The invention provides proteins from group B streptococcus (Streptococcus agalactiae) and group A streptococcus (Streptococcus pyogenes), including amino acid sequences and the corresponding nucleotide sequences. Data are given to show that the proteins are useful antigens for vaccines, immunogenic compositions, and/or diagnostics. The proteins are also targets for antibiotics.

Current U.S. Class:	424/244.1 ; 424/184.1; 424/201.1; 424/203.1; 424/242.1; 435/320.1; 435/69.1; 435/69.7; 530/350; 530/388.4; 536/23.1; 536/23.7
Current International Class:	A61K 39/09 (20060101); A61K 39/38 (20060101); C12N 15/00 (20060101); C12P 21/04 (20060101); C12P 21/06 (20060101); C07H 21/04 (20060101); A61K 39/02 (20060101)

Banner & Witcoff, Ltd.

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Claims

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The invention claimed is:

1. A recombinant expression cassette comprising an isolated nucleic acid molecule which encodes a protein which comprises the amino acid sequence shown in SEQ ID NO:8780.

2. The recombinant expression cassette of claim 1 which comprises SEQ ID NO:8779.

3. A recombinant expression cassette comprising an isolated nucleic acid molecule which encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO:8780.

4. The recombinant expression cassette of claim 3 wherein the amino acid sequence has at least 90% sequence identity to SEQ ID NO:8780.

5. The recombinant expression cassette of claim 3 wherein the amino acid sequence has at least 95% sequence identity to SEQ ID NO:8780.

6. The recombinant expression cassette of claim 3 wherein the amino acid sequence has at least 99% sequence identity to SEQ ID NO:8780.

7. A composition comprising an isolated protein which comprises the amino acid sequence shown in SEQ ID NO:8780.

8. The composition of claim 7, further comprising one or more of the following antigens: a protein antigen from Helicobacter pylori; a protein antigen from N. meningitidis serogroup B; an outer-membrane vesicle (OMV) preparation from N. meningitidis serogroup B; a saccharide antigen from N. meningitidis serogroup A, C, W135 and/or Y; a saccharide antigen from Streptococcus pneumoniae; an antigen from hepatitis A virus; an antigen from hepatitis B virus; a diphtheria antigen; a tetanus antigen; a saccharide antigen from Haemophilus influenzae B; an antigen from N. gonorrhoeae; an antigen from Chlamydia pneumoniae; an antigen from Chlamydia trachomatis; an antigen from Aporphyromonas gingivalis; a polio antigen; a rabies antigen; an antigen from Moraxella catarrhalis; and/or an antigen from Staphylococcus aureus.

9. The composition of claim 7 further comprising an adjuvant.

10. The composition of claim 7 which is a diagnostic composition.

11. The composition of claim 9 wherein the adjuvant is Freund's adjuvant.

12. The composition of claim 7 further comprising a carbohydrate antigen.

13. The composition of claim 7 further comprising a saccharide antigen.

14. A composition comprising two or more isolated proteins, wherein one of the two proteins comprises the amino acid sequence shown in SEQ ID NO:3922 and the other of the two proteins comprises the amino acid sequence shown in SEQ ID NO:8780.

15. A composition comprising an isolated polypeptide which comprises an amino acid sequence with at least 85% amino acid sequence identity to SEQ ID NO:8780.

16. The composition of claim 15 wherein the amino acid sequence has at least 90% sequence identity to SEQ ID NO:8780.

17. The composition of claim 15 wherein the amino acid sequence has at least 95% sequence identity to SEQ ID NO:8780.

18. The composition of claim 15 wherein the amino acid sequence has at least 99% sequence identity to SEQ ID NO:8780.

19. The composition of claim 15 further comprising one or more of the one or more of the following antigens: a protein antigen from Helicobacter pylori; a protein antigen from N. meningitidis serogroup B; an outer-membrane vesicle (OMV) preparation from N. meningitidis serogroup B; a saccharide antigen from N. meningitidis serogroup A, C, W135 and/or Y; a saccharide antigen from Streptococcus pneumoniae; an antigen from hepatitis A virus; an antigen from hepatitis B virus; a diphtheria antigen; a tetanus antigen; a saccharide antigen from Haemophilus influenzae B; an antigen from N. gonorrhoeae; an antigen from Chlamydia pneumoniae; an antigen from Chlamydia trachomatis; an antigen from Aporphyromonas gingivalis; a polio antigen; a rabies antigen; an antigen from Moraxella catarrhalis; and/or an antigen from Staphylococcus aureus.

20. The composition of claim 15 further comprising an adjuvant.

21. The composition of claim 15 which is a diagnostic composition.

22. The composition of claim 15 further comprising a carbohydrate antigen.

23. The composition of claim 15 further comprising a saccharide antigen.

24. The composition of claim 20 wherein the adjuvant is Freund's adjuvant.

25. A purified protein comprising the amino acid sequence shown in SEQ ID NO:8780.

26. A purified protein, wherein the amino acid sequence of the purified protein is at least 85% identical to the amino acid sequence shown in SEQ ID NO:8780.

27. The purified protein of claim 26 wherein the amino acid sequence is at least 90% identical to the amino acid sequence shown in SEQ ID NO:8780.

28. The purified protein of claim 26 wherein the amino acid sequence is at least 95% identical to the amino acid sequence shown in SEQ ID NO:8780.

29. The purified protein of claim 26 wherein the amino acid sequence is at least 99% identical to the amino acid sequence shown in SEQ ID NO:8780.

30. A method of raising an immune response in a patient against a group B Streptococcus which comprises a protein comprising the amino acid sequence SEQ ID NO:8780, comprising administering to the patient an effective amount of a composition comprising (i) an isolated protein comprising the amino acid sequence SEQ ID NO:8780 and (ii) an adjuvant.

31. The method of claim 30 wherein the group B Streptococcus is serotype III COH1.

32. The method of claim 30 wherein the group B Streptococcus is serotype V 2603 V/R.

33. The method of claim 30 wherein the adjuvant is Freund's adjuvant.

34. A method of raising an immune response in a patient against a group B Streptococcus which comprises a protein comprising the amino acid sequence SEQ ID NO:8780, comprising administering to the patient an effective amount of a composition comprising (i) a purified protein comprising an amino acid sequence which is at least 85% identical to the amino acid sequence shown in SEQ ID NO:8780 and (ii) an adjuvant.

35. The method of claim 34 wherein the amino acid sequence is at least 90% identical to the amino acid sequence shown in SEQ ID NO:8780.

36. The method of claim 34 wherein the amino acid sequence is at least 95% identical to the amino acid sequence shown in SEQ ID NO:8780.

37. The method of claim 34 wherein the amino acid sequence is at least 99% identical to the amino acid sequence shown in SEQ ID NO:8780.

38. The method of claim 34 wherein the group B Streptococcus is serotype III COH1.

39. The method of claim 34 wherein the group B Streptococcus is serotype V 2603 V/R.

40. The method of claim 34 wherein the adjuvant is Freund's adjuvant.

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Description

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CROSS REFERENCE TO RELATED APPLICATIONS

This application is a National Stage application of co-pending PCT application PCT/GB01/04789 filed Oct. 29, 2001, which was published in English under PCT Article 21(2) on May 2, 2002, which claims the benefit of Great Britain applications Serial No. GB0026333.5 filed Oct. 27, 2000, Serial No. GB0028727.6 filed Nov. 24, 2000, and Serial No. GB0105640.7 filed Mar. 7, 2001. These applications are incorporated herein by reference in their entireties.

REFERENCE TO A "SEQUENCE LISTING"

This application incorporates by reference a 21.0 MB text file created on Nov. 27, 2009 and labeled "10415182_sequence_listing.txt," which is the listing for this application.

All documents cited herein are incorporated by reference in their entirety.

TECHNICAL FIELD

This invention relates to nucleic acid and proteins from the bacteria Streptococcus agalactiae (GBS) and Streptococcus pyogenes (GAS).

BACKGROUND ART

Once thought to infect only cows, the Gram-positive bacterium Streptococcus agalactiae (or "group B streptococcus", abbreviated to "GBS") is now known to cause serious disease, bacteremia and meningitis, in immunocompromised individuals and in neonates. There are two types of neonatal infection. The first (early onset, usually within 5 days of birth) is manifested by bacteremia and pneumonia. It is contracted vertically as a baby passes through the birth canal. GBS colonises the vagina of about 25% of young women, and approximately 1% of infants born via a vaginal birth to colonised mothers will become infected. Mortality is between 50-70%. The second is a meningitis that occurs 10 to 60 days after birth. If pregnant women are vaccinated with type III capsule so that the infants are passively immunised, the incidence of the late onset meningitis is reduced but is not entirely eliminated.

The "B" in "GBS" refers to the Lancefield classification, which is based on the antigenicity of a carbohydrate which is soluble in dilute acid and called the C carbohydrate. Lancefield identified 13 types of C carbohydrate, designated A to O, that could be serologically differentiated. The organisms that most commonly infect humans are found in groups A, B, D, and G. Within group B, strains can be divided into 8 serotypes (Ia, Ib, Ia/c, II, III, IV, V, and VI) based on the structure of their polysaccharide capsule.

Group A streptococcus ("GAS", S. pyogenes) is a frequent human pathogen, estimated to be present in between 5-15% of normal individuals without signs of disease. When host defenses are compromised, or when the organism is able to exert its virulence, or when it is introduced to vulnerable tissues or hosts, however, an acute infection occurs. Diseases include puerperal fever, scarlet fever, erysipelas, pharyngitis, impetigo, necrotising fasciitis, myositis and streptococcal toxic shock syndrome.

S. pyogenes is typically treated using antibiotics. Although S. agalactiae is inhibited by antibiotics, however, it is not killed by penicillin as easily as GAS. Prophylactic vaccination is thus preferable.

Current GBS vaccines are based on polysaccharide antigens, although these suffer from poor immunogenicity. Anti-idiotypic approaches have also been used (e.g. WO99/54457). There remains a need, however, for effective adult vaccines against S. agalactiae infection. There also remains a need for vaccines against S. pyogenes infection.

It is an object of the invention to provide proteins which can be used in the development of such vaccines. The proteins may also be useful for diagnostic purposes, and as targets for antibiotics.

DISCLOSURE OF THE INVENTION

The invention provides proteins comprising the S. agalactiae amino acid sequences disclosed in the examples, and proteins comprising the S. pyogenes amino acid sequences disclosed in the examples. These amino acid sequences are the even SEQ IDs between 1 and 10960.

It also provides proteins comprising amino acid sequences having sequence identity to the S. agalactiae amino acid sequences disclosed in the examples, and proteins comprising amino acid sequences having sequence identity to the S. pyogenes amino acid sequences disclosed in the examples. Depending on the particular sequence, the degree of sequence identity is preferably greater than 50% (e.g. 60%, 70%, 80%, 90%, 95%, 99% or more). These proteins include homologs, orthologs, allelic variants and functional mutants. Typically, 50% identity or more between two proteins is considered to be an indication of functional equivalence. Identity between proteins is preferably determined by the Smith-Waterman homology search algorithm as implemented in the MPSRCH program (Oxford Molecular), using an affine gap search with parameters gap open penalty=12 and gap extension penalty=1.

Preferred proteins of the invention are GBS1 to GBS689 (see Table IV).

The invention further provides proteins comprising fragments of the S. agalactiae amino acid sequences disclosed in the examples, and proteins comprising fragments of the S. pyogenes amino acid sequences disclosed in the examples. The fragments should comprise at least n consecutive amino acids from the sequences and, depending on the particular sequence, n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more). Preferably the fragments comprise one or more epitopes from the sequence. Other preferred fragments are (a) the N-terminal signal peptides of the proteins disclosed in the examples, (b) the proteins disclosed in the examples, but without their N-terminal signal peptides, (c) fragments common to the related GAS and GBS proteins disclosed in the examples, and (d) the proteins disclosed in the examples, but without their N-terminal amino acid residue.

The proteins of the invention can, of course, be prepared by various means (e.g. recombinant expression, purification from GAS or GBS, chemical synthesis etc.) and in various forms (e.g. native, fusions, glycosylated, non-glycosylated etc.). They are preferably prepared in substantially pure form (i.e. substantially free from other streptococcal or host cell proteins) or substantially isolated form. Proteins of the invention are preferably streptococcal proteins.

According to a further aspect, the invention provides antibodies which bind to these proteins. These may be polyclonal or monoclonal and may be produced by any suitable means (e.g. by recombinant expression). To increase compatibility with the human immune system, the antibodies may be chimeric or humanised (e.g. Breedveld (2000) Lancet 355(9205):735-740; Gorman & Clark (1990) Semin. Immunol. 2:457-466), or fully human antibodies may be used. The antibodies may include a detectable label (e.g. for diagnostic assays).

According to a further aspect, the invention provides nucleic acid comprising the S. agalactiae nucleotide sequences disclosed in the examples, and nucleic acid comprising the S. pyogenes nucleotide sequences disclosed in the examples. These nucleic acid sequences are the odd SEQ IDs between 1 and 10966.

In addition, the invention provides nucleic acid comprising nucleotide sequences having sequence identity to the S. agalactiae nucleotide sequences disclosed in the examples, and nucleic acid comprising nucleotide sequences having sequence identity to the S. pyogenes nucleotide sequences disclosed in the examples. Identity between sequences is preferably determined by the Smith-Waterman homology search algorithm as described above.

Furthermore, the invention provides nucleic acid which can hybridise to the S. agalactiae nucleic acid disclosed in the examples, and nucleic acid which can hybridise to the S. pyogenes nucleic acid disclosed in the examples preferably under `high stringency` conditions (e.g. 65.degree. C. in 0.1.times.SSC, 0.5% SDS solution).

Nucleic acid comprising fragments of these sequences are also provided. These should comprise at least n consecutive nucleotides from the S. agalactiae or S. pyogenes sequences and, depending on the particular sequence, n is 10 or more (e.g. 12, 14, 15, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200 or more). The fragments may comprise sequences which are common to the related GAS and GBS sequences disclosed in the examples.

According to a further aspect, the invention provides nucleic acid encoding the proteins and protein fragments of the invention.

The invention also provides: nucleic acid comprising nucleotide sequence SEQ ID 10967; nucleic acid comprising nucleotide sequences having sequence identity to SEQ ID 10967; nucleic acid which can hybridise to SEQ ID 10967 (preferably under `high stringency` conditions); nucleic acid comprising a fragment of at least n consecutive nucleotides from SEQ ID 10967, wherein n is 10 or more e.g. 12, 14, 15, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1500, 2000, 3000, 4000, 5000, 10000, 100000, 1000000 or more Nucleic acids of the invention can be used in hybridisation reactions (e.g. Northern or Southern blots, or in nucleic acid microarrays or `gene chips`) and amplification reactions (e.g. PCR, SDA, SSSR, LCR, TMA, NASBA etc.) and other nucleic acid techniques.

It should also be appreciated that the invention provides nucleic acid comprising sequences complementary to those described above (e.g. for antisense or probing, or for use as primers).

Nucleic acid according to the invention can, of course, be prepared in many ways (e.g. by chemical synthesis, from genomic or cDNA libraries, from the organism itself etc.) and can take various forms (e.g. single stranded, double stranded, vectors, primers, probes, labelled etc.). The nucleic acid is preferably in substantially isolated form.

Nucleic acid according to the invention may be labelled e.g. with a radioactive or fluorescent label. This is particularly useful where the nucleic acid is to be used in nucleic acid detection techniques e.g. where the nucleic acid is a primer or as a probe for use in techniques such as PCR, LCR, TMA, NASBA etc.

In addition, the term "nucleic acid" includes DNA and RNA, and also their analogues, such as those containing modified backbones, and also peptide nucleic acids (PNA) etc.

According to a further aspect, the invention provides vectors comprising nucleotide sequences of the invention (e.g. cloning or expression vectors) and host cells transformed with such vectors.

According to a further aspect, the invention provides compositions comprising protein, antibody, and/or nucleic acid according to the invention. These compositions may be suitable as immunogenic compositions, for instance, or as diagnostic reagents, or as vaccines.

The invention also provides nucleic acid, protein, or antibody according to the invention for use as medicaments (e.g. as immunogenic compositions or as vaccines) or as diagnostic reagents. It also provides the use of nucleic acid, protein, or antibody according to the invention in the manufacture of: (i) a medicament for treating or preventing disease and/or infection caused by streptococcus; (ii) a diagnostic reagent for detecting the presence of streptococcus or of antibodies raised against streptococcus; and/or (iii) a reagent which can raise antibodies against streptococcus. Said streptococcus may be any species, group or strain, but is preferably S. agalactiae, especially serotype III or V, or S. pyogenes. Said disease may be bacteremia, meningitis, puerperal fever, scarlet fever, erysipelas, pharyngitis, impetigo, necrotising fasciitis, myositis or toxic shock syndrome.

The invention also provides a method of treating a patient, comprising administering to the patient a therapeutically effective amount of nucleic acid, protein, and/or antibody of the invention. The patient may either be at risk from the disease themselves or may be a pregnant woman (`maternal immunisation` e.g. Glezen & Alpers (1999) Clin. Infect. Dis. 28:219-224).

Administration of protein antigens is a preferred method of treatment for inducing immunity.

Administration of antibodies of the invention is another preferred method of treatment. This method of passive immunisation is particularly useful for newborn children or for pregnant women. This method will typically use monoclonal antibodies, which will be humanised or fully human.

The invention also provides a kit comprising primers (e.g. PCR primers) for amplifying a template sequence contained within a Streptococcus (e.g. S. pyogenes or S. agalactiae) nucleic acid sequence, the kit comprising a first primer and a second primer, wherein the first primer is substantially complementary to said template sequence and the second primer is substantially complementary to a complement of said template sequence, wherein the parts of said primers which have substantial complementarity define the termini of the template sequence to be amplified. The first primer and/or the second primer may include a detectable label (e.g. a fluorescent label).

The invention also provides a kit comprising first and second single-stranded oligonucleotides which allow amplification of a Streptococcus template nucleic acid sequence contained in a single- or double-stranded nucleic acid (or mixture thereof), wherein: (a) the first oligonucleotide comprises a primer sequence which is substantially complementary to said template nucleic acid sequence; (b) the second oligonucleotide comprises a primer sequence which is substantially complementary to the complement of said template nucleic acid sequence; (c) the first oligonucleotide and/or the second oligonucleotide comprise(s) sequence which is not complementary to said template nucleic acid; and (d) said primer sequences define the termini of the template sequence to be amplified. The non-complementary sequence(s) of feature (c) are preferably upstream of (i.e. 5' to) the primer sequences. One or both of these (c) sequences may comprise a restriction site (e.g. EP-B-0509612) or a promoter sequence (e.g. EP-B-0505012). The first oligonucleotide and/or the second oligonucleotide may include a detectable label (e.g. a fluorescent label).

The template sequence may be any part of a genome sequence (e.g. SEQ ID 10967). For example, it could be a rRNA gene (e.g. Turenne et al. (2000) J. Clin. Microbiol. 38:513-520; SEQ IDs 12018-12024 herein) or a protein-coding gene. The template sequence is preferably specific to GBS.

The invention also provides a computer-readable medium (e.g. a floppy disk, a hard disk, a CD-ROM, a DVD etc.) and/or a computer database containing one or more of the sequences in the sequence listing. The medium preferably contains SEQ ID 10967.

The invention also provides a hybrid protein represented by the formula NH.sub.2-A-[-X-L-].sub.n-B--COOH, wherein X is a protein of the invention, L is an optional linker amino acid sequence, A is an optional N-terminal amino acid sequence, B is an optional C-terminal amino acid sequence, and n is an integer greater than 1. The value of n is between 2 and x, and the value of x is typically 3, 4, 5, 6, 7, 8, 9 or 10. Preferably n is 2, 3 or 4; it is more preferably 2 or 3; most preferably, n=2. For each n instances, --X-- may be the same or different. For each n instances of [-X-L-], linker amino acid sequence -L- may be present or absent. For instance, when n=2 the hybrid may be NH.sub.2--X.sub.1-L.sub.1-X.sub.2-L.sub.2-COOH, NH.sub.2--X.sub.1-X.sub.2--COOH, NH.sub.2--X.sub.1-L.sub.1-X.sub.2--COOH, NH.sub.2--X.sub.1-X.sub.2-L.sub.2-COOH, etc. Linker amino acid sequence(s) -L- will typically be short (e.g. 20 or fewer amino acids i.e. 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples include short peptide sequences which facilitate cloning, poly-glycine linkers (i.e. Gly.sub.n where n=2, 3, 4, 5, 6, 7, 8, 9, 10 or more), and histidine tags (i.e. His.sub.n where n=3, 4, 5, 6, 7, 8, 9, 10 or more). Other suitable linker amino acid sequences will be apparent to those skilled in the art. -A- and --B-- are optional sequences which will typically be short (e.g. 40 or fewer amino acids i.e. 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples include leader sequences to direct protein trafficking, or short peptide sequences which facilitate cloning or purification (e.g. histidine tags i.e. His.sub.n where n=3, 4, 5, 6, 7, 8, 9, 10 or more). Other suitable N-terminal and C-terminal amino acid sequences will be apparent to those skilled in the art. In some embodiments, each X will be a GBS sequence; in others, mixtures of GAS and GBS will be used.

According to further aspects, the invention provides various processes.

A process for producing proteins of the invention is provided, comprising the step of culturing a host cell of to the invention under conditions which induce protein expression.

A process for producing protein or nucleic acid of the invention is provided, wherein the protein or nucleic acid is synthesised in part or in whole using chemical means.

A process for detecting polynucleotides of the invention is provided, comprising the steps of: (a) contacting a nucleic probe according to the invention with a biological sample under hybridising conditions to form duplexes; and (b) detecting said duplexes.

A process for detecting Streptococcus in a biological sample (e.g. blood) is also provided, comprising the step of contacting nucleic acid according to the invention with the biological sample under hybridising conditions. The process may involve nucleic acid amplification (e.g. PCR, SDA, SSSR, LCR, TMA, NASBA etc.) or hybridisation (e.g. microarrays, blots, hybridisation with a probe in solution etc.). PCR detection of Streptococcus in clinical samples, in particular S. pyogenes, has been reported [see e.g. Louie et al. (2000) CMAJ 163:301-309; Louie et al. (1998) J. Clin. Microbiol. 36:1769-1771]. Clinical assays based on nucleic acid are described in general in Tang et al. (1997) Clin. Chem. 43:2021-2038.

A process for detecting proteins of the invention is provided, comprising the steps of: (a) contacting an antibody of the invention with a biological sample under conditions suitable for the formation of an antibody-antigen complexes; and (b) detecting said complexes.

A process for identifying an amino acid sequence is provided, comprising the step of searching for putative open reading frames or protein-coding regions within a genome sequence of S. agalactiae. This will typically involve in silico searching the sequence for an initiation codon and for an in-frame termination codon in the downstream sequence. The region between these initiation and termination codons is a putative protein-coding sequence. Typically, all six possible reading frames will be searched. Suitable software for such analysis includes ORFFINDER (NCBI), GENEMARK [Borodovsky & McIninch (1993) Computers Chem. 17:122-133), GLIMMER [Salzberg et al. (1998) Nucleic Acids Res. 26:544-548; Salzberg et al. (1999) Genomics 59:24-31; Delcher et al. (1999) Nucleic Acids Res. 27:4636-4641], or other software which uses Markov models [e.g. Shmatkov et al. (1999) Bioinformatics 15:874-876]. The invention also provides a protein comprising the identified amino acid sequence. These proteins can then expressed using conventional techniques.

The invention also provides a process for determining whether a test compound binds to a protein of the invention. If a test compound binds to a protein of the invention and this binding inhibits the life cycle of the GBS bacterium, then the test compound can be used as an antibiotic or as a lead compound for the design of antibiotics. The process will typically comprise the steps of contacting a test compound with a protein of the invention, and determining whether the test compound binds to said protein. Preferred proteins of the invention for use in these processes are enzymes (e.g. tRNA synthetases), membrane transporters and ribosomal proteins. Suitable test compounds include proteins, polypeptides, carbohydrates, lipids, nucleic acids (e.g. DNA, RNA, and modified forms thereof), as well as small organic compounds (e.g. MW between 200 and 2000 Da). The test compounds may be provided individually, but will typically be part of a library (e.g. a combinatorial library). Methods for detecting a binding interaction include NMR, filter-binding assays, gel-retardation assays, displacement assays, surface plasmon resonance, reverse two-hybrid etc. A compound which binds to a protein of the invention can be tested for antibiotic activity by contacting the compound with GBS bacteria and then monitoring for inhibition of growth. The invention also provides a compound identified using these methods.

The invention also provides a composition comprising a protein or the invention and one or more of the following antigens: a protein antigen from Helicobacter pylori such as VacA, CagA, NAP, HopX, HopY [e.g. WO98/04702] and/or urease. a protein antigen from N. meningitidis serogroup B, such as those in WO99/24578, WO99/36544, WO99/57280, WO00/22430, Tettelin et al. (2000) Science 287:1809-1815, Pizza et al. (2000) Science 287:1816-1820 and WO96/29412, with protein `287` and derivatives being particularly preferred. an outer-membrane vesicle (OMV) preparation from N. meningitidis serogroup B, such as those disclosed in WO01/52885; Bjune et al. (1991) Lancet 338(8775):1093-1096; Fukasawa et al. (1999) Vaccine 17:2951-2958; Rosenqvist et al. (1998) Dev. Biol. Stand. 92:323-333 etc. a saccharide antigen from N. meningitidis serogroup A, C, W135 and/or Y, such as the oligosaccharide disclosed in Costantino et al. (1992) Vaccine 10:691-698 from serogroup C [see also Costantino et al. (1999) Vaccine 17:1251-1263]. a saccharide antigen from Streptococcus pneumoniae [e.g. Watson (2000) Pediatr Infect Dis J 19:331-332; Rubin (2000) Pediatr Clin North Am 47:269-285, v; Jedrzejas (2001) Microbiol Mol Biol Rev 65:187-207]. an antigen from hepatitis A virus, such as inactivated virus [e.g. Bell (2000) Pediatr Infect Dis J 19:1187-1188; Iwarson (1995) APMIS 103:321-326]. an antigen from hepatitis B virus, such as the surface and/or core antigens [e.g. Gerlich et al. (1990) Vaccine 8 Suppl:S63-68 & 79-80]. an antigen from hepatitis C virus [e.g. Hsu et al. (1999) Clin Liver Dis 3:901-915]. an antigen from Bordetella pertussis, such as pertussis holotoxin (PT) and filamentous haemagglutinin (FHA) from B. pertussis, optionally also in combination with pertactin and/or agglutinogens 2 and 3 [e.g. Gustafsson et al. (1996) N. Engl. J. Med. 334:349-355; Rappuoli et al. (1991) TIBTECH 9:232-238]. a diphtheria antigen, such as a diphtheria toxoid [e.g. chapter 3 of Vaccines (1988) eds. Plotkin & Mortimer. ISBN 0-7216-1946-0] e.g. the CRM.sub.197 mutant [e.g. Del Guidice et al. (1998) Molecular Aspects of Medicine 19:1-70]. a tetanus antigen, such as a tetanus toxoid [e.g. chapter 4 of Plotkin & Mortimer]. a saccharide antigen from Haemophilus influenzae B. an antigen from N. gonorrhoeae [e.g. WO99/24578, WO99/36544, WO99/57280]. an antigen from Chlamydia pneumoniae [e.g. PCT/IB01/01445; Kalman et al. (1999) Nature Genetics 21:385-389; Read et al. (2000) Nucleic Acids Res 28:1397-406; Shirai et al. (2000) J. Infect. Dis. 181(Suppl 3):S524-S527; WO99/27105; WO00/27994; WO00/37494]. an antigen from Chlamydia trachomatis [e.g. WO99/28475]. an antigen from Porphyromonas gingivalis [e.g. Ross et al. (2001) Vaccine 19:4135-4142]. polio antigen(s) [e.g. Sutter et al. (2000) Pediatr Clin North Am 47:287-308; Zimmerman & Spann (1999) Am Fam Physician 59:113-118, 125-126] such as IPV or OPV. rabies antigen(s) [e.g. Dreesen (1997) Vaccine 15 Suppl:S2-6] such as lyophilised inactivated virus [e.g. MMWR Morb Mortal Wkly Rep 1998 Jan. 16; 47(1):12, 19; RabAvert.TM.]. measles, mumps and/or rubella antigens [e.g. chapters 9, 10 & 11 of Plotkin & Mortimer]. influenza antigen(s) [e.g. chapter 19 of Plotkin & Mortimer], such as the haemagglutinin and/or neuramimidase surface proteins. an antigen from Moraxella catarrhalis [e.g. McMichael (2000) Vaccine 19 Suppl 1:S101-107]. an antigen from Staphylococcus aureus [e.g. Kuroda et al. (2001) Lancet 357(9264): 1225-1240; see also pages 1218-1219].

Where a saccharide or carbohydrate antigen is included, it is preferably conjugated to a carrier protein in order to enhance immunogenicity [e.g. Ramsay et al. (2001) Lancet 357(9251):195-196; Lindberg (1999) Vaccine 17 Suppl 2:S28-36; Conjugate Vaccines (eds. Cruse et al.) ISBN 3805549326, particularly vol. 10:48-114 etc.]. Preferred carrier proteins are bacterial toxins or toxoids, such as diphtheria or tetanus toxoids. The CRM.sub.197 diphtheria toxoid is particularly preferred. Other suitable carrier proteins include the N. meningitidis outer membrane protein [e.g. EP-0372501], synthetic peptides [e.g. EP-0378881, EP-0427347], heat shock proteins [e.g. WO93/17712], pertussis proteins [e.g. WO98/58668; EP-0471177], protein D from H. influenzae [e.g. WO00/56360], toxin A or B from C. difficile [e.g. WO00/61761], etc. Any suitable conjugation reaction can be used, with any suitable linker where necessary.

Toxic protein antigens may be detoxified where necessary (e.g. detoxification of pertussis toxin by chemical and/or genetic means).

Where a diphtheria antigen is included in the composition it is preferred also to include tetanus antigen and pertussis antigens. Similarly, where a tetanus antigen is included it is preferred also to include diphtheria and pertussis antigens. Similarly, where a pertussis antigen is included it is preferred also to include diphtheria and tetanus antigens.

Antigens are preferably adsorbed to an aluminium salt.

Antigens in the composition will typically be present at a concentration of at least 1 .mu.g/ml each. In general, the concentration of any given antigen will be sufficient to elicit an immune response against that antigen.

The invention also provides compositions comprising two or more proteins of the present invention.

The two or more proteins may comprise GBS sequences or may comprise GAS and GBS sequences.

A summary of standard techniques and procedures which may be employed to perform the invention (e.g. to utilise the disclosed sequences for vaccination or diagnostic purposes) follows. This summary is not a limitation on the invention but, rather, gives examples that may be used, but are not required.

General

The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature eg. Sambrook Molecular Cloning, A Laboratory Manual, Second Edition (1989); DNA Cloning, Volumes I and II (D. N Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gait ed, 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription and Translation (B. D. Hames & S. J. Higgins eds. 1984); Animal Cell Culture (R. I. Freshney ed. 1986); Immobilized Cells and Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide to Molecular Cloning (1984); the Methods in Enzymology series (Academic Press, Inc.), especially volumes 154 & 155; Gene Transfer Vectors for Mammalian Cells (J. H. Miller and M. P. Calos eds. 1987, Cold Spring Harbor Laboratory); Mayer and Walker, eds. (1987), Immunochemical Methods in Cell and Molecular Biology (Academic Press, London); Scopes, (1987) Protein Purification: Principles and Practice, Second Edition (Springer-Verlag, N.Y.), and Handbook of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell eds 1986).

Standard abbreviations for nucleotides and amino acids are used in this specification.

DEFINITIONS

A composition containing X is "substantially free of" Y when at least 85% by weight of the total X+Y in the composition is X. Preferably, X comprises at least about 90% by weight of the total of X+Y in the composition, more preferably at least about 95% or even 99% by weight.

The term "comprising" means "including" as well as "consisting" e.g. a composition "comprising" X may consist exclusively of X or may include something additional e.g. X+Y.

The term "heterologous" refers to two biological components that are not found together in nature. The components may be host cells, genes, or regulatory regions, such as promoters. Although the heterologous components are not found together in nature, they can function together, as when a promoter heterologous to a gene is operably linked to the gene. Another example is where a streptococcus sequence is heterologous to a mouse host cell. A further examples would be two epitopes from the same or different proteins which have been assembled in a single protein in an arrangement not found in nature.

An "origin of replication" is a polynucleotide sequence that initiates and regulates replication of polynucleotides, such as an expression vector. The origin of replication behaves as an autonomous unit of polynucleotide replication within a cell, capable of replication under its own control. An origin of replication may be needed for a vector to replicate in a particular host cell. With certain origins of replication, an expression vector can be reproduced at a high copy number in the presence of the appropriate proteins within the cell. Examples of origins are the autonomously replicating sequences, which are effective in yeast; and the viral T-antigen, effective in COS-7 cells.

A "mutant" sequence is defined as DNA, RNA or amino acid sequence differing from but having sequence identity with the native or disclosed sequence. Depending on the particular sequence, the degree of sequence identity between the native or disclosed sequence and the mutant sequence is preferably greater than 50% (eg. 60%, 70%, 80%, 90%, 95%, 99% or more, calculated using the Smith-Waterman algorithm as described above). As used herein, an "allelic variant" of a nucleic acid molecule, or region, for which nucleic acid sequence is provided herein is a nucleic acid molecule, or region, that occurs essentially at the same locus in the genome of another or second isolate, and that, due to natural variation caused by, for example, mutation or recombination, has a similar but not identical nucleic acid sequence. A coding region allelic variant typically encodes a protein having similar activity to that of the protein encoded by the gene to which it is being compared. An allelic variant can also comprise an alteration in the 5' or 3' untranslated regions of the gene, such as in regulatory control regions (eg. see U.S. Pat. No. 5,753,235).

Expression Systems

The streptococcus nucleotide sequences can be expressed in a variety of different expression systems; for example those used with mammalian cells, baculoviruses, plants, bacteria, and yeast.

i. Mammalian Systems

Mammalian expression systems are known in the art. A mammalian promoter is any DNA sequence capable of binding mammalian RNA polymerase and initiating the downstream (3') transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiating region, which is usually placed proximal to the 5' end of the coding sequence, and a TATA box, usually located 25-30 base pairs (bp) upstream of the transcription initiation site. The TATA box is thought to direct RNA polymerase II to begin RNA synthesis at the correct site. A mammalian promoter will also contain an upstream promoter element, usually located within 100 to 200 bp upstream of the TATA box. An upstream promoter element determines the rate at which transcription is initiated and can act in either orientation [Sambrook et al. (1989) "Expression of Cloned Genes in Mammalian Cells." In Molecular Cloning: A Laboratory Manual, 2nd ed].

Mammalian viral genes are often highly expressed and have a broad host range; therefore sequences encoding mammalian viral genes provide particularly useful promoter sequences. Examples include the SV40 early promoter, mouse mammary tumor virus LTR promoter, adenovirus major late promoter (Ad MLP), and herpes simplex virus promoter. In addition, sequences derived from non-viral genes, such as the murine metallotheionein gene, also provide useful promoter sequences. Expression may be either constitutive or regulated (inducible), depending on the promoter can be induced with glucocorticoid in hormone-responsive cells.

The presence of an enhancer element (enhancer), combined with the promoter elements described above, will usually increase expression levels. An enhancer is a regulatory DNA sequence that can stimulate transcription up to 1000-fold when linked to homologous or heterologous promoters, with synthesis beginning at the normal RNA start site. Enhancers are also active when they are placed upstream or downstream from the transcription initiation site, in either normal or flipped orientation, or at a distance of more than 1000 nucleotides from the promoter [Maniatis et al. (1987) Science 236:1237; Alberts et al. (1989) Molecular Biology of the Cell, 2nd ed.]. Enhancer elements derived from viruses may be particularly useful, because they usually have a broader host range. Examples include the SV40 early gene enhancer [Dijkema et al (1985) EMBO J. 4:761] and the enhancer/promoters derived from the long terminal repeat (LTR) of the Rous Sarcoma Virus [Gorman et al. (1982b) Proc. Natl. Acad. Sci. 79:6777] and from human cytomegalovirus [Boshart et al. (1985) Cell 41:521]. Additionally, some enhancers are regulatable and become active only in the presence of an inducer, such as a hormone or metal ion [Sassone-Corsi and Borelli (1986) Trends Genet. 2:215; Maniatis et al. (1987) Science 236:1237].

A DNA molecule may be expressed intracellularly in mammalian cells. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus of the recombinant protein will always be a methionine, which is encoded by the ATG start codon. If desired, the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide.

Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provides for secretion of the foreign protein in mammalian cells. Preferably, there are processing sites encoded between the leader fragment and the foreign gene that can be cleaved either in vivo or in vitro. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell. The adenovirus triparite leader is an example of a leader sequence that provides for secretion of a foreign protein in mammalian cells.

Usually, transcription termination and polyadenylation sequences recognized by mammalian cells are regulatory regions located 3' to the translation stop codon and thus, together with the promoter elements, flank the coding sequence. The 3' terminus of the mature mRNA is formed by site-specific post-transcriptional cleavage and polyadenylation [Birnstiel et al. (1985) Cell 41:349; Proudfoot and Whitelaw (1988) "Termination and 3' end processing of eukaryotic RNA. In Transcription and splicing (ed. B. D. Hames and D. M. Glover); Proudfoot (1989) Trends Biochem. Sci. 14:105]. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Examples of transcription terminater/polyadenylation signals include those derived from SV40 [Sambrook et al (1989) "Expression of cloned genes in cultured mammalian cells." In Molecular Cloning: A Laboratory Manual].

Usually, the above described components, comprising a promoter, polyadenylation signal, and transcription termination sequence are put together into expression constructs. Enhancers, introns with functional splice donor and acceptor sites, and leader sequences may also be included in an expression construct, if desired. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as mammalian cells or bacteria. Mammalian replication systems include those derived from animal viruses, which require trans-acting factors to replicate. For example, plasmids containing the replication systems of papovaviruses, such as SV40 [Gluzman (1981) Cell 23:175] or polyomavirus, replicate to extremely high copy number in the presence of the appropriate viral T antigen. Additional examples of mammalian replicons include those derived from bovine papillomavirus and Epstein-Barr virus. Additionally, the replicon may have two replication systems, thus allowing it to be maintained, for example, in mammalian cells for expression and in a prokaryotic host for cloning and amplification. Examples of such mammalian-bacteria shuttle vectors include pMT2 [Kaufman et al. (1989) Mol. Cell. Biol. 9:946] and pHEBO [Shimizu et al. (1986) Mol. Cell. Biol. 6:1074].

The transformation procedure used depends upon the host to be transformed. Methods for introduction of heterologous polynucleotides into mammalian cells are known in the art and include dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei.

Mammalian cell lines available as hosts for expression are known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC), including but not limited to, Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (eg. Hep G2), and a number of other cell lines.

ii. Baculovirus Systems

The polynucleotide encoding the protein can also be inserted into a suitable insect expression vector, and is operably linked to the control elements within that vector. Vector construction employs techniques which are known in the art. Generally, the components of the expression system include a transfer vector, usually a bacterial plasmid, which contains both a fragment of the baculovirus genome, and a convenient restriction site for insertion of the heterologous gene or genes to be expressed; a wild type baculovirus with a sequence homologous to the baculovirus-specific fragment in the transfer vector (this allows for the homologous recombination of the heterologous gene in to the baculovirus genome); and appropriate insect host cells and growth media.

After inserting the DNA sequence encoding the protein into the transfer vector, the vector and the wild type viral genome are transfected into an insect host cell where the vector and viral genome are allowed to recombine. The packaged recombinant virus is expressed and recombinant plaques are identified and purified. Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, inter alia, Invitrogen, San Diego Calif. ("MaxBac" kit). These techniques are generally known to those skilled in the art and fully described in Summers and Smith, Texas Agricultural Experiment Station Bulletin No. 1555 (1987) (hereinafter "Summers and Smith").

Prior to inserting the DNA sequence encoding the protein into the baculovirus genome, the above described components, comprising a promoter, leader (if desired), coding sequence, and transcription termination sequence, are usually assembled into an intermediate transplacement construct (transfer vector). This may contain a single gene and operably linked regulatory elements; multiple genes, each with its owned set of operably linked regulatory elements; or multiple genes, regulated by the same set of regulatory elements. Intermediate transplacement constructs are often maintained in a replicon, such as an extra-chromosomal element (e.g. plasmids) capable of stable maintenance in a host, such as a bacterium. The replicon will have a replication system, thus allowing it to be maintained in a suitable host for cloning and amplification.

Currently, the most commonly used transfer vector for introducing foreign genes into AcNPV is pAc373. Many other vectors, known to those of skill in the art, have also been designed. These include, for example, pVL985 (which alters the polyhedrin start codon from ATG to ATT, and which introduces a BamHI cloning site 32 basepairs downstream from the ATT; see Luckow and Summers, Virology (1989) 17:31.

The plasmid usually also contains the polyhedrin polyadenylation signal (Miller et al. (1988) Ann. Rev. Microbiol., 42:177) and a prokaryotic ampicillin-resistance (amp) gene and origin of replication for selection and propagation in E. coli.

Baculovirus transfer vectors usually contain a baculovirus promoter. A baculovirus promoter is any DNA sequence capable of binding a baculovirus RNA polymerase and initiating the downstream (5' to 3') transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5' end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site and a transcription initiation site. A baculovirus transfer vector may also have a second domain called an enhancer, which, if present, is usually distal to the structural gene. Expression may be either regulated or constitutive.

Structural genes, abundantly transcribed at late times in a viral infection cycle, provide particularly useful promoter sequences. Examples include sequences derived from the gene encoding the viral polyhedron protein, Friesen et al., (1986) "The Regulation of Baculovirus Gene Expression," in: The Molecular Biology of Baculoviruses (ed. Walter Doerfler); EPO Publ. Nos. 127 839 and 155 476; and the gene encoding the p10 protein, Vlak et al., (1988), J. Gen. Virol. 69:765.

DNA encoding suitable signal sequences can be derived from genes for secreted insect or baculovirus proteins, such as the baculovirus polyhedrin gene (Carbonell et al. (1988) Gene, 73:409). Alternatively, since the signals for mammalian cell posttranslational modifications (such as signal peptide cleavage, proteolytic cleavage, and phosphorylation) appear to be recognized by insect cells, and the signals required for secretion and nuclear accumulation also appear to be conserved between the invertebrate cells and vertebrate cells, leaders of non-insect origin, such as those derived from genes encoding human .alpha.-interferon, Maeda et al., (1985), Nature 315:592; human gastrin-releasing peptide, Lebacq-Verheyden et al., (1988), Molec. Cell. Biol. 8:3129; human IL-2, Smith et al., (1985) Proc. Nat'l Acad. Sci. USA, 82:8404; mouse IL-3, (Miyajima et al., (1987) Gene 58:273; and human glucocerebrosidase, Martin et al. (1988) DNA, 7:99, can also be used to provide for secretion in insects.

A recombinant polypeptide or polyprotein may be expressed intracellularly or, if it is expressed with the proper regulatory sequences, it can be secreted. Good intracellular expression of nonfused foreign proteins usually requires heterologous genes that ideally have a short leader sequence containing suitable translation initiation signals preceding an ATG start signal. If desired, methionine at the N-terminus may be cleaved from the mature protein by in vitro incubation with cyanogen bromide.

Alternatively, recombinant polyproteins or proteins which are not naturally secreted can be secreted from the insect cell by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provides for secretion of the foreign protein in insects. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the translocation of the protein into the endoplasmic reticulum.

After insertion of the DNA sequence and/or the gene encoding the expression product precursor of the protein, an insect cell host is co-transformed with the heterologous DNA of the transfer vector and the genomic DNA of wild type baculovirus--usually by co-transfection. The promoter and transcription termination sequence of the construct will usually comprise a 2-5 kb section of the baculovirus genome. Methods for introducing heterologous DNA into the desired site in the baculovirus virus are known in the art. (See Summers and Smith supra; Ju et al. (1987); Smith et al., Mol. Cell. Biol. (1983) 3:2156; and Luckow and Summers (1989)). For example, the insertion can be into a gene such as the polyhedrin gene, by homologous double crossover recombination; insertion can also be into a restriction enzyme site engineered into the desired baculovirus gene. Miller et al., (1989), Bioessays 4:91. The DNA sequence, when cloned in place of the polyhedrin gene in the expression vector, is flanked both 5' and 3' by polyhedrin-specific sequences and is positioned downstream of the polyhedrin promoter.

The newly formed baculovirus expression vector is subsequently packaged into an infectious recombinant baculovirus. Homologous recombination occurs at low frequency (between about 1% and about 5%); thus, the majority of the virus produced after cotransfection is still wild-type virus. Therefore, a method is necessary to identify recombinant viruses. An advantage of the expression system is a visual screen allowing recombinant viruses to be distinguished. The polyhedrin protein, which is produced by the native virus, is produced at very high levels in the nuclei of infected cells at late times after viral infection. Accumulated polyhedrin protein forms occlusion bodies that also contain embedded particles. These occlusion bodies, up to 15 .mu.m in size, are highly refractile, giving them a bright shiny appearance that is readily visualized under the light microscope. Cells infected with recombinant viruses lack occlusion bodies. To distinguish recombinant virus from wild-type virus, the transfection supernatant is plaqued onto a monolayer of insect cells by techniques known to those skilled in the art. Namely, the plaques are screened under the light microscope for the presence (indicative of wild-type virus) or absence (indicative of recombinant virus) of occlusion bodies. "Current Protocols in Microbiology" Vol. 2 (Ausubel et al. eds) at 16.8 (Supp. 10, 1990); Summers and Smith, supra; Miller et al. (1989).

Recombinant baculovirus expression vectors have been developed for infection into several insect cells. For example, recombinant baculoviruses have been developed for, inter alia: Aedes aegypti, Autographa californica, Bombyx mori, Drosophila melanogaster, Spodoptera frugiperda, and Trichoplusia ni (WO 89/046699; Carbonell et al., (1985) J. Virol. 56:153; Wright (1986) Nature 321:718; Smith et al., (1983) Mol. Cell. Biol. 3:2156; and see generally, Fraser, et al. (1989) In Vitro Cell. Dev. Biol. 25:225).

Cells and cell culture media are commercially available for both direct and fusion expression of heterologous polypeptides in a baculovirus/expression system; cell culture technology is generally known to those skilled in the art. See, eg. Summers and Smith supra.

The modified insect cells may then be grown in an appropriate nutrient medium, which allows for stable maintenance of the plasmid(s) present in the modified insect host. Where the expression product gene is under inducible control, the host may be grown to high density, and expression induced. Alternatively, where expression is constitutive, the product will be continuously expressed into the medium and the nutrient medium must be continuously circulated, while removing the product of interest and augmenting depleted nutrients. The product may be purified by such techniques as chromatography, eg HPLC, affinity chromatography, ion exchange chromatography, etc.; electrophoresis; density gradient centrifugation; solvent extraction, etc. As appropriate, the product may be further purified, as required, so as to remove substantially any insect proteins which are also present in the medium, so as to provide a product which is at least substantially free of host debris, eg. proteins, lipids and polysaccharides.

In order to obtain protein expression, recombinant host cells derived from the transformants are incubated under conditions which allow expression of the recombinant protein encoding sequence. These conditions will vary, dependent upon the host cell selected. However, the conditions are readily ascertainable to those of ordinary skill in the art, based upon what is known in the art.

iii. Plant Systems

There are many plant cell culture and whole plant genetic expression systems known in the art. Exemplary plant cellular genetic expression systems include those described in patents, such as: U.S. Pat. Nos. 5,693,506; 5,659,122; and 5,608,143. Additional examples of genetic expression in plant cell culture has been described by Zenk, Phytochemistry 30:3861-3863 (1991). Descriptions of plant protein signal peptides may be found in addition to the references described above in Vaulcombe et al., Mol. Gen. Genet. 209:33-40 (1987); Chandler et al., Plant Molecular Biology 3:407-418 (1984); Rogers, J. Biol. Chem. 260:3731-3738 (1985); Rothstein et al., Gene 55:353-356 (1987); Whittier et al., Nucleic Acids Research 15:2515-2535 (1987); Wirsel et al., Molecular Microbiology 3:3-14 (1989); Yu et al., Gene 122:247-253 (1992). A description of the regulation of plant gene expression by the phytohormone, gibberellic acid and secreted enzymes induced by gibberellic acid can be found in R. L. Jones and J. MacMillin, Gibberellins: in: Advanced Plant Physiology, Malcolm B. Wilkins, ed., 1984 Pitman Publishing Limited, London, pp. 21-52. References that describe other metabolically-regulated genes: Sheen, Plant Cell, 2:1027-1038 (1990); Maas et al., EMBO J. 9:3447-3452 (1990); Benkel and Hickey, Proc. Natl. Acad. Sci. 84:1337-1339 (1987).

Typically, using techniques known in the art, a desired polynucleotide sequence is inserted into an expression cassette comprising genetic regulatory elements designed for operation in plants. The expression cassette is inserted into a desired expression vector with companion sequences upstream and downstream from the expression cassette suitable for expression in a plant host. The companion sequences will be of plasmid or viral origin and provide necessary characteristics to the vector to permit the vectors to move DNA from an original cloning host, such as bacteria, to the desired plant host. The basic bacterial/plant vector construct will preferably provide a broad host range prokaryote replication origin; a prokaryote selectable marker; and, for Agrobacterium transformations, T DNA sequences for Agrobacterium-mediated transfer to plant chromosomes. Where the heterologous gene is not readily amenable to detection, the construct will preferably also have a selectable marker gene suitable for determining if a plant cell has been transformed. A general review of suitable markers, for example for the members of the grass family, is found in Wilmink and Dons, 1993, Plant Mol. Biol. Reptr, 11(2):165-185.

Sequences suitable for permitting integration of the heterologous sequence into the plant genome are also recommended. These might include transposon sequences and the like for homologous recombination as well as Ti sequences which permit random insertion of a heterologous expression cassette into a plant genome. Suitable prokaryote selectable markers include resistance toward antibiotics such as ampicillin or tetracycline. Other DNA sequences encoding additional functions may also be present in the vector, as is known in the art.

The nucleic acid molecules of the subject invention may be included into an expression cassette for expression of the protein(s) of interest. Usually, there will be only one expression cassette, although two or more are feasible. The recombinant expression cassette will contain in addition to the heterologous protein encoding sequence the following elements, a promoter region, plant 5' untranslated sequences, initiation codon depending upon whether or not the structural gene comes equipped with one, and a transcription and translation termination sequence. Unique restriction enzyme sites at the 5' and 3' ends of the cassette allow for easy insertion into a pre-existing vector.

A heterologous coding sequence may be for any protein relating to the present invention. The sequence encoding the protein of interest will encode a signal peptide which allows processing and translocation of the protein, as appropriate, and will usually lack any sequence which might result in the binding of the desired protein of the invention to a membrane. Since, for the most part, the transcriptional initiation region will be for a gene which is expressed and translocated during germination, by employing the signal peptide which provides for translocation, one may also provide for translocation of the protein of interest. In this way, the protein(s) of interest will be translocated from the cells in which they are expressed and may be efficiently harvested. Typically secretion in seeds are across the aleurone or scutellar epithelium layer into the endosperm of the seed. While it is not required that the protein be secreted from the cells in which the protein is produced, this facilitates the isolation and purification of the recombinant protein.

Since the ultimate expression of the desired gene product will be in a eucaryotic cell it is desirable to determine whether any portion of the cloned gene contains sequences which will be processed out as introns by the host's splicosome machinery. If so, site-directed mutagenesis of the "intron" region may be conducted to prevent losing a portion of the genetic message as a false intron code, Reed and Maniatis, Cell 41:95-105, 1985.

The vector can be microinjected directly into plant cells by use of micropipettes to mechanically transfer the recombinant DNA. Crossway, Mol. Gen. Genet, 202:179-185, 1985. The genetic material may also be transferred into the plant cell by using polyethylene glycol, Krens, et al., Nature, 296, 72-74, 1982. Another method of introduction of nucleic acid segments is high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface, Klein, et al., Nature, 327, 70-73, 1987 and Knudsen and Muller, 1991, Planta, 185:330-336 teaching particle bombardment of barley endosperm to create transgenic barley. Yet another method of introduction would be fusion of protoplasts with other entities, either minicells, cells, lysosomes or other fusible lipid-surfaced bodies, Fraley, et al., Proc. Natl. Acad. Sci. USA, 79, 1859-1863, 1982.

The vector may also be introduced into the plant cells by electroporation. (Fromm et al., Proc. Natl. Acad. Sci. USA 82:5824, 1985). In this technique, plant protoplasts are electroporated in the presence of plasmids containing the gene construct. Electrical impulses of high field strength reversibly permeabilize biomembranes allowing the introduction of the plasmids. Electroporated plant protoplasts reform the cell wall, divide, and form plant callus.

All plants from which protoplasts can be isolated and cultured to give whole regenerated plants can be transformed by the present invention so that whole plants are recovered which contain the transferred gene. It is known that practically all plants can be regenerated from cultured cells or tissues, including but not limited to all major species of sugarcane, sugar beet, cotton, fruit and other trees, legumes and vegetables. Some suitable plants include, for example, species from the genera Fragaria, Lotus, Medicago, Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersion, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Cichorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Hererocallis, Nemesia, Pelargonium, Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Glycine, Lolium, Zea, Triticum, Sorghum, and Datura.

Means for regeneration vary from species to species of plants, but generally a suspension of transformed protoplasts containing copies of the heterologous gene is first provided. Callus tissue is formed and shoots may be induced from callus and subsequently rooted. Alternatively, embryo formation can be induced from the protoplast suspension. These embryos germinate as natural embryos to form plants. The culture media will generally contain various amino acids and hormones, such as auxin and cytokinins. It is also advantageous to add glutamic acid and proline to the medium, especially for such species as corn and alfalfa. Shoots and roots normally develop simultaneously. Efficient regeneration will depend on the medium, on the genotype, and on the history of the culture. If these three variables are controlled, then regeneration is fully reproducible and repeatable.

In some plant cell culture systems, the desired protein of the invention may be excreted or alternatively, the protein may be extracted from the whole plant. Where the desired protein of the invention is secreted into the medium, it may be collected. Alternatively, the embryos and embryoless-half seeds or other plant tissue may be mechanically disrupted to release any secreted protein between cells and tissues. The mixture may be suspended in a buffer solution to retrieve soluble proteins. Conventional protein isolation and purification methods will be then used to purify the recombinant protein. Parameters of time, temperature pH, oxygen, and volumes will be adjusted through routine methods to optimize expression and recovery of heterologous protein.

iv. Bacterial Systems

Bacterial expression techniques are known in the art. A bacterial promoter is any DNA sequence capable of binding bacterial RNA polymerase and initiating the downstream (3') transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5' end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site and a transcription initiation site. A bacterial promoter may also have a second domain called an operator, that may overlap an adjacent RNA polymerase binding site at which RNA synthesis begins. The operator permits negative regulated (inducible) transcription, as a gene repressor protein may bind the operator and thereby inhibit transcription of a specific gene. Constitutive expression may occur in the absence of negative regulatory elements, such as the operator. In addition, positive regulation may be achieved by a gene activator protein binding sequence, which, if present is usually proximal (5') to the RNA polymerase binding sequence. An example of a gene activator protein is the catabolite activator protein (CAP), which helps initiate transcription of the lac operon in Escherichia coli (E. coli) [Raibaud et al. (1984) Annu. Rev. Genet. 18:173]. Regulated expression may therefore be either positive or negative, thereby either enhancing or reducing transcription.

Sequences encoding metabolic pathway enzymes provide particularly useful promoter sequences. Examples include promoter sequences derived from sugar metabolizing enzymes, such as galactose, lactose (lac) [Chang et al. (1977) Nature 198:1056], and maltose. Additional examples include promoter sequences derived from biosynthetic enzymes such as tryptophan (trp) [Goeddel et al. (1980) Nuc. Acids Res. 8:4057; Yelverton et al. (1981) Nucl. Acids Res. 9:731; U.S. Pat. No. 4,738,921; EP-A-0036776 and EP-A-0121775]. The g-laotamase (bla) promoter system [Weissmann (1981) "The cloning of interferon and other mistakes." In Interferon 3 (ed. I. Gresser)], bacteriophage lambda PL [Shimatake et al. (1981) Nature 292:128] and T5 [U.S. Pat. No. 4,689,406] promoter systems also provide useful promoter sequences.

In addition, synthetic promoters which do not occur in nature also function as bacterial promoters. For example, transcription activation sequences of one bacterial or bacteriophage promoter may be joined with the operon sequences of another bacterial or bacteriophage promoter, creating a synthetic hybrid promoter [U.S. Pat. No. 4,551,433]. For example, the tac promoter is a hybrid trp-lac promoter comprised of both trp promoter and lac operon sequences that is regulated by the lac repressor [Amann et al. (1983) Gene 25:167; de Boer et al. (1983) Proc. Natl. Acad. Sci. 80:21]. Furthermore, a bacterial promoter can include naturally occurring promoters of non-bacterial origin that have the ability to bind bacterial RNA polymerase and initiate transcription. A naturally occurring promoter of non-bacterial origin can also be coupled with a compatible RNA polymerase to produce high levels of expression of some genes in prokaryotes. The bacteriophage T7 RNA polymerase/promoter system is an example of a coupled promoter system [Studier et al. (1986) J. Mol. Biol. 189:113; Tabor et al. (1985) Proc Natl. Acad. Sci. 82:1074]. In addition, a hybrid promoter can also be comprised of a bacteriophage promoter and an E. coli operator region (EPO-A-0 267 851).

In addition to a functioning promoter sequence, an efficient ribosome binding site is also useful for the expression of foreign genes in prokaryotes. In E. coli, the ribosome binding site is called the Shine-Dalgarno (SD) sequence and includes an initiation codon (ATG) and a sequence 3-9 nucleotides in length located 3-11 nucleotides upstream of the initiation codon [Shine et al. (1975) Nature 254:34]. The SD sequence is thought to promote binding of mRNA to the ribosome by the pairing of bases between the SD sequence and the 3' and of E. coli 16S rRNA [Steitz et al. (1979) "Genetic signals and nucleotide sequences in messenger RNA." In Biological Regulation and Development: Gene Expression (ed. R. F. Goldberger)]. To express eukaryotic genes and prokaryotic genes with weak ribosome-binding site [Sambrook et al. (1989) "Expression of cloned genes in Escherichia coli." In Molecular Cloning: A Laboratory Manual].

A DNA molecule may be expressed intracellularly. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus will always be a methionine, which is encoded by the ATG start codon. If desired, methionine at the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide or by either in vivo on in vitro incubation with a bacterial methionine N-terminal peptidase (EP-A-0 219 237).

Fusion proteins provide an alternative to direct expression. Usually, a DNA sequence encoding the N-terminal portion of an endogenous bacterial protein, or other stable protein, is fused to the 5' end of heterologous coding sequences. Upon expression, this construct will provide a fusion of the two amino acid sequences. For example, the bacteriophage lambda cell gene can be linked at the 5' terminus of a foreign gene and expressed in bacteria. The resulting fusion protein preferably retains a site for a processing enzyme (factor Xa) to cleave the bacteriophage protein from the foreign gene [Nagai et al. (1984) Nature 309:810]. Fusion proteins can also be made with sequences from the lacZ [Jia et al. (1987) Gene 60:197], trpE [Allen et al. (1987) J. Biotechnol. 5:93; Makoff et al. (1989) J. Gen. Microbiol. 135:11], and Chey [EP-A-0 324 647] genes. The DNA sequence at the junction of the two amino acid sequences may or may not encode a cleavable site. Another example is a ubiquitin fusion protein. Such a fusion protein is made with the ubiquitin region that preferably retains a site for a processing enzyme (eg. ubiquitin specific processing-protease) to cleave the ubiquitin from the foreign protein. Through this method, native foreign protein can be isolated [Miller et al. (1989) Bio/Technology 7:698].

Alternatively, foreign proteins can also be secreted from the cell by creating chimeric DNA molecules that encode a fusion protein comprised of a signal peptide sequence fragment that provides for secretion of the foreign protein in bacteria [U.S. Pat. No. 4,336,336]. The signal sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell. The protein is either secreted into the growth media (gram-positive bacteria) or into the periplasmic space, located between the inner and outer membrane of the cell (gram-negative bacteria). Preferably there are processing sites, which can be cleaved either in vivo or in vitro encoded between the signal peptide fragment and the foreign gene.

DNA encoding suitable signal sequences can be derived from genes for secreted bacterial proteins, such as the E. coli outer membrane protein gene (ompA) [Masui et al. (1983), in: Experimental Manipulation of Gene Expression; Ghrayeb et al. (1984) EMBO J. 3:2437] and the E. coli alkaline phosphatase signal sequence (phoA) [Oka et al. (1985) Proc. Natl. Acad. Sci. 82:7212]. As an additional example, the signal sequence of the alpha-amylase gene from various Bacillus strains can be used to secrete heterologous proteins from B. subtilis [Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 244 042].

Usually, transcription termination sequences recognized by bacteria are regulatory regions located 3' to the translation stop codon, and thus together with the promoter flank the coding sequence. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Transcription termination sequences frequently include DNA sequences of about 50 nucleotides capable of forming stem loop structures that aid in terminating transcription. Examples include transcription termination sequences derived from genes with strong promoters, such as the trp gene in E. coli as well as other biosynthetic genes.

Usually, the above described components, comprising a promoter, signal sequence (if desired), coding sequence of interest, and transcription termination sequence, are put together into expression constructs. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as bacteria. The replicon will have a replication system, thus allowing it to be maintained in a prokaryotic host either for expression or for cloning and amplification. In addition, a replicon may be either a high or low copy number plasmid. A high copy number plasmid will generally have a copy number ranging from about 5 to about 200, and usually about 10 to about 150. A host containing a high copy number plasmid will preferably contain at least about 10, and more preferably at least about 20 plasmids. Either a high or low copy number vector may be selected, depending upon the effect of the vector and the foreign protein on the host.

Alternatively, the expression constructs can be integrated into the bacterial genome with an integrating vector. Integrating vectors usually contain at least one sequence homologous to the bacterial chromosome that allows the vector to integrate. Integrations appear to result from recombinations between homologous DNA in the vector and the bacterial chromosome. For example, integrating vectors constructed with DNA from various Bacillus strains integrate into the Bacillus chromosome (EP-A-0 127 328). Integrating vectors may also be comprised of bacteriophage or transposon sequences.

Usually, extrachromosomal and integrating expression constructs may contain selectable markers to allow for the selection of bacterial strains that have been transformed. Selectable markers can be expressed in the bacterial host and may include genes which render bacteria resistant to drugs such as ampicillin, chloramphenicol, erythromycin, kanamycin (neomycin), and tetracycline [Davies et al. (1978) Annu. Rev. Microbiol. 32:469]. Selectable markers may also include biosynthetic genes, such as those in the histidine, tryptophan, and leucine biosynthetic pathways.

Alternatively, some of the above described components can be put together in transformation vectors. Transformation vectors are usually comprised of a selectable market that is either maintained in a replicon or developed into an integrating vector, as described above.

Expression and transformation vectors, either extra-chromosomal replicons or integrating vectors, have been developed for transformation into many bacteria. For example, expression vectors have been developed for, inter alia, the following bacteria: Bacillus subtilis [Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 036 259 and EP-A-0 063 953; WO 84/04541], Escherichia coli [Shimatake et al. (1981) Nature 292:128; Amann et al. (1985) Gene 40:183; Studier et al. (1986) J. Mol. Biol. 189:113; EP-A-0 036 776, EP-A-0 136 829 and EP-A-0 136 907], Streptococcus cremoris [Powell et al. (1988) Appl. Environ. Microbiol. 54:655]; Streptococcus lividans [Powell et al. (1988) Appl. Environ. Microbiol. 54:655], Streptomyces lividans [U.S. Pat. No. 4,745,056].

Methods of introducing exogenous DNA into bacterial hosts are well-known in the art, and usually include either the transformation of bacteria treated with CaCl.sub.2 or other agents, such as divalent cations and DMSO. DNA can also be introduced into bacterial cells by electroporation. Transformation procedures usually vary with the bacterial species to be transformed. See eg. [Masson et al. (1989) FEMS Microbiol. Lett. 60:273; Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 036 259 and EP-A-0 063 953; WO 84/04541, Bacillus], [Miller et al. (1988) Proc. Natl. Acad. Sci. 85:856; Wang et al. (1990) J. Bacteriol. 172:949, Campylobacter], [Cohen et al. (1973) Proc. Natl. Acad. Sci. 69:2110; Dower et al. (1988) Nucleic Acids Res. 16:6127; Kushner (1978) "An improved method for transformation of Escherichia coli with ColE1-derived plasmids. In Genetic Engineering: Proceedings of the International Symposium on Genetic Engineering (eds. H. W. Boyer and S. Nicosia); Mandel et al. (1970) J. Mol. Biol. 53:159; Taketo (1988) Biochim. Biophys. Acta 949:318; Escherichia], [Chassy et al. (1987) FEMS Microbiol. Lett. 44:173 Lactobacillus]; [Fiedler et al. (1988) Anal. Biochem 170:38, Pseudomonas]; [Augustin et al. (1990) FEMS Microbiol. Lett. 66:203, Staphylococcus], [Barany et al. (1980) J. Bacteriol. 144:698; Harlander (1987) "Transformation of Streptococcus lactis by electroporation, in: Streptococcal Genetics (ed. J. Ferretti and R. Curtiss III); Perry et al. (1981) Infect. Immun. 32:1295; Powell et al. (1988) Appl. Environ. Microbiol. 54:655; Somkuti et al. (1987) Proc. 4th Evr. Cong. Biotechnology 1:412, Streptococcus].

v. Yeast Expression

Yeast expression systems are also known to one of ordinary skill in the art. A yeast promoter is any DNA sequence capable of binding yeast RNA polymerase and initiating the downstream (3') transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5' end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site (the "TATA Box") and a transcription initiation site. A yeast promoter may also have a second domain called an upstream activator sequence (UAS), which, if present, is usually distal to the structural gene. The UAS permits regulated (inducible) expression. Constitutive expression occurs in the absence of a UAS. Regulated expression may be either positive or negative, thereby either enhancing or reducing transcription.

Yeast is a fermenting organism with an active metabolic pathway, therefore sequences encoding enzymes in the metabolic pathway provide particularly useful promoter sequences. Examples include alcohol dehydrogenase (ADH) (EP-A-0 284 044), enolase, glucokinase, glucose-6-phosphate isomerase, glyceraldehyde-3-phosphate-dehydrogenase (GAP or GAPDH), hexokinase, phosphofructokinase, 3-phosphoglycerate mutase, and pyruvate kinase (PyK) (EPO-A-0 329 203). The yeast PHO5 gene, encoding acid phosphatase, also provides useful promoter sequences [Myanohara et al. (1983) Proc. Natl. Acad. Sci. USA 80: 1].

In addition, synthetic promoters which do not occur in nature also function as yeast promoters. For example, UAS sequences of one yeast promoter may be joined with the transcription activation region of another yeast promoter, creating a synthetic hybrid promoter. Examples of such hybrid promoters include the ADH regulatory sequence linked to the GAP transcription activation region (U.S. Pat. Nos. 4,876,197 and 4,880,734). Other examples of hybrid promoters include promoters which consist of the regulatory sequences of either the ADH2, GAL4, GAL10, OR PHO5 genes, combined with the transcriptional activation region of a glycolytic enzyme gene such as GAP or PyK (EP-A-0 164 556). Furthermore, a yeast promoter can include naturally occurring promoters of non-yeast origin that have the ability to bind yeast RNA polymerase and initiate transcription. Examples of such promoters include, inter alia, [Cohen et al. (1980) Proc. Natl. Acad. Sci. USA 77:1078; Henikoff et al. (1981) Nature 283:835; Hollenberg et al. (1981) Curr. Topics Microbiol. Immunol. 96:119; Hollenberg et al. (1979) "The Expression of Bacterial Antibiotic Resistance Genes in the Yeast Saccharomyces cerevisiae," in: Plasmids of Medical, Environmental and Commercial Importance (eds. K. N. Timmis and A. Puhler); Mercerau-Puigalon et al. (1980) Gene 11:163; Panthier et al. (1980) Curr. Genet. 2:109;].

A DNA molecule may be expressed intracellularly in yeast. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus of the recombinant protein will always be a methionine, which is encoded by the ATG start codon. If desired, methionine at the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide.

Fusion proteins provide an alternative for yeast expression systems, as well as in mammalian, baculovirus, and bacterial expression systems. Usually, a DNA sequence encoding the N-terminal portion of an endogenous yeast protein, or other stable protein, is fused to the 5' end of heterologous coding sequences. Upon expression, this construct will provide a fusion of the two amino acid sequences. For example, the yeast or human superoxide dismutase (SOD) gene, can be linked at the 5' terminus of a foreign gene and expressed in yeast. The DNA sequence at the junction of the two amino acid sequences may or may not encode a cleavable site. See eg. EP-A-0 196 056. Another example is a ubiquitin fusion protein. Such a fusion protein is made with the ubiquitin region that preferably retains a site for a processing enzyme (eg. ubiquitin-specific processing protease) to cleave the ubiquitin from the foreign protein. Through this method, therefore, native foreign protein can be isolated (eg. WO88/024066).

Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provide for secretion in yeast of the foreign protein. Preferably, there are processing sites encoded between the leader fragment and the foreign gene that can be cleaved either in vivo or in vitro. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell.

DNA encoding suitable signal sequences can be derived from genes for secreted yeast proteins, such as the yeast invertase gene (EP-A-0 012 873; JPO. 62,096,086) and the A-factor gene (U.S. Pat. No. 4,588,684). Alternatively, leaders of non-yeast origin, such as an interferon leader, exist that also provide for secretion in yeast (EP-A-0 060 057).

A preferred class of secretion leaders are those that employ a fragment of the yeast alpha-factor gene, which contains both a "pre" signal sequence, and a "pro" region. The types of alpha-factor fragments that can be employed include the full-length pre-pro alpha factor leader (about 83 amino acid residues) as well as truncated alpha-factor leaders (usually about 25 to about 50 amino acid residues) (U.S. Pat. Nos. 4,546,083 and 4,870,008; EP-A-0 324 274). Additional leaders employing an alpha-factor leader fragment that provides for secretion include hybrid alpha-factor leaders made with a presequence of a first yeast, but a pro-region from a second yeast alphafactor. (eg. see WO 89/02463.)

Usually, transcription termination sequences recognized by yeast are regulatory regions located 3' to the translation stop codon, and thus together with the promoter flank the coding sequence. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Examples of transcription terminator sequence and other yeast-recognized termination sequences, such as those coding for glycolytic enzymes.

Usually, the above described components, comprising a promoter, leader (if desired), coding sequence of interest, and transcription termination sequence, are put together into expression constructs. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as yeast or bacteria. The replicon may have two replication systems, thus allowing it to be maintained, for example, in yeast for expression and in a prokaryotic host for cloning and amplification. Examples of such yeast-bacteria shuttle vectors include YEp24 [Botstein et al. (1979) Gene 8:17-24], pCl/1 [Brake et al. (1984) Proc. Natl. Acad. Sci USA 81:4642-4646], and YRp17 [Stinchcomb et al. (1982) J. Mol. Biol. 158:157]. In addition, a replicon may be either a high or low copy number plasmid. A high copy number plasmid will generally have a copy number ranging from about 5 to about 200, and usually about 10 to about 150. A host containing a high copy number plasmid will preferably have at least about 10, and more preferably at least about 20. Enter a high or low copy number vector may be selected, depending upon the effect of the vector and the foreign protein on the host. See eg. Brake et al., supra.

Alternatively, the expression constructs can be integrated into the yeast genome with an integrating vector. Integrating vectors usually contain at least one sequence homologous to a yeast chromosome that allows the vector to integrate, and preferably contain two homologous sequences flanking the expression construct. Integrations appear to result from recombinations between homologous DNA in the vector and the yeast chromosome [Orr-Weaver et al. (1983) Methods in Enzymol. 101:228-245]. An integrating vector may be directed to a specific locus in yeast by selecting the appropriate homologous sequence for inclusion in the vector. See Orr-Weaver et al., supra. One or more expression construct may integrate, possibly affecting levels of recombinant protein produced [Rine et al. (1983) Proc. Natl. Acad. Sci. USA 80:6750]. The chromosomal sequences included in the vector can occur either as a single segment in the vector, which results in the integration of the entire vector, or two segments homologous to adjacent segments in the chromosome and flanking the expression construct in the vector, which can result in the stable integration of only the expression construct.

Usually, extrachromosomal and integrating expression constructs may contain selectable markers to allow for the selection of yeast strains that have been transformed. Selectable markers may include biosynthetic genes that can be expressed in the yeast host, such as ADE2, HIS4, LEU2, TRP1, and ALG7, and the G418 resistance gene, which confer resistance in yeast cells to tunicamycin and G418, respectively. In addition, a suitable selectable marker may also provide yeast with the ability to grow in the presence of toxic compounds, such as metal. For example, the presence of CUP1 allows yeast to grow in the presence of copper ions [Butt et al. (1987) Microbiol, Rev. 51:351].

Alternatively, some of the above described components can be put together into transformation vectors. Transformation vectors are usually comprised of a selectable marker that is either maintained in a replicon or developed into an integrating vector, as described above.

Expression and transformation vectors, either extrachromosomal replicons or integrating vectors, have been developed for transformation into many yeasts. For example, expression vectors have been developed for, inter alia, the following yeasts: Candida albicans [Kurtz, et al. (1986) Mol. Cell. Biol. 6:142], Candida maltosa [Kunze, et al. (1985) J. Basic Microbiol. 25:141]. Hansenula polymorpha [Gleeson, et al. (1986) J. Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet. 202:302], Kluyveromyces fragilis [Das, et al. (1984) J. Bacteriol. 158:1165], Kluyveromyces lactis [De Louvencourt et al. (1983) J. Bacteriol. 154:737; Van den Berg et al. (1990) Bio/Technology 8:135], Pichia guillerimondii [Kunze et al. (1985) J. Basic Microbiol. 25:141], Pichia pastoris [Cregg, et al. (1985) Mol. Cell. Biol. 5:3376; U.S. Pat. Nos. 4,837,148 and 4,929,555], Saccharomyces cerevisiae [Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA 75:1929; Ito et al. (1983) J. Bacteriol. 153:163], Schizosaccharomyces pombe [Beach and Nurse (1981) Nature 300:706], and Yarrowia lipolytica [Davidow, et al. (1985) Curr. Genet. 10:380471 Gaillardin, et al. (1985) Curr. Genet. 10:49].

Methods of introducing exogenous DNA into yeast hosts are well-known in the art, and usually include either the transformation of spheroplasts or of intact yeast cells treated with alkali cations. Transformation procedures usually vary with the yeast species to be transformed. See eg. [Kurtz et al. (1986) Mol. Cell. Biol. 6:142; Kunze et al. (1985) J. Basic Microbiol. 25:141; Candida]; [Gleeson et al. (1986) J. Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet. 202:302; Hansenula]; [Das et al. (1984) J. Bacteriol. 158:1165; De Louvencourt et al. (1983) J. Bacteriol. 154:1165; Van den Berg et al. (1990) Bio/Technology 8:135; Kluyveromyces]; [Cregg et al. (1985) Mol. Cell. Biol. 5:3376; Kunze et al. (1985) J. Basic Microbiol. 25:141; U.S. Pat. Nos. 4,837,148 and 4,929,555; Pichia]; [Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA 75; 1929; Ito et al. (1983) J. Bacteriol. 153:163 Saccharomyces]; [Beach and Nurse (1981) Nature 300:706; Schizosaccharomyces]; [Davidow et al. (1985) Curr. Genet. 10:39; Gaillardin et al. (1985) Curr. Genet. 10:49; Yarrowia].

Antibodies

As used herein, the term "antibody" refers to a polypeptide or group of polypeptides composed of at least one antibody combining site. An "antibody combining site" is the three-dimensional binding space with an internal surface shape and charge distribution complementary to the features of an epitope of an antigen, which allows a binding of the antibody with the antigen. "Antibody" includes, for example, vertebrate antibodies, hybrid antibodies, chimeric antibodies, humanised antibodies, altered antibodies, univalent antibodies, Fab proteins, and single domain antibodies.

Antibodies against the proteins of the invention are useful for affinity chromatography, immunoassays, and distinguishing/identifying streptococcus proteins.

Antibodies to the proteins of the invention, both polyclonal and monoclonal, may be prepared by conventional methods. In general, the protein is first used to immunize a suitable animal, preferably a mouse, rat, rabbit or goat. Rabbits and goats are preferred for the preparation of polyclonal sera due to the volume of serum obtainable, and the availability of labeled anti-rabbit and anti-goat antibodies. Immunization is generally performed by mixing or emulsifying the protein in saline, preferably in an adjuvant such as Freund's complete adjuvant, and injecting the mixture or emulsion parenterally (generally subcutaneously or intramuscularly). A dose of 50-200 .mu.g/injection is typically sufficient. Immunization is generally boosted 2-6 weeks later with one or more injections of the protein in saline, preferably using Freund's incomplete adjuvant. One may alternatively generate antibodies by in vitro immunization using methods known in the art, which for the purposes of this invention is considered equivalent to in vivo immunization. Polyclonal antisera is obtained by bleeding the immunized animal into a glass or plastic container, incubating the blood at 25.degree. C. for one hour, followed by incubating at 4.degree. C. for 2-18 hours. The serum is recovered by centrifugation (eg. 1,000 g for 10 minutes). About 20-50 ml per bleed may be obtained from rabbits.

Monoclonal antibodies are prepared using the standard method of Kohler & Milstein [Nature (1975) 256:495-96], or a modification thereof. Typically, a mouse or rat is immunized as described above. However, rather than bleeding the animal to extract serum, the spleen (and optionally several large lymph nodes) is removed and dissociated into single cells. If desired, the spleen cells may be screened (after removal of nonspecifically adherent cells) by applying a cell suspension to a plate or well coated with the protein antigen. B-cells expressing membrane-bound immunoglobulin specific for the antigen bind to the plate, and are not rinsed away with the rest of the suspension. Resulting B-cells, or all dissociated spleen cells, are then induced to fuse with myeloma cells to form hybridomas, and are cultured in a selective medium (eg. hypoxanthine, aminopterin, thymidine medium, "HAT"). The resulting hybridomas are plated by limiting dilution, and are assayed for production of antibodies which bind specifically to the immunizing antigen (and which do not bind to unrelated antigens). The selected MAb-secreting hybridomas are then cultured either in vitro (eg. in tissue culture bottles or hollow fiber reactors), or in vivo (as ascites in mice).

If desired, the antibodies (whether polyclonal or monoclonal) may be labeled using conventional techniques. Suitable labels include fluorophores, chromophores, radioactive atoms (particularly .sup.32P and .sup.125I), electron-dense reagents, enzymes, and ligands having specific binding partners. Enzymes are typically detected by their activity. For example, horseradish peroxidase is usually detected by its ability to convert 3,3',5,5'-tetramethylbenzidine (TMB) to a blue pigment, quantifiable with a spectrophotometer. "Specific binding partner" refers to a protein capable of binding a ligand molecule with high specificity, as for example in the case of an antigen and a monoclonal antibody specific therefor. Other specific binding partners include biotin and avidin or streptavidin, IgG and protein A, and the numerous receptor-ligand couples known in the art. It should be understood that the above description is not meant to categorize the various labels into distinct classes, as the same label may serve in several different modes. For example, .sup.125I may serve as a radioactive label or as an electron-dense reagent. HRP may serve as enzyme or as antigen for a MAb. Further, one may combine various labels for desired effect. For example, MAbs and avidin also require labels in the practice of this invention: thus, one might label a MAb with biotin, and detect its presence with avidin labeled with .sup.125I, or with an anti-biotin MAb labeled with HRP. Other permutations and possibilities will be readily apparent to those of ordinary skill in the art, and are considered as equivalents within the scope of the instant invention.

Pharmaceutical Compositions

Pharmaceutical compositions can comprise either polypeptides, antibodies, or nucleic acid of the invention. The pharmaceutical compositions will comprise a therapeutically effective amount of either polypeptides, antibodies, or polynucleotides of the claimed invention.

The term "therapeutically effective amount" as used herein refers to an amount of a therapeutic agent to treat, ameliorate, or prevent a desired disease or condition, or to exhibit a detectable therapeutic or preventative effect. The effect can be detected by, for example, chemical markers or antigen levels. Therapeutic effects also include reduction in physical symptoms, such as decreased body temperature. The precise effective amount for a subject will depend upon the subject's size and health, the nature and extent of the condition, and the therapeutics or combination of therapeutics selected for administration. Thus, it is not useful to specify an exact effective amount in advance. However, the effective amount for a given situation can be determined by routine experimentation and is within the judgement of the clinician.

For purposes of the present invention, an effective dose will be from about 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the molecule of the invention in the individual to which it is administered.

A pharmaceutical composition can also contain a pharmaceutically acceptable carrier. The term "pharmaceutically acceptable carrier" refers to a carrier for administration of a therapeutic agent, such as antibodies or a polypeptide, genes, and other therapeutic agents. The term refers to any pharmaceutical carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity. Suitable carriers may be large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, and inactive virus particles. Such carriers are well known to those of ordinary skill in the art.

Pharmaceutically acceptable salts can be used therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. A thorough discussion of pharmaceutically acceptable excipients is available in Remington's Pharmaceutical Sciences (Mack Pub. Co., N.J. 1991).

Pharmaceutically acceptable carriers in therapeutic compositions may contain liquids such as water, saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles. Typically, the therapeutic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. Liposomes are included within the definition of a pharmaceutically acceptable carrier.

Delivery Methods

Once formulated, the compositions of the invention can be administered directly to the subject. The subjects to be treated can be animals; in particular, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished by injection, either subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Other modes of administration include oral and pulmonary administration, suppositories, and transdermal or transcutaneous applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage treatment may be a single dose schedule or a multiple dose schedule.

Vaccines

Vaccines according to the invention may either be prophylactic (ie. to prevent infection) or therapeutic (ie. to treat disease after infection).

Such vaccines comprise immunising antigen(s), immunogen(s), polypeptide(s), protein(s) or nucleic acid, usually in combination with "pharmaceutically acceptable carriers," which include any carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition. Suitable carriers are typically large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, lipid aggregates (such as oil droplets or liposomes), and inactive virus particles. Such carriers are well known to those of ordinary skill in the art. Additionally, these carriers may function as immunostimulating agents ("adjuvants"). Furthermore, the antigen or immunogen may be conjugated to a bacterial toxoid, such as a toxoid from diphtheria, tetanus, cholera, H. pylori, etc. pathogens.

Preferred adjuvants to enhance effectiveness of the composition include, but are not limited to: (1) oil-in-water emulsion formulations (with or without other specific immunostimulating agents such as muramyl peptides (see below) or bacterial cell wall components), such as for example (a) MF59.TM. (WO90/14837; Chapter 10 in Vaccine Design--the subunit and adjuvant approach (1995) ed. Powell & Newman), containing 5% Squalene, 0.5% Tween 80, and 0.5% Span 85 (optionally containing MTP-PE) formulated into submicron particles using a microfluidizer, (b) SAF, containing 10% Squalane, 0.4% Tween 80, 5% pluronic-blocked polymer L121, and thr-MDP either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion, and (c) Ribi.TM. adjuvant system (RAS), (Ribi Immunochem, Hamilton, Mont.) containing 2% Squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL+CWS (Detox.TM.); (2) saponin adjuvants, such as QS21 or Stimulon.TM. (Cambridge Bioscience, Worcester, Mass.) may be used or particles generated therefrom such as ISCOMs (immunostimulating complexes), which ISCOMS may be devoid of additional detergent e.g. WO00/07621; (3) Complete Freund's Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA); (4) cytokines, such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12 (WO99/44636), etc.), interferons (e.g. gamma interferon), macrophage colony stimulating factor (M-CSF), tumor necrosis factor (TNF), etc.; (5) monophosphoryl lipid A (MPL) or 3-O-deacylated MPL (3dMPL) e.g. GB-2220221, EP-A-0689454; (6) combinations of 3dMPL with, for example, QS21 and/or oil-in-water emulsions e.g. EP-A-0835318, EP-A-0735898, EP-A-0761231; (7) oligonucleotides comprising CpG motifs [Krieg Vaccine 2000, 19, 618-622; Krieg Curr opin Mol Ther 2001 3:15-24; Roman et al., Nat. Med., 1997, 3, 849-854; Weiner et al., PNAS USA, 1997, 94, 10833-10837; Davis et al., J. Immunol., 1998, 160, 870-876; Chu et al., J. Exp. Med., 1997, 186, 1623-1631; Lipford et al., Eur. J. Immunol., 1997, 27, 2340-2344; Moldoveanu et al., Vaccine, 1988, 16, 1216-1224, Krieg et al., Nature, 1995, 374, 546-549; Klinman et al., PNAS USA, 1996, 93, 2879-2883; Ballas et al., J. Immunol., 1996, 157, 1840-1845; Cowdery et al., J. Immunol., 1996, 156, 4570-4575; Halpern et al., Cell. Immunol., 1996, 167, 72-78; Yamamoto et al., Jpn. J. Cancer Res., 1988, 79, 866-873; Stacey et al., J. Immunol., 1996, 157, 2116-2122; Messina et al., J. Immunol., 1991, 147, 1759-1764; Yi et al., J. Immunol., 1996, 157, 4918-4925; Yi et al., J. Immunol., 1996, 157, 5394-5402; Yi et al., J. Immunol., 1998, 160, 4755-4761; and Yi et al., J. Immunol., 1998, 160, 5898-5906; International patent applications WO96/02555, WO98/16247, WO98/18810, WO98/40100, WO98/55495, WO98/37919 and WO98/52581] i.e. containing at least one CG dinucleotide, with 5-methylcytosine optionally being used in place of cytosine; (8) a polyoxyethylene ether or a polyoxyethylene ester e.g. WO99/52549; (9) a polyoxyethylene sorbitan ester surfactant in combination with an octoxynol (e.g. WO01/21207) or a polyoxyethylene alkyl ether or ester surfactant in combination with at least one additional non-ionic surfactant such as an octoxynol (e.g. WO01/21152); (10) an immunostimulatory oligonucleotide (e.g. a CpG oligonucleotide) and a saponin e.g. WO00/62800; (11) an immunostimulant and a particle of metal salt e.g. WO00/23105; (12) a saponin and an oil-in-water emulsion e.g. WO99/11241; (13) a saponin (e.g. QS21)+3dMPL+IL-12 (optionally+a sterol) e.g. WO98/57659; (14) aluminium salts, preferably hydroxide or phosphate, but any other suitable salt may also be used (e.g. hydroxyphosphate, oxyhydroxide, orthophosphate, sulphate etc. [e.g. see chapters 8 & 9 of Powell & Newman]). Mixtures of different aluminium salts may also be used. The salt may take any suitable form (e.g. gel, crystalline, amorphous etc.); (15) other substances that act as immunostimulating agents to enhance the efficacy of the composition. Aluminium salts and/or MF59.TM. are preferred.

As mentioned above, muramyl peptides include, but are not limited to, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1'-2'-dipalmitoyl-s- n-glycero-3-hydroxyphosphoryloxy)-ethylamine (MTP-PE), etc.

The immunogenic compositions (eg. the immunising antigen/immunogen/polypeptide/protein/nucleic acid, pharmaceutically acceptable carrier, and adjuvant) typically will contain diluents, such as water, saline, glycerol, ethanol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles.

Typically, the immunogenic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. The preparation also may be emulsified or encapsulated in liposomes for enhanced adjuvant effect, as discussed above under pharmaceutically acceptable carriers.

Immunogenic compositions used as vaccines comprise an immunologically effective amount of the antigenic or immunogenic polypeptides, as well as any other of the above-mentioned components, as needed. By "immunologically effective amount", it is meant that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment or prevention. This amount varies depending upon the health and physical condition of the individual to be treated, the taxonomic group of individual to be treated (eg. nonhuman primate, primate, etc.), the capacity of the individual's immune system to synthesize antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation, and other rel-evant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials.

The immunogenic compositions are conventionally administered parenterally, eg. by injection, either subcutaneously, intramuscularly, or transdermally/transcutaneously (eg. WO98/20734). Additional formulations suitable for other modes of administration include oral and pulmonary formulations, suppositories, and transdermal applications. Dosage treatment may be a single dose schedule or a multiple dose schedule. The vaccine may be administered in conjunction with other immunoregulatory agents.

As an alternative to protein-based vaccines, DNA vaccination may be used [eg. Robinson & Torres (1997) Seminars in Immunol 9:271-283; Donnelly et al. (1997) Annu Rev Immunol 15:617-648; later herein].

Gene Delivery Vehicles

Gene therapy vehicles for delivery of constructs including a coding sequence of a therapeutic of the invention, to be delivered to the mammal for expression in the mammal, can be administered either locally or systemically. These constructs can utilize viral or non-viral vector approaches in in vivo or ex vivo modality. Expression of such coding sequence can be induced using endogenous mammalian or heterologous promoters. Expression of the coding sequence in vivo can be either constitutive or regulated.

The invention includes gene delivery vehicles capable of expressing the contemplated nucleic acid sequences. The gene delivery vehicle is preferably a viral vector and, more preferably, a retroviral, adenoviral, adeno-associated viral (AAV), herpes viral, or alphavirus vector. The viral vector can also be an astrovirus, coronavirus, orthomyxovirus, papovavirus, paramyxovirus, parvovirus, picornavirus, poxvirus, or togavirus viral vector. See generally, Jolly (1994) Cancer Gene Therapy 1:51-64; Kimura (1994) Human Gene Therapy 5:845-852; Connelly (1995) Human Gene Therapy 6:185-193; and Kaplitt (1994) Nature Genetics 6:148-153.

Retroviral vectors are well known in the art and we contemplate that any retroviral gene therapy vector is employable in the invention, including B, C and D type retroviruses, xenotropic retroviruses (for example, NZB-X1, NZB-X2 and NZB9-1 (see O'Neill (1985) J. Virol. 53:160) polytropic retroviruses eg. MCF and MCF-MLV (see Kelly (1983) J. Virol. 45:291), spumaviruses and lentiviruses. See RNA Tumor Viruses, Second Edition, Cold Spring Harbor Laboratory, 1985.

Portions of the retroviral gene therapy vector may be derived from different retroviruses. For example, retrovector LTRs may be derived from a Murine Sarcoma Virus, a tRNA binding site from a Rous Sarcoma Virus, a packaging signal from a Murine Leukemia Virus, and an origin of second strand synthesis from an Avian Leukosis Virus.

These recombinant retroviral vectors may be used to generate transduction competent retroviral vector particles by introducing them into appropriate packaging cell lines (see U.S. Pat. No. 5,591,624). Retrovirus vectors can be constructed for site-specific integration into host cell DNA by incorporation of a chimeric integrase enzyme into the retroviral particle (see WO96/37626). It is preferable that the recombinant viral vector is a replication defective recombinant virus.

Packaging cell lines suitable for use with the above-described retrovirus vectors are well known in the art, are readily prepared (see WO95/30763 and WO92/05266), and can be used to create producer cell lines (also termed vector cell lines or "VCLs") for the production of recombinant vector particles. Preferably, the packaging cell lines are made from human parent cells (eg. HT1080 cells) or mink parent cell lines, which eliminates inactivation in human serum.

Preferred retroviruses for the construction of retroviral gene therapy vectors include Avian Leukosis Virus, Bovine Leukemia, Virus, Murine Leukemia Virus, Mink-Cell Focus-Inducing Virus, Murine Sarcoma Virus, Reticuloendotheliosis Virus and Rous Sarcoma Virus. Particularly preferred Murine Leukemia Viruses include 4070A and 1504A (Hartley and Rowe (1976) J Virol 19:19-25), Abelson (ATCC No. VR-999), Friend (ATCC No. VR-245), Graffi, Gross (ATCC Nol VR-590), Kirsten, Harvey Sarcoma Virus and Rauscher (ATCC No. VR-998) and Moloney Murine Leukemia Virus (ATCC No. VR-190). Such retroviruses may be obtained from depositories or collections such as the American Type Culture Collection ("ATCC") in Rockville, Md. or isolated from known sources using commonly available techniques.

Exemplary known retroviral gene therapy vectors employable in this invention include those described in patent applications GB2200651, EP0415731, EP0345242, EP0334301, WO89/02468; WO89/05349, WO89/09271, WO90/02806, WO90/07936, WO94/03622, WO93/25698, WO93/25234, WO93/11230, WO93/10218, WO91/02805, WO91/02825, WO95/07994, U.S. Pat. No. 5,219,740, U.S. Pat. Nos. 4,405,712, 4,861,719, 4,980,289, 4,777,127, 5,591,624. See also Vile (1993) Cancer Res 53:3860-3864; Vile (1993) Cancer Res 53:962-967; Ram (1993) Cancer Res 53 (1993) 83-88; Takamiya (1992) J Neurosci Res 33:493-503; Baba (1993) J Neurosurg 79:729-735; Mann (1983) Cell 33:153; Cane (1984) Proc Natl Acad Sci 81:6349; and Miller (1990) Human Gene Therapy 1.

Human adenoviral gene therapy vectors are also known in the art and employable in this invention. See, for example, Berkner (1988) Biotechniques 6:616 and Rosenfeld (1991) Science 252:431, and WO93/07283, WO93/06223, and WO93/07282. Exemplary known adenoviral gene therapy vectors employable in this invention include those described in the above referenced documents and in WO94/12649, WO93/03769, WO93/19191, WO94/28938, WO95/11984, WO95/00655, WO95/27071, WO95/29993, WO95/34671, WO96/05320, WO94/08026, WO94/11506, WO93/06223, WO94/24299, WO95/14102, WO95/24297, WO95/02697, WO94/28152, WO94/24299, WO95/09241, WO95/25807, WO95/05835, WO94/18922 and WO95/09654. Alternatively, administration of DNA linked to killed adenovirus as described in Curiel (1992) Hum. Gene Ther. 3:147-154 may be employed. The gene delivery vehicles of the invention also include adenovirus associated virus (AAV) vectors. Leading and preferred examples of such vectors for use in this invention are the AAV-2 based vectors disclosed in Srivastava, WO93/09239. Most preferred AAV vectors comprise the two AAV inverted terminal repeats in which the native D-sequences are modified by substitution of nucleotides, such that at least 5 native nucleotides and up to 18 native nucleotides, preferably at least 10 native nucleotides up to 18 native nucleotides, most preferably 10 native nucleotides are retained and the remaining nucleotides of the D-sequence are deleted or replaced with non-native nucleotides. The native D-sequences of the AAV inverted terminal repeats are sequences of 20 consecutive nucleotides in each AAV inverted terminal repeat (ie. there is one sequence at each end) which are not involved in HP formation. The non-native replacement nucleotide may be any nucleotide other than the nucleotide found in the native D-sequence in the same position. Other employable exemplary AAV vectors are pWP-19, pWN-1, both of which are disclosed in Nahreini (1993) Gene 124:257-262. Another example of such an AAV vector is psub201 (see Samulski (1987) J. Virol. 61:3096). Another exemplary AAV vector is the Double-D ITR vector. Construction of the Double-D ITR vector is disclosed in U.S. Pat. No. 5,478,745. Still other vectors are those disclosed in Carter U.S. Pat. No. 4,797,368 and Muzyczka U.S. Pat. No. 5,139,941, Chartejee U.S. Pat. No. 5,474,935, and Kotin WO94/288157. Yet a further example of an AAV vector employable in this invention is SSV9AFABTKneo, which contains the AFP enhancer and albumin promoter and directs expression predominantly in the liver. Its structure and construction are disclosed in Su (1996) Human Gene Therapy 7:463-470. Additional AAV gene therapy vectors are described in U.S. Pat. Nos. 5,354,678, 5,173,414, 5,139,941, and 5,252,479.

The gene therapy vectors of the invention also include herpes vectors. Leading and preferred examples are herpes simplex virus vectors containing a sequence encoding a thymidine kinase polypeptide such as those disclosed in U.S. Pat. No. 5,288,641 and EP0176170 (Roizman). Additional exemplary herpes simplex virus vectors include HFEM/ICP6-LacZ disclosed in WO95/04139 (Wistar Institute), pHSVIac described in Geller (1988) Science 241:1667-1669 and in WO90/09441 and WO92/07945, HSV Us3::pgC-lacZ described in Fink (1992) Human Gene Therapy 3:11-19 and HSV 7134, 2 RH 105 and GAL4 described in EP 0453242 (Breakefield), and those deposited with the ATCC with accession numbers VR-977 and VR-260.

Also contemplated are alpha virus gene therapy vectors that can be employed in this invention. Preferred alpha virus vectors are Sindbis viruses vectors. Togaviruses, Semliki Forest virus (ATCC VR-67; ATCC VR-1247), Middleberg virus (ATCC VR-370), Ross River virus (ATCC VR-373; ATCC VR-1246), Venezuelan equine encephalitis virus (ATCC VR923; ATCC VR-1250; ATCC VR-1249; ATCC VR-532), and those described in U.S. Pat. Nos. 5,091,309, 5,217,879, and WO92/10578. More particularly, those alpha virus vectors described in U.S. Ser. No. 08/405,627, filed Mar. 15, 1995, WO94/21792, WO92/10578, WO95/07994, U.S. Pat. Nos. 5,091,309 and 5,217,879 are employable. Such alpha viruses may be obtained from depositories or collections such as the ATCC in Rockville, Md. or isolated from known sources using commonly available techniques. Preferably, alphavirus vectors with reduced cytotoxicity are used (see U.S. Ser. No. 08/679,640).

DNA vector systems such as eukaryotic layered expression systems are also useful for expressing the nucleic acids of the invention. See WO95/07994 for a detailed description of eukaryotic layered expression systems. Preferably, the eukaryotic layered expression systems of the invention are derived from alphavirus vectors and most preferably from Sindbis viral vectors.

Other viral vectors suitable for use in the present invention include those derived from poliovirus, for example ATCC VR-58 and those described in Evans, Nature 339 (1989) 385 and Sabin (1973) J. Biol. Standardization 1:115; rhinovirus, for example ATCC VR-1110 and those described in Arnold (1990) J Cell Biochem L401; pox viruses such as canary pox virus or vaccinia virus, for example ATCC VR-111 and ATCC VR-2010 and those described in Fisher-Hoch (1989) Proc Natl Acad Sci 86:317; Flexner (1989) Ann NY Acad Sci 569:86, Flexner (1990) Vaccine 8:17; in U.S. Pat. No. 4,603,112 and U.S. Pat. No. 4,769,330 and WO89/01973; SV40 virus, for example ATCC VR-305 and those described in Mulligan (1979) Nature 277:108 and Madzak (1992) J Gen Virol 73:1533; influenza virus, for example ATCC VR-797 and recombinant influenza viruses made employing reverse genetics techniques as described in U.S. Pat. No. 5,166,057 and in Enami (1990) Proc Natl Acad Sci 87:3802-3805; Enami & Palese (1991) J Virol 65:2711-2713 and Luytjes (1989) Cell 59:110, (see also McMichael (1983) NEJ Med 309:13, and Yap (1978) Nature 273:238 and Nature (1979) 277:108); human immunodeficiency virus as described in EP-0386882 and in Buchschacher (1992) J. Virol. 66:2731; measles virus, for example ATCC VR-67 and VR-1247 and those described in EP-0440219; Aura virus, for example ATCC VR-368; Bebaru virus, for example ATCC VR-600 and ATCC VR-1240; Cabassou virus, for example ATCC VR-922; Chikungunya virus, for example ATCC VR-64 and ATCC VR-1241; Fort Morgan Virus, for example ATCC VR-924; Getah virus, for example ATCC VR-369 and ATCC VR-1243; Kyzylagach virus, for example ATCC VR-927; Mayaro virus, for example ATCC VR-66; Mucambo virus, for example ATCC VR-580 and ATCC VR-1244; Ndumu virus, for example ATCC VR-371; Pixuna virus, for example ATCC VR-372 and ATCC VR-1245; Tonate virus, for example ATCC VR-925; Triniti virus, for example ATCC VR-469; Una virus, for example ATCC VR-374; Whataroa virus, for example ATCC VR-926; Y-62-33 virus, for example ATCC VR-375; O'Nyong virus, Eastern encephalitis virus, for example ATCC VR-65 and ATCC VR-1242; Western encephalitis virus, for example ATCC VR-70, ATCC VR-1251, ATCC VR-622 and ATCC VR-1252; and coronavirus, for example ATCC VR-740 and those described in Hamre (1966) Proc Soc Exp Biol Med 121:190.

Delivery of the compositions of this invention into cells is not limited to the above mentioned viral vectors. Other delivery methods and media may be employed such as, for example, nucleic acid expression vectors, polycationic condensed DNA linked or unlinked to killed adenovirus alone, for example see U.S. Ser. No. 08/366,787, filed Dec. 30, 1994 and Curiel (1992) Hum Gene Ther 3:147-154 ligand linked DNA, for example see Wu (1989) J Biol Chem 264:16985-16987, eucaryotic cell delivery vehicles cells, for example see U.S. Ser. No. 08/240,030, filed May 9, 1994, and U.S. Ser. No. 08/404,796, deposition of photopolymerized hydrogel materials, hand-held gene transfer particle gun, as described in U.S. Pat. No. 5,149,655, ionizing radiation as described in U.S. Pat. No. 5,206,152 and in WO92/11033, nucleic charge neutralization or fusion with cell membranes. Additional approaches are described in Philip (1994) Mol Cell Biol 14:2411-2418 and in Woffendin (1994) Proc Natl Acad Sci 91:1581-1585.

Particle mediated gene transfer may be employed, for example see U.S. Ser. No. 60/023,867. Briefly, the sequence can be inserted into conventional vectors that contain conventional control sequences for high level expression, and then incubated with synthetic gene transfer molecules such as polymeric DNA-binding cations like polylysine, protamine, and albumin, linked to cell targeting ligands such as asialoorosomucoid, as described in Wu & Wu (1987) J. Biol. Chem. 262:4429-4432, insulin as described in Hucked (1990) Biochem Pharmacol 40:253-263, galactose as described in Plank (1992) Bioconjugate Chem 3:533-539, lactose or transferrin.

Naked DNA may also be employed. Exemplary naked DNA introduction methods are described in WO 90/11092 and U.S. Pat. No. 5,580,859. Uptake efficiency may be improved using biodegradable latex beads. DNA coated latex beads are efficiently transported into cells after endocytosis initiation by the beads. The method may be improved further by treatment of the beads to increase hydrophobicity and thereby facilitate disruption of the endosome and release of the DNA into the cytoplasm.

Liposomes that can act as gene delivery vehicles are described in U.S. Pat. No. 5,422,120, WO95/13796, WO94/23697, WO91/14445 and EP-524,968. As described in U.S. Ser. No. 60/023,867, on non-viral delivery, the nucleic acid sequences encoding a polypeptide can be inserted into conventional vectors that contain conventional control sequences for high level expression, and then be incubated with synthetic gene transfer molecules such as polymeric DNA-binding cations like polylysine, protamine, and albumin, linked to cell targeting ligands such as asialoorosomucoid, insulin, galactose, lactose, or transferrin. Other delivery systems include the use of liposomes to encapsulate DNA comprising the gene under the control of a variety of tissue-specific or ubiquitously-active promoters. Further non-viral delivery suitable for use includes mechanical delivery systems such as the approach described in Woffendin et al (1994) Proc. Natl. Acad. Sci. USA 91(24):11581-11585. Moreover, the coding sequence and the product of expression of such can be delivered through deposition of photopolymerized hydrogel materials. Other conventional methods for gene delivery that can be used for delivery of the coding sequence include, for example, use of hand-held gene transfer particle gun, as described in U.S. Pat. No. 5,149,655; use of ionizing radiation for activating transferred gene, as described in U.S. Pat. No. 5,206,152 and WO92/11033

Exemplary liposome and polycationic gene delivery vehicles are those described in U.S. Pat. Nos. 5,422,120 and 4,762,915; in WO 95/13796; WO94/23697; and WO91/14445; in EP-0524968; and in Stryer, Biochemistry, pages 236-240 (1975) W.H. Freeman, San Francisco; Szoka (1980) Biochem Biophys Acta 600:1; Bayer (1979) Biochem Biophys Acta 550:464; Rivnay (1987) Meth Enzymol 149:119; Wang (1987) Proc Natl Acad Sci 84:7851; Plant (1989) Anal Biochem 176:420.

A polynucleotide composition can comprises therapeutically effective amount of a gene therapy vehicle, as the term is defined above. For purposes of the present invention, an effective dose will be from about 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the DNA constructs in the individual to which it is administered.

Delivery Methods

Once formulated, the polynucleotide compositions of the invention can be administered (1) directly to the subject; (2) delivered ex vivo, to cells derived from the subject; or (3) in vitro for expression of recombinant proteins. The subjects to be treated can be mammals or birds. Also, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished by injection, either subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Other modes of administration include oral and pulmonary administration, suppositories, and transdermal or transcutaneous applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage treatment may be a single dose schedule or a multiple dose schedule.

Methods for the ex vivo delivery and reimplantation of transformed cells into a subject are known in the art and described in eg. WO93/14778. Examples of cells useful in ex vivo applications include, for example, stem cells, particularly hematopoetic, lymph cells, macrophages, dendritic cells, or tumor cells.

Generally, delivery of nucleic acids for both ex vivo and in vitro applications can be accomplished by the following procedures, for example, dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei, all well known in the art.

Polynucleotide and Polypeptide Pharmaceutical Compositions

In addition to the pharmaceutically acceptable carriers and salts described above, the following additional agents can be used with polynucleotide and/or polypeptide compositions.

A. Polypeptides

One example are polypeptides which include, without limitation: asioloorosomucoid (ASOR); transferrin; asialoglycoproteins; antibodies; antibody fragments; ferritin; interleukins; interferons, granulocyte, macrophage colony stimulating factor (GM-CSF), granulocyte colony stimulating factor (G-CSF), macrophage colony stimulating factor (M-CSF), stem cell factor and erythropoietin. Viral antigens, such as envelope proteins, can also be used. Also, proteins from other invasive organisms, such as the 17 amino acid peptide from the circumsporozoite protein of plasmodium falciparum known as RII.

B. Hormones, Vitamins, etc.

Other groups that can be included are, for example: hormones, steroids, androgens, estrogens, thyroid hormone, or vitamins, folic acid.

C. Polyalkylenes, Polysaccharides. Etc.

Also, polyalkylene glycol can be included with the desired polynucleotides/polypeptides. In a preferred embodiment, the polyalkylene glycol is polyethlylene glycol. In addition, mono-, di-, or polysaccharides can be included. In a preferred embodiment of this aspect, the polysaccharide is dextran or DEAE-dextran. Also, chitosan and poly(lactide-co-glycolide)

D. Lipids, and Liposomes

The desired polynucleotide/polypeptide can also be encapsulated in lipids or packaged in liposomes prior to delivery to the subject or to cells derived therefrom.

Lipid encapsulation is generally accomplished using liposomes which are able to stably bind or entrap and retain nucleic acid. The ratio of condensed polynucleotide to lipid preparation can vary but will generally be around 1:1 (mg DNA:micromoles lipid), or more of lipid. For a review of the use of liposomes as carriers for delivery of nucleic acids, see, Hug and Sleight (1991) Biochim. Biophys. Acta. 1097:1-17; Straubinger (1983) Meth. Enzymol. 101:512-527.

Liposomal preparations for use in the present invention include cationic (positively charged), anionic (negatively charged) and neutral preparations. Cationic liposomes have been shown to mediate intracellular delivery of plasmid DNA (Felgner (1987) Proc. Natl. Acad. Sci. USA 84:7413-7416); mRNA (Malone (1989) Proc. Natl. Acad. Sci. USA 86:6077-6081); and purified transcription factors (Debs (1990) J. Biol. Chem. 265:10189-10192), in functional form.

Cationic liposomes are readily available. For example, N[1-2,3-dioleyloxy)propyl]-N,N,N-triethyl-ammonium (DOTMA) liposomes are available under the trademark Lipofectin, from GIBCO BRL, Grand Island, N.Y. (See, also, Felgner supra). Other commercially available liposomes include transfectace (DDAB/DOPE) and DOTAP/DOPE (Boerhinger). Other cationic liposomes can be prepared from readily available materials using techniques well known in the art. See, eg. Szoka (1978) Proc. Natl. Acad. Sci. USA 75:4194-4198; WO90/11092 for a description of the synthesis of DOTAP (1,2-bis(oleoyloxy)-3-(trimethylammonio)propane) liposomes.

Similarly, anionic and neutral liposomes are readily available, such as from Avanti Polar Lipids (Birmingham, Ala.), or can be easily prepared using readily available materials. Such materials include phosphatidyl choline, cholesterol, phosphatidyl ethanolamine, dioleoylphosphatidyl choline (DOPC), dioleoylphosphatidyl glycerol (DOPG), dioleoylphoshatidyl ethanolamine (DOPE), among others. These materials can also be mixed with the DOTMA and DOTAP starting materials in appropriate ratios. Methods for making liposomes using these materials are well known in the art.

The liposomes can comprise multilammelar vesicles (MLVs), small unilamellar vesicles (SUVs), or large unilamellar vesicles (LUVs). The various liposome-nucleic acid complexes are prepared using methods known in the art. See eg. Straubinger (1983) Meth. Immunol. 101:512-527; Szoka (1978) Proc. Natl. Acad. Sci. USA 75:4194-4198; Papahadjopoulos (1975) Biochim. Biophys. Acta 394:483; Wilson (1979) Cell 17:77); Deamer & Bangham (1976) Biochim. Biophys. Acta 443:629; Ostro (1977) Biochem. Biophys. Res. Commun. 76:836; Fraley (1979) Proc. Natl. Acad. Sci. USA 76:3348); Enoch & Strittmatter (1979) Proc. Natl. Acad. Sci. USA 76:145; Fraley (1980) J. Biol. Chem. (1980) 255:10431; Szoka & Papahadjopoulos (1978) Proc. Natl. Acad. Sci. USA 75:145; and Schaefer-Ridder (1982) Science 215:166.

E. Lipoproteins

In addition, lipoproteins can be included with the polynucleotide/polypeptide to be delivered. Examples of lipoproteins to be utilized include: chylomicrons, HDL, IDL, LDL, and VLDL. Mutants, fragments, or fusions of these proteins can also be used. Also, modifications of naturally occurring lipoproteins can be used, such as acetylated LDL. These lipoproteins can target the delivery of polynucleotides to cells expressing lipoprotein receptors. Preferably, if lipoproteins are including with the polynucleotide to be delivered, no other targeting ligand is included in the composition.

Naturally occurring lipoproteins comprise a lipid and a protein portion. The protein portion are known as apoproteins. At the present, apoproteins A, B, C, D, and E have been isolated and identified. At least two of these contain several proteins, designated by Roman numerals, AI, AII, AIV; CI, CII, CIII.

A lipoprotein can comprise more than one apoprotein. For example, naturally occurring chylomicrons comprises of A, B, C & E, over time these lipoproteins lose A and acquire C & E. VLDL comprises A, B, C & E apoproteins, LDL comprises apoprotein B; and HDL comprises apoproteins A, C, & E.

The amino acid of these apoproteins are known and are described in, for example, Breslow (1985) Annu Rev. Biochem 54:699; Law (1986) Adv. Exp Med. Biol. 151:162; Chen (1986) J Biol Chem 261:12918; Kane (1980) Proc Natl Acad Sci USA 77:2465; and Utermann (1984) Hum Genet 65:232.

Lipoproteins contain a variety of lipids including, triglycerides, cholesterol (free and esters), and phospholipids. The composition of the lipids varies in naturally occurring lipoproteins. For example, chylomicrons comprise mainly triglycerides. A more detailed description of the lipid content of naturally occurring lipoproteins can be found, for example, in Meth. Enzymol. 128 (1986). The composition of the lipids are chosen to aid in conformation of the apoprotein for receptor binding activity. The composition of lipids can also be chosen to facilitate hydrophobic interaction and association with the polynucleotide binding molecule.

Naturally occurring lipoproteins can be isolated from serum by ultracentrifugation, for instance. Such methods are described in Meth. Enzymol. (supra); Pitas (1980) J. Biochem. 255:5454-5460 and Mahey (1979) J. Clin. Invest 64:743-750. Lipoproteins can also be produced by in vitro or recombinant methods by expression of the apoprotein genes in a desired host cell. See, for example, Atkinson (1986) Annu Rev Biophys Chem 15:403 and Radding (1958) Biochim Biophys Acta 30: 443. Lipoproteins can also be purchased from commercial suppliers, such as Biomedical Techniologies, Inc., Stoughton, Mass., USA. Further description of lipoproteins can be found in WO98/06437.

F. Polycationic Agents

Polycationic agents can be included, with or without lipoprotein, in a composition with the desired polynucleotide/polypeptide to be delivered.

Polycationic agents, typically, exhibit a net positive charge at physiological relevant pH and are capable of neutralizing the electrical charge of nucleic acids to facilitate delivery to a desired location. These agents have both in vitro, ex vivo, and in vivo applications. Polycationic agents can be used to deliver nucleic acids to a living subject either intramuscularly, subcutaneously, etc.

The following are examples of useful polypeptides as polycationic agents: polylysine, polyarginine, polyornithine, and protamine. Other examples include histones, protamines, human serum albumin, DNA binding proteins, non-histone chromosomal proteins, coat proteins from DNA viruses, such as (X174, transcriptional factors also contain domains that bind DNA and therefore may be useful as nucleic aid condensing agents. Briefly, transcriptional factors such as C/CEBP, c-jun, c-fos, AP-1, AP-2, AP-3, CPF, Prot-1, Sp-1, Oct-1, Oct-2, CREP, and TFIID contain basic domains that bind DNA sequences.

Organic polycationic agents include: spermine, spermidine, and purtrescine.

The dimensions and of the physical properties of a polycationic agent can be extrapolated from the list above, to construct other polypeptide polycationic agents or to produce synthetic polycationic agents.

Synthetic polycationic agents which are useful include, for example, DEAE-dextran, polybrene. Lipofectin.TM., and lipofectAMINE.TM. are monomers that form polycationic complexes when combined with polynucleotides/polypeptides.

Immunodiagnostic Assays

Streptococcus antigens of the invention can be used in immunoassays to detect antibody levels (or, conversely, anti-streptococcus antibodies can be used to detect antigen levels). Immunoassays based on well defined, recombinant antigens can be developed to replace invasive diagnostics methods. Antibodies to streptococcus proteins within biological samples, including for example, blood or serum samples, can be detected. Design of the immunoassays is subject to a great deal of variation, and a variety of these are known in the art. Protocols for the immunoassay may be based, for example, upon competition, or direct reaction, or sandwich type assays. Protocols may also, for example, use solid supports, or may be by immunoprecipitation. Most assays involve the use of labeled antibody or polypeptide; the labels may be, for example, fluorescent, chemiluminescent, radioactive, or dye molecules. Assays which amplify the signals from the probe are also known; examples of which are assays which utilize biotin and avidin, and enzyme-labeled and mediated immunoassays, such as ELISA assays.

Kits suitable for immunodiagnosis and containing the appropriate labeled reagents are constructed by packaging the appropriate materials, including the compositions of the invention, in suitable containers, along with the remaining reagents and materials (for example, suitable buffers, salt solutions, etc.) required for the conduct of the assay, as well as suitable set of assay instructions.

Nucleic Acid Hybridisation

"Hybridization" refers to the association of two nucleic acid sequences to one another by hydrogen bonding. Typically, one sequence will be fixed to a solid support and the other will be free in solution. Then, the two sequences will be placed in contact with one another under conditions that favor hydrogen bonding. Factors that affect this bonding include: the type and volume of solvent; reaction temperature; time of hybridization; agitation; agents to block the non-specific attachment of the liquid phase sequence to the solid support (Denhardt's reagent or BLOTTO); concentration of the sequences; use of compounds to increase the rate of association of sequences (dextran sulfate or polyethylene glycol); and the stringency of the washing conditions following hybridization. See Sambrook et al. [supra] Volume 2, chapter 9, pages 9.47 to 9.57.

"Stringency" refers to conditions in a hybridization reaction that favor association of very similar sequences over sequences that differ. For example, the combination of temperature and salt concentration should be chosen that is approximately 120 to 200.degree. C. below the calculated Tm of the hybrid under study. The temperature and salt conditions can often be determined empirically in preliminary experiments in which samples of genomic DNA immobilized on filters are hybridized to the sequence of interest and then washed under conditions of different stringencies. See Sambrook et al. at page 9.50.

Variables to consider when performing, for example, a Southern blot are (1) the complexity of the DNA being blotted and (2) the homology between the probe and the sequences being detected. The total amount of the fragment(s) to be studied can vary a magnitude of 10, from 0.1 to 1 .mu.g for a plasmid or phage digest to 10.sup.-9 to 10.sup.-8 g for a single copy gene in a highly complex eukaryotic genome. For lower complexity polynucleotides, substantially shorter blotting, hybridization, and exposure times, a smaller amount of starting polynucleotides, and lower specific activity of probes can be used. For example, a single-copy yeast gene can be detected with an exposure time of only 1 hour starting with 1 .mu.g of yeast DNA, blotting for two hours, and hybridizing for 4-8 hours with a probe of 10.sup.8 cpm/.mu.g. For a single-copy mammalian gene a conservative approach would start with 10 .mu.g of DNA, blot overnight, and hybridize overnight in the presence of 10% dextran sulfate using a probe of greater than 10.sup.8 cpm/.mu.g, resulting in an exposure time of -24 hours.

Several factors can affect the melting temperature (Tm) of a DNA-DNA hybrid between the probe and the fragment of interest, and consequently, the appropriate conditions for hybridization and washing. In many cases the probe is not 100% homologous to the fragment. Other commonly encountered variables include the length and total G+C content of the hybridizing sequences and the ionic strength and formamide content of the hybridization buffer. The effects of all of these factors can be approximated by a single equation: Tm=81+16.6(log.sub.10Ci)+0.4[%(G+C)]-0.6(% formamide)-600/n-1.5(% mismatch). where Ci is the salt concentration (monovalent ions) and n is the length of the hybrid in base pairs (slightly modified from Meinkoth & Wahl (1984) Anal. Biochem. 138: 267-284).

In designing a hybridization experiment, some factors affecting nucleic acid hybridization can be conveniently altered. The temperature of the hybridization and washes and the salt concentration during the washes are the simplest to adjust. As the temperature of the hybridization increases (ie. stringency), it becomes less likely for hybridization to occur between strands that are nonhomologous, and as a result, background decreases. If the radiolabeled probe is not completely homologous with the immobilized fragment (as is frequently the case in gene family and interspecies hybridization experiments), the hybridization temperature must be reduced, and background will increase. The temperature of the washes affects the intensity of the hybridizing band and the degree of background in a similar manner. The stringency of the washes is also increased with decreasing salt concentrations.

In general, convenient hybridization temperatures in the presence of 50% formamide are 42.degree. C. for a probe with is 95% to 100% homologous to the target fragment, 37.degree. C. for 90% to 95% homology, and 32.degree. C. for 85% to 90% homology. For lower homologies, formamide content should be lowered and temperature adjusted accordingly, using the equation above. If the homology between the probe and the target fragment are not known, the simplest approach is to start with both hybridization and wash conditions which are nonstringent. If non-specific bands or high background are observed after autoradiography, the filter can be washed at high stringency and reexposed. If the time required for exposure makes this approach impractical, several hybridization and/or washing stringencies should be tested in parallel.

Nucleic Acid Probe Assays

Methods such as PCR, branched DNA probe assays, or blotting techniques utilizing nucleic acid probes according to the invention can determine the presence of cDNA or mRNA. A probe is said to "hybridize" with a sequence of the invention if it can form a duplex or double stranded complex, which is stable enough to be detected.

The nucleic acid probes will hybridize to the streptococcus nucleotide sequences of the invention (including both sense and antisense strands). Though many different nucleotide sequences will encode the amino acid sequence, the native streptococcus sequence is preferred because it is the actual sequence present in cells. mRNA represents a coding sequence and so a probe should be complementary to the coding sequence; single-stranded cDNA is complementary to mRNA, and so a cDNA probe should be complementary to the non-coding sequence.

The probe sequence need not be identical to the streptococcus sequence (or its complement)--some variation in the sequence and length can lead to increased assay sensitivity if the nucleic acid probe can form a duplex with target nucleotides, which can be detected. Also, the nucleic acid probe can include additional nucleotides to stabilize the formed duplex. Additional streptococcus sequence may also be helpful as a label to detect the formed duplex. For example, a non-complementary nucleotide sequence may be attached to the 5' end of the probe, with the remainder of the probe sequence being complementary to a streptococcus sequence. Alternatively, non-complementary bases or longer sequences can be interspersed into the probe, provided that the probe sequence has sufficient complementarity with the a streptococcus sequence in order to hybridize therewith and thereby form a duplex which can be detected.

The exact length and sequence of the probe will depend on the hybridization conditions (e.g. temperature, salt condition etc.). For example, for diagnostic applications, depending on the complexity of the analyte sequence, the nucleic acid probe typically contains at least 10-20 nucleotides, preferably 15-25, and more preferably at least 30 nucleotides, although it may be shorter than this. Short primers generally require cooler temperatures to form sufficiently stable hybrid complexes with the template.

Probes may be produced by synthetic procedures, such as the triester method of Matteucci et al. [J. Am. Chem. Soc. (1981) 103:3185], or according to Urdea et al. [Proc. Natl. Acad. Sci. USA (1983) 80: 7461], or using commercially available automated oligonucleotide synthesizers.

The chemical nature of the probe can be selected according to preference. For certain applications, DNA or RNA are appropriate. For other applications, modifications may be incorporated eg. backbone modifications, such as phosphorothioates or methylphosphonates, can be used to increase in vivo half-life, alter RNA affinity, increase nuclease resistance etc. [eg. see Agrawal & Iyer (1995) Curr Opin Biotechnol 6:12-19; Agrawal (1996) TIBTECH 14:376-387]; analogues such as peptide nucleic acids may also be used [eg. see Corey (1997) TIBTECH 15:224-229; Buchardt et al. (1993) TIBTECH 11:384-386].

Alternatively, the polymerase chain reaction (PCR) is another well-known means for detecting small amounts of target nucleic acid. The assay is described in Mullis et al. [Meth. Enzymol. (1987) 155:335-350] & U.S. Pat. Nos. 4,683,195 & 4,683,202. Two "primer" nucleotides hybridize with the target nucleic acids and are used to prime the reaction. The primers can comprise sequence that does not hybridize to the sequence of the amplification target (or its complement) to aid with duplex stability or, for example, to incorporate a convenient restriction site. Typically, such sequence will flank the desired streptococcus sequence.

A thermostable polymerase creates copies of target nucleic acids from the primers using the original target nucleic acids as a template. After a threshold amount of target nucleic acids are generated by the polymerase, they can be detected by more traditional methods, such as Southern blots. When using the Southern blot method, the labelled probe will hybridize to the streptococcus sequence (or its complement).

Also, mRNA or cDNA can be detected by traditional blotting techniques described in Sambrook et al [supra]. mRNA, or cDNA generated from mRNA using a polymerase enzyme, can be purified and separated using gel electrophoresis. The nucleic acids on the gel are then blotted onto a solid support, such as nitrocellulose. The solid support is exposed to a labelled probe and then washed to remove any unhybridized probe. Next, the duplexes containing the labeled probe are detected. Typically, the probe is labelled with a radioactive moiety.

BRIEF DESCRIPTION OF DRAWINGS FIGS. 1 to 85, 119 to 188, 238 and 239 show SDS-PAGE analysis of total cell extracts from cultures of recombinant E. coli expressing GBS proteins of the invention. Lane 1 in each gel (except for FIG. 185) contains molecular weight markers. These are 94, 67, 43, 30, 20.1 & 14.4 kDa (except for FIGS. 7, 8, 10, 11, 13, 14, 15 and 119-170, which use 250, 150, 100, 75, 50, 37, 25, 15 & 10 kDa). FIG. 86A shows the pDEST15 vector and FIG. 86B shows the pDEST17-1 vector. FIGS. 88 to 118 and 247 to 319 show protein characterisation data for various proteins of the invention. FIGS. 189 to 237 and 240 to 246 show SDS-PAGE analysis of purified GBS proteins of the invention. The left-hand lane contains molecular weight markers. These are 94, 67, 43, 30, 20.1 & 14.4 kDa. MODES FOR CARRYING OUT THE INVENTION The following examples describe nucleic acid sequences which have been identified in Streptococcus, along with their inferred translation products. The examples are generally in the following format: a nucleotide sequence which has been identified in Streptococcus the inferred translation product of this sequence a computer analysis (e.g. PSORT output) of the translation product, indicating antigenicity Most examples describe nucleotide sequences from S. agalactiae. The specific strain which was sequenced was from serotype V, and is a clinical strain isolated in Italy which expresses the R antigen (ISS/Rome/Italy collection, strain.2603 V/R). For several of these examples, the corresponding sequences from S. pyogenes are also given. Where GBS and GAS show homology in this way, there is conservation between species which suggests an essential function and also gives good cross-species reactivity. In contrast, several examples describe nucleotide sequences from GAS for which no homolog in GBS has been identified. This lack of homology gives molecules which are useful for distinguishing GAS from GBS and for making GAS-specific products. The same is true for GBS sequences which lack GAS homologs e.g. these are useful for making GBS-specific products. The examples typically include details of homology to sequences in the public databases. Proteins that are similar in sequence are generally similar in both structure and function, and the homology often indicates a common evolutionary origin. Comparison with sequences of proteins of known function is widely used as a guide for the assignment of putative protein function to a new sequence and has proved particularly useful in whole-genome analyses. Various tests can be used to assess the in vivo immunogenicity of the proteins identified in the examples. For example, the proteins can be expressed recombinantly and used to screen patient sera by immunoblot. A positive reaction between the protein and patient serum indicates that the patient has previously mounted an immune response to the protein in question i.e. the protein is an immunogen. This method can also be used to identify immunodominant proteins. The mouse model used in the examples can also be used. The recombinant protein can also be conveniently used to prepare antibodies e.g. in a mouse. These can be used for direct confirmation that a protein is located on the cell-surface. Labelled antibody (e.g. fluorescent labelling for FACS) can be incubated with intact bacteria and the presence of label on the bacterial surface confirms the location of the protein. For many GBS proteins, the following data are given: SDS-PAGE analysis of total recombinant E. coli cell extracts for GBS protein expression SDS-PAGE analysis after the protein purification Western-blot analysis of GBS total cell extract using antisera raised against recombinant proteins FACS and ELISA analysis against GBS using antisera raise against recombinant proteins Results of the in vivo passive protection assay Details of experimental techniques used are presented below: Sequence Analysis Open reading frames (ORFs) within nucleotide sequences were predicted using the GLIMMER program [Salzberg et al. (1998) Nucleic Acids Res 26:544-8]. Where necessary, start codons were modified and corrected manually on the basis of the presence of ribosome-binding sites and promoter regions on the upstream DNA sequence. ORFs were then screened against the non-redundant protein databases using the programs BLASTp [Altschul et al. (1990) J. Mol. Biol. 215:403-410] and PRAZE, a modification of the Smith-Waterman algorithm [Smith & Waterman (1981) J Mol Biol 147:195-7; see Fleischmann et al (1995) Science 269:496-512]. Leader peptides within the ORFs were located using three different approaches: (i) PSORT [Nakai (1991) Bull. Inst. Chem. Res., Kyoto Univ. 69:269-291; Horton & Nakai (1996) Intellig. Syst. Mol. Biol. 4:109-115; Horton & Nakai (1997) Intellig. Syst. Mol. Biol. 5:147-152]; (ii) SignalP [Nielsen & Krogh (1998) in Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6), AAAI Press, Menlo Park, Calif., pp. 122-130; Nielsen et al. (1999) Protein Engineering 12:3-9; Nielsen et al. (1997). Int. J. Neural Sys. 8:581-599]; and (iii) visual inspection of the ORF sequences. Where a signal sequences is given a "possible site" value, the value represents the C-terminus residue of the signal peptide e.g. a "possible site" of 26 means that the signal sequence consists of amino acids 1-26. Lipoprotein-specific signal peptides were located using three different approaches: (i) PSORT [see above]; (ii) the "prokaryotic membrane lipoprotein lipid attachment site" PROSITE motif [Hofmann et al. (1999) Nucleic Acids Res. 27:215-219; Bucher & Bairoch (1994) in Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology (ISMB-94), AAAI Press, pages 53-61]; and (iii) the FINDPATTERNS program available in the GCG Wisconsin Package, using the pattern (M, L, V)x{9, 35} LxxCx. Transmembrane domains were located using two approaches: (i) PSORT [see above]; (ii) TopPred [von Heijne (1992) J. Mol. Biol. 225:487-494]. LPXTG motifs, characteristic of cell-wall attached proteins in Gram-positive bacteria [Fischetti et al. (1990) Mol Microbiol 4:1603-5] were located, with FINDPATTERNS using the pattern (L, I, V, M, Y, F)Px(T, A, S, G)(G, N, S, T, A, L). RGD motifs, characteristic of cell-adhesion molecules [D'Souza et al. (1991) Trends Biochem Sci 16:246-50] were located using FINDPATTERNS. Enzymes belonging to the glycolytic pathway were also selected as antigens, because these have been found experimentally expressed on the surface of Streptococci [e.g. Pancholi & Fischetti (1992) J Exp Med 176:415-26; Pancholi & Fischetti (1998) J Biol Chem 273:14503-15]. Cloning, Expression and Purification of Proteins GBS genes were cloned to facilitate expression in E. coli as two different types of fusion proteins: a) proteins having a hexa-histidine tag at the amino-terminus (His-gbs) b) proteins having a GST fusion partner at the amino-terminus (Gst-gbs) Cloning was performed using the Gateway.TM. technology (Life Technologies), which is based on the site-specific recombination reactions that mediate integration and excision of phage lambda into and from the E. coli genome. A single cloning experiment included the following steps: 1--Amplification of GBS chromosomal DNA to obtain a PCR product coding for a single ORF flanked by attB recombination sites. 2--Insertion of the PCR product into a pDONR vector (containing attP sites) through a BP reaction (attB.times.attP sites). This reaction gives a so called `pEntry` vector, which now contains attL sites flanking the insert. 3--Insertion of the GBS gene into E. coli expression vectors (pDestination vectors, containing attR sites) through a LR reaction between pEntry and pDestination plasmids (attL.times.attR sites). A) Chromosomal DNA Preparation For chromosomal DNA preparation, GBS strain 2603 V/R (Istituto Superiore Sanita, Rome) was grown to exponential phase in 2 liters TH Broth (Difco) at 37.degree. C., harvested by centrifugation, and dissolved in 40 ml TES (50 mM Tris pH 8, 5 mM EDTA pH 8, 20% sucrose). After addition of 2.5 ml lysozyme solution (25 mg/ml in TES) and 0.5 ml mutanolysin (Sigma M-9901, 25000 U/ml in H.sub.2O), the suspension was incubated at 37.degree. C. for 1 hour. 1 ml RNase (20 mg/ml) and 0.1 ml proteinase K (20 mg/ml) were added and incubation was continued for 30 min. at 37.degree. C. Cell lysis was obtained by adding 5 ml sarkosyl solution (10% N-laurylsarcosine in 250 mM EDTA pH 8.0), and incubating 1 hour at 37.degree. C. with frequent inversion. After sequential extraction with phenol, phenol-chloroform and chloroform, DNA was precipitated with 0.3M sodium acetate pH 5.2 and 2 volumes of absolute ethanol. The DNA pellet was rinsed with 70% ethanol and dissolved in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8). DNA concentration was evaluated by OD.sub.260. B) Oligonucleotide Design Synthetic oligonucleotide primers were designed on the basis of the coding sequence of each ORF. The aim was to express the protein's extracellular region. Accordingly, predicted signal peptides were omitted (by deducing the 5' end amplification primer sequence immediately downstream from the predicted leader sequence) and C-terminal cell-wall ancoring regions were removed (e.g. LPXTG motifs and downstream amino acids). Where additional nucleotides have been deleted, this is indicated by the suffix `d` (e.g. `GBS352d`--see Table V). Conversely, a suffix `L` refers to expression without these deletions. Deletions of C- or N-terminal residues were also sometimes made, as indicated by a `C` or `N` suffix. The amino acid sequences of the expressed GBS proteins (including `d` and `L` forms etc.) are definitively defined by the sequences of the oligonuclotides primers given in Table II. 5' tails of forward primers and 3' tails of reverse primers included attB1 and attB2 sites respectively: Forward primers: 5'-GGGGACAAGTTTGTACAAAAAAGCAGGCTCT-ORF in frame-3' (the TCT sequence preceding the ORF was omitted when the ORF's first coding triplet began with T). Reverse primers: 5'-GGGGACCACTTTGTACAAGAAAGCTGGGTT-ORF reverse complement-3'. The number of nucleotides which hybridized to the sequence to be amplified depended on the melting temperature of the primers, which was determined as described by Breslauer et al. [PNAS USA (1986) 83:3746-50]. The average melting temperature of the selected oligos was 50-55.degree. C. for the hybridizing region and 80-85.degree. C. for the whole oligos. C) Amplification The standard PCR protocol was as follows: 50 ng genomic DNA were used as template in the presence of 0.5 .mu.M each primer, 200 .mu.M each dNTP, 1.5 mM MgCl.sub.2, 1.times. buffer minus Mg.sup.++ (Gibco-BRL) and 2 units of Taq DNA polymerase (Platinum Taq, Gibco-BRL) in a final volume of 100 .mu.l. Each sample underwent a double-step of amplification: 5 cycles performed using as the hybridizing temperature 50.degree. C., followed by 25 cycles at 68.degree. C. The standard cycles were as follows: TABLE-US-00001 Denaturation: 94.degree. C., 2 min 5 cycles: Denaturation: 94.degree. C., 30 seconds Hybridization: 50.degree. C., 50 seconds Elongation: 72.degree. C., 1 min. or 2 min. and 40 sec. 25 cycles: Denaturation: 94.degree. C., 30 seconds Hybridization: 68.degree. C., 50 seconds Elongation: 72.degree. C., 1 min. or 2 min. and 40 sec. Elongation time was 1 minute for ORFs shorter than 2000 bp and 2:40 minutes for ORFs longer than 2000 bp. Amplifications were performed using a Gene Amp PCR system 9600 (Perkin Elmer). To check amplification results, 2 .mu.l of each PCR product were loaded onto 1-1.5 agarose gel and the size of amplified fragments was compared with DNA molecular weight standards (DNA marker IX Roche, 1 kb DNA ladder Biolabs). Single band PCR products were purified by PEG precipitation: 300 .mu.l of TE buffer and 200 .mu.l of 30% PEG 8000/30 mM MgCl.sub.2 were added to 100 .mu.l PCR reaction. After vortexing, the DNA was centrifuged for 20 min at 10000 g, washed with 1 vol. 70% ethanol and the pellet dissolved in 30 .mu.l TE. PCR products smaller than 350 bp were purified using a PCR purification Kit (Qiagen) and eluted with 30 .mu.l of the provided elution buffer. In order to evaluate the yield, 2 .mu.l of the purified DNA were subjected to agarose gel electrophoresis and compared to titrated molecular weight standards. D) Cloning of PCR Products into Expression Vectors Cloning was performed following the Gateway.TM. technology's "one-tube protocol", which consists of a two step reaction (BP and LR) for direct insertion of PCR products into expression vectors. BP reaction (attB.times.attP sites): The reaction allowed insertion of the PCR product into a pDONR vector. The pDONR.TM. 201 vector we used contains the killer toxin gene ccdB between attP1 and attP2 sites to minimize background colonies lacking the PCR insert, and a selectable marker gene for kanamycin resistance. The reaction resulted in a so called pEntry vector, in which the GBS gene was located between attL1 and attL2 sites. 60 fmol of PCR product and 100 ng of pDONR.TM. 201 vector were incubated with 2.5 .mu.l of BP Clonase.TM. in a final volume of 12.5 .mu.l for 4 hours at 25.degree. C. LR reaction (attL.times.attR sites): The reaction allowed the insertion of the GBS gene, now present in the pEntry vector, into E. coli expression vectors (pDestination vectors, containing attR sites). Two pDestination vectors were used (PDEST15 for N-terminal GST fusions--FIG. 86; and pDEST17-1 for N-terminal His-tagged fusions--FIG. 87). Both allow transcription of the ORF fusion coding mRNA under T7 RNA polymerase promoter [Studier et al (1990) Meth. Enzymol 185: 60ff]. To 5 .mu.l of BP reaction were added 0.25 .mu.l of 0.75 M NaCl, 100 ng of destination vector and 1.5 .mu.l of LR Clonase.TM.. The reaction was incubated at 25.degree. C. for 2 hours and stopped with 1 .mu.l of 1 mg/ml proteinase K solution at 37.degree. C. for 15 min. 1 .mu.l of the completed reaction was used to transform 50 .mu.l electrocompetent BL21-SI.TM. cells (0.1 cm, 200 ohms, 25 .mu.F). BL21-SI cells contain an integrated T7 RNA polymerase gene under the control of the salt-inducible prU promoter [Gowrishankar (1985) J. Bacteriol. 164:434ff]. After electroporation cells were diluted in 1 ml SOC medium (20 g/l bacto-tryptone, 5 g/l yeast extract, 0.58 g/l NaCl, 0.186 g/l KCl, 20 mM glucose, 10 mM MgCl.sub.2) and incubated at 37.degree. C. for 1 hour. 200 .mu.l cells were plated onto LBON plates (Luria Broth medium without NaCl) containing 100 .mu.g/ml ampicillin. Plates were then incubated for 16 hours at 37.degree. C. Entry clones: In order to allow the future preparation of Gateway compatible pEntry plasmids containing genes which might turn out of interest after immunological assays, 2.5 .mu.l of BP reaction were incubated for 15 min in the presence of 3 .mu.l 0.15 mg/ml proteinase K solution and then kept at -20.degree. C. The reaction was in this way available to transform E. coli competent cells so as to produce Entry clones for future introduction of the genes in other Destination vectors. E) Protein Expression Single colonies derived from the transformation of LR reactions were inoculated as small-scale cultures in 3 ml LBON 100 .mu.g/ml ampicillin for overnight growth at 25.degree. C. 50-200 .mu.l of the culture was inoculated in 3 ml LBON/Amp to an initial OD600 of 0.1. The cultures were grown at 37.degree. C. until OD600 0.4-0.6 and recombinant protein expression was induced by adding NaCl to a final concentration of 0.3 M. After 2 hour incubation the final OD was checked and the cultures were cooled on ice. 0.5 OD.sub.600 of cells were harvested by centrifugation. The cell pellet was suspended in 50 .mu.l of protein Loading Sample Buffer (50 mM TRIS-HCl pH 6.8, 0.5% w/v SDS, 2.5% v/v glycerin, 0.05% w/v Bromophenol Blue, 100 mM DTT) and incubated at 100 IC for 5 min. 10 .mu.l of sample was analyzed by SDS-PAGE and Coomassie Blue staining to verify the presence of induced protein band. F) Purification of the Recombinant Proteins Single colonies were inoculated in 25 ml LBON 100 .mu.g/ml ampicillin and grown at 25.degree. C. overnight. The overnight culture was inoculated in 500 ml LBON/amp and grown under shaking at 25 IC until OD.sub.600 values of 0.4-0.6. Protein expression was then induced by adding NaCl to a final concentration of 0.3 M. After 3 hours incubation at 25 IC the final OD.sub.600 was checked and the cultures were cooled on ice. After centrifugation at 6000 rpm (JA10 rotor, Beckman) for 20 min., the cell pellet was processed for purification or frozen at -20.degree. C. Proteins were purified in 1 of 3 ways depending on the fusion partner and the protein's solubility: Purification of Soluble His-Tagged Proteins from E. coli 1. Transfer pellets from -20.degree. C. to ice bath and reconstitute each pellet with 10 ml B-PER.TM. solution (Bacterial-Protein Extraction Reagent, Pierce cat. 78266), 10 .mu.l of a 100 mM MgCl.sub.2 solution, 50 .mu.l of DNAse I (Sigma D-4263, 100 Kunits in PBS) and 100 .mu.l of 100 mg/ml lysozyme in PBS (Sigma L-7651, final concentration 1 mg/ml). 2. Transfer resuspended pellets in 50 ml centrifuge tubes and leave at room temperature for 30-40 minutes, vortexing 3-4 times. 3. Centrifuge 15-20 minutes at about 30-40000.times.g. 4. Prepare Poly-Prep (Bio-Rad) columns containing 1 ml of Fast Flow Ni-activated Chelating Sepharose (Pharmacia). Equilibrate with 50 mM phosphate buffer, 300 mM NaCl, pH 8.0. 5. Store the pellet at -20.degree. C., and load the supernatant on to the columns. 6. Discard the flow through. 7. Wash with 10 ml 20 mM imidazole buffer, 50 mM phosphate, 300 mM NaCl, pH 8.0. 8. Elute the proteins bound to the columns with 4.5 ml (1.5 ml+1.5 ml+1.5 ml) 250 mM imidazole buffer, 50 mM phosphate, 300 mM NaCl, pH 8.0 and collect three fractions of .about.1.5 ml each. Add to each tube 15 .mu.l DTT 200 mM (final concentration 2 mM). 9. Measure the protein concentration of the collected fractions with the Bradford method and analyse the proteins by SDS-PAGE. 10. Store the collected fractions at +4.degree. C. while waiting for the results of the SDS-PAGE analysis. 11. For immunisation prepare 4-5 aliquots of 20-100 .mu.g each in 0.5 ml in 40% glycerol. The dilution buffer is the above elution buffer, plus 2 mM DTT. Store the aliquots at -20.degree. C. until immunisation. Purification of His-Tagged Proteins from Inclusion Bodies 1. Bacteria are collected from 500 ml cultures by centrifugation. If required store bacterial pellets at -20.degree. C. Transfer the pellets from -20.degree. C. to room temperature and reconstitute each pellet with 10 ml B-PER.TM. solution, 10 .mu.l of a 100 mM MgCl.sub.2 solution (final 1 mM), 50 .mu.l of DNAse 1 equivalent to 100 Kunits units in PBS and 100 .mu.l of a 100 mg/ml lysozime (Sigma L-7651) solution in PBS (equivalent to 10 mg, final concentration 1 mg/ml). 2. Transfer the resuspended pellets in 50 ml centrifuge tubes and let at room temperature for 30-40 minutes, vortexing 3-4 times. 3. Centrifuge 15 minutes at 30-4000.times.g and collect the pellets. 4. Dissolve the pellets with 50 mM TRIS-HCl, 1 mM TCEP {Tris(2-carboxyethyl)-phosphine hydrochloride, Pierce}, 6M guanidine hydrochloride, pH 8.5. Stir for .about.10 min. with a magnetic bar. 5. Centrifuge as described above, and collect the supernatant. 6. Prepare Poly-Prep (Bio-Rad) columns containing 1 ml of Fast Flow Ni-activated Chelating Sepharose (Pharmacia). Wash the columns twice with 5 ml of H.sub.20 and equilibrate with 50 mM TRIS-HCl, 1 mM TCEP, 6M guanidine hydrochloride, pH 8.5. 7. Load the supernatants from step 5 onto the columns, and wash with 5 ml of 50 mM TRIS-HCl buffer, 1 mM TCEP, 6M urea, pH 8.5 8. Wash the columns with 10 ml of 20 mM imidazole, 50 mM TRIS-HCl, 6M urea, 1 mM TCEP, pH 8.5. Collect and set aside the first 5 ml for possible further controls. 9. Elute proteins bound to columns with 4.5 ml buffer containing 250 mM imidazole, 50 mM TRIS-HCl, 6M urea, 1 mM TCEP, pH 8.5. Add the elution buffer in three 1.5 ml aliquots, and collect the corresponding three fractions. Add to each fraction 15 .mu.l DTT (final concentration 2 mM). 10. Measure eluted protein concentration with Bradford method and analyse proteins by SDS-PAGE. 11. Dialyse overnight the selected fraction against 50 mM Na phosphate buffer, pH 8.8, containing 10% glycerol, 0.5 M arginine, 5 mM reduced glutathione, 0.5 mM oxidized glutathione, 2 M urea. 12. Dialyse against 50 mM Na phosphate buffer, pH 8.8, containing 10% glycerol, 0.5 M arginine, 5 mM reduced glutathione, 0.5 mM oxidized glutathione. 13. Clarify the dialysed protein preparation by centrifugation and discard the non-soluble material and measure the protein concentration with the Bradford method. 14. For each protein destined to the immunization prepare 4-5 aliquot of 20-100 .mu.g each in 0.5 ml after having adjusted the glycerol content up to 40%. Store the prepared aliquots at -20.degree. C. until immunization. Purification of GST-Fusion Proteins from E. coli 1. Bacteria are collected from 500 ml cultures by centrifugation. If required store bacterial pellets at -20.degree. C. Transfer the pellets from -20.degree. C. to room temperature and reconstitute each pellet with 10 ml B-PER.TM. solution, 10 .mu.l of a 100 mM MgCl.sub.2 solution (final 1 mM), 50 .mu.l of DNAse 1 equivalent to 100 Kunits units in PBS and 100 .mu.l of a 100 mg/ml lysozime (Sigma L-7651) solution in PBS (equivalent to 10 mg, final concentration 1 mg/ml). 2. Transfer the resuspended pellets in 50 ml centrifuge tubes and let at room temperature for 30-40 minutes, vortexing 3-4 times. 3. Centrifuge 15-20 minutes at about 30-40000.times.g. 4. Discard centrifugation pellets and load supernatants onto the chromatography columns, as follows. 5. Prepare Poly-Prep (Bio-Rad) columns containing 0.5 ml of Glutathione-Sepharose 4B resin. Wash the columns twice with 1 ml of H.sub.2O and equilibrate with 10 ml PBS, pH 7.4. 6. Load supernatants on to the columns and discard the flow through. 7. Wash the columns with 10 ml PBS, pH 7.4. 8. Elute proteins bound to columns with 4.5 ml of 50 mM TRIS buffer, 10 mM reduced glutathione, pH 8.0, adding 1.5 ml+1.5 ml+1.5 ml and collecting the respective 3 fractions of .about.1.5 ml each. 9. Measure protein concentration of the fractions with the Bradford method and analyse the proteins by SDS-PAGE. 10. Store the collected fractions at +4.degree. C. while waiting for the results of the SDS-PAGE analysis. 11. For each protein destined for immunisation prepare 4-5 aliquots of 20-100 .mu.g each in 0.5 ml of 40% glycerol. The dilution buffer is 50 mM TRIS-HCl, 2 mM DTT, pH 8.0. Store the aliquots at -20.degree. C. until immunisation. FIGS. 167 to 170 and 238 to 239

For the experiments shown in FIGS. 167 to 170, FIG. 238 and lanes 2-6 of FIG. 239, the GBS proteins were fused at the N-terminus to thioredoxin and at C-terminus to a poly-His tail. The plasmid used for cloning is pBAD-DEST49 (Invitrogen Gateway.TM. technology) and expression is under the control of an L(+)-Arabinose dependent promoter. For the production of these GBS antigens, bacteria are grown on RM medium (6 g/l Na.sub.2HPO.sub.4, 3 g/l KH.sub.2PO.sub.4, 0.5 g/l NaCl, 1 g/l NH.sub.4Cl, pH7.4, 2% casaminoacids, 0.2% glucose, 1 mM MgCl.sub.2) containing 100 .mu.g/ml ampicillin. After incubation at 37.degree. C. until cells reach OD.sub.600=0.5, protein expression is induced by adding 0.2% (v/v) L(+)Arabinose for 3 hours. Immunisations with GBS Proteins The purified proteins were used to immunise groups of four CD-1 mice intraperitoneally. 20 .mu.g of each purified protein was injected in Freund's adjuvant at days 1, 21 & 35. Immune responses were monitored by using samples taken on day 0 & 49. Sera were analysed as pools of sera from each group of mice. FACScan Bacteria Binding Assay Procedure. GBS serotype V 2603 V/R strain was plated on TSA blood agar plates and incubated overnight at 37.degree. C. Bacterial colonies were collected from the plates using a sterile dracon swab and inoculated into 100 ml Todd Hewitt Broth. Bacterial growth was monitored every 30 minutes by following OD.sub.600. Bacteria were grown until OD.sub.600=0.7-0.8. The culture was centrifuged for 20 minutes at 5000 rpm. The supernatant was discarded and bacteria were washed once with PBS, resuspended in 1/2 culture volume of PBS containing 0.05% paraformaldehyde, and incubated for 1 hour at 37.degree. C. and then overnight at 4.degree. C. 50 .mu.l bacterial cells (OD.sub.600 0.1) were washed once with PBS and resuspended in 20 .mu.l blocking serum (Newborn Calf Serum, Sigma) and incubated for 20 minutes at room temperature. The cells were then incubated with 100 .mu.l diluted sera (1:200) in dilution buffer (20% Newborn Calf Serum 0.1% BSA in PBS) for 1 hour at 4.degree. C. Cells were centrifuged at 5000 rpm, the supernatant aspirated and cells washed by adding 200 .mu.l washing buffer (0.1% BSA in PBS). 50 .mu.l R-Phicoerytrin conjugated F(ab).sub.2 goat anti-mouse, diluted 1:100 in dilution buffer, was added to each sample and incubated for 1 hour at 4.degree. C. Cells were spun down by centrifugation at 5000 rpm and washed by adding 200 .mu.l of washing buffer. The supernatant was aspirated and cells resuspended in 200 .mu.l PBS. Samples were transferred to FACScan tubes and read. The condition for FACScan setting were: FL2 on; FSC-H threshold:54; FSC PMT Voltage: E 02; SSC PMT: 516; Amp. Gains 2.63; FL-2 PMT: 728. Compensation values: 0. Samples were considered as positive if they had a .DELTA. mean values>50 channel values. Whole Extracts Preparation GBS serotype III COH1 strain and serotype V 2603 V/R strain cells were grown overnight in Todd Hewitt Broth. 1 ml of the culture was inoculated into 100 ml Todd Hewitt Broth. Bacterial growth was monitored every 30 minutes by following OD.sub.600. The bacteria were grown until the OD reached 0.7-0.8. The culture was centrifuged for 20 minutes at 5000 rpm. The supernatant was discarded and bacteria were washed once with PBS, resuspended in 2 ml 50 mM Tris-HCl, pH 6.8 adding 400 units of Mutanolysin (Sigma-Aldrich) and incubated 3 hrs at 37.degree. C. After 3 cycles of freeze/thaw, cellular debris were removed by centrifugation at 14000 g for 15 minutes and the protein concentration of the supernatant was measured by the Bio-Rad Protein assay, using BSA as a standard. Western Blotting Purified proteins (50 ng) and total cell extracts (25 .mu.g) derived from GBS serotype III COH1 strain and serotype V 2603 V/R strain were loaded on 12% or 15% SDS-PAGE and transferred to a nitrocellulose membrane. The transfer was performed for 1 hours at 100V at 4.degree. C., in transferring buffer (25 mM Tris base, 192 mM glycine, 20% methanol). The membrane was saturated by overnight incubation at 4.degree. C. in saturation buffer (5% skimmed milk, 0.1% Tween 20 in PBS). The membrane was incubated for 1 hour at room temperature with 1:1000 mouse sera diluted in saturation buffer. The membrane was washed twice with washing buffer (3% skimmed milk, 0.1% Tween 20 in PBS) and incubated for 1 hour with a 1:5000 dilution of horseradish peroxidase labelled anti-mouse Ig (Bio-Rad). The membrane was washed twice with 0.1% Tween 20 in PBS and developed with the Opti-4CN Substrate Kit (Bio-Rad). The reaction was stopped by adding water. Unless otherwise indicated, lanes 1, 2 and 3 of blots in the drawings are: (1) the purified protein; (2) GBS-III extracts; and (3) GBS-V extracts. Molecular weight markers are also shown. In Vivo Passive Protection Assay in Neonatal Sepsis Mouse model. The immune sera collected from the CD1 immunized mice were tested in a mouse neonatal sepsis model to verify their protective efficacy in mice challenged with GBS serotype III. Newborn Balb/C littermates were randomly divided in two groups within 24 hrs from birth and injected subcutaneously with 25 .mu.l of diluted sera (1:15) from immunized CD1 adult mice. One group received preimmune sera, the other received immune sera. Four hours later all pups were challenged with a 75% lethal dose of the GBS serotype III COH1 strain. The challenge dose obtained diluting a mid log phase culture was administered subcutaneously in 25 .mu.l of saline. The number of pups surviving GBS infection was assessed every 12 hours for 4 days. Results are in Table III. EXAMPLE 1 A DNA sequence (GBSx1402) was identified in S. agalactiae <SEQ ID I> which encodes the amino acid sequence <SEQ ID 2>. Analysis of this protein sequence reveals the following: TABLE-US-00002 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.48 Transmembrane 169-185 (169-185) ----- Final Results ----- bacterial membrane --- Certainty = 0.1192 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-00003 >GP: CAB88235 GB: AL353012 hypothetical serine-rich repeat protein [Schizosaccharomyces pombe] Identities = 41/152 (26%), Positives = 75/152 (48%), Gaps = 4/152 (2%) Query: 22 SSIGYADTSDKNTDTSVVTTTLSEEKRSDELDQSSTGSSSENESSSSSEPETNPSTNPPT 81 - SS +++S +++D+S ++ E S+ D SS+ SSSE+ESSS ++ S++ + Sbjct: 132 SSDSESESSSEDSDSSSSSSDSESESSSEGSDSSSSSSSSESESSSEDNDSSSSSSDSES 19- 1 Query: 82 TEPSQPSPSEENKPDGRTKTE---IGNNKDISSGTKVLISEDSIKNFSKASSDQEEVDRD 138- S+ S S + D +++ ++ SS SED+ + S + S+ E D Sbjct: 192 ESSSEDSDSSSSSSDSESESSSEGSDSSSSSSSSESESSSEDNDSSSSSSDSESESSSED 25- 1 Query: 139 ESSSSKANDGK-KGHSKPKKELPKTGDSHSDT 169 SSS ++D + + SK + DS D+ Sbjct: 252 SDSSSSSSDSESESSSKDSDSSSNSSDSEDDS 283 There is also homology to SEQ ID 1984. A related GBS gene <SEQ ID 8785> and protein <SEQ ID 8786> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00004 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: 6.72 GvH: Signal Score (-7.5): -4.34 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -0.48 threshold: 0.0 INTEGRAL Likelihood = -0.48 Transmembrane 169-185 (169-185) PERIPHERAL Likelihood = 0.16 7 modified ALOM score: 0.60 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1192 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 2 (GBS4) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 9 (lane 3; MW 43.1 kDa) and FIG. 63 (lane 4; MW 50 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 12 (lane 7; MW 30 kDa), FIG. 63 (lane 3; MW 30 kDa) and in FIG. 178 (lane 3; MW 30 kDa). GBS4-GST was purified as shown in FIG. 190 (lane 6) and FIG. 209 (lane 8). Purified GBS4-His is shown in FIGS. 89A, 191 (lane 10), 209 (lane 7) and 228 (lanes 9 & 10). The purified GBS4-His fusion product was used to immunise mice (lane 2 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 89B), FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2 A DNA sequence (GBSx1100) was identified in S. agalactiae <SEQ ID 3> which encodes the amino acid sequence <SEQ ID 4>. This protein is predicted to be aggregation promoting protein. Analysis of this protein sequence reveals the following: TABLE-US-00005 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-00006 >GP:CAA69725 GB:Y08498 aggregation promoting protein [Lactobacillus gasseri] Identities = 56/103 (54%), Positives = 69/103 (66%), Gaps = 5/103 (4%) Query: 82 TASQAEAKSQPT-----IENSMNSSSNLSSSDSAAKEEIARRESNGSYTAQNGQYYGRYQ 136- T S A A+ Q T + + + + N S S++AAK +A RES G Y+A NGQY G+YQ Subj: 195 TYSTASAQKQTTQVAQKTQTTTSYTLNASGSEAAAKAWMAGRESGGPYSAGNGQYIGKYQ 254- Query: 137 LSQSYLNGDLSPENQEKVADNYVVSRYGSWSAALSFWNSNGWY 179 LS SYL GD S NQE+VADNYV SRYGSW+ A FW +NGWY Sbjct: 255 LSASYLGGDYSAANQERVADNYVKSRYGSWTGAQKFWQTNGWY 297 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8709> and protein <SEQ ID 8710> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00007 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 2.59 GvH: Signal Score (-7.5): -0.42 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 6.79 threshold: 0.0 PERIPHERAL Likelihood = 6.79 59 modified ALOM score: -1.86 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00001## A related GBS gene <SEQ ID 8711> and protein <SEQ ID 8712> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00008 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 2.59 GvH: Signal Score (-7.5): -0.42 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 6.79 threshold: 0.0 PERIPHERAL Likelihood = 6.79 59 modified ALOM score: -1.86 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00002## SEQ ID 8712 (GBS166) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 30 (lane 2; MW 13.1 kDa). The GBS166-His fusion product was purified (FIG. 200, lane 10) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 315), which confirmed that the protein is immunoaccessible on GBS bacteria. SEQ ID 4 (GBS15) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 9 (lane 5; MW 44.8 kDa), FIG. 63 (lane 5; MW 44.8 kDa) and FIG. 66 (lane 7; MW 45 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 10 (lane 4; MW 22.3 kDa). It was also expressed as GBS15L, with SDS-PAGE analysis of total cell extract is shown in FIG. 185 (lane 1; MW 50 kDa). Purified GBS15-GST is shown in FIG. 91A, FIG. 190 (lane 9), FIG. 210 (lane 4) and FIG. 245 (lanes 4 & 5). The purified GBS15-GST fusion product was used to immunise mice (lane 1+2 products; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 91B), FACS (FIG. 91C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 3 A DNA sequence (GBSx0091) was identified in S. agalactiae <SEQ ID 303> which encodes the amino acid sequence <SEQ ID 304>. Analysis of this protein sequence reveals the following: TABLE-US-00009 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.66 Transmembrane 22-38 (15-41) ----- Final Results ----- bacterial membrane --- Certainty = 0.4864(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00010 >GP: CAA72096 GB: Y11213 hypothetical protein [Streptococcus thermophilus] Identities = 149/274 (54%), Positives = 208/274 (75%), Gaps = 9/274 (3%) Query: 23 FLVSLLLSFGIFSLIIPKSNP--KLTKKDFLTKKVIPLNYVALGDSLTEGVGDTTSQGGF 80 - F + LL GI IIP S+ K++ K KK + YVA+GDSLT+GVGD+++QGGF Sbjct: 5 FFLLFLLFVGILIFIIPSSHQSSKISDKIRSVKKE-KVTYVAIGDSLTQGVGDSSNQGGF 63 Query: 81 VPLLSESLHNRYSYQVTSVNYGVSGNTSQQILKRMTTDPQIEKDLEKADLLTLTVGGNDV 140- VP+LS++L + +++QVT NYG++GNTS QILKRM I++DL+KA L+TLTVGGNDV Sbjct: 64 VPVLSQALESDFNWQVTPRNYGIAGNTSNQILKRMQEKKDIKRDLKKAKLMTLTVGGNDV 123- Query: 141 LAVIRKELSHLSLNSFEKPAEAYKERLKEILAKARQDNPKLPIYVLGIYNPFYLNFPQLT 20- 0 + VI+ +++L++N+F K A Y++RL++I+ AR++N LPIY++GIYNPFYLNEP++T Sbjct: 124 IHVIKDNITNLNVNTFSKAAVDYQKRLRQIIELARKENKTLPIYIIGIYNPFYLNFPEMT 18- 3 Query: 201 KMQTVIDNWNKATKEVVDASENVYFVPINDRLYKGINGKEGITES------SNSQASITN 25- 4 +MQT++DNWN++T+EV +NVYFVP+ND LYKGINGK G+T S + S N Sbjct: 184 EMQTIVDNWNRSTEEVSKEYDNVYFVPVNDLLYKGINGKGGVTSSDETSQPTKSSQDSLN 24- 3 Query: 255 DALFTGDHFHPNNIGYQIMSNAVMEKINETRKNW 288 DALF DHFHPNN GYQIMS+A++++IN+T+K W Sbjct: 244 DALFEEDHFNPNNTGYQIMSDAILKRINQTKKEW 277 A related DNA sequence was identified in S. pyogenes <SEQ ID 305> which encodes the amino acid sequence <SEQ ID 306>. Analysis of this protein sequence reveals the following:

TABLE-US-00011 Possible site: 39 >>> Seems to have en uncleavable N-term signal seq INTEGRAL Likelihood = -12.05 Transmembrane 18-34 (10-37) ----- Final Results ----- bacterial membrane --- Certainty = 0.5819(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9123> which encodes the amino acid sequence <SEQ ID 9124>. Analysis of this protein sequence reveals the following: TABLE-US-00012 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.05 Transmembrane 12-28 ----- Final Results ----- bacterial membrane --- Certainty = 0.5819(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00013 Identities = 178/282 (63%), Positives = 218/282 (77%) Query: 5 LLLWFVMNKKKILTGLSFFLVSLLLSFGIFSLIIPKSNPKLTKKDFLTKKVIPLNYVALG 64 L LWFVMN + + +G+ FF++SL L+F + ++IIPKSN +L K DFL K+ + + YVA+G Sbjct: 1 LRLWFVMNNRHLFSGIFFFVISLCLAFLLLNIIIPKSNSRLKKSDFLKKEQVAIQYVAIG 60 Query: 65 DSLTEGVGDTTSQGGFVPLLSESLHNRYSYQVTSVNYGVSGNTSQQILKRMTTDPQIEKD 124- DSLTEGVGD T QGGFVPLL+ L + V NYGVSG+TSQQIL RM QI+ Sbjct: 61 DSLTEGVGDLTHQGGFVPLLTNDLSEYFKANVNHQNYGVSGDTSQQILDRMIKQKQIQLS 120- Query: 125 LEKADLLTLTVGGNDVLAVIRKELSHLSLNSFEKPAEAYKERLKEILAKARQDNPKLPIY 18- 4 L+KAD++TLTVGGNDV+AVIRK L+ L ++SF KPA Y++RL++I+ AR+DN LPI+ Sbjct: 121 LKKADIMTLTVGGNDVMAVIRKNLADLQVSSFRKPARQYQKRLRQIIELARKDNKDLPIF 18- 0 Query: 185 VLGIYNPFYLNFPQLTKMQTVIDNWNKATKEVVDASENVYFVPINDRLYKGINGKEGITE 24- 4 +LGIYNPFYLNFP+LT MQ VID+WN TKEVV + VYFVPIND LYKGING+EGI Sbjct: 181 ILGIYNPFYLNFPELTDMQKVIDDWNTKTKEVVGEYDRVYFVPINDLLYKGINGQEGIVH 24- 0 Query: 245 SSNSQASITNDALFTGDHFHPNNIGYQIMSNAVMEKINETRK 286 SS Q +I NDALFTGDHFHPNN GYQIMSNAVMEKI + K Sbjct: 241 SSGDQTTIVNDALFTGDHFHPNNTGYQIMSNAVMEKIKKHEK 282 A related GBS gene <SEQ ID 5> and protein <SEQ ID 6> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00014 Lipop: Possible site: -1 Crend: 4 SRCFLG: 0 McG: Length of UR: 24 Peak Value of UR: 3.02 Net Charge of CR: 3 McG: Discrim Score: 12.27 GvH: Signal Score (-7.5): -3.44 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program Count: 1 value: -9.66 threshold: 0.0 INTEGRAL Likelihood = 9.66 Transmembrane 12-28 (5-31) PERIPHERAL Likelihood = 1.96 118 modified ALOM score: 2.43 icm1 HYPID: 7 CFP: 0.486 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4864(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00003## SEQ ID 6 (GBS103) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 36 (lane 4; MW 32 kDa). The GBS103-His fusion product was purified (FIG. 107A; see also FIG. 201, lane 9) and used to immunise mice (lane 2+3 product; 18.5 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 107B), FACS (FIG. 107C) and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 4 A DNA sequence (GBSx1316) was identified in S. agalactiae <SEQ ID 3837> which encodes the amino acid sequence <SEQ ID 3838>. Analysis of this protein sequence reveals the following: TABLE-US-00015 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.30 Transmembrane 1058-1074 (1056-1075) ----- Final Results ----- bacterial membrane --- Certainty = 0.2720(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 7> and protein <SEQ ID 8> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00016 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -13.26 GvH: Signal Score (-7.5): -5.76 Possible site: 41 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -4.30 threshold: 0.0 INTEGRAL Likelihood = -4.30 Transmembrane 489-505 (487-506) PERIPHERAL Likelihood = 3.71 97 modified ALOM score: 1.36 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2720(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 478-482 SEQ ID 8 (GBS195) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 24 (lane 8). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 31 (lane 5). GBS195C was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 175 (lane 6 & 7; MW 81 kDa). GBS195L was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 83 (lane 2; MW 123 kDa). GBS195LN was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 83 (lane 3; MW 66 kDa). GBS195-GST was purified as shown in FIG. 198, lane 5. GBS195-His was purified as shown in FIG. 222, lane 4-5. GBS195N-His was purified as shown in FIG. 222, lane 6-7. The GBS195-GST fusion product was purified (FIG. 87A) and used to immunise mice (lane 1 product; 13.6 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 87B), FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 5 A DNA sequence (GBSx0002) was identified in S. agalactiae <SEQ ID 4043> which encodes the amino acid sequence <SEQ ID 4044>. This protein is predicted to be lipoprotein MtsA. Analysis of this protein sequence reveals the following: TABLE-US-00017 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3361(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9403> which encodes amino acid sequence <SEQ ID 9404> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 3177> which encodes the amino acid sequence <SEQ ID 3178>. Analysis of this protein sequence reveals the following: TABLE-US-00018 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2412 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00019 Identities = 146/168 (86%), Positives = 161/168 (94%) Query: 1 MNLENGIIYSKNIAKQLIAKDPKNKATYEKNRDAYVAKLEKLDKEAKSKFNAIPANKKLI 60 +NLENGIIYSKNIAKQLIAKDPKNK TYEKN AYVAKLEKLDKEAKSKF+AI NKKLI Sbjct: 107 LNLENGIIYSKNIAKQLIAKDPKNKETYEKNLKAYVAKLEKLDKEAKSKFDAIAENKKLI 16- 6 Query: 61 VTSEGCFKYFSKAYGVPSAYIWEINTEEEGTPDQITSLVKKLKQVRPSALFVESSVDKRP 120- VTSEGCFKYFSKAYGVPSAYIWEINTEEEGTPDQI+SL++KLK ++PSALFVESSVD+RP Sbjct: 167 VTSEGCFKYFSKAYGVPSAYIWEINTEEEGTPDQISSLIEKLKVIKPSALFVESSVDRRP 22- 6 Query: 121 MKSVSRESGIPIYAEIFTDSIAKKGQKGDSYYAMMKWNLDKIAEGLAK 168 M++VS++SGIPIY+EIFTDSIAKKG+ GDSYYAMMKWNLDKI+EGLAK Sbjct: 227 METVSKDSGIPIYSEIFTDSIAKKGKPGDSYYAMMKWNLDKISEGLAK 274 SEQ ID 9404 (GBS679) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 164 (lane 7-9; MW 36 kDa) and in FIG. 188 (lane 8; MW 36 kDa). Purified protein is shown in FIG. 242, lanes 9 & 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 6 A DNA sequence (GBSx0003) was identified in S. agalactiae <SEQ ID 8485> which encodes the amino acid sequence <SEQ ID 8486>. This protein is predicted to be ATP-binding protein MtsB. Analysis of this protein sequence reveals the following: TABLE-US-00020 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2097 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 8765> which encodes the amino acid sequence <SEQ ID 8766>. Analysis of this protein sequence reveals the following: TABLE-US-00021 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1929 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00022 Identities = 143/238 (60%), Positives = 186/238 (78%), Gaps = 2/238 (0%) Query: 1 MIISKHLSVSYDNNL-VLEDINLRLEGSGIIGILGPNGAGKSTLMKALLGLVDSTGESGI 59 MI + +L V+YD N LE IN+ +EG I+GI+GPNGAGKST MKA+L L+D G + Sbjct: 10 MITTNNLCVTYDGNSNALEAINVTIEGPSIVGIIGPNGAGKSTFMKAILNLIDYQGHVTV 69 Query: 60 GG-DLLPLMGRVAYVEQKTNIDYQFPITVGECVSLGLYKERGLFKRLSKTDWEKVSRVID 118- G D L VAYVEQ++ IDY FPITV ECV+LG Y + GLF+R+ K +E+V +V+ Sbjct: 70 DGKDGRKLGHTVAYVEQRSMIDYNFPITVKECVALGTYSKLGLFRRVGKKQFEQVDKVLK 129- Query: 119 QVGLRGFENRPINALSGGQFQRMLMARCLVQEADYIFLDEPFVGIDSISEQIIVNLLKKL 17- 8 QVGL F +RPI +LSGGQFQRML+ARCL+QE+DYIFLDEPFVGIDS+SE+IIV+LLK+L Sbjct: 130 QVGLEDFGHRPIKSLSGGQFQRMLVARCLIQESDYIFLDEPFVGIDSVSEKIIVDLLKEL 18- 9 Query: 179 SKAGKLILVVHHDLSKVDHYFDQVIILNRHLIACGPIDQAFTRENLSAAYGDAILLGQ 236 AGK IL+VHHDLSKV+HYFD+++ILN+HL+A G + + FT + LS AYG+ ++LG+ Sbjct: 190 KMAGKTILIVHHDLSKVEHYFDKLMILNKHLVAYGNVCEVFTVDTLSKAYGNHLILGK 247 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 7 A DNA sequence (GBSx0004) was identified in S. agalactiae <SEQ ID 9> which encodes the amino acid sequence <SEQ ID 10>. Analysis of this protein sequence reveals the following: TABLE-US-00023 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 8 A DNA sequence (GBSx0005) was identified in S. agalactiae <SEQ ID 11> which encodes the amino acid sequence <SEQ ID 12>. This protein is predicted to be integral membrane protein MtsC (znuB). Analysis of this protein sequence reveals the following: TABLE-US-00024 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: 3.77 GvH: Signal Score (-7.5): -0.47 Possible site: 45 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.83 Transmembrane 138-154 (134-162) INTEGRAL Likelihood = -7.96 Transmembrane 60-76 (50-86) INTEGRAL Likelihood = -6.95 Transmembrane 95-111 (93-118) INTEGRAL Likelihood = -5.79 Transmembrane 180-196 (174-216) INTEGRAL Likelihood = -4.35 Transmembrane 198-214 (197-216) INTEGRAL Likelihood = -4.30 Transmembrane 250-266 (246-268) INTEGRAL Likelihood = -3.93 Transmembrane 222-238 (221-241) PERIPHERAL Likelihood = 5.94 116 modified ALOM score: 2.67 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5331(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 13> which encodes the amino acid sequence <SEQ ID 14>. Analysis of this protein sequence reveals the following: TABLE-US-00025 Possible site: 45 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -11.25 Transmembrane 138-154 (134-163) INTEGRAL Likelihood = -9.08 Transmembrane 66-82 (50-86) INTEGRAL Likelihood = -6.79 Transmembrane 95-111 (93-118) INTEGRAL Likelihood = -5.63 Transmembrane 180-196 (176-216) INTEGRAL Likelihood = -4.73 Transmembrane 221-237 (218-241) INTEGRAL Likelihood = -4.35 Transmembrane 250-266 (246-268) INTEGRAL Likelihood = -4.35 Transmembrane 198-214 (197-216) INTEGRAL Likelihood = -2.81 Transmembrane 48-64 (47-64) ----- Final Results ----- bacterial membrane --- Certainty = 0.5501(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00026 Identities = 224/275 (81%), Positives = 255/275 (92%) Query: 1 MFTKFFEGLLTYHFLQNAFITAIVIGIVAGAVGCFIILRSMSLMGDAISHAVLPGVAISF 60 M KFFEGL++YHFLQNA ITA+VIGIV+GAVGCFIILRSMSLMGDAISHAVLPGVA+SF Sbjct: 1 MSMKFFEGLMSYHFLQNALITAVVIGIVSGAVGCFIILRSMSLMGDAISHAVLPGVALSF 60 Query: 61 ILGINFFIGAIVFGLLSSIIITYIKENSVIKGDTAIGITFSSFLALGIILIGLANSTTDL 120- ILG+NFFIGAI+FGLL+S+IITYIKENSVIKGDTAIGITFSSFLALG+ILIG+ANS+TDL Sbjct: 61 ILGVNFFIGAIIFGLLASVIITYIKENSVIKGDTAIGITFSSFLALGVILIGVANSSTDL 120- Query: 121 FHILFGNILAVQDSDKYMTIIVGLIVLTLITIFFKELLLTSFDPVLAKSMGMRVSFYHYL 18- 0 FHILFGNILAVQDSDK++TI V + VL +I++FFKELLLTSFDP+LAKSMG++V+ YHYL Sbjct: 121 FHILFGNILAVQDSDKWITIGVSIFVLVVISLFFKELLLTSFDPILAKSMGVKVNAYHYL 18- 0 Query: 181 LMILLTLVAVTAMQSVGTILIVALLITPAATAYLYVKSLRTMLFLSSALGAVASVLGLYI 24- 0 LM+LLTLVAVTAMQSVGTILIVALLITPAATAYLY SL+ ML +SS LGA+ASVLGLY+ Sbjct: 181 LMVLLTLVAVTAMQSVGTILIVALLITPAATAYLYANSLKVMLVMSSLLGALASVLGLYL 24- 0 Query: 241 GYTFNIAAGSSIVLTSTFMFLLAFLFSPKQSLFKK 275 GYTFN+AAGSSIVLTS MFL++F SPKQ K+ Sbjct: 241 GYTFNVAAGSSIVLTSAMMFLISFFVSPKQGYLKR 275 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 9 A DNA sequence (GBSx0006) was identified in S. agalactiae <SEQ ID 15> which encodes the amino acid sequence <SEQ ID 16>. Analysis of this protein sequence reveals the following: TABLE-US-00027 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1280(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 10 A DNA sequence (GBSx0007) was identified in S. agalactiae <SEQ ID 17> which encodes the amino acid sequence <SEQ ID 18>. This protein is predicted to be peptidyl-prolyl cis-trans isomerase 10 (rotamase). Analysis of this protein sequence reveals the following: TABLE-US-00028 Lipop Possible site: 19 Crend: 2 McG: Discrim Score: 5.27 GvH: Signal Score (-7.5): -4.14 Possible site: 19 >>> May be a lipoprotein ALOM program count: 0 value: 9.34 threshold: 0.0 PERIPHERAL Likelihood = 9.34 89 modified ALOM score: -2.37 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00029 >GP: CAA19257 GB: AL023704 putative Cyclophilin-type peptidyl-prolyl cis-trans isomerase protein [Schizosaccharomyces pombe] Identities = 88/224 (39%), Positives = 123/224 (54%), Gaps = 46/224 (20%) Query: 50 NKKTKQALKADKKAFPQLDKAVAKNEAQ-----------VLIKTSKGDINIKLFPKYAPL 98 - N TK L +D+ + + V NE + +I T++GDI+IKL+P+ AP Sbjct: 419 NMSTKFTL-SDRDVYNEQVLPVTNNEGRQENGNILLGKAAIIHTTQGDISIKLYPEEAPK 47- 7 Query: 99 AVENFLTHAKEGYYNGLSFHRVIKDFMIQSGDPNGDGTGGKSIWNSKDKKKDSGNGFVNE 158- AV+NF THA+ GYY+ FHR+IK+FMIQ GDP GDGTGG+SIW KKD F +E Sbjct: 478 AVQNFTTHAENGYYDNTIFHRIIKNFMIQGGDPLGDGTGGESIW-----KKD----FEDE 52- 8 Query: 159 ISPYLYNIRG-SLAMANAGADTNGSQFFINQSQQDHSKQLSDKKVPKVIIKAYSEGGNPS 21- 7 ISP L + R +++MAN+G +TNGSQFFI P Sbjct: 529 ISPNLKHDRPFTVSMANSGPNTNGSQFFITTDL------------------------TPW 56- 4 Query: 218 LDGGYTVFGQVISGMETVDKIASVEVTKSDQPKEKITITSIKVI 261 LDG +T+F + +G++ V +I E K D+P E I +I ++ Sbjct: 565 LDGKHTIFARAYAGLDVVHRIEQGETDKYDRPLEPTKIINISIV 608 A related DNA sequence was identified in S. pyogenes <SEQ ID 19> which encodes the amino acid sequence <SEQ ID 20>. Analysis of this protein sequence reveals the following:

TABLE-US-00030 Possible site: 19 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00031 >GP: CAB88542 GB: AL353818 putative protein [Arabidopsis thaliana] Identities = 83/186 (44%), Positives = 104/186 (55%), Gaps = 34/186 (18%) Query: 78 VVMRTSQGDITLKLFPKYAPLAVENFLTHAKKGYYDNLTFHRVINDFMIQSGDPKGDGTG 137- V+M T+ GDI +KL+P+ P VENF TH + GYYDN FHRVI FMIQ+GDP GDGTG Sbjct: 476 VIMHTTLGDIHMKLYPEECPKTVENFTTHCRNGYYDNHLFHRVIRGFMIQTGDPLGDGTG 53- 5 Query: 138 GESIWKGKDPKKDAGNGFVNEISPFLYHIRG-ALAMANAGANTNGSQFYINQNKKNQSKG 19- 6 G+SIW G F +E L H R L+MANAG NTNGSQF+I Sbjct: 536 GQSIW---------GREFEDEFHKSLRHDRPFTLSMANAGPNTNGSQFFITT-------- 57- 8 Query: 197 LSSTNYPKPIISAYEHGGNPSLDGGYTVFGQVIDGMDVVDKIAATSINQNDKPEQDITIT 25- 6 P LD +TVFG+V+ GMDVV I ++ND+P QD+ I Sbjct: 579 ----------------VATPWLDNKHTVFGRVVKGMDVVQGIEKVKTDKNDRPYQDVKIL 62- 2 Query: 257 SIDIVK 262 ++ + K Sbjct: 623 NVTVPK 628 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00032 Identities = 172/267 (64%), Positives 221/267 (82%) Query: 1 MKKIIYLGLACVSILTLSGCESIERSLKGDRYVDQKLAENSSKEATEQLNKKTKQALKAD 60 MKK++ L L +S+L LS CES++R++KGD+Y+D+K A+ S+ A++ + ++ALKAD Sbjct: 1 MKKLLSLSLVAISLLNLSACESVDRAIKGDKYIDEKTAKEESEAASKAYEESIQKALKAD 60 Query: 61 KKAFPQLDKAVAKNEAQVLIKTSKGDINIKLFPKYAPLAVENFLTHAKEGYYNGLSFHRV 120- FPQL K V K EA+V+++TS+GDI +KLFPKYAPLAVENFLTHAK+GYY+ L+FHRV Sbjct: 61 ASQFPQLTKEVGKEEAKVVMRTSQGDITLKLFPKYAPLAVENFLTHAKKGYYDNLTFHRV 120- Query: 121 IKDFMIQSGDPNGDGTGGKSIWNSKDKKKDSGNGFVNEISPYLYNIRGSLAMANAGADTN 18- 0 I DFMIQSGDP GDGTGG+SIW KD KKD+GNGFVNEISP+LY+IRG+LAMANAGA+TN Sbjct: 121 INDFMIQSGDPKGDGTGGESIWKGKDPKKDAGNGFVNEISPFLYHIRGALAMANAGANTN 18- 0 Query: 181 GSQFFINQSQQDHSKQLSDKKVPKVIIKAYSEGGNPSLDGGYTVFGQVISGMETVDKIAS 24- 0 GSQF+INQ++++ SK LS PK II AY GGNPSLDGGYTVFGQVI GM+ VDKIA+ Sbjct: 181 GSQFYINQNKKNQSKGLSSTNYPKPIISAYEHGGNPSLDGGYTVFGQVIDGMDVVDKIAA 24- 0 Query: 241 VEVTKSDQPKEKITITSIKVIKDYKFK 267 + ++D+P++ ITITSI ++KDY+FK Sbjct: 241 TSINQNDKPEQDITITSIDIVKDYRFK 267 SEQ ID 18 (GBS205) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 13; MW 31 kDa). GBS205-His was purified as shown in FIG. 206, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 11 A DNA sequence (GBSx0008) was identified in S. agalactiae <SEQ ID 21> which encodes the amino acid sequence <SEQ ID 22>. This protein is predicted to be sporulation protein SpoIIIE (ftsK). Analysis of this protein sequence reveals the following: TABLE-US-00033 Lipop Possible site: -1 Crend: 10 McG: Discrim Score: -22.83 GvH: Signal Score (-7.5): -7.13 Possible site: 39 >>> Seems to have no N-terminal signal sequence ALOM program count: 5 value: -9.24 threshold: 0.0 INTEGRAL Likelihood = -9.24 Transmembrane 36-52 (27-60) INTEGRAL Likelihood = -9.18 Transmembrane 162-178 (154-188) INTEGRAL Likelihood = -4.04 Transmembrane 597-613 (595-615) INTEGRAL Likelihood = -3.77 Transmembrane 63-79 (58-83) INTEGRAL Likelihood = -2.60 Transmembrane 90-106 (88-108) PERIPHERAL Likelihood = -1.32 136 modified ALOM score: 2.35 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4694 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10035> which encodes amino acid sequence <SEQ ID 10036> was also identified. The protein has homology with the following sequences in the GENPEPT database: ##STR00004## ##STR00005## A related DNA sequence was identified in S. pyogenes <SEQ ID 23> which encodes the amino acid sequence <SEQ ID 24>. Analysis of this protein sequence reveals the following: TABLE-US-00034 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.45 Transmembrane 31-47 (25-55) INTEGRAL Likelihood = -7.17 Transmembrane 160-176 (153-183) INTEGRAL Likelihood = -4.99 Transmembrane 93-109 (86-111) INTEGRAL Likelihood = -4.04 Transmembrane 586-602 (584-604) INTEGRAL Likelihood = -1.22 Transmembrane 64-80 (64-80) ----- Final Results ----- bacterial membrane --- Certainty = 0.4779 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00035 !GB:Z99112 DNA translocase [Bacillus subtilis] 601 e-170 Identities = 354/816 (43%), Positives = 499/816 (60%), Gaps = 69/816 (8%) Query: 11 APKKRLTKAEVEKQRAIKRMILSVLMALLLIFAMLRLGVFGVTTYNMIRFLVGSLAYPFM 70 - A KKR ++ + KQ IK + +L + I A+L+LGV G T + RF G + Sbjct: 2 AKKKRKSRKKQAKQLNIKYELNGLLCIAISIIAILQLGVVGQTFIYLFRFFAGEWFILCL 61 Query: 71 FAWLIYLFCFKWLRQKDGMI----AGVVIAFLGLLVEWHAFLFA----MPRMLDQDIFLG 122- L+ W ++ ++ AG+ +L+ H LF + + Sbjct: 62 LGLLVLGVSLFWKKKTPSLLTRRKAGLYCIIASILLLSHVQLFKNLTHKGSIESASVVRN 121- Query: 123 TARLITRDLLALRVTEFVGGGMLGALLYKPIAFLFSNIGSYFIGFLFILLGLFLMTPWDI 18- 2 T L D+ + +GGGM+GALL+ FLF++ GS + + IL+G+ L+T + Sbjct: 122 TWELFLMDMNGSSASPDLGGGMIGALLFAASHFLFASTGSQIMAIVMILIGMILVTGRSL 18- 1 Query: 183 YD--------VSHFVKEA----VDKLAVAYQENKEKRFIKREEHRLQAEKEALEKQAQEE 23- 0 + + F+KE +D + +++ N + K+ + + +K A +KQ E Sbjct: 182 QETLKKWMSPIGRFIKEQWLAFIDDMK-SFKSNMQSS--KKTKAPSKKQKPARKKQQMEP 23- 8 Query: 231 EKRLAELTVDPETGEIVEDSQSQVSYDLAEDMT-KEPEILAYDSHLKDDETSLFDQ---- 28- 5 E E G+ Y+ + EP I ++ +++E+ + ++ Sbjct: 239 EP-------PDEEGD----------YETVSPLIHSEPIISSFSDRNEEEESPVIEKRAEP 28- 1 Query: 286 --EDLAYAHEEIGAYDSLSALASSEDEMDMDEPVEVDFTPKTHLLYKLPTIDLFAPDKPK 34- 3 +L E G +++SA + E++ + Y++P++DL A K Sbjct: 282 VSKPLQDIQPETGDQETVSAPPMTFTELENKD-------------YEMPSLDLLADPKHT 32- 8 Query: 344 NQSKEKNLVRKNIKVLEDTFQSFGIDVKVERAEIGPSVTKYEIKPAVGVRVNRISNLADD 40- 3 Q +K + +N + LE TFQSFG+ KV + +GP+VTKYE+ P VGV+V++I NL+DD Sbjct: 329 GQQADKKNIYENARKLERTFQSFGVKAKVTQVHLGPAVTKYEVYPDVGVKVSKIVNLSDD 38- 8 Query: 404 LALALAAKDVRIEAPIPGKSLIGIEVPNSEIATVSFRELWEQS-DANPENLLEVPLGKAV 46- 2 LALALAAKD+RIEAPIPGKS IGIEVPN+E+A VS +E+ E + P+ + + LG+ + Sbjct: 389 LALALAAKDIRIEAPIPGKSAIGIEVPNAEVAMVSLKEVLESKLNDRPDANVLIGLGRNI 44- 8 Query: 463 NGNARSFNLARMPHLLVAGSTGSGKSVAVNGIISSILMKARPDQVKFMMIDPKMVELSVY 52- 2 +G A L +MPHLLVAG+TGSGKSV VNGII+SILM+A+P +VK MMIDPKMVEL+VY Sbjct: 449 SGEAVLAELNKMPHLLVAGATGSGKSVCVNGIITSILMRAKPHEVKMMMIDPKMVELNVY 50- 8 Query: 523 NDIPHLLIPVVTNPRKASKALQKVVDEMENRYELFSKIGVRNIAGYNTKVEEFNASSEQK 58- 2 N IPHLL PVVT+P+KAS+AL+KVV+EME RYELFS G RNI GYN ++ N K Sbjct: 509 NGIPHLLAPVVTDPKKASQALKKVVNEMERRYELFSHTGTRNIEGYNDYIKRANNEEGAK 56- 8 Query: 583 QIPLPLIVVIVDELADLMMVASKEVEDAIIRLGQKARAAGIHMILATQRPSVDVISGLIK 64- 2 Q LP IVVIVDELADLMMVAS +VED+I RL Q ARAAGIH+I+ATQRPSVDVI+G+IK Sbjct: 569 QPELPYIVVIVDELADLMMVASSDVEDSITRLSQMARAAGIHLIIATQRPSVDVITGVIK 62- 8 Query: 643 ANVPSRMAFAVSSGTDSRTILDENGAEKLLGRGDMLFKPIDENHPVRLQGSFISDDDVER 70- 2 AN+PSR+AF+VSS TDSRTILD GAEKLLGRGDMLF P+ N PVR+QG+F+SDD+VE+ Sbjct: 629 ANIPSRIAFSVSSQTDSRTILDMGGAEKLLGRGDMLFLPVGANKPVRVQGAFLSDDEVEK 68- 8 Query: 703 IVNFIKDQTEADYDDAFDPGEVSDNDPGFSGNGGAAEGDPLFEEAKALVLETQKASASMI 76- 2 +V+ + Q +A Y + P E ++ + D L++EA L++ Q AS SM+ Sbjct: 689 VVDHVITQQKAQYQEEMIPEETTETHSEVT--------DELYDEAVELIVGMQTASVSML 74- 0 Query: 763 QRRLSVGFNRATRLMDELEEAGVIGPAEGTKPRKVL 798 QRR +G+ RA RL+D +EE GV+GP EG+KPR+VL Sbjct: 741 QRRFRIGYTRAARLIDAMEERGVVGPYEGSKPREVL 776 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00036 Identities = 620/818 (75%), Positives = 701/818 (84%), Gaps = 25/818 (3%) Query: 1 MVFMANKKKTKGKKTRRPTKAEIERQRAIQRMITALVLTIILFFGIIRLGIFGITVYNVI 60 MV +KK+ KK R TKAE+E+QRAI+RMI ++++ ++L F ++RLG+FG+T YN+I Sbjct: 1 MVKRNQRKKSAPKK--RLTKAEVEKQRAIKRMILSVLMALLLIFAMLRLGVFGVTTYNMI 58 Query: 61 RFMVGSLAYLFIAATLIYLYFFKWLRKKDSLVAGFLIASLGLLIEWHAYLFSMPILKDKE 120- RF+VGSLAY F+ A LIYL+ FKWLR+KD ++AG +IA LGLL+EWHA+LF+MP + D++ Sbjct: 59 RFLVGSLAYPFMFAWLIYLFCFKWLRQKDGMIAGVVIAFLGLLVEWHAFLFAMPRMLDQD 118- Query: 121 ILRSTARLIVSDLMQFKITVFAGGGMLGALIYKPIAFLFSNIGAYMIGVLFIILGLFLMS 18- 0 I TARLI DL+ ++T F GGGMLGAL+YKPIAFLFSNIG+Y IG LFI+LGLFLM+ Sbjct: 119 IFLGTARLITRDLLALRVTEFVGGGMLGALLYKPIAFLFSNIGSYFIGFLFILLGLFLMT 17- 8 Query: 181 SLEVYDIVEFIRAFKNKVAEKHEQNKKERFAKREMKKAIAEQERIERQKAEEEAYLASVN 24- 0 ++YD+ F++ +K+A +++NK++RF KRE + AE+E +E+Q EEE LA + Sbjct: 179 PWDIYDVSHFVKEAVDKLAVAYQENKEKRFIKREEHRLQAEKEALEKQAQEEEKRLAELT 23- 8 Query: 241 VDPETGEILEDQAEDNLDDALPPEVSETSTPVFEPEILAYETSPQNDPLPV---EPTIYL 29- 7 VDPETGEI+ED + +++E T EPEILAY++ ++D + E Y Sbjct: 239 VDPETGEIVEDSQSQ-----VSYDLAEDMTK--EPEILAYDSHLKDDETSLFDQEDLAYA 29- 1 Query: 298 ED----YDSPIPNMRENDEEMVYDLDDDVDDSDIENVDFTPKTTLVYKLPTIDLFAPDKP 35- 3 + YDS + + +++EM D+D+ V+ VDFTPKT L+YKLPTIDLFAPDKP Sbjct: 292 HEEIGAYDS-LSALASSEDEM--DMDEPVE------VDFTPKTHLLYKLPTIDLFAPDKP 34- 2 Query: 354 KNQSKEKDLVRKNIRVLEETFRSFGIDVKVERAEIGPSVTKYEIKPAVGVRVNRISNLSD 41- 3 KNQSKEK+LVRKNI+VLE+TF+SFGIDVKVERAEIGPSVTKYEIKPAVGVRVNRISNL+D Sbjct: 343 KNQSKEKNLVRKNIKVLEDTFQSFGIDVKVERAEIGPSVTKYEIKPAVGVRVNRISNLAD 40- 2 Query: 414 DLALALAAKDVRIETPIPGKSLIGIEVPNSEIATVSFRELWEQSDANPENLLEVPLGKAV 47- 3 DLALALAAKDVRIE PIPGKSLIGIEVPNSEIATVSFRELWEQSDANPENLLEVPLGKAV Sbjct: 403 DLALALAAKDVRIEAPIPGKSLIGIEVPNSEIATVSFRELWEQSDANPENLLEVPLGKAV 46- 2 Query: 474 NGNARSFNLARMPHLLVAGSTGSGKSVAVNGIISSILMKARPDQVKFMMIDPKMVELSVY 53- 3 NGNARSFNLARMPHLLVAGSTGSGKSVAVNGIISSILMKARPDQVKFMMIDPKMVELSVY Sbjct: 463 NGNARSFNLARMPHLLVAGSTGSGKSVAVNGIISSILMKARPDQVKFMMIDPKMVELSVY 52- 2 Query: 534 NDIPHLLIPVVTNPRKASKALQKVVDEMENRYELFSKIGVRNIAGYNTKVEEFNASSEQK 59- 3 NDIPHLLIPVVTNPRKASKALQKVVDEMENRYELFSKIGVRNIAGYNTKVEEFNASSEQK Sbjct: 523 NDIPHLLIPVVTNPRKASKALQKVVDEMENRYELFSKIGVRNIAGYNTKVEEFNASSEQK 58- 2 Query: 594 QIPLPLIVVIVDELADLMMVASKEVEDAIIRLGQKARAAGIHMILATQRPSVDVISGLIK 65- 3 QIPLPLIVVIVDELADLMMVASKEVEDAIIRLGQKARAAGIHMILATQRPSVDVISGLIK Sbjct: 583 QIPLPLIVVIVDELADLMMVASKEVEDAIIRLGQKARAAGIHMILATQRPSVDVISGLIK 64- 2 Query: 654 ANVPSRIAFAVSSGTDSRTILDENGAEKLLGRGDMLFKPIDENHPVRLQGSFISDDDVER 71- 3 ANVPSR+AFAVSSGTDSRTILDENGAEKLLGRGDMLFKPIDENHPVRLQGSFISDDDVER Sbjct: 643 ANVPSRMAFAVSSGTDSRTILDENGAEKLLGRGDMLFKPIDENHPVRLQGSFISDDDVER 70- 2 Query: 714 IVGFIKDQAEADYDDAFDPGEVSETDNGSGGGGGVPESDPLFEEAKGLVLETQKASASMI 77- 3 IV FIKDQ EADYDDAFDPGEVS+ D G G GG E DPLFEEAK LVLETQKASASMI Sbjct: 703 IVNFIKDQTEADYDDAFDPGEVSDNDPGFSGNGGAAEGDPLFEEAKALVLETQKASASMI 76- 2 Query: 774 QRRLSVGFNRATRLMEELEAAGVIGPAEGTKPRKVLMT 811 QRRLSVGFNRATRLM+ELE AGVIGPAEGTKPRKVL T Sbjct: 763 QRRLSVGFNRATRLMDELEEAGVIGPAEGTKPRKVLQT 800 SEQ ID 22 (GBS272d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 147 (lane 9; MW 55 kDa+lane 10; MW 70 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 147 (lane 11 & 13; MW 85 kDa+lane 12; MW 74 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 12 A DNA sequence (GBSx0009) was identified in S. agalactiae <SEQ ID 25> which encodes the amino acid sequence <SEQ ID 26>. This protein is predicted to be para-aminobenzoate synthetase (pabB) (pabB). Analysis of this protein sequence reveals the following: TABLE-US-00037 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4073 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00038 >GP: AAD07357 GB: AE000547 para-aminobenzoate synthetase (pabB) [Helicobacter pylori 26695] Identities = 204/580 (35%), Positives = 325/580 (55%), Gaps = 50/580 (8%) Query: 16 YRFKNPTKELIADTLEQVLEVIKEVDYYQSQNYYVVGYLSYEASAAF-DSHFKVSQQKLA 74 - ++++ K+L A L ++ + + + Y+V GYL YEA AF D +F+ L Sbjct: 6 FKYQKSVKKLTATNLNELKNALDFISQNRGNGYFV-GYLLYEARLAFLDENFQSQTPFLY 64 Query: 75 GEHLAY---FTVHKDCENEAFPLSYENVRLADNWTANVSEQEYQEAIANIKGQIRQGNTY 131- E +++ E+ +P + +++ ++ Y + +K +++ G+TY Sbjct: 65 FEQFLERKKYSLEPLKEHAFYPKIH----------SSLDQKTYFKQFKAVKERLKNGDTY 114- Query: 132 QVNYTLELSQQLCSDPFSVYERLMVEQGAGYNAYIAYDDKRILSVSPELFFKKK--DEVL 18- 9 QVN T++L + P V++ ++ Q + A+I + +LS SPELFF+ + D + Sbjct: 115 QVNLTMDLFLDTKAKPKRVFKEVVHNQNTPFKAFIENEFGSVLSFSPELFFELEFLDTAI 17- 4 Query: 190 T--TRPMKGTSARKPTYQEDVAERDWLANDPKNRSENMMIVDLLRNDMGRICDVGTVKVK 24- 7 T+PMKGT AR D R +L ND KNRSEN+MIVDLLRND+ R+ +VKV Sbjct: 175 KIITKPMKGTIARSKNPLIDEKNRLFLQNDDKNRSENVMIVDLLRNDLSRLALKNSVKVN 23- 4 Query: 248 KLCQVEQYATVWQMTSTIEGVLSPEVTLMSIFQALYPCGSITGAPKISTMAIINELEKRP 30- 7 +L ++ +V+QM S IE L + +L IF+AL+PCGS+TG PKI TM II LEKRP Sbjct: 235 QLFEIISLPSVYQMISEIEAKLPLKTSLFEIFKALFPCGSVTGCPKIKTMQIIESLEKRP 29- 4 Query: 308 RGIYCGTIGLCMPDGQAIFNVPIRTVQMKGQQ--AYYGVGGGITWESQTDSEYEETRQKS 36- 5 RG+YCG IG+ + + +A+F+VPIRT++ + + + GVG G+T++S+ EYEE+ KS Sbjct: 295 RGVYCGAIGM-VEEKKALFSVPIRTLEKRVHENFLHLGVGSGVTYKSKAPKEYEESFLKS 35- 3 Query: 366 -AVLTRVNPKFQLITTGRV--TENKLLFSQQ--HVERLVESASYFAYSFDKSKFERELKK 42- 0 V+ ++ +F+++ T ++ + KL + + H ERL+ S YF + +D++ + EL Sbjct: 354 FFVMPKI--EFEIVETMKIIKKDQKLEINNKNAHKERLMNSTRYFNFKYDENLLDFEL-- 40- 9 Query: 421 YLHQLDEKDYRLKIMLDKTGKVTFEVKQLVNLSKKFLTAEVVVQDYPI-KLSPFTYFKTS 47- 9 +EK+ L+++L+K GK+ E K L L + E+ + + PI K + F Y KT+ Sbjct: 410 ------EKEGVLRVLLNKKGKLIKEYKTLEPLK----SLEIRLSEAPIDKRNDFLYHKTT 45- 9 Query: 480 YRPHIIEGQN--------EKIFVSPEGLLLETSIGNIVLEKNGRFLTPDLSEGGLNGIYR 53- 1 Y P + + ++IF + + L E + N+VLE + R LTP S G LNG Sbjct: 460 YAPFYQKARALIKKGVMFDEIFYNQDLELTEGARSNLVLEIHNRLLTPYFSAGALNGTGV 51- 9 Query: 532 RHLLKNQKVIEAPLTLKDLESADAIYACNAVRGLYPLNLK 571 LLK V APL L+DL+ A IY NA+ GL + +K Sbjct: 520 VGLLKKGLVGHAPLKLQDLQKASKIYCINALYGLVEVKIK 559 A related DNA sequence was identified in S. pyogenes <SEQ ID 27> which encodes the amino acid sequence <SEQ ID 28>. Analysis of this protein sequence reveals the following: TABLE-US-00039 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2669 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00040 Identities = 303/572 (52%), Positives = 406/572 (70%), Gaps = 1/572 (0%) Query: 1 MHIETVIDFKELGKRYRFKNPTKELIADTLEQVLEVIKEVDYYQSQNYYVVGYLSYEASA 60 MH +T+IDFKELG+RY F P EL+A +L+QV VI++V +YQ YYVVGYLSYEA+A Sbjct: 3 MHRKTIIDFKELGQRYLFDEPLVELVAKSLDQVGPVIEKVQHYQQLGYYVVGYLSYEAAA 62 Query: 61 AFDSHFKVSQQKLAGEHLAYFTVHKDCENEAFPLSYENVRLADNWTANVSEQEYQEAIAN 120- FD+ + +L E+LAYFTVHK C+ + PL Y+++ + + W + ++ YQ+AI Sbjct: 63 FFDNALQTHNDRLGNEYLAYFTVHKTCQKKDLPLDYDSITIPNQWVSATQKEAYQKAIET 122- Query: 121 IKGQIRQGNTYQVNYTLELSQQL-CSDPFSVYERLMVEQGAGYNAYIAYDDKRILSVSPE 17- 9 I +++QGNTYQVNYTL+L+Q+L +D ++Y +L+VEQ AGYNAYIA+D+ ++S SPE Sbjct: 123 IHREMQQGNTYQVNYTLQLTQELNAADSLAIYNKLVVEQAAGYNAYIAHDEFAVISASPE 18- 2 Query: 180 LFFKKKDEVLTTRPMKGTSARKPTYQEDVAERDWLANDPKNRSENMMIVDLLRNDMGRIC 23- 9 LFFK++ LTTRPMKGT+ R D E DWL D KNRSENMMIVDLLRNDMG+IC Sbjct: 183 LFFKQEGNRLTTRPMKGTTKRGVNSWLDQQEHDWLQADGKNRSENMMIVDLLRNDMGKIC 24- 2 Query: 240 DVGTVKVKKLCQVEQYATVWQMTSTIEGVLSPEVTLMSIFQALYPCGSITGAPKISTMAI 29- 9 G+V+V +LC+VE+Y+TVWQMTSTI G L + L+ I +AL+PCGSITGAPK+STMAI Sbjct: 243 QTGSVRVDRLCEVERYSTVWQMTSTIVGDLKADCDLIDILKALFPCGSITGAPKVSTMAI 30- 2 Query: 300 INELEKRPRGIYCGTIGLCMPDGQAIFNVPIRTVQMKGQQAYYGVGGGITWESQTDSEYE 35- 9 I LE +PRGIYCG+IG+C+PDG+ FNVPIRT+Q+ QA YGVGGGITW+S+ + EYE Sbjct: 303 ITSLEPKPRGIYCGSIGICLPDGRRFFNVPIRTIQLSHNQATYGVGGGITWQSKWEDEYE 36- 2 Query: 360 ETRQKSAVLTRVNPKFQLITTGRVTENKLLFSQQHVERLVESASYFAYSFDKSKFERELK 41- 9 E QK+A L R F L TT +V K+ F +QH+ RL E+A+YFAY +++ +++L Sbjct: 363 EVHQKTAFLYRHKQIFDLKTTAKVEHKKIAFLEQHLNRLKEAATYFAYPYNEKALQKQLS 42- 2 Query: 420 KYLHQLDEKDYRLKIMLDKTGKVTFEVKQLVNLSKKFLTAEVVVQDYPIKLSPFTYFKTS 47- 9 YL + YRL I L K GK++ + L LS FLTA++ +Q + SPFTYFKTS Sbjct: 423 TYLENKNNAAYRLMIRLSKDGKISLSDQPLEPLSADFLTAQLSLQKKDVTASPFTYFKTS 48- 2 Query: 480 YRPHIIEGQNEKIFVSPEGLLLETSIGNIVLEKNGRFLTPDLSEGGLNGIYRRHLLKNQK 53- 9 YRPHI + E++F + G LLETSIGN+ ++ TP ++ G L G++R+ LL + Sbjct: 483 YRPHIEQKSYEQLFYNQAGQLLETSIGNLFVQLGQTLYTPPVAVGILPGLFRQELLATGQ 54- 2 Query: 540 VIEAPLTLKDLESADAIYACNAVRGLYPLNLK 571 E +TL DL+ A AI+ NAVRGLYPLNL+ Sbjct: 543 AQEKEVTLADLKEASAIFGGNAVRGLYPLNLE 574 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 13 A DNA sequence (GBSx0010) was identified in S. agalactiae <SEQ ID 29> which encodes the amino acid sequence <SEQ ID 30>. Analysis of this protein sequence reveals the following:

TABLE-US-00041 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1564(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 31> which encodes the amino acid sequence <SEQ ID 32>. Analysis of this protein sequence reveals the following: TABLE-US-00042 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5335(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00043 Identities = 220/267 (82%), Positives = 243/267 (90%) Query: 10 LLLEITKIARATYYYQLKKLNKPNKDKAIKSDIQSIYDEHRGNYGYRRIYLELRNRGFVI 69 - +LLEI ++R+TYYYQ+K+L + +KD +K I+ IYDEH+GNYGYRRI++ELRNRGFV+ Sbjct: 1 MLLEILDLSRSTYYYQVKRLAQGDKDIELKHVIREIYDEHKGNYGYRRIHMELRNRGFVV 60 Query: 70 NHKRVQGLMKSMGLTARIRRKRKYASYKGEVGKKADNLIQRQFEGSKPYEKCYTDVTEFA 129- NHK+VQ LMK MGL ARIRRKRKY+SYKGEVGKKADNLI+R FEGSKPYEKCYTDVTE A Sbjct: 61 NHKKVQRLMKVMGLAARIRRKRKYSSYKGEVGKKADNLIKRHFEGSKPYEKCYTDVTELA 120- Query: 130 LPEGKLYLSPVLDGYNSEIIDFTLSRSPDLKQVQTMLEBAFPAASYSETILHSDQGWQYQ 18- 9 LPEGKLYLSPVLDGYNSEIIDFTLSRSP+LKQVQTMLE+ FPA SYS TILHSDQGWQYQ Sbjct: 121 LPEGKLYLSPVLDGYNSEIIDFTLSRSPNLKQVQTMLEKTFPADSYSGTILHSDQGWQYQ 18- 0 Query: 190 HKSYHQFLEDKGIRPSMSRKGNSPDNGMMESFFGILKSEMFYGLEKSYKSLDDLEQAITD 24- 9 H+SYH FLE KGI SMSRKGNSPDNGMMESFFGILKSEMFYGLE +Y+SLD LE+AITD Sbjct: 181 HQSYHDFLESKGILASMSRKGNSPDNGMMESFFGILKSEMFYGLETTYQSLDKLEEAITD 24- 0 Query: 250 YIFYYNNKRIKAKLKGLSPVQYRTKSF 276 YIFYYNNKRIKAKLKG SPVQYRTKSF Sbjct: 241 YIFYYNNKRIKAKLKGFSPVQYRTKSF 267 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 14 A DNA sequence (GBSx0011; GBSx2234) was identified in S. agalactiae <SEQ ID 33> which encodes the amino acid sequence <SEQ ID 34>. Analysis of this protein sequence reveals the following: TABLE-US-00044 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3578(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 35> which encodes the amino acid sequence <SEQ ID 36>. Analysis of this protein sequence reveals the following: TABLE-US-00045 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3869(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00046 Identities = 107/170 (62%), Positives = 134/170 (77%) Query: 1 MKLSYEDKLEIYELRKIGMSWSQISQRYDVRISNLKYMIKLMDRYGVEIVEKGRNEYYPP 60 MK + E K++IYELR++G S IS+++D+ S+LKYMI+L+DRYGV IV+K +N YY P Sbjct: 1 MKFNQETKVKIYELRQMGESIKSISKKFDMAESDLKYMIRLIDRYGVTIVQKCKNHYYSP 60 Query: 61 ELKQEMIDKVLIHGCSQLSVSLDYALSNCSILTNWLSQFKKNGYTIVEKTRGRPSKMGRK 120- ELKQE+I+KVLI G SQ SLDYAL S+L+ W++Q+KKNGYTI+EK RGRPSKMGRK Sbjct: 61 ELKQEIINKVLIDGQSQKQTSLDYALPTSSMLSRWIAQYKKNGYTILEKPRGRPSKMGRK 120- Query: 121 RKKTWEEMTELERLQEENERLRTENAFLKKLRDLRLRDEALQSERQKQLE 170 RKK EEMTE+ERLQ+E E R ENA LKKLR+ RLRDEA E+QK + Sbjct: 121 RKKNLEEMTEVERLQKELEYPRAENAVLKKLREYRLRDEAKLKEQQKSFK 170 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 15 A DNA sequence (GBSx0012) was identified in S. agalactiae <SEQ ID 37> which encodes the amino acid sequence <SEQ ID 38>. This protein is predicted to be oxyR protein. Analysis of this protein sequence reveals the following: TABLE-US-00047 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1323(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10033> which encodes amino acid sequence <SEQ ID 10034> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00048 >GP:CAA91664 GB:Z67753 former trsE (rbcR homolog) [Odontella sinensis] Identities = 72/259 (27%), Positives = 127/259 (48%), Gaps = 7/259 (2%) Query: 5 QKLMYLESIELYSNITKAAAMLFISQPYLSKVIKQLENELEIKLIQSQGHQTFLTYAGQR 64 Q+L L++I + T+AA LF+SQP LSK IK LE+ L I L+ + + LT AG+ Sbjct: 8 QQLRILKAIATEKSFTRAAEVLFVSQPSLSKQIKTLESRLNISLLNRENNIVSLTQAGKL 67 Query: 65 YLFYLKEIDMIERQMAKELYLIRSDKKGEITLGINSGLASSILANVLPKFNLEHPEISVK 124- +L Y + I + + + L +++ +G + +G + + + ++ VL F HP+I+++ Sbjct: 68 FLEYSERILALCEESCRVLNDLKTGDRGNLIVGASQTIGTYLMPRVLALFAQNHPQINIE 127- Query: 125 LLENNQNISEQLVASGDIDLAV--GMAPILYKDGIASTTIYRDELFLMIPTTSQLYNAEK 18- 2 + ++ + V GDID+AV G P + + DEL L+IP + +K Sbjct: 128 VHVDSTRKIAKRVLEGDIDIAVVGGNIPEEIEKNLKVEDFVNDELILIIPKSHPFALKKK 18- 7 Query: 183 RGQIIPFEYPISVLD-NEPLILTPLEYGIGKTIAQFYELHHMSLNQMITTSTVPTAASLS 24- 1 + Y ++ + N + L I IA F + Q+ + + TA SL Sbjct: 188 KKINKDDLYHLNFITLNSNSTIRKLIDNILIQIA-FEPKQFNIIMQLNSIEAIKTAVSL- 24- 5 Query: 242 LSGMGATFVPQTLIHRYLD 260 G+GA FV + I + ++ Sbjct: 246 --GLGAAFVSSSAIEKEIE 262 A related DNA sequence was identified in S. pyogenes <SEQ ID 39> which encodes the amino acid sequence <SEQ ID 40>. Analysis of this protein sequence reveals the following: TABLE-US-00049 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.28 Transmembrane 109-125 (109-126) INTEGRAL Likelihood = -0.27 Transmembrane 146-162 (146-162) ----- Final Results ----- bacterial membrane --- Certainty = 0.1510(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00050 >GP:AAC22434 GB:U32761 transcriptional regulator [Haemophilus influenzae Rd] Identities = 157/303 (51%), Positives = 221/303 (72%) Query: 2 IRQGESYLDIKQIRYFIAIVENHFNLSQAAELLYVSQPTLSMMINDFEKRENVKLFKRKR 61 + +G +DI+ +RYF++IV+N FNLS+A++ LYVSQP LSMMI +FE REN+++FKR Sbjct: 9 VLRGVKMMDIRHLRYFVSIVDNDFNLSRASQNLYVSQPALSMMITEFENRENIQIFKRAS 68 Query: 62 GRIIGLTYLGDNYYKDAQKVLSLYDDMFLKLHDHSKGLKGSINIGIPPLILSVVFSEVMP 121- G+IIGLT+ G+NYY+DA++V+ Y+DM L+ KG+I IGIPPL+LS VFS V+P Sbjct: 69 GKIIGLTFAGENYYRDAKEVIKRYNDMRTNLYKSKDCKKGTITIGIPPLVLSAVFSSVLP 128- Query: 122 KLILENPGIQFNVKEIGAYQLKNELLVGNVDVAVLLSPTGIADNLVETYEIQRSELSVCL 18- 1 LIL+NP I F +KEIGAY LK+ELL+ VD+AVLL P I+ N++++ EI SEL++ L Sbjct: 129 HLILKNPDINFIIKEIGAYALKSELLLDKVDLAVLLYPERISKNIIDSIEIHSSELALFL 18- 8 Query: 182 SPRHRLASKKVIQWEDLTDEQLALFDPSFMVHHLVLEACERHQVRPNIILTSSSWDFMLN 24- 1 SP+H LA K+ I W DL +++A+FD +FM+HH + EA ER+ P+I+L SS WDF+L+ Sbjct: 189 SPKHVLAKKQQITWADLHQQKMAIFDQTFMIHHHLKEAFERNNCYPDIVLDSSCWDFLLS 24- 8 Query: 242 STKINHNVLTICPKPITELYQLKDIKCIPMERPISWRVVLTRLRKKSYSEIEAYIMDDLL 30- 1 + K N +LTI P P+ ELY K+ C +E P+ W+V L R RK Y+ +E YI D LL Sbjct: 249 AVKTNKELLTILPLPMAELYHSKEFLCRKIESPVPWKVTLCRQRKTVYTHLEEYIFDKLL 30- 8 Query: 302 QSF 304 ++F Sbjct: 309 EAF 311 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00051 Identities = 61/227 (26%), Positives = 111/227 (48%), Gaps = 10/227 (4%) Query: 9 YLESIELYSNITKAAAHLFISQPYLSKVIKQLENELEIKLIQ-SQGHQTFLTYAGQRYLF 67 ++ +E + N+++AA L++SQP LS +I E +KL + +G LTY G Y Sbjct: 17 FIAIVENHFNLSQAAELLYVSQPTLSDMMINDFEKRENVKLFKRKRGRIIGLTYLGDNYYK 76- Query: 68 YLKEIDMIERQMAKELYLIRSDKKGEITLGINSGLASSILANVLPKFNLEHPEISVKLLE 127- +++ + M +L+ KG I +GI + S + + V+PK LE+P I + E Sbjct: 77 DAQKVLSLYDDMFLKLHDHSKGLKGSINIGIPPLILSVVFSEVMPKLILENPGIQFNVKE 136- Query: 128 NNQNISEQLVASGDIDLAVGMAPILYKDGIAST-TIYRDELFLMIPTTSQLYNAEKRGQI 18- 6 + + G++D+AV ++P D + T I R EL + + +L A K+ + Sbjct: 137 IGAYQLKNELLVGNVDVAVLLSPTGIADNLVETYEIQRSELSVCLSPRHRL--ASKK--V 19- 2 Query: 187 IPFEYPISVLDNEPLILTPLEYGIGKTIAQFYELHHMSLNQMITTST 233 I +E L +E L L + + + + E H + N ++T+S+ Sbjct: 193 IQWE----DLTDEQLALFDPSFMVHHLVLEACERHQVRPNIILTSSS 235 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 16 A DNA sequence (GBSx0013) was identified in S. agalactiae <SEQ ID 41> which encodes the amino acid sequence <SEQ ID 42>. This protein is predicted to be aminoacylase (cpsA). Analysis of this protein sequence reveals the following: TABLE-US-00052 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.75 Transmembrane 385-401 (385-401) ----- Final Results ----- bacterial membrane --- Certainty = 0.1298(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00053 >GP: AAF36227 GB: AF168363 aminoacylase [Lactococcus lactis] Identities = 201/395 (50%), Positives = 274/395 (68%), Gaps = 5/395 (1%) Query: 6 LRHQLFEKLDQKCDQMVAIRRYLHENPELSFKETKTAAYISDFYKGKDCHVQTQFGGMNG 65 L + L L Q ++M+ IRR+LH+ PE+SF+E +T YI FYK DC + G G Sbjct: 3 LLNNLLTSLTQYENEMIQIRRHLHQYPEISFQEKETFKYIMGFYKELDCEPKLIGKGF-G 61 Query: 66 VVVDIYGDKATDKPIKHIALRADFDALPIQEETGLSFASKTAGVMHACGHDAHTAYLLIL 125- ++VDI G K+ K +ALRADFDAL I E+ LSF S GVMHACGHDAHTAYL++L Sbjct: 62 IIVDIEGGKSG----KTLALRADFDALAIFEDNDLSFKSVNPGVMHACGHDAHTAYLMVL 117- Query: 126 AESLIELKSEFSGHIRILHQPAEEVPPGGAKAMIEAGCLDGIDAVLGIHVMSTMEEGTVQ 18- 5 A L+++K E G +RI+HQPAEEV PGGAK+MI+AG LDG+D ++G+HVM+T++ G + Sbjct: 118 ARELVKIKQELPGRVRIVHQPAEEVSPGGAKSMIKAGALDGVDNMIGVHVMTTIKTGVIA 17- 7 Query: 186 YHAGPIQTGRATFKVILQGKGGHGSMPHRANDTIVAASSFVMAAQTIVSRRVNPFDTAVV 24- 5 YH QTGR+ F + ++G GGH SMP +ND IVAAS FV QT++SRR++PFD V Sbjct: 178 YHNKETQTGRSNFTITIKGNGGHASMPQLSNDAIVAASYFVTELQTVISRRIDPFDMGTV 23- 7 Query: 246 TIGSWDGKGSANVIKDSVTLEGDVRVMSEETRGVVEEEFKRILDGIAQTYGVSYQLDYQN 30- 5 TIGSFDG GS N I+D V L+GDVR+M E TR V+ ++ K+I G T+GV +DY + Sbjct: 238 TIGSFDGAGSFNAIQDKVLLKGDVRMMKETTRKVIRDQVKQIAKGVGVTFGVEVIVDYDD 29- 7 Query: 306 DYPVLVNNSEVTQKVANSLKSVAIKEILDVIDCDPQTPSEDFAYYAQTIPACFFYVGAHE 36- 5 +YPVL N+ +T V +SLK I E+ +++D PQ PSEDF+YY Q +P+ FFY+GA Sbjct: 298 NYPVLFNSENLTHFVVDSLKDQNISEVNNIVDLGPQNPSEDFSYYGQVVPSTFFYIGAQP 35- 7 Query: 366 EGQPYYPHHHPKFQIAESSLMVSAKSMATAALAML 400 E YPHH P F++ E S++++AK++AT + L Sbjct: 358 EDGGNYPHHSPLFKMNEKSILIAAKAVATVTINYL 392 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 17 A DNA sequence (GBSx0014) was identified in S. agalactiae <SEQ ID 43> which encodes the amino acid sequence <SEQ ID 44>. This protein is predicted to be drug transporter. Analysis of this protein sequence reveals the following: TABLE-US-00054 Lipop: Possible Site: -1 Crend: 8 McG: Discrim Score: 6.19 GvH: Signal Score (-7.5): -0.899999 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 11 value: -12.15 threshold: 0.0 INTEGRAL Likelihood = -12.15 Transmembrane 169-185 (166-190) INTEGRAL Likelihood = -8.86 Transmembrane 229-245 (224-250) INTEGRAL Likelihood = -8.65 Transmembrane 82-98 (78-111) INTEGRAL Likelihood = -8.60 Transmembrane 436-452 (428-457) INTEGRAL Likelihood = -7.48 Transmembrane 202-218 (198-222) INTEGRAL Likelihood = -4.99 Transmembrane 334-350 (332-352) INTEGRAL Likelihood = -4.88 Transmembrane 358-374 (354-376) INTEGRAL Likelihood = -4.09 Transmembrane 301-317 (301-317) INTEGRAL Likelihood = -2.81 Transmembrane 102-118 (101-119) INTEGRAL Likelihood = -2.71 Transmembrane 52-68 (50-70) INTEGRAL Likelihood = -1.70 Transmembrane 271-287 (270-288) PERIPHERAL Likelihood = 0.32 401 modified ALOM score: 2.93 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5861(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00055 >GP: CAB02058 GB: Z79702 hypothetical protein Rv2333c [Mycobacterium tuberculosis] Identities = 118/405 (29%), Positives = 199/405 (49%), Gaps = 9/405 (2%) Query: 13 KLLVGIVLAVLSFWLFAQS-ILNMG-PDVQSSLGISSGAMDIGVSSTALFSGLFIVVTGG 70 - +LL I + F +F + I+N+ PD+Q S + + V+S +L +FI+ Sbjct: 5 QLLTLIATGLGLFMIFLDALIVNVALPDIQRSFAVGEDGLQWVVASYSLGMAVFIMSAAT 64 Query: 71 LADKLGRVKFTFIGLCLNIIGSLLIVLANGAVLFIMGRIFQGLAAAFIMPSTMALVKTYY 130- LAD GR ++ IG+ L +GS+ LA + R QGL AA + +++ALV + Sbjct: 65 LADLDGRRRWYLIGVSLFTLGSIACGLAPSIAVLTTARGAQGLGAAAVSVTSLALVSAAF 124- Query: 131 -DGKDRQRAVSFWSIGSWGGSGLCSYFGGAVASTLGWRYVFIFSI-IASVVSFLLILGTP 18- 8 + K++ RA+ W+ + G+ GG + GWR +F ++ + ++V FL + Sbjct: 125 PEAKEKAPAIGIWTAIASIGTTTGPTLGGLLVDQWGWRSIFYVNLPMGALVLFLTLCYVE 18- 4 Query: 189 ESKNVGQRTHFDYLGLIIFIISMLSLNIGISMAQEHGLMNVIPLSLFTVMLIGFVLFYYV 24- 8 ES N + FD G ++FI+++ +L + + G +V + + +G LF ++ Sbjct: 185 ESCN-ERARRFDLSGQLLFIVAVGALVYAVIEGPQIGWTSVQTIVMLWTAAVGCALFVWL 24- 3 Query: 249 ETRKSNSFIDFHLFENRFY-LGATISNFLLNAVAGTLIVINTYMQQGRQLTPKVAGEMSL 30- 7 E R SN +D LF + Y L + AV G L++ ++Q R TP V G M L Sbjct: 244 ERRSSNPMMDLTLFRDTSYALAIATICTVFFAVYGMLLLTTQFLQNVRGYTPSVTGLMIL 30- 3 Query: 308 GYLVCVLIAIRVGEKILQRFGARKPMLLGAMSTFVGIFLMTLVNIQGPLYLVLVFVGYAL 36- 7 + V I + ++ R GAR P+L G +G+ ++ + LV VG L Sbjct: 304 PFSAAVAIVSPLVGHLVGRIGARVPILAGLCMLMLGLLMLIFSEHRSS---ALVLVGLGL 36- 0 Query: 368 FGTGLGIYATPSTDTAISSIPNEKVGSASGIYKMASSLGGAIGVA 412 G+G+ + TP T A++++P E+ G ASGI ++G IG A Sbjct: 361 CGSGVALCLTPITTVAMTAVPAERAGMASGIMSAQRAIGSTIGFA 405 A related DNA sequence was identified in S. pyogenes <SEQ ID 45> which encodes the amino acid sequence <SEQ ID 46>. Analysis of this protein sequence reveals the following: TABLE-US-00056 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.28 Transmembrane 169-185 (165-189) INTEGRAL Likelihood = -8.23 Transmembrane 12-28 (11-32) INTEGRAL Likelihood = -8.17 Transmembrane 429-445 (423-450) INTEGRAL Likelihood = -6.64 Transmembrane 203-219 (200-222) INTEGRAL Likelihood = -5.41 Transmembrane 227-243 (225-245) INTEGRAL Likelihood = -3.72 Transmembrane 82-98 (80-99) INTEGRAL Likelihood = -3.72 Transmembrane 136-152 (135-155) INTEGRAL Likelihood = -2.92 Transmembrane 302-318 (299-319) INTEGRAL Likelihood = -2.55 Transmembrane 261-277 (261-277) INTEGRAL Likelihood = -2.07 Transmembrane 331-347 (331-347) INTEGRAL Likelihood = -1.06 Transmembrane 56-72 (56-72) INTEGRAL Likelihood = -0.96 Transmembrane 351-367 (351-368) INTEGRAL Likelihood = -0.37 Transmembrane 104-120 (103-120) ----- Final Results ----- bacterial membrane --- Certainty = 0.4312(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00057 !GB: AJ250422 ORFC [Oenococcus oeni] 271 1e-71 Identities = 152/445 (34%), Positives = 248/445 (55%), Gaps = 7/445 (1%) Query: 1 MSHHQQTVSKQTIMAIIAIALIGFSGILSETSMNVTFPTLMSVYQLPLNSLQWMTTIYLL 60 M Q VS +AI+ +A + F G+L ETSMNVTFPTLM + + LN +QW+TT YLL Sbjct: 1 MQKDNQPVSLHVKLAILGLAGLAFCGVLIETSMNVTFPTLMQQFSISLNKVQWLTTAYLL 60 Query: 61 AVAIMMTTSATLKKNVRERPLFFMATGLFTFGTILAVLTQSFAIMLLARIFQGIGTGLVM 120- VA ++ +A ++K + +FF A LF G I + L +F I+L+ R+ Q + TGL + Sbjct: 61 LVAATISIAAFIEKRFIFKKIFFWAGLLFIIGVICSALAPNFLILLIGRLIQALSTGLAI 120- Query: 121 PQMFNIILERVPMHKVGLFMGFAGLIISLAPAFGPTYGGFMISHFSWQWIFICILPVPLI 18- 0 P + I++++P K G +M ++ P+ GPTYGG + SW+ IF +LP+ LI Sbjct: 121 PLLITEIMQQIPQKKQGSYMELVEWLLLWQPSLGPTYGGVITQDLSWRLIFWFVLPIGLI 18- 0 Query: 181 AGILAYYYLEDSPVSEKVPFDWLAFIALSISLTSALLAITSLE-NGSVNLYYLGLFILSF 23- 9 A ++ ++E K+PF W FI+L ++L S +A+ + G ++ + G +++ Sbjct: 181 AWLIGLSFIEQKSSPSKIPFAWKQFISLILALLSITVAVNNAGIYGWTSIKFYGFLLIAV 24- 0 Query: 240 IL---FLYKNLTAKQPFLDIRILKIPSLTFGLIPFFVFQLINLGINFLTPNFIVMEKIAN 29- 6 IL F+ + ++Q + I I K L+ +F+ Q I L + FL PN+ + Sbjct: 241 ILLIVFIKLSTNSRQALISISIFKKWEFVCPLLIYFLIQFIQLSLTFLLPNYAQLILKKG 30- 0 Query: 297 SSQAGMVLLPGTLLGALLAPAFGKLYDQKGARLSLYLGNALFSLSLIIMTLQTRHFMLLP 35- 6 +G++LL G+L+ A+L P G++ D ++ L +G S I T+ R+ + Sbjct: 301 VMISGIMLLCGSLISAILQPLTGRMLDSFSVKIPLVIGAFFLITSTISFTIFQRYLSVFL 36- 0 Query: 357 FTLLYILFTFGRNMGFNNSLATAIRELPAEKNADATAIFQMMQQFAGALGTAMAS-LIAN 41- 5 LY+++ G + FNNSL A+++LP + +D A+F +QQ+AG+LGT++AS L+AN Sbjct: 361 IAALYVIYMIGFSFVFNNSLTYALQKLPLKLISDGNAVFNTLQQYAGSLGTSVASALLAN 42- 0 Query: 416 SQAEFTSGVQSVYLLFTIFALLDFI 440 T G QS Y +L+FI Sbjct: 421 GIG--TDGKQSNYTGSRHIFILNFI 443 An alignment of the GAS and GBS proteins is shown below:

TABLE-US-00058 Identities = 91/369 (24%), Positives = 160/369 (42%), Gaps = 14/369 (3%) Query: 82 FIGLCLNIIGSLLIVLANGAVLFIMGRIFQGLAAAFIMPSTMALVKTYYDGKDRQRAVSF 141- F+ L G++L VL + ++ RIFQG+ +MP ++ + F Sbjct: 83 FMATGLFTFGTILAVLTQSFAIMLLARIFQGIGTGLVMPQMFNIILERVPMHKVGLFMGF 142- Query: 142 WSIGSWGGSGLCSYFGGAVASTLGWRYVFIFSIIASVVSFLLILGTPESKNVGQKTHFDY 20- 1 + +GG + S W+++FI + +++ +L E V +K FD+ Sbjct: 143 AGLIISLAPAFGPTYGGFMISHFSWQWIFICILPVPLIAGILAYYYLEDSPVSEKVPFDW 20- 2 Query: 202 LGLIIFIISMLSLNIGISMAQEHGLMNVIPLSLFTVMLIGFVLFYYVETRKSNSFIDFHL 26- 1 L I IS+ S + I+ + E+G +N+ L LF ++ F+LF Y F+D + Sbjct: 203 LAFIALSISLTSALLAIT-SLENGSVNLYYLGLF---ILSFILFLYKNLTAKQPFLDIRI 25- 8 Query: 262 FENRFYLGATISNFLLNAV-AGTLIVINTYMQQGRQLTPKVAGEMSL-GYLVCVLIAIRV 31- 9 + I F+ + G + ++ + AG + L G L+ L+A Sbjct: 259 LKIPSLTFGLIPFFVFQLINLGINFLTPNFIVMEKIANSSQAGMVLLPGTLLGALLAPAF 31- 8 Query: 320 GEKILQRFGARKPMLLGAMSTFVGIFLMTLVNIQGPLYLVLVF-VGYALFGTGLGIYATP 37- 8 G K+ + GAR + LG + + +MTL Q +++L F + Y LF G + Sbjct: 319 G-KLYDQKGARLSLYLGNALFSLSLIIMTL---QTRHFMLLPFTLLYILFTFGRNMGFNN 37- 4 Query: 379 STDTAISSIPNEKVGSASGIYKMASSLGGAIGVATSIAIYHAFSGNADFHKAALCGLILN 43- 8 S TAI +P EK A+ I++M GA+G A + I ++ A+F +L Sbjct: 375 SLATAIRELPAEKNADATAIFQMMQQFAGALGTAMASLIANS---QAEFTSGVQSVYLLF 43- 1 Query: 439 LVFCSLSIL 447 +F L + Sbjct: 432 TIFALLDFI 440 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 18 A DNA sequence (GBSx0015) was identified in S. agalactiae <SEQ ID 47> which encodes the amino acid sequence <SEQ ID 48>. This protein is predicted to be transposase. Analysis of this protein sequence reveals the following: TABLE-US-00059 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3116(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 19 A DNA sequence (GBSx0016) was identified in S. agalactiae <SEQ ID 49> which encodes the amino acid sequence <SEQ ID 50>. This protein is predicted to be L11 protein (rplK). Analysis of this protein sequence reveals the following: TABLE-US-00060 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1859(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00061 >GP: CAA53739 GB: X76134 L11 protein [Staphylococcus carnosus] Identities = 117/139 (84%), Positives = 129/139 (92%) Query: 1 MAKKVEKLVKLQIPAGKATPAPPVGPALGQAGINIMGFTKEFNARTADQAGMIIPVVISV 60 MAKKVEK+VKLQIPAGKA PAPPVGPALGQAG+NIMGF KEFNART +QAG+IIPV ISV Sbjct: 1 MAKKVEKVVKLQIPAGKANPAPPVGPALGQAGVNIMGFCKEFNARTQEQAGLIIPVEISV 60 Query: 61 YEDKSFDFITKTPPAAVLLKKAAGVEKGSGEPNKTKVATITRAQVQEIAETKMPDLNAAN 120- YED+SF FITKTPPA VLLKKAAGVEKGSGEPNK KVAT+T+ QV+EIA+TKMPDLNAA+ Sbjct: 61 YEDRSFTFITKTPPAPVLLKKAAGVEKGSGEPNKNKVATVTKDQVREIAQTKMPDLNAAD 120- Query: 121 LESAMRMIEGTARSMGFTV 139 E+AMR+IEGTARSMG TV Sbjct: 121 EEAAMRIIEGTARSMGITV 139 A related DNA sequence was identified in S. pyogenes <SEQ ID 51> which encodes the amino acid sequence <SEQ ID 52>. Analysis of this protein sequence reveals the following: TABLE-US-00062 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4276(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00063 Identities = 136/141 (96%), Positives = 139/141 (98%) Query: 1 MAKKVEKLVKLQIPAGKATPAPPVGPALGQAGINIMGFTKEFNARTADQAGMIIPVVISV 60 MAKKVEKLVKLQIPAGKATPAPPVGPALGQAGINIMGFTKEFNARTADQAGMIIPVVISV Sbjct: 25 MAKKVEKLVKLQIPAGKATPAPPVGPALGQAGINIMGFTKEFNARTADQAGMIIPVVISV 84 Query: 61 YEDKSFDFITKTPPAAVLLKKAAGVEKGSGEPNKTKVATITRAQVQEIAETKMPDLNAAN 120- YEDKSFDFITKTPPAAVLLKKAAGVEKGSG PN TKVAT+TRAQVQEIAETKMPDLNAAN Sbjct: 85 YEDKSFDFITKTPPAAVLLKKAAGVEKGSGTPNTTKVATVTRAQVQEIAETKNPDLNAAN 144- Query: 121 LESAMRMIEGTARSMGFTVTD 141 +E+AMRMIEGTARSMGFTVTD Sbjct: 145 IEAAMRMIEGTARSMGFTVTD 165 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 20 A DNA sequence (GBSx0017) was identified in S. agalactiae <SEQ ID 53> which encodes the amino acid sequence <SEQ ID 54>. This protein is predicted to be ribosomal protein L1 (rplA). Analysis of this protein sequence reveals the following: TABLE-US-00064 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2285(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00065 >GP:CAB11879 GB:Z99104 ribosomal protein L1 (BL1) [Bacillus subtilis] Identities = 144/228 (63%), Positives = 177/228 (77%) Query: 1 MAKKSKNLRAALEKIDSTKAYSVEEAVALAKETNFAKFDATVEVSYNLNIDVKKADQQIR 60 MAKK K A + +D +KAY V EAVAL K+TN AKFDATVEV++ L +D K QQIR Sbjct: 1 MAKKGKKYVEAAKLVDHSKAYDVSEAVALVKKTNTAKFDATVEVAFRLGVDPSKNHQQIR 60 Query: 61 GAMVLPAGTGKTSRVLVFARGAKAEEAKAAGADFVGEDDLVAKIQGGWLDFDVVIATPDM 120- GA+VLP GTGKT RVLVFA+G KA+EA+AAGADFVG+ D + KIQ GW DFDV++ATPDM Sbjct: 61 GAVVLPNGTGKTQRVLVFAKGEKAKEAEAAGADFVGDTDYINKIQQGWFDFDVIVATPDM 120- Query: 121 MALVGRLGRVLGPRNLMPNPKTGTVTMDVAKAVEESKGGKITYRADKAGNVQALIGKVSF 18- 0 M VG++GRVLGP+ LMPNPKTGTVT +V KA+ E K GK+ YR DKAGN+ IGKVSF Sbjct: 121 MGEVGKIGRVLGPKGLMPNPKTGTVTFEVEKAIGEIKAGKVEYRVDKAGNIHVPIGKVSF 18- 0 Query: 181 DDAKLVDNFKAFNDVIVKAKPATAKGTYITNLSITTTQGVGIKVDPNS 228 +D KLV+NF D I+KAKPA AKG Y+ N+++T+T G G+KVD ++ Sbjct: 181 EDEKLVENFTTMYDTILKAKPAAAKGVYVKNVAVTSTMGPGVKVDSST 228 A related DNA sequence was identified in S. pyogenes <SEQ ID 55> which encodes the amino acid sequence <SEQ ID 56>. Analysis of this protein sequence reveals the following: TABLE-US-00066 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2309(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00067 Identities = 208/229 (90%), Positives = 220/229 (95%) Query: 1 MAKKSKNLRAALEKIDSTKAYSVEEAVALAKETNFAKFDATVEVSYNLNIDVKKADQQIR 60 MAKKSK +RAALEK+DSTKAYSVEEAVAL KETNFAKFDA+VEV+YNLNIDV+KADQQIR Sbjct: 1 MAKKSKQMRAALEKVDSTKAYSVEEAVALVKETNFAKFDASVEVAYNLNIDVRKADQQIR 60 Query: 61 GAMVLPAGTGKTSRVLVFARGAKAEEAKAAGADFVGEDDLVAKIQGGWLDFDVVIATPDM 120- GAMVLP GTGKT RVLVFARGAKAEEAKAAGADFVGEDDLVAKI GGWLDFDVVIATPDM Sbjct: 61 GAMVLPNGTGKTQRVLVFARGAKAEEAKAAGADFVGEDDLVAKINGGWLDFDVVIATPDM 120- Query: 121 MALVGRLGRVLGPRNLMPNPKTGTVTMDVAKAVEESKGGKITYRADKAGNVQALIGKVSF 18- 0 MA+VGRLGRVLGPRNLMPNPKTGTVTMDVAKAVEESKGGKITYRADKAGNVQALIGKVSF Sbjct: 121 MAIVGRLGRVLGPRNLMPNPKTGTVTMDVAKAVEESKGGKITYRADKAGNVQALIGKVSF 18- 0 Query: 181 DDAKLVDNFKAFNDVIVKAKPATAKGTYITNLSITTTQGVGIKVDPNSL 229 D KLV+NFKAF+DV+ KAKPATAKGTY+ N+SIT+TQGVGIKVDPNSL Sbjct: 181 DADKLVENFKAFHDVMAKAKPATAKGTYMANVSITSTQGVGIKVDPNSL 229 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 21 A DNA sequence (GBSx0018) was identified in S. agalactiae <SEQ ID 57> which encodes the amino acid sequence <SEQ ID 58>. Analysis of this protein sequence reveals the following: TABLE-US-00068 Possible site: 25 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10029> which encodes amino acid sequence <SEQ ID 10030> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00069 >GP:BAB04286 GB:AP001509 nickel transport system (nickel-binding protein) [Bacillus halodurans] Identities = 209/541 (38%), Positives = 324/541 (59%), Gaps = 14/541 (2%) Query: 5 RRNILLSITCLLMVTLTACHSQDS----KSHKLNSDK-LTLAWGEDFGDVNPHRYNPDQF 59 R+ ILL + L+ L C +S + N++K +T +W D G +NPH YNP Q Sbjct: 6 RKLILLFVISLISSILVGCAESESGTVSNEGEENTEKSITFSWPRDIGPMNPHVYNPSQL 65 Query: 60 VIQDMVYEGLVRYGDNGKIEPALAKSWSISQDGKTYTFKLRNA-KYSDGSNFNAANVKRN 118- Q M+YE LV Y + G+++P LA SW+IS+DGK YTFKLR ++SDG+ FNA VK+N Sbjct: 66 FAQSMIYEPLVSYTEGGELQPHLADSWTISEDGKEYTFKLREGVQFSDGTPFNAEIVKKN 125- Query: 119 FDSIFSKSNRGNHNWFNLTNQLENYRALNQSTFEIKLKQAYSATLYDLSMIRPIRFLSDS 17- 8 FD+ S+ H+W + N LE +++ TF++ LK+ Y L DL+++RP+RFL ++ Sbjct: 126 FDTWIEHSSL--HSWLGVMNVLEKTEVVDEFTFKMVLKEPYYPALQDLAVVRPVRFLGEA 18- 3 Query: 179 AFPKGDDTTKKNVKKPIGTGQWVVKSKKQNEYITFKRNENYWGKKPKLKEVTVKVIPDAQ 23- 8 FP DT++ +K+PIGTG W++ KQ+EY F RN NYWG+ PK+ +VTVK+IPDA+ Sbjct: 184 GFPDDGDTSQ-GIKEPIGTGPWMLSDYKQDEYAVFTRNPNYWGESPKIDKVTVKIIPDAE 24- 2 Query: 239 TRALAFESGDVDLIYGNGIIGLDTFAQYTKDKKYVTAISQPMSTRLLLLNAKESIFQDKK 29- 8 TR LAFESG++DLI+G G+I +D F Q + +Y T +S+P+ TR LLLN D + Sbjct: 243 TRVLAFESGELDLIFGEGVISMDAFNQLKESGQYGTDLSEPVGTRSLLLNTSNEKLADLR 30- 2 Query: 299 VRQAMNHAIDKVSIAKNTFRGTEKPADTIFSKSTSHSDAKLNPYSYNVDKANQLLDQAGW 35- 8 VR A++H +K ++ + G E+ AD I S + ++D + P Y+V++AN LD+AGW Sbjct: 303 VRLALHHGFNKQAMVEGVTLGLEEKADNILSTNFPYTDIDVEPIEYDVEQANAYLDEAGW 36- 2 Query: 359 KMGKDK-VREKDGKTLTLRLPYIATKATDKDLVTYFQGEWRKIGINVSLIAMEEDDYWAN 41- 7 ++ K VREK+G+ L L L Y T K + Q EW IG+ + + +E Sbjct: 363 ELPAGKTVREKNGEQLELELIYDKTDPLQKAMAETMQAEWAAIGVKLDITGLELTTQIQR 42- 2 Query: 418 AKKGNFDMMLTYSWGAPWDPHAWMSALTAKADHGHPENIALENLATKTEMDRLIKSALVD 47- 7 + G+FD+ Y++GAP+DPH++++ + A+A G E A NL+ K E+D +++ L Sbjct: 423 RRAGDFDVDFWYNYGAPYDPHSFIN-VVAEAGWGVAE--AHSNLSMKEELDEQVRATLAS 47- 9 Query: 478 PKEENVDRDYKKVLELLHDEAVYIPLTYQSVISVYRKGDFKTMRFAPEENSFPLRYIEKNN 5- 38 E Y +L L +++V++P++Y VY++ + F + P I+ +N Sbjct: 480 TDETERQELYGSILNTLQEQSVFVPISYIKKTVVYQE-NVNEFIFPANRDEHPFNGIDVSN 5- 39 A related DNA sequence was identified in S. pyogenes <SEQ ID 59> which encodes the amino acid sequence <SEQ ID 60>. Analysis of this protein sequence reveals the following: TABLE-US-00070 Possible site: 24 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00071 Identities = 131/497 (26%), Positives = 220/497 (43%), Gaps = 55/497 (11%) Query: 8 ILLSITCLLMVTLTACHSQDSKSHKLN-----SDKLTLAWGEDFGDVNPHRYNP-DQFVI 61 I L +T L++V AC Q ++ + D+L ++ G PH ++P D++ + Sbjct: 13 ITLFLTGLILV---ACQQQKPQTKERQRKQRPKDELVVSMGAKL----PHEFDPKDRYGV 65 Query: 62 QD---MVYEGLVRYGDNGKIEPALAKSWSISQDGKTYTFKLRNA-KYSDGSNFNAANVKR 117- + + + L++ I+ LAK++ +S+DG T++F L + K+S+G A +VK Sbjct: 66 HNEGNITHSTLLKRSPELDIKGELAKTYHLSEDGLTWSFDLHDDFKFSNGEPVTADDVKF 125- Query: 118 NFDSIFSKSNRGNHNWFNLTNQLENYRALNQSTFEIKLKQAYSATLYDLSMIRPIRFLSD 17- 7 +D + + + ++LT ++N + ++ I L +A+S L+ I PI Sbjct: 126 TYDML-----KADGKAWDLTF-IKNVEVVGKNQVNIHLTEAHSTFTAQLTEI-PI----- 17- 3 Query: 178 SAFPKG--DDTTKKNVKKPIGTGQWVVKSKKQNEYITFKRNENYWGKKPKLKEVTVKVIP 23- 5 PK +D K N PIG+G ++VK K E F RN + GKKP K+ T V+ Sbjct: 174 --VPKKHYNDKYKSN---PIGSGPYMVKEYKAGEQAIFVRNPYWHGKKPYFKKWT-WVLL 22- 7 Query: 236 DAQTRALAFESGDVDLIYGNGIIGLDTFAQYTK----DKKYVTAISQPMSTRLLLLNAKE 29- 1 D T A ESGDVD+IY + D + T+ V +S P + ++ ++ + Sbjct: 228 DENTALAALESGDVDMIYATPELA-DKKVKGTRLLDIPSNDVRGLSLPYVKKGVITDSPD 28- 6 Query: 292 ------SIFQDKKVRQAMNHAIDKVSIAKNTFRGTEKPADTIFSKSTSHSDAKLNPYSYN 34- 5 + D +R+A+ +++ + G KPA +I K T + K Sbjct: 287 GYPVGNDVTSDPAIRKALTIGLNRQKVLDTVLNGYGKPAYSIIDK-TPFWNPKTAIKDNK 34- 5 Query: 346 VDKANQLLDQAGWKMGKDKVREKDGKTLTLRLPYIATKATDKDLVTYFQGEWRKIGINVS 40- 5 V KA QLL +AGWK D R+K L Y +L + + +GI + Sbjct: 346 VAKAKQLLTKAGWKEQADGSRKKGDLDAAFDLYYPTNDQLRANLAVEVAEQAKALGITIK 40- 5 Query: 406 LIAMEEDDYWANAKKGNFDMMLTYSWGAPWDPHAWMSALTAKADHGHPENIALENLATKT 46- 5 L A W + D L Y+ G + S + A G NI N T T Sbjct: 406 LKASN----WDEMATKSHDSALLYAGGRHHAQQFYESHHPSLAGKGW-TNITFYNNPTVT 46- 0 Query: 466 E-MDRLIKSALVDPKEE 481 + +D+ + S+ +D E Sbjct: 461 KYLDKADMTSSDLDKANE 477 A related GBS gene <SEQ ID 8469> and protein <SEQ ID 8470> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00072 Lipop: Possible site: 22 Crend: 5 McG: Discrim Score: 7.69 GvH: Signal Score (-7.5): -3.34 Possible site: 25 >>> May be a lipoprotein ALOM program count: 0 value: 7.21 threshold: 0.0 PERIPHERAL Likelihood = 7.21 273 modified ALOM score: -1.94 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00006## There is also homology to SEQ ID 318. An alignment of the GAS and GBS sequences follows: TABLE-US-00073 Identities = 44/186 (23%), Positives = 78/186 (41%), Gaps = 27/186 (14%) Query: 65 VITQMV-DGLLENDEYGNLVPSLAKDWKVSKDGLTYTYTLRDGVSWYTADGEEYAPVTAE 123- VI MV +GL+ + G + P+LAK W +S+DG TYT+ LR+ +DG + + Sbjct: 57 VIQDMVYEGLVRYGDNGKIEPALAKSWSISQDGKTYTFKLRNA---KYSDGSNFNAANVK 113- Query: 124 DFVTGLKHAVDDKSDALYVVEDSIKNLKAYQNGEVDFKEVGVKALDDKTVQYTLNKPESY 18- 3 + + + + + + ++N +AL+ T + L ++Y Sbjct: 114 RNFDSIFSKSNRGNHNWFNLTNQLEN---------------YRALNQSTFEIKLK--QAY 15- 6 Query: 184 WNSKTTYSVLFPVNAKFLKS----KGKDFGTTDPSSILVNGAYFLSAFTSKSSMEFHKNE 23- 9 S T Y + +FL KG D + + G + + + + F +NE Sbjct: 157 --SATLYDLSMIRPIRFLSDSAFPKGDDTTKKNVKKPIGTGQWVVKSKKQNEYITFKRNE 21- 4 Query: 240 NYWDAK 245 NYW K Sbjct: 215 NYWGKK 220 SEQ ID 8470 (GBS186) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 35 (lane 7; MW 60 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 41 (lane 6; MW 85.7 kDa). GBS186-GST was purified as shown in FIG. 202, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 22 A DNA sequence (GBSx0019) was identified in S. agalactiae <SEQ ID 61> which encodes the amino acid sequence <SEQ ID 62>. Analysis of this protein sequence reveals the following: TABLE-US-00074 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.95 Transmembrane 101-117 (99-123) INTEGRAL Likelihood = -4.73 Transmembrane 276-292 (275-293) INTEGRAL Likelihood = -1.12 Transmembrane 232-248 (232-248) INTEGRAL Likelihood = -0.96 Transmembrane 151-167 (150-169) ----- Final Results ----- bacterial membrane --- Certainty = 0.3378(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-00075 >GP: BAB04287 GB: AP001509 nickel transport system (permease) [Bacillus halodurans] Identities = 119/304 (39%), Positives = 174/304 (57%) Query: 5 SSIIKKILSAFLALFFISLLTFILIKLSTVNSAENYLRLSKISVSPEALKEAEHYLGLDK 64 S I K+I + + F + F+ I+LS V+ AE YL + I + E L E H GLD+ Sbjct: 3 SYIAKRIFAVIPIVLFAIFIMFVFIRLSPVDPAEAYLTAANIHPTEELLAEKRHEFGLDQ 62 Query: 65 PLWKQYWLWFQKALTGDFGYSYVLRLPVLDLVLQRFLATLFLGTSAFLLIVTISTPLGVW 124- P+ QY K DFG+SYV PV D V R ATL L S+ L V IS PLG Sbjct: 63 PMAVQYVQTIVKVFQLDFGHSYVTNQPVWDEVTARMPATLQLAVSSIFLAVLISIPLGFL 122- Query: 125 AGLHESARSDHLIRFLSFSSVSMPNFWVAYLLMLLFSAKLNLLPVSGGNDLQSLILPSIT 18- 4 + +++++ D R LS+ S+P FW+ YLL+ FS KLNL PV G L+LP++T Sbjct: 123 SAIYKNSLIDRFSRLLSYLGASIPQFWLGYLLIFFFSVKLNLFPVEGRGSWAHLVLPTVT 18- 2 Query: 185 LSFSTVGQYIALIRKAISQENRSLNVENARLRGVKERYIVTHHLLRNALPAIMTALSLTW 24- 4 LS + + Y L+R ++ ++ + V AR RG+KE+ I+ H+L+ A+ ++T L + Sbjct: 183 LSLALIAIYTRLLRASVLEQMQESYVLYARTRGIKEKVIMVKHVLKLAISPVITGLGMNV 24- 2 Query: 245 VYLLTGSIIVEEIFSWNGIGRLFVTSLRTSDLPVIQACMLIFGTLFLANNFMTQCFMNWV 30- 4 LLTG+IIVE++FSW G GR FV ++ D+PVIQ +L+ LF+ N + + Sbjct: 243 GKLLTGTIIVEQVFSWPGFGRYFVDAIFNRDIPVIQCYVLLAACLFIVCNLIVDLVQLAM 30- 2 Query: 305 DPRL 308 DPR+ Sbjct: 303 DPRI 306 A related DNA sequence was identified in S. pyogenes <SEQ ID 63> which encodes the amino acid sequence <SEQ ID 64>. Analysis of this protein sequence reveals the following: TABLE-US-00076 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.27 Transmembrane 290-306 (287-313) INTEGRAL Likelihood = -6.37 Transmembrane 12-28 (4-33) INTEGRAL Likelihood = -5.89 Transmembrane 105-121 (100-128) INTEGRAL Likelihood = -5.26 Transmembrane 145-161 (142-172) INTEGRAL Likelihood = -2.39 Transmembrane 191-207 (190-208) ----- Final Results ----- bacterial membrane --- Certainty = 0.3909(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00077 Identities = 102/324 (31%), Positives = 167/324 (51%), Gaps = 28/324 (8%) Query: 7 IIKKILSAFLALFFISLLTFILIKLSTVN---SAENYLRLSKISVSPEALKEAEHYLGLD 63 II KI+ +F +S+LTF+L+K S V+ ++ NY S++P K H+ GLD Sbjct: 8 IIWKIIRCVTLIFGVSVLTFVLLKQSPVDPVMASVNY----DTSLTPAQYKAIAHHYGLD 63 Query: 64 KPLWKQYWLWFQKALTGDFGYSYVLRLPVLDLVLQRFLATLFLGTSAFLLIVTISTPLGV 123- KP QY++W + + GD G S V R PV D++ R A+ L +++L I LG Sbjct: 64 KPALVQYFIWLKNVIQGDLGTSLVYRQPVSDIIRSRAGASFILMGLSWILSGLIGFILGT 123- Query: 124 WAGLHESARSDHLIRFLSFSSVSMPNFWVAYLLMLLFSAKLNLLPVSGGNDL-------- 17- 5 + H+ D ++R+ S+ +S+P FW+ + +L+FS +L P+ + + Sbjct: 124 LSAFHQGKLLDRVVRWFSYLQISVPTFWIGLIFLLIFSVQLGWFPIGISSPIGTLSQDIT 18- 3 Query: 176 -----QSLILPSITLSFSTVGQYIALIRKAISQENRSLNVENARLRGVKERYIVTHHLLR 23- 0 + L+LP TLS + R + S V AR RG + I HH LR Sbjct: 184 LADRVKHLMLPVFTLSILGIANVTLHTRTKMMSVLSSEYVLFARARGETQWQIFKHHCLR 24- 3 Query: 231 NALPAIMTALSLTWVY---LLTGSIIVEEIFSWNGIGRLFVTSLRTSDLPVIQACMLIFG 28- 7 N AI+ A++L + Y L GS++ E++FS+ G+G + SD P++ A ++I G Sbjct: 244 N---AIVPAITLHFSYFGELFGGSVLAEQVFSYPGLGSTLTEAGLKSDTPLLLAIVMI-G 29- 9 Query: 288 TLFL-ANNFMTQCFMNWVDPRLRK 310 TLF+ A N + + ++P+LR+ Sbjct: 300 TLFVFAGNLIADILNSIINPQLRR 323 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 23 A DNA sequence (GBSx0020) was identified in S. agalactiae <SEQ ID 65> which encodes the amino acid sequence <SEQ ID 66>. This protein is predicted to be nickel transport system (permease). Analysis of this protein sequence reveals the following: TABLE-US-00078 Possible site: 14 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.64 Transmembrane 57-73 (51-80) INTEGRAL Likelihood = -6.85 Transmembrane 173-189 (169-194) INTEGRAL Likelihood = -5.79 Transmembrane 94-110 (86-112) INTEGRAL Likelihood = -1.44 Transmembrane 221-237 (221-238) INTEGRAL Likelihood = -1.33 Transmembrane 118-134 (118-134) ----- Final Results ----- bacterial membrane --- Certainty = 0.4057(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00079 >GP: BAB04288 GB: AP001509 nickel transport system (permease) [Bacillus halodurans] Identities = 103/239 (43%), Positives = 157/239 (65%) Query: 6 AIFAPILSSFDPQYVDLSQKLLAPNNVHLLGTDQLGRDVLSRLLYGARYSLFLAIIISLL 65 AI AP ++ DP V+L+ KLL P+ + LGTDQLGR LSRLL+GAR SL A +I + Sbjct: 29 AILAPWIAPHDPIQVNLALKLLPPSWEYPLGTDQLGRCNLSRLLFGARVSLGFATLIFIS 88 Query: 66 ELTIGMFVGLIVGWYQGKLENLFLWIANIILAFPSFLLSLATVGILGHGLGNLIFAIVFV 125- L IG+ VG I G+ G ++++ + ++AFP+ +L L VG+ G GL ++ A+V V Sbjct: 89 SLGIGLLVGAIAGYRGGWIDSVLMRFCEGVMAFPNLVLVLGLVGLFGPGLWQVVLALVMV 148- Query: 126 EWVYYAKLMTNLVKSAKKEPYVINAQIMGLSVWHILRKHIFPFVYQPILVMVLMNIGNII 18- 5 +WVYYA++ +++ S K++ ++ A+I G S W I+R+HI P V PI+V+ + +G I Sbjct: 149 QWVYYARMFRSMIVSLKEQNFITAARISGSSPWKIIRRHIIPNVLPPIVVIGTLEMGWAI 20- 8 Query: 186 LMISGFSFLGIGVQPNVTEWGMMLHDARGYFRTATWMMLSPGIAIFLTVFSFNTLGDAI 244- + IS SFLG+G+QP EWG M+H+ + + R+ +ML PGI I L V +FN LG+++ Sbjct: 209 MDISALSFLGLGIQPPTPEWGAMIHEGKSFIRSHPELMLYPGIMILLVVMTFNVLGESL 267- A related DNA sequence was identified in S. pyogenes <SEQ ID 67> which encodes the amino acid sequence <SEQ ID 68>. Analysis of this protein sequence reveals the following: TABLE-US-00080 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.80 Transmembrane 182-198 (180-204) INTEGRAL Likelihood = -7.38 Transmembrane 77-93 (69-98) INTEGRAL Likelihood = -7.06 Transmembrane 112-128 (104-132) INTEGRAL Likelihood = -6.16 Transmembrane 8-24 (7-31) INTEGRAL Likelihood = -5.10 Transmembrane 239-255 (235-258) ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00081 Identities = 61/246 (24%), Positives = 127/246 (50%), Gaps = 1/246 (0%) Query: 2 LVISAIFAPILSSFDPQYVDLSQKLLAPNNVHLLGTDQLGRDVLSRLLYGARYSLFLAII 61 L++S + + P + + + LAP+ HL GTD LGRD+ R + G +SL + ++ Sbjct: 19 LILSILALNLYFYRTPLETNAALRNLAPSLNHLFGTDGLGRDMFVRTIRGLYFSLQVGLL 78 Query: 62 ISLLELTIGMFVGLIVGWYQGKLENLFLWIANIILAFPSFLLSLATVGILGHGLGNLIFA 121- +L+ + + G++ G ++ + W+ ++ + P + + ++G G +I A Sbjct: 79 GALMGVFLATVFGVLAGLGNSLIDKIIAWLVDLFIGMPHLIFMILISFVVGKGAQGVIIA 138- Query: 122 IVFVEWVYYAKLMTNLVKSAKREPYVINAQIMGLSVWHILRKHIFPFVYQPILVMVLMNI 18- 1 W A+L+ N V K + +V ++ MG + ++I+R HI P + I + ++ Sbjct: 139 TAVTHWPSLARLIRNEVYDLKNKAFVQLSKSMGKTPYYIVRHHILPLIASQIFIGFILLF 19- 8 Query: 182 GNIILMISGFSFLGIGVQPNVTEWGMMLHDARGYFRTAT-WMMLSPGIAIFLTVFSFNTL 24- 0 ++IL + +FLG G+ G++L +A + W+++ PG+ + L V +F+T+ Sbjct: 199 PHVILHEASMTFLGFGLSAEQPSVGIILSEAAKHISLGNWWLVIFPGLYLILVVNAFDTI 25- 8 Query: 241 GDAIDK 246 G+++ K Sbjct: 259 GESLKK 264 A related GBS gene <SEQ ID 8473> and protein <SEQ ID 8474> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00082 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: 7.56 GvH: Signal Score (-7.5): -1.15 Possible site: 14 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 5 value: -7.64 threshold: 0.0 INTEGRAL Likelihood = -7.64 Transmembrane 57-73 (51-80) INTEGRAL Likelihood = -6.85 Transmembrane 173-189 (169-194) INTEGRAL Likelihood = -5.79 Transmembrane 94-110 (86-112) INTEGRAL Likelihood = -1.44 Transmembrane 221-237 (221-238) INTEGRAL Likelihood = -1.33 Transmembrane 118-134 (118-134) PERIPHERAL Likelihood = 4.72 145 modified ALOM score: 2.03 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4057(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00007## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 24 A DNA sequence (GBSx0021) was identified in S. agalactiae <SEQ ID 69> which encodes the amino acid sequence <SEQ ID 70>. This protein is predicted to be peptide ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-00083 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 161-177 (161-177) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10027> which encodes amino acid sequence <SEQ ID 10028> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00084 >GP: AAF73561 GB: AE002315 peptide ABC transporter, ATP-binding protein [Chlamydia muridarum] Identities = 86/253 (33%), Positives = 154/253 (59%), Gaps = 2/253 (0%) Query: 1 METTMEQLEIRKLSLQIGEVPVLRDFSCKIDMGESLTIIGESGSGKTLLAKLLVGHIPQG 60 M T+ ++E ++++ ++ S I +SL ++GE+GSGKT ++K ++G +P Sbjct: 1 MSKTLLKIENLVVAIKESNQRLVNHLSLTIKQRQSLALVGENGSGKTTVSKAILGFLPDN 60 Query: 61 MTVR-GNIFFKGVDLGKLTVKQWQKLRGRDIAYLVQNPMSMFNPFQKIEAHILETILSHE 119- ++ G IF+ G D+ +L+ K++Q +RG+ I+ + QN M P ++ I+ET+ H Sbjct: 61 CCIQSGKIFYSGTDITRLSRKEFQSIRGKKISTIFQNAMGTLTPSMRVGTQIIETLRHHF 120- Query: 120 KCSKRVALSKALEWMKRLNLDDAISLLKKYPFELSGGMLQRIMLATILSLDPQVIILDEP 17- 9 SK A +KA E + ++++ L+ YPFELSGGM QR+ +A L+ +P++II DEP Sbjct: 121 VMSKEEAFAKARELLVSVHIESPDRCLQLYPFELSGGMCQRVSIAIALATNPELIIADEP 18- 0 Query: 180 TSAVDCHNCSTISAILQEL-QNNGKTLITVTHDYQLARDLGGQLLVISEGEVVEQGQTQA 23- 8 ++A+D + + + +L+++ QNN L+ +TH+ L +L ++ +I GE+VEQG Sbjct: 181 STALDSISQAQVLRVLKQIHQNNNTALLLITHNLALVSELCEEMAIIHHGEIVEQGPVHE 24- 0 Query: 239 ILSNPQHNYTKAL 251 +L +P H YT+ L Sbjct: 241 LLRSPSHPYTQKL 253 A related DNA sequence was identified in S. pyogenes <SEQ ID 71> which encodes the amino acid sequence <SEQ ID 72>. Analysis of this protein sequence reveals the following: TABLE-US-00085 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.50 Transmembrane 168-184 (167-184) INTEGRAL Likelihood = -1.70 Transmembrane 211-227 (211-227) ----- Final Results ----- bacterial membrane --- Certainty = 0.1999(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00086 Identities = 87/232 (37%), Positives = 138/232 (58%), Gaps = 3/232 (1%) Query: 23 LRDFSCKIDMGESLTIIGESGSGKTLLAKLLVGHIPQ-GMTVRGNIFFKGVDLGKL-TVK 80 - +R+ S ++ GE L +GESGSGK++L K G + G G+I ++G +L L T K Sbjct: 28 IRNVSLELVEGEVLAFVGESGSGKSVLTKTFTGMLESNGRIANGSIVYRGQELTDLKTNK 87 Query: 81 QWQKLRGRDIAYLVQNPMSMFNPFQKIEAHILETILSHEKCSKRVALSKALEWMKRLNLD 140- +W K+RG IA + Q+PM+ +P + I + I E I+ H+K S A AL++M ++ + Sbjct: 88 EWAKIRGSKIATIFQDPMTSLSPIKTIGSQITEVIIKHQKVSHAKAKEMALDYMNKVGIP 147- Query: 141 DAISLLKKYPFELSGGMLQRIMLATILSLDPQVIILDEPTSAVDCHNCSTISAILQELQN 20- 0 +A + YPFE SGGM QRI++A L+ P ++I DEPT+A+D + I +L+ LQ Sbjct: 148 NAKKRFEDYPFEYSGGMRQRIVIAIALACRPDILICDEPTTALDVTIQAQIVELLKSLQR 20- 7 Query: 201 NGK-TLITVTHDYQLARDLGGQLLVISEGEVVEQGQTQAILSNPQHNYTKAL 251 T+I +THD + + ++ V+ GE+VE G + I +P+H YT +L Sbjct: 208 EYHFTIIFITHDLGVVASIADKVAVMYAGEIVEFGTVEEIFYDPRHPYTWSL 259 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 25 A DNA sequence (GBSx0022) was identified in S. agalactiae <SEQ ID 73> which encodes the amino acid sequence <SEQ ID 74>. This protein is predicted to be peptide ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-00087 Possible site: 50 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10025> which encodes amino acid sequence <SEQ ID 10026> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00088 >GP: BAB05797 GB: AP001514 oligopeptide ABC transporter (ATP-binding protein) [Bacillus halodurans] Identities = 82/199 (41%), Positives = 130/199 (65%), Gaps = 2/199 (1%) Query: 19 RQEVLKDCHFHLKRGEIIGIMGKSGSGKSSLARLIIGLIDSPTCGSIYFQG-KIYTPKDGK 77- +Q++L F + GE +GI+G+SGSGKS+L RL++G++ P G IYF+G K+ Sbjct: 21 KQKILNHISFECRHGECLGIIGESGSGKSTLGRLLLGIEKPDRGHIYFEGNKVEERSVRS 80 Query: 78 AQIILVFQDALSSVNPYFSIEEILNEAFYGKKTT-FELCQILEAVGLDGTYLKYKARQLS 136- I VFQD SS+NP+F++E + E GKK ++ +L+ VGL +Y K +LS Sbjct: 81 GNISAVFQDYTSSINPFFTVETAIMEPLKGKKAAKSKVDYLLKQVGLHPSYKKKYPHELS 140- Query: 137 GGQLQRVCIARALLLKPKIIIFDESLSGLDPVTQIKMLRLLQKIKRRYELSFIMISHDPK 19- 6 GG++QRVCIARA+ +PK I+ DE++S LD Q ++L LL ++KR Y++S++ I+HD + Sbjct: 141 GGEVQRVCIARAISTEPKCIVLDEAISSLDVSIQTQVLDLLIELKRIYQMSYLFITHDIQ 20- 0 Query: 197 ICQAICNRVFLIKNGYLVE 215 IC+R+ + ++G + E Sbjct: 201 AAAYICDRIMIFRHGQIEE 219 A related DNA sequence was identified in S. pyogenes <SEQ ID 75> which encodes the amino acid sequence <SEQ ID 76>. Analysis of this protein sequence reveals the following: TABLE-US-00089 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3195(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00090 Identities = 91/238 (38%), Positives = 137/238 (57%), Gaps = 21/238 (8%) Query: 1 MKEIFLMLVCNHVGKTFGRQ----EVLKDCHFHLKRGEIIGIMGKSGSGKSSLARLIIGL 56 M E + L +H+ TF ++ E +KD H+ +G+I GI+G SG+GKS+L R+I L Sbjct: 1 MNEAIIQL--DHIDITFRQKKRVIEAVKDVTVHINQGDIYGIVGYSGAGKSTLVRVINLL 58 Query: 57 DSPTCGSI-------YFQGKIYTPKDGKAQ----IILVFQ--DALSSVNPYFSIEEILNE 103- +PT G I + QGKI D Q I ++FQ + ++ ++ L Sbjct: 59 QAPTNGKITVDGDVTFDQGKIQLSADALRQKRRDIGMIFQHFNLMAQKTAKENVAFALRH 118- Query: 104 AFYGK-KTTFELCQILEAVGLDGTYLKYKARQLSGGQLQRVCIARALLLKPKIIIFDESL 16- 2 + K + ++ ++LE VGL Y A QLSGGQ QRV IARAL PKI+I DE+ Sbjct: 119 SSLSKTEKEHKVIELLELVGLSERADNYPA-QLSGGQKQRVAIARALANDPKILISDEAT 17- 7 Query: 163 SGLDPVTQIKMLRLLQKIKRRYELSFIMISHDPKICQAICNRVFLIKNGYLVEDNEFL 220 S LDP T ++L LLQ++ R+ L+ +MI+H+ +I + ICNRV +++NG L+E+ L Sbjct: 178 SALDPKTTKQILALLQELNRKLGLTIVMITHEMQIVKDICNRVAVMQNGVLIEEGSVL 235 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 26 A DNA sequence (GBSx0023) was identified in S. agalactiae <SEQ ID 77> which encodes the amino acid sequence <SEQ ID 78>. This protein is predicted to be UMP kinase (pyrH). Analysis of this protein sequence reveals the following: TABLE-US-00091 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1935(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00092 >GP: CAB13524 GB: Z99112 uridylate kinase [Bacillus subtilis] Identities = 143/238 (60%), Positives = 193/238 (81%) Query: 2 EPKYQRILIKLSGEALAGDKGVGIDIPTVQSIAKEIAEVHNSGVQIALVIGGGNLWRGEP 61 +PKY+RI++KLSGEALAG++G GI+ +QSIAK++ E+ V++A+V+GGGN + Sbjct: 3 KPKYKRIVLKLSGEALAGEQGNGINPTVIQSIAKQVKEIAELEVEVAVVVGGGNYGAEKT 62 Query: 62 AAEAGMDRVQADYTGMLGTVMNALVMADSLQQYGVDTRVQTAIPMQTVAEPYVRGRALRH 121- ++ GMDR ADY GML TVMN+L + DSL+ G+ +RVQT+I M+ VAEPY+R +A+RH Sbjct: 63 GSDLGMDRATADYMGMLATVMNSLALQDSLETLGIQSRVQTSIEMRQVAEPYIRRKAIRH 122- Query: 122 LEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEAEAILMAKNGVDGVYNADPKKDANAVKF 18- 1 LEK R+V+F AG G+PYFSTDTTAALRAAEIEA+ ILMAKN VDGVYNADP+KD +AVK+ Sbjct: 123 LEKKRVVIFAAGTGNPYFSTDTTAALRAAEIEADVILMAKNNVDGVYNADPRKDESAVKY 18- 2 Query: 182 DELTHVEVIKRGLKIMDATASTISMDNDIDLVVFNMNETGNIKRVVLGEQIGTTVSNK 239 + L++++V+K GL++MD+TAS++ MDNDI L+VF++ E GNIKR V+GE IGT V K Sbjct: 183 ESLSYLDVLKDGLEVMDSTASSLCMDNDIPLIVFSIMEEGNIKRAVIGESIGTIVRGK 240 A related DNA sequence was identified in S. pyogenes <SEQ ID 79> which encodes the amino acid sequence <SEQ ID 80>. Analysis of this protein sequence reveals the following:

TABLE-US-00093 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1955(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00094 Identities = 224/242 (92%), Positives = 233/242 (95%) Query: 1 MEPKYQRILIKLSGEALAGDKGVGIDIPTVQSIAKEIAEVHNSGVQIALVIGGGNLWRGE 60 +EPKYQRILIKLSGEALAG+KGVGIDIPTVQ+IAKEIAEVH SGVQIALVIGGGNLWRGE Sbjct: 1 VEPKYQRILIKLSGEALAGEKGVGIDIPTVQAIAKEIAEVHVSGVQIALVIGGGNLWRGE 60 Query: 61 PAAEAGMDRVQADYTGMLGTVMNALVMADSLQQYGVDTRVQTAIPMQTVAEPYVRGRALR 120- PAA+AGMDRVQADYTGMLGTVMNALVMADSLQ YGVDTRVQTAIPMQ VAEPY+RGRALR Sbjct: 61 PAADAGMDRVQADYTGMLGTVMNALVMADSLQHYGVDTRVQTAIPMQNVAEPYIRGRALR 120- Query: 121 HLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEAEAILMAKNGVDGVYNADPKKDANAVK 18- 0 HLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEA+AILMAKNGVDGVYNADPKKDANAVK Sbjct: 121 HLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEADAILMAKNGVDGVYNADPKKDANAVK 18- 0 Query: 181 FDELTHVEVIKRGLKIMDATASTISMDNDIDLVVFNMNETGNIKRVVLGEQIGTTVSNKA 24- 0 FDELTH EVIKRGLKIMDATAST+SMDNDIDLVVFNMNE GNI+RVV GE IGTTVSNK Sbjct: 181 FDELTHGEVIKRGLKIMDATASTLSMDNDIDLVVFNMNEAGNIQRVVFGEHIGTTVSNKV 24- 0 Query: 241 SE 242 + Sbjct: 241 CD 242 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 27 A DNA sequence (GBSx0024) was identified in S. agalactiae <SEQ ID 81> which encodes the amino acid sequence <SEQ ID 82>. Analysis of this protein sequence reveals the following: TABLE-US-00095 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3712(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 28 A DNA sequence (GBSx0025) was identified in S. agalactiae <SEQ ID 83> which encodes the amino acid sequence <SEQ ID 84>. This protein is predicted to be ribosome recycling factor (frr). Analysis of this protein sequence reveals the following: TABLE-US-00096 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3522(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00097 >GP: BAB06143 GB: AP001515 ribosome recycling factor [Bacillus halodurans] Identities = 112/185 (60%), Positives = 149/185 (80%) Query: 1 MTKEIVTKAQERFEQSHQSLSREFAGIRAGRANASLLDRIQVEYYGAPTPLNQLASITVP 60 M+KE++ A++R ++ ++L RE A +RAGRAN ++LDRI VEYYGA TPLNQLA+I+VP Sbjct: 1 MSKEVLNDAEQRMTKATEALGRELAKLRAGRANPAMLDRITVEYYGAETPLNQLATISVP 60 Query: 61 EARVLLISPFDKSSIKDIERAINESDLGINPANDGSVIRLVIPALTEETRRDLAKEVKKV 120- EAR+L+I PFDKSSI DIERAI +SDLG+ P+NDG+VIR+ IP LTEE RRDL K VKK Sbjct: 61 EARLLVIQPFDKSSISDIERAIQKSDLGLTPSNDGTVIRITIPPLTEERRRDLTKLVKKS 120- Query: 121 GENAKIAIRNIRRDAMDEAKKQEKNKEITEDDLKSLEKDIQKATDDAVKHIDEMTANKEK 18- 0 E AK+A+RNIRRDA D+ KK++K+ E+TEDDL+ + +D+QK TD ++ ID+ KEK Sbjct: 121 AEEAKVAVRNIRRDANDDLKKRQKDGELTEDDLRRVTEDVQKLTDKYIEQIDQKAEAKEK 18- 0 Query: 181 ELLEV 185 E++EV Sbjct: 181 EIMEV 185 A related DNA sequence was identified in S. pyogenes <SEQ ID 85> which encodes the amino acid sequence <SEQ ID 86>. Analysis of this protein sequence reveals the following: TABLE-US-00098 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4462(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00099 Identities = 160/185 (86%), Positives = 171/185 (91%) Query: 1 MTKEIVTKAQERFEQSHQSLSREFAGIRAGRANASLLDRIQVEYYGAPTPLNQLASITVP 60 M I+ A+ERF QSHQSLSRE+A IRAGRANASLLDRIQV+YYGAPTPLNQLASITVP Sbjct: 1 MANAIIETAKERFAQSHQSLSREYASIRAGRANASLLDRIQVDYYGAPTPLNQLASITVP 60 Query: 61 EARVLLISPFDKSSIKDIERAINESDLGINPANDGSVIRLVIPALTEETRRDLAKEVKKV 120- EARVLLISPFDKSSIRDIERA+N SDLGI PANDGSVIRLVIPALTEETR++LAKEVKKV Sbjct: 61 EARVLLISPFDKSSIKDIERALNASDLGITPANDGSVIRLVIPALTEETRKELAKEVKKV 120- Query: 121 GENAKIAIRNIRRDAMDEAKKQEKNKEITEDDLKSLEKDIQKATDDAVKHIDEMTANKEK 18- 0 GENAKIAIRNIRRDAMD+AKKQEK KEITED+LK+LEKDIQKATDDA+K ID MTA KEK Sbjct: 121 GENAKIAIRNIRRDAMDDAKKQEKAKEITEDELKTLEKDIQKATDDAIKEIDRMTAEKEK 18- 0 Query: 181 ELLEV 185 ELL V Sbjct: 181 ELLSV 185 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 29 A DNA sequence (GBSx0026) was identified in S. agalactiae <SEQ ID 87> which encodes the amino acid sequence <SEQ ID 88>. Analysis of this protein sequence reveals the following: TABLE-US-00100 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1356(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10023> which encodes amino acid sequence <SEQ ID 10024> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00101 >GP: CAB12943 GB: Z99109 yitL [Bacillus subtilis] Identities = 107/269 (39%), Positives = 155/269 (56%), Gaps = 6/269 (2%) Query: 42 LVTDENKDF-YFIQKDGFTFALSKSEGEHHIGEM--VKGFAYTDMQQKARLTTKETFATR 98 - L D DF YF+ T L SE I + V+ F Y D Q++ T K + Sbjct: 25 LSIDHQTDFGYFLTDGEDTILLHNSEMTEDIEDRDEVEVFIYVDQQERLAATMKIPIISA 84 Query: 99 DHYGWGTVTEVRKDLGVFLDTGLPDKQVVVSLDVLPELKELWPKKGDRLYVCLDVDKKDR 158- D YGW V + +D+GVF+D GL K +V+ + LP +++WP+KGD+LY L V + R Sbjct: 85 DEYGWVEVVDKVEDMGVFVDVGL-SKDALVATEHLPPYEDVWPQKGDKLYCMLKVTNRGR 143- Query: 159 LWALPADPEVFQRMATPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYSE 21- 8 ++A PA ++ + T A ++ N+ VYRL SG+FV + ++ + FIHPSER E Sbjct: 144 MFAKPAPEDIISELFTDASEDLMNKELTGTVYRLIASGSFV-ITDDGIRCFIHPSERKEE 20- 2 Query: 219 PRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQMILTYLESNGGFMTLNDKSSPE 27- 8 PRLG + RVI +E D ++NLSL PR + + DA+ ILTY+ G M +DKS P+ Sbjct: 203 PRLGSRVTGRVIQVKE-DGSVNLSLLPRKQDAMSVDAECILTYMRMRNGAMPYSDKSQPD 26- 1 Query: 279 EIKATFGISKGQFKKALGGLMKAKKIKQD 307 +I+ F +SK FK+ALG LMK K+ Q+ Sbjct: 262 DIRERFNMSKAAFKRALGHLMKNGKVYQE 290 A related DNA sequence was identified in S. pyogenes <SEQ ID 89> which encodes the amino acid sequence <SEQ ID 90>. Analysis of this protein sequence reveals the following: TABLE-US-00102 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0811(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00103 Identities = 235/284 (82%), Positives = 265/284 (92%) Query: 31 MNTLLATVITGLVTDENKDFYFIQKDGFTFALSKSEGEHHIGEMVKGFAYTDMQQKARLT 90 - MN LLATVITGL+ +EN + YFI K+GFTF LSK+EGE IG+MV GFAYTD++QKARLT Sbjct: 1 MNDLLATVITGLIKEENANDYFIHKEGFTFTLSKAEGERQIGDMVTGFAYTDIEQKARLT 60 Query: 91 TKETFATRDHYGWGTVTEVRKDLGVFLDTGLPDKQVVVSLDVLPELKELWPKKGDRLYVC 150- TKE +TR YGWG VTEVR+DLGVF+DTG+P+K++VVSLDVLPE+KELWPKKGD+LY+ Sbjct: 61 TKEIRSTRTSYGWGEVTEVRRDLGVFVDTGIPNKEIVVSLDVLPEMKELWPKKGDKLYIR 120- Query: 151 LDVDKKDRLWALPADPEVFQRMATPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFI 21- 0 LDVDKKDR+W LPA+PEVFQ+MA+PAYNNMQNQ+WPAIVYRLKL+GTFVYLPENNMLGFI Sbjct: 121 LDVDKKDRIWGLPAEPEVFQKMASPAYNNMQNQHWPAIVYRLKLTGTFVYLPENNMLGFI 18- 0 Query: 211 HPSERYSEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQMILTYLESNGGFMT 27- 0 H SERY+EPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQMI+TYLE+NGGFMT Sbjct: 181 HSSERYAEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQMIVTYLEANGGFMT 24- 0 Query: 271 LNDKSSPEEIKATFGISKGQFKKALGGLMKAKKIKQDQLGTELL 314 LNDKSSPEEIKA+FGISKGQFKKALGGLMKAK+IKQD GTEL+ Sbjct: 241 LNDKSSPEEIKASFGISKGQFKKALGGLMKAKRIKQDATGTELI 284 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 30 A DNA sequence (GBSx0028) was identified in S. agalactiae <SEQ ID 91> which encodes the amino acid sequence <SEQ ID 92>. This protein is predicted to be peptide methionine sulfoxide reductase (msrA). Analysis of this protein sequence reveals the following: TABLE-US-00104 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0866(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10021> which encodes amino acid sequence <SEQ ID 10022> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00105 >GP: BAB05167 GB: AP001512 peptide methionine sulfoxide reductase [Bacillus halodurans] Identities = 102/173 (58%), Positives = 126/173 (71%), Gaps = 2/173 (1%) Query: 14 ENDMERAIFAGGCFWCMVQPFEELDGIESVLSGYTGGHVENPTYKEVCSKTTGHTEAVEI 73 - E+ A FAGGCFWCMV PFEE GI V+SGYTGGH ENPTYKEVCS+TTGH EAV+I Sbjct: 3 ESKWALATFAGGCFWCMVSPFEEEPGIHQVVSGYTGGHTENPTYKEVCSETTGHYEAVQI 62 Query: 74 IFNPEKISYADLVELYWAQTDPTDAFGQFEDRGDNYRPVIFYENEEQRQIAQKSKDKLQA 133- F+PE Y L+E+YW Q DPTD GQF DRGD+YR IFY +E+Q+Q A SK KL+ Sbjct: 63 SFDPEVFPYEKLLEIYWTQIDPTDPGGQFHDRGDSYRTAIFYHDEQQKQAADASKQKLEE 122- Query: 134 SGRFDRPIVTSIEPADTFYPAEDYHQAFYRTNPARYAL--SSARRHAFLEENW 184 SG+F+ PIVT I PA FYPAE+YHQ +++ NP Y + + R AF++++W Sbjct: 123 SGKFNAPIVTRILPAKPFYPAEEYHQKYHKKNPFHYKMYRHGSGREAFIKQHW 175 A related DNA sequence was identified in S. pyogenes <SEQ ID 93> which encodes the amino acid sequence <SEQ ID 94>. Analysis of this protein sequence reveals the following: TABLE-US-00106 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0084(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> RGD motif: 89-91 The protein has homology with the following sequences in the databases: TABLE-US-00107 >GP: BAB05167 GB: AP001512 peptide methionine sulfoxide reductase [Bacillus halodurans] Identities = 98/168 (58%), Positives = 125/168 (74%), Gaps = 4/168 (2%) Query: 4 AIFAGGCFWCMVQPFEEQAGILSVRSGYTGGHLPNPSYEQVCAKTTGHTEAVEIIFDPKQ 63 A FAGGCFWCMV PFEE+ GI V SGYTGGH NP+Y++VC++TTGH EAV+I FDP+ Sbjct: 9 ATFAGGCFWCMVSPFEEEPGIHQVVSGYTGGHTENPTYKEVCSETTGHYEAVQISFDPEV 68 Query: 64 IAYKDLVELYWTQTDPTDAFGQFEDRGDNYRPVIYYTTERQKEIAEQSKANLQASGRFDQ 123- Y+ L+E+YWTQ DPTD GQF DRGD+YR I+Y E+QK+ A+ SK L+ SG+F+ Sbjct: 69 FPYEKLLEIYWTQIDPTDPGGQFHDRGDSYRTAIFYHDEQQKQAADASKQKLEESGKFNA 128- Query: 124 PIVTTIEPAEPFYLAEDYHQGFYKKNP---KRYAQSSAIRHQFLEENW 168 PIVT I PA+PFY AE+YHQ ++KKNP K Y S R F++++W Sbjct: 129 PIVTRILPAKPFYPAEEYHQKYHKKNPFHYKMYRHGSG-REAFIKQHW 175 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00108 Identities = 130/168 (77%), Positives = 148/168 (87%) Query: 17 MERAIFAGGCFWCMVQPFEELDGIESVLSGYTGGHVENPTYKEVCSKTTGHTEAVEIIFN 76 - MERAIFAGGCFWCMVQPFEE GI SV SGYTGGH+ NP+Y++VC+KTTGHTEAVEIIF+ Sbjct: 1 MERAIFAGGCFWCMVQPFEEQAGILSVRSGYTGGHLPNPSYEQVCAKTTGHTEAVEIIFD 60 Query: 77 PEKISYADLVELYWAQTDPTDAFGQFEDRGDNYRPVIFYENEEQRQIAQKSKDKLQASGR 136- P++I+Y DLVELYW QTDPTDAFGQFEDRGDNYRPVI+Y E Q++IA++SK LQASGR Sbjct: 61 PKQIAYKDLVELYWTQTDPTDAFGQFEDRGDNYRPVIYYTTERQKEIAEQSKANLQASGR 120- Query: 137 FDRPIVTSIEPADTFYPAEDYHQAFYRTNPARYALSSARRHAFLEENW 184 FD+PIVT+IEPA+ FY AEDYHQ FY+ NP RYA SSA RH FLEENW Sbjct: 121 FDQPIVTTIEPAEPFYLAEDYHQGFYKKNPKRYAQSSAIRHQFLEENW 168 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 31 A DNA sequence (GBSx0029) was identified in S. agalactiae <SEQ ID 95> which encodes the amino acid sequence <SEQ ID 96>. Analysis of this protein sequence reveals the following: TABLE-US-00109 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2727(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00110 >GP: CAB13859 GB: Z99114 yozE [Bacillus subtilis] Identities = 24/66 (36%), Positives = 42/66 (63%) Query: 3 KSFYSWLMTQRNPKSNEPVAILADYAFDETTFPKHSSDFETVSRYLEDEASFSFNLTDFD 62 KSFY +L+ R+PK + ++ A+ A+++ +FPK S+D+ +S YLE A + + FD Sbjct: 2 KSFYHYLLKYRHPKPKDSISEFANQAYEDHSFPKTSTDYHEISSYLELNADYLHTMATFD 61 Query: 63 DIWEDY 68 + W+ Y Sbjct: 62 EAWDQY 67 A related DNA sequence was identified in S. pyogenes <SEQ ID 97> which encodes the amino acid sequence <SEQ ID 98>. Analysis of this protein sequence reveals the following: TABLE-US-00111 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2571(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00112 Identities = 59/71 (83%), Positives = 65/71 (91%) Query: 1 MRKSFYSWLMTQRNPKSNEPVAILADYAFDETTFPKHSSDFETVSRYLEDEASFSFNLTD 60 MRKSFYSWLMTQRNPKSNEPVAILAD FD+TTFPKH++DFE +SRYLED+ASFSFNL Sbjct: 3 MRKSFYSWLMTQRNPKSNEPVAILADLVFDDTTFPKHTNDFELISRYLEDQASFSFNLGQ 62 Query: 61 FDDIWEDYLNH 71 FD+IWEDYL H Sbjct: 63 FDEIWEDYLAH 73 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 32 A DNA sequence (GBSx0030) was identified in S. agalactiae <SEQ ID 99> which encodes the amino acid sequence <SEQ ID 100>. This protein is predicted to be antigen, 67 kDa (myosin-crossreactive). Analysis of this protein sequence reveals the following: TABLE-US-00113 Possible site: 14 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.57 Transmembrane 28-44 (26-45) ----- Final Results ----- bacterial membrane --- Certainty = 0.2826(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 101> which encodes the amino acid sequence <SEQ ID 102>. Analysis of this protein sequence reveals the following: TABLE-US-00114 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.62 Transmembrane 40-56 (38-57) ----- Final Results ----- bacterial membrane --- Certainty = 0.2848(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9109> which encodes the amino acid sequence <SEQ ID 9110>. Analysis of this protein sequence reveals the following: TABLE-US-00115 Possible cleavage site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.285(Affirmative) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00116 Identities = 477/590 (80%), Positives = 542/590 (91%) Query: 3 MRYTNGNFEAFARPRKPEGVDKKSAYIVGSGLAGLAAAVFLIRDGQMDGQRIHIFEELPL 62 M YT+GN+EAFA PRKPEGVD+KSAYIVG+GLAGLAAAVFLIRDG M G+RIH+FEELPL Sbjct: 15 MYYTSGNYEAFATPRKPEGVDQKSAYIVGTGLAGLAAAVFLIRDGHMAGERIHLFEELPL 74 Query: 63 SGGSLDGVKRPDIGFVTRGGREMENHFECMWDMYRSIPSLEVPDASYLDEFYWLDKDDPN 122- +GGSLDG+++P +GFVTRGGREMENHFECMWDMYRSIPSLE+P ASYLDEFYWLDKDDPN Sbjct: 75 AGGSLDGIEKPHLGFVTRGGREMENHFECMWDMYRSIPSLEIPGASYLDEFYWLDKDDPN 134- Query: 123 SSNCRLIHKQGNRLESDGDFTLGTHSKELVKLVMETEESLGAKTIEEVFSKEFFESNFWT 18- 2 SSNCRLIHK+GNR++ DG +TLG SKEL+ L+M+TEESLG +TIEE FS++FF+SNFW Sbjct: 135 SSNCRLIHKRGNRVDDDGQYTLGKQSKELIHLIMKTEESLGDQTIEEFFSEDFFKSNFWV 19- 4 Query: 183 YWGTMFAFEKWHSAIEMRRYAMRFIHHIGGLPDFTSLKFNKYNQYDSMVKPIISYLESHN 24- 2 YW TMFAFEKWHSA+EMRRYAMRFIHHI GLPDFTSLKFNKYNQYDSMVKPII+YLESH+ Sbjct: 195 YWATMFAFEKWHSAVEMRRYAMRFIHHIDGLPDFTSLKFNKYNQYDSMVKPIIAYLESHD 25- 4 Query: 243 VDVQFDSKVTNISVDFKNGQKLAKAIHLTVGGEAKTIDLTPNDFVFVTNGSITESTNYGS 30- 2 VD+QFD+KVT+I V+ G+K+AK IH+TV GEAK I+LTP+D VFVTNGSITES+ YGS Sbjct: 255 VDIQFDTKVTDIQVEQTAGKKVAKTIHMTVSGEAKAIELTPDDLVFVTNGSITESSTYGS 31- 4 Query: 303 HDTVAKPNTDLGGSWNLWENLAAQSDEFGHPKVFYKDIPKESWFVSATATIKDPAIEPYI 36- 2 H VAKP LGGSWNLWENLAAQSD+FGHPKVFY+D+P ESWFVSATATIK PAIEPYI Sbjct: 315 HHEVAKPTKALGGSWNLWENLAAQSDDFGHPKVFYQDLPAESWFVSATATIKHPAIEPYI 37- 4 Query: 363 ERLTHRDLHDGKVNTGGIVTVTDSNWMMSFAIHRQPHFKEQKENETIVWIYGLYSNVEGN 42- 2 ERLTHRDLHDGKVNTGGI+T+TDSNWMMSFAIHRQPHFKEQKENET VWIYGLYSN EGN Sbjct: 375 ERLTHRDLHDGKVNTGGIITITDSNWMMSFAIHRQPHFKEQKENETTVWIYGLYSNSEGN 43- 4 Query: 423 YIKKPIEECTGREITEEWLYHLGVPEMKIHDLSDKQYVSTVPVYMPYITSYFMPRVKGDR 48- 2 Y+ K IEECTG+EITEEWLYHLGVP KI DL+ + Y++TVPVYMPYITSYFMPRVKGDR Sbjct: 435 YVHKKIEECTGQEITEEWLYHLGVPVDKIKDLASQDYINTVPVYMPYITSYFMPRVKGDR 49- 4 Query: 483 PDVIPQGSVNLAFIGNFAESPSRDTVFTTEYSIRTAMEAVYTFLNIERGVPEVFNSAFDI 54- 2 P VIP GSVNLAFIGNFAESPSRDTVFTTEYSIRTAMEAVY+FLN+ERG+PEVFNSA+DI Sbjct: 495 PKVIPDGSVNLAFIGNFAESPSRDTVFTTEYSIRTAMEAVYSFLNVERGIPEVFNSAYDI 55- 4 Query: 543 RVLLQSLYYLNDKKSVEDMDLPIPALMRKVGMKKIRGTYLEELLREAHLL 592 R LL++ YYLNDKK+++DMDLPIPAL+ K+G KKI+ T++EELL++A+L+ Sbjct: 555 RELLKAFYYLNDKKAIKDMDLPIPALIEKIGHKKIKDTFIEELLKDANLM 604 A related GBS gene <SEQ ID 8475> and protein <SEQ ID 8476> were also identified. Analysis of this protein sequence reveals the following:

TABLE-US-00117 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -19.82 GvH: Signal Score (-7.5): -1.16 Possible site: 14 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -4.57 threshold: 0.0 INTEGRAL Likelihood = -4.57 Transmembrane 26-42 (26-45) PERIPHERAL Likelihood = 6.79 378 modified ALOM score: 1.41 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2826(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) SEQ ID 8476 (GBS90) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 18 (lane 6; MW 68.5 kDa). The GBS90-His fusion product was purified (FIG. 194, lane 11) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 256A), FACS (FIG. 256B), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 33 A DNA sequence (GBSx0031) was identified in S. agalactiae <SEQ ID 103> which encodes the amino acid sequence <SEQ ID 104>. This protein is predicted to be phoh-like protein (phoH). Analysis of this protein sequence reveals the following: TABLE-US-00118 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2339(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00119 >GP: CAB14476 GB: Z99117 phosphate starvation-induced protein [Bacillus subtilis] Identities = 191/305 (62%), Positives = 241/305 (78%), Gaps = 1/305 (0%) Query: 27 LQHPDDMMSLFGSNERHLKLIEENLDVIIHARTERVQVLGDSEEAVETARLTIEALLVLV 86 - L++PD+ +SLFG+ + LKL+E++L++ I R E + V GD +E+ + A + +LL L+ Sbjct: 12 LKNPDEALSLFGNQDSFLKLMEKDLNLNIITRGETIYVSGD-DESFQIADRLLGSLLALI 70 Query: 87 NRGMTVNTSDVVTALSMAQNGSIDKFVALYEEEIIKDSYGKPIRVKTLGQKIYVDSVKNH 146- +G+ ++ DV+ A+ MA+ ++ F ++YEEEI K++ GK IRVKT+GQ+ YV ++K + Sbjct: 71 RKGIEISERDVIYAIKMAKKNELEYFESMYEEEITKNAKGKSIRVKTMGQREYVAAMKRN 130- Query: 147 DVVFGIGPAGTGKTFLAVTLAVTALKRGQVKRIILTRPAVEAGESLGFLPGDLKEKVDPY 20- 6 D+VFGIGPAGTGKT+LAV AV ALK G +K+IILTRPAVEAGESLGFLPGDLKEKVDPY Sbjct: 131 DLVFGIGPAGTGKTYLAVVKAVHALKNGHIKKIILTRPAVEAGESLGFLPGDLKEKVDPY 19- 0 Query: 207 LRPVYDALYQILGKEQTSRLMEREIIEIAPLAYMRGRTLDDAFVILDEAQNTTIMQMKMF 26- 6 LRP+YDAL+ +LG + T RLMER IIEIAPLAYMRGRTLDDA+VILDEAQNTT QMKMF Sbjct: 191 LRPLYDALHDVLGADHTERLMERGIIEIAPLAYMRGRTLDDAYVILDEAQNTTPAQMKMF 25- 0 Query: 267 LTRLGFNSKMIVNGDVSQIDLPKNVKSGLIDAVEKLRNIKKIDFIHLSAKDVVRHPVVAE 32- 6 LTRLGF+SKMI+ GDVSQIDLPK VKSGL A E L+ I I I L DVVRHP+VA+ Sbjct: 251 LTRLGFSSKMIITGDVSQIDLPKGVKSGLAVAKEMLKGIDGISMIELDQTDVVRHPLVAK 31- 0 Query: 327 IINAY 331 II AY Sbjct: 311 IIEAY 315 A related DNA sequence was identified in S. pyogenes <SEQ ID 105> which encodes the amino acid sequence <SEQ ID 106>. Analysis of this protein sequence reveals the following: TABLE-US-00120 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.85 Transmembrane 54-70 (54-70) ----- Final Results ----- bacterial membrane --- Certainty = 0.1341(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00121 Identities = 274/322 (85%), Positives = 298/322 (92%) Query: 18 LQEYSIEITLQHPDDMMSLFGSNERHLKLIEENLDVIIHARTERVQVLGDSEEAVETARL 77 - LQEYSI+ITL HPDD+++LFGSNERHLKLIE +L VI+HARTERVQV+GD EEAVE ARL Sbjct: 1 LQEYSIDITLTHPDDVLALFGSNERHLKLIEAHLGVIVHARTERVQVIGDDEEAVELARL 60 Query: 78 TIEALLVLVNRGMTVNTSDVVTALSMAQNGSIDKFVALYEEEIIKDSYGKPIRVKTLGQK 137- TI+ALLVLV RGM VNTSDVVTALSMA++ ID+F+ALYEEEIIKD+YGK IRVKTLGQK Sbjct: 61 TIKALLVLVGRGMVVNTSDVVTALSMAESHQIDQFMALYEEEIIKDNYGKAIRVKTLGQK 120- Query: 138 IYVDSVKNHDVVFGIGPAGTGKTFLAVTLAVTALKRGQVKRIILTRPAVEAGESLGFLPG 19- 7 YVDSVK HDVVFG+GPAGTGKTFLAVTLAVTALKRGQVKRIILTRPAVEAGESLGFLPG Sbjct: 121 TYVDSVKRHDVVFGVGPAGTGKTFLAVTLAVTALKRGQVKRIILTRPAVEAGESLGFLPG 18- 0 Query: 198 DLKEKVDPYLRPVYDALYQILGKEQTSRLMEREIIEIAPLAYMRGRTLDDAFVILDEAQN 25- 7 DLKEKVDPYLRPVYDALY ILGKEQT+RLMER++IEIAPLAYMRGRTLDDAFVILDEAQN Sbjct: 181 DLKEKVDPYLRPVYDALYHILGKEQTTRLMERDVIEIAPLAYMRGRTLDDAFVILDEAQN 24- 0 Query: 258 TTIMQMKMFLTRLGFNSKMIVNGDVSQIDLPKNVKSGLIDAVEKLRNIKKIDFIHLSAKD 31- 7 TTIMQMKMFLTRLGFNSKMIVNGD SQIDLP+NVKSGLIDA +KL+ IK+IDF++ SAKD Sbjct: 241 TTIMQMKMFLTRLGFNSKMIVNGDTSQIDLPRNVKSGLIDATQKLQGIKQIDFVYFSAKD 30- 0 Query: 318 VVRHPVVAEIINAYSDSESSHK 339 VVRHPVVA+II AY S K Sbjct: 301 VVRHPVVADIIKAYETSSEEMMK 322 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 34 A DNA sequence (GBSx0032) was identified in S. agalactiae <SEQ ID 107> which encodes the amino acid sequence <SEQ ID 108>. Analysis of this protein sequence reveals the following: TABLE-US-00122 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0275(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 35 A DNA sequence (GBSx0033) was identified in S. agalactiae <SEQ ID 109> which encodes the amino acid sequence <SEQ ID 110>. This protein is predicted to be MutT/nudix family protein. Analysis of this protein sequence reveals the following: TABLE-US-00123 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2383(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00124 >Gp: AAF09597 GB: AE001864 MutT/nudix family protein [Deinococcus radiodurans] Identities = 49/136 (36%), Positives = 69/136 (50%), Gaps = 8/136 (5%) Query: 5 YISYIRSKVGHETIFLTYSGGILTDGKGRVLLQLRADKNSWGIIGGCMELGESSVDTLKR 64 Y+S +R+ GH + +L D GRVLLQ R D WGI+GG +E GE + R Sbjct: 6 YLSELRAVWGHRALPAAGVSVLLQDETGRVLLQRRGDDGQWGILGGGLEPGEDFLIAAHR 65 Query: 65 EFFEETGLRVEPIRLLNVY------TNFQDSYPNGDKAQTVGFIYEVSCPKPVNIEGFHN 118- E EETGLR +R L + F YPNGD+ VG E + P + + Sbjct: 66 ELLEETGLRCPNLRPLPLSEGLVSGPQFWHRYPNGDEVYLVGLRTEGTVPAAALTDACPD 125- Query: 119 E--ETLQLDYFSKEDV 132 + ETL+L +F+ +D+ Sbjct: 126 DGGETLELRWFALDDL 141 A related DNA sequence was identified in S. pyogenes <SEQ ID 111> which encodes the amino acid sequence <SEQ ID 112>. Analysis of this protein sequence reveals the following: TABLE-US-00125 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4375(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00126 Identities = 93/157 (59%), Positives = 123/157 (78%) Query: 1 MKQDYISYIRSKVGHETIFLTYSGGILTDGKGRVLLQLRADKNSWGIIGGCMELGESSVD 60 M QDYISYIRSKVGH+ I L ++GGILT+ G+VL+QLR DK +W I GG MELGESS++ Sbjct: 16 MPQDYISYIRSKVGHDKIILNFAGGILTNDDGKVLMQLRGDKKTWTIPGGTMELGESSLE 75 Query: 61 TLKREFFEETGLRVEPIRLLNVYTNFQDSYPNGDKAQTVGFIYEVSCPKPVNIEGFHNEE 120- T KREF EETG+ VE +RLLNVYT+F++ YPNGD QT+ FIYE++ + I+ FHNEE Sbjct: 76 TCKREFLEETGIEVEAVRLLNVYTHFEEVYPNGDAVQTIVFIYELTAVSDMAIDNFHNEE 135- Query: 121 TLQLDYFSKEDVKNITIVNEQHQLILDEYFSQTFQMG 157 TL+L +FS E++ + V+ +H+L+L+EYFS +F MG Sbjct: 136 TLKLQFFSHEEIAELESVSAKHRLMLEEYFSDSFAMG 172 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 36 A DNA sequence (GBSx0034) was identified in S. agalactiae <SEQ ID 113> which encodes the amino acid sequence <SEQ ID 114>. Analysis of this protein sequence reveals the following: TABLE-US-00127 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3690 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 37 A DNA sequence (GBSx0035) was identified in S. agalactiae <SEQ ID 115> which encodes the amino acid sequence <SEQ ID 116>. Analysis of this protein sequence reveals the following: TABLE-US-00128 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00129 >GP:AAG05249 GB:AE004612 hypothetical protein [Pseudomonas aeruginosa] Identities = 70/254 (27%), Positives = 127/254 (49%), Gaps = 2/254 (0%) Query: 2 KITLHGVAETLLITLYIRAKDAMAKHPILNDQKSLAIVEQIEYDFDKFDNSEASFYATLA 61 +ITL G +TLLITLY +A D+ IL+D+ + V QI++DF + + + A Sbjct: 5 RITLTGEKQTLLITLYAKALDSRLDDSILHDRFAEEAVRQIDFDFSRVALGKGNERALAM 64 Query: 62 RIRVMDREIKKFIRENPNSQILSIGCGLDTRFERVD-NGQIRWYNLDLPEVMEIRKLFFE 120- R D+ ++F+ +P Q+L++GCGLD+R RVD ++ W++LD PEVM++R+ + Sbjct: 65 RSHYFDQACREFLGRHPEGQVLNLGCGLDSRIYRVDPPAELPWFDLDYPEVMDLRERLYP 124- Query: 121 EHERVTNIAKSALDETWTREVNPQNAPFLIVSEGVLMFLKEDDVETFLHILTNSFSQFMA 18- 0 + ++D+ + P+ P L+++EG++ +L+E V + L + Sbjct: 125 PRAGAYRALRHSVDDDGWLQGVPRERPALVLAEGLMPYLRESQVRRLVERLVDHLGSGEL 18- 4 Query: 181 QFDLCHKEMINKGKQHDTVKYMDTEFQFGITDGHEIVDLDPKLKQINLINFTDEMSKFEL 24- 0 FD + I + + ++ + + I D E+ P L+ I + D +L Sbjct: 185 LFDGYGRLGIMLLRLYPPLRETGAQVHWSIDDPRELERWHPALRFIEEVTDYDPQDVAKL 24- 4 Query: 241 -GTLRSLLPTIRKF 253 + R +LP F Sbjct: 245 PQSSRLMLPIYNGF 258 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8477> and protein <SEQ ID 8478> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00130 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 0.37 GvH: Signal Score (-7.5): -0.97 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 4.35 threshold: 0.0 PERIPHERAL Likelihood = 4.35 143 modified ALOM score: -1.37 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm ---Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00008## SEQ ID 8478 (GBS176) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 36 (lane 5 & 6; MW 30 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 41 (lane 7; MW 55.4 kDa). The GBS176-GST fusion product was purified (FIG. 117A; see also FIG. 202, lane 5) and used to immunise mice (lane 1+2 product; 13.5 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 117B), FACS (FIG. 117C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 38 A DNA sequence (GBSx0036) was identified in S. agalactiae <SEQ ID 117> which encodes the amino acid sequence <SEQ ID 118>. Analysis of this protein sequence reveals the following: TABLE-US-00131 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3712(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10019> which encodes amino acid sequence <SEQ ID 10020> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00132 >GP: AAC38046 GB: AF000954 No definition line found [Streptococcus mutans] Identities = 140/164 (85%), Positives = 157/164 (95%) Query: 1 MYVEMIDETGQVSEDIKKQTLDLLEFAAQKTGKENKEMAVTFVTNERSHELNLEYRDTDR 60 MY+EMIDET QVSE IK QTLD+LEFAAQKTGKE+KEMAVTFVTNERSHELNL+YRDT+R Sbjct: 1 MYIEMIDETNQVSEGIKNQTLDILEFAAQKTGKEDKEMAVTFVTNERSHELNLKYRDTNR 60 Query: 61 PTDVISLEYKPEVDISFDEEDLAENPELAEMLEDFDSYIGELFISIDKAKEQAEEYGHSY 120- PTDVISLEYKPE +SFDEEDLA++P+LAE+L +FD+YIGELFIS+DKA+EQA+EYGHS+ Sbjct: 61 PTDVISLEYKPESSLSFDEEDLADDPDLAEVLTEFDAYIGELFISVDKAREQAQEYGHSF 120- Query: 121 EREMGFLAVHGFLHINGYDHYTPEEEKEMFSLQEEILTAYGLKR 164 EREMGFLAVHGFLHINGYDHYTP+EEKEMFSLQEEIL AYGLKR Sbjct: 121 EREMGFLAVHGFLHINGYDHYTPQEEKEMFSLQEEILDAYGLKR 164 A related DNA sequence was identified in S. pyogenes <SEQ ID 119> which encodes the amino acid sequence <SEQ ID 120>. Analysis of this protein sequence reveals the following: TABLE-US-00133 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1145(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00134 Identities = 138/165 (83%), Positives = 153/165 (92%) Query: 1 MYVEMIDETGQVSEDIKKQTLDLLEFAAQKTGKENKEMAVTFVTNERSHELNLEYRDTDR 60 MY+EMIDETGQVS++I +QTLDLL FAAQKTGKE KEM+VTFVTNERSHELNLEYRDTDR Sbjct: 18 MYIEMIDETGQVSQEIMEQTLDLLNFAAQKTGKEEKEMSVTFVTNERSHELNLEYRDTDR 77 Query: 61 PTDVISLEYKPEVDISFDEEDLAENPELAEMLEDFDSYIGELFISIDKAKEQAEEYGHSY 120- PTDVISLEYKPE I F +EDLA +P LAEM+ +FD+YIGELFISIDKA+EQ++EYGHS+ Sbjct: 78 PTDVISLEYKPETPILFSQEDLAADPSLAEMMAEFDAYIGELFISIDKAREQSQEYGHSF 137- Query: 121 EREMGFLAVHGFLHINGYDHYTPEEEKEMFSLQEEILTAYGLKRQ 165 EREMGFLAVHGFLHINGYDHYT EEEKEMF+LQEEILTAYGL RQ Sbjct: 138 EREMGFLAVHGFLHINGYDHYTLEEEKEMFTLQEEILTAYGLTRQ 182 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 39 A DNA sequence (GBSx0038) was identified in S. agalactiae <SEQ ID 121> which encodes the amino acid sequence <SEQ ID 122>. This protein is predicted to be phosphoglycerate dehydrogenase (serA) (serA). Analysis of this protein sequence reveals the following: TABLE-US-00135 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2817(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-00136 >GP:AAB99020 GB:U67544 phosphoglycerate dehydrogenase (serA) [Methanococcus jannaschii] Identities = 82/232 (35%), Positives = 132/232 (56%), Gaps = 14/232 (6%) Query: 3 ENPDAYIIRSQNLHNQDF---PSNLKAIARAGAGTNNIPIEEASAQGIVVFNTPGANANA 59 ++ D ++RS +D LK I RAG G +NI +E A+ +GI+V N P A++ + Sbjct: 40 KDADVLVVRSGTKVTRDVIEKAEKLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSIS 99 Query: 60 VKEAVIAALLLSARDYLGANRWVNTLTGTDIPKQIEAGKKAFAGNEIAGKKLGVIGLGAI 119- V E + +L +AR N T K+ E +K F G E+ GK LGVIGLG I Sbjct: 100 VAELTMGLMLAAAR---------NIPQATASLKRGEWDRKRFKGIELYGKTLGVIGLGRI 15- 0 Query: 120 GARIANDARRLGMTVLGYDPYVSIETAWNISSHVQRVKEIKDIFETCDYITIHVPLTNET 17- 9 G ++ A+ GM ++GYDPY+ E A ++ V+ V +I ++ + D+IT+HVPLT +T Sbjct: 151 GQQVVKRAKAFGMNIIGYDPYIPKEVAESMG--VELVDDINELCKRADFITLHVPLTPKT 20- 8 Query: 180 KHTFDAKAFSIMKKGTTIINFARAELVNNQELFEAIETGVVKRYITDFGDKE 231 +H + ++MKK I+N AR L++ + L+EA++ G ++ D ++E Sbjct: 209 RHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRAAALDVFEEE 260 A related DNA sequence was identified in S. pyogenes <SEQ ID 123> which encodes the amino acid sequence <SEQ ID 124>. Analysis of this protein sequence reveals the following: TABLE-US-00137 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2384(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00138 Identities = 52/198 (26%), Positives = 93/198 (46%), Gaps = 14/198 (7%) Query: 24 LKAIARAGAGTNNIPIEEASAQGIVVFNTPGANANAVKEAVIAALLLSARDYLGANRWVN 83 - +K IA+ A + ++ A+ I++ N P + ++ E + +L R Sbjct: 70 IKQIAQHSASVDMYNLDLATENDIIITNVPSYSPESIAEFTVTIVLNLIRHV-------- 121- Query: 84 TLTGTDIPKQIEAGKKAFAGNEIAGKKLGVIGLGAIGARIANDARRLGMTVLGYDPYVSI 143- L ++ KQ G + + +IG G IG A + G V+GYD Y S Sbjct: 122 ELIRENVKKQNFTWGLPIRGRVLGDMTVAIIGTGRIGLATAKIFKGFGCKVVGYDIYQS- 18- 0 Query: 144 ETAWNISSHVQRVKE-IKDIFETCDYITIHVPLTNETKHTFDAKAFSIMKKGTTIINFAR 20- 2 + A + + + V+E IKD D +++H+P T E H F++ F KKG ++N AR Sbjct: 181 DAAKAVLDYKESVEEAIKD----ADLVSLHMPPTAENTHLFNSDLFKSFKKGAILMNMAR 23- 6 Query: 203 AELVNNQELFEAIETGVV 220 ++ Q+L +A++ G++ Sbjct: 237 GAVIETQDLLDALDAGLL 254 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 40 A DNA sequence (GBSx0039) was identified in S. agalactiae <SEQ ID 125> which encodes the amino acid sequence <SEQ ID 126>. This protein is predicted to be alpha-glycerophosphate oxidase. Analysis of this protein sequence reveals the following: TABLE-US-00139 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2067(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00140 >GP:AAC34740 GB:U94770 alpha-glycerophosphate oxidase [Streptococcus pneumoniae] Identities = 24/49 (48%), Positives = 37/49 (74%) Query: 1 MLFMRDNLDSLIQPVIDEMAKHYQWSDQDKTFYEEELHETLKDNDLAAL 49 MLFMRD+LDS+++PV+DEM + Y W++++K Y ++ L +NDLA L Sbjct: 558 MLFMRDSLDSIVEPVLDEMGRFYDWTEEEKATYRADVEAALANNDLAEL 606 A related DNA sequence was identified in S. pyogenes <SEQ ID 127> which encodes the amino acid sequence <SEQ ID 128>. Analysis of this protein sequence reveals the following: TABLE-US-00141 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.81 Transmembrane 20-36 (20-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.1723(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00142 >GP: AAC34740 GB: U94770 alpha-glycerophosphate oxidase [Streptococcus pneumonia] Identities = 462/607 (76%), Positives = 539/607 (88%) Query: 1 MEFSRETRRLALQKMQERDLDLLIIGGGITGAGVALQAAASGLDTGLIEMQDFAQGTSSR 60 MEFS++TR L+++KMQER LDLLIIGGGITGAGVALQAAASGL+TGLIEMQDFA+GTSSR Sbjct: 1 MEFSKKTRELSIKKMQERTLDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSR 60 Query: 61 STKLVHGGLRYLKQFDVEVVSDTVSERAVVQQIAPHIPKPDPMLLPVYDEPGSTFSMFRL 120- STKLVHGGLRYLKQFDVEVVSDTVSERAVVQQIAPHIPKPDPMLLPVYDE G+TFS+FRL Sbjct: 61 STKLVHGGLRYLKQFDVEVVSDTVSERAVVQQIAPHIPKPDPMLLPVYDEDGATFSLFRL 120- Query: 121 KVAMDLYDLLAGVSNTPAANKVLTKEEVLKREPDLKQEGLLGGGVYLDFRNNDARLVIEN 18- 0 KVAMDLYDLLAGVSNTP ANKVL+K++VL+R+P+LK+EGL+GGGVYLDFRNNDARLVIEN Sbjct: 121 KVAMDLYDLLAGVSNTPTANKVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIEN 18- 0 Query: 181 IKRANRDGALIASHVKAEDFLLDDNGKIIGVKARDLLSDQEIIIKAKLVINTTGPWSDEI 24- 0 IKRAN+DGALIA+HVKAE FL D++GKI GV ARDLL+DQ IKA+LVINTTGPWSD++ Sbjct: 181 IKRANQDGALIANHVKAEGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKV 24- 0 Query: 241 RQFSHKGQPIHQMRPTKGVHLVVDRQKLPVSQPVYVDTGLNDGRMVFVLPREEKTYFGTT 30- 0 R S+KG QMRPTKGVHLVVD K+ VSQPVY DTGL DGRMVFVLPRE KTYFGTT Sbjct: 241 RNLSNKGTQFSQMRPTKGVHLVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTT 30- 0 Query: 301 DTDYTGDLEHPQVTQEDVDYLLGVVNNRFPNANVTIDDIESSWAGLRPLLSGNSASDYNG 36- 0 DTDYTGDLEHP+VTQEDVDYLLG+VNNRFP +N+TIDDIESSWAGLRPL++GNSASDYNG Sbjct: 301 DTDYTGDLEHPKVTQEDVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNG 36- 0 Query: 361 GNSGKVSDDSFDHLVDTVKAYINHEDSREAVEKAIKQVETSTSEKELDPSAVSRGSSFER 42- 0 GN+G +SD+SFD+L+ TV++Y++ E +RE VE A+ ++E+STSEK LDPSAVSRGSS +R Sbjct: 361 GNNGTISDESFDNLIATVESYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDR 42- 0 Query: 421 DENGLFTLAGGKITDYRKMAEGALTGIIQILKEEFGKSFKLINSKTYPVSGGEINPANVD 48- 0 D+NGL TLAGGKITDYRKMAEGA+ ++ ILK EF +SFKLINSKTYPVSGGE+NPANVD Sbjct: 421 DDNGLLTLAGGKITDYRKMAEGAMERVVDILKAEFDRSFKLINSKTYPVSGGELNPANVD 48- 0 Query: 481 SEIEAYAQLGTLSGLSMDDARYLANLYGSNAPKVFALTRQLTAAEGLSLAETLSLHYAMD 54- 0 SEIEA+AQLG GL +A YLANLYGSNAPKVFAL L A GLSLA+TLSLHYAM Sbjct: 481 SEIEAFAQLGVSRGLDSKEAHYLANLYGSNAPKVFALAHSLEQAPGLSLADTLSLHYAMR 54- 0 Query: 541 YEMALKPTDYFLRRTNHLLFMRDSLDALIDPVINEMAKHFEWSDQERVAQEDDLRRVIAD 60- 0 E+AL P D+ LRRTNH+LFMRDSLD++++PV++EM + ++W+++E+ D+ +A+ Sbjct: 541 NELALSPVDFLLRRTNHMLFMRDSLDSIVEPVLDEMGRFYDWTEEEKATYRADVEAALAN 60- 0 Query: 601 NDLSALK 607 NDL+ LK Sbjct: 601 NDLAELK 607 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00143 Identities = 29/49 (59%), Positives = 41/49 (83%) Query: 1 MLFMRDNLDSLIQPVIDEMAKHYQWSDQDKTFYEEELHETLKDNDLAAL 49 +LFMRD+LD+LI PVI+EMAKH++WSDQ++ E++L + DNDL+AL Sbjct: 558 LLFMRDSLDALIDPVINEMAKHFEWSDQERVAQEDDLRRVIADNDLSAL 606 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 41 A DNA sequence (GBSx0040) was identified in S. agalactiae <SEQ ID 129> which encodes the amino acid sequence <SEQ ID 130>. Analysis of this protein sequence reveals the following: TABLE-US-00144 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1011(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00145 >GP: BAB06309 GB: AP001516 unknown conserved protein [Bacillus halodurans] Identities = 70/160 (43%), Positives = 106/160 (65%), Gaps = 3/160 (1%) Query: 5 TRPTTDKVKGAIFNMIGPFFEGGRVLDLFSGSGSLAIEAISRGMDQAVLVEKDRRAQVVI 64 TRPTTDKVK AIFNMIGPFF+GG LDL+ GSG L IEA+SRG+++ + V++ +RA I Sbjct: 21 TRPTTDKVKEAIFNMIGPFFDGGIGLDLYGGSGGLGIEALSRGVERMIFVDQQKRAIETI 80 Query: 65 QENIAMTKSPEQFQLLKMEANRALEQLTGQ---FDLVLLDPPYAKEEIVKQIQIMDSKGL 121- ++N++ + ++ + +A RAL+ LT + F V LDPPYAK+ I + I+ + GL Sbjct: 81 KQNLSHCGLEGRAEVYRNDAKRALQVLTKRGIVFAYVFLDPPYAKQTIKNDLAILANHGL 140- Query: 122 LGDDIMIACETDKSVDLPEEIASFGIWKQKIYGISKVTVY 161 L + ++ CE D+ LP++I K++ YG + +T+Y Sbjct: 141 LEEGGVVVCEHDRDTMLPDQIEYAVKHKEETYGDTMITIY 180 A related DNA sequence was identified in S. pyogenes <SEQ ID 131> which encodes the amino acid sequence <SEQ ID 132>. Analysis of this protein sequence reveals the following: TABLE-US-00146 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3814(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00147 Identities = 111/160 (69%), Positives = 136/160 (84%) Query: 3 RTTRPTTDKVKGAIFNMIGPFFEGGRVLDLFSGSGSLAIEAISRGMDQAVLVEKDRRAQV 62 + TRPT+DKV+GAIFNMIGP+F GGRVLDLF+GSG LAIEA+SRGM AVLVEK+R+AQ Sbjct: 19 KITRPTSDKVRGAIFNMIGPYFNGGRVLDLFAGSGGLAIEAVSRGMSAAVLVEKNRKAQA 78 Query: 63 VIQENIAMTKSPEQFQLLKMEANRALEQLTGQFDLVLLDPPYAKEEIVKQIQIMDSKGLL 122- +IQ+NI MTK+ +F LLKMEA RA++ LTG+FDLV LDPPYAKE IV I+ + +K LL Sbjct: 79 IIQDNIIMTKAENRFTLLKMEAERAIDCLTGRFDLVFLDPPYAKETIVATIEALAAKNLL 138- Query: 123 GDDIMIACETDKSVDLPEEIASFGIWKQKIYGISKVTVYV 162 + +M+ CETDK+V LP+EIA+ GIWK+KIYGISKVTVYV Sbjct: 139 SEQVMVVCETDKTVLLPKEIATLGIWKEKIYGISKVTVYV 178 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 42 A DNA sequence (GBSx0041) was identified in S. agalactiae <SEQ ID 133> which encodes the amino acid sequence <SEQ ID 134>. This protein is predicted to be lipopolysaccharide core biosynthesis protein kdtB (kdtB). Analysis of this protein sequence reveals the following: TABLE-US-00148 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1937(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00149 >GP:BAB13272 GB:AP001119 lipopolysaccharide core biosynthesis protein kdtB [Buchnera sp. APS] Identities = 56/149 (37%), Positives = 94/149 (62%) Query: 1 MTKKALFTGSFDPVTNGHLDIIERASYLFDHVYIGLFYNLEKQGYFSIECRKKMLEEAIR 60 M K A++ G+FDP+T GHLDII RA+ +FD + I + N K+ F+++ R ++ + Sbjct: 1 MNKTAIYPGTFDPITYGHLDIITRATKIFDSITIAISNNFTKKPIFNLKERIELTRKVTL 60 Query: 61 QFKNVSVLVAQDRLAVDLAREVGAKYFVRGLRNSQDFDYEANLEFFNKQLADDIETVYLS 120- KNV ++ + L +LA++ A +RG+R DFDYE L NKQ+ D+++++L Sbjct: 61 HLKNVKKILGFNDLLANLAKKEKANILIRGVRTIFDFDYEIKLAAINKQIYPDLDSIFLL 120- Query: 121 TSPSLSPISSSRIRELIHFKASVKPFVPK 149 +S +S ISSS ++E+ +K +KP++PK Sbjct: 121 SSKEVSFISSSFVKEIAKYKGDIKPYLPK 149 A related DNA sequence was identified in S. pyogenes <SEQ ID 135> which encodes the amino acid sequence <SEQ ID 136>. Analysis of this protein sequence reveals the following: TABLE-US-00150 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1862(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00151 Identities = 88/161 (54%), Positives = 124/161 (76%) Query: 1 MTKKALFTGSFDPVTNGHLDIIERASYLFDHVYIGLFYNLEKQGYFSIECRKKMLEEAIR 60 +TK L+TGSFDPVTNGHLDI++RAS LFD +Y+G+F N K+ YF +E RK ML +A+ Sbjct: 2 LTKIGLYTGSFDPVTNGHLDIVKRASGLFDQIYVGIFDNPTKKSYFKLEVRKAMLTQALA 61 Query: 61 QFKNVSVLVAQDRLAVDLAREVGAKYFVRGLRNSQDFDYEANLEFFNKQLADDIETVYLS 120- F NV V+ + +RLA+D+A+E+ + +RGLRN+ DF+YE NLE+FN LA +IETVYL Sbjct: 62 DFTNVIVVTSHERLAIDVAKELRVTHLIRGLRNATDFEYEENLEYFNHLLAPNIETVYLI 121- Query: 121 TSPSLSPISSSRIRELIHFKASVKPFVPKSVVREVEKMSEE 161 + +SSSR+RELIHF++S++ VP+SV+ +VEKM+E+ Sbjct: 122 SRNKWQALSSSRVRELIHFQSSLEGLVPQSVIAQVEKMNEK 162 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 43 A DNA sequence (GBSx0042) was identified in S. agalactiae <SEQ ID 137> which encodes the amino acid sequence <SEQ ID 138>. Analysis of this protein sequence reveals the following: TABLE-US-00152 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1126(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 44 A DNA sequence (GBSx0043) was identified in S. agalactiae <SEQ ID 139> which encodes the amino acid sequence <SEQ ID 140>. Analysis of this protein sequence reveals the following: TABLE-US-00153 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.04 Transmembrane 20-36 (12-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.5416(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00154 >GP:CAB13378 GB:Z99111 ylbL [Bacillus subtilis] Identities = 124/344 (36%), Positives = 199/344 (57%), Gaps = 21/344 (6%) Query: 20 WIIGFAFLLLVLASLVVRLPYYLEMPGGAYDIRSVLKVNKKADKAKGSYNFVAVSVSQAT 79 - W++ L+ VL+ ++LPYY+ PG A ++ S++KV + KGS + + V V A Sbjct: 9 WMLVILILIAVLS--FIKLPYYITKPGEATELASLIKVEGGYPE-KGSLSLMTVKVGPAN 65 Query: 80 PAQVLYAWLTPFTEL----SSKEETTGGFSNDDYLRINQFYMETSQNESIYQALKLANKQ 135- P ++A + P+ E+ S KEE G S+ +Y++ M++SQ ++ A + A K+ Sbjct: 66 PFTYVWAKMHPYYEIVPDESIKEE---GESDKEYMKRQLQMMKSSQENAVIAAYQKAGKK 122- Query: 136 VSLTYKGVYVLNLAKNSTFKDRLHLADTVTGVNGKSFKNSSQLIKYVAALHLGDKVKVQY 19- 5 VS ++ G+Y ++ +N K ++ + D + +GK+++++ +LI Y+++ GDKV ++ Sbjct: 123 VSYSFNGIYASSVVENMPAKGKIEVGDKIISADGKNYQSAEKLIDYISSKKAGDKVTLKI 18- 2 Query: 196 TSQGKKKESVGKVIKLSNGKNGIGIGLTDHTE--VLSDVPVDFNTEGVGGPSAGLMFTLA 25- 3 + K+K + + + + GIG++ +T+ V + +DF E +GGPSAGLM +L Sbjct: 183 EREEKEKRVTLTLKQFPDEPDRAGIGVSLYTDRNVKVEPDIDFEIENIGGPSAGLMMSLE 24- 2 Query: 254 IYDQLVKEDLRKGRKIAGTGTIEQNGHVGDIGGAGLKVVSAAKKGMDIFFVPNNPIDKNA 31- 3 IY+QL K D KG IAGTGTI+ +G VG IGG KVV+A K G DIFF PN N Sbjct: 243 IYNQLTKPDETKGYDIAGTGTIDVDGKVGPIGGIDQKVVAADKAGKDIFFAPNQNGASN- 30- 1 Query: 314 KKGKTKVQTNYQEAKAAAKRLGTKMKIVPVQNVQQAIDYLKKTK 357 ++Y+ A AK + + MKIVPV +Q AIDYL K K Sbjct: 302 --------SDYKNAVKTAKDIDSNMKIVPVDTMQDAIDYLNKLK 337 A related DNA sequence was identified in S. pyogenes <SEQ ID 141> which encodes the amino acid sequence <SEQ ID 142>. Analysis of this protein sequence reveals the following: TABLE-US-00155 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.24 Transmembrane 10-26 (6-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.5097(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00156 >GP:CAB13378 GB:Z99111 ylbL [Bacillus subtilis] Identities = 132/348 (37%), Positives = 198/348 (55%), Gaps = 16/348 (4%) Query: 1 MKRLKKIKWWLVGLLALISLLLALFFPLPYYIEMPGGAYDIRTVLQVNGKEDKRKGAYQF 60 M R K W LV +L LI++L F LPYYI PG A ++ ++++V G + KG+ Sbjct: 1 MLRKKHFSWMLV-ILILIAVLS--FIKLPYYITKPGEATELASLIKVEGGYPE-KGSLSL 56 Query: 61 VAVGISRASLAQLLYAWLTPFTEISTAEDTTG-GYSDADFLRINQFYMETSQNAAIYQAL 119- + V + A+ ++A + P+ EI E G SD ++++ M++SQ A+ A Sbjct: 57 MTVKVGPANPFTYVWAKMHPYYEIVPDESIKEEGESDKEYMKRQLQMMKSSQENAVIAAY 116- Query: 120 SLAGKPVTLDYKGVYVLDVNNESTFKGTLHLADTVTGVNGKQFTSSAELIDYVSHLKLGD 17- 9 AGK V+ + G+Y V KG + + D + +GK + S+ +LIDY+S K GD Sbjct: 117 QKAGKKVSYSFNGIYASSVVENMPAKGKIEVGDKIISADGKNYQSAEKLIDYISSKKAGD 17- 6 Query: 180 EVTVQFTSDNKPKKGVGRIIKLKN--GKNGIGIALTDHTSVNSEDTVIFSTKGVGGPSAG 23- 7 +VT++ + K K+ + + + + GIG++L +V E + F + +GGPSAG Sbjct: 177 KVTLKIEREEKEKRVTLTLKQFPDEPDRAGIGVSLYTDRNVKVEPDIDFEIENIGGPSAG 23- 6 Query: 238 LMFTLDIYDQITKEDLRKGRTIAGTGTIGKDGEVGDIGGAGLKVVAAAEAGADIFFVPNN 29- 7 LM +L+IY+Q+TK D KG IAGTGTI DG+VG IGG KVVAA +AG DIFF PN Sbjct: 237 LMMSLEIYNQLTKPDETKGYDIAGTGTIDVDGKVGPIGGIDQKVVAADKAGKDIFFAPNQ 29- 6 Query: 298 PVDKEIKKVNPNAISNYEEAKRAAKRLKTKMKIVPVTTVQEALVYLRK 345 N + S+Y+ A + AK + + MKIVPV T+Q+A+ YL K Sbjct: 297 ---------NGASNSDYKNAVKTAKDIDSNMKIVPVDTMQDAIDYLNK 335 An alignment of the GAS and GBS proteins is shown below:

TABLE-US-00157 Identities = 229/339 (67%), Positives = 276/339 (80%) Query: 17 LKWWIIGFAFLLLVLASLVVRLPYYLEMPGGAYDIRSVLKVNKKADKAKGSYNFVAVSVS 76 - +KWW++G L+ +L +L LPYY+EMPGGAYDIR+VL+VN K DK KG+Y FVAV +S Sbjct: 7 IKWWLVGLLALISLLLALFFPLPYYIEMPGGAYDIRTVLQVNGKEDKRKGAYQFVAVGIS 66 Query: 77 QATPAQVLYAWLTPFTELSSKEETTGGFSNDDYLRINQFYMETSQNESIYQALKLANKQV 136- +A+ AQ+LYAWLTPFTE+S+ E+TTGG+S+ D+LRINQFYMETSQN +IYQAL LA K V Sbjct: 67 RASLAQLLYAWLTPFTEISTAEDTTGGYSDADFLRINQFYMETSQNAAIYQALSLAGKPV 126- Query: 137 SLTYKGVYVLNLAKNSTFKDRLHLADTVTGVNGKSFKNSSQLIKYVAALHLGDKVKVQYT 19- 6 +L YKGVYVL++ STFK LHLADTVTGVNGK F +S++LI YV+ L LGD+V VQ+T Sbjct: 127 TLDYKGVYVLDVNNESTFKGTLHLADTVTGVNGKQFTSSAELIDYVSHLKLGDEVTVQFT 18- 6 Query: 197 SQGKKKESVGKVIKLSNGKNGIGIGLTDHTEVLSDVPVDFNTEGVGGPSAGLMFTLAIYD 25- 6 S K K+ VG++IKL NGKNGIGI LTDHT V S+ V F+T+GVGGPSAGLMFTL IYD Sbjct: 187 SDNKPKKGVGRIIKLKNGKNGIGIALTDHTSVNSEDTVIFSTKGVGGPSAGLMFTLDIYD 24- 6 Query: 257 QLVKEDLRKGRKIAGTGTIEQNGHVGDIGGAGLKVVSAAKKGMDIFFVPNNPIDKNAKKG 31- 6 Q+ KEDLRKGR IAGTGTI ++G VGDIGGAGLKVV+AA+ G DIFFVPNNP+DK KK Sbjct: 247 QITKEDLRKGRTIAGTGTIGKDGEVGDIGGAGLKVVAAAEAGADIFFVPNNPVDKEIKKV 30- 6 Query: 317 KTKVQTNYQEAKAAAKRLGTKMKIVPVQNVQQAIDYLKK 355 +NY+EAK AAKRL TKMKIVPV VQ+A+ YL+K Sbjct: 307 NPNAISNYEEAKRAAKRLKTKMKIVPVTTVQEALVYLRK 345 A related GBS gene <SEQ ID 8479> and protein <SEQ ID 8480> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00158 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 8.26 GvH: Signal Score (-7.5): -4.04 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -11.04 threshold: 0.0 INTEGRAL Likelihood = -11.04 Transmembrane 20-36 (12-43) PERIPHERAL Likelihood = 4.51 70 modified ALOM score: 2.71 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5416(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00009## SEQ ID 8480 (GBS39) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 12 (lane 9; MW 65.2 kDa) and FIG. 15 (lane 3; MW 40 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 45 A DNA sequence (GBSx0044) was identified in S. agalactiae <SEQ ID 143> which encodes the amino acid sequence <SEQ ID 144>. This protein is predicted to be UDP-sugar hydrolase. Analysis of this protein sequence reveals the following: TABLE-US-00159 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3908(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00160 >GP:CAB15227 GB:Z99120 similar to hypothetical proteins [Bacillus subtilis] Identities = 114/280 (40%), Positives = 173/280 (61%), Gaps = 9/280 (3%) Query: 1 MTELIRILHLNDLHSHFENFPKVKRFFH----DNQAQPIETISLDLGDNIDKSHPLTEAS 56 M E +R+ H NDLHSHFEN+PK+ + ++Q+ ET+ D+GD++D+ +TEA+ Sbjct: 1 MKEKLRLYHTNDLHSHFENWPKIVDYIEQKRKEHQSDGEETLVFDIGDHLDRFQFVTEAT 60 Query: 57 SGKANVQLMNELGIELATIGNNEGVGLSKKDLDQVYKDSDFTVIVGNLKD-NIIEPSWAK 115- GKANV L+N L I+ A IGNNEG+ L ++L +Y ++F VIV NL D N PSWA Sbjct: 61 FGKANVDLLNRLHIDGAAIGNNEGITLPHEELAALYDNAEFPVIVSNLFDKNGNRPSWAV 120- Query: 116 PYIIYETQQGTKLAFLAYTFPYYKTYEPNGWTIEDPIDCLKCHLQINEIK-EANCRILMS 17- 4 PY I + G +AFL T PYY Y+ GWT+ D ++ +K I E+K +A+ +L+S Sbjct: 121 PYHIKSLKNGMSIAFLGVTVPYYPVYDKLGWTVTDALESIK--ETILEVKGQADIIVLLS 17- 8 Query: 175 HLGIRFDTRIAQEFSEIDLIIGAHTHHLFEEGELINGTYLAAAGKYGRFVGSIDITFDNH 23- 4 HLGI D +A+ EID+I+ +HTHHL E+G+++NG LA+A KYG +VG ++IT D+ Sbjct: 179 HLGILDDQAVAEAVPEIDVILESHTHHLLEDGQVVNGVLLASAEKYGHYVGCVEITVDS- 23- 7 Query: 235 TLKDILISTCDTKQLTGYPSDSDWLRRLSQKVKNSLEKKV 274 + I T + + + +S + + + E+K+ Sbjct: 238 VQRSINSKTASVQNMAEWTGESAETKAFLNEKEREAEEKL 277 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 46 A DNA sequence (GBSx0045) was identified in S. agalactiae <SEQ ID 145> which encodes the amino acid sequence <SEQ ID 146>. This protein is predicted to be UDP-sugar hydrolase. Analysis of this protein sequence reveals the following: TABLE-US-00161 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.48 Transmembrane 5-21 (5-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.1192(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9605> which encodes amino acid sequence <SEQ ID 9606> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00162 >GP: CAB15227 GB: Z99120 similar to hypothetical proteins [Bacillus subtilis] Identities = 29/137 (21%), Positives = 71/137 (51%), Gaps = 13/137 (9%) Query: 3 AMLFYAGADVAIINSGLIVQPFEKD-FSRKNLHESLPHQMRLAKLTVSSQELLEIYETIY 61 A+ + D++++NSG+I+ P + ++ +LH PH + + ++ +EL E ++ Sbjct: 305 ALKEWCETDISMVNSGVILGPLKAGPVTKLDLHRICPHPINPVAVRLTGEELKETI--VH 36- 2 Query: 62 QQGQFLAQQKIHGMGFRGKCFGEVLHSGFDYKN----------GKIVYNEKDIDAKEEVI 111- + + Q +I G+GFRG+ G+++++G + + +I N +DI+ ++ Sbjct: 363 AASEQMEQLRIKGLGFRGEVMGKMVYAGVEVETKRLDDGITHVTRITLNGEDIEKHKQYS 42- 2 Query: 112 LVIVDQYYFASYFECLK 128 + ++D + F ++ Sbjct: 423 VAVLDMFTLGKLFPLIR 439 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 47 A DNA sequence (GBSx0046) was identified in S. agalactiae <SEQ ID 147> which encodes the amino acid sequence <SEQ ID 148>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following: TABLE-US-00163 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3567(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein differs from AX026665 at the C-terminus: TABLE-US-00164 Query: 181 SAKQHFVIRKK 191 SAKQH + +K Sbjct: 181 SAKQHLLFVRK 191 A related DNA sequence was identified in S. pyogenes <SEQ ID 149> which encodes the amino acid sequence <SEQ ID 150>. Analysis of this protein sequence reveals the following: TABLE-US-00165 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3974(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00166 Identities = 110/205 (53%), Positives = 147/205 (71%), Gaps = 15/205 (7%) Query: 1 MRKEVTPEMLNYNKYPGPQFIHFENIVKSDDIEFQLVINEKSAFDVTVFGQRFSEILLKY 60 M+KE++PEM NYNK+PGP+FIHFE VK++ I+ L+ + K+AFD T FGQR++E+LLKY Sbjct: 9 MKKEISPEMYNYNKFPGPKFIHFEEQVKAEGIDLLLLEDVKNAFDTTSFGQRYTEVLLKY 68 Query: 61 DFIVGDWGNEQLRLRGFYKDASTIRKNSRISRLEDYIKEYCNFGCAYFVLENPNPRDIKF 120- D+IVGDWGNEQLRL+GFYKD+ I+K +RISRLEDYIKE+CNFGCAYFVLEN +P+DIKF Sbjct: 69 DYIVGDWGNEQLRLKGFYKDSDDIKKTNRISRLEDYIKEFCNFGCAYFVLENLHPQDIKF 128- Query: 121 DDERPHKRRKS------RSKSQSSKSQTRNNRSQSNA--------NAHFTSKKRKDTKRR 16- 6 ++ER +R+KS R K S Q +S+S N FTS+KR+ + Sbjct: 129 EEERQPRRKKSPKSKSNRRKPNYSNQQPATPKSKSKRASKEKQPENQAFTSQKRRSNTKH 18- 8 Query: 167 QERHIKEEQDKEMTSAKQHFVIRKK 191 +E+ K Q ++ + HF+IRKK Sbjct: 189 KEKS-KRNQTSQLNTKISHFIIRKK 212 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 48 A DNA sequence (GBSx0047) was identified in S. agalactiae <SEQ ID 151> which encodes the amino acid sequence <SEQ ID 152>. Analysis of this protein sequence reveals the following: TABLE-US-00167 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3627(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9607> which encodes amino acid sequence <SEQ ID 9608> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00168 >GP: BAB06225 GB: AP001515 unknown conserved protein [Bacillus halodurans] Identities = 205/349 (58%), Positives = 258/349 (73%), Gaps = 5/349 (1%) Query: 18 PSIYSLTRDELIAWAIEHGEKKFRASQIWDWLYKKRVQSFDEMTNISKDFIALLNENFVV 77 - PSIY+L +EL W E GE KFRA+QI++WLY+KRV+ F EMTN+SKD A L ++F + Sbjct: 17 PSIYTLQFEELEMWLKEQGEPKFRATQIFEWLYEKRVKQFQEMTNLSKDLRAKLEKHFNL 76 Query: 78 NPLKQRIVQESADGTVKYLFELPDGMLIETVLMRQHYGLSVCVTTQVGCNIGCTFCASGL 137- LK Q+S+DGT+K+LFEL DG IETV+MR +YG SVCVTTQVGC +GCTFCAS L Sbjct: 77 TTLKTVTKQQSSDGTIKFLFELHDGYSIETVVMRHNYGNSVCVTTQVGCRLGCTFCASTL 136- Query: 138 IKKQRDLNNGEITAQIMLVQKYFDERGQGERVSHIVVMGIGEPFDNYTNVLKFLRTVNDD 19- 7 +R+L GEI AQ++ Q+ DE QGERV IVVMGIGEPFDNY ++ FL+TVN D Sbjct: 137 GGLKRNLEAGEIVAQVVEAQRAMDE--QGERVGSIVVMGIGEPFDNYQALMPFLKTVNHD 19- 4 Query: 198 NGLAIGARHITVSTSGLAHKIREFANEGVQVNLAVSLHAPNNDLRSSIMRINRSFPLEKL 25- 7 GL IGARHITVSTSG+ KI +FA+EG+Q+N A+SLHAPN +LRS +M +NR++PL KL Sbjct: 195 KGLNIGARHITVSTSGVVPKIYQFADEGLQINFAISLHAPNTELRSKLMPVNRAWPLPKL 25- 4 Query: 258 FAAIEYYIETTNRRVTFEYIMLNGVNDTPENAQELADLTKKIRKLSYVNLIPYNPVSEHD 31- 7 AI YYI+ T RRVTFEY + G ND E+A+ELADL K I+ +VNLIP N V E D Sbjct: 255 MDAIRYYIDKTGRRVTFEYGLFGGENDQVEHAEELADLIKDIK--CHVNLIPVNYVPERD 31- 2 Query: 318 QYSRSPKERVEAFYDVLKKNGVNCVVRQEHGTDIDAACGQLRSNTMKRD 366 Y R+P++++ AF LK+ GVN +R+E G DIDAACGQLR+ K + Sbjct: 313 -YVRTPRDQIFAFERTLKERGVNVTIRREQGHDIDAACGQLRAKERKEE 360 A related DNA sequence was identified in S. pyogenes <SEQ ID 153> which encodes the amino acid sequence <SEQ ID 154>. Analysis of this protein sequence reveals the following: TABLE-US-00169 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2320(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00170 Identities = 316/353 (89%), Positives = 339/353 (95%) Query: 17 KPSIYSLTRDELIAWAIEHGEKKFRASQIWDWLYKKRVQSFDEMTNISKDFIALLNENFV 76 - KPSIYSLTRDELIAWA+E G+K+FRA+QIWDWLYKKRVQSF+EMTNISKDF+++LN++F Sbjct: 2 KPSIYSLTRDELIAWAVERGQKQFRATQIWDWLYKKRVQSFEEMTNISKDFVSILNDSFC 61 Query: 77 VNPLKQRIVQESADGTVKYLFELPDGMLIETVLMRQHYGLSVCVTTQVGCNIGCTFCASG 136- VNPLKQR+VQESADGTVKYLFELPDGMLIETVLMRQHYG SVCVTTQVGCNIGCTFCASG Sbjct: 62 VNPLKQRVVQESADGTVKYLFELPDGMLIETVLMRQHYGHSVCVTTQVGCNIGCTFCASG 121- Query: 137 LIKKQRDLNNGEITAQIMLVQKYFDERGQGERVSHIVVMGIGEPFDNYTNVLKFLRTVND 19- 6 LIKKQRDLN+GEITAQIMLVQKYFD+R QGERVSH+VVMGIGEPFDNY NV+ FLR +ND Sbjct: 122 LIKKQRDLNSGEITAQIMLVQKYFDDRKQGERVSHVVVMGIGEPFDNYKNVMCFLRVIND 18- 1 Query: 197 DNGLAIGARHITVSTSGLAHKIREFANEGVQVNLAVSLHAPNNDLRSSIMRINRSFPLEK 25- 6 DNGLAIGARHITVSTSGLAHKIR+FANEGVQVNLAVSLHAPNNDLRSSIMR+NRSFPLEK Sbjct: 182 DNGLAIGARHITVSTSGLAHKIRDFANEGVQVNLAVSLHAPNNDLRSSIMRVNRSFPLEK 24- 1 Query: 257 LFAAIEYYIETTNRRVTFEYIMLNGVNDTPENAQELADLTKKIRKLSYVNLIPYNPVSEH 31- 6 LF+AIEYYIE TNRRVTFEYIMLN VND+ + AQELADLTK IRKLSYVNLIPYNPVSEH Sbjct: 242 LFSAIEYYIEKTNRRVTFEYIMLNEVNDSIKQAQELADLTKTIRKLSYVNLIPYNPVSEH 30- 1 Query: 317 DQYSRSPKERVEAFYDVLKKNGVNCVVRQEHGTDIDAACGQLRSNTMKRDRQK 369 DQYSRSPKERV AFYDVLKKNGVNCVVRQEHGTDIDAACGQLRS TMK+DR+K Sbjct: 302 DQYSRSPKERVLAFYDVLKKNGVNCVVRQEHGTDIDAACGQLRSKTMKKDREK 354 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 49 A DNA sequence (GBSx0048) was identified in S. agalactiae <SEQ ID 155> which encodes the amino acid sequence <SEQ ID 156>. This protein is predicted to be VanZF. Analysis of this protein sequence reveals the following: TABLE-US-00171 Possible site: 47 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.61 Transmembrane 86-102 (77-106) INTEGRAL Likelihood = -8.60 Transmembrane 19-35 (15-42) INTEGRAL Likelihood = -5.15 Transmembrane 113-129 (109-134) ----- Final Results ----- bacterial membrane --- Certainty = 0.4843(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00172 >GP:AAF36806 GB:AF155139 VanZF [Paenibacillus popilliae] Identities = 45/154 (29%), Positives = 68/154 (43%), Gaps = 36/154 (23%) Query: 17 RRFVWMLVIIYCLIIVRMCFGPQIMIEGVSTPNVQRFGRIVAL-------LVPFNSFRSL 69 - R F+W+ V ++ L +V M G NV GR L L+PF+S Sbjct: 36 RHFLWVYVFLFYLALVYMMTG---------IGNVWVVGRYETLIRVSEINLLPFSS---- 82 Query: 70 DQLTSFKEIFWVIGQNVVNILLLFPLIIGLLSLKPSLRKYKSVILLAFLMSIFIECTQVV 129- + +T++ ++NI+L PL L ++ P R K+ F S+ IE TQ++ Sbjct: 83 EGVTTY----------ILNIILFMPLGFLLPTIWPQFRTIKNTACTGFFFSLAIELTQLL 132- Query: 130 LDILIDANRVFEIDDLWTNTLGGPFALWTYRNIK 163 +R+ +IDDL NTLG YR K Sbjct: 133 ------NHRITDIDDLLMNTLGAIIGYLLYRAFK 160 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 50 A DNA sequence (GBSx0049) was identified in S. agalactiae <SEQ ID 157> which encodes the amino acid sequence <SEQ ID 158>. This protein is predicted to be multidrug resistance-like ATP-binding protein mdl. Analysis of this protein sequence reveals the following: TABLE-US-00173 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.79 Transmembrane 18-34 (17-36) INTEGRAL Likelihood = -5.15 Transmembrane 247-263 (242-268) INTEGRAL Likelihood = -2.81 Transmembrane 160-176 (158-176) INTEGRAL Likelihood = -2.71 Transmembrane 141-157 (134-158) INTEGRAL Likelihood = -1.12 Transmembrane 56-72 (56-73) INTEGRAL Likelihood = -0.69 Transmembrane 278-294 (277-294) ----- Final Results ----- bacterial membrane --- Certainty = 0.3718(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00174 >GP:BAB06055 ABC transporter (ATP-binding protein) [Bacillus halodurans] Identities = 284/575 (49%), Positives = 406/575 (70%), Gaps = 2/575 (0%) Query: 1 MSIIKNLWWFFKEEKKRYLIGILSLSLVAVLNLIPPKIMGSVIDAITTGKLTRPQLLWNL 60 M + +LWWFFK+EKK Y GI+ L++V++L L+PP+++G ++D I G LT P LL + Sbjct: 1 MKVFVDLWWFFKQEKKSYGFGIVMLAIVSLLTLVPPRVVGIIVDHIYEGTLTMPVLLQWI 60 Query: 61 LGLVLSALAMYGLRYIWRMYILGTSYKLGQVVRYRLFEHFTKMSPSFYQKYRTGDLMAHA 120- L AL +Y RY+WR+ I G S +L +++R +L+ HFT M+ FYQK+RTGDLMAHA Sbjct: 61 GVLAALALIVYVARYLWRVMIFGASLRLARLLRNQLYTHFTNMAAPFYQKHRTGDLMAHA 120- Query: 121 TNDINSLTRLAGGGVMSAVDASITALVTLITMFFTISWQMTLIAVIPLPLMALATSKLGR 18- 0 TNDI ++ AG GV++ VD+ ++TM TISW++TLI+++P+PLMAL TS G Sbjct: 121 TNDIRAIQATAGQGVLTLVDSLTMGGFVILTMAITISWELTLISLLPMPLMALLTSYYGS 18- 0 Query: 181 KTHETFKESQAAFSELNNKVQESVSGVKVTKSFGYQEQEIASFQEVNQMTFVKNMRTMTY 24- 0 H+ F +QAAFS LN+KVQESV+GV+VTK+FG +EQ+I +F++ + KN+ Sbjct: 181 LLHKRFHHAQAAFSSLNDKVQESVTGVRVTKAFGQEEQDIEAFRKQSDDVVKKNVAVARV 24- 0 Query: 241 DVMFDPLVLLFIGASYVLTLAMGAFMISKGQVTVGDLVTFVTYLDMLVWPLMAIGFLFNM 30- 0 D +FDP + L +G SY L + GA + Q+T+G L +F YL +L+WP++A GFLFN+ Sbjct: 241 DALFDPTISLIVGLSYFLAIVFGARFVIAEQLTIGQLTSFTIYLGLLIWPMLAFGFLFNI 30- 0 Query: 301 VQRGSVSYNRINSLLEQESDITDPLNPIRPVVNGTLRYDIDFFRYDN--EETLADIHFTL 35- 8 V+RG SYNR++ LL+ + +ITD I G + ID F Y N E LAD+ F L Sbjct: 301 VERGRASYNRVSQLLQAKQEITDSRARIHVPPTGHVDVAIDQFVYPNQKEPALADVQFEL 36- 0 Query: 359 EKGQTLGLVGQTGSGKTSLIKLLLREHDVTQGKITLNKHDIRDYRLSELRQLIGYVPQDQ 41- 8 +G+TLG+VG+TG+GKT+L++LL RE+D+ QG I L+ I Y L L+ G VPQD Sbjct: 361 SEGETLGIVGKTGAGKTTLLRLLQREYDIKQGTIILDGRPIEHYTLDALKAAFGTVPQDH 42- 0 Query: 419 FLFATSILENVRFGNPTLSINAVKKATKLAHVYDDIKQMPAGFETLIGEKGVSLSGGQKQ 47- 8 FLF+ +I +N+ F P +I+ + + ++LAH++DDI Q G++T++GE+GV+LSGGQKQ Sbjct: 421 FLFSATIADNIAFAKPDATISEIIQVSQLAHIHDDIIQFEQGYDTVVGERGVTLSGGQKQ 48- 0 Query: 479 RIAMSRAMILDPDILILDDSLSAVDAKTEHAIIENLKTNRQGKSTIISAHRLSAVVHADL 53- 8 R++++RA++ +P+ILILDDSLSAVDAKTE AI+ +L+ R+GK+TII+AHRLSA+ HAD Sbjct: 481 RVSIARALLANPNILILDDSLSAVDAKTEEAILSSLRAERKGKTTIITAHRLSAIKHADH 54- 0 Query: 539 ILVMQDGRVIERGQHQELLNKGGWYAETYASQQLE 573 ILVM DGR++ERG H+ L+ GGWY Y QQLE Sbjct: 541 ILVMDDGRIVERGTHETLMEAGGWYRNMYERQQLE 575 There is also homology to SEQ ID 8. A related DNA sequence was identified in S. pyogenes <SEQ ID 159> which encodes the amino acid sequence <SEQ ID 160>. Analysis of this protein sequence reveals the following:

TABLE-US-00175 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.75 Transmembrane 176-192 (173-197) INTEGRAL Likelihood = -4.78 Transmembrane 267-283 (265-285) INTEGRAL Likelihood = -4.09 Transmembrane 18-34 (15-40) INTEGRAL Likelihood = -2.13 Transmembrane 151-167 (150-169) INTEGRAL Likelihood = -0.69 Transmembrane 85-101 (85-101) ----- Final Results ----- bacterial membrane --- Certainty = 0.4100(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00176 Identities = 172/609 (28%), Positives = 315/609 (51%), Gaps = 58/609 (9%) Query: 1 MSIIKNLWWFFKEEKKRYLIGILSLSLVAVLNLIPPKIMGSVIDAITTGKLTRPQLLWNL 60 M + W++FK + + + +++ L L + P +G + + GK+ + + + Sbjct: 2 MKTARFFWFYFKRYRFSFTVIAVAVILATYLQVKAPVFLGESLTEL--GKIGQAYYVAKM 59 Query: 61 LGLV-----LSAL--AMYGLRYIWRMYILGT---SYKLGQVV-------RYRLFEHFTKM 103- G LSA M+ L + +L S+ L +VV R LF ++ Sbjct: 60 SGQTHFSPDLSAFNAVMFKLLMTYFFTVLANLIYSFLLTRVVSHSTNRMRKGLFGKLERL 119- Query: 104 SPSFYQKYRTGDLMAHATNDINSLTRLAGGGVMSAVDASITALVTLITMFFTISWQM--- 16- 0 + +F+ +++ G++++ T+D+++ + ++++ S+ +VT I ++ + W M Sbjct: 120 TVAFFDRHKDGEILSRFTSDLDN--------IQNSLNQSLIQVVTNIALYIGLVWMMFRQ 17- 1 Query: 161 ------TLIAVIPLPLMALATS-KLGRKTHETFKESQAAFSELNNKVQESVSGVKVTKSF 21- 3 IA P+ L+ L + +L RK Q S LN + E++SG K Sbjct: 172 DSRLALLTIASTPVALIFLVINIRLARKYTNI---QQQEVSALNAFMDETISGQKAIIVQ 22- 8 Query: 214 GYQEQEIASF----QEVNQMTFVKNMRT------MTYDVMFDPLVLLFIGASYVLT-LAM 26- 2 G QE + +F + V Q TF + + + M + + +++F+G++ VL+ +M Sbjct: 229 GVQEDTMTAFLKHNERVRQATFKRRLFSGQLFPVMNGMSLINTAIVIFVGSTIVLSDKSM 28- 8 Query: 263 GAFMISKGQVTVGDLVTFVTYLDMLVWPLMAIGFLFNMVQRGSVSYNRINSLLEQESDIT 32- 2 A +G +VTFV Y P+M I + +Q +RI + ++ ++ Sbjct: 289 PA------AAALGLVVTFVQYSQQYYQPMMQIASSWGELQLAFTGAHRIQEMFDETEEVR 34- 2 Query: 323 DPLNPIRPVVNGTLRYD-IDFFRYDNEETLADIHFTLEKGQTLGLVGQTGSGKTSLIKLL 38- 1 P + + + +DF ++ L+D+ KG+ + +VG TGSGKT+++ L+ Sbjct: 343 PQNAPAFTSLKEAVAINHVDFGYLPGQKVLSDVSIVAPKGKMIAVVGPTGSGKTTIMNLI 40- 2 Query: 382 LREHDVTQGKITLHKHDIRDYRLSELRQLIGYVPQDQFLFATSILENVRFGNPTLSINAV 44- 1 R +DV G IT + DIRDY L LRQ +G V Q+ LF+ +I +N+RFG+ T+S + V Sbjct: 403 NRFYDVDAGSITFDGRDIRDYDLDSLRQKVGIVLQESVLFSGTITDNIRFGDQTISQDMV 46- 2 Query: 442 KKATKLAHVYDDIKQMPAGFETLIGEKGVSLSGGQKQRIAMSRAMILDPDILILDDSLSA 50- 1 + A + H++D I +P G+ T + + S GQKQ I+++R ++ DP++LILD++ S Sbjct: 463 ETAARATHIHDFIMSLPKGYNTYVSDDDNVFSTGQKQLISIARTLLTDPEVLILDEATSN 52- 2 Query: 502 VDAKTEHAIIENLKTNRQGKSTIISAHRLSAVVHADLILVMQDGRVIERGQHQELLNKGG 56- 1 VD TE I ++ G+++ + AHRL +++AD I+V++DG+VIE+G H ELL++ G Sbjct: 523 VDTVTESKIQRAMEAIVAGRTSFVIAHRLKTILNADHIIVLKDGKVIEQGNHHELLHQKG 58- 2 Query: 562 WYAETYASQ 570 +YAE Y +Q Sbjct: 583 FYAELYHNQ 591 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 51 A DNA sequence (GBSx0050) was identified in S. agalactiae <SEQ ID 161> which encodes the amino acid sequence <SEQ ID 162>. This protein is predicted to be mdlB (ATP-bindingprot). Analysis of this protein sequence reveals the following: TABLE-US-00177 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.65 Transmembrane 164-180 (155-183) INTEGRAL Likelihood = -5.15 Transmembrane 25-41 (21-46) INTEGRAL Likelihood = -4.88 Transmembrane 143-159 (133-163) INTEGRAL Likelihood = -1.49 Transmembrane 251-267 (251-270) INTEGRAL Likelihood = -1.33 Transmembrane 61-77 (61-77) ----- Final Results ----- bacterial membrane --- Certainty = 0.4461(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00178 >GP:BAB06054 ABC transporter (ATP-binding protein) [Bacillus halodurans] Identities = 278/582 (47%), Positives = 398/582 (67%), Gaps = 6/582 (1%) Query: 1 MMKSNQWQVFKRLISYLRPYKWFTVLALSLLLLTTVVKNIIPLIASHFIDHYLT-NVNQT 59 + Q VFKRL+SY YK ++A LL + T + +P+I FID YLT T Sbjct: 9 LSSKEQRTVFKRLLSYAAHYKGQLMVAFLLLFIATGAQLLGPIIVKIFIDDYLTPRYFPT 68 Query: 60 AVLILVG--YYSMYVLQTLIQYFGNLFFARVSYSIVRDIRRDAFANMERLGMSYFDRTPA 117- VL L+G Y +++ +I Y+ F +V+ SIV+ +R D F++++RLG+S+FD+TPA Sbjct: 69 DVLFLLGAGYLVLHLTAVIIDYYQLFLFQKVALSIVQRLRIDVFSSVQRLGLSFFDQTPA 128- Query: 118 GSIVSRITNDTEAISDMFSGILSSFISAIFIFTVTLYTMLMLDIKLTGLVALLLPVIFIL 17- 7 G +VSRITNDTE+I +++ +L++F+ I M L++ L +LLP+IF L Sbjct: 129 GGLVSRITNDTESIKELYVTVLATFVQNIIFLIGIFAAMFYLNVTLAIYCLVLLPLIFAL 18- 8 Query: 178 VNVYRKKSVTVIAKTRSLLSDINSKLSESIEGIRIVQAFGQEERLKTEFEEINKEHVVYA 23- 7 + VYRK S A LS +N +++ESI+G+ I+Q F QE R++ EF IN EH + Sbjct: 189 MQVYRKYSSRFYADMSEKLSLLNGRINESIQGMAIIQMFRQERRMRKEFSAINDEHFLAG 24- 8 Query: 238 NRSMALDSLFLRPAMSLLKLLAYAVLMAYFGFTGVKGGLTAGLMYAFIQYVNRLFDPLIE 29- 7 +SM LD L LRPA+ +L +LA ++++YFG + + G++YAF+ Y++R F+P+ + Sbjct: 249 MKSMKLDGLLLRPAVDVLSILALMLILSYFGIMSMDTAVEIGVVYAFVNYLDRFFEPVNQ 30- 8 Query: 298 VTQNFSTLQTSMVSAGRVFDLIDETGFEPSQKNTE--AFVREGNIEFKNVSFSYDGKKQI 35- 5 + S Q ++VSAGRVF L+D P ++ E A + EGN+EF+NVSFSYDGK + Sbjct: 309 MMMRLSMFQQAIVSAGRVFKLMDHRELAPDREGNEHPAIIGEGNVEFRNVSFSYDGKTNV 36- 8 Query: 356 LDNVSFSVKKGETIAFVGATGSGKSSIINVFMRFYEFQSGQVLLDGKDIRDYSQEQLRKN 41- 5 L N+SF+VKKGET+A VG TGSGK+SIINV MRFY Q G++L+DGK + + +LR Sbjct: 369 LKNISFTVKKGETVALVGHTGSGKTSIINVLMRFYPLQDGEILIDGKPLTSFENNELRAK 42- 8 Query: 416 IGLVLQDPFLYHGTIKSNIKMY-QDITDQEVQDAAEFVDADQFIQKLPDKYDAAVSERGS 47- 4 +GLVLQDPFLY GTI SNI++Y Q I+D ++ AA FV AD FI++L Y+ V+ERG+ Sbjct: 429 VGLVLQDPFLYTGTIASNIRLYDQAISDDRIKRAASFVRADGFIERLSHGYETKVTERGA 48- 8 Query: 475 SFSTGQRQLLAFARTVASKPKILILDEATANIDSETEQIVQDSLAKMRQGRTTIAIAHRL 53- 4 +FS+GQRQLL+FART+ +P ILILDEATA++D+ETE+ +Q++L +M+QGRTTIAIAHRL Sbjct: 489 TFSSGQRQLLSFARTMVREPAILILDEATASVDTETEEAIQEALERMKQGRTTIAIAHRL 54- 8 Query: 535 STIQDANCIYVLDRGKIIESGNHESLLDLKGTYYRMYQLQAG 576 STI+DA+ I VL +G+I+E G H+ L+ KG Y +MY LQ G Sbjct: 549 STIKDADQILVLHQGEIVERGTHDELIAKKGLYQKMYVLQKG 590 There is also homology to SEQ ID 160. A related GBS gene <SEQ ID 8481> and protein <SEQ ID 8482> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00179 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -4.63 GvH: Signal Score (-7.5): -5.85 Possible site: 39 >>>Seems to have no N-terminal signal sequence ALOM program count: 5 value: -8.65 threshold: 0.0 INTEGRAL Likelihood = -8.65 Transmembrane 164-180 (155-183) INTEGRAL Likelihood = -5.15 Transmembrane 25-41 (21-46) INTEGRAL Likelihood = -4.88 Transmembrane 143-159 (133-163) INTEGRAL Likelihood = -1.49 Transmembrane 251-267 (251-270) INTEGRAL Likelihood = -1.33 Transmembrane 61-77 (61-77) PERIPHERAL Likelihood = 3.02 483 modified ALOM score: 2.23 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty =0.4461 (Affirmative) < succ> bacterial outside --- Certainty =0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty =0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00010## There is also homology to SEQ IDs 330, 4634 and 5788. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 52 A DNA sequence (GBSx0051) was identified in S. agalactiae <SEQ ID 163> which encodes the amino acid sequence <SEQ ID 164>. Analysis of this protein sequence reveals the following: TABLE-US-00180 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0635(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9609> which encodes amino acid sequence <SEQ ID 9610> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00181 >GP: AAA25224 GB: M87483 anthranilate synthase beta subunit [Lactococcus lactis] Identities = 101/191 (52%), Positives = 133/191 (68%), Gaps = 4/191 (2%) Query: 14 MLLLVDNYDSFTYNLKQYLSVYKEVFVIKNDVPNLFLLAESAEAIVLSPGPGHPKDAGKM 73 - M+L++DNYDSFTYNL QY+ V +V V+KND +L +AE A+A++ SPGPG P DAGKM Sbjct: 1 MILIIDNYDSFTYNLVQYVGVLTDVAVVKNDDDSLGNMAEKADALIFSPGPGWPADAGKM 60 Query: 74 VELINQFIGKKPILGICLGHQALAECLGGRLNLANHVMHGKQSWVTINDHTSLFKGIDSP 133- LI QF G+KPILGICLG QA+ E GG+L LA+ VMHGK S V +F + S Sbjct: 61 ETLIQQFAGQKPILGICLGFQAIVEVFGGKLRLAHQVMHGKNSQVRQTSGNLIFNHLPSK 120- Query: 134 TQVMRYHSLVVTD---LPENIAVIARSNEDNEIMAFHCPSLKVYAMQFHPESIGSIDGMK 19- 0 VMRYHS+V+ + LP+ A+ A + +D EIMA ++Y +QFHPESIG++DGM Sbjct: 121 FLVMRYHSIVMDEAVALPD-FAITAVATDDGEIMAIENEKEQIYGLQFHPESIGTLDGMT 17- 9 Query: 191 MIENFLTLIND 201 MIENF+ +N+ Sbjct: 180 MIENFVNQVNE 190 A related DNA sequence was identified in S. pyogenes <SEQ ID 165> which encodes the amino acid sequence <SEQ ID 166>. Analysis of this protein sequence reveals the following: TABLE-US-00182 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3183(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00183 Identities = 104/186 (55%), Positives = 131/186 (69%) Query: 14 MLLLVDNYDSFTYNLKQYLSVYKEVFVIKNDVPNLFLLAESAEAIVLSPGPGHPKDAGKM 73 - M+LL+DNYDSFTYNL QYLS + E V+ N PNL+ +A+ A A+VLSPGPG PK+A +M Sbjct: 1 MILLIDNYDSFTYNLAQYLSEFDETIVLYNQDPNLYDMAKKANALVLSPGPGWPKEANQM 60 Query: 74 VELINQFIGKKPILGICLGHQALAECLGGRLNLANHVMHGKQSWVTINDHTSLFKGIDSP 133- +LI F KPILG+CLGHQA+AE LGG L LA VMHG+QS + SLF+ + Sbjct: 61 PKLIQDFYQTKPILGVCLGHQAIAETLGGTLRLAKRVMHGRQSTIETQGPASLFRSLPQE 120- Query: 134 TQVMRYHSLVVTDLPENIAVIARSNEDNEIMAFHCPSLKVYAMQFHPESIGSIDGMKMIE 19- 3 VMRYHS+VV LP+ +V AR +D EIMAF +L ++ +QFHPESIG+ DGM MI Sbjct: 121 ITVMRYHSIVVDQLPKGFSVTARDCDDQEIMAFEHHTLPLFGLQFHPESIGTPDGMTMIA 18- 0 Query: 194 NFLTLI 199 NF+ I Sbjct: 181 NFIAAI 186 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 53 A DNA sequence (GBSx0052) was identified in S. agalactiae <SEQ ID 167> which encodes the amino acid sequence <SEQ ID 168>. Analysis of this protein sequence reveals the following: TABLE-US-00184 Possible site: 58 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.17 Transmembrane 117-133 (108-140) INTEGRAL Likelihood = -1.70 Transmembrane 150-166 (150-166) ----- Final Results ----- bacterial membrane --- Certainty = 0.4270(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00185 >GP: CAB12877 GB: Z99109 similar to biotin biosynthesis [Bacillus subtilis] Identities = 70/168 (41%), Positives = 106/168 (62%) Query: 8 YIALMVALLIVLGFIPGIPLGFIPVPIVLQNLGVMLAGALLGSRKGFLAVAIFLLLVAIG 67 +IA+ AL+ VLGF+P + L F PVPI LQ LGVMLAG++L + FL+ +FLLLVA G Sbjct: 9 HIAIFTALMAVLGFMPPLFLSFTPVPITLQTLGVMLAGSILRPKSAFLSQLVFLLLVAFG 68 Query: 68 APFLPGGRSGLVTLFGPTAGYLLTYPFAAFFIGLGLEKVKTTKLWVQFLIIWIFGVLLID 127- AP LPGGR G FGP+AG+L+ YP A++ I L +++ + F +FG++ I Sbjct: 69 APLLPGGRGGFGVFFGPSAGFLIAYPLASWLISLAANRLRKVTVLRLFFTHIVFGIIFIY 128- Query: 128 ICGSIVLSFQTSLPLTKSLFSNLIFIPGDTLKASICLIIYRKFANRLT 175 + G V +F + L+++ F +L ++PGD +KA++ + K L+ Sbjct: 129 LLGIPVQAFIMHIDLSQAAFMSLAYVPGDLIKAAVSAFLAIKITQALS 176 A related DNA sequence was identified in S. pyogenes <SEQ ID 169> which encodes the amino acid sequence <SEQ ID 170>. Analysis of this protein sequence reveals the following: TABLE-US-00186 Possible site: 51 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.03 Transmembrane 113-129 (109-139) INTEGRAL Likelihood = -8.97 Transmembrane 55-71 (52-76) INTEGRAL Likelihood = -7.54 Transmembrane 10-26 (6-38) INTEGRAL Likelihood = -5.79 Transmembrane 86-102 (81-105) INTEGRAL Likelihood = -2.87 Transmembrane 33-49 (28-51) INTEGRAL Likelihood = -1.97 Transmembrane 150-166 (150-168) ----- Final Results ----- bacterial membrane --- Certainty = 0.5012(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00187 Identities = 80/168 (47%), Positives = 108/168 (63%), Gaps = 1/168 (0%) Query: 3 TRTTTYIALMVALLIVLGFIPGIPLGFIPVPIVLQNLGVMLAGALLGSRKGFLAVAIFLL 62 T+ +A+M L+I+LGFIP IPLGFIPVPIVLQNLGVMLAG +LG +KG L+V +F L Sbjct: 4 TKELVKVAMMTTLIIILGFIPAIPLGFIPVPIVLQNLGVMLAGLMLGGKKGTLSVFLF-L 62 Query: 63 LVAIGAPFLPGGRSGLVTLFGPTAGYLLTYPFAAFFIGLGLEKVKTTKLWVQFLIIWIFG 122- ++ + P G R+ + L GP+AGY++ Y L + + FL + I G Sbjct: 63 VIGLFLPVFSGSRTTIPVLMGPSAGYVIAYLLVPIVFSLLYRNWFSKSTPLAFLALLISG 122- Query: 123 VLLIDICGSIVLSFQTSLPLTKSLFSNLIFIPGDTLKASICLIIYRKF 170 V+L+D+ G+I LS T + L SL SNL+FIPGDT+KA I II K+ Sbjct: 123 VVLVDVLGAIWLSAYTGMSLVTSLLSNLVFIPGDTIKAIIATIIAVKY 170 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 54 A DNA sequence (GBSx0053) was identified in S. agalactiae <SEQ ID 171> which encodes the amino acid sequence <SEQ ID 172>. Analysis of this protein sequence reveals the following: TABLE-US-00188 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3914(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 55 A DNA sequence (GBSx0054) was identified in S. agalactiae <SEQ ID 173> which encodes the amino acid sequence <SEQ ID 174>. Analysis of this protein sequence reveals the following: TABLE-US-00189 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1864(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9611> which encodes amino acid sequence <SEQ ID 9612> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00190 >GP: BAB05467 GB: AP001513 biotin synthase [Bacillus halodurans] Identities = 133/316 (42%), Positives = 201/316 (63%), Gaps = 2/316 (0%) Query: 17 NYIHLADEILSGKTSISYEQALEILNS-DENWWEIYAAALYLKNQVSRNNIRLNVLLSAK 75 - N+I LA E++ GK IS +AL ILNS D+ + A ++ ++LN++++AK Sbjct: 2 NWIQLAQEVIEGKR-ISENEALAILNSPDDELLLLLQGAFTIRQTYYGKKVKLNMIMNAK 60 Query: 76 QGLCAENCGYCSQSKESTADIDKFGLLPQNVILKQAIVAHQNGASVFCIAMSGTKPSKRE 135- G C ENCGYCSQS S A ID + ++ + IL+ A AH+ +CI SG P+ R+ Sbjct: 61 SGFCPENCGYCSQSSISKAPIDAYPMVNKETILEGAKRAHELNVGTYCIVASGRGPTNRD 120- Query: 136 IEQLCQVIPEIKKSLPLEICLTAGFLDREQLHQLKQAGIDRINHNLNTPEENYPNIATTH 19- 5 I+ + + + EIK + L+IC G L EQ QLK AG+DR NHN+NT ++ I T+H Sbjct: 121 IDHVTEAVREIKDTYGLKICACLGILKPEQAEQLKAAGVDRYNHNVNTSARHHDQITTSH 18- 0 Query: 196 SFKDRCDTLERIHNEDIDVCSGFICGMGESDEGLITLAFRLKELDPYSIPVNFLLAVEGT 25- 5 +++DR +T+E + + I CSG I GM E+ E ++ +AF+L+ELD SIPVNFL A++GT Sbjct: 181 TYEDRVNTVEVVKHSGISPCSGVIVGMKETKEDVVDMAFQLRELDADSIPVNFLHAIDGT 24- 0 Query: 256 PLGKYNYLTPIKCLKIMAMLRFVFPFKELRLSAGREVHFENFESLVTLLVDSTFLGNYLT 31- 5 PL + LTPI CLK++++ R+V P KE+R+S GREV+ ++ + L +S F+G+YLT Sbjct: 241 PLQGVHELTPIYCLKVLSLFRYVCPTKEIRISGGREVNLKSLQPLGLYAANSIFIGDYLT 30- 0 Query: 316 EGGRNQHTDIEFLEKL 331 G+ + D + L+ L Sbjct: 301 TAGQEETADHQILKDL 316 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 56 A DNA sequence (GBSx0055) was identified in S. agalactiae <SEQ ID 175> which encodes the amino acid sequence <SEQ ID 176>. Analysis of this protein sequence reveals the following:

TABLE-US-00191 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3440(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9613> which encodes amino acid sequence <SEQ ID 9614> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 57 A DNA sequence (GBSx0056) was identified in S. agalactiae <SEQ ID 177> which encodes the amino acid sequence <SEQ ID 178>. Analysis of this protein sequence reveals the following: TABLE-US-00192 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1985(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 58 A DNA sequence (GBSx0057) was identified in S. agalactiae <SEQ ID 179> which encodes the amino acid sequence <SEQ ID 180>. Analysis of this protein sequence reveals the following: TABLE-US-00193 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.11 Transmembrane 347-363 (347-363) ----- Final Results ----- bacterial membrane --- Certainty = 0.1044(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00194 >GP: CAC11722 GB: AL445064 acetyl-CoA acetyltransferase related protein [Thermoplasma acidophilum] Identities = 113/388 (29%), Positives = 181/388 (46%), Gaps = 31/388 (7%) Query: 4 RDVYIGFGLRTPIGIKGKQFKHYR-PELLGAHLLNQIKKIESESNID-----SIICGNTV 57 RDV+I RT IG G+ F + P+L GA IK + E+++D +I GN + Sbjct: 2 RDVFIVAAKRTAIGKFGRSFSKLKAPQLGGA----AIKAVMDEAHVDPASVEEVIMGNVI 57 Query: 58 --GTGGNIGRLMTLFSDYESYIPVQTIDMQCASSSSALFFGYLKISTGINEKVLVGGIES 115- G G N + + T+++ CAS A+ +I+ G + V+ GG+ES Sbjct: 58 QAGNGQNPAGQAAFHGGLPNSVLKYTVNVVCASGMLAVESAAREIALGERDLVIAGGMES 117- Query: 116 SSLQPMR-----RYAKEDNRNGEYTVAQ-FSPDSYAETVMLE----GAQRVCQKYGFRRE 16- 5 S P R+ + + Y + D + E A+R +K+G RE Sbjct: 118 MSNAPFLLPADLRWGPKHLLHKNYKIDDAMLTDGLLDAFYFEHMGVSAERTSRKFGITRE 17- 7 Query: 166 MLDKLAFLSHKRALTAKQGGYLEEVILPMEGM-RDQGVRKLKETFFQKLPRLMENSPLLT 22- 4 M D+ + S++RA+ A + G + I+ EG+ D+G+RK +LP + + +LT Sbjct: 178 MADEYSVQSYERAIRATESGEFADEIVQFEGLDHDEGIRKTTMEDLARLPPAFDKNGILT 23- 7 Query: 225 IGNVCLMHDAAAFLTLQSQKT--EFRIVHIVEVAG------DPKLSPELVHTATEKLLTE 27- 6 GH + D + L + S+K E+ + I + G DP E AT KLL + Sbjct: 238 AGNSAQLSDGGSALMIASEKAINEYGLKPIARITGYEQASLDPLDFVEAPIPATRKLLEK 29- 7 Query: 277 THTKISDYDAIEWNEPFAAIDALFNHYYPEEREKFNIFGGTLAYGHPYACSGIINILHLM 33- 6 H I YD +E NE F+ + + + E+FN+ GG +A GHP SG I+ LM Sbjct: 298 QHKSIDYYDLVEHNEAFSIASVIVRNELKIDNERFNVNGGAVAIGHPIGNSGARIIVTLM 35- 7 Query: 337 QALKYKNKPMGLTAIAGAGGVGMAISIE 364 ALK+++ GL + GG +++E Sbjct: 358 NALKHRHLKTGLATLCHGGGGAHTLTLE 385 A related DNA sequence was identified in S. pyogenes <SEQ ID 181> which encodes the amino acid sequence <SEQ ID 182>. Analysis of this protein sequence reveals the following: TABLE-US-00195 Possible site: 22 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.28 Transmembrane 345-361 (345-361) ----- Final Results ----- bacterial membrane --- Certainty = 0.1510(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00196 >GP: BAB03328 GB: AB035449 acetyl-CoA c-acetyltransferase [Staphylococcus aureus] Identities = 115/382 (30%), Positives = 184/382 (48%), Gaps = 29/382 (7%) Query: 1 MTDVYIAAGLRTPIGLVGKQFAKEQPEILGAKLINALQNKYPV---PIDQVICGNTVGTG 57 M I A RT G G +PE L L + KYP ID V+ GN VG G Sbjct: 1 MNQAVIVAAKRTAFGKYGGTLKHLEPEQLLKPLFQHFKEKYPEVISKIDDVVLGNVVGNG 60 Query: 58 GNIGRLMTLYSHLGESVSALTVDMQCASAGAALSVGYAKIKAGMASNLLVGGIESSS--- 114- GNI R L + L +S+ +T+D QC S ++ I+AG + GG+ES+S Sbjct: 61 GNIARKALLEAGLKDSIPGVTIDRQCGSGLESVQYACRMIQAGAGKVYIAGGVESTSRAP 120- Query: 115 ---LQPESVYASADWRQGAYKVAQFSPDSISPFAMIEGAERVAREHGFTKEYLNHWTLRS 17- 1 +P SVY +A Y+ A F+P+ P +MI+GAE VA+ + ++E + + RS Sbjct: 121 WKIKRPHSVYETA--LPEFYERASFAPEMSDP-SMIQGAENVAKMYDVSRELQDEFAYRS 17- 7 Query: 172 HQKASYCQEQALLADLILDLSGA-----SDQGIRPRLSSKVLSKVPPILGEGHVISAANA 22- 6 HQ + + ++ IL ++ +D+ ++ + + P++ +G ++AAN+ Sbjct: 178 HQLTAENVKNGNISQEILPITVKGEIFNTDESLKSHIPKDNFGRFKPVI-KGGTVTAANS 23- 6 Query: 227 CLTHDAAAFLQLSSQPSAFKL--------IDVVEVAGDPQRSPLMVIKASQVLLEKHGLG 27- 8 C+ +D A L + + A++L D V V D + + A LL+++ L Sbjct: 237 CMKNDGAVLLLIMEKDMAYELGFEHGLLFKDGVTVGVDSNFPGIGPVPAISNLLKRNQLT 29- 6 Query: 279 MADMTAIEWNEAFAVIDGLFETHYPDLLDRYNIFGGALAYGHPYGASAAIIILHLMRALE 33- 8 + ++ IE NEAF+ + + NI+GGALA GHPYGAS A ++ L + Sbjct: 297 IENIEVIEINEAFSAQVVACQQALNISNTQLNIWGGALASGHPYGASGAQLVTRLFYMFD 35- 6 Query: 339 IKNGRYGIAAIAAAGGQGFAVL 360 + IA++ GG G A L Sbjct: 357 KET---MIASMGIGGGLGNAAL 375 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00197 Identities = 182/362 (50%), Positives = 243/362 (66%), Gaps = 2/362 (0%) Query: 5 DVYIGFGLRTPIGIKGKQFKHYRPELLGAHLLNQIKKIESESNIDSIICGNTVGTGGNIG 64 DVYI GLRTPIG+ GKQF +PE+LGA L+N ++ + ID +ICGNTVGTGGNIG Sbjct: 3 DVYIAAGLRTPIGLVGKQFAKEQPEILGAKLINALQN-KYPVPIDQVICGNTVGTGGNIG 61 Query: 65 RLMTLFSDYESYIPVQTIDMQCASSSSALFFGYLKISTGINEKVLVGGIESSSLQPMRRY 124- RLMTL+S + T+DMQCAS+ +AL GY KI G+ +LVGGIESSSLQP Y Sbjct: 62 RLMTLYSHLGESVSALTVDMQCASAGAALSVGYAKIKAGMASNLLVGGIESSSLQPESVY 121- Query: 125 AKEDNRNGEYTVAQFSPDSYAETVMLEGAQRVCQKYGFRREMLDKLAFLSHKRALTAKQG 18- 4 A D R G Y VAQFSPDS + M+EGA+RV +++GF +E L+ SH++A ++ Sbjct: 122 ASADWRQGAYKVAQFSPDSISPFAMIEGAERVAREHGFTKEYLNHWTLRSHQKASYCQEQ 18- 1 Query: 185 GYLEEVILPMEGMRDQGVR-KLKETFFQKLPRLMENSPLLTIGNVCLMHDAAAFLTLQSQ 24- 3 L ++IL + G DQG+R +L K+P ++ +++ N CL HDAAAFL L SQ Sbjct: 182 ALLADLILDLSGASDQGIRPRLSSKVLSKVPPILGEGHVISAANACLTHDAAAFLQLSSQ 24- 1 Query: 244 KTEFRIVHIVEVAGDPKLSPELVHTATEKLLTETHTKISDYDAIEWNEPFAAIDALFNHY 30- 3 + F+++ +VEVAGDP+ SP +V A++ LL + ++D AIEWNE FA ID LF + Sbjct: 242 PSAFKLIDVVEVAGDPQRSPLMVIKASQVLLEKHGLGMADMTAIEWNEAFAVIDGLFETH 30- 1 Query: 304 YPEEREKFNIFGGTLAYGHPYACSGIINILHLMQALKYKNKPMGLTAIAGAGGVGMAISIEY - 365 YP+ +++NIFGG LAYGHPY S I ILHLM+AL+ KN G+ AIA AGG G A+ ++Y Sbjct: 302 YPDLLDRYNIFGGALAYGHPYGASAAIIILHLMRALEIKNGRYGIAAIAAAGGQGFAVLLKY - 363 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 59 A DNA sequence (GBSx0058) was identified in S. agalactiae <SEQ ID 183> which encodes the amino acid sequence <SEQ ID 184>. Analysis of this protein sequence reveals the following: TABLE-US-00198 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.82 Transmembrane 149-165 (148-165) ----- Final Results ----- bacterial membrane --- Certainty = 0.2529(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00199 >GP: CAB12876 GB: Z99109 similar to long-chain fatty-acid-CoA ligase [Bacillus subtilis] Identities = 90/382 (23%), Positives = 158/382 (40%), Gaps = 24/382 (6%) Query: 47 ISTHSLLNQLVRFVSKLCQKALPIICKPNLTHNEISRLEKEV--QYAPQLADFGVLSSGT 104- IS L+ L F +KL P++ N +IS + P+ + +SG+ Sbjct: 95 ISNADLVVTLAFFKNKLTDSQTPVVLLDNCMA-DISEAAADPLPTIDPEHPFYMGFTSGS 153- Query: 105 TADAKLLWRSFTSWSDFFSIQNAYFSVTSNSKLFIQGDFSFTGNLNLALSLLLLGGTLVV 16- 4 T K RS SW + F+ FS++S+ K+ I G + L A+S L LGGT+ + Sbjct: 154 TGKPKAFTRSHRSWMESFTCTETDFSISSDDKVLIPGALMSSHFLYGAVSTLFLGGTVCL 21- 3 Query: 165 TQKNSVKYWQTLWEKTGVTHLYLLPSYLKLVEQYSKETALDNKTIITSSQYVSDSLLEGL 22- 4 +K S + + ++ LY +P+ + + K I + + + ++S + L Sbjct: 214 LKKFSPAKAKEWLCRESISVLYTVPTMTDALARIEGFPDSPVKIISSGADWPAES-KKKL 27- 2 Query: 225 YRKHPKVSVKIFYGASELNYVSWYDGRDIRDKPQYVGEIVPNVAVRIKE----------- 27- 3 P + + FYG SEL++V++ D + KP G NV + I+ Sbjct: 273 AAAWPHLKLYDFYGTSELSFVTFSSPEDSKRKPHSAGRPFHNVRIEIRNAGGERCQPGEI 33- 2 Query: 274 GRIFVKTPYSICG-----LSSEYCAGDYGELID--GKLYLFGRGGDWCNQSGIKLYLPRL 32- 6 G+IFVK+P G E+ D +D G LY+ GR G+ ++ + Sbjct: 333 GKIFVKSPMRFSGYVNGSTPDEWMTVDDMGYVDEEGFLYISGRENGMIVYGGLNIFPEEI 39- 2 Query: 327 IEKIKTCPYIKDAVAFTKESQSHGQESHCCIVLIENQMQQECLKWLSEHFEKKYGFKHYH 38- 6 + CP ++ A + G+ + V++ N + W + K + Sbjct: 393 ERVLLACPEVESAAVVGIPDEYWGEIA--VAVILGNANARTLKAWCKQKLASYKIPKKWV 45- 0 Query: 387 IVSKIPLMPSGKIDYQQLKRQL 408 +P SGKI ++K+ L Sbjct: 451 FADSLPETSSGKIARSRVKKWL 472 A related DNA sequence was identified in S. pyogenes <SEQ ID 185> which encodes the amino acid sequence <SEQ ID 186>. Analysis of this protein sequence reveals the following: TABLE-US-00200 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2487(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00201 Identities = 154/413 (37%), Positives = 235/413 (56%), Gaps = 9/413 (2%) Query: 1 MLESLKTIVKTNSDKKLFDGD-LQVSYGEFYNLVR-QDMASQDNRKHVISTHSLLNQLVR 58 ML L+ K +KK D + ++Y E + V +D +D+ ++IS LNQL+ Sbjct: 1 MLTKLEYWAKQCPNKKAIVADQISLTYQELWQAVLIKDQTIKDSVPYIISHSRYLNQLLS 60 Query: 59 FVSKLCQKALPIICKPNLT---HNEISRLEKEVQYAPQLADFGVLSSGTTADAKLLWRSF 115- F+ L + + PII PN++ +I ++ E+ + ADF VLSSGTT AKL WR Sbjct: 61 FLRGLKEGSCPIILHPNISGTFQQQIKHVDGELL---KKADFAVLSSGTTGKAKLFWRRL 117- Query: 116 TSWSDFFSIQNAYFSVTSNSKLFIQGDFSFTGNLNLALSLLLLGGTLVVTQKNSVKYWQT 17- 5 ++W+ F QN F +T NS LF+ G FSFTGNLNLAL+ L GG LV++QK S+K W + Sbjct: 118 STWTRLFDYQNKVFGMTGNSCLFLHGSFSFTGNLNLALAQLWAGGCLVLSQKLSLKTWLS 17- 7 Query: 176 LWEKTGVTHLYLLPSYLKLVEQYSKETALDNKTIITSSQYVSDSLLEGLYRKHPKVSVKI 23- 5 LW+ V+HLYLLP+YL + Y + + ++TSSQ +S LL Y+K P++ + I Sbjct: 178 LWQAKKVSHLYLLPTYLNRLLPYLTKNNMTATHLLTSSQMISQELLRHYYKKFPQLEIVI 23- 7 Query: 236 FYGASELNYVSWYDGRDIRDKPQYVGEIVPNVAVRIKEGRIFVKTPYSICGLSSEYCAGD 29- 5 FYGASEL++++W +GR VG+ P+V++ K+ IFV+TPYS+ G+S Y D Sbjct: 238 FYGASELSFITWCNGRAAVKINGLVGQPFPDVSISFKDKEIFVETPYSVEGMSQPYSVSD 29- 7 Query: 296 YGELIDGKLYLFGRGGDWCNQSGIKLYLPRLIEKIKTCPYIKDAVAFTKESQSHGQESHC 35- 5 G++ L L GR DW NQ G+K +LP L+E P +K+A A K + + Sbjct: 298 LGKMSPAGLILEGRQDDWVNQRGVKCHLPSLVELAHQAPNVKEAHAL-KIGKGENETLIL 35- 6 Query: 356 CIVLIENQMQQECLKWLSEHFEKKYGFKHYHIVSKIPLMPSGKIDYQQLKRQL 408 +VL + +L+ + K+Y ++ +PL +GKI+ + L ++ Sbjct: 357 VLVLTKKDCLAPIKDFLALYLNSGQLPKYYLVIDCLPLKDNGKINREVLLNKI 409 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 60 A DNA sequence (GBSx0059) was identified in S. agalactiae <SEQ ID 187> which encodes the amino acid sequence <SEQ ID 188>. This protein is predicted to be endonuclease III (pdg). Analysis of this protein sequence reveals the following: TABLE-US-00202 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.00 Transmembrane 25-41 (25-41) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00203 >GP: BAB05417 GB: AP001512 endonuclease III (DNA repair) [Bacillus halodurans] Identities = 95/202 (47%), Positives = 134/202 (66%) Query: 1 MLSKAKSRYIIREIIKLFPDAKPSLDFTNVFELLVAVMLSAQTTDAAVNKVTPALFERFP 60 ML+K +++ + I ++PDA+ L +N FELL+AV+LSAQ TDA VNKVTP LF ++ Sbjct: 1 MLTKKQTQEALAVIADMYPDAECELTHSNPFELLIAVVLSAQCTDALVNKVTPRLFAKYK 60 Query: 61 NPLVLAQADPKEIEPYISKIGLYRNKARFLNQCAKQLIEHFDGKVPRTRQELESLAGVGR 120- P +E+E I IGLYRNKA+ + + + L+E + G+VP+ R EL LAGVGR Sbjct: 61 TPEDYIAVPLEELEQDIRSIGLYRNKAKNIKKLCQSLLEQYGGEVPQDRDELVKLAGVGR 120- Query: 121 KTANVVMSVGFGIPAFAVDTHVTRICKHHQICKQSASPLEIEKRVMEVLPPEEWLAAHQS 18- 0 KTANVV SV FG+PA AVDTHV R+ K IC+ + ++E+ +M+ +P +EW +H Sbjct: 121 KTANVVASVAFGVPAIAVDTHVERVSKRLGICRWKDNVTQVEQTLMKKIPMDEWSISHHR 18- 0 Query: 181 MIYFGRAICHPKNPKCDQYPQL 202 +I+FGR C +NP+CD P L Sbjct: 181 LIFFGRYHCKAQNPQCDICPLL 202 A related DNA sequence was identified in S. pyogenes <SEQ ID 189> which encodes the amino acid sequence <SEQ ID 190>. Analysis of this protein sequence reveals the following: TABLE-US-00204 Possible site: 44 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00205 Identities = 91/199 (45%), Positives = 133/199 (66%) Query: 2 LSKAKSRYIIREIIKLFPDAKPSLDFTNVFELLVAVMLSAQTTDAAVNKVTPALFERFPN 61 + KA+ ++ I ++FP+AK LD+ F+LL+AV+LSAQTTD AVNKVTP L++ +P Sbjct: 3 IGKARLAKVLTIIGQMFPEAKGELDWETPFQLLIAVILSAQTTDKAVNKVTPGLWQSYPE 62 Query: 62 PLVLAQADPKEIEPYISKIGLYRNKARFLNQCAKQLIEHFDGKVPRTRQELESLAGVGRK 121- LA A+ ++E + IGLY+NKA+ + + A+ + + F G+VP+T +ELESL GVGRK Sbjct: 63 IEDLAFAELSDVENALRTIGLYKNKAKNIIKTAQAIRDDFKGQVPKTHKELESLPGVGRK 122- Query: 122 TANVVMSVGFGIPAFAVDTHVTRICKHHQICKQSASPLEIEKRVMEVLPPEEWLAAHQSM 18- 1 TANVV++ +G+PA AVDTHV R+ K I A +IE +M +P ++W+ H + Sbjct: 123 TANVVLAEVYGVPAIAVDTHVARVSKRLNISSPDADVKQIEADLMAKIPKKDWIITHHRL 18- 2 Query: 182 IYFGRAICHPKNPKCDQYP 200 I+FGR C K PKC+ P Sbjct: 183 IFFGRYHCLAKKPKCEICP 201 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 61 A DNA sequence (GBSx0060) was identified in S. agalactiae <SEQ ID 191> which encodes the amino acid sequence <SEQ ID 192>. Analysis of this protein sequence reveals the following: TABLE-US-00206 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2264 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00207 >GP:BAA96473 GB:AB036428 hypothetical 8.3 kDa protein [Streptococcus mutans] Identities = 53/67 (79%), Positives = 62/67 (92%) Query: 1 MKVLFDVQNLLKKFGIYVYIGKRLYDIEVMKIELQRLYDNGLISRDDYLKAELILRREHR 60 MK L+DVQ LLK+FGI+VY+GKRLYDIE+MKIEL+RLYDNGLIS+ DYL AELILRREHR Sbjct: 1 MKTLYDVQRLLKQFGIFVYLGKRLYDIEMMKIELERLYDNGLISKSDYLHAELILRREHR 60 Query: 61 LELEKEN 67 +E E+EN Sbjct: 61 IEKEREN 67 A related DNA sequence was identified in S. pyogenes <SEQ ID 193> which encodes the amino acid sequence <SEQ ID 194>. Analysis of this protein sequence reveals the following: TABLE-US-00208 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1962 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00209 Identities = 53/66 (80%), Positives = 60/66 (90%) Query: 1 MKVLFDVQNLLKKFGIYVYIGKRLYDIEVMKIELQRLYDNGLISRDDYLKAELILRREHR 60 MK L+DVQ LLK FGI+VY+GKRLYDIE+MKIELQRLYD+GL+ + DYL AELILRREHR Sbjct: 7 MKTLYDVQQLLKNFGIFVYLGKRLYDIEMMKIELQRLYDSGLLDKRDYLNAELILRREHR 66 Query: 61 LELEKE 66 LELEKE Sbjct: 67 LELEKE 72 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 62 A DNA sequence (GBSx0061) was identified in S. agalactiae <SEQ ID 195> which encodes the amino acid sequence <SEQ ID 196>. Analysis of this protein sequence reveals the following:

TABLE-US-00210 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.06 Transmembrane 133-149 (133-150) ----- Final Results ----- bacterial membrane --- Certainty = 0.1022(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00211 >GP: BAB05144 GB: AP001512 glucose kinase [Bacillus halodurans] Identities = 145/315 (46%), Positives = 209/315 (66%), Gaps = 2/315 (0%) Query: 6 LGIDLGGTTIKFGILTLEGEVQEKWAIETNTLENGRHIVSDIVESLKHRLSLYGLTKDDF 65 +G+D+GGTTIK LT GE+ +KW I TN + G I ++I ++L RLS + +K D Sbjct: 7 VGVDVGGTTIKMAFLTTAGEIVDKWEIPTNKQDGGALITTNIADALDKRLSGHHKSKSDL 66 Query: 66 LGIGMGSPGAVDRTSKTVTGAFNLNWADTQEVGSVIEKEVGIPFFIDNDANVAALGERWV 125- +GIG+G+PG ++ + + A N+ W D + +E+E +P +DNDAN+AALGE W Sbjct: 67 IGIGLGAPGFIEMDTGFIYHAVNIGWRDFP-LKDKLEEETKLPVIVDNDANIAALGEMWK 125- Query: 126 GAGANNPDVVFVTLGTGVGGGVIADGNLIHGVAGAGGEIGHMIVDPENGFTCTCGNKGCL 18- 5 GAG +++ +TLGTGVGGG++A+GN++HGV G GEIGH+ V PE G C CG GCL Sbjct: 126 GAGDGAKNMLLITLGTGVGGGIVANGNILHGVNGMAGEIGHITVIPEGGAPCNCGKTGCL 18- 5 Query: 186 ETVASATGVVRVARQLAEQYEGSSAIKAAIDNGDTVTSKDIFIAAEDGDKFANSVVERVS 24- 5 ETVASATG+ R+A + +++ S + D +T+KD+F AA+ D FA SVV+ ++ Sbjct: 186 ETVASATGIARIATEGVTEHK-ESQLALDYDKHGVLTAKDVFSAADASDAFALSVVDHIA 24- 4 Query: 246 RYLGLAAANISNILNPDSVVIGGGVSAAGEFLRSRVEKYFVTFAFPQVKKSTKIKIAELG 30- 5 YLG A AN++N LNP+ +VIGGGVS AG+ L ++++F +A P+V + +IA LG Sbjct: 245 YYLGFAIANLANALNPEKIVIGGGVSKAGDTLLKPIKQHFEAYALPRVADGAEFRIATLG 30- 4 Query: 306 NDAGIIGAASLANQQ 320 NDAG+IG L QQ Sbjct: 305 NDAGVIGGGWLVKQQ 319 A related DNA sequence was identified in S. pyogenes <SEQ ID 197> which encodes the amino acid sequence <SEQ ID 198>. Analysis of this protein sequence reveals the following: TABLE-US-00212 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1060(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00213 Identities = 270/319 (84%), Positives = 292/319 (90%) Query: 1 MSKKLLGIDLGGTTIKFGILTLEGEVQEKWAIETNTLENGRHIVSDIVESLKHRLSLYGL 60 MS+KLLGIDLGGTTIKFGILT GEVQEKWAIETN LE G+HIV DI+ S+KHRL LYGL Sbjct: 1 MSQKLLGIDLGGTTIKFGILTAAGEVQEKWAIETNILEGGKHIVPDIIASIKHRLDLYGL 60 Query: 61 TKDDFLGIGMGSPGAVDRTSKTVTGAFNLNWADTQEVGSVIEKEVGIPFFIDNDANVAAL 120- + DF+GIGMGSPGAVDR + TVTGAFNLNW +TQEVGSV+EKE+GIPF IDNDANVAAL Sbjct: 61 SSADFVGIGMGSPGAVDRDTNTVTGAFNLNWKETQEVGSVVEKELGIPFAIDNDANVAAL 120- Query: 121 GERWVGAGANNPDVVFVTLGTGVGGGVIADGNLIHGVAGAGGEIGHMIVDPENGFTCTCG 18- 0 GERWVGAG NNPDVVF+TLGTGVGGG+IADGNLIHGVAGAGGEIGHMIV+PENGF CTCG Sbjct: 121 GERWVGAGENNPDVVFMTLGTGVGGGIIADGNLIHGVAGAGGEIGHMIVEPENGFACTCG 18- 0 Query: 181 NKGCLETVASATGVVRVARQLAEQYEGSSAIKAAIDNGDTVTSKDIFIAAEDGDKFANSV 24- 0 + GCLETVASATGVV+VAR LAE YEG SAIKAAIDNG+ VTSKDIF+AAE GD FA+SV Sbjct: 181 SHGCLETVASATGVVKVARLLAEAYEGDSAIKAAIDNGEGVTSKDIFMAAEAGDSFADSV 24- 0 Query: 241 VERVSRYLGLAAANISNILNPDSVVIGGGVSAAGEFLRSRVEKYFVTFAFPQVKKSTKIK 30- 0 VE+V YLGLA+ANISNILNPDSVVIGGGVSAAGEFLRSR+EKYFVTF FPQV+ STKIK Sbjct: 241 VEKVGYYLGLASANISNILNPDSVVIGGGVSAAGEFLRSRIEKYFVTFTFPQVRYSTKIK 30- 0 Query: 301 IAELGNDAGIIGAASLANQ 319 IAELGNDAGIIGAASLA Q Sbjct: 301 IAELGNDAGIIGAASLARQ 319 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 63 A DNA sequence (GBSx0062) was identified in S. agalactiae <SEQ ID 199> which encodes the amino acid sequence <SEQ ID 200>. Analysis of this protein sequence reveals the following: TABLE-US-00214 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00215 >GP: CAB14385 GB: Z99116 similar to hypothetical proteins [Bacillus subtilis] Identities = 51/124 (41%), Positives = 71/124 (57%), Gaps = 1/124 (0%) Query: 3 MSVILIIVILLAFVAWASWNYWRVRRAAKFLDNESFQKEMSRGQLIDIREAGAFHRKHIL 62 MS +++++I AF+ + +Y +R K L E F+ + QLID+RE F HIL Sbjct: 1 MSNMIVLIIFPAFIIYMIASYVYQQRIMKTLTEEEFRAGYRKAQLIDVREPNEFEGGHIL 60 Query: 63 GARNIPASQFKVALSALRKDKPVLLYDASRGQSIPRIVLLLRKEGFNQLYVLKDGFNYWT 122- GARNIP SQ K + +R DKPV LY + +S R LRK G ++Y LK GF W Sbjct: 61 GARNIPLSQLKQRKNEIRTDKPVYLYCQNSVRS-GRAAQTLRKNGCTEIYNLKGGFKKWG 119- Query: 123 GRVK 126 G++K Sbjct: 120 GKIK 123 A related DNA sequence was identified in S. pyogenes <SEQ ID 201> which encodes the amino acid sequence <SEQ ID 202>. Analysis of this protein sequence reveals the following: TABLE-US-00216 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.41 Transmembrane 4-20 (1-22) ----- Final Results ----- bacterial membrane --- Certainty = 0.2763 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00217 >GP:BAB06532 GB:AP001516 unknown conserved protein [Bacillus halodurans] Identities = 46/120 (38%), Positives = 64/120 (53%) Query: 8 LWLLLVGIVGYYTWNYFSFRKMAKQVDNETFKDVMRQGQLIDLREPAAFRTKHILGARNF 67 +WL+L+ ++ Y + K K + E F R+ QLID+REP + + HILGARN Sbjct: 5 VWLVLLALLVYVLFKRLYTPKYLKTLTQEEFIQGYRKAQLIDVREPREYDSGHILGARNI 64 Query: 68 PAQQFDAAIKGLRKDKPVLIYENMRPQYRVPAVKKLKKAGFEDVYVLKDGIDYWDGKVKQ 127- P Q +K +R D+PV +Y + R A KK G EDV LK G W GK+K+ Sbjct: 65 PLSQLKQRLKEVRTDQPVYLYCQSGARSRQAAAILKKKHGVEDVNHLKGGFRKWTGKIKK 124- An alignment of the GAS and GBS proteins is shown below: TABLE-US-00218 Identities = 63/126 (50%), Positives = 85/126 (67%) Query: 1 MDMSVILIIVILLAFVAWASWNYWRVRRAAKFLDNESFQKEMSRGQLIDIREAGAFHRKH 60 M +++ ++L+ V + +WNY+ R+ AK +DNE+F+ M +GQLID+RE AF KH Sbjct: 1 MSPITLILWLLLVGIVGYYTWNYFSFRKMAKQVDNETFKDVMRQGQLIDLREPAAFRTKH 60 Query: 61 ILGARNIPASQFKVALSALRKDKPVLLYDASRGQSIPRIVLLLRKEGFNQLYVLKDGFNY 120- ILGARN PA QF A+ LRKDKPVL+Y+ R Q V L+K GF +YVLKDG +Y Sbjct: 61 ILGARNFPAQQFDAAIKGLRKDKPVLIYENMRPQYRVPAVKKLKKAGFEDVYVLKDGIDY 120- Query: 121 WTGRVK 126 W G+VK Sbjct: 121 WDGKVK 126 A related GBS gene <SEQ ID 8483> and protein <SEQ ID 8484> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00219 Lipop: Possible site: -1 Crend: 1 McG: Discrim Score: 17.55 GvH: Signal Score (-7.5): 3.36 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 8.86 threshold: 0.0 PERIPHERAL Likelihood = 8.86 99 modified ALOM score: -2.27 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00011## SEQ ID 8484 (GBS13) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 3 (lane 4; MW 16 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 9 (lane 2; MW 40.5 kDa). The GST-fusion protein was purified as shown in FIG. 190, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 64 A DNA sequence (GBSx0063) was identified in S. agalactiae <SEQ ID 203> which encodes the amino acid sequence <SEQ ID 204>. This protein is predicted to be regulatory protein TypA (typA). Analysis of this protein sequence reveals the following: TABLE-US-00220 Possible Site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1738 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00221 >GP:CAB13350 GB:Z99111 similar to GTP-binding elongation factor [Bacillus subtilis] Identities = 455/609 (74%), Positives = 534/609 (86%), Gaps = 2/609 (0%) Query: 4 LRTDIRNVAIIAHVDHGKTTLVDELLKQSHTLDERKELEERAMDSNDIEKERGITILAKN 63- LR D+RN+AIIAHVDHGKTTLVD+LL Q+ T +++ ERAMDSND+E+ERGITILAKN Sbjct: 3 LRNDLRNIAIIAHVDHGKTTLVDQLLHQAGTFRANEQVAERAMDSNDLERERGITILAKN 62- Query: 64 TAVAYNDVRINIMDTPGHADFGGEVERIMKMVDGVVLVVDAYEGTMPQTRFVLKKALEQN 12- 3 TA+ Y D RINI+DTPGHADFGGEVERIMKMVDGVVLVVDAYEG MPQTRFVLKKALEQN Sbjct: 63 TAINYKDTRINILDTPGHADFGGEVERIMKMVDGVVLVVDAYEGCMPQTRFVLKKALEQN 12- 2 Query: 124 LIPIVVVNKIDKPSARPSEVVDEVLELFIELGADDDQLDFPVVYASAINGTSSMSDDPSD 18- 3 L P+VVVNKID+ ARP EV+DEVL+LFIEL A+++QL+FPVVYASAINGT+S+ DP Sbjct: 123 LNPVVVVNKIDRDFARPEEVIDEVLDLFIELDANEEQLEFPVVYASAINGTASL--DPKQ 18- 0 Query: 184 QEKTMAPIFDTIIDHIPAPVDNSEEPLQFQVSLLDYNDFVGRIGIGRVFRGTVKVGDQVT 24- 3 Q++ M +++TII H+PAPVDN+EEPLQFQV+LLDYND+VGRIGIGRVFRGT+KVG QV+ Sbjct: 181 QDENMEALYETIIKHVPAPVDNAEEPLQFQVALLDYNDYVGRIGIGRVFRGTMKVGQQVS 24- 0 Query: 244 LSKLDGTTKNFRVTKLFGFFGLERKEIQEAKAGDLIAVSGMEDIFVGETVTPTDAIEPLP 30- 3 L KLDGT K+FRVTK+FGF GL+R EI+EAKAGDL+AVSGMEDI VGETV P D +PLP Sbjct: 241 LMKLDGTAKSFRVTKIFGFQGLKRVEIEEAKAGDLVAVSGMEDINVGETVCPVDHQDPLP 30- 0 Query: 304 VLRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAELQTDVSLRVDPTDSPDKWTV 36- 3 VLRIDEPTLQMTF+VNNSPFAGREGK++T+RK+EERL ++LQTDVSLRV+PT SPD W V Sbjct: 301 VLRIDEPTLQMTFVVNNSPFAGREGKYVTARKIEERLQSQLQTDVSLRVEPTASPDAWVV 36- 0 Query: 364 SGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGVQCEPFERVQIDTPEEYQGAIIQS 42- 3 SGRGELHLSILIE MRREGYELQVS+PEVIIKEIDGV+CEP ERVQID PEE+ G++++S Sbjct: 361 SGRGELHLSILIENMRREGYELQVSKPEVIIKEIDGVRCEPVERVQIDVPEEHTGSVMES 42- 0 Query: 424 LSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSMTRGYGIMNHTFDQYLPVVQG 48- 3 + RKG+M+DM GNGQ RLIF +P+RGLIGYSTEFLS+TRG+GI+NHTFD Y P+ G Sbjct: 421 MGARKGEMVDMINNGNGQVRLIFTVPSRGLIGYSTEFLSLTRGFGILNHTFDSYQPMQAG 48- 0 Query: 484 EIGGRHRGALVSIENGKATTYSIMRIEERGTIFVNPGIEVYEGMIVGENSRDNDLGVNIT 54- 3 ++GGR +G LVS+ENGKAT+Y I IE+RG IFV PG EVYEGMIVGE++RDNDL VN++ Sbjct: 481 QVGGRRQGVLVSMENGKATSYGIQGIEDRGVIFVEPGTEVYEGMIVGEHNRDNDLVVNVS 54- 0 Query: 544 TAKQMTNVRSATKDQTAVIKTPRILTLEESLEFLADDEYMEVTPESIRLRKQILNKAARD 60- 3 KQ TNVRSATKDQT IK RI++LEESLE+L +DEY EVTPESIRLRK+ILNK R+ Sbjct: 541 KMKQQTNVRSATKDQTTTIKKARIMSLEESLEYLNEDEYCEVTPESIRLRKKILNKNERE 60- 0 Query: 604 KANKKKKSA 612 KA KKKK+A Sbjct: 601 KAAKKKKTA 609 A related DNA sequence was identified in S. pyogenes <SEQ ID 205> which encodes the amino acid sequence <SEQ ID 206>. Analysis of this protein sequence reveals the following: TABLE-US-00222 Possible site: 36 >>> Seems to have no N-termina1 signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1738 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00223 Identities = 594/613 (96%), Positives = 607/613 (98%) Query: 1 MTNLRTDIRNVAIIAHVDHGKTTLVDELLKQSHTLDERKELEERAMDSNDIEKERGITIL 60 MTNLR DIRNVAIIAHVDHGKTTLVDELLKQSHTLDERKEL+ERAMDSND+EKERGITIL Sbjct: 1 MTNLRNDIRNVAIIAHVDHGKTTLVDELLKQSHTLDERKELQERAMDSNDLEKERGITIL 60 Query: 61 AKNTAVAYNDVRINIMDTPGHADFGGEVERIMKMVDGVVLVVDAYEGTMPQTRFVLKKAL 120- AKNTAVAYNDVRINIMDTPGHADFGGEVERIMKMVDGVVLVVDAYEGTMPQTRFVLKKAL Sbjct: 61 AKNTAVAYNDVRINIMDTPGHADFGGEVERIMKMVDGVVLVVDAYEGTMPQTRFVLKKAL 120- Query: 121 EQNLIPIVVVNKIDKPSARPSEVVDEVLELFIELGADDDQLDFPVVYASAINGTSSMSDD 18- 0 EQNLIPIVVVNKIDKPSARP+EVVDEVLELFIELGADD+QL+FPVVYASAINGTSS+SDD Sbjct: 121 EQNLIPIVVVNKIDKPSARPAEVVDEVLELFIELGADDEQLEFPVVYASAINGTSSLSDD 18- 0 Query: 181 PSDQEKTMAPIFDTIIDHIPAPVDNSEEPLQFQVSLLDYNDFVGRIGIGRVFRGTVKVGD 24- 0 P+DQE TMAPIFDTIIDHIPAPVDNS+EPLQFQVSLLDYNDFVGRIGIGRVFRGTVKVGD Sbjct: 181 PADQEHTMAPIFDTIIDHIPAPVDNSDEPLQFQVSLLDYNDFVGRIGIGRVFRGTVKVGD 24- 0 Query: 241 QVTLSKLDGTTKNFRVTKLFGFFGLERKEIQEAKAGDLIAVSGMEDIFVGETVTPTDAIE 30- 0 QVTLSKLDGTTKNFRVTKLFGFFGLER+EIQEAKAGDLIAVSGMEDIFVGET+TPTD +E Sbjct: 241 QVTLSKLDGTTKNFRVTKLFGFFGLERREIQEAKAGDLIAVSGMEDIFVGETITPTDCVE 30- 0 Query: 301 PLPVLRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAELQTDVSLRVDPTDSPDK 36- 0 LP+LRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAELQTDVSLRVDPTDSPDK Sbjct: 301 ALPILRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAELQTDVSLRVDPTDSPDK 36- 0 Query: 361 WTVSGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGVQCEPFERVQIDTPEEYQGAI 42- 0 WTVSGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGV+CEPFERVQIDTPEEYQGAI Sbjct: 361 WTVSGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGVKCEPFERVQIDTPEEYQGAI 42- 0 Query: 421 IQSLSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSMTRGYGIMNHTFDQYLPV 48- 0 IQSLSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSMTRGYGIMNHTFDQYLPV Sbjct: 421 IQSLSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSMTRGYGIMNHTFDQYLPV 48- 0 Query: 481 VQGEIGGRHRGALVSIENGKATTYSIMRIEERGTIFVNPGIEVYEGMIVGENSRDNDLGV 54- 0 VQGEIGGRHRGALVSIENGKATTYSIMRIEERGTIFVNPG EVYEGMIVGENSRDNDLGV Sbjct: 481 VQGEIGGRHRGALVSIENGKATTYSIMRIEERGTIFVNPGTEVYEGMIVGENSRDNDLGV 54- 0 Query: 541 NITTAKQMTNVRSATKDQTAVIKTPRILTLEESLEFLADDEYMEVTPESIRLRKQILNKA 60- 0 NITTAKQMTNVRSATKDQTAVIKTPRILTLEESLEFL DDEYMEVTPESIRLRKQILNKA Sbjct: 541 NITTAKQMTNVRSATKDQTAVIKTPRILTLEESLEFLNDDEYMEVTPESIRLRKQILNKA 60- 0 Query: 601 ARDKANKKKKSAE 613 ARDKANKKKKSAE Sbjct: 601 ARDKANKKKKSAE 613 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 65 A DNA sequence (GBSx0065) was identified in S. agalactiae <SEQ ID 207> which encodes the amino acid sequence <SEQ ID 208>. This protein is predicted to be D-glutamic acid adding enzyme MurD (murD). Analysis of this protein sequence reveals the following: TABLE-US-00224 RGD motif 441-443 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9615> which encodes amino acid sequence <SEQ ID 9616> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00225 >GP: AAC95449 GB: AF068902 D-glutamic acid enzyme MurD [Streptococcus pneumoniae] Identities = 341/449 (75%), Positives = 394/449 (86%) Query: 5 MKTITTFENKKVLVLGLARSGEAAARLLAKLGAIVTVNDGKPFDENPTAQSLLEEGIKVV 64 MK I F+NKKVLVLGLA+SGE+AARLL KLGAIVTVNDGKPF++NP AQ LLEEGIKV+ Sbjct: 1 MKVIDQFKNKKVLVLGLAKSGESAARLLDKLGAIVTVNDGKPFEDNPAAQCLLEEGIKVI 60 Query: 65 CGSHPLELLDEDFCYMIKNPGIPYNNPMVKKALEKQIPVLTEVELAYLVSESQLIGITGS 124- G HPLELLDE+F M+KNPGIPY+NPM++KAL K IPVLTEVELAYL+SE+ +IGITGS Sbjct: 61 TGGHPLELLDEEFALMVKNPGIPYSNPMIEKALAKGIPVLTEVELAYLISEAPIIGITGS 120- Query: 125 NGKTTTTTMIAEVLNAGGQRGLLAGNIGFPASEVVQAANDKDTLVMELSSFQLMGVKEFR 18- 4 NGKTTTTTMI EVL A GQ GLL+GNIG+PAS+V Q A DK+TLVMELSSFQLMGV+EF Sbjct: 121 NGKTTTTTMIGEVLTAAGQHGLLSGNIGYPASQVAQIATDKNTLVMELSSFQLMGVQEFH 18- 0 Query: 185 PHIAVITNLMPTHLDYHGSFEDYVAAKWNIQNQMSSSDFLVLNFNQGISKELAKTTKATI 24- 4 P IAVITNLMPTH+DYHG FE+YVAAKWNIQN+M+++DFLVLNFNQ + K+LA T+AT+ Sbjct: 181 PEIAVITNLMPTHIDYHGLFEEYVAAKWNIQNKMTAADFLVLNFNQDLVKDLASKTEATV 24- 0 Query: 245 VPFSTTEKVDGAYVQDKQLFYKGENIMSVDDIGVPGSHNVENALATIAVAKLAGISNQVI 30- 4 VPFST EKVDGAY++D QL+++GE +M+ ++IGVPGSHNVENALATIAVAKL G+ NQ I Sbjct: 241 VPFSTLEKVDGAYLEDGQLYFRGEVVMAANEIGVPGSHNVENALATIAVAKLRGVDNQTI 30- 0 Query: 305 RETLSNFGGVKHRLQSLGKVHGISFYNDSKSTNILATQKALSGFDNTKVILIAGGLDRGN 36- 4 +ETLS FGGVKHRLQ + + G+ FYNDSKSTNILATQKALSGFDN+KV+LIAGGLDRGN Sbjct: 301 KETLSAFGGVKHRLQFVDDIKGVKFYNDSKSTNILATQKALSGFDNSKVVLIAGGLDRGN 36- 0 Query: 365 EFDELIPDITGLKHMVVLGESASRVKRAAQKAGVTYSDALDVRDAVHKAYEVAQQGDVIL 42- 4 EFDEL+PDITGLK MV+LG+SA RVKRAA KAGV Y +A D+ DA KAYE+A QGDV+L Sbjct: 361 EFDELVPDITGLKKMVILGQSAERVKRAADKAGVAYVEATDIADATRKAYELATQGDVVL 42- 0 Query: 425 LSPANASWDMYKNFEVRGDEFIDTFESLR 453 LSPANASWDMY NFEVRGD FIDT L+ Sbjct: 421 LSPANASWDMYANFEVRGDLFIDTVAELK 449 A related DNA sequence was identified in S. pyogenes <SEQ ID 209> which encodes the amino acid sequence <SEQ ID 210>. Analysis of this protein sequence reveals the following: TABLE-US-00226 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> RGD motif: 436-438 An alignment of the GAS and GBS proteins is shown below:

TABLE-US-00227 Identities = 329/451 (72%), Positives = 397/451 (87%) Query: 5 MKTITTFENKKVLVLGLARSGEAAARLLAKLGAIVTVNDGKPFDENPTAQSLLEEGIKVV 64 MK I+ F+NKK+L+LGLA+SGEAAA+LL KLGA+VTVND KPFD+NP AQ+LLEEGIKV+ Sbjct: 1 MKVISNFQNKKILILGLAKSGEAAAKLLTKLGALVTVNDSKPFDQNPAAQALLEEGIKVI 60 Query: 65 CGSHPLELLDEDFCYMIKNPGIPYNNPMVKKALEKQIPVLTEVELAYLVSESQLIGITGS 124- CGSHP+ELLDE+F YM+KNPGIPY+NPMVK+AL K+IP+LTEVELAY VSE+ +IGITGS Sbjct: 61 CGSHPVELLDENFEYMVKNPGIPYDNPMVKRALAKEIPILTEVELAYFVSEAPIIGITGS 120- Query: 125 NGKTTTTTMIAEVLNAGGQRGLLAGNIGFPASEVVQAANDKDTLVMELSSFQLMGVKEFR 18- 4 NGKTTTTTMIA+VLNAGGQ LL+GNIG+PAS+VVQ A DTLVMELSSFQL+GV FR Sbjct: 121 NGKTTTTTMIADVLNAGGQSALLSGNIGYPASKVVQKAIAGDTLVMELSSFQLVGVNAFR 18- 0 Query: 185 PHIAVITNLMPTHLDYHGSFEDYVAAKWNIQNQMSSSDFLVLNFNQGISKELAKTTKATI 24- 4 PHIAVITNLMPTHLDYHGSFEDYVAAKW IQ QM+ SD+L+LN NQ IS LAKTTKAT+ Sbjct: 181 PHIAVITNLMPTHLDYHGSFEDYVAAKWMIQAQMTESDYLILNANQEISATLAKTTKATV 24- 0 Query: 245 VPFSTTEKVDGAYVQDKQLFYKGENIMSVDDIGVPGSHNVENALATIAVAKLAGISNQVI 30- 4 +PFST + VDGAY++D L++K + I++ D+GVPGSHN+ENALATIAVAKL+GI++ +I Sbjct: 241 IPFSTQKVVDGAYLKDGILYFKEQAIIAATDLGVPGSHNIENALATIAVAKLSGIADDII 30- 0 Query: 305 RETLSNFGGVKHRLQSLGKVHGISFYNDSKSTNILATQKALSGFDNTKVILIAGGLDRGN 36- 4 + LS+FGGVKHRLQ +G++ I+FYNDSKSTNILATQKALSGFDN+++ILIAGGLDRGN Sbjct: 301 AQCLSHFGGVKHRLQRVGQIKDITFYNDSKSTNILATQKALSGFDNSRLILIAGGLDRGN 36- 0 Query: 365 EFDELIPDITGLKHMVVLGESASRVKRAAQKAGVTYSDALDVRDAVHKAYEVAQQGDVIL 42- 4 EFD+L+PD+ GLK M++LGESA R+KRAA KA V+Y +A +V +A A+++AQ GD IL Sbjct: 361 EFDDLVPDLLGLKQMIILGESAERMKRAANKAEVSYLEARNVAEATELAFKLAQTGDTIL 42- 0 Query: 425 LSPANASWDMYKNFEVRGDEFIDTFESLRGE 455 LSPANASWDMY NFEVRGDEF+ TF+ LRG+ Sbjct: 421 LSPANASWDMYPNFEVRGDEFLATFDCLRGD 451 SEQ ID 208 (GBS305) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 11; MW 53.7 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 56 (lane 3; MW 79 kDa). The GBS305-GST fusion product was purified (FIG. 207, lane 8) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 270), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 66 A DNA sequence (GBSx0066) was identified in S. agalactiae <SEQ ID 211> which encodes the amino acid sequence <SEQ ID 212>. Analysis of this protein sequence reveals the following: TABLE-US-00228 RGD motif 285-287 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.65 Transmembrane 74-90 (73-93) ----- Final Results ----- bacterial membrane --- Certainty = 0.1659(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 213> which encodes the amino acid sequence <SEQ ID 214>. Analysis of this protein sequence reveals the following: TABLE-US-00229 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.33 Transmembrane 81-97 (80-100) INTEGRAL Likelihood = -0.16 Transmembrane 272-288 (271-288) ----- Final Results ----- bacterial membrane --- Certainty = 0.1532(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9141> which encodes the amino acid sequence <SEQ ID 9142>. Analysis of this protein sequence reveals the following: TABLE-US-00230 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.33 Transmembrane 74-90 INTEGRAL Likelihood = -0.16 Transmembrane 265-281 ----- Final Results ----- bacterial membrane --- Certainty = 0.1532(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> RGD motif: 286-288 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00231 Identities = 249/358 (69%), Positives = 293/358 (81%), Gaps = 1/358 (0%) Query: 1 MGKKIVFTGGGTVGHVTLNLILIPKFIKDGWEVHYIGDKNGIEHEQINQSGLDITFHSIA 60 M KKI+FTGGGTVGHVTLNLILIPKFIKDGWEVHYIGDKNGIEH +I +SGLD+TFH+IA Sbjct: 8 MPKKILFTGGGTVGHVTLNLILIPKFIKDGWEVHYIGDKNGIEHTEIEKSGLDVTFHAIA 67 Query: 61 TGKLRRYFSWQNMLDVFKVGVGVLQSIAIIAKLRPQALFSKGGFVSVPPVVAARLLKVPV 120- TGKLRRYFSWQN+ DVFKV +G+LQS+ I+AKLRPQALFSKGGFVSVPPVVAA+LL PV Sbjct: 68 TGKLRRYFSWQNLADVFKVALGLLQSLFIVAKLRPQALFSKGGFVSVPPVVAAKLLGKPV 127- Query: 121 FVHESDLSMGLANKIAYKFATIMYTTFEQSKDLIKTKHIGAVTKVM-DCKKSFENTDLTS 17- 9 F+HESD SMGLANKIAYKFAT MYTTFEQ L K KH+GAVTKV D + E+T L + Sbjct: 128 FIHESDRSMGLANKIAYKFATTMYTTFEQEDQLSKVKHLGAVTKVFKDANQMPESTQLEA 18- 7 Query: 180 IKEAFDPNLKTLLFIGGSAGAKVFNDFITQTPELEEKYNVINISGDSSLNRLKKNLYRVD 23- 9 +KE F +LKTLLFIGGSAGA VFN FI+ PEL+++YN+INI+GD LN L +LYRVD Sbjct: 188 VKEYFSRDLKTLLFIGGSAGAHVFNQFISDHPELKQRYNIINITGDPHLNELSSHLYRVD 24- 7 Query: 240 YVTDLYQPLMNLADVVVTRGGSNTIFELVAMKKLHLIIPLGREASRGDQLENAAYFEEKG 29- 9 YVTDLYQPLM +AD+VVTRGGSNT+FEL+AM KLHLI+PLG+EASRGDQLENA YFE++G Sbjct: 248 YVTDLYQPLMAMADLVVTRGGSNTLFELLAMAKLHLIVPLGKEASRGDQLENATYFEKRG 30- 7 Query: 300 YALQLPESELNINTLEKQINLLISNSESYEKNMSQSSEIKSQDEFYQLLIDDMAKVTK 357 YA QL E +L ++ ++ + L + YE M + EI+S D FY LL D++ K Sbjct: 308 YAKQLQEPDLTLHNFDQAMADLFEHQADYEATMLATKEIQSPDFFYDLLRADISSAIK 365 SEQ ID 212 (GBS306) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 12; MW 43 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 56 (lane 4; MW 68 kDa). GBS306-GST was purified as shown in FIG. 207, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 67 A DNA sequence (GBSx0067) was identified in S. agalactiae <SEQ ID 215> which encodes the amino acid sequence <SEQ ID 216>. This protein is predicted to be cell division protein DivIB. Analysis of this protein sequence reveals the following: TABLE-US-00232 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.33 Transmembrane 103-119 (96-124) ----- Final Results ----- bacterial membrane --- Certainty = 0.6731(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00233 >GP:AAC95451 GB:AF068902 cell division protein DivIB [Streptococcus pneumoniae] Identities = 119/396 (30%), Positives = 214/396 (53%), Gaps = 38/396 (9%) Query: 3 KKKSDTPEKEEVV-LTEWQKRNLEFLKKRKEDEE---EQKRINEKLRLDKRS-----KLN 53 KK D EE+ L+EWQKRN E+LKK+ E+E E+K + R+ + S K + Sbjct: 5 KKNEDKEILEELKELSEWQKRNQEYLKKKAEEEAALAEEKEKERQARMGEESEKSEDKQD 64 Query: 54 ISSPEEPQNTTKIKKLHFPKIS------------RPKIEKKQKKEKIVNSLAKTNR---- 97 S + +++ K+ K++ P+ ++K++++K ++ A + Sbjct: 65 QESETDQEDSESAKEESEEKVASSEADKEKEEKEEPESKEKEEQDKKLSKKATKEKPAKA 124- Query: 98 -------IRTAPIFVVAFLVILVSVFLLTPFSKQKTITVSGNQHTPDDILIEKTNIQKND 150- +R I + L+++VS +LL+P++ K I V G T D + + + IQ +D Sbjct: 125 KIPGIHILRAFTILFPSLLLLIVSAYLLSPYATMKDIRVEGTVQTTADDIRQASGIQDSD 18- 4 Query: 151 YFFSLIFKHKAIEQRLAAEDVWVKTAQMTYQFPNKFHIQVQENKIIAYAHTKQGYQPVLE 21- 0 Y +L+ E+++ + + WV++AQ+ YQFP KF I+V+E I+AY + + + P+L Sbjct: 185 YTINLLLDKAKYEKQIKS-NYWVESAQLVYQFPTKFTIKVKEYDIVAYYISGENHYPILS 24- 3 Query: 211 TGK-KADPVNSSELPKHFLTINLDKEDSIKLLIKDLKALDPDLISEIQVISLADSKTTPD 26- 9 +G+ + V+ + LP+ +L++ + + IK+ + +L + P+L + IQ + LA SK T D Sbjct: 244 SGQLETSSVSLNSLPETYLSVLFNDSEQIKVFVSELAQISPELKAAIQKVELAPSKVTSD 30- 3 Query: 270 LLLLDMHDGNSIRIPLSKFKERLPFYKQIKKNLKEPSIVDMEVGVYTTTNTIESTPVKAE 32- 9 L+ L M+D + + +PLS+ ++LP+Y +IK L EPS+VDME G+Y+ T + E Sbjct: 304 LIRLTMNDSDEVLVPLSEMSKKLPYYSKIKPQLSEPSVVDMEAGIYSYTVADKLIMEVEE 36- 3 Query: 330 DTKNKSTDKTQTQNGQVAENSQGQTNNSNTNQQGQQ 365 K ++ + + Q E + Q SN NQ Q+ Sbjct: 364 KAKQEAKEAEKKQE----EEQKKQEEESNRNQTTQR 395 A related DNA sequence was identified in S. pyogenes <SEQ ID 217> which encodes the amino acid sequence <SEQ ID 218>. Analysis of this protein sequence reveals the following: TABLE-US-00234 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.45 Transmembrane 106-122 (102-125) ----- Final Results ----- bacterial membrane --- Certainty = 0.4779(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00235 Identities = 152/381 (39%), Positives = 232/381 (59%), Gaps = 14/381 (3%) Query: 4 KKSDTPEKEEVVLTEWQKRNLEFLKKRKEDEEEQKRINEKLRLDKRSKLNISSPEEP--- 60 K + +++VLTEWQKRN+EFLKK+K+ EE+K++ EKL DK+++ + E Sbjct: 3 KDKEKQSDDKLVLTEWQKRNIEFLKKKKQQAEEEKKLKEKLLSDKKAQQQAQNASEAVEL 62 Query: 61 --QNTTKIKKLHFPKISRPKIEKK--QKKEKIVNSLAKTNRIRTAPIFVVAFLVILVSVF 116- T +++ S+PK KK Q KEK +A ++ P+ + A L++ VS+F Sbjct: 63 KTDEKTDSQEIESETTSKPKKTKKVRQPKEKSATQIAFQ---KSLPVLLGALLLMAVSIF 119- Query: 117 LLTPFSKQKTITVSGNQHTPDDILIEKTNIQKNDYFFSLIFKHKAIEQRLAAEDVWVKTA 17- 6 ++TP+SK+K +V GN T D LI+ + ++ +DY+ +L+ E+ + WVK+ Sbjct: 120 MITPYSKKKEFSVRGNHQTNLDELIKASKVKASDYWLTLLTSPGQYERPILRTIPWVKSV 17- 9 Query: 177 QMTYQFPNKFHIQVQENKIIAYAHTKQGYQPVLETGKKADPVNSSELPKHFLTINLDKED 23- 6 ++YQFPN F V E +IIAYA + G+QP+LE GK+ D V +SELPK FL +NL E Sbjct: 180 HLSYQFPNHFLFNVIEFEIIAYAQVENGFQPILENGKRVDKVRASELPKSFLILNLKDEK 23- 9 Query: 237 SIKLLIKDLKALDPDLISEIQVISLADSKTTPDLLLLDMHDGNSIRIPLSRFKERLPFYK 29- 6 +I+ L+K L L L+ I+ +SLA+SKTT DLLL++MHDGN +R+P S+ +LP+Y+ Sbjct: 240 AIQQLVKQLTTLPKKLVKNIKSVSLANSKTTADLLLIEMHDGNVVRVPQSQLTLKLPYYQ 29- 9 Query: 297 QIKKNLKEPSIVDMEVGVYTTTNTIESTPVKAEDTKNKSTDKTQTQNGQVAENSQGQTNN 35- 6 ++KKNL+ SIVDMEVG+YTTT IE+ P + + DK + G+ Q QT+N Sbjct: 300 KLKKNLENDSIVDMEVGIYTTTQEIENQPEVPLTPEQNAADKEGDKPGE----HQEQTDN 35- 5 Query: 357 SNTNQQGQQIATEQAPNPQNV 377 + Q + P+P+ V Sbjct: 356 DSETPANQSSPQQTPPSPETV 376 SEQ ID 216 (GBS85) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 10; MW 45.2 kDa). The GBS85-His fusion product was purified (FIG. 105A; see also FIG. 193, lane 5) and used to immunise mice (lane 1 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 105B), FACS (FIG. 105C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 68 A DNA sequence (GBSx0068) was identified in S. agalactiae <SEQ ID 219> which encodes the amino acid sequence <SEQ ID 220>. This protein is predicted to be cell division protein FtsA (ftsA). Analysis of this protein sequence reveals the following: TABLE-US-00236 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.19 Transmembrane 322-338 (321-338) ----- Final Results ----- bacterial membrane --- Certainty = 0.2275(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00237 >GP:AAC95439 GB:AF068901 cell division protein FtsA [Streptococcus pneumoniae] Identities = 292/457 (63%), Positives = 366/457 (79%), Gaps = 1/457 (0%) Query: 1 MARNGFFTGLDIGTSSIKVLVAEFIANEMNVIGVSNVPSSGVKDGIIIDIEAAATAIKEA 60 MAR GFFTGLDIGTSS+KVLVAE E+NVIGVSN S GVKDGII+DI+AAATAIK A Sbjct: 1 MAREGFFTGLDIGTSSVKVLVAEQRNGELNVIGVSNAKSKGVKDGIIVDIDAAATAIKSA 60 Query: 61 VKQAEEKAGITIDKINVGLPANLLQIEPTQGMIPVPNESKEIKDEDVESVVKSALTKSIT 120- + QAEEKAGI+I +NVGLP NLLQ+EPTQGMIPV +++KEI D+DVE+VVKSALTKS+T Sbjct: 61 ISQAEEKAGISIKSVNVGLPGNLLQVEPTQGMIPVTSDTKEITDQDVENVVKSALTKSMT 120- Query: 121 PEREVISLIPLEFIVDGFQGIRDPRGMMGIRLEMRGLIYTGPTTILHNLRKTVERAGIKV 18- 0 P+REVI+ IP EFIVDGFQGIRDPRGMMG+RLEMRGL+YTGP TILHNLRKTVERAG++V Sbjct: 121 PDREVITFIPLEFIVDGFQGIRDPRGMMGVRLEMRGLLYTGPRTILHNLRKTVERAGVQV 18- 0 Query: 181 EHVVIAPLALAKSVLNEGEREFGATVIDMGGGQTTVASMRNQELQYTNIYSEGSDYVTKD 24- 0 E+V+I+PLA+ +SVLNEGEREFGATVIDMG GQTTVA++RNQELQ+T+I EG DYVTKD Sbjct: 181 ENVIISPLAMVQSVLNEGEREFGATVIDMGAGQTTVATIRNQELQFTHILQEGGDYVTKD 24- 0 Query: 241 ISKVLRTTVEIAEALKFNFGQANVEEASTSDTVQVNVVGNEEPVEITESYLSQIISGRIR 30- 0 ISKVL+T+ ++AE LK N+G+A AS +T QV V+G E VE+TE+YLS+IIS RI+ Sbjct: 241 ISKVLKTSRKLAEGLKLNYGEAYPPLAS-KETFQVEVIGEVEAVEVTEAYLSEIISARIK 29- 9 Query: 301 QILEHVKQDLGRGRLLDLPGGIILVGGGAIMPGVVEVAQQIFGTRVKLHVPNQVGIRNPM 36- 0 ILE +KQ+L R RLLDLPGGI+L+GG AI+PG+VE+AQ++FG RVKL+VPNQVGIRNP Sbjct: 300 HILEQIKQELDRRRLLDLPGGIVLIGGNAILPGMVELAQEVFGVRVKLYVPNQVGIRNPA 35- 9 Query: 361 FANVISIVDYVGMMSEVDIIAQHAVTGDEMLRHKPVDFDYKEKTNTMSTMPYSEPLTSSM 42- 0 FA+VIS+ ++ G ++EV+++AQ A+ G+ L H+P+ F + + Sbjct: 360 FAHVISLSEFAGQLTEVNLLAQGAIKGENDLSHQPISFGGMLQKTAQFVQSTPVQPAPAP 41- 9 Query: 421 EDSNLEPIRARENAQEPTEPKANIGERIRGIFGSMFD 457 E +P + Q+ ++ K + +R RG+ GSMFD Sbjct: 420 EVEPVAPTEPMADFQQASQNKPKLADRFRGLIGSMFD 456 A related DNA sequence was identified in S. pyogenes <SEQ ID 221> which encodes the amino acid sequence <SEQ ID 222>. Analysis of this protein sequence reveals the following: TABLE-US-00238 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.35 Transmembrane 313-329 (312-329) ----- Final Results ----- bacterial membrane --- Certainty = 0.2338(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00239 >GP:AAC95439 GB:AF068901 cell division protein FtsA [Streptococcus pneumoniae] Identities = 299/448 (66%), Positives = 368/448 (81%), Gaps = 4/448 (0%) Query: 1 LDIGTSSIKVLVAEFISGEMNVIGVSNVPSTGVKDGIIIDIEAAATAIKTAVEQAEEKAG 60 LDIGTSS+KVLVAE +GE+NVIGVSN S GVKDGII+DI+AAATAIK+A+ QAEEKAG Sbjct: 10 LDIGTSSVKVLVAEQRNGELNVIGVSNAKSKGVKDGIIVDIDAAATAIKSAISQAEEKAG 69 Query: 61 MTIEKVNVGLPANLLQIEPTQGMIPVPSESKEIKDEDVDSVVKSALTKSITPERSVISLV 120- ++I+ VNVGLP NLLQ+EPTQGMIPV S++KEI D+DV++VVKSALTKS+TP+REVI+ + Sbjct: 70 ISIKSVNVGLPGNLLQVEPTQGMIPVTSDTKEITDQDVENVVKSALTKSMTPDREVITFI 129- Query: 121 PEEFIVDGFQGIRDPRGMMGIRLEMRGLIYTGPSTILHNLRKTVERAGIKVENIIISPLA 18- 0 PEEFIVDGFQGIRDPRGMMG+RLEMRGL+YTGP TILHNLRKTVERAG++VEN+IISPLA Sbjct: 130 PEEFIVDGFQGIRDPRGMMGVRLEMRGLLYTGPRTILHNLRKTVERAGVQVENVIISPLA 18- 9 Query: 181 MAKTILNEGEREFGATVIDMGGGQTTVASMRAQELQYTNIYAEGGEYITKDISKVLKTSL 24- 0 M +++LNEGEREFGATVIDMG GQTTVA++R QELQ+T+I EGG+Y+TKDISKVLKTS Sbjct: 190 MVQSVLNEGEREFGATVIDMGAGQTTVATIRNQELQFTHILQEGGDYVTKDISKVLKTSR 24- 9 Query: 241 AIAEALKFNFGQAEISEASITETVKVDVVGSEEPVEVTERYLSEIISARIRHILDRVKQD 30- 0 +AE LK N+G+A AS ET +V+V+G E VEVTE YLSEIISARI+HIL+++KQ+ Sbjct: 250 KLAEGLKLNYGEAYPPLAS-KETFQVEVIGEVEAVEVTEAYLSEIISARIKHILEQIKQE 30- 8 Query: 301 LERGRLLDLPGGIVLIGGGAIMPGVVEIAQEIFGVTVKLHVPNQVGIRNPMFSNVISLVE 36- 0 L+R RLLDLPGGIVLIGG AI+PG+VE+AQE+FGV VKL+VPNQVGIRNP F++VISL E Sbjct: 309 LDRRRLLDLPGGIVLIGGNAILPGMVELAQEVFGVRVKLYVPNQVGIRNPAFAHVISLSE 36- 8 Query: 361 YVGMMSEVDVLAQTAVSGEELLRRKPIDFSGQESYLPDYDDSRRPESTIGYEQQ---ASQ 41- 7 + G ++EV++LAQ A+ GE L +PI F G + S + E + ++ Sbjct: 369 FAGQLTEVNLLAQGAIKGENDLSHQPISFGGMLQKTAQFVQSTPVQPAPAPEVEPVAPTE 42- 8 Query: 418 TAYDSQVPSDPKQKISERVRGIFGSMFD 445 D Q S K K+++R RG+ GSMFD Sbjct: 429 PMADFQQASQNKPKLADRFRGLIGSMFD 456 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00240 Identities = 349/456 (76%), Positives = 402/456 (87%), Gaps = 19/456 (4%) Query: 10 LDIGTSSIKVLVAEFIANEMNVIGVSNVPSSGVKDGIIIDIEAAATAIKEAVKQAEEKAG 69 - LDIGTSSIKVLVAEFI+ EMNVIGVSNVPS+GVKDGIIIDIEAAATAIK AV+QAEEKAG Sbjct: 1 LDIGTSSIKVLVAEFISGEMNVIGVSNVPSTGVKDGIIIDIEAAATAIKTAVEQAEEKAG 60 Query: 70 ITIDKINVGLPANLLQIEPTQGMIPVPNESKEIKDEDVESVVKSALTKSITPEREVISLI 129- +TI+K+NVGLPANLLQIEPTQGMIPVP+ESKEIKDEDV+SVVKSALTKSITPEREVISL+ Sbjct: 61 MTIEKVNVGLPANLLQIEPTQGMIPVPSESKEIKDEDVDSVVKSALTKSITPEREVISLV 120- Query: 130 PLEFIVDGFQGIRDPRGMMGIRLEMRGLIYTGPTTILHNLRKTVERAGIKVEHVVIAPLA 18- 9 P EFIVDGFQGIRDPRGMMGIRLEMRGLIYTGP+TILHNLRKTVERAGIKVE+++I+PLA Sbjct: 121 PEEFIVDGFQGIRDPRGMMGIRLEMRGLIYTGPSTILHNLRKTVERAGIKVENIIISPLA 18- 0 Query: 190 LAKSVLNEGEREFGATVIDMGGGQTTVASMRNQELQYTNIYSEGSDYVTKDISKVLRTTV 24- 9 +AK++LNEGEREFGATVIDMGGGQTTVASMR QELQYTNIY+EG +Y+TKDISKVL+T++ Sbjct: 181 MAKTILNEGEREFGATVIDMGGGQTTVASMRAQELQYTNIYAEGGEYITKDISKVLKTSL 24- 0 Query: 250 EIAEALKFNFGQANVEEASTSDTVQVNVVGNEEPVEITESYLSQIISGRIRQILEHVKQD 30- 9 IAEALKFNFGQA + EAS ++TV+V+VVG+EEPVE+TE YLS+IIS RIR IL+ VKQD Sbjct: 241 AIAEALKFNFGQAEISEASITETVKVDVVGSEEPVEVTERYLSEIISARIRHILDRVKQD 30- 0 Query: 310 LGRGRLLDLPGGIILVGGGAIMPGVVEVAQQIFGTRVKLHVPNQVGIRNPMFANVISIVD 36- 9 L RGRLLDLPGGI+L+GGGAIMPGVVE+AQ+IFG VKLHVPNQVGIRNPMF+NVIS+V+ Sbjct: 301 LERGRLLDLPGGIVLIGGGAIMPGVVEIAQEIFGVTVKLHVPNQVGIRNPMFSNVISLVE 36- 0 Query: 370 YVGMMSEVDIIAQHAVTGDEMLRHKPVDF--------DYKEKTNTMSTMPYSEPLTSSME 42- 1 YVGMMSEVD++AQ AV+G+E+LR KP+DF DY + ST+ Y + + + Sbjct: 361 YVGMMSEVDVLAQTAVSGEELLRRKPIDFSGQESYLPDYDDSRRPESTIGYEQQASQTAY 42- 0 Query: 422 DSNLEPIRARENAQEPTEPKANIGERIRGIFGSMFD 457 DS Q P++PK I ER+RGIFGSMFD Sbjct: 421 DS-----------QVPSDPKQKISERVRGIFGSMFD 445 SEQ ID 220 (GBS73) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 5; MW 47.8 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 20 (lane 5; MW 70.1 kDa). GBS73-GST was purified as shown in FIG. 197, lane 7. The GBS73-His fusion product was purified (FIG. 103A) and used to immunise mice (lane 1 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 103B), FACS (FIG. 103C) and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 69 A DNA sequence (GBSx0069) was identified in S. agalactiae <SEQ ID 223> which encodes the amino acid sequence <SEQ ID 224>. This protein is predicted to be cell division protein FtsZ (ftsz). Analysis of this protein sequence reveals the following:

TABLE-US-00241 Possible site: 56 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -1.97 Transmembrane 117-133 (117-133) ----- Final Results ----- <\\\\\\\\\\\\\\\bacterial> membrane --- Certainty = 0.1786 (Affirmative) < succ> <\\\\\\\\\\\\\\\\bacterial> outside --- Certainty = 0.0000 (Not Clear) < succ> <\\\\\\\\\\\\\\bacterial> cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00242 >GP:AAC95440 GB:AF068901 cell division protein FtsZ [Streptococcus pneumoniae] Identities = 327/426 (76%), Positives = 363/426 (84%), Gaps = 7/426 (1%) Query: 1 MVFSFDTASVQGAVIKVIGVGGGGGNAINRMIDEGVAGVEFIAANTDIQALSSSKAETVI 60 M FSFDTA+ QGAVIKVIGVGGGGGNAINRM+DEGV GVEFIAANTD+QALSS+KAETVI Sbjct: 1 MTFSFDTAAAQGAVIKVIGVGGGGGNAINRMVDEGVTGVEFIAANTDVQALSSTKAETVI 60 Query: 61 QLGPKLTRGLGAGGQPEVGRKAAEESEEVLTEALTGADMVFITAGMGGGSGTGAAPVIAR 120- QLGPKLTRGLGAGGQPEVGRKAAEESEE LTEA++GADMVFITAGMGGGSGTGAAPVIAR Sbjct: 61 QLGPKLTRGLGAGGQPEVGRKAAEESEETLTEAISGADMVFITAGMGGGSGTGAAPVIAR 120- Query: 121 IAKSLGALTVAVITRPFGFEGNKRSNFAIEGIQELREQVDTLLIISNNNLLEIVDKKTPL 18- 0 IAK LGALTV V+TRPFGFEG+KR FA+EGI +LRE VDTLLIISNNNLLEIVDKKTPL Sbjct: 121 IAKDLGALTVGVVTRPFGFEGSKRGQFAVEGINQLREHVDTLLIISNNNLLEIVDKKTPL 18- 0 Query: 181 LEALSEADNVLRQGVQGITDLITNPGLINLDFADVKTVMANKGNALMGIGIGSGEERITE 24- 0 LEALSEADNVLRQGVQGITDLITNPGLINLDFADVKTVMANKGNALMGIGIGSGEER+ E Sbjct: 181 LEALSEADNVLRQGVQGITDLITNPGLINLDFADVKTVMANKGNALMGIGIGSGEERVVE 24- 0 Query: 241 AARKAIYSPLLETTIDGAEDVIVNVTGGMDMTLTEAEEASEIVSQAAGKGVNIWLGTSID 30- 0 AARKAIYSPLLETTIDGAEDVIVNVTGG+D+TL EAEEAS+IV+QAAG+GVNIWLGTSID Sbjct: 241 AARKAIYSPLLETTIDGAEDVIVNVTGGLDLTLIEAEEASQIVNQAAGQGVNIWLGTSID 30- 0 Query: 301 MDMKDEIRVTVVATGVRKDKTNQVSGFTTSAPTNQAPSERQSTSNSNFDRRGNFDMTESR 36- 0 M+DEIRVTVVATGVR+D+ +V + TN + + + S+ FDR +FDM E+ Sbjct: 301 ESMRDEIRVTVVATGVRQDRVEKVVAPQARSATNYRETVKPAHSH-GFDR--HFDMAETA 35- 7 Query: 361 ENPTQQNQPHAQNQQQSSAFGNWDLRRDNISRPTEGELDSKLSMSTFSENDDMDDELETP 42- 0 E+P Q P Q+SAFG+WDLRR++I R T+ + D +DEL+TP Sbjct: 358 ELPKQ--NPRRLEPTQASAFGDWDLRRESIVRTTDSVVSPVERFEAPISQD--EDELDTP 41- 3 Query: 421 PFFKNR 426 PFFKNR Sbjct: 414 PFFKNR 419 A related DNA sequence was identified in S. pyogenes <SEQ ID 225> which encodes the amino acid sequence <SEQ ID 226>. Analysis of this protein sequence reveals the following: TABLE-US-00243 Possible site: 56 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -1.81 Transmembrane 117-133 (117-133) ----- Final Results ----- <\\\\\\\\\\\\\\\bacterial> membrane --- Certainty = 0.1723 (Affirmative) < succ> <\\\\\\\\\\\\\\\\bacterial> outside --- Certainty = 0.0000 (Not Clear) < succ> <\\\\\\\\\\\\\\bacterial> cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00244 Identities = 372/439 (84%), Positives = 391/439 (88%), Gaps = 13/439 (2%) Query: 1 MVFSFDTASVQGAVIKVIGVGGGGGNAINRMIDEGVAGVEFIAANTDIQALSSSKAETVI 60 M FSFDTAS+QGA+IKVIGVGGGGGNAINRMIDEGVAGVEFIAANTDIQALSSSKAETVI Sbjct: 1 MAFSFDTASIQGAIIKVIGVGGGGGNAINRMIDEGVAGVEFIAANTDIQALSSSKAETVI 60 Query: 61 QLGPKLTRGLGAGGQPEVGRKAAEESEEVLTEALTGADMVFITAGMGGGSGTGAAPVIAR 120- QLGPKLTRGLGAGGQPEVGRKAAEESEE+LTEALTGADMVFITAGMGGGSGTGAAPVIAR Sbjct: 61 QLGPKLTRGLGAGGQPEVGRKAAEESEEILTEALTGADMVFITAGMGGGSGTGAAPVIAR 120- Query: 121 IAKSLGALTVAVITRPFGFEGNKRSNFAIEGIQELREQVDTLLIISNNNLLEIVDKKTPL 18- 0 IAKSLGALTVAV+TRPFGFEGNKR NFAIEGI+ELREQVDTLLIISNNNLLEIVDKKTPL Sbjct: 121 IAKSLGALTVAVVTRPFGFEGNKRGNFAIEGIEELREQVDTLLIISNNNLLEIVDKKTPL 18- 0 Query: 181 LEALSEADNVLRQGVQGITDLITNPGLINLDFADVKTVMANKGNALMGIGIGSGEERITE 24- 0 LEALSEADNVLRQGVQGITDLIT+PGLINLDFADVKTVMANKGNALMGIGIGSGEERI E Sbjct: 181 LEALSEADNVLRQGVQGITDLITSPGLINLDFADVKTVMANKGNALMGIGIGSGEERIVE 24- 0 Query: 241 AARKAIYSPLLETTIDGAEDVIVNVTGGMDMTLTEAEEASEIVSQAAGKGVNIWLGTSID 30- 0 AARKAIYSPLLETTIDGA+DVIVNVTGG+DMTLTEAEEASEIV QAAG+GVNIWLGTSID Sbjct: 241 AARKAIYSPLLETTIDGAQDVIVNVTGGLDMTLTEAEEASEIVGQAAGQGVNIWLGTSID 30- 0 Query: 301 MDMKDEIRVTVVATGVRKDKTNQVSGF---TTSAPTN--------QAPSERQSTSNSNFD 34- 9 MKD+IRVTVVATGVR++K QVSGF T TN A + + + FD Sbjct: 301 DTMKDDIRVTVVATGVRQEKAEQVSGFRQPRTFTQTNAQQVAGAQYASDQAKQSVQPGFD 36- 0 Query: 350 RRGN--FDMTESREMPTQQNQPHAQNQQQSSAFGNWDLRRDNISRPTEGELDSKLSMSTF 40- 7 RR N FDM ESRE+P+ Q NQ Q SAFGNWDLRRDNISRPTEGELD+ L+MSTF Sbjct: 361 RRSNFDFDMGESREIPSAQKVISNHNQNQGSAFGNWDLRRDNISRPTEGELDNHLNMSTF 42- 0 Query: 408 SENDDMDDELETPPFFKNR 426 S NDD DDELETPPFFKNR Sbjct: 421 SANDDSDDELETPPFFKNR 439 SEQ ID 224 (GBS163) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 28 (lane 7; MW 44 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 34 (lane 4; MW 69 kDa). The GBS163-GST fusion product was purified (FIG. 114A; see also FIG. 198, lane 11) and used to immunise mice (lane 1 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 114B), FACS and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 70 A DNA sequence (GBSx0070) was identified in S. agalactiae <SEQ ID 227> which encodes the amino acid sequence <SEQ ID 228>. Analysis of this protein sequence reveals the following: TABLE-US-00245 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- <\\\\\\\\\\\\\\bacterial> cytoplasm --- Certainty = 0.2750 (Affirmative) < succ> <\\\\\\\\\\\\\\\bacterial> membrane --- Certainty = 0.0000 (Not Clear) < succ> <\\\\\\\\\\\\\\\\bacterial> outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00246 >GP:AAC95441 GB:AF068901 YlmE [Streptococcus pneumoniae] Identities = 140/223 (62%), Positives = 177/223 (78%) Query: 2 MNLQENKTAIFDNVSKLALKAGRAHESVHIVAVTKYVNCQTTEALIRTGVNHIGENRVDK 61 MN++EN +F V++ +L A R SV ++AVTKYV+ T EAL+ GV+HIGENRVDK Sbjct: 1 MNVKENTELVFREVAEASLSAHRESGSVSVIAVTKYVDVPTAEALLPLGVHHIGENRVDK 60 Query: 62 FLEKYQALKDEKLTWHLIGSLQRRKVKDVINYVDYFHALDSVKLAAEIQKHAQKLIKCFL 121- FLEKY+ALKD +TWHLIG+LQRRKVKDVI YVDYFHALDSVKLA EIQK + ++IKCFL Sbjct: 61 FLEKYEALKDRDVTWHLIGTLQRRKVKDVIQYVDYFHALDSVKLAGEIQKRSDRVIKCFL 120- Query: 122 QVNISREDSKHGFTIEQIDDALNLISRYDKIELIGIMTMAPLKATKEEISSIFEETESLR 18- 1 QVNIS+E+SKHGF+ E++ + L ++R DKIE +G+MTMAP +A+ E++ IF+ + L+ Sbjct: 121 QVNISKEESKHGFSREELLEILPELARLDKIEYVGLMTMAPFEASSEQLKEIFKAAQDLQ 18- 0 Query: 182 KRLQARNIERMPFTELSMGMSRDYDIAIQNGSTFVRIGTSFFK 224 + +Q + I MP TELSMGMSRDY AIQ GSTFVRIGTSFFK Sbjct: 181 REIQEKQIPNMPMTELSMGMSRDYKEAIQFGSTFVRIGTSFFK 223 A related DNA sequence was identified in S. pyogenes <SEQ ID 229> which encodes the amino acid sequence <SEQ ID 230>. Analysis of this protein sequence reveals the following: TABLE-US-00247 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2451(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00248 Identities = 133/222 (59%), Positives = 164/222 (72%) Query: 2 MNLQENKTAIFDNVSKLALKAGRAHESVHIVAVTKYVNCQTTEALIRTGVNHIGENRVDK 61 M+L NK IF+ + A R ++SV ++AVTKYV+ LI G+ HI ENRVDK Sbjct: 1 MDLLTNKKKIFETIRLSTEAANRTNDSVSVIAVTKYVDSTIAGQLIEAGIEHIAENRVDK 60 Query: 62 FLEKYQALKDEKLTWHLIGSLQRRKVKDVINYVDYFHALDSVKLAAEIQKHAQKLIKCFL 121- FLEKY ALK + WHLIG+LQRRKVK+VINYVDYFHALDSV+LA EI K A +KCFL Sbjct: 61 FLEKYDALKYMPVKWHLIGTLQRRKVKEVINYVDYFHALDSVRLALEINKRADHPVKCFL 120- Query: 122 QVNISREDSKHGFTIEQIDDALNLISRYDKIELIGIMTMAPLKATKEEISSIFEETESLR 18- 1 QVNIS+E+SKHGF I +ID+A+ I + +KI+L+G+MTMAP A+KE I +IF + LR Sbjct: 121 QVNISKEESKHGFNISEIDEAIGEIGKMEKIQLVGLMTMAPANASKESIITIFRQANQLR 18- 0 Query: 182 KRLQARNIERMPFTELSMGMSRDYDIAIQNGSTFVRIGTSFF 223 K LQ + + MPFTELSMGMS DY IAIQ GSTF+RIG +FF Sbjct: 181 KNLQLKKRKNMPFTELSMGMSNDYPIAIQEGSTFIRIGRAEF 222 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 71 A DNA sequence (GBSx0071) was identified in S. agalactiae <SEQ ID 231> which encodes the amino acid sequence <SEQ ID 232>. This protein is predicted to be YlmF. Analysis of this protein sequence reveals the following: TABLE-US-00249 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2194(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9617> which encodes amino acid sequence <SEQ ID 9618> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00250 >GP:AAC95442 GB:AF068901 YlmF [Streptococcus pneumoniae] Identities = 86/200 (43%), Positives = 120/200 (60%), Gaps = 25/200 (12%) Query: 5 MALKDRFDKIISYFDTDDVSENEVHEVQERTSVQRDSRAATAQEASQRSHMTNSASEEMI 64 M+LKDRFD+ I YF T+D + +E +RD T+ +SQ + + + Sbjct: 1 MSLKDRFDRFIDYF-TEDEDSSLPYE-------KRDEPVFTSVNSSQEPALPMNQPSQSA 52 Query: 65 GSRPRTYTYDPNRQERQRVQRDNAYQQATPRVQNKDSVRQQREQVTIALKYPRKYEDAQE 124- G++ T RQ+ + N Q+AT ++V I ++YPRKYEDA E Sbjct: 53 GTKENNITRLHARQQ----ELANQSQRAT-------------DKVIIDVRYPRKYEDATE 95 Query: 125 IVDLLIVNECVLIDFQYMLDAQARRCLDYIDGASRVLYGSLQKVGSSMFLLTPANVMVDI 18- 4 IVDLL NE +LIDFQYM + QARRCLDY+DGA VL G+L+KV S+M+LLTP NV+V++ Sbjct: 96 IVDLLAGNESILIDFQYMTEVQARRCLDYLDGACHVLAGNLKKVASTMYLLTPVNVIVNV 155- Query: 185 EEMNIPKTGQETSFDFDMKR 204 E++ +P Q+ F FDMKR Sbjct: 156 EDIRLPDEDQQGEFGFDMKR 175 A related DNA sequence was identified in S. pyogenes <SEQ ID 233> which encodes the amino acid sequence <SEQ ID 234>. Analysis of this protein sequence reveals the following: TABLE-US-00251 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.64 Transmembrane 142-158 (142-158) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00252 >GP: AAC95442 GB: AF068901 YlmF [Streptococcus pneumoniae] Identities = 82/219 (37%), Positives = 113/219 (51%), Gaps = 46/219 (21%) Query: 5 MAFKDTFNKMISYFDTDEVNEVEEDVAASTDNVIP--RSQQSVRASSHPKQEPRNNHVQQ 62 M+ KD F++ I YF DE D+ +P + + V S + QEP Q Sbjct: 1 MSLKDRFDRFIDYFTEDE------------DSSLPYEKRDEPVFTSVNSSQEPALPMNQP 48 Query: 63 DHQARSQEQTRSQMHPKHGTSERYYQQSQPKEGHEMVDRRKRMSTSSIANRREQYQQSTC 122- A ++E +++H + +AN Q Sbjct: 49 SQSAGTKENNITRLHARQ---------------------------QELAN-----QSQRA 76 Query: 123 SDQTTIALKYPRKYEDAQEIVDLLIVNECVLIDFQFMLDAQARRCLDFIDGASKVLYGSL 18- 2 +D+ I ++YPRKYEDA EIVDLL NE +LIDFQ+M + QARRCLD++DGA VL G+L Sbjct: 77 TDKVIIDVRYPRKYEDATEIVDLLAGNESILIDFQYMTEVQARRCLDYLDGACHVLAGNL 136- Query: 183 QKVGSSMYLLAPSNVSVNIEEMTIPHTTQDIGFDFDMKR 221 +KV S+MYLL P NV VN+E++ +P Q F FDMKR Sbjct: 137 KKVASTMYLLTPVNVIVNVEDIRLPDEDQQGEFGFDMKR 175 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00253 Identities = 118/222 (53%), Positives = 145/222 (65%), Gaps = 17/222 (7%) Query: 1 MEGNMALKDRFDKIISYFDTDDVSENEVHEVQERTSV----QRDSRAATAQEAS------ 50 ME MA KD F+K+ISYFDTD+V+E E +V Q+ RA++ + Sbjct: 1 MENKMAFKDTFNKMISYFDTDEVNEVEEDVAASTDNVIPRSQQSVRASSHPKQEPRNNHV 60 Query: 51 QRSHMTNSAEEEMIGSRPRTYTYDPNRQERQRVQR----DNAYQQATPRVQNKDSVRQQR 106- Q+ H S E+ P+ T + Q+ Q + D + +T + N+ QQ Sbjct: 61 QQDHQARSQEQTRSQMHPKHGTSERYYQQSQPKEGHEMVDRRKRMSTSSIANRREQYQQS 120- Query: 107 ---EQVTIALKYPRKYEDAQEIVDLLIVNECVLIDFQYMLDAQARRCLDYIDGASRVLYG 16- 3 +Q TIALKYPRKYEDAQEIVDLLIVNECVLIDFQ+MLDAQARRCLD+IDGAS+VLYG Sbjct: 121 TCSDQTTIALKYPRKYEDAQEIVDLLIVNECVLIDFQFMLDAQARRCLDFIDGASKVLYG 18- 0 Query: 164 SLQKVGSSMFLLTPANVMVDIEEMNIPKTGQETSFDFDMKRR 205 SLQKVGSSM+LL P+NV V+IEEM IP T Q+ FDFDMKRR Sbjct: 181 SLQKVGSSMYLLAPSNVSVNIEEMTIPHTTQDIGFDFDMKRR 222 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 72 A DNA sequence (GBSx0072) was identified in S. agalactiae <SEQ ID 235> which encodes the amino acid sequence <SEQ ID 236>. This protein is predicted to be YlmH. Analysis of this protein sequence reveals the following: TABLE-US-00254 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3956(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00255 >GP: AAC95444 GB: AF068901 YlmH [Streptococcus pneumoniae] Identities = 101/255 (39%), Positives = 161/255 (62%) Query: 6 IYQHFRPEEYAFIHKIDHLAQYVENTYSFITTEFLNPREFKILESVLERRGSHYYTSGQY 65 IYQHF E+ F+ K + VE++Y+ T F+NP + K+L+ + + G +SG++ Sbjct: 5 IYQHFSIEDRPFLDKGMEWIKKVEDSYAPFLTPFINPHQEKLLKILAKTYGLACSSSGEF 64 Query: 66 FQTEYVKVIIAPEYYQLDMADFNLSLIEIKYNAKFNHLTHAKIMGTLLNYLGVKRSILGD 125- +EYV+V++ P+Y+Q + +DF +SL EI Y+ KF HLTHAKI+GT++N LG++R + GD Sbjct: 65 VSSEYVRVLLYPDYFQPEFSDFEISLQEIVYSNKFEHLTHAKILGTVINQLGIERKLFGD 124- Query: 126 ILVEEGCAQVLVDSQMTNHLVHSVTKIGTASVQLAEVPLSKLLTPKQDIQKLTVIASSLR 18- 5 ILV+E AQ++++ Q + KIG V L E P ++ + + ++L + SS R Sbjct: 125 ILVDEERAQIMINQQFLLLFQDGLKKIGRIPVSLEERPFTEKIDKLEQYRELDLSVSSFR 18- 4 Query: 186 LDKILATILKISRTQSTKLIEADKVKVNYATVNRVSEQLVEGDLISVRGYGRFTLNHNLG 24- 5 LD +L+ +LK+SR Q+ +LIE V+VNY V++ + GDLISVR +GR L + G Sbjct: 185 LDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISVRKFGRLRLLQDKG 24- 4 Query: 246 LTKNQKYKLEVDKMI 260 TK +K K+ V ++ Sbjct: 245 QTKKEKKKITVQLLL 259 A related DNA sequence was identified in S. pyogenes <SEQ ID 237> which encodes the amino acid sequence <SEQ ID 238>. Analysis of this protein sequence reveals the following: TABLE-US-00256 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.69 Transmembrane 46-62 (46-62) ----- Final Results ----- bacterial membrane --- Certainty = 0.1277(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases:

TABLE-US-00257 >GP: AAC95444 GB: AF068901 YlmH [Streptococcus pneumoniae] Identities = 110/257 (42%), Positives = 161/257 (61%) Query: 7 IYQHFHQEEYPFIDRMSDMINRVEDYYLLEVTEFLNPREVMILKSLIALTDLKMFVSTDY 66 IYQHF E+ PF+D+ + I +VED Y +T F+NP + +LK L L S ++ Sbjct: 5 IYQHFSIEDRPFLDKGMEWIKKVEDSYAPFLTPFINPHQEKLLKILAKTYGLACSSSGEF 64 Query: 67 YPSEYGRVIIAPGYYDLEQSDFQIALVEISYQAKFNQLTHSQILGTLINELGVKRNLFGD 126- SEY RV++ P Y+ E SDF+I+L EI Y KF LTH++ILGT+IN+LG++R LFGD Sbjct: 65 VSSEYVRVLLYPDYFQPEFSDFEISLQEIVYSNKFEHLTHAKILGTVINQLGIERKLFGD 124- Query: 127 VFVEMGYAQLMIKRELLDYFLGTITKIAKTSVKLREVNFDQLIRSIDNSQTLDILVSSFR 18- 6 + V+ AQ+MI ++ L F + KI + V L E F + I ++ + LD+ VSSFR Sbjct: 125 ILVDEERAQIMINQQFLLLFQDGLKKIGRIPVSLEERPFTEKIDKLEQYRELDLSVSSFR 18- 4 Query: 187 LDGVVATILKKSRTQVIALIEANKIKVNYRVANKASDNLVIGDMVSIRGHGRFTLLADNG 24- 6 LD +++ +LK SR Q LIE ++VNY V +K+ + +GD++S+R GR LL D G Sbjct: 185 LDVLLSNVLKLSRNQANQLIEKKLVQVNYHVVDKSDYTVQVGDLISVRKFGRLRLLQDKG 24- 4 Query: 247 VTKHGKQKITLSKMIHK 263 TK K+KIT+ ++ K Sbjct: 245 QTKKEKKKITVQLLLSK 261 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00258 Identities = 123/256 (48%), Positives = 177/256 (69%) Query: 6 IYQHFRPEEYAFIHKIDHLAQYVENTYSFITTEFLNPREFKILESVLERRGSHYYTSGQY 65 IYQHF EEY FI ++ + VE+ Y TEFLNPRE IL+S++ + S Y Sbjct: 7 IYQHFHQEEYPFIDRMSDMINRVEDYYLLEVTEFLNPREVMILKSLIALTDLKMFVSTDY 66 Query: 66 FQTEYVKVIIAPEYYQLDMADFNLSLIEIKYNAKFNHLTHAKIMGTLLNYLGVKRSILGD 125- + +EY +VIIAP YY L+ +DF ++L+EI Y AKFN LTH++I+GTL+N LGVKR++ GD Sbjct: 67 YPSEYGRVIIAPGYYDLEQSDFQIALVEISYQAKFNQLTHSQILGTLINELGVKRNLFGD 126- Query: 126 ILVEEGCAQVLVDSQMTNHLVHSVTKIGTASVQLAEVPLSKLLTPKQDIQKLTVIASSLR 18- 5 + VE G AQ+++ ++ ++ + ++TKI SV+L EV +L+ + Q L ++ SS R Sbjct: 127 VFVEMGYAQLMIKRELLDYFLGTITKIAKTSVKLREVNFDQLIRSIDNSQTLDILVSSFR 18- 6 Query: 186 LDKILATILKISRTQSTKLIEADKVKVNYATVNRVSEQLVEGDLISVRGYGRFTLNHNLG 24- 5 LD ++ATILK SRTQ LIEA+K+KVNY N+ S+ LV GD++S+RG+GRFTL + G Sbjct: 187 LDGVVATILKKSRTQVIALIEANKIKVNYRVANKASDNLVIGDMVSIRGHGRFTLLADNG 24- 6 Query: 246 LTKNQKYKLEVDKMIH 261 +TK+ K K+ + KMIH Sbjct: 247 VTKHGKQKITLSKMIH 262 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 73 A DNA sequence (GBSx0073) was identified in S. agalactiae <SEQ ID 239> which encodes the amino acid sequence <SEQ ID 240>. This protein is predicted to be cell division protein DivIVA (septumplacement). Analysis of this protein sequence reveals the following: TABLE-US-00259 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5418 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00260 >GP: AAC95445 GB: AF068901 cell division protein DivIVA [Streptococcus pneumoniae] Identities = 132/227 (58%), Positives = 179/227 (78%), Gaps = 2/227 (0%) Query: 1 MPLTALEIKDKTFSSKFRGYSEEEVNEFLEIVVDDYEDLIRRNREQEQYIKDLEEKIAYF 60 MP+T+LEIKDKTF ++FRG+ EEV+EFL+IVV DYEDL+R N ++ IK LEE+++YF Sbjct: 1 MPITSLEIKDKTFGTRFRGFDPEEVDEFLDIVVRDYEDLVRANHDKNLRIKSLEERLSYF 60 Query: 61 NEMKESLSQSVILAQETAERVKISAQDEASNLMGKATFDAQHLIDEAKLKANQILRDATD 120- +E+K+SLSQSV++AQ+TAERVK +A + ++N++ +A DAQ L++EAK KAN+ILR ATD Sbjct: 61 DEIKDSLSQSVLIAQDTAERVKQAAHERSNNIIHQAEQDAQRLLEEAKYKANEILRQATD 120- Query: 121 DAKRVAIETEDLKRQSRVFHQRLLSELEGQLKLANSSAWEELLKPTAIYLQNSDASFKEV 18- 0 +AK+VA+ETE+LK +SRVFHQRL S +E QL + SS WE++L+PTA YLQ SD +FKEV Sbjct: 121 NAKKVAVETEELKNKSRVFHQRLKSTIESQLAIVESSDWEDILRPTATYLQTSDEAFKEV 18- 0 Query: 181 VEKVLDEDDALPVVDDTESFDATRQFSPDEMEELQRRVEESNKQLEE 227 V +VL E P+ + E D TRQFS EM ELQ R+E ++K+L E Sbjct: 181 VSEVLGEPIPAPI--EEEPIDMTRQFSQAEMAELQARIEVADKELSE 225 A related DNA sequence was identified in S. pyogenes <SEQ ID 241> which encodes the amino acid sequence <SEQ ID 242>. Analysis of this protein sequence reveals the following: TABLE-US-00261 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6272 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00262 Identities = 180/254 (70%), Positives = 217/254 (84%), Gaps = 2/254 (0%) Query: 1 MPLTALEIKDKTFSSKFRGYSEEEVNEFLEIVVDDYEDLIRRNREQEQYIKDLEEKIAYF 60 M LT LEIKDKTF +KFRGY EEEVNEFL+IVVDDYE L+R+NR+ E IKDLEEK++YF Sbjct: 1 MALTTLEIKDKTFKTKFRGYCEEEVNEFLDIVVDDYEALVRKNRDNEARIKDLEEKLSYF 60 Query: 61 NEMKESLSQSVILAQETAERVKISAQDEASNLMGKATFDAQHLIDEAKLKANQILRDATD 120- +EMKESLSQSVILAQETAE+VK +A EA+NL+ KAT+DAQHL+DE+K KANQ+LRDATD Sbjct: 61 DEMKESLSQSVILAQETAEKVKATANAEATNLVSKATYDAQHLLDESKAKANQMLRDATD 120- Query: 121 DAKRVAIETEDLKRQSRVFHQRLLSELEGQLKLANSSAWEELLKPTAIYLQNSDASFKEV 18- 0 +AKRVAIETE+LKRQ+RVFHQRL+S +E QL L+NS W+ELL+PTAIYLQNSD +FKEV Sbjct: 121 EAKRVAIETEELKRQTRVFHQRLISSIESQLSLSNSPEWDELLQPTAIYLQNSDDAFKEV 18- 0 Query: 181 VEKVLDEDDALPVVDDTESFDATRQFSPDEMEELQRRVEESNKQLEESGLLDTNNFQMEE 24- 0 V+ VL+ED +P DD+ SFDATRQF+P+E+EELQRRV+ESNK+LE L ++ E Sbjct: 181 VKTVLNED--IPESDDSASFDATRQFTPEELEELQRRVDESNKELEAYQLDSQSDSTTEP 23- 8 Query: 241 PINLGETQTFKLNI 254 +NL ETQTFKLNI Sbjct: 239 EVNLSETQTFKLNI 252 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 74 A DNA sequence (GBSx0074) was identified in S. agalactiae <SEQ ID 243> which encodes the amino acid sequence <SEQ ID 244>. Analysis of this protein sequence reveals the following: TABLE-US-00263 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 841-857 (841-857) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00264 >GP: AAC95446 GB: AF068901 isoleucine-tRNA synthetase [Streptococcus pneumoniae] Identities = 730/929 (78%), Positives = 822/929 (87%), Gaps = 1/929 (0%) Query: 1 MKLKETLNLGQTAFPMRAGLPNKEPQWQEAWDQADIYKKRQALNEGKPAFHLHDGPPYAN 60 MKLK+TLNLG+T FPMRAGLP KEP WQ+ W+ A +Y++RQ LN+GKP F LHDGPPYAN Sbjct: 1 MKLKDTLNLGKTEFPMRAGLPTKEPVWQKEWEDAKLYQRRQELNQGKPHFTLHDGPPYAN 60 Query: 61 GNIHVGHALNKISKDIIVRSKSMSGFRAPYVPGWDTHGLPIEQVLAKKGVKRKEMDLAEY 120- GNIHVGHA+NKISKDIIVRSKSMSGF AP++PGWDTHGLPIEQVL+K+GVKRKEMDL EY Sbjct: 61 GNIHVGHAMNKISKDIIVRSKSMSGFYAPFIPGWDTHGLPIEQVLSRQGVKRKEMDLVEY 120- Query: 121 LEMCRDYALSQVDKQRDDFKRLGVSADWENPYITLTPDYEADQVRVFGAMADKGYIYRGA 18- 0 L++CR+YALSQVDKQR+DFKRLGVS DWENPY+TLTPDYEA Q+RVFG MA+KGYIYRGA Sbjct: 121 LKLCREYALSQVDKQREDFKRLGVSGDWENPYVTLTPDYEAAQIRVFGEMANKGYIYRGA 18- 0 Query: 181 KPVYWSWSSESALAEAEIEYHDIDSTSLYYANKVKDGKGILDTDTYIVVWTTTPFTVTAS 24- 0 KPVYWSWSSESALAEAEIEYHD+ STSLYYANKVKDGKG+LDTDTYIVVWTTTPFT+TAS Sbjct: 181 KPVYWSWSSESALAEAEIEYHDLVSTSLYYANKVKDGKGVLDTDTYIVVWTTTPFTITAS 24- 0 Query: 241 RGLTVGPDMEYVVVVPVGSERKYLLAEVLVDSLAAKFGWENFEIVTHHTGKELNHIVTEH 30- 0 RGLTVG D++YV+V PVG RK+++A L+ SL+ KFGW + +++ + G+ELNHIVTEH Sbjct: 241 RGLTVGADIDYVLVQPVGEARKFVVAAELLTSLSEKFGWADVQVLETYRGQELNHIVTEH 30- 0 Query: 301 PWDTEVEELVILGDHVTTDSGTGIVHTAPGFGEDDYNVGIANGLDVVVTVDSRGLMMENA 36- 0 PWDT VEELVILGDHVTTDSGTGIVHTAPGFGEDDYNVGIAN L+V VTVD RG+MM+NA Sbjct: 301 PWDTAVEELVILGDHVTTDSGTGIVHTAPGFGEDDYNVGIANNLEVAVTVDERGIMMKNA 36- 0 Query: 361 GPDFEGQFYDKVTPLVKEKLGDLLLASEVINHSYPFDWRTKKPIIWRAVPQWFASVSKFR 42- 0 GP+FEGQFY+KV P V EKLG+LLLA E I+HSYPFDWRTKKPIIWRAVPQWFASVSKFR Sbjct: 361 GPEFEGQFYEKVVPTVIEKLGNLLLAQEEISHSYPFDWRTKKPIIWRAVPQWFASVSKFR 42- 0 Query: 421 QEILDEIEKTNFQPEWGKKRLYNMIRDRGDWVISRQRAWGVPLPIFYAEDGTAIMTKEVT 48- 0 QEILDETEK F EWGK RLYNMIRDRGDWVISRQR WGVPLPIFYAEDGTAIM E Sbjct: 421 QEILDEIEKVKFHSEWGKVRLYNMIRDRGDWVISRQRTWGVPLPIFYAEDGTAIMVAETI 48- 0 Query: 481 DHVADLFAEYGSIVWWQRDAKDLLPAGYTHPGSPNGLFEKETDIMDVWFDSGSSWNGVMN 54- 0 +HVA LF ++GS +WW+RDAKDLLP G+THPGSPNG F+KETDIMDVWFDSGSSWNGV+ Sbjct: 481 EHVAQLFSKHGSSIWWERDAKDLLPEGFTHPGSPNGEFKKETDIMDVWFDSGSSWNGVVV 54- 0 Query: 541 ARENLSYPADLYLEGSDQYRGWFNSSLITSVAVNGHAPYKAVLSQGFVLDGKGEKMSKSL 60- 0 R L+YPADLYLEGSDQYRGWFNSSLITSVA +G APYK +LSQGF LDGKGEKMSKSL Sbjct: 541 NRPELTYPADLYLEGSDQYRGWFNSSLITSVANHGVAPYKQILSQGFALDGKGEKMSKSL 60- 0 Query: 601 GNTILPSDVEKQFGAEILRLWVTSVDSSNDVRISMDILEQTSETYRKIRNTLRFLIANTS 66- 0 GNTI PSDVEKQFGAEILRLWVTSVDSSNDVRISMDIL Q SETYRKIRNTLRFLIANTS Sbjct: 601 GNTIAPSDVEKQFGAEILRLWVTSVDSSNDVRISMDILSQVSETYRKIRNTLRFLIANTS 66- 0 Query: 661 DFNPKQDAVAYENLGAVDRYMTIKFNQVVDTINKAYAAYDFMAIYKAVVNFVTVDLSAFY 72- 0 DFNP QD VAY+ L +VD+YMTI+FNQ+V TI AYA ++F+ IYKA+VNF+ VDLSAFY Sbjct: 661 DFNPAQDTVAYDELRSVDKYMTIRFNQLVKTIRDAYADFEFLTIYKALVNFINVDLSAFY 72- 0 Query: 721 LDFAKDVVYIEAANSPERRPMQTVFYDILVKLTKLLTPILPHTAEEIWSYLEHEEEEFVQ 78- 0 LDFAKDVVYIE A S ERR+MQTVFYDILVK+TKLLTPILPHTAEEIWSYLE E E+FVQ Sbjct: 721 LDFAKDVVYIEGAKSLERRQMQTVFYDILVKITKLLTPILPHTAEEIWSYLEFETEDFVQ 78- 0 Query: 781 LAEMPVAQTFSGQEEILEEWSAFMTLRTQAQKALEEARNAKVIGKSLEAHLTIYASQEVK 84- 0 L+E+P QTF+ QEEIL+ W+AFM R QAQKALEEARNAKVIGKSLEAHLT+Y ++ VK Sbjct: 781 LSELPEVQTFANQEEILDTWAAFMDFRGQAQKALEEARNAKVIGKSLEAHLTVYPNEVVK 84- 0 Query: 841 TLLTALNSDIALLMIVSQLTIADEADKPADSVSFEGVAFTVEHAEGEVCERSRRIDPTTK 90- 0 TLL A+NS++A L+IVS+LTIA+E P +SFE VAFTVE A GEVC+R RRIDPTT Sbjct: 841 TLLEAVNSNVAQLLIVSELTIAEE-PAPEAALSFEDVAFTVERAAGEVCDRCRRIDPTTA 89- 9 Query: 901 MRSYGVAVCDASAAIIEQYYPEAVAQGFE 929 RSY +CD A+I+E+ + +AVA+GFE Sbjct: 900 ERSYQAVICDHCASIVEENFADAVAEGFE 928 A related DNA sequence was identified in S. pyogenes <SEQ ID 245> which encodes the amino acid sequence <SEQ ID 246>. Analysis of this protein sequence reveals the following: TABLE-US-00265 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.70 Transmembrame 849-865 (848-867) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00266 Identities = 798/929 (85%), Positives = 857/929 (91%) Query: 1 MKLKETLNLGQTAFPMRAGLPNKEPQWQEAWDQADIYKKRQALNEGKPAFHLHDGPPYAN 60 MKLKETLNLG+TAFPMRAGLPNKEPQWQ AW+QA++YKKRQ LN GKPAFHLHDGPPYAN Sbjct: 1 MKLKETLNLGKTAFPMRAGLPNKEPQWQAAWEQAELYKKRQELNAGKPAFHLHDGPPYAN 60 Query: 61 GNIHVGHALNKISKDIIVRSKSMSGFRAPYVPGWDTHGLPIEQVLAKKGVKRKEMDLAEY 120- GNIHVGHALNKISKDIIVRSKSMSGF+APYVPGWDTHGLPIEQVLAK+G+KRKEMDLAEY Sbjct: 61 GNIHVGHALNKISKDIIVRSKSMSGFQAPYVPGWDTHGLPIEQVLAKQGIKRKEMDLAEY 120- Query: 121 LEMCRDYALSQVDKQRDDFKRLGVSADWENPYITLTPDYEADQVRVFGAMADKGYIYRGA 18- 0 LEMCR YALSQVDKQRDDFKRLGVSADWENPY+TL P +EADQ+RVFGAMA+KGYIYRGA Sbjct: 121 LEMCRQYALSQVDKQRDDFKRLGVSADWENPYVTLDPQFEADQIRVFGAMAEKGYIYRGA 18- 0 Query: 181 KPVYWSWSSESALAEAEIEYHDIDSTSLYYANKVKDGKGILDTDTYIVVWTTTPFTVTAS 24- 0 KPVYWSWSSESALAEAEIEYHDIDSTSLYYANKVKDGKGILDT+TYIVVWTTTPFTVTAS Sbjct: 181 KPVYWSWSSESALAEAEIEYHDIDSTSLYYANKVKDGKGILDTNTYIVVWTTTPFTVTAS 24- 0 Query: 241 RGLTVGPDMEYVVVVPVGSERKYLLAEVLVDSLAAKFGWENFEIVTHHTGKELNHIVTEH 30- 0 RGLTVGPDM+Y+VV P GS+R+Y++AE L+DSLA KFGWE+FE + H G +L +IVTEH Sbjct: 241 RGLTVGPDMDYLVVKPAGSDRQYVVAEGLLDSLAGKFGWESFETLASHKGADLEYIVTEH 30- 0 Query: 301 PWDTEVEELVILGDHVTTDSGTGIVHTAPGFGEDDYNVGIANGLDVVVTVDSRGLMMENA 36- 0 PWDT+VEELVILGDHVT +SGTGIVHTAPGFGEDDYNVG L+V VTVD RGLMMENA Sbjct: 301 PWDTDVEELVILGDHVTLSSGTGIVHTAPGFGEDDYNVGTKYKLEVAVTVDERGLMMENA 36- 0 Query: 361 GPDFEGQFYDKVTPLVKEKLGDLLLASEVINHSYPFDWRTKKPIIWRAVPQWFASVSKFR 42- 0 GPDF GQFY+KVTP+V +KLGDLLLA EVINHSYPFDWRTKKPIIWRAVPQWFASVS FR Sbjct: 361 GPDFHGQFYNKVTPIVIDKLGDLLLAQEVINHSYPFDWRTKKPIIWRAVPQWFASVSDFR 42- 0 Query: 421 QEILDEIEKTNFQFEWGKKRLYNMIRDRGDWVISRQRAWGVPLPIFYAEDGTAIMTKEVT 48- 0 Q+ILDEIEKT F P WG+ RLYNMIRDRGDWVISRQRAWGVPLPIFYAEDGTAIMTKEVT Sbjct: 421 QDILDEIEKTTFHPSWGETRLYNMIRDRGDWVISRQRAWGVPLPIFYAEDGTAIMTKEVT 48- 0 Query: 481 DHVADLFAEYGSIVWWQRDARDLLPAGYTHPGSPNGLFEKETDIMDVWFDSGSSWNGVMN 54- 0 DHVADLF E GSI+WWQ++AKDLLP G+THPGSPNG F KETDIMDVWFDSGSSWNGVMN Sbjct: 481 DHVADLFQENGSIIWWQKEAKDLLPEGFTHPGSPNGEFTKETDIMDVWFDSGSSWNGVMN 54- 0 Query: 541 ARENLSYPADLYLEGSDQYRGWFNSSLITSVAVNGHAPYKAVLSQGFVLDGKGEKNSKSL 60- 0 +ENLSYPADLYLEGSDQYRGWFNSSLITSVAVNGHAPYKA+LSQGFVLDGKGEKMSRS Sbjct: 541 TKENLSYPADLYLEGSDQYRGWFNSSLITSVAVNGHAPYKAILSQGFVLDGKGEKMSKSK 60- 0 Query: 601 GNTILPSDVEKQFGAEILRLWVTSVDSSNDVRISMDILKQTSETYRKIRNTLRFLIANTS 66- 0 GN I P+DV KQ+GA+ILRLWV SVD+ NDVR+SM+IL Q SETYRKIRNTLRFLIANTS Sbjct: 601 GNIISPNDVAKQYGADILRLWVASVDTDNDVRVSMEILGQVSETYRKIRNTLRFLIANTS 66- 0 Query: 661 DFNPKQDAVAYENLGAVDRYMTIKFNQVVDTINKAYAAYDFMAIYKAVVNFVTVDLSAFY 72- 0 DFNP D VAY +LG VD+YMTI FNQ+V TI AY YDFMAIYKAVVNFVTVDLSAFY Sbjct: 661 DFNPATDTVAYADLGTVDKYMTIVFNQLVATITDAYERYDFMAIYKAVVNFVTVDLSAFY 72- 0 Query: 721 LDFAKDVVYIEAANSPERRRMQTVFYDILVKLTKLLTPILPHTAEEIWSYLEHEEEEFVQ 78- 0 LDFAKDVVYIEAANS ERRRMQTVFYDILVK+TKLLTPILPHT EEIWSYLEHE E FVQ Sbjct: 721 LDFAKDVVYIEAANSLERRRMQTVFYDILVKITKLLTPILPHTTEEIWSYLEHESEAFVQ 78- 0 Query: 781 LAEMPVAQTFSGQEEILEEWSAFMTLRTQAQKALEEARNAKVIGKSLEAHLTIYASQEVK 84- 0 LAEMPVA+TFS QE+ILE WSAFMTLRTQAQKALEEARNAK+IGKSLEAHLTIYAS+EVK Sbjct: 781 LAEMPVAETFSAQEDILEAWSAFMTLRTQAQKALEEARNAKIIGKSLEAHLTIYASEEVK 84- 0 Query: 841 TLLTALNSDIALLMIVSQLTIADEADKPADSVSFEGVAFTVEHAEGEVCERSRRIDPTTK 90- 0 TLLTAL+SDIALL+IVSQLTIAD AD PAD+V+FEGVAF VEHA GEVCERSRRIDPTT+ Sbjct: 841 TLLTALDSDIALLLIVSQLTIADLADAPADAVAFEGVAFIVEHAIGEVCERSRRIDPTTR 90- 0 Query: 901 MRSYGVAVCDASAAIIEQYYPEAVAQGFE 929 MRSY VCD SA IIE+ +PEAVA+GFE Sbjct: 901 MRSYNAFVCDHSAKIIEENFPEAVAEGFE 929 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 75 A DNA sequence (GBSx0075) was identified in S. agalactiae <SEQ ID 247> which encodes the amino acid sequence <SEQ ID 248>. Analysis of this protein sequence reveals the following: TABLE-US-00267 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3425(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 249> which encodes the amino acid sequence <SEQ ID 250>. Analysis of this protein sequence reveals the following: TABLE-US-00268 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3467(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00269 Identities = 77/99 (77%), Positives = 89/99 (89%) Query: 1 MRLINTTSSHPELVRNQLQNTDAKLVEVYSAGNTDVVFTKAPKHYELLISNKYRAIKDEE 60 MRLINTTSSHPEL++NQL+NTDA LVEVYSAGNTDV+FT+APKHYELLISNKYRAIK++E Sbjct: 1 MRLINTTSSHPELIKNQLKNTDAYLVEVYSAGNTDVIFTQAPKHYELLISNKYRAIKEDE 60 Query: 61 LEAIREFFLKRKIDQSIIIQEQMKSLHTAKLIEISYPTT 99 L+ IREFFLKRKID I+I Q K+LHT LIEIS+ T+ Sbjct: 61 LDIIREFFLKRKIDPRIVIPGQSKTLHTNNLIEISFQTS 99 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 76 A DNA sequence (GBSx0076) was identified in S. agalactiae <SEQ ID 251> which encodes the amino acid sequence <SEQ ID 252>. This protein is predicted to be AP4A hydrolase. Analysis of this protein sequence reveals the following: TABLE-US-00270 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1714(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00271 >GP: AAC06510 GB: AE000676 AP4A hydrolase [Aquifex aeolicus] Identities = 30/101 (29%), Positives = 48/101 (46%), Gaps = 2/101 (1%) Query: 32 KIILVQAPNGAWFLPGGEIEENENHLEALTRELIEELGYSATIGHYYGQADEYFYSRHRD 91 - +++L++ P+ W P G IE E E RE+ EE G I Y G+ Y+Y+ + Sbjct: 16 EVLLIKTPSNVWSFPKGNIEPGEKPEETAVREVWEETGVKGEILDYIGEI-HYWYTLKGE 74 Query: 92 TYYYNPAYIYEVTAYHKDQAPLEDFNHLAWFPIQEAKEKLK 132 + Y Y + + P + +FPI+EAK+ LK Sbjct: 75 RIFKTVKY-YLMKYKEGEPRPSWEVKDAKFFPIKEAKKLLK 114 A related DNA sequence was identified in S. pyogenes <SEQ ID 253> which encodes the amino acid sequence <SEQ ID 254>. Analysis of this protein sequence reveals the following:

TABLE-US-00272 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1954(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00273 Identities = 102/149 (68%), Positives = 118/149 (78%) Query: 1 MTNPTFGEKIDNVNYRSRFGVYAIIPNPTHDKIILVQAPNGAWFLPGGEIEENENHLEAL 60 M PTFG K + +Y +R+GVYAIIPN KIILVQAPNG+WFLPGGEIE E L+AL Sbjct: 1 MMIPTFGHKNAHKDYVTRYGVYAIIPNHEQTKIILVQAPNGSWFLPGGEIEAGEGQLQAL 60 Query: 61 TRELIEELGYSATIGHYYGQADEYFYSRHRDTYYYNPAYIYEVTAYHKDQAPLEDFNHLA 120- RELIEELG+SATIG YYGQADEYFYSRHRDT++Y+PAY+YEVTA+ PLEDFN+L Sbjct: 61 ERELIEELGFSATIGSYYGQADEYFYSRHRDTHFYHPAYLYEVTAFQAVSKPLEDFNNLG 120- Query: 121 WFPIQEAKEKLKRGSHRWGVQAWEKNHHS 149 WF EA KLKR SH+WGV+ W+K HHS Sbjct: 121 WFSPIEAIAKLKRESHQWGVKEWQKKHHS 149 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 77 A DNA sequence (GBSx0077) was identified in S. agalactiae <SEQ ID 255> which encodes the amino acid sequence <SEQ ID 256>. This protein is predicted to be ClpE (clpB-1). Analysis of this protein sequence reveals the following: TABLE-US-00274 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2882(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00275 >GP: AAD01782 GB: AF023421 ClpE [Lactococcus lactis] Identities = 560/752 (74%), Positives = 647/752 (85%), Gaps = 12/752 (1%) Query: 1 MLCQNCKLNESTIHLYTNVNGKQKQVDLCQNCYQIIKTDPNNPLFSGLNHVS-HAPGGIN 59 MLCQNC +NE+TIHLYT+VNG++KQ+DLCQNCYQI+K+ LF N + ++ N Sbjct: 1 MLCQNCNINEATIHLYTSVNGQKKQIDLCQNCYQIMKSGGQEALFGAGNASNGNSDEPFN 60 Query: 60 PFFDDFFGDLNNFRAFNGQDLPNTPPTQSGGNRGGGNGNGRNNNRNQTATPSQAKGILEE 119- PF +D F L + FNG TPPTQ+GG G N R Q KG+LEE Sbjct: 61 PF-NDIFSALQG-QDFNGAASNQTPPTQTGGRGPRGPQNPR---------AKQPKGMLEE 109- Query: 120 FGINVTEIARHGDIDPVIGRDSEIIRVIEILNRRTKNNPVLIGEPGVGKTAVVEGLAQKI 17- 9 FGIN+TE AR G+IDPVIGRD EI RVIEILNRRTKNNPVLIGEPGVGKTAVVEGLAQKI Sbjct: 110 FGINITESARRGEIDPVIGRDEEIKRVIEILNRRTKNNPVLIGEPGVGKTAVVEGLAQKI 16- 9 Query: 180 VDGNVPHKLQGKQVIRLDVVSLVQGTGIRGQFEERMQKLMEEIRQRQDVILFIDEIHEIV 23- 9 VDG+VP KLQ K+VIRLDVVSLVQGTGIRGQFEERMQKLM+EIR+R DVI+FIDEIHEIV Sbjct: 170 VDGDVPQKLQNKEVIRLDVVSLVQGTGIRGQFEERMQKLMDEIRKRNDVIMFIDEIHEIV 22- 9 Query: 240 GAGTAGEGSMDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDEPSVE 29- 9 GAG+AG+G+MDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDEPSV+ Sbjct: 230 GAGSAGDGNMDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDEPSVD 28- 9 Query: 300 ETITILKGIQKKYEDYHHVKYNNDAIEAAAVLSNRYIQDRFLPDKAIDLLDEAGSKMNLT 35- 9 ETITIL+GIQ +YEDYHHVKY ++AIEAAA LSNRYIQDRFLPDKAIDLLDE+GSK NLT Sbjct: 290 ETITILRGIQARYEDYHHVKYTDEAIEAAAHLSNRYIQDRFLPDKAIDLLDESGSKKNLT 34- 9 Query: 360 LNFVDPKEIDQRLIEAENLKAQATREEDYERAAYFRDQIAKYKEMQQQKVDDQDTPIITE 41- 9 L FVDP++I++R+ +AE+ K +AT+ ED+E+AA+FRDQI+K +E+Q+Q+V D+D P+ITE Sbjct: 350 LKFVDPEDINRRIADAESKKNEATKAEDFEKAAHFRDQISKLRELQKQEVTDEDMPVITE 40- 9 Query: 420 KTIEHIIEEKTNIPVGDLKEKEQSQLINLADDLKQHVIGQDDAVVKIAKAIRRNRVGLGS 47- 9 K IE I+E+KT IPVGDLKEKEQ+QLINLADDLK HVIGQD+AV KI+KAIRR+RVGLG Sbjct: 410 KDIEQIVEQKTQIPVGDLKEKEQTQLINLADDLKAHVIGQDEAVDKISKAIRRSRVGLGK 46- 9 Query: 480 PNRPIGSFLFVGPTGVGKTELSKQLAIELFGSADSMIRFDMSEYMEKHAVAKLVGAPPGY 53- 9 PNRPIG FLFVGPTGVGKTEL+KQLA ELFGS++SMIRFDMSEYMEKH+VAKL+GAPPGY Sbjct: 470 PNRPIGFFLFVGPTGVGKTELAKQLAKELFGSSESMIRFDMSEYMEKHSVAKLIGAPPGY 52- 9 Query: 540 VGYEEAGQLTEKVRRNPYSLILLDEIEKAHPDVMHMFLQVLDDGRLTDGQGRTVSFKDTI 59- 9 VGYEEAGQLTE+VRRNPYSLILLDEIEKAHPDVMHMFLQ+L+DGRLTD QGRTVSFKD++ Sbjct: 530 VGYEEAGQLTERVRRNPYSLILLDEIEKAHPDVMHMFLQILEDGRLTDAQGRTVSFKDSL 58- 9 Query: 600 IIMTSNAGSGKTEASVGFGASREGRTNSVLGQLGNFFSPEFMNRFDGIIEFKALDKENLL 65- 9 IIMTSNAG+GK EASVGFGA+REGRT SVLGQLG+FFSPEFMNRFDGIIEF AL KENLL Sbjct: 590 IIMTSNAGTGKVEASVGFGAAREGRTKSVLGQLGDFFSPEFMNRFDGIIEFSALSKENLL 64- 9 Query: 660 NIVDIMLSDVNARLAINGIHLDVTDKVKEKLVDLGYDPKMGARPLRRTIQEHIEDAITDY 71- 9 IVD+ML +VN ++ N IHL VT KEKLVDLGY+P MGARPLRR IQE+IED+I D+ Sbjct: 650 KIVDLMLDEVNEQIGRNDIHLSVTQAAKEKLVDLGYNPAMGARPLRRIIQENIEDSIADF 70- 9 Query: 720 YLENPSEKELRAIMTSNGNIIIKSSKKTEEST 751 Y+E+P K+L A + + +I +++T E+T Sbjct: 710 YIEHPEYKQLVADLIDDKIVISNQTQETAETT 741 A related DNA sequence was identified in S. pyogenes <SEQ ID 257> which encodes the amino acid sequence <SEQ ID 258>. Analysis of this protein sequence reveals the following: TABLE-US-00276 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3104(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00277 Identities = 640/751 (85%), Positives = 691/751 (91%), Gaps = 7/751 (0%) Query: 1 MLCQNCKLNESTIHLYTNVNGKQKQVDLCQNCYQIIKTDPNNPLFSGLNHVSHAPG-GIN 59 MLCQNC LNESTIHLYT+VNGKQ+QVDLCQNCYQI+K+DP N + +GL A + Sbjct: 1 MLCQNCNLNESTIHLYTSVNGKQRQVDLCQNCYQIMKSDPANSILNGLTPGYRAQDRSTS 60 Query: 60 PFFDDFFGDLNNFRAFNGQDLPNTPPTQSGGNRGGGNGNGRNNNRNQTATPS----QAKG 115- PFFDDFFGDLNNFRAF +LPNTPPTQ+G N GG G N N + A P QAKG Sbjct: 61 PFFDDFFGDLNNFRAFG--NLPNTPPTQAGQNGNGGGRYGGNYNGQRPAQPQTPNQQAKG 118- Query: 116 ILEEFGINVTEIARHGDIDPVIGRDSEIIRVIEILNRRTKNNPVLIGEPGVGKTAVVEGL 17- 5 +LEEFGINVT+IAR+G+IDPVIGRD EI RVIEILNRRTKNNPVLIGEPGVGKTAVVEGL Sbjct: 119 LLEEFGINVTDIARNGNIDPVIGRDEEITRVIEILNRRTKNNPVLIGEPGVGKTAVVEGL 17- 8 Query: 176 AQKIVDGNVPHKLQGKQVIRLDVVSLVQGTGIRGQFEERMQKLMEEIRQRQDVILFIDEI 23- 5 AQKI+DG VP KLQGKQVIRLDVVSLVQGTGIRGQFEERMQKLMEEIR R+DVILFIDEI Sbjct: 179 AQKIIDGTVPQKLQGKQVIRLDVVSLVQGTGIRGQFEERMQKLMEEIRNRKDVILFIDEI 23- 8 Query: 236 HEIVGAGTAGEGSMDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDE 29- 5 HEIVGAG+AG+G+MDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDE Sbjct: 239 HEIVGAGSAGDGNMDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDE 29- 8 Query: 296 PSVEETITILKGIQKKYEDYHHVKYNNDAIEAAAVLSNRYIQDRFLPDKAIDLLDEAGSK 35- 5 PSVEETITILKGIQ KYEDYHHVKY+ AIEAAA LSNRYIQDRFLPDKAIDLLDEAGSK Sbjct: 299 PSVEETITILKGIQPKYEDYHHVKYSPAAIEAAAHLSNRYIQDRFLPDKAIDLLDEAGSK 35- 8 Query: 356 MNLTLNFVDPKEIDQRLIEAENLKAQATREEDYERAAYFRDQIAKYKEMQQQKVDDQDTP 41- 5 MNLTLNFVDPKEID+RLIEAENLKAQATR+EDYERAAYFRDQI KYKEMQ QKVD+QD P Sbjct: 359 MNLTLNFVDPKEIDKRLIEAENLKAQATRDEDYERAAYFRDQITKYKEMQAQKVDEQDIP 41- 8 Query: 416 IITEKTIEHIIEEKTNIPVGDLKEKEQSQLINLADDLKQHVIGQDDAVVKIAKAIRRNRV 47- 5 IITEKTIE I+E+KTNIPVGDLKEKEQSQL+NLA+DLK HVIGQDDAV KIAKAIRRNRV Sbjct: 419 IITEKTIEAIVEQKTNIPVGDLKEKEQSQLVNLANDLKAHVIGQDDAVDKIAKAIRRNRV 47- 8 Query: 476 GLGSPNRPIGSFLFVGPTGVGKTELSKQLAIELFGSADSMIRFDMSEYMEKHAVAKLVGA 53- 5 GLG+PNRPIGSFLFVGPTGVGKTELSKQLAIELFGS ++MIRFDMSEYMEKHAVAKLVGA Sbjct: 479 GLGTPNRPIGSFLFVGPTGVGKTELSKQLAIELFGSTNNMIRFDMSEYMEKHAVAKLVGA 53- 8 Query: 536 PPGYVGYEEAGQLTEKVRRNPYSLILLDEIEKAHPDVMHMFLQVLDDGRLTDGQGRTVSF 59- 5 PPGY+GYEEAGQLTE+VRRNPYSLILLDE+EKAHPDVMHMFLQVLDDGRLTDGQGRTVSF Sbjct: 539 PPGYIGYEEAGQLTEQVRRNPYSLILLDEVEKAHPDVMHMFLQVLDDGRLTDGQGRTVSF 59- 8 Query: 596 KDTIIIMTSNAGSGKTEASVGFGASREGRTNSVLGQLGNFFSPEFMNRFDGIIEFKALDK 65- 5 KDTIIIMTSNAG+GK+EASVGFGA+REGRT+SVLG+L NFFSPEFMNRFDGIIEFKAL K Sbjct: 599 KDTIIIMTSNAGTGKSEASVGFGAAREGRTSSVLGELSNFFSPEFMNRFDGIIEFKALSK 65- 8 Query: 656 ENLLNIVDIMLSDVNARLAINGIHLDVTDKVKEKLVDLGYDPKMGARPLRRTIQEHIEDA 71- 5 E+LL+IVD+ML DVN RL NGIHLDVT KVKEKLVDLGYDPKMGARPLRRTIQ++IEDA Sbjct: 659 EHLLHIVDLMLEDVNERLGYNGIHLDVTQKVKEKLVDLGYDPKMGARPLRRTIQDYIEDA 71- 8 Query: 716 ITDYYLENPSEKELRAIMTSNGNIIIKSSKK 746 ITDYYLE+P+EK+LRA+MT++ NI IK+ K+ Sbjct: 719 ITDYYLEHPTEKQLRALMTNSENITIKAVKE 749 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 78 A DNA sequence (GBSx0078) was identified in S. agalactiae <SEQ ID 259> which encodes the amino acid sequence <SEQ ID 260>. This protein is predicted to be glutamine ABC transporter, permease protein (glnP). Analysis of this protein sequence reveals the following: TABLE-US-00278 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.92 Transmembrane 27-43 (15-46) INTEGRAL Likelihood = -2.50 Transmembrane 200-216 (196-217) ----- Final Results ----- bacterial membrane --- Certainty = 0.4970(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9619> which encodes amino acid sequence <SEQ ID 9620> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00279 >GP: AAB91000 GB: AE001090 glutamine ABC transporter, permease protein (glnP) [Archaeoglobus fulgidus] Identities = 92/209 (44%), Positives = 129/209 (61%), Gaps = 10/209 (4%) Query: 17 YGVMVTIMISTCVVFFGTIIGVLIALVKRTNLHFLTILANFYVWVFRGTPMVVQIMIAFA 76 - +G VT+ ++ +FFG IIG + L + + ++ YV V RGTP++VQI+I + Sbjct: 21 FGASVTLKLTLISIFFGLIIGTIAGLGRVSKNPLPFAISTAYVEVIRGTPLLVQILIVYF 80 Query: 77 WMHFNNLPTISFGVLDLDFTRLLPGIIIISLNSGAYISEIVRAGIEAVPSGQIEAAYSLG 136- LP I + GII +S+ SGAYI+EIVRAGIE++P GQ+EAA SLG Sbjct: 81 -----GLPAIGINLQPEP-----AGIIALSICSGAYIAEIVRAGIESIPIGQMEAARSLG 130- Query: 137 IRPKNTLRYVILPQAFKNILPALGNEFITIIKDSALLQTIGVMELWNGAQSVVTATYSPV 19- 6 + +RYVI PQAF+NILPALGNEFI ++KDS+LL I ++EL + +V T++ Sbjct: 131 MTYLQAMRYVIFPQAFRNILPALGNEFIALLKDSSLLSVISIVELTRVGRQIVNTTFNAW 19- 0 Query: 197 APLLFAAFYYLMLTTILSALLKQMEKYLG 225 P L A +YLM+T LS L+ +K LG Sbjct: 191 TPFLGVALFYLMMTIPLSRLVAYSQKKLG 219 A related DNA sequence was identified in S. pyogenes <SEQ ID 261> which encodes the amino acid sequence <SEQ ID 262>. Analysis of this protein sequence reveals the following: TABLE-US-00280 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.08 Transmembrane 25-41 (11-44) INTEGRAL Likelihood = -1.91 Transmembrane 202-218 (201-218) ----- Final Results ----- bacterial membrane --- Certainty = 0.4630(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00281 >GP: AAB91000 GB: AE001090 glutamine ABC transporter, permease protein (glnP) [Archaeoglobus fulgidus] Identities = 91/209 (43%), Positives = 138/209 (65%), Gaps = 12/209 (5%) Query: 15 YGVLVTIMISVSVVFFGTLIGVLVTLIKRSHVKPLTWVVNL-YVWIFRGTPMVVQIMIAF 73 - +G VT+ +++ +FFG +IG + L + S PL + ++ YV + RGTP++VQI+I + Sbjct: 21 FGASVTLKLTLISIFFGLIIGTIAGLGRVSK-NPLPFAISTAYVEVIRGTPLLVQILIVY 79 Query: 74 AWMHFNNMPTIGFGVLDLDFSRLLPGIIIISLNSGAYISEIVRAGIEAVPKGQLEAAYSL 133- +P IG ++ GII +S+ SGAYI+EIVRAGIE++P GQ+EAA SL Sbjct: 80 F-----GLPAIG-----INLQPEPAGIIALSICSGAYIAEIVRAGIESIPIGQMEAARSL 129- Query: 134 GIRPQNAMRYVILPQAFKNILPALGNEFITIIKDSALLQTIGVMELWNGAQSVVTATYSP 19- 3 G+ AMRYVI PQAF+NILPALGNEFI ++KDS+LL I ++EL + +V T++ Sbjct: 130 GMTYLQAMRYVIFPQAFRNILPALGNEFIALLKDSSLLSVISIVELTRVGRQIVNTTFNA 18- 9 Query: 194 ISPLLVAAFYYLMVTTVMAQLLAVLERHM 222 +P L A +YLM+T +++L+A ++ + Sbjct: 190 WTPFLGVALFYLMMTIPLSRLVAYSQKKL 218 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00282 Identities = 180/225 (80%), Positives = 208/225 (92%) Query: 3 MNFSFLPQYWSYFNYGVMVTIMISTCVVFFGTIIGVLIALVKRTNLHFLTILANFYVWVF 62 M+ SFLP+YW+YFNYGV+VTIMIS VVFFGT+IGVL+ L+KR+++ LT + N YVW+F Sbjct: 1 MDLSFLPKYWAYFNYGVLVTIMISVSVVFFGTLIGVLVTLIKRSHVKPLTWVVNLYVWIF 60 Query: 63 RGTPMVVQIMIAFAWMHFNNLPTISFGVLDLDFTRLLPGIIIISLNSGAYISEIVRAGIE 122- RGTPMVVQIMIAFAWMHFNN+PTI FGVLDLDF+RLLPGIIIISLNSGAYISEIVRAGIE Sbjct: 61 RGTPMVVQIMIAFAWMHFNNMPTIGFGVLDLDFSRLLPGIIIISLNSGAYISEIVRAGIE 120- Query: 123 AVPSGQIEAAYSLGIRPKNTLRYVILPQAFKNILPALGNEFITIIKDSALLQTIGVMELW 18- 2 AVP GQ+EAAYSLGIRP+N +RYVILPQAFKNILPALGNEFITIIKDSALLQTIGVMELW Sbjct: 121 AVPKGQLEAAYSLGIRPQNAMRYVILPQAFKNILPALGNEFITIIKDSALLQTIGVMELW 18- 0 Query: 183 NGAQSVVTATYSPVAPLLFAAFYYLMLTTILSALLKQMEKYLGKG 227 NGAQSVVTATYSP++PLL AAFYYLM+TT+++ LL +E+++ +G Sbjct: 181 NGAQSVVTATYSPISPLLVAAFYYLMVTTVMAQLLAVLERHMAQG 225 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 79 A DNA sequence (GBSx0079) was identified in S. agalactiae <SEQ ID 263> which encodes the amino acid sequence <SEQ ID 264>. This protein is predicted to be phosphomannomutase (manB). Analysis of this protein sequence reveals the following: TABLE-US-00283 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5400(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9621> which encodes amino acid sequence <SEQ ID 9622> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00284 >GP: BAB04825 GB: AP001510 phosphomannomutase [Bacillus halodurans] Identities = 239/548 (43%), Positives = 344/548 (62%), Gaps = 14/548 (2%) Query: 4 MNYKEIYQEWLENDSLGKDIKSDLEAIKGDESEIQDRFYKTLEFGTAGLRGKLGAGTNRN 63 M++++ Y++W + L ++K LEAI GD +++D FYK LEFGT G+RG++G G NRN Sbjct: 1 MSWRQRYEKWKGFNELELELKQSLEAIGGDEQQLEDCFYKNLEFGTGGMRGEIGPGPNRM 60 Query: 64 NTYMVGKAAQALANTIIDHGPEAIARGIAVSYDVRYQSKEFAELTCSIMAANGIKSYIYK 123- NTY + KA++ A +++ G A+G+ ++YD R++S EFA + +GIK+Y+++ Sbjct: 61 NTYTIRKASEGFARYLLEQGEHVKAQGVVIAYDSRHKSPEFAREAALTIGKHGIKAYLFE 120- Query: 124 GIRPTPMCSYAIRALGCVSGVMITASHNPQAYNGYKAYWKEGSQILDDIADQIANHMDAI 18- 3 +RPTP S+A+R LG G++ITASHNP YNG+K Y +G Q+ + A+++ ++ I Sbjct: 121 ELRPTPELSFAVRKLGAAGGIVITASHNPPEYNGFKVYGSDGCQLPPEPANRLVKFVNEI 18- 0 Query: 184 TDYQQIKQIPFEEALASGSASYIDESIEEAYKKEVLGLTINDTNID---KSVRVVYTPLN 24- 0 D I E +G+ I E ++ AY + + + +N ++ K VR+V+TPL+ Sbjct: 181 EDELVIPVGDERELKENGTLEMIGEEVDVAYHEALKTIIVNPELLEASAKDVRIVFTPLH 24- 0 Query: 241 GVGNLPVREVLRRRGFENVYVVPEQEMPDPDFTTVGYPNPEVPKAFAYSESLGKSVDADI 30- 0 G NLPVR VL GFENV VV EQE+PDP F+TV PNPE AFA + GK +AD+ Sbjct: 241 GTANLPVRRVLEAVGFENVTVVKEQELPDPQFSTVKAPNPEEHAAFALAIEYGKKTEADV 30- 0 Query: 301 LLATDPDCDRVALEVKDSKGEYIFLNGNKIGALLSYYIFSQRCALGNLPHHPVLVKSIVT 36- 0 L+ATDPD DRV + V++ GEYI L GN+ G L+ +Y+ SQ+ G LP + + +K+IVT Sbjct: 301 LIATDPDADRVGVAVQNQAGEYIVLTGNQTGGLMLHYLLSQKKEKGQLPVNGIALKTIVT 36- 0 Query: 361 GDLSKVIADKYNIETVETLTGFKNICGKANEYDISKDKTYLFGYEESIGFCYGTFVRDKD 42- 0 + + IA+ + I V+TLTGFK I K EY + S + +LFGYEES G+ G FVRDKD Sbjct: 361 SEFGRAIAEDFGIPMVDTLTGFKFIGEKIKEYEQSGEHQFLFGYEESYGYLIGDFVRDKD 42- 0 Query: 421 AVSASMMVVEMTAYYKERGQTLLDVLQTIYDKFGYYNERQFSLELEGAEGQERISRIMED 48- 0 AV A ++ EMTAYYK RG TL D L ++D++GYY E S+ L+G G E+I ++ Sbjct: 421 AVQACLLAAEMTAYYKSRGMTLYDGLLELFDRYGYYREGLTSITLKGKVGVEKIQHVLSQ 48- 0 Query: 481 FRQDPILQVGEMTLENSIDFKDGYK-----------DFPKQNCLKYYFNEGSWYALRPSG 52- 9 FRQ P QV + + D++ K P N LKY +GSW+ LRPSG Sbjct: 481 FRQSPPKQVNDQQVVVIEDYQTKEKVSVKERTVEAITLPTSNVLKYMLEDGSWFCLRPSG 54- 0 Query: 530 TEPKIKCY 537 TEPK+K Y Sbjct: 541 TEPKLKIY 548 A related DNA sequence was identified in S. pyogenes <SEQ ID 265> which encodes the amino acid sequence <SEQ ID 266>. Analysis of this protein sequence reveals the following: TABLE-US-00285 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5487(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00286 Identities = 470/564 (83%), Positives = 517/564 (91%) Query: 1 MSHMNYKEIYQEWLENDSLGKDIKSDLEAIKGDESEIQDRFYKTLEFGTAGLRGKLGAGT 60 MS+M Y E+YQEWL N+ L DIK+DL AIK +E+EIQDRFYKTLEFGTAGLRGKLGAGT Sbjct: 1 MSNMTYNEVYQEWLHNNDLSDDIKADLAAIKDNEAEIQDRFYKTLEFGTAGLRGKLGAGT 60 Query: 61 NRMNTYMVGKAAQALANTIIDHGPEAIARGIAVSYDVRYQSKEFAELTCSIMAANGIKSY 120- NRMNTYMVGKAAQALANTIIDHGPEA+ +GIAVSYDVRYQS+ FAELTCSIMAANGIK+Y Sbjct: 61 NRMNTYMVGKAAQALANTIIDHGPEAVKKGIAVSYDVRYQSRTFAELTCSIMAANGIKAY 120- Query: 121 IYKGIRPTPMCSYAIRALGCVSGVMITASHNPQAYNGYKAYWKEGSQILDDIADQIANHM 18- 0 +YKGIRPTPMCSYAIRALGC+SGVMITASHNPQAYNGYKAYW+EGSQILDDIADQIA HM Sbjct: 121 LYKGIRPTPMCSYAIRALGCISGVMITASHNPQAYNGYKAYWQEGSQILDDIADQIAQHM 18- 0 Query: 181 DAITDYQQIKQIPFEEALASGSASYIDESIEEAYKKEVLGLTINDTNIDKSVRVVYTPLN 24- 0 A+T YQ+IKQ+PFE+AL SG +YIDESIEEAYKKEVLGLTINDT+IDKSVRVVYTPLN Sbjct: 181 AALTQYQEIKQMPFEKALDSGLVTYIDESIEEAYKKEVLGLTINDTDIDKSVRVVYTPLN 24- 0 Query: 241 GVGNLPVREVLRRRGFENVYVVPEQEMPDPDFTTVGYPNPEVPKAFAYSESLGKSVDADI 30- 0 GVGNLPVREVLRRRGFENVYVVPEQEMPDPDFTTVGYPNPEVPK FAYSE LGK+VDADI Sbjct: 241 GVGNLPVREVLRRRGFENVYVVPEQEMPDPDFTTVGYPNPEVPKTFAYSEKLGKAVDADI 30- 0 Query: 301 LLATDPDCDRVALEVKDSKGEYIFLNGNKIGALLSYYIFSQRCALGNLPHHPVLVKSIVT 36- 0 L+ATDPDCDRVALEVK++ G+Y+FLNGNKIGALLSYYIFSQR LGNLP +PVLVKSIVT Sbjct: 301 LIATDPDCDRVALEVKNAVGDYVFLNGNKIGALLSYYIFSQRFDLGNLPANPVLVKSIVT 36- 0 Query: 361 GDLSKVIADKYNIETVETLTGFKNICGKANEYDISKDKTYLFGYEESIGFCYGTFVRDKD 42- 0 GDLS+ IA Y IETVETLTGFKNICGKANEYD++K K YLFGYEESIGFCYGTFVRDKD Sbjct: 361 GDLSRAIASHYGIETVETLTGFKNICGKANEYDVTKQKNYLFGYEESIGFCYGTFVRDKD 42- 0 Query: 421 AVSASMMVVEMTAYYKERGQTLLDVLQTIYDKFGYYNERQFSLELEGAEGQERISRIMED 48- 0 AVSASMM+VEM AYYK++GQ LLDVLQTIY FGYYNERQ +LELEG EGQ+RI+RIMED Sbjct: 421 AVSASMMIVEMAAYYKKKGQNLLDVLQTIYATFGYYNERQIALELEGIEGQKRIARIMED 48- 0 Query: 481 FRQDPILQVGEMTLENSIDFKDGYKDFPKQNCLKYYFNEGSWYALRPSGTEPKIKCYLYT 54- 0 FRQ PI V EM L+ +IDF DGY+DFPKQNCLK+Y ++GSWYALRPSGTEPKIK YLYT Sbjct: 481 FRQTPIASVAEMALDKTIDFIDGYQDFPKQNCLKFYLDDGSWYALRPSGTEPKIKFYLYT 54- 0 Query: 541 IGCTEADSLSKLNAIESACRAKMN 564 IG T+ +S +KL+AIE+ACR K+N Sbjct: 541 IGQTQENSATKLDAIEAACRTKIN 564 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 80 A DNA sequence (GBSx0080) was identified in S. agalactiae <SEQ ID 267> which encodes the amino acid sequence <SEQ ID 268>. This protein is predicted to be methylenetetrahydrofolate dehydrogenase (folD). Analysis of this protein sequence reveals the following:

TABLE-US-00287 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4672(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00288 >GP: AAC44612 GB: U58210 tetrahydrofolate dehydrogenase/cyclohydrolase [Streptococcus thermophilus] Identities = 209/282 (74%), Positives = 248/282 (87%) Query: 1 MTELIDGKALSQKMQAELGRKVERLKEQHGIIPGLAVILVGDNPASQVYVRNKERSALEA 60 M ++DGKAL+ MQ +L KV RLKE+ I+PGL VI+VG+NPASQVYVRNKER+A +A Sbjct: 1 MAIIMDGKALAVNMQEQLQEKVARLKEKEWIVPGLVVIMVGENPASQVYVRNKERAAKKA 60 Query: 61 GFKSETLRLSESISQEELIDIIHQYNEDKSIHGILVQLPLPQHINDKKIILAIDPKKDVD 120- GF S+T+ LSESIS+EELI++I +YN++ HGILVQLPLP HIN+ +I+LAIDPKKDVD Sbjct: 61 GFHSKTVNLSESISEEELIEVIEKYNQNPLFHGILVQLPLPNHINEMRILLAIDPKKDVD 120- Query: 121 GFHPMNTGHLWSGRPMMVPCTPAGIMEMFREYHVDLEGKHAVIIGRSNIVGKPMAQLLLD 18- 0 GFHPMNTG+LW+GRP MVPCTPAGIME+ REY+V+LEGK AVIIGRSNIVGKPMAQLLL+ Sbjct: 121 GFHPMNTGNLWNGRPQMVPCTPAGIMEILREYNVELEGKTAVIIGRSNIVGKPMAQLLLE 18- 0 Query: 181 KNATVTLTHSRTRNLSEVTKEADILIVAIGQGHFVTKDFVKEGAVVIDVGMNRDENGKLI 24- 0 KNATVTLTHSRT +L++V +AD+LIVAIG+ FVT++FVKEGAVVIDVG+NRDE GKL Sbjct: 181 KNATVTLTHSRTPHLAKVCNKADVLIVAIGRAKFVTEEFVKEGAVVIDVGINRDEEGKLC 24- 0 Query: 241 GDVVFEQVAEVASMITPVPGGVGPMTITMLLEQTYQAALRSV 282 GDV F+QV E SMITPVPGGVGPMTITML+EQTYQAALRS+ Sbjct: 241 GDVDFDQVKEKVSMITPVPGGVGPMTITMLMEQTYQAALRSL 282 A related DNA sequence was identified in S. pyogenes <SEQ ID 269> which encodes the amino acid sequence <SEQ ID 270>. Analysis of this protein sequence reveals the following: TABLE-US-00289 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3368(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00290 Identities = 230/281 (81%), Positives = 257/281 (90%) Query: 1 MTELIDGKALSQKMQAELGRKVERLKEQHGIIPGLAVILVGDNPASQVYVRNKERSALEA 60 MTELIDGKAL+QKMQ EL KV LK++ GI+PGLAVILVGD+PASQVYVRNKER+AL Sbjct: 3 MTELIDGKALAQKMQQELAAKVNNLKQKKGIVPGLAVILVGDDPASQVYVRNKERAALTV 62 Query: 61 GFKSETLRLSESISQEELIDIIHQYNEDKSIHGILVQLPLPQHINDKKIILAIDPKKDVD 120- GFKSET+RLSE I QEELI +I +YN D +IHGILVQLPLP HINDKKIILAIDPKKDVD Sbjct: 63 GFKSETVRLSEFICQEELIAVIERYNADNTIHGILVQLPLPNHINDKKIILAIDPKKDVD 122- Query: 121 GFHPMNTGHLWSGRPMMVPCTPAGIMEMFREYHVDLEGKHAVIIGRSNIVGKPMAQLLLD 18- 0 GFHPMNTGHLWSGRP+MVPCTP+GIME+ REY+V+LEGKHAVIIGRSNIVGKPMAQLLLD Sbjct: 123 GFHPMNTGHLWSGRPLMVPCTPSGIMELLREYNVNLEGKHAVIIGRSNIVGKPMAQLLLD 18- 2 Query: 181 KNATVTLTHSRTRNLSEVTKEADILIVAIGQGHFVTKDFVKEGAVVIDVGMNRDENGKLI 24- 0 KNATVTLTHSRTR L EV + AD+LIVAIGQGHF+TK ++K+GA+VIDVGMNRD+NGKLI Sbjct: 183 KNATVTLTHSRTRQLEEVCRCADVLIVAIGQGHFITKQYIKDGAIVIDVGMNRDDNGKLI 24- 2 Query: 241 GDVVFEQVAEVASMITPVPGGVGPMTITMLLEQTYQAALRS 281 GDV F++VAEVA+ ITPVPGGVGPMTI MLLEQTYQ+ALRS Sbjct: 243 GDVAFDEVAEVAAKITPVPGGVGPMTIAMLLEQTYQSALRS 283 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 81 A DNA sequence (GBSx0081) was identified in S. agalactiae <SEQ ID 271> which encodes the amino acid sequence <SEQ ID 272>. Analysis of this protein sequence reveals the following: TABLE-US-00291 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.24 Transmembrane 39-55 (38-58) ----- Final Results ----- bacterial membrane --- Certainty = 0.2296(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9623> which encodes amino acid sequence <SEQ ID 9624> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00292 >GP:AAC44613 GB:U58210 orf1091 [Streptococcus thermophilus] Identities = 149/277 (53%), Positives = 191/277 (68%) Query: 1 MIVGEQEARALIKPRPKSSHKGDYGSVLLIGGFYPYGGAIIMAALACVKTGAGLVTVATQ 60 M V + R +I+PR + SHKG YG VLL+GG YPYGGAIIMAA+ACV +GAGLVTVAT Sbjct: 1 MKVDDDLVRQVIRPRLRGSHKGSYGRVLLVGGLYPYGGAIIMAAIACVNSGAGLVTVATD 60 Query: 61 SCNIPSLHSQLPEVMAFDSDDYKWLEKSIVQSDVIVIGPGLGVSESSRKILNQTMEKIQS 120- NI +LH+ LPE MAFD + + + +DVI+IG GLG E++ L + I+S Sbjct: 61 RENIIALHAHLPEAMAFDLRETERFLDKLRAADVILIGSGLGEEETADWALELVLANIRS 120- Query: 121 HQSVILDGSALTLLSEGAFPQTKAKNLVLTPHQKEWERLSGIAVSQQTKENTQTALKSFP 18- 0 +Q++++DGSAL LL++ +L+LTPHQKEWERLSG+A+S+Q+ NTQ AL+ F Sbjct: 121 NQNLVVDGSALNLLAKKNQSSLPKCHLILTPHQKEWERLSGLAISEQSVSNTQRALEEFQ 18- 0 Query: 181 KGTILVAKSSHTRIFQDLDEKEIIVGGPYQATGGMGDTLCGMIAGMLAQFKEASPLDKVS 24- 0 GTILVAKS T ++Q + + VGGPYQATGGMGDTL GM+AG LAQF V Sbjct: 181 SGTILVAKSHKTAVYQGAEVTHLEVGGPYQATGGMGDTLAGMVAGFLAQFASTDSYKAVI 24- 0 Query: 241 VGVYLHSAIAQGLSKEAYVVLPTTISDEIPKEMARLS 277 V +LHSAIA +++ AYVVLPT IS IP M +LS Sbjct: 241 VATWLHSAIADNIAENAYVVLPTRISKAIPSWMKKLS 277 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 272 (GBS413) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 79 (lane 2; MW 34.2 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 171 (lane 7; MW 59 kDa). GBS413-GST was purified as shown in FIG. 218, lane 12. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 82 A DNA sequence (GBSx0082) was identified in S. agalactiae <SEQ ID 273> which encodes the amino acid sequence <SEQ ID 274>. This protein is predicted to be Exonuclease VII large subunit (xseA). Analysis of this protein sequence reveals the following: TABLE-US-00293 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3172(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00294 >GP:CAB14361 GB:Z99116 similar to exodeoxyribonuclease VII (large subunit) [Bacillus subtilis] Identities = 193/446 (43%), Positives = 283/446 (63%), Gaps = 10/446 (2%) Query: 4 YLSVSTLTKYLKLKFDKDPYLERVYLTGQVSNFR-RRPNHQYFSLKDDKSVIQATMWSGH 62 Y++VS LTKY+K KFD DP+LE +++ G++SN + H YF+LK+ K +Q+ M++ Sbjct: 6 YVTVSALTKYIKRKFDVDPHLENIWIKGELSNVKIHTRGHIYFTLKERKGRMQSVMFARQ 65 Query: 63 FKKLGFELEEGMKVNVVGRVQLYEPSGSYSIIVEKAEPDGIGALAIQFEQLKKKLSQAGY 122- ++L F+ E GMKV V G + +YEPSG+Y + ++ +PDG+GAL + +E+LKKKL+ G Sbjct: 66 SERLPFKPENGMKVLVRGGISVYEPSGNYQLYAKEMQPDGVGALYLAYEELKKKLAGEGL 125- Query: 123 FDDRHKQLIPQFVRKIGVVTSPSGAVIRDIITTVSRRFPGVEILLFPTKVQGEGAAQEIA 18- 2 FDDR+K+ IP F IGVVTSP+GA +RD+ITT+ RR+P V++++ P VQGE A++ I Sbjct: 126 FDDRYKKQIPAFPATIGVVTSPTGAAVRDVITTLKRRYPLVKVIVLPALVQGENASRSIV 18- 5 Query: 183 QTIALANEKKDLDLLIVGRGGGSIEDLWAFNEECVVEAIFESRLPVISSVGHETDTTLAD 24- 2 I ANEK+ D+LIVGRGGGSIE+LWAFNEE V AIF S +P+IS+VGHETD T++D Sbjct: 186 TRIEEANEKEICDVLIVGRGGGSIEELWAFNEEIVARAIFASNIPIISAVGHETDFTISD 24- 5 Query: 243 FVADRRAATPTAAAELATPVTKIDILSWITERENRMYQSSLRLIRTKEERLQKSKQSVIF 30- 2 FVAD RAATPT AAE+A P T D++ E RM ++ + + ++ R+Q + S F Sbjct: 246 FVADIRAATPTGAAEIAVPHT-TDLIERTKTAEVRMTRAMQQHLGQEKGRIQTLQSSYAF 30- 4 Query: 303 RQPERLYDGFLQKLD----NLNQQLTYSMRDKLQTVRQKQGLLHQKLQGIDLKQRIHIYQ 35- 8 R P+RLY Q+ D QLT + K + + ++ L LKQ YQ Sbjct: 305 RFPKRLYAQKEQQFDLAYQQFQAQLTALLDRKSRQLERETYRLEALHPHEQLKQARTRYQ 36- 4 Query: 359 ERVVQSRRLLSSTMTSQYDSKLARFEKAQDALISLDSSRIVARGYAIIEKNHTLVSTTNG 41- 8 E+ Q R+ M Q ++F+ L +L +++ RGY++ K L+ + + Sbjct: 365 EQTNQLRK----NMNIQMKQLHSQFQTVLGKLNALSPLQVMERGYSLAYKEDKLIKSVSQ 42- 0 Query: 419 INEGDHLQVKMQDGLLEVEVKDVRQE 444 I E D L++K++DG+L EV + R E Sbjct: 421 IEEQDRLEIKLKDGVLTCEVLEKRGE 446 A related DNA sequence was identified in S. pyogenes <SEQ ID 275> which encodes the amino acid sequence <SEQ ID 276>. Analysis of this protein sequence reveals the following: TABLE-US-00295 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3275(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00296 Identities = 321/446 (71%), Positives = 386/446 (85%) Query: 1 MSDYLSVSTLTKYLKLKFDKDPYLERVYLTGQVSNFRRRPNHQYFSLKDDKSVIQATMWS 60 M+DYL+V+ LTKYLKLKFD+DPYLERVYLTGQVSNFR+RP HQYFSLKD+ +VIQATMW+ Sbjct: 6 MADYLTVTHLTKYLKLKFDRDPYLERVYLTGQVSNFRKRPTHQYFSLKDESAVIQATMWA 65 Query: 61 GHFKKLGFELEEGMKVNVVGRVQLYEPSGSYSIIVEKAEPDGIGALAIQFEQLKKKLSQA 120- G +KKLGF+LEEGMK+NV+GRVQLYEPSGSYSI++EKAEPDGIGALA+QFEQLKKKL+ Sbjct: 66 GVYKKLGFDLEEGMKINVIGRVQLYEPSGSYSIVIEKAEPDGIGALALQFEQLKKKLTAE 125- Query: 121 GYFDDRHKQLIPQFVRKIGVVTSPSGAVIRDIITTVSRRFPGVEILLFPTKVQGEGAAQE 18- 0 GYF+ +HKQ +PQFV KIGV+TSPSGAVIRDIITTVSRRFPGVEILLFPTKVQG+GAAQE Sbjct: 126 GYFEQKHKQPLPQFVSKIGVITSPSGAVIRDIITTVSRRFPGVEILLFPTKVQGDGAAQE 18- 5 Query: 181 IAQTIALANEKKDLDLLIVGRGGGSIEDLWAFNEECVVEAIFESRLPVISSVGHETDTTL 24- 0 + I AN+++DLDLLIVGRGGGSIEDLWAFNEE VV+AIFES+LPVISSVGHETDTTL Sbjct: 186 VVANIRRANQREDLDLLIVGRGGGSIEDLWAFNEEIVVQAIFESQLPVISSVGHETDTTL 24- 5 Query: 241 ADFVADRRAATPTAAAELATPVTKIDILSWITERENRMYQSSLRLIRTKEERLQKSKQSV 30- 0 ADFVADRRAATPTAAAELATP+TK D++SWI ER+NR YQ+ LR I+ ++E + K QSV Sbjct: 246 ADFVADRRAATPTAAAELATPITKTDLMSWIVERQNRSYQACLRRIKQRQEWVDKLSQSV 30- 5 Query: 301 IFRQPERLYDGFLQKLDNLNQQLTYSMRDKLQTVRQKQGLLHQKLQGIDLKQRIHIYQER 36- 0 IFRQPERLYD +LQK+D L+ L +M+D+L + ++ + L L L+ +I YQ+R Sbjct: 306 IFRQPERLYDAYLQKIDRLSMTLMNTMKDRLSSAKENKVQLDHALANSQLQTKIERYQDR 36- 5 Query: 361 VVQSRRLLSSTMTSQYDSKLARFEKAQDALISLDSSRIVARGYAIIEKNHTLVSTTNGIN 42- 0 V ++RLL + M SQYDS+LARFEKAQDAL+SLD+SRI+ARGYA+IEKN LV++ + I Sbjct: 366 VATAKRLLMANMASQYDSQLARFEKAQDALLSLDASRIIARGYAMIEKNQALVASVSQIT 42- 5 Query: 421 EGDHLQVKMQDGLLEVEVKDVRQENI 446 +GD L +KM+DG L+VEVKDV+ ENI Sbjct: 426 KGDQLTIKMRDGQLDVEVKDVKNENI 451 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 83 A DNA sequence (GBSx0083) was identified in S. agalactiae <SEQ ID 277> which encodes the amino acid sequence <SEQ ID 278>. Analysis of this protein sequence reveals the following: TABLE-US-00297 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2913(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00298 >GP:AAG07429 GB:AE004821 exodeoxyribonuclease VII small subunit [Pseudomonas aeruginosa] Identities = 26/66 (39%), Positives = 51/66 (76%), Gaps = 2/66 (3%) Query: 1 MSDKKT--FEENLQELETIVSRLETGDVALEDAIAEFQKGMLISKELQRTLKEAEETLVK 58 M+ KKT FE++L EL+T+V RLE+G+++LE+++ F++G+ +++E Q +L +AE+ + Sbjct: 1 MARKKTLDFEQSLTELQTLVERLESGELSLEESLGAFEQGIRLTRECQTSLSQAEQKVQI 60 Query: 59 VMQADG 64 +++ DG Sbjct: 61 LLERDG 66 A related DNA sequence was identified in S. pyogenes <SEQ ID 279> which encodes the amino acid sequence <SEQ ID 280>. Analysis of this protein sequence reveals the following: TABLE-US-00299 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2796(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00300 Identities = 55/70 (78%), Positives = 65/70 (92%) Query: 1 MSDKKTFEENLQELETIVSRLETGDVALEDAIAEFQKGMLISKELQRTLKEAEETLVKVM 60 MS KTFEENLQ+LETIV++LE GDV LE+AI+EFQKGML+SKELQ+TL+ AE+TLVKVM Sbjct: 1 MSKTKTFEENLQDLETIVNKLENGDVPLEEAISEFQKGMLLSKELQKTLQAAEKTLVKVM 60 Query: 61 QADGTEVEMD 70 QADGTEV+MD Sbjct: 61 QADGTEVDMD 70 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 84 A DNA sequence (GBSx0084) was identified in S. agalactiae <SEQ ID 281> which encodes the amino acid sequence <SEQ ID 282>. Analysis of this protein sequence reveals the following: TABLE-US-00301 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2614(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00302 >GP: BAA25265 GB: AB003187 farnesyl diphosphate synthase [Micrococcus luteus] Identities = 126/258 (48%), Positives = 175/258 (66%), Gaps = 2/258 (0%) Query: 27 LIKAILYSVDGGGKRIRPRILLEILEGFGVELIDGHYDVAAALEMIHTGSLIHDDLPAMD 86 - L +AI YS+ GGKRIRP ++L L+ G DG ALEMIHT SLIHDDLPAMD Sbjct: 31 LHEAINYSLSAGGKRIRPLLVLTTLDSLGGNAHDG-LPFGIALEMIHTYSLIHDDLPAMD 89 Query: 87 NDDFRRGRLTNHKKFDEATAVLAGDSLFLDPFDLVVKAGFKADVTVRLIELLSMSAGSFG 146- NDD+RRG+LTNHK+FDEATA+LAGD+L D F ++ A++ + LI LLS ++GS G Sbjct: 90 NDDYRRGKLTNHKRFDEATAILAGDALLTDAFQCILNTQLNAEIKLSLINLLSTASGSNG 149- Query: 147 MVGGQMLDMKGENKVLSIDDLSLIHINKTGRLLAYPFVAAGILAEKSEEVKGKLHQAGLL 20- 6 MV GQMLDM+GE+K L++++L IHI+KTG L+ V+AGI+ ++ +L+ G Sbjct: 150 MVYGQMLDMQGEHKTLTLNELERIHIHKTGELIRAAIVSAGIIMNFNDAQIEQLNIIGKN 20- 9 Query: 207 IGHAFQVRDDILDVTASFEELGKTPNKDIVAEKTTYPNLLGLDKSQEILDDTLKKAQAIF 26- 6 +G FQ++DDILDV SFE +GKT D+ +K+TY +LLGL+ S+++L+D L + Sbjct: 210 VGLMFQIKDDILDVEGSFENIGKTVGSDLNNDKSTYVSLLGLEASKQLLNDKLTETYDAL 26- 9 Query: 267 QNLEKKANFNARKIIDII 284 + L+ N N + +I I Sbjct: 270 KTLQ-PINDNLKTLITYI 286 A related DNA sequence was identified in S. pyogenes <SEQ ID 283> which encodes the amino acid sequence <SEQ ID 284>. Analysis of this protein sequence reveals the following: TABLE-US-00303 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3887(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00304 Identities = 192/289 (66%), Positives = 237/289 (81%) Query: 2 MVTIEKIDEAIHRYYKQTHSVVSPDLIKAILYSVDGGGKRIRPRILLEILEGFGVELIDG 61 M + +IDEAI RYYK T + VS +LI AILYSVD GGKRIRP ILLE++EGFGV L + Sbjct: 1 MDKLARIDEAIRRYYKTTSNGVSEELIDAILYSVDSGGKRIRPLILLEMIEGFGVSLQNA 60 Query: 62 HYDVAAALEMIHTGSLIHDDLPAMDNDDFRRGRLTNHKKFDEATAVLAGDSLFLDPFDLV 121- H+D+AAALEMIHTGSLIHDDLPAMDNDD+RRGRLTNHK+F EATA+LAGDSLFLDPF L+ Sbjct: 61 HFDLAAALEMIHTGSLIHDDLPAMDNDDYRRGRLTNHKQFGEATAILAGDSLFLDPFGLI 120- Query: 122 VKAGFKADVTVRLIELLSMSAGSFGMVGGQMLDMKGENKVLSIDDLSLIHINKTGRLLAY 18- 1 +A ++V V LI+ LS+++G+FGMVGGQMLDMKGEN+ LS+ LSLIH+NKTG+LLA+ Sbjct: 121 AQAELNSEVKVALIQELSLASGTFGMVGGQMLDMKGENQALSLPQLSLIHLNKTGKLLAF 18- 0 Query: 182 PFVAAGILAEKSEEVKGKLHQAGLLIGHAFQVRDDILDVTASFEELGKTPNKDIVAEKTT 24- 1 PF AA ++ E++ V+ +L QAG+LIGHAFQ+RDDILDVTASFE+LGKTP KD+ AEK T Sbjct: 181 PFKAAALITEQAMTVRQQLEQAGMLIGHAFQIRDDILDVTASFEDLGKTPKKDLFAEKAT 24- 0 Query: 242 YPNLLGLDKSQEILDDTLKKAQAIFQNLEKKANFNARKIIDIIEGLRLN 290 YP+LLGL+ S ++L ++L +A IFQ LE F + I +IEGLRLN Sbjct: 241 YPSLLGLEASYQLLTESLDQALTIFQTLESDVGFKPQIITKLIEGLRLN 289 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 85 A DNA sequence (GBSx0085) was identified in S. agalactiae <SEQ ID 285> which encodes the amino acid sequence <SEQ ID 286>. This protein is predicted to be hemolysin-like protein (tly). Analysis of this protein sequence reveals the following:

TABLE-US-00305 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.75 Transmembrane 152-168 (151-168) ----- Final Results ----- bacterial membrane --- Certainty = 0.1298(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00306 >GP: BAB06497 GB: AP001516 hemolysin-like protein [Bacillus halodurans] Identities = 162/270 (60%), Positives = 202/270 (74%), Gaps = 3/270 (1%) Query: 3 KERVDVLAYKQGLFDTREQAKRGVMAGMVINVINGERYDKPGEKVADDTELKLKGEKLKY 62 KERVDVL ++GL +TRE+AKR +MAG+V + ER DKPG KV DT L +KGE L Y Sbjct: 4 KERVDVLLVERGLMETREKAKRSIMAGLVFS--GHERVDKPGLKVDRDTPLSVKGEVLPY 61 Query: 63 VSRGGLKLEKALQVFEISVADKLTIDIGASTGGFTDVMLQSGARLVYAVDVGTNQLVWKL 122- VSRGGLKLEKA++ F++ + D++ +DIGASTGGFTD LQ+GA VYAVDVG NQL WKL Sbjct: 62 VSRGGLKLEKAIRAFDLHLTDRVVLDIGASTGGFTDCALQNGATFVYAVDVGYNQLAWKL 121- Query: 123 RQDHRVRSMEQYNFRYAQKEDFKEGLPEFASIDVSFISLNLILPALKEILVDGGQVVALI 18- 2 RQD RV ME+ NFRY + E + GLP A+IDVSFISL LILP LK +L++ VVAL+ Sbjct: 122 RQDERVVVMERTNFRYLKPEVLERGLPNMATIDVSFISLKLILPVLKTMLLENSDVVALV 18- 1 Query: 183 KPQFEAGREQIGKNGIVKDKLVHEKVLTTVTNFTKDYGYTVKHLDFSPIQGGHGNIEFLM 24- 2 KPQFEAGRE++GK GIV+DK VH+KVL+T+ F GY V LDFSPI GG GNIEFL+ Sbjct: 182 KPQFEAGREEVGKKGIVRDKSVHQKVLSTIVEFALKEGYAVGGLDFSPITGGEGNIEFLL 24- 1 Query: 243 HLQKCQDPQNLV-LDQIQDVIEKAHKEFKK 271 HL +D ++ + + I+D +E+AH E KK Sbjct: 242 HLMWRKDKESFISQEMIRDTVERAHLELKK 271 A related DNA sequence was identified in S. pyogenes <SEQ ID 287> which encodes the amino acid sequence <SEQ ID 288>. Analysis of this protein sequence reveals the following: TABLE-US-00307 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.92 Transmembrane 150-166 (149-168) ----- Final Results ----- bacterial membrane --- Certainty = 0.2168(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00308 >GP: BAB06497 GB: AP001516 hemolysin-like protein [Bacillus halodurans] Identities = 156/270 (57%), Positives = 196/270 (71%), Gaps = 3/270 (1%) Query: 3 KERVDVLAYKQGLFETREQAKRGVMAGLVVSVINGQRYDKPGDKIDDGTELKLKGEKLKY 62 KERVDVL ++GL ETRE+AKR +MAGLV S +R DKPG K+D T L +KGE L Y Sbjct: 4 KERVDVLLVERGLMETREKAKRSIMAGLVFS--GHERVDKPGLKVDRDTPLSVKGEVLPY 61 Query: 63 VSRGGLKLEKGLHVFGVSVANQIGIDIGASTGGFTDVMLQDGAKLVYAVDVGTNQLVWKL 122- VSRGGLKLEK + F + + +++ +DIGASTGGFTD LQ+GA VYAVDVG NQL WKL Sbjct: 62 VSRGGLKLEKAIRAFDLHLTDRVVLDIGASTGGFTDCALQNGATFVYAVDVGYNQLAWKL 121- Query: 123 RQDPRVRSMEQYNFRYAQPEDFNEGQPVFASIDVSFISLSLILPALHNVLSDQGQVIALI 18- 2 RQD RV ME+ NFRY +PE G P A+IDVSFISL LILP L +L + V+AL+ Sbjct: 122 RQDERVVVMERTNFRYLKPEVLERGLPNMATIDVSFISLKLILPVLKTMLLENSDVVALV 18- 1 Query: 183 KPQFEAGREQIGKKGIVKDKQIHEKVIQKVMDFASGYGFTVKGLDFSPIQGGHGNIEFLA 24- 2 KPQFEAGRE++GKKGIV+DK +H+KV+ +++FA G+ V GLDFSPI GG GNIEFL Sbjct: 182 KPQFEAGREEVGKKGIVRDKSVHQKVLSTIVEFALKEGYAVGGLDFSPITGGEGNIEFLL 24- 1 Query: 243 HLAKSQTPET-LAPHLIQKVVAKAHKEFEK 271 HL + E+ ++ +I+ V +AH E +K Sbjct: 242 HLMWRKDKESFISQEMIRDTVERAHLELKK 271 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00309 Identities = 214/275 (77%), Positives = 238/275 (85%) Query: 1 MAKERVDVLAYKQGLFDTREQAKRGVMAGMVINVINGERYDKPGEKVADDTELKLKGEKL 60 M KERVDVLAYKQGLF+TREQAKRGVMAG+V++VING+RYDKPG+K+ D TELKLKGEKL Sbjct: 1 MPKERVDVLAYKQGLFETREQAKRGVMAGLVVSVINGQRYDKPGDKIDDGTELKLKGEKL 60 Query: 61 KYVSRGGLKLEKALQVFEISVADKLTIDIGASTGGFTDVMLQSGARLVYAVDVGTNQLVW 120- KYVSRGGLKLEK L VF +SVA+++ IDIGASTGGFTDVMLQ GA+LVYAVDVGTNQLVW Sbjct: 61 KYVSRGGLKLEKGLHVFGVSVANQIGIDIGASTGGFTDVMLQDGAKLVYAVDVGTNQLVW 120- Query: 121 KLRQDHRVRSMEQYNFRYAQKEDFKEGLPEFASIDVSFISLNLILPALKEILVDGGQVVA 18- 0 KLRQD RVRSMEQYNFRYAQ EDF EG P FASIDVSFISL+LILPAL +L D GQV+A Sbjct: 121 KLRQDPRVRSMEQYNFRYAQPEDFNEGQPVFASIDVSFISLSLILPALHNVLSDQGQVIA 18- 0 Query: 181 LIKPQFEAGREQIGKNGIVKDKLVHEKVLTTVTNFTKDYGYTVKHLDFSPIQGGHGNIEF 24- 0 LIKPQFEAGREQIGK GIVKDK +HEKV+ V +F YG+TVK LDFSPIQGGHGNIEF Sbjct: 181 LIKPQFEAGREQIGKKGIVKDKQIHEKVIQKVMDFASGYGFTVKGLDFSPIQGGHGNIEF 24- 0 Query: 241 LMHLQKCQDPQNLVLDQIQDVIEKAHKEFKKNEEE 275 L HL K Q P+ L IQ V+ KAHKEF+K+E+E Sbjct: 241 LAHLAKSQTPETLAPHLIQKVVAKAHKEFEKHEKE 275 SEQ ID 286 (GBS310) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 57 (lane 3; MW 34 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 61 (lane 4; MW 58.8 kDa). The GBS310-GST fusion product was purified (FIG. 210, lane 10) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 282), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 86 A DNA sequence (GBSx0086) was identified in S. agalactiae <SEQ ID 289> which encodes the amino acid sequence <SEQ ID 290>. Analysis of this protein sequence reveals the following: TABLE-US-00310 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1966(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00311 >GP: CAA09426 GB: AJ010954 arginine repressor [Bacillus stearothermophilus] Identities = 49/153 (32%), Positives = 84/153 (54%), Gaps = 4/153 (2%) Query: 1 MKKSERLNLIKQIVLNHAVETQHELLRRLEAYGVTLTQATISRDMNEIGIIKVPSAKGRY 60 M K +R I++I++NH +ETQ EL+ L+ G +TQAT+SRD+ E+ ++KVP A GRY Sbjct: 1 MNKGQRHIKIREIIMNHEIETQDELVDMLKKAGFNVTQATVSRDIKELQLVKVPMANGRY 60 Query: 61 IYGLSNENDPIFTTAVAKPIKTSILSISDKLLGLEQFININVIPGNSQLIKTFIMSHCQE 120- Y L +D F + +K +++ KL G + + +PGN+ I + + Sbjct: 61 KYSL--PSDQRFNP--TQKLKRALMDAFVKLDGSGNLLVLKTLPGNAHAIGVLLDNLDWN 116- Query: 121 HIFSLTADDNSLLLIAKSEADADHIRQSMIAML 153 I D++ L+I ++ DA+ + ++ ML Sbjct: 117 EIVGTICGDDTCLIICRTAEDAEKVSGQLLGML 149 A related DNA sequence was identified in S. pyogenes <SEQ ID 291> which encodes the amino acid sequence <SEQ ID 292>. Analysis of this protein sequence reveals the following: TABLE-US-00312 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1717(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00313 Identities = 87/154 (56%), Positives = 118/154 (76%), Gaps = 1/154 (0%) Query: 1 MKKSERLNLIKQIVLNHAVETQHELLRRLEAYGVTLTQATISRDMNEIGIIKVPSARGRY 60 MKKSERL LIK++VL H +ETQH+LLR L +G+ LTQATISRDMNEIGI+K+PS GRY Sbjct: 12 MKKSERLELIKKMVLTHPIETQHDLLRLLAEHGLELTQATISRDMNEIGIVKIPSGSGRY 71 Query: 61 IYGLSNENDPIFTTAVAKPIKTSILSISDKLLGLEQFININVIPGNSQLIKTFIMSHCQE 120- IYGLS ++ + IK++IL++SDK GLEQ + + V+PGNS+LIK ++++ + Sbjct: 72 IYGLSQDSGKKIVQG-PRSIKSTILAVSDKTKGLEQHLYLKVVPGNSKLIKRYLLADFSK 130- Query: 121 HIFSLTADDNSLLLIAKSEADADHIRQSMIAMLE 154 IFSL ADD+SLLLIAKS ++AD IRQ ++ ++ Sbjct: 131 AIFSLIADDDSLLLIAKSPSEADMIRQEILLWMQ 164 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 87 A DNA sequence (GBSx0088) was identified in S. agalactiae <SEQ ID 293> which encodes the amino acid sequence <SEQ ID 294>. Analysis of this protein sequence reveals the following: TABLE-US-00314 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3339(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 88 A DNA sequence (GBSx0089) was identified in S. agalactiae <SEQ ID 295> which encodes the amino acid sequence <SEQ ID 296>. This protein is predicted to be DNA repair protein recn (recN). Analysis of this protein sequence reveals the following: TABLE-US-00315 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1651 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00316 >GP: CAB14355 GB: Z99116 recN [Bacillus subtilis] Identities = 244/567 (43%), Positives = 366/567 (64%), Gaps = 18/567 (3%) Query: 1 MLLEISIKNFAIIEEISLNFETGMTVLTGETGAGKSIIIDAMNMMLGSRASVEVIRHGAN 60 ML E+SIKNFAIIEE++++FE G+TVLTGETGAGKSIIIDA+++++G R S E +R+G Sbjct: 1 MLAELSIKNFAIIEELTVSFERGLTVLTGETGAGKSIIIDAISLLVGGRGSSEFVRYGEA 60 Query: 61 KAEIEGFFSVEKNQSLVQLLEENGIELADELII-RREIFQNGRSVSRINGQMVNLSTLKA 119- KAE+EG F +E ++ + E GI+++DE+I+ RR+I +G+SV R+NG++V +++L+ Sbjct: 61 KAELEGLFLLESGHPVLGVCAEQGIDVSDEMIVMRRDISTSGKSVCRVNGKLVTIASLRE 120- Query: 120 VGHYLVDIYGQHDQEELMKPNMHILMLDEFGNTEFNVIKERYQSLFDAYRQLRKRVLDKQ 17- 9 +G L+DI+GQHD + LM+ H+ +LD+F E + YQ + Y +L K++ Sbjct: 121 IGRLLLDIHGQHDNQLLMEDENHLQLLDKFAGAEVESALKTYQEGYQRYVKLLKKLKQLS 18- 0 Query: 180 KNEQENKSRIEMLEFQIAEIESVALKSDEDQTLLKQRDKLMNHKNIADTLTNAYLMLDNE 23- 9 ++EQE +++++FQ+ EIES L+ +ED+ L ++R ++ N + I ++L NAY L +E Sbjct: 181 ESEQEMAHCLDLIQFQLEEIESAKLELNEDEQLQEERQQISNFEKIYESLQNAYNALRSE 24- 0 Query: 240 EFSSLSNVRSAMNDLMALEEFDREYKDLSTNLSEAYYVIEEVTKRLGDVIDDLDFDAGLL 29- 9 + L V A L + + + K +S ++S +YY++E+ T ++ +++D+L+FD L Sbjct: 241 Q-GGLDWVGMASAQLEDISDINEPLKKMSESVSNSYYLLEDATFQMRNMLDELEFDPERL 29- 9 Query: 300 QEIENRLDVINTITRKYGGDVNDVLDYFDNITKEYSLLTGSEESSDALEKELKILEHDLI 35- 9 IE RL+ I + RKYG V D+L+Y I +E + + +L+KEL + D+ Sbjct: 300 NYIETRLNEIKQLKRKYGATVEDILEYASKIEEEIDQIENRDSHLQSLKKELDSVGKDVA 35- 9 Query: 360 ESANQLSLERHKLAKQLENEIKQELTELYMEKADFQVQFTKG----------------KF 40- 3 A +S R AK+L +EI +EL LYMEK+ F +F + Sbjct: 360 VEAANVSQIRKTWAKKLADEIHRELKSLYMEKSTFDTEFKVRTASRNEEAPLVNGQPVQL 41- 9 Query: 404 NKEGNEIVEFYISTNPGEGFKPLVKVASGGELSRLMLAIKSAFSRKEDKTSIVFDEVDTG 46- 3 ++G ++V+F ISTN GE K L KVASGGELSR+MLAIKS FS ++D TSI+FDEVDTG Sbjct: 420 TEQGIDLVKFLISTNTGEPLKSLSKVASGGELSRVMLAIKSIFSSQQDVTSIIFDEVDTG 47- 9 Query: 464 VSGRVAQAIAQKIHKIGSHGQVLAISHLAQVIAIADYQYFIEKISSDSSTVSTVRLLSYE 52- 3 VSGRVAQAIA+KIHK+ QVL I+HL QV A+AD +I K D T + V+ LS + Sbjct: 480 VSGRVAQAIAEKIHKVSIGSQVLCITHLPQVAAMADTHLYIAKELKDGRTTTRVKPLSKQ 53- 9 Query: 524 ERVEEIAKMLAGNNVTDTARTQAKELL 550 E+V EI + +AG VTD + AKELL Sbjct: 540 EKVAEIERSIAGVEVTDLTKRHAKELL 566 A related DNA sequence was identified in S. pyogenes <SEQ ID 297> which encodes the amino acid sequence <SEQ ID 298>. Analysis of this protein sequence reveals the following: TABLE-US-00317 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1215 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00318 Identities = 403/550 (73%), Positives = 472/550 (85%) Query: 1 MLLEISIKNFAIIEEISLNFETGMTVLTGETGAGKSIIIDAMNMMLGSRASVEVIRHGAN 60 MLLEISIKNFAII+EISLNFE GMTVLTGETGAGKSIIIDAMNMMLG+RAS EVIR GAN Sbjct: 2 MLLEISIKNFAIIDEISLNFENGMTVLTGETGAGKSIIIDAMNMMLGARASTEVIRRGAN 61 Query: 61 KAEIEGFFSVEKNQSLVQLLEENGIELADELIIRREIFQNGRSVSRINGQMVNLSTLKAV 120- KAEIEGFFSV+ LV LE +GI + +ELIIRR+IF NGRSVSRINGQMVNL+TLK V Sbjct: 62 KAEIEGFFSVDATPELVACLESSGIAMEEELIIRRDIFANGRSVSRINGQMVNLATLKQV 121- Query: 121 GHYLVDIYGQHDQEELMKPNMHILMLDEFGNTEFNVIKERYQSLFDAYRQLRKRVLDKQK 18- 0 G +LVDI+GQHDQEELM+P +H +LD FG+ F +KE YQ +FD Y+ LR++V+DKQK Sbjct: 122 GQFLVDIHGQHDQEELMRPQLHQQILDAFGDKAFEQLKENYQLIFDRYKSLRRQVIDKQK 18- 1 Query: 181 NEQENKSRIEMLEFQIAEIESVALKSDEDQTLLKQRDKLMNHKNIADTLTNAYLMLDNEE 24- 0 NE+E+K RI+ML FQIAEIE+ AL ED L ++RD+LMNHK IADTLTNAY+MLDN++ Sbjct: 182 NEKEHKDRIDMLAFQIAEIEAAALSRGEDDRLNQERDRLMNHKQIADTLTNAYVMLDNDD 24- 1 Query: 241 FSSLSNVRSAMNDLMALEEFDREYKDLSTNLSEAYYVIEEVTKRLGDVIDDLDFDAGLLQ 30- 0 FSSLSN+RS+MNDL+++E+FD EYK +ST++SEAYY++EEV+K+L D ID LDFD G LQ Sbjct: 242 FSSLSNIRSSMNDLLSIEQFDSEYKGMSTSISEAYYILEEVSKQLSDTIDQLDFDGGRLQ 30- 1 Query: 301 EIENRLDVINTITRKYGGDVNDVLDYFDNITKEYSLLTGSEESSDALEKELKILEHDLIE 36- 0 EIE RLD++N++TRKYGG+VNDVLDY+DNI KEY LLTG + SS LE ELK LE L+ Sbjct: 302 EIEFRLDILNSLTRKYGGNVNDVLDYYDNIVKEYQLLTGDDLSSGDLEAELKSLEKQLVA 36- 1 Query: 361 SANQLSLERHKLAKQLENEIKQELTELYMEKADFQVQFTKGKFNKEGNEIVEFYISTNPG 42- 0 +A++LS+ RH+LA+QLE EIK EL ELYMEKADF+V FT KFN++GNE +EFYISTNPG Sbjct: 362 AASELSVSRHQLAEQLEAEIKAELKELYMEKADFKVHFTTSKFNRDGNESLEFYISTNPG 42- 1 Query: 421 EGFKPLVKVASGGELSRLMLAIKSAFSRKEDKTSIVFDEVDTGVSGRVAQAIAQKIHKIG 48- 0 EGFKPLVKVASGGELSRLMLAIK+A SRKEDKTSIVFDEVDTGVSGRVAQAIAQKI+KIG Sbjct: 422 EGFKPLVKVASGGELSRLMLAIKAAISRKEDKTSIVFDEVDTGVSGRVAQAIAQKIYKIG 48- 1 Query: 481 SHGQVLAISHLAQVIAIADYQYFIEKISSDSSTVSTVRLLSYEERVEEIAKMLAGNNVTD 54- 0 HGQVLAISHL QVIAIADYQYFI K S + STVS VRLL+ EERVEEIA M+AG ++T Sbjct: 482 RHGQVLAISHLPQVIAIADYQYFISKESKEESTVSKVRLLTPEERVEEIASMIAGTDMTQ 54- 1 Query: 541 TARTQAKELL 550 A TQA+ELL Sbjct: 542 AALTQARELL 551 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 89 A DNA sequence (GBSx0090) was identified in S. agalactiae <SEQ ID 299> which encodes the amino acid sequence <SEQ ID 300>. This protein is predicted to be degV protein. Analysis of this protein sequence reveals the following: TABLE-US-00319 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.96 Transmembrane 246-262 (246-262) ----- Final Results ----- bacterial membrane --- Certainty = 0.1383 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00320 >GP:BAB07346 GB:AP001519 unknown conserved protein [Bacillus halodurans] Identities = 93/277 (33%), Positives = 152/277 (54%), Gaps = 4/277 (1%) Query: 1 MSKIKIVTDSSITIEPELIKELDITVVPLSVMIDGTLYSDNDLKAQGEFLNLMRGSKELP 60 M+KI IVTDS+ + P+ KEL + VVPLSV+ Y + + +F ++ ++LP Sbjct: 1 MTKIAIVTDSTAYLGPKRAKELGVIVVPLSVVFGEEAYQEEVELSSADFYERLKHEEKLP 60 Query: 61 KTSQPPVGVFAEIYEKLMNEGVEHIIAIHLTHTLSGTIE-ASRQGANIAGADVTVIDSTF 119- TSQP VG+F E +E+L EG E +I+IHL+ +SGT + A G+ + G +V DS Sbjct: 61 TTSQPAVGLFVETFERLAKEGFEVVISIHLSSKISGTYQSALTAGSMVEGIEVIGYDSGI 120- Query: 120 TDQCQKFQVVEAAKLAKEGADLDTILARVEEVRQKSELFIGVSTLENLVKGGRIGRVTGL 17- 9 + + Q V EAAKL KEGAD TI+ ++EV++++ V L +L +GGR+ + Sbjct: 121 SCEPQANFVAEAAKLVKEGADPQTIIDHLDEVKKRTNALFVVHDLSHLHRGGRLNAAQLV 18- 0 Query: 180 LSSLLNIKVIMELTNHELVPIVKGR-GLKTFSKWLDNFVESAQTRKIAEIGISYCGKADM 23- 8 + SLL IK I+ + +VP+ K R K +++ + F E A + + + + + D Sbjct: 181 VGSLLKIKPILHFEDGSIVPLEKVRTEKKAWARVKELFAEEASSASSVKATVIHANRLDG 24- 0 Query: 239 ANNFREKL-AVLGAPISVLETGSIIQTHTGEDAFAV 273 A +++ +S+ G +I TH GE + + Sbjct: 241 AEKLADEIRSQFSHVDVSISHFGPVIGTHLGEGSIGL 277 A related DNA sequence was identified in S. pyogenes <SEQ ID 301> which encodes the amino acid sequence <SEQ ID 302>. Analysis of this protein sequence reveals the following: TABLE-US-00321 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.54 Transmembrane 180-196 (180-196) INTEGRAL Likelihood = -0.16 Transmembrane 21-37 (21-38) ----- Final Results ----- bacterial membrane --- Certainty = 0.1617(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below:

TABLE-US-00322 Identities = 197/279 (70%), Positives = 226/279 (80%), Gaps = 1/279 (0%) Query: 1 MSKIKIVTDSSITIEPELIKELDITVVPLSVMIDGTLYSDNDLKAQGEFLNLMRGSKELP 60 M IKIVTDSSITIEPELIK LDITVVPLSVMID LYSDNDLK +G FL+LM+ SK LP Sbjct: 5 MGTIKIVTDSSITIEPELIKALDITVVPLSVMIDSKLYSDNDLKEEGHFLSLMKASKSLP 64 Query: 61 KTSQPPVGVFAEIYEKLMNEGVEHIIAIHLTHTLSGTIEASRQGANIAGADVTVIDSTFT 120- KTSQPPVG+FAE YE L+ +GV I+AIHL+ LSGTIEASRQGA IA A VTV+DS FT Sbjct: 65 KTSQPPVGLFAETYENLVKKGVTDIVAIHLSPALSGTIEASRQGAEIAEAPVTVLDSGFT 124- Query: 121 DQCQKFQVVEAAKLAKEGADLDTILARVEEVRQKSELFIGVSTLENLVKGGRIGRVTGLL 18- 0 DQ KFQVVEAAK+AK GA L+ ILA V+ ++ K+EL+IGVSTLENLVKGGRIGRVTG+L Sbjct: 125 DQAMKFQVVEAAKMAKAGASLNEILAAVQAIKSKTELYIGVSTLENLVKGGRIGRVTGVL 18- 4 Query: 181 SSLLNIKVIMELTNHELVPIVKGRGLKTFSKWLDNFVESAQTRKIAEIGISYCGKADMAN 24- 0 SSLLN+KV+M L N EL +VKGRG KTF+KWLD+++ R IAEI ISY G+A +A Sbjct: 185 SSLLNVKVVMALKNDELKTLVKGRGNKTFTKWLDSYLAKNSHRPIAEIAISYAGEASLAL 24- 4 Query: 241 NFREKLAV-LGAPISVLETGSIIQTHTGEDAFAVMVRYE 278 +E++A ISVLETGSIIQTHTGE AFAVMVRYE Sbjct: 245 TLKERIAAYYNHSISVLETGSIIQTHTGEGAFAVMVRYE 283 SEQ ID 300 (GBS113) was expressed in E. coli as a His-fusion product. Purified protein is shown in FIG. 201, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 90 A DNA sequence (GBSx0092) was identified in S. agalactiae <SEQ ID 307> which encodes the amino acid sequence <SEQ ID 308>. Analysis of this protein sequence reveals the following: TABLE-US-00323 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00324 >GP: CAA72097 GB: Y11213 hypothetical protein [Streptococcus thermophilus] Identities = 75/185 (40%), Positives = 116/185 (62%), Gaps = 3/185 (1%) Query: 13 WKWAFLLLLAINLSFTAVIASRLIQVREPNTGKISTGVQDKVKVGTFTTNKSQLNKTIAL 72 - WKW FL LLA+NL+ +V+ R++ E + + G K+G ++ +K +L++++ Sbjct: 5 WKWLFLGLLALNLALISVVTVRIMTPVETSPVSLPKGA---TKIGKYSMSKEELDESLRG 61 Query: 73 YLKQYQTKKMNYKIYAASSSILFEGSYQLLGYEVPLYIYFEPYRLTNGAVQLKVTSFSVG 132- + + Y T KM +K+ +S I+FE SY++LG+ VPLY+YF P +GAV L+ + S G Sbjct: 62 FAQDYSTDKMRFKVKVTNSKIVFESSYKVLGHAVPLYVYFTPLVSESGAVVLQESELSAG 121- Query: 133 TLPLPEKDVLQYIKSSYKLPNFVDIKPKKSVININLQDLKNKEGIYLKATAIDLVNDNFS 19- 2 TL LP D L IK S KLP+++ I KK + +N+Q +KN +GI +A + DLVND Sbjct: 122 TLKLPILDALNMIKRSTKLPDYIVIDSKKGKVILNIQSMKNDKGITARAQSFDLVNDRSE 18- 1 Query: 193 FDIFK 197 FDI+K Sbjct: 182 FDIYK 186 A related DNA sequence was identified in S. pyogenes <SEQ ID 309> which encodes the amino acid sequence <SEQ ID 310>. Analysis of this protein sequence reveals the following: TABLE-US-00325 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00326 >GP: CAA72097 GB: Y11213 hypothetical protein [Streptococcus thermophilus] Identities = 73/185 (39%), Positives = 112/185 (60%), Gaps = 3/185 (1%) Query: 10 WKWSFLCLLAFNTAFLMVIASRLIQVREPESELIAKKPVKNIKIGTFVTTREQLNETVAS 69 - WKW FL LLA N A + V+ R++ E + K K IG + ++E+L+E++ Sbjct: 5 WKWLFLGLLALNLALISVVTVRIMTPVETSPVSLPKGATK---IGKYSMSKEELDESLRG 61 Query: 70 YLKDYQTEKMSYKFYATSSSILFEGTYQLLGYEVPLYIYFQPHRLENGAVQLQVISFSVG 129- + +DY T+KM +K T+S I+FE +Y++LG+ VPLY+YF P E+GAV LQ S G Sbjct: 62 FAQDYSTDKMRFKVKVTNSKIVFESSYKVLGHAVPLYVYFTPLVSESGAVVLQESELSAG 121- Query: 130 TLPLPEKDVLQYLKSSYKLPSFVKVMPNQSAIVVNLQDIQNDAKVYLKAKKIDLFNDEIS 18- 9 TL LP D L +K S KLP ++ + + +++N+Q ++ND + +A+ DL ND Sbjct: 122 TLKLPILDALNMIKRSTKLPDYIVIDSKKGKVILNIQSMKNDKGITARAQSFDLVNDRSE 18- 1 Query: 190 FNIYK 194 F+IYK Sbjct: 182 FDIYK 186 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00327 Identities = 129/194 (66%), Positives = 155/194 (79%) Query: 5 KTGRNLNFWKWAFLLLLAINLSFTAVIASRLIQVREPNTGKISTGVQDKVKVGTFTTNKS 64 K NLN+WKW+FL LLA N +F VIASRLIQVREP + I+ +K+GTF T + Sbjct: 2 KKKSNLNWWKWSFLCLLAFNTAFLMVIASRLIQVREPESELIAKKPVKNIKIGTFVTTRE 61 Query: 65 QLNKTIALYLKQYQTKKMNYKIYAASSSILFEGSYQLLGYEVPLYIYFEPYRLTNGAVQL 124- QLN+T+A YLK YQT+KM+YK YA SSSILFEG+YQLLGYEVPLYIYF+P+RL NGAVQL Sbjct: 62 QLNETVASYLKDYQTEKMSYKFYATSSSILFEGTYQLLGYEVPLYIYFQPHRLENGAVQL 121- Query: 125 KVTSFSVGTLPLPEKDVLQYIKSSYKLPNFVDIKPKKSVININLQDLKNKEGIYLKATAI 18- 4 +V SFSVGTLPLPEKDVLQY+KSSYKLP+FV + P +S I +NLQD++N +YLKA I Sbjct: 122 QVISFSVGTLPLPEKDVLQYLKSSYKLPSFVKVMPNQSAIVVNLQDIQNDAKVYLKAKKI 18- 1 Query: 185 DLVNDNFSFDIFKK 198 DL ND SF+I+KK Sbjct: 182 DLFNDEISFNIYKK 195 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8487> and protein <SEQ ID 8488> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00328 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: 7.47 GvH: Signal Score (-7.5): 2.42 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 5.89 threshold: 0.0 PERIPHERAL Likelihood = 5.89 120 modified ALOM score: -1.68 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 308 (GBS20) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 4 (lane 5; MW 25 kDa) and in FIG. 167 (lane 12-14; MW 37 kDa--thioredoxin fusion). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 9 (lane 7; MW 47.6 kDa). Purified Thio-GBS20-His is shown in FIG. 244, lane 12. EXAMPLE 91 A DNA sequence (GBSx0093) was identified in S. agalactiae <SEQ ID 311> which encodes the amino acid sequence <SEQ ID 312>. This protein is predicted to be histone-like DNA-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-00329 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2768(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9313> which encodes amino acid sequence <SEQ ID 9314> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00330 >GP: AAD40810 GB: L40355 histone-like DNA-binding protein [Streptococcus mutans] Identities = 43/47 (91%), Positives = 46/47 (97%) Query: 1 MANKQDLIAKVAEATELTKKDSAAAVDAVFAAVADYLAEGEKVQLIG 47 MANKQDLIAKVAEATELTKKDSAAAVDAVF+AV+ YLA+GEKVQLIG Sbjct: 1 MANKQDLIAKVAEATELTKKDSAAAVDAVFSAVSSYLAKGEKVQLIG 47 A related DNA sequence was identified in S. pyogenes <SEQ ID 313> which encodes the amino acid sequence <SEQ ID 314>. Analysis of this protein sequence reveals the following: TABLE-US-00331 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2834(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00332 Identities = 41/47 (87%), Positives = 44/47 (93%) Query: 1 MANKQDLIAKVAEATELTKKDSAAAVDAVFAAVADYLAEGEKVQLIG 47 MANKQDLIAKVAEATELTKKDSAAAVDAVF+ + +LAEGEKVQLIG Sbjct: 1 MANKQDLIAKVAEATELTKKDSAAAVDAVFSTIEAFLAEGEKVQLIG 47 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 92 A DNA sequence (GBSx0094) was identified in S. agalactiae <SEQ ID 315> which encodes the amino acid sequence <SEQ ID 316>. Analysis of this protein sequence reveals the following: TABLE-US-00333 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2722(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9293> which encodes amino acid sequence <SEQ ID 9294> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10793> which encodes amino acid sequence <SEQ ID 10794> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00334 >GP: AAD17886 GB: AF100456 hyaluronate-associated protein precursor [Streptococcus equi] Identities = 303/435 (69%), Positives = 360/435 (82%), Gaps = 1/435 (0%) Query: 1 MATKVDVSKDGLTYTATLRKGLKWSDGSKLTAKDFVYSWQRLVDPKTASQYAYLAVEGHV 60 +A KVDVS+DGLTYTATLR GLKWSDGS LTA+DFVYSWQR+VDPKTAS+YAYLA E H+ Sbjct: 87 LAEKVDVSEDGLTYTATLRDGLKWSDGSDLTAEDFVYSWQRMVDPKTASEYAYLATESHL 146- Query: 61 LNADKINEGQEKDLNKLGVKAEGDDKVVITLSSPSPQFIYYLAFTNFMPQKQEVVEKYGK 120- NA+ IN G+ DL+ LGVKA+G+ KV+ TL+ P+PQF L+F+NF+PQK+ V+ GK Sbjct: 147 KNAEDINSGKNPDLDSLGVKADGN-KVIFTLTEPAPQFKSLLSFSNFVPQKESFVKDAGK 20- 5 Query: 121 DYATTSKNTVYSGPYTVEGWNGSNGTFTLKKNKNYWDAKNVKTKEVRIQTVKKPDTAVQM 18- 0 DY TTS+ +YSGPY V+ WNG++GTF L KNKNYWDAKNVKT+ V +QTVKKPDTAVQM Sbjct: 206 DYGTTSEKQIYSGPYIVKDWNGTSGTFKLVKNKNYWDAKNVKTETVNVQTVKKPDTAVQM 26- 5 Query: 181 YKRGELDAANISNTSAIYQANKNNKDVTDVLEATTAYMEYNTTGSVKGLDNVKIRRALNL 24- 0 YK+G+LD ANIS TSAIY ANK +KDV VLEATTAY+ YN TG+++GL+++KIR+ALNL Sbjct: 266 YKQGKLDFANISGTSAIYNANKKHKDVVPVLEATTAYIVYNQTGAIEGLNSLKIRQALNL 32- 5 Query: 241 ATNRKGVVQAAVDTGSKPAIAFAPTGLAKTPDGTDLAKYVAPGYEYNKTEAAKLFKEGLA 30- 0 AT+RKG+V AAVDTGSKPA A PTGLAK DGTDL ++VAPGY+Y+ EAAKLFKEGLA Sbjct: 326 ATDRKGIVSAAVDTGSKPATALVPTGLAKLSDGTDLTEHVAPGYKYDDKEAAKLFKEGLA 38- 5 Query: 301 ESGLTKLKLTITADADAPAAKNSVDYIKSTWEAALPGLTVEEKFVTFKQRLEDSRKQNFD 36- 0 E G L +TITADADAPAAK++VDYIK TWE ALPGLTVEEKFV FKQRLED++ QNF+ Sbjct: 386 ELGKDALTITITADADAPAAKSAVDYIKETWETALPGLTVEEKFVPFKQRLEDTKNQNFE 44- 5 Query: 361 IVVSLWGGDYPEGSTFYGLFKSDSQNNDGKFANKDYDAAYNKAISEDAMKPAESAKDYKE 42- 0 + V LWGGDYP+GSTFYGLFKS S N GKF N DYDAAYNKA++ DA+ +A DYK Sbjct: 446 VAVVLWGGDYPKGSTFYGLFKSGSAYNYGKFTNADYDAAYNKALTTDALNTDAAADDYKA 50- 5 Query: 421 AEKILFEQGAYNPLY 435 AEK L++ YNPLY Sbjct: 506 AEKALYDNALYNPLY 520 A related GBS gene <SEQ ID 8489> and protein <SEQ ID 8490> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00335 Lipop:Possible site:21 Crend:4 Sequence Pattern:CGSK SRCFLG:0 McG:Length of UR:19 Peak Value of UR:2.34 Net Charge of CR:3 McG:Discrim Score:5.94 GvH:Signal Score (-7.5):0.6 Possible site:20 >>> May be a lipoprotein Amino Acid Composition:calculated from 22 ALOM program count:0 value:5.14 threshold:0.0 PERIPHERAL Likelihood = 5.14 166 modified ALOM score:-1.53 *** Reasoning Step:3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00336 >GP|4336671|gb|AAD17886.1||AF100456 hyaluronate-associated protein precursor {Streptococcus equi} Score = 721 bits (1840), Expect = 0.0 Identities = 354/515 (68%), Positives = 417/515 (80%), Gaps = 2/515 (0%) Query: 1 KNWRRVGVGVLTLASVATLAACGSK-SASQDSNGAINWAIPTEINTLDLSKVTDTYSNLA 59 K +R+G+ +TLASVA L ACG+K SAS D INW PTEI TLD+SK TDTYS LA Sbjct: 7 KACKRLGLAAVTLASVAALMACGNKQSASTDKKSEINWYTPTEIITLDISKNTDTYSALA 66 Query: 60 IGNSSSNFLRLDKDGKTRPDLATKVDVSKDGLTYTATLRKGLKWSDGSKLTAKDFVYSWQ 119- IGNS SN LR D GK +PDLA KVDVS+DGLTYTATLR GLKWSDGS LTA+DFVYSWQ Sbjct: 67 IGNSGSNLLRADAKGKLQPDLAEKVDVSEDGLTYTATLRDGLKWSDGSDLTAEDFVYSWQ 126- Query: 120 RLVDPKTASQYAYLAVEGHVLNADKINEGQEKDLNKLGVKAEGDDKVVITLSSPSPQFIY 17- 9 R+VDPKTAS+YAYLA E H+ NA+ IN G+ DL+ LGVKA+G+ KV+ TL+ P+PQF Sbjct: 127 RMVDPKTASEYAYLATESHLKNAEDINSGKNPDLDSLGVKADGN-KVIFTLTEPAPQFKS 18- 5 Query: 180 YLAFTNFMPQKQEVVEKYGKDYATTSKNTVYSGPYTVEGWNGSNGTFTLKKNKNYWDAKN 23- 9 L+F+NF+PQK+ V+ GKDY TTS+ +YSGPY V+ WNG++GTF L KNKNYWDAKN Sbjct: 186 LLSFSNFVPQKESFVKDAGKDYGTTSEKQIYSGPYIVKDWNGTSGTFKLVKNKNYWDAKN 24- 5 Query: 240 VKTKEVRIQTVKKPDTAVQMYKRGELDAANISNTSAIYQANKNNKDVTDVLEATTAYMEY 29- 9 VKT+ V +QTVKKPDTAVQMYK+G+LD ANIS TSAIY ANK +KDV VLEATTAY+ Y Sbjct: 246 VKTETVNVQTVKKPDTAVQMYKQGKLDFANISGTSAIYNANKKHKDVVPVLEATTAYIVY 30- 5 Query: 300 NTTGSVKGLDNVKIRRALNLATNRKGVVQAAVDTGSKPAIAFAPTGLAKTPDGTDLAKYV 35- 9 N TG+++GL+++KIR+ALNLAT+RKG+V AAVDTGSKPA A PTGLAK DGTDL ++V Sbjct: 306 NQTGAIEGLNSLKIRQALNLATDRKGIVSAAVDTGSKPATALVPTGLAKLSDGTDLTEHV 36- 5 Query: 360 APGYEYNKTEAAKLFKEGLAESGLTKLKLTITADADAPAAKNSVDYIKSTWEAALPGLTV 41- 9 APGY+Y+ EAAKLFKEGLAE G L +TITADADAPAAK++VDYIK TWE ALPGLTV Sbjct: 366 APGYKYDDKEAAKLFKEGLAELGKDALTITITADADAPAAKSAVDYIKETWETALPGLTV 42- 5 Query: 420 EEKFVTFKQRLEDSRKQNFDIVVSLWGGDYPEGSTFYGLFKSDSQNNDGKFANKDYDAAY 47- 9 EEKFV FKQRLED++ QNF++ V LWGGDYP+GSTFYGLFKS S N GKF N DYDAAY Sbjct: 426 EEKFVPFKQRLEDTKNQNFEVAVVLWGGDYPKGSTFYGLFKSGSAYNYGKFTNADYDAAY 48- 5 Query: 480 NKAISEDAMKPAESAKDYKEAEKILFEQGAYNPLY 514 NKA++ DA+ +A DYK AEK L++ YNPLY Sbjct: 486 NKALTTDALNTDAAADDYKAAEKALYDNALYNPLY 520 A related DNA sequence was identified in S. pyogenes <SEQ ID 317> which encodes the amino acid sequence <SEQ ID 318>. Analysis of this protein sequence reveals the following: TABLE-US-00337 Possible site: 24 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00338 Identities = 114/428 (26%), Positives = 185/428 (42%), Gaps = 63/428 (14%) Query: 7 VSKDGLTYTATLRKGLKW--SDGSK---LTAKDFVYSWQRLVDPKTASQYAYLAVEGHVL 61 VSKDGLTYT TLR G+ W +DG + +TA+DFV + VD K+ + Y VE + Sbjct: 92 VSKDGLTYTYTLRDGVSWYTADGEEYAPVTAEDFVTGLKHAVDDKSDALY---VVEDSIK 148- Query: 62 NADKINEGQEKDLNKLGVKAEGDDKVVITLSSPSPQFIYYLAFTNFMPQKQEVVEKYGKD 121- N G E D ++GVKA D V TL+ P + ++ P + ++ GKD Sbjct: 149 NLKAYQNG-EVDFKEVGVKALDDKTVQYTLNKPESYWNSKTTYSVLFPVNAKFLKSKGKD 20- 7 Query: 122 YATTSKNTV-YSGPYTVEGWNGSNGTFTLKKNKNYWDAKNVKTKEVRI--QTVKKPDTAV 17- 8 + TT +++ +G Y + + S + KN+NYWDAKNV + V++ P + Sbjct: 208 FGTTDPSSILVNGAYFLSAFT-SKSSMEFHKNENYWDAKNVGIESVKLTYSDGSDPGSFY 26- 6 Query: 179 QMYKRGELDAANISNTSAIYQANKNN--KDVT-DVLEATTAYMEYNTT------------ 22- 3 + + +GE A + Y++ K N ++T +L ++ +N Sbjct: 267 KNFDKGEFSVARLYPNDPTYKSAKKNYADNITYGMLTGDIRHLTWNLNRTSFKNTKKDPA 32- 6 Query: 224 ---GSVKGLDNVKIRRALNLATNRKGVVQAAVDTGSKPA----IAFAPT--GLAKTPDGT 27- 4 K L+N R+A+ A +R +K + PT + ++ G+ Sbjct: 327 QQDAGKKALNNKDFRQAIQFAFDRASFQAQTAGQDAKTKALRNMLVPPTFVTIGESDFGS 38- 6 Query: 275 DLAKYVAP-GYE-------------YNKTEAAKLF---KEGLAESGLT-KLKLTITADAD 31- 6 ++ K +A G E YN +A F KE L G+T ++L D Sbjct: 387 EVEKEMAKLGDEWKDVNLADAQDGFYNPEKAKAEFAKAKEALTAEGVTFPVQLDYPVDQA 44- 6 Query: 317 APAAKNSVDYIKSTWEAALPGLTV-----EEKFVTFKQR---LEDSRKQNFDIVVSLWGG 36- 8 A K + EA+L V E + T + + E +Q++DI+ S WG Sbjct: 447 NAATVQEAQSFKQSVEASLGKENVIVNVLETETSTHEAQGFYAETPEQQDYDIISSWWGP 50- 6 Query: 369 DYPEGSTF 376 DY + T+ Sbjct: 507 DYQDPRTY 514 SEQ ID 9294 (GBS663) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 137 (lane 3; MW 89.5 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 137 (lane 5-7; MW 64.5 kDa), in FIG. 179 (lane 11; MW 65 kDa) and in FIG. 65 (lane 2; MW 61 kDa). Purified GBS663-His is shown in FIG. 231, lane 34. Purified GBS324-His is shown in lane 6 of FIG. 210. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 93 A DNA sequence (GBSx0095) was identified in S. agalactiae <SEQ ID 319> which encodes the amino acid sequence <SEQ ID 320>. This protein is predicted to be transmembrane protein OppB (oppB). Analysis of this protein sequence reveals the following: TABLE-US-00339 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.77 Transmembrane 293-309 (281-313) INTEGRAL Likelihood = -9.77 Transmembrane 21-37 (14-46) INTEGRAL Likelihood = -6.32 Transmembrane 115-131 (105-132) INTEGRAL Likelihood = -4.88 Transmembrane 144-160 (140-166) INTEGRAL Likelihood = -3.03 Transmembrane 238-254 (237-255) ----- Final Results ----- bacterial membrane --- Certainty = 0.5310(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8491> which encodes amino acid sequence <SEQ ID 8492> was also identified. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-00340 >GP: AAF73091 GB: AF103793 transmembrane protein OppB [Listeria monocytogenes] Identities = 147/304 (48%), Positives = 221/304 (72%), Gaps = 1/304 (0%) Query: 13 MIKYILKRVAILLVTLWVVITLSFFLMQILPGTPYNNP-KLTEEMIALLNKQYGLDKPVW 71 - M+KY LKRV +L+TL+++ +++F LM+ LPGTPY N KL++E I + N++YGL+ + Sbjct: 1 MVKYTLKRVLYMLITLFIIASVTFVLMKFLPGTPYRNQEKLSDEQIHMTNEKYGLNDSIP 60 Query: 72 QQYLTYLWNVLHGDFGTSYQSVNQPVSRMISLRLGVSVHLGVQALVFGVLGGILVGAISA 131- QY Y+ ++ GD G S+Q N+PVS ++S +G SV L ++A+ FGV+ GIL+G I+A Sbjct: 61 VQYFNYMTGLVKGDLGVSFQLDNRPVSEILSALIGPSVQLALEAMAFGVIFGILLGVIAA 120- Query: 132 RHKNDKVDGILSVIATLGISMPSFIIGILLLDYFGFKWNLLPLSGWGTFSQTILPSLALG 19- 1 ++N D + IA LG S+PSF+ +L + G K + P++GWGTF+ TILP+ AL Sbjct: 121 MYQNRWPDYTSTFIAILGKSVPSFVFATVLQYWLGAKLQIFPVAGWGTFADTILPAFALA 18- 0 Query: 192 LPTLASVSRFFRSEMIETLNSDYVQLARSKGMTIRQVTRKHAYRNSMIPILTLIGPLAAG 25- 1 + LA+ +RF R+E+I+ SDYV LA++KG + +V KHA RN++IP++T++GPL+ Sbjct: 181 MFPLATAARFMRTELIDVFASDYVLLAKAKGNSRTEVAVKHAIRNALIPLITVLGPLSVA 24- 0 Query: 252 LLTGSALIEQIFSIPGIGQQFVTSIPTKDYPVIMGTTIVYAVMLMVAILITDVVISIVDP 31- 1 L+TGS +IE I+SIPGIG QFV+SI T DYPVIMGTTI++AVML+ IL+ D++ ++DP Sbjct: 241 LMTGSLVIENIYSIPGIGSQFVSSIQTNDYPVIMGTTILFAVMLVFVILVVDILYGLIDP 30- 0 Query: 312 RVRL 315 R+R+ Sbjct: 301 RIRV 304 There is also homology to SEQ ID 64. A related DNA sequence was identified in S. pyogenes <SEQ ID 9069> which encodes amino acid sequence <SEQ ID 9070>. Analysis of this protein sequence reveals the following: TABLE-US-00341 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.81 Transmembrane 466-482 (463-493) INTEGRAL Likelihood = -5.10 Transmembrane 419-435 (418-440) INTEGRAL Likelihood = -4.78 Transmembrane 328-344 (322-348) INTEGRAL Likelihood = -4.41 Transmembrane 366-382 (365-384) INTEGRAL Likelihood = -4.09 Transmembrane 290-306 (287-311) INTEGRAL Likelihood = -2.97 Transmembrane 17-33 (13-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.4524(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS sequences follows: TABLE-US-00342 Score = 117 bits (291), Expect = 3e-28 Identities = 61/208 (29%), Positives = 121/208 (57%), Gaps = 4/208 (1%) Query: 291 IGFFGVMFSYIVGLPLGLFMARFKNTYFDSFSTATMTFMLALPSIAV-IYVVRFLGGMVG 34- 9 +G ++F + G+ +G AR KN D + T +++PS + I ++ + G Sbjct: 99 LGVQALVFGVLGGILVGAISARHKNDKVDGILSVIATLGISMPSFIIGILLLDYFGFKWN 158- Query: 350 LPDSFPMLGASDPKSYILPALILGILNIPTTVIWFRRYLVDLQASDWVRFARSKGLSESE 40- 9 L P+ G ILP+L LG+ + + +FR +++ SD+V+ ARSKG++ + Sbjct: 159 L---LPLSGWGTFSQTILPSLALGLPTLASVSRFFRSEMIETLNSDYVQLARSKGMTIRQ 21- 5 Query: 410 IYRGHLFKNAMVPIVSGVPASIILAIGGATLTETVFAFPGMGKMLIDSIKSANNSMIVGL 46- 9 + R H ++N+M+PI++ + + G+ L E +F+ PG+G+ + SI + + +I+G Sbjct: 216 VTRKHAYRNSMIPILTLIGPLAAGLLTGSALIEQIFSIPGIGQQFVTSIPTKDYPVIMGT 27- 5 Query: 470 TFIFTVLSIVSLLLGDIVMTLVDPRIKL 497 T ++ V+ +V++L+ D+V+++VDPR++L Sbjct: 276 TIVYAVMLMVAILITDVVISIVDPRVRL 303 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 94 A DNA sequence (GBSx0096) was identified in S. agalactiae <SEQ ID 321> which encodes the amino acid sequence <SEQ ID 322>. This protein is predicted to be transmembrane protein OppC (oppC). Analysis of this protein sequence reveals the following: TABLE-US-00343 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.52 Transmembrane 311-327 (307-333) INTEGRAL Likelihood = -7.80 Transmembrane 42-58 (40-65) INTEGRAL Likelihood = -7.43 Transmembrane 142-158 (131-165) INTEGRAL Likelihood = -4.73 Transmembrane 182-198 (179-214) INTEGRAL Likelihood = -3.50 Transmembrane 257-273 (257-276) ----- Final Results ----- bacterial membrane --- Certainty = 0.5607(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00344 >GP: AAF73092 GB: AF103793 transmembrane protein OppC [Listeria monocytogenes] Identities = 157/325 (48%), Positives = 219/325 (67%), Gaps = 4/325 (1%) Query: 20 EKIEKPALSFMQDAWRRLKKNKLAVVSLYLLALLLTFSLASNLFVTQKDANGFDSKKVTT 79 - EKI +P+L+F+QD+W R++KNK A+VSL +LAL++ ++ ++++T Sbjct: 22 EKINRPSLTFLQDSWLRIRKNKAALVSLIVLALVIIMAIVGPYLSQNLGPEHNINRQITE 81 Query: 80 YRNLPPKLSS--NLPFWNGSIKYAGNTESTDAYKSQNVPEKVKYALGTDSLGRSVAKRII 137- +LPPK+ N+PFWNG G E D YK N+ E Y LG+D+LGR RI Sbjct: 82 NASLPPEVQGFENMPFWNGHQSIGG--EDVDIYKQNNIKEGTYYWLGSDTLGRDQFARIW 139- Query: 138 VGIRISLLVAIAATFIDLIIGVTYGLVSGFAGGRLDTLMQRIVEVISSIPNLVIVTMLGL 19- 7 G R+SL++A+ A DL+IGV YGL+SG+ GGR+D MQR++EVI +IPNLV+V ++ L Sbjct: 140 AGTRVSLIIAVVAALCDLVIGVAYGLISGYVGGRVDNFMQRVLEVIGAIPNLVVVILMML 19- 9 Query: 198 VLGNGITAIIISIAFTGWTSMSRQVRNLTLSYREREFVLAARSLGESPIKIAFKHILPNI 25- 7 +L GI +III+IA T W +M+R VR L + +EFV+A+ +LGES KI KH++PNI Sbjct: 200 ILEPGIVSIIIAIAMTSWITMARVVRGQVLKRKNQEFVMASMTLGESTPKILIKHLIPNI 25- 9 Query: 258 SGIIIVQIMMTIPSAIMYEAVLSAINLGVKPPTASLGSLISDAQENLQYYPYQVILPALA 31- 7 SGIII+ IM +IPSAI +EA LS I LG+ P ASLG L++D + LQ PY ++ P + Sbjct: 260 SGIIIINIMFSIPSAIFFEAFLSFIGLGLPAPAASLGVLVNDGYKTLQVLPYMILYPCIV 31- 9 Query: 318 LVMISLAFILLGDGLRDAFDPKSSD 342 L +I +AF L+ DGLRDAFDPK D Sbjct: 320 LCIIMIAFNLIADGLRDAFDPKMRD 344 A related DNA sequence was identified in S. pyogenes <SEQ ID 323> which encodes the amino acid sequence <SEQ ID 324>. Analysis of this protein sequence reveals the following: TABLE-US-00345 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.30 Transmembrane 43-59 (37-65) INTEGRAL Likelihood = -8.49 Transmembrane 111-127 (109-135) INTEGRAL Likelihood = -6.26 Transmembrane 279-295 (270-298) INTEGRAL Likelihood = -3.88 Transmembrane 172-188 (172-188) INTEGRAL Likelihood = -3.61 Transmembrane 145-161 (145-165) INTEGRAL Likelihood = -1.49 Transmembrane 223-239 (223-239) ----- Final Results ----- bacterial membrane --- Certainty = 0.5118(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00346 Identities = 91/325 (28%), Positives = 156/325 (48%), Gaps = 34/325 (10%) Query: 16 SSTQEKIEKPALSFMQDAWRRLKKNKLAVVSLYLLALLLTFSLASNLFVTQKDANGFDSK 75 - S E I+ PA S+ + +R+ K V L +L +L S +F +D Sbjct: 16 SEASEVIDTPAYSYWKSVFRQFFSKKSTVFMLVILVTVLMMSFIYPMFAN------YDFN 69 Query: 76 KVTTYRNLPPKLSSNLPFWNGSIKYAGNTESTDAYKSQNVPEKVKYALGTDSLGRSVAKR 135- V+ + + + + +Y GTD G+S+ Sbjct: 70 DVSNIND---------------------------FSKRYIWPNAEYWFGTDKNGQSLFDG 102- Query: 136 IIVGIRISLLVAIAATFIDLIIGVTYGLVSGFAGGRLDTLMQRIVEVISSIPNLVIVTML 19- 5 + G R S+L+++ AT I++ IGV G + G + D +M I +IS+IP+++I+ +L Sbjct: 103 VWYGARNSILISVIATLINITIGVVLGAIWGVSKA-FDKVMIEIYNIISNIPSMLIIIVL 16- 1 Query: 196 GLVLGNGITAIIISIAFTGWTSMSRQVRNLTLSYREREFVLAARSLGESPIKIAFKHILP 25- 5 LG G +I++ TGW ++ +R L YR+ E+ LA+++LG KIA K++LP Sbjct: 162 TYSLGAGFWNLILAFCITGWIGVAYSIRVQILRYRDLEYNLASQTLGTPMYKIAVKNLLP 22- 1 Query: 256 NISGIIIVQIMMTIPSAIMYEAVLSAINLGVKPPTASLGSLISDAQENLQYYPYQVILPA 31- 5 + +I+ + +P + EA LS +G+ T SLG I++ NL Y +P Sbjct: 222 QLVSVIMTMLSQMLPVYVSSEAFLSFFGIGLPTTTPSLGRFIANYSSNLTTNAYLFWIPL 28- 1 Query: 316 LALVMISLAFILLGDGLRDAFDPKS 340 + L+++SL ++G L DA DP+S Sbjct: 282 VTLILVSLPLYIVGQNLADASDPRS 306 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 95 A DNA sequence (GBSx0097) was identified in S. agalactiae <SEQ ID 325> which encodes the amino acid sequence <SEQ ID 326>. This protein is predicted to be ATPase OppD (oppD). Analysis of this protein sequence reveals the following: TABLE-US-00347 Possible site: 20 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.85 Transmembrane 164-180 (163-180) ----- Final Results ----- bacterial membrane --- Certainty = 0.1341(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00348 >GP: AAF73093 GB: AF103793 ATPase OppD [Listeria monocytogenes] Identities = 230/342 (67%), Positives = 283/342 (82%), Gaps = 2/342 (0%) Query: 4 ETILSVNNLHVDFHTYAGEVKAIRDVNFELKKGETLAIVGESGSGKSVTTRTLIGLNAK- 62 E +L V +L++ FHTYAGEVKAIR VNF+L KGETLAIVGESGSGKSVTT++++ L + Sbjct: 2 EKLLEVKDLNISFHTYAGEVKAIRGVNFDLYKGETLAIVGESGSGKSVTTKSIMRLLPEG 61 Query: 63 NSEI-SGNVQFKGRNLVELSEEEWTKVRGNEISMIFQDPMTSLDPTMKIGMQIAEPMMIH 121- NSEI SG + F G ++ + E++ K+RG +I+MIFQDPMTSL+PTM IG QI+EP++ H Sbjct: 62 NSEIKSGQILFNGMDIAKAHEKQMQKIRGKDIAMIFQDPMTSLNPTMTIGKQISEPLIKH 121- Query: 122 QKISKKDALKLALELMKDVGIPNAEEHINDYPHQWSGGMRQRAVIAIALAADPEILIADE 18- 1 QKISK +A K AL L++ VGI NAEE I YPHQ+SGGMRQR VIAI+LA +P+ILIADE Sbjct: 122 QKISKHEAHKTALRLLQLVGIANAEERIKQYPHQFSGGMRQRVVIAISLACNPQILIADE 18- 1 Query: 182 PTTALDVTIQAQILNLMKKIQAERDSSIVFITHDLGVVAGMADRVAVMYAGKIVEFGTVD 24- 1 PTTALDVTIQAQIL+LMK +Q + D+SI+FITHDLGVVA +ADRVAVMY GKIVE GTVD Sbjct: 182 PTTALDVTIQAQILDLMKDLQKKIDTSIIFITHDLGVVANVADRVAVMYGGKIVEIGTVD 24- 1 Query: 242 EVFYNPQHPYTWGLLNSMPTTDTESGSLESIPGTPPDLLNPPKGDAFAARNEFALDIDHE 30- 1 E+FYNPQHPYTWGL++SMPT DT+ L IPGTPPDLL+PPKGDAFAARN++A+ ID E Sbjct: 242 EIFYNPQHPYTWGLISSMPTLDTDDEELFVIPGTPPDLLHPPKGDAFAARNKYAMQIDLE 30- 1 Query: 302 EEPPYFKVSETHFAATWLLDERSPKVLPPLPIQKRWEKWNEI 343 EEPP FKVS+TH+AATWLL +P+V PP + +R E++ E+ Sbjct: 302 EEPPLFKVSDTHYAATWLLHPDAPEVTPPDAVLRRQEQFAEL 343 There is also homology to SEQ ID 72. SEQ ID 326 (GBS375) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 64 (lane 9; MW 42 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 71 (lane 3; MW 67 kDa). GBS375-GST was purified as shown in FIG. 215, lane 10. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 96 A DNA sequence (GBSx0098) was identified in S. agalactiae <SEQ ID 327> which encodes the amino acid sequence <SEQ ID 328>. Analysis of this protein sequence reveals the following: TABLE-US-00349 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3060 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00350 >GP: AAA62692 GB: M57689 sporulation protein [Bacillus subtilis] Identities = 195/308 (63%), Positives = 245/308 (79%), Gaps = 4/308 (1%) Query: 1 MTENRKKLVEVKNVSLTFNKGKANEVRAIDNVSFDIYEGEVFGLVGESGSGKTTVGRSIL 60 M E +KL+E+K++ F + V+A+D++SFDIY+GE GLVGESG GK+T GRSI+ Sbjct: 1 MNELTEKLLEIKHLKQHFVTPRGT-VKAVDDLSFDIYKGETLGLVGESGCGKSTTGRSII 59 Query: 61 KLYDISDGEITFNGEVISHLKG-KALHSFRKDAQMIFQDPQASLNGRMKIRDIVAEGLDI 119- +LY+ +DGE+ FNGE + K K L F + QMIFQDP ASLN RM + DI+AEGLDI Sbjct: 60 RLYEATDGEVLFNGENVHGRKSRKKLLEFNRKMQMIFQDPYASLNPRMTVADIIAEGLDI 119- Query: 120 HKLAKSKSDRDSKVQALLDLVGLNKDHLTRYPHEFSGGQRQRIGIARALAVEPKFIIADE 17- 9 HKLAK+K +R +V LL+ VGLNK+H RYPHEFSGGQRQRIGIARALAV+P+FIIADE Sbjct: 120 HKLAKTKKERMQRVHELLETVGLNKEHANRYPHEFSGGQRQRIGIARALAVDPEFIIADE 17- 9 Query: 180 PISALDVSIQAQVVNLMQKLQREQGLTYLFIAHDLSMVKYISDRIGVMHWGKLLEVGTSD 23- 9 PISALDVSIQAQVVNLM++LQ+E+GLTYLFIAHDLSMVKYISDRIGVM++GKL+E+ +D Sbjct: 180 PISALDVSIQAQVVNLMKELQKEKGLTYLFIAHDLSMVKYISDRIGVMYFGKLVELAPAD 23- 9 Query: 240 DVYNNPIHPYTKSLLSAIPEPDPESERQRVHQPYNPAIEQ--DGQERQMHEITPGHFVLS 29- 7 ++Y NP+HPYTKSLLSAIP PDP+ ER RV Q Y+P++ Q DG+ + E+ PGHFV+ Sbjct: 240 ELYENPLHPYTKSLLSAIPLPDPDYERNRVRQKYDPSVHQLKDGETMEFREVKPGHFVMC 29- 9 Query: 298 TPQEAEEY 305 T E + + Sbjct: 300 TEAEFKAF 307 A related DNA sequence was identified in S. pyogenes <SEQ ID 329> which encodes the amino acid sequence <SEQ ID 330>. Analysis of this protein sequence reveals the following: TABLE-US-00351 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3900(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00352 Identities = 164/306 (53%), Positives = 228/306 (73%), Gaps = 3/306 (0%) Query: 6 KKLVEVKNVSLTFNKGKANEVRAIDNVSFDIYEGEVFGLVGESGSGKTTVGRSILKLYDI 65 +KLVEVK++ ++F +GK V A+ N +F I +GE F LVGESGSGKTT+GR+I+ L D Sbjct: 3 EKLVEVKDLEISFGEGKKKFV-AVKNANFFIKKGETFSLVGESGSGKTTIGRAIIGLNDT 61 Query: 66 SDGEITFNGEVISHLKGKA-LHSFRKDAQMIFQDPQASLNGRMKIRDIVAEGLDIHKLAK 124- S G+I ++G+VI+ K K+ + + QMIFQDP ASLN R + I++EGL L K Sbjct: 62 SSGQILYDGKVINGRKSKSEANELIRKIQMIFQDPAASLNERATVDYIISEGLYNFNLFK 121- Query: 125 SKSDRDSKVQALLDLVGLNKDHLTRYPHEFSGGQRQRIGIARALAVEPKFIIADEPISAL 18- 4 ++ +R K++ ++ VGL +HLTRYPHEFSGGQRQRIGIARAL + P+F+IADEPISAL Sbjct: 122 TEEERKEKIKNMMAEVGLLSEHLTRYPHEFSGGQRQRIGIARALVMNPEFVIADEPISAL 18- 1 Query: 185 DVSIQAQVVNLMQKLQREQGLTYLFIAHDLSMVKYISDRIGVMHWGKLLEVGTSDDVYNN 24- 4 DVS++AQV+NL++++Q E+GLTYLFIAHDLS+V++ISDRI V+H G ++EV +++++NN Sbjct: 182 DVSVRAQVLNLLKRMQAEKGLTYLFIAHDLSVVRFISDRIAVIHKGVIVEVAETEELFNN 24- 1 Query: 245 PIHPYTKSLLSAIPEPDPESERQRVHQPYNPAIEQDGQER-QMHEITPGHFVLSTPQEAE 30- 3 PIHPYT+SLLSA+P PDP ERQ+ Y+P ++ M EI P HFV + E E Sbjct: 242 PIHPYTQSLLSAVPIPDPILERQKELVVYHPDQHDYTLDKPSMVEIKPNHFVWANQAEIE 30- 1 Query: 304 EYKKQI 309 +Y+K++ Sbjct: 302 KYQKEL 307 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 97 A repeated DNA sequence (GBSx0099) was identified in S. agalactiae <SEQ ID 331> which encodes the amino acid sequence <SEQ ID 332>. Analysis of this protein sequence reveals the following: TABLE-US-00353 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3021(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 98 A repeated DNA sequence (GBSx0100) was identified in S. agalactiae <SEQ ID 333> which encodes the amino acid sequence <SEQ ID 334>. Analysis of this protein sequence reveals the following: TABLE-US-00354 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0352(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 99 A repeated DNA sequence (GBSx0101) was identified in S. agalactiae <SEQ ID 335> which encodes the amino acid sequence <SEQ ID 336>. Analysis of this protein sequence reveals the following: TABLE-US-00355 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5857(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 100 A repeated DNA sequence (GBSx0103) was identified in S. agalactiae <SEQ ID 337> which encodes the amino acid sequence <SEQ ID 338>. Analysis of this protein sequence reveals the following:

TABLE-US-00356 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1472(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 101 A repeated DNA sequence (GBSx0104) was identified in S. agalactiae <SEQ ID 339> which encodes the amino acid sequence <SEQ ID 340>. Analysis of this protein sequence reveals the following: TABLE-US-00357 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0111(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 102 A repeated DNA sequence (GBSx0105) was identified in S. agalactiae <SEQ ID 341> which encodes the amino acid sequence <SEQ ID 342>. Analysis of this protein sequence reveals the following: TABLE-US-00358 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5628(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 103 A repeated DNA sequence (GBSx0106) was identified in S. agalactiae <SEQ ID 343> which encodes the amino acid sequence <SEQ ID 344>. Analysis of this protein sequence reveals the following: TABLE-US-00359 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2059(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database; No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 104 A repeated DNA sequence (GBSx0107) was identified in S. agalactiae <SEQ ID 345> which encodes the amino acid sequence <SEQ ID 346>. Analysis of this protein sequence reveals the following: TABLE-US-00360 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2045(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 105 A DNA sequence (GBSx0108) was identified in S. agalactiae <SEQ ID 347> which encodes the amino acid sequence <SEQ ID 348>. Analysis of this protein sequence reveals the following: TABLE-US-00361 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3031(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00362 >GP: CAB11822 GB: Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 125/282 (44%), Positives = 184/282 (64%) Query: 1 MKIFEKAPAKLNLGLDIKGRCDDGYHELAMIMVSIDLNDYVTISELKEDCIVIDSDSSKM 60 M+I EKAPAK+NL LD+ + DGYHE+ MIM +IDL D + ++EL ED + + S + + Sbjct: 1 MRILEKAPAKINLSLDVTRKRPDGYHEVEMIMTTIDLADRIELTELAEDEVRVSSHNRFV 60 Query: 61 PLNNDNDVFKAADIIKNQYGINKGVHIRLEKSIPVCAGLGGGSTDAAATIRALNRLWNLQ 120- P + N ++AA +IK++Y + KGV I + K IPV AGL GGS+DAAAT+R LNRLWNL Sbjct: 61 PDDQRNLAYQAAKLIKDRYNVKKGVSIMITKVIPVAAGLAGGSSDAAATLRGLNRLWNLN 120- Query: 121 MDYDEMVAIGFKIGSDVPYCLGGGCSLVLGKGEIVKPLPTLRPCWIVLVKPDFGISTKSI 18- 0 + + + +G +IGSDV +C+ GG +L G+GE +K + T CW++L KP G+ST + Sbjct: 121 LSAETLAELGAEIGSDVSFCVYGGTALATGRGEKIKHISTPPHCWVILAKPTIGVSTAEV 18- 0 Query: 181 FRDIDCKSISRVDIDLLKSAILSSDYQLMVKSMGNSLEDITITKNPVISTIKERMLNSGA 24- 0 +R + I D+ + AI +Q M +GN LE +T+ +P ++ IK +M GA Sbjct: 181 YRALKLDGIEHPDVQGMIEAIEEKSFQKMCSRLGNVLESVTLDMHPEVAMIKNQMKRFGA 24- 0 Query: 241 DVALMTGSGPTVFSMCSTEKKADRVFNSMKGFCKEVYKVRLL 282 D LM+GSGPTVF + E K R++N ++GFC +VY VR++ Sbjct: 241 DAVLMSGSGPTVFGLVQYESKVQRIYNGLRGFCDQVYAVRMI 282 A related DNA sequence was identified in S. pyogenes <SEQ ID 349> which encodes the amino acid sequence <SEQ ID 350>. Analysis of this protein sequence reveals the following: TABLE-US-00363 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.87 Transmembrane 28-44 (27-45) ----- Final Results ----- bacterial membrane --- Certainty = 0.2147(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00364 Identities = 33/52 (63%), Positives = 38/52 (72%) Query: 126 MVAIGFKIGSDVPYCLGGGCSLVLGKGEIVKPLPTLRPCWIVLVKPDFGIST 177 M+ IG IGSDVPYCL GC+ V GKGE+V + L W+VLVKPDFGIST Sbjct: 1 MMDIGIPIGSDVPYCLLSGCAQVTGKGEVVCRILGLLSSWVVLVKPDFGIST 52 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 106 A DNA sequence (GBSx0109) was identified in S. agalactiae <SEQ ID 351> which encodes the amino acid sequence <SEQ ID-352>. This protein is predicted to be AdcR protein. Analysis of this protein sequence reveals the following: TABLE-US-00365 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1264(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00366 >GP: CAA96184 GB: Z71552 AdcR protein [Streptococcus pneumoniae] Identities = 77/146 (52%), Positives = 117/146 (79%) Query: 1 MTVLEQKLDHLVSQILLKAENQHELLFGTCQSDVKLTNTQEHILMLLSQEQLTNSDLAKK 60 M L + ++ +++++L+AENQHE+L G C S+V LTNTQEHILMLLS+E LTNS+LA++ Sbjct: 1 MRQLAKDINAFLNEVILQAENQHEILIGHCTSEVALTNTQEHILMLLSEESLTNSELARR 60 Query: 61 LNISQAAVTKAVKSLISQDMLKANKDSKDARITYFELSELAKPIADEHTHHHDNTLGVYG 120- LN+SQAAVTKA+KSL+ + ML+ +KDSKDAR+ +++L++LA+PIA+EH HHH++TL Y Sbjct: 61 LNVSQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAEEHHHHHEHTLLTYE 120- Query: 121 RLVNHFSKDEKVVLERFLDLFSRELE 146 ++ F+ +E+ V++RFL E++ Sbjct: 121 QVATQFTPNEQKVIQRFLTALVGEIK 146 A related DNA sequence was identified in S. pyogenes <SEQ ID 353> which encodes the amino acid sequence <SEQ ID 354>. Analysis of this protein sequence reveals the following: TABLE-US-00367 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1536(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00368 Identities = 106/147 (72%), Positives = 126/147 (85%) Query: 1 MTVLEQKLDHLVSQILLKAENQHELLFGTCQSDVKLTNTQEHILMLLSQEQLTNSDLAKK 60 M +LE+KLD+LV+ ILLKAENQHELLFG CQSDVKLTNTQEHILMLLSQ++LTN+DLAK Sbjct: 1 MGILEKKLDNLVNTILLKAENQHELLFGACQSDVKLTNTQEHILMLLSQQRLTNTDLAKA 60 Query: 61 LNISQAAVTKAVKSLISQDMLKANKDSKDARITYFELSELAKPIADEHTHHHDNTLGVYG 120- LNISQAAVTKA+KSL+ QDML KD+ DAR+TYFEL+ELAKPIA EHTHHHD TL VY Sbjct: 61 LNISQAAVTKAIKSLVKQDMLAGTKDTVDARVTYFELTELAKPIASEHTHHHDETLNVYN 120- Query: 121 RLVNHFSKDEKVVLERFLDLFSRELEG 147 RL+ FS E ++++F+ +F+ ELEG Sbjct: 121 RLLQKFSAKELEIVDKFVTVFAEELEG 147 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 107 A DNA sequence (GBSx0110) was identified in S. agalactiae <SEQ ID 355> which encodes the amino acid sequence <SEQ ID 356>. This protein is predicted to be AdcC protein. Analysis of this protein sequence reveals the following: TABLE-US-00369 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1089(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00370 >GP: CAA96186 GB: Z71552 AdcC protein [Streptococcus pneumoniae] Identities = 182/231 (78%), Positives = 206/231 (88%) Query: 1 MRYITVSGLTFQYDSDPVLEGVNYHLDSGEFVTLTGENGAAKSTLIKATLGILTPKVGTV 60 MRYITV L+F YD +PVLE +NY +DSGEFVTLTGENGAAK+TLIKA+LGIL P++G V Sbjct: 1 MRYITVEDLSFYYDKEPVLEHINYCVDSGEFVTLTGENGAAKTTLIKASLGILQPRIGKV 60 Query: 61 NISKENKEGKKLRIAYLPQQIASFNAGFPSSVYEFVKSGRYPRNGWFRRLTKHDEEHIRV 120- ISK N +GKKLRIAYLPQQIASFNAGFPS+VYEFVKSGRYPR GWFRRL HDEEHI+ Sbjct: 61 AISKTNTQGKKLRIAYLPQQIASFNAGFPSTVYEFVKSGRYPRKGWFRRLNAHDEEHIKA 120- Query: 121 SLEAVGMWDNRHKKIGSLSGGQKQRAVIARMFASDPDIFVLDEPTTGMDAGTTEKFYELM 18- 0 SL++VGMW++R K++GSLSGGQKQRAVIARMFASDPD+F+LDEPTTGMDAG+ +FYELM Sbjct: 121 SLDSVGMWEHRDKRLGSLSGGQKQRAVIARMFASDPDVFILDEPTTGMDAGSKNEFYELM 18- 0 Query: 181 HHNAHKHGKSVLMITHDPDEVKGYADRNIHLVRNQSLPWRCFNVHTNEMEV 231 HH+AH HGK+VLMITHDP+EVK YADRNIHLVRNQ PWRCFNVH N EV Sbjct: 181 HHSAHHHGKAVLMITHDPEEVKDYADRNIHLVRNQDSPWRCFNVHENGQEV 231 A related DNA sequence was identified in S. pyogenes <SEQ ID 357> which encodes the amino acid sequence <SEQ ID 358>. Analysis of this protein sequence reveals the following: TABLE-US-00371 Possible Site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2722(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00372 Identities = 190/232 (81%), Positives = 214/232 (91%) Query: 1 MRYITVSGLTFQYDSDPVLEGVNYHLDSGEFVTLTGENGAAKSTLIKATLGILTPKVGTV 60 MRYI+V L+FQY+S+PVLEG+ YHLDSGEFVT+TGENGAAKSTLIKATLGIL PK G V Sbjct: 1 MRYISVKNLSFQYESEPVLEGITYHLDSGEFVTMTGENGAAKSTLIKATLGILQPKAGRV 60 Query: 61 NISKENKEGKKLRIAYLPQQIASFNAGFPSSVYEFVKSGRYPRNGWFRRLTKHDEEHIRV 120- I+K+NK+GK+LRIAYLPQQ+ASFNAGFPS+VYEFVKSGRYPR+GWFR L KHDEEH++ Sbjct: 61 TIAKKNKDGKQLRIAYLPQQVASFNAGFPSTVYEFVKSGRYPRSGWFRHLNKHDEEHVQA 120- Query: 121 SLEAVGMWDNRHKKIGSLSGGQKQRAVIARMFASDPDIFVLDEPTTGMDAGTTEKFYELM 18- 0 SLEAVGMW+NRHK+IGSLSGGQKQR VIARMFASDPDIFVLDEPTTGMD+GTT+ FYELM Sbjct: 121 SLEAVGMWENRHKRIGSLSGGQKQRVVIARMFASDPDIFVLDEPTTGMDSGTTDTFYELM 18- 0 Query: 181 HHNAHKHGKSVLMITHDPDEVKGYADRNIHLVRNQSLPWRCFNVHTNEMEVE 232 HH+AH+HGKSVLMITHDP+EVK YADRNIHLVRNQ LPWRCFN+H E + E Sbjct: 181 HHSAHQHGKSVLMITHDPEEVKAYADRNIHLVRNQKLPWRCFNIHEAETDDE 232 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 108 A DNA sequence (GBSx0111) was identified in S. agalactiae <SEQ ID 359> which encodes the amino acid sequence <SEQ ID 360>. Analysis of this protein sequence reveals the following: TABLE-US-00373 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2299(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 109 A DNA sequence (GBSx0112) was identified in S. agalactiae <SEQ ID 361> which encodes the amino acid sequence <SEQ ID 362>. This protein is predicted to be AdcB protein (znuB). Analysis of this protein sequence reveals the following: TABLE-US-00374 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.33 Transmembrane 145-161 (136-172) INTEGRAL Likelihood = -11.57 Transmembrane 29-45 (20-47) INTEGRAL Likelihood = -10.56 Transmembrane 261-277 (255-280) INTEGRAL Likelihood = -8.70 Transmembrane 231-247 (227-253) INTEGRAL Likelihood = -5.63 Transmembrane 101-117 (99-121) INTEGRAL Likelihood = -4.94 Transmembrane 186-202 (183-225) INTEGRAL Likelihood = -3.82 Transmembrane 55-71 (54-74) INTEGRAL Likelihood = -3.61 Transmembrane 206-222 (203-225) INTEGRAL Likelihood = -3.03 Transmembrane 78-94 (75-94) ----- Final Results ----- bacterial membrane --- Certainty = 0.6731(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9487> which encodes amino acid sequence <SEQ ID 9488> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00375 >GP: CAA96187 GB: Z71552 AdcB protein [Streptococcus pneumoniae] Identities = 197/263 (74%), Positives = 236/263 (88%) Query: 13 LLDMLSYDFMQRALLAVVAISIFAPILGIFLILRRQSLMSDTLSHVSLAGVALGVVLGIS 72 - +L +LSYDF+QRA LAV+A+S+F+P+LG FLILRRQSLMSDTLSHVSL+GVA G+VLGIS Sbjct: 1 MLSLLSYDFIQRAFLAVIAMSLFSPVLGTFLILRRQSLMSDTLSHVSLSGVAFGLVLGIS 60 Query: 73 PTWSTIFVVTLAAVVLEYLRTVYKHYMEISTAILMSMGLAISLIVMSKAHNVGNVSLEQY 132- PT STI +V +AAV LEYLRTVYK +MEI TAILMS GLA+SLIVMSK + ++SL+QY Sbjct: 61 PTVSTIAIVLIAAVFLEYLRTVYKSFMEIGTAILMSTGLAVSLIVMSKGKSSSSMSLDQY 120- Query: 133 LFGSIITIGKEQVIALFVIALITFILTILFIRPMYILTFDEDTAFVDGLPVRTMSILFNV 19- 2 LFGSI+TI +EQVI+LFVIA + ILT LF+RPMYILTFDEDTAFVDGLPVRTMSILFN+ Sbjct: 121 LFGSIVTISEEQVISLFVIAAVVLILTFLFLRPMYILTFDEDTAFVDGLPVRTMSILFNM 18- 0 Query: 193 VTGIAIALTIPAAGALLVSTIMVLPASIAMRLGRNFKTVIFLGMLIGFVGMVAGIFLSYY 25- 2 VTG+AIAL IPAAGALLVSTIMVLPASIA+RLG+NFK+V+ L IGF+GMVAG+++SYY Sbjct: 181 VTGVAIALMIPAAGALLVSTIMVLPASIALRLGKNFKSVMLLASAIGFLGMVAGLYISYY 24- 0 Query: 253 WETPASATITMIFIGIFLLVSLV 275 ETPASA+IT+IF+ +F+L+SLV Sbjct: 241 AETPASASITIIFVTVFILISLV 263 A related DNA sequence was identified in S. pyogenes <SEQ ID 363> which encodes the amino acid sequence <SEQ ID 364>. Analysis of this protein sequence reveals the following: TABLE-US-00376 Possible site: 18 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -14.97 Transmembrane 135-151 (123-162) INTEGRAL Likelihood = -9.08 Transmembrane 68-84 (44-86) INTEGRAL Likelihood = -6.95 Transmembrane 20-36 (19-37) INTEGRAL Likelihood = -6.90 Transmembrane 251-267 (245-270) INTEGRAL Likelihood = -6.58 Transmembrane 221-237 (217-243) INTEGRAL Likelihood = -6.42 Transmembrane 91-107 (89-111) INTEGRAL Likelihood = -4.78 Transmembrane 176-192 (171-215) INTEGRAL Likelihood = -3.82 Transmembrane 45-61 (44-67) INTEGRAL Likelihood = -3.61 Transmembrane 196-212 (193-215) ----- Final Results ----- bacterial membrane --- Certainty = 0.6986(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00377 >GP: CAA96187 GB: Z71552 AdcB protein [Streptococcus pneumoniae] Identities = 195/262 (74%), Positives = 239/262 (90%) Query: 3 MLDILFYDFMQRAVMAVVAISIFAPILGIFLILRRQSLMSDTLSHVSLAGVALGVVLGIS 62 ML +L YDF+QRA +AV+A+S+F+P+LG FLILRRQSLMSDTLSHVSL+GVA G+VLGIS Sbjct: 1 MLSLLSYDFIQRAFLAVIAMSLFSPVLGTFLILRRQSLMSDTLSHVSLSGVAFGLVLGIS 60 Query: 63 PTITTIIVVVLAAILLEYLRVVYKHYMEISTAILMSLGLALSLIIMSKSHSSSSMSLEQY 122- PT++TI +V++AA+ LEYLR VYK +MEI TAILMS GLA+SLI+MSK SSSSMSL+QY Sbjct: 61 PTVSTIAIVLIAAVFLEYLRTVYKSFMEIGTAILMSTGLAVSLIVMSKGKSSSSMSLDQY 120- Query: 123 LFGSIITISMEQVVALFAIAAIILILTVLFIRPMYILTFDEDTAFVDGLPVRLMSVLFNI 18- 2 LFGSI+TIS EQV++LF IAA++LILT LF+RPMYILTFDEDTAFVDGLPVR MS+LFN+ Sbjct: 121 LFGSIVTISEEQVISLFVIAAVVLILTFLFLRPMYILTFDEDTAFVDGLPVRTMSILFNM 18- 0 Query: 183 VTGVAIALTIPAAGALLVSTIMVLPASIAMRLGKNFKTVILLGIVIGFSGMLSGIFLSYF 24- 2 VTGVAIAL IPAAGALLVSTIMVLPASIA+RLGKNFK+V+LL IGF GM++G+++SY+ Sbjct: 181 VTGVAIALMIPAAGALLVSTIMVLPASIALRLGKNFKSVMLLASAIGFLGMVAGLYISYY 24- 0 Query: 243 FETPASATITMIFISIFLLVSL 264 ETPASA+IT+IF+++F+L+SL Sbjct: 241 AETPASASITIIFVTVFILISL 262 An alignment of the GAS and GBS proteins is shown below:

TABLE-US-00378 Identities = 223/270 (82%), Positives = 252/270 (92%) Query: 12 MLLDMLSYDFMQRALLAVVAISIFAPILGIFLILRRQSLMSDTLSHVSLAGVALGVVLGI 71 - ++LD+L YDFMQRA++AVVAISIFAPILGIFLILRRQSLMSDTLSHVSLAGVALGVVLGI Sbjct: 2 VMLDILFYDFMQRAVMAVVAISIFAPILGIFLILRRQSLMSDTLSHVSLAGVALGVVLGI 61 Query: 72 SPTWSTIFVVTLAAVVLEYLRTVYKHYMEISTAILMSMGLAISLIVMSKAHNVGNVSLEQ 131- SPT +TI VV LAA++LEYLR VYKHYMEISTAILMS+GLA+SLI+MSK+H+ ++SLEQ Sbjct: 62 SPTITTIIVVVLAAILLEYLRVVYKHYMEISTAILMSLGLALSLIIMSKSHSSSSMSLEQ 121- Query: 132 YLFGSIITIGKEQVIALFVIALITFILTILFIRPMYILTFDEDTAFVDGLPVRTMSILFN 19- 1 YLFGSIITI EQV+ALF IA I ILT+LFIRPMYILTFDEDTAFVDGLPVR MS+LFN Sbjct: 122 YLFGSIITISMEQVVALFAIAAIILILTVLFIRPMYILTFDEDTAFVDGLPVRLMSVLFN 18- 1 Query: 192 VVTGIAIALTIPAAGALLVSTIMVLPASIAMRLGRNFKTVIFLGMLIGFVGMVAGIFLSY 25- 1 +VTG+AIALTIPAAGALLVSTIMVLPASIAMRLG+NFKTVI LG++IGF GM++GIFLSY Sbjct: 182 IVTGVAIALTIPAAGALLVSTIMVLPASIAMRLGKNFKTVILLGIVIGFSGMLSGIFLSY 24- 1 Query: 252 YWETPASATITMIFIGIFLLVSLVGLLRKR 281 ++ETPASATITMIFI IFLLVSL G+L+KR Sbjct: 242 FFETPASATITMIFISIFLLVSLGGMLKKR 271 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 110 A DNA sequence (GBSx0113) was identified in S. agalactiae <SEQ ID 365> which encodes the amino acid sequence <SEQ ID 366>. This protein is predicted to be streptodornase. Analysis of this protein sequence reveals the following: TABLE-US-00379 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2601(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00380 >GP: CAA59264 GB: X84793 streptodornase [Streptococcus pyogenes] Identities = 58/167 (34%), Positives = 85/167 (50%), Gaps = 30/167 (17%) Query: 2 TPIYEGNNLVPSRVELQYVGIDKQGKLLEIKLGGGKEQVDEYGVTTVTLENTSPLAKIDY 61 TP+Y+G+ L+P V + + D +DE TV + N IDY Sbjct: 245 TPVYQGSELLPRAVLVSALSSDGF--------------IDE----TVRVFNNVAGFNIDY 28- 6 Query: 62 KTGMLIKEDGKQAEEGEDPNSDADENEAAIE-SASDIEENTNTNTSESDTNNVAPQNRIV 120- + G L+ E P ++ D E +E + IE+ +T+T + D N++ Q + V Sbjct: 287 QNGGLLTES---------PVTETDNVEENVEDNIETIEDEVDTDTLKKDDENISLQ-KTV 33- 6 Query: 121 YVANKGRSNTYWYSLENI-KNANTANIVQMTEQEALNQHKHHSTTEA 166 YVA+ G SN YWYS EN+ KN N +V+M+EQ AL + KHHS EA Sbjct: 337 YVASSGLSNVYWYSKENMPKNVNLDKVVEMSEQTALARGKHHSAQEA 383 A related DNA sequence was identified in S. pyogenes <SEQ ID 367> which encodes the amino acid sequence <SEQ ID 368>. Analysis of this protein sequence reveals the following: TABLE-US-00381 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00382 Identities = 51/90 (56%), Positives = 66/90 (72%), Gaps = 4/90 (4%) Query: 1 MTPIYEGNNLVPSRVELQYVGIDKQGKLLEIKLGGGKEQVDEYGVTTVTLENTSPLAKID 60 +TP+Y N LVP +V LQYVGID+ G LL+IKLG KE VD +GVT+VTL+N SPLA++D Sbjct: 182 VTPVYHKNELVPRQVVLQYVGIDENGDLLQIKLGSEKESVDNFGVTSVTLDNVSPLAELD 24- 1 Query: 61 YKTGMLIKEDGKQAEEGEDPNSDADENEAA 90 Y+TGM++ D Q E ED N + +E E A Sbjct: 242 YQTGMML--DSTQNE--EDSNLETEEFEEA 267 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 111 A DNA sequence (GBSx0114) was identified in S. agalactiae <SEQ ID 369> which encodes the amino acid sequence <SEQ ID 370>. This protein is predicted to be tyrosyl-tRNA synthetase (tyrS-1). Analysis of this protein sequence reveals the following: TABLE-US-00383 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3618(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00384 >GP: AAC00303 GB: AF008220 tyrosine tRNA synthetase [Bacillus subtilis] Identities = 234/420 (55%), Positives = 311/420 (73%), Gaps = 2/420 (0%) Query: 2 NIFDELKERGLVFQTTDEDALRKALEEGSVSYYTGYDPTADSLHLGHLVAILTSRRLQLA 61 N+ ++L RGL+ Q TDE+ L K L E + Y+G+DPTADSLH+GHL+ ILT RR QLA Sbjct: 3 NLLEDLSFRGLIQQMTDEEGLNKQLNEEKIRLYSGFDPTADSLHIGHLLPILTLRRFQLA 62 Query: 62 GHKPYALVGGATGLIGDPSFKDVERSLQTKKTVVSWGNKIRGQLSNFLEFETGDNKAVLV 121- GH P ALVGGATGLIGDPS K ER+L T V W KI+ QLS FL+FE +N AV+ Sbjct: 63 GHHPIALVGGATGLIGDPSGKKAERTLNTADIVSEWSQKIKNQLSRFLDFEAAENPAVIA 122- Query: 122 NNYDWFSNISFIDFLRDVGKYFTVNYMMSKESVKKRIETGISYTEFAYQIMQGYDFYELN 18- 1 NN+DW ++ IDFLRDVGK F +NYM++K++V RIE+GISYTEF+Y I+Q YDF L Sbjct: 123 NNFDWIGKMNVIDFLRDVGKNFGINYMLAKDTVSSRIESGISYTEFSYMILQSYDFLNLY 18- 2 Query: 182 KNYNVTLQIGGSDQWGNMTAGTELIRR--KSNGVSHVMTVPLITDSTGKKFGKSEGNAVW 23- 9 ++ N LQIGGSDQWGN+TAG ELIR+ + + +T+PL+T + G KFGK+EG A+W Sbjct: 183 RDKNCKLQIGGSDQWGNITAGLELIRKSEEEGAKAFGLTIPLVTKADGTKFGKTEGGAIW 24- 2 Query: 240 LDADKTSPYEMYQFWLNVMDADAVRFLKIFTFLSLKEIEDIRIQFEEAPHQRLAQKTLAR 29- 9 LD +KTSPYE YQFW+N D D V++LK FTFLS +EIE + E AP +R AQK LA Sbjct: 243 LDKEKTSPYEFYQFWINTDDRDVVKYLKYFTFLSKEEIEAYAEKTETAPEKREAQKRLAE 30- 2 Query: 300 EVVTLVHGEKAYKEAVNITEQLFAGNIKGLSVKELKQGLRGVPNYHVQTEDNLNIIDLLV 35- 9 EV +LVHG +A ++A+NI++ LF+GNIK LS +++K G + VP+ V + L+++D+LV Sbjct: 303 EVTSLVHGREALEQAINISQALFSGNIKELSAQDVKVGFKDVPSMEVDSTQELSLVDVLV 36- 2 Query: 360 TSGVVNSKRQAREDVSNGAIYINGDRIQDLEYTISENDKLENEITVIRRGKKKYFVLNFK 41- 9 S + SKRQARED+ NGA+YING+R ++ YT+S D++EN+ TV+RRGKKKYF++ +K Sbjct: 363 QSKLSPSKRQAREDIQNGAVYINGERQTEINYTLSGEDRIENQFTVLRRGKKKYFLVTYK 42- 2 A related DNA sequence was identified in S. pyogenes <SEQ ID 371> which encodes the amino acid sequence <SEQ ID 372>. Analysis of this protein sequence reveals the following: TABLE-US-00385 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2340(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00386 Identities = 344/418 (82%), Positives = 377/418 (89%) Query: 1 MNIFDELKERGLVFQTTDEDALRKALEEGSVSYYTGYDPTADSLHLGHLVAILTSRRLQL 60 MNIF+ELK RGLVFQTTDE AL KAL EG VSYYTGYDPTADSLHLGHLVAILTSRRLQL Sbjct: 1 MNIFEELKARGLVFQTTDEQALVKALTEGQVSYYTGYDPTADSLHLGHLVAILTSRRLQL 60 Query: 61 AGHKPYALVGGATGLIGDPSFKDVERSLQTKKTVVSWGNKIRGQLSNFLEFETGDNKAVL 120- AGHKPYALVGGATGLIGDPSFKD ERSLQTK+TV+ W +KI+GQLS FL+FE GDNKA L Sbjct: 61 AGHKPYALVGGATGLIGDPSFKDAERSLQTKETVLEWSDKIKGQLSTFLDFENGDNKAEL 120- Query: 121 VNNYDWFSNISFIDFLRDVGKYFTVNYMMSKESVKKRIETGISYTEFAYQIMQGYDFYEL 18- 0 VNNYDWFS ISFIDFLRDVGKYFTVNYMNSK+SVKKRIETGISYTEFAYQIMQGYDFYEL Sbjct: 121 VNNYDWFSQISFIDFLRDVGKYFTVNYMMSKDSVKKRIETGISYTEFAYQIMQGYDFYEL 18- 0 Query: 181 NKNYNVTLQIGGSDQWGNMTAGTELIRRKSNGVSHVMTVPLITDSTGKKFGKSEGNAVWL 24- 0 N +NVTLQIGGSDQWGNMTAGTEL+R+K++ HVMTVPLITDSTGKKFGKSEGNAVWL Sbjct: 181 NDKHNVTLQIGGSDQWGNMTAGTELLRKKADKTGHVMTVPLITDSTGKKFGKSEGNAVWL 24- 0 Query: 241 DADKTSPYEMYQEWLNVMDADAVRFLKIFTFLSLKEIEDIRIQFEEAPHQRLAQKTLARE 30- 0 DADKTSPYEMYQFWLNVMD DAVRFLKIFTFLSL EI +I QF A H+RLAQKTLARE Sbjct: 241 DADKTSPYEMYQFWLNVMDDDAVRFLKIFTFLSLDEIAEIETQFNAARHERLAQKTLARE 30- 0 Query: 301 VVTLVHGEKAYKEAVNITEQLFAGNIKGLSVKELKQGLRGVPNYHVQTEDNLNIIDLLVT 36- 0 VVTLVHGE+AYK+A+NITEQLFAGNIK LS ELKQGL VPNYHVQ+ DN NI+++LV Sbjct: 301 VVTLVHGEEAYKQALNITEQLFAGNIKNLSANELKQGLSNVPNYHVQSIDNHNIVEILVA 36- 0 Query: 361 SGVVNSKRQAREDVSNGAIYINGDRIQDLEYTISENDKLENEITVIRRGKKKYFVLNF 418 + + SKRQAREDV NGAIYINGDR+QDL+Y +S +DK+++++TVIRRGKKKY VL + Sbjct: 361 AKISPSKRQAREDVQNGAIYINGDRVQDLDYQLSNDDKIDDQLTVIRRGKKKYAVLTY 418 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 112 A DNA sequence (GBSx0115) was identified in S. agalactiae <SEQ ID 373> which encodes the amino acid sequence <SEQ ID 374>. Analysis of this protein sequence reveals the following: TABLE-US-00387 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.21 Transmembrane 36-52 (23-59) ----- Final Results ----- bacterial membrane --- Certainty = 0.5883(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00388 >GP: AAF04736 GB: AF101781 penicillin-binding protein 1b [Streptococcus pneumoniae] Identities = 445/769 (57%), Positives = 581/769 (74%), Gaps = 9/769 (1%) Query: 3 KGNKKLNSSKLGDYTP----LEFGSIFLRI---VKLLSDFIYVIILLFVMLGVGLAVGYL 55 K K K G T L+ +IF I +K L + ++V+ L MLG G+A+GY Sbjct: 21 KNKKSARPGKKGSSTKKSKTLDKSAIFPAILLSIKALFNLLFVLGFLGGMLGAGIALGYG 80 Query: 56 ASQVDSVKVPSKNSLVTQVNTLTRVSRLTYSDKSQISEIATDLQRTPVAKDAISDNIKKA 115- + D V+VP LV QV ++ +S +TYSD + I+ I +DL RT ++ + IS+N+KKA Sbjct: 81 VALFDKVRVPQTEELVNQVKDISSISEITYSDGTVIASIESDLLRTSISSEQISENLKKA 140- Query: 116 IIATEDENFNDHKGVVPKAVLRAAAGSVLGFGESSGGSTLTQQLLKQQILGDDPSFKRKS 17- 5 IIATEDE+F +HKGVVPKAV+RA G +G G SSGGSTLTQQL+KQQ++GD P+ RK+ Sbjct: 141 IIATEDEHFKEHKGVVPKAVIRATLGKFVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKA 20- 0 Query: 176 KEIIYALALERYMDKDSILSDYLNVSPFGRNNKGQNIAGIEEAAQGIFGVSAKDLTIPQA 23- 5 EI+ ALALER M+KD IL+ YLNV+PFGRNNKGQNIAG +AA+GIFGV A LT+PQA Sbjct: 201 AEIVDALALERAMNKDEILTTYLNVAPFGRNNKGQNIAGARQAAEGIFGVDASQLTVPQA 26- 0 Query: 236 AFLAGLPQSPIVYSPYTADAQLKSDKDLSFGIKRQKNVLYNMYRTRALTKDEYKSYKDYD 29- 5 AFLAGLPQSPI YSPY +LKSD+DL G++R K VLY+MYRT AL+KDEY YKDYD Sbjct: 261 AFLAGLPQSPITYSPYENTGELKSDEDLEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYD 32- 0 Query: 296 IKKDFIKPAVATTNHHDYLYYSALSEAQKVMYNYLIKKDNVSEHDLKNDETRATYRHRAI 35- 5 +K+DF+ T DYLY++ L+EAQ+ MY+YL ++DNVS +LKN+ T+ YR A Sbjct: 321 LKQDFLPSGTVTGISRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAA 38- 0 Query: 356 EEIQQGGYTIKTTINKSVYQAMQDAAAQYGGLLDDGTGKVQMGNVLTDNSSGAIIGFIGG 41- 5 +EI+ GGY I TTI++ ++ AMQ A A YG LLDDGTG+V++GNVL DN +GAI+GF+GG Sbjct: 381 KEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGG 44- 0 Query: 416 RNYSENQNNHAFDTARSPGSSIKPILPYGIAIDQGMLGSGSVLSNYPTTYSSGEKIMHAD 47- 5 RNY ENQNNHAFDT RSP S+ KP+L YGIAIDQG++GS ++LSNYPT +++G IM+A+ Sbjct: 441 RNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYAN 50- 0 Query: 476 EEGTAMVNLQESLDISWNIPAFWTYKMLRDRGVDVKNYMEKLDYPIENFGIESLPLGGGI 53- 5 +GT M+ L E+L+ SWNIPA+WTY+MLR+ GVDVK YMEK+ Y I +GIESLP+GGGI Sbjct: 501 SKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGI 56- 0 Query: 536 DTSVAQQTNLYQMIANGGVYHKQYMIESIEDSNGKVIYNHESKPVRVFSKATATILQQLL 59- 5 + +VAQ TN YQ +AN GVYH++++I IE ++G+V+Y ++ KPV+V+SKATATI+Q LL Sbjct: 561 EVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLL 62- 0 Query: 596 HGPINSGKTTTFKNRLQGLNSGLAGVDWIGKTGTTNSTSDVWLMLSTPKVTLGGWAGHDN 65- 5 ++S TTTFK+ L LN LA DWIGKTGTTN ++WLMLSTP++TLGGW GHD+ Sbjct: 621 REVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDD 68- 0 Query: 656 NASLAKLTGYNNNANYMAHLVNAINNADGNTFGKSERFRLDDSVIKAKVLKSTGLQPGVV 71- 5 N SL++ GY+NN+NYMAHLVNAI A + +G +ERF LD SV+K++VLKSTG +PG V Sbjct: 681 NHSLSRRAGYSNNSNYMAHLVNAIQQASPSIWG-NERFALDPSVVKSEVLKSTGQKPGKV 73- 9 Query: 716 TVNGRRITVGGESTTSYWA-KNGPGTMTYRFAIGGTDSDYQKAWSTLGG 763 +V G+ + V G + TSYWA K+G +YRFAIGG+D+DYQ AWS++ G Sbjct: 740 SVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVG 788 A related DNA sequence was identified in S. pyogenes <SEQ ID 375> which encodes the amino acid sequence <SEQ ID 376>. Analysis of this protein sequence reveals the following: TABLE-US-00389 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.83 Transmembrane 39-55 (32-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.2932(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00390 >GP: AAF04736 GB: AF101781 penicillin-binding protein 1b [Streptococcus pneumoniae] Identities = 438/739 (59%), Positives = 580/739 (78%), Gaps = 2/739 (0%) Query: 27 PVLLRTLRLLSNFFYIVIFLFGMMGFGMAFGYLASQIESVKVPSKESLVKQVESLTMISQ 86 - P +L +++ L N +++ FL GM+G G+A GY + + V+VP E LV QV+ ++ IS+ Sbjct: 48 PAILLSIKALFNLLFVLGFLGGMLGAGIALGYGVALFDKVRVPQTEELVNQVKDISSISE 107- Query: 87 MNYSDNSLISTLDTDLLRTPVANDAISENIKKAIVSTEDEHFQEHKGIVPKAVFRATLAS 146- + YSD ++I+++++DLLRT ++++ ISEN+KKAI++TEDEHF+EHKG+VPKAV RATL Sbjct: 108 ITYSDGTVIASIESDLLRTSISSEQISENLKKAIIATEDEHFKEHKGVVPKAVIRATLGK 16- 7 Query: 147 VLGFGEASGGSTLTQQLVKQQVLGDDPTFKRKSKEIVYALALERYMSKDNILCDYLNVSP 20- 6 +G G +SGGSTLTQQL+KQQV+GD PT RK+ EIV ALALER M+KD IL YLNV+P Sbjct: 168 FVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKAAEIVDALALERAMNKDEILTTYLNVAP 22- 7 Query: 207 FGRNNKGQNIAGVEEAARGIFGVSAKDLTVPQAAFLAGLPQSPIVYSPYLSTGQLKSEKD 26- 6 FGRNNKGQNIAG +AA GIFGV A LTVPQAAFLAGLPQSPI YSPY +TG+LKS++D Sbjct: 228 FGRNNKGQNIAGARQAAEGIFGVDASQLTVPQAAFLAGLPQSPITYSPYENTGELKSDED 28- 7 Query: 267 MAYGIKRQQNVLFNMYRTGVLSKKEYEDYKAYPIQKDFIQPGSAIVNNHDYLYYTVLADA 32- 6 + G++R + VL++MYRTG LSK EY YK Y +++DF+ G+ + DYLY+T LA+A Sbjct: 288 LEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYDLKQDFLPSGTVTGISRDYLYFTTLAEA 34- 7 Query: 327 KKAMYSYLIKRDKVSSRDLKNDETKAAYEERALTELQQGGYTITTTINKPIYNAMQTAAA 38- 6 ++ MY YL +RD VS+++LKN+ T+ Y + A E++ GGY ITTTI++ I++AMQ+A A Sbjct: 348 QERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVA 40- 7 Query: 387 QFGGLLDDGTGTVQMGNVLTDNATGAVLGFVGGRDYALNQNNHAFNTVRSPGSSIKPIIA 44- 6 +G LLDDGTG V++GNVL DN TGA+LGFVGGR+Y NQNNHAF+T RSP S+ KP++A Sbjct: 408 DYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLA 46- 7 Query: 447 YGPAIDQGLMGSASVLSNYPTTYSSGQKIMHADSEGTAMMPLQEALNTSWNIPAFWTQKL 50- 6 YG AIDQGLMGS ++LSNYPT +++G IM+A+S+GT MM L EALN SWNIPA+WT ++ Sbjct: 468 YGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRM 52- 7 Query: 507 LREKGVDVENYMTKMGYKIADYSIESLPLGGGIEVSVAQQTNAYQMLSNNGLYQKQYIVD 56- 6 LRE GVDV+ YM KMGY+I +Y IESLP+GGGIEV+VAQ TN YQ L+NNG+Y +++++ Sbjct: 528 LRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVIS 58- 7 Query: 567 KITASDGTVVYKHENKPIRIFSAATATILQELLRGPITSGATTTFKNRLAAINPWLANAD 62- 6 KI A+DG VVY++++KP++++S ATATI+Q LLR ++S TTTFK+ L ++NP LANAD Sbjct: 588 KIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANAD 64- 7 Query: 627 WIGKTGTTENYTDVWLVLSTPKVTLGGWAGHDDNTSLAPLTGYNNNSNYLAYLANAINQA 68- 6 WIGKTGTT ++WL+LSTP++TLGGW GHDDN SL+ GY+NNSNY+A+L NAI QA Sbjct: 648 WIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSRRAGYSNNSNYMAHLVNAIQQA 70- 7 Query: 687 DPNVIGVGQRFNLDPGVIKANVLKSTGLQPGTVNVNGHTFSVGGEMTTSLWSQK-GPGAM 74- 5 P++ G +RF LDP V+K+ VLKSTG +PG V+V G V G TS W+ K G A Sbjct: 708 SPSIWG-NERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPAT 76- 6 Query: 746 TYRFAIGGTDADYQKAWGN 764 +YRFAIGG+DADYQ AW + Sbjct: 767 SYRFAIGGSDADYQNAWSS 785 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00391 Identities = 531/760 (69%), Positives = 639/760 (83%), Gaps = 3/760 (0%) Query: 6 KKLNSSKLGDYTPLEFGSIFLRIVKLLSDFIYVIILLFVMLGVGLAVGYLASQVDSVKVP 65 K+++ +LG L+ G + LR ++LLS+F Y++I LF M+G G+A GYLASQ++SVKVP Sbjct: 13 KRISHQRLG---LLDLGPVLLRTLRLLSNFFYIVIFLFGMMGFGMAFGYLASQIESVKVP 69 Query: 66 SKNSLVTQVNTLTRVSRLTYSDKSQISEIATDLQRTPVAKDAISDNIKKAIIATEDENFN 125- SK SLV QV +LT +S++ YSD S IS + TDL RTPVA DAIS+NIKKAI++TEDE+F Sbjct: 70 SKESLVKQVESLTMISQMNYSDNSLISTLDTDLLRTPVANDAISENIKKAIVSTEDEHFQ 129- Query: 126 DHKGVVPKAVLRAAAGSVLGFGESSGGSTLTQQLLKQQILGDDPSFKRKSKEIIYALALE 18- 5 +HKG+VPKAV RA SVLGFGE+SGGSTLTQQL+KQQ+LGDDP+FKRKSKEI+YALALE Sbjct: 130 EHKGIVPKAVFRATLASVLGFGEASGGSTLTQQLVKQQVLGDDPTFKRKSKEIVYALALE 18- 9 Query: 186 RYMDKDSILSDYLNVSPFGRNNKGQNIAGIEEAAQGIFGVSAKDLTIPQAAFLAGLPQSP 24- 5 RYM KD+IL DYLNVSPFGRNNKGQNIAG+EEAA+GIFGVSAKDLT+PQAAFLAGLPQSP Sbjct: 190 RYMSKDNILCDYLNVSPFGRNNKGQNIAGVEEAARGIFGVSAKDLTVPQAAFLAGLPQSP 24- 9 Query: 246 IVYSPYTADAQLKSDKDLSFGIKRQKNVLYNMYRTRALTKDEYKSYKDYDIKKDFIKPAV 30- 5 IVYSPY + QLKS+KD+++GIKRQ+NVL+NMYRT L+K EY+ YK Y I+KDFI+P Sbjct: 250 IVYSPYLSTGQLKSEKDMAYGIKRQQNVLFNMYRTGVLSKKEYEDYKAYPIQKDFIQPGS 30- 9 Query: 306 ATTNHHDYLYYSALSEAQKVMYNYLIKKDNVSEHDLKNDETRATYRHRAIEEIQQGGYTI 36- 5 A N+HDYLYY+ L++A+K MY+YLIK+D VS DLKNDET+A Y RA+ E+QQGGYTI Sbjct: 310 AIVNNHDYLYYTVLADAKKAMYSYLIKRDKVSSRDLKNDETKAAYEERALTELQQGGYTI 36- 9 Query: 366 KTTINKSVYQAMQDAAAQYGGLLDDGTGKVQMGNVLTDNSSGAIIGFIGGRNYSENQNNH 42- 5 TTINK +Y AMQ AAAQ+GGLLDDGTG VQMGNVLTDN++GA++GF+GGR+Y+ NQNNH Sbjct: 370 TTTINKPIYNAMQTAAAQFGGLLDDGTGTVQMGNVLTDNATGAVLGFVGGRDYALNQNNH 42- 9 Query: 426 AFDTARSPGSSIKPILPYGIAIDQGMLGSGSVLSNYPTTYSSGEKIMHADEEGTAMVNLQ 48- 5 AF+T RSPGSSIKPI+ YG AIDQG++GS SVLSNYPTTYSSG+KIMHAD EGTAM+ LQ Sbjct: 430 AFNTVRSPGSSIKPIIAYGPAIDQGLMGSASVLSNYPTTYSSGQKIMHADSEGTAMMPLQ 48- 9 Query: 486 ESLDISWNIPAFWTYKMLRDRGVDVKNYMEKLDYPIENFGIESLPLGGGIDTSVAQQTNL 54- 5 E+L+ SWNIPAFWT K+LR++GVDV+NYM K+ Y I ++ IESLPLGGGI+ SVAQQTN Sbjct: 490 EALNTSWNIPAFWTQKLLREKGVDVENYMTKMGYKIADYSIESLPLGGGIEVSVAQQTNA 54- 9 Query: 546 YQMIANGGVYHKQYMIESIEDSNGKVIYNHESKPVRVFSKATATILQQLLHGPINSGKTT 60- 5 YQM++N G+Y KQY+++ I S+G V+Y HE+KP+R+FS ATATILQ+LL GPI SG TT Sbjct: 550 YQMLSNNGLYQKQYIVDKITASDGTVVYKHENKPIRIFSAATATILQELLRGPITSGATT 60- 9 Query: 606 TFKNRLQGLNSGLAGVDWIGKTGTTNSTSDVWLMLSTPKVTLGGWAGHDNNASLAKLTGY 66- 5 TFKNRL +N LA DWIGKTGTT + +DVWL+LSTPKVTLGGWAGHD+N SLA LTGY Sbjct: 610 TFKNRLAAINPWLANADWIGKTGTTENYTDVWLVLSTPKVTLGGWAGHDDNTSLAPLTGY 66- 9 Query: 666 NNNANYMAHLVNAINNADGNTFGKSERFRLDDSVIKAKVLKSTGLQPGVVTVNGRRITVG 72- 5 NNN+NY+A+L NAIN AD N G +RF LD VIKA VLKSTGLQPG V VNG +VG Sbjct: 670 NNNSNYLAYLANAINQADPNVIGVGQRFNLDPGVIKANVLKSTGLQPGTVNVNGHTFSVG 72- 9 Query: 726 GESTTSYWAKNGPGTMTYRFAIGGTDSDYQKAWSTLGGKR 765 GE TTS W++ GPG MTYRFAIGGTD+DYQKAW G ++ Sbjct: 730 GEMTTSLWSQKGPGAMTYRFAIGGTDADYQKAWGNFGFRK 769 SEQ ID 374 (GBS64d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 120 (lane 24; MW 107 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 120 (lane 5-7; MW 82 kDa) and in FIG. 179 (lane 2; MW 82 kDa). GBS64d-His was purified as shown in FIG. 231, lane 7-8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 113 A DNA sequence (GBSx0116) was identified in S. agalactiae <SEQ ID 377> which encodes the amino acid sequence <SEQ ID 378>. This protein is predicted to be DNA-dependent RNA polymerase subunit beta (rpoB). Analysis of this protein sequence reveals the following:

TABLE-US-00392 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3505(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00393 >GP: CAB56706 GB: Y16468 DNA-dependent RNA polymerase subunit beta [Listeria monocytogenes] Identities = 814/1173 (69%), Positives = 978/1173 (82%), Gaps = 17/1173 (1%) Query: 2 AGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFLDAGLKEVFEDVLPISNFTDT 61 +GH+V+YG+HRTRRSF+RI EVL+LPNLIEIQT S+Q FLD GL+E+F D+ PI +F Sbjct: 5 SGHDVKYGRHRTRRSFARISEVLELPNLIEIQTASYQWFLDEGLREMFRDISPIEDFAGN 64 Query: 62 MDLEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLVNKETGEIKTQEVFFGDFPIMTE 121- + LEF+ Y+L EPKY++EE++ DA+Y+AP+ V RL+NKETGE+K QEVF GDFP+MTE Sbjct: 65 LSLEFIDYDLGEPKYSVEESKNRDANYAAPLRVKLRLINKETGEVKDQEVFMGDFPLMTE 124- Query: 122 MGTFIINGGERIIVSQLVRSPGVYFNDKVDKNGKVGYGSTVIPNRGAWLELETDAKDIAY 18- 1 MGTFIING ER+IVSQLVRSPGVYFN K+DKNGK G+GSTVIPNRGAWLE ETDAKD+ + Sbjct: 125 MGTFIINGAERVIVSQLVRSPGVYFNGKLDKNGKKGFGSTVIPNRGAWLEYETDAKDVVH 18- 4 Query: 182 TRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVRNTIEKDIHKNPSDSRTDEALKEI 24- 1 RIDRTRK+P T L+RALGF D EI+D+ GD++ +RNT+EKD N ++AL EI Sbjct: 185 VRIDRTRKLPVTVLLRALGFGSDQEIIDLIGDNDYLRNTLEKDNTDN-----AEKALLEI 23- 9 Query: 242 YERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGRYKINKKLNLKTRLLNQTIAENLVD 30- 1 YERLRPGEP T D++RSLLV+RFFDP+RYDLA+VGRYKINKKL+LK RL NQT+AE LVD Sbjct: 240 YERLRPGEPPTVDNARSLLVSRFFDPKRYDLASVGRYKINKKLHLKNRLFNQTLAETLVD 29- 9 Query: 302 GETGEILVEAGTVMTRDVIDSIAEHIDGDLNKFVYTPNDYAVVTEPVILQKFKVVAPTDP 36- 1 ETGEI+ G ++ R +D I +++ + P D V+ + V++Q K+ AP D Sbjct: 300 PETGEIIASKGDILDRRNLDQIIPNLENGVGFRTLRPTD-GVMEDSVLVQSIKIYAPNDE 35- 8 Query: 362 DRVVTIVGNSNPEDKVRALTPADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGELLA 42- 1 ++ + I+GN+ E+ V+ +TP+DI++ +SYF NL G+G DDIDHLGNRR+R+VGELL Sbjct: 359 EKEINIIGNAYIEENVKHITPSDIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQ 41- 8 Query: 422 NQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNPL 48- 1 NQFRIGL+RMER VRERMS+QD +TPQQ+INIRPV A++KEFFGSSQLSQFMDQ NPL Sbjct: 419 NQFRIGLSRMERVVRERMSIQDMTTITPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPL 47- 8 Query: 482 SELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFGHL 54- 1 EL+HKRRLSALGPGGLTR+RAGYEVRDVHY+HYGRMCPIETPEGPNIGLIN+LSSF + Sbjct: 479 GELTHKRRLSALGPGGLTRERAGYEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSFAKV 53- 8 Query: 542 NKYGFIQTPYRKVDRSTGAVTNEIVWLTADEEDEFTVAQANSKLNEDGTFAEEIVMGRHQ 60- 1 NK+GFI+TPYR+VD T VT++I +LTADEED + VAQANSKL+E GTF EE VM R + Sbjct: 539 NKFGFIETPYRRVDPETNRVTDKIDYLTADEEDNYVVAQANSKLDEQGTFTEEEVMARFR 59- 8 Query: 602 GNNQEFPSSIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAPY 66- 1 N +D++DVSPKQVV+VATACIPFLENDDSNRALMGANMQRQAVPL+ P+AP+ Sbjct: 599 SENLAVEKERIDYMDVSPKQVVSVATACIPFLENDDSNRALMGANMQRQAVPLMHPEAPF 65- 8 Query: 662 VGTGMEYQAAHDSGAAVIAKHDGRVIFSDAEKVEVRRED--------GSLDVYHVQKFRR 71- 3 VGTGME+ +A DSGAAV AKHDG V +A ++ VRR G +D Y ++KF R Sbjct: 659 VGTGMEHVSAKDSGAAVTAKHDGIVEHVEAREIWVRRVSLVDGKEVTGGIDKYTLRKFVR 71- 8 Query: 714 SNSGTAYNQRTLVKVGDLVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVIM 77- 3 SN GT YNQR V GD V KG+ + +GPSM++GE+ALG+N +VA+MTW+GYN+EDA+IM Sbjct: 719 SNQGTCYNQRPNVAEGDRVVKGEILGNGPSMDSGELALGRNVLVAFMTWDGYNYEDAIIM 77- 8 Query: 774 SERLVKEDVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDSLRDLDEMGIIRIGAEVK 83- 3 SERLVK+DVYTS+H+EEFESE RDTKLGPEE+TR+IPNVGED+LRDLDE GIIR+GAEVK Sbjct: 779 SERLVKDDVYTSIHIEEFESEARDTKLGPEEMTRDIPNVGEDALRDLDERGIIRVGAEVK 83- 8 Query: 834 EGDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRAN 89- 3 + D+LVGKVTPKG +L+AEERLLHAIFG+K+REVRDTSLRVPHGG G+V DVKIFTR Sbjct: 839 DNDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVLDVKIFTREA 89- 8 Query: 894 GDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIML 95- 3 GDEL GVN LVRVYI QKRKI GDKMAGRHGNKGV+SRI+P EDMP++PDGTPVDIML Sbjct: 899 GDELPPGVNQLVRVYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPFMPDGTPVDIML 95- 8 Query: 954 NPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWETVQEAGMDSDAKTVL 10- 13 NPLGVPSRMNIGQV+ELHLGMAAR LGIH+ATPVFDGA+ ED+W TV+EAGM DAKT+L Sbjct: 959 NPLGVPSRMNIGQVLELHLGMAARALGIHVATPVFDGANEEDVWSTVEEAGMARDAKTIL 10- 18 Query: 1014 YDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGE 1- 073 YDGR+GE FDNR+SVGVMYMIKL HMVDDKLHARS GPYSLVTQQPLGGKAQFGGQRFGE Sbjct: 1019 YDGRSGEAFDNRISVGVMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1- 078 Query: 1074 MEVWALEAYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQS 1- 133 MEVWALEAYGA+ LQEILT KSDDV GR+K YEAI KG+ +P+PGVPESF+VL+KELQS Sbjct: 1079 MEVWALEAYGAAYTLQEILTIKSDDVVGRVKTYEAIVKGESVPEPGVPESFKVLIKELQS 1- 138 Query: 1134 LGLDMRVLDEDDNEVELRDLDEGEDDDVMHVDD 1166 LG+D+++L D+ E+E+RD+D DDD + +D Sbjct: 1139 LGMDVKMLSADEEEIEMRDMD---DDDFTNQND 1168 A related DNA sequence was identified in S. pyogenes <SEQ ID 379> which encodes the amino acid sequence <SEQ ID 380>. Analysis of this protein sequence reveals the following: TABLE-US-00394 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3392(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00395 Identities = 1129/1190 (94%), Positives = 1168/1190 (97%), Gaps = 3/1190 (0%) Query: 1 MAGHEVQYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFLDAGLKEVFEDVLPISNFTD 60 +AGHEV+YGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFLD+GLKEVFEDVLPISNFTD Sbjct: 1 LAGHEVRYGKHRTRRSFSRIKEVLDLPNLIEIQTDSFQDFLDSGLKEVFEDVLPISNFTD 60 Query: 61 TMDLEFVGYELKEPKYTLEEARIHDASYSAPIFVTFRLVNKETGEIKTQEVFFGDFPIMT 120- TM+LEFVGYE KEPKYTLEEARIHDASYSAPIFVTFRLVNKETGEIKTQEVFFGDFPIMT Sbjct: 61 TMELEFVGYEFKEPKYTLEEARIHDASYSAPIFVTFRLVNKETGEIKTQEVFFGDFPIMT 120- Query: 121 EMGTFIINGGERIIVSQLVRSPGVYFNDKVDKNGKVGYGSTVIPNRGAWLELETDAKDIA 18- 0 EMGTFIINGGERIIVSQLVRSPGVYFNDKVDKNGKVGYGSTVIPNRGAWLELETD+KDIA Sbjct: 121 EMGTFIINGGERIIVSQLVRSPGVYFNDKVDKNGKVGYGSTVIPNRGAWLELETDSKDIA 18- 0 Query: 181 YTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGDSELVRNTIEKDIHKNPSDSRTDEALKE 24- 0 YTRIDRTRKIPFTTLVRALGFSGDDEIVDIFG+S+LVRNTIEKDIHKNPSDSRTDEALKE Sbjct: 181 YTRIDRTRKIPFTTLVRALGFSGDDEIVDIFGESDLVRNTIEKDIHKNPSDSRTDEALKE 24- 0 Query: 241 IYERLRPGEPKTADSSRSLLVARFFDPRRYDLAAVGRYKINKKLNLKTRLLNQTIAENLV 30- 0 IYERLRPGEPKTADSSRSLL+ARFFD RRYDLAAVGRYK+NKKLN+KTRLLNQ IAENLV Sbjct: 241 IYERLRPGEPKTADSSRSLLIARFFDARRYDLAAVGRYKVNKKLNIKTRLLNQIIAENLV 30- 0 Query: 301 DGETGEILVEAGTVMTRDVIDSIAEHIDGDLNKFVYTPNDYAVVTEPVILQKFKVVAPTD 36- 0 D ETGEILVEAGT MTR VI+SI EH+DGDLNKFVYTPNDYAVVTEPV+LQKFKVV+P D Sbjct: 301 DAETGEILVEAGTEMTRSVIESIEEHLDGDLNKFVYTPNDYAVVTEPVVLQKFKVVSPID 36- 0 Query: 361 PDRVVTIVGNSNPEDKVRALTPADILAEMSYFLNLAEGIGKVDDIDHLGNRRIRAVGELL 42- 0 PDRVVTIVGN+NP+DKVRALTPADILAEMSYFLNLAEG+GKVDDIDHLGNRRIRAVGELL Sbjct: 361 PDRVVTIVGNANPDDKVRALTPADILAEMSYFLNLAEGLGKVDDIDHLGNRRIRAVGELL 42- 0 Query: 421 ANQFRIGLARMERNVRERMSVQDNEVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNP 48- 0 ANQFRIGLARMERNVRERMSVQDN+VLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNP Sbjct: 421 ANQFRIGLARMERNVRERMSVQDNDVLTPQQIINIRPVTAAVKEFFGSSQLSQFMDQHNP 48- 0 Query: 481 LSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFGH 54- 0 LSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFGH Sbjct: 481 LSELSHKRRLSALGPGGLTRDRAGYEVRDVHYTHYGRMCPIETPEGPNIGLINNLSSFGH 54- 0 Query: 541 LNKYGFIQTPYRKVDRSTGAVTNEIVWLTADEEDEFTVAQANSKLNEDGTFAEEIVMGRH 60- 0 LNKYGFIQTPYRKVDR+TG VTNEIVWLTADEEDE+TVAQANSKLNEDGTFAEEIVMGRH Sbjct: 541 LNKYGFIQTPYRKVDRATGTVTNEIVWLTADEEDEYTVAQANSKLNEDGTFAEEIVMGRH 60- 0 Query: 601 QGNNQEFPSSIVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAP 66- 0 QGNNQEF +S+VDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPRAP Sbjct: 601 QGNNQEFSASVVDFVDVSPKQVVAVATACIPFLENDDSNRALMGANMQRQAVPLIDPKAP 66- 0 Query: 661 YVGTGMEYQAAHDSGAAVIAKHDGRVIFSDAEKVEVRREDGSLDVYHVQKFRRSNSGTAY 72- 0 YVGTGMEYQAAHDSGAAVIA+ +G+V+FSDAEKVE+RR+DGSLDVYH+ KFRRSNSGTAY Sbjct: 661 YVGTGMEYQAAHDSGAAVIAQQNGKVVFSDAEKVEIRRQDGSLDVYHITKFRRSNSGTAY 72- 0 Query: 721 NQRTLVKVGDLVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKE 78- 0 NQRTLVKVGD+VEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKE Sbjct: 721 NQRTLVKVGDIVEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKE 78- 0 Query: 781 DVYTSVHLEEFESETRDTKLGPEEITREIPNVGEDSLRDLDEMGIIRIGAEVKEGDILVG 84- 0 DVYTSVHLEEFESETRDTKLGPEEITREIPNVGE++L+DLDEMGIIRIGAEVKEGDILVG Sbjct: 781 DVYTSVHLEEFESETRDTKLGPEEITREIPNVGEEALKDLDEMGIIRIGAEVKEGDILVG 84- 0 Query: 841 KVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGVVRDVKIFTRANGDELQSG 90- 0 KVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDG+VRDVKIFTRANGDELQSG Sbjct: 841 KVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVIKFTRANGDELQSG 90- 0 Query: 901 VNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPS 96- 0 VNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPS Sbjct: 901 VNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPS 96- 0 Query: 961 RMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWETVQEAGMDSDAKTVLYDGRTGE 10- 20 RMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLW+TV+EAGMDSDAKTVLYDGRTGE Sbjct: 961 RMNIGQVMELHLGMAARNLGIHIATPVFDGASSEDLWDTVREAGMDSDAKTVLYDGRTGE 10- 20 Query: 1021 PFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1- 080 PFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE Sbjct: 1021 PFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1- 080 Query: 1081 AYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQSLGLDMRV 1- 140 AYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESFRVLVKELQSLGLDMRV Sbjct: 1081 AYGASNVLQEILTYKSDDVTGRLKAYEAITKGKPIPKPGVPESERVLVKELQSLGLDNRV 1- 140 Query: 1141 LDEDDNEVELRDLDEGEDDDVMHVDDLEKARVKQEAEEKQAEQVSEVVQE 1190 LDEDDNEVELRDLDEGEDDD+MHVDDLEKAR KQ E ++VSE E Sbjct: 1141 LDEDDNEVELRDLDEGEDDDIMHVDDLEKAREKQAQE---TQEVSETTDE 1187 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 114 A DNA sequence (GBSx0118) was identified in S. agalactiae <SEQ ID 381> which encodes the amino acid sequence <SEQ ID 382>. This protein is predicted to be DNA-directed RNA polymerase, beta subunit (rpoC). Analysis of this protein sequence reveals the following: TABLE-US-00396 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1892 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 383> which encodes the amino acid sequence <SEQ ID 384>. Analysis of this protein sequence reveals the following: TABLE-US-00397 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2128 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00398 Identities = 1148/1205 (95%), Positives = 1177/1205 (97%) Query: 11 VVDVNRFKSMQITLASPSKVRSWSYGEVKKPETINYRTLKPEREGLFDEVIFGPTKDWEC 70 - VVDVNRFKSMQITLASPSKVRSWSYGEVKKPETINYRTLKPEREGLFDEVIFGPTKDWEC Sbjct: 1 VVDVNRFKSMQITLASPSKVRSWSYGEVKKPETINYRTLKPEREGLFDEVIFGPTKDWEC 60 Query: 71 ACGKYKRIRYKGIICDRCGVEVTRAKVRRERMGHIELKAPVSHIWYFKGIPSRMGLTLDM 130- ACGKYKRIRYKGI+CDRCGVEVTRAKVRRERMGHIELKAPVSHIWYFKGIPSRMGLTLDM Sbjct: 61 ACGKYKRIRYKGIVCDRCGVEVTRAKVRRERMGHIELKAPVSHIWYFKGIPSRMGLTLDM 120- Query: 131 SPRALEEVIYFAAYVVIDPMDTPLEPKSLLTEREYREKLQEYGYGSFVAKMGAEAIQDLL 19- 0 SPRALEEVIYFAAYVVIDP DTPLEPKSLLTEREYREKLQEYG+GSFVAKMGAEAIQDLL Sbjct: 121 SPRALEEVIYFAAYVVIDPKDTPLEPKSLLTEREYREKLQEYGHGSFVAKMGAEAIQDLL 18- 0 Query: 191 KRVDLDAEIAVLKEELKSATGQKRVKAVRRLDVLDAFKKSGNKPEWMVLNILPVIPPDLR 25- 0 KRVDL AEIA LKEELKSA+GQKR+KAVRRLDVLDAF KSGNKPEWMVLNILPVIPPDLR Sbjct: 181 KRVDLAAEIAELKEELKSASGQKRIKAVRRLDVLDAFNKSGNKPEWMVLNILPVIPPDLR 24- 0 Query: 251 PMVQLDGGRFAASDLNDLYRRVINRNNRLARLLELNAPGIIVQNEKRMLQEAVDALIDNG 31- 0 PMVQLDGGRFAASDLNDLYRRVINRNNRLARLLELNAPGIIVQNEKRMLQEAVDALIDNG Sbjct: 241 PMVQLDGGRFAASDLNDLYRRVINRNNRLARLLELNAPGIIVQNEKRMLQEAVDALIDNG 30- 0 Query: 311 RRGRPITGPGSRPLKSLSHMLKGKQGRFRQNLLGKRVDFSGRSVIAVGPTLKMYQCGVPR 37- 0 RRGRPITGPGSRPLKSLSHMLKGKQGRFRQNLLGKRVDFSGRSVIAVGPTLKMYQCGVPR Sbjct: 301 RRGRPITGPGSRPLKSLSHMLKGKQGRFRQNLLGKRVDFSGRSVIAVGPTLKMYQCGVPR 36- 0 Query: 371 EMAIELFKPFVMREIVARDLAGNVKAAKRMVERGDERIWDILEEVIKEHPVLLNRAPTLH 43- 0 EMAIELFKPFVMREIVA++ AGNVKAAKRMVERGDERIWDILEEVIKEHPVLLNRAPTLH Sbjct: 361 EMAIELFKPFVMREIVAKEYAGNVKAAKRMVERGDERIWDILEEVIKEHPVLLNRAPTLH 42- 0 Query: 431 RLGIQAFEPVLIDGKALRLHPLVCEAYNADFDGDQMAIHVPLSEEAQAEARLLMLAAEHI 49- 0 RLGIQAFEPVLIDGKALRLHPLVCEAYNADFDGDQMAIHVPLSEEAQAEARLLMLAAEHI Sbjct: 421 RLGIQAFEPVLIDGKALRLHPLVCEAYNADFDGDQMAIHVPLSEEAQAEARLLMLAAEHI 48- 0 Query: 491 LNPKDGKPVVTPSQDMVLGNYYLTMEDAGREGEGMIFKDHDEAVMAYQNGYVHLHTRVGI 55- 0 LNPKDGKPVVTPSQDMVLGNYYLTMEDAGREGEGMIFKD DEAVMAY+NGY HLH+RVGI Sbjct: 481 LNPKDGKPVVTPSQDMVLGNYYLTMEDAGREGEGMIFKDKDEAVMAYRNGYAHLHSRVGI 54- 0 Query: 551 AVDSMPNKPWTEEQKHKIMVTTVGKILFNDIMPEDLPYLIEPNNANLTEKTPDKYFLEPG 61- 0 AVDSMPNKPW + Q+HKIMVTTVGKILFNDIMPEDLPYL EPNNANLTE TPDKYFLEPG Sbjct: 541 AVDSMPNKPWKDNQRHKIMVTTVGKILFNDIMPEDLPYLQEPNNANLTEGTPDKYFLEPG 60- 0 Query: 611 QDIQAVIDNLEINIPFKKKNLGNIIAETFKRFRTTETSAFLDRLKDLGYYHSTLAGLTVG 67- 0 QDIQ VID L+IN+PFKKKNLGNIIAETFKRFRTTETSAFLDRLKDLGYYHSTLAGLTVG Sbjct: 601 QDIQEVIDRLDINVPFKKKNLGNIIAETFKRFRTTETSAFLDRLKDLGYYHSTLAGLTVG 66- 0 Query: 671 IADIPVIDNKAEIIDAAHHRVEDINKAFRRGLMTEEDRYVAVTTTWREAKEALEKRLIET 73- 0 IADIPVIDNKAEIIDAAHHRVE+INKAFRRGLMT++DRYVAVTTTWREAKEALEKRLIET Sbjct: 661 IADIPVIDNKAEIIDAAHHRVEEINKAFRRGLMTDDDRYVAVTTTWREAKEALEKRLIET 72- 0 Query: 731 QDPKNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGRIMELPILSNFREGLSVLEMFFS 79- 0 QDPKNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGRIMELPILSNFREGLSVLEMFFS Sbjct: 721 QDPKNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGRIMELPILSNFREGLSVLEMFFS 78- 0 Query: 791 THGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLTITAITDGKEVTETL 85- 0 THGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGL I AITDGKEVTETL Sbjct: 781 THGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLLIRAITDGKEVTETL 84- 0 Query: 851 EERLIGRYTKKSIKHPETGEILVGADTLITEDMAAKVVKAGVEEVTIRSVFTCNTRHGVC 91- 0 EERL GRYT+KS+KHPETGE+L+GAD LITEDMA K+V AGVEEVTIRSVFTC TRHGVC Sbjct: 841 EERLQGRYTRKSVKHPETGEVLIGADQLITEDMARKIVDAGVEEVTIRSVFTCATRHGVC 90- 0 Query: 911 RHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASNTDITQGLPRIQE 97- 0 RHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASNTDITQGLPRIQE Sbjct: 901 RHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASNTDITQGLPRIQE 96- 0 Query: 971 IFEARNPKGEAVITEVKGEVVAIEEDSSTRTKKVFVKGQTGEGEYVVPFTARMKVEVGDE 10- 30 IFEARNPKGEAVITEVKG VV IEED+STRTKKV+V+G+TG GEYV+PFTARMKVEVGDE Sbjct: 961 IFEARNPKGEAVITEVKGNVVEIEEDASTRTKKVYVQGKTGMGEYVIPFTARMKVEVGDE 10- 20 Query: 1031 VARGAALTEGSIQPKRLLEVRDTLSVETYLLAEVQKVYRSQGVEIGDKHVEVMVRQMLRK 1- 090 V RGAALTEGSIQPKRLLEVRDTLSVETYLLAEVQKVYRSQGVEIGDKHVEVMVRQMLRK Sbjct: 1021 VNRGAALTEGSIQPKRLLEVRDTLSVETYLLAEVQKVYRSQGVEIGDKHVEVMVRQMLRK 1- 080 Query: 1091 VRVMDPGDTDLLPGTLMDISDFTDANKDIVISGGIPATSRPVLMGITKASLETNSFLSAA 1- 150 VRVMDPGDTDLLPGTLMDISDFTDANKDIVISGGIPATSRPVLMGITKASLETNSFLSAA Sbjct: 1081 VRVMDPGDTDLLPGTLMDISDFTDANKDIVISGGIPATSRPVLMGITKASLETNSFLSAA 1- 140 Query: 1151 SFQETTRVLTDAAIRGKKDHLLGLKENVIIGKIIPAGTGMARYRNIEPLAVNEVEIIEGT 1- 210 SFQETTRVLTDAAIRGKKDHLLGLKENVIIGKIIPAGTGMARYRNIEP A+NE+E+I+ T Sbjct: 1141 SFQETTRVLTDAAIRGKKDHLLGLKENVIIGKIIPAGTGMARYRNIEPQAMNEIEVIDHT 1- 200 Query: 1211 PVDAE 1215 V AE Sbjct: 1201 EVSAE 1205 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 115 A DNA sequence (GBSx0120) was identified in S. agalactiae <SEQ ID 385> which encodes the amino acid sequence <SEQ ID 386>. This protein is predicted to be a DNA binding protein. Analysis of this protein sequence reveals the following:

TABLE-US-00399 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4727(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00400 >GP: AAC45309 GB: U81957 putative DNA binding protein [Streptococcus gordonii] Identities = 42/99 (42%), Positives = 75/99 (75%) Query: 1 MYQVVKMFGDWEPWWFIEGWEEDITEIAEYDTLSEALLYFQEEWDRGQEKWPYFQSKSSL 60 MY+VV+M+GD+EPWWF++GWE DI + ++ +AL +++ +W + + ++ ++S+S L Sbjct: 1 MYRVVEMYGDFEPWWFLDGWENDIIQEQRFEKYYDALKFYKIQWLKLETEFKEYKSRSDL 60 Query: 61 LATFWSIKEKRWCEECDEYLQQYHSLMLLKEWQEIPKEE 99 + FW+ ++RWCEECD+Y+QQY S++LL++ + IPK + Sbjct: 61 MTVFWNENDQRWCEECDDYVQQYRSIILLEDEKVIPKSK 99 A related DNA sequence was identified in S. pyogenes <SEQ ID 387> which encodes the amino acid sequence <SEQ ID 388>. Analysis of this protein sequence reveals the following: TABLE-US-00401 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4741(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00402 Identities = 61/121 (50%), Positives = 83/121 (68%) Query: 1 MYQVVKMFGDWEPWWFIEGWEEDITEIAEYDTLSEALLYFQEEWDRGQEKWPYFQSKSSL 60 MYQV+KM+GDWEPWWFI+GW++DI + ++ EAL YF +EW R + +P + S+ +L Sbjct: 1 MYQVIKMYGDWEPWWFIDGWQDDIIDEQQFSDWQEALDYFNQEWQRMKAIFPSYHSQKNL 60 Query: 61 LATFWSIKEKRWCEECDEYLQQYHSLMLLKEWQEIPKEESIERFEVFNKIAELPSACSLNL 12- 1 LATFW ++KRWCE+CDE LQQ+HSL+LLK +P I FE N ++ C LNL Sbjct: 61 LATFWEKEDKRWCEDCDEDLQQFHSLLLLKNKDIVPSNNYIPEFEQRNDSPQVAYLCKLNL 12- 1 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 116 A DNA sequence (GBSx0121) was identified in S. agalactiae <SEQ ID 389> which encodes the amino acid sequence <SEQ ID 390>. Analysis of this protein sequence reveals the following: TABLE-US-00403 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty= 0.2433(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00404 >GP: AAC45310 GB: U81957 putative ABC transporter subunit ComYA [Streptococcus gordonii] Identities = 203/319 (63%), Positives = 255/319 (79%), Gaps = 1/319 (0%) Query: 1 MVQSLAKQVIHQAVEVNAQDIYIIPKGDCYELYMRIDDERRFIDVFEFNRMASLISHFKF 60 MVQ +A+ ++ QA E AQDIY +PK DCYELYMRI DERRFI ++F+++A++ISHFKF Sbjct: 1 MVQKIAQAIVRQAKEECAQDIYFVPKDDCYELYMRIGDERRFIQTYDFDQLAAVISHFKF 60 Query: 61 VAGMNVGEKRRSQLGSCDYELSEGRLVSLRLSSVGDYRGQESLVIRILYSGHQDLKYWFD 120- +AGMNVGEKRRSQLGSCDY + + S+RLS+VGDYRG ESLVIR+L+ +LK+WF Sbjct: 61 LAGMNVGEKRRSQLGSCDYRYDD-KETSIRLSTVGDYRGYESLVIRLLHDEETELKFWFT 119- Query: 121 NIKQMKEVLGIRGLYLFSGPVGSGKTTLMYQLASEVFKNKQIITIEDPVEIKNDKMLQLQ 18- 0 + +++E RGLYLFSGPVGSGKTTLM+QLA FK +Q+++IEDPVEIK + MLQLQ Sbjct: 120 HFPELREKFKDRGLYLFSGPVGSGKTTLMHQLAQLKFKGQQVMSIEDPVEIKQEDMLQLQ 17- 9 Query: 181 LNEDIGMTYDALIKLSLRHRPDILIIGEIRDQATARAVIRASLTGVMVFSTIHAKSIPGV 24- 0 LNE IG+TY++LIKLSLRHRPD+LIIGEIRD TARAV+RASLTG VFSTIHAKSIPGV Sbjct: 180 LNETIGLTYESLIKLSLRHRPDLLIIGEIRDSETARAVVRASLTGATVFSTIHAKSIPGV 23- 9 Query: 241 YDRLIELGVNYQELENSLKLIAYQRLIGGGSLIDFETGNFKKHSSDKWNRQVDILAEEGH 30- 0 Y+RL+ELGV+ +EL+ L+ I YQRLIGGG +IDF + N+++H WN+Q+D L GH Sbjct: 240 YERLLELGVSEEELKIVLQGICYQRLIGGGGVIDFASDNYQEHEPTVWNQQIDQLLAAGH 29- 9 Query: 301 ISKKQAQVEKIIPQETTES 319 I +QA+ EKI Q+ S Sbjct: 300 IHPEQAEAEKIRNQQAKTS 318 A related DNA sequence was identified in S. pyogenes <SEQ ID 391> which encodes the amino acid sequence <SEQ ID 392>. Analysis of this protein sequence reveals the following: TABLE-US-00405 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1846(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00406 Identities = 207/312 (66%), Positives = 257/312 (82%) Query: 1 MVQSLAKQVIHQAVEVNAQDIYIIPKGDCYELYMRIDDERRFIDVFEFNRMASLISHFKF 60 MVQ+LAK ++ +A +V+AQDIYI+P+ D Y+L++RI DERR +DV++ +RMA LISHFKF Sbjct: 1 MVQALAKAILAKAEQVHAQDIYILPRADQYDLFLRIGDERRLVDVYQSDRMAPLISHFKF 60 Query: 61 VAGMNVGEKRRSQLGSCDYELSEGRLVSLRLSSVGDYRGQESLVIRILYSGHQDLKYWFD 120- VAGM VGEKRR Q+GSCDY+LS+ + +SLRLSSVGDYRGQESLVIR+L+ ++ + YWFD Sbjct: 61 VAGMIVGEKRRCQVGSCDYKLSKDKQLSLRLSSVGDYRGQESLVIRLLHHQNKSVHYWFD 120- Query: 121 NIKQMKEVLGIRGLYLFSGPVGSGKTTLMYQLASEVFKNKQIITIEDPVEIKNDKMLQLQ 18- 0 + ++ +G RGLYLF+GPVGSGKTTLMYQL S + Q+I+IEDPVEIKN ++LQLQ Sbjct: 121 GLTKVANQVGGRGLYLFAGPVGSGKTTLMYQLISNYHQEAQVISIEDPVEIKNHQILQLQ 18- 0 Query: 181 LNEDIGMTYDALIKLSLRHRPDILIIGEIRDQATARAVIRASLTGVMVFSTIHAKSIPGV 24- 0 +N+DIGMTYD LIKLSLRHRPDIL+IGEIRD TARAVIRASLTG MVFST+HAKSI GV Sbjct: 181 VNDDIGMTYDNLIKLSLRHRPDILVIGEIRDSQTARAVIRASLTGAMVFSTVHAKSISGV 24- 0 Query: 241 YDRLIELGVNYQELENSLKLIAYQRLIGGGSLIDFETGNFKKHSSDKWNRQVDILAEEGH 30- 0 Y RL+ELGV EL N L LIAYQRL+ GG+LID F+ +SS WN+Q+D L E GH Sbjct: 241 YARLLELGVTKAELSNCLALIAYQRLLNGGALIDSTQNEFEYYSSSNWNQQIDQLLEAGH 30- 0 Query: 301 ISKKQAQVEKII 312 ++ KQA++EKII Sbjct: 301 LNPKQAKLEKII 312 SEQ ID 390 (GBS63) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 5 (lane 5; MW 39 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 13 (lane 2; MW 64 kDa). The GBS63-GST fusion product was purified (FIG. 101A; see also FIG. 191, lane 3) and used to immunise mice (lane 1 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 101B), FACS (FIG. 101C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 117 A DNA sequence (GBSx0122) was identified in S. agalactiae <SEQ ID 393> which encodes the amino acid sequence <SEQ ID 394>. This protein is predicted to be competence protein (mshG). Analysis of this protein sequence reveals the following: TABLE-US-00407 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.65 Transmembrane 123-139 (113-144) INTEGRAL Likelihood = -13.53 Transmembrane 272-288 (264-295) INTEGRAL Likelihood = -8.55 Transmembrane 79-95 (75-102) INTEGRAL Likelihood = -0.00 Transmembrane 146-162 (146-162) ----- Final Results ----- bacterial membrane --- Certainty = 0.6859(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9489> which encodes amino acid sequence <SEQ ID 9490> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00408 >GP: AAC45311 GB: U81957 putative ABC transporter subunit ComYB [Streptococcus gordonii] Identities = 161/280 (57%), Positives = 219/280 (77%) Query: 19 MNKALLEGKDLSKMLGELGFSDTVITQVALADLHGNISRSLLKIESYLANLLLVRKKVIE 78 - M + L G+ S+++ LGFSD V+TQ++LA+LHGN+S +LLKIE YL NL V+KK+IE Sbjct: 1 MRQGLANGQAFSEIMASLGFSDAVVTQLSLAELHGNLSLALLKIEEYLDNLAKVKKKLIE 60 Query: 79 VATYPLILLSFLVLIMIGLRNYLMPQLGENNFATRLITNVPNIFLLLLAVVLIFSLIFYI 138- VATYP++LL FLVLIMIGLRNYL+PQL NFAT+LI ++P IFLL + ++L + Y+ Sbjct: 61 VATYPMMLLGFLVLIMIGLRNYLLPQLSSQNFATQLIGHLPTIFLLTVLMLLGLTGAIYL 120- Query: 139 IQKRLSRIKVACFLTTIPLVGSYVKLYLTAYYAREWGNLLSQGIELDQIVKVMQNQKSKL 19- 8 + K RI V FL +P VGS+V++YLTAYYAREWGN++ QG+EL QI ++MQ Q+S L Sbjct: 121 VFKGQKRIPVYSFLARLPFVGSFVRIYLTAYYAREWGNMIGQGLELSQIFQIMQEQRSVL 18- 0 Query: 199 FREIGYDMEEGFLSGKAFHQKVLDYPFFLTELSLMIEYGQVKAKLGTELDIYADEKWEDF 25- 8 F+EIG D+ + +G+ F K+ YPFF ELSL+IEYG+VK+KLG+EL+IYA + WE+F Sbjct: 181 FQEIGQDLGQALQNGQEFSDKIASYPFFKKELSLIIEYGEVKSKLGSELEIYALKTWEEF 24- 0 Query: 259 FTKLARATQLIQPVIFIFVALIIVMIYAAMLLPMYQNMEI 298 F ++ R LIQP++F+FVAL+IV++YAAMLLP+YQNME+ Sbjct: 241 FGRVNRTMNLIQPLVFVFVALMIVLLYAAMLLPLYQNMEV 280 A related DNA sequence was identified in S. pyogenes <SEQ ID 395> which encodes the amino acid sequence <SEQ ID 396>. Analysis of this protein sequence reveals the following: TABLE-US-00409 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.52 Transmembrane 317-333 (309-339) INTEGRAL Likelihood = -10.14 Transmembrane 123-139 (119-147) INTEGRAL Likelihood = -6.95 Transmembrane 164-180 (161-183) ----- Final Results ----- bacterial membrane --- Certainty = 0.6010(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00410 >GP: AAC45311 GB: U81957 putative ABC transporter subunit ComYB [Streptococcus gordonii] Identities = 139/278 (50%), Positives = 207/278 (74%) Query: 63 MEESLLKGQGLADMLSGLGFSDAILTQISLADRHGNIETTLVAIQHYLNQMARIRRKTVE 122- M + L GQ +++++ LGFSDA++TQ+SLA+ HGN+ L+ I+ YL+ +A++++K +E Sbjct: 1 MRQGLANGQAFSEIMASLGFSDAVVTQLSLAELHGNLSLALLKIEEYLDNLAKVKKKLIE 60 Query: 123 VITYPLILLLFLFVMMLGLRRYLVPQLETQNQITYFLNHFPAFFIGFCSGLILLFGMVWL 18- 2 V TYP++LL FL ++M+GLR YL+PQL +QN T + H P F+ L+ L G ++L Sbjct: 61 VATYPMMLLGFLVLIMIGLRNYLLPQLSSQNFATQLIGHLPTIFLLTVLMLLGLTGAIYL 120- Query: 183 RWRSQSRLKLYSRLSRYPFLGKLLKQYLTSYYAREWGTLIGQGLDLMTILDIMAIEKSSL 24- 2 ++ Q R+ +YS L+R PF+G ++ YLT+YYAREWG +IGQGL+L I IM ++S L Sbjct: 121 VFKGQKRIPVYSFLARLPFVGSFVRIYLTAYYAREWGNMIGQGLELSQIFQIMQEQRSVL 18- 0 Query: 243 MKELAEDIRMSLLEGQAFHIKVATYPFFKKELSLMIEYGEIKSKLGAELEIYAQESWEQF 30- 2 +E+ +D+ +L GQ F K+A+YPFFKKELSL+IEYGE+KSKLG+ELEIYA ++WE+F Sbjct: 181 FQEIGQDLGQALQNGQEFSDKIASYPFFKKELSLIIEYGEVKSKLGSELEIYALKTWEEF 24- 0 Query: 303 FSQLYQVTQLIQPAIFLVVAVTIVMIYAAILLPIYQNM 340 F ++ + LIQP +F+ VA+ IV++YAA+LLP+YQNM Sbjct: 241 FGRVNRTMNLIQPLVFVFVALMIVLLYAAMLLPLYQNM 278 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00411 Identities = 148/297 (49%), Positives = 209/297 (69%), Gaps = 2/297 (0%) Query: 1 MVTFLKRSKLLSDCYTDSMNKALLEGKDLSKMLGELGFSDTVITQVALADLHGNISRSLL 60 ++ FLKRS+LL Y M ++LL+G+ L+ ML LGFSD ++TQ++LAD HGNI +L+ Sbjct: 45 VIAFLKRSQLLQLDYVLKMEESLLKGQGLADMLSGLGFSDAILTQISLADRHGNIETTLV 104- Query: 61 KIESYLANLLLVRKKVIEVATYPLILLSFLVLIMIGLRNYLMPQLGENNFATRLITNVPN 120- I+ YL + +R+K +EV TYPLILL FL ++M+GLR YL+PQL N T + + P Sbjct: 105 AIQHYLNQMARIRRKTVEVITYPLILLLFLFVMMLGLRRYLVPQLETQNQITYFLNHFPA 16- 4 Query: 121 IFL-LLLAVVLIFSLIFYIIQKRLSRIKVACFLTTIPLVGSYVKLYLTAYYAREWGNLLS 17- 9 F+ ++L+F ++ ++ + SR+K+ L+ P +G +K YLT+YYAREWG L+ Sbjct: 165 FFIGFCSGLILLFGMV-WLRWRSQSRLKLYSRLSRYPFLGKLLKQYLTSYYAREWGTLIG 22- 3 Query: 180 QGIELDQIVKVMQNQKSKLFREIGYDMEEGFLSGKAFHQKVLDYPFFLTELSLMIEYGQV 23- 9 QG++L I+ +M +KS L +E+ D+ L G+AFH KV YPFF ELSLMIEYG++ Sbjct: 224 QGLDLMTILDIMAIEKSSLMKELAEDIRMSLLEGQAFHIKVATYPFFKKELSLMIEYGEI 28- 3 Query: 240 KAKLGTELDIYADEKWEDFFTKLARATQLIQPVIFIFVALIIVMIYAAMLLPMYQNM 296 K+KLG EL+IYA E WE FF++L + TQLIQP IF+ VA+ IVMIYAA+LLP+YQNM Sbjct: 284 KSKLGAELEIYAQESWEQFFSQLYQVTQLIQPAIFLVVAVTIVMIYAAILLPIYQNM 340 A related GBS gene <SEQ ID 8493> and protein <SEQ ID 8494> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00412 Lipop: Possible site: -1 Crend: 9 SRCFLG: 0 McG: Length of UR: 2 Peak Value of UR: 1.24 Net Charge of CR: 0 McG: Discrim Score: -8.94 GvH: Signal Score (-7.5): -4.08 Possible site: 31 >>> Seems to have no N-terminal signal sequence Amino Acid Composition: calculated from 1 ALOM program count: 4 value: -14.65 threshold: 0.0 INTEGRAL Likelihood = -14.65 Transmembrane 105-121 (95-126) INTEGRAL Likelihood = -13.53 Transmembrane 254-270 (246-277) INTEGRAL Likelihood = -8.55 Transmembrane 61-77 (57-84) PERIPHERAL Likelihood = 5.09 14 modified ALOM score: 3.43 icm1 HYPID: 7 CFP: 0.686 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6859 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00012## SEQ ID 8494 (GBS49) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 11 (lane 5; MW 15 kDa). It was also was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 15 (lane 5; MW 60 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 118 A DNA sequence (GBSx0123) was identified in S. agalactiae <SEQ ID 397> which encodes the amino acid sequence <SEQ ID 398>. This protein is predicted to be ComYD or ComGD. Analysis of this protein sequence reveals the following: TABLE-US-00413 Possible site: 55 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00414 >GP: CAA75315 GB: Y15043 homology to ComYD from Streptcoccus gordonii, and ComGD from Bacillus subtilis [Lactococcus lactis subsp. cremoris] Identities = 56/138 (40%), Positives = 92/138 (66%), Gaps = 2/138 (1%) Query: 12 KVKAFTLLECLVALVTITGALLVYQGLTKLLAQQIVVMSSSSQSEWVLLTQQLNAEFEGA 71 - K++AFTLLECLVAL+ I+G++LV GLT+++ +Q+ + + S+ +W + +Q+ +E GA Sbjct: 13 KIRAFTLLECLVALLAISGSVLVISGLTRMIEEQMKISQNDSRKDWQIFCEQMRSELSGA 72 Query: 72 HLEYLRQNKLYLRKQDKIVTFGKSNKDDFRKTGYDGRGYQPMVYGLDNCQMSQTKSMVKL 131- L+ + QN LY+ K DK + FG DDFRK+ G+GYQPM+Y L ++ ++++K+ Sbjct: 73 KLDNVNQNFLYVTK-DKKLRFGLVG-DDFRKSDDKGQGYQPMLYDLKGAKIQAEENLIKI 130- Query: 132 VFYFKDGLKRTFYYDFKE 149 F +G +R F Y F + Sbjct: 131 TIDFDNGGERVFIYRFTD 148 A related DNA sequence was identified in S. pyogenes <SEQ ID 399> which encodes the amino acid sequence <SEQ ID 400>. Analysis of this protein sequence reveals the following: TABLE-US-00415 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00416 >GP: CAA75315 GB: Y15043 homology to ComYD from Streptcoccus gordonii, and ComGD from Bacillus subtilis [Lactococcus lactis subsp. cremoris] Identities = 65/137 (47%), Positives = 84/137 (60%), Gaps = 2/137 (1%) Query: 8 IKAFTLLEALIALLVISGSLLVYQGLTRTLLKHSHYLARHDQDNWLLFSHQLREELSGAR 67 I+AFTLLE L+ALL ISGS+LV GLTR + + + +W +F Q+R ELSGA+ Sbjct: 14 IRAFTLLECLVALLAISGSVLVISGLTRMIEEQMKISQNDSRKDWQIFCEQMRSELSGAK 73 Query: 68 FYKVADNKLYVEKGKKVLAFGQFKSHDFRKSASNGKGYQPMLFGISRSHIHIEQSQICIT 127- V N LYV K KK L FG DFRKS G+GYQPML+ + + I E++ I IT Sbjct: 74 LDNVNQNFLYVTKDKK-LRFG-LVGDDFRKSDDKGQGYQPMLYDLKGAKIQAEENLIKIT 131- Query: 128 LKWKSGLERTFYYAFQD 144 + + +G ER F Y F D Sbjct: 132 IDFDNGGERVFIYRFTD 148 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00417 Identities = 58/137 (42%), Positives = 88/137 (63%) Query: 13 VKAFTLLECLVALVTITGALLVYQGLTKLLAQQIVVMSSSSQSEWVLLTQQLNAEFEGAH 72 - +KAFTLLE L+AL+ I+G+LLVYQGLT+ L + ++ Q W+L + QL E GA Sbjct: 8 IKAFTLLEALIALLVISGSLLVYQGLTRTLLKHSHYLARHDQDNWLLFSHQLREELSGAR 67 Query: 73 LEYLRQNKLYLRKQDKIVTFGKSNKDDFRKTGYDGRGYQPMVYGLDNCQMSQTKSMVKLV 132- + NKLY+ K K++ FG+ DFRK+ +G+GYQPM++G+ + +S + + Sbjct: 68 FYKVADNKLYVEKGKKVLAFGQFKSHDFRKSASNGKGYQPMLFGISRSHIHIEQSQICIT 127- Query: 133 FYFKDGLKRTFYYDFKE 149 +K GL+RTFYY F++ Sbjct: 128 LKWKSGLERTFYYAFQD 144 A related GBS gene <SEQ ID 8495> and protein <SEQ ID 8496> were also identified. Analysis of this protein sequence reveals the following:

TABLE-US-00418 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 4.86 GvH: Signal Score (-7.5): -0.22 Possible site: 55 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 12.47 threshold: 0.0 PERIPHERAL Likelihood = 12.47 127 modified ALOM score: -2.99 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00013## SEQ ID 398 (GBS6) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 1 (lane 2; MW 40 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 2 (lane 2; MW 15 kDa). The GBS6-GST fusion product was purified (FIG. 189, lane 2) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 260), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 119 A DNA sequence (GBSx0124) was identified in S. agalactiae <SEQ ID 401> which encodes the amino acid sequence <SEQ ID 402>. Analysis of this protein sequence reveals the following: TABLE-US-00419 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3831(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00420 >GP: AAC00317 GB: AF008220 YtxK [Bacillus subtilis] Identities = 106/329 (32%), Positives = 176/329 (53%), Gaps = 17/329 (5%) Query: 1 MNFEKIETAYELILENIQTIENQLKTHIYDALIEQNSYYLGSSCDLDMVVVNNQKLRQLD 60 M + + YEL+ E I+N+L+ +AL E Y D + + +QK +QL Sbjct: 1 MQKDHVGAVYELLNEAAIMIKNELQISYIEALAEAGEMYFLEKTD-QLKLPADQKTKQLQ 59 Query: 61 LSQE---------EW-RRTFQFIFIKSAQTEQLQANHQFTPDSIGFILLFLLEE-LTSQE 109- E EW R+ FQ +K + + N Q TPD+IG + +L+ + + ++ Sbjct: 60 ALLEKAEFGTYEHEWVRKAFQLAVLKGMK-DISHPNRQMTPDTIGLFISYLVNKFMADKK 118- Query: 110 TVDVLEIGSGTGNLAQTLLNN-SSKELNYMGIEVDDLLIDLSASIAEIIGSSAQFIQEDA 16- 8 + +L+ GTGNL T+LN S K N GIE+DD+L+ ++ + A ++ + +D+ Sbjct: 119 ELTILDPALGTGNLLFTVLNQLSEKTANSFGIEIDDVLLKIAYAQANLLKKELELFHQDS 17- 8 Query: 169 VRPQILKESDVIISDLPVGYYPNDGIAKRYAVSSSKEHTYAHHLLMEQSLKYLKKDGIAI 22- 8 + P + D +I DLPVGYYPND A+ + + + + H++AHHL +EQS+K+ K G Sbjct: 179 LEPLFIDPVDTVICDLPVGYYPNDEGAEAFELKADEGHSFAHHLFIEQSVKHTKPGGYLF 23- 8 Query: 229 FLAPENLLTSPQSDLLKEWLKGYADVIAVLTLPETIFGSRQNAKSIFVLKKQAEQKP--- 28- 5 F+ P +L S QS LK++ K + A+L LP++IF +AKSI VL+KQ E Sbjct: 239 FMIPNHLFESSQSGKLKQFFKDKVHINALLQLPKSIFKDEAHAKSILVLQKQGENTKAPG 29- 8 Query: 286 ETFVYPLTDLQNRENMANFIENFQKWSRE 314 + + L N++ M + + F +W ++ Sbjct: 299 QILLANLPSFSNQKAMLDMMAQFDEWFKK 327 A related DNA sequence was identified in S. pyogenes <SEQ ID 403> which encodes the amino acid sequence <SEQ ID 404>. Analysis of this protein sequence reveals the following: TABLE-US-00421 Possible site: 57 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00422 Identities = 223/315 (70%), Positives = 270/315 (84%) Query: 1 MNFEKIETAYELILENIQTIENQLKTHIYDALIEQNSYYLGSSCDLDMVVVNNQKLRQLD 60 M FEKIE AY+L+LEN Q IEN LKTHIYDA++EQNS+YLG+ V N+ KL+ L Sbjct: 16 MTFEKIEEAYQLLLENCQLIENDLKTHIYDAIVEQNSFYLGAEGASPQVAQNSDKLKALC 75 Query: 61 LSQEEWRRTFQFIFIKSAQTEQLQANHQFTPDSIGFILLFLLEELTSQETVDVLEIGSGT 120- L++EEWR+ +QF+FIK+AQTEQLQANHQFTPD+IGFILL+LLE+L+ +++++VLEIGSGT Sbjct: 76 LTKEEWRKAYQFLFIKAAQTEQLQANHQFTPDAIGFILLYLLEQLSDKDSLEVLEIGSGT 135- Query: 121 GNLAQTLLNNSSKELNYMGIEVDDLLIDLSASIAEIIGSSAQFIQEDAVRPQILKESDVI 18- 0 GNLAQTLLNN+SK L+Y+GIE+DDLLIDLSASIAEI+ SSA FIQEDAVRPQ+LKESD++ Sbjct: 136 GNLAQTLLNNTSKSLDYVGIELDDLLIDLSASIAEIMDSSAHFIQEDAVRPQLLKESDIV 19- 5 Query: 181 ISDLPVGYYPNDGIAKRYAVSSSKEHTYAHHLLMEQSLKYLKKDGIAIFLAPENLLTSPQ 24- 0 ISDLPVGYYPND IAKRY V+SS +HTYAHHLLMEQSLKYLKKDG AIFLAP NLLTSPQ Sbjct: 196 ISDLPVGYYPNDDIAKRYKVASSDKHTYAHHLLMEQSLKYLKKDGFAIFLAPVNLLTSPQ 25- 5 Query: 241 SDLLKEWLKGYADVIAVLTLPETIFGSRQNAKSIFVLKKQAEQKPETFVYPLTDLQNREN 30- 0 S LLK+WLK YA V+ ++TLP++IFG NAKSI VL+KQ + ETFVYP+ DL+ EN Sbjct: 256 SQLLKQWLKDYAQVVTLITLPDSIFGHPSNAKSIIVLQKQTDHPMETFVYPIRDLKLAEN 31- 5 Query: 301 MANFIENFQKWSREN 315 + +F+ENF+KW N Sbjct: 316 IHDFMENFKKWKLSN 330 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 120 A DNA sequence (GBSx0125) was identified in S. agalactiae <SEQ ID 405> which encodes the amino acid sequence <SEQ ID 406>. This protein is predicted to be acetate kinase (ackA-1). Analysis of this protein sequence reveals the following: TABLE-US-00423 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2384(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00424 >GP: AAC36857 GB: L17320 acetate kinase [Bacillus subtilis] Identities = 223/395 (56%), Positives = 293/395 (73%), Gaps = 3/395 (0%) Query: 1 MSKTIAINAGSSSLKWQLYEMPEEKVVAKGIIERIGLKDSISTVKFDDKKDEQILDIVDH 60 MSK IAINAGSSSLK+QL+EMP E V+ KG++ERIG+ DS+ T+ + +K+ ++ DI DH Sbjct: 1 MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDH 60 Query: 61 TQAVKILLEDLTKHGIIKDFNEITGVGHRVVAGGEYFKESALVDDKVVEQVEELSALAPL 120- AVK+LL LT+ GIIKD NEI G+GHRVV GGE F +S L+ D+ ++++E++S LAPL Sbjct: 61 AVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPL 120- Query: 121 HNPAAAAGIRAFREILPDITSVCVFDTAFHTTMQPHTYLYPIPQKYYTDYKVRKYGAHGT 18- 0 HNPA GI+AF+E+LP++ +V VFDTAFH TM +YLY +P +YY + +RKYG HGT Sbjct: 121 HNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGT 18- 0 Query: 181 SHQYVAQEAAKQLGRPLEELKLITAHVGNGVSITANYHGQSIDTSMGFTPLAGPMMGTRS 24- 0 SH+YV + AA+ LGRPL++L+LI+ H+GNG SI A G+SIDTSMGFTPLAG MGTRS Sbjct: 181 SHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRS 24- 0 Query: 241 GDIDPAIIPYLVANDPELEDAAAVVNMLNKQSGLLGVSGTSSDMRDIEAGLQSKDPNAVL 30- 0 G+IDPA+IPY++ + D V+N LNK+SGLLG+SG SSD+RDI + + A Sbjct: 241 GNIDPALIPYIMEKTGQTAD--EVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAET 29- 8 Query: 301 AYNVFIDRIKKFIGQYLAVLNGADAIIFTAGMGENAPLMRQDVIAGLSWFGIELDPE-KN 35- 9 A VF RI K+IG Y A ++G DAIIFTAG+GEN+ +R+ V+ GL + G+ DP N Sbjct: 299 ALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNN 35- 8 Query: 360 VFGYFGDITKPDSKVKVLVIPTDEELMIARDVERL 394 V G I+ P S VKV++IPTDEE+MIARDV RL Sbjct: 359 VRGEEAFISYPHSPVKVMIIPTDEEVMIARDVVRL 393 A related DNA sequence was identified in S. pyogenes <SEQ ID 407> which encodes the amino acid sequence <SEQ ID 408>. Analysis of this protein sequence reveals the following: TABLE-US-00425 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.22 Transmembrane 63-79 (63-79) ----- Final Results ----- bacterial membrane --- Certainty = 0.1086 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00426 >GP: AAC36857 GB: L17320 acetate kinase [Bacillus subtilis] Identities = 218/395 (55%), Positives = 293/395 (73%), Gaps = 3/395 (0%) Query: 1 MSKTIAINAGSSSLKWQLYQMPEEAVLAQGIIERIGLKDSISTVKYDGKKEEQILDIHDH 60 MSK IAINAGSSSLK+QL++MP E VL +G++ERIG+ DS+ T+ +G+K ++ DI DH Sbjct: 1 MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDH 60 Query: 61 TEAVKILLNDLIHFGIIAAYDEITGVGHRVVAGGELFKESVVVNDKVLEQIEELSVLAPL 120- AVK+LLN L FGII +EI G+GHRVV GGE F +SV++ D+ +++IE++S LAPL Sbjct: 61 AVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPL 120- Query: 121 HNPGAAAGIRAFRDILPDITSVCVFDTSFHTSMAKHTYLYPIPQKYYTDYKVRKYGAHGT 18- 0 HNP GI+AF+++LP++ +V VFDT+FH +M + +YLY +P +YY + +RKYG HGT Sbjct: 121 HNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGT 18- 0 Query: 181 SHKYVAQEAAKMLGRPLEELKLITAHIGNGVSITANYHGKSVDTSMGFTPLAGPMMGTRS 24- 0 SHKYV + AA++LGRPL++L+LI+ H+GNG SI A GKS+DTSMGFTPLAG MGTRS Sbjct: 181 SHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRS 24- 0 Query: 241 GDIDPAIIPYLIEQDPELKDAADVVNMLNKKSGLSGVSGISSDMRDIEAGLQEDNPDAVL 30- 0 G+IDPA+IPY++E+ + D +V+N LNKKSGL G+SG SSD+RDI +E N A Sbjct: 241 GNIDPALIPYIMEKTGQTAD--EVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAET 29- 8 Query: 301 AYNIFIDRIKKCIGQYFAVLNGADALVFTAGMGENAPLMRQDVIGGLTWFGMDIDPE-KN 35- 9 A +F RI K IG Y A ++G DA++FTAG+GEN+ +R+ V+ GL + G+ DP N Sbjct: 299 ALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNN 35- 8 Query: 360 VFGYRGDISTPESKVKVLVISTDEELCIARDVERL 394 V G IS P S VKV++I TDEE+ IARDV RL Sbjct: 359 VRGEEAFISYPHSPVKVMIIPTDEEVMIARDVVRL 393 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00427 Identities = 332/395 (84%), Positives = 365/395 (92%) Query: 1 MSKTIAINAGSSSLKWQLYEMPEEKVVAKGIIERIGLKDSISTVKFDDKKDEQILDIVDH 60 MSKTIAINAGSSSLKWQLY+MPEE V+A+GIIERIGLKDSISTVK+D KK+EQILDI DH Sbjct: 1 MSKTIAINAGSSSLKWQLYQMPEEAVLAQGIIERIGLKDSISTVKYDGKKEEQILDIHDH 60 Query: 61 TQAVKILLEDLTKHGIIKDFNEITGVGHRVVAGGEYFKESALVDDKVVEQVEELSALAPL 120- T+AVKILL DL GII ++EITGVGHRVVAGGE FKES +V+DKV+EQ+EELS LAPL Sbjct: 61 TEAVKILLNDLIHFGIIAAYDEITGVGHRVVAGGELFKESVVVNDKVLEQIEELSVLAPL 120- Query: 121 HNPAAAAGIRAFREILPDITSVCVFDTAFHTTMQPHTYLYPIPQKYYTDYKVRKYGAHGT 18- 0 HNP AAAGIRAFR+ILPDITSVCVFDT+FHT+M HTYLYPIPQKYYTDYKVRKYGAHGT Sbjct: 121 HNPGAAAGIRAFRDILPDITSVCVFDTSFHTSMAKHTYLYPIPQKYYTDYKVRKYGAHGT 18- 0 Query: 181 SHQYVAQEAAKQLGRPLEELKLITAHVGNGVSITANYHGQSIDTSMGFTPLAGPMMGTRS 24- 0 SH+YVAQEAAK LGRPLEELKLITAH+GNGVSITANYHG+S+DTSMGFTPLAGPMMGTRS Sbjct: 181 SHKYVAQEAAKMLGRPLEELKLITAHIGNGVSITANYHGKSVDTSMGFTPLAGPMMGTRS 24- 0 Query: 241 GDIDPAIIPYLVANDPELEDAAAVVNMLNKQSGLLGVSGTSSDMRDIEAGLQSKDPNAVL 30- 0 GDIDPAIIPYL+ DPEL+DAA VVNMLNK+SGL GVSG SSDMRDIEAGLQ +P+AVL Sbjct: 241 GDIDPAIIPYLIEQDPELKDAADVVNMLNKKSGLSGVSGISSDMRDIEAGLQEDNPDAVL 30- 0 Query: 301 AYNVFIDRIKKFIGQYLAVLNGADAIIFTAGMGENAPLMRQDVIAGLSWFGIELDPEKNV 36- 0 AYN+FIDRIKK IGQY AVLNGADA++FTAGMGENAPLMRQDVI GL+WFG+++DPEKNV Sbjct: 301 AYNIFIDRIKKCIGQYFAVLNGADALVFTAGMGENAPLMRQDVIGGLTWFGMDIDPEKNV 36- 0 Query: 361 FGYFGDITKPDSKVKVLVIPTDEELMIARDVERLK 395 FGY GDI+ P+SKVKVLVI TDEEL IARDVERLK Sbjct: 361 FGYRGDISTPESKVKVLVISTDEELCIARDVERLK 395 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 121 A DNA sequence (GBSx0126) was identified in S. agalactiae <SEQ ID 409> which encodes the amino acid sequence <SEQ ID 410>. This protein is predicted to be repressor protein. Analysis of this protein sequence reveals the following: TABLE-US-00428 Possible site: 17 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00429 >GP: CAB49550 GB: AJ248284 repressor protein, putative [Pyrococcus abyssi] Identities = 39/64 (60%), Positives = 49/64 (75%) Query: 1 MKNSLQKLRKSRKLSQAELAVALGVTRQTIISLEKEKYTASLELAFKIARYFDKQIEEVF 60 MKN L++ R+ L+Q ELA LGVTRQTII++EK KY SL LAFKIAR+F +IE++F Sbjct: 1 MKNRLREFREKYGLTQEELARILGVTRQTIIAIEKGKYDPSLRLAFKIARFFGVRIEDIF 60 Query: 61 IYTE 64 IY E Sbjct: 61 IYEE 64 A related DNA sequence was identified in S. pyogenes <SEQ ID 411> which encodes the amino acid sequence <SEQ ID 412>. Analysis of this protein sequence reveals the following: TABLE-US-00430 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4344(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00431 Identities = 29/66 (43%), Positives = 44/66 (65%) Query: 1 MKNSLQKLRKSRKLSQAELAVALGVTRQTIISLEKEKYTASLELAFKIARYFDKQIEEVF 60 +KN L++LR ++Q E+A GV+RQTI +E+ +YT S+ +A KIA+ F + +EEVF Sbjct: 10 LKNRLKELRARDGINQTEMAKLAGVSRQTISLIERNEYTPSVIIAMKIAKVFQEPVEEVF 69 Query: 61 IYTESE 66 E E Sbjct: 70 RLVEVE 75 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 122 A DNA sequence (GBSx0127) was identified in S. agalactiae <SEQ ID 413> which encodes the amino acid sequence <SEQ ID 414>. Analysis of this protein sequence reveals the following: TABLE-US-00432 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.97 Transmembrane 45-61 (41-66) INTEGRAL Likelihood = -8.65 Transmembrane 14-30 (11-37) INTEGRAL Likelihood = -7.80 Transmembrane 123-139 (118-145) INTEGRAL Likelihood = -3.24 Transmembrane 177-193 (177-194) INTEGRAL Likelihood = -0.85 Transmembrane 81-97 (81-97) ----- Final Results ----- bacterial membrane --- Certainty = 0.4588(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9491> which encodes amino acid sequence <SEQ ID 9492> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00433 >GP: BAA11325 GB: D78257 ORF8 [Enterococcus faecalis] Identities = 48/120 (40%), Positives = 69/120 (57%), Gaps = 5/120 (4%) Query: 104 MQGVKDTANQTVIMELTKQLPLALMLIFAIIGAPIMEEIIFRYIIPKELFAKHQKWGFVI 16- 3 MQG TAN + +++L + L+++ I APIMEEI+FR I L + +I Sbjct: 1 MQGHTTTANDSTLIKLFSGVSPVLVVLLLGIAAPIMEEIVFRGGIIGYLVENNALLAILI 60 Query: 164 GTLAFALIHSPSDIGSFIIYAGMGAILSFVYYKTEHLEYSIMIHFINN-----ALAYSVL 21- 8 + F +IH P++ SF +Y MG ILS YYKT+ L SI IHF+NN A+AY ++ Sbjct: 61 SSFLFGIIHGPTNFISFGMYFFMGIILSVSYYKTKDLRVSISIHFLNNLFPAIAIAYGLI 120- A related DNA sequence was identified in S. pyogenes <SEQ ID 415> which encodes the amino acid sequence <SEQ ID 416>. Analysis of this protein sequence reveals the following: TABLE-US-00434 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.41 Transmembrane 12-28 (1-30) INTEGRAL Likelihood = -9.98 Transmembrane 41-57 (33-64) INTEGRAL Likelihood = -8.33 Transmembrane 128-144 (121-151) INTEGRAL Likelihood = -7.96 Transmembrane 83-99 (76-103) INTEGRAL Likelihood = -3.77 Transmembrane 208-224 (207-230) INTEGRAL Likelihood = -2.13 Transmembrane 182-198 (182-199) ----- Final Results ----- bacterial membrane --- Certainty = 0.5564(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00435 >GP: BAA11325 GB: D78257 ORF8 [Enterococcus faecalis] Identities = 47/120 (39%), Positives = 70/120 (58%), Gaps = 8/120 (6%) Query: 105 GQQVSANDAAIHTLARLIKGGFPLYTALFVLVIAFIAPIMEELVFRGFPMIDLFKGKSLK 16- 4 G +AND+ TL +L G P+ L VL++ APIMEE+VFRG + L + +L Sbjct: 3 GHTTTANDS---TLIKLFSGVSPV---LVVLLLGIAAPIMEEIVFRGGIIGYLVENNAL- 55 Query: 165 VAGLVTSLVFALPHA-TNSVEFIMYSCMGIFLFVAYQRRGNLKDAILLHIFNNLIEVILL 22- 3 +A L++S +F + H TN + F MY MGI L V+Y + +L+ +I +H NNL I + Sbjct: 56 LAILISSFLFGIIHGPTNFISFGMYFFMGIILSVSYYKTKDLRVSISIHFLNNLFPAIAI 115- An alignment of the GAS and GBS proteins is shown below: TABLE-US-00436 Identities = 72/229 (31%), Positives = 114/229 (49%), Gaps = 24/229 (10%) Query: 11 KGKILALLIAFLVINQLV-PILAVWLLKNHYQTPFTSILLIGL-------ELLIIALFLY 62 - KG I L IA L+I +V +L + LL+ + P IG+ +LI+ LY Sbjct: 2 KGFINYLKIAVLIILAMVFNVLPMILLQKQHDIPMVLNWGIGIFYLVIVGSVLIVLWGLY 61 Query: 63 YAKVKQIIRWKALLTRKALVT---ILLGWLSLRVPQIIGYLIMTM-QGVKDTANQTVIME 118- AK I+ + + LV + L WL +RV I+G L+ + G + +AN I Sbjct: 62 QAKQDTFIKQQKM----RLVDWGYLALFWLIIRVIAIVGTLVNQLWSGQQVSANDAAIHT 117- Query: 119 LTKQL----PLALMLIFAIIG--APIMEEIIFRYIIPKELF-AKHQKWGFVIGTLAFALI 17- 1 L + + PL L +I APIMEE++FR +LF K K ++ +L FAL Sbjct: 118 LARLIKGGFPLYTALFVLVIAFIAPIMEELVFRGFPMIDLFKGKSLKVAGLVTSLVFALP 17- 7 Query: 172 HSPSDIGSFIIYAGMGAILSFVYYKTEHLEYSIMIHFINNALAYSVLIS 220 H+ + + FI+Y+ MG L Y + +L+ +I++H NN + +L+S Sbjct: 178 HATNSV-EFIMYSCMGIFLFVAYQRRGNLKDAILLHIFNNLIEVILLMS 225 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 123 A DNA sequence (GBSx0128) was identified in S. agalactiae <SEQ ID 417> which encodes the amino acid sequence <SEQ ID 418>. Analysis of this protein sequence reveals the following:

TABLE-US-00437 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0826(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00438 >GP: AAC06504 GB: AE000676 pyrroline carboxylate reductase [Aquifex aeolicus] Identities = 97/259 (37%), Positives = 159/259 (60%), Gaps = 4/259 (1%) Query: 1 MKIGIIGVGKM--ASAIIQGLKQTQHDIIISGSCLERSKEIAERLDVTYAESHQSLINQA 58 M++GI+G G M A A+ K + +II++ E+ + +A + + +A + L + + Sbjct: 8 MRVGIVGFGNMGQAFALCFSKKLGKENIIVTDKVQEK-RNLATEMGIAFASDVKFLADNS 66 Query: 59 DIIMLGIKPQLFEKVLLPLDITKPII-SMAAGISLARLSQLTRSDLPLIRIMPNINAQIL 117- D++++ +KP+ ++VL L K II S+ AG+S+ ++ ++ D ++R+MPN+N + Sbjct: 67 DVVLVAVKPKDSQEVLQKLKDYKGIILSIMAGVSIEKMEKILGKDKKIVRVMPNVNVAVG 126- Query: 118 QSCTAICYNNHVSDELRQLAKEITDSFGSSFDIAETNFDTFTALAGSSPAYIYLFIEALA 17- 7 AI N ++S+E R +E+ S G+ + I E FD FTALAGS PA+++ FI+ALA Sbjct: 127 SGVMAITDNGNLSEEERSKVEELLLSCGTLYRIEERLFDAFTALAGSGPAFVFSFIDALA 18- 6 Query: 178 KAGVKYGFPKEQALSIVGQTVLASSQNLLQGQNSTSDLIDNICSPGGTTIAGLLDLEKNG 23- 7 AGV GF EQAL I TV+ S++ L + Q + ++LI + SPGGTTI G+ LE+ G Sbjct: 187 LAGVHQGFSYEQALRIALDTVMGSAKLLKEFQVNPNELIAKVTSPGGTTIEGIKYLEEKG 24- 6 Query: 238 LTHSVISAIDATIEKAKKL 256 +V+ I+ T +KAKKL Sbjct: 247 FKGTVMECINRTSQKAKKL 265 A related DNA sequence was identified in S. pyogenes <SEQ ID 419> which encodes the amino acid sequence <SEQ ID 420>. Analysis of this protein sequence reveals the following: TABLE-US-00439 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1043(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00440 Identities = 180/256 (70%), Positives = 208/256 (80%) Query: 1 MKIGIIGVGKMASAIIQGLKQTQHDIIISGSCLERSKEIAERLDVTYAESHQSLINQADI 60 MKIGIIGVGKMASAII+GLKQT H++IISGS LERSKEIAE+L + YA SHQ LI+Q D+ Sbjct: 1 MKIGIIGVGKMASAIIKGLKQTPHELIISGSSLERSKEIAEQLALPYAMSHQDLIDQVDL 60 Query: 61 IMLGIKPQLFEKVLLPLDITKPIISMAAGISLARLSQLTRSDLPLIRIMPNINAQILQSC 120- ++LGIKPQLFE VL PL +PIISMAAGISL RL+ DLPL+RIMPN+NAQILQS Sbjct: 61 VILGIKPQLFETVLKPLHFKQPIISMAAGISLQRLATFVGQDLPLLRIMPNMNAQILQSS 120- Query: 121 TAICYNNHVSDELRQLAKEITDSFGSSFDIAETNFDTFTALAGSSPAYIYLFIEALAKAG 18- 0 TA+ N VS EL+ +++TDSFGS+FDI+E +FDTFTALAGSSPAYIYLFIEALAKAG Sbjct: 121 TALTGNALVSQELQARVRDLTDSFGSTFDISEKDFDTFTALAGSSPAYIYLFIEALAKAG 18- 0 Query: 181 VKYGFPKEQALSIVGQTVLASSQNLLQGQNSTSDLIDNICSPGGTTIAGLLDLEKNGLTH 24- 0 VK G PK +AL IV QTVLAS+ NL S D ID ICSPGGTTIAGL++LE+ GLT Sbjct: 181 VKNGIPKAKALEIVTQTVLASASNLKTSSQSPHDFIDAICSPGGTTIAGLMELERLGLTA 24- 0 Query: 241 SVISAIDATIEKAKKL 256 +V SAID TI+KAK L Sbjct: 241 TVSSAIDKTIDKAKSL 256 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 124 A DNA sequence (GBSx0129) was identified in S. agalactiae <SEQ ID 421> which encodes the amino acid sequence <SEQ ID 422>. Analysis of this protein sequence reveals the following: TABLE-US-00441 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3405(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00442 >GP:CAA56994 GB:X81089 glutamyl-aminopeptidase [Lactococcus lactis] Identities = 219/354 (61%), Positives = 273/354 (76%), Gaps = 1/354 (0%) Query: 3 DLFNKIKTVTELDGIAGYEHNIRNFLRQEITPLVDQVETDGLGGIFGVKNTHETNAPKVM 62 +LF+K+K +TE+ +G+E +R++L+ + L Q E DGLGGIF K + NAP++M Sbjct: 2 ELFDKVKALTEIQATSGFEGPVRDYLKARMVELGYQPEFDGLGGIFVTKASKVENAPRIM 61 Query: 63 VAAHMDEVGFMVSHIQPDGTFRVLEVGGWNPLVVSSQRFTLYTRSGDAIPVISGSVPPHF 122- VAAHMDEVGFMVS I+ DGTFRV+ +GGWNPLVVS QRFTL+TR+G IPV++G +PPH Sbjct: 62 VAAHMDEVGFMVSSIKADGTFRVVPLGGWNPLVVSGQRFTLFTRTGKKIPVVTGGLPPHL 121- Query: 123 LRGQSGGTTLPKISDIVFDGGFTDKNEAESFGIAPGDIIVPKSETILTANQKHIMSKAWD 18- 2 LRG +P ISDI+FDG F + KA FGIA GD+I+P++ETIL+AN K+I+SKAWD Sbjct: 122 LRGTGVTPQIPAISDIIFDGAFENAAEAAEFGIAQGDLIIPETETILSANGKNIISKAWD 18- 1 Query: 183 NRYGVLMVTELLKSLKDQSLSNTLIAGANVQEEVGLRGAHVSTTKFNPDIFLAVDCSPAG 24- 2 NRYG LM+ ELL+ L D+ L TLI GANVQEEVGLRGA VSTTKFNPD+F AVDCSPA Sbjct: 182 NRYGCLMILELLEFLADKELPVTLIIGANVQEEVGLRGAKVSTTKFNPDLFFAVDCSPAS 24- 1 Query: 243 DIYG-EQGKIGEGTLIRFYDPGHIMLKDMRDFLLTTAEEAGIKYQYYAANGGTDAGAAHL 30- 1 D +G + G++GEGT +RF+DPGHIML M++FLL TA A +K Q Y A GGTDAGAAHL Sbjct: 242 DTFGDDNGRLGEGTTLRFFDPGHIMLPGMKNFLLDTANHAKVKTQVYMAKGGTDAGAAHL 30- 1 Query: 302 KNSGIPSTTIGVCARYIHSHQTLYAMDDFLQAQAYLQAIVNKLDRSTVDIIKGY 355 N G+PSTTIGV ARYIHSHQT++ +DDFLQAQ +L+AI+ L+ V IK Y Sbjct: 302 ANGGVPSTTIGVVARYIHSHQTIFNIDDFLQAQTFLRAIITSLNTEKVAEIKNY 355 A related DNA sequence was identified in S. pyogenes <SEQ ID 423> which encodes the amino acid sequence <SEQ ID 424>. Analysis of this protein sequence reveals the following: TABLE-US-00443 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2747(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00444 Identities = 276/355 (77%), Positives = 322/355 (89%) Query: 1 MSDLFNKIKTVTELDGIAGYEHNIRNFLRQEITPLVDQVETDGLGGIFGVKNTHETNAPK 60 M+DLF+KIK VTELDGIAGYEH++R++LR +ITPLVD+VETDGLGGIFG++++ AP+ Sbjct: 1 MTDLFSKIKEVTELDGIAGYEHSVRDYLRTKITPLVDRVETDGLGGIFGIRDSKAEKAPR 60 Query: 61 VMVAAHMDEVGFMVSHIQPDGTFRVLEVGGWNPLVVSSQRFTLYTRSGDAIPVISGSVPP 120- ++VAAHMDEVGFMVS I+ DGT RV+ +GGWNPLVVSSQRFTLYTR+G IP+ISGSVPP Sbjct: 61 ILVAAHMDEVGFMVSDIKVDGTLRVVGIGGWNPLVVSSQRFTLYTRTGQVIPLISGSVPP 120- Query: 121 HFLRGQSGGTTLPKISDIVFDGGFTDKNEAESFGIAPGDIIVPKSETILTANQKHIMSKA 18- 0 HFLRG +G +LP I DIVFDGGFTDK EAE FGI PGDII+P+SETILTANQK+I+SKA Sbjct: 121 HFLRGANGSASLPHIEDIVFDGGFTDKAEAERFGITPGDIIIPQSETILTANQKNIISKA 18- 0 Query: 181 WDNRYGVLMVTELLKSLKDQSLSNTLIAGANVQEEVGLRGAHVSTTKFNPDIFLAVDCSP 24- 0 WDNRYGVLM+TE+L++LK Q L+NTLIAGANVQEEVGLRGAHVSTTKF+P++F AVDCSP Sbjct: 181 WDNRYGVLMITEMLEALKGQDLNNTLIAGANVQEEVGLRGAHVSTTKFDPELFFAVDCSP 24- 0 Query: 241 AGDIYGEQGKIGEGTLIRFYDPGHIMLKDMRDFLLTTAEEAGIKYQYYAANGGTDAGAAH 30- 0 AGDIYG G IG+GTL+RFYDPGH+MLKDMRDFLLTTAEEAG+ +QYY GGTDAGAAH Sbjct: 241 AGDIYGNPGTIGDGTLLRFYDPGHVMLKDMRDFLLTTAEEAGVNFQYYCGKGGTDAGAAH 30- 0 Query: 301 LKNSGIPSTTIGVCARYIHSHQTLYAMDDFLQAQAYLQAIVNKLDRSTVDIIKGY 355 L+N G+PSTTIGVCARYIHSHQTLYAMDDF++AQA+LQAI+ KLDRSTVD+IK Y Sbjct: 301 LQNGGVPSTTIGVCARYIHSHQTLYAMDDFVEAQAFLQAIIKKLDRSTVDLIKCY 355 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 125 A DNA sequence (GBSx0130) was identified in S. agalactiae <SEQ ID 425> which encodes the amino acid sequence <SEQ ID 426>. Analysis of this protein sequence reveals the following: TABLE-US-00445 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1672(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 126 A DNA sequence (GBSx0131) was identified in S. agalactiae <SEQ ID 427> which encodes the amino acid sequence <SEQ ID 428>. Analysis of this protein sequence reveals the following: TABLE-US-00446 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.28 Transmembrane 18-34 (17-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.1914(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 429> which encodes the amino acid sequence <SEQ ID 430>. Analysis of this protein sequence reveals the following: TABLE-US-00447 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.16 Transmembrane 12-28 (8-30) ----- Final Results ----- bacterial membrane --- Certainty = 0.3463(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below: TABLE-US-00448 Identities = 30/91 (32%), Positives = 48/91 (51%) Query: 13 MKNKKILFGTGLAGVGLLAAAGYTLTKKVTDYKRQQITQTLREFFSQMGDIQVFYFNEFE 72 - M KKI +G+ G L G + D +R+Q+T+ LR FFS +G I+V Y N + Sbjct: 4 MSKKKIGMISGIFGFSLAIGLGIVIKDYCQDRQRRQMTRDLRTFFSPLGQIEVLYINPCQ 63 Query: 73 SDIKMTSGGLVLEDGRIFEFIYRQGVLDYVE 103 SGG+V+ +G+ ++F Y + + E Sbjct: 64 VKQDYISGGVVMSNGKQYQFTYHSRQISFEE 94 A related GBS gene <SEQ ID 8497> and protein <SEQ ID 8498> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00449 Lipop Possible site: -1 Crend: 4 SRCFLG: 0 McG: Length of UR: 21 Peak Value of UR: 2.30 Net Charge of CR: 3 McG: Discrim Score: 6.28 GvH: Signal Score (-7.5): -1.46 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 20 ALOM program count: 0 value: 22.60 threshold: 0.0 PERIPHERAL Likelihood = 22.60 29 modified ALOM score: -5.02 *** Reasoning Step: 3 Rule gpo1 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8498 (GBS214) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 40 (lane 3; MW 13.9 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 46 (lane 6; MW 39 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 127 A DNA sequence (GBSx0132) was identified in S. agalactiae <SEQ ID 431> which encodes the amino acid sequence <SEQ ID 432>. This protein is predicted to be thioredoxin H1 (trxA). Analysis of this protein sequence reveals the following: TABLE-US-00450 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2350(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00451 >GP:BAB06972 GB:AP001518 thioredoxin H1 [Bacillus halodurans] Identities = 47/90 (52%), Positives = 66/90 (73%) Query: 14 IDSTKKVVFFFTADWCPDCQFIYPVMPSIEKDFSDFVFVRVNRDDYIELAQQWNIFGIPS 73 - + + + VVF F+ADWCPDC+ I P +P +E+ + ++ F VNRDD+IEL Q+ +IFGIPS Sbjct: 13 VKNQENVVFLFSADWCPDCRVIEPFLPELEQTYDEYQFYYVNRDDFIELCQELDIFGIPS 72 Query: 74 FVVVENGQELGRLVNKNRKTKAEITKFLAE 103 F+ NG+E R V+K+RKTK EI +FL E Sbjct: 73 FLFYSNGEERSRFVSKDRKTKEEIERFLTE 102 A related DNA sequence was identified in S. pyogenes <SEQ ID 433> which encodes the amino acid sequence <SEQ ID 434>. Analysis of this protein sequence reveals the following: TABLE-US-00452 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1997(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00453 Identities = 70/102 (68%), Positives = 81/102 (78%) Query: 1 MILPESYEEIAAYIDSTKKVVFFFTADWCPDCQFIYPVMPSIEKDFSDFVFVRVNRDDYI 60 MI P SYE +A I+ K+V FFTADWCPDCQFIYP+MP IE + +D FV VNRD +I Sbjct: 1 MIRPTSYESLATLIEKEDKLVLFFTADWCPDCQFIYPIMPEIEAELTDMTFVCVNRDQFI 60 Query: 61 ELAQQWNIFGIPSFVVVENGQELGRLVNKNRKTKAEITKFLA 102 E+AQ+WNIFGIPSFVV+E GQE+GRLVNK RKTK EI FLA Sbjct: 61 EVAQKWNIFGIPSFVVIEKGQEVGRLVNKMRKTKTEIMHFLA 102 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 128 A DNA sequence (GBSx0133) was identified in S. agalactiae <SEQ ID 435> which encodes the amino acid sequence <SEQ ID 436>. This protein is predicted to be phenylalanyl-tRNA synthetase beta subunit, non-spirochete. Analysis of this protein sequence reveals the following: TABLE-US-00454 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1310(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00455 >GP:AAC00291 GB:AF008220 YtpR [Bacillus subtilis] Identities = 78/196 (39%), Positives = 125/196 (62%), Gaps = 1/196 (0%) Query: 5 YNREHVGDTLMVIVKDSQGAKLDVDRRGQVARVYLQDSKETVAWNIFEVSSLIVIEGAGQ 64 YN+E VGDTL++ ++D +L ++ G V +++ ++KET +NIF SS + I+ G Sbjct: 5 YNKEGVGDTLLISLQDVTREQLGYEKHGDVVKIFNNETKETTGFNIFNASSYLTIDENGP 64 Query: 65 ITLSDQDIKILNAELLKEGFEDSLVNNIEPTFVVAQIKEIIDHPDSDHLHICQAEINDGK 124- + LS+ ++ +N L + G E++LV ++ P FVV ++ HP++D L +C+ + + + Sbjct: 65 VALSETFVQDVNEILNRNGVEETLVVDLSPKFVVGYVESKEKHPNADKLSVCKVNVGE-E 123- Query: 125 TVQIVCGAPNASVGLKTVAALPGAMMPNGSLIFPGKLRGEDSFGMLCSARELALPNAPQV 18- 4 T+QIVCGAPN G K V A GA+MP+G +I +LRG S GM+CSA+EL LP+AP Sbjct: 124 TLQIVCGAPNVDQGQKVVVAKVGAVMPSGLVIKDAELRGVPSSGMICSAKELDLPDAPAE 18- 3 Query: 185 RGIIELSDQVIVGESF 200 +GI+ L G++F Sbjct: 184 KGILVLEGDYEAGDAF 199 A related DNA sequence was identified in S. pyogenes <SEQ ID 437> which encodes the amino acid sequence <SEQ ID 438>. Analysis of this protein sequence reveals the following: TABLE-US-00456 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.49 Transmembrane 90-106 (90-107) ----- Final Results ----- bacterial membrane --- Certainty = 0.1595(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00457 >GP: BAB06970 GB: AP001518 phenylalanyl-tRNA synthetase (beta subunit) [Bacillus halodurans] Identities = 84/196 (42%), Positives = 124/196 (62%), Gaps = 1/196 (0%) Query: 5 YNKEQVGDVLMVILQDTKDIKRQVERKGKVARVFAEESGKTLAWNIFEASSLITIEGNGQ 64 YN++ +GD +++++ + + R ER+G V R++ +GKT +N+F AS G G Sbjct: 5 YNEKGIGDTILIVIDEVEPANRAYERQGDVVRIYHLGTGKTTGYNLFHASKYGEFNGQGL 64 Query: 65 IFLTDENLARLNAELAKEGFSERLEPIVGPVFVVGQIVEMVAHPDSDHLNICQVAIGEDQ 124- + LTD +A L K G + LE + P FVVG + HP++D L+IC+V +G D Sbjct: 65 LELTDSLVATLEQAFQKNGVNWTLEVDLSPKFVVGFVQSKDKHPNADKLSICKVDVGSD- 123- Query: 125 TVQIVAGAPNAALGLKTIVALPGAIMPNGSLIFPGKLRGEESYGMMCSPRELALPNAPQK 18- 4 T+QIV GAPN G K +VAL GA+MP+G +I P LRG S GM+CS +ELALP+AP++ Sbjct: 124 TLQIVCGAPNVEAGQKVVVALEGAVMPSGLVIKPTSLRGVSSTGMICSAKELALPDAPEE 18- 3 Query: 185 RGIIEFDESAVVGEAF 200 +GI+ D+S VG +F Sbjct: 184 KGILVLDDSYEVGTSF 199 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00458 Identities = 133/207 (64%), Positives = 167/207 (80%) Query: 1 MIFTYNREHVGDTLMVIVKDSQGAKLDVDRRGQVARVYLQDSKETVAWNIFEVSSLIVIE 60 MIF YN+E VGD LMVI++D++ K V+R+G+VARV+ ++S +T+AWNIFE SSLI IE Sbjct: 1 MIFAYNKEQVGDVLMVILQDTKDIKRQVERKGKVARVFAEESGKTLAWNIFEASSLITIE 60 Query: 61 GAGQITLSDQDIKILNAELLKEGFEDSLVNNIEPTFVVAQIKEIIDHPDSDHLHICQAEI 120- G GQI L+D+++ LNAEL KEGF + L + P FVV QI E++ HPDSDHL+ICQ I Sbjct: 61 GNGQIFLTDENLARLNAELAKEGFSERLEPIVGPVFVVGQIVEMVAHPDSDHLNICQVAI 120- Query: 121 NDGKTVQIVCGAPNASVGLKTVAALPGAMMPNGSLIFPGKLRGEDSFGMLCSARELALPN 18- 0 + +TVQIV GAPNA++GLKT+ ALPGA+MPNGSLIFPGKLRGE+S+GM+CS RELALPN Sbjct: 121 GEDQTVQIVAGAPNAALGLKTIVALPGAIMPNGSLIFPGKLRGEESYGMMCSPRELALPN 18- 0 Query: 181 APQVRGIIELSDQVIVGESFDANKHWK 207 APQ RGIIE + +VGE+FD KHWK Sbjct: 181 APQKRGIIEFDESAVVGEAFDPAKHWK 207 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 129 A DNA sequence (GBSx0135) was identified in S. agalactiae <SEQ ID 439> which encodes the amino acid sequence <SEQ ID 440>. Analysis of this protein sequence reveals the following:

TABLE-US-00459 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3052(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00460 >GP: AAB81904 GB: U92974 unknown [Lactococcus lactis] Identities = 69/241 (28%), Positives = 117/241 (47%), Gaps = 15/241 (6%) Query: 7 YKEMLAKPWGKIQYEITFAQL--SHIKNQNVLDFGAGFCLTEQHLAKEN-NVTAIEPNPK 63 Y E+ KPWG++ Y++ F QL + K+ +L FG+GF TE L ++ VT EP+ + Sbjct: 23 YAEVFEKPWGRMFYDLLFPQLLPNLTKDSKILSFGSGFGRTETFLEEQGFEVTGYEPDVE 82 Query: 64 LLYDNQSDNIYKILGSYEALRD-LPDQSFDTIICHNVLEYIDKHNHPAYFDEFSRLLKPN 122- L ++ G+++ + + ++ +D I+ HNVLEY+ + + LL Sbjct: 83 KLEMMSDQTFRQLTGTFDDFAETVKNERYDVILIHNVLEYV--LDRKVVLELLLSLLTDG 140- Query: 123 GELSLIKHNITGKILQSVIFSNDTSTAMELLTGEANFKSASFDQGNIYT-----LEELKQ 17- 7 G LS++KH+ G +++ ++ A+++ EA AS + G+I L + Sbjct: 141 GTLSIVKHSKYGSMIEMAAGRDNPQAALDVYENEA---VASHNHGDILVYDDDWLTDFVA 19- 7 Query: 178 NTNLLVERYQGIRTFYSLQPN-HFKTETGWLNKMLAIELSVADKAPYKDIAFLQHITLKKS 2- 37 N L ++ GIR FY + N K W ML +E VA +A L H+ KKS Sbjct: 198 NYKLKLQEKFGIRHFYGISQNAEIKETENWYQPMLKLEQKVAKDQTLYPVARLHHLIFKKS 2- 58 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 130 A DNA sequence (GBSx0136) was identified in S. agalactiae <SEQ ID 441> which encodes the amino acid sequence <SEQ ID 442>. Analysis of this protein sequence reveals the following: TABLE-US-00461 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3479(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00462 >GP: AAF74079 GB: AF212845 putative single stranded binding protein [Lactococcus lactis bacteriophage ul36] Identities = 64/141 (45%), Positives = 92/141 (64%), Gaps = 10/141 (7%) Query: 1 MYNKVIMIGRLTAKPEMVKTPTDKSVTRATVAVNRRFKGSNGEREADFINVVMWGRLAET 60 M N V ++GR+T +PE+ TP +K+V T+AVNR FK +NGEREADFI+ V+WG+ AE Sbjct: 1 MINNVTLVGRITKEPELRYTPQNKAVATFTLAVNRAFKNANGEREADFISCVIWGKSAEN 60 Query: 61 LASYGTKGSLISIDGELRTRKYE-KDGQTHYITEVLASSFQLLESRAQ---------RAM 110- LA++ KG LI + G ++TR YE + GQ YITEV+AS+FQ+LE Q + Sbjct: 61 LANWTHKGQLIGVIGNIQTRNYENQQGQRVYITEVVASNFQVLEKSNQANGERISNPASK 120- Query: 111 RENNVSGDLSDLVLEEEELPF 131 +NN S + + +++LPF Sbjct: 121 PQNNDSFGSDPMEISDDDLPF 141 A related DNA sequence was identified in S. pyogenes <SEQ ID 443> which encodes the amino acid sequence <SEQ ID 444>. Analysis of this protein sequence reveals the following: TABLE-US-00463 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1817(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00464 Identities = 102/131 (77%), Positives = 116/131 (87%) Query: 1 MYNKVIMIGRLTAKPEMVKTPTDKSVTRATVAVNRRFKGSNGEREADFINVVMWGRLAET 60 MYNKVI IGRL AKPE+VKT TDK V R ++AVNRRFK ++GEREADFI+VV+WG+LAET Sbjct: 1 MYNKVIAIGRLVAKPELVKTATDKHVARLSLAVNRRFKNASGEREADFISVVVWGKLAET 60 Query: 61 LASYGTKGSLISIDGELRTRKYEKDGQTHYITEVLASSFQLLESRAQRAMRENNVSGDLS 120- L SY +KGSL+SIDGELRTRKY+KDGQ HY+TEVL SFQLLESRAQRAMRENNV+ DL Sbjct: 61 LVSYASKGSLMSIDGELRTRKYDKDGQVHYVTEVLCQSFQLLESRAQRAMRENNVTNDLV 120- Query: 121 DLVLEEEELPF 131 DLVLEE+ LPF Sbjct: 121 DLVLEEDTLPF 131 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 131 A DNA sequence (GBSx0037) was identified in S. agalactiae <SEQ ID 445> which encodes the amino acid sequence <SEQ ID 446>. Analysis of this protein sequence reveals the following: TABLE-US-00465 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2235(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9493> which encodes amino acid sequence <SEQ ID 9494> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00466 >GP: CAC13072 GB: AL445503 putative hydrolase [Streptomyces coelicolor] Identities = 63/179 (35%), Positives = 91/179 (50%), Gaps = 2/179 (1%) Query: 33 IIFDMDGVIVDSEYTFLDNKTEMLREEGI-DTDVSYQYQYMGTTFEFMWQAMKEEFGLPK 91 - +IFD+DG +VDSE + + L E G+ D + Y+G + + K +GL Sbjct: 12 VIFDLDGTLVDSEPHYYEAGRRTLAEYGVPDFSWADHEAYVGISTQETVADWKRRYGLRA 71 Query: 92 TVKEYIAEMNRRRQAIVARDGVRPIKGAQRLIHWLHQHGYRLAVASSSPMVDIKRNLKEL 151- TV+E +A NR + AR R ++ + L G +AVAS S I L Sbjct: 72 TVEELLAVKNRHYLGL-ARTSARAYPEMRKFVELLAGEGVPMAVASGSSPEAIAAILART 130- Query: 152 GVTECFEYMVTGEDVSSSKPAPDVFLRAAELLDVDPKVCIVIEDTRNGSLAAKAAGMYC 210- G+ +V+ ++V+ KPAPDVFL AA L +P C+V+ED G+ AA AAGM C Sbjct: 131 GLDAHLRTVVSADEVARGKPAPDVFLEAARRLGTEPARCVVLEDAAPGAAAAHAAGMRC 189- A related DNA sequence was identified in S. pyogenes <SEQ ID 447> which encodes the amino acid sequence <SEQ ID 448>. Analysis of this protein sequence reveals the following: TABLE-US-00467 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3706(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00468 Identities = 62/202 (30%), Positives = 100/202 (48%), Gaps = 1/202 (0%) Query: 29 MEKVIIFDMDGVIVDSEYTFLDNKTEMLREEGIDTDVSYQYQYMGTTFEFMWQAMKEEFG 88 - M K IIFDMDGV+ D+E +L + + + +GI D ++G + +W+ + + Sbjct: 3 MIKGIIFDMDGVLFDTEPFYLRRREDFFKTKGIPIDHLNSKDFIGGNLQELWKELLGKNR 62 Query: 89 LPKTVKEYIAEMNRRRQAIVARDGVRPIKGAQRLIHWLHQHGYRLAVASSSPMVDIKRNL 148- VK + + +QA I + L + G +LAVAS+S D+ L Sbjct: 63 DDAIVKAITTDYDAYKQAHKPPYQKLLITEVNSCLEQLEKQGIKLAVASNSKRQDVLLAL 122- Query: 149 KELGVTECFEYMVTGEDVSSSKPAPDVFLRAAELLDVDPKVCIVIEDTRNGSLAAKAAGM 20- 8 + + + FE ++ EDVS KP PD++ +A + L + K +V+ED++ G AAKAA + Sbjct: 123 ETTQIKDYFEIILAREDVSRGKPYPDIYNKAVQKLGLQKKQLLVVEDSQKGIAAAKAANL 18- 2 Query: 209 YCFGFANPDYPPQDLSMADKVI 230 F + Y D S AD I Sbjct: 183 TVFAITDYRY-GIDQSQADHKI 203 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 132 A DNA sequence (GBSx0138) was identified in S. agalactiae <SEQ ID 449> which encodes the amino acid sequence <SEQ ID 450>. Analysis of this protein sequence reveals the following: TABLE-US-00469 Possible site: 20 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.22 Transmembrane 16-32 (16-32) ----- Final Results ----- bacterial membrane --- Certainty = 0.1086(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 133 A DNA sequence (GBSx0139) was identified in S. agalactiae <SEQ ID 451> which encodes the amino acid sequence <SEQ ID 452>. Analysis of this protein sequence reveals the following: TABLE-US-00470 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = 5.04 Transmembrane 28-44 (27-45) ----- Final Results ----- bacterial membrane --- Certainty = 0.3017(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 134 A DNA sequence (GBSx0140) was identified in S. agalactiae <SEQ ID 453> which encodes the amino acid sequence <SEQ ID 454>. Analysis of this protein sequence reveals the following: TABLE-US-00471 Possible site: 17 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.72 Transmembrane 38-54 (34-60) INTEGRAL Likelihood = -7.70 Transmembrane 4-20 (1-22) INTEGRAL Likelihood = -4.99 Transmembrane 153-169 (150-171) INTEGRAL Likelihood = -2.55 Transmembrane 179-195 (178-198) INTEGRAL Likelihood = -2.39 Transmembrane 93-109 (93-109) INTEGRAL Likelihood = -1.17 Transmembrane 116-132 (116-133) INTEGRAL Likelihood = -0.43 Transmembrane 344-360 (344-360) ----- Final Results ----- bacterial membrane --- Certainty = 0.5288(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00472 >GP: CAB14853 GB: Z99118 two-component sensor histidine kinase [Bacillus subtilis] Identities = 254/585 (43%), Positives = 371/585 (63%), Gaps = 9/585 (1%) Query: 2 LMVLLFQRLGIIMILAFLLVNNSYFRQLIEERSK-RETVVLVIIFGLFVIISNITGIEIK 60 LM+++ +R+GII+IL F+L + FRQ ++ + + +L+ IF LF IISN TGIEI+ Sbjct: 4 LMIMMLERVGIIVILGFILAHTKLFRQALQNQDGYKGKAILISIFSLFSIISNYTGIEIQ 63 Query: 61 GDRSLVERPFLTTISHSDSLANTRTLVITTASLVGGPLVGSIVGFIGGVHRFFQGSFSGS 120- + +V ++ TI S S+ANTR L + L+GGP VG+ +G + G+HRF G + Sbjct: 64 RNM-IVNNDWVFTIDPSGSIANTRILGVEIGGLLGGPFVGAGIGILAGLHRFSLGGSTAL 122- Query: 121 FYIVSSVLVGIVSGKIGDKLKENHLYPSTSQVILISIIAESIQMLFVGIFT-----GWEL 17- 5 VSS+L G+++G IG + + P+ L+ I ES+QM+ + + WEL Sbjct: 123 SCAVSSILAGVLAGLIGRYFTKRYRMPTPRIAALVGIGMESLQMIIILLMAKPFSDAWEL 18- 2 Query: 176 VKMIVIPMMILNSLGSTLFLAILKTYLSNESQLRAVQTRDVLELTRQTLPYLRQGLTPQS 23- 5 V MI IPM+++N GS +FL+I++ + E Q RA++T VL + QTLP+ RQGL S Sbjct: 183 VSMIGIPMILINGTGSFIFLSIIQAIIRKEEQARALETHRVLTIADQTLPFFRQGLNENS 24- 2 Query: 236 ARSVCEIIKRHTNFDAVGLTDRSNVLAHIGVGHDHHIAGQPVKTDLSKSVIFDGEPRIAQ 29- 5 +SV II + T DAV LTD+ +LAH+G G DHHI, + + T LSK VI G A Sbjct: 243 CKSVAAIIHKLTGTDAVSLTDKEKILAHVGAGMDHHIPSKSLITGLSKKVIKTGHIMKAI 30- 2 Query: 296 DKAAISCPDHNCQLNSAIVVPLKINDKTVGALKMYFAGDKTMSEVEENLVLGLAQIFSGQ 35- 5 + I C C L++AIV+PL N T+G LKMYF +S+VEE L GLA +FS Q Sbjct: 303 SQEEIECTHAECPLHAAIVLPLTSNGNTIGTLKMYFKSPAGLSQVEEELAEGLAMLFSTQ 36- 2 Query: 356 LAMGITEEQNKLASMAEIKALQAQINPHFFFNAINTISALIRIDSDKARYALMQLSTFFR 41- 5 L +G E Q+KL AEIKALQAQ+NPHF FNAINTISAL R D +K R L+QLS +FR Sbjct: 363 LELGEAELQSKLLKDAEIKALQAQVNPHFLFNAINTISALCRTDVEKTRKLLLQLSVYFR 42- 2 Query: 416 TSLQGGQDREVTLEQEKSHVDAYMNVEKLRFPDKYQLSYDI-SAPEKMKLPPFGLQVLVE 47- 4 ++LQG + + L +E +H++AY+++E+ RFP KY++ +I S E++++PPF LQVLVE Sbjct: 423 SNLQGARQLLIPLSKELNHLNAYLSLEQARFPGKYKIELNIDSRLEQIEIPPFVLQVLVE 48- 2 Query: 475 NAVRHAFKERKTDNHILVQIKPDGHYYCVSVSDNGQGISDTIIDKLGQETVAESKGTGTA 53- 4 NA+RHAF +++ + V + D + V+DNG+GI ++ +LG++ +GTGTA Sbjct: 483 NALRHAFPKKQDICKVTVCVLSDDASVYMKVADNGRGIPPDVLPELGKKPFPSKEGTGTA 54- 2 Query: 535 LVNLNNRLNLLYGSVSCLHFSSD-KNGTKVWYRIPNRIREDEHEN 578 L NLN RL L+G + LH SS+ GT+V +++P + ++ E+ Sbjct: 543 LYNLNQRLIGLFGQQAALHISSEVHKGTEVSFQVPMQQMKEGEEH 587 A related DNA sequence was identified in S. pyogenes <SEQ ID 455> which encodes the amino acid sequence <SEQ ID 456>. Analysis of this protein sequence reveals the following: TABLE-US-00473 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1771(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00474 Identities = 75/245 (30%), Positives = 117/245 (47%), Gaps = 22/245 (8%) Query: 348 LAQIFSGQL-----AMGITEEQNKLASMAEIKALQAQINPHFFFNAINTISALIRI-DSD 40- 1 LAQ F+ L M ++ K ++AL +QINPHF +N ++TI + DS Sbjct: 4 LAQQFNALLDQIDSLMVAVADKEKAIGQYRLQALASQINPHFLYNTLDTIIWMAEFNDSK 63 Query: 402 KARYALMQLSTFFRTSLQGGQDREVTLEQEKSHVDAYMNVEKLRFPDKYQLSYDISAPE- 46- 0 + L+ +FR +L G + + L E HV Y+ ++K R+ DK LSY++ + Sbjct: 64 RVVEVTKSLAKYFRLALNQGNEY-IRLADELDHVSQYLFIQKQRYGDK--LSYEVQGLDV 120- Query: 461 --KMKLPPFGLQVLVENAVRHAFKERKTDNHILVQIKPDGHYYCVSVSDNGQGISDTIID 51- 8 +P LQ LVENA+ H KE I V + + ++V DNG+GI D+ + Sbjct: 121 YADFVIPKLILQPLVENAIYHGIKEVDRKGMIKVTVSDTAQHLMLTVWDNGKGIEDSSLT 18- 0 Query: 519 KLGQETVAESKGTGTALVNLNNRLNLLYGS--VSCLHFSSDKNGTKVWYRIPNR---IRE 57- 3 Q +A G L N++ RL L YG +H SD+ T++ +P + + Sbjct: 181 N-SQSLLARG---GVGLKNVDQRLKLHYGEGYHMTIHSQSDQ-FTEIQLSLPKMHELMAD 23- 5 Query: 574 DEHEN 578 D EN Sbjct: 236 DTQEN 240 SEQ ID 454 (GBS248d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 124 (lane 2-4; MW 71 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 124 (lane 5-7; MW 46 kDa) and in FIG. 180 (lane 2; MW 46 kDa). GBS248d-His was purified as shown in FIG. 234, lane 3-4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 135 A DNA sequence (GBSx0141) was identified in S. agalactiae <SEQ ID 457> which encodes the amino acid sequence <SEQ ID 458>. This protein is predicted to be two-component response regulator (lytT). Analysis of this protein sequence reveals the following: TABLE-US-00475 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3230(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9495> which encodes amino acid sequence <SEQ ID 9496> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00476 >GP: CAB14852 GB: Z99118 two-component response regulator [Bacillus subtilis] Identities = 105/244 (43%), Positives = 157/244 (64%), Gaps = 6/244 (2%) Query: 3 MKILILDDEMFARQELSFLVEHSQEVDNPEIFQAEDISEAEKILFRQQIDLIFLDISLSE 62 +++LI+DDEM AR EL++L++ + D EI +AE+I A + Q+ DL+FLD+ LS Sbjct: 2 LRVLIVDDEMLARDELAYLLKRTN--DEMEINEAENIESAFDQMMDQKPDLLFLDVDLSG 59 Query: 63 ENGFTLANQLSQLAHPPLVVFATAYDNYAVKAFESNAVDYIMKPFEQQRVDMALSKVKKL 122- ENGF +A +L ++ HPP +VFATAYD YA+KAFE +A+DY+ KPF+++R+ L K KK+ Sbjct: 60 ENGFDIAKRLKKMKHPPAIVFATAYDQYALKAFEVDALDYLTKPFDEERIQQTLKKYKKV 119- Query: 123 SQLTTASDVEQAIPKKASVELLTLTLSDRSVVVKMQDIVAASVEDGELTVSTVQKTYTIR 18- 2 ++ VE A L L++ + V+V +DI+ A EDG + V T +YT+ Sbjct: 120 NR----DIVETEQNSHAGQHKLALSVGESIVIVDTKDIIYAGTEDGHVNVKTFDHSYTVS 17- 5 Query: 183 KTLNWFKSRAVAPYFLQIHRNTVINLEMIEEIQPWFNHTLLLIMSNGEKFPVGRSYLKDL 24- 2 TL + + F+++HR+ V+N E I+EIQPWFN T LIM +G K PV R+Y K+L Sbjct: 176 DTLVVIEKKLPDSDFIRVHRSFVVNTEYIKEIQPWFNSTYNLIMKDGSKIPVSRTYAKEL 23- 5 Query: 243 NEHL 246 + L Sbjct: 236 KKLL 239 A related DNA sequence was identified in S. pyogenes <SEQ ID 459> which encodes the amino acid sequence <SEQ ID 460>. Analysis of this protein sequence reveals the following: TABLE-US-00477 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3818(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below:

TABLE-US-00478 Identities = 44/148 (29%), Positives = 84/148 (56%), Gaps = 5/148 (3%) Query: 5 ILILDDEMFARQELSFLVEHSQ-EVDNPEIFQAEDISEAEKILFRQQIDLIFLDISLSEE 63 +LI++DE RQ + LV+ SQ ++D + +AE+ A + ++ D++ DI++ + Sbjct: 4 LLIVEDEYLVRQGIRSLVDFSQFKIDR--VNEAENGQLAWDLFQKEPYDIVLTDINMPKL 61 Query: 64 NGFTLANQLSQLAHPPLVVFATAYD--NYAVKAFESNAVDYIMKPFEQQRVDMALSKVKK 121- NG LA + Q + +VF T YD NYA+ A + A DY++KPF + V+ L K++K Sbjct: 62 NGIQLAELIKQESPQTHLVFLTGYDDFNYALSALKLGADDYLLKPFSKADVEDMLGKLRK 121- Query: 122 LSQLTTASDVEQAIPKKASVELLTLTLS 149 +L+ ++ Q + ++ E+ + ++ Sbjct: 122 KLELSKKTETIQELVEQPQKEVSAIAMA 149 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 136 A DNA sequence (GBSx0142) was identified in S. agalactiae <SEQ ID 461> which encodes the amino acid sequence <SEQ ID 462>. Analysis of this protein sequence reveals the following: TABLE-US-00479 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0266(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 137 A DNA sequence (GBSx0143) was identified in S. agalactiae <SEQ ID 463> which encodes the amino acid sequence <SEQ ID 464>. Analysis of this protein sequence reveals the following: TABLE-US-00480 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.89 Transmembrane 104-120 (99-134) INTEGRAL Likelihood = -5.89 Transmembrane 47-63 (46-65) INTEGRAL Likelihood = -3.29 Transmembrane 22-38 (21-39) INTEGRAL Likelihood = -2.81 Transmembrane 74-90 (70-92) ----- Final Results ----- bacterial membrane --- Certainty = 0.5755(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8499> which encodes amino acid sequence <SEQ ID 8500> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00481 >GP: CAB14851 GB: Z99118 similar to hypothetical proteins from B. subtilis [Bacillus subtilis] Identities = 50/110 (45%), Positives = 82/110 (74%), Gaps = 2/110 (1%) Query: 20 QMSIYAAILLVSQMISMLLPKSLPIPTTVIGLVLMYVLLTAKIIKVEWVDSFGALMISMI 79 - Q I+A I+LVS MI+ ++P +PIP +V+GLVL+++LL K+IK+E V++ G + S+I Sbjct: 12 QAFIFAVIMLVSNMIAAIVP--IPIPASVVGLVLLFLLLCLKVIKLEQVETLGTSLTSLI 69 Query: 80 GFMFVPSGISVAANLDILKAEGLQLVAVITISTVVMLVVVAYVARLILAI 129 GF+FVPSGISV +L +++ GLQ+V VI ++T+++L ++LIL++ Sbjct: 70 GFLFVPSGISVMNSLGVMQQYGLQIVLVILLATIILLGATGLFSQLILSL 119 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 138 A DNA sequence (GBSx0144) was identified in S. agalactiae <SEQ ID 465> which encodes the amino acid sequence <SEQ ID 466>. Analysis of this protein sequence reveals the following: TABLE-US-00482 Possible site: 44 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.21 Transmembrane 219-235 (208-241) INTEGRAL Likelihood = -11.94 Transmembrane 103-119 (99-133) INTEGRAL Likelihood = -5.57 Transmembrane 157-173 (154-175) INTEGRAL Likelihood = -1.70 Transmembrane 73-89 (73-89) ----- Final Results ----- bacterial membrane --- Certainty = 0.5883 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00483 >GP: CAB14850 GB: Z99118 similar to hypothetical proteins [Bacillus subtilis] Identities = 120/240 (50%), Positives = 159/240 (66%), Gaps = 10/240 (4%) Query: 1 MELLKTPIFGICFSLILYTIGEHLFKKSKGFFLLQPLFFAMVSGIVILWLMSKGLGTDVK 60 ME +P FGI SL + IG LFKK+KGFFL PLF AMV GI L + Sbjct: 1 MESTMSPYFGIVVSLAAFGIGTFLFKKTKGFFLFTPLFVAMVLGIAFL---------KIG 51 Query: 61 TFYTQAYKPGGDLIFWFLNPATIAFAVPLYKKNDVVKKYWVEILSSLVIGMIVSLILIVA 120- F Y GG++I +FL PATIAFA+PLYK+ D +KKYW +I++S++ G I S+ ++ Sbjct: 52 GFSYADYNNGGEIIKFFLEPATIAFAIPLYKQRDKLKKYWWQIMASIIAGSICSVTIVYL 111- Query: 121 ISKMVGLSQVGIASMLPQAATTAIALPITAAIGGNTAVTAMACILNAVIIYALGKKLVSF 18- 0 ++K + L + SMLPQAATTAIALP++ IGG + +TA A I NAVI+YALG + Sbjct: 112 LAKGIHLDSAVMKSMLPQAATTAIALPLSKGIGGISDITAFAVIFNAVIVYALGALFLKV 17- 1 Query: 181 FHLNDSKIGAGLGLGTSGHTVGAAFALELGELQGAMAAIAVVVIGLVVDLVIPIFSHLIG 24- 0 F + + I GL LGTSGH +G A +E+GE++ AMA+IAVVV+G+V LVIP+F LIG Sbjct: 172 FKVK-NPISKGLALGTSGHALGVAVGIEMGEVEAAMASIAVVVVGVVTVLVIPVFVQLIG 23- 0 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 139 A DNA sequence (GBSx0145) was identified in S. agalactiae <SEQ ID 467> which encodes the amino acid sequence <SEQ ID 468>. Analysis of this protein sequence reveals the following: TABLE-US-00484 Possible site: 22 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00485 Identities = 508/542 (93%), Positives = 523/542 (95%) Query: 1 MTKYLKYISFVALFLASIFLVACQNQNSQTKERTRKQRPKDELVVSMGAKLPHEFDPKDR 60 ++KYLKY S + LFL + LVACQ Q QTKER RKQRPKDELVVSMGAKLPHEFDPKDR Sbjct: 3 VSKYLKYFSIITLFLTGLILVACQQQKPQTKERQRKQRPKDELVVSMGAKLPHEFDPKDR 62 Query: 61 YGIHNEGNITHSTLLKRSPELDIKGELAKKYKISKDGLTWSFDLNDDFKFSNGEPVTADD 120- YG+HNEGNITHSTLLKRSPELDIKGELAK Y +S+DGLTWSFDL+DDFKFSNGEPVTADD Sbjct: 63 YGVHNEGNITHSTLLKRSPELDIKGELAKTYHLSEDGLTWSFDLHDDFKFSNGEPVTADD 122- Query: 121 VKFTYDMLKADGKAWDLTFIKNVEVVGKNQVNIHLTEAHSTFTAQLTEIPIVPKKHYNDK 18- 0 VKFTYDMLKADGKAWDLTFIKNVEVVGKNQVNIHLTEAHSTFTAQLTEIPIVPKKHYNDK Sbjct: 123 VKFTYDMLKADGKAWDLTFIKNVEVVGKNQVNIHLTEAHSTFTAQLTEIPIVPKKHYNDK 18- 2 Query: 181 YKSNPIGSGPYMVKEYKAGEQAIFVRNPYWHGKKPYFKKWTWVLLDENTALAALESGDVD 24- 0 YKSNPIGSGPYMVKEYKAGEQAIFVRNPYWHGKKPYFKKWTWVLLDENTALAALESGDVD Sbjct: 183 YKSNPIGSGPYMVKEYKAGEQAIFVRNPYWHGKKPYFKKWTWVLLDENTALAALESGDVD 24- 2 Query: 241 MIYATPELASKKVKGTRLLDIASNDVRGLSLPYVKKGVVKNSPDGYPVGNDVTSDPAIRK 30- 0 MIYATPELA KKVKGTRLLDI SNDVRGLSLPYVKKGV+ +SPDGYPVGNDVTSDPAIRK Sbjct: 243 MIYATPELADKKVKGTRLLDIPSNDVRGLSLPYVKKGVITDSPDGYPVGNDVTSDPAIRK 30- 2 Query: 301 ALTIGLNRQKVLDTVLNGYGKPAYSIIDRTPFWNPKTAIKDNKVAKAKQLLTKAGWKEQA 36- 0 ALTIGLNRQKVLDTVLNGYGKPAYSIID+TPFWNPKTAIKDNKVAKAKQLLTKAGWKEQA Sbjct: 303 ALTIGLNRQKVLDTVLNGYGKPAYSIIDKTPFWNPKTAIKDNKVAKAKQLLTKAGWKEQA 36- 2 Query: 361 DGSRKKGNLKSEFDLYYPTNDQLRANLAVEVAEQAKALGITIKLKASNWDEMATKSHDSA 42- 0 DGSRKKG+L + FDLYYPTNDQLRANLAVEVAEQAKALGITIKLKASNWDEMATKSHDSA Sbjct: 363 DGSRKKGDLDAAFDLYYPTNDQLRANLAVEVAEQAKALGITIKLKASNWDEMATKSHDSA 42- 2 Query: 421 LLYAGGRHHAQQFYESHYPSLAGKGWTNITFYNNPTVTKYLDKAMTSPDLDKANKYWKLA 48- 0 LLYAGGRHHAQQFYESH+PSLAGKGWTNITFYNNPTVTKYLDKAMTS DLDKAN+YWKLA Sbjct: 423 LLYAGGRHHAQQFYESHHPSLAGKGWTNITFYNNPTVTKYLDKAMTSSDLDKANEYWKLA 48- 2 Query: 481 QWDGKTGASTLGDLPNVWLVSLNHTYIGDKRINVGKQGVHSHGHDWSLLTNIAEWTWDES 54- 0 QWDGKTGASTLGDLPNVWLVSLNHTYIGDKRINVGKQGVHSHGHDWSLLTNIAEWTWDES Sbjct: 483 QWDGKTGASTLGDLPNVWLVSLNHTYIGDKRINVGKQGVHSHGHDWSLLTNIAEWTWDES 54- 2 Query: 541 AK 542 K Sbjct: 543 TK 544 There is also homology to SEQ ID 60. A related GBS gene <SEQ ID 8501> and protein <SEQ ID 8502> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00486 Lipop: Possible site: 22 Crend: 5 McG: Discrim Score: 10.46 GvH: Signal Score (-7.5): -1.29 Possible site: 22 >>> May be a lipoprotein ALOM program count: 0 value: 7.27 threshold: 0.0 PERIPHERAL Likelihood = 7.27 386 modified ALOM score: -1.95 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside -- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 8502 (GBS106) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 18 (lane 3; MW 61 kDa). The GBS106-His fusion product was purified (FIG. 194, lane 2) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 255A), FACS (FIG. 255B), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 140 A DNA sequence (GBSx0146) was identified in S. agalactiae <SEQ ID 469> which encodes the amino acid sequence <SEQ ID 470>. Analysis of this protein sequence reveals the following: TABLE-US-00487 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4862 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 141 A DNA sequence (GBSx0147) was identified in S. agalactiae <SEQ ID 471> which encodes the amino acid sequence <SEQ ID 472>. Analysis of this protein sequence reveals the following: TABLE-US-00488 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.27 Transmembrane 252-268 (249-275) INTEGRAL Likelihood = -5.73 Transmembrane 67-83 (62-90) INTEGRAL Likelihood = -5.26 Transmembrane 107-123 (104-134) INTEGRAL Likelihood = -3.77 Transmembrane 153-169 (152-170) ----- Final Results ----- bacterial membrane --- Certainty = 0.3909 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9295> which encodes amino acid sequence <SEQ ID 9296> was also identified. The protein differs from U78968 at the N-terminus: TABLE-US-00489 Query: 1 MASVNYDTSLTPVQYKAIAHHYGLDKPAPVQYFIWLKNFIQGHLGTSLVYRQPVIDIIRS 60 MASVNYDTSLTP QYKAIAHHYGLDKPA VQYFIWLKN IQG LGTSLVYRQPV DIIRS Sbjct: 39 MASVNYDTSLTPAQYKAIAHHYGLDKPALVQYFIWLKNVIQGDLGTSLVYRQPVSDIIRS 98 There is also homology to SEQ ID 64. A related GBS gene <SEQ ID 8471> and protein <SEQ ID 8472> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00490 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 3.72 GvH: Signal Score (-7.5): -5.37 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 5 value: -7.27 threshold: 0.0 INTEGRAL Likelihood = -7.27 Transmembrane 290-306 (287-313) INTEGRAL Likelihood = -5.89 Transmembrane 12-28 (11-33) INTEGRAL Likelihood = -5.73 Transmembrane 105-121 (100-128) INTEGRAL Likelihood = -5.26 Transmembrane 145-161 (142-172) INTEGRAL Likelihood = -3.77 Transmembrane 191-207 (190-208) PERIPHERAL Likelihood = 2.97 245 modified ALOM score: 1.95 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3909 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 8472 (GBS436) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 173 (lane 9; MW 54 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 142 A DNA sequence (GBSx0148) was identified in S. agalactiae <SEQ ID 473> which encodes the amino acid sequence <SEQ ID 474>. This protein is predicted to be transmembrane transport protein DppC (oppC). Analysis of this protein sequence reveals the following: TABLE-US-00491 Possible site: 39 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.28 Transmembrane 77-93 (68-101) INTEGRAL Likelihood = -7.80 Transmembrane 182-198 (180-204) INTEGRAL Likelihood = -7.06 Transmembrane 112-128 (104-132) INTEGRAL Likelihood = -5.10 Transmembrane 239-255 (235-258) ----- Final Results ----- bacterial membrane --- Certainty = 0.4312(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> There is homology to SEQ ID 68. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 143 A DNA sequence (GBSx0149) was identified in S. agalactiae <SEQ ID 475> which encodes the amino acid sequence <SEQ ID 476>. This protein is predicted to be ATPase protein DppD. Analysis of this protein sequence reveals the following: TABLE-US-00492 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1957(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein differs from U78968 at the C-terminus: TABLE-US-00493 Query: 241 QTEFARSLWRSLPQQEFLKGVTHDLRG 267 QTEFAR LWR+LPQQ+FLKGVTHDLRG Sbjct: 241 QTEFARRLWRTLPQQDFLKGVTHDLRG 267 A related DNA sequence was identified in S. pyogenes <SEQ ID 477> which encodes the amino acid sequence <SEQ ID 478>. Analysis of this protein sequence reveals the following: TABLE-US-00494 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1957(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00495 Identities = 255/267 (95%), Positives = 262/267 (97%) Query: 1 MTETLLSIKDLSITFTQYGRFLKPFQSTPIQALNLEIKKGELLAIIGASGSGKSLLAHAI 60 MTETLLSIKDLSITFTQYGRFLKPFQSTPIQALNLE+KKGELLAIIGASGSGKSLLAHAI Sbjct: 1 MTETLLSIKDLSITFTQYGRFLKPFQSTPIQALNLEVKKGELLAIIGASGSGKSLLAHAI 60 Query: 61 MDILPKNASVTGDMIYRGQSLNSKRIKQLRGKDITLIPQSVNYLDPSTKVKHQVRLGISE 120- MDILPKNA+VTGDMIYRGQSL SKRIKQLRGK++TLIPQSVNYLDPS KVKHQVRLGISE Sbjct: 61 MDILPKNAAVTGDMIYRGQSLTSKRIKQLRGKEMTLIPQSVNYLDPSMKVKHQVRLGISE 120- Query: 121 NSKATQEGLFQQFGLKESDGDLYPFQLSGGMLRRVLFTTCISDKVSLIIADEPTPGLHPD 18- 0 N+KATQEGLFQQFGLKESDGDLYPFQLSGGMLRRVLFTTCISD VSLIIADEPTPGLHPD Sbjct: 121 NAKATQEGLFQQFGLKESDGDLYPFQLSGGMLRRVLFTTCISDTVSLIIADEPTPGLHPD 18- 0 Query: 181 ALQMVLDQLRSFADKGISVIFITHDIVAASQIADRITIFKEGKAIETAPASFFSGNGEQL 24- 0 ALQMVLDQLRSFADKGISVIFITHDIVAASQIADRITIFKEGKAIETAPASFFSG GEQL Sbjct: 181 ALQMVLDQLRSFADKGISVIFITHDIVAASQIADRITIFKEGKAIETAPASFFSGGGEQL 24- 0 Query: 241 QTEFARSLWRSLPQQEFLKGVTHDLRG 267 QTEFAR LWR+LPQQ+FLKGVTHDLRG Sbjct: 241 QTEFARRLWRTLPQQDFLKGVTHDLRG 267 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 144 A DNA sequence (GBSx0150) was identified in S. agalactiae <SEQ ID 479> which encodes the amino acid sequence <SEQ ID 480>. This protein is predicted to be ATPase protein DppE. Analysis of this protein sequence reveals the following: TABLE-US-00496 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3783(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 481> which encodes the amino acid sequence <SEQ ID 482>. Analysis of this protein sequence reveals the following: TABLE-US-00497 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3383(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00498 Identities = 188/205 (91%), Positives = 197/205 (95%) Query: 1 MTLEAKKLGFYHKKDQWLFKEINLEVAPGQVLGIFGQSGCGKTSLSRVLAGFLHPKSGEV 60 MTLEAKKLGFYHKKDQWLFKEI+LEVAPGQ+LGIFGQSGCGKTSLSRVLAGFL PKSGEV Sbjct: 1 MTLEAKKLGFYHKKDQWLFKEIDLEVAPGQILGIFGQSGCGKTSLSRVLAGFLQPKSGEV 60 Query: 61 LVDGSNLPSKAFRPVQLIQQHPEKTMNPLWPMKKSLEEAYYPSRDLLDAFGIQEKWLNRR 120- LVDGS+LP+KAFRPVQLIQQHPE+TMNPLWPMKKSLEEAYYPS+DL DAFGIQEKWL RR Sbjct: 61 LVDGSHLPNKAFRPVQLIQQHPEQTMNPLWPMKKSLEEAYYPSQDLRDAFGIQEKWLKRR 120- Query: 121 PSELSGGELQRFSIVRSLHPETKYLIADEMTTMLDSITQASVWKSLLEIVKDRNLGLIVI 18- 0 PSELSGGELQRFSIVRSLHPETKYLIADEMTTMLDSITQASVWKSLLEIVKDRNLGLI+I Sbjct: 121 PSELSGGELQRFSIVRSLHPETKYLIADEMTTMLDSITQASVWKSLLEIVKDRNLGLIII 18- 0 Query: 181 SHDFAMLEKLCNQCYMIEENRIVSF 205 SH+F MLEKLC+ CYMIEENR F Sbjct: 181 SHEFDMLEKLCDACYMIEENRTQLF 205 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 145 A DNA sequence (GBSx0151) was identified in S. agalactiae <SEQ ID 483> which encodes the amino acid sequence <SEQ ID 484>. This protein is predicted to be PTS system, trehalose-specific IIBC component (treB). Analysis of this protein sequence reveals the following:

TABLE-US-00499 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.14 Transmembrane 468-484 (462-489) INTEGRAL Likelihood = -8.23 Transmembrane 279-295 (275-306) INTEGRAL Likelihood = -6.05 Transmembrane 112-128 (105-130) INTEGRAL Likelihood = -3.35 Transmembrane 204-220 (203-222) INTEGRAL Likelihood = -1.75 Transmembrane 255-271 (255-271) INTEGRAL Likelihood = -1.54 Transmembrane 327-343 (326-344) INTEGRAL Likelihood = -0.37 Transmembrane 422-438 (422-438) INTEGRAL Likelihood = -0.06 Transmembrane 304-320 (304-320) ----- Final Results ----- bacterial membrane --- Certainty = 0.5055(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00500 >GP: AAF94072 GB: AE004175 PTS system, trehalose-specific IIBC component [Vibrio cholerae] Identities = 225/484 (46%), Positives = 318/484 (65%), Gaps = 28/484 (5%) Query: 5 KHDAKALLEAIGGKENISAVTHCATRMRFVLNDSSKAKVKVIEELPSVKGTFTNAGQFQV 64 K D L+E +GG+ NI++VTHC TR+RFVLN +A +E L VKG FTNAGQFQV Sbjct: 10 KQDVTRLIELVGGESNIASVTHCLTRLRFVLNQPEQADKAGLEALSMVKGCFTNAGQFQV 69 Query: 65 IIGNDVPIFYNAFVAVSGIEGVSKEAAKSAAQKNQNPLQRVLTMLAEIFTPIIPAIIVGG 124- +IG +V Y + +G + VSK+ AK AA++N N L+R ++ LAEIF P++PAII GG Sbjct: 70 VIGTEVDQVYKMLLEQTGKQAVSKDDAKVAARQNMNVLERGISHLAEIFVPLLPAIITGG 129- Query: 125 LILGFRNILDAVPFEFLGQKVVDGVRQVDSSGHPIWNTLVDVSTFWSGVDSFLWLPGEAI 18- 4 LILGFRN++ + ++ DG TL ++S FW+ V +FLWL GEAI Sbjct: 130 LILGFRNVIGDI-------RMFDG------------KTLTEISQFWASVHAFLWLIGEAI 17- 0 Query: 185 FHFLPVGIVWSVTRKMGTTQILGIVLGICLVSPQLLNAYSVASTSAADIAKNWSWNFGYF 24- 4 F FLPVG+ WS +K+G T ILGI LG+ LVSPQL+NAY + W+FG F Sbjct: 171 FFFLPVGVCWSTVKKLGGTPILGITLGVTLVSPQLMNAYLIGKEVPE------VWDFGLF 22- 4 Query: 245 TVQKIGYQAQVIPALLAGLSLSYLEIFWRKHIPEVVSMIFVPFLSLVPAIILAHTVLGPI 30- 4 ++K+GYQAQVIPA+LAG++L+++E R+ +P + ++ VPF+S++ +++LAH +GP Sbjct: 225 AIEKVGYQAQVIPAILAGVALAFIENNLRRVVPSYLYLVVVPFVSIIVSVVLAHAFIGPF 28- 4 Query: 305 GWTLGKWISAIVLIGLTGPVKWLFGAIFGALYAPFVITGLHHMTNAIDTQLIADTKTHTT 36- 4 G +G ++ +TG + +FG +YAP VITG+HH TNA+D QL+ + T Sbjct: 285 GRVIGDGVAFAAKAAMTGDFAVIGSTLFGFMYAPLVITGIHHTTNAVDLQLMQE--LGGT 34- 2 Query: 365 GLWPMIALSNIAQGSAVLAYYFMHRHDEKEAQISLPAAISAYLGVTEPALFGVNVKYIYP 42- 4 +WP+IALSNIAQ SAV+ + + + E IS+PAAISAYLGVTEPA++G+N+KY +P Sbjct: 343 PIWPLIALSNIAQASAVVGIIIISK-KQGERDISVPAAISAYLGVTEPAMYGINLKYKFP 40- 1 Query: 425 FVAGMIGSSVAGLLATTFNVQANSIGVGGLPGFLSINVKYMGYFFICMAVAIFIPLFLTL 48- 4 ++ MIGS++A + + V AN IGVGGLPG LSI ++ + + M +AI +P LTL Sbjct: 402 MLSAMIGSALAAAVCGSAGVMANGIGVGGLPGILSIQPQFWSIYLVAMLIAILVPAALTL 46- 1 Query: 485 FFKK 488 K Sbjct: 462 LMYK 465 A related DNA sequence was identified in S. pyogenes <SEQ ID 485> which encodes the amino acid sequence <SEQ ID 486>. Analysis of this protein sequence reveals the following: TABLE-US-00501 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.61 Transmembrane 466-482 (457-488) INTEGRAL Likelihood = -8.01 Transmembrane 279-295 (275-306) INTEGRAL Likelihood = -6.05 Transmembrane 112-128 (105-130) INTEGRAL Likelihood = -3.35 Transmembrane 204-220 (203-222) INTEGRAL Likelihood = -3.13 Transmembrane 255-271 (255-272) INTEGRAL Likelihood = -2.07 Transmembrane 327-343 (325-344) INTEGRAL Likelihood = -0.59 Transmembrane 422-438 (422-438) ----- Final Results ----- bacterial membrane --- Certainty = 0.4843(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00502 >GP: AAF94072 GB: AE004175 PTS system, trehalose-specific IIBC component [Vibrio cholerae] Identities = 231/484 (47%), Positives = 322/484 (65%), Gaps = 28/484 (5%) Query: 5 EQDAKSLLTAIGGKENIKVVTHCATRMRFVLNDNNKANVKEIEKISVVKGTFTNAGQFQV 64 +QD L+ +GG+ NI VTHC TR+RFVLN +A+ +E +S+VKG FTNAGQFQV Sbjct: 10 KQDVTRLIELVGGESNIASVTHCLTRLRFVLNQPEQADKAGLEALSMVKGCFTNAGQFQV 69 Query: 65 IIGNDVPVFYNDFTAVSSIEGVSKEAAKSAAKSNQNALQRVMTMLAEIFTPIIPAIIVGG 124- +IG +V Y + + VSK+ AK AA+ N N L+R ++ LAEIF P++PAII GG Sbjct: 70 VIGTEVDQVYKMLLEQTGKQAVSKDDAKVAARQNMNVLERGISHLAEIFVPLLPAIITGG 129- Query: 125 LILGFRNILESVPFEFLGQQVEKGKLVFDAAGDPVWNTIVRVSPFWSGVNHFLWLPGEAI 18- 4 LILGFRN++ + +FD T+ +S FW+ V+ FLWL GEAI Sbjct: 130 LILGFRNVIGDI-------------RMFDG------KTLTEISQFWASVHAFLWLIGEAI 17- 0 Query: 185 FHFLPVGITWSVTRKMGTTQILGIVLGICLVSPQLLNAYAVAGTPAAEIAKNWVWDFGFF 24- 4 F FLPVG+ WS +K+G T ILGI LG+ LVSPQL+NAY + G E VWDFG F Sbjct: 171 FFFLPVGVCWSTVKKLGGTPILGITLGVTLVSPQLMNAYLI-GKEVPE-----VWDFGLF 22- 4 Query: 245 TINRIGYQAQVIPALLAGLSLAYLEIFWRKRIPEVVSMIFVPFLSLIPALILAHTVLGPI 30- 4 I ++GYQAQVIPA+LAG++LA++E R+ +P + ++ VPF+S+I +++LAH +GP Sbjct: 225 AIEKVGYQAQVIPAILAGVALAFIENNLRRVVPSYLYLVVVPFVSIIVSVVLAHAFIGPF 28- 4 Query: 305 GWTIGKGISFVVLAGLTGPVKWLFGAIFGALYAPLVITGLHHMTNAIDTQLIADTATRTT 36- 4 G IG G++F A +TG + +FG +YAPLVITG+HH TNA+D QL+ + T Sbjct: 285 GRVIGDGVAFAAKAAMTGDFAVIGSTLFGFMYAPLVITGIHHTTNAVDLQLMQELG--GT 34- 2 Query: 365 GLWPMIALSNIAQGSAVFAYYLMNRHEEREAEISLPAAISAYLGVTEPALFGVNVKYVYP 42- 4 +WP+IALSNIAQ SAV ++++ ++ E +IS+PAAISAYLGVTEPA++G+N+KY +P Sbjct: 343 PIWPLIALSNIAQASAVVGIIIISK-KQGERDISVPAAISAYLGVTEPAMYGINLKYKFP 40- 1 Query: 425 FVAGMIGSGIAGLLSTTFNVQANSIGVGGLPGFMAINVKYMIPFFICMAVAIVVPMFLTF 48- 4 ++ MIGS +A + + V AN IGVGGLPG ++I ++ + + M +AI+VP LT Sbjct: 402 MLSAMIGSALAAAVCGSAGVMANGIGVGGLPGILSIQPQFWSIYLVAMLIAILVPAALTL 46- 1 Query: 485 FFRK 488 K Sbjct: 462 LMYK 465 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00503 Identities = 501/675 (74%), Positives = 573/675 (84%), Gaps = 2/675 (0%) Query: 1 MEQFKHDAKALLEAIGGKENISAVTHCATRMRFVLNDSSKAKVKVIEELPSVKGTFTNAG 60 M +F+ DAK+LL AIGGKENI VTHCATRMRFVLND++KA VK IE++ VKGTFTNAG Sbjct: 1 MGKFEQDAKSLLTAIGGKENIKVVTHCATRMRFVLNDNNKANVKEIEKISVVKGTFTNAG 60 Query: 61 QFQVIIGNDVPIFYNAFVAVSGIEGVSKEAAKSAAQKNQNPLQRVLTMLAEIFTPIIPAI 120- QFQVIIGNDVP+FYN F AVS IEGVSKEAAKSAA+ NQN LQRV+TMLAEIFTPIIPAI Sbjct: 61 QFQVIIGNDVPVFYNDFTAVSSIEGVSKEAAKSAAKSNQNALQRVMTMLAEIFTPIIPAI 120- Query: 121 IVGGLILGFRNILDAVPFEFLGQRVVDGVRQVDSSGHPIWNTLVDVSTFWSGVDSFLWLP 18- 0 IVGGLILGFRNIL++VPFEFLGQ+V G D++G P+WNT+V VS FWSGV+ FLWLP Sbjct: 121 IVGGLILGFRNILESVPFEFLGQQVEKGKLVFDAAGDPVWNTIVRVSPFWSGVNHFLWLP 18- 0 Query: 181 GEAIFHFLPVGIVWSVTRKMGTTQILGIVLGICLVSPQLLNAYSVASTSAADIAKNWSWN 24- 0 GEAIFHFLPVGI WSVTRKNGTTQILGIVLGICLVSPQLLNAY+VA T AA+IAKNW W+ Sbjct: 181 GEAIFHFLPVGITWSVTRKMGTTQILGIVLGICLVSPQLLNAYAVAGTPAAEIAKNWVWD 24- 0 Query: 241 FGYFTVQKIGYQAQVIPALLAGLSLSYLEIFWRKHIPEVVSMIFVPFLSLVPAIILAHTV 30- 0 FG+FT+ +IGYQAQVIPALLAGLSL+YLEIFWRK IPEVVSMIFVPFLSL+PA+ILAHTV Sbjct: 241 FGFFTINRIGYQAQVIPALLAGLSLAYLEIFWRKRIPEVVSMIFVPFLSLIPALILAHTV 30- 0 Query: 301 LGPIGWTLGKWISAIVLIGLTGPVKWLFGAIFGALYAPFVITGLHHMTNAIDTQLIADTK 36- 0 LGPIGWT+GK IS +VL GLTGPVKWLFGAIFGALYAP VITGLHHMTNAIDTQLIADT Sbjct: 301 LGPIGWTIGKGISFVVLAGLTGPVKWLFGAIFGALYAPLVITGLHHMTNAIDTQLIADTA 36- 0 Query: 361 THTTGLWPMIALSNIAQGSAVLAYYFMHRHDEKEAQISLPAAISAYLGVTEPALFGVNVK 42- 0 T TTGLWPMIALSNIAQGSAV AYY M+RH+E+EA+ISLPAAISAYLGVTEPALFGVNVK Sbjct: 361 TRTTGLWPMIALSNIAQGSAVFAYYLMNRHEEREAEISLPAAISAYLGVTEPALFGVNVK 42- 0 Query: 421 YIYPFVAGMIGSSVAGLLATTFNVQANSIGVGGLPGFLSINVKYMGYFFICMAVAIFIPL 48- 0 Y+YPFVAGMIGS +AGLL+TTFNVQANSIGVGGLPGF++INVKYM FFICMAVAI +P+ Sbjct: 421 YVYPFVAGMIGSGIAGLLSTTFNVQANSIGVGGLPGFMAINVKYMIPFFICMAVAIVVPM 48- 0 Query: 481 FLTLFFKKSGILTKTEEEKLVPDAVIASTTETKSAKEKAVVSGTKLSVVSPLSGLAKPLD 54- 0 FLT FF+KS I+TKTE+E +P+ + S +A K + GT +++ SPL+G K L Sbjct: 481 FLTFFFRKSHIMTKTEDEAKLPETPV-SDAPVATAPHK-TMQGTVITLTSPLTGEVKALS 53- 8 Query: 541 QASDPVFSQGIMGKGVVIDPSDGELVSPVDATVSVLFPTKHAIGLLTSEGVEFLIHIGMD 60- 0 +A DPVF+QG+MG+G ++ P++G LV+P DA VSVLFPTKHAI L+T+EG+E L+HIGMD Sbjct: 539 EAVDPVFAQGVMGQGALLQPTEGVLVAPCDAEVSVLFPTKHAICLVTTEGLELLMHIGMD 59- 8 Query: 601 TVNLEGKGFTSHVAQGDTVKVGDKLITFDIPMIKEEGYIVETPILITNQQEFRPEELIDL 66- 0 TVNL+G+GF + V QGD VK G LI FDI I E GY ETP+++TNQ F L Sbjct: 599 TVNLDGQGFEALVKQGDQVKAGQTLIQFDIAAISEAGYATETPLVVTNQDVFTVTVEGSL 65- 8 Query: 661 PKQIKRGQALMVAKK 675 P+QIK L VA K Sbjct: 659 PRQIKVNDKLAVAVK 673 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 146 A DNA sequence (GBSx0052) was identified in S. agalactiae <SEQ ID 487> which encodes the amino acid sequence <SEQ ID 488>. This protein is predicted to be dextran glucosidase DexS (treC). Analysis of this protein sequence reveals the following: TABLE-US-00504 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3493(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00505 >GP: AAB65079 GB: U35633 dextran glucosidase DexS [Streptococcus suis] Identities = 383/547 (70%), Positives = 439/547 (80%), Gaps = 13/547 (2%) Query: 1 MTIDKRKVVYQIYPKSYKDTTGNGVGDLRGIIEKLPYLAELGIDMVWLNPFYPSPQRDNG 60 MTIDKRKVVYQIYPKSYKDTTGNGVGDLRGIIEKLPYL ELGIDM+WLNPFYPSPQRDNG Sbjct: 1 MTIDKRKVVYQIYPKSYKDTTGNGVGDLRGIIEKLPYLKELGIDMIWLNPFYPSPQRDNG 60 Query: 61 YDISDYTAINPDFGTMDDFEEMIEVGRQYRIDFMLDMVLNHCSIEHEWFKKALAGDRYYQ 120- YDISDYTA+NPDFGTM DFEEM+ VG++ I+FMLDMVLNHCS +HEWF+KAL+GD+YYQ Sbjct: 61 YDISDYTAVNPDFGTMADFEEMVTVGKELGIEFMLDMVLNHCSTDHEWFQKALSGDQYYQ 120- Query: 121 DFFILRDNPTDWVSKFGGNAWAPFGDTGKYYLHLFDITQADLNWRNADVRKELFKVVNFW 18- 0 DFFILRD PTDWVSKFGGNAWAPFGDTGKYYLHLFD+TQADLNWRN +R+ELFKVVNFW Sbjct: 121 DFFILRDQPTDWVSKFGGNAWAPFGDTGKYYLHLFDVTQADLNWRNPHIREELFKVVNFW 18- 0 Query: 181 RDKGVKGFRFDVINLIGKDEILENCPINDGKPAYTDRPITHDYLKMLNNASFGQDDSFMT 24- 0 +DKGVKGFRFDVINLIGKDE E+CPINDGKPAYTDRPITHDYLKM+NNA+FG + FMT Sbjct: 181 KDKGVKGFRFDVINLIGKDEAREDCPINDGKPAYTDRPITHDYLKMMNNATFGSEKGFMT 24- 0 Query: 241 VGEMSSTTIANCILYTAPEREELSMAFNFHHLKVDYKDGQKWTIMAFDFPALRDLFHSWG 30- 0 VGEMS+TTI NCILYTAPER+ELSMAFNFHHLKVDYKDGQKWTIM FDF L+ LFH+WG Sbjct: 241 VGEMSATTIENCILYTAPERKELSMAFNFHHLKVDYKDGQKWTIMDFDFEELKHLFHTWG 30- 0 Query: 301 EGMSEGNGWNALFYNNHDQPRALNRFVDVKRFRNEGATMLAASIHLSRGTPYIYMGEEIG 36- 0 E MS GNGWNALFYNNHDQPRALNRF+DV+ FR EGATMLAASIHLSRG Sbjct: 301 EEMSVGNGWNALFYNNHDQPRALNRFIDVENFRKEGATMLAASIHLSRGNNLTST----- 35- 5 Query: 361 MLDPDYSSMDDYVDIESLNAYQIMLDEGKSQEEAFSIIRAKSRDNSRVPMQWDDS----- 41- 5 + SS + + + + + S + + R SR + P+ Sbjct: 356 WVRRSVSSTLTTIAWTTTWTWSLSMPTRCSWTKVTRLSR-PSRLSRPSPVTIPAPRCNGT 41- 4 Query: 416 --TNAGFSEGAPWLKVGKSYKEINVAKEKTGLIFTFYQELIRLRKQLPIIADGNYKAAFK 47- 3 T + PWLK GKSY+ INV +EKTG IFTFY+ LRK+LP+I++G+YKAA+K Sbjct: 415 LLTMQASQQATPWLKAGKSYQTINVEQEKTGPIFTFYKRTHPLRKELPLISEGDYKAAYK 47- 4 Query: 474 DNEKVYAFERHLDKEKLLVLNNFFAEKVKIKLPENYLQGQVLLSNYKDVTLDETVTLQPY 53- 3 D++KVYAFER L+ EKLLVLNNFFAE+V++ L ++Y GQVL+SNY D L + + L+PY Sbjct: 475 DSQKVYAFERLLNDEKLLVLNNFFAEEVELDLADDYAHGQVLISNYPDNKLGKKIILKPY 53- 4 Query: 534 QTLAILV 540 Q LAI V Sbjct: 535 QALAIQV 541 A related DNA sequence was identified in S. pyogenes <SEQ ID 489> which encodes the amino acid sequence <SEQ ID 490>. Analysis of this protein sequence reveals the following: TABLE-US-00506 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3631(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00507 Identities = 431/539 (79%), Positives = 486/539 (89%) Query: 1 MTIDKRKVVYQIYPKSYKDTTGNGVGDLRGIIEKLPYLAELGIDMVWLNPFYPSPQRDNG 60 MTIDK+KVVYQIYPKSYKDTTGNGVGDL GII+KLPYL ELGIDM+WLNPFYPSPQRDNG Sbjct: 1 MTIDKKKVVYQIYPKSYKDTTGNGVGDLLGIIDKLPYLQELGIDMIWLNPFYPSPQRDNG 60 Query: 61 YDISDYTAINPDFGTMDDFEEMIEVGRQYRIDFMLDMVLNHCSIEHEWFKKALAGDRYYQ 120- YD+SDYTA+NPDFGTM DFE +++ ++++I+ MLDMVLNHCS +HEWF+KALAGD YYQ Sbjct: 61 YDVSDYTAVNPDFGTMADFENLVKAAKEHQIELMLDMVLNHCSTDHEWFQKALAGDPYYQ 120- Query: 121 DFFILRDNPTDWVSKFGGNAWAPFGDTGKYYLHLFDITQADLNWRNADVRKELFKVVNFW 18- 0 DFFILRD PTDWVSKFGGNAWAPFGDTGKYYLHLFD+TQADLNWRN VR+EL KVVNFW Sbjct: 121 DFFILRDQPTDWVSKFGGNAWAPFGDTGKYYLHLFDVTQADLNWRNPHVREELAKVVNFW 18- 0 Query: 181 RDKGVKGFRFDVINLIGKDEILENCPINDGKPAYTDRPITHDYLKMLNNASFGQDDSFMT 24- 0 RDKGVKGFRFDVINLIGKDE L +CP+NDGKPAYTDRPITH YL LN ASFGQDDSFMT Sbjct: 181 RDKGVKGFRFDVINLIGKDEELVDCPVNDGKPAYTDRPITHTYLHDLNQASFGQDDSFMT 24- 0 Query: 241 VGEMSSTTIANCILYTAPEREELSMAFNFHHLKVDYKDGQKWTIMAFDFPALRDLFHSWG 30- 0 VGEMS+TTI NC+LYTAPEREELSMAFNFHHLKVDY++GQKWTIMAFDF ALRDLFH+WG Sbjct: 241 VGEMSATTIDNCLLYTAPEREELSMAFNFHHLKVDYENGQKWTIMAFDFAALRDLFHAWG 30- 0 Query: 301 EGMSEGNGWNALFYNNHDQPRALNRFVDVKRFRNEGATMLAASIHLSRGTPYIYMGEEIG 36- 0 EGMS+GNGWNALFYNNHDQPRALNRFVDV FRNEGATMLAASIHLSRGTPYIYMGEEIG Sbjct: 301 EGMSQGNGWNALFYNNHDQPRALNRFVDVTHFRNEGATMLAASIHLSRGTPYIYMGEEIG 36- 0 Query: 361 MLDPDYSSMDDYVDIESLNAYQIMLDEGKSQEEAFSIIRAKSRDNSRVPMQWDDSTNAGF 42- 0 MLDPD+ SMDDYVD+ESLNAY +L GKS EEAF+II+AKSRDN+R PMQWD S +AGF Sbjct: 361 MLDPDFDSMDDYVDVESLNAYSSLLVSGKSAEEAFAIIKAKSRDNARTPMQWDASEHAGF 42- 0 Query: 421 SEGAPWLKVGKSYKEINVAKEKTGLIFTFYQELIRLRKQLPIIADGNYKAAFKDNEKVYA 48- 0 + G PWL+VGKSY++INV EK G IF FYQ LI LRK+LPIIA+G+Y+AAFKD++ VYA Sbjct: 421 TTGKPWLEVGKSYRDINVETEKEGRIFPFYQRLIALRKELPIIAEGDYRAAFKDSQAVYA 48- 0 Query: 481 FERHLDKEKLLVLNNFFAEKVKIKLPENYLQGQVLLSNYKDVTLDETVTLQPYQTLAIL 539- FERHL + LLVLN+F+A++V+++LP Y GQVL+SNY+ V++ E V L+PYQTLAIL Sbjct: 481 FERHLGDQCLLVLNHFYADEVELELPPRYQHGQVLISNYEKVSICEKVILKPYQTLAIL 539- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 147 A DNA sequence (GBSx0153) was identified in S. agalactiae <SEQ ID 491> which encodes the amino acid sequence <SEQ ID 492>. Analysis of this protein sequence reveals the following: TABLE-US-00508 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.03 Transmembrane 8-24 (8-25) ----- Final Results ----- bacterial membrane --- Certainty = 0.2211(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 148 A DNA sequence (GBSx0154) was identified in S. agalactiae <SEQ ID 493> which encodes the amino acid sequence <SEQ ID 494>. Analysis of this protein sequence reveals the following: TABLE-US-00509 Possible site: 57 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00510 >GP: BAB03939 GB: AP001507 unknown conserved protein [Bacillus halodurans] Identities = 190/639 (29%), Positives = 331/639 (51%), Gaps = 34/639 (5%) Query: 6 TVVIMLVFLARKNLSLYELTVQTKFSIKVIIEQINYLNSFLAKNHLPAIAHSAGRYQLLG 65 T ++ + AR L + ELT + S + + + +NS+L + L A+ + L+ Sbjct: 8 TFILTQLLHARSYLPIQELTQKLNVSRRTVYNDLEKINSWLEEQGLKAV-YKVRSQGLIL 66 Query: 66 DEKEHDKI---VSLLEAEQFYLTQEERVCLIYLYSFCRREFVSNVHYQDFLKVSKNTTLS 122- DE+ ++I + L++ + + +ER + +Y R E + H D VS+NTT+ Sbjct: 67 DERAKEEIPTKLRSLKSWHYEYSAQERKAWVVIYLLTRLEPLFLEHLMDRTGVSRNTTID 126- Query: 123 DIKMLRSKLAKRGISLTYTRAKGYSLVGDEMDKHQVAFQMITQLLE--------SPIGFW 17- 4 DIK L+ +L ++L + R GY++ GDE DK + ++Q L SPI + Sbjct: 127 DIKCLKDELNNFHLALEFERKDGYTISGDETDKRKALVYYLSQALPQQNWETELSPIRIF 18- 6 Query: 175 SLNYILSSWKFALSYEKLEKTVEYFYESFQLSPIQ---DRLEKSLYFIILILCRYQRSVD 23- 1 + F + E+L+K + ES ++ IQ D L +L + R + Sbjct: 187 LRTKRDNGRIFTI--EELQKVYDVISESEKVLKIQYTDDVLHSLSLRFLLFMKRVAKG-- 24- 2 Query: 232 RVLQGSPIVSEQLK-----ELTTIIVTNLSQDISLSKPLDQKEKDYITLILSGCF----- 28- 1 + ++ P+ + LK E ++ L Q + P D++ T ILS Sbjct: 243 KFIKVHPLEKQVLKGTKEYEAAKVMSFKLEQAFGVHYP-DEEVLYLTTHILSSKINYANG 30- 1 Query: 282 EGEGTKDDDFFEALAKAIVDEMETVSLLNFSNKEELLQGLKRHIIPAYFRLKYGLTGDSG 34- 1 E E K+ + ++V++ + + + F KE L + L HI PA++R+KYGL ++ Sbjct: 302 EIESRKESQELTHIVTSMVNDFQKYACVVFEEKELLEKNLFFHIKPAFYRIKYGLEVENN 36- 1 Query: 342 YTQNIKEHYSDLFLLVKKALRPLEEQVGL-IPDSEISYFVIHFGGYLRQSGGTQSMSYKA 40- 0 ++IK Y +LFLL +K + LE VG + D+E+++ +HF G++R+ G + KA Sbjct: 362 IAESIKTSYPELFLLTRKVVHYLERYVGKSVNDNEVAFITMHFVGWMRREGTIPTKRKKA 42- 1 Query: 401 LILCPNGVSSSLVIKEKLRGLFPQIHFHRVSKIEQLKLIDNQTYDMVFSTIFVETKKPNY 46- 0 LI+C NGV +S +K +L GLFP + + I + + + ++ +T E P + Sbjct: 422 LIVCANGVGTSQFLKNQLEGLFPAVDIIKTCSIREYEKTPVEVDFIISTTSIPEKNVPIF 48- 1 Query: 461 LVSLMMT-AEQVQQLKELVISDFPKACLDDFQLDQLIATIKKYAHVHCEEELKLALRTMV 51- 9 +V+ ++T E+ + LK + ++ + + ++ L+ IK++ +V E+ L LR Sbjct: 482 IVNPILTETEKERLLKSVHVALDELGAMKGYSIEGLMDVIKRHGNVDDEKALYQDLRRFF 54- 1 Query: 520 KQD--ILRKDVRPLLHQLITEETYQTSSEQMNWKEAIRLAAKPLLASGKITESYPEAMIE 57- 7 Q I K +P L+QL+TE+ Q + +W+EAI+LAAKPLL G +TESY + MI+ Sbjct: 542 TQPTPIGPKQEKPDLNQLLTEDMIQLREQVTHWQEAIQLAAKPLLLKGMVTESYVKKMIK 60- 1 Query: 578 KVEEFGPFINLGKGIAIPHARPEDGVNSVGMSMLVLEQP 616 +E+FGP++ + AIPHA+PEDGV +GMS+L L++P Sbjct: 602 NIEKFGPYMIIAPHFAIPHAKPEDGVRQLGMSLLWLKKP 640 A related DNA sequence was identified in S. pyogenes <SEQ ID 495> which encodes the amino acid sequence <SEQ ID 496>. Analysis of this protein sequence reveals the following:

TABLE-US-00511 Possible site: 57 or 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.64 Transmembrane 123-139 (123-139) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00512 Identities = 187/624 (29%), Positives = 327/624 (51%), Gaps = 20/624 (3%) Query: 1 MVDNKTVVIMLVFLARKNLSLYELTVQTKFSIKVIIEQINYLNSFLAKNHLPAIAHSAGR 60 M+ ++ + +F K SL K S + I+ I +N L+ LP IA Sbjct: 35 MLSHELIRNYQLFSKYKGHSLEAFESILKASKRHILADIAKINDTLSLYQLPLIALDR-- 92 Query: 61 YQLL--GDEKEHDKIVSLLEAEQFYLTQEERVCLIYLYSFCRREFVSNVHYQDFLKVSKN 118- QL+ D E D + +L YL Q+ER+ +I +Y +EF+S H + L++S+N Sbjct: 93 -QLVYPPDLTEKDLLNRMLPTLDDYLFQDERLDMIIIYIMMAKEFISINHLESLLRLSRN 151- Query: 119 TTLSDIKMLRSKLAKRGISLTYTRAKGYSLVGDEMDKHQVAFQMITQLLESPIGFWSLNY 17- 8 + ++D+ ++R ++ ++L Y R GY G+ + ++ ++ LL+ G W +Y Sbjct: 152 SVIADLNLVRDRVQAFQVTLAYNRQDGYFFEGEPLALRRLLESAVSSLLQVTSGPWVFSY 21- 1 Query: 179 ILSSWKFALSYEKLEKTVEYFYESFQLSPIQDRLEKSLYFIILILCR-YQRSVD-RVLQG 23- 6 +L + + T+E L+ I ++L +YF L+ R + R+V + Sbjct: 212 LLHELGLPDQKKVMAATLEELSRENHLTFISEKLRDLIYFFCLLAHRPFSRNVRAEAVDT 27- 1 Query: 237 SPIVSEQLKELTTIIVTNLSQDISLSKPLDQKEKDYITLILSGCFEG--EGTKDDDFFEA 29- 4 P+ S ++ + ++ N P +EK + L GC +G E ++ Sbjct: 272 FPLASPAVETMVDQLLVNF--------PSLTEEKYLVQSRLLGCIQGDLELVFQQPIYDI 32- 3 Query: 295 LAKAIVDEMETVSLLNFSNKEELLQGLKRHIIPAYFRLKYGLTGDSGYTQNIKEHYSDLF 35- 4 + + I++ + + L+ ++ EL Q L H++PAY+RL Y + + + IK+ Y LF Sbjct: 324 MEE-IINSVAVNTGLSITDTPELRQNLYSHLLPAYYRLYYDINLTNPLKEQIKQDYESLF 38- 2 Query: 355 LLVKKALRPLEEQVGL-IPDSEISYFVIHFGGYLRQSGGTQSMSYKALILCPNGVSSSLV 41- 3 LVK++L PLE+Q+G + + E++YF IHFG +L+ S AL +CPNG+SSSL+ Sbjct: 383 YLVKRSLSPLEKQLGKSVNEDEVAYFTIHFGRWLQAPKKRPSNQLVALSVCPNGISSSLM 44- 2 Query: 414 IKEKLRGLFPQIHFHRVSKIEQLKLIDNQTYDMVFSTIFVETKKPNYLVSLMMTAEQVQQ 47- 3 ++ L+ LFPQ+ F R+ +++++KL+D ++D++FST+ + KP Y+ +M + Sbjct: 443 LEATLKELFPQLQFIRIHQLDKIKLLDPASFDLIFSTVAFDCAKPVYVTQALMGPVEKMM 50- 2 Query: 474 LKELVISDFPKACLDDFQLDQLIATIKKYAHVHCEEELKLAL-RTMVKQDILRKDVRPLL 53- 2 LK++V DF + F LD L++ I K+ + +E L L R ++ + + L Sbjct: 503 LKKMVCDDFHLPLSEQFALDDLLSIIHKHTTITNKEGLVSDLSRYLIGNHLTIEKGGLGL 56- 2 Query: 533 HQLITEETYQTSSEQMNWKEAIRLAAKPLLASGKITESYPEAMIEKVEEFGPFINLGKGI 59- 2 L+T + + + +W+EAIRLAA+PLL I SY + MI+ V E G +I L + Sbjct: 563 LDLLTADFIRQADAVSDWQEAIRLAAQPLLEHQMIETSYIDGMIDSVNELGAYIVLAPKV 62- 2 Query: 593 AIPHARPEDGVNSVGMSMLVLEQP 616 A+PHA PE G +GMS+L L++P Sbjct: 623 AVPHAAPEKGTRQLGMSLLQLKEP 646 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 149 A DNA sequence (GBSx0155) was identified in S. agalactiae <SEQ ID 497> which encodes the amino acid sequence <SEQ ID 498>. Analysis of this protein sequence reveals the following: TABLE-US-00513 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3665(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 499> which encodes the amino acid sequence <SEQ ID 500>. Analysis of this protein sequence reveals the following: TABLE-US-00514 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3665(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00515 Identities = 33/35 (94%), Positives = 35/35 (99%) Query: 1 MEKEAKQIIDLKRNLFKIDVRAQKDEEKVFMRTAW 35 +EKEAKQ+IDLKRNLFKIDVRAQKDEEKVFMRTAW Sbjct: 1 LEKEAKQMIDLKRNLFKIDVRAQKDEEKVFMRTAW 35 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 150 A repeated DNA sequence (GBSx0156) was identified in S. agalactiae <SEQ ID 501> which encodes the amino acid sequence <SEQ ID 502>. This protein is predicted to be a repeat-associated protein in rhsc-phrb intergenic region. Analysis of this protein sequence reveals the following: TABLE-US-00516 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.57 Transmembrane 29-45 (28-48) ----- Final Results ----- bacterial membrane --- Certainty = 0.2826(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A closely-related DNA sequence was identified in S. agalactiae <SEQ ID 1035> which encodes the amino acid sequence <SEQ ID 1036>. Further related GBS sequences are: <SEQ ID 9067>, <SEQ ID 9068>, <SEQ ID 9497>, <SEQ ID 9498>, <SEQ ID 9733>, <SEQ ID 9734> A related repeated DNA sequence was identified in S. pyogenes <SEQ ID 503> which encodes the amino acid sequence <SEQ ID 504>. Analysis of this protein sequence reveals the following: TABLE-US-00517 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.57 Transmembrane 29-45 (28-48) ----- Final Results ----- bacterial membrane --- Certainty = 0.2826(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS gene <SEQ ID 8547> and protein <SEQ ID 8548> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00518 Lipop Possible site: -1 Crend: 5 McG: Discrim Score: -7.73 GvH: Signal Score (-7.5): -3.88 Possible site: 44 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -4.57 threshold: 0.0 INTEGRAL Likelihood = -4.57 Transmembrane 26-42 (25-45) PERIPHERAL Likelihood = 2.12 334 modified ALOM score: 1.41 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2826(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 7071> which encodes the amino acid sequence <SEQ ID 7072>. An alignment of the GAS and GBS sequences follows: TABLE-US-00519 Score = 767 bits (1960), Expect = 0.0 Identities = 375/377 (99%), Positives = 375/377 (99%) Query: 4 MIDFIISIDDCAVELDSRQSWKIRSPLSTILFLVFVCQLAGIETWKEMEDFIEMNEPLFA 63 MIDFIISIDDCAVELDSRQSWKIR PLSTILFLVFVCQLAGIETWKEMEDFIEMNEPLFA Sbjct: 1 MIDFIISIDDCAVELDSRQSWKIRYPLSTILFLVFVCQLAGIETWKEMEDFIEMNEPLFA 60 Query: 64 TYVDLSEGCSSHDTLERVISLVNSDRLKELKVQFEQSLTSLDAVHQLISVDGKTIRGNRG 123- TYVDLSEGC SHDTLERVISLVNSDRLKELKVQFEQSLTSLDAVHQLISVDGKTIRGNRG Sbjct: 61 TYVDLSEGCPSHDTLERVISLVNSDRLKELKVQFEQSLTSLDAVHQLISVDGKTIRGNRG 120- Query: 124 KNQKPVHIVTAYDGGHHLSLGQVAVEEKSNEIVAIPQLLRTIDIRKSIVTIDAMGTQTAI 18- 3 KNQKPVHIVTAYDGGHHLSLGQVAVEEKSNEIVAIPQLLRTIDIRKSIVTIDAMGTQTAI Sbjct: 121 KNQKPVHIVTAYDGGHHLSLGQVAVEEKSNEIVAIPQLLRTIDIRKSIVTIDAMGTQTAI 18- 0 Query: 184 VDTIIKGKADYCLAVKGNQETLYDDIALYFSDVNLLEELQENAQYYQTVEKSRGQIEVRE 24- 3 VDTIIKGKADYCLAVKGNQETLYDDIALYFSDVNLLEELQENAQYYQTVEKSRGQIEVRE Sbjct: 181 VDTIIKGKADYCLAVKGNQETLYDDIALYFSDVNLLEELQENAQYYQTVEKSRGQIEVRE 24- 0 Query: 244 YWVSSDIKWLCQNHPKWHKLRGIGMTRNTIDKDGQLSQENRYFIFSFKPDVLTFANCVRG 30- 3 YWVSSDIKWLCQNHPKWHKLRGIGMTRNTIDKDGQLSQENRYFIFSFKPDVLTFANCVRG Sbjct: 241 YWVSSDIKWLCQNHPKWHKLRGIGMTRNTIDKDGQLSQENRYFIFSFKPDVLTFANCVRG 30- 0 Query: 304 HWQIESMHWLLDVVYHEDHHQTLDKRAAFNLNLIRKMCLYFLKVMVFPKKDLSYRRKQRY 36- 3 HWQIESMHWLLDVVYHEDHHQTLDKRAAFNLNLIRKMCLYFLKVMVFPKKDLSYRRKQRY Sbjct: 301 HWQIESMHWLLDVVYHEDHHQTLDKRAAFNLNLIRKMCLYFLKVMVFPKKDLSYRRKQRY 36- 0 Query: 364 ISVHLEDYLVQLFGERG 380 ISVHLEDYLVQLFGERG Sbjct: 361 ISVHLEDYLVQLFGERG 377 A further related DNA sequence was identified in S. pyogenes <SEQ ID 9087> which encodes the amino acid sequence <SEQ ID 9088>. A further related DNA sequence was identified in S. pyogenes <SEQ ID 9089> which encodes the amino acid sequence <SEQ ID 9090>. The GAS and GBS proteins are 100% identical. There is also homology to SEQ IDs 7018 and 8548. SEQ ID 8548 (GBS318) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 46 (lane 5; MW 70 kDa). GBS318-GST was purified as shown in FIG. 203, lane 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 151 A DNA sequence (GBSx0157) was identified in S. agalactiae <SEQ ID 505> which encodes the amino acid sequence <SEQ ID 506>. Analysis of this protein sequence reveals the following: TABLE-US-00520 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 496. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 152 A repeated DNA sequence (GBSx0158) was identified in S. agalactiae <SEQ ID 507> which encodes the amino acid sequence <SEQ ID 508>. Analysis of this protein sequence reveals the following: TABLE-US-00521 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1054(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00522 >GP: BAB03941 GB: AP001507 unknown conserved protein [Bacillus halodurans] Identities = 26/82 (31%), Positives = 52/82 (62%), Gaps = 2/82 (2%) Query: 2 LRIGTACGSGLGSSFMVQMNIESILKDLGVSDVEVEHYDLGGADPSAADVWIVGRDLEDS 61 ++I CG G G+S +++MN+E++L LG++ +V++ D+ A +D I ++L +S Sbjct: 1 MKILCVCGLGQGTSLILKMNVETVLSQLGIA-ADVDNTDVSSASSEQSDFIITSKELAES 59 Query: 62 -AGHLGDVRILNSIIDMDELRE 82 A H + I+N+ DM+E+++ Sbjct: 60 LASHPSKIVIVNNYFDMEEIKQ 81 A related DNA sequence was identified in S. pyogenes <SEQ ID 509> which encodes the amino acid sequence <SEQ ID 510>. Analysis of this protein sequence reveals the following: TABLE-US-00523 Possible site: 48 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00524 Identities = 27/90 (30%), Positives = 51/90 (56%), Gaps = 1/90 (1%) Query: 1 MLRIGTACGSGLGSSFMVQMNIESILKDLGVSDVEVEHYDLGGADPSAADVWIVGRDLED 60 M++I T CG+G+GSS +++M +E+I LG+ DV+ E D A AD+++ ++ +D Sbjct: 8 MIKIVTVCGNGIGSSLLLRMKVEAIASSLGI-DVDAESCDSNAAVGKGADLFVTVKEFKD 66 Query: 61 SAGHLGDVRILNSIIDMDELRELVTGICQE 90 V I+ S + ++ E + + +E Sbjct: 67 IFPEDAKVCIVKSYTNRKKIEEDLVPVLKE 96 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 153 A DNA sequence (GBSx0159) was identified in S. agalactiae <SEQ ID 511> which encodes the amino acid sequence <SEQ ID 512>. Analysis of this protein sequence reveals the following: TABLE-US-00525 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 154 A DNA sequence (GBSx0160) was identified in S. agalactiae <SEQ ID 513> which encodes the amino acid sequence <SEQ ID 514>. This protein is predicted to be sgaT. Analysis of this protein sequence reveals the following: TABLE-US-00526 Possible site: 16 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -14.97 Transmembrane 424-440 (411-447) INTEGRAL Likelihood = -8.86 Transmembrane 224-240 (221-248) INTEGRAL Likelihood = -7.27 Transmembrane 134-150 (124-167) INTEGRAL Likelihood = -7.11 Transmembrane 321-337 (314-349) INTEGRAL Likelihood = -6.64 Transmembrane 379-395 (370-397) INTEGRAL Likelihood = -6.21 Transmembrane 96-112 (94-115) INTEGRAL Likelihood = -6.05 Transmembrane 267-283 (257-289) INTEGRAL Likelihood = -3.13 Transmembrane 18-34 (17-35) INTEGRAL Likelihood = -2.55 Transmembrane 151-167 (151-167) INTEGRAL Likelihood = -0.32 Transmembrane 42-58 (42-58) ----- Final Results ----- bacterial membrane --- Certainty = 0.6986(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00527 >GP: CAB52363 GB: AL109747 putative integral membrane protein [Streptomyces coelicolor A3(2)] Identities = 202/453 (44%), Positives = 292/453 (63%), Gaps = 22/453 (4%) Query: 7 FLVN-IASTPAILVALIAIIGLVLQKKGVPDIVKGGIKTFVGFLVVSGGTGIVQNSLNPF 65 FLVN I S PA L+ +I +GL KK V V G IK +G L+V G G+V +SL+P Sbjct: 10 FLVNEILSQPAYLIGIITAVGLAALKKSVGQTVGGAIKATLGLLLVGAGAGLVSSSLDPL 69 Query: 66 GKMFEHAFHLVGVVPNNEAIVAVALTKYGSATALIMLAGMIFNILIARFTKFKYIFLTGH 125- G+M + GV+P NEAIV +A +++G+ A +M+ G + ++ +ARFT +Y+FLTGH Sbjct: 70 GRMIQGTTGTHGVIPTNEAIVGIAQSEFGARVAWLMILGFLVSLALARFTPLRYVFLTGH 129- Query: 126 HTLYMACMIAVIFAVAGFTSFSLILFGGLALGIIMSVSPAFVQKYMIQLTGNDKVALGHF 18- 5 H L+MA ++ ++ A AG S +++L GG+ +GI++ PAF + ++TGND +A+GHF Sbjct: 130 HMLFMATLLTIVMATAGQGSVAVVLGGGVLVGILLVALPAFAHPWTKKVTGNDTLAIGHF 18- 9 Query: 186 GSLGYWLSGFIGGIVGDKSKSTEDIKFPKSLSFLRDSTVSITISMAIIYLIVAV------ 23- 9 G+ GY +SG G +VG S+STE++K P+ L FLRDS V+ +SM +IYL++++ Sbjct: 190 GTAGYIVSGATGQLVGKNSRSTEEMKLPEGLRFLRDSMVATALSMVLIYLVMSLLFLAKV 24- 9 Query: 240 --------FAGEAYIAKEISNGVNGLVYALQLAGQFAAGVFVILAGVRLILGEIVPAFKG 29- 1 FAG ++ N L+ ++ QF GV VIL GVR ILGE+VPAF+G Sbjct: 250 GQDAAFKAFAGSG--GDPAADVGNYLMQSVMQGLQFGIGVAVILFGVRTILGELVPAFQG 30- 7 Query: 292 ISEKLVPNSKPALDCPIVYPYAPNAVLIGFISSFVGGLVSMIVMI-----VTGTTVILPG 34- 6 I+ ++VP +KPALD PIV+PYA NAVLIGFI SF+GGL + +I G ++LPG Sbjct: 308 IAGRVVPGAKPALDAPIVFPYAQNAVLIGFIFSFLGGLTGLAALIWVFNPAFGLALVLPG 36- 7 Query: 347 VVPHFFCGATAGVIGNASGGVRGATIGAFVQGILISFLPIFLMPVLGGLGFKGSTFSDAD 40- 6 +VPHFF G AGV GNA+GG RGA +G+F+ G+LI+FLP L+ LG G +TF DAD Sbjct: 368 LVPHFFTGGAAGVYGNATGGRRGAAVGSFLNGLLITFLPAILLKALGSFGEANTTFGDAD 42- 7 Query: 407 FGLTGIILGALNHVGGAIAIVIGIVVILIGLFG 439 FG G +LG++ + G ++ ++ L+ L G Sbjct: 428 FGWFGAVLGSIGKLDGTAGLIGMLIFGLLILAG 460 A related DNA sequence was identified in S. pyogenes <SEQ ID 515> which encodes the amino acid sequence <SEQ ID 516>. Analysis of this protein sequence reveals the following:

TABLE-US-00528 Possible site: 34 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.33 Transmembrane 330-346 (315-353) INTEGRAL Likelihood = -8.17 Transmembrane 227-243 (221-246) INTEGRAL Likelihood = -4.62 Transmembrane 127-143 (126-145) INTEGRAL Likelihood = -4.25 Transmembrane 269-285 (266-291) INTEGRAL Likelihood = -3.77 Transmembrane 43-59 (41-62) INTEGRAL Likelihood = -3.66 Transmembrane 98-114 (91-116) INTEGRAL Likelihood = -2.76 Transmembrane 146-162 (145-163) INTEGRAL Likelihood = -1.59 Transmembrane 308-324 (308-324) ----- Final Results ----- bacterial membrane --- Certainty = 0.4333(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00529 >GP: CAB52363 GB: AL109747 putative integral membrane protein [Streptomyces coelicolor A3(2)] Identities = 162/387 (41%), Positives = 245/387 (62%), Gaps = 17/387 (4%) Query: 8 IRDILKEPAFLMGLIAFAGLVALKTPAHKVLTGTLGPILGYLMLVAGAGVIVTNLDPLAK 67 + +IL +PA+L+G+I GL ALK + + G + LG L++ AGAG++ ++LDPL + Sbjct: 12 VNEILSQPAYLIGIITAVGLAALKKSVGQTVGGAIKATLGLLLVGAGAGLVSSSLDPLGR 71 Query: 68 LIEHGFSITGVVPNNEAVTSVAQKILGVETMSILVVGLLLNLAFARFTRFKYIFLTGHHS 127- +I+ GV+P NEA+ +AQ G ++++G L++LA ARFT +Y+FLTGHH Sbjct: 72 MIQGTTGTHGVIPTNEAIVGIAQSEFGARVAWLMILGFLVSLALARFTPLRYVFLTGHHM 131- Query: 128 FFMACLLSAVLGAVGFKGSLLIIL-DGFLLGAWSAISPAIGQQYTLKVTDGDEIAMGHFG 18- 6 FMA LL+ V+ G +GS+ ++L G L+G PA +T KVT D +A+GHFG Sbjct: 132 LFMATLLTIVMATAG-QGSVAVVLGGGVLVGILLVALPAFAHPWTKKVTGNDTLAIGHFG 19- 0 Query: 187 SLGYYLSAWVGSKVGKDSKDTEDLQISEKWSFLRNTTISTGLIMVIFYLVAT---VASVL 24- 3 + GY +S G VGK+S+ TE++++ E FLR++ ++T L MV+ YLV + +A V Sbjct: 191 TAGYIVSGATGQLVGKNSRSTEEMKLPEGLRFLRDSMVATALSMVLIYLVMSLLFLAKVG 25- 0 Query: 244 RNASVAEELAAGQNP-------FIFAIKSGLTFAVGVAIVYAGVRMILADLIPAFQGIAN 29- 6 ++A+ +G +P + ++ GL F +GVA++ GVR IL +L+PAFQGIA Sbjct: 251 QDAAFKAFAGSGGDPAADVGNYLMQSVMQGLQFGIGVAVILFGVRTILGELVPAFQGIAG 31- 0 Query: 297 KLIPNAIPAVDCAVFFPYAPTAVIIGFASSFVGGLLGMLIL-----GVAGGVLIIPGMVP 35- 1 +++P A PA+D + FPYA AV+IGF SF+GGL G+ L G L++PG+VP Sbjct: 311 RVVPGAKPALDAPIVFPYAQNAVLIGFIFSFLGGLTGLAALIWVFNPAFGLALVLPGLVP 37- 0 Query: 352 HFFCGATAEIFGNSTGGRRGAMIGASL 378 HFF G A ++GN+TGGRRGA +G+ L Sbjct: 371 HFFTGGAAGVYGNATGGRRGAAVGSFL 397 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00530 Identities = 174/376 (46%), Positives = 258/376 (68%), Gaps = 2/376 (0%) Query: 1 MKGLLDFLVNIASTPAILVALIAIIGLVLQKKGVPDIVKGGIKTFVGFLVVSGGTGIVQN 60 M+ LL F+ +I PA L+ LIA GLV K ++ G + +G+L++ G G++ Sbjct: 1 MEALLSFIRDILKEPAFLMGLIAFAGLVALKTPAHKVLTGTLGPILGYLMLVAGAGVIVT 60 Query: 61 SLNPFGKMFEHAFHLVGVVPNNEAIVAVALTKYGSATALIMLAGMIFNILIARFTKFKYI 120- +L+P K+ EH F + GVVPNNEA+ +VA G T I++ G++ N+ ARFT+FKYI Sbjct: 61 NLDPLAKLIEHGFSITGVVPNNEAVTSVAQKILGVETMSILVVGLLLNLAFARFTRFKYI 120- Query: 121 FLTGHHTLYMACMIAVIFAVAGFTSFSLILFGGLALGIIMSVSPAFVQKYMIQLTGNDKV 18- 0 FLTGHH+ +MAC+++ + GF LI+ G LG ++SPA Q+Y +++T D++ Sbjct: 121 FLTGHHSFFMACLLSAVLGAVGFKGSLLIILDGFLLGAWSAISPAIGQQYTLKVTDGDEI 18- 0 Query: 181 ALGHFGSLGYWLSGFIGGIVGDKSKSTEDIKFPKSLSFLRDSTVSITISMAIIYLI--VA 23- 8 A+GHFGSLGY+LS ++G VG SK TED++ + SFLR++T+S + M I YL+ VA Sbjct: 181 AMGHFGSLGYYLSAWVGSKVGKDSKDTEDLQISEKWSFLRNTTISTGLIMVIFYLVATVA 24- 0 Query: 239 VFAGEAYIAKEISNGVNGLVYALQLAGQFAAGVFVILAGVRLILGEIVPAFKGISEKLVP 29- 8 A +A+E++ G N ++A++ FA GV ++ AGVR+IL +++PAF+GI+ KL+P Sbjct: 241 SVLRNASVAEELAAGQNPFIFAIKSGLTFAVGVAIVYAGVRMILADLIPAFQGIANKLIP 30- 0 Query: 299 NSKPALDCPIVYPYAPNAVLIGFISSFVGGLVSMIVMIVTGTTVILPGVVPHFFCGATAG 35- 8 N+ PA+DC + +PYAP AV+IGF SSFVGGL+ M+++ V G +I+PG+VPHFFCGATA Sbjct: 301 NAIPAVDCAVFFPYAPTAVIIGFASSFVGGLLGMLILGVAGGVLIIPGMVPHFFCGATAE 36- 0 Query: 359 VIGNASGGVRGATIGA 374 + GN++GG RGA IGA Sbjct: 361 IFGNSTGGRRGAMIGA 376 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 155 A DNA sequence (GBSx0161) was identified in S. agalactiae <SEQ ID 517> which encodes the amino acid sequence <SEQ ID 518>. This protein is predicted to be transketolase, N-terminal subunit (tkt). Analysis of this protein sequence reveals the following: TABLE-US-00531 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3680(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00532 >GP: AAB98676 GB: U67515 transketolase' [Methanococcus jannaschii] Identities = 106/269 (39%), Positives = 158/269 (58%), Gaps = 4/269 (1%) Query: 11 LRRFATEIRLNTLETLNHLGFGHYGGSLSIVEALAVLYGDIMDINPEKFKESDRDYMVLS 70 - L + A ++R N ++ + GH GGSLS + + LY +M+ +P+ + DRD VLS Sbjct: 10 LEKIAKKVRYNIVKMVGLAKSGHPGGSLSATDIIVALYFKLMNYSPDNPYKKDRDRFVLS 69 Query: 71 KGHAGPALYSTLYLKGFFDKTFLHSLNTNGTKLPSHPDRNLTPGIDVTTGSLGQGISIAT 130- KGHA PALY+ L G ++ L L KL HP + TPG+++ TGSLGQG S A Sbjct: 70 KGHAAPALYAVLSELGIIEEEELWKLRRLEGKLQGHPSMD-TPGVEICTGSLGQGFSAAV 128- Query: 131 GIAYAQKIENSSYYTYTIVGDGELNEGQCWEAIQFAAHHQLHHLIVFVDDNKKQLDGLTA 19- 0 G+A +++ + Y Y ++GDGE EG WEA AAH++L +LI F+D NK Q+DG T Sbjct: 129 GMALGCRLDKLNNYVYVLLGDGECQEGIVWEAAMAAAHYKLDNLIAFIDRNKLQIDGCTE 18- 8 Query: 191 DICNPGDFVAKFEAFGFDAVRVKGDDIEAIDKAIKTFQDSNSVRPKCIVLDSIKGQGVKE 25- 0 D+ + GD AKFEAFG+D + G + E I ++ + + +PK I+ ++KG+GV Sbjct: 189 DVMSLGDIKAKFEAFGWDVFEIDGHNFEEIINTVEKAKSMKNGKPKMIIAYTVKGKGVSF 24- 8 Query: 251 LEELASNHHLRPDLQQKTMLERALISLRE 279 +E + H P+ +Q L++AL L E Sbjct: 249 MENNVAFHGKAPNEEQ---LKQALEELSE 274 A related DNA sequence was identified in S. pyogenes <SEQ ID 519> which encodes the amino acid sequence <SEQ ID 520>. Analysis of this protein sequence reveals the following: TABLE-US-00533 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.75 Transmembrane 58-74 (57-74) ----- Final Results ----- bacterial membrane --- Certainty = 0.1298(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9165> which encodes the amino acid sequence <SEQ ID 9166>. Analysis of this protein sequence reveals the following: TABLE-US-00534 Possible site: 54 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.75 Transmembrane 40-56 (39-56) ----- Final Results ----- bacterial membrane --- Certainty = 0.130(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00535 Identities = 82/246 (33%), Positives = 129/246 (52%), Gaps = 15/246 (6%) Query: 18 IRLNTLETLNHLGFGHYGGSLSIVEALAVLYGDIMDINPEKFKE-SDRDYMVLSKGHAGP 76 - +R +++ + GH G + VL+ M+INP+ + S+RD +LS GH Sbjct: 82 VRTLSMDAIQAANSGHPGLPMGAAPMAYVLWNHFMNINPKTSRNWSNRDRFILSAGHGSA 141- Query: 77 ALYSTLYLKGF-FDKTFLHSLNTNGTKLPSHPDRNLTPGIDVTTGSLGQGISIATGIAYA 135- LYS L+L G+ L + G+K P HP+ N T G++ TTG LGQGI+ A G+A A Sbjct: 142 MLYSLLHLAGYDLSVEDLKNFRQWGSKTPGHPEVNHTDGVEATTGPLGQGIANAVGMAMA 20- 1 Query: 136 QK----------IENSSYYTYTIVGDGELNEGQCWEAIQFAAHHQLHHLIVFVDDNKKQL 18- 5 + + +YT+ + GDG+L EG EA A H +L L++ D N L Sbjct: 202 EAHLAAKFNKPGFDIVDHYTFALNGDGDLMEGVSQEAASMAGHLKLGKLVLLYDSNDISL 26- 1 Query: 186 DGLTADICNPGDFVAKFEAFGFDAVRVK-GDDIEAIDKAIKTFQDSNSVRPKCIVLDSIK 24- 4 DG T+ + D +FEA+G+ + VK G+D+E I AI+ + + + +P I + +I Sbjct: 262 DGPTS-MAFTEDVKGRFEAYGWQHILVKDGNDLEEIAAAIEAAK-AETEKPTIIEVKTII 31- 9 Query: 245 GQGVKE 250 G G ++ Sbjct: 320 GFGAEK 325 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 156 A DNA sequence (GBSx0162) was identified in S. agalactiae <SEQ ID 521> which encodes the amino acid sequence <SEQ ID 522>. Analysis of this protein sequence reveals the following: TABLE-US-00536 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.27 Transmembrane 53-69 (53-69) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9499> which encodes amino acid sequence <SEQ ID 9500> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00537 >GP: AAB98674 GB: U67515 transketolase`` [Methanococcus jannaschii] Identities = 100/301 (33%), Positives = 171/301 (56%), Gaps = 7/301 (2%) Query: 6 KEMRLVYRDFLLQANQENKQITVLEADLSSSMSTNALASEFGKRYINLGIMEAEMVGLAA 65 K MR Y + L++ ++ + + VL+ADLS S T A EF +R+ N G+ E M+G+AA Sbjct: 9 KGMRKGYGETLIELGKKYENLVVLDADLSGSTQTAMFAKEFPERFFNAGVAEQNMIGMAA 68 Query: 66 GLAIKGYKPYLHTFGPFASRRVFDQVFLSLGYSQLSATIIGSDAGISAEMNGGTHMPFEE 125- GLA G + +F FAS R ++ + + Y +L+ I+ + AGI+ +G +H E+ Sbjct: 69 GLATTGKIVFASSFSMFASGRAWEIIRNLVAYPKLNVKIVATHAGITVGEDGASHQMCED 128- Query: 126 LGLLRLIPKATIFEVSDDIQFEAILKQTLSIDGLKYIRTIRKAPTAVYEGRE----DFSK 18- 1 + ++R IP + +D + +++ G Y+R R+ +YE E + K Sbjct: 129 IAIMRAIPNMVVIAPTDYYHTKNVIRTIAEYKGPVYVRMPRRDTEIIYENEEEATFEIGK 18- 8 Query: 182 GFIQLRQGKDITLVASGIMVSRAIEAADYLKELGIEASVIDLFKIKPLPEELKPLLIDQS 24- 1 G I L G+D+T++A+G V A+ A + LKE GI A ++++ IKP+ EE+ D Sbjct: 189 GKI-LVDGEDLTIIATGEEVPEALRAGEILKENGISAEIVEMATIKPIDEEIIKKSKD-F 24- 6 Query: 242 IVTIENHNRIGGIGSALCEWL-SMEKDTTVSRMGIDERFGQVGQMEYLLEEYGLAVKDIVQ 3- 01 +VT+E+H+ IGG+G A+ E + S + + R+GI++ FG+ G+ + LL+ YGL + I + Sbjct: 247 VVTVEDHSIIGGLGGAVAEVIASNGLNKKLLRIGINDVFGRSGKADELLKYYGLDGESIAK 3- 07 There is also homology to SEQ ID 520. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 157 A DNA sequence (GBSx0163) was identified in S. agalactiae <SEQ ID 523> which encodes the amino acid sequence <SEQ ID 524>. Analysis of this protein sequence reveals the following: TABLE-US-00538 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2517 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 158 A DNA sequence (GBSx0164) was identified in S. agalactiae <SEQ ID 525> which encodes the amino acid sequence <SEQ ID 526>. Analysis of this protein sequence reveals the following: TABLE-US-00539 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.42 Transmembrane 119-135 (114-145) INTEGRAL Likelihood = -5.10 Transmembrane 33-49 (32-50) INTEGRAL Likelihood = -4.30 Transmembrane 94-110 (94-111) INTEGRAL Likelihood = -3.66 Transmembrane 67-83 (60-83) ----- Final Results ----- bacterial membrane --- Certainty = 0.3569 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8503> and protein <SEQ ID 8504> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00540 Lipop: Possible site: -1 Crend: 4 SRCFLG: 0 McG: Length of UR: 22 Peak Value of UR: 2.96 Net Charge of CR: 2 McG: Discrim Score: 10.55 GvH: Signal Score (-7.5): -4.31 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 6 value: -6.42 threshold: 0.0 INTEGRAL Likelihood = -6.42 Transmembrane 154-170 (149-180) INTEGRAL Likelihood = -5.10 Transmembrane 68-84 (67-85) INTEGRAL Likelihood = -5.04 Transmembrane 6-22 (2-24) INTEGRAL Likelihood = -4.30 Transmembrane 129-145 (129-146) INTEGRAL Likelihood = -3.66 Transmembrane 102-118 (95-118) INTEGRAL Likelihood = -3.56 Transmembrane 29-45 (29-46) PERIPHERAL Likelihood = 0.79 285 modified ALOM score: 1.78 icm1 HYPID: 7 CFP: 0.357 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3569 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00014## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 159 A DNA sequence (GBSx0165) was identified in S. agalactiae <SEQ ID 527> which encodes the amino acid sequence <SEQ ID 528>. This protein is predicted to be 30S ribosomal protein S15 (rpsO). Analysis of this protein sequence reveals the following: TABLE-US-00541 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4074(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00542 >GP: CAB13541 GB: Z99112 ribosomal protein S15 (BS18) [Bacillus subtilis] Identities = 55/89 (61%), Positives = 71/89 (78%) Query: 1 MAISKEKKNEIIAQYARHEGDTGSVEVQVAVLTWEINHLNDHIKQHKKDHATYRGLMKKI 60 MAI++E+KN++I ++ HE DTGS EVQ+A+LT IN+LN+H++ HKKDH + RGL+K + Sbjct: 1 MAITQERKNQLINEFKTHESDTGSPEVQIAILTDSINNLNEHLRTHKKDHHSRRGLLKMV 60 Query: 61 GHRRNLLAYLRRTDVNRYRELIQSLGLRR 89 G RRNLL YLR DV RYRELI LGLRR Sbjct: 61 GKRRNLLTYLRNKDVTRYRELINKLGLRR 89 A related DNA sequence was identified in S. pyogenes <SEQ ID 529> which encodes the amino acid sequence <SEQ ID 530>. Analysis of this protein sequence reveals the following: TABLE-US-00543 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3746(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00544 Identities = 88/89 (98%), Positives = 88/89 (98%) Query: 1 MAISKEKKNEIIAQYARHEGDTGSVEVQVAVLTWEINHLNDHIKQHKKDHATYRGLMKKI 60 MAISKEKKNEIIAQYARHEGDTGSVEVQVAVLTWEINHLN HIKQHKKDHATYRGLMKKI Sbjct: 1 MAISKEKKNEIIAQYARHEGDTGSVEVQVAVLTWEINHLNSHIKQHKKDHATYRGLMKKI 60 Query: 61 GHRRNLLAYLRRTDVNRYRELIQSLGLRR 89 GHRRNLLAYLRRTDVNRYRELIQSLGLRR Sbjct: 61 GHRRNLLAYLRRTDVNRYRELIQSLGLRR 89 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 160 A DNA sequence (GBSx0166) was identified in S. agalactiae <SEQ ID 531> which encodes the amino acid sequence <SEQ ID 532>. This protein is predicted to be polyribonucleotide nucleotidyltransferase (pnp). Analysis of this protein sequence reveals the following: TABLE-US-00545 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.64 Transmembrane 448-464 (448-464) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9501> which encodes amino acid sequence <SEQ ID 9502> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00546 >GP: AAC43595 GB: U29668 polynucleotide phosphorylase [Bacillus subtilis] Identities = 428/694 (61%), Positives = 532/694 (75%), Gaps = 4/694 (0%) Query: 7 KQVFEMIFAGKKLVVETGQVAKQANGSVVVRYGDSTVLTAAVMSKKMSTGDFFPLQVNYE 66 K VF + +AG+ L VETGQ+AKQANG+V++RYGD+ VL+ A SK+ DFFPL VNYE Sbjct: 5 KHVFTIDWAGRTLTVETGQLAKQANGAVMIRYGDTAVLSTATASKEPKPLDFFPLTVNYE 64 Query: 67 EKMYAAGKFPGGFNKREGRPSTDATLTARLIDRPIRPMFAEGFRNEVQVINTVLSFDENA 126- E++YA GK PGGF KREGRPS A L +RLIDRPIRP+FA+GFRNEVQVI+ V+S D+N Sbjct: 65 ERLYAVGKIPGGFIKREGRPSEKAVLASRLIDRPIRPLFADGFRNEVQVISIVMSVDQNC 124- Query: 127 SAPMAAMFGSSLALSISDIPFNGPIAGVQVAYVDGNFIINPTAQEQEASALELTVAGTKE 18- 6 S+ MAAMFGSSLALS+SDIPF GPIAGV V +D FIINPT + E S + L VAGTK+ Sbjct: 125 SSEMAAMFGSSLALSVSDIPFEGPIAGVTVGRIDDQFIINPTVDQLEKSDINLVVAGTKD 18- 4 Query: 187 AINMVESGAKELSEEIMLEALLKGHEAVCELIAFQEEIVTAIGKEKAEVELLQVDPELQA 24- 6 AINMVE+GA E+ EEIMLEA++ GHE + LIAFQEEIV A+GKEK+E++L ++D EL Sbjct: 185 AINMVEAGADEVPEEIMLEAIMFGHEEIKRLIAFQEEIVAAVGKEKSEIKLFEIDEELNE 24- 4 Query: 247 EIIATHNIALQAAVQVEEKKAREAATEAVKEVVIGEYEARYAEHEEYDRIMRDVAEILEQ 30- 6 ++ A L A+QV EK ARE A VK V+ ++E EH+E ++ V +IL + Sbjct: 245 KVKALAEEDLLKAIQVHEKHAREDAINEVKNAVVAKFEDE--EHDE--DTIKQVKQILSK 30- 0 Query: 307 MEHAEVRRLITEDKIRPDGRRVDEIRPLDAEIDFLPQVHGSGLFTRGQTQALSVLTLAPM 36- 6 + EVRRLITE+K+RPDGR VD+IRPL +E+ LP+ HGSGLFTRGQTQALSV TL + Sbjct: 301 LVKNEVRRLITEEKVRPDGRGVDQIRPLSSEVGLLPRTHGSGLFTRGQTQALSVCTLGAL 36- 0 Query: 367 GEAQIIDGLTPEYKKRFMHHYNFPQYSVGETGRYGAAGRREIGHGALGERALEQVLPRLE 42- 6 G+ QI+DGL E KRFMHHYNFPQ+SVGETG GRREIGHGALGERALE V+P + Sbjct: 361 GDVQILDGLGVEESKRFMHHYNFPQFSVGETGPMRGPGRREIGHGALGERALEPVIPSEK 42- 0 Query: 427 EFPYAIRLVAEVLESNGSSSQASICAGTLALMAGGVPIKAPVAGIAMGLISDGTNYTVLT 48- 6 +FPY +RLV+EVLESNGS+SQASICA TLA+M GVPIKAPVAGIAMGL+ G +YTVLT Sbjct: 421 DFPYTVRLVSEVLESNGSTSQASICASTLAMMDAGVPIKAPVAGIAMGLVKSGEHYTVLT 48- 0 Query: 487 DIQGLEDHFGDMDFKVAGTREGITALQMDIKIEGITPQILEEALAQAKKARFEILDVLHG 54- 6 DIQG+ED GDMDFKVAGT +G+TALQMDIKIEG++ +ILEEAL QAKK R EIL+ + Sbjct: 481 DIQGMEDALGDMDFKVAGTEKGVTALQMDIKIEGLSREILEEALQQAKKGRMEILNSMLA 54- 0 Query: 547 AIAEPRPQLAPTAPKIDMIKIDVDKIKVVIGKGGETIDKIIAETGVKIDIDEEGNVSIFS 60- 6 ++E R +L+ APKI + I+ DKI+ VIG G+ I+KII ETGVKIDI+++G + I S Sbjct: 541 TLSESRKELSRYAPKILTMTINPDKIRDVIGPSGKQINKIIEETGVKIDIEQDGTIFISS 60- 0 Query: 607 SDQAAIDRTKDIIASLVREAKVGEVYHAKVVRIEKFGAFVNLFDKTDALVHISEIAWTRT 66- 6 +D++ + K II LVRE +VG++Y KV RIEKFGAFV +F D LVHISE+A R Sbjct: 601 TDESGNQKAKKIIEDLVREVEVGQLYLGKVKRIEKFGAFVEIFSGKDGLVHISELALERV 66- 0 Query: 667 ANVADVLEIGEEVDVKVIKIDDKGRVDASMKALL 700 V DV++IG+E+ VKV +ID +GRV+ S KA+L Sbjct: 661 GKVEDVVKIGDEILVKVTEIDKQGRVNLSRKAVL 694 A related DNA sequence was identified in S. pyogenes <SEQ ID 533> which encodes the amino acid sequence <SEQ ID 534>. Analysis of this protein sequence reveals the following:

TABLE-US-00547 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.64 Transmembrane 444-460 (444-460) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00548 Identities = 631/708 (89%), Positives = 664/708 (93%), Gaps = 2/708 (0%) Query: 5 MSKQVFEMIFAGKKLVVETGQVAKQANGSVVVRYGDSTVLTAAVMSKKMSTGDFFPLQVN 64 MSKQ F FAGK LVVE GQVAKQANG+ VVRYGDSTVLTAAVMSKKM+TGDFFPLQVN Sbjct: 1 MSKQTFTTTFAGKPLVVEVGQVAKQANGATVVRYGDSTVLTAAVMSKKMATGDFFPLQVN 60 Query: 65 YEEKMYAAGKFPGGFNKREGRPSTDATLTARLIDRPIRPMFAEGFRNEVQVINTVLSFDE 124- YEEKNYAAGKFPGGF KREGRPSTDATLTARLIDRPIRPMFAEGFRNEVQVINTVLS+DE Sbjct: 61 YEEKMYAAGKFPGGFMKREGRPSTDATLTARLIDRPIRPMFAEGFRNEVQVINTVLSYDE 120- Query: 125 NASAPMAAMFGSSLALSISDIPFNGPIAGVQVAYVDGNFIINPTAQEQEASALELTVAGT 18- 4 NASAPMAAMFGSSLALSISDIPFNGPIAGVQV Y+DG FIINP ++ EAS LELTVAG+ Sbjct: 121 NASAPMAAMFGSSLALSISDIPFNGPIAGVQVGYIDGEFIINPDKEQMEASLLELTVAGS 18- 0 Query: 185 KEAINMVESGAKELSEEIMLEALLKGHEAVCELIAFQEEIVTAIGKEKAEVELLQVDPEL 24- 4 KEAINMVESGAKELSE+IMLEALLKGH+A+ ELIAFQE+IV +GKEKAEVELLQVD +L Sbjct: 181 KEAINMVESGAKELSEDIMLEALLKGHQAIQELIAFQEQIVAVVGKEKAEVELLQVDVDL 24- 0 Query: 245 QAEIIATHNIALQAAVQVEEKKAREAATEAVKEVVIGEYEARYAEHEEYDRIMRDVAEIL 30- 4 QA+I+A +N LQ AVQVEEKKAREAATEAVKE+V EYE RYAE E IMRDVAEIL Sbjct: 241 QADIVAKYNAQLQKAVQVEEKKAREAATEAVKEMVKAEYEERYAEDENLATIMRDVAEIL 30- 0 Query: 305 EQMEHAEVRRLITEDKIRPDGRRVDEIRPLDAEIDFLPQVHGSGLFTRGQTQALSVLTLA 36- 4 EQMEHAEVRRLITEDKIRPDGR++DEIRPLDA +DFLP+VHGSGLFTRGQTQALSVLTLA Sbjct: 301 EQMEHAEVRRLITEDKIRPDGRKIDEIRPLDAVVDFLPKVHGSGLFTRGQTQALSVLTLA 36- 0 Query: 365 PMGEAQIIDGLTPEYKKRFMHHYNFPQYSVGETGRYGAAGRREIGHGALGERALEQVLPR 42- 4 PMGE QIIDGL PEYKKRF+HHYNFPQYSVGETGRYGAAGRREIGHGALGERALEQVLP Sbjct: 361 PMGETQIIDGLAPEYKKRFLHHYNFPQYSVGETGRYGAAGRREIGHGALGERALEQVLPS 42- 0 Query: 425 LEEFPYAIRLVAEVLESNGSSSQASICAGTLALMAGGVPIKAPVAGIAMGLISDGTNYTV 48- 4 LEEFPYAIRLVAEVLESNGSSSQASICAGTLALMAGGVPIKAPVAGIAMGLISDGTNYTV Sbjct: 421 LEEFPYAIRLVAEVLESNGSSSQASICAGTLALMAGGVPIKAPVAGIAMGLISDGTNYTV 48- 0 Query: 485 LTDIQGLEDHFGDMDFKVAGTREGITALQMDIKIEGITPQILEEALAQAKKARFEILDVL 54- 4 LTDIQGLEDHFGDMDFKVAGTREGITALQMDIKI GITPQILEEALAQAKKARFEILDV+ Sbjct: 481 LTDIQGLEDHFGDMDFKVAGTREGITALQMDIKIAGITPQILEEALAQAKKARFEILDVI 54- 0 Query: 545 HGAIAEPRPQLAPTAPKIDMIKIDVDKIKVVIGKGGETIDKIIAETGVKIDIDEEGNVSI 60- 4 IAEPRP+LAPTAPKID IKIDVDKIKVVIGKGGETIDKIIAETGVKIDID+EGNVSI Sbjct: 541 EATIAEPRPELAPTAPKIDTIKIDVDKIKVVIGKGGETIDKIIAETGVKIDIDDEGNVSI 60- 0 Query: 605 FSSDQAAIDRTKDIIASLVREAKVGEVYHAKVVRIEKFGAFVNLFDKTDALVHISEIAWT 66- 4 +SSDQAAIDRTK+IIA LVREAKVGEVYHAKVVRIEKFGAFVNLFDKTDALVHISEIAWT Sbjct: 601 YSSDQAAIDRTKEIIAGLVREAKVGEVYHAKVVRIEKFGAFVNLFDKTDALVHISEIAWT 66- 0 Query: 665 RTANVADVLEIGEEVDVKVIKIDDKGRVDASMKALLPRPPKADNPKKE 712 RT NV+DVLE+GE+VDVKVIKID+KGRVDASMKAL+PRPPK + KKE Sbjct: 661 RTTNVSDVLEVGEDVDVKVIKIDEKGRVDASMKALIPRPPKPE--KKE 706 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 161 A DNA sequence (GBSx0167) was identified in S. agalactiae <SEQ ID 535> which encodes the amino acid sequence <SEQ ID 536>. Analysis of this protein sequence reveals the following: TABLE-US-00549 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1293 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 537> which encodes the amino acid sequence <SEQ ID 538>. Analysis of this protein sequence reveals the following: TABLE-US-00550 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 83-99 (83-99) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below: TABLE-US-00551 Identities = 172/248 (69%), Positives = 211/248 (84%) Query: 1 MTSTNELDIRLRAFINAPDNFLDSIGLVNALHHSTVWASKEPYAIQVDGQEVVPVFTDIT 60 MT +NELDIRLRAFINAPDNFLDS+ LVNA H+ VWA+KEPY I+V+G +V PVFTD Sbjct: 1 MTKSNELDIRLRAFINAPDNFLDSLALVNAFHNFPVWAAKEPYVIEVEGVKVTPVFTDKE 60 Query: 61 DLNHFKEEQESARDMFWESRRSLDVLDEAISHGLAGLVYNLKKEGDFGNSTIFYCEDMVQ 120- D+ FKEEQ+SA+ +W R +L VL+E I+ G AGL++NLKK+GDFGNSTIF DM+Q Sbjct: 61 DMARFKEEQKSAQSQYWLERSALAVLEEVITSGAAGLIFNLKKKGDFGNSTIFKSSDMIQ 120- Query: 121 FMNNYTTILNQLLNEDNIVADIMDKTYLVPAFVHPREEGSFDRLFPTMSTPEGKSYVPVF 18- 0 FMN+YTT+LN L+++DN+ AD M+K YLVPAFV+P++ +DRLFPTMSTPEGKSYVP F Sbjct: 121 FMNHYTTVLNTLMSDDNVAADTMEKVYLVPAFVYPKDNNHYDRLFPTMSTPEGKSYVPAF 18- 0 Query: 181 SNLLSFEKWYNHNDFGGAFRKAQGVILAWTIDDIYKPRNGENEIDDTFGVAINPFDEQQV 24- 0 SNL SF KWYN +DFGG FRKA+GVIL WTIDDIY+PRNGENE+D+TFGVAINPFD+QQ+ Sbjct: 181 SNLQSFAKWYNQDDFGGLFRKAEGVILTWTIDDIYQPRNGENELDETFGVAINPFDDQQI 24- 0 Query: 241 LVDWSDVE 248 LVDWS+++ Sbjct: 241 LVDWSELD 248 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 162 A DNA sequence (GBSx0168) was identified in S. agalactiae <SEQ ID 539> which encodes the amino acid sequence <SEQ ID 540>. This protein is predicted to be serine acetyltransferase (cysE). Analysis of this protein sequence reveals the following: TABLE-US-00552 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.02 Transmembrane 150-166 (147-168) ----- Final Results ----- bacterial membrane --- Certainty = 0.1808 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9503> which encodes amino acid sequence <SEQ ID 9504> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00553 >GP: CAB71304 GB: AJ130879 serine acetyltransferase [Clostridium sticklandii] Identities = 92/169 (54%), Positives = 125/169 (73%) Query: 9 KESIAIVKEQDPAARSSLEVILTYPGIKALAAHRLSHFLWNHNFKLLARMHSQFWRFWTQ 68 KE+I + +E+DPAA+ ++ +++ PGI A+ HR++H L+N +AR+ SQ RF T Sbjct: 20 KETIEVAREKDPAAKGAINILVNTPGIHAIMFHRVAHSLYNRKHFFIARLISQISRFLTG 79 Query: 69 IEIHPGATISEGVFIDHGSGLVIGETAIVEKGAMLYHGVTLGGTGKDKGKRHPTIRKGAL 128- IEIHPGA I FIDHG G+VIGETA + ML+H VTLGGTGKDKGKRHPT+ + Sbjct: 80 IEIHPGAQIGRRFFIDHGMGVVIGETAEIGDDVMLFHQVTLGGTGKDKGKRHPTVENNVI 139- Query: 129 ISAHSQIIGPIEVGENAKVGAAAVVLADVPADVTVVGVPAKVVRVHGQK 177 ISA +++GPI +GEN+K+GA AVVL D+P + T VG+PAKVVR++G+K Sbjct: 140 ISAGVKVLGPIVIGENSKIGANAVVLHDIPKNATAVGIPAKVVRLNGEK 188 A related DNA sequence was identified in S. pyogenes <SEQ ID 541> which encodes the amino acid sequence <SEQ ID 542>. Analysis of this protein sequence reveals the following: TABLE-US-00554 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0141 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00555 Identities = 162/193 (83%), Positives = 178/193 (91%) Query: 5 MGWWKESIAIVKEQDPAARSSLEVILTYPGIKALAAHRLSHFLWNHNFKLLARMHSQFWR 64 MGWWKESIAIVK DPAAR+SLEVILTYPGIKALAAHRLSHFLW H+FKLLARMHSQFWR Sbjct: 1 MGWWKESIAIVKALDPAARNSLEVILTYPGIKALAAHRLSHFLWRHHFKLLARMHSQFWR 60 Query: 65 FWTQIEIHPGATISEGVFIDHGSGLVIGETAIVEKGAMLYHGVTLGGTGKDKGKRHPTIR 124- FWTQIEIHPGA I+ GVFIDHG+GLVIGETAIVEKG MLYHGVTLGGTGKD GKRHPT+R Sbjct: 61 FWTQIEIHPGAQIAPGVFIDHGAGLVIGETAIVEKGVMLYHGVTLGGTGKDCGKRHPTVR 120- Query: 125 KGALISAHSQIIGPIEVGENAKVGAAAVVLADVPADVTVVGVPAKVVRVHGQKDDLQIRS 18- 4 +GALISAH+Q+IGPI++G NAKVGAAAVVL+DVP DVTVVGVPAK+VRVHGQKD+ QI+S Sbjct: 121 QGALISAHAQVIGPIDIGANAKVGAAAVVLSDVPEDVTVVGVPAKIVRVHGQKDNRQIQS 18- 0 Query: 185 IEHDREESYYSSK 197 ++ RE SY SK Sbjct: 181 LQKQREVSYQLSK 193 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 163 A DNA sequence (GBSx0169) was identified in S. agalactiae <SEQ ID 543> which encodes the amino acid sequence <SEQ ID 544>. Analysis of this protein sequence reveals the following: TABLE-US-00556 Possible site: 29 >>> May be a lipoprotein INTEGRAL Likelihood = -5.89 Transmembrane 32-48 (29-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.3357 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 164 A DNA sequence (GBSx0170) was identified in S. agalactiae <SEQ ID 545> which encodes the amino acid sequence <SEQ ID 546>. This protein is predicted to be cysteinyl-tRNA synthetase (cysS). Analysis of this protein sequence reveals the following: TABLE-US-00557 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2227 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00558 >GP: CAB11870 GB: Z99104 cysteinyl-tRNA synthetase [Bacillus subtilis] Identities = 246/465 (52%), Positives = 322/465 (68%), Gaps = 23/465 (4%) Query: 2 IKIYDTMTRSLQDFIPLNEGKVNMYVCGPTVYNYIHIGNARSVVAFDTIRRYFEYCGYQV 61 I +Y+T+TR + F+PL EGKV MYVCGPTVYNYIHIGNAR + +DT+R Y EY GY V Sbjct: 3 ITLYNTLTRQKETFVPLEEGKVKMYVCGPTVYNYIHIGNARPAIVYDTVRNYLEYKGYDV 62 Query: 62 NYISNFTDVDDKIIKGAAEAGMDTKSFSDKFISAFMEDVAALGVKPATKNPRVIDYMDEI 121- Y+SNFTDVDDK+IK A E G D + S++FI A+ EDV ALG + A +PRV++ MD I Sbjct: 63 QYVSNFTDVDDKLIKAANELGEDVPTISERFIKAYFEDVGALGCRKADLHPRVMENMDAI 122- Query: 122 IDFVKVLVDKEFAYEANGDVYFRVSKSHHYAKLANKTLEDLEIGASGRVDGEGEIKENPL 18- 1 I+FV LV K +AYE+ GDVYF+ Y KL+ +++++L GA RV GE KE+ L Sbjct: 123 IEFVDQLVKKGYAYESEGDVYFKTRAFEGYGKLSQQSIDELRSGARIRV---GEKKEDAL 17- 9 Query: 182 DFALWKSAKSGEVSWESPWGKGRPGWHIECSVMATEILGDTIDIHGGGADLEFPHHTNEI 24- 1 DFALWK+AK GE+SW+SPWGKGRPGWHIECS M + LGD IDIH GG DL FPHH NEI Sbjct: 180 DFALWKAAKEGEISWDSPWGKGRPGWHIECSAMVKKYLGDQIDIHAGGQDLTFPHHENEI 23- 9 Query: 242 AQSEAKTGKTFANYWMHNGFVNVDNEKMSKSLGNFITVHDMLKSVDGQVIRFFLATQQYR 30- 1 AQSEA TGKTFA YW+HNG++N+DNEKMSKSLGNF+ VHD++K D Q++RFF+ + YR Sbjct: 240 AQSEALTGKTFAKYWLHNGYINIDNEKMSKSLGNFVLVHDIIKQHDPQLLRFFMLSVHYR 29- 9 Query: 302 KPVNFTEKAVHDAEVNLKYLKNTF-----------NLPIQENANDEELEQFVKAFQGAMD 35- 0 P+N++E+ + + + LK + NL ++ E++E+ KAF+ MD Sbjct: 300 HPINYSEELLENTKSAFSRLKTAYSNLQHRLNSSTNLTEDDDQWLEKVEEHRKAFEEEMD 35- 9 Query: 351 DDFNTANGITVIFEMAKWIN--------SGHYTSRVKETFAELLEIFGI-VFQEEVLDAD 40- 1 DDFNTAN I+V+F++AK N + H + E F ++ + G + ++E+LD + Sbjct: 360 DDFNTANAISVLFDLAKHANYYLQKDHTADHVITAFIEMFDRIVSVLGFSLGEQELLDQE 41- 9 Query: 402 IESLIEQRQEARANRDFATADRIRDELAKQGIKLLDTKDGVRWTR 446 IE LIE+R EAR NRDFA +D+IRD+L I L DT G RW R Sbjct: 420 IEDLIEKRNEARRNRDFALSDQIRDQLKSMNIILEDTAQGTRWKR 464 A related DNA sequence was identified in S. pyogenes <SEQ ID 547> which encodes the amino acid sequence <SEQ ID 548>. Analysis of this protein sequence reveals the following: TABLE-US-00559 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1765(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00560 Identities = 357/447 (79%), Positives = 401/447 (88%) Query: 1 MIKIYDTMTRSLQDFIPLNEGKVNMYVCGPTVYNYIHIGNARSVVAFDTIRRYFEYCGYQ 60 MIKIYDTMTRSL+ F+PL E VN+YVCGPTVYNYIHIGNARS VAFDTIRRYFEY GYQ Sbjct: 1 MIKIYDTMTRSLRKFVPLTENTVNIYVCGPTVYNYIHIGNARSAVAFDTIRRYFEYTGYQ 60 Query: 61 VNYISNFTDVDDKIIKGAAEAGMDTKSFSDKFISAFMEDVAALGVKPATKNPRVIDYMDE 120- VNYISNFTDVDDKIIK A +AG+ K SD+FI+AF+ED ALGVKPAT+NPRV+DY+ E Sbjct: 61 VNYISNFTDVDDKIIKAATQAGVSPKELSDRFIAAFIEDTKALGVKPATQNPRVMDYIAE 120- Query: 121 IIDFVKVLVDKEFAYEANGDVYFRVSKSHHYAKLANKTLEDLEIGASGRVDGEGEIKENP 18- 0 II FV+ L++K+FAYEA+GDVYFRV KS HYAKLANKTL +LE+GASGR D E +KENP Sbjct: 121 IISFVESLIEKDFAYEADGDVYFRVEKSEHYAKLANKTLSELEVGASGRTDAETALKENP 18- 0 Query: 181 LDFALWKSAKSGEVSWESPWGKGRPGWHIECSVMATEILGDTIDIHGGGADLEFPHHTNE 24- 0 LDFALWKSAK+GEVSW+SPWG GRPGWHIECSVMATEILGDTIDIHGGGADLEFPHHTNE Sbjct: 181 LDFALWKSAKAGEVSWDSPWGFGRPGWHIECSVMATEILGDTIDIHGGGADLEFPHHTNE 24- 0 Query: 241 IAQSEAKTGKTFANYWMHNGFVNVDNEKMSKSLGNFITVHDMLKSVDGQVIRFFLATQQY 30- 0 IAQSEAKTGKTFANYWMHNGFV VDNEKMSKSLGNF+TVHDML++VDGQV+RFFLATQQY Sbjct: 241 IAQSEAKTGKTFANYWMHNGFVTVDNEKMSKSLGNFVTVHDMLQTVDGQVLRFFLATQQY 30- 0 Query: 301 RKPVNFTEKAVHDAEVNLKYLKNTFNLPIQENANDEELEQFVKAFQGAMDDDFNTANGIT 36- 0 RKP+NFTEK +HDAE+NLKYLKNT P+ E A+++EL+QFV AFQ AMDDDFNTANGIT Sbjct: 301 RKPINFTEKTIHDAEINLKYLKNTLQQPLTETADEQELKQFVIAFQDAMDDDFNTANGIT 36- 0 Query: 361 VIFEMAKWINSGHYTSRVKETFAELLEIFGIVFQEEVLDADIESLIEQRQEARANRDFAT 42- 0 V+F+MAKWINSG YT VK F ++L +FGI+F+EEVL+ DIE+LI +RQEARANRDFAT Sbjct: 361 VVFDMAKWINSGSYTEPVKSAFEKMLAVFGIIFEEEVLEVDIEALIAKRQEARANRDFAT 42- 0 Query: 421 ADRIRDELAKQGIKLLDTKDGVRWTRD 447 AD IRD+LA QGIKLLDTKDGVRW RD Sbjct: 421 ADAIRDQLAVQGIKLLDTKDGVRWLRD 447 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 165 A DNA sequence (GBSx0171) was identified in S. agalactiae <SEQ ID 549> which encodes the amino acid sequence <SEQ ID 550>. Analysis of this protein sequence reveals the following: TABLE-US-00561 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0259(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9505> which encodes amino acid sequence <SEQ ID 9506> was also identified. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-00562 >GP: CAB11871 GB: Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 58/122 (47%), Positives = 87/122 (70%) Query: 3 DVRLINGIALAFEGDAVYSLYIRRHLIMQGFTKPNQLHRKATQYVSANAQALLINAMLEE 62 D + +NG+ALA+ GDA++ +Y+R HL+ QGFTKPN LH+K+++ VSA +QA ++ + + Sbjct: 9 DSKQLNGLALAYIGDAIFEVYVRHHLLKQGFTKPNDLHKKSSRIVSAKSQAEILFFLQNQ 68 Query: 63 NILTDEEQLIYKRGRNANSHTKAKNADIITYRMSTGFEALMGYLDMTGQIKRLETLIQWC 122- + T+EE+ + KRGRNA S T KN D+ TYR ST FEAL+GYL + + +RL L+ Sbjct: 69 SFFTEEEEAVLKRGRNAKSGTTPKNTDVQTYRYSTAFEALLGYLFLEKKEERLSQLVAEA 128- Query: 123 IE 124 I+ Sbjct: 129 IQ 130 A related DNA sequence was identified in S. pyogenes <SEQ ID 551> which encodes the amino acid sequence <SEQ ID 552>. Analysis of this protein sequence reveals the following: TABLE-US-00563 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00564 Identities = 99/127 (77%), Positives = 111/127 (86%) Query: 2 IDVRLINGIALAFEGDAVYSLYIRRHLIMQGFTKPNQLHRKATQYVSANAQALLINAMLE 61 +DV LINGIALAFEGDAVYS Y+RRHLI QG TKP+QLHR AT+YVSA AQA LI AMLE Sbjct: 5 VDVNLINGIALAFEGDAVYSYYVRRHLIFQGKTKPSQLHRLATRYVSAKAQANLIQAMLE 64 Query: 62 ENILTDEEQLIYKRGRNANSHTKAKNADIITYRMSTGFEALMGYLDMTGQIKRLETLIQW 121- +LT++E+ IYKRGRN NSHTKAKNADIITYRMSTGFEA+MGYLDM GQ +RLE LI+W Sbjct: 65 AQLLTEKEEDIYKRGRNTNSHTKAKNADIITYRMSTGFEAIMGYLDMMGQKERLEELIRW 124- Query: 122 CIETIEK 128 CIE +EK Sbjct: 125 CIEYVEK 131 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 166 A DNA sequence (GBSx0172) was identified in S. agalactiae <SEQ ID 553> which encodes the amino acid sequence <SEQ ID 554>. This protein is predicted to be spoU rRNA methylase family protein. Analysis of this protein sequence reveals the following: TABLE-US-00565 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1478 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00566 >GP: CAB11872 GB: Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 113/244 (46%), Positives = 163/244 (66%), Gaps = 6/244 (2%) Query: 11 ESSDLVYGLHAVTESLRANTG-NKLYLQDDLRGKNVDKVKALATEKKVSISWTPKKTLSD 69 - + D V G +AV E+L+++ KL++ ++ +V LA ++ ++I + P+K L Sbjct: 3 QQHDYVIGKNAVIETLKSDRKLYKLWMAENTVKGQAQQVIELAKKQGITIQYVPRKKLDQ 62 Query: 70 MTNGGVHQGFVLKVSEFAYADLSEIMTKAENE-ENPLILILDGLTDPHNLGSILRTADAT 128- M G HQG V +V+ + YA+L ++ AE + E P LILD L DPHNLGSI+RTADA Sbjct: 63 MVTGQ-HQGVVAQVAAYEYAELDDLYKAAEEKNEQPFFLILDELEDPHNLGSIMRTADAV 121- Query: 129 NVTGIIIPKHRSVGVTPVVSKTSTGAVEHVPIARVTNLSQTLDTLKDKEFWIFGTDMNGT 18- 8 GI+IPK R+VG+T V+K STGA+EH+P+ARVTNL++TL+ +K++ W+ GTD + Sbjct: 122 GAHGIVIPKRRAVGLTTTVAKASTGAIEHIPVARVTNLARTLEEMKERGIWVVGTDASAR 18- 1 Query: 189 PSHKWNTKGK--LALVIGNEGKGISHNIKKQVDEMITIPMNGHVQSLNASVAAAILMYEV 24- 6 + N G LALVIG+EGKG+ +K++ D +I +PM G V SLNASVAA +LMYEV Sbjct: 182 EDFR-NMDGNMPLALVIGSEGKGMGRLVKEKCDFLIKLPMAGKVTSLNASVAAGLLMYEV 24- 0 Query: 247 FRNR 250 +R R Sbjct: 241 YRKR 244 A related DNA sequence was identified in S. pyogenes <SEQ ID 555> which encodes the amino acid sequence <SEQ ID 556>. Analysis of this protein sequence reveals the following: TABLE-US-00567 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1037 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00568 Identities = 206/248 (83%), Positives = 225/248 (90%), Gaps = 1/248 (0%) Query: 3 MKDKQFKEESSDLVYGLHAVTESLRANTGNKLYLQDDLRGKNVDKVKALATEKKVSISWT 62 M+DK E++D+VYG+HAVTESL+ANTGNKLY+Q+DLRGK VD +K+LAT+KKV+ISWT Sbjct: 10 MEDKD-TIETNDIVYGVHAVTESLQANTGNKLYIQEDLRGKKVDNIKSLATQKKVAISWT 68 Query: 63 PKKTLSDMTNGGVHQGFVLKVSEFAYADLSEIMTKAENEENPLILILDGLTDPHNLGSIL 122- PKKTLS MT+G VHQGFVL+VS FAY D+ EI+ AE E NPLILILDGLTDPHNLGSIL Sbjct: 69 PKKTLSQMTDGAVHQGFVLRVSAFAYTDVDEILEIAEQEANPLILILDGLTDPHNLGSIL 128- Query: 123 RTADATNVTGIIIPKHRSVGVTPVVSKTSTGAVEHVPIARVTNLSQTLDTLKDKEFWIFG 18- 2 RTADATNV G+IIPKHRSVGVTPVVSKTSTGAVEH+PIARVTNLSQTLD LK + FWIFG Sbjct: 129 RTADATNVCGVIIPKHRSVGVTPVVSKTSTGAVEHIPIARVTNLSQTLDKLKARGFWIFG 18- 8 Query: 183 TDMNGTPSHKWNTKGKLALVIGNEGKGISHNIKKQVDEMITIPMNGHVQSLNASVAAAIL 24- 2 TDMNGTPS WNT GKLALVIGNEGKGIS NIKKQVDEMITIPMNGHVQSLNASVAAAIL Sbjct: 189 TDMNGTPSDCWNTNGKLALVIGNEGKGISTNIKKQVDEMITIPMNGHVQSLNASVAAAIL 24- 8 Query: 243 MYEVFRNR 250 MYEVFRNR Sbjct: 249 MYEVFRNR 256 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 167 A DNA sequence (GBSx0173) was identified in S. agalactiae <SEQ ID 557> which encodes the amino acid sequence <SEQ ID 558>. Analysis of this protein sequence reveals the following: TABLE-US-00569 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2187 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00570 >GP: CAB11873 GB: Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 67/147 (45%), Positives = 94/147 (63%), Gaps = 2/147 (1%) Query: 6 ILLVDGYNMIAFWKDTRQLFKSNRLEEAREVLLRKLNHYAHFEHIDIICVFDAQYVPGVR 65 ILLVDGYNMI W + L K+N EEAR+VL++K+ Y + +I VFDA V G+ Sbjct: 3 ILLVDGYNMIGAWPQLKDL-KANSFEEARDVLIQKMAEYQSYTGNRVIVVFDAHLVKGLE 61 Query: 66 QRYDQYKISVIFTEEDETADSYIERAAAELNQSVLNLVSVATSDLNEQWTIFSQGALRVS 125- ++ +++ VIFT+E+ETAD IE+ A LN ++ + VATSD EQW IF QGALR S Sbjct: 62 KKQTNHRVEVIFTKENETADERIEKLAQALN-NIATQIHVATSDYTEQWAIFGQGALRKS 120- Query: 126 ARELEQRVATVKSDLDKMSSQIDLSTP 152 AREL + V T++ +++ +I P Sbjct: 121 ARELLREVETIERRIERRVRKITSEKP 147 A related DNA sequence was identified in S. pyogenes <SEQ ID 559> which encodes the amino acid sequence <SEQ ID 560>. Analysis of this protein sequence reveals the following: TABLE-US-00571 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2465(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00572 Identities = 130/167 (77%), Positives = 149/167 (88%), Gaps = 1/167 (0%) Query: 3 KHSILLVDGYNMIAEWKDTRQLFKSNRLEEAREVLLRKLNHYAHFEHIDIICVFDAQYVP 62 K ILLVDGYNMIAFW+ TRQLFK+N+L++AR LL KLNHYAHFE+I+IICVFDAQYVP Sbjct: 2 KKRILLVDGYNMIAFWQSTRQLFKTNQLDQARNTLLTKLNHYAHFENINIICVFDAQYVP 61 Query: 63 GVRQRYDQYKISVIFTEEDETADSYIERAAAELNQSVLNLVSVATSDLNEQWTIFSQGAL 122- G+RQRYDQY ISV+FTEEDETADSYIER AAELN + +++V VATSDLNEQWTIFSQGAL Sbjct: 62 GLRQRYDQYYISVVFTEEDETADSYIERMAAELN-TAIHMVEVATSDLNEQWTIFSQGAL 120- Query: 123 RVSARELEQRVATVKSDLDKMSSQIDLSTPKLRPWNDEQLGKLKDFL 169 RV+ARELEQRV TVK+DLDKMS IDL TPKLRP++ QL +LKDF+ Sbjct: 121 RVTARELEQRVHTVKADLDKMSRDIDLKTPKLRPFDQGQLIQLKDFM 167 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 168 A DNA sequence (GBSx0174) was identified in S. agalactiae <SEQ ID 561> which encodes the amino acid sequence <SEQ ID 562>. Analysis of this protein sequence reveals the following: TABLE-US-00573 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4889(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00574 >GP: CAB12951 GB: Z99109 yits [Bacillus subtilis] Identities = 100/284 (35%), Positives = 157/284 (55%), Gaps = 6/284 (2%) Query: 1 MTFKILTDSTSDLDEKWAQEHNVDIIGLTIELDGKTYETVGDEKITSDFLLERMQEGAKP 60 MT ++ DS +DL + +E + I L +L K +E I +D + E MQ G P Sbjct: 1 MTVHLIADSATDLPRSYFEEKGIGFIPLRVSLGDKEFEDA--VTIHADQIFEAMQNGETP 58 Query: 61 TTSQINVGQFEEVFSTYAENDHALLYLALSSHLSGTYQSATIAREMVLDKYPDAQIEIVD 120- TSQ + + VF YAE LY+A SS LSGTYQ+A + V +++PD + ++D Sbjct: 59 KTSQASPQTIKNVFLQYAETGDPALYIAFSSGLSGTYQTAVMIANEVKEEFPDFDLRVID 118- Query: 121 TMAASCGEGVLAMLATKERQEGKSLEEVKQKIESLLPKLNTYFLVDDLNHLMRSGRLSKG 18- 0 + AS G G+ A G +++E++ +++ +L F VDDL +L R GR+SK Sbjct: 119 SKCASLGYGLAVRHAADLCINGNTIQEIETSVKNFCSQLEHIFTVDDLTYLARGGRISKT 17- 8 Query: 181 AAIIGSVAKIKPLLKLDSEGKLVPFAKTRGRKKGIK---EIVTQATKTLSYSTLIIAYSG 23- 7 +A +G + IKPLL+++ +GKLVP K RG+KK K E++ + S T+ I+Y+ Sbjct: 179 SAFVGGLLNIKPLLQME-DGKLVPLEKIRGQKKLFKRIIELMKERGDDWSNQTVGISYAA 23- 7 Query: 238 EKDSAQVMKEQLLADERIEEVIIRPLGPVISAHVGSGALALFSL 281 K+ A MK + + +E+I+ P+ I +H G G LA+F L Sbjct: 238 NKEKATDMKHLIEEAFKPKEIIMHPISSAIGSHAGPGTLAIFFL 281 A related DNA sequence was identified in S. pyogenes <SEQ ID 563> which encodes the amino acid sequence <SEQ ID 564>. Analysis of this protein sequence reveals the following: TABLE-US-00575 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3247(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00576 Identities = 167/286 (58%), Positives = 227/286 (78%) Query: 1 MTFKILTDSTSDLDEKWAQEHNVDIIGLTIELDGKTYETVGDEKITSDFLLERMQEGAKP 60 MTF I+TDST+DL++ WA++H++ +IGLTI DG+ YETVG +I+SD+LL++M+ G+ P Sbjct: 1 MTFTIMTDSTADLNQTWAEDHDIVLIGLTILCDGEVYETVGPNRISSDYLLKKMKAGSHP 60 Query: 61 TTSQINVGQFEEVFSTYAENDHALLYLALSSHLSGTYQSATIAREMVLDKYPDAQIEIVD 120- TSQINVG+FE+VF +A N+ ALLYLA SS LSGTYQSA +AR++V + YPDA IEIVD Sbjct: 61 QTSQINVGEFEKVFREHARNNKALLYLAFSSVLSGTYQSALMARDLVREDYPDAVIEIVD 120- Query: 121 TMAASCGEGVLAMLATKERQEGKSLEEVKQKIESLLPKLNTYFLVDDLNHLMRSGRLSKG 18- 0 T+AA+ GEG L +LA + R GK+L E K +E+++P+L TYFLVDDL HLMR GRLSKG Sbjct: 121 TLAAAGGEGYLTILAAEARDSGKNLLETKDIVEAVIPRLRTYFLVDDLFHLMRGGRLSKG 18- 0 Query: 181 AAIIGSVAKIKPLLKLDSEGKLVPFAKTRGRKKGIKEIVTQATKTLSYSTLIIAYSGEKD 24- 0 +A +GS+A IKPLL +D EGKLVP AK RGR+K IKE+V Q K ++ ST+I++Y+ ++ Sbjct: 181 SAFLGSLASIKPLLWIDEEGKLVPIAKIRGRQKAIKEMVAQVEKDIADSTVIVSYTSDQG 24- 0 Query: 241 SAQVMKEQLLADERIEEVIIRPLGPVISAHVGSGALALFSLGEENR 286 SA+ ++E+LLA E I +V++ PLGPVISAHVG LA+F +G+ +R Sbjct: 241 SAEKLREELLAHENISDVLMMPLGPVISAHVGPNTLAVFVIGQNSR 286 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 169 A DNA sequence (GBSx0175) was identified in S. agalactiae <SEQ ID 565> which encodes the amino acid sequence <SEQ ID 566>. Analysis of this protein sequence reveals the following: TABLE-US-00577 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.76 Transmembrane 43-59 (40-62) ----- Final Results ----- bacterial membrane --- Certainty = 0.4503(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 170 A DNA sequence (GBSx0176) was identified in S. agalactiae <SEQ ID 567> which encodes the amino acid sequence <SEQ ID 568>. This protein is predicted to be ribosomal protein L13 (rplM). Analysis of this protein sequence reveals the following: TABLE-US-00578 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3426(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9507> which encodes amino acid sequence <SEQ ID 9508> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00579 >GP: BAB03887 GB: AP001507 ribosomal protein L13 [Bacillus halodurans] Identities = 89/144 (61%), Positives = 113/144 (77%) Query: 36 KTTFMAKPGQVERKWYVVDAADVPLGRLSAVVASVLRGKNKPTFTPHTDTGDFVIVINAE 95 - +TT+MAKP +VERKWYVVDA LGRL++ VAS+LRGK+KPT+TPH DTGD VI+INAE Sbjct: 2 RTTYMAKPNEVERKWYVVDAEGQTLGRLASEVASILRGKHKPTYTPHVDTGDHVIIINAE 61 Query: 96 KVKLTGKKASDKIYYTHSMYPGGLKQISAGELRSKNAVRLIEKSVKGMLPHNTLGRAQGM 155- K+ LTG K DKIYY HS +PGGLK+ A ++R+ +++E ++KGMLP NTLGR QGM Sbjct: 62 KIHLTGNKLQDKIYYRHSGHPGGLKETRAADMRANKPEKMLELAIKGMLPKNTLGRKQGM 121- Query: 156 KLKVFVGGEHTHAAQQPEVLDISG 179 KL V+ G EH H AQ+PEV ++ G Sbjct: 122 KLHVYAGSEHKHQAQKPEVYELRG 145 A related DNA sequence was identified in S. pyogenes <SEQ ID 569> which encodes the amino acid sequence <SEQ ID 570>. Analysis of this protein sequence reveals the following: TABLE-US-00580 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4249(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00581 Identities = 167/184 (90%), Positives = 171/184 (92%), Gaps = 4/184 (2%) Query: 1 MFTPFVRPRNLSNTLVDRNIHT--CKQ-KRIRIGEIMNKTTFMAKPGQVERKWYVVDAAD 57 +FTPF RPRNL NT D H CKQ RIRIGEIMNKTTFMAKPGQVERKWYVVDAAD Sbjct: 1 LFTPFERPRNLPNTF-DGTEHPSPCKQILRIRIGEIMNKTTFMAKPGQVERKWYVVDAAD 59 Query: 58 VPLGRLSAVVASVLRGKNKPTFTPHTDTGDFVIVINAEKVKLTGKKASDKIYYTHSMYPG 117- VPLGRLSAVVASVLRGKNKPTFTPHTDTGDFVIVINAEKVKLTGKKA+DK+YYTHSMYPG Sbjct: 60 VPLGRLSAVVASVLRGKNKPTFTPHTDTGDFVIVINAEKVKLTGKKATDKVYYTHSMYPG 119- Query: 118 GLKQISAGELRSKNAVRLIEKSVKGMLPHNTLGRAQGMKLKVFVGGEHTHAAQQPEVLDI 17- 7 GLK I+AGELRSKNAVRLIEKSVKGMLPHNTLGRAQGMKLKVFVGGEHTHAAQQPEVLDI Sbjct: 120 GLKSITAGELRSKNAVRLIEKSVKGMLPHNTLGRAQGMKLKVFVGGEHTHAAQQPEVLDI 17- 9 Query: 178 SGLI 181 SGLI Sbjct: 180 SGLI 183 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 171 A DNA sequence (GBSx0177) was identified in S. agalactiae <SEQ ID 571> which encodes the amino acid sequence <SEQ ID 572>. This protein is predicted to be 30S ribosomal protein S9 (rpsI). Analysis of this protein sequence reveals the following: TABLE-US-00582 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1761(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00583 >GP: CAB11926 GB: Z99104 ribosomal protein S9 [Bacillus subtilis] Identities = 88/130 (67%), Positives = 105/130 (80%) Query: 1 MAQAQYAGTGRRKNAVARVRLVPGTGKITINKKDVEEYIPHADLRLVINQPFAVTSTQGS 60 MAQ QY GTGRRK++VARVRLVPG G+I +N +++ E+IP A L I QP +T T G+ Sbjct: 1 MAQVQYYGTGRRKSSVARVRLVPGEGRIVVNNREISEHIPSAALIEDIKQPLTLTETAGT 60 Query: 61 YDVFVNVVGGGYAGQSGAIRHGISRALLEVDPDFRDSLKRAGLLTRDARMVERKKPGLKK 120- YDV VNV GGG +GQ+GAIRHGI+RALLE DP++R +LKRAGLLTRDARM ERKK GLK Sbjct: 61 YDVLVNVHGGGLSGQAGAIRHGIARALLEADPEYRTTLKRAGLLTRDARMKERKKYGLKG 120- Query: 121 ARKASQFSKR 130 AR+A QFSKR Sbjct: 121 ARRAPQFSKR 130 A related DNA sequence was identified in S. pyogenes <SEQ ID 573> which encodes the amino acid sequence <SEQ ID 574>. Analysis of this protein sequence reveals the following: TABLE-US-00584 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1865(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00585 Identities = 124/130 (95%), Positives = 129/130 (98%) Query: 1 MAQAQYAGTGRRKNAVARVRLVPGTGKITINKKDVEEYIPHADLRLVINQPFAVTSTQGS 60 MAQAQYAGTGRRKNAVARVRLVPGTGKIT+NKKDVEEYIPHADLRL+INQPFAVTST+GS Sbjct: 1 MAQAQYAGTGRRKNAVARVRLVPGTGKITVNKKDVEEYIPHADLRLIINQPFAVTSTEGS 60 Query: 61 YDVFVNVVGGGYAGQSGAIRHGISRALLEVDPDFRDSLKRAGLLTRDARMVERKKPGLKK 120- YDVFVNVVGGGY GQSGAIRHGI+RALL+VDPDFRDSLKRAGLLTRDARMVERKKPGLKK Sbjct: 61 YDVFVNVVGGGYGGQSGAIRHGIARALLQVDPDFRDSLKRAGLLTRDARMVERKKPGLKK 120- Query: 121 ARKASQFSKR 130 ARKASQFSKR Sbjct: 121 ARKASQFSKR 130 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 172 A DNA sequence (GBSx0078) was identified in S. agalactiae <SEQ ID 575> which encodes the amino acid sequence <SEQ ID 576>. This protein is predicted to be recombinase (b1345). Analysis of this protein sequence reveals the following:

TABLE-US-00586 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1939(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00587 >GP: AAG29618 GB: AF217235 integrase-like protein [Staphylococcus aureus] Identities = 127/386 (32%), Positives = 205/386 (52%), Gaps = 18/386 (4%) Query: 3 IHKYPSKKAKNGYLYFVKIYMVKD---SQRADHIKRGFRTRKEAKDYEARLIYLKASGKL 59 I KY K Y++ Y+ D ++ +RGF+T +EAK EA+L + Sbjct: 2 IKKYKKKDGSTAYMFVA--YLGTDPITGKQKRTTRRGFKTEREAKIAEAKL---QTEVSQ 56 Query: 60 EEFIKPTHKTYNEIFEKWYQAYQDMVEPTTASRTLDMFRLHILPVMGDLPISKISPLDCQ 119- F+ T+ E++E W + YQ+ V +T R L +F IL D+PI KI+ CQ Sbjct: 57 NGFLNNDITTFKEVYELWLEQYQNTVRESTYQRVLTLFDTAILEHFQDVPIKKITVPYCQ 116- Query: 120 NFITDKAKTFKNIKQIKSYTGKVFDFAIKMKLLKHNPMAEIIMPKRKKTRIE---NYWTV 17- 6 I K + +IK I+ YT VF +A+ +K++ NP A P++K+ + + Y++ Sbjct: 117 KVINKWNKKYSDIKAIRIYTSNVFKYAVSLKIIVDNPFAHTKAPRKKEAQQDASTKYYSS 17- 6 Query: 177 QELQEFLAIVLQEEPYKHYALFRLLAYSGLRKGELYALKWADIDFQTETLSVDKSLGR-L 23- 5 EL++FL V E+ +YA+FR LA++G R+GEL AL W DIDF +T+S++K+ R Sbjct: 177 DELKQFLTFV--EDDPLYYAIFRTLAFTGFRRGELMALTWNDIDFTKQTISINKTCARGA 23- 4 Query: 236 DGQAIEKGTKNDFSVRKIKLDSETISILQEWKSISQKEKAQLAVAPLSIEQDFLFTYCTR 29- 5 + + + + K S R I +D +T S+L+ W++ + E + S + +FT Sbjct: 235 NYKLVIQEPKTKSSHRTISIDDKTASVLKSWRTHQRVESLKYG-HNTSDKHQHVFTTVRD 29- 3 Query: 296 SGSIEPLHADYINNVLSRIIRKHGLKKISPHGFRHTHATLMIEIGVDPVNTAKRLGHASS 35- 5 + +PL+ ++ N L I K+ K+I HGFRHTH +L+ E G+ RLGH Sbjct: 294 N---KPLYPEHCNKALDLICEKNSFKRIKVHGFRHTHCSLLFEAGLSIQEVQDRLGHGDI 35- 0 Query: 356 QMTLDTYSHSTTTGEDRSVKQFADYL 381 + T+D Y+H T D+ +FA Y+ Sbjct: 351 KTTMDIYAHVTEKQRDQVADKFAKYI 376 A related DNA sequence was identified in S. pyogenes <SEQ ID 577> which encodes the amino acid sequence <SEQ ID 578>. Analysis of this protein sequence reveals the following: TABLE-US-00588 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3445(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00589 Identities = 109/386 (28%), Positives = 185/386 (47%), Gaps = 28/386 (7%) Query: 3 IHKYPSKKAKNGYL-YFVKIYMVKDSQRADHIKRGF--RTRKEA--KDYEARLIYLKASG 57 I K K KNG + Y IY+ D +K RTRKE K A+ +L Sbjct: 6 IMKITEHKKKNGTIVYRASIYLGIDQMTGKRVKTSITGRTRKEVNQKAKHAQFDFLSNGS 65 Query: 58 KLEEFIKPTHKTYNEIFEKWYQAYQDMVEPTTASRTLDMFRLHILPVMGDLPISKISPLD 117- ++ K KT+ E+ W + Y+ V+P T T+ HI+P +G++ + KI+ D Sbjct: 66 TIKR--KVVIKTFKELSHLWLETYKLTVKPQTYDATVTRLNRHIMPTLGNMKVDKITASD 123- Query: 118 CQNFITDKAKTFKNIKQIKSYTGKVFDFAIKMKLLKHNPMAEIIMPKRK---KTRIENYW 17- 4 Q I +K + N ++S KV + + L+ +N +II+P+++ K +++ + Sbjct: 124 IQMLINRLSKYYVNYTAVRSVIRKVLQQGVLLGLIDYNSARDIILPRKQPNAKKKVK-FI 18- 2 Query: 175 TVQELQEFLAIVLQEEPYKHY------ALFRLLAYSGLRKGELYALKWADIDFQTETLSV 22- 8 +L+ FL L+ +K Y L++LL +GLR GE AL+W DID + T+++ Sbjct: 183 DPSDLKSFLE-HLETSQHKRYNLYFDAVLYQLLLSTGLRIGEACALEWGDIDLENGTIAI 24- 1 Query: 229 DKSLGRLDGQAIEKGTKNDFSVRKIKLDSETISILQEWKSISQKEKAQLAVAPLSIEQDF 28- 8 +K+ + K R I +D +T+ L+ + Q + QL + + Sbjct: 242 NKTYNK--NLKFLSTAKTQSGNRVISVDKKTLRSLK----LYQMRQRQLFNEVGARVSEV 29- 5 Query: 289 LFTYCTRSGSIEPLHADYINNVLSRIIRKHGLKKISPHGFRHTHATLMIEIGVDPVNTAK 34- 8 +F TR + +A + L ++ G+++ + H FRHTHA+L++ G+ Sbjct: 296 VFATPTR----KYFNASVRQSALDTRCKEAGIERFTFHAFRHTHASLLLNAGISYKELQY 35- 1 Query: 349 RLGHASSQMTLDTYSHSTTTGEDRSV 374 RLGHA+ MTLDTY H + E +V Sbjct: 352 RLGHANISMTLDTYGHLSKGKEKEAV 377 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 173 A DNA sequence (GBSx0179) was identified in S. agalactiae <SEQ ID 579> which encodes the amino acid sequence <SEQ ID 580>. Analysis of this protein sequence reveals the following: TABLE-US-00590 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2477(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00591 >GP: AAF63067 GB: AF158600 putative DNA binding protein [Streptococcus thermophilus bacteriophage Sfill] Identities = 32/70 (45%), Positives = 46/70 (65%), Gaps = 3/70 (4%) Query: 3 NRLKELRKDKGLTQADLAKVINTNQSQYGKYENGKTSLSIENSKILADFFGVSIPYLLGL 62 NRL LR+ + +T+ +LA+ I ++ K E+G + +S +K LADFFGVS+ YLLGL Sbjct: 2 NRLYLLRESRKITRVELAEKIGVSKLTVLKLEHGTSKISRREAKKLADFFGVSVGYLLGL 61 Query: 63 D---NNSKIA 69 D N+S IA Sbjct: 62 DTTENDSLIA 71 A related DNA sequence was identified in S. pyogenes <SEQ ID 581> which encodes the amino acid sequence <SEQ ID 582>. Analysis of this protein sequence reveals the following: TABLE-US-00592 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0680(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00593 Identities = 21/61 (34%), Positives = 34/61 (55%) Query: 1 MYNRLKELRKDKGLTQADLAKVINTNQSQYGKYENGKTSLSIENSKILADFFGVSIPYLL 60 MY R++ LR+D TQ +A +++ + + Y K E G+ +L + + +VSI YLL Sbjct: 1 MYPRIRNLREDNDFTQKFVANLLSFSHANYAKIERGEVALMADVLVQFYKLYNVSIDYLL 60 Query: 61 G 61 G Sbjct: 61 G 61 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 174 A DNA sequence (GBSx0180) was identified in S. agalactiae <SEQ ID 583> which encodes the amino acid sequence <SEQ ID 584>. Analysis of this protein sequence reveals the following: TABLE-US-00594 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5278(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 175 A DNA sequence (GBSx0181) was identified in S. agalactiae <SEQ ID 585> which encodes the amino acid sequence <SEQ ID 586>. Analysis of this protein sequence reveals the following: TABLE-US-00595 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3762(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 176 A DNA sequence (GBSx0182) was identified in S. agalactiae <SEQ ID 587> which encodes the amino acid sequence <SEQ ID 588>. Analysis of this protein sequence reveals the following: TABLE-US-00596 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.66 Transmembrane 40-56 (33-65) INTEGRAL Likelihood = -5.79 Transmembrane 62-78 (59-81) ----- Final Results ----- bacterial membrane --- Certainty = 0.4864(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8505> and protein <SEQ ID 8506> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00597 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: -16.96 GvH: Signal Score (-7.5): -2.95 Possible site: 57 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -9.66 threshold: 0.0 INTEGRAL Likelihood = -9.66 Transmembrane 33-49 (26-58) INTEGRAL Likelihood = -5.79 Transmembrane 55-71 (52-74) PERIPHERAL Likelihood = 10.87 14 modified ALOM score: 2.43 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4864(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 177 A DNA sequence (GBSx0183) was identified in S. agalactiae <SEQ ID 589> which encodes the amino acid sequence <SEQ ID 590>. Analysis of this protein sequence reveals the following: TABLE-US-00598 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3276 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 178 A DNA sequence (GBSx0184) was identified in S. agalactiae <SEQ ID 591> which encodes the amino acid sequence <SEQ ID 592>. Analysis of this protein sequence reveals the following: TABLE-US-00599 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3482 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9509> which encodes amino acid sequence <SEQ ID 9510> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00600 >GP: CAA30291 GB: X07371 RepM protein (AA 1-314) [Staphylococcus aureus] Identities = 89/283 (31%), Positives = 145/283 (50%), Gaps = 26/283 (9%) Query: 67 KVSLDNITMTAYIKSKKYLAMKQLIETHLAITVQTAMTDMFRATTGDGIHVVLHMNYDKQ 126- K+S D +T+ + + + I + + F+A + +++ YDK Sbjct: 42 KLSFDAMTIVGNLNKNSAKKLSDFMSLDPQIRLWDILQTKFKAKA---LQEKVYIEYDKV 98 Query: 127 KGQDRKARPFRLEFNPNKLRLVDSEII---DTIIPFLEDISISRADLAFDLFEVDCSEF- 18- 2 K R R+EFNPNKL E++ II ++ED +R DLAFD FE D S++ Sbjct: 99 KADTWDRRNMRVEFNPNKL--THDEMLWLKHNIIDYMEDDGFTRLDLAFD-FEDDLSDYY 155- Query: 183 -VLEKKGRPTATKEFRSSTGTLETKYLGAPRSEKQVRLYNKKKEQLQNGTDKDKDFASQF 24- 1 + EK + T F +TG ETKY G+ S + +R+YNKKKE+ +N D D +++ Sbjct: 156 ALSEKALKRTV---FFGTTGKAETKYFGSRDSNRFIRIYNKKKERKENA---DVDVSAE- 20- 8 Query: 242 KHWWRLEFQLRSRSIDEIFEVI-DTIIFKP--FNLKGLSIETQIYLTALIHDKNIWKKLH 29- 8 H WR+E +L+ +D D I KP L+ L + +YL L+H+++ W +LH Sbjct: 209 -HLWRVEIELKRDMVDYWNNCFNDLHILKPAWATLESLKEQAMVYL--LLHEESKWGELH 26- 5 Query: 299 RNTRARYKKILETHQTSDTDYLGLLKDLLKHERPRLENQLAYY 341 RN+R +YK+I++ + S D L+K L L+ Q+ ++ Sbjct: 266 RNSRRKYKQIIQ--EISSIDLTDLMKSTLTDNEENLQKQINFW 306 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 179 A DNA sequence (GBSx0185) was identified in S. agalactiae <SEQ ID 593> which encodes the amino acid sequence <SEQ ID 594>. Analysis of this protein sequence reveals the following: TABLE-US-00601 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.55 Transmembrane 137-153 (133-157) ----- Final Results ----- bacterial membrane --- Certainty = 0.7220 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9511> which encodes amino acid sequence <SEQ ID 9512> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8507> and protein <SEQ ID 8508> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00602 Lipop: Possible site: -1 Crend: 2 McG: Discrim Score: -16.84 GvH: Signal Score (-7.5): -5.3 Possible site: 32 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -15.55 threshold: 0.0 INTEGRAL Likelihood = -15.55 Transmembrane 137-153 (133-157) PERIPHERAL Likelihood = 10.93 60 modified ALOM score: 3.61 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.7220 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00015## SEQ ID 8508 (GBS405) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 171 (lane 4; MW 46 kDa-2 bands) and in FIG. 177 (lane 7; MW 46 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 76 (lane 5; MW 21 kDa). GBS405-GST was purified as shown in FIG. 218, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 180 A DNA sequence (GBSx0186) was identified in S. agalactiae <SEQ ID 595> which encodes the amino acid sequence <SEQ ID 596>. Analysis of this protein sequence reveals the following: TABLE-US-00603 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3406 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00604 >GP:CAA33713 GB:X15669 pre protein (AA 1-494) [Streptococcus agalactiae] Identities = 171/402 (42%), Positives = 250/402 (61%), Gaps = 46/402 (11%) Query: 1 MSYVVARMAKYKSGQLTAIYNHNERIFKNHSNKEIDVEKSHLNYELTNRDQAQNYHKQIK 60 MSY+VARM K K+G L + HNER+F+ HSNK+I+ +SHLNYELT+RD++ +Y KQIK Sbjct: 1 MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLNYELTDRDRSVSYEKQIK 60 Query: 61 EHINENRLSTRGVRKDAILCNEWIITSDKTFFDSLDEKQTREFFETAKDYFAEKYGDANI 120- +++NEN++S R +RKDA+LC+EWIITSDK FF+ LDE+QTR FFETAK+YFAE YG++NI Sbjct: 61 DYVNENKVSNRAIRKDAVLCDEWIITSDKDFFEKLDEEQTRTFFETAKNYFAENYGESNI 120- Query: 121 AYARVHLDESTPHMHLGIVPMKNGKLSSKALFGNKEKLVAIQDELPKYLNEHGFNLQRGE 18- 0 AYA VHLDESTPHMH+G+VP +NGKLSSKA+F ++E+L IQ++LP+Y+++HGF L+RG+ Sbjct: 121 AYASVHLDESTPHMHMGVVPFENGKLSSKAMF-DREELKHIQEDLPRYMSDHGFELERGK 17- 9 Query: 181 IGSKKKHLETAEFKEKQRLLDNADRKLADKHEELKALDDKISNV-NDTIA---------- 22- 9 + S+ KH AEFK ++ +L +K+ +D++ + NDT A Sbjct: 180 LNSEAKHKTVAEFKRAMADME-LKEELLEKYHAPPFVDERTGELNNDTEAFWHEKEFADM 23- 8 Query: 230 -DKESRLKEL---EAKEWDAVGDLKQYELEKQSLAESIEDIKDIELLQLDRIQKEDLVKQ 28- 5 + +S ++E E +W KQY+ E + L S + ++D D E+L+ + Sbjct: 239 FEVQSPIRETTNQEKMDWLR----KQYQEELKKLESSKKPLED------DLSHLEELLDK 28- 8 Query: 286 SFDGKLKMDKETYNRLFQTASKHASSNAELKRDLVKAQSQNNHLSRELLNHRKTAEKNIK 34- 5 +K+D E AS+ AS +L KA+ N L NH K+ E I+ Sbjct: 289 KTKEYIKIDSE--------ASERAS-------ELSKAEGYINTLE----NHSKSLEAKIE 32- 9 Query: 346 LSQENRKLKDKVKMLDEQVKILNKSLSVWKEKAKEFMPKQVY 387 + + +K K + K LN+S + K F+ K+ Y Sbjct: 330 CLESDNLQLEKQKATKLEAKALNESELRELKPKKNFLGKEHY 371 A related DNA sequence was identified in S. pyogenes <SEQ ID 597> which encodes the amino acid sequence <SEQ ID 598>. Analysis of this protein sequence reveals the following:

TABLE-US-00605 LPXTG motif: 2025-2030 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.08 Transmembrane 2034-2050 (2030-2053) INTEGRAL Likelihood = -6.05 Transmembrane 21-37 (20-39) ----- Final Results ----- bacterial membrane --- Certainty = 0.5034 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00606 >GP: AA003320 GB: AF067776 extracellular matrix binding protein [Abiotrophia defectiva] Identities = 362/1396 (25%), Positives = 591/1396 (41%), Gaps = 87/1396 (6%) Query: 636 KAEVKLREAHEATKQAIEKDPWLSPEQKKAQKEKAKARLDEGLKALKAADSLEILKVTEE 69- 5 +A+ + A +A AI+ + L+ E+K A+K K +A + L + A K T Sbjct: 636 EAKNAVNNAAKAKNTAIDNNNNLTAEEKAAEKAKVEAAKNATLAGIDQA------KTTAA 68- 9 Query: 696 AFVDKEKNPDSIPNQHKAGTADQARKQALDSLDKEVQKELESIDNDNTLTTDEKAAAKKK 75- 5 + K I + A A AL+ + ++ I LT +EK A + Sbjct: 690 RNAAQNKGTTDINAVNPVPVAKPAANAALE---QAAVNKINEISQRPDLTREEKQAFMDQ 74- 6 Query: 756 VNDAYDVARQTAMEANSYEDLTTIKDEFLS---NLPHKQGTPLKDQQSDAIAELEKKQQE 81- 2 V A D A A + + +T+ +D+ L+ NLP TP + +A+ + + Sbjct: 747 VRTARDAAMAKVASAANNQAVTSARDQGLNAVNNLP----TPAA-KYPEALGHVRQAADA 80- 1 Query: 813 IEKAIEGDKTLPRDEKEKQIADSKERLKSDTQKVKDAKNADAIKKAFEEGKVNIPQAHIP 87- 2 +AI + L +E+ + + + + KA +G I Sbjct: 802 KRQAIRDNANLTAEEQADALRQVDAAQTAAEAAINQNHTNATLAKADSDGVKAI------ 85- 5 Query: 873 GDLN---KDKEKLLAELKQKADDTEKAIDVDKTLTEDEKKEQKVKTKAELEKAKTDVKNT 92- 9 D+N + K L+Q A +AI+ + LT++EK + + L AKT V+ Sbjct: 856 NDINPQPRSKPAANQALEQVAAAKRQAINNNNQLTDEEKAQAIQQVDQALANAKTQVQAA 91- 5 Query: 930 QTREELDKKVPELKKAIEDTHVKGNLEGVKNKAIEDLKKAHTETVAKINGDDTLDKATKE 98- 9 +++ AI + + +G K +AI ++ A ++ G + L + Sbjct: 916 NDNNGVNQAKTAGTTAINNINPQGTQ---KAQAIAAIEAAEQAKRLELQGRNDLTTEERN 97- 2 Query: 990 AQVKEADKALAAGKDAITKADDADKVSTAVTEHTPKIKAAHKTGDLKKAQVDANTALDKA 10- 49 + + A KDA+ +A + V+ A +I+ + T +K DA A+D+A Sbjct: 973 NALADLTAKAQAAKDAVNQARNNTGVAGAKDNGVAQIQGINPTAVVKP---DARNAIDQA 10- 29 Query: 1050 AEKERGEINKDATLTTEDKAKQLKEVETALTKAKDNVKAAKTADAINDARDKGVATIDAV 1- 109 A + E + LT E+KA +K+V+ A AK + A + +N+A ++G A I A+ Sbjct: 1030 ARDKEAEFQANTKLTDEEKAAAIKKVQDAARDAKAAIDRAGSNGDVNNAVNQGKAAIQAI 1- 089 Query: 1110 HKAGQDLGARKSGQVAKLEEAAKATKDKISADPTLTSKEKEEQSKAVDAELKKAIEAVNA 1- 169 + K A ++ AA A K I+A+ LT +EK K V+ E KA AV+A Sbjct: 1090 KALDDSQPSAKDTAKAAIQNAADAKKAAITANNALTQEEKAAAIKQVEDEAAKAQAAVDA 1- 149 Query: 1170 ADTADKVDDALGEGVTDIKNQHKSGDSIDARREAHGKELDRVAQETKGAIEKDPTLTTEE 1- 229 + + VD A +G+ I + ++ + +D+ A + K I D TLT EE Sbjct: 1150 SRSKADVDRAKDQGLQKISDV----PAVQPPKLNAIAAVDQAATDKKAVINNDTTLTQEE 1- 205 Query: 1230 KAKQVKDVDAAKERGMAKLNEAKDADALDKAYGEGVTDIKNQHKSGDPVDARRGLHNKSI 1- 289 K ++ VD + +N+A + +G I N ++ A + ++ Sbjct: 1206 KEAAIRKVDEEAAKARQAINDATSNADVAAKQAQGTQAINNVPQT----PAAKNAAKAAV 1- 261 Query: 1290 DEVAQATKDAITADTTLTEAEKETQRGNVDKEATKAKEELAKAKDADALDKAYGDGVTSI 1- 349 ++ A A K AI D LT EK+ VD+E KA++ + A + +G +I Sbjct: 1262 EQAADAKKQAIENDPNLTRQEKDAAIAKVDQETNKARQAIDAATTNADVTAKQNEGTQAI 1- 321 Query: 1350 KNQHKSGKGLDVRKDEHKKALEAVAKRVTAEIEADPTLTPEVREQQKAEVQKELELATDK 1- 409 ++ K K + K A+ A+ + IE DP LT E ++ KA+V E A + Sbjct: 1322 NAVPQTPKA----KTDAKNAVTQAAEDKKSAIENDPNLTREEKDAAKAKVDAEATKAKNA 1- 377 Query: 1410 IAEAKDADEADKAYGDGVTAIENAHVIGKGIEARKDLAKKDLAEAAAKTKALIIEDKTLT 1- 469 I A D+ +G AI + + + +A+ D AK + +AA + K I D LT Sbjct: 1378 IDAATSNDDETAKQNEGTQAI---NAVPQTPKAKTD-AKNAVTQAADRKKDAIENDPNLT 1- 433 Query: 1470 DDQRKEQLLGVDTEYAKGIENIDAAKDAAGVDKAYSDGVRDILAQYKEGQNLNDRRNAAK 1- 529 +++ VD E K + IDAA A V ++G + I + + AK Sbjct: 1434 REEKVAAKAKVDAEAKKAKDAIDAATSNADVTAKQNEGTKAI----NDVPQTPTAKTDAK 1- 489 Query: 1530 EFLLKEADKVTKLINDDPTLTHDQKVDQINKVEQAKLDAIKSVDDAQTADAINDALGKGI 1- 589 + + AD I DP LT ++K KV+ A ++D A + + +G Sbjct: 1490 NAVTQAADAKKDAIEKDPNLTREEKDAAKAKVDAEAKKAKDAIDAATSNADVTAKQNEGT 1- 549 Query: 1590 ENINNQYQHGDGVDVRKATAKGDLEKEAAKVKALIAKDPTLTQADKDKQTAAVDAAKNTA 1- 649 + IN+ Q K AK + + A K I KDP LT+ +KD A VDA A Sbjct: 1550 KAINDVPQ----TPTAKTDAKNAVTQAADAKKDAIEKDPNLTREEKDAAKAKVDAEAKKA 1- 605 Query: 1650 IAAVDKATTTEGINQELGKGITAINKAYRPGEGVKARKEAAKADLEKEAAKVKALITNDP 1- 709 A+D AT+ + + G AIN + K AK + + A K I ND Sbjct: 1606 KDAIDAATSNADVTAQKDAGKNAINAVPQ----TPTAKTDAKNAVTQAADAKKDAIENDA 1- 661 Query: 1710 TLTKADK-AKQTEAVAKALKAAIAAVDKATTAEGINQELGKGITAINKAYRPGEGVKARK 1- 768 LT+ +K A + + A+A KA A+D AT+ + + +G AIN + K Sbjct: 1662 NLTREEKDAAKAKVDAEATKAK-NAIDAATSNADVTAKQNEGTKAINDVPQ----TPTAK 1- 716 Query: 1769 EAAKADLEREAAKVREAIANDPTLTKADK-AKQTEAVAKALKAAIAAVDKATTAEGINQE 1- 827 AK +++ A + AI NDP LT+ +K A + + A+A KA A+D AT+ + + Sbjct: 1717 TDAKNAVDQAATDKKSAIENDPALTREEKDAAKAKVDAEATKAK-NAIDAATSNADVTAQ 1- 775 Query: 1828 LGKGITAINKAYRPGEGVEAHKEAAKANLEKVAKETKALISGDRYLSKTEKAVQKQAVEQ 1- 887 G AIN + K AK +++ A + KA I D L+ EK K V+ Sbjct: 1776 KDAGKNAINAVPQ----TPTAKTDAKNAVDQAATDKKAAIENDPALTREEKDAAKAKVDA 1- 831 Query: 1888 ALAKALGQVEAAKTVEAVKLAENLGTVAIRSAYVAGLAKDTDQATAALNEAKQAAIEALK 1- 947 KA ++AA + V ++ G KD A AK A A+ Sbjct: 1832 EAKKAKDAIDAATSNADVTAQKDAG-------------KDAINAVPQTPTAKTDAKNAVD 1- 878 Query: 1948 QAAAETLAKITTDAKLTEAQKAEQSENVSLALKTAIATVRSAQSIASVKEAKDKGITAIR 2- 007 QAA + + I D LT +K V K A + +A S A V + +G AI Sbjct: 1879 QAATDKKSAIENDPALTREEKDAVKAKVDAEAKKAKDAIDAATSNADVTAKQTEGTQAIN 1- 938 Query: 2008 AAYVPNKAVAKSSSAN 2023 A VP AK+ + N Sbjct: 1939 A--VPQTPTAKTDAKN 1952 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00607 Identities = 77/396 (19%), Positives = 157/396 (39%), Gaps = 48/396 (12%) Query: 42 LNYELTNRDQAQNYHKQIKEHINENRLSTRGVRKDAILCNEWIITSDKTFFDSLDEKQTR 101- L++E+ + ++QN K+I + + D E +I K +++ EK T Sbjct: 338 LDFEILH-PRSQNVSKKISKQVEAKPF-------DPASYKEKVIAKLKPVYEATSEKITN 38- 9 Query: 102 EFF--ETAKDYFAEKYGDANIAYARVHLDESTPHMHLGIVPMKNGKLSSKALFG--NKEK 15- 7 + + E AKD +K + I+ G V + +A+ NK Sbjct: 390 DAWLDENAKDLQKQKLEEQYIS---------------GKVAISEAGTKQEAIDAAYNKYS 43- 4 Query: 158 LVAIQDELPKYLNEHGFNLQRGEIGSKKKHLETAEFKEKQRLLDN---ADRKLADKHEEL 21- 4 D LP + N + + ++ ++T + K D K K E L Sbjct: 435 SQTDPDSLPSQYKQG--NKENEQEKGRQDLIQTRDLTLKAIQEDKWLTEQEKTIQKEEAL 49- 2 Query: 215 KALDDKISNVNDTIADKESRLKELEAKEWDAVGDLKQYE----------LEKQSLAESIE 26- 4 KA + I +VN T++ ++ + + + K + + K+Y EK+ A E Sbjct: 493 KAFETGIESVNQTVSLEQLKQRLIVYKASEKDSEKKEYPESIPNQHIPGKEKEVKAAKQE 55- 2 Query: 265 DIKDIELLQLDRIQKEDLVKQSFDGKLKMDKETYNRLFQTASKHASSNAELKRDLVKAQS 32- 4 ++K + L++I ++ + + +E + Q A K A + +L+ DL S Sbjct: 553 ELKKLHDTTLEKINQDKWLTPDQQAEQLKQAEVTFKKGQEAIKSAQTLTQLETDLADYVS 61- 2 Query: 325 QNNHLSRELLNHRKTAEKNIKLSQENRKLKDKVKMLDEQVK----ILNKSLSVWKEKAKE 38- 0 +N + + K+ K+ +++ KLK+ + + ++ + + KEKAK Sbjct: 613 ENEGKGNSIPDKYKSGNKDDLVNKAEVKLKEAHEATKQAIEKDPWLSPEQKKAQKEKAKA 67- 2 Query: 381 FMPKQVYRETLSIINTLNPIGLAKTAIRQVKKMVDS 416 + + + + L ++L + + + A +K DS Sbjct: 673 RLDEGL--KALKAADSLEILKVTEEAFVDKEKNPDS 706 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 181 A DNA sequence (GBSx0187) was identified in S. agalactiae <SEQ ID 599> which encodes the amino acid sequence <SEQ ID 600>. Analysis of this protein sequence reveals the following: TABLE-US-00608 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2544 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 182 A DNA sequence (GBSx0188) was identified in S. agalactiae <SEQ ID 601> which encodes the amino acid sequence <SEQ ID 602>. Analysis of this protein sequence reveals the following: TABLE-US-00609 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2045 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 603> which encodes the amino acid sequence <SEQ ID 604>. Analysis of this protein sequence reveals the following: TABLE-US-00610 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2045 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00611 Identities = 102/111 (91%), Positives = 107/111 (95%) Query: 1 MDYKKYQIIYAPDVLEKLKEIRDYISQNYSSTSGQHKMEQIISDIEKLEVFPEVGFDADE 60 +DYKKYQIIYAPDVLEKLKEIRDYISQNYSSTSGQ KMEQIISDIEKLEVFPEVGFDADE Sbjct: 1 LDYKKYQIIYAPDVLEKLKEIRDYISQNYSSTSGQRKMEQIISDIEKLEVFPEVGFDADE 60 Query: 61 KYGSKISKYHSTRGYTLSKDYIVLYHIEEEENRVVIDYLLPTRSDYMKLFK 111 KYGSKI YHST+GYTLSKDYIVLYHIE EENR+VIDYLLPT+SDY+KLFK Sbjct: 61 KYGSKIIHYHSTKGYTLSKDYIVLYHIEGEENRIVIDYLLPTQSDYIKLFK 111 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 183 A DNA sequence (GBSx0189) was identified in S. agalactiae <SEQ ID 605> which encodes the amino acid sequence <SEQ ID 606>. Analysis of this protein sequence reveals the following: TABLE-US-00612 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1621(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 607> which encodes the amino acid sequence <SEQ ID 608>. Analysis of this protein sequence reveals the following: TABLE-US-00613 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1596(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00614 Identities = 91/95 (95%), Positives = 93/95 (97%) Query: 1 MVTAEKNRAVTFQANKELVSEAMTVLNKKNLTLSSALRLFLQNVVVTNEVDLLTEEELEK 60 M T +KNRAVTFQANKELVSEAMTVLNKKNLTLSSALRLFLQNVVVTNEVDLLTEEELEK Sbjct: 1 MTTVKKNRAVTFQANKELVSEAMTVLNKKNLTLSSALRLFLQNVVVTNEVDLLTEEELEK 60 Query: 61 EKLFKQFQAEINKNIEDVRQGKFYTSEEVRSELGL 95 EKLFKQFQAEINKNIEDVRQGKFYTSEEVR+ELGL Sbjct: 61 EKLFKQFQAEINKNIEDVRQGKFYTSEEVRAELGL 95 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 184 A DNA sequence (GBSx0190) was identified in S. agalactiae <SEQ ID 609> which encodes the amino acid sequence <SEQ ID 610>. Analysis of this protein sequence reveals the following: TABLE-US-00615 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4568(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9513> which encodes amino acid sequence <SEQ ID 9514> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00616 >GP:CAA46375 GB:X65276 ORFA1 [Clostridium acetobutylicum] Identities = 36/91 (39%), Positives = 51/91 (55%) Query: 2 MSQIKLTPEELRISAQKYTTGSQSITDVLTVLTQEQAVIDENWDGTAFDSFEAQFNELSP 61 M+QI +TPEEL+ AQ Y + I + + + I E W G AF ++ Q+N+L Sbjct: 1 MAQISVTPEELKSQAQVYIQSKEEIDQAIQKVNSMNSTIAEEWKGQAFQAYLEQYNQLHQ 60 Query: 62 KITQFAQLLEDINQQLLKVADVVEQTDSDIA 92 + QF LLE +NQQL K AD V + D+ A Sbjct: 61 TVVQFENLLESVNQQLNKYADTVAERDAQDA 91 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 185 A DNA sequence (GBSx0191) was identified in S. agalactiae <SEQ ID 611> which encodes the amino acid sequence <SEQ ID 612>. Analysis of this protein sequence reveals the following: TABLE-US-00617 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4523(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 186 A DNA sequence (GBSx0192) was identified in S. agalactiae <SEQ ID 613> which encodes the amino acid sequence <SEQ ID 614>. Analysis of this protein sequence reveals the following: TABLE-US-00618 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5339(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 187 A DNA sequence (GBSx0193) was identified in S. agalactiae <SEQ ID 615> which encodes the amino acid sequence <SEQ ID 616>. This protein is predicted to be chromosome assembly protein. Analysis of this protein sequence reveals the following: TABLE-US-00619 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4620(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 188 A DNA sequence (GBSx0194) was identified in S. agalactiae <SEQ ID 617> which encodes the amino acid sequence <SEQ ID 618>. Analysis of this protein sequence reveals the following: TABLE-US-00620 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4511(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 189 A DNA sequence (GBSx0195) was identified in S. agalactiae <SEQ ID 619> which encodes the amino acid sequence <SEQ ID 620>. Analysis of this protein sequence reveals the following: TABLE-US-00621 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5249(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 190 A DNA sequence (GBSx0196) was identified in S. agalactiae <SEQ ID 621> which encodes the amino acid sequence <SEQ ID 622>. Analysis of this protein sequence reveals the following:

TABLE-US-00622 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3542(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9515> which encodes amino acid sequence <SEQ ID 9516> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 191 A DNA sequence (GBSx0197) was identified in S. agalactiae <SEQ ID 623> which encodes the amino acid sequence <SEQ ID 624>. Analysis of this protein sequence reveals the following: TABLE-US-00623 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3098 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 192 A DNA sequence (GBSx0198) was identified in S. agalactiae <SEQ ID 625> which encodes the amino acid sequence <SEQ ID 626>. This protein is predicted to be rgg protein. Analysis of this protein sequence reveals the following: TABLE-US-00624 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3177 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00625 >GP: AAA26968 GB: M89776 rgg [Streptococcus gordonii] Identities = 74/277 (26%), Positives = 142/277 (50%) Query: 7 IFREFRLNRQFSLKQVASNELSVSQLSRFERGESDLSLTKFLGALEAIDLSISEFMDRVN 66 I + R ++ SLK+VA+ ++SV+QLSR+ERG S L++ F L + +S++EF + Sbjct: 10 ILKIIRESKNMSLKEVAAGDISVAQLSRYERGISSLTVDSFYSCLRNMSVSLAEFQYVYH 69 Query: 67 KYQKSDQISLMSQMAQYHYQRDVAGLEKMISVEEGKLKKDSSDIRCRLNIVLFRGMICEC 126- Y+++D + L ++++ + ++ LE +++ E ++ +LN ++ R + C Sbjct: 70 NYREADDVVLSQKLSEAQRENNIVKLESILAGSEAMAQEFPEKKNYKLNTIVIRATLTSC 129- Query: 127 DSSRKMSEEDLCFLSDYLFQKDSWEISDYILIGNLYRYYNTRHICQLVKEVINQKEYYRD 18- 6 + ++S+ D+ FL+DYLF + W + L N + E+IN+ ++Y + Sbjct: 130 NPDYQVSKGDIEFLTDYLFSVEEWGRYELWLFTNSVNLLTLETLETFASEMINRTQFYNN 18- 9 Query: 187 IYTNRNVVEATLLNVVETLIERRALEEATFFLEKVEALLNNERNAYHRIILLYEKGFLAY 24- 6 + NR + LLNVV IE L+ A FL ++ E + Y R+++ Y K +Y Sbjct: 190 LPENRRRIIKMLLNVVSACIENNHLQVAMKFLNYIDNTKIPETDLYDRVLIKYHKALYSY 24- 9 Query: 247 AKGDSRGIQSMKQAIFCFQAIGSKHHVENFQEHFNRV 283 G+ ++Q + F+ + S +E F R+ Sbjct: 250 KVGNPHARHDIEQCLSTFEYLDSFGVARKLKEQFERI 286 A related DNA sequence was identified in S. pyogenes <SEQ ID 627> which encodes the amino acid sequence <SEQ ID 628>. Analysis of this protein sequence reveals the following: TABLE-US-00626 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3792 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00627 Identities = 79/275 (28%), Positives = 146/275 (52%), Gaps = 11/275 (4%) Query: 9 REFRLNRQFSLKQVASNELSVSQLSRFERGESDLSLTKFLGALEAIDLSISEFMDRVNKY 68 R R +Q S+ +A LS SQ+SRFERGES+++ ++ L L+ ++++I EF+ +K Sbjct: 15 RRLRKGKQVSISFLADEYLSKSQISRFERGESEITCSRLLNLLDKLNITIDEFVSAHSKT 74 Query: 69 QKSDQISLMSQMAQYHYQRDVAGLEKMISVEEGKLKKDSSDIRCRLNIVLFRGMICECDS 128- + +L+SQ + + +++V L K++ + KD R + +LF DS Sbjct: 75 H-THFFTLLSQARKCYAEKNVVKLTKLL---KDYAHKDYE--RTMIKAILF-----SIDS 123- Query: 129 SRKMSEEDLCFLSDYLFQKDSWEISDYILIGNLYRYYNTRHICQLVKEVINQKEYYRDIY 18- 8 S S+E+L L+DYLF+ + W + IL+GN R+ N + L KE++ Y Sbjct: 124 SIAPSQEELTRLTDYLFKVEQWGYYEIILLGNCSRFMNYNTLFLLTKEMVASFAYSEQNK 18- 3 Query: 189 TNRNVVEATLLNVVETLIERRALEEATFFLEKVEALLNNERNAYHRIILLYEKGFLAYAK 24- 8 TN+ +V +N + I+ E + + + K++ LL +E N Y + + LY G+ + Sbjct: 184 TNKMLVTQLSINCLIISIDHSCFEHSRYLINKIDLLLRDELNFYEKTVFLYVHGYYKLKQ 24- 3 Query: 249 GDSRGIQSMKQAIFCFQAIGSKHHVENFQEHFNRV 283 + G + M+QA+ F+ +G +++EH+ ++ Sbjct: 244 EEMSGEEDMRQALQIFKYLGEDSLYYSYKEHYRQI 278 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 193 A DNA sequence (GBSx0199) was identified in S. agalactiae <SEQ ID 629> which encodes the amino acid sequence <SEQ ID 630>. This protein is predicted to be permease. Analysis of this protein sequence reveals the following: TABLE-US-00628 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.07 Transmembrane 217-233 (215-238) INTEGRAL Likelihood = -7.96 Transmembrane 163-179 (158-185) INTEGRAL Likelihood = -7.75 Transmembrane 71-87 (69-91) INTEGRAL Likelihood = -7.22 Transmembrane 369-385 (356-389) INTEGRAL Likelihood = -5.15 Transmembrane 279-295 (275-299) INTEGRAL Likelihood = -4.88 Transmembrane 252-268 (250-270) INTEGRAL Likelihood = -4.78 Transmembrane 140-156 (139-157) INTEGRAL Likelihood = -3.56 Transmembrane 343-359 (340-367) INTEGRAL Likelihood = -3.13 Transmembrane 40-56 (39-56) INTEGRAL Likelihood = -2.28 Transmembrane 94-110 (92-112) ----- Final Results ----- bacterial membrane --- Certainty = 0.4227(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00629 >GP: AAD36408 GB: AE001788 permease, putative [Thermotoga maritima] Identities = 97/396 (24%), Positives = 194/396 (48%), Gaps = 15/396 (3%) Query: 1 MNINGIKLLSSRAVSKLGDVFYDYGNSTWIASMGGLGQKILGIYQIVELLVSIVLNPFGG 60 MN N + S VS +G Y + W+ S G + + G++ I L +I+++PF G Sbjct: 1 MNRNLLLFASGSFVSLIGTRIYQVALAWWLYSKTGSSEYV-GLFMISSFLPAIIVSPFAG 59 Query: 61 ALADRFQRRKILLITDAICAIM---CFLLSFIGDDKVMVYGLIVANAILAVSNAFSSPAY 117- + DR RR ++++ D + ++ FL+ + + + + L++ +++V ++F +PA Sbjct: 60 TVVDRHSRRNMMVVMDILRGVLFMYLFLMEYFSELTMAL--LLIVTVLVSVFDSFFNPAV 117- Query: 118 KSYIPEIVDKADIITYNANLETIVQIISVSSPVLGFLIFNNFGIRITLIVDAITFLISFL 17- 7 S +P++V K +++ N+ + + + P LG L+ G+ +++++++FLIS + Sbjct: 118 DSLLPDLVRKENLVRANSLYRLLKNLSKILGPALGSLLLKVVGLAGVILINSLSFLISGI 17- 7 Query: 178 FLYAIKVERVQLSKQEKVAIKNILADIADGFTYIKKEKEIMFFLIIAALLNTFLAMFNYL 23- 7 F IKVE L K K +N+ DI YI+ + I+ +++ A++N F + L Sbjct: 178 FEMFIKVEEKHLKKVSKE--RNMWQDIKSALLYIRSVRFILVTILVIAIMNFFTGSMHVL 23- 5 Query: 238 LP-FTNSLLKTSGAYATILSISAIGSIIGALIARKI--KSSINSMLSMLVFSSLGVIVMG 29- 4 LP + L K+ Y T++S+ + G +I + I ++S+ ++ LV L V V Sbjct: 236 LPEHVSKLGKSEWVYGTLMSMLSFGGLIVTFLMATIRTRASVKTLGLNLVGYGLAVFVFA 29- 5 Query: 295 FPSLFELPIWIPYSGSFLFNSLLTMFNIHFFSQVQIRVDEAYMGRVMSTIFTIAIMFMPI 35- 4 W+ ++ FL T+FNI+ + +Q+ + E G++ S I ++ +P+ Sbjct: 296 MTGNH----WLMFAMYFLIGIFQTLFNINVITLLQLAIPEEMRGKIFSLISAVSFSLLPV 35- 1 Query: 355 GTLFMTIFSFALSNVSFIVIGCAIAILGGLGFSYSK 390 F S ++ + I GG+ S + Sbjct: 352 SYGFFGFLSSYVATAHIFITTSMALIAGGVLISLQR 387 A related DNA sequence was identified in S. pyogenes <SEQ ID 631> which encodes the amino acid sequence <SEQ ID 632>. Analysis of this protein sequence reveals the following: TABLE-US-00630 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.17 Transmembrane 172-188 (161-194) INTEGRAL Likelihood = -8.07 Transmembrane 220-236 (218-242) INTEGRAL Likelihood = -7.22 Transmembrane 311-327 (303-329) INTEGRAL Likelihood = -5.26 Transmembrane 98-114 (96-118) INTEGRAL Likelihood = -4.99 Transmembrane 347-363 (342-370) INTEGRAL Likelihood = -4.62 Transmembrane 154-170 (151-171) INTEGRAL Likelihood = -4.25 Transmembrane 284-300 (281-306) INTEGRAL Likelihood = -3.66 Transmembrane 378-394 (378-396) INTEGRAL Likelihood = -3.56 Transmembrane 74-90 (73-92) INTEGRAL Likelihood = -2.39 Transmembrane 50-66 (49-66) ----- Final Results ----- bacterial membrane --- Certainty = 0.4270(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00631 >GP: AAD36408 GB: AE001788 permease, putative [Thermotoga maritima] Identities = 85/345 (24%), Positives = 171/345 (48%), Gaps = 8/345 (2%) Query: 40 SLSLVAVYQSLESVIGVLFNLFGGVIADSFKRKKIIITTNILCGTACLVLSFLTKEQWLV 99 - S V ++ + ++ + F G + D R+ +++ +IL G + L + L Sbjct: 36 SSEYVGLFMISSFLPAIIVSPFAGTVVDRHSRRNMMVVMDILRGVLFMYLFLMEYFSELT 95 Query: 100 YAIVL-TNVILAFMSAFSSPSYKAFTKEIVKKDSISQLNSLLETTSTVIKVTVPMVAIFL 15- 8 A++L V+++ +F +P+ + ++V+K+++ + NSL + K+ P + L Sbjct: 96 MALLLIVTVLVSVFDSFFNPAVDSLLPDLVRKENLVRANSLYRLLKNLSKILGPALGSLL 155- Query: 159 YKLLGIHGVLLLDGLSFLIAALLISFILPVNDEVVIKEKVTIREIFNDLKIGFKYVYSHK 21- 8 K++G+ GV+L++ LSFLI+ + FI +E +K+ R ++ D+K Y+ S + Sbjct: 156 LKVVGLAGVILINSLSFLISGIFEMFIKV--EEKHLKKVSKERNMWQDIKSALLYIRSVR 21- 3 Query: 219 SIFIITVLSALVNFFLAAYNLLLPYSNQMFGEISTGLYGTFLTAEAIGGFIGAILSGFVN 27- 8 I + ++ A++NFF + ++LLP G+ S +YGT ++ + GG I L + Sbjct: 214 FILVTILVIAIMNFFTGSMHVLLPEHVSKLGK-SEWVYGTLMSMLSFGGLIVTFLMATIR 27- 2 Query: 279 KELSSMRLILFLSLSGLMLMLAPPFYIMFHNAIILALSPALFSLFLSIFNIQFFSLVQKD 33- 8 S L L L GL + + + M N ++ L +F ++FNI +L+Q Sbjct: 273 TRASVKTLGLNLVGYGLAVFV----FAMTGNHWLMFAMYFLIGIFQTLFNINVITLLQLA 32- 8 Query: 339 VDNDFLGRVFGIIFTITILFMPIGTGFFSVALNPNNSFNLFIIGS 383 + + G++F +I ++ +P+ GFF + + ++FI S Sbjct: 329 IPEEMRGKIFSLISAVSFSLLPVSYGFFGFLSSYVATAHIFITTS 373 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00632 Identities = 136/379 (35%), Positives = 229/379 (59%), Gaps = 6/379 (1%) Query: 8 LLSSRAVSKLGDVFYDYGNSTWIASMGGLGQKILGIYQIVELLVSIVLNPFGGALADRFQ 67 L+ S+ + ++GDV +D+ N+T++A + ++ +YQ +E ++ ++ N FGG +AD F+ Sbjct: 11 LVYSKVIYRIGDVMFDFANNTFLAGLNPASLSLVAVYQSLESVIGVLFNLFGGVIADSFK 70 Query: 68 RRKILLITDAICAIMCFLLSFIGDDKVMVYGLIVANAILAVSNAFSSPAYKSYIPEIVDK 127- R+KI++ T+ +C C +LSF+ ++ +VY +++ N ILA +AFSSP+YK++ EIV K Sbjct: 71 RKKIIITTNILCGTACLVLSFLTKEQWLVYAIVLTNVILAFMSAFSSPSYKAFTKEIVKK 130- Query: 128 ADIITYNANLETIVQIISVSSPVLGFLIFNNFGIRITLIVDAITFLISFLFLYAIKVERV 18- 7 I N+ LET +I V+ P++ ++ GI L++D ++FLI+ L + I Sbjct: 131 DSISQLNSLLETTSTVIKVTVPMVAIFLYKLLGIHGVLLLDGLSFLIAALLISFILPVND 19- 0 Query: 188 QLSKQEKVAIKNILADIADGFTYIKKEKEIMFFLIIAALLNTFLAMFNYLLPFTNSLLK- 24- 6 ++ +EKV I+ I D+ GF Y+ K I +++AL+N FLA +N LLP++N + Sbjct: 191 EVVIKEKVTIREIFNDLKIGFKYVYSHKSIFIITVLSALVNFFLAAYNLLLPYSNQMFGE 25- 0 Query: 247 -TSGAYATILSISAIGSIIGALIARKIKSSINSMLSMLVFSSLGVIVMGFPS---LFELP 30- 2 ++G Y T L+ AIG IGA+++ + ++SM +L S G+++M P +F Sbjct: 251 ISTGLYGTFLTAEAIGGFIGAILSGFVNKELSSMRLILFLSLSGLMLMLAPPFYIMFHNA 31- 0 Query: 303 IWIPYSGSFLFNSLLTMFNIHFFSQVQIRVDEAYMGRVMSTIFTIAIMFMPIGTLFMTIF 36- 2 I + S + LF+ L++FNI FFS VQ VD ++GRV IFTI I+FMPIGT F ++ Sbjct: 311 IILALSPA-LFSLFLSIFNIQFFSLVQKDVDNDFLGRVFGIIFTITILFMPIGTGFFSVA 36- 9 Query: 363 SFALSNVSFIVIGCAIAIL 381 ++ + +IG I L Sbjct: 370 LNPNNSFNLFIIGSCITTL 388 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 194 A DNA sequence (GBSx0200) was identified in S. agalactiae <SEQ ID 633> which encodes the amino acid sequence <SEQ ID 634>. This protein is predicted to be membrane permease OpuCD. Analysis of this protein sequence reveals the following: TABLE-US-00633 Possible site: 46 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.68 Transmembrane 91-107 (88-110) INTEGRAL Likelihood = -4.30 Transmembrane 15-31 (9-37) INTEGRAL Likelihood = -3.72 Transmembrane 72-88 (72-88) INTEGRAL Likelihood = -3.19 Transmembrane 124-140 (123-142) ----- Final Results ----- bacterial membrane --- Certainty = 0.3272(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8509> which encodes amino acid sequence <SEQ ID 8510> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-00634 Lipop: Possible site: -1 Crend: 1 McG: Discrim Score: -10.69 GvH: Signal Score (-7.5): -3.79 Possible site: 39 >>> Seems to have no N-terminal signal sequence ALOM program count: 5 value: -9.02 threshold: 0.0 INTEGRAL Likelihood = -9.02 Transmembrane 35-51 (25-53) INTEGRAL Likelihood = -5.68 Transmembrane 151-167 (148-170) INTEGRAL Likelihood = -4.30 Transmembrane 75-91 (69-97) INTEGRAL Likelihood = -3.72 Transmembrane 132-148 (132-148) INTEGRAL Likelihood = -3.19 Transmembrane 184-200 (183-202) PERIPHERAL Likelihood = 2.17 58 modified ALOM score: 2.30 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4609(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00635 >GP: AAF91342 GB: AF249729 membrane permease OpuCD [Listeria monocytogenes] Identities = 104/154 (67%), Positives = 133/154 (85%) Query: 3 IANVIQTIPSLAMISIIMLGLGLGIKTVVATVFLYSLLPIITNTYTGIRNVDSDLLDAAK 62 IAN+IQTIP+LAM++++ML +GLG TVV ++FLYSLLPI+ NTYTGIRNVD LL++ K Sbjct: 60 IANIIQTIPALAMLAVLMLIMGLGTNTVVLSLFLYSLLPILKNTYTGIRNVDGALLESGK 119- Query: 63 GMGMTKRQRLFMVELPLSISVIMAGLRNALVVAIGITAIGAFVGGGGLGDIIIRGTNATN 122- MGMTK Q L ++E+PL++SVIMAG+RNALV+AIG+ AIG FVG GGLGDII+RGTNATN Sbjct: 120 AMGMTKWQVLRLIEMPLALSVIMAGIRNALVIAIGVAAIGTFVGAGGLGDIIVRGTNATN 17- 9 Query: 123 GGAIILAGSLPTALMAIFSDLILGGIQRMLEPRK 156 G AIILAG++PTA+MAI +D++LG ++R L P K Sbjct: 180 GTAIILAGAIPTAVMAILADVLLGWVERTLNPVK 213 A related DNA sequence was identified in S. pyogenes <SEQ ID 635> which encodes the amino acid sequence <SEQ ID 636>. Analysis of this protein sequence reveals the following: TABLE-US-00636 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.24 Transmembrane 39-55 (31-59) INTEGRAL Likelihood = -7.17 Transmembrane 190-206 (188-211) INTEGRAL Likelihood = -4.62 Transmembrane 93-109 (75-110) INTEGRAL Likelihood = -3.66 Transmembrane 76-92 (75-92) INTEGRAL Likelihood = -2.87 Transmembrane 221-237 (220-237) INTEGRAL Likelihood = -2.44 Transmembrane 168-184 (165-184) ----- Final Results ----- bacterial membrane --- Certainty = 0.4694(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00637 >GP: AAD45530 GB: AF162656 choline transporter [Streptococcus pneumoniae] Identities = 344/508 (67%), Positives = 425/508 (82%), Gaps = 2/508 (0%) Query: 13 MPSLFVTFQNRFNEWLAALGEHLQISLLSLMIALLIGVPLAALLSRSKRWSDIMLQVTGV 72 - M +L TFQ+RF++WL AL +HLQ+SLL+L++A+L+ +PLA L ++ +D +LQ+ G+ Sbjct: 1 MTNLIATFQDRFSDWLTALSQHLQLSLLTLLLAILLAIPLAVFLRYHEKLADWVLQIAGI 60 Query: 73 FQTIPSLALLGLFIPLMGIGTLPAVTALVIYAIFPILQNTITGLNGIDPSLVEAGIAFGM 132- FQTIPSLALLGLFIPLMGIGTLPA+TALVIYAIFPILQNTITGL GIDP+L EAGIAFGM Sbjct: 61 FQTIPSLALLGLFIPLMGIGTLPALTALVIYAIFPILQNTITGLKGIDPNLQEAGIAFGM 120- Query: 133 TKWERLKTFEIPIAMPVIMSGVRTSAVMIIGTATLASLIGAGGLGSFILLGIDRNNANLI 19- 2 T+WERLK FEIP+AMPVIMSG+RT+AV+IIGTATLA+LIGAGGLGSFILLGIDRNNA+LI Sbjct: 121 TRWERLKKFEIPLAMPVIMSGIRTAAVLIIGTATLAALIGAGGLGSFILLGIDRNNASLI 18- 0 Query: 193 LIGAISSALLAIIFNSLLQYLEKASLRRIMISFGITLLALLASYTPMALSQFSKGKDTVV 25- 2 LIGA+SSA+LAI FN LL+ +EKA LR I F + L L SY+P L Q K K+ +V Sbjct: 181 LIGALSSAVLAIAFNFLLKVMEKAKLRTIFSGFALVALLLGLSYSPALLVQ--KEKENLV 23- 8 Query: 253 IAGKLGAEPDILINLYKELIEDQSDISVELKSNFGKTSFLYEALKSGDIDMYPEFTGTIT 31- 2 IAGK+G EP+IL N+YK LIE+ + ++ +K NFGKTSFLYEALK GDID+YPEFTGT+T Sbjct: 239 IAGKIGPEPEILANMYKLLIEENTSMTATVKPNFGKTSFLYEALKKGDIDIYPEFTGTVT 29- 8 Query: 313 SSLLRDKPPLSNDPKQVYEDAKKGIAKQDKLTLLKPFAYQNTYAVAMPEKLAKEYQIETI 37- 2 SLL+ P +S++P+QVY+ A+ GIAKQD L LKP +YQNTYAVA+P+K+A+EY ++TI Sbjct: 299 ESLLQPSPKVSHEPEQVYQVARDGIAKQDHLAYLKPMSYQNTYAVAVPKKIAQEYGLKTI 35- 8 Query: 373 SDLKAHADTLKAGFTLEFKDRADGYKGMQSQYGLQLSVATMEPALRYQAIQSGDIQVTDA 43- 2 SDLK LKAGFTLEF DR DG KG+QS YGL L+VAT+EPALRYQAIQSGDIQ+TDA Sbjct: 359 SDLKKVEGQLKAGFTLEFNDREDGNKGLQSMYGLNLNVATIEPALRYQAIQSGDIQITDA 41- 8 Query: 433 YSTDAEITKYHLKVLKDDKQLFPPYQGAPLMKTSLLTKHPELKGILNQLAGKITEKEMQD 49- 2 YSTDAE+ +Y L+VL+DDKQLFPPYQGAPLMK +LL KHPEL+ +LN LAGKITE +M Sbjct: 419 YSTDAELERYDLQVLEDDKQLFPPYQGAPLMKEALLKKHPELERVLNTLAGKITESQMSQ 47- 8 Query: 493 MNYEVSVKGADANKVARDYLLKTGLIQK 520 +NY+V V+G A +VA+++L + GL++K Sbjct: 479 LNYQVGVEGKSAKQVAKEFLQEQGLLKK 506 An alignment of the GAS and GBS proteins is shown below:

TABLE-US-00638 Identities = 53/148 (35%), Positives = 93/148 (62%), Gaps = 1/148 (0%) Query: 3 IANVIQTIPSLAMISIIMLGLGLGIKTVVATVFLYSLLPIITNTYTGIRNVDSDLLDAAK 62 + V QTIPSLA++ + + +G+G V + +Y++ PI+ NT TG+ +D L++A Sbjct: 69 VTGVFQTIPSLALLGLFIPLMGIGTLPAVTALVIYAIFPILQNTITGLNGIDPSLVEAGI 128- Query: 63 GMGMTKRQRLFMVELPLSISVIMAGLRNALVVAIGITAIGAFVGGGGLGDIIIRGTNATN 122- GMTK +RL E+P+++ VIM+G+R + V+ IG + + +G GGLG I+ G + N Sbjct: 129 AFGMTKWERLKTFEIPIAMPVIMSGVRTSAVMIIGTATLASLIGAGGLGSFILLGIDRNN 18- 8 Query: 123 GGAIILAGSLPTALMAIFSDLILGGIQR 150 +IL G++ +AL+AI + +L +++ Sbjct: 189 AN-LILIGAISSALLAIIFNSLLQYLEK 215 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 195 A DNA sequence (GBSx0201) was identified in S. agalactiae <SEQ ID 637> which encodes the amino acid sequence <SEQ ID 638>. This protein is predicted to be choline transporter-related. Analysis of this protein sequence reveals the following: TABLE-US-00639 Possible site: 44 >>> May be a lipoprotein INTEGRAL Likelihood = -3.03 Transmembrane 306-322 (306-327) ----- Final Results ----- bacterial membrane --- Certainty = 0.2211(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9517> which encodes amino acid sequence <SEQ ID 9518> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00640 >GP: CAB15386 GB: Z99121 glycine betaine/carnitine/choline ABC transporter (osmoprotectant-binding protein) [Bacillus subtilis] Identities = 168/303 (55%), Positives = 224/303 (73%), Gaps = 1/303 (0%) Query: 2 LKKSHFLQIFTLCLALLTISGCQLTDTKKSGHTTIKVAAQSSTESSIMANIITELIHHEL 61 + K +L F L +L + GC L + TIK+ AQS TES I+AN+I +LI H+ Sbjct: 1 MTKIKWLGAFALVFVML-LGGCSLPGLGGASDDTIKIGAQSMTESEIVANMIAQLIEHDT 59 Query: 62 GYNTTLISNLGSSTVTHQALLRGDADIAATRYTGTDITGTLGLKAVKDPKEASKIVKTEF 121- NT L+ NLGS+ V HQA+L GD DI+ATRY+GTD+T TLG +A KDPK+A IV+ EF Sbjct: 60 DLNTALVKNLGSNYVQHQAMLGGDIDISATRYSGTDLTSTLGKEAEKDPKKALNIVQNEF 119- Query: 122 QKRYNQTWYPTYGFSDTYAFMVTKEFARQNKITKISDLKKLSTTMKAGVDSSWMNREGDG 18- 1 QKR++ W+ +YGF +TYAF VTK+FA + I +SDLKK ++ K GVD++W+ R+GDG Sbjct: 120 QKRFSYKWFDSYGFDNTYAFTVTKKFAEKEHINTVSDLKKNASQYKLGVDNAWLKRKGDG 17- 9 Query: 182 YTDFAKTYGFEFSHIYPMQIGLVYDAVESNKMQSVLGYSTDGRISSYDLEILRDDKKFFP 24- 1 Y F TYGFEF YPMQIGLVYDAV++ KM +VL YSTDGRI +YDL+IL+DDK+FFP Sbjct: 180 YKGFVSTYGFEFGTTYPMQIGLVYDAVKNGKMDAVLAYSTDGRIKAYDLKILKDDKRFFP 23- 9 Query: 242 PYEASMVVNNSIIKKDPKLKKLLHRLDGKINLKTMQNLNYMVDDKLLEPSVVAKQFLEKN 30- 1 PY+ S V+ ++K+ P+L+ ++++L G+I+ +TMQ LNY VD KL EPSVVAK+FLEK+ Sbjct: 240 PYDCSPVIPEKVLKEHPELEGVINKLIGQIDTETMQELNYEVDGKLKEPSVVAKEFLEKH 29- 9 Query: 302 HYF 304 HYF Sbjct: 300 HYF 302 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8511> and protein <SEQ ID 8512> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00641 Lipop: Possible site: 22 Crend: 5 McG: Discrim Score: 10.26 GvH: Signal Score (-7.5): -4.19 Possible site: 44 >>> May be a lipoprotein ALOM program count: 0 value: 8.65 threshold: 0.0 PERIPHERAL Likelihood = 8.65 66 modified ALOM score: -2.23 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00016## SEQ ID 8512 (GBS23) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 14 (lane 8; MW 35 kDa). The GBS23-His fusion product was purified (FIG. 194, lane 9) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 251). These tests confirm that the protein is immunoaccessible on GBS bacteria. EXAMPLE 196 A DNA sequence (GBSx0202) was identified in S. agalactiae <SEQ ID 639> which encodes the amino acid sequence <SEQ ID 640>. This protein is predicted to be membrane permease OpuCB (opuBB). Analysis of this protein sequence reveals the following: TABLE-US-00642 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.66 Transmembrane 25-41 (18-45) INTEGRAL Likelihood = -7.96 Transmembrane 182-198 (174-202) INTEGRAL Likelihood = -4.83 Transmembrane 61-77 (57-95) INTEGRAL Likelihood = -4.09 Transmembrane 78-94 (78-95) INTEGRAL Likelihood = -1.22 Transmembrane 134-150 (134-150) ----- Final Results ----- bacterial membrane --- Certainty = 0.4864 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00643 >GP: AAF91340 GB: AF249729 membrane permease OpuCB [Listeria monocytogenes] Identities = 121/208 (58%), Positives = 160/208 (76%) Query: 1 MVNFLSQYGMQILVKTWEQVYISFFAIALGIAIAVPLGVVLTRFPKVAKIIIAIASMLQT 60 +V F + G +LV+TW+ ++IS A+ LGIA+AVP G++LTR PKVA +I + S+LQT Sbjct: 4 IVTFFQENGHNLLVQTWQHLFISLSAVILGIAVAVPTGILLTRSPKVANFVIGVVSVLQT 63 Query: 61 IPSLALLALMIPLFGIGKIPAIVALFIYSLLPILRNTYIGMNNVNPTLKDCAKGMGMKPI 120- +PSLA+LA +IP G+G +PAI+ALFIY+LLPILRNT+IG+ V+ L + +GMGM Sbjct: 64 VPSLAILAFIIPFLGVGTLPAIIALFIYALLPILRNTFIGVRGVDKNLIESGRGMGMTNW 123- Query: 121 QSIFQVELPLATPIIMAGIRLSTIYVIAWATLASYIGAGGLGDLIFSGLNLFQSKLILGG 18- 0 Q I VE+P + +IMAGIRLS +YVIAWATLASYIGAGGLGD IF+GLNL++ LILGG Sbjct: 124 QLIVNVEIPNSISVIMAGIRLSAVYVIAWATLASYIGAGGLGDFIFNGLNLYRPDLILGG 18- 3 Query: 181 TIPVIILSLIIDYLLGLLETALTPRTTR 208 IPV IL+L++++ LG LE LTP+ R Sbjct: 184 AIPVTILALVVEFALGKLEYRLTPKAIR 211 A related GBS gene <SEQ ID 8513> and protein <SEQ ID 8514> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00644 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: -9.08 GvH: Signal Score (-7.5): -1.86 Possible site: 37 >>> Seems to have no N-terminal signal sequence ALOM program count: 5 value: -8.60 threshold: 0.0 INTEGRAL Likelihood = -8.60 Transmembrane 25-41 (18-45) INTEGRAL Likelihood = -7.96 Transmembrane 182-198 (174-202) INTEGRAL Likelihood = -4.83 Transmembrane 61-77 (57-95) INTEGRAL Likelihood = -4.09 Transmembrane 78-94 (78-95) INTEGRAL Likelihood = -1.22 Transmembrane 134-150 (134-150) PERIPHERAL Likelihood = 2.70 156 modified ALOM score: 2.22 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4439 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00017## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 197 A DNA sequence (GBSx0203) was identified in S. agalactiae <SEQ ID 641> which encodes the amino acid sequence <SEQ ID 642>. Analysis of this protein sequence reveals the following: TABLE-US-00645 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3531 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00646 >GP: AAF91339 GB: AF249729 ATPase OpuCA [Listeria monocytogenes] Identities = 230/380 (60%), Positives = 298/380 (77%), Gaps = 4/380 (1%) Query: 6 IIEYQNINKVY-GENVAVEDINLKIYPGDFVCFIGTSGSGKTTLMRMVNHMLKPTNGTLL 64 +++++++ K Y G AV D+ L I G+FVCFIG SG GKTT M+M+N +++PT G + Sbjct: 1 MLKFEHVTKTYKGGKKAVNDLTLNIDKGEFVCFIGPSGCGKTTTMKMINRLIEPTEGKIF 60 Query: 65 FKGKDISTINPIELRRRIGYVIQNIGLMPHMTIYENIVLVPKLLKWSEEAKRAKARELIK 124- KDI +P++LRR IGYVIQ IGLMPHMTI ENIVLVPKLLKWSEE K+ +A+ELIK Sbjct: 61 INDKDIMAEDPVKLRRSIGYVIQQIGLMPHMTIRENIVLVPKLLKWSEEKKQERAKELIK 120- Query: 125 LVELPEEYLDRYPSELSGGQQQRIGVIRALAADQDIILMDEPFGALDPITREGIQDLVKS 18- 4 LV+LPEE+LDRYP ELSGGQQQRIGV+RALAA+Q++ILMDEPFGALDPITR+ +Q+ K+ Sbjct: 121 LVDLPEEFLDRYPYELSGGQQQRIGVLRALAAEQNLILMDEPFGALDPITRDSLQEEFKN 18- 0 Query: 185 LQEEMGKTIILVTHDMDEALKLATKIIVMDNGKMVQEGTPNDLLHHPATSFVEQMIGEER 24- 4 LQ+E+GKTII VTHDMDEA+KLA +I++M +G++VQ TP+++L +PA SFVE IG++R Sbjct: 181 LQKELGKTIIFVTHDMDEAIKLADRIVIMKDGEIVQFDTPDEILRNPANSFVEDFIGKDR 24- 0 Query: 245 LLHAQADITPVKQIMLNNPVSITAEKTLTEAITLMRQKRVDSLLVTDNGKLI-GFIDLES 30- 3 L+ A+ D+T V QIM NPVSITA+K+L AIT+M++KRVD+LLV D G ++ GFID+E Sbjct: 241 LIEAKPDVTQVAQIMNTNPVSITADKSLQAAITVMKEKRVDTLLVVDEGNVLKGFIDVEQ 30- 0 Query: 304 LSSKYKKDRLVSDILKHTDFYVMEDDLLRNTAERILKLGLKYAPVVDHENNLKGIVTRAS 36- 3 + + V DI++ FYV ED LLR+T +RILK G KY PVVD + L GIVTRAS Sbjct: 301 IDLNRRTATSVMDIIEKNVFYVYEDTLLRDTVQRILKRGYKYIPVVDKDKRLVGIVTRAS 36- 0 Query: 364 LVDMLYDIIWGDTE--TEDQ 381 LVD++YD IWG E TE+Q Sbjct: 361 LVDIVYDSIWGTLEDATENQ 380 A related DNA sequence was identified in S. pyogenes <SEQ ID 643> which encodes the amino acid sequence <SEQ ID 644>. Analysis of this protein sequence reveals the following: TABLE-US-00647 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3619(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00648 Identities = 102/237 (43%), Positives = 165/237 (69%), Gaps = 1/237 (0%) Query: 6 IIEYQNINKVYGENVAVEDINLKIYPGDFVCFIGTSGSGKTTLMRMVNHMLKPTNGTLLF 65 +I + N++K +G+ +++ +I +F +G SGSGKTTL++M+N +++P++G +L Sbjct: 1 MIRFNNVSKTFGQTKVLQEQTFQINDREFFVLVGPSGSGKTTLLKMINCLIEPSSGDILL 60 Query: 66 KGKDISTINPIELRRRIGYVIQNIGLMPHMTIYENIVLVPKLLKWSEEAKRAKARELIKL 125- + ++ E+R IGYV+Q I L P++T+ ENI ++P++ +WS E R K EL+ Sbjct: 61 NNVPQTELDLREMRLSIGYVLQQIALFPNLTVAENIAIIPEMKQWSAEEIRQKTEELLDK 120- Query: 126 VELP-EEYLDRYPSELSGGQQQRIGVIRALAADQDIILMDEPFGALDPITREGIQDLVKS 18- 4 V LP ++YLDRYPS+LSGG+QQRIG++RA+ + I+LMDEPF ALDPI+R+ +Q+L+ S Sbjct: 121 VGLPAKDYLDRYPSDLSGGEQQRIGIVRAIISHPKILLMDEPFSALDPISRKQLQELMLS 18- 0 Query: 185 LQEEMGKTIILVTHDMDEALKLATKIIVMDNGKMVQEGTPNDLLHHPATSFVEQMIG 241 L +E TI+ VTHD+DEA+KL ++ +++ G++VQ P + HPA +FV + G Sbjct: 181 LHKEFDMTIVFVTHDIDEAIKLGDRVAILNEGEIVQLDRPEMIKTHPANAFVVNLFG 237 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 198 A repeated DNA sequence (GBSx0212) was identified in S. agalactiae <SEQ ID 645> which encodes the amino acid sequence <SEQ ID 646>. Analysis of this protein sequence reveals the following: TABLE-US-00649 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4736(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 199 A DNA sequence (GBSx0213) was identified in S. agalactiae <SEQ ID 647> which encodes the amino acid sequence <SEQ ID 648>. Analysis of this protein sequence reveals the following: TABLE-US-00650 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.06 Transmembrane 18-34 (18-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.1426(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty= 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8515> and protein <SEQ ID 8516> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00651 Lipop: Possible site: 20 Crend: 5 Sequence Pattern: CQMN SRCFLG: 0 McG: Length of UR: 19 Peak Value of UR: 2.60 Net Charge of CR: 3 McG: Discrim Score: 7.77 GvH: Signal Score (-7.5): -4.89 Possible site: 25 >>> May be a lipoprotein Amino Acid Composition: calculated from 21 ALOM program count: 0 value: 13.21 threshold: 0.0 PERIPHERAL Likelihood = 13.21 115 modified ALOM score: -3.14 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00018## SEQ ID 8516 (GBS389) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 74 (lane 6; MW 18 kDa). The GBS389-His fusion product was purified (FIG. 214, lane 4) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 313), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 200 A DNA sequence (GBSx0214) was identified in S. agalactiae <SEQ ID 649> which encodes the amino acid sequence <SEQ ID 650>. Analysis of this protein sequence reveals the following: TABLE-US-00652 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3766 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 201 A DNA sequence (GBSx0215) was identified in S. agalactiae <SEQ ID 651> which encodes the amino acid sequence <SEQ ID 652>. Analysis of this protein sequence reveals the following: TABLE-US-00653 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3882 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 202 A DNA sequence (GBSx0216) was identified in S. agalactiae <SEQ ID 653> which encodes the amino acid sequence <SEQ ID 654>. This protein is predicted to be lectin, alpha subunit precursor. Analysis of this protein sequence reveals the following: TABLE-US-00654 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0653 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 203 A DNA sequence (GBSx0217) was identified in S. agalactiae <SEQ ID 655> which encodes the amino acid sequence <SEQ ID 656>. Analysis of this protein sequence reveals the following: TABLE-US-00655 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6569(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 204 A DNA sequence (GBSx0218) was identified in S. agalactiae <SEQ ID 657> which encodes the amino acid sequence <SEQ ID 658>. Analysis of this protein sequence reveals the following: TABLE-US-00656 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5736(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 205 A DNA sequence (GBSx0219) was identified in S. agalactiae <SEQ ID 659> which encodes the amino acid sequence <SEQ ID 660>. Analysis of this protein sequence reveals the following:

TABLE-US-00657 Possible site: 52 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.11 Transmembrane 146-162 (138-170) INTEGRAL Likelihood = -12.90 Transmembrane 13-29 (9-32) INTEGRAL Likelihood = -9.50 Transmembrane 108-124 (104-129) INTEGRAL Likelihood = -7.75 Transmembrane 40-56 (33-61) INTEGRAL Likelihood = -6.64 Transmembrane 177-193 (170-195) INTEGRAL Likelihood = -3.35 Transmembrane 77-93 (77-97) ----- Final Results ----- bacterial membrane --- Certainty = 0.6243(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8517> which encodes amino acid sequence <SEQ ID 8518> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 206 A DNA sequence (GBSx0220) was identified in S. agalactiae <SEQ ID 661> which encodes the amino acid sequence <SEQ ID 662>. Analysis of this protein sequence reveals the following: TABLE-US-00658 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2374(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00659 >GP: AAB89623 GB: AE000990 repressor protein [Archaeoglobus fulgidus] Identities = 34/62 (54%), Positives = 46/62 (73%) Query: 11 LKQVREDIGMTQQELAIRIGVRRETIGHLENNRYNPSLEMALKIVKIFDMKIEDIFQLRK 70 - +K+ R MTQ+ELA R+GVRRETI LE +YNPSL++A KI ++F+ KIEDIF + Sbjct: 5 IKEFRAKFNMTQEELAKRVGVRRETIVFLEKGKYNPSLKLAYKIARVFNAKIEDIFIFDE 64 Query: 71 ED 72 E+ Sbjct: 65 EE 66 There is also homology to SEQ ID 412. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 207 A DNA sequence (GBSx0221) was identified in S. agalactiae <SEQ ID 663> which encodes the amino acid sequence <SEQ ID 664>. Analysis of this protein sequence reveals the following: TABLE-US-00660 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3794 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00661 >GP: CAB61817 GB: AL133236 putative acetyl transferase [Streptomyces coelicolor A3(2)] Identities = 30/97 (30%), Positives = 52/97 (52%), Gaps = 1/97 (1%) Query: 82 VGMLNIVTLARADMQWGELGYVFHNQFWSNGYAFESILALLNSTYEKLGFHHIEAQITPG 141- VGM ++ + Q GE+ Y+ H + W G E +LL+ +++ G H I A P Sbjct: 72 VGMGDLHVRSHTQRQ-GEISYIVHPRVWGQGIGTEIGRSLLSLGFDRWGLHRIRATCDPR 130- Query: 142 NERSEKLVRRLGLTYETTRKDFSFENGKWTDKLIYSI 178 N+ S +++ +LG+TYE + ++ W D L++SI Sbjct: 131 NQASSRVLTKLGMTYEGRHRHTAWIRDGWRDSLVFSI 167 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 208 A DNA sequence (GBSx0222) was identified in S. agalactiae <SEQ ID 665> which encodes the amino acid sequence <SEQ ID 666>. This protein is predicted to be p20 protein. Analysis of this protein sequence reveals the following: TABLE-US-00662 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1044 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00663 >GP: CAA30415 GB: X07542 P20 (AA 1-178) [Bacillus licheniformis] Identities = 56/175 (32%), Positives = 94/175 (53%), Gaps = 6/175 (3%) Query: 16 TVLTERLRLQPVELTNVNDFLEFSSDSETVFYMQRYKANTVEEAQVVLA---NVCMKSPL 72 - T+ TERL L+ +EL + + ++ SD E YM V +A+ ++ ++ ++ Sbjct: 3 TLYTERLTLRKMELEDADVLCQYWSDPEVTKYMNITPFTDVSQARDMIQMINDLSLEGQA 62 Query: 73 GIYAMIEKESQKMIGIIELEIRDEFS--AEFGYILNKNYNGKGYMTEACSKLMSIGFEHL 130- +++I KE+ ++IG + D+ + AE GY L +N+ GKG+ +EA KL+ GF L Sbjct: 63 NRFSIIVKETDEVIGTCGFNMIDQENGRAEIGYDLGRNHWGKGFASEAVQKLIDYGFTSL 122- Query: 131 DLERIYARFDINNKKSGNVMERIGMKKEGELRHLAKNPKGEWKTRAYYSILKEEY 185 +L RI A+ + N S ++ + +KEG LR K KG +S+LK EY Sbjct: 123 NLNRIEAKVEPENTPSIKLLNSLSFQKEGLLRDYEK-AKGRLIDVYMFSLLKREY 176 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 209 A DNA sequence (GBSx0223) was identified in S. agalactiae <SEQ ID 669> which encodes the amino acid sequence <SEQ ID 670>. Analysis of this protein sequence reveals the following: TABLE-US-00664 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5180 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00665 >GP: CAA87001 GB: Z46902 unknown [Saccharomyces cerevisiae] Identities = 105/224 (46%), Positives = 148/224 (65%), Gaps = 3/224 (1%) Query: 1 MGDVVENFTEGKNPKIDTLNGKTVRIEKINPD-HFEDLFQVYGELSTEDSLTYISFSKFN 59 +G VE +T P+ L G T R+E ++ + H +LF Y E + TY+ F Sbjct: 11 VGADVEGWTTRAFPEKVVLKGNTCRLEPLDRERHGSELFSAYSEAG-QKLWTYLPAGPFT 69 Query: 60 SKNEFDVFFQTLLKSEDPYYLAIVDNNTGKVLGTFSLMRIDTKNRVVEMGWVVYSSKLKQ 119- + E+ F + L +++D AI++ T + +GT L+RID N +E+G+VV+S +L++ Sbjct: 70 NLEEYLEFIKELNETKDTVPFAIINKETERAVGTLCLIRIDEANGSLEVGYVVFSPELQK 129- Query: 120 TRIATEAQYLVMKYVFEELCYRRYEWKCDSLNAPSNNSAKRLGFTFEGTFRQAVVYKGRN 17- 9 T IATEAQ+L+MKYVF++L YRRYEWKCDSLN PS +A RLGF +EGTFRQ VVYKGR Sbjct: 130 TIIATEAQFLLMKYVFDDLQYRRYEWKCDSLNGPSRRAAMRLGFKYEGTFRQVVVYKGRT 18- 9 Query: 180 RDTNWYSILDKEWPEKKTRFEKWLDDSNFAVNGYQIRSLSSIEQ 223 RDT W+SI+DKEW + FE+WLD +NF NG Q R +++I + Sbjct: 190 RDTQWFSIIDKEWLRIRKTFEEWLDKTNFE-NGKQKRGIAAIRE 232 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 210 A DNA sequence (GBSx0224) was identified in S. agalactiae <SEQ ID 671> which encodes the amino acid sequence <SEQ ID 672>. Analysis of this protein sequence reveals the following: TABLE-US-00666 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.15 Transmembrane 25-41 (20-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.5861 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8519> and protein <SEQ ID 8520> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00667 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -3.31 GvH: Signal Score (-7.5): -4.44 Possible site: 39 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -12.15 threshold: 0.0 INTEGRAL Likelihood = -12.15 Transmembrane 25-41 (20-49) PERIPHERAL Likelihood = 11.94 59 modified ALOM score: 2.93 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5861 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 672 (GBS43) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 5 (lane 4; MW 34 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 13 (lane 9; MW 58 kDa) and in FIG. 15 (lane 4; MW 59 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 211 A DNA sequence (GBSx0225) was identified in S. agalactiae <SEQ ID 673> which encodes the amino acid sequence <SEQ ID 674>. Analysis of this protein sequence reveals the following: TABLE-US-00668 Possible site: 32 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9519> which encodes amino acid sequence <SEQ ID 9520> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 212 A DNA sequence (GBSx0226) was identified in S. agalactiae <SEQ ID 675> which encodes the amino acid sequence <SEQ ID 676>. Analysis of this protein sequence reveals the following: TABLE-US-00669 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.54 Transmembrane 165-181 (164-181) INTEGRAL Likelihood = -0.85 Transmembrane 67-83 (67-84) ----- Final Results ----- bacterial membrane --- Certainty = 0.1617 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00670 >GP: CAA82211 GB: Z28353 similar to a B. subtilis gene (GB: BACHEMEHY_5) [Clostridium pasteurianum] Identities = 40/185 (21%), Positives = 87/185 (46%), Gaps = 6/185 (3%) Query: 18 MPKGKQKVILSAIELFASQGFHGTSTAQLAKNAEVSQATIYKYFETKDKLLVFILELIVQ 77 - M K K + SAI++F++ G++G + ++A NA V++ T+Y +F++K+++ +I+E V Sbjct: 1 MNKTKDNIFYSAIKVFSNNGYNGATMDEIASNAGVAKGTLYYHFKSKEEIFKYIIEEGVN 60 Query: 78 TIGRPFFTELSTFSTKEELIHFFVQDRFKFIEKNNDLIKILMQELLINSETSTIFTKLIN 137- + T E + + + I KN D K++ +L ++ Sbjct: 61 LMKNEIDEATDKEKTALEKLKAVCRVQLNLIYKNRDFFKVIASQLWGKELRQLELRDIMR 120- Query: 138 STDPNITKIFNCLSEGNSL---NKMEILRAVIGQFITFFIQLY-ILNIKPENLEEELKQI 19- 3 + +I + E S+ N + + A +G + + LY ++N + +N+ ++ + Sbjct: 121 NYVVHIEEFVKDAMEAGSIKKGNSLFVAYAFLGTLCS--VSLYEVINAENDNINNTIENL 17- 8 Query: 194 EKQIL 198 IL Sbjct: 179 MNYIL 183 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 213 A DNA sequence (GBSx0227) was identified in S. agalactiae <SEQ ID 677> which encodes the amino acid sequence <SEQ ID 678>. Analysis of this protein sequence reveals the following: TABLE-US-00671 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2389(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 214 A DNA sequence (GBSx0228) was identified in S. agalactiae <SEQ ID 679> which encodes the amino acid sequence <SEQ ID 680>. Analysis of this protein sequence reveals the following: TABLE-US-00672 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.32 Transmembrane 341-357 (333-361) INTEGRAL Likelihood = -10.93 Transmembrane 253-269 (238-277) INTEGRAL Likelihood = -10.77 Transmembrane 172-188 (166-196) INTEGRAL Likelihood = -8.01 Transmembrane 225-241 (215-251) INTEGRAL Likelihood = -7.01 Transmembrane 21-37 (18-42) INTEGRAL Likelihood = -2.66 Transmembrane 285-301 (283-301) ----- Final Results ----- bacterial membrane --- Certainty = 0.6328(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00673 >GP: CAB42664 GB: AL049819 putative integral membrane protein [Streptomyces coelicolor A3(2)] Identities = 60/156 (38%), Positives = 101/156 (64%), Gaps = 1/156 (0%) Query: 176 LMGFMVFFFVFLISGMALLKERTSGTLDRLLATPVKRSDIVFGYMLSYGILAIIQTIVIV 23- 5 L+G +FL++ +A L+ERTSGTL+RLLA P+ + D++ GY L++G LAI+Q+ + Sbjct: 77 LLGIFPLITMFLVTSIATLRERTSGTLERLLAMPLGKGDLIAGYALAFGALAIVQSALAT 136- Query: 236 LSTIWLLDIQVVGSIFSVIIVNFILALVALSLGILMSTLAKSEFQMMQFIPLIIMPQLFF 29- 5 +W L + V GS + +++V + AL+ +LG+ +S A SEFQ +QF+P +I PQL Sbjct: 137 GLAVWFLGLDVTGSPWLLLLVALLDALLGTALGLFVSAFAASEFQAVQFMPAVIFPQLLL 19- 6 Query: 296 SGII-PLENMASWAQTVGKILPLSYSGDALTKIIMY 330 G+ P +NM + V +LP+SY+ D + +++ + Sbjct: 197 CGLFTPRDNMHPALEAVSDVLPMSYAVDGMNEVLRH 232 There is also homology to a DNA sequence which was identified in S. pyogenes <SEQ ID 681> which encodes the amino acid sequence <SEQ ID 682>. Analysis of this protein sequence reveals the following: TABLE-US-00674 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.41 Transmembrane 263-279 (246-284) INTEGRAL Likelihood = -7.70 Transmembrane 231-247 (224-258) INTEGRAL Likelihood = -4.99 Transmembrane 20-36 (18-39) INTEGRAL Likelihood = -3.72 Transmembrane 349-365 (345-368) INTEGRAL Likelihood = -3.45 Transmembrane 187-203 (182-204) ----- Final Results ----- bacterial membrane --- Certainty = 0.5564(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00675 >GP: CAB12662 GB: Z99108 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 92/369 (24%), Positives = 180/369 (47%), Gaps = 25/369 (6%) Query: 12 IKRKKTSYVTFFLMPILTTLLALSLSFSNNNQAKIGILDKDNSQISKQFIAQLKQNKKYD 71 - I +K +Y+ F P+L T + S+ N+++ ++ I+D+D++ +S+ +I QLK + Sbjct: 15 IFKKPQNYLIMFAAPLLLTFVFGSMLSGNDDKVRLAIVDQDDTILSQHYIRQLKAHDDMY 74 Query: 72 IFTKIKKEHIDHYLQDKSLEAVLTIDKGFSDKVLQGKSQKLNIRSIANSEITEWVKAQTN 131- +F + + L+ K + ++ I + F ++ +GK +L R VK Sbjct: 75 VFENMSESKASEKLKQKKIAGIIVISRSFQTQLEKGKHPELIFRHGPELSEAPMVKQYAE 134- Query: 132 YLLENYNIIGDVALGNEDTFNR---------ILQKNQQLNYDVKQVTLTDRSRSKAVSST 18- 2 L NI A T +K++ + V + TL+D+ S T Sbjct: 135 SALATLNIQVTAAKTASQTAGENWKAAYKTVFAKKHEDIVPAVTRQTLSDKKEGAEASDT 19- 4 Query: 183 TT---GFLLILMLGSTSVIYSGILADKSSQLYHRLMLSNLSRFR----YMLSYVCVGFVA 23- 5 + GF ++ ++ + IL + + ++ RL+ +++SR Y+LS+ +G++ Sbjct: 195 ASRAAGFSILFVMLTMMGAAGTILEARKNGVWSRLLTASVSRAEIGAGYVLSFFVIGWIQ 25- 4 Query: 236 FTIQIVIMLSLLKVFNISFFVPTSLLLIIFFLFSLLAIGFGLLIGAITQNSQQSSQLANL 29- 5 F I ++LS +F I++ P ++++++ LF L +G GL+I A + +Q NL Sbjct: 255 FGI---LLLSTHWLFGINWGNPAAVIVLVS-LFLLTVVGIGLMIAANVRTPEQQLAFGNL 31- 0 Query: 296 IVMPTSMLAGCLWPLSITPSYMQAIGKLLPQNWVLSAIA-IFQSGGTLSQAWPYLLALMG 35- 4 V+ T M++G WP+ I P +MQ+I + LPQ W +S + I +G ++ +L + G Sbjct: 311 FVIATCMVSGMYWPIDIEPKFMQSIAEFLPQKWAMSGLTEIIANGARVTD----ILGICG 36- 6 Query: 355 TALALISFS 363 LA + + Sbjct: 367 ILLAFAAIT 375 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00676 Identities = 92/375 (24%), Positives = 164/375 (43%), Gaps = 66/375 (17%) Query: 11 IKELF----RDKRTLAMMFLAPILIMFLMNVMFSANSNTKVKIGTINVNTKVVSNLDNIK 66 - IK LF R K + FL PIL L+ + S ++N + KIG ++ + +S Sbjct: 5 IKTLFVKIKRKKTSYVTFFLMPILTT-LLALSLSFSNNNQAKIGILDKDNSQISK----- 58 Query: 67 HIQVRSFKFNSSAKKALKSNKIDALISEDNKSYTVFYANTDSSKTTLT-RQAFKTAVNTM 125- +F + LK NK + ++ K + Y S + LT + F V Sbjct: 59 -------QFIAQ----LKQNKKYDIFTKIKKEHIDHYLQDKSLEAVLTIDKGFSDKVLQG 107- Query: 126 NSKELISQVKILANKNPKLAQSLQTRSKYIKEKYNY------GNKNT-----------GF 16- 8 S++L I + N ++ + ++ ++ Y+ E YN GN++T + Sbjct: 108 KSQKL----NIRSIANSEITEWVKAQTNYLLENYNIIGDVALGNEDTFNRILQKNQQLNY 16- 3 Query: 169 FAKMIPIL------------MGFMVFFFVFLISGM--ALLKERTSGTLDRLLATPVKRSD 21- 4 K + + GF++ + S + +L +++S RL+ + + R Sbjct: 164 DVKQVTLTDRSRSKAVSSTTTGFLLILMLGSTSVIYSGILADKSSQLYHRLMLSNLSR-- 22- 1 Query: 215 IVFGYMLSY---GILAIIQTIVIVLSTIWLLDIQVVGSIFSVIIVNFILALVALSLGILM 27- 1 F YMLSY G +A IVI+LS + + +I ++I+ F+ +L+A+ G+L+ Sbjct: 222 --FRYMLSYVCVGFVAFTIQIVIMLSLLKVFNISFFVPTSLLLIIFFLFSLLAIGFGLLI 27- 9 Query: 272 STLAKSEFQMMQFIPLIIMPQLFFSGII-PLENMASWAQTVGKILPLSYSGDALTKIIMY 33- 0 + ++ Q Q LI+MP +G + PL S+ Q +GK+LP ++ A+ I Sbjct: 280 GAITQNSQQSSQLANLIVMPTSMLAGCLWPLSITPSYMQAIGKLLPQNWVLSAIA-IFQS 33- 8 Query: 331 GQGLPNVSSNLLVLL 345 G L LL L+ Sbjct: 339 GGTLSQAWPYLLALM 353 A further related DNA sequence was identified in S. pyogenes <SEQ ID 9081> which encodes the amino acid sequence <SEQ ID 9082>. Analysis of this protein sequence reveals the following:

TABLE-US-00677 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.52 Transmembrane 21-37 (17-43) INTEGRAL Likelihood = -10.30 Transmembrane 351-367 (346-371) INTEGRAL Likelihood = -5.36 Transmembrane 262-278 (260-285) INTEGRAL Likelihood = -2.60 Transmembrane 288-304 (288-305) INTEGRAL Likelihood = -1.81 Transmembrane 229-245 (229-246) ----- Final Results ----- bacterial membrane --- Certainty = 0.6010(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS sequences follows: TABLE-US-00678 Score = 62.5 bits (149), Expect = 9e-12 Identities = 72/382 (18%), Positives = 166/382 (42%), Gaps = 32/382 (8%) Query: 1 MVLFHLIKKESLQIFRNRTALLMMVIFPILMIVILSFAFKSSFNTATTVPKLTIRYQLEG 60 M + + +K ++FR++ L MM + PIL++ +++ F ++ NT + + + ++ Sbjct: 1 MRIIAITEKVIKELFRDKRTLAMMFLAPILIMFLMNVMFSANSNTKVKIGTINVNTKVVS 60 Query: 61 EKTDYQKNFLAFLKVLNQKLHLETKPSNSLEKDRQRVSEGALTAVLEVKKNQTIKVITNN 120- L+ H++ + ++ + + A++ + N++ V N Sbjct: 61 N--------------LDNIKHIQVRSFKFNSSAKKALKSNKIDALIS-EDNKSYTVFYAN 105- Query: 121 INQQNADLINMLVKNYVDNAKTYDSIAALY------PQQLNHIRKRSVDYVKVSSIQTSK 17- 4 + L K V+ + + I+ + P+ ++ RS Y+K + + Sbjct: 106 TDSSKTTLTRQAFKTAVNTMNSKELISQVKILANKNPKLAQSLQTRS-KYIKE---KYNY 16- 1 Query: 175 GMTSADYYA----ISMFTMITFYSMMSAMNLVLSDRQQRITNRIHLTGVSPSFLVFGKLI 23- 0 G + ++A I M M+ F+ + + +L +R +R+ T V S +VFG ++ Sbjct: 162 GNKNTGFFAKMIPILMGFMVFFFVFLISGMALLKERTSGTLDRLLATPVKRSDIVFGYML 22- 1 Query: 231 GAMLATTVQLSLLYIFTRFVLRVNWGTNEWMLIGITASLVYLSVAIGIGLGISIKNEAFL 29- 0 + +Q ++ + T ++L + + + +I + L +++++GI + K+E + Sbjct: 222 SYGILAIIQTIVIVLSTIWLLDIQVVGSIFSVIIVNFILALVALSLGILMSTLAKSEFQM 28- 1 Query: 291 TVASNTIIPIFAFLGGSYVPLTTLHSSIINQLSNISPIKWVNDSLFYLIFGGQYNP-IPV 34- 9 II F G +PL + +S + I P+ + D+L +I GQ P + Sbjct: 282 MQFIPLIIMPQLFFSG-IIPLENM-ASWAQTVGKILPLSYSGDALTKIIMYGQGLPNVSS 33- 9 Query: 350 TLIVNISIGTIFIILALIGMRK 371 L+V + I I + G+++ Sbjct: 340 NLLVLLLFLIILTIANIFGLKR 361 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 215 A DNA sequence (GBSx0229) was identified in S. agalactiae <SEQ ID 683> which encodes the amino acid sequence <SEQ ID 684>. This protein is predicted to be CG1718 gene product (b0794). Analysis of this protein sequence reveals the following: TABLE-US-00679 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.17 Transmembrane 118-134 (117-134) ----- Final Results ----- bacterial membrane --- Certainty = 0.1468(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8521> which encodes amino acid sequence <SEQ ID 8522> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-00680 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -10.96 GvH: Signal Score (-7.5): -4.84 Possible site: 15 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -1.17 threshold: 0.0 INTEGRAL Likelihood = -1.17 Transmembrane 142-158 (141-158) PERIPHERAL Likelihood = 4.98 197 modified ALOM score: 0.73 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1468(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00681 >GP:AAF50837 GB:AE003568 CG1718 gene product [Drosophila melanogaster] Identities = 80/204 (39%), Positives = 123/204 (60%), Gaps = 3/204 (1%) Query: 7 EIIGLIGPSGAGKSTLIKTMLGMEKADKGTALV--LDTQMPDRNILNQIGYMAQSDALYE 64 E GL+G +GAGK+T K M G E+ G A V L + +I IGY Q DAL + Sbjct: 1394 ECFGLLGVNGAGKTTTFKMMTGDERISSGAAYVQGLSLESNMNSIYKMIGYCPQFDALLD 1- 453 Query: 65 SLTGLENLLFFGKMKGIQKTELKQQITHISKVVDLENQLDKFVSGYSGGMKRRLSLAIAL 124- LTG E L F ++G+Q++ ++Q ++K +DK YSGG KR+LS AIA+ Sbjct: 1454 DLTGREVLRIFCMLRGVQESRIRQLSEDLAKSFGFMKHIDKQTHAYSGGNKRKLSTAIAV 1- 513 Query: 125 LGNPTVLILDEPTVGIDPSLRRKIWQELINIKDEGHSIFITTHVMDEAE-LTSKVALLLR 18- 3 +G+P+V+ LDEPT G+DP+ RR++W + I+D G SI +T+H M+E E L +++A+++ Sbjct: 1514 IGSPSVIYLDEPTTGMDPAARRQLWNMVCRIRDSGKSIVLTSHSMEECEALCTRLAIMVN 1- 573 Query: 184 GNIIAFDTPLHLKKQFNVSTIEEV 207 G + HLK +F+ I ++ Sbjct: 1574 GEFKCIGSTQHLKNKFSKGLILKI 1597 Identities = 73/216 (33%), Positives = 128/216 (58%), Gaps = 9/216 (4%) Query: 1 MEVFKGEIIGLIGPSGAGKSTLIKTMLGMEKADKGTALV--LDTQMPDRNILNQIGYMAQ 58 M +F+ EI L+G +GAGK+T I + GM GTA++ D + +G Q Sbjct: 536 MNMFEDEITVLLGHNGAGKTTTISMLTGMFPPTSGTAIINGSDIRTNIEGARMSLGICPQ 59- 5 Query: 59 SDALYESLTGLENLLFFGKMKGIQKTELKQQITHISKVVDLENQLDKFVSGYSGGMKRRL 118- + L++ ++ ++ FF +MKG++ ++Q++ K+++LE++ + S SGGMKR+L Sbjct: 596 HNVLFDEMSVSNHIRFFSRMKGLRGKAVEQEVAKYLKMIELEDKANVASSKLSGGMKRKL 65- 5 Query: 119 SLAIALLGNPTVLILDEPTVGIDPSLRRKIWQELINIKDEGHSIFITTHVMDEAE-LTSK 17- 7 S+ AL G+ V++ DEP+ G+DPS RR++W +L+ + G ++ +TTH MDEA+ L + Sbjct: 656 SVCCALCGDTKVVLCDEPSSGMDPSARRQLW-DLLQQEKVGRTLLLTTHFMDEADVLGDR 71- 4 Query: 178 VALLLRGNIIAFDTPLHLKKQFN-----VSTIEEVF 208 +A++ G + T LKKQ+ VS ++ +F Sbjct: 715 IAIMCDGELKCQGTSFFLKKQYGSGYRLVSGVQNLF 750 A related DNA sequence was identified in S. pyogenes <SEQ ID 685> which encodes the amino acid sequence <SEQ ID 686>. Analysis of this protein sequence reveals the following: TABLE-US-00682 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 49-65 (49-65) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00683 >GP:CAB12660 GB:Z99108 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 151/316 (47%), Positives = 202/316 (63%), Gaps = 18/316 (5%) Query: 4 VQLTNVVKSYKNGKKA-VNDVSLSIEAGNIYGLLGPNGAGKSTLINLILGLIPLSSGKIT 62 +Q N+ K+Y GKK V +S S++ G +GLLGPNGAGKST I++I GL+P SG IT Sbjct: 2 LQAENIKKAY--GKKTIVKGISFSLKKGESFGLLGPNGAGKSTTISMISGLVPHDSGNIT 59 Query: 63 VLGQS-QKTIRKISSQIGYVPQDIAVYPDLTAYENVELFGSLYGLKGAQLKKQVLKSLEF 121- V G K K +IG VPQ+IA+YP LTA+EN+ +G +YGL + KK+ + LE+ Sbjct: 60 VGGYVIGKETAKAKQKIGIVPQEIALYPTLTAHENLMFWGKMYGLTHDEAKKRAAEVLEY 119- Query: 122 VGLHSQAKQFPSQFSGGMKRRLNIACALVHSPKLIIFDEPTVGIDPQSRNHILESIRLLN 18- 1 VGL +AK FSGGMKRR+NI AL+H P+L+I DEPTVGIDPQSRNHILE+++ LN Sbjct: 120 VGLTERAKDKIETFSGGMKRRINIGAALMHKPELLIMDEPTVGIDPQSRNHILETVKQLN 17- 9 Query: 182 KEGATVIYTTHYMEEVEALCDYIFIMDHGQVIEEGPKFELEKRYVANLANQIIVTLTDSR 24- 1 + G TVIYT+HYMEEVE LCD I I+D G++I G K +L R + Q+ V+ + Sbjct: 180 ETGMTVIYTSHYMEEVEFLCDRIGIIDQGEMIAIGTKTDLCSRLGGDTIIQLTVSGINEA 23- 9 Query: 242 HL----ELADKPDWSLIEDGEKLMLKIDNSD------MTSVVHQLTQANITFSEIRHNHL 29- 1 L LA D ++ E L LKID S +TS++ + T +I ++ Sbjct: 240 FLVAIRSLAHVNDVTVHE----LELKIDISAAHHEKVVTSLLAEATAHHINLLSLQVQEP 29- 5 Query: 292 NLEEIFLHLTGKKLRD 307 NLE +FL+LTG+ LRD Sbjct: 296 NLERLFLNLTGRTLRD 311 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00684 Identities = 81/211 (38%), Positives = 125/211 (58%), Gaps = 2/211 (0%) Query: 1 MEVFKGEIIGLIGPSGAGKSTLIKTMLGMEKADKGTALVL-DTQMPDRNILNQIGYMAQS 59 + + G I GL+GP+GAGKSTLI +LG+ G VL +Q R I +QIGY+ Q Sbjct: 25 LSIEAGNIYGLLGPNGAGKSTLINLILGLIPLSSGKITVLGQSQKTIRKISSQIGYVPQD 84 Query: 60 DALYESLTGLENLLFFGKMKGIQKTELKQQITHISKVVDLENQLDKFVSGYSGGMKRRLS 119- A+Y LT EN+ FG + G++ +LK+Q+ + V L +Q +F S +SGGMKRRL+ Sbjct: 85 IAVYPDLTAYENVELFGSLYGLKGAQLKKQVLKSLEFVGLHSQAKQFPSQFSGGMKRRLN 144- Query: 120 LAIALLGNPTVLILDEPTVGIDPSLRRKIWQELINIKDEGHSIFITTHVMDEAE-LTSKV 17- 8 +A AL+ +P ++I DEPTVGIDP R I + + + EG ++ TTH M+E E L + Sbjct: 145 IACALVHSPKLIIFDEPTVGIDPQSRNHILESIRLLNKEGATVIYTTHYMEEVEALCDYI 20- 4 Query: 179 ALLLRGNIIAFDTPLHLKKQFNVSTIEEVFL 209 ++ G +I L+K++ + ++ + Sbjct: 205 FIMDHGQVIEEGPKFELEKRYVANLANQIIV 235 SEQ ID 8522 (GBS391) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 74 (lane 7; MW 30 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 83 (lane 4; MW 55 kDa). GBS391-GST was purified as shown in FIG. 217, lane 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 216 A DNA sequence (GBSx0230) was identified in S. agalactiae <SEQ ID 687> which encodes the amino acid sequence <SEQ ID 688>. Analysis of this protein sequence reveals the following: TABLE-US-00685 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6732(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 217 A repeated DNA sequence (GBSx0231) was identified in S. agalactiae <SEQ ID 689> which encodes the amino acid sequence <SEQ ID 690>. This protein is predicted to be ISL2 protein. Analysis of this protein sequence reveals the following: TABLE-US-00686 Possible site: 58 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00687 >GP:CAC18596 GB:AJ278419 IS1381 transposase [Streptococcus pneumoniae] Identities = 111/129 (86%), Positives = 117/129 (90%) Query: 1 MKAQAIVTSQGRIVSLDIAVNYCHDMKLFKMSRRNIGQAAKILADSGYQGIMKMYSQAQT 60 MK QAIVTSQGRIVSLDI VNYCHDMKLFKMSRRNIGQA KILADSGYQG+MK+Y QAQT Sbjct: 1 MKTQAIVTSQGRIVSLDITVNYCHDMKLFKMSRRNIGQAGKILADSGYQGLMKIYPQAQT 60 Query: 61 PRKSSKLKPLTLEDKTYNHTLSKERIKVENIFAKVKTFKIFSTTYRNRRKRFGLRMNLIA 120- RKSSKLKPLT+EDK NH LSKER KVENIFAKVKTFK+FSTTYR+ RKRFGLRMNL A Sbjct: 61 SRKSSKLKPLTVEDKACNHALSKERSKVENIFAKVKTFKMFSTTYRSHRKRFGLRMNLSA 120- Query: 121 GMINRELGF 129 G+IN ELGF Sbjct: 121 GIINHELGF 129 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 218 A repeated DNA sequence (GBSx0232) was identified in S. agalactiae <SEQ ID 691> which encodes the amino acid sequence <SEQ ID 692>. This protein is predicted to be ISL2 protein. Analysis of this protein sequence reveals the following: TABLE-US-00688 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3996(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00689 >GP:CAC18595 GB:AJ278419 IS1381 transposase [Streptococcus pneumoniae] Identities = 110/125 (88%), Positives = 119/125 (95%) Query: 1 MNYEASKQLTDVRFKRLVGVQRTTFEEMLAVLKTAYQRKHAKGGRTPKLSLEDLLMATLQ 60 MNYEASKQLTD RFKRLVGVQRTTFEEMLAVLKTAYQ KHAKGGR PKLSLEDLLMATLQ Sbjct: 1 MNYEASKQLTDARFKRLVGVQRTTFEEMLAVLKTAYQLKHAKGGRKPKLSLEDLLMATLQ 60 Query: 61 YMREYRTYEQIAADFGIHESNLIRRSQWVESTLIQSGFTISKTHLSAEDTVIVDATEVKI 120- Y+REYRTYE+IAADFG+HESNL+RRSQWVE TL+QSG TIS+T LS+EDTV++DATEVKI Sbjct: 61 YVREYRTYEEIAADFGVHESNLLRRSQWVEVTLVQSGVTISRTPLSSEDTVMIDATEVKI 120- Query: 121 NRPKK 125 NRPKK Sbjct: 121 NRPKK 125 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 219 A DNA sequence (GBSx0233) was identified in S. agalactiae <SEQ ID 693> which encodes the amino acid sequence <SEQ ID 694>. Analysis of this protein sequence reveals the following: TABLE-US-00690 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.40 Transmembrane 130-146 (123-156) INTEGRAL Likelihood = -7.86 Transmembrane 169-185 (167-191) INTEGRAL Likelihood = -6.90 Transmembrane 100-116 (95-118) INTEGRAL Likelihood = -5.52 Transmembrane 199-215 (189-216) ----- Final Results ----- bacterial membrane --- Certainty = 0.5161(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00691 >GP:BAB04126 GB:AP001508 unknown conserved protein in others [Bacillus halodurans] Identities = 47/207 (22%), Positives = 95/207 (45%), Gaps = 14/207 (6%) Query: 7 LQKENTLLEGRIDNSNNQTYTDMIVYLRGA-SISPYHQELIRNDIVNMLLEAQERQASLV 65 L K+N + N + Y D+++Y+R A S S E + ++++ LLEAQ + S Sbjct: 6 LIKDNNEKRKLLTEENLKVYEDLLLYIRLAHSKSEQETEELLTELLDHLLEAQAKGKSAK 65 Query: 66 SVFGEDRHDFINQVIKSTPKISKKEE-TLQRWDLAILLLTIQMIIFLGGYLITEALQQSV 124- +VFG++ + +++I PK+ KE L + L++ T+ ++F G Y + V Sbjct: 66 AVFGDNPKQYADEIIGEIPKMVTKERFGLFAYGLSMFFATV--LVFSGIYRMLRYYVFQV 123- Query: 125 PDLIPITLLDVLFAIFISIIAVKIADTIIYATYNFDK----SKEKKYFFRYIFLILSLII 18- 0 + + + A+ +I ++ IA ++ + + + K F +I + +I Sbjct: 124 GEAVSEVYVGT--ALITTIASIVIAWMFVFVVFQYFRWSCFRTINKVFEFFILWLGGMIP 18- 1 Query: 181 AYILIGKYYHLP----FINIPLWIYLI 203 + Y P I IP+++Y + Sbjct: 182 FALFFALLYFTPNVGRMIEIPVYLYFV 208 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 220 A DNA sequence (GBSx0234) was identified in S. agalactiae <SEQ ID 695> which encodes the amino acid sequence <SEQ ID 696>. This protein is predicted to be minor extracellular protease epr precursor (epr). Analysis of this protein sequence reveals the following: TABLE-US-00692 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.72 Transmembrane 10-26 (5-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.5288(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8523> which encodes amino acid sequence <SEQ ID 8524> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-00693 Lipop Possible site: -1 Crend: 8 McG: Discrim Score: 12.11 GvH: Signal Score (-7.5): -4.02 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -10.72 threshold: 0.0 INTEGRAL Likelihood = -10.72 Transmembrane 8-24 (5-33) PERIPHERAL Likelihood = 13.74 219 modified ALOM score: 2.64 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5288(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-00694 !GB:Z99123 extracellular serine protease [Bacillus s . . . >GP:CAB15866 GB:Z99123 extracellular serine protease [Bacillus subtilis] Identities = 44/150 (29%), Positives = 80/150 (53%), Gaps = 14/150 (9%) Query: 37 QMDTVESSVNHVSDSQLTEAQDMLDKFEKKPSEKLLKDVELALNKLSNSSKKEALQKRFK 96 - ++D V+S N + +A+D + K EK +++ + + A+NKL N + K+ LQKR Sbjct: 428 RLDKVQSYRN------VKDAKDKVAKAEKYKTQQTVDTAQTAINKLPNGTDKKNLQKRLD 48- 1 Query: 97 KAKDKYLKDEADKKATKDATDLVEILEQAPSEENVLKAEAAVNKLTVKESKEALQKRIDT 156- + K +Y+ A+K A D V E++ + +V A++A+ KL K +LQKR++ Sbjct: 482 QVK-RYI-------ASKQAKDKVAKAEKSKKKTDVDSAQSAIGKLPASSEKTSLQKRLNK 53- 3 Query: 157 VKTQYGLIGNQTPSSSVAETTEQGTANPAS 186 VK+ Q+ S++ ++T+ A S Sbjct: 534 VKSTNLKTAQQSVSAAEKKSTDANAAKAQS 563 Identities = 39/124 (31%), Positives = 64/124 (51%), Gaps = 2/124 (1%) Query: 35 TTQMDTVESSVNHVSDSQLTEAQDMLDKFEKKPSEKLLKDVELALNKLSNSSKKEALQKR 94 - +++ +++ +N V + L AQ + EKK ++ + A+N+L K ALQKR Sbjct: 521 SSEKTSLQKRLNKVKSTNLKTAQQSVSAAEKKSTDANAAKAQSAVNQLQAGKDKTALQKR 58- 0 Query: 95 FKKAKDKYLKDEADKKATKDATDLVEILEQAPSEENVLKAEAAVNKLTVKESKEALQKRI 154- K K K EA K T A V+ E+ ++++ A++AVN+L K LQKR+ Sbjct: 581 LDKVKKKVAAAEAKKVETAKAK--VKKAEKDKTKKSKTSAQSAVNQLKASNEKTKLQKRL 63- 8 Query: 155 DTVK 158 + VK Sbjct: 639 NAVK 642 A related DNA sequence was identified in S. pyogenes <SEQ ID 697> which encodes the amino acid sequence <SEQ ID 698>. Analysis of this protein sequence reveals the following: TABLE-US-00695 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.99 Transmembrane 24-40 (23-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.2996(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00696 >CAB15866 GB:Z99123 extracellular serine protease [Bacillus subtilis] Identities = 43/130 (33%), Positives = 71/130 (54%), Gaps = 8/130 (6%) Query: 41 GSHPQTQDKVA---KHSKSAASLLKKAVKAVNDADRLATAAAIQEAQKAVDKLAESSKKK 97 - G P + +K + + +K ++ LK A ++V+ A++ +T A +AQ AV++L K Sbjct: 516 GKLPASSEKTSLQKRLNKVKSTNLKTAQQSVSAAEKKSTDANAAKAQSAVNQLQAGKDKT 57- 5 Query: 98 TLQEQLN-----VAKAKQEQEDAATQAVKAAEETLNQNLKDIAQKAVNDLSNKGKKAALQ 152- LQ++L+ VA A+ ++ + A VK AE+ + K AQ AVN L +K LQ Sbjct: 576 ALQKRLDKVKKKVAAAEAKKVETAKAKVKKAEKDKTKKSKTSAQSAVNQLKASNEKTKLQ 63- 5 Query: 153 SRLDAILPAK 162 RL+A+ P K Sbjct: 636 KRLNAVKPKK 645 Identities = 31/105 (29%), Positives = 53/105 (49%), Gaps = 1/105 (0%) Query: 54 SKSAASLLKKAVKAVNDADRLATAAAIQEAQKAVDKLAESSKKKTLQEQLNVAKAKQEQE 113- +++ S A +AV A++ I +A++ + +L S K L ++L+ ++ + + Sbjct: 380 AQATDSAYAAAEQAVKKAEQTKAQIDINKARELISQLPNSDAKTALHKRLDKVQSYRNVK 43- 9 Query: 114 DAATQAVKAAEETLNQNLKDIAQKAVNDLSNKGKKAALQSRLDAI 158 DA + KA E+ Q D AQ A+N L N K LQ RLD + Sbjct: 440 DAKDKVAKA-EKYKTQQTVDTAQTAINKLPNGTDKKNLQKRLDQV 483 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00697 Identities = 61/233 (26%), Positives = 115/233 (49%), Gaps = 13/233 (5%) Query: 2 SMKIDKKELLALIASIILLIFASVTFFLFKDHGTTQMDTVESSVNHVSDSQLTEAQDMLD 61 SM +KE L + S++ + + +F H TQ + S + + S L +A ++ Sbjct: 12 SMTKSQKEALYWMLSVLTITLIGGSCLIFGSHPQTQDKVAKHSKS--AASLLKKAVKAVN 69 Query: 62 KFEKKPSEKLLKDVELALNKLSNSSKKEALQKRFKKAKDKYLKDEADKKATKDATDLVEI 121- ++ + +++ + A++KL+ SSKK+ LQ++ AK K +++A AT V+ Sbjct: 70 DADRLATAAAIQEAQKAVDKLAESSKKKTLQEQLNVAKAKQEQEDA-------ATQAVKA 122- Query: 122 LEQAPSEENVLKAEAAVNKLTVKESKEALQKRIDTVKTQYGLIGNQTPSSSVAETTEQGT 18- 1 E+ ++ A+ AVN L+ K K ALQ R+D + +I ++ P S E T+ Sbjct: 123 AEETLNQNLKDIAQKAVNDLSNKGKKAALQSRLDAILPAKPII-DEFPRQS-GEITDNSY 18- 0 Query: 182 ANPASQDTSSYVNQNVAPTYE-QPQANNTPVTPGVNNTVP-TPGTGTVPATNG 232 P D S + + +PT + +++ + VTP ++ P P T + P+ +G Sbjct: 181 WTPFPGDVSDTYDNSQSPTLDPSSESSASDVTPQPSHPDPIPPQTSSEPSDSG 233 SEQ ID 8524 (GBS278) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 52 (lane 6; MW 40 kDa). The GBS278-His fusion product was purified (FIG. 206, lane 10) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 305), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 221 A DNA sequence (GBSx0235) was identified in S. agalactiae <SEQ ID 699> which encodes the amino acid sequence <SEQ ID 700>. Analysis of this protein sequence reveals the following: TABLE-US-00698 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1466 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 222 A DNA sequence (GBSx0236) was identified in S. agalactiae <SEQ ID 701> which encodes the amino acid sequence <SEQ ID 702>. This protein is predicted to be N-acetylglucosamine-6-phosphate deacetylase (nagA). Analysis of this protein sequence reveals the following: TABLE-US-00699 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4607 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9297> which encodes amino acid sequence <SEQ ID 9298> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00700 >GP:AAG21688 GB:AY007718 N-acetylglucosamine-6-phosphate deacetylase [Lactococcus lactis subsp. cremoris] Identities = 113/178 (63%), Positives = 135/178 (75%) Query: 131 GIYFEGPYFTEEYKGAQNPIYMRNPNLEEFAQWQKAAKGLITKIALAPEREGVEEFVSAI 19- 0 GI+FEGP+FTEE KGAQNP YMR+ + E WQ+AA G++ KI LAPEREG E+F+ Sbjct: 1 GIFFEGPFFTEEKKGAQNPKYMRDAKMWELEDWQEAAHGMLKKIGLAPEREGSEDFIRKA 60 Query: 191 TKQGVTVALGHSNGTYKEAKKAVKAGASVWVHAYNGMRGLTHREPGMVGAVYNLPNTYAE 25- 0 T+ GV +ALGHSN TYK+A V+AGASVWVH +NGM G+TH+EPGMVGA+ N PNTYAE Sbjct: 61 TESGVVIALGHSNATYKQAVAGVQAGASVWVHTFNGMSGMTHQEPGMVGAILNTPNTYAE 120- Query: 251 LICDGHHVDPVACDILMTQKGHNHVALITDCMAAGGAPDGDYMLGELPVVVSNGTARL 308 LICDGHHV P A +I++ KG +HV LITD M A G PDG YMLGE V V +G A L Sbjct: 121 LICDGHHVRPEAAEIVVKMKGADHVVLITDSMRAAGLPDGPYMLGEYEVEVRDGAAWL 178 A related DNA sequence was identified in S. pyogenes <SEQ ID 703> which encodes the amino acid sequence <SEQ ID 704>. Analysis of this protein sequence reveals the following: TABLE-US-00701 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3114 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00702 Identities = 227/300 (75%), Positives = 262/300 (86%) Query: 9 MTKYIKADRFFYADHVKENGYLEIKDNHFGKWIENISGQEEILDYSGYQIAPGLVDTHIH 68 MT Y+KAD F+Y V+ GYL + D FG+W E + +I+DY+GYQIAPGLVDTHIH Sbjct: 1 MTCYLKADCFYYPTEVRPAGYLSLHDGVFGEWTEIVPADAQIIDYTGYQIAPGLVDTHIH 60 Query: 69 GFAGADVMDCDSEGILRMSAGLLSTGVTSFLPTTLTSDTKRLEEASKSVAAVAGKEQGAK 128- G+AGADVMD ++GI +MS GLL+TGVTSFLPTTLTS ++LE+ S ++A+VA + +GAK Sbjct: 61 GYAGADVMDNSAQGIHQMSEGLLATGVTSFLPTTLTSTFEQLEKVSGTIASVADQVKGAK 120- Query: 129 IQGIYFEGPYFTEEYKGAQNPIYMRNPNLEEFAQWQKAAKGLITKIALAPEREGVEEFVS 18- 8 IQGIYFEGPYFTEEYKGAQNP YM+ P LEEF WQKAAKGLI KIALAPER+GV+EFVS Sbjct: 121 IQGIYFEGPYFTEEYKGAQNPSYMKTPRLEEFDAWQKAAKGLIKKIALAPERDGVKEFVS 18- 0 Query: 189 AITKQGVTVALGHSNGTYKEAKKAVKAGASVWVHAYNGMRGLTHREPGMVGAVYNLPNTY 24- 8 A+TKQGVTVALGHSNGTY+EAK+AV+AGASVWVHAYNGMRGLTHREPGMVGAVYNLPNTY Sbjct: 181 AVTKQGVTVALGHSNGTYQEAKEAVQAGASVWVHAYNGMRGLTHREPGMVGAVYNLPNTY 24- 0 Query: 249 AELICDGHHVDPVACDILMTQKGHNHVALITDCMAAGGAPDGDYMLGELPVVVSNGTARL 30- 8 AELICDGHHV P+ACDILM QKGH+HVA+ITDCM AGG+PDGDY+LGE VVV+NGTARL Sbjct: 241 AELICDGHHVSPIACDILMQQKGHDHVAMITDCMRAGGSPDGDYLLGEFSVVVANGTARL 30- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 223 A DNA sequence (GBSx0237) was identified in S. agalactiae <SEQ ID 705> which encodes the amino acid sequence <SEQ ID 706>. Analysis of this protein sequence reveals the following: TABLE-US-00703 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3709(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9307> which encodes amino acid sequence <SEQ ID 9308> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00704 >GP:CAB16112 GB:Z99124 yyaQ [Bacillus subtilis] Identities = 40/110 (36%), Positives = 62/110 (56%), Gaps = 12/110 (10%) Query: 121 IAKTFEDSVDYPFAKHPQYASYRVSG--KWYALLFPLKMGKLENVPAQLSED---EVEVL 17- 5 + + + S DYP+ K+P YAS R + KWY L+ + +P +L D E+++L Sbjct: 11 VKEKYGTSPDYPWEKYPNYASLRHTSNKKWYGLIMNV-------LPEKLGLDGHGEIDIL 63 Query: 176 NIKVNPQDMEILLQKEGIYPSYHMSKKTWVSIVLDNTLSDIEIFKLVSDS 225 N+K P+ + L E I P YHM K+ W+SIVL+ T + EI+ L+ S Sbjct: 64 NLKCPPEISDRLRNGENILPGYHMDKEHWISIVLERTDPEGEIYNLIEQS 113 A related DNA sequence was identified in S. pyogenes <SEQ ID 707> which encodes the amino acid sequence <SEQ ID 708>. Analysis of this protein sequence reveals the following: TABLE-US-00705 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2541(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00706 Identities = 114/247 (46%), Positives = 169/247 (68%), Gaps = 1/247 (0%) Query: 7 MSIESDFFRKKRFIFSSLEEFGFIKSDQEYIYCQTFMDNDFKAIITISLDGKIAGKVIDS 66 MS+ +D+F ++ I L +GF K D Y Y +FM+ +F+A + I G I +VID Sbjct: 1 MSLATDYFSRQTPIVEKLMAYGFEKRDNGYFYNERFMEGEFEAQLRIDEAGNIWDRVIDC 60 Query: 67 ALEEEYLPLRAANYNGSFVGEVRSAYMAILGDISDSCCKDLLFTKDQSNRLAEKIAKTFE 126- LEE+YLPL+ A + G++ G+VR+AY+ +L +S +C + F Q+NRLA+ I K + Sbjct: 61 DLEEDYLPLQQAAWQGTYTGQVRAAYLELLERLSVACFEATPFQSMQANRLAKHITKEWS 120- Query: 127 DSVDYPFAKHPQYASYRVSGKWYALLFPLKMGKLENVPAQLSEDEVEVLNIKVNPQDMEI 18- 6 D +DYPF KHP A+YRV GKWYA++F L KL+ + P +L EV+ +KVNP+ Sbjct: 121 DPMDYPFEKHPDLATYRVGGKWYAMIFSLLADKLDQIPERLVGQTCEVMTVKVNPKAFPQ 18- 0 Query: 187 LLQKEGIYPSYHMSKKTWVSIVLDNTLSDIEIFKLVSDSRKLVSHNKKSN-SEPEFWIIP 24- 5 LLQ+EGIYP+YHMSKK W+SI+LD+ ++D +++ LV+ SR+LV+ N SN + P++W+IP Sbjct: 181 LLQQEGIYPAYHMSKKNWISIILDDKVTDDKLWTLVTQSRQLVNPNGLSNPNGPDYWVIP 24- 0 Query: 246 ANPKFYD 252 AN K+YD Sbjct: 241 ANLKYYD 247 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 224 A DNA sequence (GBSx0238) was identified in S. agalactiae <SEQ ID 709> which encodes the amino acid sequence <SEQ ID 710>. This protein is predicted to be transposase for insertion sequence element is 905. Analysis of this protein sequence reveals the following: TABLE-US-00707 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1824(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9601> which encodes amino acid sequence <SEQ ID 9602> was also identified. A related GBS nucleic acid sequence <SEQ ID 9595> which encodes amino acid sequence <SEQ ID 9596> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00708 >GP:AAA25167 GB:L20851 transposase [Lactococcus lactis] Identities = 325/391 (83%), Positives = 365/391 (93%) Query: 12 MTQFTTELLNFLAQKQDIDEFFRSSLETAMNDLLQVELSAFLGYEPYDKAGYNTGNSRNG 71 - MTQFTTELLNFLAQKQDIDEFFR+SLETAMNDLLQ ELSAFLGYEPYDK GYN+GNSRNG Sbjct: 1 MTQFTTELLNFLAQKQDIDEFFRTSLETAMNDLLQAELSAFLGYEPYDKVGYNSGNSRNG 60 Query: 72 AYTRRFETKYGVVNLLIPRDRNGEFSPALIPSYGRRDNHLEEMVIKLYRTGVTTREISDI 131- +Y+R+FETKYG V L IPRDRNG FSPAL+P+YGRRD+HLEEMVIKLY+TGVTTREISDI Sbjct: 61 SYSRQFETKYGTVQLSIPRDRNGNFSPALLPAYGRRDDHLEEMVIKLYQTGVTTREISDI 120- Query: 132 IERMYGHHYSPATVSNISKATQENVASFHERSLEANYTVLYLDGTYLPLRRGTVSKECIH 19- 1 IERMYGHHYSPAT+SNISKATQENVA+FHERSLEANY+VL+LDGTYLPLRRGTVSKECIH Sbjct: 121 IERMYGHHYSPATISNISKATQENVATFHERSLEANYSVLFLDGTYLPLRRGTVSKECIH 18- 0 Query: 192 IALGVTSYGHKAILGYDIAPNENNASWSDLLERFKGQGVQQVSLVVSDGFNGLDQLIQQA 25- 1 IALG+T G KA+LGY+IAPNENNASWS LL++ + QG+QQVSLVV+DGF GL+Q+I QA Sbjct: 181 IALGITPEGQKAVLGYEIAPNENNASWSTLLDKLQNQGIQQVSLVVTDGFKGLEQIISQA 24- 0 Query: 252 FPMAKQQRCLVHIGRNIASKVKRADRALILEQFKTIYRAINVEEAKQALDSFINEWKPHY 31- 1 +P+AKQQRCL+HI RN+ASKVKRADRA+ILEQFKTIYRA N+E A QAL++FI EWKP Y Sbjct: 241 YPLAKQQRCLIHISRNLASKVKRADRAVILEQFKTIYRAENLEMAVQALENFIAEWKPKY 30- 0 Query: 312 KKVIETLESIENLLIFYEFPHQIWGSIYSTNLIESLNKEIKRQTKKKVVFPNEESLERYL 37- 1 +KV+E+LE+ +NLL FY+FP+QIW SIYSTNLIESLNKEIKRQTKKKV+FPNEE+LERYL Sbjct: 301 RKVMESLENTDNLLTFYQFPYQIWHSIYSTNLIESLNKEIKRQTKKKVLFPNEEALERYL 36- 0 Query: 372 VTLFSDYNFKQGQRIHKGFGQCTDTLESLFD 402 VTLF DYNFKQ QRIHKGFGQC DTLESLFD Sbjct: 361 VTLFEDYNFKQSQRIHKGFGQCADTLESLFD 391 A related DNA sequence was identified in S. pyogenes <SEQ ID 711> which encodes the amino acid sequence <SEQ ID 712>. Analysis of this protein sequence reveals the following: TABLE-US-00709 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3054 (Atfirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00710 Identities = 111/128 (86%), Positives = 122/128 (94%) Query: 12 MTQFTTELLNFLAQKQDIDEFFRSSLETAMNDLLQVELSAFLGYEPYDKAGYNTGNSRNG 71 - MTQFTTELLNFLAQKQDIDEFFRSSLE AMNDLLQVELSAFLGYEPY+K GYNTGNSRNG Sbjct: 1 MTQFTTELLNFLAQKQDIDEFFRSSLEIAMNDLLQVELSAFLGYEPYEKEGYNTGNSRNG 60 Query: 72 AYTRRFETKYGVVNLLIPRDRNGEFSPALIPSYGRRDNHLEEMVIKLYRTGVTTREISDI 131- Y+R+FETKYG+VNL+IPRDRNGEFSP L+PSY RR++HLEE+VIKLY+TGVTTREISDI Sbjct: 61 TYSRQFETKYGLVNLIIPRDRNGEFSPVLLPSYARREDHLEEIVIKLYQTGVTTREISDI 120- Query: 132 IERMYGHH 139 I+RMYG H Sbjct: 121 IKRMYGDH 128 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 225 A DNA sequence (GBSx0239) was identified in S. agalactiae <SEQ ID 713> which encodes the amino acid sequence <SEQ ID 714>. Analysis of this protein sequence reveals the following: TABLE-US-00711 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.42 Transmembrane 268-284 (260-286) INTEGRAL Likelihood = -6.32 Transmembrane 232-248 (231-254) ----- Final Results ----- bacterial membrane --- Certainty = 0.5967 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00712 >GP:AAD40365 GB:AF036485 hypothetical protein [Piasmid pNZ4000] Identities = 69/283 (24%), Positives = 133/283 (46%), Gaps = 9/283 (3%) Query: 11 INVDDLSLQEERF-LPSELLAYARDENESS-FVRDIEGHLALVYQLLDTQGHVDDVRHVP 68 - IN ++ + E+++ + +++ Y D +ES+ +V DI L L D +R++ Sbjct: 19 INAEERATLEDQYGIDEDIIEYVTDNDESTNYVYDINEDDQLFIFLAPYALDKDALRYIT 78 Query: 69 RVIPVTLFLKEDGLFVLANHKNINLVKKALNRV---EKVDSPKHLLLSLVTAFSKQYFDV 125- + P + L + LF N I V AL +V S +L + + + Sbjct: 79 Q--PFGMLLHKGVLFTF-NQSGIPEVNTALYSALDNPEVKSVDAFILETLFTVVVSFIPI 135- Query: 126 LDTISEERDKLINDLRKRPNKSNLARLANLQSGTVHLMMGTKQNFEMLTDLQNIEQDKEN 18- 5 I+++R+ L L ++ S+L L+ LQ L + N L L Sbjct: 136 SRAITKKRNYLDKMLNRKTKNSDLVSLSYLQQTLTFLSSAVQTNLSELDRLPKTHFGVGA 19- 5 Query: 186 TRNEKMQLQDAIIEARQLSNMCSLNSQVFQELS-SYNNVLSNNLNDNVTTLTIISIGISI 24- 4 +++ +D IE Q+ M + +QV + + N++ +NNLND + LTI S+ +++ Sbjct: 196 DQDKIDLFEDVQIEGEQVQRMFEIETQVVDRIDHTLNSLANNNLNDTMKFLTIWSLTMAV 25- 5 Query: 245 IAMVTSFYGMNVKLPFDSVDAVWVLIILITTIITIMLSIVMYI 287 +++ FYGMNVKLP + W+L + I+ ++ + + I++ + Sbjct: 256 PTIISGFYGMNVKLPLAGMQYAWMLTLGISVVLIVAMLIMLKV 298 SEQ ID 714 (GBS422) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 172 (lane 7; MW 60 kDa). GBS422-GST was purified as shown in FIG. 219, lane 12. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 226 A DNA sequence (GBSx0240) was identified in S. agalactiae <SEQ ID 717> which encodes the amino acid sequence <SEQ ID 718>. Analysis of this protein sequence reveals the following:

TABLE-US-00713 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0783(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00714 >GP: CAB61731 GB: AL133220 putative oxidoreductase. [Streptomyces coelicolor A3(2)] Identities = 100/306 (32%), Positives = 152/306 (48%), Gaps = 3/306 (0%) Query: 3 KVRYGVVSTAKVAPRFIEGVRLAGNGEVVAVSSRTLESAQAFANKYHLPKAYDKLEDMLA 62 KVR+G+++T +A RF + + EVVAV+SRT SA+ FA ++ +P+AY E + Sbjct: 8 KVRWGILATGGMAARFTADLVDLPDAEVVAVASRTEASAKTFAERFGIPRAYGGWETLAR 67 Query: 63 DESIDVIYVATINQDHYKVAKAALLAGKHVLVEKPFTLTYDQANELFALAESCNLFLMEA 122- DE +DV+YVAT + H A L AG++VL EKPFTL +A EL ALA +FLMEA Sbjct: 68 DEDVDVVYVATPHSAHRTAAGLCLEAGRNVLCEKPFTLNAREAAELVALARENGVFLMEA 127- Query: 123 QKSVFIPMTQVIKKLLASGEIGEVISISSTTAYPN-IDHVTWFRELELGGGTVHFMAPYA 18- 1 P+ + +K+L+A G IGEV S+ + R+ GGG + + Y Sbjct: 128 MWMYCNPLVRRLKELVADGAIGEVRSLQADFGLAGPFPAAHRLRDPAQGGGALLDLGVYP 18- 7 Query: 182 LSYLQYLFDATITHASGTATFPKGQSDSQSKLLLQLSNGVLVDIFLTTRLNLPHEMIIYG 24- 1 +S+ Q L T + A + D Q+ LL N L I + P+ I G Sbjct: 188 VSFAQLLLGEP-TDVAARAVLSEEGVDLQTGALLSYGNDALASIHCSITGGTPNSASITG 24- 6 Query: 242 TEGRLIIPH-FWKTTHAKLVRNDTSARTIQVDMVSDFEKEAYHVSQMILEGQRVSHIMTP 30- 0 +EGR+ +P+ F+ H L R + + D + H ++ ++ R +P Sbjct: 247 SEGRIDVPNGFFFPDHFVLHRTGRDPQEFRADPADGPRESLRHEAEEVMRALRAGETESP 30- 6 Query: 301 QLTLSG 306 + L G Sbjct: 307 LVPLDG 312 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 227 A DNA sequence (GBSx0241) was identified in S. agalactiae <SEQ ID 721> which encodes the amino acid sequence <SEQ ID 722>. This protein is predicted to be valyl-tRNA synthetase (valS). Analysis of this protein sequence reveals the following: TABLE-US-00715 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.00 Transmembrane 794-810 (794-810) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00716 >GP: AAA57558 GB: L08854 valyl-tRNA synthetase [Lactobacillus casei] Identities = 543/881 (61%), Positives = 679/881 (76%), Gaps 12/881 (1%) Query: 5 LSPKYNPAEVEEGRYQTWLDQDVFKPSGDTEAKPYSIVIPPPNVTGKLHLGHAWDTTLQD 64 L+PKY+ VEEGRYQ WLD+DVFKPSGD +AKPYSIVIPPPNVTGKLH+GHAWDTTLQD Sbjct: 27 LAPKYDHKAVEEGRYQEWLDEDVFKPSGDKKAKPYSIVIPPPNVTGKLHMGHAWDTTLQD 86 Query: 65 IIIRQKRMQGFDTLWLPGMDHAGIATQAKVEERLREQGISRYDLGREKFLDKVWEWKDEY 124- I+IRQKR++GFDTLWLPGMDHAGIATQAKVE +LR++GISRYDLGREKF+ KVWEWKDE+ Sbjct: 87 IVIRQKRIEGFDTLWLPGMDHAGIATQAKVEAKLRKEGISRYDLGREKFVQKVWEWKDEF 146- Query: 125 AATIKSQWGKMGLSVDYSRERFTLDEGLSKAVRKVFVDLYNKGWIYRGEFIINWDPAART 18- 4 A TI QW KMGLS+DYSRERFTLD+GL++AVR+VFVDLYN+G IYRGE+I+NWDP ART Sbjct: 147 AKTIHGQWAKMGLSLDYSRERFTLDKGLNQAVRRVFVDLYNQGLIYRGEYIVNWDPQART 20- 6 Query: 185 ALSDIEVIHKDVEGAFYHMNYMLEDGSRALEVATTRPETMFGDVAVAVNPEDARYKDLIG 24- 4 ALSDIEVIHKD +GAFYH+ Y DGS +E+ATTRPETM GD AVAV+P D RYKD++G Sbjct: 207 ALSDIEVIHKDDKGAFYHVKYPFADGSGYIEIATTRPETMMGDTAVAVHPGDERYKDMVG 26- 6 Query: 245 QNVILPIINKPIPIVADEHADPEFGTGVVKITPAHDPNDFAVGQRHNLPQVNVMNDDGTM 30- 4 +ILP+ N+ IPI+ D + DPEFGTG VKITPAHDPNDF VG RH+L ++N MNDDGTM Sbjct: 267 TELILPLANRKIPIIEDAYVDPEFGTGAVKITPAHDPNDFQVGNRHDLKRINTMNDDGTM 32- 6 Query: 305 NELADEFNGMDRFEARKAVVAKLESLGNLVKIKKTTHSVGHSERTGVVVEPRLSTQWFVK 36- 4 NE A ++ GMDRFEARKA+VA L+ G L+K++ HSVGHSERTGV VE RLSTQWFVK Sbjct: 327 NENAGKYQGMDRFEARKAMVADLDKAGLLLKVEPIVHSVGHSERTGVQVEARLSTQWFVK 38- 6 Query: 365 MDQLAKNAI-ANQDTEDKVEFYPPRFNDTFMSWMENVHDWVISRQLWWGHQIPAWYN-VN 42- 2 M LA+ AI A Q+ + KV F P RF T++ WMEN+HDWVISRQLWWGHQIPAWYN Sbjct: 387 MKPLAEAAIKAQQEPDKKVTFVPERFEHTYLQWMENIHDWVISRQLWWGHQIPAWYNKQT 44- 6 Query: 423 GEMYVGEDAPEG-DGWTQDEDVLDTWFSSALWPFSTMGWPDTEAADFKRYFPTSTLVTGY 48- 1 GE YVG +AP+ + W QD DVLDTWFSSALWPFSTMGWP+T+A D+KRY+PT TLVTGY Sbjct: 447 GETYVGMEAPKDIENWKQDPDVLDTWFSSALWPFSTMGWPNTDAPDYKRYYPTDTLVTGY 50- 6 Query: 482 DIIFFWVSRMIFQSLEFTGRQPFSNVLIHGLIRDEEGRKMSKSLGNGIDPMDVIEKYGAD 54- 1 DII FWV+RMIFQ L FT ++PF LIHGL+RDE+GRKMSKSLGNGIDPMDVIEKYGAD Sbjct: 507 DIIPFWVARMIFQGLHFTHQRPFQYTLIHGLMRDEQGRKMSKSLGNGIDPMDVIEKYGAD 56- 6 Query: 542 ALRWFLSNGSAPGQDVRFSYEKMDASWNFINKIWNISRYILMNNEGLTLDQARENVEKVV 60- 1 ALRWFL G+ PGQD RFSY++++A+WNFINKIWNISR+++MN L Q + Sbjct: 567 ALRWFLITGNKPGQDTRFSYKQVEAAWNFINKIWNISRFVMMNLGDLDTPQQPD------ 62- 0 Query: 602 NSQVGNVTDRWILHNLNETVGKVTENFDKFEFGVAGHILYNFIWEEFANWYVELTKEVLY 66- 1 +++D+W+ LNET+ +V + +FEFG G LYNF W A+WYVE++KEVLY Sbjct: 621 -PSTFDLSDKWLFAQLNETIKQVMDLSARFEFGEMGRTLYNFTWNVLADWYVEMSKEVLY 67- 9 Query: 662 SDNEDEKVITRSVLLYTLDQILRLLHPINPFVTEEIF--GQYAEGSIVLASYPQVNATFE 71- 9 D+E K R L Y LDQILRLLHP+NPFV +++ + SIV ASYP N FE Sbjct: 680 GDDEQAKAAKRVNLAYALDQILRLLHPVMPFVHGKLWLALPHTGKSIVTASYPVANTAFE 73- 9 Query: 720 NQTAHKGVESLKDLIRSVRNSRAEVNVAPSKPITILVKTSDSELESFFKDNSNYIKRFTN 77- 9 N A ++++ LIR VR R E + ILVK +D L+ F+ N ++I RF N Sbjct: 740 NADATSAMDAIIALIRGVRGIRKEAGAPLKTKVDILVKLTDPALKPIFEQNFDFIDRFVN 79- 9 Query: 780 PETLEISSAIATPELAMSSVITGAEIFLPLADLLNVEEELARLEKELAKWQKELDNVGKK 83- 9 + + + +A P++A S+VITGA IF+PL +L++++EE A+L K+ K ++E+ + KK Sbjct: 800 SKAFTVGTDVAEPKMAGSAVITGATIFVPLNELIDLDEEKAKLTKDAKKLEQEIARIDKK 85- 9 Query: 840 LSNERFVANAKPEVVQKEKDKQTDYQTKYDATIARIEEMKK 880 L+N+ F++ A VV +++ K++D++ + +T R+E++++ Sbjct: 860 LNNQGFLSKAPEAVVAEQRTKRSDFEDQLTSTKQRLEQLQR 900 A related DNA sequence was identified in S. pyogenes <SEQ ID 723> which encodes the amino acid sequence <SEQ ID 724>. Analysis of this protein sequence reveals the following: TABLE-US-00717 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5062 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00718 Identities = 782/878 (89%), Positives = 818/878 (93%) Query: 4 ELSPKYNPAEVEEGRYQTWLDQDVFKPSGDTEAKPYSIVIPPPNVTGKLHLGHAWDTTLQ 63 ELSPKYNPAEVE GRYQ WLD DVFKPSGD +AKPYSIVIPPPNVTGKLHLGHAWDTTLQ Sbjct: 3 ELSPKYNPAEVEAGRYQKWLDADVFKPSGDQKAKPYSIVIPPPNVTGKLHLGHAWDTTLQ 62 Query: 64 DIIIRQKRMQGFDTLWLPGMDHAGIATQAKVEERLREQGISRYDLGREKFLDKVWEWKDE 123- DIIIRQKRMQGFDTLWLPGMDHAGIATQAKVEERLREQGISRYDLGR+KFLDKVWEWKDE Sbjct: 63 DIIIRQKRMQGFDTLWLPGMDHAGIATQAKVEERLREQGISRYDLGRDKFLDKVWEWKDE 122- Query: 124 YAATIKSQWGKMGLSVDYSRERFTLDEGLSKAVRKVFVDLYNKGWIYRGEFIINWDPAAR 18- 3 YA TIK QWGKMGLSVDYSRERFTLDEGLSKAVRKVFVDLY KGWIYRGEFIINWDPAAR Sbjct: 123 YATTIKEQWGKMGLSVDYSRERFTLDEGLSKAVRKVFVDLYKKGWIYRGEFIINWDPAAR 18- 2 Query: 184 TALSDIEVIHKDVEGAFYHMNYMLEDGSRALEVATTRPETMFGDVAVAVNPEDARYKDLI 24- 3 TALSDIEVIHKDVEGAFYHMNYMLEDGSRAL+VATTRPETMFGDVAVAVNPED RYKDLI Sbjct: 183 TALSDIEVIHKDVEGAFYHMNYMLEDGSRALQVATTRPETMFGDVAVAVNPEDPRYKDLI 24- 2 Query: 244 GQNVILPIINKPIPIVADEHADPEFGTGVVKITPAHDPNDFAVGQRHNLPQVNVMNDDGT 30- 3 G+NVILPI+NK IPIV DEHADPEFGTGVVKITPAHDPNDF VGQRHNLPQVNVMNDDGT Sbjct: 243 GKNVILPIVNKLIPIVGDEHADPEFGTGVVKITPAHDPNDFEVGQRHNLPQVNVMNDDGT 30- 2 Query: 304 MNELADEFNGMDRFEARKAVVAKLESLGNLVKIKKTTHSVGHSERTGVVVEPRLSTQWFV 36- 3 MNELA +F GMDRFEAR+A VAKLE LG LV I+K HSVGHSER+G VVEPRLSTQWFV Sbjct: 303 MNELAGDFAGMDRFEARQATVAKLEELGALVNIEKRVHSVGHSERSGAVVEPRLSTQWFV 36- 2 Query: 364 KMDQLAKNAIANQDTEDKVEFYPPRFNDTFMSWMENVHDWVISRQLWWGHQIPAWYNVNG 42- 3 KMD+LAK A+ NQ+T+D+V+FYPPRFNDTF+ WMENVHDWVISRQLWWGHQIPAWYN G Sbjct: 363 KMDELAKQAMDNQETDDRVDFYPPRFNDTFLQWMENVHDWVISRQLWWGHQIPAWYNAEG 42- 2 Query: 424 EMYVGEDAPEGDGWTQDEDVLDTWFSSALWPFSTMGWPDTEAADFKRYFPTSTLVTGYDI 48- 3 E+YVGE+APEGD WTQDEDVLDTWFSSALWPFSTMGWPDT+ DFKRYFPTSTLVTGYDI Sbjct: 423 EIYVGEEAPEGDDWTQDEDVLDTWFSSALWPFSTMGWPDTDVEDFKRYFPTSTLVTGYDI 48- 2 Query: 484 IFFWVSRMIFQSLEFTGRQPFSNVLIHGLIRDEEGRKMSKSLGNGIDPMDVIEKYGADAL 54- 3 IFFWVSRMIFQSLEFTGRQPF NVLIHGLIRDEEGRKMSKSLGNGIDPMDVIEKYGAD+L Sbjct: 483 IFFWVSRMIFQSLEFTGRQPFQNVLIHGLIRDEEGRKMSKSLGNGIDPMDVIEKYGADSL 54- 2 Query: 544 RWFLSNGSAPGQDVRFSYEKMDASWNFINKIWNISRYILMNNEGLTLDQARENVEKVVNS 60- 3 RWFLSNGSAPGQDVRFSYEKMDASWNFINKIWNISRYILMNNEGLTL+ A NV KV S Sbjct: 543 RWFLSNGSAPGQDVRFSYEKMDASWNFINKIWNISRYILMNNEGLTLEDAESNVAKVAAS 60- 2 Query: 604 QVGNVTDRWILHNLNETVGKVTENFDKFEFGVAGHILYNFIWEEFANWYVELTKEVLYSD 66- 3 + GNVTD+WILHNLNET+ KVTENFDKFEFGVAGHILYNFIWEEFANWYVELTKEVLYSD Sbjct: 603 EAGNVTDQWILHNLNETIAKVTENFDKFEFGVAGHILYNFIWEEFANWYVELTKEVLYSD 66- 2 Query: 664 NEDEKVITRSVLLYTLDQILRLLHPIMPFVTEEIFGQYAEGSIVLASYPQVNATFENQTA 72- 3 NE EKVITRSVLLYTLD+ILRLLHPIMPFVTEEI+ QYA+GSIV YP V FEN+ A Sbjct: 663 NEAEKVITRSVLLYTLDKILRLLHPIMPFVTEEIYAQYAQGSIVTVDYPVVRPAFENEAA 72- 2 Query: 724 HKGVESLKDLIRSVRNSRAEVNVAPSKPITILVKTSDSELESFFKDNSNYIKRFTNPETL 78- 3 HKGVESLKDLIR+VRN+RAEVNVAPSKPITILVKT+DSELE FF N NYIK FTNPE L Sbjct: 723 HKGVESLKDLIRAVRNARAEVNVAPSKPITILVKTADSELEDFFNSNINYIKCFTNPEKL 78- 2 Query: 784 EISSAIATPELAMSSVITGAEIFLPLADLLNVEEELARLEKELAKWQKELDMVGKKLSNE 84- 3 EISSAIA PELAM+S+ITGAEI+LPLADLLNVEEELARL+KELAKWQKELDMVGKKL NE Sbjct: 783 EISSAIAAPELAMTSIITGAEIYLPLADLLNVEEELARLDKELAKWQKELDMVGKKLGNE 84- 2 Query: 844 RFVANAKPEVVQKEKDKQTDYQTKYDATIARIEMKKL 881 RFVANAKPEVVQKEKDKQ DYQ KYDAT RI EMKK+ Sbjct: 843 RFVANAKPEVVQKEKDKQADYQAKYDATQERIAEMKKI 880 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 228 A DNA sequence (GBSx0242) was identified in S. agalactiae <SEQ ID 725> which encodes the amino acid sequence <SEQ ID 726>. Analysis of this protein sequence reveals the following: TABLE-US-00719 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0669 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 727> which encodes the amino acid sequence <SEQ ID 728>. Analysis of this protein sequence reveals the following: TABLE-US-00720 Possible site: 57 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below: TABLE-US-00721 Identities = 148/191 (77%), Positives = 165/191 (85%) Query: 14 GEKKKMNIIIIGAQASGKMTIGQEIAKQTGMTLFHNHDSIDFVLRFMPWSPDSIALTESI 73 - G + KMN+IIIGAQASGKMTIGQE+A+QTGMTLFHNHDSIDFVLRFMPWS +S AL E I Sbjct: 3 GAETKMNLIIIGAQASGKMTIGQEVARQTGMTLFHNHDSIDFVLRFMPWSQESTALIERI 62 Query: 74 RFKFFETFAKTGQEMIFTIVIDFNDSRDVVFLEKIQIVFQSHNQEVLFVELETELSERLK 133- RF FFETFAKTGQ+MIFTIVIDFND DV LEKIQ VFQS++QEVLFVEL+T++ ERLK Sbjct: 63 RFAFFETFAKTGQDMIFTIVIDFNDPNDVAMLEKIQAVFQSYDQEVLFVELKTDIEERLK 122- Query: 134 RNRTENRLKHKPSKRDIKWSESDICSTMDYAIFNPEVAPEALTYYHKINNTCLTATETAY 19- 3 RNRTENRLKHKP KR+I+WSE DI STM YA+FNPE P+ LT+Y KINNT LTA ETA Sbjct: 123 RNRTENRLKHKPLKRNIEWSEQDIQSTMAYAVFNPEEPPKTLTHYQKINNTQLTAAETAQ 18- 2 Query: 194 LIIQKINQIKE 204 LIIQK+ IKE Sbjct: 183 LIIQKMTHIKE 193 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 229 A DNA sequence (GBSx0243) was identified in S. agalactiae <SEQ ID 729> which encodes the amino acid sequence <SEQ ID 730>. Analysis of this protein sequence reveals the following: TABLE-US-00722 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3614(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00723 >GP: BAB04556 GB: AP001510 unknown conserved protein [Bacillus halodurans] Identities = 60/189 (31%), Positives = 102/189 (53%), Gaps = 3/189 (1%) Query: 7 EIVDNQLPVVETNRLLLRQRKLEDAKEIFEFVKLDEVSYPAGFPAVKSLEEEITYIQEIY 66 E + LP +ET RL LR+ +DA I+++ ++V+ + +S+++ ++ + Sbjct: 4 EDIYGDLPTLETERLRLRKFYKDDAAAIYDYASNEQVTKYVLWETHQSIKDSEAFLA--F 61 Query: 67 PTNLEKEKLPSGYAITLKGDDKVIGSVDFNH-RHEDDIFEIGYLLHPDYWGQGIVPEAAS 125- N EK S +AI LK ++++IG+VDF + +D E+GY+L YWGQGI+ EA + Sbjct: 62 ALNKYDEKDVSPWAIELKRNERMIGTVDFVWWKPKDKTAELGYVLSEPYWGQGIMTEAVN 121- Query: 126 ALVEIGFTLLGLHKIELGCYDYNKQSQAVARKLGFTLEANIRDRRDAQGKRCGDMRFGLL 18- 5 ALVE GF + L +I+ C+ N S V K G E R +G + ++ Sbjct: 122 ALVEFGFNNMELERIQAKCFAENISSARVMEKAGLIYEGTHRRAIYVKGAHRDFKVYAII 18- 1 Query: 186 RSEWEKKRR 194 R ++E+K + Sbjct: 182 REDYEQKHQ 190 A related DNA sequence was identified in S. pyogenes <SEQ ID 731> which encodes the amino acid sequence <SEQ ID 732>. Analysis of this protein sequence reveals the following: TABLE-US-00724 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1864(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00725 Identities = 50/58 (86%), Positives = 56/58 (96%) Query: 137 LHKIELGCYDYNKQSQAVARKLGFTLEANIRDRRDAQGKRCGDMRFGLLRSEWEKKRR 194 - LHKIELGCYDYNKQSQAVARKLGFTLEAN RDR+D QG+RCGDMRFGLLRSEWE++++ Sbjct: 1 LHKIELGCYDYNKQSQAVARKLGFTLEANARDRKDVQGRRCGDMRFGLLRSEWEEQKQ 58 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 230 A DNA sequence (GBSx0244) was identified in S. agalactiae <SEQ ID 733> which encodes the amino acid sequence <SEQ ID 734>. This protein is predicted to be ribosomal-protein-alanine N-acetyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-00726 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4066(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9599> which encodes amino acid sequence <SEQ ID 9600> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00727 >GP: BAB04418 GB: AP001509 ribosomal-protein-alanine N-acetyltransferase [Bacillus halodurans] Identities = 63/185 (34%), Positives = 95/185 (51%), Gaps = 11/185 (5%) Query: 53 KALPKLETDRLILRQRTVGDVPAMFDYVCLEEVAYPAGLSPIASLEDEYDYFENRYYQNL 112- K P LET RLILR+ T D ++ Y+ +EV GL P +LED E +Y+++ Sbjct: 6 KRFPILETKRLILRKITTDDARSILSYLSDKEVMKYFGLEPFQTLEDALG--EIAWYESI 63 Query: 113 EKAKLPSGYGITVKGSDRIIGSCAFN-----HRHEDDVFEICYLLHPDYWGHGYMTEAVA 16- 7 + +GIT+KG D +IGSC F+ H + FE+ L YWG G +EA+ Sbjct: 64 LHEQTGIRWGITLKGQDEVIGSCGFHQWVPKHHRAEIGFELSKL----YWGQGIASEAIR 119- Query: 168 ALIEVGFTLLNLHKIEIRCYDYNKQSRRVAEKLGFTLEATIRDRKDNQDNRCVNLIYGLL 22- 7 A+I+ GF L L +I+ N S+R+ EK GF E +R + +Y LL Sbjct: 120 AVIQYGFEHLELQRIQALIEPPNIPSQRLVEKQGFISEGLLRSYEYTCGKFDDLYMYSLL 17- 9 Query: 228 RSEWE 232 + +++ Sbjct: 180 KRDFD 184 There is also homology to SEQ ID 732: TABLE-US-00728 Identities = 39/54 (72%), Positives = 44/54 (81%) Query: 179 LHKIEIRCYDYNKQSRRVAEKLGFTLEATIRDRKDNQDNRCVNLIYGLLRSEWE 232 LHKIE+ CYDYNKQS+ VA KLGFTLEA RDRKD Q RC ++ +GLLRSEWE Sbjct: 1 LHKIELGCYDYNKQSQAVARKLGFTLEANARDRKDVQGRRCGDMRFGLLRSEWE 54 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 231 A DNA sequence (GBSx0245) was identified in S. agalactiae <SEQ ID 735> which encodes the amino acid sequence <SEQ ID 736>. Analysis of this protein sequence reveals the following: TABLE-US-00729 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2719(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 232 A DNA sequence (GBSx0246) was identified in S. agalactiae <SEQ ID 737> which encodes the amino acid sequence <SEQ ID 738>. Analysis of this protein sequence reveals the following:

TABLE-US-00730 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3250(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9597> which encodes amino acid sequence <SEQ ID 9598> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 739> which encodes the amino acid sequence <SEQ ID 740>. Analysis of this protein sequence reveals the following: TABLE-US-00731 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3293(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00732 Identities = 24/55 (43%), Positives = 38/55 (68%) Query: 56 LLEGLTANKQDVLKEAGLVSLEAFAKVSEADVLALKGIGPAAIKQLVDNGVVFAK 110 ++ G+ ++ + L G+ S +AF + +E D+LALKGIGPA +K+LV+NG F K Sbjct: 77 VVAGIRSDLVETLYAEGIHSAQAFKEWTEKDLLALKGIGPATVKKLVENGASFKK 131 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 233 A DNA sequence (GBSx0247) was identified in S. agalactiae <SEQ ID 741> which encodes the amino acid sequence <SEQ ID 742>. Analysis of this protein sequence reveals the following: TABLE-US-00733 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2901(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 743> which encodes the amino acid sequence <SEQ ID 744>. Analysis of this protein sequence reveals the following: TABLE-US-00734 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2536(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00735 Identities = 57/84 (67%), Positives = 73/84 (86%) Query: 1 MSYEQEFLKDFEEWLQSQISINQMAMDSAKKVLEEDKDERAADAYIRYESKLDAYRFLQG 60 MSYE+EFLKDFE+W+++QI +NQ+AM ++++V +ED DERA DA+IRYESKLDAY FL G Sbjct: 1 MSYEKEFLKDFEDWVKTQIQVNQLAMATSQEVAQEDGDERAKDAFIRYESKLDAYEFLLG 60 Query: 61 KFNNYHNQKSFHDLPDGLFGQRHY 84 KF+NY N K+FHD+PD LFG RHY Sbjct: 61 KFDNYKNGKAFHDIPDELFGARHY 84 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 234 A DNA sequence (GBSx0248) was identified in S. agalactiae <SEQ ID 745> which encodes the amino acid sequence <SEQ ID 746>. This protein is predicted to be methyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-00736 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2469(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 747> which encodes the amino acid sequence <SEQ ID 748>. Analysis of this protein sequence reveals the following: TABLE-US-00737 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3352(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00738 Identities = 26/60 (43%), Positives = 37/60 (61%) Query: 23 LKNERCPHPKLINVLERKLEIILGDQKHILEKDSLISLSPQETHHLRAIENSKFLQIELD 82 - + E P K+I VLE +L L DQK +L ++SLI++ Q+ HHL A + K LQ+ LD Sbjct: 42 ISQETSPRDKVILVLEGQLIFDLEDQKQVLTQESLIAIPAQKVHHLEAKTDCKLLQVLLD 101- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 235 A DNA sequence (GBSx0249) was identified in S. agalactiae <SEQ ID 749> which encodes the amino acid sequence <SEQ ID 750>. This protein is predicted to be integrase (codV). Analysis of this protein sequence reveals the following: TABLE-US-00739 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3842(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 236 A DNA sequence (GBSx0250) was identified in S. agalactiae <SEQ ID 751> which encodes the amino acid sequence <SEQ ID 752>. Analysis of this protein sequence reveals the following: TABLE-US-00740 Possible site: 22 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 752 (GBS128) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 23 (lane 5; MW 15 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 32 (lane 4; 2 bands). The GBS128-GST fusion product was purified (FIG. 198, lane 2) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 288), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 237 A DNA sequence (GBSx0251) was identified in S. agalactiae <SEQ ID 753> which encodes the amino acid sequence <SEQ ID 754>. Analysis of this protein sequence reveals the following: TABLE-US-00741 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2940 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 755> which encodes the amino acid sequence <SEQ ID 756>. Analysis of this protein sequence reveals the following: TABLE-US-00742 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2518 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00743 Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 10/90 (11%) Query: 3 TVAVRVDDQLKDDATELFQSLGLDMSTAVKMFLIQSVKTQSIPFEIK--------NKSSV 54 - T+ +RVDD +K A ++ + LG+ MSTA+ MFL Q + T IPF++ N + Sbjct: 15 TLNLRVDDSVKSAADDILKRLGIPMSTAIDMFLNQIILTGGIPFDVSLPEAPQRVNVDYM 74 Query: 55 SDEEFQNLVETKLKGIRVKASDPESVNAFF 84 S E+F + + T + K +P+ V F+ Sbjct: 75 SQEKFYDKLITSFED--AKTCNPQDVGKFY 102 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 238 A DNA sequence (GBSx0252) was identified in S. agalactiae <SEQ ID 757> which encodes the amino acid sequence <SEQ ID 758>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-00744 Possible site: 24 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.81 Transmembrane 370-386 (368-388) ----- Final Results ----- bacterial membrane --- Certainty = 0.2126 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> A related GBS nucleic acid sequence <SEQ ID 9593> which encodes amino acid sequence <SEQ ID 9594> was also identified. A related GBS nucleic acid sequence <SEQ ID 10773> which encodes amino acid sequence <SEQ ID 10774> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 759> which encodes the amino acid sequence <SEQ ID 760>. Analysis of this protein sequence reveals the following: TABLE-US-00745 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.57 Transmembrane 354-370 (353-371) ----- Final Results ----- bacterial membrane --- Certainty = 0.2826 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> LPXTG motif: 344-348 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00746 Identities = 64/277 (23%), Positives = 99/277 (35%), Gaps = 31/277 (11%) Query: 126 SIGNLPDLPKGTTVAFETPVDTATPGDKPAKVVVTYPDGSKDTVDVTVKVVDPRTDADKN 18- 5 ++ +LP + TT E PV + V + D+ + T P A Sbjct: 121 AVKDLPASTESTTQPVEAPVQETQASASDSMVTGDSTSVTTDSPEETPSSESPVAPALSE 18- 0 Query: 186 DPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVAFETPVDTATPGDKPAKVVVTYPDGSK 24- 5 PA Q E P S P T A ETP + A P P + S+ Sbjct: 181 APA----QPAESEEPSVAASSEETPS--PSTPAAPETPEEPAAPSPSPESEEPSVAAPSE 23- 4 Query: 246 DTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVAFETPVDT 30- 5 +T P A + PA ++ T + P P + +TP Sbjct: 235 ETPSPET----PEEPAAPSQPAESEESSVAATTSPS-------PSTPAESET--QTPPAV 28- 1 Query: 306 ATPGDKPAKVVVTYPDGSKDTVDVTVKVVDPRTDADK----------NDPAGKDQQVNGK 35- 5 DKP+ P S + TV+ + +DK N + + + Sbjct: 282 TKDSDKPSSAAEK-PAASSLVSEQTVQQPTSKRSSDKKEEQEQSYSPNRSLSRQVRAHES 34- 0 Query: 356 GNKLPATGENATPFFNVVALTIMSSVGLLSVSKKKED 392 G LP+TGE A P F + +T+MS G L V+K++++ Sbjct: 341 GKYLPSTGEKAQPLF-IATMTLMSLFGSLLVTKRQKE 376 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 239 A DNA sequence (GBSx0253) was identified in S. agalactiae <SEQ ID 761> which encodes the amino acid sequence <SEQ ID 762>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-00747 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5289 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 240 A DNA sequence (GBSx0254) was identified in S. agalactiae <SEQ ID 763> which encodes the amino acid sequence <SEQ ID 764>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-00748 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.06 Transmembrane 39-55 (39-55) ----- Final Results ----- bacterial membrane --- Certainty = 0.1426 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> A related GBS nucleic acid sequence <SEQ ID 9591> which encodes amino acid sequence <SEQ ID 9592> was also identified. The protein differs significantly from U58333 in several places: TABLE-US-00749 Query: 157 TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK 20- 1 T PDG D V+V++ + + DK D K KAED P +G+ Sbjct: 683 TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA 74- 2 Query: 202 VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV 25- 8 +D T D K T D + +VT K++ PR DADKNDPAGKDQQVNV Sbjct: 743 FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV 79- 8 Query: 157 TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK 20- 1 T PDG D V+V++ + + DK D K KAED P +G+ Sbjct: 841 TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA 90- 0 Query: 202 VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV 25- 8 +D T D K T D + +VT K++ PR DADKNDPAGKDQQVNV Sbjct: 901 FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV 95- 6 Query: 157 TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK 20- 1 T PDG D V+V++ + + DK D K KAED P +G+ Sbjct: 288 TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA 34- 7 Query: 202 VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV 25- 8 +D T D K T D + +VT K++ PR DADKNDPAGKDQQVNV Sbjct: 348 FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV 40- 3 Query: 157 TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK 20- 1 T PDG D V+V++ + + DK D K KAED P +G+ Sbjct: 604 TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA 66- 3 Query: 202 VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV 25- 8 +D T D K T D + +VT K++ PR DADKNDPAGKDQQVNV Sbjct: 664 FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV 71- 9 Query: 157 TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK 20- 1 T PDG D V+V++ + + DK D K KAED P +G+ Sbjct: 446 TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA 50- 5 Query: 202 VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV 25- 8 +D T D K T D + +VT K++ PR DADKNDPAGKDQQVNV Sbjct: 506 FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV 56- 1 Query: 157 TKPDGQVDIVNVSLTIYNSSALRDKIDEVKK----------KAED-----PKWDEGSRDK 20- 1 T PDG D V+V++ + + DK D K KAED P +G+ Sbjct: 920 TYPDGSKDTVDVTVKVVDPRTDADKNDPAGKDQQVNVGETPKAEDSIGNLPDLPKGTTVA 97- 9 Query: 202 VLISLDDIKTDIDNNPK---TQSDIANKITEVTNLEKILVPRIPDADKNDPAGKDQQVNV 25- 8 +D T D K T D + +VT K++ PR DADKNDPAGKDQQVNV Sbjct: 980 FETPVDTA-TPGDKPAKVVVTYPDGSKDTVDVT--VKVVDPRT-DADKNDPAGKDQQVNV 10- 35 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 241 A DNA sequence (GBSx0255) was identified in S. agalactiae <SEQ ID 765> which encodes the amino acid sequence <SEQ ID 766>. This protein is predicted to be ara-C-like activator. Analysis of this protein sequence reveals the following: TABLE-US-00750 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 8-24 (8-25) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9589> which encodes amino acid sequence <SEQ ID 9590> was also identified. There is homology to SEQ ID 460. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 242 A DNA sequence (GBSx0256) was identified in S. agalactiae <SEQ ID 767> which encodes the amino acid sequence <SEQ ID 768>. Analysis of this protein sequence reveals the following: TABLE-US-00751 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1200(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9587> which encodes amino acid sequence <SEQ ID 9588> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 769> which encodes the amino acid sequence <SEQ ID 770>. Analysis of this protein sequence reveals the following: TABLE-US-00752 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0679 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below:

TABLE-US-00753 Identities = 135/176 (76%), Positives = 161/176 (90%) Query: 1 MSYMVKDRQIQKTKVAIYNAFISLLQENDYSKITVQDVIGLANVGRSTFYSHYESKEVLL 60 +S M KDRQI+KTK AIY+AFI+LLQ+ +YSKITV+D+I LANVGRSTFY+HYESKE+LL Sbjct: 1 VSDMTKDRQIKKTKTAIYSAFIALLQKKEYSKITVRDMITLANVGRSTFYAHYESKEMLL 60 Query: 61 KELCEDLFHHLFKQGRDVTFEEYLVHILKHFEQNQDSIATLLLSDDPYFLLRFRSELEHD 120- KELCE+LFHHLF+Q R+VTFE+YLVHILKHFEQN+DSIATLLLS+DPYFLLRF++ELEHD Sbjct: 61 KELCEELFHHLFRQKRNVTFEDYLVHILKHFEQNKDSIATLLLSNDPYFLLRFKNELEHD 120- Query: 121 VYPRLREEYITKVDIPEDFLKQFLLSSFIETLKWWLHQRQKMTVEDLLKYYLTMVE 176 VYP LR +YI K IPE FLKQF+LSSFIETLKWWLHQRQ+M+ +LLKYYL +++ Sbjct: 121 VYPNLRCKYIDKTTIPEVFLKQFVLSSFIETLKWWLHQRQRMSANELLKYYLELIK 176 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 243 A DNA sequence (GBSx0257) was identified in S. agalactiae <SEQ ID 771> which encodes the amino acid sequence <SEQ ID 772>. Analysis of this protein sequence reveals the following: TABLE-US-00754 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3573 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 244 A DNA sequence (GBSx0258) was identified in S. agalactiae <SEQ ID 773> which encodes the amino acid sequence <SEQ ID 774>. Analysis of this protein sequence reveals the following: TABLE-US-00755 Possible site: 35 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.19 Transmembrane 112-128 (107-131) INTEGRAL Likelihood = -8.07 Transmembrane 77-93 (71-97) INTEGRAL Likelihood = -6.10 Transmembrane 144-160 (138-165) INTEGRAL Likelihood = -3.03 Transmembrane 165-181 (164-182) ----- Final Results ----- bacterial membrane --- Certainty = 0.5076 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 775> which encodes the amino acid sequence <SEQ ID 776>. Analysis of this protein sequence reveals the following: TABLE-US-00756 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.13 Transmembrane 112-128 (107-130) INTEGRAL Likelihood = -5.89 Transmembrane 144-160 (138-163) INTEGRAL Likelihood = -5.47 Transmembrane 7-23 (6-29) INTEGRAL Likelihood = -3.50 Transmembrane 77-93 (74-94) INTEGRAL Likelihood = -2.07 Transmembrane 166-182 (165-183) ----- Final Results ----- bacterial membrane --- Certainty = 0.4652 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00757 Identities = 212/287 (73%), Positives = 245/287 (84%) Query: 1 MTSNKKVAIAFILNISFSVLEFIFGSLFFSGAILADAVHDFGDAIAIGISATLEKKSKKD 60 M ++KKV I FILN+SFS++EFIFG+LFFSGAILADAVHDFGDAIAIGISA LE+K+ K Sbjct: 1 MPASKKVTIIFILNLSFSLIEFIFGTLFFSGAILADAVHDFGDAIAIGISAILERKAVKK 60 Query: 61 EDTIFSLGYKRFSLLGALITSLILISGSILVMIENIPKLWHPTPVNYHGMFILAVIAIII 120- E FSLGYKRFSLLGAL T+LILISGS+LVMIE IPKLWHPT VNY GMF+LA+ AIII Sbjct: 61 ESPNFSLGYKRFSLLGALTTNLILISGSLLVMIETIPKLWHPTIVNYDGMFVLAIFAIII 120- Query: 121 NGLASFILHSGQSKHEEILSLHFLEDILGWLAIIVISLILNWKPLYILDPLLSVAISTFI 18- 0 NG ASFI+HS Q+K+EEILSLHFLEDILGWLAII++SLIL WKP YILDPLLS+AI++FI Sbjct: 121 NGFASFIIHSNQTKNEEILSLHFLEDILGWLAIIILSLILKWKPWYILDPLLSIAIASFI 18- 0 Query: 181 LSKALPKLLSTLKLFLDGVPDSIDYAALHDELKGLSQVRSINQLNIWSMDGIDNRAIIHC 24- 0 LSKALPKL++T +FLDGVPDSIDY LH EL L + S+NQLN+WSMDGID+RA IHC Sbjct: 181 LSKALPKLVATANIFLDGVPDSIDYCTLHHELSQLPHIVSVNQLNVWSMDGIDHRATIHC 24- 0 Query: 241 CLNQLISEKDCKRAIRTICQHYKINDVTVEIDYSLREHQNHCKPLKN 287 CL + +EK CK++IR ICQ Y IN VTVEID SL EHQ+HC L + Sbjct: 241 CLRESTTEKHCKKSIRLICQRYNINSVTVEIDTSLNENQHHCSSLSS 287 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 245 A DNA sequence (GBSx0259) was identified in S. agalactiae <SEQ ID 777> which encodes the amino acid sequence <SEQ ID 778>. Analysis of this protein sequence reveals the following: TABLE-US-00758 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.22 Transmembrane 221-237 (221-237) ----- Final Results ----- bacterial membrane --- Certainty = 0.1489 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> There is also homology to SEQ ID 780. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 246 A DNA sequence (GBSx0260) was identified in S. agalactiae <SEQ ID 781> which encodes the amino acid sequence <SEQ ID 782>. Analysis of this protein sequence reveals the following: TABLE-US-00759 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.50 Transmembrane 2-18 (1-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.1999(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 247 A DNA sequence (GBSx0261) was identified in S. agalactiae <SEQ ID 783> which encodes the amino acid sequence <SEQ ID 784>. This protein is predicted to be dehydrogenase (Zn-dependent). Analysis of this protein sequence reveals the following: TABLE-US-00760 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.77 Transmembrane 171-187 (170-187) ----- Final Results ----- bacterial membrane --- Certainty = 0.2508(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00761 >GP:AAG20655 GB:AE005134 alcohol dehydrogenase; Adh2 [Halobacterium sp. NRC-1] Identities = 169/348 (48%), Positives = 232/348 (66%), Gaps = 9/348 (2%) Query: 1 MKVATFIEPGKMVITDTPKPVIEQETDAVIKIVRACVCGSDLWWYRGISKRESGSFAGHE 60 M+ A + PG++ + + PKP IE DAVI++ VCGSDLW+YRG S RE+GS GHE Sbjct: 1 MRAAVYQGPGEIAVEEVPKPDIESPEDAVIRVTHTAVCGSDLWFYRGDSDREAGSRVGHE 60 Query: 61 AIGIVEEVGTKVTDVSKGDFVIVPFTHGCGQCPSCKAGFDGNCTNHQA---AKNVGYQGQ 117- +GIVEEVG VT V+ GD VI PF CG+C C+ G +C ++ N G QG+ Sbjct: 61 PMGIVEEVGDDVTSVAPGDRVIAPFAISCGECEFCRQGLYTSCVEDESWGSEANGGGQGE 120- Query: 118 YLRYTNANWALVKIPGQPSDYDNETLNSLLTLSDVMATGYHAAATAEVKEGDTVVVMGDG 17- 7 Y++ A+ LV++P + +D D + L SLL L+DVM TG+HAA +A V EGDT VV+GDG Sbjct: 121 YVKCPFADGTLVRVPDRYAD-DEDVLESLLPLTDVMGTGHHAAVSAGVGEGDTAVVVGDG 17- 9 Query: 178 AVGLCGVIAAKMLGANRIIAMSRHKDRQELALTFGATDIVEERGDEAVKRVLDLTNQAGA 23- 7 AVGLCGV+AA+ LGA RIIAM H+DR ELA FGATD + RGD+A++R DLT+ GA Sbjct: 180 AVGLCGVLAAQRLGAERIIAMGHHEDRLELAAEFGATDTISARGDDAIERARDLTH-GGA 23- 8 Query: 238 DAVLECVGTEQSVDTATQIARPGAVIGRVGIP---QNPDMNTNNLFWKNIGLRGGIASVT 29- 4 + V+ECVG ++D+A IARPG +G VG+P ++ ++ +F NI +RGG+A V Sbjct: 239 NHVMECVGAASAMDSAIAIARPGGTVGYVGVPYGVEDGGLDVFTMFSDNITIRGGVAPVR 29- 8 Query: 295 TFDKSVLLDAVLTHKINPGLVFTKSFVLDDIQKAYEAMDKRDAIKSLV 342 + + ++ D VL ++P +FTK+ LD + + Y AMD R+AIK LV Sbjct: 299 AYAEELMAD-VLQGTLDPSPIFTKTVDLDGVPEGYAAMDDREAIKVLV 345 There is also homology to SEQ ID 786. A related sequence was also identified in GAS <SEQ ID 9145> which encodes the amino acid sequence <SEQ ID 9146>. Analysis of this protein sequence reveals the following: TABLE-US-00762 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.41 Transmembrane 170-186 ----- Final Results ----- bacterial membrane --- Certainty = 0.3166(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00763 Identities = 121/353 (34%), Positives = 182/353 (51%), Gaps = 16/353 (4%) Query: 1 MKVATFIEPGKMVITDTPKPVIEQETDAVIKIVRACVCGSDLWWYRG-ISKRESGSFAGH 59- MK AT++ G + + D PKPVI + TDA++++V+ + CG+DL G + + G+ GH Sbjct: 15 MKAATYLSTGNLQLIDKPKPVIIKPTDAIVQLVKTTICGTDLHILGGDVPACKEGTILGH 74- Query: 60 EAIGIVEEVGTKVTDVSKGDFVIVPFTHGCGQCPSCKAGFDGNCTNHQAAKN---VGYQG 11- 6 E IGIV+EVG VT+ GD VI+ C C CK G +C + G Q Sbjct: 75 EGIGIVKEVGDAVTNFKIGDKVIISCVTSCHTCYYCKRGLSSHCQDGGWILGHLINGTQA 13- 4 Query: 117 QYLRYTNANWALVKIPGQPSDYDNETLNSLLTLSDVMATGYH-AAATAEVKEGDTVVVMG 17- 5 +Y+ +A+ +L P D +L+ LSD++ T Y + VK GD V ++G Sbjct: 135 EYVHIPHADGSLYHAPDTIDD------EALVMLSDILPTSYEIGVLPSHVKPGDNVCIVG 18- 8 Query: 176 DGAVGLCGVIAAKMLGANRIIAMSRHKDRQELALTFGATDIVEERGDEAVKRVL-DLTNQ 23- 4 G VGL ++ + II + ++R E A TFGAT + E VK ++ D+TN Sbjct: 189 AGPVGLAALLTVQFFSPANIIMVDLSQNRLEAAKTFGATHTICSGSSEEVKAIIDDITNG 24- 8 Query: 235 AGADAVLECVGTEQSVDTATQIARPGAVIGRVGIPQNP-DMNTNNLFWKNIGLRGGIASV 29- 3 G D +ECVG + D +I G I VG+ P D N + L+ KNI L G+ + Sbjct: 249 RGVDISMECVGYPATFDICQKIISVGGHIANVGVHGKPVDFNLDELWIKNITLNTGLVNA 30- 8 Query: 294 TTFDKSVLLDAVLTHKINPGLVFTKSFVLDDIQKAYEAMDKRDAIKSL-VIVD 345 T + +LL+ + T KI+ + T F L +++KAYE A +L VI+D Sbjct: 309 NTTE--MLLNVLKTGKIDATRLITHHFKLSEVEKAYETFKHAGANNALKVIID 359 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 248 A DNA sequence (GBSx0262) was identified in S. agalactiae <SEQ ID 787> which encodes the amino acid sequence <SEQ ID 788>. Analysis of this protein sequence reveals the following: TABLE-US-00764 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2169 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00765 >GP:AAD36075 GB:AE001762 hypothetical protein [Thermotoga maritima] Identities = 55/128 (42%), Positives = 72/128 (55%), Gaps = 8/128 (6%) Query: 8 IFPKGEKNPYGEFFIGQSYLAALAKSPDG--NVSVGNVTFEAGCRNNWHVHLDGYQILLV 65- IF +G K +FF G ++ L +G N V +V FE G R +WH H G QIL+V Sbjct: 5 IFERGSKGS-SDFFTGNVWVKMLVTDENGVFNTQVYDVVFEPGARTHWHSHPGG-QILIV 62- Query: 66 TEGSGWYQEEGKEAVSLKPGDVIVTDKGVRHWHGAKKDSEFAHIAITA----GKSEFYEA 12- 1 T G G+YQE GK A LK GDV+ V HWHGA D E HI I+ G +E+ + Sbjct: 63 TRGKGFYQERGKPARILKKGDVVEIPPNVVHWHGAAPDEELVHIGISTQVHLGPAEWLGS 12- 2 Query: 122 VSDEEYSR 129 V++EEY + Sbjct: 123 VTEEEYRK 130 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 249 A DNA sequence (GBSx0263) was identified in S. agalactiae <SEQ ID 789> which encodes the amino acid sequence <SEQ ID 790>. This protein is predicted to be gamma-carboxymuconolactone decarboxylase. Analysis of this protein sequence reveals the following: TABLE-US-00766 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4089 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00767 >GP:CAA20070 GB:AL031155 3-oxoadipate enol-lactone hydrolase/ 4-carboxymuconolactone decarboxylase [Streptomyces coelicolor A3(2)] Identities = 33/93 (35%), Positives = 59/93 (62%), Gaps = 1/93 (1%) Query: 11 QLEEFAPEFARYNDDILFGEVWAKEDHLTDKTRSIITISALISGGNLEQLEHHLQFAKQN 70- Q +EF+ +F + +GE+W + L ++RS +T++AL++GG+L++L HL+ A +N Sbjct: 349 QADEFSGDFQEFLTRYAWGEIWDRPG-LDRRSRSCVTLTALVAGGHLDELAPHLRAALRN 40- 7 Query: 71 GVTKEEIADIITHLAFYVGWPKAWSAFNKAKEI 103 G+T EI+++ A Y G P A AF A+++ Sbjct: 408 GLTPGEIKEVLLQAAVYCGVPAANGAFRVAQQV 440 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 250 A DNA sequence (GBSx0265) was identified in S. agalactiae <SEQ ID 791> which encodes the amino acid sequence <SEQ ID 792>. Analysis of this protein sequence reveals the following: TABLE-US-00768 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5529 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 251 A DNA sequence (GBSx0266) was identified in S. agalactiae <SEQ ID 793> which encodes the amino acid sequence <SEQ ID 794>. This protein is predicted to be probable transcriptional regulator. Analysis of this protein sequence reveals the following: TABLE-US-00769 Possible site: 58 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9585> which encodes amino acid sequence <SEQ ID 9586> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00770 >GP: AAG08263 GB: AE004901 probable transcriptional regulator [Pseudomonas aeruginosa] Identities = 36/148 (24%), Positives = 68/148 (45%), Gaps = 22/148 (14%) Query: 5 QIVEKPAMILAG-------------------VTLENVKSNQEGIQQAIGICKTQPDFRFD 45 +IVE+PA + G + E+ + + + + GIC QP+ F Sbjct: 123 RIVERPAFSVVGMEYFGSAPGDTIGQLWERFIPREHEIAGKHDPEVSYGICAQQPNGEFH 18- 2 Query: 46 YSATYQVETSVQAPKGLEIIRIPSATYAVISVKGPMPSSLQETWRKIIQGFFQENNLKPA 105- Y A ++V+ P+G+ ++P+ YAV + KG P + E+++ I E L+P Sbjct: 183 YVAGFEVQEGWPVPEGMVRFQVPAQKYAVFTHKGTAP-QIAESFQAIYSHLLAERGLEPK 24- 1 Query: 106 NSPNLEIYSSQH--PQDTDYQMEIWLAI 131 + E Y + P D + Q+++++ I Sbjct: 242 AGVDFEYYDQRFRGPLDPNSQVDLYIPI 269 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 252 A DNA sequence (GBSx0267) was identified in S. agalactiae <SEQ ID 795> which encodes the amino acid sequence <SEQ ID 796>. Analysis of this protein sequence reveals the following: TABLE-US-00771 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0887(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00772 >GP: AAB84919 GB: AE000825 conserved protein [Methanothermobacter thermoautotrophicus] Identities = 42/130 (32%), Positives = 71/130 (54%), Gaps = 3/130 (2%) Query: 1 MITQEMKEIINSQLAMVATVDAKGQPNIGPKRSMRLWDDKTFIYNENTDGQTRINIEDNG 60 M+T EM + I +L VAT D +G PN+ P R D++T + +N +T N+ +N Sbjct: 1 MMTPEMMDAIEKELVFVATADEEGTPNVVPIGFARPLDERTILIADNYMKKTIRNLHENP 60 Query: 61 KIEIAFVDRERLLGYRFVGTAEIQTEGTYYEAAKKWAEGRMG--VPKAVGIIHVERIFNL 118- +I + R Y+F GT EI G Y++ +WA+ M PK+ ++ VE I+++ Sbjct: 61 RIAL-IPQNARECPYQFKGTVEIFKSGKYFDMVVEWAQNVMTELEPKSAILMTVEEIYSV 119- Query: 119 QSGANAGKEI 128 + G AG+++ Sbjct: 120 KPGPEAGEKV 129 A related DNA sequence was identified in S. pyogenes <SEQ ID 797> which encodes the amino acid sequence <SEQ ID 798>. Analysis of this protein sequence reveals the following: TABLE-US-00773 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0789(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00774 Identities = 123/128 (96%), Positives = 127/128 (99%) Query: 1 MITQEMKEIINSQLAMVATVDAKGQPNIGPKRSMRLWDDKTFIYNENTDGQTRINIEDNG 60 MITQEMK++IN+QLAMVATVDAKGQPNIGPKRSMRLWDDKTFIYNENTDGQTRINIEDNG Sbjct: 1 MITQEMKDLINNQLAMVATVDAKGQPNIGPKRSMRLWDDKTFIYNENTDGQTRINIEDNG 60 Query: 61 KIEIAFVDRERLLGYRFVGTAEIQTEGTYYEAAKKWAEGRMGVPKAVGIIHVERIFNLQS 120- KIEIAFVDRERLLGYRFVGTAEIQTEG YYEAAKKWA+GRMGVPKAVGIIHVERIFNLQS Sbjct: 61 KIEIAFVDRERLLGYRFVGTAEIQTEGAYYEAAKKWAQGRMGVPKAVGIIHVERIFNLQS 120- Query: 121 GANAGKEI 128 GANAGKEI Sbjct: 121 GANAGKEI 128 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 253 A DNA sequence (GBSx0268) was identified in S. agalactiae <SEQ ID 799> which encodes the amino acid sequence <SEQ ID 800>. Analysis of this protein sequence reveals the following:

TABLE-US-00775 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.47 Transmembrane 1028-1044 (1027-1048) ----- Final Results ----- bacterial membrane --- Certainty = 0.3187(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00776 !GB: AF054892 surface antigen BspA [Bacteroides forsy . . . !GB: AF054892 surface antigen BspA [Bacteroides forsy . . . !GB: AF054892 surface antigen BspA [Bacteroides forsy . . . !GB: AF054892 surface antigen BspA [Bacteroides forsy . . . !GB: AF054892 surface antigen BspA [Bacteroides forsy . . . >GP: AAC82625 GB: AF054892 surface antigen BspA [Bacteroides forsythus] Identities = 143/566 (25%), Positives = 243/566 (42%), Gaps = 52/566 (9%) Query: 95 VPKAKPEVTQEASNSSNDASKVEVPKQDTASKKETLETSTWEAKDFVTRGDTLVG----F 150- +P + + + A + + +P TA + L T + T +G F Sbjct: 120 IPNSVTTIGEWAFKGCSGLKSITLPNSLTAIGQSALSGCTGLTSITIPNSVTTIGEWAFF 17- 9 Query: 151 SKSGINKLSQTSHLVLPSHAA--DGTQLTQVASFAFTPDKKTAIAEYTSRLGENGKPSRL 20- 8 SG+ ++ + L +A LT + PD T I E + G +G S Sbjct: 180 GCSGLTSITFPNSLTAIGESAFYGCGALTSIT----LPDALTTIGESAFK-GCSGLKSIT 23- 4 Query: 209 DIDQKEIIDEGEIFNAYQLTKLTIPNGYKSIGQDAFVDNKNIAEVNLPESLETISDYAFA 26- 8 + I E ++ LT +T+P+ +IG+ AF + + P SL TI + AF Sbjct: 235 FPNSLTTIGESAFYDCGALTSITLPDALTTIGRSAFYGCSGLKSITFPNSLTTIGESAFY 29- 4 Query: 269 HM-SLKQVKLPDNLKVIGELAFFDNQIGGKLYLPRHLIKLAERAFKSNRIQTVEFLGSKL 32- 7 + SL + +P+++ IG AF+ + LP L + ERAF + + T + + + Sbjct: 295 NCGSLTSITIPNSVTTIGRSAFYGCSGLKSITLPDGLTTIEERAFYNCGVLTSITIPNSV 35- 4 Query: 328 KVIGEASFQD-NNLRNVMLPDGLEKIESEAFTGNPGDEHYNNQVVLRTRTGQNPHQLATE 38- 6 IGE++F + L+++ LPDGL IE AF N L + T N E Sbjct: 355 ATIGESAFYGCSGLKSITLPDGLTTIEWGAFY---------NCGALTSITIPNSVSTIGE 40- 5 Query: 387 NTYVNPDKSLWRATPDMDYTKWLEEDFTYQKNSVTGFS---NKGLQKVRRNKNLEIPKQH 44- 3 + + +L T D ++ D +++ +++G G + V K ++ K+ Sbjct: 406 SAFYGCG-ALKDVTVAWDTPIDIQRD-VFRELTLSGIRLHVPAGKKTVYEAK--DVWKEF 46- 1 Query: 444 NGITITEIGDNAFRNVDFQSKTLRKYDLEEIKLPSTIRKIGAFAFQSNNLKSFEASEDLE 50- 3 N + + G + N D +KTL + P T + + FA ++ L Sbjct: 462 NIVEDDDFGGLQW-NYDAATKTLTITN----PTPDTPKPMPNFATPNDQLW--------- 50- 7 Query: 504 EIKEGAFMNNRIGTLDLKDKLIKIGDAAFH-INHIYAIVLPESVQEIGRSAFRQNGALHL 56- 2 GAF I + + D + +GD AF + + +I LP+SV IG+SAF L Sbjct: 508 ----GAFQKE-IQKITIGDGVTSVGDFAFSGCDALKSITLPKSVTTIGQSAFSGCWDLRS 56- 2 Query: 563 MFIGNKVKTIGEMAFLSNKLESVNLSEQKQLKTIEVQAFS-DNALSEVVLPPNLQTIREE 62- 1 + + + V TIGE AF + LE +++ K + I + F +L+ + LP L I ++ Sbjct: 563 LTLPDGVNTIGEKAFY-DCLELTSITIPKSVTAIGQETFHYCVSLTSLTLPDALTAIGKK 62- 1 Query: 622 AF-KRNHLKEVKGSSTLSQITFNAFD 646 AF N L V +++ I NAFD Sbjct: 622 AFYSCNALTSVTFPKSITTIGENAFD 647 Identities = 109/407 (26%), Positives = 175/407 (42%), Gaps = 48/407 (11%) Query: 222 FNAYQLTKLTIPNGYKSIGQDAFVDNKNIAEVNLPESLETISDYAFAHMS-LKQVKLPDN 28- 0 F+ LT +T+PN +IG AF + + +P S+ TI ++AF S LK + LP++ Sbjct: 87 FSDCALTSVTLPNSLTAIGDHAFKGCSGLTSITIPNSVTTIGEWAFKGCSGLKSITLPNS 146- Query: 281 LKVIGELAFFDNQIGGKLYLPRHLIKLAERAFKSNRIQTVEFLGSKLKVIGEASFQD-NN 33- 9 L IG+ A + +P + + E AF T + L IGE++F Sbjct: 147 LTAIGQSALSGCTGLTSITIPNSVTTIGEWAFFGCSGLTSITFPNSLTAIGESAFYGCGA 20- 6 Query: 340 LRNVMLPDGLEKIESEAFTGNPGDEHYNNQVVLRTRTGQNPHQLATENTYVNPDKSLWRA 39- 9 L ++ LPD L I AF G G L++ T N E+ + + Sbjct: 207 LTSITLPDALTTIGESAFKGCSG---------LKSITFPNSLTTIGESAFYDCGALTSIT 25- 7 Query: 400 TPDMDYTKWLEEDFTYQKNSVTGFSNKGLQKVRRNKNLEIPKQHNGITITEIGDNAFRNV 45- 9 PD ++T K++ P ++T IG++AF N Sbjct: 258 LPD----------------ALTTIGRSAFYGCSGLKSITFPN-----SLTTIGESAFYNC 29- 6 Query: 460 DFQSKTLRKYDLEEIKLPSTIRKIGAFAFQS-NNLKSFEASEDLEEIKEGAFMNNRIGT- 51- 7 L I +P+++ IG AF + LKS + L I+E AF N + T Sbjct: 297 G---------SLTSITIPNSVTTIGRSAFYGCSGLKSITLPDGLTTIEERAFYNCGVLTS 34- 7 Query: 518 LDLKDKLIKIGDAAFH-INHIYAIVLPESVQEIGRSAFRQNGALHLMFIGNKVKTIGEMA 57- 6 + + + + IG++AF+ + + +I LP+ + I AF GAL + I N V TIGE A Sbjct: 348 ITIPNSVATIGESAFYGCSGLKSITLPDGLTTIEWGAFYNCGALTSITIPNSVSTIGESA 40- 7 Query: 577 FLS-NKLESVNLSEQKQLKTIEVQAFSDNALSEVVL--PPNLQTIRE 620 F L+ V ++ + I+ F + LS + L P +T+ E Sbjct: 408 FYGCGALKDVTVAWDTPI-DIQRDVFRELTLSGIRLHVPAGKKTVYE 453 Identities = 111/465 (23%), Positives = 185/465 (38%), Gaps = 56/465 (12%) Query: 141 VTRGDTLVGFSKSGINKLSQTSHLVLPSHAADGTQLTQVASFAF----------TPDKKT 19- 0 +T D L +S S + P+ LT + AF PD T Sbjct: 210 ITLPDALTTIGESAFKGCSGLKSITFPN------SLTTIGESAFYDCGALTSITLPDALT 26- 3 Query: 191 AIAEYTSRLGENGKPSRLDIDQKEIIDEGEIFNAYQLTKLTIPNGYKSIGQDAFVDNKNI 25- 0 I ++ G +G S + I E +N LT +TIPN +IG+ AF + Sbjct: 264 TIGR-SAFYGCSGLKSITFPNSLTTIGESAFYNCGSLTSITIPNSVTTIGRSAFYGCSGL 32- 2 Query: 251 AEVNLPESLETISDYAFAHMS-LKQVKLPDNLKVIGELAFFDNQIGGKLYLPRHLIKLAE 30- 9 + LP+ L TI + AF + L + +P+++ IGE AF+ + LP L + Sbjct: 323 KSITLPDGLTTIEERAFYNCGVLTSITIPNSVATIGESAFYGCSGLKSITLPDGLTTIEW 38- 2 Query: 310 RAFKSNRIQTVEFLGSKLKVIGEASFQD-NNLRNVMLP-DGLEKIESEAF-----TGNPG 36- 2 AF + T + + + IGE++F L++V + D I+ + F +G Sbjct: 383 GAFYNCGALTSITIPNSVSTIGESAFYGCGALKDVTVAWDTPIDIQRDVFRELTLSGIRL 44- 2 Query: 363 DEHYNNQVVLRTRTGQNPHQLATEN-------TYVNPDKSLWRATPDMDYTKWLEEDFTY 41- 5 + V + + ++ Y K+L P D K + +F Sbjct: 443 HVPAGKKTVYEAKDVWKEFNIVEDDDFGGLQWNYDAATKTLTITNPTPDTPKPM-PNFAT 50- 1 Query: 416 QKNSVTGFSNKGLQKVRRNKNLEIPKQHNGITITEIGDNAFRNVDFQSKTLRKYDLEEIK 47- 5 + + G K +QK+ G +T +GD AF D L+ I Sbjct: 502 PNDQLWGAFQKEIQKIT-----------IGDGVTSVGDFAFSGCD---------ALKSIT 54- 1 Query: 476 LPSTIRKIGAFAFQSN-NLKSFEASEDLEEIKEGAFMN-NRIGTLDLKDKLIKIGDAAFH 53- 3 LP ++ IG AF +L+S + + I E AF + + ++ + + IG FH Sbjct: 542 LPKSVTTIGQSAFSGCWDLRSLTLPDGVNTIGEKAFYDCLELTSITIPKSVTAIGQETFH 60- 1 Query: 534 -INHIYAIVLPESVQEIGRSAFRQNGALHLMFIGNKVKTIGEMAF 577 + ++ LP+++. IG+ AF AL + + TIGE AF Sbjct: 602 YCVSLTSLTLPDALTAIGKKAFYSCNALTSVTFPKSITTIGENAF 646 Identities = 98/351 (27%), Positives = 152/351 (42%), Gaps = 53/351 (15%) Query: 315 NRIQTVEFLGSKLKVIGEASFQDNNLRNVMLPDGLEKIESEAFTGNPGDEHYNNQVVLRT 37- 4 ++IQTV +G + +G +F D L +V LP+ L I AF G G L + Sbjct: 68 SKIQTVT-IGDGVTSVGNNAFSDCALTSVTLPNSLTAIGDHAFKGCSG---------LTS 117- Query: 375 RTGQNPHQLATENTYVNPDKSLWRATPDMDYTKWLEEDFTYQKNSVTGFSNKGLQKVRRN 43- 4 T P+ + T + S ++ NS+T L Sbjct: 118 IT--IPNSVTTIGEWAFKGCSGLKSIT--------------LPNSLTAIGQSALSGCTGL 16- 1 Query: 435 KNLEIPKQHNGITITEIGDNAF------RNVDFQSKTLRKYD--------LEEIKLPSTI 48- 0 ++ IP ++T IG+ AF ++ F + + L I LP + Sbjct: 162 TSITIPN-----SVTTIGEWAFFGCSGLTSITFPNSLTAIGESAFYGCGALTSITLPDAL 21- 6 Query: 481 RKIGAFAFQS-NNLKSFEASEDLEEIKEGAFMN-NRIGTLDLKDKLIKIGDAAFH-INHI 53- 7 IG AF+ + LKS L I E AF + + ++ L D L IG +AF+ + + Sbjct: 217 TTIGESAFKGCSGLKSITFPNSLTTIGESAFYDCGALTSITLPDALTTIGRSAFYGCSGL 27- 6 Query: 538 YAIVLPESVQEIGRSAFRQNGALHLMFIGNKVKTIGEMAFLS-NKLESVNLSEQKQLKTI 59- 6 +I P S+ IG SAF G+L + I N V TIG AF + L+S+ L + L TI Sbjct: 277 KSITFPNSLTTIGESAFYNCGSLTSITIPNSVTTIGRSAFYGCSGLKSITLPD--GLTTI 33- 4 Query: 597 EVQAFSD-NALSEVVLPPNLQTIREEAFKR-NHLKEVKGSSTLSQITFNAF 645 E +AF + L+ + +P ++ TI E AF + LK + L+ I + AF Sbjct: 335 EERAFYNCGVLTSITIPNSVATIGESAFYGCSGLKSITLPDGLTTIEWGAF 385 Identities = 78/282 (27%), Positives = 123/282 (42%), Gaps = 46/282 (16%) Query: 111 NDASKVEVPKQDTASKKETLETSTWEAKDFVTRGDTLVGFSKSGINKLSQTSHLVLPS-- 16- 8 N+AS E+P SK +T VT GD + + + + TS + LP+ Sbjct: 56 NNAS--EIPWHSLQSKIQT-----------VTIGDGVTSVGNNAFSDCALTS-VTLPNSL 101- Query: 169 -----HAADG----------TQLTQVASFAFT----------PDKKTAIAEYTSRLGENG 20- 3 HA G +T + +AF P+ TAI + ++ G G Sbjct: 102 TAIGDHAFKGCSGLTSITIPNSVTTIGEWAFKGCSGLKSITLPNSLTAIGQ-SALSGCTG 16- 0 Query: 204 KPSRLDIDQKEIIDEGEIFNAYQLTKLTIPNGYKSIGQDAFVDNKNIAEVNLPESLETIS 26- 3 S + I E F LT +T PN +IG+ AF + + LP++L TI Sbjct: 161 LTSITIPNSVTTIGEWAFFGCSGLTSITFPNSLTAIGESAFYGCGALTSITLPDALTTIG 22- 0 Query: 264 DYAFAHMS-LKQVKLPDNLKVIGELAFFDNQIGGKLYLPRHLIKLAERAFKS-NRIQTVE 32- 1 + AF S LK + P++L IGE AF+D + LP L + AF + ++++ Sbjct: 221 ESAFKGCSGLKSITFPNSLTTIGESAFYDCGALTSITLPDALTTIGRSAFYGCSGLKSIT 28- 0 Query: 322 FLGSKLKVIGEASFQD-NNLRNVMLPDGLEKIESEAFTGNPG 362 F S L IGE++F + +L ++ +P+ + I AF G G Sbjct: 281 FPNS-LTTIGESAFYNCGSLTSITIPNSVTTIGRSAFYGCSG 321 Identities = 43/144 (29%), Positives = 70/144 (47%), Gaps = 4/144 (2%) Query: 220 EIFNAYQ--LTKLTIPNGYKSIGQDAFVDNKNIAEVNLPESLETISDYAFAHM-SLKQVK 76- +++ A+Q + K+TI +G S+G AF + + LP+S+ TI AF+ L+ + Sbjct: 505 QLWGAFQKEIQKITIGDGVTSVGDFAFSGCDALKSITLPKSVTTIGQSAFSGCWDLRSLT 56- 4 Query: 277 LPDNLKVIGELAFFDNQIGGKLYLPRHLIKLAERAFKSNRIQTVEFLGSKLKVIGEASFQ 33- 6 LPD + IGE AF+D + +P+ + + + F T L L IG+ +F Sbjct: 565 LPDGVNTIGEKAFYDCLELTSITIPKSVTAIGQETFHYCVSLTSLTLPDALTAIGKKAFY 62- 4 Query: 337 D-NNLRNVMLPDGLEKIESEAFTG 359 N L +V P + I AF G Sbjct: 625 SCNALTSVTFPKSITTIGENAFDG 648 Identities = 43/134 (32%), Positives = 66/134 (49%), Gaps = 12/134 (8%) Query: 511 MNNRIGTLDLKDKLIKIGDAAFHINHIYAIVLPESVQEIGRSAFRQNGALHLMFIGNKVK 57- 0 + ++I T+ + D + +G+ AF + ++ LP S+ IG AF+ L + I N V Sbjct: 66 LQSKIQTVTIGDGVTSVGNNAFSDCALTSVTLPNSLTAIGDHAFKGCSGLTSITIPNSVT 125- Query: 571 TIGEMAFLS-NKLESVNLSEQKQLKTIEVQAFSD-NALSEVVLPPNLQTIREEAFKRNHL 62- 8 TIGE AF + L+S+ L L I A S L+ + +P ++ TI E AF Sbjct: 126 TIGEWAFKGCSGLKSITL--PNSLTAIGQSALSGCTGLTSITIPNSVTTIGEWAF----- 17- 8 Query: 629 KEVKGSSTLSQITF 642 G S L+ ITF Sbjct: 179 ---FGCSGLTSITF 189 A related DNA sequence was identified in S. pyogenes <SEQ ID 801> which encodes the amino acid sequence <SEQ ID 802>. Analysis of this protein sequence reveals the following: TABLE-US-00777 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -2.44 Transmembrane 984-1000 (984-1001) ----- Final Results ----- bacterial membrane --- Certainty = 0.1977 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> LPXTG motif: 975-979 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00778 Identities = 751/1050 (71%), Positives 861/1050 (81%), Gaps = 45/1050 (4%) Query: 3 KKHLKTLALALTTVSVVTYSQEVYGLEREESVKQEQTQSA-SEDDWFEEDNERKTNVSKE 61 KKHLKT+AL LTTVSVVT++QEV+ L +E +K Q Q S+ S D+ E + K +++ Sbjct: 2 KKHLKTVALTLTTVSVVTHNQEVFSLVKEPILKQTQASSSISGADYAESSGKSKLKINET 61 Query: 62 NSTVDETVSDLFSDGNSWNSSSKTESVVSDPKQVPKAKPEVTQEASWSSNDASKVEVPKQ 121- + VD+TV+DLFSD + K +Q KA E T E+ S++E K+ Sbjct: 62 SGPVDDTVTDLFSDKRTTPEKIKDNLAKGPREQELKAVTENT-ESEKQITSGSQLEQSKE 120- Query: 122 DTASKKETLETSTWEAKDFVTRGDTLVGFSKSGIWKLSQTSHLVLPSHAADGTQLTQVAS 18- 1 + K TS WE DF+T+G+TLVG SKSG+ KLSQT NLVLPS AADGTQL QVAS Sbjct: 121 SLSLNKTVPSTSNWEICDFITKGWTLVGLSKSGVEKLSQTDHLVLPSQAADGTQLIQVAS 18- 0 Query: 182 FAFTPDKKTAIAEYTSRLGENGKPSRLDIDQKEIIDEGEIFWAYQLTKLTIPNGYKSIGQ 24- 1 FAFTPDKKTAIAEYTSR GENG+ S+LD+D KEII+EGE+FN+Y L K+TIP GYK IGQ Sbjct: 181 FAFTPDKKTAIAEYTSRAGENGEISQLDVDGKEIINEGEVFWSYLLKKVTIPTGYKHIGQ 24- 0 Query: 242 DAFVDNKNIAEVNLPESLETISDYAFAHMSLKQVKLPDWLKVIGELAFFDNQIGGKLYLP 30- 1 DAFVDNKNIAEVWLPESLETISDYAFAH++LKQ+ LPDWLK IGELAFFDNQI GKL LP Sbjct: 241 DAFVDNKNIAEVNLPESLETISDYAFAHLALKQIDLPDWLKAIGELAFFDWQITGKLSLP 30- 0 Query: 302 RHLIKLAERAFKSNRIQTVEFLGSKLKVIGEASFQDWNLRNVMLPDGLEKIESEAFTGNF 36- 1 R L++LAERAFKSN I+T+EF G+ LKVIGEASFQDN+L +MLPDGLEKIESEAFTGNP Sbjct: 301 RQLMRLAERAFKSNHIKTIEFRGNSLKVIGEASFQDWDLSQLMLPDGLEKIESEAFTGNP 36- 0 Query: 362 GDEHYNNQVVLRTRTGQNPHQLATENTYVNPDKSLWRATPDMDYTKWLEEDFTYQKWSVT 42- 1 GD+HYNN+VVL T++G+NP LATENTYVNPDKSLW+ +P++DYTKWLEEDFTYQKNSVT Sbjct: 361 GDDHYWNRVVLWTKSGKNPSGLATENTYVNPDKSLWQESPEIDYTKWLEEDFTYQKWSVT 42- 0 Query: 422 GFSNKGLQKVRRNKNLEIPKQHNGITITEIGDNAFRNVDFQSKTLRKYDLEEIKLPSTIR 48- 1 GFSNKGLQKV+RNKNLEIPKQHNG+TITEIGDNAFRNVDFQ+KTLRKYDLEE+KLPSTIR Sbjct: 421 GFSNKGLQKVKRNKNLEIPKQHNGVTITEIGDNAFRNVDFQNKTLRKYDLEEVKLPSTIR 48- 0 Query: 482 KIGAFAFQSNNLKSFEASEDLEEIKEGAFMNNRIGTLDLKDKLIKIGDAAFHINHIYAIV 54- 1 KIGAFAFQSNNLKSFEAS+DLEEIKEGAFMNNRI TL+LKDKL+ IGDAAFHINHIYAIV Sbjct: 481 KIGAFAFQSNNLKSFEASDDLEEIKEGAFMNNRIETLELKDKLVTIGDAAFHINHIYAIV 54- 0 Query: 542 LPESVQEIGRSAFRQNGALHLMFIGNKVKTIGSMAFLSNKLSSVNLSEQKQLKTIEVQAF 60- 1 LPESVQEIGRSAFRQNGA +L+F+G+KVKT+GEMAFLSN+LE ++LSEQKQL I VQAF Sbjct: 541 LPESVQEIGRSAFRQNGANNLIFNGSKVKTLGEMAFLSNRLEHLDLSEQKQLTSIPVQAF 60- 0 Query: 602 SDNALSEVVLPPNLQTIREEAFKRNHLKEVKGSSTLSQITFNAFDQNDGDKRFGKKVVVR 66- 1 SDNAL EV+LP +L+TIREEAFK+NHLK+++ +S LS I FNA D NDGD++F KVVV+ Sbjct: 601 SDNALKEVLLFASLKTIREEAFKKNHLKQLEVASALSHIAFNALDDNDGDEQFDNKVVVK 66- 0 Query: 662 THNNSHMLADGERFIIDPDKLSSTMVDLEKVLKIIEGLDYSTLRQTTQTQFREMTTAGKA 72- 1 TH+NS+ LADGE FI+DPDKLSST+VDLEK+LK+IEGLDYSTLRQTTQTQFR+MTTAGKA Sbjct: 661 THHNSYALADGEHFIVDPDKLSSTIVDLEKILKLIEGLDYSTLRQTTQTQFRDMTTAGKA 72- 0 Query: 722 LLSKSNLRQGEKQKFLQEAQFFLGRVDLDKAIAKAEKALVTKKATKNGHLLERSINKAVL 78- 1 LLSKSNLRQGEKQKFLQEAQFFLGRVDLDKAIAKAEKALVTKKATKNG LLERSINKAVL Sbjct: 721 LLSKSNLRQGEKQKFLQEAQFFLGRVDLDKAIAKAEKALVTKKATKNGQLLERSINKAVL 78- 0 Query: 782 AYNNSAIKKANVKRLEKELDLLTDLVEGKGPLAQATMVQGVYLLKTPLPLFEYYIGLNVY 84- 1 AYNNSAIKKANVKRLEKELDLLT LVEGKGPLAQATMVQGVYLLKTPLPLPEYYIGLNVY Sbjct: 781 AYNNSAIKKANVKRLEKELDLLTGLVEGKGPLAQATMVQGVYLLKTPLPLPEYYIGLNVY 84- 0 Query: 842 FDKSGKLIYALDMSDTIGEGQKDAYGNPILNVDEDNEGYHTLAVATLADYEGLYIKDILN 90- 1 FDKSGKLIYALDMSDTIGEGQKDAYGNPILNVDEDNEGYH LAVATLADYEGL IK ILN Sbjct: 841 FDKSGKLIYALDMSDTIGEGQKDAYGNPILNVDEDNEGYHALAVATLADYEGLDIKTILN 90- 0 Query: 902 SSLDKIKAIRQIPLAKYHRLGIFQAIRNAAAEADRLLPKTPKGYLNEVPNYRKKQVEKNL 96- 1 S L ++ +IRQ+P A YHR GIFQAI+NAAAEA++LLPK Sbjct: 901 SKLSQLTSIRQVPTAAYHRAGIFQAIQNAAAEAEQLLPK--------------------- 93- 9 Query: 962 KPVDYKTPIFNKALPNEKVDGDRAAKGHNINAETNNSVAVTPIRSEQQLHKSQSDVNLPQ 10- 21 ++++ + N++ ++S + ++ + LP+ Sbjct: 940 ----------------PGTHSEKSSSSESANSKDRG------LQSNPKTNRGRHSAILPR 97- 7 Query: 1022 TSSKNNFIYEILGYVSLCLLFLVTAGKKGK 1051 T SK +F+Y ILGY S+ LL L+TA KK K Sbjct: 978 TGSKGSFVYGILGYTSVALLSLITAIKKKK 1007 SEQ ID 800 (GBS97) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 12; MW 113.4 kDa). GBS97-His was purified as shown in FIG. 193, lane 6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 254 A DNA sequence (GBSx0269) was identified in S. agalactiae <SEQ ID 803> which encodes the amino acid sequence <SEQ ID 804>. This protein is predicted to be ribonucleoside-diphosphate reductase alpha chain (nrdE). Analysis of this protein sequence reveals the following: TABLE-US-00779 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4274 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00780 >GP:AAB96160 GB:AE000050 ribonucleoside-diphosphate reductase alpha chain~MPN324 (new), 513 (Himmelreich et al., 1996) [Mycoplasma pneumoniae] Identities = 476/725 (65%), Positives = 586/725 (80%), Gaps = 20/725 (2%) Query: 2 TQSD--AYLSLNAKTRFRDRTGNYHFTSDKEAVEQYMIEHVEPNTHVFTSLIEKLDYLVS 59 TQ D +Y+SLNA T+ F D AVE Y+ EHV+P T VF S E+LD+LV Sbjct: 12 TQEDLESYISLNAYTKVYG-----DFKMDLHAVEAYIQEHVKPKTKVFHSTKERLDFLVK 66 Query: 60 NNYYESDLLKQYNLEFICQIFEHAYAKKFAFLNFHGALKFYNAYALKTEDNRYYLEHYED 119- N+YY+ +++ Y+ E +I AYA +F + NFMGA KFYNAYALKT D ++ YLE+YED Sbjct: 67 NDYYDENIINMYSFEQFEEITRRAYAYRFRYANFHGAFKFYNAYALKTFDGKWYLENYED 126- Query: 120 RVVMNALFLAAGDEKAAYDLVDDMLANRFQPATPTFLNAGKKRRGEYISCYLLRIEDNME 17- 9 RVVMN LFLA G+ A L+ ++ NRFQPATPTFLNAG+K+RGE++SCYLLRIEDNME Sbjct: 127 RVVMNVLFLANGNYNKALKLLKQIITNRFQPATPTFLNAGRKKRGEFVSCYLLRIEDNME 18- 6 Query: 180 SISRAISTSLQLSRRGGGVALCLTNLREFGAFIRGIKNQATGIVPVNKLLEDSFSYANQL 23- 9 SI RAI+T+LQLSKR GGVAL LTN+RE GAPIK I+NQ++GI+P+MKLLEDSFSYANQL Sbjct: 187 SIGRAITTTLQLSRRDGGVALLLTNIRESGAPIRRIENQSSGIIPIMRLLEDSFSYANQL 24- 6 Query: 240 GQRQGAGAVYLHAHHPEVLTFLDTRRENADEKIRIKSLSLGLVIPDITFELAKANKDMAL 29- 9 GQRQGAGAVYLHAHHP+V+ FLDTKRENADEEIRIRSLSLGLVIPDITF LAK N++MAL Sbjct: 247 GQRQGAGAVYLHAHHPDVMQFLDTKRENADEKIRIKSLSLGLVIPDITFTLAKNNEEMAL 30- 6 Query: 300 FSPYDIERVYGKPMSDISITEEYETLLANADIRKTFISARKLFQTIAELHFESGYPYILF 35- 9 FSPYD+ YGKP+SDIS+TE Y LLAN I+KTFI+ARK FQT+AELHFESGYPYILF Sbjct: 307 FSPYDVYEEYGKPLSDISVTEMYYELLANQRIKKTFINARKFFQTVAELHFESGYPYILF 36- 6 Query: 360 EDTVNAKNPHKKEGRIVMSNLCSEIAQVNTASQFSEDLTFTKVGHDVCCNLGSINIARAM 41- 9 +DTVN +N H RIVMSNLCSEI Q +T S+F DL F KVG+D+ CNLGS+NIA+AM Sbjct: 367 DDTVNRRNAH--PNRIVMSNLCSEIVQPSTPSEFHHDLAFKKVGNDISCNLGSLNIARAM 42- 4 Query: 420 DQAADFEKLIANSIRALDRVSRTSDLDSAPSIKKGNAANHAVGLGANNLHGFLATNHIYY 47- 9 + +F +L+ +I +LD VSR S+L++APSI+KGN+ NHA+GLGAMNLHGFLATH IYY Sbjct: 425 ESGPEFSELVKLAIESLDLVSRVSNLETAPSIQKGNSENHALGLGANNLHGFLATNQIYY 48- 4 Query: 480 DSQEAIDFTDCFFYANAYYAFKASNHLAKEKGTFEGFSESSYADGSYFYQY--TEQNF-E 53- 6 +S EAIDFT+ FFY +AY+AFKAS+ LA ERG F+ F + +ADGSYF +Y E +F Sbjct: 485 NSFEAIDFTNIFFYTVAYHAFKASSELALEKGKFKNFENTKFADGSYFDKYIKVEPDFWT 54- 4 Query: 537 PKTQRVKNLLAEYGLTLPSQEDWRKLVQSIKEIGLANAHLLAVAPTGSISYLSSCTPSLQ 59- 6 PKT+RVK L +Y + +P++E+W++L +I++ GLAN+HLLA+APTGSISYLSSCTPSLQ Sbjct: 545 PKTERVKALFQKYQVEIPTRENWKELALNIQKNGLANSHLLAIAPTGSISYLSSCTPSLQ 60- 4 Query: 597 PVVSPVEVRKEGALGRVYVPAYKIDADNYVYYKKGAYEVGSEAIINIAAAAQKHIDQAIS 65- 6 PVVSPVEVRKEG LGR+YVPAY+++ D+Y +YK GAYE+G E IINIAAAAQ+H+DQAIS Sbjct: 605 PVVSPVEVRKEGRLGRIYVPAYQLNEDSYPFYKDGAYELGPEPIINIAAAAQQHVDQAIS 66- 4 Query: 657 LTLFMTDQATTRDLNKAYIQAFKQKCASIYYVRVRQDILEGSESYDDMLDDFTSSDLEDC 71- 6 LTLFMTD+ATTRDLNKAYI AFK+ C+SIYYVRVRQ++LE SE + + ++ C Sbjct: 665 LTLFMTDKATTRDLNKAYIYAFKKGCSSIYYVRVRQEVLEDSEDH--------TIQMQQC 71- 6 Query: 717 QSCMI 721 ++C+I Sbjct: 717 EACVI 721 A related DNA sequence was identified in S. pyogenes <SEQ ID 805> which encodes the amino acid sequence <SEQ ID 806>. Analysis of this protein sequence reveals the following:

TABLE-US-00781 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1843 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00782 >GP:AAC82625 GB:AF054892 surface antigen BspA [Bacteroides forsythus] Identities = 124/451 (27%), Positives = 202/451 (44%), Gaps = 65/451 (14%) Query: 221 FNSYLLKKVTIPTGYKHIGQDAFVDNKNIAEVNLPSSLETISDYAFAHLA-LKQIDLPDN 27- 9 F+ L VT+P IG AF + + +P S+ TI ++AF + LK I LP++ Sbjct: 87 FSDCALTSVTLPNSLTAIGDHAFKGCSGLTSITIPNSVTTIGEWAFKGCSGLKSITLPNS 146- Query: 280 LKAIGELAFFDNQITGKLSLPRQLMRLAERA-FKSNHIKTISFRGNSLKVIGEASFQD-N 33- 7 L AIG+A +++P + + E A F + + +I F NSL IGE++F Sbjct: 147 LTAIGQSALSGCTGLTSITIPNSVTTIGEWAFFGCSGLTSITF-PNSLTAIGESAFYGCG 20- 5 Query: 338 DLSQLMLPDGLEKIESEAFTGNPGDDHYNNRVVLWTKSGKNPSGLATENTYVNPDKSLWQ 39- 7 L+ + LPD L I AF G G KS P+ L T +S + Sbjct: 206 ALTSITLPDALTTIGESAFKGCSG-----------LKSITFPNSLTTIG------ESAFY 24- 8 Query: 398 SSPEIDYTKWLEEDFTYQKNSVTGFSNKGLQKVKRNKNLSIPKQHNGVTITEIGDNAFRN 45- 7 + + + T +++ G S GL K++ P ++T IG++AF N Sbjct: 249 DCGALTSITLPDALTTIGRSAFYGCS--GL------KSITFPN-----SLTTIGESAFYN 29- 5 Query: 458 VDFQNKTLRKYDLEEVKLPSTIRKIGAFAFQS-NNLKSFEASDDLEEIKEGAFMNNRIET 51- 6 L + +P+++ IG AF + LKS D L I+E AF N + T Sbjct: 296 CG---------SLTSITIPNSVTTIGRSAFYGCSGLKSITLPDGLTTIEERAFYNCGVLT 34- 6 Query: 517 -LELKDKLVTIGDAAFH-INHIYAIVLPESVQEIGRSAFRQNGANNLIFNGSKVKTLGEM 57- 4 + + + + TIG++AF+ + + +I LP+ + I AF GA I + + V T+GE Sbjct: 347 SITIPNSVATIGESAFYGCSGLKSITLPDGLTTIEWGAFYNCGALTSITIPNSVSTIGES 40- 6 Query: 575 AFLS-NRLEHLDLSEQKQLTEIPVQAFSDNALKEVLL--PASLKTIREEAFKKNHLKQLE 63- 1 AF L+ + ++ + +I F + L + L PA KT+ E K+ K+ Sbjct: 407 AFYGCGALKDVTVAWDTPI-DIQRDVFRELTLSGIRLHVPAGKKTVYE---AKDVWKE-- 46- 0 Query: 632 VASALSHIAFNALDDND-GDEQFDNKVVVRT 661 FN ++D+D G Q++ KT Sbjct: 461 ---------FNIVEDDDFGGLQWNYDAATKT 482 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00783 Identities = 534/726 (73%), Positives = 614/726 (84%), Gaps = 5/726 (0%) Query: 1 HTQSDA-YLSLNAKTRFRDRTGNYHFTSDKSAVEQYHIEHVEPNTMVFTSLIEKLDYLVS 59 M+Q++A YLSLNA TRF+ G+YHF SDKEAV +Y+ EHV PN M F SL +KL YL++ Sbjct: 1 MSQTNASYLSLNALTRFKKPDGSYHFDSDKEAVRRYLEEHVSPNQMAFNSLEDKLAYLIN 60 Query: 60 NNYYESDLLKQYNLEFICQIFEHAYAKKFAFLNFMGALKFYNAYALKTEDNRYYLEHYED 119- YYE + Y + I + F +AY + + FLN MGA+KFY +YALKT D + YLE +ED Sbjct: 61 EGYYEQAIFDAYPNDLIKEAFHYAYQQGYRFLNLNGAMKFYQSYALKTLDGKQYLETFED 120- Query: 120 RVVMNALFLAAGDEKAAYDLVDDMLANRFQPATPTFLNAGKERRGEYISCYLLRIEDNME 17- 9 R VMNALFLA GD+ +D++D +L RFQPATPTFLNAGKKRRGEYISCYLLR+EDNME Sbjct: 121 PAVMNALFLADGDQTFVFDVIDAILHRRFQPATPTFLNAGKKRRGEYISCYLLRVEDNME 18- 0 Query: 180 SISRAISTSLQLSKRGGGVALCLTNLREFGAPIKGIKNQATGIVPVMKLLEDSFSYANQL 23- 9 SISRAISTSLQLSKRGGGVALCLTNLRE GAPIKGI+NQATGIVPVMKLLEDSFSYANQL Sbjct: 181 SISRAISTSLQLSKRGGGVALCLTNLREIGAPIKGIENQATGIVPVMKLLEDSFSYANQL 24- 0 Query: 240 GQRQGAGAVYLHAHHPEVLTFLDTKRENADEKIRIKSLSLGLVIPDITFELAKANKDMAL 29- 9 GQRQGAGAVYLHAHHPEVLTFLDTKRENADEKIRIKSL+LGLVIPDITF+LAK NKDMAL Sbjct: 241 GQRQGAGAVYLHAHHPEVLTFLDTKRENADEKIRIKSLALGLVIPDITFQLAKENKDMAL 30- 0 Query: 300 FSPYDIERVYGKPMSDISITEEYETLLANADIRKTFISARKLFQTIAELHFESGYPYILF 35- 9 FSPYDI+R Y K MSDISITEEY+ LLAN I+KT+ISARK FQ IAELHFESGYPY+LF Sbjct: 301 FSPYDIKRAYGKDMSDISITEEYDKLLANPAIKKTYISARKFFQLIAELHFSSGYPYLLF 36- 0 Query: 360 EDTVNAKNPHKKEGRIVIASNLCSEIAQVNTASQFSEDLTFTKVGHDVCCNLGSINIARM 41- 9 +DTVN +NPH K+GRIVMSNLCSEIAQV+T S F EDL+F +G D+CCNLGSINIA+AN Sbjct: 361 DDTVNKRNPHAKKGRIVMSNLCSEIAQVSTPSTFKEDLSFETIGEDICCNLGSINIAQAN 42- 0 Query: 420 DQAADFEKLIANSIRALDRVSRTS0LDSAPSIKKGNAANHAVGLGAMNLHGFLATNNIYY 47- 9 A FE+LI SIRALDRVSR SDL+ APS++ GNAANHAVGLGAMNLHGFLATNHIYY Sbjct: 421 ADAPHFEQLITTSIRALDRVSRVSDLNCAPSVETGNAANHAVGLGAMNLHGFLATNNIYY 48- 0 Query: 480 DSQEAIDFTDCFFYAMAYYAFKASNHLAKEKGTFEGFSESSYADGSYFYQYTEQNFEPKT 53- 9 D++EA+DFTD FF+AMAYYAFKAS LAKEKG F GFS S+Y+DG+YF +Y +++ +P+T Sbjct: 481 DTKEAVDFTDLFFHAMAYYAFKASCQLAKEKGAFAGFSLSTYSDGTYFAKYLQEDAKPQT 54- 0 Query: 540 QRVKNLLAEYGLTLPSQEDWRKLVQSIKEIGLANAHLLAVAPTGSISYLSSCTPSLQPVV 59- 9 +V LL +YG TLP+ DW+ LV IK+ GLANAHLLAVAPTGSISYLSSCTPSLQPVV Sbjct: 541 AKVATLLQDYGFTLPTVADWQALVADIKQFGLANAHLLAVAPTGSISYLSSCTPSLQPVV 60- 0 Query: 600 SPVEVRKEGALGRVYVPAYKIDADNYVYYKRGAYEVGSEAIINIAAAAQKHIDQAISLTL 65- 9 +PVEVRKEG+LGR+YVPAY+ID NY YY++GAYEVG +AII++ AAAQKH+DQAISLTL Sbjct: 601 APVEVRKEGSLGRIYVPAYQIDQANYAYYERGAYEVGPKAIIDVVAAAQKHVDQAISLTL 66- 0 Query: 660 FMTDQATTRDLNKAYIQAFKQKCASIYYVRVRQDILEGSESYDD----MLDDFTSSDLED 71- 5 FMTDQATTRDLN++YIQAFKQ CASIYYVRVRQD+L GSE YD+ + + Sbjct: 661 FMTDQATTRDLNRSYIQAFKQNCASIYYVRVRQDVLAGSEQYDEDSLVTAPGASDETTTE 72- 0 Query: 716 CQSCMI 721 CQSCMI Sbjct: 721 CQSCMI 726 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 255 A DNA sequence (GBSx0270) was identified in S. agalactiae <SEQ ID 807> which encodes the amino acid sequence <SEQ ID 808>. This protein is predicted to be nrdI protein (nrdI). Analysis of this protein sequence reveals the following: TABLE-US-00784 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ---- bacterial cytoplasm --- Certainty = 0.2952 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00785 >GP:AAC71451 GB:U39702 nrdI protein (nrdI) [Mycoplasma genitalium] Identities = 77/127 (60%), Positives = 104/127 (81%), Gaps = 1/127 (0%) Query: 7 VVYFSSKSNNTHRFVQKLACSNQRIPSD-GSSILVTEDYILIVPTYAGGGDDTKGAVPKQ 65 +VYFSS SNNTHRF++KL ++RIP D SI V+ +Y+LI PTY+GGG+ +GAVPKQ Sbjct: 22 IVYFSSISNNTHRFIEKLGFQHKRIPVDITQSITVSNEYVLICPTYSGGGNQVEGAVPKQ 81 Query: 66 VVQFLNVRQNREHCQGVISSGNTNFGDTYAIAGPIIARKLNVPLLHQFELLGTQEDVTRV 125- V+QFLN + NRE C+GVI+SGNTNFGDT+ +AG +I++KLNVPLL+QFELLGT+ DV + Sbjct: 82 VIQFLNNKHNRELCRGVIASGNTNFGDTFCLAGTVISKKLNVPLLYQFELLGTKNDVEQT 141- Query: 126 KELLCQF 132 ++++ F Sbjct: 142 QKIIANF 148 A related DNA sequence was identified in S. pyogenes <SEQ ID 809> which encodes the amino acid sequence <SEQ ID 810>. Analysis of this protein sequence reveals the following: TABLE-US-00786 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0089 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00787 Identities = 84/125 (67%), Positives = 100/125 (79%) Query: 7 VVYFSSKSNNTHRFVQKLACSNQRIPSDGSSILVTEDYILIVPTYAGGGDDTKGAVPKQV 66 +VYFSSKS NTHRFVQKL QRIP D + V+ Y+LIVPTYA GG D KGAV KQV Sbjct: 6 IVYFSSKSNNTHRFVQKLGLPAQRIPVDNRPLEVSTHYLLIVPTYAAGGSDAKGAVSKQV 65 Query: 67 VQFLNVRQNREHCQGVISSGNTNFGDTYAIAGPIIARKLNVPLLHQFELLGTQEDVTRVK 126- ++FLN NR+HC+GVISSGNTNFGDT+A+AGPII++KL VPLLHQFELLGT DV +V+ Sbjct: 66 IRFLNNPNNRKHCKGVISSGNTNFGDTFALAGPIISQKLQVPLLHQFELLGTATDVKKVQ 125- Query: 127 ELLCQ 131 ++ Sbjct: 126 AIFAR 130 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 256 A DNA sequence (GBSx0271) was identified in S. agalactiae <SEQ ID 811> which encodes the amino acid sequence <SEQ ID 812>. This protein is predicted to be ribonucleoside-diphosphate reductase beta chain (nrdF). Analysis of this protein sequence reveals the following: TABLE-US-00788 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3889 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00789 >GP:AAB96162 GB:AE000050 ribonucleoside-diphosphate reductase beta chain [Mycoplasma pneumoniae] Identities = 261/335 (77%), Positives = 301/335 (88%) Query: 2 QSYYDRSQSPLDYALSEKAFPMRSVNWNKLNDDKDLEVWNRVTQNFWLPSKIPVSNDLNS 61 + Y+ S SPL+YA + +RSVNWN ++D+KDLEVWNR+TQNFWLPEKIPVSND+ S Sbjct: 5 KKYFLESVSPLEYAQKKPQGNLRSVNWNLVDDEKDLEVWNRITQNFWLPEKIPVSNDIPS 64 Query: 62 WRTLDADWQQLITRTFTGLTLLDSVQATVGDIAQIKHSQTDHSQVIYANFAFMVAIHARS 121- W+ L +WQ LIT+TFTGLTLLD++QAT+GDI QI ++ TDHSQVIYANFAFMV +HARS Sbjct: 65 WKQLSKEWQDLITKTFTGLTLLDTIQATIGDIKQIDYALTDHEQVIYANFAFMVGVHARS 124- Query: 122 YGTIFSTLCTSQQIEEAHEWVVDTESLQARSRILIPFYTGDDPLKSKVAAAMMPGFLLYG 18- 1 YGTIFSTLCTS+QI EAHEWVV TESLQ R++ LIP+YTG DPLKSKVAAA+MPGFLLYG Sbjct: 125 YGTIFSTLCTSEQITEAHEWVVKTESLQKRAKALIPYYTGKDPLKSKVAAALMPGFLLYG 18- 4 Query: 182 GFYLPFYLSARGKLPNTSDIIRLILRDKVIHNYYSGYKYQQKVAKLSVEKQAEMKTFVFD 24- 1 GFYLPFYLS+R +LPNTSDIIRLILRDKVIHNYYSGYK+Q+KV K+S EKQAEMK FVFD Sbjct: 185 GFYLPFYLSSRKQLPNTSDIIRLILRDKVIHNYYSGYKFQRKVEKMSKEKQAEMKRFVFD 24- 4 Query: 242 LLYQLIDLEKAYLYELYDGEDLAEDAIRFSIYNAGKFLQNLGYDSPFTEEETRISPEVFA 30- 1 L+Y+LI+LEKAYL ELY+GF + EDAI+FSIYNAGKFLQNLGYDSPFTEESTRI PE+FA Sbjct: 245 LMYELIELEKAYLKELYEGEGIVEDAIKFSIYNAGKFLQNLGYDSPFTSEETRIKPEIFA 30- 4 Query: 302 QLSARADENHDFFSGMGSSYIMGITEETLDEDWEF 336 QLSARADENHDFFSGNGSSY+MGI+EET D+DW+F Sbjct: 305 QLSARADENHDFFSGNGSSYVMGISEETEDKDWDF 339 A related DNA sequence was identified in S. pyogenes <SEQ ID 813> which encodes the amino acid sequence <SEQ ID 814>. Analysis of this protein sequence reveals the following: TABLE-US-00790 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3779 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00791 Identities = 292/335 (87%), Positives = 318/335 (94%) Query: 2 QSYYDRSQSPLDYALSEKAFPMRSVNWNKLNDDKDLEVWNRVTQNFWLPEKIPVSNDLNS 61 Q YY+RSQSP++YALSE +RS+NWN LNDDKDLEVWNRVTQNFWLPEK+PVSNDLNS Sbjct: 3 QHYYERSQSPIEYALSETQKQLRSINWNYLNDDKDLEVWNRVTQNFWLPEKVPVSNDLNS 62 Query: 62 WRTLDADWQQLITRTFTGLTLLDSVQATVGDIAQIKHSQTDHEQVIYANFAFMVAIHARS 121- WR+L DWQQLITRT+TGLTLLD+VQATVGD+AQI+HSQTDHEQVIY NFAFMV IHARS Sbjct: 63 WRSLGEDWQQLITRTYTGLTLLDTVQATVGDVAQIQHSQTDHEQVIYTNFAFMVGIHARS 122- Query: 122 YGTIFSTLCTSQQIEEAHEWVVDTESLQARSRILIPFYTGDDPLKSKVAAAMMPGFLLYG 18- 1 YGTIFSTLC+S+QIEEAHEWVV T+SLQ R+R+LIP+YTGDDPLKSKVAAAMMPGFLLYG Sbjct: 123 YGTIFSTLCSSEQIEEAHEWVVSTQSLQDRARVLIPYYTGDDPLKSKVAAAMMPGFLLYG 18- 2 Query: 182 GFYLPFYLSARGKLPNTSDIIRLILRDKVIHNYYSGYKYQQKVAKLSVEKQAEMKTFVFD 24- 1 GFYLPFYLSARGK+PNTSDIIRLILRDKVIHNYYSGYKYQQKVA+LS EKQAEMK FVFD Sbjct: 183 GFYLPFYLSARGKMPNTSDIIRLILRDKVIHNYYSGYKYQQKVARLSPEEQAEMKAFVFD 24- 2 Query: 242 LLYQLIDLEKAYLYELYDGFDLAEDAIRWSIYNAGKFLQNLGYDSPFTEEETRISPEVFA 30- 1 LLY+LIDLEKAYL ELY GFDLAEDAIRFS+YNAGKFLQNLGY+SPFT+EETR+SPEVFA Sbjct: 243 LLYELIDLEKAYLRELYAGFDLAEDAIRFSLYNAGKFLQNLGYESPFTDEETRVSPEVFA 30- 2 Query: 302 QLSARADENHDFFSGNGSSYIMGITEETLDEDWEF 336 QLSARADENHDFFSGNGSSY+MGITEET D+DWEF Sbjct: 303 QLSARADENHDFFSGNGSSYVHGITEETTDDDWEF 337 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 257 A DNA sequence (GBSx0272) was identified in S. agalactiae <SEQ ID 815> which encodes the amino acid sequence <SEQ ID 816>. This protein is predicted to be rhamnosyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-00792 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1741 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9583> which encodes amino acid sequence <SEQ ID 9584> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00793 >GP:BAA32090 GB:AB010970 rhamnosyltransferase [Streptococcus mutans] Identities = 104/309 (33%), Positives = 173/309 (55%), Gaps = 21/309 (6%) Query: 11 QINICLATYNGQKYLRQQLDSIIQQGYTDWICLIRDDGSTDDTVAIIKEYVNRDSRFIFI 70 - ++NI ++TYNGQ+++ QQ+ SI +Q + +W LIRDDGS+D T II ++ D+R FI Sbjct: 2 KVNILMSTYNGQEFIAQQIQSIQKQTFENWNLLIRDDGSSDGTPKIIADFAKSDARIRFI 61 Query: 71 NSNDDRKLGSHRSFYELVNYKKADFYVFSDQDDVWKENRLERYLEEAEKFNQELPLLVYS 130- N++ G ++FY L+ Y+KAD+Y FSDQDDVW +LE L EK N ++PL+VY+ Sbjct: 62 NADKRENFGVIKNFYTLLKYEKADYYFFSDQDDVWLPQKLELTLASVEKENNQIPLNVYT 121- Query: 131 NWTSVDEKLTVL-------KEHNPATVIQEQIAFNQINGMVINMNNELAKLWE--YRQIG 18- 1 + T VD L VL + H+ T + E++ N + G +M+NH LAK W+ Y + Sbjct: 122 DLTVVDRDLQVLHDSMIKTQSHHANTSLLEELTENTVTGGTMMVNHCLAKQWKQCYDDLI 18- 1 Query: 182 AHDSYVGTLAYAVGNVAYISDSTVLWRRQ----VGAES----LNNYGRQYG-VATFWQMI 23- 2 HD Y+ LA ++G + Y+ ++T L+R+ +GA + L N+ R + V +W ++ Sbjct: 182 MHDWYLALLAASLGKLIYLDETTELYRQHESNVLGARTWSKRLKNWLRPHRLVKKYWWLV 24- 1 Query: 233 NTSFDRASLIFAQVSDKNSLERKLFFSRFIELKNANLMRRIYLLSKLKLRRKSLKETVAN 29- 2 +S +AS + + + K ++ L + + + RI L + + T Sbjct: 242 TSSQQQASHL---LELDLPAANKAIIRAYVTLLDQSFLNRIKWLKQYGFAKNRAFHTFVF 29- 8 Query: 293 TILLLTGYG 301 L++T +G Sbjct: 299 KTLIITKFG 307 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 258 A DNA sequence (GBSx0273) was identified in S. agalactiae <SEQ ID 819> which encodes the amino acid sequence <SEQ ID 820>. Analysis of this protein sequence reveals the following: TABLE-US-00794 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.19 Transmembrane 1213-1229 (1211-1230) ----- Final Results ----- bacterial membrane --- Certainty = 0.2678 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9581> which encodes amino acid sequence <SEQ ID 9582> was also identified. There is also homology to SEQ ID 822. A related GBS gene <SEQ ID 8525> and protein <SEQ ID 8526> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00795 Lipop: Possible site: -1 Crend: 7 SRCFLG: 0 McG: Length of UR: 3 Peak Value of UR: 2.28 Net Charge of CR: 4 McG: Discrim Score: 1.29 GvH: Signal Score (-7.5): 2.84 Possible site: 30 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 31 ALOM program count: 0 value: 1.16 threshold: 0.0 PERIPHERAL Likelihood = 1.16 344 modified ALOM score: -0.73 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> LPXTG motif: 1197-1201 SEQ ID 8526 (GBS147) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 29 (lane 4; MW 132 kDa). The GBS147-His fusion product was purified (FIG. 200, lane 5) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 286), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 259 A DNA sequence (GBSx0274) was identified in S. agalactiae <SEQ ID 823> which encodes the amino acid sequence <SEQ ID 824>. This protein is predicted to be Acetyltransferase (GNAT) family. Analysis of this protein sequence reveals the following:

TABLE-US-00796 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2781 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00797 >GP: AAG03505 GB: AE004449 conserved hypothetical protein [Pseudomonas aeruginosa] Identities = 66/143 (46%), Positives = 94/143 (65%), Gaps = 5/143 (3%) Query: 2 WNVKTFDNLTTHELFQIYKLRVSVFVVEQDCPYQEVDDEDLI--CLHGMNWVDGQLAAYY 59 W K +LT EL+ + +LR VFVVEQ CPYQEVD DL+ H M W DGQL AY Sbjct: 5 WTCKHHADLTLKELYALLQLRTEVFVVEQKCPYQEVDGLDLVGDTHHLMAWRDGQLLAYL 64 Query: 60 RLIP---EDDKVHLGRVIVNPDFRKKGLGNQLVEYAIKFSEANYPNKPIYAQAQAYLQDF 116- RL+ + +V +GRV+ + R +GLG+QL+E A++ +E + + P+Y AQA+LQ + Sbjct: 65 RLLDPVRHEGQVVIGRVVSSSAARGQGLGHQLMERALQAAERLWLDTPVYLSAQAHLQAY 124- Query: 117 YQSFGFQPVSDIYLEDNIPHLDM 139 Y +GF V+++YLED+IPH+ M Sbjct: 125 YGRYGFVAVTEVYLEDDIPHIGM 147 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 260 A DNA sequence (GBSx0275) was identified in S. agalactiae <SEQ ID 825> which encodes the amino acid sequence <SEQ ID 826>. Analysis of this protein sequence reveals the following: TABLE-US-00798 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2010(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 261 A DNA sequence (GBSx0276) was identified in S. agalactiae <SEQ ID 827> which encodes the amino acid sequence <SEQ ID 828>. Analysis of this protein sequence reveals the following: TABLE-US-00799 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2935(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00800 >GP: CAB12631 GB: Z99108 similar to RNA methyltransferase [Bacillus subtilis] Identities = 217/448 (48%), Positives = 298/448 (66%), Gaps = 4/448 (0%) Query: 7 QRIPLKIKRMGINGEGIGFYKKTLIFVPGALKGEEVFCQISSVRRNFAEAKLLKINKKSK 66 Q PL IKR+GINGEG+G++KK ++FVPGAL GEEV Q + V+ F+E ++ KI K S+ Sbjct: 16 QTFPLTIKRLGINGEGVGYFKKKVVFVPGALPGEEVVVQATKVQPKFSEGRIKKIRKASE 75 Query: 67 NRVEPPCSIYKECGGCQIMHLQYDKQLEFKTDVIRQALMKFKPEGYENYEIRKTIGMSEP 126- +RV PPC +Y++CGGCQ+ HL Y +QL K D++ Q+L + EN EI++TIGM P Sbjct: 76 HRVAPPCPVYEQCGGCQLQHLAYSQQLREKRDIVIQSLERHTKFKVENMEIKETIGMDNP 135- Query: 127 EHYRAKLQFQV-RSFGGNVKAGLYAQGTHRLIDIKDCLVQDSLTQEMINRVAELLGKYKL 18- 5 +YR K QFQ+ RS G++ AGLY +H ++ IKDC+VQ T + V +L + + Sbjct: 136 WNYRNKSQFQIGRSQSGSIIAGLYGLDSHDIVPIKDCIVQHPATNKTTGIVRRILEDFNV 19- 5 Query: 186 PIYNERKIAG-VRTVMIRRAQASGEVQLIFITSKRL--DFDDVVIELVREFPELKTVAVN 24- 2 +YNERK G VRT++ R +GEVQ++ +T+K +++V + + PE+K++ N Sbjct: 196 SVYNERKRKGDVRTIVTRVGFETGEVQVVLVTAKETLPHKEEIVKAIQKRLPEVKSIIQN 25- 5 Query: 243 INASKTSDIYGQITEVIWGQESINEEVLDYGFSLSPRAFYQLNPKQTQILYSEAVKALDV 30- 2 +N +KTS I+G+ T+ + G+ I E + D F LS RAF+QLNP+QT LY E KA + Sbjct: 256 VNGAKTSVIFGEKTKQLAGKTVIQEVLGDVSFELSARAFFQLNPEQTVKLYDEVKKAAQL 31- 5 Query: 303 KEDDDLIDAYCGVGTIGLAFAGKVKSVRGMDIIPEAIQDAKENALYMGFTNTHYEAGKAE 36- 2 + ++DAYCGVGTIG+ A K VRGMD+I E+I DAK+NA G N Y G AE Sbjct: 316 TGKEKVVDAYCGVGTIGMWVADGAKEVRGMDVIKESIDDAKKNAKKHGMANATYVTGTAE 37- 5 Query: 363 DIIPRWYSEGFRANALIVDPPRTGLDDKLLNTILKMPPEKMVYVSCNTSTLARDLVTLTK 42- 2 +P+W EGFR + +IVDPPRTG D L+TI K+ P++ VYVSCN STLA+DL TL+K Sbjct: 376 HWLPKWTKEGFRPDVVIVDPPRTGCDSTFLDTIKKVKPKRFVYVSCNPSTLAKDLQTLSK 43- 5 Query: 423 VYHVHYIQSVDMFPHTARTEAVVKLQRK 450 Y V YIQ VDMFP TA EAV +L K Sbjct: 436 DYRVDYIQPVDMFPQTAHVEAVARLVLK 463 A related DNA sequence was identified in S. pyogenes <SEQ ID 829> which encodes the amino acid sequence <SEQ ID 830>. Analysis of this protein sequence reveals the following: TABLE-US-00801 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2980(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00802 Identities = 327/450 (72%), Positives = 397/450 (87%) Query: 1 MNVVLKQRIPLKIKRMGINGEGIGFYKKTLIFVPGALKGEEVFCQISSVRRNFAEAKLLK 60 M V +KQ+IPLKIKRMGINGEGIGFY+KTL+FVPGALKGE++FCQI++V+RNFAEAKLL Sbjct: 1 MVVKVKQKIPLKIKRMGINGEGIGFYQKTLVFVPGALKGEDIFCQITAVKRNFAEAKLLT 60 Query: 61 INKKSKNRVEPPCSIYKECGGCQIMHLQYDKQLEFKTDVIRQALMKFKPEGYENYEIRKT 120- +NK SKNRV+P CS+Y+ CGGCQIMHL Y KQL+FK DVIRQAL KFEP GYE +EIR T Sbjct: 61 VNKASKNRVKPACSVYETCGGCQIMHLAYPKQLDFKDDVIRQALKKFKPTGYEQFEIRPT 120- Query: 121 IGMSEPEHYRAKLQFQVRSFGGNVKAGLYAQGTHRLIDIKDCLVQDSLTQEMINRVAELL 18- 0 +GM +P+HYRAKLQFQ+RSFGG VKAGL++QG+HRL+ I +CLVQD LTQ++IN++ +L+ Sbjct: 121 LGMKKPDHYRAKLQFQLRSFGGTVKAGLFSQGSHRLVPIDNCLVQDQLTQDIINKITQLV 18- 0 Query: 181 GKYKLPIYNERKIAGVRTVMIRRAQASGEVQLIFITSKRLDFDDVVIELVREFPELKTVA 24- 0 KYKLPIYNERKIAG+RT+M+R+AQAS +VQ+I ++SK + + + EL + FP++KTVA Sbjct: 181 DKYKLPIYNERKIAGIRTIMVRKAQASDQVQIIVVSSKEVRLANFIGELTKAFPQVKTVA 24- 0 Query: 241 VNINASKTSDIYGQITEVIWGQESINEEVLDYGFSLSPRAFYQLNPKQTQILYSEAVKAL 30- 0 +N N SK+S+IYG TE++WGQE+I+EEVLDYGF+LSPRAFYQLNP+QT++LY E VKAL Sbjct: 241 LNSNRSKSSEIYGDETEILWGQEAIHEEVLDYGFALSPRAFYQLNPQQTEVLYGEVVKAL 30- 0 Query: 301 DVKEDDDLIDAYCGVGTIGLAFAGKVKSVRGMDIIPEAIQDAKENALYMGFTNTHYEAGK 36- 0 DV D +IDAYCGVG+IG AFAGKVKSVRGMDIIPEAI+DA++NA MGF N +YEAGK Sbjct: 301 DVGSKDHIIDAYCGVGSIGFAFAGKVKSVRGMDIIPEAIEDAQKNAKAMGFDNAYYEAGK 36- 0 Query: 361 AEDIIPRWYSEGFRANALIVDPPRTGLDDKLLNTILKMPPEKMVYVSCNTSTLARDLVTL 42- 0 AEDII +WY +G+RA+A+IVDPPRTGLDDKLL TIL P++MVYVSCNTSTLARDLV L Sbjct: 361 AEDIISKWYKQGYRADAVIVDPPRTGLDDKLLKTILHYQPKQMVYVSCNTSTLARDLVQL 42- 0 Query: 421 TKVYHVHYIQSVDMFPHTARTEAVVKLQRK 450 TKVY VHYIQSVDMFPHTARTEAVVKLQ++ Sbjct: 421 TKVYDVHYIQSVDMFPHTARTEAVVKLQKR 450 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 262 A DNA sequence (GBSx0277) was identified in S. agalactiae <SEQ ID 831> which encodes the amino acid sequence <SEQ ID 832>. Analysis of this protein sequence reveals the following: TABLE-US-00803 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3505(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00804 >GP: BAB04643 GB: AP001510 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 74/263 (28%), Positives = 141/263 (53%), Gaps = 9/263 (3%) Query: 3 ITKIEKKKR---LYTLEL-DNTENLY---ITEDTIVHFMLSKGMIINAEKLENIKKFAQL 55 IT+IE +KR Y + + N +++Y + E ++ L KG+ I+AE+++ I ++ Sbjct: 4 ITRIEVQKRNNERYNIFIHQNGQDVYAFSVDEQVLIKQGLRKGLDIDAEQMKQILYEDEV 63 Query: 56 SYGKNLGLYYISFKQRTEKEVIKYLQQHDIDSKIIPQIIDNLKSENWINDKNYVQSFIQQ 115- NL L+Y+S++ R+ EV YL++ D + II ++ L + ++D + ++FIQ Sbjct: 64 QKTFNLALHYLSYRMRSVHEVRTYLKKKDREEPIIEHVLHRLTEQRLLDDHAFAEAFIQT 123- Query: 116 NLNTGDKGPYVIKQKLLQKGIKSKIIESELQAINFQDLASKISQKLYKKYQNKLPLKAL- 17- 4 T KGP +KQ+L +KG+ K IE L ++++ ++ L K+ +L Sbjct: 124 KRATTSKGPLKLKQELAEKGVSEKTIEGALTTFSYEEQVEQVKAWLEKQKGRTFKGSSLA 18- 3 Query: 175 -KDKLMQSLTTKGFDYQIVHTVIQNLEIEKDQELEEDLIYKELDKQYQKLSKKHDQYELK 23- 3 K KL + L KG+ ++ ++ I++++E E + + +K +K + K +EL+ Sbjct: 184 WKQKLSRQLLAKGYTSPVIEEAFADVPIKQEEEEEWEALKAFGEKAMRKYAGKKTGWELQ 24- 3 Query: 234 QRIINALMRKGYQYEDIKSALRE 256 Q++ AL RKG+ E I+ L + Sbjct: 244 QKVKQALYRKGFSLEMIERYLND 266 A related DNA sequence was identified in S. pyogenes <SEQ ID 833> which encodes the amino acid sequence <SEQ ID 834>. Analysis of this protein sequence reveals the following: TABLE-US-00805 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2388(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00806 Identities = 146/258 (56%), Positives = 190/258 (73%) Query: 1 MKITKIEKKKRLYTLELDNTENLYITEDTIVHFMLSKGMIINAEKLENIKKFAQLSYGKN 60 MKITKIEKKKRLY +ELDN E+LY+TEDTIV FMLSK +++ ++LE++K FAQLSYGKN Sbjct: 1 MKITKIEKKKRLYLIELDNDESLYVTEDTIVRFMLSKDKVLDNDQLEDMKHFAQLSYGKN 60 Query: 61 LGLYYISFKQRTEKEVIKYLQQHDIDSKIIPQIIDNLKSENWINDKNYVQSFIQQNLNTG 120- L LY++SF+QR+ K+V YL++H+I+ II II L+ E WI+D ++I+QN G Sbjct: 61 LALYFLSFQQRSNKQVADYLRKHEIEEHIIADIITQLQEEQWIDDTKLADTYIRQNQLNG 120- Query: 121 DKGPYVIKQKLLQKGIKSKIIESELQAINFQDLASKISQKLYKKYQNKLPLKALKDKLMQ 18- 0 DKGP V+KQKLLQKGI S I+ L +F LA K+SQKL+ KYQ KLP KALKDK+ Q Sbjct: 121 DKGPQVLKQKLLQKGIASHDIDPILSQTDFSQLAQKVSQKLFDKYQEKLPPKALKDKITQ 18- 0 Query: 181 SLTTKGFDYQIVHTVIQNLEIEKDQELEEDLIYKELDKQYQKLSKKHDQYELKQRIINAL 24- 0 +L TKGF Y + + +L ++D + EDL+ KELDKQY+KLS+K+D Y LKQ++ AL Sbjct: 181 ALLTKGFSYDLAKHSLNHLNFDQDNQEIEDLLDKELDKQYRKLSRKYDGYTLKQKLYQAL 24- 0 Query: 241 MRKGYQYEDIKSALREYL 258 RKGY +DI LR YL Sbjct: 241 YRKGYNSDDINCKLRNYL 258 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 263 A DNA sequence (GBSx0278) was identified in S. agalactiae <SEQ ID 835> which encodes the amino acid sequence <SEQ ID 836>. Analysis of this protein sequence reveals the following: TABLE-US-00807 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3912(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00808 >GP: BAB04659 GB: AP001510 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 96/175 (54%), Positives = 122/175 (68%) Query: 1 MRLPKEGDFITIQSYKHDGSLHRTWRDTMVLKTTENALIGVNDHTLVTENDGRRWVTREP 60 M PK G I IQSYKH+GS+HR W +T+VLK T +IG ND LV E+DGR W TREP Sbjct: 1 MNFPKVGSKIQIQSYKHNGSIHRIWEETIVLKGTSKVVIGGNDRILVKESDGRHWRTREP 60 Query: 61 AIVYFHKKYWFNIIAMIRETGVSYYCNLASPYILDPEALKYIDYDLDVKVFADGEKRLLD 120- AI YF + WFN I MIR G+ +YCNL +P+ D EALKYIDYDLD+KVF D +LLD Sbjct: 61 AICYFDSEQWFNTIGMIRADGIYFYCNLGTPFTWDEEALKYIDYDLDIKVFPDMTFKLLD 120- Query: 121 VDEYEQHKAQMNYPTDIDYILKENVKILVEWINENKGPFSSSYINIWYKRYLELK 175 DEY H+ M YP +ID IL+ +V LV WI++ KGPF+ ++ WY+R+L+ + Sbjct: 121 EDEYAMHRKMMKYPPEIDRILQRSVDELVSWIHQRKGPFAPQFVESWYERFLQYR 175 A related DNA sequence was identified in S. pyogenes <SEQ ID 837> which encodes the amino acid sequence <SEQ ID 838>. Analysis of this protein sequence reveals the following: TABLE-US-00809 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3912(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00810 Identities = 155/177 (87%), Positives = 165/177 (92%) Query: 1 MRLPKEGDFITIQSYKHDGSLHRTWRDTMVLKTTENALIGVNDHTLVTENDGRRWVTREP 60 M+LPKEGDFITIQSYKHDGSLHRTWRDTMVLKTTENALIGVNDHTLVTE+DGRRWVTREP Sbjct: 1 MKLPKEGDFITIQSYKHDGSLHRTWRDTMVLKTTENALIGVNDHTLVTESDGRRWVTREP 60 Query: 61 AIVYFHKKYWFNIIAMIRETGVSYYCNLASPYILDPEALKYIDYDLDVKVFADGEKRLLD 120- AIVYFHKKYWFNIIAMIR+ GVSYYCNLASPY++D EALKYIDYDLDVKVFADGEKRLLD Sbjct: 61 AIVYFHKKYWFNIIAMIRDNGVSYYCNLASPYMMDTEALKYIDYDLDVKVFADGEKRLLD 120- Query: 121 VDEYEQHKAQMNYPTDIDYILKENVKILVEWINENKGPFSSSYINIWYKRYLELKKR 177 VDEYE HK +M Y D+D+ILKENVKILV+WIN KGPFS +YI IWYKRYLELK R Sbjct: 121 VDEYEIHKKEMQYSADMDFILKENVKILVDWINHEKGPFSKAYITIWYKRYLELKNR 177 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 264 A DNA sequence (GBSx0288) was identified in S. agalactiae <SEQ ID 839> which encodes the amino acid sequence <SEQ ID 840>. This protein is predicted to be jag protein. Analysis of this protein sequence reveals the following: TABLE-US-00811 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1666(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00812 >GP: BAB07782 GB: AP001520 spoIIIJ-associated protein [Bacillus halodurans] Identities = 54/198 (27%), Positives = 98/198 (49%), Gaps = 6/198 (3%) Query: 100 DVVEEYIEEVDETLEKEDVSQPELPKIDDKNVVTTSEAIEKIDLLPNIEVAAAQVTKYVE 15- 9 + VE+ I E+ T E+ + E PK ++ + A+ ++ + P+ + ++E Sbjct: 13 EAVEQAIIELGTTRERITYTVVEEPKSGLFGILGSKPAVIEVVVKPD---PVDRAKAFLE 69 Query: 160 NIIYEMDLDA--TIETTTSKRQINLQIETPEAGRIIGYHGKVLKSLQLLAQNYLHDRFSK 21- 7 ++ EMD++ TIE + N+ E + G +IG G+ L SLQ L + + Sbjct: 70 ELLQEMDMEVEVTIEKDPATVLFNISGEQ-DLGTLIGKRGQTLDSLQYLVNLVANKEEGE 128- Query: 218 SFSVSINVHDYVEHRTETLIDFSKKIARRVLETNEPYHMDPMSNSERKTVHKTIATIEGV 27- 7 + ++ +Y R E L+ ++++A + L T P ++PMS ERK +H + + V Sbjct: 129 FIRIKLDAENYRARRKEALVQLAERLASKALRTKRPVSLEPMSAHERKIIHTALQELGDV 18- 8 Query: 278 ESYSEGNDPNRFVVVTKK 295 E+YSEG R VV+ K Sbjct: 189 ETYSEGQGIGRHVVIAPK 206 A related DNA sequence was identified in S. pyogenes <SEQ ID 841> which encodes the amino acid sequence <SEQ ID 842>. Analysis of this protein sequence reveals the following: TABLE-US-00813 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3721(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00814 Identities = 176/302 (58%), Positives = 223/302 (73%), Gaps = 32/302 (10%) Query: 23 MVLFTGATVEEAIEKGLQELNISRLRAHIKVVSREKKGFLGFGKKPAKVEIEGITDEVTD 82 - MVLFTG TVEEAIE GLQEL +SRL+AHIKV+S+EKKGFLGFGKKPA+V+IEGI+D+ Sbjct: 1 MVLFTGKTVEEAIETGLQELGLSRLKAHIKVISKEKKGFLGFGKKPAQVDIEGISDKTVY 60 Query: 83 INESVALKNI------KNVPS--SVDVVEEYIEEVDETLEKEDVSQPELPKIDDK----- 129- + A + + +N P+ S DV E I+ + LE ED L D Sbjct: 61 KADKKATRGVPEDINRQNTPAVNSADVEPEEIKAT-QRLEAEDTKVVPLMSEDSPAQTPS 119- Query: 130 ---NVVTTSEA------IEKIDL---------LPNIEVAAAQVTKYVENIIYEMDLDATI 17- 1 VT ++A +E+ ++ +IE AA +V+ YV IIYEMD++AT+ Sbjct: 120 NLAETVTETKAQQPSIPVEESEVPQDAGNDGFSKDIEKAAQEVSDYVTKIIYEMDIEATV 17- 9 Query: 172 ETTTSKRQINLQIETPEAGRIIGYHGKVLKSLQLLAQNYLHDRFSKSFSVSINVHDYVEH 23- 1 ET+ ++RQINLQIETPEAGR+IGYHGKVLKSLQLLAQN+LHDR+SK+FSVS+NVHDYVEH Sbjct: 180 ETSNNRRQINLQIETPEAGRVIGYHGKVLKSLQLLAQNFLHDRYSKNFSVSLNVHDYVEH 23- 9 Query: 232 RTETLIDFSKKIARRVLETNEPYHMDPMSNSERKTVHKTIATIEGVESYSEGNDPNRFVV 29- 1 RTETLIDF++K+A+RVLE+ + Y MDPMSNSERK VHKT+++IEGV+SYSEGNDPNR+VV Sbjct: 240 RTETLIDFTQKVAKRVLESGQDYTMDPMSNSERKIVHKTVSSIEGVDSYSEGNDPNRYVV 29- 9 Query: 292 VT 293 V+ Sbjct: 300 VS 301 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 265 A DNA sequence (GBSx0290) was identified in S. agalactiae <SEQ ID 843> which encodes the amino acid sequence <SEQ ID 844>. This protein is predicted to be 60 kd inner-membrane protein (yidC). Analysis of this protein sequence reveals the following:

TABLE-US-00815 Possible site: 42 >>> May be a lipoprotein INTEGRAL Likelihood = -7.38 Transmembrane 54-70 (52-75) INTEGRAL Likelihood = -5.20 Transmembrane 193-209 (192-211) INTEGRAL Likelihood = -3.61 Transmembrane 125-141 (124-144) INTEGRAL Likelihood = -2.44 Transmembrane 168-184 (167-184) ----- Final Results ----- bacterial membrane --- Certainty = 0.3951(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00816 >GP: CAA78595 GB: Z14225 SpoIIIJ [Bacillus subtilis] Identities = 79/243 (32%), Positives = 142/243 (57%), Gaps = 5/243 (2%) Query: 1 MKKKLKTFSLILLTGSLLVACG--RGEVSSHSATLWEQ-IVYAFAKSIQWLS--FNHSIG 55 MK+++ ++ LL C + +++ S W++ +VY ++ I +++ + G Sbjct: 1 MKRRIGLLLSMVGVFMLLAGCSSVKEPITADSPHFWDKYVVYPLSELITYVAKLTGDNYG 60 Query: 56 LGIILFTLIIRAIMMPLYNMQMKSSQKMQEIQPRLKELQKKYPGKDPDNRLKLNDEMQSM 115- L IIL T++IR +++PL Q++SS+ MQ +QP +++L++KY KD + KL E ++ Sbjct: 61 LSIILVTILIRLLILPLMIKQLRSSKAMQALQPEMQKLKEKYSSKDQKTQQKLQQETMAL 120- Query: 116 YKAEGVNPYASVLPLLIQLPVLWALFQALTRVSFLKVGTFLSLELSQPDPYYILPVLAAL 17- 5 ++ GVNP A P+LIQ+P+L + A+ R + +FL +L + DPYYILP++A + Sbjct: 121 FQKHGVNPLAGCFPILIQMPILIGFYHAIMRTQAISEHSFLWFDLGEKDPYYILPIVAGV 18- 0 Query: 176 FTFLSTWLTNKAAVEKNIALTLMTYVMPFIILVTSFNFASGVVLYWTVSNAFQVFQILLL 23- 5 TF+ L ++N + +M ++MP +I+V + NF + + LYW V N F + Q L+ Sbjct: 181 ATFVQQKLMMAGNAQQNPQMAMMLWIMPIMIIVFAINFPAALSLYWVVGNLFMIAQTFLI 24- 0 Query: 236 NNP 238 P Sbjct: 241 KGP 243 A related GBS sequence was identified <SEQ ID 10783> which encodes amino acid sequence <SEQ ID 10784>. A related DNA sequence was identified in S. pyogenes <SEQ ID 845> which encodes the amino acid sequence <SEQ ID 846>. Analysis of this protein sequence reveals the following: TABLE-US-00817 Possible site: 49 >>> May be a lipoprotein INTEGRAL Likelihood = -6.32 Transmembrane 198-214 (197-220) INTEGRAL Likelihood = -5.52 Transmembrane 59-75 (57-80) INTEGRAL Likelihood = -4.25 Transmembrane 130-146 (129-150) INTEGRAL Likelihood = -2.28 Transmembrane 173-189 (170-189) ----- Final Results ----- bacterial membrane --- Certainty = 0.3527 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00818 >GP: BAA05234 GB: D26185 stage III sporulation [Bacillus subtilis] Identities = 90/249 (36%), Positives = 150/249 (60%), Gaps = 6/249 (2%) Query: 16 IVPLVLLLVACG--RGEVTAQSSSGWDQ-LVYLFARAIQWLS--FDGSIGVGIILFTLTI 70 - +V + +LL C + +TA S WD+ +VY + I +++ + G+ IIL T+ I Sbjct: 13 MVGVFMLLAGCSSVKEPITADSPHFWDKYVVYPLSELITYVAKLTGDNYGLSIILVTILI 72 Query: 71 RLMLMPLFNMQIKSSQKMQDIQPELRELQRKYAGKDTQTRMKLAEESQALYKKYGVNPYA 130- RL+++PL Q++SS+ MQ +QPE+++L+ KY+ KD +T+ KL +E+ AL++K+GVNP A Sbjct: 73 RLLILPLMIKQLRSSKAMQALQPEMQKLKEKYSSKDQKTQQKLQQETMALFQKHGVNPLA 132- Query: 131 SLLPLLIQMPVMIALFQALTRVSFLKTGTFLWVELAQHDHLYLLPVLAAVFTFLSTWLTN 19- 0 P+LIQMP++I + A+ R + +FLW +L + D Y+LP++A V TF+ L Sbjct: 133 GCFPILIQMPILIGFYHAIMRTQAISEHSFLWFDLGEKDPYYILPIVAGVATFVQQKLMM 19- 2 Query: 191 LAAKEKNVMMTVMIYVMPLMIFFMGFNLASGVVLYWTVSNAFQVVQLLLLNNP-FKIIAE 24- 9 ++N M +M+++MP+MI N + + LYW V N F + Q L+ P K E Sbjct: 193 AGNAQQNPQMAMMLWIMPIMIIVFAINFPAALSLYWVVGNLFMIAQTFLIKGPDIKKNPE 25- 2 Query: 250 RQRLANEEK 258 Q+ ++K Sbjct: 253 PQKAGGKKK 261 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00819 Identities = 172/270 (63%), Positives = 217/270 (79%), Gaps = 1/270 (0%) Query: 1 MKKKLKTFSLILLTGSLLVACGRGEVSSHSATLWEQIVYAFAKSIQWLSFNHSIGLGIIL 60 +KK +K ++ L LLVACGRGEV++ S++ W+Q+VY FA++IQWLSF+ SIG+GIIL Sbjct: 7 VKKNIKIARIVPLV-LLLVACGRGEVTAQSSSGWDQLVYLFARAIQWLSFDGSIGVGIIL 65 Query: 61 FTLIIRAIMMPLYNMQMKSSQKMQEIQPRLKELQKKYPGKDPDNRLKLNDEMQSMYKAEG 120- FTL IR ++MPL+NMQ+KSSQKMQ+IQP L+ELQ+KY GKD R+KL +E Q++YK G Sbjct: 66 FTLTIRLMLMPLFNMQIKSSQKMQDIQPELRELQRKYAGKDTQTRMKLAEESQALYKKYG 125- Query: 121 VNPYASVLPLLIQLPVLWALFQALTRVSFLKVGTFLSLELSQPDPYYILPVLAALFTFLS 18- 0 VNPYAS+LPLLIQ+PV+ ALFQALTRVSFLK GTFL +EL+Q D Y+LPVLAA+FTFLS Sbjct: 126 VNPYASLLPLLIQMPVMIALFQALTRVSFLKTGTFLWVELAQHDHLYLLPVLAAVFTFLS 18- 5 Query: 181 TWLTNKAAVEKNIALTLMTYVMPFIILVTSFNFASGVVLYWTVSNAFQVFQILLLNNPYK 24- 0 TWLTN AA EKN+ +T+M YVMP +I FN ASGVVLYWTVSNAFQV Q+LLLNNP+K Sbjct: 186 TWLTNLAAKEKNVMMTVMIYVMPLMIFFMGFNLASGVVLYWTVSNAFQVVQLLLLNNPFK 24- 5 Query: 241 IIKVREEAVRVAHEKEQRVKRAKRKASKKR 270 II R+ E+ R +RA++KA K++ Sbjct: 246 IIAERQRLANEEKERRLRERRARKKAMKRK 275 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8527> and protein <SEQ ID 8528> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00820 Lipop: Possible site: 20 Crend: 5 McG: Discrim Score: 4.90 GvH: Signal Score (-7.5): -0.39 Possible site: 42 >>> May be a lipoprotein ALOM program count: 4 value: -7.38 threshold: 0.0 INTEGRAL Likelihood = -7.38 Transmembrane 54-70 (52-75) INTEGRAL Likelihood = -5.20 Transmembrane 193-209 (192-211) INTEGRAL Likelihood = -3.61 Transmembrane 125-141 (124-144) INTEGRAL Likelihood = -2.44 Transmembrane 168-184 (167-184) PERIPHERAL Likelihood = 2.54 217 modified ALOM score: 1.98 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3951 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00019## EXAMPLE 266 A DNA sequence (GBSx0291) was identified in S. agalactiae <SEQ ID 847> which encodes the amino acid sequence <SEQ ID 848>. Analysis of this protein sequence reveals the following: TABLE-US-00821 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3778 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9579> which encodes amino acid sequence <SEQ ID 9580> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00822 >GP: CAA44400 GB: X62539 homologous to E. coli rnpA [Bacillus subtilis] Identities = 52/109 (47%), Positives = 77/109 (69%), Gaps = 1/109 (0%) Query: 21 LKKTYRVKSDKDFQMIFSRGKNVANRKFVIYYLEK-EQKHFRVGISVSKKLGNAVVRNAI 79 - LKK R+K ++DFQ +F G +VANR+FV+Y L++ E RVG+SVSKK+GNAV+RN I Sbjct: 4 LKKRNRLKKNEDFQKVFKHGTSVANRQFVLYTLDQPENDELRVGLSVSKKIGNAVMRNRI 63 Query: 80 KRKIRHVLLSQKTALQDYDFVVIARKGVEELDYQALEKNLIHVLKIAGL 128 KR IR L +K L++ D+++IARK +L Y+ +K+L H+ + + L Sbjct: 64 KRLIRQAFLEEKERLKEKDYIIIARKPASQLTYEETKKSLQHLFRKSSL 112 A related DNA sequence was identified in S. pyogenes <SEQ ID 849> which encodes the amino acid sequence <SEQ ID 850>. Analysis of this protein sequence reveals the following: TABLE-US-00823 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3820 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00824 Identities = 73/109 (66%), Positives = 88/109 (79%) Query: 21 LKKTYRVKSDKDFQMIFSRGKNVANRKFVIYYLEKEQKHFRVGISVSKKLGNAVVRNAIK 80 - LKKTYRVK +KDFQ IF GK+ ANRKFVIY+L + Q HFRVGISV KK+GNAV RNA+K Sbjct: 1 LKKTYRVKREKDFQAIFKDGKSTANRKFVIYHLNRGQDHFRVGISVGKKIGNAVTRNAVK 60 Query: 81 RKIRHVLLSQKTALQDYDFVVIARKGVEELDYQALEKNLIHVLKIAGLI 129 RKIRHV+++ L+ DFVVIARKGV L+YQ L++NL HVLK+A L+ Sbjct: 61 RKIRHVIMALGHQLKSEDFVVIARKGVHSLEYQELQQNLHHVLKLAQLL 109 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 267 A DNA sequence (GBSx0292) was identified in S. agalactiae <SEQ ID 851> which encodes the amino acid sequence <SEQ ID 852>. This protein is predicted to be glycerol-3-phosphate dehydrogenase, NAD-dependent (gpsA). Analysis of this protein sequence reveals the following: TABLE-US-00825 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1429 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8529> which encodes amino acid sequence <SEQ ID 8530> was also identified. There is a signal peptide at residues 1-19. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00826 >GP: AAA86746 GB: U32164 NAD(P)H-dependent dihydroxyacetone-phosphate reductase [Bacillus subtilis] Identities = 177/333 (53%), Positives = 241/333 (72%) Query: 18 QKIAVLGPGSWGTALAQVLNDNGHEVRLWGNVVEQIEEINTNHTNQRYFKDITLDSKIKA 77 - +K+ +LG GSWGTALA VL DHG+EV +W + + I +IN H N+ Y ++ L + IK Sbjct: 2 KKVTMLGAGSWGTALALVLTDNGNEVCVWAHRADLIHQINELHENKDYLPNVKLSTSIKG 61 Query: 78 YTNLEEAINNVDSILFVVPTKVTRLVAKQVANLLKHKVVLMHASKGLEPGTHERLSTILE 137- T+++EA+++ D I+ VPTK R V +Q + K V +H SKG+EP + R+S I+E Sbjct: 62 TTDMKEAVSDADVIIVAVPTKAIREVLRQAVPFITKKAVFVHVSKGIEPDSLLRISEIME 121- Query: 138 EEISEQYRSDIVVVSGPSHAEEAIVRDITLITAASKDIEAAKYVQKLFSNHYFRLYTNTD 19- 7 E+ R DIVV+SGPSHAEE +R T +TA+SK + AA+ VQ LF NH FR+YTN D Sbjct: 122 IELPSDVRRDIVVLSGPSHAEEVGLRHATTVTASSKSMRAAEEVQDLFINHNFRVYTNPD 18- 1 Query: 198 VVGVETAGALKNIIAVGAGALHGLGYGDNAKAAIITRGLAEITRLGVQLGADPLTFSGLS 25- 7 ++GVE GALKNIIA+ AG GLGYGDNAKAA+ITRGLAEI RLG ++G +PLTFSGL+ Sbjct: 182 IIGVEIGGALKNIIALAAGITDGLGYGDNAKAALITRGLAEIARLGTKMGGNPLTFSGLT 24- 1 Query: 258 GVGDLIVTGTSVHSRNWRAGDALGRGEKLEDIEKNMGMVIEGISTTKVAYEIAQNLNVYM 31- 7 GVGDLIVT TSVHSRNWRAG+ LG+G KLED+ + MGMV+EG+ TTK AY++++ +V M Sbjct: 242 GVGDLIVTCTSVHSRNWRAGNLLGKGYKLEDVLEEMGMVVEGVRTTKAAYQLSKKYDVKM 30- 1 Query: 318 PITEAIYKSIYEGANIKDSILDMMSNEFRSENE 350 PITEA+++ ++ G ++ ++ +M+ E E Sbjct: 302 PITEALHQVLFNGQKVETAVESLMARGKTHEME 334 A related DNA sequence was identified in S. pyogenes <SEQ ID 853> which encodes the amino acid sequence <SEQ ID 854>. Analysis of this protein sequence reveals the following: TABLE-US-00827 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0882(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00828 Identities = 287/338 (84%), Positives = 316/338 (92%) Query: 15 MTKQKIAVLGPGSWGTALAQVLNDNGHEVRLWGNVVEQIEEINTNHTNQRYFKDITLDSK 74 - MTKQK+A+LGPGSWGTAL+QVLNDNGH+VRLWGN+ +QIEEINT HTN+ YFKDI LD Sbjct: 1 MTKQKVAILGPGSWGTALSQVLNDNGHDVRLWGNIPDQIEEINTKHTNRHYFKDIVLDKN 60 Query: 75 IKAYTNLEEAINNVDSILFVVPTKVTRLVAKQVANLLKHKVVLMHASKGLEPGTHERLST 134- I A +L +A+++VD++LFVVPTKVTRLVA+QVA +L HKVV+MHASKGLEP THERLST Sbjct: 61 ITATLDLGQALSDVDAVLFVVPTKVTRLVARQVAAILDHKVVVMHASKGLEPETHERLST 120- Query: 135 ILEEEISEQYRSDIVVVSGPSHAEEAIVRDITLITAASKDIEAAKYVQKLFSNHYFRLYT 19- 4 ILEEEI +RS++VVVSGPSHAEE IVRDITLITAASKDIEAAKYVQ LFSNHYFRLYT Sbjct: 121 ILEEEIPAHFRSEVVVVSGPSHAEETIVRDITLITAASKDIEAAKYVQSLFSNHYFRLYT 18- 0 Query: 195 NTDVVGVETAGALKNIIAVGAGALHGLGYGDNAKAAIITRGLAEITRLGVQLGADPLTFS 25- 4 NTDV+GVETAGALKNIIAVGAGALHGLGYGDNAKAA+ITRGLAEITRLGV+LGADPLT+S Sbjct: 181 NTDVIGVETAGALKNIIAVGAGALHGLGYGDNAKAAVITRGLAEITRLGVKLGADPLTYS 24- 0 Query: 255 GLSGVGDLIVTGTSVHSRNWRAGDALGRGEKLEDIEKNMGMVIEGISTTKVAYEIAQNLN 31- 4 GLSGVGDLIVTGTSVHSRNWRAG ALGRGEKLEDIE+NMGMVIEGI+TTKVAYEIAQ+L Sbjct: 241 GLSGVGDLIVTGTSVHSRNWRAGAALGRGEKLEDIERNMGMVIEGIATTKVAYEIAQDLG 30- 0 Query: 315 VYMPITEAIYKSIYEGANIKDSILDMMSNEFRSENEWH 352 VYMPIT AIYKSIYEGA+IK+SIL MMSNEFRSENEWH Sbjct: 301 VYMPITTAIYKSIYEGADIKESILGMMSNEFRSENEWH 338 SEQ ID 8530 (GBS291) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 59 (lane 5; MW 38.9 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 77 (lane 2; MW 64 kDa). GBS291-GST was purified as shown in FIG. 226, lane 10-11. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 268 A DNA sequence (GBSx0293) was identified in S. agalactiae <SEQ ID 855> which encodes the amino acid sequence <SEQ ID 856>. This protein is predicted to be glucose-1-phosphate uridylyltransferase (gtaB). Analysis of this protein sequence reveals the following: TABLE-US-00829 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00830 >GP:BAA28714 GB:AB001562 glucose-1-phosphate uridylyltransferase [Streptococcus mutans] Identities = 263/296 (88%), Positives = 285/296 (95%) Query: 2 KVRKAVIPAAGLGTRFLPATKALAKEMLPIVDKPTIQFIVEEALKSGIEDILVVTGKSKR 61 KVRKAVIPAAGLGTRFLPATKALAKEMLPIVDKPTIQFIVEEALKSGIEDILVVTGKSKR Sbjct: 5 KVRKAVIPAAGLGTRFLPATKALAKEMLPIVDKPTIQFIVEEALKSGIEDILVVTGKSKR 64 Query: 62 SIEDEFDSNFELEYNLKEKGKNELLKLVDETTGIRLHFIRQSHPRGLGDAVLQAKAFVGN 121- SIEDHFDSNFELEYNL++KGK +LLKLV++TT I LHFIRQSHPRGLGDAVLQAKAFVGN Sbjct: 65 SIEDHFDSNFELEYNLEQKGKTDLLKLVNDTTAINLHFIRQSHPRGLGDAVLQAKAFVGN 124- Query: 122 EPFVVNLGDDLMDITNNKVIPLTKQLINDFEATHASTIAVMEVPHEDVSAYGVIAPQGEG 18- 1 EPFVVMLGDDLMDIT++K IPLT+QL+ND+E THASTIAVMEVPHEDVSAYGVIAPQGEG Sbjct: 125 EPFVVMLGDDLMDITDDKAIPLTRQLMNDYEETHASTIAVMEVPHEDVSAYGVIAPQGEG 18- 4 Query: 182 VNGLYSVNTFVEKPSPEEAPSNLAIIGRYLLTPEIFNILETQKPGAGNEIQLTDAIDTLN 24- 1 V+GLYSV+TWVEKP+P+EAPSNLAIIGRYLLTPEIF ILETQ+PGAGNE+QLTDAIDTLN Sbjct: 185 VSGLYSVDTWVEKPAPKEAPSNLAIIGRYLLTFEIFTILETQEPGAGNEVQLTDAIDTLN 24- 4 Query: 242 KTQRVFARKFTGDRYDVGDKFGFMKTSIDYALQHPQVKDDLKKYIIDLGKSLEKTS 297 KTQRVFAR+F G RYDVGDKFGFMKTSIDYAL+HPQVK+DLK YII+LGK L++ S Sbjct: 245 KTQRVFAREFRGKRYDVGDKFGFMKTSIDYALKHPQVKEDLEAYIIELGKKLDQKS 300 A related DNA sequence was identified in S. pyogenes <SEQ ID 857> which encodes the amino acid sequence <SEQ ID 858>. Analysis of this protein sequence reveals the following: TABLE-US-00831 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00832 Identities = 257/295 (87%), Positives = 277/295 (93%) Query: 2 KVRKAVIPAAGLGTRFLPATKALAKEMLPIVDKPTIQFIVEEALKSGIEDILVVTGKSKR 61 KVRKA+IPAAGLGTRFLPATKALAKEMLPIVDKPTIQFIVEEALKSGIE+ILVVTGK+KR Sbjct: 3 KVRKAIIPAAGLGTRFLPATKALAKEMLPIVDKPTIQFIVEEALKSGIEEILVVTGKAKR 62 Query: 62 SIEDHFDSNFELEYNLKEKGKNELLKLVDETTGIRLHFIRQSHPRGLGDAVLQAKAFVGN 121- SIEDHFDSNFELEYNL+ KGKNSLLKLVDETT I LHFIRQSHPRGLGDAVLQAKAFVGN Sbjct: 63 SIEDHFDSNFELEYNLQAKGKNELLKLVDETTAINLHFIRQSHPRGLGDAVLQAKAFVGN 122- Query: 122 EPFVVNLGDDLMDITNNKVIPLTKQLINDFEATHASTIAVMEVPHEDVSAYGVIAPQGEG 18- 1 EPFVVMLGDDLMDITN PLTKQL+ D++ THASTIAVM+VPHEDVS+YGVIAPQG+ Sbjct: 123 EPFVVMLGDDLMDITNASAKPLTKQLMEDYDKTHASTIAVMKVPHEDVSSYGVIAPQGKA 18- 2 Query: 182 VNGLYSVNTFVEKPSPEEAPSNLAIIGRYLLTPEIFNILETQKPGAGNEIQLTDAIDTLN 24- 1 V GLYSV+TFVEKP PE+APS+LAIIGRYLLTPEIF ILE Q PGAGNE+QLTDAIDTLN Sbjct: 183 VKGLYSVDTFVEKPQPEDAPSDLAIIGRYLLTPEIFGILERQTPGAGNEVQLTDAIDTLN 24- 2 Query: 242 KTQRVFARKFTGDRYDVGDKFGFMKTSIDYALQHPQVKDDLKKYIIDLGKSLSKT 296 KTQRVFAR+F G+RYDVGDKFGFMKTSIDYAL+HPQVK+DLK YII LGK+LEK+ Sbjct: 243 KTQRVFAREFKGNRYDVGDKFGFMKTSIDYALEHPQVKEDLKNYIIKLGKALEKS 297 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 269 A DNA sequence (GBSx0294) was identified in S. agalactiae <SEQ ID 859> which encodes the amino acid sequence <SEQ ID 860>. Analysis of this protein sequence reveals the following:

TABLE-US-00833 Possible Site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.94 Transmembrane 28-44 (27-45) ----- Final Results ----- bacterial membrane --- Certainty = 0.2975 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00834 >GP:CAB15143 GB:Z99120 similar to ABC transporter (lipoprotein) [Bacillus subtilis] Identities = 148/346 (42%), Positives = 222/346 (63%), Gaps = 16/346 (4%) Query: 31 LTLLSLSVLTLTACGNRSDKSAN---KSDIKVAMVTNQGGVDDKSFNQSAWEGLQKWGKK 87 - ++L+ + L ACGN S + K+ VAMVT+ GGVDDKSFNQSAWEG+Q +GK+ Sbjct: 1 MSLVIAAGTILGACGNSEKSSGSGEGKNKESVAMVTDVGGVDDKSFNQSAWEGIQAFGKE 60 Query: 88 KGLTKG-NGFDYFQSSNESDHANNLDTAASSGYNLIFGIGFGLHDTIEKVSENNKDVKYV 146- GL KG NG+DY QS +++D+ NL+ A ++LI+G+G+ + D+I ++++ K+ + Sbjct: 61 NGLKKGKNGYDYLQSKSDADYTTNLNKLARENFDLIYGVGYLMEDSISEIADQRKNTNFA 120- Query: 147 IVDDIIKGKENVASVTFADNEAAYLAGVAAAKTTKTKTVGFIGGMEGVVVKRFEAGFKAG 20- 6 I+D ++ K+NVAS+TF + E ++L GVAAA ++K+ +GF+GGNE ++K+FE GF+AG Sbjct: 121 IIDAVVD-KDNVASITFKEQEGSFLVGVAAALSSKSGKIGFVGGMESELIKKFEVGFRAG 17- 9 Query: 207 VKSIDPAIKVAVSYAGSFTDAAKGKTIAATQYATGVDVIYQAAGGTGAGIFSEAKTENET 26- 6 V++++P V V YAG F A GK A + Y +GVDVIY +AG TG G+F+EAK Sbjct: 180 VQAVNPKAVVEVKYAGGFDKADVGKATAESMYKSGVDVIYHSAGATGTGVFTEAK---NL 23- 6 Query: 267 RKESNK--VWVIGVDRDQSQEGNYVSKDGKKANFVLASTIKEVGKSLQSVAELTEKKQYP 32- 4 +KE K VWVIGVD+DQ EG +G N L S +K+V ++ V + ++P Sbjct: 237 KKEDPKRDVWVIGVDKDQYAEGQV---EGTDDNVTLTSMVKKVDTVVEDVTKKASDGKFP 29- 3 Query: 325 GGKVTVFGLKDSGVDI--KEHQLSSEGSVAVKKAKEDIVSGKIQVP 368 GG+ +GL GV I + LS + AV K K+ I+ G +++P Sbjct: 294 GGETLTYGLDQDGVGISPSKQNLSDDVIKAVDKWKKKIIDG-LEIP 338 There is also homology to SEQ ID 862. A related GBS gene <SEQ ID 8531> and protein <SEQ ID 8532D were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00835 Lipop: Possible site: 20 Crend: 3 Sequence Pattern: CGNR SRCFLG: 0 McG: Length of UR: 19 Peak Value of UR: 2.31 Net Charge of CR: 2 McG: Discrim Score: 5.09 GvH: Signal Score (-7.5): -3.29 Possible site: 19 >>> May be a lipoprotein Amino Acid Composition: calculated from 21 ALOM program count: 0 value: 5.20 threshold: 0.0 PERIPHERAL Likelihood = 5.20 90 modified ALOM score: -1.54 Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00020## A related GBS nucleic acid sequence <SEQ ID 10947> which encodes amino acid sequence <SEQ ID 10948> was also identified. SEQ ID 8532 (GBS108) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 38 (lane 7; MW 39.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 41 (lane 9; MW 64.6 kDa). The GBS108-GST fusion product was purified (FIG. 202, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 273), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 270 A DNA sequence (GBSx0295) was identified in S. agalactiae <SEQ ID 863> which encodes the amino acid sequence <SEQ ID 864>. Analysis of this protein sequence reveals the following: TABLE-US-00836 Possible site: 35 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.74 Transmembrane 206-222 (197-224) INTEGRAL Likelihood = -3.72 Transmembrane 174-190 (171-194) INTEGRAL Likelihood = -3.19 Transmembrane 98-114 (98-116) INTEGRAL Likelihood = -1.54 Transmembrane 120-136 (120-139) INTEGRAL Likelihood = -0.90 Transmembrane 157-173 (157-173) ----- Final Results ----- bacterial membrane --- Certainty = 0.6095 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00837 >GP: CAB90755 GB: AJ400707 hypothetical protein [Streptococcus uberis] Identities = 126/218 (57%), Positives = 166/218 (75%) Query: 8 KEYPTTVLLVSLTTLVFLLMQLTYGSQAESSQVIFQFGGIQGDYLKAYPTNLWRLISPIF 67 KE P T +S+T L+F++MQ+ YGS A+S QV+FQFGG+ G +K+ P+ LWRL++PIF Sbjct: 5 KEKPVTFFFLSVTILLFIVMQVFYGSWAKSPQVVFQFGGMFGLVVKSMPSQLWRLVTPIF 64 Query: 68 VHIGWEHFLLNGLALYFVGQMGESIWGSLRFLILYILSGLMGNIFTLFFTPHVVAAGAST 127- +HIGWEHFL+N L LYFVGQ+ ESIWGS FL+LY+LSG+MGN+ TLFFTPHVVAAGAST Sbjct: 65 IHIGWEHFLINSLTLYFVGQLAESIWGSRFFLLLYVLSGIMGNVLTLFFTPHVVAAGAST 124- Query: 128 SLFGVFSAIAIAGYFGKNPYLKQVGKSYQVMILLNLFFNIFTPGVSLAGHVGGLVGGVLV 18- 7 SLFG+F+AI + GYFG N LK +GKSYQ +I+LNL N+F P V + GH+GG +GG L Sbjct: 125 SLFGLFAAIVVVGYFGHNQLLKSIGKSYQTLIILNLVMNLFMPNVGIVGHLGGALGGALA 18- 4 Query: 188 AIFLTKQNGSLLFKTWQSILALMIFIIVSISLIGLSLV 225 A+FL + LF Q AL+ ++ +++ LI LSL+ Sbjct: 185 AVFLPTLLDAELFTKKQKTSALLSYLTLALVLITLSLM 222 A related DNA sequence was identified in S. pyogenes <SEQ ID 865> which encodes the amino acid sequence <SEQ ID 866>. Analysis of this protein sequence reveals the following: TABLE-US-00838 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.92 Transmembrane 214-230 (212-232) INTEGRAL Likelihood = -5.36 Transmembrane 135-151 (128-153) INTEGRAL Likelihood = -1.81 Transmembrane 101-117 (100-117) INTEGRAL Likelihood = -1.44 Transmembrane 183-199 (182-199) INTEGRAL Likelihood = -0.53 Transmembrane 166-182 (166-182) ----- Final Results ----- bacterial membrane --- Certainty = 0.4970(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00839 >GP: CAB90755 GB: AJ400707 hypothetical protein [Streptococcus uberis] Identities = 72/128 (56%), Positives = 94/128 (73%) Query: 106 FLLLYVLSGVMGNAFTFWLTPETVAAGASTSLFGLFAAIVVLSFLGKNQALKDLGKSYQT 16- 5 FLLLYVLSG+MGN T + TP VAAGASTSLFGLFAAIVV+ + G NQ LK +GKSYQT Sbjct: 95 FLLLYVLSGIMGNVLTLFFTPHVVAAGASTSLFGLFAAIVVVGYFGHNQLLKSIGKSYQT 154- Query: 166 LIVVNLLMNLFMPNVSMAGHIGGVVGGALLSIVFPTKMRVITVKKTKRMLALVSYGIILV 22- 5 LI++NL+MNLFMPNV + GH+GG +GGAL ++ PT + K ++ AL+SY + + Sbjct: 155 LIILNLVMNLFMPNVGIVGHLGGALGGALAAVFLPTLLDAELFTKKQKTSALLSYLTLAL 21- 4 Query: 226 GVLVLGFL 233 ++ L + Sbjct: 215 VLITLSLM 222 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00840 Identities = 63/132 (47%), Positives = 92/132 (68%) Query: 94 GSLRFLILYILSGLMGNIFTLFFTPHVVAAGASTSLFGVFSAIAIAGYFGKNPYLKQVGK 153- G FL+LY+LSG+MGN FT + TP VAAGASTSLFG+F+AI + + GKN LK +GK Sbjct: 102 GLTPFLLLYVLSGVMGNAFTFWLTPETVAAGASTSLFGLFAAIVVLSFLGKNQALKDLGK 16- 1 Query: 154 SYQVMILLNLFFNIFTPGVSLAGHVGGLVGGVLVAIFLTKQNGSLLFKTWQSILALMIFI 21- 3 SYQ +I++NL N+F P VS+AGH+GG+VGG L++I + + K + +LAL+ + Sbjct: 162 SYQTLIVVNLLMNLFMPNVSMAGHIGGVVGGALLSIVFPTKMRVITVKKTKRMLALVSYG 22- 1 Query: 214 IVSISLIGLSLV 225 I+ + ++ L + Sbjct: 222 IILVGVLVLGFL 233 A further corresponding DNA sequence was identified in S. pyogenes <SEQ ID 9083> which encodes the amino acid sequence <SEQ ID 9084>. Analysis of this protein sequence reveals the following: TABLE-US-00841 Possible site: 52 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.70 Transmembrane 12-28 (7-30) ----- Final Results ----- bacterial membrane --- Certainty = 0.4079(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS sequences follows: TABLE-US-00842 Score = 74.5 bits (180), Expect = 5e-16 Identities = 37/96 (38%), Positives = 48/96 (49%) Query: 1 MTQLLKRYPXXXXXXXXXXXXXXAMQVVYGHLATGAQAIYQVGGMFGLLVKAMPDQLWRL 60 M + K YP MQ+ YG A +Q I+Q GG+ G +KA P LWRL Sbjct: 3 MKKFAKEYPTTVLLVSLTTLVFLLMQLTYGSQAESSQVIFQFGGIQGDYLKAYPTNLWRL 62 Query: 61 VTPXXXXXXXXXXXVNGLTLYFVGQIVEDLWGSRLF 96 ++P +NGL LYFVGQ+ E +WGS F Sbjct: 63 ISPIFVHIGWEHFLLNGLALYFVGQMGESIWGSLRF 98 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 271 A DNA sequence (GBSx0296) was identified in S. agalactiae <SEQ ID 867> which encodes the amino acid sequence <SEQ ID 868>. Analysis of this protein sequence reveals the following: TABLE-US-00843 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2055(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00844 >GP: BAA28715 GB: AB001562 hypothetical protein [Streptococcus mutans] Identities = 96/173 (55%), Positives = 129/173 (74%) Query: 1 MEKKLLRKEVLITLKSQPQAYKSEVDCKLLEAFIKTKAYQNSCVIATYLSFDYEYNTQLL 60 M KK R +V+ LK Q +A K D +LLE I+ +AYQ + VIATYL+F +E++T LL Sbjct: 1 MMKKDYRTQVIEDLKKQDKAKKVLRDEQLLEELIQLEAYQKAHVIATYLAFPFEFDTSLL 60 Query: 61 IKQALCDGKRVLVPKTYPKGKMIFVDYQKDNLRTTPFGLLEPVNDRAVEKASIDLIHVPG 120- I+QA D K ++VPKTYP+ KMIFV Y + +L+ T FGL EP ++ A+EK++IDLIHVPG Sbjct: 61 IEQAQRDNKSIVVPKTYPQRKMIFVVYDEADLQITKFGLKEPRSEEALEKSAIDLIHVPG 120- Query: 121 LIFNNKGFRIGYGAGYFDRYLSDFEGDTISTIYRCQRQDFVEEKHDVAVKEVL 173 L FNN+G+RIG+GAGY+D+YL+DF+GDT+STIY Q+ F D+ VKEVL Sbjct: 121 LAFNNEGYRIGFGAGYYDQYLADFQGDTVSTIYSFQQFTFEPSFFDIPVKEVL 173 A related GBS nucleic acid sequence <SEQ ID 10925> which encodes amino acid sequence <SEQ ID 10926> was also identified. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 272 A DNA sequence (GBSx0297) was identified in S. agalactiae <SEQ ID 869> which encodes the amino acid sequence <SEQ ID 870>. Analysis of this protein sequence reveals the following: TABLE-US-00845 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.44 Transmembrane 161-177 (161-177) INTEGRAL Likelihood = -0.22 Transmembrane 29-45 (28-45) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9305> which encodes amino acid sequence <SEQ ID 9306> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00846 >GP: AAD33517 GB: AF132127 glucose-6-phosphate isomerese [Streptococcus mutans] Identities = 344/401 (85%), Positives = 374/401 (92%) Query: 1 MDLPENYDKEEFSRIQKAAEKIKSDSEVLVVIGIGGSYLGAKAAIDFLNNHFANLQTAEE 60 ++LP+NYDKEEF+RI+KAAEKIKSDSEVLVVIGIGGSYLGA+AAIDFLN+ F NL+ EE Sbjct: 49 LNLPQNYDKEEFARIKKAAEKIKSDSEVLVVIGIGGSYLGARAAIDFLNSSFVNLENKEE 108- Query: 61 RKAPQILYAGNSISSTYLADLVEYVQDKEFSVNVISKSGTTTEPAIAFRVFKELLVKKYG 120- RKAPQILYAGNSISS YLADLV+YV DK+FSVNVISKSGTTTEPAIAFRVFK+LLVKKYG Sbjct: 109 RKAPQILYAGNSISSNYLADLVDYVADKDFSVNVISKSGTTTEPAIAFRVFKDLLVKKYG 16- 8 Query: 121 QEEANKRIYATTDKVKGAVKVEADANNWETFVVPDNVGGRFSVLTAVGLLPIAASGADIT 18- 0 QEEAN+RIYATTD+VKGAVKVEADAN WETFVVPD+VGGRF+VLTAVGLLPIAASGAD+ Sbjct: 169 QEEANQRIYATTDRVKGAVKVEADANGWETFVVPDSVGGRFTVLTAVGLLPIAASGADLD 22- 8 Query: 181 ALMEGANAARKDLSSDKISENIAYQYAAVRNVLYRKGYITEILANYEPSLQYFGEWWKQL 24- 0 LM GA AAR+D SS ++SEN AYQYAA+RN+LYRKGY+TE+LANYEPSLQYF EWWKQL Sbjct: 229 QLMAGAEAARQDYSSAELSENEAYQYAAIRNILYRKGYVTEVLANYEPSLQYFSEWWKQL 28- 8 Query: 241 AGESEGKDQKGIYPTSANFSTDLHSLGQFIQEGYRNLFETVVRVEKPRKNVTIPELTEDL 30- 0 AGESEGKDQKGIYPTSANFSTDLHSLGQFIQEG RNLFETV+RVEK RKN+ +PE EDL Sbjct: 289 AGESEGKDQKGIYPTSANFSTDLHSLGQFIQEGNRNLFETVIRVEKARKNILVPEAAEDL 34- 8 Query: 301 DGLGYLQGKDVDFVNKKATDGVLLAHTDGGVPNMFVTLPTQDAYTLGYTIYFFELAIGLS 36- 0 DGL YLQGKDVDFVNKKATDGVLLAHTDGGVPN F+T+P QD +TLGY IYFFELAIGLS Sbjct: 349 DGLAYLQGKDVDFVNKKATDGVLLAHTDGGVPNTFLTIPEQDEFTLGYVIYFFELAIGLS 40- 8 Query: 361 GYLNSVNPFDQPGVEAYKRNMFALLGKPGFEELSAELNARL 401 GYLN VNPFDQPGVEAYK+NMFALLGKPGFEEL AELNARL Sbjct: 409 GYLNGVNPFDQPGVEAYKKNMFALLGKPGFEELGAELNARL 449 A related DNA sequence was identified in S. pyogenes <SEQ ID 871> which encodes the amino acid sequence <SEQ ID 872>. Analysis of this protein sequence reveals the following: TABLE-US-00847 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.44 Transmembrane 209-225 (209-225) INTEGRAL Likelihood = -0.22 Transmembrane 77-93 (76-93) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00848 >GP: AAD33517 GB: AF132127 glucose-6-phosphate isomerase [Streptococcus mutans] Identities = 369/449 (82%), Positives = 408/449 (90%) Query: 1 MSHITFDYSKVLESFAGQHEIDFLQGQVTEADKLLREGTGPGSDFLGWLDLPENYDKDEF 60 M+HI FDYSKVL F HE+D++Q QVT AD+ LR+GTGPG++ GWL+LP+NYDK+EF Sbjct: 1 MTHIKFDYSKVLGKFLASHELDYIQMQVTAADEALRKGTGPGAEMTGWLNLPQNYDKEEF 60 Query: 61 ARILTAAEKIKADSEVLVVIGIGGSYLGAKAAIDFLNHHFANLQTAKERKAPQILYAGNS 120- ARI AAEKIK+DSEVLVVIGIGGSYLGA+AAIDFLN F NL+ +ERKAPQILYAGNS Sbjct: 61 ARIKKAAEKIKSDSEVLVVIGIGGSYLGARAAIDFLNSSFVNLENKEERKAPQILYAGNS 120- Query: 121 ISSTYLADLVEYVQDKEFSVNVISKSGTTTEPAIAFRVFKELLVKKYGQEEANKRIYATT 18- 0 ISS YLADLV+YV DK+FSVNVISKSGTTTEPAIAFRVFK+LLVKKYGQEEAN+RIYATT Sbjct: 121 ISSNYLADLVDYVADKDFSVNVISKSGTTTEPAIAFRVFKDLLVKKYGQEEANQRIYATT 18- 0 Query: 181 DKVKGAVKVEADANNWETFVVPDNVGGRFSVLTAVGLLPIAASGADITALMEGANAARKD 24- 0 D+VKGAVKVEADAN WETFVVPD+VGGRF+VLTAVGLLPIAASGAD+ LM GA AAR+D Sbjct: 181 DRVKGAVKVEADANGWETFVVPDSVGGRFTVLTAVGLLPIAASGADLDQLMAGAEAARQD 24- 0 Query: 241 LSSDKISENIAYQYAAVRNVLYRKGYITEILANYEPSLQYFGEWWKQLAGESEGKDQKGI 30- 0 SS ++SEN AYQYAA+RN+LYRKGY+TE+LANYEPSLQYF EWWKQLAGESEGKDQKGI Sbjct: 241 YSSAELSENEAYQYAAIRNILYRKGYVTEVLANYEPSLQYFSEWWKQLAGESEGKDQKGI 30- 0 Query: 301 YPTSANFSTDLHSLGQFIQEGYRNLFETVIRVDNPRKNVIIPELAEDLDGLGYLQGKDVD 36- 0 YPTSANFSTDLHSLGQFIQEG RNLFETVIRV+ RKN+++PE AEDLDGL YLQGKDVD Sbjct: 301 YPTSANFSTDLHSLGQFIQEGNRNLFETVIRVEKARKNILVPEAAEDLDGLAYLQGKDVD 36- 0 Query: 361 FVNKKATDGVLLAHTDGGVPNMFVTLPAQDEFTLGYTIYFFELAIAVSGYMNAVNPFDQP 42- 0 FVNKKATDGVLLAHTDGGVPN F+T+P QDEFTLGY IYFFELAI +SGY+N VNPFDQP Sbjct: 361 FVNKKATDGVLLAHTDGGVPNTFLTIPEQDEFTLGYVIYFFELAIGLSGYLNGVNPFDQP 42- 0 Query: 421 GVEAYKRNMFALLGKPGFEALSAELNARL 449 GVEAYK+NMFALLGKPGFE L AELNARL Sbjct: 421 GVEAYKKNMFALLGKPGFEELGAELNARL 449 The protein has homology with the following sequences in the databases: TABLE-US-00849 >GP: CAB90755 GB: AJ400707 hypothetical protein [Streptococcus uberis] Identities = 58/91 (63%), Positives = 69/91 (75%) Query: 6 KRYPITIFLLGLTGLIFIAMQVVYGHLATGAQAIYQVGGMFGLLVKAMPDQLWRLVTPIF 65 K P+T F L +T L+FI MQV YG A Q ++Q GGMFGL+VK+MP QLWRLVTPIF Sbjct: 5 KEKPVTFFFLSVTILLFIVMQVFYGSWAKSPQVVFQFGGMFGLVVKSMPSQLWRLVTPIF 64 Query: 66 IHIGFGHFFVNGLTLYFVGQIVEDLWGSRLF 96 IHIG+ HF +N LTLYFVGQ+ E +WGSR F Sbjct: 65 IHIGWEHFLINSLTLYFVGQLAESIWGSRFF 95 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00850 Identities = 380/401 (94%), Positives = 392/401 (96%) Query: 1 MDLPENYDKEEFSRIQKAAEKIKSDSEVLVVIGIGGSYLGAKAAIDFLNNHFANLQTAEE 60 +DLPENYDK+EF+RI AAERIK+DSEVLVVIGIGGSYLGAKAAIDFLN+HFANLQTA+E Sbjct: 49 LDLPENYDKDEFARILTAAEKIKADSEVLVVIGIGGSYLGAKAAIDFLNHHFANLQTAKE 108- Query: 61 RKAPQILYAGNSISSTYLADLVEYVQDKEFSVNVISKSGTTTEPAIAFRVFKELLVKKYG 120- RKAPQILYAGNSISSTYLADLVEYVQDKEFSVNVISKSGTTTEPAIAFRVFKELLVKKYG Sbjct: 109 RKAPQILYAGNSISSTYLADLVEYVQDKEFSVNVISKSGTTTEPAIAFRVFKELLVKKYG 16- 8 Query: 121 QEEANKRIYATTDKVKGAVKVEADANNWETFVVPDNVGGRFSVLTAVGLLPIAASGADIT 18- 0 QEEANKRIYATTDKVKGAVKVEADANNWETFVVPDNVGGRFSVLTAVGLLPIAASGADIT Sbjct: 169 QEEANKRIYATTDKVKGAVKVEADANNWETFVVPDNVGGRFSVLTAVGLLPIAASGADIT 22- 8 Query: 181 ALMEGANAARKDLSSDKISENIAYQYAAVRNVLYRKGYITEILANYEPSLQYFGEWWKQL 24- 0 ALMEGANAARKDLSSDKISENIAYQYAAVRNVLYRKGYITEILANYEPSLQYFGEWWKQL Sbjct: 229 ALMEGANAARKDLSSDKISENIAYQYAAVRNVLYRKGYITEILANYEPSLQYFGEWWKQL 28- 8 Query: 241 AGESEGKDQKGIYPTSANFSTDLHSLGQFIQEGYRNLFETVVRVEKPRKNVTIPELTEDL 30- 0 AGESEGKDQKGIYPTSANFSTDLHSLGQFIQEGYRNLFETV+RV+ PRKNV IPEL EDL Sbjct: 289 AGESEGKDQKGIYPTSANFSTDLHSLGQFIQEGYRNLFETVIRVDNPRKNVIIPELAEDL 34- 8 Query: 301 DGLGYLQGKDVDFVNKKATDGVLLAHTDGGVPNMFVTLPTQDAYTLGYTIYFFELAIGLS 36- 0 DGLGYLQGKDVDFVNKKATDGVLLAHTDGGVPNMFVTLP QD +TLGYTIYFFELAI +S Sbjct: 349 DGLGYLQGKDVDFVNKKATDGVLLAHTDGGVPNMFVTLPAQDEFTLGYTIYFFELAIAVS 40- 8 Query: 361 GYLNSVNPFDQPGVEAYKRNMFALLGKPGFEELSAELNARL 401 GY+N+VNPFDQPGVEAYKRNMFALLGKPGFE LSAELNARL Sbjct: 409 GYMNAVNPFDQPGVEAYKRNMFALLGKPGFEALSAELNARL 449 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 273 A DNA sequence (GBSx0298) was identified in S. agalactiae <SEQ ID 873> which encodes the amino acid sequence <SEQ ID 874>. Analysis of this protein sequence reveals the following:

TABLE-US-00851 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.66 Transmembrane 654-670 (653-671) INTEGRAL Likelihood = -1.65 Transmembrane 113-129 (113-129) ----- Final Results ----- bacterial membrane --- Certainty = 0.2062 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9463> which encodes amino acid sequence <SEQ ID 9464> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00852 >GP: AAA81906 GB: U04863 alcohol dehydrogenase 2 [Entamoeba histolytica] Identities = 536/864 (62%), Positives = 663/864 (76%), Gaps = 3/864 (0%) Query: 20 ETTDVALAIDTLVQNGLKALDEMR--QLNQEQVDYIVAKASVAALDAHGELALHAVEETG 77 - +T V I+ LV+ AL E + QE++DYIV KASVAALD H LA AVEETG Sbjct: 5 QTMTVDEHINQLVRKAQVALKEYLKPEYTQEKIDYIVKKASVAALDQHCALAAAAVEETG 64 Query: 78 RGVFEDKATKNLFACEHVVNNMRHTKTVGVIEEDDVTGLTLIAEPVGVVCGITPTTNPTS 137- RG+FEDKATKN+FACEHV + MRH KTVG+I D + G+T IAEPVGVVCG+TP TNPTS Sbjct: 65 RGIFEDKATKNIFACEHVTHEMRHAKTVGIINVDPLYGITEIAEPVGVVCGVTPVTNPTS 124- Query: 138 TAIFKSLISLKTRNPIIFAFHPSAQESSAHAARIVRDAAIAAGAPENCVQWIEQPSIDAT 19- 7 TAIFKSLIS+KTRNPI+F+FHPSA + S AA+IVRDAAIAAGAPENC+QWIE I+A+ Sbjct: 125 TAIFKSLISIKTRNPIVFSFHPSALKCSIMAAKIVRDAAIAAGAPENCIQWIEFGGIEAS 18- 4 Query: 198 NALMNHDGIATILATGGNAMVKAAYSCGKPALGVGAGNVPAYVEKSANIRQAAHDIVMSK 25- 7 N LMNH G+ATILATGGNAMVKAAYS GKPALGVGAGNVP Y+EK+ NI+QAA+D+VMSK Sbjct: 185 NKLMNHPGVATILATGGNAMVKAAYSSGKPALGVGAGNVPTYIEKTCNIKQAANDVVMSK 24- 4 Query: 258 SFDNGMVCASEQAVIIDKEIYKEFVEEFKSYHTYFVNKKEKALLEEFCFGAKANSKNCAG 31- 7 SFDNGM+CASEQA IIDKEIY + VEE K+ YF+N++EKA LE+F FG A S + Sbjct: 245 SFDNGMICASEQAAIIDKEIYDQVVEEMKTLGAYFINEEEKAKLEKFMFGVNAYSADVNN 30- 4 Query: 318 AKLNPNIVGKSAVWIAEQAGFTVPEGTNILAAECTEVSEKEPLTREKLSPVIAVLKAEST 37- 7 A+LNP G S W AEQ G VPE NI+ A C EV EPLTREKLSPV+A+LKAE+T Sbjct: 305 ARLNPKCPGMSPQWFAEQVGIKVPEDCNIICAVCKEVGPNEPLTREKLSPVLAILKAENT 36- 4 Query: 378 EDGVEKARQMVEFNGLGHSAAIHTKDADLAREFGTRIRAIRVIWNSPSTFGGIGDVYNAF 43- 7 +DG++KA MVEFNG GHSAAIH+ D + ++ ++A R++ N+PS+ GGIG +YN Sbjct: 365 QDGIDKAEAMVEFNGRGHSAAIHSNDKAVVEKYALTMKACRILHNTPSSQGGIGSIYNYI 42- 4 Query: 438 LPSLTLGCGSYGRNSVGDNVSAINLLNIKKVGRRRNNMQWFKVPSKTYFERDSIQYLQKC 49- 7 PS TLGCGSYG NSV NV+ NLLNIK++ RRNN+QWF+VP K +FE SI+YL + Sbjct: 425 WPSFTLGCGSYGGNSVSANVTYHNLLNIKRLADRRNNLQWFRVPPKIFFEPHSIRYLAEL 48- 4 Query: 498 RDVERVMIVTDHAMVELGFLDRIIEQLDLRRNKVVYQIFAEVEPDPDITTVMKGTDLMRT 55- 7 +++ ++ IV+D M +LG++DR+++ L R N+V +IF +VEPDP I TV KG +M T Sbjct: 485 KELSKIFIVSDRMMYKLGYVDRVMDVLKRRSNEVEIEIFIDVEPDPSIQTVQKGLAVMNT 54- 4 Query: 558 FKPDTIIALGGGSPMDAAKVMWLFYEQPEVDFHDLVQKFMDIRKRAFKFPELGKKTKFVA 61- 7 F PD IIA+GGGS MDAAK+MWL YE PE DF + QKF+D+RKRAFKFP +GKK + + Sbjct: 545 FGPDNIIAIGGGSAMDAAKIMWLLYEHPEADFFAMKQKFIDLRKRAFKFPTMGKKARLIC 60- 4 Query: 618 IPTTSGTGSEVTPFAVISDKANNRKYPIADYSLTPTVAIVDPALVMTVPGFIAADTGMDV 67- 7 IPTTSGTGSEVTPFAVISD +KYP+ADYSLTP+VAIVDP M++P ADTG+DV Sbjct: 605 IPTTSGTGSEVTPFAVISDHETGKKYPLADYSLTPSVAIVDPMFTMSLPKRAIADTGLDV 66- 4 Query: 678 LTHATEAYVSQMANDYTDGLALQAIKIVFDYLERSVKDADFEAREKMHNASTMAGMAFAN 73- 7 L HATEAYVS MAN+YTDGLA +A+K+VF+ L +S + D EAREKMHNA+T+AGMAFA+ Sbjct: 665 LVHATEAYVSVMANEYTDGLAREAVKLVFENLLKSY-NGDLEAREKMHNAATIAGMAFAS 72- 3 Query: 738 AFLGISHSMAHKIGAQFHTVHGRTNAILLPYVIRYNGTRPAKTATWPKYNYYRADEKYQD 79- 7 AFLG+ HSMAHK+GA FH HGR A+LLP+VIRYNG +P K A WPKYN+Y+AD++Y + Sbjct: 724 AFLGMDHSMAHKVGAAFHLPHGRCVAVLLPHVIRYNGQKPRKLAMWPKYNFYKADQRYME 78- 3 Query: 798 IAKLLGLPAATPEEAVESYAKAVYDLGTRLGIKMNFRDQGIDEKEWKEKSRELAFLAYED 85- 7 +A+++GL TP E VE++AKA +L F+ IDE W K E+A LA+ED Sbjct: 784 LAQMVGLKCNTPAEGVEAFAKACEELMKATETITGFKKANIDEAAWMSKVPEMALLAFED 84- 3 Query: 858 QCSPANPRLPMVDHMQEIIEDAYY 881 QCSPANPR+PMV M++I++ AYY Sbjct: 844 QCSPANPRVPMVKDMEKILKAAYY 867 A related DNA sequence was identified in S. pyogenes <SEQ ID 875> which encodes the amino acid sequence <SEQ ID 876>. Analysis of this protein sequence reveals the following: TABLE-US-00853 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.66 Transmembrane 643-659 (642-660) INTEGRAL Likelihood = -1.81 Transmembrane 102-118 (102-118) ----- Final Results ----- bacterial membrane --- Certainty = 0.2466(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00854 >GP: AAA81906 GB: U04863 alcohol dehydrogenase 2 [Entamoeba histolytica] Identities = 535/870 (61%), Positives = 669/870 (76%), Gaps = 3/870 (0%) Query: 6 NTVETTSVSVTIDALVQKGLAALEEMRKLD--QEQVDYIVAKASVAALDAHGELAKHAYE 63 +T +T +V I+ LV+K AL+E K + QE++DYIV KASVAALD H LA A E Sbjct: 2 STQQTMTVDEHINQLVRKAQVALKEYLKPEYTQEKIDYIVKKASVAALDQHCALAAAAVE 61 Query: 64 ETGRGVFEDKATKHLFACEHVVNNMRHQKTVGIIEEDDVTGLTLIAEPVGVICGITPTTN 123- ETGRG+FEDKATK++FACEHV + MRH KTVGII D + G+T IAEPVGV+CG+TP TN Sbjct: 62 ETGRGIFEDKATKNIFACEHVTHEMRHAKTVGIINVDPLYGITEIAEPVGVVCGVTPVTN 121- Query: 124 PTSTAIFKSLISLKTRNPIIFAFHPSAQESSAHAARIVRDAAIAAGAPENCVQWVETPSL 18- 3 PTSTAIFKSLIS+KTRNPI+F+FHPSA + S AA+IVRDAAIAAGAPENC+QW+E + Sbjct: 122 PTSTAIFKSLISIKTRNPIVFSFHPSALKCSIMAAKIVRDAAIAAGAPENCIQWIEFGGI 18- 1 Query: 184 EATNALMNHDGIATILATGGNAMVKAAYSCGKPALGVGAGNVPAYVEKSANIRQAAHDIV 24- 3 EA+N LMNH G+ATILATGGNAMVKAAYS GKPALGVGAGNVP Y+EK+ NI+QAA+D+V Sbjct: 182 EASNKLMNHPGVATILATGGNAMVKAAYSSGKPALGVGAGNVPTYIEKTCNIKQAANDVV 24- 1 Query: 244 MSKSFDNGMVCASEQAVIIDKEIYDDFVAEFKSYHTYFVNKKEKALLEEFCFGAKANSKN 30- 3 MSKSFDNGM+CASEQA IIDKEIYD V E K+ YF+N++EKA LE+F FG A S + Sbjct: 242 MSKSFDNGMICASEQAAIIDKEIYDQVVEEMKTLGAYFINEEEKAKLEKFMFGVNAYSAD 30- 1 Query: 304 CAGAKLNPNIVGKPATWIAEQAGFTVPEGTNILAAECKEVSENEPLTREKLSPVIAVLKS 36- 3 A+LNP G W AEQ G VPE NI+ A CKEV NEPLTREKLSPV+A+LK+ Sbjct: 302 VNNARLNPKCPGMSPQWFAEQVGIKVPEDCNIICAVCKEVGPNEPLTREKLSPVLAILKA 36- 1 Query: 364 ESREDGVEKARQMVEFNGLGHSAAIHTADAELAKEFGTRIRAIRVIWNSPSTFGGIGDVY 42- 3 E+ +DG++KA MVEFNG GHSAAIH+ D + +++ ++A R++ N+PS+ GGIG +Y Sbjct: 362 ENTQDGIDKAEAMVEFNGRGHSAAIHSNDKAVVEKYALTMKACRILHNTPSSQGGIGSIY 42- 1 Query: 424 NAFLPSLTLGCGSYGRNAVGDNVSAINLLNIKKVGRRRNNMQWFKVPSKTYFERDSIQYL 48- 3 N PS TLGCGSYG N+V NV+ NLLNIK++ RRNN+QWF+VP K +FE SI+YL Sbjct: 422 NYIWPSFTLGCGSYGGNSVSANVTYHNLLNIKRLADRRNNLQWFRVPPKIFFEPHSIRYL 48- 1 Query: 484 QKCRDVERVMIVTDHAMVELGFLDRIIEQLDLRRNKVVYQIFAEVEPDPDITTVMKGTEL 54- 3 + +++ ++ IV+D M +LG++DR+++ L R N+V +IF +VEPDP I TV KG + Sbjct: 482 AELKELSKIFIVSDRMMYKLGYVDRVMDVLKRRSNEVEIEIFIDVEPDPSIQTVQKGLAV 54- 1 Query: 544 MRTFKPDTIIALGGGSPMDAAKVMWLFYEQPEVDFHDLVQKFMDIRKRAFKFPELGKKTK 60- 3 M TF PD IIA+GGGS MDAAK+MWL YE PE DF + QKF+D+RKRAFKFP +GKK + Sbjct: 542 MNTFGPDNIIAIGGGSAMDAAKIMWLLYEHPEADFFAMKQKFIDLRKRAFKFPTMGKKAR 60- 1 Query: 604 FVAIPTTSGTGSEVTPFAVISDKANNRKYPIADYSLTPTVAIVDPALVLTVPGFIAADTG 66- 3 + IPTTSGTGSEVTPFAVISD +KYP+ADYSLTP+VAIVDP +++P ADTG Sbjct: 602 LICIPTTSGTGSEVTPFAVISDHETGKKYPLADYSLTPSVAIVDPMFTMSLPKRAIADTG 66- 1 Query: 664 MDVLTHATEAYVSQMANDFTDGLALQAIKIVFDNLEKSVKTADFEAREKMHNASTMAGMA 72- 3 +DVL HATEAYVS MAN++TDGLA +A+K+VF+NL KS D EAREKMHNA+T+AGMA Sbjct: 662 LDVLVHATEAYVSVMANEYTDGLAREAVKLVFENLLKSY-NGDLEAREKMHNAATIAGMA 72- 0 Query: 724 FANAFLGISHSMAHKIGAQFHTVHGRTNAILLPYVIRYNGTRPAKTATWPKYNYYRADEK 78- 3 FA+AFLG+ HSMAHK+GA FH HGR A+LLP+VIRYNG +P K A WPKYN+Y+AD++ Sbjct: 721 FASAFLGMDHSMAHKVGAAFHLPHGRCVAVLLPHVIRYNGQKPRKLAMWPKYNFYKADQR 78- 0 Query: 784 YQDIAKLLGLPASTPEEAVESYAKAVYDLGCRVGIQMNFKAQGIDENEWKEHSRELAYLA 84- 3 Y ++A+++GL +TP E VE++AKA +L FK IDE W E+A LA Sbjct: 781 YMELAQMVGLKCNTPAEGVEAFAKACEELMKATETITGFKKANIDEAAWMSKVPEMALLA 84- 0 Query: 844 YEDQCSPANPRLPMVDHMQEIIEDAYYGYA 873 +EDQCSPANPR+PMV M++I++ AYY A Sbjct: 841 FEDQCSPANPRVPMVKDMEKILKAAYYPIA 870 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00855 Identities = 827/880 (93%), Positives = 852/880 (95%) Query: 12 MTEKTKAVETTDVALAIDTLVQNGLKALDEMRQLNQEQVDYIVAKASVAALDAHGELALH 71- MTE VETT V++ ID LVQ GL AL+EMR+L+QEQVDYIVAKASVAALDAHGELA H Sbjct: 1 MTEGHNTVETTSVSVTIDALVQKGLAALEEMRKLDQEQVDYIVAKASVAALDAHGELAKH 60- Query: 72 AVEETGRGVFEDKATKNLFACEHVVNNMRHTKTVGVIEEDDVTGLTLIAEPVGVVCGITP 13- 1 A EETGRGVFEDKATK+LFACEHVVNNMRH KTVG+IEEDDVTGLTLIAEPVGV+CGITP Sbjct: 61 AYEETGRGVFEDKATKHLFACEHVVNNMRHQKTVGIIEEDDVTGLTLIAEPVGVICGITP 12- 0 Query: 132 TTNPTSTAIFKSLISLKTRNPIIFAFHPSAQESSAHAARIVRDAAIAAGAPENCVQWIEQ 19- 1 TTNPTSTAIFKSLISLKTRNPIIFAFHPSAQESSAHAARIVRDAAIAAGAPENCVQW+E Sbjct: 121 TTNPTSTAIFKSLISLKTRNPIIFAFHPSAQESSAHAARIVRDAAIAAGAPENCVQWVET 18- 0 Query: 192 PSIDATNALMNHDGIATILATGGNAMVKAAYSCGKPALGVGAGNVPAYVEKSANIRQAAH 25- 1 PS++ATNALMNHDGIATILATGGNAMVKAAYSCGKPALGVGAGNVPAYVEKSANIRQAAH Sbjct: 181 PSLEATNALMNHDGIATILATGGNAMVKAAYSCGKPALGVGAGNVPAYVEKSANIRQAAH 24- 0 Query: 252 DIVMSKSFDNGMVCASEQAVIIDKEIYKEFVEEFKSYHTYFVNKKEKALLEEFCFGAKAN 31- 1 DIVMSKSFDNGMVCASEQAVIIDKEIY +FV EFKSYHTYFVNKKEKALLEEFCFGAKAN Sbjct: 241 DIVMSKSFDNGMVCASEQAVIIDKEIYDDFVAEFKSYHTYFVNKKEKALLEEFCFGAKAN 30- 0 Query: 312 SKNCAGAKLNPNIVGKSAVWIAEQAGFTVPEGTNILAAECTEVSEKEPLTREKLSPVIAV 37- 1 SKNCAGAKLNPNIVGK A WIAEQAGFTVPEGTNILAAEC EVSE EPLTREKLSPVIAV Sbjct: 301 SKNCAGAKLNPNIVGKPATWIAEQAGFTVPEGTNILAAECKEVSENEPLTREKLSPVIAV 36- 0 Query: 372 LKAESTEDGVEKARQMVEFNGLGHSAAIHTKDADLAREFGTRIRAIRVIWNSPSTFGGIG 43- 1 LK+ES EDGVEKARQMVEFNGLGHSAAIHT DA+LA+EFGTRIRAIRVIWNSPSTFGGIG Sbjct: 361 LKSESREDGVEKARQMVEFNGLGHSAAIHTADAELAKEFGTRIRAIRVIWNSPSTFGGIG 42- 0 Query: 432 DVYNAFLPSLTLGCGSYGRNSVGDNVSAINLLNIKKVGRRRNNMQWFKVPSKTYFERDSI 49- 1 DVYNAFLPSLTLGCGSYGRN+VGDNVSAINLLNIKKVGRRRNNNQWFKVPSKTYFERDSI Sbjct: 421 DVYNAFLPSLTLGCGSYGRNAVGDNVSAINLLNIKKVGRRRNNMQWFKVPSKTYFERDSI 48- 0 Query: 492 QYLQKCRDVERVMIVTDHAMVELGFLDRIIEQLDLRRNKVVYQIFAEVEPDPDITTVMKG 55- 1 QYLQKCRDVERVMIVTDHAMVELGFLDRIIEQLDLRRNKVVYQIFAEVEPDPDITTVMKG Sbjct: 481 QYLQKCRDVERVMIVTDHAMVELGFLDRIIEQLDLRRNKVVYQIFAEVEPDPDITTVMKG 54- 0 Query: 552 TDLMRTFKPDTIIALGGGSPMDAAKVMWLFYEQPEVDFHDLVQKFMDIRKRAFKFPELGK 61- 1 T+LMRTFKPDTIIALGGGSPMDAAKVMWLFYEQPEVDEHDLVQKFNDIRKRAFKFPELGK Sbjct: 541 TELMRTFKPDTIIALGGGSPMDAAKVMWLFYEQPEVDEHDLVQKFNDIRKRAFKFPELGK 60- 0 Query: 612 KTKFVAIPTTSGTGSEVTPFAVISDKANNRKYPIADYSLTPTVAIVDPALVMTVPGFIAA 67- 1 KTKFVAIPTTSGTGSEVTPFAVISDKANNRKYPIADYSLTPTVAIVDPALV+TVPGFIAA Sbjct: 601 KTKFVAIPTTSGTGSEVTPFAVISDKANNRKYPIADYSLTPTVAIVDPALVLTVPGFIAA 66- 0 Query: 672 DTGMDVLTHATEAYVSQMANDYTDGLALQAIKIVFDYLERSVKDADFEAREKMHNASTMA 73- 1 DTGMDVLTHATEAYVSQMAND+TDGLALQAIKIVFD LE+SVK ADFEAREKMHNASTMA Sbjct: 661 DTGMDVLTHATEAYVSQMANDFTDGLALQAIKIVFDNLEKSVKTADFEAREKMHNASTMA 72- 0 Query: 732 GMAFANAFLGISHSMAHKIGAQFHTVHGRTNAILLPYVIRYNGTRPAKTATWPKYNYYRA 79- 1 GMAFANAFLGISHSMAHKIGAQFHTVHGRTNAILLPYVIRYNGTRPAKTATWPKYNYYRA Sbjct: 721 GMAFANAFLGISHSMAHKIGAQFHTVHGRTNAILLPYVIRYNGTRPAKTATWPKYNYYRA 78- 0 Query: 792 DEKYQDIAKLLGLPAATPEEAVESYAKAVYDLGTRLGIKMNFRDQGIDEKEWKEKSRELA 85- 1 DEKYQDIAKLLGLPA+TPEEAVESYAKAVYDLG R+GI+MNF+ QGIDE EWKE SRELA Sbjct: 781 DEKYQDIAKLLGLPASTPEEAVESYAKAVYDLGCRVGIQMNFKAQGIDENEWKEHSRELA 84- 0 Query: 852 FLAYEDQCSPANPRLPMVDHMQEIIEDAYYGYEERPGRRK 891 +LAYEDQCSPANPRLPMVDHMQEIIEDAYYGY ERPGRRK Sbjct: 841 YLAYEDQCSPANPRLPMVDHMQEIIEDAYYGYAERPGRRK 880 A related GBS gene <SEQ ID 8533> and protein <SEQ ID 8534> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00856 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -4.68 GvH: Signal Score (-7.5): -2.48 Possible site: 21 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -2.66 threshold: 0.0 INTEGRAL Likelihood = -2.66 Transmembrane 100-116 (99-117) PERIPHERAL Likelihood = 3.61 173 modified ALOM score: 1.03 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2062 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 8534 (GBS432) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 173 (lane 5; MW 66 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 77 (lane 7; MW 41 kDa). GBS432-GST was purified as shown in FIG. 223, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 274 A DNA sequence (GBSx0299) was identified in S. agalactiae <SEQ ID 877> which encodes the amino acid sequence <SEQ ID 878>. Analysis of this protein sequence reveals the following: TABLE-US-00857 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3444 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 880. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 275 A DNA sequence (GBSx0300) was identified in S. agalactiae <SEQ ID 881> which encodes the amino acid sequence <SEQ ID 882>. Analysis of this protein sequence reveals the following: TABLE-US-00858 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.39 Transmembrane 74-90 (69-94) INTEGRAL Likelihood = -5.31 Transmembrane 168-184 (163-186) INTEGRAL Likelihood = -4.83 Transmembrane 34-50 (29-52) INTEGRAL Likelihood = -0.75 Transmembrane 202-218 (202-219) ----- Final Results ----- bacterial membrane --- Certainty = 0.4354 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00859 >GP:CAA17305 GB:AL021926 hypothetical protein Rv0111 [Mycobacterium tuberculosis] Identities = 70/218 (32%), Positives = 104/218 (47%), Gaps = 12/218 (5%) Query: 9 VRITGLLLVLLYHFFKNSFPGGFVGVDIFFTFSGFLITALLIDEFSKTKKIDFVSFCRRR 68- +R + LVL H GGF+GVD FF SGFLIT+LL+DE +T +ID F RR Sbjct: 39 LRAIAVALVLASHGGIPGMGGGFIGVDAFFVLSGFLITSLLLDELGRTGRIDLSGFWIRR 98- Query: 69 FYRIFPPLVLMVLVTIPFVFLVKSDFRASIGSQIMTALGFTSNFYEILTGGNYESQFI-P 12- 7 R+ P LVLMVL L + S + A +T+N+ + +Y +Q P Sbjct: 99 ARRLLPALVLMVLTVSAARALFPDQALTGLRSDAIAAFLWTANWRFVAQNTDYFTQGAPP 15- 8 Query: 128 HLFVHTWSLSIEVHFYVLWGL----TVWLLSKRSKDQKQLRGTLFLISMGIFGVSFLTMF 18- 3 HTWSL +E +YV+W L LL+ R++ ++ R T+ + F ++ L Sbjct: 159 SPLQHTWSLGVEEQYYVVWPLLLIGATLLLAARAR-RRCRRATVGGVRFAAFLIASLGTM 21- 7 Query: 184 VRAFFVDNFST------IYFSTLSHIFPFFLGAMVATI 215 A F++ IYF T + +G+ A + Sbjct: 218 ASATAAVAFTSAATRDRIYFGTDTRAQALLIGSAAAAL 255 A related DNA sequence was identified in S. pyogenes <SEQ ID 879> which encodes the amino acid sequence <SEQ ID 880>. Analysis of this protein sequence reveals the following: TABLE-US-00860 Possible site: 46 >>>Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.83 Transmembrane 325-341 (313-346) INTEGRAL Likelihood = -9.29 Transmembrane 237-253 (234-258) INTEGRAL Likelihood = -7.91 Transmembrane 166-182 (162-188) INTEGRAL Likelihood = -6.10 Transmembrane 72-88 (68-92) INTEGRAL Likelihood = -4.09 Transmembrane 264-280 (260-281) INTEGRAL Likelihood = -2.87 Transmembrane 371-387 (370-390) INTEGRAL Likelihood = -2.66 Transmembrane 34-50 (32-50) INTEGRAL Likelihood = -1.91 Transmembrane 3-19 (3-19) INTEGRAL Likelihood = -0.85 Transmembrane 136-152 (136-154) ----- Final Results ----- bacterial membrane --- Certainty = 0.5331 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00861 Identities = 167/226 (73%), Positives = 195/226 (85%) Query: 1 MRIKWFSLVRITGLLLVLLYHFFKNSFPGGFVGVDIFFTFSGFLITALLIDEFSKTKKID 60- MRIKWFS VR+TGLLLVLLYHFFKN FPGGF+GVDIFFTFSG+LITALLIDE++K +ID Sbjct: 1 MRIKWFSFVRVTGLLLVLLYHFFKNVFPGGFIGVDIFFTFSGYLITALLIDEYTKKESID 60- Query: 61 FVSFCRRRFYRIFPPLVLMVLVTIPFVFLVKSDFRASIGSQIMTALGFTSNFYEILTGGN 12- 0 + F +RRFYRI PPLVLM+L+TIPF FL+K DF A+IGSQI LGFT+N YEILTG + Sbjct: 61 IIGFLKRRFYRIVPPLVLMILLTIPFTFLIKKDFIANIGSQITAVLGFTTNIYEILTGSS 12- 0 Query: 121 YESQFIPHLFVHTWSLSIEVHFYVLWGLTVWLLSKRSKDQKQLRGTLFLISMGIFGVSFL 18- 0 YESQFIPHLFVHTWSL+IEVHFY+ WG+ VWLL++R + QKQLRG LFLIS+GIF +SFL Sbjct: 121 YESQFIPHLFVHTWSLAIEVHFYLFWGVFVWLLARRKETQKQLRGLLFLISLGIFAISFL 18- 0 Query: 181 TMFVRAFFVDNFSTIYFSTLSHIFPFFLGAMVATISGIREITGRFK 226 +MF+R+F NFS IYFS+LSH FPFFLGAM ATI+GI E T RF+ Sbjct: 181 SMFIRSFMTSNFSLIYFSSLSHSFPFFLGAMFATITGINETTVRFQ 226 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 276 A DNA sequence (GBSx0302) was identified in S. agalactiae <SEQ ID 883> which encodes the amino acid sequence <SEQ ID 884>. Analysis of this protein sequence reveals the following:

TABLE-US-00862 Possible site: 38 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00863 !GB:AE004818 hypothetical protein [Pseudomonas aerug . . . !GB:AE004818 hypothetical protein [Pseudomonas aerug . . . !GB:AE004818 hypothetical protein [Pseudomonas aerug . . . !GB:AE004818 hypothetical protein [Pseudomonas aerug . . . !GB:AE004818 hypothetical protein [Pseudomonas aerug . . . >GP:AAG07403 GB:AE004818 hypothetical protein [Pseudomonas aeruginosa] Identities = 33/80 (41%), Positives = 50/80 (62%) Query: 45 KYVGSIVNHHMTGKGKLTYENGDYYKGDFVNGVFEGKGTFVSVHGWSYTGDFKKGQPDGQ 10- 4 +Y G +V+ + G+G+L Y+NG +Y G F +G+ G GT+ G Y+G F G DGQ Sbjct: 39 RYRGELVDGRLEGQGRLDYDNGAWYAGRFEHGLLHGHGTWQGADGSRYSGGFAAGLFDGQ 98- Query: 105 GRLNAKNKKVYKGTFKQGIY 124 GRL + VY+G F+QG+ Sbjct: 99 GRLAMADGSVYQGGFRQGLF 118 Identities = 31/91 (34%), Positives = 46/91 (50%), Gaps = 2/91 (2%) Query: 34 QGVFSYDGGKIKYVGSIVNHHMTGKGKLTYENGDYYKGDFVNGVFEGKGTFVSVHGWSYT 93- QG YD G Y G + + G G +G Y G F G+F+G+G G Y Sbjct: 52 QGRLDYDNGAW-YAGRFEHGLLHGHGTWQGADGSRYSGGFAAGLFDGQGRLAMADGSVYQ 11- 0 Query: 94 GDFKKGQPDGQGRLNAKNKKVYKGTFKQGIY 124 G F++G DG+G L + + Y+G F++G+Y Sbjct: 111 GGFRQGLFDGEGSLEQQGTR-YRGGFRKGLY 140 Identities = 31/91 (34%), Positives = 42/91 (46%), Gaps = 1/91 (1%) Query: 32 SSQGVFSYDGGKIKYVGSIVNHHMTGKGKLTYENGDYYKGDFVNGVFEGKGTFVSVHGWS 91- S QG G +Y GS + G+G + G+ Y G F +G GKG + G Sbjct: 141 SGQGTLDGSDGS-RYQGSFRQGRLEGEGSFSDSQGNQYAGTFRDGQLNGKGRWSGPDGDR 19- 9 Query: 92 YTGDFKKGQPDGQGRLNAKNKKVYKGTFKQG 122 Y G FK Q GQGR + + V+ G F +G Sbjct: 200 YVGQFKDNQFHGQGRYESASGDVWIGRFSEG 230 Identities = 31/91 (34%), Positives = 45/91 (49%), Gaps = 4/91 (4%) Query: 34 QGVFSYDGGK----IKYVGSIVNHHMTGKGKLTYENGDYYKGDFVNGVFEGKGTFVSVHG 89- QG+F +G +Y G +G+G L +G Y+G F G EG+G+F G Sbjct: 115 QGLFDGEGSLEQQGTRYRGGFRKGLYSGQGTLDGSDGSRYQGSFRQGRLEGEGSFSDSQG 17- 4 Query: 90 WSYTGDFKKGQPDGQGRLNAKNKKVYKGTFK 120 Y G F +GQ +G+GR + + Y G FK Sbjct: 175 NQYAGTFRDGQLNGKGRWSGPDGDRYVGQFK 205 Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 1/87 (1%) Query: 34 QGVFSYDGGKIKYVGSIVNHHMTGKGKLTYENGDYYKGDFVNGVFEGKGTFVSVHGWSYT 93- +G FS G +Y G+ + + GKG+ + +GD Y G F + F G+G + S G + Sbjct: 166 EGSFSDSQGN-QYAGTFRDGQLNGKGRWSGPDGDRYVGQFKDNQFHGQGRYESASGDVWI 22- 4 Query: 94 GDFKKGQPDGQGRLNAKNKKVYKGTFK 120 G F +G +G G L + Y+G F+ Sbjct: 225 GRFSEGALNGPGELLGADGSRYRGGFQ 251 Identities = 28/89 (31%), Positives = 43/89 (47%), Gaps = 2/89 (2%) Query: 34 QGVFSYDGGKIKYVGSIVNHHMTGKGKLTYENGDYYKGDFVNGVFEGKGTFVSVHGWSYT 93- QG + G + Y G G+G L + G Y+G F G++ G+GT G Y Sbjct: 98 QGRLAMADGSV-YQGGFRQGLFDGEGSLE-QQGTRYRGGFRKGLYSGQGTLDGSDGSRYQ 15- 5 Query: 94 GDFKKGQPDGQGRLNAKNKKVYKGTFKQG 122 G F++G+ +G+G + Y GTF+ G Sbjct: 156 GSFRQGRLEGEGSFSDSQGNQYAGTFRDG 184 Identities = 25/80 (31%), Positives = 37/80 (46%) Query: 45 KYVGSIVNHHMTGKGKLTYENGDYYKGDFVNGVFEGKGTFVSVHGWSYTGDFKKGQPDGQ 10- 4 +YVG ++ G+G+ +GD + G F G G G + G Y G F+ + GQ Sbjct: 199 RYVGQFKDNQFHGQGRYESASGDVWIGRFSEGALNGPGELLGADGSRYRGGFQFWRFHGQ 25- 8 Query: 105 GRLNAKNKKVYKGTFKQGIY 124 G L + Y+G F G Y Sbjct: 259 GLLEQLDGTRYEGGFAAGAY 278 A related DNA sequence was identified in S. pyogenes <SEQ ID 885> which encodes the amino acid sequence <SEQ ID 886>. Analysis of this protein sequence reveals the following: TABLE-US-00864 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.16 Transmembrane 20-36 (12-41) ----- Final Results ----- bacterial membrane --- Certainty = 0.6265 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00865 >GP:BAA16606 GB:D90899 hypothetical protein [Synechocystis sp.] Identities = 37/89 (41%), Positives = 49/89 (54%), Gaps = 6/89 (6%) Query: 48 KGRMHYT------GYVINHKMNGEGKLVYPNGDIYEGTFKDGLFEGKGTFTAKTGWLYNG 10- 1 KG YT G V+ ++NG GK Y NGD YEGT K+G +G+G F G Y G Sbjct: 141 KGTFIYTNGDRCSGTVVQGELNGSGKCEYNNGDQYEGTLKNGQPDGEGIFRFAAGGEYEG 20- 0 Query: 102 EFHKGQANGKGVLKAKNNKVYKGIFKQGI 130 EF G+ +G+G N ++G FKQG+ Sbjct: 201 EFQSGEFSGQGTRIFANGNRFQGQFKQGL 229 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00866 Identities = 68/126 (53%), Positives = 93/126 (72%) Query: 1 MKNFKITRTHLEILSLIIIVVFGLSVFTLTTSSQGVFSYDGGKIKYVGSIVNHHMTGKGK 60- +K + ITR LEI+S+I+I+V +SVF++ S++ +YD G++ Y G ++NH M G+GK Sbjct: 8 VKKWSITRAKLEIVSVIVILVCAISVFSVRISNKTSLTYDKGRMHYTGYVINHKMNGEGK 67- Query: 61 LTYENGDYYKGDFVNGVFEGKGTFVSVHGWSYTGDFKKGQPDGQGRLNAKNKKVYKGTFK 12- 0 L Y NGD Y+G F +G+FEGKGTF + GW Y G+F KGQ +G+G L AKN KVYKG FK Sbjct: 68 LVYPNGDIYEGTFKDGLFEGKGTFTAKTGWLYNGEFHKGQANGKGVLKAKNNKVYKGIFK 12- 7 Query: 121 QGIYQK 126 QGI+QK Sbjct: 128 QGIFQK 133 SEQ ID 884 (GBS139) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 19 (lane 3; MW 13 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 22 (lane 2; MW 38.2 kDa), in FIG. 24 (lane 7; MW 38 kDa) and in FIG. 33 (lane 7; MW 38.2 kDa). The GBS139-GST fusion product was purified (FIG. 200, lane 2) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 287), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 277 A DNA sequence (GBSx0303) was identified in S. agalactiae <SEQ ID 887> which encodes the amino acid sequence <SEQ ID 888>. This protein is predicted to be holliday junction dna helicase ruvb (ruvB). Analysis of this protein sequence reveals the following: TABLE-US-00867 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4386 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00868 >GP:CAB75331 GB:Y15896 RuvB protein [Bacillus subtilis] Identities = 196/322 (60%), Positives = 254/322 (78%) Query: 3 RFLDSDAMGDEELVERTLRPQYLREYIGQDKVKDQLKIFIEAAKLRDESLDHVLLFGPPG 62- R + S+A E ++E++LRPQ L +YIGQ KVK+ L++FI+AAK+R E+LDHVLL+GPPG Sbjct: 4 RLVSSEADNHESVIEQSLRPQNLAQYIGQHKVKENLRVFIDAAKMRQETLDHVLLYGPPG 63- Query: 63 LGKTTMAFVIANELGVNLKQTSGPAIEKSGDLVAILNDLEPGDVLFIDEIHRMPMAVEEV 12- 2 LGKTT+A ++ANE+GV L+ TSGPAIE+ GDL AlL LEPGDVLFIDEIHR+ ++EEV Sbjct: 64 LGKTTLASIVANEMGVELRTTSGPAIERPGDLAAILTALEPGDVLFIDEIHRLHRSIEEV 12- 3 Query: 123 LYSAMEDFYIDIMIGAGETSRSVHLDLPPFTLIGATTRAGMLSNPLRARFGITGHMEYYE 18- 2 LY AMEDF +DI+IG G ++RSV LDLPPFTL+GATTR G+L+ PLR RFG+ +EYY Sbjct: 124 LYPAMEDFCLDIVIGKGPSARSVRLDLPPFTLVGATTRVGLLTAPLRDRFGVMSRLEYYT 18- 3 Query: 183 ENDLTEIIERTADIFEMKITYEAASELARRSRGTPRIANRLLKRVRDYAQIMGDGLIDDN 24- 2 + +L +I+ RTAD+FE++I +A E+ARRSRGTPR+ANRLL+RVRD+AQ++GD I ++ Sbjct: 184 QEELADIVTRTADVFEVEIDKPSALEIARRSRGTPRVANRLLRRVRDFAQVLGDSRITED 24- 3 Query: 243 ITDKALTMLDVDHEGLDYVDQKILRTMIEMYNGGPVGLGTLSVNIAEERDTVEDMYEPYL 30- 2 I+ AL L VD GLD++D K+L MIE +NGGPVGL T+S I EE T+ED +YEPYL Sbjct: 244 ISQNALERLQVDRLGLDHIDHKLLMGMIEKFNGGPVGLDTISATIGEESHTIEDVYEPYL 30- 3 Query: 303 IQKGFIMRTRTGRVATVKAYEH 324 +Q GFI RT GR+ T Y H Sbjct: 304 LQIGFIQRTPRGRIVTPAVYHH 325 A related GBS nucleic acid sequence <SEQ ID 10943> which encodes amino acid sequence <SEQ ID 10944> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 889> which encodes the amino acid sequence <SEQ ID 890>. Analysis of this protein sequence reveals the following: TABLE-US-00869 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0686 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00870 Identities = 282/327 (86%), Positives = 306/327 (93%) Query: 1 MTRFLDSDAMGDEELVERTLRPQYLREYIGQDKVKDQLKIFIEAAKLRDESLDHVLLFGP 60- M R LD++ MG+EE +RTLRPQYL EYIGQDKVK+Q IFIEAAK RDESLDHVLLFGP Sbjct: 25 MARILDNNVMGNEEFSDRTLRPQYLHEYIGQDKVKEQFAIFIEAAKRRDESLDHVLLFGP 84- Query: 61 PGLGKTTMAFVIANELGVNLKQTSGPAIEKSGDLVAILNDLEPGDVLFIDEIHRMPMAVE 12- 0 PGLGKTTMAFVIANELGVNLKQTSGPA+EK+GDLVAILN+LEPGD+LFIDEIHRMPM+VE Sbjct: 85 PGLGKTTMAFVIANELGVNLKQTSGPAVEKAGDLVAILNELEPGDILFIDEIHRMPMSVE 14- 4 Query: 121 EVLYSAMEDFYIDIMIGAGETSRSVHLDLPPFTLIGATTRAGMLSNPLRARFGITGHMEY 18- 0 EVLYSAMEDFYIDIMIGAG+TSRS+HLDLPPFTLIGATTRAGMLSNPLRARFGITGHMEY Sbjct: 145 EVLYSAMEDFYIDIMIGAGDTSRSIHLDLPPFTLIGATTRAGMLSNPLRARFGITGHMEY 20- 4 Query: 181 YEENDLTEIIERTADIFEMKITYEAASELARRSRGTPRIANRLLKRVRDYAQIMGDGLID 24- 0 Y+E DLTEI+ERTA IFE+KI +EAA +LA RSRGTPRIANRLLKRVRDYAQI+GDG+I Sbjct: 205 YQEKDLTEIVERTATIFEIKIDHEAARKLACRSRGTPRIANRLLKRVRDYAQIIGDGIIT 26- 4 Query: 241 DNITDKALTMLDVDHEGLDYVDQKILRTMIEMYNGGPVGLGTLSVNIAEERDTVEDMYEP 30- 0 ITD+ALTMLDVD EGLDY+DQKILRTMIEMY GGPVGLGTLSVNIAEER+TVE+MYEP Sbjct: 265 AQITDRALTMLDVDREGLDYIDQKILRTMIEMYQGGPVGLGTLSVNIAEERNTVEEMYEP 32- 4 Query: 301 YLIQKGFIMRTRTGRVATVKAYEHLGY 327 YLIQKGF+MRTRTGRVAT KAY HLGY Sbjct: 325 YLIQKGFLMRTRTGRVATQKAYRHLGY 351 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 278 A DNA sequence (GBSx0304) was identified in S. agalactiae <SEQ ID 891> which encodes the amino acid sequence <SEQ ID 892>. Analysis of this protein sequence reveals the following: TABLE-US-00871 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.87 Transmembrane 157-173 (157-174) INTEGRAL Likelihood = -1.49 Transmembrane 205-221 (205-222) ----- Final Results ----- bacterial membrane --- Certainty = 0.2147 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 893> which encodes the amino acid sequence <SEQ ID 894>. Analysis of this protein sequence reveals the following: TABLE-US-00872 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3097 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00873 Identities = 130/303 (42%), Positives = 202/303 (65%) Query: 1 MLKHFGSKVRNLRVTRNITREDFCGDETELSVRQLARIESGQSIPNLTKAHYIAKQLNVK 60- ML+HFG KV+ LR+ + I+RED CGDE+ELSVRQLARIE GQSIP+L+K +IAK LNV Sbjct: 1 MLEHFGGKVKVLRLEKRISREDLCGDESELSVRQLARIELGQSIPSLSKVIFIAKALNVS 60- Query: 61 LDILTGGESLELPKRYKELKYLILRIPTYADAERLKLRECQFDHIFEEFYDNLPEDECLA 12- 0 + LT G LELPKRYKELKYLILR PTY D +L++RE QFD IFE++YD LPE+E + Sbjct: 61 VGYLTDGADLELPKRYKELKYLILRTPTYMDDGKLQVREEQFDEIFEDYYDKLPEEEKII 12- 0 Query: 121 IDSLQAKFEVYQTGDINFGVEVLCECFDKVKYKEKYTLNDLIIIDLFLTCAVVSKFNNRA 18- 0 ID LQA + + + NFG+++L E F+++K K ++ NDLI+++L+L + + + Sbjct: 121 IDCLQATLDTLLSENTNFGIDLLQEYFNQIKTKVRFRQNDLILLELYLAYLDIEGMDGQY 18- 0 Query: 181 FTKEVFQTICKTLISQNHKLTAEDLFWFNHVLLNCVFVGLCLNSEECLAEMLEVSRQTMV 24- 0 K + ++ L Q + ++LF N ++++ + L N + L + +E+S++`M Sbjct: 181 SDKIFYDSLLDNLSEQFEQFELDELFIVNKIIIDISSLSLKNNRLDNLEKAIEMSQKIMA 24- 0 Query: 241 STHDFHKMPLYFMYQWKYFITIDNDIKSAENAYQQSIMFSKMIDDKHLIKKLELEWQEDI 30- 0 D+++MP+ + +WKYF+ DI AE ++ ++ +F++M D++L KL EW++D+ Sbjct: 241 KIQDWNRMPILKLIEWKYFLIKQKDIIKAEQSFMKACLFAQMTADQYLENKLIQEWEKDV 30- 0 Query: 301 TGH 303 + Sbjct: 301 KSY 303 SEQ ID 892 (GBS319) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 40 (lane 4; MW 37 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 46 (lane 7; MW 62 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 279 A DNA sequence (GBSx0305) was identified in S. agalactiae <SEQ ID 895> which encodes the amino acid sequence <SEQ ID 896>. This protein is predicted to be adenylosuccinate lyase (purB). Analysis of this protein sequence reveals the following: TABLE-US-00874 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3358 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00875 >GP:BAB04344 GB:AP001509 adenylosuccinate lyase [Bacillus halodurans] Identities = 326/430 (75%), Positives = 366/430 (84%) Query: 1 MIERYSRPEMAAIWTEENKYRAWLEVEILADEAWAELGEIPKEDVAKIREKADFDIDRIL 60- MIERY+RPEM AIWTEEN+Y+AWLEVEI+A EAWAELGEIPKEDV KIRE A FD++RIL Sbjct: 1 MIERYTRPEMGAIWTEENRYQAWLEVEIVACEAWAELGEIPKEDVKKIREHASFDVERIL 60- Query: 61 EIEQDTRHDVVAFTRAVSETLGEERKWVHYGLTSTDVVDTAYGYLYKQANDIIRRDLENF 12- 0 EIEQ+TRHDVVAFTRAVSETLGEERKWVHYGLTSTDVVDTA YL KQAN+II DL F Sbjct: 61 EIEQETRHDVVAFTRAVSETLGEERKWVHYGLTSTDVVDTALSYLLKQANEIIEADLVRF 12- 0 Query: 121 TNIVADKAKEHKFTIMMGRTHGVHAEPTTFGLKLATWYSEMKRNIERFEHAAAGVEAGKI 18- 0 +I+ +KA EHK+T+MMGRTHGVHAEPTTFGLKLA WY EMKRN+ERF AA GV GK+ Sbjct: 121 LDILKEKALEHKYTVMMGRTHGVHAEPTTFGLKLALWYEEMKRNLERFRLAAEGVRVGKL 18- 0 Query: 181 SGAVGNFANIPPFVEQYVCDKLGIRPQEISTQVLPRDLHAEYFAVLASIATSIERMATEI 24- 0 SGAVG +ANI PFVEQYVC+KLG+ ISTQ L RD HAEY A LA IATSIE+ A EI Sbjct: 181 SGAVGTYANIDPFVEQYVCEKLGLERAPISTQTLQRDRHAEYMATLALIATSIEKFAVEI 24- 0 Query: 241 RGLQKSEQREVEEFFAKGQKGSSAMPHKRNPIGSENMTGLARVIRGHMVTAYENVALWHE 30- 0 RGLQKSE REVEE+FAKGQKGSSAMPHKRNPIGSENMTG+ARV+RGHM+ AYENV LWHE Sbjct: 241 RGLQKSETREVEEYFAKGQKGSSAMPHKRNPIGSENMTGIARVVRGHMLAAYENVPLWHE 30- 0 Query: 301 RDISHSSAERIITPDTTILIDYMLNRFGNIVKNLTVFPENMMRNMESTFGLIYSQRVMLK 36- 0 RDISHSSAERII PD TI I+YMLNRFGNIVKNLTVFPENM RNM T+GLIYSQRV+L Sbjct: 301 RDISHSSAERIILPDATIAINYMLNRFGNIVKNLTVFPENMKRNMTRTYGLIYSQRVLLS 36- 0 Query: 361 LIEKGMTREEAYDLVQPKTAYSWDNQVDFKPLLEEDTKVTSCLTQEEIDELFNPIYYTKR 42- 0 LI+KGM REEAYDLVQPK +W+ V F+ L+E++ ++TS L+ EEI+ F+ ++ K Sbjct: 361 LIDKGMVREEAYDLVQPKAMEAWEKGVQFRELVEQEERITSVLSPEEIEACFDYNHHLKH 42- 0 Query: 421 VDDIFERLGL 430 VD IFERLGL Sbjct: 421 VDTIFERLGL 430 A related DNA sequence was identified in S. pyogenes <SEQ ID 897> which encodes the amino acid sequence <SEQ ID 898>. Analysis of this protein sequence reveals the following: TABLE-US-00876 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3358(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00877 Identities = 422/430 (98%), Positives = 428/430 (99%) Query: 1 MIERYSRPEMAAIWTEENKYRAWLEVEILADEAWAELGEIPKEDVAKIREKADFDIDRIL 60 M+ERYSRPEMAAIWTEENKY AWLEVEILADEAWAELGEIPKEDVAKIREKADFDIDRIL Sbjct: 1 MLERYSRPEMAAIWTEENKYHAWLEVEILADEAWAELGEIPKEDVAKIREKADFDIDRIL 60 Query: 61 EIEQDTRHDVVAFTRAVSETLGEERKWVHYGLTSTDVVDTAYGYLYKQANDIIRRDLENF 120- EIEQDTRHDVVAFTRAVSETLGEERKWVHYGLTSTDVVDTAYGYLYKQANDIIRRDLENF Sbjct: 61 EIEQDTRHDVVAFTRAVSETLGEERKWVHYGLTSTDVVDTAYGYLYKQANDIIRRDLENF 120- Query: 121 TNIVADKAKEHKFTIMMGRTHGVHAEPTTFGLKLATWYSEMKRNIERFEHAAAGVEAGKI 18- 0 TNIVADKA+EHK TIMMGRTHGVHAEPTTFGLKLATWYSEMKRNIERFEHAAAGVEAGKI Sbjct: 121 TNIVADKAREHKMTIMMGRTHGVHAEPTTFGLKLATWYSEMKRNIERFEHAAAGVEAGKI 18- 0 Query: 181 SGAVGNFANIPPFVEQYVCDKLGIRPQEISTQVLPRDLHAEYFAVLASIATSIERMATEI 24- 0 SGAVGNFANIPPFVE+YVCDKLGIRPQEISTQVLPRDLHAEYFAVLASIATSIERMATEI Sbjct: 181 SGAVGNFANIPPFVEEYVCDKLGIRPQEISTQVLPRDLHAEYFAVLASIATSIERMATEI 24- 0 Query: 241 RGLQKSEQREVEEFFAKGQKGSSAMPHKRNPIGSENMTGLARVIRGHMVTAYENVALWHE 30- 0 RGLQKSEQREVEEFFAKGQKGSSAMPHKRNPIGSENMTGLARVIRGHMVTAYENV+LWHE Sbjct: 241 RGLQKSEQREVEEFFAKGQKGSSAMPHKRNPIGSENMTGLARVIRGHMVTAYENVSLWHE 30- 0 Query: 301 RDISHSSAERIITPDTTILIDYMLNRFGNIVKNLTVFPENMMRNMESTFGLIYSQRVMLK 36- 0 RDISHSSAERIITPDTTILIDYMLNRFGNIVKNLTVFPENMMRNMESTFGLIYSQRVMLK Sbjct: 301 RDISHSSAERIITPDTTILIDYMLNRFGNIVKNLTVFPENMMRNMESTFGLIYSQRVMLK 36- 0 Query: 361 LIEKGMTREEAYDLVQPKTAYSWDNQVDFKPLLEEDTKVTSCLTQEEIDELFNPIYYTKR 42- 0 LIEKGMTREEAYDLVQPKTAYSWDNQVDFKPLLEEDTKVTSCLTQEEIDELFNPIYYTKR Sbjct: 361 LIEKGMTREEAYDLVQPKTAYSWDNQVDFKPLLEEDTKVTSCLTQEEIDELFNPIYYTKR 42- 0 Query: 421 VDDIFERLGL 430 VDDIF+RLG+ Sbjct: 421 VDDIFKRLGI 430 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 280 A DNA sequence (GBSx0306) was identified in S. agalactiae <SEQ ID 899> which encodes the amino acid sequence <SEQ ID 900>. Analysis of this protein sequence reveals the following:

TABLE-US-00878 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -16.24 Transmembrane 145-161 (119-167) INTEGRAL Likelihood = -9.98 Transmembrane 125-141 (119-144) INTEGRAL Likelihood = -9.29 Transmembrane 28-44 (23-51) INTEGRAL Likelihood = -7.01 Transmembrane 196-212 (193-220) INTEGRAL Likelihood = -6.21 Transmembrane 96-112 (88-116) INTEGRAL Likelihood = -5.79 Transmembrane 249-265 (246-266) INTEGRAL Likelihood = -2.87 Transmembrane 222-238 (222-238) INTEGRAL Likelihood = -2.28 Transmembrane 279-295 (278-295) ----- Final Results ----- bacterial membrane --- Certainty = 0.7456(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty= 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00879 >GP:BAB13498 GB:AB028634 RNA polymerase [Flammulina velutipes] Identities = 83/336 (24%), Positives = 150/336 (43%), Gaps = 40/336 (11%) Query: 152 ILLLIAFVSIGKNR-VYNFVQNLNYFEEVIWNYFEENPVKIKEKSLIIK-----FLLTIS 20- 5 IL L SI NR + ++ N ++ N+F+ + +K K L+I F++ +S Sbjct: 133 ILFLYLIYSILINRFILKWLDNSGIIYKININWFKNHMIKHINKMLVINIKFFNFIIKLS 19- 2 Query: 206 FVFVIDFAMVRL-----LNFNIKFSTILACSAILLAWLYQN-----------KSVTEPFL 24- 9 + +I +++ L +NF+I+ I I ++ S+ F Sbjct: 193 IITIIGISIMELFGIFGINFDIRIIIINYLKTINSGKIHLTIINMDQYSVLENSIHTIFY 25- 2 Query: 250 LKKLVIYFIFFIATLIGNLKN-ELSILETPLLFISIFFTMDRIIALSKEMRDLI--ISKS 30- 6 + L+I+ IF L N+KN + +I +L+I IF I ++DL+ ++K Sbjct: 253 INLLIIFLIFISLILYRNVKNIDTNIKRWIILYILIFLINIIFIFNHIYIKDLMDNLNKY 31- 2 Query: 307 ILFYYDHENIKPSILLSEIKEIKYLENVDIGE---LELVRQMVIRLRLELEEEFLILSDI 36- 3 IL Y D I S+ L ++K L+ ++I + V+ + I+ ++E L + I Sbjct: 313 ILDYMDLHIIVNSLFLFNKFDVK-LKRINIYKSYSTVTVKDLEIKSKIEERSNELDIKLI 37- 1 Query: 364 YMKNG-YEKYIQFVQGNVYFINLE--LDKIPNYTNLKLILESIFD----HNNQKIFIPKL 41- 6 K G YE YI ++ N+ ++ E L P Y N +E + + + F+ K+ Sbjct: 372 IAKYGSYENYINSIE-NINIVDEEFILKNYPEYINDSKFIEFLMELEPLFRDHTEFVKKI 43- 0 Query: 417 YEEYIYILISLGEVEKAKEIL---KEVSDYLTEESL 449 YE L + K+IL KE+ DY+ + +L Sbjct: 431 YENLNSTNEKLEFLLANKDILSENKEIFDYVLQLNL 466 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 281 A DNA sequence (GBSx0308) was identified in S. agalactiae <SEQ ID 901> which encodes the amino acid sequence <SEQ ID 902>. Analysis of this protein sequence reveals the following: TABLE-US-00880 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3307 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 282 A DNA sequence (GBSx0309) was identified in S. agalactiae <SEQ ID 903> which encodes the amino acid sequence <SEQ ID 904>. This protein is predicted to be purK (purK). Analysis of this protein sequence reveals the following: TABLE-US-00881 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0334 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9461> which encodes amino acid sequence <SEQ ID 9462> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00882 >GP:CAA04376 GB:AJ000883 purk [Lactococcus lactis] Identities = 208/347 (59%), Positives = 258/347 (73%), Gaps = 3/347 (0%) Query: 14 NSFKTIGIIGGGQLGQMMAIAAIYMGHKVITLDPASDCPASRVS-EVIVAPYDDVEALGT 72 - N+ +TIGIIGGGQLGQMMAIAA YMGHKVITLDP +C A++VS E+IVAPYDDVE L Sbjct: 4 NTKQTIGIIGGGQLGQMMAIAAQYMGHKVITLDPNPNCSAAKVSDELIVAPYDDVENLLR 63 Query: 73 LAARCDVLTYEFENVDADGLDAVVSAGQLPQGTDLLRISQNRIFEKDFLANKAGVTVAPY 132- LA CDV+TYEFENV A L + ++PQG LL I+QNR FEK+FL N+A V VAP+ Sbjct: 64 LAYACDVITYEFENVSAKALHEIEGCVRIPQGIRLLEITQNRRFEKEFLTNEAKVNVAPW 123- Query: 133 KVVTSSLDLEGLDLTKTYVLKTATGGYDGHGQKVIRSAEDLPEAQQLANSAQCVLEEFVN 19- 2 ++V S+ L +T+ VLKT TGGYDGHGQ V+ + E L A+ L ++CVLE+F++ Sbjct: 124 QLVDSAEKLPET-VTRKQVLKTTTGGYDGHGQVVLNTDEKLSAAKSLTELSECVLEDFIS 18- 2 Query: 193 FDLEISVIVSGNGQDVTVFPVQENIHRNNILSKTIVPARISDQLADKAKEMAVQIAKKLQ 25- 2 F+ EISVI+SGNG + VFP+ EN HR NIL +TI PARIS ++ + A ++A IA+KL+ Sbjct: 183 FEREISVIISGNGHEYVVFPLAENEHRENILHQTISPARISAEITENAYKIATSIAEKLE 24- 2 Query: 253 LSGTLCVEMFATAD-DIIVNEIAPRPHNSGHYSIEACDFSQFDTHILGVLGAPLPPIKLH 31- 1 LSG LCVEMF TAD I VNE+APRPHNSGH++IEACDF+QFD HI G+LG LP KL Sbjct: 243 LSGVLCVEMFLTADGQIYVNELAPRPHNSGHFTIEACDFNQFDLHIKGILGEDLPEPKLL 30- 2 Query: 312 APAVMFNVLGQHVQQAIDHVAQNPSAHLHMYGKLEAKHNRKMGHVTV 358 PA+M NVLGQHV+ ++ H H YGK +AKHNRKMGHVT+ Sbjct: 303 KPAIMLNVLGQHVEAVKKLNHEHADWHQHDYGKADAKHNRKMGHVTI 349 A related DNA sequence was identified in S. pyogenes <SEQ ID 905> which encodes the amino acid sequence <SEQ ID 906>. Analysis of this protein sequence reveals the following: TABLE-US-00883 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0334 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00884 Identities = 344/369 (93%), Positives = 353/369 (95%) Query: 1 MRNKEKSQRSQAMNSFKTIGIIGGGQLGQMMAIAAIYMGHKVITLDPASDCPASRVSEVI 60 MRNKEKSQRSQ +NSFKTIGIIGGGQLGQMMAIAAIYMGHKVITLDPASD PASRVSEVI Sbjct: 1 MRNKEKSQRSQVVNSFKTIGIIGGGQLGQMMAIAAIYMGHKVITLDPASDSPASRVSEVI 60 Query: 61 VAPYDDVEALGTLAARCDVLTYEFENVDADGLDAVVSAGQLPQGTDLLRISQNRIFEKDF 120- VAPYDDVEALG LAARCDVLTYEFENVDADGLDAVVSA QLPQGTDLLRISQNRI EKDF Sbjct: 61 VAPYDDVEALGQLAARCDVLTYEFENVDADGLDAVVSACQLPQGTDLLRISQNRIVEKDF 120- Query: 121 LANKAGVTVAPYKVVTSSLDLEGLDLTKTYVLRTATGGYDGHGQKVIRSAEDLPEAQQLA 18- 0 LANKAGVTVAPYKVVTSSLDL GLDLTKTYVLKT TGGYDGHGQK+IRSAEDLPEAQQLA Sbjct: 121 LANKAGVTVAPYKVVTSSLDLGGLDLTKTYVLKTETGGYDGHGQKIIRSAEDLPEAQQLA 18- 0 Query: 181 NSAQCVLEEFVNFDLEISVIVSGNGQDVTVFPVQENIHRNNILSKTIVPARISDQLADKA 24- 0 NSAQCVLEEFVNFDLEISVIVSGNG+DVTVFPVQENIHRNNILSKTIVPARISDQLADKA Sbjct: 181 NSAQCVLEEFVNFDLEISVIVSGNGKDVTVFPVQENIHRNNILSKTIVPARISDQLADKA 24- 0 Query: 241 KEMAVQIAKKLQLSGTLCVEMFATADDIIVNEIAPRPHNSGHYSIEACDFSQFDTHILGV 30- 0 K+ AVQIAKKLQLSGTLCVEMF TADDIIVNEIAPRPHNSG YSIEACDFSQFDTHILGV Sbjct: 241 KKTAVQIAKKLQLSGTLCVEMFTTADDIIVNEIAPRPHNSGRYSIEACDFSQFDTHILGV 30- 0 Query: 301 LGAPLPPIKLHAPAVMFNVLGQHVQQAIDHVAQNPSAHLHMYGKLEAKHNRKMGHVTVFS 36- 0 LGAPLP I+LHAPAVM NVLGQHVQQA D+VA+NPSAHLHMYGKLEAKHNRKMGHVTVF+ Sbjct: 301 LGAPLPQIQLHAPAVMLNVLGQHVQQATDYVAKNPSAHLHMYGKLEAKHNRKMGHVTVFA 36- 0 Query: 361 DVPDEVEEF 369 DEV+EF Sbjct: 361 KDADEVKEF 369 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 283 A DNA sequence (GBSx0310) was identified in S. agalactiae <SEQ ID 907> which encodes the amino acid sequence <SEQ ID 908>. This protein is predicted to be phosphoribosylaminoimidazole carboxylase catalytic subunit (purE). Analysis of this protein sequence reveals the following: TABLE-US-00885 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3572(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00886 >GP:CAB12462 GB:Z99107 phosphoribosylaminoimidazole carboxylase I [Bacillus subtilis] Identities = 106/162 (65%), Positives = 128/162 (78%) Query: 33 MQPIISIIMGSKSDWTTMQKTAEVLDNFGIAYEKKVVSAHRTPDLMFKHAEEARGRGIKI 92 - MQP++ IIMGS SDW TM+ ++LD + YEKKVVSAHRTPD MF++AE AR RGIK+ Sbjct: 1 MQPLVGIIMGSTSDWETMKHACDILDELNVPYEKKVVSAHRTPDFMFEYAETARERGIKV 60 Query: 93 IIAGAGGAAHLPGMVAAKTTLPVIGVPVKSRALSGLDSLYSIVQMPGGVPVATMAIGEAG 152- IIAGAGGAAHLPGM AAKTTLPVIGVPV+S+AL+G+DSL SIVQMPGGVPVAT +IG+AG Sbjct: 61 IIAGAGGAAHLPGMTAAKTTLPVIGVPVQSKALNGMDSLLSIVQMPGGVPVATTSIGKAG 120- Query: 153 ATNAALTALRILSIEDQNLADALAHFHEEQGKIAEESSNELI 194 A NA L A +ILS D++LA L E + ESS++L+ Sbjct: 121 AVNAGLLAAQILSAFDEDLARKLDERRENTKQTVLESSDQLV 162 A related DNA sequence was identified in S. pyogenes <SEQ ID 909> which encodes the amino acid sequence <SEQ ID 910>. Analysis of this protein sequence reveals the following: TABLE-US-00887 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.08 Transmembrane 36-52 (34-52) ----- Final Results ----- bacterial membrane --- Certainty = 0.2232(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00888 >GP:CAA04375 GB:AJ000883 purE [Lactococcus lactis] Identities = 105/158 (66%), Positives = 131/158 (82%) Query: 46 ISIIMGSKSDWATMQKTAEVLDNFGIAYEKKVVSAHRTPDLMFKHAEEARGRGIKIIIAG 105- ++IIMG SDWATM++TA++LD+FG+AYEKKVVSAHRTP LM + + +AR RG K+IIAG Sbjct: 4 VAIIMGCSSDWATMKETAKILDDFGLAYEKKVVSAHRTPALMAEFSSQARERGYKVIIAG 63 Query: 106 AGGAAHLPGMVAAKTTLPVIGVPVKSRALSGLDSLYSIVQMPGGVPVATMAIGEAGATNA 16- 5 AGGAAHLPGMV+A+T +PVIGVP+KSRALSGLDSLYSIVQMP GVPVATMAIGEAGA NA Sbjct: 64 AGGAAHLPGMVSAQTLVPVIGVPIKSRALSGLDSLYSIVQMPAGVPVATMAIGEAGAKNA 123- Query: 166 ALTALRILSIEDQNLADALAHFHEEQGKIAEESSGELI 203 AL AL++L+ ++NL L + ++ EES+ L+ Sbjct: 124 ALFALQLLANTNENLIQKLLVYRAAAQEMVEESNKALL 161 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00889 Identities = 162/169 (95%), Positives = 164/169 (96%), Gaps = 1/169 (0%) Query: 27 PLYLNIMQ-PIISIIMGSKSDWTTMQKTAEVLDNFGIAYEKKVVSAHRTPDLMFKHAEEA 85 - PL + IM+ PIISIIMGSKSDW TMQKTAEVLDNFGIAYEKKVVSAHRTPDLMFKHAEEA Sbjct: 35 PLCILIMKTPIISIIMGSKSDWATMQKTAEVLDNFGIAYEKKVVSAHRTPDLMFKHAEEA 94 Query: 86 RGRGIKIIIAGAGGAAHLPGMVAAKTTLPVIGVPVKSRALSGLDSLYSIVQMPGGVPVAT 145- RGRGIKIIIAGAGGAAHLPGMVAAKTTLPVIGVPVKSRALSGLDSLYSIVQMPGGVPVAT Sbjct: 95 RGRGIKIIIAGAGGAAHLPGMVAAKTTLPVIGVPVKSRALSGLDSLYSIVQMPGGVPVAT 154- Query: 146 MAIGEAGATNAALTALRILSIEDQNLADALAHFHEEQGKIAEESSNELI 194 MAIGEAGATNAALTALRILSIEDQNLADALAHFHEEQGKIAEESS ELI Sbjct: 155 MAIGEAGATNAALTALRILSIEDQNLADALAHFHEEQGKIAEESSGELI 203 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 284 A DNA sequence (GBSx0311) was identified in S. agalactiae <SEQ ID 911> which encodes the amino acid sequence <SEQ ID 912>. This protein is predicted to be phosphoribosylglycinamide synthetase (purD). Analysis of this protein sequence reveals the following: TABLE-US-00890 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1966(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00891 >GP:CAA04374 GB:AJ000883 purD [Lactococcus lactis] Identities = 236/419 (56%), Positives = 298/419 (70%), Gaps = 7/419 (1%) Query: 1 MKLLVVGSGGREHAIAKKLLASKDVDQVFVAPGNDGMTLDGLDLVNIGISEHSRLIDFVK 60 MK+LV+GSGGREHA+AKK + S V++VFVAPGN GM DG+ +V+I + +L+ F + Sbjct: 1 MKILVIGSGGREHALAKKFMESPQVEEVFVAPGNSGMEKDGIQIVHISELSNDKLVKFAQ 60 Query: 61 ENEIAWTLIGPDDALAAGIVDGFNSAGLRAFGPTKAAAELEWSKDFAKEIMVKYNVPTAA 120- I T +GP+ AL G+VD F A L FGP K AAELE SKDFAK IM KY VPTA Sbjct: 61 NQNIGLTFVGPETALMNGVVDAFIKAELPIFGPNKMAAELEGSKDFAKSIMKKYGVPTAD 120- Query: 121 YGTFSDFEKAKAYIEEQGAPIVVKADGLALGKGVVVAETVEQAVEAAQEMLLDNKFGDSG 18- 0 Y TF E A AY++E+G P+V+KADGLA GKGV VA +E A A ++ F S Sbjct: 121 YATFDSLEPALAYLDEKGVPLVIKADGLAAGKGVTVAFDIETAKSALADI-----FSGSQ 17- 5 Query: 181 ARVVIEEFLDGEEFSLFAFANGDKFYIMPTAQDHKRAYDGDKGLNTGGMGAYAPVPHLPQ 24- 0 +VVIEEFLDGEEFSLF+F + K Y MP AQDHKRA+D DKG NTGGMGAY+PV H+ + Sbjct: 176 GKVVIEEFLDGEEFSLFSFIHDGKIYPMPIAQDHKRAFDEDKGPNTGGMGAYSPVLHISK 23- 5 Query: 241 SVVDTAVETIVKPVLEGMIAEGRPYLGVLYAGLILTADGPKVIEFNSRFGDPETQIILPR 30- 0 VV+ A+E +VKP + GMI EG+ + GVLYAGLILT DG K IEFN+RFGDPETQ++LPR Sbjct: 236 EVVNEALEKVVKPTVAGMIEEGKSFTGVLYAGLILTEDGVKTIEFNARFGDPETQVVLPR 29- 5 Query: 301 LTSDFAQNIDDIMMGIEPYITWQKDGVTLGVVVASEGYPLDYEKGVPLPEKTDGDIITYY 36- 0 L SD AQ I DI+ G EP + W + GVTLGVVVA+EGYP + G+ LPE +G + YY Sbjct: 296 LKSDLAQAIIDILAGNEPTLEWLESGVTLGVVVAAEGYPSQAKLGLILPEIPEG-LNVYY 35- 4 Query: 361 AGAKFAENSKALLSNGGRVYMLVTTEDSVKAGQDKIYTQLAQQDTTGLFYRNDIGSKAI 419- AG EN++ L+S+GGRVY++ T + VK+ Q +Y +L + + G FYR+DIGS+AI Sbjct: 355 AGVSKNENNQ-LISSGGRVYLVSETGEDVKSTQKLLYEKLDKLENDGFFYRHDIGSRAI 412- A related DNA sequence was identified in S. pyogenes <SEQ ID 913> which encodes the amino acid sequence <SEQ ID 914>. Analysis of this protein sequence reveals the following: TABLE-US-00892 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.80 Transmembrane 5-21 (5-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.1319(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00893 >GP:CAA04374 GB:AJ000883 purD [Lactococcus lactis] Identities = 236/419 (56%), Positives = 301/419 (71%), Gaps = 7/419 (1%) Query: 50 LKLLVVGSGGREHAIAKKLLASKGVDQVFVAPGNDGMTLDGLDLVNIVVSEHSRLIAFAK 109- +K+LV+GSGGREHA+AKK + S V++VFVAPGN GM DG+ +V+I + +L+ FA+ Sbjct: 1 MKILVIGSGGREHALAKKFMESPQVEEVFVAPGNSGMEKDGIQIVHISELSNDKLVKFAQ 60 Query: 110 ENEISWAFIGPDDALAAGIVDDFNSAGLRAFGPTKAAAELEWSKDFAKEIMVKYNVPTAA 16- 9 I F+GP+ AL G+VD F A L FGP K AAELE SKDFAK IM KY VPTA Sbjct: 61 NQNIGLTFVGPETALMNGVVDAFIKAELPIFGPNKMAAELEGSKDFAKSIMKKYGVPTAD 120- Query: 170 YGTFSDFEKAKAYIEEQGAPIVVKADGLALGKGVVVAETVEQAVEAAQEMLLDNKFGDSG 22- 9 Y TF E A AY++E+G P+V+KADGLA GKGV VA +E A A ++ F S Sbjct: 121 YATFDSLEPALAYLDEKGVPLVIKADGLAAGKGVTVAFDIETAKSALADI-----FSGSQ 17- 5 Query: 230 ARVVIEEFLDGEEFSLFAFANGDKFYIMPTAQDHKRAFDGDKGPNTGGMGAYAPVPHLPQ 28- 9 +VVIEEFLDGEEFSLF+F + K Y MP AQDHKRAFD DKGPNTGGMGAY+PV H+ + Sbjct: 176 GKVVIEEFLDGEEFSLFSFIHDGKIYPMPIAQDHKRAFDEDKGPNTGGMGAYSPVLHISK 23- 5 Query: 290 SVVDTAVEMIVRPVLEGMVAEGRPYLGVLYVGLILTADGPKVIEFNSRFGDPETQIILPR 34- 9 VV+ A+E +V+P + GM+ EG+ + GVLY GLILT DG K IEFN+RFGDPETQ++LPR Sbjct: 236 EVVNEALEKVVKPTVAGMIEEGKSFTGVLYAGLILTEDGVKTIEFNARFGDPETQVVLPR 29- 5 Query: 350 LTSDFAQNIDDIMMGIEPYITWQKDGVTLGVVVASEGYPFDYEKGVPLPEKTDGDIITYY 40- 9 L SD AQ I DI+ G EP + W + GVTLGVVVA+EGYP + G+ LPE +G + YY Sbjct: 296 LKSDLAQAIIDILAGNEPTLEWLESGVTLGVVVAAEGYPSQAKLGLILPEIPEG-LNVYY 35- 4 Query: 410 AGVKFSENSELLLSNGGRVYMLVTTEDSVKAGQDKIYTQLAQQDTTGLFYRNDIGSKAI 468- AGV +EN++ L+S+GGRVY++ T + VK+ Q +Y +L + + G FYR+DIGS+AI Sbjct: 355 AGVSKNENNQ-LISSGGRVYLVSETGEDVKSTQKLLYEKLDKLENDGFFYRHDIGSRAI 412- An alignment of the GAS and GBS proteins is shown below: TABLE-US-00894 Identities = 399/421 (94%), Positives = 408/421 (96%) Query: 1 MKLLVVGSGGREHAIAKKLLASKDVDQVFVAPGNDGMTLDGLDLVNIGISEHSRLIDFVK 60 +KLLVVGSGGREHAIAKKLLASK VDQVFVAPGNDGMTLDGLDLVNI +SEHSRLI F K Sbjct: 50 LKLLVVGSGGREHAIAKKLLASKGVDQVFVAPGNDGMTLDGLDLVNIVVSEHSRLIAFAK 109- Query: 61 ENEIAWTLIGPDDALAAGIVDGFNSAGLRAFGPTKAAAELEWSKDFAKEIMVKYNVPTAA 120- ENEI+W IGPDDALAAGIVD FNSAGLRAFGPTKAAAELEWSKDFAKEIMVKYNVPTAA Sbjct: 110 ENEISWAFIGPDDALAAGIVDDFNSAGLRAFGPTKAAAELEWSKDFAKEIMVKYNVPTAA 16- 9 Query: 121 YGTFSDFEKAKAYIEEQGAPIVVKADGLALGKGVVVAETVEQAVEAAQEMLLDNKFGDSG 18- 0 YGTFSDFEKAKAYIEEQGAPIVVKADGLALGKGVVVAETVEQAVEAAQEMLLDNKFGDSG Sbjct: 170 YGTFSDFEKAKAYIEEQGAPIVVKADGLALGKGVVVAETVEQAVEAAQEMLLDNKFGDSG 22- 9 Query: 181 ARVVIEEFLDGEEFSLFAFANGDKFYIMPTAQDHKRAYDGDKGLNTGGMGAYAPVPHLPQ 24- 0 ARVVIEEFLDGEEFSLFAFANGDKFYIMPTAQDHKRA+DGDKG NTGGMGAYAPVPHLPQ Sbjct: 230 ARVVIEEFLDGEEFSLFAFANGDKFYIMPTAQDHKRAFDGDKGPNTGGMGAYAPVPHLPQ 28- 9 Query: 241 SVVDTAVETIVKPVLEGMIAEGRPYLGVLYAGLILTADGPKVIEFNSRFGDPETQIILPR 30- 0 SVVDTAVE IV+PVLEGM+AEGRPYLGVLY GLILTADGPKVIEFNSRFGDPETQIILPR Sbjct: 290 SVVDTAVEMIVRPVLEGMVAEGRPYLGVLYVGLILTADGPKVIEFNSRFGDPETQIILPR 34- 9 Query: 301 LTSDFAQNIDDIMMGIEPYITWQKDGVTLGVVVASEGYPLDYEKGVPLPEKTDGDIITYY 36- 0 LTSDFAQNIDDIMMGIEPYITWQKDGVTLGVVVASEGYP DYEKGVPLPEKTDGDIITYY Sbjct: 350 LTSDFAQNIDDIMMGIEPYITWQKDGVTLGVVVASEGYPFDYEKGVPLPEKTDGDIITYY 40- 9 Query: 361 AGAKFAENSKALLSNGGRVYMLVTTEDSVKAGQDKIYTQLAQQDTTGLFYRNDIGSKAIKE 4- 21 AG KF+ENS+ LLSNGGRVYMLVTTEDSVKAGQDKIYTQLAQQDTTGLFYRNDIGSKAI+E Sbjct: 410 AGVKFSENSELLLSNGGRVYMLVTTEDSVKAGQDKIYTQLAQQDTTGLFYRNDIGSKAIRE 4- 70 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 285 A DNA sequence (GBSx0312) was identified in S. agalactiae <SEQ ID 915> which encodes the amino acid sequence <SEQ ID 916>. Analysis of this protein sequence reveals the following:

TABLE-US-00895 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.28 Transmembrane 235-251 (235-251) ----- Final Results ----- bacterial membrane --- Certainty = 0.1510(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00896 >GP: AAA23257 GB: M81878 unknown [Clostridium perfringens] Identities = 66/258 (25%), Positives = 119/258 (45%), Gaps = 9/258 (3%) Query: 1 MTIYDQIESALDLMTDLEREIACYFMGQPISKDALASTIVTKQLHISQAALTRFAKKCGF 60 M I +Q+E+ T E+ + Y + + +I+ K+ + +A +TRF KK GF Sbjct: 1 MGILEQLENPKFKATKSEKTLIEYIKSDLDNIIYKSISIIAKESGVGEATITRFTKKLGF 60 Query: 61 KGYREFVFEYLKS-HETISQQLYGLQNDNTKKVFMNYQEMISKSADI-------IDEEQL 112- G+++F K + + L + V +M+ S +I ID + + Sbjct: 61 NGFQDFKVTLAKEISNKKNTSIINLHVHRDESVTETANKMLKSSINILEQTVKQIDLDLM 120- Query: 113 LEVSHMIEQADRVYFYGKGSSSLVAKEFKIRLMRLGVICEALDDTDSFSWTNSIVNDRCL 17- 2 + +I A RVYF G G S + A + + MR+G + D+ + +SI ND + Sbjct: 121 CKCRDLIMNAKRVYFIGIGYSGIAATDINYKFMRIGFTTVPVTDSHTMVIMSSITNDDDV 18- 0 Query: 173 VIAFSLSGNTNSVIGALKIASCHGAKTVLFTK-QPHTIDYAFDKIIQVASARHLDYGNRI 23- 1 ++A S SG T VI +K A +G K + T+ + + D + SA + I Sbjct: 181 IVAISNSGTTKEVIKTVKQAKENGTKIITLTEDSDNPLRKLSDYELTYTSAETIFETGSI 24- 0 Query: 232 SPQIPMLIMVDIIYAQFL 249 S +IP + ++D++Y + + Sbjct: 241 SSKIPQIFLLDLLYTEVI 258 A related DNA sequence was identified in S. pyogenes <SEQ ID 917> which encodes the amino acid sequence <SEQ ID 918>. Analysis of this protein sequence reveals the following: TABLE-US-00897 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.88 Transmembrane 243-259 (242-261) ----- Final Results ----- bacterial membrane --- Certainty = 0.2954(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified <SEQ ID 9093> which encodes the amino acid sequence <SEQ ID 9094>. Analysis of this protein sequence reveals the following: TABLE-US-00898 Possible cleavage site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.88 Transmembrane 239-255 (238-257) ----- Final Results ----- bacterial membrane --- Certainty = 0.295(Affirmative) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00899 Identities = 138/263 (52%), Positives = 189/263 (71%), Gaps = 2/263 (0%) Query: 6 QIESALDLMTDLEREIACYFMGQPISKDALASTIVTKQLHISQAALTRFAKKCGFKGYRE 65 +IE++L+ MT LE+ IA +F+ ++ L ++ + K+LHISQAALTRFAKKCGF GYR Sbjct: 14 KIEASLEHMTSLEKGIAHFFITTDLTPQELTASEIVKRLHISQAALTRFAKKCGFTGYRA 73 Query: 66 FVFEYLKSHETISQQLYGLQNDNTKKVFMNYQEMISKSADIIDEEQLLEVSHMIEQADRV 125- F F+YL S + + + + TK+V M+Y +I+K+ ++++EE+LL ++ +I+ ++RV Sbjct: 74 FAFDYLHSLQESQETFQSIHLELTKRVLMDYDALINKTYELVNEEKLLNLAKLIDSSERV 133- Query: 126 YFYGKGSSSLVAKEFKIRLMRLGVICEALDDTDSFSWTNSIVNDRCLVIAFSLSGNTNSV 18- 5 YF+GKGSS LVA+E K+R MRLG+IC+A DTD F+W NS+VN+ CLV FSLSG TNSV Sbjct: 134 YFFGKGSSGLVAREMKLRFMRLGLICDAYSDTDGFTWANSLVNENCLVFGFSLSGRTNSV 19- 3 Query: 186 IGALKIASCHGAKTVLFTKQPHT-IDYAFDKIIQVASARHLDYGNRISPQIPMLIMVDII 24- 4 I AL AS GAKTVL T T D + D II V+S L YGNR+SPQ P+LIM+DII Sbjct: 194 ITALHQASQRGAKTVLLTTDNQTEFDDSLD-IIPVSSTHQLHYGNRVSPQFPLLIMMDII 25- 2 Query: 245 YAQFLDINKIEKERIFRETIIQR 267 YA L I+K KE+IF+ TII + Sbjct: 253 YAYVLAIDKPHKEKIFKNTIIDK 275 SEQ ID 916 (GBS320) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 40 (lane 5; MW 33 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 85 (lane 7; MW 58 kDa) and in FIG. 160 (lane 7 & 8; MW 58 kDa). GBS320-GST was purified as shown in FIG. 224, lane 3-4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 286 A DNA sequence (GBSx0313) was identified in S. agalactiae <SEQ ID 919> which encodes the amino acid sequence <SEQ ID 920>. This protein is predicted to be xylan esterase 1 (cephalosporin-C). Analysis of this protein sequence reveals the following: TABLE-US-00900 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4981(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00901 >GP:AAB68821 GB:AF001926 xylan esterase 1 [Thermoanaerobacterium sp. `JW/SL YS485`] Identities = 133/299 (44%), Positives = 188/299 (62%), Gaps = 1/299 (0%) Query: 5 MSLDDMREYLGQDQIPEDFDDFWKKQTMKYQG-NIEYRLDKKDFNITFAQAYDLHFKGSN 63 M L +REY G + PEDFD++W + + + + + L + F ++FA+ YDL+F G Sbjct: 6 MPLQKLREYTGTNPCPEDFDEYWNRALDEMRSVDPKIELKESSFQVSFAECYDLYFTGVR 65 Query: 64 NSIVYAKCLFPKTNKPYPVVFYFHGYQNQSPDWSDQLNYVAAGYGVVSMDVRGQAGQSQD 123- + ++AK + PKT +P + FHGY + S DW+D+LNYVAAG+ VV+MDVRGQ GQSQD Sbjct: 66 GARIHAKYIKPKTEGKHPALIRFHGYSSNSGDWNDKLNYVAAGFTVVAMDVRGQGGQSQD 125- Query: 124 KGHFDGITVKGQIVRGMISGPNHLFYKDIYLDVFQLIDIIATLESVDSNQLYSYGWSQGG 18- 3 G G T+ G I+RG+ +++ ++ I+LD QL I+ + VD +++ G SQGG Sbjct: 126 VGGVTGNTLNGHIIRGLDDDADNMLFRHIFLDTAQLAGIVMNMPEVDEDRVGVMGPSQGG 18- 5 Query: 184 ALALIAAALNPKIVKTVAVYPFLSDFRRVLDLGGVSEPYDELFRYFKYSDPFHKTENNVL 24- 3 L+L AAL P++ K V+ YPFLSD++RV DL Y E+ YF+ DP H+ EN V Sbjct: 186 GLSLACAALEPRVRKVVSEYPFLSDYKRVWDLDLAKNAYQEITDYFRLFDPRHERENEVF 24- 5 Query: 244 KTLAYIDVKNFAHRISCPVVLLTALKDDICPPSTQFAIFNRLTSTKKHLLLPDYGHDPM 302- L YIDVKN A RI V++ L D +CPPST FA +N + S K + PDYGH+PM Sbjct: 246 TKLGYIDVKNLAKRIKGDVLMCVGLMDQVCPPSTVFAAYNNIQSKKDIKVYPDYGHEPM 304- No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 287 A DNA sequence (GBSx0314) was identified in S. agalactiae <SEQ ID 921> which encodes the amino acid sequence <SEQ ID 922>. Analysis of this protein sequence reveals the following: TABLE-US-00902 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.73 Transmembrane 128-144 (126-145) ----- Final Results ----- bacterial membrane --- Certainty = 0.3293(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00903 >GP:AAA23256 GB:M81878 unknown [Clostridium perfringens] Identities = 78/160 (48%), Positives = 110/160 (68%) Query: 131 CLTIGTGIGGCLIIDKTVFHGFSNSACEVGYMHLSDGDFQDLASTTALIADVAKAHGDEI 19- 0 CLTIGTGIGG LIID V HGFSNSA E+GYM ++ + QD+AS +AL+ +VA G E Sbjct: 18 CLTIGTGIGGALIIDGKVLHGFSNSAGEIGYMMVNGENIQDIASASALVKNVALRKGVEP 77 Query: 191 SRWDGRRIFQEAKKGNEKCIASIDRMINYLGQGIANMVYVVNPEKVVLGGGIMAQKDYLQ 25- 0 S DGR + + G+ C ++++ + L GI+N+VY++NPE VVLGGGIMA+++ + Sbjct: 78 SSIDGRYVLDNYENGDLICKEEVEKLADNLALGISNIVYLINPEVVVLGGGIMAREEVFR 137- Query: 251 DKLSESLKRNLVTSLAEKTAIVFAQHENQAGMLGAYYHFK 290 + SL++ L+ S+ T I FA+ +N AGM GAYY+FK Sbjct: 138 PLIENSLRKYLIESVYNNTKIAFAKLKNTAGMKGAYYNFK 177 A related DNA sequence was identified in S. pyogenes <SEQ ID 923> which encodes the amino acid sequence <SEQ ID 924>. Analysis of this protein sequence reveals the following: TABLE-US-00904 Possible site: 22 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.30 Transmembrane 128-144 (127-145) INTEGRAL Likelihood = -0.11 Transmembrane 227-243 (227-243) ----- Final Results ----- bacterial membrane --- Certainty = 0.2720(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00905 >GP:BAB04516 GB:AP001509 glucose kinase [Bacillus halodurans] Identities = 97/291 (33%), Positives = 155/291 (52%), Gaps = 14/291 (4%) Query: 5 LAIDIGGTAIKYGLISETGDLLEKEEMATEAYKGGPSILEKVKGLVKTYQDQMDLAGVAI 64 + ID+GGT IK L+S+ G+++ +E TEA +G ++ K+ L + D AG+ I Sbjct: 3 VGIDLGGTKIKAALVSDAGEIISVQECPTEAAQGPEEVMNKMMSLTEKVTDHQPFAGIGI 62 Query: 65 SSAGMVNPDEGEIFYAGPQIPNYAGTQFKKEIEETFGLPCEVENDVNCAGLAEAISGSAK 124- + G ++ EG I + P +P + +E F P +++ND N A LAEA+ GS + Sbjct: 63 GAPGPLSSTEGTIL-SPPNLPGWDHIHLVDRFQEQFQCPVKLDNDANVAALAEALLGSGQ 121- Query: 125 DYPVALCLTIGTGIGGCLLFNSQVFHGSSHSACEVG----------YLHLSDGQFQDLAS 17- 4 + LTI TGIGG + + + HG+S A E+G + +L+ G + LAS Sbjct: 122 GFTSVFYLTISTGIGGGYVLDGSIVHGASDYAGEIGNMIVQPNGYQHANLNPGSLEGLAS 18- 1 Query: 175 TTALVQEVVLAYGDDISQWDGRRIFEQAKAGDAICIAAISKQVDYLGQGIANICYVVNPN 23- 4 TA+ + +G + R +F+Q + GD + + +DYL GIANI + +NP+ Sbjct: 182 GTAIGRMARERFG---VEGGTREVFDQIRRGDHDMQRLVEEAMDYLAIGIANIAHTINPD 23- 8 Query: 235 VVVLGGGIMAQKDYLADKLKTALDSYLVSSLAKKTQLKFASHGNNAGILGA 285 V VLGGG+M D + +K + YL LA+ T + A G ++G+LGA Sbjct: 239 VFVLGGGVMNADDLILPIVKEKVSRYLYPGLAQSTTIVKAKLGGDSGVLGA 289 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00906 Identities = 192/292 (65%), Positives = 237/292 (80%) Query: 1 MTRTVAIDIGGTMIKHGIVDNLGCIVEASELATEAYKGGPGILQKVCQIIDNYLAEGSID 60 M +AIDIGGT IK+G++ G ++E E+ATEAYKGGP IL+KV ++ Y + + Sbjct: 1 MKHYLAIDIGGTAIKYGLISETGDLLEKEEMATEAYKGGPSILEKVKGLVKTYQDQNDLA 60 Query: 61 GIAISSAGMVDPDEGCIFYSGPQIPNYAGTQFKKVLEDTYQVRTEIENDVNCAGLAEAVS 120- G+AISSAGMV+PDEG IFY+GPQIPNYAGTQFKK +E+T+ + E+ENDVNCAGLAEA+S Sbjct: 61 GVAISSAGMVNPDEGEIFYAGPQIPNYAGTQFKKEIEETFGLPCEVENDVNCAGLAEAIS 120- Query: 121 GSAKDSSIALCLTIGTGIGGCLIIDKTVFHGFSNSACEVGYMHLSDGDFQDLASTTALIA 18- 0 GSAKD +ALCLTIGTGIGGCL+ + VFHG S+SACEVGY+HLSDG FQDLASTTAL+ Sbjct: 121 GSAKDYPVALCLTIGTGIGGCLLFNSQVFHGSSHSACEVGYLHLSDGQFQDLASTTALVQ 18- 0 Query: 181 DVAKAHGDEISRWDGRRIFQEAKKGNEKCIASIDRMINYLGQGIANMVYVVNPEKVVLGG 24- 0 +V A+GD+IS+WDGRRIF++AK G+ CIA+I + ++YLGQGIAN+ YVVNP VVLGG Sbjct: 181 EVVLAYGDDISQWDGRRIFEQAKAGDAICIAAISKQVDYLGQGIANICYVVNPNVVVLGG 24- 0 Query: 241 GIMAQKDYLQDKLSESLKRNLVTSLAEKTAIVFAQHENQAGMLGAYYHFKNR 292 GIMAQKDYL DKL +L LV+SLA+KT + FA H N AG+LGAYYHFK + Sbjct: 241 GIMAQKDYLADKLKTALDSYLVSSLAKKTQLKFASHGNNAGILGAYYHFKQK 292 SEQ ID 922 (GBS331) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 60 (lane 2; MW 35.9 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 67 (lane 3; MW 61 kDa). The GBS331-GST fusion product was purified (FIG. 209, lane 3) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 309), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 288 A DNA sequence (GBSx0315) was identified in S. agalactiae <SEQ ID 925> which encodes the amino acid sequence <SEQ ID 926>. This protein is predicted to be a acylneuraminate lyase (nanA). Analysis of this protein sequence reveals the following: TABLE-US-00907 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0894(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00908 >GP: CAA69950 GB: Y08695 putative acylneuraminate lyase [Clostridium tertium] Identities = 162/225 (72%), Positives = 191/225 (84%) Query: 1 MKDLQKYQGIIPAFYACYDDKGDICPERVKALTNYFIDKGVQGLYVNGSSGECIYQSVAD 60 M++L+KY+GIIPAFYACYDD+G I PER + T Y IDKGV+GLYV GSSGECIYQS + Sbjct: 1 MRNLEKYKGIIPAFYACYDDEGKISPERTQMFTQYLIDKGVKGLYVCGSSGECIYQSKEE 60 Query: 61 RKLVLENVMSVAKGKLTVIAHVACNNTKDSVELAMHAEAIGVDAIAAIPPIYPRLPEYAI 120- RK+ LENVM VAKGK+T+IAHV CNNT+DS ELA HAE+IGVDAIA+IPPIYF LP+Y+I Sbjct: 61 RKITLENVMKVARGKITIIAHVGCNNTRDSEELAEHAESIGVDAIASIFPIYFHLPDYSI 120- Query: 121 ADYWNTISQAAPQTDFIIYNIPQLAGVALTSDLYRKMLQNPQVIGVKNSSMPVQDIQNFV 18- 0 A+YWN IS AAP TDFIIYNIPQLAGV L +LY++ML+NP+VIGVKNSSMPVQDIQ F Sbjct: 121 AEYWNDISNAAPNTDFIIYNIPQLAGVGLGINLYKQMLKNPRVIGVKNSSMPVQDIQMFK 18- 0 Query: 181 AIGGENHIVFNGPDEQFLGGRLMGAAAGIGGTYGVMPELYLTLNQ 225 I G+ +VFNGPDEQF+ GR+MGA GIGGTY VMPEL+L ++ Sbjct: 181 DISGDESVVFNGPDEQFVAGRIMGADGGIGGTYAVMPELFLAADK 225 A related DNA sequence was identified in S. pyogenes <SEQ ID 927> which encodes the amino acid sequence <SEQ ID 928>. Analysis of this protein sequence reveals the following: TABLE-US-00909 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0981(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00910 Identities = 238/304 (78%), Positives = 263/304 (86%) Query: 1 MKDLQKYQGIIPAFYACYDDKGDICPERVKALTNYFIDKGVQGLYVNGSSGECIYQSVAD 60 M DL KYQGIIPAFYACYDD+G+I PERV+ALT Y+IDKGVQGLY+NGSSGECIYQSV D Sbjct: 1 MTDLTKYQGIIPAFYACYDDQGNISPERVRALTQYYIDKGVQGLYINGSSGECIYQSVFD 60 Query: 61 RKLVLENVMSVAKGKLTVIAHVACNNTKDSVELANHAEAIGVDAIAAIPPIYFRLPEYAI 120- R+LVLENVM+VAKGKLT+I HVACNNTKDS+ELA H+E +GVDAIAAIPPIYFRLPEYA+ Sbjct: 61 RQLVLENVMAVAKGKLTIINHVACNNTKDSIELAAHSERLGVDAIAAIPPIYFRLPEYAV 120- Query: 121 ADYWNTISQAAPQTDFIIYNIPQLAGVALTSDLYRKMLQNPQVIGVKNSSMPVQDIQNFV 18- 0 ADYWN IS AAP TDFIIYNIPQLAGVALT LY+ ML N +VIGVKNSSMFVQDIQ F Sbjct: 121 ADYWNAISSAAPHTDFIIYNIPQLAGVALTPSLYKTMLANKRVIGVKNSSMPVQDIQTFC 18- 0 Query: 181 AIGGENHIVFNGPDEQFLGGRLMGAAAGIGGTYGVMPELYLTLNQLIVDKDLEKARELQF 24- 0 AIGG++HIVFNGPDEQFLGGRLMGAAAGIGGTYG MPEL+L LNQLI DKDLEKA+ LQ+ Sbjct: 181 AIGGDDHIVFNGPDEQFLGGRLMGAAAGIGGTYGAMPELFLRLNQLIADKDLEKAKALQY 24- 0 Query: 241 TINDIITKLCSGHGNMYAVIKAVLEINEQLTIGSVRLPLASVTEEDKPIIKEAAEMIRHA 30- 0 TIN+II L S HGNMY VIK VL INE L IGSVR PLA + EED+ I + AA +I A Sbjct: 241 TINEIIGVLVSAHGNMYGVIKEVLRINEGLDIGSVRSPLAELVEEDRVICQRAAALINQA 30- 0 Query: 301 KKQF 304 K+ F Sbjct: 301 KETF 304 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 289 A DNA sequence (GBSx0317) was identified in S. agalactiae <SEQ ID 929> which encodes the amino acid sequence <SEQ ID 930>. Analysis of this protein sequence reveals the following: TABLE-US-00911 Possible site: 46 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.45 Transmembrane 82-98 (79-111) INTEGRAL Likelihood = -6.85 Transmembrane 24-40 (21-52) INTEGRAL Likelihood = -5.26 Transmembrane 180-196 (172-200) INTEGRAL Likelihood = -5.10 Transmembrane 160-176 (158-179) INTEGRAL Likelihood = -4.35 Transmembrane 110-126 (106-130) ----- Final Results ----- bacterial membrane --- Certainty = 0.4779(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-00912 >GP: BAB05827 GB: AP001514 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 40/148 (27%), Positives = 74/148 (49%), Gaps = 4/148 (2%) Query: 14 VNNPFMQGCNVVFDLALLNLLFMI-TCLPLVTIG--AAKISLYRTLWQKLEGD-QTNLLI 69 - +++ F Q C+ ++ LA +NLL++ T L LV +G A +++ L + G+ + Sbjct: 6 MSSRFYQTCDWIWKLAYINLLWLSGTLLGLVVLGFLPATTAMFTVLRKWFTGNPDVAITR 65 Query: 70 LYIKHLKKEWFQGMLLGLVELSILVVIIFDLTILHYQIGFIVSFLKITCYAFLLLTVMTS 129- + + K E+ + LLG V L ++ F+ L G + L + YAFL+L ++T Sbjct: 66 TFFQAYKNEFLKINLLGAVLLLGAYILYFNYMYLGTVEGTVHMVLSLGWYAFLILYIITL 125- Query: 130 IYLFPMAARYEMSLLDTVKKSFIMACLN 157 Y+ P Y + L +K + I+ +N Sbjct: 126 FYIIPAYVHYNLKLFQYIKTALIIGFVN 153 A related DNA sequence was identified in S. pyogenes <SEQ ID 931> which encodes the amino acid sequence <SEQ ID 932>. Analysis of this protein sequence reveals the following: TABLE-US-00913 Possible site: 24 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.86 Transmembrane 117-133 (108-139) INTEGRAL Likelihood = -7.48 Transmembrane 30-46 (21-54) INTEGRAL Likelihood = -6.90 Transmembrane 88-104 (83-105) INTEGRAL Likelihood = -6.26 Transmembrane 165-181 (151-187) INTEGRAL Likelihood = -5.89 Transmembrane 189-205 (182-207) ----- Final Results ----- bacterial membrane --- Certainty = 0.6944(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00914 >GP: BAB05582 GB: AP001513 unknown conserved protein in bacilli [Bacillus halodurans] Identities = 59/194 (30%), Positives = 93/194 (47%), Gaps = 11/194 (5%) Query: 17 SKWMRASAALFDLLVFNLLFVL-SCLPLLTIGV--AKMALYASLLDWREGQVS-QLVTTY 72 - +K M+ + L+ NLL++L S + + +GV A +L+A W + + L TY Sbjct: 8 TKIMKLFEWIMRLVYLNLLWLLFSFIGGIILGVMPATASLFAVFRKWYQKEDDFPLFQTY 67 Query: 73 SSHFKYYFKSGLRLGLIELGIMTICLLDLFLIRNQSGLVFQGFKVLCVAVLFLVVILFLY 132- + FK FK +GL + I I LD+ L+ S + Q + A+ F+ ++ LY Sbjct: 68 LNEFKRSFKIANLVGLTLVLIGGILYLDVLLLLGTSHWIGQLLLMGVGALSFIYLVTLLY 127- Query: 133 AYPQAVKRDLSLSTLFKRSFLLAGLFFPWSFAFLAFICLTIFSLQL----SLLTLFGGVS 18- 8 +P V DLS FK SFLL G+ P+ L I L++ +L LL LF S Sbjct: 128 IFPTLVHFDLSYKQYFKHSFLL-GVLQPFR-TLLLMITLSLSALLFLTFPILLPLF-AAS 18- 4 Query: 189 LLAIIGISSLTYLY 202 +A + + S + Y Sbjct: 185 FMAALTMWSFLFGY 198 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00915 Identities = 68/210 (32%), Positives = 117/210 (55%) Query: 3 KANQLIAAIFDVNNPFMQGCNVVFDLALLNLLFMITCLPLVTIGAAKISLYRTLWQKLEG 62- K L+ ++F +++ +M+ +FDL + NLLF+++CLPL+TIG AK++LY +L EG Sbjct: 4 KKQGLLHSLFKLDSKWMRASAALFDLLVFNLLFVLSCLPLLTIGVAKMALYASLLDWREG 63- Query: 63 DQTNLLILYIKHLKKEWFQGMLLGLVELSILVVIIFDLTILHYQIGFIVSFLKITCYAFL 12- 2 + L+ Y H K + G+ LGL+EL I+ + + DL ++ Q G + K+ C A L Sbjct: 64 QVSQLVTTYSSHFKYYFKSGLRLGLIELGIMTICLLDLFLIRNQSGLVFQGFKVLCVAVL 12- 3 Query: 123 LLTVMTSIYLFPMAARYEMSLLDTVKKSFIMACLNLKWTGVLMFLLIMTWFIMVQSSLLF 18- 2 L V+ +Y +P A + ++SL K+SF++A L W+ + + +T F + S L Sbjct: 124 FLVVILFLYAYPQAVKRDLSLSTLFKRSFLLAGLFFPWSFAFLAFICLTIFSLQLSLLTL 18- 3 Query: 183 MLTVSAIFIFAYTAFAYFKIIILQKQFAYF 212 VS + I ++ Y +II++ F Sbjct: 184 FGGVSLLAIIGISSLTYLYLIIMESLLRRF 213 A related GBS gene <SEQ ID 8535> and protein <SEQ ID 8536> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00916 Lipop: Possible site: -1 Crend: 2 McG: Discrim Score: 3.27 GvH: Signal Score (-7.5): -4.23 Possible site: 46 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 5 value: -9.45 threshold: 0.0 INTEGRAL Likelihood = -9.45 Transmembrane 82-98 (79-111) INTEGRAL Likelihood = -6.85 Transmembrane 24-40 (21-52) INTEGRAL Likelihood = -5.26 Transmembrane 180-196 (172-200) INTEGRAL Likelihood = -5.10 Transmembrane 160-176 (158-179) INTEGRAL Likelihood = -4.35 Transmembrane 110-126 (106-130) PERIPHERAL Likelihood = 5.89 142 modified ALOM score: 2.39 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4779 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: ##STR00021## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 290 A DNA sequence (GBSx0318) was identified in S. agalactiae <SEQ ID 933> which encodes the amino acid sequence <SEQ ID 934>. Analysis of this protein sequence reveals the following: TABLE-US-00917 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1827 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00918 >GP: AAC44392 GB: U43526 ORF-1 [Streptococcus pneumoniae] Identities = 48/151 (31%), Positives = 66/151 (42%), Gaps = 5/151 (3%) Query: 1 MIYDHLLNLTHYKDINPNLDLAIDYLLSHDLRNLDIGTYHISPEVILMVQSNQLSES-FD 59 MI + L Y +NP+ ID+L L NL G+ I + L++ Sbjct: 1 MIITKISRLGTYVGVNPHFATLIDFLEKTGLENLTEGSIAIDGNRLFGNCFTYLADGQAG 60 Query: 60 HIFEYHKKYLDIHYVIEGHEVIKLGKGDKVEV-EEY--LGDIGFIKCSEETSFDLRDNYI 116- FE H+KYLDIH V+E E + + + V V +EY DI E LR Sbjct: 61 AFFETHQKYLDIHLVLENEEAMAVTSPENVSVTQEYDEEKDIELYTGKVEQLVHLRAGEC 120- Query: 117 AFFFPEEAHQPNGMGSLGNYVKKGVLKVLMA 147 FPE+ HQP + VKK V KV ++ Sbjct: 121 LITFPEDLHQPK-VRINDEPVKKVVFKVAIS 150 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 291 A DNA sequence (GBSx0319) was identified in S. agalactiae <SEQ ID 935> which encodes the amino acid sequence <SEQ ID 936>. This protein is predicted to be sugar ABC transporter, permease protein (araQ). Analysis of this protein sequence reveals the following: TABLE-US-00919 Possible site: 35 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.38 Transmembrane 245-261 (239-265) INTEGRAL Likelihood = -3.72 Transmembrane 140-156 (139-158) INTEGRAL Likelihood = -3.61 Transmembrane 76-92 (71-94) INTEGRAL Likelihood = -2.81 Transmembrane 112-128 (107-128) INTEGRAL Likelihood = -1.59 Transmembrane 188-204 (186-204) ----- Final Results ----- bacterial membrane --- Certainty = 0.3951(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00920 >GP: AAD35515 GB: AE001721 sugar ABC transporter, permease protein [Thermotoga maritima] Identities = 94/262 (35%), Positives = 158/262 (59%), Gaps = 1/262 (0%) Query: 15 LILCLLTVLFIFPFYWIMTGAFKSQPDTIIIPPQWWPKAPTLENFKALTVQNPALRWLWN 74 - + + + V+F+ P ++ + +FK + PP +PK P+LE + + + L +L N Sbjct: 9 IFIVFMLVVFMLPVFYAVVSSFKPMSEIYSYPPTIFPKKPSLEGYINVIKEYDLLTYLRN 68 Query: 75 SVFISIMTMFLVCCTSSMAGYVLAKKRFYGQKILFSLFIAAMALPKQVVLVPLVRIINFM 134- ++F++ + + S M GY LAK +F+G + + S+F M + QV++VPL +I + Sbjct: 69 TLFVATVATVITVLVSVMTGYGLAKGKFWGIRPVNSMFTMTMFVSAQVIMVPLFVVIRSL 128- Query: 135 GIHDTLWAVILPLVGWPFGVFLMKQFSENIPTELLESAKIDGCGEIRTFINVAFPIVKPG 19- 4 G+ ++LW +I+P V P G+F+ Q+ ++IP ELLESAKIDG E + F + FP+ KP Sbjct: 129 GLINSLWGLIIPAVYTPTGMFMAVQYMKDIPDELLESAKIDGANEWQIFWRIVFPLSKPL 18- 8 Query: 195 FAALAIFTFINTWNDYFMQLVMLTSRNNLTISLGVATMQAEM-ATNYGLIMAGAALAAVP 25- 3 AALAIF+F WND+ + L+++ RN T+ L +AT+Q E + I+A + L +P Sbjct: 189 VAALAIFSFTWRWNDFVLPLLVVNRRNLYTLQLALATIQEEYGGAEWNTILAFSTLTIIP 24- 8 Query: 254 IVTVFLVFQKSFTQGITMGAVK 275 + +FL+FQ+ F +GI G +K Sbjct: 249 TLIIFLLFQRLFMKGIMAGGLK 270 A related DNA sequence was identified in S. pyogenes <SEQ ID 937> which encodes the amino acid sequence <SEQ ID 938>. Analysis of this protein sequence reveals the following: TABLE-US-00921 Possible site: 40 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.37 Transmembrane 245-261 (240-265) INTEGRAL Likelihood = -5.15 Transmembrane 140-156 (139-158) INTEGRAL Likelihood = -2.97 Transmembrane 111-127 (107-128) INTEGRAL Likelihood = -2.87 Transmembrane 76-92 (75-93) INTEGRAL Likelihood = -1.59 Transmembrane 188-204 (186-204) ----- Final Results ----- bacterial membrane --- Certainty = 0.3548(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00922 >GP: CAB59597 GB: AL132662 probable sugar transport inner membrane protein [Streptomyces coelicolor A3(2)] Identities = 88/262 (33%), Positives = 147/262 (55%) Query: 15 VMLCVLTILFIFPFYWIMTGAFKAQADTIMIPPQWWPKAPTIENFKALVVQNPALKWLWN 74 - ++L L ++F P W++ + + A+ PP WP + ++ ++ +W N Sbjct: 38 LLLAPLALVFAVPLVWLVLSSVMSNAEINRFPPALWPSGIDLGGYRYVLGNAMFPRWFVN 97 Query: 75 SVFISVATMFLVCGTSSLAGYALAKKRFYGQRLLFSIFIAAMALPKQVVLVPLVRIVNFM 134- S+ +S T+ SLAGYA A+ RF G R+L + +A MA+P Q+ ++P ++ + Sbjct: 98 SLIVSAVTVAANLVFGSLAGYAFARMRFAGSRVLMGLMLATMAVPFQLTMIPTFLVMKKL 157- Query: 135 GIHDTLAAVILPLVGWPFGVFLMKQFSENIPTELLESAKIDGCGEIRTFFNVAFPIVKPG 19- 4 G+ DTL A+I+P + PF VFL++QF ++P EL E+A IDGC +R + + P+ +P Sbjct: 158 GLIDTLGALIVPSLVTPFAVFLLRQFFLSLPRELEEAAWIDGCSRLRVLWRIVLPLSRPA 21- 7 Query: 195 FAALAIFTFINTWNDYFMQLVMLTSRENLTISLGVATMQAEMATNYGLIMAGAAMAAVPI 25- 4 A +A+ TF+ TWND L+ + T+ LG+ T Q + T + +MAG + +P+ Sbjct: 218 LATVAVLTFLTTWNDLTWPLIAINHDTQYTLQLGLTTFQGQHHTQWAAVMAGNVITVLPV 27- 7 Query: 255 VTVFLVFQKSFTQGITMGAVKG 276 + FL QK+F Q IT +KG Sbjct: 278 LLAFLGAQKTFIQSITSSGLKG 299 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00923 Identities = 245/276 (88%), Positives = 262/276 (94%) Query: 1 MKKKTFSAYNFLTALILCLLTVLFIFPFYWIMTGAFKSQPDTIIIPPQWWPKAPTLENFK 60 M KK +A + LT ++LC+LT+LFIFPFYWIMTGAFK+Q DTI+IPPQWWPKAPT+ENFK Sbjct: 1 MTKKKLTASDILTTVMLCVLTILFIFPFYWIMTGAFKAQADTIMIPPQWWPKAPTIENFK 60 Query: 61 ALTVQNPALRWLWNSVFISIMTMFLVCCTSSMAGYVLAKKRFYGQKILFSLFIAAMALPK 120- AL VQNPAL+WLWNSVFIS+ TMFLVC TSS+AGY LAKKRFYGQ++LFS+FIAAMALPK Sbjct: 61 ALVVQNPALKWLWNSVFISVATMFLVCGTSSLAGYALAKKRFYGQRLLFSIFIAAMALPK 120- Query: 121 QVVLVPLVRIINFMGIHDTLWAVILPLVGWPFGVFLMKQFSENIPTELLESAKIDGCGEI 18- 0 QVVLVPLVRI+NFMGIHDTL AVILPLVGWPFGVFLMKQFSENIPTELLESAKIDGCGEI Sbjct: 121 QVVLVPLVRIVNFMGIHDTLAAVILPLVGWPFGVFLMKQFSENIPTELLESAKIDGCGEI 18- 0 Query: 181 RTFINVAFPIVKPGFAALAIFTFINTWNDYFMQLVMLTSRNNLTISLGVATMQAEMATNY 24- 0 RTF NVAFPIVKPGFAALAIFTFINTWNDYFMQLVMLTSR NLTISLGVATMQAEMATNY Sbjct: 181 RTFFNVAFPIVKPGFAALAIFTFINTWNDYFMQLVMLTSRENLTISLGVATMQAEMATNY 24- 0 Query: 241 GLIMAGAALAAVPIVTVFLVFQKSFTQGITMGAVKG 276 GLIMAGAA+AAVPIVTVFLVFQKSFTQGITMGAVKG Sbjct: 241 GLIMAGAAMAAVPIVTVFLVFQKSFTQGITMGAVKG 276 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 292 A DNA sequence (GBSx0320) was identified in S. agalactiae <SEQ ID 939> which encodes the amino acid sequence <SEQ ID 940>. Analysis of this protein sequence reveals the following: TABLE-US-00924 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.83 Transmembrane 74-90 (64-96) INTEGRAL Likelihood = -6.37 Transmembrane 108-124 (107-126) INTEGRAL Likelihood = -5.84 Transmembrane 270-286 (265-290) INTEGRAL Likelihood = -5.20 Transmembrane 161-177 (156-182) INTEGRAL Likelihood = -0.16 Transmembrane 219-235 (219-235) ----- Final Results ----- bacterial membrane --- Certainty = 0.5331(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00925 >GP: BAB05584 GB: AP001513 sugar transport system (permease) (binding protein dependent transporter) [Bacillus halodurans] Identities = 106/289 (36%), Positives = 168/289 (57%), Gaps = 6/289 (2%) Query: 9 RETMIAYAFLAPILLFFLIFVFAPMVMGFVTSFFNYSM-TQFTFIGLANYNRMF-HDSIF 66 +E Y F+AP ++ F IF PM+ SF ++ + + + G NY R+F D +F Sbjct: 25 KEYFWGYLFIAPPIIGFAIFALGPMLYSIYVSFTDFDLYNEPVWTGADNYYRLFVTDDLF 84 Query: 67 MKSLINTVIIVIGSVPVVVFFSLFVAANTYEKNVFSRSFYRCVFFLPVVTGSVAVTVVWK 126- K++ NT +G +P+ + SL +A +K V + +R FFLP V+ VA+T++W+ Sbjct: 85 RKTVFNTFYAALG-IPIGMAVSLGIAVALNQK-VKGIALFRTAFFLPAVSSVVAITLLWR 142- Query: 127 WIYDPMSGILNYILKSGHVIEQNISWLGDKHWALLAIIIILLTTSVGQPIILYIAAMGNI 18- 6 WI++ G+LN +L +V WL D+ WA+ A+II + +G +ILY+AA+ + Sbjct: 143 WIFNADFGLLNIMLN--YVGIHGPGWLSDEKWAMPAMIIQGVWGGLGINMILYLAALQGV 20- 0 Query: 187 DNSLCEAARVDGANEMQVFWQIKWPSLLPTTLYIAVITTINSFQCFALIQLLTSGGPNYS 24- 6 + +L EAA +DG N Q F I PS+ PTT +I + +TI + Q F ++T GGPNYS Sbjct: 201 NPALYEAADIDGGNAWQKFIHITVPSISPTTFFILITSTIGALQDFQRFMIMTEGGPNYS 26- 0 Query: 247 TSTLMYYLYEKAFKLSEYGYANTMGVFLAVMIALISFAQFKILGNDVEY 295 T+T++YYL+ AF+ E GYA+ M L ++I +I+ FK+ V Y Sbjct: 261 TTTVVYYLFLNAFRYMEMGYASAMAWVLGIIILIITIINFKLAKKWVHY 309 A related DNA sequence was identified in S. pyogenes <SEQ ID 941> which encodes the amino acid sequence <SEQ ID 942>. Analysis of this protein sequence reveals the following: TABLE-US-00926 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.74 Transmembrane 55-71 (44-78) INTEGRAL Likelihood = -10.83 Transmembrane 109-125 (98-130) INTEGRAL Likelihood = -6.21 Transmembrane 304-320 (299-324) INTEGRAL Likelihood = -6.00 Transmembrane 142-158 (141-160) INTEGRAL Likelihood = -5.04 Transmembrane 196-212 (190-216) INTEGRAL Likelihood = -0.16 Transmembrane 253-269 (253-269) ----- Final Results ----- bacterial membrane --- Certainty = 0.6095(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00927 >GP: BAB05584 GB: AP001513 sugar transport system (permease) (binding protein dependent transporter) [Bacillus halodurans] Identities = 113/310 (36%), Positives = 176/310 (56%), Gaps = 9/310 (2%) Query: 25 KVEQKKEVFQVNVNKLKMR---ETLISYAFLAPVLVFFVIFVLIPMIMGFVTSFFNYSM- 80 - +VE +E K K R E Y F+AP ++ F IF L PM+ SF ++ + Sbjct: 4 EVETPRETKTTKARKQKRRLNKEYFWGYLFIAPPIIGFAIFALGPMLYSIYVSFTDFDLY 63 Query: 81 TEFTFVGFANYARMF-QDPIFMKSLINTLIIVIGSVPVVVFFSLFVAAKTYDKNVVARSF 139- E + G NY R+F D +F K++ NT +G +P+ + SL +A K V + Sbjct: 64 NEPVWTGADNYYRLFVTDDLFRKTVFNTFYAALG-IPIGMAVSLGIAVALNQK-VKGIAL 121- Query: 140 YRAVFFLPVVTGSVAVTVVWKWIYDPMSGILNYVLKYAHVIEQNISWLGDKHWALLAIIV 19- 9 +R FFLP V+ VA+T++W+WI++ G+LN +L Y + WL D+ WA+ A+I+ Sbjct: 122 FRTAFFLPAVSSVVAITLLWRWIFNADFGLLNIMLNYVGI--HGPGWLSDEKWAMPAMII 17- 9 Query: 200 ILLTTSVGQPIILYIAAMGNIDNSLVEAARVDGATEFQVFWNIKWPSLLPTTLYIAVITT 25- 9 + +G +ILY+AA+ ++ +L EAA +DG +Q F +I PS+ PTT +I + +T Sbjct: 180 QGVWGGLGINMILYLAALQGVNPALYEAADIDGGNAWQKFIHITVPSISPTTFFILITST 23- 9 Query: 260 INSFQCFALIQLLTSGGPNYSTSTLMYYLYEKAFKLSEYGYANTMGVFLAVMIAIISFAQ 31- 9 I + Q F ++T GGPNYST+T++YYL+ AF+ E GYA+ M L ++I II+ Sbjct: 240 IGALQDFQRFMIMTEGGPNYSTTTVVYYLFLNAFRYMEMGYASAMAWVLGIIILIITIIN 29- 9 Query: 320 FKILGNDVEY 329 FK+ V Y Sbjct: 300 FKLAKKWVHY 309 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00928 Identities = 263/295 (89%), Positives = 278/295 (94%) Query: 1 MRTNKLKMRETMIAYAFLAPILLFFLIFVFAPMVMGFVTSFFNYSMTQFTFIGLANYNRM 60- + NKLKMRET+I+YAFLAP+L+FF+IFV PM+MGFVTSFFNYSMT+FTF+G ANY RM Sbjct: 35 VNVNKLRMRETLISYAFLAPVLVFFVIFVLIPMIMGFVTSFFNYSMTEFTFVGFANYARM 94- Query: 61 FHDSIFMKSLINTVIIVIGSVPVVVFFSLFVAANTYEKNVFSRSFYRCVFFLPVVTGSVA 12- 0 F D IFMKSLINT+IIVIGSVPVVVFFSLFVAA TY+KNV +RSFYR VFFLPVVTGSVA Sbjct: 95 FQDPIFMKSLINTLIIVIGSVPVVVFFSLFVAAKTYDKNVVARSFYRAVFFLPVVTGSVA 15- 4 Query: 121 VTVVWKWIYDPMSGILNYILKSGHVIEQNISWLGDKHWALLAIIIILLTTSVGQPIILYI 18- 0 VTVVWKWIYDPMSGILNY+LK HVIEQNISWLGDKHWALLAII+ILLTTSVGQPIILYI Sbjct: 155 VTVVWKWIYDPMSGILNYVLKYAHVIEQNISWLGDKHWALLAIIVILLTTSVGQPIILYI 21- 4 Query: 181 AAMGNIDNSLCEAARVDGANEMQVFWQIKWPSLLPTTLYIAVITTINSFQCFALIQLLTS 24- 0 AAMGNIDNSL EAARVDGA E QVFW IKWPSLLPTTLYIAVITTINSFQCFALIQLLTS Sbjct: 215 AAMGNIDNSLVEAARVDGATEFQVFWNIKWPSLLPTTLYIAVITTINSFQCFALIQLLTS 27- 4 Query: 241 GGPNYSTSTLMYYLYEKAFKLSEYGYANTMGVFLAVMIALISFAQFKILGNDVEY 295 GGPNYSTSTLMYYLYEKAFKLSEYGYANTMGVFLAVMIA+ISFAQFKILGNDVEY Sbjct: 275 GGPNYSTSTLMYYLYEKAFKLSEYGYANTMGVFLAVMIAIISFAQFKILGNDVEY 329 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 293 A DNA sequence (GBSx0321) was identified in S. agalactiae <SEQ ID 943> which encodes the amino acid sequence <SEQ ID 944>. Analysis of this protein sequence reveals the following:

TABLE-US-00929 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00930 >GP:CAB12516 GB:Z99107 similar to sugar-binding protein [Bacillus subtilis] Identities = 54/187 (28%), Positives = 90/187 (47%), Gaps = 14/187 (7%) Query: 19 MFACVDSSQSVMAAEKD-KVEITWWAFPTFTQEKAKDGVGTYEKKVIKAFEKKNPNIKVK 77- MF+ + + ++D + I WW + D Y KVI+ +EKKNP++ ++ Sbjct: 1 MFSGCSAGEEASGKKEDVTLRIAWWG-----GQPRHD----YTTKVIELYEKKNPHVHIE 51- Query: 78 LETIDFTSGPEKITTAIEAGTAPDVLFDAPGRIIQYGKNGKLADLNDLFTDQFIKDVN-- 13- 5 E ++ +K+ AG PDV+ + QYGK +L DL D I DV+ Sbjct: 52 AEFANWDDYWKKLAPMSAAGQLPDVIQMDTAYLAQYGKKNQLEDLTPYTKDGTI-DVSSI 11- 0 Query: 136 NKNIIQASKSGDKAYMYPISSAPFYMAFNKKMLKDAGVLKLVKEGWTTSDFEKVLKALKN 19- 5 ++N++ K +K Y + + + N+ +LK AGV + +E WT D+EK+ L+ Sbjct: 111 DENMLSGGKIDNKLYGFTLGVNVLSVIANEDLLKKAGV-SINQENWTWEDYEKLAYDLQE 16- 9 Query: 196 KGYTPGS 202 K GS Sbjct: 170 KAGVYGS 176 A related DNA sequence was identified in S. pyogenes <SEQ ID 945> which encodes the amino acid sequence <SEQ ID 946>. Analysis of this protein sequence reveals the following: TABLE-US-00931 Possible site: 20 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: TABLE-US-00932 !GB:Z99107 similar to sugarbinding protein [Bacillu. . . 82 2e-14 >GP:CAB12516 GB:Z99107 similar to sugar-binding protein [Bacillus subtilis] Identities = 105/446 (23%), Positives = 176/446 (38%), Gaps = 71/446 (15%) Query: 24 GKSQKEAGASKSDTAKTEITWWAFPVFTQEKAEDGVGTYEKKLIAAFEKANPEIKVKLET 83- G S E + K + I WW + D Y K+I +EK NP + ++ E Sbjct: 4 GCSAGEEASGKKEDVTLRIAWWG-----GQPRHD----YTTKVIELYEKKNPHVHIEAEF 54- Query: 84 IDFTSGPEKITTAIEAGTAPDVLFDAPGRIIQYGKNGKLADLNDLFTEEFTKDVN--NDK 14- 1 ++ +K+ AG PDV+ + QYGK +L DL +T++ T DV+ ++ Sbjct: 55 ANWDDYWKKLAPMSAAGQLPDVIQMDTAYLAQYGKKNQLEDLTP-YTKDGTIDVSSIDEN 11- 3 Query: 142 LIQASKAGDTAYMYPISSAPFYMALNKKMLKDAGVLDLVKEGWTTDDFEKVLKALKDK-- 19- 9 ++ K + Y + + + N+ +LK AGV + +E WT +D+EK+ L++K Sbjct: 114 MLSGGKIDNKLYGFTLGVNVLSVIANEDLLKKAGV-SINQENWTWEDYEKLAYDLQEKAG 17- 2 Query: 200 -----GYNPGSFFANGQGGDQGPRAFFANLYSSHITDDKV---------------TKYTT 23- 9 G +P F +G R+ + DD++ T T Sbjct: 173 VYGSNGMHPPDIFFPYYLRTKGERFYKEDGTGLAYQDDQLFVDYFERQLRLVKAKTSPTP 23- 2 Query: 240 DDANSIKAMTKISNWIKDGLMMNGSQYDGSADIQNFANGQTSFTILWAPAQPGIQAKLLE 29- 9 D++ IK M +D ++ G SA N++N F A+L+ Sbjct: 233 DESAQIKGM-------EDDFIVKGK----SAITWNYSNQYLGF------------ARLTD 26- 9 Query: 300 ASKVDYLEIPFPSDDGKPELEYLVNGFAVFNNKDEQKVAASKTFIQFIADDKEWGPKNVV 35- 9 + YL P + L + E K A+K FI F +++E + + Sbjct: 270 SPLSLYLP---PEQMQEKALTLKPSMLFSIPKSSEHKKEAAK-FINFFVNNEE-ANQLIK 32- 4 Query: 360 RTGAFPVRTSYGDLYKDKRMEK---IAEWTKFYSPYYNTID-----GFAEMRTLWFPMVQ 41- 1 PV D K K E+ I E+ + S + D G AE+ L Sbjct: 325 GERGVPVSDKVADAIKPKLNEEETNIVEYVETASKNISKADPPEPVGSAEVIKLLKDTSD 38- 4 Query: 412 AVSNGDEKPEDALKAFTEKANKTIKK 437 + PE A K F +KAN+ +++ Sbjct: 385 QILYQKVSPEKAAKTFRKKANEILER 410 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00933 Identities = 352/438 (80%), Positives = 384/438 (87%), Gaps = 4/438 (0%) Query: 1 MSIKKSVIGFCLGAAALSMFACVDSSQSVMAAEKD---KVEITWWAFPTFTQEKAKDGVG 57- M++KK LGA+ L + AC SQ A K K EITWWAFP FTQEKA+DGVG Sbjct: 1 MNMKKLASLAMLGASVLGLAACGGKSQKEAGASKSDTAKTEITWWAFPVFTQEKAEDGVG 60- Query: 58 TYEKKVIKAFEKKNPNIKVKLETIDFTSGPEKITTAIEAGTAPDVLFDAPGRIIQYGKNG 11- 7 TYEKK+I AFEK NP IKVKLETIDFTSGPEKITTAIEAGTAPDVLFDAPGRIIQYGKNG Sbjct: 61 TYEKKLIAAFEKANPEIKVKLETIDFTSGPEKITTAIEAGTAPDVLFDAPGRIIQYGKNG 12- 0 Query: 118 KLADLNDLFTDQFIKDVNNKNIIQASKSGDKAYMYPISSAPFYMAFNKKMLKDAGVLKLV 17- 7 KLADLNDLFT++F KDVUN +IQASK+GD AYMYPISSAPFYMA NKKMLKDAGVL LV Sbjct: 121 KLADLNDLFTEEFTKDVNNDKLIQASKAGDTAYMYPISSAPFYMALNKKMLKDAGVLDLV 18- 0 Query: 178 KEGWTTSDFEKVLKALKNKGYTPGSFFANGQGGDQGPRAFFANLYSAPITDKEVTKYTTD 23- 7 KEGWTT DFEKVLKALK+KGY PGSFFANGQGGDQGPRAFFANLYS+ ITD +VTKYTTD Sbjct: 181 KEGWTTDDFEKVLKALKDKGYNPGSFFANGQGGDQGPRAFFANLYSSHITDDKVTKYTTD 24- 0 Query: 238 TKNSVKSMKKIVEWIKKGYLMNGSQYDGSADIQNFANGQTAFTILWAPAQPKTQAKLLES 29- 7 NS+K+M KI WIK G +MNGSQYDGSADIQNFANGQT+FTILWAPAQP QAKLLE+ Sbjct: 241 DANSIKANTKISNWIKDGLMNNGSQYDGSADIQNFANGQTSFTILWAPAQPGIQAKLLEA 30- 0 Query: 298 SKVDYLEVPFPSEDGKPDLEYLVNGFAVFNNKDENKVKASKKFITFIADDKKWGPKDVIR 35- 7 SKVDYLE+PFPS+DGKP+LEYLVNGFAVFNNKDE KV ASK FI FIADDK+WGPK+V+R Sbjct: 301 SKVDYLEIPFPSDDGKPELEYLVNGFAVFNNKDEQKVAASKTFIQFIADDKEWGPKNVVR 36- 0 Query: 358 TGAFPVRTSFGDLYKGDKRNNKISKWTQYYSPYYNTIDGFSEMRTLWFPNVQSVSNGDEK 41- 7 TGAFPVRTS+GDLYK DKRN KI++WT++YSPYYNTIDGF+EMRTLWFPNVQ+VSNGDEK Sbjct: 361 TGAFPVRTSYGDLYK-DKRNEKIAEWTKFYSPYYNTIDGFAEMRTLWFPMVQAVSNGDEK 41- 9 Query: 418 PADALKDFTQKANDTIKK 435 P DALK FT+KAN TIKK Sbjct: 420 PEDALKAFTEKANKTIKK 437 A related GBS gene <SEQ ID 8537> and protein <SEQ ID 8538> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00934 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 5.05 GvH: Signal Score (-7.5): 4.69 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 7.69 threshold: 0.0 PERIPHERAL Likelihood = 7.69 90 modified ALOM score: -2.04 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00022## SEQ ID 944 (GBS16) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 3 (lane 9; MW 49 kDa). The GBS16-His fusion product was purified (FIG. 92A; see also FIG. 189, lane 9) and used to immunise mice (lane 1+2 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 92B), FACS (FIG. 92C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 294 A DNA sequence (GBSx0322) was identified in S. agalactiae <SEQ ID 947> which encodes the amino acid sequence <SEQ ID 948>. Analysis of this protein sequence reveals the following: TABLE-US-00935 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9459> which encodes amino acid sequence <SEQ ID 9460> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00936 >GP:AAC66999 GB:AE001166 conserved hypothetical protein [Borrelia burgdorferi] Identities = 107/225 (47%), Positives = 147/225 (64%), Gaps = 6/225 (2%) Query: 12 QIKNGIIVSCQALPGEPLYTESGGVMPLLALAAQEAGAVGIRANSVRDIKEIQEVTNLPI 71 - +IK G+IVSCQAL EPL+ S +M +ALAA+ GA+GIRAN V DI +I+ +LPI Sbjct: 6 KIKRGLIVSCQALENEPLH--SSFIMSKMALAAKIGGAIGIRANGVNDISQIKLEVDLPI 63 Query: 72 IGIIKREYPPQEPFITATMTEVDQLASLDIAVIALDCTLRERHDGLSVVEFIQKIKRKYP 131- IGIIK+ Y + FIT TM E+D+L + + +IALD T R R DG+ + +F + IK+KYP Sbjct: 64 IGIIKKNYNNCDVFITPTMKEIDELCNEGVDIIALDATFRNRPDGVLLDDFFENIKKKYP 123- Query: 132 EQLLMADISTFEEGKNAFEAGVDFVGTTLSGYTDYSR--QEEGPDIELLNKLCQAGI--D 18- 7 +Q LMADIS+ +E NA + G DF+GTTL GYT + D L L + + Sbjct: 124 KQCLMADISSLDEAINADKLGFDFIGTTLYGYTKNTNGLNIADNDFNFLRTLLNSNLKST 18- 3 Query: 188 VIAEGKIHTPKQANEINHIGVAGIVVGGAITRPKEIAERFISGLS 232 +I EGKI TP +A + +GV +VVGGAITRP EI ++F+ ++ Sbjct: 184 LIVEGKIDTPLKAQKCFEMGVDLVVVGGAITRPAEITKKFVEKIN 228 A related DNA sequence was identified in S. pyogenes <SEQ ID 949> which encodes the amino acid sequence <SEQ ID 950>. Analysis of this protein sequence reveals the following: TABLE-US-00937 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.49 Transmembrane 175-191 (175-192) ----- Final Results ----- bacterial membrane --- Certainty = 0.1595 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00938 >GP:AAD28762 GB:AF130859 putative N-acetylmannosamine-6-P epimerase [Clostridium perfringens] Identities = 113/225 (50%), Positives = 148/225 (65%), Gaps = 5/225 (2%) Query: 10 LMEQLKGGIIVSCQALPGEPLYSETGGIMPLMAKAAQEAGAVGIRANSVRDIKEIQAITD 69 - +++ +KG +IVSCQAL EPL+S IM MA AA++ GA IRA + DI EI+ +T Sbjct: 1 MLDVVKGNLIVSCQALSDEPLHSSF--IMGRMAIAAKQGGAAAIRAQGIDDINEIKEVTK 58 Query: 70 LPIIGIIKKDYPPQEPFITATMTEVDQLAALNIAVIAMDCTKRDRHDGLDIASFIRQVKE 129- LPIIGIIK++Y E +IT TM EVD+L + +I +D TKR R +G +I + + Sbjct: 59 LPIIGIIKRNYDDSEIYITPTMKEVDELLKTDCEMIGLDATKRKRPNGENIKDLVDAIHA 118- Query: 130 KYPNQLLMADISTFDEGLVAHQAGIDFVGTTLSGYTPYSRQEAGPDVALIEALCK-AGIA 18- 8 K +L MADIST +EG+ A + G D V TTLSGYTPYS+Q D L+E L K I Sbjct: 119 K--GRLAMADISTLEEGIEAEKLGFDCVSTTLSGYTPYSKQSNSVDFELLEELVKTVKIP 17- 6 Query: 189 VIAEGKIHSPEEAKKINDLGVAGIVVGGAITRPKEIAERFIEALK 233 VI EG+I++PEE KK DLG VVGGAITRP++I +RF + LK Sbjct: 177 VICEGRINTPEELKKALDLGAYSAVVGGAITRPQQITKRFTDILK 221 An alignment of the GAS and GBS proteins is shown below: TABLE-US-00939 Identities = 172/227 (75%), Positives = 202/227 (88%) Query: 5 SKEAFKKQIKNGIIVSCQALPGEPLYTESGGVMPLLALAAQEAGAVGIRANSVRDIKEIQ 64 +KE +Q+K GIIVSCQALPGEPLY+E+GG+MPL+A AAQEAGAVGIRANSVRDIKEIQ Sbjct: 6 TKEKLMEQLKGGIIVSCQALPGEPLYSETGGIMPLMAKAAQEAGAVGIRANSVRDIKEIQ 65 Query: 65 EVTNLPIIGIIKREYPPQEPFITATMTEVDQLASLDIAVIALDCTLRERHDGLSVVEFIQ 124- +T+LPIIGIIK++YPPQEPFITATMTEVDQLA+L+IAVIA+DCT R+RHDGL + FI+ Sbjct: 66 AITDLPIIGIIKKDYPPQEPFITATMTEVDQLAALNIAVIAMDCTKRDRHDGLDIASFIR 125- Query: 125 KIKRKYPEQLLMADISTFEEGKNAFEAGVDFVGTTLSGYTDYSRQEEGPDIELLNKLCQA 18- 4 ++K KYP QLLMADISTF+EG A +AG+DFVGTTLSGYT YSRQE GPD+ L+ LC+A Sbjct: 126 QVKEKYPNQLLMADISTFDEGLVAHQAGIDFVGTTLSGYTPYSRQEAGPDVALIEALCKA 18- 5 Query: 185 GIDVIAEGKIHTPKQANEINHIGVAGIVVGGAITRPKEIAERFISGL 231 GI VIAEGKIH+P++A +IN +GVAGIVVGGAITRPKEIAERFI L Sbjct: 186 GIAVIAEGKIHSPEEAKKINDLGVAGIVVGGAITRPKEIAERFIEAL 232 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 295 A DNA sequence (GBSx0323) was identified in S. agalactiae <SEQ ID 951> which encodes the amino acid sequence <SEQ ID 952>. This protein is predicted to be group B streptococcal surface immunogenic protein. Analysis of this protein sequence reveals the following: TABLE-US-00940 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 953> which encodes the amino acid sequence <SEQ ID 954>. Analysis of this protein sequence reveals the following: TABLE-US-00941 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00942 Identities = 182/437 (41%), Positives = 240/437 (54%), Gaps = 53/437 (12%) Query: 1 MKMNKKVLLTSTMAASLLSVASVQAQETDTTWTARTVSEVKADLVKQDNKSSYTVKYGDT 60 M + KK L +++A SL+ +A+ QAQE WT R+V+E+K++LV DN +YTVKYGDT Sbjct: 1 MIITKKSLFVTSVALSLVPLATAQAQE----WTPRSVTEIKSELVLVDNVFTYTVKYGDT 56 Query: 61 LSVISEAMSIDMNVLAKINNIADINLIYPETTLTVTYDQKSHTATSMKIETPATNAAGQT 120- LS I+EAM ID++VL IN+IA+I+LI+P+T LT Y+Q AT++ ++ PA++ A + Sbjct: 57 LSTIAEAMGIDVHVLGDINHIANIDLIFPDTILTANYNQHGQ-ATNLTVQAPASSPASVS 115- Query: 121 TATVDLKTNQVSVADQKVSLNTISEGMTP-EAATTIVSPMKTYSSAPALKSKEVLAQEQA 17- 9 Q S Q ++ TP + TT + K SS A S E+ + Sbjct: 116 HVPSSEPLPQASATSQPTV--PMAPPATPSDVPTTPFASAKPDSSVTA--SSELTSSTND 17- 1 Query: 180 VSQAAANEQVSPAPVKSITSEVPAAKEEVKPTQTSVSQSTTVSPASVAAETPAPVAKVAP 23- 9 VS ++E V P A E T V T +S A +A P P + Sbjct: 172 VSTELSSESQKQPEVPQEAVPTPKAAE-----TTEVEPKTDISEAPTSANRPVPNESASE 22- 6 Query: 240 VRTVAAPRVASVKVVTPKVETGASPEHVSAPAVP---VTTTSPATDSKLQATEVKSVPVA 29- 6 + AAP + A E SAPA TTS AT + L Sbjct: 227 EVSSAAP-----------AQAPAEKEETSAPAAQKAVADTTSVATSNGL----------- 26- 4 Query: 297 QKAPTATPVAQPASTTNAVAAHPENAGLQPHVAAYKEKVASTYGVNEFSTYRAGDPGDHG 35- 6 AP A +P NAGLQP AA+KE+VAS +G+ FS YR GDPGDHG Sbjct: 265 SYAPNH-------------AYNPMNAGLQPQTAAFKEEVASAFGITSFSGYRPGDPGDHG 31- 1 Query: 357 KGLAVDFIVGTNQALGNKVAQYSTQNMAANNISYVIWQQKFYSNTNSIYGPANTWNAMPD 41- 6 KGLA+DF+V N ALG++VAQY+ +MA ISYVIW+Q+FY+ SIYGPA TWN MPD Sbjct: 312 KGLAIDFMVPENSALGDQVAQYAIDHMAERGISYVIWKQRFYAPFASIYGPAYTWNPMPD 37- 1 Query: 417 RGGVTANHYDHVHVSFN 433 RG +T NHYDHVHVSFN Sbjct: 372 RGSITENHYDHVHVSFN 388 A related GBS gene <SEQ ID 8539> and protein <SEQ ID 8540> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00943 Lipop: Possible site: -1 Crend: 3 SRCFLG: 0 McG: Length of UR: 20 Peak Value of UR: 1.96 Net Charge of CR: 2 McG: Discrim Score: 2.95 GvH: Signal Score (-7.5): 3.84 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 24 ALOM program count: 0 value: 4.29 threshold: 0.0 PERIPHERAL Likelihood = 4.29 58 modified ALOM score: -1.36 *** Reasoning Step: 3 Rule gpo1 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrame --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 8540 (GBS322) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 77 (lane 9; MW 52 kDa). The GBS322-His fusion product was purified (FIG. 214, lane 10) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 267), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 296 A DNA sequence (GBSx0324) was identified in S. agalactiae <SEQ ID 955> which encodes the amino acid sequence <SEQ ID 956>. Analysis of this protein sequence reveals the following: TABLE-US-00944 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.86 Transmembrane 5-21 (4-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.1744 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00945 >GP:AAC46072 GB:U50357 zoocin A endopeptidase [Streptococcus zooepidemicus] Identities = 163/274 (59%), Positives = 196/274 (71%), Gaps = 11/274 (4%) Query: 25 VLADTYVRPIDNGRITTGFNGYPGHCGVDYAVPTGTIIRAVADGTVKFAGAGANFSWMTD 84- V A TY RP+D G ITTGFNGYPGH GVDYAVP GT +RAVA+GTVKFAG GAN WM Sbjct: 21 VSAATYTRPLDTGNITTGFNGYPGHVGVDYAVPVGTPVRAVANGTVKFAGNGANHPWMLW 80- Query: 85 LAGNCVMIQHADGMHSGYAHMSRVVARTGEKVKQGDIIGYVGATGMATGPHLHFEFLPAN 14- 4 +AGNCV+IQHADGMH+GYAH+S++ T VKQG IIGY GATG TGPHLHFE LPAN Sbjct: 81 MAGNCVLIQHADGMHTGYAHLSKISVSTDSTVKQGQIIGYTGATGQVTGPHLHFEMLPAN 14- 0 Query: 145 PNFQNGFHGRINPTSLIANVATFSGKTQASAPSIKPLQSAPVQNQSSKLKVYRVDELQKV 20- 4 PN+QNGF GRI+PT IAN F+G T + P N LK+Y+VD+LQK+ Sbjct: 141 PNWQNGFSGRIDPTGYIANAPVFNGTTPTE-------PTTPTTN----LKIYKVDDLQKI 18- 9 Query: 205 NGVWLVKNNTLTPTGFDWNDNGIPASEIDEVDANGNLTADQVLQKGGYFIFNPKTLKTVE 26- 4 NG+W V+NN L PT F W DNGI A ++ EV +NG T+DQVLQKGGYF+ NP +K+V Sbjct: 190 NGIWQVRNNILVPTDFTWVDNGIAADDVIEVTSNGTRTSDQVLQKGGYFVINPNNVKSVG 24- 9 Query: 265 KPIQGTAGLTWAKTRFANGSSVWLRVDNSQELLY 298 P++G+ GL+WA+ F G +VWL + LLY Sbjct: 250 TPMKGSGGLSWAQVNFTTGGNVWLNTTSKDNLLY 283 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8541> and protein <SEQ ID 8542> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00946 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: 6.63 GvH: Signal Score (-7.5): -2.97 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -1.86 threshold: 0.0 INTEGRAL Likelihood = -1.86 Transmembrane 5-21 (4-21) PERIPHERAL Likelihood = 5.57 50 modified ALOM score: 0.87 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1744 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: ##STR00023## SEQ ID 8542 (GBS36) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 11 (lane 4; MW 34.1 kDa). GBS36-His was purified as shown in FIG. 192, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 297 A DNA sequence (GBSx0325) was identified in S. agalactiae <SEQ ID 957> which encodes the amino acid sequence <SEQ ID 958>. This protein is predicted to be phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohyd. Analysis of this protein sequence reveals the following:

TABLE-US-00947 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2815(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00948 >GP:BAB04352 GB:AP001509 phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase [Bacillus halodurans] Identities = 310/515 (60%), Positives = 390/515 (75%), Gaps = 4/515 (0%) Query: 1 MTKRALISVSDKSGIIDFAKELKNLGWDIISTGGTKVALDDAGVETIAIDDVTGFPEMMD 60- M +RAL+SVS+K GI+ FAK L +I+STGGTK AL +AG+ I DVTGFPE++D Sbjct: 1 MKRRALVSVSNREGIVPFAKALVEHEVEIVSTGGTKRALQEAGIPVTGISDVTGFPEILD 60- Query: 61 GRVKTLHPNIHGGLLARRDADSHLQAAKDNNIELIDLVVVNLYPFKETILRPDVTYDLAV 12- 0 GRVKTLHPNIHGGLLA R+ D HL +++I ID VVVNLYPF++TI +P+ T+ A+ Sbjct: 61 GRVKTLHPNIHGGLLAMRERDEHLAQLNEHHIRPIDFVVVNLYPFQQTIAKPEATFADAI 12- 0 Query: 121 ENIDIGGPSMLRSAAKNHASVTVVVDSADYATVLGELADASQTTFKTRQRLAAKAFRHTA 18- 0 ENIDIGGPSMLR+AAKNH VTVVVD DY TVL ELAD +T++RLAAK FRHTA Sbjct: 121 ENIDIGGPSMLRAAAKNHQHVTVVVDPVDYETVLKELADQGMVATETKRRLAAKVFRHTA 18- 0 Query: 181 AYDALIAEYFTAQVGEAKPEKLTITYDLKQAMRYGENPQQDADFYQKALPTDYSIASAKQ 24- 0 AYDA+IAEY T VGE PE LT+T++ KQ +RYGENP Q A FYQE L SIA AKQ Sbjct: 181 AYDAMIAEYLTDAVGEESPESLTVTFE-KQDLRYGENPHQKATFYQKPLGAKASIAHAKQ 24- 0 Query: 241 LNGKELSFNNIRDADAAIRIIRDFKDSPTVVALKHMNPCGIGQADDIETAWDYAYEADPV 30- 0 L+GKELS+NNI DADAA+I+++FK+ P VA+KHMNPCG+G + I+ A+D AYEADPV Sbjct: 241 LHGKELSYNNINDADAALSIVKEFKE-PAAVAVKHMNPCGVGTGETIKEAFDRAYEADPV 29- 9 Query: 301 SIFGGIVVLNREVDAATAEKMHPIFLEIIIAPSYSEEALAILTNKKKNLRILELPFDAQA 36- 0 SIFGGI+LNREVD TA+ + IFLEIIIAPS+SEEAL +LT+ KKNLR+L LP + + Sbjct: 300 SIFGGIIALNREVDVETAKTLKEIFLEIIIAPSFSEEALDVLTS-KKNLRLLTLPLNEE- 35- 7 Query: 361 ASEVEAEYTGVVGGLLVQNQDVVAENPSDWQVVTDRQPTEQEATALEFAWKAIKYVKSNG 42- 0 ++ E T + GG LVQ +D ++ ++ T R+PTE E AL+ AW+ +K+VKSN Sbjct: 358 -NQAEKRITSIHGGALVQEEDTYGFEEAEIKIPTKREPTEAEWEALKLAWRVVKHVRSNA 41- 6 Query: 421 IIITNDHMTLGLGAGQTMRVGSVKIAIEQAKDHLDGAVLASDAFFPFADNIEEIAAAGIK 48- 0 I++ + MT+G+GAGQ NRVG+ KIAIEQA + G+V+ SDAFFP D +E A AGI Sbjct: 417 IVLADGQMTVGVGAGQMNRVGAAKIAIEQAGEKAAGSVMGSDAFFPMGDTVELAAKAGIT 47- 6 Query: 481 AIIQPGGSVRDQESIDAANKHGLTMIFTGVRHFRH 515 AIIQPGGS+RD+ESI+ A+KHG+ M+FTGVRHF+H Sbjct: 477 AIIQPGGSIRDEESIENADKHGIAMVFTGVRHFKH 511 A related DNA sequence was identified in S. pyogenes <SEQ ID 959> which encodes the amino acid sequence <SEQ ID 960>. Analysis of this protein sequence reveals the following: TABLE-US-00949 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2932(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00950 Identities = 500/515 (97%), Positives = 507/515 (98%) Query: 1 MTKRALISVSDKSGIIDFAKELKNLGWDIISTGGTKVALDDAGVETIAIDDVTGFPEMMD 60- MTKRALISVSDKSGI+DFAKELKNLGWDIISTGGTKV LDDAGVETIAIDDVT FPEMMD Sbjct: 1 MTKRALISVSDKSGIVDFAKELKNLGWDIISTGGTKVTLDDAGVETIAIDDVTRFPEMMD 60 Query: 61 GRVKTLHPNIHGGLLARRDADSHLQAAKDNNIELIDLVVVNLYPFKETILRPDVTYDLAV 12- 0 GRVKTLHPNIHGGLLARRDADSHLQAAKDNNIELIDLVVVNLYPFKETILRPD+TYDLAV Sbjct: 61 GRVKTLHPNIHGGLLARRDADSHLQAAKDNNIELIDLVVVNLYPFKETILRPDITYDLAV 12- 0 Query: 121 ENIDIGGPSMLRSAAKNHASVTVVVDSADYATVLGELADASQTTFKTRQRLAAKAFRHTA 18- 0 ENIDIGGPSNLRSAAKNHASVTVVVD ADYATVLGELADA QTTF+TRQRLAAK FRHTA Sbjct: 121 ENIDIGGPSMLRSAAKNHASVTVVVDPADYATVLGELADAGQTTFETRQRLAAKVFRHTA 18- 0 Query: 181 AYDALIAEYFTAQVGEAKPEKLTITYDLKQAMRYGENPQQDADFYQKALPTDYSIASAKQ 24- 0 AYDALIAEYFT QVGEAKPEKLTITYDLKQAMRYGENPQQDADFYQKALPTDYSIASAKQ Sbjct: 181 AYDALIAEYFTTQVGEAKPEKLTITYDLKQAMRYGENPQQOADFYQKALPTDYSIASAKQ 24- 0 Query: 241 LNGKELSFNNIRDADAAIRIIRDFKDSPTVVALKHMNPCGIGQADDIETAWDYAYEADPV 30- 0 LNGKELSFNNIRDADAAIRIIRDFKD PTVVALKHMNPCGIGQADDIETAWDY Y+ADPV Sbjct: 241 LNGKELSFNNIRDADAAIRIIRDFKDRPTVVALKHMNPCGIGQADDIETAWDYTYKADPV 30- 0 Query: 301 SIFGGIVVLNREVDAATAEKMHPIFLEIIIAPSYSEEALAILTNKKKNLRILELPFDAQA 36- 0 SIFGGI+VLNREVDAATA+KMHPIFLEIIIAPSYSEEALAILTNKKKNLRILELPFDAQA Sbjct: 301 SIFGGIIVLNREVDAATAKKMHPIFLEIIIAPSYSEEALAILTNKKKNLRILELPFDAQA 36- 0 Query: 361 ASEVEAEYTGVVGGLLVQNQDVVAENPSDWQVVTDRQPTEQEATALEFAWKAIKYVKSNG 42- 0 ASEVEAEYTGVVGGLLVQNQDVVAENPSDWQVVTDRQPTEQEATALEFAWKAIKYVKSNG Sbjct: 361 ASEVEAEYTGVVGGLLVQNQDVVAENPSDWQVVTDRQPTEQEATALEFAWKAIKYVKSNG 42- 0 Query: 421 IIITNDHMTLGLGAGQTNRVGSVKIAIEQAKDHLDGAVLASDAFFPFADNIEEIAAAGIK 48- 0 IIITNDHMTLGLGAGQTNRVGSVKIAIEQAKDHLDGAVLASDAFFPFADNIEEIAAAGIK Sbjct: 421 IIITNDHMTLGLGAGQTNRVGSVKIAIEQAKDHLDGAVLASDAFFPFADNIEEIAAAGIK 48- 0 Query: 481 AIIQPGGSVRDQESIDAANKHGLTMIFTGVRHFRH 515 AIIQPGGSVRDQ+SIDAANKHGLTMIFTGVRHFRH Sbjct: 481 AIIQPGGSVRDQDSIDAANKHGLTMIFTGVRHFRH 515 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 298 A DNA sequence (GBSx0326) was identified in S. agalactiae <SEQ ID 961> which encodes the amino acid sequence <SEQ ID 962>. This protein is predicted to be similar to antibiotic resistance protein. Analysis of this protein sequence reveals the following: TABLE-US-00951 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1842(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00952 >GP: CAB12342 GB: Z99106 similar to antibiotic resistance protein [Bacillus subtilis] Identities = 65/263 (24%), Positives = 117/263 (43%), Gaps = 34/263 (12%) Query: 5 KNLEIVESIFGD-WDETIIWSCV-QGIMGEVFVDSLDQPKSSLAKLGRKSSFGFLAGQPT 62 K ++++F D + T ++S + Q I G V+ D PKS +G +S F+AG Sbjct: 10 KKYSSLKTMFDDKYCPTFVYSILDQTIPGAVYADDQTFPKSFF--IGTESGIYFIAGDQG 67 Query: 63 ----------LFLLEVCSGEDIILVPQHKGWSDLIESTYGQNAHSFKRYATKKDTLFERS 112- + +V S + L W +++ + + +R A + Sbjct: 68 NRDFHDFIAGYYEEQVKSSKRFTLFSSSDTWDSVLKPILKDDLNQMRRAAFSY-----QP 122- Query: 113 RLEKFVTQLPNGFELRAIDEKV------YNSCLEKEWSQDLVANYATYQYYKKQGIGYVV 16- 6 + K QLP G L+ IDE + +NS +E+ + + + +G G+ V Sbjct: 123 KSFKKTLQLPKGLVLKRIDEDIISHSTAFNSAYYEEY-------WNSVSQFASKGFGFAV 17- 5 Query: 167 YYQGNIIAGASSYSTYKNGIEIEVDTHPDFRRRGLATIVAAQLILTCLDKGIYPSWDAH- 22- 5 + ++++ +S N E+++ T ++R GLA VA + I C++ GI PSWD Sbjct: 176 LHGNHVVSECTSIFLGHNRAEMDIYTLEEYRGLGLAYCVANRFIAFCMENGIVPSWDCDI 23- 5 Query: 226 -TRTSLNLSEKLGYEFSHEYIAY 247 +S+ L+ KLG++ EY Y Sbjct: 236 CNNSSIALAAKLGFKTVTEYTIY 258 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 299 A DNA sequence (GBSx0328) was identified in S. agalactiae <SEQ ID 963> which encodes the amino acid sequence <SEQ ID 964>. This protein is predicted to be phosphoribosylglycinamide formyltransferase homolog (purN). Analysis of this protein sequence reveals the following: TABLE-US-00953 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0736(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 965> which encodes the amino acid sequence <SEQ ID 966>. Analysis of this protein sequence reveals the following: TABLE-US-00954 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.53 Transmembrane 75-91 (75-91) ----- Final Results ----- bacterial membrane --- Certainty = 0.1213(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-00955 >GP: CAA04374 GB: AJ000883 purD [Lactococcus lactis] Identities = 236/419 (56%), Positives = 301/419 (71%), Gaps = 7/419 (1%) Query: 50 LKLLVVGSGGREHAIAKKLLASKGVDQVFVAPGNDGMTLDGLDLVNIVVSEHSRLIAFAK 109- +K+LV+GSGGREHA+AKK + S V++VFVAPGN GM DG+ +V+I + +L+ FA+ Sbjct: 1 MKILVIGSGGREHALAKKFMESPQVEEVFVAPGNSGMEKDGIQIVHISELSNDKLVKFAQ 60 Query: 110 ENEISWAFIGPDDALAAGIVDDFNSAGLRAFGPTKAAAELEWSKDFAKEIMVKYNVPTAA 16- 9 I F+GP+ AL G+VD F A L FGP K AAELE SKDFAK IM KY VPTA Sbjct: 61 NQNIGLTFVGPETALMNGVVDAFIKAELPIFGPNKMAAELEGSKDFAKSIMKKYGVPTAD 120- Query: 170 YGTFSDFEKAKAYIEEQGAPIVVKADGLALGKGVVVAETVEQAVEAAQEMLLDNKFGDSG 22- 9 Y TF E A AY++E+G P+V+KADGLA GKGV VA +E A A ++ F S Sbjct: 121 YATFDSLEPALAYLDEKGVPLVIKADGLAAGKGVTVAFDIETAKSALADI-----FSGSQ 17- 5 Query: 230 ARVVIEEFLDGEEFSLFAFANGDKFYIMPTAQDHKRAFDGDKGPNTGGMGAYAPVPHLPQ 28- 9 +VVIEEFLDGEEFSLF+F + K Y MP AQDHKRAFD DKGPNTGGMGAY+PV H+ + Sbjct: 176 GKVVIEEFLDGEEFSLFSFIHDGKIYPMPIAQDHKRAFDEDKGPNTGGMGAYSPVLHISK 23- 5 Query: 290 SVVDTAVEMIVRPVLEGMVAEGRPYLGVLYVGLILTADGPKVIEFNSRFGDPETQIILPR 34- 9 VV+ A+E +V+P + GM+ EG+ + GVLY GLILT DG K IEFN+RFGDPETQ++LPR Sbjct: 236 EVVNEALEKVVKPTVAGMIEEGKSFTGVLYAGLILTEDGVKTIEFNARFGDPETQVVLPR 29- 5 Query: 350 LTSDFAQNIDDIMMGIEPYITWQKDGVTLGVVVASEGYPFDYEKGVPLPEKTDGDIITYY 40- 9 L SD AQ I DI+ G EP + W + GVTLGVVVA+EGYP + G+ LPE +G + YY Sbjct: 296 LKSDLAQAIIDILAGNEPTLEWLESGVTLGVVVAAEGYPSQAKLGLILPEIPEG-LNVYY 35- 4 Query: 410 AGVKFSENSELLLSNGGRVYMLVTTEDSVKAGQDKIYTQLAQQDTTGLFYRNDIGSKAI 468- AGV +EN++ L+S+GGRVY++ T + VK+ Q +Y +L + + G FYR+DIGS+AI Sbjct: 355 AGVSKNENNQ-LISSGGRVYLVSETGEDVKSTQKLLYEKLDKLENDGFFYRHDIGSRAI 412- An alignment of the GAS and GBS proteins is shown below: TABLE-US-00956 Identities = 172/182 (94%), Positives = 176/182 (96%) Query: 1 MKIAVFASGNGSNFQVIAEQFQVSFVFSDHRDAYVLERAQNLAIPSFAFELKEFENKAAY 60 MKIAVFASGNGSNFQVIAEQF VSFVFSDHRDAYVLERAQNLAIPSFAFELKEFENK AY Sbjct: 1 MKIAVFASGNGSNFQVIAEQFPVSFVFSDHRDAYVLERAQNLAIPSFAFELKEFENKVAY 60 Query: 61 EQAVVDLLDKHEIDLVCLAGYMKIVGETLLSAYEGRIINIHPTYLPEFPGAHGIKDAWEA 120- EQA+VDLLDKHEIDLVCLAGYMKIVGETLL AYE RIINIHP YLPEFPGAHGI+DAWEA Sbjct: 61 EQAIVDLLDKHEIDLVCLAGYMKIVGETLLLAYERRIINIHPAYLPEFPGAHGIEDAWEA 120- Query: 121 GVDQSGVTIHWVDSGVDTGQVIQQVHVPRLADDSLESFETRIHETEYQLYPAVLDSLGIK 18- 0 GVDQSGVTIHWVDSGVDTGQVIQQV VPRLADDSLESFETRIHETEYQLYPAVLDSLG++ Sbjct: 121 GVDQSGVTIHWVDSGVDTGQVIQQVRVPRLADDSLESFETRIHETEYQLYPAVLDSLGVE 18- 0 Query: 181 RK 182 RK Sbjct: 181 RK 182 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 300 A DNA sequence (GBSx0329) was identified in S. agalactiae <SEQ ID 967> which encodes the amino acid sequence <SEQ ID 968>. Analysis of this protein sequence reveals the following: TABLE-US-00957 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.59 Transmembrane 121-137 (121-137) ----- Final Results ----- bacterial membrane --- Certainty = 0.1235(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00958 >GP: AAC16901 GB: AF016634 phosphoribosylformylglycinamide cyclo-ligase [Lactococcus lactis subsp. cremoris] Identities = 253/338 (74%), Positives = 288/338 (84%), Gaps = 4/338 (1%) Query: 4 KNAYAQSGVDVEAGYEVVERIKKHVARTERAGVMGALGGFGGMFDLSQTGVKEPVLISGT 63 +NAYA+SGVDVEAGYEVV RIKKHVA+TER GV+GALGGFGG FDLS VKEPVLISGT Sbjct: 5 ENAYAKSGVDVEAGYEVVSRIKKHVAKTERLGVLGALGGFGGSFDLSVLDVKEPVLISGT 64 Query: 64 DGVGTKLMLAIKYDKHDTIGQDCVAMCVNDIIAAGAEPLYFLDYVATGKNEPAKLEQVVA 123- DGVGTKLMLAI+ DKHDTIG DCVAMCVNDIIAAGAEPLYFLDY+ATGKN P KLEQVVA Sbjct: 65 DGVGTKLMLAIRADKHDTIGIDCVAMCVNDIIAAGAEPLYFLDYIATGKNIPEKLEQVVA 124- Query: 124 GVAEGCVQASAALIGGETAEMPGMYGEDDYDLAGFAVGVAEKSQIIDGSK-VKEGDILLG 18- 2 GVAEGC+QA AALIGGETAEMPGMY EDDYDLAGFAVGVAEKSQ+IDG K V+ GD+LLG Sbjct: 125 GVAEGCLQAGAALIGGETAEMPGMYDEDDYDLAGFAVGVAEKSQLIDGEKDVEAGDVLLG 18- 4 Query: 183 LASSGIHSNGYSLVRRVFADYTGDEVLPELEGKQLKDVLLEPTRIYVKAALPLIKEELVN 24- 2 LASSGIHSNGYSLVR+VFAD+ +E LPEL+ + L D LL PT+IYVK LPLIK+ + Sbjct: 185 LASSGIHSNGYSLVRKVFADFDLNESLPELD-QSLIDTLLTPTKIYVKELLPLIKQNKIK 24- 3 Query: 243 GIAHITGGGFIENVPRMFADDLAAEIDEDKVPVLPIFKALEKYGDIKHEEMFEIFNMGVG 30- 2 GIAHITGGGF EN+PRMF + L+AEI E VLPIFKALEKYG IKHEEM+EIFNMG+G Sbjct: 244 GIAHITGGGFHENLPRMFGNSLSAEIVEGSWDVLPIFKALEKYGSIKHEEMYEIFNMGIG 30- 3 Query: 303 LMLDVNPENVDRVKELLDEPVYEIGRIIKKADDSVVIK 340 +++ V PEN +K+ L+ +EIG+++ + + VVIK Sbjct: 304 MVIAVAPENAAALKKELN--AFEIGQMVNRQEAPVVIK 339 A related DNA sequence was identified in S. pyogenes <SEQ ID 969> which encodes the amino acid sequence <SEQ ID 970>. Analysis of this protein sequence reveals the following: TABLE-US-00959 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3236(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00960 Identities = 321/340 (94%), Positives = 332/340 (97%) Query: 1 MSEKNAYAQSGVDVEAGYEVVERIKKHVARTERAGVMGALGGFGGMFDLSQTGVKEPVLI 60 MSEKNAYA+SGVDVEAGYEVVERIKKHVARTERAGVMGALGGFGGMFDLS+TGVKEPVL+ Sbjct: 1 MSEKNAYAKSGVDVEAGYEVVERIKKHVARTERAGVMGALGGFGGMFDLSKTGVKEPVLV 60 Query: 61 SGTDGVGTKLMLAIKYDKHDTIGQDCVAMCVNDIIAAGAEPLYFLDYVATGKNEPAKLEQ 120- SGTDGVGTKLMLAIKYDKHDTIGQDCVAMCVNDIIAAGAEPLYFLDY+ATGKN P KLE+ Sbjct: 61 SGTDGVGTKLMLAIKYDKHDTIGQDCVAMCVNDIIAAGAEPLYFLDYIATGKNNPVKLEE 120- Query: 121 VVAGVAEGCVQASAALIGGETAEMPGMYGEDDYDLAGFAVGVAEKSQIIDGSKVKEGDIL 18- 0 VV+GVAEGCVQA AALIGGETAEMPGMYG+DDYDLAGFAVGVAEKSQIIDGSKVKEGDIL Sbjct: 121 VVSGVAEGCVQAGAALIGGETAEMPGMYGQDDYDLAGFAVGVAEKSQIIDGSKVKEGDIL 18- 0 Query: 181 LGLASSGIHSNGYSLVRRVFADYTGDEVLPELEGKQLKDVLLEPTRIYVKAALPLIKEEL 24- 0 LGLASSGIHSNGYSLVRRVFADYTG E+LPELEGKQLKDVLLEPTRIYVKAALPLIKEEL Sbjct: 181 LGLASSGIHSNGYSLVRRVFADYTGKELLPELEGKQLKDVLLEPTRIYVKAALPLIKEEL 24- 0 Query: 241 VNGIAHITGGGFIENVPRMFADDLAAEIDEDKVPVLPIFKALEKYGDIKHEEMFEIFNMG 30- 0 V GI HITGGGFIEN+PRMFADDLAAEIDEDKVPVLPIFKALEKYGDIKHEEMFEIFNMG Sbjct: 241 VKGIGHITGGGFIENIPRMFADDLAAEIDEDKVPVLPIFKALEKYGDIKHEEMFEIFNMG 30- 0 Query: 301 VGLMLDVNPENVDRVKELLDEPVYEIGRIIKKADDSVVIK 340 VGLML V+PENV+RVKELLDEPVYEIGRIIKKAD SVVIK Sbjct: 301 VGLMLAVSPENVNRVKELLDEPVYEIGRIIKKADASVVIK 340 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 301 A DNA sequence (GBSx0330) was identified in S. agalactiae <SEQ ID 971> which encodes the amino acid sequence <SEQ ID 972>. This protein is predicted to be phosphoribosylpyrophosphate amidotransferase (purF). Analysis of this protein sequence reveals the following: TABLE-US-00961 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1112(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00962 >GP: AAD12627 GB: U64311 phosphoribosylpyrophosphate amidotransferase [Lactococcus lactis] Identities = 340/470 (72%), Positives = 404/470 (85%), Gaps = 6/470 (1%) Query: 3 YEVKSLNEECGVFGIWGYPQAAQVTYFGLHSLQHRGQEGAGIISNDNGKLYGYRNVGLLS 62 +E K+LNEECG+FG+WG+P AA++TYFGLH+LQHRGQEGAGI+ N+NGKL +R +GL++ Sbjct: 37 FEAKTLNEECGLFGVWGHPDAARLTYFGLHALQHRGQEGAGILVNNNGKLNRHRGLGLVT 96 Query: 63 EVFKNQSELDNLTGNAAIGHVRYATAGSADIRNIQPFLYKFHDGQFALCHNGNLTNAISS 122- EVF+++ +L+ LTG++AIGHVRYATAGSA+I NIQPF ++FHDG L HNGNLTNA S Sbjct: 97 EVFRHEKDLEELTGSSAIGHVRYATAGSANINNIQPFQFEFHDGSLGLAHNGNLTNAQSL 156- Query: 123 RKELEKQGAIFNASSDTEILMHLIRRSHNPSFMGKVKEALSTVKGGFAYLLMTEDKLIAA 18- 2 R ELEK GAIF+++SDTEILMHLIRRSH+P FMG+VKEAL+TVKGGFAYL+MTE+ ++AA Sbjct: 157 RCELEKSGAIFSSNSDTEILMHLIRRSHHPEFMGRVKEALNTVKGGFAYLIMTENSIVAA 21- 6 Query: 183 LDPNAFRPLSIGQMQNGAWVISSETCAFEVVGAKWVRDVEPGEVILIDDSGIQCDRYTDE 24- 2 LDPN FRPLSIG+M NGA V++SETCAF+VVGA W++DV+PGE+I I+D GI D++TD Sbjct: 217 LDPNGFRPLSIGKMSNGALVVASETCAFDVVGATWIQDVQPGEIIEINDDGIHVDQFTDS 27- 6 Query: 243 TQLAICSMEYVYFARPDSTIHGVNVHTARKNMGKRLAQEFKQDADIVIGVPNSSLSAAMG 30- 2 T + ICSMEY+YFARPDS I GVNVHTARK GK LAQE K DADIVIGVPNSSLSAA G Sbjct: 277 TNMTICSMEYIYFARPDSNIAGVNVHTARKRSGKILAQEAKIDADIVIGVPNSSLSAASG 33- 6 Query: 303 FAEESGLPNEMGLVKNQYTQRTFIQPTQELREQGVRMKLSAVSGVVKGKRVVMIDDSIVR 36- 2 +AEESGLP EMGL+KNQY RTFIQPTQELREQGVRMKLSAV GVV+GKRV+M+DDSIVR Sbjct: 337 YAEESGLPYEMGLIKNQYVARTFIQPTQELREQGVRMKLSAVRGVVEGKRVIMVDDSIVR 39- 6 Query: 363 GTTSRRIVGLLREAGATEVHVAIASPELKYPCFYGIDIQTRRELISANHAVDEVCDIIGA 42- 2 GTTSRRIV LL++AGA EVHVAIASP LKYPCFYGIDIQ R ELI+A H DE+ + IGA Sbjct: 397 GTTSRRIVKLLKDAGAAEVHVAIASPALKYPCFYGIDIQDRDELIAATHTTDEIREAIGA 45- 6 Query: 423 DSLTYLSIDGLIKSIGLETKAPNGGLCVAYFDGHYPTPLYDYEEEYLRSL 472 DSLTYLS GL+++IG + LC++YFDG YPTPLYDYE +YL SL Sbjct: 457 DSLTYLSQSGLVEAIG------HDKLCLSYFDGEYPTPLYDYEADYLESL 500 A related DNA sequence was identified in S. pyogenes <SEQ ID 973> which encodes the amino acid sequence <SEQ ID 974>. Analysis of this protein sequence reveals the following:

TABLE-US-00963 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0610(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00964 Identities = 473/484 (97%), Positives = 481/484 (98%) Query: 1 MTYEVKSLNEECGVFGIWGYPQAAQVTYFGLHSLQHRGQEGAGIISNDNGKLYGYRNVGL 60- MTYEVKSLNEECGVFGIWG+PQAAQVTYFGLHSLQHRGQEGAGI+SNDNGKLYGYRNVGL Sbjct: 20 MTYEVKSLNEECGVFGIWGHPQAAQVTYFGLHSLQHRGQEGAGIVSNDNGKLYGYRNVGL 79- Query: 61 LSEVFKNQSELDNLTGNAAIGHVRYATAGSADIRNIQPFLYKFHDGQFALCHNGNLTNAI 12- 0 LSEVFKNQSELDNLTGNAAIGHVRYATAGSADIRNIQPFLYKFHDGQFALCHNGNLTNAI Sbjct: 80 LSEVFKNQSELDNLTGNAAIGHVRYATAGSADIRNIQPFLYKFHDGQFALCHNGNLTNAI 13- 9 Query: 121 SSRKELEKQGAIFNASSDTEILMHLIRRSHNPSFMGKVKEALSTVKGGFAYLLMTEDKLI 18- 0 S RKELEKQGAIFNASSDTEILMHLIRRSHN SFMGKVKEAL+TVKGGFAYLLMTE+KLI Sbjct: 140 SLRKELEKQGAIFNASSDTEILMHLIRRSHNSSFMGKVKEALNTVKGGFAYLLMTEWKLI 19- 9 Query: 181 AALDPNAFRPLSIGQMQNGAWVISSETCAFEVVGAKWVRDVEPGEVILIDDSGIQCDRYT 24- 0 AALDPNAFRPLSIGQMQNGAWVISSETCAFEVVGARWVRDVEPGEVILIDD GIQCDRYT Sbjct: 200 AALDPNAFRPLSIGQMQNGAWVISSETCAFEVVGAKWVROVEPGEVILIDDRGIQCDRYT 25- 9 Query: 241 DETQLAICSMEYVYFARPDSTIHGVNVHTARKNMGKRLAQEFKQDADIVIGVFNSSLSAA 30- 0 DETQLAICSMEYVYFARPDSTIHGVNVHTARKNMGKRLAQEFKQDADIVIGVPNSSLSAA Sbjct: 260 DETQLAICSMEYVYFARPDSTIHGVNVHTARKNMGKRLAQEFKQDADIVIGVPNSSLSAA 31- 9 Query: 301 MGFAEESGLPNEMGLVKNQYTQRTFIQPTQSLREQGVRMKLSAVSGVVKGKRVVMIDDSI 36- 0 MGFAEESGLPNEMGLVKNQYTQRTFIQPTQELREQGVPMKLSAVSGVVKGKRVVMIDDSI Sbjct: 320 MGFAEESGLPNEMGLVKNQYTQRTFIQPTQELREQGVRMKLSAVSGVVKGKRVVMIDDSI 37- 9 Query: 361 VRGTTSRRIVGLLREAGATEVHVAIASPELKYPCFYGIDIQTRRELISANHAVDEVCDII 42- 0 VRGTTSRRIVGLLREAGA+EVHVAIASPELKYPCFYGIDIQTRRELISANH+VDEVCDII Sbjct: 380 VRGTTSRRIVGLLREAGASEVHVAIASPELKYPCFYGIDIQTRRELISANHSVDEVCDII 43- 9 Query: 421 GADSLTYLSIDGLIKSIGLETKAPNGGLCVAYFDGHYPTPLYDYEEEYLRSLEEKTSFYI 48- 0 GADSLTYLS+DGLI+SIGLETKAPNGGLCVAYFDGHYPTPLYDYEEEYLRSLEEKTSFYI Sbjct: 440 GADSLTYLSLDGLIESIGLSTKAPNGGLCVAYFDGHYPTPLYDYEEEYLRSLEEKTSFYI 49- 9 Query: 481 QKVK 484 QKVK Sbjct: 500 QKVK 503 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 302 A DNA sequence (GBSx0331) was identified in S. agalactiae <SEQ ID 975> which encodes the amino acid sequence <SEQ ID 976>. Analysis of this protein sequence reveals the following: TABLE-US-00965 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4797(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 303 A DNA sequence (GBSx0332) was identified in S. agalactiae <SEQ ID 977> which encodes the amino acid sequence <SEQ ID 978>. Analysis of this protein sequence reveals the following: TABLE-US-00966 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3489(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 304 A DNA sequence (GBSx0333) was identified in S. agalactiae <SEQ ID 979> which encodes the amino acid sequence <SEQ ID 980>. Analysis of this protein sequence reveals the following: TABLE-US-00967 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1690(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00968 >GP:CAC12194 GB:AL445066 phosphoribosylformylglycinamidine synthase related protein [Thermoplasma acidophilum] Identities = 199/746 (26%), Positives = 329/746 (43%), Gaps = 103/746 (13%) Query: 202 ADD--FAAYKAEQGLAMEVDDLLFIQDYFKSIGRVPTETELKVLDTYWSDHCRHTTFETE 25- 9 ADD A GLA+ +D++ ++ YF+ +GR P + E+ + WS+HC + + + Sbjct: 11 ADDARLKAISKRLGLALSLDEMKAVRSYFERLGRDPIDAEIHAVAQSWSEHCSYKSSKYY 70- Query: 260 LKNIDFSASKFQKQLQATYDKYIAMRDELGRSEKPQTLMDMATIFGRYERANGRLDDMEV 31- 9 LK K+ L+ Y +AM D+ G Sbjct: 71 LK-------KYLGSLKTDYT-ILAMEDDAG------------------------------ 92- Query: 320 SDEINACSVEIEVDVDGVKEPWLLMFKNETHNHPTEIEPFGGAATCIGGAIRDPLSGRSY 37- 9 VD DG + + K E+HNHP+ +EP+GGAAT IGG +RD L + Sbjct: 93 -----------VVDFDG---EYAYVLKMESHNHPSAVEPYGGAATGIGGIVRDVLCMGAQ 13- 8 Query: 380 VYQAMRISGAGDITTPIAETRAGKLPQQVISKTAAHGYSSYGNQIGLATTYVREYFHPGF 43- 9 + GD+++ E G L + I G YGN+IG+ YF + Sbjct: 139 PVALIDSLFLGDVSSDRYE---GLLSPRYIFGGVVGGIRDYGNRIGIPNVAGSLYFDKLY 19- 5 Query: 440 VAKRMELGAVVGAAPKENVVREKP-EAGDVVVLLGGKTGRDGVGGATGSSKVQTVESVET 49- 8 + + VG ++ +VR K + GDV+VL+GGKTGRDG+ G +S + ++ Sbjct: 196 NSNPLVNAGCVGIVRRDRIVRSKSYKPGDVLVLMGGKTGRDGIHGVNFASTTLG-KVTKS 25- 4 Query: 499 AGAEVQKGNAIEERKIQRLFRDGNVTRLIKKSNDFGAGGVCVAIGELAD----GLEIDLD 55- 4 + +Q GN I E+ + + + N LI+ D G GG+ A E+ G EI LD Sbjct: 255 SRLAIQLGNPIVEQPMIKAVLEANDAGLIRAMKDLGGGGLSSAATEMVYAGGFGAEITLD 31- 4 Query: 555 KVPLKYQGLNGTEIAISESQERMSVVVGPSDVDAFIAACNKENIDAVVVATVTEKPNLVM 61- 4 + LK ++G EI ISESQERM + P DV+ K N+D V+ VT + + Sbjct: 315 DIKLKESNMSGWEIWISESQERMLMECYPEDVEKIRQIAEKWNLDFSVIGQVTADRRIRV 37- 4 Query: 615 TWNGETIVDLERCFLDTNGV-RVVVDAKVVDKDLTVPEARTTSAETLEADMLKVLSDLNH 67- 3 + I+D++ FLD + V + K V+K +TVP+ E L + + ++ LN Sbjct: 375 YYKKRKIIDMDIEFLDDSPVYQRPYRIKEVEKSVTVPQ----EPEDLNSFVRDFMARLNT 43- 0 Query: 674 ASQKGLQTIFDSSVGRSTVNHPIGGR-YQITPTESSVQKLPVQYGVTTTASVMAQGYNPY 73- 2 ++ + +D +V ST+ P GR + T +++V K P++ + V+ G P Sbjct: 431 CARFNVVRQYDHTVRGSTIVTPFVGRPNKETHADATVIK-PLENSM--RGLVLTSGSRPN 48- 7 Query: 733 IAEWSPYHGAAYAVIEATARLVATGADWSRARFSYQEYFERMDKQAERFGQPVSALLGSI 79- 2 + PY G + EA +++TG R ++ E GQ V ++ Sbjct: 488 MVSVDPYAGTLLTLAEAYKNILSTG---GRPHSVVDALNFGNPEREEIMGQFVESVRAIG 54- 4 Query: 793 EAQIQFGLPSIGGKDSMSGTFEELTVPPTLVAFGVTTADS-RKVLSPEFKAAGENIY--- 84- 8 + + GLP + G S + + + PT V D R+ + K +G IY Sbjct: 545 DFCRKMGLPVVAGNVSFYNEYRKTDIMPTPTIMMVGLIDDVRRSRTTYMKGSGNAIYLIG 60- 4 Query: 849 ----------------YIPGQAISEDIDFDLIKANF--SQFEAIQAQHKITAASAVKYGG 89- 0 Y G + D+D +F S+ + I + H +++ GG Sbjct: 605 EPCDNLTGSEYSRMHGYTDGFLPAPDLDELTRIRDFLSSKADMILSSHDVSS------GG 65- 8 Query: 891 VLESLALMTFGNRIGASVEIAELDSS 916 + +L+ M+FG+ IG V+I+ + ++ Sbjct: 659 LFAALSEMSFGSGIGFHVDISNVSAA 684 A related DNA sequence was identified in S. pyogenes <SEQ ID 981> which encodes the amino acid sequence <SEQ ID 982>. Analysis of this protein sequence reveals the following: TABLE-US-00969 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1415(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00970 Identities = 1219/1256 (97%), Positives = 1226/1256 (97%) Query: 11 SSYFRVAPLSDLVSYMNKRIFVEKKADFGIKSASLVKELTHNLQLASLKDLRIVQVYDVF 7- 0 SSYF VAPLSDLVSYMNKRIFVEKKADFGIKSASLVKELTHNLQL SLK LRIVQVYDVF Sbjct: 2 SSYFPVAPLSDLVSYMNKRIFVEKKADFGIKSASLVKELTHNLQLTSLKALRIVQVYDVF 6- 1 Query: 71 NLAEDLLARAEKHIFSEQVTDRLLTEAEITAELDKVAFFAIEALPGQFDQRAASSQEALL 1- 30 NLAEDLLARAEKHIFSEQVTD LLTE EITAELDKVAFFAIEALPGQFDQRAASSQEALL Sbjct: 62 NLAEDLLARAEKHIFSEQVTDCLLTETEITAELDKVAFFAIEALPGQFDQRAASSQEALL 1- 21 Query: 131 LLGSDSQVKVNTAQLYLVNKDIAEAELEAVKNYLLNPVDSRFKDITLPLEVQAFSVSDKT 1- 90 L GSDSQVKVNTAQLYLVNKDI EAELEAVKNYLLNPVDSRFKDITLPLE QAFSVSDKT Sbjct: 122 LFGSDSQVKVNTAQLYLVNKDITEAELEAVKNYLLNPVDSRFKDITLPLEEQAFSVSDKT 1- 81 Query: 191 ISNLDFFETYQADDFAAYKAEQGLAMEVDDLLFIQDYFKSIGRVPTETELKVLDTYWSDH 2- 50 I NLDFFETYQADDFA YKAEQGLAMEVDDLLFIQ+YFKSIG VPTETELKVLDTYWSDH Sbjct: 182 IPNLDFFETYQADDFATYKAEQGLAMEVDDLLFIQNYFKSIGCVPTETELKVLDTYWSDH 2- 41 Query: 251 CRHTTFETELKNIDFSASKFQKQLQATYDKYIAMRDELGRSEKPQTLMDMATIFGRYERA 3- 10 CRHTTFETELKNIDFSASKFQKQLQ TYDKYIAMRDELGRSEKPQTLMDMATIFGRYERA Sbjct: 242 CRHTTFETELKNIDFSASKFQKQLQTTYDKYIAMRDELGRSEKPQTLMDMATIFGRYERA 3- 01 Query: 311 NGRLDDMEVSDEINACSVEIEVDVDGVKEPWLLMFKNETHNHPTEIEPFGGAATCIGGAI 3- 70 NGRLDDMEVSDEINACSVEIEVDVDGVKEPWLLMFKNETHNHPTEIEPFGGAATCIGGAI Sbjct: 302 NGRLDDMEVSDEINACSVEIEVDVDGVKEPWLLMFKNETHNHPTEIEPFGGAATCIGGAI 3- 61 Query: 371 RDPLSGRSYVYQAMRISGAGDITTPIAETRAGKLPQQVISKTAAHGYSSYGNQIGLATTY 4- 30 RDPLSGRSYVYQAMRISGAGDITTPIAETRAGKLPQQVISKTAAHGYSSYGNQIGLATTY Sbjct: 362 RDPLSGRSYVYQAMRISGAGDITTPIAETRAGKLPQQVISKTAAHGYSSYGNQIGLATTY 4- 21 Query: 431 VREYFHPGFVAKRMELGAVVGAAPKENVVREKPEAGDVVVLLGGKTGRDGVGGATGSSKV 4- 90 VREYFHPGFVAKRMELGAVVGAAPKENVVREKPEAGDVV+LLGGKTGRDGVGGATGSSKV Sbjct: 422 VREYFHPGFVAKRMELGAVVGAAPKENVVREKPEAGDVVILLGGKTGRDGVGGATGSSKV 4- 81 Query: 491 QTVESVETAGAEVQKGNAIEERKIQRLFRDGNVTRLIKKSNDFGAGGVCVAIGELADGLE 5- 50 QTVESVETAGAEVQKGNAIEERKIQRLFRDGNVTRLIKKSNDFGAGGVCVAIGELADGLE Sbjct: 482 QTVESVETAGAEVQKGNAIEERKIQRLFRDGNVTRLIKKSNDFGAGGVCVAIGELADGLE 5- 41 Query: 551 IDLDKVPLKYQGLNGTEIAISESQERMSVVVGPSDVDAFIAACNKENIDAVVVATVTEKP 6- 10 IDLDKVPLKYQGLNGTEIAISESQERMSVVV P+DVDAFIAACNKENIDAVVVATVTEKP Sbjct: 542 IDLDKVPLKYQGLNGTEIAISESQERMSVVVRPNDVDAFIAACNKENIDAVVVATVTEKP 6- 01 Query: 611 NLVMTWNGETIVDLERCFLDTNGVRVVVDAKVVDKDLTVPEARTTSAETLEADMLKVLSD 6- 70 NLVMTWNGE IVDLER FLDTNGVRVVVDAKVVDKDLTVPEARTTSAETLEAD LKVLSD Sbjct: 602 NLVMTWNGEIIVDLERRFLDTNGVRVVVDAKVVDKDLTVPEARTTSAETLEADTLKVLSD 6- 61 Query: 671 LNHASQKGLQTIFDSSVGRSTVNHPIGGRYQITPTESSVQKLPVQYGVTTTASVMAQGYN 7- 30 LNHASQKGLQTIFDSSVGRSTVNHPIGGRYQITPTESSVQKLPVQ+GVTTTASVMAQGYN Sbjct: 662 LNHASQKGLQTIFDSSVGRSTVNHPIGGRYQITPTESSVQKLPVQHGVTTTASVMAQGYN 7- 21 Query: 731 PYIAEWSPYHGAAYAVIEATARLVATGADWSRARFSYQEYFERMDKQAERFGQPVSALLG 7- 90 PYIAEWSPYHGAAYAVIEATARLVATGADWSRARFSYQEYFERMDKQAERFGQPVSALLG Sbjct: 722 PYIAEWSPYHGAAYAVIEATARLVATGADWSRARFSYQEYFERMDKQAERFGQPVSALLG 7- 81 Query: 791 SIEAQIQFGLPSIGGKDSMSGTFEELTVPPTLVAFGVTTADSRKVLSPEFKAAGENIYYI 8- 50 SIEAQIQ GLPSIGGKDSMSGTFE+LTVPPTLVAFGVTTADSRKVLSPEFKAAGENIYYI Sbjct: 782 SIEAQIQLGLPSIGGKDSMSGTFEDLTVPPTLVAFGVTTADSRKVLSPEFKAAGENIYYI 8- 41 Query: 851 PGQAISEDIDFDLIKANFSQFEAIQAQHKITAASAVKYGGVLESLALMTFGNRIGASVEI 9- 10 PGQAISEDIDFDLIK NFSQFEAIQAQHKITAASA KYGGVLESLALMTFGNRIGASVEI Sbjct: 842 PGQAISEDIDFDLIKDNFSQFEAIQAQHKITAASAAKYGGVLESLALMTFGNRIGASVEI 9- 01 Query: 911 AELDSSLTAQLGGFVFTSVEEIADVVKIGQTQADFTVTVNGNDLAGASLLSAFEGKLEEV 9- 70 AELDSSLTAQLGGFVFTS EEIAD VKIGQTQADFTVTVNGNDLAGASLL+AFEGKLEEV Sbjct: 902 AELDSSLTAQLGGFVFTSAEEIADVVKIGQTQADFTVTVNGNDLAGASLLAAFEGKLEEV 9- 61 Query: 971 YPTEFEQVDAIEEVPAVVSDVVIKAKEIIEKPVVYIPVFPGTNSEYDSAKAFEQVGASVN 1- 030 YPTEFEQ D +EEVPAVVSD VIKAKE IEKPVVYIPVFPGTNSEYDSAKAFEQVGASVN Sbjct: 962 YPTEFEQTDVIEEVPAVVSDTVIKAKETIEKPVVYIPVFPGTNSEYDSAKAFEQVGASVN 1- 081 Query: 1031 LVPFVTLNEAAIAESVDTMVANIAKANIIFFAGGFSAADEPDGSAKFIVNILLNEKVRAA 1- 150 LVPFVTLNE AIAESVDTMVANIAKANIIFFAGGFSAADEPDGSAKFIVNILLNEKVRAA Sbjct: 1022 LVPFVTLNEVAIAESVDTMVANIAKANIIFFAGGFSAADEPDGSAKFIVNILLNEKVRAA 1- 081 Query: 1091 IDSFIEKGGLIIGICNGFQALVKSGLLPYGNFEEAGETSPTLFYNDANQHVAKMVETRIA 1- 150 IDSFIEKGGLIIGICNGFQALVKSGLLPYGNFEEAGETSPTLFYNDANQHVAKMVETRIA Sbjct: 1082 IDSFIEKGGLIIGICNGFQALVKSGLLPYGNFEEAGETSPTLFYNDANQHVAKMVETRIA 1- 141 Query: 1151 NTNSPWLAGVEVGDIHVIPVSHGEGKFVVSASEFAELRDNGQIWSQYVDFDGQPSMDSKY 1- 210 NTNSPWLAGVEVGDIH IPVSHGEGK VVSASEFAELRDNGQIWSQYVDFDGQPSMDSKY Sbjct: 1142 NTNSPWLAGVEVGDIHAIPVSHGEGKLVVSASEFAELRDNGQIWSQYVDFDGQPSMDSKY 1- 201 Query: 1211 NPNGSVNAIEGITSKNGQIIGKMGHSERWEDGLFQNIPGNKDQKLFESAVKYFTGK 1266 NPNGSVNAIEGITSKNGQIIGKMGHSERWEDGLFQNIPGNKDQ LF SAVKYFTGK Sbjct: 1202 NPNGSVNAIEGITSKNGQIIGKMGHSERWEDGLFQNIPGNKDQILFASAVKYFTGK 1257 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 305 A DNA sequence (GBSx0334) was identified in S. agalactiae <SEQ ID 983> which encodes the amino acid sequence <SEQ ID 984>. This protein is predicted to be phosphoribosylaminoimidazole-succinocarboxamide synthase (purC). Analysis of this protein sequence reveals the following: TABLE-US-00971 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4783(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00972 >GP:AAA03540 GB:L15190 SAICAR synthetase [Streptococcus pneumoniae] Identities = 183/231 (79%), Positives = 203/231 (87%) Query: 1 MTNQLIYTGKAKDIYSTKDENVIRTVYKDQATMLNGARKETIDGKGALNNQISSLIFEKL 60- M+ QLIY+GKAKDIY+T+DEN+I + YRDQAT NG +KE I GKG LNNQISS IFEKL Sbjct: 1 MSKQLIYSGKAKDIYTTEDENLIISTYKDQATAFNGVKKEQIAGKGVLNNQISSFIFEKL 60- Query: 61 NMAGVVTHYIEQISKNEQLNKKVDIIPLEVVLRNVTAGSFSKRFGVEEGHVLETPIVEFY 12- 0 N AGV TH++E++S EQLNKKV IIPLEVVLRN TAGSFSKRFGV+EG LETFIVEFY Sbjct: 61 NAAGVATHFVEKLSDTEQLNKKVKIIPLEVVLRNYTAGSFSKRFGVDEGIALETPIVEFY 12- 0 Query: 121 YKNDNLNDPFINDENVKFLGIVNDEEIAYLKGETRHINELLKDWFAQIGLNLIDFKLEFG 18- 0 YKND+L+DPFINDENVKFL I +D++IAYLK E R INELLK WFA+IGL LIDFKLEFG Sbjct: 121 YKNDDLDDPFINDEHVKFLQIADDQQIAYLKEEARRINELLKVWFAEIGLKLIDFKLEFG 18- 0 Query: 181 FDKDGKIILADEFSPDNCRLWDADGNHMDKDVFRRDLGSLTDVYQVVLEKL 231 FDKDGKIILADEFSPDNCRLWDADGNHMDKDVFRR LG LTDVY++V EKL Sbjct: 181 FDKDGKIILADEFSPDNCRLWDADGNHMDKDVFRRGLGELTDVYEIVWEKL 231 A related DNA sequence was identified in S. pyogenes <SEQ ID 985> which encodes the amino acid sequence <SEQ ID 986>. Analysis of this protein sequence reveals the following: TABLE-US-00973 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3935(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00974 Identities = 221/234 (94%), Positives = 228/234 (96%) Query: 1 MTNQLIYTGKAKDIYSTKDENVIRTVYKDQATMLNGARKETIDGKGALNNQISSLIFEKL 60- +TNQLIY GKAKDIYSTKDENVIRTVYKDQATMLNGARKETIDGKGALNNQISSLIFEKL Sbjct: 11 VTNQLIYKGRAKDIYSTKDENVIRTVYRDQATMLNGARKETIDGKGALNNQISSLIFEKL 70- Query: 61 NMAGVVTHYIEQISKNEQLNKKVDIIPLEVVLRNVTAGSFSKRFGVEEGHVLETPIVEFY 12- 0 N AGVVTHYIEQISKNEQLNKKVDIIPLEVVLRNVTAGSFSKRFGVEEGHVLETPIVEFY Sbjct: 71 NKAGVVTHYIEQISKNEQLNKKVDIIPLEVVLRNVTAGSFSKRFGVEEGHVLETPIVEFY 13- 0 Query: 121 YKNDNLNDPFINDEHVKFLGIVNDEEIAYLKGETRHINELLKDWFAQIGLNLIDFKLEFG 18- 0 YKND+L+DPFINDEHVKFLGIVNDEEIAYLKGETR INELLK WFAQIGLNLIDFKLEFG Sbjct: 131 YKNDDLDDPFINDEHVKFLGIVNDEEIAYLKGETRRINELLKGWFAQIGLNLIDFKLEFG 19- 0 Query: 181 FDKDGKIILADEFSPDNCRLWDADGNHMDKDVFRRDLGSLTDVYQVVLEKLIAL 234 FD++G IILADEFSPDNCRLWD +GNHMDKDVFRRDLG+LTDVYQVVLEKLIAL Sbjct: 191 FDQEGTIILADEFSPDNCRLWDKNGNHMDKDVFRRDLGNLTDVYQVVLEKLIAL 244 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 306 A DNA sequence (GBSx0335) was identified in S. agalactiae <SEQ ID 987> which encodes the amino acid sequence <SEQ ID 988>. Analysis of this protein sequence reveals the following: TABLE-US-00975 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2779(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9457> which encodes amino acid sequence <SEQ ID 9458> was also identified. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-00976 >GP:AAC35700 GB:AF041468 acyl carrier protein [Guillardia theta] Identities = 27/75 (36%), Positives = 52/75 (69%) Query: 12 MSRDEVFEKMLELLRQQLGDPQLDITPESSLHDDLAIDSIALTEFIINLEDVFHLEIPDE 71 - M+ E+FEK+ ++ +QLG + +T +++ +DL DS+ E ++ +E+ F++EIPD Sbjct: 1 MNEQEIFEKVQTIISEQLGVDKSQVTKDANFANDLGADSLDTVELVMAIEEAFNIEIPDD 60 Query: 72 AVEHMSSVQQLLDYI 86 A E +S++QQ +D+I Sbjct: 61 AAEQISNLQQAVDFI 75 A related DNA sequence was identified in S. pyogenes <SEQ ID 989> which encodes the amino acid sequence <SEQ ID 990>. Analysis of this protein sequence reveals the following: TABLE-US-00977 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1917(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00978 Identities = 36/77 (46%), Positives = 57/77 (73%) Query: 12 MSRDEVFSKMLELLRQQLGDPQLDITPESSLHDDLAIDSIALTEFIINLEDVFHLEIPDE 71 - M+R E+FE+++ L+++Q + IT ++ L +DLA+DSI L EFIIN+ED FH+ IPDE Sbjct: 1 MTRQEIFERLINLIQKQRSYLSVAITEQTHLRNDLAVDSIELVEFIINVEDEFHIAIPDE 60 Query: 72 AVEHMSSVQQLLDYIIE 88 VE M ++ +LDY+++ Sbjct: 61 DVEDMVFMRDILDYLVQ 77 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 307 A DNA sequence (GBSx0336) was identified in S. agalactiae <SEQ ID 991> which encodes the amino acid sequence <SEQ ID 992>. This protein is predicted to be fatty acid/phospholipid synthesis protein (plsX). Analysis of this protein sequence reveals the following: TABLE-US-00979 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.64 Transmembrane 101-117 (101-117) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9455> which encodes amino acid sequence <SEQ ID 9456> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00980 >GP:CAB13462 GB:Z99112 alternate gene name: ylpD [Bacillus subtilis] Identities = 174/329 (52%), Positives = 238/329 (71%), Gaps = 2/329 (0%) Query: 8 KIAIDAMGGDYAPKAIVEGVNQAISDFSDIEVQLYGDQKKIEKYLTVT-ERVSIIHTEEK 66- +IA+DAMGGD+APKA+++GV + I F D+ + L GD+ IE +LT T +R++++H +E Sbjct: 2 RIAVDAMGGDHAPKAVIDGVIKGIEAFDDLHITLVGDKTTIESHLTTTSDRITVLHADEV 61- Query: 67 INSDDEPAKAVRRKKQSSMVLGAKAVKDGVAQAFISAGNTGALLAAGLFVVGRIKGVDRP 12- 6 I DEP +AVRRKK SSMVL A+ V + A A ISAGNTGAL+ AGLF+VGRIKG+DRP Sbjct: 62 IEPTDEPVRAVRRKKNSSMVLMAQEVAENRADACISAGNTGALMTAGLFIVGRIRGIDRP 12- 1 Query: 127 GLMSTMPTLDGVGFDMLDLGANAENTASHLHQYAILGSFYAKNVRGIEVPRVGLLNNGTE 18- 6 L T+PT+ G GF +LD+GAN + HL QYAI+GS Y++ VRG+ PRVGLLN GTE Sbjct: 122 ALAPTLPTVSGDGFLLLDVGANVDAKPEHLVQYAIMGSVYSQQVRGVTSPRVGLLNVGTE 18- 1 Query: 187 ETKGDSLHKEAYELLAAEPSINFIGNIEARDLMSSVADVVVTDGFTGNAVLRTMEGTAMS 24- 6 + KG+ L K+ +++L +INFIGN+EARDL+ VADVVVTDGFTGN LKT+EG+A+S Sbjct: 182 DKKGNELTRQTFQILKETANINFIGNVEARDLLDDVADVVVTDGETGNVTLKTLEGSALS 24- 1 Query: 247 IMGSLKSSIKSGGVKAKLGALLLKDSLYQLKDSMDYSSAGGAVLFGLKAPIVKCHGSSDS 30- 6 I ++ + + + +KL A +LK L ++K M+YS+ GGA LFGLKAP++K HGSSDS Sbjct: 242 IFKMMR-DVMTSTLTSKLAAAVLKPKLKEMKMKMEYSNYGGASLFGLKAPVIKAHGSSDS 30- 0 Query: 307 KAVYSTLKQVRTMLETQVVDQLVDAFTDE 335 AV+ ++Q R M+ V + + +E Sbjct: 301 NAVFHAIRQAREMVSQNVAALIQEEVKEE 329 A related DNA sequence was identified in S. pyogenes <SEQ ID 993> which encodes the amino acid sequence <SEQ ID 994>. Analysis of this protein sequence reveals the following: TABLE-US-00981 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.07 Transmembrane 121-137 (120-138) ----- Final Results ----- bacterial membrane --- Certainty = 0.1829(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9127> which encodes the amino acid sequence <SEQ ID 9128>. Analysis of this protein sequence reveals the following: TABLE-US-00982 Possible cleavage site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.07 Transmembrane 95-111 (94-112) ------ Final Results ----- bacterial membrane --- Certainty = 0.183(Affirmative) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00983 Identities = 254/330 (76%), Positives = 290/330 (86%) Query: 6 MKKIAIDAMGGDYAPKAIVEGVNQAISDFSDIEVQLYGDQKKIEKYLTVTERVSIIHTEE 65 MK+IAIDAMGGD APKAIVEGVNQAI FSDIE+QLYGDQ KI YL ++RV+IIHT+E Sbjct: 27 MKRIAIDAMGGDNAPKAIVEGVNQAIEAFSDIEIQLYGDQTKINSYLIQSDRVAIIHTDE 86 Query: 66 KINSDDEPAKAVRRKKQSSMVLGAKAVKDGVAQAFISAGNTGALLAAGLFVVGRIKGVDR 125- KI SDDEPAKAVRRKK++SMVL AKAVK+G A A ISAGNTGALLA GLFVVGRIKGVDR Sbjct: 87 KIMSDDEPAKAVRRKKKASMVLAAKAVKEGKADAIISAGNTGALLAVGLFVVGRIKGVDR 146- Query: 126 PGLMSTMPTLDGVGFDMLDLGANAENTASHLHQYAILGSFYAKNVRGIEVPRVGLLNNGT 18- 5 PGL+ST+PT+ G+GFDMLDLGANAENTA HLHQYAILGSFYAKNVRGI PRVGLLNNGT Sbjct: 147 PGLLSTIPTVTGLGFDMLDLGANAENTAKHLHQYAILGSFYAKNVRGIANPRVGLLNNGT 20- 6 Query: 186 EETKGDSLHKEAYELLAAEPSINFIGNIEARDLMSSVADVVVTDGFTGNAVLKTMEGTAM 24- 5 EETKGD L K YELL A+ +I+F+GN+EAR+LMS VADV+V+DGFTGNAVLK++EGTA+ Sbjct: 207 EETKGDPLRKATYELLTADNTISFVGNVEARELMSGVADVIVSDGFTGNAVLKSIEGTAI 26- 6 Query: 246 SIMGSLKSSIKSGGVKAKLGALLLKDSLYQLKDSMDYSSAGGAVLFGLKAPIVKCHGSSD 30- 5 SIMG LK I SGG+K K+GA LLK SLY++K ++DYSSAGGAVLFGLKAP+VK HGSSD Sbjct: 267 SIMGQLKQIINSGGIKTKIGASLLKSSLYEMKKTLDYSSAGGAVLFGLKAPVVKSHGSSD 32- 6 Query: 306 SKAVYSTLKQVRTMLETQVVDQLVDAFTDE 335 KA++ST+KQVRTML+T VV QLV+ F E Sbjct: 327 VKAIFSTIKQVRTMLDTNVVGQLVEEFAKE 356 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 308 A DNA sequence (GBSx0337) was identified in S. agalactiae <SEQ ID 995> which encodes the amino acid sequence <SEQ ID 996>. Analysis of this protein sequence reveals the following: TABLE-US-00984 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4668(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 309 A DNA sequence (GBSx0338) was identified in S. agalactiae <SEQ ID 997> which encodes the amino acid sequence <SEQ ID 998>. Analysis of this protein sequence reveals the following: TABLE-US-00985 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.84 Transmembrane 61-77 (55-82) INTEGRAL Likelihood = -10.14 Transmembrane 26-42 (19-51) INTEGRAL Likelihood = -9.77 Transmembrane 192-208 (186-211) INTEGRAL Likelihood = -5.79 Transmembrane 267-283 (262-286) INTEGRAL Likelihood = -3.77 Transmembrane 100-116 (99-116) ----- Final Results ----- bacterial membrane --- Certainty = 0.6137(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9453> which encodes amino acid sequence <SEQ ID 9454> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00986 >GP: CAA22372 GB: AL034446 putative transmembrane protein [Streptomyces coelicolor A3(2)] Identities = 47/154 (30%), Positives = 69/154 (44%), Gaps = 12/154 (7%) Query: 120 SGFVEISSSNSFSFGPFFFLFLAYFIQSLTEEILFRGYVMTTVTKFKGSFAGVLCNSMLF 17- 9 SG+ E+ S F+A + TEE++FRG + + + G++ + ++F Sbjct: 118 SGYYEVDGLGSVQGAIGLVGFMA--AAAATEEVVFRGVLFRIIEEHIGTYLALGLTGLVF 17- 5 Query: 180 SFIHFRN-----YGITAIALFNLFLLGIIFSILFNMTKNILFVTGVHTTWNFTMGCVLGN 23- 4 +H N +G AIA+ F+L ++ T+N+ GVH WNF G V Sbjct: 176 GLMHLLNEDATLWGALAIAIEAGFMLAAAYAA----TRNLWLTIGVHFGWNFAAGGVFST 23- 1 Query: 235 KVSGGDSPVSLFRITENSSFALWNGGDFGFEGGV 268 VSG L T S L GGDFG EG V Sbjct: 232 VVSGNGDSEGLLDAT-MSGPKLLTGGDFGPEGSV 264 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 310 A DNA sequence (GBSx0339) was identified in S. agalactiae <SEQ ID 999> which encodes the amino acid sequence <SEQ ID 1000>. Analysis of this protein sequence reveals the following: TABLE-US-00987 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2665(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9451> which encodes amino acid sequence <SEQ ID 9452> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00988 >GP:BAB05088 GB:AP001511 unknown conserved protein [Bacillus halodurans] Identities = 81/242 (33%), Positives = 124/242 (50%), Gaps = 3/242 (1%) Query: 8 GLVLYNRNYREDDKLVKIFTETEGKRMFFVKHAS--KSKFNAVLQPLTIAHFILKINDNG 65- G+V+ +Y E +K+V +FT GK + A KS+ AV Q T + + N G Sbjct: 7 GIVIRTVDYGESNKIVTVFTREYGKIALMARGAKRPKSRLTAVTQLFTYGMMMFQKNA-G 65- Query: 66 LSYIDDYKEVLAFQETNSDLFKLSYASYITSLADVAISDNVADAQLFIFLKKTLELIEDG 12- 5 L + + + +F+E +DLF+ SY SY+T L + D + LF L +T+ + +G Sbjct: 66 LGTLTQGEIIQSFREVRNDLFRASYVSYVTDLTNKLTEDEKRNPYLFELLYQTIHYMNEG 12- 5 Query: 126 LDYEILTNIFEVQLLERFGVALNFHDCVFCHRVGLPFDFSHKYSGLLCPNHYYKDERRNH 18- 5 +D ++LT IFEV++ G+ CV C +P FS K +G LC KD Sbjct: 126 MDPDVLTRIFEVKMFTVAGIKPELDQCVSCRSTDVPVGFSIKEAGFLCKRCIEKDPHAYK 18- 5 Query: 186 LDPNMLYLINRFQSIQFDDLQTISVKPEMKLKIRQFLDMIYDEYVGIHLKSKKFIDDLSSWG - 247 + + L+ F L TIS+KPE K ++ + YDEY G+HLKS++F+D L S G Sbjct: 186 ITAQVAKLLRLFYHFDLQRLGTISLKPETKATLKTIIHQYYDEYSGLHLKSRRFLDQLESMG - 247 A related DNA sequence was identified in S. pyogenes <SEQ ID 1001> which encodes the amino acid sequence <SEQ ID 1002>. Analysis of this protein sequence reveals the following: TABLE-US-00989 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1566 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00990 Identities = 159/251 (63%), Positives = 210/251 (83%) Query: 1 MRVSQTYGLVLYNRNYREDDKLVKIFTETEGKRMFFVKHASKSKFNAVLQPLTIAHFILK 60- M+++++ G+VL+NRNYREDDKLVKIFTE GK+MFFVKH S+SK ++++QPLTIA FI K Sbjct: 1 MQLTESLGIVLFNRNYREDDKLVKIFTEVAGKQMFFVKHISRSKMSSIIQPLTIADFIFK 60- Query: 61 INDNGLSYIDDYKEVLAFQETNSDLFKLSYASYITSLADVAISDNVADAQLFIFLKKTLE 12- 0 +ND GLSY+ DY V ++ N+D+F+L+YASY+ +LAD AI+DN +D+ LF FLKKTL+ Sbjct: 61 LNDTGLSYVVDYSNVNTYRYINNDIFRLAYASYVLALADAAIADNESDSHLFTFLKKTLD 12- 0 Query: 121 LIEDGLDYEILTNIFEVQLLERFGVALNFHDCVFCHRVGLPFDFSHKYSGLLCPNHYYKD 18- 0 L+E+GLDYEILTNIFE+Q+L+RFG++LNFH+C CHR LP DFSH++S +LC HYYKD Sbjct: 121 LMEEGLDYEILTNIFEIQILDRFGISLNFHECAICHRTDLPLDFSHRFSAVLCSEHYYKD 18- 0 Query: 181 ERRNHLDPNMLYLINRFQSIQFDDLQTISVKPEMKLKIRQFLDMIYDEYVGIHLKSKKFI 24- 0 RRNHLDPN++YL++RFQ I FDDL+TIS+ ++K K+RQF+D +Y +YVGI LKSK FI Sbjct: 181 NRRNHLDPNVIYLLSRFQKITFDDLRTISLNKDIKKKLRQFIDELYHDYVGIKLKSKTFI 24- 0 Query: 241 DDLSSWGSIMK 251 D+L WG IMK Sbjct: 241 DNLVKWGDIMK 251 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 311 A DNA sequence (GBSx0340) was identified in S. agalactiae <SEQ ID 1003> which encodes the amino acid sequence <SEQ ID 1004>. This protein is predicted to be aromatic amino acid aminotransferase (patA). Analysis of this protein sequence reveals the following: TABLE-US-00991 Possible site: 14 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.13 Transmembrane 141-157 (140-159) ----- Final Results ----- bacterial membrane --- Certainty = 0.2253 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> A related GBS nucleic acid sequence <SEQ ID 9449> which encodes amino acid sequence <SEQ ID 9450> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00992 >GP:AAF06954 GB:AF146529 aromatic amino acid aminotransferase [Lactococcus lactis subsp. cremoris] Identities = 261/391 (66%), Positives = 323/391 (81%) Query: 38 MTLEKRFNKYLDRIEVSLIRQFDQSISDIPGMVKLTLGEPDFTTPDHVKEAAKSAIDANQ 97- M L K+FN LD+IE+SLIRQFDQ +S IP ++KLTLGEPDF TP+HVK+A +AI+ NQ Sbjct: 1 MDLLKKFNPNLDKIEISLIRQFDQQVSSIPDIIKLTLGEPDFYTPEHVKQAGIAAIENNQ 60- Query: 98 SYYTGMSGLLALRQAAADFAKDKYNLTYNPDCEILVTIGATEALSASLIAILEAGDVVLL 15- 7 S+YTGM+GLL LRQAA++F KY L+Y + EILVT+G TEA+S+ L++IL AGD VL+ Sbjct: 61 SHYTGMAGLLELRQAASEFLLKKYGLSYAAEDEILVTVGVTEAISSVLLSILVAGDEVLI 12- 0 Query: 158 PAPAYPGYEPIVNLVGADIVEIDTRENDFRLTPEMLETAIIQQGEKLKAVLLNYPTNPTG 21- 7 PAPAYPGYEP++ L G +VEIDTR NDF LTPEML+ AII++ K+KAV+LNYP NPTG Sbjct: 121 PAPAYPGYEPLITLAGGSLVEIDTRANDFVLTPEMLDQAIIEREGKVKAVILNYPANPTG 18- 0 Query: 218 ITYSRQEIAALAEVLKKYDIFVISDEVYSELTYTGQQHVSIAEYLPNQTILINGLSKSHA 27- 7 +TY+R++I LAEVLKK+++FVI+DEVYSEL YT Q HVSIAEY P QTI++NGLSKSHA Sbjct: 181 VTYNREQIKDLAEVLKKHEVFVIADEVYSELNYTDQPHVSIAEYAPEQTIVLNGLSKSHA 24- 0 Query: 278 MTGWRVGLVYAPEAFIAQIIKSHQYMVTAASTISQFAGVEALSVGKNDTLPMRQGYIKRR 33- 7 MTGWR+GL++A +AQIIK+HQY+VT+AST SQFA +EAL G +D LPM++ Y+KRR Sbjct: 241 MTGWRIGLIFAARELVAQIIKTHQYLVTSASTQSQFAAIEALKNGADDALPMKKEYLKRR 30- 0 Query: 338 DYIIDKMSKLGFKIIKPSGAFYIFAKIPDSYPQDSFKFCQDFAYQQAVAIIPGVAFGKYG 39- 7 DYII+KMS LGFKII+P GAFYIFAKIP QDSFKF DFA + AVAIIPG+AFG+YG Sbjct: 301 DYIIEKMSALGFKIIEPDGAFYIFAKIPADLEQDSFKFAVDFAKENAVAIIPGIAFGQYG 36- 0 Query: 398 EGYIRLSYAASMEVIETAMARLKVFMESYEG 428 EG++RLSYAASM+VIE AMARL ++ G Sbjct: 361 EGFVRLSYAASMDVIEQAMARLTDYVTKKRG 391 There is also homology to SEQ ID 1006. SEQ ID 1004 (GBS332) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 60 (lane 3; MW 50.7 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 67 (lane 4; MW 76 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 312 A DNA sequence (GBSx0341) was identified in S. agalactiae <SEQ ID 1007> which encodes the amino acid sequence <SEQ ID 1008>. This protein is predicted to be ribose-phosphate pyrophosphokinase (prsA). Analysis of this protein sequence reveals the following: TABLE-US-00993 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3118(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9447> which encodes amino acid sequence <SEQ ID 9448> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00994 >GP: AAA62181 GB: N92842 prs [Listeria monocytogenes] Identities = 209/312 (66%), Positives = 266/312 (84%), Gaps = 3/312 (0%) Query: 10 LKLFALSSNKELARKVSQTIGIPLGQSTVRQFSDGEIQVNIEESIRGHHVFILQSTSSPV 69 - LK+F+L+SN+ELA+++++ +GI LG+S+V FSDGEIQ+NIEESIRG HV+++QSTS+PV Sbjct: 10 LKIFSLNSNRELAEEIAKEVGIELGKSSVTHFSDGEIQINIEESIRGCHVYVIQSTSNPV 69 Query: 70 NDNLMEILIMVDALKRASAESVSVVMPYYGYARQDRKARSREPITSKLVANNLEVAGVDR 129- N NLME+LIM+DALKRASA ++++VMPYYGYARQDRKARSREPIT+KLVAN++E AG R Sbjct: 70 NQNLNELLIMIDALRRASAATINIVMPYYGYARQDRKARSREPITAKLVANLIETAGATR 129- Query: 130 LLTVDLHAAQIQGFFDIPVDHLMGAPLIADYFDRQGLVGDDVVVVSPDHGGVTRARKLAQ 18- 9 ++T+D+HA QIQGFFDIP+DHL L++DYF + L GDD+VVVSPDHGGVTRARK+A Sbjct: 130 MITLDMHAPQIQGFFDIPIDHLNAVRLLSDYFSERHL-GDDLVVVSPDHGGVTRARKMAD 18- 8 Query: 190 CLKTPIAIIDKRRSVTKMNTSEVMNIIGNIKGKKCILIDDMIDTAGTICHAADALAEAGA 24- 9 LK PIAIIDKRR + N +EVMNI+GN++GK CI+IDD+IDTAGTI AA AL EAGA Sbjct: 189 RLKAPIAIIDKRR--PRPNVAEVMNIVGNVEGKVCIIIDDIIDTAGTITLAAKALREAGA 24- 6 Query: 250 TAVYASCTHPVLSGPALDNIQNSAIEKLIVLDTIYLPEERLIDKIEQISIAELIGEAIIR 30- 9 T VYA C+HPVLSGPA+ I+ S IEKL+V ++I LPEE+ IDK+EQ+S+A L+GEAI+R Sbjct: 247 TKVYACCSHPVLSGPAMKRIEESPIEKLVVTNSIALPEEKWIDKMEQLSVAALLGEAIVR 30- 6 Query: 310 IHEKRPLSPLFE 321 +HE +S LFE Sbjct: 307 VHENASVSSLFE 318 A related DNA sequence was identified in S. pyogenes <SEQ ID 1009> which encodes the amino acid sequence <SEQ ID 1010>. Analysis of this protein sequence reveals the following:

TABLE-US-00995 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2685(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-00996 Identities = 298/322 (92%), Positives = 311/322 (96%) Query: 1 MEEIMSYSNLKLFALSSNKELAKKVSQTIGIPLGQSTVRQFSDGEIQVNIEESIRGHHVF 60 +EE MSYS+LKLFALSSNKELA+KV+ +GI LG+STVRQFSDGEIQVNIEESIRGHHVF Sbjct: 1 LEEKMSYSDLKLFALSSNKELAEKVASAMGIQLGKSTVRQFSDGEIQVNIEESIRGHHVF 60 Query: 61 ILQSTSSPVNDNLMEILIMVDALKRASAESVSVVMPYYGYARQDRKARSREPITSKLVAN 120- ILQSTSSPVNDNLMEILIMVDALKRASAE +SVVMPYYGYARQDRKARSREPITSKLVAN Sbjct: 61 ILQSTSSPVNDNLMEILIMVDALKRASAEKISVVMPYYGYARQDRKARSREPITSKLVAN 120- Query: 121 MLEVAGVDRLLTVDLHAAQIQGFFDIPVDHLMGAPLIADYFDRQGLVGDDVVVVSPDHGG 18- 0 MLEVAGVDRLLTVDLHAAQIQGFFDIPVDHLMGAPLIADYFDR GLVG+DVVVVSPDHGG Sbjct: 121 MLEVAGVDRLLTVDLHAAQIQGFFDIPVDHLMGAPLIADYFDRHGLVGEDVVVVSPDHGG 18- 0 Query: 181 VTRARKLAQCLKTPIAIIDKRRSVTKMNTSEVMNIIGNIKGKKCILIDDMIDTAGTICHA 24- 0 VTRARKLAQ L+TPIAIIDKRRSV KMNTSEVMNIIGN+ GKKCILIDDMIDTAGTICHA Sbjct: 181 VTRARKLAQFLQTPIAIIDKRRSVDKMNTSEVMNIIGNVSGKKCILIDDMIDTAGTICHA 24- 0 Query: 241 ADALAEAGATAVYASCTHPVLSGPALDNIQNSAIEKLIVLDTIYLPEERLIDKIEQISIA 30- 0 ADALAEAGATAVYASCTHPVLSGPALDNIQ SAIEKLIVLDTIYLP+ERLIDKIEQISIA Sbjct: 241 ADALAEAGATAVYASCTHPVLSGPALDNIQRSAIEKLIVLDTIYLPKERLIDKIEQISIA 30- 0 Query: 301 ELIGEAIIRIHEKRPLSPLFEM 322 +L+ EAIIRIHEKRPLSPLFEM Sbjct: 301 DLVAEAIIRIHEKRPLSPLFEM 322 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 313 A DNA sequence (GBSx0342) was identified in S. agalactiae <SEQ ID 1011> which encodes the amino acid sequence <SEQ ID 1012>. This protein is predicted to be a secreted protein. Analysis of this protein sequence reveals the following: TABLE-US-00997 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3751(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9277> which encodes amino acid sequence <SEQ ID 9278> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-00998 >GP: AAD00288 GB: U78607 putative secreted protein [Streptococcus mutans] Identities = 111/157 (70%), Positives = 130/157 (82%), Gaps = 1/157 (0%) Query: 1 MTAIKGQVGALESQQSELEAQNAQLEAVSQQLGQEIQTLSNKIVARNESLKKQVRSAQKG 60 + I+GQV AL++QQ+EL+A+N +LEA S LGQ+IQTLS+KIVARNESLK+Q RSAQK Sbjct: 55 LITIQGQVSALQTQQAELQAENQRLEAQSATLGQQIQTLSSKIVARNESLKQQARSAQKS 114- Query: 61 NL-TNYINTILNSKSVSDAVNRVVAIREVVSANEKMLAQQEADKAALEAKQIENQNAINT 119- N T+YIN I+NSKSVSDA+NRV AIREVVSANEKML QQE DKAA+E KQ ENQ AINT Sbjct: 115 NAATSYINAIINSKSVSDAINRVSAIREVVSANEKMLQQQEQDKAAVEQKQQENQAAINT 17- 4 Query: 120 VAANKQAIENNKAALATQRAQLEAAQLELSAQLTTVQ 156 VAAN++ I N AL TQ+AQLEAAQL L A+LTT Q Sbjct: 175 VAANQETIAQNTNALNTQQAQLEAAQLNLQAELTTAQ 211 A related GBS gene <SEQ ID 8543> and protein <SEQ ID 8544> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-00999 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 8.29 GvH: Signal Score (-7.5): 0.8 Possible site: 49 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 6.74 threshold: 0.0 PERIPHERAL Likelihood = 6.74 400 modified ALOM score: -1.85 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) The protein has homology with the following sequences in the databases: ##STR00024## SEQ ID 8544 (GBS65) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 5 (lane 6; MW 47.5 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 13 (lane 3; MW 72 kDa) and in FIG. 175 (lane 2 & 3; MW 72 kDa). The GBS65-GST fusion product was purified (FIG. 102A; see also FIG. 191, lane 4) and used to immunise mice (lane 1 product; 20 kg/mouse). The resulting antiserum was used for Western blot (FIG. 102B), FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 314 A DNA sequence (GBSx0343) was identified in S. agalactiae <SEQ ID 1015> which encodes the amino acid sequence <SEQ ID 1016>. Analysis of this protein sequence reveals the following: TABLE-US-01000 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1184 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 315 A DNA sequence (GBSx0344) was identified in S. agalactiae <SEQ ID 1017> which encodes the amino acid sequence <SEQ ID 1018>. Analysis of this protein sequence reveals the following: TABLE-US-01001 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4736 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 316 A DNA sequence (GBSx0345) was identified in S. agalactiae <SEQ ID 1019> which encodes the amino acid sequence <SEQ ID 1020>. This protein is predicted to be elongation factor Tu (tufA). Analysis of this protein sequence reveals the following: TABLE-US-01002 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3012 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9737> which encodes amino acid sequence <SEQ ID 9738> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01003 >GP: BAB03851 GB: AP001507 translation elongation factor Tu (EF-Tu) [Bacillus halodurans] Identities = 302/397 (76%), Positives = 350/397 (88%), Gaps = 2/397 (0%) Query: 7 MAKEKYDRSKPHVNIGTIGHVDHGKTTLTAAITTVLARRLPTSVNQPKDYASIDAAPEER 66 MAKEK+DRSK H NIGTIGHVDHGKTTLTAAITTVLA+R V Y +ID APEER Sbjct: 1 MAKEKFDRSKTHANIGTIGHVDHGKTTLTAAITTVLAKRSGKGVAMA--YDAIDGAPEER 58 Query: 67 ERGITINTAHVEYETEKRHYAHIDAPGHADYVKNMITGAAQMDGAILVVASTDGPMPQTR 126- ERGITI+TAHVEYET+ RHYAH+D PGHADYVKNMITGAAQMDG ILVV++ DGPMPQTR Sbjct: 59 ERGITISTAHVEYETDNRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAADGPMPQTR 118- Query: 127 EHILLSRQVGVKHLIVFMNKVDLVDDEELLELVEMEIRDLLSEYDFPGDDLPVIQGSALK 18- 6 EHILLSRQVGV +L+VF+NK D+VDDEELLELVEME+RDLLSEYDFPGDD+PVI+GSALK Sbjct: 119 EHILLSRQVGVPYLVVFLNKCDMVDDEELLELVEMEVRDLLSEYDFPGDDVPVIRGSALK 17- 8 Query: 187 ALEGDEKYEDIIMELMSTVDEYIPEPERDTDKPLLLPVEDVFSITGRGTVASGRIDRGTV 24- 6 ALEGD ++E+ I+ELM+ VD+YIP PERDT+KP ++PVEDVFSITGRGTVA+GR++RG + Sbjct: 179 ALEGDAEWEEKIIELMAAVDDYIPTPERDTEKPFMMPVEDVFSITGRGTVATGRVERGQL 23- 8 Query: 247 RVNDEVEIVGIKEDIQKAVVTGVEMFRKQLDEGLAGDNVGVLLRGVQRDEIERGQVLAKP 30- 6 V DEVEI+G++E+ +K VTGVEMFRK LD AGDN+G LLRGV R+E++RGQVLAKP Sbjct: 239 NVGDEVEIIGLEEEAKKTTVTGVEMFRKLLDYAEAGDNIGALLRGVSREEVQRGQVLAKP 29- 8 Query: 307 GSINPHTRFKGEVYILSKEEGGRHTPFFNNYRPQFYFRTTDVTGSIELPAGTEMVMPGDN 36- 6 G+I PHT FK EVY+LSKEEGGRHTPFF+NYRPQFYFRTTDVTG I+LP G EMVMPGDN Sbjct: 299 GTITPHTNFKAEVYVLSKEEGGRHTPFFSNYRPQFYFRTTDVTGIIQLPDGVEMVMPGDN 35- 8 Query: 367 VTIEVELIHPIAVEQGTTFSIREGGRTVGSGIVSEIE 403 V + VELI PIA+E+GT FSIREGGRTVG+G+V+ I+ Sbjct: 359 VEMTVELIAPIAIEEGTKFSIREGGRTVGAGVVASIQ 395 A related DNA sequence was identified in S. pyogenes <SEQ ID 1021> which encodes the amino acid sequence <SEQ ID 1022>. Analysis of this protein sequence reveals the following: TABLE-US-01004 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1367(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01005 Identities = 386/404 (95%), Positives = 396/404 (97%) Query: 1 MEAFPKMAKEKYDRSKPHVNIGTIGHVDHGKTTLTAAITTVLARRLPTSVNQPKDYASID 60 +EAFPKMAKEKYDRSKPHVNIGTIGHVDHGKTTLTAAITTVLARRLP+SVNQPKDYASID Sbjct: 12 LEAFPKMAKEKYDRSKPHVNIGTIGHVDHGKTTLTAAITTVLARRLPSSVNQPKDYASID 71 Query: 61 AAPEERERGITINTAHVEYETEKRHYAHIDAPGHADYVKNMITGAAQMDGAILVVASTDG 120- AAPEERERGITINTAHVEYET RHYAHIDAPGHADYVKNMITGAAQMDGAILVVASTDG Sbjct: 72 AAPEERERGITINTAHVEYETATRHYAHIDAPGHADYVKNMITGAAQMDGAILVVASTDG 131- Query: 121 PMPQTREHILLSRQVGVKHLIVFMNKVDLVDDEELLELVEMEIRDLLSEYDFPGDDLPVI 18- 0 PMPQTREHILLSRQVGVKHLIVFMNKVDLVDDEELLELVEMEIRDLLSEYDFPGDDLPVI Sbjct: 132 PMPQTREHILLSRQVGVKHLIVFMNKVDLVDDEELLELVEMEIRDLLSEYDFPGDDLPVI 19- 1 Query: 181 QGSALKALEGDEKYEDIIMELMSTVDEYIPEPERDTDKPLLLPVEDVFSITGRGTVASGR 24- 0 QGSALKALEGD K+EDIIMELM TVD YIPEPERDTDKPLLLPVEDVFSITGRGTVASGR Sbjct: 192 QGSALKALEGDTKFEDIIMELMDTVDSYIPEPERDTDKPLLLPVEDVFSITGRGTVASGR 25- 1 Query: 241 IDRGTVRVNDEVEIVGIKEDIQKAVVTGVEMFRKQLDEGLAGDNVGVLLRGVQRDEIERG 30- 0 IDRGTVRVNDE+EIVGIKE+ +KAVVTGVEMFRKQLDEGLAGDNVG+LLRGVQRDEIERG Sbjct: 252 IDRGTVRVNDEIEIVGIKEETKKAVVTGVEMFRKQLDEGLAGDNVGILLRGVQRDEIERG 31- 1 Query: 301 QVLAKPGSINPHTRFKGEVYILSKEEGGRHTPFFNNYRPQFYFRTTDVTGSIELPAGTEM 36- 0 QV+AKP SINPHT+FKGEVYILSK+EGGRHTPFFNNYRPQFYFRTTDVTGSIELPAGTEM Sbjct: 312 QVIAKPSSINPHTKFKGEVYILSKDEGGRHTPFFNNYRPQFYFRTTDVTGSIELPAGTEM 37- 1 Query: 361 VMPGDNVTIEVELIHPIAVEQGTTFSIREGGRTVGSGIVSEIEA 404 VMPGDNVTI VELIHPIAVEQGTTFSIREGGRTVGSGIVSEIEA Sbjct: 372 VMPGDNVTINVELIHPIAVEQGTTFSIREGGRTVGSGIVSEIEA 415 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 317 A DNA sequence (GBSx0346) was identified in S. agalactiae <SEQ ID 1023> which encodes the amino acid sequence <SEQ ID 1024>. Analysis of this protein sequence reveals the following: TABLE-US-01006 Possible site: 36 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -0.64 Transmembrane 90-106 (90-106) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 318 A DNA sequence (GBSx0347) was identified in S. agalactiae <SEQ ID 1025> which encodes the amino acid sequence <SEQ ID 1026>. This protein is predicted to be ftsW. Analysis of this protein sequence reveals the following: TABLE-US-01007 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.15 Transmembrane 44-60 (35-70) INTEGRAL Likelihood = -4.73 Transmembrane 76-92 (74-98) INTEGRAL Likelihood = -3.86 Transmembrane 117-133 (113-134) ----- Final Results ----- bacterial membrane --- Certainty = 0.5458 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01008 >GP: AAB39929 GB: U58049 putative cell division protein ftsW [Enterococcus hirae] Identities = 78/159 (49%), Positives = 107/159 (67%), Gaps = 4/159 (2%) Query: 1 MANSXYAMSNGGWFGRGLGNSIEKLGYLPEATTDFVFSIVIEELGVIGAGFILALVFFLI 60 M+NS YA+ NGG FGRG+GNSI K GYLPE+ TDF+FS++ EE G+IGA +L L+F L Sbjct: 240 MSNSYYALYNGGLFGRGMGNSITKKGYLPESETDFIFSVIAEEFGLIGALLVLFLLFLLC 29- 9 Query: 61 LRIMHVGIKAKDPFNSMIALGIGAMLLMQVFVNIGGISGLIPSTGVTFPFLSQGGNSLLV 120- +RI K K+ ++I +G+G +L+Q +NIG I GLIP TGV PF+S GG S L+ Sbjct: 300 MRIFQKSTKQKNQQANLILIGVGTWILVQTSINIGSILGLIPMTGVPLPFVSYGGTSYLI 35- 9 Query: 121 LSVAIGFVLNIDANEKKELIMKEAEEQYKPQEKNEKIIN 159 LS AIG LNI + + KE + ++ + Q K K++N Sbjct: 360 LSFAIGLALNISSRQVKE----KNKQVERLQLKKPKLLN 394 A related DNA sequence was identified in S. pyogenes <SEQ ID 1027> which encodes the amino acid sequence <SEQ ID 1028>. Analysis of this protein sequence reveals the following: TABLE-US-01009 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.93 Transmembrane 312-328 (303-338) INTEGRAL Likelihood = -8.23 Transmembrane 22-38 (17-47) INTEGRAL Likelihood = -6.85 Transmembrane 192-208 (187-211) INTEGRAL Likelihood = -5.10 Transmembrane 218-234 (212-236) INTEGRAL Likelihood = -4.83 Transmembrane 86-102 (85-107) INTEGRAL Likelihood = -3.72 Transmembrane 385-401 (383-402) INTEGRAL Likelihood = -3.45 Transmembrane 61-77 (61-79) INTEGRAL Likelihood = -2.39 Transmembrane 344-360 (344-360) ----- Final Results ----- bacterial membrane --- Certainty = 0.5373 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: TABLE-US-01010 >GP: CAB59721 GB: AJ250603 FtsW protein [Enterococcus faecium] Identities = 131/397 (32%), Positives = 223/397 (55%), Gaps = 23/397 (5%) Query: 15 KRHLLNYSILLPYLILSVIGLIMVYSTTSVSLIQAHANPFKSVINQGVFWIISLVAITFI 74 - KR +++ IL PYL LS+IGL+ VYS +S L+QA N ++ Q +F +S I Sbjct: 3 KRKKIDWWILGPYLTLSMIGLLEVYSASSYRLLQADENTKSLLLRQLIFIFLSWGVIFLA 62 Query: 75 YKLKLNFLTNTRVLTVVMLGEAFLLIIAR--FFTTAIKGAHGWIVIGPVSFQPAEYLKII 132- +KL++L + ++ + F LI+ R F + GA WI + + FQP+E + Sbjct: 63 RSIKLHYLLHPKIAGYGLALSIFFLILVRVGIFGVTVNGAQRWISLFGIQFQPSELANLF 122- Query: 133 MVWYLALTFAKIQKNISLYDYQALTRRKWWPTQWNDLRDWRVYSLLMVLLVAAQPDLGNA 19- 2 +++YL+ F P + +L+ + ++ + LL+ QP + A Sbjct: 123 LIFYLSWFFRDGNN----------------PPK--NLKKPFLITVSITLLILFQPKIAGA 16- 4 Query: 193 SIIVLTAIIMFSISGIGYRWFSAILVMITGLSTVFLGTIAVIGVERVAKIP-VFGYVAKR 25- 1 +I+ A ++F + + ++ ++V + L G + +G + +P +F + +R Sbjct: 165 LMILSIAWVIFWAAAVPFKKGIYLIVTFSALLIGAAGGVLYLGNK--GWLPQMFNHAYER 22- 2 Query: 252 FSAFFNPFHDLTDSGHQLANSYYAMSNGGWFGQGLGNSIEKRGYLPEAQTDFVFSVVIEE 31- 1 + +PF D +G+Q+ +S+YA+ NGG +G+GLGNSI K+GYLPE +TDF+FS++ EE Sbjct: 223 IATLRDPFIDSHGAGYQMTHSFYALYNGGIWGRGLGNSITKKGYLPETETDFIFSIITEE 28- 2 Query: 312 LGLIGAGFILALVFFLILRIMNVGIKAKNPFNAMMALGVGGMMLMQVFVNIGGISGLIPS 37- 1 LGLIGA +L L+F L +RI + + KN + LG G ++ +Q +N+G I+GL+P Sbjct: 283 LGLIGALCVLFLLFSLCMRIFCLSSRCKNQQAGLFLLGFGTLLFVQTIMNVGSIAGLMPM 34- 2 Query: 372 TGVTFPFLSQGGNSLLVLSVAVGFVLNIDASEKRDDI 408 TGV PF+S GG S L+LS+ +G LNI + + +++ Sbjct: 343 TGVPLPFVSYGGTSYLILSLGIGITLNISSKIQAEEL 379 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01011 Identities = 130/166 (78%), Positives = 152/166 (91%), Gaps = 2/166 (1%) Query: 1 MANSXYAMSNGGWFGRGLGNSIEKLGYLPEATTDFVFSIVIEELGVIGAGFILALVFFLI 60 +ANS YAMSNGGWFG+GLGNSIEK GYLPEA TDFVFS+VIEELG+IGAGFILALVFFLI Sbjct: 269 LANSYYAMSNGGWFGQGLGNSIEKRGYLPEAQTDFVFSVVIEELGLIGAGFILALVFFLI 32- 8 Query: 61 LRIMHVGIKAKDPFNSMIALGIGAMLLMQVFVNIGGISGLIPSTGVTFPFLSQGGNSLLV 120- LRIM+VGIKAK+PFN+M+ALG+G M+LMQVFVNIGGISGLIPSTGVTFPFLSQGGNSLLV Sbjct: 329 LRIMNVGIKAKNPFNAMMALGVGGMMLMQVFVNIGGISGLIPSTGVTFPFLSQGGNSLLV 38- 8 Query: 121 LSVAIGFVLNIDANEKKELIMKEAEEQYK--PQEKNEKIINLDAFK 164 LSVA+GFVLNIDA+EK++ I KEAE Y+ +++N K++N+ F+ Sbjct: 389 LSVAVGFVLNIDASEKRDDIFKEAELSYRKDTRKENSKVVNIKQFQ 434 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 319 A DNA sequence (GBSx0348) was identified in S. agalactiae <SEQ ID 1029> which encodes the amino acid sequence <SEQ ID 1030>. This protein is predicted to be probable cell division protein ftsw (ftsW). Analysis of this protein sequence reveals the following: TABLE-US-01012 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.77 Transmembrane 12-28 (7-37) INTEGRAL Likelihood = -7.22 Transmembrane 76-92 (74-97) INTEGRAL Likelihood = -6.53 Transmembrane 182-198 (178-201) INTEGRAL Likelihood = -4.62 Transmembrane 51-67 (46-69) INTEGRAL Likelihood = -2.87 Transmembrane 202-218 (202-218) ----- Final Results ----- bacterial membrane --- Certainty = 0.4906 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9327> which encodes amino acid sequence <SEQ ID 9328> was also identified. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-01013 >GP: CAA44490 GB: X62621 ORF2 N-terminal [Lactococcus lactis] Identities = 82/199 (41%), Positives = 122/199 (61%), Gaps = 9/199 (4%) Query: 1 MKIDKRHLLNYSILIPYLILSILGLIVIYSTTSATLIQLGANPFRSVINQGVFWAVSLVA 60 M ++K + LNYSILIPYLIL+ +G+++I+STT +Q G NP++ VINQ F +S++ Sbjct: 1 MNLNKNNFLNYSILIPYLILAGIGIVMIFSTTVPDQLQKGLNPYKLVINQTAFVLLSIIM 60 Query: 61 IIFIYKLKLNFLKNSKVLTMAVLVEVFLLLIARF------FTQEVNGAHGWIVIGPI-SF 113- I IY+LKL LKN K++ + +++ + L+ R T VNGA GWI I I + Sbjct: 61 IAVIYRLKLRALKNRKMIGIIMVILILSLIFCRIMPSSFALTAPVNGARGWIHIPGIGTV 120- Query: 114 QPAEYLKVIIVWYLAFTFARRQKKIEIYDYQALTKGRWLPRSLSDLKDWRFYSLFMIGLV 17- 3 QPAE+ KV I+WYLA F+ +Q++IE D + KG+ L + L WR + ++ + Sbjct: 121 QPAEFAKVFIIWYLASVFSTKQEEIEKNDINEIFKGKTLTQKL--FGGWRLPVVAILLVD 17- 8 Query: 174 IAQPDLGNGSIIVLTVIIM 192 + PDLGN II +IM Sbjct: 179 LIMPDLGNTMIIGAVALIM 197 There is also homology to SEQ ID 1028. A related GBS gene <SEQ ID 8545> and protein <SEQ ID 8546> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01014 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: 15.18 GvH: Signal Score (-7.5): -3.58 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 5 value: -9.77 threshold: 0.0 INTEGRAL Likelihood = -9.77 Transmembrane 12-28 (7-37) INTEGRAL Likelihood = 7.22 Transmembrane 76-92 (74-97) INTEGRAL Likelihood = 6.69 Transmembrane 210-226 (201-227) INTEGRAL Likelihood = 6.53 Transmembrane 182-198 (178-201) INTEGRAL Likelihood = 4.62 Transmembrane 51-67 (46-69) PERIPHERAL Likelihood = 1.32 116 modified ALOM score: 2.45 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4906 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: ##STR00025## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 320 A DNA sequence (GBSx0349) was identified in S. agalactiae <SEQ ID 1031> which encodes the amino acid sequence <SEQ ID 1032>. Analysis of this protein sequence reveals the following: TABLE-US-01015 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3665(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1033> which encodes the amino acid sequence <SEQ ID 1034>. Analysis of this protein sequence reveals the following: TABLE-US-01016 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2373(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01017 Identities = 35/41 (85%), Positives = 37/41 (89%) Query: 1 MEKEAKQIIDLKRNLFKIDVRAQKDEEKVFMRTACCYSPFY 41 +EKEAKQ+IDLKRNLFKIDVRAQKDEEKVFMRTAC S Y Sbjct: 1 LEKEAKQMIDLKRNLFKIDVRAQKDEEKVFMRTACRQSRVY 41 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 321 A DNA sequence (GBSx0351) was identified in S. agalactiae <SEQ ID 1037> which encodes the amino acid sequence <SEQ ID 1038>. Analysis of this protein sequence reveals the following: TABLE-US-01018 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.65 Transmembrane 78-94 (78-95) INTEGRAL Likelihood = -1.33 Transmembrane 421-437 (420-437) ----- Final Results ----- bacterial membrane --- Certainty = 0.1659(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01019 >GP: CAA00827 GB: A09073 phosphoenol pyruvate carboxylase [Corynebacterium glutamicum] Identities = 335/958 (34%), Positives = 539/958 (55%), Gaps = 80/958 (8%) Query: 22 EIITEEVGLLKQLLDEATQKLIGSESFDKIE--KIVSLSLTD---DYTGLKETISALSNE 76 - + + +++ L Q+L E + G E ++ +E ++ S + + L + ++ Sbjct: 3 DFLRDDIRFLGQILGEVIAEQEGQEVYELVEQARLTSFDIAKGNAEMDSLVQVFDGITPA 62 Query: 77 EMVIVSRYFSILPLLINISEDVDLAYEINYKNNLNQDYLGKLST----TIDVV------- 125- + ++R FS LL N++ED+ Y L + L T T+D Sbjct: 63 KATPIARAFSHFALLANLAEDL-------YDEELREQALDAGDTPPDSTLDATWLKLNEG 115- Query: 126 -AGHENAKDILEHVNVVPVLTAHPTQVQRKTVLELTSKIHDLLRKYRDVKAGIVNQ---- 18- 0 G E D+L + V PVLTAHPT+ +R+TV + I +R+ +++ Sbjct: 116 NVGAEAVADVLRNAEVAPVLTAHPTETRRRTVFDAQKWITTHMRERHALQSAEPTARTQS 17- 5 Query: 181 --EKWYADLRRYIGIIMQTDTIREKKLKVKNEITNVMEYYNRSLIKAVTKLTAEYKALAA 23- 8 ++ ++RR I I+ QT IR + ++++EI + YY SL++ + ++ + Sbjct: 176 KLDEIEKNIRRRITILWQTALIRVARPRIEDEIEVGLRYYKLSLLEEIPRINRDVAVELR 23- 5 Query: 239 KK---GIHLENPKPLTM-GMWIGGDRDGNPFVTAETLRLSAMVQSEVIINHYIEQLNELY 29- 4 ++ G+ L KP+ G WIGGD DGNP+VTAET+ S +E ++ +Y QL+ L Sbjct: 236 ERFGEGVPL---KPVVKPGSWIGGDHDGNPYVTAETVEYSTHRAAETVLKYYARQLHSLE 29- 2 Query: 295 RNMSLSINLTEVSPELVTLANQSQDNSVYRENEPYRKAFNFIQDKLVQTLLNLKVGSSPK 35- 4 +SLS + +V+P+L+ LA+ ++ R +EPYR+A + ++ +++ T Sbjct: 293 HELSLSDRMNKVTPQLLALADAGHNDVPSRVDEPYRRAVHGVRGRILAT----------- 34- 1 Query: 355 EKFVSRQESSDIVGRYIKSHIAQVASDIQTEELPAYATAEEFKQDLLLVKQSLVQYGQDS 41- 4 +++++G + + YA+ EEF D L + SL + Sbjct: 342 --------TAELIGE-------DAVEGVWFKVFTPYASPEEFLNDALTIDHSLRESKDVL 38- 6 Query: 415 LVDGELACLIQAVDIFGFYLATIDMRQDSSINEACVAELLKSANIVDDYSSLSEEEKCQL 47- 4 + D L+ LI A++ FGF L +D+RQ+S E +EL + A + +Y LSE EK ++ Sbjct: 387 IADDRLSVLISAIESFGFNLYALDLRQNSESYEDVLTELFERAQVTANYRELSEAEKLEV 44- 6 Query: 475 LLKELTEDPRTLSSTHAPKSELLQKELAIFQTARELKDQLGEDIINQHIISHTESVSDMF 53- 4 LLKEL + SE+ +EL IF+TA E + G ++ IIS SV+D+ Sbjct: 447 LLKELRSPRPLIPHGSDEYSEVTDRELGIFRTASEAVKKFGPRMVPHCIISMASSVTDVL 50- 6 Query: 535 ELAIMLKEVGLIDAN----QARIQIVPLFETIEDLDNSRDIMTQYLHYELVKKWIATNNN 59- 0 E ++LKE GLI AN + + ++PLFETIEDL I+ + +L + ++ +N Sbjct: 507 EPMVLLKEFGLIAANGDNPRGTVDVIPLFETIEDLQAGAGILDELWKIDLYRNYLLQRDN 56- 6 Query: 591 YQEIMLGYSDSNKDGGYLSSGWTLYKAQNELTKIGEENGIKITFFHGRGGTVGRGGGPSY 65- 0 QE+MLGYSDSNKDGGY S+ W LY A+ +L ++ G+K+ FHGRGGTVGRGGGPSY Sbjct: 567 VQEVMLGYSDSNKDGGYFSANWALYDAELQLVELCRSAGVKLRLFHGRGGTVGRGGGPSY 62- 6 Query: 651 EAITSQPFGSIKDRIRLTEQGEIIENKYGNQDAAYYNLEMLISASIDRMVTRMITNPNEI 71- 0 +AI +QP G+++ +R+TEQGEII KYGN + A NLE L+SA+++ + + +E+ Sbjct: 627 DAILAQPRGAVQGSVRITEQGEIISAKYGNPETARRNLEALVSATLE----ASLLDVSEL 68- 2 Query: 711 DNFRETMDGIVSESNAV----YRNLVFDNPYFYDYFFEASPIKEVSSLNIGSRPAARKTI 76- 6 + + D I+SE + + Y +LV ++ F DYF +++P++E+ SLNIGSRP++RK Sbjct: 683 TDHQRAYD-IMSEISELSLKKYASLVHEDQGFIDYFTQSTPLQEIGSLNIGSRPSSRKQT 74- 1 Query: 767 TEISGLRAIFWVFSWSQNRIMFPGWYGVGSAFKHFI---EQDEANLAKLQTMYQKWPFFN 82- 3 + + LRAIPWV SWSQ+R+M PGW+GVG+A + +I EQ +A+LQT+ + WPFF Sbjct: 742 SSVEDLRAIPWVLSWSQSRVMLPGWFGVGTALSQWIGEGEQATQRIAELQTLNESWPFFT 80- 1 Query: 824 SLLSNVDMVLSKSNMNIALQYAQLAGSKEVRD-VFNIILNEWQLTKDMILAIEQHDNLLE 88- 2 S+L N+ V+SK+ + +A YA L EV + V+++I E+ LTK M I D+LL+ Sbjct: 802 SVLDNMAQVMSKAELRLAKLYADLIPDTEVAERVYSVIREEYFLTKKMFCVITGSDDLLD 86- 1 Query: 883 ENPMLHASLDYRLPYFNVLNYVQIELIKRLRSNQLDEDYEKLIHITINGIATGLRNSG 940 +NP+L S+ R PY LN +Q+E+++R R E + I +T+NG++T LRNSG Sbjct: 862 DNPLLARSVQRRYPYLLPLNVIQVEMMRRYRKGDQSEQVSRNIQLTMNGLSTALRNSG 919 A related GBS nucleic acid sequence <SEQ ID 10961> which encodes amino acid sequence <SEQ ID 10962> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 1039> which encodes the amino acid sequence <SEQ ID 1040>. Analysis of this protein sequence reveals the following: TABLE-US-01020 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1613(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01021 Identities = 659/927 (71%), Positives = 779/927 (83%), Gaps = 11/927 (1%) Query: 14 KLESSSNKEIITEEVGLLKQLLDEATQKLIGSESFDKIEKIVSLSLTDDYTGLKETISAL 73 - KLESS+N++II EEV LLK++L+ T+++IG ++F IE I+ LS DY L++ ++ + Sbjct: 5 KLESSNNQDIIAEEVALLKEMLENITRRMIGDDAFTVIESIMVLSEKQDYIELEKVVANI 64 Query: 74 SNEEMVIVSRYFSILPLLINISEDVDLAYEINYKNNLNQDYLGKLSTTIDVVAGHENAKD 133- SN+EM ++SRYFSILPLLINISEDVDLAYEINY+NN + DYLGKL+ TI +AG +N KD Sbjct: 65 SNQEMEVISRYFSILPLLINISEDVDLAYEINYQNNTDTDYLGKLALTIKDLAGKDNGKD 124- Query: 134 ILEHVNVVPVLTAHPTQVQRKTVLELTSKIHDLLRKYRDVKAGIVNQEKWYADLRRYIGI 19- 3 ILE VNVVPVLTAHPTQVQRKT+LELT+ IH LLRKYRD KAG++N EKW +L RYI + Sbjct: 125 ILEQVNVVPVLTAHPTQVQRKTILELTTHIHKLLRKYRDAKAGVINLEKWRQELYRYIEM 18- 4 Query: 194 IMQTDTIREKKLKVKNEITNVMEYYNRSLIKAVTKLTAEYKALAAKKGIHLENPKPLTMG 25- 3 IMQTD IREKKL+VKNEI NVM+YY+ SLI+AVTKLT EYK LA K G+ L+NPKP+TMG Sbjct: 185 IMQTDIIREKKLQVKNEIKNVMQYYDGSLIQAVTKLTTEYKNLAQKHGLELDNPKPITMG 24- 4 Query: 254 MWIGGDRDGNPFVTAETLRLSAMVQSEVIINHYIEQLNELYRNMSLSINLTEVSPELVTL 31- 3 MWIGGDRDGNPFVTAETL LSA VQSEVI+N+YI++L LYR SLS L + + E+ L Sbjct: 245 MWIGGDRDGNPFVTAETLCLSATVQSEVILNYYIDELAALYRTFSLSSTLVQPNSEVERL 30- 4 Query: 314 ANQSQDNSVYRENEPYRKAFNFIQDKLVQTLLNLKVGSSPKEKFVSRQESSDIVGRYIKS 37- 3 A+ SQD S+YR NEPYR+AF++IQ +L QT + L + + SS + S Sbjct: 305 ASLSQDQSIYRGNEPYRRAFHYIQSRLKQTQIQLT------NQPAASMSSSVGLNTSAWS 35- 8 Query: 374 HIAQVASDIQTEELPAYATAEEFKQDLLLVKQSLVQYGQDSLVDGELACLIQAVDIFGFY 43- 3 A + + I AY + +FK DL ++QSL+ G +L++G+L ++QAVDIFGF+ Sbjct: 359 SPASLENPIL-----AYDSPVDFKADLKAIEQSLLDNGNSALIEGDLREVMQAVDIFGFF 41- 3 Query: 434 LATIDMRQDSSINEACVAELLKSANIVDDYSSLSEEEKCQLLLKELTEDPRTLSSTHAPK 49- 3 LA+IDMRQDSS+ EACVAELLK ANIVDDYSSLSE EKC +LL++L E+PRTLSS K Sbjct: 414 LASIDMRQDSSVQEACVAELLKGANIVDDYSSLSETEKCDVLLQQLMEEPRTLSSAAVAK 47- 3 Query: 494 SELLQKELAIFQTARELKDQLGEDIINQHIISHTESVSDMFELAIMLKEVGLIDANQARI 55- 3 S+LL+KELAI+ TARELKD+LGE++I QHIISHTESVSDMFELAIMLKEVGL+D +AR+ Sbjct: 474 SDLLEKELAIYTTARELKDKLGEEVIKQHIISHTESVSDMFELAIMLKEVGLVDQQRARV 53- 3 Query: 554 QIVPLFETIEDLDNSRDIMTQYLHYELVKKWIATNNNYQEIMLGYSDSNKDGGYLSSGWT 61- 3 QIVPLFETIEDLDN+RDIM YL +++VK WIATN NYQEIMLGYSDSNKDGGYL+SGWT Sbjct: 534 QIVPLFETIEDLDNARDIMAAYLSHDIVKSWIATNRNYQEIMLGYSDSNKDGGYLASGWT 59- 3 Query: 614 LYKAQNELTKIGEENGIKITFFHGRGGTVGRGGGPSYEAITSQPFGSIKDRIRLTEQGEI 67- 3 LYKAQNELT IGEE+G+KITFFHGRGGTVGRGGGPSY+AITSQPFGSIKDRIRLTEQGEI Sbjct: 594 LYKAQNELTAIGEEHGVKITFFHGRGGTVGRGGGPSYDAITSQPFGSIKDRIRLTEQGEI 65- 3 Query: 674 IENKYGNQDAAYYNLEMLISASIDRMVTRMITNPNEIDNFRETMDGIVSESNAVYRNLVF 73- 3 IENKYGN+D AYY+LEMLISASI+RMVT+MIT+PNEID+FRE MD IV++SN +YR LVF Sbjct: 654 IENKYGNKDVAYYHLEMLISASINRMVTQMITDPNEIDSFREIMDSIVADSNIIYRKLVF 71- 3 Query: 734 DNPYFYDYFFEASPIKEVSSLNIGSRPAARKTITEISGLRAIPWVFSWSQNRIMFPGWYG 79- 3 DNP+FYDYFFEASPIKEVSSLNIGSRPAARKTITEI+GLRAIPWVFSWSQNRIMFPGWYG Sbjct: 714 DNPHFYDYFFEASPIKEVSSLNIGSRPAARKTITEITGLRAIPWVFSWSQNRIMFPGWYG 77- 3 Query: 794 VGSAFKHFIEQDEANLAKLQTMYQKWPFFNSLLSNVDMVLSKSNMNIALQYAQLAGSKEV 85- 3 VGSAFK +I++ + NL +LQ MYQ WPFF+SLLSNVDMVLSKSNMNIA QYAQLA ++V Sbjct: 774 VGSAFKRYIDRAQGNLERLQHMYQTWPFFHSLLSNVDMVLSKSNMNIAFQYAQLAERQDV 83- 3 Query: 854 RDVFNIILNEWQLTKDMILAIEQHDNLLEENPMLHASLDYRLPYFNVLNYVQIELIKRLR 91- 3 RDVF IL+EWQLTK++ILAI+ HD+LLE+NP L SL RLPYFNVLNY+QIELIKR R Sbjct: 834 RDVFYEILDEWQLTKNVILAIQDHDDLLEDNPSLKHSLKSRLPYFNVLNYIQIELIKRWR 89- 3 Query: 914 SNQLDEDYEKLIHITINGIATGLRNSG 940 +NQLDE+ EKLIH TINGIATGLRNSG Sbjct: 894 NNQLDENDEKLIHTTINGIATGLRNSG 920 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 322 A DNA sequence (GBSx0352) was identified in S. agalactiae <SEQ ID 1041> which encodes the amino acid sequence <SEQ ID 1042>. This protein is predicted to be Bacillus licheniformis Pz-peptidase homologue (pepF). Analysis of this protein sequence reveals the following: TABLE-US-01022 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3012 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 1043> which encodes the amino acid sequence <SEQ ID 1044>. Analysis of this protein sequence reveals the following: TABLE-US-01023 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3137 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01024 Identities = 512/593 (86%), Positives = 564/593 (94%) Query: 1 MKLKKRSEFPENELWDLTALYKDRQDFLLAIEKALEDIKVFKKNYEGKLNCVEDFTSALM 60 M+LKKRSEFPENELWDLTALYKDRQDFLLAIEKAL+DI +FK+NYEG+L V+DFT AL+ Sbjct: 26 MELKKRSEFPENELWDLTALYKDRQDFLLAIEKALQDIDLFKRNYEGRLTSVDDFTQALI 85 Query: 61 EIEHIYIQMSHIDTYAFMPQTTDFSNEEFAQISQAGSDFATKANVLLSFFNTALANADIK 120- EIEHIYIQMSHI TYAFMPQTTDFS+E FAQI+QAG DF TKA+V LSFF+TALANAD+ Sbjct: 86 EIEHIYIQMSHIGTYAFMPQTTDFSDESFAQIAQAGDDFMTKASVALSFFDTALANADLD 145- Query: 121 ILDSLENNPHFKATIRQAKIQKQHLLSPEVEKALTNLNEVLNTPYDIYTKMRAGDFDMED 18- 0 +LD+LE NP+F A IR AKIQK+HLLSP+VEKAL NL EV+N PYDIYTKMRAGDFDM+D Sbjct: 146 VLDTLEKNPYFSAAIRMAKIQKEHLLSPDVEKALANLREVINAPYDIYTKMRAGDFDMDD 20- 5 Query: 181 FEVDGKTYKNSFVTYENYFQNHENAEIREKSFRSFSKGLRKHQNAAAAAYLAKVKSEKLI 24- 0 FEVDGKTYKNSFV+YEN++QNHENAEIREK+FRSFSKGLRKHQN AAAAYLAKVKSEKL+ Sbjct: 206 FEVDGKTYKNSFVSYENFYQNHENAEIREKAFRSFSKGLRKHQNTAAAAYLAKVKSEKLL 26- 5 Query: 241 ADMRGYDSVFDYLLSEQEVDRSMFDRQIDLIMDEFGPVAQRFLKHIADVNGIEKMTFADW 30- 0 ADM+GY SVFDYLL+EQEVDRS+FDRQIDLIM EFGPVAQ+FLKH+A VNG+EKMTFADW Sbjct: 266 ADMKGYASVFDYLLAEQEVDRSLFDRQIDLIMTEFGPVAQKFLKHVAQVNGLEKMTFADW 32- 5 Query: 301 KLDIDNELNPEVSINDAYDLVMKSVAPLGKEYSQEVERYQKERWVDFAANANKDSGGYAA 36- 0 KLDIDN+LNPEVSI+ AYDLVMKS+APLG+EY++E+ERYQ ERWVDFAANANKDSGGYAA Sbjct: 326 KLDIDNDLNPEVSIDGAYDLVMKSLAPLGQEYTKEIERYQTERWVDFAANANKDSGGYAA 38- 5 Query: 361 DPYKVHPYVLMSWTGRMSDVYTLIHEIGHSGQFIFSDNHQSFFNTHMSTYYVEAPSTFNE 42- 0 DPYKVHPYVLMSWTGRMSDVYTLIHEIGHSGQFIFSDNHQS+FNTHMSTYYVEAPSTFNE Sbjct: 386 DPYKVHPYVLMSWTGRMSDVYTLIHEIGHSGQFIFSDNHQSYFNTHMSTYYVEAPSTFNE 44- 5 Query: 421 LLLSDYLENQFDTARQKRFALAHRLTDTYFHNFITHLLEAAFQRKVYTLIEEGGTFGAEQ 48- 0 L+LSDYLE+QFD RQKRFALAHRLTDTYFHNFITHLLEAAFQRKVYTLIEEGGTFGA+Q Sbjct: 446 LMLSDYLEHQFDDPRQKRFALAHRLTDTYFHNFITHLLEAAFQRKVYTLIEEGGTFGADQ 50- 5 Query: 481 LNAIMKEVLTQFWGDAIEIDDDAALTWMRQAHYYMGLYSYTYSAGLVISTAGYLNLKNNP 54- 0 LNA+MKEVLT FWGDA++IDDDAALTWMRQAHYYMGLYSYTYSAGLVISTAGYLNLK+NP Sbjct: 506 LNAMMKEVLTDFWGDAVDIDDDAALTWMRQAHYYMGLYSYTYSAGLVISTAGYLNLKHNP 56- 5 Query: 541 NGAKEWLAFLKSGGSRTPLETALLISADISTDKPLRDTINFLSNTVDQIINYS 593 NGAKEWL FLKSGGSRTPL+TA+LI ADI+T+KPLRDTI FLS+TVDQII+Y+ Sbjct: 566 NGAKEWLDFLKSGGSRTPLDTAMLIGADIATEKPLRDTIQFLSDTVDQIISYT 618 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 323 A DNA sequence (GBSx0353) was identified in S. agalactiae <SEQ ID 1045> which encodes the amino acid sequence <SEQ ID 1046>. Analysis of this protein sequence reveals the following: TABLE-US-01025 Possible site: 19 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1047> which encodes the amino acid sequence <SEQ ID 1048>. Analysis of this protein sequence reveals the following: TABLE-US-01026 Possible site: 19 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below:

TABLE-US-01027 Identities = 72/127 (56%), Positives = 85/127 (66%) Query: 1 MKKYIKLFLLTVFATTLVACGQPSTSNKTTTSSTLEVGKVELVVKEDTNVLSEKVVYHKG 60 + K K L + A LVAC Q + +TT S V LVVKEDTN + EKV + KG Sbjct: 1 VNKRFKTGFLALVAMLLVACSQGTKQIQTTPSVPKADHHVRLVVKEDTNTVDEKVSFGKG 60 Query: 61 DTVLDVLKANYKVKEKDGFITSIDGISQDETKGLYWMFKVNNKLAPKAANQIKVKKNDKI 120- DTVL+VLK NY+VKEKDGFIT+IDGI QD YW+FKVN K+A K A+QI VK D I Sbjct: 61 DTVLEVLKDNYEVKEKDGFITAIDGIEQDTKANKYWLFKVNGKMADKGADQITVKDGDSI 120- Query: 121 EFYQEVY 127 EFYQEV+ Sbjct: 121 EFYQEVF 127 SEQ ID 1046 (GBS185) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 28 (lane 6; MW 15.7 kDa). GBS185-His was purified as shown in FIG. 199, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 324 A DNA sequence (GBSx0354) was identified in S. agalactiae <SEQ ID 1049> which encodes the amino acid sequence <SEQ ID 1050>. Analysis of this protein sequence reveals the following: TABLE-US-01028 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.46 Transmembrane 75-91 (67-94) INTEGRAL Likelihood = -4.41 Transmembrane 33-49 (30-49) INTEGRAL Likelihood = -2.60 Transmembrane 53-69 (52-70) INTEGRAL Likelihood = -1.38 Transmembrane 108-124 (106-124) INTEGRAL Likelihood = -0.06 Transmembrane 149-165 (149-165) ----- Final Results ----- bacterial membrane --- Certainty = 0.2784 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9731> which encodes amino acid sequence <SEQ ID 9732> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10929> which encodes amino acid sequence <SEQ ID 10930> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1051> which encodes the amino acid sequence <SEQ ID 1052>. Analysis of this protein sequence reveals the following: TABLE-US-01029 Possible site: 48 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.96 Transmembrane 50-66 (49-71) INTEGRAL Likelihood = -5.73 Transmembrane 101-117 (99-124) INTEGRAL Likelihood = -4.41 Transmembrane 141-157 (139-159) INTEGRAL Likelihood = -4.25 Transmembrane 73-89 (67-92) ----- Final Results ----- bacterial membrane --- Certainty = 0.4185 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below: TABLE-US-01030 Identities = 82/163 (50%), Positives = 120/163 (73%), Gaps = 3/163 (1%) Query: 10 LTRVAILSALCVVLRYAFAPLPNIQPITAIFLITVVLFDLKEGVATVTITMLVSSFLMGF 69 - ++R+AI+SALCVVLR F+ LPN+QP+TA L ++ F L E V + + + +S+FL+GF Sbjct: 6 MSRIAIMSALCVVLRMVFSSLPNVQPVTAFLLSYLLYFGLAEAVLVMMLCLFLSAFLLGF 65 Query: 70 GPWVFLQIISFTLILCLWKFLIYPLTKAVCFGKITEVVLQTFFAGGLGVVYGVIIDTCFA 129- GPWVF Q+ F L+L LW+F++YPL++ F K ++ Q F G++YGV+IDTCFA Sbjct: 66 GPWVFWQVTCFVLVLLLWRFVLYPLSQQ--FPKY-QLGCQAFLVALCGLLYGVLIDTCFA 122- Query: 130 WLYHMPWWTYVLAGLSFNMAHALSTCLFYPLLLPILRRFRNEK 172 +LY MPWW+YVLAG+ FN+AHALST +F+P+++ + RR E+ Sbjct: 123 YLYSMPWWSYVLAGMPFNIAHALSTLVFFPVVMMLFRRLIGEQ 165 A related GBS gene <SEQ ID 8549> and protein <SEQ ID 8550> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01031 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 6.79 GvH: Signal Score (-7.5): -0.91 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 3 value: -4.46 threshold: 0.0 INTEGRAL Likelihood = -4.46 Transmembrane 35-51 (29-54) INTEGRAL Likelihood = -1.38 Transmembrane 68-84 (66-84) INTEGRAL Likelihood = -0.06 Transmembrane 109-125 (109-125) PERIPHERAL Likelihood = 7.53 88 modified ALOM score: 1.39 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2784 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00026## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 325 A DNA sequence (GBSx0355) was identified in S. agalactiae <SEQ ID 1053> which encodes the amino acid sequence <SEQ ID 1054>. This protein is predicted to be endolysin. Analysis of this protein sequence reveals the following: TABLE-US-01032 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01033 >GP: CAA72266 GB: Y11477 endolysin [Bacteriophage Bastille] Identities = 64/210 (30%), Positives = 95/210 (44%), Gaps = 15/210 (7%) Query: 66 KPIIDVSGWQLPKEIDYDTLSKNISGVVIRVFGGSKISKTNNAAYTTGIDKSFKTHIKEF 12- 5 K I+D+S +ID+DT +S + R G + + +N +D+ +KT + Sbjct: 12 KTIVDISHHNA--DIDFDTAKNYVSMFIARTGDGHRYN--SNGELQGVVDRKYKTFVANM 67 Query: 126 QKRNIPVAVYSYALGSSVKEMKEEAQIFYKNAAPYKPTFYWIDVEEETMSNMNKGVQAFR 18- 5 + R IP Y + S V K+EA+ F+ N T + D E T NM + +Q F Sbjct: 68 KARGIPFGNYMFNRFSGVASAKQEAEFFW-NYGDKDATVWVCDAEVSTAPNMKECIQVFI 12- 6 Query: 186 KELKRLGAKNVGIYIGTYFMTEQGISVKGFDAVWIPTYGSDSGYYEAAPQTELKYDLHQY 24- 5 LK LGAK VG+YIG + E G D WIP YG+ + DL Q+ Sbjct: 127 DRLKELGAKKVGLYIGHHKYQEFGGKDVNCDFTWIPRYGNKPAF---------ACDLWQW 17- 7 Query: 246 TSQGYLPGFNQPLDLNQIAVNKDKKKTYEK 275 T G + G + D+N + +K EK Sbjct: 178 TEYGNIAGIGK-CDINVLYGDKPMSFFTEK 206 A related DNA sequence was identified in S. pyogenes <SEQ ID 1055> which encodes the amino acid sequence <SEQ ID 1056>. Analysis of this protein sequence reveals the following: TABLE-US-01034 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -16.98 Transmembrane 8-24 ( 3-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.7793(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01035 Identities = 198/278 (71%), Positives = 225/278 (84%) Query: 1 MRRRIKPIVVAVFFSLFGLLLIIGHLHSTNTLKKELVEAKKTIPSVKASKVPQKSTSSKD 60 MRR+IKPIVV VFF L ++LIIG + + +KE+ +AK IP ++ K+++S+ Sbjct: 1 MRRKIKPIVVLVFFILLAMVLIIGKRQANHAKQKEVEDAKSHIPIATSNPGKAKTSTSET 60 Query: 61 KEFVLKPIIDVSGWQLPKEIDYDTLSKNISGVVIRVFGGSKISKTNNAAYTTGIDKSFKT 12- 0 ++F+L PI+DVSGWQLP+EIDYDTLS++ISG ++RV+GGS+I+ NNAA+TTGIDKSFKT Sbjct: 61 EDFILNPIVDVSGWQLPEEIDYDTLSRHISGAIVRVYGGSQITAHNNAAFTTGIDKSFKT 12- 0 Query: 121 HIKEFQKRNIPVAVYSYALGSSVKEMKEEAQIFYKNAAPYKPTFYWIDVEEETMSNMNKG 18- 0 HIKEFQKRN+PVAVYSYALG S KEMKEEA+ FYKNAAPY PT+YWIDVEE TM +MNKG Sbjct: 121 HIKEFQKRNVPVAVYSYALGRSTKEMKEEARAFYKNAAPYNPTYYWIDVEEATMKDMNKG 18- 0 Query: 181 VQAFRKELKRLGAKNVGIYIGTYFMTEQGISVKGFDAVWIPTYGSDSGYYEAAPQTELKY 24- 0 V AFR+ELK+LGA+NVG+YIGTYFM EW IS KGFD+VWIPTYGSDSGYYEAAP T L Y Sbjct: 181 VTAFREELKKLGAENVGLYIGTYFMAEQDISTKGFDSVWIPTYGSDSGYYEAAPNTTLDY 24- 0 Query: 241 DLHQYTSQGYLPGFNQPLDLNQIAVNKDKKKTYELKFG 278 DLHQYTSQGYL GFN LDLNQIAV KD KKT+EKLFG Sbjct: 241 DLHQYTSQGYLSGFNNALDLNQIAVTKDTKKTFEKLFG 278 A related GBS gene <SEQ ID 8551> and protein <SEQ ID 8552> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01036 Lipop Possible site: -1 Crend: 5 McG: Discrim Score: 13.20 GvH: Signal Score (-7.5): -0.72 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 7.05 threshold: 0.0 PERIPHERAL Likelihood = 7.05 196 modified ALOM score: -1.91 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00027## SEQ ID 8552 (GBS206) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 6; MW 31.7 kDa). GBS206-His was purified as shown in FIG. 206, lane 6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 326 A DNA sequence (GBSx0356) was identified in S. agalactiae <SEQ ID 1057> which encodes the amino acid sequence <SEQ ID 1058>. Analysis of this protein sequence reveals the following: TABLE-US-01037 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.44 Transmembrane 183-199 (183-200) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9729> which encodes amino acid sequence <SEQ ID 9730> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01038 >GP: AAG20117 GB: AE005090 NADH dehydrogenase/oxidoreductase-like protein; NolA [Halobacterium sp. NRC-1] Identities = 38/156 (24%), Positives = 83/156 (52%), Gaps = 13/156 (8%) Query: 19 TMEILIAGGSGFLGKQIIKAALTKGHKVAYLSRHEGKGDIFKDPRLTYIRGDITEADKIH 78 - +M++L+ GG+GF+G + + +GH V +R + D +T I GD+T + + Sbjct: 8 SMDVLVTGGTGFIGTHLCRELDDRGHDVTAFAREPADAALPAD--VTRIVGDVTVKETVA 65 Query: 79 LEDRTFDILIDCIGA---IKPNQLD----ELNVKATQKAVALCHKNQIPKLVYISA---- 127- D +++ + KP+ D ++++ T+ VA + + ++ +SA Sbjct: 66 NAIDGHDAVVNLVALSPLFKPSGGDSRHLDVHLGGTENVVAAASEAGVEYILQLSALDAD 125- Query: 128 NSGYSAYIKSKRKAEQIIKASGLDYLFVRPGLMYGE 163 +G +AY+++K +AE+ +++S L + VRP +++G+ Sbjct: 126 PTGPTAYLRAKGRAEEAVRSSDLHHTIVRPSVVFGD 161 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8553> and protein <SEQ ID 8554> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01039 Lipop Possible site: -1 Crend: 5 McG: Discrim Score: -7.99 GvH: Signal Score (-7.5): -6.34 Possible site: 41 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -1.44 threshold: 0.0 INTEGRAL Likelihood = -1.44 Transmembrane 183-199 (183-200) PERIPHERAL Likelihood = 4.29 20 modified ALOM score: 0.79 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> RGD motif 68-70 The protein has homology with the following sequences in the databases: ##STR00028## SEQ ID 8554 (GBS303) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 5; MW 28.3 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 55 (lane 5; MW 53.2 kDa). The GBS303-GST fusion product was purified (FIG. 207, lane 6) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 275), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 327 A DNA sequence (GBSx0357) was identified in S. agalactiae <SEQ ID 1059> which encodes the amino acid sequence <SEQ ID 1060>. Analysis of this protein sequence reveals the following: TABLE-US-01040 Possible site: 4 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2850(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01041 >GP: AAC36853 GB: L23802 regulatory protein [Enterococcus faecalis] Identities = 61/164 (37%), Positives = 96/164 (58%), Gaps = 13/164 (7%) Query: 1 MSKKNKIKKTLVDQILDKAKIEH---------DSLQLDALQGDLPNGIQKQDIFKTLALI 51 M+KK +KT +++++ K+ + D L +++ L GI+K IFKTL + Sbjct: 1 MAKKKTQQKTNAMRMVEQHKVPYKEYEFAWSEDHLSAESVAESL--GIEKGRIFKTLVTV 58 Query: 52 GDKTGPIIGILPLTEHLSEKKLAKISGNKKVQMIPQKDLQKITGYIHGANNPIGIRQKHN 11- 1 G+KTGP++ ++P + L KKLAK SGNKKV+M+ KDL+ TGIY G +P G+ K Sbjct: 59 GNKTGPVVAVIPGNQELDLKKLAKSAGNKKVEMLHLKDLEATTGYIRGGCSPTGM--KKQ 11- 6 Query: 112 YPIFIDTIALEKQELIVSAGEIGRSIRINSEVLADFVNAKFADI 155 +P ++ A + +IVSAG+ G I + E + N +FA+I Sbjct: 117 FPTYLAEEAQQYSAIIVSAGKRGMQIELAPEAILSLTNGQFAEI 160 A related DNA sequence was identified in S. pyogenes <SEQ ID 1061> which encodes the amino acid sequence <SEQ ID 1062>. Analysis of this protein sequence reveals the following: TABLE-US-01042 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2651(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01043 Identities = 114/157 (72%), Positives = 139/157 (87%) Query: 1 MSKKNKIKKTLVDQILDKAKIEHDSLQLDALQGDLPNGIQKQDIFKTLALIGDKTGPIIG 60 M+KK K+VVTLV+QILDKA I H L+L+AL+GD P+ +Q DI+KTLAL GD+TGP+IG Sbjct: 1 MAKKTKLKKTLVEQILDKANIAHQGLKLNALEGDFPDDLQPSDIYKTLALTGDQTGPLIG 60 Query: 61 ILPLTEHLSEKKLAKISGNKKVQMIPQKDLQKITGYIHGANNPIGIRQKHNYPIFIDTIA 12- 0 I+PLTEHLSEK+LAK+SGNKKV M+PQKDLQK TGYIHGANNP+GIRQKH+YPIFID A Sbjct: 61 IIPLTEHLSEKQLAKVSGNKKVSMVPQKDLQKTTGYIHGANNPVGIRQKHSYPIFIDQTA 12- 0 Query: 121 LEKQELIVSAGEIGRSIRINSEVLADFVNAKFADIKE 157 LEK ++IVSAGE+GRSI+I+S+ LADFV A FAD+K+ Sbjct: 121 LEKGQIIVSAGEVGRSIKISSQALADFVGASFADLKK 157 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 328 A DNA sequence (GBSx0358) was identified in S. agalactiae <SEQ ID 1063> which encodes the amino acid sequence <SEQ ID 1064>. Analysis of this protein sequence reveals the following: TABLE-US-01044 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4719(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) >c succ> A related GBS nucleic acid sequence <SEQ ID 8555> which encodes amino acid sequence <SEQ ID 8556> was also identified. This protein belongs to the glycolysis/gluconeogenesis pathway, and such proteins have been experimentally detected as surface-exposed in Streptococci. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01045 >GP: AAD36444 GB: AE001791 phosphoglycerate mutase [Thermotoga maritima] Identities = 65/191 (34%), Positives = 93/191 (48%), Gaps = 13/191 (6%) Query: 5 MKFYLVRHGKTQWNLEGRFQGANGDSPLLEEAIEELEELGQYLSSIHFDAVYSSDLGRAR 64 MK YL+RHG+T WN +G +QG D PL E E+ +L L + DA+YSS R+ Sbjct: 1 MKLYLIRHGETIWNEKGLWQGVT-DVPLNERGREQARKLANSLKRV--DAIYSSPLKRSL 57 Query: 65 DTVNILNDANSCPKEIHYTPQLREWALGTLEGCKIATMQAIYPRQMTAFYQNPLQFKHDM 12- 4 +T + A KEI LRE + G + YP + + +P M Sbjct: 58 ETAEEI--ARRFEKEIIVEEDLRECEISLWNGLTVEEAIREYPVEFKKWSSDP---NFGM 11- 2 Query: 125 FGAESLYQTTHRVESFLRSLASK----NYDKVLIVGHGANLTASIRSLLGYQYGSLHYKD 18- 0 G ES+ +RV + + S+ + V+IV H +L A I +LG LH Sbjct: 113 EGLESMRNVQNRVVKAIMKIVSQEKLNGSENVVIVSHSLSLRAFICWILGLPL-YLHRNF 17- 1 Query: 181 KLDNASLTIIE 191 KLDNASL+++E Sbjct: 172 KLDNASLSVVE 182 A related DNA sequence was identified in S. pyogenes <SEQ ID 1065> which encodes the amino acid sequence <SEQ ID 1066>. Analysis of this protein sequence reveals the following: TABLE-US-01046 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3628(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01047 Identities = 127/205 (61%), Positives = 152/205 (73%) Query: 5 MKFYLVRHGKTQWNLEGRFQGANGDSPLLEEAIEELEELGQYLSSIHFDAVYSSDLGRAR 64 MK Y VRHGKT WNLEGRFQGA GDSPLLEEA +E+ LG+ L+ + FDAVY+SDL RA Sbjct: 1 MKLYFVRHGKTLWNLEGRFQGAGGDSPLLEEAKDEIHLLGKELAKVAFDAVYTSDLQRAM 60 Query: 65 DTVNILNDANSCPKEIHYTPQLREWALGTLEGCKIATMQAIYPRQMTAFYQNPLQFKHDM 124- T I+ DA ++++T QLREW LG LEG KIATM AIYP+QM AF +N QFK D Sbjct: 61 ATAAIILDAFDQQPKLYHTDQLREWRLGKLEGAKIATMAAIYPQQMLAFRENLAQFKPDQ 120- Query: 125 FGAESLYQTTHRVESFLRSLASKNYDKVLIVGHGANLTASIRSLLGYQYGSLHYKDKLDN 18- 4 F AES+YQTT RV ++S K+Y VLIVGHGANLTA+IRSLLG++ L K LDN Sbjct: 121 FEAESIYQTTQRVCHLIQSFKDKHYQNVLIVGHGANLTATIRSLLGFEPALLLAKGGLDN 18- 0 Query: 185 ASLTIIETHDFKDFNCLTWNDKSYL 209 ASLTI+ET D+ ++CL WNDKS+L Sbjct: 181 ASLTILETKDYLTYDCLIWNDKSFL 205 SEQ ID 8556 (GBS314) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 4; MW 27.2 kDa) and in FIG. 169 (lane 15-17; MW 41.6 kDa) and in FIG. 239 (lane 4; MW 41.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 55 (lane 4; MW 52.1 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 329 A DNA sequence (GBSx0359) was identified in S. agalactiae <SEQ ID 1067> which encodes the amino acid sequence <SEQ ID 1068>. Analysis of this protein sequence reveals the following:

TABLE-US-01048 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3014(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01049 >GP: CAB12562 GB: Z99108 similar to hypothetical proteins [Bacillus subtilis] Identities = 69/232 (29%), Positives = 108/232 (45%), Gaps = 9/232 (3%) Query: 4 SIVFDVDDTIYDQQAPYRIAVEKCFPDFDMSAINQAYIRFRHYSDIGFPRVMAGEWTTEY 63 +++FDVDDTI D QA +A+ F D ++ N +++ + + G+ T + Sbjct: 6 TLLFDVDDTILDFQAAEALALRLLFEDQNIPLTNDMKAQYKTINQGLWRAFEEGKMTRDE 65 Query: 64 FRFWRCKETLLEFGYREIDEATGIYFQEIYEHELENITMLDEMRMTLDFLKSKNVPMGII 123- R L E+GY EA G ++ Y LE L + L + + I+ Sbjct: 66 VVNTRFSALLKEYGY----EADGALLEQKYRRFLEEGHQLIDGAFDLISNLQQQFDLYIV 121- Query: 124 TNGPTEHQLKKVKKLGLYDYVDPKRVIVSQATGFQKPEKEIFNLAAEQF-DMNPSTTLYV 18- 2 TNG + Q K+++ GL+ + K + VS+ TGFQKP KE FN E+ + TL + Sbjct: 122 TNGVSHTQYKRLRDSGLFPFF--KDIFVSEDTGFQKPMKEYFNYVFERIPQFSAEHTLII 17- 9 Query: 183 GDSYDNDIMGAFNGGWHSMWFNHRGRSLKPGIKPVYDVAIDNFEQLFGAVKV 234 GDS DI G G + W N + P I P Y+ I E+L+ + + Sbjct: 180 GDSLTADIKGGQLAGLDTCWMNPDMKPNVPEIIPTYE--IRKLEELYHILNI 229 A related DNA sequence was identified in S. pyogenes <SEQ ID 1069> which encodes the amino acid sequence <SEQ ID 1070>. Analysis of this protein sequence reveals the following: TABLE-US-01050 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3216(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01051 Identities = 276/300 (92%), Positives = 292/300 (97%) Query: 1 MITSIVFDVDDTIYDQQAPYRIAVEKCFPDFDMSAINQAYIRFRHYSDIGFPRVMAGEWT 60 MIT+IVFDVDDTIYDQQAPYRIA+EKCFPDFDMS +NQAYIRFRHYSD+GFPRVMAGEWT Sbjct: 1 MITAIVFDVDDTIYDQQAPYRIAMEKCFPDFDMSVMNQAYIRFRHYSDVGFPRVMAGEWT 60 Query: 61 TEYFRFWRCKETLLEFGYREIDEATGIYFQEIYEHELENITMLDEMRMTLDFLKSKNVPM 120- TEYFRFWRCKETLLEFGYREIDEA G++FQE+YEHELENITMLDEMRMTLDFLKSKNVPM Sbjct: 61 TEYFRFWRCKETLLEFGYREIDEAAGVHFQEVYEHELENITMLDEMRMTLDFLKSKNVPM 120- Query: 121 GIITNGPTEHQLKKVKKLGLYDYVDPKRVIVSQATGFQKPEKEIFNLAAEQFDMNPSTTL 18- 0 GIITNGPTEHQLKKV+KLGLYDY+D KRVIVSQATGFQKPEKEIFNLAAEQFDMNP TTL Sbjct: 121 GIITNGPTEHQLKKVRKLGLYDYIDAKRVIVSQATGFQKPEKEIFNLAAEQFDMNPQTTL 18- 0 Query: 181 YVGDSYDNDIMGAFNGGWHSMWFNHRGRSLKPGIKPVYDVAIDNFEQLFGAVKVLFDLPD 24- 0 YVGDSYDNDIMGAFNGGWHSMWFNHRGR LKPG KPVYDVAIDNFEQLFGAVKVLFDLPD Sbjct: 181 YVGDSYDNDIMGAFNGGWHSMWFNHRGRQLKPGTKPVYDVAIDNFEQLFGAVKVLFDLPD 24- 0 Query: 241 NKFIFDINDKSNPVLEMGLNNGLMMAAERLLESNMSVDKVVILLRLTAKQEKVLRMKYAR 30- 0 NKFIFD+NDK NP+L+MG+NNGLMMAAERLLESNMS+DKVVILLRLT +QEKVLR+KYAR Sbjct: 241 NKFIFDVNDKKNPILQMGINNGLMMAAERLLESNMSIDKVVILLRLTKQQEKVLRLKYAR 30- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 330 A DNA sequence (GBSx0360) was identified in S. agalactiae <SEQ ID 1071> which encodes the amino acid sequence <SEQ ID 1072>. Analysis of this protein sequence reveals the following: TABLE-US-01052 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2451(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9727> which encodes amino acid sequence <SEQ ID 9728> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01053 >GP: CAB11858 GB: Z99104 lysyl-tRNA synthetase [Bacillus subtilis] Identities = 318/490 (64%), Positives = 390/490 (78%), Gaps = 1/490 (0%) Query: 44 EELNDQQIVRREKMAALTEQGIDPFGKRFERTATSGQLNEKYADKSKEDLHDIEETATIA 103- EELNDQ VRR+KM L + GIDPFG RFERT S ++ Y D +KE+L + TIA Sbjct: 9 EELNDQLQVRRDKMNQLRDNGIDPFGARFERTHQSQEVISAYQDLTKEELEEKAIEVTIA 68 Query: 104 GRLMTKRGKGKVGFAHIQDREGQIQIYVRKDSVGEENYEIFKKADLGDFLGVEGQVMRTD 16- 3 GR+MTKRGKGK GFAH+QD EGQIQIYVRKDSVG++ YEIFK +DLGD +GV G+V +T+ Sbjct: 69 GRMMTKRGKGKAGFAHLQDLEGQIQIYVRKDSVGDDQYEIFKSSDLGDLIGVTGKVFKTN 128- Query: 164 MGELSIKATHITHLSKALRPLPEKFHGLTDIETIYRKRHLDLISNRDSFDRFVTRSKIIS 22- 3 +GELS+KAT L+KALRPLP+K+HGL D+E YR+R+LDLI N DS F+TRSKII Sbjct: 129 VGELSVKATSFELLTKALRPLPDKYHGLKDVEQRYRQRYLDLIVNPDSKHTFITRSKIIQ 18- 8 Query: 224 EIRRFMDSNGFLEVETPVLHNEAGGASARPFITHHNAQDIDMVLRIATELHLKRLIVGGM 28- 3 +RR++D +G+LEVETP +H+ GGASARPFITHHNA DI + +RIA ELHLKRLIVGG+ Sbjct: 189 AMRRYLDDHGYLEVETPTMHSIPGGASARPFITHHNALDIPLYMRIAIELHLKRLIVGGL 24- 8 Query: 284 ERVYEIGRIFRNEGMDATHNPEFTSIEAYQAYADYQDIMDLTEGIIQHVTKTVKGDGPIN 34- 3 E+VYEIGR+FRNEG+ HNPEFT IE Y+AYADY+DIM LTE ++ H+ + V G I Sbjct: 249 EKVYEIGRVFRNEGVSTRHNPEFTMIELYEAYADYKDIMSLTENLVAHIAQEVLGTTTIQ 30- 8 Query: 344 YQGTEIKINEPFKRVHMVDAVKEITGIDFWKEMTLEEAQALAQEKNVPLEKHFTTVGHII 40- 3 Y +I + +KR+HMVDAVKE TG+DFW+E+T+E+A+ A+E V + K TVGHII Sbjct: 309 YGEEQIDLKPEWKRIHMVDAVKEATGVDFWEEVTVEQAREYAKEHEVEI-KDSMTVGHII 36- 7 Query: 404 NAFFEEFVEDTLIQPTFVFGHPVEVSPLAKKNDTDPRFTDRFELFIMTKEYANAFTELND 46- 3 N FFE+ +E+TLIQPTF++GHPVE+SPLAKKN DPRFTDRFELFI+ +E+ANAFTELND Sbjct: 368 NEFFEQKIEETLIQPTFIYGHPVEISPLAKKNPEDPRFTDRFELFIVGREHANAFTELND 42- 7 Query: 464 PIDQLSRFEAQASAKELGDDEATGVDYDYVEALEYGMPPTGGLGIGIDRLCMLLTDTTTI 52- 3 PIDQ RFEAQ +E G+DEA +D D+VEALEYGMPPTGGLGIGIDRL MLLT+ +I Sbjct: 428 PIDQRERFEAQLKEREAGNDEAHLMDEDFVEALEYGMPPTGGLGIGIDRLVMLLTNAPSI 48- 7 Query: 524 RDVLLFPTMK 533 RDVLLFP M+ Sbjct: 488 RDVLLFPQMR 497 A related DNA sequence was identified in S. pyogenes <SEQ ID 1073> which encodes the amino acid sequence <SEQ ID 1074>. Analysis of this protein sequence reveals the following: TABLE-US-01054 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4694(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01055 Identities = 439/500 (87%), Positives = 474/500 (94%) Query: 34 LEEIMSNQHIEELNDQQIVRREKMAALTEQGIDPFGKRFERTATSGQLNEKYADKSKEDL 93 LEE MSNQHIEELNDQQIVRREKM AL EQGIDPFGKRF+RTA S +L EKYADK+KE+L Sbjct: 1 LEENMSNQHIEELNDQQIVRREKMTALAEQGIDPFGKRFDRTANSAELKEKYADKTKEEL 60 Query: 94 HDIEETATIAGRLMTKRGKGKVGFAHIQDREGQIAIYVRKDSVGEENYEIFKKADLGDFL 15- 3 H++ ETA +AGRLMTKRGKGKVGFAH+QDREGQIQ+YVRKDSVGE+NYEIFKKADLGDF+ Sbjct: 61 HELNETAIVAGRLMTKRGKGKVGFAHLQDREGQIQLYVRKDSVGEDNYEIFKKADLGDFI 12- 0 Query: 154 GVEGQVMRTDMGELSIKATHITHLSKALRPLPEKFHGLTDIETIYRKRHLDLISNRDSFD 21- 3 GVEG+VMRTDMGELSIKAT +THLSK+LRPLPEKFHGLTDIETIYRKRHLDLISNR+SFD Sbjct: 121 GVEGEVMRTDMGELSIKATKLTHLSKSLRPLPEKFHGLTDIETIYRKRHLDLISNRESFD 18- 0 Query: 214 RFVTRSKIISEIRRFMDSNGFLEVETPVLHNEAGGASARPFITHHNAQDIDMVLRIATEL 27- 3 RFVTRSK+ISEIRR++D FLEVETPVLHNEAGGA+ARPF+THHNAQ+IDMVLRIATEL Sbjct: 181 RFVTRSKMISEIRRYLDGLDFLEVETPVLHNEAGGAAARPFVTHHNAQNIDMFLRIATEL 24- 0 Query: 274 HLKRLIVGGMERVYEIGRIFRNEGMDATHNPEFTSIEAYQAYADYQDIMDLTEGIIQHVT 33- 3 HLKRLIVGGMERVYEIGRIFRNEGMDATHNPEFTSIE YQAYADY DIM+LTEGIIQH Sbjct: 241 HLKRLIVGGMERVYEIGRIFRNEGMDATHNPEFTSIEVYQAYADYLDIMNLTEGIIQHAA 30- 0 Query: 334 KTVKGDGPINYQGTEIKINEPFKRVHMVDAVKEITGIDFWKEMTLEEAQALAQEKNVPLE 39- 3 K V+GDGPI+YQGTEI+INEPFKRVHMVDA+KE+TG DFW EMT+EEA ALA+EK VPLE Sbjct: 301 KAVRGDGPIDYQGTEIRINEPFKRVHMVDAIKEVTGADFWPEMTVEEAIALAKEKQVPLE 36- 0 Query: 394 KHFTTVGHIINAFFEEFVEDTLIQPTFVFGHPVEVSPLAKKNDTDPRFTDRFELFIMTKE 45- 3 KHF +VGHIINAFFEEFVE+TL+QPTFVFGHPVEVSPLAKKN D RFTDRFELFIMTKE Sbjct: 361 KHFISVGHIINAFFEEFVEETLVQPTFVFGHPVEVSPLAKKNPEDTRFTDRFELFIMTKE 42- 0 Query: 454 YANAFTELNDPIDQLSRFEAQASAKELGDDEATGVDYDYVEALEYGMPPTGGLGIGIDRL 51- 3 YANAFTELNDPIDQLSRFEAQA AKELGDDEATG+DYD+VEALEYGMPPTGGLGIGIDRL Sbjct: 421 YANAFTELNDPIDQLSRFEAQAQAKELGDDEATGIDYFDVEALEYGMPPTGGLGIGIDRL 48- 0 Query: 514 CMLLTDTTTIRDVLLRPTMK 533 CMLLT+TTTIRDVLLFPTMK Sbjct: 481 CMLLTNTTTIRDVLLFPTMK 500 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 331 A DNA sequence (GBSx0361) was identified in S. agalactiae <SEQ ID 1075> which encodes the amino acid sequence <SEQ ID 1076>. This protein is predicted to be 6,7-dimethyl-8-ribityllumazine synthase (ribH). Analysis of this protein sequence reveals the following: TABLE-US-01056 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1042(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01057 >GP: CAB14257 GB: Z99116 riboflavin synthase (beta subunit) [Bacillus subtilis] Identities = 103/151 (68%), Positives = 120/151 (79%) Query: 1 MTIIEGQLVANEMKIGIVVSRFNELITSKLLSGAVDGLLRHGVSEEDIDIVWVPGAFEIP 60 M II+G LV +KIGIVV RFN+ ITSKLLSGA D LLRHGV DID+ WVPGAFEIP Sbjct: 1 MNIIQGNLVGTGLKIGIVVGRFNDFITSKLLSGAEDALLRHGVDTNDIDVAWVPGAFEIP 60 Query: 61 YMARKMALYKDYDAIICLGVVIKGSTDHYDYVCNEVTKGIGHLNSQSDIPHIFGVLTTDN 12- 0 + A+KMA K YDAII LG VI+G+T HYDYVCNE KGI + + +P IFG++TT+N Sbjct: 61 FAAKKMAETKKYDAIITLGTVIRGATTHYDYVCNEAAKGIAQAANTTGVPVIFGIVTTEN 12- 0 Query: 121 IEQAIERAGTKAGNKGYDCALSAIEMVNLDK 151 IEQAIERAGTKAGNKG DCA+SAIEM NL++ Sbjct: 121 IEQAIERAGTKAGNKGVDCAVSAIEMANLNR 151 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 332 A DNA sequence (GBSx0362) was identified in S. agalactiae <SEQ ID 1077> which encodes the amino acid sequence <SEQ ID 1078>. This protein is predicted to be GTP cyclohydrolase ii (ribA/B). Analysis of this protein sequence reveals the following: TABLE-US-01058 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1918(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9725> which encodes amino acid sequence <SEQ ID 9726> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01059 >GP: AAA86524 GB: U27202 GTP cyclohydrase II/ 3,4-dihydroxy-2-butanone-4-phosphate synthase [Actinobacillus pleuropneumoniae] Identities = 230/395 (58%), Positives = 307/395 (77%) Query: 19 FSPIKKLLQDIKSGKMVVLMDDENRENEGDLICAAEMVTKESINFMAKFGKGLICLPLSN 78 FS ++ ++ I+ GK++++ DDE+RENEGD ICAAE T E+INFMA +GKGLIC P+S Sbjct: 6 FSKVEDAIEAIRQGKIILVTDDEDRENEGDFICAAEFATPENINFMATYGKGLICTPIST 65 Query: 79 YYAEKLELAQMASHNTDNHETAFTISIDHLSTSTGISAEDRALTAKMVANDSSKAKFDRR 13- 8 A+KL M + N DNHETAFT+S+DH+ T TGISA +R++TA + +D++KA DFRR Sbjct: 66 EIAKKLNFHPMVAVNQDNHETAFTVSVDHIDTGTGISAFERSITAMKIVDDNAKATDFRR 12- 5 Query: 139 PGHLFPLLAKEGGVLARNGHTEATVDLCRLAGLKECGLCCEIMAEDGSMMRKDELLAFAQ 19- 8 PGH+FPL+AKEGGVL RNGHTEATVDL RLAGLK GLCCEIMA+DG+MM +L FA Sbjct: 126 PGHMFPLIAKEGGVLVRNGHTEATVDLARLAGLKHAGLCCEIMADDGTMMTMPDLQKFAV 18- 5 Query: 199 KHDLAIATIKQLQDYRRQEEGGVVREIEIQLPTQFGHFTAYGYSEVVANKEHVALVKGDI 25- 8 +H++ TI+QLQ+YRR+ + V + +++PT++G F A+ + EV++ KEHVALVKGD+ Sbjct: 186 EHNMPFITIQQLQEYRRKHDSLVKQISVVKMPTKYGEFMAHSFVEVISGKEHVALVKGDL 24- 5 Query: 259 SSGEDVLCRLHSECLTGDVFHSLRCDCGEQLANALQQIEAEGRGVLLYMRQEGRGIGLIN 31- 8 + GE VL R+HSECLTGD F S RCDCG+Q A A+ QIE EGRGV+LY+RQEGRGIGLIN Sbjct: 246 TDGEQVLARIHSECLTGDAFGSQRCDCGQQFAAAMTQIEQEGRGVILYLRQEGRGIGLIN 30- 5 Query: 319 KLKAYHLQEEGLDTLEANLALGFEGDERDYGVSAQLLKDLGINSINLLTNNPDKIQQLEA 37- 8 KL+AY LQ++G+DT+EAN+ALGF+ DER+Y + AQ+ + LG+ SI LLTNNP KI+ L+ Sbjct: 306 KLRAYELQDKGMDTVEANVALGFKEDEREYYIGAQMFQQLGVKSIRLLTNNPAKIEGLKE 36- 5 Query: 379 EGICVKNRVPLQVAVTAYDLNYLKTKKEKMGHLLD 413 +G+ + R P+ V D++YLK K+ KMGH+ + Sbjct: 366 QGLNIVAREPIIVEPNKNDIDYLKVKQIKMGHMFN 400 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 333 A DNA sequence (GBSx0363) was identified in S. agalactiae <SEQ ID 1079> which encodes the amino acid sequence <SEQ ID 1080>. This protein is predicted to be riboflavin synthase alpha chain (ribE). Analysis of this protein sequence reveals the following: TABLE-US-01060 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3517(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9723> which encodes amino acid sequence <SEQ ID 9724> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01061 >GP: BAB05274 GB: AP001512 riboflavin synthase alpha subunit [Bacillus halodurans] Identities = 98/216 (45%), Positives = 147/216 (67%), Gaps = 2/216 (0%) Query: 1 MFTGIIEEMGQVSRIRNGIKSQQLSIDAPKLVPLLRKGDSVAVNGVCLTVLDKSETAFIA 60 MFTGIIE++G + I+ ++ ++I + K+V ++ GDS+AVNGVCLTV ++T F Sbjct: 1 MFTGIIEDVGTIDAIQQTGEAIVMTITSKKIVSDVQLGDSIAVNGVCLTVTSFTDTQFTV 60 Query: 61 DVMPESMMRTSLAALRLHSKVNLELALRSDSRLGGHFVLGHVDGVGKIEKIQKDDIAVRF 12- 0 D+MPE++ TSL L S+VNLE A+ ++ R GGH V GHVDG+G I K ++ D AV + Sbjct: 61 DLMPETVRATSLRLLSKGSRVNLERAMVANGRFGGHIVSGHVDGIGTIRKKERKDNAVYY 12- 0 Query: 121 SIDAPPSIMSYIIEKGSVALDGISLTVVSFTEHSFEVSVIPHTMAQTNLSLKKVGDLLNI 18- 0 +I+ S+ Y+I KGSVA+DG SLT+ ++ +F +S+IPHTM +T + LKK GD++NI Sbjct: 121 TIEVSSSLRRYMIHKGSVAVDGTSLTIFDVSDKTFTISIIPHTMEETIIGLKKAGDIVNI 18- 0 Query: 181 EVDLVGKYAEKFLAPTNRTNHTSSVMDWSFLSENGY 216 E D++GKY E+F+ N + +FL+E+GY Sbjct: 181 ECDLIGKYIEQFVQQGKPVNEGG--LTKAFLTEHGY 214 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 334 A DNA sequence (GBSx0364) was identified in S. agalactiae <SEQ ID 1081> which encodes the amino acid sequence <SEQ ID 1082>. This protein is predicted to be riboflavin-specific deaminase (ribD). Analysis of this protein sequence reveals the following: TABLE-US-01062 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.01 Transmembrane 307-323 ( 307-323) ----- Final Results ----- bacterial membrane --- Certainty = 0.1404(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01063 >GP: AAA86522 GB: U27202 riboflavin-specific deaminase [Actinobacillus pleuropneumoniae] Identities = 182/353 (51%), Positives = 259/353 (72%) Query: 6 DYMALALKEAEKGMGFVAPNPLVGAVIVKDDRIISKGYHKRFGDLHAERQAIKNADEDIS 65 DYM A+ A++G+G+ PVPLVG VIVK+ I+++GYH++ G HAER A+ + ED+S Sbjct: 51 DYMRRAIALAKQGLGWTNPNPLVGCVIVKNGEIVAEGYHEKIGGWHAERNAVLHCKEDLS 11- 0 Query: 66 GSTLYVTLEPCCHVGKQPPCTEALIKSGIKKVVVGSLDPNPLVSGKGIALLRKEGLNVEV 12- 5 G+T YVTLEPCCH G+ PPC++ LI+ GIKKV +GS DPNPLV+G+G LR+ G+ V Sbjct: 111 GATAYVTLEPCCHHGRTPPCSDLLIERGIKKVFIGSSDPNPLVAGRGANQLRQAGVEVVE 17- 0 Query: 126 GILREECDALNERFIFHMTYKQPFVYLKYAMTLDGKIATKTGDSKWISNEHSRQSVQKLR 18- 5 G+L+EECDALN F ++ K+P+V +KYAMT DGKIAT +G+SKWI+ E +R VQ+ R Sbjct: 171 GLLKEECDALNPIFFHYIQTKRPYVLMKYAMTADGKIATGSGESKWITGESARARVQQTR 23- 0 Query: 186 QKCSAIMVGINTVLADNPRLTCRIPKGEALVRIVCDSQLKIPLDSYLVKSAKTIPTWIAT 24- 5 + SAIMVG++TVLADNP L R+P + VRIVCDSQL+ PLD LV++AK T IAT Sbjct: 231 HQYSAIMVGVDTVLADNPMLNSRMPNAKQPVRIVCDSQLRTPLDCQLVQTAKEYRTVIAT 29- 0 Query: 246 CSDNLAQQQTLKEMGCRLIKVPRKDGKLDLKVLMTILGQEGIDSLLIEGGSSLHFSALKA 30- 5 SD+L + + + +G ++ ++ ++DL+ L+ LG+ IDSLL+EGGSSL+FSAL++ Sbjct: 291 VSDDLQKIEQFRPLGVDVLVCKARNKRVDLQDLLQKLGEMQIDSLLLEGGSSLNFSALES 35- 0 Query: 306 GIVNRLIVFIAPKIIGGLKAKTAISGEGLDWLNQARFVKDIELSRMDSDVVIE 358 GIVNR+ +IAPK++GG +AKT I GEG+ ++QA ++K + D++++ Sbjct: 351 GIVNRVHCYIAPKLVGGKQAKTPIGGEGIQQIDQAVKLKLKSTELIGEDILLD 403 A related DNA sequence was identified in S. pyogenes <SEQ ID 1083> which encodes the amino acid sequence <SEQ ID 1084>. Analysis of this protein sequence reveals the following:

TABLE-US-01064 Possible site: 25 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.17 Transmembrane 88-104 ( 88-105) ----- Final Results ----- bacterial membrane --- Certainty = 0.1468(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.C000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01065 >GP: CAB11794 GB: Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 71/161 (44%), Positives = 109/161 (67%) Query: 13 LEEQTYFMQEALKEAEKSLQKAEIPIGCVIVKDGEIIGRGHNAREESNQAIMHAEMMAIN 72 + + +M+EA+KEA+K+ +K E+PIG V+V +GEII R HN RE ++I AHEM+ I+ Sbjct: 1 MTQDELYMKEAIKEAKKAEEKGEVPIGAVLVINGEIIARAHNLRETEQRSIAHAEMLVID 60 Query: 73 EANAHEGNWRLLDTTLFVTEIPCVMCSGAIGLARIPHVIYGASNQKFGGVDSLYQILTDE 13- 2 EA G WRL TL+VT+EPC MC+GA+ L+R+ V++GA + K G +L +L +E Sbjct: 61 EACKALGTWRLEGATLYVTLEPCPMCAGAVVLSRVEKVVFGAFDPKGGCSGTLMNLLQEE 12- 0 Query: 133 RLNHRVQVERGLLAADCANIMQTFFRQGRERKKIAKHLIKE 173 R NH+ +V G+L +C ++ FFR+ R++KK A+ + E Sbjct: 121 RFNHQAEVVSGVLEEECGGMLSAFFRELRKKKKAARKNLSE 161 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01066 Identities = 48/146 (32%), Positives = 71/146 (47%), Gaps = 21/146 (14%) Query: 7 YMALALKEAEKGMGFVAPNPLVGAVIVKDDRIISKGYHKRFGD----LHAERQAIKNADE 62 +M ALKEAEK + A P +G VIVKD II +G++ R +HAE AI A+ Sbjct: 19 FMQEALKEAEKSLQ-KAEIP-IGCVIVKDGEIIGRGHNAREESNQAIMHAEMMAINEANA 76 Query: 63 D-----ISGSTLYVTLEPCCHVGKQPPCTEALIKSGIKKVVVGSLDPNPLVSGKGIALLR 11- 7 + +TL+VT+EPC C+ A+ + I V+ G+ + +L Sbjct: 77 HEGNWRLLDTTLFVTIEPCV------MCSGAIGLARIPHVIYGASNQKFGGVDSLYQILT 13- 0 Query: 118 KEGLN----VEVGILREECDALNERF 139 E LN----VE G+L +C + + F Sjbct: 131 DERLNHRVQVERGLLAADCANIMQTF 156 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 335 A DNA sequence (GBSx0365) was identified in S. agalactiae <SEQ ID 1085> which encodes the amino acid sequence <SEQ ID 1086>. This protein is predicted to be Nramp metal ion transporter. Analysis of this protein sequence reveals the following: TABLE-US-01067 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.89 Transmembrane 169-185 ( 160-191) INTEGRAL Likelihood = -11.09 Transmembrane 140-156 ( 128-165) INTEGRAL Likelihood = -6.85 Tranamembrane 359-375 ( 354-379) INTEGRAL Likelihood = -6.48 Transmernbrane 269-285 ( 263-287) INTEGRAL Likelihood = -6.16 Transmembrane 426-442 ( 423-445) INTEGRAL Likelihood = -5.57 Transmembrane 62-78 ( 58-80) INTEGRAL Likelihood = -4.94 Transmembrane 107-123 ( 103-127) INTEGRAL Likelihood = -4.46 Transmembrane 391-407 ( 389-408) INTEGRAL Likelihood = -4.35 Transmembrane 310-326 ( 307-328) ----- Final Results ----- bacterial membrane --- Certainty = 0.5755(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01068 >GP: AAF83825 GB: AE003939 manganese transport protein [Xylella fastidiosa] Identities = 192/436 (44%), Positives = 274/436 (62%), Gaps = 14/436 (3%) Query: 10 SLSEVNQSVEVPHNSSFWNTLRAFLGPGALVAVGYMDPGNWITSVIGGATYRYLLLFVVL 69 - SL E++ SV V + L AFLGPG +V+VGYMDPGNW T + GG+ + Y+LL V+L Sbjct: 39 SLGEMHASVAVSRRGHWGFRLLAFLGPGYMVSVGYMDPGNWATGLAGGSRFGYMLLSVIL 98 Query: 70 VSSLMAMQLQQMAGKLGIVTRQDLAQATASRLPKPLRYLLFIIIELALIATDLAEVIGSA 129- +S++MA+ LQ +A +LGI + DLAQA +R + L+++ ELA+IA DLAEVIG+A Sbjct: 99 LSNVMAIVLQALAARLGIASDMDLAQACRARYSRGTTLALWVVCELAIIACDLAEVIGTA 158- Query: 130 IALHLLFGWPLLLSIMITILDVFLLLLLMKLGVQKIEAFVSVLILTILIIFTYLVVLSQP 18- 9 IAL+LL G P++ ++IT +DV L+LLLM G + +EAFV L+L I F +VL+ P Sbjct: 159 IALNLLLGVPIIWGVVITAVDVVLVLLLMHRGFRALEAFVIALLLVIFGCFVVQIVLAAP 21- 8 Query: 190 DLDAMFKGFLPHHELFNISHEGKNSPLTLALGIIGATVMPHNLYLHSSLSQTRRVDYHNK 24- 9 L + GF+P ++ L LA+GI+GATVMPHNLYLHSS+ QTR Sbjct: 219 PLQEVLGGFVPRWQVV-----ADPQALYLAIGIVGATVMPHNLYLHSSIVQTRAYP-RTP 27- 2 Query: 250 SSIKKAVRFMTLDSNIQLSLAFVVNSLLLVLGASLFYG-HANDISAFSQMYLALSDKTIT 30- 8 + A+R+ DS + L LA +N+ +L+L A++F+ H D+ Q Y L+ Sbjct: 273 VGRRSALRWAVADSTLALMLALFINASILILAAAVFHAQHHFDVEEIEQAYQLLAPVLGV 33- 2 Query: 309 GAVASSFLSTLFAVALLASGQNSTITGTLTGQIVMEGFLHFKLPQWLIRLCTRLLTLLPI 36- 8 G A TLFA ALLASG NST+T TL GQIVMEGFL +L WL R+ TR L ++P+ Sbjct: 333 GVAA-----TLFATALLASGINSTVTATLAGQIVMEGFLRLRLRPWLRRVLTRGLAIVPV 38- 7 Query: 369 FVIALLVGGEENTLDQLIVYSQVFLSLALPFSIFPLIYFTSQKSIMGEHANAKWNTYLAY 42- 8 V+ L G E +L++ SQV LS+ LPF++ PL+ + + +MG +W +A+ Sbjct: 388 IVVVALYG--EQGTGRLLLLSQVILSMQLPFAVIPLLRCVADRKVMGALVAPRWLMVVAW 44- 5 Query: 429 LVAIILTLLNLKLIMD 444 L+A ++ +LN+KL+ D Sbjct: 446 LIAGVIVVLNVKLLGD 461 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 336 A DNA sequence (GBSx0366) was identified in S. agalactiae <SEQ ID 1087> which encodes the amino acid sequence <SEQ ID 1088>. Analysis of this protein sequence reveals the following: TABLE-US-01069 Possible site: 54 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -14.12 Transmembrane 113-129 (98-132) INTEGRAL Likelihood = -12.15 Transmembrane 228-244 (220-249) INTEGRAL Likelihood = -10.83 Transmembrane 175-191 (167-195) INTEGRAL Likelihood = -5.04 Transmembrane 57-73 (55-75) INTEGRAL Likelihood = -3.93 Transmembrane 146-162 (142-166) INTEGRAL Likelihood = -1.38 Transmembrane 199-215 (199-215) INTEGRAL Likelihood = -0.32 Transmembrane 82-98 (82-98) ----- Final Results ----- bacterial membrane --- Certainty = 0.6647(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01070 >GP: AAF11325 GB: AE002018 hypothetical protein [Deinococcus radiodurans] Identities = 63/215 (29%), Positives = 108/215 (49%), Gaps = 13/215 (6%) Query: 11 LLLVFILTIIVNYLSATGFLTGNSQKSLSDRYQTLLTPAPLAFSIWSVIYL-LTFLVILR 69 - LL +LT++VNYLS L GNS +SDR TPA L F++W I+L L + + Sbjct: 10 LLAATVLTLVVNYLSNALPLFGNSNAEVSDRLPNAFTPAGLTFTVWGPIFLGLLVFAVYQ 69 Query: 70 AIFSKSQSYQDNFASIFPYFLGLLLVNNIWTVFFTSNLIGLSTIIIFAYCILLV-IIIKI 128- A+ ++ + D +P+ LG LL N W + F S IGLS +I+ A +LV + + + Sbjct: 70 ALPAQRGARLDRL--FWPFLLGNLL-NVAWLLAFQSLNIGLSVVIMLALLAVLVRLYLSV 126- Query: 129 LS---KNKSKLLLRITFGIHAGWLLVASLVNLAVYLVKI----DFNYPLPKVYIAIIALI 18- 1 S + + L++ ++ W+ VA++ N+ +LV F V+ A++ ++ Sbjct: 127 RSLPPQGAERWTLQLPVSLYLAWISVATIANITAFLVSAGVTQSFLGIAGPVWSALLLVV 18- 6 Query: 182 FITVLSLYLARVLQNAYLILSVFWAWLMVFKAHLE 216 + +L R A+ + + WA+ V+ A E Sbjct: 187 AAAIGVFFLWRFRDYAFAAV-LLWAFYGVYVARPE 220 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 337 A DNA sequence (GBSx0367) was identified in S. agalactiae <SEQ ID 1089> which encodes the amino acid sequence <SEQ ID 1090>. Analysis of this protein sequence reveals the following: TABLE-US-01071 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3401(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01072 >GP: AAC65352 GB: AE001215 T. pallidum predicted coding region TP0352 [Treponema pallidum] Identities = 28/64 (43%), Positives = 41/64 (63%) Query: 3 EFTFEIVEKLLVLSENEKGWTKELNRVSFNGAPAKFDLRTWSPDHTKMGKGITLSNEEFK 62 +F +E+ LS + GW+ EL +S+NG P K+D+R WSPD +KMGKG+TL+ E Sbjct: 12 DFHYEVTRNWGTLSTSGNGWSLELKSISWNGRPEKYDIRAWSPDKSKMGKGVTLTRAEIV 71 Query: 63 VILD 66 + D Sbjct: 72 ALRD 75 A related DNA sequence was identified in S. pyogenes <SEQ ID 1091> which encodes the amino acid sequence <SEQ ID 1092>. Analysis of this protein sequence reveals the following: TABLE-US-01073 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4021(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01074 Identities = 59/70 (84%), Positives = 64/70 (91%) Query: 1 MSEFTFEIVEKLLVLSENEKGWTKELNRVSFNGAPAKFDLRTWSPDHTKMGKGITLSNEE 60 M+EFTF I E LL LSEN+KGWTKELNRVSFNGA AK+D+RTWSPDHTKMGKGITL+NEE Sbjct: 1 MAEFTFNIEEHLLTLSENDKGWTKELNRVSFNGAEAKWDIRTWSPDHTKNGKGITLTNEE 60 Query: 61 FKVILDAFRK 70 FK ILDAFRK Sbjct: 61 FKTILDAFRK 70 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 338 A DNA sequence (GBSx0368) was identified in S. agalactiae <SEQ ID 1093> which encodes the amino acid sequence <SEQ ID 1094>. Analysis of this protein sequence reveals the following: TABLE-US-01075 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.66 Transmembrane 92-108 (92-110) ----- Final Results ----- bacterial membrane --- Certainty = 0.2062(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01076 >GP: CAB14676 GB: Z99117 similar to protease [Bacillus subtilis] Identities = 201/407 (49%), Positives = 277/407 (67%), Gaps = 2/407 (0%) Query: 4 VKKRPEVLSPAGTLEKLKVAIDYGADAVFVGGQAYGLRSRAGNFSMEELQEGINYAHARD 63 + K+PE+L+PAG LEKLK+A+ YGADAVF+GGQ YGLRS A NF++EE+ EG+ +A Sbjct: 18 ITKKPELLAPAGNLEKLKIAVHYGADAVFIGGQEYGLRSNADNFTIEEIAEGVEFAKKYG 77 Query: 64 AKVYVAANMVTHEGNELGAGPWFRELRDMGLDAVIVSDPALIVICATEAPGLEIHLSTQA 123- AK+YV N+ H N G + + L D + +IV+DP +I C AP +E+HLSTQ Sbjct: 78 AKIYVTTNIFAHNENMDGLEDYLKALGDANVAGIIVADPLIIETCRRVAPNVEVHLSTQQ 137- Query: 124 SSTNYETFEFWKEMGLTRVVLAREVTMAELAEIRKRTDVEIEAFVHGAMCISYSGRCVLS 18- 3 S +N++ +FWKE GL RVVLARE + E+ E++++ D+EIE+F+HGAMCI+YSGRCVLS Sbjct: 138 SLSNWKAVQFWKEEGLDRVVLARETSALEIREMKEKVDIEIESFIHGAMCIAYSGRCVLS 19- 7 Query: 184 NHMSHRDANRGGCSQSCRWKYDLYDMPFGQERQSLKGEIPEPFSMSAVDMCMIEHIPDMI 24- 3 NHM+ RD+NRGGC QSCRW YDLY G +L GE PF+MS D+ +IE IP MI Sbjct: 198 NHMTARDSNRGGCCQSCRWDYDLYQTD-GANAVALYGEEDAPFAMSPKDLKLIESIPKMI 25- 6 Query: 244 ENGVDSLKIEGRMKSIHYVSTVTNCYKAAVDAYMESPEAFEAIKEDLIDELWKVAQRELA 30- 3 E G+DSLKIEGRMKSIHYV+TV + Y+ +DAY PE F I+++ ++EL K A R+ A Sbjct: 257 EMGIDSLKIEGRMKSIHYVATVVSVYRKVIDAYCADPENF-VIQKEWLEELDKCANRDTA 31- 5 Query: 304 TGFYYHTPTENEQLFGARRKIPQYKFVGEVVSFDNAKMEATIRQRNVIMEGDRVEFYGPG 36- 3 T F+ TP EQ+FG K Y FVG V+++D T++QRN +GD VEF+GP Sbjct: 316 TAFFEGTPGYEEQMFGEHAKKTTYDFVGLVLNYDEDTQMVTLQQRNFFKKGDEVEFFGPE 37- 5 Query: 364 FRHFECFIDGLRDAEGNKIDRAPNPMELLTITLPNPVKKGDMIRACK 410 +F I+ + D +GN++D A +P++++ L + +M+R K Sbjct: 376 IENFTHTIETIWDEDGNELDAARHPLQIVKFKLDKKIYPSNMMRKGK 422 A related DNA sequence was identified in S. pyogenes <SEQ ID 1095> which encodes the amino acid sequence <SEQ ID 1096>. Analysis of this protein sequence reveals the following: TABLE-US-01077 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.66 Transmembrane 92-108 (92-110) ----- Final Results ----- bacterial membrane --- Certainty = 0.2062(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01078 >GP: BAB04993 GB: AP001511 protease [Bacillus halodurans] Identities = 201/403 (49%), Positives = 280/403 (68%), Gaps = 4/403 (0%) Query: 6 KRPEVLSPAGTLEKLKVAIDYGADAVFVGGQAYGLRSRAGNFSMEELQEGIDYAHARGAK 65 K+PE+L+PAG+LEKLKVAI YGADAV++GGQ +GLRS A NFS+EE++EG+++A+ GAK Sbjct: 17 KKPELLAPAGSLEKLKVAIHYGADAVYIGGQEFGLRSNADNFSIEEMREGVEFANKYGAK 76 Query: 66 VYVAANMVTHEGNEIGAGEWFRQLRDMGLDAVIVSDPALIVICSTEAPGLEIHLSTQASS 125- VYV N+ H N G E+ L+++G+ +IV+DP +I C AP +E+HLSTQ S Sbjct: 77 VYVTTNIYAHNENMDGLEEYLSALQEVGVTGIIVADPLIIETCKRVAPKVEVHLSTQQSL 136- Query: 126 TNYETFEFWKAMGLTRVVLAREVNMAELAEIRKRTDVEIEAFVHGAMCISYSGRCVLSNH 18- 5 +N+ +FWK GL RVVLAREV + E+ E++K D+EIE FVHGAMCISYSGRCVLSNH Sbjct: 137 SNWLAVKFWKEEGLHRVVLAREVGLEEMLEMKKHVDIEIETFVHGAMCISYSGRCVLSNH 19- 6 Query: 186 MSHRDANRGGCSQSCRWKYDLYDMPFGGE-RRSLKGEIPEDYSMSSVDMCMIDHIPDLIE 24- 4 M+ RD+NRGGC QSCRW YDLY+ E +G++P Y+MS D+ +I IP LIE Sbjct: 197 MTARDSNRGGCCQSCRWDYDLYEQQDSAEIPLFAEGDVP--YTMSPKDLNLIQAIPQLIE 25- 4 Query: 245 NGVDSLKIEGRMKSIHYVSTVTNCYKAAVGAYMESPEAFYAIKEELIDELWKVAQRELAT 30- 4 G+DSLK+EGRMKSIHYV+TVT+ Y+ + AY P+ F IK E ++EL K A R+ A Sbjct: 255 AGIDSLKVEGRMKSIHYVATVTSVYRKVIDAYCSDPDNF-KIKREWLEELEKCANRDFAP 31- 3 Query: 305 GFYYGIPTENEQLFGARRKIPQYKFVGEVVAFDSASMTATIRQRNVIMEGDRIECYGPGF 36- 4 F+ G PT EQ++G K +Y FVG V+ ++ + T++QRN +GD +E +GP Sbjct: 314 QFFEGTPTYKEQMYGIHPKRTKYDFVGLVLDYNEKTGIVTLQQRNHFKQGDEVEFFGPEI 37- 3 Query: 365 RHFETVVKDLHDADGQKIDRAPNPMELLTISLPREVKPGDMIR 407 F V+ + D DG ++D A +P++++ + ++V P +M+R Sbjct: 374 NRFTQTVEKIWDEDGNELDAARHPLQIVKFKVDQKVYPQNMMR 416 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01079 Identities = 386/427 (90%), Positives = 404/427 (94%) Query: 1 MSNVKKRPEVLSPAGTLEKLKVAIDYGADAVFVGGQAYGLRSRAGNFSMEELQEGINYAH 60 MS++KKRPEVLSPAGTLEKLKVAIDYGADAVFVGGQAYGLRSRAGNFSMEELQEGI+YAH Sbjct: 1 MSHMKKRPEVLSPAGTLEKLKVAIDYGADAVFVGGQAYGLRSRAGNFSMEELQEGIDYAH 60 Query: 61 ARDAKVYVAANMVTHEGNELGAGPWFRELRDMGLDAVIVSDPALIVICATEAPGLEIHLS 120- AR AKVYVAANMVTHEGNE+GAG WFR+LRDMGLDAVIVSDPALIVIC+TEAPGLEIHLS Sbjct: 61 ARGAKVYVAANMVTHEGNEIGAGEWFRQLRDMGLDAVIVSDPALIVICSTEAPGLEIHLS 120- Query: 121 TQASSTNYETFEFWKEMGLTRVVLAREVTMAELAEIRKRTDVEIEAFVHGAMCISYSGRC 18- 0 TQASSTNYETFEFWK MGLTRVVLAREV MAELAEIRKRTDVEIEAFVHGAMCISYSGRC Sbjct: 121 TQASSTNYETFEFWKAMGLTRVVLAREVNMAELAEIRKRTDVEIEAFVHGAMCISYSGRC 18- 0 Query: 181 VLSNHMSHRDANRGGCSQSCRWKYDLYDMPFGQERQSLRGEIPEPFSMSAVDMCMIEHIP 24- 0 VLSNHMSHRDANRGGCSQSCRWKYDLYDMPFG ER+SLKGEIPE +SMS+VDMCMI+HIP Sbjct: 181 VLSNHMSHRDANRGGCSQSCRWKYDLYDMPFGGERRSLKGEIPEDYSMSSVDMCMIDHIP 24- 0 Query: 241 DMIENGVDSLKIEGRMKSIHYVSTVTNCYKAAVDAYMESPEAFEAIKEDLIDELWKVAQR 30- 0 D+IENGVDSLKIEGRNKSIHYVSTVTNCYKAAV AYMESPEAF AIKE+LIDELWKVAQR Sbjct: 241 DLIENGVDSLKIEGRMKSIHYVSTVTNCYKAAVGAYMESPEAFYAIKEELIDELWKVAQR 30- 0 Query: 301 ELATGFYYHTPTENEQLFGARRKIPQYKFVGEVVSFDNAKMEATIRQRNVIMEGDRVEFY 36- 0 ELATGFYY PTENEQLFGARRKIPQYKFVGEVV+FD+A M ATIRQRNVIMEGDR+E Y Sbjct: 301 ELATGFYYGIPTENEQLFGARRKIPQYKFVGEVVAFDSASMTATIRQRNVIMEGDRIECY 36- 0 Query: 361 GPGFRHFECFIDGLRDAEGNKIDPAPNPMELLTITLPNPVKKGDMIRACKEGLVNLYQND 42- 0 GPGFRHFE + L DA+G KIDRAPNPMELLTI+LP VK GDMIRACKEGLVNLYQ D Sbjct: 361 GPGFRHFETVVRDLHDADGQKIDRAPNPMELLTISLPREVKPGDMIRACKEGLVNLYQKD 42- 0 Query: 421 GTSKTVR 427 GTSKTVR Sbjct: 421 GTSKTVR 427 SEQ ID 1094 (GBS385) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 69 (lane 3; MW 50 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 7; MW 75.7 kDa). The GBS385-GST fusion product was purified (FIG. 213, lane 7) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 312), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 339 A DNA sequence (GBSx0369) was identified in S. agalactiae <SEQ ID 1097> which encodes the amino acid sequence <SEQ ID 1098>. This protein is predicted to be collagenase. Analysis of this protein sequence reveals the following: TABLE-US-01080 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2208(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-01081 >GP: CAB14677 GB: Z99117 similar to protease [Bacillus subtilis] Identities = 92/304 (30%), Positives = 161/304 (52%), Gaps = 5/304 (1%) Query: 1 MEKIILTATAESIEQVKQLLAIGIDRIYVGEENYGLRLPHSFSDDELREIAKLVHDAGKE 60 M+K L T S + L+ G VGE+ YGLRL FS +++ + ++ H G + Sbjct: 1 MKKPELLVTPTSTADILPLIQAGATAFLVGEQRYGLRLAGEFSREDVTKAVEIAHKEGAK 60 Query: 61 LTVACNALMHQEMMDNIKPFLELMKEINVDYLVVGDAGVFYINKRDGYNFKLIYDTSVFV 120- + VA NA+ H + + + +L + E VD V GD V + + KL + T Sbjct: 61 VYVAVNAIFHNDKVGELGEYLAFLAEAGVDAAVFGDPAVLMAARESAPDLKLHWSTETTG 120- Query: 121 TSSRQVNFWGQHGAVETVLAREIPSEELFKMSENLEFPAEILVYGASVIHHSKRPLLQNY 18- 0 T+ N+WG+ GA +VLARE+ + + ++ EN E EI V+G + + SKR L+ NY Sbjct: 121 TNYYTCNYWGRKGAARSVLARELNMDSIVEIKENAEVEIEIQVHGMTCMFQSKRSLIGNY 18- 0 Query: 181 YNF---THITDEKTRERGLFLAEPGOFESHYSIYEDKHGTHIFINNDINMMTKVTELVEH 23- 7 + + + K +E G+FL + + ++ Y I+ED++GTHI ND+ ++ ++ EL++ Sbjct: 181 FEYQGKVMDIERKKKESGMFLHDK-ERDNKYPIFEDENGTHIMSPNDVCIIDELEELIDA 23- 9 Query: 238 HFTHWKLDGIYCPGDNFVAIAEIFVETARL-IENGTFTQDQAFLFDERIRKLHPKGRGLD 29- 6 +K+DG+ + + + +++ E L +EN + + + ERI + P R +D Sbjct: 240 GIDSFKIDGVLKMPEYLIEVTKMYREAIDLCVENRDEYEAKKEDWIERIESIQPVNRKID 29- 9 Query: 297 TGFY 300 TGF+ Sbjct: 300 TGFF 303 A related GBS nucleic acid sequence <SEQ ID 10949> which encodes amino acid sequence <SEQ ID 10950> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 1099> which encodes the amino acid sequence <SEQ ID 1100>. Analysis of this protein sequence reveals the following: TABLE-US-01082 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1716(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01083 Identities = 245/308 (79%), Positives = 273/308 (88%) Query: 1 MEKIILTATAESIEQVKQLLAIGIDRIYVGEENYGLRLPHSFSDDELREIAKLVHDAGKE 60 MEKII+TATAESIEQVK LLA G+DRIYVGE NYGLRLPH+FS DELR+IAKLVHDAGKE Sbjct: 1 MEKIIITATAESIEQVKALLAAGVDRIYVGEANYGLRLPHNFSYDELRQIAKLVHDAGKE 60 Query: 61 LTVACNALMHQEMMDNIKPFLELMKEINVDYLVVGDAGVFYINKRDGYNFKLIYDTSVFV 120- LTVACNALMHQ+MMD IKPFL+LM EI VDYLVVGDAGVFY+NKRDGYNFKLIYDTSVFV Sbjct: 61 LTVACNALMHQDMMDQIKPFLDLMIEIAVDYLVVGDAGVFYVNKRDGYNFKLIYDTSVFV 120- Query: 121 TSSRQVNFWGQHGAVETVLAREIPSEELFKMSENLEFPAEILVYGASVIHHSKRPLLQNY 18- 0 TSSRQVNFWGQHGAVE+VLAREIPS ELF ++ENLEFPAE+LVYGASVIHHSKRPLL+NY Sbjct: 121 TSSRQVNFWGQHGAVESVLAREIPSAELFTLAENLEFPAEVLVYGASVIHHSKRPLLENY 18- 0 Query: 181 YNFTHITDEKTRERGLFLAEPGDPESHYSIYEDKHGTHIFINNDINMMTKVTELVEHHFT 24- 0 Y+FT I DE +RERGLFLAEPGD SHYSIYED HGTHIFINNDI+MM+K+ EL H T Sbjct: 181 YHFTKIDDEVSRERGLFLAEPGDASSHYSIYEDNHGTHIFINNDIDMMSKLGELYAHGLT 24- 0 Query: 241 HWKLDGIYCPGDNFVAIAEIFVETARLIENGTFTQDQAFLFDERIRKLHPKGRGLDTGFY 30- 0 HWKLDGIYCPGD+FVAI ++F++ L+E G FTQ++A D+ + HP GRGLDTGFY Sbjct: 241 HWKLDGIYCPGDDFVAITKLFIQAKTLLEAGQFTQEEAEKLDQAVHAHHPAGRGLDTGFY 30- 0 Query: 301 DFDPSTVK 308 +FDP TVK Sbjct: 301 EFDPKTVK 308 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 340 A DNA sequence (GBSx0371) was identified in S. agalactiae <SEQ ID 1101> which encodes the amino acid sequence <SEQ ID 1102>. This protein is predicted to be cDNA EST yk542c12.5 comes from this gene. Analysis of this protein sequence reveals the following: TABLE-US-01084 Possible site: 16 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01085 >GP:AAD15622 GB:U75480 unknown [Streptococcus mutans] Identities = 69/152 (45%), Positives = 101/152 (66%), Gaps = 12/152 (7%) Query: 1 MSKLFKTLVISAASGAAAAYFLTTKKGKELRKNAEKFYGEYKENPEEYHQIAKDKASEYS 60 MSK KT +I A +GAAAAYFL+T KGK+ +K + + +YKENP+EYHQ A DK +EY Sbjct: 1 MSKFLKTAIIGAGTGAAAAYFLSTDKGKQFKKKIHQTFTDYKENPKEYHQYAADKVNEYK 60 Query: 61 NLAVDTFKDYKGKFESGELTTEDIVSAVKEKSGEVVDFANDFVNQAKSKFSDEDTAKKED 120- ++AV +FKDYK KFE+GELT ++I+S+VKEK+ + FAN ++Q K + T +K + Sbjct: 61 DVAVHSFKDYKDKFETGELTKDNIISSVKEKASQAGKFANSKLSQVKDHLA--QTVEKAE 118- Query: 121 KAP----------ETKVEDIVIDYKENTEDKE 142 + + +V+DIVIDY+ + K+ Sbjct: 119 ASTNDAGIPLGEMKAQVDDIVIDYQAEEKTKK 150 A related DNA sequence was identified in S. pyogenes <SEQ ID 1103> which encodes the amino acid sequence <SEQ ID 1104>. Analysis of this protein sequence reveals the following: TABLE-US-01086 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.81 Transmembrane 15-31 (14-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.1723(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9117> which encodes the amino acid sequence <SEQ ID 9118>. Analysis of this protein sequence reveals the following: TABLE-US-01087 Possible cleavage site: 19 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.300(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01088 Identities = 69/140 (49%), Positives = 91/140 (64%), Gaps = 8/140 (5%) Query: 1 MSKLFKTLVISAASGAAAAYFLTTKKGKELRKNAEKFYGEYKENPEEYHQIAKDKASEYS 60 M+K FK LVI A SG AAAYFL+T+KGK L+ AEK Y YKE+P++YHQ AK+K SEYS Sbjct: 8 MNKSFKNLVIGAVSGVAAAYFLSTEKGKALKNPAEKAYQAYKESPDDYHQFAKEKGSEYS 67 Query: 61 NLAVDTFKDYKGKFESGELTTEDIVSAVKEKSGEVVDFANDFVNQAKSKFSD-EDTAKKE 119- +LA DTF D K K SG+LT ED++ +K+K+ FV + K ++ E K++ Sbjct: 68 HLARDTFYDVKDKLASGDLTKEDMLDLLKDKT-------TAFVQKTKETLAEVEAKEKQD 120- Query: 120 DKAPETKVEDIVIDYKENTE 139 D + EDI+IDY E E Sbjct: 121 DVIIDLNEEDIIIDYTEQDE 140 SEQ ID 1102 (GBS164) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 30 (lane 4; MW 17.4 kDa). The GBS164-His fusion product was purified (FIG. 115A; see also FIG. 200, lane 4) and used to immunise mice (lane 1+2+3 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot, FACS (FIG. 115B), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 341 A DNA sequence (GBSx0372) was identified in S. agalactiae <SEQ ID 1105> which encodes the amino acid sequence <SEQ ID 1106>. Analysis of this protein sequence reveals the following: TABLE-US-01089 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -16.93 Transmembrane 6-22 (1-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.7771(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01090 >GP:AAD15621 GB:U75480 unknown [Streptococcus mutans] Identities = 88/129 (68%), Positives = 112/129 (86%) Query: 1 MIEIAVLIIAIAFVVLVLGILFVLKKVSETIEETKQTIKVLTSDVNVTLYQTNEILAKAN 60 M EIA+LI+AIAF VLV+ ++ +L+K+S+T++E++QT+K+LTSDVNVTLYQTNE+LAKAN Sbjct: 1 MWEIALLIVAIAFAVLVIYLILLLRKISDTVDESRQTLKILTSDVNVTLYQTNELLAKAN 60 Query: 61 VLVDDVNGKVSTIDPLFVAIADLSESVSDLNLQARHIGQKASSATSSVTKAGSALAIGKA 120- VLV+DVNGKV TIDPLF AIADLS SVSDLN QAR+ G+K +T++V KAG+A GK Sbjct: 61 VLVEDVNGKVETIDPLFTAIADLSVSVSDLNRQARYFGKKTRKSTANVGKAGAAYTFGKV 120- Query: 121 ASKIFRKKG 129 ASK+FRKKG Sbjct: 121 ASKLFRKKG 129 A related DNA sequence was identified in S. pyogenes <SEQ ID 1107> which encodes the amino acid sequence <SEQ ID 1108>. Analysis of this protein sequence reveals the following: TABLE-US-01091 Possible Site: 16 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -0.85 Transmembrane 18-34 (17-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.1341(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01092 >GP:AAD15621 GB:U75480 unknown [Streptococcus mutans] Identities = 83/128 (64%), Positives = 110/128 (85%) Query: 6 ISLMIIALAFVALVIFLIIVLKKVSETIDEAKKTISVLTSDVNVTLHQTNDILAKANILV 65 I+L+I+A+AF LVI+LI++L+K+S+T+DE+++T+ +LTSDVNVTL+QTN++LAKAN+LV Sbjct: 4 IALLIVAIAFAVLVIYLILLLRKISDTVDESRQTLKILTSDVNVTLYQTNELLAKANVLV 63 Query: 66 EDVNGKVATIDPLFVAIADLSESLSDLNSQARHFGQKATNATGNVSKAGKLALVGKVASK 125- EDVNGKV TIDPLF AIADLS S+SDLN QAR+FG+K +T NV KAG GKVASK Sbjct: 64 EDVNGKVETIDPLFTAIADLSVSVSDLNRQARYFGKKTRKSTANVGKAGAAYTFGKVASK 123- Query: 126 VFGKKGEK 133 +F KKG++ Sbjct: 124 LFRKKGKQ 131 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01093 Identities = 92/131 (70%), Positives = 116/131 (88%) Query: 1 MIEIAVLIIAIAFVVLVLGILFVLKKVSETIEETKQTIKVLTSDVNVTLYQTNEILAKAN 60 ++ I+++IIA+AFV LV+ ++ VLKKVSETI+E K+TI VLTSDVNVTL+QTN+ILAKAN Sbjct: 3 LVGISLMIIALAFVALVIFLIIVLKKVSETIDEAKKTISVLTSDVNVTLHQTNDILAKAN 62 Query: 61 VLVDDVNGKVSTIDPLFVAIADLSESVSDLNLQARHIGQKASSATSSVTKAGSALAIGKA 120- +LV+DVNGKV+TIDPLFVAIADLSES+SDLN QARH GQKA++AT +V+KAG +GK Sbjct: 63 ILVEDVNGKVATIDPLFVAIADLSESLSDLNSQARHFGQKATNATGNVSKAGKLALVGKV 122- Query: 121 ASKIFRKKGDK 131 ASK+F KKG+K Sbjct: 123 ASKVFGKKGEK 133 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 342 A DNA sequence (GBSx0373) was identified in S. agalactiae <SEQ ID 1109> which encodes the amino acid sequence <SEQ ID 1110>. Analysis of this protein sequence reveals the following: TABLE-US-01094 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0462(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 343 A DNA sequence (GBSx0374) was identified in S. agalactiae <SEQ ID 1111> which encodes the amino acid sequence <SEQ ID 1112>. This protein is predicted to be prolipoprotein diacylglyceryl transferase (Igt). Analysis of this protein sequence reveals the following: TABLE-US-01095 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.39 Transmembrane 231-247 (225-251) INTEGRAL Likelihood = -7.64 Transmembrane 89-105 (87-107) INTEGRAL Likelihood = -5.20 Transmembrane 18-34 (13-36) INTEGRAL Likelihood = -1.86 Transmembrane 46-62 (46-64) ----- Final Results ----- bacterial membrane --- Certainty = 0.4354(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9721> which encodes amino acid sequence <SEQ ID 9722> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01096 >GP:AAC80171 GB:U75480 putative prolipoprotein diacylglycerol transferase [Streptococcus mutans] (ver 3) Identities = 184/257 (71%), Positives = 226/257 (87%) Query: 2 MINPVAIRLGPFSIRWYAICIVSGMLLAVYLAMKEAPRKNIKSDDILDFILMAFPLSIVG 61 MINP+AI+LGP +IRWY+ICIV+G++LAVYL ++EAP+KNIKSDD+LDFIL+AFPL+IVG Sbjct: 1 MINPIAIKLGPLTIRWYSICIVTGLILAVYLTIREAPKKNIKSDDVLDFILIAFPLAIVG 60 Query: 62 ARIYYVIFEWAYYSKHPVEIIAIWNGGIAIYGGLITGAILLVIFSYRRLINPIDFLDIAA 121- AR+YYVIF+W YY K+P EI IW+GGIAIYGGL+TGA++L IFSY R+I PIDFLD+AA Sbjct: 61 ARLYYVIFDWDYYLKNPSEIPVIWHGGIAIYGGLLTGALVLFIFSYYRMIKPIDFLDVAA 120- Query: 122 PGVMIAQAIGRWGNFINQEAYGRAVKNLNYVPNFIKNQMYIDGAYRVPTFLYESLWNFLG 18- 1 PGVM+AQ+IGRWGNF+NQEAYG+ V LNY+P+FI+ QMYIDG YR PTFLYESLWN LG Sbjct: 121 PGVMLAQSIGRWGNFVNQEAYGKTVTQLNYLPDFIRKQMYIDGHYRTPTFLYESLWNLLG 18- 0 Query: 182 FVIIMSIRHRPRTLKQGEVACFYLVWYGCGRFIIEGMRTDSLYLAGLRVSQWLSVILVII 24- 1 F+IIM +R RP LK+GEVA FYL+WYG GRF+IEGMRTDSL A LRVSQWLSV+LV++ Sbjct: 181 FIIIMILRRRPNLLKEGEVAFFYLIWYGSGRFVIEGMRTDSLMFASLRVSQWLSVLLVVV 24- 0 Query: 242 GIVMIIYRRREQHISYY 258 G+++++ RRR I YY Sbjct: 241 GVILMVIRRRNHAIPYY 257 A related DNA sequence was identified in S. pyogenes <SEQ ID 1113> which encodes the amino acid sequence <SEQ ID 1114>. Analysis of this protein sequence reveals the following: TABLE-US-01097 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.01 Transmembrane 229-245 (222-249) INTEGRAL Likelihood = -6.90 Transmembrane 45-61 (40-68) INTEGRAL Likelihood = -4.41 Transmembrane 17-33 (11-35) INTEGRAL Likelihood = -4.14 Transmembrane 87-103 (86-106) INTEGRAL Likelihood = -0.27 Transmembrane 170-186 (170-186) ----- Final Results ----- bacterial membrane --- Certainty = 0.3803(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01098 >GP:AAC80171 GB:U75480 putative prolipoprotein diacylglycerol transferase [Streptococcus mutans] (ver 3) Identities = 176/258 (68%), Positives = 217/258 (83%) Query: 1 MINPIALKCGPLAIHWYALCILSGLVLAVYLASKEAPKKGISSDAIFDFILIAFPLAIVG 60 MINPIA+K GPL I WY++CI++GL+LAVYL +EAPKK I SD + DFILIAFPLAIVG Sbjct: 1 MINPIAIKLGPLTIRWYSICIVTGLILAVYLTIREAPKKNIKSDDVLDFILIAFPLAIVG 60 Query: 61 ARIYYVIFEWSYYVKHLDEIIAIWNGGIAIYGGLITGALVLLAYCYNKVLNPIHFLDIAA 120- AR+YYVIF+W YY+K+ EI IW+GGIAIYGGL+TGALVL + Y +++ PI FLD+AA Sbjct: 61 ARLYYVIFDWDYYLKNPSEIPVIWHGGIAIYGGLLTGALVLFIFSYYRMIKPIDFLDVAA 120- Query: 121 PSVMVAQAIGRWGNFINQEAYGKAVSQLNYLPSFIQKQMFIEGSYRIPTFLYESLWNLLG 18- 0 P VM+AQ+IGRWGNF+NQEAYGK V+QLNYLP FI+KQM+I+G YR PTFLYESLWNLLG Sbjct: 121 PGVMLAQSIGRWGNFVNQEAYGKTVTQLNYLPDFIRKQMYIDGHYRTPTFLYESLWNLLG 18- 0 Query: 181 FVIIMMWRRKPKSLLDGEIFAFYLIWYGSGRLVIEGMRTDSLMFLGIRISQYVSALLIII 24- 0 F+IIM+ RR+P L +GE+ FYLIWYGSGR VIEGMRTDSLMF +R+SQ++S LL+++ Sbjct: 181 FIIIMILRRRPNLLKEGEVAFFYLIWYGSGRFVIEGMRTDSLMFASLRVSQWLSVLLVVV 24- 0 Query: 241 GLIFVIKRRRQKGISYYQ 258 G+I ++ RRR I YYQ Sbjct: 241 GVILMVIRRRNHAIPYYQ 258 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01099 Identities = 176/257 (68%), Positives = 221/257 (85%) Query: 2 MINPVAIRLGPFSIRWYAICIVSGMLLAVYLAMKEAPRKNIKSDDILDFILMAFPLSIVG 61 MINP+A++ GP +I WYA+CI+SG++LAVYLA KEAP+K I SD I DFIL+AFPL+IVG Sbjct: 1 MINPIALKCGPLAIHWYALCILSGLVLAVYLASKEAPKKGISSDAIFDFILIAFPLAIVG 60 Query: 62 ARIYYVIFEWAYYSKHPVEIIAIWNGGIAIYGGLITGAILLVIFSYRRLINPIDFLDIAA 121- ARIYYVIFEW+YY KH EIIAIWNGGIAIYGGLITGA++L+ + Y +++NPI FLDIAA Sbjct: 61 ARIYYVIFEWSYYVKHLDEIIAIWNGGIAIYGGLITGALVLLAYCYNKVLNPIHFLDIAA 120- Query: 122 PGVMIAQAIGRWGNFINQEAYGRAVKNLNYVFNFIKHQMYIDGAYRVPTFLYESLWNFLG 18- 1 P VM+AQAIGRWGNFINQEAYG+AV LNY+P+FI+ QM+I+G+YR+PTFLYESLWN LG Sbjct: 121 PSVMVAQAIGRWGNFINQEAYGKAVSQLNYLPSFIQKQMFIEGSYRIPTFLYESLWNLLG 18- 0 Query: 182 FVIIMSIRHRPRTLKQGEVACFYLVWYGCGRFIIEGMRTDSLYLAGLRVSQWLSVILVII 24- 1 FVIIM R +P++L GE+ FYL+WYG GR +IEGMRTDSL G+R+SQ++S +L+II Sbjct: 181 FVIIMMWRRKPKSLLDGEIFAFYLIWYGSGRLVIEGMRTDSLMFLGIRISQYVSALLIII 24- 0 Query: 242 GIVMIIYRRREQHISYY 258 G++ +I RRR++ ISYY Sbjct: 241 GLIFVIKRRRQKGISYY 257 A related GBS gene <SEQ ID 8557> and protein <SEQ ID 8558> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01100 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: 2.45 GvH: Signal Score (-7.5): -2.9 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 3 value: -8.39 threshold: 0.0 INTEGRAL Likelihood = -8.39 Transmembrane 209-225 (203-229) INTEGRAL Likelihood = -7.64 Transmembrane 67-83 (65-85) INTEGRAL Likelihood = -1.86 Transmembrane 24-40 (24-42) PERIPHERAL Likelihood = 0.79 92 modified ALOM score: 2.18 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4354(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00029## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 344 A DNA sequence (GBSx0375) was identified in S. agalactiae <SEQ ID 1115> which encodes the amino acid sequence <SEQ ID 1116>. Analysis of this protein sequence reveals the following:

TABLE-US-01101 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2817(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01102 >GP:BAA77782 GB:AB027460 Hpr kinase [Streptococcus bovis] Identities = 264/309 (85%), Positives = 292/309 (94%) Query: 1 MAVTVQMLVDRLRLNVIYGDEHLLSKRITTADISRPGLEMTGYFDYYAPERLQLVGMKEW 60 M+VTV+MLVD++KL+VIYGD+ LLSK ITT+DISRPGLEMTGYFDYY+PERLQL+GMKEW Sbjct: 1 MSVTVKMLVDKVKLDVIYGDDDLLSKEITTSDISRPGLEMTGYFDYYSPERLQLLGMKEW 60 Query: 61 SYLMAMTGHNRYQVLREMFQKETPAIVVARDLEIPEEMYEAAKDTGIAILQSKAPTSRLS 120- SYL MT HNR VLREM + ETPAI+VAR+L IPEEM AAK+ GIAILQS PTSRLS Sbjct: 61 SYLTRMTSHNRRHVLREMIKPETPAIIVARNLAIPEEMISAAKEKGIAILQSHVPTSRLS 120- Query: 121 GEVSWYLDSCLAERTSVHGVLMDIYGMGVLIQGDSGIGKSETGLELVKRGHRLVADDRVD 18- 0 GE+SWYLDSCLAERTSVHGVLMDIYGMGVLIQGDSGIGKSETGLELVKRGHRLVADDRVD Sbjct: 121 GEMSWYLDSCLAERTSVHGVLMDIYGMGVLIQGDSGIGKSETGLELVKRGHRLVADDRVD 18- 0 Query: 181 VYAKDEETLWGEPAEILRHLLEIRGVGIIDIMSLYGASAVKDSSQVQLAIYLENFETGKV 24- 0 V+AKDEETLWGEPAEILRHLLEIRGVGIID+MSLYGASAVKDSSQVQLAIYLEN+E+GKV Sbjct: 181 VFAKDEETLWGEPAEILRHLLEIRGVGIIDVMSLYGASAVKDSSQVQLAIYLENYESGKV 24- 0 Query: 241 FDRLGNGNEEIELSGVKVPRIRIPVRTGRNVSVVIEAAAMNHRAKQMGFDATQTFEDRLT 30- 0 FDRLGNGNEE+ELSGVK+PR+RIPV+TGRN+SVVIEAAAMN+RAKQMGFDAT+TFE+RLT Sbjct: 241 FDRLGNGNEELELSGVKIPRLRIPVQTGRNMSVVIEAAAMNYRAKQMGFDATKTFEERLT 30- 0 Query: 301 HLISQNEVN 309 LI++NE N Sbjct: 301 QLITKNEGN 309 A related DNA sequence was identified in S. pyogenes <SEQ ID 1117> which encodes the amino acid sequence <SEQ ID 1118>. Analysis of this protein sequence reveals the following: TABLE-US-01103 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2391(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01104 Identities = 255/309 (82%), Positives = 288/309 (92%) Query: 1 MAVTVQMLVDRLKLNVIYGDEHLLSKRITTADISRPGLEMTGYFDYYAPERLQLVGMKEW 60 M VTV+MLV ++KL+V+Y ++LLSK ITT+DISRPGLEMTGYFDYYAPERLQL GMKEW Sbjct: 32 MTVTVKMLVQKVKLDVVYATDNLLSKEITTSDISRPGLEMTGYFDYYAPERLQLFGMKEW 91 Query: 61 SYLMAMTGHNRYQVLREMFQKETPAIVVARDLEIPEEMYEAAKDTGIAILQSKAPTSRLS 120- SYL MT HNRY VL+EMF+K+TPA+VV+R+L IP+EM +AAK+ GI++L S+ TSRL+ Sbjct: 92 SYLTQMTSHNRYSVLKEMFKKDTPAVVVSRNLAIPKEMVQAAKEEGISLLSSRVSTSRLA 151- Query: 121 GEVSWYLDSCLAERTSVHGVLMDIYGMGVLIQGDSGIGKSETGLELVKRGHRLVADDRVD 18- 0 GE+S++LD+ LAERTSVHGVLMDIYGMGVLIQGDSGIGKSETGLELVKRGHRLVADDRVD Sbjct: 152 GEMSYFLDASLAERTSVHGVLMDIYGMGVLIQGDSGIGKSETGLELVKRGHRLVADDRVD 21- 1 Query: 181 VYAKDEETLWGEPAEILRHLLEIRGVGIIDIMSLYGASAVKDSSQVQLAIYLENFETGKV 24- 0 VYAKDEETLWGEPAEILRHLLEIRGVGIID+MSLYGASAVKDSSQVQLAIYLENFE GKV Sbjct: 212 VYAKDEETLWGEPAEILRHLLEIRGVGIIDVMSLYGASAVKDSSQVQLAIYLENFEAGKV 27- 1 Query: 241 FDRLGNGNEEIELSGVKVPRIRIPVKTGRNVSVVIEAAAMNHRAKQMGFDATQTFEDRLT 30- 0 FDRLGNGNEEI SGV++PRIRIPVKTGRNVSVVIEAAAMNHRAK+MGFDAT+TFEDRLT Sbjct: 272 FDRLGNGNEEITFSGVRIPRIRIPVKTGRNVSVVIEAAAMNHRAKEMGFDATKTFEDRLT 33- 1 Query: 301 HLISQNEVN 309 LI++NEV+ Sbjct: 332 QLITKNEVS 340 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 345 A DNA sequence (GBSx0376) was identified in S. agalactiae <SEQ ID 1119> which encodes the amino acid sequence <SEQ ID 1120>. Analysis of this protein sequence reveals the following: TABLE-US-01105 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1836(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9719> which encodes amino acid sequence <SEQ ID 9720> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 346 A DNA sequence (GBSx0377) was identified in S. agalactiae <SEQ ID 1121> which encodes the amino acid sequence <SEQ ID 1122>. Analysis of this protein sequence reveals the following: TABLE-US-01106 Possible site: 37 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.88 Transmembrane 35-51 (31-59) ----- Final Results ----- bacterial membrane --- Certainty = 0.2954(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01107 >GP:AAC67275 GB:AF017113 YvlC [Bacillus subtilis] Identities = 21/63 (33%), Positives = 36/63 (56%), Gaps = 2/63 (3%) Query: 3 SSFYKQRKGKLVCGVVAGLADKYNWDLALSRVLIALILYFTKF--GLLLYILLAVFLPYK 60 + Y+ K K + GV+ GLA+ +NWD +L RV+ ++ T LL+YI+ +P + Sbjct: 2 NKLYRSEKNKKIAGVIGGLAEYFNWDASLLRVITVILAIMTSVLPVLLIYIIWIFIVPSE 61 Query: 61 EDI 63 D+ Sbjct: 62 RDM 64 A related DNA sequence was identified in S. pyogenes <SEQ ID 1123> which encodes the amino acid sequence <SEQ ID 1124>. Analysis of this protein sequence reveals the following: TABLE-US-01108 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.26 Transmembrane 39-55 (31-61) ----- Final Results ----- bacterial membrane --- Certainty = 0.3102(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01109 Identities = 60/90 (66%), Positives = 77/90 (84%), Gaps = 3/90 (3%) Query: 1 MKSSFYKQRKGKLVCGVVAGLADKYNWDLALSRVLIALILYFTKFGLLLYILLAVFLPYK 60 +++ FYKQRK +LV GV+AGLADKY WDLAL+RVL AL++Y T FG+LLYILLA+FLPYK Sbjct: 1 VETKFYKQRKNRLVAGVIAGLADKYGWDLALARVLAALLIYGTGFGVLLYILLAIFLPYK 60 Query: 61 EDIIETR-RQGPRRRKDAEPV--DDDGWFW 87 ED++E R +GPRRRKDA+ + ++DGWFW Sbjct: 61 EDLLEERYGRGPRRRKDADVLNEEEDGWFW 90 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 347 A DNA sequence (GBSx0378) was identified in S. agalactiae <SEQ ID 1125> which encodes the amino acid sequence <SEQ ID 1126>. Analysis of this protein sequence reveals the following: TABLE-US-01110 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3577(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9717> which encodes amino acid sequence <SEQ ID 9718> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01111 >GP:BAB04250 GB:AP001508 unknown conserved protein [Bacillus halodurans] Identities = 379/729 (51%), Positives = 515/729 (69%), Gaps = 25/729 (3%) Query: 29 ENLNITQIAIDLGIKASQIEKVLELTDEGNTIPFIARYRKEMTGNLDEVQIKSIIDLDKS 88 - E I +A +L +K + I++V++L EGNT+PFIARYRKE+TG +DEV+I+ + + Sbjct: 8 EEHTIKTLAKELSLKPNYIKQVIQLLHEGNTVPFIARYRKELTGGMDEVKIREVSEKWTY 67 Query: 89 MTALSDRKTTVLAKIEEQGKLTQELKKAIEEATKLADVEELYLPYKEKRRTKATIAREAG 148- L +RK V+ +EEQGKLT E KK +E+A KL +VE+LY PYK+KRRT+AT+A+E G Sbjct: 68 ANQLHERKEEVIRLVEEQGKLTDEWKKTVEQAQKLQEVEDLYRPYKQKRRTRATVAKEKG 127- Query: 149 LFPLARLI--LQNKDNLEEEAQNYLTDGFETTT--KALSGAVDILIEAFSEDNKLRSWTY 20- 4 L PLA + L + +EA+ YL+ E T L GA DI+ E ++D LR Sbjct: 128 LEPLAEWLFSLPRDGDPLQEAEVYLSVEHELTKVEDVLQGAQDIIAEWIADDADLRKRIR 18- 7 Query: 205 NEIWNYSSITAVVKDESLDEKQVFKIYYDFSEKISKLHGYQVLALNRGEKMGVLKVNFEH 26- 4 + + S+ A VK E LDEK V+++YYD+ E + L ++ LALNRGEK VL+V Sbjct: 188 SLGFKEGSVIAKVKKEELDEKGVYEMYYDYEEPVRTLVPHRTLALNRGEKEDVLRVTIRF 24- 7 Query: 265 NLEKMFRF----FAVRFKETS-QYIDDLIVQTVKKKIVPAMERRIRTELSEGAEDGAISL 31- 9 ++++ F RF + Y+ I K+ I P++ER IR EL+E AE+ AI + Sbjct: 248 PVDRIIEMSEKTFIRRFGSPAVPYVKAAIEDGYKRLIEPSIEREIRHELTEKAEEQAIHI 30- 7 Query: 320 FSENLRNLLLVSPLKGKMVLGFDPAFRTGAKLAVVDQTGKLMTTQVIYPVPPANQAKIEQ 37- 9 F+ENLR+LLL P+KGK+VLG DPA+RTG KLA+VD+TGK++ QVIYP PP N+ + Sbjct: 308 FAENLRSLLLQPPIKGKVVLGLDPAYRTGCKLAIVDETGKVLDIQVIYPTPPKNE--VAA 36- 5 Query: 380 SKIELAKLIKEFNIEIIAIGNGTASRESEAFVAEVLQDFPD-VSYVIVNESGASVYSASE 43- 8 +K + KLI ++ +E+IAIGNGTASRESE F+A++++D P + Y+IVNE+GASVYSASE Sbjct: 366 AKKIVKKLIADYGVEMIAIGNGTASRESEQFIADLIKDLPQTIYYLIVNEAGASVYSASE 42- 5 Query: 439 LARHEFPDLTVEKRSAISIARRLQDPLAELVKIDPKSIGVGQYQHDVSQKKLAENLDFVV 49- 8 + R EFPDL VE+RSA+SIARRLQDPLAELVKIDPKS+GVGQYQHDVSQK+L E+L FVV Sbjct: 426 IGREEFPDLQVEERSAVSIARRLQDPLAELVKIDPKSVGVGQYQHDVSQKRLNESLTFVV 48- 5 Query: 499 ETVVNQVGVNVNTASPALLAHVSGLNKTISENIVKYREENGQIKSRAEIKKVPRLGAKAF 55- 8 ETVVNQVGVNVNTASP+LL +V+GL+KT+++NIVK REE G+ +RA++K +PRLGAK + Sbjct: 486 ETVVNQVGVNVNTASPSLLQYVAGLSKTVAKNIVKKREEAGRFTARAQLKDIPRLGAKTY 54- 5 Query: 559 EQAAGFLRIPNAKNFLDNTGVHPESYEAVKKLLDQLTIKELD---DLAKEKLQNLDLIAT 61- 5 EQ GFLRI + N LD T +HPESY+ KLL ++ D + K+KLQ LD+ A Sbjct: 546 EQCIGFLRIMDGDNLLDATAIHPESYKVTDKLLSEVGATAADVGIEDLKKKLQALDVSAM 60- 5 Query: 616 AESIGVGQETLKDIIEDLLKPGRDLRDDFEAPVLRHDVLDVSDLKVGQELQGTVRNVVDF 67- 5 A ++ VG TLKD+I+ L++P RD RD+ P+L+ DVL + DL G ELQGTVRNVVDF Sbjct: 606 AATLDVGVPTLKDMIDALIRPTRDPRDEVAKPLLKQDVLQLEDLLPGMELQGTVRNVVDF 66- 5 Query: 676 GAFVDIGVHEDGLIHQSRLIKRKRDKKTRKMPPLQHPSKYLSVGDIVTVWVVEVDAERSR 73- 5 G FVDIGV +DGL+H S+L R ++HP + ++VG+IVTVWV +VD ++ R Sbjct: 666 GVFVDIGVKQDGLVHISKLANRY----------IKHPLEVVTVGEIVTVWVEDVDIKKGR 71- 5 Query: 736 IGLSLIKPD 744 I L++++P+ Sbjct: 716 IALTMLRPE 724 A related DNA sequence was identified in S. pyogenes <SEQ ID 1127> which encodes the amino acid sequence <SEQ ID 1128>. Analysis of this protein sequence reveals the following: TABLE-US-01112 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2207(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01113 Identities = 532/716 (74%), Positives = 619/716 (86%), Gaps = 10/716 (1%) Query: 28 MENLNITQIAIDLGIKASQIEKVLELTDEGNTIPFIARYRKEMTGNLDEVQIKSIIDLDK 87 - MEN N IA L + QIE+VL LT +GNTIPFIARYRKE+TGNLDEV IKSIID+DK Sbjct: 1 MENNNNHNIAEALSVSLHQIEQVLALTAQGNTIPFIARYRKEVTGNLDEVVIKSIIDMDK 60 Query: 88 SMTALSDRKTTVLAKIEEQGKLTQELKKAIEEATKLADVEELYLPYKEKRRTKATIAREA 147- S+T L++RK T+LAKIEEQGKLT +L+ +IE KLAD+EELYLPYKEKRRTKATIAREA Sbjct: 61 SLTTLNERKATILAKIEEQGKLTDQLRTSIEATEKLADLEELYLPYKEKRRTKATIAREA 120- Query: 148 GLFPLARLILQNKDNLEEEAQNYLTDGFETTTKALSGAVDILIEAFSEDNKLRSWTYNEI 20- 7 GLFPLARLILQN NLE A+ ++T+GF + +AL+GAVDIL+EA SED KLRSWTYNEI Sbjct: 121 GLFPLARLILQNAQNLETAAEPFVTEGFASPQEALAGAVDILVEAMSEDAKLRSWTYNEI 18- 0 Query: 208 WNYSSITAVVKDESLDEKQVFKIYYDFSEKISKLHGYQVLALNRGEKMGVLKVNFEHNLE 26- 7 W YS + + +KDE LDEK+VF+IYYDFS+++S + GY+ LALNRGEK+G+LKV+FEHNLE Sbjct: 181 WQYSRLVSTLKDEQLDEKKVFQIYYDFSDQVSNMQGYRTLALNRGEKLGILKVSFEHNLE 24- 0 Query: 268 KMFRFFAVRFKETSQYIDDLIVQTVKKKIVPAMERRIRTELSEGAEDGAISLFSENLRNL 32- 7 KM RFF+VRFKET+ YI+++I QT+KKKIVPAMERR+R+ELS+ AEDGAI LFSENLR+L Sbjct: 241 KMQRFFSVRFKETNPYIEEVINQTIKKKIVPAMERRVRSELSDAAEDGAIHLFSENLRHL 30- 0 Query: 328 LLVSPLKGKMVLGFDPAFRTGAKLAVVDQTGKLMTTQVIYPVPPANQAKIEQSKIELAKL 38- 7 LLVSPLKGKMVLGFDPAFRTGAKLA+VDQTGKL+TTQVIYPV PA+Q KI+ +K L +L Sbjct: 301 LLVSPLKGKMVLGFDPAFRTGAKLAIVDQTGKLLTTQVIYPVAPASQTKIQAAKETLTQL 36- 0 Query: 388 IKEFNIEIIAIGNGTASRESEAFVAEVLQDFPDVSYVIVNESGASVYSASELARHEFPDL 44- 7 I+ + I+IIAIGNGTASRESEAFVA+VL+DFP+ SYVIVNESGASVYSASELARHEFPDL Sbjct: 361 IETYQIDIIAIGNGTASRESEAFVADVLKDFPNTSYVIVNESGASVYSASELARHEFPDL 42- 0 Query: 448 TVEKRSAISIARRLQDPLAELVKIDPKSIGVGQYQHDVSQKKLAENLDFVVETVVNQVGV 50- 7 TVEKRSAISIARRLQDPLAELVKIDPKSIGVGQYQHDVSQKKL+ENL FVV+TVVNQVGV Sbjct: 421 TVEKRSAISIARRLQDPLAELVKIDPKSIGVGQYQHDVSQKKLSENLGFVVDTVVNQVGV 48- 0 Query: 508 NVNTASPALLAHVSGLNKTISENIVKYREENGQIKSRAEIKKVPRLGAKAFEQAAGFLRI 56- 7 NVNTASP+LLAHVSGLNKTISENIVKYREENG + SRA+IKKVPRLGAKAFEQAAGFLRI Sbjct: 481 NVNTASPSLLAHVSGLNKTISENIVKYREENGALTSRADIKKVPRLGAKAFEQAAGFLRI 54- 0 Query: 568 PNAKNFLDNTGVHPESYEAVKKLLDQLTIKELDDLAKEKLQNLDLIATAESIGVGQETLK 62- 7 P AKN LDNTGVHPESY AVK+L L I++LDD AK L + + AE++ +GQETLK Sbjct: 541 PGAKNILDNTGVHPESYPAVKELFKVLGIQDLDDAAKATLAAVQVPQMAETLAIGQETLK 60- 0 Query: 628 DIIEDLLKPGRDLRDDFEAPVLRHDVLDVSDLKVGQELQGTVRNVVDFGAFVDIGVHEDG 68- 7 DII DLLKPGRDLRDDFEAP+LR D+LD+ DL++GQ+L+GTVRNVVDFGAFVDIGVHEDG Sbjct: 601 DIIADLLKPGRDLRDDFEAPILRQDILDLKDLEIGQKLEGTVRNVVDFGAFVDIGVHEDG 66- 0 Query: 688 LIHQSRLIKRKRDKKTRKMPPLQHPSKYLSVGDIVTVWVVEVDAERSRIGLSLIKP 743 LIH S + K + HPS+ +SVGD+VTVWV ++D +R ++ LSL+ P Sbjct: 661 LIHISEMSKTF----------VNHPSQVVSVGDLVTVWVSKIDLDRHKVNLSLLPP 706 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 348 A DNA sequence (GBSx0379) was identified in S. agalactiae <SEQ ID 1129> which encodes the amino acid sequence <SEQ ID 1130>. This protein is predicted to be N5,N10-methylenetetrahydromethanopterin reductase homolog. Analysis of this protein sequence reveals the following: TABLE-US-01114 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4864(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01115 >GP:AAB94650 GB:U96107 N5,N10-methylenetetrahydromethanopterin reductase homolog [Staphylococcus carnosus] Identities = 164/300 (54%), Positives = 217/300 (71%), Gaps = 1/300 (0%) Query: 45 VYGIGEHHREDFAVSAPEIVLAAGAVRTNNIRLSSAVTILSSNDPIRVYQQFSTIDALSN 104- +YG+GEHHR D+AVS P VLAA A T I+LSSAVT+LSS+DP+ VY++F+T+DA+SN Sbjct: 1 MYGLGEHHRSDYAVSDPVTVLAAAASLTQRIKLSSAVTVLSSDDPVCVYERFATLDAVSN 60 Query: 105 GRAEIMAGRGSFIESFPLFGYDLADYDDLFNEKMDMLLAINSATNLDWKGHLTQTVNERP 16- 4 GRAEIM GRGSFIESFPLFGYDL DYD LF EK+++L IN + W+G + + Sbjct: 61 GRAEIMVGRGSFIESFPLFGYDLDDYDRLFVEKLELLKEINQHEVVTWEGTMRPAIKGLG 120- Query: 165 IYPRALQRQLPIWVATGGNVDSTIRIAEQGLPIVYATIGGNPKAFRQLVHIYKEVGSRNG 22- 4 +YPRA+Q ++PIW+ATGG +S+IR AE GLPI YA IGGNPK F++ + IY+ V G Sbjct: 121 VYPRAVQDEIPIWLATGGTPESSIRAAEFGLPITYAIIGGNPKRFKRNIAIYRAVAESRG 18- 0 Query: 225 HKPEQLKVAAHSWGWIEEDNQTAIDRYFFPTKQTVDNIAKGRPHWSEMTKEQYLRSVGPE 28- 4 + + VA HSWG+I + ++ A ++ PTK + IAK R +W T+ + R + E Sbjct: 181 YDLADMPVAVHSWGYIADTDEQAQREFYEPTKVHHEIIAKER-NWPPYTEAHFQREISDE 23- 9 Query: 285 GAIFVGSPEVVAHKIIGLVEALELDRFMLHLPVGSMPHKDVLNAIKLYGKEVAPIVRKYF 34- 4 GA+FVGSPE VA K+I ++E L L+RFMLH+PVGSMPH+ ++ AIKLYGK V PI+ YF Sbjct: 240 GAMFVGSPETVARKMIKVIEELGLNRFMLHIPVGSMPHERIMKAIKLYGKRVKPIIEDYF 29- 9 No corresponding DNA-sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 349 A DNA sequence (GBSx0380) was identified in S. agalactiae <SEQ ID 1131> which encodes the amino acid sequence <SEQ ID 1132>. Analysis of this protein sequence reveals the following: TABLE-US-01116 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1310(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9715> which encodes amino acid sequence <SEQ ID 9716> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1133> which encodes the amino acid sequence <SEQ ID 1134>. Analysis of this protein sequence reveals the following: TABLE-US-01117 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0915(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below:

TABLE-US-01118 Identities = 20/40 (50%), Positives = 27/40 (67%), Gaps = 3/40 (7%) Query: 4 MAITHKRQDDLESMFASFAKVP---KPKKVDSDSKPEQKD 40 MAITHK+ D+LE M A FA +P KP +V++D K K+ Sbjct: 1 MAITHKKNDELEKMLAGFASIPSFDKPLEVNTDGKLATKE 40 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 350 A DNA sequence (GBSx0381) was identified in S. agalactiae <SEQ ID 1135> which encodes the amino acid sequence <SEQ ID 1136>. Analysis of this protein sequence reveals the following: TABLE-US-01119 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1453(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 351 A DNA sequence (GBSx0382) was identified in S. agalactiae <SEQ ID 1137> which encodes the amino acid sequence <SEQ ID 1138>. Analysis of this protein sequence reveals the following: TABLE-US-01120 Possible site: 37 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.15 Transmembrane 216-232 (210-240) INTEGRAL Likelihood = -9.18 Transmembrane 15-31 (10-39) INTEGRAL Likelihood = -9.02 Transmembrane 283-299 (276-299) INTEGRAL Likelihood = -8.76 Transmembrane 128-144 (119-150) INTEGRAL Likelihood = -4.62 Transmembrane 243-259 (237-265) INTEGRAL Likelihood = -2.44 Transmembrane 65-81 (65-81) INTEGRAL Likelihood = -2.44 Transmembrane 94-110 (93-111) ----- Final Results ----- bacterial membrane --- Certainty = 0.5458(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01121 >GP:CAB12119 GB:Z99105 ycgR [Bacillus subtilis] Identities = 141/283 (49%), Positives = 198/283 (69%), Gaps = 3/283 (1%) Query: 10 SVLQWFAIFISIIIEALPFVLLGTILSGIIEVFITPDIVNKFLPKNKFLRVLFGTFVGFV 69 - S LQ +IFISI+IEA+PF+L+G ILSGII++F++ +++ + +PKN+FL VLFG G + Sbjct: 6 SFLQLNSIFISILIEAIPFILIGVILSGIIQMFVSEEMIARIMPKNRFLAVLFGALAGVL 65 Query: 70 FPSCECGIIPIINRFLEKKVPSYTAVPFLATAPIINPIVLFATYSAFGNSIRFLILRFVG 129- FP+CECGIIPI R L K VP + V F+ TAPIINPIVLF+TY AFGN + R Sbjct: 66 FPACECGIIPITRRLLLKGVPLHAGVAFMLTAPIINPIVLFSTYIAFGNRWSVVFYRGGL 125- Query: 130 ATIVAIALGVMLAFLVDDNILKEDAKPTHFHDYSDKKWYQKIFLALAHAIDEFFDTGRYL 18- 9 A V++ +GV+L++ DN L + +P H H + QK+ L HAIDEFF G+YL Sbjct: 126 ALAVSLIIGVILSYQFKDNQLLKPDEPGHHHHHHGTL-LQKLGGTLRHAIDEFFSVGKYL 18- 4 Query: 190 VFGTLIASAMQIYLPTRVLTTIGHSPITAILVMMLLAFILSLCSEADAFIGASLLSTFGI 24- 9 + G IA+AMQ Y+ T L IG + +++ LVMM LAF+LSLCSE DAFI +S STF + Sbjct: 185 IIGAFIAAAMQTYVKTSTLLAIGQNDVSSSLVMMGLAFVLSLCSEVDAFIASSFSSTFSL 24- 4 Query: 250 APVMAFLLIGPMIDIKNLMMMVNSFKTRFIVQFISVSSLIIII 292 ++AFL+ G M+DIKNL+MM+ +FK RF+ F+ ++ +++I+ Sbjct: 245 GSLIAFLVFGAMVDIKNLLMMLAAFKKRFV--FLLITYIVVIV 285 A related DNA sequence was identified in S. pyogenes <SEQ ID 1139> which encodes the amino acid sequence <SEQ ID 1140>. Analysis of this protein sequence reveals the following: TABLE-US-01122 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.92 Transmembrane 216-232 (211-237) INTEGRAL Likelihood = -9.45 Transmembrane 283-299 (276-299) INTEGRAL Likelihood = -8.76 Transmembrane 128-144 (119-150) INTEGRAL Likelihood = -7.80 Transmembrane 15-31 (10-39) INTEGRAL Likelihood = -5.47 Transmembrane 243-259 (237-265) INTEGRAL Likelihood = -2.44 Transmembrane 65-81 (65-81) INTEGRAL Likelihood = -2.44 Transmembrane 94-110 (93-111) ----- Final Results ----- bacterial membrane --- Certainty = 0.4970(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01123 >GP:CAB12119 GB:Z99105 ycgR [Bacillus subtilis] Identities = 143/288 (49%), Positives = 196/288 (67%), Gaps = 1/288 (0%) Query: 10 SVLQWFAIFMSIIIEALPFVLLGTILSGCIEVFVTPELVQKYLPKQKCLRILFGTFVGFV 69 - S LQ +IF+SI+IEA+PF+L+G ILSG I++FV+ E++ + +PK + L +LFG G + Sbjct: 6 SFLQLNSIFISILIEAIPFILIGVILSGIIQMFVSEEMIARIMPKNRFLAVLFGALAGVL 65 Query: 70 FPSCECGIIPIINRFLEKKVPSYTAVPFLATAPIINPIVLFATYSAFGNSLRFLILRLVG 129- FP+CECGIIPI R L K VP + V F+ TAPIINPIVLF+TY AFGN + R Sbjct: 66 FPACECGIIPITRRLLLKGVPLHAGVAFMLTAPIINPIVLFSTYIAFGNRWSVVFYRGGL 125- Query: 130 AALVAITLGVMLAFIVDDNILKDNAQPVHFHDYSHESLPKRIYLALVHAIDEFFDTGRYL 18- 9 A V++ +GV+L++ DN L +P H H + H +L +++ L HAIDEFF G+YL Sbjct: 126 ALAVSLIIGVILSYQFKDNQLLKPDEPGH-HHHHHGTLLQKLGGTLRHAIDEFFSVGKYL 18- 4 Query: 190 VFGTLIASAMQIYVPTRVLTTIGHNPLTAILIMMLMAFILSLCSEADAFIGASLLSTFGV 24- 9 + G IA+AMQ YV T L IG N +++ L+MM +AF+LSLCSE DAFI +S STF + Sbjct: 185 IIGAFIAAAMQTYVKTSTLLAIGQNDVSSSLVMMGLAFVLSLCSEVDAFIASSFSSTFSL 24- 4 Query: 250 APVLAFLLIGPMVDIKNLMMMVKAFKGRFIVQFIGVSVLMIAVYCLLV 297 ++AFL+ G MVDIKNL+MM+ AFK RF+ I V+++ LLV Sbjct: 245 GSLIAFLVFGAMVDIKNLLMMLAAFKKRFVFLLITYIVVIVLAGSLLV 292 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01124 Identities = 248/300 (82%), Positives = 278/300 (92%) Query: 1 MDIFNQLPDSVLQWFAIFISIIIEALPFVLLGTILSGIIEVFITPDIVNKFLPKNKFLRV 60 M +F+ LP SVLQWFAIF+SIIIEALPFVLLGTILSG IEVF+TP++V K LPK K LR+ Sbjct: 1 MSLFSNLPPSVLQWFAIFMSIIIEALPFVLLGTILSGCIEVFVTPELVQKYLPKQKCLRI 60 Query: 61 LFGTFVGFVFPSCECGIIPIINRFLEKKVPSYTAVPFLATAPIINPIVLFATYSAFGNSI 120- LFGTFVGFVFPSCECGIIPIINRFLEKKVPSYTAVPFLATAPIINPIVLFATYSAFGNS+ Sbjct: 61 LFGTFVGFVFPSCECGIIPIINRFLEKKVPSYTAVPFLATAPIINPIVLFATYSAFGNSL 120- Query: 121 RFLILRFVGATIVAIALGVMLAFLVDDNILKEDAKPTHFHDYSDKKWYQKIFLALAHAID 18- 0 RFLILR VGA +VAI LGVMLAF+VDDNILK++A+P HFHDYS + ++I+LAL HAID Sbjct: 121 RFLILRLVGAALVAITLGVMLAFIVDDNILKDNAQPVHFHDYSHESLPKRIYLALVHAID 18- 0 Query: 181 EFFDTGRYLVFGTLIASAMQIYLPTRVLTTIGHSPITAILVMMLLAFILSLCSEADAFIG 24- 0 EFFDTGRYLVFGTLIASAMQIY+PTRVLTTIGH+P+TAIL+MML+AFILSLCSEADAFIG Sbjct: 181 EFFDTGRYLVFGTLIASAMQIYVPTRVLTTIGHNPLTAILIMMLMAFILSLCSEADAFIG 24- 0 Query: 241 ASLLSTFGIAPVMAFLLIGPMIDIKNLMMMVNSFKTRFIVQFISVSSLIIIIYCLFVGVI 30- 0 ASLLSTFG+APV+AFLLIGPM+DIKNLMMMV +FK RFIVQFI VS L+I +YCL VGV+ Sbjct: 241 ASLLSTFGVAPVLAFLLIGPMVDIKNLMMMVKAFKGRFIVQFIGVSVLMIAVYCLLVGVL 30- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 352 A DNA sequence (GBSx0383) was identified in S. agalactiae <SEQ ID 1141> which encodes the amino acid sequence <SEQ ID 1142>. Analysis of this protein sequence reveals the following: TABLE-US-01125 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4703(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 353 A DNA sequence (GBSx0384) was identified in S. agalactiae <SEQ ID 1143> which encodes the amino acid sequence <SEQ ID 1144>. Analysis of this protein sequence reveals the following: TABLE-US-01126 Possible site: 50 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.44 Transmembrane 45-61 (39-65) INTEGRAL Likelihood = -8.12 Transmembrane 83-99 (77-101) INTEGRAL Likelihood = -0.00 Transmembrane 2-18 (1-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.4376(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8559> which encodes amino acid sequence <SEQ ID 8560> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-01127 Lipop Possible site: -1 Crend: 2 SRCFLG: 0 McG: Length of UR: 8 Peak Value of UR: 2.23 Net Charge of CR: 1 McG: Discrim Score: 0.46 GvH: Signal Score (-7.5): -3.54 Possible site: 42 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 2 value: -8.44 threshold: 0.0 INTEGRAL Likelihood = -8.44 Transmembrane 37-53 (31-57) INTEGRAL Likelihood = -8.12 Transmembrane 75-91 (69-93) PERIPHERAL Likelihood = 2.76 200 modified ALOM score: 2.19 icm1 HYPID: 7 CFP: 0.438 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4376(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01128 >GP:CAB12118 GB:Z99105 ycgQ [Bacillus subtilis] Identities = 100/290 (34%), Positives = 159/290 (54%), Gaps = 25/290 (8%) Query: 9 MIRFLILAGYFELSMYLKLSGKLNQYINTHYTYLAYISMVLSFILAIVQLIIWVKNMKMH 68 M R L+L G+ +L SG L +YIN Y YL++I++ L IL VQ +++K+ + Sbjct: 1 MFRLLVLMGFTFFFYHLHASGNLTKYINMKYAYLSFIAIFLLAILTAVQAYLFIKSPEKS 60 Query: 69 SHLHGKIA----------KSTSP--------MILVFPVLVGLLVPTVSLDSTTVSAKGYN 110- H H + P ++ +FP++ G+ P +LDS+ V KG++ Sbjct: 61 GHHHDHDCGCGHDHEHDHEQNKPFYQRYLIYVVFLFPLVSGIFFPIATLDSSIVKTKGFS 120- Query: 111 FPLAAGSTGTVSQDGTRVQYLKPDTSTYFTSSAYEKEMQKELKKYKGSGTLTITTENYME 17- 0 F A S SQ QYL+PD S Y+ +Y+K+M++ KY +++T +++++ Sbjct: 121 FK-AMESGDHYSQ----TQYLRPDASLYYAQDSYDKQMKQLFNKYSSKKEISLTDDDFLK 17- 5 Query: 171 VMELIYLYPEQFMDRQIQYTGFVY-NEPKHEGYQFIFRFGIIHCIADSGVYGLLTT-GNQ 22- 8 ME IY YP +F+ R I++ GF Y ++ F+ RFGIIHCIADSGVYG+L Sbjct: 176 GMETIYNYPGEFLGRTIEFHGFAYKGNAINKNQLFVLRFGIIHCIADSGVYGMLVEFPKD 23- 5 Query: 229 KSYPDNTWVTVRGTIKSEYNQLLQQNLPVLHIEESRQVSKANNPYVYRVF 278 D+ W+ ++GT+ SEY Q + LPV+ + + + K ++PYVYR F Sbjct: 236 MDIKDDEWIHIKGTLASEYYQPFKSTLPVVKVTDWNTIKKPDDPYVYRGF 285 A related DNA sequence was identified in S. pyogenes <SEQ ID 1145> which encodes the amino acid sequence <SEQ ID 1146>. Analysis of this protein sequence reveals the following: TABLE-US-01129 Possible site: 60 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.33 Transmembrane 83-99 (74-101) INTEGRAL Likelihood = -6.21 Transmembrane 42-58 (39-62) ----- Final Results ----- bacterial membrane --- Certainty = 0.4333(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9115> which encodes the amino acid sequence <SEQ ID 9116>. Analysis of this protein sequence reveals the following: TABLE-US-01130 Possible cleavage site: 54 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.33 Transmembrane 75-91 (66-93) INTEGRAL Likelihood = -6.21 Transmembrane 34-50 (31-54) PERIPHERAL Likelihood = 2.76 ----- Final Results ----- bacterial membrane --- Certainty = 0.433(Affirmative) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01131 Identities = 208/279 (74%), Positives = 244/279 (86%), Gaps = 1/279 (0%) Query: 1 MFICGGNIMIRFLILAGYFELSMYLKLSGKLNQYINTHYTYLAYISMVLSFILAIVQLII 60 +F CGG +MIRFLILAGYFEL+MYL+LSGKL+QYIN Y+YLAYISM+LSFILA+VQL Sbjct: 1 LFTCGGALMIRFLILAGYFELTMYLQLSGKLDQYINVRYSYLAYISMILSFILALVQLYT 60 Query: 61 WVKNMKMHSHLHGKIAKSTSPMILVFPVLVGLLVPTVSLDSTTVSAKGYNFPLAAGSTGT 120- W+KN+K+HSHL GKIA+ TSP ILVFPVL+GLLVPTV+LDSTTVSAKGY FPLAAG++ T Sbjct: 61 WMKNIKVHSHLTGKIARLTSPFILVFPVLIGLLVPTVTLDSTTVSAKGYTFPLAAGASKT 120- Query: 121 -VSQDGTRVQYLKPDTSTYFTSSAYEKEMQKELKKYKGSGTLTITTENYMEVMELIYLYP 17- 9 VS DGT +QYLKPDTS YFT SAY+KEM++EL KYKG +TITTENYMEVMELIYLYP Sbjct: 121 GVSDDGTTIQYLKPDTSLYFTKSAYQKEMRQELHKYKGKKPVTITTENYMEVMELIYLYP 18- 0 Query: 180 EQFMDRQIQYTGFVYNEPKHEGYQFIFRGIIHCIADSGVYGLLTTGNQKSYPDNTWVTV 239- ++F+DR IQYTGFVYNEP H+ YQF+FRFGIIHCIADSGVYGLLTTGNQ SYP+NTW+TV Sbjct: 181 DEFLDRDIQYTGFVYNEPGHDNYQFLFRFGIIHCIADSGVYGLLTTGNQTSYPNNTWLTV 24- 0 Query: 240 RGTIKSEYNQLLQQNLPVLHIEESRQVSKANNPYVYRVF 278 +G + EY++ L+Q+LPVL + E Q + NNPYVYRVF Sbjct: 241 KGRLHMEYDKNLEQHLPVLQLAEVHQTKEPNNPYVYRVF 279 SEQ ID 8560 (GBS235d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 146 (lane 14 & 15; MW 48.5 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 146 (lane 17 & 18; MW 23.4 kDa), in FIG. 150 (lane 15; MW 23 kDa) and in FIG. 182 (lane 5; MW 23 kDa). GBS235d-His was purified as shown in FIG. 235, lane 6-7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 354 A DNA sequence (GBSx0385) was identified in S. agalactiae <SEQ ID 1147> which encodes the amino acid sequence <SEQ ID 1148>. This protein is predicted to be signal recognition particle (ftsY). Analysis of this protein sequence reveals the following: TABLE-US-01132 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3301(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01133 >GP: BAB06205 GB: AP001515 signal recognition particle (docking protein) [Bacillus halodurans] Identities = 175/304 (57%), Positives = 227/304 (74%) Query: 233 EKYNRSLKKTRTGFSARLNAFLSNFRRVDEEFFEELEEMLILSDVGVNVATQLTEDLRYE 29- 2 EK+ L+KTR F+ ++N + +R VDE+FFEELEE+LI +DVGV L E+L+ E Sbjct: 20 EKFKAGLEKTRDSFAGKMNDLVYKYRSVDEDFFEELEEILIGADVGVTTVMDLVEELKDE 79 Query: 293 AKLENAKKSEDLKRVIVEKLVEIYEKDGIYNEAINFQEGLTVMLFVGVNGVGKTTSIGKL 35- 2 + +N K S+D++ +I EKL E+ EK+G E GL+V+L VGVNGVGKTTSIGKL Sbjct: 80 VRRQNIKDSKDIQPIISEKLAELLEKEGGETEVNLQPAGLSVILVVGVNGVGKTTSIGKL 139- Query: 353 AHQYKSQGKKVMLVAADTFRAGAVAQLVEWGRRVDVPVVTGEEKADPASVVFDGMEKAVA 41- 2 AH YK QGKKV+L A DTFRAGA+ QL WG R V V+ E +DPA+V+FD ++ A + Sbjct: 140 AHMYKQQGKKVILAAGDTFRAGAIEQLEVWGERAGVDVIKQSEGSDPAAVMFDAIQAAKS 19- 9 Query: 413 QGVDVLLIDTAGRLQNKENLMAELEKIGRIIKRVVPDAPHETLLALDASTGQNALSQAKE 47- 2 + D+L+ DTAGRLQNK NLM ELEK+ R+I R +P APHE L+ALDA+TGQNA+SQAK Sbjct: 200 READILICDTAGRLQNKVNLMKELEKVKRVISREIPGAPHEVLIALDATTGQNAMSQAKT 25- 9 Query: 473 FSKITPLTGLILTKIDGTAKGGVVLAIRQELDIPVKFIGFGEKIDDIGEFNSEDFMRGLL 53- 2 F + T +TG+ILTK+DGTAKGG+VLAIR ELDIPVKF+G GEKIDD+ F+SE F+ GL Sbjct: 260 FKETTDVTGIILTKLDGTAKGGIVLAIRHELDIPVKFVGLGEKIDDLQPFDSEQFVYGLF 31- 9 Query: 533 EGIL 536 + ++ Sbjct: 320 KDMV 323 A related DNA sequence was identified in S. pyogenes <SEQ ID 1149> which encodes the amino acid sequence <SEQ ID 1150>. Analysis of this protein sequence reveals the following: TABLE-US-01134 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4384(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01135 Identities = 339/549 (61%), Positives = 404/549 (72%), Gaps = 46/549 (8%) Query: 1 MGLFDRLFGHKKKDKEPEIEASESVVLEDEDSVIDKEEGSNFSKESTLNRTSEVPVAEDD 60 MGLFDRLFG K+ K E + E+++ E KEE S + E ++ + + Sbjct: 1 MGLFDRLFGKKETPKVAEEKLEENLLTE----TTQKEELSEKANEQ-----DKIEAVQQE 51 Query: 61 SFLELERDTALSESHQPVTSEIHPLESEDTDEIPVKEDDSFLELEDRAKTKVADTSEVEN 120- ++ + A S + P + ++ L E+T D + DT+E Sbjct: 52 ---DVSSEGAGSVENGPEAASVNALVEEETG--------------DNSNHPSEDTNEF-- 92 Query: 121 VVPDSTTLSDNVSAKSEASFSDKEQLSDSQASDQFSETPLQEEMS--SGKTEVQTESEDT 17- 8 D T L VS S+++ S+ + L D +QF Q + S S E S++ Sbjct: 93 -AADKTDLK--VSELSQSTASEPKDLVDQPVVEQFPTKQAQADASNDSANEEAVDTSKEQ 149- Query: 179 SAADAFLADYYAKRKAIEKEISSNSLST---------DESEFSEAQEVLSQSQA--DTIK 22- 7 S++ + DYY ++ A+EK + + +T E++ S + E SQ++A DTI Sbjct: 150 SSSQQVMEDYYRRKAALEKSLQEKAAATVPVMPEEVPQENQASTSAEA-SQNKATHDTIP 20- 8 Query: 228 AESQEEKYNRSLKKTRTGFSARLNAFLSNFRRVDEEFFEELEEMLILSDVGVNVATQLTE 28- 7 E+ +EKY RSLKKTRTGFSARLN+F +NFRRVDEEFFE+LEEMLILSDVGV+VAT LTE Sbjct: 209 -ETDQEKYKRSLKKTRTGFSARLNSFFANFRRVDEEFFEDLEEMLILSDVGVHVATTLTE 26- 7 Query: 288 DLRYEAKLENAKKSEDLKRVIVEKLVEIYEKDGIYNEAINFQEGLTVMLFVGVNGVGKTT 34- 7 +LRYEAKLENAKK + LKRVIVEKLV+IYEKDG YNEAIN+Q+GLTVMLFVGVNGVGKTT Sbjct: 268 ELRYEAKLENAKKPDALKRVIVEKLVDIYEKDGRYNEAINYQDGLTVMLFVGVNGVGKTT 32- 7 Query: 348 SIGKLAHQYKSQGKKVMLVAADTFRAGAVAQLVEWGRRVDVPVVTGEEKADPASVVFDGM 40- 7 SIGKLA++YK +GKKVMLVAADTFRAGAVAQLVEWGRRVDVPV+TG EKADPASVVFDGM Sbjct: 328 SIGKLAYRYKQEGKKVMLVAADTFRAGAVAQLVEWGRRVDVPVITGPEKADPASVVFDGM 38- 7 Query: 408 EKAVAQGVDVLLIDTAGRLQNKENLMAELEKIGRIIKRVVPDAPHETLLALDASTGQNAL 46- 7 EKAVA+GVD+LLIDTAGRLQNKENLMAELEK+GRIIKRV+PDAPHETLLALDASTGQNAL Sbjct: 388 EKAVAKGVDILLIDTAGRLQNKENLMAELEKMGRIIKRVLPDAPHETLLALDASTGQNAL 44- 7 Query: 468 SQAKEFSKITPLTGLILTKIDGTAKGGVVLAIRQELDIPVKFIGFGEKIDDIGEFNSEDF 52- 7 SQAKEFSKITPLTGLILTKIDGTAKGGVVLAIRQELDIPVKFIGFGEK+DDIGEF+SEDF Sbjct: 448 SQAKEFSKITPLTGLILTKIDGTAKGGVVLAIRQELDIPVKFIGFGEKVDDIGEFHSEDF 50- 7 Query: 528 MRGLLEGIL 536 M+GLLEGIL Sbjct: 508 MKGLLEGIL 516 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 355 A DNA sequence (GBSx0386) was identified in S. agalactiae <SEQ ID 1151> which encodes the amino acid sequence <SEQ ID 1152>. Analysis of this protein sequence reveals the following:

TABLE-US-01136 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3592(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01137 >GP: AAA62048 GB: L10328 f270 [Escherichia coli] Identities = 101/273 (36%), Positives = 160/273 (57%), Gaps = 10/273 (3%) Query: 4 IKILALDLDGTLFTTDKKVSEENKVALKAAREKGIKVVITTGRPLKAIGNLLEDLELVSD 63 IK++A+D+DGTL D +S K A+ AAR +G+ VV+TTGRP + N L++L + Sbjct: 3 IKLIAIDMDGTLLLPDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKELHMEQP 62 Query: 64 EDYSITFNGGLVQQNT-GKILAKTAMTRQEVEDIHEELYQVGLPTDILSEGTVYS----I 118- DY IT+NG LVQ+ G +A+TA++ + + + +VG L T+Y+ I Sbjct: 63 GDYCITYNGALVQKAADGSTVAQTALSYDDYRXLEKLSREVGSHFHALDRTTLYTANRDI 122- Query: 119 ANKGHHSQYHLANPLLEFIEVDDLEQVPKDVVYNKIVSVIDATYLDQQIAKLPDRLKVDY 17- 8 + H + PL+ F E E++ + + K++ + + LDQ IA++P +K Y Sbjct: 123 SYYTVHESFVATIPLV-FCEA---EKMDPNTQFLKVMMIDEPAILDQAIARIPQXVKEKY 17- 8 Query: 179 EMFKSRDIILELMPKGVHKAVGLELLTKHLGLDSSQVMAMGDEANDLSMLEWAGLGVAMA 23- 8 + KS LE++ K V+K G++ L LG+ ++MA+GD+ ND++M+E+AG+GVAM Sbjct: 179 TVLKSAPYFLEILDKRVNKGTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVAMD 23- 8 Query: 239 NGIPEAKAIAKATTICNNDESGVAEAIGKYILS 271 N IP K +A T +N E GVA AI KY+L+ Sbjct: 239 NAIPSVKEVANFVT-KSNLEDGVAFAIEKYVLN 270 A related DNA sequence was identified in S. pyogenes <SEQ ID 1153> which encodes the amino acid sequence <SEQ ID 1154>. Analysis of this protein sequence reveals the following: TABLE-US-01138 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3502(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01139 Identities = 180/273 (65%), Positives = 218/273 (78%), Gaps = 1/273 (0%) Query: 3 DIKILALDLDGTLFTTDKKVSEENKVALKAAREKGIKVVITTGRPLKAIGNLLEDLELVS 62 +I+ILALDLDGTL+ T+K V++ NK AL AAREKG+KVVITTGRPLKAIGNLLE+L+L+ Sbjct: 2 NIRILALDLDGTLYNTEKIVTDANKKALAAAREKGVKVVITTGRPLKAIGNLLEELDLLD 61 Query: 63 DEDYSITFNGGLVQQNTGKILAKTAMTRQEVEDIHEELYQVGLPTDILSEGTVYSIANK- 121- +DYSITFNGGLVQ+NTG++L K++++ +V I + L VGLPTDI+S G VYSI +K Sbjct: 62 HDDYSITFNGGLVQRNTGEVLDKSSLSFDQVCQIQQALEAVGLPTDIISGGDVYSIPSKD 121- Query: 122 GHHSQYHLANPLLEFIEVDDLEQVPKDVVYNKIVSVIDATYLDQQIAKLPDRLKVDYEMF 18- 1 G HSQYHLANPLL FIEV + ++PKD+ YNKIV+V D +LDQQI KL L D+E F Sbjct: 122 GRHSQYHLANPLLTFIEVTSVAELPKDITYNKIVTVTDPDFLDQQIIKLSPSLFEDFEAF 18- 1 Query: 182 KSRDIILELMPKGVHKAVGLELLTKHLGLDSSQVMAMGDEANDLSMLEWAGLGVAMANGI 24- 1 KSRDII E+MPKG+ KA GL LL +HLGLD+ VMAMGDEAND +MLEWAGLGVAMANG+ Sbjct: 182 KSRDIIFEIMPKGIDKAFGLNLLCQHLGLDARHVMAMGDEANDFAMLEWAGLGVAMANGV 24- 1 Query: 242 PEAKAIAKATTICNNDESGVAEAIGKYILSEEN 274 AKA A A T NDESGVAEA+ +IL EE+ Sbjct: 242 SGAKADADAVTTLTNDESGVAEAVKTFILEEES 274 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 356 A DNA sequence (GBSx0387) was identified in S. agalactiae <SEQ ID 1155> which encodes the amino acid sequence <SEQ ID 1156>. Analysis of this protein sequence reveals the following: TABLE-US-01140 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4648(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01141 >GP: BAA35556 GB: D90723 Hypothetical 30.2 kd protein in idh-deoR intergenic region. [Escherichia coli] Identities = 91/264 (34%), Positives = 146/264 (54%), Gaps = 4/264 (1%) Query: 2 IKLVATDMDGTFLDENGTYDKKRLANVLKKFKEQGIVFTAASGRSLLSLEQLFADFRDQM 61 IKL+A DMDGTFL + TY+++R ++ K QGI F ASG L F + +++ Sbjct: 4 IKLIAVDMDGTFLSDQKTYNRERFMAQYQQMKAQGIRFVVASGNQYYQLISFFPEIANEI 63 Query: 62 AFIAENGSAAVLFNRLAYEQHLSREQYLDIIDHLSKSPYMENNEYVLSGKDGAYILSDAN 121- AF+AENG V + + LS++ + +++HL P + E + GK+ AY L + Sbjct: 64 AFVAENGGWVVSEGKDVFNGELSKDAFATVVEHLLTRPEV---EIIACGKNSAYTLKKYD 120- Query: 122 PDYIEFITHYYDNLQKVSHFEDVDDIIFKVTANFTEETVRQAEEWVNQAI-PYATAVTTG 18- 0 YY L+ V +F++++DI FK N ++E + Q ++ +++AI +V TG Sbjct: 121 DAMKTVAEMYYHRLEYVDNFDNLEDIFFKFGLNLSDELIPQVQKALHEAIGDIMVSVHTG 18- 0 Query: 181 FKSIDIILSSVNKRNGLEHLCEQYGIRAEEVLSFGDNINDLEMLEWSGKAIATENARPEV 24- 0 SID+I+ V+K NGL L + +GI EV+ FGD ND+EML +G + A ENA V Sbjct: 181 NGSIDLIIPGVHKANGLRQLQKLWGIDDSEVVVFGDGGNDIEMLRQAGFSFAMENAGSAV 24- 0 Query: 241 KEIADCIIGHHNNQAVMAYLESMV 264 A G +N + V+ ++ ++ Sbjct: 241 VAAAKYRAGSNNREGVLDVIDKVL 264 A related DNA sequence was identified in S. pyogenes <SEQ ID 1157> which encodes the amino acid sequence <SEQ ID 1158>. Analysis of this protein sequence reveals the following: TABLE-US-01142 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3401(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01143 Identities = 138/265 (52%), Positives = 193/265 (72%), Gaps = 1/265 (0%) Query: 1 MIKLVATDMDGTFLDENGTYDKKRLANVLKKFKEQGIVFTAASGRSLLSLEQLFADFRDQ 60 MIKL+ATDMDGTFL E+GTY++++LA +L K E+GI+F +SGRSLL+++QLF F DQ Sbjct: 1 MIKLIATDMDGTFLAEDGTYNQEQLAALLPKLAEKGILFAVSSGRSLLAIDQLFEPFLDQ 60 Query: 61 MAFIAENGSAAVLFNRLAYEQHLSREQYLDIIDHLSKSPYMENNEYVLSGKDGAYILSDA 120- +A IAENGS + + +++EQY ++ + +P+ V SG+ AYIL A Sbjct: 61 IAVIAENGSVVQYRGEILFADMMTKEQYTEVAKKILANPHYVETGMVFSGQKAAYILKGA 120- Query: 121 NPDYIEFITHYYDNLQKVSHFEDVD-DIIFKVTANFTEETVRQAEEWVNQAIPYATAVTT 17- 9 + +YI+ HYY N++ ++ FED++ D IFKV+ NFT TV + +W+NQA+PYATAVTT Sbjct: 121 SEEYIQKTKHYYANVKVINGFEDMENDAIFKVSTNFTGHTVLEGSDWLNQALPYATAVTT 18- 0 Query: 180 GFKSIDIILSSVNKRNGLEHLCEQYGIRAEEVLSFGDNINDLEMLEWSGKAIATENARPE 23- 9 GF SIDIIL VNK G+EHLC+ GI+ E ++FGDN ND +MLE++G+AIATENARPE Sbjct: 181 GFDSIDIILKEVNKGFGMEHLCQALGIKKAETIAFGDNFNDYQMLEFAGRAIATENARPE 24- 0 Query: 240 VKEIADCIIGHHNNQAVMAYLESMV 264 +K I+D +IGH N+ AV+ YL+ +V Sbjct: 241 IKVISDQVIGHCNDGAVLTYLKGLV 265 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 357 A DNA sequence (GBSx0388) was identified in S. agalactiae <SEQ ID 1159> which encodes the amino acid sequence <SEQ ID 1160>. Analysis of this protein sequence reveals the following: TABLE-US-01144 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2428(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 358 A DNA sequence (GBSx0389) was identified in S. agalactiae <SEQ ID 1161> which encodes the amino acid sequence <SEQ ID 1162>. This protein is predicted to be p115 protein (smc). Analysis of this protein sequence reveals the following: TABLE-US-01145 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.99 Transmembrane 1092-1108 (1088-1110) ----- Final Results ----- bacterial membrane --- Certainty = 0.2996(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9713> which encodes amino acid sequence <SEQ ID 9714> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01146 >GP: CAB13467 GB: Z99112 chromosome segregation SMC protein homolg [Bacillus subtilis] Identities = 458/1193 (38%), Positives = 728/1193 (60%), Gaps = 27/1193 (2%) Query: 1 MFLKEIEMQGFKSFADKTKVEFDQGVTAVVGPNGSGKSNITESLRWALGESSAKSLRGGK 60 MFLK +++ GFKSFA++ V+F +GVTAVVGPNGSGKSNIT+++RW LGE SA+SLRGGK Sbjct: 1 MFLKRLDVIGFKSFAERISVDFVKGVTAVVGPNGSGKSNITDAIRWVLGEQSARSLRGGK 60 Query: 61 MPDVIFAGTENRKPLNYAQVSVTLDNSDHFIENIADEVRVERRIFRNGDSEYLIDGRKVR 120- M D+IFAG+++RK LN A+V++TLDN DHF+ EV V RR++R+G+SE+LI+ + R Sbjct: 61 MEDIIFAGSDSRKRLNLAEVTLTLDNDDHFLPIDFHEVSVTRRVYRSGESEFLINNQPCR 120- Query: 121 LRDIHDLFMDTGLGRDSFSIISQGRVEAIFNSKPEERRAIFEEAAGVLKYKTRKKETQSK 18- 0 L+DI DLFMD+GLG+++FSIISQG+VE I +SK E+RR+IFEEAAGVLKYKTRKK+ ++K Sbjct: 121 LKDIIDLFMDSGLGKEAFSIISQGKVEEILSSKAEDRRSIFEEAAGVLKYKTRKKKAENK 18- 0 Query: 181 LEQTQGNLDRLEDIIYELDMQVQPLEKQASIAKRFLVLDEERQGLHLSILIEDILQHQSD 24- 0 L +TQ NL+R+EDI++EL+ QV+PL+ QASIAK +L +E + + +++ DI + Sbjct: 181 LFETQDNLNRVEDILHELEGQVEPLKIQASIAKDYLEKKKELEHVEIALTAYDIEKLHGK 24- 0 Query: 241 LTTVEEKLLTVRKELATYYQQRQSLEDENQSLKQKRHHLSEEIEAKQLALLDVTKLKSDL 30- 0 +T++EK+ ++E + E + + + K L E + Q LL ++ L Sbjct: 241 WSTLKEKVQMAKEEELAESSAISAKEAKIEDTRDKIQALDESVNELQQVLLVTSEELEKL 30- 0 Query: 301 ERQIDLIRLESNQKAEKKEEAGQRLAELEIKAKDCSDQITQKNIELTTLSEKIAQIRSEI 36- 0 E + ++++ + +E+ + + + + K ++++++ TL ++ Q+R+++ Sbjct: 301 EGRKEVLKERKKNAVQNQEQLEEAIVQFQQKETVLKEELSKQEAVFETLQAEVKQLRAQV 36- 0 Query: 361 VSTESSLERFSTNPDQIIEKLREDFVTLMQEEADTSNALTALLADIENQKQASQAKSQEI 42- 0 + +L + N ++ IE+L+ D+ L+ +A N L LL D +Q + + + Sbjct: 361 KEKQQALSLHNENVEEKIEQLKSDYFELLWSQASIRNEL-QLLDDQMSQSAVTLQRLADN 41- 9 Query: 421 QEVSKNLEVLKSNAKVALE-RFEAAKKNVRQLLSHYQDLGQTLQNLEGEYKWQQSILFDH 47- 9 E S K A E F ++ + + Y+D+ + + +Y+ +S L+ Sbjct: 420 NEKHLQERHDISARKAACETEFARIEQEIHSQVGAYRDMQTKYEQKKRQYEKNESALYQA 47- 9 Query: 480 LDEIKSKQARISSLESILKNHSNFYAGVKSVLQAKDQLGGIIGAVSEHLSFDKHYQTALE 53- 9 ++ +++ LE++ + S FY GVK VL+AK++LGGI GAV E +S ++ Y+TA+E Sbjct: 480 YQYVQQARSKKDMLETMQGDFSGFYQGVKEVLKAKERLGGIRGAVLELISTEQKYETAIE 53- 9 Query: 540 IALGGSSQHIIVEDESAAKRSIAFLKKNRQGRATFLPLTTIKPRELAQHYLSKLQSSQGF 59- 9 IALG S+QH++ +DE +A+++I +LK+N GRATFLPL+ I+ R+L F Sbjct: 540 IALGASAQHVVTDDEQSARKAIQYLKQNSFGRATFLPLSVIRDRQLQSRDAETAARHSSF 59- 9 Query: 600 LGIASELVTYDQRLSNIFKNNLGLTAIFDTVDNANVAARQLNYQVRLVTLDGTELRPGGS 65- 9 LG+ASELVT+D ++ +N LG I + + AN A+ L ++ R+VTL+G + PGGS Sbjct: 600 LGVASELVTFDPAYRSVIQNLLGTVLITEDLKGANELAKLLGHRYRIVTLEGDVVNPGGS 65- 9 Query: 660 YSGGANRQNNTVFI--KPELDNLKKELKQAQSKQLIQEKEVATLLEQLKEKQETLAQLKN 71- 7 +GGA ++ N + EL+++ K L + + K + E+EV TL +++ ++ LA L+ Sbjct: 660 MTGGAVKKKNNSLLGRSRELEDVTKRLAEMEEKTALLEQEVKTLKHSIQDMEKKLADLRE 71- 9 Query: 718 DGEQARLEEQRADIEYQQLSEKLADLNKLYNGLQLSSGALEQTTSENE--KNRLEKELEQ 77- 5 GE RL++Q + +L ++N AL ++ E + K +LE+EL Sbjct: 720 TGEGLRLKQQDVKGQLYELQVAEKNINTHLELYDQEKSALSESDEERKVRKRKLEEELSA 77- 9 Query: 776 FAIKKEELTTSIAQIKEDKDSIQEKVNNLTTLLSEAQLEERDLLNEQKFERANCTRL--- 83- 2 + K ++L I ++ + K + +L+ L+E ++ K E N RL Sbjct: 780 VSEKMKQLEEDIDRLTKQKQTQSSTKESLSNELTELKIAAAKKEQACKGEEDNLARLKKE 83- 9 Query: 833 ----EITLSEIKRDISNLQTLLSHQDSQLDKEELPRIEKQLLQVNNRRENDEEKLVSLRF 88- 8 E+ L E K D+S L + +S S E++L + + ND+ K + L Sbjct: 840 LTETELALKEAKEDLSFLTSEMSSSTSG---------EEKLEEAAKHKLNDKTKTIELIA 89- 0 Query: 889 ELEDCEAALDDLAASLAKEGQKNESLIRQQAQL----ESQCEQLSQQLMIFSRQLSEDYQ 94- 4 D L + +E ++ + L +Q+ L E + ++ +L + L E+Y Sbjct: 891 LRRDQRIKLQHGLDTYERELKEMKRLYKQKTTLLKDEEVKLGRMEVELDNLLQYLREEYS 95- 0 Query: 945 MTLDEAKVKANVLEDILMAREQLKSLQAKIKALGPVNIDAIAQFEEVHERLTFLNTQRDD 10- 04 ++ + AK K + D AR+++K ++ I+ LG VN+ +I +FE V+ER FL+ Q++D Sbjct: 951 LSFEGAKEKYQLETDPEEARKRVKLIKLAIEELGTVNLGSIDEFERVNERYKFLSEQKED 10- 10 Query: 1005 LVHAKNLLLETITDMDDEVKTRFKSTFEAIRHSFKETFVQMFGGGSADLILTE-GDLLSA 1- 063 L AKN L + I +MD+E+ RF TF IR F + F +FGGG A+L LT+ DLL + Sbjct: 1011 LTEAKNTLFQVIEEMDEEMTKRFNDTFVQIRSHFDQVFRSLFGGGRAELRLTDPNDLLHS 1- 070 Query: 1064 GVDISVQPPGKKIQSLNLMSGGEKALSALALLFAIIRVKTIPFVILDEVEAALDEANVKR 1- 123 GV+I QPPGKK+Q+LNL+SGGE+AL+A+ALLF+I++V+ +PF +LDEVEAALDEANV R Sbjct: 1071 GVEIIAQPPGKKLQNLNLLSGGERALTAIALLFSILKVRPVPFCVLDEVEAALDEANVFR 1- 130 Query: 1124 FGDYLNRFDKSSQFIVVTHRKGTMSAADSIYGVTMQESGVSKIVSVKLKEAQE 1176 F YL ++ +QFIV+THRKGTM AD +YGVTMQESGVSK++SVKL+E +E Sbjct: 1131 FAQYLKKYSSDTQFIVITHRKGTMEEADVLYGVTMQESGVSKVISVKLEETKE 1183 A related DNA sequence was identified in S. pyogenes <SEQ ID 1163> which encodes the amino acid sequence <SEQ ID 1164>. Analysis of this protein sequence reveals the following: TABLE-US-01147 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.99 Transmembrane 1092-1108 (1088-1110) ----- Final Results ----- bacterial membrane --- Certainty = 0.2996(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01148 >GP: CAB13467 GB: Z99112 chromosome segregation SMC protein homolg [Bacillus subtilis] Identities = 441/1192 (36%), Positives = 729/1192 (60%), Gaps = 25/1192 (2%) Query: 1 MFLKEIEMEGFKSFADKTKIEFDKGVTAVVGPNGSGKSNITESLRWALGESSAKNLRGGK 60 MFLK +++ GFKSFA++ ++F KGVTAVVGPNGSGKSNIT+++RW LGE SA++LRGGK Sbjct: 1 MFLKRLDVIGFKSFAERISVDFVKGVTAVVGPNGSGKSNITDAIRWVLGEQSARSLRGGK 60 Query: 61 MPDVIFAGTQNRNPLNYAKVAVVLDNSDHFIKTAKKEIRVERHIYRNGDSDYLIDGRKVR 120- M D+IFAG+ +R LN A+V + LDN DHF+ E+ V R +YR+G+S++LI+ + R Sbjct: 61 MEDIIFAGSDSRKRLNLAEVTLTLDNDDHFLPIDFHEVSVTRRVYRSGESEFLINNQPCR 120- Query: 121 LRDIHDLFMDTGLGRDSFSIISQGRVEEIFNSKPEERRAIFEEAAGVLKYKTRKKETQIK 18- 0 L+DI DLFMD+GLG+++FSIISQG+VEEI +SK E+RR+IFEEAAGVLKYKTRKK+ + K Sbjct: 121 LKDIIDLFMDSGLGKEAFSIISQGKVEEILSSKAEDRRSIFEEAAGVLKYKTRKKKAENK 18- 0 Query: 181 LNQTQDNLDRLEDIIYELDTQLAPLEKQAKVAKQFLELDANRKQLQLDILVKDIDIAQER 24- 0 L +TQDNL+R+EDI++EL+ Q+ PL+ QA +AK +LE + +++ + DI+ + Sbjct: 181 LFETQDNLNRVEDILHELEGQVEPLKIQASIAKDYLEKKKELEHVEIALTAYDIEKLHGK 24- 0 Query: 241 QTKDTEALAALQQDLASYYAKRQSMEEDYQKFKQKKQVLSQESDQTQTTLLELTKLIADL 30- 0 + E + +++ + + + E + + K Q L + ++ Q LL ++ + L Sbjct: 241 WSTLKEKVQMAKEEELAESSAISAKEAKIEDTRDKIQALDESVNELQQVLLVTSEELEKL 30- 0 Query: 301 EKQIELVKLESGQSAEKKAEAKKHLEQLQEQLDGFQAEEKQCTEQLLH-------IDQQL 35- 3 E + E++K E+K A ++ EQL+E + FQ +E E+L + ++ Sbjct: 301 EGRKEVLK-------ERKKNAVQNQEQLEEAIVQFQQKETVLKEELSKQEAVFETLQAEV 35- 3 Query: 354 CDVKQQLNELSNALERFSSDPDQLMETLREEFVLLMQKEAALSNQLTALKAHLDKEKQAR 41- 3 ++ Q+ E AL + + ++ +E L+ ++ L+ +A++ N+L L + + Sbjct: 354 KQLRAQVKEKQQALSLHNENVEEKIEQLKSDYFELLNSQASIRNELQLLDDQMSQSAVTL 41- 3 Query: 414 QHKAQEYQLLVTKLDQLNDESQKAQAHYKAQKEQVEMLLQNYQEGDKRVQELERDYQLNQ 47- 3 Q A + + + ++ + + ++++ + Y++ + ++ +R Y+ N+ Sbjct: 414 QRLADNNEKHLQERHDISARKAACETEFARIEQEIHSQVGAYRDMQTKYEQKKRQYEKNE 47- 3 Query: 474 ERLFDLLDQKKGKEARKASLESIQKSHSQFYAGVRAVLQSQKKLGGIIGAVSEHLSFDSD 53- 3 L+ + ++K LE++Q S FY GV+ VL+++++LGGI GAV E +S + Sbjct: 474 SALYQAYQYVQQARSKKDMLETMQGDFSGFYQGVKEVLKAKERLGGIRGAVLELISTEQK 53- 3 Query: 534 YQTALEVALGANSQHIIVTDEAAAKRAIAYLKKNRQGRATFLPLTTIKARSLSEHYHRQL 59- 3 Y+TA+E+ALGA++QH++ DE +A++AI YLK+N GRATFLPL+ I+ R L Sbjct: 534 YETAIEIALGASAQHVVTDDEQSARKAIQYLKQNSFGRATFLPLSVIRDRQLQSRDAETA 59- 3 Query: 594 ATCEGYLGTAESLIRYDDSLSAIIQNLLSSTAIFETIDQANIAARLLGYKVRIVTLDGTE 65- 3 A +LG A L+ +D + ++IQNLL + I E + AN A+LLG++ RIVTL+G Sbjct: 594 ARHSSFLGVASELVTFDPAYRSVIQNLLGTVLITEDLKGANELAKLLGHRYRIVTLEGDV 65- 3 Query: 654 LRPGGSFSGGANRQSNTTFI--KPELEQISEELTRLVEQLKITEKEVAALQSDLIAKKEE 71- 1 + PGGS +GGA ++ N + + ELE +++ L + E+ + E+EV L+ + +++ Sbjct: 654 VNPGGSMTGGAVKRKNNSLLGRSRELEDVTKRLAEMEEKTALLEQEVKTLKHSIQDMEKK 71- 3 Query: 712 LTQLKLAGDQARLAEQ--RAQMAYQQLQEKQEDSKALLAALDQSQTTHSDESLLAEQARI 76- 9 L L+ G+ RL +Q + Q+ Q+ EK ++ L ++S + SDE + ++ Sbjct: 714 LADLRETGEGLRLRQQDVKGQLYELQVAEKNINTHLELYDQEKSALSESDEERKVRKRKL 77- 3 Query: 770 EEALTAIAKKKNALTCDIDDIKENKDLIRQKTQNIHQALSQARLQERDLLNEKKFEQANQ 82- 9 EE L+A+++K L DID + + K +++ L++ ++ K E+ N Sbjct: 774 EEELSAVSEKMKQLEEDIDRLTKQKQTQSSTKESLSNELTELKIAAAKKEQACKGEEDNL 83- 3 Query: 830 SRLRTQLKQCQQNILKLESILNNNVSQDSIQRLPQWQKQLQDATEHKSGAQKRLVQLRFE 88- 9 +RL+ +L + + + + + L+ S+ S +++L++A +HK + + ++L Sbjct: 834 ARLKKELTETELALKEAKEDLSFLTSEMSSS--TSGEEKLEEAAKHKLNDKTKTIELIAL 89- 1 Query: 890 IEDYEARLEETAEKITKESEKNDTFIRRQTKL----ETHLEQVANRLRAYAKSLSEDFQM 94- 5 D +L+ + +E ++ +++T L E L ++ L + L E++ + Sbjct: 892 RRDQRIKLQHGLDTYERELKEMKRLYKQKTTLLKDEEVKLGRMEVELDNLLQYLREEYSL 95- 1 Query: 946 TLADAKEVTNSIDHLESAKEKLHHLQKTIRALGPINSDAINQYEEVHERLTFLTSQKTDL 10- 05 + AKE E A++++ ++ I LG +N +I+++E V+ER FL+ QK DL Sbjct: 952 SFEGAKEKYQLETDPEEARKRVKLIKLAIEELGTVNLGSIDEFERVNERYKFLSEQKEDL 10- 11 Query: 1006 TKAKNLLLETINSMDSEVKARFKVTFEAIQKSFKETFTQMFGGGSADLVLTE-TDLLSAG 1- 064 T+AKN L + I MD E+ RF TF I+ F + F +FGGG A+L LT+ DLL +G Sbjct: 1012 TEAKNTLFQVIEEMDEEMTKRFNDTFVQIRSHFDQVFRSLFGGGRAELRLTDPNDLLHSG 1- 071 Query: 1065 IEISVQPPGKKIQSLNLMSGGEKALSALALLFAIIRVKTIPFVILDEVEAALDEANVKRF 1- 124 +EI QPPGKK+Q+LNL+SGGE+AL+A+ALLF+I++V+ +PF +LDEVEAALDSANV RF Sbjct: 1072 VEIIAQPPGKKLQNLNLLSGGERALTAIALLFSILKVRPVPFCVLDEVEAALDEANVFRF 1- 131 Query: 1125 GDFLNRFDKDSQFIVVTHRKGTMAAADSIYGITMQESGVSKIVSVKLKEAQE 1176 +L ++ D+QFIV+THRKGTM AD +YG+TMQESGVSK++SVKL+E +E Sbjct: 1132 AQYLKKYSSDTQFIVITHRKGTMEEADVLYGVTMQESGVSKVISVKLEETKE 1183 An alignment of the GAS and GBS proteins is shown below:

TABLE-US-01149 Identities = 732/1179 (62%), Positives = 911/1179 (77%) Query: 1 MFLKEIEMQGFKSFADKTKVEFDQGVTAVVGPNGSGKSNITESLRWALGESSAKSLRGGK 60 MFLKEIE++GFKSFADKTK+EFD+GVTAVVGPNGSGKSNITESLRWALGESSAK+LRGGK Sbjct: 1 MFLKEIELEGFKSFADKTKIEFDKGVTAVVGPNGSGKSNITESLRWALGESSAKNLRGGK 60 Query: 61 MPDVIFAGTENRKPLNYAQVSVTLDNSDHFIENIADEVRVERRIFRNGDSEYLIDGRKVR 120- MPDVIFAGT+NR PLNYA+V+V LDNSDHFI+ E+RVER I+RNGDS+YLIDGRKVR Sbjct: 61 MPDVIFAGTQNRNPLNYAKVAVVLDNSDHFIKTAKKEIRVERHIYRNGDSDYLIDGRKVR 120- Query: 121 LRDIHDLFMDTGLGRDSFSIISQGRVEAIFNSKPEERRAIFEEAAGVLKYKTRKKETQSK 18- 0 LRDIHDLFMDTGLGRDSFSIISQGRVE IFNSKPEERRAIFEEAAGVLKYKTRKKETQ K Sbjct: 121 LRDIHDLFMDTGLGRDSFSIISQGRVEEIFNSKPEERRAIFEEAAGVLKYKTRKKETQIK 18- 0 Query: 181 LEQTQGNLDRLEDIIYELDMQVQPLEKQASIAKRFLVLDEERQGLHLSILIEDILQHQSD 24- 0 L QTQ NLDRLEDIIYELD Q+ PLEKQA +AK+FL LD R+ L L IL++DI Q Sbjct: 181 LNQTQDNLDRLEDIIYELDTQLAPLEKQAKVAKQFLELDANRKQLQLDILVKDIDIAQER 24- 0 Query: 241 LTTVEEKLLTVRKELATYYQQRQSLEDENQSLKQKRHHLSEEIEAKQLALLDVTKLKSDL 30- 0 T E L ++++LA+YY +RQS+E++ Q KQK+ LS+E + Q LL++TKL +DL Sbjct: 241 QTKDTEALAALQQDLASYYAKRQSMEEDYQKFKQKKQVLSQESDQTQTTLLELTKLIADL 30- 0 Query: 301 ERQIDLIRLESNQKAEKKEEAGQRLAELEIKAKDCSDQITQKNIELTTLSEKIAQIRSEI 36- 0 E+QI+L++LES Q+AEKK EA + L +L+ + + Q +L + +++ ++ ++ Sbjct: 301 EKQIELVKLESGQEAEKKAEAKKHLEQLQEQLDGFQAEEKQCTEQLLHIDQQLCDVKQQL 36- 0 Query: 361 VSTESSLERFSTNPDQIIEKLREDFVTLMQEEADTSNALTALLADIENQKQASQAKSQEI 42- 0 ++LERFS++PDQ++E LRE+FV LMQ+EA SN LTAL A ++ +KQA Q K+QE Sbjct: 361 NELSNALERFSSDPDQLMETLREEFVLLMQKEAALSNQLTALKAHLDKEKQARQHKAQEY 42- 0 Query: 421 QEVSKNLEVLKSNAKVALERFEAAKKNVRQLLSHYQDLGQTLQNLEGEYKNQQSILFDHL 48- 0 Q + L+ L ++ A ++A K+ V LL +YQ+ + +Q LE +Y+ Q LFD L Sbjct: 421 QLLVTKLDQLNDESQKAQAHYKAQKEQVEMLLQNYQEGDKRVQELERDYQLNQERLFDLL 48- 0 Query: 481 DEIKSKQARISSLESILKNHSNFYAGVKSVLQAKDQLGGIIGAVSEHLSFDKHYQTALEI 54- 0 D+ K K+AR +SLESI K+HS FYAGV++VLQ++ +LGGIIGAVSEHLSFD YQTALE+ Sbjct: 481 DQKKGKEARKASLESIQKSHSQFYAGVRAVLQSQKKLGGIIGAVSEHLSFDSDYQTALEV 54- 0 Query: 541 ALGGSSQHIIVEDESAAKRSIAFLKKNRQGRATFLPLTTIKPRELAQHYLSKLQSSQGFL 60- 0 ALG +SQHIIV DE+AAKR+IA+LKKNRQGRATFLPLTTIK R L++HY +L + +G+L Sbjct: 541 ALGANSQHIIVTDEAAAKRAIAYLKKNRQGRATFLPLTTIKARSLSEHYHRQLATCEGYL 60- 0 Query: 601 GIASELVTYDQRLSNIFKNNLGLTAIFDTVDNANVAARQLNYQVRLVTLDGTELRPGGSY 66- 0 G A L+ YD LS I +N L TAIF+T+D AN+AAR L Y+VR+VTLDGTELRPGGS+ Sbjct: 601 GTAESLIRYDDSLSAIIQNLLSSTAIFETIDQANIAARLLGYKVRIVTLDGTELRPGGSF 66- 0 Query: 661 SGGANRQNNTVFIKPELDNLKKELKQAQSKQLIQEKEVATLLEQLKEKQETLAQLKNDGE 72- 0 SGGANRQ+NT FIKPEL+ + +EL + + I EKEVA L L K+E L QLK G+ Sbjct: 661 SGGANRQSNTTFIKPELEQISEELTRLVEQLKITEKEVAALQSDLIAKKEELTQLKLAGD 72- 0 Query: 721 QARLEEQRADIEYQQLSEKLADLNKLYNGLQLSSGALEQTTSENEKNRLEKELEQFAIKK 78- 0 QARL EQRA + YQQL EK D L L S + E+ R+E+ L A KK Sbjct: 721 QARLAEQRAQMAYQQLQEKQEDSKALLAALDQSQTTHSDESLLAEQARIEEALTAIAKKK 78- 0 Query: 781 EELTTSIAQIKEDKDSIQEKVNNLTTLLSEAQLEERDLLNEQKFERANCTRLEITLSEIK 84- 0 LT I IKE+KD I++K N+ LS+A+L+ERDLLNE+KFE+AN +RL L + + Sbjct: 781 NALTCDIDDIKENKDLIRQKTQNIHQALSQARLQERDLLNEKKFEQANQSRLRTQLKQCQ 84- 0 Query: 841 RDISNLQTLLSHQDSQLDKEELPRIEKQLLQVNNRRENDEEKLVSLRFELEDCEAALDDL 90- 0 ++I L+++L++ SQ + LP+ +KQL + +++LV LRFE+ED EA L++ Sbjct: 841 QNILKLESILNNNVSQDSIQRLPQWQKQLQDATEHKSGAQKRLVQLRFEIEDYEARLEET 90- 0 Query: 901 AASLAKEGQKNESLIRQQAQLESQCEQLSQQLMIFSRQLSEDYQMTLDEAKVKANVLEDI 96- 0 A + KE +KN++ IR+Q +LE+ EQ++ +L +++ LSED+QMTL +AK N ++ + Sbjct: 901 AEKITKESEKNDTFIRRQTKLETHLEQVANRLRAYAKSLSEDFQMTLADAKEVTNSIDHL 96- 0 Query: 961 LMAREQLKSLQAKIKALGPVNIDAIAQFEEVHERLTFLNTQRDDLVHAKNLLLETITDMD 10- 20 A+E+L LQ I+ALGP+N DAI Q+EEVHERLTFL +Q+ DL AKNLLLETI MD Sbjct: 961 ESAKEKLHHLQKTIRALGPINSDAINQYEEVHERLTFLTSQKTDLTKAKNLLLETINSMD 10- 20 Query: 1021 DEVKTRFKSTFEAIRHSFKETFVQMFGGGSADLILTEGDLLSAGVDISVQPPGKKIQSLN 1- 080 EVK RFK TFEAI+ SFKETF QMFGGGSADL+LTE DLLSAG++ISVQPPGKKIQSLN Sbjct: 1021 SEVKARFKVTFEAIQKSFKETFTQMFGGGSADLVLTETDLLSAGIEISVQPPGKKIQSLN 1- 080 Query: 1081 LMSGGEKALSALALLFAIIRVKTIPFVILDEVEAALDEANVKRFGDYLNRFDKSSQFIVV 1- 140 LMSGGEKALSALALLFAIIRVKTIPFVILDEVEAALDEANVKRFGD+LNRFDK SQFIVV Sbjct: 1081 LMSGGEKALSALALLFAIIRVKTIPFVILDEVEAALDEANVKRFGDFLNRFDKDSQFIVV 1- 140 Query: 1141 THRKGTMSAADSIYGVTMQESGVSKIVSVKLKEAQEMTN 1179 THRKGTM+AADSIYG+TMQESGVSKIVSVKLKEAQEMTN Sbjct: 1141 THRKGTMAAADSIYGITMQESGVSKIVSVKLKEAQEMTN 1179 SEQ ID 1162 (GBS199) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 52 (lane 2; MW 75 kDa). GBS199-GST was purified as shown in FIG. 208, lane 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 359 A DNA sequence (GBSx0390) was identified in S. agalactiae <SEQ ID 1165> which encodes the amino acid sequence <SEQ ID 1166>. This protein is predicted to be ribonuclease III (rnc). Analysis of this protein sequence reveals the following: TABLE-US-01150 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3372(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9711> which encodes amino acid sequence <SEQ ID 9712> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01151 >GP: CAB13466 GB: Z99112 ribonuclease III [Bacillus subtilis] Identities = 115/230 (50%), Positives = 154/230 (66%), Gaps = 1/230 (0%) Query: 13 KKMKELRSKLEKDYGIVFANQELLDTAFTHTSYANEHRLLNISHNERLEFLGDAVLQLLI 72 - KK+++ + E+ + F N++LL AFTH+SY NEHR NERLEFLGDAVL+L I Sbjct: 15 KKVEQFKEFQER-ISVHFQNEKLLYQAFTHSSYVNEHRKKPYEDNERLEFLGDAVLELTI 73 Query: 73 SQYLFTKYPQKAEGDLSKLRSMIVREESLAGFSRLCGFDHYIKLGKGEEKSGGRNRDTIL 132- S++LF KYP +EGDL+KLR+ IV E SL + F + LGKGEE +GGR R +L Sbjct: 74 SRFLFAKYPAMSEGDLTKLRAAIVCEPSLVSLAHELSFGDLVLLGKGEEMTGGRKRPALL 133- Query: 133 GDLFEAFLGALLLDKGVEVVHAFVNKVMIPHVEKGTYERVKDYKTSLQELLQSHGDVKID 19- 2 D+FEAF+GAL LD+G+E V +F+ + P + G + V D+K+ LQE +Q G ++ Sbjct: 134 ADVFEAFIGALYLDQGLEPVESFLKVYVFPKINDGAFSHVMDFKSQLQEYVQRDGKGSLE 19- 3 Query: 193 YQVTNESGPAHAKEFEVTVSVNQENLSQGIGRSKKAAEQDAAKNALATLQ 242 Y+++NE GPAH +EFE VS+ E L G GRSKK AEQ AA+ ALA LQ Sbjct: 194 YKISNEKGPAHNREFEAIVSLKGEPLGVGNGRSKKEAEQHAAQEALAKLQ 243 A related DNA sequence was identified in S. pyogenes <SEQ ID 1167> which encodes the amino acid sequence <SEQ ID 1168>. Analysis of this protein sequence reveals the following: TABLE-US-01152 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1414(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01153 Identities = 170/227 (74%), Positives = 192/227 (83%) Query: 15 MKELRSKLEKDYGIVFANQELLDTAFTHTSYANEHRLLNISHNERLEFLGDAVLQLLISQ 74 - MK+L L + I F + LL+TAFTHTSYANEHRLLN+SHNERLEFLGDAVLQL+IS+ Sbjct: 1 MKQLEELLSTSFDIQFNDLTLLETAFTHTSYANEHRLLNVSHNERLEFLGDAVLQLIISE 60 Query: 75 YLFTKYPQKAEGDLSKLRSMIVREESLAGFSRLCGFDHYIKLGKGEEKSGGRNRDTILGD 134- YLF KYP+K EGD+SKLRSMIVREESLAGFSR C FD YIKLGKGEEKSGGR RDTILGD Sbjct: 61 YLFAKYPKKTEGDMSKLRSMIVREESLAGFSRFCSFDAYIKLGKGEEKSGGRRRDTILGD 120- Query: 135 LFEAFLGALLLDKGVEVVHAFVNKVMIPHVEKGTYERVKDYKTSLQELLQSHGDVKIDYQ 19- 4 LFEAFLGALLLDKG++ V F+ +VMIP VEKG +ERVKDYKT LQE LQ+ GDV IDYQ Sbjct: 121 LFEAFLGALLLDKGIDAVRRFLKQVMIPQVEKGNFERVKDYKTCLQEFLQTKGDVAIDYQ 18- 0 Query: 195 VTNESGPAHAKEFEVTVSVNQENLSQGIGRSKKAAEQDAAKNALATL 241 V +E GPAHAK+FEV++ VN LS+G+G+SKK AEQDAAKNALA L Sbjct: 181 VISEKGPAHAKQFEVSIVVNGAVLSKGLGKSKKLAEQDAAKNALAQL 227 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 360 A DNA sequence (GBSx0391) was identified in S. agalactiae <SEQ ID 1169> which encodes the amino acid sequence <SEQ ID 1170>. Analysis of this protein sequence reveals the following: TABLE-US-01154 Possible site: 43 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.19 Transmembrane 100-116 (99-117) INTEGRAL Likelihood = -2.44 Transmembrane 81-97 (81-97) ----- Final Results ----- bacterial membrane --- Certainty = 0.2678(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01155 >GP: CAC12789 GB: AJ279090 hypothetical protein [Staphylococcus carnosus] Identities = 50/114 (43%), Positives = 72/114 (62%) Query: 3 KIFYISLGFISLGIGIAGIVLPVVPTTPLVLLSAFCFSRSSEKFDIWLRQTKVYKYYAAD 62 K ++LG I GIG GIV+P++PTTP +LL+A CFSRSS+KF+ WL TK++ Y Sbjct: 2 KYVLMTLGLIFAGIGFVGIVVPLLPTTPFLLLAAICFSRSSKKFNRWLVNTKIHDEYVES 61 Query: 63 FVESRSIAPARKKSMIWQIYILMGISIYFAPLMWLKLGLLIGTIVGTYVLFYVV 116 F + +K ++ +YILMGISI+ +++++ LLI V T VLF V Sbjct: 62 FKRDKGFTLKKKFKLLTSLYILMGISIFIIDNLYIRITLLIMLFVQTVVLFTFV 115 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 361 A DNA sequence (GBSx0392) was identified in S. agalactiae <SEQ ID 1171> which encodes the amino acid sequence <SEQ ID 1172>. Analysis of this protein sequence reveals the following: TABLE-US-01156 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1908(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 1173> which encodes the amino acid sequence <SEQ ID 1174>. Analysis of this protein sequence reveals the following: TABLE-US-01157 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1610(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01158 Identities = 225/269 (83%), Positives = 248/269 (91%) Query: 1 MSEIGFKYSILASGSTGNCFYIETPQKRLLIDAGLTGKKVTSLLAEINRKPEDLDAILVT 60 M+E GFKYSILASGSTGNCFY+ETP+KRLLIDAGLTGKK+TSLLAEI+RKPEDLDAIL+T Sbjct: 1 MNESGFKYSILASGSTGNCFYLETPKKRLLIDAGLTGKKITSLLAEIDRKPEDLDAILIT 60 Query: 61 HEHSDHIKGVGVLARKYHLDIYANEQTWKVMDERNMLGKVDVSQKHVFGRGKTLTFGDLD 120- HEHSDHIKGVGV+ARKYHLDIYANE+TW++MDE NMLGK+D SQKH+F R K LTFGD+D Sbjct: 61 HEHSDHIKGVGVMARKYHLDIYANEKTWQLMDECNMLGKLDASQKHIFQRDKVLTFGDVD 120- Query: 121 IESFGVSHDAVDPQFYRMMKDDKSFVMLTDTGYVSDRMAGLIENADGYLIESNHDIEILR 18- 0 IESFGVSHDA+DPQFYR+MKD+KSFVMLTDTGYVSDRM G+IENADGYLIESNHDIEILR Sbjct: 121 IESFGVSHDAIDPQFYRIMKDNKSFVMLTDTGYVSDRMTGIIENADGYLIESNHDIEILR 18- 0 Query: 181 SGSYPWTLKQRILSDKGHLSNEDGSETMIRTIGNRTKHIYLGHLSKENNIKELAHMTMEN 24- 0 SGSYPW+LKQRILSD GHLSNEDG+ MIR++G TK IYLGHLSKENNIKELAHMTM N Sbjct: 181 SGSYPWSLKQRILSDLGHLSNEDGAGAMIRSLGYNTKKIYLGHLSKENNIKELAHMTMVN 24- 0 Query: 241 NLMRADFGVGTDFSVHDTSPDSATPLTRI 269 L AD VGTDF+VHDTSPD+A PLT I Sbjct: 241 QLAMADLAVGTDFTVHDTSPDTACPLTDI 269 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 362 A DNA sequence (GBSx0393) was identified in S. agalactiae <SEQ ID 1175> which encodes the amino acid sequence <SEQ ID 1176>. Analysis of this protein sequence reveals the following: TABLE-US-01159 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.94 Transmembrane 15-31 (5-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.5776(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 1177> which encodes the amino acid sequence <SEQ ID 1178>. Analysis of this protein sequence reveals the following: TABLE-US-01160 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01161 Identities = 335/443 (75%), Positives = 392/443 (87%) Query: 7 NIRSFELALLFLLVFVAVYFVYLAVRDFKMSKNIRLLNWKVRDLIAGNYSDSILIQGDAD 66 N+ +FELA+L LLVFVA YF++LAVRD++ ++ IR+++ K+RDLI G Y+D I + D + Sbjct: 8 NLSTFELAILILLVFVAFYFIHLAVRDYRNARIIRMMSHKIRDLINGRYTDIIDEKADIE 67 Query: 67 LVELGESLNDLSDVFRMAHDNLEQEKNRLASILTYMTDGVLATDRSGKIVMINETAQQQF 126- L+EL + LNDLSDVFR+ H+NL QEKNRLASIL YM+DGVLATDRSGKI+MINETA++Q Sbjct: 68 LMELSDQLNDLSDVFRLTHENLAQEKNRLASILAYMSDGVLATDRSGKIIMINETARKQL 127- Query: 127 NLAYDEALSMNIVDMLGSGSPYSFQDLVSKTPEVVLNRRDENGEFVTLRIRFALNRRESG 18- 6 NL+ +EAL NI D+L + Y+++DLVSKTP V +N R++ GEFV+LR+RFALNRRESG Sbjct: 128 NLSKEEALKKNITDLLEGDTSYTYRDLVSKTPVVTVNSRNDMGEFVSLRLRFALNRRESG 18- 7 Query: 187 FISGLVAVSHDATEQEKEERERRLFVSNVSHELRTPLTSVKSYLEALDEGALNEEVAPSF 24- 6 FISGLV V HD TEQEKEERERRLFVSNVSHELRTPLTSVKSYLEALDEGAL E++APSF Sbjct: 188 FISGLVVVLHDTTEQEKEERERRLFVSNVSHELRTPLTSVKSYLEALDEGALKEDIAPSF 24- 7 Query: 247 IKVSLDETNRMMRMISDLLSLSRIDNEVTHLDVEMTNFTAFMTSILNRFDQIRNQKTVTG 30- 6 IKVSLDETNRMMRMISDLL+LSRIDN+VT L VEMTNFTAF+TSILNRFD ++NQ T TG Sbjct: 248 IKVSLDETNRMMRMISDLLNLSRIDNQVTQLAVEMTNFTAFITSILNRFDLVKNQHTGTG 30- 7 Query: 307 KVYEIVRDYPLKSIWVEIDTDKMTQVIDNILNNAVKYSPDGGKITVNLRTTKTQMILSIS 36- 6 KVYEIVRDYP+ S+W+EID DKMTQVI+NILNNA+KYSPDGGKITV ++TT TQ+I+SIS Sbjct: 308 KVYEIVRDYPITSVWIEIDNDKMTQVIENILNNAIKYSPDGGKITVRMKTTDTQLIISIS 36- 7 Query: 367 DQGLGIPKKDLPLIFDRFYRVDKARSRKQGGTGLGLSIAKEIVKQHKGFIWAKSEYGKGS 42- 6 DQGLGIPK DLPLIFDRFYRVDKARSR QGGTGLGL+IAKEI+KQH GFIWAKS+YGKGS Sbjct: 368 DQGLGIPKTDLPLIFDRFYRVDKARSRAQGGTGLGLAIAKEIIKQHHGFIWAKSDYGKGS 42- 7 Query: 427 TFTIVLPYDKDAVTYEEWEDVED 449 TFTIVLPY+KDA YEEWE+ D Sbjct: 428 TFTIVLPYEKDAAIYEEWEEDVD 450 A related GBS gene <SEQ ID 8561> and protein <SEQ ID 8562> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01162 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 8.59 GvH: Signal Score (-7.5): -3.38 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -11.94 threshold: 0.0 INTEGRAL Likelihood = -11.94 Transmembrane 15-31 (5-34) PERIPHERAL Likelihood = 8.27 178 modified ALOM score: 2.89 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5776(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00030## SEQ ID 1176 (GBS41) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 4 (lane 7; MW 50 kDa), in FIG. 168 (lane 24; MW 65 kDa--thioredoxin fusion) and in FIG. 238 (lane 4; MW 65 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 13 (lane 7; MW 75 kDa). Purified Thio-GBS41-His is shown in FIG. 244, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 363 A DNA sequence (GBSx0394) was identified in S. agalactiae <SEQ ID 1179> which encodes the amino acid sequence <SEQ ID 1180>. This protein is predicted to be VicR protein (regX3). Analysis of this protein sequence reveals the following:

TABLE-US-01163 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2754(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 1181> which encodes the amino acid sequence <SEQ ID 1182>. Analysis of this protein sequence reveals the following: TABLE-US-01164 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2754(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01165 Identities = 205/236 (86%), Positives = 221/236 (92%) Query: 1 MKKILIVDDEKPISDIIKFNLTKEGYETATAFDGREALVQYAEFQPDLIILDLMLPELDG 60 MKKILIVDDEKPISDIIKFNLTKEGY+ TAFDGREA+ + E +PDLIILDLMLPELDG Sbjct: 1 MKKILIVDDEKPISDIIKFNLTKEGYDIVTAFDGREAVTIFEEEKPDLIILDLMLPELDG 60 Query: 61 LEVAKEVRKTSHIPIIMLSAKDSEFDKVIGLEIGADDYVTKPFSNRELLARVKAHLRRTE 120- LEVAKE+RKTSH+PIIMLSAKDSEFDKVIGLEIGADDYVTKPFSNRELLARVKAHLRRTE Sbjct: 61 LEVAKEIRKTSHVPIIMLSAKDSEFDKVIGLEIGADDYVTKPWSNRELLARVKAHLRRTE 120- Query: 121 NIETAVAEESAQNASSDITIGELQILPDAFIAKKRGEEIELTHREFELLHHLATHIGQVM 18- 0 IETAVAEE+A + + ++TIG LQILPDAF+AKK G+E+ELTHREFELLHHLA H+GQVM Sbjct: 121 TIETAVAEENASSGTQELTIGNLQILPDAFVAKKHGQEVELTHREFELLHHLANHMGQVM 18- 0 Query: 181 TREHLLETVWGYDYFGDVRTVDVTVRRLREKIEDTPGRPEYILTRRGVGYYMKSYE 236 TREHLLE VWGYDYFGDVRTVDVTVRRLREKIEDTP RPEYILTRRGVGYYMKSY+ Sbjct: 181 TREHLLEIVWGYDYFGDVRTVDVTVRRLREKIEDTPSRFEYILTRRGVGYYMKSYD 236 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 364 A DNA sequence (GBSx0395) was identified in S. agalactiae <SEQ ID 1183> which encodes the amino acid sequence <SEQ ID 1184>. This protein is predicted to be amino acid ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-01166 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3791(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01167 >GP: CAB14701 GB: Z99118 glutamine ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 149/244 (61%), Positives = 200/244 (81%), Gaps = 2/244 (0%) Query: 3 LISYKNVNKYYGDYHALRQINLEIEPGQVVVLLGPSGSGKSTLIRTMNALESIDDGSLVV 62 +I+++NVNK+YGD+H L+QINL+IE G+VVV++GPSGSGKSTL+R +N LESI++G L V Sbjct: 1 MITFQNVNKHYGDFHVLRQINLQIEKGEVVVIIGPSGSGKSTLLRCINRLESINEGVLTV 60 Query: 63 NGHELANISSKELVNLRKEVGMVFQHFNLYPHKTVLENITLAPIKVLKQSKKEAMEIASK 122- NG + N ++ +R+ +GMVFQHF+LYPHKTVL+NI LAP+KVL+QS ++A E A Sbjct: 61 NGTAI-NDRKTDINQVRQNIGMVFQHFHLYPHKTVLQNIMLAPVKVLRQSPEQAKETARY 119- Query: 123 YLKFVNMWERKDSYPSMLSGGQKQRIAIARGLAMHPKLLLFDEPTSALDPETIGDVLSVM 18- 2 YL+ V + ++ D+YPS LSGGQ+QR+AIARGLAM P+++LFDEPTSALDPE IG+VL VM Sbjct: 120 YLEKVGIPDKADAYPSQLSGGQQQRVAIARGLAMKPEVMLFDEPTSALDPEMIGEVLDVM 17- 9 Query: 183 QKLANDGMNMVVVTHEMGFAREVADRIIFMADGEILVDTTDVQDFFDNPREPRAKQFLSN 24- 2 + LA +GM MVVVTHEMGFA+EVADRI+F+ +G+IL + +F+ NP+E RA+ FLS Sbjct: 180 KTLAKEGMTMVVVTHEMGFAKEVADRIVFIDEGKILEEAVPA-EFYANPKEERARLFLSR 23- 8 Query: 243 IINH 246 I+NH Sbjct: 239 ILNH 242 A related DNA sequence was identified in S. pyogenes <SEQ ID 1185> which encodes the amino acid sequence <SEQ ID 1186>. Analysis of this protein sequence reveals the following: TABLE-US-01168 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3763(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01169 Identities = 131/243 (53%), Positives = 179/243 (72%), Gaps = 2/243 (0%) Query: 2 SLISYKNVNKYYGDYHALRQINLEIEPGQVVVLLGPSGSGKSTLIRTMNALESIDDGSLV 61 ++IS K+++KYYG L+ I+L+I PG+VVV++GPSGSGKSTL+RTMN LE G + Sbjct: 5 AIISIKDLHKYYGHNEVLKGIDLDIMPGEVVVIIGPSGSGKSTLLRTMNLLEVPTKGQIR 64 Query: 62 VNGHELANISSKELVNLRKEVGMVFQHFNLYPHKTVLENITLAPIKVLKQSKKEAMEIAE 121- G ++ + ++ ++R+++GMVFQ FNL+P+ T+LENITL+PIK +K EA + A Sbjct: 65 FEGIDITD-KKNDIFSMREKMGMVFQQFNLFPNMTILENITLSPIKTKGMAKAEADKTAL 123- Query: 122 KYLKFVNMWERKDSYPSMLSGGQKQRIAIARGLAMHPKLLLFDEPTSALDPETIGDVLSV 18- 1 L V + E+ +YP+ LSGGQ+QRIAIARGLAM P +LLFDEPTSALDPE +G+VL+V Sbjct: 124 SLLDKVGLSEKAKAYPASLSGGQQQRIAIARGLAMDPDVLLFDEPTSALDPEMVGEVLAV 18- 3 Query: 182 MQKLANDGMNMVVVTHEMGFAREVADRIIFMADGEILVDTTDVQDFFDNPREPRAKQFLS 24- 1 MQ LA GM MV+VTHEMGFA+EVADR++FM DG ++V+ FD +E R K FLS Sbjct: 184 MQDLAKSGMTMVIVTHEMGFAKEVADRVMFM-DGGVIVEEGSPNQLFDLTKEERTKDFLS 24- 2 Query: 242 NII 244 ++ Sbjct: 243 RVL 245 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 365 A DNA sequence (GBSx0396) was identified in S. agalactiae <SEQ ID 1187> which encodes the amino acid sequence <SEQ ID 1188>. This protein is predicted to be glutamine-binding. Analysis of this protein sequence reveals the following: TABLE-US-01170 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01171 >GP: CAB73178 GB: AL139076 probable ABC-type aminoacid transporter periplasmic solute-binding protein [Campylobacter jejuni] Identities = 99/240 (41%), Positives = 141/240 (58%), Gaps = 3/240 (1%) Query: 1 MLRRKRLTFYLLSCIFIFLLFYPNSTSANQLSEIKKSGVLKVGVKQDVPNFGYYNAETNQ 60 M+ RK L + + + F + + +L IK G L VGVK DVP++ + T + Sbjct: 1 MVFRKSLLKLAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGE 60 Query: 61 YEGMEIDIAKKIAKSL---GVKPVFVPTTAQTREPLMDNGQIDILIATYTITPERKANYN 117- +G E+D+AK +AKS+ K V A+TR PL+DNG +D +IAT+TITPERK YN Sbjct: 61 IKGFEVDVAKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRIYN 120- Query: 118 ISKAYYHDEIGFLVRKNSHIKTIKELDGKHIGVAQGATTKVNLEKYAKEHKLKFSYAQLG 17- 7 S+ YY D IG LV K K++ ++ G +IGVAQ ATTK + + AK+ + +++ Sbjct: 121 FSEPYYQDAIGLLVLKEKKYKSLADMKGANIGVAQAATTKKAIGEAAKKIGIDVKFSEFP 18- 0 Query: 178 SFPELAISLYANRIDAFSVDKSILSGYLSPHTTILKEGFNTQEYGIATSKQDKVLIPYVN 23- 7 +P + +L A R+DAFSVDKSIL GY+ + IL + F Q YGI T K D YV+ Sbjct: 181 DYPSIKAALDAKRVDAFSVDKSILLGYVDDKSEILPDSFEPQSYGIVTKKDDPAFAKYVD 24- 0 A related DNA sequence was identified in S. pyogenes <SEQ ID 1189> which encodes the amino acid sequence <SEQ ID 1190>. Analysis of this protein sequence reveals the following: TABLE-US-01172 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = 6.16 Transmembrane 17-33 (15-35) ----- Final Results ----- bacterial membrane --- Certainty = 0.3463(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9097> which encodes the amino acid sequence <SEQ ID 9098>. Analysis of this protein sequence reveals the following: TABLE-US-01173 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01174 Identities = 66/251 (26%), Positives = 111/251 (43%), Gaps = 27/251 (10%) Query: 23 PNSTSANQLSEIKKSGVLKVGVKQDVPNFGYYNAETNQYEGMEIDIAKKIAKSLGVKPVF 82 - P+ + + IK+ GVLKV +YN + N+ G E+D+ K+I K L +K F Sbjct: 34 PHQSQKSSWDTIKEKGVLKVATPGTYQPTSFYN-DNNELVGYEVDMVKEIGKRLNIKVKF 92 Query: 83 VPTTAQTREPLMDNGQIDILIATYTITPERKANYNISKAYYHDEIGFLVR----KNSHIK 138- V T +D+G++DI + + ITP+R+ YNIS Y + G +VR N K Sbjct: 93 VETGFDQAFTSVDSGRVDISLNNFDITPKRQKKYNISTPYKYGVGGMIVRADGSSNIAKK 152- Query: 139 TIKELDGKHIGVAQGATTKVNLEKYAKEHKLKFSYAQLGSFPELAISLYANRI------- 19- 1 + + GK A G +K A+L ++ + +Y N + Sbjct: 153 DLSDWKGKKAAGASGTEYMKVAQKQG---------AELVTYDNVTGDVYLNDVANGRTDF 20- 3 Query: 192 --DAFSVDKSILSGYLSPHTTILKE----GFNTQEYGIATSKQDKVLIPYVNKLLVSWEK 24- 5 + + K + LS + + + +N E GI +K+D L ++ ++ K Sbjct: 204 IPNDYPAQKLFVDYMLSQNPNLNVKMSDVQYNPTEQGIVMNKKDDSLKKKIDAVIKDMIK 26- 3 Query: 246 DGSLKHIYQKF 256 DGSLK I + + Sbjct: 264 DGSLKKISETY 274 SEQ ID 1188 (GBS136) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 29 (lane 5; MW 29.9 kDa). The GBS136-His fusion product was purified (FIG. 200, lane 6) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 284), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 366 A DNA sequence (GBSx0397) was identified in S. agalactiae <SEQ ID 1191> which encodes the amino acid sequence <SEQ ID 1192>. This protein is predicted to be integral membrane. Analysis of this protein sequence reveals the following: TABLE-US-01175 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.34 Transmembrane 32-48 (27-55) INTEGRAL Likelihood = -5.04 Transmembrane 200-216 (196-219) INTEGRAL Likelihood = -3.13 Transmembrane 93-109 (93-113) INTEGRAL Likelihood = -2.02 Transmembrane 74-90 (74-92) ----- Final Results ----- bacterial membrane --- Certainty = 0.4736(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01176 >GP: CAB73177 GB: AL139076 putative ABC-type amino-acid transporter permease protein [Campylobacter jejuni] Identities = 112/226 (49%), Positives = 160/226 (70%), Gaps = 3/226 (1%) Query: 5 NISPFAISRWGAFFNHFDLFFKGFLYTLGISFGALLLALILGILSGGLSTSKSKVGKLIS 64 +ISPFA+ ++ ++ D F GF+YTL +S ALL+A I G + G ++TS+ K+ + + Sbjct: 25 SISPFAVWKFLDALDNKDAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYT 84 Query: 65 RIYVEVFQNTPLLVQMVFVYYGLAIISNGHVMISAFFTAVLCVGLYHGAYISEVIRSGIE 124- RIYVE+FQN PL++Q+ F++Y L ++ + + F VL VG YHGAY+SEV+RSGI Sbjct: 85 RIYVELFQNVPLVIQIFFLFYALPVLG---IRLDIFTIGVLGVGAYHGAYVSEVVRSGIL 141- Query: 125 AVPKGQTEAALAQGFTANQTMQLIILPQAVRTILPPMTNQVVNLIKNTSTVAIISGADIM 18- 4 AVP+GQ EA+ +QGFT Q M+ II+PQ +R ILPPMTNQ+VNLIKNTS + I+ GA++M Sbjct: 142 AVPRGQFEASASQGFTYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELM 20- 1 Query: 185 FVAKAWAYDTTNYIPAFAGAAIFYFVICFPLASWARKQEELNKKTY 230 A ++A D NY PA+ AA+ YF+IC+PLA +A+ E KK + Sbjct: 202 HSADSYAADYGNYAPAYIFAAVLYFIICYPLAYFAKAYENKLKKAH 247 A related DNA sequence was identified in S. pyogenes <SEQ ID 1193> which encodes the amino acid sequence <SEQ ID 1194>. Analysis of this protein sequence reveals the following: TABLE-US-01177 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.26 Transmembrane 307-323 ( 303-327) INTEGRAL Likelihood = -5.89 Transmembrane 485-501 ( 479-502) INTEGRAL Likelihood = -1.12 Transmembrane 375-391 ( 375-391) ----- Final Results ----- bacterial membrane --- Certainty = 0.3506(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01178 >GP:BAA17584 GB:D90907 glutamine binding periplasmic protein [Synechocystis sp.] Identities = 146/532 (27%), Positives = 244/532 (45%), Gaps = 59/532 (11%) Query: 6 YMKKLILSCLVALALLFGGMSRAQANQYLRVGMEAAYAPFNWTQDDASNGAVPIEGTSQY 65 Y L L L+A+A+ + Q + V E + PF T E T Q Sbjct: 16 YYLLLALGVLLAIAIPLLPAFSQVSRQTIIVATEPTFPPFEMTD----------EATGQL 65 Query: 66 ANGYDVQVAKKVAKAMNKELLVVKTSWTGLIPALTSGKIDMIAAGMSPTKERRNEISFSN 125- G+DV + + + +A + + + G+IPAL S + + ++ T ER +SFS+ Sbjct: 66 T-GFDVDLIQAIGEAAQVTVDIQGYPFDGIIPALQSNTVGAAISAITITPERAQSVSFSS 124- Query: 126 SSYTSQPVLVVTANGRYADATSLKDFSGAKVTAQQGVWHVNLLTQLKGAKLQTPMGDFSQ 18- 5 + S VL + +LKD G ++ G + T + GAK+ T + Sbjct: 125 PYFKS--VLAIAVQDGNDTIKNLKDLEGKRLAVAIGTTGAMVATNVPGAKV-TNFDSITS 18- 1 Query: 186 MRQALTSGVIDAYISERPEAMTAEAADSRLKMITLKKGFAVAESDAAIAVGMKKNDDRMA 24- 5 Q L +G DA I++RP + A D+L+ + + +E IA+ + + Sbjct: 182 ALQELVNGNADAVINDRPVLLYA-IKDAGLRNVKISADVG-SEDYYGIAMPLAPPGE--- 23- 6 Query: 246 TVNQVLEGFSQTDRMALMDDMVTKQPVEKKAEDAKASFLGQMWAIFKGN----------- 29- 4 +NQ E +Q ++++ EK + FL + G Sbjct: 237 -INQTREVLNQ-GLFQIIENGTYNAIYEKWFGEKNPPFLPLVAPSLVGKVGTAQSLTERS 29- 4 Query: 295 ------------WKQFLRGTGMTLLISMVGTITGLFIGLLIGIFRTAPKAKHKVAALGQK 34- 2 ++ +G+ +T+L++ GL G + I + K Sbjct: 295 QANPNDNFLITLFRNLFKGSILTVLLTAFSVFFGLIGGTGVAIALISDI-----------K 3- 44 Query: 343 LFGWLLTIYIEIFRGTPMIVQSMVIYYGTAQAF-----GISIDRTLAAIFIVSINTGAYM 39- 7 + IY+E FRGTPM+VQ +IY+G F GI+IDR AAI +S+N AY+ Sbjct: 345 PLQLIFRIYVEFFRGTPMLVQLFIIYFGLPALFKEIGLGITIDRFPAAIIALSLNVAAYL 40- 4 Query: 398 SEIVRGGIFAVDKGQFKAATALGFTHGQTMRKIVLPQVVRNILPATGNEFVINIKDTSVL 45- 7 +EI+RGGI ++D+GQ++A +LG + QTM++++ PQ R ILP GNEF+ IKDTS+ Sbjct: 405 AEIIRGGIQSIDQGQWEACESLGMSPWQTMKEVIFPQAFRRILPPLGNEFITLIKDTSLT 46- 4 Query: 458 NVISVVELYFSGNTVATQTYQYFQTFTIIAIIYFVLTFTVTRILRYIERRFD 509 VI EL+ G + TY+ F+ + +A++Y +LT + + +++E D Sbjct: 465 AVIGFQELFREGQLIVATTYRAFEVYIAVALVYLLLTTISSFVFKWLENYMD 516 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01179 Identities = 82/210 (39%), Positives = 113/210 (53%), Gaps = 12/210 (5%) Query: 14 WGAFFNHFDLFFKGFLYTLGISFGALLLALILGILSGGLSTS---KSKVGKL-------I 63 - W F ++ F +G TL IS + L +G+L G T+ K KV L + Sbjct: 288 WAIFKGNWKQFLRGTGMTLLISMVGTITGLFIGLLIGIFRTAPKAKHKVAALGQKLFGWL 34- 7 Query: 64 SRIYVEVFQNTPLLVQMVFVYYGLAIISNGHVMISAFFTAVLCVGLYHGAYISEVIRSGI 123- IY+E+F+ TP++VQ + +YYG A + I A+ V + GAY+SE++R GI Sbjct: 348 LTIYIEIFRGTPMIVQSMVIYYGTAQAFG--ISIDRTLAAIFIVSINTGAYMSEIVRGGI 40- 5 Query: 124 EAVPKGQTEAALAQGFTANQTMQLIILPQAVRTILPPMTNQVVNLIKNTSTVAIISGADI 18- 3 AV KGQ +AA A GFT QTM+ I+LPQ VR ILP N+ V IK+TS + +IS ++ Sbjct: 406 FAVDKGQFKAATALGFTHGQTMRKIVLPQVVRNILPATGNEFVINIKDTSVLNVISVVEL 46- 5 Query: 184 MFVAKAWAYDTTNYIPAFAGAAIFYFVICF 213 F A T Y F AI YFV+ F Sbjct: 466 YFSGNTVATQTYQYFQTFTIIAIIYFVLTF 495 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 367 A DNA sequence (GBSx0398) was identified in S. agalactiae <SEQ ID 1195> which encodes the amino acid sequence <SEQ ID 1196>. This protein is predicted to be amino acid ABC transporter, permease protein. Analysis of this protein sequence reveals the following: TABLE-US-01180 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.95 Transmembrane 25-41 ( 16-42) INTEGRAL Likelihood = -3.61 Transmembrane 66-82 ( 65-86) INTEGRAL Likelihood = -2.44 Transmembrane 184-200 ( 182-201) INTEGRAL Likelihood = -0.59 Transmembrane 119-135 ( 119-135) ----- Final Results ----- bacterial membrane --- Certainty = 0.3781(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01181 >GP: CAB14704 GB: Z99118 glutamine ABC transporter (integral membrane protein) [Bacillus subtilis] Identities = 84/206 (40%), Positives = 129/206 (61%), Gaps = 6/206 (2%) Query: 10 ILFLLQGFGLTLYISFISILLSMFFGTLLAIMRNSKNPIWKLIASIYIEFVRNVPNLLWI 69 - + FL GF +TLY++FISI+LS FFG + +R +K P+ + ++ +E +RN+P LL I Sbjct: 12 LAFLWDGFLVTLYVAFISIILSFFFGLIAGTLRYAKVPVLSQLIAVLVETIRNLPLLLII 71 Query: 70 FIIFLVF-----QMKSVSAGITSFTIFTSAALAEIIRGGLNGVDKGQTEAGLSQGFTYLQ 124- F F +++ +A IT+ TIF SA L+EIIR GL +DKGQ EA S G +Y Q Sbjct: 72 FFTFFALPEIGIKLEITAAAITALTIFESAMLSEIIRSGLKSIDKGQIEAARSSGLSYTQ 131- Query: 125 VFIIIIFPQAFRKMLPAIISQFVTVIKDTSLLYSVIAIQEIFGKSQILMGRYFEAGQVFT 18- 4 I+ PQA R+M+P I+SQF++++KDTSL VIA+ E+ +QI+ G+ + F Sbjct: 132 TLFFIVMPQALRRMVPPIVSQFISLLKDTSLAV-VIALPELIHNAQIINGQSADGSYFFP 19- 0 Query: 185 LYAIITAVYFITNFIISSFSRKLSKR 210 ++ + +YF N+ +S +R+L R Sbjct: 191 IFLLAALMYFAVNYSLSLAARRLEVR 216 A related DNA sequence was identified in S. pyogenes <SEQ ID 1197> which encodes the amino acid sequence <SEQ ID 1198>. Analysis of this protein sequence reveals the following:

TABLE-US-01182 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.51 Transmembrane 529-545 (517-551) INTEGRAL Likelihood = -10.30 Transmembrane 697-713 (693-719) INTEGRAL Likelihood = -4.41 Transmembrane 560-576 (555-585) INTEGRAL Likelihood = -0.32 Transmembrane 662-678 (662-678) ----- Final Results ----- bacterial membrane --- Certainty = 0.5203(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01183 >GP: BAA17584 GB: D90907 glutamine binding periplasmic protein [Synechocystis sp.] Identities = 153/475 (32%), Positives = 251/475 (52%), Gaps = 27/475 (5%) Query: 273 IVSDSSFAPFEFQN-GKGKYVGIDIELIKAIAKQQGFKIEIANPGFDAALNAVQSSQADG 33- 1 + ++ +F PFE + G+ G D++LI+AI + ++I FD + A+QS+ Sbjct: 46 VATEPTFPPFEMTDEATGQLTGFDVDLIQAIGEAAQVTVDIQGYPFDGIIPALQSNTVGA 105- Query: 332 VIAGATITDARKAIFDFSDPYYTSNIILAVKAGKN-IKNYEDLDRKTVGAKNGTSSYSWL 39- 0 I+ TIT R FS PY+ S + +AV+ G + IKN +DL+ K + GT+ + + Sbjct: 106 AISAITITPERAQSVSFSSPYFKSVLAIAVQDGNDTIKNLKDLEGKRLAVAIGTTG-AMV 16- 4 Query: 391 KENAPKYGYNVKAFDDGSSMYDSLNSGSVDAIMDDEAVLKYAISQG--RRFETPLEGIST 44- 8 N P G V FD +S L +G+ DA+++D VL YAI R + + S Sbjct: 165 ATNVP--GAKVTNFDSITSALQELVNGNADAVINDRPVLLYAIKDAGLRNVKISADVGSE 22- 2 Query: 449 GEVGFAVKKGTNPELI---EMFNNGLAALKKSGQYDDIIDKYLDSKKA-----ATPSEKG 50- 0 G A+ E+ E+ N GL + ++G Y+ I +K+ K PS G Sbjct: 223 DYYGIAMPLAPPGEINQTREVLNQGLFQIIENGTYNAIYEKWFGEKNPPFLPLVAPSLVG 28- 2 Query: 501 -----------ADESTISGLLSNNYKQLLAGLGTTLSLTLISFAIAIIIGIIFGMMAVSP 54- 9 + + L ++ L G T+ LT S +I G + +S Sbjct: 283 KVGTAQSLTERSQANPNDNFLITLFRNLFKGSILTVLLTAFSVFFGLIGGTGVAIALISD 34- 2 Query: 550 TKSLRLISTVFVDVVRGIPLMIVAAFIFWGVPNLIESMTGHQSPINDFLAATIALSLNGG 60- 9 K L+LI ++V+ RG P+++ I++G+P L + + G I+ F AA IALSLN Sbjct: 343 IKPLQLIFRIYVEFFRGTPMLVQLFIIYFGLPALFKEI-GLGITIDRFPAAIIALSLNVA 40- 1 Query: 610 AYIAEIVRGGIEAVPAGQMEASRSLGLSYGTTMRKVILPQAVKLMLPNFINQFVISLKDT 66- 9 AY+AEI+RGGI+++ GQ EA SLG+S TM++VI PQA + +LP N+F+ +KDT Sbjct: 402 AYLAEIIRGGIQSIDQGQWEACESLGMSPWQTMKEVIFPQAFRRILPPLGNEFITLIKDT 46- 1 Query: 670 TIVSAIGLVELFQTGKIIIARNYQSFRMYAILAIIYLIMIILLTRLAKRLEKRLN 724 ++ + IG ELF+ G++I+A Y++F +Y +A++YL++ + + + K LE ++ Sbjct: 462 SLTAVIGFQELFREGQLIVATTYRAFEVYIAVALVYLLLTTISSFVFKWLENYMD 516 Identities = 68/247 (27%), Positives = 106/247 (42%), Gaps = 11/247 (4%) Query: 7 VLLLAIMSIFLTCNIASAETIAIVSDTAYAPFEFKD--SDQIYKGIDVDIINEVAKRQSW 64 VLL + + + S +TI + ++ + PFE D + Q+ G DVD+I + + Sbjct: 24 VLLAIAIPLLPAFSQVSRQTIIVATEPTFPPFEMTDEATGQL-TGFDVDLIQAIGEAAQV 82 Query: 65 DFSMSFPGFDAAVNAVQSGQASALMAGTTITNARKKVFHFSEPYYDTKIVIATRKAN-AI 123- + FD + A+QS A ++ TIT R + FS PY+ + + IA + N I Sbjct: 83 TVDIQGYPFDGIIPALQSNTVGAAISAITITPERAQSVSFSSPYFKSVLAIAVQDGNDTI 142- Query: 124 KKYSDLKGKTVGVKNGTAAQAFLNNYKKKYDYTVKTFDTGDLMYNSLSAGSIAAVMDDEA 18- 3 K DL+GK + V GT N V FD+ L G+ AV++D Sbjct: 143 KNLKDLEGKRLAVAIGTTGAMVATNVP---GAKVTNFDSITSALQELVNGNADAVINDRP 19- 9 Query: 184 VIQYAIS----QNQDIAINMKGEPIGSFGFAVKKGSGYDYLVNDFNTALKAMKADGTYQA 23- 9 V+ YAI +N I+ ++ E + + N L + +GTY A Sbjct: 200 VLLYAIKDAGLRNVKISADVGSEDYYGIAMPLAPPGEINQTREVLNQGLFQIIENGTYNA 25- 9 Query: 240 IMTKWLG 246 I KW G Sbjct: 260 IYEKWFG 266 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01184 Identities = 68/210 (32%), Positives = 113/210 (53%), Gaps = 16/210 (7%) Query: 13 LLQGFGLTLYISFISILLSMFFGTLLAIMRNSKNPIWKLIASIYIEFVRNVPNLLWIFII 72 - LL G G TL ++ IS +++ G + +M S +LI++++++ VR +P ++ I Sbjct: 517 LLAGLGTTLSLTLISFAIAIIIGIIFGMMAVSPTKSLRLISTVFVDVVRGIPLMIVAAFI 57- 6 Query: 73 F-----LVFQMKSVSAGITSFTIFT-------SAALAEIIRGGLNGVDKGQTEAGLSQGF 120- F L+ M + I F T A +AEI+RGG+ V GQ EA S G Sbjct: 577 FWGVPNLIESMTGHQSPINDFLAATIALSLNGGAYIAEIVRGGIEAVPAGQMEASRSLGL 63- 6 Query: 121 TYLQVFIIIIFPQAFRKMLPAIISQFVTVIKDTSLLYSVIAIQEIFGKSQILMGRYFEAG 18- 0 +Y +I PQA + MLP I+QFV +KDT+++ S I + E+F +I++ R + Sbjct: 637 SYGTTMRKVILPQAVKLMLPNFINQFVISLKDTTIV-SAIGLVELFQTGKIIIARNY--- 69- 2 Query: 181 QVFTLYAIITAVYFITNFIISSFSRKLSKR 210 Q F +YAI+ +Y I +++ +++L KR Sbjct: 693 QSFRMYAILAIIYLIMIILLTRLAKRLEKR 722 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 368 A DNA sequence (GBSx0399) was identified in S. agalactiae <SEQ ID 1199> which encodes the amino acid sequence <SEQ ID 1200>. Analysis of this protein sequence reveals the following: TABLE-US-01185 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.21 Transmembrane 7-23 (1-30) ----- Final Results ----- bacterial membrane --- Certainty = 0.5883(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01186 >GP:BAB04094 GB:AP001508 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 43/157 (27%), Positives = 83/157 (52%), Gaps = 9/157 (5%) Query: 26 YQSQFQKTTNQALAIAYKDAKVAKK--DVIHQKIDKEFENFRGSYEIEFNTKSAEYSYHV 83 - +Q++ N+L+A ++ + + + +K+ +N R YEIE EY++ Sbjct: 38 HQAESVSADNEGLTLAEASDIALERAGNGVVTEAEKDRDNGRVVYEIEVKNDDDEYDFKI 97 Query: 84 DVKTGQILERDMDNNGFSKSTSQSSSSSSQKSHKISQEEAKKIAFKDANIEESEVSNLKI 143- D +TG+IL+ + SK SSS ++ IS +EAK+IA K+ + ++ ++++ Sbjct: 98 DQQTGEILKEKQEQRKGSKPREGHSSSKGSEAVISMDEAKEIALKEVS----GKIDDIEL 153- Query: 144 KEEIENGKSVYDIDF-VDLKNKNEVDYQIDAETGKII 179 E ENG VY+++ D + ++V +DA TG ++ Sbjct: 154 --ERENGSLVYEVEIESDHYDODDVTVYVDANTGNVL 188 A related DNA sequence was identified in S. pyogenes <SEQ ID 1201> which encodes the amino acid sequence <SEQ ID 1202>. Analysis of this protein sequence reveals the following: TABLE-US-01187 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.15 Transmembrane 42-58 ( 41-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.3060(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below: TABLE-US-01188 Identities = 37/96 (38%), Positives = 63/96 (65%), Gaps = 5/96 (5%) Query: 94 DMDNNGFSKSTSQSSSSSSQKSHKISQEEAKKIAFKDANIEESEVSNLKIKEEIENGKSV 153- DMD+ +Q +S + K K+S+++AK IA KDA++E++ L + ++ E+GK+V Sbjct: 59 DMDDKD-DHMDNQPKTSQTSKKVKLSEDKAKSIALKDASVTEADAQMLSVTQDNEDGKAV 117- Query: 154 YDIDWVDLKNKN-EVDYQIDAETGKIIERSRDHMND 188 Y+I+F +NK+ E Y IDA +G I+E+S + +ND Sbjct: 118 YEIEF---QNKDQEYSYTIDANSGDIVEKSSEPIND 150 Identities = 23/62 (37%), Positives = 37/62 (59%) Query: 35 NQALAIAYKDAKVAKKDVIHQKIDKEFENFRGSYEIEFNTKSAEYSYHVDVKTGQILERD 94 - ++A +IA KDA V + D + ++ E+ + YEIEF K EYSY +D +G I+E+ Sbjct: 85 DKAKSIALKDASVTEADAQMLSVTQDNEDGKAVYEISFQNKDQEYSYTIDANSGDIVEKS 144- Query: 95 MD 96 + Sbjct: 145 SE 146 A related GBS gene <SEQ ID 8563> and protein <SEQ ID 8564> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01189 Lipop: possible site: = -1 Crend: 9 McG: Discrim Score: 14.45 GyM: Signal Score (-7.5): -5.92 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -8.92 threshold: 0.0 INTEGRAL Likelihood = -8.92 Transmembrane 7-23 ( 2-28) PERIPHERAL Likelihood = 10.93 37 modified ALOM score: 2.28 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4567(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00031## SEQ ID 8564 (GBS37) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 14 (lane 4; MW 22 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 10; MW 47 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 369 A DNA sequence (GBSx0400) was identified in S. agalactiae <SEQ ID 1203> which encodes the amino acid sequence <SEQ ID 1204>. Analysis of this protein sequence reveals the following: TABLE-US-01190 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1499(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9709> which encodes amino acid sequence <SEQ ID 9710> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1205> which encodes the amino acid sequence <SEQ ID 1206>. Analysis of this protein sequence reveals the following: TABLE-US-01191 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2808(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01192 Identities = 128/297 (43%), Positives = 180/297 (60%), Gaps = 9/297 (3%) Query: 54 IDDIKVGSPIFKYFWT-SLSLQAPLKALEFVLEQAKMPTELSGELSETQYLVAQFSDELA 112- I D ++GSP F W Q+ + L F+L+ +MP ELSG+L ETQ L+ +F L Sbjct: 46 IIDNRLGSPTFWVIWPIEKENQSAKQLLTFLLDLVEMPFELSGQLHETQTLLTRFHPSLL 105- Query: 113 PHDDFWIALSQVIYDSFPGNSLAEDTVLNRKLHQFRYLISSQQAQYVRRYFKDVGMTDRD 17- 2 P FW L+ ++ +FPG +L++ L ++LHQFRY+ISSQQAQ +R ++K + MTD Sbjct: 106 PDHMFWKELASLVDQAFPGKTLSQAGELEKRLHQFRYVISSQQAQSIRNHYKMIEMTDAQ 16- 5 Query: 173 ALVNYL-----SCL-REPDSIAYYESARLHNKRRRNGEIFGFPDDEPVINSKLLISFHTE 22- 6 AL +L CL R+ +SARLHNK R FP E N K+L+ FHTE Sbjct: 166 ALALFLRSKKGPCLWRQAPDYTLMDSARLHNKLRFEDNKVIFPSQEVSYNIKVLLWFHTE 22- 5 Query: 227 FIIDDKGNFLNEIDAEVITRNGIINGASFNYAFKNNTRHKELDVDPVK-LDPKFRNDMTR 28- 5 F +D G FLNE+DAEV+T GI+NGASFNY + RH +LDVDP+ DP+FR D + Sbjct: 226 FTLDSTGFFLNEVDAEVVTEKGIVNGASFNYG-TDGPRHWDLDVDPISHHDPQFRRDTLK 28- 4 Query: 286 GYRSPNLSRRKWFFFKEEDYDCSYFNKKGYYAFGRRSAKQSVDKQVKYLKKAVQKMR 342 G+RSP R+WF +++D+ SYFN KG +A+ +S+ V K K K+ + ++ Sbjct: 285 GFRSPKRVFRQWFRAQKDDFMFSYFNAKGLFAYHNKSSFARVKKSAKQFKRQIHPIK 341 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 370 A DNA sequence (GBSx0401) was identified in S. agalactiae <SEQ ID 1207> which encodes the amino acid sequence <SEQ ID 1208>. This protein is predicted to be similar to two-component response regulator [YcbM] (ompr-likeprotei). Analysis of this protein sequence reveals the following: TABLE-US-01193 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3129(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01194 >GP: CAA55264 GB: X78502 gtcR [Brevibacillus brevis] Identities = 99/228 (43%), Positives = 149/228 (64%), Gaps = 3/228 (1%) Query: 2 RTVLVVQGDDETIELLRSYLEGALYKVVMASDGEEAFSLFQQHQIDLAIIDITLPKIDGY 61 +T+L+ + E IELL+ +LE Y+++ A DGE+A++ +QH +DLAIIDI +P +DG+ Sbjct: 3 KTILIADDEPEIIELLKLFLERESYRIIEAYDGEQAWNYIRQHPVDLAIIDIMMPALDGF 62 Query: 62 ELTRLIRQDSQIPIIMLAAKTTDMDRILGLNIGADDFITKPFNSLEVLARINSQLRRYYE 121- +L + + + ++P+I+L+AK D D+ILGL +GADDFI+KPFN LE +ARI +QLRR +E Sbjct: 63 QLIKRLTNEYKLPVIILSAKNRDSDKILGLGLGADDFISKPFNPLEAVARIQAQLRRAFE 122- Query: 122 FNSLAKP--KNQFIKIGELELDEEHVELTKNGKHIKLTATEFKILHILMS-SPGRIYTKT 17- 8 FN + Q +G L L + + + +T E+++L+ M S I+TK Sbjct: 123 FNEPEEKAISTQSTTVGRLTLLHTACVVYRGDETYSVTPLEYRLLNTFMQCSRTSIFTKQ 18- 2 Query: 179 QLYEKINGRYLEGDETTIMVHISNIRDKIEDDSKYPKYIKTLRGVGYK 226 QL+E+ D+ TIMV IS +RDKIED + P YIKT+RG+GYK Sbjct: 183 QLFEQAWSETYWEDDNTIMVQISRLRDKIEDQPRQPVYIKTVRGLGYK 230 There is also homology to SEQ ID 1182: TABLE-US-01195 Identities = 87/230 (37%), Positives = 144/230 (61%), Gaps = 5/230 (2%) Query: 1 MRTVLVVQGDDETIELLRSYLEGALYKVVMASDGEEAFSLFQQHQIDLAIIDITLPKIDG 60 M+ +L+V + ++++ L Y +V A DG EA ++F++ + DL I+D+ LP++DG Sbjct: 1 MKKILIVDDEKPISDIIKFNLTKEGYDIVTAFDGREAVTIFEEEKPDLIILDLMLPELDG 60 Query: 61 YELTRLIRQDSQIPIIMLAAKTTDMDRILGLNIGADDFITKPFNSLEVLARINSQLRRYY 120- E+ + IR+ S +PIIML+AK ++ D+++GL IGADD++TKPF++ E+LAR+ + LRR Sbjct: 61 LEVAKEIRKTSHVPIIMLSAKDSEFDKVIGLEIGADDYVTKPFSNRELLARVKAHLRRTE 120- Query: 121 EFNSLAKPKN-----QFIKIGELELDEEHVELTKNGKHIKLTATEFKILHILMSSPGRIY 17- 5 + +N Q + IG L++ + K+G+ ++LT EF++LH L + G++ Sbjct: 121 TIETAVAEENASSGTQELTIGNLQILPDAFVAKKHGQEVELTHREFELLHHLANHMGQVM 18- 0 Query: 176 TKTQLYEKINGRYLEGDETTIMVHISNIRDKIEDDSKYPKYIKTLRGVGY 225 T+ L E + G GD T+ V + +R+KIED P+YI T RGVGY Sbjct: 181 TREHLLEIVWGYDYFGDVRTVDVTVRRLREKIEDTPSRPEYILTRRGVGY 230 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 371 A DNA sequence (GBSx0402) was identified in S. agalactiae <SEQ ID 1209> which encodes the amino acid sequence <SEQ ID 1210>. This protein is predicted to be threonyl-tRNA synthetase 1 (thrS). Analysis of this protein sequence reveals the following: TABLE-US-01196 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2353(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01197 >GP: BAB06860 GB: AP001517 threonyl-tRNA synthetase 1 [Bacillus halodurans] Identities = 413/638 (64%), Positives = 506/638 (78%), Gaps = 7/638 (1%) Query: 1 MIKITFPDGAIREFESGITTFEIAQSISNSLAKKALAGKFNGQLIDTTRAIEEDGSIEIV 60 MI ITFPDGA++EF G TT EIA SIS L KKALAG +G L+D IE+DG+I IV Sbjct: 4 MINITFPDGAVKEFPKGTTTAEIAGSISPGLKKKALAGMLDGTLLDLNTPIEQDGTITIV 63 Query: 61 TPDHEDALGVLRHSAAHLFAQAAKRLFPD--LCLGVGPAIQDGFYYDTDNKSGQISNDDL 118- TP+ ++AL VLRHS AH+ AQA KRLF D + LGVGP I+ GFYYD D ++ +DL Sbjct: 64 TPESDEALEVLRHSTAHVMAQALKRLFKDRNVKLGVGPVIEGGFYYDVDMDES-LTPEDL 122- Query: 119 PRIEEEMKKIVKENHPCIREEISKEEALELFKD--DPYKVELISEHAEDG-LTVYRQGEF 17- 5 P+IE+EMKKI+ EN P R +S+EEAL +++ DPYK+ELI++ ED +T+Y QGEF Sbjct: 123 PKIEKEMKKIIGENLPIERVVVSREEALARYEEVGDPYKIELINDLPEDETITIYEQGEF 18- 2 Query: 176 VDLCRGPHVPSTGRIQVFHLLNVAGAYWRGNSDNAMMQRVYGTAWFDKKDLKAYLKRREE 23- 5 DLCRG HVPSTG+++ F LLN+AGAYWRG+S N M+QR+YGTA+F K DL +L+ EE Sbjct: 183 FDLCRGVHVPSTGKLKEFKLLNLAGAYWRGDSSNKMLQRIYGTAFFKKADLDEHLRLLEE 24- 2 Query: 236 AKERDHRKLGKELDLFMVNPEVGQGLPFWLPNGATIRRELERYIVDKEIASGYQHVYTPP 29- 5 AKERDHRKLGKEL +F ++ +VGQGLP WLP GATIRR +ERYIVDKE GYQHVYTP Sbjct: 243 AKERDHRKLGKELGIFALSQKVGQGLPLWLPKGATIRRIIERYIVDKEEKLGYQHVYTPV 30- 2 Query: 296 MASVEFYKTSGHWDHYREDMFPTMDMGDGEEFVLRPMNCPHHIEVYKHHVHSYRELPIRI 35- 5 +AS E YKTSGHWDHY++DMFPTM+M + EE VLRPMNCPHH+ VYK + SYR+LP+RI Sbjct: 303 LASSELYKTSGHWDHYKDDMFPTMEM-ENEELVLRPMNCPHHMMVYKTEMRSYRQLPLRI 36- 1 Query: 356 AELGMMHRYEKSGALTGLQRVREMTLNDAHIFVTPEQIKDEFLKALNLIAEIYEDFNLTD 41- 5 AELG+MHRYE SGA++GLQRVR MTLNDAHIF P+QIKDEF++ + LI +YEDF L + Sbjct: 362 AELGLMHRYEMSGAVSGLQRVRGMTLNDAHIFCRPDQIKDEFVRVVRLIQAVYEDFGLKN 42- 1 Query: 416 YRFRLSYRDPEDKHKYYDNDEMWENAQAMLKEAMDDFGLDYFEAEGEAAFYGPKLDIQVK 47- 5 Y FRLSYRDPEDK KY+D+D MW AQ MLKEAMD+ L+YFEAEGEAAFYGPKLD+QV+ Sbjct: 422 YSFRLSYRDPEDKEKYFDDDNMWNKAQGMLKEAMDELELEYFEAEGEAAFYGPKLDVQVR 48- 1 Query: 476 TALGNEETLSTIQLDFLLPERFDLKYIGADGEEHRPIMIHRGGISTMERFTAILIETYKG 53- 5 TALG +ETLST+QLDFLLPERFDL Y+G DG+ HRP+++HRG +STMERF A L+E YKG Sbjct: 482 TALGKDETLSTVQLDFLLPERFDLTYVGEDGQPHRPVVVHRGVVSTMERFVAFLLEEYKG 54- 1 Query: 536 AFPTWLAPQQVSVIPISNEAHIDYAWEVARVLKDRGIRAEVDDRNEKMQYKIRAAQTQKI 59- 5 AFPTWLAP QV VIP+S EAH++YA V L+ GIR E+D+R+EK+ YKIR AQ QKI Sbjct: 542 AFPTWLAPVQVQVIPVSPEAHLEYAKNVQETLQQAGIRVEIDERDEKIGYKIREAQMQKI 60- 1 Query: 596 PYQLIVGDKEMEEKAVNVRRYGSKATETKSIEEFVESI 633 PY L++GDKE+E VNVR+YG K + + ++EFV + Sbjct: 602 PYMLVLGDKEVEANGVNVRKYGEKDSSSMGLDEFVRHV 639 A related DNA sequence was identified in S. pyogenes <SEQ ID 1211> which encodes the amino acid sequence <SEQ ID 1212>. Analysis of this protein sequence reveals the following:

TABLE-US-01198 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2566(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01199 Identities = 564/644 (87%), Positives = 608/644 (93%) Query: 1 MIKITFPDGAIREFESGITTFEIAQSISNSLAKKALAGKFNGQLIDTTRAIEEDGSIEIV 60 MIKITFPDGA+REFESG+TTF+IA+SIS SLAKKALAGKFN QLIDTTRAIEEDGSIEIV Sbjct: 1 MIKITFPDGAVREFESGVTTFDIAESISKSLAKKALAGKFNDQLIDTTRAIEEDGSIEIV 60 Query: 61 TPDHEDALGVLRHSAAHLFAQAAKRLFPDLCLGVGPAIQDGFYYDTDNKSGQISNDDLPR 120- TPDH+DA VLRHSAAHLFAQAAKRLFP+L LGVGPAI +GFYYDTDN GQISN+DLPR Sbjct: 61 TPDHKDAYEVLRHSAAHLFAQAAKRLFPNLHLGVGPAIAEGFYYDTDNAEGQISNEDLPR 120- Query: 121 IEEEMKKIVKENHPCIREEISKEEALELFKDDPYKVELISEHAEDGLTVYRQGEFVDLCR 18- 0 IE EM+KIV EN+PCIREE++KEEALELFKDDPYKVELI+EHA GLTVYRQGEFVDLCR Sbjct: 121 IEAEMQKIVTENYPCIREEVTKEEALELFKDDPYKVELINEHAGAGLTVYRQGEFVDLCR 18- 0 Query: 181 GPHVPSTGRIQVFHLLNVAGAYWRGNSDNAMMQRVYGTAWFDKKDLKAYLKRREEAKERD 24- 0 GPHVPSTGRIQVFHLLNVAGAYWRGNSDN MMQR+YGTAWFDKKDLKAYL R EEAKERD Sbjct: 181 GPHVPSTGRIQVFHLLNVAGAYWRGNSDNNMMQRIYGTAWFDKKDLKAYLTRLEEAKERD 24- 0 Query: 241 HRKLGKELDLFMVNPEVGQGLPFWLPNGATIRRELERYIVDKEIASGYQHVYTPPMASVE 30- 0 HRKLGKELDLFM++ EVGQGLPFWLP+GATIRR LERYI DKE+ASGYQHVYTPP+ASVE Sbjct: 241 HRKLGKELDLFMISQEVGQGLPFWLPDGATIRRTLERYITDKELASGYQHVYTPPLASVE 30- 0 Query: 301 FYKTSGHWDHYREDMFPTMDMGDGEEFVLRPMNCPHHIEVYKHHVHSYRELPIRIAELGM 36- 0 YKTSGHWDHY+EDMFP MDMGDGEEFVLRPMNCPHHI+VYK+HV SYRELPIRIAELGM Sbjct: 301 LYKTSGHWDHYQEDMFPVMDMGDGEEFVLRPMNCPHHIQVYKNHVRSYRELPIRIAELGM 36- 0 Query: 361 MHRYEKSGALTGLQRVREMTLNDAHIFVTPEQIKDEFLKALNLIAEIYEDFNLTDYRFRL 42- 0 MHRYEKSGAL+GLQRVREMTLND HIFVTPEQI++EF +AL LI ++Y DFNLTDYRFRL Sbjct: 361 MHRYEKSGALSGLQRVREMTLNDGHIFVTPEQIQEEFQRALQLIIDVYADFNLTDYRFRL 42- 0 Query: 421 SYRDPEDKHKYYDNDEMWENAQAMLKEAMDDFGLDYFEAEGEAAFYGPKLDIQVKTALGN 48- 0 SYRDP D HKYYDNDEMWENAQ+MLK A+D+ G+DYFEAEGEAAFYGPKLDIQVKTALGN Sbjct: 421 SYRDPNDTHKYYDNDEMWENAQSMLKAALDEMGVDYFEAEGEAAFYGPKLDIQVKTALGN 48- 0 Query: 481 EETLSTIQLDFLLPERFDLKYIGADGEEHRPIMIHRGGISTMERFTAILIETYKGAFPTW 54- 0 EETLSTIQLDFLLPERFDLKYIGADGEEHRP+MIHRG ISTMERFTAILIETYKGAFPTW Sbjct: 481 EETLSTIQLDFLLPERFDLKYIGADGEEHRPVMIHRGVISTMERFTAILIETYKGAFPTW 54- 0 Query: 541 LAPQQVSVIPISNEAHIDYAWEVARVLKDRGIRAEVDDRNEKMQYKIRAAQTQKIPYQLI 60- 0 LAP QV+VIPISNEAHIDYAWEVA+ L+DRG+RA+VDDRNEKMQYKIRA+QT KIPYQLI Sbjct: 541 LAPHQVTVIPISNEAHIDYAWEVAKTLRDRGVRADVDDRNEKMQYKIRASQTSKIPYQLI 60- 0 Query: 601 VGDKEMEEKAVNVRRYGSKATETKSIEEFVESILADIARKSRPD 644 VGDKEME+K+VNVRRYGSK T T+S+EEFVE+ILADIARKSRPD Sbjct: 601 VGDKEMEDKSVNVRRYGSKTTHTESVEEFVENILADIARKSRPD 644 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 372 A DNA sequence (GBSx0403) was identified in S. agalactiae <SEQ ID 1213> which encodes the amino acid sequence <SEQ ID 1214>. Analysis of this protein sequence reveals the following: TABLE-US-01200 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1985(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01201 >GP:CAA72250 GB:Y11463 ORF5 [Streptococcus pneuinoniae] Identities = 189/290 (65%), Fesitives = 234/290 (80%) Query: 1 MRIGLFTDTYFFQVSGVSTSIRTLKEGLEKEGHEVYIFTTTDRNVKRFEDPTIIRLPSVP 60 MRIGLFTDTYFPQVSGV+TSIRTLK LEK+GH V+IFTTTD++V R+ED IIR+PSVP Sbjct: 1 MRIGLFTDTYFPQVSGVATSIRTLKTELEKQGHAVFIFTTTDKDVNRYEDWQIIRIPSVP 60 Query: 61 FISFTDRRVVYRGLISAYRIAKDYELDIIHTQTEFSLGLLGRLVAKALRIPVVHTYHTQY 120- F +F DRR YRG A IAK Y+LDIIHTQTEFSLGLLG +A+ L+IPV+HTYHTQY Sbjct: 61 FFAFKDRRFAYRGFSKALEIAKQYQLDIIHTQTEFSLGLLGIWIARELKIPVIHTYHTQY 120- Query: 121 EDYVGYIAKGKLIKPSDVKYIMRTYLSDLDGVICPSRIVLNLLDGYGVKIPKQVIPTGIP 18- 0 EDYV YIAKG LI+PSMVKY++R +L D+DGVICPS IV +LL Y VK+ K+VIPTGI Sbjct: 121 EDYVHYIAKGMLIRPSMVKYLVRGFLHDVDGVICPSEIVRDLLSDYKVKVEKRVIPTGIE 18- 0 Query: 181 VENYRREDISEETIKNLRTELGLADNDTMLLSLSRVSFERNIQAILMHLSAVVDENPHVK 24- 0 + + R +I +E +K LR++LG+ D + LLSLSR+S+EKNIQA+L+ + V+ E VK Sbjct: 181 LAKFERPEIKQENLKELRSKLGIQDGEKTLLSLSRISYEKNIQAVLVAFADVLKEEDKVK 24- 0 Query: 241 LVIVGDGPYLSDLKELVHSLELENSVIFTGMVEHSQVAIYYKACDFFISA 290 LV+ GDGPYL+DLKE +LE+++SVIFTGM+ S+ A+YYKA DFFISA Sbjct: 241 LVVAGDGPYLNDLKEQAQNLEIQDSVIFTGMIAPSETALYYKAADFFISA 290 A related DNA sequence was identified in S. pyogenes <SEQ ID 1215> which encodes the amino acid sequence <SEQ ID 1216>. Analysis of this protein sequence reveals the following: TABLE-US-01202 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1074(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01203 Identities = 309/444 (69%), Positives = 370/444 (82%) Query: 1 MRIGLFTDTYFPQVSGVSTSIRTLKEGLEKEGHEVYIFTTTDRNVKRFEDPTIIRLPSVP 60 MRIGLFTDTYWPQVSGV+TSIRTLKE LEKEGHEVYIFTTTDR+VKRFSDPTIIRLPSVP Sbjct: 1 MRIGLFTDTYFPQVSGVATSIRTLKEELEKEGHEVYIFTTTDRDVKRFSDPTIIRLPSVP 60 Query: 61 FISFTDRRVVYRGLISAYRIAKDYELDIIHTQTEFSLGLLGKLVAKALRIPVVHTYHTQY 120- F+SFTDRRVVYRGLIS+Y+IAK Y LDIIHTQTEFSLGLLGK++ KALRIPVVHTYHTQY Sbjct: 61 FVSFTDRRVVYRGLISSYKIAKHYNLDIIHTQTEFSLGLLGKMIGKALRIPVVHTYHTQY 120- Query: 121 EDYVGYIAKGKLTKPSMVRYIMRTYLSDLDGVICPSRIVLNLLDGYGVKIPKQVIPTGIP 18- 0 EDYV YIA GK+I+PSMVK ++R YL DLDGVICPSRIVLNLL+GY V IPK+VIPTGIP Sbjct: 121 EDYVSYIANGKIIRPSMVKFLLRGYLKOLDGVICPSRIVLNLLEGYEVTIPKRVIPTGIP 18- 0 Query: 181 VENYRREDISEETIKNLRTELGLADNDTMLLSLSRVSFEKNIQAILMHLSAVVDENPHVK 24- 0 +E Y R+DI+ E + NL+ ELG+A ++TMLLSLSR+S+EKNIQAI+ + A++ EN +K Sbjct: 181 LEKYIRDDITAEEVTNLKAELGIAGDETMLLSLSRISYEKNIQAIINQMPAILAENAKIK 24- 0 Query: 241 LVIVGDGPYLSDLKELVHSLELENSVIFTGMVEHSQVAIYYKACDFFISASTSETQGLTY 30- 0 L+IVG+GPYL DLK L LE++ V FTGMV H +VA+YYKACDFFISASTSETQGLTY Sbjct: 241 LIIVGNGPYLQDLKHLAMQLEVDKHVTFTGMVPHDKVALYYKACDFFISASTSETQGLTY 30- 0 Query: 301 IESLASGRPIIAQSNPYLDDVISDKMFGTLYKKESDLADAILDAIAETPKMTQEAYEQKL 36- 0 IESLASG PIIA NPYLDDV++DKMFGTLY E+DL DAI+DAI +TP M + +K Sbjct: 301 IESLASGTPIIAHGNPYLDDVVTDKMFGTLYYAETDLTDAIIDAILKTPVMDKRLLAKKR 36- 0 Query: 361 YEISAENFSKSVYAFYLDFLISQKASVKEKVSLTIGNKDSHSTLRFVRKAVYLPKKVFTF 42- 0 YEISA++F KS+Y FYLD LI++ + +K+SL + + S+L+ V+ A++LPK+ Sbjct: 361 YEISAQHFGKSIYTFYLDTLIARNSKEAQKLSLYLNHSGKSSSLKLVQGAIHLPKRAAKV 42- 0 Query: 421 TGPASKKVVKAPKRRISSIRDFLD 444 T S KVVKAP + + +I+DFLD Sbjct: 421 TAITSVKVVKAPIRLVHAIKDFLD 444 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 373 A DNA sequence (GBSx0404) was identified in S. agalactiae <SEQ ID 1217> which encodes the amino acid sequence <SEQ ID 1218>. This protein is predicted to be lipopolysaccharide biosynthesis protein-related protein. Analysis of this protein sequence reveals the following: TABLE-US-01204 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4076(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01205 >GP: AAG19110 GB: AE005009 Vng0600c [Halobacterium sp. NRC-1] Identities = 117/350 (33%), Positives = 178/350 (50%), Gaps = 29/350 (8%) Query: 1 MKVLLYLEAEEYLKKSGIGRAIKHQEKALQIAGIDYTTNPT------------------- 41 M+ L YLEA E L+ G+ A Q AL+ ++ P Sbjct: 2 MRALNYLEAAEALR-GGMVTATNQQRAALETTDVEVVETPWRAGDPVRSIGSLAAGGSCF 60 Query: 42 DDFDLVHMNTYGIRSWLLMSKAKKTGKKVIMHGHSTEEDFRNSFIGSNLVSPLFKWYLCR 101- FD+ H N G S + A++T +++H H T EDF SF GS+ ++P + YL Sbjct: 61 TAFDVAHCNLVGPGSVAVARHARRTDTPLVLHAHLTREDFAQSFRGSSTIAPALEPYLRW 120- Query: 102 FYQKADAIITPTDYSKQLIKAYGIKKPIFVLSNGIDLSRYQRSEKKESAFRHYFHLSKDD 16- 1 FY +AD ++ P++Y+K +++AY + PI LSNG+DL Q E + R F L D Sbjct: 121 FYSQADLVLCPSEYTKDVLRAYPVDAPIRQLSNGVDLESMQGYESFRADTRARFDL--DG 17- 8 Query: 162 KVVMGAGLYFMRKGIDQFVEVAAKMPDIRFIWFGETNKWVIPRKVRQIVTKQHPSNVTFA 22- 1 VV G F RKG+ F E+ AK D F WFG ++ + P+NVTF Sbjct: 179 TVVYAVGEVFERKGLTMFCEL-AKATDHEFAWFGPYDEGPQAGAATRKWVADPPANVTFT 23- 7 Query: 222 GYIKGDVYEGAMSASDAFFFPSREETEGIVVLEALASHQHVVLRDIPVYHGWVTE-DSVE 28- 0 GY++ A A D + FP++ E +GI VLEA+A + VVLRDIPV+ + T+ + Sbjct: 238 GYMEDK--RAAFGAGDIYLFPAKVENQGIAVLEAMACGKPVVLRDIPVFREFFTDGEDCL 29- 5 Query: 281 LATDVDGFVEKLDKVLSGKSDKIKEGYH---VAESRSIERIAHELASVYQ 327 + + + F + +D++ + + G + AES S++RI ELAS+Y+ Sbjct: 296 MCSTFEAFRDAIDRLADDPELRTRLGENARETAESHSLDRIGEELASIYE 345 A related-DNA sequence was identified in S. pyogenes <SEQ ID 1219> which encodes the amino acid sequence <SEQ ID 1220>. Analysis of this protein sequence reveals the following: TABLE-US-01206 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4088(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01207 Identities = 236/332 (71%), Positives = 276/332 (83%) Query: 1 MKVLLYLEAEEYLKKSGIGRAIKHQEKALQIAGIDYTTNPTDDFDLVHMNTYGIRSWLLM 60 MKVLLYLEAE YL+KSGIGRAIKHQ KAL + G +TTNP + +DLVH+NTYG++SWLLM Sbjct: 1 MKVLLYLEAENYLRKSGIGRAIKHQAKALSLVGQHFTTNPRETYDLVHLNTYGLKSWLLM 60 Query: 61 SKAKKTGKKVIMHGHSTEEDFRNSFIGSNLVSPLFKWYLCRFYQKADAIITPTDYSKQLI 120- KA+K GKKVIMHGHSTEEDFRNSFI SNL+SP FK YLC FY KADAIITPT YSK LI Sbjct: 61 IKAQKAGKKVIMHGHSTEEDFRNSFIFSNLLSPWFKKYLCHFYNKADAIITPTLYSKSLI 120- Query: 121 KAYGIKKPIFVLSNGIDLSRYQRSEKKESAFRHYFHLSKDDKVVMGAGLYFMRKGIDQFV 18- 0 ++YG+K PIF +SNGIDL +Y KKE+AFR YF + + +KVVMGAGL+F+RKGID FV Sbjct: 121 ESYGVKSPIFAVSNGIDLEQYGADPKKEAAFRRYFDIKEGEKVVMGAGLFFLRKGIDDFV 18- 0 Query: 181 EVAAKMPDIRFIWFGETNKWVIPRKVRQIVTKQHPSNVTFAGYIKGDVYEGAMSASDAFF 24- 0 +VA MPD+RFIWFGETNKWVIP +VRQ+V HP N+ F GYIKGDVYEGAM+ +DAFF Sbjct: 181 KVAQAMPDVRFIWFGETNKWVIPAQVRQMVNGNHPKNLIFPGYIKGDVYEGAMTGADAFF 24- 0 Query: 241 FPSREETEGIVVLEALASHQHVVLRDIPVYHGWVTEDSVELATDVDGFVEKLDKVLSGKS 30- 0 FPSREETEGIVVLEALAS QH+VLRDIPVY+GWV + S ELATD+ GF+E L KV SG S Sbjct: 241 FPSREETEGIVVLEALASRQHLVLRDIPVYYGWVDQSSAELATDIPGFIEALKKVFSGAS 30- 0 Query: 301 DKIKEGYHVAESRSIERIAHELASVYQKVMEL 332 +K++ GY VA+SR +E + H L VY+KVMEL Sbjct: 301 NKVEAGYKVAQSRRLETVGHALVDVYKKVMEL 332 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 374 A DNA sequence (GBSx0405) was identified in S. agalactiae <SEQ ID 1221> which encodes the amino acid sequence <SEQ ID 1222>. Analysis of this protein sequence reveals the following: TABLE-US-01208 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5487(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01209 >GP: AAC35010 GB: AF055987 intracellular a-amylase [Streptococcus mutans] Identities = 308/483 (63%), Positives = 378/483 (77%) Query: 1 MTNELIMQAFEWYLPSDGNHWKKLEESISDLKKLGISKIWLPPAFKGTSSDDVGYGVYDL 60 MTNE +MQ FEWYLP+DG HW+L E S LK +GISK+W+PPAFKGT S+DVGYGVYDL Sbjct: 1 MTNETMMQYFEWYLPNDGKHWQHLAEDASHLKNIGISKVWMPPAFKGTGSNDVGYGVYDL 60 Query: 61 FDLGEFDQNGTIRTKYGRKEEYLKLIKSLKANGIKPFADIVLNHKANGDHKEKFQVIKVN 120- +DLGEF+QNGT+RTKYG +E+YL + +LK I P +DIVLNHKANGD KE+FQV+KVN Sbjct: 61 YDLGEFNQNGTVRTKYGSREDYLNAVNALKEQEIMPISDIVLNHKANGDAKERFQVVKVN 120- Query: 121 PENRQEALSEPYEIEGWTGFDFPGRQGEYNDFKWHWYHFTGLDYDAKNNETDIFMIVGDN 18- 0 P NRQE +SEPYEIEGWT F+FPGRQ Y+DFKWHWYHFTG+DYDA +NE I+MI+GDN Sbjct: 121 PSNRQEKISEPYEIEGWTQFNFPGRQDNYSDFKWHWYHFTGVDYDALHNENGIYMILGDN 18- 0 Query: 181 KGWADDDLIDDENGNFDYLMYNDIDFKHPEVIKNLQDWAKWFIETTGIEGFRLDAVKHID 24- 0 KGWA + ID ENGN+DYLMY+DIDFKHPEV ++L+DW WF+ET+G+ GFRLDA+KHID Sbjct: 181 KGWASQENIDQENGNYDYLMYDDIDFKHPEVQEHLRDWVAWFLETSGVGGFRLDAIKHID 24- 0 Query: 241 SYFIQTFINDIRTKIKPDLEVFGEYWKSDQTSMKDYLEATQFQFSLVDVTLHMNFFDASH 30- 0 F+ FI IR +K DL VFGEYWK + DYL + QF L+DV LHM+ F+A Sbjct: 241 KTFMAQFIRYIREHLKADLYVFGEYWKDSHFDITDYLHSVDLQFDLIDVMLHMSLFEAGQ 30- 0 Query: 301 QNRDFDMRTIFDDSLVIDNPEYAVTFVENHDTQSGQALESRVEDWFKPLAYGLILLRQQG 36- 0 + DFD+ TI DDSL+ +P++AVTFV+NHD+Q GQALES V +WFKPLAYGLILLRQ+G Sbjct: 301 KGSDFDLSTILDDSLMKSHPDEAVTFVDNHDSQRGQALESTVAEWFKPLAYGLILLRQEG 36- 0 Query: 361 TPCLFYGDYYGIQGEFGQPSFKEVIDKMAELRQNYVFGKQVDYFTHSNCIGWTCLGDEEH 42- 0 PC+FYGDYYGI GEF Q SF+ V+DK+ +RQ +V+G + T NCIGWTCLGDEEH Sbjct: 361 IPCVFYGDYYGISGEFAQESFQTVLDKLLYIRQYHVYGSKKIILTMPNCIGWTCLGDEEH 42- 0 Query: 421 NSCLAVVLTNGDQGWKHMEVGEIYAGKTFVDYLGNCEQEVVIGDDGWGDFLVESASISAW 48- 0 +AV+++NG+ K M +GE K FVDYL NC +EV++ D GWGDF V+ AS+SAW Sbjct: 421 PDGVAVIISNGEANCKRMNMGEFNRNKVFVDYLNNCTEEVILDDQGWGDFPVQEASLSAW 48- 0 Query: 481 VPK 483 V K Sbjct: 481 VNK 483 A related DNA sequence was identified in S. pyogenes <SEQ ID 1223> which encodes the amino acid sequence <SEQ ID 1224>. Analysis of this protein sequence reveals the following: TABLE-US-01210 Possible site: 30 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01211 >GP: AAB00845 GB: M57692 alpha-cyclodextrin glycosyltransferase [Thermoanaerobacterium thermosulfurigenes] Identities = 356/710 (50%), Positives = 468/710 (65%), Gaps = 16/710 (2%) Query: 7 KTYKLLTKSAVLLGLISFPLT--VSAADNASVTNKADFSTDTIYQIVTDRFNDGNTSNNG 64 KT+KL+ + L L+ F LT + AA + +V+N ++STD IYQIVTDRF DGNTSNN Sbjct: 3 KTFKLILVLMLSLTLV-FGLTAPIQAASDTAVSNVVNYSTDVIYQIVTDRFVDGNTSNNP 61 Query: 65 KTDVFDKN--DLKKYHGGDWQGIIAKIKDGYLTDMGISAIWISSPVENIDSIDPSN---G 119- D++D LKKY GGDWQGII KI DGYLT MG++AIWIS PVENI ++ P + G Sbjct: 62 TGDLYDPTHTSLKKYFGGDWQGIINKINDGYLTGMGVTAIWISQPVENIYAVLPDSTFGG 121- Query: 120 SAAYHGYWAKDFFKTNQHFGTEADFQQLVKVAHQHHIKVVIDFAPNHTSTAEKEGTTFKE 17- 9 S +YHGYWA+DF +TN +FG+ DFQ L+ AH H+IKV+IDFAPNHTS A + T+ E Sbjct: 122 STSYHGYWARDFKRTNPYFGSFTDFQNLINTAHAHNIKVIIDFAPNHTSPASETDPTYAE 18- 1 Query: 180 DGALYKNGKLVGKFSDDKDKIFNHESWTDFSTYENSIYHSMYGLADLNNINPKVDQYMKE 23- 9 +G LY NG L+G +++D + F+H TDFS+YE+ IY +++ LADLN N +D Y+K Sbjct: 182 NGRLYDNGTLLGGYTNDTNGYFHHYGGTDFSSYEDGIYRNLFDLADLNQQNSTIDSYLKS 24- 1 Query: 240 AIDKWLDLGVDGIRVDAVKHMSQGWQKNWLSHIYEKHNVFVFGEWFSGHTDDDYDMTTFA 29- 9 AI WLD+G+DGIR+DAVKHM GWQKN++ I VF FGEWF G + D + T FA Sbjct: 242 AIKVWLDMGIDGIRLDAVKHMPFGWQKNFMDSILSYRPVFTFGEWFLGTNEIDVNNTYFA 30- 1 Query: 300 NNSGMGLLDFRFANAIRQLYTGFSTFTMRDFYKVLENRDQVTNEVTDQVTFIDNHDMERF 35- 9 N SGM LLDFRF+ +RQ++ +T TM ++++ N + D VTFIDNHDM+RF Sbjct: 302 NESGMSLLDFRFSQKVRQVFRD-NTDTMYGLDSMIQSTASDYNFINDMVTFIDNHDMDRF 36- 0 Query: 360 ATKVANNQTAVNQAYALLLTSRGVPNIYYGTEQYATGDKDPNNRGDMPSFNKESQAYKVI 41- 9 + V QA A LTSRGVP IYYGTEQY TG+ DP NR M SFN + AY VI Sbjct: 361 YN--GGSTRPVEQALAFTLTSRGVPAIYYGTEQYMTGNGDPYNRAMMTSFNTSTTAYNVI 41- 8 Query: 420 SKLAPLRKQNQALAYGTTEQRWISDHVLVFERKFGNHVALVAINRDQTNGYTITNAKTAL 47- 9 KLAPLRK N A+AYGTT+QRWI++ V ++ERKFGN+VALVAINR+ + Y IT TAL Sbjct: 419 KKLAPLRKSNPAIAYGTTQQRWINNDVYIYERKFGNNVALVAINRNLSTSYNITGLYTAL 47- 8 Query: 480 PQNSYKDKLEGLLGGQELIVGADGTISSFELGAGQVAVWTYEGEDKTPQLGDVDASVGIA 53- 9 P +Y D L GLL G + V +DG+++ F L AG+VAVW Y +P +G V ++ A Sbjct: 479 PAGTYTDVLGGLLNGNSISVASDGSVTPFTLSAGEVAVWQYVSSSNSPLIGHVGPTMTKA 53- 8 Query: 540 GNKITISGQGFGNSKGQVTFGEISAEILSWSDTLITLKVPTVPANYYNISVTTADKQTSN 59- 9 G ITI G+GFG + GQV FG + I+SW DT + +KVP+V YNIS+ T+ TSN Sbjct: 539 GQTITIDGRGFGTTSGQVLFGSTAGTIVSWDDTEVKVKVPSVTPGKYNISLKTSSGATSN 59- 8 Query: 600 SYQAFEVLTDKQIPVRLLINDFKTVPGEQLYLMGDVFEMGANDAKNAVGPLFNNTQTIAK 65- 9 +Y +LT QI VR ++N+ TV GE +YL G+V E+G D A+GP+FN Q + + Sbjct: 599 TYNNINILTGNQICVRFVVNNASTVYGENVYLTGNVAELGNWDTSKAIGPMFN--QVVYQ 65- 6 Query: 660 YPNWFFDTHLPINKEIAVKLVKKDSIGNVLWT--SPETYSIKTGHEAQTI 707 YP W++D +P I K +KK+ + W S TY++ + I Sbjct: 657 YPTWYYDVSVPAGTTIQFKFIKKNG-NTITWEGGSNHTYTVPSSSTGTVI 705 An alignment of the GAS and GBS proteins is shown below:

TABLE-US-01212 Identities = 112/509 (22%), Positives = 193/509 (37%), Gaps = 103/509 (20%) Query: 18 GNHWKKLEESISD--LKKLGISKIWLPPAFKGTSSDDV--------GYGVYDLFDLGEFD 67 - G W+ + I D L +GIS IW+ + S D GY D F + Sbjct: 79 GGDWQGIIAKIKDGYLTDMGISAIWISSPVENIDSIDPSNGSAAYHGYWAKDFFKTNQH- 137- Query: 68 QNGTIRTKYGRKEEYLKLIKSLKANGIKPFADIVLNHKANGDHKEKFQVIKVNPENRQEA 127- +G + ++ +L+K + IK D NH + + + Sbjct: 138 --------FGTEADFQQLVKVAHQHHIKVVIDFAPNHTSTAEKE---------------- 17- 3 Query: 128 LSEPYEIEGWTGFDFPGRQGEYNDFKWHWYHFTGLDYDAKNNETDIFMIVGDNKGWADDD 18- 7 G F Y + K G D K+ + +++ W D Sbjct: 174 -----------GTTFKEDGALYKNGK-----LVGKFSDDKDK-------IFNHESWTDFS 21- 0 Query: 188 LIDDE--NGNFDYLMYNDIDFKHPEVIKNLQDWAKWFIETTGIEGFRLDAVKHIDSYFIQ 24- 5 ++ + + N+I+ K + +K D KW G++G R+DAVKH+ + + Sbjct: 211 TYENSIYHSMYGLADLNNINPKVDQYMKEAID--KWL--DLGVDGIRVDAVKHMSQGWQK 26- 6 Query: 246 TFINDIRTKIKPDLEVFGEYWKSDQTSMKDYLEATQFQFSLVDVTLHMNFFDASHQ-NRD 30- 4 +++ I K ++ VFGE W S T D + T F + L F +A Q Sbjct: 267 NWLSHIYE--KHNVFVFGE-WFSGHTD--DDYDMTTFANNSGMGLLDFRFANAIRQLYTG 32- 1 Query: 305 FDMRTIFDDSLVIDNPEYA-------VTFVENHDTQSGQALESRVEDWFKPLAYGLILLR 35- 7 F T+ D V++N + VTF++NHD + + + AY L LL Sbjct: 322 FSTFTMRDFYKVLENRDQVTNEVTDQVTFIDNHDMERFATKVANNQTAVNQ-AYAL-LLT 37- 9 Query: 358 QQGTPCLFYGDYYGIQGE------FGQPSFK------EVIDKMAELR---QNYVFGKQVD 40- 2 +G P ++YG G+ PSF +VI K+A LR Q +G Sbjct: 380 SRGVPNIYYGTEQYATGDKDPNNRGDMPSFNKESQAYKVISKLAPLRKQNQALAYGTTEQ 43- 9 Query: 403 YFTHSNCIGWTCLGDEEHNSCLAVVLTWGDQ--GWKHMEVGEIYAGKTFVDYLGNC--EQ 45- 8 + + + + + + + +A+V N DQ G+ ++ D L Q Sbjct: 440 RWISDHVL----VFERKFGNHVALVAINRDQTNGYTITNAKTALPQNSYKDKLEGLLGGQ 49- 5 Query: 459 EVVIGDDGW-GDFLVESASISAWVPKIEE 486 E+++G DG F + + ++ W + E+ Sbjct: 496 ELIVGADGTISSFELGAGQVAVWTYEGED 524 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 375 A DNA sequence (GBSx0406) was identified in S. agalactiae <SEQ ID 1225> which encodes the amino acid sequence <SEQ ID 1226>. This protein is predicted to be catabolite control protein A. Analysis of this protein sequence reveals the following: TABLE-US-01213 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2154(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9707> which encodes amino acid sequence <SEQ ID 9708> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01214 >GP: BAA88121 GB: AB028599 catabolite control protein A [Streptococcus bovis] (ver 3) Identities = 304/332 (91%), Positives = 320/332 (95%) Query: 1 MNTDDTITIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARGLA 60 MNTDDTITIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARGLA Sbjct: 1 MNTDDTITIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARGLA 60 Query: 61 SKKTTTVGVVIPNIANSYFSILARGIDDIAAMYKYNIVLASSDEDDDKEVNVVNTLFAKQ 120- SKKTTTVGVVIPNIANSYFSILA+GIDDIAAMYKYNIVLASSDEDDDKEVNVVNTLFAKQ Sbjct: 61 SKKTTTVGVVIPNIANSYFSILAKGIDDIAAMYKYNIVLASSDEDDDKEVNVVNTLFAKQ 120- Query: 121 VDGIIFMGHHLTEKIRAEFSRSRTPIVLAGTVDLEHQLPSVNIDYKAAAVDVIDILAGNH 18- 0 VDGIIFMGHHLTEKIRAEFSRSRTP+VLAGTVDLEHQLPSVNIDYKAA DV+DILA N+ Sbjct: 121 VDGIIFMGHHLTEKIRAEFSRSRTPVVLAGTVDLEHQLPSVNIDYKAAVADVVDILAKNN 18- 0 Query: 181 KDIAFVSGPLIDDINGKVRLAGYKEGLKKNGLNFKEGLVFEANYRYAEGFALAQRVINAG 24- 0 KDIAFVSGPLIDDINGKVRLAGYKEGL+KN L+FKEGLVFEANY Y +G+ LAQRV+N+G Sbjct: 181 KDIAFVSGPLIDDINGKVRLAGYKEGLEKNNLSFKEGLVFEANYNYKDGYELAQRVMNSG 24- 0 Query: 241 ATAAYVAEDELAAGLLNGLFEAGKRVPEDFEIITSNDSPIAQYTRPNLTSISQPVYDLGA 30- 0 ATAAYVAEDELAAGLLNGLF AGK+VPEDFEI+TSNDSPI YTRPNL+SISQPVYDLGA Sbjct: 241 ATAAYVAEDELAAGLLNGLFAAGKKVPEDFEILTSNDSPITSYTRPNLSSISQPVYDLGA 30- 0 Query: 301 VSMRMLTKIMHKEELEEKEIVLNHGIVKRGTT 332 VSMRMLTKIM+KEELEEKEI+LNHG+ RGTT Sbjct: 301 VSMRMLTKIMNKEELEEKEIILNHGLKLRGTT 332 A related DNA sequence was identified in S. pyogenes <SEQ ID 1227> which encodes the amino acid sequence <SEQ ID 1228>. Analysis of this protein sequence reveals the following: TABLE-US-01215 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2154(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01216 Identities = 307/332 (92%), Positives = 320/332 (95%) Query: 1 MNTDDTITIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARGLA 60 MNTDD +TIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARGLA Sbjct: 1 MNTDDPLTIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARGLA 60 Query: 61 SKKTTTVGVVIPNIANSYFSILARGIDDIAAMYKYNIVLASSDEDDDKEVNVVNTLFAKQ 120- SKKTTTVGVVIPNIANSYFSILA+GIDDIAAMYKYNIVLASSDEDDDKEVNVVNTLFAKQ Sbjct: 61 SKKTTTVGVVIPNIANSYFSILAKGIDDIAAMYKYNIVLASSDEDDDKEVNVVNTLFAKQ 120- Query: 121 VDGIIFMGHHLTEKIRAEFSRSRTPIVLAGTVDLEHQLPSVNIDYKAAAVDVIDILAGNH 18- 0 VDGIIFMGHHLTEKIRAEFSRSRTP+VLAGTVDL+HQLPSVNIDY+AA +V+DILA NH Sbjct: 121 VDGIIFMGHHLTEKIRAEFSRSRTPVVLAGTVDLDHQLPSVNIDYRAAVSNVVDILAENH 18- 0 Query: 181 KDIAFVSGPLIDDINGKVRLAGYKEGLKKNGLNFKEGLVFEANYRYAEGFALAQRVINAG 24- 0 K IAFVSGPLIDDINGKVRLAGYKEGLK N L+FKEGLVFEANY Y EGF LAQRVIN+G Sbjct: 181 KCIAFVSGPLIDDINGKVRLAGYKEGLKHNKLDFKEGLVFEANYSYKEGFELAQRVINSG 24- 0 Query: 241 ATAAYVAEDELAAGLLNGLFEAGKRVPEDFEIITSNDSPIAQYTRPNLTSISQPVYDLGA 30- 0 ATAAYVAEDELAAGLLNGLFEAGKRVPEDFEIITSNDSP+ QYTRPNL+SISQPVYDLGA Sbjct: 241 ATAAYVAEDELAAGLLNGLFEAGKRVPEDFEIITSNDSPVVQYTRPNLSSISQPVYDLGA 30- 0 Query: 301 VSMRMLTKIMHKEELEEKEIVLNHGIVKRGTT 332 VSMRMLTKIM+KEELEEKEI+LNHGI KRGTT Sbjct: 301 VSMRMLTKIMNKEELEEKEILLNHGIKKRGTT 332 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 376 A DNA sequence (GBSx0407) was identified in S. agalactiae <SEQ ID 1229> which encodes the amino acid sequence <SEQ ID 1230>. This protein is predicted to be PepQ (pepQ-2). Analysis of this protein sequence reveals the following: TABLE-US-01217 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1118(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01218 >GP:AAC46293 GB:AF014460 PepQ [Streptococcus mutans] Identities = 257/359 (71%), Positives = 304/359 (84%) Query: 1 MSKLNRIRHHLHSVQAELAVFSDPVTVNYLTGFFCDPHERQMFLFVYEDRDPILFVPALE 60 MSKL +I L E AV SDPV++NYLTGF+ DPHER MFLF++ D++ +LF+P L+ Sbjct: 1 MSKLAQIVQKLKKQGIEAAVLSDPVSINYLTGFYSDPHERLMFLFLFADQETLLFLPELD 60 Query: 61 VSRAKQSVPFPVFGYIDSENPWQKIASNLPSFSVSKVLAEFDNLNVTKFQGLQTVFDGHF 120- RAK + V GY+D ENP +KI + LP + SK+ EFDNLNVTKF+GL+T+F G F Sbjct: 61 ALRAKSILDISVTGYLDFENPLEKIKTLLPKTNYSKIALEFDNLNVTKFKGLETIFSGQF 120- Query: 121 ENLTPYIQNMRLIKSRDEIEKNLVAGEFADKAVQVGFDNISLNNTETDIIAQIEFEMKKQ 18- 0 NLTP I MRLIKS DEI+K+L+AGE ADKAVQ+GFD+ISLN TETDIIAQIEFEMKK Sbjct: 121 TNLTPLINRNRLIKSADEIQKLLIAGELADKAVQIGFDSISLNATETDIIAQIEFEMKKL 18- 0 Query: 181 GINKNSFDTMVLTGNNAANPHGIPGTNKIENNALLLFDLGVETLGYTSDMTRTVAVGKPD 24- 0 G++KMSF+TMVLTG+NAANPHG+P ++KIENN LLLFDLGVE+ GY SDMTRTVAVG+PD Sbjct: 181 GVDKMSFETNVLTGSNAANPHGLPASHKIENNHLLLFDLGVESTGYVSDMTRTVAVGQPD 24- 0 Query: 241 QFKKDIYHLCLEANQAAIDFIKPGVLASEVDAAARNVIEKAGYGQYFNHRLGHGLGMDVH 30- 0 QFKKDIY++CLEA A+DFIKPGV A++VDAAAR+VIEKAGYG YFNHRLGHG+GM +H Sbjct: 241 QFKKDIYNICLEAQLTALDFIKPGVSAAQVDAAARSVIEKAGYGDYFNHRLGHGIGMGLH 30- 0 Query: 301 EFPSIMAGNDMEIQEGMCFSVEPGIYIPDKVGVRIEDCGYVTKTGFEVFTKTPKELLYF 359- EFPSIMAGNDM ++EGMCFSVEPGIYIP+KVGVRIEDCG+VTK GFEVFT+TPKELLYF Sbjct: 301 SFPSIMAGNDMLLEEGMCFSVEPGIYIPSKVGVRIEDCGHVTKNGFEVFTQTPKELLYF 359- A related DNA sequence was identified in S. pyogenes <SEQ ID 1231> which encodes the amino acid sequence <SEQ ID 1232>. Analysis of this protein sequence reveals the following: TABLE-US-01219 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.90 Transmembrane 42-58 (42-59) ----- Final Results ----- bacterial membrane --- Certainty = 0.1362(Atfirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01220 >GP:AAC46293 GB:AF014460 PepQ [Streptococcus mutans] Identities = 264/359 (73%) , Positives = 304/359 (84%) Query: 1 MTKLDQIRLYLDQKGAELAIFSDPVTINYLTGFFCDPHERQLFLFVYHDLAPVLFVPALE 60 M+KL QI L ++G S A+ SDPV+INYLTGF+ DPHER +FLF++ D +LF+P L+ Sbjct: 1 MSKLAQIVQKLKKQGIEAAVLSDPVSINYLTGFYSDPHERLMFLFLFADQETLLFLPELD 60 Query: 61 VARASQAISFPVFGYVDSENPWEKIKAVLPNTAAKTIYAEFDHLNVNKFHGLQTIFSGQF 120- RA + V GY+D ENP EKIK +LP T+ I EFD+LNV KF GL+TIFSGQF Sbjct: 61 ALRAKSILDISVTGYLDFENPLEKIKTLLPSTNYSKIALEFDNLNVTKFKGLETIFSGQF 120- Query: 121 NNLTPYVQGMRLVKSADEINKMMIAGQFADKAVQVGFDNISLDATETDVIAQIEFEMKKQ 18- 0 NLTP + MRL+KSADEI K++IAG+ ADKAVQ+GFD+ISL+ATETD+IAQIEFEMKK Sbjct: 121 TNLTPLINRMRLIKSADEIQKLLIAGELADKAVQIGFDSISLHATETDIIAQIEFEMKKL 18- 0 Query: 181 GIHKMSFDTMVLTGNNAANPHGIPGTNNIENNALLLFDLGVETLGYTSDMTRTVAVGQPD 24- 0 G+ KMSF+TMVLTG+NAANPHG+P ++ IENN LLLFDLGVE+GY SDMTRTVAVGQPD Sbjct: 181 GVDKMSFETMVLTGSNAANPHGLPASHKIENNHLLLFDLGVESTGYVSDMTRTVAVGQPD 24- 0 Query: 241 QFKIDIYNLCLSAQLAAIDFIKPGVTAAQVDAAARQVIEKAGYGEYFNHRLGHGIGMDVH 30- 0 QFK DIYN+CLEAQL A+DFIKPGV+AAQVDAAAR VIEKAGYG+YFNHRLGHGIGM +H Sbjct: 241 QFKKDIYNICLEAQLTALDFIKPGVSAAQVDAAARSVIEKAGYGDYFNHRLGHGIGMGLH 30- 0 Query: 301 EFPSIMAGNDLVLEEGMCFSVEPGIYIPGKVGVRIEDCGHVTKNGFEVFTHTPKELLYF 359- EFPSIMAGND++LEEGMCFSVEPGIYIP KVGVRIEDCGHVTKNGFEVFT TPKELLYF Sbjct: 301 EFPSIMAGNDMLLEEGMCFSVEPGIYIPEKVGVRIEDCGHVTKNGFEVFTQTPKELLYF 359- An alignment of the GAS and GBS proteins is shown below: TABLE-US-01221 Identities = 288/361 (79%), Positives = 325/361 (89%) Query: 1 MSKLNRIRHHLHSVQAELAVFSDPVTVNYLTGFFCDPHERQMFLFVYEDRDPILFVPALE 60 M+KL++IR +L AELA+FSDPVT+NYLTGFFCDPHERQ+FLFVY D P+LFVPALE Sbjct: 1 MTKLDQIRLYLDQKGAELAIFSDPVTINYLTGFFCDPHERQLFLFVYHDLAPVLFVPALE 60 Query: 61 VSRAKQSVPFPVFGYIDSENPWQKIASNLPSFSVSKVLAEFDNLNVTKFQGLQTVFDGHF 120- V+RA Q++ FPVFGY+DSENPW+KI + LP+ + + AEFD+LNV KF GLQT+F G F Sbjct: 61 VARASQAISFPVFGYVDSENPWEKIKAVLPNTAAKTIYAEFDHLNVNKFHGLQTIFSGQF 120- Query: 121 ENLTPYIQNMRLIKSRDEIEKMLVAGEFADKAVQVGFDNISLNNTETDIIAQIEFEMKKQ 18- 0 NLTPY+Q MRL+KS DEI KM++AG+FADKAVQVGFDNISL+ TETD+IAQIEFEMKKQ Sbjct: 121 NNLTPYVQGMRLVKSADEINKMMIAGQFADKAVQVGFDNISLDATETDVIAQIEFEMKKQ 18- 0 Query: 181 GINKMSFDTMVLTGNNAANPHGIPGTNKIENNALLLFDLGVETLGYTSDMTRTVAVGKPD 24- 0 GI+KMSFDTMVLTGNNAANPHGIPGTN IENNALLLFDLGVETLGYTSDMTRTVAVG+PD Sbjct: 181 GIHKMSFDTMVLTGNNAANPHGIPGTNNIENNALLLFDLGVETLGYTSDMTRTVAVGQPD 24- 0 Query: 241 QFKKDIYHLCLEAHQAAIDFIKPGVLASEVDAAARNVIEKAGYGQYFNHRLGHGLGMDVH 30- 0 QFK DIY+LCLEA AAIDFIKPGV A++VDAAAR VIEKAGYG+YFNHRLGHG+GMDVH Sbjct: 241 QFKIDIYNLCLEAQLAAIDFIKPGVTAAQVDAAARQVIEKAGYGEYFNHRLGHGIGMDVH 30- 0 Query: 301 EFPSIMAGNDMEIQEGMCFSVEPGIYIPDKVGVRIEDCGYVTKTGFEVFTKTPKELLYFEG 3- 61 EFPSIMAGND+ ++EGMCFSVEPGIYIP KVGVRIEDCG+VTK GFEVFT TPKELLYFEG Sbjct: 301 EFPSIMAGNDLVLEEGMCFSVEPGIYIPGKVGVRIEDCGHVTKNGFEVFTHTPKELLYFEG 3- 61 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 377 A DNA sequence (GBSx0408) was identified in S. agalactiae <SEQ ID 1233> which encodes the amino acid sequence <SEQ ID 1234>. Analysis of this protein sequence reveals the following: TABLE-US-01222 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3629(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 378 A DNA sequence (GBSx0409) was identified in S. agalactiae <SEQ ID 1235> which encodes the amino acid sequence <SEQ ID 1236>. This protein is predicted to be beta-hexosamidase A precursor. Analysis of this protein sequence reveals the following: TABLE-US-01223 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3279(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01224 >GP:CAB11942 GB:Z99104 alternate gene name: yzbA~similar to beta-hexosaminidase [Bacillus subtilis] Identities = 151/602 (25%), Positives = 268/602 (44%), Gaps = 69/602 (11%) Query: 26 INEMTLDEKIGQLF------FNMGASRSEEYLTDVLDRYHIAAVRYNRGSSSEIYDQNL- 78 - +N M+LDEK+GQ+ + S + LT + D +Y G ++ +N+ Sbjct: 39 VNRMSLDEKLGQMLMPDFRNWQKEGESSPQALTKMNDEVASLVKKYQFGGII-LFAENVK 97 Query: 79 -----------ILQTKSKLPMLIAANTEAGGDGAVTDGTKVGDEIKVAATNDPKYAYEMG 127- + K+P++++ + E G + +GT + + A AY+ G Sbjct: 98 TTKQTVQLTDDYQKASPKIPLMLSIDQEGGIVTRLGEGTNFPGNMALGAARSRINAYQTG 157- Query: 128 RIAGMEASAVGCNASFSPIVDLTRNWRNPIIASRNWGANVDQIISLSKEYMKGIMQYNIV 18- 7 I G E SA+G N FSP+VD+ N NP+I R++ +N + L MKG+ + +I Sbjct: 158 SIIGKELSALGINTDFSPVVDINNNPDNPVIGVRSFSSNRELTSRLGLYTMKGLQRQDIA 21- 7 Query: 188 PFAKHFPGDGIDERDHHLSFASNPMSKEEWMSTFGRIYGELADAGLPGVMAGHIHLPNVE 24- 7 KHFPG G + D H +E + + DAG VM H+ P + Sbjct: 218 SALKHFPGHGDTDVDSHYGLPLVSHGQERLREVELYPFQKAIDAGADMVMTAHVQFPAFD 27- 7 Query: 248 KEMHPER--DLDDMLPASLNKTLLDELLRGELGYNGAIVTDASHMVGMTASMARRDLLPT 30- 5 + + D ++PA+L+K ++ LLR E+G+NG IVTDA +M + + + + Sbjct: 278 DTTYKSKLDGSDILVPATLSKKVMTGLLRQEMGFNGVIVTDALNMKAIADHFGQEEAVVM 33- 7 Query: 306 AIEAGCDLFLF---FNDPDED------IQWMKEGYEKGILTEERLHDALRRTLGLKAKLG 35- 6 A++AG D+ L E+ IQ+ KE + G+ E+++++++ R + LK K G Sbjct: 338 AVKAGVDIALMPASVTSLKEEQKFARVIQALKEAVKNGDIPEQQINNSVERIISLKIKRG 39- 7 Query: 357 LHNYEGRRQELFMPK-DKAMALINTLESQKIADEVADKAVTLVKDKQKDIFPVNPERYRH 41- 5 + Y R + K KA ++ + + K ++A+KAVT++K++Q + P P++ Sbjct: 398 M--YPARNSDSTKEKIAKAKKIVGSKQHLKAEKKLAEKAVTVLKNEQHTL-PFKPKKGSR 45- 4 Query: 416 ILLVNVSGYKGGFGAMIAGNKQRASDYMKE------LLEARGHEVTVWESTEERIMKLPQ 46- 9 IL+V + A +Q D +K L V+++ E+ +K Sbjct: 455 ILIV------APYEEQTASIEQTIHDLIKRKKIKPVSLSKMNFASQVFKTEHEKQVK--- 50- 5 Query: 470 EERAAAIANVYAQK-QPIANLTEHYDLIINLVDVNAGGTTQRIIWPAAKGTPDQPFYVHE 52- 8 E I Y K P+ N D +I+ D + + ++P A + H Sbjct: 506 -EADYIITGSYVVKNDPVVN-----DGVID--DTISDSSKWATVFPRA---VMKAALQHN 55- 4 Query: 529 IPSIVISVQHAFALADMPQVGTYINAYD--------GLPSTISAVVAKLAGESEFTGVSP 58- 0 P +++S+++ + A+ + I Y L I A V + G+++ G P Sbjct: 555 KPFVLMSLRNPYDAANFEEAKALIAVYGFKGYANGRYLQPNIPAGVMAIFGQAKPKGTLP 61- 4 Query: 581 VD 582 VD Sbjct: 615 VD 616 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8565> and protein <SEQ ID 8566> were also identified. Analysis of this protein sequence reveals the following homology to a lipoprotein, with homology with the following sequences in the databases: ##STR00032## SEQ ID 1236 (GBS50) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 11 (lane 8; MW 69.2 kDa). GBS50-His was purified as shown in FIG. 192, lane 5. The GBS50-His fusion product was purified (FIG. 192, lane 5) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 264), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 379 A DNA sequence (GBSx0410) was identified in S. agalactiae <SEQ ID 1237> which encodes the amino acid sequence <SEQ ID 1238>. Analysis of this protein sequence reveals the following:

TABLE-US-01225 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2266(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 380 A DNA sequence (GBSx0411) was identified in S. agalactiae <SEQ ID 1239> which encodes the amino acid sequence <SEQ ID 1240>. Analysis of this protein sequence reveals the following: TABLE-US-01226 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2279(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9705> which encodes amino acid sequence <SEQ ID 9706> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01227 >GP:AAC21726 GB:U32690 oxidoreductase [Haemophilus influenzae Rd] Identities = 197/271 (72%), Positives = 229/271 (83%) Query: 26 NKVVVITGAGGVLCGYMAKEFAKAGAKVALLDLNQEAAQTFADEIVEEGGIAKAYKANVL 85 - NK+++ITGAGGVLC ++AK+ A A +ALLDLN EAA A EI + GG AKAYK NVL Sbjct: 15 NKLIIITGAGGVLCSFLAKQLAYTKANIALLDLNFEAADKVAKEINQSGGKAKAYKTNVL 74 Query: 86 SKENLEEVHQAVLEDLGPTDILVNGAGGNNPKATTDNEFHELDLPSETKTFFELDEAGIS 145- EN++EV + D G DIL+NGAGGNNPKATTDNEFH+ DL T+TFF+LD++GI Sbjct: 75 ELENIKEVRNQIETDFGTCDILINGAGGNNPKATTDNEFHQFDLNETTRTFFDLDKSGIE 134- Query: 146 FVFNLNYLGTLLPTQVFAQDMVGREGANIINISSMNAFTPLTKIPAYSGAKAAISNFTQW 20- 5 FVFNLNYLG+LLPTQVFA+DM+G++GANIINISSMNAFTPLTKIPAYSGAKAAISNFTQW Sbjct: 135 FVFNLNYLGSLLPTQVFAKDMLGKQGANIINISSMNAFTPLTKIPAYSGAKAAISNFTQW 19- 4 Query: 206 LAVHFSKVGIRCNAIAFGFLVTNQNRSLLFTEDGQPTARAEKILNNTPMGRFGEASELIG 26- 5 LAV+FSKVGIRCNAIAPGFLV+NQN +LLF +G+PT RA KIL NTPMGRFGE+ EL+G Sbjct: 195 LAVYFSKVGIRCNAIAPGFLVSNQNLALLFDTEGKPTDRANKILTNTPMGRFGESEELLG 25- 4 Query: 266 GLFFLADEKSSSFVNGVVLPIDGGFAAYSGV 296 L FL DE S+FVNGVVLP+DGGF+AYSGV Sbjct: 255 ALLFLIDENYSAFVNGVVLPVDGGFSAYSGV 285 A related DNA sequence was identified in S. pyogenes <SEQ ID 1241> which encodes the amino acid sequence <SEQ ID 1242>. Analysis of this protein sequence reveals the following: TABLE-US-01228 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0358(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01229 Identities = 77/279 (27%), Positives = 125/279 (44%), Gaps = 19/279 (6%) Query: 18 MSKTITFTNKVVVITGAGGVLCGYMAKEFAKAGARVALLDLNQEAAQTFADEIVEEGGIA 77 - M + K+ +ITGA + +AK +A+AGA + D+ QE E G A Sbjct: 1 MENMFSLQGKIALITGASYGIGFEIAKAYAQAGATIVFNDIKQELVDKGLAAYRELGIEA 60 Query: 78 KAYKANVLSKENLEEVHQAVLEDLGPTDILVNGAGGNNPKATTDNEFHELDLPSETKTFF 137- Y +V + ++++ + +++G DILVN AG Sbjct: 61 HGYVCDVTDEAGIQQMVSQIEDEVGAIDILVNNAG-----------------IIRRTPML 103- Query: 138 ELDEAGISFVFNLNYLGTLLPTQVFAQDMVGREGANIINISSMNAFTPLTKIPAYSGAKA 19- 7 E+ V +++ + ++ M+ + IINI SM + + AY+ AK Sbjct: 104 EMAAEDFRQVIDIDLMAPFIVSKAVLPSMIAKGHGKIINICSMMSELGRETVSAYAAAKG 16- 3 Query: 198 AISNFTQWLAVHFSKVGIRCNAIAPGFLVTNQNRSLLFTE-DGQPTARAEKILNNTPMGR 25- 6 + T+ +A F + I+CN I PG++ T Q L + DG + I+ TP R Sbjct: 164 GLKNLTKNIASEFGEANIQCNGIGPGYIATPQTAPLRERQADGSRHPFDQFIIAKTPAAR 22- 3 Query: 257 FGEASELIGGLFFLADEKSSSFVNGVVLPIDGGFAAYSG 295 +G +L G FLA + +S+FVNG +L +DGG AY G Sbjct: 224 WGTTEDLAGPAVFLASD-ASNFVNGHILYVDGGILAYIG 261 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 381 A DNA sequence (GBSx0412) was identified in S. agalactiae <SEQ ID 1243> which encodes the amino acid sequence <SEQ ID 1244>. This protein is predicted to be D-mannonate dehydrolase (uxuA). Analysis of this protein sequence reveals the following: TABLE-US-01230 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3188(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01231 >GP:BAB04425 GB:AP001509 D-mannonate dehydrolase [Bacillus halodurans] Identities = 202/343 (58%), Positives = 261/343 (75%) Query: 1 MEMSFRWYGEDDPVTLENIGQIPTMKGIVTAIYDVPVGEVWSRERIQQLKEKVEAAGLKI 60 M ++ RW+G D V LE I QIP MKGIV+AIYDV VG VW +E+I LK +E GL + Sbjct: 1 MRLTMRWFGPSDKVKLEYIKQIPGMKGIVSAIYDVAVGGVWPKEKILALKNNIERHGLTL 60 Query: 61 SVIESVPVHEDIKLGRPTRDLLIDNYIQTVKNLAAEGIDTICYNFMPVFDWTRTDLAYQY 120- VIESVPVHEDIKLG+PTRD I+NY QT+++LA GIDT+CYNFMPVFDWTR+ L ++ Sbjct: 61 DVIESVPVHEDIKLGKPTRDRYIENYKQTLRHLAECGIDTVCYNFMPVFDWTRSQLDFKL 120- Query: 121 PDGSTALIFDETVSKKMDPVNGELSLPGWDASYSKEEMKAIMDAYAEIDEEKLWENLTYF 18- 0 DGS ALI++E V + +P++GEL LPGWD SY E +K ++ AY +I EE LW++LTYF Sbjct: 121 EDGSEALIYEEDVISRTNPLSGELELPGWDTSYENESLKGVLQAYKKISEEDLWDHLTYF 18- 0 Query: 181 IKRIIPEAEAVGVKMAIHPDDPPYSIFGLPRIITGLEAIERFVKLYDSKSNGITLCVGSY 24- 0 ++ I+P A+ VG+KMAIHPDDPP+SIFGLPRI+T +ER + LYDS ++GIT+C GS Sbjct: 181 VQAIMPVADEVGIKMAIHPDDPPWSIEGLPRIVTNKANLERLLSLYDSPNHGITMCSGSL 24- 0 Query: 241 ASDPQNDVLEISRRAFELDRVNFVHARNIKLGDGKSFKESAHPSEYGSIDMYEVIKLCHE 30- 0 ++ ND+ E+ R R++F HARNIK +SF+ESAH SE GS++M ++K H+ Sbjct: 241 GANEANDLPEMIRHFGGQGRIHFAHARNIKRTGPRSFQESAHLSEAGSVNMVAMLKAYHD 30- 0 Query: 301 FGFEGAIRPDHGRMIWGETGRPGYGLYDRALGATYVSGLYEAV 343 GF G +RPDHGRMIWGE GRPGYGLYDRALGATY++G++EAV Sbjct: 301 IGFTGPLRPDHGRMIWGEKGRPGYGLYDRALGATYLNGIWEAV 343 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 382 A DNA sequence (GBSx0413) was identified in S. agalactiae <SEQ ID 1245> which encodes the amino acid sequence <SEQ ID 1246>. Analysis of this protein sequence reveals the following: TABLE-US-01232 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2447(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 383 A DNA sequence (GBSx0414) was identified in S. agalactiae <SEQ ID 1247> which encodes the amino acid sequence <SEQ ID 1248>. This protein is predicted to be uronate isomerase. Analysis of this protein sequence reveals the following: TABLE-US-01233 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3066(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01234 >GP:BAB04424 GB:AP001509 uronate isomerase [Bacillus halodurans] Identities = 215/465 (46%), Positives = 294/465 (62%), Gaps = 7/465 (1%) Query: 3 FNTETFMLKNQAAIQLYEE-VKRQPIFDYHCHLDPKDIFEDHIFDNIVDLWLGGDHYKWR 61 F +E F+L N+ +LY K PI DYHCHL P++I+E+ F+N+ WLGGDHYKWR Sbjct: 4 FLSEDFLLMNEYDRELYYTFAKNMPICDYHCHLSPQEIWENKPFENMTKAWLGGDHYKWR 63 Query: 62 LMRANGISEAEITGPASNLEKFKAFARTLERAYGNPVYHWSAMELKNVFGVNEILTESNA 121- MR NG+ E ITG A + KF A+A+T+ + GNP+YHW+ MELK F ++ L E+N Sbjct: 64 AMRLNGVREEFITGGAPDKEKFLAWAKTVPKTIGNPLYHWTHMELKTYFHFHQPLDETNG 123- Query: 122 EEIYHRLNHFLKEHKISPRRLIADSKVMFIGTTDHPLDTLEWHKKLAADESFKTVVAPTF 18- 1 E ++ N L++ +PR LI S V IGTTD P D+L +H+KL AD++F V PTF Sbjct: 124 ENVWDACNRLLQQEAFTPRALIERSNVRAIGTTDDPTDSLLYHQKLQADDTFHVKVIPTF 18- 3 Query: 182 RPDEAF-IEHRHFVDFITKLGDITQKEITDFSTFIAAMEERIAYFAQNGCRASDISFTEI 24- 0 RPD A IE F D++ KL D+T + + F+ A++ER+ +F ++GCR+SD TE+ Sbjct: 184 RPDGALKIEQDSFADWVAKLSDVTGESLDTLDAFLHALKERLTFFDEHGCRSSDHDMTEV 24- 3 Query: 241 VFEQTDELELNDLFNKVCEGYIPNQSEISKWQTAVFMELCRLYKKYGFVTQVHFGALRNN 30- 0 F + +E E +F K + E K++T + L + Y G+V Q H G +RNN Sbjct: 244 PFVEVNEQEAQHIFRKRLANEGLTKVENEKYKTFLMTWLGKEYAARGWVMQWHIGVMRNN 30- 3 Query: 301 HSTIFEKLGADVGVDSLGD-QVALTVNMNRLLDSLVKKDSLPKMIWYNLNPAYNIAVANT 35- 9 +S + KLG D G DS+GD Q+A +LLD L K+ +LPK I Y +NP N A+ Sbjct: 304 NSRMLHKLGPDTGFDSIGDGQIAHAT--AKLLDLLDKQGALPKTILYCVNPNANYILASM 36- 1 Query: 360 LANFQANELGVRSYLQFGAGWWFADTKLGMISQMNALAEQGMLANFIGMLTDSRSFLSYQ 41- 9 + NF E GVR +QFG+ WWF D GM Q+ LA G+L+NFIGMLTDSRSFLSY Sbjct: 362 IGNF-TESGVRGKVQFGSAWWFNDHIDGMRRQLTDLASVGLLSNFIGMLTDSRSFLSYP 419- Query: 420 RHDYFRRILCTYLGEWIEEGEVPEDYQALGSMAKDIAYQNAVNYF 464 RHDYFRRILC +G WI+EG++P D + G + +DI Y N V+YF Sbjct: 420 RHDYFRRILCQLIGSWIKEGQLPPDMERWGQIVQDICYNNVVDYF 464 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 384 A DNA sequence (GBSx0415) was identified in S. agalactiae <SEQ ID 1249> which encodes the amino acid sequence <SEQ ID 1250>. This protein is predicted to be 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate al. Analysis of this protein sequence reveals the following: TABLE-US-01235 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3883(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9703> which encodes amino acid sequence <SEQ ID 9704> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01236 >GP:AAD35160 GB:AE001693 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase [Thermotoga maritima] Identities = 93/199 (46%), Positives = 125/199 (62%), Gaps = 6/199 (3%) Query: 37 KNNYFFAVIRGKSSEDALEIAKHAILGGIRNIEVTFSTPEASKVIKQLSDDFKNNKEIIV 96 - K + AV+R S E+A E A GG+ IE+TF+ P+A VIK+LS F K I+ Sbjct: 8 KKHKIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELS--FLKEKGAII 65 Query: 97 GAGTVMTTELAKEAIDAGAKFLVSPHFDSDIANLANENKVYYFPGCATATEIVVARKYKC 156- GAGTV + E ++A+++GA+F+VSPH D +I+ E V+Y PG T TE+V A K Sbjct: 66 GAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGH 125- Query: 157 QIIKLFPGGVVGPGFIKDIHGPIPDVDLMPSGGVSVSNVVEWRKAGAVAVGVGSALSSKV 21- 6 I+KLFPG VVGP F+K + GP P+V +P+GGV++ NV EW KAG +AVGVGSAL Sbjct: 126 TILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGT 18- 5 Query: 217 ATEGYDSVTKIAKQFVSAL 235 D V + AK FV + Sbjct: 186 P----DEVREKAKAFVEKI 200 A related DNA sequence was identified in S. pyogenes <SEQ ID 1251> which encodes the amino acid sequence <SEQ ID 1252>. Analysis of this protein sequence reveals the following: TABLE-US-01237 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1039(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01238 Identities = 82/204 (40%), Positives = 132/204 (64%) Query: 32 MLNQLKNNYFFAVIRGKSSEDALEIAKHAILGGIRNIEVTFSTPEASKVIKQLSDDFKNN 91 - +L +LK N V+RG+SSE+AL + +I GGI+ IEVT++ P AS+VI QL++ FK + Sbjct: 6 ILTKLKANRLVLVVRGESSEEALACSLASIEGGIKTIEVTYTNPFASEVIGQLAERFKED 65 Query: 92 KEIIVGAGTVMTTELAKEAIDAGAKFLVSPHFDSDIANLANENKVYYFPGCATATEIVVA 151- E+++GAGTV+ A++AI AGA+F+V P+F+ +A + + + Y PGC T E+V A Sbjct: 66 PEVLIGAGTVLDDVTARQAILAGAQFIVGPNFNRAVALICHRYSIPYLPGCMTVNEVVTA 125- Query: 152 RKYKCQIIKLFPGGVVGPGFIKDIHGPIPDVDLMPSGGVSVSNVVEWRKAGAVAVGVGSA 21- 1 + ++K+FPG VG FI+ I P+P V++M +GGVS N+ +W AG +G+G Sbjct: 126 LESGVDMVKIFPGSTVGISFIRAIKSPLPQVEVMVTGGVSSDNLKDWLAAGVDVLGIGGE 18- 5 Query: 212 LSSKVATEGYDSVTKIAKQFVSAL 235 + + + Y+ +TK A ++ +L Sbjct: 186 FNQLASQKQYNLITKKAAHYIKSL 209 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 385 A DNA sequence (GBSx0416) was identified in S. agalactiae <SEQ ID 1253> which encodes the amino acid sequence <SEQ ID 1254>. This protein is predicted to be pyruvate dehydrogenase complex repressor. Analysis of this protein sequence reveals the following: TABLE-US-01239 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2827(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01240 >GP:CAB12044 GB:Z99105 similar to transcriptional regulator (GntR family) [Bacillus subtilis] Identities = 67/225 (29%), Positives = 119/225 (52%), Gaps = 17/225 (7%) Query: 3 RPLVEQTADRLLHLILEREYPVGAKLPNEYELAEDLDVGRSTIREAVRSLATRNILEVRQ 62 + L +Q +R++HL+ + G KLP E EL + L V R +REA+ SL T ++ + Sbjct: 16 KTLAKQVIERIVHLLSSGQLRAGDKLPTEMELMDILHVSRPVLREALSSLETLGVITRKT 75 Query: 63 GSGTYISSKKGVSEDPLGFSLIKDTDRLTSDLFELRLLLEPRIAELVAYRITDDQLQLLE 122- GTY + K G+ P L TD L + + E R+ LE + + A +I +++LQ L+ Sbjct: 76 RGGTYFNDKIGM--QPFSVMLALATDNLPA-IIEARMALELGLVTIAAEKINEEELQRLQ 132- Query: 123 KLVGDIEDAV--HAGDPKHLLLDVEFHSMLAKYSGNIAMDSLLPVINQSIHLINANYTNR 18- 0 K + DI ++ H G+ D EFH ++A + N ++ ++ QS+ + +A ++ Sbjct: 133 KTIDDIANSTDNHYGE-----ADKEFHRIIALSANNPVVEGMI----QSLLITHAKIDSQ 18- 3 Query: 181 ---QMKSDSLEAHREIIKAIREKNPVAAHDAMLMHIMSVRRSALK 222 + + ++E H++I A+ +++P AH M H+ VR LK Sbjct: 184 IPYRERDVTVEYHKKIYDALAQRDPYKAHYHMYEHLKFVRDKILK 228 A related DNA sequence was identified in S. pyogenes <SEQ ID 1255> which encodes the amino acid sequence <SEQ ID 1256>. Analysis of this protein sequence reveals the following: TABLE-US-01241 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2161(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01242 Identities = 24/51 (47%), Positives = 35/51 (68%) Query: 22 YPVGAKLPNEYELAEDLDVGRSTIREAVRSLATRNILEVRQGSGTYISSKK 72 +P+G++LP+E LAE V R T+R+A+ L ILE R GSGTY++S + Sbjct: 30 WPIGSRLPSERHLAEHFTVSRMTLRQAITLLVEEGILERRIGSGTYVASHR 80 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 386 A DNA sequence (GBSx0417) was identified in S. agalactiae <SEQ ID 1257> which encodes the amino acid sequence <SEQ ID 1258>. Analysis of this protein sequence reveals the following: TABLE-US-01243 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2178(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9701> which encodes amino acid sequence <SEQ ID 9702> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01244 >GP:CAA58911 GB:X84105 gluceronidase [synthetic construct] Identities = 258/602 (42%), Positives = 357/602 (58%), Gaps = 31/602 (5%) Query: 23 MLYPLLTKTRNTYDLGGIWNFKLGEHNPN-------ELLPSDEVMVIPTSFNDLMVSKEK 75 - ML P+ T TR L G+W F L N L + +P SFND + Sbjct: 1 MLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADI 60 Query: 76 RDYIGDFWYEKVIEVPKVSEDEEMVLRFGSVTHQAKIYVDGVLVGEHKGGFTPFEVLVPE 135- R+Y G+ WY++ + +PK + +VLRF +VTH K++V+ V EH+GG+TPFE V Sbjct: 61 RNYAGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVMEHQGGYTPFEADVTP 120- Query: 136 CKYNNEKIKVSICANNVLDYTTLPVGNYSEIIQEDGSIKKKVRENFDFFNYAGVHRPLKL 19- 5 + +++++C NN L++ T+P G I E+G KKK DFFNYAG+HR + L Sbjct: 121 YVIAGKSVRITVCVNNELNWQTIPPGMV--ITDENG--KKKQSYFHDFFNYAGIHRSVML 17- 6 Query: 196 MIRPKNHIFDITITSRLSDDLQSADLHFLVETNQKVDEVRISVFDEDNKLV--GETKDSR 25- 3 P + DIT+ + ++ D A + + V N +V + + D D ++V G+ Sbjct: 177 YTTPNTWVDDITVVTHVAQDCNHASVDWQVVAN---GDVSVELRDADQQVVATGQGTSGT 23- 3 Query: 254 LFLSDVHLWEVLNAYLYTARVEIFVDNQLQDVYEENFGLREIEVTNGQFLLNRKPIYFKG 31- 3 L + + HLW+ YLY V + D+Y G+R + V QFL+N KP YF G Sbjct: 234 LQVVNPHLWQPGEGYLYELCVTAKSQTEC-DIYPLRVGIRSVAVKGEQFLINHKPFYFTG 29- 2 Query: 314 FGKHEDTFINGRGLNEAANLMDLNLLKDMGANSFRTSHYPYSEEMMRLADRMGVLVIDEV 37- 3 FG+HED + G+G + + D L+ +GANS+RTSHYPY+EEM+ AD G++VIDE Sbjct: 293 FGRHEDADLRGKGFDNVLMVHDHALMDWIGANSYRTSHYFYAEEMLDWADEHGIVVIDET 35- 2 Query: 374 PAVGLFQNFNASLDLS------PKDNGTWNLM--QTKAAHEQAIQELVKRDKNHPSVVMW 42- 5 AVG FN SL + PK+ + + +T+ AH QAI+EL+ RDKNHPSVVMW Sbjct: 353 AAVG----FNLSLGIGFEAGNKPKELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVMW 40- 8 Query: 426 VVANEPASHEAGAHDYFEPLVKLYKDLDPQKRPVTLVNILMATPDRDQVMDLVDVVCLNR 48- 5 +ANEP + GA +YF PL + + LDP RP+T VN++ D + DL DV+CLNR Sbjct: 409 SIANEPDTRPQGAREYFAPLAEATRKLDPT-RPITCVNVMFCDAHTDTISDLFDVLCLNR 46- 7 Query: 486 YYGWYVDHGDLTNAEVGIRKELLEWQDKFPDKPIIITEYGADTLPGLHSTWNIPYTEEFQ 54- 5 YYGWYV GDL AE + KELL WQ+K +PIIITEYG DTL GLHS + ++EE+Q Sbjct: 468 YYGWYVQSGDLETAEKVLEKELLAWQEKL-HQPIIITEYGVDTLAGLHSMYTDMWSEEYQ 52- 6 Query: 546 CDFYEMSHRVFDGIPNLVGEQVWNFADFETNLMILRVQGNHKGLFSRNRQPKQVVKEFKK 60- 5 C + +M HRVFD + +VGEQVWNFADF T+ ILRV GN KG+F+R+R+PK +K Sbjct: 527 CAWLDMYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQK 58- 6 Query: 606 RW 607 RW Sbjct: 587 RW 588 A related DNA sequence was identified in S. pyogenes <SEQ ID 1259> which encodes the amino acid sequence <SEQ ID 1260>. Analysis of this protein sequence reveals the following:

TABLE-US-01245 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.04 Transmembrane 1131-1147 (1130-1147) ----- Final Results ----- bacterial membrane --- Certainty = 0.2614(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01246 >GP:AAF97242 GB:AF282987 beta-galactosidase precursor [Streptococcus pneumoniae] Identities = 303/921 (32%), Positives = 463/921 (49%), Gaps = 86/921 (9%) Query: 5 QKSSEIVT----RTITKPSRATSNVKQEIDMTPDSKEQTVTGYQYHYIDQ--EGRKQPFN 58 +K E VT + KP ++ + ++ ++Q E RK FN Sbjct: 96 KKEDEAVTPKEEKVSAKPEEKAPRIESQASNQEKPLKEDAKAVTNEEVNQMIEDRKVDFN 155- Query: 59 QGWRF-LMADVACAQDPSFDDSNWQVIHLPHDFSLTQPYTRNGEA--ESAYKLGGVGWYR 115- Q W F L A+ A P D S W+ + LP+D+S+ + A E GG WYR Sbjct: 156 QNWYFKLNANSKEAIKPDADVSTWKKLDLPYDWSIFNDFDHESPAQNEGGQLNGGEAWYR 21- 5 Query: 116 HYLVLDEVLAGCHVAITFEGSYMETEIYVNGQFIGKHLNGYQEFTYDISDVVTF-GAENL 17- 4 LDE +V +TF+G YM++++YVNGQ +G + NGY +F+YDI+ + G EN+ Sbjct: 216 KTFKLDEKDLKKNVRLTFDGVYMDSQVYVNGQLVGHYPNGYNQFSYDITKYLQKDGRENV 27- 5 Query: 175 LAVRVENKVPSSRWYSGSGLYREVSLSVLPQLHFVADQVAMTLADTAVQEKGQQKVDLRF 23- 4 +AV NK PSSRWYSGSG+YR+V+L V ++H + + Q+ G+ + + Sbjct: 276 IAVHAVNKQPSSRWYSGSGIYRDVTLQVTDKVHVEKNGTTILTPKLEEQQHGEVETHVTS 33- 5 Query: 235 ALNQSIQTCHYQLSLCLWEQSHCSKDKKLLYQETEVPLADLAFQRQYGLT--LSLEELQL 29- 2 + + H ++ E + + L L L +E +L Sbjct: 336 KIVNTDDKDHELVA----EYQIVERGGHAVTGLVRTASRTLKAHESTSLDAILSVERPKL 39- 1 Query: 293 WSP--DNPHLYDLELTLYYQGQVIDCFCLETGFRQLTFMANQGLFVNGRAVKLKGVCLHH 35- 0 W+ D P LY+L +Y GQ++D G+R + N+G +NG +K GV LHH Sbjct: 392 WTVLNDKPALYELITRVYRDGQLVDAKKDLFGYRYYHWTPNEGFSLNGERIKFHGVSLHH 45- 1 Query: 351 DQGGLGACAYEDALARQLVLLKDMGANTIRSTHNPSSPKLRQLANRLGFFVIEEAFDTWT 41- 0 D G LGA A R+L +K+MG N+IR+THNP+S + Q+A LG V EEAFDTW Sbjct: 452 DHGALGAEENYKAEYRRLKQMKEMGVNSIRTTHNPASEQTLQIAAELGLLVQEEAFDTWY 51- 1 Query: 411 YAKNGNVNDFSNYFHQTIGTENANYLQRVRSPETSWAQYSIEAMVWSAKNDPSVLMWSIG 47- 0 K D+ +F + A ++ W+ + + MV KN+P++ MWSIG Sbjct: 512 GGK--KPYDYGRFFEKDATHPEARKGEK-------WSDFDLRTMVERGKNNPAIFMWSIG 56- 2 Query: 471 NELMEGFSADVSHYPELTRQMCQWITAIDTSRPITFGDNKLKEADFC-WHEEVSQMATLL 52- 9 NE+ G + +H +++ + I +D +R +T G +K + + HE+++ Sbjct: 563 NEI--GEANGDAHSLATVKRLVKVIKDVDKTRYVTMGADKFRFGNGSGGHEKIA------ 61- 4 Query: 530 SQLDHPQGLIGLNYADGKDYDRLHEEHSDWLLYGSETVSAITSR-AYYKETKKVLDS--- 58- 5 +LD +G NY++ +Y L +H WL+YGSET SA +R +YY+ +++ S Sbjct: 615 DELD----AVGFNYSE-DNYKALRAKHPKWLIYGSETSSATRTRGSYYRPERELKHSNGP 66- 9 Query: 586 --GYHLTSYDHAKVDWGAFASQAWYDTITRDFV--AGECVWTGFDYLGEPTPWNKTDSGV 64- 1 Y + Y + +V WG A+ +W T RD AG+ +WTG DY+GEPTPW+ + Sbjct: 670 ERNYEQSDYGNDRVGWGKTATASW--TFDRDNAGYAGQFIWTGTDYIGEPTPWHNQNQTP 72- 7 Query: 642 VGLWPSPKNAYFGILDTAGFPKDSYYFYQSQW--AQGQTTLHLLPVWQKD-----QLCFD 69- 4 V K++YFGI+DTAG PK +Y YQSQW + + +HLLP W + D Sbjct: 728 V------KSSYFGIVDTAGIPKHDFYLYQSQWVSVKKKPMVHLLPHWNWENKELASKVAD 78- 1 Query: 695 EQGLVEVVVYSNAASVQLMFEDEQGNLTDYGRKAFHTYSTPTGHTYQLYQGADAAKNPHE 75- 4 +G + V YSNA+SV+L N G K F+ T G TYQ +GA+A Sbjct: 782 SEGKIPVRAYSNASSVELFL-----NGKSLGLKTFNKKQTSDGRTYQ--EGANA-----N 82- 9 Query: 755 NLYLTWRVPYQKGLLRAVAYDISGKSIPKTSGRSQVRTYGSVAKLSWKAFEAPIDAPW-E 81- 3 LYL W+V YQ G L A+A D SGK I R ++ T G A + + I A + Sbjct: 830 ELYLEWKVAYQPGTLEAIARDESGKEI----ARDKITTAGKPAAVRLIKEDHAIAADGKD 88- 5 Query: 814 LLYLDLSLLDSRGELVSHAQDWLQVQVEGPARLLALDNGNPTDHTPYQEP-----LRQAY 86- 8 L Y+ ++DS+G +V A + ++ Q+ G +L+ +DNG Y+ +R+A+ Sbjct: 886 LTYIYYEIVDSQGNVVPTANNLVRFQLHGQGQLVGVDNGEQASRERYEAQADGSWIRKAF 94- 5 Query: 869 GGKLLAILALTGEAGHIKVTA 889 GK +AI+ T +AG +TA Sbjct: 946 NGKGVAIVKSTEQAGKFTLTA 966 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01247 Identities = 98/414 (23%), Positives = 175/414 (41%), Gaps = 64/414 (15%) Query: 54 LPSDEVMVIPTSFNDLMVSKEKRDYIGDFWYEKVIEVPKVSEDEEMVLRFGSVTHQAKIY 113- LP D + P + N S K +G WY + + +V + + F + +IY Sbjct: 86 LPHDFSLTQPYTRNGEAESAYKLGGVG-WYRHYLVLDEVLAGCHVAITFEGSYMETEIY 143 Query: 114 VDGVLVGEHKGGFTPFEVLVPECKYNNEKIKVSICANNVLDYTTLPVGNYSEIIQEDGSI 17- 3 V+G +G+H G+ F + + V+ A N+L + Sbjct: 144 VNGQFIGKHLNGYQEFTYDISDV--------VTFGAENLLAVR----------------V 17- 9 Query: 174 KKKVRENFDFFNYAGVHRPLKLMIRPKNHIFDITITSRLSDDL------QSADLHFLVET 22- 7 + KV + +++ +G++R + L + P+ H + L+D Q DL F + Sbjct: 180 ENKVPSS-RWYSGSGLYREVSLSVLPQLHFVADQVAMTLADTAVQEKGQQKVDLRFALNQ 23- 8 Query: 228 NQKVDEVRISVF-------DEDNKLVGETKDS-------------RLFLSDVNLWEVLNA 26- 7 + + ++S+ +D KL+ + + L L ++ LW N Sbjct: 239 SIQTCHYQLSLCLWEQSHCSKDKKLLYQETEVPLADLAFQRQYGLTLSLEELQLWSPDNP 29- 8 Query: 268 YLYTARVEIFVDNQLQDVYEENFGLREIE-VTNGQFLLNRKPIYFKGFGKHEDTFINGRG 32- 6 +LY + ++ Q+ D + G R++ + N +N + + KG H D G Sbjct: 299 HLYDLELTLYYQGQVIDCFCLETGFRQLTFMANQGLFVNGRAVKLKGVCLHHDQGGLGAC 35- 8 Query: 327 LNEAANLMDLNLLKDMGANSFRTSHYPYSEEMMRLADRMGVLVIDEVPAVGLFQ---NFN 38- 3 E A L LLKDMGAN+ R++H P S ++ +LA+R+G VI+E + N N Sbjct: 359 AYEDALARQLVLLKDMGANTIRSTHNPSSPKLRQLANRLGFFVIEEAFDTWTYAKNGNVN 41- 8 Query: 384 ASLDLSPKDNGTWN---LMQTKAAH----EQAIQELVKRDKNHPSVVMWVVANE 430 + + GT N L + ++ + +I+ +V KN PSV+MW + NE Sbjct: 419 DFSNYFHQTIGTENANYLQRVRSPETSWAQYSIEAMVWSAKNDPSVLMWSIGNE 472 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 387 A DNA sequence (GBSx0418) was identified in S. agalactiae <SEQ ID 1261> which encodes the amino acid sequence <SEQ ID 1262>. This protein is predicted to be 2-keto-3-deoxygluconate kinase. Analysis of this protein sequence reveals the following: TABLE-US-01248 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.53 Transmembrane 197-213 (197-213) ----- Final Results ----- bacterial membrane --- Certainty = 0.1213(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9699> which encodes amino acid sequence <SEQ ID 9700> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01249 >GP:AAD35161 GB:AE001693 2-keto-3-deoxygluconate kinase [Thermotoga maritima] Identities = 115/342 (33%), Positives = 180/342 (52%), Gaps = 16/342 (4%) Query: 14 KIISLGEVLLRLSPPQYHTLMQANHLKCQFGGSELNVLASLAQLGYHVGLVSALPDNDLG 73 - K+++ GE++LRLSPP + + Q + +GG+E NV A LAQ+G V+ LP+N LG Sbjct: 2 KVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLG 61 Query: 74 KMASQFILSQQISPAAIIKKEGRLGIYYYEQGFSVRTNKVIYDRNYSSFWESTLSDYDFT 133- A+ + + I + R+GIY+ E G S R +KV+YDR +S+ E+ D+D+ Sbjct: 62 DAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121- Query: 134 SIFKGVDWFHVSGITPALTKDLYEVTRFLMTKAKEGGVKVSIDLNFRESLWSSFQEAREQ 19- 3 I G WFH SGITP L K+L + + A E GV VS DLN+R LW+ +EA++ Sbjct: 122 KILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTK-EEAQKV 18- 0 Query: 194 LSPLLGLLDVCFGLEPIYLAGESEDLKDELGLSRPYLDI-------ELLEKITQKIVQEY 24- 6 + P + +DV L ED++ LG+S LD+ E KI +++ ++Y Sbjct: 181 MIPFMEYVDV--------LIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKY 23- 2 Query: 247 GLDYIAFTQREMEYTNQYMLKSYLYHNNMLYQTDKTGVEVLDRVGTGDAFAAGLIHALLE 30- 6 + T RE ++ N + +++ + ++DRVG GD+FA LI+ L Sbjct: 233 NFKTVGITLRESISATVNYWSVMVFENGQPHFSNRYEIHIVDRVGAGDSFAGALIYGSLM 29- 2 Query: 307 KETPQRALEIAMATFKYKHTIQGDINIMTRDDIAYLIEKETN 348 Q+ E A A KHTI GD +++ ++I L T+ Sbjct: 293 GFDSQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASGATS 334 A related DNA sequence was identified in S. pyogenes <SEQ ID 1263> which encodes the amino acid sequence <SEQ ID 1264>. Analysis of this protein sequence reveals the following: TABLE-US-01250 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0708(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01251 Identities = 111/319 (34%), Positives = 168/319 (51%), Gaps = 7/319 (2%) Query: 12 MAKIISLGEVLLRLSPPQYHTLMQANHLKCQFGGSELNVLASLAQLGYHVGLVSALPDND 71 - M+K++ +GE L+R+SP Q+ L A + FGGSE+N+ +L G L +ALPDN Sbjct: 14 MSKLLLVGEPLIRVSPNQFQPLTNACEAQLFFGGSEVNIARTLGGFGLEARLFTALPDNP 73 Query: 72 LGKMASQFILSQQISPAAIIKKEGRLGIYYYEQGFSVRTNKVIYDRNYSSFWESTLSDYD 131- +G QF+ + + + R+G+YY E GF R ++V YDR SSF D Sbjct: 74 VGHAFHQFLKQSGVDMSLTAWQGHRVGLYYLENGFGCRASQVYYDRCGSSFSALDKDSLD 133- Query: 132 FTSIFKGVDWFHVSGITPALTKDLYEVTRFLMTKAKEGGVKVSIDLNFRESLWSSFQEAR 19- 1 +IF+G+ FH SGI+ AL K ++ L+ +AK+ + +S DLNFR S+ + +A+ Sbjct: 134 LAAIFEGISHFHFSGISLALGKKTQDLIEVLVREAKKRDICISFDLNFRSSM-IAVADAK 19- 2 Query: 192 EQLSPLLGLLDVCFGLEPIYLAGESEDLKDELGLSRPYLDIELLEKITQKIVQEYGLDYI 25- 1 S D+ FG+EP+ L + D+ D R D + + + Q Y L I Sbjct: 193 RLFSHFAQYADIIFGMEPLLLDSDDFDMFD-----RKKADTTTIRERLAGLYQRYQLQAI 24- 7 Query: 252 AFTQREMEYTNQYMLKSYLYHNNMLYQTDKTGVEVLDRVGTGDAFAAGLIHALLEKETPQ 31- 1 T+R + K+Y Y + Y++ + VL RVG+GDAF AGL++ LLE Q Sbjct: 248 YHTERSNDAQGSNHFKAYAY-DRQFYESCEVTTPVLQRVGSGDAFVAGLLYQLLEGNEKQ 30- 6 Query: 312 RALEIAMATFKYKHTIQGD 330 R L+ A+AT K T+ D Sbjct: 307 RNLDFAVATASLKCTVAED 325 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 388 A DNA sequence (GBSx0419) was identified in S. agalactiae <SEQ ID 1265> which encodes the amino acid sequence <SEQ ID 1266>. Analysis of this protein sequence reveals the following: TABLE-US-01252 Possible Site: 15 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.17 Transmembrane 5-21 (5-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.1468(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 389 A DNA sequence (GBSx0420) was identified in S. agalactiae <SEQ ID 1267> which encodes the amino acid sequence <SEQ ID 1268>. Analysis of this protein sequence reveals the following: TABLE-US-01253 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.05 Transmembrane 198-214 (191-220) INTEGRAL Likelihood = -11.68 Transmembrane 446-462 (437-467) INTEGRAL Likelihood = -9.55 Transmembrane 94-110 (91-116) INTEGRAL Likelihood = -7.43 Transmembrane 291-307 (283-309) INTEGRAL Likelihood = -4.88 Transmembrane 265-281 (257-282) INTEGRAL Likelihood = -4.62 Transmembrane 321-337 (318-339) INTEGRAL Likelihood = -3.93 Transmembrane 406-422 (405-426) INTEGRAL Likelihood = -1.59 Transmembrane 121-137 (121-137) INTEGRAL Likelihood = -1.12 Transmembrane 345-361 (345-362) INTEGRAL Likelihood = -0.48 Transmembrane 43-59 (43-59) ----- Final Results ----- bacterial membrane --- Certainty = 0.5819(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01254 >GP:CAB13641 GB:Z99113 similar to H+-symporter [Bacillus subtilis] Identities = 105/452 (23%), Positives = 182/452 (40%), Gaps = 37/452 (8%) Query: 36 IYLFTFMFVTYFSTGVLGSAAIFVSQIMGYIRIFDGFIDPAIGIMIDKTDTKFGKYRPIL 95 - IY ++ +F T V G +A + +RI D DP IG ++D+T+++F ++RP L Sbjct: 27 IYATVSTYLLFFYTDVFGLSAAAAGTMFLVVRIIDALADPFIGTIVDRTNSRFARFRPYL 86 Query: 96 IIGNVITALSLIFLLALRGVDENIRFPLFILVLIIHKIGYSHQQTITKAGQTALTNDPKQ 155- + G A + L L + ++ I +G S+ T ALT+ Sbjct: 87 LFG----AFPFVILAILCFTTPDFSDMGKLIYAYITYVGLSLTYTTINVPYGALTS-AMT 141- Query: 156 RPIFNIVDAVMTTSLMTGGQFVVSVFLVPKFGNFTPQFFNVLIFGTILISAILAIV--AI 21- 3 R +V L +V F VP + G L IL ++ + Sbjct: 142 RNNQEVVSITSVRMLFANLGGLVVAFFVPLLAAYLSDTSGNESLGWQLTMGILGMIGGCL 20- 1 Query: 214 IGIWAKDRKEFFGLGENTQKTALKDYWKVLKGNKPLQILSIAAALVKFAIQFFGDSV-VM 27- 2 + K KE L ++ +K D ++ + N+PL +LSI ++ F + +SV + Sbjct: 202 LIFCFKSTKERVTLQKSEEKIKFTDIFEQFRVNRPLVVLSIFFIII-FGVNSISNSVGIY 26- 0 Query: 273 VLLFGI----LFGNYALSGQFSLLFIVPGVIINILFSTIARKKGLRFSYVRAIQIGMIGL 32- 8 + + + L Y L G L I+P I L + +KK L + A+ + +IGL Sbjct: 261 YVTYNLEREDLVKWYGLIGSLPALVILP--FIPRLHQFLGKKKLLNY----ALLLNIIGL 31- 4 Query: 329 LAFGAVLYVGKPGDLSLTSLNLYTILFIVTNIIARYASQAPASLVLTMGADISDYETSES 38- 8 LA L + N+Y IL V +IA S + + + +Y + Sbjct: 315 LAL-----------LFVPPSNVYLIL--VCRLIAAAGSLTAGGYMWALIPETIEYGEYRT 36- 1 Query: 389 GRYVSGMIGTIFSLTDSIASSFAPMVVGFVLAGIGFSKSFPTIETPLPPDLKMAAISILV 44- 8 G+ + G+I I + +V G VL G+ P M + Sbjct: 362 GKRMGGLIYAIIGFFFKFGMALGGVVPGLVLDKFGY-----VANQAQTPAALMGILITTT 41- 6 Query: 449 AIPFIALSIALLLMKFYKLDKEEMVRIQEKIQ 480 IP L +AL+ + FY LD+++ + +++ Sbjct: 417 IIPVFLLVLALIDINFYNLDEKKYKNMVRELE 448 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 390 A DNA sequence (GBSx0422) was identified in S. agalactiae <SEQ ID 1269> which encodes the amino acid sequence <SEQ ID 1270>. Analysis of this protein sequence reveals the following: TABLE-US-01255 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3375(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01256 >GP:AAB17663 GB:U31175 D-specific D-2-hydroxyacid dehydrogenase [S. aureus] Identities = 165/331 (49%), Positives = 231/331 (68%), Gaps = 1/331 (0%) Query: 1 MMKLKVFNVREEEATLAQDWANRNHVELSMSEGPLTLETVNEVEGFDGIANAQIEPLDDA 60 M K+ F R+ E +A +W +N+VE++ S+ L+ TV++++ +DG+ Q L++ Sbjct: 1 MTKIMFFGTRDYEKEMALNWGKKNNVEVTTSKELLSSATVDQLKDYDGVTTMQFGKLEND 60 Query: 61 IYPLLKEMGIKQIAQRSAGVDMYNLELAKQHGIIISNVPSYSPESIAEFTVTIALNLIRK 120- +YP L+ GIKQIAQR+AG DMY+L+LAK+H I+ISNVPSYSPE+IAE++V+IAL L+R+ Sbjct: 61 VYPKLESYGIKQIAQRTAGFDMYDLDLAKKHNIVISNVPSYSPETIAEYSVSIALQLVRR 120- Query: 121 VELIRANVREQNFSWTLPIRGRVLGNMTVAIIGTGRIGLATAKIFKGFGCRVIGYDIYHN 18- 0 I V+ +F+W I + + NMTVAIIGTGRIG ATAKI+ GFG + YD Y N Sbjct: 121 FPDIERRVQAHDFTWQAEIMSKPVKNMTVAIIGTGRIGAATAKIYAGFGATITAYDAYPN 18- 0 Query: 181 PMADGILEYVNSVEEAVEEADLVSLHMPPTAENTHLFNLDMFKQFKKGAILMNMARGALV 24- 0 D L Y +SV+EA+++AD++SLH+P E+ HLF+ MF KKGAIL+N ARGA++ Sbjct: 181 KDLD-FLTYKDSVKEAIKDADIISLHVPANKESYHLFDKAMFDHVKKGAILVNAARGAVI 23- 9 Query: 241 ETKDLLEALDQGLLEGAGIDTYEFEGPYIPKNCQGQDISDKDFLRLINHPKVIYTPHAAY 30- 0 T DL+ A++ G L GA IDTYE E Y + +DI DK L LI H +++ TPH A+ Sbjct: 240 NTPDLIAAVNDGTLLGAAIDTYENEAAYFTNDWTNKDIDDKTLLELIEHERILVTPHIAF 29- 9 Query: 301 YTDEAVKNLVEGALNACVEVIETGTTTTKVN 331 ++DEAV+NLVEG LNA + VI TGT T++N Sbjct: 300 FSDEAVQNLVEGGLNAALSVINTGTCETRLN 330 There is also homology to SEQ ID 124. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 391 A DNA sequence (GBSx0423) was identified in S. agalactiae <SEQ ID 1271> which encodes the amino acid sequence <SEQ ID 1272>. Analysis of this protein sequence reveals the following:

TABLE-US-01257 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2364(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 392 A DNA sequence (GBSx0424) was identified in S. agalactiae <SEQ ID 1273> which encodes the amino acid sequence <SEQ ID 1274>. This protein is predicted to be regulatory protein (pfoS/R). Analysis of this protein sequence reveals the following: TABLE-US-01258 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.90 Transmembrane 64 - 80 (53 - 89) ----- Final Results ----- bacterial membrane --- Certainty = 0.6158(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9325> which encodes amino acid sequence <SEQ ID 9326> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01259 >GP:AAC65034 GB:AE001189 regulatory protein (pfoS/R) [Treponema pallidum] Identities = 33/91 (36%), Positives = 55/91 (60%), Gaps = 1/91 (1%) Query: 1 MANVLAKPKIMLPMISSAAILGILGALFNIQGTPASAGFGISGLIGPINALNLAKGGWSV 60 M N + P + +P++ + + G+L LFN+QGTPASAGFG GL+GPINA L V Sbjct: 250 MPNWIRYPILNIPLLLNGLVCGVLAWLFNLQGTPASAGFGFIGLVGPINAYRLMAYTPMV 30- 9 Query: 61 MNMLLIIIIFVAAPIILNFIFNYLFIKVLKI 91 +L ++ FV + + ++ +++ + LK+ Sbjct: 310 RAGILFLVYFVLS-FLAAYLIDFILVDRLKL 339 A related DNA sequence was identified in S. pyogenes <SEQ ID 1275> which encodes the amino acid sequence <SEQ ID 1276>. Analysis of this protein sequence reveals the following: TABLE-US-01260 Possible site: 51 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.31 Transmembrane 141-157 (133-166) INTEGRAL Likelihood = -6.00 Transmembrane 92-108 (88-112) ----- Final Results ----- bacterial membrane --- Certainty = 0.5925(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01261 >GP: AAC65034 GB: AE001189 regulatory protein (pfoS/R) [Treponema pallidum] Identities = 63/178 (35%), Positives = 107/178 (59%), Gaps = 10/178 (5%) Query: 2 IGQGIASLLGLQPILMSLLIAMIFCFLIVSPITTVGIALAINLSGIGSGAASFG------ 55 +G+ IA+ + LQP+LMS+L++M F +I+SP+++V + +A+ L+G+ SGAA+ G Sbjct: 164 VGRVIATFIALQPLLMSILLSMSFSLIIISPVSSVAVGIAVGLTGLASGAANIGVSSCAM 22- 3 Query: 56 -LCLAGWAVNSKGTSLAHVLRSPKISMANVLSKPKIMLPMLCSAAVLGVIGAIFNIQGTP 114- L + VN G LA + K+ M N + P + +P+L + V GV+ +FN+QGTP Sbjct: 224 TLIVGTMRVNKIGVPLAMFAGAMKMLMPNWIRYPILNIPLLLNGLVCGVLAWLFNLQGTP 28- 3 Query: 115 ASAGFGISGLIGPINALNLAKGGWCP-VNILLIIIIFVGAPIVLNMIFNYLFIKVLKV 171 ASAGFG GL+GPINA L + P V ++ +++ + + +++ + LK+ Sbjct: 284 ASAGFGFIGLVGPINAYRLM--AYTPMVRAGILFLVYFVLSFLAAYLIDFILVDRLKL 339 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01262 Identities = 86/101 (85%), Positives = 96/101 (94%) Query: 1 MANVLAKPKIMLPMISSAAILGILGALFNIQGTPASAGFGISGLIGPINALNLAKGGWSV 60 MANVL+KPKIMLPM+ SAA+LG++GA+FNIQGTPASAGFGISGLIGPINALNLAKGGW Sbjct: 81 MANVLSKPKIMLPMLCSAAVLGVIGAIFNIQGTPASAGFGISGLIGPINALNLAKGGWCP 140- Query: 61 MNMLLIIIIFVAAPIILNFIFNYLFIKVLKIIDPMDYKLDI 101 +N+LLIIIIFV API+LN IFNYLFIKVLK+IDPMDYKLDI Sbjct: 141 VNILLIIIIFVGAPIVLNMIFNYLFIKVLKVIDPMDYKLDI 181 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 393 A DNA sequence (GBSx0426) was identified in S. agalactiae <SEQ ID 1277> which encodes the amino acid sequence <SEQ ID 1278>. This protein is predicted to be regulatory protein (pfoS/R). Analysis of this protein sequence reveals the following: TABLE-US-01263 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.58 Transmembrane 148-164 (145-169) INTEGRAL Likelihood = -5.26 Transmembrane 33-49 (25-52) INTEGRAL Likelihood = -4.73 Transmembrane 70-86 (62-88) INTEGRAL Likelihood = -3.45 Transmembrane 124-140 (122-143) INTEGRAL Likelihood = -1.33 Transmembrane 96-112 (96-112) ----- Final Results ----- bacterial membrane --- Certainty = 0.3633(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9735> which encodes amino acid sequence <SEQ ID 9736> was also identified. A related GBS nucleic acid sequence <SEQ ID 9697> which encodes amino acid sequence <SEQ ID 9698> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01264 >GP: AAC65034 GB: AE001189 regulatory protein (pfoS/R) [Treponema pallidum] Identities = 61/158 (38%), Positives = 92/158 (57%) Query: 24 KSFIMNVLNGLALGTVIVLIPGAILGELMKALLPMWSGFATLIAATAVATSMMGLVIGIM 83 - + F+M +LNG + G VI L+P AI GEL +AL P+ FA L + +IG + Sbjct: 9 RQFMMKILNGSSAGIVIGLVPPAIAGELFRALAPLSPLFAALYHVVLPIQFSVPALIGTL 68 Query: 84 VGLNFKFNPIQSASLGLAVMFAGGAATFLKGAIMLKGTGDIINMGITAALGVLLIQFLSD 143- VGL F + + A+L + A G T GA ++ G GD+IN+ + +AL ++L++ L Sbjct: 69 VGLQFHCSAPEVATLAFVSVIASGNVTLQNGAWLITGIGDVINVMLISALAIILVRALRG 128- Query: 144 KTKSFTLIVIPTVTLLLVGGVGHVLLPYVKMITTIGQ 181 K S T+I +P + ++ GGVG LPYVKMIT +G+ Sbjct: 129 KLGSLTIIALPVIVAVVAGGVGSFSLPYVKMITLFVGR 166 A related DNA sequence was identified in S. pyogenes <SEQ ID 1279> which encodes the amino acid sequence <SEQ ID 1280>. Analysis of this protein sequence reveals the following: TABLE-US-01265 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.06 Transmembrane 314-330 (301-335) INTEGRAL Likelihood = -11.30 Transmembrane 185-201 (178-215) INTEGRAL Likelihood = -8.01 Transmembrane 22-38 (11-42) INTEGRAL Likelihood = -3.29 Transmembrane 266-282 (265-285) INTEGRAL Likelihood = -2.66 Transmembrane 141-157 (141-159) INTEGRAL Likelihood = -2.13 Transmembrane 53-69 (53-69) INTEGRAL Likelihood = -1.33 Transmembrane 114-130 (113-131) INTEGRAL Likelihood = -0.80 Transmembrane 206-222 (206-222) ----- Final Results ----- bacterial membrane --- Certainty = 0.6222(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01266 >GP: AAC65034 GB: AE00189 regulatory protein (pfoS/R) [Treponema pallidum] Identities = 137/346 (39%), Positives = 217/346 (62%), Gaps = 14/346 (4%) Query: 12 FMNKVLAGTAIAIVVALIPNAILATFLKPLLP-NMAAAEFLHIVQVFQFFTPIMAGFLIG 70 - FM K+L G++ IV+ L+P AI + L P + A H+V QF P + G L+G Sbjct: 11 FMMKILNGSSAGIVIGLVPPAIAGELFRALAPLSPLFAALYHVVLPIQFSVPALIGTLVG 70 Query: 71 QQFKFNPMQQLAVGGAAYIGSGAWAYTEVIQKGVATGTFQLRGIGDLINMMITASLAVLA 130- QF + + + + I SG + G + + GIGD+IN+M+ ++LA++ Sbjct: 71 LQFHCSAPEVATLAFVSVIASG--------NVTLQNGAWLITGIGDVINVMLISALAIIL 122- Query: 131 VKYFGNKFGSLTIILLPITIGTGVGYIGWKFLPYVSYVTTLIGQGINSFTTLQPILMSIL 19- 0 V+ K GSLTII LP+ + G +G LPYV +T +G+ I +F LQP+LMSIL Sbjct: 123 VRALRGKLGSLTIIALPVIVAVVAGGVGSFSLPYVKMITLFVGRVIATFIALQPLLMSIL 18- 2 Query: 191 IAVAFSLIIVSPISTVAIGLAIGLNGMAAGAASMGIASTAAVLVWATLKVNKSGVPIAIA 25- 0 ++++FSLII+SP+S+VA+G+A+GL G+A+GAA++G++S A L+ T++VNK GVP+A+ Sbjct: 183 LSMSFSLIIISPVSSVAVGIAVGLTGLASGAANIGVSSCAMTLIVGTMRVNKIGVPLAMF 24- 2 Query: 251 LGAMKMMMPNFLKHPIMAIPMVFTAAISSLTVPLFNLVGTPASSGFGLVGAVGPIAS--L 30- 8 GAMKM+MPN++++PI+ IP++ + + LFNL GTPAS+GFG +G VGPI + L Sbjct: 243 AGAMKMLMPNWIRYPILNIPLLLNGLVCGVLAWLFNLQGTPASAGFGFIGLVGPINAYRL 30- 2 Query: 309 AGGSSIL---IIILAWIIVPFAVAFAAHKVSKDILKLYKEDIFVFE 351 + ++ I+ L + ++ F A+ + D LKLY+ ++F+ E Sbjct: 303 MAYTPMVRAGILFLVYFVLSFLAAYLIDFILVDRLKLYRRELFIPE 348 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01267 Identities = 65/172 (37%), Positives = 95/172 (54%), Gaps = 9/172 (5%) Query: 19 EKQTTKSFIMNVLNGLALGTVIVLIPGAILGELMKALLPMWSGFATLIAATAVATSMMGL 78 - +K+T SF+ VL G A+ V+ LIP AIL +K LLP + A + V + Sbjct: 5 DKETFSSFMNKVLAGTAIAIVVALIPNAILATFLKPLLPNMAA-AEFLHIVQVFQFFTPI 63 Query: 79 VIGIMVGLNFKFNPIQSASLGLAVMFAGGAATFLK--------GAIMLKGTGDIINMGIT 130- + G ++G FKFNP+Q ++G A GA + + G L+G GD+INM IT Sbjct: 64 MAGFLIGQQFKFNPMQQLAVGGAAYIGSGAWAYTEVIQKGVATGTFQLRGIGDLINMMIT 123- Query: 131 AALGVLLIQFLSDKTKSFTLIVIPTVTLLLVGGVGHVLLPYVKMITTMIGQG 182 A+L VL +++ +K S T+I++P VG +G LPYV +TT+IGQG Sbjct: 124 ASLAVLAVKYFGNKFGSLTIILLPITIGTGVGYIGWKFLPYVSYVTTLIGQG 175 A related GBS gene <SEQ ID 8567> and protein <SEQ ID 8568> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01268 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -13.49 GvH: Signal Score (-7.5): -5.82 Possible site: 48 >>> Seems to have no N-terminal signal sequence ALOM program count: 5 value: -6.58 threshold: 0.0 INTEGRAL Likelihood = -6.58 Transmembrane 148-164 (145-169) INTEGRAL Likelihood = -5.26 Transmembrane 33-49 (25-52) INTEGRAL Likelihood = -4.73 Transmembrane 70-86 (62-88) INTEGRAL Likelihood = -3.45 Transmembrane 124-140 (122-143) INTEGRAL Likelihood = -1.33 Transmembrane 96-112 (96-112) PERIPHERAL Likelihood = 1.85 51 modified ALOM score: 1.82 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3633(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00033## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 394 A DNA sequence (GBSx0428) was identified in S. agalactiae <SEQ ID 1281> which encodes the amino acid sequence <SEQ ID 1282>. This protein is predicted to be cyn operon transcriptional activator. Analysis of this protein sequence reveals the following: TABLE-US-01269 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01270 >GP: CAB15857 GB: Z99123 alternate gene name: ipa-24d~similar to transcriptional regulator (LysR family) [Bacillus subtilis] Identities = 87/282 (30%), Positives = 152/282 (53%), Gaps = 5/282 (1%) Query: 1 MDIRQLTYFIAVAEAKNYSRAAKSLFVTQPTLSQSIKKLEAELNTILFLQNGRQLALTEA 60 MDIR LTYF+ VA K++++A++SL+V+QPT+S+ IK LE EL LF +NGRQ+ LT+A Sbjct: 1 MDIRHLTYFLEVARLKSFTKASQSLYVSQPTISKMIKNLEEELGIELFYRNGRQVELTDA 60 Query: 61 GEILYEKGQLLMTNVNQMVTEIQQLNQEKKEGIRVGLTSLFAIQFMKQI-STFMATHSNV 119- G +Y + Q ++ + + +E+ + + KK +R+GL + F ++ F + NV Sbjct: 61 GHSMYVQAQEIIKSFQNLTSELNDIMEVKKGHVRIGLPPMIGSGFFPRVLGDFRENYPNV 120- Query: 120 EVSLIQDGSRKLQELLAKGKIDIGLLSFPSTRNDITIEPLQTSTKGYKVSIVMPKSHPLA 17- 9 L++DGS K+QE + G +DIG++ P+ + + T + +V+ SH LA Sbjct: 121 TFQLVEDGSIKVQEGVGDGSLDIGVVVLPANEDIFHSFTIVKET----LMLVVHPSHRLA 17- 6 Query: 180 TLPEIELNDLRDYKVASLNEHYMLGEMLPRKCRALGFDPHIVFKHNDWEVLIHSLQDLNA 23- 9 E +L +L+D E ++L + +C GF PHI+++ + W+ + + Sbjct: 177 DEKECQLRELKDEPFIFFREDFVLHNRIMTECIKAGFRPHIIYETSQWDFISEMVSANLG 23- 6 Query: 240 VTILPSEFESISQVQDLCWVPLKDKNNFYPIGIAYRNDTSFS 281 + +LP + + +PL D + + I +R D S Sbjct: 237 IGLLPERICRGLDPEKVKVIPLVDPVIPWHLAIIWRKDRYLS 278 A related DNA sequence was identified in S. pyogenes <SEQ ID 1283> which encodes the amino acid sequence <SEQ ID 1284>. Analysis of this protein sequence reveals the following: TABLE-US-01271 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1101(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01272 Identities = 125/160 (78%), Positives = 144/160 (89%) Query: 135 LAKGKIDIGLLSFPSTRNDITIEPLQTSTKGYKVSIVMPKSHPLATLPEIELNDLRDYKV 19- 4 L++GKIDIGLLSF S R DITIE LQTSTKGYKVSIV+ K HPLA P+++L DL+ YK+ Sbjct: 1 LSQGKIDIGLLSFLSIRKDITIELLQTSTKGYKVSIVLLKQHPLAQHPQLKLKDLKGYKI 60 Query: 195 ASLNEHYMLGEMLPRKCRALGFDPHIVFKHNDWEVLIHSLQDLNAVTILPSEFESISQVQ 25- 4 ASLN+HYMLGEMLPRKCRALGF+P IVFKHNDWEVLIHSL DLN +TILPS+FES++QV Sbjct: 61 ASLNDHYMLGEMLPRKCRALGFEPDIVFKHNDWEVLIHSLHDLNTLTILPSDFESLNQVD 120- Query: 255 DLCWVPLKDKNNFYPIGIAYRNDTSFSPMIEEFLSLLKTN 294 +L W+PL+DKNNFYPIGIAYR+D SFSP+IEEFLSLLKTN Sbjct: 121 NLVWIPLQDKNNFYPIGIAYRDDASFSPVIEEFLSLLKTN 160 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 395 A DNA sequence (GBSx0429) was identified in S. agalactiae <SEQ ID 1285> which encodes the amino acid sequence <SEQ ID 1286>. Analysis of this protein sequence reveals the following: TABLE-US-01273 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1833(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> Signal peptide: 1-21 A related GBS nucleic acid sequence <SEQ ID 8569> which encodes amino acid sequence <SEQ ID 8570> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8570 (GBS271) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 8; MW 31.3 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 55 (lane 6; MW 56.3 kDa) and in FIG. 62 (lane 10; MW 56.3 kDa). GBS271-GST was purified as shown in FIG. 210, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 396 A DNA sequence (GBSx0430) was identified in S. agalactiae <SEQ ID 1287> which encodes the amino acid sequence <SEQ ID 1288>. Analysis of this protein sequence reveals the following: TABLE-US-01274 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.74 Transmembrane 9-25 (5-28) INTEGRAL Likelihood = -5.84 Transmembrane 97-113 (92-122) INTEGRAL Likelihood = -5.47 Transmembrane 37-53 (35-61) INTEGRAL Likelihood = -2.55 Transmembrane 220-236 (220-238) INTEGRAL Likelihood = -1.65 Transmembrane 64-80 (63-81) INTEGRAL Likelihood = -1.28 Transmembrane 193-209 (192-209) INTEGRAL Likelihood = -0.53 Transmembrane 125-141 (125-141) ----- Final Results ----- bacterial membrane --- Certainty = 0.3697(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01275 >GP: AAC73593 GB: AE000155 putative metal resistance protein [Escherichia coli K12] Identities = 128/252 (50%), Positives = 186/252 (73%) Query: 5 NSISLMSLLMASSLVLITLFFSYWQKLNLEKEVIISAIRAVIQLLAVGFLLDYIFGYQNP 64 ++I+ SL +A LV++ + S+ +KL LEK+++ S RA+IQL+ VG++L YIF + Sbjct: 13 HNITNESLALALMLVVVAILISHKEKLALEKDILWSVGRAIIQLIIVGYVLKYIFSVDDA 72 Query: 65 IFTALLMLFMIINASYNAAKRGKGINKGFVISFIAIGSGTIITLSVLIFSGILKFVPNQM 124- T L++LF+ NA++NA KR K I K F+ SFIAI G ITL+VLI SG ++F+P Q+ Sbjct: 73 SLTLLMVLFICFNAAWNAQKRSKYIAKAFISSFIAITVGAGITLAVLILSGSIEFIPMQV 132- Query: 125 IPVGGMIISNSMVAIGLCYKQLLSEFRSKQEEVETKLALGADILPASIDIIRDVIKTGMV 18- 4 IP+ GMI N+MVA+GLCY L S+Q++++ KL+LGA AS +IRD I+ ++ Sbjct: 133 IPIAGMIAGNAMVAVGLCYNNLGQRVISEQQQIQEKLSLGATPKQASAILIRDSIRAALI 19- 2 Query: 185 PTIDSAKTLGIVSLPGMMTGLILAGTSPIQAVKYQMMVTFMLLATTSIASFVATYLAYKI 24- 4 PT+DSAKT+G+VSLPGMM+GLI AG P++A+KYQ+MVTFMLL+T S+++ +A YL Y+ Sbjct: 193 PTVDSAKTVGLVSLPGMMSGLIFAGIDPVKAIKYQIMVTFMLLSTASLSTIIACYLTYRK 25- 2 Query: 245 FFNNRKQLVVTK 256 F+N+R QLVVT+ Sbjct: 253 FYNSRHQLVVTQ 264 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 397 A DNA sequence (GBSx0431) was identified in S. agalactiae <SEQ ID 1289> which encodes the amino acid sequence <SEQ ID 1290>. This protein is predicted to be SUGAR TRANSPORT ATP-BINDING PROTEIN. (b0490). Analysis of this protein sequence reveals the following:

TABLE-US-01276 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1903(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01277 >GP: AAC73592 GB: AE000155 putative ATP-binding component of a transport system [Escherichia coli K12] Identities = 95/202 (47%), Positives = 142/202 (70%), Gaps = 2/202 (0%) Query: 4 LTFKHVDFKTDDKLVLNDINFAIDEGDFVSIVGPSGSGKSTVLKLASGLMSPTAGHIFFD 63 L ++V + D +LN+INF++ G+F I GPSG GKST+LK+ + L+SPT+G + F+ Sbjct: 8 LQLQNVGYLAGDAKILNNINFSLRAGEFKLITGPSGCGKSTLLKIVASLISPTSGTLLFE 67 Query: 64 GKDLNQLEPIESRKMISYCFQTPHLFGNTVEDNISFPYHIRHEKVDYRRVDDLFQRFEMD 123- G+D++ L+P R+ +SYC QTP LFG+TV DN+ FP+ IR+ + D D +RF + Sbjct: 68 GEDVSTLKPEIYRQQVSYCAQTPTLFGDTVYDNLIFPWQIRNRQPDPAIFLDFLERFALP 127- Query: 124 QSYLKQDVKKLSGGEKQRIALIRQLLFEPKVLLLDEVTSALDNHNKAIVEKVI-KSLHDK 18- 2 S L +++ +LSGGEKQRI+LIR L F PKVLLLDE+TSALD NK V ++I + + ++ Sbjct: 128 DSILTKNIAELSGGEKQRISLIRNLQFMPKVLLLDEITSALDESNKHNVNEMIHRYVREQ 18- 7 Query: 183 GITILWITHDEEQSRRFANKVL 204 I +LW+THD+++ A+KV+ Sbjct: 188 NIAVLWVTHDKDEINH-ADKVI 208 A related DNA sequence was identified in S. pyogenes <SEQ ID 1291> which encodes the amino acid sequence <SEQ ID 1292>. Analysis of this protein sequence reveals the following: TABLE-US-01278 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2053(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01279 Identities = 73/214 (34%), Positives = 133/214 (62%), Gaps = 9/214 (4%) Query: 4 LTFKHVD--FKTDDKLVLNDINFAIDEGDFVSIVGPSGSGKSTVLKLASGLMSPTAGHIF 61 +TF +V F+ VL +INF ++EG F +++G SGSGKST+L + +GL+ ++G I+ Sbjct: 6 ITFNNVSKTFEDSGTQVLKNINFDLEEGKFYTLLGASGSGKSTILNIMAGLLDASSGDIY 65 Query: 62 FDGKDLNQLEPIESRKMISYCFQTPHLFGN-TVEDNISFPYHIR--HEKVDYRRVDDLFQ 118- DG+ +N L PI R I FQ LF + TV +N++F ++ +K +RV + + Sbjct: 66 LDGERINDL-PINKRD-IHTVFQNYALFPHMTVFENVAFALKLKKVDKKEIAKRVKETLK 123- Query: 119 RFEMDQSYLKQDVKKLSGGEKQRIALIRQLLFEPKVLLLDEVTSALDNHNKAIVEKVIKS 17- 8 ++ + + + ++KLSGG++QR+A+ R ++ +P+V+LLDE SALD + ++ ++ Sbjct: 124 MVQL-EGFENRSIQKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTEMQYELRE 18- 2 Query: 179 LHDK-GITILWITHDEEQSRRFANKVLKVVNGSI 211 L + GIT +++THD+E++ ++ + + G I Sbjct: 183 LQQRLGITFVFVTHDQEEALAMSDWIFVMNEGEI 216 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 398 A DNA sequence (GBSx0432) was identified in S. agalactiae <SEQ ID 1293> which encodes the amino acid sequence <SEQ ID 1294>. Analysis of this protein sequence reveals the following: TABLE-US-01280 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0658(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 399 A DNA sequence (GBSx0434) was identified in S. agalactiae <SEQ ID 1295> which encodes the amino acid sequence <SEQ ID 1296>. This protein is predicted to be deda protein (dedA). Analysis of this protein sequence reveals the following: TABLE-US-01281 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.05 Transmembrane 186-202 (178-208) INTEGRAL Likelihood = -8.81 Transmembrane 65-81 (61-89) INTEGRAL Likelihood = -7.54 Transmembrane 26-42 (24-47) INTEGRAL Likelihood = -0.37 Transmembrane 152-168 (152-168) ----- Final Results ----- bacterial membrane --- Certainty = 0.5819(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01282 >GP: AAC75377 GB: AE000320 orf, hypothetical protein [Escherichia coli K12] Identities = 91/211 (43%), Positives = 131/211 (61%), Gaps = 7/211 (3%) Query: 2 FLIDFILHIDTHIYAMANTVGNWTYLLLFLVIFVETGAVIFPFLPGDSLLFAAGALAANP 61 FLIDFILHID H+ + G W Y +LFL++F ETG V+ PFLPGDSLLF AGALA+ Sbjct: 6 FLIDFILHIDVHLAELVAEYGVWVYAILFLILFCETGLVVTPFLPGDSLLFVAGALASLE 65 Query: 62 KMSFNIVTFLIIFFIAAFIGDSCNFLIGRTFGYRFIKHP---FFRRFIKEKNIRDAELYF 118- N+ +++ IAA +GD+ N+ IGR FG + +P FRR +K ++ Sbjct: 66 TNDLNVHMMVVLMLIAAIVGDAVNYTIGRLFGEKLFSNPNSKIFRRSYLDK----THQFY 121- Query: 119 EKKGTAAIILGRYIPIIRTFVPFVAGISQLPPKVFIKRAFIAALSWSVIATGSGFLFGNI 17- 8 EK G IIL R++PI+RTF PFVAG+ + + F I AL W ++ T +G+ FG I Sbjct: 122 EKHGGKTIILARFVPIVRTFAPFVAGMGHMSYRHFAAYNVIGALLWVLLFTYAGYFFGTI 18- 1 Query: 179 PFVKQHFSLIILGIVFVTLIPVLISGVKSYR 209 P V+ + L+I+GI+ V+++P +I ++ R Sbjct: 182 PMVQDNLKLLIVGIIVVSILPGVIEIIRHKR 212 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 400 A DNA sequence (GBSx0435) was identified in S. agalactiae <SEQ ID 1297> which encodes the amino acid sequence <SEQ ID 1298>. Analysis of this protein sequence reveals the following: TABLE-US-01283 Possible Site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3100(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 401 A DNA sequence (GBSx0436) was identified in S. agalactiae <SEQ ID 1299> which encodes the amino acid sequence <SEQ ID 1300>. This protein is predicted to be DNA-entry nuclease. Analysis of this protein sequence reveals the following: TABLE-US-01284 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3990(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9323> which encodes amino acid sequence <SEQ ID 9324> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01285 >GP: CAA38134 GB: X54225 membrane nuclease [Streptococcus pneumoniae] Identities = 87/157 (55%), Positives = 110/157 (69%), Gaps = 1/157 (0%) Query: 1 MLDRTIRQYQNRRDTTLPDANWKPLGWHQVAT-NDHYGHAVDKGHLIAYALAGNFKGWDA 59 +L + RQY+NR++T +W P GWHQV Y HAVD+GHL+ YAL G G+DA Sbjct: 116 LLSKATRQYKNRKETGNGSTSWTPPGWHQVKNLKGSYTHAVDRGHLLGYALIGGLDGFDA 17- 5 Query: 60 SVSNPQNVVTQTAHSNQSNQKINRGQNYYESLVRKAVDQNKRVRYRVTPLYRNDTDLVPF 119- S SNP+N+ QTA +NQ+ + + GQNYYES VRKA+DQNKRVRYRVT Y ++ DLVP Sbjct: 176 STSNPKNIAVQTAWANQAQAEYSTGQNYYESKVRKALDQNKRVRYRVTLYYASNEDLVPS 23- 5 Query: 120 AMHLEAKSQDGTLEFNVAIPNTQASYTMDYATGEITL 156 A +EAKS DG LEFNV +PN Q +DY TGE+T+ Sbjct: 236 ASQIEAKSSDGELEFNVLVPNVQKGLQLDYRTGEVTV 272 A related DNA sequence was identified in S. pyogenes <SEQ ID 1301> which encodes the amino acid sequence <SEQ ID 1302>. Analysis of this protein sequence reveals the following: TABLE-US-01286 Possible site: 42 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01287 >GP: CAA38134 GB: X54225 membrane nuclease [Streptococcus pneumoniae] Identities = 89/135 (65%), Positives = 104/135 (76%), Gaps = 1/135 (0%) Query: 25 SPAGWHRLHHLKGSYDHAVDRGHLLGYALVGGLKGFDASTGNPDNIATQLSWANQANKPY 84 - +P GWH++ +LKGSY HAVDRGHLLGYAL+GGL GFDAST NP NIA Q +WANQA Y Sbjct: 138 TPPGWHQVKNLKGSYTHAVDRGHLLGYALIGGLDGFDASTSNPKNIAVQTAWANQAQAEY 19- 7 Query: 85 LTGQNYYEGLVRRALDKGHRVRYRVTLLY-DGDNLLASGSHLEAKSSDDSLTFNVFVPNV 143- TGQNYYE VR+ALD+ RVRYRVTL Y ++L+ S S +EAKSSD L FNV VPNV Sbjct: 198 STGQNYYESKVRKALDQNKRVRYRVTLYYASNEDLVPSASQIEAKSSDGELEFNVLVPNV 25- 7 Query: 144 QAGLTADYRTGQIAI 158 Q GL DYRTG++ + Sbjct: 258 QKGLQLDYRTGEVTV 272 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01288 Identities = 73/135 (54%), Positives = 92/135 (68%), Gaps = 2/135 (1%) Query: 24 PLGWHQVA-TNDHYGHAVDKGHLIAYALAGNFKGWDASVSNPQNVVTQTAHSNQSNQKIN 82 - P GWH++ Y HAVD+GHL+ YAL G KG+DAS NP N+ TQ + +NQ+N+ Sbjct: 26 PAGWHRLHHLKGSYDHAVDRGHLLGYALVGGLKGFDASTGNPDNIATQLSWANQANKPYL 85 Query: 83 RGQNYYESLVRKAVDQNKRVRYRVTPLYRNDTDLVPFAMHLEAKSQDGTLEFNVAIPNTQ 142- GQNYYE LVR+A+D+ RVRYRVT LY D +L+ HLEAKS D +L FNV +PN Q Sbjct: 86 TGQNYYEGLVRRALDKGHRVRYRVTLLYDGD-NLLASGSHLEAKSSDDSLTFNVFVPNVQ 144- Query: 143 ASYTMDYATGEITLN 157 A T DY TG+I +N Sbjct: 145 AGLTADYRTGQIAIN 159 SEQ ID 9324 (GBS656) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 186 (lane 10; MW 57 kDa). GBS656-GST was purified as shown in FIG. 236, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 402 A DNA sequence (GBSx0437) was identified in S. agalactiae <SEQ ID 1303> which encodes the amino acid sequence <SEQ ID 1304>. Analysis of this protein sequence reveals the following: TABLE-US-01289 Possible site: 13 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9321> which encodes amino acid sequence <SEQ ID 9322> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1305> which encodes the amino acid sequence <SEQ ID 1306>. Analysis of this protein sequence reveals the following: TABLE-US-01290 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5350(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01291 Identities = 24/73 (32%), Positives = 37/73 (49%), Gaps = 2/73 (2%) Query: 1 MFYMKLANRLSLAATIVNEANANSPFGIIIHSDKAENVEWNDFETQFPDLFNSPKKEESP 60 + YMKLA L TI+ E + SPF I+H+D A N++ E N +++P Sbjct: 80 ILYMKLAKENHLPVTIITETHMTSPFAFILHTDHAINLKETRLEVILKQTKNDQLSKQTP 139- Query: 61 K--KSLWQHFFSQ 71 + KS W+ F + Sbjct: 140 EKTKSFWKRFLKK 152 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 403 A DNA sequence (GBSx0438) was identified in S. agalactiae <SEQ ID 1307> which encodes the amino acid sequence <SEQ ID 1308>. This protein is predicted to be Isopentenyl-diphosphate delta-isomerase. Analysis of this protein sequence reveals the following: TABLE-US-01292 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1649(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01293 >GP: AAG20030 GB: AE005083 isopentenyl pyrophosphate isomerase; Idi [Halobacterium sp. NRC-1] Identities = 24/77 (31%), Positives = 40/77 (51%) Query: 14 TGLTLNRDQNIPQGLFHLVVDVILFHEDGDVLMMKRHPKKKAFPAYFEATAGGSALKGEN 73 - TGL D + G+ H +LF EDG VL+ +R +K+ + +++ T ++G++ Sbjct: 42 TGLANRLDAHTGDGVRHRAFTCLLFDEDGRVLLAQRADRKRLWDTHWDGTVASHPIEGQS 101- Query: 74 AKQAILRELKEETGIVP 90 A + L EE GI P Sbjct: 102 QVDATRQRLAEELGIEP 118 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 404 A DNA sequence (GBSx0439) was identified in S. agalactiae <SEQ ID 1309> which encodes the amino acid sequence <SEQ ID 1310>. This protein is predicted to be phosphoserine phosphatase (serB). Analysis of this protein sequence reveals the following: TABLE-US-01294 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0613(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01295 >GP: CAB50876 GB: AL096844 putative phosphoserine phosphatase [Streptomyces coelicolor A3(2)] Identities = 96/193 (49%), Positives = 132/193 (67%) Query: 5 LLVMDVDSTLIMEEAIDLLAIEAGVGKQVAALTDAAMRGELDFEEALKKRVALLKGLPVT 64 L+VMDVDSTLI +E I+L A AG +VA +T AAMRGELDFE++L RVALL GL + Sbjct: 183 LVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVALLAGLDAS 24- 2 Query: 65 ILTDILSSIHFTPGAYELIKECHKRQMKVGLVSGGFHETIDILAKQLQVDYVKANRLGVK 124- ++ + + + TPGA LI+ + +VG+VSGGF + D L +QL +D+ +AN L + Sbjct: 243 VVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFAQANTLEIV 30- 2 Query: 125 GGFLTGEVEGEIVTKEVKKIKLKEWASENHLDLSQTIAMGDGANDLPMIKSAGVGIAFCA 18- 4 G LTG V GEIV + K L+ +A+ + LSQT+A+GDGANDL M+ +AG+G+AF A Sbjct: 303 DGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAAGLGVAFNA 36- 2 Query: 185 KPIVREEAAYQIN 197 KP+VRE A +N Sbjct: 363 KPVVREAAHTAVN 375 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 405 A DNA sequence (GBSx0440) was identified in S. agalactiae <SEQ ID 1311> which encodes the amino acid sequence <SEQ ID 1312>. Analysis of this protein sequence reveals the following: TABLE-US-01296 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -17.88 Transmembrane 5-21 (1-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.8153(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01297 >GP: BAB06924 GB: AP001518 unknown conserved protein [Bacillus halodurans] Identities = 122/553 (22%), Positives = 265/553 (47%), Gaps = 12/553 (2%) Query: 7 LLLVAIVLLVIIAYVVGVVIRKRNDTLIANLETRKQELVDLPVQEEIEQVKLLHLIGQSQ 66 +++ ++++L + +V G + RK + LE K +++ P+ +EI +VK L + G+++ Sbjct: 3 IVVFSLLVLTVTFFVYGALRRKAFYKRVDKLEDWKNDILQRPIPDEIGKVKGLTMSGETE 62 Query: 67 STFREWNQKWTDLSTNSFKDIDFHLVEAENLNDSFNFVRAKHEIDNVDSQLTIIEEDIVS 126- F W W D+ +++ L + E+ + + F +AK +D ++ +L IEE + Sbjct: 63 EKFEVWRSDWDDIVGVILPNVEEQLFDVEDFANKYRFQKAKALLDTIEQRLHSIEEQLKI 122- Query: 127 IREALEVLKEQEEKNSARVTHALDLYETLQKSISEKEDNYGTTMPEIEKQLKNIEAEFSH 18- 6 + + ++VL + EE+N + +L + L K + + ++ +++L+ Sbjct: 123 MVDDIQVLVQSEEQNRTEIGSVRELQQKLIKEAITRRGSLSSSAKVFDEKLEKANELLQA 18- 2 Query: 187 FVTLNSTGDPIEASEVLNKAEEHTIALGQITEQIPAIVAKLEDDFPDQLDDLETGYRRLL 24- 6 F G+ I+ASEVL +A+E + + + +P + +L+ + P +L +L+ G R + Sbjct: 183 FDERTEKGNYIQASEVLEEAKELLGQIEHLLKIVPGLFVELQTNIPAELTNLKNGLRDME 24- 2 Query: 247 EENYHFPEKDIEQRFQEVREAIRSNSDGLVSLDLDRARDENEHIQEKIDKLYDIFEREIA 30- 6 E + I+ + + + E + L L+ + +E I+E +++++++ E+E+ Sbjct: 243 EAGFFLETFAIDSQMERLEEKRVELLEQLTVLECNGMEEEINFIEESMEQMFELLEKEVE 30- 2 Query: 307 AYKVAHKDSKIIPQFLAHAKSNNEQLGH---EIKRLSAKYILNENESLSLRSFTNDLEEI 36- 3 A ++ + ++P E+L H E + + Y L E E + + +L+E+ Sbjct: 303 A---KNEITILLPNLREDLTKTEEKLTHLKEETESVQLSYRLAEEELVFQQKLGKELKEL 35- 9 Query: 364 ETKVLPSVENFGQEASPYTHLQILFERTLKTLTTVEENQMEVFEAVKTIESVETRARQNM 42- 3 ++ E ++ ++ ++ + E + LT + + E++ ++ E +A++ + Sbjct: 360 RQQLQVIDEVTEEQKQTFSSVRSMLEEWREGLTACQNKIEQAQESLNSLRKDELKAKEEL 41- 9 Query: 424 DKYVNKLHMIKRFMEKRNLPGIPQDFLSTFFTTSSQIEALINELSRGRIDIEAVSRLNDV 48- 3 + KL KR ++K N+PG+P+ L ++ I +LS +++ V+ L D Sbjct: 420 KQLKEKLLEDKRLVQKSNIPGLPETLLHRLEDGEQKLAQAIAKLSDVPLEMGRVTALVDE 47- 9 Query: 484 TTNAIANLEQATYLVVQDATLTEQLLQYSNRYRSFEQNVQKSFEQALYLFEVEHNYKASF 54- 3 I + ++ A L E ++QY NRYRS V+K A LF + Sbjct: 480 AQGLIHENSSILHETIEKARLAEHVIQYGNRYRSRSAEVKKRLSNAEELFRA-----FEY 53- 4 Query: 544 DE-ISYALETVEP 555 DE I A++ +EP Sbjct: 535 DEAIEMAVQAIEP 547 A related DNA sequence was identified in S. pyogenes <SEQ ID 1313> which encodes the amino acid sequence <SEQ ID 1314>. Analysis of this protein sequence reveals the following:

TABLE-US-01298 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -18.04 Transmembrane 5-21 (1-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.8217(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01299 >GP: BAB06924 GB: AP001518 unknown conserved protein [Bacillus halodurans] Identities = 131/555 (23%), Positives = 269/555 (47%), Gaps = 16/555 (2%) Query: 7 LLIVAIVLLVIIAYLVGVIIRKRNDSLITSLEERKQALFALPVNDEIEEVKSLHLIGQSQ 66 +++ ++++L + ++ G + RK + LE+ K + P+ DEI +VK L + G+++ Sbjct: 3 IVVFSLLVLTVTFFVYGALRRKAFYKRVDKLEDWKNDILQRPIPDEIGKVKGLTMSGETE 62 Query: 67 TSFREWNQKWVDLTVNSFADIENHIFEAENLNDTFNFIRAKHEINSVESQLNLVEEDIAS 126- F W W D+ ++E +F+ E+ + + F +AK ++++E +L+ +EE + Sbjct: 63 EKFEVWRSDWDDIVGVILPNVEEQLFDVEDFANKYRFQKAKALLDTIEQRLHSIEEQLKI 122- Query: 127 IREALNILKEQEEKNSARVTHALDLYEKLQASISENEDNFGSTMPEIDKQMKNIETEFSQ 18- 6 + + + +L + EE+N + +L +KL + S+ D++++ Sbjct: 123 MVDDIQVLVQSEEQNRTEIGSVRELQQKLIKEAITRRGSLSSSAKVFDEKLEKANELLQA 18- 2 Query: 187 FVALNSSGDPVEASEVLDRAEEHTIALGQITEQIPAIVAKLEDDFPDQLDDLETGYRRLL 24- 6 F G+ ++ASEVL+ A+E + + + +P + +L+ + P +L +L+ G R + Sbjct: 183 FDERTEKGNYIQASEVLEEAKELLGQIEHLLKIVPGLFVELQTNIPAELTNLKNGLRDME 24- 2 Query: 247 EENYHFPEKNIEARFQEIRESIRANSSELVTLDLDRAREENTHIQERIDSLYEVFEREIA 30- 6 E + I+++ + + E +L L+ + EE I+E ++ ++E+ E+E Sbjct: 243 EAGFFLETFAIDSQMERLEEKRVELLEQLTVLECNGMEEEINFIEESMEQMFELLEKE-- 30- 0 Query: 307 AYKVAAKN--SKMLPRYLEHVKRNNEQ---LKDEIARLSRKYILSETESLTVKAFEKDIK 36- 1 V AKN + +LP E + + E+ LK+E + Y L+E E + + K++K Sbjct: 301 ---VEAKNEITILLPNLREDLTKTEEKLTHLKEETESVQLSYRLAEEELVFQQKLGKELK 35- 7 Query: 362 EIEDSTLAVAEQFGLQEKPFSELQVTFERSIKTLTNVESGQMDVFAAVKDIEKIESQARH 42- 1 E+ + E Q++ FS ++ E + LT ++ ++ + K E +A+ Sbjct: 358 ELRQQLQVIDEVTEEQKQTFSSVRSMLEEWREGLTACQNKIEQAQESLNSLRKDELKAKE 41- 7 Query: 422 NLDVYVTQLHMIKRYMEKRHLPGIPQDFLSAFFTTSSQLEALMDELSRGRINIEAVSRLS 48- 1 L +L KR ++K ++PG+P+ L +L + +LS + + V+ L Sbjct: 418 ELKQLKEKLLEDKRLVQKSNIPGLPETLLHRLEDGEQKLAQAIAKLSDVPLEMGRVTALV 47- 7 Query: 482 EVATVAIANLEDLTYQVVQNATLTEQLLQYSNRYRSFEAGVQSSFEHALRLFEVENDYQA 54- 1 + A I + ++ ++ A L E ++QY NRYRS A V+ +A LF Sbjct: 478 DEAQGLIHENSSILHETIEKARLAEHVIQYGNRYRSRSAEVKKRLSNAEELFRA-----F 53- 2 Query: 542 SFDE-ISYALETVEP 555 +DE I A++ +EP Sbjct: 533 EYDEAIEMAVQAIEP 547 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01300 Identities = 429/574 (74%), Positives = 503/574 (86%) Query: 1 MSSGIILLLVAIVLLVIIAYVVGVVIRKRNDTLIANLETRKQELVDLPVQEEIEQVKLLH 60 MSSGIILL+VAIVLLVIIAY+VGV+IRKRND+LI +LE RKQ L LPV +EIE+VK LH Sbjct: 1 MSSGIILLIVAIVLLVIIAYLVGVIIRKRNDSLITSLEERKQALFALPVNDEIEEVKSLH 60 Query: 61 LIGQSQSTFREWNQKWTDLSTNSFKDIDFHLVEAENLNDSFNFVRAKHEIDNVDSQLTII 120- LIGQSQ++FREWNQKW DL+ NSF DI+ H+ EAENLND+FNF+RAKHEI++V+SQL ++ Sbjct: 61 LIGQSQTSFREWNQKWVDLTVNSFADIENHIFEAENLNDTFNFIRAKHEINSVESQLNLV 120- Query: 121 EEDIVSIREALEVLKEQEEKNSARVTHALDLYETLQKSISEKEDNYGTTMPEIEKQLKNI 18- 0 EEDI SIREAL +LKEQEEKNSARVTHALDLYE LQ SISE EDN+G+TMPEI+KQ+KNI Sbjct: 121 EEDIASIREALNILKEQEEKNSARVTHALDLYEKLQASISENEDNFGSTMPEIDKQMKNI 18- 0 Query: 181 EAEFSHFVTLNSTGDPIEASEVLNKAEEHTIALGQITEQIPAIVAKLEDDFPDQLDDLET 24- 0 E EFS FV LNS+GDP+EASEVL++AEEHTIALGQITEQIPAIVAKLEDDFPDQLDDLET Sbjct: 181 ETEFSQFVALNSSGDPVEASEVLDRAEEHTIALGQITEQIPAIVAKLEDDFPDQLDDLET 24- 0 Query: 241 GYRRLLEENYHFPEKDIEQRFQEVREAIRSNSDGLVSLDLDRARDENEHIQEKIDKLYDI 30- 0 GYRRLLEENYHFPEK+IE RFQE+RE+IR+NS LV+LDLDRAR+EN HIQE+ID LY++ Sbjct: 241 GYRRLLEENYHFPEKNIEARFQEIRESIRANSSELVTLDLDRAREENTHIQERIDSLYEV 30- 0 Query: 301 FEREIAAYKVAHKDSKIIPQFLAHAKSNNEQLGHEIKRLSAKYILNENESLSLRSFTNDL 36- 0 FEREIAAYKVA K+SK++P++L H K NNEQL EI RLS KYIL+E ESL++++F D+ Sbjct: 301 FEREIAAYKVAAKNSKMLPRYLEHVKRNNEQLKDEIARLSRKYILSETESLTVKAFEKDI 36- 0 Query: 361 EEIETKVLPSVENFGQEASPYTHLQILFERTLKTLTTVEENQMEVFEAVKTIESVETRAR 42- 0 +EIE L E FG + P++ LQ+ FER++KTLT VE QM+VF AVK IE +E++AR Sbjct: 361 KEIEDSTLAVAEQFGLQEKPFSELQVTFERSIKTLTNVESGQMDVFAAVKDIEKIESQAR 42- 0 Query: 421 QNMDKYVNKLHMIKRFMEKRNLPGIPQDFLSTFFTTSSQIEALINELSRGRIDIEAVSRL 48- 0 N+D YV +LHMIKR+MEKR+LPGIPQDFLS FFTTSSQ+EAL++ELSRGRI+IEAVSRL Sbjct: 421 HNLDVYVTQLHMIKRYMEKRHLPGIPQDFLSAFFTTSSQLEALMDELSRGRINIEAVSRL 48- 0 Query: 481 NDVTTNAIANLEQATYLVVQDATLTEQLLQYSNRYRSFEQNVQKSFEQALYLFEVEHNYK 54- 0 ++V T AIANLE TY VVQ+ATLTEQLLQYSNRYRSFE VQ SFE AL LFEVE++Y+ Sbjct: 481 SEVATVAIANLEDLTYQVVQNATLTEQLLQYSNRYRSFEAGVQSSFEHALRLFEVENDYQ 54- 0 Query: 541 ASFDEISYALETVEPGVTDRFVTSYEKTQERIRF 574 ASFDEISYALETVEPGVTDRFV SYEKT+E IRF Sbjct: 541 ASFDEISYALETVEPGVTDRFVNSYEKTREHIRF 574 SEQ ID 1312 (GBS642) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 142 (lane 24; MW 27 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 406 A DNA sequence (GBSx0441) was identified in S. agalactiae <SEQ ID 1315> which encodes the amino acid sequence <SEQ ID 1316>. Analysis of this protein sequence reveals the following: TABLE-US-01301 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2471(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9671> which encodes amino acid sequence <SEQ ID 9672> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01302 >GP: CAA91553 GB: Z67740 DNA gyrase [Streptococcus pneumoniae] Identities = 574/650 (88%), Positives = 618/650 (94%), Gaps = 2/650 (0%) Query: 1 MTEETKNMEQRAQEYDASQIQVLEGLEAVRMRPGMYIGSTSKEGLHHLVWEIVDNSIDEA 60 MTEE KN++ AQ+YDASQIQVLEGLEAVRMRPGMYIGSTSKEGLHHLVWEIVDNSIDEA Sbjct: 1 MTEEIKNLQ--AQDYDASQIQVLEGLEAVRMRPGMYIGSTSKEGLHHLVWEIVDNSIDEA 58 Query: 61 LAGFAGHIKVYIEPDNSITVVDDGRGIPVDIQEKTGRPAVETVFTVLHAGGKFGGGGYKV 120- LAGFA HI+V+IEPD+SITVVDDGRGIPVDIQEKTGRPAVETVFTVLHAGGKFGGGGYKV Sbjct: 59 LAGFASHIQVFIEPDDSITVVDDGRGIPVDIQEKTGRPAVETVFTVLHAGGKFGGGGYKV 118- Query: 121 SGGLHGVGSSVVNALSTQLDVKVYKNGKVHYQEYQRGVVVNDLEIIGDTDLSGTTVHFTP 18- 0 SGGLHGVGSSVVNALSTQLDV V+KNGK+HYQEY+RG VV DLE++GDTD +GTTVHFTP Sbjct: 119 SGGLHGVGSSVVNALSTQLDVHVHKNGKIHYQEYRRGHVVADLEVVGDTDRTGTTVHFTP 17- 8 Query: 181 DPEIFTETTVFDFDKLAKRIQELAFLNRGLRISISDKREGQEVEKEYHYEGGIGSYVEFI 24- 0 DPEIFTETT+FDFDKL KRIQELAFLNRGL+ISI+DKR+G E K YHYEGGI SYVE+I Sbjct: 179 DPEIFTETTIFDFDKLNKRIQELAFLNRGLQISITDKRQGLEQTKHYHYEGGIASYVEYI 23- 8 Query: 241 NENKEVIFENPIYTDGELDGISVEVAMQYTTGYQETVMSFANNIHTHEGGTHEQGFRTAL 30- 0 NENK+VIF+ PIYTDGE+D I+VEVAMQYTTGY E VMSFANNIHTHEGGTHEQGFRTAL Sbjct: 239 NENKDVIFDTPIYTDGEMDDITVEVAMQYTTGYHENVMSFANNIHTHEGGTHEQGFRTAL 29- 8 Query: 301 TRVINDYAKKNKILKENEDNLTGEDVREGLTAVISVKHPNPQFEGQTKTKLGNSEVVKIT 36- 0 TRVINDYA+KNK+LK+NEDNLTGEDVREGLTAVISVKHPNPQFEGQTKTKLGNSEVVKIT Sbjct: 299 TRVINDYARKNKLLKDNEDNLTGEDVREGLTAVISVKHPNPQFEGQTKTKLGNSEVVKIT 35- 8 Query: 361 NRLFSEAFNRFLLENPQVAKKIVEKGILASKARIAAKRAREVTRKKSGLEISNLPGKLAD 42- 0 NRLFSEAF+ FL+ENPQ+AK+IVEKGILA+KAR+AAKRAREVTRKKSGLEISNLPGKLAD Sbjct: 359 NRLFSEAFSDFLMENPQIAKRIVEKGILAAKARVAAKRAREVTRKKSGLEISNLPGKLAD 41- 8 Query: 421 CSSNNAEMNELFIVEGDSAGGSAKSGRNREFQAILPIRGKILNVEKATMDKILANEEIRS 48- 0 CSSNN ELFIVEGDSAGGSAKSGRNREFQAILPIRGKILNVEKA+MDKILANEEIRS Sbjct: 419 CSSNNPAETELFIVEGDSAGGSAKSGRNREFQAILPIRGKILNVEKASMDKILANEEIRS 47- 8 Query: 481 LFTAMGTGFGADFDVSKVRYQKLVIMTDADVDGAHIRTLLLTLIYRFMRPVLEAGYVYIA 54- 0 LFTAMGTGFGA+FDVSK RYQKLV+MTDADVDGAHIRTLLLTLIYR+M+P+LEAGYVYIA Sbjct: 479 LFTAMGTGFGAEFDVSKARYQKLVLMTDADVDGAHIRTLLLTLIYRYMKPILEAGYVYIA 53- 8 Query: 541 QPPIYGVKVGSEIKAYIQPGVNQEEELRQALDTYSSGRSKPTVQRYKGLGEMDDHQLWET 60- 0 QPPIYGVKVGSEIK YIQPG +QE +L++AL YS GR+KPT+QRYKGLGEMDDHQLWET Sbjct: 539 QPPIYGVKVGSEIKEYIQPGADQEIKLQEALARYSEGRTKPTIQRYKGLGEMDDHQLWET 59- 8 Query: 601 TMDPENRLMARVSVDDAAEADKIFDMLMGDRVEPRREFIEANAVYSNLDI 650 TMDPE+RLMARVSVDDAAEADKIFDMLMGDRVEPRREFIE NAVYS LD+ Sbjct: 599 TMDPEHRLMARVSVDDAAEADKIFDMLMGDRVEPRREFIEENAVYSTLDV 648 A related DNA sequence was identified in S. pyogenes <SEQ ID 1317> which encodes the amino acid sequence <SEQ ID 1318>. Analysis of this protein sequence reveals the following: TABLE-US-01303 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1698(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01304 Identities = 584/650 (89%), Positives = 618/650 (94%) Query: 1 MTEETKNMEQRAQEYDASQIQVLEGLEAVRMRPGMYIGSTSKEGLHHLVWEIVDNSIDEA 60 M EE K+ E++ QEYDASQIQVLEGLEAVRMRPGMYIGST+KEGLHHLVWEIVDNSIDEA Sbjct: 1 MIEENKHFEKKMQEYDASQIQVLEGLEAVRMRPGMYIGSTAKEGLHHLVWEIVDNSIDEA 60 Query: 61 LAGFAGHIKVYIEPDNSITVVDDGRGIPVDIQEKTGRPAVETVFTVLHAGGKFGGGGYKV 120- LAGFA HIKV+IE DNSITVVDDGRGIPVDIQ KTGRPAVETVFTVLHAGGKFGGGGYKV Sbjct: 61 LAGFASHIKVFIEADNSITVVDDGRGIPVDIQAKTGRPAVETVFTVLHAGGKFGGGGYKV 120- Query: 121 SGGLHGVGSSVVNALSTQLDVKVYKNGKVHYQEYQRGVVVNDLEIIGDTDLSGTTVHFTP 18- 0 SGGLHGVGSSVVNALSTQLDV+VYKNG++HYQE++RG VV DLE+IG TD++GTTVHFTP Sbjct: 121 SGGLHGVGSSVVNALSTQLDVRVYKNGQIHYQEFKRGAVVADLEVIGTTDVTGTTVHFTP 18- 0 Query: 181 DPEIFTETTVFDFDKLAKRIQELAFLNRGLRISISDKREGQEVEKEYHYEGGIGSYVEFI 24- 0 DPEIFTETT FD+ LAKRIQELAFLNRGL+ISI+DKR G E E+ + YEGGIGSYVEF+ Sbjct: 181 DPEIFTETTQFDYSVLAKRIQELAFLNRGLKISITDKRSGMEQEEHFLYEGGIGSYVEFL 24- 0 Query: 241 NENKEVIFENPIYTDGELDGISVEVAMQYTTGYQETVMSFANNIHTHEGGTHEQGFRTAL 30- 0 N+ K+VIFE PIYTDGEL+GI+VEVAMQYTT YQETVMSFANNIHTHEGGTHEQGFR AL Sbjct: 241 NDKKDVIFETPIYTDGELEGIAVEVAMQYTTSYQETVMSFANNIHTHEGGTHEQGFRAAL 30- 0 Query: 301 TRVINDYAKKNKILKENEDNLTGEDVREGLTAVISVKHPNPQFEGQTKTKLGNSEVVKIT 36- 0 TRVINDYAKKNKILKENEDNLTGEDVREGLTAVISVKHPNPQFEGQTKTKLGNSEVVKIT Sbjct: 301 TRVINDYAKKNKILKENEDNLTGEDVREGLTAVISVKHPNPQFEGQTKTKLGNSEVVKIT 36- 0 Query: 361 NRLFSEAFNRFLLENPQVAKKIVEKGILASKARIAAKRAREVTRKKSGLEISNLPGKLAD 42- 0 NRLFSEAF RFLLENPQVA+KIVEKGILASKARIAAKRAREVTRKKSGLEISNLPGKLAD Sbjct: 361 NRLFSEAFQRFLLENPQVARKIVEKGILASKARIAAKRAREVTRKKSGLEISNLPGKLAD 42- 0 Query: 421 CSSNNAEMNELFIVEGDSAGGSAKSGRNREFQAILPIRGKILNVEKATMDKILANEEIRS 48- 0 CSSN+A NELFIVEGDSAGGSAKSGRNREFQAILPIRGKILNVEKATMDKILANEEIRS Sbjct: 421 CSSNDANQNELFIVEGDSAGGSAKSGRNREFQAILPIRGKILNVEKATMDKILANEEIRS 48- 0 Query: 481 LFTAMGTGFGADFDVSKVRYQKLVIMTDADVDGAHIRTLLLTLIYRFMRPVLEAGYVYIA 54- 0 LFTAMGTGFGADFDVSK RYQKLVIMTDADVDGAHIRTLLLTLIYRFMRPVLEAGYVYIA Sbjct: 481 LFTAMGTGFGADFDVSKARYQKLVIMTDADVDGAHIRTLLLTLIYRFMRPVLEAGYVYIA 54- 0 Query: 541 QPPIYGVKVGSEIKAYIQPGVNQEEELRQALDTYSSGRSKPTVQRYKGLGEMDDHQLWET 60- 0 QPPIYGVKVGSEIK YIQPG++QE++L+ AL+ YS GRSKPTVQRYKGLGEMDDHQLWET Sbjct: 541 QPPIYGVKVGSEIKEYIQPGIDQEDQLKTALEKYSIGRSKPTVQRYKGLGEMDDHQLWET 60- 0 Query: 601 TMDPENRLMARVSVDDAAEADKIFDMLMGDRVEPRREFIEANAVYSNLDI 650 TMDPENRLMARV+VDDAAEADK+FDMLMGDRVEPRR+FIE NAVYS LDI Sbjct: 601 TMDPENRLMARVTVDDAAEADKVFDMLMGDRVEPRRDFIEENAVYSTLDI 650 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 407 A DNA sequence (GBSx0442) was identified in S. agalactiae <SEQ ID 1319> which encodes the amino acid sequence <SEQ ID 1320>. Analysis of this protein sequence reveals the following: TABLE-US-01305 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3186(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01306 >GP: CAA91552 GB: Z67740 unidentified [Streptococcus pneumoniae] Identities = 82/142 (57%), Positives = 105/142 (73%) Query: 45 LKESTADAIAYFIPEEADFLKEYKANEAKVLETPILFQGAKELLAKIQRQGSRNFLVSHR 104- LK ST AI F P +FL++YK NEA+ LE PILF+G +LL I QG R+FLVSHR Sbjct: 2 LKVSTPFAIETFAPNLENFLEKYKENEARELEHPILFEGVSDLLEDILNQGGRHFLVSHR 61 Query: 105 DNQVIVILEKTEIIDYFTEVVTADNGFSRKPSPESMLYLKEKYQIDNCLVIGDRDIDKQA 16- 4 ++QV+ ILEKT I YFTEVVT+ +GF RKP+PESMLYL+ERYQI + LVIGDR ID +A Sbjct: 62 NDQVLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKYQISSGLVIGDRPIDIEA 121- Query: 165 GESAGFDTLLVDGSKSLMEIIE 186 G++AG DT L +L ++++ Sbjct: 122 GQAAGLDTHLFTSIVNLRQVLD 143 A related DNA sequence was identified in S. pyogenes <SEQ ID 1321> which encodes the amino acid sequence <SEQ ID 1322>. Analysis of this protein sequence reveals the following: TABLE-US-01307 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2472(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01308 Identities = 122/185 (65%), Positives = 145/185 (77%) Query: 1 MNYHDYIWDLGGTLLDNYESSTRAFVETLKEFGYQADHDSVYQKLKESTADAIAYFIPEE 60 MNY DYIWDLGGTLLDNYE ST+AFV+TL F DHD+VYQKLKESTA A+A F P E Sbjct: 4 MNYQDYIWDLGGTLLDNYELSTQAFVQTLAFFSLPGDHDAVYQKLKESTAIAVAMFAPNE 63 Query: 61 ADFLKEYKANEAKVLETPILFQGAKELLAKIQRQGSRNFLVSHRDNQVIVILEKTEIIDY 120- +FL Y+ EA L PI GAKE+L KI GSRNFL+SHRD QV +LE+ ++ Y Sbjct: 64 PEFLHVYRLREADKLAQPIWCLGAKEILGKIATSGSRNFLISHRDCQVNQLLEQAGLLIY 123- Query: 121 FTEVVTADNGFSRKPSPESMLYLKEKYQIDNCLVIGDRDIDKQAGESAGFDTLLVDGSKS 18- 0 FTEVVTA NGF+RKP+PES+ YLKEKY I++ LVIGDR IDKQAG++AGF+TLLVDG K+ Sbjct: 124 FTEVVTASNGFARKPNPESLFYLKEKYDINSGLVIGDRLIDKQAGQAAGFNTLLVDGRKN 18- 3 Query: 181 LMEII 185 L+EI+ Sbjct: 184 LLEIV 188 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 408 A DNA sequence (GBSx0443) was identified in S. agalactiae <SEQ ID 1323> which encodes the amino acid sequence <SEQ ID 1324>. This protein is predicted to be stage V sporulation protein E (rodA). Analysis of this protein sequence reveals the following: TABLE-US-01309 Possible site: 42 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -11.15 Transmembrane 206-222 (177-226) INTEGRAL Likelihood = -10.14 Transmembrane 58-74 (50-82) INTEGRAL Likelihood = -9.34 Transmembrane 182-198 (177-205) INTEGRAL Likelihood = -8.55 Transmembrane 158-174 (156-177) INTEGRAL Likelihood = -8.12 Transmembrane 300-316 (299-324) INTEGRAL Likelihood = -2.66 Transmembrane 86-102 (83-102) INTEGRAL Likelihood = -2.34 Transmembrane 338-354 (338-357) ----- Final Results ----- bacterial membrane --- Certainty = 0.5458(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9669> which encodes amino acid sequence <SEQ ID 9670> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01310 >GP: CAB15838 GB: Z99123 alternate gene name: ipa-42d~similar to cell-division protein [Bacillus subtilis] Identities = 142/392 (36%), Positives = 237/392 (60%), Gaps = 23/392 (5%) Query: 10 QKSNYFKGQIDYAVVIPVFFLLMIGLASIYVA-TMNDYPSNIYIAMFQQVSWIIMGCIIA 68 - Q+S +++G D + VFF+ I + SIY A Y + +I QQ+ + ++G + Sbjct: 7 QQSPFYQG--DLIFIFGVFFI--ISVVSIYAAGQFGQYGNTDWI---QQIVFYLLGAVAI 59 Query: 69 FVVMLFSTEFLWKATPYLYALGLTLMVLPLIFYSPQLFAAT--GAKNWVTIGSVTLFQPS 126- V++ F E L K + Y++ +G+ +++ I SP+ A GAK+W IG +T+ QPS Sbjct: 60 TVLLYFDLEQLEKLSLYIFIIGILSLIILKI--SPESIAPVIKGAKSWFRIGRITI-QPS 116- Query: 127 EFMKISYILMLSRITVSFHQKNRKTFQDDWKLL-GLFGLVTLPVMILLMLQKDLGTALVF 18- 5 EFMK+ I+ML+ + + K +T +DD LL + G+ +PV ++LM +D GTA + Sbjct: 117 EFMKVGLIMMLASVIGKANPKGVRTLRDDIHLLLKIAGVAVIPVGLILM--QDAGTAGIC 17- 4 Query: 186 LAILSGLILLSGISWWIILPILSTIVLFIASFLMIFISPNGKEWFYNLGMDTYQINRLSA 24- 5 + I+ ++ +SGI+W +I I + +L I+ L++ I N + ++G+ YQI R+++ Sbjct: 175 MFIVLVMVFMSGINWKLIAIIAGSGILLISLILLVMI--NFPDVAKSVGIQDYQIKRVTS 23- 2 Query: 246 WIDPFSFAD---SIAYQQTQGMVSIGSGGVTGKGFNILELSVPVRESDMIFTVIAENFGF 30- 2 W+ + + ++Q Q +++IGSGG+ G G + L++ VP +D IF++I E+FGF Sbjct: 233 WVSASNETQEDSNDSWQVDQAIMAIGSGGILGNGISNLKVYVPESTTDFIFSIIGESFGF 29- 2 Query: 303 IGSAIVLGLYLIIIYRMLRIT--IESNNQFYTFISTGFIMMIVFHVFENIGAAVGILPLT 36- 0 IG AIV+ ++ +IYR++ + I N+F +F G+ +IV H F+NIG +GI+P+T Sbjct: 293 IGCAIVVIMFFFLIYRLVVLIDKIHPFNRFASFFCVGYTALIVIHTFQNIGMNIGIMPVT 35- 2 Query: 361 GIPLPFISQGGSSLLSNLIGIGLVLSMSYQNT 392 GIPL F+S GGSS LS LIG G+V + S Q T Sbjct: 353 GIPLLFVSYGGSSTLSTLIGFGIVYNASVQLT 384 There is also homology to SEQ ID 1028. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 409 A DNA sequence (GBSx0444) was identified in S. agalactiae <SEQ ID 1325> which encodes the amino acid sequence <SEQ ID 1326>. Analysis of this protein sequence reveals the following:

TABLE-US-01311 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3195(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1327> which encodes the amino acid sequence <SEQ ID 1328>. Analysis of this protein sequence reveals the following: TABLE-US-01312 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2735(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01313 Identities = 38/55 (69%), Positives = 48/55 (87%) Query: 8 DEFKEAIDKGYISGNTVAIVRKNGKIFDYVLLHEEVREEEVVTVERVLDVLRKLS 62 DEFK+AID GYI+G+TVAIVRK+G+IFDYVL HE+V+ EVVT E+V +VL +LS Sbjct: 5 DEFKQAIDNGYIAGDTVAIVRKDGQIFDYVLPHEKVKNGEVVTKEKVEEVLVELS 59 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 410 A DNA sequence (GBSx0445) was identified in S. agalactiae <SEQ ID 1329> which encodes the amino acid sequence <SEQ ID 1330>. Analysis of this protein sequence reveals the following: TABLE-US-01314 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4241(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1331> which encodes the amino acid sequence <SEQ ID 1332>. Analysis of this protein sequence reveals the following: TABLE-US-01315 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4551(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01316 Identities = 57/66 (86%), Positives = 63/66 (95%) Query: 1 MSQEKLKSKLDQAKGGAKEGFGKITGDKELEAKGFIEKTIAKGKELADDAKDAVEGAVDA 60 - MS+EKLKSK++QA GG KEG GK+TGDKELEAKGF+EKTIAKGKELADDAK+AVEGAVDA Sbjct: 1 MSEEKLKSKIEQASGGLKEGAGKLTGDKELEAKGFVEKTIAKGKELADDAKEAVEGAVDA 60 Query: 61 VKEKLK 66 VKEKLK Sbjct: 61 VKEKLK 66 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 411 A DNA sequence (GBSx0447) was identified in S. agalactiae <SEQ ID 1333> which encodes the amino acid sequence <SEQ ID 1334>. This protein is predicted to be TnpA (orfB). Analysis of this protein sequence reveals the following: TABLE-US-01317 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3961(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9667> which encodes amino acid sequence <SEQ ID 9668> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 1335> which encodes the amino acid sequence <SEQ ID 1336>. Analysis of this protein sequence reveals the following: TABLE-US-01318 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3365(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01319 Identities = 152/160 (95%), Positives = 154/160 (96%) Query: 1 MKNMALPKMATVKTKTALKKTQKTYPQNLLNQKFNPDKPNQVWSTDFTYISIGYKKYVYL 60 MKNMALPKMATVK KTALK+TQKTYPQNLLNQKFNPDKPNQVWSTDFTYISIGYKKYVYL Sbjct: 194 MKNMALPKMATVKPKTALKRTQKTYPQNLLNQKFNPDKPNQVWSTDFTYISIGYKKYVYL 25- 3 Query: 61 CAIIDLYSRKYIAWKLSHRMDAKLACDTLELALNKRKIEGTLLFHSDQGSQFKAREFRKI 120- CAI+DLYSRK IAWKLSHRMDAKLACDTLELALNKRKIEGTLLFHSDQGSQFKARE RKI Sbjct: 254 CAILDLYSRKCIAWKLSHRMDAKLACDTLELALNKRKIEGTLLFHSDQGSQFKARELRKI 31- 3 Query: 121 IDDNNIMHSFSKPRYPYDNAVTEAFFKYLKHRQINQKNYQ 160 IDDN IMHSFSKP YPYDNAVTEAFFKYLKHRQINQK YQ Sbjct: 314 IDDNTIMHSFSKPGYPYDNAVTEAFFKYLKHRQINQKKYQ 353 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 412 A DNA sequence (GBSx0448) was identified in S. agalactiae <SEQ ID 1337> which encodes the amino acid sequence <SEQ ID 1338>. Analysis of this protein sequence reveals the following: TABLE-US-01320 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1090(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 413 A DNA sequence (GBSx0449) was identified in S. agalactiae <SEQ ID 1339> which encodes the amino acid sequence <SEQ ID 1340>. This protein is predicted to be histidine kinase (resE). Analysis of this protein sequence reveals the following: TABLE-US-01321 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.57 Transmembrane 17-33 (6-38) INTEGRAL Likelihood = -4.67 Transmembrane 147-163 (142-166) ----- Final Results ----- bacterial membrane --- Certainty = 0.5628(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01322 >GP: AAD25109 GB: AF140356 VncS [Streptococcus pneumoniae] Identities = 178/435 (40%), Positives = 281/435 (63%), Gaps = 1/435 (0%) Query: 1 MKKLKIFPKMFIQIFSILGILIILVHSLFFFIFPKTYLETRKVKIHIMADEISKNMNGKE 60 MK+ +F K+FI FSI +L+I +H +F+FP TYL R+ I A I++++ GK+ Sbjct: 1 MKRTGLFAKIFIYTFSIFSVLVICLHLAIYFLFPSTYLSHRQETIGQKATAIAQSLEGKD 60 Query: 61 LKYLDQTLELYSKSSDIKVFIKKNNNKNELQINDNINVNVKSDSNSLIIEEREIKLHDGK 120- + ++Q L+LYS++SDIK +K +++L++ D++ ++ + SL IEERE+K DG Sbjct: 61 RQSIEQVLDLYSQTSDIKGTVKGEMTEDKLEVKDSLPLDTDRQTTSLFIEEREVKTQDGG 120- Query: 121 KIHLQFVSTADMQKDAKDLSLKFLPYSLSISFLFSIVISLIYAKSIKNNIQEITMVTDKM 18- 0 + LQF+++ D+QK+A+ +SL+FLPY+L SFL S++++ IYA++I I EI VT +M Sbjct: 121 TMILQFLASMDLQKEAEQISLQFLPYTLLASFLISLLVAYIYARTIVAPILEIKRVTRRM 18- 0 Query: 181 IKLDKETRLKISSNDEIGQLKQQINDLYCALLNTINDLEFKNKEILKLEKLKYDFFKGAS 24- 0 + LD + RL++ S DEIG LK+QIN LY LL I DL KN+ IL+LEK+K +F +GAS Sbjct: 181 MDLDSQVRLRVDSKDEIGNLKEQINSLYQHLLTVIADLHEKNEAILQLEKMKVEFLRGAS 24- 0 Query: 241 HELKTPLSSLKILLENMKYNIGKYKDRDFYISECINIVDNLTKNVSQILSFYSIKDLNND 30- 0 HELKTPL+SLKIL+ENM+ NIG+YKDRD Y+ + IVD L +V QILS S+++L +D Sbjct: 241 HELKTPLASLKILIENMRENIGRYKDRDQYLGVALGIVDELNHHVLQILSLSSVQELRDD 30- 0 Query: 301 EEYLNVGDTLDEVLEKYSILVNQKKININKELLDYNIYIGKTALNIVFSNLISNAVKYTN 36- 0 E +++ +++ Y++L ++++ I+ L Y+ + + ++ SNLISNA+K++ Sbjct: 301 RETIDLLQMTQNLVKDYALLAKERELQIDNSLTHQQAYLNPSVMKLILSNLISNAIKHSV 36- 0 Query: 361 RNGIINIKIANDWLLIENSYDKNKISKINKILDASFDLKLDNSNGLGLNIVKNILNKYNI 42- 0 G++ I L IENS + K+ + + K+ S G+GL +VK++L + Sbjct: 361 PGGLVRIGEREGELFIENSCSSEEQEKLAQSFSDNASRKVKGS-GMGLFVVKSLLEHEKL 41- 9 Query: 421 KYEILHGENYFIFKI 435 Y EN F I Sbjct: 420 AYRFEMEENSLTFFI 434 A related DNA sequence was identified in S. pyogenes <SEQ ID 1341> which encodes the amino acid sequence <SEQ ID 1342>. Analysis of this protein sequence reveals the following: TABLE-US-01323 Possible site: 37 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.83 Transmembrane 14-30 (6-35) INTEGRAL Likelihood = -2.44 Transmembrane 157-173 (156-174) ----- Final Results ----- bacterial membrane --- Certainty = 0.5734(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01324 >GP: AAD25109 GB: AF140356 VncS [Streptococcus pneumoniae] Identities = 123/455 (27%), Positives = 223/455 (48%), Gaps = 23/455 (5%) Query: 3 LIKKTFLVINGLIIVVVTSILLVLYFAMPIYYTKVKDKEVKCEFDQTSKQIKGKTVTEIR 62 L K F+ + V+V + L +YF P Y + + + + ++ ++GK I Sbjct: 6 LFAKIFIYTFSIFSVLVICLHLAIYFLFPSTYLSHRQETIGQKATAIAQSLEGKDRQSIE 65 Query: 63 DILTKKINKDNIWYSLVDSDNQLLYPSLQLLDGVSESKDSQNVNIVTTFDNSYSNVKVMS 122- +L +I ++ ++ L++ D + D Q ++ + Sbjct: 66 QVLDLYSQTSDIKGTV---KGEMTEDKLEVKDSLPLDTDRQTTSLF-----------IEE 111- Query: 123 QKVTLRDGKKMTLLGQSSLQPVTDASKVLLDLYPSLLIFSVTVGSIVAYLYSRTSSRRIL 18- 2 ++V +DG M L +S+ +A ++ L P L+ S + +VAY+Y+RT IL Sbjct: 112 REVKTQDGGTMILQFLASMDLQKEAEQISLQFLPYTLLASFLISLLVAYIYARTIVAPIL 17- 1 Query: 183 SMSQTAKKMVNLEPNLTCTIHGKDEIAMLASDINRLYASLSTSIKSLQKEYEKASDSERE 24- 2 + + ++M++L+ + + KDEI L IN LY L T I L ++ E E+ Sbjct: 172 EIKRVTRRMMDLDSQVRLRVDSKDEIGNLKEQINSLYQHLLTVIADLHEKNEAILQLEKM 23- 1 Query: 243 KSEFLRMTSHELKTPITSVIGMIDGMLYNVGDFADRDKYLRKCRDVLEGQAQLVQSILSL 30- 2 K EFLR SHELKTP+ S+ +I+ M N+G + DRD+YL +++ V ILSL Sbjct: 232 KVEFLRGASHELKTPLASLKILIENMRENIGRYKDRDQYLGVALGIVDELNHHVLQILSL 29- 1 Query: 303 SKIETLASQNQELFSLKSSLEEEMEVFLVLSELKHLKVTINLEEQFVKANKVYLLKAIKN 36- 2 S ++ L ++E L + ++ + +L++ + L++ +L Q N + + N Sbjct: 292 SSVQEL-RDDRETIDLLQMTQNLVKDYALLAKERELQIDNSLTHQQAYLNPSVMKLILSN 35- 0 Query: 363 IIDNAFHYTKSGGQVMIQLKDNQLVIKNEAETLLTQQQMKQLFQPFYRPDYSRNRKDGGT 42- 2 +I NA ++ GG V I ++ +L I+N + ++ ++L Q F + +RK G+ Sbjct: 351 LISNAIKHSVPGGLVRIGEREGELFIENSC----SSEEQEKLAQSF---SDNASRKVKGS 40- 3 Query: 423 GLGLFITHQILDQHHLAYRFVVLDQRWMVFTIDFP 457 G+GLF+ +L+ LAYRF +++ + F IDFP Sbjct: 404 GMGLFVVKSLLEHEKLAYRF-EMEENSLTFFIDFP 437 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01325 Identities = 108/454 (23%), Positives = 220/454 (47%), Gaps = 22/454 (4%) Query: 4 LKIFPKMFIQIFSILGILIILVHSLFFFIFPKTYLETRKVKIHIMADEISKNMNGKELKY 63 +++ K F+ I ++ +++ + + +F P Y + + ++ D+ SK + GK + Sbjct: 1 VRLIKKTFLVINGLIIVVVTSILLVLYFAMPIYYTKVKDKEVKCEFDQTSKQIKGKTVTE 60 Query: 64 LDQTLELYSKSSDIKVFIKKNNNK------------NELQINDNINVNVKSDSN--SLII 109- + L +I + ++N+ +E + + N+N+ D++ ++ + Sbjct: 61 IRDILTKKINKDNIWYSLVDSDNQLLYPSLQLLDGVSESKDSQNVNIVTTFDNSYSNVKV 120- Query: 110 EEREIKLHDGKKIHLQFVSTADMQKDAKDLSLKFLPYSLSISFLFSIVISLIYAKSIKNN 16- 9 +++ L DGKK+ L S+ DA + L P L S +++ +Y+++ Sbjct: 121 MSQKVTLRDGKKMTLLGQSSLQPVTDASKVLLDLYPSLLIFSVTVGSIVAYLYSRTSSRR 18- 0 Query: 170 IQEITMVTDKMIKLDKETRLKISSNDEIGQLKQQINDLYCALLNTINDLEFKNKEILKLE 22- 9 I ++ KM+ L+ I DEI L IN LY +L +I L+ + ++ E Sbjct: 181 ILSMSQTAKKMVNLEPNLTCTIHGKDEIAMLASDINRLYASLSTSIKSLQKEYEKASDSE 24- 0 Query: 230 KLKYDFFKGASHELKTPLSSLKILLENMKYNIGKYKDRDFYISECINIVDNLTKNVSQIL 28- 9 + K +F + SHELKTP++S+ +++ M YN+G + DRD Y+ +C ++++ + V IL Sbjct: 241 REKSEFLRMTSHELKTPITSVIGMIDGMLYNVGDFADRDKYLRKCRDVLEGQAQLVQSIL 30- 0 Query: 290 SFYSIKDL-NNDEEYLNVGDTLDEVLEKYSILVNQKKININKELLDYNIYIGKTALNIVF 34- 8 S I+ L + ++E ++ +L+E +E + +L K + + L + + K L Sbjct: 301 SLSKIETLASQNQELFSLKSSLEEEMEVFLVLSELKHLKVTINLEEQFVKANKVYLLKAI 36- 0 Query: 349 SNLISNAVKYTNRNGIINIKIANDWLLIENSYDKNKISKINKILDASF------DLKLDN 40- 2 N+I NA YT G + I++ ++ L+I+N + + K L F + D Sbjct: 361 KNIIDNAFHYTKSGGQVMIQLKDNQLVIKNEAETLLTQQQMKQLFQPFYRPDYSRNRKDG 42- 0 Query: 403 SNGLGLNIVKNILNKYNIKYE-ILHGENYFIFKI 435 GLGL I IL+++++ Y ++ + + +F I Sbjct: 421 GTGLGLFITHQILDQHHLAYRFVVLDQRWMVFTI 454 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 414 A DNA sequence (GBSx0450) was identified in S. agalactiae <SEQ ID 1343> which encodes the amino acid sequence <SEQ ID 1344>. This protein is predicted to be response regulator (regX3). Analysis of this protein sequence reveals the following: TABLE-US-01326 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.80 Transmembrane 50-66 (50-66) ----- Final Results ----- bacterial membrane --- Certainty = 0.1319(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9665> which encodes amino acid sequence <SEQ ID 9666> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01327 >GP: AAD25108 GB: AF140356 VncR [Streptococcus pneumoniae] Identities = 131/218 (60%), Positives = 176/218 (80%), Gaps = 1/218 (0%) Query: 5 MKILTVEDDKLIREGISEYLSEFGYTVIQAKDGREALSKFNS-DINLVILDIQIPFINGL 63 MKIL VED+++IREG+S+YL++ GY I+A DG+EAL +F+S ++ LV+LDIQ+P +NGL Sbjct: 1 MKILIVEDEEMIREGVSDYLTDCGYETIEAADGQEALEQFSSYEVALVLLDIQMPKLNGL 60 Query: 64 EVLKEIRKKSNLPILILTAFSDEEYKIDAFTNLVDGYVEKPFSLPVLKARIDSLIKKNFG 123- EVL EIRK S +P+L+LTAF DEEYK+ AF +L DGY+EKPFSL +LK R+D++ K+ + Sbjct: 61 EVLAEIRKTSQVPVLMLTAFQDEEYKMSAFASLADGYLEKPFSLSLLKVRVDAIFKRYYD 120- Query: 124 HLEKFEYKNLSVNFNSYTAKINDEKIDVNAKELEILKCLLDNDGQVLTRMQIIDYVWKDS 18- 3 F YK+ V+F SY+A + +++ +NAKELEIL L+ N+G+ LTR QIID VWK + Sbjct: 121 TGRIFSYKDTKVDFESYSASLAGQEVPINAKELEILDYLVKNEGRALTRSQIIDAVWKAT 18- 0 Query: 184 EEIPYDRVVDVYIKELRKKLQLDCITTIRNVGYKLERK 221 +E+P+DRV+DVYIKELRKKL LDCI T+RNVGYKLERK Sbjct: 181 DEVPFDRVIDVYIKELRKKLDLDCILTVRNVGYKLERK 218 A related DNA sequence was identified in S. pyogenes <SEQ ID 1345> which encodes the amino acid sequence <SEQ ID 1346>. Analysis of this protein sequence reveals the following: TABLE-US-01328 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.60 Transmembrane 48-64 (48-64) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01329 >GP: AAF72358 GB: AF192329 VanRB [Enterococcus faecalis] Identities = 88/215 (40%), Positives = 128/215 (58%), Gaps = 2/215 (0%) Query: 3 KILVVEDDDTISQVICEFLKANNYDPDCVFDGQAALDKWQTTSYDLIILDIMLPSLSGLE 62 +IL+VEDDD I + FL Y D DG A K+ +Y L+ILDIMLP ++G E Sbjct: 4 RILLVEDDDHICNTVRGFLAEAGYQVDACTDGNEAYTKFYENTYQLVILDIMLPGMNGHE 63 Query: 63 VLKTIRKTSDVPIIMLTALDDEYTQLVSFNHLISDYVTKPFSPLILIKRIENVLRVSTPD 122- +L+ R +D PI+M+TAL D+ Q+ +F+ DYVTKPF IL+KR+E +LR S Sbjct: 64 LLREFRAKNDTPILMMTALSDDENQIRAFDAEADDYVTKPFKMQILLKRVEALLRRSGAL 123- Query: 123 EKR-QIGDLLVDETEHSVYWQGTLVKLTKKEYDIIDYLAKRHQKIVTRDQLMDDIWGYS- 18- 0 K ++G L + + +V GT + LT+KE++I+ L + + +T + ++ IWGY Sbjct: 124 AKEIRVGRLTLLPEDFTVLCDGTELPLTRKEFEILLLLVQNKGRTLTHEIILSRIWGYDF 18- 3 Query: 181 ELDTRVLDNHIKNLRKKMTGIPLKTITGMGYLLGE 215 E D + HIKNLR K+ +KTI G+GY L E Sbjct: 184 EGDGSTVHTHIKNLRAKLPENIIKTIRGVGYRLEE 218 An alignment of the GAS and GBS proteins is shown below:

TABLE-US-01330 Identities = 80/214 (37%), Positives = 126/214 (58%), Gaps = 4/214 (1%) Query: 6 KILTVEDDKLIREGISEYLSEFGYTVIQAKDGREALSKFNS-DINLVILDIQIPFINGLE 64 KIL VEDD I + I E+L Y DG+ AL K+ + +L+ILDI +P ++GLE Sbjct: 3 KILVVEDDDTISQVICEFLKANNYDPDCVFDGQAALDKWQTTSYDLIILDIMLPSLSGLE 62 Query: 65 VLKEIRKKSNLPILILTAFSDEEYKIDAFTNLVDGYVEKPFSLPVLKARIDSLIKKNFGH 124- VLK IRK S++PI++LTA DE ++ +F +L+ YV KPFS +L RI+++++ + Sbjct: 63 VLKTIRKTSDVPIIMLTALDDEYTQLVSFNHLISDYVTKPFSPLILIKRIENVLRVSTPD 122- Query: 125 LEKFEYKNLSVNFNSYTAKINDEKIDVNAKELEILKCLLDNDGQVLTRMQIIDYVWKDSE 18- 4 EK + +L V+ ++ + + KE +I+ L +++TR Q++D +W SE Sbjct: 123 -EKRQIGDLLVDETEHSVYWQGTLVKLTKKEYDIIDYLAKRHQKIVTRDQLMDDIWGYSE 18- 1 Query: 185 EIPYDRVVDVYIKELRKKLQLDCITTIRNVGYKL 218 RV+D +IK LRKK+ + TI +GY L Sbjct: 182 --LDTRVLDNHIKNLRKKMTGIPLKTITGMGYLL 213 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 415 A DNA sequence (GBSx0451) was identified in S. agalactiae <SEQ ID 1347> which encodes the amino acid sequence <SEQ ID 1348>. This protein is predicted to be Vexp3. Analysis of this protein sequence reveals the following: TABLE-US-01331 Possible site: 49 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.68 Transmembrane 423-439 (413-447) INTEGRAL Likelihood = -10.67 Transmembrane 16-32 (12-37) INTEGRAL Likelihood = -9.77 Transmembrane 303-319 (301-326) INTEGRAL Likelihood = -3.13 Transmembrane 343-359 (343-367) ----- Final Results ----- bacterial membrane --- Certainty = 0.6074(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01332 >GP: AAD47594 GB: AF140784 Vexp3 [Streptococcus pneumoniae] Identities = 280/458 (61%), Positives = 363/458 (79%), Gaps = 3/458 (0%) Query: 1 MIKNAFAYVTRKSLKSLIIILVILSMATLSIISLSIKDATDRASKETFANITNSFSMEIN 60 M+ NAFAYVTRK KS++I L+IL MA+LS++ LSIK AT +AS+ETF NITNSFSM+IN Sbjct: 1 MLHNAFAYVTRKFFKSIVIFLIILLMASLSLVGLSIKGATAKASQETFKNITNSFSMQIN 60 Query: 61 RQVNPGTPRGGGNVKGEDIKKISQTNSIDSYVKRINSVADLVDHDIIETQDTLANQSPER 120- R+VN GTPRG GN+KGEDIKKI++ +I+SYVKRIN++ DL +D+IET +T N + +R Sbjct: 61 RRVNQGTPRGAGNIKGEDIKKITENKAIESYVKRINAIGDLTGYDLIETPETKKNLTADR 120- Query: 121 AKNFKRTVMLTGVNDSAKETKFVSEAYKLVEGKHLENKDKNKILMHKDLAKKNNLKVGDK 18- 0 AK F ++M+TGVNDS+KE KFVS +YKLVEG+HL N DK+KIL+HKDLA K+ KVGDK Sbjct: 121 AKRFGSSLMITGVNDSSKEDKFVSGSYKLVEGEHLTNDDKDKILLHKDLAAKHGWKVGDK 18- 0 Query: 181 IKIKSNLFDADNEKVANETVEVEIKGLFDGHNSGGVSAAQELYENTLITDVHSAAKVYGN 24- 0 +K+ SN++DADNEK A ETVEV IKGLFDGHN V+ +QELYENT ITD+H+AAK+YG Sbjct: 181 VKLDSNIYDADNEKGAKETVEVTIKGLFDGHNKSAVTYSQELYENTAITDIHTAAKLYGY 24- 0 Query: 241 TEDTAVYQDATFFVKGDKNLDSVIKDL-GKLDINWREYNLIKSSSNYPALQQSISGIYSI 29- 9 TEDTA+Y DATFFV DKNLD V+K+L G INW+ Y L+KSSSNYPAL+QSISG+Y + Sbjct: 241 TEDTAIYGDATFFVTADKNLDDVMKELNGISGINWKSYTLVKSSSNYPALEQSISGMYKM 30- 0 Query: 300 SNKLFVGSLIFAGVVVSLLLFLWMNARKKEIAVLLSLGISKLEIFGQFIIEMVFISIPAL 35- 9 +N LF GSL F+ ++++LLL LW+NAR+KE+ +LLS+G+ + I GQFI E + I+IPAL Sbjct: 301 ANLLFWGSLSFSVLLLALLLSLWINARRKEVGILLSIGLKQASILGQFITESILIAIPAL 36- 0 Query: 360 LGSYFLAQYTADKLGNNILNKVTGDIAKQIARQSASSQLGGGAEAEGFNKTLSGLDINV- 41- 8 + +YFLA YTA +GN +L VT +AKQ ++ + +S LGGGAE +GF+KTLS LDI++ Sbjct: 361 VSAYFLANYTARAIGNTVLANVTSGVAKQASKAAQASNLGGGAEVDGFSKTLSSLDISIQ 42- 0 Query: 419 LPKFIIYVVIFMSFVLLVSLILSSIYTLRKNPKELLID 456 FII V+ + V+LV + L+S LRK PKELL+D Sbjct: 421 TSDFIIIFVLALVLVVLV-MALASSNLLRKQPKELLLD 457 A related DNA sequence was identified in S. pyogenes <SEQ ID 1349> which encodes the amino acid sequence <SEQ ID 1350>. Analysis of this protein sequence reveals the following: TABLE-US-01333 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.90 Transmembrane 19-35 (16-43) INTEGRAL Likelihood = -7.27 Transmembrane 371-387 (359-392) INTEGRAL Likelihood = -7.01 Transmembrane 335-351 (326-357) INTEGRAL Likelihood = -6.21 Transmembrane 282-298 (276-308) ----- Final Results ----- bacterial membrane --- Certainty = 0.6158(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01334 >GP: AAC24912 GB: AF012285 YknZ [Bacillus subtilis] Identities = 176/408 (43%), Positives = 250/408 (61%), Gaps = 16/408 (3%) Query: 1 MENWKFALSSIWGHKMRSILTMLGIIIGVAAVVIIMGLGNAMKNSVTSTFSSKQKDIQLY 60 +EN + ALSS+ HKMRSILTMLGIIIGV +V++++ +G + + + S ++LY Sbjct: 4 LENIRMALSSVLAHKMRSILTMLGIIIGVGSVIVVVAVGQGGEQMLKQSISGPGNTVELY 63 Query: 61 FQEKGEE--EDLYAGLHTHENNHEVKPEWLEQIVKDIDGIDSYYFTNSATSTISYEKKKV 118- + EE + A + +++K +K I+GI + S + Y +++ Sbjct: 64 YMPSDEELASNPNAAAESTFTENDIKG------LKGIEGIKQVVASTSESMKARYHEEET 117- Query: 119 DNASIIGVSKDYFNIKNYDIVAGRTLTDNDYSNFSRIILLDTVLADDLFGKGNYKSALNK 17- 8 D A++ G++ Y N+ + I +GRT TDND+ +R+ ++ +A +LF K S L + Sbjct: 118 D-ATVNGINDGYMNVNSLKIESGRTFTDNDFLAGNRVGIISQKMAKELFDK---TSPLGE 17- 3 Query: 179 VVSLSDKDYLVIGVYKTDQTPVSFDGLSGGAVMANTQVASEFGTKEIGSIYIHVNDIQNS 23- 8 VV ++ + +IGV K +SFD LS V N + S FGT + ++ + V + Sbjct: 174 VVWINGQPVEIIGVLKKVTGLLSFD-LSEMYVPFN-MMKSSFGTSDFSNVSLQVESADDI 23- 1 Query: 239 MNLGNQAADMLTNISHIKDGQYAVPDNSKIVEEINSQFSIMTTVIGSIAAISLLVGGIGV 29- 8 + G +AA L N +H + Y V + +I I +IMTT+IGSIA ISLLVGGIGV Sbjct: 232 KSAGKEAAQ-LVNDNHGTEDSYQVMNMEEIAAGIGKVTAIMTTIIGSIAGISLLVGGIGV 29- 0 Query: 299 MNIMLVSVTERTREIGLRKALGATRLKILSQFLIESVVLTVLGGLIGLLLAQLSVGALGN 35- 8 MNIMLVSVTERTREIG+RK+LGATR +IL+QFLIESVVLT++GGL+G+ + AL + Sbjct: 291 MNIMLVSVTERTREIGIRKSLGATRGQILTQFLIESVVLTLIGGLVGIGIG-YGGAALVS 34- 9 Query: 359 AMTLKGACISLDVALIAVLFSASIGVFFGMLPANKASKLDPIEALRYE 406 A+ + IS V VLFS IGV FGMLPANKA+KLDPIEALRYE Sbjct: 350 AIAGWPSLISWQVVCGGVLFSMLIGVIFGMLPANKAAKLDPIEALRYE 397 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01335 Identities = 56/247 (22%), Positives = 101/247 (40%), Gaps = 42/247 (17%) Query: 147 YKLVEGKHLENKDKNKI--------LMHKDLAKKNNLK--------VGDKIKIKSNLFDA 19- 0 Y +V G+ L + D + ++ DL K N K + DK + ++ Sbjct: 136 YDIVAGRTLTDNDYSNFSRIILLDTVLADDLFGKGNYKSALNKVVSLSDKDYLVIGVYKT 19- 5 Query: 191 DNEKVANETVEVEIKGLFDGHNSGGVSAAQELYENTLITDVHSAAKVYGNTEDTAVYQDA 25- 0 D V+ FDG + G V A NT + A +G E ++Y Sbjct: 196 DQTPVS-----------FDGLSGGAVMA------NTQV------ASEFGTKEIGSIYIHV 23- 2 Query: 251 TFFVKGDKNLDSVIKDL--GKLDINWREYNLIKSSSNYPALQQSISGIYSISNKLFVGSL 30- 8 ++ NL + D+ I +Y + +S + S + ++ + SL Sbjct: 233 ND-IQNSMNLGNQAADMLTNISHIKDGQYAVPDNSKIVEEINSQFSIMTTVIGSIAAISL 29- 1 Query: 309 IFAGVVVSLLLFLWMNARKKEIAVLLSLGISKLEIFGQFIIEMVFISIPALLGSYFLAQY 36- 8 + G+ V ++ + + R +EI + +LG ++L+I QF+IE V +++ L LAQ Sbjct: 292 LVGGIGVMNIMLVSVTERTREIGLRKALGATRLKILSQFLIESVVLTVLGGLIGLLLAQL 35- 1 Query: 369 TADKLGN 375 + LGN Sbjct: 352 SVGALGN 358 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 416 A DNA sequence (GBSx0452) was identified in S. agalactiae <SEQ ID 1351> which encodes the amino acid sequence <SEQ ID 1352>. This protein is predicted to be Vexp2 (b0879). Analysis of this protein sequence reveals the following: TABLE-US-01336 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3194(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01337 >GP: AAD47593 GB: AF140784 Vexp2 [Streptococcus pneumoniae] Identities 142/207 (68%), Positives = 169/207 (81%) Query: 1 MDILEIKNVNYSYANSKEKVLSGVNQKFELGKFYAIVGKSGTGKSTLLSLLAGLDKVQTG 60- M +L++++V Y Y N+ E VL +N FE GKFY+I+G+SG GKSTLLSLLAGLD G Sbjct: 1 MTLLQLQDVTYRYKNTAEAVLYQINYNFEPGKFYSIIGESGAGKSTLLSLLAGLDSPVEG 60- Query: 61 KILFKNEDIEKKGYSNHRKNNISLVFQNYNLIDYLSPIENIRLVNKSVDESILFELGLDK 12- 0 ILF+ EDI KKGYS HR ++ISLVFQNYNLIDYLSP+ENIRLVNK ++ L ELGLD+ Sbjct: 61 SILFQGEDIRKKGYSYHRMHHISLVFQNYNLIDYLSPLENIRLVNKKASKNTLLELGLDE 12- 0 Query: 121 KQIKRNVMKLSGGQQQRVAIARALVSDAPIILADEPTGNLDSVTAGEIINILKELAQDRN 18- 0 QIKRNV++LSGGQQQRVAIAR+LVS+AP+ILADEPTGNLD TAG+I+ +LK LAQ Sbjct: 121 SQIKRNVLQLSGGQQQRVAIARSLVSEAPVILADEPTGNLDPKTAGDIVELLKSLAQKTG 18- 0 Query: 181 KCVIVVTHSKEVADSADIILELSGKKL 207 KCVIVVTHSKEVA ++DI LEL KKL Sbjct: 181 KCVIVVTHSKEVAQASDITLELKDKKL 207 A related DNA sequence was identified in S. pyogenes <SEQ ID 1353> which encodes the amino acid sequence <SEQ ID 1354>. Analysis of this protein sequence reveals the following: TABLE-US-01338 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2717(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01339 Identities = 83/230 (36%), Positives = 135/230 (58%), Gaps = 13/230 (5%) Query: 1 MDILEIKNVNYSYANSKEKVLSGVNQKFEL--GKFYAIVGKSGTGKSTLLSLLAGLDKVQ 58- M +E+K V+ SY + V + FE+ G+ I+G SG GKST+L++L G+D V Sbjct: 5 MAFIELKQVSKSYQIGETTVFANHEVSFEINKGELVVILGASGAGKSTVLNILGGMDTVD 64- Query: 59 TGKILFKNEDIE---KKGYSNHRKNNISLVFQNYNLIDYLSPIENIRLVNKSVDES---- 11- 1 G+++ +DI K + +R+N I VFQ YNL+ L+ EN+ L + V ++ Sbjct: 65 AGQVIIDGKDIAHYTSKALTQYRRNAIGFVFQFYNLVPNLTAKENVELAVEIVADALDPV 12- 4 Query: 112 -ILFELGLDKKQIKRNVMKLSGGQQQRVAIARALVSDAPIILADEPTGNLDSVTAGEIIN 17- 0 IL E+GL + + +LSGG+QQRV+IARAL + ++L DEPTG LD T +I+ Sbjct: 125 TILKEVGLSHR-LDHFPAQLSGGEQQRVSIARALAKNPKLLLCDEPTGALDYQTGKQILT 18- 3 Query: 171 ILKELAQDRNKCVIVVTHSKEVADSADIILELSGKKLKK--VNKMNLEVE 218 +L+++AQ + V++VTH+ +A AD ++ + ++ K +NK +E Sbjct: 184 LLQDMAQTKGTTVVIVTHNAAIAPIADRVIFMHDAQVTKTVINKEPASIE 233 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 417 A DNA sequence (GBSx0453) was identified in S. agalactiae <SEQ ID 1355> which encodes the amino acid sequence <SEQ ID 1356>. Analysis of this protein sequence reveals the following: TABLE-US-01340 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.35 Transmembrane 17-33 (17-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.2338(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 418 A DNA sequence (GBSx0454) was identified in S. agalactiae <SEQ ID 1357> which encodes the amino acid sequence <SEQ ID 1358>. This protein is predicted to be Vexp1. Analysis of this protein sequence reveals the following: TABLE-US-01341 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.52 Transmembrane 294-310 (285-312) INTEGRAL Likelihood = -10.67 Transmembrane 396-412 (385-417) INTEGRAL Likelihood = -8.76 Transmembrane 17-33 (14-38) INTEGRAL Likelihood = -4.14 Transmembrane 335-351 (333-357) ----- Final Results ----- bacterial membrane --- Certainty = 0.5607(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01342 >GP:AAD47592 GB:AF140784 Vexpl [Streptococcus pneumoniae] Identities = 165/425 (38%), Positives = 271/425 (62%), Gaps = 4/425 (0%) Query: 2 IKNAIAYITRKKNRTLIIFAILTIVLSCLYSCLTIMKSSNEIEKALYESSNSSISITK-K 60 I+ + AY++RK+ R+ I+F IL ++L+ + +CLT+MKS+ +E LY+S N+S SI K + Sbjct: 4 IQRSWAYVSRKRLRSFILFLILLVLLAGISACLTLMKSNKTVESNLYKSLNTSFSIKKIE 63 Query: 61 DGKYFNINQFKNIEKIKEVEEKIFQYDGLAKLKDLKVVSGEQSINREDLSDEFKNVVSLE 120- +G+ F ++ ++ KIK +E + + +AKLKD + V+GEQS+ R+DLS N+VSL Sbjct: 64 NGQTFKLSDLASVSKIKGLENVSPELETVAKLKDKEAVTGEQSVERDDLSAADNNLVSLT 123- Query: 121 ATSNTKRNLLFSSGVFSFKEGKNIEENDKNSILVHEEFAKQNKLKLGDEIDLELLDTEKS 18- 0 A ++ +++ F+S F+ KEG+++++ D IL+HEE AK+N L L D+I L+ +E S Sbjct: 124 ALEDSSKDVTFTSSAFNLKEGRHLQKGDSKKILIHEELAKKNGLSLHDKIGLDAGQSE-S 18- 2 Query: 181 GKIKSHKFKIIGIFSGKKQETYTGLSSDFSENMVFVDYSTSQEILNKSENNRIANKILMY 24- 0 GK ++ +F+IIGIFSGKKQE +TGLSSDFSEN VF DY +SQ +L SE A + Y Sbjct: 183 GKGQTVEFEIIGIFSGKKQEKFTGLSSDFSENQVFTDYESSQTLLGNSEAQVSAARF--Y 24- 0 Query: 241 SGSLESTELALNKLKDFKIDKSKYSIKKDNKAFEESLESVSGIKHIIKIMTYSIMLGGIV 30- 0 + + + + ++++ ++ Y ++K+NKAFE+ +SV+ + + I Y +++ G Sbjct: 241 VENPKEMDGLMKQVENLALENQGYQVEKENKAFEQIKDSVATFQTFLTIFLYGMLIAGAG 30- 0 Query: 301 VLSLILILWLRERIYEIGIFLSIGTTKIQIIRQFIFELIFISIPSIISSLFLGNLLLKVI 36- 0 L L+L LWLRER+YE+GI L++G K I QF E++ +S+ +++ + GN + + Sbjct: 301 ALILVLSLWLRERVYEVGILLALGKGKSSIFLQFCLEVVLVSLGALLPAFVAGNAITTYL 36- 0 Query: 361 VEGFINSENSMIFGGSLINKSSFMLNITTLAESYLILISIIVLSVVMASSLILFKKPKEI 42- 0 ++ + S + +L SS +I + AESY+ L+ + LSV + + K PKEI Sbjct: 361 LQTLLASGDQASLQDTLAKASSLSTSILSFAESYVFLVLLSCLSVALCFLFLFRKSPKEI 42- 0 Query: 421 LSKIS 425 LS IS Sbjct: 421 LSSIS 425 A related DNA sequence was identified in S. pyogenes <SEQ ID 1359> which encodes the amino acid sequence <SEQ ID 1360>. Analysis of this protein sequence reveals the following: TABLE-US-01343 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.57 Transmembrane 23-39 (16-43) INTEGRAL Likelihood = -11.36 Transmembrane 371-387 (362-396) INTEGRAL Likelihood = -8.12 Transmembrane 331-347 (324-360) INTEGRAL Likelihood = -7.70 Transmembrane 280-296 (277-308) ----- Final Results ----- bacterial membrane --- Certainty = 0.5628(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01344 >GP:AAB97962 GB:U96166 ATP-binding cassette transporter-like protein [Streptococcus cristatus] Identities = 222/311 (71%), Positives = 278/311 (89%) Query: 16 MRSILTMLGIIIGIGAIIAIFSIIEGNTENTKRQLIGGSNNTINIVFNKKSSIDPKFPDK 75 - MRS+LTMLGIIIGIGAIIAIFSIIEGNTENTKRQLIGGSNNTI +V++KKS+IDP P+K Sbjct: 1 MRSMLTMLGIIIGIGAIIAIFSIIEGNTENTKRQLIGGSNNTIKVVYDKKSAIDPSIPEK 60 Query: 76 SNAKKPDYLPFMAEEELSKIQQVKGVKNALISYGIDDKVYHLGQKSSAKISAITKNVAEV 135- S A+KP Y+PFM E+ LSKI+++ GVKNAL++YG D+K+Y+L QKSS+K+ A++++VA++ Sbjct: 61 SQAQKPSYIPFMGEDVLSKIKEIPGVKNALMTYGADEKIYYLSQKSSSKVQAVSQSVADI 120- Query: 136 RRMTFIKGSDFSDKDFIDQKQVIYLEKSLYESLFPKDDGLGKFVEVMGNPFRVIGVFESK 19- 5 ++ ++G F + F +Q+QV YLEKSLY++LFPK DG+GK+VEV GNPF+VIGVFES Sbjct: 121 KQQRLLEGEGFDSEAFKNQEQVAYLEKSLYDTLFPKGDGIGKYVEVKGNPFKVIGVFEST 18- 0 Query: 196 EQSGLTSGTEKIAYIPLHQWYNINGVVDATPEITIQTYRADDLKPVAKRVSDMLNQTIPK 25- 5 EQSGLTSG+EK+AYIPL QW+ I ++ +PE+T+QT++ADDLK VAK+VSD LNQ +P+ Sbjct: 181 EQSGLTSGSEKVAYIPLQQWHRIFDTINVSPEVTVQTHKADDLKKVAKKVSDYLNQQMPQ 24- 0 Query: 256 SDYMFGVMNLKEFERQLDNLNKSNFVLLAGIASISLIVGGIGVMNIMLVSVTERTREIGI 31- 5 SDYMFGV+NL+EFERQLDNLN+SNFVLLAGIASISL+VGGIGVMNIMLVSVTERTREIGI Sbjct: 241 SDYMFGVLNLQEFERQLDNLNQSNFVLLAGIASISLLVGGIGVMNIMLVSVTERTREIGI 30- 0 Query: 316 KKALGARRKLI 326 KKALGARRK++ Sbjct: 301 KKALGARRKIL 311 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01345 Identities = 79/386 (20%), Positives = 170/386 (43%), Gaps = 38/386 (9%) Query: 5 AIAYITRKKNRTLIIFAILTIVLSCLYSCLTIMKSSNE-IEKALYESSNSSISITKKDGK 63 A++ I K R+++ + I + + + +I++ + E ++ L SN++I+I Sbjct: 7 ALSSILSHKMRSILTMLGIIIGIGAIIAIFSIIEGNTENTKRQLIGGSNNTINIV----- 61 Query: 64 YFNINQFKNIEKIKEVEEKIFQYDGLAKLKDLKVVSGEQSINREDLSDEFKNVVSLEATS 123- FN K ++ K F AK D E+ +++ KN + Sbjct: 62 -FN--------KKSSIDPK-FPDKSNAKKPDYLPFMAEEELSKIQQVKGVKNALISYGID 111- Query: 124 NTKRNLLFSSGVFSFKEGKNIEENDKNSILVHEEFAKQNKLKLGDEIDLELLDTE----- 17- 8 + +L S KN+ E + + + +F+ ++ + I LE E Sbjct: 112 DKVYHLGQKSSAKISAITKNVAEVRRMTFIKGSDFSDKDFIDQKQVIYLEKSLYESLFPK 17- 1 Query: 179 -----KSGKIKSHKFKIIGIFSGKKQETYTGLSSDFSENMVFVDYSTSQEILNKSENNRI 23- 3 K ++ + F++IG+F K+Q +GL+S +E + ++ I + Sbjct: 172 DDGLGKFVEVMGNPFRVIGVFESKEQ---SGLTSG-TEKIAYIPLHQWYNINGVVDATPE 22- 7 Query: 234 ANKILMYSGSLESTELALNKLKDFKIDKSKYSIKKDN-KAFEESLESVSGIKHIIK--IM 29- 0 + L+ ++ + + I KS Y N K FE L++++ ++ I Sbjct: 228 ITIQTYRADDLKPVAKRVSDMLNQTIPKSDYMFGVMNLKEFERQLDNLNKSNFVLLAGIA 28- 7 Query: 291 TYSIMLGGIVVLSLILILWLRERIYEIGIFLSIGTTKIQIIRQFIFELIFIS----IPSI 34- 6 + S+++GGI V++++L+ + ER EIGI ++G + I++QF+ E + ++ + + Sbjct: 288 SISLIVGGIGVMNIMLVS-VTERTREIGIKKALGARRKLILKQFLIEAVILTLLGGVIGV 34- 6 Query: 347 ISSLFLGNLLLKVIVEGFINSENSMI 372 IS + G ++ + + +I S S++ Sbjct: 347 ISGMVSGLIITRSLEYPYILSLFSVV 372 A related GBS gene <SEQ ID 8571> and protein <SEQ ID 8572> were also identified. Analysis of this protein sequence reveals the following:

TABLE-US-01346 Lipop Possible site: -1 Crend: 10 McG: Discrim Score: 5.59 GvH: Signal Score (-7.5): -5.97 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 4 value: -11.52 threshold: 0.0 INTEGRAL Likelihood = -11.52 Transmembrane 294-310 (285-312) INTEGRAL Likelihood = -10.67 Transmembrane 396-412 (385-417) INTEGRAL Likelihood = -8.76 Transmembrane 17-33 (14-38) INTEGRAL Likelihood = -4.14 Transmembrane 335-351 (333-357) PERIPHERAL Likelihood = -4.51 315 modified ALOM score: 2.80 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5607(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00034## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 419 A DNA sequence (GBSx0455) was identified in S. agalactiae <SEQ ID 1361> which encodes the amino acid sequence <SEQ ID 1362>. Analysis of this protein sequence reveals the following: TABLE-US-01347 Possible site: 42 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.04 Transmembrane 19-35 (14-42) ----- Final Results ----- bacterial membrane --- Certainty = 0.3011(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 420 A DNA sequence (GBSx0456) was identified in S. agalactiae <SEQ ID 1363> which encodes the amino acid sequence <SEQ ID 1364>. Analysis of this protein sequence reveals the following: TABLE-US-01348 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 421 A DNA sequence (GBSx0457) was identified in S. agalactiae <SEQ ID 1365> which encodes the amino acid sequence <SEQ ID 1366>. Analysis of this protein sequence reveals the following: TABLE-US-01349 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01350 >GP: AAA74029 GB: U30715 ORFB [Bacillus anthracis] Identities = 33/76 (43%), Positives = 44/76 (57%), Gaps = 1/76 (1%) Query: 11 IRRVSHACTKAGDRFYEENILNREFTATAHNQKWCTDVTYLQYGLGAKAYLSAIKDLYNG 70 - ++R R EN+LNR F A N+KW TD+TYL +G YL +I DLYN Sbjct: 86 VKRKRRTWINGESRIVVENLLNRNFQANKPNEKWVTDITYLPFGT-EMLYLLSIMDLYNN 144- Query: 71 SIIAYEISHNNEIHLL 86 IIAYEIS+ ++ L+ Sbjct: 145 EIIAYEISNRQDVTLV 160 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 422 A DNA sequence (GBSx0458) was identified in S. agalactiae <SEQ ID 1367> which encodes the amino acid sequence <SEQ ID 1368>. Analysis of this protein sequence reveals the following: TABLE-US-01351 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.69 Transmembrane 10-26 (10-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.1277(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 423 A DNA sequence (GBSx0459) was identified in S. agalactiae <SEQ ID 1369> which encodes the amino acid sequence <SEQ ID 1370>. Analysis of this protein sequence reveals the following: TABLE-US-01352 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4170(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01353 >GP: AAA56999 GB: U09558 ORFA, putative Helix-Turn-Helix motif from amino acid 21 through 42 and from amino acid 78 through 99 [Lactobacillus johnsonii] Identities = 28/116 (24%), Positives = 59/116 (50%), Gaps = 6/116 (5%) Query: 3 YSTLAKEQGVQGYLDGKGSLRDICKWYDISSRSVLQKWIKRYTSGEDLKATSRGYSRMKQ 62 YST K + V YL+ + S++ + K Y+I +++++W+ + + L A S +++ Sbjct: 4 YSTELKIEIVSKYLNHEDSIKGLAKQYNIHW-TLIRRWVDK-AKCQGLAALSVKHTKTTY 61 Query: 63 GRQATFEERVEIVNYTIAHGKDYQAAIEKFGVSYQQIYSWVRKLEKNGSQGLVDRR 118 + ++ +V Y + H KF +S Q+Y+W +K + G GL+ ++ Sbjct: 62 SS----DFKLNVVRYYLTHSIGVSKVAAKFNISDSQVYNWAKKFNEEGYAGLLPKQ 113 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 424 A DNA sequence (GBSx0460) was identified in S. agalactiae <SEQ ID 1371> which encodes the amino acid sequence <SEQ ID 1372>. Analysis of this protein sequence reveals the following: TABLE-US-01354 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.69 Transmembrane 2-18 (2-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.1277(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 425 A DNA sequence (GBSx0461) was identified in S. agalactiae <SEQ ID 1373> which encodes the amino acid sequence <SEQ ID 1374>. This protein is predicted to be integrase (phage-relatedpr). Analysis of this protein sequence reveals the following: TABLE-US-01355 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01356 >GP: AAC79517 GB: U88974 ORF1 [Streptococcus thermophilus temperate bacteriophage O1205] Identities = 104/172 (60%), Positives = 127/172 (73%), Gaps = 11/172 (6%) Query: 10 QHQSYAALYLIAKTGMRFAECLGLTVNDIDYTNKYLSINKTWDYHFNQRYLPTKNKSSIR 69 - ++ SYAALY+I+KTG+RFAECLGLTV+DI LS+NKTWDY N ++PTK KSSIR Sbjct: 186 EYASYAALYIISKTGIRFAECLGLTVDDIKRDTGMLSVNKTWDYKNNTGFMPTKTKSSIR 24- 5 Query: 70 NIPIDNDTLFFLHEFTKNKNDRLFDKLSNNAVNKTIRKITGREVRVHSLRHTFASY---- 125- IP+D++ + F+ + + RL LSNNAVNKT+RKI GREVRVHSLRHT+ASY Sbjct: 246 EIPLDDEFINFIDQLPPTDDGRLLPSLSNNAVNKTLRKIVGREVRVHSLRHTYASYLIAH 30- 5 Query: 126 ---LISISQVLDHENLNITLEVYAHQLQEQKDRNDKLNQRNLGRIWGKIALN 174 LIS+SQVL HENLNITLEVYAHQLQEQK RND+ + ++W K N Sbjct: 306 DIDLISVSQVLGHENLNITLEVYAHQLQEQKSRNDE----KIKQMWTKCGQN 353 There is also homology to SEQ ID 578 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 426 A DNA sequence (GBSx0462) was identified in S. agalactiae <SEQ ID 1375> which encodes the amino acid sequence <SEQ ID 1376>. Analysis of this protein sequence reveals the following: TABLE-US-01357 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3206(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 1328. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 427 A DNA sequence (GBSx0463) was identified in S. agalactiae <SEQ ID 1377> which encodes the amino acid sequence <SEQ ID 1378>. Analysis of this protein sequence reveals the following: TABLE-US-01358 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6542(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01359 >GP: CAB52541 GB: AJ131519 hypothetical protein [Lactobacillus bacteriophage phi adh] Identities = 24/55 (43%), Positives = 36/55 (64%) Query: 12 MDKELTPQEKANKKWAENNREHRTYLSKRSTARSFINKNATKEDLLELKQLIESK 66 M K + KANKKW E N+ + Y++KRSTA+SFI AT+EDL +++ + + Sbjct: 1 MAKITEARAKANKKWDEKNKARKLYINKRSTAKSFILNLATEEDLANIEEYVAER 55 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 428 A DNA sequence (GBSx0464) was identified in S. agalactiae <SEQ ID 1379> which encodes the amino acid sequence <SEQ ID 1380>. Analysis of this protein sequence reveals the following: TABLE-US-01360 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4417(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 1332. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 429 A DNA sequence (GBSx0465) was identified in S. agalactiae <SEQ ID 1381> which encodes the amino acid sequence <SEQ ID 1382>. Analysis of this protein sequence reveals the following: TABLE-US-01361 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 430 A DNA sequence (GBSx0466) was identified in S. agalactiae <SEQ ID 1383> which encodes the amino acid sequence <SEQ ID 1384>. Analysis of this protein sequence reveals the following: TABLE-US-01362 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.30 Transmembrane 205-221 (202-223) INTEGRAL Likelihood = -3.56 Transmembrane 296-312 (294-312) ----- Final Results ----- bacterial membrane --- Certainty = 0.2720(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9663> which encodes amino acid sequence <SEQ ID 9664> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8573> and protein <SEQ ID 8574> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01363 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -8.80 GvH: Signal Score (-7.5): -4.03 Possible site: 47 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -4.30 threshold: 0.0 INTEGRAL Likelihood = -4.30 Transmembrane 205-221 (202-223) INTEGRAL Likelihood = -3.56 Transmembrane 296-312 (294-312) PERIPHERAL Likelihood = 2.97 20 modified ALOM score: 1.36 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2720(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8574 (GBS366) was expressed in E. coli as a GST-fusion product. The purified fusion protein (FIG. 215, lane 5) was used to immunise mice. The resulting antiserum was used for FACS (FIG. 281), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 431 A DNA sequence (GBSx0467) was identified in S. agalactiae <SEQ ID 1385> which encodes the amino acid sequence <SEQ ID 1386>. This protein is predicted to be N-acetylmuramoyl-L-alanine amidase. Analysis of this protein sequence reveals the following: TABLE-US-01364 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1471(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8575> which encodes amino acid sequence <SEQ ID 8576> was also identified. This has an RGD motif at residues 81-83. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01365 >GP: CAB07986 GB: Z93946 N-acetylmuramoyl-L-alanine amidase [bacteriophage Dp-1] Identities = 99/140 (70%), Positives = 120/140 (85%) Query: 10 MVINIEQAIAWMASRKGKVTYSMDYRNGPSSYDCSSSVYFALRSAGASDNGWAVNTEYEH 69 - M ++IE+ +AWM +RKG+V+YSMD+R+GP SYDCSSS+Y+ALRSAGAS GWAVNTEY H Sbjct: 1 MGVDIEKGVAWMQARKGRVSYSMDFRDGPDSYDCSSSMYYALRSAGASSAGWAVNTEYMH 60 Query: 70 DWLIKNGYVLIAENTNWNAQRGDIFIWGKRGASAGAFGHTGMFVDPDNIIHCNYGYNSIT 129- WLI+NGY LI+EN W+A+RGDIFIWG++GASAGA GHTGMF+D DNIIHCNY Y+ I+ Sbjct: 61 AWLIENGYELISENAPWDAKRGDIFIWGRKGASAGAGGHTGMFIDSDNIIHCNYAYDGIS 120- Query: 130 VNNHDEIWGYNGQPYVYAYR 149 VN+HDE W Y GQPY Y YR Sbjct: 121 VNDHDERWYYAGQPYYYVYR 140 A related DNA sequence was identified in S. pyogenes <SEQ ID 1387> which encodes the amino acid sequence <SEQ ID 1388>. Analysis of this protein sequence reveals the following: TABLE-US-01366 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.06 Transmembrane 79-95 (77-95) ----- Final Results ----- bacterial membrane --- Certainty = 0.1426(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01367 Identities = 56/91 (61%), Positives = 68/91 (74%) Query: 158 KVDNQSVVSKFEKELDVNTPLSNSNMPYYEATISEDYYVESKPDVNSTDKELLVAGTRVR 21- 7 K+D F ++LD NT L NSN+PYYEAT+ DYYVESKP+ +S DKE + AGTRVR Sbjct: 354 KIDKPQSQLTFNQKLDTNTKLDNSNVPYYEATLRTDYYVESKPNASSADKEFIKAGTRVR 41- 3 Query: 218 VYEKVKGWARIGAPQSNQWVEDAYLIDATDM 248 VYEKV GW+RI A QS+QWVED YL +AT + Sbjct: 414 VYEKVNGWSRINASQSDQWVEDKYLSNATQV 444 SEQ ID 8576 (GBS301) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 44 (lane 9; MW 30 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 3; MW 55 kDa). The GBS301-GST fusion product was purified (FIG. 205, lane 4) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 300), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 432 A DNA sequence (GBSx0468) was identified in S. agalactiae <SEQ ID 1389> which encodes the amino acid sequence <SEQ ID 1390>. Analysis of this protein sequence reveals the following:

TABLE-US-01368 Possible site: 53 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.53 Transmembrane 8-24 (3-25) ----- Final Results ----- bacterial membrane --- Certainty = 0.3612(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 433 A DNA sequence (GBSx0469) was identified in S. agalactiae <SEQ ID 1391> which encodes the amino acid sequence <SEQ ID 1392>. Analysis of this protein sequence reveals the following: TABLE-US-01369 Possible site: 34 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 434 A DNA sequence (GBSx0470) was identified in S. agalactiae <SEQ ID 1393> which encodes the amino acid sequence <SEQ ID 1394>. Analysis of this protein sequence reveals the following: TABLE-US-01370 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0120(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 435 A DNA sequence (GBSx0471) was identified in S. agalactiae <SEQ ID 1395> which encodes the amino acid sequence <SEQ ID 1396>. Analysis of this protein sequence reveals the following: TABLE-US-01371 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4757(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9661> which encodes amino acid sequence <SEQ ID 9662> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 436 A DNA sequence (GBSx0472) was identified in S. agalactiae <SEQ ID 1397> which encodes the amino acid sequence <SEQ ID 1398>. This protein is predicted to be a minor structural protein. Analysis of this protein sequence reveals the following: TABLE-US-01372 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.39 Transmembrane 349-365 (347-366) ----- Final Results ----- bacterial membrane --- Certainty = 0.1956(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01373 >GP: AAF43531 GB: AF145054 ORF39 [Streptococcus thermophilus bacteriophage 7201] Identities = 212/666 (31%), Positives = 323/666 (47%), Gaps = 52/666 (7%) Query: 10 WGNNLTLEILSAWNKP---NIASNTSTVNVQVFL-----KMSSYGYISIGETRPLKITVD 61 - W NN + W +I +NTS V +++ L + Y + E ++ Sbjct: 5 WSNNDRGYRIRLWVDQVGQDIQNNTSQVRLRLSLLNTTTTFAQYSCSAFVEFNGQRLNWS 64 Query: 62 GRAETINVNPSINYGQRKLLFAKDYIVNHNSDGNKPLFNISAYYPIN--FSNYGEATANQ 119- G + N +I L + V H DG+ +F + A++ + +S NQ Sbjct: 65 GSPSVLGWNQTIQ------LIDQTITVRHADDGSG-VFGVHAHFNGSGGWSPGNLDIGNQ 117- Query: 120 SISLPKINRLSVSSAISGVLGNAVTITINRYSTSFTHNLKYDFKGSTGTIATGVGTSYLW 17- 9 I+L I R S G +GN V I+I+R TH L+Y ++ G IA VGTSY W Sbjct: 118 QITLTTIPRGSSVRVSDGFIGNQVDISIDRKIGGATHTLRYAWENKQGKIADNVGTSYKW 17- 7 Query: 180 TIPPTFANLLPNELTGTGNLIVETMDGSAKIGETKYTLSITIPNTATYKPKLSSITLSDT 23- 9 TIP FAN +PN +G G + V+T I TL+ ++ T KP + TL+DT Sbjct: 178 TIPEDFANDIPNSTSGRGTIYVDTYINGNFIQTQSTTLTASV-ITNNLKPSFTGFTLTDT 23- 6 Query: 240 NTLTSSIVSG-NNFVRIISKVKVDFGSAIGNNGSTITSYNAEIVGKSNSIIGNGSVFDKL 29- 8 N + IV G +FV I+S VKV F A +G+TI Y AEIVG +NSI NG V ++ Sbjct: 237 NPTSQRIVPGQTHFVSIMSLVKVVFNGAQAKSGATIVGYYAEIVGANNSISSNGGVLREV 29- 6 Query: 299 DFFGSA--TIRATVTDSRGLTSEPVDTKINVIDYFLPIVTSAKVVRSQQNPDILQVLPFV 35- 6 T+R V DSRG+ S+ V+TK+ + YF P + +V RS + DIL + F Sbjct: 297 SVNQDTEMTLRGRVQDSRGIWSDWVETKLTFLFYFSPAL-RFEVKRSDKKLDILTIKRFA 35- 5 Query: 357 KIAPIIVGGIQKNQLKMSVSVAPYNTGIYAVDSGAATNTWSTISQMSGAPLNLGGTYDKS 41- 6 KIAP+ V GIQ+N +K++ S A + VD+G A WS+IS+ + + LG +Y Sbjct: 356 KIAPLSVNGIQRNVMKLTFSTAKVGWDNFVVDNGQAGGVWSSISEFNASDAKLGNSYPAD 41- 5 Query: 417 KSWLVKISVSDNLMSATPIIQPVASEFVLVTKAPSGVAFGKIWEHGIIDAKGDVYVDGTI 47- 6 S++V + D S T V ++ V++T GV GK E G +D GD I Sbjct: 416 TSYVVIGKLEDEFTS-TSFQATVPTDEVIMTYDRQGVGIGKYRERGALDVNGD------I 46- 8 Query: 477 YCGDKAIQQKPLALNNGGSFRHDDTDLNSLQDTGFYCVFRGANRPAGAGPGYVTVVRHET 53- 6 Y + IQQ L NNG ++ N+++D G Y +F A P + + H + Sbjct: 469 YANNSPIQQYQLTNNNGSPKMTNNA--NTIEDPGQYYLFSAA--PGNPSGQWGHLFHHSS 52- 4 Query: 537 ------ANYAYQQFYDRTNKTI-----FTRLLENGVWSGWSEYVKKD--SLQTTGWITIG 58- 3 A Q F+ + ++R++++ W W E+ + D +L TGW G Sbjct: 525 YGKGSMYKEAIQIFWSNDGRLFSRHHRWSRIIDD--WEPWKEFARNDNTNLINTGWQPAG 58- 2 Query: 584 -NGFKYKRKGDDIDLMYNFASNGLQRWSVGNMPSGLI--PQELMFAITGWTLAPDKSIHL 64- 0 +G YKR GD + + +NF G + + ++P + PQ MF +TGW++ +K ++ Sbjct: 583 VDGSFYKRVGDVLTIKFNFTGTG-GDFLLASVPPEIFKAPQSYMFVVTGWSVWANKQYNV 64- 1 Query: 641 QINASG 646 Q+N G Sbjct: 642 QVNEGG 647 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 1398 (GBS365) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 82 (lane 2; MW 102 kDa). GBS365-GST was purified as shown in FIG. 216, lane 11. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 437 A DNA sequence (GBSx0473) was identified in S. agalactiae <SEQ ID 1399> which encodes the amino acid sequence <SEQ ID 1400>. This protein is predicted to be a minor structural protein. Analysis of this protein sequence reveals the following: TABLE-US-01374 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3481(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01375 >GP: AAC34413 GB: AF158600 putative minor structural protein [Streptococcus thermophilus bacteriophage Sfill] Identities = 504/998 (50%), Positives = 675/998 (67%), Gaps = 56/998 (5%) Query: 1 MLTIHGPDLKPVLFLDNDKQGALNYFNHKWYRKQKTGSSVLEFSVYKKDLLGDSPLSHKY 60 +LTIH +L+ V ++DN+KQ LN+FN KW R ++G+SV EFSV+KK + DS + Y Sbjct: 2 LLTIHDNNLQKVAYIDNEKQSTLNFFNDKWTRSLESGTSVFEFSVFKKSIKSDSKVEISY 61 Query: 61 HVLNDQAFVSFVHKGKVQLLNIMKIDEDEKQIDCYCENLNLELLNEYCNAYKATKAMSFE 120- LN++AFVSF HKGK L N+MKI+EDE+ I CYCENL+LELL EY AYKA+K M+F+ Sbjct: 62 KYLNERAFVSFKHKGKSYLFNVMKIEEDEQIIRCYCENLSLELLLEYRGAYKASKPMTFK 121- Query: 121 EYLVQFDILSWGALTVGTNEVKDKKLTLEWTSQETKLARLLSIANNFDAEIEFETKLNFN 18- 0 EY + + + LT+G NEV D+K TLEW QET LARL+S+A NFDAEIEF+T+L N Sbjct: 122 EYFDDWGMGQFAKLTLGVNEVSDQKRTLEWEGQETTLARLISLARNFDAEIEFDTRLKPN 18- 1 Query: 181 HTFKQLIINIYKEYEEGKSYGVDRDKTDVILRYQKNISGIRKTVDKRQIYNAIRPYGKK- 23- 9 + ++N+YK Y+ GK+ GV R ++DVIL+Y KNI+GI+++VDK QIYN I PYG+K Sbjct: 182 SQLDEFVLNVYKAYD-GKNQGVGRRRSDVILKYGKNINGIKRSVDKTQIYNMITPYGRKS 24- 0 Query: 240 -TVRGERVISNPVTRKVTKTVGSNRT---YLGGDLKYYGHTIKKANVQAIINYAVQYNIL 29- 5 T + + IS+PVT + V S R Y GGDL Y GHT+ + VQ I N VQ N+L Sbjct: 241 DTKKETKRISDPVTIQNPVVVPSARVEKRYAGGDLTYAGHTLSASLVQTIFNLCVQRNLL 30- 0 Query: 296 PSGIITQLYLESFWGDSTVGKRDNNWAGMSGGAQTRPSGVKVTTGMARPANEGGTYMHYA 35- 5 PSG+I+QLYLESFWG S V +RDNNW+GM+GGAQTRPSGV VTTG RPA+EGGTYMHYA Sbjct: 301 PSGVISQLYLESFWGSSNVARRDNNWSGMTGGAQTRPSGVVVTTGSPRPASEGGTYMHYA 36- 0 Query: 356 SVDDFLKDYTYLLAKQG-----IYNVVGKKNIADYTKGLFRAGGAKYDYAAAGYQSYTNL 41- 0 SVDDF+KDYTYLLA Q +Y V GK+NI +YTKGLFR GGA YDYAAAGY Y L Sbjct: 361 SVDDFMKDYTYLLADQTSGGRKMYGVKGKQNIEEYTKGLFRIGGALYDYAAAGYNHYIYL 42- 0 Query: 411 MTNIRNGINKVTGNILNTIDKLWQTPVKPITAVNVARRATKTIQA------INEATKLKG 46- 4 M +IRNGIN+ GNIL+ +D LW+ P IT N ++ T+T++A +NE LKG Sbjct: 421 MRDIRNGINRSNGNILDKLDDLWRQPDNQITQPN--KQVTRTVKADRVIAVLNEMQGLKG 47- 8 Query: 465 RRIGSGQCYALSGWYAKKLDGAWIDSSIGGIRGRIGGGMAAALIGTDYNWGAYGWKVDKS 52- 4 RR+G+GQCYAL+ WY+ KL G + + + G G IG GMAAA IGTDY W +GW V + Sbjct: 479 RRVGNGQCYALAAWYSMKLGGPGLGAGVTGKSGVIGAGMAAAKIGTDYAWDRFGWSVVRP 53- 8 Query: 525 PNAGNLKAGGIYNVRANRGAPFYTTGWGHTGIIKSVSKTRVTVLEQNFVGRMYVVENSYD 58- 4 + LK G I N++A T+ WGH II S + + VTVLEQN+ GR YVV+NSY Sbjct: 539 TSVDQLKPGAIANIKAYNSY-LGTSVWGHVSIIISNNGSTVTVLEQNYAGRQYVVQNSYP 59- 7 Query: 585 INSFASGLQTVCYPREIAQGMSVNGATTQQVSGGTQISYEEVVQEAQTESYEEEQIIYID 64- 4 +++ ++T+CYP E+ +G +V G T + ++ E+ + E + ID Sbjct: 598 ASAYLGAVETLCYPPELKEGKTVEGRTETVSTPNVEVQKVEIPPIDVEVTTESTAALTID 65- 7 Query: 645 NSIYKEWKDENGKVEYYLKNGFLYAPLSRDRYPSVLTGNETRDNWIRKDMEVETDSQEVL 70- 4 + +EW++ENG+VE+YL+NG LYAP+S++ YPS+LTG E DNWIRKDME++TDS++VL Sbjct: 658 SKRKQEWRNENGQVEFYLENGSLYAPISKELYPSILTGKENGDNWIRKDMEIDTDSEDVL 71- 7 Query: 705 MSTGLKDLKAHAYPAITYEVDGYVDLELGDVVRIQDDGYEPPLILTARVVEQEISITNPS 76- 4 +ST L++L+ YPAITYEVDG++DL++GD V+IQD G+ P L+L ARV EQ+IS TNP Sbjct: 718 ISTALRNLRKFCYPAITYEVDGFLDLDIGDTVKIQDTGFSPMLMLEARVSEQQISFTNPV 77- 7 Query: 765 SNKTKFSNFVEKESQLASDLISDMLRLYDESIPYEIKLATSNGVAFKNGTGESVLTPSLQ 82- 4 NKT F+NF +++++ L+S M +L +E+IPYE+KL+T NG FKN TG+SVL +L+ Sbjct: 778 ENKTVFANFQTLQNKVSDSLLSRMTKLAEEAIPYELKLSTDNGTTFKNSTGQSVLKATLE 83- 7 Query: 825 KNGKDYEAVYFYKNGDSLIDIGPSLIVKASDFNHVLNITVEAYLNEELVASTQISFTDTE 88- 4 KNG+ Y+ ++F+KNGDS+I G L+VK +DF + L +TVEAYL++ELVAS +I+FTD Sbjct: 838 KNGEVYQPIFFFKNGDSIIGTGNQLVVKPTDFENTLQVTVEAYLDDELVASAEITFTDVS 89- 7 Query: 885 DGADGKDGAPGPQGPPGVNGLQGPKGDQGIQGPAGADGKATYTHIAYALDENGSTGFSVS 94- 4 DG QGPKGD G+ L S G+ Sbjct: 898 DGK------------------QGPKGDDGVS--------------PINLIIESSNGYQFK 92- 5 Query: 945 DNVGKTYI--GMYVDDNIIDSNDPK-KYKWNLIKGADG 979 +N+ T +Y D+ ID + + Y W+ + ADG Sbjct: 926 NNIINTTFTAKLYQDNKEIDKDGTRYAYLWSKV-NADG 962 A related DNA sequence was identified in S. pyogenes <SEQ ID 1401> which encodes the amino acid sequence <SEQ ID 1402>. Analysis of this protein sequence reveals the following: TABLE-US-01376 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -3.56 Transmembrane 325-341 (323-343) ----- Final Results ----- bacterial membrane --- Certainty = 0.2423(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial Cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01377 Identities = 23/55 (41%), Positives = 27/55 (48%) Query: 886 GADGKDGAPGPQGPPGVNGLQGPKGDQGIQGPAGADGKATYTHIAYALDENGSTG 940 G GKDGAPG G PG G +G +G+ G QGP G G+ T G G Sbjct: 181 GEAGKDGAPGKDGAPGEKGEKGDRGETGAQGPVGPQGEKGETGAQGPAGPQGEAG 235 Identities = 48/151 (31%), Positives = 58/151 (37%), Gaps = 19/151 (12%) Query: 852 KASDFNHVLNITVEAYLNE--ELVASTQISFTDTEDGADGKDGAPGPQGPPGVNGLQGPK 90- 9 K DF L E L E +L+ + I + G G G GPQG G G QGPK Sbjct: 82 KEEDFQKELKDFTEKRLKEILDLIGKSGIK---GDRGETGPAGPAGPQGKTGERGAQGPK 138- Query: 910 GD---QGIQGPAGADGKATYTHIAYALDENGSTGFS----VSDNVGKTYIGMYVDDNIID 96- 2 GD QGIQG AG G+ E G G + GK D sbjct: 139 GDRGEQGIQGKAGEKGERGEKGDKGETGERGEKGEAGIQGPQGEAGK-------DGAPGK 19- 1 Query: 963 SNDPKKYKWNLIKGADGARGIQGPAGADGKT 993 P + +G GA+G GP G G+T Sbjct: 192 DGAPGEKGEKGDRGETGAQGPVGPQGEKGET 222 Identities = 25/50 (50%), Positives = 29/50 (58%), Gaps = 9/50 (18%) Query: 884 EDGADGKDGAPGPQGPPGVNGL---------QGPKGDQGIQGPAGADGKA 924 +DGA GRDGAPG +G G G QG KG+ G QGPAG G+A Sbjct: 185 KDGAPGKDGAPGEKGEKGDRGETGAQGPVGPQGEKGETGAQGPAGPQGEA 234 SEQ ID 1400 was expressed in four different forms. SDS-PAGE analysis of total cell extract is shown in FIG. 122 (GBS105dN--lane 5 & 7; MW 102 kDa), FIG. 122 (GBS105dC--lane 8-10; MW 81 kDa), FIG. 179 (GBS105d--lane 8; MW 102 kDa) and in FIG. 181 (GBS105C--lane 2; MW 56 kDa). GBS105dN-His was purified as shown in FIG. 232 (lanes 9 & 10). GBS105dC-His was purified as shown in FIG. 233 (lanes 3 & 4). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 438 A DNA sequence (GBSx0474) was identified in S. agalactiae <SEQ ID 1403> which encodes the amino acid sequence <SEQ ID 1404>. This protein is predicted to be a minor structural protein. Analysis of this protein sequence reveals the following: TABLE-US-01378 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2502(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01379 >GP: AAC34412 GB: AF158600 putative minor structural protein [Streptococcus thermophilus bacteriophage Sfill] Identities = 163/433 (37%), Positives = 244/433 (55%), Gaps = 21/433 (4%) Query: 80 LSSKKPKMLMFSHIPGRYYLAVQVGDLNFKEIKMNGFGEIT--FIVADAYAHSTSYRRIK 137- L +KK L P RYYLA+ G+++ K I + + E T F+V D AHST+Y+R+ Sbjct: 93 LHTKKAVKLFLPTEPERYYLALVKGEVSLKGIS-DWYDEATIEFLVPDGVAHSTTYKRVT 151- Query: 138 DYTQDGNKMTFKIKNNGTAPAFPIFRIKHLGENGYIGITNETGAFAVGSPEEEDGTIVHR 19- 7 DY + KM F I N G+ A+PI +K ENGY G+ ++ AF G+ EE DG I+ + Sbjct: 152 DYQEKDGKMIFSIDNEGSTDAYPIITLKANAENGYYGLVSDKFAFEAGNIEEADGKIISK 21- 1 Query: 198 NETLFDY-SKAIAQAL-EGAPNVAKLNYMPPTFDSELKRMRLDNILGSGKGGEYVAIGAR 25- 5 E L+D+ I QA +GA NV N + + + N+ G IG + Sbjct: 212 AEVLYDFRDDRIPQAFAKGAKNVGITNVTGDLHGT----LEIQNVWGRPH------IGLK 26- 1 Query: 256 GTTPGYGE-HVGTRTFIINPDSNGEY-TLNEHLWWKQIFIATAQDQKGFLKLCVTGENDE 31- 3 + + T I PDS+G LNE++WW+QIF A + Q GFLKL V+ + Sbjct: 262 NPNANINQLQTASLTLDIPPDSSGNVGALNEYIWWRQIFWAGSISQYGFLKLTVSDADGN 32- 1 Query: 314 FLYGIETYKRKNGFETEYNFFALDDDGVGWRFYKQFEFQA-DRNYHNPFSMNRSRAVEIF 37- 2 FLYG+ET+KR G E+EYN A D G G+RF KQ+ F A + HNPF+ R + +I Sbjct: 322 FLYGVETFKRSLGLESEYNALASDGYG-GFRFLKQWSFLATEYEDHNPFNEPRGWS-DIK 37- 9 Query: 373 REEDKFRIYFNGAHHHVTVPSLKGKKSRKIHLAMGTCSDSSKYINYNLFEKVNFEKMGVS 43- 2 RE+DK Y+ G ++ T+P +KGKKS KIHL + S ++ + F+++ + K + Sbjct: 380 REDDKVTFYWWGTYNTFTIPEIKGKKSAKIHLTISNI-PSKSFVTHAYFDQLLYIKTNNA 43- 8 Query: 433 HYNNIVNKYQPGDEVIINFENDTVSTKDIDSIQDVVLGSKMISIPPGESELVVHLSSWVA 49- 2 + +I N+Y G +IIN E+DT++ ++ ++ ++V GS IPPGES++ V S W Sbjct: 439 FFEDIPNRYIQGSNLIINSEDDTLTLNNLLNLDEIVDGSLWPVIPPGESQIEVVQSPWAK 49- 8 Query: 493 ALPDISIDFEERY 505 P ++I+FEER+ Sbjct: 499 KKPSVTIEFEERW 511 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 439 A DNA sequence (GBSx0475) was identified in S. agalactiae <SEQ ID 1405> which encodes the amino acid sequence <SEQ ID 1406>. This protein is predicted to be PblA. Analysis of this protein sequence reveals the following: TABLE-US-01380 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.11 Transmembrane 427-443 (424-445) INTEGRAL Likelihood = -4.99 Transmembrane 449-465 (448-469) INTEGRAL Likelihood = -2.71 Transmembrane 41-57 (38-57) INTEGRAL Likelihood = -0.37 Transmembrane 361-377 (361-377) INTEGRAL Likelihood = -0.22 Transmembrane 324-340 (324-340) ----- Final Results ----- bacterial membrane --- Certainty = 0.3845(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-01381 >GP: AAG18638 GB: AY007505 Pb1A [Streptococcus mitis] Identities = 233/401 (58%), Positives = 296/401 (73%), Gaps = 17/401 (4%) Query: 1 MATNLGQAYVQIMPSAKGISGSISKTLDPEASSAGSSAGSLLGGKLIGILGSVIAAAKIG 60- MAT + QAYVQ++PSA+GI+G I L+PEAS+AG SAG LG L+G++ VIAAA IG Sbjct: 1 MATEIAQAYVQLIPSARGITGKIQSILNPEASAAGQSAGQSLGSSLVGVMTKVIAAAGIG 60- Query: 61 EMVTKAISSSISEGAALQQSLGGVETLFKSNANLVKKYADEAYKTTGLSANAYMESVTGF 12- 0 KA S++ISEGAALQQSLGG+ETLFK +A+ VK YA+EAYKTTGLSANAYME+VTGF Sbjct: 61 ----KAFSAAISEGAALQQSLGGIETLFKGSADKVKGYANEAYKTTGLSANAYMENVTGF 11- 6 Query: 121 SASLLQSLGGDTAKAAKVANMAMIDMADNSNKMGTSMESIQYAYQGFAKQNYTMLDNLKL 18- 0 SASLLQSLGGDT KAA+ ANMAMIDM+DN+NKMGTSMESIQ AYQGFAKQNYTMLDNLKL Sbjct: 117 SASLLQSLGGDTNKAAETANMAMIDMSDNANKMGTSMESIQMAYQGFAKQNYTMLDNLKL 17- 6 Query: 181 GYGGTQEEMKRLLSDAQKLTGKKYDISNLSDVYEAIHAIQGKIGITGTTAKEAATTFTGS 24- 0 GYGGT++EM+RLL+DA+KLTG KYDI+NLSDVY AIHAIQ + ITGTTAKEAA+TF+GS Sbjct: 177 GYGGTKQEMQRLLADAEKLTGVKYDINNLSDVYSAIHAIQENLDITGTTAKEAASTFSGS 23- 6 Query: 241 FEAMKAASKNLLGKMALGEDIKPSLKALFDTTSNFVLNNFIPMLTNVFKGFGSVISLTFS 30- 0 FE+MKAA++N+LGK+ALGE+I PSL AL TTS F+ +NF+PM+ NVF G G V++ S Sbjct: 237 FESMKAAAQNVLGKLALGENILPSLHALLKTTSTFLFDNFLPMIGNVFSGLGLVLTEGIS 29- 6 Query: 301 ELIPKIVGFMQTSGPSLMQSGISFIISFVNGFLTAYPAFLTVAGKIFTDFVSFVMQSIPG 36- 0 ++ ++G S + +S + G + F + G + ++ +I G Sbjct: 297 QIASQLFG-------DAFGSAVFDQLSRITGIFETF--FDMIFGSLSKQDNIDILNTI-G 34- 6 Query: 361 LLQAGATLVLNLIDGILANLPQIATS---AVSVISSFISML 398 + AT ++N+ D I I ++ V ++ F+ L Sbjct: 347 FSEEAATQIVNIADNIRVTFENIGSAIGDVVGIVGDFVGDL 387 Identities = 112/386 (29%), Positives = 172/386 (44%), Gaps = 18/386 (4%) Query: 235 TTFTGSFEAMKAASKNLLGKMA-LGEDIKPSLKA---LFDTTSNFVLNNFIPMLTNVFKG 29- 0 TT+ E++KA ++ + L E IK + L T V+ FI N++ Sbjct: 580 TTWNAYVESLKAMWNAVVTFFSDLWESIKEAASTAWTLITTAVMMVVQPFIDGFMNIWNN 63- 9 Query: 291 FGSVISLTFSELIPKIVGFMQTSGPSLMQSGISFIISFVNGFLTAYPAFLTVAGKIFTDF 35- 0 ++ + + G + S+ I II V G A L++ + + Sbjct: 640 ISEGLTQVWEGIKLIFEGAWEFI-KSIFLGAILIIIDLVTGNFGQLGADLSLIWEGIKNG 69- 8 Query: 351 VSFVMQSIPGLLQAGATLVLNLIDGILANLPQIATSAVSVISSFISMLQANYPAILKKGF 41- 0 +S + + I +++ G+ N + ++ I + SM + I Sbjct: 699 ISLIWSGIKTYFSGVVDVIVGYATGVFENFSNVLSTIWEFIKTAASMA---WEWIKSTVS 75- 5 Query: 411 EILSYLVQGIIARLPDIVITVGKL---IAILAGAIASNLPKVLALGVQLLITFVKGILSV 46- 7 +++ L+QG + V + L I A A S L K L LG + V G + Sbjct: 756 NLITGLIQGAQNLWNNFVSFLSGLWENIKSTASAAWSGL-KSLVLG--FINGLVSGAQTA 81- 2 Query: 468 IGKINETANNIGEK---LINAIKSIDLLSAGRAIMRGFLRGLEDVWGDIQNFVGDIAGWI 52- 4 + + +++ K + N IK+I+L AG+AI+ GFL GL+ W + NFVG IA WI Sbjct: 813 WNNMKQAVSDLVTKVTNIFNGIKNINLWEAGKAILNGFLGGLKSAWEGVTNFVGGIANWI 87- 2 Query: 525 KDHKGPISYDRRLLIPAGNAIMQGLHQGLVDKFKPVKNLVNGMAEEIQSSFGNPQLAFDM 58- 4 +DHKGPI YDR+LLIPAGNAIM L GL D FK VK V GM+ EI F L + Sbjct: 873 RDHKGPIEYDRKLLIPAGNAIMGSLDNGLKDGFKDVKKTVGGMSGEISDVFSGDNLDLNS 93- 2 Query: 585 DTNVNNGFE-RIGTLNKNLSSQVTST 609 +V E R+ + L Q + T Sbjct: 933 TASVTKNLEARLAMPSAQLEVQESKT 958 A related DNA sequence was identified in S. pyogenes <SEQ ID 1407> which encodes the amino acid sequence <SEQ ID 1408>. Analysis of this protein sequence reveals the following: TABLE-US-01382 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.76 Transmembrane 458-474 (458-474) INTEGRAL Likelihood = -2.60 Transmembrane 483-499 (482-499) INTEGRAL Likelihood = -2.02 Transmembrane 429-445 (429-445) INTEGRAL Likelihood = -1.28 Transmembrane 397-413 (397-413) INTEGRAL Likelihood = -0.53 Transmembrane 739-755 (738-755) INTEGRAL Likelihood = -0.27 Transmembrane 356-372 (356-372) ----- Final Results ----- bacterial membrane --- Certainty = 0.2105(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01383 >GP: AAB18717 GB: U38906 ORF42 [Bacteriophage rlt] Identities = 261/579 (45%), Positives = 359/579 (61%), Gaps = 63/579 (10%) Query: 184 MKRLLSDAEKLPAAMGKKFDLSNYADVVEAIHLVQDNMGIAGVAAEEAKTTFSGSLAAMK 24- 3 M+RLL+DA+KL G+K+D+SN++D+ +AIH +Q M I G A+EA TTFSGS +MK Sbjct: 1 MQRLLTDAQKLT--GQKYDISNFSDITQAIHAIQTEMDITGTTAKEASTTFSGSFDSMK 57 Query: 244 SSFTNVMAGLSLGDDIRPALRGLAETTSNFLFGNFIPMVANIFKGLPSAIGTFIGAAAPI 30- 3 ++ +NV+ LSLG D++ L L TTS FLF NFIPMV NIFK LP AI TF+ AA Sbjct: 58 AAMSNVLGNLSLGRDLQGPLNALVSTTSTFLFKNFIPMVGNIFKALPGAISTFVSAAGKE 11- 7 Query: 304 ITSQ-------------------------------------FQGLMSSLG-ISIDLSPIT 32- 5 ++SQ F L+SS+G IS + + Sbjct: 118 LSSQLGNGIGSGFSDFTAKFSSILSPLQGSFQTIVSGLKPVFDSLLSSIGPISTQIMGVF 17- 7 Query: 326 AKFAQIGQNLQ----PVFNGLKTAFSQLPSFFTSIGSAVAPVIDTIISGLARLDFSGFEA 38- 1 +K Q+ N+ PV + L AF QLPS F +I AV P+IDTI SG++RLDFSG +A Sbjct: 178 SKLPQLFSNVISAVIPVISTLSVAFGQLPSLFEAISVAVQPMIDTISSGISRLDFSGIQA 23- 7 Query: 382 LISAILPALQAGFSNFAAIVGPAISGVVDSFVGMWNAAQPLISILSDALMPVFQILGSFL 44- 1 +ISA++PA+ G + I+GP+I +V+SFV MWN+ QPL ++++ ALMP FQ+LG+F+ Sbjct: 238 IISALVPAITTGITTMMGIIGPSIDTLVNSFVKMWNSIQPLATVIAGALMPAFQVLGAFI 29- 7 Query: 442 GGVVKGALMGVSFAFDAVKVAIQLVTPIIDLLVQGLNFVQPVLSVIAEWIGVAIGMFGNL 50- 1 GGV+KGA++ +S FD ++V + +TPII ++ PVL+ +A+W+G AIG F N Sbjct: 298 GGVLKGAMLALSATFDTIRVVVGFLTPIIAAVLAKFQEFAPVLATVAQWVGTAIGFFANF 35- 7 Query: 502 GTAGQGLSAFIKSAWTNIQTAISTAGTIISTVIDYIKLAFSGAGSAVGVLKNIFSLAWMA 56- 1 G AG L I SAW I++ IS+ + I +I+ K F+G GSA G L+++ S AW Sbjct: 358 GAAGTSLKGLITSAWNGIKSIISSVVSGIGGIINTAKAIFTGLGSAGGALRSMISGAWSG 41- 7 Query: 562 MGDAINVAKGIISSVINGIKSAFSSFS-------SLVSSVGSAVNGVIDSISSTIRG--- 61- 1 + I+ G IS INGIKS FSS S++S V S + G+I SSTI G Sbjct: 418 IRSIISSVGGSISGTINGIKSFFSSLGGSGNGLRSVMSGVWSGITGIISGASSTISGIID 47- 7 Query: 612 --------LANIDISGAGAAIMNGFLNGLKSAWGAVKSFVSGIANWIAEHKGPISYDRVL 66- 3 L NID++GAG A+++GF+ GLKS W A K FV GIA+WI +HKGPISYDR + Sbjct: 478 GIKNIFNSLKNIDLAGAGRAVIDGFVGGLKSTWEAGKKFVGGIADWIKDHKGPISYDRKI 53- 7 Query: 664 LKPAGKAIMGGLNTSLIDGFKEVKSNVSGMADDLASTMT 702 L PAG+AIMGG N SL++ FK V+ NVSG+A + S +T Sbjct: 538 LIPAGQAIMGGFNDSLMENFKAVQKNVSGIAKQIQSAIT 576 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01384 Identities = 272/701 (38%), Positives = 371/701 (52%), Gaps = 91/701 (12%) Query: 1 MATNLGQAYVQIMPSAKGISGSISKTLDPEASSAGSSAGSLLGGKLIGILGSVIAAAKIG 60- MAT LGQAYVQIMPSA+GISG+ISK LDPEA SAG SAGSL+GG L+ ++G IAAA IG Sbjct: 1 MATELGQAYVQIMPSARGISGAISKQLDPEARSAGLSAGSLIGGNLVKMIGGAIAAAGIG 60- Query: 61 EMVTKAISSSISEGAALQQSLGGVETLFKSNANLVKKYADEAYKTTGLSANAYMESVTGF 12- 0 +M ISS++S GA LQQS GG++TL+K VK +A EAYK G+SAN Y E Sbjct: 61 KM----ISSALSAGADLQQSFGGIDTLYKGAETAVKGFAKEAYKA-GISANTYASQAVSM 11- 5 Query: 121 SASLLQSLGGDTAKAAKVANMAMIDMADNSNKMGTSMESIQYAYQGFAKQNYTMLDNLKL 18- 0 ASL QSLGGD AAK ANMA++DMADNS KMGT + SIQ AYQGFAKQNYTMLDNL+L Sbjct: 116 GASLKQSLGGDAVAAAKAANMAIMDMADNSAKMGTDITSIQMAYQGFAKQNYTMLDNLRL 17- 5 Query: 181 GYGGTQEEMKRLLSDAQKL---TGKKYDISNLSDVYEAIHAIQGKIGITGTTAKEAATTF 23- 7 GYGGT+EEMKRLLSDA+KL GKK+D+SN +DV EAIH +Q +GI G A+EA TTF Sbjct: 176 GYGGTKEEMKRLLSDAEKLPAAMGKKFDLSNYADVVEAIHLVQDNMGIAGVAAEEAKTTF 23- 5 Query: 238 TGSFEAMKAASKNLLGKMALGEDIKPSLKALFDTTSNFVLNNFIPMLTNVFKGFGSVISL 29- 7 +GS AMK++ N++ ++LG+DI+P+L+ L +TTSNF+ NFIPM+ N+FKG S I Sbjct: 236 SGSLAAMKSSFTNVMAGLSLGDDIRPALRGLAETTSNFLFGNFIPMVANIFKGLPSAIGT 29- 5 Query: 298 TFSELIPKIV----GFMQTSGPSLMQSGISFIISFV--------NGFLTAY---PAFLTV 34- 2 P I G M + G S+ S I+ + + NG TA+ P+F T Sbjct: 296 FIGAAAPIITSQFQGLMSSLGISIDLSPITAKFAQIGQNLQPVFNGLKTAFSQLPSFFTS 35- 5 Query: 343 AGKIFTDFVSFVMQSIPGL----LQAGATLVLNLIDGILANLPQIATSAVS-VISSFISM 39- 7 G + ++ + L +A + +L + +N I A+S V+ SF+ M Sbjct: 356 IGSAVAPVIDTIISGLARLDFSGFEALISAILPALQAGFSNFAAIVGPAISGVVDSFVGM 41- 5 Query: 398 LQANYPAI------LKKGFEILSYLVQGI---------------------IARLPDIVIT 43- 0 A P I L F+IL + G+ + + D+++ Sbjct: 416 WNAAQPLISILSDALMPVFQILGSFLGGVVKGALMGVSFAFDAVKVAIQLVTPIIDLLVQ 47- 5 Query: 431 ----VGKLIAILAGAIASNLPKVLALGV--QLLITFVKGILSVIGKINETANNIGEKLIN 48- 4 V +++++A I + LG Q L F+K + I TA I +I+ Sbjct: 476 GLNFVQPVLSVIAEWIGVAIGMFGNLGTAGQGLSAFIKSAWTNIQTAISTAGTIISTVID 53- 5 Query: 485 AIKSI-----------------------DLLSAGRAIMRGFLRGLEDVWGDIQNFVGDIA 52- 1 IK D ++ + I+ + G++ + + V + Sbjct: 536 YIKLAFSGAGSAVGVLKNIFSLAWMAMGDAINVAKGIISSVINGIKSAFSSFSSLVSSVG 59- 5 Query: 522 GWIKDHKGPISYDRRLLI-----PAGNAIMQGLHQGLVDKFKPVKNLVNGMAEEIQSSFG 57- 6 + IS R L AG AIM G GL + VK+ V+G+A I G Sbjct: 596 SAVNGVIDSISSTIRGLANIDISGAGAAIMNGFLNGLKSAWGAVKSFVSGIANWIAEHKG 65- 5 Query: 577 NPQLAFDMDTMVNNGFERIGTLNKNLSSQVTSTDNYTSGNA 617 +++D G +G LN +L + SG A Sbjct: 656 --PISYDRVLLKPAGKAIMGGLNTSLIDGFKEVKSNVSGMA 694 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 440 A DNA sequence (GBSx0477) was identified in S. agalactiae <SEQ ID 1409> which encodes the amino acid sequence <SEQ ID 1410>. Analysis of this protein sequence reveals the following: TABLE-US-01385 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2565(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01386 >GP: AAG18637 GB: AY007505 unknown [Streptococcus mitis] Identities = 64/119 (53%), Positives = 87/119 (72%), Gaps = 2/119 (1%) Query: 1 MLKMDEDALVCDLAETYHIYDYKQLPPLKVAVFSLGLREESRINRVISGNRVSFERRILA 60 M++ DEDAL+CDLAETY I+DY+QLP +VAVF+ GLR++SRI ++ ++V FE +LA Sbjct: 1 MIQTDEDALICDLAETYGIFDYRQLPADQVAVFAFGLRDDSRIKLAMTNSKVPFETFLLA 60 Query: 61 GMFDRLGMLIWMKTTDGQKGKNRPEMVSTMF--DNQQKDSEVVSFGSGKDFEETRNNIL 117 G+ DRL L+W KTTDGQKG N+P MV+ + K+S+ + F SG+DFEE R IL Sbjct: 61 GVLDRLSALVWFKTTDGQKGINKPLMVTEELTGKTKAKESKEMIFDSGEDFEEYRQKIL 119 A related DNA sequence was identified in S. pyogenes <SEQ ID 1411> which encodes the amino acid sequence <SEQ ID 1412>. Analysis of this protein sequence reveals the following: TABLE-US-01387 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2905(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01388 Identities = 60/123 (48%), Positives = 82/123 (65%), Gaps = 2/123 (1%) Query: 1 MLKMDEDALVCDLAETYHIYDYKQLPPLKVAVFSLGLREESRINRVISGNRVSFERRILA 60 M+ D+DAL CDLAETY IYDY+QLP +VAVF++GLR SRI +SG + + +LA Sbjct: 1 MIAKDDDALTCDLAETYGIYDYRQLPAYQVAVFAVGLRSNSRIKMALSGETEALDTVLLA 60 Query: 61 GMFDRLGMLIWMKTTDGQKGKNRPEMV--STMFDNQQKDSEVVSFGSGKDFEETRNNILG 118- G++D +L W KT DGQ G+N+P+ V + QK ++V+SF SG+DFE R +LG Sbjct: 61 GIYDNTNLLFWSKTKDGQSGQNKPKSVVEAISGSKSQKANDVISFVSGEDFENARKQLLG 120- Query: 119 FGG 121 G Sbjct: 121 GDG 123 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 441 A DNA sequence (GBSx0478) was identified in S. agalactiae <SEQ ID 1413> which encodes the amino acid sequence <SEQ ID 1414>. Analysis of this protein sequence reveals the following: TABLE-US-01389 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2280(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01390 >GP: AAG18636 GB: AY007505 unknown [Streptococcus mitis] Identities = 40/80 (50%), Positives = 62/80 (77%), Gaps = 1/80 (1%) Query: 3 TSSGFEYKIEESRLKNYELVEALADLESNPLSLPKVLRLLLGDQVESLKNHLRASDGTVS 62 TS+GF ++I + RL+NYEL+EA++++++NP LPKV++L+LG++ E LKNH+R +DG V Sbjct: 24 TSTGFPFEITKERLENYELLEAISEVDTNPAVLPKVVKLMLGNKSEDLKNHVRTADGIVP 83 Query: 63 TEALMEEVKEIFES-GQLKK 81 + + E+ EIF S QLKK Sbjct: 84 LDKMGAEISEIFSSQNQLKK 103 A related DNA sequence was identified in S. pyogenes <SEQ ID 1415> which encodes the amino acid sequence <SEQ ID 1416>. Analysis of this protein sequence reveals the following: TABLE-US-01391 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4365(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01392 Identities = 42/75 (56%), Positives = 60/75 (80%) Query: 2 KTSSGFEYKIEESRLKNYELVEALADLESNPLSLPKVLRLLLGDQVESLKNHLRASDGTV 61 KT+SGFEY+I + RLKN+ELVEA+A+ E++P ++ K++ LLLGD +SLK H+R ++G V Sbjct: 7 KTTSGFEYEIPKKRLKNFELVEAIAEEETDPTAVVKIVNLLLGDAAKSLKEHVRDAEGIV 66 Query: 62 STEALMEEVKEIFES 76 EA+ E+KEIFES Sbjct: 67 DVEAIGVEIKEIFES 81 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 442 A DNA sequence (GBSx0479) was identified in S. agalactiae <SEQ ID 1417> which encodes the amino acid sequence <SEQ ID 1418>. This protein is predicted to be Structural protein. Analysis of this protein sequence reveals the following: TABLE-US-01393 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3461(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01394 >GP: AAG18635 GB: AY007505 unknown [Streptococcus mitis] Identities = 114/183 (62%), Positives = 142/183 (77%) Query: 2 VANSSNVTTAKPKIGGAIYTAPLGTELPKDTASELNEAFKSLGYISEDGLSNEDKRESEE 61 +A +NVTTAKPKIGGA+Y+APLGT LP D ++L++AF++LGYIS+DG++N + ESE Sbjct: 1 MATEANVTTAKPKIGGAVYSAPLGTALPTDATTKLDQAFEALGYISDDGMTNSNSPESEN 60 Query: 62 IQAWGGDVVESAQKSKADKFTYTLIEALNIEVLKEIYGKDNVTGDLKTGITVKSNSKPLE 121- I+AWGG VV S QK K D F Y LIEALN+ VLKE+YG DNV+GDL +GIT+K+NSK L Sbjct: 61 IKAWGGVVVSSVQKEKTDTFKYMLIEALNLHVLKEVYGPDNVSGDLSSGITIKANSKELP 120- Query: 122 EHCLVIEMILKNNTVKRIVIPKGKVSEVGEIKYVDNEAAGYETTLQAFPDAEGNTHYEYI 18- 1 HCLVIE +LK +KRIVIP GKV+ + EI Y D GY TT+ AFP+A +THYEYI Sbjct: 121 HHCLVIETVLKGGVLKRIVIPSGKVTAIDEITYNDGSVLGYGTTVTAFPNAADDTHYEYI 18- 0 Query: 182 KGA 184 KGA Sbjct: 181 KGA 183 A related DNA sequence was identified in S. pyogenes <SEQ ID 1419> which encodes the amino acid sequence <SEQ ID 1420>. Analysis of this protein sequence reveals the following: TABLE-US-01395 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2379(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01396 Identities = 119/182 (65%), Positives = 142/182 (77%) Query: 4 NSSNVTTAKPKIGGAIYTAPLGTELPKDTASELNEAFKSLGYISEDGLSNEDKRESEEIQ 63 ++ NVT+AKPK GGAIY+APLGTELPKD SELN FK+LGY+SEDG+ NED R SE I+ Sbjct: 6 DTKNVTSAKPKTGGAIYSAPLGTELPKDAKSELNTKFKNLGYVSEDGVVNEDTRSSENIK 65 Query: 64 AWGGDVVESAQKSKADKFTYTLIEALNIEVLKEIYGKDNVTGDLKTGITVKSNSKPLEEH 123- AWGGD+V + Q K DKFTY LIE+LN+EVLKE+YG NVTGDL GI +KSNSK LE H Sbjct: 66 AWGGDIVGAVQTEKEDKFTYKLIESLNVEVLKEVYGAVNVTGDLSGGIQIKSNSKELEAH 125- Query: 124 CLVIEMILKNNTVKRIVIPKGKVSEVGEIKYVDNEAAGYETTLQAFPDAEGNTHYEYIKG 18- 3 +V++MI+ +KRIV+P KV EVGEIKYVD E GYETTL+ FPD +G+TH EYI Sbjct: 126 VIVVDMIMNGGILKRIVLPNAKVDEVGEIKYVDGEVVGYETTLKCFPDKDGDTHREYIVK 18- 5 Query: 184 AG 185 G Sbjct: 186 PG 187 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 443 A DNA sequence (GBSx0480) was identified in S. agalactiae <SEQ ID 1421> which encodes the amino acid sequence <SEQ ID 1422>. Analysis of this protein sequence reveals the following: TABLE-US-01397 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2214(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-01398 >GP: AAB18710 GB: U38906 ORF35 [Bacteriophage rlt] Identities = 52/78 (66%), Positives = 66/78 (83%) Query: 1 MSKFKFKLNKAGVAELMKSSEMQQVLTTKATAIRERCGDGYAQDIHVGKNRANAMVSAKT 60 - M+K FKLN++GVA +MKS EMQ +L KA+A+++RCG GY QD+HVGKNRANAMV A+T Sbjct: 1 MAKNLFKLNRSGVASMMKSPEMQAILKEKASAVKQRCGPGYGQDMHVGKNRANAMVFAET 60 Query: 61 IKAKKDNSKNNTLLKAVR 78 +AK+DN KNNT+LKAVR Sbjct: 61 YQAKRDNMKNNTILRAVR 78 A related DNA sequence was identified in S. pyogenes <SEQ ID 1423> which encodes the amino acid sequence <SEQ ID 1424>. Analysis of this protein sequence reveals the following: TABLE-US-01399 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2446(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01400 Identities = 75/78 (96%), Positives = 76/78 (97%) Query: 1 MSKFKFKLNKAGVASLMKSSEMQQVLTTKATAIRERCGDGYAQDIHVGKNRANAMVSAKT 60 - MSKFKFKLN+AGVAELMKSSEMQQVLTTKATAIRERCGDGY QDIHVGKNRANAMVS KT Sbjct: 1 MSKFKFKLNRAGVAELMKSSEMQQVLTTKATAIRERCGDGYVQDIHVGKNRANAMVSTKT 60 Query: 61 IKAKKDNSKNNTLLKAVR 78 IKAKKDNSKNNTLLKAVR Sbjct: 61 IKAKKDNSKNNTLLKAVR 78 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 444 A DNA sequence (GBSx0481) was identified in S. agalactiae <SEQ ID 1425> which encodes the amino acid sequence <SEQ ID 1426>. Analysis of this protein sequence reveals the following: TABLE-US-01401 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2888(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01402 >GP: AAB18709 GB: U38906 ORF34 (Bacteriophage rlt] Identities = 41/59 (69%), Positives = 45/59 (75%) Query: 1 MTGKKVEYILAIPKGDKHDWEDKEVCFFDKKWRTVGLALEGIEELIPLEWNKKVMVERY 59 +TGKK Y LAIPK D HDWE+K+V FF K WRT G LEGIE LIPL+WNKKV VE Y Sbjct: 56 LTGKKAIYTLAIPKKDTHDWENKKVRFFGKTWRTFGEPLEGIEGLIPLDWNKKVTVEHY 114 A related DNA sequence was identified in S. pyogenes <SEQ ID 1427> which encodes the amino acid sequence <SEQ ID 1428>. Analysis of this protein sequence reveals the following: TABLE-US-01403 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2779(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01404 Identities = 51/60 (85%), Positives = 57/60 (95%) Query: 1 MTGKKVEYILAIPKGDKHDWEDKEVCFFDKKWRTVGLALEGIEELIPLEWNKKVMVERYE 60 - +TGKKVEY+LAIPKGD+HDWE+KEV FF KKWRTVG+ LEGIEELIPL+WNKKVMVERYE Sbjct: 50 LTGKKVEYVLAIPKGDEHDWENKEVRFFGKKWRTVGIPLEGIEELIPLDWNKKVMVERYE 109- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 445 A DNA sequence (GBSx0482) was identified in S. agalactiae <SEQ ID 1429> which encodes the amino acid sequence <SEQ ID 1430>. Analysis of this protein sequence reveals the following: TABLE-US-01405 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2770(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01406 >GP: AAB18708 GB: U38906 ORF33 [Bacteriophage r1t] Identities = 89/130 (68%), Positives = 106/130 (81%), Gaps = 1/130 (0%) Query: 1 MTNFATTDDVILLWRQLSVDEIKRAEALLETVSDTLRLEASKVGKNLDEMILETP-YFAT 59 M FAT DD+ +LWR L DE +RAE LLE VSD+LR EA KVG++L MI E P YFA+ Sbjct: 1 MNPFATVDDLTMLWRPLKGDEKERAEKLLEIVSDSLREEADKVGRDLYAMIAEKPSYFAS 60 Query: 60 VLKSVTVDIVARTLMTATQGEPMSQESQSALGYTWSGTYLVPGGGLFIKDSELKRLGLKK 119- V+KSVTVDIVARTLMT+T EPM+Q ++SALGY+ SG+YLVPGGGLFIK+SEL RLGLKK Sbjct: 61 VVKSVTVDIVARTLMTSTDQEPMTQTTESALGYSVSGSYLVPGGGLFIKNSELSRLGLKK 120- Query: 120 QRYGGIELYG 129 QR+G I+ YG Sbjct: 121 QRFGVIDFYG 130 A related DNA sequence was identified in S. pyogenes <SEQ ID 1431> which encodes the amino acid sequence <SEQ ID 1432>. Analysis of this protein sequence reveals the following: TABLE-US-01407 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2061(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01408 Identities = 116/138 (84%), Positives = 129/138 (93%) Query: 3 NFATTDDVILLWRQLSVDEIKRAEALLETVSDTLRLEASKVGKNLDEMILETPYFATVLK 62 NFATTDDVILLWR LSVDE+KRA ALL+ VSDTLR+EA KVGK+LD+ +++ PYF V+K Sbjct: 3 NFATTDDVILLWRPLSVDELKRANALLKVVSDTLRMEADKVGKDLDKTMVDKPYFVNVIK 62 Query: 63 SVTVDIVARTLMTATQGEPMSQESQSALGYTWSGTYLVPGGGLFIKDSELKRLGLKKQRY 122- SVTVDIVARTLMT+T+GEPM+QESQSALGYTWSGTYLVPGGGLFIKDSELKRLGLKKQRY Sbjct: 63 SVTVDIVARTLMTSTRGEPMAQESQSALGYTWSGTYLVPGGGLFIKDSELKRLGLKKQRY 122- Query: 123 GGIELYGEIERNNSYFSR 140 GGIELYGEIER+NS FSR Sbjct: 123 GGIELYGEIERDNSCFSR 140 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 446 A DNA sequence (GBSx0483) was identified in S. agalactiae <SEQ ID 1433> which encodes the amino acid sequence <SEQ ID 1434>. This protein is predicted to be Structural protein. Analysis of this protein sequence reveals the following: TABLE-US-01409 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3015(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01410 >GP: AAB18706 GB: U38906 Structural protein [Bacteriophage r1t] Identities = 132/296 (44%), Positives = 189/296 (63%), Gaps = 8/296 (2%) Query: 5 IKAGTLFKPELVTEIMSKVKGHSTLAKLSGQTPIPFNGVEQFVFNLDGNAQIVGEGEQKL 64 + GTLF P LVT+++SKV G S++A+LS Q PIPFNG + F F +D +V E +K Sbjct: 3 LNKGTLFDPTLVTDLISKVAGKSSIARLSAQKPIPFNGEKVFTFTMDSEIDVVAESGKKT 62 Query: 65 GNTAKVTSKIIKPLKFVYQARMTDEFKYASEEKRLNFLKHYADGFAKKMAEAFDIAAIHG 124- + + + P+K Y AR++DEF YAS+E+++N L+ + DGFAKK+A D+ A HG Sbjct: 63 HGGVTLAPQTMVPIKVEYGARISDEFMYASDEEKINILQEFNDGFAKKVARGIDLMAFHG 122- Query: 125 LEPRTMTDASFKATNSFDGVVTGNVIKYEADK--IDDN--IDAAVTTIVANGNDVTGIAL 18- 0 + PR T ++ TN FD VT K EA + D N I+ AV + DVTGIA+ Sbjct: 123 VNPRLGTASAVIGTNHFDSKVTQ---KVEAPRGIADPNGAIENAVELLTGVDADVTGIAI 17- 9 Query: 181 SPQAGQDMSKRKDKFDNVMYPEFRFGQRPSNFFNMTLDINKTLTMKGGTAKDDHAIVGDF 24- 0 +P ++K+KD DN ++PE ++G P + +D+NKT++ T + D AI+GDF Sbjct: 180 NPSFRSALAKQKDLQDNALFPELKWGATPDTINGLPVDVNKTVSDMSLTQR-DRAIIGDF 23- 8 Query: 241 QNMFKWGYAENIPMEIIEYGDPDGSGRDLKAYNEILLRTEAFIGWGILDEKAFSRV 296 N FKWGYA+ +P+E+I+YGDPD SG DLK YN++ +R E F+GWGILD F+RV Sbjct: 239 ANGFKWGYAKEVPLEVIQYGDPDNSGLDLKGYNQVYIRAELFLGWGILDATKFARV 294 A related DNA sequence was identified in S. pyogenes <SEQ ID 1435> which encodes the amino acid sequence <SEQ ID 1436>. Analysis of this protein sequence reveals the following: TABLE-US-01411 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2772(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01412 Identities = 133/298 (44%), Positives = 187/298 (62%), Gaps = 2/298 (0%) Query: 1 MAESIKAGTLFKPELVTEIMSKVKGHSTLAKLSGQTPIPFNGVEQFVFNLDGNAQIVGEG 60 M +LF LV+++++KVKGHS+LAKLS Q PIPFNG ++F F LD + +V E Sbjct: 1 MGTETSKASLFDKHLVSDLINKVKGHSSLAKLSSQKPIPFNGSKEFTFTLDSDIDVVAEN 60 Query: 61 EQKLGNTAKVTSKIIKPLKFVYQARMTDEFKYASEEKRLNFLKHYADGFAKKMAEAFDIA 120- +K + I P+K Y AR++DEF YA+EE++++ LK + +GFAKK+A D+ Sbjct: 61 GKKTHGGLSLEPVTIVPIKVEYGARLSDEFLYATEEEKIDILKAFNEGFAKKLARGIDLM 120- Query: 121 AIHGLEPRTMTDASFKATNSFDGVVTGNVIKYEADKIDDNIDAAVTTIVANGNDVTGIAL 18- 0 A+HG+ PRT + TN FD VT V E++ D NI+AAV I + VTG+A+ Sbjct: 121 AMHGINPRTKKASDVIGTNHFDSKVTQVVKFTESEDADANIEAAVNLIQGSEGVVTGLAM 18- 0 Query: 181 SPQAGQDMSK-RKDKFDNVMYPEFRFGQRPSNFFNMTLDINKTLTMKGGTAKD-DHAIVG 23- 8 + ++K + MYPE +G P + + +N T+ A+ D I+G Sbjct: 181 DTEFSTALAKVTNGEMGPKMYPELAWGANPDSINGLKSSVNTTVGAGADEAESKDLVIIG 24- 0 Query: 239 DFQNMFKWGYAENIPMEIIEYGDPDGSGRDLKAYNEILLRTEAFIGWGILDEKAFSRV 296 DF++MFKWGYA+ IPMEII+YGDPD SG+DLK YN+I LR EA+IGWGILD K+F+RV Sbjct: 241 DFESMFKWGYAKQIPMEIIKYGDPDNSGKDLKGYNQIYLRAEAYIGWGILDAKSFARV 298 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 447 A DNA sequence (GBSx0484) was identified in S. agalactiae <SEQ ID 1437> which encodes the amino acid sequence <SEQ ID 1438>. Analysis of this protein sequence reveals the following: TABLE-US-01413 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2224(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9659> which encodes amino acid sequence <SEQ ID 9660> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01414 >GP: AAB18705 GB: U38906 ORF30 [Bacteriophage rlt] Identities = 64/158 (40%), Positives = 101/158 (63%), Gaps = 8/158 (5%) Query: 43 MSEFKVIETQEELDTIVKARIARERE----KYQDYDQLKTRVEELETENSSLQTALNDAK 98 - MSE + +TQEEL+ I++ R+AR++E + DYD+LKT++ LE +N++ Q + ++K Sbjct: 1 MSENNLPKTQEELNQIIETRLARQKETIEANFADYDELKTKIAALEADNTAYQATIEESK 60 Query: 99 SNTDSYTEKITTLENQIAGYEAANLRTKVALQYGLPIDLANRLQGDDEDGLKVDAERLAS 158- S + ++ E QI+GY+ L+ +A++ GLP+DLA+RL GDDE+ LK DAER + Sbjct: 61 S----WEQEKADYEKQISGYKTTQLKQSIAIKAGLPLDLADRLSGDDEESLKADAERFSG 116- Query: 159 FIKPSQPQPPTKSNEPIITDQKEAGWIEMARNLVNKGE 196 FIKP P P K EP + D K+ + ++ L +GE Sbjct: 117 FIKPKTPPAPLKDVEPNLGDGKDGAYRKLVDGLKTEGE 154 A related DNA sequence was identified in S. pyogenes <SEQ ID 1439> which encodes the amino acid sequence <SEQ ID 1440>. Analysis of this protein sequence reveals the following: TABLE-US-01415 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3476(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01416 Identities = 128/149 (85%), Positives = 136/149 (90%) Query: 43 MSEFKVIETQEELDTIVKARIAREREKYQDYDQLKTRVEELETENSSLQTALNDAKSNTD 102- MSEFKVIETQEELDTIVKARIAREREKYQDYDQLKTRVEELETENSSLQTALNDAKSNTD Sbjct: 1 MSEFKVIETQEELDTIVKARIAREREKYQDYDQLKTRVEELETENSSLQTALNDAKSNTD 60 Query: 103 SYTEKITTLENQIAGYEAANLRTKVALQYGLPIDLANRLQGDDEDGLKVDAERLASFIKP 16- 2 SYTE+I+TL+NQIA YE ANLRTKVALQYGLPIDLA+RLQGDDEDGLKVDAERLASFIKP Sbjct: 61 SYTEEISTLKNQIADYETANLRTKVALQYGLPIDLADRLQGDDEDGLKVDAERLASFIKP 120- Query: 163 SQPQPPTKSNEPIITDQKEAGWIEMARNL 191 SQPQPP KSNEP I +A + + + L Sbjct: 121 SQPQPPAKSNEPNIDSNADANYRALVQGL 149 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 448 A DNA sequence (GBSx0485) was identified in S. agalactiae <SEQ ID 1441> which encodes the amino acid sequence <SEQ ID 1442>. Analysis of this protein sequence reveals the following: TABLE-US-01417 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2888(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01418 >GP: AAB18704 GB: U38906 ORF29 [Bacteriophage rlt] Identities = 322/461 (69%), Positives = 383/461 (82%) Query: 8 KLGNQRPTQSVNLHFAKTLAHEAINYYKKTGLSCYLWQENMLIPMMAINEDNLWVHQKYG 67 + GNQ PTQSV L F +T EAI Y+K+ CY WQ+N+L +MAI+ED LW HQK+G Sbjct: 6 RFGNQYPTQSVILPFTETKYQEAIEIYEKSKHECYPWQKNLLKEVMAIDEDGLWTHQKFG 65 Query: 68 YAIPRRNGKTEVVYILELWALHKGLKILHTAHRISTSHSSFEKVKKYLEMSGYVDGEDFI 127- Y+IPRRNGKTE+VYILELW+L +GL ILHTAHRISTSHSS+EK+KKYLE SGYV+GEDF Sbjct: 66 YSIPRRNGKTEIVYILELWSLVQGLSILHTAHRISTSHSSYEKLKKYLEDSGYVEGEDFK 125- Query: 128 SNKAKGQERIEFKSSGSVIQFRTRTSNGGLGEGFDLLIIDEAQEYTAEQESALKYTVTDS 18- 7 S KAKGQER+E SG VIQFRTRTS+GGLGEGFD+L+IDEAQEYT EQESALKYTVTDS Sbjct: 126 SIKAKGQERLELIESGGVIQFRTRTSSGGLGEGFDILVIDEAQEYTTEQESALKYTVTDS 18- 5 Query: 188 DNPMTIMCGTPPTMVSTGTVFESYRKECLKGDRRYSGWAEWSVDEMQPIHDVKSWYVANP 24- 7 DNPMTIMCGTPPT VS+GTVF +YR + G +YSGWAEWSV++++ IHDV++WY +NP Sbjct: 186 DNPMTIMCGTPPTPVSSGTVFTNYRDNTIAGKAKYSGWAEWSVEDVKDIHDVEAWYNSNP 24- 5 Query: 248 SMGYHLNERKIEAELGEDEIDHNIQRLGYWPSFNQKSVISEKEWAKLKVEQVPELKSKLF 30- 7 SMGYHLNERKIEAELGED++DHN+QRLGYWP +NQKSVISE+EW LKV ++P +K KLF Sbjct: 246 SMGYHLNERKIEAELGEDKLDHNVQRLGYWPKYNQKSVISEQEWNALKVNRLPVIKGKLF 30- 5 Query: 308 VGIKFGQDGNNVSLSIAARASENKVFVEAIDCLSVRNGTQWIINFLKSADIAKVVVDGAS 36- 7 VGIK+G DG NV++SIA + KVFVE IDC S+RNG QWIINFLK AD+ KVV+DG S Sbjct: 306 VGIKYGNDGANVAMSIAVKTLSGKVFVETIDCQSIRNGNQWIINFLKKADVEKVVIDGQS 36- 5 Query: 368 GQELLAQEMREHGLKKPELPKVAEIITANTMWEQGIMQETICHNDQPSLTAVVTNCEKRQ 42- 7 GQ +L EM++ LK+P LP V EII AN++WEQGI Q+ CH+ QPSL+ VVTNC+KR Sbjct: 366 GQSILTSEMKDFKLKEPILPTVKEIINANSLWEQGIFQKNFCHSGQPSLSTVVTNCDKRN 42- 5 Query: 428 IGSNGGFGYKSLYDDRDISLMDSALLAHWICYTTKPKRKQR 468 IG++GGFGYKS +DD DISLMDSALLAHW C KPK+KQ+ Sbjct: 426 IGTSGGFGYKSQFDDMDISLMDSALLAHWACSNNKPKKKQQ 466 A related DNA sequence was identified in S. pyogenes <SEQ ID 1443> which encodes the amino acid sequence <SEQ ID 1444>. Analysis of this protein sequence reveals the following: TABLE-US-01419 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3133(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01420 Identities = 437/471 (92%), Positives = 459/471 (96%) Query: 1 MVTKTKAKLGNQRPTQSVNLHFAKTLAHEAINYYKKTGLSCYLWQENMLIPMMAINEDNL 60 MVTKTK KLGNQRPTQSVNLHFAK+LAHEAINYYKKTGLSCY WQ NMLIP+MAI+E+ L Sbjct: 6 MVTKTKTKLGNQRPTQSVNLHFAKSLAHEAINYYKKTGLSCYPWQVNMLIPIMAIDENGL 65 Query: 61 WVHQKYGYAIPRRNGKTEVVYILELWALHKGLKILHTAHRISTSHSSFEKVKKYLEMSGY 120- WVHQKYGYAIPRRNGKTEVVYI++LWALHKGLKILHTAHRISTSH+SFEKVKKYLEMSGY Sbjct: 66 WVHQKYGYAIPRRNGKTEVVYIVQLWALHKGLKILHTAHRISTSHASFEKVKKYLEMSGY 125- Query: 121 VDGEDFISNKAKGQERIEFKSSGSVIQFRTRTSNGGLGEGFDLLIIDEAQEYTAEQESAL 18- 0 VDGEDFISNKAKGQERIEFK+SG+VIQFRTRTSNGGLGEGFDLLIIDEAQEYT+EQESAL Sbjct: 126 VDGEDFISNKAKGQERIEFKASGAVIQFRTRTSNGGLGEGFDLLIIDEAQEYTSEQESAL 18- 5 Query: 181 KYTVTDSDNPMTIMCGTPPTMVSTGTVFESYRKECLKGDRRYSGWAEWSVDEMQPIHDVK 24- 0 KYTVTDSDNPMTIMCGTPPTMVSTGTVFE+YRK+CLKG++RYSGWAEWSV EM I+DV Sbjct: 186 KYTVTDSDNPMTIMCGTPPTMVSTGTVFEAYRKDCLKGNKRYSGWAEWSVPEMVKINDVS 24- 5 Query: 241 SWYVANPSMGYHLNERKIEAELGEDEIDHNIQRLGYWPSFNQKSVISEKEWAKLKVEQVP 30- 0 SWY++NPSMG+HLNERKIEAELGEDEIDHNIQRLGYWPSFNQKSVISEKEWAKLKVEQVP Sbjct: 246 SWYISNPSMGFHLNERKIEAELGEDEIDHNIQRLGYWPSFNQKSVISEKEWAKLKVEQVP 30- 5 Query: 301 ELKSKLFVGIKFGQDGNNVSLSIAARASENKVFVEAIDCLSVRNGTQWIINFLKSADIAK 36- 0 ELKSKLFVGIKFGQDGNNVSLSIAAR SENKVFVE IDCLSVRNGTQWIINFLKSADIAK Sbjct: 306 ELKSKLFVGIKFGQDGNNVSLSIAARTSENKVFVETIDCLSVRNGTQWIINFLKSADIAK 36- 5 Query: 361 VVVDGASGQELLAQEMREHGLKKPELPKVAEIITANTMWEQGIMQETICHNDQPSLTAVV 42- 0 VV+DGASGQELLAQEM++ GLKKPELPKVAEIITAN MWEQGIMQETICH+DQPSLTAVV Sbjct: 366 VVIDGASGQELLAQEMKDQGLKKPELPKVAEIITANMMWEQGIMQETICHSDQPSLTAVV 42- 5 Query: 421 TNCEKRQIGSNGGFGYKSLYDDRDISLMDSALLAHWICYTTKPKRKQRTSC 471 TNCEKRQIGSNGGFGYKSLYDDRDISLMDSALLAHWICYTTKPKRKQRTSC Sbjct: 426 TNCEKRQIGSNGGFGYKSLYDDRDISLMDSALLAHWICYTTKPKRKQRTSC 476 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 449 A DNA sequence (GBSx0486) was identified in S. agalactiae <SEQ ID 1445> which encodes the amino acid sequence <SEQ ID 1446>. Analysis of this protein sequence reveals the following: TABLE-US-01421 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2745(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 450 A DNA sequence (GBSx0487) was identified in S. agalactiae <SEQ ID 1447> which encodes the amino acid sequence <SEQ ID 1448>. Analysis of this protein sequence reveals the following:

TABLE-US-01422 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2568(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01423 >GP: AAB18703 GB: U38906 ORF28 [Bacteriophage r1t] Identities = 124/250 (49%), Positives = 164/250 (65%), Gaps = 3/250 (1%) Query: 2 VDDVLPKLLKSVQQDFEKHFGKSEVVAKAFAELQAKKATYKTVNEFAVEVGRLLSLALAN 61 ++D+LP LL+ + QDF++ S+ + ++ L+ KKATY NEF VEVG++LS L Sbjct: 1 MEDILPPLLEKINQDFDERAANSKKLKQSMELLKTKKATYIQANEFGVEVGQILSDVLGT 60 Query: 62 SVISDELPDGKMYYNIANRLVNDTLRHNYKLISDYAGDVQQNLNKQAKISLKIQRPPLNQ 121- V D LPDGKMY+NIA+RL+N L+ N+ LIS Y+ DVQ LN+ A LK Q P LNQ Sbjct: 61 HVTVDVLPDGKMYFNIADRLLNSILKKNFDLISGYSTDVQSELNQLAGFKLKSQVPELNQ 120- Query: 122 DKIDGLVNRLASEPVFDDVKWLLDEPIVNFSQSIVDDCIRANADFHFKTGLKPTIERIST 18- 1 D+IDG+VNR++SE F+ + WLL EPIV FSQS+VDD ++ N DF K GLKP I R Sbjct: 121 DRIDGIVNRISSEDDFEKILWLLKEPIVTFSQSVVDDTLKKNIDFQAKAGLKPKIVRKLV 18- 0 Query: 182 GKCCDWCDRLAGRYVYHEEPKDFYKRHQHCQCVIDYHPK--NGKRQNSWSKKWTKETTDI 23- 9 GK CDWC LAG Y Y P D Y RH+ C+C ++Y P+ + KRQ+ WSK W D Sbjct: 181 GKACDWCRNLAGSYDYPNVPSDVYHRHERCRCTVEYDPRDIDKKRQDVWSKNWVDPDKDA 24- 0 Query: 240 -LERRKQMNI 248 + RK +N+ Sbjct: 241 KIAERKNLNL 250 A related DNA sequence was identified in S. pyogenes <SEQ ID 1449> which encodes the amino acid sequence <SEQ ID 1450>. Analysis of this protein sequence reveals the following: TABLE-US-01424 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3099(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01425 Identities = 169/261 (64%), Positives = 207/261 (78%), Gaps = 2/261 (0%) Query: 1 MVDDVLPKLLKSVQQDFEKHFGKSEVVAKAFAELQAKKATYKTVNEFAVEVGRLLSLALA 60 MVDDVLPKLLKSV+QDFEK+FG+S+VV KAFAELQAKK TYKTVNEFA+EVGRLLSLAL Sbjct: 1 MVDDVLPKLLKSVRQDFEKYFGESDVVTKAFAELQAKKVTYKTVNEFAIEVGRLLSLALT 60 Query: 61 NSVISDELPDGKMYYNIANRLVNDTLRHNYKLISDYAGDVQQNLNKQAKISLKIQRPPLN 120- SV SD+LPDGKMYYNIA RL+++T+ NYKLIS YAGDVQ+ LN+ A+I LK+QRPPLN Sbjct: 61 GSVSSDKLPDGKMYYNIAKRLLDETMGRNYKLISGYAGDVQRILNENAQIGLKVQRPPLN 120- Query: 121 QDKIDGLVNRLASEPVFDDVKWLLDEPIVNFSQSIVDDCIRANADFHFKTGLKPTIERIS 18- 0 +DKI+G+VNRL SE FDDVKWL EPIVNFSQSIVDD I+ANAD +KTG+ P + R Sbjct: 121 RDKINGMVNRLDSENTFDDVKWLFGEPIVNFSQSIVDDTIKANADLQYKTGMTPQVVRTE 18- 0 Query: 181 TGKCCDWCDRLAGRYVYHEEPKDFYKRHQHCQCVIDYHPKNGKRQNSWSKKWTK--ETTD 23- 8 +G CC+WC + G Y Y + PKD ++RHQ C+C +DY PKNGK Q++WSK W K +T + Sbjct: 181 SGNCCEWCREVVGTYSYPKVPKDVWRRHQRCRCTLDYDPKNGKVQSAWSKIWRKKEKTQE 24- 0 Query: 239 ILERRKQMNIDIRDNNRKSDI 259 +ER ++ + K+DI Sbjct: 241 SIERVEKFKESALVESIKNDI 261 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 451 A DNA sequence (GBSx0488) was identified in S. agalactiae <SEQ ID 1451> which encodes the amino acid sequence <SEQ ID 1452>. This protein is predicted to be Structural protein. Analysis of this protein sequence reveals the following: TABLE-US-01426 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 93-109 (93-110) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01427 >GP: AAC39307 GB: AF022773 ORF5 [Lactococcus bacteriophage phi31] Identities = 271/410 (66%), Positives = 326/410 (79%), Gaps = 2/410 (0%) Query: 1 MNYMGMGYLQRKLALFKTGVDKRYRYYAMDDRDNTRSIVMPDNVREMYRSVIEWTAKGVD 60 M G+GYL+ KL++ K + RY YAM D + I +P + + YRS++ W AKGVD Sbjct: 1 MTEKGIGYLRFKLSVHKRRAEMRYEQYAMKHVDRFKGITIPQALSQQYRSILGWCAKGVD 60 Query: 61 SLADRIIFREFANDDFNAWEIFKANNPDIFFDTAIQSALIASCCFVYIMPGKEDSLPKMQ 120- SLADR+IFREF NDDF EIF+ NNPDIFFD+A+ SALIASC F+YI G+ D++ ++Q Sbjct: 61 SLADRLIFREFENDDFTVNEIFEENNPDIFFDSAVLSALIASCSFIYISKGENDAV-RLQ 119- Query: 121 VIEASKATGILDPTTFLLTEGYAVLESDSNENPTLEAYFTGEKTWYYPKDEKP-YSIDNS 17- 9 VIEA ATGI+DP T LLTEGYAVLE D N N LEA+F ++T YY +D + SI N Sbjct: 120 VIEAVNATGIIDPITGLLTEGYAVLERDENNNVVLEAHFLPDRTDYYYRDSRNNISIANP 17- 9 Query: 180 TGHPLLVPVIHRPDAVRPFGRSRITKAGMYHQKAAKRTLERAEVTAEFYSFPQKYVLGMD 23- 9 TGHPLLVP+IHRPDAVRPFGRSRIT++GMY Q AKRTLERA+VTAEFYSFPQKYV G+ Sbjct: 180 TGHPLLVPIIHRPDAVRPFGRSRITRSGMYWQSNAKRTLERADVTAEFYSFPQKYVTGLS 23- 9 Query: 240 PDAEPMEKWRATVSTLLEISKDEDGDKPTVGQFTTASMAPFMDHLKMYASLFAGGSGLTL 29- 9 DAEPME W+ATVS++L+ +KDEDGDKPT+GQFT SM+PF + L+ A+ FAG +GLTL Sbjct: 240 DDAEPMETWKATVSSMLQFTKDEDGDKPTLGQFTQPSMSPFTEQLRTAAAGFAGETGLTL 29- 9 Query: 300 DDLGFPSDNPSSVEAIKAAHENLRAAGRKAQRSFSSGFLNVAYIAVCLRDDFPYLRNQFM 35- 9 DDLGF SDNPSSVEAIKA+HENLR AGRKAQRS +G LNVAY+A CLRDD PYLR QF Sbjct: 300 DDLGFVSDNPSSVEAIKASHENLRLAGRKAQRSLGAGLLNVAYLAACLRDDVPYLREQFS 35- 9 Query: 360 DTEIKWEPLFEADANMLTLVGDGAIKLNQAIPGFMDADVIRDLTGVKGSD 409 T+ KWEPLFEADA+ML+L+GDGAIKLNQAIP F++ D IRDLTG+KG++ Sbjct: 360 KTKPKWEPLFEADASMLSLIGDGAIKLNQAIPEFINKDTIRDLTGIKGAE 409 A related DNA sequence was identified in S. pyogenes <SEQ ID 1453> which encodes the amino acid sequence <SEQ ID 1454>. Analysis of this protein sequence reveals the following: TABLE-US-01428 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 93-109 (93-110) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01429 Identities = 395/422 (93%), Positives = 407/422 (95%) Query: 1 MNYMGMGYLQRKLALFKTGVDKRYRYYAMDDRDNTRSIVMPDNVREMYRSVIEWTAKGVD 60 MNYMGMGYL+RKLALFKTGVDKRYRYYAMDDRD+TRSIVMP+NVREMYRSV+EWTAKGVD Sbjct: 1 MNYMGMGYLRRKLALFKTGVDKRYRYYAMDDRDDTRSIVMPNNVREMYRSVLEWTAKGVD 60 Query: 61 SLADRIIFREFANDDFNAWEIFKANNPDIFFDTAIQSALIASCCFVYIMPGKEDSLPKMQ 120- SLADRIIFREF NDDFNAWEIFKANNPDIFFDTAIQSALIASCCFVYIMPG ED LPKMQ Sbjct: 61 SLADRIIFREFTNDDFNAWEIFKANNPDIFFDTAIQSALIASCCFVYIMPGAEDGLPKMQ 120- Query: 121 VIEASKATGILDPTTFLLTEGYAVLESDSNENPTLEAYFTGEKTWYYPKDEKPYSIDNST 18- 0 VIEASKATGILDPTTFLLTEGYA+LESDSN NPTLEAYFT + WYYPK KPY+I N T Sbjct: 121 VIEASKATGILDPTTFLLTEGYAILESDSNGNPTLEAYFTDKDIWYYPKKGKPYNIKNPT 18- 0 Query: 181 GHPLLVPVIHRPDAVRPFGRSRITKAGMYHQKAAKRTLERAEVTAEFYSFPQKYVLGMDP 24- 0 GHPLLVP+IHRPDAVRPFGRSRITKAGMYHQKAAKRTLERAEVTAEFYSFPQKYVLGMDP Sbjct: 181 GHPLLVPIIHRPDAVRPFGRSRITKAGMYHQKAAKRTLERAEVTAEFYSFPQKYVLGMDP 24- 0 Query: 241 DAEPMEKWRATVSTLLEISKDEDGDKPTVGQFTTASMAPFMDHLKMYASLFAGGSGLTLD 30- 0 DAEPMEKWRATVSTLLEISKDEDGDKPTVGQFTTASMAPFM+HLKMYASLFAGGSGLTLD Sbjct: 241 DAEPMEKWRATVSTLLEISKDEDGDKPTVGQFTTASMAPFMEHLKMYASLFAGGSGLTLD 30- 0 Query: 301 DLGFPSDNPSSVEAIKAAHENLRAAGRKAQRSFSSGFLNVAYIAVCLRDDFPYLRNQFMD 36- 0 DLGFPSDNPSSVE+IKAAHENLRAAGRKAQRSFSSGFLNVAYIAVCLRD+FPYLRNQFMD Sbjct: 301 DLGFPSDNPSSVESIKAAHENLRAAGRKAQRSFSSGFLNVAYIAVCLRDEFPYLRNQFMD 36- 0 Query: 361 TEIKWEPLFEADANMLTLVGDGAIKLNQAIPGFMDADVIRDLTGVKGSDNPIPKATEVTT 42- 0 T IKWEPLFEADANMLTLVGDGAIKLNQAIPGFMDADVIRDLTGVKG+D PIP TEVTT Sbjct: 361 TVIKWEPLFEADANMLTLVGDGAIKLNQAIPGFMDADVIRDLTGVKGADKPIPAITEVTT 42- 0 Query: 421 DG 422 DG Sbjct: 421 DG 422 SEQ ID 1452 (GBS364) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 73 (lane 6; MW 50 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 81 (lane 11; MW 75 kDa). GBS364-GST was purified as shown in FIG. 216, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 452 A DNA sequence (GBSx0489) was identified in S. agalactiae <SEQ ID 1455> which encodes the amino acid sequence <SEQ ID 1456>. Analysis of this protein sequence reveals the following: TABLE-US-01430 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4063(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1457> which encodes the amino acid sequence <SEQ ID 1458>. Analysis of this protein sequence reveals the following: TABLE-US-01431 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4120(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01432 Identities = 101/118 (85%), Positives = 110/118 (92%) Query: 1 MKKKCLICKKTFQAKTNRSLYCSEECRKKGIREKQRKLMKQKRADKKKEKIKVLNTNADV 60 +KKKCLICKK FQAKTNR+LYCSEECRKKG REKQRKLMKQKRA+++KEK KVLN N DV Sbjct: 1 LKKKCLICKKNFQAKTNRTLYCSEECRKKGNREKQRKLMKQKRAEQRKEKKKVLNPNTDV 60 Query: 61 TEKPKKIRNLVQHYKKLKREILDNESEFGFTGIALVEGIDIHEENFVDLVMQKIKEQQ 118 TEKPKKIRNL QHYKKLK+EIL NESEFGFTGI L+EGID+HEENFVDLVMQKIKEQ+ Sbjct: 61 TEKPKKIRNLAQHYKKLKKEILANESEFGFTGITLIEGIDVHEENFVDLVMQKIKEQK 118 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 453 A DNA sequence (GBSx0490) was identified in S. agalactiae <SEQ ID 1459> which encodes the amino acid sequence <SEQ ID 1460>. Analysis of this protein sequence reveals the following: TABLE-US-01433 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0633(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01434 >GP: AAC39305 GB: AF022773 ORF3 [Lactococcus bacteriophage phi31] Identities = 75/109 (68%), Positives = 87/109 (79%), Gaps = 1/109 (0%) Query: 29 LRADKKGTHRVAFEKNKRRLLKTAHLCGICGRPVDKSLKYPHPLSAAIDHIVPIAKGGHP 88 - LRAD+ G HRVAF+KN++ LLKT + CGICG+P+DK LK P PLS +DHI+PI KGGHP Sbjct: 3 LRADRTGAHRVAFDKNRKILLKTQNTCGICGKPIDKRLKAPDPLSPVVDHIIPINKGGHP 62 Query: 89 SSIDNLQLTHWQCNRQKSDKLFINQTAVRATVVGNRNLPQSRDWSSYAS 137 S++DNLQL HW CNRQKSDKLF N V+GNRNLPQSRDWSSY S Sbjct: 63 SAMDNLQLAHWTCNRQKSDKLF-NVKQEEPKVLGNRNLPQSRDWSSYVS 110 A related DNA sequence was identified in S. pyogenes <SEQ ID 1461> which encodes the amino acid sequence <SEQ ID 1462>. Analysis of this protein sequence reveals the following: TABLE-US-01435 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4185(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01436 Identities = 88/112 (78%), Positives = 102/112 (90%) Query: 28 KLRADKKGTHRVAFEKNKRRLLKTAHLCGICGRPVDKSLKYPHPLSAAIDHIVPIAKGGH 87 - +LRADKKGTHRVAF++NK++LLK A +CGICG+PVDKSLKYPHPLSAAIDHIVPIAKGGH Sbjct: 3 QLRADKKGTHRVAFDRNKKKLLKAATVCGICGKPVDKSLKYPHPLSAAIDHIVPIAKGGH 62 Query: 88 PSSIDNLQLTHWQCNRQKSDKLFINQTAVRATVVGNRNLPQSRDWSSYASKE 139 PS+++NLQLTHWQCNRQKSDKLF NQ + +GNRNLPQSRDWSS+A K+ Sbjct: 63 PSALENLQLTHWQCNRQKSDKLFANQASNEPKTIGNRNLPQSRDWSSFAFKK 114 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 454 A DNA sequence (GBSx0491) was identified in S. agalactiae <SEQ ID 1463> which encodes the amino acid sequence <SEQ ID 1464>. Analysis of this protein sequence reveals the following: TABLE-US-01437 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4481(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 455 A DNA sequence (GBSx0492) was identified in S. agalactiae <SEQ ID 1465> which encodes the amino acid sequence <SEQ ID 1466>. Analysis of this protein sequence reveals the following: TABLE-US-01438 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2907(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01439 >GP: AAF43508 GB: AF145054 ORF15 [Streptococcus thermophilus bacteriophage 7201] Identities = 61/187 (32%), Positives = 90/187 (47%), Gaps = 31/187 (16%) Query: 1 MNIEEAKKLIDKQSIGKGGVGDIPVVKTHIVKVLLDQIDQPQPEVPRFVADWYEKHKDSL 60 MN +EA K I K+ + + L D I +P VP++VADWYE+HKD Sbjct: 1 MNRDEAVKKIAKEGY----------ISIEHAEDLYDSIIT-KPVVPQYVADWYEEHKDEF 49 Query: 61 ECDL------YLYHMSIY--DEEVEKDDFYYWMQTSKNPVYTLINMHQFGYTIQKEKLYT 112- +L + H++ Y +E DF W +KN + L+NMHQFGY ++KEK YT Sbjct: 50 YLNLHRVVRDFFEHLNAYYFNENPIDYDFACWYYNTKNAIQILVNMHQFGYEVKKEKRYT 109- Query: 113 VEIPN--PNERQLSFVLMRQLSGNVSIKVMHRDNLDLLKTDNDLQLTESEIRKDFDWAWQ 17- 0 V I N E L++ R+ + RDN D +T + T E+ ++ + W Sbjct: 110 VRIRNLDDEETYLNYDKFRE-----TWVFYSRDNTDRFRTIH----THKEL-EEGGFGWV 15- 9 Query: 171 FREEVVE 177 F E +E Sbjct: 160 FDCEGIE 166 A related GBS nucleic acid sequence <SEQ ID 10927> which encodes amino acid sequence <SEQ ID 10928> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 1467> which encodes the amino acid sequence <SEQ ID 1468>. Analysis of this protein sequence reveals the following: TABLE-US-01440 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3815(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01441 Identities = 70/180 (38%), Positives = 98/180 (53%), Gaps = 30/180 (16%) Query: 1 MNIEEAKKLIDKQSI-GKGGVGDIPVVKTHIVKVLLDQIDQPQPEVPRFVADWYEKHKDS 59 MNIEEAK+L+D GK V+K V+ ++DQ++QP+PEVP+ VADW E+ K+ Sbjct: 1 MNIEEAKELVDNSKFYGKTS----SVIKAE-VRDIIDQLNQPKPEVPQCVADWIEECKEE 55 Query: 60 LECDLYLYHMSIYDEEVEKDDFYYWMQTSKNPVYTLINMHQFGYTIQKEKLYTVEIPN-- 117- DL L ++ + W+ S + GYT++KEKLYTV++PN Sbjct: 56 ---DLTL--KGLFSNSDMPAKIFDWIFGSDENCRLMAEAWINGYTVEKEKLYTVDLPNGQ 110- Query: 118 PNERQLSFVLMRQLSGNVSIKVMHRDNLDLLKTDNDLQLTESEIRKDFDWAWQFREEVVE 17- 7 P R ++ + Q L T+N ++LTESEIRKDF+WAWQF EEV E Sbjct: 111 PLVRGINTLYFSQN----------------LATEN-VKLTESEIRKDFEWAWQFAEEVTE 15- 3 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 456 A DNA sequence (GBSx0493) was identified in S. agalactiae <SEQ ID 1469> which encodes the amino acid sequence <SEQ ID 1470>. Analysis of this protein sequence reveals the following: TABLE-US-01442 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5365(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 457 A DNA sequence (GBSx0494) was identified in S. agalactiae <SEQ ID 1471> which encodes the amino acid sequence <SEQ ID 1472>. Analysis of this protein sequence reveals the following:

TABLE-US-01443 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.55 Transmembrane 34-50 (31-54) ----- Final Results ----- bacterial membrane --- Certainty = 0.4418(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9657> which encodes amino acid sequence <SEQ ID 9658> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1473> which encodes the amino acid sequence <SEQ ID 1474>. Analysis of this protein sequence reveals the following: TABLE-US-01444 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.25 Transmembrane 26-42 (20-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.5501(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below: TABLE-US-01445 Identities = 56/89 (62%), Positives = 71/89 (78%) Query: 8 MTEQQMIDCLLYELAKKDKLNIRRNNIITFLSIVLMAISILNVALQDHYKSQITELRTQL 67 MTE+QMIDCLLYEL KKDK +++ II L+++L+ +S L V+L+ +Y+ QI LRTQL Sbjct: 1 MTEEQMIDCLLYELVKKDKAIKKKSIIIAALTVMLIVVSGLCVSLKSYYEPQIYGLRTQL 60 Query: 68 SRTQKQLKRASDDRARQTKRIAELTGNGG 96 SRTQKQLKRAS+ RQTKRIA+LT NGG Sbjct: 61 SRTQKQLKRASEQNQRQTKRIADLTNNGG 89 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 458 A DNA sequence (GBSx0495) was identified in S. agalactiae <SEQ ID 1475> which encodes the amino acid sequence <SEQ ID 1476>. Analysis of this protein sequence reveals the following: TABLE-US-01446 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2040(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 459 A DNA sequence (GBSx0496) was identified in S. agalactiae <SEQ ID 1477> which encodes the amino acid sequence <SEQ ID 1478>. Analysis of this protein sequence reveals the following: TABLE-US-01447 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3044(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01448 >GP: AAD37108 GB: AF109874 unknown [Bacteriophage Tuc2009] Identities = 50/143 (34%), Positives = 67/143 (45%), Gaps = 29/143 (20%) Query: 1 MIPNFRAFNKETKKM-YG-VDGFELSVRKIYRCSLADDEFRCGRLETFHFVEDNFDDYIL 58- MIP RA++K+ ++M YG V+ F+ S+ YR HF +D Sbjct: 1 MIPKLRAWDKQDERMSYGEVEYFDDSIN--YRFD--------------HFCTGADEDVEF 44- Query: 59 MQSTGMFDKNGVEIFDGDIVLTTRL-------IDY-TYKNFKGVVKMLEGRWLIDTGKDA 11- 0 MQSTG+ DKNGVEI++GDI+ + I Y Y G + EG L + Sbjct: 45 MQSTGIKDKNGVEIYEGDILKLHAIFLAPDDKIGYLEYSPKYGYSIICEGNRLY---RQE 10- 1 Query: 111 VGLWTEVDENEAIGNIYQNSELL 133 T E IGHIY+N ELL Sbjct: 102 YWASTNKLNYEVIGNIYENPELL 124 A related DNA sequence was identified in S. pyogenes <SEQ ID 1479> which encodes the amino acid sequence <SEQ ID 1480>. Analysis of this protein sequence reveals the following: TABLE-US-01449 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4779(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01450 Identities = 44/52 (84%), Positives = 47/52 (89%) Query: 1 MIPNFRAFNKETKKMYGVDGFELSVRKIYRCSLADDEFRCGRLETFHFVEDN 52 MIPNFR FNK+TKKMY +DGF+ S RKIYRCSLADDEFR GRLETFHFVEDN Sbjct: 1 MIPNFRGFNKKTKKMYSIDGFKSSERKIYRCSLADDEFRSGRLETFHFVEDN 52 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 460 A DNA sequence (GBSx0497) was identified in S. agalactiae <SEQ ID 1481> which encodes the amino acid sequence <SEQ ID 1482>. Analysis of this protein sequence reveals the following: TABLE-US-01451 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3843(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9655> which encodes amino acid sequence <SEQ ID 9656> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 461 A DNA sequence (GBSx0498) was identified in S. agalactiae <SEQ ID 1483> which encodes the amino acid sequence <SEQ ID 1484>. Analysis of this protein sequence reveals the following: TABLE-US-01452 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5189(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9653> which encodes amino acid sequence <SEQ ID 9654> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01453 >GP: AAF43503 GB: AF145054 ORF10 [Streptococcus thermophilus bacteriophage 7201] Identities = 92/147 (62%), Positives = 121/147 (81%) Query: 15 IEPKPQTRPKFSKFGTYEDPKMKRWRKEVSGWIEKNYDGPFFDDCIKVEVTFYMKAPKTL 74 - IEPKPQTRP+FSKFGTYEDPKMK WR+E S IE+ YDG FF I V+VTFYMKAP ++ Sbjct: 7 IEPKPQTRPRFSKFGTYEDPKMKAWRRECSRLIEQEYDGQFFYGPISVDVTFYMKAPLSV 66 Query: 75 SKEPTQRSKGKTIQIYQNFVRELIWHAKKPDIDNLIKAVFDSISDAGYDRIQKSGIVWSD 134- SK+PT +++ KT ++ F+ E +WH++KPDIDNLIKA+FDSIS AGY+++ K GIVW+D Sbjct: 67 SKKPTPKARAKTWDAFKKFMAERLWHSRKPDIDNLIKALFDSISTAGYNKVDKKGIVWTD 126- Query: 135 DNIVCDLRAKKKYSQNPRIKVRIEEID 161 D+IVC L A+K+YS+NPRI+ I+E++ Sbjct: 127 DSIVCKLSAQKRYSENPRIEFEIKELE 153 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 462 A DNA sequence (GBSx0499) was identified in S. agalactiae <SEQ ID 1485> which encodes the amino acid sequence <SEQ ID 1486>. Analysis of this protein sequence reveals the following: TABLE-US-01454 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4007(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 463 A DNA sequence (GBSx0500) was identified in S. agalactiae <SEQ ID 1487> which encodes the amino acid sequence <SEQ ID 1488>. This protein is predicted to be pXO1-07. Analysis of this protein sequence reveals the following: TABLE-US-01455 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3664(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01456 >GP: AAC38715 GB: AF030367 maturase-related protein [Streptococcus pneumoniae] Identities = 146/373 (39%), Positives = 216/373 (57%), Gaps = 18/373 (4%) Query: 35 LYDKVYRKDILKVAWFYVKRNKGSAGIDDFTIEEIEAYGVQKFLDEIEDQLRNKKYQPKA 94 - L DK+ ++ + A+ VK NKGSAGID TIEE++ Y Q + ++ ++ +KY+P+ Sbjct: 4 LLDKILSRENMLEAYNQVKSNKGSAGIDGMTIEEMDNYLRQNWR-LTKELIKQRKYKPQP 62 Query: 95 VKRVYIPKANGKKRPLGIPTVRDRVVQTAVKIVIEPIFEADFQEFSYGFRPKRSANQAIR 154- V +V IPK +G R LGIPTV DR++Q A+ V+ PI E F + SYGFRP RS +AI Sbjct: 63 VLKVEIPKPDGGIRQLGIPTVMDRMIQQAIVQVMSPICEPHFSDTSYGFRPNRSCEKAIM 122- Query: 155 EIYKYLNYGCEWVIDADLKGYFDTIPHDKLLLLVKERVTDKSIIKLLSLWLEAGIMEDNQ 21- 4 ++ +YLN G EW++D DL+ +FDT+P D+L+ LV + D L+ +L +G++ + Q Sbjct: 123 KLLEYLNDGYEWIVDIDLEKFFDTVPQDRLMSLVHNIIEDGDTESLIRKYLHSGVIINGQ 18- 2 Query: 215 VRSNILGTPQGGVISPLLANIYLNALDRYWKNNRLEGRGHDAHLIRYADDFVI-LCSNNP 27- 3 ++GTPQGG +SPLL+NI LN LD+ LE RG +RYADD VI + S Sbjct: 183 RYKTLVGTPQGGNLSPLLSNIMLNELDK-----ELEKRG--LRFVRYADDCVITVGSEAA 23- 5 Query: 274 KKYYQYAKQRI--DKLGLTLNEEKTRIVHATEGFDFLGYTLRKSKSHKSGKYKTYYYPSR 33- 1 K Y+ R +LGL +N KT+I E +LG+ KS + P + Sbjct: 236 AKRVMYSVSRFIEKRLGLKVNMTKTKITRPRE-LKYLGFGFWKSSDGWKSR------PHQ 28- 8 Query: 332 KSMKSIKGKVKDVIQTGQHLNLPDVMERLNPMLRGWANYFKAGNSKQHFKSIDNYVIYNL 39- 1 S++ K K+K + Q ++L +E+LN +RGW NYF GN K SID + L Sbjct: 289 DSVRRFKLKLKKLTQRKWSIDLTRRIEQLNLSIRGWINYFSLGNMKSIVASIDERLRTRL 34- 8 Query: 392 TIMLRKKHKKSGK 404 +++ K+ KK + Sbjct: 349 RMIIWKQWKKKSR 361 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 464 A DNA sequence (GBSx0501) was identified in S. agalactiae <SEQ ID 1489> which encodes the amino acid sequence <SEQ ID 1490>. Analysis of this protein sequence reveals the following: TABLE-US-01457 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3833(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9651> which encodes amino acid sequence <SEQ ID 9652> was also identified. A further related DNA sequence (GBSx2517) was identified in S. agalactiae <SEQ ID 7217> which encodes the amino acid sequence <SEQ ID 7218>. Analysis of this protein sequence reveals the following: TABLE-US-01458 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3833(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 1491> which encodes the amino acid sequence <SEQ ID 1492>. Analysis of this protein sequence reveals the following: TABLE-US-01459 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2299(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) <succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01460 Identities = 113/163 (69%), Positives = 128/163 (78%), Gaps = 25/163 (15%) Query: 1 MINNIVLVGRMTKDAELRYTPSNQAVATFSLAVNRNFKNQSGEREADFINCVIWRQQAEN 60 MINN+VLVGRMTKDAELRYTPS AVATF+LAVNR FK+Q+GEREADFINCVIWRQ AEN Sbjct: 1 MINNVVLVGRMTKDAELRYTPSQVAVATFTLAVNRTFKSQNGEREADFINCVIWRQPAEN 60 Query: 61 LANWAKKGALVGITGRIQTRNYENQQGQRIYVTEVVAENFQLLESRNSQQ---------Q 11- 1 LANWAKKGAL+G+TGRIQTRNYENQQGQR+YVTEVVA+NFQ+LESR +++ Sbjct: 61 LANWAKKGALIGVTGRIQTRNYENQQGQRVYVTEVVADNFQMLESRATREGGSTGSFNGG 12- 0 Query: 112 TNQSGNSSNSY----------------FGNANKMDISDDDLPF 138 N + +SSNSY FGN+N MDISDDDLPF Sbjct: 121 FNNNTSSSNSYSAPAQQTPNFGRDDSPFGNSNPMDISDDDLPF 163 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 465 A DNA sequence (GBSx0502) was identified in S. agalactiae <SEQ ID 1493> which encodes the amino acid sequence <SEQ ID 1494>. Analysis of this protein sequence reveals the following: TABLE-US-01461 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.33 Transmembrane 17-33 ( 17-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.1532(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 466 A DNA sequence (GBSx0503) was identified in S. agalactiae <SEQ ID 1495> which encodes the amino acid sequence <SEQ ID 1496>. This protein is predicted to be p22 erf-like protein. Analysis of this protein sequence reveals the following: TABLE-US-01462 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2469(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01463 >GP: BAA97824 GB: AB044554 orf 17 [Staphylococcus aureus prophage phiPV83] Identities = 93/183 (50%), Positives = 120/183 (64%), Gaps = 5/183 (2%) Query: 1 MRKSESITEYAKAFCKAQLEVKQPLKDKDNPFFKSKYVPLENVTEAITTAFANNGISFSQ 60 M KSE++ E KA + EVKQPLKDK+NPFFKSKYVPLENV EAI A +G+S++Q Sbjct: 1 MNKSETVVEINKAMVAFRKEVKQPLKDKNNPFFKSKYVPLENVVEAIDEAATPHGLSYTQ 60 Query: 61 DPTTNTENGYIDVATLVMHTSGEWVEYGPLSVKPTKNDVQGAGSAITYAKRYALSAIFGI 120- N +G + VAT++MH SGE++EY P+ + KN QGAGS I+Y KRY+LSAIFGI Sbjct: 61 W-ALNDVDGRVGVATMLMHESGEYIEYDPVFMNAEKNTPQGAGSLISYLKRYSLSAIFGI 119- Query: 121 TSDQDDDGNEDSKPNNSRQSPKATTKKTQKTGYQTPKISNIQIETYKSDLNDIAKATNQN 18- 0 TSDQDDDGNE S NN +PK T +TQ +T I ++ ++ + K QN Sbjct: 120 TSDQDDDGNEASGKNN---NPKQQT-RTQWASSETIGILRKEVISFTKLIKGTDKEAPQN 17- 5 Query: 181 VEE 183 + E Sbjct: 176 IVE 178 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 467 A DNA sequence (GBSx0504) was identified in S. agalactiae <SEQ ID 1497> which encodes the amino acid sequence <SEQ ID 1498>. This protein is predicted to be gp157. Analysis of this protein sequence reveals the following: TABLE-US-01464 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3148(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01465 >GP: AAD44102 GB: AF115103 orf157 gp [Streptococcus thermophilus] bacteriophage Sfi21] Identities = 59/160 (36%), Positives = 100/160 (61%), Gaps = 3/160 (1%) Query: 1 MAYLYELEGIYAQLQSMDLDEETFQDTLDSIDFQSDLENNIEYFVKMLKNVQADAEKYKA 60 MA LYEL G + ++ +M++D+ET DTL++ID+ SD EN +E +VK++K+++AD E K Sbjct: 1 MATLYELTGQFLEIYNMEIDDETKLDTLEAIDWTSDYENKVEGYVKVIKSLEADIEARKN 60 Query: 61 EKEAFYKKQKQAEAKAEKYKETIRLAMELSQKKKVDAGMFKVSLRRSKKVEILDETKIPL 120- EK+ K ++K +K K + ++M + + +VD +FK+ +SK V +++E K+P Sbjct: 61 EKKRLDGLNKSDQSKIDKLKAALAISMTETGQTRVDTTLFKIGFHKSKAV-VVNEEKLPK 119- Query: 121 DYMQEKIEYKPMKAEISKALKSGIDISGVELIETESLQVK 160 +Y + YKP K + + LKSG I G L E +L ++ Sbjct: 120 EY--QIATYKPDKKTLKELLKSGKHIEGATLEERRNLNIR 157 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 468 A DNA sequence (GBSx0505) was identified in S. agalactiae <SEQ ID 1499> which encodes the amino acid sequence <SEQ ID 1500>. This protein is predicted to be tropomyosin 2. Analysis of this protein sequence reveals the following: TABLE-US-01466 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4474(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 469 A DNA sequence (GBSx0506) was identified in S. agalactiae <SEQ ID 1501> which encodes the amino acid sequence <SEQ ID 1502>. Analysis of this protein sequence reveals the following:

TABLE-US-01467 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4114(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9649> which encodes amino acid sequence <SEQ ID 9650> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 470 A DNA sequence (GBSx0507) was identified in S. agalactiae <SEQ ID 1503> which encodes the amino acid sequence <SEQ ID 1504>. Analysis of this protein sequence reveals the following: TABLE-US-01468 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3799(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1505> which encodes the amino acid sequence <SEQ ID 1506>. Analysis of this protein sequence reveals the following: TABLE-US-01469 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3775(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01470 Identities = 43/46 (93%), Positives = 46/46 (99%) Query: 1 MTKQHRETLIWYRASHQEREKLLDFGLVDKSQYVTLLRQLRKKYAI 46 MTKQHRETLIWYRASHQERE+LLDFGLVDK++YVTLLRQLRKKYAI Sbjct: 1 MTKQHRETLIWYRASHQERERLLDFGLVDKARYVTLLRQLRKKYAI 46 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 471 A DNA sequence (GBSx0508) was identified in S. agalactiae <SEQ ID 1507> which encodes the amino acid sequence <SEQ ID 1508>. Analysis of this protein sequence reveals the following: TABLE-US-01471 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4308(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1509> which encodes the amino acid sequence <SEQ ID 1510>. Analysis of this protein sequence reveals the following: TABLE-US-01472 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4308(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01473 Identities = 76/77 (98%), Positives = 76/77 (98%) Query: 1 MDQEIFNFFNKQIKKDFGKTASKETFAKFASYCAEGIEKNGVKPIFNWINLYAFGTGMTT 60 MDQEIFNFFNKQIKKDFGKTASKETFAKFASYCAEGIEKNGVKPIFNWINLYAFGTGMTT Sbjct: 1 MDQEIFNFFNKQIKKDFGKTASKETFAKFASYCAEGIEKNGVKPIFNWINLYAFGTGMTT 60 Query: 61 AEADRLRIERYKQENTL 77 AEADRLRIERYKQEN L Sbjct: 61 AEADRLRIERYKQENAL 77 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 472 A DNA sequence (GBSx0509) was identified in S. agalactiae <SEQ ID 1511> which encodes the amino acid sequence <SEQ ID 1512>. Analysis of this protein sequence reveals the following: TABLE-US-01474 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2706(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 1513> which encodes the amino acid sequence <SEQ ID 1514>. Analysis of this protein sequence reveals the following: TABLE-US-01475 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3316(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01476 Identities = 52/127 (40%), Positives = 75/127 (58%), Gaps = 1/127 (0%) Query: 160 EDRFVDVVEANLGRGLVKFEFDMINDYLIGQNVSKDLFLEAVKVAVANNVRKFNYIARIL 21- 9 E + + + GR + FE + I ++ N+ ++ A++ AV NN + YI +IL Sbjct: 3 EKKLFENFQLTFGRMISPFEIEDIQKWIHEDNMPIEVVNLALREAVENNKISWKYINKIL 62 Query: 220 DNWINDGIKTPEQAYQAQRDFKAKKANKTMQSQSNVPSWSNPDYKGPDLKEFALGSIDDI 27- 9 +W G T E+ + F K +++ + SNVPSWSNPDYK PDL+EFALGS+D I Sbjct: 63 VDWYKSGDTTVEKVRDRLQRFDDSKKQRSVTT-SNVPSWSNPDYKEPDLEEFALGSMDGI 121- Query: 280 EDGSGDF 286 EDGSGDF Sbjct: 122 EDGSGDF 128 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 473 A DNA sequence (GBSx0510) was identified in S. agalactiae <SEQ ID 1515> which encodes the amino acid sequence <SEQ ID 1516>. Analysis of this protein sequence reveals the following: TABLE-US-01477 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.63 Transmembrane 13-29 (11-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.3251(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9647> which encodes amino acid sequence <SEQ ID 9648> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 474 A DNA sequence (GBSx0511) was identified in S. agalactiae <SEQ ID 1517> which encodes the amino acid sequence <SEQ ID 1518>. Analysis of this protein sequence reveals the following: TABLE-US-01478 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5822(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 475 A DNA sequence (GBSx0512) was identified in S. agalactiae <SEQ ID 1519> which encodes the amino acid sequence <SEQ ID 1520>. Analysis of this protein sequence reveals the following: TABLE-US-01479 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4175(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 476 A DNA sequence (GBSx0513) was identified in S. agalactiae <SEQ ID 1521> which encodes the amino acid sequence <SEQ ID 1522>. This protein is predicted to be P1-antirepressor homolog. Analysis of this protein sequence reveals the following: TABLE-US-01480 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3411(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9645> which encodes amino acid sequence <SEQ ID 9646> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01481 >GP: AAG31333 GB: AF182207 ORF 169a [Bacteriophage mv4] Identities = 88/167 (52%), Positives = 122/167 (72%) Query: 100 MLQRNEKSKQVRKYFIQVEKDFNSPEKIMARALLMADKKITNLTMENNQLQLDLKEAQKQ 15- 9 M+ + K K++R+YFIQVEK++NSPE I+ RAL +++ +I L +N L L L+E+ K+ Sbjct: 1 MMSKTAKGKEIRQYFIQVEKNWNSPEMIIQRALEISNARIQELQAQNKSLTLQLEESNKK 60- Query: 160 ARYLDLIIESKGALRVTQIAADYGMSVNKFNKTLLEFGVQHKVNGQWILYKRHMGKGYTD 21- 9 A YLD+I+ + L TQIAADYG S FN+ L E G+QHKVNGQWILYK +MGKGY Sbjct: 61 ASYLDIILGTPDLLATTQIAADYGYSARTFNQLLKEVGIQHKVNGQWILYKAYMGKGYVQ 12- 0 Query: 220 SHTFDYQDKNGHTRANVTTTWTQKGRLFLYELLKDNNILPLIEQEDI 266 S +F ++D+ GH R+ +T WTQKGR +Y++LK+N LPLIE++DI Sbjct: 121 SKSFAFKDRKGHDRSKPSTYWTQKGRKLIYDVLKENGTLPLIERDDI 167 A related DNA sequence was identified in S. pyogenes <SEQ ID 1523> which encodes the amino acid sequence <SEQ ID 1524>. Analysis of this protein sequence reveals the following: TABLE-US-01482 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4214(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01483 Identities = 130/249 (52%), Positives = 163/249 (65%), Gaps = 14/249 (5%) Query: 19 MNQLINITLNENQEPVVSGRDLHNVLNIKTQYTKWLERMSEYGFEENVDYIAISQKRLTA 78- MNQLIN+TLNENQEPVVSGRDLH VL IKTQYTKWLERMSEYGF EN D++AISQKRLTA Sbjct: 1 MNQLINVTLNENQEPVVSGRDLHKVLEIKTQYTKWLERMSEYGFVENEDFMAISQKRLTA 60- Query: 79 QGNRTEYIDHVLKLDMAKEIAMLQRNEKSKQVRKYFIQVEKDFNSPEKIMARALLMADKK 13- 8 QGN+TEY DHVLKLDMAKEIAMLQRNEKSK+VRKYFIQVEKDFNSPEKIMARALLMADKK Sbjct: 61 QGNQTEYTDHVLKLDMAKEIAMLQRNEKSKEVRKYFIQVEKDFNSPEKIMARALLMADKK 12- 0 Query: 139 ITNLTMENNQLQLDLKEAQKQARYLDLIIESKGALRVTQIAA-----DYGMSVNKFNKTL 19- 3 + ++L+ ++ + + + D + S ++ V ++A + + L Sbjct: 121 V-------HKLEAQIEADRPKVLFADAVSASHTSILVGELAKLLKQNGVNIGATRLFTWL 17- 3 Query: 194 LEFGVQHKVNGQ-WIL-YKRHMGKGYTDSHTFDYQDKNGHTRANVTTTWTQKGRLFLYEL 25- 1 + G K NG+ W + ++ + G +GH + T T KG+ + Sbjct: 174 RKHGYLIKRNGRDWNMPTQKSVELGLIRVKETSITHSDGHITVSKTPLVTGKGQQYFINK 23- 3 Query: 252 LKDNNILPL 260 + LP+ Sbjct: 234 FLNQEYLPV 242 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 477 A DNA sequence (GBSx0514) was identified in S. agalactiae <SEQ ID 1525> which encodes the amino acid sequence <SEQ ID 1526>. Analysis of this protein sequence reveals the following: TABLE-US-01484 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4205(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1527> which encodes the amino acid sequence <SEQ ID 1528>. Analysis of this protein sequence reveals the following: TABLE-US-01485 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial Cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01486 Identities = 21/63 (33%), Positives = 31/63 (48%), Gaps = 1/63 (1%) Query: 1 MQQFNLKQLREKKGFTQNELADKANVSRSLVVGLETGSYSETSTASLKKLAKALDVKIKD 60 M+ LK R K +Q LAD VSR + +E G Y+ T + + + LD + D Sbjct: 1 MKNLKLKAARAGKDLSQQALADLVGVSRQTIAAVEKGDYNPTINLCI-AICRVLDKTLDD 59 Query: 61 LFF 63 LF+ Sbjct: 60 LFW 62 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 478 A DNA sequence (GBSx0515) was identified in S. agalactiae <SEQ ID 1529> which encodes the amino acid sequence <SEQ ID 1530>. Analysis of this protein sequence reveals the following: TABLE-US-01487 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0396(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01488 >GP: BAA17582 GB: D90907 hypothetical protein [Synechocystis sp.] Identities = 45/164 (27%), Positives = 79/164 (47%), Gaps = 33/164 (20%) Query: 102 EEEELRNLFTKLIASSMDKSKNEFNHPSFIEIIKQFDKIDAQNFKIISDLYFKKGFVATG 16- 1 ++E L+ L+ L+AS++ +S + SF+E++KQ D +DA+ ++ L+ + Sbjct: 97 DDENLQTLWANLLASALTESDRTNSTKSFVEVLKQVDIVDAELLNVLYLLHLRV------ 150- Query: 162 TYYTTIIGQDKPLEHIASHVFVDNLEQNDIAIQSSSLTNLERLGLIQINY--KAHVDEKE 21- 9 KP E ++ D+ + N + I S +L NLERLGL+ I+ VDE+ Sbjct: 151 --------MAKPDEFTYAN---DSRKYNIVQI-SVALNNLERLGLLIIHKYDDTPVDEEA 19- 8 Query: 220 YYNILNNSFITKKNSELKEQNKRVLTNLGMITLTLFGVRFSKTC 263 +I ++ N K ++LTLFG+ F + C Sbjct: 199 RISIW---YMQDGNRSFKAH----------VSLTLFGIHFMRVC 229 A related DNA sequence was identified in S. pyogenes <SEQ ID 1531> which encodes the amino acid sequence <SEQ ID 1532>. Analysis of this protein sequence reveals the following: TABLE-US-01489 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0151(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01490 Identities = 64/215 (29%), Positives = 105/215 (48%), Gaps = 23/215 (10%) Query: 65 QKLAKEIQDVVSKNIE-NLQEPSLSIAGPALEASKFYLEEEELRNLFTKLIASSMDKSKN 123- +K EI SK + +L+EP I PA+ S+ YL E LRN+F + IAS+ ++ K Sbjct: 72 EKFKNEIDCEFSKIPQTSLKEPVEYILYPAINESEQYLSNETLRNMFARTIASTFNQDKE 131- Query: 124 EFNHPSFIEIIKQFDKIDAQNFKIISDLYFKKGFVATGTYYTTIIGQDKPLEHI------ 17- 7 + H +F++IIKQ +DAQN +I+ IG E++ Sbjct: 132 KDLHSAFVQIIKQMTPLDAQNLLLINQ-------EGNNLIANLQIGVHYSKENLSGTVNK 18- 4 Query: 178 ASHVFVDNLEQNDIAIQSSSLTNLERLGLIQINYKAHVDEKEYYNILNNSFITKKNSELK 23- 7 A+++++ L+ + I +SS+ NL RLGLI+++Y + + Y +I + SE+ Sbjct: 185 ANNIYLSKLDYSPDII-ASSIDNLTRLGLIKVDYLHYPLDSNYESIKQTTIYKSLESEIN 24- 3 Query: 238 EQNKRVLTNL--------GMITLTLFGVRFSKTCL 264 N +N G ++LT FG +F CL Sbjct: 244 TLNLFKTSNTKYDIKIEKGKVSLTDFGKKFISVCL 278 SEQ ID 1530 (GBS261) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 44 (lane 8; MW 31 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 479 A DNA sequence (GBSx0516) was identified in S. agalactiae <SEQ ID 1533> which encodes the amino acid sequence <SEQ ID 1534>. Analysis of this protein sequence reveals the following: TABLE-US-01491 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.55 Transmembrane 3-19 (1-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.4418(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 480 A DNA sequence (GBSx0517) was identified in S. agalactiae <SEQ ID 1535> which encodes the amino acid sequence <SEQ ID 1536>. Analysis of this protein sequence reveals the following:

TABLE-US-01492 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.99 Transmembrane 35-51 (30-51) ----- Final Results ----- bacterial membrane --- Certainty = 0.2996(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1537> which encodes the amino acid sequence <SEQ ID 1538>. Analysis of this protein sequence reveals the following: TABLE-US-01493 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.94 Transmembrane 31-47 (30-51) ----- Final Results ----- bacterial membrane --- Certainty = 0.2975(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01494 Identities = 45/52 (86%), Positives = 48/52 (91%) Query: 1 MNWKKLMLGDLEHTFTSRDGKEKTSVEFEGGVLPALLVLGGITWLIAWLITK 52 MNWKKLM GDLEHTFT+ DGKEKTS+EFEGGVLPALLVLGGI W+IAW ITK Sbjct: 1 MNWKKLMFGDLEHTFTNHDGKEKTSIEFEGGVLPALLVLGGIAWMIAWFITK 52 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 481 A DNA sequence (GBSx0518) was identified in S. agalactiae <SEQ ID 1539> which encodes the amino acid sequence <SEQ ID 1540>. Analysis of this protein sequence reveals the following: TABLE-US-01495 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3445(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 482 A DNA sequence (GBSx0519) was identified in S. agalactiae <SEQ ID 1541> which encodes the amino acid sequence <SEQ ID 1542>. Analysis of this protein sequence reveals the following: TABLE-US-01496 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3934(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 483 A DNA sequence (GBSx0520) was identified in S. agalactiae <SEQ ID 1543> which encodes the amino acid sequence <SEQ ID 1544>. This protein is predicted to be repressor protein. Analysis of this protein sequence reveals the following: TABLE-US-01497 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0905(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9643> which encodes amino acid sequence <SEQ ID 9644> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 1545> which encodes the amino acid sequence <SEQ ID 1546>. Analysis of this protein sequence reveals the following: TABLE-US-01498 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3117(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01499 Identities = 175/264 (66%), Positives = 207/264 (78%), Gaps = 19/264 (7%) Query: 34 LGKYIKKYRDTNNLSMAEFAKESGISKAY--VSILEKNRDPRNGKEIIPSIPIIKKVSDT 91 - LG I+K R+ N++ E ++ G+ K Y VS EKN + GK++ KK+++ Sbjct: 24 LGDRIRKLREGRNMTQTELSEILGM-KTYTTVSKWEKNENFPKGKDL-------KKLAEI 75 Query: 92 IGISFDDLLNSLDENQIVALNETKTEKNLTSSTLQKITSTSSQLEQPRQEKVLSFANEQL 151- ++ D LL L ++K K + +I S +QLEQPRQEKVL+FANEQL Sbjct: 76 FNVTSDYLLG---------LTDSKLGKITIQNEQPEIVSIYNQLEQPRQEKVLNFANEQL 126- Query: 152 EEQNKVVSMFDRKVEETENYITDYVEGLVAAGLGAYQEDNLHMEVKLRADDVPDKYDTIA 21- 1 EEQNK VS+FD+K EETE+YITDYVEGLVAAGLGAYQEDNLHM+VKLR+DDVPD+YDTIA Sbjct: 127 EEQNKTVSIFDKKSEETEDYITDYVEGLVAAGLGAYQEDNLHMKVKLRSDDVPDEYDTIA 18- 6 Query: 212 KVAGNSMEPLIQDNDLLFVKVSSQVDMNDIGIFQVNGKNFVKKLKRDYDGAWYLQSLNKS 27- 1 KVAG+SMEPLIQDNDLLF+KVSSQVDMNDIGIFQVNGKNFVKKLKRDYDGAWYLQSLNKS Sbjct: 187 KVAGDSMEPLIQDNDLLFIKVSSQVDMNDIGIFQVNGKNFVKKLKRDYDGAWYLQSLNKS 24- 6 Query: 272 YEEIYLSENDNIRTIGEVVDIYRE 295 YEEIYLS++D+IRTIGEVVDIYRE Sbjct: 247 YEEIYLSKDDDIRTIGEVVDIYRE 270 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 484 A DNA sequence (GBSx0521) was identified in S. agalactiae <SEQ ID 1547> which encodes the amino acid-sequence <SEQ ID 1548>. Analysis of this protein sequence reveals the following: TABLE-US-01500 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3760(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 485 A DNA sequence (GBSx0522) was identified in S. agalactiae <SEQ ID 1549> which encodes the amino acid sequence <SEQ ID 1550>. This protein is predicted to be integrase (ripX). Analysis of this protein sequence reveals the following: TABLE-US-01501 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2719(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01502 >GP: CAB96616 GB: AJ400629 integrase [Streptococcus pneumoniae bacteriophage MM1] Identities = 36/59 (61%), Positives = 48/59 (81%), Gaps = 1/59 (1%) Query: 2 KIYGDYHTHLFRHSHISFLAEKGIPLNAIMDRVGHSDPKTTLSIYSHTTVNMKE-IINK 59 KI + +H+FRHSHISFLAE G+P+ +IMDRVGHS+ K TL IYSHTT +M++ ++NK Sbjct: 312 KIEKNLSSHIFRHSHISFLAESGLPIKSIMDRVGHSNAKMTLEIYSHTTEDMEDKLVNK 370- A related DNA sequence was identified in S. pyogenes <SEQ ID 1551> which encodes the amino acid sequence <SEQ ID 1552>. Analysis of this protein sequence reveals the following: TABLE-US-01503 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2719(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01504 Identities = 63/71 (88%), Positives = 66/71 (92%) Query: 1 MKIYGDYHTHLFRHSHISFLAEKGIPLNAIMDRVGHSDPKTTLSIYSHTTVNMKEIINKQ 60 +KIYGDYHTHLFRHSHISFLAEKGIPLNAIMDRVGHSDPKTTLSIYSHTTVNMKEIINKQ Sbjct: 1 LKIYGDYHTHLFRHSHISFLAEKGIPLNAIMDRVGHSDPKTTLSIYSHTTVNMKEIINKQ 60 Query: 61 TAPFVPLLKSE 71 T PF +K + Sbjct: 61 TDPFKTGIKQK 71 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 486 A DNA sequence (GBSx0523) was identified in S. agalactiae <SEQ ID 1553> which encodes the amino acid sequence <SEQ ID 1554>. This protein is predicted to be 50S ribosomal protein L19 (rplS). Analysis of this protein sequence reveals the following: TABLE-US-01505 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3331(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9641> which encodes amino acid sequence <SEQ ID 9642> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01506 >GP: AAC01534 GB: U88973 ribosomal protein L19 [Streptococcus thermophilus] Identities = 110/115 (95%), Positives = 112/115 (96%) Query: 25 MNPLIQSLTEGQLRSDIPEFRAGDTVRVHAKVVEGTRERIQIFEGVVISRKGQGISEMYT 84 - MNPLIQSLTEGQLR+DIP FR GDTVRVHAKVVEGTRERIQIFEGVVISRKGQGISEMYT Sbjct: 1 MNPLIQSLTEGQLRTDIPSFRPGDTVRVHAKVVEGTRERIQIFEGVVISRKGQGISEMYT 60 Query: 85 VRKISGGIGVERTFPIHTPRVDKIEVVRYGKVRRAKLYYLRALQGKAARIKEIRR 139 VRKIS GIGVERTFPIHTPRVDKIEVVRYGKVRRAKLYYLRALQGKAARIKEIR+ Sbjct: 61 VRKISSGIGVERTFPIHTPRVDKIEVVRYGKVRRAKLYYLRALQGKAARIKEIRK 115 A related DNA sequence was identified in S. pyogenes <SEQ ID 1555> which encodes the amino acid sequence <SEQ ID 1556>. Analysis of this protein sequence reveals the following: TABLE-US-01507 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4849(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01508 Identities = 111/115 (96%), Positives = 113/115 (97%) Query: 25 MNPLIQSLTEGQLRSDIPEFRAGDTVRVHAKVVEGTRERIQIFEGVVISRKGQGISEMYT 84 - MNPLIQSLTEGQLRSDIP FR GDTVRVHAKVVEGTRERIQIFEGVVISRKGQGISEMYT Sbjct: 1 MNPLIQSLTEGQLRSDIPNFRPGDTVRVHAKVVEGTRERIQIFEGVVISRKGQGISEMYT 60 Query: 85 VRKISGGIGVERTFPIHTPRVDKIEVVRYGKVRRAKLYYLRALQGKAARIKEIRR 139 VRKISGGIGVERTFPIHTPRVDKIEV+R+GKVRRAKLYYLRALQGKAARIKEIRR Sbjct: 61 VRKISGGIGVERTFPIHTPRVDKIEVIRHGKVRRAKLYYLRALQGKAARIKEIRR 115 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 487 A DNA sequence (GBSx0524) was identified in S. agalactiae <SEQ ID 1557> which encodes the amino acid sequence <SEQ ID 1558>. This protein is predicted to be ISL2 protein. Analysis of this protein sequence reveals the following: TABLE-US-01509 Possible site: 58 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01510 >GP: CAC18596 GB: AJ278419 IS1381 transposase [Streptococcus pneumoniae] Identities = 111/129 (86%), Positives = 117/129 (90%) Query: 1 MKAQAIVTSQGRIVSLDIAVNYCHDMKLFKMSRRNIGQAAKILADSGYQGIMKNYSQAQT 60- MK QAIVTSQGRIVSLDI VNYCHDMKLFKMSRRNIGQA KILADSGYQG+MK+Y QAQT Sbjct: 1 MKTQAIVTSQGRIVSLDITVNYCHDMKLFKMSRRNIGQAGKILADSGYQGLMKIYPQAQT 60- Query: 61 PRKSSKLKPLTLEDKTYNHTLSKERIKVENIFAKVKTFKIFSTTYRNRRKRFGLRMNLIA 12- 0 RKSSKLKPLT+EDK NH LSKER KVENIFAKVKTFK+FSTTYR+ RKRFGLRMNL A Sbjct: 61 SRKSSKLKPLTVEDKACNHALSKERSKVENIFAKVKTFKMFSTTYRSHRKRFGLRMNLSA 12- 0 Query: 121 GMINRELGF 129 G+IN ELGF Sbjct: 121 GIINHELGF 129 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 488 A DNA sequence (GBSx0526) was identified in S. agalactiae <SEQ ID 1559> which encodes the amino acid sequence <SEQ ID 1560>. Analysis of this protein sequence reveals the following: TABLE-US-01511 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.99 Transmembrane 81-97 (67-107) INTEGRAL Likelihood = -6.32 Transmembrane 8-24 (6-25) INTEGRAL Likelihood = -2.76 Transmembrane 120-136 (120-136) ----- Final Results ----- bacterial membrane --- Certainty = 0.5394(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01512 >GP: BAB04382 GB: AP001509 unknown conserved protein in others [Bacillus halodurans] Identities = 53/150 (35%), Positives = 82/150 (54%), Gaps = 1/150 (0%) Query: 1 MLNPYKRIFTLGLLATFLLFIFHFGRYSGLGTNLIEASFTNKNLYDYDWLLKLCLTVITL 60- M N R F GL+ L +I Y+G G +++E SFT +++ Y +L KL T +T+ Sbjct: 251 MKNHTVRAFVGGLIIVALTYIIGSYDYNGRGLDMLEDSFT-QDVPPYAFLAKLVFTAVTM 30- 9 Query: 61 AAGYQGGEVTPLFAIGASLGVIIAPILGLPVILVAALGYTSVFGSATNTLLGPILIGGEV 12- 0 G+ GGE PLF +GA+LG + + LP+ +AALG FG NT + L+G E+ Sbjct: 310 GMGFVGGEAIPLFFVGATLGNTLHAFIDLPLSFLAALGMIVTFGGGANTPIAAFLLGVEM 36- 9 Query: 121 FGFANTPYFVIVCLVAYSISHAHTIYGAQS 150 F +F + CL +Y S H ++ +Q+ Sbjct: 370 FNGKGIEFFFVACLTSYLFSGHHGLNPSQT 399 A related DNA sequence was identified in S. pyogenes <SEQ ID 1561> which encodes the amino acid sequence <SEQ ID 1562>. Analysis of this protein sequence reveals the following: TABLE-US-01513 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.99 Transmembrane 56-72 (53-76) INTEGRAL Likelihood = -7.17 Transmembrane 337-353 (327-355) INTEGRAL Likelihood = -6.74 Transmembrane 264-280 (260-282) INTEGRAL Likelihood = -6.16 Transmembrane 167-183 (161-187) INTEGRAL Likelihood = -5.26 Transmembrane 223-239 (217-242) INTEGRAL Likelihood = -5.10 Transmembrane 20-36 (19-42) INTEGRAL Likelihood = -0.37 Transmembrane 102-118 (102-119) INTEGRAL Likelihood = -0.16 Transmembrane 300-316 (300-316) ----- Final Results ----- bacterial membrane --- Certainty = 0.5798(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01514 >GP: BAB04382 GB: AP001509 unknown conserved protein in others [Bacillus halodurans] Identities = 129/397 (32%), Positives = 210/397 (52%), Gaps = 14/397 (3%) Query: 20 VLGLVGLALPIGGAVGVVDVIFGKGLLFLSEYRDHHLFLLLPFLALAGLVIVFLYDKLG- 78- +L + + IG VG + L E R++ + +L FL LAGL + +LY K G Sbjct: 9 LLTWIFFGIMIGAIVGSATALLLTVNDHLGETRENRPWFVL-FLPLAGLALGYLYMKAGT 67- Query: 79 ---KEVRQGMGLVFQVGHGQKNQIPPMLIPLILFSTWVTHLFGASAGREGVAVQIGATIS 13- 5 E+ +G LV + G K ++ L PL+ T++T LFG S GREG A+Q+G +++ Sbjct: 68 SAGNELYKGNNLVIESVQG-KGKMLLRLGPLVYLGTFMTILFGGSTGREGAAIQMGGSVA 12- 6 Query: 136 HYCRR-FVTSQEAARHLLIMGMAAGFAGLFQTPIAAVVFALEVLLVGTLRYSALLPSLVA 19- 4 + F R LL+ G++AGF F TPI A +F +E+ +G L++ AL+P LVA Sbjct: 127 EAVNKLFKVKLIDTRILLMGGISAGFGAAFGTPITAAIFGMEMASLGRLKFEALVPCLVA 18- 6 Query: 195 AYVASWTSHALG-LEKFTIVLEETLTITPLTLVKLIGLGLIFGLVGNSFAYLL-GWFKPY 25- 2 ++V +T+ +E ++ ++ LT K+I L ++F LV + L G K Sbjct: 187 SFVGHYTTEKFWHVEHEKFIIATVPEVSALTFSKVILLAIVFSLVSVLYCQLRHGIHKLS 24- 6 Query: 253 LSQKLPNPYFRIAFIGALLSICL--MIGHVGRYSGLGTNLIAAAFSGQTILTYDWLLKMI 31- 0 + N R AF+G L+ + L +IG Y+G G +++ +F+ Q + Y +L K++ Sbjct: 247 EKYTMKNHTVR-AFVGGLIIVALTYIIGSYD-YNGRGLDMLEDSFT-QDVPPYAFLAKLV 30- 3 Query: 311 VTVISLSAGFQGGEVTPLFAIGASLGIVLAPYLGLPVLLVAALGYTTVFGSATNTFWAPI 37- 0 T +++ GF GGE PLF +GA+LG L ++ LP+ +AALG FG NT A Sbjct: 304 FTAVTMGMGFVGGEAIPLFFVGATLGNTLHAFIDLPLSFLAALGMIVTFGGGANTPIAAF 36- 3 Query: 371 FIGIEVFGPENALAYFVTSAAAYMVSHRHSIYSYQKV 407 +G+E+F + +FV +Y+ S H ++ Q + Sbjct: 364 LLGVEMFNGKGIEFFFVACLTSYLFSGHHGLWPSQTI 400 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01515 Identities = 91/147 (61%), Positives = 111/147 (74%) Query: 3 NPYKRIFTLGLLATFLLFIFHFGRYSGLGTNLIEASFTNKNLYDYDWLLKLCLTVITLAA 62 NPY RI +G L + L I H GRYSGLGTNLI A+F+ + + YDWLLK+ +TVI+L+A Sbjct: 259 NPYFRIAFIGALLSICLMIGHVGRYSGLGTNLIAAAFSGQTILTYDWLLKMIVTVISLSA 31- 8 Query: 63 GYQGGEVTPLFAIGASLGVIIAPILGLPVILVAALGYTSVFGSATNTLLGPILIGGEVFG 122- G+QGGEVTPLFAIGASLG+++AP LGLPV+LVAALGYT+VFGSATNT PI IG EVFG Sbjct: 319 GFQGGEVTPLFAIGASLGIVLAPYLGLPVLLVAALGYTTVFGSATNTFWAPIFIGIEVFG 37- 8 Query: 123 FANTPYFVIVCLVAYSISHAHTIYGAQ 149 N + + AY +SH H+IY Q Sbjct: 379 PENALAYFVTSAAAYMVSHRHSIYSYQ 405 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 489 A DNA sequence (GBSx0527) was identified in S. agalactiae <SEQ ID 1563> which encodes the amino acid sequence <SEQ ID 1564>. Analysis of this protein sequence reveals the following:

TABLE-US-01516 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.65 Transmembrane 47-63 (45-70) INTEGRAL Likelihood = -5.04 Transmembrane 219-235 (208-237) INTEGRAL Likelihood = -3.35 Transmembrane 168-184 (168-187) INTEGRAL Likelihood = -0.48 Transmembrane 141-157 (141-157) ----- Final Results ----- bacterial membrane --- Certainty = 0.4461(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9317> which encodes amino acid sequence <SEQ ID 9318> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01517 >GP: BAB04382 GB: AP001509 unknown conserved protein in others [Bacillus halodurans] Identities = 75/223 (33%), Positives = 119/223 (52%), Gaps = 18/223 (8%) Query: 17 FSLLIGGVVGAITAVFGRVLLFLTAFRSDYIAYLLPFLSIVGLFIVFVYQKFGGKS---- 72 - F ++IG +VG+ TA+ V L R + ++L FL + GL + ++Y K G + Sbjct: 15 FGIMIGAIVGSATALLLTVNDHLGETRENRPWFVL-FLPLAGLALGYLYMKAGTSAGNEL 73 Query: 73 VKGMGLVFEVGHGNEETIPKRLVPLVILTTWLTHLFGGSAGREGVAVQIGATVSHYFQKY 132- KG LV E G + + RL PLV L T++T LFGGS GREG A+Q+G +V+ K Sbjct: 74 YKGNNLVIESVQGKGKML-LRLGPLVYLGTFMTILFGGSTGREGAAIQMGGSVAEAVNKL 132- Query: 133 CRLQNASQLFLVM-GMAAGFAGLFQTPLAATFFAIEVLVVGRLMVSYVLPSLIAALTANF 19- 1 +++ L+M G++AGF F TP+ A F +E+ +GRL ++P L+A+ ++ Sbjct: 133 FKVKLIDTRILLMGGISAGFGAAFGTPITAAIFGMEMASLGRLKFEALVPCLVASFVGHY 19- 2 Query: 192 VSHSLGLEKFSH------SIATSMALTPDIILKLLVLGLCFGL 228 + EKF H IAT ++ K+++L + F L Sbjct: 193 TT-----EKFWHVEHEKFIIATVPEVSALTFSKVILLAIVFSL 230 There is also homology to SEQ ID 1562. A related GBS gene <SEQ ID 8577> and protein <SEQ ID 8578> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01518 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: 9.66 GvH: Signal Score (-7.5): -1.12 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 7 value: -10.99 threshold: 0.0 INTEGRAL Likelihood = -10.99 Transmembrane 328-344 (314-354) INTEGRAL Likelihood = -8.65 Transmembrane 47-63 (45-70) INTEGRAL Likelihood = -6.32 Transmembrane 255-271 (253-272) INTEGRAL Likelihood = -4.41 Transmembrane 214-230 (208-238) INTEGRAL Likelihood = -3.35 Transmembrane 168-184 (168-187) INTEGRAL Likelihood = -2.76 Transmembrane 367-383 (367-383) INTEGRAL Likelihood = -0.48 Transmembrane 141-157 (141-157) PERIPHERAL Likelihood = 0.42 94 modified ALOM score: 2.70 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5394(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00035## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 490 A DNA sequence (GBSx0528) was identified in S. agalactiae <SEQ ID 1565> which encodes the amino acid sequence <SEQ ID 1566>. Analysis of this protein sequence reveals the following: TABLE-US-01519 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3568(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01520 >GP: AAB98234 GB: U67480 chorismate mutase/prephenate dehydratase (pheA) [Methanococcus jannaschii] Identities = 26/85 (30%), Positives = 46/85 (53%), GapS = 1/85 (1%) Query: 2 ELEEIRQEIDEIDQQLVSLLETRMGLILEVIAFKKKHRLPVLDNNRENEVLNNVLKKVQN 61 - +L EIR++IDEID +++ L+ R L +V K + +P+ D RE + + + K + Sbjct: 4 KLAEIRKKIDEIDNKILKLIAERNSLAKDVAEIKNQLGIPINDPEREKYIYDRIRKLCKE 63 Query: 62 HQFDDVIRATFKDIMTE-SRVYQKE 85 H D+ I I+ E ++ QK+ Sbjct: 64 HNVDENIGIKIFQILIEHNKALQKQ 88 A related DNA sequence was identified in S. pyogenes <SEQ ID 1567> which encodes the amino acid sequence <SEQ ID 1568>. Analysis of this protein sequence reveals the following: TABLE-US-01521 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2356(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01522 Identities = 45/91 (49%), Positives = 62/91 (67%) Query: 1 MELEEIRQEIDEIDQQLVSLLETRMGLILEVIAFKKKHRLPVLDNNRENEVLNNVLKKVQ 60 - M LE+IRQEI+ ID LV+LLE RM L+ +V A+K + LPVLD REN++L+ V V+ Sbjct: 1 MRLEKIRQEINGIDHHLVALLEKRMALVEQVTAYKLANHLPVLDQARENQILDRVSYLVK 60 Query: 61 NHQFDDVIRATFKDIMTESRVYQKENIVDGD 91 + F+ I TFK IM+ SR YQ +++ GD Sbjct: 61 DQAFEPAIHETFKTIMSLSRQYQTQHLTGGD 91 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 491 A DNA sequence (GBSx0529) was identified in S. agalactiae <SEQ ID 1569> which encodes the amino acid sequence <SEQ ID 1570>. This protein is predicted to be neuramimidase. Analysis of this protein sequence reveals the following: TABLE-US-01523 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.35 Transmembrane 28-44 (28-47) ----- Final Results ----- bacterial membrane --- Certainty = 0.2338(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certaimty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10191> which encodes amino acid sequence <SEQ ID 10192> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01524 >GP: CAA51473 GB: X72967 neuraminidase [Streptococcus pneumoniae] Identities = 294/504 (58%), Positives = 380/504 (75%), Gaps = 10/504 (1%) Query: 303 EDIKSYFQYYCHLNHQLKLPKGAILSAKTEVYRGGDFGRKNKDNVFGYRIPSLLKTEKGT 36- 2 E+++ Q + + + KLP+GA L+ KT+++ G G+ NKD + YRIP+LLKT+KGT Sbjct: 299 EEVQKRSQLFKRSDLEKKLPEGAALTEKTDIFESGRNGKPNKDGIKSYRIPALLKTDKGT 35- 8 Query: 363 LLVGADERIEQACDWGNIGMVIRRSEDDGVTWGKRETIVNLRNNPRVPLVTSGDYSGSPI 42- 2 L+ GADER + DWG+IGMVIRRSED+G TWG R TI NLR+NP+ S GSP+ Sbjct: 359 LIAGADERRLHSSDWGDIGMVIRRSEDNGKTWGDRVTITNLRDNPKA----SDPSIGSPV 41- 4 Query: 423 NMDMALVQDTSSKTKRIFSIYDMFPEGRGVISIANTPEKEYTQIGGQSYLNLYNNGKKSK 48- 2 N+DM LVQD +TKRIFSIYDMFPEG+G+ +++ E+ Y +I G++Y LY G+K Sbjct: 415 NIDMVLVQDP--ETKRIFSIYDMFPEGKGIFGMSSQKEEAYKKIDGKTYQILYREGEKG- 47- 1 Query: 483 VFTIRDKGIVYNFKGKKTDYHVITETTKSDHSNLGDIYKGKQLLGNIYFTKHKTSPFRLA 54- 2 +TIR+ G VY GK TDY V+ + K +S+ GD+YKG QLLGNIYFT +KTSPFR+A Sbjct: 472 AYTIRENGTVYTPDGKATDYRVVVDPVKPAYSDKGDLYKGNQLLGNIYFTTNKTSPFRIA 53- 1 Query: 543 KSSYVWMSYSDDDGRTWSSPRDITASLRQKGMKFLGIGPGKGIVLKWGPHAGRIIIPAYS 60- 2 K SY+WMSYSDDDG+TWS+P+DIT ++ MKFLG+GPG GIVL+ GPH GRI+IP Y+ Sbjct: 532 KDSYLWMSYSDDDGKTWSAPQDITPMVKADWMKFLGVGPGTGIVLRNGPHKGRILIPVYT 59- 1 Query: 603 TNWKSHLRGSQSSRLIYSDDHGKTWHTGKAVNDNRILSNGEKIHSLTMDNKKEQNTESVP 66- 2 TN SHL GSQSSR+IYSDDHGKTWH G+AVNDNR + +G+KIHS TM+N++ QNTES Sbjct: 592 TNNVSHLNGSQSSRIIYSDDHGKTWHAGEAVNDNRQV-DGQKIHSSTMNNRRAQNTESTV 65- 0 Query: 663 VQLKNGDIKLFMRNLTGNLEVATSKDGGETWQNHVKRYKEVHDAYVQLSAIRFEHDKKEY 72- 2 VQL NGD+KLFMR LTG+L+VATSKDGG TW+ +KRY +V D YVQ+SAI H+ KEY Sbjct: 651 VQLNNGDVKLFMRGLTGDLQVATSKDGGVTWEKDIKRYPQVKDVYVQMSAIHTMHEGKEY 71- 0 Query: 723 ILLVNANGPGKKRQDGYARLAQVNRNGSFKWLYHHHIQDGSFAYNSVQQLNNDKFGVLYE 78- 2 I+L NA GP KR++G LA+V NG WL H+ IQ G FAYNS+Q+L N ++G+LYE Sbjct: 711 IILSNAGGP--KRENGMVHLARVEENGELTWLKHNPIQKGEFAYNSLQELGNGEYGILYE 76- 8 Query: 783 HREKHQNSFTLNYKVFNWSFLSQN 806 H EK QN++TL+++ FNW FLS++ Sbjct: 769 HTEKGQNAYTLSFRKFNWDFLSKD 792 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 492 A DNA sequence (GBSx0530) was identified in S. agalactiae <SEQ ID 1571> which encodes the amino acid sequence <SEQ ID 1572>. This protein is predicted to be unnamed protein product (gatC). Analysis of this protein sequence reveals the following: TABLE-US-01525 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.63 Transmembrane 154-170 (149-178) INTEGRAL Likelihood = -11.99 Transmembrane 103-119 (98-123) INTEGRAL Likelihood = -7.91 Transmembrane 21-37 (14-40) INTEGRAL Likelihood = -6.53 Transmembrane 448-464 (444-467) INTEGRAL Likelihood = -5.89 Transmembrane 47-63 (45-68) INTEGRAL Likelihood = -5.10 Transmembrane 356-372 (352-373) INTEGRAL Likelihood = -4.78 Transmembrane 330-346 (328-350) INTEGRAL Likelihood = -4.41 Transmembrane 376-392 (375-393) INTEGRAL Likelihood = -3.72 Transmembrane 243-259 (235-266) INTEGRAL Likelihood = -2.55 Transmembrane 277-293 (275-293) ----- Final Results ----- bacterial membrane --- Certainty = 0.6052(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 1573> which encodes the amino acid sequence <SEQ ID 1574>. Analysis of this protein sequence reveals the following: TABLE-US-01526 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.31 Transmembrane 154-170 (150-179) INTEGRAL Likelihood = -11.68 Transmembrane 104-120 (99-124) INTEGRAL Likelihood = -9.82 Transmembrane 447-463 (442-469) INTEGRAL Likelihood = -7.91 Transmembrane 22-38 (11-41) INTEGRAL Likelihood = -7.11 Transmembrane 377-393 (375-403) INTEGRAL Likelihood = -5.89 Transmembrane 48-64 (46-69) INTEGRAL Likelihood = -4.78 Transmembrane 331-347 (329-351) INTEGRAL Likelihood = -3.88 Transmembrane 357-373 (353-373) INTEGRAL Likelihood = -2.55 Transmembrane 278-294 (276-294) INTEGRAL Likelihood = -1.22 Transmembrane 240-256 (240-257) ----- Final Results ----- bacterial membrane --- Certainty = 0.5925(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01527 Identities = 419/482 (86%) , Positives = 447/482 (91%) Query: 1 MQVFLNIVNKFFDPIIHMGSGVVMLIVMTGLAMIFGVKFSKALEGGIKLAIALTGIGAII 60- MQ FL+I+NK I +GSGVVMLIVMTGLAMIFGVKF+KALEGGIKLAIALTGIGAII Sbjct: 2 MQPFLDIINKILGFPIQLGSGVVMLIVMTGLAMIFGVKFTKALEGGIKLAIALTGIGAII 61- Query: 61 GILTGAFSESLQAFVKNTGINLSIIDVGWAPLATITWGSPYTLYFLLIMLIVNIVMIVMK 12- 0 GILTGAFSESLQAFVKNTGI+L+IIDVGWAPLATITWGSPYTLYFLL+ML+VNIVMIVMK Sbjct: 62 GILTGAFSESLQAFVKNTGISLNIIDVGWAPLATITWGSPYTLYFLLVMLVVNIVMIVMK 12- 1 Query: 121 KTDTLDVDIFDIWHLSITGLLIMWYAKKNNLPTLLSVIIATVAIIFVGVLKIINSDLMKP 18- 0 KTDTLDVDIFDIWHLSITGLLIMWYA +N+LP +S++IATVA+I VGVLKIINSDLMKP Sbjct: 122 KTDTLDVDIFDIWHLSITGLLIMWYAARNHLPVFVSLLIATVAVILVGVLKIINSDLMKP 18- 1 Query: 181 TFDDLLGTGPTSPMTSTHMNYMMNPIIMVLDKLFDKVFPGLDKYDFDAAKLNKAIGFWGS 24- 0 TFDDLLGTGP SPMTSTHMNYMMNPIIMVLDK+FDKVFPGLDKYDFDAAKLNK IGFWGS Sbjct: 182 TFDDLLGTGPQSPMTSTHMNYMMNPIIMVLDKIFDKVFPGLDKYDFDAAKLNKKIGFWGS 24- 1 Query: 241 KFFIGMILGLVIGIMGNPVFSFAALGGWFSLGFTAGACLELFSLIGSWFIAAVEPLSQGI 30- 0 KFFIGM LG VIGIMG+P F+ ++ WF LGFTAGACLELFSLIGSWFIAAVEPLSQGI Sbjct: 242 KFFIGMALGFVIGIMGDPHFTVESIKNWFGLGFTAGACLELFSLIGSWFIAAVEPLSQGI 30- 1 Query: 301 TNFANGKMHGRRFNIGLDWPFIAGRAEIWACANILAPIMLVEAILLSKVGNGILPLAGII 36- 0 TNFAN +MHGRRFNIGLDWPFIAGRAEIWACANILAPIML+EA+LLSKVGNGILPLAGII Sbjct: 302 TNFANARMHGRRFNIGLDWPFIAGRAEIWACANILAPIMLIEAVLLSKVGNGILPLAGII 36- 1 Query: 361 AMGVTPALLVVTRGRLIRMITFGTLLLPLFLLSGTMIAPFATELAKKVGAFPAGARAGSL 42- 0 AMG+TPALLVVTRGRLIRMI FG+LLLPLFLLSGTMIAPFATELAKKVGAFPAG AGSL Sbjct: 362 AMGMTPALLVVTRGRLIRMIIFGSLLLPLFLLSGTMIAPFATELAKKVGAFPAGTSAGSL 42- 1 Query: 421 ITHSTLEGPMEKIFGYVIGKATTGQLSAIITLIIFATAYLGLFMWYAKQMKRRNAEYAAN 48- 0 ITHSTLEGPMEKIFGYVIG+ATTGQ+++IITLIIF YL LF WYA QMK RNAEYA Sbjct: 422 ITHSTLEGPMEKIFGYVIGQATTGQIASIITLIIFVAIYLSLFAWYANQMKARNAEYAKT 48- 1 Query: 481 QK 482 K Sbict: 482 MK 483 A related GBS gene <SEQ ID 8579> and protein <SEQ ID 8580> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01528 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 4.31 GvH: Signal Score (-7.5): -2.64 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 6 value: -12.63 threshold: 0.0 INTEGRAL Likelihood = -12.63 Transmembrane 154-170 (149-178) INTEGRAL Likelihood = -11.99 Transmembrane 103-119 (98-123) INTEGRAL Likelihood = -7.91 Transmembrane 21-37 (14-40) INTEGRAL Likelihood = -5.89 Transmembrane 47-63 (45-68) INTEGRAL Likelihood = -4.88 Transmembrane 243-259 (235-265) INTEGRAL Likelihood = -1.22 Transmembrane 268-284 (268-284) PERIPHERAL Likelihood = 0.85 127 modified ALOM score: 3.03 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6052(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00036## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 493 A DNA sequence (GBSx0531) was identified in S. agalactiae <SEQ ID 1575> which encodes the amino acid sequence <SEQ ID 1576>. Analysis of this protein sequence reveals the following: TABLE-US-01529 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0302(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1577> which encodes the amino acid sequence <SEQ ID 1578>. Analysis of this protein sequence reveals the following: TABLE-US-01530 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0302(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01531 Identities = 85/100 (85%), Positives = 96/100 (96%) Query: 1 MIKILAACGAGVNSSHQIKDAIETQLGDRGYNVHCDAVMVKDITEEMVNKYDIFTPIAKT 60 - MIKILAACGAGVNSSHQIKDAIETQ+ DRGY+VHCDAVMVKDITEE+V++YDIFTPIAKT Sbjct: 1 MIKILAACGAGVNSSHQIKDAIETQMSDRGYDVHCDAVMVKDITEELVSRYDIFTPIAKT 60 Query: 61 DLGFNVPIPVVEAGPILYRIPVMSEPVFTALEQVIKEHNL 100 DLGF +PIP+VEAGPILYRIP+MSEPVF LE+VIKE++L Sbjct: 61 DLGFEMPIPIVEAGPILYRIPIMSEPVFAELERVIKENHL 100 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 494 A DNA sequence (GBSx0532) was identified in S. agalactiae <SEQ ID 1579> which encodes the amino acid sequence <SEQ ID 1580>. This protein is predicted to be GatA. Analysis of this protein sequence reveals the following: TABLE-US-01532 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2078(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10193> which encodes amino acid sequence <SEQ ID 10194> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01533 >GP: AAG09977 GB: AF248038 GatA [Streptococcus agalactiae] Identities = 39/135 (28%), Positives = 76/135 (55%), Gaps = 9/135 (6%) Query: 16 QEELFDLVSKALIKQHYVSPNYRQAVKEREREFPTGLKIDLKDGTPIQYVAIPHTETQYC 75- Q L +++S+ L+++ YV + +A+ +RE+++PTGL+++ VAIPHT ++Y Sbjct: 20 QTNLLEVLSQYLLQKGYVKTEFSKAILQREKDYPTGLQLE------NMAVAIPHTYSEYV 73- Query: 76 LVDRIFYVKNSQPITFKHMINPEEECRVQDFFFIINSRN-SNQSDILSNLITFFITKGNL 13- 4 L I+ K +PI+F M E+E + + ++ N +Q+ +L+ L+T F + Sbjct: 74 LKPFIYINKLKEPISFIQM-GTEDEIVMARYVIVLGISNPKDQAGLLAELMTLFSNPKIV 13- 2 Query: 135 DRLHELGDNKEKINH 149 +L E KE + + Sbjct: 133 QQL-EMAQTKEALKN 146 A related DNA sequence was identified in S. pyogenes <SEQ ID 1581> which encodes the amino acid sequence <SEQ ID 1582>. Analysis of this protein sequence reveals the following:

TABLE-US-01534 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3130(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01535 Identities = 102/154 (66%), Positives = 122/154 (78%) Query: 4 VTQDILFIDAHSQEELFDLVSKALIKQHYVSPNYRQAVKEREREFPTGLKIDLKDGTPIQ 63- V +ILF +A +Q ELFDLV+ L K YV+ Y QA+ ERE FPTGLK+DLKDG+ I Sbjct: 1 VFPNILFTEARTQPELFDLVASHLEKVGYVTQEYHQALVEREAVFPTGLKVDLKDGSDIL 60- Query: 64 YVAIPHTETQYCLVDRIFYVKNSQPITFKHMINPEEECRVQDFFFIINSRNSNQSDILSN 12- 3 Y AIPHTET+YCLVD++ YV+NSQ +TFKHMINPEE+C V DFFFIINS+N Q+ ILSN Sbjct: 61 YAAIPHTETKYCLVDQVVYVRNSQALTFKHMINPEEDCLVTDFFFIINSQNEGQTTILSN 12- 0 Query: 124 LITFFITKGNLDRLHELGDNKEKINHYLIEKGVF 157 LITFFITKGNL L L D+K+ I++YLIEKGVF Sbjct: 121 LITFFITKGNLSYLASLKDDKQAISNYLIEKGVF 154 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 495 A DNA sequence (GBSx0533) was identified in S. agalactiae <SEQ ID 1583> which encodes the amino acid sequence <SEQ ID 1584>. Analysis of this protein sequence reveals the following: TABLE-US-01536 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1429(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01537 >GP:AAA25176 GB:M60447 repressor protein [Lactococcus lactis] Identities = 139/255 (54%), Positives = 189/255 (73%), Gaps = 6/255 (2%) Query: 1 MLKRERLQKIIEKVNINGIVTVNEIMEELDVSDMTVRRDLDELDKAGLLIRIHGGAQKVN 60 M K+ RL+KI++ + I+G +T+ EI++ELD+SDMT RRDLD L+ GLL R HGGAQ ++ Sbjct: 7 MNKKRRLEKILDMLKIDGTITIREIIDELDISDMTARRDLDALEADGLLTRTHGGAQLLS 66 Query: 61 ASPTPQNYEKSNTEKYDIQTNEKLEIAQFAKQFINDGETIFIGPGTTLEKLATQLLD--- 117- + + EK++ EK + T EK++IA+ A I DG+TIFIGPGTTL +LA +L Sbjct: 67 SK---KPLEKTHIEKKSLNTKEKIDIAKKACSLIKDGDTIFIGPGTTLVQLALELKGRKG 123- Query: 118 FKIRVVTNSLPVFNILNQSSTLDLILVGGEYREITGAFVGSVTINSIKSLNFSKAFVSSN 17- 7 +KIRV+TNSLPVF ILN S T+DL+L+GGEYREITGAFVGS+ ++K++ F+KAFV +N Sbjct: 124 YKIRVITNSLPVFLILNDSETIDLLLLGGEYREITGAFVGSMASTNLKAMRFAKAFVRAN 18- 3 Query: 178 GVFEKSIATYDEGEGEIQRIALNNSFEKFLLVDSQKFGKYDFYTFYQLDDIDFVLTDHNI 23- 7 V SIATY + EG IQ++ALNN+ EKFLLVDS EF +YDF+ FY LD +D ++TD+ I Sbjct: 184 AVTHNSIATYSDKEGVIQQLALNNAVEKFLLVDSTKFDRYDFFNFYNLDQLDTIITDNQI 24- 3 Query: 238 DNVVKEQYSSFTKIL 252 E++S +T IL Sbjct: 244 SPQHLEEFSQYTTIL 258 A related DNA sequence was identified in S. pyogenes <SEQ ID 1585> which encodes the amino acid sequence <SEQ ID 1586>. Analysis of this protein sequence reveals the following: TABLE-US-01538 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0740(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01539 Identities = 161/252 (63%), Positives = 195/252 (76%), Gaps = 3/252 (1%) Query: 1 MLKRERLQKIIEKVNINGIVTVNEIMEELDVSDMTVRRDLDELDKAGLLIRIHGGAQKVN 60 MLKRERL KI E VN GIVTVN+I++ L+VSDNTVRRDLDEL+KAG LIRIHGGAQ + Sbjct: 1 MLKRERLLKITEIVNEQGIVTVNDIIQTLNVSDMTVRRDLDELEKAGRLIRIHGGAQSIT 60 Query: 61 ASPTPQNYEKSNTEKYDIQTNEKLEIAQFAKQFINDGETIFIGPGTTLEKLATQLLDWKI 120- P E+SN EK +QT EK E+A +A Q +NDGETIFIGPGTTLE A QL ++I Sbjbt: 61 M---PNKKERSNIEKQTVQTKEKWELASYATQLVNDGETIFIGPGTTLECFAEQLKNRQI 117- Query: 121 RVVTNSLPVFNILNQSSTLDLILVGGEYREITGAFVGSVTINSIRSLNFSKAFVSSNGVF 18- 0 R+VTNSLPVFNIL S T+DLIL+GGEYR ITGAFVGS+ +I SL F+KAF+S NG++ Sbjct: 118 RIVTNSLPVFNILQDSETIDLILIGGEYRSITGAFVGSLASQNISSLKFAKAFISCNGIY 17- 7 Query: 181 EKSIATYDEGEGEIQRIALNNSFEKFLLVDSQKFGKYDFYTFYQLDDIDFVLTDHNIDNV 24- 0 + IATY E EGEIQ++A NNS EK+LLVD+QKF YDF+ FY L++ID V+TD I Sbjct: 178 KNDIATYSETEGEIQKLAFNNSIEKYLLVDNQKFNAYDFFIFYHLNNIDAVVTDSQITED 23- 7 Query: 241 VKEQYSSFTKIL 252 V E+YS FT++L Sbjct: 238 VIERYSQFTQLL 249 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 496 A DNA sequence (GBSx0534) was identified in S. agalactiae <SEQ ID 1587> which encodes the amino acid sequence <SEQ ID 1588>. Analysis of this protein sequence reveals the following: TABLE-US-01540 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3436(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01541 >GP:AAD13797 GB:AF062533 unknown [Streptococcus agalactiae] Identities = 86/371 (23%), Positives = 136/371 (36%), Gaps = 79/371 (21%) Query: 11 DLSESELKAAQEFLSGKSEANQDKPKTGKTAQEIYEAIEPKAIVKPEDLLFGIAQATDYK 70 - DL++ + L K D TG IEP+ V L AT Sbjct: 526 DLTQIAFAEQELMLKDKKHYRYDIVDTG---------IEPRLAVDVSSLPHHAGHATYDT 57- 6 Query: 71 NGTFVIPHKDHYHYVELKWFDEEKDLLADSDKTYSLEDYLATAKYYMMHPSKRPKVEGWG 130- +FVIPH DH H V W + +AT KY M HPE RP V W Sbjct: 577 GSSFVIPHIDHIHVVPYSWLTRNQ---------------IATIKYVMQHPEVRPDV--IS 61- 9 Query: 131 KDAEIYKEKDSNKADKPSPAPTDNKSTSNSSDKNLSAAEVFKQAKPEKIVPLDKIAAHMA 19- 0 K + + + P+ P D ++ + SA EV +K + + AA Sbjct: 620 KPGH-----EESGSVIPNVTPLDKRAGMPHWQIIHSAEEV------QKALAEGRFAA--- 66- 5 Query: 191 YAVGFEDDQLIVPHHDHYHNVPMAWFDKGGLWKAPEGYTLQQLFST--IKYYMEHPHELP 24- 8 D I D W D +G +L+ + + + + EL Sbjct: 666 ------PDGYIFDPRDVLAKETFVWKDGSFSIPRADGSSLRTINKSDLSQAEWQQAQELL 71- 9 Query: 249 KEKGWGHDSDHNKGSNKDNKAKNYAPDEEPEDSGKVTHNYGFYDVNKGSDEEEP-EKQED 30- 7 +K G +D +K P+E+ + +K ++ ++P E ++ Sbjct: 720 AKKHAGDATDTDK------------PEEKQQ-------------ADKSNENQQPSEASKE 75- 4 Query: 308 ESELDEYELGMAQNAKKYGMDRQSFEKQLIQLSNKYSVSFESFNYIHGSQVQVTKKDGSK 36- 7 E E D++ + YG+DR + E + QL+ K ++ + VQ K+G Sbjct: 755 EKESDDF----IDSLPDYGLDRATLEDHIHQLAQKANID-PKYLIFQPEGVQFYNKHGEL 80- 9 Query: 368 VLVDIKTLTEV 378 V DIKTL ++ Sbjct: 810 VTYDIKTLQQI 820 A related DNA sequence was identified in S. agalactiae <SEQ ID 6983> which encodes the amino acid sequence <SEQ ID 6984>. Analysis of this protein sequence reveals the following: TABLE-US-01542 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS gene <SEQ ID 8581> and protein <SEQ ID 8582> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01543 Lipop Possible site: -1 Crend: 2 McG: Discrim Score: 6.06 GvH: Signal Score (-7.5): -5.61 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 0 value: 2.23 threshold: 0.0 PERIPHERAL Likelihood = 2.23 6 modified ALOM score: -0.95 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 1589> which encodes the amino acid sequence <SEQ ID 1590>. Analysis of this protein sequence reveals the following: TABLE-US-01544 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-01545 Identities = 808/825 (97%), Positives = 816/825 (97%), Gaps = 3/825 (0%) Query: 2 KKTYGYIGSVAAILLATHIGSYQLGKHHMGLATKDNQIAYIDDSKGKVKAPKTNKTMDQ 60 KKTYGYIGSVAAILLATHIGSYQLGKHHMG ATKDNQIAYIDDSKGK KAPKTNKTMDQ Sbjct: 2 KKTYGYIGSVAAILLATHIGSYQLGKHHMGSATKDNQIAYIDDSKGKAKAPKTNKTMDQ 60 Query: 61 ISAEEGISAEQIVVKITDQGYVTSHGDHYHFYNGKVPYDAIISEELLMTDPNYHFKQSDV 120- ISAEEGISAEQIVVKITDQGYVTSHGDHYHFYNGKVPYDAIISEELLMTDPNY FKQSDV Sbjct: 61 ISAEEGISAEQIVVKITDQGYVTSHGDHYHFYNGKVPYDAIISEELLMTDPNYRFKQSDV 120- Query: 121 INEILDGYVIKVNGNYYVYLKPGSKRKNIRTKQQIAEQVAKGTKEAKEKGLAQVAHLSKE 18- 0 INEILDGYVIKVNGNYYVYLKPGSKRKNIRTKQQIAEQVAKGTKEAKEKGLAQVAHLSKE Sbjct: 121 INEILDGYVIKVNGNYYVYLKPGSKRKNIRTKQQIAEQVAKGTKEAKEKGLAQVAHLSKE 18- 0 Query: 181 EVAAVNEAKRQGRYTTDDGYIFSPTDIIDDLGDAYLVPHGNHYHYIPKKDLSPSELAAAQ 24- 0 EVAAVNEAKRQGRYTTDDGYIFSPTDIIDDLGDAYLVPHGNHYHYIPKKDLSPSELAAAQ Sbjct: 181 EVAAVNEAKRQGRYTTDDGYIFSPTDIIDDLGDAYLVPHGNHYHYIPKKDLSPSELAAAQ 24- 0 Query: 241 AYWSQKQGRGARPSDYRPTPAP--GRRKAPIPDVTPNPGQGHQPDNGGYHPAPPRPNDAS 29- 8 AYWSQKQGRGARPSDYRPTPAP GRRKAPIPDVTPNPGQGHQPDNGGYHPAPPRPNDAS Sbjct: 241 AYWSQKQGRGARPSDYRPTPAPAPGRRKAPIPDVTPNPGQGHQPDNGGYHPAPPRPNDAS 30- 0 Query: 299 QNKHQRDEFKGKTFKELLDQLHRLDLKYRHVEEDGLIFEPTQVIKSNAFGYVVPHGDHYH 35- 8 QNKHQRDEFKGKTFKELLDQLHRLDLKYRHVEEDGLIFEPTQVIKSNAFGYVVPHGDHYH Sbjct: 301 QNKHQRDEFKGKTFKELLDQLHRLDLKYRHVEEDGLIFEPTQVIKSNAFGYVVPHGDHYH 36- 0 Query: 359 IIPRSQLSPLEMELADRYLAGQTDDNDSGSDHSKPSDKEVTHTFLGHRIKAYGKGLDGKP 41- 8 IIPRSQLSPLEMELADRYLAGQT+D+DSGSDHSKPSDKEVTHTFLGHRIKAYGKGLDGKP Sbjct: 361 IIPRSQLSPLEMELADRYLAGQTEDDDSGSDHSKPSDKEVTHTFLGHRIKAYGKGLDGKP 42- 0 Query: 419 YDTSDAYVFSKESIHSVDKSGVTAKHGDHFHYIGFGELEQYELDEVANWVKAKGQADELV 47- 8 YDTSDAYVFSKESIHSVDKSGVTAKHGDHFHYIGFGELEQYELDEVANWVKAKGQADEL Sbjct: 421 YDTSDAYVFSKESIHSVDKSGVTAKHGDHFHYIGFGELEQYELDEVANWVKAKGQADELA 48- 0 Query: 479 AALDQEQGKEKPLFDTKKVSRKVTKDGKVGYIMPKDGKDYFYARYQLDLTQIAFAEQELM 53- 8 AALDQEQGKEKPLFDTKKVSRKVTKDGKVGY+MPKDGKDYFYAR QLDLTQIAFAEQELM Sbjct: 481 AALDQEQGKEKPLFDTKKVSRKVTKDGKVGYMMPKDGKDYFYARDQLDLTQIAFAEQELM 54- 0 Query: 539 LKDKKHYRYDIVDTGIEPRLAVDLSSLPMHAGNATYDTGSSFVIPHIDHIHVVPYSWLTR 59- 8 LKDKKHYRYDIVDTGIEPRLAVD+SSLPMHAGNATYDTGSSFVIPHIDHIHVVPYSWLTR Sbjct: 541 LKDKKHYRYDIVDTGIEPRLAVDVSSLPMHAGNATYDTGSSFVIPHIDHIHVVPYSWLTR 60- 0 Query: 599 NQIATIKYVMQHPEVRPDVWSKPGHEESGSVIPNVTPLDKRAGMPNWQIIHSAEEVQKAL 65- 8 +QIATIKYVMQHPEVRPD+WSKPGHEESGSVIPNVTPLDKRAGMPNWQIIHSAEEVQKAL Sbjct: 601 DQIATIKYVMQHPEVRPDIWSKPGHEESGSVIPNVTPLDKRAGMPNWQIIHSAEEVQKAL 66- 0 Query: 659 AEGRFAAPDGYIFDPRDVLAKETFVWKDGSFSIPRADGSSLRTINKSDLSQAEWQQAQEL 71- 8 AEGRFA PDGYIFDPRDVLAKETFVWKDGSFSIPRADGSSLRTINKSDLSQAEWQQAQEL Sbjct: 661 AEGRFATPDGYIFDPRDVLAKETFVWKDGSFSIPRADGSSLRTINKSDLSQAEWQQAQEL 72- 0 Query: 719 LAKKNAGDATDTDKPEEKQQADKSNENQQPSEASK-EEKESDDFIDSLPDYGLDRATLED 77- 7 LAKKNAGDATDTDKP+EKQQADKSNENQQPSEASK EEKESDDFIDSLPDYGLDRATLED Sbjct: 721 LAKKNAGDATDTDKPKEKQQADKSNENQQPSEASKEEEKESDDFIDSLPDYGLDRATLED 78- 0 Query: 778 HINQLAQKANIDPKYLIFQPEGVQFYNKNGELVTYDIKTLQQINP 822 HINQLAQKANIDPKYLIFQPEGVQFYNKNGELVTYDIKTLQQINP Sbjct: 781 HINQLAQKANIDPKYLIFQPEGVQFYNKNGELVTYDIKTLQQINP 825 SEQ ID 8582 was expressed in E. coli in two different forms. GBS293dNterm was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 147 (lane 14; MW 74 kDa+lanes 17 & 18; MW 48.8 kDa). GBS293C was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIGS. 148 (lane 24; MW 71 kDa+lanes 5 & 7; MW 46 kDa) and 182 (lane 7; MW 46 kDa). Purified GBS293C-His is shown in FIG. 241, lanes 8& 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 497 A DNA sequence (GBSx0535) was identified in S. agalactiae <SEQ ID 1591> which encodes the amino acid sequence <SEQ ID 1592>. Analysis of this protein sequence reveals the following: TABLE-US-01546 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01547 >GP: AAD13797 GB: AF062533 unknown [Streptococcus agalactiae] Identities = 213/463 (46%), Positives = 277/463 (59%), Gaps = 41/463 (8%) Query: 4 KKTV-IISALSVALFGTGVGAYQLGSYNA--QKSDNSVSYVKTDKSDSKAQATAVNKTPD 60 KKT I +++ L T +G+YQLG ++ DN ++Y+ D S K +A NKT D Sbjct: 2 KKTYGYIGSVAAILLATHIGSYQLGKHHMGLATKDNQIAYI--DDSKGKVKAPKTNKTMD 59 Query: 61 QISKEEGISAEQIVVKITDDGYVTSHGDHYHYYNGKVPYDAIISEELIMKDPSYVFNKAD 120- QIS EEGISAEQIVVKITD GYVTSHGDHYH+YNGKVPYDAIISEEL+M DP+Y F ++D Sbjct: 60 QISAEEGISAEQIVVKITDQGYVTSHGDHYHFYNGKVPYDAIISEELLMTDPNYHFKQSD 119- Query: 121 VINEVKDGYIIKVNGKYYLYLKEGSKRTNVRTKEQIQKQREEWSKGGSKGESGKHSSAKT 18- 0 VINE+ DGY+IKVNG YY+YLK GSKR N+RTK+QI +Q + +K E+ + A+ Sbjct: 120 VINEILDGYVIKVNGNYYVYLKPGSKRKNIRTKQQIAEQVAKGTK-----EAKEKGLAQV 17- 4 Query: 181 QALS----ASVREAKASGRYTTDDGYVFSPTDVIDDMGDAFLVPHGDHFHYIPKADLSPS 23- 6 LS A+V EAK GRYTTDDGY+FSPTD+IDD+GDA+LVPHG+H+HYIPK DLSPS Sbjct: 175 AHLSKEEVAAVNEAKRQGRYTTDDGYIFSPTDIIDDLGDAYLVPHGNHYHYIPKKDLSPS 23- 4 Query: 237 ELSAAQAYWNRKTGRSGNSS--KPSNSSSYIHASAPSGNVSTGRHANAPISIPRVTHANH 29- 4 EL+AAQAYW++K GR S +P+ + A P + G+ H Sbjct: 235 ELAAAQAYWSQKQGRGARPSDYRPTPAPGRRKAPIPDVTPNPGQGHQPD------NGGYH 28- 8 Query: 295 WSKPAGNHATAPKHHAPTTKPINKDSALDKMLKRLYAQPLYARHVESDGLVYDPAQVNAF 35- 4 + P N A+ KH + K ++L +L+ L RHVE DGL+++P QV Sbjct: 289 PAPPRPNDASQNKHQ----RDEFKGKTFKELLDQLHRLDLKYRHVEEDGLIFEPTQVIKS 34- 4 Query: 355 TAIGVSIPHGNHFHFIHYKDMSPLELE-ATRMVAEHRGHHIDALGKKDSTEKPKHISHEP 41- 3 A G +PHG+H+H I +SPLE+E A R +A G+ D + S Sbjct: 345 NAFGYVVPHGDHYHIIPRSQLSPLEMELADRYLA----------GQTDDNDSGSDHSKPS 39- 4 Query: 414 NKE-PHTEEEHHAVTPKDQRKGKP---NSQIVYSAQEIEEAKK 452 +KE HT H GKP + V+S + I K Sbjct: 395 DKEVTHTFLGHRIKAYGKGLDGKPYDTSDAYVFSKESIHSVDK 437 There is also homology to SEQ ID 1590. SEQ ID 1592 (GBS94) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 3; MW 52.5 kDa). GBS94-His was purified as shown in FIG. 194, lane 8. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 498 A DNA sequence (GBSx0536) was identified in S. agalactiae <SEQ ID 1593> which encodes the amino acid sequence <SEQ ID 1594>. This protein is predicted to be Lmb. Analysis of this protein sequence reveals the following: TABLE-US-01548 Possible site: 24 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> There is also homology to SEQ IDs 1596 and 5548. A related GBS gene <SEQ ID 8583> and protein <SEQ ID 8584> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01549 Lipop: Possible site: 22 Crend: 5 McG: Discrim Score: 13.64 GvH: Signal Score (-7.5): -5.75 Possible site: 24 >>> May be a lipoprotein ALOM program count: 0 value: 4.83 threshold: 0.0 PERIPHERAL Likelihood = 4.83 33 modified ALOM score: -1.47 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8584 (GBS22) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 14 (lane 6; MW 35 kDa). The GBS22-His fusion product was purified (FIG. 94A; see also FIG. 193, lane 4) and used to immunise mice (lane 2 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 94B), FACS (FIG. 94C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. SEQ ID 9584 (GBS22) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 183 (lane 7 & 8; MW 35 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 499 A DNA sequence (GBSx0537) was identified in S. agalactiae <SEQ ID 1597> which encodes the amino acid sequence <SEQ ID 1598>. Analysis of this protein sequence reveals the following: TABLE-US-01550 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.59 Transmembrane 19-35 (19-35) ----- Final Results ----- bacterial membrane --- Certainty = 0.1235(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-01551 >GP: CAA51352 GB: X72832 ORF1 [Streptococcus equisimilis] Identities = 104/145 (71%), Positives = 126/145 (86%) Query: 1 MKIIIQRVNQASVSIEDDVVGSIEKGLVLLVGIAPEDTTEDIAYAVRKITSMRIFSDDEG 60 MK+++QRV +ASVSI+ + G+I +GL+LLVG+ P+D ED+AYAVRKI +MRIFSD +G Sbjct: 1 MKLVLQRVKEASVSIDGKIAGAINQGLLLLVGVGPDDAAEDLAYAVRKIVNMRIFSDADG 60 Query: 61 KMNLSIQDIKGSVLSISQFTLFADTKKGNRPAFTGAADPVKANQFYDIFNQELANHVSVE 120- KMN SIQDIKGS+LS+SQFTL+ADTKKGNRPAFTGAA P A+QFYD FN++LA+ V VE Sbjct: 61 KMNQSIQDIKGSILSVSQFTLYADTKKGNRPAFTGAAKPDMASQFYDRFNEQLADFVPVE 120- Query: 121 TGQFGADMQVSLINDGPVTIVLDTK 145 G FGADMQVSLINDGPVTI+LDTK Sbjct: 121 RGVFGADMQVSLINDGPVTIILDTK 145 A related DNA sequence was identified in S. pyogenes <SEQ ID 1599> which encodes the amino acid sequence <SEQ ID 1600>. Analysis of this protein sequence reveals the following: TABLE-US-01552 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1430(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01553 Identities = 103/145 (71%), Positives = 124/145 (85%) Query: 1 MKIIIQRVNQASVSIEDDVVGSIEKGLVLLVGIAPEDTTEDIAYAVRKITSMRIFSDDEG 60 MK+++QRV +ASVSI+ + G+I +GL+LLVG+ P+D ED+AYAVRKI +MRIFSD +G Sbjct: 1 MKLVLQRVKEASVSIDGKIAGAINQGLLLLVGVGPDDNAEDLAYAVRKIVNMRIFSDADG 60 Query: 61 KMNLSIQDIKGSVLSISQFTLFADTKKGNRPAFTGAADPVKANQFYDIFNQELANHVSVE 120- KMN SIQDIKGS+LS+SQFTL+ADTKKGNRPAFTGAA P A+Q YD FN++LA V VE Sbjct: 61 KMNQSIQDIKGSILSVSQFTLYADTKKGNRPAFTGAAKPDLASQLYDSFNEQLAEFVPVE 120- Query: 121 TGQFGADMQVSLINDGPVTIVLDTK 145 G FGADMQVSLINDGPVTI+LDTK Sbjct: 121 RGVFGADMQVSLINDGPVTIILDTK 145 SEQ ID 1598 (GBS368) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 64 (lane 4; MW 20 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 70 (lane 4; MW 45 kDa). GBS368-GST was purified as shown in FIG. 215, lane 6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 500 A DNA sequence (GBSx0538) was identified in S. agalactiae <SEQ ID 1601> which encodes the amino acid sequence <SEQ ID 1602>. This protein is predicted to be stringent response-like protein (rel) (relA). Analysis of this protein sequence reveals the following: TABLE-US-01554 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 60-76 (60-76) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01555 >GP: CAA51353 GB: X72832 stringent response-like protein [Streptococcus equisimilis] Identities = 647/739 (87%), Positives = 696/739 (93%), Gaps = 1/739 (0%) Query: 1 MVKEINLTGEEVVAITSQYMSETDVAFVKFALNYATAAHYYQARKSGEPYIIHPIQVAGI 60 M KEINLTGEEVVA+ ++YM+ETD AFVK AL+YATAAH+YQ RKSGEPYI+HPIQVAGI Sbjct: 1 MAKEINLTGEEVVALAAKYMNETDAAFVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGI 60 Query: 61 LADLHLDAVTVACGFLHDVVEDTEITLDEIETDFGKDVRDIIDGVTKLGKVEYKSHEEQL 120- LADLHLDAVTVACGFLHDVVEDT+ITLD IE DFGKDVRDI+DGVTKLGKVEYKSHEEQL Sbjct: 61 LADLHLDAVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKLGKVEYKSHEEQL 120- Query: 121 AENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGI 18- 0 AENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGI Sbjct: 121 AENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGI 18- 0 Query: 181 SRIKWELEDLSFRYLNETEFYKISHMMSEKRREREELVDIIVDKIRSYTEEQGLYGDIYG 24- 0 SRIKWELEDL+FRYLNETEFYKISHMM+EKRRERE LVD IV KI+SYT EQGL+GD+YG Sbjct: 181 SRIKWELEDLAFRYLNETEFYKISHMMNEKRREREALVDDIVTKIKSYTTEQGLFGDVYG 24- 0 Query: 241 RPKHIYSIYRKMRDKKKRFDQIYDLIAIRCIMETASDVYAMVGYIHELWRPMPGRFKDYI 30- 0 RPKHIYSIYRKMRDKKKRFDQI+DLIAIRC+MET SDVYAMVGYIHELWRPMPGRFKDYI Sbjct: 241 RPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSDVYAMVGYIHELWRPMPGRFKDYI 30- 0 Query: 301 AAPKANGYQSIHTTVYGPKGPIEIQIRTKEMHQVAEFGVAAHWAYKKGITSKVNQAEQSV 36- 0 AAPKANGYQSIHTTVYGPKGPIEIQIRTKEMHQVAE+GVAAHWAYKKG+ KVNQAEQ V Sbjct: 301 AAPKANGYQSIHTTVYGPKGPIEIQIRTKEMHQVAEYGVAAHWAYKKGVRGKVNQAEQKV 36- 0 Query: 361 GMGWIQELVELQDESK-DAKDFVDSVKEDIFTERIYVFTPNGAVQELPRESGPIDFAYAI 41- 9 GM WI+ELVELQD S DA DFVDSVKEDIF+ERIYVFTP GAVQELP++SGPIDFAYAI Sbjct: 361 GMNWIKELVELQDASNGDAVDFVDSVKEDIFSERIYVFTPTGAVQELPKDSGPIDFAYAI 42- 0 Query: 420 HTQVGEKATGAKVNGRMVPLTAKLKTGDVVEIITNPNSFGPSRDWIKIVKTNKARNKIRQ 47- 9 HTQVGEKA GAKVNGRMVPLTAKLKTGDVVEI+TNPNSFGPSRDWIK+VKTNKARNKIRQ Sbjct: 421 HTQVGEKAIGAKVNGRMVPLTAKLKTGDVVEIVTNPNSFGPSRDWIKLVKTNKARNKIRQ 48- 0 Query: 480 FFKNQDKETSINKGRELLVDYFQEQGYVPNKYLDKKHIEEILPRVSVKSEEALYAAVGFG 53- 9 FFKNQDKE S+NKGR++LV YFQEQGYV NKYLDKK IE ILP+VSVKSEE+LYAAVGFG Sbjct: 481 FFKNQDKELSVNKGRDMLVSYFQEQGYVANKYLDKKRIEAILPKVSVKSEESLYAAVGFG 54- 0 Query: 540 DLSPISIFNKLTEKERREEERAKAKAEADELINGGEIKTDKRDVLKVKSENGVIIQGASG 59- 9 D+SP+S+FNKLTEKERREEERAKAKAEA+EL+NGGEIK + +DVLKV+SENGVIIQGASG Sbjct: 541 DISPVSVFNKLTEKERREEERAKAKAEAEELVNGGEIKHENKDVLKVRSENGVIIQGASG 60- 0 Query: 600 LLMRIAKCCNPVPGDLIEGYITKGRGVAIHRSDCQNLKSQENYEQRLIDVEWDDDGSKKE 65- 9 LLMRIAKCCNPVPGD IEGYITKGRG+AIHR+DC N+KSQ+ Y++RLI+VEWD D S K+ Sbjct: 601 LLMRIAKCCNPVPGDPIEGYITKGRGIAIHRADCNNIKSQDGYQERLIEVEWDLDNSSKD 66- 0 Query: 660 YMAEIDIYGLNRSGLLNDVLQTLSNATKLVSTVNAQPTKDMKFANIHVSFGISNLAQLTT 71- 9 Y AEIDIYGLNR GLLNDVLQ LSN+TK +STVNAQPTKDMKFANIHVSFGI NL LTT Sbjct: 661 YQAEIDIYGLNRRGLLNDVLQILSNSTKSISTVNAQPTKDMKFANIHVSFGIPNLTHLTT 72- 0 Query: 720 VVDKIKIIPDVYSVKRTNG 738 VV+KIK +PDVYSVKRTNG Sbjct: 721 VVEKIKAVPDVYSVKRTNG 739 A related DNA sequence was identified in S. pyogenes <SEQ ID 1603> which encodes the amino acid sequence <SEQ ID 1604>. Analysis of this protein sequence reveals the following: TABLE-US-01556 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 64-80 (64-80) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01557 >GP: CAA51353 GB: X72832 stringent response-like protein [Streptococcus equisimilis] Identities = 700/739 (94%), Positives = 721/739 (96%) Query: 5 MAKIMNVTGEEVIALAATYMTKADVAFVAKALAYATAAHFYQVRKSGEPYIVHPIQVAGI 64 MAK +N+TGEEV+ALAA YM + D AFV KAL YATAAHFYQVRKSGEPYIVHPIQVAGI Sbjct: 1 MAKEINLTGEEVVALAAKYMNETDAAFVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGI 60 Query: 65 LADLHLDAVTVACGFLHDVVEDTDITLDEIEADFGHDARDIVDGVTKLGEVEYKSHEEQL 124- LADLHLDAVTVACGFLHDVVEDTDITLD IE DFG D RDIVDGVTKLG+VEYKSHEEQL Sbjct: 61 LADLHLDAVTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKLGKVEYKSHEEQL 120- Query: 125 AENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGI 18- 4 AENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGI Sbjct: 121 AENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGI 18- 0 Query: 185 SRIKWELEDLAFRYLNETEFYKISHMMKEKRREREALVEAIVSKVKTYTTQQGLFGDVYG 24- 4 SRIKWELEDLAFRYLNETEFYKISHMM EKRREREALV+ IV+K+K+YTT+QGLFGDVYG Sbjct: 181 SRIKWELEDLAFRYLNETEFYKISHMMNEKRREREALVDDIVTKIKSYTTEQGLFGDVYG 24- 0 Query: 245 RPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSDVYAMVGYIHELWRPMPGRFKDYI 30- 4 RPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSDVYAMVGYIHELWRPMPGRFKDYI Sbjct: 241 RPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSDVYAMVGYIHELWRPMPGRFKDYI 30- 0 Query: 305 AAPKANGYQSIHTTVYGPKGPIEIQIRTKDMHQVAEYGVAAHWAYKKGVRGKVNQAEQAV 36- 4 AAPKANGYQSIHTTVYGPKGPIEIQIRTK+MHQVAEYGVAAHWAYKKGVRGKVNQAEQ V Sbjct: 301 AAPKANGYQSIHTTVYGPKGPIEIQIRTKEMHQVAEYGVAAHWAYKKGVRGKVNQAEQKV 36- 0 Query: 365 GMNWIKELVELQDASNGDAVDFVDSVKEDIFSERIYVFTPTGAVQELPKESGPIDFAYAI 42- 4 GMNWIKELVELQDASNGDAVDFVDSVKEDIFSERIYVFTPTGAVQELPK+SGPIDFAYAI Sbjct: 361 GMNWIKELVELQDASNGDAVDFVDSVKEDIFSERIYVFTPTGAVQELPKDSGPIDFAYAI 42- 0 Query: 425 HTQIGEKATGAKVNGRMVPLTAKLKTGDVVEIITNANSFGPSRDWVKLVKTNKARNKIRQ 48- 4 HTQ+GEKA GAKVNGRMVPLTAKLKTGDVVEI+TN NSFGPSRDW+KLVKTNKARNKIRQ Sbjct: 421 HTQVGEKAIGAKVNGRMVPLTAKLKTGDVVEIVTNPNSFGPSRDWIKLVKTNKARNKIRQ 48- 0 Query: 485 FFKNQDKELSVNKGRDLLVSYFQEQGYVANKYLDKKRIEAILPKVSVKSEESLYAAVGFG 54- 4 FFKNQDKELSVNKGRD+LVSYFQEQGYVANKYLDKKRIEAILPKVSVKSEESLYAAVGFG Sbjct: 481 FFKNQDKELSVNKGRDMLVSYFQEQGYVANKYLDKKRIEAILPKVSVKSEESLYAAVGFG 54- 0 Query: 545 DISPISVFNKLTEKERREEERAKAKAEAEELVKGGEVKHENKDVLKVRSENGVIIQGASG 60- 4 DISP+SVFNKLTEKERREEERAKAKAEAEELV GGE+KHENKDVLKVRSENGVIIQGASG Sbjct: 541 DISPVSVFNKLTEKERREEERAKAKAEAEELVNGGEIKHENKDVLKVRSENGVIIQGASG 60- 0 Query: 605 LLMRIAKCCNPVPGDPIDGYITKGRGIAIHRSDCHNIKSQDGYQERLIEVEWDLDNSSKD 66- 4 LLMRIAKCCNPVPGDPI+GYITKGRGIAIHR+DC+NIKSQDGYQERLIEVEWDLDNSSKD Sbjct: 601 LLMRIAKCCNPVPGDPIEGYITKGRGIAIHRADCNNIKSQDGYQERLIEVEWDLDNSSKD 66- 0 Query: 665 YQAEIDIYGLNRSGLLNDVLQILSNSTKSISTVNAQPTKDMKFANIHVSFGIPNLTHLTT 72- 4 YQAEIDIYGLNR GLLNDVLQILSNSTKSISTVNAQPTKDMKFANIHVSFGIPNLTHLTT Sbjct: 661 YQAEIDIYGLNRRGLLNDVLQILSNSTKSISTVNAQPTKDMKFANIHVSFGIPNLTHLTT 72- 0 Query: 725 VVEKIKAVPDVYSVKRTNG 743 VVEKIKAVPDVYSVKRTNG Sbjct: 721 VVEKIKAVPDVYSVKRTNG 739 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01558 Identities = 635/739 (85%), Positives = 691/739 (92%), Gaps = 1/739 (0%) Query: 1 MVKEINLTGEEVVAITSQYMSETDVAFVKFALNYATAAHYYQARKSGEPYIIHPIQVAGI 60 M K +N+TGEEV+A+ + YM++ DVAFV AL YATAAH+YQ RKSGEPYI+HPIQVAGI Sbjct: 5 MAKIMNVTGEEVIALAATYMTKADVAFVAKALAYATAAHFYQVRKSGEPYIVHPIQVAGI 64 Query: 61 LADLHLDAVTVACGFLHDVVEDTEITLDEIETDFGKDVRDIIDGVTKLGKVEYKSHEEQL 120- LADLHLDAVTVACGFLHDVVEDT+ITLDEIE DFG D RDI+DGVTKLG+VEYKSHEEQL Sbjct: 65 LADLHLDAVTVACGFLHDVVEDTDITLDEIEADFGHDARDIVDGVTKLGEVEYKSHEEQL 124- Query: 121 AENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGI 18- 0 AENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGI Sbjct: 125 AENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGI 18- 4 Query: 181 SRIKWELEDLSFRYLNETEFYKISHMMSEKRREREELVDIIVDKIRSYTEEQGLYGDIYG 24- 0 SRIKWELEDL+FRYLNETEFYKISHMM EKRRERE LV+ IV K+++YT +QGL+GD+YG Sbjct: 185 SRIKWELEDLAFRYLNETEFYKISHMMKEKRREREALVEAIVSKVKTYTTQQGLFGDVYG 24- 4 Query: 241 RPKHIYSIYRKMRDKKKRFDQIYDLIAIRCIMETASDVYAMVGYIHELWRPMPGRFKDYI 30- 0 RPKHIYSIYRKMRDKKKRFDQI+DLIAIRC+MET SDVYAMVGYIHELWRPMPGRFKDYI Sbjct: 245 RPKHIYSIYRKMRDKKKRFDQIFDLIAIRCVMETQSDVYAMVGYIHELWRPMPGRFKDYI 30- 4 Query: 301 AAPKANGYQSIHTTVYGPKGPIEIQIRTKEMHQVAEFGVAAHWAYKKGITSKVNQAEQSV 36- 0 AAPKANGYQSIHTTVYGPKGPIEIQIRTK+MHQVAE+GVAAHWAYKKG+ KVNQAEQ+V Sbjct: 305 AAPKANGYQSIHTTVYGPKGPIEIQIRTKDMHQVAEYGVAAHWAYKKGVRGKVNQAEQAV 36- 4 Query: 361 GMGWIQELVELQDESK-DAKDFVDSVKEDIFTERIYVFTPNGAVQELPRESGPIDFAYAI 41- 9 GM WI+ELVELQD S DA DFVDSVKEDIF+ERIYVFTP GAVQELP+ESGPIDFAYAI Sbjct: 365 GMNWIKELVELQDASNGDAVDFVDSVKEDIFSERIYVFTPTGAVQELPKESGPIDFAYAI 42- 4 Query: 420 HTQVGEKATGAKVNGRMVPLTAKLKTGDVVEIITNPNSFGPSRDWIKIVKTNKARNKIRQ 47- 9 HTQ+GEKATGAKVNGRMVPLTAKLKTGDVVEIITN NSFGPSRDW+K+VKTNKARNKIRQ Sbjct: 425 HTQIGEKATGAKVNGRMVPLTAKLKTGDVVEIITNANSFGPSRDWVKLVKTNKARNKIRQ 48- 4 Query: 480 FFKNQDKETSINKGRELLVDYFQEQGYVPNKYLDKKHIEEILPRVSVKSEEALYAAVGFG 53- 9 FFKNQDKE S+NKGR+LLV YFQEQGYV NKYLDKK IE ILP+VSVKSEE+LYAAVGFG Sbjct: 485 FFKNQDKELSVNKGRDLLVSYFQEQGYVANKYLDKKRIEAILPKVSVKSEESLYAAVGFG 54- 4 Query: 540 DLSPISIFNKLTEKERREEERAKAKAEADELINGGEIKTDKRDVLKVKSENGVIIQGASG 59- 9 D+SPIS+FNKLTEKERREEERAKAKAEA+EL+ GGE+K + +DVLKV+SENGVIIQGASG Sbjct: 545 DISPISVFNKLTEKERREEERAKAKAEAEELVKGGEVKHENKDVLKVRSENGVIIQGASG 60- 4 Query: 600 LLMRIAKCCNPVPGDLIEGYITKGRGVAIHRSDCQNLKSQENYEQRLIDVEWDDDGSKKE 65- 9 LLMRIAKCCNPVPGD I+GYITKGRG+AIHRSDC N+KSQ+ Y++RLI+VEWD D S K+ Sbjct: 605 LLMRIAKCCNPVPGDPIDGYITKGRGIAIHRSDCHNIKSQDGYQERLIEVEWDLDNSSKD 66- 4 Query: 660 YMAEIDIYGLNRSGLLNDVLQTLSNATKLVSTVNAQPTKDMKFANIHVSFGISNLAQLTT 71- 9 Y AEIDIYGLNRSGLLNDVLQ LSN+TK +STVNAQPTKDMKFANIHVSFGI NL LTT Sbjct: 665 YQAEIDIYGLNRSGLLNDVLQILSNSTKSISTVNAQPTKDMKFANIHVSFGIPNLTHLTT 72- 4 Query: 720 VVDKIKIIPDVYSVKRTNG 738 VV+KIK +PDVYSVKRTNG Sbjct: 725 VVEKIKAVPDVYSVKRTNG 743 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 501 A DNA sequence (GBSx0539) was identified in S. agalactiae <SEQ ID 1605> which encodes the amino acid sequence <SEQ ID 1606>. This protein is predicted to be 2',3'-cyclic-nucleotide 2'-phosphodiesterase precursor (cpdB). Analysis of this protein sequence reveals the following: TABLE-US-01559 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.79 Transmembrane 779-795 (778-797) ----- Final Results ----- bacterial membrane --- Certainty = 0.3314(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01560 >GP: CAB12613 GB: Z99108 similar to 2',3'-cyclic-nucleotide 2'-phosphodiesterase [Bacillus subtilis] Identities = 297/630 (47%), Positives = 419/630 (66%), Gaps = 21/630 (3%) Query: 102 KVDLRIMSTTDLHTNLVNYDYYQDKESQKIGLAKTAVLIEEAKKENPNTVLVDNGDVIQG 16- 1 +V L I++TTD+H N+++YDYY DKE+ GLA+TA LI++ +++NPNT+LVDNGD+IQG Sbjct: 42 QVHLSILATTDIHANMMDYDYYSDKETADFGLARTAQLIQKHREQNPNTLLVDNGDLIQG 101- Query: 162 TPLGTYKAIVKP---VAENEEHPMYQAMNALGYDASTLGNHEFNYGLDYLKKIIATANLP 21- 8 PLG Y + ++ + HP+ MNAL YDA TLGNHEFNYGLD+L I A+ P Sbjct: 102 NPLGEYAVKYQKDDIISGTKTHPIISVMNALKYDAGTLGNHEFNYGLDFLDGTIKGADFP 16- 1 Query: 219 ILNANVLDFKTHQPVFKTYDIITKTFKDSTGRAVALNIGITGIVPPQILNWDKANLEGKV 27- 8 I+NANV + + + Y I KT D G + +G G VPPQI+ WDK NLEG+V Sbjct: 162 IVNANVKT-TSGENRYTPYVINEKTLIDENGNEQKVKVGYIGFVPPQIMTWDKKNLEGQV 22- 0 Query: 279 IVKDSVKAIEEIVPTMRAKGADVILVLSHSGIGDDRYEEGEENVGYQIAS-IKGVDAVVT 33- 7 V+D V++ E +P M+A+GADVI+ L+H+GI G EN + +A+ KG+DA+++ Sbjct: 221 QVQDIVESANETIPKMKAEGADVIIALAHTGIEKQAQSSGAENAVFDLATKTKGIDAIIS 28- 0 Query: 338 GHSHAEFPSGNGTGFYEKYTGVDGIN---GKINGTPVTMAGKYGDHLGIIDLGLSYTNGK 39- 4 GH H FPS +Y GV N G ING PV M +G +LG+IDL L +G Sbjct: 281 GHQHGLFPSA-------EYAGVAQFNVEKGTINGIPVVMPSSWGKYLGVIDLKLEKADGS 33- 3 Query: 395 WQVSESSAKIRKIDMNSTTADERIIALAKEAHDGTINYVRQQVGTTTAPITSYFALVKDD 45- 4 W+V++S I I N T+ +E + ++ H T+ YVR+ VG T A I S+FA VKDD Sbjct: 334 WKVADSKGSIESIAGNVTSRNETVTNTIQQTHQNTLEYVRKPVGKTEADINSFFAQVKDD 39- 3 Query: 455 PSVQIVNNAQRWYVANELKGTPEANLPLLSAAAPFKAGTRGDATAYTDIPAGPVAIKNVA 51- 4 PS+QIV +AQ+WY E+K T NLP+LSA APFKAG R A YT+IPAG +AIKNV Sbjct: 394 PSIQIVTDAQKWYAEKEMKDTEYKNLPILSAGAPFKAGGRNGANYYTNIPAGDLAIKNVG 45- 3 Query: 515 DLYLYDNVTALLKVTGADLREWLEMSAGQFNQIDPNNKAPQNIINTEYRTYNFDVIDGLT 57- 4 DLYLYDN ++K+TG+++++WLEMSAGQFNQIDP Q ++N +R+YNFDVIDG+T Sbjct: 454 DLYLYDNTVQIVKLTGSEVKDWLEMSAGQFNQIDPAKGGDQALLNENFRSYNFDVIDGVT 51- 3 Query: 575 YKFDITQPNKYNKDGKVVNSQASRVRDLMYNGKPVADKQEFMIVTNNYRASGTFPGAKNA 63- 4 Y+ D+T+P KYN++GKV+N+ +SR+ +L Y GKP++ QEF++VTNNYRASG G + Sbjct: 514 YQVDVTKPAKYNENGKVINADSSRIINLSYEGKPISPSQEFLVVTNNYRASGG-GGFPHL 57- 2 Query: 635 TMNRLLN---LENRQTIINYIISEKTINPTADNNWGFTESIKDLDLRFQTADKAKNLVTN 69- 1 T +++++ +ENRQ +++YII +KT+NP ADNNW + +L F+++ AK Sbjct: 573 TSDKIVHGSAVENRQVLMDYIIEQKTVNPKADNNWSIA-PVSGTNLTFESSLLAKPFADK 63- 1 Query: 692 SKDIQYIASSTKDEGFGDYRFVYTEQEKVD 721 + D+ Y+ S +EG+G Y+ + + D Sbjct: 632 ADDVAYVGKSA-NEGYGVYKLQFDDDSNPD 660 Identities = 133/567 (23%), Positives = 214/567 (37%), Gaps = 147/567 (25%) Query: 104 DLRIMSTTDLHTNLVNYDYYQDKESQKIGLAKTAVLIEEAKKENPNTVLVDNGDVIQGTP 16- 3 DL +M T D H +L + A+ I E + E + +L+D GDV G Sbjct: 668 DLTVMHTNDTHAHLDD-------------AARRMTKINEVRSETNHNILLDAGDVFSGD- 71- 3 Query: 164 LGTYKAIVKPVAENEEHPMYQAMNALGYDASTLGNHEFNYG----LDYLKKIIATAN--- 21- 6 Y +A+ + MN +GYDA T GNHEF+ G D+L AT + Sbjct: 714 --LYFTKWNGLAD------LKMMNMMGYDAMTFGNHEFDKGPTVLSDFLSGNSATVDPAN 76- 5 Query: 217 --------LPILNANVLDFKTHQPVFKTYDIITKTF----KDSTGRAVALNIGITG--IV 26- 2 PI++ANV +++P K++ +TF K G + + + G + Sbjct: 766 RYHFEAPEFPIVSANV--DVSNEPKLKSFVKKPQTFTAGEKKEAGIHPYILLDVDGEKVA 82- 3 Query: 263 PPQILNWDKANLE--GKVIV--------KDSVKAIEEIVPTMRAKGADVILVLSHSGIGD 31- 2 + D A GK IV +++VKAI+E + + I+ L+H G Sbjct: 824 VFGLTTEDTATTSSPGKSIVFNDAFETAQNTVKAIQE------EEKVNKIIALTHIG--- 87- 4 Query: 313 DRYEEGEENVGYQIA-SIKGVDAVVTGHSHAEFPSGNGTGFYEKYTGVDGINGKINGTP- 37- 0 N ++A +KG+D ++ GH+H T VD + N P Sbjct: 875 -------HNRDLELAKKVKGIDLIIGGHTH---------------TLVDKMEVVNNEEPT 91- 2 Query: 371 -VTMAGKYGDHLGIIDLGLSYTNGKWQVSESSAKIRKIDMNSTTADERIIALAKEAHDGT 42- 9 V A +YG LG +D+ G Q +S+ + ID ++ E AK+ D Sbjct: 913 IVAQAKEYGQFLGRVDVAFD-EKGVVQTDKSNLSVLPIDEHTEENPE-----AKQELDQF 96- 6 Query: 430 INYV----RQQVGTTTAPITSYFALVKDDPSVQIVNNAQRWYVANELKGTPEANLPLLSA 48- 5 N + ++VG T + + QR +V + + A Sbjct: 967 KNELEDVKNEKVGYT-----------------DVALDGQREHVRTKETNLGNFIADGMLA 10- 09 Query: 486 AAPFKAGTRGDAT----AYTDIPAGPVAIKNVADLYLYDNVTALLKVTGADLREWLEMSA 54- 1 A AG R T I G + + V ++ + N + +TG ++E LE Sbjct: 1010 KAKEAAGARIAITNGGGIRAGIDKGDITLGEVLNVMPFGNTLYVADLTGKQIKEALE--- 1- 066 Query: 542 GQFNQIDPNNKAPQNIINTEYRTYNFDVIDGLTYKFDITQPNKYNKDGKVVNSQASRVRD 60- 1 Q + N E F + G+ Y F + NK G + V+ Sbjct: 1067 -------------QGLSNVENGGGAFPQVAGIEYTFTLN-----NKPG----HRVLEVKI 1- 104 Query: 602 LMYNGKPVADKQE--FMIVTNNYRASG 626 NG VA + + + TNN+ +G Sbjct: 1105 ESPNGDKVAINTDDTYRVATNNFVGAG 1131 There is also homology to SEQ ID 1608. A related sequence was also identified in GAS <SEQ ID 9129> which encodes the amino acid sequence <SEQ ID 9130>. Analysis of this protein sequence reveals the following:

TABLE-US-01561 Possible cleavage site: 27 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.67 Transmembrane 649-665 (648-666) INTEGRAL Likelihood = -2.02 Transmembrane 6-22 (5-22) PERIPHERAL Likelihood = 1.85 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8585> and protein <SEQ ID 8586> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01562 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: 6.68 GvH: Signal Score (-7.5): 0.87 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 1 value: -5.79 threshold: 0.0 INTEGRAL Likelihood = -5.79 Transmembrane 779-795 (778-797) PERIPHERAL Likelihood = 0.53 251 modified ALOM score: 1.66 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3314(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 769-773 The protein has homology with the following sequences in the databases: ##STR00037## SEQ ID 8586 (GBS53) was expressed in E. coli as a His-fusion product. The purified protein is shown in FIG. 196, lane 9. EXAMPLE 502 A DNA sequence (GBSx0540) was identified in S. agalactiae <SEQ ID 1609> which encodes the amino acid sequence <SEQ ID 1610>. Analysis of this protein sequence reveals the following: TABLE-US-01563 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0296(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 503 A DNA sequence (GBSx0541) was identified in S. agalactiae <SEQ ID 1611> which encodes the amino acid sequence <SEQ ID 1612>. Analysis of this protein sequence reveals the following: TABLE-US-01564 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1504(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10195> which encodes amino acid sequence <SEQ ID 10196> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01565 >GP: CAB12860 GB: Z99109 similar to glucanase [Bacillus subtilis] Identities = 212/345 (61%), Positives = 268/345 (77%), Gaps = 1/345 (0%) Query: 30 SMETTLNYIKTLTSIPSPTGFTQTIMTYIIKELEAFGYSPIRTNKGGVMVSLKGKNDTKH 89 - S+ T+ IK L SIPSPTG T ++ YI L+ + +R +KGG++ +L G++ ++H Sbjct: 3 SVRKTMELIKELVSIPSPTGNTYEVINYIESLLKEWKVETVRNHKGGLIATLPGRDTSRH 62 Query: 90 RMITAHLDTLGAMVRAIKPDGRLKIDLIGGYTYNAIEGENCTIHLSKNGKEISGTALIHQ 149- RM+TAH+DTLGAMV+ IK DGRLKIDLIGG+ YN+IEGE C I + +GK +GT L+HQ Sbjct: 63 RMLTAHVDTLGAMVKEIKADGRLKIDLIGGFRYNSIEGEYCQIETA-SGKMYTGTILMHQ 121- Query: 150 TSVHVYKDAGTAERNQTNMEIRLDEKVTTADETRALGIQVGDFISFDPRTIITDSGFIKS 20- 9 TSVHVYKDAG AERNQ NMEIRLDE V +T LGI VGDF+SFDPR IT SGFIKS Sbjct: 122 TSVHVYKDAGKAERNQENMEIRLDEPVHCRKDTEELGIGVGDFVSFDPRVEITSSGFIKS 18- 1 Query: 210 RYLDDKVSAGILMELLSVYKKEDIQLPYTTHFYFSAFEELGHGANSSIPNETVEYLAVDM 26- 9 R+LDDK S +L+ L+ + EDI+LPYTTHF S EE+G+G NS+IP ETVEYLAVDM Sbjct: 182 RHLDDKASVALLLRLIHEIQTEDIELPYTTHFLISNNEEIGYGGNSNIPPETVEYLAVDM 24- 1 Query: 270 GAMGDDQETDEYTVSICVKDASGPYHYELRQHLVSLAENNNIPYKLDIYPYYGSDASAAM 32- 9 GA+GD Q TDEY+VSICVKDASGPYHY+LR+HLV LAE ++I YKLDIYPYYGSDASAA+ Sbjct: 242 GAIGDGQATDEYSVSICVKDASGPYHYQLRKHLVQLAEKHHIDYKLDIYPYYGSDASAAI 30- 1 Query: 330 RAGAEVKHALLGAGIESSHSYERTHIDSIQATELLVDAYLKSNMV 374 ++G ++ H L+G GI++SH++ERTH S++ T L+ Y++S MV Sbjct: 302 KSGHDIVHGLIGPGIDASHAFERTHKSSLRHTAKLLYYYVQSPMV 346 There is also homology to SEQ ID 424. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 504 A DNA sequence (GBSx0542) was identified in S. agalactiae <SEQ ID 1613> which encodes the amino acid sequence <SEQ ID 1614>. Analysis of this protein sequence reveals the following: TABLE-US-01566 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3157(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01567 >GP: AAF11472 GB: AE002031 conserved hypothetical protein [Deinococcus radiodurans] Identities = 55/150 (36%), Positives = 85/150 (56%), Gaps = 2/150 (1%) Query: 5 LIIIRGNSASGKSTIAKQLQAELGENTLLLSQDYLRREMLGTKDGENTTTIPLLINLLNY 64 LI++RGNS SGKS++A+ L+ G + QDYLRR +L D I L+ + Y Sbjct: 23 LIVLRGNSGSGKSSVARALRERFGYGLAWVEQDYLRRVLLREHDVAGGKNIGLIETNVRY 82 Query: 65 GYHNCSYIILEGILRSDWYTPVWKHILKHNPNNTYAYYYDLSFQETVKRHSTRLKSLEFG 124- S +LEGIL S Y P+ + + H + +Y+DL F+ETV+RH+TR ++ +FG Sbjct: 83 CLSAGSVTVLEGILFSRHYGPMLERL--HADFGGHWFYFDLPFEETVRRHATRPQAADFG 140- Query: 125 EDSLARWWLEKDFLKEIPEKILTKAMSLED 154 + W+ +D L + E+++ A SL D Sbjct: 141 VQDMQAWFQARDVLPFVQEQLIGPASSLAD 170 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 505 A DNA sequence (GBSx0543) was identified in S. agalactiae <SEQ ID 1615> which encodes the amino acid sequence <SEQ ID 1616>. This protein is predicted to be periplasmic-iron-binding protein BitC. Analysis of this protein sequence reveals the following: TABLE-US-01568 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.46 Transmembrane 9-25 (5-30) ----- Final Results ----- bacterial membrane --- Certainty = 0.5585(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01569 >GP: AAD18094 GB: U75349 periplasmic-iron-binding protein BitA [Brachyspira hyodysenteriae] (ver 2) Identities = 114/331 (34%), Positives = 184/331 (55%), Gaps = 3/331 (0%) Query: 11 YILLVVSIIFISVFTYSISQPSKLLPPKELVILSPNSQAILTGTIPAFEEKY-GIKVKLI 69 - +I+ + ++ +++F S SK LVI + ++ + F+ K I V+++ Sbjct: 4 FIIFCMLMLSMTLFYSCSSGDSK--NANSLVIYCSHPLDLMNTILDDFKAKNPDINVEVV 61 Query: 70 QGGTGQLIDRLSKEGKQLKADIFFGGNYTQFESHKALFESYVSKNVHTVIPDYIHPSDTA 129- GTG+L+ R+ E D+ +GG +S LFE+Y S N ++ ++ + Sbjct: 62 TAGTGELLKRVEAEKMNPLGDVLWGGTLNSVKSKTDLFENYTSTNEANILDEFKNTEGPF 121- Query: 130 TPYTINGSVLIVNNELAKGLTIKSYEDLLQPSLKGKIAFADPNTSSSAFSQLTNILLAKG 18- 9 T ++ S+L+VN LA + I+ YEDLL P LKGKIA ADP+ SSSAF L N+L A G Sbjct: 122 TRFSAIPSILMVNTNLAGNIKIEGYEDLLNPELKGKIAAADPSASSSAFEHLVNMLYAMG 18- 1 Query: 190 GYTNPKAWNYVKKLQHNINAIKSSSSSEVYQSVAEGKMIVGLTYEDPSVNLQKSGANVSI 24- 9 K W+YV+KL N++ S SS VY+ VA+G+ VGLTYE+P ++ SG+ V + Sbjct: 182 KGDPEKGWDYVQKLCANLDGKLLSGSSAVYKGVADGEYTVGLTYEEPGISYMSSGSPVKV 24- 1 Query: 250 VYPTEGTVFVPSSVAIIKNAPSMKEAKLFINFMLSLDVQNAFGQSTSNRPIRKDAQTSNG 30- 9 +Y EG + P V IIK +++ AK FI++ +SLD QN + S R IR DA ++ Sbjct: 242 IYMKEGVISKPDGVYIIKGGKNLENAKKFIDYCVSLDAQNMLVEKLSRRSIRSDAVVTDM 30- 1 Query: 310 MKALKDIATLKEDYRYVTKHKGQILKTYNRI 340 +K + +I ++ ++ V + + + L + I Sbjct: 302 VKPMSEIYSITDNADVVEESRQKWLDKFKDI 332 A related DNA sequence was identified in S. pyogenes <SEQ ID 1617> which encodes the amino acid sequence <SEQ ID 1618>. Analysis of this protein sequence reveals the following: TABLE-US-01570 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.16 Transmembrane 9-25 (4-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.6265(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01571 >GP: AAB95371 GB: U75349 periplasmic-iron-binding protein BitC [Brachyspira hyodysenteriae] Identities = 115/324 (35%), Positives = 177/324 (54%), Gaps = 8/324 (2%) Query: 15 VIIILAIVNVAMYIF-----SSSKKDSAKELVILTPNSQTILTGTIPAFEEKY-GVKVRL 68 - +++I + ++++IF S S S LVI P+ + + F+ K G+ V + Sbjct: 4 IVLIFTSLLLSVFIFYSCSSSESGAQSGNSLVIYCPHPLEFINPLVDDFKAKNPGINVDI 63 Query: 69 IQGGTGQLIDQL-GRKDKPLNADIFFGGNYTQFESHKDLFESYVSPQVSTVISDYQLPSH 127- I GTG+L+ ++ KD PL DI +GG + + DLFESY S + Y+ Sbjct: 64 IAAGTGELLKRVESEKDNPLG-DILWGGTISMAKPKIDLFESYTSTNEENIAEIYKNTEG 122- Query: 128 RATPYTINGSVLIVNNELARGLHITSYEDLLQPALKGKIAFADPNSSSSAFSQLTNILLA 18- 7 T T S+L+VN LA + I YEDLL P LKGKIAFADP++SSS+F L N+L A Sbjct: 123 ALTRCTAVPSILMVNTNLAGDIKIEGYEDLLNPELKGKIAFADPSASSSSFEHLVNMLYA 18- 2 Query: 188 KGGYTNADAWAYMKRLLVNMNSIRATSSSEVYQSVAEGKMIVGLTYEDPCINLQKSGANV 24- 7 G W Y+ +L N++ + SS VY+ VA+G+ VGLT+E+ N +G+ V Sbjct: 183 IGKGDPEKGWDYVSKLCANLDGKLLSGSSAVYKGVADGEYTVGLTFEEGGANYVSAGSPV 24- 2 Query: 248 SIVYPKEGTVFVPSSVAIIKHAPNMTEAKLFINFMLSRDVQNAFGQSTSNRPIRQDAQTS 30- 7 +VY KEG + P + IIK+A N+ AK F+++ S D Q + R +R D S Sbjct: 243 KLVYMKEGVIIKPDGIYIIKNAKNLENAKKFVDYATSYDAQKTITDKLNRRSVRGDLPPS 30- 2 Query: 308 HDMKALETIATLKEDYAYVTKHKK 331 +++++TI + +D A V ++K+ Sbjct: 303 AILQSVDTINVITDDEAVVDQNKQ 326 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01572 Identities = 257/345 (74%), Positives = 295/345 (85%), Gaps = 1/345 (0%) Query: 1 MKEKQSKRLIYILLVVSIIFISVFTYSISQPSKLLPPKELVILSPNSQAILTGTIPAFEE 60 +K K+ L ++L+++ + ++V Y S SK KELVIL+PNSQ ILTGTIPAFEE Sbjct: 2 LKLKRKWLLSFLLVIIILAIVNVAMYIFSS-SKKDSAKELVILTPNSQTILTGTIPAFEE 60 Query: 61 KYGIKVKLIQGGTGQLIDRLSKEGKQLKADIFFGGNYTQFESHKALFESYVSKNVHTVIP 120- KYG+KV+LIQGGTGQLID+L ++ K L ADIFFGGNYTQFESHK LFESYVS V TVI Sbjct: 61 KYGVKVRLIQGGTGQLIDQLGRKDKPLNADIFFGGNYTQFESHKDLFESYVSPQVSTVIS 120- Query: 121 DYIHPSDTATPYTINGSVLIVNNELAKGLTIKSYEDLLQPSLKGKIAFADPNTSSSAFSQ 18- 0 DY PS ATPYTINGSVLIVNNELA+GL I SYEDLLQP+LKGKIAFADPN+SSSAFSQ Sbjct: 121 DYQLPSHRATPYTINGSVLIVNNELARGLHITSYEDLLQPALKGKIAFADPNSSSSAFSQ 18- 0 Query: 181 LTNILLAKGGYTNPKAWNYVKKLQHNINAIKSSSSSEVYQSVAEGKMIVGLTYEDPSVNL 24- 0 LTNILLAKGGYTN AW Y+K+L N+N+I+++SSSEVYQSVAEGKMIVGLTYEDP +NL Sbjct: 181 LTNILLAKGGYTNADAWAYMKRLLVNMNSIRATSSSEVYQSVAEGKMIVGLTYEDPCINL 24- 0 Query: 241 QKSGANVSIVYPTEGTVFVPSSVAIIKNAPSMKEAKLFINFMLSLDVQNAFGQSTSNRPI 30- 0 QKSGANVSIVYP EGTVFVPSSVAIIK+AP+M EAKLFINFMLS DVQNAFGQSTSNRPI Sbjct: 241 QKSGANVSIVYPKEGTVFVPSSVAIIKHAPNMTEAKLFINFMLSRDVQNAFGQSTSNRPI 30- 0 Query: 301 RKDAQTSNGMKALKDIATLKEDYRYVTKHKGQILKTYNRIRRNAD 345 R+DAQTS+ MKAL+ IATLKEDY YVTKHK +I+ TYN++R+ + Sbjct: 301 RQDAQTSHDMKALETIATLKEDYAYVTKHKKKIVATYNQLRQRLE 345 SEQ ID 1616 (GBS263) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 4; MW 63 kDa). The GBS263-GST fusion product was purified (FIG. 205, lane 5) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 301), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 506 A DNA sequence (GBSx0544) was identified in S. agalactiae <SEQ ID 1619> which encodes the amino acid sequence <SEQ ID 1620>. This protein is predicted to be response regulator. Analysis of this protein sequence reveals the following: TABLE-US-01573 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4733(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01574 >GP: AAF31452 GB: AF221126 putative response regulator [Streptococcus pneumoniae] Identities = 85/252 (33%), Positives = 147/252 (57%), Gaps = 17/252 (6%) Query: 2 YRLLIVEDEHLIRKWLRYAIDYQSLNILVVGEAKDGKEGAQLIQEEQPDIVLSDINMPIM 61 Y +LIVEDE+L+R+ L ++ + ++ ++G+A++G++ +LIQ++ PDI+L+DINMP + Sbjct: 3 YTILIVEDEYLVRQGLTKLVNVAAYDMEIIGQAENGRQAWELIQKQVPDIILTDINMPHL 62 Query: 62 TAFDMFEATKGQSYAK---IILSGYADFPNAQSAIHYGVLEFLTKPLEKQALIDCLKTIM 118- + + ++Y + + L+GY DF A SA+ GV ++L KP +Q + + L I Sbjct: 63 NGIQLASLVR-ETYPQVHLVFLTGYDDFDYALSAVKLGVDDYLLKPFSRQDIEEMLGKIK 121- Query: 119 ARIE-EHKEKHLQEHTELYLPLPQANDQVPEVIKDMLAWIHSHFHGKIVISQLAHDLGYS 17- 7 +++ E KE+ LQ+ L + + + I+ LA + + LA DLG+S Sbjct: 122 QKLDKEEKEEQLQD-----LLTNRFEGNMAQKIQSHLA------DSQFSLKSLASDLGFS 17- 0 Query: 178 ESYLYTVTKKHLHITLSDYINQYRINQAIQLMFREPDLMVYQIAEAVGIYDYRYFDRVFK 23- 7 +YL ++ KK L + DY+ + R+ QA +L+ DL +Y+IAE VG D YF + FK Sbjct: 171 PTYLSSLIKKELGLPFQDYLVRERVKQA-KLLLLTTDLKIYEIAEKVGFEDMNYFTQRFK 22- 9 Query: 238 KYLGQTVKAFKE 249 + G T + FK+ Sbjct: 230 QIAGVTPRQFKK 241 A related DNA sequence was identified in S. pyogenes <SEQ ID 1621> which encodes the amino acid sequence <SEQ ID 1622>. Analysis of this protein sequence reveals the following: TABLE-US-01575 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4239(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01576 Identities = 193/257 (75%), Positives = 226/257 (87%) Query: 1 MYRLLIVEDEHLIRKWLRYAIDYQSLNILVVGEAKDGKEGAQLIQEEQPDIVLSDINMPI 60 MY+L+I+EDEH+IRKWLRYAIDY++L+ILV+GEAKDGKEGA LI+E QPDIVL+DINMPI Sbjct: 1 MYKLVIIEDEHIIRKWLRYAIDYKALDILVIGEAKDGKEGAVLIKESQPDIVLTDINMPI 60 Query: 61 MTAFDMFEATKGQSYAKIILSGYADFPNAQSAIHYGVLEFLTKPLEKQALIDCLKTIMAR 120- MTAFDMFE TK Q+YAKIILSGYADFPNA+SAIHYGVLEFLTKP+EK AL +CL+TI+A+ Sbjct: 61 MTAFDMFEVTKDQTYAKIILSGYADFPNARSAIHYGVLEFLTKPIEKAALWECLQTIIAK 120- Query: 121 IEEHKEKHLQEHTELYLPLPQANDQVPEVIKDMLAWIHSHFHGKIVISQLAHDLGYSESY 18- 0 IE+ K + + +Y+PLPQ DQ+PEV+KD+L W+H+HF KI S+LAHDLGYSESY Sbjct: 121 IEKQKGSNQKTDACVYIPLPQMTDQIPEVVKDILEWVHAHFQDKISTSRLAHDLGYSESY 18- 0 Query: 181 LYTVTKKHLHITLSDYINQYRINQAIQLMFREPDLMVYQIAEAVGIYDYRYFDRVFKKYL 24- 0 +Y KKHL + LSDYINQYRINQAIQLM +EPDLMVY+IA+AVGIYDYRYFDRVFKKYL Sbjct: 181 IYQNIKKHLQMPLSDYINQYRINQAIQLMQQEPDLMVYEIAQAVGIYDYRYFDRVFKKYL 24- 0 Query: 241 GQTVKAFKEEHIFKQMD 257 GQTVKAFKEEH K D Sbjct: 241 GQTVKAFKEEHFMKDTD 257 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 507 A DNA sequence (GBSx0545) was identified in S. agalactiae <SEQ ID 1623> which encodes the amino acid sequence <SEQ ID 1624>. Analysis of this protein sequence reveals the following: TABLE-US-01577 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2964(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 508 A DNA sequence (GBSx0546) was identified in S. agalactiae <SEQ ID 1625> which encodes the amino acid sequence <SEQ ID 1626>. This protein is predicted to be two-component sensor histidine kinase. Analysis of this protein sequence reveals the following: TABLE-US-01578 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.80 Transmembrane 266-282 (257-285) INTEGRAL Likelihood = -12.90 Transmembrane 29-45 (24-51) ----- Final Results ----- bacterial membrane --- Certainty = 0.6519(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10197> which encodes amino acid sequence <SEQ ID 10198> was also identified. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-01579 >GP: BAB05628 GB: AP001513 two-component sensor histidine kinase [Bacillus halodurans] Identities = 84/258 (32%), Positives = 138/258 (52%), Gaps = 23/258 (8%) Query: 298 SSAINQMVLDMDAISRQEKSSIELDSQDEFQYLSVQINQMVSRLKDLHEKTLDLETQKLL 35- 7 S INQ+ S K+ I +D +DE LSVQ NQMV+ L+ L + + QK L Sbjct: 327 SERINQVA------SGDLKTKIVVDGKDEIGQLSVQFNQMVANLRSLIHQVHETNRQKRL 38- 0 Query: 358 FEK-------RMLEAQFNPHFLYNTLETILITSHYDSQL-TERIVIQLTKLLRYSLSGST 40- 9 EK +ML +Q NPHFL+NTLE+I + SH + ++V QL KL+R SL + Sbjct: 381 LEKSQNEIKLKMLASQINPHFLFNTLESIRMKSHMKGETEIAKVVKQLGKLMRKSLEVTG 44- 0 Query: 410 EAAVLKDDLAIIESYLLINQVRF-EELTYTISVSPELEHMRVPKLFLLPLIENAIKYGLK 46- 8 L+++L ++ YL I R+ + L Y + + P+ E + + L + PL+ENA+ +GL+ Sbjct: 441 HHIPLRNELDMVRCYLEIQTFRYGDRLHYELYIDPQSEMVEILPLIIQPLVENAVIHGLE 50- 0 Query: 469 ERHD-VAINIDIWQDSDGIWFTVSNNGSGISLARQQAIRTMLRSTH----SHHGLINSYR 52- 3 D + I + + + V+++G G+ + +AI+ ML + GL+N ++ Sbjct: 501 RTEDGGTVTISTIVNGNDLTVIVNDDGCGMDEEKLEAIQNMLHHPQEVDGNKIGLLNVHK 56- 0 Query: 524 RLQYQF---STVLLEFTK 538 RLQ + S +++E K Sbjct: 561 RLQLTYGKTSGLIIESAK 578 A related DNA sequence was identified in S. pyogenes <SEQ ID 1627> which encodes the amino acid sequence <SEQ ID 1628>. Analysis of this protein sequence reveals the following: TABLE-US-01580 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.88 Transmembrane 27-43 (22-49) INTEGRAL Likelihood = -9.08 Transmembrane 263-279 (258-282) ----- Final Results ----- bacterial membrane --- Certainty = 0.5352(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01581 >GP: BAB05628 GB: AP001513 two-component sensor histidine kinase [Bacillus halodurans] Identities = 85/270 (31%), Positives = 139/270 (51%), Gaps = 20/270 (7%) Query: 276 IFVILQRKSSGLANRIAAKNSRAINQMVRDMSAISRQEKRRIDLESQDEFQYLSDQINQM 33- 5 + V+L S L ++ + S INQ+ S K +I ++ +DE LS Q NQM Sbjct: 307 VAVLLIVHFSWLISKRLSHLSERINQVA------SGDLKTKIVVDGKDEIGQLSVQFNQM 36- 0 Query: 336 VERLQQLHDKTLDLETQKLLFEK-------RMLEAQFNPHFLYNTLETILITSHYDSAL- 38- 7 V L+ L + + QK L EK +ML +Q NPHFL+NTLE+I + SH Sbjct: 361 VANLRSLIHQVHETNRQKRLLEKSQNEIKLKMLASQINPHFLFNTLESIRMKSHMKGETE 42- 0 Query: 388 TEKIVIQLTKLLRYSLTDSSKPVLLKDDLSVIESYLVINQVRF-EELQYSINLSPDLDSL 44- 6 K+V QL KL+R SL + + L+++L ++ YL I R+ + L Y + + P + + Sbjct: 421 IAKVVKQLGKLMRKSLEVTGHHIPLRNELDMVRCYLEIQTFRYGDRLHYELYIDPQSEMV 48- 0 Query: 447 EVPKLFLLPLIENAIKYGLKERHD-VKINIACYYQDDHIIFSVRDNGSGIDAHHQKVIRE 50- 5 E+ L + PL+ENA+ +GL+ D + I+ + + V D+G G+D + I+ Sbjct: 481 EILPLIIQPLVENAVIHGLERTEDGGTVTISTIVNGNDLTVIVNDDGCGMDEEKLEAIQN 54- 0 Query: 506 QL----EAGESHHGLINSYRRLKYHFSEVS 531 L E + GL+N ++RL+ + + S Sbjct: 541 MLHHPQEVDGNKIGLLNVHKRLQLTYGKTS 570 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01582 Identities = 369/549 (67%), Positives = 449/549 (81%) Query: 3 MRGYRNEERFKKRLQDDISKHFSRQSLILSLLLIALFVLFSLAPQQIGLYKDVNSVSYSY 62 MRG ++EE FKK+LQDDIS+HFS QSL+LSLLLI LF++FSLAPQQ+GLY+D+N+ + Y Sbjct: 1 MRGEQVEEHFKKQLQDDISRHFSYQSLMLSLLLIGLFIIFSLAPQQLGLYRDINATATRY 60 Query: 63 KQLIQKHDTLLDDLGKNSLKPFVSGHLGSADLSKQYYHLRNHLQSQTELLVFSPNQELLF 122- +LI K + LLDDLGKNSL PF++ +L +ADLSK Y+HLR+ Q+ ELL+FSP+Q+LLF Sbjct: 61 HRLISKQEALLDDLGKNSLLPFLNKNLSTADLSKHYFHLRHSSQTSPELLLFSPSQDLLF 120- Query: 123 ASNSHLGNFFSKSIYISEVLDKAKINQRLLKIIVDSEGGHYLALIKPIIVNKKVSGYAFL 18- 2 ASM HLGN FSKS+YI EVL + L K +DSE GHYL +I P+I ++ GYAFL Sbjct: 121 ASNPHLGNVFSKSVYIQEVLRATHSPKTLFKDAMDSEDGHYLMIIMPMIDQNQLKGYAFL 18- 0 Query: 183 LMNGKDFLLPTKAINSDLIIADQLNNSFTFTNRDFISSSLDKVDSQFLTRYFSFHDHRAF 24- 2 +M+GKDFL PTK + S+L+IAD+L+N+FTF+NR+FI+SSLDK++SQ+L YF F D+RAF Sbjct: 181 VMSGKDFLHPTKTLTSELVIADKLDNTFTFSNRSFIASSLDKINSQYLHHYFVFQDNRAF 24- 0 Query: 243 VVRKVALQDNILLYMYRPLIPVTLVVLFSLVSSVIIFVILRQKSRVLADRIAVKNSSAIN 30- 2 + RKVALQ + LYMYRPLIP+ V+LFSL+SS +IFVIL++KS LA+RIA KNS AIN Sbjct: 241 ITRKVALQGGLWLYMYRPLIPMVSVMLFSLISSAVIFVILQRKSSGLANRIAAKNSRAIN 30- 0 Query: 303 QMVLDMDAISRQEKSSIELDSQDEFQYLSVQINQMVSRLKDLHEKTLDLETQKLLFEKRM 36- 2 QMV DM AISRQEK I+L+SQDEFQYLS QINQMV RL+ LH+KTLDLETQKLLFEKRM Sbjct: 301 QMVRDMSAISRQEKRRIDLESQDEFQYLSDQINQMVERLQQLHDKTLDLETQKLLFEKRM 36- 0 Query: 363 LEAQFNPHFLYNTLETILITSHYDSQLTERIVIQLTKLLRYSLSGSTEAAVLKDDLAIIE 42- 2 LEAQFNPHFLYNTLETILITSHYDS LTE+IVIQLTKLLRYSL+ S++ +LKDDL++IE Sbjct: 361 LEAQFNPHFLYNTLETILITSHYDSALTEKIVIQLTKLLRYSLTDSSKPVLLKDDLSVIE 42- 0 Query: 423 SYLLINQVRFEELTYTISVSPELEHMRVPKLFLLPLIENAIKYGLKERHDVAINIDIWQD 48- 2 SYL+INQVRFEEL Y+I++SF+L+ + VPKLFLLPLIENAIKYGLKERHDV INI + Sbjct: 421 SYLVINQVRFEELQYSINLSPDLDSLEVPKLFLLPLIENAIKYGLKERHDVKINIACYYQ 48- 0 Query: 483 SDGIWFTVSNNGSGISLARQQAIRTMLRSTHSHHGLINSYRRLQYQFSTVLLEFTKTDDA 54- 2 D I F+V +NGSGI Q+ IR L + SHHGLINSYRRL+Y FS V L F + D Sbjct: 481 DDHIIFSVRDNGSGIDAHHQKVIREQLEAGESHHGLINSYRRLKYHFSEVSLVFDQGDKQ 54- 0 Query: 543 FRVSYIVKE 551 F VSY VKE Sbjct: 541 FNVSYHVKE 549 A related GBS gene <SEQ ID 8587> and protein <SEQ ID 8588> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01583 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 6.23 GvH: Signal Score (-7.5): -0.0500002 Possible site: 38 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 1 value: -13.80 threshold: 0.0 INTEGRAL Likelihood - -13.80 Transmernbrane 259-275 ( 250-278) PERIPHERAL Likelihood - 2.70 404 modified ALOM score: 3.26 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6519(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00038## SEQ ID 8588 (GBS47) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 14 (lane 2; MW 84 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 85 (lane 4; MW 59.3 kDa). GBS47-His was purified as shown in FIG. 221, lane 4-5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 509 A DNA sequence (GBSx0547) was identified in S. agalactiae <SEQ ID 1629> which encodes the amino acid sequence <SEQ ID 1630>. This protein is predicted to be phosphotransferase enzyme II, D component. Analysis of this protein sequence reveals the following: TABLE-US-01584 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.46 Transmembrane 258-274 ( 252-274) INTEGRAL Likelihood = -9.13 Transmembrane 232-248 ( 227-251) INTEGRAL Likelihood = -5.31 Transmembrane 142-158 ( 140-161) INTEGRAL Likelihood = -2.50 Transmembrane 119-135 ( 118-139) ----- Final Results ----- bacterial membrane --- Certainty = 0.5182(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01585 >GP:AAC74889 GB:AE000276 PTS en yme IID, mannoses--pecific [Escherichia coli K12] Identities = 94/280 (33%), Positives = 156/280 (55%), Gaps = 13/280 (4%) Query: 3 SQDNLTKEDRKHLRSVFWRSWTMNASRTGATQYHAVGVIYTLLPVINRFYKTDKD-KAEA 61 ++ LT+ D +R VF RS S + A+G ++++P I R Y + + + +A Sbjct: 12 TEKKLTQSD---IRGVFLRSNLFQGS-WNFERMQALGFCFSMVPAIRRLYPENNEARKQA 67 Query: 62 LVRHTTWFNATMHINNFIMGLVASMEKKNSEDPDFDASAITAVKASLMGPISGVGDSFFW 121- + RH +FN + I+G+ ++E++ + + D AI +K LMGP++GVGD FW Sbjct: 68 IRRHLEFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVGDPIFW 127- Query: 122 GILRVIAAGIGISLASTGSAMGAVVFLLLYNIPAFLIHYYSLYGGYSVGAGFIKKLYESG 18- 1 G +R + A +G +A +GS +G ++F +L+N+ YY + GYS G +K + G Sbjct: 128 GTVRPVFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIVKDM-GGG 18- 6 Query: 182 GIKIVTKTSSMLGLMNVGSM----TASNVKFKTILTVAAKGAKEAASIQSYLDQLFVGVV 23- 7 ++ +T+ +S+LGL ++G++ T N+ G + ++Q+ LDQL G+V Sbjct: 187 FLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILDQLMPGLV 24- 6 Query: 238 PLLVTILAFWLLRKRVNINWIMFGIMVLGI---VLGLLGI 274 PLL+T WLLRKKVN WI+ G V+GI GLLG+ Sbjct: 247 PLLLTFACMWLLRKKVNPLWIIVGFFVIGIAGYACGLLGL 286 A related DNA sequence was identified in S. pyogenes <SEQ ID 1631> which encodes the amino acid sequence <SEQ ID 1632>. Analysis of this protein sequence reveals the following: TABLE-US-01586 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.98 Transmembrane 255-271 (251-274) INTEGRAL Likelihood = -7.01 Transmembrane 232-248 (228-250) INTEGRAL Likelihood = -5.68 Transmembrane 142-158 (140-161) INTEGRAL Likelihood = -2.50 Transmembrane 119-135 (118-139) ----- Final Results ----- bacterial membrane --- Certainty = 0.4991(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01587 >GP: AAC74889 GB: AE000276 PTS enzyme IID, mannose-specific [Escherichia coli] Identities = 94/281 (33%), Positives = 157/281 (55%), Gaps = 13/281 (4%) Query: 2 TSQDNLTKEDRKMLRSVFWRSWTMNASRTGATQYHAVGVIYTLLPVINRFYKTDKD-KAE 60 T++ LT+ D +R VF RS S + A+G ++++P I R Y + + + + Sbjct: 11 TTEKKLTQSD---IRGVFLRSNLFQGS-WNFERMQALGFCFSMVPAIRRLYPENNEARKQ 66 Query: 61 ALVRHTTWFNATMHINNFIMGLVASMEKKNSEDPDFDASAITAVKASLMGPISGVGDSFF 120- A+ RH +FN + I+G+ ++E++ + + D AI +K LMGP++GVGD F Sbjct: 67 AIRRHLEFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVGDPIF 126- Query: 121 WGILRVIAAGIGISLASAGSAMGAVVFLLLYNIPAFIIHYYSLYGGYSVGAGFIKKLYES 18- 0 WG +R + A +G +A +GS +G ++F +L+N+ YY + GYS G +K + Sbjct: 127 WGTVRPVFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIVKDM-GG 18- 5 Query: 181 GGIKIVTKTSSMLGLMMVGSM----TASNVKFKTILTVAAKGAKEAASIQDYLDQLFIGI 23- 6 G ++ +T+ +S+LGL ++G++ T N+ G + ++Q LDQL G+ Sbjct: 186 GFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILDQLMPGL 24- 5 Query: 237 VPLMVTLAAFWLLRKKVNIIWIMFGIMFLGI---ILGLLGI 274 VPL++T A WLLRKKVN +WI+ G +GI GLLG+ Sbjct: 246 VPLLLTFACMWLLRKKVNPLWIIVGFFVIGIAGYACGLLGL 286 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01588 Identities = 263/275 (95%), Positives = 269/275 (97%) Query: 1 MKSQDNLTKEDRKMLRSVFWRSWTMNASRTGATQYHAVGVIYTLLPVINRFYKTDKDKAE 60 M SQDNLTKEDRKMLRSVFWRSWTMNASRTGATQYHAVGVIYTLLPVINRFYKTDKDKAE Sbjct: 1 MTSQDNLTKEDRKMLRSVFWRSWTMNASRTGATQYHAVGVIYTLLPVINRFYKTDKDKAE 60 Query: 61 ALVRHTTWFNATMHINNFIMGLVASMEKKNSEDPDFDASAITAVKASLMGPISGVGDSFF 120- ALVRHTTWFNATMHINNFIMGLVASMEKKNSEDPDFDASAITAVKASLMGPISGVGDSFF Sbjct: 61 ALVRHTTWFNATMHINNFIMGLVASMEKKNSEDPDFDASAITAVKASLMGPISGVGDSFF 120- Query: 121 WGILRVIAAGIGISLASTGSAMGAVVFLLLYNIPAFLIHYYSLYGGYSVGAGFIKKLYES 18- 0 WGILRVIAAGIGISLAS GSAMGAVVFLLLYNIPAF+IHYYSLYGGYSVGAGFIKKLYES Sbjct: 121 WGILRVIAAGIGISLASAGSAMGAVVFLLLYNIPAFIIHYYSLYGGYSVGAGFIKKLYES 18- 0 Query: 181 GGIKIVTKTSSMLGLMMVGSMTASNVKFKTILTVAAKGAKEAASIQSYLDQLFVGVVPLL 24- 0 GGIKIVTKTSSMLGLMMVGSMTASNVKFKTILTVAAKGAKEAASIQ YLDQLF+G+VPL+ Sbjct: 181 GGIKIVTKTSSMLGLMMVGSMTASNVKFKTILTVAAKGAKEAASIQDYLDQLFIGIVPLM 24- 0 Query: 241 VTILAFWLLRKKVNINWIMFGIMVLGIVLGLLGIC 275 VT+ AFWLLRKKVNI WIMFGIM LGI+LGLLGIC Sbjct: 241 VTLAAFWLLRKKVNIIWIMFGIMFLGIILGLLGIC 275 There is also homology to SEQ ID 5236. A further related DNA sequence was identified in S. pyogenes <SEQ ID 9077> which encodes the amino acid sequence <SEQ ID 9078>. An alignment of the GAS and GBS sequences follows: TABLE-US-01589 Score = 178 bits (448), Expect = 3e-47 Identities = 83/136 (61%), Positives = 108/136 (79%) Query: 2 IMEEITIYHNPNCGTSRNVLAMIRHAGIEPTIIEYLQTPPNRETLIELLQSMGISARELL 61 +ME+I IYHNPNCGTSRNVLA+IRH GIEP II YL+TPP+R L+ELL M +SARELL Sbjct: 1 MMEKIRIYHNPNCGTSRNVLAIIRHCGIEPEIIYYLKTPPSRMELVELLLEMKLSARELL 60 Query: 62 RTNVPEFEAYGLANQAVAEKDIINAMLADPILINRPIVVTRKGVKLCRPSETLLDILPVP 121- RT+VP +E + L + +V ++++I+AM+ DPILINRPIVVT KG KLCRP E +L ILPV Sbjct: 61 RTDVPAYEKFNLESSSVTDEEMIDAMIQDPILINRPIVVTSKGAKLCRPCEAILTILPVK 120- Query: 122 LPSPYIKEDGESVNPI 137 + ++KEDG+ + + Sbjct: 121 MEKDFVKEDGQIIQSL 136 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 510 A DNA sequence (GBSx0548) was identified in S. agalactiae <SEQ ID 1633> which encodes the amino acid sequence <SEQ ID 1634>. This protein is predicted to be PTS permease for mannose subunit IIPMan. Analysis of this protein sequence reveals the following: TABLE-US-01590 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.70 Transmembrane 144-160 (140-165) INTEGRAL Likelihood = -8.07 Transmembrane 220-236 (215-239) INTEGRAL Likelihood = -7.27 Transmembrane 95-111 (91-116) INTEGRAL Likelihood = -3.77 Transmembrane 2-18 (1-18) INTEGRAL Likelihood = -1.44 Transmembrane 180-196 (179-196) INTEGRAL Likelihood = -1.33 Transmembrane 32-48 (30-49) INTEGRAL Likelihood = -0.53 Transmembrane 198-214 (198-214) ----- Final Results ----- bacterial membrane --- Certainty = 0.4482(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01591 >GP: AAC44680 GB: U65015 PTS permease for mannose subunit IIPMan [Vibrio furnissii] Identities = 70/251 (27%), Positives = 132/251 (51%), Gaps = 6/251 (2%) Query: 2 IMPATMAALAVLICFGGNYLTGQSMMERPLVVGLVTGMLLGDIKVGILMGASLEALFLGN 61 + A M L + G + G + RP+V+G + G++LGD+ GIL+G +LE +++G Sbjct: 5 LFQALMLGLLAFLA-GLDLFNGLTHFHRPVVLGPLVGLILGDLHTGILVGGTLELIWMGL 63 Query: 62 VNIGGVIAAEPVTATAMATTFTIISNIDQKAAMTLAVPIGMLAAFVVMFLKNVFMNIFAP 121- + G + T + TTF I +N++ A+ +AVP + + L + + + Sbjct: 64 APLAGAQPPNVIIGTIVGTTFAITTNVEPNVAVGVAVPFAVAVQMGITLLFSAMSAVMSK 123- Query: 122 MVDKAAAANHQGKLVMLHYGTWII--YYLIIASISFIGILVGSGPVNSFVHHIPQNLMNG 17- 9 + A A+ +G + ++ ++ +Y + A F+ I +G+ + V +P+ L++G Sbjct: 124 CDEYAKNADTRGIERVNYFALAVLGSFYFLCA---FLPIYLGADHAGAMVAALPKALIDG 18- 0 Query: 180 LSAAGGLLPAVGFAMLMKLLWTNKLAVFYLLGFVLTAYLKLPAVAVAALGAVICVISSQR 23- 9 L AGG++PA+GFA+LMK++ N +++LGFV A+L+LP +A+ + +I R Sbjct: 181 LGVAGGIMPAIGFAVLMKIMMKNAYIPYFILGFVAAAWLQLPILAIRCAATAMAIIDFMR 24- 0 Query: 240 DIELDAITRGA 250 E + A Sbjct: 241 KSEPTPVNASA 251 A related DNA sequence was identified in S. pyogenes <SEQ ID 1635> which encodes the amino acid sequence <SEQ ID 1636>. Analysis of this protein sequence reveals the following: TABLE-US-01592 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.70 Transmembrane 144-160 (140-165) INTEGRAL Likelihood = -8.07 Transmembrane 220-236 (215-239) INTEGRAL Likelihood = -7.27 Transmembrane 95-111 (91-116) INTEGRAL Likelihood = -4.62 Transmembrane 2-18 (1-19) INTEGRAL Likelihood = -1.44 Transmembrane 180-196 (179-196) INTEGRAL Likelihood = -0.96 Transmembrane 32-48 (31-49) INTEGRAL Likelihood = -0.53 Transmembrane 198-214 (198-214) ----- Final Results ----- bacterial membrane --- Certainty = 0.4482(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01593 >GP: AAC44680 GB: U65015 PTS permease for mannose subunit IIPMan [Vibrio furnissii] Identities = 72/251 (28%), Positives = 132/251 (51%), Gaps = 6/251 (2%) Query: 2 LVPATMAALAVLICFGGNYLTGQSMMERPLVVGLVTGLLLGDMKVGILMGASLEALFLGN 61 L A M L + G + G + RP+V+G + GL+LGD+ GIL+G +LE +++G Sbjct: 5 LFQALMLGLLAFLA-GLDLFNGLTHFHRPVVLGPLVGLILGDLHTGILVGGTLELIWMGL 63 Query: 62 VNIGGVIAAEPVTATAMATTFTIISHIDQKAAMTLAVPIGMLAAFVVMFLKNVFMNIFAP 121- + G + T + TTF I ++++ A+ +AVP + + L + + + Sbjct: 64 APLAGAQPPNVIIGTIVGTTFAITTNVEPNVAVGVAVPFAVAVQMGITLLFSAMSAVMSK 123- Query: 122 MVDKAAAANHQGKLVMLHYGTWII--YYLIIASISFIGILVGSGPVNAFVEHIPQNLMNG 17- 9 + A A+ +G + ++ ++ +Y + A F+ I +G+ A V +P+ L++G Sbjct: 124 CDEYAKNADTRGIERVNYFALAVLGSFYFLCA---FLPIYLGADHAGAMVAALPKALIDG 18- 0 Query: 180 LSAAGGLLPAVGFAMLMKLLWTNKLAVFYLLGFVLTAYLKLPAVAVAALGAVICVISSQR 23- 9 L AGG++PA+GFA+LMK++ N +++LGFV A+L+LP +A+ + +I R Sbjct: 181 LGVAGGIMPAIGFAVLMKIMMKNAYIPYFILGFVAAAWLQLPILAIRCAATAMAIIDFMR 24- 0 Query: 240 DLELDAITRGA 250 E + A Sbjct: 241 KSEPTPVNASA 251 An alignment of the GAS and GBS proteins is shown below:

TABLE-US-01594 Identities = 261/269 (97%), Positives = 268/269 (99%) Query: 1 MIMPATMAALAVLICFGGNYLTGQSMMERPLVVGLVTGMLLGDIKVGILMGASLEALFLG 60 M++PATMAALAVLICFGGNYLTGQSMMERPLVVGLVTG+LLGD+KVGILMGASLEALFLG Sbjct: 1 MLVPATMAALAVLICFGGNYLTGQSMMERPLVVGLVTGLLLGDMKVGILMGASLEALFLG 60 Query: 61 NVNIGGVIAAEPVTATAMATTFTIISNIDQKAAMTLAVPIGMLAAFVVMFLKNVFMNIFA 120- NVNIGGVIAAEPVTATAMATTFTIIS+IDQKAAMTLAVPIGMLAAFVVMFLKNVFMNIFA Sbjct: 61 NVNIGGVIAAEPVTATAMATTFTIISHIDQKAAMTLAVPIGMLAAFVVMFLKNVFMNIFA 120- Query: 121 PMVDKAAAANHQGKLVMLHYGTWIIYYLIIASISFIGILVGSGPVNSFVHHIPQNLMNGL 18- 0 PMVDKAAAANHQGKLVMLHYGTWIIYYLIIASISFIGILVGSGPVN+FV HIPQNLMNGL Sbjct: 121 PMVDKAAAANHQGKLVMLHYGTWIIYYLIIASISFIGILVGSGPVNAFVEHIPQNLMNGL 18- 0 Query: 181 SAAGGLLPAVGFAMLMKLLWTNKLAVFYLLGFVLTAYLKLPAVAVAALGAVICVISSQRD 24- 0 SAAGGLLPAVGFAMLMKLLWTNKLAVFYLLGFVLTAYLKLPAVAVAALGAVICVISSQRD Sbjct: 181 SAAGGLLPAVGFAMLMKLLWTNKLAVFYLLGFVLTAYLKLPAVAVAALGAVICVISSQRD 24- 0 Query: 241 IELDAITRGAISKQTTFDSKESEEEDFFA 269 +ELDAITRGAISKQTTFDSKESEEEDFFA Sbjct: 241 LELDAITRGAISKQTTFDSKESEEEDFFA 269 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 511 A DNA sequence (GBSx0549) was identified in S. agalactiae <SEQ ID 1637> which encodes the amino acid sequence <SEQ ID 1638>. This protein is predicted to be pts system, sorbose-specific iib component. Analysis of this protein sequence reveals the following: TABLE-US-01595 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1874(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01596 >GP: CAA46858 GB: X66059 EIII-B Sor PTS [Klebsiella pneumoniae] Identities = 49/158 (31%), Positives = 94/158 (59%), Gaps = 8/158 (5%) Query: 2 ITQIRVDDRLIHGQVAVVWTKELNAPLLVVANDEAAKNEITQMTLKMAVPNGMKLLIRSV 61 IT R+DDRLIHGQV VW+K NA +++ ND+ +E+ + L+ A P GMK+ + S+ Sbjct: 3 ITLARIDDRLIHGQVTTVWSKVANAQRIIICNDDVFNDEVRRTLLRQAAPPGMKVNVVSL 62 Query: 62 EESIALFKDPRATDKRIFVIVNSVKDACTIAKNITDLEAVNVANVGRFDKSDPATKVKLT 121- E+++A++ +P+ D+ +F + + D T+ + + +N+ + + K +LT Sbjct: 63 EKAVAVYHNPQYQDETVFYLFTNPHDVLTMVRQGVQIATLNIGGM-----AWRPGKKQLT 117- Query: 122 SSLLLNTEELEAAKELASL-PDLDVFNQVLPSNTKVNL 158 ++ L+ ++++A +EL L LD+ +V+ S+ VN+ Sbjct: 118 KAVSLDPQDIQAFRELDKLGVKLDL--RVVASDPSVNI 153 A related DNA sequence was identified in S. pyogenes <SEQ ID 1639> which encodes the amino acid sequence <SEQ ID 1640>. Analysis of this protein sequence reveals the following: TABLE-US-01597 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1874(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01598 Identities = 145/162 (89%), Positives = 152/162 (93%) Query: 1 MITQIRVDDRLIHGQVAVVWTKELNAPLLVVANDEAAKNEITQMTLKMAVPNGMKLLIRS 60 MITQIRVDDRLIHGQVAVVWTKELNAPLLVVANDEAAKNEITQMTLKMAVPNGMKLLIRS Sbjct: 1 MITQIRVDDRLIHGQVAVVWTKELNAPLLVVANDEAAKNEITQMTLKMAVPNGMKLLIRS 60 Query: 61 VEESIALFKDPRATDKRIFVIVNSVKDACTIAKNITDLEAVNVANVGRFDKSDPATKVKL 120- VE+SI LF DPRA DKRIFVIVNSVKDAC IAK + DLEAVNVANVGRFDKSDPA+KVK+ Sbjct: 61 VEDSIKLFNDPRAKDKRIFVIVNSVKDACAIAKEVPDLEAVNVANVGRFDKSDPASKVKV 120- Query: 121 TSSLLLNTEELEAAKELASLPDLDVFNQVLPSNTKVNLSQLV 162 T SLLLN EE+ AAKEL SLP+LDVFNQVLPSNTKV+LSQLV Sbjct: 121 TPSLLLNPEEMAAAKELVSLPELDVFNQVLPSNTKVHLSQLV 162 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 512 A DNA sequence (GBSx0550) was identified in S. agalactiae <SEQ ID 1641> which encodes the amino acid sequence <SEQ ID 1642>. Analysis of this protein sequence reveals the following: TABLE-US-01599 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.22 Transmembrane 87-103 (87-104) ----- Final Results ----- bacterial membrane --- Certainty = 0.1489(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1643> which encodes the amino acid sequence <SEQ ID 1644>. Analysis of this protein sequence reveals the following: TABLE-US-01600 Possible site: 33 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.44 Transmembrane 87-103 (87-104) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below: TABLE-US-01601 Identities = 115/141 (81%), Positives = 125/141 (88%) Query: 1 MKRKFLIGSHGKLASGLQSSIDILTGKGQEIQTIDAYIDDSDYTKSIVEFIDEIAPDEQG 60 MKRKFLIGSHG+LASGLQSSIDIL G GQ ++TIDAY+DDSDYT I +FI +A DEQG Sbjct: 1 MKRKFLIGSHGRLASGLQSSIDILAGMGQALETIDAYVDDSDYTSQIDDFIAGVAADEQG 60 Query: 61 LIFTDLLGGSVNQKMATAVMNSGKNNIFLITNSNLATLLSLLFLKPEEELTKEEIVTVIN 120- LIFTDLLGGSVNQKM TAVMNSGK+NIFLITNSNLATLLSL+FLKP E LTK+EIVTVIN Sbjct: 61 LIFTDLLGGSVNQKMVTAVMNSGKDNIFLITNSNLATLLSLVFLKPGEALTKDEIVTVIN 120- Query: 121 ESQVQLVDLSFKAGSEDDFFD 141 ESQVQLVDL + SEDDFFD Sbjct: 121 ESQVQLVDLVPETNSEDDFFD 141 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 513 A DNA sequence (GBSx0551) was identified in S. agalactiae <SEQ ID 1645> which encodes the amino acid sequence <SEQ ID 1646>. Analysis of this protein sequence reveals the following: TABLE-US-01602 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2469(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 514 A DNA sequence (GBSx0552) was identified in S. agalactiae <SEQ ID 1647> which encodes the amino acid sequence <SEQ ID 1648>. This protein is predicted to be racemase. Analysis of this protein sequence reveals the following: TABLE-US-01603 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.65 Transmembrane 319-335 (316-339) INTEGRAL Likelihood = -6.10 Transmembrane 18-34 (17-37) INTEGRAL Likelihood = -5.68 Transmembrane 230-246 (227-248) INTEGRAL Likelihood = -3.98 Transmembrane 254-270 (254-271) INTEGRAL Likelihood = -3.56 Transmembrane 110-126 (110-129) INTEGRAL Likelihood = -3.19 Transmembrane 161-177 (156-177) INTEGRAL Likelihood = -1.97 Transmembrane 132-148 (132-153) INTEGRAL Likelihood = -1.33 Transmembrane 286-302 (286-302) INTEGRAL Likelihood = -0.59 Transmembrane 53-69 (52-69) ----- Final Results ----- bacterial membrane --- Certainty = 0.4461(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01604 >GP: AAF71283 GB: AF253562 racemase [Enterococcus faecalis] Identities = 78/262 (29%), Positives = 129/262 (48%), Gaps = 29/262 (11%) Query: 13 KQHNTSMISLLQYLFSILVILVHSGRLFS-QDVIHFTFKSFLGRMAVPYFLICTAFFLRG 71 - K + S I +++ ++L++ +H+ LFS + +F F + +AVP+F + + FFL Sbjct: 3 KNESYSGIDYFRFIAALLIVAIHTSPLFSFSETGNFIFTRIVAPVAVPFFFMTSGFFL-- 60 Query: 72 RIQQGLCNHSYFRKLIKK----YSMWTIIYLPY----GYFFFESLNIAKIYLLPGFIVAF 123- I + CN IKK Y + ++Y+P GYF ++L LP I Sbjct: 61 -ISRYTCNAEKLGAFIKKTTLIYGVAILLYIPINVYNGYFKMDNL-------LPNIIKDI 112- Query: 124 LYLGMSHTLWYIPAVILGWVIIQGLLKYVGTRGTFITVVVLYCIGAV-ETYSVFIQSTKF 18- 2 ++ G + LWY+PA I+G I L+K V R F+ +LY IG ++Y ++S Sbjct: 113 VFDGTLYHLWYLPASIIGAAIAWYLVKKVHYRKAFLIASILYIIGLFGDSYYGIVKSVSC 17- 2 Query: 183 YPLMSTYMSIFQT---TRNGLFYTPVYLLAGYLLYDYFNTDLFTKSRGLK-YILFLLLLA 23- 8 L Y IFQ TRNG+F+ P++ + G + D + + + K ++ Y LF L+ Sbjct: 173 --LNVFYNLIFQLTDYTRNGIFFAFIFFVLGGYISD--SPNRYRKKNYIRIYSLFCLMFG 22- 8 Query: 239 LENVLIYFN-QGLDKNFFLLAP 259 L +F+ Q D + LL P Sbjct: 229 KTLTLQHFDIQKHDSMYVLLLP 250 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8589> and protein <SEQ ID 8590> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01605 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: 0.23 GvH: Signal Score (-7.5): -5.77 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 3 value: -5.68 threshold: 0.0 INTEGRAL Likelihood = -5.68 Transmembrane 41-57 (38-59) INTEGRAL Likelihood = -3.98 Transmembrane 65-81 (65-82) INTEGRAL Likelihood = -1.33 Transmembrane 97-113 (97-113) PERIPHERAL Likelihood = 5.78 10 modified ALOM score: 1.64 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3272(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm = Certainty = 0.0000(Not Clear) < succ> A related GBS gene <SEQ ID 8591> and protein <SEQ ID 8592> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01606 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: 11.50 GvH: Signal Score (-7.5): -2.69 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 9 value: -8.65 threshold: 0.0 INTEGRAL Likelihood = -8.65 Transmembrane 310-326 ( 307-330) INTEGRAL Likelihood = -6.10 Transmembrane 9-25 ( 8-28) INTEGRAL Likelihood = -5.68 Transmembrane 221-237 ( 218-239) INTEGRAL Likelihood = -3.98 Transmembrane 245-261 ( 245-262) INTEGRAL Likelihood = -3.56 Transmembrane 101-117 ( 101-120) INTEGRAL Likelihood = -3.19 Transmembrane 152-168 ( 147-168) INTEGRAL Likelihood = -1.97 Transmembrane 123-139 ( 123-144) INTEGRAL Likelihood = -1.33 Transmembrane 277-293 ( 277-293) INTEGRAL Likelihood = -0.59 Transmembrane 44-60 ( 43-60) PERIPHERAL Likelihood = 5.78 190 modified ALOM score: 2.23 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4461(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00039## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 515 A DNA sequence (GBSx0553) was identified in S. agalactiae <SEQ ID 1649> which encodes the amino acid sequence <SEQ ID 1650>. Analysis of this protein sequence reveals the following: TABLE-US-01607 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3088(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 516 A DNA sequence (GBSx0554) was identified in S. agalactiae <SEQ ID 1651> which encodes the amino acid sequence <SEQ ID 1652>. Analysis of this protein sequence reveals the following: TABLE-US-01608 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1446(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 517 A DNA sequence (GBSx0555) was identified in S. agalactiae <SEQ ID 1653> which encodes the amino acid sequence <SEQ ID 1654>. Analysis of this protein sequence reveals the following: TABLE-US-01609 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 8.28 GvH: Signal Score (-7.5): -2.11 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 6 value: -8.33 threshold: 0.0 INTEGRAL Likelihood = -8.33 Transmembrane 358-374 (354-376) INTEGRAL Likelihood = -8.23 Transmembrane 264-280 (257-290) INTEGRAL Likelihood = -6.37 Transmembrane 210-226 (206-232) INTEGRAL Likelihood = -5.95 Transmembrane 163-179 (160-180) INTEGRAL Likelihood = -5.10 Transmembrane 23-39 (21-40) INTEGRAL Likelihood = -1.70 Transmembrane 297-313 (296-314) PERIPHERAL Likelihood = 1.75 322 modified ALOM score: 2.17 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4333(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 518 A DNA sequence (GBSx0556) was identified in S. agalactiae <SEQ ID 1655> which encodes the amino acid sequence <SEQ ID 1656>. This protein is predicted to be ABC transporter (ATP-bindingprot). Analysis of this protein sequence reveals the following: TABLE-US-01610 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1510(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10199> which encodes amino acid sequence <SEQ ID 10200> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01611 >GP: CAB88481 GB: AL353816 putative ABC transport system ATP-binding protein [Streptomyces coelicolor A3(2)] Identities = 104/284 (36%), Positives = 159/284 (55%), Gaps = 18/284 (6%) Query: 6 TMLLQLDNITKSYGKKIVLNQISYQFTPGLYGLLGANGTGKTTLLNLMSHFTLADSGNIY 65 T + ++ YG+ L+ +S + TPG+ GLLG NG GKTTLL +++ AD G Sbjct: 2 TPTVSASGLSLHYGRTRALDDVSLRLTPGVTGLLGPNGAGKTTLLRVLATAVPADRGAFT 61 Query: 66 WNGQEQS-----EEFYRHIGFLPQHFRYYDQFTGIAFLNYIATLKGV-DKKKAKQEIPRL 119- G + +E R +G+LPQ ++ FT F++Y+A LK + D+++ +E+ R+ Sbjct: 62 VLGHDPGSSRGRQEVRRRLGYLPQTPGFHPDFTAFEFVDYVAILKELADRRERHREVRRV 121- Query: 120 LELVGLGDVGKKKISSYSGGMKQRLGIAQALINDPEILILDEPTVGLDPKERVKFRHILS 17- 9 LE V LG+V ++I SGGM+QR+ +A AL+ DP L+LDEPTVGLDP++R++FR +++ Sbjct: 122 LEEVDLGEVRGRRIKKLSGGMRQRVALAAALVGDPGFLVLDEPTVGLDPEQRMRFRELIA 18- 1 Query: 180 QLSTNKIIILSTHIVSDVEAVAKEIIVLKNGKFIEHGNTAQLLKTIEGKVWEIT-TEPGL 23- 8 + ++LSTH DV + +IV+ G G A+L G+VW T +PG Sbjct: 182 GAGEGRTVLLSTHQTEDVAMLCHRVIVMAAGAVRFDGTPAELTARAAGRVWSSTEKDPG- 24- 0 Query: 239 SQIPNIAIVNEKVFSDSRVFRVVSDICPSDSAQLVVPTLEDFYI 282 A + + S FR V D P A+ PTLED Y+ Sbjct: 241 ------AKAGWRTGTGS--FRNVGD--PPPGAEPAEPTLEDGYL 274 There is also homology to SEQ ID 686. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 519 A DNA sequence (GBSx0557) was identified in S. agalactiae <SEQ ID 1657> which encodes the amino acid sequence <SEQ ID 1658>. This protein is predicted to be response regulator. Analysis of this protein sequence reveals the following: TABLE-US-01612 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3781(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(N0t Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01613 >GP: CAC10170 GB: AJ278301 response regulator [Streptococcus pneumoniae] Identities = 136/242 (56%), Positives = 183/242 (75%) Query: 1 MNIFILEDDFVQQAHFEKIIKEIRVQYNLHFKTVETFAKPVQLLESIYEIGLHNLFFLDI 60 M IF+LEDDF QQ E I+++ ++++ + E F KP QLL ++E G H LFFLDI Sbjct: 1 MRIFVLEDDFSQQTRIETTIEKLLKEHHITLSSFEVFGKPDQLLAEVHEKGAHQLFFLDI 60 Query: 61 EIKNDSQMGLSVAKQIRQVDPYAQIVFVTTHSELMPLTFRYQVSALDYIDKGLSQEEFSQ 120- EI+N+E GLEVA++IR+ DPYA IVFVTTHSE MPL+FRYQVSALDYIDK LS EEF Sbjct: 61 EIRNEEMKGLEVARKIREQDPYALIVFVTTHSEFMPLSFRYQVSALDYIDKALSAEEFES 120- Query: 121 RIEEVLLYVDGICNKPLVENSFYFKSRYSQVQLPFNDLLYIETSSRSHRVVLYTEKDRME 18- 0 RIE LLY + +K L E+ FYFKS+++Q Q PF ++ Y+ETS R HRV+LYT+ DR+E Sbjct: 121 RIETALLYANSQDSKSLAEDCFYFKSKFAQFQYPFKEVYYLETSPRPHRVILYTKTDRLE 18- 0 Query: 181 FTATLGDILKQEPRLFQCHRSFLVNPLNIFKVDRIDRLVYFQNGTTCLVSRNKVRDIVSI 24- 0 FTA+L ++ KQEPRL QCHRSFL+NP N+ +D+ ++L++F NG +CL++R KVR++ Sbjct: 181 FTASLEEVFKQEPRLLQCHRSFLINPANVVHLDKKEKLLFFPNGGSCLIARYKVREVSEA 24- 0 Query: 241 VD 242 ++ Sbjct: 241 IN 242 A related DNA sequence was identified in S. pyogenes <SEQ ID 1659> which encodes the amino acid sequence <SEQ ID 1660>. Analysis of this protein sequence reveals the following:

TABLE-US-01614 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2098(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01615 Identities = 106/235 (45%), Positives = 159/235 (67%) Query: 1 MNIFILEDDFVQQAHFEKIIKEIRVQYNLHFKTVETFAKPVQLLESIYEIGLHNLFFLDI 60 MNIFILEDDF+QQ E I+ I + + +E F+ P +L ESI E G H L+FLDI Sbjct: 2 MNIFILEDDFIQQTRIESIVVGILKETRIPCNQLEVFSTPQKLFESIQERGDHQLYFLDI 61 Query: 61 EIKNDEQMGLEVAKQIRQVDPYAQIVFVTTHSELMPLTFRYQVSALDYIDKGLSQEEFSQ 120- EI + GLE+A IRQ DP A IVFVTTHSE P++F+Y+VSALD+IDK Q++F + Sbjct: 62 EIGEYTRCGLELAAAIRQKDPNAVIVFVTTHSEFAPISFKYKVSALDFIDKAGGQKQFKE 121- Query: 121 RIEEVLLYVDGICNKPLVENSFYFKSRYSQVQLPFNDLLYIETSSRSHRVVLYTEKDRME 18- 0 +IEE + Y + + ++ F F++ ++++LP+ D+LY T++ H+V L+T+ +R+E Sbjct: 122 QIEECIRYTYDMMSSRESKDMFLFETPQTRLKLPYKDILYFATATTPHKVCLWTQTERLE 18- 1 Query: 181 FTATLGDILKQEPRLFQCHRSFLVNPLNIFKVDRIDRLVYFQNGTTCLVSRNKVR 235 F L +I P+LF CHRS+LVN + ++D+ +L+YF+NG +C+VSR K++ Sbjct: 182 FYGNLSEIQAVAPKLFLCHRSYLVNLDKVVRIDKSKQLLYFENGDSCMVSRLKMK 236 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 520 A DNA sequence (GBSx0558) was identified in S. agalactiae <SEQ ID 1661> which encodes the amino acid sequence <SEQ ID 1662>. Analysis of this protein sequence reveals the following: TABLE-US-01616 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2651(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1663> which encodes the amino acid sequence <SEQ ID 1664>. Analysis of this protein sequence reveals the following: TABLE-US-01617 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0535(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01618 Identities = 177/269 (65%), Positives = 219/269 (80%) Query: 6 MAKCLTLNTHSWMEVNALKKLFDLAEHIFREKYDIICLQEVNQSISSPLAKSSPNYHPIE 65 M K LTLNTHSWM+ N LKKL LAEHI EKYDIICLQE+NQ I S LA P Y + Sbjct: 1 MTKVLTLNTHSWMQANTLKKLVALAEHILAEKYDIICLQEINQLIESELATDLPRYQALS 60 Query: 66 GTPALHQDNFALQLVHYLNLQGLHYHWTWAYNHIGYSKYHEGVAILSLKPLKPEDILVSA 125- GTP++H+D+FAL L+HYL +G HY+W+WAYNHIGY Y EGVAILS +P+ DILVSA Sbjct: 61 GTPSIHKDHFALLLIHYLQKRGQHYYWSWAYNHIGYDIYQEGVAILSKQPIHVSDILVSA 120- Query: 126 VDDETDYHTRRALVAETTLNDKVVTVVSLHFSWFEKGFAEEWKRLETTLLEVETPLLLMG 18- 5 +DDETDYHTRR+L+A+TTL+ K V VV++H SWF+KGF EW++LE LL + PLLLMG Sbjct: 121 MDDETDYHTRRSLIAKTTLDGKEVAVVNVHLSWFDKGFLGEWEKLEKELLTLNCPLLLMG 18- 0 Query: 186 DFNNPTGNQGYELVLNSPLALKDSHQIANHVFGDHTIMADIDGWEGNKKALKVDHIFTSE 24- 5 DFNNPT GY++++ SPL L+DSH+ A+HVFGDH+I+ADIDGW+GNK+ALKVDH+FTS+ Sbjct: 181 DFNNPTDQDGYQVMMGSPLDLQDSHKGADHVFGDHSIVADIDGWQGNKEALKVDHVFTSK 24- 0 Query: 246 DLSISSSQVVFEGGEAPVVSDHYGLEITM 274 D I SS++ FEGG+APVVSDHYGLE+T+ Sbjct: 241 DFIIRSSKITFEGGDAPVVSDHYGLEVTL 269 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 521 A DNA sequence (GBSx0559) was identified in S. agalactiae <SEQ ID 1665> which encodes the amino acid sequence <SEQ ID 1666>. This protein is predicted to be PTS system, glucose-specific enzyme 11, A component (ptsG). Analysis of this protein sequence reveals the following: TABLE-US-01619 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.07 Transmembrane 193-209 (189-217) INTEGRAL Likelihood = -7.86 Transmembrane 28-44 (24-48) INTEGRAL Likelihood = -6.48 Transmembrane 431-447 (421-449) INTEGRAL Likelihood = -2.92 Transmembrane 153-169 (153-170) INTEGRAL Likelihood = -2.81 Transmembrane 93-109 (93-111) INTEGRAL Likelihood = -2.39 Transmembrane 370-386 (370-388) INTEGRAL Likelihood = -2.28 Transmembrane 68-84 (68-84) ----- Final Results ----- bacterial membrane --- Certainty = 0.4227(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10201> which encodes amino acid sequence <SEQ ID 10202> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01620 >GP: AAD00281 GB: U78600 putative ptsG protein [Streptococcus mutans] Identities = 294/409 (71%), Positives = 342/409 (82%), Gaps = 7/409 (1%) Query: 293 DLINLKGS-NSSQYHHLLTSVTPARFKVGQMIGASGILMGLSYAMYRNVDKDKKLKYKSM 35- 1 DLI+LKG+ + SQYHHLLTSVTPARFKVGQMIG+SGILMGL+ AMYRNVD DKK KYK M Sbjct: 3 DLIHLKGAGHMSQYHHLLTSVTPARFKVGQMIGSSGILMGLTLAMYRNVDPDKKEKYKGM 62 Query: 352 FISAAAATFLTGVTEPIEYMFMFAAMPLYLVYAVVQGCAFAMADIVNLRVHSFGNIEFLT 41- 1 F+SAA A FLTGVTEP+EYMFMFAA+PLYLVYAVVQG AFA AD+++LRVHSFGNIEFLT Sbjct: 63 FLSAAVAVFLTGVTEPLEYMFMFAALPLYLVYAVVQGLAFASADLIHLRVHSFGNIEFLT 122- Query: 412 RVPMGIKAGLGGDIFNFVWVTLLFAVLMYFIANFMIKKFNLATAGRNGNYDNEEVDNAPS 47- 1 + PM IKAGL DI NF+ V+++F V MYFI NFMIKKFNLAT+GRNGNYD + D + Sbjct: 123 KTPMAIKAGLAMDIVNFIVVSVVFGVAMYFITNFMIKKFNLATSGRNGNYDTGD-DASDE 18- 1 Query: 472 TAS----GSADANSQVVQVINLLGGRDNIEDVDACMTRLRVTVKDGNSVGSEAAWKKAGA 52- 7 TAS G+A+ANSQ+V++INLLGG++NI DVDACMTRLR+TV D VG EAAWKKAGA Sbjct: 182 TASNSNAGTANANSQIVKIINLLGGKENISDVDACMTRLRITVTDVAKVGDEAAWKKAGA 24- 1 Query: 528 MGLVLKGNGVQAIYGPKADVLKSDIQDLLDSGTVIPIVDLETGQPVAAAPVTTYKGITEE 58- 7 MGL++KGNGVQA+YGPKADVLKSDIQDLLDSG IP D+ + A V ++KG+TEE Sbjct: 242 MGLIVKGNGVQAVYGPKADVLKSDIQDLLDSGVDIPKTDVTAPEEDKTADV-SFKGVTEE 30- 0 Query: 588 IVSVANGQVEALDVVKDPVFSQKMMGDGFAVEPTDGNIYVPVSGTVTSVFPTKHAFGLLT 64- 7 + +VA+GQV + V DPVFSQKMMGDGFAVEP +GNIY PV+G VTSVFPTKHA GLLT Sbjct: 301 VATVADGQVLPITQVHDPVFSQKMMGDGFAVEPENGNIYSPVAGLVTSVFPTKHALGLLT 36- 0 Query: 648 ESGLEVLVHIGLDTVALDGQPFEVKISSGQKVVAGDLAVVADLEAIKAA 696 + GLEVLVH+GLDTVAL+G PF K+ GQ+V GDL +VADLEAIK+A Sbjct: 361 DDGLEVLVHVGLDTVALNGAPFSAKVKDGQRVALGDLLLVADLEAIKSA 409 A related DNA sequence was identified in S. pyogenes <SEQ ID 1667> which encodes the amino acid sequence <SEQ ID 1668>. Analysis of this protein sequence reveals the following: TABLE-US-01621 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -13.43 Transmembrane 186-202 (181-213) INTEGRAL Likelihood = -6.79 Transmembrane 419-435 (412-442) INTEGRAL Likelihood = -5.52 Transmembrane 61-77 (57-82) INTEGRAL Likelihood = -3.56 Transmembrane 363-379 (363-381) INTEGRAL Likelihood = -1.97 Transmembrane 143-159 (142-160) INTEGRAL Likelihood = -0.16 Transmembrane 343-359 (343-359) ----- Final Results ----- bacterial membrane --- Certainty = 0.6371(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01622 >GP: AAD00281 GB: U78600 putative ptsG protein [Streptococcus mutans] Identities = 288/407 (70%), Positives = 331/407 (80%), Gaps = 2/407 (0%) Query: 286 DLVHLKGSD-ASAYSHLMDSVTPARFKVGQHIGATGTLMGVALAMYRNVDADKKHTYKMM 34- 4 DL+HLKG+ S Y HL+ SVTPARFKVGQMIG++G LMG+ LAMYRNVD DKK YK M Sbjct: 3 DLIHLKGAGHMSQYHHLLTSVTPARFKVGQMIGSSGILMGLTLAMYRNVDPDKKEKYKGM 62 Query: 345 FISAAAAVFLTGVTEPLEYLFMFAAMPLYIVYALVQGASFAMADLVNLRVHSFGNIELLT 40- 4 F+SAA AVFLTGVTEPLEY+FMFAA+PLY+VYA+VQG +FA ADL++LRVHSFGNIE LT Sbjct: 63 FLSAAVAVFLTGVTEPLEYMFMFAALPLYLVYAVVQGLAFASADLIHLRVHSFGNIEFLT 122- Query: 405 RTPMALKAGLGMDVINFVWVSVLFAVIMYFIADMMIKKMHLATAGRLGNYDA-DILGDRN 46- 3 +TPMA+KAGL MD++NF+ VSV+F V MYFI + MIKK +LAT+GR GNYD D D Sbjct: 123 KTPMAIKAGLAMDIVNFIVVSVVFGVANMFITNFMIKKFNLATSGRNGNYDTGDDASDET 18- 2 Query: 464 TQTRPTQVADSNSQVVQIVNLLGGAGNIDDVDACMTRLRVTVKDPAKVGAEDDWKKAGAI 52- 3 A++NSQ+V+I+NLLGG NI DVDACMTRLR+TV D AKVG E WKKAGA+ Sbjct: 183 ASNSNAGTANANSQIVKIINLLGGKENISDVDACMTRLRITVTDVAKVGDEAAWKKAGAM 24- 2 Query: 524 GLIQKGNGVQAVYGPKADILKSDIQDLLDSGALIPEVNMSQLTSKPTPAKDFKHVTEDVL 58- 3 GLI KGNGVQAVYGPKAD+LKSDIQDLLDSG IP+ +++ T FK VTE+V Sbjct: 243 GLIVKGNGVQAVYGPKADVLKSDIQDLLDSGVDIPKTDVTAPEEDKTADVSFKGVTEEVA 30- 2 Query: 584 SVADGMVLPITGVKDQVFAAKMMGDGFAVEPTHGNIYAPVAGLVTSVFPTKHAFGLLTDN 64- 3 +VADG VLPIT V D VF+ KMMGDGFAVEP +GNIY+PVAGLVTSVFPTKHA GLLTD+ Sbjct: 303 TVADGQVLPITQVHDPVFSQKMMGDGFAVEPENGNIYSPVAGLVTSVFPTKHALGLLTDD 36- 2 Query: 644 GLEVLVHVGLDTVALNGVPFSVKVSEGQRVHAGDLLVVADLAAIKSA 690 GLEVLVHVGLDTVALNG PFS KV +GQRV GDLL+VADL AIKSA Sbjct: 363 GLEVLVHVGLDTVALNGAPFSAKVKDGQRVALGDLLLVADLEAIKSA 409 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01623 Identities = 517/731 (70%), Positives = 606/731 (82%), Gaps = 7/731 (0%) Query: 8 MKNNVKQLFSFEFWQKFGKALMVVIAVMPAAGLMVSIGNSISLLDPSNVLLGRIANVIAQ 67 MK + KQLF FEFWQKFGK LMVVIAVNPAAGLM+SIGNSI +++ + L + N+IAQ Sbjct: 1 MKTSFKQLFRFEFWQKFGKCLMVVIAVMPAAGLMINIGMSIPMINHDSAFLASLGNIIAQ 60 Query: 68 IGWGVIGNLHILFALAIGGSWAKERAGGAFAAGLSFILINLITGNFFGVKTDMLADSKAT 127- IGW VI NLH+LFALAIGGSWAKERAGGAFA+GL+F+LIN ITG F+GV + MLAD +A Sbjct: 61 IGWAVIVNLHLLFALAIGGSWAKERAGGAFASGLAFVLINRITGAFYGVSSTMLADPEAK 120- Query: 128 VQTVFGATIRVSDYFVNVLGQPALNMGVFVGIISGFVGATAFNKYYNYRKLPDALTFFNG 18- 7 + ++ G + V DYF +VL PALN GVFVGII+GFVGATA+NKYYNYRKLP+ LTFFNG Sbjct: 121 ITSLLGTQMIVKDYFTSVLESPALNTGVFVGIIAGFVGATAYNKYYNYRKLPEVLTFFNG 18- 0 Query: 188 KRFVPFVVIYRSVIVALILSVFWPVVQSGINGFGKWIASSQDSAPILAPFVYGTLERLLL 24- 7 KRFVPFVVI RS+ VALIL V WPV+QSGIN FG WIASSQDSAPILAPF+YGTLERLLL Sbjct: 181 KRFVPFVVILRSIFVALILVVVWPVIQSGINSFGMWIASSQDSAPILAPFLYGTLERLLL 24- 0 Query: 248 PFGLHHMLTIPMNYTQLGGTYTVLTGATKGAQVLGQDPLWLAWVGDLINLKGSNSSQYHH 30- 7 PFGLHHMLTIPMNYT LGGTY V+TGA G +V GQDPLWLAWV DL++LKGS++S Y H Sbjct: 241 PFGLHHMLTIPMNYTALGGTYEVMTGAAAGTKVFGQDPLWLAWVTDLVHLKGSDASAYSH 30- 0 Query: 308 LLTSVTPARFKVGQMIGASGILMGLSYAMYRNVDKDKKLKYKSMFISAAAATFLTGVTEP 36- 7 L+ SVTPARFKVGQMIGA+G LMG++ AMYRNVD DKK YK MFISAAAA FLTGVTEP Sbjct: 301 LMDSVTPARFKVGQMIGATGTLMGVALAMYRNVDADKKHTYKMMFISAAAAVFLTGVTEP 36- 0 Query: 368 IEYMFMFAAMPLYLVYAVVQGCAFAMADIVNLRVHSFGNIEFLTRVPMGIKAGLGGDIFN 42- 7 +EY+FMFAAMPLY+VYA+VQG +FAMAD+VNLRVHSFGNIE LTR PM +KAGLG D+ N Sbjct: 361 LEYLFMFAAMPLYIVYALVQGASFAMADLVNLRVHSFGNIELLTRTPMALKAGLGMDVIN 42- 0 Query: 428 FVWVTLLFAVLMYFIANFMIKKFNLATAGRNGNYDNEEVD--NAPSTASGSADANSQVVQ 48- 5 FVWV++LFAV+MYFIA+ MIKK +LATAGR GNYD + + N + + AD+NSQVVQ Sbjct: 421 FVWVSVLFAVIMYFIADMMIRKMHLATAGRLGNYDADILGDRNTQTRPTQVADSNSQVVQ 48- 0 Query: 486 VINLLGGRDNIEDVDACMTRLRVTVKDGNSVGSEAAWKKAGAMGLVLKGNGVQAIYGPKA 54- 5 ++NLLGG NI+DVDACMTRLRVTVKD VG+E WKKAGA+GL+ KGNGVQA+YGPKA Sbjct: 481 IVNLLGGAGNIDDVDACMTRLRVTVKDPAKVGAEDDWKKAGAIGLIQKGNGVQAVYGPKA 54- 0 Query: 546 DVLKSDIQDLLDSGTVIPIVDLE--TGQPVAAAPVTTYKGITEEIVSVANGQVEALDVVK 60- 3 D+LKSDIQDLLDSG +IP V++ T +P P +K +TE+++SVA+G V + VK Sbjct: 541 DILKSDIQDLLDSGALIPEVNMSQLTSKP---TPAKDFKHVTEDVLSVADGMVLPITGVK 59- 7 Query: 604 DPVFSQKMMGDGFAVEPTDGNIYVPVSGTVTSVFPTKHAFGLLTESGLEVLVHIGLDTVA 66- 3 D VF+ KMMGDGFAVEPT GNIY PV+G VTSVFPTKHAFGLLT++GLEVLVH+GLDTVA Sbjct: 598 DQVFAAKMMGDGFAVEPTHGNIYAPVAGLVTSVFPTKHAFGLLTDNGLEVLVHVGLDTVA 65- 7 Query: 664 LDGQPFEVKISSGQKVVAGDLAVVADLEAIKAAGKETSVIIVFTNVSDIKTVKLEKSGPQ 72- 3 L+G PF VK+S GQ+V AGDL VVADL AIK+A +ET +++ FTN ++I+ V L G Q Sbjct: 658 LNGVPFSVKVSEGQRVHAGDLLVVADLAAIKSAERETIIVVAFTNTTEIQDVTLTSLGAQ 71- 7 Query: 724 IAKTVVAKVEL 734 AKT VA VEL Sbjct: 718 PAKTKVATVEL 728 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 522 A DNA sequence (GBSx0560) was identified in S. agalactiae <SEQ ID 1669> which encodes the amino acid sequence <SEQ ID 1670>. Analysis of this protein sequence reveals the following: TABLE-US-01624 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2266(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 523 A DNA sequence (GBSx0561) was identified in S. agalactiae <SEQ ID 1671> which encodes the amino acid sequence <SEQ ID 1672>. This protein is predicted to be alkaline phosphatase synthesis sensor protein phor (hpyA). Analysis of this protein sequence reveals the following: TABLE-US-01625 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.96 Transmernbrane 160-176 ( 148-183) INTEGRAL Likelihood = -8.65 Transmembrane 20-36 ( 13-41) ----- Final Results ----- bacterial membrane --- Certainty = 0.6583(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8595> which encodes amino acid sequence <SEQ ID 8596> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-01626 Lipop: Possible site: -1 Crend: 6 SRCFLG: 0 McG: Length of UR: 26 Peak Value of UR: 3.27 Net Charge of CR: 3 McG: Discrim Score: 14.63 GvH: Signal Score (-7.5): -5.64 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 2 value: -13.96 threshold: 0.0 INTEGRAL Likelihood = -13.96 Transmembrane 152-168 ( 140-175) INTEGRAL Likelihood = -8.65 Transmembrane 12-28 ( 5-33) PERIPHERAL Likelihood = -1.59 135 modified ALOM score: 3.29 icml HYPID: 7 CFP: 0.658 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6583(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS gene <SEQ ID 8593> and protein <SEQ ID 8594> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01627 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: 14.63 GvH: Signal Score (-7.5): -5.64 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 2 value: -13.96 threshold: 0.0 INTEGRAL Likelihood = -13.96 Transmembrane 152-168 ( 140-175) INTEGRAL Likelihood = -8.65 Transmembrane 12-28 ( 5-33) PERIPHERAL Likelihood = -1.59 135 modified ALOM score: 3.29 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6583(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00040## The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01628 >GP: BAB06875 GB: AP001517 two-component sensor histidine kinase involved in phosphate regulation [Bacillus halodurans] Identities = 176/589 (29%), Positives = 315/589 (52%), Gaps = 47/589 (7%) Query: 9 MTKKIFRTTLSASLGIVLVTILMIMG------------FLYNYFNHIQREQLRTQTALAS 56 MTK +R L+ ++ VT+L++ G +L N + +++E + + + Sbjct: 1 MTKFRYRLVLA----VLTVTLLVMAGLGLVIGQIFKNVYLENLTDRLKKETYLAASMVEN 56 Query: 57 QGISF-EGKDYFENLKTS-NVRITWVDNKGQVLYDTQSDAKHMKNHANRQEIKEAIKSGY 114- + + F E + E + + R+T + G V+ ++ +D M+NHA+R E E ++ G Sbjct: 57 EAVLFNEVQTLTEEISQKLDARVTIILADGTVVGESAADPAEMENHADRPEFTE-LEEGI 115- Query: 115 GESTRWSATL-TEKSIYAAQRLN--NGTI--VRLSVAQQTIFYLLLGMISPLAIIILLAI 16- 9 R+S T+ TE YA N N TI VRL + + + + + + L + +A Sbjct: 116 ---VRYSTTVETELLFYAVPIQNEANETIGYVRLGLPIEAVNSVNRTLWAILIVSFTIAF 17- 2 Query: 170 ILSVLIARYIAKKVSEPLNNI----------DLDHPLSNDSYEEITPLLRRLDSHQAKIQ 21- 9 ++ V + IA ++ P+ + D S +S +E+ L R ++ ++ Sbjct: 173 LVIVSVTYRIANQMIRPIESATVVANKLAEGDYQARTSEESRDEVGQLNRSINVLAYNLE 23- 2 Query: 220 HQKLLLQKRQKEFDTIISKIKEGMILLDDQARIVSINAEALKLFQINDD-WHGRFMMEVS 27- 8 Q +++ +T+I + G+IL++ + I IN +FQ + D W + +V Sbjct: 233 QLTKRHQVQKERLETLIENMGSGLILINTRGDISLINKTCHDIFQEDTDLWLHQLYHDVI 29- 2 Query: 279 RDLTLKDLIDQGLKGKKKEAN-----IGIENNHYRVLVRPTT-DNNRVTGLVVLLFDVTD 33- 2 + + ++ +K++ I +E H+ V P +N ++ G+ ++ D+T+ Sbjct: 293 KHKEIIKIVQDIFLTEKRQRRQVKLPIHLEYRHFDVHGAPIVRENGKLKGIALVFHDITE 35- 2 Query: 333 QLQMEQLQREFTANVSHELKTPLHVISGYSELLANQMVPNEEV-PQFAAKIHKESERLVK 39- 1 ++EQ++++F ANVSHELKTP+ I G++E L + + +E++ QF I KESERL Sbjct: 353 LKKLEQVRKDFVANVSHELKTPVTSIKGFTETLLDGAMHDEQLRDQFLHIIWKESERLQS 41- 2 Query: 392 LVEDIINLSHLDEQE-KLPQETVNLYDLTQKVLEGLQAKADKKHIQINFNGEEAI-LRGN 44- 9 L+ D++ LS +++ +L + NL+ + +V+ L+ KA++K I I+ + E + L G+ Sbjct: 413 LIHDLLELSKIEQNYFQLNWQQTNLFAVVSEVMTLLKGKAEEKGIDISLSAEGSFDLEGD 47- 2 Query: 450 PVLLNSLVYNLCDNAITYNHEKGQVNVTLKNSPDTITLEVSDTGLGIAEKDKKRIFERFY 50- 9 P L + NL +NAITY G++++ LK+ D + EV+DTG+GI E + RIFERFY Sbjct: 473 PERLKQIAINLVNNAITYTSNGGRIDLALKDHGDVVEFEVNDTGIGIRESEIPRIFERFY 53- 2 Query: 510 RVDKSRSKIVGGTGLGLSIVKSALDFHNGSIKVDSHLGQGTTMTVLLHK 558 RVD++RS+ GGTGLGL+IVK ++ H G I V+S G+GTT T+ H+ Sbjct: 533 RVDRARSRNSGGTGLGLAIVKHLVEAHQGKILVESEFGKGTTFTIQFHR 581 There is also homology to SEQ ID 1178. SEQ ID 8594 (GBS340) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 173 (lane 10; MW 86 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 11 (lane 7; MW 61.5 kDa) and in FIG. 77 (lane 10; MW 62 kDa). Purified GBS340-GST is shown in FIG. 223, lane 2; purified GBS340-His is shown in FIG. 191, lane 9. The purified GBS340-GST fusion product was used to immunise mice. The resulting antiserum was used for Western blot (FIG. 254A), FACS (FIG. 254B), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 524 A DNA sequence (GBSx0562) was identified in S. agalactiae <SEQ ID 1673> which encodes the amino acid sequence <SEQ ID 1674>. This protein is predicted to be phosphate regulon transcriptional regulatory protein phob (phoB). Analysis of this protein sequence reveals the following:

TABLE-US-01629 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2617(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10203> which encodes amino acid sequence <SEQ ID 10204> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01630 >GP: AAC73502 GB: AE000146 positive response regulator for pho regulon, sensor is PhoR (or CreC) [Escherichia coli K12] Identities = 98/224 (43%), Positives = 138/224 (60%), Gaps = 2/224 (0%) Query: 2 IYCVEDDADIREMMLYTLQMAGFKAQGFSSSELFWEAIQEKVPDLILLDIMLPGDDGLTI 61 I VED+A IREM+ + L+ GF+ + + E PDLILLD MLPG G+ Sbjct: 5 ILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQF 64 Query: 62 LERLRRKHQTEMIPVIMTTAKGSEYDKVKGLDLGADDYLVKPFGMMEMISRIKAVLRRSR 121- ++ L+R+ T IPV+M TA+G E D+V+GL+ GADDY+ KPF E+++RIKAV+RR Sbjct: 65 IKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRIS 124- Query: 122 QVDSKAHIIIGNLEIDPTNYWVKRGTEKIHLTLKEFELLVLFFRNPNRVFTRQELLDKVW 18- 1 + + I + L +DPT++ V G E + + EF+LL F +P RV++R++LL+ VW Sbjct: 125 PMAVEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVW 18- 4 Query: 182 GEQFLGETRTVDVHIGTLRTKLGEDGY--LIATVRGVGYRLEER 223 G E RTVDVHI LR L G+ ++ TVRG GYR R Sbjct: 185 GTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTR 228 There is also homology to SEQ ID 1182. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 525 A DNA sequence (GBSx0563) was identified in S. agalactiae <SEQ ID 1675> which encodes the amino acid sequence <SEQ ID 1676>. This protein is predicted to be phosphate transport system regulatory protein (phoU). Analysis of this protein sequence reveals the following: TABLE-US-01631 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1188(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01632 >GP: AAG08750 GB: AE004948 phosphate uptake regulatory protein PhoU [Pseudomonas aeruginosa] Identities = 66/213 (30%), Positives = 119/213 (54%), Gaps = 4/213 (1%) Query: 2 IRSRFASQLNDLNKEIIFMGALCEDIIGKSLGALTNSNDVYLDDISETYHKIEQMERDIE 61 I +F ++L D+ ++ MG L E + ++ AL +++ + E +I QMER+I+ Sbjct: 11 ISQQFNAELEDVRSHLLAMGGLVEKQVNDAVNALIDADSGLAQQVREIDDQINQMERNID 70 Query: 62 ERCLKLLLRQQPVAKDLRRISSALKMVYDMKRIGAQAYEIAEIVSLGHIIQGSGSERD-- 119- E C+++L R+QP A DLR I S K V D++RIG +A ++A + + S R Sbjct: 71 EECVRILARRQPAASDLRLIISISKSVIDLERIGDEASKVARRAI--QLCEEGESPRGYV 128- Query: 120 QLNSMSNNVISMLTKSIDAFIYDNEEQAHQVIEQDRTVNQEFDTIKKQLVLYFSVQDVDG 17- 9 ++ + + V M+ +++DAF + + A V + D+TV++E+ T ++LV Y Sbjct: 129 EVRHIGSQVQKMVQEALDAFARFDADLALSVAQYDKTVDREYKTALRELVTYMMEDPRAI 18- 8 Query: 180 EYPIDVLMIAKYLERIGDHTVNIAKWVLFSITG 212 ++++ + LERIGDH NIA+ V++ + G Sbjct: 189 SRVLNIIWALRSLERIGDHARNIAELVIYLVRG 221 There is also homology to SEQ ID 1678. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 526 A DNA sequence (GBSx0564) was identified in S. agalactiae <SEQ ID 1679> which encodes the amino acid sequence <SEQ ID 1680>. This protein is predicted to be ATP-binding cassette protein PstB (pstB-2). Analysis of this protein sequence reveals the following: TABLE-US-01633 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2432(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10205> which encodes amino acid sequence <SEQ ID 10206> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01634 >GP: AAD22041 GB: AF118229 ATP-binding cassette protein PstB [Streptococcus pneumoniae] Identities = 166/245 (67%), Positives = 211/245 (85%), Gaps = 1/245 (0%) Query: 10 INNLDLYYGEFHALKDVNLDIEEKEITAFIGPSGCGKSTLLKSINRMNDLVKNCKITGDI 69 - + +LDL+YG+F ALK++++ + E++ITA IGPSGCGKST LK++NRMNDLV +C I G + Sbjct: 6 VRHLDLFYGDFQALKNISIQLPERQITALIGPSGCGKSTFLKTLNRMNDLVPSCHIEGQV 65 Query: 70 TLEGEDVYR-QLDINQLRKKVGMVFQKPNPFPMSIYDNVAFGPRTHGIHSKAELDDIVER 128- L+ +D+Y + ++NQLRK+VGMVFQ+PNPF MSIYDNVA+GPRTHGI K +LD +VE+ Sbjct: 66 LLDEQDIYSSKFNLNQLRKRVGMVFQQPNPFAMSIYDNVAYGPRTHGIRDKKQLDALVEK 125- Query: 129 SLKQAALWDEVKDRLHKSALGMSGGQQQRLCIARALAIEPDVLLMDEPTSALDPISTAKI 18- 8 SLK AA+W+EVKD L KSA+ +SGGQQQRLCIARALA+EPD+LLMDEPTSALDPIST KI Sbjct: 126 SLKGAAIWEEVKDDLKKSAMSLSGGQQQRLCIARALAVEPDILLMDEPTSALDPISTLKI 18- 5 Query: 189 EELVIQLKKNYTIVIVTHNMQQAVRISDKTAFFLMGEVVEYNKTSQLFSLPQDERTENYI 24- 8 E+L+ QLKK+YTI+IVTHNMQQA RISDKTAFFL GE+ E+ T +F+ P+D+RTE+YI Sbjct: 186 EDLIQQLKKDYTIIIVTHNMQQASRISDKTAFFLTGEICEFGDTVDVFTNPKDQRTEDYI 24- 5 Query: 249 TGRFG 253 +GRFG Sbjct: 246 SGRFG 250 There is also homology to SEQ ID 1682. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 527 A DNA sequence (GBSx0565) was identified in S. agalactiae <SEQ ID 1683> which encodes the amino acid sequence <SEQ ID 1684>. This protein is predicted to be transmembrane protein PstA (pstA-2). Analysis of this protein sequence reveals the following: TABLE-US-01635 Possible site: 38 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -13.11 Transmembrane 265-281 (255-286) INTEGRAL Likelihood = -8.81 Transmembrane 79-95 (68-100) INTEGRAL Likelihood = -4.78 Transmembrane 195-211 (192-213) INTEGRAL Likelihood = -4.67 Transmembrane 147-163 (143-164) INTEGRAL Likelihood = -2.92 Transmembrane 122-138 (120-138) INTEGRAL Likelihood = -0.90 Transmembrane 40-56 (39-56) ----- Final Results ----- bacterial membrane --- Certainty = 0.6243(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01636 >GP: AAD22040 GB: AF118229 transmembrane protein PstA [Streptococcus pneumoniae] Identities = 135/263 (51%), Positives = 203/263 (76%) Query: 23 FFLFAIVYLGAILSFATIAFVVIYILVKGLPHVNTGLFAWTYNTQNVSLLPAFINTIFII 82 - + L +VY + L+F ++ ++ +IL+KGLPH++ LF+WTY ++N+SL+PA I+T+ ++ Sbjct: 4 YLLKLLVYCFSALTFGSLFLIIGFILIKGLPHLSLSLFSWTYTSENISLMPAIISTVILV 63 Query: 83 ALTLLFAVPLGIGGSIYLTEYARRDNPYLKIIRVATETLAGIPSIIYGLFGALFFVKYTH 142- LL A+P+GI YL EY ++D+ +KI+R+A++TL+GIPSI++GLFG LFFV + Sbjct: 64 FGALLLALPIGIFAGFYLVEYTKKDSLCVKIMRLASDTLSGIPSIVFGLFGMLFFVVFLG 123- Query: 143 LGLSLISGSLTLSIMILPLIMRTTEEALLSVPDSYREGAFALGAGKLRTIFKIVLPSAMS 20- 2 SL+SG LT IM+LP+I+R+TEEALLSV DS R+ ++ LGAGKLRT+F+IVLP AM Sbjct: 124 FQYSLLSGILTSVIMVLPVIIRSTEEALLSVSDSMRQASYGLGAGKLRTVFRIVLPVAMP 18- 3 Query: 203 GIFAGIILAVGRIIGESAALIFTAGTVAKVAHSVFSSSRTLAVHMYAISGEGLYVDQTYA 26- 2 GI AG+ILA+GRI+GE+AAL++T GT S+ SS R+LA+HMY +S EGL+V++ YA Sbjct: 184 GILAGVILAIGRIVGETAALMYTLGTSTNTPSSLMSSGRSLALHMYMLSSEGLHVNEAYA 24- 3 Query: 263 TAVILLLLVIIVNFVSGLVAKRL 285 T VIL++ V+++N +S L++++L Sbjct: 244 TGVILIITVLMINTLSSLLSRKL 266 There is also homology to SEQ ID 1686. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 528 A DNA sequence (GBSx0566) was identified in S. agalactiae <SEQ ID 1687> which encodes the amino acid sequence <SEQ ID 1688>. Analysis of this protein sequence reveals the following: TABLE-US-01637 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2687(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 529 A DNA sequence (GBSx0567) was identified in S. agalactiae <SEQ ID 1689> which encodes the amino acid sequence <SEQ ID 1690>. This protein is predicted to be transmembrane protein PstC (pstC-2). Analysis of this protein sequence reveals the following: TABLE-US-01638 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.67 Transmembrane 256-272 (251-279) INTEGRAL Likelihood = -8.86 Transmembrane 141-157 (133-162) INTEGRAL Likelihood = -4.99 Transmembrane 111-127 (109-132) INTEGRAL Likelihood = -4.30 Transmembrane 76-92 (72-95) INTEGRAL Likelihood = -1.86 Transmembrane 25-41 (24-42) INTEGRAL Likelihood = -1.33 Transmembrane 59-75 (59-75) INTEGRAL Likelihood = -0.27 Transmembrane 203-219 (202-219) --- Final Results ----- bacterial membrane --- Certainty = 0.5267(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01639 >GP: AAD22039 GB: AF118229 transmembrane protein PstC [Streptococcus pneumoniae] Identities = 162/266 (60%), Positives = 212/266 (78%), Gaps = 3/266 (1%) Query: 15 ITACVSVISAILICLFLFSSGLPAITKIGWGNFIFGKVWHPSN--NIFGIFPMIVGSLYV 72 - ++A V+V++ +LIC F+FS+GLP I G+ F+ G W P+N +GI PMIVGSL + Sbjct: 1 MSATVAVVAILLICFFIFSNGLPFIANYGFARFLLGSDWSPTNIPASYGILPMIVGSLLI 60 Query: 73 TAGALLLGGPIGILTAVFMAYFCPENIYKPLKSAINLMAGIPSVVYGFFGLVVIVPMIRQ 132- T GA+++G P GILT+VFM Y+CP+ +Y LKSAINLMA IPS+VYGFFGL ++VP IR Sbjct: 61 TLGAIVIGVPTGILTSVFMVYYCPKPVYGFLKSAINLMAAIPSIVYGFFGLQLLVPWIRS 120- Query: 133 YIGGFGMGVLAASILLGIMILPTIVSISESSLRAVPESYYEGGIALGASHERSVFFAVLP 19- 2 ++G GM VL AS+LLGIMILPTI+S+SES++R VP++YY G +ALGASHERS+F +LP Sbjct: 121 FLGN-GMSVLTASLLLGIMILPTIISLSESAIRTVPKTYYSGSLALGASHERSIFSVILP 17- 9 Query: 193 AAKRGILASVVLGIGRAIGETMAVIMVAGNQAVLPQSLTSGVRTLTTNIVMEMGYSSGLH 25- 2 AA+ GIL++V+LGIGRA+GETMAVI+VAGNQ ++P L SG RTLTTNIV+EM Y+SG H Sbjct: 180 AARSGILSAVILGIGRAVGETMAVILVAGNQPIIPSGLFSGTRTLTTNIVLEMAYASGQH 23- 9 Query: 253 RQALIGTAVVLFIFILMINISFSALQ 278 R+ALI T+ VLF IL+IN F+ L+ Sbjct: 240 REALIATSAVLFFLILLINAYFAYLK 265 There is also homology to SEQ ID 1692. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 530 A DNA sequence (GBSx0568) was identified in S. agalactiae <SEQ ID 1693> which encodes the amino acid sequence <SEQ ID 1694>. This protein is predicted to be probable hemolysin precursor (pstS). Analysis of this protein sequence reveals the following: TABLE-US-01640 Possible site: 34 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01641 >GP: AAD22038 GB: AF118229 phosphate binding protein PstS [Streptococcus pneuxnoniae] Identities = 134/295 (45%), Positives = 185/295 (62%), Gaps = 9/295 (3%) Query: 1 MKKHKMLSLLAVSGLMGIGILAGCSNDSSSSSK---GTINIVSREEGSGTRGAFIELFGI 57 MK KML+L A+ GL G G++A C N S++S + GTI ++SRE GSGTRGAF E+ GI Sbjct: 1 MKFKKMLTLAAI-GLSGFGLVA-CGNQSAASKQSASGTIEVISRENGSGTRGAFTEITGI 58 Query: 58 ESKNKKGEKVDHTSDAATVTNSTSVMLTTVSKDPSAIGYSSLGSLNSSVKVLKIDGKNAT 117- K+ +K+D+T+ A + NST +L+ V + +AIGY SLGSL SVK L+IDG A+ Sbjct: 59 LKKDGD-KKIDNTAKTAVIQNSTEGVLSAVQGNANAIGYISLGSLTKSVKALEIDGVKAS 117- Query: 118 VKDIKSGSYKISRPFNIVTKEGKEKEATKDFIDYILSKDGQAVVEKNGYIPL-DNAKAYQ 17- 6 + G Y + RPFNIV K +DFI +I SK GQ VV N +I Y Sbjct: 118 RDTVLDGEYPLQRPFNIVWSSNLSK-LGQDFISFIHSKQGQQVVTDNKFIEAKTETTEYT 17- 6 Query: 177 AKVSSGKVVIAGSSSVTPVMEKIKEAYHKVNAKVDVEIQQSDSSTGITSAIDGSADIGMA 23- 6 ++ SGK+ + GS+SV+ +MEK+ EAY K N +V ++I + SS GIT+ + +ADIGM Sbjct: 177 SQHLSGKLSVVGSTSVSSLMEKLAEAYKKENPEVTIDITSNGSSAGITAVKEKTADIGMV 23- 6 Query: 237 SRELDKTESSKGVKATVIATDGIAVVVNKKNKVNDLSTKQVKDIFTGKTTSWSDL 291 SREL E K + IA DGIAVVVN NK + +S ++ D+F+GK T+W + Sbjct: 237 SREL-TPEEGKSLTHDAIALDGIAVVVNNDNKASQVSMAELADVFSGKLTTWDKI 290 There is also homology to SEQ ID 1696. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8597> and protein <SEQ ID 8598> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01642 Lipop: Possible site: 23 Crend: 4 McG: Discrim Score: 7.91 GvH: Signal Score (-7.5): -3.72 Possible site: 34 >>> May be a lipoprotein ALOM program count: 0 value: 2.44 threshold: 0.0 PERIPHERAL Likelihood = 2.44 248 modified ALOM score: -0.99 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 1694 (GBS24) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 14 (lane 9; MW 33 kDa). GBS24-His was purified as shown in FIG. 194, lane 10. EXAMPLE 531 A DNA sequence (GBSx0569) was identified in S. agalactiae <SEQ ID 1697> which encodes the amino acid sequence <SEQ ID 1698>. Analysis of this protein sequence reveals the following: TABLE-US-01643 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1725(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 532 A DNA sequence (GBSx0570) was identified in S. agalactiae <SEQ ID 1699> which encodes the amino acid sequence <SEQ ID 1700>. Analysis of this protein sequence reveals the following:

TABLE-US-01644 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2741(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01645 >GP: BAB05069 GB: AP001511 unknown conserved protein [Bacillus halodurans] Identities = 119/250 (47%), Positives = 149/250 (59%), Gaps = 9/250 (3%) Query: 1 MQQYFVNGE--AGAYVTIEDKDTIKHMFNVMRLTEDDQVVLVFDDAIKRLAKVVDSSAHR 58 MQ+YFV E YVTI D +KH+ VMR+T D+ L+ D R + A+ Sbjct: 1 MQRYFVPKEQMTDTYVTITGDD-VKHIIKVMRMTIGDE--LICSDGHGRTVRCEIEKAND 57 Query: 59 FQIL----EELDNNVEMPVQVTIASGFPKGDKLDFVTQKATELGAAAIWGFPADWSVVKW 114- ++L E L N E+P++VTIA PKGDKLD++ QK TELGA A W F A S+VKW Sbjct: 58 SEVLARVIEPLIPNTELPIRVTIAQALPKGDKLDYIVQKGTELGAQAFWPFSASRSIVKW 117- Query: 115 DGKKLAKKEDKLAKIALGAAEQSKRNRLPQVRLFEKKADFQAELAGFDKIFIAYEESAKE 17- 4 D KK KK ++L KIA AAEQS R R+P + + E++GF K +AYEE AKE Sbjct: 118 DEKKGRKKTERLMKIAKEAAEQSYRERIPSIETPLAFSKLLQEISGFTKTIVAYEEEAKE 17- 7 Query: 175 GELSALAQNLQTVKAGDKLLFIFGPEGGISPKEIAAFEEVGAIKVGLGPRIMRTETAPLY 23- 4 G L A L + GD LL I GPEGG + +EI A + G GLGPRI+RTETA LY Sbjct: 178 GRLMTFAACLNELHHGDSLLVIIGPEGGFTTEEIDAIQRAGGAPAGLGPRILRTETASLY 23- 7 Query: 235 ALSVISYSAE 244 AL+ ISY E Sbjct: 238 ALAAISYHFE 247 A related DNA sequence was identified in S. pyogenes <SEQ ID 1701> which encodes the amino acid sequence <SEQ ID 1702>. Analysis of this protein sequence reveals the following: TABLE-US-01646 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2274(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01647 Identities = 173/245 (70%), Positives = 202/245 (81%) Query: 1 MQQYFVNGEAGAYVTIEDKDTIKHMFNVMRLTEDDQVVLVFDDAIKRLAKVVDSSAHRFQ 60 MQQYF+ G+A VTI DKDTIKHMF VMRL ++ +VVLVFDD +K LAKV +S AN + Sbjct: 1 NQQYFIKGKAEKKVTITDKDTIKHMFQVMRLADEAEVVLVFDDGVKYLAKVTNSMAHELE 60 Query: 61 ILEELDNNVEMPVQVTIASGFPKGDKLDFVTQKATELGAAAIWGFPADWSVVKWDGKKLA 120- I+E L + VE+PV+VTIASGFPKGDKLD + QK TELGA+A+WG+PADWSVVKWDGKKLA Sbjct: 61 IIEALPDQVELPVKVTIASGFPKGDKLDTIAQKVTELGASALWGYPADWSVVKWDGKKLA 120- Query: 121 KKEDKLAKIALGAAEQSKRNRLPQVRLFEKKADFQAELAGFDKIFIAYEESAKEGELSAL 18- 0 KKEDKLAKI LGAAEQSKRNR+P+V LFE KA+F L+ FD IFIAYEE+AK G+L+ L Sbjct: 121 KKEDKLAKIVLGAAEQSKRNRVPEVHLFEHKAEFLKSLSSFDHIFIAYEETAKAGQLATL 18- 0 Query: 181 AQNLQTVKAGDKLLFIFGPEGGISPKEIAAFEEVGAIKVGLGPRIMRTETAPLYALSVIS 24- 0 A+ ++ VK G K+LFIFGPEGGISP EI FE AIKVGLGPRIMR ETAPLYALS +S Sbjct: 181 AREVKEVKPGAKILFIFGPEGGISPTEITQFEAASAIKVGLGPRIMRAETAPLYALSALS 24- 0 Query: 241 YSAEL 245 Y+ EL Sbjct: 241 YALEL 245 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 533 A DNA sequence (GBSx0571) was identified in S. agalactiae <SEQ ID 1703> which encodes the amino acid sequence <SEQ ID 1704>. Analysis of this protein sequence reveals the following: TABLE-US-01648 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.28 Transmembrane 238-254 (237-254) ----- Final Results ----- bacterial membrane --- Certainty = 0.1914(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01649 >GP: BAA82791 GB: AB023064 orf35 [Listeria monocytogenes] Identities = 138/309 (44%), Positives = 193/309 (61%), Gaps = 5/309 (1%) Query: 4 WNELTVHVNREAEEAVSNLLIETGSQGVAISDSADYLGQ-EDRFGELYP---EVEQSDMI 59 W+E+ VH EA E V+N+L E G+ GV+I D AD+L + ED+FGE+Y E D + Sbjct: 3 WSEVEVHTTNEAVEPVANVLTEFGAAGVSIEDVADFLREREDKFGEIYALRREDYPEDGV 62 Query: 60 AITAYYPDTLDIEAVKADLADRLANFEGFGLATGSVNLDSQELVEEDWADNWKKYYEPAR 119- I AY+ T + ++ L N F + G ++ +E+WA WKKYY P + Sbjct: 63 IIKAYFLKTTEFVEQIPEIEQTLKNLSTFDIPLGKFQFVVNDVDDEEWATAWKKYYHPVQ 122- Query: 120 ITHDLTIVPSWTDYEAKAGEKIIKMDPGMAFGTGTHPTTKMSLFALEQVLRGGETVIDVG 17- 9 IT +TIVPSW Y A E II++DPGMAFGTGTHPTT++ + AL L+ G+ VIDVG Sbjct: 123 ITDRITIVPSWESYTPSANEIIIELDPGMAFGTGTHPTTQLCIRALSNYLQPGDEVIDVG 18- 2 Query: 180 TGSGVLSIASSLLGAKDIYAYDLDDVAVRVAQENIDMNPGTENIHVAAGDLLKGVQQ-EV 23- 8 TGSGVLSIAS+ LGAK I A DLD++A R A+ENI +N I V +LL+ + + V Sbjct: 183 TGSGVLSIASAKLGAKSILATDLDEIATRAAEENITLNKTEHIITVKQNNLLQDINKTNV 24- 2 Query: 239 DVIVANILADILIHLTDDAYRLVKDEGYLIMSGIISEKWDMVRESAEKAGFFLETHMVQG 29- 8 D++VANILA++++ +D Y+ +K G I SGII +K +V E+ + AG +E QG Sbjct: 243 DIVVANILAEVILLFPEDVYKALKPGGVFIASGIIEDKAKVVEEALKNAGLIIEKMEQQG 30- 2 Query: 299 EWNACVFKK 307 +W A + K+ Sbjct: 303 DWVAIISKR 311 A related DNA sequence was identified in S. pyogenes <SEQ ID 1705> which encodes the amino acid sequence <SEQ ID 1706>. Analysis of this protein sequence reveals the following: TABLE-US-01650 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.57 Transmembrane 238-254 (237-257) ----- Final Results ----- bacterial membrane --- Certainty = 0.2826(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01651 >GP: BAA82791 GB: AB023064 orf35 [Listeria monocytogenes] Identities = 139/309 (44%), Positives = 203/309 (64%), Gaps = 5/309 (1%) Query: 4 WQEVTVHVHRDAQEAVSHVLIETGSQGVAIADSADYIGQK-DRFGELYP---DVEQSDMI 59 W EV VH +A E V++VL E G+ GV+I D AD++ ++ D+FGE+Y + D + Sbjct: 3 WSEVEVHTTNEAVEPVANVLTEFGAAGVSISDVADFLREREDKFGEIYALRREDYPEDGV 62 Query: 60 AITAYYPSSTNLADIIATINEQLAELASFGLQVGQVTVDSQELAEEDWADNWKKYYEPAR 119- I AY+ +T + I I + L L++F + +G+ ++ + E+WA WKKYY P+ Sbjct: 63 IIKAYFLKTTEFVEQIPEIEQTLKNLSTFDIPLGKFQFVVNDVDDEEWATAWKKYYHPVQ 122- Query: 120 ITHDLTIVPSWTDYDASAGEKVIKLDPGMAFGTGTHPTTKMSLFALEQILRGGETVIDVG 17- 9 IT +TIVPSW Y SA E +I+LDPGMAFGTGTHPTT++ + AL L+ G+ VIDVG Sbjct: 123 ITDRITIVPSWESYTPSANEIIIELDPGMAFGTGTHPTTQLCIRALSNYLQPGDEVIDVG 18- 2 Query: 180 TGSGVLSIASSLLGAKTIYAYDLDDVAVRVAQDNIDLNQGTDNIHVAAGDLLKGVSQ-EA 23- 8 TGSGVLSIAS+ LGAK+I A DLD++A R A++NI LN+ I V +LL+ +++ Sbjct: 183 TGSGVLSIASAKLGAKSILATDLDEIATRAAEENITLNKTEHIITVKQNNLLQDINKTNV 24- 2 Query: 239 DVIVANILADILVLLTDDAYRLVKKEGYLILSGIISEKLDMVLEAAFSAGFFLETHMVQG 29- 8 D++VANILA++++L +D Y+ +K G I SGII +K +V EA +AG +E QG Sbjct: 243 DIVVANILAEVILLFPEDVYKALKPGGVFIASGIIEDKAKVVEEALKNAGLIIEKMEQQG 30- 2 Query: 299 EWNALVFKK 307 +W A++ K+ Sbjct: 303 DWVAIISKR 311 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01652 Identities = 259/317 (81%), Positives = 287/317 (89%) Query: 1 MNTWNELTVHVNREAEEAVSNLLIETGSQGVAISDSADYLGQEDRFGELYPEVEQSDMIA 60 M TW E+TVHV+R+A+EAVS++LIETGSQGVAI+DSADY+GQ+DRFGELYP+VEQSDMIA Sbjct: 1 METWQEVTVHVHRDAQEAVSHVLIETGSQGVAIADSADYIGQKDRFGELYPDVEQSDMIA 60 Query: 61 ITAYYPDTLDIEAVKADLADRLANFEGFGLATGSVNLDSQELVEEDWADNWKKYYEPARI 120- ITAYYP + ++ + A + ++LA FGL G V +DSQEL EEDWADNWKKYYEPARI Sbjct: 61 ITAYYPSSTNLADIIATINEQLAELASFGLQVGQVTVDSQELAEEDWADNWKKYYEPARI 120- Query: 121 THDLTIVPSWTDYEAKAGEKIIKMDPGMAFGTGTHPTTKMSLFALEQVLRGGETVIDVGT 18- 0 THDLTIVPSWTDY+A AGEK+IK+DPGMAFGTGTHPTTKMSLFALEQ+LRGGETVIDVGT Sbjct: 121 THDLTIVPSWTDYDASAGEKVIKLDPGMAFGTGTHPTTKMSLFALEQILRGGETVIDVGT 18- 0 Query: 181 GSGVLSIASSLLGAKDIYAYDLDDVAVRVAQENIDMNPGTENIHVAAGDLLKGVQQEVDV 24- 0 GSGVLSIASSLLGAK IYAYDLDDVAVRVAQ+NID+N GT+NIHVAAGDLLKGV QE DV Sbjct: 181 GSGVLSIASSLLGAKTIYAYDLDDVAVRVAQDNIDLNQGTDNIHVAAGDLLKGVSQEADV 24- 0 Query: 241 IVANILADILIHLTDDAYRLVKDEGYLIMSGIISEKWDMVRESAEKAGFFLETHMVQGEW 30- 0 IVANILADIL+ LTDDAYRLVK EGYLI+SGIISEK DMV E+A AGFFLETHMVQGEW Sbjct: 241 IVANILADILVLLTDDAYRLVKKEGYLILSGIISEKLDMVLEAAFSAGFFLETHMVQGEW 30- 0 Query: 301 NACVFKKTDDISGVIGG 317 NA VFKKTDDISGVIGG Sbjct: 301 NALVFKKTDDISGVIGG 317 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 534 A DNA sequence (GBSx0572) was identified in S. agalactiae <SEQ ID 1707> which encodes the amino acid sequence <SEQ ID 1708>. Analysis of this protein sequence reveals the following: TABLE-US-01653 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4198(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 535 A DNA sequence (GBSx0573) was identified in S. agalactiae <SEQ ID 1709> which encodes the amino acid sequence <SEQ ID 1710>. This protein is predicted to be transcriptional activator tipa. Analysis of this protein sequence reveals the following: TABLE-US-01654 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0683(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01655 >GP: CAB15677 GB: Z99122 transcriptional regulator [Bacillus subtilis] Identities = 87/246 (35%), Positives = 139/246 (56%), Gaps = 13/246 (5%) Query: 4 VKEVSILSGVSVRTLHHYDKIGLFPPTALSEAGYRLYDDEALIRLQEILLFRELEFPLKD 63 VK+V+ +SGVS+RTLHHYD I L P+AL++AGYRLY D L RLQ+IL F+E+ F L + Sbjct: 5 VKQVAEISGVSIRTLHHYDNIELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDE 64 Query: 64 IKYLLEQAKEERQDLLAQQIKLLEWKRSHLEQVITHAKR--LQEKGDDYMN----FDVYN 117- IK +L+ +R+ L Q ++L K+ ++++I R L G + MN F + Sbjct: 65 IKEMLDHPNFDRKAALQSQKEILMKKKQRMDEMIQTIDRTLLSVDGGETMNKRDLFAGLS 124- Query: 118 KTELEQLQA----EAKEKWGQTAA--YKEFAQKHASDDFAQISQEMAKIMVQFGQLKTQN 17- 1 ++E+ Q E ++ +G+ A ++ +++DD+ I E I + Sbjct: 125 MKDIEEHQQTYADEVRKLYGKEIAEETEKRTSAYSADDWRTIMAEFDSIYRRIAARMKHG 18- 4 Query: 172 VSDESVQMCVKRLQDYISQNFYTCTNEILAGLGQMYQSDDRFSQSIDKAGGAGTSEFVSQ 23- 1 D +Q V +D+I Q Y CT +I GLG++Y +D+RF+ SI++ G G + F+ + Sbjct: 185 PDDAEIQAAVGAFRDHICQYHYDCTLDIFRGLGEVYITDERFTDSINQY-GEGLAAFLRE 24- 3 Query: 232 AIAYYC 237 AI YC Sbjct: 244 AIIIYC 249 A related DNA sequence was identified in S. pyogenes <SEQ ID 1711> which encodes the amino acid sequence <SEQ ID 1712>. Analysis of this protein sequence reveals the following: TABLE-US-01656 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.28 Transmembrane 146-162 (143-167) INTEGRAL Likelihood = -2.92 Transmembrane 172-188 (171-190) ----- Final Results ----- bacterial membrane --- Certainty = 0.4312(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01657 >GP: CAB15677 GB: Z99122 transcriptional regulator [Bacillus subtilis] Identities = 40/107 (37%), Positives = 69/107 (64%), Gaps = 6/107 (5%) Query: 7 YSTGELANLAGVSIRTVQYYDQRGILIPTALTAGGRRLYTDSDLEQLRMICFLRDLGFSI 66 Y ++A ++GVSIRT+ +YD +L P+ALT G RLY+D+DLE+L+ I F +++GF + Sbjct: 3 YQVKQVAEISGVSIRTLHHYDNIELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRL 62 Query: 67 EQIRKVLAEENAAQVLELLLVDHIATAKEDLAAKEQQVDIAVKILDR 113 ++I+++L N + L + KE L K+Q++D ++ +DR Sbjct: 63 DEIKEMLDHPNFDRKAAL------QSQKEILMKKKQRMDEMIQTIDR 103 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01658 Identities = 40/133 (30%), Positives = 71/133 (53%), Gaps = 6/133 (4%) Query: 6 EVSILSGVSVRTLHHYDKIGLFPPTALSEAGYRLYDDEALIRLQEILLFRELEFPLKDIK 65 E++ L+GVS+RT+ +YD+ G+ PTAL+ G RLY D L +L+ I R+L F ++ I+ Sbjct: 11 ELANLAGVSIRTVQYYDQRGILIPTALTAGGRRLYTDSDLEQLRMICFLRDLGFSIEQIR 70 Query: 66 YLL--EQAKEERQDLLAQQIKL----LEWKRSHLEQVITHAKRLQEKGDDYMNFDVYNKT 119- +L E A + + LL I L K ++ + RL+++ ++F + Sbjct: 71 KVLAEENAAQVLELLLVDHIATAKEDLAAKEQQVDIAVKILDRLRKQDPQSLDFLMDISL 130- Query: 120 ELEQLQAEAKEKW 132 ++ +A K +W Sbjct: 131 SMKNQKAWKKLQW 143 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 536 A DNA sequence (GBSx0575) was identified in S. agalactiae <SEQ ID 1713> which encodes the amino acid sequence <SEQ ID 1714>. Analysis of this protein sequence reveals the following: TABLE-US-01659 Possible site: 24 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.06 Transmembrane 57-73 (57-73) ----- Final Results ----- bacterial membrane --- Certainty = 0.1022(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01660 >GP: CAB14586 GB: Z99117 yrkN [Bacillus subtilis] Identities = 38/136 (27%), Positives = 60/136 (43%), Gaps = 3/136 (2%) Query: 2 ITLQKAEASDLEKIIA-IQRASFKAVYEKYHDQYDPYVEEVEQIRWKLVERPDCFYHFVL 60 + L+ A+ SDL + +Q A AV E + D D + ++ + P + +L Sbjct: 9 VILELAKESDLPEFQKKLQEAFAIAVIETFGDCEDGPIPSDNDVQ-ESFNAPGAVVYHIL 67 Query: 61 VDETIVGFLRLVIKDEEKRAWLGTAAILPQYQGQGYGSAAMALLEKTYPKLTKWDLCTIA 120- D VG + I + L + P+Y QG G +A +E YP W+ T Sbjct: 68 QDGKNVGGAVVRINSQTNHNSLDLFYVSPEYHSQGIGLSAWKAIEAQYPDTVLWETVTPY 127- Query: 121 QEKLMVSFY-EKCGYH 135 EK ++FY KCG+H Sbjct: 128 FEKRNINFYVNKCGFH 143 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 537 A DNA sequence (GBSx0576) was identified in S. agalactiae <SEQ ID 1715> which encodes the amino acid sequence <SEQ ID 1716>. This protein is predicted to be Bacterial mutT protein. Analysis of this protein sequence reveals the following: TABLE-US-01661 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2417(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01662 >GP: AAG06568 GB: AE004742 hypothetical protein [Pseudomonas aeruginosa] Identities = 57/131 (43%), Positives = 82/131 (62%) Query: 10 FSGAKIALFCEGKILTSLRDDFPDLPYAGFWDLPGGGREDNETPLECLFREVDEELSLTL 69 - FSGAK+ALF ++ RD+ P +P+ G+WD PGGGRE ETP EC RE++EE S+ L Sbjct: 7 FSGAKLALFYGDHLVVYKRDEKPGIPFPGYWDFPGGGREGLETPAECALRELEEEFSIRL 66 Query: 70 TRNHIDWVKTYRGMLKPDKLSVFMVGHISQKEYDSIVLGDEGQDYKLMSIDEFLSHKKVI 129- I+W + Y + F+V + +E+++I GDEGQ ++LM +D +L+H + Sbjct: 67 EEPRIEWQRQYPSTSGSAPFAYFLVARLEDREFEAIRFGDEGQYWRLMEVDAYLAHAMAV 126- Query: 130 PQLQERLRDYL 140 P LQ RL DYL Sbjct: 127 PYLQSRLGDYL 137 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 538 A DNA sequence (GBSx0577) was identified in S. agalactiae <SEQ ID 1717> which encodes the amino acid sequence <SEQ ID 1718>. Analysis of this protein sequence reveals the following: TABLE-US-01663 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3299(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1719> which encodes the amino acid sequence <SEQ ID 1720>. Analysis of this protein sequence reveals the following: TABLE-US-01664 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5527(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below:

TABLE-US-01665 Identities = 111/156 (71%), Positives = 128/156 (81%) Query: 1 MAKFGFLSVLEEELDKHLQYDFAMDWDKKNHTVEVTFILEAQNSSAIETVDDQGETSSED 60 MA +GFLSVLEEE+DKH QYD+AMDWDKKNH VEVTF+LEAQN AI+T+DD GE + +D Sbjct: 1 MATYGFLSVLEEEMDKHFQYDYAMDWDKKNHAVEVTFVLEAQNKEAIKTIDDSGEVTQDD 60 Query: 61 IVFEDYVLFYNPVKSRFDAEDYLVTIPYEPKKGLSREFLAYFAETLNEVATEGLSDLMDF 120- IVFEDYVLFYNP KS+FDA DYLVTIP++ KKG SREFLAYFA+ LN+VA EG SDLMDF Sbjct: 61 IVFEDYVLFYNPAKSQFDAADYLVTIPFDAKKGFSREFLAYFAQFLNDVAIEGHSDLMDF 120- Query: 121 LTDDSIEEFGLSWDTDAFENGRAELKETEFYPYPRY 156 L DDS +F L W+ AFE G+ L+E YPYPRY Sbjct: 121 LADDSKADFFLEWNAQAFEEGQQGLEEAASYPYPRY 156 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 539 A DNA sequence (GBSx0578) was identified in S. agalactiae <SEQ ID 1721> which encodes the amino acid sequence <SEQ ID 1722>. Analysis of this protein sequence reveals the following: TABLE-US-01666 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2846(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01667 >GP: CAB51273 GB: AL096872 putative acetyltransferase [Streptomyces coelicolor A3(2)] Identities = 35/109 (32%), Positives = 62/109 (56%), Gaps = 1/109 (0%) Query: 51 VAEVDDKIAGVLDFGPYYPFPAGKHVATF-GILIAEPYQGQGLGKALLKALLTEAKAQGY 109- VAE+D + G + G P + HV G+ +A +G G+G+AL++A + EA+ +G+ Sbjct: 56 VAELDGAVVGYVRLGFPTPLASNTHVRQIRGLAVAGAARGHGVGRALVRAAVEEARHEGF 115- Query: 110 IKIAMHVMGNNSRAISLYQKYGFTEEARITKAFFIENHYVDALIFAKDL 158 +I + V+G+N+ A LY+ GF E + F ++ YVD ++ + L Sbjct: 116 RRITLRVLGHNTAARGLYESEGFVVEGVQPEEFHLDGRYVDDVLMGQML 164 A related DNA sequence was identified in S. pyogenes <SEQ ID 1723> which encodes the amino acid sequence <SEQ ID 1724>. Analysis of this protein sequence reveals the following: TABLE-US-01668 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0229(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01669 Identities = 34/108 (31%), Positives = 59/108 (54%), Gaps = 7/108 (6%) Query: 35 TESDLEKNLANGMSFFV-----AEVDDKIAGVLDFGPYYPFPAGKHVATFGILIAEPYQG 89 - T +L L+ + F+ A +D+K+ G+L+ G+ A +L+A+ Y+G Sbjct: 43 TPQELSDFLSRSQTSFIDFCLLARLDEKVVGLLNLSGEV-LSQGQAEADVFMLVAKTYRG 101- Query: 90 QGLGKALLKALLTEAKAQGYIK-IAMHVMGNNSRAISLYQKYGFTEEA 136 G+G+ LL+ L A+ YI+ + + V N++AI LY+KYGF E+ Sbjct: 102 YGIGQLLLEIALDWAEENPYIESLKLDVQVRNTKAIYLYKKYGFRIES 149 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 540 A DNA sequence (GBSx0579) was identified in S. agalactiae <SEQ ID 1725> which encodes the amino acid sequence <SEQ ID 1726>. Analysis of this protein sequence reveals the following: TABLE-US-01670 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2056(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01671 >GP: CAB14712 GB: Z99118 similar to hypothetical proteins [Bacillus subtilis] Identities = 248/417 (59%), Positives = 314/417 (74%), Gaps = 4/417 (0%) Query: 5 LALRMRPRNINEVIGQQHLVGNGKIIDRMVAANMLSSMILYGPPGIGKTSIASAIAGTTK 64 LA RMRP I ++IGQQHLV KII RMV A LSSMILYGPPGIGKTSIA+AIAG+T Sbjct: 4 LAYRMRPTKIEDIIGQQHLVAEDKIIGRMVQAKHLSSMILYGPPGIGKTSIATAIAGSTS 63 Query: 65 YAFRTFNATVDSKKRLQEIAEEAKFSGGLVLLLDEIHRLDKTKQDFLLPLLENGNIIMIG 124- AFR NA +++KK ++ +A+EAK SG ++L+LDE+HRLDK KQDFLLP LENG II+IG Sbjct: 64 IAFRKLNAVINNKKDMEIVAQEAKMSGQVILILDEVHRLDKGKQDFLLPYLENGMIILIG 123- Query: 125 ATTENPFFSVTPAIRSRVQIFELEPLSNEDIKKAIQLAISDKERGF-PFLVTIDDEALDF 18- 3 ATT NP+ ++ PAIRSR QIFELEPL+ E IK+A++ A+ D+ RG + V+IDD+A++ Sbjct: 124 ATTANPYHAINPAIRSRTQIFELEPLTPELIKQALERALHDEHRGLGTYSVSIDDQAMEH 18- 3 Query: 184 IVTATNGDLRSAYNSLDLAVMSTSPNEDGSRHISLETMENSLQCSYITMDKNGDGHYDIL 24- 3 GD+RSA N+L+LAV+ST + DG HI+LET E LQ + DK+GD HYD+L Sbjct: 184 FAHGCGGDVRSALNALELAVLSTKESADGEIHITLETAEECLQKKSFSHDKDGDAHYDVL 24- 3 Query: 244 SALQKSIRGSDVNASLHYAARLVEAGDLPSLARRLTIIAYEDIGLANPEAQIHTVTALEA 30- 3 SA QKSIRGSD NA+LHY ARL+EAGDL S+ARRL +IAYEDIGLA+P+A + A++ Sbjct: 244 SAFQKSIRGSDANAALHYLARLIEAGDLESIARRLLVIAYEDIGLASPQAGPRVLNAIQT 30- 3 Query: 304 AQRIGFPEARILIANIVVDLALSPKSNSAYLAMDAALADLRRSGNLPIPRHLRDGHYSGS 36- 3 A+R+GFPEART +AN V++L LSPKSNSA LA+D ALAD+R +P+HL+D HY G+ Sbjct: 304 AERVGFPEARIPLANAVIELCLSPKSNSAILAIDEALADIRAGKIGDVPKHLKDAHYKGA 36- 3 Query: 364 KTLGNARDYKYPHAYPEKWVKQQYLPDKLVGHNYFEANETGKYERALGSNKERIDKL 420 + LG DYKYPH Y WV+QQYLPD L Y++ +TGK+E AL K+ DKL Sbjct: 364 QELGRGIDYKYPHNYDNGWVEQQYLPDPLKNKQYYKPKQTGKFESAL---KQVYDKL 417 A related DNA sequence was identified in S. pyogenes <SEQ ID 1727> which encodes the amino acid sequence <SEQ ID 1728>. Analysis of this protein sequence reveals the following: TABLE-US-01672 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2374(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01673 Identities = 394/422 (93%), Positives = 409/422 (96%) Query: 1 MADNLALRMRPRNINEVIGQQHLVGNGKIIDRMVAANMLSSMILYGPPGIGKTSIASAIA 60 M D+LALRMRP+ I+EVIGQ+HLVG GKII RMV AN LSSMILYGPPGIGKTSIASAIA Sbjct: 1 MPDHLALRMRPKTISEVIGQKHLVGEGKIIRRMVEANRLSSMILYGPPGIGKTSIASAIA 60 Query: 61 GTTKYAFRTFNATVDSKKRLQEIAEEAKFSGGLVLLLDEIHRLDKTKQDFLLPLLENGNI 120- GTT+YAFRTFNAT+DSKKRLQEIAEEAKFSGGLVLLLDEIHRLDKTKQDFLLPLLENG I Sbjct: 61 GTTRYAFRTFNATIDSKKRLQEIAEEAKFSGGLVLLLDEIHRLDKTKQDFLLPLLENGTI 120- Query: 121 IMIGATTENPFFSVTPAIRSRVQIFELEPLSNEDIKKAIQLAISDKERGFPFLVTIDDEA 18- 0 IMIGATTENPFFSVTPAIRSRVQIFELEPLSNEDIK AIQLAISDKERGFPFLVTIDDEA Sbjct: 121 IMIGATTENPFFSVTPAIRSRVQIFELEPLSNEDIKTAIQLAISDKERGFPFLVTIDDEA 18- 0 Query: 181 LDFIVTATNGDLRSAYNSLDLAVMSTSPNEDGSRHISLETMENSLQCSYITMDKNGDGHY 24- 0 LDFIVTATNGDLRSAYNSLDLAVMSTSPNEDGSRHISLETMENSLQ SYITMDKNGDGHY Sbjct: 181 LDFIVTATNGDLRSAYNSLDLAVMSTSPNEDGSRHISLETMENSLQRSYITMDKNGDGHY 24- 0 Query: 241 DILSALQKSIRGSDVNASLHYAARLVEAGDLPSLARRLTIIAYEDIGLANPEAQIHTVTA 30- 0 D+LSALQKSIRGSDVNASLHYAARLVEAGDLPSLARRLTIIAYEDIGLANP+AQ+HTVTA Sbjct: 241 DVLSALQKSIRGSDVNASLHYAARLVEAGDLPSLARRLTIIAYEDIGLANPDAQVHTVTA 30- 0 Query: 301 LEAAQRIGFPEARILIANIVVDLALSPKSNSAYLAMDAALADLRRSGNLPIPRHLRDGHY 36- 0 L+AAQRIGFPEARI IAN+V+DLALSPKSNSAYLAMDAALADLR SGNLPIPRHLRDGHY Sbjct: 301 LDAAQRIGFPEARIPIANVVIDLALSPKSNSAYLAMDAALADLRTSGNLPIPRHLRDGHY 36- 0 Query: 361 SGSKTLGNARDYKYPHAYPEKWVKQQYLPDKLVGHNYFEANETGKYERALGSNKERIDKL 42- 0 +GSK LGNA+DY YPHAYPEKWVKQQYLPDKLVGH+YFEANETGKYERALGSNKERIDKL Sbjct: 361 AGSKDLGNAKDYLYPHAYPEKWVKQQYLPDKLVGHHYFEANETGKYERALGSNKERIDKL 42- 0 Query: 421 SD 422 SD Sbjct: 421 SD 422 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 541 A DNA sequence (GBSx0580) was identified in S. agalactiae <SEQ ID 1729> which encodes the amino acid sequence <SEQ ID 1730>. Analysis of this protein sequence reveals the following: TABLE-US-01674 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2991(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10207> which encodes amino acid sequence <SEQ ID 10208> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 542 A DNA sequence (GBSx0581) was identified in S. agalactiae <SEQ ID 1731> which encodes the amino acid sequence <SEQ ID 1732>. Analysis of this protein sequence reveals the following: TABLE-US-01675 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2402(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 543 A DNA sequence (GBSx0582) was identified in S. agalactiae <SEQ ID 1733> which encodes the amino acid sequence <SEQ ID 1734>. Analysis of this protein sequence reveals the following: TABLE-US-01676 Possible site: 49 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.40 Transmembrane 231-247 (225-250) INTEGRAL Likelihood = -9.92 Transmembrane 159-175 (151-179) INTEGRAL Likelihood = -9.08 Transmembrane 21-37 (18-43) INTEGRAL Likelihood = -9.08 Transmembrane 181-197 (176-201) INTEGRAL Likelihood = -3.35 Transmembrane 111-127 (110-130) INTEGRAL Likelihood = -2.81 Transmembrane 74-90 (74-93) ----- Final Results ----- bacterial membrane --- Certainty = 0.5161(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01677 >GP: CAB15891 GB: Z99123 yxlG [Bacillus subtilis] Identities = 54/203 (26%), Positives = 100/203 (48%), Gaps = 7/203 (3%) Query: 1 MTGLIPMLKKEWLENSRSHKALALLLISIIFGILGPLTALLMPEIMA--GILPKKLQEAI 58 M ++ +L+KEWLE +S K + L + +I G+ PLT MPEI+A G LP ++ + Sbjct: 1 MKVMMALLQKEWLEGWKSGKLIWLPIAMMIVGLTQPLTIYYMPEIIAHGGNLPDGMKISF 60 Query: 59 PDPTYLDSYSQYFKNINQLGLILLVFLFSGSLTQEFTRGTLINLITKGLSKKAIILAKFI 118- P+ + N LG+ L++F GS+ E +G ++++ ++ I++K++ Sbjct: 61 TMPSGSEVMVSTLSQFNTLGMALVIFSVMGSVANERNQGVTALIMSRPVTAAHYIVSKWL 120- Query: 119 MMTLIWSISYILGSLTQYAYTLYYFNNHGQHKLIV-YGTSWIFGLLLLSLILFYSVIFRK 17- 7 + ++I +S+ G Y Y F + + G ++ + +++ L S IFR Sbjct: 121 IQSVIGIMSFAAGYGLAYYYVRLLFEDASFSRFAASLGLYALWVIFIVTAGLAGSTIFR- 17- 9 Query: 178 TAGVLIAC---LMTIVAFFISGF 197 + G AC L V+F + F Sbjct: 180 SVGAAAACGIGLTAAVSFAVHYF 202 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 544 A DNA sequence (GBSx0583) was identified in S. agalactiae <SEQ ID 1735> which encodes the amino acid sequence <SEQ ID 1736>. This protein is predicted to be ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-01678 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1344(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01679 >GP: CAB15892 GB: Z99123 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 116/303 (38%), Positives = 175/303 (57%), Gaps = 18/303 (5%) Query: 4 ISLQNLSKSFGDQIILNQVSLELEENKIYGFVGPNGAGKTTTIKMILGLLKVDSGTISVM 63 +S+++L KS+ + VS + EN+ +GPNGAGKTTT++M+ GLL SGTI ++ Sbjct: 2 LSIESLCKSYRHHEAVKNVSFHVNENECVALLGPNGAGKTTTLQMLAGLLSPTSGTIKLL 61 Query: 64 GNPVTFGQTKSNQVIGYLPDVPEFYDYMTAQEYLQLC---AGLAQNKTSLPIADLLEQVG 120- G + ++IGYLP P FY +MTA E+L +GL++ K I ++LE VG Sbjct: 62 GE-----KKLDRRLIGYLPQYPAFYSWMTANEFLTFAGRLSGLSKRKCQEKIGEMLEFVG 116- Query: 121 LADN-QQRISTYSRGMKQRLGLAQALIHNPKILICDEPTSALDPQGRQEILSIISQLRGQ 17- 9 L + +RI YS GMKQRLGLAQAL+H PK LI DEP SALDP GR E+L ++ +L+ Sbjct: 117 LHEAAHKRIGGYSGGMKQRLGLAQALLHKPKFLILDEPVSALDPTGRFEVLDMMRELKKH 17- 6 Query: 180 KTVIFSTHILSDVEKVCDQVLILTKSGIH---NLEDLRDKASASVNQLNLLIKVSDNEAQ 23- 6 V+FSTH+L D E+VCDQV+I+ I L++L+ + +V L++ K+ + Sbjct: 177 MAVLFSTHVLHDAEQVCDQVVIMKNGEISWKGELQELKQQQQTNVFTLSVKEKLEGWLEE 23- 6 Query: 237 KLALRFPLNQKDQYYKVHLELSEANNREQALASFYRYLVEQEITPYFIELLEDSLEDFYL 29- 6 K + + + + EL + + L+ + + +T E +SLED YL Sbjct: 237 KPYVSAIVYKNPS--QAVFELPDIHAGRSLLSD----CIRKGLTVTRFEQKTESLEDVYL 29- 0 Query: 297 EVI 299 +V+ Sbjct: 291 KVV 293 There is also homology to SEQ ID 686. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 545 A DNA sequence (GBSx0584) was identified in S. agalactiae <SEQ ID 1737> which encodes the amino acid sequence <SEQ ID 1738>. Analysis of this protein sequence reveals the following: TABLE-US-01680 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4383(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01681 >GP: AAB71491 GB: U53767 ORF6 [Bacillus pumilus] Identities = 25/60 (41%), Positives = 41/60 (67%) Query: 2 IGDTILFERTRLGMTQEKLSDYLHLTKATISKWENNQAKPDIDYLILMAKLFDMTLDELV 61 +G I +R L ++QE +++ L +++ ISKWE NQ++P +D LI +A+LFD + ELV Sbjct: 4 LGSNISNKRKSLKLSQEYVAEQLGVSRQAISKWETNQSEPSMDNLIRLAELFDSDIKELV 63 There is also homology to SEQ ID 1740. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 546 A DNA sequence (GBSx0585) was identified in S. agalactiae <SEQ ID 1741> which encodes the amino acid sequence <SEQ ID 1742>. Analysis of this protein sequence reveals the following: TABLE-US-01682 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4241(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01683 >GP: CAB15470 GB: Z99121 yvdC [Bacillus subtilis] Identities = 59/104 (56%), Positives = 76/104 (72%) Query: 1 MDITAYQKWVSEFYKKRNWYQYNSFIRSNFLCEEVGELAQAIRKYEIGRDRPDEIEKSNN 60 M + +KW+ EFY+KR W +Y FIR FL EE GELA+A+R YEIGRDRPDE E S Sbjct: 1 MQLADAEKWMKEFYEKRGWTEYGPFIRVGFLMEEAGELARAVRAYEIGRDRPDEKESSRA 60 Query: 61 ENLNDIKEELGDVLDNIFILADQYNISLEEIIEAHKNKLEKRFE 104 E ++ EE+GDV+ NI ILAD Y +SLE++++AH+ KL KRFE Sbjct: 61 EQKQELIEEMGDVIGNIAILADMYGVSLEDVMKAHQEKLTKRFE 104 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 547 A DNA sequence (GBSx0586) was identified in S. agalactiae <SEQ ID 1743> which encodes the amino acid sequence <SEQ ID 1744>. Analysis of this protein sequence reveals the following: TABLE-US-01684 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0453(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01685 >GP: BAB06803 GB: AP001517 unknown conserved protein [Bacillus halodurans] Identities = 87/187 (46%), Positives = 125/187 (66%) Query: 1 MKITVFCGASNGNNPIYSQKIVELGEWMIKNNHDLVYGGGKVGLMGVIADTVINNGGQAI 60 MKI VFCG+SNG + +Y + +LG+ + + LVYGG VG+MG +AD+V+ GG+ I Sbjct: 1 MKIAVFCGSSNGASDVYKEGARQLGKELARRGITLVYGGASVGIMGAVADSVLEAGGEVI 60 Query: 61 GVIPTFLKDREIAHTNLSKLIVVENMPQRKGKMMSLGEAYIALPGGPGTLEEISEVISWS 120- GV+P FL++ EI+H +L+KLIVVE M +RK KM L + ++ALPGGPGTLEE E+ +W+ Sbjct: 61 GVMPRFLEEPEISHPHLTKLIVVETMHERKAKMAELADGFLALPGGPGTLEEFFEIFTWA 120- Query: 121 RIGQNDSPCILYNINGYFNHLESMFDHMVSEGFLSQNDRNNVLFSDDIIEIEKFIKDYQS 18- 0 +IG + PC L NIN YF+ L ++ HM +E FL + R+ L D I + Y+ Sbjct: 121 QIGLHQKPCGLLNINHYFDPLVTLLHHMSNEQFLHEKYRSMALVHTDPILLLDQFSTYEP 18- 0 Query: 181 PTIRKYS 187 PT++ YS Sbjct: 181 PTVKAYS 187 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 548 A DNA sequence (GBSx0587) was identified in S. agalactiae <SEQ ID 1745> which encodes the amino acid sequence <SEQ ID 1746>. Analysis of this protein sequence reveals the following:

TABLE-US-01686 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5288(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 549 A DNA sequence (GBSx0588) was identified in S. agalactiae <SEQ ID 1747> which encodes the amino acid sequence <SEQ ID 1748>. This protein is predicted to be integrase. Analysis of this protein sequence reveals the following: TABLE-US-01687 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3685(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01688 >GP: AAF12706 GB: AF066865 integrase [bacteriophage TPW22] Identities = 106/377 (28%), Positives = 199/377 (52%), Gaps = 31/377 (8%) Query: 4 ARYRRRGNQNLWAYEIREEGKTVAYNS----GFKTKKLAEAEAEPILQKLRTGSIITKNI 59 A +R+RG W + + + Y G+KTKK AEA A+ ++L S +I Sbjct: 2 ANFRKRGKT--WQFRLSYKDNNGEYKKFEKGGYKTKKEAEAAADEAKKRLNNHSEFDNDI 59 Query: 60 SLPELYQEWLDLKIMPSNRSDVTKKKYLSRKVTLEKLFGDKPISQIRPSEYQRIMNNYGQ 119- SL + +++W + P + ++ T + Y ++K DKPI++I P+ YQ ++N Sbjct: 60 SLYDFFEKWAKVYKKP-HVTEATWRTYKRTLNLIDKYIKDKPIAEITPTFYQAVLNKMSL 118- Query: 120 RVSRNFLGRLNTGVKQSLQMAIADKVMIEDFTQNVELFSTVKSQDADSKYLHSEKAYLDL 17- 9 + L + +K ++++A+ +KV+ E+F + S + ++ + KYLH+++ YL L Sbjct: 119 LYRQESLDKFYFQIKSAMKIAVHEKVISENFADFTKAKSKLAARPVEEKYLHADE-YLKL 17- 7 Query: 180 INAVKDKFNYKKSVVPYIIYFLLKTGMRYGELIALTWEDIDFDKGIFKTYRRFN-SETSQ 23- 8 + ++K Y + Y TGMR+ EL+ LTW +DFDK R ++ S T+ Sbjct: 178 LAIAEEKMEYTSY---FACYLTAVTGMRFAELLGLTWSHVDFDKKEISIQRTWDYSITNN 23- 4 Query: 239 FVPPKNKTSIRIVPVDNECLEILKNLKIEQNQSNKELGLQNTNNMVFQHFGYPNSVPSTN 29- 8 F KN++S R +P+ ++ +++LK K KE +N + V + S N Sbjct: 235 FAETKNESSKRKIPISSKTIKLLKKYK-------KEYWHENKYDRVIYNL-------SNN 28- 0 Query: 299 GTNKVLRGIVQELNIEPIITTKGARHTYGSFLWHRGYDLGIIAKILGHKDISMLIEVYGH 35- 8 G NK ++ ++ + P RH++ S+L ++G DL ++K+LGH+++++ ++VY H Sbjct: 281 GLNKTIK-VIAGRKVHP----HSLRHSFASYLIYKGIDLLTVSKLLGHENLNVTLKVYAH 33- 5 Query: 359 TLEEKIQEEYNEIKQLW 375 L+E QE + I++++ Sbjct: 336 QLKEMEQENNDVIRKIF 352 There is also homology to SEQ ID 578. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 550 A DNA sequence (GBSx0589) was identified in S. agalactiae <SEQ ID 1749> which encodes the amino acid sequence <SEQ ID 1750>. Analysis of this protein sequence reveals the following: TABLE-US-01689 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2710(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 551 A DNA sequence (GBSx0590) was identified in S. agalactiae <SEQ ID 1751> which encodes the amino acid sequence <SEQ ID 1752>. Analysis of this protein sequence reveals the following: TABLE-US-01690 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2534(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01691 >GP: BAA06248 GB: D29979 ORF3 [Bacillus stearothermophilus] Identities = 81/263 (30%), Positives = 135/263 (50%), Gaps = 14/263 (5%) Query: 65 MGVHVELKGQGCRQYEEFIEGNDNNWTSLVKRLI-DNNSNFTRLDIANDIFDESLNVQRL 123- MG+HVE+ GQGCR +E NW L RL+ + N TRLD+A D F + L Sbjct: 1 MGIHVEMTGQGCRLFELH---TSINWYELFYRLVYEYEVNITRLDVAVDDFKGYFKINTL 57 Query: 124 YEYSKKGLCITTARHAEYHEKFVIDSGELVGETVVFGARGNQQWCVYNKLMEQNGKLQTD 18- 3 + K + + A + E VI+ GE +G T+ FGA + + + E+N ++ D Sbjct: 58 VKKLKDDEVTSRFKKARHIENIVIEGGETIGHTLYFGAPSSD---IQVRFYEKNVQMGMD 114- Query: 184 IDINSWVRAELRCWQEKANLIAHQL-NDMRPLASIYFEAINGHYRFVSPKARDKNKRRRE 24- 2 ID+ W R E++ ++A+++A + +D+ PL I + + +F + KA DKNK+R Sbjct: 115 IDV--WNRTEIQLRDDRAHVVAQIIADDVLPLGEIVAGLLRNYIQFRTRKATDKNKKRWP 17- 2 Query: 243 SVRWWQNYINTEEKTRLSIVREKPTLRQSEAWTDKQVSKTIAKVYMAKYEAYGIDQAEVF 30- 2 R+W N++ + R++ K ++ + W D QVSK+ +Y E ++ + F Sbjct: 173 LARFWLNFLGDVQPLRIAKQMPKTSIEKKYRWIDSQVSKSFFMIYYCLNE----EEKQRF 22- 8 Query: 303 LQDLLRRGVEKFTDNDEKEIEQY 325 + D+L G K T D + I Q+ Sbjct: 229 IDDVLAEGASKLTKADLQVINQF 251 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 552 A DNA sequence (GBSx0591) was identified in S. agalactiae <SEQ ID 1753> which encodes the amino acid sequence <SEQ ID 1754>. Analysis of this protein sequence reveals the following: TABLE-US-01692 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2700(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 553 A DNA sequence (GBSx0592) was identified in S. agalactiae <SEQ ID 1755> which encodes the amino acid sequence <SEQ ID 1756>. Analysis of this protein sequence reveals the following: TABLE-US-01693 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3121(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 1757> which encodes the amino acid sequence <SEQ ID 1758>. Analysis of this protein sequence reveals the following: TABLE-US-01694 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2913(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01695 Identities = 19/52 (36%), Positives = 33/52 (62%) Query: 8 FGPNLTRLRKERGISQVELSNQLQIGKQSISDYEKQKAFPTFANLDKIAEYF 59 F NL L ++ I Q+++ N+L I K +I+ Y K ++ PT N+ K+A++F Sbjct: 15 FSTNLNMLMAKKNIKQIDIHNKLGIPKSTITGYVKGRSLPTAGNVQKLADFF 66 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 554 A DNA sequence (GBSx0593) was identified in S. agalactiae <SEQ ID 1759> which encodes the amino acid sequence <SEQ ID 1760>. Analysis of this protein sequence reveals the following: TABLE-US-01696 Possible site: 54 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01697 >GP:AAA98584 GB:L44593 ORF536; putative [Lactococcus phage BK5-T] Identities = 248/532 (46%), Positives = 359/532 (66%), Gaps = 16/532 (3%) Query: 1 MNFIEQISENNQFPIIFVGSGITQRYFENAPTWEKLLKDIWLELFDEESYYAK--AFELR 58 MNFIE I +NNQFPIIFVGSG+T+RYF+N WE+LL ++W + +E+++Y + FE Sbjct: 1 MNFIENIKDNNQFPIIFVGSGVTKRYFKNGLKWEQLLLELWNLVEEEKAFYTQYHVFENL 60 Query: 59 ERFEN-----NDFDIYTNLASLLEKEVSKAFINGNIQVDNLDLKTAYELNISPFKQLVAN 113- + +N +F+I +A +LE++++ AF + + +DNL L A+ +ISPF+Q +AN Sbjct: 61 LKSKNLSKSDKEFEINLMMAGILEEKINNAFYSDELNIDNLTLAQAHTENISPFRQCIAN 120- Query: 114 RFSNLKIREEKIEEIKQFSQMLSKARIIITTNYDNFIEECLKTINVSVKINVGNKGLFLK 17- 3 FSNL ++ EEI FS+ML KAR I+TTNYDNFIEEC NVS+K+NVGN GLF+K Sbjct: 121 TFSNLDRKKGFDEEIISFSKMLVKARFIVTTNYDNFIEECFSKRNVSIKVNVGNSGLFVK 18- 0 Query: 174 SSDYGELYKIHGTVDDASTITITKEDYEKNVTKSALINAKILSNLVESPILFLGYSLTDE 23- 3 S+DYGELYKIHG+V + +TI IT EDY+N +K AL+NAKILSNL ESPILF+GYSLTD+ Sbjct: 181 SNDYGELYKIHGSVKNPNTICITSEDYKNNESKLALVNAKILSNLTESPILFIGYSLTDK 24- 0 Query: 234 NIRKLLTDFAENSPFDISESAQKIGVVEYLPDSESIETVVSSLPDLSVYYSCLKTDNFTN 29- 3 NIR+LLT ++EN P++ISE+A +IGVVEY PD I+ +VS++PDL ++Y+ +TDN+ Sbjct: 241 NIRELLTSYSENLPYEISEAAARIGVVEYTPDKIEIQDIVSNIPDLGIHYTKISTDNYKK 30- 0 Query: 294 IYRLISKINQGFLPSEIAKYENVFRRIIEVKGESKDLKTVLTSYEDLANLTEDEIRSKNI 35- 3 IY IS+I QG+LPSEIAK+E FRKIIEVKG+ K+L TVLTS+ D++ + +E+++KNI Sbjct: 301 IYDEISQIEQGYLPSEIAKFEGAFRKIIEVKGKEKELDTVLTSFIDISKINTEELKNKNI 36- 0 Query: 354 VVAFGDERYIYKFPDFKEYVRSYFLDKETIPQEIVIRFIATQPVASHLPIKKYMFAMSEY 41- 3 VVAFGD +YIYK P +K+Y+R YF + + I + F+ + +P KK+M + + Sbjct: 361 VVAFGDSKYIYRMPTYKDYIREYFSNSMELDTRIALLFLKKRSANYPVPYKKHMGVIESW 42- 0 Query: 414 --ISKDSNKYTENIKKRLSKEEELSLDDFTSSIGVPLL--HSKTLERQTEIVGILE-ADV 46- 8 I D + E++K R+S E + ++ L + L + + I ++ ++V Sbjct: 421 GSIPNDLVQEVESLKTRISNFPESIVRTYSIKANKDLAKKYLPYLNKTSTIEDVMSLSNV 48- 0 Query: 469 PDNVRYNFIATHIKNFPKEELFLLVEKIID----EGIFETSRRRFLKAFDLL 516 P + FI I F EEL +K ID +GI T R+ + ++ ++ Sbjct: 481 PLYNKLRFILFKIDKFKVEELKDFIVKNIDMGEGKGISSTLYRKIVMSYSII 532 A related GBS gene <SEQ ID 8599> and protein <SEQ ID 8600> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01698 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 1.55 GvH: Signal Score (-7.5): 0.27 Possible site: 54 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 2.44 threshold: 0.0 PERIPHERAL Likelihood = 2.44 214 modified ALON score: -0.99 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00041## No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8600 (GBS142) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 18 (lane 5; MW 54 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 33 (lane 6; MW 79.8 kDa). The GBS142-GST fusion product was purified (FIG. 195, lane 3) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 249). These tests confirm that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 555 A DNA sequence (GBSx0594) was identified in S. agalactiae <SEQ ID 1761> which encodes the amino acid sequence <SEQ ID 1762>. This protein is predicted to be integrase. Analysis of this protein sequence reveals the following: TABLE-US-01699 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2933(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01700 <GP: AAA98585 GB: L44593 integrase [Lactococcus phage BK5-T] Identities = 124/382 (32%), Positives = 202/382 (52%), Gaps = 21/382 (5%) Query: 1 MATYRQRGKKKLWDYRIFNEKSELVA-SGSGFKTKREAMNEAMRIE---QQKLLVNSISS 56 MATY++RGK W Y I K L + GF TK +A EAM IE ++ +V+ I Sbjct: 1 MATYQKRGKT--WQYSISRTKQGLPRLTKGGFSTKSDAQAEAMDIESKLKKGFIVDPIKQ 58 Query: 57 DITLYDL-WFEWYSLIIKPSNLAETTKNKYFTRGSVIRKLFGNQKVNKIKHSAYQRKLNT 115- +I+ Y W E Y K + + E T Y ++ N +++I S+YQR LN Sbjct: 59 EISEYFKDWMELY----KKNAIDEMTYKGYEQTLKYLKTYMPNVLISEITASSYQRALNK 114- Query: 116 YAEKYTKNHVRRLNSDIKKAIQFAKRDGVLLSDFTDGVVIAGRKFVKDADDKYLHSIFD- 17- 4 +AE + K + ++ ++ +IQ +G L DFT V+ G K DK+++ FD Sbjct: 115 FAETHAKASTKGFHTRVRASIQPLIEEGRLQKDFTTRAVVKGNGNDKAEQDKFVN--FDE 17- 2 Query: 175 YKKVISYLENNLD--YSNSIVYYLLLVLFKTGLRVGEALALTWDDVNFEDLEIKTYR--R 23- 0 YK+++ Y N L+ YS+ + +++ + TG+R EA L WDD++F + IK R Sbjct: 173 YKQLVDYFRNRLNPNYSSPTMLFIISI---TGMRASEAFGLVWDDIDFNNNTIKCRRTWN 22- 9 Query: 231 FSGDKGTFSPPKTKTSIRTIPISQSLALILRDLKDDQQVMLKNLKIVNMNNQIFYDYRYG 29- 0 + G F PKT IR I I +L+D ++ Q+ + ++L I +++ + Y Sbjct: 230 YRNKVGGFKKPKTDAGIRDIVIDDESMQLLKDFREQQKTLFESLGIKPIHDFVCYHPYRK 28- 9 Query: 291 VSTNSAINKSLKNVLKILNINSKMTATGARHTYGSYLLAKGVDIWVVARLMGHKDITQLL 35- 0 + T SA+ +L + LK LNI++ +T G RHT+ S LL GVDI V++ +GH + Sbjct: 290 IITLSALQNTLDHALKKLNISTPLTIHGLRHTHASVLLYHGVDIMTVSKRLGHASVAITQ 34- 9 Query: 351 ETYGHVLTEVINKEYETVRSLV 372 +TY H++ E+ NK+ + + L+ Sbjct: 350 QTYIHIIKELENKDKDKIIELL 371 There is also homology to SEQ ID 578. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 556 A DNA sequence (GBSx0595) was identified in S. agalactiae <SEQ ID 1763> which encodes the amino acid sequence <SEQ ID 1764>. Analysis of this protein sequence reveals the following: TABLE-US-01701 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1603(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10209> which encodes amino acid sequence <SEQ ID 10210> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01702 >GP: BAB07266 GB: AP001519 unknown conserved protein in others [Bacillus halodurans] Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 6/71 (8%) Query: 37 WWDIDNLQELLGIGRSKLINDILLNPDIKKEVDLSINPNGFIVYPKGKGSRYKILATK-- 94 - WW + +L+E G L +ILL+P K +D I GF+ YP+ KG R+ +A+ Sbjct: 4 WWSMQDLKERTGYSEDWLKENILLHPRYKPMLD--IENGGFVYYPEKKGERWCFIASSME 61 Query: 95 --ARKYFEDNF 103 +KYF+D F Sbjct: 62 EFLKKYFKDIF 72 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 557 A DNA sequence (GBSx0596) was identified in S. agalactiae <SEQ ID 1765> which encodes the amino acid sequence <SEQ ID 1766>. Analysis of this protein sequence reveals the following: TABLE-US-01703 Possible site: 14 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.88 Transmembrane 12-28 (11-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.2550(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01704 >GP: AAB99663 GB: U67604 chromosome segretation protein (smc1) [Methanococcus jannaschii] Identities = 53/210 (25%), Positives = 95/210 (45%), Gaps = 33/210 (15%) Query: 20 IFTNVGVLISNSRDNKAIQRELELLEEGQEKLVDEFSKISTNQYDKYV----------LI 69 - +F +G+L N + + + + + K++DE S I+ K LI Sbjct: 133 LFRRLGLLGDNVISQGDLLKIINISPIERRKIIDEISGIAEFDEKKKKAEEELKKARELI 19- 2 Query: 70 Q------SNLSNNIEKNKQELVQKNSYVK--EDTKYIRDEMLIEKKSK-----EEVYNHV 116- + S + NN++K K+E Y+K E+ K + ++++K S E + N + Sbjct: 193 EMIDIRISEVENNLKKLKKEKEDAEKYIKLNEELKAAKYALILKKVSYLNVLLENIQNDI 25- 2 Query: 117 KNGDKLIEKMAFANELILKFGEVSRENQMLGLKVNSLEEKIVDLSNQPKNDEISKLRKSI 17- 6 KN ++L NE + K E+ E + L L++N+ I++ N+ N+E+ +L KSI Sbjct: 253 KNLEEL------KNEFLSKVREIDVEIENLKLRLNN----IINELNEKGNEEVLELHKSI 30- 2 Query: 177 SSFERELSRFEDVGYSEAEEIKSTLRRILN 206 E E+ + V S E+K I N Sbjct: 303 KELEVEIENDKKVLDSSINELKKVEVEIEN 332 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 1766 (GBS315) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 42 (lane 4; MW 26.7 kDa) and in FIG. 239 (lane 5; MW 41 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 47 (lane 5; MW 52 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 558 A DNA sequence (GBSx0597) was identified in S. agalactiae <SEQ ID 1767> which encodes the amino acid sequence <SEQ ID 1768>. This protein is predicted to be surface protein. Analysis of this protein sequence reveals the following:

TABLE-US-01705 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.70 Transmembrane 229-245 (226-248) ----- Final Results ----- bacterial membrane --- Certainty = 0.4079(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01706 >GP: CAA47097 GB: X66468 orf iota [Streptococcus pyogenes] Identities = 90/262 (34%), Positives = 138/262 (52%), Gaps = 26/262 (9%) Query: 4 VKVLSLITV-SGLFLMAGNLSASADVVISGGDTIMLSGVDAGVSDSIMPPPSSINPV--- 59 +K L+L+T+ S L++ + + AD S D +L+ D V P + ++PV Sbjct: 1 MKKLALLTLFSTTLLVSAPIVSFADETASSSDINILADDDPVVPVEPTDPTTPVDPVDPV 60 Query: 60 -----------TDTTEPSAPTPSTDPI--TDTTEPSAPTPSTDPI--TDTTEPSAPTPST 104- T+ TEP+ PT T+P T+ TEP+ PT T+P T+ TEP+ PT T Sbjct: 61 DPVDPVDPVDPTEPTEPTEPTEPTEPTEPTEPTEPTEPTEPTEPTEPTEPTEPTEPTEPT 120- Query: 105 DQTTGTTDSS-TPSSSTTNPVDGITDNGTKPNAGIDKPSTNKPSDHSESSI--KPVTKPT 16- 1 + T T + T S T P + T+P + +PS +E ++ KPV Sbjct: 121 EPTEPTEPTEPTEPSKPTEPTE--PSKPTEPTEPTEPSKPTEPSKPTEPTVPNKPVDTNP 17- 8 Query: 162 INQPITTVTGDQVIGTQDGKVLVQTPSGTQLK-DAAEVGGNVQKDGTVAIKKSDGKIEVL 22- 0 I P+ T TG ++ +D K ++Q GT K +A E+G +VQKDGTV +K SDGK++VL Sbjct: 179 IENPVNTDTGVVIVAVEDSKPIIQLADGTTKKVEAKEIGADVQKDGTVTVKGSDGKMKVL 23- 8 Query: 221 PKTGEGKTI-FTIVGLLLIAGA 241 PKTGE I +++G L++ G+ Sbjct: 239 PKTGETANIALSVLGSLMVLGS 260 There is also homology to SEQ ID 760. SEQ ID 1768 (GBS141) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 19 (lane 4; MW 35 kDa). The GBS141-His fusion product was purified (FIG. 194, lane 3) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 295), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 559 A DNA sequence (GBSx0598) was identified in S. agalactiae <SEQ ID 1769> which encodes the amino acid sequence <SEQ ID 1770>. Analysis of this protein sequence reveals the following: TABLE-US-01707 Possible site: 18 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8601> and protein <SEQ ID 8602> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01708 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 14.39 GvH: Signal Score (-7.5): -1.23 Possible site: 18 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 8.96 threshold: 0.0 PERIPHERAL Likelihood = 8.96 104 modified ALOM score: -2.29 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 1770 (GBS17) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 4 (lane 2; MW 24 kDa). The His-fusion protein was purified as shown in FIG. 189, lane 10. EXAMPLE 560 A DNA sequence (GBSx0599) was identified in S. agalactiae <SEQ ID 1771> which encodes the amino acid sequence <SEQ ID 1772>. Analysis of this protein sequence reveals the following: TABLE-US-01709 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS gene <SEQ ID 10779> and protein <SEQ ID 10780> were also identified. A further related GBS nucleic acid sequence <SEQ ID 10957> which encodes amino acid sequence <SEQ ID 10958> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 1772 (GBS643) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 129 (lane 2-4; MW 79 kDa) and in FIG. 186 (lane 2; MW 79 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 129 (lane 5-7; MW 54 kDa) and in FIG. 176 (lane 5; MW 54 kDa). GBS643-GST was purified as shown in FIG. 236, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 561 A DNA sequence (GBSx0600) was identified in S. agalactiae <SEQ ID 1773> which encodes the amino acid sequence <SEQ ID 1774>. Analysis of this protein sequence reveals the following: TABLE-US-01710 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5815(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 562 A DNA sequence (GBSx0601) was identified in S. agalactiae <SEQ ID 1775> which encodes the amino acid sequence <SEQ ID 1776>. This protein is predicted to be membrane protein. Analysis of this protein sequence reveals the following: TABLE-US-01711 Possible site: 33 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.32 Transmembrane 311-327 (282-332) INTEGRAL Likelihood = -10.46 Transmembrane 293-309 (282-310) INTEGRAL Likelihood = -8.55 Transmembrane 390-406 (388-410) INTEGRAL Likelihood = -7.64 Transmembrane 49-65 (40-69) INTEGRAL Likelihood = -5.68 Transmembrane 100-116 (98-122) INTEGRAL Likelihood = -4.35 Transmembrane 130-146 (127-148) INTEGRAL Likelihood = -3.88 Transmembrane 344-360 (342-363) ----- Final Results ----- bacterial membrane --- Certainty = 0.6328(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01712 >GP: CAB70618 GB: AJ243106 membrane protein [Streptococcus thermophilus] Identities = 234/665 (35%), Positives = 379/665 (56%), Gaps = 59/665 (8%) Query: 13 FAKVKDVDIFALKAYMEITH-GAETGAQSILLDVFVNFPFFLLNLIVGLFSVILRFFENF 71 - FAK+K VDIF+LK+YME T+ G+ GA ++ ++FVN FF+LN +VG FS+++R E Sbjct: 5 FAKLKGVDIFSLKSYMEPTNFGSFNGAWVLINELFVNLFFFILNAVVGFFSLLIRILEKI 64 Query: 72 SLYDTYKQTVYHSSQKLWENLSGN--GSYTS-SLLYLLVAISAFSIFISYLFSKGDFSKR 128- LY TYK V+H + +W +G+ G+ T+ SL+ L+ + AF +F Y FSKG FS+ Sbjct: 65 DLYATYKTYVFHGASSIWHGFTGSNTGNITNKSLVGTLLLVLAFYLFYQYFFSKGSFSRT 124- Query: 129 LIHLFVVIILGMGYFGTIQSTSGGIYILDTVHQLAGSFSDAVTNLSLDNPSGGKTKITQK 18- 8 L+H+ +V++L +GYFGT+ TSGG+Y+LDTV+ ++ + + + +D KI + Sbjct: 125 LLHVCLVLLLALGYFGTVAGTSGGLYLLDTVNNVSKDVTKKIAGIKVDYAKDKSIKIGK- 18- 3 Query: 189 SSVADNYVMKTSYTAYLFVNTGQLNGKFHNNQTGKEEKFDNEQVLGKYDKSGKFITPKQK 24- 8 S++D+Y+ +TSY AY+FVNTGQ NGK+ N+Q GKEE FD+ +VLG DK+G F K K Sbjct: 184 -SMSDSYIAETSYKAYVFVNTGQENGKYKNSQDGKEEAFDDSKVLGTSDKNGNFKAVKAK 24- 2 Query: 249 DILNYTDNLGDKATEGEEKNRWLSAVNDYLWIKSGYVILKIFEAVILAVPLILIQLIAFM 30- 8 + Y D+LG+ A + EKNRW+SA+ D+++ + YVI KI EA +LAVP+ILIQL+ + Sbjct: 243 ERSKYLDDLGEGANDDGEKNRWVSAMPDFIFTRVFYVIFKIVEAFVLAVPIILIQLLNVV 30- 2 Query: 309 ADVLVIILMFIFPLALLVSFLPRMQDIIFNVLKVMFGAVSFPALAGFLTLIVFYTQTLIA 36- 8 A +LV+ ++ +FP+ LL+SF+PRMQ+++F VLKVMFG + FPA+ LTL++FY + +I Sbjct: 303 AQILVLTMILLFPVVLLMSFVPRMQELVFGVLKVMFGGLIFPAITTLLTLLIFYIEKMIE 36- 2 Query: 369 TFVKKKFTDGSLLSGSNFKGQAILFMLLITVFVQGCVFWGIWKYKETFLRLIIGSRASQV 42- 8 V F DG L + + ++F LL++V +G +++ IW++K L+ I+GS+A V Sbjct: 363 NIVTNGF-DGVLKTLPSLLLFGLVFKLLVSVVSKGVIYFLIWRFKGQLLQFILGSKARMV 42- 1 Query: 429 -------INQSVDKINEKAENLGITPKSIYERAHDMSSLAMMGAGYGVGTMMNAQ---DN 47- 8 + V K E A + P A + + + GAG+G G MMNA+ N Sbjct: 422 ATDIGTKVEHGVTKSKEVASQV---PTRSLATAQHLGNFTLAGAGFGTGVMMNAKSHFQN 47- 8 Query: 479 WNAFKERQQANLDDGQSKTNDADKYDEANADDTVISKEAELTNEGEYQSELPKEASKRIE 53- 8 +F R++ + + + + + + +I ++ P + K I Sbjct: 479 AGSFFTRKEPSQPETVMPSGPTEAPITPESPEPIIP-----------PTQTPPDNFKTIG 52- 7 Query: 539 QLGKESSYELSFISEGNSTEEILKNVKSDNHTFQEGDGDTSLTNQDMITNDIENHSNNYT 59- 8 + + +SEG + E ++ + + Sbjct: 528 EEKPTPPSDSPIMSEGTPSSE----------------------------DEFQTLKEEWM 55- 9 Query: 599 SPLKQRKLNKLEGELSQFNSDVSMTKNHGKNAFEKGFNASKTKEVRKQHNLERQSKVLEE 65- 8 SP KQ ++N LE L + +M K G NAF + + + T++ + + N+ER+ ++ + Sbjct: 560 SPFKQHRINTLERRLDAYKDPQAMYKAQGSNAFTRAYRKTLTRDDKIRANIERRDRLTQR 61- 9 Query: 659 LEKLR 663 L +LR Sbjct: 620 LNQLR 624 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 563 A DNA sequence (GBSx0602) was identified in S. agalactiae <SEQ ID 1777> which encodes the amino acid sequence <SEQ ID 1778>. This protein is predicted to be conjugative protein. Analysis of this protein sequence reveals the following: TABLE-US-01713 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3714(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01714 >GP: CAB70617 GB: AJ243106 conjugative protein [Streptococcus thermophilus] Identities = 515/757 (68%), Positives = 612/757 (80%), Gaps = 1/757 (0%) Query: 1 MSDFEADLADDVKELGLETLDFTVDTLTHEMEIPYQFDWLIGVDLGKGQYNANIKEFIYN 60 M DF LADD +ELG E L +TVD LT EMEIPYQFDW+IGV L K + A +K+ Y Sbjct: 78 MRDFSEALADDSRELGEELLLYTVDRLTDEMEIPYQFDWVIGVTLRKQNHGATVKDLAYE 137- Query: 61 QFESIASNFASLAGYEVEVDEDWYKEHSEEELLVYSLLSTLKAKRLTDVDLFYYQRMQFL 120- F + A GYE + WY ++ +E ++ S L+AKRLT+ +LFYYQRMQ+L Sbjct: 138 SFNEFSEKIAKGLGYEYALSPTWYDDYRSDEFTIFQAFSVLRAKRLTNEELFYYQRMQYL 19- 7 Query: 121 RYVPHTKSEVIANRNMLNVTDTLIKSLEGGFLKLESAYGSSFVSVLPVGRFSTIFNGFHL 18- 0 RY+PH K EV+ANR+ N+TDTLIK L+GGFL+LES YGSSFV++LPVG+F FNGFHL Sbjct: 198 RYIPHYKKEVLANRSQFNITDTLIKVLKGGFLELESPYGSSFVTILPVGKFPVQFNGFHL 25- 7 Query: 181 GELVQRMSFPVELRFKAEFIDKTKLGGTMGRSNTRYDQIMKEAYNTNTVQQDDILMGAYS 24- 0 GE VQR++FPVELR KAEFID K+ G MGRSNTRY IM+EA NT+TVQQD+I+MG+ S Sbjct: 258 GEFVQRLNFPVELRIKAEFIDTNKIKGRMGRSNTRYRNIMEEAENTDTVQQDEIIMGSIS 31- 7 Query: 241 LKDLMKKVGNKEEIIEYGCYLVVAGSSLNQLKQRRYAILSYFDDMKVNVYEASHDTPYLF 30- 0 LKDLMKKVGNKE+IIEYG YL+V+ SS+NQL+QRR IL+YFDDM V + EAS D PYLF Sbjct: 318 LKDLMKKVGNKEDIIEYGAYLIVSASSVNQLRQRRQVILNYFDDMGVEISEASQDGPYLF 37- 7 Query: 301 QALLYGQDLQKTTRKWNHLVTARGFSELMLFTNTQSGNRIGWYIGRVDNRLTAWDSIDEA 36- 0 QALLYG++LQK TR W H+VTARGFSELM FTNT SGNRIGWYIGRVDN + WDSI +A Sbjct: 378 QALLYGENLQKKTRTWTHMVTARGFSELMPFTNTSSGNRIGWYIGRVDNWIGRWDSIAKA 43- 7 Query: 361 IMGSKNLVLFNATVANKEDVAGKVTKNPHVIITGATGQGKSYLAQMIFLHTAQQNVRVLY 42- 0 I SKN+VL+NATV NKED+AGK+TKNPH+IITGATGQGKS+LAQ+IFL A QNV+ LY Sbjct: 438 IDSSKNIVLYNATVGNKEDIAGKITKNPHIIITGATGQGKSFLAQIIFLSVALQNVKTLY 49- 7 Query: 421 VDPKRELRQHYLKVVSDPEYARKFPLRKKQIEETNFVTLDSSVKENHGVLDPIVILDKEG 48- 0 +DPKRELR HY +V++ PE+AR++P RKKQI+ NFVTLDSS+ NHGVLDPIV+LDKE Sbjct: 498 IDPKRELRNHYQEVINSPEFARRYPERKKQIDNFNFVTLDSSLPSNHGVLDPIVVLDKEQ 55- 7 Query: 481 ASSTAKNMLLYLLKNATEIKLDQTTALTEAISQVIAKREAGEVVGFNQVIEVLIDSESDE 54- 0 A AKNML +LL+ ++ +DQ TA+TEAI+ ++ +R AGE VGF V+E L ++ S E Sbjct: 558 AVEVAKNMLEFLLQAVDDVTMDQKTAITEAINTIVERRVAGENVGFKHVLETLRNASSSE 61- 7 Query: 541 VQSVGRYFKAIIQNSILELAFSDGDVAGLSYEERVTVLEVADLSLPKDGSDHISDHESNS 60- 0 + SVGRY +I+ NSILELAFSDG GL+YE RVT+LEV +L LPKD S ISDHE NS Sbjct: 618 IASVGRYLTSIVTNSILELAFSDGTTPGLNYESRVTILEVNNLKLPKDDSTKISDHERNS 67- 7 Query: 601 IALMFALGAFCKHFGERSDDE-TVEIFDEAWVLMQSSEGKAVIKSMRRVGRSKYNVLMLV 65- 9 IALMFALGAFC HFGER+++E T+E FDEAW+LM+S+EGKAVIK+MRR+GRSK N L L+ Sbjct: 678 IALMFALGAFCTHFGERNENEDTIEFFDEAWILMKSAEGKAVIKNMRRIGRSKNNTLALI 73- 7 Query: 660 SQSVHDAENDDDTTGFGTIFSFYEKSEREDILSHVGLEVTPKNLEWIDNMISGQCLYYDV 71- 9 +QSVHDAENDDDTTGFGTIF+FYEKSEREDIL HV LEVT NLEWIDNMISGQCLYYDV Sbjct: 738 TQSVHDAENDDDTTGFGTIFAFYEKSEREDILRHVNLEVTESNLEWIDNMISGQCLYYDV 79- 7 Query: 720 YGNLNMISIHNIHPDIDPLLKPMKKTVSSHLENKYAS 756 YGNLNMIS+HN+ DID LLKPMK TVSS LENKYAS Sbjct: 798 YGNLNMISVHNLFEDIDMLLKPMKATVSSSLENKYAS 834 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 564 A DNA sequence (GBSx0604) was identified in S. agalactiae <SEQ ID 1779> which encodes the amino acid sequence <SEQ ID 1780>. This protein is predicted to be ISL2 protein. Analysis of this protein sequence reveals the following: TABLE-US-01715 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3469(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01716 >GP: CAC18595 GB: AJ278419 IS1381 transposase [Streptococcus pneumoniae] Identities = 110/125 (88%), Positives = 119/125 (95%) Query: 81 MNYEASKQLTDVRFKRLVGVQRTTFEEMLAVLKTAYQRKHAKGGRTPKLSLEDLLMATLQ 140- MNYEASKQLTD RFKRLVGVQRTTFEEMLAVLKTAYQ KHAKGGR PKLSLEDLLMATLQ Sbjct: 1 MNYEASKQLTDARFKRLVGVQRTTFEEMLAVLKTAYQLKHAKGGRKPKLSLEDLLMATLQ 60 Query: 141 YMREYRTYEQIAADFGIHESNLIRRSQWVESTLIQSGFTISKTHLSAEDTVIVDATEVKI 20- 0 Y+REYRTYE+IAADFG+HESNL+RRSQWVE TL+QSG TIS+T LS+EDTV++DATEVKI Sbjct: 61 YVREYRTYEEIAADFGVHESNLLRRSQWVEVTLVQSGVTISRTPLSSEDTVMIDATEVKI 120- Query: 201 NRPKK 205 NRPKK Sbjct: 121 NRPKK 125 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 565 A DNA sequence (GBSx0605) was identified in S. agalactiae <SEQ ID 1781> which encodes the amino acid sequence <SEQ ID 1782>. Analysis of this protein sequence reveals the following: TABLE-US-01717 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.58 Transmembrane 39-55 (32-66) ----- Final Results ----- bacterial membrane --- Certainty = 0.6031(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 566 A DNA sequence (GBSx0606) was identified in S. agalactiae <SEQ ID 1783> which encodes the amino acid sequence <SEQ ID 1784>. This protein is predicted to be Cag-W. Analysis of this protein sequence reveals the following: TABLE-US-01718 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.82 Transmembrane 50-66 (49-66) INTEGRAL Likelihood = -3.72 Transmembrane 25-41 (23-45) ----- Final Results ----- bacterial membrane --- Certainty = 0.2529(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 567 A DNA sequence (GBSx0607) was identified in S. agalactiae <SEQ ID 1785> which encodes the amino acid sequence <SEQ ID 1786>. Analysis of this protein sequence reveals the following:

TABLE-US-01719 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.80 Transmembrane 36-52 (32-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01720 >GP: CAB12298 GB: Z99106 similar to transposon protein [Bacillus subtilis] Identities = 68/339 (20%), Positives = 133/339 (39%), Gaps = 49/339 (14%) Query: 16 KKEEGGKQPKTKEVKQRTANFIV--YGILGLLFIVGFFGSLRAIGLSNQVQHLKETVIAV 73 - K+ E ++ K K + R+ V + +G L + L +I +Q+ +K+ Sbjct: 24 KRIERPEKDKQKVPRDRSKLIAVTLWSCVGSLLFICLLAVLLSINTRSQLNDMKDETNKP 83 Query: 74 EKKSKHKKTDDSLDISRIQYYMNNFVYYYINYS--QDTADQRKTELENY--------YSF 123- K K + ++ + +++ F+ Y+N Q++ ++R LE+Y + Sbjct: 84 TNDDKQK-----ISVTAAENFLSGFINEYMNVKNDQESIEKRMQSLESYMVKQEDNHFED 138- Query: 124 STASMTDDVRKSRTLQTQRLISVEKEKDYYIALMRIGYEV-------------------- 16- 3 D ++ R L+ L +V++ + ++ YE Sbjct: 139 EERFNVDGLKGDRELKGYSLYNVKEGDKNSLFQYKVTYENLYPVEKEVEKEVKDGKKKKK 19- 8 Query: 164 --------DKKSYQMNLAVPFQMQRGLLAIVSQPYTVAEDLYLGKSKAFEKKTLDQVKEL 21- 5 +K QM L +P + A+ + PY +Y K K + E Sbjct: 199 VKEKVKTNEKYEKQMLLNIPVTNKGDSFAVSAVPYFT--QIYDLKGDIAFKGKEETRDEY 25- 6 Query: 216 SKEQVSSIQKFLPVFFNKYALINKTDLKLLMKTPELMGKGFKVSELDLNNAIYYQEKKHQ 27- 5 + E+ SI+ FL FF KYA K ++ +MK PE + E + + ++ KK Sbjct: 257 AGEKKESIESFLQNFFEKYASEKKEEMVYMMKKPEALEGNLLFGE--VQSVKIFETKKGF 31- 4 Query: 276 VVQLSVTFEDLVTGGTRSENFTLYLFKADNGWYVEEMYH 314 V +V F++ +E F+L + + +YV ++ H Sbjct: 315 EVFCAVRFKEKENDIPVNEKFSLEITENSGQFYVNKLKH 353 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 1786 (GBS333d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 145 (lane 8-10; MW 58 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 145 (lane 11 & 13; MW 33 kDa), in FIG. 182 (lane 2; MW 33 kDa) and in FIG. 185 (lane 3; MW 58 kDa). GBS333d-GST was purified as shown in FIG. 236, lane 2. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 568 A DNA sequence (GBSx0608) was identified in S. agalactiae <SEQ ID 1787> which encodes the amino acid sequence <SEQ ID 1788>. Analysis of this protein sequence reveals the following: TABLE-US-01721 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4177(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01722 >GP: CAB38326 GB: Y17736 hypothetical protein [Streptomyces coelicolor A3(2)] Identities = 45/80 (56%), Positives = 56/80 (69%) Query: 4 FTEEAWKDYVSWQQEDKKILKRINRLIEDIKRDPFEGIGKPEPLKYHYSGAWSRRITEEH 63 FT W+DYV W + D+K+ KRINRLI DI RDPF+G+GKPEPLK SG WSRRI + H Sbjct: 5 FTSHGWEDYVHWAESDRKVTKRINRLIADIARDPFKGVGKPEPLKGDLSGYWSRRIDDTH 64 Query: 64 RLIYMIEDGEIYFLSFRDHY 83 RL+Y D ++ + R HY Sbjct: 65 RLVYKPTDDQLVIVQARYHY 84 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 569 A DNA sequence (GBSx0609) was identified in S. agalactiae <SEQ ID 1789> which encodes the amino acid sequence <SEQ ID 1790>. Analysis of this protein sequence reveals the following: TABLE-US-01723 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5669(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10211> which encodes amino acid sequence <SEQ ID 10212> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01724 >GP: AAD17306 GB: AF121418 putative Phd protein [Francisella tularensis subsp. novicida] Identities = 26/84 (30%), Positives = 45/84 (52%) Query: 4 MEAIVYSHFRNNLKDYMKKVNDEFEPLIVVNKNPDENIVVLSQDSWESLQETIRLMENDY 63 M+ + YS FRN L D M +V P+IV + E +V++S + +++ +ET LM + Sbjct: 1 MQTVNYSTFRNELSDSMDRVTKNHSPMIVTRGSKKEAVVMMSLEDFKAYEETAYLMRSMN 60 Query: 64 LSHKVINGISQVKEKQVTKHGLIE 87 ++ N I +V+ + LIE Sbjct: 61 NYKRLQNSIDEVESGLAIQKELIE 84 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 570 A DNA sequence (GBSx0610) was identified in S. agalactiae <SEQ ID 1791> which encodes the amino acid sequence <SEQ ID 1792>. Analysis of this protein sequence reveals the following: TABLE-US-01725 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2407(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 571 A DNA sequence (GBSx0611) was identified in S. agalactiae <SEQ ID 1793> which encodes the amino acid sequence <SEQ ID 1794>. Analysis of this protein sequence reveals the following: TABLE-US-01726 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1274(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10213> which encodes amino acid sequence <SEQ ID 10214> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01727 >GP: AAB60015 GB: U09422 ORF18 [Enterococcus faecalis] Identities = 41/140 (29%), Positives = 73/140 (51%), Gaps = 3/140 (2%) Query: 23 FPVEMSELKLALGLREEDDLEYIIADSDCQL-LKEHDSIEMINQFVELVENVDSELVKAV 81 - FP++ E+K +GL +E + EY I D + + E+ SI +N+ E+V + EL + Sbjct: 26 FPIDFEEVKEKIGLNDEYE-EYAIHDYELPFTVDEYTSIGELNRLWEMVSELPEELQSEL 84 Query: 82 HQVIGYTASDFVDYDFNFGDCCLLSDVTTRRELGEYYFDELGVQGVGKEALEMYFDHEAY 141- ++ + +S + + D + SD ++ YY +E G G +L+ Y D++AY Sbjct: 85 SALLTHFSS-IEELSEHQEDIIIHSDCDDMYDVARYYIEETGALGEVPASLQNYIDYQAY 143- Query: 142 GRDIDLESQGGFSDYGYVEI 161 GRD+DL +++G EI Sbjct: 144 GRDLDLSGTFISTNHGIFEI 163 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 572 A DNA sequence (GBSx0612) was identified in S. agalactiae <SEQ ID 1795> which encodes the amino acid sequence <SEQ ID 1796>. Analysis of this protein sequence reveals the following: TABLE-US-01728 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1366(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 573 A DNA sequence (GBSx0613) was identified in S. agalactiae <SEQ ID 1797> which encodes the amino acid sequence <SEQ ID 1798>. Analysis of this protein sequence reveals the following: TABLE-US-01729 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1484(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 574 A DNA sequence (GBSx0614) was identified in S. agalactiae <SEQ ID 1799> which encodes the amino acid sequence <SEQ ID 1800>. This protein is predicted to be abortive phage resistance protein. Analysis of this protein sequence reveals the following: TABLE-US-01730 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2205(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10215> which encodes amino acid sequence <SEQ ID 10216> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01731 >GP: AAB53710 GB: U94520 abortive phage resistance protein [Lactococcus lactis] Identities = 131/499 (26%), Positives = 210/499 (41%), Gaps = 97/499 (19%) Query: 3 MFSKIEFKNFMSFSNLT------------------FDLLNRGKCKDIIAIYGENGSGKTN 44 M F+NF+SF L+ D+ N K + IYG N SGK++ Sbjct: 1 MLVNFRFENFLSFDKLSTFSMAPGKSRQHMEDLIELDIKNNQKLLKLSTIYGANASGKSS 60 Query: 45 IVEAF---KLLVL-----SLQSMESLNENTRLQSLLKEQTNKE---ENQKTNFGDISEIL 93 V+A K L++ L S N+NT SL + + E E++ ++G S IL Sbjct: 61 FVDAIGISKSLIIRGFYNGLVLSNSYNKNTVDNSLNETKFEYEIVIEDKVYSYG-FSVIL 119- Query: 94 DKISFFTTFKGIAKNTHRIASEGNTILKYYFNIEKDNGYYLLEYNENNELVKEELVFKIK 153- F + + N ++ Y KDN YN N+E L + Sbjct: 120 SLKKFMSEWLYDITNDEKM---------IYTIDRKDN-----SYNINDEF----LNLDEQ 16- 1 Query: 154 SNKGVHFSITNIDGLSQSLNKTIFKNTIFKDLTEQIEKYWGKHTFLSIFN--NYCLEV-- 20- 9 SN + I + S + N +F N++ D + IE F +FN N LEV Sbjct: 162 SNNRISIYIDD----SANDNTQLFLNSL-NDGKKTIESKDNSTIFKKVFNWFNNTLEVLG 21- 6 Query: 210 ---------------NEEF---INEQVSINFQKVVDEFDKIFIWSGNFRGPFHSTELLLK 25- 1 EEF + + + +N V+D N P E +L Sbjct: 217 PGDEARGSIASLTQEEEEFKEDLGKYLELNDTGVIDIVQVPVDNLSNV--PAKLQERILD 27- 4 Query: 252 DISKGKIDKSEKEKLSYTEEIIYKYFSALYIDIKDVKYKQDAQGQEIKYELMIRKNIGGD 31- 1 +I+ I K +KE+ E I F+ + +++ Q+ Q +EL K+ G Sbjct: 275 NITT-DIKKKKKER-----EDIEISFNTILNTSQNIYIIQNNDEQFEYFELKF-KHKNGT 32- 7 Query: 312 LLDVPISLESQGTKNLLDLLKV-FNNVLDGKICIVDEIDSGIHDLLMNSILNDLK--GSV 36- 8 L +S ES GT L++L V F+N D K+ ++DEID +H LL + + K S+ Sbjct: 328 LYS--LSEESDGTVRLIELFSVLFHN--DEKVFVIDEIDRSLHPLLTYNFIESFKKQKSI 38- 3 Query: 369 NGQLIFTTHDTTLL--KELSPSSAYFLNVDIKGNKVIISGNEADKKIGVNNNLEKLYLSG 42- 6 N QLI TTH+ +L + L +F++ + +GN + S E ++ + ++ YL+G Sbjct: 384 N-QLIVTTHEDYILNFELLRRDEVWFVDKNFEGNSSMFSLEEFKERF--DKDINTSYLNG 44- 0 Query: 427 FFGAVPDPLDIDFSDLFLD 445 +G +P+ L FS+ D Sbjct: 441 RYGGIPN-LSCLFSEFAKD 458 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 575 A DNA sequence (GBSx0615) was identified in S. agalactiae <SEQ ID 1801> which encodes the amino acid sequence <SEQ ID 1802>. This protein is predicted to be repressor (rstR-1). Analysis of this protein sequence reveals the following: TABLE-US-01732 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3724(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01733 >GP: AAB84427 GB: AF027868 transcription regulator [Bacillus subtilis] Identities = 31/81 (38%), Positives = 53/81 (65%), Gaps = 2/81 (2%) Query: 9 QKLKELRKEKKLTQTELASKLNISQKSYSNWESGKAEPTLDNIIKLANILDVTVDYLLGR 68 Q+L++LRK KLT +LA K+ I++ SY +E+ +P LD ++ LA + DV+VDY+LG Sbjct: 4 QRLRQLRKAHKLTMEQLAEKIGIAKSSYGGYEAESKKPPLDKLVILARLYDVSVDYILGL 63 Query: 69 SDNFSNTIVLSKNNMKSFSKR 89 +D+ + + N+K F ++ Sbjct: 64 TDDPDPKV--ERKNLKEFLEK 82 There is also homology to SEQ ID 1740. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 576 A DNA sequence (GBSx0616) was identified in S. agalactiae <SEQ ID 1803> which encodes the amino acid sequence <SEQ ID 1804>. Analysis of this protein sequence reveals the following: TABLE-US-01734 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3607(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes; could be useful antigens for vaccines or diagnostics. EXAMPLE 577 A DNA sequence (GBSx0617) was identified in S. agalactiae <SEQ ID 1805> which encodes the amino acid sequence <SEQ ID 1806>. Analysis of this protein sequence reveals the following: TABLE-US-01735 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0564(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10217> which encodes amino acid sequence <SEQ ID 10218> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01736 >GP:CAB12294 GB:Z99106 similar to transposon protein [Bacillus subtilis] Identities = 93/348 (26%), Positives = 164/348 (46%), Gaps = 28/348 (8%) Query: 81 SRLQVMIDYVRITLKDVRDLEFFCRNFLHCAFKEFQPFESKLMNYNHLWKRGDIWIFDFA 140- S L M+DY+R++ K D++ LH + +S Y ++ I +F A Sbjct: 26 SPLVSMVDYIRVSFK-THDVDRIIEEVLHLSKDFMTEKQSGFYGYVGTYELDYIKVFYSA 84 Query: 141 DKHETGNFQITVQLSGRGCRQLELLMETEKFTWHDWLSYLRNSYRDDMNVTRFDIAIDEL 20- 0 G + +++SG+GCRQ E +E K TW+D + ++ + + TRFD+AID+ Sbjct: 85 PDDNRG---VLIEMSGQGCRQFESFLECRKKTWYD---FFQDCMQQGGSFTRFDLAIDD- 137- Query: 201 YLGKDRENEQFHLSDMISKYYRHELDFESLRTWNYIGGGSLNFSDMEEIEQNRQGISLYF 26- 0 + F + +++ K + E R ++ GS + SD G ++YF Sbjct: 138 ------KRTYFSIPELLKKAQKGEC-ISRFRKSDF-NGSFDLSD------GITGGTTIYF 18- 3 Query: 261 GSRQSEMYFNFYEKRYEIAKQEGITVEEALEIFELWNRYEIRLSQSKANAAVDEFISGVP 32- 0 GS++SE Y FYEK YE A++ I +EE + WNRYE+RL +A A+D + Sbjct: 184 GSKKSEAYLCFYEKNYEQAEKYNIPLEELGD----WNRYELRLKNERAQVAIDALLKTKD 23- 9 Query: 321 IGEISRGLIVSKIDVYDGKNEY--GSFQADRKWQLMFGGVEPLKFVTKPEAYSIERTLRW 37- 8 + I+ +I + + D ++ W G V L KP+ +++ W Sbjct: 240 LTLIAMQIINNYVRFVDADENITREHWKTSLFWSDFIGDVGRLPLYVKPQKDFYQKSRNW 29- 9 Query: 379 LSDSVSPSLAMIREYDMIVDGDYLQTILNSGEVNERGEKILDSIKASL 426 L +S +P++ M+ E D + L ++ E+ ++ +K+LD A + Sbjct: 300 LRNSCAPTMKMVLEADEHLGKTDLSDMIAEAELADKHKKMLDVYMADV 347 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8603> and protein <SEQ ID 8604> were also identified. Analysis of this protein sequence reveals a RGD motif at residues 131-133. The protein has homology with the following sequences in the databases: ##STR00042## SEQ ID 8604 (GBS294) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 167 (lane 6 & 7; MW 65 kDa--thioredoxin fusion), in FIG. 238 (lane 2; MW 65 kDa) and in FIG. 40 (lane 6; MW 37 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 47 (lane 3; MW 76 kDa). Purified Thio-GBS294-His is shown in FIG. 244, lane 2. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 578 A DNA sequence (GBSx0618) was identified in S. agalactiae <SEQ ID 1807> which encodes the amino acid sequence <SEQ ID 1808>. Analysis of this protein sequence reveals the following: TABLE-US-01737 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.61 Transmembrane 24 - 40 (20 - 41) INTEGRAL Likelihood = -1.97 Transmembrane 53 - 69 (52 - 72) ----- Final Results ----- bacterial membrane --- Certainty = 0.2444(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-01738 >GP:AAB60012 GB:U09422 ORF21 [Enterococcus faecalis] Identities = 136/473 (28%), Positives = 228/473 (47%), Gaps = 40/473 (8%) Query: 9 RGIKVKPYMRYMSYYL-FSFLFILFLTPVGVYSYYYLDL-------LKMMDKMSM----I 56 RG +++P + + ++ + L +FL VG++ + L DK+ + I Sbjct: 4 RGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLII 63 Query: 57 SVGTGLFLAFFVSWYLTWFLQEANPLFNKLDRLKRMSKFLYENGYVYEKR-------KKS 109- S + + V++ F + +L ++++K + EN + ++ K S Sbjct: 64 SFSVAILICLLVAFV---FKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDS 120- Query: 110 NKKTKTKYR-FPKVYVKQGKYDLSVSFEMAGGKFQKKFKDIGGELEDTFFMDFMEKTDDP 16- 8 +TK K FPK+Y + + + E+ GK+Q + + +LE + + +K Sbjct: 121 AGRTKEKITYFPKMYYRLKNGLIQIRVEITLGRYQDQLLHLEKKLESGLYCELTDKELKD 18- 0 Query: 169 RFKIYKLAYSAFLSRITVKDVIWNKDKGIKLMDGYYWDFINDPHLLVAGGTGGGKTVLLR 22- 8 + Y L Y SRI++ D + KD ++LM +W++ PH+L+AGGTGGGKT + Sbjct: 181 SYVEYTLLYDTIASRISI-DEVEAKDGKLRLMKNVWWEYDKLPHMLIAGGTGGGKTYFIL 23- 9 Query: 229 SILRCLAEI-GVCDICDPKRADFVTMSDLSAFEGRIAFEKADIIEKFENAVTIMFARYDF 28- 7 +++ L I DPK AD ++DL + + + K D++ E M R + Sbjct: 240 TLIEALLHTDSKLYILDPKNAD---LADLGSVMANVYYRKEDLLSCIETFYEEMMKRSE- 29- 5 Query: 288 VRNEMKRLGHKDMKKFYDY-GLEPYFFVCDEYNALMSSLSYQEREIVDNAFTQYILLGRQ 34- 6 EMK++ + K Y Y GL +F + DEY A M L +E V N Q ++LGRQ Sbjct: 296 ---EMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLGRQ 35- 2 Query: 347 VGCNAIIAMQKPSADDLPTKIRSNMMHHISVGRLDDGGYVMMFGDENRNKEFRFIKYLAG 40- 6 G I+A Q+P A L IR +++GR+ + GY MMFG + + K+F F+K Sbjct: 353 AGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQ-KDF-FLK---- 40- 6 Query: 407 RRVYGRGYSAVFGEVAREFYSPLLPKNFSFYDAFEKINRHENPFDPTENQEVS 459 R+ GRGY V V EFY+PL+PK + F + +K++ T EV+ Sbjct: 407 -RIKGRGYVDVGTSVISEFYTPLVFKGYDFLEEIKKLSNSRQSTQATCEAEVA 458 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8605> and protein <SEQ ID 8606> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01739 Lipop Possible site: -1 Crend: 8 McG: Discrim Score: -10.05 GvH: Signal Score (-7.5): -3.42 Possible site: 40 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -3.61 threshold: 0.0 INTEGRAL Likelihood = -3.61 Transmembrane 24 - 40 (20 - 41) INTEGRAL Likelihood = -1.97 Transmembrane 53 - 69 (52 - 72) PERIPHERAL Likelihood - 1.01 224 modified ALOM score: 1.22 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2444(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00043## SEQ ID 8606 (GBS216) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 42 (lane 3; MW 66.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 47 (lane 2; MW 91 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 579 A DNA sequence (GBSx0619) was identified in S. agalactiae <SEQ ID 1809> which encodes the amino acid sequence <SEQ ID 1810>. Analysis of this protein sequence reveals the following: TABLE-US-01740 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4095(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 580 A DNA sequence (GBSx0620) was identified in S. agalactiae <SEQ ID 1811> which encodes the amino acid sequence <SEQ ID 1812>. Analysis of this protein sequence reveals the following: TABLE-US-01741 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0944(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10219> which encodes amino acid sequence <SEQ ID 10220> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 581 A DNA sequence (GBSx0621) was identified in S. agalactiae <SEQ ID 1813> which encodes the amino acid sequence <SEQ ID 1814>. Analysis of this protein sequence reveals the following: TABLE-US-01742 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.94 Transmembrane 810-826 (808-830) ----- Final Results ----- bacterial membrane --- Certainty = 0.2975(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01743 !GB: D90354 surface protein antigen precursor [Strept . . . >GP: BAA14368 GB: D90354 surface protein antigen precursor [Streptococcus sobrinus] Identities = 151/408 (37%), Positives = 219/408 (53%), Gaps = 27/408 (6%) Query: 451 PSKAVIDEAGQSVNGKTVLPNAELNYVAKQDFSQYKGMTASQGKIAKNFVFIDDYKDDAL 51- 0 P K +E G ++GK+VL Y D QYKG +++ I K F ++DDY ++AL Sbjct: 1162 PHKVNKNENGVVIDGKSVLAGTTNYYELTWDLDQYKGDKSAKETIQKGFFYVDDYPEEAL 1- 221 Query: 511 DGKSMKVNSIKASDGTDVSQL-LEMRHVLSTDTLDEKLQTLIKEAGISPVGEFYMWTAKD 56- 9 D ++ + IK +D + + + S + +Q ++K+A I+P G F ++TA D Sbjct: 1222 D---LRTDLIKLTDANGKAVTGVSVADYASLEAAPAAVQDMLKKANITPKGAFQVFTADD 1- 278 Query: 570 PQAFYKAYVQKGLDVTYNLSFKVKKEFTK--GQIQNGVAQIDFGNGYTGNIVVNDLTTPE 62- 7 PQAFY AYV G D+T VK E K G +N QIDFGNGY NIV+N++ Sbjct: 1279 PQAFYDAYVVTGTDLTIVTPMTVKAEMGKIGGSYENKAYQIDFGNGYESNIVINNVPQIN 1- 338 Query: 628 IHKDV---LDKEDGKSINNGTVKLGDEVTYKLEGWVVPTGRSYDLFEYKFVDQLQRTPDL 68- 4 KDV +D D +++ T+ L Y+L G ++P + +LFEY F D +T D Sbjct: 1339 PEKDVTLTMDPADSTNVDGQTIALNQVFNYRLIGGIIPADHAEELFEYSFSDDYDQTGDQ 1- 398 Query: 685 YLRD-KVVAKVDVTLKDGTVIKKGTNLGEYTETVYNKKTGLYELVFKKDFLEKVARSSEF 74- 3 Y K AKVD+TLKDGT+IK GT+L YTE ++ G + FK+DFL V+ S F Sbjct: 1399 YTGQYKAFAKVDLTLKDGTIIKAGTDLTSYTEAQVDEANGQIVVTFKEDFLRSVSVDSAF 1- 458 Query: 744 GADDFVVVKRIKAGDVYNTADFFINGNKVKTETVVTHTPE--KPKPVEPQ---------- 79- 1 A+ ++ +KRI G NT +NG + TV T TPE +P PV+P+ Sbjct: 1459 QAEVYLQMKRIAVGTFANTYVNTVNGITYSSNTVRTSTPEPKQPSPVDPKTTTTVVFQPR 1- 518 Query: 792 --KATPKAPAKG--LPQTGEASVAPLTALGAIILSA-IGLAGFKKRKE 834 KA AP G LP TG++S A L LG + L+A L G +++++ Sbjct: 1519 QGKAYQPAPPAGAQLPATGDSSNAYLPLLGLVSLTAGFSLLGLRRKQD 1566 Identities = 75/242 (30%), Positives = 120/242 (48%), Gaps = 33/242 (13%) Query: 11 SADQVTTQATTQTVTQNQAETVTSTQLDKAVATAKKAAVAVTTTAAVNHATTTDAQADLA 70 - S+ T+QA T + V++++LD+A +A++A V V+ A VN T + D A Sbjct: 73 SSQAETSQAQAGQKTGAMSVDVSTSELDEAAKSAQEAGVTVSQDATVNKGTVETS--DEA 130- Query: 71 NQTQT-VKDVTAKAQANTQAIKDATAENAKIDAENKAESQRVSQLNAQTKAKID---AEN 126- NQ +T +KD +K A+ I+ T + A N+AE+ R++Q NA KA+ + A N Sbjct: 131 NQKETEIKDDYSKQAAD---IQKTTEDYKAAVAANQAETDRITQENAAKKAQYEQDLAAN 18- 7 Query: 127 KDAQAKADATNAQLQKDYQAKLAKIKSVEAYNAGVRQRNKDAQA--------------KA 17- 2 K + NAQ + DY+AKLA+ + A V+Q N D+QA + Sbjct: 188 KAEVERITNENAQAKADYEAKLAQYQKDLA---AVQQANNDSQAAYAAAKEAYDKELARV 24- 4 Query: 173 DATNAQLQKDYQAKLA---LYNQALKAKAEADKQSINNVAFDIKAQ----AKGVDNAEYG 22- 5 A NA +K+Y+ LA N+ +KA+ A +Q D +A+ K + A+ G Sbjct: 245 QAANAAAKKEYEEALAANTTKNEQIKAENAAIQQRNAQAKADYEAKLAQYEKDLAAAQSG 30- 4 Query: 226 NS 227 N+ Sbjct: 305 NA 306 Identities = 63/223 (28%), Positives = 100/223 (44%), Gaps = 31/223 (13%) Query: 2 ITTLQTSQVSADQVTTQATTQTVTQNQAETVTSTQLDKAVATAK-----------KAAVA 50 + +Q + +A + +A T+N+ + + + A AK K A Sbjct: 241 LARVQAANAAAKKEYEEALAANTTKNEQIKAENAAIQQRNAQAKADYEAKLAQYEKDLAA 30- 0 Query: 51 VTTTAAVNHATTTDAQADLANQTQTVKDVTAKA-QANTQAIKDATAENAKIDAENKAESQ 109- + A N A +A + V+ A A QA QA+ TA+NA+I AEN+A Q Sbjct: 301 AQSGNATNEADYQAKKAAYEQELARVQAANAAAKQAYEQALAANTAKNAQITAENEAIQQ 36- 0 Query: 110 RVSQLNAQTKAKIDAENKDAQAKADATNAQLQKDYQAKLA----KIKSVEAYNAGVRQRN 16- 5 R +Q A +AK+ KD A A + NA + DYQ KLA ++ V+A NA +Q Sbjct: 361 RNAQAKANYEAKLAQYQKDL-AAAQSGNAANEADYQEKLAAYEKELARVQAANAAAKQEY 41- 9 Query: 166 KDAQAKADATNAQL--------------QKDYQAKLALYNQAL 194 + +A+A NA++ + DY+ KL+ Y + L Sbjct: 420 EQKVQEANAKNAEITEANRAIRERNAKAKTDYELKLSKYQEEL 462 Identities = 75/243 (30%), Positives = 101/243 (40%), Gaps = 56/243 (23%) Query: 8 SQVSAD-QVTTQATTQTVTQNQAETVTSTQLDKAVATAKKAAVAVTTTAAVNHATTTDAQ 66 S+ +AD Q TT+ V NQAET TQ + A A+ A V T +AQ Sbjct: 142 SKQAADIQKTTEDYKAAVAANQAETDRITQ-ENAAKKAQYEQDLAANKAEVERITNENAQ 20- 0 Query: 67 ADL---ANQTQTVKDVTAKAQANT--------------------------------QAIK 91 A A Q KD+ A QAN +A+ Sbjct: 201 AKADYEAKLAQYQKDLAAVQQANNDSQAAYAAAKEAYDKELARVQAANAAAKKEYEEALA 26- 0 Query: 92 DATAENAKIDAENKAESQRVSQLNAQTKAKIDAENKDAQAKADATNAQLQKDYQAKLA-- 149- T +N +I AEN A QR +Q A +AK+ KD A A + NA + DYQAK A Sbjct: 261 ANTTKNEQIKAENAAIQQRNAQAKADYEAKLAQYEKDL-AAAQSGNATNEADYQAKKAAY 31- 9 Query: 150 --KIKSVEAYNAGVRQRNKDAQAKADATNAQL--------------QKDYQAKLALYNQA 19- 3 ++ V+A NA +Q + A A A NAQ+ + +Y+AKLA Y + Sbjct: 320 EQELARVQAANAAAKQAYEQALAANTAKNAQITAENEAIQQRNAQAKANYEAKLAQYQKD 37- 9 Query: 194 LKA 196 L A Sbjct: 380 LAA 382 There is also homology to SEQ ID 598. SEQ ID 1814 (GBS191) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 176 (lane 2; MW 91 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 582 A DNA sequence (GBSx0622) was identified in S. agalactiae <SEQ ID 1815> which encodes the amino acid sequence <SEQ ID 1816>. This protein is predicted to be TnpA. Analysis of this protein sequence reveals the following: TABLE-US-01744 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2935(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10221> which encodes amino acid sequence <SEQ ID 10222> was also identified. A related GBS nucleic acid sequence <SEQ ID 9921> which encodes amino acid sequence <SEQ ID 9922> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01745 >GP: AAC82523 GB: AF027768 TnpA [Serratia marcescens] Identities = 168/385 (43%), Positives = 232/385 (59%), Gaps = 13/385 (3%) Query: 26 MMFKVEAVGPPERCPECGFD-KLYKHSSRNQLIMDLPIRLKRVGLHLNRRRYKCRECGST 84 - M F+V+ V P C ECG + + R+ DLPI KRV L + RRRY CR C +T Sbjct: 1 MHFQVD-VPDPIACEECGVQGEFVRFGKRDVPYRDLPIHGKRVTLWVVRRRYTCRACKTT 59 Query: 85 IS------VDEKRSMTKRLLKSIQEQSMSKTFVEVAESVGVDEKTIRNVFKDYVALKERE 138- VD R MT RL + ++++S + + VA G+DEKT+R++F R Sbjct: 60 FRPQLPEMVDGFR-MTLRLHEYVEKESFNHPYTFVAAQTGLDEKTVRDIFNARAEFLGRW 118- Query: 139 YQFETPKWLGIDEIHIIRRPRLVLTNIERRTIYDIKPNRNKETVIQRLSEISDRTYIEYV 19- 8 ++FETP+ LGIDE+++ +R R +LTNIE RT+ D+ R ++ V L ++ DR +E V Sbjct: 119 HRFETPRILGIDELYLNKRYRCILTNIEERTLLDLLATRRQDVVTNYLMKLKDRQKVEIV 17- 8 Query: 199 TMDMWKPYKDAVNTILPQAKVVVDKFHVVRMANQALDNVRKSLKAHMSQKERRTLMRERF 25- 8 +MDMW PY+ AV +LPQA++VVDKFHVVRMAN AL+ VRK L+ + + RTL +R Sbjct: 179 SMDMWNPYRAAVKAVLPQARIVVDKFHVVRMANDALERVRKGLRKELKPSQSRTLKGDRK 23- 8 Query: 259 ILLKRKHDLNERESFLLDTWLGNLPALKEAYELKEEFYWIWDTPDPDEGHLRYSQWRHRC 31- 8 ILLKR H++++RE +++TW G P L AYE KE FY IWD + +W Sbjct: 239 ILLKRAHEVSDRERLIMETWTGAFPQLLAAYEHKERFYGIWDATTRLQAEAALDEWI-AT 29- 7 Query: 319 MSSNSKDAYKDLVRAVDNWHVEIFNYF--DKRLTNAYTESINSIIRQVERMGRGYSFDAL 37- 6 + K+ + DLVRAV NW E YF D +TNAYTESIN + + R GRGYSF+ + Sbjct: 298 IPKGQKEVWSDLVRAVGNWREETMTYFETDMPVTNAYTESINRLAKDKNREGRGYSFEVM 35- 7 Query: 377 RAKILFNEKLHKKRKPRFNSSAFNK 401 RA++L+ K HKK+ P S F K Sbjct: 358 RARMLYTTK-HKKKAPTAKVSPFYK 381 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 583 A DNA sequence (GBSx0623) was identified in S. agalactiae <SEQ ID 1817> which encodes the amino acid sequence <SEQ ID 1818>. This protein is predicted to be mercuric reductase. Analysis of this protein sequence reveals the following: TABLE-US-01746 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2115(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01747 >GP: CAA70224 GB: Y09024 mercuric reductase [Bacillus cereus] Identities = 411/546 (75%), Positives = 483/546 (88%) Query: 1 MNKFKVNISGMTCTGCEKHVESALEKIGAKNIESSYRRGEAVFELPDDIEVESAIKAIDE 60 M K++V++ GMTCTGCE+HV ALE +GA IE +RRGEAVFELP+ + VE+A KAI + Sbjct: 1 MKKYRVDVQGMTCTGCEEHVAVALENMGATGIEVDFRRGEAVFELPNALGVETAKKAISD 60 Query: 61 ANYQAGEIEEVSSLENVALINEDNYDLLIIGSGAAAFSSAIKAIEYGAKVGMIERGTVGG 120- A YQ G+ EEV S E V L NE +YD +IIGSG AAFSSAI+A++YGAKV MIERGT+GG Sbjct: 61 AKYQPGKAEEVQSQEMVQLGNEGDYDYIIIGSGGAAFSSAIEAVKYGAKVAMIERGTIGG 120- Query: 121 TCVNIGCVPSKTLLRAGEINHLSKDNPFIGLQTSAGEVDLASLITQKDKLVSELRNQKYM 18- 0 TCVNIGCVPSKTLLRAGEINHL+K+NPF+GL TSAGEVDLA LI QK++LV+ELRN KY+ Sbjct: 121 TCVNIGCVPSKTLLRAGEINHLAKNNPFVGLHTSAGEVDLAPLIKQKNELVTELRNSKYV 18- 0 Query: 181 DLIDEYNFDLIKGEAKFVDASTVEVNGTKLSAKRFLIATGASPSLPQISGLEKMDYLTST 24- 0 DLID+Y F+LI+GEAKFVD TVEVNG +SAKRFLIATGASP+ P I GL ++DYLTST Sbjct: 181 DLIDDYGFELIEGEAKFVDEKTVEVNGAPISAKRFLIATGASPAKPNIPGLNEVDYLTST 24- 0 Query: 241 TLLELKKIPKRLTVIGSGYIGMELGQLFHHLGSEITLMQRSERLLKEYDPEISESVEKAL 30- 0 +LLELKK+PKRL VIGSGYIGMELGQLFH+LGSE+TL+QRSERLLKEYDPEISESVEK+L Sbjct: 241 SLLELKKVPKRLVVIGSGYIGMELGQLFHNLGSEVTLIQRSERLLKEYDPEISESVEKSL 30- 0 Query: 301 IEQGINLVKGATFERVEQSGEIKRVYVTVNGSREVIESDQLLVATGRKPNTDSLNLSAAG 36- 0 +EQGINLVKGAT+ER+EQ+G+IK+V+V VNG + +IE+DQLLVATGR PNT +LNL AAG Sbjct: 301 VEQGINLVKGATYERIEQNGDIKKVHVEVNGKKRIIEADQLLVATGRTPNTATLNLRAAG 36- 0 Query: 361 VETGKNNEILINDFGQTSNEKIYAAGDVTLGPQFVYVAAYEGGIITDNAIGGLNKKIDLS 42- 0 VE G EI+I+D+ +T+N +IYAAGDVTLGPQFVYVAAY+GG+ NAIGGLNKK++L Sbjct: 361 VEIGSRGEIIIDDYSRTTNTRIYAAGDVTLGPQFVYVAAYQGGVAAPNAIGGLNKKLNLE 42- 0 Query: 421 VVPAVTFTNPTVATVGLTEEQAKEKGYDVKTSVLPLGAVPRAIVNRETTGVFKLVADAET 48- 0 VVP VTFT P +ATVGLTE+QAKE GY+VKTSVLPL AVPRA+VNRETTGVFKLVAD++T Sbjct: 421 VVPGVTFTAPAIATVGLTEQQAKENGYEVKTSVLPLDAVPRALVNRETTGVFKLVADSKT 48- 0 Query: 481 LKVLGVHIVSENAGDVIYAASLAVKFGLTIEDLTETLAPYLTMAEGLKLVALTFDKDISK 54- 0 +KVLG H+V+ENAGDVIYAA+LAVKFGLT++D+ ETLAPYLTMAEGLKL ALTFDKDISK Sbjct: 481 MKVLGAHVVAENAGDVIYAATLAVKFGLTVDDIRETLAPYLTMAEGLKLAALTFDKDISK 54- 0 Query: 541 LSCCAG 546 LSCCAG Sbjct: 541 LSCCAG 546 There is also homology to SEQ ID 1820. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 584 A DNA sequence (GBSx0624) was identified in S. agalactiae <SEQ ID 1821> which encodes the amino acid sequence <SEQ ID 1822>. This protein is predicted to be regulatory protein. Analysis of this protein sequence reveals the following: TABLE-US-01748 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4529(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01749 >GP: AAA83973 GB: AF138877 mercury resistance operon negative regulator MerR1 [Bacillus sp. RC607] Identities = 84/129 (65%), Positives = 105/129 (81%) Query: 1 MIYRISEFADKCGVNKETIRYYERKNLLQEPHRTEAGYRIYSYDDVKRVGFIKRIQELGF 60 M +RI E ADKCGVNKETIRYYER L+ EP RTE GYR+YS V R+ FIKR+QELGF Sbjct: 1 MKFRIGELADKCGVNKETIRYYERLGLIPEPERTEKGYRMYSQQTVDRLHFIKRMQELGF 60 Query: 61 SLSEIYKLLGVVDKDEVRCQDMFEFVSKKQKEVQKQIEDLKRIETMLDDLKQRCPDEKKL 120- +L+EI KLLGVVD+DE +C+DM++F K +++Q++IEDLKRIE ML DLK+RCP+ K + Sbjct: 61 TLNEIDKLLGVVDRDEAKCRDMYDFTILKIEDIQRKIEDLKRIERMLMDLKERCPENKDI 120- Query: 121 HSCPIIETL 129 + CPIIETL Sbjct: 121 YECPIIETL 129 There is also homology to SEQ ID 1712. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 585 A DNA sequence (GBSx0625) was identified in S. agalactiae <SEQ ID 1823> which encodes the amino acid sequence <SEQ ID 1824>. This protein is predicted to be Nramp metal ion transporter. Analysis of this protein sequence reveals the following:

TABLE-US-01750 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.85 Transmembrane 175-191 (169-201) INTEGRAL Likelihood = -11.94 Transmembrane 150-166 (132-173) INTEGRAL Likelihood = -9.45 Transmembrane 491-507 (481-509) INTEGRAL Likelihood = -8.92 Transmembrane 375-391 (374-396) INTEGRAL Likelihood = -8.39 Transmembrane 72-88 (69-93) INTEGRAL Likelihood = -7.96 Transmembrane 280-296 (274-299) INTEGRAL Likelihood = -7.17 Transmembrane 413-429 (411-431) INTEGRAL Likelihood = -6.79 Transmembrane 327-343 (322-346) INTEGRAL Likelihood = -3.40 Transmembrane 444-460 (443-462) INTEGRAL Likelihood = -3.24 Transmembrane 132-148 (132-149) INTEGRAL Likelihood = -0.96 Transmembrane 115-131 (114-131) ----- Final Results ----- bacterial membrane --- Certainty = 0.6540(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01751 >GP: AAF83825 GB: AE003939 manganese transport protein [Xylella fastidiosa] Identities = 185/450 (41%), Positives = 278/450 (61%), Gaps = 29/450 (6%) Query: 16 ANGPSLEEINGTIEVPKDLSFFKTLLAYSGPGALVAVGYMDPGNWSTSITGGQNFQYLLI 75 - ++ PSL E++ ++ V + + LLA+ GPG +V+VGYMDPGNW+T + GG F Y+L+ Sbjct: 35 SDSPSLGEMHASVAVSRRGHWGFRLLAFLGPGYMVSVGYMDPGNWATGLAGGSRFGYMLL 94 Query: 76 SIILMSSLIAMLLQYMSAKLGIVTQMDLAQAIRARTSKQLGIVLWILTELAIMATDIAEV 135- S+IL+S+++A++LQ ++A+LGI + MDLAQA RAR S+ + LW++ ELAI+A D+AEV Sbjct: 95 SVILLSNVMAIVLQALAARLGIASDMDLAQACRARYSRGTTLALWVVCELAIIACDLAEV 154- Query: 136 IGGAIALYLLFHIPLAIAVFITVFDVLLLLLLTKIGFRKIEALVVALILVIFLVFAYQVA 19- 5 IG AIAL LL +P+ V IT DV+L+LLL GFR +EA V+AL+LVIF F Q+ Sbjct: 155 IGTAIALNLLLGVPIIWGVVITAVDVVLVLLLMHRGFRALEAFVIALLLVIFGCFVVQIV 21- 4 Query: 196 LSHPIWTDIFKGLVPTSEAFSTSHTVNGQTPLSGALGIIGATVMPHNLYLHSSVVQSRKL 25- 5 L+ P ++ G VP + V L A+GI+GATVMPHNLYLHSS+VQ+R Sbjct: 215 LAAPPLQEVLGGFVPRWQ------VVADPQALYLAIGIVGATVMPHNLYLHSSIVQTRAY 26- 8 Query: 256 DHNNKKDIAR--AIRFSTFDSNIQLTVAFFVNSLLLIMGVAVFKTGSVTDPSFFGLFKAL 31- 3 + + R A+R++ DS + L +A F+N+ +LI+ AVF D Sbjct: 269 P---RTPVGRRSALRWAVADSTLALMLALFINASILILAAAVFHAQHHFD---------- 31- 5 Query: 314 SNSTIMSNSILAHIASSGILSLLFAIALLASGQNSTITGTLTGQIIMEGFIHMKVPIWFR 37- 3 + +LA + G+ + LFA ALLASG NST+T TL GQI+MEGF+ +++ W R Sbjct: 316 VEEIEQAYQLLAPVLGVGVAATLFATALLASGINSTVTATLAGQIVMEGFLRLRLRPWLR 37- 5 Query: 374 RIITRLISVIPVMICVLVTSGRSTVEEHIAINNLMNNSQVFLAFALPFSMLPLLIFTNSK 43- 3 R++TR ++++PV++ V + + T L+ SQV L+ LPF+++PLL + Sbjct: 376 RVLTRGLAIVPVIVVVALYGEQGT-------GRLLLLSQVILSMQLPFAVIPLLRCVADR 42- 8 Query: 434 VEMDDDFKNTWIIKILGWLSVIGLIYLNMK 463 M W++ ++ WL ++ LN+K Sbjct: 429 KVMGALVAPRWLM-VVAWLIAGVIVVLNVK 457 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 586 A DNA sequence (GBSx0626) was identified in S. agalactiae <SEQ ID 1825> which encodes the amino acid sequence <SEQ ID 1826>. Analysis of this protein sequence reveals the following: TABLE-US-01752 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2590(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 587 A DNA sequence (GBSx0627) was identified in S. agalactiae <SEQ ID 1827> which encodes the amino acid sequence <SEQ ID 1828>. Analysis of this protein sequence reveals the following: TABLE-US-01753 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.82 Transmembrane 212-228 (204-233) INTEGRAL Likelihood = -8.39 Transmembrane 98-114 (94-125) INTEGRAL Likelihood = -7.22 Transmembrane 132-148 (122-154) INTEGRAL Likelihood = -6.42 Transmembrane 159-175 (155-188) INTEGRAL Likelihood = -4.78 Transmembrane 54-70 (51-72) INTEGRAL Likelihood = -2.97 Transmembrane 18-34 (15-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.4927(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01754 >GP: CAB16051 GB: Z99124 yydJ [Bacillus subtilis] Identities = 97/239 (40%), Positives = 154/239 (63%), Gaps = 3/239 (1%) Query: 4 LEFRKSIRGRTLFYIISTVALTYVLGYILPVGIDKIRHLTLGEFYFSTYTVFTQFGFLIF 63 LEF+KSI + + + + ++LGY L VGIDK+ ++T F+FS+YTV TQFG ++F Sbjct: 3 LEFKKSISNKVIIILGAMFVFLFLLGYFLLVGIDKVSNVTPEMFFFSSYTVATQFGLMLF 62 Query: 64 GFVIVYFFNKDYSDKCILYHYFSGYHLTKYFYTKLLVLFSEFFIAIIVCNILASLLWGYS 123- FVI +F N++YS+K IL++ G ++ +FY K+ VLF E F I + ++ SL++ + Sbjct: 63 SFVIAFFINREYSNKNILFYKLIGENIYTFFYKKIAVLFLECFAFITLGLLIISLMY-HD 121- Query: 124 LFYFLTTTILFSLVVLQYLLVVSTISILFSNMLVSIGVTIFYWITSIILVAIGG-IFKVS 18- 2 +F LFS V+LQY+L++ TIS+L N+L+SIGV+I YW+TS+ILVAI F Sbjct: 122 FSHFALLLFLFSAVILQYILIIGTISVLCPNILISIGVSIVYWMTSVILVAISNKTFGFI 18- 1 Query: 183 AIFDASNSLYKIIGK-LFSHPMTIDLTDFFIIVPYMICLSVISFLIVCLSNRRWLLNGM 240- A F+A N++Y I + L S MT+ D I+ Y++ + +I+ +++ S RW+ G+ Sbjct: 182 APFEAGNTMYPRIERVLQSDNMTLGSNDVLFIILYLVSIIIINAIVLRFSKTRWIKMGL 240- No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 588 A DNA sequence (GBSx0628) was identified in S. agalactiae <SEQ ID 1829> which encodes the amino acid sequence <SEQ ID 1830>. This protein is predicted to be antibiotic epidermin immunity protein F. Analysis of this protein sequence reveals the following: TABLE-US-01755 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2901(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01756 >GP:CAB16052 GB:Z99124 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 100/209 (47%), Positives = 150/209 (70%), Gaps = 4/209 (1%) Query: 1 MFINNYTLKIGNRILLENTNLDFEEGEINHLLGRNGSGKSQLAKDFIINRGNYFSNDIYE 60 M I NYTLK+ + LL++T+L F G+INH++G+NG GKSQLAKDF++N DI + Sbjct: 1 MNIANYTLKVKGKTLLQDTDLHFSSGKINHVVGKNGVGKSQLAKDFLLNNSERIGRDIRQ 60 Query: 61 DTLIISSYSNLPSDVT----INDLERTIPWKLSKEIYQLLNINQISKTVKLKQLSDGQKQ 116- + +ISS SN+P+DV+ ++ L + K+ +I LLN++ I V +K LSDGQKQ Sbjct: 61 NVSLISSSSNIPNDVSKDFLLHFLSKKFDAKMIDKIAYLLNLDNIDGKVLIKNLSDGQKQ 120- Query: 117 KVKLLVLLSLDKHIIILDEITNALDKKSVDEINVFLQNYIQYYPEKIIINISHDINNIRS 17- 6 K+KLL L DK+II+LDEITN+LDKK+V EI+ FL YIQ PEKIIINI+HD++++++ Sbjct: 121 KLKLLSFLLEDKNIIVLDEITNSLDKKTVIEIHGFLNKYIQENPEKIIINITHDLSDLKA 18- 0 Query: 177 LKGNYFLIDNQKICKVDTLDDAISWYLGE 205 ++G+Y++ ++Q+I + ++D I Y+ E Sbjct: 181 IEGDYYIFNHQEIQQYHSVDKLIEVYINE 209 A related DNA sequence was identified in S. pyogenes <SEQ ID 1831> which encodes the amino acid sequence <SEQ ID 1832>. Analysis of this protein sequence reveals the following: TABLE-US-01757 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2760(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01758 Identities = 49/174 (28%), Positives = 82/174 (46%), Gaps = 27/174 (15%) Query: 3 INNYTLKIGNRILLENTNLDFEEGEINHLLGRNGSGKSQLAK----------DFIINRGN 52 I N G R +L N N++ +G++ L+G NG+GKS + K II G Sbjct: 23 IQNLKKSYGKRTILNNVNMNIPKGKVYALIGPNGAGKSTIMKILTGLVSKTSGSIIFEGR 82 Query: 53 YFS-------NDIYEDTLI---ISSYSNLPSDVTINDL-ERTIPWKLSKEIYQLLNINQI 101- +S I E+ + +S+Y N+ T+ + E TI L+K + + I Sbjct: 83 EWSRRDLRKIGSIIEEPPLYKNLSAYDNMKVVTTMLGVSESTILPLLNK-----VGLGNI 137- Query: 102 SKTVKLKQLSDGQKQKVKLLVLLSLDKHIIILDEITNALDKKSVDEINVFLQNY 155 K +KQ S G KQ++ + + L ++ILDE TN LD + E+ ++++ Sbjct: 138 DKR-PVKQFSLGMKQRLGIAISLINSPKLLILDEPTNGLDPIGIQELREIIESF 190 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 589 A DNA sequence (GBSx0629) was identified in S. agalactiae <SEQ ID 1833> which encodes the amino acid sequence <SEQ ID 1834>. This protein is predicted to be aminoglycoside 6-adenylyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-01759 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1780(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01760 >GP:CAA29839 GB:X06627 ORF (str) [Staphylococcus aureus] Identities = 91/289 (31%), Positives = 146/289 (50%), Gaps = 14/289 (4%) Query: 1 MRDEQEIYNLVLNIANQDKRIEAVLLNGSRANPNVPKDDFQDYDIVFVTNFIEDIISDTN 60 MR E+EI NLV A Q ++ + L GSR N N+ KD FQDYD F + IE + + Sbjct: 1 MRTEKEILNLVSEFAYQRSNVKIIALEGSRTNENIKKDKFQDYDFAFFVSDIEYFTHEES 60 Query: 61 YHKKFGDILIMQKPNE---FRNKTEYNCFAYLMQFQDLTRIDLRLIKPEFLEDYLDDA-- 115- + FG++L +QKP + F +Y ++Y+M F+D ++D+ LI + L Y D+ Sbjct: 61 WLSLFGELLFIQKPEDMELFPPDLDYG-YSYIMYFKDGIKMDITLINLKDLNRYFSDSDG 119- Query: 116 FSKVLLDKKNKYLDYNFERSSLYETKQLSEDEINKILNEIYWVSTYVVKGIARNDIIYSE 17- 5 K+L+DK N S Y K+ +E E NE + VSTYV KG+ R +I+++ Sbjct: 120 LVKILVDKDNLVTQEIVPDDSNYWLKKPTEREFYDCCNEFWSVSTYVARGVFRREILFAL 17- 9 Query: 176 FMISNPIKNAFIKLLKQKILIEKELDSLSFGKLDKDILQYITDKD--QLLKIFSNKSLKD 23- 3 +N ++ ++++ I + D S GK K I +Y+TDK+ LL F + Sbjct: 180 DHFNNILRPELLRMISWYIGFNRGFD-FSLGKNYKFINKYLTDKEFNMLLATFEMNGYRK 23- 8 Query: 234 IEANLRFLLDETNQMAKYISINRKLNLNQGEYQSAMKFMNIFLSNSYQN 282 + + ++ KY S N+ L Y + K + F+ N+Y+N Sbjct: 239 TYQSFKLCC----ELFKYYS-NKVSCLGNYNYPNYEKNIENFIRNNYEN 282 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8607> and protein <SEQ ID 8608> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01761 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: -5.26 GvH: Signal Score (-7.5): -6.14 Possible site: 33 >>> Seems to have no N-terminal signal sequence ALOM program count: 0 value: 6.10 threshold: 0.0 PERIPHERAL Likelihood = 6.10 151 modified ALOM score: -1.72 *** Reasoning Step: 3 ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1780(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00044## SEQ ID 1834 (GBS46) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 11 (lane 6; MW 34.9 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 3; MW 59.8 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 590 A DNA sequence (GBSx0630) was identified in S. agalactiae <SEQ ID 1835> which encodes the amino acid sequence <SEQ ID 1836>. Analysis of this protein sequence reveals the following: TABLE-US-01762 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1179(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 591 A DNA sequence (GBSx0631) was identified in S. agalactiae <SEQ ID 1837> which encodes the amino acid sequence <SEQ ID 1838>. Analysis of this protein sequence reveals the following: TABLE-US-01763 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.81 Transmembrane 177-193 (177-194) INTEGRAL Likelihood = -0.27 Transmembrane 129-145 (129-145) ----- Final Results ----- bacterial membrane --- Certainty = 0.2126(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8609> which encodes amino acid sequence <SEQ ID 8610> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-01764 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: -19.59 GvH: Signal Score (-7.5): -4.49 Possible site: 44 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -2.81 threshold: 0.0 INTEGRAL Likelihood = -2.81 Transmembrane 172-188 (172-189) INTEGRAL Likelihood = -0.27 Transmembrane 124-140 (124 140) PERIPHERAL Likelihood = 8.01 30 modified ALOM score: 1.06 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2126(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 592 A DNA sequence (GBSx0632) was identified in S. agalactiae <SEQ ID 1839> which encodes the amino acid sequence <SEQ ID 1840>. Analysis of this protein sequence reveals the following: TABLE-US-01765 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10223> which encodes amino acid sequence <SEQ ID 10224> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01766 >GP: CAB49414 GB: AJ248284 hypothetical protein [Pyrococcus abyssi] Identities = 29/86 (33%), Positives = 52/86 (59%), Gaps = 4/86 (4%) Query: 14 TYYILLALFE--EAHGYAIMQKVEEMSGGDVRIAAGTMYGAIENLLKQKWIKSIPSD--D 69 - +Y ILL L E + HGYAI +++EE++ G + + G +Y ++ L K K ++ ++ Sbjct: 19 SYLILLILNENEKLHGYAIRKRLEELTDGKLVPSEGALYSILKMLKKYKLVEDYWAEVGG 78 Query: 70 RRRKVYIITETGKEIVELETNRLRKL 95 R R+ Y ITE GKE+++ +R++ Sbjct: 79 RVRRYYQITELGKEVLDEIKEEIREI 104 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 593 A DNA sequence (GBSx0633) was identified in S. agalactiae <SEQ ID 1841> which encodes the amino acid sequence <SEQ ID 1842>. Analysis of this protein sequence reveals the following: TABLE-US-01767 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0510(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10225> which encodes amino acid sequence <SEQ ID 10226> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01768 >GP: AAF22299 GB: AF185571 putative N-acetyltransferase Camello 2 [Homo sapiens] Identities = 32/110 (29%), Positives = 54/110 (49%), Gaps = 4/110 (3%) Query: 67 IKMAEQDDIFQIENYYQNRKGQ-FWIALENERVVGSIALLRIDDKTAVLKKFFTYPKYRG 125- + +A + D+ I Y + G FW+A EKVVG++ L +DD T K+ + Sbjct: 86 VDIALRTDHSDITKSYLSECGSCFWVAESEEKVVGTVGALPVDDFTLREKRLQLFHLSVD 145- Query: 126 NPVR---LGRKLFERFMLFARASKFTRIVLDTPEKEKRSHFFYENQGFKQ 172 N R + + L + FAR ++ +VLDT + + Y++ GFK+ Sbjct: 146 NEHRGQGIAKALVRTVLQFARDQGYSEVVLDTSNIQLSAMGLYQSLGFKK 195 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 594 A DNA sequence (GBSx0634) was identified in S. agalactiae <SEQ ID 1843> which encodes the amino acid sequence <SEQ ID 1844>. Analysis of this protein sequence reveals the following:

TABLE-US-01769 Possible site: 47 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -11.94 Transmembrane 159-175 (151-180) INTEGRAL Likelihood = -11.62 Transmembrane 231-247 (225-251) INTEGRAL Likelihood = -9.98 Transmembrane 182-198 (177-203) INTEGRAL Likelihood = -7.11 Transmembrane 118-134 (106-136) INTEGRAL Likelihood = -1.49 Transmembrane 74-90 (74-93) ----- Final Results ----- bacterial membrane --- Certainty = 0.5776(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10227> which encodes amino acid sequence <SEQ ID 10228> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01770 >GP:CAB15891 GB:Z99123 yxlG [Bacillus subtilis] Identities = 42/188 (22%), Positives = 94/188 (49%), Gaps = 4/188 (2%) Query: 1 MKSLAVMLKKEWMENVRTYKVISILITCSIFGILGPLTALMMPDIMA--GILPKKLQGAI 58 MK + +L+KEW+E ++ K+I + I I G+ PLT MP+I+A G LP ++ + Sbjct: 1 MKVMMALLQKEWLEGWKSGKLIWLPIAMMIVGLTQPLTIYYMPEIIANGGNLPDGMKISF 60 Query: 59 PEPTYIDSYIQYFKNMNQLGLVILVFLFSSTLTQEFSKGTLINLVTKGLAKKVIILAKFI 118- P+ + + N LG+ +++F ++ E ++G ++++ + I++K++ Sbjct: 61 TMPSGSEVMVSTLSQFNTLGMALVIFSVMGSVANERNQGVTALIMSRPVTAAHYIVSKWL 120- Query: 119 VITLLWTVSYLLSVVIHFSYTLYYFSNEGSHKLMVYGATWFIGILFI-SLILFFSVLFRK 17- 7 + +++ +S+ + + Y F + + + + ++FI + L S +FR Sbjct: 121 IQSVIGIMSFAAGYGLAYYYVRLLFEDASFSRFAASLGLYALWVIFIVTAGLAGSTIFR- 17- 9 Query: 178 TLGGLLGC 185 ++G C Sbjct: 180 SVGAAAAC 187 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 595 A DNA sequence (GBSx0635) was identified in S. agalactiae <SEQ ID 1845> which encodes the amino acid sequence <SEQ ID 1846>. This protein is predicted to be ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-01771 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3431(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10229> which encodes amino acid sequence <SEQ ID 10230> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01772 >GP:CAB12736 GB:Z99108 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 105/299 (35%), Positives = 175/299 (58%), Gaps = 11/299 (3%) Query: 4 ISFQNVTKSFGPKKILNNVSFDLEENMIYGFVGPNGAGKTTTIKMILGLLKFDTGFITIF 63 + +NVTK+ + I++++SF + E ++GF+GPNGAGKTTTI+N++GL+K G + I Sbjct: 5 LELKNVTKNIRGRTIIDDLSFTIREGEVFGFLGPNGAGKTTTIRMMVGLMKLSKGDVLIC 64 Query: 64 GKKVNFGRTDTNQLIGYLPDVPEYYDYMTALEYLDLCSGLARSKHKLSNKELLRSVGLDD 123- G+ + + IG + + PE Y +++ + L + + + K E++ VGLD Sbjct: 65 GQSITKEYAKAIKHIGAIVENPELYKFLSGYKNLQQFARMVKGVTKEKIDEVVELVGLTD 124- Query: 124 N-HQKIATYSRGMKQRLGLAQALVHDPKIIICDEPTSALDPKGRQDILDIISNLRGEK-- 18- 0 H K+ TYS GM+QRLGLAQ L+HDPK++I DEPT+ LDP G ++I D + L E+ Sbjct: 125 RIHDKVKTYSLGMRQRLGLAQCLLHDPKVLILDEPTNGLDPAGIREIRDHLKKLTRERGM 18- 4 Query: 181 TVIFSTHILSDVEKICDHVLVLTKCGIYSLEELKGKKSEENYSVRILIKVTKSEAKVLSH 24- 0 VI S+H+LS++E +CD + +L K + ++ +K + +EN + ++ SEA ++ Sbjct: 185 AVIVSSHLLSEMELMCDRIAILQKGKLIDIQNVKDENIDENDTYFFQVE-QPSEAATVLN 24- 3 Query: 241 NYQIEKKDNEYALTLKGSKMDNKADLLAGFYQDLVSLKISPSAIEVIDNSLEELYLEVT 299- Y + K N + L ++ +L LV +I ++VI SLE+ +LE+T Sbjct: 244 QYDLLSKTNGVEIKLAKEEVPAVIEL-------LVMQQIRIYEVKVITKSLEDRFLEMT 295- There is also homology to SEQ ID 686. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 596 A DNA sequence (GBSx0636) was identified in S. agalactiae <SEQ ID 1847> which encodes the amino acid sequence <SEQ ID 1848>. Analysis of this protein sequence reveals the following: TABLE-US-01773 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4040(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01774 >GP:AAB71491 GB:U53767 ORF6 [Bacillus pumilus] Identities = 39/134 (29%), Positives = 71/134 (52%), Gaps = 16/134 (11%) Query: 2 LGENIYLQRTQIGMTQENLSDYLHLTKTTISKWENNQAKPDIDYLILMANLFDISLDDLV 61 LG NI +R + ++QE +++ L +++ ISKWE NQ++P +D LI +A LFD + +LV Sbjct: 4 LGSNISNKRKSLKLSQEYVAEQLGVSRQAISKWETNQSEPSMDNLIRLAELFDSDIKELV 63 Query: 62 GYQKTLSDDQRNQLIKDLKIKANVLSERDFFQEVKELSKQFPNDFKTLLIMINM--VLSN 119- S +Q ++ KDL+ + K++ Q F +L++I+ + Sbjct: 64 ------SPEQYSEEQKDLETRIE--------HGQKDIKMQNSAVFGRILMLISFFGYIGA 109- Query: 120 LTNLNDSEMKEWSL 133 L +L+ ++ W L Sbjct: 110 LFDLSSYQLPIWXL 123 There is also homology to SEQ ID 1740. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 597 A DNA sequence (GBSx0637) was identified in S. agalactiae <SEQ ID 1849> which encodes the amino acid sequence <SEQ ID 1850>. Analysis of this protein sequence reveals the following: TABLE-US-01775 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.59 Transmembrane 152 - 168 (145 - 173) INTEGRAL Likelihood = -9.71 Transmembrane 7 - 23 (3 - 27) INTEGRAL Likelihood = -6.95 Transmembrane 125 - 141 (122 - 146) INTEGRAL Likelihood = -4.51 Transmembrane 85 - 101 (83 - 102) INTEGRAL Likelihood = -3.35 Transmembrane 55 - 71 (54 - 75) ----- Final Results ----- bacterial membrane --- Certainty = 0.6434(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01776 >GP:CAA79986 GB:Z21972 ORF2 [Bacillus megaterium] Identities = 51/186 (27%), Positives = 106/186 (56%), Gaps = 5/186 (2%) Query: 5 SFFQCVILLVSFLVLTLAVKSQSDMISYLDNITSAFFQSIRNPDLTNLMTIISTVVSPLT 64 +F V+ L+ F + + S ++ + + +++ S Q +P LT++M + + S + Sbjct: 10 AFIISVLSLIGFSFMAFTI-SANEYLKFDEDVIS-LVQGWESPLLTDIMKFFTYIGSTAS 67 Query: 65 TSLIALVILGYQY-FLNQRIAVWLFM-LFFGTNALALLLKDIIARHRP-MNQLVFDSGYS 121- +++LVIL + Y L R+ + LF + G+ L L++K R RP +++L+ GYS Sbjct: 68 LIILSLVILFFLYRILKHRLELVLFTAVMVGSPLLNLMVKLFFQRARPDLHRLIDIGGYS 127- Query: 122 FPSGHTISAFLLMILVLVVARQRLRRVLSQVVFVIFALVILASVIFSRLYLENHFLTDIL 18- 1 FPSGH ++AF L ++ + + + ++++ ++F+++++ S+ SR+YL H+ +DI+ Sbjct: 128 FPSGHAMNAFSLYGILTFLLWRHITARWARILLILFSMLMILSIGISRIYLGVHYPSDII 18- 7 Query: 182 GSLLLG 187 L G Sbjct: 188 AGYLAG 193 There is also homology to SEQ ID 1852. A related GBS gene <SEQ ID 8611> and protein <SEQ ID 8612> were also identified. Analysis of this TABLE-US-01777 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 11.91 GvH: Signal Score (-7.5): -4.6 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 5 value: -13.59 threshold: 0.0 INTEGRAL Likelihood = -13.59 Transmembrane 152 - 168 (145 - 173) INTEGRAL Likelihood = -9.71 Transmembrane 7 - 23 (3 - 27) INTEGRAL Likelihood = -6.95 Transmembrane 125 - 141 (122 - 146) INTEGRAL Likelihood = -4.51 Transmembrane 85 - 101 (83 - 102) INTEGRAL Likelihood = -3.35 Transmembrane 55 - 71 (54 - 75) PERIPHERAL Likelihood = -1.16 184 modified ALOM score: 3.22 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6434(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00045## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 598 A DNA sequence (GBSx0638) was identified in S. agalactiae <SEQ ID 1853> which encodes the amino acid sequence <SEQ ID 1854>. Analysis of this protein sequence reveals the following: TABLE-US-01778 Possible Site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4288(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01779 >GP:CAB15470 GB:Z99121 yvdC [Bacillus subtilis] Identities = 53/96 (55%), Positives = 70/96 (72%) Query: 1 MDITDYQKWVSEFYKKRNWYQYNSFIRSNFLSEEVGELAQAIRKYEIGRDRPDETEQTDL 60 M + D +KW+ EFY+KR W +Y FIR FL EE GELA+A+R YEIGRDRPDE E + Sbjct: 1 MQLADAEKWMKEFYEKRGWTEYGPFIRVGFLMEEAGELARAVRAYEIGRDRPDEKESSRA 60 Query: 61 ENLNDIKEELGDVLDNIFILADQYNISLEEIISAHR 96 E ++ EE+GDV+ NI ILAD Y +SLE+++ AH+ Sbjct: 61 EQKQELIEEMGDVIGNIAILADMYGVSLEDVMKAHQ 96 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 599 A DNA sequence (GBSx0639) was identified in S. agalactiae <SEQ ID 1855> which encodes the amino acid sequence <SEQ ID 1856>. Analysis of this protein sequence reveals the following: TABLE-US-01780 Possible Site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0635(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01781 >GP:BAB06803 GB:AP001517 unknown conserved protein [Bacillus halodurans] Identities = 83/186 (44%), Positives = 117/186 (62%) Query: 1 MRITIFCGASTGENPVYSEKTVALAQWMAQNKHSLVYGGGKVGLMGVMADTVIANGGYTT 60 M+I +FCG+S G + VY E L + +A+ +LVYGG VG+MG +AD+V+ GG Sbjct: 1 MKIAVFCGSSNGASDVYKEGARQLGKELARRGITLVYGGASVGIMGAVADSVLEAGGEVI 60 Query: 61 GVIPTFLRDREIAHENLSELIIVNNMPERKAKMMLLGDAFIALPGGPGTLEEISEVISWS 120- GV+P FL + EI+H +L++LI+V M ERKAKM L D F+ALPGGPGTLEE E+ +W+ Sbjct: 61 GVMPRFLEEPEISHPHLTKLIVVETMHERKAKMAELADGFLALPGGPGTLEEFFEIFTWA 120- Query: 121 RIGQNDNPCILYNVNGYFNDLKNMFDHMVGEGFLSLEDRENVLFSDDITEIEDFITNYKV 18- 0 +IG + PC L N+N YF+ L + HM E FL + R L D + D + Y+ Sbjct: 121 QIGLHQKPCGLLNINHYFDPLVTLLHHMSNEQFLHEKYRSMALVHTDPILLLDQFSTYEP 18- 0 Query: 181 PSTRQY 186 P+ + Y Sbjct: 181 PTVKAY 186 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 600 A DNA sequence (GBSx0640) was identified in S. agalactiae <SEQ ID 1857> which encodes the amino acid sequence <SEQ ID 1858>. Analysis of this protein sequence reveals the following: TABLE-US-01782 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.86 Transmembrane 222-238 (214-239) INTEGRAL Likelihood = -6.69 Transmembrane 39-55 (36-58) INTEGRAL Likelihood = -4.25 Transmembrane 266-282 (266-284) INTEGRAL Likelihood = -1.28 Transmembrane 166-182 (166-182) INTEGRAL Likelihood = -1.01 Transmembrane 190-206 (190-206) INTEGRAL Likelihood = -0.96 Transmembrane 70-86 (70-86) ----- Final Results ----- bacterial membrane --- Certainty = 0.4142(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01783 >GP: CAB12420 GB: Z99107 ydiL [Bacillus subtilis] Identities = 40/132 (30%), Positives = 63/132 (47%), Gaps = 8/132 (6%) Query: 107 ESQNYDATFNI-----LMISYSVVVGPFFEEVLYRGIVLNLL-SKYGKWFAIITSGILFG 16- 0 ES+N A ++ LMI S +VGP EE+++R I+ L K +FA + S ++FG Sbjct: 114 ESENTQAILDVIQAVPLMIIVSSIVGPILEEIIFRKIIFGALYEKTNFFFAGLISSVIFG 17- 3 Query: 161 LMHQDISQLLTTSIAGIIMGFI-AYHYSFKVALLLHICNNFIVEIFTQLSTVNELYGTYF 21- 9 ++H D+ LL + G F+ A V + H+ N V + QL V Sbjct: 174 IVHADLKHLLLYTAMGFTFAFLYARTKRIWVPIFAHLMMNTFV-VIMQLEPVRNYLEQQS 23- 2 Query: 220 ENILLILAILFI 231 + LI+ LF Sbjct: 233 TQMQLIIGGLFL 244 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8613> and protein <SEQ ID 8614> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01784 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: 12.52 GvH: Signal Score (-7.5): -1.74 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 2 value: -6.69 threshold: 0.0 INTEGRAL Likelihood = -6.69 Transmembrane 39-55 ( 36-58) INTEGRAL Likelihood = -0.96 Transmembrane 70-86 ( 70-86) PERIPHERAL Likelihood = 4.56 21 modified ALOM score: 1.84 ***Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3675(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01785 Query: 10 LIGLILLAQAIVLSLATTLFAEILQNDVWIGIASTLIALLIPCF 53 L+ L LL ++++LS++ +L +W+ +A+ L+A ++ CF Sbjct: 21 LLCLCLLVRSLLLSVSLYSALILLVLILWVTVATPLLAFVVSCF 64 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 601 A DNA sequence (GBSx0641) was identified in S. agalactiae <SEQ ID 1859> which encodes the amino acid sequence <SEQ ID 1860>. This protein is predicted to be capa protein. Analysis of this protein sequence reveals the following: TABLE-US-01786 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.80 Transmembrane 27-43 ( 22-50) ----- Final Results ----- bacterial membrane --- Certainty = 0.6519(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9385> which encodes amino acid sequence <SEQ ID 9386> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01787 >GP: AAF13661 GB: AF188935 pXO2-56 [Bacillus anthracis] Identities = 68/224 (30%), Positives = 118/224 (52%), Gaps = 10/224 (4%) Query: 95 FKEVKSWIESADLAIGDYEGTISSE----YPLAGYPL-FNAPNEIATTMKETGYDVVDLA 14- 9 F+ V +++++D G++E + E Y A + +A E +KE G+ V++LA Sbjct: 87 FRHVSPYLKNSDYVSGNFEHPVLLEDKKNYQKADKNIHLSAKEETVKAVKEAGFTVLNLA 14- 6 Query: 150 HNHILDSQLAGAINTVKTFNRLGLKTIGVYLKDRNKEDILIKHVNGIKIAILGYSYGY-N 20- 8 +NH+ D G +Y+K F LD +G ++ ++I+ ++VNG+++A G++ + Sbjct: 147 NNHMTDYGAKGTKDTIKAFKEADLDYVGAGENFKDVKNIVYQNVNGVRVATLGFTDAFVA 20- 6 Query: 209 GMEANVSKSDYEKHMSDLDTKKIKQDIKKAEKEADITIVMPQMGIEYQKKPTTEQVMLYH 26- 8 G A + D+ K+I + + AD+ +V G EY KP+ Q L Sbjct: 207 GAIATKEQPGSLSMNPDVLLKQISKAKDPKKGNADLVVVNTHWGEEYDNKPSPRQEALAK 26- 6 Query: 269 SMIKWGADIIFGGHPHVVEPSEVIKKDGQKKFIIYSMGNFISNQ 312 +M+ GADII G HPHV++ +V K+ I YS+GNF+ +Q Sbjct: 267 AMVDAGADIIVGHHPHVLQSFDVYKQG----IIFYSLGNFVGDQ 306 A related DNA sequence was identified in S. pyogenes <SEQ ID 1861> which encodes the amino acid sequence <SEQ ID 1862>. Analysis of this protein sequence reveals the following: TABLE-US-01788 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.05 Transmembrane 44-60 ( 40-68) ----- Final Results ----- bacterial membrane --- Certainty = 0.5819(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9119> which encodes the amino acid sequence <SEQ ID 9120>. Analysis of this protein sequence reveals the following: TABLE-US-01789 Possible cleavage site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.582(Affirmative) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below:

TABLE-US-01790 Identities = 232/334 (69%), Positives = 273/334 (81%), Gaps = 4/334 (1%) Query: 24 YQKTLIFCVAVIIAIFILGLSKDLAQSKGQKVANNNT----VKTARVVANGDILLHDVLY 79 Y+KT+ VA+I+A+ + GL DL + ++A + VKTARVVANGDIL+HD+LY Sbjct: 40 YKKTMATVVALIVALLLFGLIYDLLGVQKNELAAQKSAQPKVKTARVVANGDILIHDILY 99 Query: 80 ASARQPDGTYNFTPYFKEVKSWIESADLAIGDYEGTISSEYPLAGYPLFNAPNEIATTMK 13- 9 SAR+ D TY+FTPYF+ VK WI ADLAIGDYEGTIS +YPLAGYPLFNAP EIA +K Sbjct: 100 MSARKADDTYDFTPYFEYVKDWISGADLAIGDYEGTISPDYPLAGYPLFNAPEEIAGALK 15- 9 Query: 140 ETGYDVVDLAHNHILDSQLAGAINTVKTFNRLGLDTIGVYLKDRNKEDILIKHVNGIKIA 19- 9 TGYDVVDLAHNHILDSQL GA+NT K F++LG+D+IG+Y KDR+KE LIK+VNGIKIA Sbjct: 160 NTGYDVVDLAHNHILDSQLDGALNTKKVFHQLGIDSIGIYDKDRSKEDFLIKNVNGIKIA 21- 9 Query: 200 ILGYSYGYNGMEANVSKSDYEKHMSDLDTKKIKQDIKKAEKEADITIVMPQMGIEYQKKP 25- 9 ILGYSYGYNGMEA +S+ DYEKHMSDLD KIK++++ AEK+AD+TIVMPQMG EY +P Sbjct: 220 ILGYSYGYNGMEATLSQEDYEKHMSDLDEAKIKKELQLAEKKADVITVMPQMGTEYALEP 27- 9 Query: 260 TTEQVMLYHSMIKWGADIIFGGHPHVVEPSEVIKKDGQKKFIIYSMGNFISNQRLETVDD 31- 9 T EQ LYH MI WGAD++ GGHPHV+EPSE + K QKKFIIYSMGNFISNQRLETVDD Sbjct: 280 TAEQKELYHKMIDWGADVVLGGHPHVIEPSETVIKGRQKKFIIYSMGNFISNQRLETVDD 33- 9 Query: 320 IWTERGLLMDVTIEKKGQKTVIKKVKAHPTLVEA 353 IWTERGLLMD+T EKK KT IK V+AHPT+V A Sbjct: 340 IWTERGLLMDLTFEKKDNKTKIKTVEAHPTMVLA 373 A related GBS gene <SEQ ID 8615> and protein <SEQ ID 8616> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01791 Lipop Possible site: -1 Crend: 7 SRCFLG: 0 McG: Length of UR: 18 Peak Value of UR: 3.83 Net Charge of CR: 2 McG: Discrim Score: 15.36 GvH: Signal Score (-7.5): -1.52 Possible site: 32 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 33 ALOM program count: 0 value: 4.35 threshold: 0.0 PERIPHERAL Likelihood = 4.35 170 modified ALOM score: -1.37 *** Reasoning Step: 3 Rule gpol ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00046## SEQ ID 8616 (GBS289) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 57 (lane 5; MW 40 kDa), in FIG. 181 (lane 6; MW 47 kDa), in FIG. 169 (lane 13 & 14; MW 54.5 kDa--thioredoxin fusion) and in FIG. 239 (lane 3; MW 54.5 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 61 (lane 5; MW 65 kDa). SEQ ID 8616 (GBS289L) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 126 (lane 2; MW 72 kDa) and in FIG. 184 (lane 5; MW 72 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 126 (lane 5-7; MW 47 kDa). GBS289L-His was purified as shown in FIG. 234, lane 9-10. Purified GBS289L-GST is shown in FIG. 245, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 602 A DNA sequence (GBSx0642) was identified in S. agalactiae <SEQ ID 1863> which encodes the amino acid sequence <SEQ ID 1864>. This protein is predicted to be thiamin biosynthesis protein ThiI (thiI). Analysis of this protein sequence reveals the following: TABLE-US-01792 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2720(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9971> which encodes amino acid sequence <SEQ ID 9972> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01793 >GP: AAC00308 GB: AF008220 YtbJ [Bacillus subtilis] Identities 184/354 (51%), Positives = 249/354 (69%) Query: 11 MQYSEIMIRYGELSTKKKNRMRFINKLKNNMEHVLSIYPDVSVKTDRDRGHVYLNGTDYH 70 M Y I+IR+GE+STK KNR FI +LK N+ VL YP++ ++RDR + LNG D Sbjct: 1 MNYDHILIRFGEISTKGKNRKSFIERLKQNIRLVLKDYPNLKYFSNRDRMTITLNGEDPE 60 Query: 71 EVAESLKEIFGIQAFSPSFKVEKNVDTLVKAVQEIMTSVYKDGMTFKITAKRSDHSFELD 13- 0 + LK++FGIQ+FS + K + +D + + + YK G TFK+ KR+ FELD Sbcjt: 61 ALFPHLKQVFGIQSFSLAIKCDSRLDDIKATALKAIKDQYKPGDTFKVATKRAYKQFELD 12- 0 Query: 131 SRALNHTLGDAVFSVLPNIKAQMKQPDINLKVEIRDEAAYISYEDIRGAGGLPVGTSGKG 19- 0 + +N +G + + ++ PDI L++EIR+EA +++ D +GAGGLPVG++GK Sbjct: 121 TNQMNAEIGGHILRNTEGLTVDVRNPDIPLRIEIREEATFLTIRDEKGAGGLPVGSAGKA 18- 0 Query: 191 MLMLSGGIDSPVAGYLALKRGVDIEAVHFASPPYTSPGALKKAHDLTRKLTKFGGNIQFI 25- 0 MLMLSGG DSPVAG+ A+KRG+ +EAVHF SPPYTS A +K DL + L++FGG++ Sbjct: 181 MLMLSGGFDSPVAGFYAMKRGLSVEAVHFFSPPYTSERAKQKVMDLAKCLSRFGGSMTLH 24- 0 Query: 251 EVPFTEIQEEIKAKAPEAYLMTLTRRFMMRITDRIREDRNGLVIINGESLGQVASQTLES 31- 0 VPFT+ QE I+ + PE Y MT TRR M++I DRIRE RNGL II GESLGQVASQTLES Sbjct: 241 IVPFTKTQELIQKQIPENYTMTATRRLMLQIADRIREKRNGLAIITGESLGQVASQTLES 30- 0 Query: 311 MQAINAVTATPIIRPVVTMDKLEIIDIAQKIDTFDISIQPFEDCCTIFAPDRPK 364 M AINAVT+TPI+RP++ MDK EII+ +++I T++ SIQPFEDCCTIF +P+ Sbjct: 301 MYAINAVTSTPILRPLIAMDKTEIIEKSREIGTYETSIQPFEDCCTIFTTAKPR 354 A related DNA sequence was identified in S. pyogenes <SEQ ID 1865> which encodes the amino acid sequence <SEQ ID 1866>. Analysis of this protein sequence reveals the following: TABLE-US-01794 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4897(Affirmative) <succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01795 Identities = 316/404 (78%), Positives = 362/404 (89%) Query: 11 MQYSEIMIRYGELSTKKKNRMRFINKLKNNMEHVLSIYPDVSVKTDRDRGHVYLNGTDYH 70 M YSEIM+R+GELSTK KNRMRFINKLKNN++ VL+ +P ++V++DRDR HV LNGTDY Sbjct: 1 MDYSEIMVRHGELSTKGKNRMRFINKLKNNIQDVLAPFPAITVRSDRDRTHVSLNGTDYQ 60 Query: 71 EVAESLKEIFGQQAFSPSFKVEKNVDTLVKAVQEIMTSVYKDGMTFKITAKRSDHSFELD 13- 0 + E+LK +FG+QA SP +K+EK+V LV AVQ+IMTS+Y+DG+TFKI KRSDH+FELD Sbjct: 61 PIVEALKLVFGVQALSPVYKLEKSVPLLVTAVQDIMTSLYRDGLTFKIATKRSDHAFELD 12- 0 Query: 131 SRALNHTLGDAVFSVLPNIAKQMKQPDINLKVEIRDEAAYISYEDIRGAGGLPVGTSGKG 19- 0 SR LN LG AVF VLPNI+AQMK PD+ LKVEIRDEAAYISYE+I+GAGGLPVGTSGKG Sbjct: 121 SRELNSLLGGAVFEVLPNIQAQMKHPDVTLKVEIRDEAAYISYEEIKGAGGLPVGTSGKG 18- 0 Query: 191 MLMLSGGIDSPVAGYLALKRGVDIEAVHFASPPYTSPGALKKAHDLTRKLTKFGGNIQFI 25- 0 MLMLSGGIDSPVAGYLALKRG+DIE VHFASPPYTSPGAL KA DLTR+LT+FGGNIQFI Sbjct: 181 MLMLSGGIDSPVAGYLALKRGDLIEVVHFASPPYTSPGALAKAQDLTRRLTRFGGNIQFI 24- 0 Query: 251 EVPFTEIQEEIKAKAPEAYLMTLTRRFMMRITDRIREDRNGLVIINGESLGQVASQTLES 31- 0 EVPFTEIQEEIK KAPEAYLMTLTRRFMMRITD IRE R GLVI+NGESLGQVASQTLES Sbjct: 241 EVPFTEIQEEIKNKAPEAYLMTLTRRFMMRITDAIREQRKGLVIVNGESLGQVASQTLES 30- 0 Query: 311 MQAINAVTATPIIRPVVTMDKLEIIDIAQKIDTFDISIQPFEDCCTIFAPDRPKTNPKIK 37- 0 MQAINAVT+TPIIRPVVTMDKLEII++AQ IDTFDISIQPFEDCCTIFAPDRPKTNPK+ Sbjct: 301 MQAINAVTSTPIIRPVVTMDKLEIIEMAQAIDTFDISIQPFEDCCTIFAPDRPKTNPKLG 36- 0 Query: 371 NTEQYEKRMDVEGLVERAVAGIMVTTIQPQADSDDVDDLIDDLL 414 N E+YE+ D++GLV+RAV+GI+VT I P+ +D+V++LID LL Sbjct: 361 NAEKYEECFDIDGLVQRAVSGIVVTEITPEIVNDEVENLIDALL 404 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 603 A DNA sequence (GBSx0643) was identified in S. agalactiae <SEQ ID 1867> which encodes the amino acid sequence <SEQ ID 1868>. This protein is predicted to be nifs protein homolog, fragment. Analysis of this protein sequence reveals the following: TABLE-US-01796 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.27 Transmembrane 131-147 (131-147) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01797 >GP: CAA43493 GB: X61190 nifS-like gene [Lactobacillus delbrueckii] Identities = 177/353 (50%), Positives = 234/353 (66%), Gaps = 1/353 (0%) Query: 14 PEVLRTYQEVASKIYGNPSSLHELGTTSSRILEASRKQIASLLELKANEIFFTSGGTEAD 73 - P+ L TY +V +KI+GNPSSLH+LG + +LEASRKQ+A LL + +EI+FTSGGTE++ Sbjct: 3 PKALETYSQVVTKIWGNPSSLHKLGDRAHGLLEASRKQVADLLGVNTDEIYFTSGGTESN 62 Query: 74 NWVIKGLAFEKQHFGNHIIVSDIEHPAVKESAKWLGEYGFEIDYAPVDDKGFVDVEALVK 133- N IKG A+ K+ FG HII S +EH +V + L GF + PVD +G V+ E L Sbjct: 63 NTAIKGTAWAKREFGKHIITSSVEHASVANTFTELENLGFRVTRLPVDKEGRVNPEDLKA 122- Query: 134 LIKPETILISIMAINNEIGSIQPIKAISDLLSDKPTISFHVDAVQAIGKIPTKDYLTERV 19- 3 + +T L+SIM +NNEIG+IQPIK IS++L+D P I FHVD VQA+GK T RV Sbjct: 123 ALDKDTTLVSIMGVNNEIGTIQPIKEISEILADYPNIHFHVDNVQALGKGIWDQVFTSRV 18- 2 Query: 194 DFASFSSHKFHGVRGVGFLYIKEGKRISPLLTGGGQETDLRSTTENVAGIAATAKALRMV 25- 3 D SFSSHKFHG RG+G LY K G+ + PL GGGQE LRS TEN+A IAA AKA R++ Sbjct: 183 DMMSFSSHKFHGPRGIGILYKKRGRMLMPLCEGGGQEKGLRSGTENLAAIAAMAKAARLL 24- 2 Query: 254 MDKEVVAIPKISKMKTIIHDELAKYEDITLFSG-KEDFSPNIITFGIKGVRGEVLVHAFE 31- 2 + E + +K I LA I +FS K DF+P+I+ F ++G+RGE LVH E Sbjct: 243 LTDEKEKADREYAIKEKISKYLAGKPGIHIFSPLKADFAPHILCFALEGIRGETLVHTLE 30- 2 Query: 313 GHDIFISTTSACSSKAGKPAGTLIAMGISTKLAQTAVRISLDDDNDMGQVEQF 365 DI+ISTTSAC+SK A TL+AM +A +AVR+S D+ N + + ++F Sbjct: 303 DQDIYISTTSACASKKADEASTLVAMKTPDAIATSAVRLSFDESNTLEEADEF 355 A related DNA sequence was identified in S. pyogenes <SEQ ID 1869> which encodes the amino acid sequence <SEQ ID 1870>. Analysis of this protein sequence reveals the following: TABLE-US-01798 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3067 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01799 Identities = 268/370 (72%), Positives = 322/370 (86%) Query: 1 MIYFDNSATTIPYPEVLRTYQEVASKIYGNPSSLHELGTTSSRILEASRKQIASLLELKA 60 MIYFDN+ATTIPY E L+TYQEVA+KIYGNPSSLH+LGT +SRILEASRKQIA LL +K+ Sbjct: 1 MIYFDNAATTIPYGEALKTYQEVATKIYGNPSSLHQLGTNASRILEASRKQIAGLLGVKS 60 Query: 61 NEIFFTSGGTEADNWVIKGLAFEKQHFGNHIIVSDIEHPAVKESAKWLGEYGFEIDYAPV 120- EIFFTSGGTE+ NW IKG+AFEK FG HII+S IEHPAV ES KWL GFE+ YAPV Sbjct: 61 EEIFFTSGGTESANWAIKGIAFEKNAFGKHIIISAIEHPAVSESVKWLLTQGFEVSYAPV 120- Query: 121 DDKGFVDVEALVKLIKPETILISIMAINNEIGSIQPIKAISDLLSDKPTISFHVDAVQAI 18- 0 +G VDV AL +LI+P+TILISIMA+NNE+G+IQPI+AIS+LL+++PTI+FHVDAVQAI Sbjct: 121 TTQGVVDVNALAELIRPDTILISIMAVNNEMGAIQPIRAISNLLANQPTITFHVDAVQAI 18- 0 Query: 181 GKIPTKDYLTERVDFASFSSHKFHGVRGVGFLYIKEGKRISPLLTGGGQETDLRSTTENV 24- 0 GKIP DY+T RVD ASFS HKFH VRGVGFLY K GKR++PLL+GGGQE +LRSTTENV Sbjct: 181 GKIPLCDYMTNRVDLASFSGHKFHSVRGVGFLYKKAGKRLNPLLSGGGQEQELRSTTENV 24- 0 Query: 241 AGIAATAKALRMVMDKEVVAIPKISKMKTIIHDELAKYEDITLFSGKEDFSPNIITFGIK 30- 0 AGIA+ AKALR+V +K+V +PK++ M+ +I+ L+ Y D+T+FS +E F+PNI+TFGI+ Sbjct: 241 AGIASMAKALRIVTEKQVSVLPKLTAMRDVIYKSLSAYPDVTVFSAQEGFAPNILTFGIR 30- 0 Query: 301 GVRGEVLVHAFEGHDIFISTTSACSSKAGKPAGTLIAMGISTKLAQTAVRISLDDDNDMG 36- 0 GVRGEV+VHAFE ++I+ISTTSACSSKAG+PAG+L+AMGI K AQTAVRISLDDDNDMG Sbjct: 301 GVRGEVIVHAFEKYEIYISTTSACSSKAGEPAGSLVAMGIPVKTAQTAVRISLDDDNDMG 36- 0 Query: 361 QVEQFLTIFK 370 QVEQFLTIF+ Sbjct: 361 QVEQFLTIFQ 370 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 604 A DNA sequence (GBSx0644) was identified in S. agalactiae <SEQ ID 1871> which encodes the amino acid sequence <SEQ ID 1872>. Analysis of this protein sequence reveals the following: TABLE-US-01800 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1539 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 605 A DNA sequence (GBSx0645) was identified in S. agalactiae <SEQ ID 1873> which encodes the amino acid sequence <SEQ ID 1874>. This protein is predicted to be glutathione reductase (gor). Analysis of this protein sequence reveals the following: TABLE-US-01801 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.25 Transmembrane 170-186 (169-187) ----- Final Results ----- bacterial membrane --- Certainty = 0.2699 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01802 >GP: BAA76640 GB: AB019579 glutathione reductase (GR) [Streptococcus mutans] Identities = 274/450 (60%), Positives = 346/450 (76%), Gaps = 1/450 (0%) Query: 1 MSKQYDYIVIGGGSAGSGTANRAAMYGAKVLLIEGGQVGGTCVNLGCVPKKIMWYGAQVS 60 M+KQYDYIVIGGGS G +ANRAAM+GAKV+L EG QVGGTCVN+GCVPKK+MWYGAQV+ Sbjct: 1 MTKQYDYIVIGGGSGGIASANRAAMHGAKVILFEGKQVGGTCVNVGCVPKKVMWYGAQVA 60 Query: 61 ETLHKYSSGYGFEVNNLNFDFTTLKANRDAYVQRSRQSYAANFERNGVEKIDGFARFIDN 120- ET++ Y++ YGF+V F F LK NR AY+ R + SY F+ NGVE++ +A F+D Sbjct: 61 ETINNYAADYGFDVTTQTFHFDALKQNRQAYIDRIQDSYERGFDSNGVERVYSYATFVDA 120- Query: 121 HTIEVNGQQYKAPHITIATGGHPLYPDIIGSELGETSDDFFGWETLPDSILIVGAGYIAA 18- 0 HT+EV G+ Y APHI IATGGH L PDI GSE G TSD FF + +P +VGAGYIA Sbjct: 121 HTVEVAGEHYTAPHILIATGGHALLPDIPGSEYGITSDGFFELDAIPKRTAVVGAGYIAV 18- 0 Query: 181 ELAGVVNELGVETHLAFRKDHILRGFDDMVTSEVMAEMEKSGISLHANHVPKSLKRDEGG 24- 0 E++GV++ LG ETHL R+D LR FD + ++ EM+K G LH VPK + ++ Sbjct: 181 EISGVLHALGGETHLFVRRDRPLRKFDKEIVGTLVDEMKKDGPHLHTFSVPKEVIKNTDN 24- 0 Query: 241 KLIFEAENGKTLVVDRVIWAIGRGPNV-DMGLENTDIVLNDKGYIKADEFENTSVDGVYA 29- 9 L ENG+ VD +IWAIGR N LE T + L+ +G+I D FENT+V+G+YA Sbjct: 241 SLTLILENGEEYTVDTLIWAIGRAANTKGFNLEVTGVTLDSRGFIATDAFENTNVEGLYA 30- 0 Query: 300 IGDVNGKIALTPVAIAAGRRLSERLFNHKDNEKLDYHNVPSVIFTHPVIGTVGLSEAAAI 35- 9 +GDVNGK+ LTPVA+ AGR+LSERLFNHK K+DY +V +VIF+HPVIG++GLSE A+ Sbjct: 301 LGDVNGKLELTPVAVKAGRQLSERLFNHKPQAKMDYKDVATVIFSHPVIGSIGLSEEVAL 36- 0 Query: 360 EQFGEDNIKVYTSTFTSMYTAVTTNRQAVKMKLITLGKEEKVIGLHGVGYGIDEMIQGFS 41- 9 +Q+GE+N+ VY STFTSMYTAVT++RQA KMKL+T+G++EK++GLHG+GYG+DEMIQGF+ Sbjct: 361 DQYGEENVTVYRSTFTSMYTAVTSHRQACKMKLVTVGEDEKIVGLHGIGYGVDEMIQGFA 42- 0 Query: 420 VAIKMGATKADFDDTVAIHPTGSEEFVTMR 449 VAIKMGATKADFD+TVAIHPTGSEEFVTMR Sbjct: 421 VAIKMGATKADFDNTVAIHPTGSEEFVTMR 450 A related DNA sequence was identified in S. pyogenes <SEQ ID 1875> which encodes the amino acid sequence <SEQ ID 1876>. Analysis of this protein sequence reveals the following: TABLE-US-01803 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.33 Transmembrane 173-189 (173-191) ----- Final Results ----- bacterial membrane --- Certainty = 0.1532 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01804 Identities = 268/446 (60%), Positives = 340/446 (76%), Gaps = 1/446 (0%) Query: 5 YDYIVIGGGSAGSGTANRAAMYGAKVLLIEGGQVGGTCVNLGCVPKKIMWYGAQVSETLH 64 YDYIVIGGGSAG +ANRAAM+GAKVLL EG ++GGTCVNLGCVPKK+MWYGAQV++ L Sbjct: 8 YDYIVIGGGSAGIASANRAAMHGAKVLLAEGKEIGGTCVNLGCVPKKVMWYGAQVADILG 67 Query: 65 KYSSGYGFEVNNLNFDFTTLKANRDAYVQRSRQSYAANFERNGVEKIDGFARFIDNHTIE 124- Y+ YGF+ FDF LKANR AY+ R SY FE+NGV++I +A F D HT+E Sbjct: 68 TYAKDYGFDFKEKAFDFKQLKANRQAYIDRIHASYERGFEQNGVDRIYDYAVFKDAHTVE 127- Query: 125 VNGQQYKAPHITIATGGHPLYPDIIGSELGETSDDFFGWETLPDSILIVGAGYIAAELAG 18- 4 + GQ Y APHI IATGGHP++PDI G++ G +SD FF + +P +VGAGYIA ELAG Sbjct: 128 IAGQLYTAPHILIATGGHPVFPDIEGAQYGISSDGFFALDEVPKRTAVVGAGYIAVELAG 18- 7 Query: 185 VVNELGVETHLAFRKDHILRGFDDMVTSEVMAEMEKSGISLHANHVPKSLKRDEGGKLIF 24- 4 V++ LG +T L R D LR FD + ++ EM +G LH + + ++ L Sbjct: 188 VLHALGSKTDLFIRHDRPLRSFDKTIVDVLVDEMAVNGPRLHTHAEVAKVVKNTDESLTL 24- 7 Query: 245 EAENGKTLVVDRVIWAIGRGPNVD-MGLENTDIVLNDKGYIKADEFENTSVDGVYAIGDV 30- 3 ++G+ + VD++IWAIGR PN++ L+ T + LNDKGYI+ D +ENTSV G+YA+GDV Sbjct: 248 YLKDGQEVEVDQLIWAIGRKPNLEGFSLDKTGVTLNDKGYIETDAYENTSVKGIYAVGDV 30- 7 Query: 304 NGKIALTPVAIAAGRRLSERLFNHKDNEKLDYHNVPSVIFTHPVIGTVGLSEAAAIEQFG 36- 3 NGK+ALTPVA+AAGRRLSERLFN K +EKLDY NV +VIF+HPVIG+VGLSE AA++Q+G Sbjct: 308 NGKLALTPVAVAAGRRLSERLFNGKTDEKLDYQNVATVIFSHPVIGSVGLSEEAAVKQYG 36- 7 Query: 364 EDNIKVYTSTFTSMYTAVTTNRQAVKMKLITLGKEEKVIGLHGVGYGIDEMIQGFSVAIK 42- 3 ++ +K Y S FTSM+TA+T +RQ MKL+T+G EK++GLHG+GYG+DEMIQGF+VAIK Sbjct: 368 QEAVKTYQSRFTSMFTAITNHRQPCLMKLVTVGDTEKIVGLHGIGYGVDEMIQGFAVAIK 42- 7 Query: 424 MGATKADFDDTVAIHPTGSEEFVTMR 449 MGATKADFD+TVAIHPTGSEEFVTMR Sbjct: 428 MGATKADFDNTVAIHPTGSEEFVTMR 453 SEQ ID 1874 (GBS417) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 79 (lane 5; MW 53 kDa). GBS417-His was purified as shown in FIG. 216, lane 2. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 606 A DNA sequence (GBSx0646) was identified in S. agalactiae <SEQ ID 1877> which encodes the amino acid sequence <SEQ ID 1878>. Analysis of this protein sequence reveals the following:

TABLE-US-01805 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3122 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01806 >GP: AAC62417 GB: AF084104 hypothetical protein [Bacillus firmus] Identities = 33/110 (30%), Positives = 66/110 (60%) Query: 1 MANVYDLANELERAVRALPEYQAVLTAKSAIESDADAQVLWQDFLATQSKVQEMMQSGQM 60 M+NVYD A+EL++A+ E+ A+ + IE+D A+ + ++F Q ++Q+ G Sbjct: 1 MSNVYDKAHELKKAIAESEEFSALKSMHEEIEADEIAKKMLENFRNLQLELQQKQMQGIQ 60 Query: 61 PSQEEQDEMSKLGEKIESNDLLKVYFDQQQRLSVYMSDIEKIVFAPMQDL 110 ++EE + + E ++ ++L+ + +QRLSV + DI KI+ P++++ Sbjct: 61 ITEEEAQKAQQQFELVQQHELISKLMEAEQRLSVIIGDINKIITEPLEEI 110 A related DNA sequence was identified in S. pyogenes <SEQ ID 1879> which encodes the amino acid sequence <SEQ ID 1880>. Analysis of this protein sequence reveals the following: TABLE-US-01807 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4058 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01808 Identities = 68/108 (62%), Positives = 86/108 (78%) Query: 4 VYDLANELERAVRALPEYQAVLTAKSAIESDADAQVLWQDFLATQSKVQEMMQSGQMPSQ 63 +YD AN+LERAVRALPEYQ VL K AI++D A L+ +F+A Q K+Q MMQSGQMP+ Sbjct: 5 IYDYANQLERAVRALPEYQKVLEVKEAIQADVSASELFDEFVAMQEKIQGMMQSGQMPTA 64 Query: 64 EEQDEMSKLGEKIESNDLLKVYFDQQQRLSVYMSDIEKIVFAPMQDLM 111 EEQ + +L +KIE+ND LK YF+ QQ LSVYMSDIE+IVFAP++DL+ Sbjct: 65 EEQTSIQELSQKIEANDQLKAYFEAQQALSVYMSDIERIVFAPLKDLV 112 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 607 A DNA sequence (GBSx0647) was identified in S. agalactiae <SEQ ID 1881> which encodes the amino acid sequence <SEQ ID 1882>. This protein is predicted to be chorismate synthase (aroC). Analysis of this protein sequence reveals the following: TABLE-US-01809 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.67 Transmembrane 343-359 (341-364) ----- Final Results ----- bacterial membrane --- Certainty = 0.2869 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01810 >GP: BAB05375 GB: AP001512 chorismate synthase [Bacillus halodurans] Identities = 227/381 (59%), Positives = 282/381 (73%), Gaps = 2/381 (0%) Query: 1 MRYLTAGESHGPSLTAIIEGIPAGLKLSAKDINEDLKRRQGGYGRGNRMKIETDQVIISS 60 MRYLTAGESHGP LT IIEG PA L+L A DIN DL RRQGG+GRG RM+IE DQV I Sbjct: 1 MRYLTAGESHGPQLTTIIEGAPAQLELVADDINVDLARRQGGHGRGRRMQIEKDQVQIVG 60 Query: 61 GVRHGKTLGSPITLTVTNKDHSKWLDIMSVEDI--EERLKQKRRIKHPRPGHADLVGGIK 118- G+RHGKT G+PI L V NKD W IM E + +E + KR+I PRPGHADL G IK Sbjct: 61 GIRHGKTTGAPIALVVENKDWKHWTKIMGAEPLTGDEEKEIKRKITRPRPGHADLNGAIK 120- Query: 119 YRFDDLRNALERSSARETTMRVAIGAIAKRILKEIGIEIANHIVVFGGKEITVPDKLTVQ 17- 8 Y D+RN LERSSARETT+RVA GA+AK+IL+ GIE+ +H++ GG + + Sbjct: 121 YGHRDMRNVLERSSARETTVRVAAGAVAKKILRTFGIEVGSHVLEIGGVKAEKTSYDQLS 18- 0 Query: 179 QIKVLSSQSQVAIVNPSFEQEIKDYIDSVKKAGDTIGGVVETIVGGVPVGLGSYVHWDRK 23- 8 +K L+ S V ++ EQE+ ID K+ GD+IGGVVE IV GVP+GLGS+VH+DRK Sbjct: 181 NLKELAEASPVRCLDKEAEQEMIAAIDQAKENGDSIGGVVEVIVEGVPIGLGSHVHYDRK 24- 0 Query: 239 LDAKIAQAVVSINAFKGVEFGLGFKSGFLKGSQVMDSISWTKDQGYIRQSNNLGGFEGGM 29- 8 LDAKIA AV+SINAFKGVEFG+GF++ GS+V D I+W +++GY R+SNNLGGFEGGM Sbjct: 241 LDAKIAAAVMSINAFKGVEFGIGFEAASKPGSEVHDEIAWDEERGYYRKSNNLGGFEGGM 30- 0 Query: 299 TNGEPIIVRGVMKPIPTLYKPLMSVDIDTHEPYRATVERSDPTALPAAGVVMEAVVATVL 35- 8 TNG PI+VRGVMKPIPTLYKPL SVDI T EP+ A++ERSD A+PAA VV EAVVA + Sbjct: 301 TNGMPIVVRGVMKPIPTLYKPLQSVDIATKEPFAASIERSDSCAVPAAAVVAEAVVAWEV 36- 0 Query: 359 VTEVLEKFSSDNMYELKEAVK 379 +LE+F +D + E+++ ++ Sbjct: 361 ANALLERFGADQVEEIEKNIR 381 A related DNA sequence was identified in S. pyogenes <SEQ ID 1883> which encodes the amino acid sequence <SEQ ID 1884>. Analysis of this protein sequence reveals the following: TABLE-US-01811 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.75 Transmembrane 342-358 (342-359) INTEGRAL Likelihood = -0.16 Transmembrane 155-171 (155-171) ----- Final Results ----- bacterial membrane --- Certainty = 0.1298 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01812 >GP: BAB05375 GB: AP001512 chorismate synthase [Bacillus halodurans] Identities = 213/390 (54%), Positives = 277/390 (70%), Gaps = 2/390 (0%) Query: 1 LRYLTAGESHGPSLTAIIEGIPAGLTLHPADIDHELQRRQGGYGRGARMSIETDRVQISS 60 +RYLTAGESHGP LT IIEG PA L L DI+ +L RRQGG+GRG RM IE D+VQI Sbjct: 1 MRYLTAGESHGPQLTTIIEGAPAQLELVADDINVDLARRQGGHGRGRRMQIEKDQVQIVG 60 Query: 61 GVRHGKTTGAPITLTVINKDHQKWLDVMAVGDI--EETLKLKRRVKHPRPGHADLVGGIK 118- G+RHGKTTGAPI L V NKD + W +M + +E ++KR++ PRPGHADL G IK Sbjct: 61 GIRHGKTTGAPIALVVENKDWKHWTKIMGAEPLTGDEEKEIKRKITRPRPGHADLNGAIK 120- Query: 119 YHFNDLRDALERSSARETTMRVAVGAVAKRILAELGIDMLHHILIFGGITITIPSKLSFR 17- 8 Y D+R+ LERSSARETT+RVA GAVAK+IL GI++ H+L GG+ S Sbjct: 121 YGHRDMRNVLERSSARETTVRVAAGAVAKKILRTFGIEVGSHVLEIGGVKAEKTSYDQLS 18- 0 Query: 179 ELQERALHSELSIVNPKQEEEIKTYIDKIKKEGDTIGGIIETIVQGVPAGLGSYVQWDKK 23- 8 L+E A S + ++ + E+E+ ID+ K+ GD+IGG++E IV+GVP GLGS+V +D+K Sbjct: 181 NLKELAEASPVRCLDKEAEQEMIAAIDQAKENGDSIGGVVEVIVEGVPIGLGSHVHYDRK 24- 0 Query: 239 LDAKLAQAVLSINAFKGVEFGAGFDMGFQKGSQVMDEITWTPTQGYGRQTNHLGGFEGGM 29- 8 LDAK+A AV+SINAFKGVEFG GF+ + GS+V DEI W +GY R++N+LGGFEGGM Sbjct: 241 LDAKIAAAVMSINAFKGVEFGIGFEAASKPGSEVHDEIAWDEERGYYRKSNNLGGFEGGM 30- 0 Query: 299 TTGQPLVVKGVMKPIPTLYKPLMSVDIDSHEPYKATVERSDPTALPAAGVIMENVVATVL 35- 8 T G P+VV+GVMKPIPTLYKPL SVDI + EP+ A++ERSD A+PAA V+ E VVA + Sbjct: 301 TNGMPIVVRGVMKPIPTLYKPLQSVDIATKEPFAASIERSDSCAVPAAAVVAEAVVAWEV 36- 0 Query: 359 AKEILETFSSTTMSELQKAFSDYRAYVKQF 388 A +LE F + + E++K ++ + F Sbjct: 361 ANALLERFGADQVEEIEKNIREFNEKARLF 390 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01813 Identities = 284/388 (73%), Positives = 333/388 (85%) Query: 1 MRYLTAGESHGPSLTAIIEGIPAGLKLSAKDINEDLKRRQGGYGRGNRMKIETDQVIISS 60 +RYLTAGESHGPSLTAIIEGIPAGL L DI+ +L+RRQGGYGRG RM IETD+V ISS Sbjct: 1 LRYLTAGESHGPSLTAIIEGIPAGLTLHPADIDHELQRRQGGYGRGARMSIETDRVQISS 60 Query: 61 GVRHGKTLGSPITLTVTNKDHSKWLDIMSVEDIEERLKQKRRIKHPRPGHADLVGGIKYR 120- GVRHGKT G+PITLTV NKDH KWLD+M+V DIEE LK KRR+KHPRPGHADLVGGIKY Sbjct: 61 GVRHGKTTGAPITLTVINKDHQKWLDVMAVGDIEETLKLKRRVKHPRPGHADLVGGIKYH 120- Query: 121 FDDLRNALERSSARETTMRVAIGAIAKRILKEIGIEIANHIVVFGGKEITVPDKLTVQQI 18- 0 F+DLR+ALERSSARETTMRVA+GA+AKRIL E+GI++ +HI++FGG IT+P KL+ +++ Sbjct: 121 FNDLRDALERSSARETTMRVAVGAVAKRILAELGIDMLHHILIFGGITITIPSKLSFREL 18- 0 Query: 181 KVLSSQSQVAIVNPSFEQEIKDYIDSVKKAGDTIGGVVETIVGGVPVGLGSYVHWDRKLD 24- 0 + + S+++IVNP E+EIK YID +KK GDTIGG++ETIV GVP GLGSYV WD+KLD Sbjct: 181 QERALHSELSIVNPKQEEEIKTYIDKIKKEGDTIGGIIETIVQGVPAGLGSYVQWDKKLD 24- 0 Query: 241 AKIAQAVVSINAFKGVEFGLGFKSGFLKGSQVMDSISWTKDQGYIRQSNNLGGFEGGMTN 30- 0 AK+AQAV+SINAFKGVEFG GF GF KGSQVMD I+WT QGY RQ+N+LGGFEGGMT Sbjct: 241 AKLAQAVLSINAFKGVEFGAGFDMGFQKGSQVMDEITWTPTQGYGRQTNHLGGFEGGMTT 30- 0 Query: 301 GEPIIVRGVMKPIPTLYKPLMSVDIDTHEPYRATVERSDPTALPAAGVVMEAVVATVLVT 36- 0 G+P++V+GVMKPIPTLYKPLMSVDID+HEPY+ATVERSDPTALPAAGV+ME VVATVL Sbjct: 301 GQPLVVKGVMKPIPTLYKPLMSVDIDSHEPYKATVERSDPTALPAAGVIMENVVATVLAK 36- 0 Query: 361 EVLEKFSSDNMYELKEAVKLYRNYVDHF 388 E+LE FSS M EL++A YR YV F Sbjct: 361 EILETFSSTTMSELQKAFSDYRAYVKQF 388 A related GBS gene <SEQ ID 8617> and protein <SEQ ID 8618> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01814 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: -2.42 GvH: Signal Score (-7.5): -3.23 Possible site: 15 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -4.67 threshold: 0.0 INTEGRAL Likelihood = -4.67 Transmembrane 343-359 (341-364) PERIPHERAL Likelihood = 0.69 214 modified ALOM score: 1.43 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2869 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00047## SEQ ID 8618 (GBS192) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 18 (lane 4; MW 44 kDa). GBS192-His was purified as shown in FIG. 196, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 608 A DNA sequence (GBSx0648) was identified in S. agalactiae <SEQ ID 1885> which encodes the amino acid sequence <SEQ ID 1886>. This protein is predicted to be 3-dehydroquinate synthase (aroB). Analysis of this protein sequence reveals the following: TABLE-US-01815 Possible site: 24 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.82 Transmembrane 99-115 (98-116) ----- Final Results ----- bacterial membrane --- Certainty = 0.2529 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01816 >GP: BAA18068 GB: D90911 3-dehydroquinate synthase [Synechocystis sp.] Identities = 138/351 (39%), Positives = 200/351 (56%), Gaps = 4/351 (1%) Query: 3 VEVDLPNHPYHIKIEEGCFSEAGDWVSHLWQKQMITIITDSNVEILYGESLVNQLKKQGF 62 + V LP PY ++I G + D ++ L + I ++++ + YGE ++ L++ G+ Sbjct: 5 IPVPLPQSPYQVQIVPGGLAAIADHLAPLGLGKKIMVVSNPEIYDYYGEVVIQALQRAGY 64 Query: 63 TVHVFSFAAGEASKTLEVANRIYAFLAKHHMTRSDGIIALGGGVVGDLAAFVASTYMRGI 122- V AGE KTL N +Y + ++ R+ +++LGGGV+GD+ F A+T++RGI Sbjct: 65 EVFQHLIPAGETHKTLASINELYDVAFQANLERNSTLLSLGGGVIGDMTGFGAATWLRGI 124- Query: 123 HFLQIPTSLTAQVDSSIGGKTGVNTSFAKNMVGTFAQPDGVLIDPVTLKTLGNRELVEGM 18- 2 +F+Q+PTSL A VD+SIGGKTGVN KN++G F QP V IDPV LKTL RE GM Sbjct: 125 NFVQVPTSLLAMVDASIGGKTGVNHPQGKNLIGAFYQPRLVYIDPVVLKTLPEREFRAGM 18- 4 Query: 183 GEVIKYGLIDDIKLWHILEEMD--GTIDSILDNALA-IIYHSCQVKRKHVLADQYDKGLR 23- 9 EVIKYG+I D +L+ LEE + +ID + D L II SCQ K V D+ + GLR Sbjct: 185 AEVIKYGVIWDSELFTALEEAEDLSSIDRLPDELLTKIIQRSCQAKVDVVSQDEKEAGLR 24- 4 Query: 240 MHLNFGHTIGHAIEVHAGYGEIMHGEAVAIGMIQLSRVAERKNLMPRGISQDIYNMCLKF 29- 9 LN+GHT+GH +E GYG I HGEAVAIGM +++A L + + + LK Sbjct: 245 AILNYGHTVGHGVESLTGYGVINHGEAVAIGMEAAAKIAHYLGLCDQSLGDRQRQLLLKT 30- 4 Query: 300 GLPVHY-AEWDKDVLFDILSHDKKASGQFIKIVILPQLGSATVHQIPLEEM 349 LP + L L HDKK ++ ++ +G T+ +E+ Sbjct: 305 KLPTEMPPTLAVENLLASLLHDKKVKAGKVRFILPTAIGQVTISDAVTDEV 355 A related DNA sequence was identified in S. pyogenes <SEQ ID 1887> which encodes the amino acid sequence <SEQ ID 1888>. Analysis of this protein sequence reveals the following: TABLE-US-01817 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 97-113 (97-114) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01818 >GP: BAA18068 GB: D90911 3-dehydroquinate synthase [Synechocystis sp.] Identities = 123/349 (35%), Positives = 190/349 (54%), Gaps = 9/349 (2%) Query: 1 MPQTLHVHSRVKDYDILFTDHVLKTLADCLGERKQ-RKLLFITDQTVYHLYQTLFEEFAQ 59 M T+ V Y + L +AD L +K++ +++ +Y Y + + Q Sbjct: 1 MATTIPVPLPQSPYQVQIVPGGLAAIADHLAPLGLGKKIMVVSNPEIYDYYGEVVIQALQ 60 Query: 60 Q--YNAFVHVCPPGGQSKSLERVSAIYDQLIAENFSKKDMIVTIGGGVVGDLGGFVAATY 117- + Y F H+ P G K+L ++ +YD N + ++++GGGV+GD+ GF AAT+ Sbjct: 61 RAGYEVFQHLIPAGETHKTLASINELYDVAFQANLERNSTLLSLGGGVIGDMTGFGAATW 120- Query: 118 YRGIPYIQIPTTLLSQVDSSIGGKVGVHFKGLTNMIGSIYPPEAIIISTTFLETLPQREF 17- 7 RGI ++Q+PT+LL+ VD+SIGGK GV+ N+IG+ Y P + I L+TLP+REF Sbjct: 121 LRGINFVQVPTSLLAMVDASIGGKTGVNHPQGKNLIGAFYQPRLVYIDPVVLKTLPEREF 18- 0 Query: 178 SCGISEMLKIGFIHDRPLFQQLRDFQ-----KETDKQGLERLIYQSISNKKRIVEQDEFE 23- 2 G++E++K G I D LF L + + + L ++I +S K +V QDE E Sbjct: 181 RAGMAEVIKYGVIWDSELFTALEEAEDLSSIDRLPDELLTKIIQRSCQAKVDVVSQDEKE 24- 0 Query: 233 NGLRMSLNFGHTLGHAIESLCHHDFYHHGEAIAIGMVVDAKLAVSKGLLPKEDLDSLLQV 29- 2 GLR LN+GHT+GH +ESL + +HGEA+AIGM AK+A GL + D Q+ Sbjct: 241 AGLRAILNYGHTVGHGVESLTGYGVINHGEAVAIGMEAAAKIAHYLGLCDQSLGDRQRQL 30- 0 Query: 293 FERYQLPTTLERADVSATSLFDVFKTDKKNSEQHIIFILPTETGFTTLA 341 + +LPT + ++ +L DKK + FILPT G T++ Sbjct: 301 LLKTKLPTEMP-PTLAVENLLASLLHDKKVKAGKVRFILPTAIGQVTIS 348 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01819 Identities = 121/332 (36%), Positives = 182/332 (54%), Gaps = 7/332 (2%) Query: 12 YHIKIEEGCFSEAGDWVSHLWQKQMITIITDSNVEILYGESLVNQLKKQGFTVHVFSFAA 71 - Y I + D + Q++++ ITD V LY ++L + +Q + V Sbjct: 14 YDILFTDHVLKTLADCLGERKQRKLL-FITDQTVYHLY-QTLFEEFAQQ-YNAFVHVCPP 70 Query: 72 GEASKTLEVANRIYAFLAKHHMTRSDGIIALGGGVVGDLAAFVASTYMRGIHFLQIPTSL 131- G SK+LE + IY L + ++ D I+ +GGGVVGDL FVA+TY RGI ++QIPT+L Sbjct: 71 GGQSKSLERVSAIYDQLIAENFSKKDMIVTIGGGVVGDLGGFVAATYYRGIPYIQIPTTL 130- Query: 132 TAQVDSSIGGKTGVNTSFAKNMVGTFAQPDGVLIDPVTLKTLGNRELVEGMGEVIKYGLI 19- 1 +QVDSSIGGK GV+ NM+G+ P+ ++I L+TL RE G+ E++K G I Sbjct: 131 LSQVDSSIGGKVGVHFKGLTNMIGSIYPPEAIIISTTFLETLPQREFSCGISEMLKIGFI 19- 0 Query: 192 DDIKLWHILEEMDGTIDSILDNALAIIYHSCQVKRKHVLADQYDKGLRMHLNFGHTIGHA 25- 1 D L+ L + D +IY S K++ V D+++ GLRM LNFGHT+GHA Sbjct: 191 HDRPLFQQLRDFQKETDK--QGLERLIYQSISNKKRIVEQDEFENGLRMSLNFGHTLGHA 24- 8 Query: 252 IEVHAGYGEIMHGEAVAIGMIQLSRVAERKNLMPRGISQDIYNMCLKFGLP--VHYAEWD 30- 9 IE + HGEA+AIGM+ +++A K L+P+ + + ++ LP + A+ Sbjct: 249 IESLCHHDFYHHGEAIAIGMVVDAKLAVSKGLLPKEDLDSLLQVFERYQLPTTLERADVS 30- 8 Query: 310 KDVLFDILSHDKKASGQFIKIVILPQLGSATV 341 LFD+ DKK S Q I ++ + G T+ Sbjct: 309 ATSLFDVFKTDKKNSEQHIIFILPTETGFTTL 340 SEQ ID 1886 (GBS336) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 62 (lane 2; MW 42.7 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 67 (lane 5; MW 68 kDa). The GBS336-GST fusion product was purified (FIG. 209, lane 4) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 310), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 609 A DNA sequence (GBSx0649) was identified in S. agalactiae <SEQ ID 1889> which encodes the amino acid sequence <SEQ ID 1890>. Analysis of this protein sequence reveals the following: TABLE-US-01820 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3884 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9973> which encodes amino acid sequence <SEQ ID 9974> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01821 >GP: CAB14240 GB: Z99116 3-dehydroquinate dehydratase [Bacillus subtilis] Identities = 70/233 (30%), Positives = 127/233 (54%), Gaps = 12/233 (5%) Query: 2 KIVVPVMPRSLEEA-QEIDLSKFDSVDIIEWRADALPK----DDIINVAPAIFEKFAGHE 56 KI++P+M ++ ++ E + K + DI+EWR D K + + + + + Sbjct: 17 KIIIPLMGKTEKQILNEAEAVKLLNPDIVEWRVDVFEKANDREAVTKLISKLRKSLEDKL 76 Query: 57 IIFTLRTTREGGNIVLSDAEYVELIQKINSIYNPDYIDFEYFSHKEVFQEMLEFPN---- 112- +FT RT +EGG++ + ++ Y+ L++ + D ID E FS + ++ Sbjct: 77 FLFTFRTHKEGGSMEMDESSYLALLESAIQTKDIDLIDIELFSGDANVKALVSLAEENNV 136- Query: 113 -LVLSYHNFQETP--ENIMEIFSELTALAPRVVKIAVMPKNEQDVLDVMNYTRGFKTINP 16- 9 +V+S H+F++TP + I+ ++ L + K+AVMP + D+L +++ T KTI Sbjct: 137 YVVMSNHDFEKTPVKDEIISRLRKMQDLGAHIPKMAVMPNDTGDLLTLLDATYTMKTIYA 19- 6 Query: 170 DQVYATVSMSKIGRISRFAGDVTGSSWTFAYLDSSIAPGQITISEMKRVKALL 222 D+ T+SM+ G ISR +G+V GS+ TF + + APGQI +SE++ V +L Sbjct: 197 DRPIITMSMAATGLISRLSGEVFGSACTFGAGEEASAPGQIPVSELRSVLDIL 249 A related DNA sequence was identified in S. pyogenes <SEQ ID 1891> which encodes the amino acid sequence <SEQ ID 1892>. Analysis of this protein sequence reveals the following: TABLE-US-01822 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3248 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below:

TABLE-US-01823 Identities = 160/225 (71%), Positives = 198/225 (87%) Query: 1 MKIVVPVMPRSLEEAQEIDLSKFDSVDIIEWRADALPKDDIINVAPAIFEKFAGHEIIFT 60 M+IV PVMPR +EAQ ID+SK++ V++IEWRAD LPKD+I+ VAPAIFEKFAG EIIFT Sbjct: 1 MRIVAPVMPRHFDEAQAIDISKYEDVNLIEWRADFLPKDEIVAVAPAIFEKFAGKEIIFT 60 Query: 61 LRTTREGGNIVLSDAEYVELIQKINSIYNPDYIDFEYFSHKEVFQEMLEFPNLVLSYHNF 120- LRT +EGGNI LS EYV++I++IN+IYNPDYIDFEYF+HK VFQEML+FPNL+LSYHNF Sbjct: 61 LRTVQEGGNITLSSQEYVDIIKEINAIYNPDYIDFEYFTHKSVFQEMLDFPNLILSYHNF 120- Query: 121 QETPENIMEIFSELTALAPRVVKIAVMPKNEQDVLDVMNYTRGFKTINPDQVYATVSMSK 18- 0 +ETPEN+ME FSE+T LAPRVVKIAVMP++EQDVLD+MNYTRGFKT+NP+Q +AT+SM K Sbjct: 121 EETPENLMEAFSEMTKLAPRVVKIAVMPQSEQDVLDLMNYTRGFKTLNPEQEFATISMGK 18- 0 Query: 181 IGRISRFAGDVTGSSWTFAYLDSSIAPGQITISEMKRVKALLDAD 225 +GR+SRFAGDV GSSWT+ LD PGQ+T+++MKR+ +L+ D Sbjct: 181 LGRLSRFAGDVIGSSWTYVSLDHVSGPGQVTLNDMKRIIEVLEMD 225 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 610 A DNA sequence (GBSx0650) was identified in S. agalactiae <SEQ ID 1893> which encodes the amino acid sequence <SEQ ID 1894>. Analysis of this protein sequence reveals the following: TABLE-US-01824 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1195 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 611 A DNA sequence (GBSx0651) was identified in S. agalactiae <SEQ ID 1895> which encodes the amino acid sequence <SEQ ID 1896>. Analysis of this protein sequence reveals the following: TABLE-US-01825 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3431 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01826 >GP: CAB15862 GB: Z99123 alternate gene name: ipa-19d~similar to hypothetical proteins [Bacillus subtilis] Identities = 161/396 (40%), Positives = 235/396 (58%), Gaps = 11/396 (2%) Query: 1 MNKLKVNSVVERKIKSGAQLLEKKDFDTSLVNQ----LVQLFSQSN-QFLGMAYLSPQNK 55 M L + KIK G L+EK+ S + LV + S+S +FL Y QNK Sbjct: 1 MKLLTLKKAHAAKIKKGYPLIEKEALAGSAGHMKEGDLVDIVSESGGEFLARGYYGLQNK 60 Query: 56 GIGWLLSRQVFD-FNHDYFVSLFEKSREKRQKFEKSSQTTAYRLFNQDGDNFGGLTIDFY 114- G+GW L+R + + +F+S K+ + R K ++ TTA+RLFN +GD GG+TID+Y Sbjct: 61 GVGWTLTRNKHEQIDQAFFLSKLTKAAQARAKLFEAQDTTAFRLFNGEGDGVGGVTIDYY 120- Query: 115 SDYALFSWYNEFVYTNRQMIVAAFKQVYPNIKGAYEKIRFKGLDF---ESAHLYGQEAPE 17- 1 Y L WY++ +YT + M+++A ++ + K YEK RF + + G+ Sbjct: 121 DGYLLIQWYSKGIYTFKDMLISALDEMDLDYKAIYEKKRFDTAGQYVEDDDFVKGRRGEF 18- 0 Query: 172 SFLILENNIKYSVFLNDGLMTGIFLDQHDVRKALATNLSEGKKVLNMFSYTAAFSVAAAV 23- 1 +I EN I+Y+V LN+G MTGIFLDQ VRKA+ ++GK VLN FSYT AFSVAAA+ Sbjct: 181 PIIIQENGIQYAVDLNEGAMTGIFLDQRHVRKAIRDRYAKGKTVLNTFSYTGAFSVAAAL 24- 0 Query: 232 GGALETTSVDLAKRSRELSKAHFDANQIVTDNHRFIVMDVFEYYKYAKRKHLSYDVIVID 29- 1 GGA +TTSVD+A RS + F N++ + H VMDVF Y+ YA +K L +D+I++D Sbjct: 241 GGAEKTTSVDVANRSLAKTIEQFSVNKLDYEAHDIKVMDVFNYFSYAAKKDLRFDLIILD 30- 0 Query: 292 PPSFARNKKQTFSVTKDYYKLIEQALDILTPGGTIIASTNAANLTVSQFKKQLEKGFGKA 35- 1 PPSFAR KK+TFS KDY L+++ + I G I+ASTN++ + +FK ++ F + Sbjct: 301 PPSFARTKKRTFSAAKDYKNLLKETIAITADKGVIVASTNSSAFGMKKFKGFIDAAFKET 36- 0 Query: 352 SHNYISLQQ-LPEDFTINDKDQQSNYLKVFTIKVK 385 + Y +++ LPEDF + NYLKV ++ K Sbjct: 361 NERYTIIEEFTLPEDFKTISAFPEGNYLKVVLLQKK 396 A related DNA sequence was identified in S. pyogenes <SEQ ID 1897> which encodes the amino acid sequence <SEQ ID 1898>. Analysis of this protein sequence reveals the following: TABLE-US-01827 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2699 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01828 Identities = 259/386 (67%), Positives = 315/386 (81%), Gaps = 1/386 (0%) Query: 1 MNKLKVNSVVERKIKSGAQLLEKKDFDT-SLVNQLVQLFSQSNQFLGMAYLSPQNKGIGW 59 MNKL ++S VE+K+ +G QLL++KDF NQLVQL ++SN+ +G AY+S QNKGIGW Sbjct: 1 MNKLYIDSFVEKKLTAGVQLLDEKDFSNIKEKNQLVQLVTKSNRPIGTAYISKQNKGIGW 60 Query: 60 LLSRQVFDFNHDYFVSLFEKSREKRQKFEKSSQTTAYRLFNQDGDNFGGLTIDFYSDYAL 119- L + D + YFVSLF ++ KRQ F +S +T AYRLFNQ+GD FGG+TID Y D+A+ Sbjct: 61 YLGPEKIDLSISYFVSLFSVAKAKRQDFAQSDETNAYRLFNQEGDGFGGVTIDLYKDFAV 120- Query: 120 FSWYNEFVYTNRQMIVAAFKQVYPNIKGAYEKIRFKGLDFESAHLYGQEAPESFLILENN 17- 9 FSWYN FVY ++MI+ AF+QV+P +KGAYEK RFKG D E+AHLYG+ A E+F ILEN Sbjct: 121 FSWYNAFVYDKKEMIMEAFQQVFPEVKGAYEKCRFKGPDTETAHLYGELAQETFSILENG 18- 0 Query: 180 IKYSVFLNDGLMTGIFLDQHDVRKALATNLSEGKKVLNMFSYTAAFSVAAAVGGALETTS 23- 9 I Y VFLN+GLMTGIFLDQHDVR+AL L+ GK +LN+FSYTAAFSVAAA+GGA+ETTS Sbjct: 181 IAYQVFLNEGLMTGIFLDQHDVRRALVDGLAMGKSLLNLFSYTAAFSVAAAMGGAIETTS 24- 0 Query: 240 VDLAKRSRELSKAHFDANQIVTDNHRFIVMDVFEYYKYAKRKHLSYDVIVIDPPSFARNK 29- 9 VDLAKRSRELS AHF+ NQ+ +H F+VMDVFEY+KYAKRK L +DVIVIDPPSFARNK Sbjct: 241 VDLAKRSRELSLAHFEHNQLNLASHHFVVMDVFEYFKYAKRKKLIFDVIVIDPPSFARNK 30- 0 Query: 300 KQTFSVTKDYYKLIEQALDILTPGGTIIASTNAANLTVSQFKKQLEKGFGKASHNYISLQ 35- 9 KQTFSV++DY+KLI +ALDIL+P GTIIASTNAAN+TVSQFKKQ+ KGFG ++LQ Sbjct: 301 KQTFSVSRDYHKLITEALDILSPKGTIIASTNAANMTVSQFKKQIIKGFGSRRPESMTLQ 36- 0 Query: 360 QLPEDFTINDKDQQSNYLKVFTIKVK 385 QLP DFTIN D++SNYLKVFTIKV+ Sbjct: 361 QLPSDFTINKADERSNYLKVFTIKVR 386 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 612 A DNA sequence (GBSx0652) was identified in S. agalactiae <SEQ ID 1899> which encodes the amino acid sequence <SEQ ID 1900>. This protein is predicted to be minimal change nephritis transmembrane glycoprotein. Analysis of this protein sequence reveals the following: TABLE-US-01829 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.85 Transmembrane 129-145 (126-152) INTEGRAL Likelihood = -4.88 Transmembrane 48-64 (46-69) INTEGRAL Likelihood = -4.83 Transmembrane 75-91 (74-97) INTEGRAL Likelihood = -4.62 Transmembrane 16-32 (15-34) INTEGRAL Likelihood = -2.28 Transmembrane 163-179 (163-182) ----- Final Results ----- bacterial membrane --- Certainty = 0.3739 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01830 >GP: CAB12545 GB: Z99107 alternate gene name: yetP~similar to hypothetical proteins [Bacillus subtilis] Identities = 299/676 (44%), Positives = 415/676 (61%), Gaps = 33/676 (4%) Query: 2 KKIKDFASRAINTRLGFILLLVVIYWLKTIWAYHTDFNLGLENSYQLFLTIINPIPLGLL 61 KK++ + + +L F +L V+++W KT +Y T+FNLG++ + Q L I NP + Sbjct: 9 KKVEVAMKKLFSYKLSFFVLAVILFWAKTYLSYKTEFNLGVKGTTQEILLIFNPFSSAVF 68 Query: 62 IIGLALYVKRTKAFYITAFITYAIVNILLIANAIYYREFSDFITVSAVLASSKTSAGLGD 121- +GLAL K K+ I I + ++ +L AN ++YR F DF+T + S +GD Sbjct: 69 FLGLALLAKGRKSAIIMLIIDF-LMTFVLYANILFYRFFDDFLTFPNIKQSGNVG-NMGD 126- Query: 122 SALNLLRIWDLVYVFDFIILIFLFATKKIHLDDRPFNKRASFSITALSGL-LFSINLFLA 18- 0 +++ D+ Y D IILI + + L + KR + S+ LSG+ LF INL A Sbjct: 127 GIFSIMAGHDIFYFLDIIILIAVLIWRP-ELKEYKMKKRFA-SLVILSGIALFFINLHYA 18- 4 Query: 181 EIDRPELLSRGFSNTYIVKALGLPSFSIYSGNQTYQAQKERNGATAQELATAKKYVAEHY 24- 0 E DRP+LL+R F YIVK LGL +++IY G QT Q + +R A++ +L + + Y HY Sbjct: 185 EKDRPQLLTRTFDRHYIVKYLGLYNYTIYDGVQTAQTETQRAYASSDDLTSVENYTTSHY 24- 4 Query: 241 AKPNPEYYGIGKGRNVIMIHLESFQQFLIDYRLNIDGKEHVVTPFINSLYHSKETVS-FS 29- 9 AKPN EY+G KG+N+I IHLESFQ FLIDYKLN G+E VTPF+N L H E V+F Sbjct: 245 AKPNAEYFGSARGKNIIKIHLESFQSFLIDYKLN--GEE--VTPFLNKLAHGGEDVTYFD 30- 0 Query: 300 NFFHQVKAGKTSDAETLMENSLFGLSSGSFMVNYGGENTQFAAPHILAQNGGYSSAVFHG 35- 9 NFFHQ GKTSDAE M+NS+FGL GS V GENT + P IL Q GY+SAV HG Sbjct: 301 NFFHQTGQGKTSDAELTMDNSIFGLPEGSAFVT-KGENTYQSLPAILDQKEGYTSAVLHG 35- 9 Query: 360 NVGTFWNRNNAYKQWGYDYFFDSSYFSKQTKDNSFQYGLNDKYMFADSIKYLEHMQQPFY 41- 9 + +FWNR+ YK GYD FFD+S + + +N GL DK F +SI LE ++QPFY Sbjct: 360 DYKSFWNRDQIYKHIGYDKFFDASTYD-MSDENVINMGLKDKPFFTESIPKLESLKQPFY 41- 8 Query: 420 TKFITVSNHYPYTSLKGESDEEGFPLAKTNDETINGYFATANYLDTALKSFFEYLKAAGV 47- 9 IT++NHYP+ + + A T D T++ YF TA YLD AL+ FF+ LK AG+ Sbjct: 419 AHLITLTNHYPFNL---DEKDASLKKATTGDNTVDSYFQTARYLDEALEQFFKELKEAGL 47- 5 Query: 480 YDNSIIVMYGDHYGISNTRNPSLAELLGKDPETWSEYDNAMLQRVPYMIHIPGYSKGFIS 53- 9 YDNS+I++YGDH GIS N ++ E+LGK+ ++Y NA QRVP MI +PG KG ++ Sbjct: 476 YDNSVIMIYGDHNGISENHNRAMKEILGKE---ITDYQNAQNQRVPLMIRVPG-KKGGVN 53- 1 Query: 540 NTYGGEVDNLPTLLHILGIDTSKYTQLGQDLLSKDNKQMVAMRTTGQYITPKYTNYSGHL 59- 9 +TYGGE+D +PTLLH+ GID+ KY G DL SKD+ VA R G ++TPKYT+ + Sbjct: 532 HTYGGEIDVMPTLLHLEGIDSQKYINFGTDLFSKDHDDTVAFR-NGDFVTPKYTSVDNII 59- 0 Query: 600 YYTDSGQEITNPDETTKAEIKAIRDATNKQLSTSDSIQTGDLLRFDENNGLKTVEVEKFN 65- 9 Y T +G+++ +ET K ++ N+QLS SDS+ DLLRF + N K V+ ++ Sbjct: 591 YDTKTGEKLKANEET-----KNLKTRVNQQLSLSDSVLYKDLLRFHKLNDFKAVDPSDYH 64- 5 Query: 660 YTHSLKALKAKERKLK 675 Y KE+++K Sbjct: 646 Y--------GKEKEIK 653 A related DNA sequence was identified in S. pyogenes <SEQ ID 1901> which encodes the amino acid sequence <SEQ ID 1902>. Analysis of this protein sequence reveals the following: TABLE-US-01831 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.85 Transmembrane 90-106 (88-112) INTEGRAL Likelihood = -5.68 Transmembrane 146-162 (139-165) INTEGRAL Likelihood = -4.99 Transmembrane 63-79 (60-84) INTEGRAL Likelihood = -3.98 Transmembrane 178-194 (176-197) INTEGRAL Likelihood = -0.59 Transmembrane 31-47 (31-47) ----- Final Results ----- bacterial membrane --- Certainty = 0.3739 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01832 Identities = 533/713 (74%), Positives = 603/713 (83%) Query: 1 MKKIKDFASRAINTRLGFILLLVVIYWLKTIWAYHTDFNLGLENSYQLFLTIINPIPLGL 60 +KK K + INTRLGFI+ L+ YW+KT+WAYHTDF+L L N YQ+FLTIINPIPL Sbjct: 16 VKKFKTLITGFINTRLGFIITLLFCYWIKTLWAYHTDFSLDLGNIYQVFLTIINPIPLAF 75 Query: 61 LIIGLALYVKRTKAFYITAFITYAIVNILLIANAIYYREFSDFITVSAVLASSKTSAGLG 120- L++G+ALYVK T+AFYI +++ Y I+NILLI+N+IYYREFSDFITVSA+LASSK SAGLG Sbjct: 76 LLLGVALYVKNTRAFYICSWVVYIILNILLISNSIYYREFSDFITVSAMLASSKVSAGLG 135- Query: 121 DSALNLLRIWDLVYVFDFIILIFLFATKKIHLDDRPFNKRASFSITALSGLLFSINLFLA 18- 0 DSALNLLRIWD++Y+ DFIILI L KKI D RPFNKRA+F+ITALS LL SINLFLA Sbjct: 136 DSALNLLRIWDIIYILDFIILISLSIAKKIKNDQRPFNKRAAFAITALSSLLLSINLFLA 19- 5 Query: 181 EIDRPELLSRGFSNTYIVKALGLPSFSIYSGNQTYQAQKERNGATAQELATAKKYVAEHY 24- 0 EIDRPELL+RGFSNTYIV+ALGLP+F++YSGNQTYQAQKERNGATA+EL K YV HY Sbjct: 196 EIDRPELLTRGFSNTYIVRALGLPAFTLYSGNQTYQAQKERNGATAEELIDVKTYVKGHY 25- 5 Query: 241 AKPNPEYYGIGKGRNVIMIHLESFQQFLIDYKLNIDGKEHVVTPFINSLYHSKETVSFSN 30- 0 A P+P+Y+GIGKG+N+I++HLESFQQFLIDYKL KE+ VTPFINSLYHS T++F N Sbjct: 256 AAPDPQYFGIGKGKNIIVLHLESFQQFLIDYKLKEGDKEYEVTPFINSLYHSNATLAFPN 31- 5 Query: 301 FFHQVKAGKTSDAETLMENSLFGLSSGSFMVNYGGENTQFAAPHILAQNGGYSSAVFHGN 36- 0 FFHQVKAGKTSDAET+MENSLFGL+SGSFMVNYGGENTQFA P ILAQ GGY+SAVFHGN Sbjct: 316 FFHQVKAGKTSDAETMMENSLFGLNSGSFMVNYGGENTQFATPSILAQKGGYTSAVFHGN 37- 5 Query: 361 VGTFWNRNNAYKQWGYDYFFDSSYFSKQTKDNSFQYGLNDKYMFADSIKYLEHMQQPFYT 42- 0 VGTFWNRNNAYKQWGY+YFFDSSYFSKQ NSFQYGLNDKYMF DSIKYLE MQQPFYT Sbjct: 376 VGTFWNRNNAYKQWGYNYFFDSSYFSKQNSKNSFQYGLNDKYMFKDSIKYLEQMQQPFYT 43- 5 Query: 421 KFITVSNHYPYTSLKGESDEEGFPLAKTNDETINGYFATANYLDTALKSFFEYLKAAGVY 48- 0 KFITVSNHYPYTSLKGES EEGFPLAKT+DETINGYFATANYLD ALKSFF+YLKA G+Y Sbjct: 436 KFITVSNHYPYTSLKGESSEEGFPLAKTDDETINGYFATANYLDAALKSFFDYLKATGLY 49- 5 Query: 481 DNSIIVMYGDHYGISNTRNPSLAELLGKDPETWSEYDNAMLQRVPYMIHIPGYSKGFISN 54- 0 DNSI V+YGDHYGISN+RN SLA LLGKD ETWSEYDNAMLQRVPYMIHIPGY+ G I Sbjct: 496 DNSIFVLYGDHYGISNSRNSSLAPLLGKDSETWSEYDNAMLQRVPYMIHIPGYTNGSIKE 55- 5 Query: 541 TYGGEVDNLPTLLHILGIDTSKYTQLGQDLLSKDNKQMVAMRTTGQYITPKYTNYSGHLY 60- 0 T+GGE+D LPTLLHILGIDTS++ QLGQDLLS N Q+VA RT+G Y+TP+YTNYSG LY Sbjct: 556 TFGGEIDALPTLLHILGIDTSQFVQLGQDLLSPQNSQIVAQRTSGTYMTPEYTNYSGRLY 61- 5 Query: 601 YTDSGQEITNPDETTKAEIKAIRDATNKQLSTSDSIQTGDLLRFDENNGLKTVEVEKFNY 66- 0 T +G EITNPDE T A+ K IR A +QL+ SD+IQTGDLLRFD NGLK ++ +F Y Sbjct: 616 NTQTGLEITNPDEMTIAKTKEIRSAVAQQLAASDAIQTGDLLRFDTQNGLKAIDPNQFIY 67- 5 Query: 661 THSLKALKAKERKLKDRSTSIYSKHNNKSTVDLFHAPSYLELQDPNKTHKTSK 713 T LK LK KL STS+YSK+ +KST LF APSYLEL TS+ Sbjct: 676 TKQLKQLKDISAKLGSESTSLYSKNGHKSTQKLFKAPSYLELNPVEADAATSE 728 A related GBS gene <SEQ ID 8619> and protein <SEQ ID 8620> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01833 Lipop Possible site: -1 Crend: 9 McG: Discrim Score: 12.63 GvH: Signal Score (-7.5): -2.99 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 5 value: -6.85 threshold: 0.0 INTEGRAL Likelihood = -6.85 Transmembrane 129-145 (126-152) INTEGRAL Likelihood = -4.88 Transmembrane 48-64 (46-69) INTEGRAL Likelihood = -4.83 Transmembrane 75-91 (74-97) INTEGRAL Likelihood = -4.62 Transmembrane 16-32 (15-34) INTEGRAL Likelihood = -2.28 Transmembrane 163-179 (163-182) PERIPHERAL Likelihood = 3.76 103 modified ALOM score: 1.87 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3739 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00048## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 613 A DNA sequence (GBSx0653) was identified in S. agalactiae <SEQ ID 1903> which encodes the amino acid sequence <SEQ ID 1904>. This protein is predicted to be 50S ribosomal protein L20 (rplT). Analysis of this protein sequence reveals the following: TABLE-US-01834 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3392 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9387> which encodes amino acid sequence <SEQ ID 9388> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01835 >GP: CAB14845 GB: Z99118 ribosomal protein L20 [Bacillus subtilis] Identities = 70/89 (78%), Positives = 78/89 (86%) Query: 1 MFRTAKEQVMNSYYYAYRDRRQKKRDFRKLWITRINAAARMNGLSYSQLMHGLKLAEIEV 60 +++ A +QVM S YA+RDRRQKKRDFRKLWITRINAAARMNGLSYS+LMHGLKL+ IEV Sbjct: 31 LYKVANQQVMKSGNYAFRDRRQKKRDFRKLWITRINAAARMNGLSYSRLMHGLKLSGIEV 90 Query: 61 NRKMLADLAVNDAAAFTALADAAKAKLGK 89 NRKMLADLAVND AF LADAAKA+L K Sbjct: 91 NRKMLADLAVNDLTAFNQLADAAKAQLNK 119 A related DNA sequence was identified in S. pyogenes <SEQ ID 1905> which encodes the amino acid sequence <SEQ ID 1906>. Analysis of this protein sequence reveals the following: TABLE-US-01836 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.06 Transmembrane 94-110 (94-110) ----- Final Results ----- bacterial membrane --- Certainty = 0.1022 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01837 Identities = 87/89 (97%), Positives = 88/89 (98%) Query: 1 MFRTAKEQVMNSYYYAYRDRRQKKRDFRKLWITRINAAARMNGLSYSQLMHGLKLAEIEV 60 +FRTAKEQVMNSYYYAYRDRRQKKRDFRKLWITRINAAARMNGLSYSQLMHGLKLAEIEV Sbjct: 31 LFRTAKEQVMNSYYYAYRDRRQKKRDFRKLWITRINAAARMNGLSYSQLMHGLKLAEIEV 90 Query: 61 NRKMLADLAVNDAAAFTALADAAKAKLGK 89 NRKMLADLAV DAAAFTALADAAKAKLGK Sbjct: 91 NRKMLADLAVADAAAFTALADAAKAKLGK 119 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 614 A DNA sequence (GBSx0654) was identified in S. agalactiae <SEQ ID 1907> which encodes the amino acid sequence <SEQ ID 1908>. Analysis of this protein sequence reveals the following: TABLE-US-01838 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.64 Transmembrane 32-48 (32-48) INTEGRAL Likelihood = -0.32 Transmembrane 3-19 (3-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 615 A DNA sequence (GBSx0655) was identified in S. agalactiae <SEQ ID 1909> which encodes the amino acid sequence <SEQ ID 1910>. Analysis of this protein sequence reveals the following:

TABLE-US-01839 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.63 Transmembrane 747-763 (743-772) INTEGRAL Likelihood = -12.52 Transmembrane 840-856 (835-856) INTEGRAL Likelihood = -11.20 Transmembrane 447-463 (440-466) INTEGRAL Likelihood = -5.79 Transmembrane 351-367 (346-372) INTEGRAL Likelihood = -4.25 Transmembrane 517-533 (516-537) INTEGRAL Likelihood = -1.49 Transmembrane 397-413 (396-413) INTEGRAL Likelihood = -0.96 Transmembrane 799-815 (799-817) ----- Final Results ----- bacterial membrane --- Certainty = 0.6052 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9349> which encodes amino acid sequence <SEQ ID 9350> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01840 >GP: AAB89436 GB: AE000977 A. fulgidus predicted coding region AF1820 [Archaeoglobus fulgidus] Identities = 100/483 (20%), Positives = 210/483 (42%), Gaps = 61/483 (12%) Query: 351 LFPIILYLVAALVTLTTMTRFVEEERTNAGILKALGYSDRQVIFKFIIYGFIAGTLGTTL 41- 0 LFP LV+ +T ++R + N +++ALG++ +++ ++ Y + G +T Sbjct: 276 LFPAFFILVSIFMTYALLSRIFRLQLGNIAVMRALGFTRNEIMLHYLQYPLLMGFFASTA 33- 5 Query: 411 GIIGGHYLLPRIISDIISKDLTIPNTQYHLFLNYSLLAFVFSLLSIVLPVFVI------- 46- 3 G++ G + + S I+ L +P L L+ + L+ + F++ Sbjct: 336 GLVAGFFASQLLTSQYIT-FLNLPYYVSKPHLEVYSLSLMAGTLTPTISGFLVAYQASRV 39- 4 Query: 464 ----TRRELKEKAAFLLLPKPPAKGSKIALEYINWIWKKLSFTQKVTARNIFRYKQRMIM 51- 9 R E AA + + A S+I W ++ ++ RNIFR K+R + Sbjct: 395 DIVKALRGYAEVAAVSFIARIDALFSRI------W---RMRLIFRLALRNIFRSKRRTAI 44- 5 Query: 520 TIFGVAGSVALLFSGLGIQSSLKQTVNEHFGRIMPYDILLTYNTNASPPKILELLSKDSK 57- 9 +IF + +L+ + + S + FG++ YDI ++ E+L K K Sbjct: 446 SIFSIVACTSLILNSMVFVDSFDYVMQLQFGKVYAYDIKVSLEGYDGK----EVLEKVRK 50- 1 Query: 580 IDKY--------QPIHLENLDESIPGQINKQSISLFITDKKQLLPFIYLQEATTNKSLHL 63- 1 +D PI++E E++P +L I Q L +Y E + Sbjct: 502 MDGVLFAEPAVEMPIYVEKGGEAVP--------TLLIASNFQTLYNVYNAEG----EKLI 54- 9 Query: 632 NNKGIIISKKLAQFYHVNTGDFIHL------SHSQTLPSRKLKITGVVNANVGHYIFMTK 68- 5 ++GII SK + + G+ + + ++ + + V A++ Sbjct: 550 PSEGIIFSKTAMKNLSLVEGEKVSVYTEFGKLEAEVEDVEMIPLLSVATASL-------- 60- 1 Query: 686 QYYRTIFKKEAKDNAFLVKLTKHKIANNLAEKLLEINGVESLTQNALQLASVEAVVRSLD 74- 5 Y+ I + N +V + +IA +AEK+ +++GV+ ++ S+E ++ Sbjct: 602 DYFSRISGVDG-FNRIVVDADEGRIA-EIAEKIRQMDGVKKVSTVIEAQESIEELMGFFY 65- 9 Query: 746 GSMTILVVVSLLLAIVILYNLTNINLAERKRELSTIKVLGFYNEEVTLYIYRETIILSTI 80- 5 + + + L ++N T+I++ ER REL+T+++LG+ + E+ + + E + ++ + Sbjct: 660 AFIAFSLFFGVSLGFAAVFNTTSISVIERSRELATLRMLGYTSREIIISLILENLFVAIL 71- 9 Query: 806 GVI 808 G++ Sbjct: 720 GLV 722 A related DNA sequence was identified in S. pyogenes <SEQ ID 1911> which encodes the amino acid sequence <SEQ ID 1912>. Analysis of this protein sequence reveals the following: TABLE-US-01841 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.33 Transmembrane 749-765 (739-775) INTEGRAL Likelihood = -10.88 Transmembrane 845-861 (834-865) INTEGRAL Likelihood = -6.64 Transmembrane 350-366 (344-369) INTEGRAL Likelihood = -6.53 Transmembrane 22-38 (19-42) INTEGRAL Likelihood = -6.32 Transmembrane 520-536 (515-537) INTEGRAL Likelihood = -4.99 Transmembrane 446-462 (445-465) INTEGRAL Likelihood = -2.92 Transmembrane 396-412 (395-413) INTEGRAL Likelihood = -0.80 Transmembrane 800-816 (800-819) ----- Final Results ----- bacterial membrane --- Certainty = 0.6731(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01842 >GP: AAB89436 GB: AE000977 A. fulgidus predicted coding region AF1820 [Archaeoglobus fulgidus] Identities = 101/542 (18%), Positives = 237/542 (43%), Gaps = 42/542 (7%) Query: 350 IFPVVLYLVAALVAFTTMTRYVDEERTSSGLLKAIGYSNKDISLKFLIYGLLASFLGTTL 40- 9 +FP LV+ + + ++R + + +++A+G++ +I L +L Y LL F +T Sbjct: 276 LFPAFFILVSIFMTYALLSRIFRLQLGNIAVMRALGFTRNEIMLHYLQYPLLMGFFASTA 33- 5 Query: 410 GIIGGTYLLSTLISEILTGA---LTIGKTHLYSYWFYNGIAYLLAMLSAVLPAYLIVKKE 46- 6 G++ G + L S+ +T + K HL Y L +S L AY + + Sbjct: 336 GLVAGFFASQLLTSQYITFLNLPYYVSKPHLEVYSLSLMAGTLTPTISGFLVAYQASRVD 39- 5 Query: 467 LFLN-------AAQLLLPKPPSKGAKIWLEHLTFVWKALSFTHKVTIRNIFRYKQRMLMT 51- 9 + AA + + + ++IW L F ++ +RNIFR K+R ++ Sbjct: 396 IVKALRGYAEVAAVSFIARIDALFSRIWRMRLIF---------RLALRNIFRSKRRTAIS 44- 6 Query: 520 IVGVAGSVALLFAGLGIQSSLAKVVEHQFGDLTTYDILAVGSAKATATEQTDLASYLKQE 57- 9 I + +L+ + S V++ QFG + YDI + L Y +E Sbjct: 447 IFSIVACTSLILNSMVFVDSFDYVMQLQFGKVYAYDI------------KVSLEGYDGKE 49- 4 Query: 580 PITGYQKVSYASLTLPVKGLP---DKQSISILSSS-ATSLSPYFNLLDSQEQKKVPIPTS 63- 5 + +K+ P +P +K ++ + A++ +N+ +++ +K IP+ Sbjct: 495 VLEKVRKMDGVLFAEPAVEMPIYVEKGGEAVPTLLIASNFQTLYNVYNAEGEKL--IPSE 55- 2 Query: 636 GVLISEKLASYYKVKPGDQLVLTDRKGQSYKVTIKQVIDMTVGHYLIMSDTYFKNHFKGL 69- 5 G++ S+ + G+++ + G+ ++ ++ L+ T ++F + Sbjct: 553 GIIFSKTAMKNLSLVEGEKVSVYTEFGK-----LEAEVEDVEMIPLLSVATASLDYFSRI 60- 7 Query: 696 EAAPAYLIKVKDKDSKHIKETASDLLTLKAIRAVSQNVNHIKSVQLVVTSLNQVMTLLVF 75- 5 + V D D I E A + + ++ VS + +S++ ++ + +F Sbjct: 608 SGVDGFNRIVVDADEGRIAEIAEKIRQMDGVKKVSTVIEAQESIEELMGFFYAFIAFSLF 66- 7 Query: 756 LSILLAIVILYNLTTINIAERIRELSTIKVLGFYDQEVTLYIYRETISLSLVGILLGIYL 81- 5 + L ++N T+I++ ER REL+T+++LG+ +E+ + + E + ++++G++ + + Sbjct: 668 FGVSLGFAAVFNTTSISVIERSRELATLRMLGYTSREIIISLILENLFVAILGLVFALPI 72- 7 Query: 816 GKGLHTYIMTMISTGDIQFGVKVDAYVYLVPILVILSLLAVLGIWVNRHLKKVDMLEALK 87- 5 + + + + + + +L + +++ + + R + ++D+ + K Sbjct: 728 AYSTAYFFFSSFESELYYMPMVIYPRTFAATVLAVFAIILLALLPSARRVSEMDIAKVTK 78- 7 Query: 876 SI 877 I Sbjct: 788 EI 789 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01843 Identities = 377/857 (43%), Positives = 543/857 (62%), Gaps = 7/857 (0%) Query: 3 KTFWKDIYRSITTSKGRFSSILLLMMLGSFAFIGLKVSAPNMQRTAQNYLAHHHVMDITV 62 KT WKDI R+I SKGRF S+ LM LGSFA +GLKV+ P+M+RTA YL H VMD+TV Sbjct: 4 KTLWKDILRAIKNSKGRFISLFFLMALGSFALVGLKVTGPDMERTASRYLERHQVMDLTV 63 Query: 63 FNSWGLDKHDQTVLESLKGSQVEFSYFVDTTPQQNSKSYRLYSNTKTISTFDLVKGRLPL 122- S + D+ L++LKG+ +E+ + +D + N KS RLYS K +S LVKG P Sbjct: 64 LASHQFSQADKQELDTLKGAHLEYGHLLDVSLTSNQKSLRLYSVPKKVSKPVLVKGSWPK 123- Query: 123 NKSEIALSFQERKKYAIGDKINFKQDKNKLFSNTGPLTIVGFVNSTEIWSKTNLGSSQTG 18- 2 ++++ LS K Y IGD++ L + T +VGF NS+E+WSK+NLGSS TG Sbjct: 124 RETDLVLSSSLAKNYQIGDELAVTSPMEGLLTTTH-FQVVGFANSSEVWSKSNLGSSSTG 18- 2 Query: 183 DGDLDSYGVLDKTAFHSPVYTMARVTFKDLRLINPFSISYKEKVAKYQEKVSRKLNIHNK 24- 2 DG L +Y ++ F S + + R+ F LRL N FS Y+++V + Q + L + + Sbjct: 183 DGSLYAYAFVNPNVFKS-AFNLLRIRFSHLRLTNAFSKDYQKRVTQNQAHLDNLLKDNGQ 24- 1 Query: 243 IRYTKTKKESLRKIDEEEKSLLKAQKQINRLDNDSLAMPLSQRQAIQMKIKQDRLSLLKR 30- 2 RY + + + +L K ++ + + + S Q + +I+Q + +L K Sbjct: 242 KRYDDLQNQYDLALKNGRAALAKETVKLAASEENLTFLEGSALQEAKHQIEQGKQALAKE 30- 1 Query: 303 TKELLKLRHNTQIMESPQIIVYNRTTFPGGQGYNTFDSSTNSTSKISNLFPIILYLVAAL 36- 2 K+L +++ +E P + YNR+T PGG+GY+T+ +ST S S + N+FP++LYLVAAL Sbjct: 302 EKQLEQVQATKDKLEKPSYLTYNRSTLPGGEGYHTYATSTTSISNVGNIFPVVLYLVAAL 36- 1 Query: 363 VTLTTMTRFVEEERTNAGILKALGYSDRQVIFKFIIYGFIAGTLGTTLGIIGGHYLLPRI 42- 2 V TTMTR+V+EERT++G+LKA+GYS++ + KF+IYG +A LGTTLGIIGG YLL + Sbjct: 362 VAFTTMTRYVDEERTSSGLLKAIGYSNKDISLKFLIYGLLASFLGTTLGIIGGTYLLSTL 42- 1 Query: 423 ISDIISKDLTIPNTQYHLFLNYSLLAFVFSLLSIVLPVFVITRRELKEKAAFLLLPKPPA 48- 2 IS+I++ LTI T + + Y+ +A++ ++LS VLP ++I ++EL AA LLLPKPP+ Sbjct: 422 ISEILTGALTIGKTHLYSYWFYNGIAYLLAMLSAVLPAYLIVKKELFLNAAQLLLPKPPS 48- 1 Query: 483 KGSKIALEYINWIWKKLSFTQKVTARNIFRYKQRMIMTIFGVAGSVALLFSGLGIQSSLK 54- 2 KG+KI LE++ ++WK LSFT KVT RNIFRYKQRM+MTI GVAGSVALLF+GLGIQSSL Sbjct: 482 KGAKIWLEHLTFVWKALSFTHKVTIRNIFRYKQRMLMTIVGVAGSVALLFAGLGIQSSLA 54- 1 Query: 543 QTVNEHFGRIMPYDILLTYNTNASPPKILELLS--KDSKIDKYQPIHLENLDESIPGQIN 60- 0 + V FG + YDIL + A+ + +L S K I YQ + +L + G + Sbjct: 542 KVVEHQFGDLTTYDILAVGSAKATATEQTDLASYLKQEPITGYQKVSYASLTLPVKGLPD 60- 1 Query: 601 KQSISLFITDKKQLLPFIYLQEATTNKSLHLNNKGIIISKKLAQFYHVNTGDFIHLSHSQ 66- 0 KQSIS+ + L P+ L ++ K + + G++IS+KLA +Y V GD + L+ + Sbjct: 602 KQSISILSSSATSLSPYFNLLDSQEQKKVPIPTSGVLISEKLASYYKVKPGDQLVLTDRK 66- 1 Query: 661 TLPSRKLKITGVVNANVGHYIFMTKQYYRTIFKKEAKDNAFLVKL--TKHKIANNLAEKL 71- 8 S K+ I V++ VGHY+ M+ Y++ FK A+L+K+ K A L Sbjct: 662 G-QSYKVTIKQVIDMTVGHYLIMSDTYFKNHFKGLEAAPAYLIKVKDKDSKHIKETASDL 72- 0 Query: 719 LEINGVESLTQNALQLASVEAVVRSLDGSMTILVVVSLLLAIVILYNLTNINLAERKREL 77- 8 L + + +++QN + SV+ VV SL+ MT+LV +S+LLAIVILYNLT IN+AER REL Sbjct: 721 LTLKAIRAVSQNVNHIKSVQLVVTSLNQVMTLLVFLSILLAIVILYNLTTINIAERIREL 78- 0 Query: 779 STIKVLGFYNEEVTLYIYRETIILSTIGVILGTISGTYLHRQMMLLIGSDQILFGEKVSP 83- 8 STIKVLGFY++EVTLYIYRETI LS +G++LG G LH +M +I + I FG KV Sbjct: 781 STIKVLGFYDQEVTLYIYRETISLSLVGILLGIYLGKGLHTYIMTMISTGDIQFGVKVDA 84- 0 Query: 839 TTFIIPISVVVIILXXL 855 +++PI V++ +L L Sbjct: 841 YVYLVPILVILSLLAVL 857 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 616 A DNA sequence (GBSx0656) was identified in S. agalactiae <SEQ ID 1913> which encodes the amino acid sequence <SEQ ID 1914>. This protein is predicted to be ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-01844 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2757 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01845 >GP: AAB89431 GB: AE000977 ABC transporter, ATP-binding protein [Archaeoglobus fulgidus] Identities = 112/230 (48%), Positives = 167/230 (71%) Query: 4 IEMKHSYKRYQTGETEIVANNDISFSIERGELVVILGASGAGKSTVLNILGGMDSNSEGE 63 + ++ +K YQ G+ E+ A I+ IERGE +V+LG SG GK+T+LNI+GG+D + G Sbjct: 2 LRLEDVWKVYQMGKVEVSALRGINLEIERGEFMVVLGPSGCGKTTMLNIIGGIDRPTRGR 61 Query: 64 VLIDGKNIANYTIRELTRYRRYDVGFVFQFYNLVPNLTALENVELASEIVPKALDAQQAL 123- V+ DGK+I NY LT +RR +VGF +FQF+NL+P LTA ENVE+A+++V D + L Sbjct: 62 VIFDGKDITNYNEDRLTMHRRNNVGFIFQFFNLIPTLTARENVEIAADLVESPRDVDEVL 121- Query: 124 ENVGLGHRINHFPAQLSGGEQQRVAIARAIAKKPKLLLCDEPTGALDYQTGKQVLAILQK 18- 3 + VGL R HFPA+LSGGEQQRVAIARA+ K P ++L DEPTG+LD++TGK VL ++++ Sbjct: 122 KMVGLADRAEHFPAELSGGEQQRVAIARALVKNPPIILADEPTGSLDFETGKAVLKVMRE 18- 1 Query: 184 MAQSKETTVIIVTHNTALAPIANRVIHMHDSKISDIVINENPSDIQNIEY 233 + + + T ++VTHN+A+A IA+RV+++ D K+ + N +P+D I++ Sbjct: 182 INRKEGITFVLVTHNSAIAAIADRVVYLRDGKVERVERNLHPADPDEIQW 231 There is also homology to SEQ ID 1354. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 617 A DNA sequence (GBSx0657) was identified in S. agalactiae <SEQ ID 1915> which encodes the amino acid sequence <SEQ ID 1916>. This protein is predicted to be DNA topoisomerase I (topA). Analysis of this protein sequence reveals the following: TABLE-US-01846 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4716 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9821> which encodes amino acid sequence <SEQ ID 9822> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01847 >GP: CAB13485 GB: Z99112 DNA topoisomerase I [Bacillus subtilis] Identities = 442/690 (64%), Positives = 535/690 (77%), Gaps = 10/690 (1%) Query: 27 LVIVESPAKAKTIEKYLGRNYKVVASVGHIRDLKKSSMSIDFENNYEPQYINIRGKGPLI 86 - LVIVESPAKAKTIE+YLG+ YKV AS+GH+RDL KS M +D E N+EP+YI IRGKGP++ Sbjct: 5 LVIVESPAKAKTIERYLGKKYKVKASMGHVRDLPKSQMGVDIEQNFEPKYITIRGKGPVL 64 Query: 87 NDLKKEAKKAKKVYLASDPDREGEAISWHLAHILDLDKEDRNRVVFNEITKDAVKNAFVE 146- +LK AKKAKKVYLA+DPDREGEAI+WHLAH LDLD RVVFNEITKDA+K +F Sbjct: 65 KELKTAAKKAKKVYLAADPDREGEAIAWHLAHSLDLDLNSDCRVVFNEITKDAIKESFKH 124- Query: 147 PRQINMDLVDAQQARRVLDRIVGYSISPILWKKVKKGLSAGRVQSVALKLIIDRENEIKA 20- 6 PR INMDLVDAQQARR+LDR+VGY ISPILWKKVKKGLSAGRVQSVAL+LIIDRE EI Sbjct: 125 PRMINMDLVDAQQARRILDRLVGYKISPILWKKVKKGLSAGRVQSVALRLIIDREKEIND 18- 4 Query: 207 FQPEEYWTIDGSFKKGTRKFNATFYGLDGKKFKLSNNEDVKTVLKRIKTDEFLVEKVEKK 26- 6 F+PEEYWTIDG+F KG F A+F+G +GKK L++ DVK +L ++K +++ VEKV KK Sbjct: 185 FKPEEYWTIDGTFLKGQETFEASFFGKNGKKLPLNSEADVKEILSQLKGNQYTVEKVTKK 24- 4 Query: 267 ERRRNAPLPYTTSSLQQDAANKINFRTRKTMMIAQQLYEGLSLGTAGHQGLITYMRTDST 32- 6 ER+RN LP+TTS+LQQ+AA K+NFR +KTMMIAQQLYEG+ LG G GLITYMRTDST Sbjct: 245 ERKRNPALPFTTSTLQQEAARKLNFRAKKTMMIAQQLYEGIDLGREGTVGLITYMRTDST 30- 4 Query: 327 RISPLAQNEATEFITNRFGANYSKHGNK-VKNASGAQDAHEAIRPSSVNHTPESIAKYLD 38- 5 RIS A +EA FI +G + K K AQDAHEAIRP+SV P + L Sbjct: 305 RISNTAVDEAAAFIDQTYGKEFLGGKRKPAKKNENAQDAHEAIRPTSVLRKPSELKAVLG 36- 4 Query: 386 KDQLKLYTLIWNRFIASQMTAAVFDTMKVNLTQNGVTFIANGSQVKFDGYMAVYND---- 44- 1 +DQ++LY LIW RF+ASQM AV DTM V+LT NG+TF ANGS+VKF G+M VY + Sbjct: 365 RDQMRLYKLIWERFVASQMAPAVLDTMSVDLTNNGLTFRANGSKVKFSGFMKVYVEGKDD 42- 4 Query: 442 --TDKNKMLPDMEEGESVKKVNTNPEQHFTQPPARFSEASLIKTLEENGVGRPSTYAPTL 49- 9 +K++MLPD++EG++V + PEQHFTQPP R++EA L+KTLEE G+GRPSTYAPTL Sbjct: 425 QMEEKDRMLPDLQEGDTVLSKDIEPEQHFTQPPPRYTEARLVKTLEERGIGRPSTYAPTL 48- 4 Query: 500 ETIQKRYYVKLAAKRFEPTELGEIVNSLIVEFFPDIVDVTFTAEMEGKLDEVEIGKEQWQ 55- 9 +TIQ+R YV L KRF PTELG+IV LI+EFFP+I++V FTA+ME LD VE G +W Sbjct: 485 DTIQRRGYVALDNKRFVPTELGQIVLDLIMEFFPEIINVEFTAKMERDLDHVEEGNTEWV 54- 4 Query: 560 KIIDEFYKPFEKELAKAETEMEKIQIKDEPAGFDCELCGSPMVIKLGRYGKFYACSNFPE 61- 9 KIID FY FEK + KAE+EM++++I+ E AG DCELC SPMV K+GRYGKF ACSNFP+ Sbjct: 545 KIIDNFYTDFEKRVKKAESEMKEVEIEPEYAGEDCELCSSPMVYKMGRYGKFLACSNFPD 60- 4 Query: 620 CHNTKAITKEIGVICPICQKGQVIERKTKRNRIFYGCDRYPECEFTSWDKPIGRTCPKSN 67- 9 C NTK I K+IGV CP C +G ++ERK+K+ R+FYGCDRYP+CEF SWDKPI R CPK Sbjct: 605 CRNTKPIVKQIGVKCPSCGEGNIVERKSKKKRVFYGCDRYPDCEFVSWDKPIERKCPKCG 66- 4 Query: 680 DFLVEKKVRGGGKQVVCSNEKCDYQEEKIK 709 LVEKK++ G QV C +CDY+EE K Sbjct: 665 KMLVEKKLK-KGIQVQC--VECDYKEEPQK 691 A related DNA sequence was identified in S. pyogenes <SEQ ID 1917> which encodes the amino acid sequence <SEQ ID 1918>. Analysis of this protein sequence reveals the following: TABLE-US-01848 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5445 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01849 Identities = 595/704 (84%), Positives = 656/704 (92%), Gaps = 1/704 (0%) Query: 6 TTTKTSTKKTSKKKSATAKKNLVIVESPAKAKTIEKYLGRNYKVVASVGHIRDLKKSSMS 65 T KT TKK++ KK +TAKKNLVIVESPAKAKTIEKYLGR+YKVVASVGHIRDLKKSSMS Sbjct: 7 TKPKTGTKKSTTKKKSTAKKNLVIVESPAKAKTIEKYLGRSYKVVASVGHIRDLKKSSMS 66 Query: 66 IDFENNYEPQYINIRGKGPLINDLKKEAKKAKKVYLASDPDREGEAISWHLAHILDLDKE 125- IDF+NNYEPQYINIRGKGPLIN LKKEAK AKKVYLASDPDREGEAISWHL+HIL LD + Sbjct: 67 IDFDNNYEPQYINIRGKGPLINSLKKEAKAAKKVYLASDPDREGEAISWHLSHILGLDPQ 126- Query: 126 DRNRVVFNEITKDAVKNAFVEPRQINMDLVDAQQARRVLDRIVGYSISPILWKKVKKGLS 18- 5 D NRVVFNEITKDAVK+AFVEPRQI+MDLVD+QQARRVLDRIVGYSISPILWKKVKKGLS Sbjct: 127 DNNRVVFNEITKDAVKHAFVEPRQIDMDLVDSQQARRVLDRIVGYSISPILWKKVKKGLS 18- 6 Query: 186 AGRVQSVALKLIIDRENEIKAFQPEEYWTIDGSFKKGTRKFNATFYGLDGKKFKLSNNED 24- 5 AGRVQSVALKLIIDREN+IKAF P+EYW+IDG FKKGT+KF ATFYG++GKK KL NN D Sbjct: 187 AGRVQSVALKLIIDRENDIKAFVPKEYWSIDGLFKKGTKKFQATFYGINGKKTKLDNNND 24- 6 Query: 246 VKTVLKRIKTDEFLVEKVEKKERRRNAPLPYTTSSLQQDAANKINFRTRKTMMIAQQLYE 30- 5 VK VL ++ ++FLV KV+KKERRRNAPLPYTTSSLQQDAANKINFRTRKTMM+AQQLYE Sbjct: 247 VKEVLAKLTNEDFLVSKVDKKERRRNAPLPYTTSSLQQDAANKINFRTRKTMMVAQQLYE 30- 6 Query: 306 GLSLGTAGHQGLITYMRTDSTRISPLAQNEATEFITNRFGANYSKHGNKVKNASGAQDAH 36- 5 G+ LG G QGLITYMRTDSTRISP+AQN+A +FI NRFGANYSKHGN+VKN SG QDAH Sbjct: 307 GIHLGENGTQGLITYMRTDSTRISPVAQNDAAQFIINRFGANYSKHGNRVKNTSGVQDAH 36- 6 Query: 366 EAIRPSSVNHTPESIAKYLDKDQLKLYTLIWNRFIASQMTAAVFDTMKVNLTQNGVTFIA 42- 5 EAIRPSSVNHTP+SIAKYL+KDQLKLYTLIWNRF+ASQMTAAVFDT+KVNL QNGV F+A Sbjct: 367 EAIRPSSVNHTPDSIAKYLNKDQLKLYTLIWNRFVASQMTAAVFDTVKVNLEQNGVIFVA 42- 6 Query: 426 NGSQVKFDGYMAVYNDTDKNKMLPDMEEGESVKKVNTNPEQHFTQPPARFSEASLIKTLE 48- 5 NGSQ+KFDGYMAVYND+DKNKMLP+M EGE+VKK++T+PEQHFTQPPAR+SEA+LIKTLS Sbjct: 427 NGSQMKFDGYMAVYNDSDKNKMLPEMAEGETVKKISTSPEQHFTQPPARYSEATLIKTLE 48- 6 Query: 486 ENGVGRPSTYAPTLETIQKRYYVKLAAKRFEPTELGEIVNSLIVEFFPDIVDVTFTAEME 54- 5 ENGVGRPSTYAPTLE IQ+RYYVKL+AKRFEPTELGEIVN LIVEFFPDIVDV FTAEME Sbjct: 487 ENGVGRPSTYAPTLEVIQRRYYVKLSAKRFEPTELGEIVNKLIVEFFPDIVDVAFTAEME 54- 6 Query: 546 GKLDEVEIGKEQWQKIIDEFYKPFEKELAKAETEMEKIQIKDEPAGFDCELCGSPMVIKL 60- 5 GKLD+VEIG+EQWQ +ID+FY+PF KEL KAE+E+EKIQIKDEPAGFDC++CG PMVIKL Sbjct: 547 GKLDQVEIGEEQWQHVIDQFYQPFVKELNKAESEIEKIQIKDEPAGFDCDVCGHPMVIKL 60- 6 Query: 606 GRYGKFYACSNFPECHNTKAITKEIGVICPICQKGQVIERKTKRNRIFYGCDRYPECEFT 66- 5 GR+GKFYACSNFPEC NTKAITKEIGV CP+C KGQVIERKTK+NRIFYGCD+YP+CEF Sbjct: 607 GRFGKFYACSNFPECRNTKAITKEIGVTCPVCHKGQVIERKTKKNRIFYGCDQYPDCEFI 66- 6 Query: 666 SWDKPIGRTCPKSNDFLVEKKVRGGGKQVVCSNEKCDYQEEKIK 709 SWD PIGR CPKS D+L+EKKVR GGKQV+CSNE CDY+EEKIK Sbjct: 667 SWDLPIGRACPKSGDYLIEKKVR-GGKQVMCSNETCDYKEEKIK 709 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 618 A DNA sequence (GBSx0658) was identified in S. agalactiae <SEQ ID 1919> which encodes the amino acid sequence <SEQ ID 1920>. Analysis of this protein sequence reveals the following:

TABLE-US-01850 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2578 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01851 >GP: AAD35341 GB: AE001708 DNA processing chain A [Thermotoga maritima] Identities = 97/231 (41%), Positives = 149/231 (63%), Gaps = 2/231 (0%) Query: 51 FIENYKQLDLKKLRQEFKKFPV--LSILDSNYPLELKEIYNPPVLLFYQGNIELLSKPKL 108- F+E + +L++ ++ +K V +S + +YP L+EI PP +LF +G+ ELL + + Sbjct: 41 FLEKCGKEELERQKELIRKHNVKLVSFWEDDYPQHLREIRYPPAVLFVRGDAELLKEKCV 100- Query: 109 AVVGARQASQIGCQSVKKIIKETNNQFVIVSGLARGIDTAAHVSALKNGGSSIAVIGSGL 16- 8 VVG R+ + G K+ +K + FVIVSG+A GID+ AH AL +GG ++AV+G+G+ Sbjct: 101 GVVGTRRPTSYGVNVTKRFVKLLSEYFVIVSGMAFGIDSVAHKEALSSGGKTVAVLGTGV 16- 0 Query: 169 DVYYPTENKKLQEYMSYNHLVLSEYFTGEQPLKFHFPERNRIIAGLCQGIVVAEAKMRSG 22- 8 DV YP N++L + N V+SEY G + K HFP RNRIIAGL I+V EA ++SG Sbjct: 161 DVVYPRSNERLFHEIVKNGCVVSEYPMGTRARKHHFPARNRIIAGLSDAIIVTEAPIKSG 22- 0 Query: 229 SLITCERALEEGREVFAIPGNIIDGKSDGCHHLIQEGAKCIISGKDILSEY 279 +LIT + ALE GR+VFA+PG+I S+G ++LI+ GA + +D+ + + Sbjct: 221 ALITVKFALESGRDVFAVPGDIDRKTSEGTNYLIKSGAYPLTDEEDLETHF 271 A related DNA sequence was identified in S. pyogenes <SEQ ID 1921> which encodes the amino acid sequence <SEQ ID 1922>. Analysis of this protein sequence reveals the following: TABLE-US-01852 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2856 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01853 Identities = 185/279 (66%), Positives = 238/279 (84%), Gaps = 1/279 (0%) Query: 1 MNHFELFKLKKAGLTNLNIHNIINYLKKNSLTSLSVRNMAVVSKCKNPTFFIENYKQLDL 60 +NHFEL+KLKKAGLTN NI NI++Y +K+ SLS+R+MAVVS CK+P+ FIE YKQLD+ Sbjct: 1 VNHFELYKLKKAGLTNKNILNILDY-QKHQEKSLSLRDMAVVSGCKHPSHFIEAYKQLDI 59 Query: 61 KKLRQEFKKFPVLSILDSNYPLELKEIYNPPVLLFYQGNIELLSKPKLAVVGARQASQIG 120- + L+ EFK+FP +SILD +YP+ LKEIYNPPVLLF+QGN++LL KPKLA+VG+R++S G Sbjct: 60 QNLKMEFKQFPSISILDKHYPMALKEIYNPPVLLFFQGNLDLLEKPKLAIVGSRRSSDTG 119- Query: 121 CQSVKKIIKETNNQFVIVSGLARGIDTAAHVSALKNGGSSIAVIGSGLDVYYPTENKKLQ 18- 0 +SV+KI+KE N+FVIVSGLARGIDT+AH++ LKNGG +IA+IG+GLD +YP EN++LQ Sbjct: 120 VKSVRKILKELGNRFVIVSGLARGIDTSAHLACLKNGGQTIAIIGTGLDRFYPKENRELQ 17- 9 Query: 181 EYMSYNHLVLSEYFTGEQPLKFHFPERNRIIAGLCQGIVVAEAKMRSGSLITCERALEEG 24- 0 ++ NHLVL+EY GE+ L +HFPERNRIIAGL +GI+V EAK RSGSLITC+ +EEG Sbjct: 180 TFLGKNHLVLTEYGPGEEALSYHFPERNRIIAGLSRGILVVEAKNRSGSLITCQIGIEEG 23- 9 Query: 241 REVFAIPGNIIDGKSDGCHHLIQEGAKCIISGKDILSEY 279 R++FA+PGNI+DGKS+GC LI+EGA C+ SG DILSEY Sbjct: 240 RDIFAVPGNILDGKSEGCLQLIKEGATCVTSGMDILSEY 278 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 619 A DNA sequence (GBSx0659) was identified in S. agalactiae <SEQ ID 1923> which encodes the amino acid sequence <SEQ ID 1924>. This protein is predicted to be lipoprotein (ceuE). Analysis of this protein sequence reveals the following: TABLE-US-01854 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01855 >GP: CAA06500 GB: AJ005352 lipoprotein [Staphylococcus aureus] Identities = 122/348 (35%), Positives = 201/348 (57%), Gaps = 16/348 (4%) Query: 1 MTKKLIIAILALCTILTTSQAVLAKEKSQ--------TVTIKNNYSVYIKKEKRDKPDNK 52 M K ++ +LA+ +L KE+S+ TV I+NNY + + EK+D D K Sbjct: 1 MKKTVLYLVLAVMFLLAACGNNSDKEQSKSETKGSKDTVKIENNYKM--RGEKKDGSDAK 58 Query: 53 KQISETLKVPLKPKKVVVFDMGALDTITALGAEKSVIGIPKAKNALSLLPNNVKSVYKAK 112- K + ET++VP P+ VV D GALD + +G V +PK + SL PN ++S +K Sbjct: 59 K-VKETVEVPKNPENAVVLDYGALDVMKEMGLSDKVKALPKGEGGKSL-PNFLES-FKDD 115- Query: 113 RYQDVGSLFEPNFEAIARMQPDVVFLGARMASVDNIEKLKEAAPKAALVYAGVDSKKVFD 17- 2 +Y +VG+L E NF+ IA +P+V+F+ R A+ N+++ K+AAPKA +VY G D K + Sbjct: 116 KYTNVGNLKEVNFDKIAATKPEVIFISGRTANQKNLDEFKKAAPKAKIVYVGADEKNLIG 17- 5 Query: 173 KGVAERVTMLGKIFDQNKKAKTFNKDIAQAVLKLQKTIEKKGKPTALFVMANSGELLTQS 23- 2 + + +GKI+D+ KAK NKD+ + ++ + K T ++++ N GEL T Sbjct: 176 S-MKQNTENIGKIYDKEVKAKELNKDLDNKIASMKDKTKNFNK-TVMYLLVNEGELSTFG 23- 3 Query: 233 PSGRFGW-IFSVGGFKAVNENEKLSSHGTPVSYEYIAEKNPNYLFVLDRGATIGQGASSK 29- 1 P GRFG ++ GF AV++ S+HG VS EY+ ++NP+ + +DRG + +++K Sbjct: 234 PKGRFGGLVYDTLGFNAVDKKVSNSNHGQNVSNEYVNKENPDVILAMDRGQAVSGKSTAK 29- 3 Query: 292 ELFNNDVIKATDAVKNKRVHEVDGKDWYINSGGSRVTLRMIKDVQNFV 339 + NN V+K A+K +V+ +D K WY +G + T++ I+++ V Sbjct: 294 QALNNPVLKNVKAIKEDKVYNLDPKLWYFAAGSTTTTIKQIEELDKVV 341 A related DNA sequence was identified in S. pyogenes <SEQ ID 1925> which encodes the amino acid sequence <SEQ ID 1926>. Analysis of this protein sequence reveals the following: TABLE-US-01856 Possible site: 32 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01857 Identities = 57/255 (22%), Positives = 104/255 (40%), Gaps = 30/255 (11%) Query: 66 KKVVVFDMGALDTITALGAEKSVIGIPKAKNALSLLPNNVKSVYKAKRYQDVGSLFEPNF 125- +++V + +D L + ++G+ +K L LP +V + VG P+ Sbjct: 45 QRIVATSVAVVDICDRLNLD--LVGVCDSK--LYTLPKRYDAVKR------VGLPMNPDI 94 Query: 126 EAIARMQPDVVFLGARMASVDNIEKLKEAAPKAALVYAGVDSKKVFDKGVAERVTMLGKI 18- 5 E IA ++P + + E L+ K Y ++ + V +G+ + + LG + Sbjct: 95 ELIASLKPTWILSPNSLQ-----EDLEPKYQKLDTEYGFLNLRSV--EGMYQSIDDLGNL 147- Query: 186 FDQNKKAKTFNKDIAQAVLKLQKTIEKKGKPTALFVMANSGELLTQSPSGRFGWIFSVGG 24- 5 F + ++AK + Q + K KP L +M G L + G + + G Sbjct: 148 FQRQQEAKELRQQYQDYYRAFQAKRKGKKKPKVLILMGLPGSYLVATNQSYVGNLLDLAG 20- 7 Query: 246 FKAV---NENEKLSSHGTPVSYEYIAEKNPNYLFVLDRGATIGQGAS---SKELFNNDVI 29- 9 + V +E E LS++ E + K P+ +L I KE ND+ Sbjct: 208 GENVYQSDEKEFLSANP-----EDMLAKEPD--LILRTAHAIPDKVKVMFDKEFAENDIW 26- 0 Query: 300 KATDAVKNKRVHEVD 314 K AVK +V+++D Sbjct: 261 KHFTAVKEGKVYDLD 275 SEQ ID 1924 (GBS181) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 39 (lane 5; MW 38.7 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 46 (lane 3; MW 64 kDa). The GBS181-GST fusion product was purified (FIG. 204, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 299), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 620 A DNA sequence (GBSx0660) was identified in S. agalactiae <SEQ ID 1927> which encodes the amino acid sequence <SEQ ID 1928>. This protein is predicted to be iron(III) ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-01858 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3231(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01859 >GP: CAB12190 GB: Z99106 similar to ferrichrome ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 125/247 (50%), Positives = 187/247 (75%) Query: 1 MIQINNLHKFYGQKEILKDINISIPKGKVTAILGPNGSGKSTLLSCISRLEPYDNGEIFL 60 M+++ N+ K YG K +L++ +++I KGK+T+ +GPNG+GKSTLLS +SRL D+GEI++ Sbjct: 1 MVEVRNVSKQYGGKVVLEETSVTIQKGKITSFIGPNGAGKSTLLSIMSRLIKKDSGEIYI 60 Query: 61 DKVPLAHYSSNDLAKTLAILRQSNHLTLKIKVRDLIGFGRFPYSKGRLSQKDKAVIESVI 120- D + S +LAK ++IL+Q+N + +++ ++DL+ FGRFPYS+GRL+++D I + Sbjct: 61 DGQEIGACDSKELAKKMSILKQANQINIRLTIKDLVSFGRFPYSQGRLTEEDWVHINQAL 120- Query: 121 SYMDLNDIADEFINNLSGGQIQRAFIAMTMAQDTQYICLDEPLNNLDMKYAVQMMDLIKR 18- 0 SYM L DI D++++ LSGGQ QRAFIAM +AQDT YI LDEPLNNLDMK++V++M L+KR Sbjct: 121 SYMKLEDIQDKYLDQLSGGQCQRAFIAMVIAQDTDYIFLDEPLNNLDMKHSVEIMKLLKR 18- 0 Query: 181 YAYEFNKTIVIIIHDINFATHYADNVVALKEGQVVTCGTVEDVMQEKILSHLFDMPIRIE 24- 0 E KTIVI+IHDINFA+ Y+D +VALK G++V G E++++ +L ++DM I I+ Sbjct: 181 LVEELGKTIVIVIHDINFASVYSDYIVALKNGRIVKEGPPEEMIETSVLEEIYDMTIPIQ 24- 0 Query: 241 TVDGKPI 247 T+D + I Sbjct: 241 TIDNQRI 247 There is also homology to SEQ ID 1930. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 621 A DNA sequence (GBSx0661) was identified in S. agalactiae <SEQ ID 1931> which encodes the amino acid sequence <SEQ ID 1932>. Analysis of this protein sequence reveals the following: TABLE-US-01860 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.74 Transmembrane 271-287 (266-295) INTEGRAL Likelihood = -8.55 Transmembrane 49-65 (47-69) INTEGRAL Likelihood = -8.07 Transmembrane 185-201 (178-207) INTEGRAL Likelihood = -7.70 Transmembrane 112-128 (105-132) INTEGRAL Likelihood = -7.38 Transmembrane 231-247 (227-261) INTEGRAL Likelihood = -2.50 Transmembrane 139-155 (135-156) INTEGRAL Likelihood = -1.97 Transmembrane 302-318 (301-319) ----- Final Results ----- bacterial membrane --- Certainty = 0.6095(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01861 >GP: CAB12189 GB: Z99106 similar to ferrichrome ABC transporter (permease) [Bacillus subtilis] Identities = 138/315 (43%), Positives = 222/315 (69%), Gaps = 6/315 (1%) Query: 9 KLLILLILLIAAIILFLIYGIPTDANEFLIIYILKTRYQKLIALILVGICIGSSSLIFQT 68 K+ +L+ L I I LFL Y + Y L R +K+ A++L G I S++IFQT Sbjct: 6 KIALLVGLAIVCIGLFLFYDLGNWD------YTLPRRIKKVAAIVLTGGAIAFSTMIFQT 59 Query: 69 LTNNRLLTPSIIGLDSLYILIQTGLMYLIGAQRVIKFSSFSSFLLSLLLMVGFAYLLFTI 128- +TNNR+LTPSI+GLDSLY+LIQTG+++L G+ ++ + +F++S+LLM+ F+ +L+ I Sbjct: 60 ITNNRILTPSILGLDSLYMLIQTGIIFLFGSANMVIMNKNINFIISVLLMILFSLVLYQI 119- Query: 129 LFRNKKQSLYFVLLAGLIFNTLFSSISSFIQAIMDPNDFMILQNQLFASFNAINTKILWI 18- 8 +F+ + ++++F+LL G++F TLFSS+SSF+Q ++DPN+F ++Q+++FASFN INT +LW+ Sbjct: 120 MFKGEGRNIFFLLLIGIVFGTLFSSLSSFMQMLIDPNEFQVVQDKMFASFNNINTDLLWL 17- 9 Query: 189 SFIIIVVSFVINWPFIKELDVLLLGKENAISLGISYQKLTTRFFLWLALMVAIATALVGP 24- 8 +FII +++ V W F K DVL LG+E+A++LGI Y K+ + + +A++V+++TALVGP Sbjct: 180 AFIIFLLTGVYVWRFTKFFDVLSLGREHAVNLGIDYDKVVKQMLIVVAILVSVSTALVGP 23- 9 Query: 249 ITFLGLLVAHITYHSFHTFRHQILVPIAIVICIFTLVLGQHLVQNLLHLTVQLSVLLNLI 30- 8 I FLGLLV ++ T++H L+ ++ I I LV GQ +V+ + + LSV++N Sbjct: 240 IMFLGLLVVNLAREFLKTYKHSYLIAGSVFISIIALVGGQFVVEKVFTFSTTLSVIINFA 29- 9 Query: 309 GGSYFIFTLIKGRKN 323 GG YFI+ L+K K+ Sbjct: 300 GGIYFIYLLLKENKS 314 A related DNA sequence was identified in S. pyogenes <SEQ ID 1933> which encodes the amino acid sequence <SEQ ID 1934>. Analysis of this protein sequence reveals the following: TABLE-US-01862 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.64 Transmembrane 33-49 (26-61) INTEGRAL Likelihood = -8.97 Transmembrane 259-275 (246-286) INTEGRAL Likelihood = -8.65 Transmembrane 296-312 (294-316) INTEGRAL Likelihood = -8.39 Transmembrane 83-99 (78-104) INTEGRAL Likelihood = -6.26 Transmembrane 212-228 (210-231) INTEGRAL Likelihood = -4.04 Transmembrane 113-129 (110-132) INTEGRAL Likelihood = -3.61 Transmembrane 140-156 (134-157) INTEGRAL Likelihood = -2.71 Transmembrane 165-181 (165-181) INTEGRAL Likelihood = -1.06 Transmembrane 327-343 (327-343) INTEGRAL Likelihood = -0.22 Transmembrane 50-66 (50-66) ----- Final Results ----- bacterial membrane --- Certainty = 0.6456(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9175> which encodes the amino acid sequence <SEQ ID 9176>. Analysis of this protein sequence reveals the following: TABLE-US-01863 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.64 Transmembrane 24-40 (17-52) INTEGRAL Likelihood = -8.97 Transmembrane 250-266 (237-277) INTEGRAL Likelihood = -8.65 Transmembrane 287-303 (285-307) INTEGRAL Likelihood = -8.39 Transmembrane 74-90 (69-95) INTEGRAL Likelihood = -6.26 Transmembrane 203-219 (201-222) INTEGRAL Likelihood = -4.04 Transmembrane 104-120 (101-123) INTEGRAL Likelihood = -3.61 Transmembrane 131-147 (125-148) INTEGRAL Likelihood = -2.71 Transmembrane 156-172 (156-172) INTEGRAL Likelihood = -1.06 Transmembrane 318-334 (318-334) INTEGRAL Likelihood = -0.22 Transmembrane 41-57 (41-57) ----- Final Results ----- bacterial membrane --- Certainty = 0.646(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01864 Identities = 80/326 (24%), Positives = 157/326 (47%), Gaps = 34/326 (10%) Query: 10 LLILLILLIAAIILFLIYGIPTDANEFL----------IIYILKTRYQKLIALILVGICI 59 - +L++L LL A+I + G+ + + I R+ +++ +L G I Sbjct: 34 VLLILSLLFLAVIALSLGGLAVSYGAIVKGLFVAYDPQVALIYDLRFPRIVIALLAGAGI 93 Query: 60 GSSSLIFQTLTNNRLLTPSIIGL---DSLYILIQTGLMYLIGAQRVIKFSSFSSFL---L 113- S ++FQ + N + P+IIG+ S +L+ + L+ +++ + SFL + Sbjct: 94 AVSGVLFQAVLKNPISDPAIIGICSGASFMVLVSSLLL-----PQLLLYGPIVSFLGGGV 148- Query: 114 SLLLMVGFAYLLFTILFRNKKQSLYFVLLAGLIFNTLFSSISSFIQAIMDPNDFMILQNQ 17- 3 S LL+ G A+ K + ++L G+ N LF +S+ + + M+ N Sbjct: 149 SFLLIYGLAW--------KKGLNPIRLILTGIAINALFMGLSTALTSFFTSASPMV--NA 19- 8 Query: 174 LFASFNAINTKI-LWISFIIIVVSFVINWPFIKELDVLLLGKENAISLGISYQKLTTRFF 23- 2 L A + T + + F + ++ K ++LLL + LGI L Sbjct: 199 LLAGHISQKTWADVGVLFPYTFIGLLLALLLSKTCNLLLLDDQVIRHLGIDATALRLGIS 25- 8 Query: 233 LWLALMVAIATALVGPITFLGLLVAHITYHSFHTFRHQILVPIAIVICIFTLVLGQHLVQ 29- 2 L L+ ++AT++VG ++FLGL+V H++ + +HQIL+P + ++ F +L L + Sbjct: 259 LVAVLLASVATSIVGVVSFLGLIVPHMSRLLVGS-KHQILIPFSALLGAFVFLLADTLGR 31- 7 Query: 293 NLLH-LTVQLSVLLNLIGGSYFIFTL 317 +L + L + +++++++GG YFI+ L Sbjct: 318 SLAYPLEISPAIIMSIVGGPYFIYLL 343 A related DNA sequence was identified in S. pyogenes <SEQ ID 2491> which encodes amino acid sequence <SEQ ID 2492>. An alignment of the GAS and GBS sequences follows: TABLE-US-01865 Score = 51.9 bits (122), Expect = 5e-08 Identities = 73/327 (22%), Positives = 137/327 (41%), Gaps = 38/327 (11%) Query: 494 IISSLGTAISTVAQGIGTGLAIAFRGLGAAIAMVPPTTWLALGTAILMVGAAFALAGTQA 55- 3 +I L T + G L IA +GA + +V A+ L++ A Sbjct: 573 VILGLVTTAVMMLLGAIAPLVIAIGAIGAPVGIVVAAIVGAIAVITLIIQAIMNWGA--- 62- 9 Query: 554 DGISQILRTIGDXXXXXXXXXTDSLATLLTIIANAIGSMLPIVAGAISQIVG-------A 60- 6 I++ L++ D ++ T T A + ++G S +V + Sbjct: 630 --ITEWLQSTWDSCAAWXSELWTNIVTTAT---TAWSNFTAWLSGLWSSVVSTGQSLWSS 68- 4 Query: 607 VAGGLSQLIIAVSTGVSLVIGAFTGLLGGI-SGVINSISAVIQSLTGVITAVFNGIATVI 66- 5 LS + ++ TG + +FT L + SG++++ S + +L+ I+ +FNGI + Sbjct: 685 FTSSLSNIFSSLITGAQSLWSSFTSTLSNLWSGLVSTGSNLFNNLSSTISGIFNGILSTA 74- 4 Query: 666 SSVGSTIKDVLTGLGTAFEGFGNGVKSALEGVGAVIESFGSAVR--------NVLDGVAN 71- 7 S++ ++IK ++ A +G N V + GV A+ F ++ + G AN Sbjct: 745 SNIWNSIKSTIS---NAIDGAKNAVSN---GVNAIKNLFNFQIKWPHIPLPHFRVSGSAN 79- 8 Query: 718 ILDSM--GTAALNAGRGVKEMAKGIKMLVDLSLGDLVATLAAVASGLGKMASSAGEMTTL 77- 5 LD + G ++ G+ AKG ++ +L + A V G A +TL Sbjct: 799 PLDWLKGGLPSI----GIDWYAKG-GIMTKPTLFGMNGNRAMVGGEAGAEAILPLNKSTL 85- 3 Query: 776 GSAMSKVANGMTRLATSATIAITGLTV 802 G+ +AN M + + + +G+T+ Sbjct: 854 GAIGQSIANTM-NTSNNINVNFSGVTI 879 Score = 33.2 bits (74), Expect = 0.019 Identities = 83/477 (17%), Positives = 175/477 (36%), Gaps = 103/477 (21%) Query: 420 GSFLDKISTKFGLFGKKAKEGTD--------------QAANGSRKSGGIISQIFNGLGNI 46- 5 G + +++T+FGL G+K K ++ +A ++++ LG + Sbjct: 313 GDAVGELNTQFGLTGEKLKSASELLIKYAEINETDISSSAISAKQAIEAYGLTAEDLGMV 37- 2 Query: 466 VKSAGTAISTAAKGIGTGIKTALSGAPPIISSLGTAISTVA--------QGIGTGLAIA- 51- 6 + + A + + T ++ A+ GAP I LG + A G+ + A++ Sbjct: 373 LDNVTKAAQDTGQSVDTIVQKAIDGAPQ-IKGLGLSFEEGAALIGKFEKSGVDSSAALSS 43- 1 Query: 517 ---------------FRGLGAAIAMVPPTT--WLALGTAILMVGAAFALAGTQA------ 55- 3 GL ++ + +T AL A + G+ A A Sbjct: 432 LSKAAVIYAKDGKTLTDGLNETVSAIQNSTSETEALSIASEIFGSKAAPRMVDAIQRGAF 49- 1 Query: 554 --DGISQILRTIGDXXXXXXXXXTDSLATLLTI-------IANAIGSMLPIVAGAISQIV 60- 4 D +++ ++ D + L +A G +L V A+ ++ Sbjct: 492 SFDDLAEAAKSSSGTVSTTFDETLDPIDKLTQYSNQAKEGMAELGGKLLETVIPALEPLM 55- 1 Query: 605 GAVAGGLS----------QLII---AVSTGVSLVIGAFTGL---LGGISGVINSISAVIQ 64- 8 G + ++ Q I+ V+T V +++GA L +G I + + A I Sbjct: 552 GMLESSVNWFTSLNETDQQTIVILGLVTTAVMMLLGAIAPLVIAIGAIGAPVGIVVAAIV 61- 1 Query: 649 SLTGVITAVFNGI-----------------ATVISSVGSTIKDVLTGLGTAFEGFGNGVK 69- 1 VIT + I A S + + I T + F + +G+ Sbjct: 612 GAIAVITLIIQAIMNWGAITEWLQSTWDSCAAWXSELWTNIVTTATTAWSNFTAWLSGLW 67- 1 Query: 692 SALEGVG-AVIESFGSAVRNV----LDGVANILDSMGTAALNAGRGVKEMAKGIKMLVDL 74- 6 S++ G ++ SF S++ N+ + G ++ S + N G+ + Sbjct: 672 SSVVSTGQSLWSSFTSSLSNIFSSLITGAQSLWSSFTSTLSNLWSGLVSTGSNL------ 72- 5 Query: 747 SLGDLVATLAAVASGLGKMASSAGEMTTLGSAMSKVANGMTRLATSATIAITGLTVF 803 +L +T++ + +G+ +++++ ++ S +S +G ++ AI L F Sbjct: 726 -FNNLSSTISGIFNGI--LSTASNIWNSIKSTISNAIDGAKNAVSNGVNAIKNLFNF 779 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 622 A DNA sequence (GBSx0662) was identified in S. agalactiae <SEQ ID 1935> which encodes the amino acid sequence <SEQ ID 1936>. Analysis of this protein sequence reveals the following:

TABLE-US-01866 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2277 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 623 A DNA sequence (GBSx0663) was identified in S. agalactiae <SEQ ID 1937> which encodes the amino acid sequence <SEQ ID 1938>. This protein is predicted to be membrane protein (ceuB). Analysis of this protein sequence reveals the following: TABLE-US-01867 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.30 Transmembrane 241-257 (237-274) INTEGRAL Likelihood = -6.42 Transmembrane 127-143 (118-149) INTEGRAL Likelihood = -5.79 Transmembrane 152-168 (150-174) INTEGRAL Likelihood = -5.47 Transmembrane 312-328 (309-330) INTEGRAL Likelihood = -4.83 Transmembrane 289-305 (287-308) INTEGRAL Likelihood = -4.67 Transmembrane 24-40 (22-46) INTEGRAL Likelihood = -4.35 Transmembrane 69-85 (68-86) INTEGRAL Likelihood = -4.19 Transmembrane 200-216 (198-216) INTEGRAL Likelihood = -2.76 Transmembrane 107-123 (107-123) INTEGRAL Likelihood = -0.85 Transmembrane 258-274 (258-274) ----- Final Results ----- bacterial membrane --- Certainty = 0.5522 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8621> which encodes amino acid sequence <SEQ ID 8622> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-01868 Lipop: Possible site: -1 Crend: 2 SRCFLG: 0 NcG: Length of UR: 23 Peak Value of UR: 2.64 Net Charge of CR: 2 McG: Discrim Score: 8.59 GvH: Signal Score (-7.5): -4.6 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 9 value: -11.30 threshold: 0.0 INTEGRAL Likelihood = -11.30 Transmembrane 226-242 (222-259) INTEGRAL Likelihood = -6.42 Transmembrane 112-128 (103-134) INTEGRAL Likelihood = -5.79 Transmembrane 137-153 (135-159) INTEGRAL Likelihood = -4.67 Transmembrane 9-25 (7-31) INTEGRAL Likelihood = -4.35 Transmembrane 54-70 (53-71) INTEGRAL Likelihood = -4.19 Transmembrane 185-201 (183-201) INTEGRAL Likelihood = -3.08 Transmembrane 268-284 (265-284) INTEGRAL Likelihood = -2.76 Transmembrane 92-108 (92-108) INTEGRAL Likelihood = -0.85 Transmembrane 243-259 (243-259) PERIPHERAL Likelihood = 5.73 203 modified ALOM score: 2.76 icml HYPID: 7 CFP: 0.552 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5522 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01869 >GP: CAB12188 GB: Z99106 similar to ferrichrome ABC transporter (permease) [Bacillus subtilis] Identities = 149/304 (49%), Positives = 234/304 (76%) Query: 29 LVILSLTSLFVGVKSIPLEQITHLDQSQVOIFLTSRLPRTISILISGASLSVCGLLMQQL 88 - L+IL++TS+F+GV+ + + L + + SRLPR ISI+I+G S+S+CGL+MQQ+ Sbjct: 10 LIILAVTSVFIGVEDLSPLDLFDLSKQEASTLFASRLPRLISIVIAGLSMSICGLIMQQI 69 Query: 89 TQNKFVSPTTSGTMDWAKLGVVVTLIFFKNTSIFIQLCIASGFAILGSLLFVTILKMITF 148- ++NKFVSPTT+GTMDWA+LG++++L+ F + S I++ +A FA+ G+ LF+ IL+ I F Sbjct: 70 SRNKFVSPTTAGTMDWARLGILISLLLFTSASPLIKMLVAFVFALAGNFLFMKILERIKF 129- Query: 149 KDNIFIPLIGLMLGQIVAAATVFLGTHFQVLQSVNSWLQGNFSIMTSHRYEILYLALPCL 20- 8 D IFIPL+GLMLG IV++ F+ + ++Q+V+SWLQG+FS++ RYE+LYL++P + Sbjct: 130 NDTIFIPLVGLMLGNIVSSIATFIAYKYDLIQNVSSWLQGDFSLVVKGRYELLYLSIPLV 18- 9 Query: 209 FLVYFFAHQFTIVGLGESFAKNLGVAYEKMIYFGLVLVSIMTSLVIIIVGALPFLGLIVP 26- 8 + Y +A +FT+ G+GESF+ NLG+ Y++++ GL++VS++TSLVI+ VG LPFLGLI+P Sbjct: 190 IIAYVYADKFTLAGMGESFSVNLGLKYKRVVNIGLIIVSLITSLVILTVGMLPFLGLIIP 24- 9 Query: 269 NLISITKGDHMSSTILETSLLGACIVMICDLFGRLVIFPYEVSIGVTLGVLGSAFFLISI 32- 8 N++SI +GD++ S++ T LLGA V+ CD+ GR++IFPYE+SIG+ +G++GS FL + Sbjct: 250 NIVSIYRGDNLKSSLPHTVLLGAVFVLFCDILGRIIIFPYEISIGLMVGIIGSGIFLFML 30- 9 Query: 329 IRNE 332 +R + Sbjct: 310 LRRK 313 There is also homology to SEQ ID 1940. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 624 A DNA sequence (GBSx0664) was identified in S. agalactiae <SEQ ID 1941> which encodes the amino acid sequence <SEQ ID 1942>. Analysis of this protein sequence reveals the following: TABLE-US-01870 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.90 Transmembrane 140-156 (140-156) ----- Final Results ----- bacterial membrane --- Certainty = 0.1362 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01871 >GP: BAB06720 GB: AP001517 maltose transacetylase (maltose O-acetyltransferase) [Bacillus halodurans] Identities = 93/182 (51%), Positives = 125/182 (68%), Gaps = 2/182 (1%) Query: 2 TEKEKMLAGQYYRPSAPELRKDREVALKNMQAFNN--EDNSSKRNVILQKWFGATGKSIH 59 TEKEKMLAG+ Y+ PEL KDRE A + + FN E +R ++++ FG+ G+S++ Sbjct: 3 TEKEKMLAGERYKAWDPELVKDRERARRLTRLFNQTTETEEKQRTELIKELFGSMGESVN 62 Query: 60 MEQRFVCDYGCNIYVGENFYANFNQTFLDVCEIRIGDNCMFGPNCQLLTPLHPLDPIERN 119- +E F CDYG NI+VG NF+ANF+ LDVCE+RIG NCM P + T HP+ P+ER Sbjct: 63 IEPTFRCDYGYNIHVGNNFFANFDCVILDVCEVRIGANCMLAPGVHIYTATHPIHPLERV 122- Query: 120 SGLEYGAPIQIGNNVWLGGGVTILPGVVLGDNVVVGAGSVVTKSFENNVVIAGNPAKIIKKL - 182 G EYG P+ I NNVW+GG + PGV +G+N V+ +GSVVTK NVV+AGNPAK+I+ + Sbjct: 123 EGPEYGKPVTIRNNVWIGGRAIVNPGVTIGNNAVIASGSVVTKDVPENVVVAGNPAKVIQTI - 184 A related DNA sequence was identified in S. pyogenes <SEQ ID 1943> which encodes the amino acid sequence <SEQ ID 1944>. Analysis of this protein sequence reveals the following: TABLE-US-01872 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4052 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01873 Identities = 68/188 (36%), Positives = 101/188 (53%), Gaps = 13/188 (6%) Query: 2 TEKEKMLAGQYYRPSAPELRKDREVALKNMQAFN--------NEDNSSKRNVILQKWFGA 53 TE +KM G++Y + D E+ K M A + +R+ +L + FG Sbjct: 3 TEFDKMTRGEWY-----DANFDSELIQKRMMAQDLCFDLNQLKPSREEERSAVLNQLFGQ 57 Query: 54 TGKSIHMEQRFVCDYGCNIYVGENFYANFNQTFLDVCEIRIGDNCMFGPNCQLLTPLHPL 113- + + + + F+CDYG NI G+N + N N F+D +I +GDN GP+ T HPL Sbjct: 58 SFEGLVLLSPFICDYGKNITFGKNCFINSNCYFMDGAKIALGDNVFVGPSTGFYTANHPL 117- Query: 114 DPIERNSGLEYGAPIQIGNNVWLGGGVTILPGVVLGDNVVVGAGSVVTKSFENNVVIAGN 17- 3 D RN GLE PI IG+NVW G V ++PGV +G V+ +GSVVT N + AG Sbjct: 118 DYKRRNEGLEKALPITIGDNVWFGANVNVMPGVTIGSGCVIASGSVVTHDIPVNSLAAGV 17- 7 Query: 174 PAKIIKKL 181 P ++++K+ Sbjct: 178 PCQVVRKI 185 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 625 A DNA sequence (GBSx0665) was identified in S. agalactiae <SEQ ID 1945> which encodes the amino acid sequence <SEQ ID 1946>. This protein is predicted to be ribonuclease H (rnhB-2). Analysis of this protein sequence reveals the following: TABLE-US-01874 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 79-95 (79-95) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9823> which encodes amino acid sequence <SEQ ID 9824> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01875 >GP: CAB13479 GB: Z99112 ribonuclease H [Bacillus subtilis] Identities = 128/249 (51%), Positives = 168/249 (67%) Query: 4 TIKEIKAILETIVDLKDKRWQEYQTDSRAGVQKAILQRKKNIQSDLDEEARLEQMLVYEK 63 T+K+IK L+ + D +D + + D R VQ + Q K + + + M YE+ Sbjct: 5 TVKDIKDRLQEVKDAQDPFIAQCENDPRKSVQTLVEQWLKKQAKEKALKEQWVNMTSYER 64 Query: 64 KLYIEHINLIAGIDEVGRGPLAGPVVAAAVILPPNCKIKHLNDSKKIPKKKHQEIYQNIL 123- + LIAG+DEVGRGPLAGPVVA+AVILP C+I L DSKK+ +KK +E Y+ I+ Sbjct: 65 LARNKGFRLIAGVDEVGRGPLAGPVVASAVILPEECEILGLTDSKKLSEKKREEYYELIM 124- Query: 124 DQALAVGIGIQDSQCIDDINIYEATKHAMIDAVSHLSVAPEHLLIDAMVLDLSIPQTKII 18- 3 +ALAVGIGI ++ ID+INIYEA+K AM+ A+ LS P++LL+DAM L L Q II Sbjct: 125 KEALAVGIGIVEATVIDEINIYEASKMAMVKAIQDLSDTPDYLLVDAMTLPLDTAQASII 18- 4 Query: 184 KGDANSLSIAAASIVAKVTRDKIMSDYDSTYPGYAFSKNAGYGTKEHLEGLQKYGITPIH 24- 3 KGDA S+SIAA + +AKVTRD++MS Y TYP Y F KN GYGTKEHLE L YG T +H Sbjct: 185 KGDAKSVSIAAGACIAKVTRDRMMSAYAETYPMYGFEKNKGYGTKEHLEALAAYGPTELH 24- 4 Query: 244 RKSFEPIKS 252 RK+F P++S Sbjct: 245 RKTFAPVQS 253 A related DNA sequence was identified in S. pyogenes <SEQ ID 1947> which encodes the amino acid sequence <SEQ ID 1948>. Analysis of this protein sequence reveals the following: TABLE-US-01876 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.53 Transmembrane 79-95 (79-95) ----- Final Results ----- bacterial membrane --- Certainty = 0.1213(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01877 >GP: CAB13479 GB: Z99112 ribonuclease H [Bacillus subtilis] Identities = 130/252 (51%), Positives = 176/252 (69%), Gaps = 3/252 (1%) Query: 4 SIKAIKESLEAVTSLLDPLFQELATDTRSGVQKALKSRQKVIQAELAEEERLEAMLSYEK 63 ++K IK+ L+ V DP + D R VQ ++ K E A +E+ M SYE+ Sbjct: 5 TVKDIKDRLQEVKDAQDPFIAQCENDPRKSVQTLVEQWLKKQAKEKALKEQWVNMTSYER 64 Query: 64 ALYKKGYKAIAGIDEVGRGPLAGPVVAACVILPKYCKIKGLNDSKKIPKAKHETIYQAVK 123- KG++ IAG+DEVGRGPLAGPVVA+ VILP+ C+I GL DSKK+ + K E Y+ + Sbjct: 65 LARNKGFRLIAGVDEVGRGPLAGPVVASAVILPEECEILGLTDSKKLSEKKREEYYELIM 124- Query: 124 EKALAIGIGIIDNQLIDEVNIYEATKLAMLEAIKQLEGQLTQPDYLLIDAMTLDIAISQQ 18- 3 ++ALA+GIGI++ +IDE+NIYEA+K+AM++AI+ L PDYLL+DAMTL + +Q Sbjct: 125 KEALAVGIGIVEATVIDEINIYEASKMAMVKAIQDLS---DTPDYLLVDAMTLPLDTAQA 18- 1 Query: 184 SILKGDANSLSIAAASIVAKVTRDQMMANYDRIFPGYDFAKNAGYGTKEHLQGLKAYGIT 24- 3 SI+KGDA S+SIAA + +AKVTRD+MM+ Y +P Y F KN GYGTKEHL+ L AYG T Sbjct: 182 SIIKGDAKSVSIAAGACIAKVTRDRMMSAYAETYPMYGFEKNKGYGTKEHLEALAAYGPT 24- 1 Query: 244 PIHRKSFEPVKS 255 +HRK+F PV+S Sbjct: 242 ELHRKTFAPVQS 253 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01878 Identities = 168/256 (65%), Positives = 203/256 (78%), Gaps = 3/256 (1%) Query: 1 MMATIKEIKAILETIVDLKDKRWQEYQTDSRAGVQKAILQRKKNIQSDLDEEARLEQMLV 60 M +IK IK LE + L D +QE TD+R+GVQKA+ R+K IQ++L EE RLE ML Sbjct: 1 MPTSIKAIKESLEAVTSLLDPLFQELATDTRSGVQKALKSRQKVIQAELAEEERLEAMLS 60 Query: 61 YEKKLYIEHINLIAGIDEVGRGPLAGPVVAAAVILPPNCKIKHLNDSKKIPKKKHQEIYQ 120- YEK LY + IAGIDEVGRGPLAGPVVAA VILP CKIK LNDSKKIPK KH+ IYQ Sbjct: 61 YEKALYKKGYKAIAGIDEVGRGPLAGPVVAACVILPKYCKIKGLNDSKKIPKAKHETIYQ 120- Query: 121 NILDQALAVGIGIQDSQCIDDINIYEATKHAMIDAVSHLS---VAPEHLLIDAMVLDLSI 17- 7 + ++ALA+GIGI D+Q ID++NIYEATK AM++A+ L P++LLIDAM LD++I Sbjct: 121 AVKEKALAIGIGIIDNQLIDEVNIYEATKLAMLEAIKQLEGQLTQPDYLLIDAMTLDIAI 18- 0 Query: 178 PQTKIIKGDANSLSIAAASIVAKVTRDKIMSDYDSTYPGYAFSKNAGYGTKEHLEGLQKY 23- 7 Q I+KGDANSLSIAAASIVAKVTRD++M++YD +PGY F+KNAGYGTKEHL+GL+ Y Sbjct: 181 SQQSILKGDANSLSIAAASIVAKVTRDQMMANYDRIFPGYDFAKNAGYGTKEHLQGLKAY 24- 0 Query: 238 GITPIHRKSFEPIKSM 253 GITPIHRKSFEP+KSM Sbjct: 241 GITPIHRKSFEPVKSM 256 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 626 A DNA sequence (GBSx0666) was identified in S. agalactiae <SEQ ID 1949> which encodes the amino acid sequence <SEQ ID 1950>. Analysis of this protein sequence reveals the following: TABLE-US-01879 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1865(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 627 A DNA sequence (GBSx0667) was identified in S. agalactiae <SEQ ID 1951> which encodes the amino acid sequence <SEQ ID 1952>. Analysis of this protein sequence reveals the following: TABLE-US-01880 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3034(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01881 >GP: BAB06195 GB: AP001515 unknown conserved protein [Bacillus halodurans] Identities = 140/281 (49%), Positives = 195/281 (68%), Gaps = 5/281 (1%) Query: 3 TIQWFPGHMSKARRQVQENIKHVDFVTILVDARLPLSSQNPMLTKIVGDKPKLMILNKAD 62 TIQWFPGHM+KARR+V E +K +D V L+DAR+PLSS+NPM+ +IV KP+L++LNK D Sbjct: 2 TIQWFPGHMAKARREVTEKLKLIDVVIELLDARVPLSSRNPMMDEIVAHKPRLVLLNKDD 61 Query: 63 LADPIRTKEWRDFYESQGLKTLAINSKEQSTVKKVTDIAKILMSDKIANLRGRGIQKETL 122- LADP +TKEW F+E G L IN++ V +++ + L I R +G++ + Sbjct: 62 LADPSKTKEWTRFFEEGGATVLPINAQTGQGVSRISPACQTLAQALIEKQRAKGMKPRAI 121- Query: 123 RTMIIGIPNAGKSTLMNRLAGKKIAVVGNKPGVTKGQQWLKSNKELEILDTPGILWPKFE 18- 2 R MI+GIPN GKSTL+NRLA K+IA VG++PG+TK QQW+K KELE+LDTPGILWPKF+ Sbjct: 122 RAMILGIPNVGKSTLINRLASKRIAKVGDRPGITKQQQWIKVGKELELLDTPGILWPKFD 18- 1 Query: 183 DELVGLKLALTGAIKDQLLPMDEVTIFGLNYFKTYYPDRLKERFKSINLEDEAPEIIMAL 24- 2 D+ G +LA TGAIKD+LL +V +F L Y + YPDRL +R+K L ++ + A+ Sbjct: 182 DQATGFRLAATGAIKDELLDFQDVALFVLRYMREMYPDRLMDRYKLNELPEDGVTLFDAI 24- 1 Query: 243 TQKLGY-----RDDYDRFYNLFVKEVRDGKLGRYTLDIVGE 278 +K G+ DYD+ + ++E+R G LGR TL++ G+ Sbjct: 242 GKKRGHLLSGGYIDYDKTAEMILRELRAGTLGRITLEVPGK 282 A related DNA sequence was identified in S. pyogenes <SEQ ID 1953> which encodes the amino acid sequence <SEQ ID 1954>. Analysis of this protein sequence reveals the following:

TABLE-US-01882 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2688(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01883 Identities = 247/282 (87%), Positives = 265/282 (93%) Query: 1 MATIQWFPGHMSKARRQVQENIKHVDFVTILVDARLPLSSQNPMLTKIVGDKPKLMILNK 60 MA IQWFPGHMSKARRQVQEN+KHVDFVTILVDARLPLSSQNPMLTKIVGDKPKLMILNK Sbjct: 1 MAMIQWFPGHMSKARRQVQENVKHVDFVTILVDARLPLSSQNPMLTKIVGDKPKLMILNK 60 Query: 61 ADLADPIRTKEWRDFYESQGLKTLAINSKEQSTVKKVTDIAKILMSDKIANLRGRGIQKE 120- ADLAD RTKEW+ +YESQG+KTLAINSKEQSTVKKVT+ AK LM+DKI LR RGIQKE Sbjct: 61 ADLADATRTKEWKAYYESQGIKTLAINSKEQSTVKKVTEAAKELMADKIQRLRERGIQKE 120- Query: 121 TLRTMIIGIPNAGKSTLMNRLAGKKIAVVGNKPGVTKGQQWLKSNKELEILDTPGILWPK 18- 0 TLRTMIIGIPNAGKSTLMNRLAGKKIAVVGNKPGVTKGQQWLKSNKELEILDTPGILWPK Sbjct: 121 TLRTMIIGIPNAGKSTLMNRLAGKKIAVVGNKPGVTKGQQWLKSNKELEILDTPGILWPK 18- 0 Query: 181 FEDELVGLKLALTGAIKDQLLPMDEVTIFGLNYFKTYYPDRLKERFKSINLEDEAPEIIM 24- 0 FEDELVGLKLALTGAIKDQLLPMDEVTIFGLNYF+ YYP+RL +RFK+I LE+EAPEIIM Sbjct: 181 FEDELVGLKLALTGAIKDQLLPMDEVTIFGLNYFREYYPNRLTKRFKNIPLEEEAPEIIM 24- 0 Query: 241 ALTQKLGYRDDYDRFYNLFVKEVRDGKLGRYTLDIVGEHDGN 282 LT++LG++DDYDRFY LFVKEVRDGKLG+YTLD VG+ D + Sbjct: 241 TLTRQLGFKDDYDRFYTLFVKEVRDGKLGQYTLDQVGDMDAD 282 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 628 A DNA sequence (GBSx0668) was identified in S. agalactiae <SEQ ID 1955> which encodes the amino acid sequence <SEQ ID 1956>. Analysis of this protein sequence reveals the following: TABLE-US-01884 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9825> which encodes amino acid sequence <SEQ ID 9826> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01885 >GP: CAB12129 GB: Z99105 similar to hypothetical proteins [Bacillus subtilis] Identities = 69/173 (39%), Positives = 102/173 (58%), Gaps = 13/173 (7%) Query: 29 DKAKEKASV-----IKQASQTSQTSKKEVLQKKT----YPNLNKYSNLEIHVSSTRQTMT 79 - D A+E AS+ ++ + +T+K + K YP++ K ++ I V+ Q Sbjct: 22 DHAEEHASINTKKTVENITDVRKTAKTSIDWTKPSGGEYPDI-KQKHVWIDVNVKEQKAY 80 Query: 80 ITSNDKVIFKTIVSTG---AKESPTPKGTFVIEPERGDFFYNASSKEGAYYWVSFKEHGI 136- I I+ ++S+G K+ TPKGTF +EPERG++F++ +EGA YWVS+K HG Sbjct: 81 IKEGSNTIYTMMISSGLDQTKDDATPKGTFYVEPERGEWFFSEGYQEGAEYWVSWKNHGE 140- Query: 137 YLFHSVPTDQQGNEIPEEAKQLGKAASHGCVRMSRADAKWFYENIPQGTTVTI 189 +LFHSVP + I EA++LG SHGC+R++ DAKW YENIP+ T V I Sbjct: 141 FLFHSVPMTKDQKVIKTEAEKLGTKVSHGCIRLTIPDAKWVYENIPEHTKVVI 193 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 1956 (GBS644) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 130 (lane 2 & 3; MW 49.6 kDa) and in FIG. 186 (lane 3; MW 50 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 130 (lane 5-7; MW 24.6 kDa) and in FIG. 177 (lane 3; MW 25 kDa). GBS644-GST was purified as shown in FIG. 236, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 629 A DNA sequence (GBSx0669) was identified in S. agalactiae <SEQ ID 1957> which encodes the amino acid sequence <SEQ ID 1958>. This protein is predicted to be carbon starvation protein A. Analysis of this protein sequence reveals the following: TABLE-US-01886 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.25 Transmembrane 129-145 (122-151) INTEGRAL Likelihood = -9.92 Transmembrane 316-332 (305-342) INTEGRAL Likelihood = -6.42 Transmembrane 164-180 (157-181) INTEGRAL Likelihood = -5.73 Transmembrane 443-459 (441-466) INTEGRAL Likelihood = -5.57 Transmembrane 416-432 (414-435) INTEGRAL Likelihood = -4.88 Transmembrane 190-206 (183-209) INTEGRAL Likelihood = -4.83 Transmembrane 78-94 (70-95) INTEGRAL Likelihood = -3.13 Transmembrane 362-378 (359-379) INTEGRAL Likelihood = -2.34 Transmembrane 228-244 (227-245) INTEGRAL Likelihood = -2.02 Transmembrane 2-18 (1-18) INTEGRAL Likelihood = -1.28 Transmembrane 393-409 (393-410) ----- Final Results ----- bacterial membrane --- Certainty = 0.5501 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01887 >GP: AAF93852 GB: AE004154 carbon starvation protein A, putative [Vibrio cholerae] Identities = 220/470 (46%), Positives = 311/470 (65%), Gaps = 16/470 (3%) Query: 1 MVTFLGGVALLIVGYFTYGRYIEKNFQIDENRQTPAEALRDGYDFVPMPKWKNGMIELLN 60 M+ FL VA L+ GYF YG ++EK F I+E RQTPA DG D+VPM K +++LLN Sbjct: 1 MLWFLTCVAALVGGYFIYGAFVEKVFGINEKRQTPAHTKTDGVDYVPMSTPKVYLVQLLN 60 Query: 61 IAGTGPIFGPILGALYGPVAYIWIVLGCIFAGAVHDYMIGMISLRNNGAYLPELASRYLG 120- IAG GPIFGPI+GALYGP A +WIV+GCIFAGAVHDY GM+S+RN GA +P + RYLG Sbjct: 61 IAGVGPIFGPIMGALYGPAAMLWIVVGCIFAGAVHDYFSGMLSIRNGGASVPSITGRYLG 120- Query: 121 KSMKHVINIFSMLLLILVATVFVVTPANLILSILPAG---TLSLPWIIGLIFVYYLISTV 17- 7 KH +NIF+++LL+LV VFV PA +I +++ T+S+ ++ +IF YY+++T+ Sbjct: 121 NGAKHFMNIFAIVLLLLVGVVFVSAPAGMITNLINQQTDFTVSMTTMVVIIFAYYILATI 18- 0 Query: 178 LPIDKALGKVYPVF-------CVILMVSTAAVGFRLLTGGFDMPNLTFETFKNMHPAGLG 23- 0 +P+DK +G+ YP+F V LM + A + GGF++ ++ KN++P + Sbjct: 181 VPVDKIIGRFYPLFGALLIFMSVGLMTAIAFSSEHQVLGGFEISDMV----KNLNPNDMP 23- 6 Query: 231 IFPALFFTISCGAISGFHATQAPMVSRTTVNEREGRFTFYGMMIAEGVIAMIWAGASMSL 29- 0 ++PALF TI+CGAISGFHATQ+P+++R NE+ GRF FYG MI EG+IA+IW ++S Sbjct: 237 LWPALFITIACGAISGFHATQSPLMARCMENEKNGRFVFYGAMIGEGIIALIWCTVALSF 29- 6 Query: 291 FKG-QNLYEMIAAGTPSAVVNQVMLMLLGSVIGTIAIIGVIVLPVSSGLSAFRSLRTIVA 34- 9 F + L E + G P VV LLG G IA +GV++LP++SG +AFRS R I+A Sbjct: 297 FGSLEALSEAVKNGGPGNVVYGASFGLLGVFGGVIAFLGVVILPITSGDTAFRSSRLILA 35- 6 Query: 350 DYIHVKQDTLPKIFAVTIPLYVISFVLTHVDFNLLWRYFNWANQVTAVIGLLVATRYLIL 40- 9 +Y +++Q TL + +PL+VI VLT VDF ++WRYF +ANQ TAV+ L AT YL+ Sbjct: 357 EYFNMEQKTLRNRLLMAVPLFVIGAVLTQVDFGIIWRYFGFANQATAVMMLWTATAYLMR 41- 6 Query: 410 KRRNYWVTFVPAMFMLYAVVVYIL-SQPIGFNMGLGILTYSLALVLTGIL 458 + +W+ VPA+FM + +IL S +GF + + I T + L G L Sbjct: 417 HNKLHWICTVPALFMTTVCISFILNSSTLGFGLPMQISTIAGVLASLGAL 466 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8623> and protein <SEQ ID 8624> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01888 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: 6.07 GvH: Signal Score (-7.5): -3.54 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 11 value: -11.25 threshold: 0.0 INTEGRAL Likelihood = -11.25 Transmembrane 129-145 (122-157) INTEGRAL Likelihood = -9.92 Transmembrane 316-332 (305-342) INTEGRAL Likelihood = -6.42 Transmembrane 164-180 (157-181) INTEGRAL Likelihood = -5.57 Transmembrane 416-432 (414-435) INTEGRAL Likelihood = -4.88 Transmembrane 190-206 (183-209) INTEGRAL Likelihood = -4.83 Transmembrane 78-94 (70-95) INTEGRAL Likelihood = -4.67 Transmembrane 445-461 (441-463) INTEGRAL Likelihood = -3.13 Transmembrane 362-378 (359-379) INTEGRAL Likelihood = -2.34 Transmembrane 228-244 (227-245) INTEGRAL Likelihood = -2.02 Transmembrane 2-18 (1-18) INTEGRAL Likelihood = -1.28 Transmembrane 393-409 (393-410) PERIPHERAL Likelihood = 0.21 272 modified ALOM score: 2.75 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5501 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00049## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 630 A DNA sequence (GBSx0670) was identified in S. agalactiae <SEQ ID 1959> which encodes the amino acid sequence <SEQ ID 1960>. This protein is predicted to be lytR (lytT). Analysis of this protein sequence reveals the following: TABLE-US-01889 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.80 Transmembrane 27-43 (27-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.1319 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01890 >GP: AAB48183 GB: L42945 lytR [Staphylococcus aureus] Identities = 93/245 (37%), Positives = 150/245 (60%), Gaps = 3/245 (1%) Query: 1 MKVLVVDDEPVARNELIYLLNKYDSNLVIAEAHDMATALAILLRETFDVALLDIHLRDDS 60 MK L++DDEP+ARNEL YLLN+ I EA ++ L LL +D+ LD++L D++ Sbjct: 1 MKALIIDDEPLARNELTYLLNEIGGFEEINEAENVKETLEALLINQYDIIFLDVNLMDEN 60 Query: 61 GLQLAEYINKMPKPPLLIFATAYDQYAIQAFEHDARDYLLKPYDFDRLKQAMDRVKGALS 120- G++L I KM +PP +IFATA+DQYA+QAFE +A DY+LKP+ R++QA+++V+ + Sbjct: 61 GIELGAKIQKMKEPPAIIFATAHDQYAVQAFELNATDYILKPFGQKRIEQAVNKVRATKA 120- Query: 121 TSTIIESVTSGPL---FKQQYPLTVEDRIYLVSADDILLIEAMQGKLIIQTPDKNYEIDG 17- 7 S + + F Q P+ ++D+I+++ +I+ I G I T + YE Sbjct: 121 KDDNNASAIANDMSANFDQSLPVEIDDKIHMLKQQNIIGIGTHNGITTIHTTNHKYETTE 18- 0 Query: 178 SLQQWQDKLPSSQFVRVHRSYIVNINAIKTIEPWFNQTLQLHLCNKITVPVSRANVKPLK 23- 7 L +++ +L + F+R+HRSYI+N IK ++ WFN T + L N + + V R+ +K K Sbjct: 181 PLNRYEKRLNPTYFIRIHRSYIINTKHIKEVQQWFNYTYMVILTNGVKMQVGRSFMKDFK 24- 0 Query: 238 QMLGI 242 +G+ Sbjct: 241 ASIGL 245 There is also homology to SEQ ID 460. SEQ ID 1960 (GBS399) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 75 (lane 7; MW 30.4 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 84 (lane 2; MW 55 kDa). Purified GBS399-GST is shown in FIG. 217, lane 9; purified GBS399d-GST is shown in FIG. 236, lane 3. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 631 A DNA sequence (GBSx0671) was identified in S. agalactiae <SEQ ID 1961> which encodes the amino acid sequence <SEQ ID 1962>. Analysis of this protein sequence reveals the following: TABLE-US-01891 Possible site: 51 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.59 Transmembrane 95-111 (86-116) INTEGRAL Likelihood = -5.95 Transmembrane 155-171 (152-176) INTEGRAL Likelihood = -2.28 Transmembrane 189-205 (187-206) INTEGRAL Likelihood = -1.49 Transmembrane 122-138 (121-138) ----- Final Results ----- bacterial membrane --- Certainty = 0.4036 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01892 >GP: AAB48182 GB: L42945 lytS [Staphylococcus aureus] Identities = 264/570 (46%), Positives = 389/570 (67%), Gaps = 2/570 (0%) Query: 1 MTLFLIMMERAGLIILLAYAFVHIPFIKQTLKQPELKKHQYILLILFSLFAIISNFTGVE 60 ++L ++++ER GLII+LAY ++IP+ K + + K ++ L I+FSLFA++SN TG+ Sbjct: 2 LSLTMLLLERVGLIIILAYVLMNIPYFKNLMNRRRTWKARWQLCIIFSLFALMSNLTGIV 61 Query: 61 IQSDLSIIPQTLNHIADQSSVANTRVLTIGVSGLIGGPIVGIIVGLLSVFVRYLQGGLAP 120- I S+ + D S+ANTRVLTIGV+GL+GGP VG+ VG++S R GG Sbjct: 62 IDHQHSLSGSVYFRLDDDVSLANTRVLTIGVAGLVGGPFVGLFVGVISGIFRVYMGGADA 121- Query: 121 HIYVISSLLIGLCSGLSGNYLRKNYNKIRVLDAMVVGFGMEILQMICILIFSVDFNQALR 18- 0 +Y+ISS+ IG+ +G G ++ + + ++G ME++QM+ IL FS D A+ Sbjct: 122 QVYLISSIFIGIIAGYFGLQAQRRKRYPSIAKSAMIGIVMEMIQMLSILTFSHDKAYAVD 18- 1 Query: 181 LVSFISMPMILSNTLGLGIFISIISSTQKLEEHAKAFQTHQVLELANLTLPYLRKGLTTE 24- 0 L+S I++PMI+ N++G IF+SII T K E+ K QTH VL+L N T PY ++GL E Sbjct: 182 LISLIALPMIIVNSVGPAIFIMSIIIPTLKQEDQMKPVQTHDVLQLMNQTFPYFKEGLNRE 2- 41 Query: 241 SCQPVAEIIHKHMDVSAVSLTSQSAILAYVGDGADHHLPNTQILTKLAKRAIDTGKVSVA 30- 0 S Q +A II M VS+V++TS++ IL++VG G+DHH+P +ILT L+K + +GK+ Sbjct: 242 SAQQIAMIIKNLMKVSSVAITSKNEILSHVGGGSDHHIPTNEILTSLSKDVLKSGKLKEV 30- 1 Query: 301 TDKSEIECDHKNCPLSSAIVIPLHIHDVIVGTLKLYFSDAQHMTYVDRQLAEGLGNIFST 36- 0 K EI C H NCPL +AIVIPL +H IVGTLK+YF++ +T+V+RQLAEGL NIFS+ Sbjct: 302 HTKEEIGCSHPNCPLRAAIVIPLEMHGSIVGTLKMYFTNPNDLTFVERQLAEGLANIFSS 36- 1 Query: 361 QLALGQAEEATRLLQDAEMKSLQAQVNPHFLFNALNTIYGLIRMDSEKARKLVQDFSKVI 42- 0 Q+ LG+AE ++LL+DAE+KSLQAQV+PHF FN++N I L+R++SEKAR+L+ + S Sbjct: 362 QIELGEAETQSKLLKDAEIKSLQAQVSPHFFFNSINPISALVRINSEKARELLLELSYFF 42- 1 Query: 421 RANLQRAKQNLIPLHDELEQVNAYLALEEARFPNMVAFNLDNQTNSDDNLMIPPFTLQVL 48- 0 RANLQ +KQ+ I L EL QV AYL+LE+AR+P N++ + D +++PPF +Q+L Sbjct: 422 RANLQGSKQHTITLDKELSQVRAYLSLEQARYPGRFNININVEDKYRD-VLVPPFLIQIL 48- 0 Query: 481 IENSYKHAFKHVNKNNQLKVTIARNN-DRLHIIVQDNGIGIPKEKLITLGKKTQISKQGS 53- 9 +EN+ KHAF + + N + V++ + + IIVQDNG GI K+K+ LG+ + S+ G+ Sbjct: 481 VENAIKHAFTNRKQGNDIDVSVIKETATHVRIIVQDNGQGISKDKMHLLGETSVESESGT 54- 0 Query: 540 GTAIENLVRRLNIIYDGQASLKFESNDSGT 569 G+A+ENL RL ++ A+L+FES SGT Sbjct: 541 GSALENLNLRLKGLFGKSAALQFESTSSGT 570 A related DNA sequence was identified in S. pyogenes <SEQ ID 1963> which encodes the amino acid sequence <SEQ ID 1964>. Analysis of this protein sequence reveals the following: TABLE-US-01893 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.79 Transmembrane 283-299 (276-307) INTEGRAL Likelihood = -5.57 Transmembrane 27-43 (24-48) ----- Final Results ----- bacterial membrane --- Certainty = 0.3718 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01894 >GP: CAB54576 GB: AJ006396 histidine kinase [Streptococcus pneumoniae] Identities = 115/231 (49%), Positives = 159/231 (68%), Gaps = 7/231 (3%) Query: 351 MLASIKAYIDEVYVLEVEQRDAQMRALQSQINPHFLYNTLEYIRMYALSCQQEELADVIY 41- 0 ML ++ I ++Y LE+ Q+DA MRALQ+QINPHF+YNTLE++RMYA+ Q+ELAD+IY Sbjct: 1 MLDRLEKNIHDIYQLELSQRDANMRALQAQINPHFMYNTLEFLRMYAVMQSQDELADIIY 60 Query: 411 AFASLLRNNISQDKMTTLKEELAFCEKYIYLYQMRYPDSFAYHVKIDESVADLAIPKFVI 47- 0 F+SLLRNNIS ++ T LK+EL FC KY YL +RYP S AY KID + ++ IPKF + Sbjct: 61 EFSSLLRNNISDERETLLKQELEFCRKYSYLCMVRYPKSIAYGFKIDPELENMKIPKFTL 120- Query: 471 QPLVENYFVHGIDYSRHDNALSIKALDETDHLLIQVLDNGRGISQERLADMEKRLQ---- 52- 6 QPLVENYF HG+D+ R DN +SIKAL + + I V+DNGRG+S E+LA++ ++L Sbjct: 121 QPLVENYFAHGVDHRRTDNVISIKALKQDGFVEILVVDNGRGMSAEKLANIREKLSQRYF 18- 0 Query: 527 EHQTT---GNSSIGLQNVYLRLFHHFRDRVSWSMAKEPNGGFIIQIRIRKD 574 EHQ + SIG+ NV+ R +F DR + ++ G +I I+ + Sbjct: 181 EHQASYSDQRQSIGIVNVHERFVLYFGDRYAITIESAEQAGVQYRITIQDE 231 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01895 Identities = 59/180 (32%), Positives = 97/180 (53%), Gaps = 8/180 (4%) Query: 375 QDAEMKSLQAQVNPHFLFNALNTI--YGLIRMDSEKARKLVQDFSKVIRANLQRAKQNLI 43- 2 +DA+M++LQ+Q+NPHFL+N L I Y L E A ++ F+ ++R N+ + K + Sbjct: 370 RDAQMRALQSQINPHFLYNTLEYIRMYALSCQQEELA-DVIYAFASLLRNNISQDK--MT 42- 6 Query: 433 PLHDELEQVNAYLALEEARFPNMVAFNLDNQTNSDDNLMIPPFTLQVLIENSYKHAFKHV 49- 2 L +EL Y+ L + R+P+ A+++ + D L IP F +Q L+EN + H + Sbjct: 427 TLKEELAFCEKYIYLYQMRYPDSFAYHVKIDESVAD-LAIPKFVIQPLVENYFVHGIDYS 48- 5 Query: 493 NKNNQLKVTIARNNDRLHIIVQDNGIGIPKEKLITLGKKTQISKQ--GSGTAIENLVRRL 55- 0 +N L + D L I V DNG GI +E+L + K+ Q + S ++N+ RL Sbjct: 486 RHDNALSIKALDETDHLLIQVLDNGRGISQERLADMEKRLQEHQTTGNSSIGLQNVYLRL 54- 5 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 632 A DNA sequence (GBSx0672) was identified in S. agalactiae <SEQ ID 1965> which encodes the amino acid sequence <SEQ ID 1966>. Analysis of this protein sequence reveals the following:

TABLE-US-01896 Possible site: 24 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9827> which encodes amino acid sequence <SEQ ID 9828> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 633 A DNA sequence (GBSx0673) was identified in S. agalactiae <SEQ ID 1967> which encodes the amino acid sequence <SEQ ID 1968>. Analysis of this protein sequence reveals the following: TABLE-US-01897 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.55 Transmembrane 52-68 (45-74) INTEGRAL Likelihood = -9.18 Transmembrane 83-99 (76-106) INTEGRAL Likelihood = -8.76 Transmembrane 126-142 (118-146) INTEGRAL Likelihood = -7.48 Transmembrane 174-190 (170-191) INTEGRAL Likelihood = -3.66 Transifiembrane 195-211 (193-212) INTEGRAL Likelihood = -1.28 Transmembrane 24-40 (24-40) ----- Final Results ----- bacterial membrane --- Certainty = 0.4821 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8625> and protein <SEQ ID 8626> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01898 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -8.54 GvH: Signal Score (-7.5): -5.6 Possible site: 57 >>> Seems to have no N-terminal signal sequence ALOM program count: 6 value: -9.55 threshold: 0.0 INTEGRAL Likelihood = -9.55 Transmembrane 52-68 (45-74) INTEGRAL Likelihood = -9.18 Transmembrane 83-99 (76-106) INTEGRAL Likelihood = -8.76 Transmembrane 126-142 (118-146) INTEGRAL Likelihood = -7.48 Transmembrane 174-190 (170-191) INTEGRAL Likelihood = -3.66 Transmembrane 195-211 (193-212) INTEGRAL Likelihood = -1.28 Transmembrane 24-40 (24-40) PERIPHERAL Likelihood = 13.05 100 modified ALOM score: 2.41 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4821 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 634 A DNA sequence (GBSx0674) was identified in S. agalactiae <SEQ ID 1969> which encodes the amino acid sequence <SEQ ID 1970>. Analysis of this protein sequence reveals the following: TABLE-US-01899 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.53 Transmembrane 83-99 (83-99) ----- Final Results ----- bacterial membrane --- Certainty = 0.1213 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 635 A DNA sequence (GBSx0675) was identified in S. agalactiae <SEQ ID 1971> which encodes the amino acid sequence <SEQ ID 1972>. Analysis of this protein sequence reveals the following: TABLE-US-01900 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1902 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 636 A DNA sequence (GBSx0676) was identified in S. agalactiae <SEQ ID 1973> which encodes the amino acid sequence <SEQ ID 1974>. Analysis of this protein sequence reveals the following: TABLE-US-01901 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4763 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 637 A DNA sequence (GBSx0677) was identified in S. agalactiae <SEQ ID 1975> which encodes the amino acid sequence <SEQ ID 1976>. Analysis of this protein sequence reveals the following: TABLE-US-01902 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5089 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 638 A DNA sequence (GBSx0678) was identified in S. agalactiae <SEQ ID 1977> which encodes the amino acid sequence <SEQ ID 1978>. Analysis of this protein sequence reveals the following: TABLE-US-01903 Possible site: 25 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 1978 (GBS184) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 26 (lane 7; MW 21 kDa), in FIG. 168 (lane 14-16; MW 36 kDa--thioredoxin fusion) and in FIG. 238 (lane 9; MW 36 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 37 (lane 7; MW 46.4 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 639 A DNA sequence (GBSx0679) was identified in S. agalactiae <SEQ ID 1979> which encodes the amino acid sequence <SEQ ID 1980>. Analysis of this protein sequence reveals the following: TABLE-US-01904 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2179(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 640 A DNA sequence (GBSx0680) was identified in S. agalactiae <SEQ ID 1981> which encodes the amino acid sequence <SEQ ID 1982>. This protein is predicted to be immunogenic secreted protein precursor. Analysis of this protein sequence reveals the following: TABLE-US-01905 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2166(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9351> which encodes amino acid sequence <SEQ ID 9352> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 1983> which encodes the amino acid sequence <SEQ ID 1984>. Analysis of this protein sequence reveals the following: TABLE-US-01906 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.77 Transmembrane 9-25 (5-27) ----- Final Results ----- bacterial membrane --- Certainty = 0.2508(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01907 Identities = 64/86 (74%), Positives = 76/86 (87%) Query: 1 MGNGGDWKNKPGYQTTHEAKTGYAISFSPGQAGADRTYGHVAIVEDVKEDGSIPISESNV 60 MGNGGDW+ KPG+ TTH+ K GY +SF+PGQAGAD TYGHVA+VE +KEDGSI ISESNV Sbjct: 452 MGNGGDWQRKPGFVTTHKPKVGYVVSFAPGQAGADATYGHVAVVEQIKEDGSILISESNV 51- 1 Query: 61 LGLGTISYRTFSAAEAAQLTYVVGEK 86 +GLGTISYRTF+A +A+ LTYVVG+K Sbjct: 512 MGLGTISYRTFTAEQASLLTYVVGDK 537 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 641 A DNA sequence (GBSx0681) was identified in S. agalactiae <SEQ ID 1985> which encodes the amino acid sequence <SEQ ID 1986>. This protein is predicted to be immunogenic secreted protein precursor. Analysis of this protein sequence reveals the following: TABLE-US-01908 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2495(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01909 AAB52379 GB: U31811 immunogenic secreted protein precursor [Streptococcus pyogenes] Identities = 133/259 (51%), Positives = 170/259 (65%), Gaps = 4/259 (1%) Query: 3 PSQPQVTATPQKSEVVTPAITSGIDLPDVAIPTAMASAAYVKHWIGNDAYTHNLLSHRYG 62 P QP + A + V P S DL + P++ +SAAYV+HW G+ AYTHNLLS RYG Sbjct: 174 PIQPPLGAA---APVFAPWRESDKDLSKLK-PSSRSSAAYVRHWTGDSAYTHNLLSRRYG 22- 9 Query: 63 ITAAQLDGFLQSTGITYDSSRIDGQKILDREKSSGLDARAIIAIAIAESSLGTQGVATAP 122- ITA QLDGFL S GI YD R++G+++L+ EK +GLD RAI+AIA+AESSLGTQGVA Sbjct: 230 ITAEQLDGFLNSLGIHYDKERLNGKRLLEWEKLTGLDVRAIVAIAMAESSLGTQGVAKEK 28- 9 Query: 123 GANMFGFGAVDNNTTNAQNFSDDKAVIKMTQETIIQNQNTSFAIQDQKAQFLSTGNLNVA 18- 2 G+NMFG+GA D N NA+ +SD+ A+ M ++TII N+N +F QD KA+ S G L+ Sbjct: 290 GSNMFGYGAFDFNPNNAKKYSDEVAIRHMVEDTIIANKNQTFERQDLKAKKWSLGQLDTL 34- 9 Query: 183 ARGGVYFTDASGSGKRRAAIMESIDKWIDAHGGISEISKELLNTSSVAMMAVPTSYSVSR 24- 2 GGVYFTD SGSG+RRA IM +D+WID HG +I + L TS VP Y S+ Sbjct: 350 IDGGVYFTDTSGSGQRRADIMTKLDQWIDDHGNTPDIPEHLKITSGTQFSEVPVGYKRSQ 40- 9 Query: 243 ANQAGNYVAGTYPWGQRTW 261 Y + TY +GQ TW Sbjct: 410 PQNVLTYKSETYSFGQCTW 428 A related DNA sequence was identified in S. pyogenes <SEQ ID 1987> which encodes the amino acid sequence <SEQ ID 1988>. Analysis of this protein sequence reveals the following: TABLE-US-01910 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01911 Identities = 143/265 (53%), Positives = 184/265 (68%), Gaps = 5/265 (1%) Query: 2 VPSQPQVTATPQKSEVVTPA-----ITSGIDLPDVAIPTAMASAAYVKHWIGNDAYTHNL 56 V + P + + Q E TP S +DL ++ IP+ AAYV+HW G +AYTH+L Sbjct: 135 VDTAPASSLSKQLPEARTPIQSLSPYVSDLDLSEIDIPSVNTYAAYVEHWSGKNAYTHHL 19- 4 Query: 57 LSHRYGITAAQLDGFLQSTGITYDSSRIDGQKILDREKSSGLDARAIIAIAIAESSLGTQ 116- LS RYGI A Q+D +L+STGI YDS+RI+G+K+L EK SGLD RAI+AIA++ESSLGTQ Sbjct: 195 LSRRYGIKADQIDSYLKSTGIAYDSTRINGEKLLQWEKKSGLDVRAIVAIAMSESSLGTQ 25- 4 Query: 117 GVATAPGANMFGFGAVDNNTTNAQNFSDDKAVIKMTQETIIQNQNTSFAIQDQKAQFLST 17- 6 G+AT GANMFG+ A D + T A F+DD A++KMTQ+TII+N+N++FA+QD KA S Sbjct: 255 GIATLLGANMFGYAAFDLDPTQASKFNDDSAIVKMTQDTIIKNKNSNFALQDLKAAKFSR 31- 4 Query: 177 GNLNVAARGGVYFTDASGSGKRRAAIMESIDKWIDAHGGISEISKELLNTSSVAMMAVPT 23- 6 G LN A+ GGVYFTD +GSGKRRA IME +DKWID HGG I EL SS + +VP Sbjct: 315 GQLNFASDGGVYFTDTTGSGKRRAQIMEDLDKWIDDHGGTPAIPAELKVQSSASFASVPA 37- 4 Query: 237 SYSVSRANQAGNYVAGTYPWGQRTW 261 Y +S++ Y A +Y WGQ TW Sbjct: 375 GYKLSKSYDVLGYQASSYAWGQCTW 399 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 642 A DNA sequence (GBSx0682) was identified in S. agalactiae <SEQ ID 1989> which encodes the amino acid sequence <SEQ ID 1990>. Analysis of this protein sequence reveals the following: TABLE-US-01912 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8627> and protein <SEQ ID 8628> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-01913 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 11.56 GvH: Signal Score (-7.5): 0.870001 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 11.88 threshold: 0.0 PERIPHERAL Likelihood = 11.88 63 modified ALOM score: -2.88 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8628 (GBS159) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 28 (lane 4; MW 26 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 34 (lane 2; MW 41 kDa). GBS159-GST was purified as shown in FIG. 198, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 643 A DNA sequence (GBSx0683) was identified in S. agalactiae <SEQ ID 1991> which encodes the amino acid sequence <SEQ ID 1992>. Analysis of this protein sequence reveals the following: TABLE-US-01914 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2668(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01915 >GP: BAB04699 GB: AP001510 unknown conserved protein [Bacillus halodurans] Identities = 32/76 (42%), Positives = 54/76 (70%) Query: 7 LGSVIELKNDSQKVMITSRFPLYDNEGQLGYFDYSGCIFPISIVGNETYFFNLEDIDKVL 66 +GS++ LK + K+MI +R P+ + G+ FDYSGC +P +V ++ ++FN E+ID+V+ Sbjct: 4 IGSIVYLKEGTSKLMILNRGPILEANGENKMFDYSGCFYPQGLVPDKVFYFNHENIDEVV 63 Query: 67 FEGYYDENEEEMQKIF 82 FEG+ D+ E+ QK+F Sbjct: 64 FEGFQDDEEQRFQKLF 79 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 644 A DNA sequence (GBSx0684) was identified in S. agalactiae <SEQ ID 1993> which encodes the amino acid sequence <SEQ ID 1994>. Analysis of this protein sequence reveals the following: TABLE-US-01916 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.81 Transmembrane 75-91 (69-99) INTEGRAL Likelihood = -14.38 Transmembrane 134-150 (129-179) INTEGRAL Likelihood = -8.49 Transmembrane 157-173 (151-179) INTEGRAL Likelihood = -1.17 Transmembrane 50-66 (46-67) ----- Final Results ----- bacterial membrane --- Certainty = 0.6922 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 645 A DNA sequence (GBSx0685) was identified in S. agalactiae <SEQ ID 1995> which encodes the amino acid sequence <SEQ ID 1996>. Analysis of this protein sequence reveals the following: TABLE-US-01917 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.11 Transmembrane 40-56 (40-56) ----- Final Results ----- bacterial membrane --- Certainty = 0.1044 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 1996 (GBS204) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 13; MW 32 kDa) and FIG. 53 (lane 2; MW 14.7 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 54 (lane 6; MW 39.7 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 646 A DNA sequence (GBSx0686) was identified in S. agalactiae <SEQ ID 1997> which encodes the amino acid sequence <SEQ ID 1998>. Analysis of this protein sequence reveals the following:

TABLE-US-01918 Possible site: 38 >>> Seems to have no N-terminal signal sequence (or signal = aa 1-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01919 >GP: CAC16670 GB: AJ302698 hypothetical protein [Staphylococcus haemolyticus] Identities = 60/254 (23%), Positives = 109/254 (42%), Gaps = 14/254 (5%) Query: 2 VKVSVSSVGTQASTVAISMFSRVSALNDAITKLSSFAEAATLQGTAYSNAKSYATGTLTP 61 + + V +Q+S V ++ S S + + F A+ LQG AY + K + + + P Sbjct: 3 IDMYVGKSKSQSSDVGSTVKSISSGYDSLQKGIMQFVGASELQGQAYDSGKQFFSAVIAP 62 Query: 62 MLQGMILFSETLSEKCTELQTLYVSICGDEDLDSVVLESKLASDRASLKIAEALLEHLND 121- + + + E + C + Y S + L L + + EA+ L Sbjct: 63 LTESIKTLGELTEQACNDFVDQYQSEVDSQSLKESELLEDIEELNKQISQLEAMNASLKH 122- Query: 122 DPEPSKSAISSTKSNIKKLKKRIKSNQKKLDNLNEFNAHSATVFADISNAQSTVNQALAA 18- 1 + S +S I L+++ K ++KL L +F+A S +F ++ + Q TV Q + Sbjct: 123 KSSKNSSLLSGNHQMISSLEQQKKELEEKLRKLRQFDAKSPNIFKEVESFQKTVQQGINQ 18- 2 Query: 182 VSTGFSGYNSKTGAFGKPTSGQMEWTKTVKKNWKEREDAKAEELKSKKAEESKKASKIEN 24- 1 T ++ F P MEW K ++ E K +++ ++KA++ KK SK + Sbjct: 183 AKT---AWDPGKQTFNIPAGKDMEWAKVSQQKALE---VKMDKI-NQKAKDGKKLSKNDI 23- 5 Query: 242 TT-------KKSNV 248 T KKSN+ Sbjct: 236 FTIIAYQQQKKSNI 249 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 1998 (GBS270) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 2; MW 34.3 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 54 (lane 7; MW 59.2 kDa). The GBS270-GST fusion product was purified (FIG. 206, lane 3) and used to immunise mice. The resulting antiserun was used for FACS (FIG. 265), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 647 A DNA sequence (GBSx0687) was identified in S. agalactiae <SEQ ID 1999> which encodes the amino acid sequence <SEQ ID 2000>. This protein is predicted to be outer surface protein F. Analysis of this protein sequence reveals the following: TABLE-US-01920 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3323(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 2000 (GBS316) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 3; MW 23 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 55 (lane 2; MW 41.8 kDa). GBS316-GST was purified as shown in FIG. 206, lane 4. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 648 A DNA sequence (GBSx0688) was identified in S. agalactiae <SEQ ID 2001> which encodes the amino acid sequence <SEQ ID 2002>. This protein is predicted to be actin-like protein arp3 (act4). Analysis of this protein sequence reveals the following: TABLE-US-01921 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0217(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 649 A DNA sequence (GBSx0689) was identified in S. agalactiae <SEQ ID 2003> which encodes the amino acid sequence <SEQ ID 2004>. This protein is predicted to be diarrheal toxin. Analysis of this protein sequence reveals the following: TABLE-US-01922 Possible site: 25 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.65 Transmembrane 65-81 (61-84) INTEGRAL Likelihood = -3.98 Transmembrane 89-105 (85-106) ----- Final Results ----- bacterial membrane --- Certainty = 0.4461(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01923 >GP: CAB15175 GB: Z99120 alternate gene name: yueA~similar to hypothetical proteins [Bacillus subtilis] Identities = 452/1058 (42%), Positives = 664/1058 (62%), Gaps = 39/1058 (3%) Query: 98 VTMIFSITGYFKNRKQYKQDLQERIDSYHDYLSDKSIELQKLAKEQKRGQHYHYPTIEGL 157- +T+I S YF+++ Q K+ ++R Y YL +K ELQ LA++QK+ +H+P+ E + Sbjct: 1 MTLITSTVQYFRDKNQRKKREEKRERVYKLYLDNKRKELQALAEKQKQVLEFHFPSFEQM 60 Query: 158 QEMADTYHHRIYEKTPLHFDFLYYRLGLGEVPTSYNIHYSQPERSGKK-DPLENEGYNLY 21- 6 + + RI+EK+ D+L RLG G VP+SY I+ S + + + D L + ++ Sbjct: 61 KYLTSEISDRIWEKSLESKDYLQLRLGTGTVPSSYEINMSGGDLANRDIDDLMEKSQHMQ 120- Query: 217 FNNRYIKNMPIVANLSHGPVGYIGPRGLVLEQLQLMVNQLAFFHSYHDVQFITIVPEEEM 27- 6 + I+N P+ +L+ GP+G +G +V ++ ++ QL+FF+SYHD++F+ I EEE Sbjct: 121 RVYKDIRNAPVTVDLAEGPMGLVGKSQIVKNEIHQLIGQLSFFNSYHDLRFVFIFHEEEY 18- 0 Query: 277 DKWSWMRWLPHETLQDVNVRGFVYNQRSRDQVLNSLNQILKLRRTQREDKSAKEGTLFSP 33- 6 W WM+ +P + + +GF+YN+++RDQ+L+SL ++++ +R+ + KE F P Sbjct: 181 KDWEWMKCVPQFQMPHIYAKGFIYNEQTRDQLLSSLYELIR----ERDLEDDKEKLQFKP 23- 6 Query: 337 HYVVIVTDEKLILDHVIMEFFTEDPTELGCSLIFVQDVMSSLSENIKTIINIKDRNTGQL 39- 6 H+V ++T+++LI +HVI+E+ LG S I + SLSENI T++ + + G + Sbjct: 237 HFVFVITNQQLISEHVILEYLEGQHEHLGISTIVAAETKESLSENITTLVRYINEHEGDI 29- 6 Query: 397 VIEEGELKETDFELDHFLEDYDKENISRRLAPLNHLQNLKSSIPEAVTFMEMYQAEEFED 45- 6 +I++ + F LDH + D E SR L LNH + +SIPE V+F+E++ A+E ++ Sbjct: 297 LIQKKKAVRIPFRLDHHQRE-DNERFSRTLRTLNHQVGITNSIPETVSFLELFHAKEVKE 35- 5 Query: 457 LHVQERWISHAPYKSSAVPLGLRGQDDIVYLNLHEKAHGPHGLVAGTTGSGKSEIIQSYI 51- 6 + +Q+RW++ KS +VP+G +G+DDIVYLNLHEKAHGPHGL+AGTTGSGKSE +Q+YI Sbjct: 356 IGIQQRWLTSESSKSLSVPIGYKGKDDIVYLNLHEKAHGPHGLLAGTTGSGKSEFLQTYI 41- 5 Query: 517 LSLAVNFHPHDVAFLLIDYKGGGMANLFKDLPHLLGTITNLDGAQ--SMRALVSINAELK 57- 4 LSLAV+FHPH+ AFLLIDYKGGGMA F+++PHLLGTITN++G++ SMRAL SI +ELK Sbjct: 416 LSLAVHFHPHEAAFLLIDYKGGGMAQPFRNIPHLLGTITNIEGSKNFSMRALASIKSELK 47- 5 Query: 575 RRQRLFAKADVNHINQYQKKYKLGEVSEPMPHLFLISDEFAELKSNQPEFMKELVSTARI 63- 4 +RQRLF + VNHIN Y K YK G+ MPHLFLISDEFAELKS +P+F++ELVS ARI Sbjct: 476 KRQRLFDQYQVNHINDYTKLYKQGKAEVAMPHLFLISDEFAELKSEEPDFIRELVSAARI 53- 5 Query: 635 GRSLGIHLILATQKPSGVVDDQIWSNSRFKLALKVADRGDSMEMLHTPDAAEITQAGRAY 69- 4 GRSLG+HLILATQKP G++DDQIWSNSRFK+ALKV D DS E+L DAA IT GR Y Sbjct: 536 GRSLGVHLILATQKPGGIIDDQIWSNSRFKVALKVQDATDSKEILKNSDAANITVTGRGY 59- 5 Query: 695 LQVGNNEVYELFQSAWSGADYQPEKDDQGIEDHTIYSINDLGQYEILNDDLSGLDQAENI 75- 4 LQVGNNEVYELFQSAWSGA Y E G ED I + D G LS +D +N Sbjct: 596 LQVGNNEVYELFQSAWSGAPYLEEV--YGTEDE-IAIVTDTGLI-----PLSEVDTEDNA 64- 7 Query: 755 -KEVPTELDAIVENIQALTKEMGISDLPQPWLPPLSNQIAVTDLRKEGSVDLWSKAPSYK 81- 3 K+V TE++A+V+ I+ + EMGI LP PWLPPL+ +I T L+ Sbjct: 648 KKDVQTEIEAVVDEIERIQDEMGIEKLPSPWLPPLAERIPRT---------LFPSNEKDH 69- 8 Query: 814 AVLGFMDIPSQQAQEVAYHDFEDDGHLSIFAGPSMGKSTALQTVTMDLARHNSPEFLNLY 87- 3 ++D P Q Q + +DG++ IF GKS A T M A +PE L++Y Sbjct: 699 FHFAYVDEPDLQRQAPIAYKMMEDGNIGIFGSSGYGKSIAAATFLMSFADVYTPEELHVY 75- 8 Query: 874 LFDFGTNGLLPLRRLPHVADFFTIDDDEKIAKFIARIKVEMSDRKKALSRYNVATAKLYR 93- 3 +FDFG LLPL +LPH AD+F +D KI KF+ RIK E+ RK+ ++ K+Y Sbjct: 759 IFDFGNGTLLPLAKLPHTADYFLMDQSRKIEKFMIRIKEEIDRRKRLFREKEISHIKMYN 81- 8 Query: 934 QVSGETMPQILIVIDSYEGLREAQTPTNLEACFQNISRDGSSLGISLVISAGRTAALRSS 99- 3 +S E +P I I ID+++ +++ LE+ F +SRDG SLGI +++A R A+R S Sbjct: 819 ALSEEELPFIFITIDNFDIVKDEM--HELESEFVQLSRDGQSLGIYFMLTATRVNAVRQS 87- 6 Query: 994 LMANLKERIALKLTDDSESRTLVGRHQHIMEDIPGRGLIKRDDIEVLQVALSTEGTETFD 10- 53 L+ NLK +I L D SE ++ GR + +E IPGR +I+++++ Q+ L + + Sbjct: 877 LLNNLKTKIVHYLMDQSEGYSIYGRPKFNLEPIPGRVIIQKEELYFAQMFLPVDADDDIG 93- 6 Query: 1054 IINNIQNESDAMNSKWTG-PRPKAIPIVPEELTFDDFMATDSVQADLSANRL--PLGLEM 1- 110 + N ++++ + ++ +P IP++PE L+ + S++ L L P+GL Sbjct: 937 MFNELKSDVQKLQGRFASMEQPAPIPMLPESLSTREL----SIRFKLERKPLSVPIGLHE 99- 2 Query: 1111 VDVESYSLALNRFKHMLYMSDSDESLEAVGSHIIKVLL 1148 V L + KH L + + ++++KV+L Sbjct: 993 ETVSPVYFDLGKHKHCLILGQTQRG----KTNVLKVML 1026 There is also homology to SEQ ID 24. A related GBS gene <SEQ ID 8629> and protein <SEQ ID 8630> were also identified. Analysis of this protein sequence reveals the following: Homology to a bacterial toxin The protein has homology with the following sequences in the databases: TABLE-US-01924 >OMNI|NT01BS3725 diarrheal toxin Score = 203 bits (511), Expect = 4e-51 Identities = 123/377 (32%), Positives = 198/377 (51%), Gaps = 22/377 (5%) Query: 1 MGISDLPQPWLPPLSNQIAVTDLRKEGSVDLWSKAPSYKAVLGFMDIPSQQAQEVAYHDF 60 MGI LP PWLPPL+ +I T L+ ++D P Q Q + Sbjct: 704 MGIEKLPSPWLPPLAERIPRT---------LFPSNEKDHFHFAYVDEPDLQRQAPIAYEM 75- 4 Query: 61 EDDGHLSIFAGPSMGKSTALQTVTMDLARHNSPEFLNLYLFDFGTNGLLPLRRLPHVADF 120- +DG++ IF GKS A T M A +PE L++Y+FDFG LLPL +LPH AD+ Sbjct: 755 MEDGNIGIFGSSGYGKSIAAATFLMSFADVYTPEELHVYIFDFGNGTLLPLAKLPHTADY 81- 4 Query: 121 FTIDDDEKIAKFIARIKVEMSDRKKALSRYNVATAKLYRQVSGETMPQILIVIDSYEGLR 18- 0 F +D KI KF+ RIK E+ RK+ ++ K+Y +S E +P I I ID+++ ++ Sbjct: 815 FLMDQSRKIEKFMIRIKEEIDRRKRLFREKEISHIKMYNALSEEELPFIFITIDNFDIVK 87- 4 Query: 181 EAQTPTNLEACFQNISRDGSSLGISLVISAGRTAALRSSLMANLKERIALKLTDDSESRT 24- 0 + LE+ F +SRDG SLGI +++A R A+R SL+ NLK +I L D SE + Sbjct: 875 DEM--HELESEFVQLSRDGQSLGIYFMLTATRVNAVRQSLLNNLKTKIVHYLMDQSEGYS 93- 2 Query: 241 LVGRHQHIMEDIPGRGLIKRDDIEVLQVALSTEGTETFDIINNIQNESDAMNSKWTG-PR 29- 9 + GR + +E IPGR +I+++++ Q+ L + + + N ++++ + ++ + Sbjct: 933 IYGRPKFNLEPIPGRVIIQKEELYFAQMFLPVDADDDIGMFNELKSDVQKLQGRFASMEQ 99- 2 Query: 300 PKAIPIVPEELTFDDFMATDSVQADLSANRL--PLGLEMVDVESYSLALNRFKHMLYMSD 35- 7 P IP++PE L+ + S++ L L P+GL V L + KH L + Sbjct: 993 PAPIPMLPESLSTREL----SIRFKLERKPLSVPIGLHEETVSPVYFDLGKHKHCLILGQ 10- 48 Query: 358 SDESLEAVGSHIIKVLL 374 + ++++KV+L Sbjct: 1049 TQRG----KTNVLKVML 1061 SEQ ID 8630 (GBS326) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 65 (lane 5; MW 66 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 71 (lane 5; MW 91 kDa). GBS326-GST was purified as shown in FIG. 212, lane 5. GBS326LN was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 127 (lane 24; MW 114 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 184 (lane 6; MW 114 kDa). The purified protein is shown in FIG. 236, lane 12. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 650 A DNA sequence (GBSx0690) was identified in S. agalactiae <SEQ ID 2005> which encodes the amino acid sequence <SEQ ID 2006>. Analysis of this protein sequence reveals the following: TABLE-US-01925 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2693 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 651 A DNA sequence (GBSx0691) was identified in S. agalactiae <SEQ ID 2007> which encodes the amino acid sequence <SEQ ID 2008>. Analysis of this protein sequence reveals the following: TABLE-US-01926 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3933 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 652 A DNA sequence (GBSx0692) was identified in S. agalactiae <SEQ ID 2009> which encodes the amino acid sequence <SEQ ID 2010>. Analysis of this protein sequence reveals the following: TABLE-US-01927 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.32 Transmembrane 225-241 (219-246) ----- Final Results ----- bacterial membrane --- Certainty = 0.3930 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01928 >GP: BAB04693 GB: AP001510 unknown conserved protein [Bacillus halodurans] Identities = 83/320 (25%), Positives = 162/320 (49%), Gaps = 1/320 (0%) Query: 103 VNFILHPSNLFLTKNATAKIAYRSLPGIMRPEKFGPEEFLYQFKCFVFALLTQHDYIELY 16- 2 ++ I+ P N+ ++ + + + P + PE + + + LL + Y Sbjct: 106 LHLIVSPENVLVSDGLDVTFIHYGVKDSIPPYETDPERLFLELRATLLVLLDGNHRFHEY 16- 5 Query: 163 NGAISVIEVSDFLKSIYHAETIQAVRDIITIDYEQQVEVETHTLAKVSRAKYKLYKYISV 22- 2 +++S KS+ T++ +R++I + Q+ E + L KV + K+ + K+ + Sbjct: 166 MNYHDTLKLSPEAKSLVQQTTLEGLRELIR-HWIQEHEQQEKQLHKVPKTKWTIQKWAGI 22- 4 Query: 223 WLGALSTILLIPLVYLVFIHNPFKEKMLAADTSFIKVDYNQVINRLEHVKVSKLPYTQKY 28- 2 L A +I +VY++ P +E A+ +++ +Y+QVI+ LE + +P KY Sbjct: 225 GLIAALVPAIIYIVYVLAFLQPRQEAFTASHAAYLNENYSQVIDTLEPYSPNSMPRVVKY 28- 4 Query: 283 ELAYSYINGMSFSEEQREVILNNVTLKTDELYLDYWINIGRGLDDDAIDAAKRLDDSDLV 34- 2 +LA SY+ RE + N + L+ E Y DYWI IGRG ++ AID A+ L D + + Sbjct: 285 QLAQSYVAIEPLQAYHRENLKNVLVLQAAESYFDYWIAIGRGENEKAIDIARGLQDKEWL 34- 4 Query: 343 IYAIVQKMDQVRKDNSLSGKDREQKLSELQTDYDKYWKDRKTALTDEESKSKNSNNHSTN 40- 2 +YA V++ ++V+ D +LSGK+RE + E++ + D Y ++ + + E+ N+ ++N Sbjct: 345 VYANVKRREEVKSDENLSGKEREDLIKEIEAEIDDYMRELEELAEEGEAFQPNAEPAASN 40- 4 Query: 403 SNKESSESSSTTASTSSKTK 422 +E + S + + K Sbjct: 405 ELEEDEGDTEEDDSDNQEAK 424 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 2010 (GBS337) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 62 (lane 3; MW 50.3 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 653 A DNA sequence (GBSx0693) was identified in S. agalactiae <SEQ ID 2011> which encodes the amino acid sequence <SEQ ID 2012>. Analysis of this protein sequence reveals the following: TABLE-US-01929 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -14.01 Transmembrane 131-147 (122-153) ----- Final Results ----- bacterial membrane --- Certainty = 0.6604 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8631> which encodes amino acid sequence <SEQ ID 8632> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-01930 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 13.38 GvH: Signal Score (-7.5): -1.25 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 1 value: -14.01 threshold: 0.0 INTEGRAL Likelihood = -14.01 Transmembrane 127-143 (118-149) PERIPHERAL Likelihood = 16.13 113 modified ALOM score: 3.30 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6604(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8632 (GBS140) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 32 (lane 3; MW 43 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 8; MW 18 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 654 A DNA sequence (GBSx0694) was identified in S. agalactiae <SEQ ID 2013> which encodes the amino acid sequence <SEQ ID 2014>. Analysis of this protein sequence reveals the following:

TABLE-US-01931 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1486(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 655 A DNA sequence (GBSx0695) was identified in S. agalactiae <SEQ ID 2015> which encodes the amino acid sequence <SEQ ID 2016>. Analysis of this protein sequence reveals the following: TABLE-US-01932 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.59 Transmembrane 984-1000 (976-1009) INTEGRAL Likelihood = -9.71 Transmembrane 19-35 (15-42) INTEGRAL Likelihood = -9.50 Transmembrane 872-888 (865-890) INTEGRAL Likelihood = -6.37 Transmembrane 927-943 (924-951) INTEGRAL Likelihood = -4.19 Transmembrane 831-847 (828-847) INTEGRAL Likelihood = -2.87 Transmembrane 899-915 (899-916) ----- Final Results ----- bacterial membrane --- Certainty = 0.6838(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8633> which encodes amino acid sequence <SEQ ID 8634> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-01933 Lipop Possible site: -1 Crend: 6 SRCFLG: 0 McG: Length of UR: 20 Peak Value of UR: 3.40 Net Charge of CR: 3 McG: Discrim Score: 13.67 GvH: Signal Score (-7.5): -3.27 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 6 value: -14.59 threshold: 0.0 INTEGRAL Likelihood = -14.59 Transmembrane 973-989 (965-998) INTEGRAL Likelihood = -9.71 Transmembrane 8-24 (4-31) INTEGRAL Likelihood = -9.50 Transmembrane 861-877 (854-879) INTEGRAL Likelihood = -6.37 Transmembrane 916-932 (913-940) INTEGRAL Likelihood = -4.19 Transmembrane 820-836 (817-836) INTEGRAL Likelihood = -2.87 Transmembrane 888-904 (888-905) PERIPHERAL Likelihood = 3.82 936 modified ALOM score: 3.42 icm1 HYPID: 7 CFP: 0.684 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6838(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01934 >GP: AAB86324 GB: AE000938 phage infection protein homolog [Methanothermobacter thermoautotrophicus] Identities = 96/454 (21%), Positives = 190/454 (41%), Gaps = 63/454 (13%) Query: 1 MLKIKYILGRIMKR-NNFRILWYIIAVALFLVAIAGLNLKLQGDHAKENKTTQSATNTKL 59 M K I + MK N ++ ++IAV + + A+ + +Q ++T+ + Sbjct: 1 MRKALEIFWKDMKTVKNSPVVLFVIAVIICIPALYAV-FNIQATLDPYSRTSS------I 53 Query: 60 NIALVNEDQNVSNGKESYNLGASYIKSIERDNSQNWSVVSRGTAQNGLDKGDYQLMVIIP 119- +A+VNED N+GA ++ + ++ + +W V R A +GL KG Y ++IIP Sbjct: 54 EVAVVNEDMGADFNGTHLNVGAEFVSELRKNRNFDWQFVDRSDAMDGLRKGKYYAVLIIP 113- Query: 120 NNFSQKLLDVNKANAEQTTISYKVNAKGNLALEKKATEKEKDIVSELNSHLVNMYMASIL 17- 9 NFS LL + Q +I Y VN K N + + +++NS +V + Sbjct: 114 GNFSSDLLSIKNGTPRQASIKYMVNDKLNPVAPRITNAGADALQAKINSEVVKTIDGIVF 17- 3 Query: 180 SNLYTAQENVQA----------MVNVQSGNISNYQKNLLDSATNF---QNIFPAL----- 22- 1 + A E +A VN +GN+ + L + ++ QN++ +L Sbjct: 174 GKISEAGELARANRDDILRTKRFVNELNGNLGKIDETLSTANSDLEKGQNLWSSLKTDLP 23- 3 Query: 222 -VNQSSSSITANESLKKS------------LEASDNMFNDLVTTQTNTGKDLSSL----- 26- 3 + +++ + SL +S +++ ++ ++ +T+ L+SL Sbjct: 234 EIRDNANFVKEKYSLLESYIGKDPAKALSTVQSMESHLSEAITSMKYLRAVLASLYSATG 29- 3 Query: 264 -------IEQRHQDSISYEAFSTSLLEMNNELLEKQLSDIITQAQKDQETLSSQLNSIMG 31- 6 I+Q + + L + ++L K +D I + + + + S LN +M Sbjct: 294 DPKLKTAIDQIDTNIEKASSVLGILQTIESDLKTKGTTDRIVKLKASIDRMDSALNKLMD 35- 3 Query: 317 D-DNNHNHKENSSAYLNVARQKIQELSEALKSQDNIAKDQSEQLDKIVREGLASYFAKNN 37- 5 D +++SA L +A + + A+ +D S +L+ I + L S + Sbjct: 354 SRDEIDAAMQDASAKLGIANARWPTMRSAI-------QDASRKLNMISDDDLNSLVKLAD 40- 6 Query: 376 KDNITLLELLKSHSTNEK----TLKDFKAKVADF 405 D + E +S EK +K++ + +A F Sbjct: 407 IDPSAVREYFRSPVRMEKEHIYPVKNYGSALAPF 440 SEQ ID 8634 (GBS250) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 47 (lane 4; MW 136 kDa). GBS250-GST was purified as shown in FIG. 203, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 656 A DNA sequence (GBSx0696) was identified in S. agalactiae <SEQ ID 2019> which encodes the amino acid sequence <SEQ ID 2020>. Analysis of this protein sequence reveals the following: TABLE-US-01935 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5009(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01936 >GP: CAA46375 GB: X65276 ORFA1 [Clostridium acetobutylicum] Identities = 35/91 (38%), Positives = 53/91 (57%) Query: 1 MAQIKLTPEELRSSAQKYTAGSQQVTEVLNLLTQEQAVIDENWDGSTFDSFEAQFNELSP 60 MAQI +TPEEL+S AQ Y +++ + + + + I E W G F ++ Q+N+L Sbjct: 1 MAQISVTPEELKSQAQVYIQSKEEIDQAIQKVNSMNSTIAEEWKGQAFQAYLEQYNQLHQ 60 Query: 61 KITEFAQLLEDINQQLLKVADIIEQTDADIA 91 + +F LLE +NQQL K AD + + DA A Sbjct: 61 TVVQFENLLESVNQQLNKYADTVAERDAQDA 91 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 657 A DNA sequence (GBSx0697) was identified in S. agalactiae <SEQ ID 2021> which encodes the amino acid sequence <SEQ ID 2022>. Analysis of this protein sequence reveals the following: TABLE-US-01937 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3741(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 658 A repeated DNA sequence (GBSx0698) was identified in S. agalactiae <SEQ ID 2023> which encodes the amino acid sequence <SEQ ID 2024>. This protein is predicted to be carbamoylphosphate synthetase (carB). Analysis of this protein sequence reveals the following: TABLE-US-01938 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -1.33 Transmembrane 807-823 (807-823) ----- Final Results ----- bacterial membrane --- Certainty = 0.1532(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01939 >GP: CAA03928 GB: AJ000109 carbamoylphosphate synthetase [Lactococcus lactis] Identities = 771/1062 (72%), Positives = 901/1062 (84%), Gaps = 5/1062 (0%) Query: 1 MPKRTDIRKIMVIGSGPIVIGQAAEFDYSGTQACLSLKEEGYQVVLVNSNPATIMTDKDI 60 MPKR DI+KIM+IGSGPI+IGQAAEFDY+GT+ACL+LKEEGY+VVLVNSNPATIMTD++I Sbjct: 1 MPKRNDIKKIMIIGSGPIIIGQAAEFDYAGTEACLALKEEGYEVVLVNSNPATIMTDREI 60 Query: 61 ADKVYIEPITLEFVTRILRKERPDALLPTLGGQTGLNMAMALSKNGILEELNVELLGTKL 120- AD VYIEPITLEFV++ILRKERPDALLPTLGGQTGLNMAM LSK GILEELNVELLGTKL Sbjct: 61 ADTVYIEPITLEFVSKILRKERPDALLPTLGGQTGLNMAMELSKTGILEELNVELLGTKL 120- Query: 121 SAIDKAEDRDLFKQLMEELNQPIPESEIVNSVEEAIQFAEQIGYPLIVRPAFTLGGTGGG 18- 0 SAID+AEDR+LFK+L E +N+P+ S+I +VEEAI A++IGYP+IV PAFT+GGTGGG Sbjct: 121 SAIDQAEDRELFKELCESINEPLCASDIATTVEEAINIADKIGYPIIVGPAFTMGGTGGG 18- 0 Query: 181 MCDNQEQLVDITTKGLKLSPVTQCLIERSIAGFKEIEYEVMRDAADNALVVCNMENFDPV 24- 0 +CD +E+L +I GLKLSPVTQCLIE SIAG+KEIEYEVMRD+ADNA+VVCNMENFDPV Sbjct: 181 ICDTEEELREIVANGLKLSPVTQCLIEESIAGYKEIEYEVMRDSADNAIVVCNMENFDPV 24- 0 Query: 241 GIHTGDSIVFAPAQTLSDVENQLLRDASLDIIRALKIEGGCNVQLALDPNSFKYYVIEVN 30- 0 G+HTGDSIVFAP+QTLSD E Q+LRDASL+IIRALKIEGGCNVQLALDPNS++Y VIEVN Sbjct: 241 GVHTGDSIVFAPSQTLSDNEYQMLRDASLNIIRALKIEGGCNVQLALDPNSYEYRVIEVN 30- 0 Query: 301 PRVSRSSALASKATGYPIAKLAAKIAVGLTLDEVINPITKTTYAMFEPALDYVVAKMPRF 36- 0 PRVSRSSALASKATGYPIAK++AKIA+G+TLDE+INP+T TYAMFEPALDYVVAK+ RF Sbjct: 301 PRVSRSSALASKATGYPIAKMSAKIAIGMTLDEIINPVTNKTYAMFEPALDYVVAKIARF 36- 0 Query: 361 PFDKFESGDRKLGTQMKATGEVMAIGRNIEESLLKACRSLEIGVDHIKIADLDNVSDDVL 42- 0 PFDKFE+GDR LGTQMKATGEVMAIGRNIEESLLKA RSLEIGV H ++ + D+ L Sbjct: 361 PFDKFENGDRHLGTQMKATGEVMAIGRNIEESLLKAVRSLEIGVFHNEMTEAIEADDEKL 42- 0 Query: 421 LEKIRKAEDDRLFYLAEALRRHYSIEKLASLTSIDSFFLDKLRVIVELEDLLSKNRLDIN 48- 0 EK+ K +DDRLFY++EA+RR IE++A LT ID FFLDKL IVE+E+ L N + Sbjct: 421 YEKMVKTQDDRLFYVSEAIRRGIPIEEIADLTKIDIFFLDKLLYIVEIENQLKVNIFEPE 48- 0 Query: 481 ILKKVKNKGFSDKAIASLWQINEDQVRNMRKEAGILPVYKMVDTCASEFDSATPYFYSTY 54- 0 +LK K GFSD+ IA LW + ++VR R+E I+PVYKMVDTCA+EF+S+TPYFYSTY Sbjct: 481 LLKTAKKNGFSDREIAKLWNVTPEEVRRRRQENKIIPVYKMVDTCAAEFESSTPYFYSTY 54- 0 Query: 541 AVENESLISDKASILVLGSGPIRIGQGVEFDYATVHSVKAIRESGFEAIIMNSNPETVST 60- 0 ENES SDK I+VLGSGPIRIGQGVEFDYATVH VKAI+ G EAI++NSNPETVST Sbjct: 541 EWENESKRSDKEKIIVLGSGPIRIGQGVEFDYATVHCVKAIQALGKEAIVINSNPETVST 60- 0 Query: 601 DFSISDKLYFEPLTFEDVMNVIDLEKPEGVILQFGGQTAINLAKDLNKAGVKILGTQLED 66- 0 DFSISDKLYFEPLTFEDVMNVIDLE+P VI+QFGGQTAINLA+ L+KAGVKILGTQ+ED Sbjct: 601 DFSISDKLYFEPLTFEDVMNVIDLEEPLVVIVQFGGQTAINLAEHLSKAGVKILGTQVED 66- 0 Query: 661 LDRAENRKQFEATLQALNIPQPPGFTATTEEEAVNAAQKIGYPVLVRPSYVLGGRAMKIV 72- 0 LDRAE+R FE LQ L+IPQPPG TAT EEEAV A KIGYPVL+RPS+VLGGRAM+I+ Sbjct: 661 LDRAEDRDLFEKALQDLDIPQPPGATATNEEEAVANANKIGYPVLIRPSFVLGGRAMEII 72- 0 Query: 721 ENEEDLRHYMTTAVKASPDHPVLIDAYLIGKECEVDAISDGQNILIPGIMEHIERSGVHS 78- 0 NE+DLR YM AVKASP+HPVL+D+YL G+ECEVDAI DG+ +L+PGIMEHIER+GVHS Sbjct: 721 NNEKDLRDYMNRAVKASPEHPVLVDSYLQGQECEVDAICDGKEVLLPGIMEHIERAGVHS 78- 0 Query: 781 GDSMAVYPPQTLSETIIETIVDYTKRLAIGLNCIGMMNIQFVIKDQKVYVIEVNPRASRT 84- 0 GDSMAVYPPQ LS+ II+TIVDYTKRLAIGLNCIGMMNIQFVI +++VYVIEVNPRASRT Sbjct: 781 GDSMAVYPPQNLSQAIIDTIVDYTKRLAIGLNCIGMMNIQFVIYEEQVYVIEVNPRASRT 84- 0 Query: 841 LPFLSKVTHIPMAQVATKVILGDKLCNFTYGYDLYPASDMVHIKAPVFSFTKLAKVDSLL 90- 0 +PFLSKVT+IPMAQ+AT++ILG+ L + Y L P DMVH+KAPVFSFTKLAKVDSLL Sbjct: 841 VPFLSKVTNIPMAQLATQMILGENLKDLGYEAGLAPTPDMVHVKAPVFSFTKLAKVDSLL 90- 0 Query: 901 GPEMKSTGEVMGSDINLQKALYKAFEAAYLHMPDYGNIVFTVDDTDKEEALELAKVYQSI 96- 0 GPEMKSTG MGSD+ L+KALYK+FEAA LHM DYG+++FTV D DKEE L LAK + I Sbjct: 901 GPEMKSTGLAMGSDVTLEKALYKSFEAAKLHMADYGSVLFTVADEDKEETLALAKDFAEI 96- 0 Query: 961 GYRIYATQGTAIYFDANGLETVLVGKL--GENDRNHIPDLIKNGKIQAVINTVGQNNID- 10- 17 GY + AT GTA + NGL V KL GE++ + + I+ G++QAV+NT+G Sbjct: 961 GYSLVATAGTAAFLKENGLYVREVEKLAGGEDEEGTLVEDIRQGRVQAVVNTMGNTRASL 10- 20 Query: 1018 --NHDALIIRRSAIEQGVPLFTSLDTAHAMFKVLESRAFTLK 1057 D IR+ AI +G+PLFTSLDT A+ KV++SR+FT K Sbjct: 1021 TTATDGFRIRQEAISRGIPLFTSLDTVAAILKVMQSRSFTTK 1062 A related DNA sequence was identified in S. pyogenes <SEQ ID 2025> which encodes the amino acid sequence <SEQ ID 2026>. Analysis of this protein sequence reveals the following: TABLE-US-01940 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.17 Transmembrane 773-789 (773-789) ----- Final Results ----- bacterial membrane --- Certainty = 0.1468(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01941 >GP: CAA03928 GB: AJ000109 carbamoylphosphate synthetase [Lactococcus lactis] Identities = 753/1030 (73%), Positives = 876/1030 (84%), Gaps = 6/1030 (0%) Query: 1 LALKEEGYKVILVNSNPATIMTDKEIADKVYIEPLTLEFVNRIIRKERPDAILPTLGGQT 60 LALKEEGY+V+LVNSNPATIMTD+EIAD VYIEP+TLEFV++I+RKERPDA+LPTLGGQT Sbjct: 35 LALKEEGYEVVLVNSNPATIMTDREIADTVYIEPITLEFVSKILRKERPDALLPTLGGQT 94 Query: 61 GLNMAMALSKAGILDDLEIELLGTKLSAIDQAEDRDLFKQLMQELDQPIPESTIVKTVDE 120- GLNMAM LSK GIL++L +ELLGTKLSAIDQAEDR+LFK+L + +++P+ S I TV+E Sbjct: 95 GLNMAMELSKTGILEELNVELLGTKLSAIDQAEDRELFKELCESINEPLCASDIATTVEE 154- Query: 121 AVTFARDIGYPVIVRPAFTLGGTGGGICSSEEELCEITENGLKLSPVTQCLIERSIAGFK 18- 0 A+ A IGYP+IV PAFT+GGTGGGIC +EEEL EI NGLKLSPVTQCLIE SIAG+K Sbjct: 155 AINIADKIGYPIIVGPAFTMGGTGGGICDTEEELREIVANGLKLSPVTQCLIEESIAGYK 21- 4 Query: 181 EIEYEVMRDSADNALVVCNMENFDPVGIHTGDSIVFAPTQTLSDIENQMLRDASLKIIRA 24- 0 EIEYEVMRDSADNA+VVCNMENFDPVG+HTGDSIVFAP+QTLSD E QMLRDASL IIRA Sbjct: 215 EIEYEVMRDSADNAIVVCNMENFDPVGVHTGDSIVFAPSQTLSDNEYQMLRDASLNIIRA 27- 4 Query: 241 LKIEGGCNVQLALDPYSFKYYVIEVNPRVSRSSALASKATGYPIAKLAAKIAVGLTLDEM 30- 0 LKIEGGCNVQLALDP S++Y VIEVNPRVSRSSALASKATGYPIAK++AKIA+G+TLDE+ Sbjct: 275 LKIEGGCNVQLALDPNSYEYRVIEVNPRVSRSSALASKATGYPIAKMSAKIAIGMTLDEI 33- 4 Query: 301 INPITGTTYAMFEPALDYVVAKIPRFPFDKFEHGERQLGTQMKATGEVMAIGRNLEESLL 36- 0 INP+T TYAMFEPALDYVVAKI RFPFDKFE+G+R LGTQMKATGEVMAIGRN+EESLL Sbjct: 335 INPVTNKTYAMFEPALDYVVAKIARFPFDKFENGDRHLGTQMKATGEVMAIGRNIEESLL 39- 4 Query: 361 KACRSLEIGVCHNEMTSLSNISDEELVTKVIKAQDDRLFYLSEAIRRGYSIEELESLTKI 42- 0 KA RSLEIGV HNEMT DE+L K++K QDDRLFY+SEAIRRG IEE+ LTKI Sbjct: 395 KAVRSLEIGVFHNEMTEAIEADDEKLYEKMVKTQDDRLFYVSEAIRRGIPIEEIADLTKI 45- 4 Query: 421 DLFFLDKLLHIVEIEQELQMHVDHLESLKKAKRYGFSDQKIAEIWQKDESDIRAMRHSHS 48- 0 D+FFLDKLL+IVEIE +L++++ E LK AK+ GFSD++IA++W ++R R + Sbjct: 455 DIFFLDKLLYIVEIENQLKVNIFEPELLKTAKKNGFSDREIAKLWNVTPEEVRRRRQENK 51- 4 Query: 481 LYPVYKMVDTCAAEFDAKTPYFYSTYELENESVQSNKESILVLGSGPIRIGQGVEFDYAT 54- 0 + PVYKMVDTCAAEF++ TPYFYSTYE ENES +S+KE I+VLGSGPIRIGQGVEFDYAT Sbjct: 515 IIPVYKMVDTCAAEFESSTPYFYSTYEWENESKRSDKEKIIVLGSGPIRIGQGVEFDYAT 57- 4 Query: 541 VHSVKAIQKAGYEAIIMNSNPETVSTDFSVSDKLYFEPLTFEDVMNVIDLEQPKGVIVQF 60- 0 VH VKAIQ G EAI++NSNPETVSTDFS+SDKLYFEPLTFEDVMNVIDLE+P VIVQF Sbjct: 575 VHCVKAIQALGKEAIVINSNPETVSTDFSISDKLYFEPLTFEDVMNVIDLEEPLVVIVQF 63- 4 Query: 601 GGQTAINLAQALSEAGVTILGTQVEDLDRAEDRDLFEKALKELGIPQPQGQTATNEEEAL 66- 0 GGQTAINLA+ LS+AGV ILGTQVEDLDRAEDRDLFEKAL++L IPQP G TATNEEEA+ Sbjct: 635 GGQTAINLAEHLSKAGVKILGTQVEDLDRAEDRDLFEKALQDLDIPQPPGATATNEEEAV 69- 4 Query: 661 EAAKKIGFPVLVRPSYVLGGRAMEIVENKEDLREYIRTAVKASPEHPILVDSYIFGKECE 72- 0 A KIG+PVL+RPS+VLGGRAMEI+ N++DLR+Y+ AVKASPEHP+LVDSY+ G+ECE Sbjct: 695 ANANKIGYPVLIRPSFVLGGRAMEIINNEKDLRDYMNRAVKASPEHPVLVDSYLQGQECE 75- 4 Query: 721 VDAISDGKSVLIPGIMEHIERAGVHSGDSMAVYPPQQLSKQIQETIAEYTKRLAIGLNCI 78- 0 VDAI DGK VL+PGIMEHIERAGVHSGDSMAVYPPQ LS+ I +TI +YTKRLAIGLNCI Sbjct: 755 VDAICDGKEVLLPGIMEHIERAGVHSGDSMAVYPPQNLSQAIIDTIVDYTKRLAIGLNCI 81- 4 Query: 781 GMMNVQFVIKNEQVYVIEVNPRASRTVPFLSKVTGIPMAQIATKLILGQTLKDLGYEDGL 84- 0 GMMN+QFVI EQVYVIEVNPRASRTVPFLSKVT IPMAQ+AT++ILG+ LKDLGYE GL Sbjct: 815 GMMNIQFVIYEEQVYVIEVNPRASRTVPFLSKVTNIPMAQLATQMILGENLKDLGYEAGL 87- 4 Query: 841 YPQSPLVHIKAPVFSFTKLAQVDSLLGPEMKSTGEVMGSDTSLEKALYKAFEANNSHLSE 90- 0 P +VH+KAPVFSFTKLA+VDSLLGPEMKSTG MGSD +LEKALYK+FEA H+++ Sbjct: 875 APTPDMVHVKAPVFSFTKLAKVDSLLGPEMKSTGLAMGSDVTLEKALYKSFEAAKLHMAD 93- 4 Query: 901 FGQIVFTIADDSKAEALSLARRFKAIGYQIMATQGTAAYFAEQGLSACLVGKIGDAANDI 96- 0 +G ++FT+AD+ K E L+LA+ F IGY ++AT GTAA+ E GL V K+ ++ Sbjct: 935 YGSVLFTVADEDKEETLALAKDFAEIGYSLVATAGTAAFLKENGLYVREVEKLAGGEDEE 99- 4 Query: 961 PTLV---RHGHVQAIVNTVGIKR---TADKDGQMIRSSAIEQGVPLFTALDTAKAMLTVL 10- 14 TLV R G VQA+VNT+G R T DG IR AI +G+PLFT+LDT A+L V+ Sbjct: 995 GTLVEDIRQGRVQAVVNTMGNTRASLTTATDGFRIRQEAISRGIPLFTSLDTVAAILKVM 10- 54 Query: 1015 ESRCFNIEAI 1024 +SR F + I Sbjct: 1055 QSRSFTTKNI 1064 Identities = 141/389 (36%), Positives = 222/389 (56%), Gaps = 16/389 (4%) Query: 518 ESILVLGSGPIRIGQGVEFDYATVHSVKAIQKAGYEAIIMNSNPETVSTDFSVSDKLYFE 57- 7 + I+++GSGPI IGQ EFDYA + A+++ GYE +++NSNP T+ TD ++D +Y E Sbjct: 8 KKIMIIGSGPIIIGQAAEFDYAGTEACLALKEEGYEVVLVNSNPATIMTDREIADTVYIE 67 Query: 578 PLTFEDVMNVIDLEQPKGVIVQFGGQTAINLAQALSEAG------VTILGTQVEDLDRAE 63- 1 P+T E V ++ E+P ++ GGQT +N+A LS+ G V +LGT++ +D+AE Sbjct: 68 PITLEFVSKILRKERPDALLPTLGGQTGLNMAMELSKTGILEELNVELLGTKLSAIDQAE 127- Query: 632 DRDLFEKALKELGIPQPQGQTATNEEEALEAAKKIGFPVLVRPSYVLGGRAMEIVENKED 69- 1 DR+LF++ + + P AT EEA+ A KIG+P++V P++ +GG I + +E+ Sbjct: 128 DRELFKELCESINEPLCASDIATTVEEAINIADKIGYPIIVGPAFTMGGTGGGICDTEEE 18- 7 Query: 692 LREYIRTAVKASPEHPILVDSYIFG-KECEVDAISD-GKSVLIPGIMEHIERAGVHSGDS 74- 9 LRE + +K SP L++ I G KE E + + D + ++ ME+ + GVH+GDS Sbjct: 188 LREIVANGLKLSPVTQCLIEESIAGYKEIEYEVMRDSADNAIVVCNMENFDPVGVHTGDS 24- 7 Query: 750 MAVYPPQQLSKQIQETIAEYTKRLAIGLNCIGMMNVQFVI--KNEQVYVIEVNPRASRTV 80- 7 + P Q LS + + + + + L G NVQ + + + VIEVNPR SR+ Sbjct: 248 IVFAPSQTLSDNEYQMLRDASLNIIRALKIEGGCNVQLALDPNSYEYRVIEVNPRVSRSS 30- 7 Query: 808 PFLSKVTGIPMAQIATKLILGQTLKDL--GYEDGLY----PQSPLVHIKAPVFSFTKLAQ 86- 1 SK TG P+A+++ K+ +G TL ++ + Y P V K F F K Sbjct: 308 ALASKATGYPIAKMSAKIAIGMTLDEIINPVTNKTYAMFEPALDYVVAKIARFPFDKFEN 36- 7 Query: 862 VDSLLGPEMKSTGEVMGSDTSLEKALYKA 890 D LG +MK+TGEVM ++E++L KA Sbjct: 368 GDRHLGTQMKATGEVMAIGRNIEESLLKA 396 An alignment of the GAS and GBS proteins is shown below:

TABLE-US-01942 Identities = 777/1025 (75%), Positives = 896/1025 (86%), Gaps = 1/1025 (0%) Query: 35 LSLKEEGYQVVLVNSNPATIMTDKDIADKVYIEPITLEFVTRILRKERPDALLPTLGGQT 94 - L+LKEEGY+V+LVNSNPATIMTDK+IADKVYIEP+TLEFV RI+RKERPDA+LPTLGGQT Sbjct: 1 LALKEEGYKVILVNSNPATIMTDKEIADKVYIEPLTLEFVNRIIRKERPDAILPTLGGQT 60 Query: 95 GLNMAMALSKNGILEELNVELLGTKLSAIDKAEDRDLFKQLMEELNQPIPESEIVNSVEE 154- GLNMAMALSK GIL++L +ELLGTKLSAID+AEDRDLFKQLM+EL+QPIPES IV +V+E Sbjct: 61 GLNMAMALSKAGILDDLEIELLGTKLSAIDQAEDRDLFKQLMQELDQPIPESTIVKTVDE 120- Query: 155 AIQFAEQIGYPLIVRPAFTLGGTGGGMCDNQEQLVDITTKGLKLSPVTQCLIERSIAGFK 21- 4 A+ FA IGYP+IVRPAFTLGGTGGG+C ++E+L +IT GLKLSPVTQCLIERSIAGFK Sbjct: 121 AVTFARDIGYPVIVRPAFTLGGTGGGICSSEEELCEITENGLKLSPVTQCLIERSIAGFK 18- 0 Query: 215 EIEYEVMRDAADNALVVCNMENFDPVGIHTGDSIVFAPAQTLSDVENQLLRDASLDIIRA 27- 4 EIEYEVMRD+ADNALVVCNMENFDPVGIHTGDSIVFAP QTLSD+ENQ+LRDASL IIRA Sbjct: 181 EIEYEVMRDSADNALVVCNMENFDPVGIHTGDSIVFAPTQTLSDIENQMLRDASLKIIRA 24- 0 Query: 275 LKIEGGCNVQLALDPNSFKYYVIEVNPRVSRSSALASKATGYPIAKLAAKIAVGLTLDEV 33- 4 LKIEGGCNVQLALDP SFKYYVIEVNPRVSRSSALASKATGYPIAKLAAKIAVGLTLDE+ Sbjct: 241 LKIEGGCNVQLALDPYSFKYYVIEVNPRVSRSSALASKATGYPIAKLAAKIAVGLTLDEM 30- 0 Query: 335 INPITKTTYAMFEPALDYVVAKMPRFPFDKFESGDRKLGTQMKATGEVMAIGRNIEESLL 39- 4 INPIT TTYAMFEPALDYVVAK+PRFPFDKFE G+R+LGTQMKATGEVMAIGRN+EESLL Sbjct: 301 INPITGTTYAMFEPALDYVVAKIPRFPFDKFEHGERQLGTQMKATGEVMAIGRNLEESLL 36- 0 Query: 395 KACRSLEIGVDHIKIADLDNVSDDVLLEKIRKAEDDRLFYLAEALRRHYSIEKLASLTSI 45- 4 KACRSLEIGV H ++ L N+SD+ L+ K+ KA+DDRLFYL+EA+RR YSIE+L SLT I Sbjct: 361 KACRSLEIGVCHNEMTSLSNISDEELVTKVIKAQDDRLFYLSEAIRRGYSIEELESLTKI 42- 0 Query: 455 DSFFLDKLRVIVELEDLLSKNRLDINILKKVKNKGFSDKAIASLWQINEDQVRNMRKEAG 51- 4 D FFLDKL IVE+E L + + LKK K GFSD+ IA +WQ +E +R MR Sbjct: 421 DLFFLDKLLHIVEIEQELQMHVDHLESLKKAKRYGFSDQKIAEIWQKDESDIRAMRHSHS 48- 0 Query: 515 ILPVYKMVDTCASEFDSATPYFYSTYAVENESLISDKASILVLGSGPIRIGQGVEFDYAT 57- 4 + PVYKMVDTCA+EFD+ TPYFYSTY +ENES+ S+K SILVLGSGPIRIGQGVEFDYAT Sbjct: 481 LYPVYKMVDTCAAEFDAKTPYFYSTYELENESVQSNKESILVLGSGPIRIGQGVEFDYAT 54- 0 Query: 575 VHSVKAIRESGFEAIIMNSNPETVSTDFSISDKLYFEPLTFEDVMNVIDLEKPEGVILQF 63- 4 VHSVKAI+++G+EAIIMNSNPETVSTDFS+SDKLYFEPLTFEDVMNVIDLE+P+GVI+QF Sbjct: 541 VHSVKAIQKAGYEAIIMNSNPETVSTDFSVSDKLYFEPLTFEDVMNVIDLEQPKGVIVQF 60- 0 Query: 635 GGQTAINLAKDLNKAGVKILGTQLEDLDRAENRKQFEATLQALNIPQPPGFTATTEEEAV 69- 4 GGQTAINLA+ L++AGV ILGTQ+EDLDRAE+R FE L+ L IPQP G TAT EEEA+ Sbjct: 601 GGQTAINLAQALSEAGVTILGTQVEDLDRAEDRDLFEKALKELGIPQPQGQTATNEEEAL 66- 0 Query: 695 NAAQKIGYPVLVRPSYVLGGRAMKIVENEEDLRHYMTTAVKASPDHPVLIDAYLIGKECE 75- 4 AA+KIG+PVLVRPSYVLGGRAM+IVEN+EDLR Y+ TAVKASP+HP+L+D+Y+ GKECE Sbjct: 661 EAAKKIGFPVLVRPSYVLGGRAMEIVENKEDLREYIRTAVKASPEHPILVDSYIFGKECE 72- 0 Query: 755 VDAISDGQNILIPGIMEHIERSGVHSGDSMAVYPPQTLSETIIETIVDYTKRLAIGLNCI 81- 4 VDAISDG+++LIPGIMEHIER+GVHSGDSMAVYPPQ LS+ I ETI +YTKRLAIGLNCI Sbjct: 721 VDAISDGKSVLIPGIMEHIERAGVHSGDSMAVYPPQQLSKQIQETIAEYTKRLAIGLNCI 78- 0 Query: 815 GMMNIQFVIKDQKVYVIEVNPRASRTLPFLSKVTHIPMAQVATKVILGDKLCNFTYGYDL 87- 4 GMMN+QFVIK+++VYVIEVNPRASRT+PFLSKVT IPMAQ+ATK+ILG L + Y L Sbjct: 781 GMMNVQFVIKNEQVYVIEVNPRASRTVPFLSKVTGIPMAQIATKLILGQTLKDLGYEDGL 84- 0 Query: 875 YPASDMVHIKAPVFSFTKLAKVDSLLGPEMKSTGEVMGSDINLQKALYKAFEAAYLHMPD 93- 4 YP S +VHIKAPVFSFTKLA+VDSLLGPEMKSTGEVMGSD +L+KALYKAFEA H+ + Sbjct: 841 YPQSPLVHIKAPVFSFTKLAQVDSLLGPEMKSTGEVMGSDTSLEKALYKAFEANNSHLSE 90- 0 Query: 935 YGNIVFTVDDTDKEEALELAKVYQSIGYRIYATQGTAIYFDANGLETVLVGKLGENDRNH 99- 4 +G IVFT+ D K EAL LA+ +++IGY+I ATQGTA YF GL LVGK+G+ N Sbjct: 901 FGQIVFTIADDSKAEALSLARRFKAIGYQIMATQGTAAYFAEQGLSACLVGKIGD-AAND 95- 9 Query: 995 IPDLIKNGKIQAVINTVGQNNIDNHDALIIRRSAIEQGVPLFTSLDTAHAMFKVLESRAF 10- 54 IP L+++G +QA++NTVG + D +IR SAIEQGVPLFT+LDTA AM VLESR F Sbjct: 960 IPTLVRHGHVQAIVNTVGIKRTADKDGQMIRSSAIEQGVPLFTALDTAKAMLTVLESRCF 10- 19 Query: 1055 TLKVL 1059 ++ + Sbjct: 1020 NIEAI 1024 Identities = 145/387 (37%), Positives = 229/387 (58%), Gaps = 16/387 (4%) Query: 10 IMVIGSGPIVIGQAAEFDYSGTQACLSLKEEGYQVVLVNSNPATIMTDKDIADKVYIEPI 69 - I+V+GSGPI IGQ EFDY+ + ++++ GY+ +++NSNP T+ TD ++DK+Y EP+ Sbjct: 520 ILVLGSGPIRIGQGVEFDYATVHSVKAIQKAGYEAIIMNSNPETVSTDFSVSDKLYFEPL 57- 9 Query: 70 TLEFVTRILRKERPDALLPTLGGQTGLNMAMALSKNGILEELNVELLGTKLSAIDKAEDR 129- T E V ++ E+P ++ GGQT +N+A ALS+ G V +LGT++ +D+AEDR Sbjct: 580 TFEDVMNVIDLEQPKGVIVQFGGQTAINLAQALSEAG------VTILGTQVEDLDRAEDR 63- 3 Query: 130 DLFKQLMEELNQPIPESEIVNSVEEAIQFAEQIGYPLIVRPAFTLGGTGGGMCDNQEQLV 18- 9 DLF++ ++EL P P+ + + EEA++ A++IG+P++VRP++ LGG + +N+E L Sbjct: 634 DLFEKALKELGIPQPQGQTATNEEEALEAAKKIGFPVLVRPSYVLGGRAMEIVENKEDLR 69- 3 Query: 190 DITTKGLKLSPVTQCLIERSIAGFKEIEYEVMRDAADNALVVCNMENFDPVGIHTGDSIV 24- 9 + +K SP L++ I G KE E + + D + L+ ME+ + G+H+GDS+ Sbjct: 694 EYIRTAVKASPEHPILVDSYIFG-KECEVDAISD-GKSVLIPGIMEHIERAGVHSGDSMA 75- 1 Query: 250 FAPAQTLSDVENQLLRDASLDIIRALKIEGGCNVQLALDPNSFKYYVIEVNPRVSRSSAL 30- 9 P Q LS + + + + + L G NVQ + + + YVIEVNPR SR+ Sbjct: 752 VYPPQQLSKQIQETIAEYTKRLAIGLNCIGMMNVQFVI--KNEQVYVIEVNPRASRTVPF 80- 9 Query: 310 ASKATGYPIAKLAAKIAVGLTLDEVINPITKTTYAMFEPALDYVVAKMPRFPFDKFESGD 36- 9 SK TG P+A++A K+ +G TL ++ Y P V K P F F K D Sbjct: 810 LSKVTGIPMAQIATKLILGQTLKDL--GYEDGLY----PQSPLVHIKAPVFSFTKLAQVD 86- 3 Query: 370 RKLGTQMKATGEVMAIGRNIEESLLKA 396 LG +MK+TGEVM ++E++L KA Sbjct: 864 SLLGPEMKSTGEVMGSDTSLEKALYKA 890 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 659 A DNA sequence (GBSx0699) was identified in S. agalactiae <SEQ ID 2027> which encodes the amino acid sequence <SEQ ID 2028>. This protein is predicted to be carbamoyl phosphate synthetase small subunit (carA). Analysis of this protein sequence reveals the following: TABLE-US-01943 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2401 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01944 >GP: CAB89872 GB: AJ132624 carbamoyl phosphate synthetase small subunit [Lactococcus lactis] Identities = 242/355 (68%), Positives = 305/355 (85%) Query: 2 KRLLLLEDGSVFEGEAFGADVETSGEIVFSTGMTGYQESITDQSYNGQIITFTYPLIGNY 61 KRLL+LEDG++FEGEA GA+++ +GE+VF+TGMTGYQESITDQSYNGQI+TFTYP++GNY Sbjct: 3 KRLLILEDGTIFEGEALGANLDVTGELVFNTGMTGYQESITDQSYNGQILTFTYPIVGNY 62 Query: 62 GINRDDYESIRPTCKGVVIYEWAEYPSNWRQQMTLDEFLKLKGIPGISGIDTRALTKIIR 121- G+NRDDYESI PTCK VV++E A PSNWR QM+ DEFLK K IPGI+G+DTRA+TKI+R Sbjct: 63 GVNRDDYESIHPTCKAVVVHEAARRPSNWRMQMSFDEFLKSKNIPGITGVDTRAITKIVR 122- Query: 122 KHGTMKACLINEGNSIHEALENLQKSVLLNDQIEQVSTKLAYASPGVGKNIVLVDFGLKH 18- 1 +HGTMKA L+ + + + LQ +VL +Q+E ST AY SP G+ +V+VDFGLKH Sbjct: 123 EHGTMKASLVQARDEVDHQMSQLQATVLPTNQVETSSTATAYPSPNTGRKVVVVDFGLKH 18- 2 Query: 182 SILRELSQRQCHITVVPHTTTAQEILNLNPDGVLLSNGPGNPEQLPNALQMIQEIQGKIP 24- 1 SILRELS+R+C++TVVP+ T+A+EIL + PDGV+L+NGPG+P +P A++MI+E+QGKIP Sbjct: 183 SILRELSKRECNLTVVPYNTSAKEILEMEPDGVMLTNGPGDPTDVPEAIEMIKEVQGKIP 24- 2 Query: 242 IFGICMGHQLFAKANGAKTYKMTFGHRGFNHAVRHLQTGQVDFTSQNHGYAVSREDFPEA 30- 1 IFGIC+GHQLF+ ANGA TYKM FGHRGFNHAVR + TG++DFTSQNHGYAVS E+ PE Sbjct: 243 IFGICLGHQLFSLANGATTYKMKFGHRGFNHAVREVATGRIDFTSQNHGYAVSSENLPED 30- 2 Query: 302 LFITHEEINDKTVEGVRHKYYPAFSVQFHPDAAPGPHDTSYLFDEFINMIDDFQQ 356 L ITH EIND +VEGVRHKY+PAFSVQFHPDAAPGPHD SYLFD+F++++D+F++ Sbjct: 303 LMITHVEINDNSVEGVRHKYFPAFSVQFHPDAAPGPHDASYLFDDFMDLMDNFKK 357 A related DNA sequence was identified in S. pyogenes <SEQ ID 2029> which encodes the amino acid sequence <SEQ ID 2030>. Analysis of this protein sequence reveals the following: TABLE-US-01945 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3534 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01946 Identities = 265/354 (74%), Positives = 309/354 (86%) Query: 2 KRLLLLEDGSVFEGEAFGADVETSGEIVFSTGMTGYQESITDQSYNGQIITFTYPLIGNY 61 KRLL+LEDG++FEGE FGAD++ +GEIVF+TGMTGYQESITDQSYNGQI+TFTYPLIGNY Sbjct: 3 KRLLILEDGTIFEGEPFGADIDVTGEIVFNTGMTGYQESITDQSYNGQILTFTYPLIGNY 62 Query: 62 GINRDDYESIRPTCKGVVIYEWAEYPSNWRQQMTLDEFLKLKGIPGISGIDTRALTKIIR 121- GINRDDYESI PTCKGVV+ E + SNWR+QMTLD FLK+KGIPGISGIDTRALTKIIR Sbjct: 63 GINRDDYESISPTCKGVVVSEVSRLASNWRKQMTLDAFLKIKGIPGISGIDTRALTKIIR 122- Query: 122 KHGTMKACLINEGNSIHEALENLQKSVLLNDQIEQVSTKLAYASPGVGKNIVLVDFGLKH 18- 1 +HGTMKA + ++G+SI + L+ +VL + IEQVSTK AY +PG+GKNIVLVDFGLKH Sbjct: 123 QHGTMKATMADDGDSIQHLKDQLRATVLPTNTIEQVSTKTAYPAPGIGKNIVLVDFGLKH 18- 2 Query: 182 SILRELSQRQCHITVVPHTTTAQEILNLNPDGVLLSNGPGNPEQLPNALQMIQEIQGKIP 24- 1 SILRE S+RQC+ITVVP TA+E+L LNPDG++LSNGPGNPE LP AL MI+ +QGKIP Sbjct: 183 SILREFSKRQCNITVVPFNITAEEVLQLNPDGLMLSNGPGNPEDLPEALDMIRGVQGKIP 24- 2 Query: 242 IFGICMGHQLFAKANGAKTYKMTFGHRGFNHAVRHLQTGQVDFTSQNHGYAVSREDFPEA 30- 1 IFGICMGHQLF+ ANGAKT KMTFGHRGFNHAVR + TG++DFTSQNHGYAV R P+ Sbjct: 243 IFGICMGHQLFSLANGAKTCKMTFGHRGFNHAVREIATGRIDFTSQNHGYAVERSSLPDT 30- 2 Query: 302 LFITHEEINDKTVEGVRHKYYPAFSVQFHPDAAPGPHDTSYLFDEFINMIDDFQ 355 L +THE+INDKTVEGV+H+ +PAFSVQFHPDAAPGPHD SYLFDEF+ MID ++ Sbjct: 303 LMVTHEDINDKTVEGVKHRDFPAFSVQFHPDAAPGPHDASYLFDEFLEMIDSWR 356 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 660 A DNA sequence (GBSx0700) was identified in S. agalactiae <SEQ ID 2031> which encodes the amino acid sequence <SEQ ID 2032>. This protein is predicted to be aspartate carbamoyltransferase (pyrB). Analysis of this protein sequence reveals the following: TABLE-US-01947 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3260 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01948 >GP: AAF72727 GB: AF264709 aspartate transcarbamoylase [Enterococcus faecalis] Identities = 197/303 (65%), Positives = 250/303 (82%) Query: 5 TQTLSLEHFVSLEELSNQEVMSLIKRSIEVKENPSNIGFDKDYYVSNLFFENSTRTHKSF 64 ++ +SL+H ++ E L+++EVM LI+R+ E K+ ++ Y+ +NLFFENSTRTHKSF Sbjct: 5 SERISLKHLLTAEALTDREVMGLIRRAGEFKQGAKWHPEERQYFATNLFFENSTRTHKSF 64 Query: 65 EMAELKLGLKTIEFNADTSSVNKGETLYDTILTMSALGLDVCVIRHPDIDYYKELIASPN 124- E+AE KLGL+ IEF A SSV KGETLYDT+LTMSA+G+DV VIRH +YY ELI S Sbjct: 65 EVAEKKLGLEVIEFEASRSSVQKGETLYDTVLTMSAIGVDVAVIRHGKENYYDELIQSKT 124- Query: 125 IHSAIVNGGDGSGQHPSQSLLDLVTIYEEFGYFKGLKIAIVGDLTHSRVAKSNMQVLKRL 18- 4 I +I+NGGDGSGQHP+Q LLDL+TIYEEFG F+GLK+AIVGD+THSRVAKSNMQ+L RL Sbjct: 125 IQCSIINGGDGSGQHPTQCLLDLMTIYEEFGGFEGLKVAIVGDITHSRVAKSNMQLLNRL 18- 4 Query: 185 GAEIFFSGPKEWYSSQFDEYGQYLPIDQLVDQIDVLMLLRVQHERHDGKGVFSKESYHQQ 24- 4 GAEI+FSGP+EWY QFD YGQY+P+D++V+++DV+MLLRVQHERHDGK FSKE YH + Sbjct: 185 GAEIYFSGPEEWYDHQFDVYGQYVPLDEIVEKVDVMMLLRVQHERHDGKESFSKEGYHLE 24- 4 Query: 245 FGLTKERYKHLRDTAIIMHPAPVNRDVEIASDLVEADKARIVKQMSNGVYARIAILEAVL 30- 4 +GLT ER L+ AIIMHPAPVNRDVE+A +LVE+ ++RIV QMSNGV+ R+AILEA+L Sbjct: 245 YGLTNERATRLQKHAIIMHPAPVNRDVELADELVESLQSRIVAQMSNGVFMRMAILEAIL 30- 4 Query: 305 NSR 307 + + Sbjct: 305 HGK 307 A related DNA sequence was identified in S. pyogenes <SEQ ID 2033> which encodes the amino acid sequence <SEQ ID 2034>. Analysis of this protein sequence reveals the following: TABLE-US-01949 Possible site: 38 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01950 Identities = 208/300 (69%), Positives = 249/300 (82%) Query: 8 LSLEHFVSLEELSNQEVMSLIKRSIEVKENPSNIGFDKDYYVSNLFFENSTRTHKSFEMA 67 ++L + VS+E L+ +EV+ LI R E K I + V+NLFFENSTRTHKSFE+A Sbjct: 26 VALTNLVSMEALTTEEVLGLINRGSEYKAGKVVISDHQKDLVANLFFENSTRTHKSFEVA 85 Query: 68 ELKLGLKTIEFNADTSSVNKGETLYDTILTMSALGLDVCVIRHPDIDYYKELIASPNIHS 127- E KLGL ++FNAD S+VNKGE+LYDT+LTMSALG D+CVIRHP+ DYYKEL+ SP I + Sbjct: 86 EKKLGLTVLDFNADASAVNKGESLYDTVLTMSALGTDICVIRHPEDDYYKELVESPTITA 145- Query: 128 AIVNGGDGSGQHPSQSLLDLVTIYEEFGYFKGLKIAIVGDLTHSRVAKSNMQVLKRLGAE 18- 7 +IVNGGDGSGQHPSQ LLDL+TIYEEFG F+GLKIAI GDLTHSRVAKSNMQ+LKRLGAE Sbjct: 146 SIVNGGDGSGQHPSQCLLDLLTIYEEFGRFEGLKIAIAGDLTHSRVAKSNMQILKRLGAE 20- 5 Query: 188 IFFSGPKEWYSSQFDEYGQYLPIDQLVDQIDVLMLLRVQHERHDGKGVFSKESYHQQFGL 24- 7 ++F GP+EWYS F+ YG Y+ IDQ++ ++DVLMLLRVQHERHDG FSKE YHQ FGL Sbjct: 206 LYFYGPEEWYSEAFNAYGTYIAIDQIIKELDVLMLLRVQHERHDGHQSFSKEGYHQAFGL 26- 5 Query: 248 TKERYKHLRDTAIIMHPAPVNRDVEIASDLVEADKARIVKQMSNGVYARIAILEAVLNSR 30- 7 T+ERY+ L+D+AIIMHPAPVNRDVEIA LVEA KARIV QM+NGV+ R+AI+EA+LN R Sbjct: 266 TQERYQQLKDSAIIMHPAPVNRDVEIADSLVEAPKARIVSQMANGVFVRMAIIEAILNGR 32- 5 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 661 A DNA sequence (GBSx0701) was identified in S. agalactiae <SEQ ID 2035> which encodes the amino acid sequence <SEQ ID 2036>. Analysis of this protein sequence reveals the following: TABLE-US-01951 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2392(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01952 >GP: AAC06948 GB: AE000708 dihydroorotase [Aquifex aeolicus] Identities = 176/422 (41%), Positives = 255/422 (59%), Gaps = 8/422 (1%) Query: 11 IIKNGLIIDPQSGFNQVSDMLIDQGKIKQISKEIDIKGIPIIDASNKIVAPGLVDIHVHF 70 - I+KNG +IDP D+L++ GKIK+I K I + IIDA IV PG +DIHVH Sbjct: 5 IVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHL 64 Query: 71 REPGQTHKENIHTGALSAAVGGFTTVLMMANTNPTISSPEIVKQVKESAAKEAI-KIETV 129- R+PGQT+KE+I +G+ A GGFTT++ M NTNP I + +V + + + + ++ Sbjct: 65 RDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPT 124- Query: 130 ATITKSLNGKDLVNFEELLEAGVAGFSDDGIPLTDTKVLQEAMNLARKHDVVLSLHEEDP 18- 9 TITK GK++ +F L EAG F+DDG P+ D+ V+++A+ LA + V + H ED Sbjct: 125 GTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDHCEDD 18- 4 Query: 190 SLN-GVLGINEHIAQKIYHVCGASGLAEYSMIARDAMIAYQTQAKVHIQHLSSSESVEVV 24- 8 L GV INE + + + AE IARD ++A +T VHIQH+S+ S+E++ Sbjct: 185 KLAYGV--INEGEVSALLGLSSRAPEAEEIQIARDGILAQRTGGHVHIQHVSTKLSLEII 24- 2 Query: 249 DFAQKLGANLTAEVTPQHFSKTENLLLTKGANAKLNPPLRLEKDRQALIDGLKSGVISII 30- 8 +F ++ G +T EV P H TE +L GANA++NPPLR ++DR ALI+G+K G+I Sbjct: 243 EFFKEKGVKITCEVNPNHLLFTEREVLNSGANARVNPPLRKKEDRLALIEGVKRGIIDCF 30- 2 Query: 309 ASDHAPHHIMEKAADNISQAPSGMTGLETSLALGITYLVSTKELSMIDFLAKMTCNPAQL 36- 8 A+DHAPH EK + + A G+ GL+T+L + L +S+ + T NPA++ Sbjct: 303 ATDHAPHQTFEK--ELVEFAMPGIIGLQTALPSALE-LYRKGIISLKKLIEMFTINPARI 35- 9 Query: 369 YGFDAGYLREGGPADIVIFDQAEERIIKAEF-ASKSSNSPFIGDKLKGVIHYTICNGEIV 42- 7 G D G L+ G PADI IFD +E I+ E SKS N+P G LKG + YTI +G++V Sbjct: 360 IGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMV 41- 9 Query: 428 YQ 429 Y+ Sbjct: 420 YK 421 A related DNA sequence was identified in S. pyogenes <SEQ ID 2037> which encodes the amino acid sequence <SEQ ID 2038>. Analysis of this protein sequence reveals the following:

TABLE-US-01953 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.80 Transmembrane 76-92 (76-92) INTEGRAL Likelihood = -0.00 Transmembrane 286-302 (286-302) ----- Final Results ----- bacterial membrane --- Certainty = 0.132(Affirmative) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-01954 !GB: AE000708 dihydroorotase [Aquifex aeolicus] 316 3e-85 >GP: AAC06948 GB: AE000708 dihydroorotase [Aquifex aeolicus] Score = 316 bits (801), Expect = 3e-85 Identities = 177/422 (41%), Positives = 254/422 (59%), Gaps = 8/422 (1%) Query: 2 ILIKNGRVMDPKSQRDQVADVLIDGKQIVKIASAIECQEAQVIDASGLIVAPGLVDIHVH 61 +++KNG V+DP + D+L++ +I KI I EA++IDA GLIV PG +DIHVH Sbjct: 4 LIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVH 63 Query: 62 FREPGQTHKEDIHTGALAAAAGGVTTVVMMANTNPVISDVETLQEVLASAAKEKI-HIYT 120- R+PGQT+KEDI +G+ A AGG TT+V M NTNP I + + +L + + + Sbjct: 64 LRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLP 123- Query: 121 NASVTQAFNGKDVTDFKALLEAGAVSFSDDGIPLESSKVLKEAFDLANANQTFISLHEED 18- 0 ++T+ GK++ DF +L EAG V+F+DDG P+ S V+++A +LA+ I H ED Sbjct: 124 TGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDHCED 18- 3 Query: 181 PQL-NGVLGFNEGIAEEHFHFCGATGVAEYSMIARDVMIAYDRQAHVHIQHLSKAESVQV 23- 9 +L GV+ NEG AE IARD ++A HVHIQH+S S+++ Sbjct: 184 DKLAYGVI--NEGEVSALLGLSSRAPEAEEIQIARDGILAQRTGGHVHIQHVSTKLSLEI 24- 1 Query: 240 VAFAQQLGAKVTAEVSPQHFSTTEDLLLIAGTSAKMNPPLRTQRDRLAVIEGLKSGVITV 29- 9 + F ++ G K+T EV+P H TE +L +G +A++NPPLR + DRLA+IEG+K G+I Sbjct: 242 IEFFKEKGVKITCEVNPNHLLFTEREVLNSGANARVNPPLRKKEDRLALIEGVKRGIIDC 30- 1 Query: 300 IATDHAPHHKDEKTVDDMTKAPSGMTGLETSLSLGLTHLVEPGHLTLMSLLEKMTLNPAL 35- 9 ATDHAPH EK + + A G+ GL+T+L L L G ++L L+E T+NPA Sbjct: 302 FATDHAPHQTFEKELVEF--AMPGIIGLQTALPSAL-ELYRKGIISLKKLIEMFTINPAR 35- 8 Query: 360 LYGFDAGYLAENGPADLVIFADKQERLITENF-ASKASNSPFIGNKLKGVVKYTIADGEV 41- 8 + G D G L PAD+ IF +E ++ E SK+ N+P G LKG V YTI DG++ Sbjct: 359 IIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKM 41- 8 Query: 419 VY 420 VY Sbjct: 419 VY 420 An alignment of the GAS and GBS proteins is shown below: TABLE-US-01955 Identities = 269/420 (64%), Positives = 338/420 (80%) Query: 9 MYIIKNGLIIDPQSGFNQVSDMLIDQGKIKQISKEIDIKGIPIIDASNKIVAPGLVDIHV 68 M +IKNG ++DP+S +QV+D+LID +I +I+ I+ + +IDAS IVAPGLVDIHV Sbjct: 1 MILIKNGRVMDPKSQRDQVADVLIDGKQIVKIASAIECQEAQVIDASGLIVAPGLVDIHV 60 Query: 69 HFREPGQTHKENIHTGALSAAVGGFTTVLMMANTNPTISSPEIVKQVKESAAKEAIKIET 128- HFREPGQTHKE+IHTGAL+AA GG TTV+MMANTNP IS E +++V SAAKE I I T Sbjct: 61 HFREPGQTHKEDIHTGALAAAAGGVTTVVMMANTNPVISDVETLQEVLASAAKEKIHIYT 120- Query: 129 VATITKSLNGKDLVNFEELLEAGVAGFSDDGIPLTDTKVLQEAMNLARKHDVVLSLHEED 18- 8 A++T++ NGKD+ +F+ LLEAG FSDDGIPL +KVL+EA +LA + +SLHEED Sbjct: 121 NASVTQAFNGKDVTDFKALLEAGAVSFSDDGIPLESSKVLKEAFDLANANQTFISLHEED 18- 0 Query: 189 PSLNGVLGINEHIAQKIYHVCGASGLAEYSMIARDAMIAYQTQAKVHIQHLSSSESVEVV 24- 8 P LNGVLG NE IA++ +H CGA+G+AEYSMIARD MIAY QA VHIQHLS +ESV+VV Sbjct: 181 PQLNGVLGFNEGIAEEHFHFCGATGVAEYSMIARDVMIAYDRQAHVHIQHLSKAESVQVV 24- 0 Query: 249 DFAQKLGANLTAEVTPQHFSKTENLLLTKGANAKLNPPLRLEKDRQALIDGLKSGVISII 30- 8 FAQ+LGA +TAEV+PQHFS TE+LLL G +AK+NPPLR ++DR A+I+GLKSGVI++I Sbjct: 241 AFAQQLGAKVTAEVSPQHFSTTEDLLLIAGTSAKMNPPLRTQRDRLAVIEGLKSGVITVI 30- 0 Query: 309 ASDHAPHHIMEKAADNISQAPSGMTGLETSLALGITYLVSTKELSMIDFLAKMTCNPAQL 36- 8 A+DHAPHH EK D++++APSGMTGLETSL+LG+T+LV L+++ L KMT NPA L Sbjct: 301 ATDHAPHHKDEKTVDDMTKAPSGMTGLETSLSLGLTHLVEPGHLTLMSLLEKMTLNPALL 36- 0 Query: 369 YGFDAGYLREGGPADIVIFDQAEERIIKAEFASKSSNSPFIGDKLKGVIHYTICNGEIVY 42- 8 YGFDAGYL E GPAD+VIF +ER+I FASK+SNSPFIG+KLKGV+ YTI +GE+VY Sbjct: 361 YGFDAGYLAENGPADLVIFADKQERLITENFASKASNSPFIGNKLKGVVKYTIADGEVVY 42- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 662 A DNA sequence (GBSx0702) was identified in S. agalactiae <SEQ ID 2039> which encodes the amino acid sequence <SEQ ID 2040>. This protein is predicted to be orotate phosphoribosyltransferase PyrE (pyrE). Analysis of this protein sequence reveals the following: TABLE-US-01956 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2214(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01957 >GP: AAC95453 GB: AF068902 orotate phosphoribosyltransferase PyrE [Streptococcus pneumoniae] Identities = 152/208 (73%), Positives = 180/208 (86%) Query: 1 MDLARQIAMELLDIQAVYLRPQQPFTWASGVKSPIYTDNRVTLSYPETRTLIENGFVKQI 60 M LA+ IA LL IQAVYL+P++PFTWASG+KSPIYTDNRVTL+YPETRTLIENGFV I Sbjct: 1 MTLAKDIASHLLKIQAVYLKPEEPFTWASGIKSPIYTDNRVTLAYPETRTLIENGFVDAI 60 Query: 61 QKHFPNVDIIAGTATAGIPHGAIIADKMNLPFAYIRSKAKDHGVGNQIEGRVYSGQKMVI 120- ++ FP V++IAGTATAGIPHGAIIADKMNLPFAYIRSK KDHG GNQIEGRV GQKMV+ Sbjct: 61 KEAFPEVEVIAGTATAGIPHGAIIADKMNLPFAYIRSKPKDHGAGNQIEGRVAQGQKMVV 120- Query: 121 IEDLISTGGSVLEAVTAAQSQGIEVLGVVAIFTYQLAKAEQAFREADIPLVTLTDYNQLI 18- 0 +EDLISTGGSVLEAV AA+ +G +VLGVVAIF+YQL KA++ F +A + LVTL++Y++LI Sbjct: 121 VEDLISTGGSVLEAVAAAKREGADVLGVVAIFSYQLPKADKNFADAGVKLVTLSNYSELI 18- 0 Query: 181 KVAKVNGYITADQLVLLKKFKEDQMNWQ 208 +A+ GYIT + L LLK+FKEDQ NWQ Sbjct: 181 HLAQEEGYITPEGLDLLKRFKEDQENWQ 208 A related DNA sequence was identified in S. pyogenes <SEQ ID 2041> which encodes the amino acid sequence <SEQ ID 2042>. Analysis of this protein sequence reveals the following: TABLE-US-01958 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1612(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01959 Identities = 158/208 (75%), Positives = 179/208 (85%) Query: 1 MDLARQIAMELLDIQAVYLRPQQPFTWASGVKSPIYTDNRVTLSYPETRTLIENGFVKQI 60 M LA QIA +LLDI+AVYL+P+ PFTWASG+KSPIYTDNRVTLSYP+TR LIENGFV+ I Sbjct: 1 MTLASQIATQLLDIKAVYLKPEDPFTWASGIKSPIYTDNRVTLSYPKTRDLIENGFVETI 60 Query: 61 QKHFPNVDIIAGTATAGIPHGAIIADKMNLPFAYIRSKAKDHGVGNQIEGRVYSGQKMVI 120- + HFP V++IAGTATAGIPHGAIIADKM LPFAYIRSK KDHG GNQIEGRV GQKMVI Sbjct: 61 KAHFPEVEVIAGTATAGIPHGAIIADKMTLPFAYIRSKPKDHGAGNQIEGRVLKGQKMVI 120- Query: 121 IEDLISTGGSVLEAVTAAQSQGIEVLGVVAIFTYQLAKAEQAFREADIPLVTLTDYNQLI 18- 0 IEDLISTGGSVL+A AA +G +VLGVVAIFTY+L KA Q F+EA I L+TL++Y +LI Sbjct: 121 IEDLISTGGSVLDAAAAASREGADVLGVVAIFTYELPKASQNFKEAGIKLITLSNYTELI 18- 0 Query: 181 KVAKVNGYITADQLVLLKKFKEDQMNWQ 208 VAK+ GYIT D L LLKKFKEDQ+NWQ Sbjct: 181 AVAKLQGYITNDGLHLLKKFKEDQVNWQ 208 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 663 A DNA sequence (GBSx0703) was identified in S. agalactiae <SEQ ID 2043> which encodes the amino acid sequence <SEQ ID 2044>. This protein is predicted to be orotidine 5'-phosphate decarboxylase (pyrF). Analysis of this protein sequence reveals the following: TABLE-US-01960 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9829> which encodes amino acid sequence <SEQ ID 9830> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01961 >GP: AAC95452 GB: AF068902 orotidine-5'-decarboxylase PyrF [Streptococcus pneumoniae] Identities = 149/231 (64%), Positives = 176/231 (75%), Gaps = 1/231 (0%) Query: 19 MLEKCPIIALDFSDLASVTTFLEHFPKEELLFVKIGMELYYSEGPSIIRYIKSLGHRIFL 78 - M E PIIALDF +V FL FP EE L++K+GMELYY+ GP I+ Y+K LGH +FL Sbjct: 1 MREHRPIIALDFPSFEAVKEFLALFPAEESLYLKVGMELYYAAGPEIVSYLKGLGHSVFL 60 Query: 79 DLKLHDIPNTVRSSMSVLAKLGIDMTNVHAAGGVEMMKAAREGLGKGPILLAVTQLTSTS 138- DLKLHDIPNTV+S+M VL++LG+DMTNVHAAGGVEMMKAAREGLG L+AVTQLTSTS Sbjct: 61 DLKLHDIPNTVKSAMKVLSQLGVDMTNVHAAGGVEMMKAAREGLGSQAKLIAVTQLTSTS 120- Query: 139 QEQMQVDQHINLSVVDSVCHYAQKAQEAGLDGVVASAQEGMQIKKQTNEHFICLTPGIRP 19- 8 + QMQ Q+I S+ +SV HYA+K EAGLDGVV SAQE IK+ TN FICLTPGIRP Sbjct: 121 EAQMQEFQNIQTSLQESVIHYAKKTAEAGLDGVVCSAQEVQVIKQATNPDFICLTPGIRP 18- 0 Query: 199 PQTNQLDDQKRTMTPEQARIVGADYIVVGRPITKAENPYQAYLEIKEEWNR 249 + DQKR MTP A +G+DYIVVGRPIT+AE+P AY IK+EW + Sbjct: 181 AGV-AVGDQKRVMTPADAYQIGSDYIVVGRPITQAEDPVAAYHAIKDEWTQ 230 A related DNA sequence was identified in S. pyogenes <SEQ ID 2045> which encodes the amino acid sequence <SEQ ID 2046>. Analysis of this protein sequence reveals the following: TABLE-US-01962 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1934(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01963 Identities = 149/229 (65%), Positives = 180/229 (78%), Gaps = 1/229 (0%) Query: 19 MLEKCPIIALDFSDLASVTTFLEHFPKEELLFVKIGMELYYSEGPSIIRYIKSLGHRIFL 78 - M E+ PIIALDFS FL+ FP EE L+VKIGMELYY++GP I+RYIKSLGH +FL Sbjct: 1 MKEERPIIALDFSSFEETKAFLDLFPAEEKLYVKIGMELYYAQGPDIVRYIKSLGHNVFL 60 Query: 79 DLKLHDIPNTVRSSMSVLAKLGIDMTNVHAAGGVEMMKAAREGLGKGPILLAVTQLTSTS 138- DLKLHDIPNTVR++M+VL +L IDM VHAAGGVEM+KAAREGLG+GP L+AVTQLTSTS Sbjct: 61 DLKLHDIPNTVRAAMAVLKELDIDMATVHAAGGVEMLKAAREGLGQGPTLIAVTQLTSTS 120- Query: 139 QEQMQVDQHINLSVVDSVCHYAQKAQEAGLDGVVASAQEGMQIKKQTNEHFICLTPGIRP 19- 8 ++QM+ DQ+I S+++SV HY++ A +A LDG V SAQE IK T F CLTPGIRP Sbjct: 121 EDQMRGDQNIQTSLLESVLHYSKGAAKAQLDGAVCSAQEVEAIKAVTPTGFTCLTPGIRP 18- 0 Query: 199 PQTNQLDDQKRTMTPEQARIVGADYIVVGRPITKAENPYQAYLEIKEEW 247 +N + DQKR MTP QAR +G+DYIVVGRPIT+A++P AY IK EW Sbjct: 181 KGSN-IGDQKRVMTPNQARRIGSDYIVVGRPITQAKDPVAAYQAIKAEW 228 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 664 A DNA sequence (GBSx0704) was identified in S. agalactiae <SEQ ID 2047> which encodes the amino acid sequence <SEQ ID 2048> in others. Analysis of this protein sequence reveals the following: TABLE-US-01964 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.70 Transmembrane 192-208 (190-211) INTEGRAL Likelihood = -7.64 Transmembrane 226-242 (218-250) INTEGRAL Likelihood = -3.77 Transmembrane 388-404 (378-404) INTEGRAL Likelihood = -3.08 Transmembrane 293-309 (292-311) INTEGRAL Likelihood = -2.87 Transmembrane 165-181 (162-182) INTEGRAL Likelihood = -2.13 Transmembrane 267-283 (267-284) INTEGRAL Likelihood = -0.90 Transmembrane 114-130 (114-130) INTEGRAL Likelihood = -0.75 Transmembrane 318-334 (318-334) INTEGRAL Likelihood = -0.53 Transmembrane 140-156 (140-156) ----- Final Results ----- bacterial membrane --- Certainty = 0.4482(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01965 >GP: BAB03800 GB: AP001507 unknown conserved protein in others [Bacillus halodurans] Identities = 63/243 (25%), Positives = 120/243 (48%) Query: 5 MSVVLRAGKLLIESGAEVYRVEDTMKHFAKALQIENFEAYVVSSSIIASGINRYGKQEAK 64 M + + AG++++ +GAE YRVE+T++ AKA Q N ++V ++ I S + Sbjct: 8 MDICMLAGEIMLINGAETYRVEETLERMAKAGQFRNVHSFVTTTGIFLSFEEEGAGDVMQ 67 Query: 65 VCNTDGVTANLGRLEAVNNLSRQIAKQDLVSPEEIVKQLDLIEHQKDYSLLVTLISYFCG 124- + D +L ++ VN +SR+ ++ + E + K ++ + +YS L+ + Sbjct: 68 MIRVDDRMQDLNKVTLVNQVSREFVNGEIDAAEALTKLQNIAKQPMNYSPLLLHTASGVA 127- Query: 125 AGSFSLALGSSLLDSFSAAVTGLILGYFLNLMESRIHTGFLLTILGSSVVALSANLLYFS 18- 4 G+FS G +L D+ A + G + + ++S + F + + A LL Sbjct: 128 GGAFSYLFGGNLFDTLPAFIAGFVASMAVVHLQSYLKVRFFAEFMAAFTGGAVAILLVLI 18- 7 Query: 185 GLGEHRSIIILGALMVMVPGAAFVNSVREFSQNNFSTGLALIMSALLICISISAGVAITI 24- 4 GLGE+ +I+G LM +VPG N+VR+ + G+ + +SI+ G+A+ I Sbjct: 188 GLGENVDQVIIGTLMPLVPGIPLTNAVRDLISGDLLAGVTRGAECFVTSLSIATGIALAI 24- 7 Query: 245 EII 247 ++ Sbjct: 248 ALL 250 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 665 A DNA sequence (GBSx0705) was identified in S. agalactiae <SEQ ID 2049> which encodes the amino acid sequence <SEQ ID 2050>. This protein is predicted to be ABC transporter. Analysis of this protein sequence reveals the following: TABLE-US-01966 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5134(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9353> which encodes amino acid sequence <SEQ ID 9354> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01967 >GP: CAB12571 GB: Z99108 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 193/288 (67%), Positives = 231/288 (80%) Query: 1 MNDVINIVYHVENQDLVRYSGDYTNFESVYAMKKAQLEAAYERQQKEIADLQDFVNRNKA 60 +N VIN++YHVENQ+L RY GDY F VY +KK QLEAAY++QQ+E+A+L+DFV RNKA Sbjct: 222 LNSVINLIYHVENQELTRYVGDYHQFMEVYEVKKQQLEAAYKKQQQEVAELKDFVARNKA 28- 1 Query: 61 RVATRNMAMSRQKKLDKMDIIELQAEKPKPSFEFKESRTPGRFIFQAKDLQIGYDRALTK 120- RV+TRNMAMSRQKKLDKMD+IEL AEKPKP F FK +RT G+ IF+ KDL IGYD L++ Sbjct: 282 RVSTRNMAMSRQKKLDKMDMIELAAEKPKPEFHFKPARTSGKLIFETKDLVIGYDSPLSR 34- 1 Query: 121 PLNLTFERNQKIAIVGANGIGKTTLLKSLLGIIPPISGNVERGDFIDLGYFEQEVPGGNR 18- 0 PLNL ER QKIA+ GANGIGKTTLLKSLLG I P+ G+VERG+ I GYFEQEV N Sbjct: 342 PLNLRMERGQKIALYGANGIGKTTLLKSLLGEIQPLEGSVERGEHIYTGYFEQEVKETNN 40- 1 Query: 181 QTPLEAVWDAFPALNQAEVRAALARCGLTSKHIESQIQVLSGGEQSKVRFCLLMNRENNV 24- 0 T +E VW FP+ Q E+RAA A+CGLT+KHIES++ VLSGGE++KVR C L+N E N+ Sbjct: 402 NTCIEEVWSEFPSYTQYEIRAAPAKCGLTTKHIESRVSVLSGGEKAKVRLCKLINSETNL 46- 1 Query: 241 LVLDEPTNHLDVDAKDELKRALKAYKGSILMVCHEPDFYEGWMDDVWD 288 LVLDEPTNHLD DAK+ELKRALK YKGSIL++ HEPDFY + W+ Sbjct: 462 LVLDEPTNHLDADAKEELKRALKEYKGSILLISHEPDFYMDIATETWN 509 Identities = 56/219 (25%), Positives = 97/219 (43%), Gaps = 44/219 (20%) Query: 104 IFQAKDLQIGY-DRALTKPLNLTFERNQKIAIVGANGIGKTTLLKSLLGIIPPISGNVER 16- 2 I KDL G+ DRA+ ++ + + + ++GANG GK+T + + G + P G VE Sbjct: 3 ILSVKDLSHGFGDRAIFNNVSFRLLKGEHVGLIGANGEGKSTFMNIITGKLEPDEGKVEW 62 Query: 163 GDFIDLGYFEQEVPGGNRQTPLEAVWDAFPALNQAE------------------------ 19- 8 + +GY +Q ++ + + DAF L E Sbjct: 63 SKNVRVGYLDQHTVLEKGKSIRDVLKDAFHYLFAMEEEMNEIYNKMGEADPDELEKLLEE 122- Query: 199 ---VRAALAR----------------CGLTSKHIESQIQVLSGGEQSKVRFCLLMNRENN 23- 9 ++ AL GL+ +E + LSGG+++KV L+ + Sbjct: 123 VGVIQDALTNNDFYVIDSKVEEIARGLGLSDIGLERDVTDLSGGQRTKVLLAKLLLEKPE 18- 2 Query: 240 VLVLDEPTNHLDVDAKDELKRALKAYKGSILMVCHEPDF 278 +L+LDEPTN+LD + LKR L+ Y+ + +++ H+ F Sbjct: 183 ILLLDEPTNYLDEQHIEWLKRYLQEYENAFILISHDIPF 221 A related DNA sequence was identified in S. pyogenes <SEQ ID 2051> which encodes the amino acid sequence <SEQ ID 2052>. Analysis of this protein sequence reveals the following: TABLE-US-01968 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2794 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01969 Identities = 246/294 (83%), Positives = 274/294 (92%), Gaps = 1/294 (0%) Query: 1 MNDVINIVYHVENQDLVRYSGDYTNFESVYAMKKAQLEAAYERQQKEIADLQDFVNRNKA 60 +NDVINIVYHVENQ LVRY+GDY F++VY MK++QLEAAYERQQKEIA+LQDFVNRNKA Sbjct: 233 LNDVINIVYHVENQSLVRYTGDYYQFQAVYEMKQSQLEAAYERQQKEIANLQDFVNRNKA 29- 2 Query: 61 RVATRNMAMSRQKKLDKMDIIELQAEKPKPSFEFKESRTPGRFIFQAKDLQIGYDRALTK 120- RVATRNMAMSRQKKLDKMDIIELQAEKPKP+FEFK++RTP RFIFQ K+L IGYD LTK Sbjct: 293 RVATRNMAMSRQKKLDKMDIIELQAEKPKPNFEFKQARTPSRFIFQTKNLVIGYDYPLTK 35- 2 Query: 121 -PLNLTFERNQKIAIVGANGIGKTTLLKSLLGIIPPISGNVERGDFIDLGYFEQEVPGGN 17- 9 PLN+TFERNQKIAIVGANGIGK+TLLKSLLG+I P+ G++ GDF+++GYFEQEV G N Sbjct: 353 EPLNITFERNQKIAIVGANGIGKSTLLKSLLGVIEPLEGHIVTGDFLEVGYFEQEVTGVN 41- 2 Query: 180 RQTPLEAVWDAFPALNQAEVRAALARCGLTSKHIESQIQVLSGGEQSKVRFCLLMNRENN 23- 9 RQTPLE VWDAFPALNQAEVRAALARCGLTSKHIESQIQVLSGGEQ+KVRFCLLMNRENN Sbjct: 413 RQTPLEVVWDAFPALNQAEVRAALARCGLTSKHIESQIQVLSGGEQAKVRFCLLMNRENN 47- 2 Query: 240 VLVLDEPTNHLDVDAKDELKRALKAYKGSILMVCHEPDFYEGWMDDVWDFNQLS 293 VL+LDEPTNHLD+DAK+ELKRALKAYKGSILMVCHEPDFY GW+ D WDF++L+ Sbjct: 473 VLILDEPTNHLDIDAKNELKRALKAYKGSILMVCHEPDFYNGWVTDTWDFSKLT 526 Identities = 60/218 (27%), Positives = 102/218 (46%), Gaps = 43/218 (19%) Query: 104 IFQAKDLQIGY-DRALTKPLNLTFERNQKIAIVGANGIGKTTLLKSLLGIIPPISGNVER 16- 2 I + K L G+ DRA+ + ++ + + I +VGANG GK+T + + G + P G VE Sbjct: 15 ILEVKQLSHGFGDRAIFENVSFRLLKGEHIGLVGANGEGKSTFMSIVTGHLQPDEGKVEW 74 Query: 163 GDFIDLGYFEQEVPGGNRQTPLEAVWDAFPALNQAEVR-----AALA------------- 20- 4 ++ GY +Q + QT + + AF L + E R A++A Sbjct: 75 SKYVTAGYLDQHTVLESGQTVRDVLRTAFDELFKTENRINEIYASMADDKADIAVLMEEV 134- Query: 205 ------------------------RCGLTSKHIESQIQVLSGGEQSKVRFCLLMNRENNV 24- 0 G+ +ES + LSGG+++KV L+ + ++ Sbjct: 135 GELQDRLESRDFYTLDAKIDEVARALGVMDFGMESDVTSLSGGQRTKVLLAKLLLEKPDI 19- 4 Query: 241 LVLDEPTNHLDVDAKDELKRALKAYKGSILMVCHEPDF 278 L+LDEPTNHLD + + LKR L+ Y+ + +++ H+ F Sbjct: 195 LLLDEPTNHLDAEHIEWLKRYLQHYENAFVLISHDISF 232 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 666 A DNA sequence (GBSx0706) was identified in S. agalactiae <SEQ ID 2053> which encodes the amino acid sequence <SEQ ID 2054>. This protein is predicted to be lipoprotein Nlp1 precursor (pstS). Analysis of this protein sequence reveals the following:

TABLE-US-01970 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2637 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01971 >GP: CAB14429 GB: Z99116 alternate gene name: yzmB~similar to phosphate ABC transporter (binding protein) [Bacillus subtilis] Identities = 42/62 (67%), Positives = 49/62 (78%) Query: 15 SITSVGSTALQPLVEAAADEFGKTNLGKTINVQGGGSGTGLSQVQSGAVQIGNSDLFAEE 74 - S+T GS+A+QPLV AAA++F + N I VQ GGSGTGLSQV GAVQIGNSD+FAEE Sbjct: 45 SLTISGSSAMQPLVLAAAEKFMEENPDADIQVQAGGSGTGLSQVSEGAVQIGNSDVFAEE 104- Query: 75 KE 76 KE Sbjct: 105 KE 106 A related DNA sequence was identified in S. pyogenes <SEQ ID 1695> which encodes the amino acid sequence <SEQ ID 1696>. Analysis of this protein sequence reveals the following: TABLE-US-01972 Possible site: 24 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01973 Identities = 63/74 (85%), Positives = 71/74 (95%) Query: 3 LSGCANWIDKGQSITSVGSTALQPLVEAAADEFGKTNLGKTINVQGGGSGTGLSQVQSGA 62 LS C++WIDKG+SIT+VGSTALQPLVEA ADEFG +NLGKT+NVQGGGSGTGLSQVQSGA Sbjct: 20 LSACSSWIDKGESITAVGSTALQPLVEAVADEFGSSNLGKTVNVQGGGSGTGLSQVQSGA 79 Query: 63 VQIGNSDLFAEEKE 76 VQIGNSD+FAEEK+ Sbjct: 80 VQIGNSDVFAEEKD 93 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 667 A DNA sequence (GBSx0707) was identified in S. agalactiae <SEQ ID 2055> which encodes the amino acid sequence <SEQ ID 2056>. This protein is predicted to be lipoprotein Nlp1 precursor (pstS). Analysis of this protein sequence reveals the following: TABLE-US-01974 Possible site: 60 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9343> which encodes amino acid sequence <SEQ ID 9344> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01975 >GP: CAB14429 GB: Z99116 alternate gene name: yzmB~similar to phosphate ABC transporter (binding protein) [Bacillus subtilis] Identities = 95/184 (51%), Positives = 126/184 (67%), Gaps = 1/184 (0%) Query: 3 DHQVAVAGLAVIVNKKVNVKNLTTHQLRDIFAGKIKINWKEVGGQDLDISIINRAASSGSR 62 - DHQVAV G+A VN VK+++ +L+ IF GKIKNWKE+GG+D I+++NR SSG+R Sbjct: 115 DHQVAVVGMAAAVNPDAGVKDISKDELKKIFTGKIKNWKELGGKDQKITLVNRPDSSGTR 17- 4 Query: 63 ATFDNTIMGNVAPIQSQEQDSNGMVKSIVSQTPGAISYLAFAYV-DKSVGTLKLNGFAPT 121- ATF + P + +DS+ VK I++ TPGAI YLAF+Y+ D V L ++G P Sbjct: 175 ATFVKYALDGAEPAEGITEDSSNTVKKIIADTPGAIGYLAFSYLTDDKVTALSIDGVKPE 23- 4 Query: 122 AKNVTTDNWKLWSYEHMYTKGNETGLTKEFLDYMKSDKVQSSIVQHMGYISINDMKVVKD 18- 1 AKNV T + +W+Y+H YTKG TGL KEFLDY+KS+ +Q SIV GYI + DMKV +D Sbjct: 235 AKNVATGEYPIWAYQHSYTKGEATGLAKEFLDYLKSEDIQKSIVTDQGYIPVTDMKVTRD 29- 4 Query: 182 AEGK 185 A GK Sbjct: 295 ANGK 298 There is also homology to SEQ ID 1696. SEQ ID 9344 (GBS659) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 135 (lane 2 & 3; MW 60 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 135 (lane 5-7; MW 35 kDa) and in FIG. 178 (lane 11; MW 35 kDa). GBS659-His was purified as shown in FIG. 228, lane 6-8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 668 A DNA sequence (GBSx0708) was identified in S. agalactiae <SEQ ID 2057> which encodes the amino acid sequence <SEQ ID 2058>. This protein is predicted to be phosphate transporter permease PstC (pstC-2). Analysis of this protein sequence reveals the following: TABLE-US-01976 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.50 Transmembrane 35-51 (27-61) INTEGRAL Likelihood = -7.64 Transmembrane 167-183 (154-186) INTEGRAL Likelihood = -6.37 Transmembrane 282-298 (277-302) INTEGRAL Likelihood = -5.52 Transmembrane 85-101 (81-116) INTEGRAL Likelihood = -3.24 Transmembrane 133-149 (131-155) ----- Final Results ----- bacterial membrane --- Certainty = 0.7198 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8635> which encodes amino acid sequence <SEQ ID 8636> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-01977 Lipop: Possible site: -1 Crend: 8 SRCFLG: 0 McG: Length of UR: 5 Peak Value of UR: -0.12 Net Charge of CR: 2 McG: Discrim Score: -16.22 GvH: Signal Score (-7.5): -4.26 Possible site: 41 >>> Seems to have no N-terminal signal sequence Amino Acid Composition: calculated from 1 ALOM program count: 5 value: -15.50 threshold: 0.0 INTEGRAL Likelihood = -15.50 Transmembrane 29-45 (21-55) INTEGRAL Likelihood = -7.64 Transmembrane 161-177 (148-180) INTEGRAL Likelihood = -6.37 Transmembrane 276-292 (271-296) INTEGRAL Likelihood = -5.52 Transmembrane 79-95 (75-110) INTEGRAL Likelihood = -3.24 Transmembrane 127-143 (125-149) PERIPHERAL Likelihood = 0.69 205 modified ALOM score: 3.60 icm1 HYPID: 7 CFP: 0.720 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.7198 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01978 >GP: CAB14428 GB: Z99116 alternate gene name: yzmC~similar to phosphate ABC transporter (permease) [Bacillus subtilis] Identities = 145/303 (47%), Positives = 209/303 (68%), Gaps = 4/303 (1%) Query: 8 KNQELAKKLTSPSKNSRLEKFGKGITFLSLALIVFIVAM-ILIFVAQKGLSTFFVDGVKL 66 +N ++++L S +N +L++ + + ALI+ ++ I IF+ KGL +F V+GV Sbjct: 6 ENMSVSERLISSRQNRQLDEVRGRMIVTACALIMIAASVAITIFLGVKGLQSFLVNGVSP 65 Query: 67 TDFLFNTKWEP--SAKSFGAFPMIAGSFIVTILSAIIATPFAIGAAVFMTEISPKYGSKI 124- +FL + W P S +G P I GSF VTILSA+IA P I +FMTEI+P +G K+ Sbjct: 66 IEFLTSLNWNPTDSDPKYGVLPFIFGSFAVTILSALIAAPLGIAGPIFMTEIAPNWGKKV 125- Query: 125 LQPAVELLVGIPSVVYGFIGLQIIVPFVRSI-FGGTGFGILSGVCVLFVMILPTVTFMTV 18- 3 LQP +ELLVGIPSVVYGFIGL ++VPF+ GTG +L+G VL VMILPT+T ++ Sbjct: 126 LQPVIELLVGIPSVVYGFIGLTVLVPFIAQFKSSGTGHSLLAGTIVLSVMILPTITSISA 18- 5 Query: 184 DSLRAVPRHYKEASLAMGATRWQTIWRVILNAARPGIFTAIVFGMARAFGEALAIQMVVG 24- 3 D++ ++P+ +E S A+GATRWQTI +V++ AA P + TA+V GMARAFGEALA+QMV+G Sbjct: 186 DAMASLPKSLREGSYALGATRWQTIRKVLVPAAFPTLMTAVVLGMARAFGEALAVQMVIG 24- 5 Query: 244 NSAILPTSLTTPAATLTSVLTMGIGNTVMGTVQNNVLWSLALVLLIMSLAFNTVIKLITR 30- 3 N+ +LP S A TLT+++T+ +G+T G+V+NN LWS+ LVLL+MS F +I+ ++ Sbjct: 246 NTRVLPESPFDTAGTLTTIITLNMGHTTYGSVENNTLWSMGLVLLVMSFLFILLIRYLSS 30- 5 Query: 304 EGK 306 K Sbjct: 306 RRK 308 A related DNA sequence was identified in S. pyogenes <SEQ ID 1691> which encodes the amino acid sequence <SEQ ID 1692>. Analysis of this protein sequence reveals the following: TABLE-US-01979 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -17.25 Transmembrane 29-45 (21-55) INTEGRAL Likelihood = -7.22 Transmernbrane 162-178 (154-84) INTEGRAL Likelihood = -5.57 Transmembrane 282-298 (277-302) INTEGRAL Likelihood = -5.41 Transmembrane 96-112 (81-116) INTEGRAL Likelihood = -3.08 Transmembrane 133-149 (131-152) ----- Final Results ----- bacterial membrane --- Certainty = 0.7899 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01980 Identities = 266/311 (85%), Positives = 290/311 (92%), Gaps 6/311 (1%) Query: 7 MKNQELAKKLTSPSKNSRLEKFGKGITFLSLALIVFIVAMILIFVAQKGLSTFFVDGVKL 66 M+NQELAKKL SPSKNSRLE FG+ ITFL LALIVFIVAMILIVAQKGLSTFFVD V L Sbjct: 1 MENQELAKKLASPSKNSRLETFGRTITFLCLALIVFIVAMILIFVAQKGLSTFFVDKVNL 60 Query: 67 TDFLFNTKWEPSAKS------FGAFPMIAGSFIVTILSAIIATPFAIGAAVFMTEISPKY 120- DFLF +W+PS K+ GA PMI GSF+VTILSAIIATPFAIGAAVFMTEISPKY Sbjct: 61 FDFLFGKEWQPSVKNAAGIPYLGALPMITGSFLVTILSAIIATPFAIGAAVFMTEISPKY 120- Query: 121 GSKILQPAVELLVGIPSVVYGFIGLQIIVPFVRSIFGGTGFGILSGVCVLFVMILPTVTF 18- 0 G+K+LQPAVELLVGIPSVVYGFIGLQ+IVPF+RSIFGGTGFGILSGVCVLFVMILPTVTF Sbjct: 121 GAKLLQPAVELLVGIPSVVYGFIGLQVIVPFMRSIFGGTGFGILSGVCVLFVMILPTVTF 18- 0 Query: 181 MTVDSLRAVPRHYKEASLAMGATRWQTIWRVILNAARPGIFTAIVFGMARAFGEALAIQM 24- 0 MT DSLRAVPRHY+EAS+AMGATRWQTIWRV+LNAARPGIFTA++FGMARAFGEALAIQM Sbjct: 181 MTTDSLRAVPRHYREASMAMGATRWQTIWRVVLNAARPGIFTAVIFGMARAFGEALAIQM 24- 0 Query: 241 VVGNSAILPTSLTTPAATLTSVLTMGIGNTVMGTVQNNVLWSLALVLLIMSLAFNTVIKL 30- 0 VVGNSA++P+SLTTPAATLTSVLTMGIGNTVMGTVQNNVLWSLALVLL+MSLAFN+++KL Sbjct: 241 VVGNSAVMPSSLTTPAATLTSVLTMGIGNTVMGTVQNNVLWSLALVLLLMSLAFNSLVKL 30- 0 Query: 301 ITREGKKNYER 311 IT+E K+NYER Sbjct: 301 ITKERKRNYER 311 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 669 A DNA sequence (GBSx0709) was identified in S. agalactiae <SEQ ID 2059> which encodes the amino acid sequence <SEQ ID 2060>. Analysis of this protein sequence reveals the following: TABLE-US-01981 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2469 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 670 A DNA sequence (GBSx0710) was identified in S. agalactiae <SEQ ID 2061> which encodes the amino acid sequence <SEQ ID 2062>. This protein is predicted to be probable abc transporter permease protein in soda-comga intergenic reg. Analysis of this protein sequence reveals the following: TABLE-US-01982 Possible site: 18 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.24 Transmembrane 20-36 (19-41) INTEGRAL Likelihood = -8.28 Transmembrane 66-82 (57-88) INTEGRAL Likelihood = -6.90 Transmembrane 260-276 (258-285) INTEGRAL Likelihood = -5.47 Transmembrane 109-125 (106-129) INTEGRAL Likelihood = -2.87 Transmembrane 181-197 (178-198) ----- Final Results ----- bacterial membrane --- Certainty = 0.4694 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01983 >GP: CAB14427 GB: Z99116 alternate gene name: yzmD~similar to phosphate ABC transporter (permease) [Bacillus subtilis] Identities = 157/294 (53%), Positives = 225/294 (76%) Query: 1 MNAKKADKLATTILYSIAAIIVTILASLLIFILVRGLPHVSWSFLTGKSSSYEAGGGIGI 60 MN K DKLAT + AAII IL L +I++ G+ +S+ F+T KSS+ AGGGI Sbjct: 1 MNRKITDKLATGMFGLCAAIIAAILVGLFSYIIINGVSQLSFQFITTKSSAIAAGGGIRD 60 Query: 61 QLYNSFFLLIVTLIISIPLSLGAGIYLSEYAKKGRLTNFVRTCIEILSSLPSVVVGLFGY 120- QL+NSF++L +T++I+IPL +G G++++EYA ++T+F+RTCIE+LSSLPS+V+G+FG Sbjct: 61 QLFNSFYILFITMLITIPLGVGGGVFMAEYAPNNKVTDFIRTCIEVLSSLPSIVIGMFGL 120- Query: 121 LIFVVQFQYGFSIISGALALTVFNLPQMTRSVEDSLQNVHHTQREAGLALGISRWETVIY 18- 0 L+FV +G++II GALALTVFNLP M R ED++++V +EA LALG+SRW TV Sbjct: 121 LMFVNLTGWGYTIIGGALALTVFNLPVMVRVTEDAIRSVPKDLKEASLALGVSRWHTVKT 18- 0 Query: 181 VVVPEALPSIVTGVVLASGRIFGEAAALIYTAGQSAPALDWSNWNVLSVTSPISIFRQAE 24- 0 V++P A+PSI+TG +LASGR+FGEAAAL++TAG + P L+++ WN S TSP++IFR AE Sbjct: 181 VLIPSAIPSIITGAILASGRVFGEAAALLFTAGLTTPRLNFTEWNPFSETSPLNIFRPAE 24- 0 Query: 241 TLAVHIWKVNSEGTIPDATQVSAGSAAVLLVVILIFNLSARSIGKKLHSKLTSS 294 TLAVHIW VN++G IPDA ++ G + VL++ +L+FNL+AR +G ++ KLT++ Sbjct: 241 TLAVHIWNVNTQGMIPDAEAIANGGSPVLVISVLVFNLAARWLGTMIYKKLTAN 294 A related DNA sequence was identified in S. pyogenes <SEQ ID 1685> which encodes the amino acid sequence <SEQ ID 1686>. Analysis of this protein sequence reveals the following: TABLE-US-01984 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.89 Transmembrane 17-33 (8-40) INTEGRAL Likelihood = -10.19 Transmembrane 260-276 (257-285) INTEGRAL Likelihood = -5.89 Transmembrane 66-82 (57-87) INTEGRAL Likelihood = -5.47 Transmembrane 109-125 (106-129) INTEGRAL Likelihood = -2.02 Transmembrane 181-197 (180-197) ----- Final Results ----- bacterial membrane --- Certainty = 0.5755 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01985 Identities = 257/294 (87%), Positives = 278/294 (94%) Query: 1 MNAKKADKLATTILYSIAAIIVTILASLLIFILVRGLPHVSWSFLTGKSSSYEAGGGIGI 60 MNAKK DK+AT LY+IA IIV ILASL+++ILVRGLPH+SWSFLTGKSSSYEAGGGIGI Sbjct: 1 MNAKKVDKVATGTLYTIAGIIVAILASLILYILVRGLPHISWSFLTGKSSSYEAGGGIGI 60 Query: 61 QLYNSFFLLIVTLIISIPLSLGAGIYLSEYAKKGRLTNFVRTCIEILSSLPSVVVGLFGY 120- QLYNSFFLLIVTLIISIPLS GAGIYL+EYAKKG +TNF+RTCIEILSSLPSVVVGLFGY Sbjct: 61 QLYNSFFLLIVTLIISIPLSTGAGIYLAEYAKKGPVTNFIRTCIEILSSLPSVVVGLFGY 120- Query: 121 LIFVVQFQYGFSIISGALALTVFNLPQMTRSVEDSLQNVHHTQREAGLALGISRWETVIY 18- 0 LIFVVQF+YGFSIISGALALTVFNLPQMTR+VEDSL +VHHTQREAGLALG+SRWETV Y Sbjct: 121 LIFVVQFEYGFSIISGALALTVFNLPQMTRNVEDSLLHVHHTQREAGLALGLSRWETVFY 18- 0 Query: 181 VVVPEALPSIVTGVVLASGRIFGEAAALIYTAGQSAPALDWSNWNVLSVTSPISIFRQAE 24- 0 VV+PEALP +VTG+VLASGRIFGEAAALIYTAGQSAPALDWSNWN LSVTSPISIFRQ+E Sbjct: 181 VVIPEALPGMVTGIVLASGRIFGEAAALIYTAGQSAPALDWSNWNPLSVTSPISIFRQSE 24- 0 Query: 241 TLAVHIWKVNSEGTIPDATQVSAGSAAVLLVVILIFNLSARSIGKKLHSKLTSS 294 TLAVHIWKVNSEGTIPDAT VSAGSAAVLL+ ILIFN SA IGKKLHSK+T++ Sbjct: 241 TLAVHIWKVNSEGTIPDATLVSAGSAAVLLIFILIFNFSAHFIGKKLHSKMTAA 294 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 671 A DNA sequence (GBSx0711) was identified in S. agalactiae <SEQ ID 2063> which encodes the amino acid sequence <SEQ ID 2064>. This protein is predicted to be phosphate ABC transporter, ATP-binding protein (pstB) (pstB-2). Analysis of this protein sequence reveals the following: TABLE-US-01986 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4506 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-01987 >GP: AAB99016 GB: U67544 phosphate specific transport complex component (pstB) [Methanococcus jannaschii] Identities = 154/247 (62%), Positives = 204/247 (82%) Query: 21 LTTKDLHVYYGEKEAIKGIDMQFEKNKITALIGPSGCGKSTYLRSLNRMNDTIDIARVTG 80 - + TK+L+++YGEK+A+ I++ +NKITALIGPSGCGKST+LR LNR+ND I R+ G Sbjct: 6 METKNLNLWYGEKQALFDINLPIYENKITALIGPSGCGKSTFLRCLNRLNDLIPNVRIEG 65 Query: 81 QIMYEGIDVNAQDINVYEMRKHIGMVFQRPNPFAKSIYKNITFAYERAGVKDKKFLDEVV 140- +++ +G ++ +D++VYE+RK +GMVFQ+PNPFA SIY N+ F G+KDKK LD++V Sbjct: 66 EVLLDGKNIYDKDVDVYELRKRVGMVFQKPNPFAMSIYDNVAFGPRIHGIKDKKELDKIV 125- Query: 141 ETSLKQAALWDQVKDDLHKSAFTLSGGQQQRLCIARAIAVKPEILLMDEPASALDPIATM 20- 0 E +LK+AALWD+VKD+LHK+A +LSGGQQQRLCIARAIAVKPE+LLMDEP SALDPI+T+ Sbjct: 126 EWALKKAALWDEVKDELHKNALSLSGGQQQRLCIARAIAVKPEVLLMDEPTSALDPISTL 18- 5 Query: 201 QLEETMFELKKNYTIIIVTHNMQQAARASDYTAFFYLGDLIEYDKTNNIFQNAKCQSTSD 26- 0 ++EE M EL K+YTI++VTHNMQQA+R SDYTAFF +G LIE+ +T IF N + + T D Sbjct: 186 KIEELMVELAKDYTIVVVTHNMQQASRVSDYTAFFLMGKLIEFGETEQIFLNPQKKETDD 24- 5 Query: 261 YVSGRFG 267 Y+SGRFG Sbjct: 246 YISGRFG 252 A related DNA sequence was identified in S. pyogenes <SEQ ID 1681> which encodes the amino acid sequence <SEQ ID 1682>. Analysis of this protein sequence reveals the following: TABLE-US-01988 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2796 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01989 Identities = 242/267 (90%), Positives = 258/267 (95%) Query: 1 MAEYNWDERHIITFPEENSALTTKDLHVYYGEKEAIKGIDMQFEKNKITALIGPSGCGKS 60 M EYNW+ERHIITFPEE AL TKDLHVYYG KEAIKGIDMQFEK+KITALIGPSGCGKS Sbjct: 1 MTEYNWNERHIITFPEETLALATKDLHVYYGAKEAIKGIDMQFEKHKITALIGPSGCGKS 60 Query: 61 TYLRSLNRMNDTIDIARVTGQIMYEGIDVNAQDINVYEMRKHIGMVFQRPNPFAKSIYKN 120- TYLRSLNRMNDTIDIARVTG+I+Y+GIDVN +D+NVYE+RKH+GMVFQRPNPFAKSIYKN Sbjct: 61 TYLRSLNRMNDTIDIARVTGEILYQGIDVNRKDMNVYEIRKHLGMVFQRPNPFAKSIYKN 120- Query: 121 ITFAYERAGVKDKKFLDEVVETSLKQAALWDQVKDDLHKSAFTLSGGQQQRLCIARAIAV 18- 0 ITFA+ERAGVKDKK LDE+VETSLKQAALWDQVKDDLHKSAFTLSGGQQQRLCIARAI+V Sbjct: 121 ITFAHERAGVKDKKVLDEIVETSLKQAALWDQVKDDLHKSAFTLSGGQQQRLCIARAISV 18- 0 Query: 181 KPEILLMDEPASALDPIATMQLEETMFELKKNYTIIIVTHNMQQAARASDYTAFFYLGDL 24- 0 KP+ILLMDEPASALDPIATMQLEETMFELKKNYTIIIVTHNMQQAARASDYTAFFYLG+L Sbjct: 181 KPDILLMDEPASALDPIATMQLEETMFELKKNYTIIIVTHNMQQAARASDYTAFFYLGNL 24- 0 Query: 241 IEYDKTNNIFQNAKCQSTSDYVSGRFG 267 IEYDKT NIFQNA+CQST+DYVSG FG Sbjct: 241 IEYDKTRNIFQNAQCQSTNDYVSGHFG 267 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 672 A DNA sequence (GBSx0712) was identified in S. agalactiae <SEQ ID 2065> which encodes the amino acid sequence <SEQ ID 2066>. This protein is predicted to be phosphate ABC transporter, ATP-binding protein (pstB-1). Analysis of this protein sequence reveals the following: TABLE-US-01990 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3806 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9815> which encodes amino acid sequence <SEQ ID 9816> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01991 >GP: CAB14426 GB: Z99116 alternate gene name: yzmE~similar to phosphate ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 148/248 (59%), Positives = 189/248 (75%) Query: 5 ILQVSDLSVYYNKKKALKEVSMDFYPNEITALIGPSGSGKSTLLRAINRMGDLNPEVTLT 64 +L+V DLS+YY K+A+ V+MD N +TALIGPSG GKST LR INRM DL P Sbjct: 22 VLEVKDLSIYYGNKQAVHHVNMDIEKNAVTALIGPSGCGKSTFLRNINRMNDLIPSARAE 81 Query: 65 GAVMYNGHNVYSPRTDTVELRKEIGMVFQQPNPFPMSVFENVVYGLRLKGIKDKATLDEA 124- G ++Y G N+ + V LR+EIGMVFQ+PNPFP S++ N+ + L+ G ++KA LDE Sbjct: 82 GEILYEGLNILGGNINVVSLRREIGMVFQKPNPFPKSIYANITHALKYAGERNKAVLDEI 141- Query: 125 VETSLKGASIWDEVKDRLHDSALGLSGGQQQRVCIARTLATKPKIILLDEPTSALDPISA 18- 4 VE SL A++WDEVKDRLH SAL LSGGQQQR+CIARTLA KP ++LLDEP SALDPIS Sbjct: 142 VEESLTKAALWDEVKDRLHSSALSLSGGQQQRLCIARTLAMKPAVLLLDEPASALDPISN 20- 1 Query: 185 GKIEETLHGLKDQYTMLLVTRSMQQASRISDRTGFFLDGNLIEYGNTKEMFMNPKHKETE 24- 4 KIEE + GLK +Y++++VT +MQQA R+SDRT FFL+G L+EYG T+++F +PK ++TE Sbjct: 202 AKIEELITGLKREYSIIIVTHNMQQALRVSDRTAFFLNGELVEYGQTEQIFTSPKKQKTE 26- 1 Query: 245 DYITGKFG 252 DYI GKFG Sbjct: 262 DYINGKFG 269 A related DNA sequence was identified in S. pyogenes <SEQ ID 2067> which encodes the amino acid sequence <SEQ ID 2068>. Analysis of this protein sequence reveals the following: TABLE-US-01992 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3590 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01993 Identities = 208/252 (82%), Positives = 235/252 (92%) Query: 1 MTQPILQVSDLSVYYNKKKALKEVSMDFYPNEITALIGPSGSGKSTLLRAINRMGDLNPE 60 MT+PILQ+ DLSVYYN+KK LK+VS+D YPNEITALIGPSGSGKSTLLR+INRN DLNPE Sbjct: 2 MTEPILQIRDLSVYYNQKKTLKDVSLDLYPNEITALIGPSGSGKSTLLRSINRMNDLNPE 61 Query: 61 VTLTGAVMYNGHNVYSPRTDTVELRKEIGMVFQQPNPFPHSVFENVVYGLRLKGIKDKAT 120- VT+TG+++YNGHN+YSPRTDTV+LRKEIGMVFQQPNPFPMS++ENVVYGLRLKGI+DK+ Sbjct: 62 VTITGSIVYNGHNIYSPRTDTVDLRKEIGMVFQQPNPFPMSIYENVVYGLRLKGIRDKSI 121- Query: 121 LDEAVETSLKGASIWDEVKDRLHDSALGLSGGQQQRVCIARTLATKPKIILLDEPTSALD 18- 0 LD AVE+SLKGASIW+EVKDRLHDSA+GLSGGQQQRVCIAR LAT P+IILLDEPTSALD Sbjct: 122 LDHAVESSLKGASIWNEVKDRLHDSAVGLSGGQQQRVCIARVLATSPRIILLDEPTSALD 18- 1 Query: 181 PISAGKIEETLHGLKDQYTMLLVTRSMQQASRISDRTGFFLDGNLIEYGNTKEMFMNPKH 24- 0 PISAGKIEETL LK YT+ +VTRSMQQASR+SDRTGFFL+G+L+E G TK MFMNPK Sbjct: 182 PISAGKIEETLLLLKKDYTLAIVTRSMQQASRLSDRTGFFLEGDLLECGPTKAMFMNPKR 24- 1 Query: 241 KETEDYITGKFG 252 KETEDYI+GKFG Sbjct: 242 KETEDYISGKFG 253 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for, vaccines or diagnostics. EXAMPLE 673 A DNA sequence (GBSx0713) was identified in S. agalactiae <SEQ ID 2069> which encodes the amino acid sequence <SEQ ID 2070>. Analysis of this protein sequence reveals the following: TABLE-US-01994 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1937 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01995 >GP: AAD22042 GB: AF118229 PhoU [Streptococcus pneumoniae] Identities = 75/216 (34%), Positives = 126/216 (57%), Gaps = 1/216 (0%) Query: 2 LRSKFDEELDKLHNQFYAMGIEAIGQIKKTVRAFVSHDRELAKEVIEDDVTLNNFETKLE 61 +R++FD EL +L F +G + K + A S D+E+A+ +I D +N ++ +E Sbjct: 1 MRNQFDLELHELEQSFLGLGQLVLETASKALLALASKDKEMAELIINKDHAINQGQSAIE 60 Query: 62 KKSLEIIALQQPVSQDLRTVITVLKATSDVERMGDHAAAVAKATIRMKGEERIPAVELEI 121- ++ALQQP DLR VI+++ + SD+ERMGDH A +AKA +++K E ++ E ++ Sbjct: 61 LTCARLLALQQPQVSDLRFVISIMSSCSDLERMGDHMAGIAKAVLQLK-ENQLAPDEEQL 119- Query: 122 NNMGKAVKNMLEEALTAYINGDDEKAYEVAAMDEIVDDYFRDIQKMVVETIQKHPDVAFA 18- 1 + MGK +ML + L A+ KA +A DE +D Y+ + K ++ ++ Sbjct: 120 HQMGKLSLSMLADLLVAFPLHQASKAISIAQKDEQIDQYYYALSKEIIGLMKDQETSIPN 17- 9 Query: 182 AKEYFQVLMHLERIGDYGKNICEWIVYLKTGKIIEL 217 +Y ++ HLER DY NICE +VYL+TG++++L Sbjct: 180 GTQYLYIIGHLERFADYIANICERLVYLETGELVDL 215 A related DNA sequence was identified in S. pyogenes <SEQ ID 1677> which encodes the amino acid sequence <SEQ ID 1678>. Analysis of this protein sequence reveals the following: TABLE-US-01996 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2229 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-01997 Identities = 174/217 (80%), Positives = 194/217 (89%) Query: 1 MLRSKFDEELDKLHNQFYAMGIEAIGQIKKTVRAFVSHDRELAKEVIEDDVTLNNFETKL 60 MLR+KF+EELDKLHNQFY+MG+E + QI KTVRAFVSHDRELAKEVIE+D T+NNFETKL Sbjct: 1 MLRTKFEEELDKLHNQFYSMGMEVLAQINKTVRAFVSHDRELAKEVIEEDDTINNFETKL 60 Query: 61 EKKSLEIIALQQPVSQDLRTVITVLKATSDVERMGDHAAAVAKATIRMKGEERIPAVELE 120- EKKSLEIIALQQPVS DLR VITVLKA+SD+ERMGDHAA++AKATIRMKGEERIP VE + Sbjct: 61 EKKSLEIIALQQPVSNDLRMVITVLKASSDIERMGDHAASIAKATIRMKGEERIPVVEEQ 120- Query: 121 INNMGKAVKNMLEEALTAYINGDDEKAYEVAAMDEIVDDYFRDIQKMVVETIQKHPDVAF 18- 0 IN MGKAVK M+EEAL AYIN DD KAYE+AA DEI+D YFR+IQ + VE I+K PD F Sbjct: 121 INLMGKAVKQMVEEALNAYINADDTKAYEIAASDEIIDQYFRNIQTLAVEEIRKSPDAVF 18- 0 Query: 181 AAKEYFQVLMHLERIGDYGKNICEWIVYLKTGKIIEL 217 A KEYFQVLM+LERIGDY +NICEWIVYLKTGKIIEL Sbjct: 181 AGKEYFQVLMYLERIGDYARNICEWIVYLKTGKIIEL 217 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 674 A DNA sequence (GBSx0714) was identified in S. agalactiae <SEQ ID 2071> which encodes the amino acid sequence <SEQ ID 2072>. This protein is predicted to be aminopeptidase N. Analysis of this protein sequence reveals the following: TABLE-US-01998 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2845(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-01999 >GP:CAB50785 GB:AJ007700 aminopeptidase N [Streptococcus thermophilus] Identities = 556/847 (65%), Positives = 673/847 (78%), Gaps = 4/847 (0%) Query: 3 TVEHFVTKFVPENYNLFLDINRQTKTFSGNVAVSGEALDNNISFHQKGLTIKSVLLDNQP 62 +V F+ F+PENYNLFLDINR KTF+GNVA++GEA+DN+IS HQK LTI SVLLDN+ Sbjct: 4 SVARFIESFIPENYNLFLDINRSEKTFTGNVAITGEAIDNHISLHQKDLTINSVLLDNES 63 Query: 63 LDFQLDEDNEAMHIQLHETGSMVLVFEFSGHITDNMTGMYPSYYTVNGIKKEVISTQFES 122- L+FQ+D+ NEA HI+L ETG + + EFSG ITDNMTG+YPSYYT NG KKE+ISTQFES Sbjct: 64 LNFQMDDANEAFHIELPETGVLTIFIEFSGRITDNMTGIYPSYYTYNGEKKEIISTQFES 123- Query: 123 HFAREVFPSIDEPEAKATFDLSLKFDQKEGEIALSNMPEINAEQRQETGLWTFDTTPKMS 18- 2 HFARE FP +DEPEAKATFDLSLKFD +EG+ ALSNMPEIN+ R+ETG+WTF+TTP+MS Sbjct: 124 HFAREAFPCVDEPEAKATFDLSLKFDAEEGDTALSNMPEINSHLREETGVWTFETTPRMS 18- 3 Query: 183 SYLLAFALGELHGKTTHTKNGTLVGSYATKAHQLNELDFSLDIVVRVIEFYEDYFGVRYP 24- 2 +YLLAF G LHGKT TKNGT VG +AT A N +DF+LDI VRVIEFYEDYF V+YP Sbjct: 184 TYLLAFGFGALHGKTAKTKNGTEVGVFATVAQAENSVDFALDIAVRVIEFYEDYFQVKYP 24- 3 Query: 243 IPQSLHVALPDFSAGAMENWGLVTYREVYLLVDENSSVSSRQQVALVVAHEIAHQWFGNL 30- 2 IP S H+ALPD SAGAMENWGLVTYREVYLLVDENSS +SRQQVALVVAHE+AHQWFGNL Sbjct: 244 IPLSYHLALPDLSAGAMENWGLVTYREVYLLVDENSSAASRQQVALVVAHELAHQWFGNL 30- 3 Query: 303 VTMKWWDDLWLNESFANMMEYVSIDYIEPKLNIFEDFQTG-GLPLALKRDATDGVQSVHV 36- 1 VTMKWWDDLWLNESFANMMEYVS++ IEP NIFE F G+P AL+RDATDGVQSVH+ Sbjct: 304 VTMKWWDDLWLNESFANMMEYVSVNAIEPSWNIFEGFPNKLGVPNALQRDATDGVQSVHM 36- 3 Query: 362 EVNHPDEINTLFDPAIVYAKGSRLMHMLRRWLGDTDFAAGLKIYFEKHQYQNTIGRDLWN 42- 1 EVNHPDEINTLFD AIVYAKGSRLMHMLRRWLGD FA GLK YFEKHQY NT+GRDLWN Sbjct: 364 EVNHPDEINTLFDSAIVYAKGSRLMHMLRRWLGDEAFAKGLKAYFEKHQYNNTVGRDLWN 42- 3 Query: 422 ALSQTSGKDVAAFMDSWLEQPGYPVMAAKIEEDELILTQKQFFIGEHEDKSRLWQIPLNS 48- 1 ALS+ SGKDV++FMD+WLEQPGYPV++A++ +D LIL+QKQFFIGEHEDK RLW+IPLN+ Sbjct: 424 ALSEASGKDVSSFMDTWLEQPGYPVVSAEVVDDTLILSQKQFFIGEHEDKGRLWEIPLNT 48- 3 Query: 482 NWEGIPEILTEETVVIPNFSQLAEKNKENGALRFNTENTAHYITNYQGQLLEHIISDLPL 54- 1 NW G+P+ L+EE + IPN+SQLA +N NG LR NT NTAHYIT+YQGQLL++I+ D Sbjct: 484 NWNGLPDTLSEERIEIPNYSQLATEN--NGVLRLNTANTAHYITDYQGQLLDNILEDFAN 54- 1 Query: 542 MDNISKLQIVQERHLLAESGMISYSSLIPLVSLLSQETSYLVNSAIKSVIDGLSLFVQED 60- 1 +D +SKLQI+QER LLAESG ISY+SL+ L+ L+ +E S+L++ A ++ GL F+ ED Sbjct: 542 LDTVSKLQILQERRLLAESGRISYASLVGLLDLVEKEESFLISQAKSQILAGLKRFIDED 60- 1 Query: 602 SQDEFDFKEFVNKLSAFNFNRLGFEKREGEGDDSEMVRHLSLSLALYSDNEHAIEEAHHI 66- 1 ++ E +K V++ +F RLGF+ +EGE D+ EMVR +LS + +D + + A ++ Sbjct: 602 TEAEVHYKALVSRQFQNDFERLGFDAKEGESDEDEMVRQTALSYLIEADYQPTVLAAANV 66- 1 Query: 662 FKAHENNIAAIPAAIRLLVLTNEMKHFESKELSHLLLETYSTTTDGNFKRQLASALSHTT 72- 1 F+AH+ NI +IPA+IR LVL N+MK S L + Y T D NF+RQL ALS+ Sbjct: 662 FQAHKENIESIPASIRGLVLINQMKQENSLSLVEEYINAYVATNDSNFRRQLTQALSYLK 72- 1 Query: 722 DSKTLKKLLSDWKNKDIVKPQDLAMSWYATFLKNSFTQESVWEWAQENWEWIKATLGGDM 78- 1 + + L +L K+K++VKPQDL + WY FL SF QE+VW+WA+ENWEWIKA LGGDM Sbjct: 722 NQEGLDYVLGQLKDKNVVKPQDLYL-WYMNFLSKSFAQETVWDWAKENWEWIKAALGGDM 78- 0 Query: 782 SFDKFVIYPSSSFKTEERLEQYKNFFEPQLSDMAISRNISMGIKEISARVLLITKQKEEV 84- 1 SFD FV P+ FK +ERL+QY FFEPQ SD A+ RNI MGIK I+ARV LI K+K V Sbjct: 781 SFDSFVNIPAGIFKNQERLDQYIAFFEPQTSDKALERNILMGIKTIAARVDLIEKEKAAV 84- 0 Query: 842 INTIKKY 848 + +K Y Sbjct: 841 ESALKDY 847 A related DNA sequence was identified in S. pyogenes <SEQ ID 2073> which encodes the amino acid sequence <SEQ ID 2074>. Analysis of this protein sequence reveals the following: TABLE-US-02000 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1098(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02001 Identities = 576/848 (67%), Positives = 692/848 (80%), Gaps = 3/848 (0%) Query: 1 MKTVEHFVTKFVPENYNLFLDINRQTKTFSGNVAVSGEALDNNISFHQKGLTIKSVLLDN 60 MKTVEH + FVPENYN+FLDINRQTKTF+GNVA++GEALDN+++FHQK L IKS+LLDN Sbjct: 21 MKTVEHLIETFVPENYNIFLDINRQTKTFTGNVAINGEALDNHVAFHQKDLDIKSILLDN 80 Query: 61 QPLDFQLDEDNEAMHIQLHETGSMVLVFEFSGHITDNMTGMYPSYYTVNGIKKEVISTQF 120- + + +Q+D DNE + ++L ETG M LV EFSG ITDNMTG+YPSYYT NG KKEVISTQF Sbjct: 81 EAVIYQVDNDNEVVRVELPETGMMTLVIEFSGSITDNMTGIYPSYYTKNGEKKEVISTQF 140- Query: 121 ESHFAREVFPSIDEPEAKATFDLSLKFDQKEGEIALSNMPEINAEQRQETGLWTFDTTPK 18- 0 ESHFARE FP IDEP+AKATFDLSL FDQ+ GEIALSNMPE+N ++R+ETGLWTFDTT + Sbjct: 141 ESHFAREAFPCIDEPQAKATFDLSLTFDQEIGEIALSNMPEVNIDRREETGLWTFDTTLR 20- 0 Query: 181 MSSYLLAFALGELHGKTTHTKNGTLVGSYATKAHQLNELDFSLDIVVRVIEFYEDYFGVR 24- 0 MSSYLLAFALGELHGKT +K GT VG YAT AH L+ LDFSLDI VRVI FYEDYFGV Sbjct: 201 MSSYLLAFALGELHGKTVESKKGTTVGVYATTAHPLSSLDFSLDIAVRVINFYEDYFGVH 26- 0 Query: 241 YPIPQSLHVALPDFSAGAMENWGLVTYREVYLLVDENSSVSSRQQVALVVAHEIAHQWFG 30- 0 YPIPQSL++ALPDFS+GAMENWGL+TYRE+YLLVDENS+V SRQQVALV+AHEIAHQWFG Sbjct: 261 YPIPQSLNIALPDFSSGAMENWGLITYREIYLLVDENSTVQSRQQVALVIAHEIAHQWFG 32- 0 Query: 301 NLVTMKWWDDLWLNESFANMMEYVSIDYIEPKLNIFEDFQTGGLPLALKRDATDGVQSVH 36- 0 NLVTMKWWDDLWLNESFANMMEYVSI+ IEP I EDFQTGG+PLALKRDATDGVQSVH Sbjct: 321 NLVTMKWWDDLWLNESFANMMEYVSIEAIEPSWKIIEDFQTGGIPLALKRDATDGVQSVH 38- 0 Query: 361 VEVNHPDEINTLFDPAIVYAKGSRLMHMLRRWLGDTDFAAGLKIYFEKHQYQNTIGRDLW 42- 0 VEVNHPDEINTLFDPAIVYAKGSRLMHMLRR++GD DFA GL YFEK+QY+NT+GRDLW Sbjct: 381 VEVNHPDEINTLFDPAIVYAKGSRLMHMLRRFIGDRDFAIGLHHYFEKYQYRNTVGRDLW 44- 0 Query: 421 NALSQTSGKDVAAFMDSWLEQPGYPVMAAKIEEDELILTQKQFFIGEHEDKSRLWQIPLN 48- 0 N LS TSGKDVAAFMD+WLEQPGYPV+ A++E D+LIL+QKQFFIG+ E+K RLW IPLN Sbjct: 441 NILSDTSGKDVAAFMDAWLEQPGYPVLTARLENDQLILSQKQFFIGKGEEKGRLWPIPLN 50- 0 Query: 481 SNWEGIPEILTEETVVIPNFSQLAEKNKENGALRFNTENTAHYITNYQGQLLEHIISDLP 54- 0 +NW G+PE LTE +VIPNFSQLA +N+ GALRFN +NTAHYIT+YQG LL+ ++++L Sbjct: 501 TNWHGLPETLTEAEMVIPNFSQLAAENE--GALRFNIDNTAHYITDYQGSLLDALVTELA 55- 8 Query: 541 LMDNISKLQIVQERHLLAESGMISYSSLIPLVSLLSQETSYLVNSAIKSVIDGLSLFVQE 60- 0 +DN S LQ++QER LLA+SG+ISY+ L+ L++ L SY+V A++ V+ GL F+ E Sbjct: 559 QLDNTSALQVIQERRLLADSGLISYAELVDLIAQLDDSKSYMVAEAVQQVVSGLKRFIDE 61- 8 Query: 601 DSQDEFDFKEFVNKLSAFNFNRLGFEKREGEGDDSEMVRHLSLSLALYSDNEHAIEEAHH 66- 0 S E F V + +FN+ GFEK+ E D+ EMVR ++L ++N+ I+ Sbjct: 619 GSLAEKSFNRLVTTIYQEDFNQHGFEKKADESDEDEMVRQVALGRLWLAENQTIIDGLRT 67- 8 Query: 661 IFKAHENNIAAIPAAIRLLVLTNEMKHFESKELSHLLLETYSTTTDGNFKRQLASALSHT 72- 0 IF+A++NNIA+IPAA+R LVL N+MK+FE+ L + ETY TTD N + L A S T Sbjct: 679 IFEAYQNNIASIPAAVRRLVLANQMKYFETDSLVDIYFETYVATTDNNLRSDLTVAFSQT 73- 8 Query: 721 TDSKTLKKLLSDWKNKDIVKPQDLAMSWYATFLKNSFTQESVWEWAQENWEWIKATLGGD 78- 0 T++++L K+KDI+KPQDL+ WY L SFTQ+ +WEWA+ENW+WIK+ LGGD Sbjct: 739 KQPTTIRRILVSLKDKDIIKPQDLSY-WYNALLGQSFTQDIIWEWARENWDWIKSALGGD 79- 7 Query: 781 MSFDKFVIYPSSSFKTEERLEQYKNFFEPQLSDMAISRNISMGIKEISARVLLITKQKEE 84- 0 MSFDKFVIYP+S+FKT + L +YK+FFEP+L DMAISRNI+MGI EI ARV LITK+KE Sbjct: 798 MSFDKFVIYPASNFKTPKHLAEYKSFFEPKLDDMAISRNITMGINEIEARVALITKEKEA 85- 7 Query: 841 VINTIKKY 848 VI + Y Sbjct: 858 VIAALSHY 865 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 675 A DNA sequence (GBSx0715) was identified in S. agalactiae <SEQ ID 2075> which encodes the amino acid sequence <SEQ ID 2076>. This protein is predicted to be response regulator (trcR). Analysis of this protein sequence reveals the following:

TABLE-US-02002 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2741(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02003 >GP:CAA54465 GB:X77249 response regulator [Streptococcus pneumoniae] Identities = 198/224 (88%), Positives = 213/224 (94%) Query: 1 MIKILLIEDDLSLSNSVFDFLDDFADVMQIFDGEEGLYEAESGVYDLILLDLMLPEKNGF 60 MIKILL+EDDL LSNSVFDFLDDFADVMQ+FDGEEGLYEAESGVYDLILLDLMLPEKNGF Sbjct: 1 MIKILLVEDDLGLSNSVFDFLDDFADVMQVFDGEEGLYEAESGVYDLILLDLMLPEKNGF 60 Query: 61 QVLKELREKGITTPVLIMTAKESIDDKGQGFDLGADDYLTKPFYLEELKMRIQALLKRSG 120- QVLKELREKGITTPVLIMTAKES+DDKG GF+LGADDYLTKPFYLEELKMRIQALLKRSG Sbjct: 61 QVLKELREKGITTPVLIMTAKESLDDKGHGFELGADDYLTKPFYLEELKMRIQALLKRSG 120- Query: 121 KFNDNSLIYGDIRVDMSTNSTFVNQTEVELLGKEFDLLVYFLQNQNVILPKSQIFDRIWG 18- 0 KFN+N+L YG+I V++STN+ V T VELLGKEFDLLVYFLQNQNVILPK+QIFDR+WG Sbjct: 121 KFNENTLTYGNIVVNLSTNTVKVEDTPVELLGKEFDLLVYFLQNQNVILPKTQIFDRLWG 18- 0 Query: 181 FDSDTTISVVEVYVSKVRKKLKGTLFSENLQTLRSVGYILKHVE 224 FDSDTTISVVEVYVSKVRKKLKGT F+ENLQTLRSVGY+LK V+ Sbjct: 181 FDSDTTISVVEVYVSKVRKKLKGTTFAENLQTLRSVGYLLKDVQ 224 A related DNA sequence was identified in S. pyogenes <SEQ ID 2077> which encodes the amino acid sequence <SEQ ID 2078>. Analysis of this protein sequence reveals the following: TABLE-US-02004 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2689(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02005 Identities = 180/224 (80%), Positives = 200/224 (88%) Query: 1 MIKILLIEDDLSLSNSVFDFLDDFADVMQIFDGEEGLYEAESGVYDLILLDLMLPEKNGF 60 MIKILL+EDDLSLSNS+FDFLDDFADVMQ+FDG+EGLYEAESG+YDLILLDLMLPEKNGF Sbjct: 1 MIKILLVEDDLSLSNSIFDFLDDFADVMQVFDGDEGLYEAESGIYDLILLDLMLPEKNGF 60 Query: 61 QVLKELREKGITTPVLIMTAKESIDDKGQGFDLGADDYLTKPFYLEELKMRIQALLKRSG 120- QVLKELREK I PVLIMTAKE +DDKG GF+LGADDYLTKPFYLEELKMRIQALLKR+G Sbjct: 61 QVLKELREKDIKIPVLIMTAKEGLDDKGHGFELGADDYLTKPFYLEELKMRIQALLKRTG 120- Query: 121 KFNDNSLIYGDIRVDMSTNSTFVNQTEVELLGKEFDLLVYFLQNQNVILPKSQIFDRIWG 18- 0 KF D ++ +G++ VD++ V VELLGKEFDLLVY LQNQNVILPK+QIFDR+WG Sbjct: 121 KFADKNISFGNLVVDLARKEVKVEGKVVELLGKEFDLLVYLLQNQNVILPKTQIFDRLWG 18- 0 Query: 181 FDSDTTISVVEVYVSKVRKKLKGTLFSENLQTLRSVGYILKHVE 224 FDSDTTISVVEVY+SK+RKKLKGT F LQTLRSVGYILK+ E Sbjct: 181 FDSDTTISVVEVYISKIRKKLKGTCFVNRLQTLRSVGYILKNNE 224 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 676 A DNA sequence (GBSx0716) was identified in S. agalactiae <SEQ ID 2079> which encodes the amino acid sequence <SEQ ID 2080>. This protein is predicted to be histidine kinase. Analysis of this protein sequence reveals the following: TABLE-US-02006 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.18 Transmembrane 22-38 (17-46) INTEGRAL Likelihood = -4.94 Transmembrane 182-198 (178-201) ----- Final Results ----- bacterial membrane --- Certainty = 0.4673(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02007 >GP:CAA54466 GB:X77249 histidine kinase [Streptococcus pneumoniae] Identities = 218/420 (51%), Positives = 305/420 (71%), Gaps = 4/420 (0%) Query: 17 SHFIHFFTVFSGIFLVMTVIILQVMRYGVYSSVDSSLKYISTHPKNYINMVMSRTAAY-- 74 - S+FI F VF+ IF MT+IILQVM +Y+SVD L +S +P+ I + ++R Sbjct: 15 SYFIRNFGVFTLIFSTMTLIILQVMHSSLYTSVDDKLHGLSENPQAVIQLAINRATEEIK 74 Query: 75 -LDNSNIASVKLKPGGQTVANTDIILFTSEEEVINYFDAFSNYQFLKPNKKNLGGISELT 133- L+N+ + K++ +NT++ILF + + + F +K KK LG I ++ Sbjct: 75 DLENARADASKVEIKPNVSSNTEVILFDKDFTQLLSGNRFLGLDKIKLEKKELGHIYQIQ 134- Query: 134 LTNIFGQDETYHAVTVKVN-NPAYPNVTYMTAIVNIDQLVNAKERYEKIIIFVMTTFWII 19- 2 + N +GQ+E Y + ++ N + N+ Y ++N QL A +++E++I+ VM +FWI+ Sbjct: 135 VFNSYGQEEIYRVILMETNISSVSTNIKYAAVLINTSQLEQASQKHEQLIVVVMASFWIL 19- 4 Query: 193 SIGASIYLAKWAQKPIIENYERQKAFVENASHELRTPLAVLQNRLETLFRKPNATILENS 25- 2 S+ AS+YLA+ + +P++E+ ++Q++FVENASHELRTPLAVLQNRLETLFRKP ATI++ S Sbjct: 195 SLLASLYLARVSVRPLLESMQKQQSFVENASHELRTPLAVLQNRLETLFRKPEATIMDVS 25- 4 Query: 253 ENIASSLDEVRNMRILTTNLLNLARRDDGIKPELAVIKPTLFDSIFENYDLITQENGKNF 31- 2 E+IASSL+EVRNMR LTT+LLNLARRDDGIKPELA + + F++ F NY++I EN + F Sbjct: 255 ESIASSLEEVRNMRFLTTSLLNLARRDDGIKPELAEVPTSFFNTTFTNYEMIASENNRVF 31- 4 Query: 313 TGHNMIQDSFKTDKTLLKQLMTILFDNAIKYTDNDGSIDFTISETDKYLFLEIADNGPGI 37- 2 N I + TD+ LLKQLMTILFDNA+KYT+ DG IDF IS TD+ L+L ++DNG GI Sbjct: 315 RFENRIHRTIVTDQLLLKQLMTILFDNAVKYTEEDGEIDFLISATDRNLYLLVSDNGIGI 37- 4 Query: 373 SEEDKVRIFDRFYRVDKARTRQQGGFGLGLSLAQQIVNSLRGNITVIDNKPRGSIFKIKL 43- 2 S EDK +IFDRFYRVDKARTRQ+GGFGLGLSLA+QIV++L+G +TV DNKP+G+IF++K+ Sbjct: 375 STEDKKKIFDRFYRVDKARTRQKGGFGLGLSLAKQIVDALKGTVTVKDNKPKGTIFEVKI 43- 4 A related DNA sequence was identified in S. pyogenes <SEQ ID 2081> which encodes the amino acid sequence <SEQ ID 2082>. Analysis of this protein sequence reveals the following: TABLE-US-02008 Possible site: 57 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.09 Transmembrane 19-35 (14-44) INTEGRAL Likelihood = -10.24 Transmembrane 185-201 (182-206) ----- Final Results ----- bacterial membrane --- Certainty = 0.5437(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02009 >GP: CAA54466 GB: X77249 histidine kinase [Streptococcus pneumoniae] Identities = 223/436 (51%), Positives = 313/436 (71%), Gaps = 5/436 (1%) Query: 2 NKLKKEILSDNYNHFFHFFAVFTGIFVIMTIIILQIMRFGVYSSVDSSLVSVSNNASSYA 61 +KLKK +D++++F F VFT IF MT+IILQ+M +Y+SVD L +S N + Sbjct: 3 SKLKKTWYADDFSYFIRNFGVFTLIFSTMTLIILQVMHSSLYTSVDDKLHGLSENPQAVI 62 Query: 62 NRTMARISSFYFDTENNIIKALPDSDSSKLLGTPAANTDIILFSANGTILNAFDAFSNYQ 121- + R + D EN A D+ ++ ++NT++ILF + T L + + F Sbjct: 63 QLAINRATEEIKDLEN----ARADASKVEIKPNVSSNTEVILFDKDFTQLLSGNRFLGLD 118- Query: 122 NFHLDKRRLGSIETTSLMNFYGQEEKYHTITVGVHIKNYPA-VAYMMAVVNVEQLDRANE 18- 0 L+K+ LG I + N YGQEE Y I + +I + + Y ++N QL++A++ Sbjct: 119 KIKLEKKELGHIYQIQVFNSYGQEEIYRVILMETNISSVSTNIKYAAVLINTSQLEQASQ 17- 8 Query: 181 RYERIIIIVMSVFWLISILASIYLAKWSRKPILESYEKQKMFVENASHELRTPLAVLQNR 24- 0 ++E++I++VM+ FW++S+LAS+YLA+ S +P+LES +KQ+ FVENASHELRTPLAVLQNR Sbjct: 179 KHEQLIVVVMASFWILSLLASLYLARVSVRPLLESMQKQQSFVENASHELRTPLAVLQNR 23- 8 Query: 241 LESLFRKPNETILENSEHLASSLDEVRNMRILTTNLLNLARRDDGINPQWTHLDTDFFNA 30- 0 LE+LFRKP TI++ SE +ASSL+EVRNMR LTT+LLNLARRDDGI P+ + T FFN Sbjct: 239 LETLFRKPEATIMDVSESIASSLEEVRNMRFLTTSLLNLARRDDGIKPELAEVPTSFFNT 29- 8 Query: 301 IFENYELVAKEYGKIFYFQNQVNRSLRMDKALLKQLITILFDNAIKYTDKNGIIEIIVKT 36- 0 F NYE++A E ++F F+N+++R++ D+ LLKQL+TILFDNA+KYT+++G I+ ++ Sbjct: 299 TFTNYEMIASENNRVFRFENRIHRTIVTDQLLLKQLMTILFDNAVKYTEEDGEIDFLISA 35- 8 Query: 361 TDKNLLISVIDNGPGITDEEKKKIFDRFYRVDKARTRQTGGFGLGLALAQQIVMSLKGNI 42- 0 TD+NL + V DNG GI+ E+KKKIFDRFYRVDKARTRQ GGFGLGL+LA+QIV +LKG + Sbjct: 359 TDRNLYLLVSDNGIGISTEDKKKIFDRFYRVDKARTRQKGGFGLGLSLAKQIVDALKGTV 41- 8 Query: 421 TVKDNDPKGSIFEVKL 436 TVKDN PKG+IFEVK+ Sbjct: 419 TVKDNKPKGTIFEVKI 434 An alignment of the GAS and GBS proteins is shown below: TABLE-US-02010 Identities = 265/436 (60%), Positives = 334/436 (75%), Gaps = 10/436 (2%) Query: 7 ISKFKKNV-SDS--HFIHFFTVFSGIFLVMTVIILQVMRYGVYSSVDSSLKYISTHPKNY 63 ++K KK + SD+ HF HFF VF+GIF++MT+IILQ+MR+GVYSSVDSSL +S + +Y Sbjct: 1 MNKLKKEILSDNYNHFFHFFAVFTGIFVIMTIIILQIMRFGVYSSVDSSLVSVSNNASSY 60 Query: 64 INMVMSRTAAYLDNSNIASVKLKPG-------GQTVANTDIILFTSEEEVINYFDAFSNY 116- N M+R +++ ++ +K P G ANTDIILF++ ++N FDAFSNY Sbjct: 61 ANRTMARISSFYFDTENNIIKALPDSDSSKLLGTPAANTDIILFSANGTILNAFDAFSNY 120- Query: 117 QFLKPNKKNLGGISELTLTNIFGQDETYHAVTVKVNNPAYPNVTYMTAIVNIDQLVNAKE 17- 6 Q +K+ LG I +L N +GQ+E YH +TV V+ YP V YM A+VN++QL A E Sbjct: 121 QNFHLDKRRLGSIETTSLMNFYGQEEKYHTITVGVHIKNYPAVAYMMAVVNVEQLDRANE 18- 0 Query: 177 RYERIIIFVMTTFWIISIGASIYLAKWAQKPIIENYERQKAFVENASHELRTPLAVLQNR 23- 6 RYE+III VM+ FW+ISI ASIYLAKW++KPI+E+YE+QK FVENASHELRTPLAVLQNR Sbjct: 181 RYERIIIIVMSVFWLISILASIYLAKWSRKPILESYEKQKMFVENASHELRTPLAVLQNR 24- 0 Query: 237 LETLFRKPNATILENSENIASSLDEVRNMRILTTNLLNLARRDDGIKPELAVIKPTLFDS 29- 6 LE+LFRKPN TILENSE++ASSLDEVRNMRILTTNLLNLARRDDGI P+ + F++ Sbjct: 241 LESLFRKPNETILENSEHLASSLDEVRNMRILTTNLLNLARRDDGINPQWTHLDTDFFNA 30- 0 Query: 297 IFENYDLITQENGKNFTGHNMIQDSFKTDKTLLKQLMTILFDNAIKYTDNDGSIDFTISE 35- 6 IFENY+L+ +E GK F N + S + DK LLKQL+TILFDNAIKYTD +G I+ + Sbjct: 301 IFENYELVAKEYGKIFYFQNQVNRSLRMDKALLKQLITILFDNAIKYTDKNGIIEIIVKT 36- 0 Query: 357 TDKYLFLEIADNGPGISEEDKVRIFDRFYRVDKARTRQQGGFGLGLSLAQQIVNSLRGNI 41- 6 TDK L + + DNGPGI++E+K +IFDRFYRVDKARTRQ GGFGLGL+LAQQIV SL+GNI Sbjct: 361 TDKNLLISVIDNGPGITDEEKKKIFDRFYRVDKARTRQTGGFGLGLALAQQIVMSLKGNI 42- 0 Query: 417 TVIDNKPRGSIFKIKL 432 TV DN P+GSIF++KL Sbjct: 421 TVKDNDPKGSIFEVKL 436 SEQ ID 2080 (GBS339d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 146 (lane 9; MW 73 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 185 (lane 5; MW 73 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 677 A DNA sequence (GBSx0717) was identified in S. agalactiae <SEQ ID 2083> which encodes the amino acid sequence <SEQ ID 2084>. Analysis of this protein sequence reveals the following: TABLE-US-02011 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1783(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9813> which encodes amino acid sequence <SEQ ID 9814> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02012 >GP: AAB48049 GB: U88582 YlxM [Streptococcus mutans] Identities = 95/110 (86%), Positives = 103/110 (93%) Query: 1 MEIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIAEESGVSRQAVYDNIKRTE 60 MEIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIAEE VSRQAVYDNIKRTE 60 Sbjct: 1 MEIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIAEEFDVSRQAVYDNIKRTE 60 Query: 61 KILEAYEMKLHMYSDYIVRSQIFDDILEKYTDDAFLQEKISILSSIDNRD 110 KILE YEMKLHMYSDY+VRS+IFD I++KY +D +LQ KISIL++IDNRD Sbjct: 61 KILEDYEMKLHMYSDYVVRSEIFDAIMKKYPNDPYLQNKISILTTIDNRD 110 A related DNA sequence was identified in S. pyogenes <SEQ ID 2085> which encodes the amino acid sequence <SEQ ID 2086>. Analysis of this protein sequence reveals the following: TABLE-US-02013 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1767(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02014 Identities = 95/110 (86%), Positives = 103/110 (93%) Query: 1 MEIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIAEESGVSRQAVYDNIKRTE 60 MEIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIA+E GVSRQAVYDNIKRTE Sbjct: 4 MEIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTE 63 Query: 61 KILEAYEMKLHMYSDYIVRSQIFDDILEKYTDDAFLQEKISILSSIDNRD 110 KILE YEMKLHMYSDY+VRS+IFDD++ Y D +LQEKISIL+SIDNR+ Sbjct: 64 KILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSIDNRE 113 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 678 A DNA sequence (GBSx0719) was identified in S. agalactiae <SEQ ID 2087> which encodes the amino acid sequence <SEQ ID 2088>. This protein is predicted to be signal recognition particle protein (ffh). Analysis of this protein sequence reveals the following: TABLE-US-02015 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.22 Transmembrane 37-53 (37-53) ----- Final Results ----- bacterial membrane --- Certainty = 0.1086(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02016 >GP: AAB48050 GB: U88582 Ffh [Streptococcus mutans] Identities = 437/522 (83%), Positives = 484/522 (92%), Gaps = 7/522 (1%) Query: 1 MAFESLTERLQGVFKNIRGKKKLSEKDVQEVTKEIRLALLEADVALPVVKTFIKHVRERA 60 MAFESLTERLQGVFKN+RGK+KLSEKDVQEVTKEIRLALLEADVALPVVK FIK VR+RA Sbjct: 1 MAFESLTERLQGVFKNLRGKRKLSEKDVQEVTKEIRLALLEADVALPVVKEFIKRVRKRA 60 Query: 61 VGHEIIDTLDPTQQIVKIVNEELTDLLGAETSEIEKSPKIPTIIMMVGLQGAGKTTFAGK 120- VGHE+IDTLDP+QQI+KIVNEELT +LG+ET+EIEKS KIPTIIMMVGLQGAGKTTFAGK Sbjct: 61 VGHEVIDTLDPSQQIIKIVNEELTAVLGSETAEIEKSSKIPTIIMMVGLQGAGKTTFAGK 120- Query: 121 LANKLIKEDNARPMMIAADIYRPAAIDQLKTLGSQINVPVFDMGTNHSAVEIVTKGLEQA 18- 0 LANKL+KE+NARP+MIAADIYRPAAIDQLK LG QINVPVFDMGT HSAVEIV++GL QA Sbjct: 121 LANKLVKEENARPLMIAADIYRPAAIDQLKILGQQINVPVFDMGTEHSAVEIVSQGLAQA 18- 0 Query: 181 RENRNDYVLIDTAGRLQIDATLMQELHDVKAIAQPNEILLVVDSMIGQEAANVAEEFNRQ 24- 0 +ENRNDYVLIDTAGRLQID LM EL D+KA+A PNEILLVVDSMIGQEAANVA EFN+Q Sbjct: 181 KENRNDYVLIDTAGRLQIDEKLMTELRDIKALANPNEILLVVDSMIGQEAANVAREFNQQ 24- 0 Query: 241 LSISGVVLTKIDGDTRGGAALSVREITGKPIKFTGTGEKITDIETFHPDRMASRILGMGD 30- 0 L ++GV+LTKIDGDTRGGAALSVR+ITGKPIKFTGTGEKITDIETFHPDRM+SRILGMGD Sbjct: 241 LEVTGVILTKIDGDTRGGAALSVRQITGKPIKFTGTGEKITDIETFHPDRMSSRILGMGD 30- 0 Query: 301 LLTLIERASQEYDEKRSMELAEKMRENTFDFNDFIDQLDQVQNMGPMEDLLKMLPGMANN 36- 0 LLTLIE+ASQ+YDE++S ELAEKMREN+FDFNDFI+QLDQVQNMG MED+LKM+PGMANN Sbjct: 301 LLTLIEKASQDYDEQKSAELAEKMRENSFDFNDFIEQLDQVQNMGSMEDILKMIPGMANN 36- 0 Query: 361 PAMKNFKVDENEIARKRAIVSSMTPEERENPDLLNPSRRRRIAAGSGNTFVDVNKFIKDF 42- 0 PA+ N +VDE EIARKRAIVSSMTPEERENPDLL PSRRRRIA+GSGNTFV+VNKFIKDF Sbjct: 361 PALANVEVDEGEIARKRAIVSSMTPEERENPDLLTPSRRRRIASGSGNTFVNVNKFIKDF 42- 0 Query: 421 NQAKQMMQGVMSGDMNKMMKKMGIDPNNLPKDMPGMDGMDMSNLEGMMGQNGMPDLSSL- 47- 9 NQAK+MMQGVMSGDMNK+MK+MGI+PNN+P + MD S LEGMMGQ GMPD+S L Sbjct: 421 NQAKKMMQGVMSGDMNKVMKQMGINPNNMP------NNMDSSALEGMMGQGGMPDMSGLS 47- 4 Query: 480 GGDMDFSQMFGGGLKGKVGAFAAKQSMKRMANKMKKAKKKRK 521 G +MD SQMFGGGLKGKVG FA KQSMK+MA +MKKAKK++K Sbjct: 475 GANMDVSQMFGGGLKGKVGEFAMKQSMKKMAKRMKKAKKRKK 516 A related DNA sequence was identified in S. pyogenes <SEQ ID 2089> which encodes the amino acid sequence <SEQ ID 2090>. Analysis of this protein sequence reveals the following: TABLE-US-02017 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.22 Transmembrane 39-55 (39-55) ----- Final Results ----- bacterial membrane --- Certainty = 0.1086(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02018 Identities = 458/522 (87%), Positives = 489/522 (92%), Gaps = 4/522 (0%) Query: 1 MAFESLTERLQGVFKNIRGKKKLSEKDVQEVTKEIRLALLEADVALPVVKTFIKHVRERA 60 MAFESLT+RLQ VFK+IRGKKKLSE DVQEVTKEIRLALLEADVALPVVKTFIK VRERA Sbjct: 3 MAFESLTQRLQDVFKHIRGKKKLSESDVQEVTKEIRLALLEADVALPVVKTFIKRVRERA 62 Query: 61 VGHEIIDTLDPTQQIVKIVNEELTDLLGAETSEIEKSPKIPTIIMMVGLQGAGKTTFAGK 120- +GHEIIDTLDPTQQI+KIVNEELT +LG+ET+EI+KSPKIPTIIMMVGLQGAGKTTFAGK Sbjct: 63 IGHEIIDTLDPTQQILKIVNEELTSILGSETAEIDKSPKIPTIIMMVGLQGAGKTTFAGK 122- Query: 121 LANKLIKEDNARPMMIAADIYRPAAIDQLKTLGSQINVPVFDMGTNHSAVEIVTKGLEQA 18- 0 LANKLIKE+NARP+MIAADIYRPAAIDQLKTLG QINVPVFDMGT+HSAV+IV KGLEQA Sbjct: 123 LANKLIKEENARPLMIAADIYRPAAIDQLKTLGQQINVPVFDMGTDHSAVDIVRKGLEQA 18- 2 Query: 181 RENRNDYVLIDTAGRLQIDATLMQELHDVKAIAQPNEILLVVDSMIGQEAANVAEEFNRQ 24- 0 REN NDYVLIDTAGRLQID LM EL DVKA+AQPNEILLVVDSMIGQEAANVA EFN Q Sbjct: 183 RENHNDYVLIDTAGRLQIDEKLMGELRDVKALAQPNEILLVVDSMIGQEAANVAYEFNHQ 24- 2 Query: 241 LSISGVVLTKIDGDTRGGAALSVREITGKPIKFTGTGEKITDIETFHPDRMASRILGMGD 30- 0 LSI+GVVLTKIDGDTRGGAALSVREITGKPIKFTG GEKITDIETFHPDRM+SRILGMGD Sbjct: 243 LSITGVVLTKIDGDTRGGAALSVREITGKPIKFTGIGEKITDIETFHPDRMSSRILGMGD 30- 2 Query: 301 LLTLIERASQEYDEKRSMELAEKMRENTFDFNDFIDQLDQVQNMGPMEDLLKMLPGMANN 36- 0 LLTLIE+ASQEYDEK+S+ELAEKMRENTFDFNDFI+QLDQVQNMGPMEDLLKM+PGMA N Sbjct: 303 LLTLIEKASQEYDEKKSLELAEKMRENTFDFNDFIEQLDQVQNMGPMEDLLKMIPGMAGN 36- 2 Query: 361 PAMKNFKVDENEIARKRAIVSSMTPEERENPDLLNPSRRRRIAAGSGNTFVDVNKFIKDF 42- 0 PA+ N KVDEN+IARKRAIVSSMTP ERENPDLLNPSRRRRIAAGSGN+FVD NKFIKDF Sbjct: 363 PALANIKVDENQIARKRAIVSSMTPAERENPDLLNPSRRRRIAAGSGNSFVD-NKFIKDF 42- 1 Query: 421 NQAKQMMQGVMSGDMNKMMKKMGIDPNNLPKDMPGMDGM-DMSNLEGMMGQNGMPDLSSL 47- 9 NQAK MMQGVMSGDM+KMMK MGI+PNNLPK+MP GM DMS+LEGMMGQ GMPDLS L Sbjct: 422 NQAKSMMQGVMSGDMSKMMKDMGINPNNLPKNMPA--GMPDMSSLEGMMGQGGMPDLSGL 47- 9 Query: 480 GGDMDFSQMFGGGLKGKVGAFAAKQSMKRMANKMKKAKKKRK 521 GGDMD SQ+FG G KGK+G FA KQ+MKR ANK+KKAKKKRK Sbjct: 480 GGDMDMSQLFGKGFKGKIGQFAMKQAMKRQANKLKKAKKKRK 521 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 679 A DNA sequence (GBSx0721) was identified in S. agalactiae <SEQ ID 2091> which encodes the amino acid sequence <SEQ ID 2092>. This protein is predicted to be SatD. Analysis of this protein sequence reveals the following:

TABLE-US-02019 Possible site: 49 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.28 Transmembrane 3-19 (2-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.1510(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9811> which encodes amino acid sequence <SEQ ID 9812> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02020 >GP:AAG28336 GB:U88582 SatD [Streptococcus mutans] Identities = 106/222 (47%), Positives = 162/222 (72%), Gaps = 2/222 (0%) Query: 13 MYLALIGDIINSKQILERETFQQSFQQLMTELSDVYGEELISPFTITAGDEFQALLKPSK 72 - +Y+A+IGD+I+SK I R Q+ + L+ +++ Y E L S FTIT GDEFQALL P+ Sbjct: 2 IYIAIIGDLISSKAITNRPKSQKQLKNLLNQINKKYKELLKSAFTITTGDEFQALLVPNP 61 Query: 73 KVFQIIDHIQLALKPVNVRFGLGTGNIITSINSNESIGADGPAYWHARSAINHIHDKNDY 132- ++FQIID I L KP +RFG+G+G+I+T IN +SIG+DGPAYWHAR+AI++IHDKNDY Sbjct: 62 QIFQIIDEIALGFKPYQIRFGVGSGSILTEINPEQSIGSDGPAYWHARAAIDYIHDKNDY 121- Query: 133 GTVQVAICLDDEDQNLELTLNSLISAGDFIKSKWTTNHFQMLEHLILQDNYQEQFQHQKL 19- 2 G+ +A+ L+D + + + +N++++A +FIKSKWT +++++ L+ Y+E+F H+K+ Sbjct: 122 GSNHLAVDLEDTETSQQ--INAILAACEFIKSKWTVTQYEVIDGLLQAGIYEEKFSHKKM 17- 9 Query: 193 AQLENIEPSALTKRLKASGLKIYLRTRTQAADLLVKSCTQTK 234 A+ ++ PS+ KRLK+SGLKIYLR + A LL+ + + K Sbjct: 180 AEKLDLSPSSFNKRLKSSGLKIYLRNKKVATTLLLNAIRKEK 221 A related DNA sequence was identified in S. pyogenes <SEQ ID 2093> which encodes the amino acid sequence <SEQ ID 2094>. Analysis of this protein sequence reveals the following: TABLE-US-02021 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3744(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02022 Identities = 94/213 (44%), Positives = 137/213 (64%), Gaps = 3/213 (1%) Query: 14 YLALIGDIINSKQILERETFQQSFQQLMTELSDVYGEELISPFTITAGDEFQALLKPSKK 73 - Y+ALIGDII SKQ+ +R Q++ + +L+ + +IS ++T GDEFQ L + Sbjct: 3 YIALIGDIIQSKQLTDRSKVQKTLAAYLDDLNKTFAPYIISKLSLTLGDEFQGLFQVDTP 62 Query: 74 VFQIIDHIQLALKPVNVRFGLGTGNIITSINSNESIGADGPAYWHARSAINHIHDKNDYG 133- +F +ID I + + +RFG+G G+I+T IN + SIGADGPAYWHAR AI +IH KNDYG Sbjct: 63 IFHLIDLINHHMD-IPIRFGVGVGSILTDINPDISIGADGPAYWHAREAIRYIHQKNDYG 121- Query: 134 TVQVAICLDDEDQNLELTLNSLISAGDFIKSKWTTNHFQMLEHLILQDNYQEQFQHQKLA 19- 3 +A L N + LNSL++AGD IK+ W + +++ + L+ Y+E F Q+L Sbjct: 122 NTTLA--LRTGHHNQDDVLNSLLAAGDAIKANWRASQWEIFDTLLDLGIYEEYFDQQRLG 17- 9 Query: 194 QLENIEPSALTKRLKASGLKIYLRTRTQAADLL 226 + ++ SAL+KRLK+S +KIYLRTR A + L Sbjct: 180 KQLSLSSSALSKRLKSSHVKIYLRTRQSALNCL 212 A related GBS gene <SEQ ID 8637> and protein <SEQ ID 8638> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02023 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: 4.96 GvH: Signal Score (-7.5): -5.46 Possible site: 49 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -1.28 threshold: 0.0 INTEGRAL Likelihood = -1.28 Transmembrane 3-19 (1-19) PERIPHERAL Likelihood = 5.99 74 modified ALOM score: 0.76 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1510(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8638 (GBS338) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 62 (lane 5; MW 30 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 68 (lane 11; MW 55 kDa). GBS338-GST was purified as shown in FIG. 215, lane 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 680 A DNA sequence (GBSx0722) was identified in S. agalactiae <SEQ ID 2095> which encodes the amino acid sequence <SEQ ID 2096>. Analysis of this protein sequence reveals the following: TABLE-US-02024 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6082 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 681 A DNA sequence (GBSx0723) was identified in S. agalactiae <SEQ ID 2097> which encodes the amino acid sequence <SEQ ID 2098>. Analysis of this protein sequence reveals the following: TABLE-US-02025 Possible site: 30 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.87 Transmembrane 126-142 (124-154) INTEGRAL Likelihood = -8.23 Transmembrane 45-61 (41-66) INTEGRAL Likelihood = -5.10 Transmembrane 241-257 (236-257) INTEGRAL Likelihood = -4.04 Transmembrane 199-215 (198-218) INTEGRAL Likelihood = -0.22 Transmembrane 96-112 (96-112) ----- Final Results ----- bacterial membrane --- Certainty = 0.4949 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02026 >GP:AAG28337 GB:U88582 SatE [Streptococcus mutans] Identities = 54/103 (52%), Positives = 70/103 (67%), Gaps = 2/103 (1%) Query: 1 MISDFLRDNPILTLLFCAHFLADFQWQSQSLADSKSHSWRGLWRHLLIVFLPLAALMILI 60 +IS FL NP+LTLL AHFLADFQWQSQ +AD KS +W L RHL+IV LPL L ++I Sbjct: 6 VISQFLSGNPVLTLLLIAHFLADFQWQSQKMADLKSSNWTYLIRHLIIVALPLILLSVVI 65 Query: 61 PETTLLNLSIWGSHIVIDSIKKLSYPWVEEGHF--QKAAFIID 101 P + L+ I+ SH++IDS K L + ++ F KA F+ID Sbjct: 66 PHSFLVLSLIFLSHVLIDSGKLLLNSFYKDRSFIKTKAVFLID 108 A related DNA sequence was identified in S. pyogenes <SEQ ID 2099> which encodes the amino acid sequence <SEQ ID 2100>. Analysis of this protein sequence reveals the following: TABLE-US-02027 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.59 Transmembrane 125-141 (120-144) INTEGRAL Likelihood = -6.58 Transmembrane 222-238 (215-238) INTEGRAL Likelihood = -5.04 Transmembrane 47-63 (45-77) INTEGRAL Likelihood = -4.62 Transmembrane 179-195 (178-199) INTEGRAL Likelihood = -0.43 Transmembrane 67-83 (67-83) ----- Final Results ----- bacterial membrane --- Certainty = 0.4036(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below: TABLE-US-02028 Identities = 109/256 (42%), Positives = 146/256 (56%), Gaps = 28/256 (10%) Query: 2 ISDFLRDNPILTLLFCAHFLADFQWQSQSLADSKSHSWRGLWRHLLIVFLPLAALMILIP 61 +S +L P LTL H L+D+Q QSQ +AD K L HL+ V +PL L ++IP Sbjct: 5 VSHYLAQTPTLTLFLICHVLSDYQLQSQQVADLKEKHLTYLGYHLIGVSIPLICLTLIIP 64 Query: 62 ETTLLNLSIWGSHIVIDSIKKL---SYPWVEEGHFQKAAFIIDQLAHYTCIIVFYHALPT 118- + L++L + SH +ID +K S W E F++DQ H L Sbjct: 65 QAWLMSLLVMISHALIDWLKPKMANSLKWKREW-----IFLLDQCLHIAISSFAGLRLAG 119- Query: 119 YLPPNHWLLPIKHFIVIALVFIIITKPINIVFKIFFNKFQAKELSSLLTQEKTKIMKEKS 17- 8 PN WL PI ++ L ++ITKP NIVFK+FF K+Q + + Sbjct: 120 VTLPN-WL-PIS-ILMTVLFILLITKPTNIVFKLFFIKYQPDQGEKM------------- 16- 3 Query: 179 EDHEETIEGAGAMIGNLERLIMAILLISGQYAAIGLVFTAKSIARYDKISKSQVFAEYYL 23- 8 +TI GAGA IG LER+++ + +I GQ+A+IGLVFTAKSIARY+KIS+S FAEYYL Sbjct: 164 ----DTIIGAGATIGILERIVIGVCMIMGQFASIGLVFTAKSIARYNKISESPAFAEYYL 21- 9 Query: 239 IGSLFSIISVLITHWL 254 IGSLFSI+SV I W+ Sbjct: 220 IGSLFSILSVFIAAWI 235 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 682 A DNA sequence (GBSx0724) was identified in S. agalactiae <SEQ ID 2101> which encodes the amino acid sequence <SEQ ID 2102>. Analysis of this protein sequence reveals the following: TABLE-US-02029 Possible site: 30 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02030 >GP:AAD17886 GB:AF100456 hyaluronate-associated protein precursor [Streptococcus equi] Identities = 358/521 (68%), Positives = 426/521 (81%), Gaps = 2/521 (0%) Query: 1 MSSFNRKKLKFLGISLATLTATTVTLVACGNESKNSGDNKV-INWYIPTEISTLDISKNT 59 M+ K K LG++ TL A+ L+ACGN+ S D K INWY PTEI TLDISKNT Sbjct: 1 MTVLGTKACKRLGLAAVTL-ASVAALMACGNKQSASTDKKSEINWYTPTEIITLDISKNT 59 Query: 60 DAYSNLAIGNSGSNLLRIDKEGKPKPDLAKKVSVSSDGLTYTATLRDNLKWSDGSKLSAE 119- D YS LAIGNSGSNLLR D +GK +PDLA+KV VS DGLTYTATLRD LKWSDGS L+AE Sbjct: 60 DTYSALAIGNSGSNLLRADAKGKLQPDLAEKVDVSEDGLTYTATLRDGLKWSDGSDLTAE 119- Query: 120 DFVYTWRRIVDPKTASEYAYLATESHLLNADKINSGDIKDLNKLGVTAKGNQVTFKLTSP 17- 9 DFVY+W+R+VDPKTASEYAYLATESHL NA+ INSG DL+ LGV A GN+V F LT P Sbjct: 120 DFVYSWQRMVDPKTASEYAYLATESHLKNAEDINSGKNPDLDSLGVKADGNKVIFTLTEP 17- 9 Query: 180 CPQFKYYLAFSNFMPQKQSYVEKVGKDYGTTSKNQIYSGPYLVKDWNGSNGKFKLVKNKY 23- 9 PQFK L+FSNF+PQK+S+V+ GKDYGTTS+ QIYSGPY+VKDWNG++G FKLVKNK Sbjct: 180 APQFKSLLSFSNFVPQKESFVKDAGKDYGTTSEKQIYSGPYIVKDWNGTSGTFKLVKNKN 23- 9 Query: 240 YWDSKHVKTNSVIVQTIKKPDTAVQMYKQGQIDFAEISGTSAIYQANKNNKDVVDASDAR 29- 9 YWD+K+VKT +V VQT+KKPDTAVQMYKQG++DFA ISGTSAIY ANK +KDVV +A Sbjct: 240 YWDAKNVKTETVNVQTVKKPDTAVQMYKQGKLDFANISGTSAIYNANKKHKDVVPVLEAT 29- 9 Query: 300 TTYIIYNQTGSVKALTNQKIRQALNLATDRKGVVKAAVDTGSTPAESLVPKKLAKLPNGE 35- 9 T YI+YNQTG+++ L + KIRQALNLATDRKG+V AAVDTGS PA +LVP LAKL +G Sbjct: 300 TAYIVYNQTGAIEGLNSLKIRQALNLATDRKGIVSAAVDTGSKPATALVPTGLAKLSDGT 35- 9 Query: 360 DLSKYTAPGYTYNTSKAQKLFKEGLAEVGQSSLKLTITADSDSPAAKNAVDYVKSTWESA 41- 9 DL+++ APGY Y+ +A KLFKEGLAE+G+ +L +TITAD+D+PAAK+AVDY+K TWE+A Sbjct: 360 DLTEHVAPGYKYDDKEAAKLFKEGLAELGKDALTITITADADAPAAKSAVDYIKETWETA 41- 9 Query: 420 LPGLTVEEKFVTFKQRLEDAKNENFDVVLFSWGGDYPEGSTFYGLFTTNSAYNYGKFSSK 47- 9 LPGLTVEEKFV FKQRLED KN+NF+V + WGGDYP+GSTFYGLF + SAYNYGKF++ Sbjct: 420 LPGLTVEEKFVPFKQRLEDTKNQNFEVAVVLWGGDYPKGSTFYGLFKSGSAYNYGKFTNA 47- 9 Query: 480 EYDNAYQKAITTDALKPGDAANDYKTAEKALFDQSYYNPVY 520 +YD AY KA+TTDAL AA+DYK AEKAL+D + YNP+Y Sbjct: 480 DYDAAYNKALTTDALNTDAAADDYKAAEKALYDNALYNPLY 520 There is also homology to SEQ ID 318. An alignment of the GAS and GBS proteins is shown below: TABLE-US-02031 Identities = 138/524 (26%), Positives = 222/524 (42%), Gaps = 73/524 (13%) Query: 7 KKLKFLG-ISLATLTATTVTLVACGNESKNSGDN--KVINWYIPTEISTLDISKNTDAYS 63 KK K+L +S+A L+ + L ACGN++ + G K + + +LD + Sbjct: 5 KKSKWLAAVSVAILSVSA--LAACGNKNASGGSEATKTYKYVFVNDPKSLDYILTNGGGT 62 Query: 64 NLAIGNSGSNLLRIDKEGKPKPDLAKKVSVSSDGLTYTATLRDNLKW--SDGSK---LSA 118- I LL D+ G P LAK VS DGLTYT TLRD + W +DG + ++A Sbjct: 63 TDVITQMVDGLLENDEYGNLVPSLAKDWKVSKDGLTYTYTLRDGVSWYTADGEEYAPVTA 122- Query: 119 EDFVYTWRRIVDPKTASEYAYLATESHLLNADKINSGDIKDLNKLGVTAKGNQ-VTFKLT 17- 7 EDFV + VD K+ + Y E + N +G++ D ++GV A ++ V + L Sbjct: 123 EDFVTGLKHAVDDKSDALY---VVEDSIKNLKAYQNGEV-DFKEVGVKALDDKTVQYTLN 17- 8 Query: 178 SPCPQFKYYLAFSNFMPQKQSYVEKVGKDYGTTSKNQI-YSGPYLVKDWNGSNGKFKLVK 23- 6 P + +S P +++ GKD+GTT + I +G Y + + S + K Sbjct: 179 KPESYWNSKTTYSVLFPVNAKFLKSKGKDFGTTDPSSILVNGAYFLSAFT-SKSSMEFHK 23- 7 Query: 237 NKYYWDSKHVKTNSV--IVQTIKKPDTAVQMYKQGQIDFAEISGTSAIYQ-ANKNNKDVV 29- 3 N+ YWD+K+V SV P + + + +G+ A + Y+ A KN D + Sbjct: 238 NENYWDAKNVGIESVKLTYSDGSDPGSFYKNFDKGEFSVARLYPNDPTYKSAKKNYADNI 29- 7 Query: 294 D----ASDARTTYIIYN---------------QTGSVKALTNQKIRQALNLATDRKG--- 33- 1 D R ++ +N Q KAL N+ RQA+ A DR Sbjct: 298 TYGMLTGDIR--HLTWNLNRTSFKNTKKDPAQQDAGKKALNNKDFRQAIQFAFDRASFQA 35- 5 Query: 332 ----------------VVKAAVDTGSTPAESLVPKKLAKL-PNGEDLSKYTAPGYTYNTS 37- 4 V V G + S V K++AKL +D++ A YN Sbjct: 356 QTAGQDAKTKALRNMLVPPTFVTIGESDFGSEVEKEMAKLGDEWKDVNLADAQDGFYNPE 41- 5 Query: 375 KAQKLF---KEGLAEVGQS-SLKLTITADSDSPAAKNAVDYVKSTWESALPGLTV----- 42- 5 KA+ F KE L G + ++L D + A K + E++L V Sbjct: 416 KAKAEFAKAKEALTAEGVTFPVQLDYPVDQANAATVQEAQSFKQSVEASLGKENVIVNVL 47- 5 Query: 426 EEKFVTFKQR---LEDAKNENFDVVLFSWGGDYPEGSTFYGLFT 466 E + T + + E + +++D++ WG DY + T+ + + Sbjct: 476 ETETSTHEAQGFYAETPEQQDYDIISSWWGPDYQDPRTYLDIMS 519 SEQ ID 2102 (GBS323) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 62 (lane 4; MW 61.3 kDa). The GBS323-His fusion product was purified (FIG. 209, lane 5) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 306), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 683 A DNA sequence (GBSx0725) was identified in S. agalactiae <SEQ ID 2103> which encodes the amino acid sequence <SEQ ID 2104>. Analysis of this protein sequence reveals the following: TABLE-US-02032 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.54 Transmembrane 199-215 (198-215) ----- Final Results ----- bacterial membrane --- Certainty = 0.1617(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02033 >GP:AAC17173 GB:AF065141 unknown [Streptococcus mutans] Identities = 304/356 (85%), Positives = 334/356 (93%) Query: 1 MKRELLLEKIDELKEIMPWYVLEYYQSKLSVPYSFTTLYEYLKEYRRFLEWLLDSGVANC 60 M+RELLLEKIDELKE+MPWYVLEYYQSKL+VPYSFTTLYEYLKEYRRF EWL+DSGV+N Sbjct: 1 MRRELLLEKIDELKELMPWYVLEYYQSKLTVPYSFTTLYEYLKEYRRFFEWLIDSGVSNA 60 Query: 61 HHIAEIELSVLENLTKKDMEAFILYLRERPLLNANTRQNGVSQTTINRTLSALSSLFKYL 120- + +A+I L LE+L+KKDME+FILYLRER LLN ++ GVSQTTINRTLSALSSL+KYL Sbjct: 61 NKLADIPLETLEHLSKKDMESFILYLRERTLLNTKNKRQGVSQTTINRTLSALSSLYKYL 120- Query: 121 TEEVENADGEPYFYRNVMKKVSTKKKKETLASRAENIKQKLFLGNETIEFLEYIDCEYQN 18- 0 TEEVENADGEPYFYRNVMKKVSTKKKKETLA+RAENIKQKLFLGNET+EFLEY+DCEY+ Sbjct: 121 TEEVENADGEPYFYRNVMKKVSTKKKKETLAARAENIKQKLFLGNETMEFLEYVDCEYEQ 18- 0 Query: 181 KLSKRALAFFNKNKERDLAIIALLLASGVRLSEAVNLDLKDINLNVMVIDVTRKGGKRDS 24- 0 KLSKRAL+ F KNKERDLAIIALLLASGVRLSEAVNLDLKD+NLN+M+I+VTRKGGK DS Sbjct: 181 KLSKRALSSFRKNKERDLAIIALLLASGVRLSEAVNLDLKDVNLNMMIIEVTRKGGKHDS 24- 0 Query: 241 VNVASFAKPYLANYLDIRKNRYKAENQDIALFLSEYRGVPNRIDASSVEKMVAKYSQDFK 30- 0 VNVA FAKPYL NY+ IR+ RYKA+ D+A FLSEYRGVPNR+DASS+EKMVAKYSQDFK Sbjct: 241 VNVAGFAKPYLENYITIRRGRYKAKKTDLAFFLSEYRGVPNRMDASSIEKMVAKYSQDFK 30- 0 Query: 301 VRVTPHKLRHTLATRLYDATKSQVLVSHQLGHASTQVTDLYTHIVNDEQKNALDKL 356 +RVTPHKLRHTLATRLYDATKSQVLVSHQLGHASTQVTDLYTHIVNDEQKNALDKL Sbjct: 301 IRVTPHKLRHTLATRLYDATKSQVLVSHQLGHASTQVTDLYTHIVNDEQKNALDKL 356 A related DNA sequence was identified in S. pyogenes <SEQ ID 2105> which encodes the amino acid sequence <SEQ ID 2106>. Analysis of this protein sequence reveals the following: TABLE-US-02034 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.54 Transmembrane 211-227 (210-227) ----- Final Results ----- bacterial membrane --- Certainty = 0.1617(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9139> which encodes the amino acid sequence <SEQ ID 9140>. Analysis of this protein sequence reveals the following:

TABLE-US-02035 Possible cleavage site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.54 Transmembrane 199-215 (198-215) ----- Final Results ----- bacterial membrane --- Certainty = 0.162(Affirmative) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02036 Identities = 283/356 (79%), Positives = 321/356 (89%) Query: 1 MKRELLLEKIDELKEIMPWYVLEYYQSKLSVPYSFTTLYEYLKEYRRFLEWLLDSGVANC 60 M+RELLLEKI+ K IMPWYVL+YYQSKL+VPYSFTTLYEYLKEY+RF +WL+D+ + Sbjct: 13 MRRELLLEKIETYKAIMPWYVLDYYQSKLAVPYSFTTLYEYLKEYKRFFDWLMDADLTQA 72 Query: 61 HHIAEIELSVLENLTKKDMEAFILYLRERPLLNANTRQNGVSQTTINRTLSALSSLFKYL 120- IA+I+LS LE+LTKKD+EAF+LYLRERP LN + + G+SQTTINRTLSALSSL+KYL Sbjct: 73 PKIADIDLSTLEHLTKKDLEAFVLYLRERPSLNTYSTKEGLSQTTINRTLSALSSLYKYL 132- Query: 121 TEEVENADGEPYFYRNVMKKVSTKKKKETLASRAENIKQKLFLGNETIEFLEYIDCEYQN 18- 0 TEEVEN GEPYFYRNVMKKVSTKKKKETLASRAENIKQKLFLG+ET+ FL+Y+D EY+ Sbjct: 133 TEEVENDQGEPYFYRNVMKKVSTKKKKETLASRAENIKQKLFLGDETLAFLDYVDKEYEQ 19- 2 Query: 181 KLSKRALAFFNKNKERDLAIIALLLASGVRLSEAVNLDLKDINLNVMVIDVTRKGGKRDS 24- 0 KLS RA + F KNKERDLAIIALLLASGVRLSEAVNLDLKD+NLN+M+I+V REGGERDS Sbjct: 193 KLSNRAKSSFRKNKERDLAIIALLLASGVRLSEAVNLDLKDVNLNMMIIEVIRKGGKRDS 25- 2 Query: 241 VNVASFAKPYLANYLDIRKNRYKAENQDIALFLSEYRGVPNRIDASSVEKMVAKYSQDFK 30- 0 VNVA FAK YL +YL +R+ RYKAE QD+A FL+EYRGVPNR+DASS+EKMV KYS+DFK Sbjct: 253 VNVAGFAKGYLESYLAVRQRRYKAEKQDLAFFLTEYRGVPNRMDASSIEKMVGKYSEDFK 31- 2 Query: 301 VRVTPHKLRHTLATRLYDATKSQVLVSHQLGHASTQVTDLYTHIVNDEQKNALDKL 356 +RVTPHKLRHTLATRLYDATKSQVLVSHQLGH+STQVTDLYTHIVNDEQKNALD L Sbjct: 313 IRVTPHKLRHTLATRLYDATKSQVLVSHQLGHSSTQVTDLYTHIVNDEQKNALDNL 368 SEQ ID 2104 (GBS420) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 172 (lane 5; MW 68 kDa). GBS420-GST was purified as shown in FIG. 219, lane 9-10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 684 A DNA sequence (GBSx0726) was identified in S. agalactiae <SEQ ID 2107> which encodes the amino acid sequence <SEQ ID 2108>. This protein is predicted to be a sensor-like histidine kinase in idh 3'region. Analysis of this protein sequence reveals the following: TABLE-US-02037 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.75 Transmembrane 10-26 (8-34) INTEGRAL Likelihood = -3.93 Transmembrane 37-53 (35-54) ----- Final Results ----- bacterial membrane --- Certainty = 0.4100(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02038 >GP:CAB16001 GB:Z99124 similar to two-component sensor histidine kinase [YxdJ] [Bacillus subtilis] Identities = 96/320 (30%), Positives = 172/320 (53%), Gaps = 16/320 (5%) Query: 2 IRQFLREHLIWYILYIM--MFVLFFISFYLYHLPMPYLFNSLGLNVIVLLGISIWQYSRY 59 ++ FLR H + +L+++ +FV F+ F H +LF LG+ +++L G +++ + Sbjct: 1 MKLFLRSHAVLILLFLLQGLFVFFYYWFAGLH-SFSHLFYILGVQLLILAGYLAYRWYKD 59 Query: 60 RKKMLHLKYFNSSQDPSFELQPSDYAYFNIITQLEA--REAQKVSETIEQTNHVALMIKM 117- R L D + L S + Q+E + QK+ ET + + + Sbjct: 60 RGVYHWLSSGQEGTDIPY-LGSSVFCSELYEKQMELIRLQHQKLHETEAKLDARVTYMNQ 118- Query: 118 WSHQMKVPLAAISLMAQTNHLDP--KEVEQQLLKLQHYLETLLAFLKFRQYRDDFRFEAV 17- 5 W HQ+K PL+ I+L+ Q +P +++++++ +++ LETLL + + DF+ EAV Sbjct: 119 WVHQVKTPLSVINLIIQEED-EPVFEQIKKEVRQIEFGLETLLYSSRLDLFERDFKIEAV 17- 7 Query: 176 SLREVVVEIIKSYKVICLSKSL--SIIIEGDNIWKTDKKWLTFALSQVLDNAIKYSNPES 23- 3 SL E++ +I+SYK + + + + D+ TD KWL FA+ QV+ NA+KYS +S Sbjct: 178 SLSELLQSVIQSYKRFFIQYRVYPKMNVCDDHQIYTDAKWLKFAIGQVVTNAVKYSAGKS 23- 7 Query: 234 -----KIIISIGEESIRIQDYGIGILEEDIPRLFEDGFTGYNGHEHQKATGMGLYMTKEV 28- 8 + + ++DYG+GI +DI R+F+ +TG NG Q++TG+GL++ KE+ Sbjct: 238 DRLELNVFCDEDRTVLEVKDYGVGIPSQDIKRVFDPYYTGENGRRFQESTGIGLHLVKEI 29- 7 Query: 289 LSSLNLSISVDSKINYGTAV 308 LN ++ + S GT+V Sbjct: 298 TDKLNHTVDISSSPGEGTSV 317 SEQ ID 2108 (GBS421) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 172 (lane 6; MW 63 kDa). GBS421-GST was purified as shown in FIG. 219, lane 11. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 685 A DNA sequence (GBSx0727) was identified in S. agalactiae <SEQ ID 2111> which encodes the amino acid sequence <SEQ ID 2112>. Analysis of this protein sequence reveals the following: TABLE-US-02039 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1310 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.00000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02040 >GP:AAD10258 GB:AF036964 putative response regulator [Lactobacillus sakei] Identities = 94/222 (42%), Positives = 140/222 (62%), Gaps = 8/222 (3%) Query: 7 KIYIVEDDMTIVSLLKDHLSASYHVSSV--SNFRDVKQEIIAFQPDLILMDITLPYFNGF 64 +I IVEDD TI +L+ ++L + + ++ +F + + +P L+L+DI LP ++GF Sbjct: 3 EIMIVEDDPTIANLIAENLE-KWQLKAIIPDDFDTIFDRFLTDKPHLVLLDINLPVYDGF 61 Query: 65 YWTAELRKFLTIPIIFISSSNDEMDMVMALNMGGDDFISKPFSLAVLDAKLTAILRRSQQ 124- YW ++R+ +PIIFISS + MDMVM++NMGGDDF++KPFS+ VL AK+ A+LRR+ Sbjct: 62 YWCRKIREVSKVPIIFISSRSTNMDMVMSMNMGGDDFVNKPFSMEVLIAKINALLRRTYN 121- Query: 125 FIQQE---LTFGGFTLT-REGLLSSQDKEVILSPTENRILSILLMHPKQVVSKESLLEKL 18- 0 ++ Q + G + + G D V LS E K+L L+ Q+VS+E LL L Sbjct: 122 YVDQNTDVIEHNGLLINLQSGGAQVGDTVVDLSKNEYKLLQFLMRQHGQIVSREKLLRAL 18- 1 Query: 181 WENDSFIDQNTLNVNMTRLRKKIVPIGF-DYIHTVRGVGYLL 221 W+++ F+D NTL VN+ RLRKKI G DYI T G GY++ Sbjct: 182 WDDERFVDDNTLTVNINRLRKKIEQAGLEDYIQTKIGQGYII 223 There is also homology to SEQ ID 1182. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 686 A DNA sequence (GBSx0728) was identified in S. agalactiae <SEQ ID 2113> which encodes the amino acid sequence <SEQ ID 2114>. This protein is predicted to be permease OrfY. Analysis of this protein sequence reveals the following: TABLE-US-02041 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.62 Transmembrane 55-71 (49-75) INTEGRAL Likelihood = -10.30 Transmembrane 197-213 (192-218) INTEGRAL Likelihood = -9.13 Transmembrane 152-168 (141-172) INTEGRAL Likelihood = -8.70 Transmembrane 624-640 (619-645) INTEGRAL Likelihood = -8.44 Transmembrane 222-238 (219-250) INTEGRAL Likelihood = -7.75 Transmembrane 283-299 (280-307) INTEGRAL Likelihood = -7.70 Transmembrane 533-549 (526-552) INTEGRAL Likelihood = -6.95 Transmembrane 108-124 (99-140) INTEGRAL Likelihood = -4.88 Transmembrane 585-601 (581-610) INTEGRAL Likelihood = -3.82 Transmembrane 25-41 (21-47) INTEGRAL Likelihood = -0.48 Transmembrane 602-618 (602-618) ----- Final Results ----- bacterial membrane --- Certainty = 0.5649 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9809> which encodes amino acid sequence <SEQ ID 9810> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02042 >GP:AAF99695 GB:AF267498 permease OrfY [Streptococcus mutans] Identities = 154/665 (23%), Positives = 299/665 (44%), Gaps = 40/665 (6%) Query: 4 MFYLKIAWHNLKHSIDQYIPFLLASLLLYSLTCSTLLILMSAVGRDMGTAAT---VLFLG 60 MF KI++HNL + +P+ + + L + ++ TA +L G Sbjct: 1 MFLPKISFHNLIVNKSLTLPYFAIMTIFSGFNYVLINFLTNPSFYNIPTARILIDILIFG 60 Query: 61 VIVLSIFAVVMEHYSYMILMKQRSSEFGLYNILGMNKRQVARVASLELFIIYIFLISIGS 120- I++S+ ++ Y+ + +R+S G++ +LGM K+Q+ ++ LE ++ G Sbjct: 61 FILISLLMLLYGRYANRFISDERNSNMGIFLMLGMGKRQLLKIIYLEKLYLFTGTFFGGL 120- Query: 121 LFSAFFAKFIYLIFVNIINYHALNLSLSLWPFIICIVIFTGIFLTLEVPVIRHVHLSSPL 18- 0 +F ++K +L N+I + SL +++ I+ + + R + S Sbjct: 121 IFGFVYSKIFFLFIRNLIVIGDVREQYSLTAISWLLILTFFIYFIIYLSEYRLLKRQSIT 18- 0 Query: 181 SLFRKKQQGEKEPKGNLILAILALVAIAIAYTMALTSGKAPALAVIY-RFFFAVLLVIAG 23- 9 +F K + + K ++ + + L A+ + Y ALTS P + + RF +A LV G Sbjct: 181 VIFNSKAKRDNPRKTSVFVGLFGLFALLMGYHFALTS---PNVTTSFSRFIYAACLVTLG 23- 7 Query: 240 TYLFYISFMTWYLKRLRQNKHYYYKSEHFVSTSQMIFRMKQNAVGLASITLLAVMALVTI 29- 9 + + S + L +++ + YY FV + + R++ NA+ LA+I + + LV++ Sbjct: 238 IFCTFSSGVIMLLTVIKKRRAIYYNQRRFVVIASLFHRIRSNALSLATICIFSTATLVSL 29- 7 Query: 300 ATTVSLYSNTQNVVTGLFPKSVSLSIDNSKGDAKNIFEEKILKKLGKSSKEAITYNQTMI 35- 9 + SLY N+V P+ V++ S D E L + + +T Q Sbjct: 298 SVLASLYLAKDNMVRLSSPRDVTVL---STTDI-----EPNLMDIATKNHVTLTNRQ--- 34- 6 Query: 360 SMPVSQSSELNITSKNVKHVDITKTGFNY------LITQNDFRRLGHQLPKLKDNQVAYF 41- 3 ++ VSQS NI H+ + G M +I+ + F + +LK++++ + Sbjct: 347 NLKVSQSVYGNIKGS---HLSVDPNGGMANDYQITVISLDSFNASNNTHYRLKNHEILTY 40- 3 Query: 414 VQKGDSRLKKINLLGNKFDVVKNLKEA-YVPETTNTYNPGLIIFANNKQI-DNIRKAYLP 47- 1 V G + G K VK +K ++ + P I +N++I I K L Sbjct: 404 VSNGAAAPSSYTTNGVKLTNVKQIKRINFIFSPLRSMQPNFFIITDNREIIQTILKEELT 46- 3 Query: 472 YTKNINTFPKTFKAYLDLNSQEINSISKNDIIEVDG--KYVGNISTKQSFLKEGYQMFGG 52- 9 + T Y + +++N D +E ++ N+ + + +FGG Sbjct: 464 WG--------TMAGY-HVKGKKMNQKDFYDELETTNFRQFSANVVSIRQVKSMFNALFGG 51- 4 Query: 530 LLFTGFLLGISFLLGIALIVYYKQYSEGHEDKRSYRILQEVGMSKKLVKRTINSQIMIFF 58- 9 LLF G + G F + A+ +YY+Q SEG D+ Y+ + ++GM+ K ++ +I QI F Sbjct: 515 LLFVGIIFGTIFAILTAITIYYQQLSEGIRDRDDYKAMIKLGMTNKTIQDSIKVQINFVF 57- 4 Query: 590 FQPLVVAVIHFGVAIPMLKQMLLVFGVLNSTIVYVVSGLTVLAISIIYFIIYRITSRTYY 64- 9 P+ A+++ A+P+L +++ FG ++ + G ++ Y+ I TS+ YY Sbjct: 575 ILPIAFALLNLIFALPILYKIMTTFGFNDAGLFLRAVGTCLIVYLFFYWFICHCTSKLYY 63- 4 Query: 650 HIIER 654 +I + Sbjct: 635 RLISK 639 A related DNA sequence was identified in S. pyogenes <SEQ ID 2115> which encodes the amino acid sequence <SEQ ID 2116>. Analysis of this protein sequence reveals the following: TABLE-US-02043 Possible site: 35 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -13.59 Transmembrane 602-618 (592-630) INTEGRAL Likelihood = -12.26 Transmembrane 59-75 (50-81) INTEGRAL Likelihood = -12.21 Transmembrane 235-251 (224-262) INTEGRAL Likelihood = -9.82 Transmembrane 159-175 (146-177) INTEGRAL Likelihood = -9.02 Transmembrane 201-217 (198-223) INTEGRAL Likelihood = -8.97 Transmembrane 510-526 (507-540) INTEGRAL Likelihood = -6.42 Transmembrane 569-585 (564-589) INTEGRAL Likelihood = -5.95 Transmembrane 109-125 (102-138) INTEGRAL Likelihood = -4.09 Transmembrane 294-310 (290-315) INTEGRAL Likelihood = -1.86 Transmembrane 126-142 (126-142) ----- Final Results ----- bacterial membrane --- Certainty = 0.6434 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02044 >GP:BAB03337 GB:AB035452 ABC transporter [Staphylococcus aureus] Identities = 141/657 (21%), Positives = 289/657 (43%), Gaps = 66/657 (10%) Query: 5 ITKSNIKKNFSLYRIYFLATIGLLSIFIAFLNFISDKII--TEKIGDSGQALVIANGSL- 61 I N+++N Y +Y L S+F + + + S + T+ + + +I G+L Sbjct: 6 IVFKNLRQNLKHYAMY------LFSLFFSIVLYFSFTTLQFTKGVNNDDSMAIIKKGALV 59 Query: 62 --IFLIVFLVVFLIYFNNFFVKKRSQELGVLAILGFSKRELTKLLTLENLVILVLSYLVS 119- IFL + +V+FL+Y N+ FVK+R++E + ++G +++ + K+L LE +++ +++ +V Sbjct: 60 GSIFLFIIIVIFLMYANHLFVKRRTREFALFQLIGLTRQNILKMLALEQMIVFLITGVVG 119- Query: 120 LLLGPTLYFLAVLAITHLLNLTMEVQWFITVNEIIESLGILVVVFLINVITNGLIISKQS 17- 9 +L G L + ++ L++L++ + ++ ++ +L++ +++ + + L + ++S Sbjct: 120 VLCGIAGAQLLLSIVSKLMSLSINLSIHFEPMALVLTIFMLIIAYVLILFQSALFLKRRS 17- 9 Query: 180 LIEFVNFSRKAE----KKIKIRKVRAIIAITALLLSYILCLATVFSSTRNMLLSIGMVPV 23- 5 ++ + S K + K + ++ I + L Y +AT T L P Sbjct: 180 ILSMMKDSIKTDATTAKVTTAEVISGVLGIAMIALGYY--MATEMFGTFKALTMAMTSP- 23- 6 Query: 236 SLLIIVLVVLGTVFTIRYGLAFVVSLLKENKKRLYRPLSNIIYPKFNYRIATKNKLLTVL 29- 5 +I+ L V+G R ++ + LK++K + YR+ LT++ Sbjct: 237 -FIILFLTVVGAYLFFRSSVSLIFKTLKKSKNGRVSITDVVFTSSIMYRMKKNAMSLTII 29- 5 Query: 296 GGLLTVTVSVAGMMVMLYAYSLNGIERLTPSAIEYNVESENGQVNVTTILENDQVSL--- 35- 2 + VTV+V + + + + + P+ E+NV + T L Q++ Sbjct: 296 AIISAVTVTVLCFAALSKSNTDQTLTSMAPN--EFNVVATQDAKQFETKLSQQQITFSKN 35- 3 Query: 353 ----VDVGLLRLNTIPEVTITDSGQTIPYFDIINYSDYKELMKAQGRTNSIEGSKSLPLL 40- 8 + V ++ I +DSG+T N K G I +KSLP + Sbjct: 354 AYETITVDNVKDQVITLENGSDSGRTNSILSANN--------KVTGNNAIITNTKSLPNI 40- 5 Query: 409 INYYPTEISLGKTFNLGNAYDVT--VKQVSTNNVFSFSTSVTTLV--VSDKLYAKLSSRF 46- 4 IN I L K + + T V Q V+ + S + V VS + Y +L + Sbjct: 406 IN-----IHLNKDLVVKGTKNETFRVTQEDKGRVYPLNLSFNSPVVEVSPEKYQQLKT-- 45- 8 Query: 465 PEKEMTIRTFNGTSIR------SSEAFYNQFSMVPDVISSYSKEHTVKTANIATYIFIT- 51- 7 + + TF G I+ ++A QF D + +Y + A IF+T Sbjct: 459 ---QNNVHTFYGYDIKQTSQKEKAQAIAKQFG---DKVITYDEMKKEVDATNGILIFVTS 51- 2 Query: 518 FLSILFIICTGSILYFTSLIEIMENKEEYGYLSKLGYSKKMIHRILRYETGILFLIPVFI 57- 7 FL + F++ G I+Y + E + + L ++G++ + + L + F +P+ I Sbjct: 513 FLGLAFLVAAGCIIYIKQMDETEDELSNFRILKRIGFTHTDMLKGLLLKITFNFGLPLLI 57- 2 Query: 578 GIVNGGMLLIYYKYLFMDTLVAGNIIMLSLLLCLLFFLIIYGTFYVLTLRLVTSIIK 634 I++ I + L GNI + +++ ++ + +IY TF ++ +IK Sbjct: 573 AILHAVFAAIAFMKLM------GNISFMPVIVVIVVYTLIYITFALIAFVHSNKLIK 623 An alignment of the GAS and GBS proteins is shown below: TABLE-US-02045 Identities = 145/678 (21%), Positives = 277/678 (40%), Gaps = 89/678 (13%) Query: 13 NLKHSIDQYIPFLLASLLLYSLTCSTL-----LILMSAVGRDMGTAATVLFLGVIVLSIF 67 - N+K + Y + LA++ L S+ +L I+ +G D G A + +I L +F Sbjct: 9 NIKKNFSLYRIYFLATIGLLSIFIAFLNFISDKIITEKIG-DSGQALVIANGSLIFLIVF 67 Query: 68 AVVMEHYSYNILMKQRSSEFGLYNILGMNKRQVARVASLELFIIYIFLISIGSLFSAFFA 127- VV Y N +K+RS E G+ ILG +KR++ ++ +LE +I + + L S Sbjct: 68 LVVFLIYFNNFFVKKRSQELGVLAILGFSKRELTKLLTLENLVILV----LSYLVSLLLG 123- Query: 128 KFIYLIFVNIINYHALNLSLSLWPFIICIVIFTGIFLTLEVPVIRHV------HLSSPLS 18- 1 +Y + V I H LNL++ + FI I + + + V +I + S + Sbjct: 124 PTLYFLAVLAIT-HLLNLTMEVQWFITVNEIIESLGILVVVFLINVITNGLIISKQSLIE 18- 2 Query: 182 LFRKKQQGEKEPKGNLILAILALVAIAIAYTMAL------TSGKAPALAVIYRFFFAVLL 23- 5 ++ EK+ K + AI+A+ A+ ++Y + L T ++ ++ ++L Sbjct: 183 FVNFSRKAEKKIKIRKVRAIIAITALLLSYILCLATVFSSTRNMLLSIGMVPVSLLIIVL 24- 2 Query: 236 VIAGTYLFYISFMTWYLKRLRQNKHYYYKSEHFVSTSQMIFRMKQNAVGLASITLLAVMA 29- 5 V+ GT + + + L++NK Y+ + + +R+ A +T+L + Sbjct: 243 VVLGTVFTIRYGLAFVVSLLKENKKRLYRPLSNIIYPKFNYRI---ATKNKLLTVLGGLL 29- 9 Query: 296 LVTIATT---VSLYSNTQNVVTGLFPKSVSLSIDNSKGDAKNIFEEKILKKLGKSSKEAI 35- 2 VT++ V LY+ + N + L P ++ ++++ G + I Sbjct: 300 TVTVSVAGMMVMLYAYSLNGIERLTPSAIEYNVESENGQV---------------NVTTI 34- 4 Query: 353 TYNQTMISMPVSQSSELNITSKNVKHVDITKTG----FMYLITQNDFRRL------GHQL 40- 2 N + + V + + V IT +G + +I +D++ L + + Sbjct: 345 LENDQVSLVDVGL-----LRLNTIPEVTITDSGQTIPYFDIINYSDYKELMKAQGRTNSI 39- 9 Query: 403 PKLKDNQVAYFVQKGDSRLKKINLLGNKFDVVKNLKEAYVPETTNTYNPGLIIFANNKQI 46- 2 K + + L K LGN +DV +K+ + + ++K Sbjct: 400 EGSKSLPLLINYYPTEISLGKTFNLGNAYDVT--VKQVSTNNVFSFSTSVTTLVVSDKLY 45- 7 Query: 463 DNIRKAYLPYTKNINTFPKT-------FKAYLDLNSQEINSISKNDIIEVDGKYVGNIST 51- 5 + + I TF T F + I+S SK ++ NI+T Sbjct: 458 AKLSSRFPEKEMTIRTFNGTSIRSSEAFYNQFSMVPDVISSYSKEHTVKT-----ANIAT 51- 2 Query: 516 KQSFLKEGYQMFGGLLFTGFLLGISFLLGIALIVYYKQYSEGHEDKRSYRILQEVGMSKK 57- 5 +F FL I F++ I+Y+ E E+K Y L ++G SKK Sbjct: 513 --------------YIFITFL-SILFIICTGSILYFTSLIEIMENKEEYGYLSKLGYSKK 55- 7 Query: 576 LVKRTINSQIMIFFFQPLVVAVIHFGVAIPMLKQMLLVFGVLNSTIVYVVSGLTVLAISI 63- 5 ++ R + + I F P+ + +++ G+ + K L + ++ I+ + L +L I Sbjct: 558 MIHRILRYETGILFLIPVFIGIVNGGMLLIYYK-YLFMDTLVAGNIIMLSLLLCLLFFLI 61- 6 Query: 636 IYFIIYRITSRTYYHIIE 653 IY Y +T R II+ Sbjct: 617 IYGTFYVLTLRLVTSIIK 634 A related GBS gene <SEQ ID 8639> and protein <SEQ ID 8640> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02046 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: -11.64 GvH: Signal Score (-7.5): -3.52 Possible site: 37 >>> Seems to have no N-terminal signal sequence ALOM program count: 11 value: -11.62 threshold: 0.0 INTEGRAL Likelihood = -11.62 Transmembrane 55-71 (49-75) INTEGRAL Likelihood = -10.30 Transmembrane 197-213 (192-218) INTEGRAL Likelihood = -9.13 Transmembrane 152-168 (141-172) INTEGRAL Likelihood = -8.70 Transmembrane 624-640 (619-645) INTEGRAL Likelihood = -8.44 Transmembrane 222-238 (219-250) INTEGRAL Likelihood = -7.75 Transmembrane 283-299 (280-307) INTEGRAL Likelihood = -7.70 Transmembrane 533-549 (526-552) INTEGRAL Likelihood = -6.95 Transmembrane 108-124 (99-140) INTEGRAL Likelihood = -4.88 Transmembrane 585-601 (581-610) INTEGRAL Likelihood = -3.82 Transmembrane 25-41 (21-47) INTEGRAL Likelihood = -0.48 Transmembrane 602-618 (602-618) PERIPHERAL Likelihood = 1.16 129 modified ALOM score: 2.82 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5649 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00050## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 687 A DNA sequence (GBSx0729) was identified in S. agalactiae <SEQ ID 2117> which encodes the amino acid sequence <SEQ ID 2118>. This protein is predicted to be ABC transporter OrfX. Analysis of this protein sequence reveals the following:

TABLE-US-02047 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5121 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02048 >GP:AAF99694 GB:AF267498 ABC transporter OrfX [Streptococcus mutans] Identities = 118/242 (48%), Positives = 175/242 (71%), Gaps = 1/242 (0%) Query: 5 INHLEKVFRTRFSKEETRALQDVDFKVEQGEFIAIMGESGSGKTTLLNILATLEKPTNGQ 64 ++HL+KV++T+ AL+D+ F V++GEFIAIMGESGSGK+TLLNILA ++ P++G Sbjct: 6 VSHLKKVYKTQEGLTN-EALKDITFSVQEGEFIAIMGESGSGKSTLLNILACMDYPSSGH 64 Query: 65 VILNGEDITKIKEAKLASFRLKNLGFVFQDFNLLDTLSVRDNIYLPLVLDRKRYKEMDHR 124- +I N + K+K+ + A FR +++GF+FQ+FNLL+ + +DN+ +P+++ + + R Sbjct: 65 IIFNNYQLEKVKDEEAAVFRSRHIGFIFQNFNLLNIFNNKDNLLIPVIISGSKVNSYEKR 124- Query: 125 LSELSSHLRIDDLLDKRPFELSGGQKQRVAIARSLITNPQILLADEPTAALDYRNSEDLL 18- 4 L +L++ + I+ LL K P+ELSGGQ+QR+AIAR+LI NP ++LADEPT LD + S+ +L Sbjct: 125 LRDLAAVVGIESLLSKYPYELSGGQQQRLAIARALIMNPDLILADEPTGQLDSKTSQRIL 18- 4 Query: 185 NLFETINLDGQTILMVTHSANAASHAKRVLFIKDGRIFHQLYRGNKNNSEFNKDISLTMS 24- 4 NL IN +TILMVTHS AAS+A RVLFIKDG IF+QL RG K+ F I + + Sbjct: 185 NLLSNINAKRKTILMVTHSPKAASYANRVLFIKDGVIENQLVRGCKSREGFLDQIIMAQA 24- 4 Query: 245 AI 246 ++ Sbjct: 245 SL 246 A related DNA sequence was identified in S. pyogenes <SEQ ID 2119> which encodes the amino acid sequence <SEQ ID 2120>. Analysis of this protein sequence reveals the following: TABLE-US-02049 Possible Site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2131 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02050 Identities = 91/222 (40%), Positives = 142/222 (62%), Gaps = 2/222 (0%) Query: 2 LLEINHLEKVFRTRFSKEETRALQDVDFKVEQGEFIAIMGESGSGKTTLLNILATLEKPT 61 LL + + K + EE L+ +D +V +G+F+AIMG SGSGK+TL+NI+ L+KP Sbjct: 1 LLNLKDIRKSYH--LGTEEFAILKGIDLEVNEGDFLAIMGPSGSGKSTLMNIIGCLDKPG 58 Query: 62 NGQVILNGEDITKIKEAKLASFRLKNLGFVFQDFNLLDTLSVRDNIYLPLVLDRKRYKEM 121- +G + G D++ + + +LA R + +GFVFQ+FNL+ L+ N+ LPL KE Sbjct: 59 SGSYAIEGRDVSSLSDNELADLRNQKIGFVFQNFNLMPKLTACQNVELPLTYMNVPKKER 118- Query: 122 DHRLSELSSHLRIDDLLDKRPFELSGGQKQRVAIARSLITNPQILLADEPTAALDYRNSE 18- 1 R E+ + +++ + +P ELSGGQKQRVAIAR+L+TNP +L DEPT ALD + S Sbjct: 119 RKRALEMLKLVGLEERSEFKPMELSGGQKQRVAIARALVTNPSFILGDEPTGALDTKTSV 17- 8 Query: 182 DLLNLFETINLDGQTILMVTHSANAASHAKRVLFIKDGRIFH 223 +++LF+ N +G+TI+++TH A+ K+ + ++DG I H Sbjct: 179 QIMDLFKQFNDNGKTIIIITHEPEVAALCKKTVILRDGNIEH 220 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 688 A DNA sequence (GBSx0730) was identified in S. agalactiae <SEQ ID 2121> which encodes the amino acid sequence <SEQ ID 2122>. This protein is predicted to be nisin-resistance protein. Analysis of this protein sequence reveals the following: TABLE-US-02051 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.16 Transmembrane 8-24 (1-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.6265 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02052 >GP:AAB08491 GB:U25181 nisin-resistance protein [Lactococcus lactis] Identities = 108/318 (33%), Positives = 190/318 (58%), Gaps = 8/318 (2%) Query: 3 RKIVLLFVVPMLIVLGILGVVVHYYGSALNIYLLPPSSERYGRVILDRVEQRGLYSQGRQ 62 ++I+L V + LGI ++++G NIYL+PPS ++Y RV L +++ GL++ ++ Sbjct: 5 KRILLGLVAVCALFLGI----IYFWGYKFNIYLVPPSPQKYVRVALKNMDELGLFTDSKE 60 Query: 63 WQIIRQRSEKKLKTSKSYQESRNIVQEAVRYGGGKHSQILSKETVRRDTLDSRYPEYRRL 122- W ++++ ++ +K+Y E+ +Q+A++ GGKHS I +E + + ++ + Sbjct: 61 WVETKKKTIEETSNAKNYAETIPFLQKAIKVAGGKHSFIEHEEDISKRSITKYIKPKAEI 120- Query: 123 NEDILLITIPSISKLDKRSISHYSGKLQNILMEKSYKGLILDLSNNTGGNMIPMIGGVAS 18- 2 + L++TIP + D ++ S Y+ L++ + +Y G+I+DL N GG++ PM+ G++ Sbjct: 121 EGNTLILTIPEFTGNDSQA-SDYANFLESSFHKNNYNGVIVDLRGNRGGDLSPMVLGLSP 17- 9 Query: 183 ILPNDTLFHYTDKYGNKKTITMKNIPLEALKISRKTINTKHV---PIAIITNHKTASSAE 23- 9 +LP+ TLF Y DK + K + ++N + + S K + K + PIA++ ++ T SS E Sbjct: 180 LLPDGTLFTYVDKSSHSKPVELQNGEINSGGSSTKVSDNKKIKKAPIAVLIDNNTGSSGE 23- 9 Query: 240 MTFLSFKGLPNVKSFGQATAGYTTVNETFMLYDGARLALTTGIVSDRQGYKYENTPILPD 299 +T L FKG+PNVK G +AGYT+ N+T LYDG+ L +T+ V DR Y+N PI PD Sbjct: 240 LTALCFKGIPNVKFLGSDSAGYTSANQTVYLYDGSTLQITSAFVKDRTNNIYKNFPISPD 29- 9 Query: 300 QVTSLPLQESQSWLKSRI 317 T+ + W+KS+I Sbjct: 300 IQTNNAKSSAIEWIKSQI 317 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8641> and protein <SEQ ID 8642> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02053 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 12.71 GvH: Signal Score (-7.5): -5.64 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -13.16 threshold: 0.0 INTEGRAL Likelihood = -13.16 Transmembrane 8-24 (1-31) PERIPHERAL Likelihood = 4.03 174 modified ALOM score: 3.13 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6265 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00051## SEQ ID 2122 (GBS38) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 14 (lane 7; MW 37 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 12; MW 62 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 689 A DNA sequence (GBSx0731) was identified in S. agalactiae <SEQ ID 2123> which encodes the amino acid sequence <SEQ ID 2124>. Analysis of this protein sequence reveals the following: TABLE-US-02054 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2125> which encodes the amino acid sequence <SEQ ID 2126>. Analysis of this protein sequence reveals the following: TABLE-US-02055 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1369 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02056 Identities = 31/49 (63%), Positives = 43/49 (87%) Query: 6 KKLTKSLGPIGKLISIIPDTTELIGKAIDNSRPIIEKELDRRHEKKTDL 54 K++ K+LG +GKL+SI+PDTTE+IGK IDNSRPIIEK ++++HEK+ L Sbjct: 3 KRIRKALGVVGKLMSIVPDTTEIIGKTIDNSRPIIEKRMEQKHEKEMQL 51 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 690 A DNA sequence (GBSx0732) was identified in S. agalactiae <SEQ ID 2127> which encodes the amino acid sequence <SEQ ID 2128>. Analysis of this protein sequence reveals the following: TABLE-US-02057 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3644 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 2126. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 691 A DNA sequence (GBSx0733) was identified in S. agalactiae <SEQ ID 2129> which encodes the amino acid sequence <SEQ ID 2130>. This protein is predicted to be 28 kd outer membrane protein precursor (yaeC). Analysis of this protein sequence reveals the following: TABLE-US-02058 Possible site: 16 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02059 >GP:CAB59827 GB:AJ012388 hypothetical protein [Lactococcus lactis] Identities = 123/290 (42%), Positives = 178/290 (60%), Gaps = 18/290 (6%) Query: 1 MKIKKLLGLTTTVVISALILGAC------GQSKNEDAKVVRVGTMVKSKTEKARWDKIEE 54 +K +++L +T +++ +I+G G +K+V++G M K E W ++++ Sbjct: 3 VKNRRIL-ITIIILVFIIIVGGIFAFSHSGNKSKVSSKIVKIGLMPGGKQEDVIWKQVQK 61 Query: 55 LVKKK-GVKLKFTEFTDYTQPNKALESDEIDINAFQHYNYLNNWNKANKTNLVSVAETYF 113- K + G+ LKF FTD +PNKAL + E+D+NAFQHY YL +WNKAN N+VS+ +T Sbjct: 62 NAKDQFGITLKFVNFTDGDEPNKALVNHEVDLNAFQHYAYLKSWNKANNGNIVSIGDTII 121- Query: 114 TSFRLYSGTKNGKGKYQTVSEIPNKATITIPNDAVNESRSLYLLQSAGLLKLKVSGDALA 17- 3 T LYS KY+ V EIP+K+TI IPND NESR+LY+L++AGL+KL S LA Sbjct: 122 TPIHLYST------KYKKVDEIPDKSTIAIPNDITNESRALYVLKNAGLIKLDTSRGVLA 17- 5 Query: 174 TMSDVVSNPKSLDLKEVDAAQTARSLDSTDAAVINNDFVTEAGINPKSAIFIEPKSKNAK 23- 3 T+ D+ NPKSL +KE+DA+QT R+LDS AAVIN +F A + K +I+ EP ++++ Sbjct: 176 TVKDIRENPKSLIIKEIDASQTPRALDSVAAAVINYNFAISAKNSDKESIYQEPLNEDSA 23- 5 Query: 234 QWYNLLVAQKGWQDKSKAKAIKEVVKAYHTDAVKKVIEKT-SQGLDQPVW 282 QW N + A Q K KEVVKAY + +I+K G + P W Sbjct: 236 QWINFIAAN---QSDKNNKVYKEVVKAYEQKNIADIIKKEYPDGGELPAW 282 A related DNA sequence was identified in S. pyogenes <SEQ ID 2131> which encodes the amino acid sequence <SEQ ID 2132>. Analysis of this protein sequence reveals the following: TABLE-US-02060 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1766 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02061 Identities = 145/264 (54%), Positives = 203/264 (75%), Gaps = 2/264 (0%) Query: 20 LGACGQSKNEDAKVVRVGTMVKSKTEKARWDKIEELVKKKGVKLKFTEFTDYTQPNKALE 79 - L AC + K +D + +G M K+++++ARWDK+EEL+KK + LK+ EFTDY+QPNKA+ Sbjct: 1 LVACSE-KQDDKNTLTIGVMTKTESDQARWDKVEELLKKDNITLKYKEFTDYSQPNKAVA 59 Query: 80 SDEIDINAFQHYNYLNNWNKANKTNLVSVAETYFTSFRLYSGT-KNGKGKYQTVSEIPNK 138- + E+DINAFQHYN+LNNWNK NK +LV++A+TY + L+SGT ++GK KY++V+++PN Sbjct: 60 NGEVDINAFQHYNFLNNWNKENKEHLVAIADTYISPINLFSGTSQDGKAKYKSVADLPNG 119- Query: 139 ATITIPNDAVNESRSLYLLQSAGLLKLKVSGDALATMSDVVSNPKSLDLKEVDAAQTARS 19- 8 I +PNDA NESR+LY+LQSAGL+KL VSGD LAT++++ N K LD+KE+DA+QTAR+ Sbjct: 120 TQIAVPNDATNESRALYVLQSAGLIKLNVSGDQLATIANISENKKKLDIKELDASQTARA 17- 9 Query: 199 LDSTDAAVINNDFVTEAGINPKSAIFIEPKSKNAKQWYNLLVAQKGWQDKSKAKAIKEVV 25- 8 L S DAAV+NN + A I+ K+++F E N+KQW N++ QK W+ KA AIK+++ Sbjct: 180 LVSADAAVVNNSYAVPAKIDYKTSLFKEKADDNSKQWINIIAGQKDWEKSEKADAIKKLI 23- 9 Query: 259 KAYHTDAVKKVIEKTSQGLDQPVW 282 KAY TD VKKV+EKTS G+D VW Sbjct: 240 KAYQTDEVKKVVEKTSNGIDVSVW 263 SEQ ID 2130 (GBS96) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 19 (lane 7; MW 32 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 22 (lane 3; MW 57.2 kDa). The GBS96-GST fusion product was purified (FIG. 195, lane 10) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 290), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 692 A DNA sequence (GBSx0734) was identified in S. agalactiae <SEQ ID 2133> which encodes the amino acid sequence <SEQ ID 2134>. Analysis of this protein sequence reveals the following: TABLE-US-02062 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5103 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9807> which encodes amino acid sequence <SEQ ID 9808> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 693 A DNA sequence (GBSx0735) was identified in S. agalactiae <SEQ ID 2135> which encodes the amino acid sequence <SEQ ID 2136>. This protein is predicted to be glucose-inhibited division protein (gid). Analysis of this protein sequence reveals the following: TABLE-US-02063 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0656 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02064 >GP:CAB13486 GB:Z99112 glucose-inhibited division protein [Bacillus subtilis] Identities = 289/439 (65%), Positives = 352/439 (79%), Gaps = 10/439 (2%) Query: 1 MSQSYINVIGAGLAGSEAAYQIAKRGIPVKLYEMRGVESTPQHKTDNFAELVCSNSFRGD 60 M+Q +NVIGAGLAGSEAA+Q+ARRGI VKLYEMR VR TP H TD FAELVCSNS R + Sbjct: 1 MNQQTVNVIGAGLAGSEAAWQLAKRGIQVKLYEMRPVKQTPAHHTDKFAELVCSNSLRSN 60 Query: 61 SLTNAVGLLKEEMRRLDSIIMRNGEAHRVPAGGAMAVDREGYSEAVTEEIHKHPLIEVIR 120- +L NAVG+LKEEMR LDS I+ + VPAGGA+AVDR ++ +VT + HP + VI Sbjct: 61 TLANAVGVLKEEMRALDSAIIAAADECSVPAGGALAVDRHEFAASVTNRVKNHPNVTVIN 120- Query: 121 DEITDIPGDAITVIATGPLTSDSLAAKIHELNGGDGFYFYDAAAPIVDKNTIDINKVYLK 18- 0 +E+T+IP + T+IATGPLTS+SL+A++ EL G D YFYDAAAPIV+K+++D++KVYLK Sbjct: 121 EEVTEIP-EGPTIIATGPLTSESLSAQLKELTGEDYLYFYDAAAPIVEKDSLDMDKVYLK 17- 9 Query: 181 SRYDKGEAAYLNCPMTKEEFMAFHEALTTAEEAPLNSFEKEKYFEGCMPIEVMAKRGIKT 24- 0 SRYDKGEAAYLNCPMT+EEF FHEALT+AE PL FEKE +FEGCMPIEVMAKRG KT Sbjct: 180 SRYDKGEAAYLNCPMTEEEFDRFHEALTSAETVPLKEFEKEIFFEGCMPIEVMAKRGKKT 23- 9 Query: 241 MLYGPMKPVGLEYPEDYKGPRDGEFKTPYAVVQLRQDNAAGSLYNIVGFQTHLKWGEQKR 30- 0 ML+GPMKPVGLE+P K PYAVVQLRQD+AAG+LYNIVGFQTHLKWG+QK Sbjct: 240 MLFGPMKPVGLEHPVTGK--------RPYAVVQLRQDDAAGTLYNIVGFQTHLKWGDQKE 29- 1 Query: 301 VFQMIPGLENAEFVRYGVMHRNSYMDSPNLLNQTFATRKNPNLFFAGQMTGVEGYVESAA 36- 0 V ++IPGLEN E VRYGVMHRN++++SP+LL T+ + +LFFAGQMTGVEGYVESAA Sbjct: 292 VLKLIPGLENVEIVRYGVMHRNTFINSPSLLKPTYQFKNRSDLFFAGQMTGVEGYVESAA 35- 1 Query: 361 SGLVAGINAVRRFNGESEVVFPQTTAIGALPHYITHTDSKHFQPMNVNFGIIKELEGPRI 42- 0 SGLVAGINA + GE V+FPQ TAIG++ HYIT T+K+FQPMN NFG++KEL +I Sbjct: 352 SGLVAGINAAKLVLGEELVIFPQETAIGSMAHYITTTNQKNFQPMNANFGLLKELP-VKI 41- 0 Query: 421 RDKKERYEAIATRALKDLE 439 ++KKER E A RA++ ++ Sbjct: 411 KNKKERNEQYANRAIETIQ 429 A related DNA sequence was identified in S. pyogenes <SEQ ID 2137> which encodes the amino acid sequence <SEQ ID 2138>. Analysis of this protein sequence reveals the following:

TABLE-US-02065 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.44 Transmembrane 12-28 (9-32) ----- Final Results ----- bacterial membrane --- Certainty = 0.4376 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 111-113 The protein has homology with the following sequences in the databases: TABLE-US-02066 >GP:CAB13486 GB:Z99112 glucose-inhibited division protein [Bacillus subtilis] Identities = 292/435 (67%), Positives = 350/435 (80%), Gaps = 10/435 (2%) Query: 59 INVIGAGLAGSEAAYQIAKRGIPVKLYEMRGVKATPQHKTTNFAELVCSNSFRGDSLTNA 118- +NVIGAGLAGSEAA+Q+AKRGI VKLYEMR VK TP H T FAELVCSNS R ++L NA Sbjct: 6 VNVIGAGLAGSEAAWQLAKRGIQVKLYEMRPVKQTPAHHTDKFAELVCSNSLRSNTLANA 65 Query: 119 VGLLKEEMRRLDSIIMRNGEANRVPAGGAMAVDREGYAESVTAELENHPLIEVIRGEITE 17- 8 VG+LKEEMR LDS I+ + VPAGGA+AVDR +A SVT ++NHP + VI E+TE Sbjct: 66 VGVLKEEMRALDSAIIAAADECSVPAGGALAVDRHEFAASVTNRVKNHPNVTVINEEVTE 125- Query: 179 IPDDAITVIATGPLTSDALAEKIHALNGGDGFYFYDAAAPIIDKSTIDMSKVYLKSRYDK 23- 8 IP+ T+IATGPLTS++L+ ++ L G D YFYDAAAPI++K ++DM KVYLKSRYDK Sbjct: 126 IPEGP-TIIATGPLTSESLSAQLKELTGEDYLYFYDAAAPIVEKDSLDMDKVYLKSRYDK 18- 4 Query: 239 GEAAYLNCPMTKEEFMAFHEALTTAEEAPLNAFEKEKYFEGCMPIEVMAKRGIKTMLYGP 29- 8 GEAAYLNCPMT+EEF FHEALT+AE PL FEKE +FEGCMPIEVMAKRG KTML+GP Sbjct: 185 GEAAYLNCPMTEEEFDRFHEALTSAETVPLKEFEKEIFFEGCMPIEVMAKRGKKTMLFGP 24- 4 Query: 299 MKPVGLEYPDDYTGPRDGEFKTPYAVVQLRQDNAAGSLYNIVGFQTHLKWGEQKRVFQMI 35- 8 MKPVGLE+P TG R PYAVVQLRQD+AAG+LYNIVGFQTHLKWG+QK V ++I Sbjct: 245 MKPVGLEHP--VTGKR------PYAVVQLRQDDAAGTLYNIVGFQTHLKWGDQKEVLKLI 29- 6 Query: 359 PGLENAEFVRYGVMHRNSYMDSPNLLTETFQSRSNPNLFFAGQMTGVEGYVESAASGLVA 41- 8 PGLEN E VRYGVMHRN++++SP+LL T+Q ++ +LFFAGQMTGVEGYVESAASGLVA Sbjct: 297 PGLENVEIVRYGVMHRNTFINSPSLLKPTYQFKNRSDLFFAGQMTGVEGYVESAASGLVA 35- 6 Query: 419 GINAARLFKREEALIFPQTTAIGSLPHYVTHADSKHFQPMNVNFGIIKELEGPRIRDKKE 47- 8 GINAA+L EE +IFPQ TAIGS+ HY+T + K+FQPMN NFG++KEL +I++KKE Sbjct: 357 GINAAKLVLGEELVIFPQETAIGSMAHYITTTNQKNFQPMNANFGLLKELP-VKIKNKKE 41- 5 Query: 479 RYEAIASRALADLDT 493 R E A+RA+ + T Sbjct: 416 RNEQYANRAIETIQT 430 An alignment of the GAS and GBS proteins is shown below: TABLE-US-02067 Identities = 395/439 (89%), Positives = 417/439 (94%) Query: 4 SYINVIGAGLAGSEAAYQIAKRGIPVKLYEMRGVKSTPQHKTDNFAELVCSNSFRGDSLT 63 +YINVIGAGLAGSEAAYQIAKRGIPVKLYEMRGVK+TPQHKT NFAELVCSNSFRGDSLT Sbjct: 57 TYINVIGAGLAGSEAAYQIAKRGIPVKLYEMRGVKATPQHKTTNFAELVCSNSFRGDSLT 116- Query: 64 NAVGLLKEEMRRLDSIIMRNGEAHRVPAGGAMAVDREGYSEAVTEEIHKHPLIEVIRDEI 123- NAVGLLKEEMRRLDSIIMRNGEA+RVPAGGAMAVDREGY+E+VT E+ HPLIEVIR EI Sbjct: 117 NAVGLLKEEMRRLDSIIMRNGEANRVPAGGAMAVDREGYAESVTAELENHPLIEVIRGEI 17- 6 Query: 124 TDIPGDAITVIATGPLTSDSLAAKIHELNGGDGFYFYDAAAPIVDKNTIDINKVYLKSRY 18- 3 T+IP DAITVIATGPLTSD+LA KIH LNGGDGFYFYDAAAPI+DK+TID++KVYLKSRY Sbjct: 177 TEIPDDAITVIATGPLTSDALAEKIHALNGGDGFYFYDAAAPIIDKSTIDMSKVYLKSRY 23- 6 Query: 184 DKGEAAYLNCPMTKEEFMAFHEALTTAEEAPLNSFEKEKYFEGCMPIEVMAKRGIKTMLY 24- 3 DKGEAAYLNCPMTKEEFMAFHEALTTAEEAPLN+FEKEKYFEGCMPIEVMAKRGIKTMLY Sbjct: 237 DKGEAAYLNCPMTKEEFMAFHEALTTAEEAPLNAFEKEKYFEGCMPIEVMAKRGIKTMLY 29- 6 Query: 244 GPMKPVGLEYPEDYKGPRDGEFKTPYAVVQLRQDNAAGSLYNIVGFQTHLKWGEQKRVFQ 30- 3 GPMKPVGLEYP+DY GPRDGEFKTPYAVVQLRQDNAAGSLYNIVGFQTHLKWGEQKRVFQ Sbjct: 297 GPMKPVGLEYPDDYTGPRDGEFKTPYAVVQLRQDNAAGSLYNIVGFQTHLKWGEQKRVFQ 35- 6 Query: 304 MIPGLENAEFVRYGVMHRNSYMDSPNLLNQTFATRKNPNLFFAGQMTGVEGYVESAASGL 36- 3 MIPGLENAEFVRYGVMHRNSYMDSPNLL +TF +R NPNLFFAGQMTGVEGYVESAASGL Sbjct: 357 MIPGLENAEFVRYGVMHRNSYMDSPNLLTETFQSRSNPNLFFAGQMTGVEGYVESAASGL 41- 6 Query: 364 VAGINAVRRFNGESEVVFPQTTAIGALPHYITHTDSKHFQPMNVNFGIIKELEGPRIRDK 42- 3 VAGINA R F E ++FPQTTAIG+LPHY+TH DSKHFQPMNVNFGIIKELEGPRIRDK Sbjct: 417 VAGINAARLFKREEALIFPQTTAIGSLPHYVTHADSKHFQPMNVNFGIIKELEGPRIRDK 47- 6 Query: 424 KERYEAIATRALKDLEKFL 442 KERYEAIA+RAL DL+ L Sbjct: 477 KERYEAIASRALADLDTCL 495 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 694 A DNA sequence (GBSx0736) was identified in S. agalactiae <SEQ ID 2139> which encodes the amino acid sequence <SEQ ID 2140>. This protein is predicted to be transcriptional regulator (GntRfamily). Analysis of this protein sequence reveals the following: TABLE-US-02068 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5103(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02069 >GP:BAB04138 GB:AP001508 transcriptional regulator (GntR family) [Bacillus halodurans] Identities = 83/229 (36%), Positives = 133/229 (57%), Gaps = 1/229 (0%) Query: 2 LPAYIKIHDAIKKEIDKGTWKIGQRLPSERDLADDYSVSRMTLRQSITLLVEEGILERRV 61 LP Y +I + IK++I+ G K G L SER+ A+ Y VSRMT+RQ+I LV +G + ++ Sbjct: 8 LPIYYQIEEQIKQQIESGVLKPGDMLKSEREYAEYYDVSRMTVRQAINNLVNQGYIYKKK 67 Query: 62 GSGTYVASHRVQEKMRGTTSFTEIVNSQGRKPSSKLISFQRKLANETEIQKLNLSQSDYV 121- GSGTYV ++++ + G TSFTE + +G +PSS+L+ F+ A ++LNL ++ V Sbjct: 68 GSGTYVQEKKIEQALNGLTSFTEDMRKRGMEPSSRLLKFELIPATAKIAKELNLKENTPV 127- Query: 122 VRMERVRYADKVPLVYEVASIPENLIKGFEQSEVTEHFFKTLTEN-GYEIGKSQQTIYAR 18- 0 ++R+RY D VP+ E +P NL+KG + + + ++ + E I + Q I A Sbjct: 128 TEIKRIRYGDGVPIAIERNLLPANLVKGLNEEIINQSLYQYIEEELNLRIADALQVIEAS 18- 7 Query: 181 NASERVASHLEVNAGHAILALTQVSYFTDGKPFEYVHGQYVGDRFEFYL 229 AS+ A LE+ G IL + + ++ DG E V Y DR++F + Sbjct: 188 TASKTEADLLEIQKGSPILLIERKTFLADGTVLELVKSAYRADRYKFMI 236 There is also homology to SEQ ID 1256. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 695 A DNA sequence (GBSx0737) was identified in S. agalactiae <SEQ ID 2141> which encodes the amino acid sequence <SEQ ID 2142>. This protein is predicted to be GMP synthase (guaA). Analysis of this protein sequence reveals the following: TABLE-US-02070 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.96 Transmembrane 228-244 (228-245) ----- Final Results ----- bacterial membrane --- Certainty = 0.1383(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02071 >GP:AAD15805 GB:AF058326 GMP synthase [Lactococcus lactis] Identities = 416/511 (81%), Positives = 467/511 (90%), Gaps = 3/511 (0%) Query: 10 IQKIIVLDYGSQYNQLIARRIREFGVFSELKSHKITADEIRDINPIGIVLSGGPNSVYAD 69 - ++KIIVLDYGSQYNQLIARRIRE GVFSEL SHK+TA EIR+INPIGI+LSGGPNSVY + Sbjct: 6 LEKIIVLDYGSQYNQLIARRIREIGVFSELMSHKVTAKEIREINPIGIILSGGPNSVYDE 65 Query: 70 GAFGIDEEIFELGIPILGICYGMQLITHKLGGKVLPAGEAGHREYGQSALRLRSESALFA 129- G+F ID EIFELG+P+LGICYGMQL+++KLGG V AGE REYG + L+L +SALFA Sbjct: 66 GSFDIDPEIFELGLPVLGICYGMQLMSYKLGGMVEAAGE---REYGVAPLQLTEKSALFA 122- Query: 130 GTPQEQLVLMSHGDAVTEIPEGFHLVGDSVDCPFAAMENTEKQFYGIQFHPEVRHSVYGN 18- 9 GTP+ Q VLMSHGD VT IPEGFH+VG S + PFAA+ENTE+ YGIQFHPEVRHSV+G Sbjct: 123 GTPEVQDVLMSHGDRVTAIPEGFHVVGTSPNSPFAAVENTERNLYGIQFHPEVRHSVHGT 18- 2 Query: 190 DILKNFAVNICGARGDWSMDNFIDMEIAKIRETVGDRKVLLGLSGGVDSSVVGVLLQRAI 24- 9 ++L+NFA+NICGA+G+WSM+NFIDM+I IRE VGD+KVLLGLSGGVDSSVVGVLLQRAI Sbjct: 183 EMLRNFALNICGAKGNWSMENFIDMQIKDIREKVGDKKVLLGLSGGVDSSVVGVLLQRAI 24- 2 Query: 250 GDQLTCIFVDHGLLRKNEGDQVMDMLGGKFGLNIIRVDASKRFLDLLSGVEDPERKRKII 30- 9 GDQLT IFVDHG LRK E DQVM+ LGGKFGLNII+VDA KRF+D L G+ DPE +RKII Sbjct: 243 GDQLTSIFVDHGFLRKGEADQVMETLGGKFGLNIIKVDAQKRFMDKLVGLSDPETQRKII 30- 2 Query: 310 GNEFVYVFDDEASKLKGVDFLAQGTLYTDIIESGTETAQTIKSHHNVGGLPEDMQFELIE 36- 9 GNEFVYVFDDEA+KL+GVDFLAQGTLYTD+IESGT+TAQTIKSHHNVGGLPEDMQF+LIE Sbjct: 303 GNEFVYVFDDEANKLEGVDFLAQGTLYTDVIESGTDTAQTIKSHHNVGGLPEDMQFQLIE 36- 2 Query: 370 PLNTLFKDEVRALGTALGMPDEVVWRQPFPGPGLAIRVMGEITEEKLETVRESDAILREE 42- 9 PLNTLFKDEVRALGT LGMPDE+VWRQPFPGPGLAIRV+G++TEEKLETVRESDAILREE Sbjct: 363 PLNTLFKDEVRALGTQLGMPDEIVWRQPFPGPGLAIRVLGDLTEEKLETVRESDAILREE 42- 2 Query: 430 IAKAGLDRDVWQYFTVNTGVRSVGVMGDGRTYDYTIAIRAITSIDGMTADFAQLPWDVLK 48- 9 IA +GL+RDVWQYFTVNT V+SVGVMGD RTYDYT+AIRAITSIDGMTADFAQLPWD+L+ Sbjct: 423 IAASGLERDVWQYFTVNTDVKSVGVMGDQRTYDYTLAIRAITSIDGMTADFAQLPWDLLQ 48- 2 Query: 490 KISTRIVNEVDHVNRIVYDITSKPPATVEWE 520 KIS RIVNEVDHVNRIVYDITSKPPATVEW+ Sbjct: 483 KISKRIVNEVDHVNRIVYDITSKPPATVEWQ 513 A related DNA sequence was identified in S. pyogenes <SEQ ID 2143> which encodes the amino acid sequence <SEQ ID 2144>. Analysis of this protein sequence reveals the following: TABLE-US-02072 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.96 Transmembrane 228-244 (228-245) ----- Final Results ----- bacterial membrane --- Certainty = 0.1383(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> RGD motif: 203-205 The protein has homology with the following sequences in the databases: TABLE-US-02073 >GP:AAD15805 GB:AF058326 GMP synthase [Lactococcus lactis] Identities = 411/511 (80%), Positives = 464/511 (90%), Gaps = 3/511 (0%) Query: 10 VQKIIVLDYGSQYNQLIARRIREFGVFSELKSHKITAQELREINPIGIVLSGGPNSVYAD 69 - ++KIIVLDYGSQYNQLIARRIRE GVFSEL SHK+TA+E+REINPIGI+LSGGPNSVY + Sbjct: 6 LEKIIVLDYGSQYNQLIARRIREIGVFSELMSHKVTAKEIREINPIGIILSGGPNSVYDE 65 Query: 70 NAFGIDPEIFELGIPILGICYGMQLITHKLGGKVVPAGQAGNREYGQSTLHLRETSKLFS 129- +F IDPEIFELG+P+LGICYGMQL+++KLGG V AG+ REYG + L L E S LF+ Sbjct: 66 GSFDIDPEIFELGLPVLGICYGMQLMSYKLGGMVEAAGE---REYGVAPLQLTEKSALFA 122- Query: 130 GTPQEQLVLMSHGDAVTEIPEGFHLVGDSNDCPYAAIENTEKNLYGIQFHPEVRHSVYGN 18- 9 GTP+ Q VLMSHGD VT IPEGFH+VG S + P+AA+ENTE+NLYGIQFHPEVRHSV+G Sbjct: 123 GTPEVQDVLMSHGDRVTAIPEGFHVVGTSPNSPFAAVENTERNLYGIQFHPEVRHSVHGT 18- 2 Query: 190 DILKNFAISICGARGDWSMDNFIDMEIAKIRETVGDRKVLLGLSGGVDSSVVGVLLQKAI 24- 9 ++L+NFA++ICGA+G+WSM+NFIDM+I IRE VGD+KVLLGLSGGVDSSVVGVLLQ+AI Sbjct: 183 EMLRNFALNICGAKGNWSMENFIDMQIKDIREKVGDKKVLLGLSGGVDSSVVGVLLQRAI 24- 2 Query: 250 GDQLTCIFVDHGLLRKDEGDQVMGMLGGKFGLNIIRVDASKRFLDLLADVEDPEKKRKII 30- 9 GDQLT IFVDHG LRK E DQVM LGGKFGLNII+VDA KRF+D L + DPE +RKII Sbjct: 243 GDQLTSIFVDHGFLRKGEADQVMETLGGKFGLNIIKVDAQKRFMDKLVGLSDPETQRKII 30- 2 Query: 310 GNEFVYVFDDEASKLKGVDFLAQGTLYTDIIESGTETAQTIKSHHNVGGLPEDMQFELIE 36- 9 GNEFVYVFDDEA+KL+GVDFLAQGTLYTD+IESGT+TAQTIKSHHNVGGLPEDMQF+LIE Sbjct: 303 GNEFVYVFDDEANKLEGVDFLAQGTLYTDVIESGTDTAQTIKSHHNVGGLPEDMQFQLIE 36- 2 Query: 370 PLNTLFKDEVRALGIALGMPEEIVWRQPFPGPGLAIRVMGAITEEKLETVRESDAILREE 42- 9 PLNTLFKDEVRALG LGMP+EIVWRQPFPGPGLAIRV+G +TEEKLETVRESDAILREE Sbjct: 363 PLNTLFKDEVRALGTQLGMPDEIVWRQPFPGPGLAIRVLGDLTEEKLETVRESDAILREE 42- 2 Query: 430 IAKAGLDRDVWQYFTVNTGVRSVGVMGDGRTYDYTIAIRAITSIDGMTADFAQLPWDVLK 48- 9 IA +GL+RDVWQYFTVNT V+SVGVMGD RTYDYT+AIRAITSIDGMTADFAQLPWD+L+ Sbjct: 423 IAASGLERDVWQYFTVNTDVKSVGVMGDQRTYDYTLAIRAITSIDGMTADFAQLPWDLLQ 48- 2 Query: 490 KISTRIVNEVDHVNRIVYDITSKPPATVEWE 520 KIS RIVNEVDHVNRIVYDITSKPPATVEW+ Sbjct: 483 KISKRIVNEVDHVNRIVYDITSKPPATVEWQ 513 An alignment of the GAS and GBS proteins is shown below: TABLE-US-02074 Identities = 487/520 (93%), Positives = 505/520 (96%) Query: 1 MTDISILNDIQKIIVLDYGSQYNQLIARRIREFGVFSELKSHKITADEIRDINPIGIVLS 60 MT+ISILND+QKIIVLDYGSQYNQLIARRIREFGVFSELKSHKITA E+R+INPIGIVLS Sbjct: 1 MTEISILNDVQKIIVLDYGSQYNQLIARRIREFGVFSELKSHKITAQELREINPIGIVLS 60 Query: 61 GGPNSVYADGAFGIDEEIFELGIPILGICYGMQLITHKLGGKVLPAGEAGHREYGQSALR 120- GGPNSVYAD AFGID EIFELGIPILGICYGMQLITHKLGGKV+PAG+AG+REYGQS L Sbjct: 61 GGPNSVYADNAFGIDPEIFELGIPILGICYGMQLITHKLGGKVVPAGQAGNREYGQSTLH 120- Query: 121 LRSESALFAGTPQEQLVLMSHGDAVTEIPEGFHLVGDSVDCPFAAMENTEKQFYGIQFHP 18- 0 LR S LF+GTPQEQLVLMSHGDAVTEIPEGFHLVGDS DCP+AA+ENTEK YGIQFHP Sbjct: 121 LRETSKLFSGTPQEQLVLMSHGDAVTEIPEGFHLVGDSNDCPYAAIENTEKNLYGIQFHP 18- 0 Query: 181 EVRHSVYGNDILKNFAVNICGARGDWSMDNFIDMEIAKIRETVGDRKVLLGLSGGVDSSV 24- 0 EVRHSVYGNDILKNFA++ICGARGDWSMDNFIDMEIAKIRETVGDRKVLLGLSGGVDSSV Sbjct: 181 EVRHSVYGNDILKNFAISICGARGDWSMDNFIDMEIAKIRETVGDRKVLLGLSGGVDSSV 24- 0 Query: 241 VGVLLQRAIGDQLTCIFVDHGLLRKNEGDQVMDMLGGKFGLNIIRVDASKRFLDLLSGVE 30- 0 VGVLLQ+AIGDQLTCIFVDHGLLRK+EGDQVM MLGGKFGLNIIRVDASKRFLDLL+ VE Sbjct: 241 VGVLLQKAIGDQLTCIFVDHGLLRKDEGDQVMGMLGGKFGLNIIRVDASKRFLDLLADVE 30- 0 Query: 301 DPERKRKIIGNEFVYVFDDEASKLKGVDFLAQGTLYTDIIESGTETAQTIKSHHNVGGLP 36- 0 DPE+KRKIIGNEFVYVFDDEASKLKGVDFLAQGTLYTDIIESGTETAQTIKSHHNVGGLP Sbjct: 301 DPEKKRKIIGNEFVYVFDDEASKLKGVDFLAQGTLYTDIIESGTETAQTIKSHHNVGGLP 36- 0 Query: 361 EDMQFELIEPLNTLFKDEVRALGTALGMPDEVVWRQPFPGPGLAIRVMGEITEEKLETVR 42- 0 EDMQFELIEPLNTLFKDEVRALG ALGMP+E+VWRQPFPGPGLAIRVMG ITEEKLETVR Sbjct: 361 EDMQFELIEPLNTLFKDEVRALGIALGMPEEIVWRQPFPGPGLAIRVMGAITEEKLETVR 42- 0 Query: 421 ESDAILREEIAKAGLDRDVWQYFTVNTGVRSVGVMGDGRTYDYTIAIRAITSIDGMTADF 48- 0 ESDAILREEIAKAGLDRDVWQYFTVNTGVRSVGVMGDGRTYDYTIAIRAITSIDGMTADF Sbjct: 421 ESDAILREEIAKAGLDRDVWQYFTVNTGVRSVGVMGDGRTYDYTIAIRAITSIDGMTADF 48- 0 Query: 481 AQLPWDVLKKISTRIVNEVDHVNRIVYDITSKPPATVEWE 520 AQLPWDVLKKISTRIVNEVDHVNRIVYDITSKPPATVEWE Sbjct: 481 AQLPWDVLKKISTRIVNEVDHVNRIVYDITSKPPATVEWE 520 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 696 A DNA sequence (GBSx0740) was identified in S. agalactiae <SEQ ID 2145> which encodes the amino acid sequence <SEQ ID 2146>. This protein is predicted to be branched chain amino acid ABC transporter, periplasmic amino acid-bind. Analysis of this protein sequence reveals the following: TABLE-US-02075 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0957(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9409> which encodes amino acid sequence <SEQ ID 9410> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02076 >GP:AAD36211 GB:AE001771 branched chain amino acid ABC transporter, periplasmic amino acid-binding protein [Thermotoga maritima] Identities = 31/92 (33%), Positives = 51/92 (54%), Gaps = 4/92 (4%) Query: 26 AKAFHDHYVKAYGEEPSMFSALSYDAVYMAAKSAKGAKTSID---IKKALAKLKDFKGVT 82 - AK F + Y + YG+EP+ +AL YDA YM A S D I + + K ++F G + Sbjct: 275 AKKFVEVYKEKYGKEPAALNALGYDA-YMVLLDAIERAGSFDREKIAEEIRKTRNFNGAS 33- 3 Query: 83 GKMSIDKNHNVVKSAYVVKLEDGKTSSVNIIS 114 G ++ID+N + +KS V +++G +I+ Sbjct: 334 GIINIDENGDAIKSVVVNIVKNGSVDFEAVIN 365 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 9410 (GBS660) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 135 (lane 8 & 9; MW 71.5 kDa)+ 10 ; MW 27 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 141 (lane 2; MW 46.5 kDa) and in FIG. 181, (lane 3; MW 46 kDa). GBS660-His was purified as shown in FIG. 233, lane 5-6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 697 A DNA sequence (GBSx0741) was identified in S. agalactiae <SEQ ID 2147> which encodes the amino acid sequence <SEQ ID 2148>. Analysis of this protein sequence reveals the following: TABLE-US-02077 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.61 Transmembrane 140-156 (129-158) INTEGRAL Likelihood = -9.55 Transmembrane 60-76 (53-80) INTEGRAL Likelihood = -7.59 Transmembrane 264-280 (257-285) INTEGRAL Likelihood = -5.79 Transmembrane 232-248 (219-251) INTEGRAL Likelihood = -2.23 Transmembrane 190-206 (190-207) INTEGRAL Likelihood = -1.75 Transmembrane 90-106 (90-110) ----- Final Results ----- bacterial membrane --- Certainty = 0.5246(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10059> which encodes amino acid sequence <SEQ ID 10060> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02078 >GP:AA036212 GB:AE001771 branched chain amino acid ABC transporter, permease protein [Thermotoga maritima] Identities = 140/295 (47%), Positives = 200/295 (67%), Gaps = 7/295 (2%) Query: 2 LQQLVNGLILGSIYALLALGYTMVYGIIKLINFAHGDIYMMGAFMGYYLINHLHLNFFLA 61 LQ L NG++LG +YAL+A+GYTMVYGI++LINFAHGD+ MMG + +Y L LN + Sbjct: 5 LQNLFNGIMLGGLYALIAIGYTMVYGILRLINFAHGDVMMMGVYFAFYAATLLSLNPLFS 64 Query: 62 LLIAMLGSAFLGVVIEYLAYRPLRKSTRIAALITAIGVSFLLEYGMVYLVGADTRAFPQA 121- ++A+LG+A LG +I+ +AY+PLR + RI+ALITAIGVSF LE V + GA ++F + Sbjct: 65 AIVAILGAALLGFLIDRVAYKPLRNAPRISALITAIGVSFFLESLAVVVFGAIPKSFLKV 124- Query: 122 IHTVKYNLGPITITNVQL-----IILGIALLLMLTLQFIVQKTKMGKAMRALSVDSDAAQ 17- 6 +T+ ++ +++ I ++++ L FIV +TK+G AMRA+S+D Sbjct: 125 FKDRTILNKVLTVAGARIPLLTFLVIFITAVILIVLFFIVYRTKIGMAMRAISMDIPTTA 18- 4 Query: 177 LMGINVNRTISFTFALGSALAGAGGVLIGLYYNSVQPLMGVTPGLKAFVAAVLGGIGIIP 23- 6 LMG+NV+ I FTFALGSALA A G++ + + +V P MG PGLKAF+AAV GGIG IP Sbjct: 185 LMGVNVDAVIGFTFALGSALAAASGIMWAMRFPNVHPYMGFMPGLKAFIAAVFGGIGSIP 24- 4 Query: 237 GAAIGGFVIGILETLATAL--GVSDFRDGIVYAILILIFLIRPAGILGKNIKEKV 289 GA +GG ++G++E A V +RD + ILI+I L++P+G+LGK I EKV Sbjct: 245 GAVLGGVLLGLIEIFLAAYFPAVMGYRDAFAFIILIIILLVKPSGLLGKKIVEKV 299 There is also homology to SEQ ID 2150. A related sequence was also identified in GAS <SEQ ID 9171> which encodes the amino acid sequence <SEQ ID 9172>. Analysis of this protein sequence reveals the following:

TABLE-US-02079 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.74 Transmembrane 196-212 (191-219) INTEGRAL Likelihood = -12.42 Transmembrane 12-28 (5-36) INTEGRAL Likelihood = -7.22 Transmembrane 106-122 (102-126) INTEGRAL Likelihood = -4.78 Transmembrane 242-258 (240-260) INTEGRAL Likelihood = -2.50 Transmembrane 61-77 (60-77) INTEGRAL Likelihood = -2.34 Transmembrane 293-309 (291-309) INTEGRAL Likelihood = -1.44 Transmembrane 139-155 (138-156) INTEGRAL Likelihood = -1.33 Transmembrane 317-333 (317-333) ----- Final Results ----- bacterial membrane --- Certainty = 0.609(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02080 Identities = 35/147 (23%), Positives = 71/147 (47%), Gaps = 6/147 (4%) Query: 134 ITNVQLIILGI--ALLLMLTLQFIVQKTKMGKAMRALSVDSDAAQLMGINVNRTISFTFA 19- 1 +TN I +GI A++ + + F++ KT +G +R++ ++ A++ G++ RTI + Sbjct: 197 LTNNSRINIGIFFAIIAIALIWFLLNKTTLGFEIRSVGLNPHASEYAGMSSKRTIILSMI 25- 6 Query: 192 LGSALAGAGGVL--IGLYYNSVQPLMGVTPGLKAFVAAVLGGIGIIPGAAIGGFVIGILE 24- 9 + ALAG GGV+ +G + N + G ++L + G F+ G+L Sbjct: 257 ISGALAGLGGVVEGLGTFENVFVQGSSLAVGFDGMAVSLLAANSPL-GIFFSSFLFGVLN 31- 5 Query: 250 TLATALGVSDFRDGIVYAILI-LIFLI 275 A + ++ +V + +IF + Sbjct: 316 IGAPGMNIAGIPPELVKVVTASIIFFV 342 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 698 A DNA sequence (GBSx0742) was identified in S. agalactiae <SEQ ID 2151> which encodes the amino acid sequence <SEQ ID 2152>. This protein is predicted to be branched chain amino acid ABC transporter, permease protein (livM). Analysis of this protein sequence reveals the following: TABLE-US-02081 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.76 Transmembrane 90-106 (84-113) INTEGRAL Likelihood = -8.23 Transmembrane 12-28 (5-33) INTEGRAL Likelihood = -8.17 Transmembrane 205-221 (200-224) INTEGRAL Likelihood = -7.86 Transmembrane 276-292 (273-300) INTEGRAL Likelihood = -6.32 Transmembrane 159-175 (154-176) INTEGRAL Likelihood = -6.05 Transmembrane 236-252 (232-264) INTEGRAL Likelihood = -5.95 Transmembrane 42-58 (38-60) INTEGRAL Likelihood = -5.84 Transmembrane 120-136 (119-138) INTEGRAL Likelihood = -4.35 Transmembrane 255-271 (253-274) INTEGRAL Likelihood = -1.59 Transmembrane 66-82 (66-85) ----- Final Results ----- bacterial membrane --- Certainty = 0.4503(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02082 >GP:AAD36213 GB:AE001771 branched chain amino acid ABC transporter, permease protein [Thermotoga maritima] Identities = 119/332 (35%), Positives = 191/332 (56%), Gaps = 33/332 (9%) Query: 12 LAIVVLDYLLISVLISMGIFNLYHIQIIETIGINVILAVGLNLIVGCSGQFSLGHAGFMA 71 - L +V L ++ + + ++ + Y ++++ I I I+AV LNLI G +G FSLGHAGF+ Sbjct: 16 LTVVFLIFMALLLYLADRYMDSYKLRVVRLIAIYGIMAVSLNLINGITGIFSLGHAGFIL 75 Query: 72 IGAYAVAIIGVKMP-----------------TYVGFLIAILVGTLVAGGIALGVGIPTLR 114- IGAY +++ + + F A + G ++A A +G P LR Sbjct: 76 IGAYTASLLTLSPEQKAMSFIIEPIVPWLANAHTDFFTATVAGGVLAAVFAFLIGWPVLR 135- Query: 115 LKGDYLAIATLGVAEIIRILLVNGGDITNGAAGIMGIPPFTTWSLVYGVAVVSLILAMNF 17- 4 L GDYLAIA+LG AE+IRI+ +N ITNG G+ GIP ++ YG V+++ + Sbjct: 136 LSGDYLAIASLGFAEVIRIIALNAISITNGPLGLKGIPEYSNIWWCYGWLFVTVLFMASL 19- 5 Query: 175 LRSPLGRNTIAIREDEIAAESMGVDTTKVKVIVFVFGAILASIAGSLQAGYVGTVMPKDF 23- 4 + S GR AIRED IAAE+MG++ K +++ FV GA A ++GSL A ++ T+ P+ Sbjct: 196 VNSSYGRALKAIREDRIAAEAMGINVFKHQLLSFVIGAFFAGVSGSLYAHWLTTIDPRTT 25- 5 Query: 235 SF--MMSVNVLIIVVLGGLGSMTGTVLAAILLGLLNMLLQD--------------YASVR 27- 8 + M++ VLI++VLGGLGS++G+++ A L +L L+D +R Sbjct: 256 TLGPMLTFYVLIMIVLGGLGSISGSLIGAALFAILFEWLRDLEEPFTFFGIHVPGIKGMR 31- 5 Query: 279 MIIYALALILIMIFRPSGLLGTKELTLSHLFR 310 +++ + IL+MIF G++G +ELT ++L+R Sbjct: 316 ILVISAIFILVMIFWQRGIMGREELTWNNLYR 347 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 699 A DNA sequence (GBSx0743) was identified in S. agalactiae <SEQ ID 2153> which encodes the amino acid sequence <SEQ ID 2154>. This protein is predicted to be branched chain amino acid ABC transporter, ATP-binding protein (livG). Analysis of this protein sequence reveals the following: TABLE-US-02083 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2057(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02084 >GP:AAD36214 GB:AE001771 branched chain amino acid ABC transporter, ATP-binding protein [Thermotoga maritima] Identities = 136/271 (50%), Positives = 189/271 (69%), Gaps = 21/271 (7%) Query: 3 LLEVKNLSKHFGGLTAVGDVSMKLHKGELIGLIGPNGAGKTTLFNLLTGVYLPSKGTISI 62 LL + +++ FGGL AV D + ++ +GEL+GLIGPNGAGKTT+FN++TG+Y P+KG I Sbjct: 11 LLLLDHVTMQFGGLVAVDDFTNEIREGELVGLIGPNGAGKTTVFNVITGIYTPTKGRIVF 70 Query: 63 DGKILNGRKPAKIASLGLGRTFQNIRLFKNMTVLDNVLVGLSNHHLSHPIASFLRLPK-- 120- + + G +P +I LG+ RTFQNIRLF +MTVL+NVLV +H LS+P A + + Sbjct: 71 NDIDITGLRPYQITHLGIARTFQNIRLFSDMTVLENVLVA-QHHVLSNPDADRILVKHGK 129- Query: 121 ------------------YYHSEKALRKKALELLEIFGLKAYQDALAKNLPYGKQRRLEI 16- 2 Y EK + ++A +L++ GL+ A +LPYG+QR+LEI Sbjct: 130 PRKGHGRFWFWRAVTRIGYLKKEKEMVERAKDLIKRVGLEKVMYEKASSLPYGEQRKLEI 18- 9 Query: 163 VRALATEPKILFLDEPAAGMNPQETAELTQLISQIKSDFDITIMLIEHDMNLVMQVTERI 22- 2 RALATEPK++ LDEPAAGMNP+ET +L + I QI+ DF++T++LIEHDM +VM + ERI Sbjct: 190 ARALATEPKLILLDEPAAGMNPKETEDLMEFIKQIRKDFNLTVLLIEHDMKVVMGICERI 24- 9 Query: 223 YVLEYGRLIAHGTPEEIKNNKRVIEAYLGGE 253 V++YGR+IA GTP+EI+N+ RVIEAYLG E Sbjct: 250 IVMDYGRIIAEGTPKEIQNDPRVIEAYLGRE 280 There is also homology to SEQ ID 644. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 700 A DNA sequence (GBSx0744) was identified in S. agalactiae <SEQ ID 2155> which encodes the amino acid sequence <SEQ ID 2156>. Analysis of this protein sequence reveals the following: TABLE-US-02085 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2216(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02086 >GP:CAB52068 GB:AL109732 putative branched chain amino acid transport ATP-binding protein [Streptomyces coelicolor A3(2)] Identities = 136/233 (58%), Positives = 181/233 (77%) Query: 3 MLKVENLSIHYGVIQAVNDVSFEVNQGEVVTLIGANGAGKTSILRTISGLVRPSQGSISF 62 +L+VE+L + YG I+AV +SF+V+ GEVVTLIG NGAGKT+ LRT+SGL++P G I F Sbjct: 4 LLEVEDLRVAYGKIEAVKGISFKVDAGEVVTLIGTNGAGKTTTLRTLSGLLKPVGGQIRF 63 Query: 63 MGKPIHKLAARKIVGNGLAQVPEGRHVFSSLSVMENLEMGAFLQKDREQNQKMLKKVFDR 122- GK + K+ A +IV GLA PEGRH+F +++ +NL +GAFL+ DR +K +++ +D Sbjct: 64 GGKSLKKVPAHQIVSLGLAHSPEGRHIFPRMTIEDNLRLGAFLRSDRPGIEKDIQRAYDL 123- Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSRPKLLLLDEPSMGLAPIFIQEIFNIIEDI 18- 2 FP L ER+ Q A TLSGGEQQMLAMGRALMS+PKLL+LDEPSMGL+PI +Q+I I ++ Sbjct: 124 FPILGERRKQAAGTLSGGEQQMLAMGRALMSQPKLLMLDEPSMGLSPIMMQKIMATIAEL 18- 3 Query: 183 KKQGTTVLLVEQNANKALTIADKAYVLETGKVVLSGTGKELLVSDQVRKAYLG 235 K QGTT+LLVEQNA AL++AD +V+E G +VLSG+G++LL + VRKAYLG Sbjct: 184 KSQGTTILLVEQNAQAALSLADHGHVMEVGNIVLSGSGQDLLHDESVRKAYLG 236 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 701 A DNA sequence (GBSx0745) was identified in S. agalactiae <SEQ ID 2159> which encodes the amino acid sequence <SEQ ID 2160>. Analysis of this protein sequence reveals the following: TABLE-US-02087 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0415(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02088 >GP:AAD36216 GB:AE001771 conserved hypothetical protein [Thermotoga maritima] Identities = 72/166 (43%), Positives = 116/166 (69%), Gaps = 2/166 (1%) Query: 1 MPVKDFMTKKLVYVSPDTTVAEAADLLREHHLRRLPVVENDQLVGLVTEGTMAEAQPSKA 60 M VRDFMT+ + ++P+T+ +EA L++++ ++RL V++N+++VG+VTE + A PSKA Sbjct: 1 MLVKDFMTRNPITIAPETSFSEALKLMKQNKIKRLIVMKNEKIVGIVTEKDLLYASPSKA 60 Query: 61 TSLSIYEMNYLLNKTKIRDIMIKDIVTVSQYASLEDAIYLMMSRKIGVLPVVDN-GQLYG 119- T+L+I+E++YLL+K KI +IM KD+VTV++ +EDA +M + I LPVVD+ G+L G Sbjct: 61 TTLNIWELHYLLSKLKIEEIMTKDVVTVNENTPIEDAARIMEEKDISGLPVVDDAGRLVG 120- Query: 120 IVTDRDVFKAFLEIAGYGQE-SYRLVILADEGIGVLSKVLNRLSSA 164 I+T D+FK F+EI G +E + R + + G L +V R+ A Sbjct: 121 IITQTDIFKVFVEIFGTKREGTIRYTMEMPDKPGELLEVAKRIYEA 166 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 702 A DNA sequence (GBSx0746) was identified in S. agalactiae <SEQ ID 2163> which encodes the amino acid sequence <SEQ ID 2164>. Analysis of this protein sequence reveals the following: TABLE-US-02089 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5585(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 703 A DNA sequence (GBSx0747) was identified in S. agalactiae <SEQ ID 2165> which encodes the amino acid sequence <SEQ ID 2166>. This protein is predicted to be a transposase. Analysis of this protein sequence reveals the following: TABLE-US-02090 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.65 Transmembrane 53-69 (53-70) ----- Final Results ----- bacterial membrane --- Certainty = 0.1659(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02091 >GP:AAA85003 GB:U28972 SpV1 ORF3; putative transposase [Spiroplasma citri] Identities = 49/154 (31%), Positives = 80/154 (51%), Gaps = 11/154 (7%) Query: 39 WLEMDTVIGRIGGKVLLTFNVAFCNFIFAKLMDSKTAIETAKHIQ--VIKRTLYDNKRDF 96 - WLEMDTV+G+ +L FA +++ TA E K + +IK L + Sbjct: 174 WLEMDTVVGKDHKSAILVLVEQLSKKYFAIKLENHTAREVEKKFKDIIIKNNLIGKIKG- 23- 2 Query: 97 FELFPVILTDNGGEFARVDDIEIDVCGQSQLFFCDPNRSDQKARIEKNHTLVRDILPKGT 156- I+TD G EF++ ++EI ++Q++FCD QK IE ++ +R PKGT Sbjct: 233 ------IITDRGKEFSKWREMEI--FAETQVYFCDAGSPQQKPLIEYMNSELRHWFPKGT 28- 4 Query: 157 SFDNLTQEDINLALSHINSVKRQALNGKTAYELF 190 F+ ++Q+ I+ ++ IN R LN ++ E+F Sbjct: 285 DFNKVSQKQIDWVVNVINDKLRPCLNWISSKEMF 318 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 704 A DNA sequence (GBSx0748) was identified in S. agalactiae <SEQ ID 2167> which encodes the amino acid sequence <SEQ ID 2168>. Analysis of this protein sequence reveals the following: TABLE-US-02092 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3116(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10055> which encodes amino acid sequence <SEQ ID 10056> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 705 A DNA sequence (GBSx0749) was identified in S. agalactiae <SEQ ID 2169> which encodes the amino acid sequence <SEQ ID 2170>. This protein is predicted to be thymidylate kinase (tmk). Analysis of this protein sequence reveals the following: TABLE-US-02093 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1876(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10053> which encodes amino acid sequence <SEQ ID 10054> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02094 >GP: BAB03761 GB: AP001507 thymidylate kinase [Bacillus halodurans] Identities = 112/210 (53%), Positives = 148/210 (70%), Gaps = 1/210 (0%) Query: 17 MKKGLMISFEGPDGAGKTTVLEAVLPLLREKLSQDILTTREPGGVTISEEIRHIILDVKH 76 - M KG I+ EG +GAGKT+ L+A+ +LRE ++ TREPGG+ I+E+IR IILDV H Sbjct: 1 MTKGCFITVEGGEGAGKTSALDAIEEMLREN-GLSVVRTREPGGIPIAEQIRSIILDVDH 59 Query: 77 TQMDKKTELLLYMAARRQHLVEKVLPALEEGKIVLMDRFIDSSVAYQGSGRGLDKSHIKW 136- T+MD +TE LLY AARRQHLVEKVLPALE G +VL DRFIDSS+AYQG RG+ I Sbjct: 60 TRMDPRTEALLYAAARRQHLVEKVLPALEAGHVVLCDRFIDSSLAYQGYARGIGFEDILA 119- Query: 137 LNDYATDSHKPDLTLYFDVPSEVGLERIQKSVQREVNRLDLEQLDMHQRVRQGYLELADS 19- 6 +N++A + PDLTL F V +VGL RI + RE NRLD E L HQ+V++GY + ++ Sbjct: 120 INEFAIEGRYPDLTLLFRVDPDVGLSRIHRDQSREQNRLDQEALTFHQKVKEGYERIVET 17- 9 Query: 197 EPNRIVTIDASQQLDEVIAETFSIILDRIN 226 P R+V IDA+Q D+V+A+ +I R++ Sbjct: 180 YPERVVEIDANQSFDQVVADAVRMIKQRLS 209 A related DNA sequence was identified in S. pyogenes <SEQ ID 2171> which encodes the amino acid sequence <SEQ ID 2172>. Analysis of this protein sequence reveals the following: TABLE-US-02095 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.75 Transmembrane 215-231 (215-231) ----- Final Results ----- bacterial membrane --- Certainty = 0.1298(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02096 >GP:BAB03761 GB:AP001507 thymidylate kinase [Bacillus halodurans] Identities = 109/205 (53%), Positives = 148/205 (72%), Gaps = 1/205 (0%) Query: 22 MITGKLITVEGPDGAGKTTVLEQLIPLLKQKVAQDILTTREPGGVAISEHIRELILDINH 81 - M G ITVEG +GAGKT+ L+ + +L++ ++ TREPGG+ I+E IR +ILD++H Sbjct: 1 MTKGCFITVEGGEGAGKTSALDAIEEMLREN-GLSVVRTREPGGIPIAEQIRSIILDVDH 59 Query: 82 TAMDPKTELLLYIAARRQHLVEKVLPALEAGQLVFIDRFIDSSVAYQGAGRGLIKADIQW 141- T MDP+TE LLY AARRQHLVEKVLPALEAG +V DRFIDSS+AYQG RG+ DI Sbjct: 60 TRMDPRTEALLYAAARRQHLVEKVLPALEAGHVVLCDRFIDSSLAYQGYARGIGFEDILA 119- Query: 142 LNEFATDGLEPDLTLYFDVPSEIGLARINANQQREVNRLDLETIEIHQRVRKGYLALAKE 20- 1 +NEFA +G PDLTL F V ++GL+RI+ +Q RE NRLD E + HQ+V++GY + + Sbjct: 120 INEFAIEGRYPDLTLLFRVDPDVGLSRIHRDQSREQNRLDQEALTFHQKVKEGYERIVET 17- 9 Query: 202 HPKRIVTIDATKPLKEVVSVALEHV 226 +P+R+V IDA + +VV+ A+ + Sbjct: 180 YPERVVEIDANQSFDQVVADAVRMI 204 An alignment of the GAS and GBS proteins is shown below: TABLE-US-02097 Identities = 145/219 (66%), Positives = 181/219 (82%) Query: 4 FDRIVVIINKGCTMKKGLMISFEGPDGAGKTTVLEAVLPLLREKLSQDILTTREPGGVTI 63 FD+I ++ ++G M G +I+ EGPDGAGKTTVLE ++PLL++K++QDILTTREPGGV I Sbjct: 9 FDKIELLKSEGNKMITGKLITVEGPDGAGKTTVLEQLIPLLKQKVAQDILTTREPGGVAI 68 Query: 64 SEEIRHIILDVKHTQMDKKTELLLYMAARRQHLVEKVLPALEEGKIVLMDRFIDSSVAYQ 123- SE IR +ILD+ HT MD KTELLLY+AARRQHLVEKVLPALE G++V +DRFIDSSVAYQ Sbjct: 69 SEHIRELILDINHTAMDPKTELLLYIAARRQHLVEKVLPALEAGQLVFIDRFIDSSVAYQ 128- Query: 124 GSGRGLDKSHIKWLNDYATDSHKPDLTLYFDVPSEVGLERIQKSVQREVNRLDLEQLDMH 18- 3 G+GRGL K+ I+WLN++ATD +PDLTLYFDVPSE+GL RI + QREVNRLDLE +++H Sbjct: 129 GAGRGLIKADIQWLNEFATDGLEPDLTLYFDVPSEIGLARINANQQREVNRLDLETIEIH 18- 8 Query: 184 QRVRQGYLELADSEPNRIVTIDASQQLDEVIAETFSIIL 222 QRVR+GYL LA P RIVTIDA++ L EV++ +L Sbjct: 189 QRVRKGYLALAKEHPKRIVTIDATKPLKEVVSVALEHVL 227 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 706 A DNA sequence (GBSx0750) was identified in S. agalactiae <SEQ ID 2173> which encodes the amino acid sequence <SEQ ID 2174>. This protein is predicted to be DNA polymerase III delta' subunit (dnaZX). Analysis of this protein sequence reveals the following:

TABLE-US-02098 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2603(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02099 >GP:BAB03763 GB:AP001507 DNA polymerase III delta' subunit [Bacillus halodurans] Identities = 78/189 (41%), Positives = 113/189 (59%), Gaps = 3/189 (1%) Query: 2 DLKRTQPKLLEKFNTILQSDRMSHAYLFSGNFAS--LDMALYLAQSQFCEKRQSGLPCQE 59 +L + QP + L R++HAY+F GN + MAL+LA+S FC +R PCQ Sbjct: 5 NLAKNQPFVATMLKNSLAKGRLAHAYIFDGNRGTGKKRMALHLAKSFFCAQRAGVEPCQT 64 Query: 60 CRACRLIANGEFSDVKIIEPQGQLIKTETIKELTKDFSRSGFEGKSQVFIIKDCEKMHVN 119- C+ C+ I +G DV IEP GQ IK ++ L K+FS G E +V+I+ +KM + Sbjct: 65 CKECKRIEHGNHPDVHFIEPDGQSIKKHQVEHLQKEFSYRGMESAKKVYIVNHADKMTTS 124- Query: 120 AANSLLKFIEEPQSSSYVILLTNDENNVLPTIKSRTQIFRF-PKQLDMLVHQAEQAGLLK 17- 8 AANSLLKF+EEP + + ILLT N+LPTIKSR+Q+ F P ++ E+ G+ + Sbjct: 125 AANSLLKFLEEPLADTVAILLTEQLQNMLPTIKSRSQVLSFAPLEVQAFAKLLEEEGISE 18- 4 Query: 179 SQASLLAQV 187 S ++LLA + Sbjct: 185 SVSNLLASL 193 A related DNA sequence was identified in S. pyogenes <SEQ ID 2175> which encodes the amino acid sequence <SEQ ID 2176>. Analysis of this protein sequence reveals the following: TABLE-US-02100 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2685(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02101 Identities = 151/290 (52%), Positives = 213/290 (73%), Gaps = 3/290 (1%) Query: 1 MDLKRTQPKLLEKFNTILQSDRMSHAYLFSGNFASLDMALYLAQSQFCEKRQSGLPCQEC 60 MDL + P + + F TIL+ DR++HAYLFSG+FA+ +MAL+LA+ FCE+++ PC C Sbjct: 1 MDLAQKAPNVYQAFQTILKKDRLNHAYLFSGDFANEEMALFLAKVIFCEQKKDQTPCGHC 60 Query: 61 RACRLIANGEFSDVKIIEPQGQLIKTETIKELTKDFSRSGFEGKSQVFIIKDCEKMHVNA 120- R+C+LI G+F+DV ++EP GQ+IKT+ +KE+ +FS++G+E K QVFIIKDC+KMH+NA Sbjct: 61 RSCQLIEQGDFADVTVLEPTGQVIKTDVVKEMMANFSQTGYENKRQVFIIKDCDKMHINA 120- Query: 121 ANSLLKFIEEPQSSSYVILLTNDENNVLPTIKSRTQIFRFPKQLDMLVHQAEQAGLLKSQ 18- 0 ANSLLK+IEEPQ +Y+ LLTND+N VLPTIKSRTQ+F+FPK L A++ GLL Q Sbjct: 121 ANSLLKYIEEPQGEAYIFLLTNDDNKVLPTIKSRTQVFQFPKNEAYLYQLAQEKGLLNHQ 18- 0 Query: 181 ASLLAQVADDPKHLEILLTNKKLLDYLNLSQQFVTTLAKDRQTAYLEVSRLTSQVVDKND 24- 0 A L+A++A + HLE LL KLL+ + +++FV+ KD+ AYL ++RL +K + Sbjct: 181 AKLVAKLATNTSHLERLLQTSKLLELITQAERFVSIWLKDQLQAYLALNRLVQLATEKEE 24- 0 Query: 241 QAFVFQWLTIMLAKE---GQLYDLENTYRAQQMWKSNVSFQNSLEYMVLS 287 Q V LT++LA+E L LE Y+A+ MW+SNV+FQN+LEYMV+S Sbjct: 241 QDLVLTLLTLLLARERAQTPLTQLEAVYQARLMWQSNVNFQNTLEYMVMS 290 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 707 A DNA sequence (GBSx0751) was identified in S. agalactiae <SEQ ID 2177> which encodes the amino acid sequence <SEQ ID 2178>. Analysis of this protein sequence reveals the following: TABLE-US-02102 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2016(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02103 >GP:BAB03765 GB:AP001507 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 45/116 (38%), Positives = 62/116 (52%), Gaps = 8/116 (6%) Query: 1 MDKKDLFDAFDDFSQNLLVGLSEIETMKKQIQKLLEENTVLRIENGKLRERLSVIEAET- 59 M+KK +F + + E+ +K+Q+ L+EEN L IEN LRERL E E Sbjct: 1 MNKKAIFTQVSQLEERIGELHRELGGLKEQLAYLIEENHFLTIENEHLRERLGEPELEET 60 Query: 60 ---ETAVKNSK----QGRELLEGIYNDGFHICNTFYGQRRENDEECAFCIELLYRD 108 E K K +G + L +Y +GFHICNT YG R+N E+C FC+ L +D Sbjct: 61 EEKEQVTKERKPFVGEGYDNLARLYQEGFHICNTHYGSLRKNGEDCLFCLSFLNQD 116 A related DNA sequence was identified in S. pyogenes <SEQ ID 2179> which encodes the amino acid sequence <SEQ ID 2180>. Analysis of this protein sequence reveals the following: TABLE-US-02104 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0700(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02105 Identities = 75/107 (70%), Positives = 89/107 (83%), Gaps = 1/107 (0%) Query: 1 MDKKDLFDAFDDFSQNLLVGLSEIETMKKQIQKLLEENTVLRIENGKLRERLSVIEAETE 60 ++KK+LFDAFD FSQNL+V L+EIE MKKQ+Q L+EENT+LR+EN KLRERLS +E ET Sbjct: 1 VNKKELFDAFDGFSQNLMVTLAEIEAMKKQVQSLVEENTILRLENTKLRERLSHLEHET- 59 Query: 61 TAVKNSKQGRELLEGIYNDGFHICNTFYGQRRENDEECAFCIELLYR 107 A SKQ ++ LEGIY++GFHICN FYGQRRENDEEC FC ELL R Sbjct: 60 VAKNPSKQRKDHLEGIYDEGFHICNFFYGQRRENDEECMFCRELLDR 106 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 708 A DNA sequence (GBSx0752) was identified in S. agalactiae <SEQ ID 2181> which encodes the amino acid sequence <SEQ ID 2182>. Analysis of this protein sequence reveals the following: TABLE-US-02106 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.28 Transmembrane 119-135 (119-135) ----- Final Results ----- bacterial membrane --- Certainty = 0.1510(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10051> which encodes amino acid sequence <SEQ ID 10052> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02107 >GP:BAB03768 GB:AP001507 unknown conserved protein [Bacillus halodurans] Identities = 138/287 (48%), Positives = 189/287 (65%), Gaps = 2/287 (0%) Query: 4 MQVQKSFKSNIHYGTLYLVPTPIGNLDDMTFRAIRILREVDFICAEDTRNTGLLLKHFDI 63 M+ Q+S++ GTLYLV TPIGNL+D+TFRAIR L+E D I AEDTR T LL HFDI Sbjct: 1 MKTQQSYQQRDDKGTLYLVATPIGNLEDVTFRAIRTLKEADQIAAEDTRQTKKLLNHFDI 60 Query: 64 TTKQISFHEHNAYDKISGLIDLLKEGKSLAQVSDAGMPSISDPGHDLVKAAIEGDIPVVS 123- TK +S+HEHN LID L EG+++A VSDAGMP+ISDPG++LV +AI+ I V+ Sbjct: 61 ATKLVSYHEHNKETMGKRLIDDLIEGRTIALVSDAGMPAISDPGYELVVSAIKEGIAVIP 120- Query: 124 IPGASAGITALIASGLAPQPHIFYGFLPRKKGQQITFFETKQDYPETQIFYESPFRVSDT 18- 3 IPGA+A +TALIASGL + F GFLPR+K Q+ E + T IFYESP R+ DT Sbjct: 121 IPGANAAVTALIASGLPTESFQFIGFLPRQKKQRRQALEETKPTKATLIFYESPHRLKDT 18- 0 Query: 184 LKHMKEIYGDRQVVLVRELTKLYEEYQRGTISQLLEHIEKVPLKGECLIIVDGKRDTERV 24- 3 L M I G+R V + RELTK YEE+ RGT+ + + + +KGE +IV+G + Sbjct: 181 LDDMLLILGNRHVSICRELTKTYEEFLRGTLEEAVHWAREATIKGEFCLIVEGNGEKVEP 24- 0 Query: 244 KDS--SQQDPLVLVKEYIANGDKTNQAIKKVAKEFNLNRQELYASFH 288 ++ P+ V+ YIA G ++ +AIK+VA + + ++++Y +H Sbjct: 241 EEVWWESLSPVQHVEHYIALGFRSKEAIKQVATDRGVPKRDIYNIYH 287 A related DNA sequence was identified in S. pyogenes <SEQ ID 2183> which encodes the amino acid sequence <SEQ ID 2184>. Analysis of this protein sequence reveals the following: TABLE-US-02108 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.09 Transmembrane 116-132 (116-134) ----- Final Results ----- bacterial membrane --- Certainty = 0.2635(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02109 >GP:BAB03768 GB:AP001507 unknown conserved protein [Bacillus halodurans] Identities = 139/287 (48%), Positives = 189/287 (65%), Gaps = 2/287 (0%) Query: 1 MQVQKSFKDKKTSGTLYLVPTPIGNLQDMTFRAVATLKEVDFICAEDTRNTGLLLKHFDI 60 M+ Q+S++ + GTLYLV TPIGNL+D+TFRA+ TLKE D I AEDTR T LL HFDI Sbjct: 1 MKTQQSYQQRDDKGTLYLVATPIGNLEDVTFRAIRTLKEADQIAAEDTRQTKKLLNHFDI 60 Query: 61 ATKQISFHEHNAYEKIPDLIDLLISGRSLAQVSDAGMPSISDPGHDLVKAAIDSDIAVVA 120- ATK +S+HEHN LID LI GR++A VSDAGMP+ISDPG++LV +AI IAV+ Sbjct: 61 ATKLVSYHEHNKETMGKRLIDDLIEGRTIALVSDAGMPAISDPGYELVVSAIKEGIAVIP 120- Query: 121 LPGASAGITALIASGLAPQPHVFYGFLPRKAGQQKAFFEDKHHYPETQMFYESPYRIKDT 18- 0 +PGA+A +TALIASGL + F GFLPR+ Q++ E+ T +FYESP+R+KDT Sbjct: 121 IPGANAAVTALIASGLPTESFQFIGFLPRQKKQRRQALEETKPTKATLIFYESPHRLKDT 18- 0 Query: 181 LTNMLACYGDRQVVLVRELTKLFEEYQRGSISEILSYLEETPLKGECLLIVA--GAQADS 23- 8 L +ML G+R V + RELTK +EE+ RG++ E + + E +KGE LIV G + + Sbjct: 181 LDDMLLILGNRHVSICRELTKTYEEFLRGTLEEAVHWAREATIKGEFCLIVEGNGEKVEP 24- 0 Query: 239 EVELTADVDLVSLVQKEIQAGAKPNQAIKTIAKAYQVNRQELYQQFH 285 E + V V+ I G + +AIK +A V ++++Y +H Sbjct: 241 EEVWWESLSPVQHVEHYIALGFRSKEAIKQVATDRGVPKRDIYNIYH 287 An alignment of the GAS and GBS proteins is shown below: TABLE-US-02110 Identities = 208/287 (72%), Positives = 238/287 (82%) Query: 4 MQVQKSFKSNIHYGTLYLVPTPIGNLDDMTFRAIRILREVDFICAEDTRNTGLLLKHFDI 63 MQVQKSFK GTLYLVPTPIGNL DMTFRA+ L+EVDFICAEDTRNTGLLLKHFDI Sbjct: 1 MQVQKSFKDKKTSGTLYLVPTPIGNLQDMTFRAVATLKEVDFICAEDTRNTGLLLKHFDI 60 Query: 64 TTKQISFHEHNAYDKISGLIDLLKEGKSLAQVSDAGMPSISDPGHDLVKAAIEGDIPVVS 123- TKQISFHEHNAY+KI LIDLL G+SLAQVSDAGMPSISDPGHDLVKAAI+ DI VV+ Sbjct: 61 ATKQISFHEHNAYEKIPDLIDLLISGRSLAQVSDAGMPSISDPGHDLVKAAIDSDIAVVA 120- Query: 124 IPGASAGITALIASGLAPQPHIFYGFLPRKKGQQITFFETKQDYPETQIFYESPFRVSDT 18- 3 +PGASAGITALIASGLAPQPH+FYGFLPRK GQQ FFE K YPETQ+FYESP+R+ DT Sbjct: 121 LPGASAGITALIASGLAPQPHVFYGFLPRKAGQQKAFFEDKHHYPETQMFYESPYRIKDT 18- 0 Query: 184 LKHMKEIYGDRQVVLVRELTKLYEEYQRGTISQLLEHIEKVPLKGECLIIVDGKRDTERV 24- 3 L +M YGDRQVVLVRELTKL+EEYQRG+IS++L ++E+ PLKGECL+IV G + V Sbjct: 181 LTNMLACYGDRQVVLVRELTKLFEEYQRGSISEILSYLEETPLKGECLLIVAGAQADSEV 24- 0 Query: 244 KDSSQQDPLVLVKEYIANGDKTNQAIKKVAKEFNLNRQELYASFHDL 290 + ++ D + LV++ I G K NQAIK +AK + +NRQELY FHDL Sbjct: 241 ELTADVDLVSLVQKEIQAGAKPNQAIKTIAKAYQVNRQELYQQFHDL 287 A related GBS gene <SEQ ID 8643> and protein <SEQ ID 8644> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02111 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -6.92 GvH: Signal Score (-7.5): -9.26 Possible site: 48 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -1.28 threshold: 0.0 INTEGRAL Likelihood = -1.28 Transmembrane 118-134 (118-134) PERIPHERAL Likelihood = 6.89 32 modified ALOM score: 0.76 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1510 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00052## SEQ ID 8644 (GBS343) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 11; MW 35.4 kDa). The GBS343-His fusion product was purified (FIG. 215, lane 4) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 277), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 709 A DNA sequence (GBSx0753) was identified in S. agalactiae <SEQ ID 2185> which encodes the amino acid sequence <SEQ ID 2186>. This protein is predicted to be bA483F11.3 (cutC). Analysis of this protein sequence reveals the following: TABLE-US-02112 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2568 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02113 >GP:CAB88199 GB:AL133353 bA483F11.3 (CGI-32 protein) [Homo sapiens] Identities = 79/203 (38%), Positives = 116/203 (56%), Gaps = 7/203 (3%) Query: 3 LREFCAENLTDLTRLDKAIISRVELCDNLAVGGTTPSYGVIKEANQYLHEKGISVAVMIR 62 L E C +++ ++ R+ELC L+ GGTTPS GV++ Q + I V VMIR Sbjct: 27 LMEVCVDSVESAVNAERGGADRIELCSGLSEGGTTPSMGVLQVVKQSVQ---IPVFVMIR 83 Query: 63 PRGGNFVYNDLELRIMEEDILRAVELESDALVLGILTSNNHIDTEAIEQLLPATQGLPLV 122- PRGG+F+Y+D E+ +M+ DI A +D LV G LT + HID E L+ + LP+ Sbjct: 84 PRGGDFLYSDREIEVMKADIRLAKLYGADGLVFGALTEDGHIDKELCMSLMAICRPLPVT 143- Query: 123 FHMAFDVIPKSDQKKSIDQLVALGFTRILLHGSSNGEPIIENIKHIKALVEYANNRIEIM 18- 2 FH AFD++ D +++ L+ LGF R+L G + +E + IK L+E A RI +M Sbjct: 144 FHRAFDMV--HDPMAALETLLTLGFERVLTSGCDSS--ALEGLPLIKRLIEQAKGRIVVM 19- 9 Query: 183 VGGGVTAENYQYICQETGVKQAH 205 GGG+T N Q I + +G + H Sbjct: 200 PGGGITDRNLQRILEGSGATEFH 222 A related DNA sequence was identified in S. pyogenes <SEQ ID 2187> which encodes the amino acid sequence <SEQ ID 2188>. Analysis of this protein sequence reveals the following: TABLE-US-02114 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2372 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02115 Identities = 143/208 (68%), Positives = 168/208 (80%) Query: 2 ILREFCAENLTDLTRLDKAIISRVELCDNLAVGGTTPSYGVIKEANQYLHEKGISVAVMI 61 +++EFCAENLT L LD ISRVELCDNLAVGGTTPSYGVIKEA Q LH+K ISVA MI Sbjct: 1 MIKEFCAENLTLLPTLDAGQISRVELCDNLAVGGTTPSYGVIKEACQLLHDKKISVATMI 60 Query: 62 RPRGGNFVYNDLELRIMEEDILRAVELESDALVLGILTSNNHIDTEAIEQLLPATQGLPL 121- RPRGG+FVYNDLEL+ MEEDIL+AVE SDALVLG+LT+ N +DT+AIEQLLPATQGLPL Sbjct: 61 RPRGGDFVYNDLELKAMEEDILKAVEAGSDALVLGLLTTENQLDTDAIEQLLPATQGLPL 120- Query: 122 VFHMAFDVIPKSDQKKSIDQLVALGFTRILLHGSSNGEPIIENIKHIKALVEYANNRIEI 18- 1 VFHMAFD IP Q +++DQL+ GF R+L HGS PI +N++ +K+LV YAN RIEI Sbjct: 121 VFHMAFDRIPTDHQHQALDQLIDYGFVRVLTHGSPEATPITDNVEQLKSLVTYANKRIEI 18- 0 Query: 182 MVGGGVTAENYQYICQETGVKQAHGTRI 209 M+GGG+TAEN Q + Q TG HGT+I Sbjct: 181 MIGGGITAENCQSLSQLTGTAIVHGTKI 208 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 710 A DNA sequence (GBSx0754) was identified in S. agalactiae <SEQ ID 2189> which encodes the amino acid sequence <SEQ ID 2190>. Analysis of this protein sequence reveals the following: TABLE-US-02116 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1216 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02117 >GP:BAA12206 GB:D84061 phosphoserine aminotransferase [Spinacia oleracea] Identities = 65/109 (59%), Positives = 79/109 (71%), Gaps = 1/109 (0%) Query: 3 IYNFSAGPAVLPKPVLVKAQSELLNYQGSSMSVLEVSHRSKEFDDIIKGAERYLRDLMGI 62 ++NF+AGPAVLP+ VL KAQSELLN++GS MSV+E+SHR KEF II AE LR L+ I Sbjct: 69 VFNFAAGPAVLPENVLQKAQSELLNWRGSGMSVMEMSHRGKEFTSIIDKAEADLRTLLNI 128- Query: 63 PDNYKVIFLQGGASLQFSMIPLNIARGRKAY-YHVAGSWGEKSLYRGCK 110 P +Y V+FLQGGAS QFS IPLN+ A Y V GSWG+K+ K Sbjct: 129 PSDYTVLFLQGGASTQFSAIPLNLCTPDSAVDYIVTGSWGDKAAKEAAK 177 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 711 A DNA sequence (GBSx0755) was identified in S. agalactiae <SEQ ID 2191> which encodes the amino acid sequence <SEQ ID 2192>. Analysis of this protein sequence reveals the following: TABLE-US-02118 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 712 A DNA sequence (GBSx0756) was identified in S. agalactiae <SEQ ID 2193> which encodes the amino acid sequence <SEQ ID 2194>. This protein is predicted to be phosphoserine aminotransferase (serC). Analysis of this protein sequence reveals the following:

TABLE-US-02119 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3380 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10049> which encodes amino acid sequence <SEQ ID 10050> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02120 >GP:AAF94318 GB:AE004196 phosphoserine aminotransferase [Vibrio cholerae] Identities = 104/210 (49%), Positives = 152/210 (71%), Gaps 3/210 (1%) Query: 4 NNTIEGTSLYDIPKTNEVPVIADMSSNILAVKYKVEDFAMIYAGAQKNIGPAGVTVVIIR 63 N TI+G + D+P T++ P++ADMSS IL+ + V + +IYAGAQKNIGPAG+ + I+R Sbjct: 170 NETIDGIEINDLPVTDK-PIVADMSSTILSREIDVSKYGVIYAGAQKNIGPAGICIAIVR 22- 8 Query: 64 EDMIN-EEPTLSSMLDYKIQSDAGSLYNTPPAYSIYIAKLVFEWVKSLGGVDAMEKANRE 122- +D+++ L +L+YKI ++ S++NTPP ++ Y++ LVF+W+K+ GGV A+E+ NR Sbjct: 229 DDLLDLASDLLPGVLNYKILAEQESMFNTPPTFAWYLSGLVFQWLKAQGGVKAIEEVNRA 28- 8 Query: 123 KSGLLYDYIDSSEFYSNPVRDKKSRSLCNIPFITINKDLDEKFVKEATERGFKNIKGHRS 18- 2 K+ LLY YIDSS+FY N + +RSL N+PF +LD+ F++ A RG ++KGHR Sbjct: 289 KAALLYGYIDSSDFYRNEIH-PDNRSLMNVPFQLAKPELDDTFLELAEARGLVSLKGHRV 34- 7 Query: 183 VGGMRASLYNAFPKQGVIELIDFMKTFEAE 212 VGGMRAS+YNA P +GV L+DFMK FEA+ Sbjct: 348 VGGMRASIYNAMPLEGVQALVDFMKEFEAQ 377 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 713 A DNA sequence (GBSx0757) was identified in S. agalactiae <SEQ ID 2195> which encodes the amino acid sequence <SEQ ID 2196>. Analysis of this protein sequence reveals the following: TABLE-US-02121 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0466 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10047> which encodes amino acid sequence <SEQ ID 10048> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02122 >GP:CAB73701 GB:AL139079 putative acetyltransferase [Campylobacter jejuni] Identities = 46/170 (27%), Positives = 78/170 (45%), Gaps = 13/170 (7%) Query: 7 IRLAFPNEIDQIMLLIEEARAEIAKTGSDQWQKEDGYPNRNDIIDDILNGYAWVGIEDGM 66 I+ A +++ I+ + ++A + QW ++ YPN +DI +V E+ Sbjct: 6 IQKAVNKDLNSILEITKDALNAMKTMNFHQW--DENYPNEIVFQEDIQAQELYVFKENDE 63 Query: 67 LATYAAVIDGHE-EVYDAIYEGKWLHDNHRYLTFHRIAISNQFRGRGLAQTFLQGL---- 121- + + + + +E Y + K D YL HR+A+ +G+G+AQ L Sbjct: 64 ILGFICINEKFKPEFYKQVIFNKNYDDKAFYL--HRLAVKQNAKGKGVAQKLLNFCENFA 121- Query: 122 IEGHKGPDFRCDTHEKNVTMQHILNKLGYQYCGKVPLDGVR---LAYQKI 168 +E HK R DTH KN M + KL + +CG + + LAY+KI Sbjct: 122 LENHKA-SLRADTHSKNFPMNSLFKKLDFNFCGNFDIPNYQDPFLAYEKI 170 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 714 A DNA sequence (GBSx0758) was identified in S. agalactiae <SEQ ID 2197> which encodes the amino acid sequence <SEQ ID 2198>. Analysis of this protein sequence reveals the following: TABLE-US-02123 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2968 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 7151 A DNA sequence (GBSx0759) was identified in S. agalactiae <SEQ ID 2199> which encodes the amino acid sequence <SEQ ID 2200>. This protein is predicted to be D-3-phosphoglycerate dehydrogenase (serA). Analysis of this protein sequence reveals the following: TABLE-US-02124 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3102 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10045> which encodes amino acid sequence <SEQ ID 10046> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02125 >GP:AAB99020 GB:U67544 phosphoglycerate dehydrogenase (serA) [Methanococcus jannaschii] Identities = 102/313 (32%), Positives = 168/313 (53%), Gaps = 21/313 (6%) Query: 31 ENPDAYIIRSQNLHNQDF---PSNLKAIARAGAGTNNIPIEEASAQGIVVFNTPGANANA 87 - ++ D ++RS +D LK I RAG G +NI +E A+ +GI+V N P A++ + Sbjct: 40 KDADVLVVRSGTKVTRDVIEKAEKLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSIS 99 Query: 88 VKEAVIAALLLSARDYLGANRWVNTLTGTDIPKQIEAGKKAFAGNEIAGKKLGVIGLGAI 147- V E + +L +AR N T K+ E +K F G E+ GK LGVIGLG I Sbjct: 100 VAELTMGLMLAAAR---------NIPQATASLKRGEWDRKRFKGIELYGKTLGVIGLGRI 15- 0 Query: 148 GARIANDARRLGMTVLGYDPYVSIETAWNISSHVQRVKEIKDIFETCDYITIHVPLTNET 20- 7 G ++ A+ GM ++GYDPY+ E A ++ V+ V +I ++ + D+IT+HVPLT +T Sbjct: 151 GQQVVKRAKAFGMNIIGYDPYIPKEVAESMG--VELVDDINELCKRADFITLHVPLTPKT 20- 8 Query: 208 KHTFDAKAFSIMKKGTTIINFARAELVNNQELFEAIETGVVKRYITDFGDKE------LL 26- 1 +H + ++MKK I+N AR L++ + L+EA++ G ++ D ++E LL Sbjct: 209 RHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRAAALDVFEEEPPKDNPLL 26- 8 Query: 262 NQKGITVFPHVGGSTDEAELNCAIMASQTIRCFMETGEITNSVNFPNVHQIQTAPFR-IT 32- 0 + PH G ST+EA+ + ++ I+ + N VN PN+ Q + + Sbjct: 269 TLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVLRGELAENVVNMPNIPQEKLGKLKPYM 32- 8 Query: 321 LINKNVPNIVAKI 333 L+ + + NIV ++ Sbjct: 329 LLAEMLGNIVMQV 341 There is also homology to SEQ ID 124. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 716 A DNA sequence (GBSx0760) was identified in S. agalactiae <SEQ ID 2201> which encodes the amino acid sequence <SEQ ID 2202>. This protein is predicted to be methylated-DNA--protein-cysteine S-methyltransferase (ogt). Analysis of this protein sequence reveals the following: TABLE-US-02126 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2460(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02127 >GP:AAF96913 GB:AE004427 methylated-DNA--protein-cysteine S-methyltransferase [Vibrio cholerae] Identities = 73/156 (46%), Positives = 99/156 (62%), Gaps = 9/156 (5%) Query: 7 YQSPLGEIRLLADNLGLSGLYFVGQKYDMLAVNQEEIVNMSNSYTLLGK--KWLDAYFSQ 64 Y SPLG + L A + GL G++F Q E + + +L K + LD YFS Sbjct: 7 YSSPLGPMTLQASSQGLLGVWFATQ-----TTQPEHLGDYVKECPILNKTIRQLDEYFSG 61 Query: 65 QNLP-SIPLSLRGTAFQTRVWQELQKIPFGDTKTYGELAKEL-NCQSAQAVGGAIGKNSI 122- Q +PL+ GTAFQ VW L KIP+G+ +Y +LA+ + N ++ +AVG A GKN I Sbjct: 62 QRTQFELPLAASGTAFQQSVWHALCKIPYGEIWSYQQLAEAIGNPKAVRAVGLANGKNPI 121- Query: 123 SLIIPCHRVLGRYGQLTGYAGGLERKSWLLEYEKEK 158 S+I+PCHRV+G+ GQLTGYAGGLERK++LLE EK + Sbjct: 122 SIIVPCHRVVGKNGQLTGYAGGLERKAFLLELEKRR 157 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 717 A DNA sequence (GBSx0761) was identified in S. agalactiae <SEQ ID 2203> which encodes the amino acid sequence <SEQ ID 2204>. Analysis of this protein sequence reveals the following: TABLE-US-02128 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3137(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02129 >GP:BAB07204 GB:AP001518 arsenate reductase [Bacillus halodurans] Identities = 56/107 (52%), Positives = 74/107 (68%), Gaps = 1/107 (0%) Query: 3 TFYEYPKCTTCRSAKKELTELGLTFEAIDIKSNPPKVSLLKELLENSPYDLKKFFNTSGN 62 TFY+YPKC TC+ AKK L + G+ ++ I PP LK+L E S +LKKFFNTSG Sbjct: 4 TFYQYPKCGTCQKAKKWLDQHGIEVNSVHIVEQPPSKEELKQLYEQSGLELKKFFNTSGK 63 Query: 63 SYRELGLKDKFDDLTLDQALDLLASDGMLIKRPLLVKDNKILQIGYR 109 YRELGLKDK + + D+ L+ LASDGMLIKRP+L +K+ +G++ Sbjct: 64 KYRELGLKDKVKEASEDELLETLASDGMLIKRPILTDGDKV-TVGFK 109 A related DNA sequence was identified in S. pyogenes <SEQ ID 2205> which encodes the amino acid sequence <SEQ ID 2206>. Analysis of this protein sequence reveals the following: TABLE-US-02130 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3969(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02131 Identities = 64/99 (64%), Positives = 79/99 (79%) Query: 19 ELTELGLTFEAIDIKSNPPKVSLLKELLENSPYDLKKFFNTSGNSYRELGLKDKFDDLTL 78 - EL +L FEAIDIK+NPPK LK +E S Y +K FFNTSGNSYRELGLKDK D L+L Sbjct: 3 ELKQLVSDFEAIDIKANPPKAQDLKHWMETSGYTIKNFFNTSGNSYRELGLKDKIDQLSL 62 Query: 79 DQALDLLASDGMLIKRPLLVKDNKILQIGYRTKYKDLNL 117 D+A +LLA+DGMLIKRP+L+KD +LQ+GYR Y++L+L Sbjct: 63 DKAAELLATDGMLIKRPILIKDGNVLQVGYRKPYQELDL 101 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 718 A DNA sequence (GBSx0762) was identified in S. agalactiae <SEQ ID 2207> which encodes the amino acid sequence <SEQ ID 2208>. This protein is predicted to be exodeoxyribonuclease (exoA). Analysis of this protein sequence reveals the following: TABLE-US-02132 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1859(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02133 >GP:AAA26879 GB:J04234 exodeoxyribonuclease [Streptococcus pneumoniae] Identities = 217/275 (78%), Positives = 245/275 (88%) Query: 1 MKLISWNIDSLNAALTSESTRALMSRQVIDTLVAEDADIIAIQETKLSAKGPTKKHLEVL 60 MKLISWNIDSLNAALTS+S RA +S++V+ TLVAE+ADIIAIQETKLSAKGPTKKH+E+L Sbjct: 1 MKLISWNIDSLNAALTSDSARAKLSQEVLQTLVAENADIIAIQETKLSAKGPTKKHVEIL 60 Query: 61 ETYFPEYDLVWRSSVEPARKGYAGTMFLYRKGLNPIVSFPEIDAPTTMDNEGRIITLELE 120- E FP Y+ WRSS EPARKGYAGTMFLY+K L P +SFPEI AP+TMD EGRIITLE + Sbjct: 61 EELFPGYENTWRSSQEPARKGYAGTMFLYKKELTPTISFPEIGAPSTMDLEGRIITLEFD 120- Query: 121 NCYITQVYTPNAGDGLKRLADRQIWDIKYAEYLATLDSQKPVLATGDYNVAHKEIDLANP 18- 0 ++TQVYTPNAGDGLKRL +RQ+WD KYAEYLA LD +KPVLATGDYNVAH EIDLANP Sbjct: 121 AFFVTQVYTPNAGDGLKRLEERQVWDAKYAEYLAELDKEKPVLATGDYNVAHNEIDLANP 18- 0 Query: 181 SSNRRSAGFTAEERQGFTNLLAKGFTDTFRYLHGDVPNVYSWWAQRSRTSKINNTGWRID 24- 0 +SNRRS GFT EER GFTNLLA GFTDTFR++HGDVP Y+WWAQRS+TSKINNTGWRID Sbjct: 181 ASNRRSPGFTDEERAGFTNLLATGFTDTFRHVHGDVPERYTWWAQRSKTSKINNTGWRID 24- 0 Query: 241 YWLTSNRVADKITKSEMIHSGDRQDHTPIILEIEL 275 YWLTSNR+ADK+TKS+MI SG RQDHTPI+LEI+L Sbjct: 241 YWLTSNRIADKVTKSDMIDSGARQDHTPIVLEIDL 275 A related DNA sequence was identified in S. pyogenes <SEQ ID 2209> which encodes the amino acid sequence <SEQ ID 2210>. Analysis of this protein sequence reveals the following: TABLE-US-02134 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2181(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02135 Identities = 221/275 (80%), Positives = 251/275 (90%) Query: 1 MKLISWNIDSLNAALTSESTRALMSRQVIDTLVAEDADIIAIQETKLSAKGPTKKHLEVL 60 MKLISWNIDSLNAALT ES RAL+SR V+DTLVA+DADIIAIQETKLSAKGPTKKH+E L Sbjct: 1 MKLISWNIDSLNAALTGESPRALLSRAVLDTLVAQDADIIAIQETKLSAKGPTKKHIETL 60 Query: 61 ETYFPEYDLVWRSSVEPARKGYAGTMFLYRKGLNPIVSFPEIDAPTTMDNEGRIITLELE 120- +YFP Y VWRSSVEPARKGYAGTMFLY+ LNP+++FPEI APTTMD EGRIITLE E Sbjct: 61 LSYFPNYLHVWRSSVEPARKGYAGTMFLYKNTLNPVITFPEIGAPTTMDAEGRIITLEFE 120- Query: 121 NCYITQVYTPNAGDGLKRLADRQIWDIKYAEYLATLDSQKPVLATGDYNVAHKEIDLANP 18- 0 + ++TQVYTPNAGDGL+RL DRQIWD KYA+YL LD+QKPVLATGDYNVAHKEIDLANP Sbjct: 121 DFFVTQVYTPNAGDGLRRLDDRQIWDHKYADYLTELDAQKPVLATGDYNVAHKEIDLANP 18- 0 Query: 181 SSNRRSAGFTAEERQGFTNLLAKGFTDTFRYLHGDVPNVYSWWAQRSRTSKINNTGWRID 24- 0 +SNRRS GFT EERQGFTNLLA+GFTDTFR++HGD+P+VY+WWAQRS+TSKINNTGWRID Sbjct: 181 NSNRRSPGFTDEERQGFTNLLARGFTDTFRHVHGDIPHVYTWWAQRSKTSKINNTGWRID 24- 0 Query: 241 YWLTSNRVADKITKSEMIHSGDRQDHTPIILEIEL 275 YWL SNR+ DK+ +SEMI SG+RQDHTPI+L+I+L Sbjct: 241 YWLASNRLVDKVKRSEMISSGERQDHTPILLDIDL 275 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 719 A DNA sequence (GBSx0763) was identified in S. agalactiae <SEQ ID 2211> which encodes the amino acid sequence <SEQ ID 2212>. Analysis of this protein sequence reveals the following: TABLE-US-02136 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.96 Transmembrane 28-44 (22-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.4185(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8645> which encodes amino acid sequence <SEQ ID 8646> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-02137 Lipop Possible site: -1 Crend: 5 McG: Discrim Score: 17.78 GvH: Signal Score (-7.5): -4.56 Possible site: 55 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -7.96 threshold: 0.0 INTEGRAL Likelihood = -7.96 Transmembrane 8-24 (2-29) PERIPHERAL Likelihood = 9.28 138 modified ALOM score: 2.09 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4185(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02138 >GP:AAD11512 GB:U60828 unknown [Lactococcus lactis] Identities = 53/240 (22%), Positives = 102/240 (42%), Gaps = 24/240 (10%) Query: 65 PTILIPGSSATQERFNSMLAQL----NQMGEKHSVLKLTVKKDNSIIYNGQISGNDHKPY 120- PTI I GS + ++ +L N +K V+ + K+ + GQIS ++ P Sbjct: 64 PTIYIGGSGGNVTSIDWLVERLLPIKNISSQKSLVMTSNITKNYELKVEGQISQDNKYPI 123- Query: 121 IVIGFENNEDGYSNIKKQTKWLQIAMNDLQKKYKFKRFNAIGHSNGGLSWTIFLEDYYDS 18- 0 I G ++ + +K LQ + L + Y+ N +G+S+G ++ D ++ Sbjct: 124 IEFA---TVKGTNSGELFSKGLQKIIVYLTENYQVPWINLVGYSSGATGAVYYMMDTGNN 18- 0 Query: 181 DEFD-MKSLLTMGTPFNFEES-----NTSN--------HTQMLKDLISNKGNIPSSLMVY 22- 6 F + +++ +N E + + SN T+M + + N + S + Sbjct: 181 PNFPPVNKYVSLDGEYNNETNLQLGESLSNVLKEGPIVKTEMYQYIADNYQKVSSKTQML 24- 0 Query: 227 NLAGT--NSYDGDKIVPFASVETGKYIFQETAKHYTQLTVTGNNATHSDLPDNPEVIQYV 28- 4 L G + D +P+A + ++F++ T T+ +HS P NP V++YV Sbjct: 241 LLEGNFNSEKQTDSAIPWADSFSIYHLFKKNGNEITT-TLYPTKTSHSQAPKNPTVVKYV 29- 9 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8646 (GBS219) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 43 (lane 3; MW 31.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 47 (lane 7; MW 56 kDa). GBS219-GST was purified as shown in FIG. 203, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 720 A DNA sequence (GBSx0764) was identified in S. agalactiae <SEQ ID 2213> which encodes the amino acid sequence <SEQ ID 2214>. This protein is predicted to be PTS system, cellobiose-specific IIC component. Analysis of this protein sequence reveals the following:

TABLE-US-02139 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.64 Transmembrane 263-279 (260-282) INTEGRAL Likelihood = -6.26 Transmembrane 200-216 (197-226) INTEGRAL Likelihood = -5.95 Transmembrane 157-173 (156-175) INTEGRAL Likelihood = -5.79 Transmembrane 307-323 (306-332) INTEGRAL Likelihood = -5.68 Transmembrane 131-147 (126-148) INTEGRAL Likelihood = -4.73 Transmembrane 375-391 (370-396) INTEGRAL Likelihood = -3.61 Transmembrane 101-117 (98-119) INTEGRAL Likelihood = -1.75 Transmembrane 326-342 (324-342) INTEGRAL Likelihood = -0.37 Transmembrane 25-41 (25-41) INTEGRAL Likelihood = -0.16 Transmembrane 71-87 (71-88) ----- Final Results ----- bacterial membrane --- Certainty = 0.4057(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02140 >GP:AAC74807 GB:AE000268 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin [Escherichia coli K12] Identities = 60/197 (30%), Positives = 83/197 (41%), Gaps = 12/197 (6%) Query: 209 LAIFLTLSGLFVPDIL--FRPYSYFSVVSENLNAALSQHTDKIPYLYTFYTVKNSFAMFG 26- 6 LA+ +G+ P L Y + V L A + H P L +SF G Sbjct: 253 LALTALDNGIMTPWALENIATYQQYGSVEAALAAGKTFHIWAKPML-------DSFIFLG 30- 5 Query: 267 GIGILLSLFLAVLYESRKLQSKNYYKLTLLTLTPLIFDQNLPFLVGLPVILQPILFIPMV 32- 6 G G L L LA+ SR+ +Y ++ L L IF N P L GLP+I+ P++FIP V Sbjct: 306 GSGATLGLILAIFIASRRA---DYRQVAKLALPSGIFQINEPILFGLPIIMNPVMFIPFV 36- 2 Query: 327 LTTIFAEAFGALMLYLKFVDPAVYTVPSGTPSLLFGFLASNGDWRYLPVTAIILVVGFFI 38- 6 L A Y+ + P P P+ L F +NG L V L + I Sbjct: 363 LVQPILAAITLAAYYMGIIPPVTNIAPWTMPTGLGAFFNTNGSVAALLVALFNLGIATLI 42- 2 Query: 387 YRPFVKIAFAKEEQYEK 403 Y PFV +A + +K Sbjct: 423 YLPFVVVANKAQNAIDK 439 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 721 A DNA sequence (GBSx0765) was identified in S. agalactiae <SEQ ID 2217> which encodes the amino acid sequence <SEQ ID 2218>. Analysis of this protein sequence reveals the following: TABLE-US-02141 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1991(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 722 A DNA sequence (GBSx0766) was identified in S. agalactiae <SEQ ID 2219> which encodes the amino acid sequence <SEQ ID 2220>. Analysis of this protein sequence reveals the following: TABLE-US-02142 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.79 Transmembrane 188-204 (179-206) INTEGRAL Likelihood = -5.36 Transmembrane 105-121 (104-127) INTEGRAL Likelihood = -4.41 Transmembrane 212-228 (210-229) INTEGRAL Likelihood = -3.45 Transmembrane 72-88 (69-89) INTEGRAL Likelihood = -0.48 Transmembrane 124-140 (124-140) ----- Final Results ----- bacterial membrane --- Certainty = 0.3314(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8647> which encodes amino acid sequence <SEQ ID 8648> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-02143 Lipop Possible site: -1 Crend: 6 SRCFLG: 0 McG: Length of UR: 5 Peak Value of UR: 2.99 Net Charge of CR: 4 McG: Discrim Score: 6.88 GvH: Signal Score (-7.5): -2.86 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 5 value: -5.79 threshold: 0.0 INTEGRAL Likelihood = -5.79 Transmembrane 179-195 (170-197) INTEGRAL Likelihood = -5.36 Transmembrane 96-112 (95-118) INTEGRAL Likelihood = -4.41 Transmembrane 203-219 (201-220) INTEGRAL Likelihood = -3.45 Transmembrane 63-79 (60-80) PERIPHERAL Likelihood = 0.10 18 modified ALOM score: 1.66 icm1 HYPID: 7 CFP: 0.331 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3314(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2221> which encodes the amino acid sequence <SEQ ID 2222>. Analysis of this protein sequence reveals the following: TABLE-US-02144 Possible site: 30 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -11.20 Transmembrane 179-195 (173-201) INTEGRAL Likelihood = -3.66 Transmembrane 96-112 (95-113) INTEGRAL Likelihood = -1.44 Transmembrane 203-219 (203-219) INTEGRAL Likelihood = -0.96 Transmembrane 115-131 (115-131) INTEGRAL Likelihood = -0.64 Transmembrane 63-79 (63-79) ----- Final Results ----- bacterial membrane --- Certainty = 0.5479(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below: TABLE-US-02145 Identities = 160/228 (70%), Positives = 185/228 (80%) Query: 10 MSKKSHRQYQIYEGLRCAVALCFISGYINAFTYVTQGKRFAGVQTGNLLSFAIHLSNKHY 69 - MSKK + YQ+YEGLRCA+ LCFISGY+NAFTY+TQGKRFAGVQTGNLLSFAI LS + Sbjct: 1 MSKKKRKHYQVYEGLRCAMTLCFISGYVNAFTYMTQGKRFAGVQTGNLLSFAIRLSEQQL 60 Query: 70 SQALAFLLPIMVFMLGQSFTYFMNRWANKHQLHWYLLSSFALTQVAIVTIILTPFLPSSF 129- +AL FLLP++VFMLGQSFTYFM+RWA K LHWYLLSS LT +A T + TPFLPS+ Sbjct: 61 KEALQFLLPMIVFMLGQSFTYFMHRWATKKGLHWYLLSSVILTGIAFGTALFTPFLPSNV 120- Query: 130 TVAGLAFFASIQVDTFKSLRGAPYANMMMTGNIKNAAYLLTKGLYEKNSDIFLIARNTII 18- 9 TVA LAFFASIQVDTFK+LRGA YAN+MMTGNIKNAAYLLTKGLYEKN ++ I RNT+I Sbjct: 121 TVAALAFFASIQVDTFKTLRGASYANVMMTGNIKNAAYLLTKGLYEKNHELTHIGRNTLI 18- 0 Query: 190 IIGGFIFGVVCSTYFSSKLGEWSLSLILIPLLYVNLLLGHEFYNLQVE 237 +I F GVVCST GE++L IL+PLLYVN LL EFY++Q + Sbjct: 181 VILAFAVGVVCSTLLCIAYGEYALMPILMPLLYVNYLLAQEFYHIQTK 228 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 723 A DNA sequence (GBSx0767) was identified in S. agalactiae <SEQ ID 2223> which encodes the amino acid sequence <SEQ ID 2224>. This protein is predicted to be tellurite resistance protein. Analysis of this protein sequence reveals the following: TABLE-US-02146 Possible site: 20 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.00 Transmembrane 190-206 (190-206) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02147 >GP:AAC22923 GB:U32807 tellurite resistance protein (tehB) [Haemophilus influenzae Rd] Identities = 164/282 (58%), Positives = 205/282 (72%), Gaps = 1/282 (0%) Query: 7 LLPYKTMPVWTAQSIPKAFLEKHNTKEGTWAKLTILSGSLVFYQLSPDGEEISRHIFDAS 66 L+ YK MPVWT ++P+ F EKHNTK GTW KLT+L G L FY+L+ +G+ I+ HIF Sbjct: 5 LICYKQMPVWTKDNLPQMFQEKHNTKVGTWGKLTVLKGKLKFYELTENGDVIAEHIFTPE 64 Query: 67 SDIPFVDPQVWHKVSPNSPDLSCYLTFYCQKEDYFHKKYGLTRTHSEVIASAPLLSEKSN 126- S IPFV+PQ WH+V S DL C L FYC+KEDYF KKY T H +V+ +A ++S Sbjct: 65 SHIPFVEPQAWHRVEALSDDLECTLGFYCKKEDYFSKKYNTTAIHGDVVDAAKIISP-CK 123- Query: 127 ILDLGCGQGRNSLYLSLLGHQVTSVDSNGQSLVALENMALEEELPYNIKRYDINTAAIEG 18- 6 +LDLGCGQGRNSLYLSLLG+ VTS D N S+ L +E L + YDIN A I+ Sbjct: 124 VLDLGCGQGRNSLYLSLLGYDVTSWDHNENSIAFLNETKEKENLNISTALYDINAANIQE 18- 3 Query: 187 HYDFILSTVVFMFLNPDCISDIILQMQSHTQIGGYNLIVSAMDTAENPCPLPFPFTFKEG 24- 6 +YDFI+STVVFMFLN + + II M+ HT +GGYNLIV+AM T + PCPLPF FTF E Sbjct: 184 NYDFIVSTVVFMFLNRERVPSIIKNMKEHTNVGGYNLIVAAMSTDDVPCPLPFSFTFAEN 24- 3 Query: 247 QLKSYYNDWEIIKYNENLGELHRVDENGNRLKLQFATLLARK 288 +LK YY DWE ++YNEN+GELH+ DENGNR+K++FAT+LARK Sbjct: 244 ELKEYYKDWEFLEYNENMGELHKTDENGNRIKMKFATMLARK 285 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 2224 (GBS95) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 5 (lane 3; MW 35.6 kDa) and in FIG. 12 (lane 4; MW 35.6 kDa). The GBS95-His fusion product was purified (FIG. 191, lane 7) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 292), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 724 A DNA sequence (GBSx0768) was identified in S. agalactiae <SEQ ID 2225> which encodes the amino acid sequence <SEQ ID 2226>. This protein is predicted to be methionyl-tRNA synthetase (metS). Analysis of this protein sequence reveals the following: TABLE-US-02148 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 473-489 (473-489) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10043> which encodes amino acid sequence <SEQ ID 10044> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02149 >GP:CAB11814 GB:Z99104 methionyl-tRNA synthetase [Bacillus subtilis] Identities = 395/667 (59%), Positives = 501/667 (74%), Gaps = 12/667 (1%) Query: 20 EKKSFYITTPIYYPSGKLHIGSAYTTIACDVLARYKRMMGFDVQYLTGLDEHGQKIQQKA 79 - E +FYITTPIYYPSGKLHIG AYTT+A D +ARYKR+ GFDV+YLTG DEHGQKIQQKA Sbjct: 4 ENNTFYITTPIYYPSGKLHIGHAYTTVAGDAMARYKRLKGFDVRYLTGTDEHGQKIQQKA 63 Query: 80 EEAGITPQEYVDGMAESVKTLWELLDISYDKFIRTTDTYHEEAVAKIFEQLLAQGDIYLG 139- E+ ITPQEYVD A ++ LW+ L+IS D FIRTT+ H+ + K+F++LL GDIYL Sbjct: 64 EQENITPQEYVDRAAADIQKLWKQLEISNDDFIRTTEKRHKVVIEKVFQKLLDNGDIYLD 123- Query: 140 EYTGWYSVSDEEFFTESQLAEVYRDENGNMIGGVAP-SGHEVEKVSEESYFFRMSKYADR 19- 8 EY GWYS+ DE F+TE+QL ++ R+E G +IGG +P SGH VE + EESYFFRM KYADR Sbjct: 124 EYEGWYSIPDETFYTETQLVDIERNEKGEVIGGKSPDSGHPVELIKEESYFFRMGKYADR 18- 3 Query: 199 LKAYYAEHPEFIQPDGRMNEMLKNFIEPGLEDLAVSRTTYTWGVQVPSNPKHVIYVWIDA 25- 8 L YY E+P FIQP+ R NEM+ NFI+PGLEDLAVSRTT+ WGV+VP NPKHV+YVWIDA Sbjct: 184 LLKYYEENPTFIQPESRKNEMINNFIKPGLEDLAVSRTTFDWGVKVPENPKHVVYVWIDA 24- 3 Query: 259 LMNYISALGYGWSDDLSQYHKFWPADIHMIGKDILRFHSIYWPIMLMALDLPLPKRLVAH 31- 8 L NY++ALGY +D Y K+WPAD+H++GK+I+RFH+IYWPIMLMALDLPLPK++ AH Sbjct: 244 LFNYLTALGYDTEND-ELYQKYWPADVHLVGKEIVRFHTIYWPIMLMALDLPLPKQVFAH 30- 2 Query: 319 GWFVMQDGKMSKSKGNVVYPEMLVERFGLDPLRYYLMRSLPVGSDGTFTPEDYVGRINYE 37- 8 GW +M+DGKMSKSKGNVV P L+ER+GLD LRYYL+R +P GSDG FTPE +V RINY+ Sbjct: 303 GWLLMKDGKMSKSKGNVVDPVTLIERYGLDELRYYLLREVPFGSDGVFTPEGFVERINYD 36- 2 Query: 379 LANDLGNLLNRTIAMVNKYFDGEVPRF-AVATDFDADLASVATDSIENYHKQMEAVDFPR 43- 7 LANDLGNLLNRT+AM+NKYFDG++ + T+FD L SVA ++++ Y K ME ++F Sbjct: 363 LANDLGNLLNRTVAMINKYFDGQIGSYKGAVTEFDHTLTSVAEETVKAYEKAMENMEFSV 42- 2 Query: 438 ALEAVWNLISRTNKYIDETAPWVLAKDETDRDKLAAVMSHLVASLRVVAHLIQPFMMETS 49- 7 AL +W LISRTNKYIDETAPWVLAKD ++L +VM HL SLR+ A L+QPF+ +T Sbjct: 423 ALSTLWQLISRTNKYIDETAPWVLAKDPAKEEELRSVMYHLAESLRISAVLLQPFLTKTP 48- 2 Query: 498 DAIMEQLGL--GATFDLEKLT-FADLPEGVRVVAKGSPIFPRLDMEDEITYIKEQMNAGK 55- 4 + + EQLG+ + + +T F L + V KG P+FPRL+ E+EI YIK +M G Sbjct: 483 EKMFEQLGITDESLKAWDSITAFGQLKD--TKVQKGEPLFPRLEAEEEIAYIKGKMQ-GS 53- 9 Query: 555 APVEKEWVPEEVELTSSKGQIKFEDFDAVEIRVAEVIEVEKVEGSDKLLRFRLDAGDEGH 61- 4 AP ++E EE + +I + F VE+RVAEVIE E V+ +D+LL+ +LD G E Sbjct: 540 APAKEETKEEEPQEVDRLPEITIDQFMDVELRVAEVIEAEPVKKADRLLKLQLDLGFE-K 59- 8 Query: 615 RQILSGIAKFYPNEQELVGKKLQIVANLKPRKMMKKYVSQGMILSAEHDGKLTVLTVDSA 67- 4 RQ++SGIAK Y E ELVGKKL V NLKP K ++ +SQGMIL+ E DG L V+++D + Sbjct: 599 RQVVSGIAKHYTPE-ELVGKKLVCVTNLKPVK-LRGELSQGMILAGEADGVLKVVSIDQS 65- 6 Query: 675 VANGSII 681 + G+ I Sbjct: 657 LPKGTRI 663 A related DNA sequence was identified in S. pyogenes <SEQ ID 2227> which encodes the amino acid sequence <SEQ ID 2228>. Analysis of this protein sequence reveals the following: TABLE-US-02150 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1245(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02151 Identities = 516/665 (77%), Positives = 573/665 (85%), Gaps = 4/665 (0%) Query: 21 KKSFYITTPIYYPSGKLHIGSAYTTIACDVLARYKRMMGFDVQYLTGLDEHGQKIQQKAE 80 - KK FYITTPIYYPSGKLHIGSAYTTIACDVLARYKR+MG +V YLTGLDEHGQKIQ KA+ Sbjct: 3 KKPFYITTPIYYPSGKLHIGSAYTTIACDVLARYKRLMGHEVFYLTGLDEHGQKIQTKAK 62 Query: 81 EAGITPQEYVDGMAESVKTLWELLDISYDKFIRTTDTYHEEAVAKIFEQLLAQGDIYLGE 140- EAGITPQ YVD MA+ VK LW+LLDISYD FIRTTD YHEE VA +FE+LLAQ DIYLGE Sbjct: 63 EAGITPQTYVDNMAKDVKALWQLLDISYDTFIRTTDDYHEEVVAAVFEKLLAQDDIYLGE 122- Query: 141 YTGWYSVSDEEFFTESQLAEVYRDENGNMIGGVAPSGHEVEKVSEESYFFRMSKYADRLK 20- 0 Y+GWYSVSDEEFFTESQL EV+RDE+G +IGG+APSGHEVE VSEESYF R+SKY DRL Sbjct: 123 YSGWYSVSDEEFFTESQLKEVFRDEDGQVIGGIAPSGHEVEWVSEESYFLRLSKYDDRLV 18- 2 Query: 201 AYYAEHPEFIQPDGRMNEMLKNFIEPGLEDLAVSRTTYTWGVQVPSNPKHVIYVWIDALM 26- 0 A++ E P+FIQPDGRMNEM+KNFIEPGLEDLAVSRTT+TWGV VPS+PKHV+YVWIDAL+ Sbjct: 183 AFFKERPDFIQPDGRMNEMVKNFIEPGLEDLAVSRTTFTWGVPVPSDPKHVVYVWIDALL 24- 2 Query: 261 NYISALGYGWSDDLSQYHKFWPADI-HMIGKDILRFHSIYWPIMLMALDLPLPKRLVAHG 31- 9 NY +ALGY ++ + + KFW + HM+GKDILRFHSIYWPI+LM LDLP+P RL+AHG Sbjct: 243 NYATALGYRQANH-ANFDKFWNGTVFHMVGKDILRFHSIYWPILLMMLDLPMPDRLIAHG 30- 1 Query: 320 WFVMQDGKMSKSKGNVVYPEMLVERFGLDPLRYYLMRSLPVGSDGTFTPEDYVGRINYEL 37- 9 WFVM+DGKMSKSKGNVVYPEMLVERFGLDPLRYYLMRSLPVGSDGTFTPEDYVGRINYEL Sbjct: 302 WFVMKDGKMSKSKGNVVYPEMLVERFGLDPLRYYLMRSLPVGSDGTFTPEDYVGRINYEL 36- 1 Query: 380 ANDLGNLLNRTIAMVNKYFDGEVPRFA-VATDFDADLASVATDSIENYHKQMEAVDFPRA 43- 8 ANDLGNLLNRT+AM+NKYFDG VP + T FDADL+ + + +YHK MEAVD+PRA Sbjct: 362 ANDLGNLLNRTVAMINKYFDGTVPAYVDNGTAFDADLSQLIDAQLADYHKHMEAVDYPRA 42- 1 Query: 439 LEAVWNLISRTNKYIDETAPWVLAKDETDRDKLAAVMSHLVASLRVVAHLIQPFMMETSD 49- 8 LEAVW +I+RTNKYIDETAPWVLAK++ D+ +LA+VM+HL ASLR+VAH+IQPFMMETS Sbjct: 422 LEAVWTIIARTNKYIDETAPWVLAKEDGDKAQLASVMAHLAASLRLVAHVIQPFMMETSA 48- 1 Query: 499 AIMEQLGLGATFDLEKLTFADLPEGVRVVAKGSPIFPRLDMEDEITYIKEQMNAGKA-PV 55- 7 AIM QLGL DL L AD P +VVAKG+PIFPRLDME EI YIK QM A Sbjct: 482 AIMAQLGLEPVSDLSTLALADFPANTKVVAKGTPIFPRLDMEAEIDYIKAQMGDSSAISQ 54- 1 Query: 558 EKEWVPEEVELTSSKGQIKFEDFDAVEIRVAEVIEVEKVEGSDKLLRFRLDAGDEGHRQI 61- 7 EKEWVPEEV L S K I FE FDAVEIRVAEV EV KVEGS+KLLRFR+DAGD RQI Sbjct: 542 EKEWVPEEVALKSEKDVITFETFDAVEIRVAEVKEVSKVEGSEKLLRFRVDAGDGQDRQI 60- 1 Query: 618 LSGIAKFYPNEQELVGKKLQIVANLKPRKMMKKYVSQGMILSAEHDGKLTVLTVDSAVAN 67- 7 LSGIAKFYPNEQELVGKKLQIVANLKPRKMMKKY+SQGMILSAEH +LTVLTVDS+V N Sbjct: 602 LSGIAKFYPNEQELVGKKLQIVANLKPRKMMKKYISQGMILSAEHGDQLTVLTVDSSVPN 66- 1 Query: 678 GSIIG 682 GSIIG Sbjct: 662 GSIIG 666 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 725 A DNA sequence (GBSx0769) was identified in S. agalactiae <SEQ ID 2229> which encodes the amino acid sequence <SEQ ID 2230>. Analysis of this protein sequence reveals the following: TABLE-US-02152 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2633(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 726 A DNA sequence (GBSx0770) was identified in S. agalactiae <SEQ ID 2231> which encodes the amino acid sequence <SEQ ID 2232>. This protein is predicted to be branched chain amino acid transport system II carrier protein (brnQ). Analysis of this protein sequence reveals the following: TABLE-US-02153 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -14.91 Transmembrane 279-295 (269-303) INTEGRAL Likelihood = -9.98 Transmembrane 82-98 (74-102) INTEGRAL Likelihood = -6.58 Transmembrane 345-361 (340-364) INTEGRAL Likelihood = -6.00 Transmembrane 157-173 (153-179) INTEGRAL Likelihood = -4.30 Transmembrane 48-64 (45-66) INTEGRAL Likelihood = -4.14 Transmembrane 251-267 (250-278) INTEGRAL Likelihood = -4.09 Transmembrane 308-324 (305-326) INTEGRAL Likelihood = -2.55 Transmembrane 218-234 (216-237) INTEGRAL Likelihood = -1.38 Transmembrane 126-142 (126-142) ----- Final Results ----- bacterial membrane --- Certainty = 0.6965(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9407> which encodes amino acid sequence <SEQ ID 9408> was also identified. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-02154 22 GP:AAC00400 GB:AF008220 branch-chain amino acid transporter [Bacillus subtilis] Identities = 130/367 (35%), Positives = 204/367 (55%), Gaps = 12/367 (3%) Query: 1 MSEKFSPWFSLTFLVILYLTIGPLFAIPRTATVSFEIGVAPIVGHSP--IALLCFTACFF 58 +++K P F F V+LYL+IGPLFAIPRT TVS+EIG P + P ++LL FT FF Sbjct: 73 LADKAHPVFGTIFTVVLYLSIGPLFAIPRTGTVSYEIGAVPFLTGVPERLSLLIFTLIFF 132- Query: 59 AAAYYLAIRPNGILDSVGKILTPVFAFLILSLVVVGAIAYGNLESAKASADYAGKAFGSG 118- YYLA+ P+ ++D VGKILTP+ F I+ ++V+ AI + Y G G Sbjct: 133 GVTYYLALNPSKVVDRVGKILTPI-KFTIILIIVLKAIFTPMGGLGAVTEAYKGTPVFKG 19- 1 Query: 119 VLAGYNTLDALAAVAFCLVATETLKKFGFKTKKEYLSTIWIVGIVTSLAFSILYIGLGFL 17- 8 L GY T+DALA++ F +V +K G K + G++ +L + +Y+ L +L Sbjct: 192 FLEGYKTMDALASIVFGVVVVNAVKSKGVTQSKALAAACIKAGVIAALGLTFIYVSLAYL 25- 1 Query: 179 GNKFPVPADILADPNVNKGAYVLSQASYKLFGNFGRYFLSIMVTLTCFTTTVGLIVSVSE 23- 8 G A V +GA +LS +S+ LFG+ G L +T+ C TT++GL+ S + Sbjct: 252 G-----ATSTNAIGPVGEGAKILSASSHYLFGSLGNIVLGAAITVACLTTSIGLVTSCGQ 30- 6 Query: 239 FFDKNFRFGNYKLFATVFTLIGFLIANLGLNAVITFSVPVLTLLYPIVIVIVLIILINKW 29- 8 +F K +YK+ T+ TL +IAN GL +I FSVP+L+ +YP+ IVI+++ I+K Sbjct: 307 YFSKLIPALSYKIVVTIVTLFSLIIANFGLAQIIAFSVPILSAIYPLAIVIIVLSFIDKI 36- 6 Query: 299 LPLSKK---GMSLTIGLVTLVSFVEVLAGQWQEKTLTQLVGFLPFHTISMGWLVPMLIGI 35- 5 ++ + GL +++ ++ AG L LP +++ +GW++P ++G Sbjct: 367 FKERREVYIACLIGTGLFSILDGIKA-AGFSLGSLDVFLNANLPLYSLGIGWVLPGIVGA 42- 5 Query: 356 VFSLVLS 362 V VL+ Sbjct: 426 VIGYVLT 432 There is also homology to SEQ ID 2234. A related GBS gene <SEQ ID 8649> and protein <SEQ ID 8650> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02155 Lipop: Possible site: -1 Crend: 3 SRCFLG: 0 McG: Length of UR: 30 Peak Value of UR: 2.99 Net Charge of CR: 2 McG: Discrim Score: 13.17 GvH: Signal Score (-7.5): -3.3 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 11 value: -14.91 threshold: 0.0 INTEGRAL Likelihood = -14.91 Transmembrane 347-363 (337-371) INTEGRAL Likelihood = -9.98 Transmembrane 150-166 (142-170) INTEGRAL Likelihood = -7.54 Transmembrane 40-56 (36-61) INTEGRAL Likelihood = -6.64 Transmembrane 79-95 (76-97) INTEGRAL Likelihood = -6.00 Transmembrane 225-241 (221-247) INTEGRAL Likelihood = -4.30 Transmembrane 116-132 (113-134) INTEGRAL Likelihood = -4.14 Transmembrane 319-335 (318-346) INTEGRAL Likelihood = -4.09 Transmembrane 376-392 (373-394) INTEGRAL Likelihood = -2.92 Transmembrane 7-23 (6-28) INTEGRAL Likelihood = -2.55 Transmembrane 286-302 (284-305) INTEGRAL Likelihood = -1.38 Transmembrane 194-210 (194-210) PERIPHERAL Likelihood = 2.49 402 modified ALOM score: 3.48 icm1 HYPID: 7 CFP: 0.696 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6965 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00053## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 727 A DNA sequence (GBSx0771) was identified in S. agalactiae <SEQ ID 2235> which encodes the amino acid sequence <SEQ ID 2236>. Analysis of this protein sequence reveals the following: TABLE-US-02156 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3291 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10041> which encodes amino acid sequence <SEQ ID 10042> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 728 A DNA sequence (GBSx0772) was identified in S. agalactiae <SEQ ID 2237> which encodes the amino acid sequence <SEQ ID 2238>. Analysis of this protein sequence reveals the following: TABLE-US-02157 Possible site: 39 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.33 Transmembrane 117-133 (112-136) INTEGRAL Likelihood = -3.77 Transmembrane 53-69 (53-70) INTEGRAL Likelihood = -3.40 Transmembrane 98-114 (97-115) ----- Final Results ----- bacterial membrane --- Certainty = 0.4333 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 729 A DNA sequence (GBSx0773) was identified in S. agalactiae <SEQ ID 2239> which encodes the amino acid sequence <SEQ ID 2240>. Analysis of this protein sequence reveals the following: TABLE-US-02158 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.19 Transmembrane 22-38 (20-44) ----- Final Results ----- bacterial membrane --- Certainty = 0.2678 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8651> which encodes amino acid sequence <SEQ ID 8652> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-02159 Lipop Possible site: -1 Crend: 3 SRCFLG: 0 McG: Length of UR: 21 Peak Value of UR: 3.11 Net Charge of CR: 2 McG: Discrim Score: 11.30 GvH: Signal Score (-7.5): -5.35 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 1 value: -4.19 threshold: 0.0 INTEGRAL Likelihood = -4.19 Transmembrane 5-21 (3-27) PERIPHERAL Likelihood = 6.74 53 modified ALOM score: 1.34 icm1 HYPID: 7 CFP: 0.268 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2678 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02160 >GP:CAB15623 GB:Z99122 spore coat protein (inner) [Bacillus subtilis] Identities = 71/359 (19%), Positives = 148/359 (40%), Gaps = 49/359 (13%) Query: 127 ISYRGNTSRYFDKKSLKVKFVTNKLKEKKHRLAGMPKESEWVLHGPFLDRTLLRNYLSYN 18- 6 I+YRG+ R F KKS + F K + L+ + D +L+RN LS + Sbjct: 47 IAYRGSHIRDFKKKSYHISFYQPKTFRGAREIH---------LNAEYKDPSLMRNKLSLD 97 Query: 187 IAGEIMSYAPNVRYCELFVNGEYQGVYLAVENIEQGEQRVPIEKSDKKLHKTPYIVAWDR 24- 6 E+ + +P + + +NG+ +GVYL +E++++ + +KL A D Sbjct: 98 FFSELGTLSPKAEFAFVKMNGKNEGVYLELESVDE------YYLAKRKLADGAIFYAVDD 151- Query: 247 EHKAKQKLDNYVHYTHQSGISALDVKYPGKQRLTSKQLEFINKD----INHIEKVLYSYD 30- 2 + D + ++L++ Y +++ +++ +F +D IN + K + Sbjct: 152 DANFSLMSD-----LERETKTSLELGY--EKKTGTEEDDFYLQDMIFKINTVPKAQFK-- 20- 2 Query: 303 FSQYPKYIDRESFANYFVINEFFRNVDAGKFSTYLYKDLRDRA-KLVVWDFNNAFDNQIE 36- 1 S+ K++D + + + F N D + LY+ +++ WD++ + I Sbjct: 203 -SEVTKHVDVDKYLRWLAGIVFTSNYDGFVHNYALYRSGETGLFEVIPWDYDATWGRDIH 26- 1 Query: 362 GRVDEADFTLTDAPWFNMLIKDKAFIDLVVHRYKELRKGVLATEYLSNYIDETRHFLGPA 42- 1 G AD+ FN L YK L + L + + Y++ P Sbjct: 262 GERMAADYVRIQG--FNTLTARILDESEFRKSYKRLLEKTLQSLFTIEYME-------PK 31- 2 Query: 422 IDRNYKKWGYVFDLKNTDPRNYLIPTERN-VTSYHKSVEQLKDFIKKRGRWMDRNIETL 479- I Y++ P + P ++N + + + + + ++IK R +++ ++ L Sbjct: 313 IMAMYER---------IRPFVLMDPYKKNDIERFDREPDVICEYIKNRSQYLKDHLSIL 362- No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 730 A DNA sequence (GBSx0774) was identified in S. agalactiae <SEQ ID 2241> which encodes the amino acid sequence <SEQ ID 2242>. Analysis of this protein sequence reveals the following: TABLE-US-02161 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 731 A DNA sequence (GBSx0775) was identified in S. agalactiae <SEQ ID 2243> which encodes the amino acid sequence <SEQ ID 2244>. Analysis of this protein sequence reveals the following: TABLE-US-02162 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.62 Transmembrane 5-21 (3-24) ----- Final Results ----- bacterial membrane --- Certainty = 0.2848 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02163 >GP:BAB05949 GB:AP001514 unknown [Bacillus halodurans] Identities = 199/697 (28%), Positives = 322/697 (45%), Gaps = 58/697 (8%) Query: 57 KPFVVKGVDVESSLAGYHHNDFPITQKTYREWFHLISNMGANTVRVKVPMNVAFYDALYH 116- K + GV++ G + I +K Y WF I MG N +RV FY AL Sbjct: 414 KKLQIHGVNLGMGKPGTFPGEAAIKEKDYYRWFEQIGEMGGNAIRVYTLHPPGFYHALKR 47- 3 Query: 117 HNKASKRPLYLLQGIRIDSYRNNASITAFNDNYRGYLKREAKGVVDILHGRKQVWNTDLG 17- 6 +N+ + P+YL G+ ID ++ AF++ ++E K +VD++HG V + + G Sbjct: 474 YNEQHENPIYLFHGVWIDEEPLEDTLDAFDEETNEEFQQEMKRIVDVIHGNAVV-DPNPG 53- 2 Query: 177 SRH--YHYDLSPWVLGYVVGDDWNSGTVAYTNHQEKKT-QYKGRYFKTSVAANPFEVMLA 23- 3 H Y D+SP+ +G+++G +W TV TN Y G+Y +T A PFE LA Sbjct: 533 HAHGVYQADVSPYTIGWIIGIEWYPHTVKATNKNNPDIGDYDGKYVETK-DAEPFEYWLA 59- 1 Query: 234 QVMDELTHYETAKYGWQHLISFSNSPTTDPF-HYRKPFEAQAPKYVQLNVENIQANSNVK 29- 2 D L YE +Y W +SF+N TTD H +P E + V NV +++ + + Sbjct: 592 NQFDILLSYEIEQYNWIRPVSFTNWVTTDLLTHPAEPNEDEDLVGVDPNVIHLKGPA-TE 65- 0 Query: 293 AGMFAAYKAIDFHPRYKDYLLFDKENISKEDRQKIKELSLSQGYVKLLNAYHKIPVLVTG 35- 2 FA+Y +P Y D+L ++++ I D + EL+ GY+K L+ H +P+L+ Sbjct: 651 TNQFASYHV---YPYYPDFLNYEEDYIHYVDHR--GELNNYAGYLKDLHDAHDLPILIAE 70- 5 Query: 353 YGYSTARGIA-QKEIDKRPLPINEKEQGQRLLEDYESFISSGSFGATINAWQDDWNARAW 41- 1 +G +RG+ + K ++E+EQG+ ++E +E I G I WQD+W R W Sbjct: 706 FGVPASRGLTHENPFGKNQGFLSEEEQGKIVVELFEDIIEEKLLGGLIFTWQDEWFKRTW 76- 5 Query: 412 NTSFATNKHSQFLWGDAQVFNQGYGLLGFKNAKHHYQVDGKRGKG-----EWKHPLMTSA 46- 6 NT N + W +AQ Q +GLL F K D + + E HP + Sbjct: 766 NTMDYDNPDRRPFWSNAQTNEQQFGLLSFDRLKVKVNGDDQDWEDASLLYEEDHPYVKR- 82- 4 Query: 467 TGDDLYASSDESYLYLAIKTKPEKLKE-----KRLLPIDITPKSGSRKMNGSK-VTFSKS 52- 0 LY DE YLY I K + +L +D P G+ + + VTF Sbjct: 825 ----LYMDHDERYLYFRIDMKSGSTDDFFKDGFPILVLDTLPGQGNEHIKEVEGVTFDHG 88- 0 Query: 521 SDFVLSIDPNGKSELFVQERYNALKANYLRQLNGKDFYAFPPKKNSSNFEQINMVLRNTK 58- 0 DF++ + +S + V Y+ Y + + + P+ N+ F++I+ L N + Sbjct: 881 IDFIIELKGYDESRVKVDAYYDFFTYQYSQIYQMIEETSIEPQNNTGVFQKIHYAL-NQE 93- 9 Query: 581 IVEDMEKVKATERFLP--THPTGLLKTGTTDRHQKTFDSQTD--ISFGKDFIEVRIPWQL 63- 6 I ++ +T +P + TG L+ G D +DS D ++ K IEVRIPW L Sbjct: 940 I-----RIPSTNEVIPFSYYETGELRHGNGDPEADDYDSLADFFVNEEKGMIEVRIPWLL 99- 4 Query: 637 LNFSDPSSQKIHDDYFKHYGVKELE-IESI-ALGLGANSKENTLIKMAD----------- 68- 3 L+F DPS +++ ++ G + E IE + A L K++ ++ D Sbjct: 995 LSFKDPSQREVMSAIYEGEGGETSEIIEGVRAAVLFVEPKDDDSYQVVDALPALDGDRLT 10- 54 Query: 684 ------YRLKNWERPDTKTFLKDSYYSIKKEWSKERE 714 Y + W+ P + LK SY +K+ ++ +E Sbjct: 1055 DEVMNMYTWETWDIPLYEERLKQSYDLVKEAFTSIKE 1091 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8653> and protein <SEQ ID 8654> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02164 Lipop: Possible site: -1 Crend: 2 McG: Discrim Score: 12.00 GvH: Signal Score (-7.5): -5.46 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -4.62 threshold: 0.0 INTEGRAL Likelihood = -4.62 Transmembrane 5-21 (3-24) PERIPHERAL Likelihood = 7.32 223 modified ALOM score: 1.42 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2848 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 2244 (GBS62) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 5 (lane 7; MW 80.5 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 13 (lane 4; MW 105 kDa). The GBS62-GST fusion product was purified (FIG. 100A; see also FIG. 193, lane 7) and used to immunise mice (lane 1 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 100B), FACS (FIG. 100C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 732 A DNA sequence (GBSx0778) was identified in S. agalactiae <SEQ ID 2245> which encodes the amino acid sequence <SEQ ID 2246> in others. Analysis of this protein sequence reveals the following: TABLE-US-02165 Possible site: 14 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.48 Transmembrane 310-326 (302-335) INTEGRAL Likelihood = -7.32 Transmembrane 362-378 (361-380) INTEGRAL Likelihood = -7.11 Transmembrane 334-350 (329-355) INTEGRAL Likelihood = -2.28 Transmembrane 381-397 (380-397) ----- Final Results ----- bacterial membrane --- Certainty = 0.3994 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10039> which encodes amino acid sequence <SEQ ID 10040> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02166 >GP:BAB05950 GB:AP001514 unknown conserved protein in others [Bacillus halodurans] Identities = 143/405 (35%), Positives = 226/405 (55%), Gaps = 5/405 (1%) Query: 11 IVPAYNESTTIVSSIDSLLHLDYEAYEIIVVDDGSSDNTSDVLKEEFALMKISNTIDSII 70 - +VPAYNE T I+ ++ SLL L Y EI+VV+DGS+D T +V+ E F ++K+ I I Sbjct: 69 LVPAYNEETGIIETVRSLLSLKYPQTEIVVVNDGSTDQTLEVIIEHFQMVKVGKVIRKQI 128- Query: 71 ATQTCKDVFQRQVGKVKLTLIVKENGGKGDALNMGINAANYDYFLCLDADSMLQVDSLSQ 130- T+ K V+Q + L L+ K NGGK DALN G+N + Y YF +D DS+L+ D+L + Sbjct: 129 ETEPIKGVYQSTIFP-HLLLVDKSNGGKADALNAGLNVSKYPYFCSIDGDSILETDALLK 18- 7 Query: 131 ISKSIQV----DPTVIAVGGLVQVAQGVKIEQGKVASYRLPWRIIPCAQALEYDSSFLGA 18- 6 + K I + VIA GG V++A G I+ G V S +L + Q +EY +FL Sbjct: 188 VMKPIVTSRDDEDEVIASGGNVRIANGSDIQMGSVLSVQLAKNPLVVMQVIEYLRAFLMG 24- 7 Query: 187 RIFLDYLRANLIISGAFGLFKKDLVKAVGGYDTQTLGEDMELVMKLHFFCRNNNIPYRIC 24- 6 RI L LIISGAF +F K V GGY +T+GEDMELV++LH + + RI Sbjct: 248 RIGLSRHNMVLIISGAFSVFAKKWVMEAGGYSKKTVGEDMELVVRLHRLVKEKRLKKRIT 30- 7 Query: 247 YETDAVCWSQAPTNLGDLRKQRRRWYLGLYQCLKKYKSIFANYRFGAVGSISYIYYILFE 30- 6 + D VCW++AP L++QR RW+ GL + L ++ + N ++G VG+ S Y+ + E Sbjct: 308 FVPDPVCWTEAPATFRVLQRQRSRWHRGLMESLWLHRGMTFNPKYGLVGTASIPYFWIVE 36- 7 Query: 307 LLTPFIECFGIVIIFLSLLFNQLNIPFFISLVSLYIFYCVLITLSSFLHRIYSQQLVIGI 36- 6 P +E G + I + F L + F ++L L++ Y + ++++ + +S + + Sbjct: 368 FFGPVVELMGYLYIVFAFFFGGLYVEFALALFLLFVLYGTVFSMTAVILEGWSLKRYPKV 42- 7 Query: 367 LDIVKVFYIAVFRYLILHPVLTFVKVASVIGYKNKKMVWGHITRE 411 D+ ++ ++F L P+ + ++I + WG +TR+ Sbjct: 428 SDMSRLMIFSLFEALWYRPLTVLWRFGAIIEALFRSKAWGEMTRK 472 A related DNA sequence was identified in S. pyogenes <SEQ ID 2247> which encodes the amino acid sequence <SEQ ID 2248>. Analysis of this protein sequence reveals the following: TABLE-US-02167 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.04 Transmembrane 33-49 (24-57) INTEGRAL Likelihood = -10.77 Transmembrane 376-392 (370-399) INTEGRAL Likelihood = -7.86 Transmembrane 344-360 (342-372) INTEGRAL Likelihood = -4.94 Transmembrane 63-79 (55-81) INTEGRAL Likelihood = -2.07 Transmembrane 403-419 (403-419) ----- Final Results ----- bacterial membrane --- Certainty = 0.5416 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below:

TABLE-US-02168 Identities = 84/397 (21%), Positives = 173/397 (43%), Gaps = 71/397 (17%) Query: 6 FRRKSIVPAYNEST-TIVSSIDSLLHLDYEAYEIIVVDDGSSDNTSDVLKEEFALMKISN 64 ++ +++P+YNE +++ ++ S+L Y EI +VDDGSS+ + L EE+ ++ Sbjct: 90 YKVAAVIPSYNEDAESLLETLKSVLAQTYPLSEIYIVDDGSSNTDAIQLIEEY----VNR 145- Query: 65 TIDSIIATQTCKDVFQRQVGKVKLTLIVKENGGKGDALNMGINAANYDYFLCLDADSMLQ 124- +D C++V V +L+ N GK A ++ D FL +D+D+ + Sbjct: 146 EVD------ICRNVI------VHRSLV---NKGKRHAQAWAFERSDADVFLTVDSDTYIY 19- 0 Query: 125 VDSLSQISKSIQVDPTVIAVGGLVQVAQGVKIEQGKVASYRLPWRIIPCAQALEYDSSFL 18- 4 ++L ++ KS D TV A G + + ++ + YD++F Sbjct: 191 PNALEELLKSFN-DETVYAA-------------TGHLNARNRQTNLLTRLTDIRYDNAF- 23- 5 Query: 185 GARIFLDYLRANLII-SGAFGLFKKD-LVKAVGGYDTQT-------LGEDMELVMKLHFF 23- 5 G L N+++ SG +++++ ++ + Y QT +G+D L Sbjct: 236 GVERAAQSLTGNILVCSGPLSIYRREVIIPNLERYKNQTFLGLPVSIGDDRCLT------ 28- 9 Query: 236 CRNNNIPY-RICYETDAVCWSQAPTNLGDLRKQRRRWYLGLY-QCLKKYKSIFANYRFGA 29- 3 N I R Y++ A C + P L KQ+ RW + + + K I +N Sbjct: 290 --NYAIDLGRTVYQSTARCDTDVPFQLKSYLKQQNRWNKSFFKESIISVKKILSN----P 34- 3 Query: 294 VGSISYIYYILFELLTPFIECFGIVIIFLSLLFNQLNIPFFISLVSLYIFYCV--LITLS 35- 1 + ++ I+ ++ ++ +++ +LLFNQ + L+ L+ F + ++ L Sbjct: 344 IVALWTIFEVVMFMM--------LIVAIGNLLFNQ---AIQLDLIKLFAFLSIIFIVALC 39- 2 Query: 352 SFLHRIYSQQLVIGILDIVKVFYIAVFRYLILHPVLT 388 +H + + + + ++ V + L L+ + T Sbjct: 393 RNVHYMIKHPASFLLSPLYGILHLFVLQPLKLYSLCT 429 A related GBS gene <SEQ ID 8655> and protein <SEQ ID 8656> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02169 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -5.18 GvH: Signal Score (-7.5): -4.91 Possible site: 14 >>> Seems to have no N-terminal signal sequence ALOM program count: 4 value: -7.48 threshold: 0.0 INTEGRAL Likelihood = -7.48 Transmembrane 310-326 (302-335) INTEGRAL Likelihood = -7.32 Transmembrane 362-378 (361-380) INTEGRAL Likelihood = -7.11 Transmembrane 334-350 (329-355) INTEGRAL Likelihood = -2.28 Transmembrane 381-397 (380-397) PERIPHERAL Likelihood = 1.22 140 modified ALOM score: 2.00 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3994(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00054## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 733 A DNA sequence (GBSx0779) was identified in S. agalactiae <SEQ ID 2249> which encodes the amino acid sequence <SEQ ID 2250>. Analysis of this protein sequence reveals the following: TABLE-US-02170 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2014(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02171 >GP:CAA22725 GB:AL035161 hypothetical protein SC9C7.13c [Streptomyces coelicolor A3(2)] Identities = 35/153 (22%), Positives = 64/153 (40%), Gaps = 5/153 (3%) Query: 5 IRRARLGDEVNLAYIQTESWKAAFGKILPEDIIQKTTEIEPAITMYQQLLHKEVGKGYIL 64 +R L D ++ I+ W++A+ ++P+ + A G+ ++ Sbjct: 10 VREMTLADCDRVSLIRVRGWQSAYRGLMPQPYLDAMDPAADAERRRSLFARPPEGRVNLV 69 Query: 65 EVDSNPHCMAWWD----KSREDGMLDYAELICIHSLKEGWGKGYGSQMMNHVLSEIQQAG 120- D + W + E D AEL ++ +G G G + + + AG Sbjct: 70 AEDEGGEVVGWACHGPYRDGEARTAD-AELYALYVDAARFGAGIGRALAGESVRRCRAAG 128- Query: 121 YNKVILWVFTENTRARKFYDRFGFSFKGKSKTY 153 + +++LWV N RAR+FYDR GF G + + Sbjct: 129 HARMLLWVLKGNVRARRFYDRAGFRPDGAEEPF 161 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 734 A DNA sequence (GBSx0780) was identified in S. agalactiae <SEQ ID 2251> which encodes the amino acid sequence <SEQ ID 2252>. This protein is predicted to be a DNA-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-02172 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1162(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 735 A DNA sequence (GBSx0781) was identified in S. agalactiae <SEQ ID 2253> which encodes the amino acid sequence <SEQ ID 2254>. Analysis of this protein sequence reveals the following: TABLE-US-02173 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2589(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10037> which encodes amino acid sequence <SEQ ID 10038> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2255> which encodes the amino acid sequence <SEQ ID 2256>. Analysis of this protein sequence reveals the following: TABLE-US-02174 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2767(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02175 Identities = 80/86 (93%), Positives = 84/86 (97%) Query: 6 LKTIKENNMTFEEILPGLKAKKKYVRTGWGGAENYVQLFDTLEVNGKVLQATPYFLINVT 65 + +IKENNMTFEEILPGLKAKKKYVRTGWGGAENYVQLFDTLEV+GKVLQATPYFLI+VT Sbjct: 3 ISSIKENNMTFEEILPGLKAKKKYVRTGWGGAENYVQLFDTLEVDGKVLQATPYFLIHVT 62 Query: 66 GEGEGFSMWAPTPCDVLAEDWIEVND 91 G GEGFSMWAPTPCDVLAEDWIEVND Sbjct: 63 GAGEGFSMWAPTPCDVLAEDWIEVND 88 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 736 A DNA sequence (GBSx0782) was identified in S. agalactiae <SEQ ID 2257> which encodes the amino acid sequence <SEQ ID 2258>. Analysis of this protein sequence reveals the following: TABLE-US-02176 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02177 >GP:BAA85256 GB:AB021978 3-oxoacyl-[acyl carrier protein] reductase homolog [Moritella marina] Identities = 82/239 (34%), Positives = 125/239 (51%), Gaps = 15/239 (6%) Query: 2 TKVVLVTGCASGIGYAQAQYFLKQGYQVYGVDKSDKPNLN-----GNFNF-IKLDLSSDL 55 +K VLVTG + GIG A A++F K G V G S + G+ F ++L+++S Sbjct: 5 SKTVLVTGASRGIGRAIAEHFAKLGATVIGTATSAQGAERIGAYLGDAGFGLELNVTSQD 64 Query: 56 S------PLFTMVPTVDILCNTAGILDAYKPLLEVSDEELEHLFDINFFVTVRLTRHYLR 109- S + T V +DIL N AGI A L + ++E ++ D N RL + LR Sbjct: 65 SVDALYAEIKTQVGHIDILVNNAGIT-ADNIFLRMKEDEWCNVIDTNLTSLYRLCKPCLR 123- Query: 110 RMVEKKSGIIINMCSIASFIAGGGGAAYTSSKHALAGFTRQLALDYAKDCIQIFGIAPGA 16- 9 M++++ G IIN+ S+ GG A Y ++K L GFT+ LA + A I + +APG Sbjct: 124 GMMKQRHGRIINIGSVVGTTGNGGQANYAAAKSGLLGFTKSLASEVASRGITVNAVAPGF 18- 3 Query: 170 VQTAMTASDFEPGGLAEWVASETPIGRWTKPSEVAELTGFLASGKARSMQGEIVKIDGG 228- ++T MTA E + + ++ P R +E+AE GFLAS A + GE + ++GG Sbjct: 184 IETDMTAELTEE--QKQTILAQVPTSRLGSTTEIAETVGFLASDGASYITGETIHVNGG 240- There is also homology to SEQ IDs 2628 and 7170. A related sequence was also identified in GAS <SEQ ID 9107> which encodes the amino acid sequence <SEQ ID 9108>. Analysis of this protein sequence reveals the following: TABLE-US-02178 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02179 Identities = 206/232 (88%), Positives = 224/232 (95%) Query: 1 MTKVVLVTGCASGIGYAQAQYFLKQGYQVYGVDKSDKPNLNGNFNFIKLDLSSDLSPLFT 60 MTKVVLVTGCASGIGYAQA+YFLKQG+ VYGVDKSDKP+L+GNF+FIKLDLSS+L+PLF Sbjct: 4 MTKVVLVTGCASGIGYAQARYFLKQGHHVYGVDKSDKPDLSGNFHFIKLDLSSELAPLFK 63 Query: 61 MVPTVDILCNTAGILDAYKPLLEVSDEELEHLFDINFFVTVRLTRHYLRRMVEKKSGIII 120- +VP+VDILCNTAGILDAYKPLL+VSDEE+EHLFDINFF TV+LTRHYLRRMVEK+SG+II Sbjct: 64 VVPSVDILCNTAGILDAYKPLLDVSDEEVEHLFDINFFATVKLTRHYLRRMVEKQSGVII 123- Query: 121 NMCSIASFIAGGGGAAYTSSKHALAGFTRQLALDYAKDCIQIFGIAPGAVQTAMTASDFE 18- 0 NMCSIASFIAGGGG AYTSSKHALAGFTRQLALDYAKD I IFGIAPGAV+TAMTA+DFE Sbjct: 124 NMCSIASFIAGGGGVAYTSSKHALAGFTRQLALDYAKDQIHIFGIAPGAVKTAMTANDFE 18- 3 Query: 181 PGGLAEWVASETPIGRWTKPSEVAELTGFLASGKARSMQGEIVKIDGGWSLK 232 PGGLA+WVA ETPIGRWTKP EVAELTGFLASGKARSMQGEIVKIDGGW+LK Sbjct: 184 PGGLADWVARETPIGRWTKPDEVAELTGFLASGKARSMQGEIVKIDGGWTLK 235 A related DNA sequence was identified in S. pyogenes <SEQ ID 9063> which encodes amino acid sequence <SEQ ID 9064>. An alignment of the GAS and GBS sequences follows: TABLE-US-02180 Score = 83.1 bits (202), Expect = 4e-18 Identities = 72/258 (27%), Positives = 106/258 (40%), Gaps = 36/258 (13%) Query: 6 EVAFITGAASGIGKQIGETLLKEGKTVVFSDINQE-----KLDQVVADYTKEGYDAFSVV 60 +V +TG ASGIG + LK+G V D + + + + D + + F++V Sbjct: 3 KVVLVTGCASGIGYAQAQYFLKQGYQVYGVDKSDKPNLNGNFNFIKLDLSSDLSPLFTMV 62 Query: 61 CDVTKEEAINAAIDTVVEKYGRIDILVNNAG-LQHVAMIEDFPTEKFEFMIKIMLTAPFI 119- +DIL N AG L + + E+ E + I Sbjct: 63 --------------------PTVDILCNTAGILDAYKPLLEVSDEELEHLFDINFFVTVR 102- Query: 120 AIKRAFPTMKAQKHGRIINMASINGVIGFAGKSAYNSAKHGLIGLTKVTALEAADSGITV 17- 9 + M +K G IINM SI I G +AY S+KH L G T+ AL+ A I + Sbjct: 103 LTRHYLRRMVEKKSGIIINMCSIASFIAGGGGAAYTSSKHALAGFTRQLALDYAKDCIQI 16- 2 Query: 180 NAICPGYVDTPLVRGQFEDLSKTRGIPLENVLEEVLYPLVPQKRLIDVQEIADYVSFLAS 23- 9 I PG V T + FE L E + P R E+A+ FLAS Sbjct: 163 FGIAPGAVQTAMTASDFE----------PGGLAEWVASETPIGRWTKPSEVAELTGFLAS 21- 2 Query: 240 DKAKGVTGQACILDGGYT 257 KA+ + G+ +DGG++ Sbjct: 213 GKARSMQGEIVKIDGGWS 230 A further related DNA sequence was identified in S. pyogenes <SEQ ID 2259> which encodes the amino acid sequence <SEQ ID 2260>. An alignment of the GAS and GBS sequences follows: TABLE-US-02181 Score = 427 bits (1086), Expect = e-122 Identities = 206/232 (88%), Positives = 224/232 (95%) Query: 4 MTKVVLVTGCASGIGYAQARYFLKQGHHVYGVDKSDKPDLSGNFHFIKLDLSSELAPLFK 63 MTKVVLVTGCASGIGYAQA+YFLKQG+ VYGVDKSDKP+L+GNF+FIKLDLSS+L+PLF Sbjct: 1 MTKVVLVTGCASGIGYAQAQYFLKQGYQVYGVDKSDKPNLNGNFNFIKLDLSSDLSPLFT 60 Query: 64 VVPSVDILCNTAGILDAYKPLLDVSDEEVEHLFDINFFATVKLTRHYLRRMVEKQSGVII 123- +VP+VDILCNTAGILDAYKPLL+VSDEE+EHLFDINFF TV+LTRHYLRRMVEK+SG+II Sbjct: 61 MVPTVDILCNTAGILDAYKPLLEVSDEELEHLFDINFFVTVRLTRHYLRRMVEKKSGIII 120- Query: 124 NMCSIASFIAGGGGVAYTSSKHALAGFTRQLALDYAKDQIHIFGIAPGAVKTAMTANDFE 18- 3 NMCSIASFIAGGGG AYTSSKHALAGFTRQLALDYAKD I IFGIAPGAV+TAMTA+DFE Sbjct: 121 NMCSIASFIAGGGGAAYTSSKHALAGFTRQLALDYAKDCIQIFGIAPGAVQTAMTASDFE 18- 0 Query: 184 PGGLADWVARETPIGRWTKPDEVAELTGFLASGKARSMQGEIVKIDGGWTLK 235 PGGLA+WVA ETPIGRWTKP EVAELTGFLASGKARSMQGEIVKIDGGW+LK Sbjct: 181 PGGLAEWVASETPIGRWTKPSEVAELTGFLASGKARSMQGEIVKIDGGWSLK 232 SEQ ID 2258 (GBS251) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 43 (lane 2; MW 21.7 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 47 (lane 6; MW 52 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 737 A DNA sequence (GBSx0783) was identified in S. agalactiae <SEQ ID 2261> which encodes the amino acid sequence <SEQ ID 2262>. Analysis of this protein sequence reveals the following: TABLE-US-02182 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.82 Transmembrane 62-78 (62-79) ----- Final Results ----- bacterial membrane --- Certainty = 0.2529(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 738 A DNA sequence (GBSx0784) was identified in S. agalactiae <SEQ ID 2263> which encodes the amino acid sequence <SEQ ID 2264>. Analysis of this protein sequence reveals the following: TABLE-US-02183 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1495(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02184 >GP: CAA20397 GB: AL031317 SC6G4.19c, unknown, len: 190 aa; contains Pro-Ser-rich domain at N-terminus [Streptomyces coelicolor A3(2)] Identities = 26/80 (32%), Positives = 44/80 (54%), Gaps = 5/80 (6%) Query: 1 MDSNDEAICIIEITKVDIVPFKDVSADHAFKEGEGDKTLEWWRKAHIDFF-----KPYFE 55 +DS + + +IE+T+V +VP +V HA EGEGD ++ WR H F+ + Sbjct: 103 VDSRERPVAVIEVTEVRVVPLAEVDLAHAVDEGEGDTSVAGWRAGHERFWHGAEMRAALG 16- 2 Query: 56 EFGLMFSEDSRIVLEEFQVV 75 + G + + +VLE F++V Sbjct: 163 DPGFTVDDATPVVLERFRIV 182 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 739 A DNA sequence (GBSx0785) was identified in S. agalactiae <SEQ ID 2265> which encodes the amino acid sequence <SEQ ID 2266>. Analysis of this protein sequence reveals the following: TABLE-US-02185 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.49 Transmembrane 3-19 (3-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.1595(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02186 >GP: BAB06422 GB: AP001516 unknown conserved protein [Bacillus halodurans] Identities = 133/315 (42%), Positives = 191/315 (60%), Gaps = 4/315 (1%) Query: 1 MKLAVLGTGMIVKEVLPVLQKIEGIDLVAILSTVRSLETAKDLAKEYNMSLATSEYKAVL 60 MK+A +GTG IV+ L L I+G VA+ S R TAK LA +YN+ + + +L Sbjct: 1 MKIATVGTGPIVEAFLSALDDIDGPMCVAMYS--RKETTAKPLADQYNIPTIYTHFDHML 58 Query: 61 DNEEIDTVYIGLPNHLHFDYAKEALLAGKHVICEKPFTLEASQLEELVSIANTRQLILLE 120- + ++ VY+ PN LH+ +A +AL KHVICEKPFT A +LE L+S+A +L+L E Sbjct: 59 ADPNVEVVYVASPNSLHYQHALQALEHRKHVICEKPFTSTARELEHLISVARKNELMLFE 118- Query: 121 AITNQYLPNFDLVKEHLSNLGDIKIVECNYSQYSSRYDAFKRGEIAPAFNPEMGGGALRD 18- 0 AIT +LPN+ L+KE++ LG IK+++CNYSQYSSRYD F GE FNP GGAL D Sbjct: 119 AITTIHLPNYQLIKENIHKLGSIKMIQCNYSQYSSRYDRFLSGETPNVFNPAFSGGALMD 17- 8 Query: 181 LNIYNLHLVIGLFGEPITAQYLPNIE-RGIDTSGVLVLDYGHFKTVCIGAKDCSAEVKST 23- 9 +N+YN+H V+ LFG P A Y+ N GIDTSGVLVL Y HF + C+G KD + Sbjct: 179 INVYNIHFVMNLFGPPEAAHYIANQHANGIDTSGVLVLKYPHFISECVGCKDTQSMNFVL 23- 8 Query: 240 IQGDKGSIAILGPTNTMPKISLTMNGQESHVYQLNGDRHRMHDEFVIFEGIISNLDFKRA 29- 9 IQG+KG I + N + + ++ Q S + D ++ +E + +F++ Sbjct: 239 IQGEKGYIHVENGANGCRNVKIYLDDQTSELNAQTNDNLLYYETRTFYE-MYQAKNFEKC 29- 7 Query: 300 AQALEHSRTVMKVLD 314 + L +S +VM+V++ Sbjct: 298 YELLSYSHSVMRVME 312 A related DNA sequence was identified in S. pyogenes <SEQ ID 719> which encodes the amino acid sequence <SEQ ID 720>. Analysis of this protein sequence reveals the following: TABLE-US-02187 Possible site: 40 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below:

TABLE-US-02188 Identities = 233/314 (74%), Positives = 269/314 (85%) Query: 1 MKLAVLGTGMIVKEVLPVLQKIEGIDLVAILSTVRSLETAKDLAKEYNMSLATSEYKAVL 60 MKLAVLGTGMIVKEVLPVLQKI+GIDLVAILSTVRSL TAKDLAK ++M LATS+Y+A+L Sbjct: 1 MKLAVLGTGMIVKEVLPVLQKIDGIDLVAILSTVRSLTTAKDLAKAHHMPLATSKYEAIL 60 Query: 61 DNEEIDTVYIGLPNHLHFDYAKEALLAGKHVICEKPFTLEASQLEELVSIANTRQLILLE 120- NEEIDTVYIGLPNHLHF YAKEALLAGKHVICEKPFT+ A +L+ELV IA R+LILLE Sbjct: 61 GNEEIDTVYIGLPNHLHFAYAKEALLAGKHVICEKPFTMTAGELDELVVIARKRKLILLE 120- Query: 121 AITNQYLPNFDLVKEHLSNLGDIKIVECNYSQYSSRYDAFKRGEIAPAFNPEMGGGALRD 18- 0 AITNQYL N +KEHL LGDIKIVECNYSQYSSRYDAFKRG+IAPAFNP+MGGGALRD Sbjct: 121 AITNQYLSNMTFIKEHLDQLGDIKIVECNYSQYSSRYDAFKRGDIAPAFNPKMGGGALRD 18- 0 Query: 181 LNIYNLHLVIGLFGEPITAQYLPNIERGIDTSGVLVLDYGHFKTVCIGAKDCSAEVKSTI 24- 0 LNIYN+H V+GLFG P T QYL N+E+GIDTSG+LV+DY FK VCIGAKDC+AE+KSTI Sbjct: 181 LNIYNIHFVVGLFGRPKTVQYLANVEKGIDTSGMLVMDYEQFKVVCIGAKDCTAEIKSTI 24- 0 Query: 241 QGDKGSIAILGPTNTMPKISLTMNGQESHVYQLNGDRHRMHDEFVIFEGIISNLDFKRAA 30- 0 QG+KGS+A+LG TNT+P++ L+++G E V N HRM++EFV F +I DF++ Sbjct: 241 QGNKGSLAVLGATNTLPQVQLSLHGHEPQVINHNKHDHRMYEEFVAFRDMIDQRDFEKVN 30- 0 Query: 301 QALEHSRTVMKVLD 314 QALEHSR VM VL+ Sbjct: 301 QALEHSRAVMAVLE 314 SEQ ID 2266 (GBS342) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 10; MW 36.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 81 (lane 2; MW 61 kDa). GBS342-GST was purified as shown in FIG. 226, lane 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 740 A DNA sequence (GBSx0786) was identified in S. agalactiae <SEQ ID 2267> which encodes the amino acid sequence <SEQ ID 2268>. Analysis of this protein sequence reveals the following: TABLE-US-02189 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0499(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02190 >GP: CAB12535 GB: Z99107 similar to hypothetical proteins [Bacillus subtilis] Identities = 41/127 (32%), Positives = 63/127 (49%), Gaps = 11/127 (8%) Query: 1 MISSIGQVMLYVSNVEASADFWKNKVGFERVEKQTQGDYVTYI-VAPKLDSEVSFVLHDK 59 MI IG V +YV + + + FW KVGF+ G +++ VAPK +E V++ K Sbjct: 1 MIKQIGTVAVYVEDQQKAKQFWTEKVGFDIAADHPMGPEASWLEVAPK-GAETRLVIYPK 59 Query: 60 AIIAQMSPELDLATPSILFETTDIDSTYQELTAN--EVMTNP-IVDMGSMRVFNFSDNDN 116- A M + SI+FE DI TY+++ N E + P ++ G+ F D D Sbjct: 60 A----MMKGSEQMKASIVFECEDIFGTYEKMKTNGVEFLGEPNQMEWGTF--VQFKDEDG 113- Query: 117 NYFAIRE 123 N F ++E Sbjct: 114 NVFLLKE 120 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 741 A DNA sequence (GBSx0787) was identified in S. agalactiae <SEQ ID 2269> which encodes the amino acid sequence <SEQ ID 2270>. Analysis of this protein sequence reveals the following: TABLE-US-02191 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3402(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02192 >GP: BAB04569 GB: AP001510 unknown conserved protein in others [Bacillus halodurans] Identities = 46/144 (31%), Positives = 83/144 (56%), Gaps = 10/144 (6%) Query: 1 MVKALETYIVTNGNGRQAVDFYKDVFQADLVNMMTWEEM--DPNC--LEDRKDLIINAQL 56 M+ + Y++ +G+G+ A++FY+D A+++ + T+ ++ PN KDLI++A L Sbjct: 1 MILTMNPYLMLDGDGQAAIEFYQDALNAEVITIQTYGDLPEQPNSPMASVNKDLILHAHL 60 Query: 57 IFDGIRLQISDENPD-----FVYQAGKNVTAAIIVGSVEEAREIYEKLKKSAQEVQLELQ 111- + L ISD+ D F +G VT A+ +VE E+++KL +E+ L+ Sbjct: 61 KLGEMDLMISDQCLDVDPERFPQHSGSPVTIALTTNNVEMTTEVFQKLASGGEEIA-PLE 119- Query: 112 ETFWSPAYANLVDQFGVMWQISTE 135 +TF+SP Y + D+FG+ W +ST+ Sbjct: 120 KTFFSPLYGQVTDKFGITWHVSTQ 143 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 742 A DNA sequence (GBSx0788) was identified in S. agalactiae <SEQ ID 2271> which encodes the amino acid sequence <SEQ ID 2272>. Analysis of this protein sequence reveals the following: TABLE-US-02193 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02194 >GP: BAB03784 GB: AP001507 UDP-N-acetylglucosamine pyrophosphorylase [Bacillus halodurans] Identities = 238/453 (52%), Positives = 322/453 (70%), Gaps = 1/453 (0%) Query: 1 MSN-YAIILAAGKGTRMKSDLPKVMHKVSGITMLEHVFRSVQAIEPSKIVTVIGHKAELV 59 MSN +A+ILAAG+GTRMKS L KV+H V G M++HV V A+ +IVT+IGH A+ V Sbjct: 1 MSNRFAVILAAGQGTRMKSKLYKVLHSVCGKPMVQHVVDQVSALGFDEIVTIIGHGADAV 60 Query: 60 RDVLGDKSEFVMQTEQLGTGHAVMMAEEELATSKGHTLVIAGDTPLITGESLKNLIDFHV 119- + LG++ + +Q EQLGTGHAV+ AE L +G T+V+ GDTPL+T E++ +++ +H Sbjct: 61 KSQLGERVSYALQEEQLGTGHAVLQAESALGGRRGVTIVLCGDTPLLTAETIDHVMSYHE 120- Query: 120 NHKNVATILTADAANPFGYGRIIRNSDDEVTKIVEQKDANDFEQQVKEINTGTYVFDNQS 17- 9 + AT+LTA+ A+P GYGRI+RN V +IVE KDA E+Q+ E+NTGTY FDN++ Sbjct: 121 EEQAKATVLTAELADPTGYGRIVRNDKGLVERIVEHKDATSEEKQITEVNTGTYCFDNEA 18- 0 Query: 180 LFEALKDINTNNAQGEYYLTDVIGIFKEAGKKVGAYKLRDFDESLGVNDRVALATAEKVM 23- 9 LF+ALK++ NNAQGEYYL DVI I + G+KV AYK +E+LGVNDRVALA AE+VM Sbjct: 181 LFQALKEVGNNNAQGEYYLPDVIQILQTKGEKVAAYKTAHVEETLGVNDRVALAQAEQVM 24- 0 Query: 240 RHRIARQHMVNGVTVVNPDSAYIDIDVEIGEESVIEPNVTLKGQTKIGKGTLLTNGSYLV 29- 9 + RI M GVT ++P+ Y+ D IG+++VI P + GQT IG+G +L + L Sbjct: 241 KRRINEAWMRKGVTFIDPEQTYVSPDATIGQDTVIYPGTMVLGQTTIGEGCVLGPHTELK 30- 0 Query: 300 DAQVGNDVTITNSMVEESIISDGVTVGPYAHIRPGTSLAKGVHIGNFVEVKGSQIGENTK 35- 9 D+++GN + S+V S + + V++GP++HIRP + + V IGNFVEVK S IG+ +K Sbjct: 301 DSKIGNKTAVKQSVVHNSEVGERVSIGPFSHIRPASMIHDDVRIGNFVEVKKSTIGKESK 36- 0 Query: 360 AGHLTYIGNAEVGCDVNFGAGTITVNYDGQNKFKTEIGSNVFIGSNSTLIAPLEIGDNAL 41- 9 A HL+YIG+AEVG VNF G+ITVNYDG+NKF T+I + FIG NS LIAP+ IG AL Sbjct: 361 ASHLSYIGDAEVGERVNFSCGSITVNYDGKNKFLTKIEDDAFIGCNSNLIAPVTIGKGAL 42- 0 Query: 420 TAAGSTITDNVPIDSIAIGRGRQVNKEGYANKK 452 AAGSTIT++VP D+++I R RQ NKE Y KK Sbjct: 421 IAAGSTITEDVPSDALSIARARQTNKEHYVTKK 453 A related DNA sequence was identified in S. pyogenes <SEQ ID 2273> which encodes the amino acid sequence <SEQ ID 2274>. Analysis of this protein sequence reveals the following: TABLE-US-02195 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0461(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02196 Identities = 345/458 (75%), Positives = 398/458 (86%) Query: 1 MSNYAIILAAGKGTRMKSDLPKVMHKVSGITMLEHVFRSVQAIEPSKIVTVIGHKAELVR 60 M+NYAIILAAGKGTRM SDLPKV+HKVSG+TMLEHVFRSV+AI P K VTVIGHK+E+VR Sbjct: 1 MTNYAIILAAGKGTRMTSDLPKVLHKVSGLTMLEHVFRSVKAISPEKSVTVIGHKSEMVR 60 Query: 61 DVLGDKSEFVMQTEQLGTGHAVMMAEEELATSKGHTLVIAGDTPLITGESLKNLIDFHVN 120- VL D+S FV QTEQLGTGHAVMMAE +L +GHTLVIAGDTPLITGESLK+LIDFHVN Sbjct: 61 AVLADQSAFVHQTEQLGTGHAVMMAETQLEGLEGHTLVIAGDTPLITGESLKSLIDFHVN 120- Query: 121 HKNVATILTADAANPFGYGRIIRNSDDEVTKIVEQKDANDFEQQVKEINTGTYVFDNQSL 18- 0 HKNVATILTA A +PFGYGRI+RN D EV KIVEQKDAN++EQQ+KEINTGTYVFDN+ L Sbjct: 121 HKNVATILTATAQDPFGYGRIVRNKDGEVIKIVEQKDANEYEQQLKEINTGTYVFDNKRL 18- 0 Query: 181 FEALKDINTNNAQGEYYLTDVIGIFKEAGKKVGAYKLRDFDESLGVNDRVALATAEKVMR 24- 0 FEALK I TNNAQGEYYLTDV+ IF+ +KVGAY LRDF+ESLGVNDRVALA AE VMR Sbjct: 181 FEALKCITTNNAQGEYYLTDVVAIFRANKEKVGAYILRDFNESLGVNDRVALAIAETVMR 24- 0 Query: 241 HRIARQHMVNGVTVVNPDSAYIDIDVEIGEESVIEPNVTLKGQTKIGKGTLLTNGSYLVD 30- 0 RI ++HMVNGVT NP++ YI+ DVEI + +IE NVTLKG+T IG GT+LTNG+Y+VD Sbjct: 241 QRITQKHMVNGVTFQNPETVYIESDVEIAPDVLIEGNVTLKGRTHIGSGTVLTNGTYIVD 30- 0 Query: 301 AQVGNDVTITNSMVEESIISDGVTVGPYAHIRPGTSLAKGVHIGNFVEVKGSQIGENTKA 36- 0 +++G++ +TNSM+E S+++ GVTVGPYAH+RPGT+L + VHIGNFVEVKGS IGE TKA Sbjct: 301 SEIGDNCVVTNSMIESSVLAAGVTVGPYAHLRPGTTLDREVHIGNFVEVKGSHIGEKTKA 36- 0 Query: 361 GHLTYIGNAEVGCDVNFGAGTITVNYDGQNKFKTEIGSNVFIGSNSTLIAPLEIGDNALT 42- 0 GHLTYIGNA+VG VN GAGTITVNYDGQNK++T IG + FIGSNSTLIAPLE+GD+ALT Sbjct: 361 GHLTYIGNAQVGSSVNVGAGTITVNYDGQNKYETVIGDHAFIGSNSTLIAPLEVGDHALT 42- 0 Query: 421 AAGSTITDNVPIDSIAIGRGRQVNKEGYANKKPHHPSQ 458 AAGSTI+ VPIDSIAIGR RQV KEGYA + HHPS+ Sbjct: 421 AAGSTISKTVPIDSIAIGRSRQVTKEGYAKRLAHHPSR 458 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 743 A DNA sequence (GBSx0790) was identified in S. agalactiae <SEQ ID 2275> which encodes the amino acid sequence <SEQ ID 2276>. Analysis of this protein sequence reveals the following: TABLE-US-02197 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1366(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02198 >GP: CAB14293 GB: Z99116 similar to hypothetical proteins [Bacillus subtilis] Identities = 92/177 (51%), Positives = 124/177 (69%), Gaps = 4/177 (2%) Query: 4 EEKTINRQTVFDGQIIKVAVDDVELPNGLGQSKRELVFHGGAVATLAVTPEHKIVLVKQY 63 EEKTI ++ +F G++I + V+DVELPNG SKRE+V H GAVA LAVT E KI++VKQ+ Sbjct: 5 EEKTIAKEQIFSGKVIDLYVEDVELPNGKA-SKREIVKHPGAVAVLAVTDEGKIIMVKQF 63 Query: 64 RKAIEGISYEIPAGKLETGESGSKEEAALRELEEETGYTG-NLEILYSFYTAIGFCNEKI 122- RK +E EIPAGKLE GE E ALRELEEETGYT L + +FYT+ GF +E + Sbjct: 64 RKPLERTIVEIPAGKLEKGE--EPEYTALRELEEETGYTAKKLTKITAFYTSPGFADEIV 121- Query: 123 VLYLATDLQKVENPRPQDDDEVLELLELSYEDCMQMVEKGMIQDAKTIIALQYYGLK 179 ++LA +L +E R D+DE +E++E++ ED +++VE + DAKT A+QY LK Sbjct: 122 HVFLAEELSVLEEKRELDEDEFVEVMEVTLEDALKLVESREVYDAKTAYAIQYLQLK 178 A related DNA sequence was identified in S. pyogenes <SEQ ID 2277> which encodes the amino acid sequence <SEQ ID 2278>. Analysis of this protein sequence reveals the following: TABLE-US-02199 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1120 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02200 Identities = 136/182 (74%), Positives = 153/182 (83%) Query: 1 MDFEEKTINRQTVFDGQIIKVAVDDVELPNGLGQSKRELVFHGGAVATLAVTPEHKIVLV 60 M FEEKT+ RQTVFDG I KV VDDVELPN LGQSKREL+FH GAVA LA+TPE KIVLV Sbjct: 1 MKFEEKTLKRQTVFDGHIFKVVVDDVELPNNLGQSKRELIFHRGAVAVLAITPERKIVLV 60 Query: 61 KQYRKAIEGISYEIPAGKLETGESGSKEEAALRELEEETGYTGNLEILYSFYTAIGFCNE 120- KQYRKAIE +SYEIPAGKLE GE GSK +AA RELEEET YTG L LY FYTAIGFCNE Sbjct: 61 KQYRKAIERVSYEIPAGKLEIGEEGSKLKAAARELEEETAYTGTLTFLYEFYTAIGFCNE 120- Query: 121 KIVLYLATDLQKVENPRPQDDDEVLELLELSYEDCMQMVEKGMIQDAKTIIALQYYGLKM 18- 0 KI L+LATDL +V NP+PQDDDEV+E+LEL+Y++CM +V +G + DAKT+IALQYY L Sbjct: 121 KITLFLATDLIQVANPKPQDDDEVIEVLELTYQECMDLVAQGKLADAKTLIALQYYALHF 18- 0 Query: 181 GG 182 GG Sbjct: 181 GG 182 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 744 A DNA sequence (GBSx0791) was identified in S. agalactiae <SEQ ID 2279> which encodes the amino acid sequence <SEQ ID 2280>. Analysis of this protein sequence reveals the following: TABLE-US-02201 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.44 Transmembrane 70-86 (64-88) ----- Final Results ----- bacterial membrane --- Certainty = 0.7177 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2281> which encodes the amino acid sequence <SEQ ID 2282>. Analysis of this protein sequence reveals the following: TABLE-US-02202 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.60 Transmembrane 65-81 (58-83) ----- Final Results ----- bacterial membrane --- Certainty = 0.7241 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02203 Identities = 39/89 (43%), Positives = 61/89 (67%), Gaps = 6/89 (6%) Query: 1 MGKPLLTDDMIERSNRGEKVSGQTILDQETKIISTEDGMEQLTDENGKHIYKSRRIENAK 60 MG+PLLTDD+IE++ R E ++ +TK+++ + ++ IYKSRRIENAK Sbjct: 2 MGRPLLTDDIIEKARRMETFEPDDAVNFDTKVMTLPE------KDDKARIYKSRRIENAK 55 Query: 61 RNEFQRKLNLVLFILLILLALLFYAIFKL 89 R++ Q KLN++L +++L+A+L YAIF L Sbjct: 56 RSQLQSKLNVILIAVMLLIAILVYAIFYL 84 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 745 A DNA sequence (GBSx0792) was identified in S. agalactiae <SEQ ID 2283> which encodes the amino acid sequence <SEQ ID 2284>. This protein is predicted to be pfs protein (pfs). Analysis of this protein sequence reveals the following: TABLE-US-02204 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 56-72 (56-72) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02205 >GP: AAC22869 GB: U32801 pfs protein (pfs) [Haemophilus influenzae Rd] Identities = 100/229 (43%), Positives = 144/229 (62%) Query: 1 MKIGIIAAMEEELKLLVENLEDKSQETVLSNVYYSGRYGEHELVLVQSGVGKVMSAMSVA 60 MKIGI+ AM +E+++L + D+++ V S V + G+ ++ L+QSG+GKV +A+ Sbjct: 1 MKIGIVGAMAQEVEILKNLMADRTETRVASAVIFEGKINGKDVALLQSGIGKVAAAIGTT 60 Query: 61 ILVESFKVDAIINTGSAGAVATGLNVGDVVVADTLVYHDVDLTAFGYDYGQMSMQPLYFH 120- L++ K D +INTGSAG VA GL VGD+V++D YHD D+TAFGY+ GQ+ P F Sbjct: 61 ALLQLAKPDCVINTGSAGGVAKGLKVGDIVISDETRYHDADVTAFGYEKGQLPANPAAFL 120- Query: 121 SDKTFVSTFEAVLSKEEMISKVGLIATGDSFIAGQEKIDVIKGHFPQVLAVEMEGAAIAQ 18- 0 SDK + + K+ K GLI +GDSFI ++KI IK FP V VEME AIAQ Sbjct: 121 SDKKLADLAQEIAEKQGQSVKRGLICSGDSFINSEDKIAQIKADFPNVTGVEMEATAIAQ 18- 0 Query: 181 AAQATGKPFVVVRAMSDTAAHDANITFDEFIIEAGKRSAQVLMAFLKAL 229 A PFVVVRA+SD A+++F+EF+ A K+S+ +++ + L Sbjct: 181 VCYAFNVPFVVVRAISDGGDGKASMSFEEFLPLAAKQSSALVLGMIDRL 229 A related DNA sequence was identified in S. pyogenes <SEQ ID 2285> which encodes the amino acid sequence <SEQ ID 2286>. Analysis of this protein sequence reveals the following: TABLE-US-02206 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1245 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02207 Identities = 169/229 (73%), Positives = 189/229 (81%) Query: 1 MKIGIIAAMEEELKLLVENLEDKSQETVLSNVYYSGRYGEHELVLVQSGVGKVMSAMSVA 60 MKIGIIAAMEEEL LL+ NL D + VLS YY+GR+G+HEL+LVQSGVGKVMSAM+VA Sbjct: 1 MKIGIIAAMEEELSLLLANLLDAQEHQVLSKTYYTGRFGKHELILVQSGVGKVMSAMTVA 60 Query: 61 ILVESFKVDAIINTGSAGAVATGLNVGDVVVADTLVYHDVDLTAFGYDYGQMSMQPLYFH 120- ILVE FK AIINTGSAGAVA+ L +GDVVVAD LVYHDVD TAFGY YGQM+ QPLY+ Sbjct: 61 ILVEHFKAQAIINTGSAGAVASHLAIGDVVVADRLVYHDVDATAFGYAYGQMAGQPLYYD 120- Query: 121 SDKTFVSTFEAVLSKEEMISKVGLIATGDSFIAGQEKIDVIKGHFPQVLAVEMEGAAIAQ 18- 0 D FV+ F+ VL E+ +VGLIATGDSF+AGQ+KID IK F VLAVEMEGAAIAQ Sbjct: 121 CDPQFVAIFKQVLKHEKTNGQVGLIATGDSFVAGQDKIDQIKTAFSDVLAVEMEGAAIAQ 18- 0 Query: 181 AAQATGKPFVVVRAMSDTAAHDANITFDEFIIEAGKRSAQVLMAFLKAL 229 AA GKPF+VVRAMSDTAAHDANITFD+FIIEAGKRSAQ LM FL+ L Sbjct: 181 AAHTAGKPFIVVRAMSDTAAHDANITFDQFIIEAGKRSAQTLMTFLENL 229 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 746 A DNA sequence (GBSx0793) was identified in S. agalactiae <SEQ ID 2287> which encodes the amino acid sequence <SEQ ID 2288>. This protein is predicted to be SloR. Analysis of this protein sequence reveals the following:

TABLE-US-02208 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3777 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9405> which encodes amino acid sequence <SEQ ID 9406> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02209 >GP: AAF81675 GB: AF232688 SloR [Streptococcus mutans] Identities = 97/175 (55%), Positives = 134/175 (76%) Query: 1 MSEMIKKMISEQLIVKDKDLGYYLTKQGLLVVSDLYRKHRLVEVFLVNHLHYTADDIHEE 60 +SEM+KK++ E L++KDK GY LTK+G ++ S LYRKHRL+EVFL+NHL+YTAD+IHEE Sbjct: 38 VSEMVKKLLLEDLVLKDKQAGYLLTKKGQILASSLYRKHRLIEVFLMNHLNYTADEIHEE 97 Query: 61 AEVLEHTVSTTFVDQLEKLLDFPQFCPHGGTIPKKGEFLVEINQMTLDQISQLGTYVISR 120- AEVLEHTVS FV++L+K L++P+ CPHGGTIP+ G+ LVE + TL ++++G Y++ R Sbjct: 98 AEVLEHTVSDVFVERLDKFLNYPKVCPHGGTIPQHGQPLVERYRTTLKGVTEMGVYLLKR 157- Query: 121 VHDDFQLLKYLEQHRLHINDTIELTQIDPYAKTYHITYNDENLTIPERIASQIYV 175 V D+FQLLKY+EQH L I D + L + D +A Y I + E L + +ASQIY+ Sbjct: 158 VQDNFQLLKYMEQHHLKIGDELRLLEYDAFAGAYTIEKDGEQLQVTSAVASQIYI 212 A related DNA sequence was identified in S. pyogenes <SEQ ID 2289> which encodes the amino acid sequence <SEQ ID 2290>. Analysis of this protein sequence reveals the following: TABLE-US-02210 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2910 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02211 Identities = 44/75 (58%), Positives = 59/75 (78%) Query: 1 MSEMIKKMISEQLIVKDKDLGYYLTKQGLLVVSDLYRKHRLVEVFLVNHLHYTADDIHEE 60 +SEMIKKMIS+ IVKDK GY L +G +V++LYRK RL+EVFL++ L Y ++H+E Sbjct: 38 VSEMIKKMISQGWIVKDKAKGYLLKDKGYALVANLYRKLRLIEVFLIHQLGYNTQEVHQE 97 Query: 61 AEVLEHTVSTTFVDQ 75 AEVLEHTVS +F+D+ Sbjct: 98 AEVLEHTVSDSFIDR 112 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 747 A DNA sequence (GBSx0794) was identified in S. agalactiae <SEQ ID 2291> which encodes the amino acid sequence <SEQ ID 2292>. This protein is predicted to be undecaprenyl pyrophosphate synthetase (uppS). Analysis of this protein sequence reveals the following: TABLE-US-02212 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3569 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9435> which encodes amino acid sequence <SEQ ID 9436> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02213 >GP: CAB13526 GB: Z99112 similar to hypothetical proteins [Bacillus subtilis] Identities = 88/165 (53%), Positives = 118/165 (71%), Gaps = 4/165 (2%) Query: 1 MNLPVKFFDKYVPELDKNNVRVQVIGDTHKLPKATYDAMQRACLRTKHNSGLVLNFALNY 60 M LP +F + Y+PEL + NV+V++IGD LP T A+++A T N G++LNFALNY Sbjct: 100 MKLPEEFLNTYLPELVEENVQVRIIGDETALPAHTLRAIEKAVQDTAQNDGMILNFALNY 15- 9 Query: 61 GGRSEITNAIKEIAQDVLEAKLNPDDITEDLVANHLMTNSLPYLYRDPDLIIRTSGELRL 120- GGR+EI +A K +A+ V E LN +DI E L + +LMT SL +DP+L+IRTSGE+RL Sbjct: 160 GGRTEIVSAAKSLAEKVKEGSLNIEDIDESLFSTYLMTESL----QDPELLIRTSGEIRL 21- 5 Query: 121 SNFLPWQSAYSEFYFTPVLWPDFKKDELHKAIVDYNQRHRRFGSV 165 SNF+ WQ AYSEF FT VLWPDFK+D +A+ ++QR RRFG + Sbjct: 216 SNFMLWQVAYSEFVFTDVLWPDFKEDHFLQALGEFQQRGRRFGGI 260 A related DNA sequence was identified in S. pyogenes <SEQ ID 2293> which encodes the amino acid sequence <SEQ ID 2294>. Analysis of this protein sequence reveals the following: TABLE-US-02214 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2073 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02215 Identities = 125/165 (75%), Positives = 145/165 (87%) Query: 1 MNLPVKFFDKYVPELDKNNVRVQVIGDTHKLPKATYDAMQRACLRTKHNSGLVLNFALNY 60 MNLPV FFDKYVP L +NNV++Q+IG+T +LP+ T A+ A +TK N+GL+LNFALNY Sbjct: 85 MNLPVTFFDKYVPVLHENNVKIQMIGETSRLPEDTLAALNAAIDKTKRNTGLILNFALNY 144- Query: 61 GGRSEITNAIKEIAQDVLEAKLNPDDITEDLVANHLMTNSLPYLYRDPDLIIRTSGELRL 120- GGR+EIT+A++ IAQDVL+AKLNP DITEDL+AN+LMT+ LPYLYRDPDLIIRTSGELRL Sbjct: 145 GGRAEITSAVRFIAQDVLDAKLNPGDITEDLIANYLMTDHLPYLYRDPDLIIRTSGELRL 20- 4 Query: 121 SNFLPWQSAYSEFYFTPVLWPDFKKDELHKAIVDYNQRHRRFGSV 165 SNFLPWQSAYSEFYFTPVLWPDFKK EL KAI DYN+R RRFG V Sbjct: 205 SNFLPWQSAYSEFYFTPVLWPDFKKAELLKAIADYNRRQRRFGKV 249 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 748 A DNA sequence (GBSx0795) was identified in S. agalactiae <SEQ ID 2295> which encodes the amino acid sequence <SEQ ID 2296>. This protein is predicted to be phosphatidate cytidylyltransferase (cdsA). Analysis of this protein sequence reveals the following: TABLE-US-02216 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.65 Transmembrane 201-217 (194-222) INTEGRAL Likelihood = -7.96 Transmembrane 175-191 (170-197) INTEGRAL Likelihood = -5.89 Transmembrane 81-97 (74-99) INTEGRAL Likelihood = -3.03 Transmembrane 26-42 (23-42) INTEGRAL Likelihood = -2.92 Transmembrane 136-152 (135-153) INTEGRAL Likelihood = -2.02 Transmembrane 49-65 (47-66) INTEGRAL Likelihood = -0.64 Transmembrane 248-264 (248-264) ----- Final Results ----- bacterial membrane --- Certainty = 0.4461 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02217 >GP: BAB06141 GB: AP001515 phosphatidate cytidylyltransferase [Bacillus halodurans] Identities = 116/266 (43%), Positives = 172/266 (64%), Gaps = 6/266 (2%) Query: 1 MKERVIWGAVALAIFIPFLVMGGLPFQFLVGLLAMIGVSELLRMRRLEIFSFEGALAMIG 60 MK+RV+ + +F+ F+V+GGLPF + ++A I +SELL+M+++ FS GA +++ Sbjct: 1 MKQRVVTAIIFGLVFLTFVVVGGLPFTMFIIVVATIAMSELLKMKKIAPFSPMGAFSLLP 60 Query: 61 AFVLTVPLDSYLSFLPVDASLSAYGIVIFMILAGTVLNSNSYSFEDAAFPIASSFYVGIG 120- ++L +P D + +P + + I +L TVL N+++F++A F I SS Y+G G Sbjct: 61 MWMLLLPNDWFKVVIPDFTKVEIFIFFILFLLLLTVLTKNTFTFDEAGFVILSSAYIGYG 120- Query: 121 FQNLVSARMA---GIDKVLLALFIVWATDIGAYMIGRQFGQRKLLPSVSPNKTIEGSLGG 17- 7 F L+ +R G+ V LF++WATD GAY GR FG+ KL P +SPNKTIEGS+GG Sbjct: 121 FHFLLLSREIPEIGLPLVFFVLFVIWATDSGAYFAGRAFGKHKLWPHISPNKTIEGSIGG 18- 0 Query: 178 IASAIVVAFFFMLFDKTVYAPHSFLVMLVLVAIFSIFGQFGDLVESSIKRHFGVKDSGKL 23- 7 I A+++ F S+ V L ++ + S+FGQ GDLVES++KRH+ VKDSG + Sbjct: 181 IILAVIIGSLFYWIMPLF---SSYGVALAVIVVASVFGQLGDLVESALKRHYAVKDSGTV 23- 7 Query: 238 IPGHGGILDRFDSMIFVFPIMHFFGL 263 +PGHGGILDRFDS+I+V PI+H L Sbjct: 238 LPGHGGILDRFDSLIYVMPILHLLHL 263 A related DNA sequence was identified in S. pyogenes <SEQ ID 2297> which encodes the amino acid sequence <SEQ ID 2298>. Analysis of this protein sequence reveals the following: TABLE-US-02218 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.98 Transmembrane 175-191 (170-197) INTEGRAL Likelihood = -8.97 Transmembrane 5-21 (4-42) INTEGRAL Likelihood = -6.85 Transmembrane 201-217 (197-222) INTEGRAL Likelihood = -6.53 Transmembrane 81-97 (79-99) INTEGRAL Likelihood = -4.73 Transmembrane 49-65 (47-71) INTEGRAL Likelihood = -3.40 Transmembrane 136-152 (135-153) INTEGRAL Likelihood = -3.24 Transmembrane 26-42 (22-42) INTEGRAL Likelihood = -1.17 Transmembrane 248-264 (248-264) ----- Final Results ----- bacterial membrane --- Certainty = 0.4991 (Afffirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02219 >GP: BAB06141 GB: AP001515 phosphatidate cytidylyltransferase [Bacillus halodurans] Identities = 125/266 (46%), Positives = 177/266 (65%), Gaps = 6/266 (2%) Query: 1 MKERVVWGGVAVAIFLPFLIIGNLPFQLFVGVLAMIGVSELLKMKRLEVFSFEGVFAMLA 60 MK+RVV + +FL F+++G LPF +F+ V+A I +SELLKMK++ FS G F++L Sbjct: 1 MKQRVVTAIIFGLVFLTFVVVGGLPFTMFIIVVATIAMSELLKMKKIAPFSPMGAFSLLP 60 Query: 61 AFVLAVPMDHYLTFLPIDANVAFYSLMVFFILAGTVLNSRAYSFDDAAFPIATSFYVGIG 120- ++L +P D + +P V + + F+L TVL ++FD+A F I +S Y+G G Sbjct: 61 MWMLLLPNDWFKVVIPDFTKVEIFIFFILFLLLLTVLTKNTFTFDEAGFVILSSAYIGYG 120- Query: 121 FQHLINAR---LSGIDKVFLALFIVWATDIGAYLIGRQFGRRKLLPTVSPNKTIEGSLGG 17- 7 F L+ +R G+ VF LF++WATD GAY GR FG+ KL P +SPNKTIEGS+GG Sbjct: 121 FHFLLLSREIPEIGLPLVFFVLFVIWATDSGAYFAGRAFGKHKLWPHISPNKTIEGSIGG 18- 0 Query: 178 IACAVLVSFIFMVIDRSVYAPHHFLTMLVLVALFSIFAQFGDLVESALKRHFGVKDSGKL 23- 7 I AV++ +F I +++ + +++VA S+F Q GDLVESALKRH+ VKDSG + Sbjct: 181 IILAVIIGSLFYWI-MPLFSSYGVALAVIVVA--SVFGQLGDLVESALKRHYAVKDSGTV 23- 7 Query: 238 IPGHGGILDRFDSMIFVFPIMHLFGL 263 +PGHGGILDRFDS+I+V PI+HL L Sbjct: 238 LPGHGGILDRFDSLIYVMPILHLLHL 263 An alignment of the GAS and GBS proteins is shown below: TABLE-US-02220 Identities = 204/264 (77%), Positives = 243/264 (91%) Query: 1 MKERVIWGAVALAIFIPFLVMGGLPFQFLVGLLAMIGVSELLRMRRLEIFSFEGALAMIG 60 MKERV+WG VA+AIF+PFL++G LPFQ VG+LAMIGVSELL+M+RLE+FSFEG AM+ Sbjct: 1 MKERVVWGGVAVAIFLPFLIIGNLPFQLFVGVLAMIGVSELLKMKRLEVFSFEGVFAMLA 60 Query: 61 AFVLTVPLDSYLSFLPVDASLSAYGIVIFMILAGTVLNSNSYSFEDAAFPIASSFYVGIG 120- AFVL VP+D YL+FLP+DA+++ Y +++F ILAGTVLNS +YSF+DAAFPIA+SFYVGIG Sbjct: 61 AFVLAVPMDHYLTFLPIDANVAFYSLMVFFILAGTVLNSRAYSFDDAAFPIATSFYVGIG 120- Query: 121 FQNLVSARMAGIDKVLLALFIVWATDIGAYMIGRQFGQRKLLPSVSPNKTIEGSLGGIAS 18- 0 FQ+L++AR++GIDKV LALFIVWATDIGAY+IGRQFG+RKLLP+VSPNKTIEGSLGGIA Sbjct: 121 FQHLINARLSGIDKVFLALFIVWATDIGAYLIGRQFGRRKLLPTVSPNKTIEGSLGGIAC 18- 0 Query: 181 AIVVAFFFMLFDKTVYAPHSFLVMLVLVAIFSIFGQFGDLVESSIKRHFGVKDSGKLIPG 24- 0 A++V+F FM+ D++VYAPH FL MLVLVA+FSIF QFGDLVES++KRHFGVKDSGKLIPG Sbjct: 181 AVLVSFIFMVIDRSVYAPHHFLTMLVLVALFSIFAQFGDLVESALKRHFGVRDSGKLIPG 24- 0 Query: 241 HGGILDRFDSMIFVFPIMHFFGLF 264 HGGILDRFDSMIFVFPIMH FGLF Sbjct: 241 HGGILDRFDSMIFVFPIMHLFGLF 264 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 749 A DNA sequence (GBSx0796) was identified in S. agalactiae <SEQ ID 2299> which encodes the amino acid sequence <SEQ ID 2300>. Analysis of this protein sequence reveals the following: TABLE-US-02221 Possible site: 46 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.09 Transmembrane 2-18 (1-25) INTEGRAL Likelihood = -9.39 Transmembrane 394-410 (390-415) INTEGRAL Likelihood = -8.01 Transmembrane 181-197 (173-198) INTEGRAL Likelihood = -2.97 Transmembrane 343-359 (342-360) ----- Final Results ----- bacterial membrane --- Certainty = 0.5437 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02222 >GP: AAD47948 GB: AF152237 Eep [Enterococcus faecalis] Identities = 229/425 (53%), Positives = 298/425 (69%), Gaps = 9/425 (2%) Query: 1 MLGILTFIIIFGVIVVVHEFGHFYFAKKSGILVREFAIGMGPKIFSHIDKEGTTYTIRIL 60 M I+TFII+FG++V+VHEFGHFYFAK++GILVREFAIGMGPKIF+H K+GTTYTIR+L Sbjct: 1 MKTIITFIIVFGILVLVHEFGHFYFAKRAGILVREFAIGMGPKIFAHRGKDGTTYTIRLL 60 Query: 61 PLGGYVRMAGWGDDKTEIKTGTPASLTLNKEGIVTRINLSGKQLDNTSLPINVTAYDLED 120- P+GGYVRMAG G+D TEI G P S+ LN G V +IN S K S+P+ V +DLE Sbjct: 61 PIGGYVRMAGMGEDMTEITPGMPLSVELNAVGNVVKINTSKKVQLPHSIPMEVVDFDLEK 120- Query: 121 KLTITGLV---LSETKTYSVDHDATIIEEDGTEIRIAPLDMQYQNASVWGRLITNFAGPM 17- 7 +L I G V E Y VDHDATIIE DGTE+RIAPLD+Q+Q+A + R++TNFAGPM Sbjct: 121 ELFIKGYVNGNEEEETVYKVDHDATIIESDGTEVRIAPLDVQFQSAKLSQRILTNFAGPM 18- 0 Query: 178 NNFILGLVVFIALAFIQGGVQDLSTNQV-RVSENGPAASAGLKNNDRILQIGSHKVSNWE 23- 6 NNFILG ++F F+QGGV DL+TNQ+ +V NGPAA AGLK ND++L I +K+ +E Sbjct: 181 NNFILGFILFTLAVFLQGGVTDLNTNQIGQVIPNGPAAEAGLKENDKVLSINNQKIKKYE 24- 0 Query: 237 QLTAAVEKSTRHLEKKQKLALKIKSKEVVKTINVKPQKVDKSYI--IGIMPALKTSFKDK 29- 4 T V+K+ EK ++ KE T+ + QKV+K I +G+ P +KT K Sbjct: 241 DFTTIVQKNP---EKPLTFVVERNGKEEQLTVTPEKQKVEKQTIGKVGVYPYMKTDLPSK 29- 7 Query: 295 LLGGLKLAWESFFRILNELKKLIAHFSINKLGGPVALYQASSQAAKNGFVTVLNLMGLIS 35- 4 L+GG++ S +I L L FS+NKLGGPV +++ S +A+ G TV+ LM ++S Sbjct: 298 LMGGIQDTLNSTTQIFKALGSLFTGFSLNKLGGPVMMFKLSEEASNAGVSTVVFLMAMLS 35- 7 Query: 355 INLGIMNLIPIPALDGGKIVMNILEAIRRKPLKQETETYITLAGVAVMLVLMIAVTWNDI 41- 4 +NLGI+NL+PIPALDGGKIV+NI+E +R KP+ E E ITL G ++VLM+ VTWNDI Sbjct: 358 MNLGIINLLPIPALDGGKIVLNIIEGVRGKPISPEKEGIITLIGFGFVMVLMVLVTWNDI 41- 7 Query: 415 MRAFF 419 R FF Sbjct: 418 QRFFF 422 A related DNA sequence was identified in S. pyogenes <SEQ ID 2301> which encodes the amino acid sequence <SEQ ID 2302>. Analysis of this protein sequence reveals the following: TABLE-US-02223 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.41 Transmembrane 2-18 (1-25) INTEGRAL Likelihood = -9.77 Transmembrane 394-410 (390-415) INTEGRAL Likelihood = -9.61 Transmembrane 180-196 (173-201) INTEGRAL Likelihood = -2.66 Transmembrane 347-363 (343-363) ----- Final Results ----- bacterial membrane --- Certainty = 0.5564 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02224 >GP: AAD47948 GB: AF152237 Eep [Enterococcus faecalis] Identities = 230/427 (53%), Positives = 298/427 (68%), Gaps = 13/427 (3%) Query: 1 MLGIITFIIIFGILVIVHEFGHFYFAKKSGILVREFAIGMGPKIFSHVDQGGTLYTLRML 60 M IITFII+FGILV+VHEFGHFYFAK++GILVREFAIGMGPKIF+H + GT YT+R+L Sbjct: 1 MKTIITFIIVFGILVLVHEFGHFYFAKRAGILVREFAIGMGPKIFAHRGKDGTTYTIRLL 60 Query: 61 PLGGYVRMAGWGDDKTEIKTGTPASLTLNEQGFVKRINLSQSKLDPTSLPMHVTGYDLED 120- P+GGYVRMAG G+D TEI G P S+ LN G V +IN S+ P S+PM V +DLE Sbjct: 61 PIGGYVRMAGMGEDMTEITPGMPLSVELNAVGNVVKINTSKKVQLPHSIPMEVVDFDLEK 120- Query: 121 QLSITGLV---LEETKTYKVAHDATIVEEDGTEIRIAPLDVQYQNASIGGRLITNFAGPM 17- 7 +L I G V EE YKV HDATI+E DGTE+RIAPLDVQ+Q+A + R++TNFAGPM Sbjct: 121 ELFIKGYVNGNEEEETVYKVDHDATIIESDGTEVRIAPLDVQFQSAKLSQRILTNFAGPM 18- 0 Query: 178 NNFILGIVVFILLVFLQGGMPDFSSNHV-RVQENGAAAKAGLRDNDQIVAINGYKVTSWN 23- 6 NNFILG ++F L VFLQGG+ D ++N + +V NG AA+AGL++ND++++IN K+ + Sbjct: 181 NNFILGFILFTLAVFLQGGVTDLNTNQIGQVIPNGPAAEAGLKENDKVLSINNQKIKKYE 24- 0 Query: 237 DLTEAVDLATRDLGPSQTIKVTYKSHQRLKTVAVKPQKH-AKTYTI---GVKASLKTGFK 29- 2 D T V P + + + + + + + V P+K + TI GV +KT Sbjct: 241 DFTTIV-----QKNPEKPLTFVVERNGKEEQLTVTFPEKQKVEKQTIGKVGVYPYMKTDLP 2- 95 Query: 293 DKLLGGLELAWSRAFTILNALKGLITGFSLNKLGGPVAMYDMSNQAAQNGLESVLSLMAM 35- 2 KL+GG++ + I AL L TGFSLNKLGGPV M+ +S +A+ G+ +V+ LMAM Sbjct: 296 SKLMGGIQDTLNSTTQIFKALGSLFTGFSLNKLGGPVMMFKLSEEASNAGVSTVVFLMAM 35- 5 Query: 353 LSINLGIFNLIPIPALDGGKILMNIIEAIRRKPIKQETEAYITLAGVAIMVVLMIAVTWN 41- 2 LS+NLGI NL+PIPALDGGKI++NIIE +R KPI E E ITL G ++VLM+ VTWN Sbjct: 356 LSMNLGIINLLPIPALDGGKIVLNIIEGVRGKPISPEKEGIITLIGFGFVMVLMVLVTWN 41- 5 Query: 413 DIMRVFF 419 DI R FF Sbjct: 416 DIQRFFF 422 An alignment of the GAS and GBS proteins is shown below: TABLE-US-02225 Identities = 306/419 (73%), Positives = 359/419 (85%) Query: 1 MLGILTFIIIFGVIVVVHEFGHFYFAKKSGILVREFAIGMGPKIFSHIDKEGTTYTIRIL 60 MLGI+TFIIIFG++V+VHEFGHFYFAKKSGILVREFAIGMGPKIFSH+D+ GT YT+R+L Sbjct: 1 MLGIITFIIIFGILVIVHEFGHFYFAKKSGILVREFAIGMGPKIFSHVDQGGTLYTLRML 60 Query: 61 PLGGYVRMAGWGDDKTEIKTGTPASLTLNKEGIVTRINLSGKQLDNTSLPINVTAYDLED 120- PLGGYVRMAGWGDDKTEIKTGTPASLTLN++G V RINLS +LD TSLP++VT YDLED Sbjct: 61 PLGGYVRMAGWGDDKTEIKTGTPASLTLNEQGFVKRINLSQSKLDPTSLPMHVTGYDLED 120- Query: 121 KLTITGLVLSETKTYSVDHDATIIEEDGTEIRIAPLDMQYQNASVWGRLITNFAGPMNNF 18- 0 +L+ITGLVL ETKTY V HDATI+EEDGTEIRIAPLD+QYQNAS+ GRLITNFAGPMNNF Sbjct: 121 QLSITGLVLEETKTYKVAHDATIVEEDGTEIRIAPLDVQYQNASIGGRLITNFAGPMNNF 18- 0 Query: 181 ILGLVVFIALAFIQGGVQDLSTNQVRVSENGPAASAGLKNNDRILQIGSHKVSNWEQLTA 24- 0 ILG+VVFI L F+QGG+ D S+N VRV ENG AA AGL++ND+I+ I +KV++W LT Sbjct: 181 ILGIVVFILLVFLQGGMPDFSSNHVRVQENGAAAKAGLRDNDQIVAINGYKVTSWNDLTE 24- 0 Query: 241 AVEKSTRHLEKKQKLALKIKSKEVVKTINVKPQKVDKSYIIGIMPALKTSFKDKLLGGLK 30- 0 AV+ TR L Q + + KS + +KT+ VKPQK K+Y IG+ +LKT FKDKLLGGL+ Sbjct: 241 AVDLATRDLGPSQTIKVTYKSHQRLKTVAVKPQKHAKTYTIGVKASLKTGFKDKLLGGLE 30- 0 Query: 301 LAWESFFRILNELKKLIAHFSINKLGGPVALYQASSQAAKNGFVTVLNLMGLISINLGIM 36- 0 LAW F ILN LK LI FS+NKLGGPVA+Y S+QAA+NG +VL+LM ++SINLGI Sbjct: 301 LAWSRAFTILNALKGLITGFSLNKLGGPVAMYDMSNQAAQNGLESVLSLMAMLSINLGIF 36- 0 Query: 361 NLIPIPALDGGKIVMNILEAIRRKPLKQETETYITLAGVAVMLVLMIAVTWNDIMRAFF 419- NLIPIPALDGGKI+MNI+EAIRRKP+KQETE YITLAGVA+M+VLMIAVTWNDIMR FF Sbjct: 361 NLIPIPALDGGKILMNIIEAIRRKPIKQETEAYITLAGVAIMVVLMIAVTWWDIMRVFF 419- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 750 A DNA sequence (GBSx0797) was identified in S. agalactiae <SEQ ID 2303> which encodes the amino acid sequence <SEQ ID 2304>. This protein is predicted to be prolyl-tRNA synthetase (proS). Analysis of this protein sequence reveals the following:

TABLE-US-02226 Possible site: 18 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 473-489 (473-490) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10181> which encodes amino acid sequence <SEQ ID 10182> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02227 >GP: CAB13530 GB: Z99112 prolyl-tRNA synthetase [Bacillus subtilis] Identities = 301/608 (49%), Positives = 410/608 (66%), Gaps = 52/608 (8%) Query: 1 MKQSKMLIPTLREMPSDAQVISHALMVRAGYVRQVSAGIYAYLPLANRTIEKFKTIMRQE 60 M+QS LIPTLRE+P+DA+ SH L++RAG++RQ ++G+Y+Y+PLA + I+ + I+R+E Sbjct: 1 MRQSLTLIPTLREVPADAEAKSHQLLLRAGFIRQNTSGVYSYMPLAYKVIQNIQQIVREE 60 Query: 61 FEKIGAVEMLAPALLTADLWRESGRYETYGEDLYKLKNRDQSDFILGPTHEETFTTLVRD 120- EKI AVEML PAL A+ W+ESGR+ TYG +L +LK+R +F LG THEE T+LVRD Sbjct: 61 MEKIDAVEMLMPALQQAETWQESGRWYTYGPELMRLKDRHGREFALGATHEEVITSLVRD 120- Query: 121 AVKSYKQLPLNLYQIQSKYRDEKRPRNGLLRTREFIMKDGYSFHKDYEDLDVTYEDYREA 18- 0 VKSYK+LPL LYQIQSK+RDEKRPR GLLR REFIMED YSFH E LD TY+ +A Sbjct: 121 EVKSYKRLPLTLYQIQSKFRDEKRPRFGLLRGREFIMKDAYSFHASAESLDETYQKMYEA 18- 0 Query: 181 YEAIFTRAGLDFKGIIGDGGAMGGKDSQEFMAVTPNRTDLNRWLVLDKTIPSIDDIPEDV 24- 0 Y IF R G++ + +I D GAMGGKD+ EFMA++ Sbjct: 181 YSNIFARCGINVRPVIADSGAMGGKDTHEFMALS-------------------------- 21- 4 Query: 241 LEEIKVELSAWLVSGEDTIAYSTESSYAANLEMATNEYKPSTKAATFEEVTKVETPNCKS 30- 0 GEDTIAYS ES YAAN+EMA ++ + + KV TPN K+ Sbjct: 215 ------------AIGEDTIAYSDESQYAANIEMAEVLHQEVPSDEEPKALEKVHTPHVKT 26- 2 Query: 301 IDEVAGFLSIDENQTIKTLLFIADEQPVVALLVGNDQVNDVKLKNYLAADFLEPASEEQA 36- 0 I+E+ FL + IK++LF AD++ V+ L+ G+ +VND+K+KN L A+ +E A+ E+ Sbjct: 263 IEELTAFLQVSAEACIKSVLFKADDRFVLVLVRGDHEVNDIKVKNLLHAEVVELATHEEV 32- 2 Query: 361 KEIFGAGFGSLGPVNLPDSVKIIADRKVQDLANAVSGANQDGYHFTGVNPERDFTA-EYV 41- 9 + G G +GPV + V++ AD+ V+ + NAV+GAN+ +H+ VN RD E+ Sbjct: 323 IQQLGTEPGFVGPVGIHQDVEVYADQAVKAMVNAVAGANEGDHHYKNVNVNRDAQIKEFA 38- 2 Query: 420 DIREVKEGEISPDGKGTLKFARGIEIGHIFKLGTRYSDSMGANILDENGRSNPIVMGCYG 47- 9 D+R +KEG+ SPDGKGT++FA GIE+G +FKLGTRYS++M A LDENGR+ P++MGCYG Sbjct: 383 DLRFIKEGDPSPDGKGTIRFAEGIEVGQVFKLGTRYSEAMNATYLDENGRAQPMLMGCYG 44- 2 Query: 480 IGVSRILSAVIEQHARLFVNKTPKGAYRFAWGINFPEELAPFDVHLITVNVKDQESQDLT 53- 9 IGVSR LSA+ EQH G+ +P+ +AP+D+H++ +N+K+ ++L Sbjct: 443 IGVSRTLSAIAEQH-------------HDEKGLIWPKSVAPYDLHILALNMKNDGQRELA 48- 9 Query: 540 EKIEADLMLKGYEVLTDDRNERVGSKFSDSDLIGLPIRVTVGKKASEGIVEVKIKASGDT 59- 9 EK+ ADL +GYEVL DDR ER G KF+DSDLIGLPIR+TVGK+A EGIVEVKI+ +G++ Sbjct: 490 EKLYADLKAEGYEVLYDDRAERAGVKFADSDLIGLPIRITVGKRADEGIVEVEIRQTGES 54- 9 Query: 600 IEVHADNL 607 E+ D L Sbjct: 550 TEISVDEL 557 A related DNA sequence was identified in S. pyogenes <SEQ ID 2305> which encodes the amino acid sequence <SEQ ID 2306>. Analysis of this protein sequence reveals the following: TABLE-US-02228 Possible site: 18 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = 0.32 Transmembrane 473-489 (473-490) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02229 Identities = 535/617 (86%), Positives = 584/617 (93%) Query: 1 MKQSKMLIPTLREMPSDAQVISHALMVRAGYVRQVSAGIYAYLPLANRTIEKFKTIMRQE 60 MKQSK+LIPTLREMPSDAQVISHALMVRAGYVRQVSAGIYAYLPLANRTIEKFKTIMR+E Sbjct: 1 MKQSKLLIPTLREMPSDAQVISHALMVRAGYVRQVSAGIYAYLPLANRTIEKFKTIMREE 60 Query: 61 FEKIGAVEMLAPALLTADLWRESGRYETYGEDLYKLKNRDQSDFILGPTHEETFTTLVRD 120- FEKIGAVEMLAPALLTADLWRESGRYETYGEDLYKLKNRD SDFILGPTHEETFTTLVRD Sbjct: 61 FEKIGAVEMLAPALLTADLWRESGRYETYGEDLYKLKNRDNSDFILGPTHEETFTTLVRD 120- Query: 121 AVKSYKQLPLNLYQIQSKYRDEKRPRNGLLRTREFIMKDGYSFHKDYEDLDVTYEDYRKA 18- 0 AVKSYKQLPLNLYQIQSKYRDEKRPRNGLLRTREFIMKDGYSFH +YEDLDVTYEDYR+A Sbjct: 121 AVKSYKQLPLNLYQIQSKYRDEKRPRNGLLRTREFIMKDGYSFHHNYEDLDVTYEDYRQA 18- 0 Query: 181 YEAIFTRAGLDFKGIIGDGGAMGGKDSQEFMAVTPNRTDLNRWLVLDKTIPSIDDIPEDV 24- 0 YEAIFTRAGLDFKGIIGDGGAMGGKDSQEFMA+TP RTDL+RW+VLDK+I S+DDIP++V Sbjct: 181 YEAIFTRAGLDFKGIIGDGGAMGGKDSQEFMAITPNRTDLNRWVVLDKSIASMDDIPKEV 24- 0 Query: 241 LEEIKVELSAWLVSGEDTIAYSTESSYAANLEMATNEYKPSTKAATFEEVTKVETPNCKS 30- 0 LE+IK EL+AW++SGEDTIAYSTESSYAANLEMATNEYKPS+K A + + +VETP+CK+ Sbjct: 241 LEDIKAELAAWMISGEDTIAYSTESSYAANLEMATNEYKPSSKVAAEDALAEVETPHCKT 30- 0 Query: 301 IDEVAGFLSIDENQTIKTLLFIADEQPVVALLVGNDQVNDVKLKNYLAADFLEPASEEQA 36- 0 IDEVA FLS+DE QTIKTLLF+AD +PVVALLVGND +N VKLENYLAADFLEPASEE+A Sbjct: 301 IDEVAAFLSVDETQTIKTLLFVADNEPVVALLVGNDHINTVKLKNYLAADFLEPASEEEA 36- 0 Query: 361 KEIFGAGFGSLGPVNLPDSVKIIADRKVQDLANAVSGANQDGYHFTGVNPERDFTAEYVD 42- 0 + FGAGFGSLGPVNL +I+ADRKVQ+L NAV+GAN+DG+H TGVNP RDF AEYVD Sbjct: 361 RAFFGAGFGSLGPVNLAQGSRIVADRKVQNLTNAVAGANKDGFHMTGVNPGRDFQAEYVD 42- 0 Query: 421 IREVKEGEISPDGKGTLKFARGIEIGHIFKLGTRYSDSMGANILDENGRSNPIVMGCYGI 48- 0 IREVKEGE+SPDG G L+FARGIE+GHIFKLGTRYSDSMGA ILDENGR+ PIVMGCYGI Sbjct: 421 IREVEEGEMSPDGHGVLQFARGIEVGHIFKLGTRYSDSMGATILDENGRTVPIVMGCYGI 48- 0 Query: 481 GVSRILSAVIEQHARLFVNKTPKGAYRFAWGINFPEELAPFDVHLITVNVKDQESQDLTE 54- 0 GVSRILSAVIEQHARLFVNKTPKG YR+AWGINFP+ELAPFDVHLITVNVKDQ +QDLT Sbjct: 481 GVSRILSAVIEQHARLFVNKTPKGDYRYAWGINFPKELAPFDVHLITVNVKDQVAQDLTA 54- 0 Query: 541 KIEADLMLKGYEVLTDDRNERVGSKFSDSDLIGLPIRVTVGKKASEGIVEVKIKASGDTI 60- 0 K+EADLM KGY+VLTDDRNERVGSKFSDSDLIGLPIRVTVGKKA+EGIVE+KIKA+GD+I Sbjct: 541 KLEADLMAKGYDVLTDDRNERVGSKFSDSDLIGLPIRVTVGKKAAEGIVEIKIKATGDSI 60- 0 Query: 601 EVHADNLIETLEILTKK 617 EV+A+NLIETLEILTK+ Sbjct: 601 EVNAENLIETLEILTKE 617 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 751 A DNA sequence (GBSx0798) was identified in S. agalactiae <SEQ ID 2307> which encodes the amino acid sequence <SEQ ID 2308>. This protein is predicted to be peptidoglycan hydrolase (flgJ). Analysis of this protein sequence reveals the following: TABLE-US-02230 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.86 Transmembrane 9-25 (9-25) ----- Final Results ----- bacterial membrane --- Certainty = 0.1744 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02231 >GP: CAB94815 GB: AJ245582 peptidoglycan hydrolase [Streptococcus thermophilus] Identities = 101/201 (50%), Positives = 122/201 (60%), Gaps = 9/201 (4%) Query: 2 KSRKKDKLVLRLTT-----TLLVFGL----GGVWFYNYKNDNVEPTVTSASDQTTTFIQT 52 KS+KK K VL +L+ GL G + N+ +E +T +T FI Sbjct: 16 KSKKKKKSVLLFPKFFQKWSLIFIGLFSLLGLLASLNFPRLTMEKNMTPTDETTVAFIAE 75 Query: 53 ISPTAIEISKTYDLYASVLLAQAILESSSGQSDLSKAPNYNLFGIKGEYKGKSVQMPTLE 112- I T+ ++ DLYASV++AQAILES SGQS LS+ P YN FGIKGEY G+SV +PT E Sbjct: 76 IGETSRYLAARNDLYASVMIAQAILESDSGQSQLSQKPLYNFFGIKGEYNGQSVTLPTWE 135- Query: 113 DDGKGNMTQIQAPFRAYPNYSASLYDYAELVSSQKYASVWKSNTSSYKDATAALTGLYAT 17- 2 DDGKGN I A FR+Y + SL DY E + Y V +S T SYKDATAALTG+YAT Sbjct: 136 DDGKGNPYHIDAAFRSYGSVENSLQDYVEFLEGSYYVGVHRSKTRSYKDATAALTGVYAT 19- 5 Query: 173 DTAYASKLNQIIETYSLDAYD 193 DT Y KLN IIE Y L YD Sbjct: 196 DTTYGDKLNSIIEQYQLTIYD 216 A related DNA sequence was identified in S. pyogenes <SEQ ID 2309> which encodes the amino acid sequence <SEQ ID 2310>. Analysis of this protein sequence reveals the following: TABLE-US-02232 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02233 >GP: CAB94815 GB: AJ245582 peptidoglycan hydrolase [Streptococcus thermophilus] Identities = 103/189 (54%), Positives = 126/189 (66%), Gaps = 4/189 (2%) Query: 4 KKGKLVLISLFVLAACLGAYSAMRQSHKTSNVSAETIASSSTRHFIDEIGPTASTIGQER 63 +K L+ I LF L L + + R+ + + T +T FI EIG T+ + Sbjct: 32 QKWSLIFIGLFSLLGLLASLNFPRLTMEKNM----TPTDETTVAFIAEIGETSRYLAARN 87 Query: 64 DLYASVMIAQAILESSNGKSSLSQAPYYNFFGIKGAYNGSSVTMSTWEDDGNGNTYTIDQ 123- DLYASVMIAQAILES +G+S LSQ P YNFFGIKG YNG SVT+ TWEDDG GN Y ID Sbjct: 88 DLYASVMIAQAILESDSGQSQLSQKPLYNFFGIKGEYNGQSVTLPTWEDDGKGNPYHIDA 147- Query: 124 AFRAYPSIADSLNDYADLLSSSTYIGARKSNTLSYQDATAALTGLYATDTSYNLKLNNII 18- 3 AFR+Y S+ +SL DY + L S Y+G +S T SY+DATAALTG+YATDT+Y KLN+II Sbjct: 148 AFRSYGSVENSLQDYVEFLEGSYYVGVHRSKTRSYKDATAALTGVYATDTTYGDKLNSII 20- 7 Query: 184 ATYGLTAYD 192 Y LT YD Sbjct: 208 EQYQLTIYD 216 An alignment of the GAS and GBS proteins is shown below: TABLE-US-02234 Identities = 108/192 (56%), Positives = 124/192 (64%), Gaps = 2/192 (1%) Query: 3 SRKKDKLVL-RLTTTLLVFGLGGVWFYNYKNDNVEPTVTSASDQTTTFIQTISPTAIEIS 61 ++KK KLVL L G ++K NV T AS T FI I PTA I Sbjct: 2 TKKKGKLVLISLFVLAACLGAYSAMRQSHKTSNVSAE-TIASSSTRHFIDEIGPTASTIG 60 Query: 62 KTYDLYASVLLAQAILESSSGQSDLSKAPNYNLFGIKGEYKGKSVQMPTLEDDGKGNMTQ 121- + DLYASV++AQAILESS+G+S LS+AP YN FGIKG Y G SV M T EDDG GN Sbjct: 61 QERDLYASVMIAQAILESSNGKSSLSQAPYYNFFGIKGAYNGSSVTMSTWEDDGNGNTYT 120- Query: 122 IQAPFRAYPNYSASLYDYAELVSSQKYASVWKSNTSSYKDATAALTGLYATDTAYASKLN 18- 1 I FRAYP+ + SL DYA+L+SS Y KSNT SY+DATAALTGLYATDT+Y KLN Sbjct: 121 IDQAFRAYPSIADSLNDYADLLSSSTYIGARKSNTLSYQDATAALTGLYATDTSYNLKLN 18- 0 Query: 182 QIIETYSLDAYD 193 II TY L AYD Sbjct: 181 NIIATYGLTAYD 192 A further related DNA sequence was identified in S. pyogenes <SEQ ID 9073> which encodes the amino acid sequence <SEQ ID 9074>. Analysis of this protein sequence reveals the following: TABLE-US-02235 Possible site: 58 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty=0.0000 (Not Clear) < succ> An alignment of the GAS and GBS sequences follows: TABLE-US-02236 Score = 130 bits (323), Expect = 2e-32 Identities = 68/169 (40%), Positives = 96/169 (56%), Gaps = 3/169 (1%) Query: 30 MWTLKLGNQRLAPY---ADHETLTFVRKISHAAQSVAQKKQLYSSVMMAQAILESNNGKS 86 - +W N + P A +T TF++ IS A +++ LY+SV++AQAILES++G+S Sbjct: 25 VWFYNYKNDNVEPTVTSASDQTTTFIQTISPTAIEISKTYDLYASVLLAQAILESSSGQS 84 Query: 87 QLSQKPYYNFFGIKGSYKERSVIFPTLEDDGQGNLYQIDAAFRSYGSLTACFLDYARVLN 146- LS+ P YN FGIKG YK +SV PTLEDDG+GN+ QI A FR+Y + +A DYA +++ Sbjct: 85 DLSKAPNYNLFGIKGEYKGKSVQMPTLEDDGKGNMTQIQAPFRAYPNYSASLYDYAELVS 144- Query: 147 DPLYDKTHKKFWSHYQXXXXXXXXXXXXXXXXXXKLNELIEWYQLTNFD 195 Y K S Y+ KLN++IE Y L +D Sbjct: 145 SQKYASVWKSNTSSYKDATAALTGLYATDTAYASKLNQIIETYSLDAYD 193 A further related DNA sequence was identified in S. pyogenes <SEQ ID 9075> which encodes the amino acid sequence <SEQ ID 9076>. An alignment of the GAS and GBS sequences follows: TABLE-US-02237 Score = 69.1 bits (166), Expect = 1e-13 Identities = 52/151 (34%), Positives = 79/151 (51%), Gaps = 10/151 (6%) Query: 2 TFLDKIKQGCLDGWAKYKILPSLTAAQAILESGWGKH----APHNALFGIKADSSWTGKS 57 TF+ I ++ Y + S+ AQAILES G+ AP+ LFGIK + + GKS Sbjct: 48 TFIQTISPTAIEISKTYDLYASVLLAQAILESSSGQSDLSKAPNYNLFGIKGE--YKGKS 105- Query: 58 FDTKTQEEYQAGVVTDIVDRFRAYDSWDESIADHGQFLVDNPRYEAV--IGETDYKKACY 115- T E+ G +T I FRAY ++ S+ D+ +LV + +Y +V + YK A Sbjct: 106 VQMPTLEDDGKGNMTQIQAPFRAYPNYSASLYDYAE-LVSSQKYASVWKSNTSSYKDATA 16- 4 Query: 116 AIKAAGYATASSYVELLIQLIEENDLQSWDR 146 A+ YAT ++Y L Q+IE L ++D+ Sbjct: 165 ALTGL-YATDTAYASKLNQIIETYSLDAYDK 194 SEQ ID 2308 (GBS275) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 52 (lane 4; MW 22.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 58 (lane 4; MW 47.5 kDa). The GBS275-GST fusion product was purified (FIG. 208, lane 5) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 276), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 752 A DNA sequence (GBSx0799) was identified in S. agalactiae <SEQ ID 2311> which encodes the amino acid sequence <SEQ ID 2312>. Analysis of this protein sequence reveals the following: TABLE-US-02238 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 876-892 (876-892) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2313> which encodes the amino acid sequence <SEQ ID 2314>. Analysis of this protein sequence reveals the following: TABLE-US-02239 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 873-889 (873-889) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02240 >GP: CAB94815 GB: AJ245582 peptidoglycan hydrolase [Streptococcus thermophilus] Identities = 96/202 (47%), Positives = 127/202 (62%), Gaps = 10/202 (4%) Query: 4 KKRRRRAKSSV---------NRLVLGLV-LLNLIVSMWTLKLGNQRLAPYADHETLTFVR 53 KK +++ KS + + + +GL LL L+ S+ +L ++ D T+ F+ Sbjct: 15 KKSKKKKKSVLLFPKFFQKWSLIFIGLFSLLGLLASLNFPRLTMEKNMTPTDETTVAFIA 74 Query: 54 KISHAAQSVAQKKQLYSSVMMAQAILESNNGKSQLSQKPYYNFFGIKGSYKERSVIFPTL 113- +I ++ +A + LY+SVM+AQAILES++G+SQLSQKP YNFFGIKG Y +SV PT Sbjct: 75 EIGETSRYLAARNDLYASVMIAQAILESDSGQSQLSQKPLYNFFGIKGEYNGQSVTLPTW 134- Query: 114 EDDGQGNLYQIDAAFRSYGSLTACFLDYARVLNDPLYDKTHKKFWSHYQDATATLTGTYA 17- 3 EDDG+GN Y IDAAFRSYGS+ DY L Y H+ Y+DATA LTG YA Sbjct: 135 EDDGKGNPYHIDAAFRSYGSVENSLQDYVEFLEGSYYVGVHRSKTRSYKDATAALTGVYA 19- 4 Query: 174 TDTTYHTKLNELIEWYQLTNFD 195 TDTTY KLN +IE YQLT +D Sbjct: 195 TDTTYGDKLNSIIEQYQLTIYD 216 An alignment of the GAS and GBS proteins is shown below: TABLE-US-02241 Identities = 1244/1468 (84%), Positives = 1351/1468 (91%), Gaps = 3/1468 (0%) Query: 1 MSELFKKLMDQIEMPLEIKNSSVFSSADIIEVKVHSLSRLWEFHFSFPELLPIEVYRELQ 60 MS+LF KLMDQIEMPL+++ SS FSSADIIEVKVHS+SRLWEFHF+F +LPI YREL Sbjct: 1 MSDLFAKLMDQIEMPLDMRRSSAFSSADIIEVKVHSVSRLWEFHFAFAAVLPIATYRELH 60 Query: 61 TRLVNSFEKADIKATFDIRAETIDFSDDLLQDYYQQAFCEPLCNSASFKSSFSQLKVHYN 120- RL+ +FE ADIK TFDI+A +D+SDDLLQ YYQ+AF CNSASFKSSFS+LKV Y Sbjct: 61 DRLIRTFEAADIKVTFDIQAAQVDYSDDLLQAYYQEAFEHAPCNSASFKSSFSKLKVTYE 120- Query: 121 GSQMIISAPQFVNNNHFRQNHLPRLEQQFSLFGFGKLAIDMVSDEQMTQDLKSSFETNRE 18- 0 ++II+AP FVNN+HFR NHLP L +Q FGFG L IDMVSD++MT+ L +F ++R+ Sbjct: 121 DDKLIIAAPGFVNNDHFRNNHLPNLVKQLEAFGFGILTIDMVSDQEMTEHLTKNFVSSRQ 18- 0 Query: 181 QLLEKANQEAMQALEAQKSLEDSAPPSEEVTPTQNYDFKERIKQRQAGFEKAEITPMIEV 24- 0 L++KA Q+ LEAQKSLE PP EE TP +D+KER +RQAGFEKA ITPMIE+ Sbjct: 181 ALVKKAVQDN---LEAQKSLEAMMPPVEEATPAPKFDYKERAAKRQAGFEKATITPMIEI 23- 7 Query: 241 TTEENRIVFEGMVFSVERKTTRTGRHIINFKMTDYTSSFAMQKWAKDDEELKKYDMISKG 30- 0 TEENRIVFEGMVF VERKTTRTGRHIINFKMTDYTSSFA+QKWAKDDEEL+K+DMI+KG Sbjct: 238 ETEENRIVFEGMVFDVERKTTRTGRHIINFKMTDYTSSFALQKWAKDDEELRKFDMIAKG 29- 7 Query: 301 SWLRVRGNIENNNFTKSLTMNVQDIKEIVHHERKDLMPADQKRVEFHAHTNMSTMDALPT 36- 0 +WLRV+GNIE N FTKSLTMNVQ +KEIV HERKDLMP QKRVE HAHTNMSTMDALPT Sbjct: 298 AWLRVQGNIETNPFTKSLTMNVQQVKEIVRHERKDLMPEGQKRVELHAHTNMSTMDALPT 35- 7 Query: 361 VESLIDTAAKWGHPAIAITDHANVQSFPHGYHRAKKAGIKAIFGLEANIVEDKVPISYNE 42- 0 VESLIDTAAKWGH AIAITDHANVQSFPHGYHRA+KAGIKAIFGLEANIVEDKVPISY Sbjct: 358 VESLIDTAAKWGHKAIAITDHANVQSFPHGYHRARKAGIKAIFGLEANIVEDKVPISYEP 41- 7 Query: 421 VDMNLHEATYVVFDVETTGLSAANNDLIQIAASKMFKGNIIEQFDEFIDPGHPLSAFTTE 48- 0 VDM+LHEATYVVFDVETTGLSA NNDLIQIAASKMFKGNI+EQFDEFIDPGHPLSAFTTE Sbjct: 418 VDMDLHEATYVVFDVETTGLSAMNNDLIQIAASKMFKGNIVEQFDEFIDPGHPLSAFTTE 47- 7 Query: 481 LTGITDNHVRGSKPILQVLQEFQNFCQGTVLVAHNATFDVGFMNANYERHNLPLITQPVI 54- 0 LTGITD H++G+KP++ VL+ FQ+FC+ ++LVAHNA+FDVGFMNANYERH+LP ITQPVI Sbjct: 478 LTGITDKHLQGAKPLVTVLKAFQDFCKDSILVAHNASFDVGFMNANYERHDLPKITQPVI 53- 7 Query: 541 DTLEFARNLYPEYKRHGLGPLTKRFQVALEHHHMANYDAEATGRLLFIFLKEARENRDVT 60- 0 DTLEFARNLYPEYKRHGLGPLTKRFQV+L+HHHMANYDAEATGRLLFIFLK+ARE + Sbjct: 538 DTLEFARNLYPEYKRHGLGPLTKRFQVSLDHHHMANYDAEATGRLLFIFLKDAREKHGIK 59- 7 Query: 601 NLMELNTKLVAEDSYKKARIKHATIYVQNQVGLKNIFKLVSLSNVKYFEGVARIPRSVLD 66- 0 NL++LNT LVAEDSYKKARIKHATIYVQNQVGLKN+FKLVSLSN+KYFEGV RIPR+VLD Sbjct: 598 NLLQLNTDLVAEDSYKKARIKHATIYVQNQVGLKNMFKLVSLSNIKYFEGVPRIPRTVLD 65- 7 Query: 661 AHREGLLLGTACSDGEVFDALLSNGIDAAVTLAKYYDFIEVMPPAIYRPLVVRDLIKDEV 72- 0 AHREGLLLGTACSDGEVFDA+L+ GIDAAV LA+YYDFIE+MPPAIY+PLVVR+LIKD+ Sbjct: 658 AHREGLLLGTACSDGEVFDAVLTKGIDAAVDLARYYDFIEIMPPAIYQPLVVRELIKDQA 71- 7 Query: 721 GIQQIIRDLIEVGRRLDKPVLATGNVHYIEPEDEIYREIIVRSLGQGAMINRTIGRGEDA 78- 0 GI+Q+IRDLIEVG+R KPVLATGNVHY+EPE+EIYREIIVRSLGQGAMINRTIGRGE A Sbjct: 718 GIEQVIRDLIEVGKRAKKPVLATGNVHYLEPEEEIYREIIVRSLGQGAMINRTIGRGEGA 77- 7 Query: 781 QPAPLPKAHFRTTNEMLDEFAFLGKDLAYEIVVTNTNTFADRFEDVEVVKGDLYTPFVDR 84- 0 QPAPLPKAHFRTTNEMLDEFAFLGKDLAY++VV NT FADR E+VEVVKGDLYTP++D+ Sbjct: 778 QPAPLPKAHFRTTNEMLDEFAFLGKDLAYQVVVQNTQDFADRIEEVEVVKGDLYTPYIDK 83- 7 Query: 841 AEERVAELTYAKAFEIYGNPLPDIIDLRIEKELASILGNGFAVIYLASQMLVQRSNERGY 90- 0 AEE VAELTY KAFEIYGNPLPDIIDLRIEKEL SILGNGFAVIYLASQMLV RSNERGY Sbjct: 838 AEETVAELTYQKAFEIYGNPLPDIIDLRIEKELTSILGNGFAVIYLASQMLVNRSNERGY 89- 7 Query: 901 LVGSRGSVGSSFVATMIGITEVNPMPPHYVCPNCQHSEFITDGSCGSGYDLPNKNCPKCG 96- 0 LVGSRGSVGSSFVATMIGITEVNPMPPHYVCP+CQHSEFITDGS GSGYDLPNK CPKCG Sbjct: 898 LVGSRGSVGSSFVATMIGITEVNPMPPHYVCPSCQHSEFITDGSVGSGYDLPNKPCPKCG 95- 7 Query: 961 TLYKKDGQDIPFETFLGFDGDKVPDIDLNFSGDDQPSAHLDVRDIFGEEYAFRAGTVGTV 10- 20 T Y+KDGQDIPFETFLGFDGDKVPDIDLNFSGDDQPSAHLDVRDIFG+EYAFRAGTVGTV Sbjct: 958 TPYQKDGQDIPFETFLGFDGDKVPDIDLNFSGDDQPSAHLDVRDIFGDEYAFRAGTVGTV 10- 17 Query: 1021 AEKTAFGFVKGYERDYNKFYNDAEVERLATGAAGVKRSTGQHPGGIVVIPNYMDVYDFTP 1- 080 AEKTA+GFVKGYERDY KFY DAEV+RLA GAAGVKR+TGQHPGGIVVIPNYMDVYDFTP Sbjct: 1018 AEKTAYGFVKGYERDYGKFYRDAEVDRLAAGAAGVKRTTGQHPGGIVVIPNYMDVYDFTP 1- 077 Query: 1081 VQYPADDMTAAWQTTHFNFHDIDENVLKLDILGHDDPTMIRKLQDLSGIDPSNILPDDPD 1- 140 VQYPADD+TA+WQTTHFNFHDIDENVLKLDILGHDDPTMIRKLQDLSGIDP I DDP Sbjct: 1078 VQYPADDVTASWQTTHFNFHDIDENVLKLDILGHDDPTMIRKLQDLSGIDPITIPADDPG 1- 137 Query: 1141 VMKLFSGTEVLGVTEEQIGTPTGMLGIPEFGTNFVRGMVNETHPTTFAELLQLSGLSHGT 1- 200 VM LFSGTEVLGVT EQIGTPTGMLGIPEFGTNFVRGMVNETHPTTFAELLQLSGLSHGT Sbjct: 1138 VMALFSGTEVLGVTPEQIGTPTGMLGIPEFGTNFVRGMVNETHPTTFAELLQLSGLSHGT 1- 197 Query: 1201 DVWLGNAQDLIKEGIATLSTVIGCRDDIMVYLMHAGLQPKMAFTIMERVRKGLWLKISED 1- 260 DVWLGNAQDLIKEGIATL TVIGCRDDIMVYLMHAGL+PKMAFTIMERVRKGLWLKISE+ Sbjct: 1198 DVWLGNAQDLIKEGIATLKTVIGCRDDIMVYLMHAGLEPKMAFTIMERVRKGLWLKISEE 1- 257 Query: 1261 ERNGYIQAMRDNNVPDWYIESCGKIKYMFPKAHAAAYVLMALRVAYFKVHYPIFYYCAYF 1- 320 ERNGYI AMR+NNVPDWYIESCGKIKYMFPKAHAAAYVLMALRVAYFKVH+PI YYCAYF Sbjct: 1258 ERNGYIDAMRENNVPDWYIESCGKIKYMFPKAHAAAYVLMALRVAYFKVHHPIMYYCAYF 1- 317 Query: 1321 SIRAKAFELRTMSAGLDAVKARMKDITEKRQRNEATNVENDLFTTLELVNEMLERGFKFG 1- 380 SIRAKAFEL+TMS GLDAVKARM+DIT KR+ NEATNVENDLFTTLE+VNEMLERGFKFG Sbjct: 1318 SIRAKAFELKTMSGGLDAVKARMEDITIKRKNNEATNVENDLFTTLEIVNEMLERGFKFG 1- 377 Query: 1381 KLDLYRSHATDFIIEEDTLIPPFVAMEGLGENVAKQIVRAREDGEFLSKTELRKRGGVSS 1- 440 KLDLY+S A +F I+ DTLIPPF+A+EGLGENVAKQIV+AR++GEFLSK ELRKRGG SS Sbjct: 1378 KLDLYKSDAIEFQIKGDTLIPPFIALEGLGENVAKQIVKARQEGEFLSKMELRKRGGASS 1- 437 Query: 1441 TLVEKFDEMGILGNLPEDNQLSLFDDFF 1468 TLVEK DEMGILGN+PEDNQLSLFDDFF Sbjct: 1438 TLVEKMDEMGILGNMPEDNQLSLFDDFF 1465 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 753 A DNA sequence (GBSx0800) was identified in S. agalactiae <SEQ ID 2315> which encodes the amino acid sequence <SEQ ID 2316>. Analysis of this protein sequence reveals the following:

TABLE-US-02242 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1505 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10179> which encodes amino acid sequence <SEQ ID 10180> was also identified. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02243 >GP: CAB13207 GB: Z99111 similar to transcriptional regulator (MarR family) [Bacillus subtilis] Identities = 49/124 (39%), Positives = 73/124 (58%) Query: 18 VMRKAFRTIDGKVSESFKEFELTPTQFAVLDVLYAKGTMKIGELIENMLATSGNMTVVIK 77 - V +AF+++ KE PT+FAVL++LY +G K+ ++ +L SGN+T VI Sbjct: 20 VFARAFKSVSEHSIRDSKEHGFNPTEFAVLELLYTRGPQKLQQIGSRLLLVSGNVTYVID 79 Query: 78 NMEKKGWVLRHSCPNDKRAFLVSLTTEGEEVIKKALPEHIKRVEDAFSVLTETEQEDLIN 137- +E+ G+++R P DKR+ LT +G E + K P H R+ AFS L+ EQ+ LI Sbjct: 80 KLERNGFLVREQDPKDKRSVYAHLTDKGNEYLDKIYPIHALRIARAFSGLSPDEQDQLIV 139- Query: 138 LLKK 141 LLKK Sbjct: 140 LLKK 143 A related DNA sequence was identified in S. pyogenes <SEQ ID 2317> which encodes the amino acid sequence <SEQ ID 2318>. Analysis of this protein sequence reveals the following: TABLE-US-02244 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0537 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below: TABLE-US-02245 Identities = 80/145 (55%), Positives = 111/145 (76%), Gaps = 1/145 (0%) Query: 2 GDEMGNF-KNSAVKSMVVMRKAFRTIDGKVSESFKEFELTPTQFAVLDVLYAKGTMKIGE 60 G++M + KN+A+K+MVV RKA RT+D ++ FK+ +LT TQF+VL+VLY KG M+I Sbjct: 8 GNQMSHLDKNTALKAMVVFRKAQRTLDAFGADIFKKADLTATQFSVLEVLYTKGCMRINH 67 Query: 61 LIENMLATSGNMTVVIKNMEKKGWVLRHSCPNDKRAFLVSLTTEGEEVIKKALPEHIKRV 120- LI+++LATSGNMTVV+ NME+ GW+ + DKRA++V+LT +G +I+ LP+H+ RV Sbjct: 68 LIDSLLATSGNMTVVLNNMERNGWISKCKDKTDKRAYVVTLTDKGTRLIEAVLPKHVARV 127- Query: 121 EDAFSVLTETEQEDLINLLKKFKTL 145 E+AF+VLTE EQ LI LLKKFK L Sbjct: 128 EEAFAVLTEKEQLCLIELLKKFKQL 152 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 754 A DNA sequence (GBSx0801) was identified in S. agalactiae <SEQ ID 2319> which encodes the amino acid sequence <SEQ ID 2320>. Analysis of this protein sequence reveals the following: TABLE-US-02246 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3741 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02247 >GP: AAG05963 GB: AE004686 hypothetical protein [Pseudomonas aeruginosa] Identities = 115/203 (56%), Positives = 143/203 (69%), Gaps = 7/203 (3%) Query: 2 SFLEELKNRRSIYALGRNTEVSDEKIVEIIKEAVRQSPSAFNSQTSRVVILLNDEVTKFW 61 +FL +KNRR+IYAL + VS EKIVE++KEAV SPSAFNSQ+SRVV+L E +FW Sbjct: 4 AFLSSIKNRRTIYALDKQLPVSQEKIVELVKEAVSHSPSAFNSQSSRVVVLFGAEHEQFW 63 Query: 62 DELVANDLVETMKVQGAPETAIAGTKEKLASFGASKGTVLFFEDQDVVKSLQEQFVLYAD 121- + +A D E K+ P A A T+ KL SF A GTVLFFEDQ VV+ LQEQF LYAD Sbjct: 64 N--IAKD--ELKKI--VPADAFAATETKLNSFAAGAGTVLFFEDQTVVRQLQEQFALYAD 117- Query: 122 NFPVWSEQSTGIASVNTWTALSAELGLGGNLQHYNPVIDASVQAVYGVPASWKLRGQLNF 18- 1 NFPVWSEQ++G+A WTAL AE +G +LQHYNP++DA + +P SWKLR Q+ F Sbjct: 118 NFPVWSEQASGMAQFAVWTAL-AEHKVGASLQHYNPLVDAQTHKTWNLPESWKLRAQMPF 17- 6 Query: 182 GSIEAETGEKEFMNDDDRFKVIG 204 G+I A GEK F+ + +RFKV G Sbjct: 177 GAIAAPAGEKAFIAESERFKVFG 199 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 755 A DNA sequence (GBSx0802) was identified in S. agalactiae <SEQ ID 2321> which encodes the amino acid sequence <SEQ ID 2322>. Analysis of this protein sequence reveals the following: TABLE-US-02248 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2730 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02249 >GP: CAB62846 GB: AL035475 hypothetical protein [Plasmodium falciparum] (ver 2) Identities = 112/529 (21%), Positives = 217/529 (40%), Gaps = 67/529 (12%) Query: 3 NKKHKLLKNIEEFKTITQKRLTERGKFPYDTVHSTFEIKDENFIMERLKSSGLSNGKP-- 60 N K+ +K + ++ Q + E+ KF D H E + E FI E + + K Sbjct: 1063 NVKYNEMKGAKN-DSLNQNEIIEKEKF--DLQH---ENRSERFIEEEKQICIVDDKKNNI 1- 116 Query: 61 --VDYMGVNGIPIYTKTLSIVNKFAFENNSKDSSYSSNINISEDKIKENDQKILDLIVKS 118- VD + P Y + L + +N + YS+ DKI +N++ ++ K Sbjct: 1117 MNVDEKRKSDHPSYERVLKMEG-----SNKNEEGYSNT-----DKILKNEKNEKNVNEKK 1- 166 Query: 119 GANNQNLTDEEKVIAFTKYIGEITNYDNEAYRARNVDTEYYRASDLFSVTERKLAMCVGY 17- 8 G N++ +E+K K + E + ++E D + F +C Sbjct: 1167 GENDEKNENEKKEENDEKNVNEKKDENDEKNENEKKDENDNNNNSYFYNNSDTFELCTNS 1- 226 Query: 179 SVTAARAFNIMGIPSYVVSGKSPQGISHAAVRAYYNRSWHIIDITASTYWKNGNYKTTYS 23- 8 + N + IPS ++ +GI + N S I+ KN N ++ YS Sbjct: 1227 LIFINNKKNSILIPS-----ENEKGIIGSQKEEEQNISPVKINNKKKDLCKNIN-ESDYS 1- 280 Query: 239 DFIKEYCIDGYD--VYDPAKTNNRFK-VKYMESNEAFENWIHNNGSKSML-------FIN 28- 8 D ++ + +Y +N++ + ++ + NE + + + N S++ L ++ Sbjct: 1281 DKQYSVLLNSIEKKIYKKCSSNSKIRGIEKKKINEDYVDLKNINCSRNTLEFFLTKKYLK 1- 340 Query: 289 ESAALKDKKPKDDFVPVTEKEKNELIDKYKKLLSQIPENTQNPGEKNIRDYLKNEYEEIL 34- 8 S + ++ + V EK+K + K KKL +I N P + I + + +EY + Sbjct: 1341 SSELIINEHDCQNINNVYEKKKKKEQAK-KKLNRKI--NVNIPNDSIIEENMSSEYNFVK 1- 397 Query: 349 KKDN----LFEHEHAE-------FKESLNLNESFYLQLKKEE-------MKPSDNLKKEE 39- 0 KK+N FE + ++ F N + L +E+ ++ +N K+ E Sbjct: 1398 KKNNNCMVKFETKRSKSILSSEIFAVKKNKKRATNLMRSEEQFISSIGLVEKGENKKRIE 1- 457 Query: 391 KPRENSVKERETPAENNDFVSVTEKNNLIDKYKELLSKIPENTQNPGEKNIRN--YLEKE 44- 8 + E +KE+ + N+F KNNL ++ L K EN G N ++++ Sbjct: 1458 EKDEEYIKEK-IKNKKNEF-----KNNLTEQL--LFFKSAENINTSGSFNTEKIRHVKRT 1- 509 Query: 449 YEELLQKDKLFKHEYTEFTKSLNLNETFYSQLKEGEMKLSENPEKGETN 497 ++ + + ++ K L E ++ E + ++++N EKGE N Sbjct: 1510 KRKVNLSNNFILNNFSNILKKLQRMEEDKIKMDEQKKEINKNNEKGEFN 1558 There is also homology to SEQ ID 598. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 756 A DNA sequence (GBSx0803) was identified in S. agalactiae <SEQ ID 2323> which encodes the amino acid sequence <SEQ ID 2324>. Analysis of this protein sequence reveals the following: TABLE-US-02250 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1243 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 757 A DNA sequence (GBSx0804) was identified in S. agalactiae <SEQ ID 2325> which encodes the amino acid sequence <SEQ ID 2326>. This protein is predicted to be 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate al. Analysis of this protein sequence reveals the following: TABLE-US-02251 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1057 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02252 >GP: AAD35160 GB: AE001693 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase [Thermotoga maritima] Identities = 78/192 (40%), Positives = 118/192 (60%), Gaps = 6/192 (3%) Query: 14 KIVAVIRGNSQEEAFQAAQACIKGGISAIEIAYTNSKASQVIEQLVTQYTNQEQVVVGAG 73 - KIVAV+R NS EEA + A A +GG+ IEI +T A VI++L + ++ ++GAG Sbjct: 11 KIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKEL--SFLKEKGAIIGAG 68 Query: 74 TVLDSETARMAILAGAKFIVSPAFNLQTAKLCNRYAIPYLPGCMTLSEVTTALEAGCEII 133- TV E R A+ +GA+FIVSP + + ++ C + Y+PG MT +E+ A++ G I+ Sbjct: 69 TVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTIL 128- Query: 134 KIFPGGTLGTSFISSLKAPLPQVQIMVTGGVNLTNAKDWFLSGVTAIGIGGEFNKLAALG 19- 3 K+FPG +G F+ ++K P P V+ + TGGVNL N +WF +GV A+G+G K G Sbjct: 129 KLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVK----G 18- 4 Query: 194 EFDKITEMAKQY 205 D++ E AK + Sbjct: 185 TPDEVREKAKAF 196 There is also homology to SEQ ID 1252. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 758 A DNA sequence (GBSx0805) was identified in S. agalactiae <SEQ ID 2327> which encodes the amino acid sequence <SEQ ID 2328>. This protein is predicted to be 2-keto-3-deoxygluconate kinase. Analysis of this protein sequence reveals the following: TABLE-US-02253 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4113 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02254 >GP: AAD35161 GB: AE001693 2-keto-3-deoxygluconate kinase [Thermotoga maritima] Identities = 94/329 (28%), Positives = 169/329 (50%), Gaps = 7/329 (2%) Query: 3 KILFFGEPLIRITPKENDYFADSISTKLFYGGSEVNTARALQGFGQDTKLLSALPNNPIG 62 K++ FGE ++R++P ++ + S + YGG+E N A L G D ++ LPNNP+G Sbjct: 2 KVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLG 61 Query: 63 NSFLQFLKAQGIDTHSIQWVGERVGLYFLEDSFACRKGEVVYDRDHSSLHDFRINQIDFD 122- ++ L+ G+ T I G R+G+YFLE + R +VVYDR HS++ + + D++ Sbjct: 62 DAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121- Query: 123 QLFEGVSLFHFSGITLSLDESIQEITLLLLKEAKKREITISLDLNFRSKLISPKNAKILF 18- 2 ++ +G FHFSGIT L + + I LK A ++ +T+S DLN+R++L + + A+ + Sbjct: 122 KILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEAQKVM 18- 1 Query: 183 SQFATFADICFG----IEPLMVDSQDTTFFNRDEATIEDVKERMISLINHFDFQVIFHTK 23- 8 F + D+ IE ++ S + + E + + ++F+ + T Sbjct: 182 IPFMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKYNFKTVGITL 24- 1 Query: 239 RLQDEWGRNHYQAYI-ANRKQEFVTSKEITTAVNQRIGSGDAFVAGALYQLLQHSDSKTV 29- 7 R N++ + N + F EI + R+G+GD+F +Y L DS+ Sbjct: 242 RESISATVNYWSVMVFENGQPHFSNRYEI--HIVDRVGAGDSFAGALIYGSLMGFDSQKK 29- 9 Query: 298 IDFAVASASLKCALEGDNMFETVTAVNKV 326 +FA A++ LK + GD + ++ + K+ Sbjct: 300 AEFAAAASCLKHTIPGDFVVLSIEEIEKL 328 There is also homology to SEQ ID 1264. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 759 A DNA sequence (GBSx0806) was identified in S. agalactiae <SEQ ID 2329> which encodes the amino acid sequence <SEQ ID 2330>. Analysis of this protein sequence reveals the following: TABLE-US-02255 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.22 Transmembrane 53-69 (53-70) ----- Final Results ----- bacterial membrane --- Certainty = 0.1086 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-02256 >GP: AAD36157 GB: AE001768 sugar-phosphate isomerase [Thermotoga maritima] Identities = 41/125 (32%), Positives = 61/125 (48%), Gaps = 10/125 (8%) Query: 1 MKIALINENSQASKNTIIYKELKAVSDEKGFEVFNYGMYGKEEESQLTYVQNGLLTAILL 60 MKIA+ ++++ + +++K KG EV ++G Y +E Y + ++ +IL Sbjct: 1 MKIAIASDHAAFE----LKEKVKNYLLGKGIEVEDHGTYSEESVDYPDYAKK-VVQSILS 55 Query: 61 NSGAADFVITGCGTGIGAMLACNSFPGVVCGFAADPVDAYLFSQVNGGNALSLPFAKGFG 120- N ADF I CGTG+G +A N + G+ P A L N N L LP G Sbjct: 56 NE--ADFGILLCGTGLGMSIAANRYRGIRAALCLFPDMARLARSHNNANILVLP---GRL 110- Query: 121 WGAEL 125 GAEL Sbjct: 111 IGAEL 115 A related DNA sequence was identified in S. pyogenes <SEQ ID 2331> which encodes the amino acid sequence <SEQ ID 2332>. Analysis of this protein sequence reveals the following: TABLE-US-02257 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2599 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02258 Identities = 159/212 (75%), Positives = 186/212 (87%) Query: 1 MKIALINENSQASKNTIIYKELKAVSDEKGFEVFNYGMYGKEEESQLTYVQNGLLTAILL 60 MKIALINENSQA+KN IIY L V+D+ G++VFNYGMYG E ESQLTYVQNGLL +ILL Sbjct: 1 MKIALINENSQAAKNGIIYDALTTVTDKHGYQVFNYGMYGTEGESQLTYVQNGLLASILL 60 Query: 61 NSGAADFVITGCGTGIGAMLACNSFPGVVCGFAADPVDAYLFSQVNGGNALSLPFAKGFG 120- + AADFV+TGCGTG+GAMLA NSFPGV CGFA++P +AYLFSQ+NGGNALS+PFAKGFG Sbjct: 61 TTKAADFVVTGCGTGVGAMLALNSFPGVTCGFASEPTEAYLFSQINGGNALSIPFAKGFG 120- Query: 121 WGAELNLRYLFERLFEDEKGGGYPKERAVPEQRNARILSEIKQITYRDLLSVLKEIDQDF 18- 0 WGAELNL +FERLF + GGGYPKERA+PEQRNARILS++K+ITYRDLL+++K+IDQDF Sbjct: 121 WGAELNLTLIFERLFAEPMGGGYPKERAIPEQRNARILSDLKKITYRDLLAIVKDIDQDF 18- 0 Query: 181 LKETISGEHFQEYFFANCQNQNIADYLKSVLD 212 LKETISG HFQEYFFAN + + YLKSVL+ Sbjct: 181 LKETISGAHFQEYFFANAEPSELVTYLKSVLE 212 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 760 A DNA sequence (GBSx0807) was identified in S. agalactiae <SEQ ID 2333> which encodes the amino acid sequence <SEQ ID 2334>. Analysis of this protein sequence reveals the following: TABLE-US-02259 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 10-26 (8-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 761 A DNA sequence (GBSx0808) was identified in S. agalactiae <SEQ ID 2335> which encodes the amino acid sequence <SEQ ID 2336>. This protein is predicted to be gluconate 5-dehydrogenase (fabG). Analysis of this protein sequence reveals the following: TABLE-US-02260 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1117 (Affirmative) < succ> bacterial membrane --- Certainty = 0.000 (Not Clear) < succ> bacterial outside --- Certainty = 0.000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02261 >GP: AAC77223 GB: AE000497 5-keto-D-gluconate 5-reductase [Escherichia coli K12] Identities = 116/260 (44%), Positives = 165/260 (62%), Gaps = 6/260 (2%) Query: 6 LKDNFSLEGKVALITGASYGIGFSIATAFARAGATIVFNDIKQELVDKGISAYKKLGIKA 65 + D FSL GK LITG++ GIGF +AT + GA I+ NDI E + + + GI+A Sbjct: 1 MNDLFSLAGKNILITGSAQGIGFLLATGLGKYGAQIIINDITAERAELAVEKLHQEGIQA 60 Query: 66 HGYVCDVTDEDGINEMVDKISQDVGVIDILVNNAGIIKRTPMLEMSAADFRQVIDIDLNA 125- +VT + I+ V+ I +D+G ID+LVNNAGI +R P E ++ VI ++ A Sbjct: 61 VAAPFNVTHKHEIDAAVEHIEKDIGPIDVLVNNAGIQRRHPFTEFPEQEWNDVIAVNQTA 120- Query: 126 PFIVSKAVLPGMIQKGHGKIINICSMMSELGRETVAAYAAAKGGLKMLTKNIASEYGSAN 18- 5 F+VS+AV M+++ GK+INICSM SELGR+T+ YAA+KG +KMLT+ + E N Sbjct: 121 VFLVSQAVTRHMVERKAGRVINICSMQSELGRDTITPYAASKGAVKMLTRGMCVELARHN 18- 0 Query: 186 IQCNGIGPGYIATPQTAPLRERQDDGSRHPFDQFIIAKTPAARWGEAEDLGAPAIFLASD 24- 5 IQ NGI PGY T T L E + F ++ +TPAARWG+ ++L A+FL+S Sbjct: 181 IQVNGIAPGYFKTEMTKALVEDE------AFTAWLCKRTPAARWGDPQELIGAAVFLSSK 23- 4 Query: 246 ASNFINGHILYVDGGILAYI 265 AS+F+NGH+L+VDGG+L + Sbjct: 235 ASDFVNGHLLFVDGGMLVAV 254 There is also homology to SEQ ID 1242: TABLE-US-02262 Identities = 225/264 (85%), Positives = 246/264 (92%) Query: 6 LKDNFSLEGKVALITGASYGIGFSIATAFARAGATIVFNDIKQELVDKGISAYKKLGIKA 65 +++ FSL+GK+ALITGASYGIGF IA A+A+AGATIVFNDIKQELVDKG++AY++LGI+A Sbjct: 1 MENMFSLQGKIALITGASYGIGFEIAKAYAQAGATIVFNDIKQELVDKGLAAYRELGIEA 60 Query: 66 HGYVCDVTDEDGINEMVDKISQDVGVIDILVNNAGIIKRTPMLEMSAADFRQVIDIDLNA 125- HGYVCDVTDE GI +MV +I +VG IDILVNNAGII+RTPMLEM+A DFRQVIDIDLNA Sbjct: 61 HGYVCDVTDEAGIQQMVSQIEDEVGAIDILVNNAGIIRRTPMLEMAAEDFRQVIDIDLNA 120- Query: 126 PFIVSKAVLPGMIQRGHGKIINICSMMSELGRETVAAYAAAKGGLKMLTKNIASEYGSAN 18- 5 PFIVSKAVLP MI KGHGKIINICSMMSELGRETV+AYAAAKGGLKMLTKNIASE+G AN Sbjct: 121 PFIVSKAVLPSMIAKGHGKIINICSMMSELGRETVSAYAAAKGGLKMLTKNIASEFGEAN 18- 0 Query: 186 IQCNGIGPGYIATPQTAPLRERQDDGSRHPFDQFIIAKTPAARWGEAEDLGAPAIFLASD 24- 5 IQCNGIGPGYIATPQTAPLRERQ DGSRHPFDQFIIAKTPAARWG EDL PA+FLASD Sbjct: 181 IQCNGIGPGYIATPQTAPLRERQADGSRHPFDQFIIAKTPAARWGTTEDLAGPAVFLASD 24- 0 Query: 246 ASNFINGHILYVDGGILAYIGKQP 269 ASNF+NGHILYVDGGILAYIGKQP Sbjct: 241 ASNFVNGHILYVDGGILAYIGKQP 264 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 762 A DNA sequence (GBSx0809) was identified in S. agalactiae <SEQ ID 2337> which encodes the amino acid sequence <SEQ ID 2338>. This protein is predicted to be mannose-specific phosphotransferase system component IIAB. Analysis of this protein sequence reveals the following: TABLE-US-02263 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0886 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02264 >GP: AAD46485 GB: AF130465 mannose-specific phosphotransferase system component IIAB [Streptococcus salivarius] Identities = 43/107 (40%), Positives = 61/107 (56%), Gaps = 3/107 (2%) Query: 2 IKIIIVAHGNFPDGILSSLELIAGHQEYVVGINFIAGMSSNDVRVALQREVIDFK---EI 58 I III +HG F +GI S +I G QE V + F+ +D+ + F EI Sbjct: 3 IGIIIASHGKFAEGIHQSGSMIFGDQEKVQVVTFMPSEGPDDLYAHFNDAIAQFDADDEI 62 Query: 59 LVLTDLLGGTPFNVSSALSVEYTDKKIKVLSGLNLSMLMEAVLSRTM 105 LVL DL G+PFN +S ++ E D+KI +++GLNL ML++A R M Sbjct: 63 LVLADLWSGSPFNQASRIAGENPDRKIAIITGLNLPMLIQAYTERMM 109 A related DNA sequence was identified in S. pyogenes <SEQ ID 2339> which encodes the amino acid sequence <SEQ ID 2340>. Analysis of this protein sequence reveals the following: TABLE-US-02265 Possible site: 41 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02266 >GP: AAF81086 GB: AF228498 AgaF [Escherichia coli] Identities = 48/127 (37%), Positives = 71/127 (55%), Gaps = 6/127 (4%) Query: 1 MIAIIVMGNGHFASGIVSALELIAGKQEKVTAIDFTTEMTAADVQDQLSRALIP---EEE 57 M++II+ GHG FASG+ A++ I G+Q + AID + A + QL A+ E+ Sbjct: 1 MLSIILTGHGGFASGMEKAMKQILGEQSQFIAIDVPETSSTALLTSQLEEAIAQLDCEDG 60 Query: 58 TLVLCDLLGGTPFKVAATLMESLPNTTCNVLSGLNLAMLIEASFARQTAASFDDLVSGLI 117- + L DLLGGTPF+VA+TL P C V++G NL +L+E R+ + + V L Sbjct: 61 IVFLTDLLGGTPFRVASTLAMQKPG--CEVITGTNLQLLLEMVLEREGLSGEEFRVQAL- 117- Query: 118 TCSKEGI 124 C G+ Sbjct: 118 ECGHRGL 124 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02267 Identities = 73/146 (50%), Positives = 94/146 (64%), Gaps = 3/146 (2%) Query: 1 MIKIIIVAHGNFPDGILSSLELIAGHQEYVVGINFIAGMSSNDVRVALQREVIDFKEILV 60 MI II++ HG+F GI+S+LELIAG QE V I+F M++ DV+ L R +I +E LV Sbjct: 1 MIAIIVMGHGHFASGIVSALELIAGKQEKVTAIDFTTEMTAADVQDQLSRALIPEEETLV 60 Query: 61 LTDLLGGTPFNVSSALSVEYTDKKIKVLSGLNLSMLMEAVLSRTMFEHVDDLVDKVITSS 120- L DLLGGTPF V++ L + VLSGLNL+ML+EA +R DDLV +IT S Sbjct: 61 LCDLLGGTPFKVAATLMESLPNTTCNVLSGLNLAMLIEASFARQTAASFDDLVSGLITCS 120- Query: 121 HEGIVDFSTCLATQTAEATFE--GGI 144 EGIVD+ T L+ Q AT + GGI Sbjct: 121 KEGIVDWKT-LSQQEDGATDDELGGI 145 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 763 A DNA sequence (GBSx0811) was identified in S. agalactiae <SEQ ID 2341> which encodes the amino acid sequence <SEQ ID 2342>. This protein is predicted to be unsaturated glucuronyl hydrolase. Analysis of this protein sequence reveals the following: TABLE-US-02268 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.11 Transmembrane 172-188 (172-188) ----- Final Results ----- bacterial membrane --- Certainty = 0.1044 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02269 >GP: BAB05773 GB: AP001514 unsaturated glucuronyl hydrolase [Bacillus halodurans] Identities = 156/370 (42%), Positives = 219/370 (59%), Gaps = 3/370 (0%) Query: 30 EEAIEKALKQLYINIDYFGEEYPTPATFNNIYKVMDNTEWTNGFWTGCLWLAYEYNQDKK 89 - ++A+ ++ NI F +P + Y++ +N EWTNGFW+G LWL YEY D Sbjct: 4 KQAMTDVAEKTLTNIKRFNGRFPHVSEDGEHYELNNNNEWTNGFWSGILWLCYEYTNDPA 63 Query: 90 LKNIAHKNVLSFLNRINNRIALDHHDLGFLYTPSCTAEYRINGDVKALEATIKAADKLME 149- + A V SF R+ + LDHHD+GFLY+ S A++ I D +A + TI+AAD LM+ Sbjct: 64 FRQAAASTVRSFQQRMEQNLELDHHDIGFLYSLSSKAQWIIERDERAKQLTIEAADVLMK 123- Query: 150 RYQEKGGFIQAWGELG-YKEHYRLIIDCLLNIQLLFFAYEQTGDEKYRQVAVNHFYASAN 20- 8 R++EK QAWG G R+I+DCL+N+ LLF+A E TG+ YR+ A+ H + Sbjct: 124 RWREKIELFQAWGPEGDLSNGGRIIVDCLMNLPLLFWASEVTGNPDYREAAIIHADKTRR 18- 3 Query: 209 NVVRDDSSAFHTFYFDPETGEPLKGVTRQGYSDESSWARGQAWGIYGIPLSYRKMKDYQQ 26- 8 +VR D S +HTFYF+ ETGE L+G T QGY D S+W+RGQAW IYG ++YR + + Sbjct: 184 FIVRGDDSTYHTFYFNQETGEALRGGTHQGYEDGSTWSRGQAWAIYGFAIAYRYTGNERY 24- 3 Query: 269 IILFKGMTNYFLNRLPEDKVSYWDLIFTDGSGQPRDTSATATAVCGIHEMLKYLPEVDPD 32- 8 + K YF+ LP D V+YWD RD+SA+A A CGI E+L +L E DPD Sbjct: 244 LETAKRTAKYFIENLPADYVAYWDFNAPITPDTKRDSSASAIASCGILELLSHLQETDPD 30- 3 Query: 329 KETYKYAMHTMLRSLIEQYSNNELIAGRPLLLHGVYSWHSGKGVDEGNIWGDYYYLEALI 38- 8 K ++ ++ + SL+E Y++ + G L+ G YS G D+ IWGDY+Y EAL+ Sbjct: 304 KAFFQQSVQKQMTSLVENYASEKDAQG--LIKRGSYSVRIGHAPDDYVIWGDYFYTEALM 36- 1 Query: 389 RFYKDWELYW 398 R K YW Sbjct: 362 RLEKLRNGYW 371 A related DNA sequence was identified in S. pyogenes <SEQ ID 2343> which encodes the amino acid sequence <SEQ ID 2344>. Analysis of this protein sequence reveals the following: TABLE-US-02270 Possible site: 33 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 173-189 (173-189) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02271 Identities = 273/395 (69%), Positives = 336/395 (84%) Query: 4 IKPVKVESIENPKRFLNSRLLTKIEVEEAIEKALKQLYINIDYFGEEYPTPATFNNIYKV 63 +K + +E I+ P+RF L++ ++ +A++ ALKQ+ +N+DYF E++PTPAT +N Y + Sbjct: 5 LKTIALEPIKQPERFTKEDFLSQEDITQALDLALKQVRLNMDYFKEDFPTPATKDNQYAI 64 Query: 64 MDNTEWTNGFWTGCLWLAYEYNQDKKLKNIAHKNVLSFLNRINNRIALDHHDLGFLYTPS 123- MDNTEWTN FWTGCLWLAYEY+ D +K +A N LSFL+R+ I LDHHDLGFLYTPS Sbjct: 65 MDNTEWTNAFWTGCLWLAYEYSGDDAIKALAQANDLSFLDRVTRDIELDHHDLGFLYTPS 124- Query: 124 CTAEYRINGDVKALEATIKAADKLMERYQEKGGFIQAWGELGYKEHYRLIIDCLLNIQLL 18- 3 C AE+++ ++ EA +KAADKL++RYQ+KGGFIQAWGELG KE YRLIIDCLLNIQLL Sbjct: 125 CMAEWKLLKTPESREAALKAADKLVQRYQDKGGFIQAWGELGKKEDYRLIIDCLLNIQLL 18- 4 Query: 184 FFAYEQTGDEKYRQVAVNHFYASANNVVRDDSSAFHTFYFDPETGEPLKGVTRQGYSDES 24- 3 FFA ++TGD +YR +A+NHFYASAN+V+RDD+SA+HTFYFDPETG+P+KGVTRQGYSD+S Sbjct: 185 FFASQETGDNRYRDMAINHFYASANHVIRDDASAYHTFYFDPETGDPVKGVTRQGYSDDS 24- 4 Query: 244 SWARGQAWGIYGIPLSYRKMKDYQQIILFKGMTNYFLNRLPEDKVSYWDLIFTDGSGQPR 30- 3 +WARGQAWGIYGIPL+YR +K+ + I LFKGMT+YFLNRLP+D+VSYWDLIF DGS Q R Sbjct: 245 AWARGQAWGIYGIPLTYRFLKEPELIQLFKGMTHYFLNRLPKDQVSYWDLIFGDGSEQSR 30- 4 Query: 304 DTSATATAVCGIHEMLKYLPEVDPDKETYKYAMHTMLRSLIEQYSNNELIAGRPLLLHGV 36- 3 D+SATA AVCGIHEMLK LP+ DPDK+TY+ AMH+MLR+LI+ Y+N +L G PLLLHGV Sbjct: 305 DSSATAIAVCGIHEMLKTLFDHDPDKKTYEAAMHSMLRALIKDYANKDLKPGAPLLLHGV 36- 4 Query: 364 YSWHSGKGVDEGNIWGDYYYLEALIRFYKDWELYW 398 YSWHSGKGVDEGNIWGDYYYLEAL+RFYKDW YW Sbjct: 365 YSWHSGKGVDEGNIWGDYYYLEALLRFYKDWNPYW 399 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 764 A DNA sequence (GBSx0812) was identified in S. agalactiae <SEQ ID 2345> which encodes the amino acid sequence <SEQ ID 2346>. Analysis of this protein sequence reveals the following: TABLE-US-02272 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3035 (Atfirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02273 >GP: AAC44679 GB: U65015 PTS permease for mannose subunit IIIMan C terminal domain [Vibrio furnissii] Identities = 63/125 (50%), Positives = 89/125 (70%), Gaps = 1/125 (0%) Query: 5 PNIVMTRVDERLIHGQ-GQLWVKFLSCNTVIVANDDVSKDHLQQTLMKTVVPESIALRFF 63 PNIV++R+DERL+HGQ G WV F N V+VAND+V+ D +QQ LM+ V+ + IA+RF+ Sbjct: 2 PNIVLSRIDERLVHGQVGVQWVGFADANIVVVANDEVAADTIQQNLMEMVLADGIAIRFW 61 Query: 64 DIQKVIDIIHKANPAQTIFIIVKDLKDVYRLVAGGVPIKEINIGNIHNGEGKEQVSRSIF 123- +QK ID IHKA+ Q I ++ K D RLV GGVPI IN+GN+H +GK Q+S+++ Sbjct: 62 TVQKTIDTIHKASDRQRILLVCKTPHDFRRLVEGGVPIAAINVGNMHYIDGKTQISKTVS 121- Query: 124 LGMKD 128 + +D Sbjct: 122 VDAED 126 A related DNA sequence was identified in S. pyogenes <SEQ ID 2347> which encodes the amino acid sequence <SEQ ID 2348>. Analysis of this protein sequence reveals the following: TABLE-US-02274 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2511 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02275 >GP: BAA84216 GB: AB019619 unsaturated glucuronyl hydrolase [Bacillus sp. GL1] Identities = 161/369 (43%), Positives = 220/369 (58%), Gaps = 1/369 (0%) Query: 32 QALDLALKQVRLNMDYFKEDFPTPATKDNQYAIMDNTEWTNAFWTGCLWLAYEYSGDDAI 91 - QA+ AL N+ F + FP + N+Y + DNT+WT+ FW+G LWL YEY+GD+ Sbjct: 4 QAIGDALGITARNLKKFGDRFPHVSDGSNKYVLNDNTDWTDGFWSGILWLCYEYTGDEQY 63 Query: 92 KALAQANDLSFLDRVTRDIELDHHDLGFLYTPSCMAEWKLLKTPESREAALKAADKLVQR 151- + A SF +R+ R LDHHD+GFLY+ S A+W + K +R+ AL AAD L++R Sbjct: 64 REGAVRTVASFRERLDRFENLDHHDIGFLYSLSAKAQWIVEKDESARKLALDAADVLMRR 123- Query: 152 YQDKGGFIQAWGELGKKEDY-RLIIDCLLNIQLLFFASQETGDNRYRDMAINHFYASANH 21- 0 ++ G IQAWG G E+ R+IIDCLLN+ LL +A ++TGD YR +A H S Sbjct: 124 WRADAGIIQAWGPKGDPENGGRIIIDCLLNLPLLLWAGEQTGDPEYRRVAEAHALKSRRF 18- 3 Query: 211 VIRDDASAYHTFYFDPETGDPVKGVTRQGYSDDSAWARGQAWGIYGIPLTYRFLKEPELI 27- 0 ++R D S+YHTFYFDPE G+ ++G T QG +D S W RGQAWGIYG L R+L +L+ Sbjct: 184 LVRGDDSSYHTFYFDPENGNAIRGGTHQGNTDGSTWTRGQAWGIYGFALNSRYLGNADLL 24- 3 Query: 271 QLFKGMTHYFLNRLPKDQVSYWDLIFGDGSEQSRDSSATAIAVCGIHEMLKTLPDHDPDK 33- 0 + K M +FL R+P+D V YWD RDSSA+AI CG+ E+ L + DP++ Sbjct: 244 ETAKRMARHFLARVPEDGVVYWDFEVPQEPSSYRDSSASAITACGLLEIASQLDESDPER 30- 3 Query: 331 KTYEAAMHSMLRALIKDYANKDLKPGAPLLLHGVYSWHSGKGVDEGNIWGDYYYLEALLR 39- 0 + + A + + AL YA +D + G Y G D+ IWGDYYYLEALLR Sbjct: 304 QRFIDAAKTTVTALRDGYAERDDGEAEGFIRRGSYHVRGGISPDDYTIWGDYYYLEALLR 36- 3 Query: 391 FYKDWNPYW 399 + YW Sbjct: 364 LERGVTGYW 372 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-02276 Identities = 112/160 (70%), Positives = 132/160 (82%), Gaps = 1/160 (0%) Query: 5 PNIVMTRVDERLIHGQGQLWVKFLSCNTVIVANDDVSKDHLQQTLMKTVVPESIALRFFD 64 PNI+MTRVDERLIHGQGQLWVKFL+CNTVIVAND VS+D +QQ+LMKTV+P SIA+RFF Sbjct: 4 PNIIMTRVDERLIHGQGQLWVKFLNCNTVIVANDAVSEDKIQQSLMKTVIPSSIAIRFFS 63 Query: 65 IQKVIDIIHKANPAQTIFIIVKDLKDVYRLVAGGVPIKEINIGNIHNGEGKEQVSRSIFL 124- IQKVIDIIHKA+PAQ+IFI+VKDL+ D LV GGVPI EINIGNIH + K +++ I L Sbjct: 64 IQKVIDIIHKASPAQSIFIVVKDLQDAKLLVEGGVPITEINIGNIHKTDDKVAITQFISL 123- Query: 125 GMKDKEIIRKLNQEYHIAFNTKTTPTGNDGAVEVNILDYI 164 G DK IR L ++H+ FNTKTTP GN A +V+ILDYI Sbjct: 124 GETDKSAIRCLAHDHHVVFNTKTTPAGN-SASDVDILDYI 162 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 765 A DNA sequence (GBSx0813) was identified in S. agalactiae <SEQ ID 2349> which encodes the amino acid sequence <SEQ ID 2350>. This protein is predicted to be AgaW (agaC). Analysis of this protein sequence reveals the following: TABLE-US-02277 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.95 Transmembrane 251-267 (244-269) INTEGRAL Likelihood = -4.30 Transmembrane 213-229 (208-230) INTEGRAL Likelihood = -2.71 Transmembrane 149-165 (148-165) INTEGRAL Likelihood = -1.81 Transmembrane 31-47 (31-49) INTEGRAL Likelihood = -1.49 Transmembrane 173-189 (173-189) ----- Final Results ----- bacterial membrane --- Certainty = 0.3781 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02278 >GP: AAF81084 GB: AF228498 AgaW [Escherichia coli] Identities = 93/295 (31%), Positives = 140/295 (46%), Gaps = 48/295 (16%) Query: 1 MDISILQAVLIGLWTAFCFSGMLLGL-YTNRCIVLSLGVGVILGDIQTALAVGAISELAY 59 M+IS+LQA +G+ M GL + +R +VL VG++LGD+ T + G EL + Sbjct: 1 MEISLLQAFALGIIAFIAGLDMFNGLTHMHRPVVLGPLVGLVLGDLHTGILTGGTLELVW 60 Query: 60 MGFGVGAGGTVPPNPIGPGIFGTLMAITTAGTKGKITPEAALALSTPIAVGIQFLQTATY 119- MG AG PPN I I GT AITT + P+ A+ ++ P AV +Q T + Sbjct: 61 MGLAPLAGAQ-PPNVIIGTIVGTAFAITTG-----VKPDVAVGVAVPFAVAVQMGITFLF 114- Query: 120 TAFAGAPETAKK--------ALQAGNFRGFKIAANGT-IWAFAGLGFGLGVLGALSTQTL 17- 0 + +G + AL A N+ N + AF + FG A +T+ Sbjct: 115 SVMSGVMSRCARMPRTPILAALNACNYLALLALGNFYFLCAFLPIYFG-----AEHAKTI 16- 9 Query: 171 TDLFALIPPVLLNGLTLAGKMLPAIGFAMILSVMAKKELIPYILLGYVLAVYFGLPVLTP 23- 0 D+ +P L++GL +AG ++PAIGFA++L +M K IPY +LG+V A + LPVL Sbjct: 170 IDV---LPQRLIDGLGVAGGIMPAIGFAVLLKIMMKNVYIPYFILGFVAAAWLKLPVL-- 22- 4 Query: 231 TANGDGVLTSVATNSVLGVPTIGVAIIATIFALLDIFRKPAAPTKETKTEGDNQD 285 +A A AL+D+ RK PT+ + + +D Sbjct: 225 ----------------------AIACPALAMALIDLLRKSPEPTQPAAQKEEFED 257 A related DNA sequence was identified in S. pyogenes <SEQ ID 2351> which encodes the amino acid sequence <SEQ ID 2352>. Analysis of this protein sequence reveals the following: TABLE-US-02279 Possible site: 52 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.37 Transmembrane 220-236 (214-241) INTEGRAL Likelihood = -5.10 Transmembrane 146-162 (144-165) INTEGRAL Likelihood = -1.59 Transmembrane 184-200 (184-202) ----- Final Results ----- bacterial membrane --- Certainty = 0.3548 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02280 >GP: AAC44680 GB: U65015 PTS permease for mannose subunit IIPMan [Vibrio furnissii] Identities = 86/255 (33%), Positives = 137/255 (53%), Gaps = 11/255 (4%) Query: 1 MDINLLQALLIGLWTAFCFSGMLLGI-YTNRCIILSFGVGIILGDLPTALSMGAISELAY 59 M+I L QAL++GL + G+ + +R ++L VG+ILGDL T + +G EL + Sbjct: 1 MEIGLFQALMLGLLAFLAGLDLFNGLTHFHRPVVLGPLVGLILGDLHTGILVGGTLELIW 60 Query: 60 MGFGVGAGGTVPPNPIGPGIFGTLMAITSAGKVTPEAALALSTPIAVAIQFLQTFAYTAF 119- MG AG PPN I I GT AIT+ V P A+ ++ P AVA+Q T ++A Sbjct: 61 MGLAPLAGAQ-PPNVIIGTIVGTTFAITT--NVEPNVAVGVAVPFAVAVQMGITLLFSAM 117- Query: 120 AGAPETAKKQLQKGNIRGFK---FAANGTIWAFAFIGLGLGLLGALSMDTLLHLVDYIPP 17- 6 + + + + RG + + A + +F F+ L + L D +V +P Sbjct: 118 SAVMSKCDEYAKNADTRGIERVNYFALAVLGSFYFLCAFLPIY--LGADHAGAMVAALPK 17- 5 Query: 177 VLLNGLTVAGKMLPAIGFAMILSVMAKKELIPFVLIGYVCAAYLQIPTIGIAIIGIIFAL 23- 6 L++GL VAG ++PAIGFA+++ +M K IP+ ++G+V AA+LQ+P + I A+ Sbjct: 176 ALIDGLGVAGGIMPAIGFAVLMKIMMKNAYIPYFILGFVAAAWLQLPILAIRCAATAMAI 23- 5 Query: 237 NEFYNK--PKQVDAT 249 +F K P V+A+ Sbjct: 236 IDFMRKSEPTPVNAS 250 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02281 Identities = 203/288 (70%), Positives = 225/288 (77%), Gaps 28/288 (9%) Query: 1 MDISILQAVLIGLWTAFCFSGMLLGLYTNRCIVLSLGVGVILGDIQTALAVGAISELAYM 60 MDI++LQA+LIGLWTAFCFSGMLLG+YTNRCI+LS GVG+ILGD+ TAL++GAISELAYM Sbjct: 1 MDINLLQALLIGLWTAFCFSGMLLGIYTNRCIILSFGVGIILGDLPTALSMGAISELAYM 60 Query: 61 GFGVGAGGTVPPNPIGPGIFGTLMAITTAGTKGKITPEAALALSTPIAVGIQFLQTATYT 120- GFGVGAGGTVPPNPIGPGIFGTLMAIT+AG K+TPEAALALSTPIAV IQFLQT YT Sbjct: 61 GFGVGAGGTVPPNPIGPGIFGTLMAITSAG---KVTPEAALALSTPIAVAIQFLQTFAYT 117- Query: 121 AFAGAPETAKKALQAGNFRGFKIAANGTIWAFAGLGFGLGVLGALSTQTLTDLFALIPPV 18- 0 AFAGAPETAKI LQ GN RGFK AANGTIWAFA +G GLG+LGALS TL L IPPV Sbjct: 118 AFAGAPETAKKQLQKGNIRGFKFAANGTIWAFAFIGLGLGLLGALSMDTLLHLVDYIPPV 17- 7 Query: 181 LLNGLTLAGKMLPAIGFAMILSVMAKKELIPYILLGYVLAVYFGLPVLTPTANGDGVLTS 24- 0 LLNGLT+AGKMLPAIGFAMILSVMAKKELIP++L+GYV A Y Sbjct: 178 LLNGLTVAGKMLPAIGFAMILSVMAKKELIPFVLIGYVCAAY------------------ 21- 9 Query: 241 VATNSVLGVPTIGVAIIATIFALLDIFRKPAAPTKETKTEGDNQDDWI 288 L +PTIG+AII IFAL + + KP T +G QDDWI Sbjct: 220 ------LQIPTIGIAIIGIIFALNEFYNKP-KQVDATTVQGGQQDDWI 260 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 766 A DNA sequence (GBSx0814) was identified in S. agalactiae <SEQ ID 2353> which encodes the amino acid sequence <SEQ ID 2354>. Analysis of this protein sequence reveals the following: TABLE-US-02282 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2442 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 767 A DNA sequence (GBSx0815) was identified in S. agalactiae <SEQ ID 2355> which encodes the amino acid sequence <SEQ ID 2356>. This protein is predicted to be PTS permease for mannose subunit IIBMan. Analysis of this protein sequence reveals the following: TABLE-US-02283 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.28 Transmembrane 278-294 (272-294) INTEGRAL Likelihood = -3.45 Transmembrane 155-171 (155-174) INTEGRAL Likelihood = -1.59 Transmembrane 250-266 (250-267) ----- Final Results ----- bacterial membrane --- Certainty = 0.4312 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8657> which encodes amino acid sequence <SEQ ID 8658> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-02284 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -9.70 GvH: Signal Score (-7.5): -6.12 Possible site: 19 >>> Seems to have no N-terminal signal sequence ALOM program count: 3 value: -8.28 threshold: 0.0 INTEGRAL Likelihood = -8.28 Transmembrane 254-270 (248-270) INTEGRAL Likelihood = -3.45 Transmembrane 131-147 (131-150) INTEGRAL Likelihood = -1.59 Transmembrane 226-242 (226-243) PERIPHERAL Likelihood = 0.37 175 modified ALOM score: 2.16 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4312 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02285 >GP: AAA57943 GB: U18997 ORF_o290; Geneplot suggests frameshift linking to o267, not found [Escherichia coli] Identities = 101/278 (36%), Positives = 164/278 (58%), Gaps = 6/278 (2%) Query: 17 LRQKETTKMTGSKKLAKSDYTKTALRAFYLQNGFNYSNYQGLGYANVIYPALKKYYGDDK 76 - ++ K+ T GS+ ++K D T+ R+ LQ FNY Q G+ + P LKK Y DDK Sbjct: 19 VKMKKRTTAMGSE-ISKKDITRLGFRSSLLQASFNYERMQAGGFTWAMLPILKKIYKDDK 77 Query: 77 KALAGALEENVEFYNTNPHFLPFVTSLHLAMLDNERPEEEIRGIKMALMGPLAGIGDSLS 136- L+ A+++N+EF NT+P+ + F+ L ++M + + I+G+K+AL GP+AGIGD++ Sbjct: 78 PGLSAAMKDNLEFINTHPNLVGFLMGLLISMEEKGENRDTIKGLKVALFGPIAGIGDAIF 137- Query: 137 QFCLAPLFSTIAASLATDGLVMGPILFFVAMNTILTGIKLVTGMYGYRLGTSFIDKLSEQ 19- 6 F L P+ + I +S A+ G ++GPILFF A+ ++ +++ GY +G IDK+ E Sbjct: 138 WFTLLPIMAGICSSFASQGNLLGPILFF-AVYLLIFFLRVGWTHVGYSVGVKAIDKVREN 19- 6 Query: 197 MSVISRAANIVGVTVISSLAATQVKLTIPYTFAPEKVTSTTQKIVTVQGMLDKIAPALLP 25- 6 +I+R+A I+G+TVI L A+ V + + +FA T + Q DK+ P +LP Sbjct: 197 SQMIARSATILGITVIGGLIASYVHINVVTSFA----IDNTHSVALQQDFFDKVFPNILP 25- 2 Query: 257 ALYTFLMFYLIKNKKWTTYKLVILTVIIGILGSWLGIL 294 YT LM+Y ++ KK L+ +T ++ I+ S GIL Sbjct: 253 MAYTLLMYYFLRVKKAHPVLLIGVTFVLSIVCSAFGIL 290 A related DNA sequence was identified in S. pyogenes <SEQ ID 2357> which encodes the amino acid sequence <SEQ ID 2358>. Analysis of this protein sequence reveals the following: TABLE-US-02286 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.49 Transmembrane 276-292 (270-292) INTEGRAL Likelihood = -7.01 Transmembrane 151-167 (149-176) INTEGRAL Likelihood = -3.03 Transmembrane 202-218 (202-220) INTEGRAL Likelihood = -2.13 Transmembrane 249-265 (248-265) ----- Final Results ----- bacterial membrane --- Certainty = 0.4397 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02287 >GP: AAA57943 GB: U18997 ORF_o290; Geneplot suggests frameshift linking to o267, not found [Escherichia coli] Identities = 104/285 (36%), Positives = 162/285 (56%), Gaps = 7/285 (2%) Query: 8 NKSMQQLSKEANKMTGSNKLTKKDYLKTALRAFFLQNGFNYNNYQGIGYANVIYPALKKH 67 N+S + + ++++KKD + R+ LQ FNY Q G+ + P LKK Sbjct: 13 NRSPLPVKMKKRTTAMGSEISKKDITRLGFRSSLLQASFNYERMQAGGFTWAMLPILKKI 72 Query: 68 FGNDKKGLYQALEDNCEFYNTNPHFLPFITSLHLVMLENNRPEEETRNIKMALMGPLAGI 127- + +DK GL A++DN EF NT+P+ + F+ L + M E + + +K+AL GP+AGI Sbjct: 73 YKDDKPGLSAAMKDNLEFINTHPNLVGFLMGLLISMEEKGENRDTIKGLKVALFGPIAGI 132- Query: 128 GDSLSQFCLAPLFSTIAASLASDGLVLGPILFFLAMNIILTAIKIGSGLYGYKVGTSFID 18- 7 GD++ F L P+ + I +S AS G +LGPILFF A+ +++ +++G GY VG ID Sbjct: 133 GDAIFWFTLLPIMAGICSSFASQGNLLGPILFF-AVYLLIFFLRVGWTHVGYSVGVKAID 19- 1 Query: 188 KLSEQMAVVSRMANIVGVTVIAGLAATSVKITVPITFAAGKVDAANTAQKFVTIQGMLDK 24- 7 K+ E +++R A I+G+TVI GL A+ V I V +FA + Q F DK Sbjct: 192 KVRENSQMIARSATILGITVIGGLIASYVHINVVTSFAIDNTHSVALQQDF------FDK 24- 5 Query: 248 IAPALLPALFTLLMYYLIKNKKWTTYKLVILTVIIGVIGSWLGIL 292 + P +LP +TLLMYY ++ KK L+ +T ++ ++ S GIL Sbjct: 246 VFPNILPMAYTLLMYYFLRVKKAHPVLLIGVTFVLSIVCSAFGIL 290 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02288 Identities = 224/288 (77%), Positives = 255/288 (87%), Gaps = 4/288 (1%) Query: 12 HLLKKLRQ--KETTKMTGSKKLAKSDYTKTALRAFYLQNGFNYSNYQGLGYANVIYPALK 69 - +L K ++Q KE KMTGS KL K DY KTALRAF+LQNGFNY+NYQG+GYANVIYPALK Sbjct: 6 NLNKSMQQLSKEANKMTGSNKLTKKDYLKTALRAFFLQNGFNYNNYQGIGYANVIYPALK 65 Query: 70 KYYGDDKKALAGALEENVEFYNTNPHFLPFVTSLHLAMLDNERPEEEIRGIKMALMGPLA 129- K++G+DKK L ALE+N EFYNTNPHFLPF+TSLHL ML+N RPEEE R IKMALMGPLA Sbjct: 66 KHFGNDKKGLYQALEDNCEFYNTNPHFLPFITSLHLVMLENNRPEEETRNIKMALMGPLA 125- Query: 130 GIGDSLSQFCLAPLFSTIAASLATDGLVMGPILFFVAMNTILTGIKLVTGMYGYRLGTSF 18- 9 GIGDSLSQFCLAPLFSTIAASLA+DGLV+GPILFF+AMN ILT IK+ +G+YGY++GTSF Sbjct: 126 GIGDSLSQFCLAPLFSTIAASLASDGLVLGPILFFLAMNIILTAIKIGSGLYGYKVGTSF 18- 5 Query: 190 IDKLSEQMSVISRAANIVGVTVISSLAATQVKLTIPYTFAPEKV--TSTTQKIVTVQGML 24- 7 IDKLSEQM+V+SR ANIVGVTVI+ LAAT VK+T+P TFA KV +T QK VT+QGML Sbjct: 186 IDKLSEQMAVVSRMANIVGVTVIAGLAATSVKITVPITFAAGKVDAANTAQKFVTIQGML 24- 5 Query: 248 DKIAPALLPALYTFLMFYLIKNKKWTTYKLVILTVIIGILGSWLGILA 295 DKIAPALLPAL+T LM+YLIKNKKWTTYKLVILTVIIG++GSWLGILA Sbjct: 246 DKIAPALLPALFTLLMYYLIKNKKWTTYKLVILTVIIGVIGSWLGILA 293 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 768 A DNA sequence (GBSx0816) was identified in S. agalactiae <SEQ ID 2359> which encodes the amino acid sequence <SEQ ID 2360>. Analysis of this protein sequence reveals the following: TABLE-US-02289 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 135-151 (135-151) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02290 >GP: CAB01924 GB: Z79691 OrfA [Streptococcus pneumoniae] Identities = 76/206 (36%), Positives = 124/206 (59%), Gaps = 1/206 (0%) Query: 428 SWTYNSYPKCDYCQLTSKDRYHLVEGQLHVQRASDIYYHKRWLLTLPQAITLVIDKVSCP 48- 7 SW Y YP +C ++ H +EG Y HKR +L L + + L++D + C Sbjct: 2 SWEYEYYPHSLFCHHKEREGMHYIEGAYWSAEPDLPYLHKRKILMLVEDVWLLVDDIRCQ 61 Query: 488 GEHVLTNQYILDDQVIYENGFVNDLKLVSPTTFNLEDCLISKRYNQLTESHKLVKKIKFV 54- 7 G+H Q+ILD V Y++G +N L+L S F+LED +IS +YN+L S KL K+ F Sbjct: 62 GQHEALTQFILDKDVTYQDGKINQLRLWSEVDFDLEDTIISPKYNELERSSKLTKRQFFE 121- Query: 548 DEVMDYTLIVDRNCQVKYVPLVQTNSHKELSNSIAFDIRSQDFHYLIGVLMDDIIFGDKL 60- 7 ++++DYT+I + ++ + QT+ +E+ N++AF++++ + LI +L +DI G+KL Sbjct: 122 NQMLDYTIIAHESFEIIRHSVYQTDD-REVENALAFEVKNDETDKLILLLSEDIRVGEKL 18- 0 Query: 608 YLMQGIKCKGKVIVYDKNNGKMSRLK 633 L+ G K +GK +VYDK N +M RL+ Sbjct: 181 CLVDGTKMRGKCLVYDKINERMIRLQ 206 A related DNA sequence was identified in S. pyogenes <SEQ ID 2361> which encodes the amino acid sequence <SEQ ID 2362>. Analysis of this protein sequence reveals the following: TABLE-US-02291 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.55 Transmembrane 477-493 (477-493) ----- Final Results ----- bacterial membrane --- Certainty = 0.2020 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02292 >GP: CAB01924 GB: Z79691 OrfA [Streptococcus pneumoniae] Identities = 75/207 (36%), Positives = 125/207 (60%), Gaps = 2/207 (0%) Query: 434 SWAYLSYPKSNYCHLRQNGHVYFIEGSYQTQFSDRNNYQHDRQILILPPGIFLIIDTIQA 49- 3 SW Y YP S +CH ++ +++IEG+Y + D Y H R+IL+L ++L++D I+ Sbjct: 2 SWEYEYYPHSLFCHHKEREGMHYIEGAYWSAEPDLP-YLHKRKILMLVEDVWLLVDDIRC 60 Query: 494 QGNHCLVSQFILDNHLDVKTDHLSDLRLISDCPFTIEETILSKKYNQYLTSHKLIKRKPF 55- 3 QG H ++QFILD + + ++ LRL S+ F +E+TI+S KYN+ S KL KR+ F Sbjct: 61 QGQHEALTQFILDKDVTYQDGKINQLRLWSEVDFDLEDTIISPKYNELERSSKLTKRQFF 120- Query: 554 KDKGCTSTLLVPDDTKVTPLTPLQTGKRNPIETALSWHLKGKQFDYSICVLQEDLIKGEK 61- 3 +++ T++ + ++ + QT R +E AL++ +K + D I +L ED+ GEK Sbjct: 121 ENQMLDYTIIAHESFEIIRHSVYQTDDRE-VENALAFEVKNDETDKLILLLSEDIRVGEK 17- 9 Query: 614 LVLLNSHKIRGKVVVINHITNEIIRLK 640 L L++ K+RGK +V + I +IRL+ Sbjct: 180 LCLVDGTKMRGKCLVYDKINERMIRLQ 206 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02293 Identities = 282/631 (44%), Positives = 414/631 (64%), Gaps = 2/631 (0%) Query: 6 YNKFKD-FDREFCQKYIKTYQSNAYQEMKASVNLMMRNTFVFNDNWDMEPCSKAYCLDPL 64 + +FK+ + +FC+ Y+ YQ+++Y + K +L++ NTF+F DNWDMEPC Y LDP+ Sbjct: 11 FARFKETVNPDFCRNYLLDYQTDSYADQKRIADLLLTNTFLFEDNWDMEPCHIPYHLDPI 70 Query: 65 EWDKPVTDDPEWLYMLNRQTYLFKFLVVYIVEGDKSYLRQMKYFMYHWIDCQFTLKPEGA 124- W + V DDPEW +MLNRQTYL K ++VY+VE D+ YL K F+ +WI+ L P+G Sbjct: 71 TWQEAVIDDPEWNFMLNRQTYLQKLILVYLVERDERYLLTAKGFILNWIESAIPLDPKGL 130- Query: 125 VSRTIDTGIRCMSWLKVLIFLDYFGLITETKKIKLLTSLREQITYMRDYYREKDSLSNWG 18- 4 +RT+DTGIRC +W+K LI+L+ F +T+ ++ +L SL +Q+ ++ Y +K SLSNWG Sbjct: 131 ATRTLDTGIRCFAWVKCLIYLNLFNALTKQEESLILASLEKQLQFLHANYLDKYSLSNWG 19- 0 Query: 185 ILQTTAILACLYYYEDELNLPEIQSFAEEELLLQIKLQILDDGSQYEQSIMYHVEVLKSL 24- 4 ILQTTAIL Y+ +L++ +FA +EL QI LQIL+DGSQ+EQS MYHVEVLK+L Sbjct: 191 ILQTTAILLADAYFGSDLDIAAATAFARKELTQQIALQILEDGSQFEQSTMYHVEVLKAL 25- 0 Query: 245 MELVILAPKYYLPLEETIEKMVTYLIAMTGPDYCQLAIGDSDVTDTRDILTLATLVLKSS 30- 4 +EL L P Y L T+ M YL+ MTGPD+ Q+ +GDSDVTDTRDILTLA +L+ Sbjct: 251 LELTALVPDYLPQLRPTLLAMSDYLLKMTGPDHKQIPLGDSDVTDTRDILTLAATILEEP 31- 0 Query: 305 KTKSFSFDNVNLETLLLFGKPSIYLFEEIPRATIGESAYLFPDSGHVCLRDDRRYIFFKN 36- 4 K+ +F +++++LLL G+ ++ FE++P T+ A+ F SGH+ + + Y+FFKN Sbjct: 311 HLKAAAFPTLDIDSLLLLGEKGVHTFEQLPVQTLPTFAHHFEHSGHITINQENYYLFFKN 37- 0 Query: 365 GPFGSAHTHSDNNSVCLYDKKKPIFIDAGRYTYKEEQLRYDFKRSTSHSTCTLDGQPLEM 42- 4 GP GS+HTHSD NS+CLY K +P+F DAGRYTYKEE LRY K ++ HST L+ Q E Sbjct: 371 GPIGSSHTHSDQNSLCLYYKGQPLFCDAGRYTYKEEPLRYALKSASHHSTAFLEEQLPEQ 43- 0 Query: 425 IKDSWTYNSYPKCDYCQLTSKDRYHLVEGQLHVQRAS-DIYYHKRWLLTLPQAITLVIDK 48- 3 I SW Y SYPK +YC L + +EG Q + + Y H R +L LP I L+ID Sbjct: 431 IDSSWAYLSYPKSNYCHLRQNGHVYFIEGSYQTQFSDRNNYQHDRQILILPPGIFLIIDT 49- 0 Query: 484 VSCPGEHVLTNQYILDDQVIYENGFVNDLKLVSPTTFNLEDCLISKRYNQLTESHKLVKK 54- 3 + G H L +Q+ILD+ + + ++DL+L+S F +E+ ++SK+YNQ SHKL+K+ Sbjct: 491 IQAQGNHCLVSQFILDNHLDVKTDHLSDLRLISDCPFTIEETILSKKYNQYLTSHKLIKR 55- 0 Query: 544 IKFVDEVMDYTLIVDRNCQVKYVPLVQTNSHKELSNSIAFDIRSQDFHYLIGVLMDDIIF 60- 3 F D+ TL+V + +V + +QT + ++++ ++ + F Y I VL +D+I Sbjct: 551 KPFKDKGCTSTLLVPDDTKVTPLTPLQTGKRNPIETALSWHLKGKQFDYSICVLQEDLIK 61- 0 Query: 604 GDKLYLMQGIKCKGKVIVYDKNNGKMSRLKN 634 G+KL L+ K +GKV+V + ++ RLK+ Sbjct: 611 GEKLVLLNSHKIRGKVVVINHITNEIIRLKH 641 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 769 A DNA sequence (GBSx0817) was identified in S. agalactiae <SEQ ID 2363> which encodes the amino acid sequence <SEQ ID 2364>. This protein is predicted to be RegR (kdgR). Analysis of this protein sequence reveals the following:

TABLE-US-02294 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2545 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02295 >GP: CAB01925 GB: Z79691 RegR [Streptococcus pneumoniae] Identities = 222/333 (66%), Positives = 279/333 (83%) Query: 1 MSKKMTINDIAQLSKTSKTTVSFFLNQKFEKMSDETRQRIQEVIDETGYRPSTIARSLNS 60 M KK+TI DIA++++TSKTTVSF+LN K+EKMS ETR++I++VI ET Y+PS +ARSLNS Sbjct: 1 MEKKLTIKDIAEMAQTSKTTVSFYLNGKYEKMSQETREKIEKVIHETNYKPSIVARSLNS 60 Query: 61 KKTKLLGVLIGDITNTFSNQIVKGIEHITKQKGYQIIVGNSNYDAKSEEDYIENMLNLGV 120- K+TKL+GVLIGDITN+FSNQIVKGIE I Q GYQ+++GNSNY +SE+ YIE+ML LGV Sbjct: 61 KRTKLIGVLIGDITNSFSNQIVKGIEDIASQNGYQVMIGNSNYSQESEDRYIESMLLLGV 120- Query: 121 DGFIIQPTSNFRKYSRILKEKKKPMVFFDSQLYEHKTSWVKANNYDAVYDMTQECLNRGY 18- 0 DGFIIQPTSNFRKYSRI+ EKKK MVFFDSQLYEH+TSWVK NNYDAVYDMTQ C+ +GY Sbjct: 121 DGFIIQPTSNFRKYSRIIDEKKKKMVFFDSQLYEHRTSWVKTNNYDAVYDMTQSCIEKGY 18- 0 Query: 181 KKFIMITADTSLLSTRIERASGFMDALKDNGFGYDTLVIEDDDHSKSDIEDFLKAVVPDK 24- 0 + F++ITADTS LSTRIERASGF+DAL D + +L IED + I++FL+ + Sbjct: 181 EYFLLITADTSRLSTRIERASGFVDALTDANMRHASLTIEDKHTNLEQIKEFLQKEIDPD 24- 0 Query: 241 EETLVFAPNCWALPMVFTAMKNLNFDMPRVGLVGFDNIEWTDFSSPKVSTIVQPAYEEGE 30- 0 E+TLVF PNCWALP+VFT +K LN+++P+VGL+GFDN EWT FSSP VST+VQP++EEG+ Sbjct: 241 EKTLVFIPNCWALPLVFTVIKELNYNLPQVGLIGFDNTEWTCFSSPSVSTLVQPSFEEGQ 30- 0 Query: 301 QVAQILINRIEGDDSVDNQQIVDCQMFWKESTF 333 Q +ILI++IEG + + QQ++DC + WKESTF Sbjct: 301 QATKILIDQIEGRNQEERQQVLDCSVNWKESTF 333 A related DNA sequence was identified in S. pyogenes <SEQ ID 2365> which encodes the amino acid sequence <SEQ ID 2366>. Analysis of this protein sequence reveals the following: TABLE-US-02296 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2928 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02297 Identities = 214/333 (64%), Positives = 266/333 (79%), Gaps = 2/333 (0%) Query: 1 MSKKMTINDIAQLSKTSKTTVSFFLNQKFEKMSDETRQRIQEVIDETGYRPSTIARSLNS 60 M +K+TI DIA+L+KTSKTTVSF+LN +F+KMS+ET+ RI E I T Y+PS ARSLN+ Sbjct: 13 MQRKVTIKDIAELAKTSKTTVSFYLNGRFDKMSEETKNRISESIKATNYKPSIAARSLNA 72 Query: 61 KKTKLLGVLIGDITNTFSNQIVKGIEHITKQKGYQIIVGNSNYDAKSEEDYIENMLNLGV 120- K TKL+GV+IGDITN+FSNQIVKGIE ++ GYQII+GNSNYD E++ IE MLNLGV Sbjct: 73 KSTKLIGVVIGDITNSFSNQIVKGIESKAQEFGYQIIIGNSNYDPSREDELIEKMLNLGV 132- Query: 121 DGFIIQPTSNFRKYSRILKEKKKPMVFFDSQLYEHKTSWVKANNYDAVYDMTQECLNRGY 18- 0 DGFIIQPTSNFRKYSRI+ KKK +VFFDSQLYEH+T+WVK NNYDAVYD Q+C+++GY Sbjct: 133 DGFIIQPTSNFRKYSRIIDIKKKKVVFFDSQLYEHRTNWVKTNNYDAVYDTIQQCIDKGY 19- 2 Query: 181 KKFIMITADTSLLSTRIERASGFMDALKDNGFGYDTLVIEDDDHSKSDIEDFLKAVVPDK 24- 0 + FIMIT + +LLSTRIERASGF+D L+ N + ++I+++ S I FL+ + K Sbjct: 193 EHFIMITGNPNLLSTRIERASGFIDVLEANHLTHQEMIIDENQTSSEAIAQFLQGSLTKK 25- 2 Query: 241 EETLVFAPNCWALPMVFTAMKNLNFDMPRVGLVGFDNIEWTDFSSPKVSTIVQPAYEEGE 30- 0 +LVF PNCWALP VFTAMK+L F++P +GLVGFDNIEWT FSSP ++TI+QPAYEEGE Sbjct: 253 --SLVFVPNCWALPKVFTAMKSLKFNIPEIGLVGFDNIEWTKFSSPTLTTIIQPAYEEGE 31- 0 Query: 301 QVAQILINRIEGDDSVDNQQIVDCQMFWKESTF 333 Q +ILI+ IEG QQI DCQ+ W+ESTF Sbjct: 311 QATKILIDDIEGHSQEAKQQIFDCQVNWQESTF 343 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 770 A DNA sequence (GBSx0818) was identified in S. agalactiae <SEQ ID 2367> which encodes the amino acid sequence <SEQ ID 2368>. This protein is predicted to be polypeptide defromylase (def-1). Analysis of this protein sequence reveals the following: TABLE-US-02298 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2339 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02299 >GP: CAC15392 GB: AJ278785 polypeptide deformylase [Streptococcus pneumoniae] Identities = 169/204 (82%), Positives = 192/204 (93%), Gaps = 1/204 (0%) Query: 1 MSAIDKLVKASHLIDMNDIIREGNPTLRKVAEEVTFPLSEKEEILGEKMMQFLKHSQDPI 60 MSAI+++ KA+HLIDMNDIIREGNPTLR +AEEVTFPLS++E ILGEKMMQFLKHSQDP+ Sbjct: 1 MSAIERITKAAHLIDMNDIIREGNPTLRAIAEEVTFPLSDQEIILGEKMMQFLKHSQDPV 60 Query: 61 MAEKLGLRGGVGLAAPQLDISKRIIAVLVPNVEDAQGNPPKEAYSLQEVMYNPKVVSHSV 120- MAEK+GLRGGVGLAAPQLDISKRIIAVLVPN+ + +G P+EAY L+ +MYNPK+VSHSV Sbjct: 61 MAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIVE-EGETPQEAYDLEAIMYNPKIVSHSV 119- Query: 121 QDAALSDGEGCLSVDREVPGYVVRHARVTIEYFDKTGEKHRLKLKGYNSIVVQHEIDHID 18- 0 QDAAL +GEGCLSVDR VPGYVVRHARVT++YFDK GEKHR+KLKGYNSIVVQHEIDHI+ Sbjct: 120 QDAALGEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHIN 17- 9 Query: 181 GIMFYDRINEKNPFAVKEGLLILE 204 GIMFYDRINEK+PFAVK+GLLILE Sbjct: 180 GIMFYDRINEKDPFAVKDGLLILE 203 A related DNA sequence was identified in S. pyogenes <SEQ ID 2369> which encodes the amino acid sequence <SEQ ID 2370>. Analysis of this protein sequence reveals the following: TABLE-US-02300 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1745 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02301 Identities = 160/204 (78%), Positives = 186/204 (90%) Query: 1 MSAIDKLVKASHLIDMNDIIREGNPTLRKVAEEVTFPLSEKEEILGEKMMQFLKHSQDPI 60 MSA DKL+K SHLI M+DIIREGNPTLR VA+EV+ PL +++ +LGEKMMQFLKHSQDP+ Sbjct: 1 MSAQDKLIKPSHLITMDDIIREGNPTLRAVAKEVSLPLCDEDILLGEKMMQFLKHSQDPV 60 Query: 61 MAEKLGLRGGVGLAAPQLDISKRIIAVLVPNVEDAQGNPPKEAYSLQEVMYNPKVVSHSV 120- MAEKLGLR GVGLAAPQ+D+SKRIIAVLVPN+ D +GNPPKEAYS QEV+YNPK+VSHSV Sbjct: 61 MAEKLGLRAGVGLAAPQIDVSKRIIAVLVPNLPDKEGNPPKEAYSWQEVLYNPKIVSHSV 120- Query: 121 QDAALSDGEGCLSVDREVPGYVVRHARVTIEYFDKTGEKHRLKLKGYNSIVVQHEIDHID 18- 0 QDAALSDGEGCLSVDR V GYVVRHARVT++Y+DK G++HR+KLKGYN+IVVQHEIDHI+ Sbjct: 121 QDAALSDGEGCLSVDRVVEGYVVRHARVTVDYYDKEGQQHRIKLKGYNAIVVQHEIDHIN 18- 0 Query: 181 GIMFYDRINEKNPFAVKEGLLILE 204 G++FYDRIN KNPF KE LLIL+ Sbjct: 181 GVLFYDRINAKNPFETKEELLILD 204 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 771 A DNA sequence (GBSx0819) was identified in S. agalactiae <SEQ ID 2371> which encodes the amino acid sequence <SEQ ID 2372>. Analysis of this protein sequence reveals the following: TABLE-US-02302 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3620 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10177> which encodes amino acid sequence <SEQ ID 10178> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02303 >GP: AAC75224 GB: AE000305 putative transcriptional regulator [Escherichia coli K12] Identities = 58/191 (30%), Positives = 98/191 (50%) Query: 37 DLQVITLTAGQSVCKQGEQLEYLHYIVKGRFKIVRRLFNGKEHILDIKTKPTLIGDIELL 96 - D ++ A + ++G+Q +L Y+ +GR ++ L NG+ ++D P IG+IEL+ Sbjct: 17 DTRLFHFLARDYIVQEGQQPSWLFYLTRGRARLYATLANGRVSLIDFFAAPCFIGEIELI 76 Query: 97 TNRQIVSSVIALEDLTVIQLSLKGRKEKLLTDATFLLKLSQELAQAFHDQNIKASTNLGY 156- +V A+E+ + L +K + LL D FL KL L+ + + + N + Sbjct: 77 DKDHEPRAVQAIEECWCLALPMKHYRPLLLNDTLFLRKLCVTLSHKNYRNIVSLTQNQSF 136- Query: 157 TVKELLASHILAIEEQGYFQLELSSLADSFGVSYRHLLRVIHDMVKEGLIQKEKPKYFIK 21- 6 + LA+ IL +E + + + A+ GVSYRHLL V+ + +GL+ K K Y IK Sbjct: 137 PLVNRLAAFILLSQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIHDGLLIKSKKGYLIK 19- 6 Query: 217 NRFALESLNIQ 227 NR L L ++ Sbjct: 197 NRKQLSGLALE 207 A related DNA sequence was identified in S. pyogenes <SEQ ID 2373> which encodes the amino acid sequence <SEQ ID 2374>. Analysis of this protein sequence reveals the following: TABLE-US-02304 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3809 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02305 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%) Query: 146 QNIKASTNLGYTVKELLASHILAIEEQGYFQLELSSLADSFGVSYRHLLRVIHDMVKEGL 20- 5 QN+ N+ YTVKE AS+ L + L L+ LA+ FG S RHL V+ + + + Sbjct: 3 QNV-CQQNITYTVKERFASYTLEAQANQEVHLNLTLLANRFGTSDRHLKHVLKQPIFQRI 61 Query: 206 IQK 208 I++ Sbjct: 62 IER 64 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 772 A DNA sequence (GBSx0820) was identified in S. agalactiae <SEQ ID 2375> which encodes the amino acid sequence <SEQ ID 2376>. Analysis of this protein sequence reveals the following: TABLE-US-02306 Possible site: 54 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.24 Transmembrane 163-179 (159-185) INTEGRAL Likelihood = -8.49 Transmembrane 204-220 (201-226) INTEGRAL Likelihood = -7.80 Transmembrane 272-288 (269-296) INTEGRAL Likelihood = -6.00 Transmembrane 333-349 (331-352) INTEGRAL Likelihood = -5.41 Transmembrane 75-91 (73-92) INTEGRAL Likelihood = -4.94 Transmernbrane 245-261 (240-262) INTEGRAL Likelihood = -4.41 Transmernbrane 362-378 (359-380) INTEGRAL Likelihood = -4.14 Transmembrane 96-112 (95-113) INTEGRAL Likelihood = -2.44 Transmembrane 141-157 (141-158) INTEGRAL Likelihood = -1.81 Transmembrane 302-318 (301-320) ----- Final Results ----- bacterial membrane --- Certainty = 0.4694 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8659> which encodes amino acid sequence <SEQ ID 8660> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-02307 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: -3.52 GvH: Signal Score (-7.5): 0.340001 Possible site: 25 >>> Seems to have no N-terminal signal sequence ALOM program count: 11 value: -9.24 threshold: 0.0 INTEGRAL Likelihood = -9.24 Transmembrane 134-150 (130-156) INTEGRAL Likelihood = -8.60 Transmembrane 17-33 (13-37) INTEGRAL Likelihood = -8.49 Transmembrane 175-191 (172-197) INTEGRAL Likelihood = -7.80 Transmembrane 243-259 (240-267) INTEGRAL Likelihood = -6.00 Transmembrane 304-320 (302-323) INTEGRAL Likelihood = -5.41 Transmembrane 46-62 (44-63) INTEGRAL Likelihood = -4.94 Transmembrane 216-232 (211-233) INTEGRAL Likelihood = -4.41 Transmembrane 333-349 (330-351) INTEGRAL Likelihood = -4.14 Transmembrane 67-83 (66-84) INTEGRAL Likelihood = -2.44 Transmembrane 112-128 (112-129) INTEGRAL Likelihood = -1.81 Transmembrane 273-289 (272-291) PERIPHERAL Likelihood = 3.45 193 modified ALOM score: 2.35 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4694 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02308 >GP: CAB50057 GB: AJ248286 TRANSPORT PROTEIN, permease [Pyrococcus abyssi] Identities = 94/382 (24%), Positives = 173/382 (44%), Gaps = 30/382 (7%) Query: 5 MEKLSLLSL-SLILLSTFSTSPALPQMISYY-RDKGLPSPQVELLFSIPSMAIIFILLIT 62 MEKL +L L SL + +S A+P + +D G+ + ++ LL + + I + Sbjct: 1 MEKLIILILISLGWIFNYSHRMAVPSLAPIIMKDLGINNAEIGLLMTSLLLPYSLIQVPA 60 Query: 63 PWLSKKLSEKHMIIFGLLLTALGGGLPVVSQNYLLVFVSRLLLGSGIGFINTRAISVISE 122- ++ K+ K ++ +L +L L V++++Y + R L G G A ++ISE Sbjct: 61 GYIGDKIGRKKLLTISILGYSLSSALIVLTRDYWDLVTVRALYGFFAGLYYAPATALISE 120- Query: 123 YYQGKERRKLLGLRGSFEVLGNA---GLTAL--VGLLLTFGWSKSFMIYFLALPILVLYL 17- 7 ++ ++ L F ++G A G+T L V + LT W +F++ + I+ + L Sbjct: 121 LFRERKGSAL-----GFFMVGPAIGSGITPLIVVPVALTLSWRYAFLVLSIMSSIVGILL 17- 5 Query: 178 VFAPKKVVKDTNDKIKTKGQKIPKADLTYIVALAILAGFVITINTGINLRIPLLVVEFGL 23- 7 + A K + IK +G K ++++LA G + + LV G+ Sbjct: 176 MVAIK------GEPIKVEGVKFKIPRGVFLLSLANFLGLGAFFAM-LTFLVSYLVSR-GV 22- 7 Query: 238 GTPAQASLVLSAMMLMGIIAGMSFGQLIAMFHKQLIPICLVLFS-LTLLGVGLPSNLNVL 29- 6 G +ASL+ S + L+GI+ + G L K + + L S LT L + +PS L ++ Sbjct: 228 GME-KASLMFSMLSLVGILGSIIAGFLYDHLGKVSVLLAYALNSLLTFLVIVIPSPLFLI 28- 6 Query: 297 TISAMASGFLYSL--MVTAVFSLVADRVEYSLVGSATTLVLVF-CNIGGASAAILLSCFD 35- 3 + + LYS+ ++TA S A R +V +V F IG L+ Sbjct: 287 PLGLV----LYSVGGIMTAYTSEKASRENLGVVMGFVNMVGFFGATIGPYIVGFLIDRLG 34- 2 Query: 354 HLLGQINAVFYVYAILSLAVGM 375 + L + +V Y + ++ +G+ Sbjct: 343 YSLALL-SVPLAYLVSAVIIGL 363 There is also homology to SEQ ID 2378. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 773 A DNA sequence (GBSx0821) was identified in S. agalactiae <SEQ ID 2379> which encodes the amino acid sequence <SEQ ID 2380>. Analysis of this protein sequence reveals the following: TABLE-US-02309 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 171-187 (171-187) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02310 >GP: CAB61731 GB: AL133220 putative oxidoreductase. [Streptomyces coelicolor A3(2)] Identities = 101/327 (30%), Positives = 169/327 (50%), Gaps = 12/327 (3%) Query: 8 WATLGTGVIANEL-AQALEARGQKLYSVANRTYDKGLEFATKYGIQKVYDHIDQVFEDPE 66 W L TG +A A ++ ++ +VA+RT FA ++GI + Y + + D + Sbjct: 11 WGILATGGMAARFTADLVDLPDAEVVAVASRTEASAKTFAERFGIPRAYGGWETLARDED 70 Query: 67 VDIIYISTPHNTHISFLRKALANGKHVLCEKSITLNSTELKEAIDLAETNHVVLAEAMTI 126- VD++Y++TPH+ H + L G++VLCEK TLN+ E E + LA N V L EAM + Sbjct: 71 VDVVYVATPHSAHRTAAGLCLEAGRNVLCEKPFTLNAREAAELVALARENGVFLMEAMWM 130- Query: 127 FHMPIYRQLKTLVDSGKLGPLKMIQMNFGSYKEYDMTNRFFSRDLAGGALLDIGVYALSC 18- 6 + P+ R+LK LV G +G ++ +Q FG + +R GGALLD+GVY +S Sbjct: 131 YCNPLVRRLKELVADGAIGEVRSLQADFGLAGPFPAAHRLRDPAQGGGALLDLGVYPVSF 19- 0 Query: 187 IRWFMSEAPHNITSQVTFAPTGVDEQVGILLTNPANEMATVSLSLHAKQPKRATIAYDKG 24- 6 + + E P ++ ++ + GVD Q G LL+ + +A++ S+ P A+I +G Sbjct: 191 AQLLLGE-PTDVAARAVLSEEGVDLQTGALLSYGNDALASIHCSITGGTPNSASITGSEG 24- 9 Query: 247 YIEL---FEYPRGQKAVITYTEDGHQDIL--EAGKTENALQYEVADMEEAV-SGKTNH-- 29- 8 I++ F +P V+ T Q+ A +L++E ++ A+ +G+T Sbjct: 250 RIDVPNGFFFP--DHFVLHRTGRDPQEFRADPADGPRESLRHEAEEVMRALRAGETESPL 30- 7 Query: 299 MYLNYTKDVMDIMTQLRQEWGFTYPEE 325 + L+ T VM + +R G YP E Sbjct: 308 VPLDGTLAVMRTLDAIRDRVGVRYPGE 334 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 774 A DNA sequence (GBSx0822) was identified in S. agalactiae <SEQ ID 2381> which encodes the amino acid sequence <SEQ ID 2382>. This protein is predicted to be oligopeptidase. Analysis of this protein sequence reveals the following:

TABLE-US-02311 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2881 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02312 >GP: CAC14579 GB: AJ249396 oligopeptidase [Streptococcus thermophilus] Identities = 504/631 (79%), Positives = 563/631 (88%) Query: 1 MIKYQDDFYQAVNGEWAKTAVIPDDKPRTGGFSDLADDIEALMLSTTDKWLADENKPSDT 60 M + QDDFY A+NGEW KTAVIPDDKP TGGFSDLAD+IE LML TTD+WLA EN P + Sbjct: 1 MTRLQDDFYHAINGEWEKTAVIPDDKPCTGGFSDLADEIEDLMLETTDQWLAGENVPDNA 60 Query: 61 ILNHFIAFHKMTADYQKREEVGVSPVLPLIEEYKGLQSFSEFASKVAEYELEGKPNEFPF 120- IL +FI FH+MTADY +RE VG+ PV PLIEEYK L SFSEFASK+AEYE+ GKPNEFPF Sbjct: 61 ILQNFIKFHRMTADYDRREAVGIEPVKPLIEEYKKLSSFSEFASKIAEYEMSGKPNEFPF 120- Query: 121 GVAPDFMNAQLNVLWAEAPGIILPDTTYYSEDNEKGKELLAFWRKSQEDLLPLFGLSEQE 18- 0 V+PDFMNAQLNVLWA+APGIILPDTTYY+EDNEKGKELL WR+ QE+LL +G + +E Sbjct: 121 SVSPDFMNAQLNVLWADAPGIILPDTTYYTEDNEKGKELLEIWREMQEELLGKYGFTAEE 18- 0 Query: 181 IKDILDKVLALDAKLAQYVLSREESSEYVKLYHPYNWEDFTKLAPELPLDAIFQKILGQK 24- 0 IKD+LDKV+ LDAKLA+YVLS EESSEYV+LYHPY+W DFTKLAPELPLD+IF +ILGQ Sbjct: 181 IKDLLDKVIDLDAKLAKYVLSHEESSEYVELYHPYDWADFTKLAPELPLDSIFTEILGQV 24- 0 Query: 241 PDKVIVPEERFWTEFASDYYSESNWELLKADLILSAANAYNAYLTDDIRIKSGVYSRALS 30- 0 PDKVIV EE FWTEFA++YYSE+NWELLKA L++ A ++NAYLTD++R+ SG YSRALS Sbjct: 241 PDKVIVSEESFWTEFAAEYYSEANWELLKAVLLIDATTSWNAYLTDELRVLSGKYSRALS 30- 0 Query: 301 GTPQAMDKKKAAYYLASGPYNQALGLWYAGEKFSPEAKADVEHKIATMIDVYKSRLEKAD 36- 0 GTPQAMDKKKAA+YLA GPYNQALGLWYAGEKFSPEAKADVE K+ATMIDVYKSRL+ AD Sbjct: 301 GTPQAMDKKKAAFYLAQGPYNQALGLWYAGEKFSPEAKADVEAKVATMIDVYKSRLQTAD 36- 0 Query: 361 WLAQSTREKAIMKLNVITPHIGYPEKLPETYTKKIIDPKLSLVENATNLDKISIAYGWSK 42- 0 WLA TREKAI KLNVITPHIGYPEKLPETY KKIID LSLVENA L +ISIA+ WSK Sbjct: 361 WLAPETREKAITKLNVITPHIGYPEKLPETYDKKIIDENLSLVENAQKLVEISIAHSWSK 42- 0 Query: 421 WNKPVDRSEWHMPAHMVNAYYDPQQNQIVFPAAILQEPFYALEQSSSANYGGIGAVIAHE 48- 0 WNKPVDRSEWHMPAHMVNAYYDPQQNQIVFPAAILQ PFY + QSSSANYGGIGAVIAHE Sbjct: 421 WNKPVDRSEWHMPAHMVNAYYDPQQNQIVFPAAILQAPFYDIAQSSSANYGGIGAVIAHE 48- 0 Query: 481 ISHAFDTNGASFDEHGSLNNWWTDEDFEAFKKLTDKVVEQFDGLESYGAKVNGKLTVSEN 54- 0 ISHAFDTNGASFDE+GSL NWWT++D+ AFK+ TDK+V+QF+GL+SYGAKVNGKLTVSEN Sbjct: 481 ISHAFDTNGASFDENGSLKNWWTEDDYAAFKERTDKIVDQFEGLDSYGAKVNGKLTVSEN 54- 0 Query: 541 VADLGGVACALEAAQRESDFSARDFFINFATIWRMKARDEYMQMLASVDVHAPAQWRTNI 60- 0 VADLGGVACALEAA+R+ DFS R+FFINFATIWR KAR+EYMQMLASVDVHAPA+WRTN+ Sbjct: 541 VADLGGVACALEAAKRDEDFSVREFFINFATIWRTKAREEYMQMLASVDVHAPAKWRTNV 60- 0 Query: 601 TVTNFEEFHKEFDVKDGDNMWRPVEKRVIIW 631 VTNF+EFHKEFDVK+GD MWR E RVIIW Sbjct: 601 IVTNFDEFHKEFDVKEGDGMWPAPEDRVIIW 631 Endopeptidases are often exposed antigens. A related DNA sequence was identified in S. pyogenes <SEQ ID 2383> which encodes the amino acid sequence <SEQ ID 2384>. Analysis of this protein sequence reveals the following: TABLE-US-02313 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial Cytoplasm --- Certainty = 0.2622 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02314 Identities = 504/631 (79%), Positives = 564/631 (88%) Query: 1 MIKYQDDFYQAVNGEWAKTAVIPDDKPRTGGFSDLADDIEALMLSTTDKWLADENKPSDT 60 M YQDDFYQAVNG+WA+TAVIPDDKPRTGGFSDLAD+IEALML TTD WLA EN P D Sbjct: 1 MTTYQDDFYQAVNGKWAETAVIPDDKPRTGGFSDLADEIEALMLDTTDAWLAGENIPDDA 60 Query: 61 ILNHFIAFHKMTADYQKREEVGVSPVLPLIEEYKGLQSFSEFASKVAEYELEGKPNEFPF 120- IL +F+ FH++ ADY KR+EVGVSP+LPLIEEY+ L+SFSEF + +A+YEL G PNEFPF Sbjct: 61 ILKNFVKFHRLVADYAKRDEVGVSPILPLIEEYQSLKSFSEFVANIAKYELAGLPNEFPF 120- Query: 121 GVAPDFMNAQLNVLWAEAPGIILPDTTYYSEDNEKGKELLAFWRKSQEDLLPLFGLSEQE 18- 0 VAPDFMNAQLNVLWAEAP I+LPDTTYY E NEK +EL WR+SQE LLP FG S +E Sbjct: 121 SVAPDFMNAQLNVLWAEAPSILLPDTTYYEEGNEKAEELRGIWRQSQEKLLPQFGFSTEE 18- 0 Query: 181 IKDILDKVLALDAKLAQYVLSREESSEYVKLYHPYNWEDFTKLAPELPLDAIFQKILGQK 24- 0 IKD+LDKV+ LD +LA+YVLSREE SEY KLYHPY W DF KLAPELPLD+IF+KILGQ Sbjct: 181 IKDLLDKVIELDKQLAKYVLSREEGSEYAKLYHPYVWADFKKLAPELPLDSIFEKILGQV 24- 0 Query: 241 PDKVIVPEERFWTEFASDYYSESNWELLKADLILSAANAYNAYLTDDIRIKSGVYSRALS 30- 0 PDKVIVPEERFWTEFA+ YYSE+NW+LLKA+LI+ AANAYNAYLTDDIR++SG YSRALS Sbjct: 241 PDKVIVPEERFWTEFAATYYSEANWDLLKANLIVDAANAYNAYLTDDIRVESGAYSRALS 30- 0 Query: 301 GTPQAMDKKKAAYYLASGPYNQALGLWYAGEKFSPEAKADVEHKIATMIDVYKSRLEKAD 36- 0 GTPQAMDK+KAA+YLA GP++QALGLWYAG+KFSPEAKADVE K+A MI+VYKSRLE AD Sbjct: 301 GTPQAMDKQKAAFYLAQGPFSQALGLWYAGQKFSPEAKADVESKVARMIEVYKSRLETAD 36- 0 Query: 361 WLAQSTREKAIMKLNVITPHIGYPEKLPETYTKKIIDPKLSLVENATNLDKISIAYGWSK 42- 0 WLA +TREKAI KLNVITPHIGYPEKLPETY KK+ID LSLVENA NL KI+IA+ WSK Sbjct: 361 WLAPATREKAITKLNVITPHIGYPEKLPETYAKKVIDESLSLVENAQNLAKITIAHTWSK 42- 0 Query: 421 WNKPVDRSEWHMPAHMVNAYYDPQQNQIVFPAAILQEPFYALEQSSSANYGGIGAVIAHE 48- 0 WNKPVDRSEWHMPAH+VNAYYD QQNQIVFPAAILQEPFY+L+QSSSANYGGIGAVIAHE Sbjct: 421 WNKPVDRSEWHMPAHLVNAYYDLQQNQIVFPAAILQEPFYSLDQSSSANYGGIGAVIAHE 48- 0 Query: 481 ISHAFDTNGASFDEHGSLNNWWTDEDFEAFKKLTDKVVEQFDGLESYGAKVNGKLTVSEN 54- 0 ISHAFDTNGASFDEHGSLN+WWT ED+ AFK+ TDK+V QFDGLES+GAKVNGKLTVSEN Sbjct: 481 ISHAFDTNGASFDEHGSLNDWWTQEDYAAFKERTDKIVAQFDGLESHGAKVNGKLTVSEN 54- 0 Query: 541 VADLGGVACALEAAQRESDFSARDFFINFATIWRMKARDEYMQMLASVDVHAPAQWRTNI 60- 0 VADLGGVACALEAAQ E DFSARDFFINFATIWRMKAR+EYMQMLAS+DVHAP + RTN+ Sbjct: 541 VADLGGVACALEAAQSEEDFSARDFFINFATIWRMKAREEYMQMLASIDVHAPGELRTNV 60- 0 Query: 601 TVTNFEEFHKEFDVKDGDNMWRPVEKRVIIW 631 T+TNF+ FH+ FD+K+GD MWR + RVIIW Sbjct: 601 TLTNFDAFHETFDIKEGDAMWRAPKDRVIIW 631 SEQ ID 2382 (GBS193) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 23 (lane 3; MW 73 kDa). The GBS193-His fusion product was purified (FIG. 196, lane 5) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 253). These tests confirm that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 775 A DNA sequence (GBSx0823) was identified in S. agalactiae <SEQ ID 2385> which encodes the amino acid sequence <SEQ ID 2386>. This protein is predicted to be immunity protein (mccF-1). Analysis of this protein sequence reveals the following: TABLE-US-02315 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1627 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9433> which encodes amino acid sequence <SEQ ID 9434> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02316 >GP: AAB84435 GB: AF027868 YocD [Bacillus subtilis] Identities = 114/270 (42%), Positives = 170/270 (62%), Gaps = 4/270 (1%) Query: 1 MSFSKHYLENDILYSASITSRVEDLHEAFADPSVDAILATIGGFNSNELLPYLDYDLISK 60 ++ ++H E + S+SI SRV DLH AF DP V AIL T+GGFNSN+LL YLDY+ I + Sbjct: 43 VTIAEHANECNEFDSSSIESRVHDLHAAFFDPGVKAILTTLGGFNSNQLLRYLDYEKIKR 102- Query: 61 NPKIICGYSDSTAFLNAIFAKAKIQTYMGPAYSSFKMKEGQPYQTQAWLT-AMTENHYEL 119- +PKI+CGYSD TA NAI+ K + TY GP +S+F MK+G Y + +L+ +++ +E+ Sbjct: 103 HPKILCGYSDITALCNAIYQKTGLVTYSGPHFSTFAMKKGLDYTEEYFLSCCASDDPFEI 16- 2 Query: 120 WPSEEWSSDPWYDPSKPRQFFPTEWK-IYNHGKASGTIIGGNLSTFGLLRGTPYAPKIER 17- 8 PS EWS D W+ + R+F+P + G A GT+IGGNL T LL+GT Y P+ E Sbjct: 163 HPSSEWSDDRWFLDQENRRFYPNNGPVVIQEGYAEGTLIGGNLCTLNLLQGTEYFPETEH 22- 2 Query: 179 YVLLIEEAEESNFYEFDRNLAAI--LQAYPHPQAILMGRFPKECGMTPQVFEYILSKHAI 23- 6 +LLIE+ S+ + FDR+L ++ L A+ H +AIL+GRF K ++ + + ++ Sbjct: 223 TILLIEDDYMSDIHMFDRDLQSLIHLPAFSHVKAILIGRFQKASNVSIDLVKAMIETKKE 28- 2 Query: 237 FKEIPVIYDMDFAHTQPLLTVTIGAELSVD 266 IP+I +++ HT P+ T IG ++ Sbjct: 283 LSGIPIIANINAGHTSPIATFPIGGTCRIE 312 A related DNA sequence was identified in S. pyogenes <SEQ ID 2387> which encodes the amino acid sequence <SEQ ID 2388>. Analysis of this protein sequence reveals the following: TABLE-US-02317 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1162 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02318 Identities = 75/252 (29%), Positives = 125/252 (48%), Gaps = 22/252 (8%) Query: 34 VDAILATIGGFNSNELLPYLDYDLISKNPKIICGYSDSTAFLNAIFAKAKIQTYMGPAYS 93 - VD I+ +IGG+NSN +L Y+DYDL + I GYSD+TA A++ K TY+ + Sbjct: 1 VDVIMTSIGGYNSNSVLKYIDYDLFKQKFPIFIGYSDTTALALALYKKTGCITYLSQSVI 60 Query: 94 SFKMKEGQP----------YQTQAWLTAMTENHYELWPSEEWSSDPWYDPSKPRQFFPTE 143- S E +P + Q+ + ++W ++EW + W + ++ E Sbjct: 61 S-NFGEFEPFNELNYFYFDFMLQSKCETLMVQIPDVW-TDEWIN--WETYERTKKTNKNE 116- Query: 144 WKIYNHGKASGTIIGGNLSTFGLLRGTPYAPKIERYVLLIEEAEESNFYEFDRNLA--AI 20- 1 W I+N G+ +GT+IGGNL T + GT Y PKI +L+ E ++ RN A+ Sbjct: 117 WIIFNKGEFNGTLIGGNLDTIVGIIGTEYMPKITEDTILLLEDVYTDLGRLYRNFTTLAL 17- 6 Query: 202 LQAYPHPQAILMGRFPKECGMTPQVFEYILSKHAIFKEIPVIYDMDFAHTQPLLTVTIGA 26- 1 + +++ +F + G V I+++ ++IP++ + D HT P + IG Sbjct: 177 HGIFDKIGGLIISKF-ETIGENSDVINDIINEFVGHRKIPILLNFDCGHTHPSCLMPIGG 23- 5 Query: 262 ELSVDTTTLSLS 273 ++ TLSLS Sbjct: 236 KI-----TLSLS 242 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 776 A DNA sequence (GBSx0824) was identified in S. agalactiae <SEQ ID 2389> which encodes the amino acid sequence <SEQ ID 2390>. Analysis of this protein sequence reveals the following: TABLE-US-02319 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3112 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 777 A DNA sequence (GBSx0825) was identified in S. agalactiae <SEQ ID 2391> which encodes the amino acid sequence <SEQ ID 2392>. Analysis of this protein sequence reveals the following: TABLE-US-02320 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6171 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10175> which encodes amino acid sequence <SEQ ID 10176> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 778 A DNA sequence (GBSx0826) was identified in S. agalactiae <SEQ ID 2393> which encodes the amino acid sequence <SEQ ID 2394>. Analysis of this protein sequence reveals the following: TABLE-US-02321 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.19 Transmembrane 83-99 (80-113) INTEGRAL Likelihood = -9.71 Transmembrane 4-20 (1-24) INTEGRAL Likelihood = -9.45 Transmembrane 315-331 (307-337) INTEGRAL Likelihood = -8.33 Transmembrane 186-202 (180-210) INTEGRAL Likelihood = -7.75 Transmembrane 233-249 (227-255) INTEGRAL Likelihood = -3.98 Transmembrane 390-406 (382-407) INTEGRAL Likelihood = -3.61 Transmembrane 27-43 (27-45) INTEGRAL Likelihood = -3.29 Transmembrane 107-123 (105-125) INTEGRAL Likelihood = -1.75 Transmembrane 273-289 (273-290) ----- Final Results ----- bacterial membrane --- Certainty = 0.5076 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02322 >GP: CAB15347 GB: Z99121 similar to hypothetical proteins [Bacillus subtilis] Identities = 174/524 (33%), Positives = 275/524 (52%), Gaps = 13/524 (2%) Query: 1 MEETILIVSFLLFLILSNVINRIFPKLPLPFIQLVFGILSGLVFHKSQVHIDPELFLAFV 60 M+ ++++ L + +SN++NR P +P+P IQ+ GIL+ ++ ELF Sbjct: 1 MDIFLVVLVLLTIIAISNIVNRFIPFIPVPLIQVALGILAASFPQGLHFELNTELFFVLF 60 Query: 61 IAPLNFREGQESDIGSFIKYRAIILYLILPTVFLTAIVVGYVAGHLLPVSLPLAACFALG 120- IAPL F +G+ + RA IL L L VF T IV GY ++P ++PLAA F L Sbjct: 61 IAPLLFNDGKRTPRAELWNLRAPILLLALGLVFATVIVGGYTIHWMIP-AIPLAAAFGLA 119- Query: 121 AALGPTDAVAFISIAKRFQFPKRAENILKLEGLLNDASGLVSFQFALTALVTGYFSLAKA 18- 0 A L PTD VA +++ R + PK +L+ EGL+NDASGLV+F+FA+ A VTG FSLA+A Sbjct: 120 AILSPTDVVAVSALSGRVKMPKGILRLLEGEGLMNDASGLVAFKFAIAAAVTGAFSLAQA 17- 9 Query: 181 SLKLALAIMGGFLIGLLFAFLMRLCLTVLEKFDAADVTGALLLELTLPFVAYFVADLLGF 24- 0 ++ +GG L G++ +FL+ L + DVT +L+++ PFV Y A+ +G Sbjct: 180 AVSFVFISLGGLLCGVVISFLIIRFRLFLRRLGMQDVTMHMLIQILTPFVIYLAAEEIGV 23- 9 Query: 241 SAIIAVVVAGVMQANRLKKVTLFDAQVDRVTSVIWETLNFILNGLVFLIFGRELTRIIGP 30- 0 S I+AVV G+ A ++ ++ V+S W + FILNGLVF+I G ++ +I Sbjct: 240 SGILAVVAGGITHAVEQDRLESTMIKLQIVSSSTWNIILFILNGLVFVILGTQIPDVISV 29- 9 Query: 301 LLTSNAYSNFDLISIVVLVTCTLFLVRFLAVSCFY--AWRSFKYHKSFKKYWREIQLLTF 35- 8 + A SN +I ++++T TL L+RFL V F+ W K +K R L++ Sbjct: 300 IFNDTAISNMKVIGYILVITFTLMLLRFLWVLFFWNGKWFFNKDQNIYKPGLRSTLLISI 35- 9 Query: 359 SGVKGSVSIATILLLPKHSVIGE--LGYSLILFTVGAVTLMSFLTGLLVLPKLAPPLQVK 41- 6 SGV+G+V++A +P G +LILF V L + + +VLP L + Sbjct: 360 SGVRGAVTLAGSFSIPYFLEDGTPFPERNLILFLAAGVILCTLVIATVVLPILTEKEEED 41- 9 Query: 417 DD-----YLIRLSILTKVLSVLEEDGKSSENQASFYAVIDNYNSRIRHLILEQ--ESSDI 46- 9 ++ R ++ L ++ED + AS AVI YN ++++L +Q S+ I Sbjct: 420 EERNKKLLTARRKLIKTALQTIKEDMNETNKTASL-AVIAEYNEKMKNLRFQQYTSSNRI 47- 8 Query: 470 KKDLAELQLMMLSIESDGLEAAYRYGNISIKEYRIYQRYLKYLE 513 KK +++ + E + L G+I + + Q LE Sbjct: 479 KKHERKVRAQGVKAEQEALMKMLERGDIPEETANVLQERFNELE 522 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 779 A DNA sequence (GBSx0827) was identified in S. agalactiae <SEQ ID 2395> which encodes the amino acid sequence <SEQ ID 2396>. Analysis of this protein sequence reveals the following: TABLE-US-02323 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3494 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 780 A DNA sequence (GBSx0828) was identified in S. agalactiae <SEQ ID 2397> which encodes the amino acid sequence <SEQ ID 2398>. This protein is predicted to be integrase (phage-relatedpr). Analysis of this protein sequence reveals the following: TABLE-US-02324 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5094 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10173> which encodes amino acid sequence <SEQ ID 10174> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02325 >GP: AAF12706 GB: AF066865 integrase [bacteriophage TPW22] Identities = 171/353 (48%), Positives = 253/353 (71%), Gaps = 1/353 (0%) Query: 21 MASYRKRENGLWEYRISYKTIDGKYKRKEKGGFKTKKLAQAAAIEIEKKLTQNILTNDEV 80 - MA++RKR W++R+SYK +G+YK+ EKGG+KTKK A+AAA E +K+L + ++++ Sbjct: 1 MANFRKRGK-TWQFRLSYKDNNGEYKKFEKGGYKTKKEAEAAADEAKKRLNNHSEFDNDI 59 Query: 81 TLYDFVKTWSEVYKRPYVKDKTWETYSKNFKHIKNYFQELKVKDITPLYYQKKLNEFGEK 140- +LYDF + W++VYK+P+V + TW TY + I Y ++ + +ITP +YQ LN+ Sbjct: 60 SLYDFFEKWAKVYKKPHVTEATWRTYKRTLNLIDKYIKDKPIAEITPTFYQAVLNKMSLL 119- Query: 141 YAQETLEKFHYQIKGAMKVAVREQVVTFNFAEGAKVKSQVEPKNEEEDFLEEREYKALLA 20- 0 Y QE+L+KF++QIK AMK+AV E+V++ NFA+ K KS++ + EE +L EY LLA Sbjct: 120 YRQESLDKFYFQIKSAMKIAVHEKVISENFADFTKAKSKLAARPVEEKYLHADEYLKLLA 17- 9 Query: 201 LTRENIQYVSYFTLYLLAVTGLRFSEAMGLTWSDIDFKNGILDINKSFDYSNTQDFADLK 26- 0 + E ++Y SYF YL AVTG+RF+E +GLTWS +DF + I +++DYS T +FA+ K Sbjct: 180 IAEEKMEYTSYFACYLTAVTGMRFAELLGLTWSHVDFDKKEISIQRTWDYSITNNFAETK 23- 9 Query: 261 NESSKRKVPIDSNTIDILREYKKNHWQANIKNRVCFGVSNSACNKLIKKIVGRKVRNHSL 32- 0 NESSKRK+PI S TI +L++YKK +W N +RV + +SN+ NK IK I GRKV HSL Sbjct: 240 NESSKRKIPISSKTIKLLKKYKKEYWHENKYDRVIYNLSNNGLNKTIKVIAGRKVHPHSL 29- 9 Query: 321 RHTYASFLILNGVDIVTISKLLGHESPDITLKVYTHQMEALAERNFEKIKNIF 373 RH++AS+LI G+D++T+SKLLGHE+ ++TLKVY HQ++ + + N + I+ IF Sbjct: 300 RHSFASYLIYKGIDLLTVSKLLGHENLNVTLKVYAHQLKEMEQENNDVIRKIF 352 There is also homology to SEQ ID 578. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 781 A DNA sequence (GBSx0829) was identified in S. agalactiae <SEQ ID 2399> which encodes the amino acid sequence <SEQ ID 2400>. Analysis of this protein sequence reveals the following:

TABLE-US-02326 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3377 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 782 A DNA sequence (GBSx0830) was identified in S. agalactiae <SEQ ID 2401> which encodes the amino acid sequence <SEQ ID 2402>. This protein is predicted to be homology to cl-like repressor. Analysis of this protein sequence reveals the following: TABLE-US-02327 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0827 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02328 >GP: AAD44097 GB: AF115103 orf122 gp [Streptococcus thermophilus bacteriophage Sfi21] Identities = 57/125 (45%), Positives = 77/125 (61%), Gaps = 5/125 (4%) Query: 3 MKLDQLCKEFGVELCLFDASDWHSSGFYNPITKVLGVDVNLSEQEQKQVALHELQHKNHF 62 M +L ++FGV LC F +S W GF +P+ +V+ ++ +L + + +V LHEL H H Sbjct: 1 MNESELLEQFGVSLCEFSSSQWTRDGFLDPVNRVVYINRDLPTERRLKVLLHELGHLEHD 60 Query: 63 PYQYQLFRERCELDANRNMIHHLLKEELEIAEDHTQFNYLVFMEKYKLKTIADEAMIKEE 122- P QY+ RE+ E ANRNMIH LLK E+ FNY+ FMEKY L TI DE +K E Sbjct: 61 PKQYERLREKYEAQANRNMIHELLKN-----ENLDNFNYVHFMEKYNLTTICDETFVKNE 115- Query: 123 YLNLV 127 YL L+ Sbjct: 116 YLKLI 120 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 783 A DNA sequence (GBSx0831) was identified in S. agalactiae <SEQ ID 2403> which encodes the amino acid sequence <SEQ ID 2404>. This protein is predicted to be EpsR protein. Analysis of this protein sequence reveals the following: TABLE-US-02329 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4692 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02330 >GP: AAF12710 GB: AF066865 repressor protein [bacteriophage TPW22] Identities = 36/101 (35%), Positives = 62/101 (60%), Gaps = 7/101 (6%) Query: 4 LIDRIRELSNKKGMSLNDLEDTLGYSRNSLYSLNE-NSKMGKPKEIAQYFNVSLDYLLGL 62 L ++I+EL+++K +S+ +E+ LG++ ++ + N + K K++A+YFNVS+D+LLGL Sbjct: 3 LYEKIKELASQKNVSIRQVEEKLGFANGTIRQWGKKNPGINKVKDVAKYFNVSVDFLLGL 62 Query: 63 TDNPRIAS--DETAIIDGQVVDLREAAAHTMLFDGKPLDED 101 DN R D +D V+ E + FDGKPL ++ Sbjct: 63 DDNQRKKEPVDLADFVDDNKVNWDEWVS----FDGKPLSDE 99 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 784 A DNA sequence (GBSx0832) was identified in S. agalactiae <SEQ ID 2405> which encodes the amino acid sequence <SEQ ID 2406>. Analysis of this protein sequence reveals the following: TABLE-US-02331 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4079 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 785 A DNA sequence (GBSx0833) was identified in S. agalactiae <SEQ ID 2407> which encodes the amino acid sequence <SEQ ID 2408>. Analysis of this protein sequence reveals the following: TABLE-US-02332 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2942 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10171> which encodes amino acid sequence <SEQ ID 10172> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 786 A DNA sequence (GBSx0834) was identified in S. agalactiae <SEQ ID 2409> which encodes the amino acid sequence <SEQ ID 2410>. This protein is predicted to be a replication initiation protein Rep (RC). Analysis of this protein sequence reveals the following: TABLE-US-02333 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3335 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 787 A DNA sequence (GBSx0835) was identified in S. agalactiae <SEQ ID 2411> which encodes the amino acid sequence <SEQ ID 2412>. This protein is predicted to be antirepressor. Analysis of this protein sequence reveals the following: TABLE-US-02334 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3380 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02335 >GP: BAA97816 GB: AB044554 antirepressor [Staphylococcus aureus prophage phiPV83] Identities = 70/153 (45%), Positives = 93/153 (60%), Gaps = 15/153 (9%) Query: 3 EIFVFHGQEVRTVTINNEPWFVGKDVADILGYSKSRNAIALHVDEDDALKQGITDNLGRM 62 + F F VRTV I NEP+FVGKD+A+ILGY+++ NAI HVD +D L + + G+ Sbjct: 5 QTFNFKELPVRTVEIENEPYFVGKDIAEILGYARTDNAIRNHVDSEDKLTHQFSAS-GQN 63 Query: 63 QETIIINESGLYSLIL----SSKLPQVKE----FKRWVTSEVLPQIRQQGAYVPENLSDE 114- + IIINESGLYSLI SK +++E FKRWVTS+VLP IR+ G Y +N+ ++ Sbjct: 64 RNMIIINESGLYSLIFDASKQSKNEKIRETARKFKRWVTSDVLPAIRKHGIYATDNVIEQ 123- Query: 115 A------FIALFTGQKKLKEHQLALAQDVDYLK 141 I + T KK KE L L Q V+ K Sbjct: 124 TLKDPDYIITVLTEYKKEKEQNLVLQQQVEVNK 156 A related DNA sequence was identified in S. pyogenes <SEQ ID 2413> which encodes the amino acid sequence <SEQ ID 2414>. Analysis of this protein sequence reveals the following: TABLE-US-02336 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4609 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02337 Identities = 54/142 (38%), Positives = 73/142 (51%), Gaps = 7/142 (4%) Query: 11 EVRTVTINNEPWFVGKDVADILGYSKSRNAIALHVDEDDALKQGITDNLGRMQETIIINE 70 - EVRT TINN+ +F D IL S R I +++D I D+LGR Q+ INE Sbjct: 13 EVRTATINNQIYFNLNDCCQILELSNPRKTIE-RLNKDGVTTSDIIDSLGRTQQANFINE 71 Query: 71 SGLYSLILSSKLPQVKEFKRWVTSEVLPQIRQQGAYVPENLSDEA------FIALFTGQK 124- S Y L+ S+ P+ ++F WVTSEVLP IR+ GAY+ E ++A I L K Sbjct: 72 SNFYKLVFQSRKPEAEKFADWVTSEVLPSIRKHGAYMTEQTLEQALTSPDFLIRLANELK 131- Query: 125 KLKEHQLALAQDVDYLKNEQPI 146 + KE L + L E + Sbjct: 132 EEKERSRQLEAEKSILSVENMV 153 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 788 A DNA sequence (GBSx0836) was identified in S. agalactiae <SEQ ID 2415> which encodes the amino acid sequence <SEQ ID 2416>. This protein is predicted to be e11. Analysis of this protein sequence reveals the following: TABLE-US-02338 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3281 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02339 >GP: AAC27227 GB: AF009630 e11 [bacteriophage bIL170] Identities = 66/161 (40%), Positives = 93/161 (56%), Gaps = 13/161 (8%) Query: 15 YQVSNLGRVRSIGRTVNAKQRTRKTKGRILKQSL-SSGYAIVTLSVNGLRKSIRVHRLVA 73 - Y+VSNLG+VR+I GRILK + +GY + L N +K++ +HR++A Sbjct: 16 YEVSNLGKVRNI------------KSGRILKPWIVPNGYLMHQLCENNKKKNLFLHRIIA 63 Query: 74 EAFIPNPINKRTINHIDENKLNNRVDNLEWATDKENANHGNRTTKSSLGRCKPVEQFTLE 133- AFI NP K +NHIDENKLNN ++NLEW T KEN HG R + + K V Q L Sbjct: 64 TAFIDNPEEKPQVNHIDENKLNNDLNNLEWCTVKENNIHGTRMKRIAEKHFKKVIQLDLN 123- Query: 134 GEFINTFDSIKSASMKTGISSQRITATAMGHQKQTHGYKWR 174 +N F+S+ A +TG+S + I++ G +K +KWR Sbjct: 124 DNVLNEFESMVQAEQETGVSRRNISSCCNGKRKSAGRFKWR 164 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 789 A DNA sequence (GBSx0837) was identified in S. agalactiae <SEQ ID 2417> which encodes the amino acid sequence <SEQ ID 2418>. Analysis of this protein sequence reveals the following: TABLE-US-02340 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2357 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10169> which encodes amino acid sequence <SEQ ID 10170> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 790 A DNA sequence (GBSx0838) was identified in S. agalactiae <SEQ ID 2419> which encodes the amino acid sequence <SEQ ID 2420>. Analysis of this protein sequence reveals the following: TABLE-US-02341 Possible site: 57 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.47 Transmembrane 21-37 (19-38) ----- Final Results ----- bacterial membrane --- Certainty = 0.3187 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 791 A DNA sequence (GBSx0839) was identified in S. agalactiae <SEQ ID 2421> which encodes the amino acid sequence <SEQ ID 2422>. This protein is predicted to be DNA polymerase III delta prime subunit (dnaB). Analysis of this protein sequence reveals the following: TABLE-US-02342 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0544 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02343 AAF98347 AF280763 DNA polymerase III delta prime subunit [Streptococcus pyogenes] Identities = 284/444 (63%), Positives = 357/444 (79%), Gaps = 4/444 (0%) Query: 3 ELKVLPHDIQAEQSVLGSIFIKPEKMIEVAEYLKPNDFYRPAHKILFKAMVSLADRGEAI 62 EL+V P D+ AEQSVLGSIFI P+K+I V E++ P+DFY+ AHKI+F+AM++L+DR +AI Sbjct: 8 ELRVQPQDLLAEQSVLGSIFISPDKLIAVREFISPDDFYKYAHKIIFRAMITLSDRNDAI 67 Query: 63 DIVTIKSTLESTDELGMVGGISYIAEIVNAVPTSSHAEHYAKIVAKKAQLRSIIDNLSDS 122- D TI++ L+ D+L +GG+SYI E+VN+VPTS++AE+YAKIVA+KA LR II L++S Sbjct: 68 DATTIRTILDDQDDLQSIGGLSYIVELVNSVPTSANAEYYAKIVAEKAMLRDIIARLTES 127- Query: 123 IGNAYDEDMDIDEIIAKAERSLIEVSQASNKSSFRPIHDVLLENHSKIEERSNNTSQITG 18- 2 + AYDE + +E+IA ER+LIE+++ SN+S FR I DVL N+ +E RS TS +TG Sbjct: 128 VNLAYDEILKPEEVIAGVERALIELNEHSNRSGFRKISDVLKVNYEALEARSKQTSNVTG 18- 7 Query: 183 IETGFYDFDKLITGLHEDQLIVLAARPAMGKTALALNIAQNVATKSNKAVAVFSLEMGAE 24- 2 + TGF D DK+ TGLH DQL++LAARPA+GKTA LNIAQNV TK K VA+FSLEMGAE Sbjct: 188 LPTGFRDLDKITTGLHPDQLVILAARPAVGKTAFVLNIAQNVGTKQKKTVAIFSLEMGAE 24- 7 Query: 243 SLVERMLSAEGTIINHHIRTGNLTVNEWQRLIYAQGQLAEAPIFIDDTAGVKITDIRARA 30- 2 SLV+RML+AEG + +H +RTG LT +W + AQG LAEAPI+IDDT G+KIT+IRAR+ Sbjct: 248 SLVDRMLAAEGMVDSHSLRTGQLTDQDWNNVTIAQGALAEAPIYIDDTPGIKITEIRARS 30- 7 Query: 303 RRLSQETD-GLGLIVIDYLQLIQGSRSDNRQQEVSEISRQLKIIAKELKVPVIALSQLSR 36- 1 R+LSQE D GLGLIVIDYLQLI G++ +NRQQEVS+ISRQLKI+AKELKVPVIALSQLSR Sbjct: 308 RKLSQEVDGGLGLIVIDYLQLITGTKPENRQQEVSDISRQLKILAKELKVPVIALSQLSR 36- 7 Query: 362 GVEQRNDKRPIMSDLRESGSIEQDADIVAFLYRDAYYQ---DKKEGQPENDITELIIRKN 41- 8 GVEQR DKRP++SD+RESGSIEQDADIVAFLYRD YY+ D E E++ E+I+ KN Sbjct: 368 GVEQRQDKRPVLSDIRESGSIEQDADIVAFLYRDDYYRKECDDAEEAVEDNTIEVILEKN 42- 7 Query: 419 RHGNLGTVKLYFHKEYTKFSSVEE 442 R G GTVKL F KEY KFSS+ + Sbjct: 428 RAGARGTVKLMFQKEYNKFSSIAQ 451 There is also homology to SEQ ID 2424: TABLE-US-02344 Identities = 284/444 (63%), Positives = 357/444 (79%), Gaps = 4/444 (0%) Query: 3 ELKVLPHDIQAEQSVLGSIFIKPEKMIEVAEYLKPNDFYRPAHKILFKAMVSLADRGEAI 62 EL+V P D+ AEQSVLGSIFI P+K+I V E++ P+DFY+ AHKI+F+AM++L+DR +AI Sbjct: 11 ELRVQPQDLLAEQSVLGSIFISPDKLIAVREFISPDDFYKYAHKIIFRAMITLSDRNDAI 70 Query: 63 DIVTIKSTLESTDELGMVGGISYIAEIVNAVPTSSHAEHYAKIVAKKAQLRSIIDNLSDS 122- D TI++ L+ D+L +GG+SYI E+VN+VPTS++AE+YAKIVA+KA LR II L++S Sbjct: 71 DATTIRTILDDQDDLQSIGGLSYIVELVNSVPTSANAEYYAKIVAEKAMLRDIIARLTES 130- Query: 123 IGNAYDEDMDIDEIIAKAERSLIEVSQASNKSSFRPIHDVLLENHSKIEERSNNTSQITG 18- 2 + AYDE + +E+IA ER+LIE+++ SN+S FR I DVL N+ +E RS TS +TG Sbjct: 131 VNLAYDEILKPEEVIAGVERALIELNEHSNRSGFRKISDVLKVNYEALEARSKQTSNVTG 19- 0 Query: 183 IETGFYDFDKLITGLHEDQLIVLAARPAMGKTALALNIAQNVATKSNKAVAVFSLEMGAE 24- 2 + TGF D DK+ TGLH DQL++LAARPA+GKTA LNIAQNV TK K VA+FSLEMGAE Sbjct: 191 LPTGFRDLDKITTGLHPDQLVILAARPAVGKTAFVLNIAQNVGTKQKKTVAIFSLEMGAE 25- 0 Query: 243 SLVERMLSAEGTIINHHIRTGNLTVNEWQRLIYAQGQLAEAPIFIDDTAGVKITDIRARA 30- 2 SLV+RML+AEG + +H +RTG LT +W + AQG LAEAPI+IDDT G+KIT+IRAR+ Sbjct: 251 SLVDRMLAAEGMVDSHSLRTGQLTDQDWNNVTIAQGALAEAPIYIDDTPGIKITEIRARS 31- 0 Query: 303 RRLSQETD-GLGLIVIDYLQLIQGSRSDNRQQEVSEISRQLKIIAKELKVPVIALSQLSR 36- 1 R+LSQE D GLGLIVIDYLQLI G++ +NRQQEVS+ISRQLKI+AKELKVPVIALSQLSR Sbjct: 311 RKLSQEVDGGLGLIVIDYLQLITGTKPENRQQEVSDISRQLKILAKELKVPVIALSQLSR 37- 0 Query: 362 GVEQRNDKRPIMSDLRESGSIEQDADIVAFLYRDAYYQ---DKKEGQPENDITELIIRKN 41- 8 GVEQR DKRP++SD+RESGSIEQDADIVAFLYRD YY+ D E E++ E+I+ KN Sbjct: 371 GVEQRQDKRPVLSDIRESGSIEQDADIVAFLYRDDYYRKECDDAEEAVEDNTIEVILEKN 43- 0 Query: 419 RHGNLGTVKLYFHKEYTKFSSVEE 442 R G GTVKL F KEY KFSS+ + Sbjct: 431 RAGARGTVKLMFQKEYNKFSSIAQ 454 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 792 A DNA sequence (GBSx0840) was identified in S. agalactiae <SEQ ID 2425> which encodes the amino acid sequence <SEQ ID 2426>. Analysis of this protein sequence reveals the following: TABLE-US-02345 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2146 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10167> which encodes amino acid sequence <SEQ ID 10168> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 793 A DNA sequence (GBSx0841) was identified in S. agalactiae <SEQ ID 2427> which encodes the amino acid sequence <SEQ ID 2428>. Analysis of this protein sequence reveals the following: TABLE-US-02346 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2774 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 794 A DNA sequence (GBSx0842) was identified in S. agalactiae <SEQ ID 2429> which encodes the amino acid sequence <SEQ ID 2430>. Analysis of this protein sequence reveals the following:

TABLE-US-02347 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.91 Transmembrane 63-79 (62-79) ----- Final Results ----- bacterial membrane --- Certainty = 0.1765 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8661> which encodes amino acid sequence <SEQ ID 8662> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-02348 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -11.31 GvH: Signal Score (-7.5): -1.86 Possible site: 28 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -1.91 threshold: 0.0 INTEGRAL Likelihood = -1.91 Transmembrane 61-77 (60-77) PERIPHERAL Likelihood = 9.92 19 modified ALOM score: 0.88 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1765 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02349 >GP: AAB18686 GB: U38906 ORF11 [Bacteriophage r1t] Identities = 101/249 (40%), Positives = 157/249 (62%), Gaps = 21/249 (8%) Query: 3 MAQRRMFSRKITETDRFLEMPLSSQALYFHLNMGADDEGFIDKAKTIQRTIGASDDDMKL 62 MAQRRM ++ +T +FL +PL +QALYFHL + ADD+G ++ A + R +GA++D + L Sbjct: 1 MAQRRMIDKRTIQTQKFLRLPLETQALYFHLMLNADDDGVVE-AFPVVRMVGAAEDSLGL 59 Query: 63 LIAKGFLIPFDSGVV-VIRHWRIHNYIQSDRFQSTLYQSEKAQLEYDKSKTASLKPIGNC 121- L+ K F+ P + +V I ++ N I+ DR++++ Y AQL ++ ++P N Sbjct: 60 LVVKQFIKPLNEEMVYFIIDFKEQNTIKKDRYKASKY----AQLLTNEEFGTEMEPKRNQ 115- Query: 122 IQNVSKMETQVRLSKGSLDKDSLTTYPTVSDNEEEDIPYKEIISYLNEKANRNYRPNIQK 18- 1 + K RL K LDK++ +S ++ IPY EI+ YLN+K R++R N++ Sbjct: 116 LGTSDKN----RLDKNRLDKNN-----NMSGKPDDVIPYSEILEYLNKKTGRSFR-NVEA 16- 5 Query: 182 NKTLIKARWSEGFRLDDFKHVIDTTVKDWSGTKY-----EKYLRPETLFGSKFEGYLNQA 23- 6 NK LIKARW+EG++L+DFK V+D V +WSG + E YL+P+TLF +KF+ YLNQ Sbjct: 166 NKKLIKARWNEGYKLEDFKTVVDNMVSNWSGKMFNGVPAENYLQPKTLFSNKFDSYLNQV 22- 5 Query: 237 PRIKTETID 245 PRI+ + I+ Sbjct: 226 PRIEQKEIN 234 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8662 (GBS344) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 12; MW 30.9 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 81 (lane 3; MW 59 kDa). The GBS344-GST fusion product was purified (FIG. 213, (lane 3; FIG. 226, lanes 4-6) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 271), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 795 A DNA sequence (GBSx0843) was identified in S. agalactiae <SEQ ID 2431> which encodes the amino acid sequence <SEQ ID 2432>. Analysis of this protein sequence reveals the following: TABLE-US-02350 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2549 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database: TABLE-US-02351 >GP: AAG31329 GB: AF182207 ORF 272 [Bacteriophage mv4] Identities = 70/241 (29%), Positives = 125/241 (51%), Gaps = 30/241 (12%) Query: 12 VLEETCEVHGCQLWLTKVPIKGRLEELKQCPECTKAAINIFENKLNSQSKINSKLADTYA 71 - VLE+ C HG L +T +G E++ CP+C A+ + + + + +++ S +A Sbjct: 16 VLEQKCSKHGLNL-ITYKNHEG--EQVTCCPQCQAEALEVLQERFDQKAR-QSIIARK-- 69 Query: 72 VFERDSLVSDKLRAKSLENYE---------IKDEIDQHAINYAKRMEQFYRQDRTGNAII 122- F +SL + K+ + + +E IK ++ A+ +A + + A++ Sbjct: 70 -FRENSLANSKMWKCTFDTFEAQPGSAEELIKGQVRNAAVAFATKPVAHH-------AVL 121- Query: 123 TGPSGVGKSHLTYGLAKFMNEQFKAYESPKSVLFISLVSLFTKIKESFKVDNGY-RQADM 18- 1 G G GKSHL A M ++ + K++ FI++ LF+KIK SF + Y + Sbjct: 122 YGQPGAGKSHL----AMAMMQEIHKHRPTKTMAFINISRLFSKIKNSFDDPSEYWTKEKA 17- 7 Query: 182 IELLTRVDYLFLDDLGKESRKGDS--QNNEWTHQILYEILDNRSNTIINTNLSSKEIKALY 2- 40 +E++ VD L +DDLG ES G + + +W ++Y++L+N+ II TNLS +E+K +Y Sbjct: 178 LEIMRGVDLLCIDDLGTESSMGRTGQEATKWAQDVIYDVLENQDRIIITTNLSERELKRVY 2- 38 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 796 A DNA sequence (GBSx0844) was identified in S. agalactiae <SEQ ID 2433> which encodes the amino acid sequence <SEQ ID 2434>. This protein is predicted to be methyl transferase. Analysis of this protein sequence reveals the following: TABLE-US-02352 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1241 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10165> which encodes amino acid sequence <SEQ ID 10166> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02353 >GP: AAC98421 GB: L29323 methyl transferase [Streptococcus pneumoniae] Identities = 262/474 (55%), Positives 313/474 (65%), Gaps = 71/474 (14%) Query: 2 MKFLDLFAGIGGFRLGMEQAGHECIGFCEINKFARASYKVIHDTEGEIELHDITRVSD-E 60 M+F+DLF+GIGGFRLGME GHECIGFCEI+KFAR SYK I TEGEIE HDI VSD E Sbjct: 1 MRFIDLFSGIGGFRLGMESVGHECIGFCEIDKFARESYKSIFQTEGEIEFHDIRDVSDDE 60 Query: 61 FIRGIGSVDVICGGFPCQAFSIAGNRRGFEDTRGTLFFEIARFASILRPKYLFLENVKGL 120- F + G VDVICGGFPCQAFSIAG R GFEDTRGTLFFEIAR A ++P++LFLENVKGL Sbjct: 61 FKKLRGKVDVICGGFPCQAFSIAGRRLGFEDTRGTLFFEIARAAKQIQPRFLFLENVKGL 120- Query: 121 LNHEGGATFETIIRTLDELGYNVEWQIFNSKNFGVPQNRERVFIIGHLRGEGTRPIFPFE 18- 0 LNH+ G TF TI+ TLDELG++VEWQ+ NSK+FGVPQNRERVFIIGH R GTR FPF Sbjct: 121 LNHDKGRTFTTILTTLDELGFDVEWQMLNSKDFGVPQNRERVFIIGHSRKRGTRLGFPFR 18- 0 Query: 181 SSITENYPIHTRKIGNVNPSGNGMNGEVYDSEGLSPTLTTNKGEGVKIAVN--------- 23- 1 P + +GN+NPS +GM+G+VY SEGL+PTL KGEG KIA+ Sbjct: 181 REGQATNPETLKILGNLNPSKSGMSGKVYYSEGLAPTLVRGKGEGFKIAIPCMTPDRLDK 24- 0 Query: 232 --------------------------VVGRLPGKFEMPNRVYDPDGLAPTIRTMQGGGLE 26- 5 VVG LP F+ RVY +GL+PT+ TMQGG Sbjct: 241 RQNGRRFKDNQEPMFTLNTQDRHGIVVVGDLPTSFKETGRVYGSEGLSPTLTTMQGGDKI 30- 0 Query: 266 PKIIQRGRGYNQGGEYEISPTVTCNSWQENNLLKIKEATKKGYSEAEAGDSVNLSHPNSE 32- 5 PKI+ + LK++EATKKGY++AE GDS+NL P+S+ Sbjct: 301 PKILIP---------------------EPIQFLKVREATKKGYAQAEIGDSINLERPSSQ 33- 9 Query: 326 TRRGRVGKGIANTLLTGEEQGVVV--YDLYNRRKKDIVGTLTASGHNGNTTTGTFGISNG 38- 3 RRGRVGKGIANTL T + GVVV Y+ +++ + G L G Sbjct: 340 HRRGRVGKGIANTLTTSGQMGVVVASYEGEDKQVYQVAGVLID------------GQFYR 38- 7 Query: 384 FRIRKLTPRECWRLQGFPDWAFDKASQVNSNSQLYKQAGNSVTVNVIAAIARRL 437 RIR++TP+EC+RLQGFPDWAF+ A +V+SNSQLYKQAGNSVTV VIAAIA++L Sbjct: 388 LRIRRITPKECFRLQGFPDWAFEAARKVSSNSQLYKQAGNSVTVPVIAAIAKKL 441 There is also homology to SEQ ID 2436: TABLE-US-02354 Identities = 53/75 (70%), Positives = 62/75 (82%), Gaps = 1/75 (1%) Query: 2 MKFLDLFAGIGGFRLGMEQAGHECIGFCEINKFARASYKVIHDTEGEIELHDITRVSDEF 61 MKFLDLFAGIGGFRLG+ HECIGFCEI+KFAR SYK I++TEGEIE HDI +V+D+ Sbjct: 4 MKFLDLFAGIGGFRLGLINQCHECIGFCEIDKFARQSYKAIYETEGEIEFHDIRQVTDQD 63 Query: 62 IRGI-GSVDVICGGF 75 R + G VD+ICGGF Sbjct: 64 FRQLRGQVDIICGGF 78 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 797 A DNA sequence (GBSx0845) was identified in S. agalactiae <SEQ ID 2437> which encodes the amino acid sequence <SEQ ID 2438>. Analysis of this protein sequence reveals the following: TABLE-US-02355 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2585 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 798 A DNA sequence (GBSx0846) was identified in S. agalactiae <SEQ ID 2439> which encodes the amino acid sequence <SEQ ID 2440>. This protein is predicted to be arpR protein. Analysis of this protein sequence reveals the following: TABLE-US-02356 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5070 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02357 >GP: AAB09197 GB: U24159 orf12 [Bacteriophage HP1] Identities = 34/69 (49%), Positives = 47/69 (67%), Gaps = 1/69 (1%) Query: 1 MTKTMTLEEKVEQWFIDRNLHE-ANPVKQFQKLIEETGELYSGIAKGKSEIIRDSLGDMQ 59 M L + +EQW DRNL E + P KQF KL+EE GEL SG+AK K ++I+DS+GD Sbjct: 1 MADLQQLIKNIEQWAEDRNLVEDSTPQKQFIKLMEEFGELCSGVAKNKPDVIKDSIGDCF 60 Query: 60 VVLIGIEQQ 68 VV++ + +Q Sbjct: 61 VVMVILAKQ 69 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 799 A DNA sequence (GBSx0847) was identified in S. agalactiae <SEQ ID 2441> which encodes the amino acid sequence <SEQ ID 2442>. Analysis of this protein sequence reveals the following: TABLE-US-02358 Possible site: 58 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.10 Transmembrane 13-29 (10-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.3039 (Affirmative) < succ> bacterial outside --- Certainty= 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty= 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02359 >GP: AAD21919 GB: AF085222 unknown [Streptococcus thermophilus bacteriophage DT1] Identities = 31/67 (46%), Positives = 49/67 (72%), Gaps = 1/67 (1%) Query: 42 HQEADRVIIYVADNAGAEMFGKITDKEIIEGRHTVTAGAYGKFLVTEEQYNEITVGDDIP 101- ++ + ++++ ADN E+ GK+T K ++ +T+ GAYGKFLV++EQY+ + VGD+IP Sbjct: 34 NRPVEAIVVHKADNF-VELHGKVTGKSMVGKLYTIDCGAYGKFLVSKEQYDSVQVGDEIP 92 Query: 102 DYLKGRG 108 YLKGRG Sbjct: 93 SYLKGRG 99 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 800 A DNA sequence (GBSx0848) was identified in S. agalactiae <SEQ ID 2443> which encodes the amino acid sequence <SEQ ID 2444>. This protein is predicted to be gene 17 protein. Analysis of this protein sequence reveals the following: TABLE-US-02360 Possible Site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5428 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02361 > GP: CAA24397 GB: V01146 gene 1.7 [Bacteriophage T7] Identities = 30/72 (41%), Positives = 40/72 (54%) Query: 47 DNVNYPSHYQGKYGLESIDVLRNFMTPEMLKGFYLGNALKYQLRYRKKNGLEDLKKARKN 106- + V PSHY +E+I+V+ MT E KG+ GN LKY+LR KK+ L L+K Sbjct: 120 EGVTKPSHYMLFDDIEAIEVIARSMTVEQFKGYCFGNILKYRLRAGKKSELAYLEKDLAK 17- 9 Query: 107 LDWLIEEMEKEK 118 D+ E EK K Sbjct: 180 ADFYKELFEKHK 191 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 801 A DNA sequence (GBSx0849) was identified in S. agalactiae <SEQ ID 2445> which encodes the amino acid sequence <SEQ ID 2446>. Analysis of this protein sequence reveals the following: TABLE-US-02362 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1375 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 802 A DNA sequence (GBSx0850) was identified in S. agalactiae <SEQ ID 2447> which encodes the amino acid sequence <SEQ ID 2448>. Analysis of this protein sequence reveals the following: TABLE-US-02363 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0087(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10163> which encodes amino acid sequence <SEQ ID 10164> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02364 >GP: AAF26608 GB: AF145054 ORF9 [Streptococcus thermophilus bacteriophage 7201] Identities = 99/148 (66%), Positives = 116/148 (77%), Gaps = 10/148 (6%) Query: 5 MINNVVLIGRLTRDVELRYTPSNIANATFNLAVNRNFKNAAGDREADFINCVMWRQQAEN 64 MINN VL+GRLT+D E +YT SNIA A+F+LAVNRNFK+A G+READFINCV+WRQQAEN Sbjct: 1 MINNTVLVGRLTKDPEFKYTGSNIAVASFSLAVNRNFKDANGEREADFINCVIWRQQAEN 60 Query: 65 LANWTKKGMLIGITGRIQTRSYENQQGQRIYVTEVVADSFQILEKR----DNSTNQASMD 120- LANW KKG LIGITGRIQTRSYENQQGQR+YVTEVVA++FQ+LE R + N + Sbjct: 61 LANWAKKGALIGITGRIQTRSYENQQGQRVYVTEVVAENFQMLESRAAREGGNANNSYSQ 120- Query: 121 DQLP------PSFGNSQPMDISDDDLPF 142 Q+P + N QP+DIS DDLPF Sbjct: 121 QQVPNFARKNTEYSNKQPLDISSDDLPF 148 There is also homology to SEQ ID 1492. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 803 A DNA sequence (GBSx0851) was identified in S. agalactiae <SEQ ID 2449> which encodes the amino acid sequence <SEQ ID 2450>. This protein is predicted to be puff C4B protein. Analysis of this protein sequence reveals the following: TABLE-US-02365 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1203(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10161> which encodes amino acid sequence <SEQ ID 10162> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 804 A DNA sequence (GBSx0852) was identified in S. agalactiae <SEQ ID 2451> which encodes the amino acid sequence <SEQ ID 2452>. This protein is predicted to be F5M15.19. Analysis of this protein sequence reveals the following: TABLE-US-02366 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.34 Transmembrane 7-23 (6-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.1935(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 805 A DNA sequence (GBSx0853) was identified in S. agalactiae <SEQ ID 2453> which encodes the amino acid sequence <SEQ ID 2454>. Analysis of this protein sequence reveals the following: TABLE-US-02367 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4398(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10159> which encodes amino acid sequence <SEQ ID 10160> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 806 A DNA sequence (GBSx0855) was identified in S. agalactiae <SEQ ID 2455> which encodes the amino acid sequence <SEQ ID 2456>. Analysis of this protein sequence reveals the following:

TABLE-US-02368 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2992(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 807 A DNA sequence (GBSx0856) was identified in S. agalactiae <SEQ ID 2457> which encodes the amino acid sequence <SEQ ID 2458>. Analysis of this protein sequence reveals the following: TABLE-US-02369 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4639(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02370 >GP: BAB07758 GB: AP001520 unknown conserved protein [Bacillus halodurans] Identities = 65/184 (35%), Positives = 102/184 (55%), Gaps = 6/184 (3%) Query: 1 MNIVEPLRDKDDIQAMKDYLSSWNEKYYMLFLLGINTGFRVGDILKLKVKDVQGWHIKVR 60 M V P RD D IQA+K L + + Y+LF +GINTG R+ +L LK+KDV Sbjct: 1 MEYVVPFRDVDQIQAIKRSLKKKSPRDYLLFTIGINTGLRISQLLALKIKDVYDGQKPKD 60 Query: 61 EQKTGKYKSIKMTRPLKNELR---EFVKDKELHEYLFQSRVGKNKALSYKTVYWFLKRAA 117- + + + + +K L+ F++ +E H LF S ++ ++ + Y +K+AA Sbjct: 61 YLQLESGEIVYLNDQVKKALQFYAHFIEFQEQH-CLFAS-TNPDQPMTRQHAYRIIKQAA 118- Query: 118 EDLGI-DNVGTHTMRKTFGYHYYKKYKNVADLMSLFNHSSPAVTLIYICVRQDELDTKMS 17- 6 +G+ D +GTHT+RKTFGYH Y++ ++ L FNH +PA TL YI + ++E Sbjct: 119 LQVGLTDQIGTHTLRKTFGYHAYRQGVALSLLQQRFNHQTPAQTLRYIDIAKNEQTIPRI 17- 8 Query: 177 NFSL 180 N +L Sbjct: 179 NVNL 182 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 808 A DNA sequence (GBSx0857) was identified in S. agalactiae <SEQ ID 2459> which encodes the amino acid sequence <SEQ ID 2460>. Analysis of this protein sequence reveals the following: TABLE-US-02371 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3582(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 809 A DNA sequence (GBSx0858) was identified in S. agalactiae <SEQ ID 2461> which encodes the amino acid sequence <SEQ ID 2462>. Analysis of this protein sequence reveals the following: TABLE-US-02372 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2732(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 810 A DNA sequence (GBSx0859) was identified in S. agalactiae <SEQ ID 2463> which encodes the amino acid sequence <SEQ ID 2464>. Analysis of this protein sequence reveals the following: TABLE-US-02373 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1720(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 811 A DNA sequence (GBSx0860) was identified in S. agalactiae <SEQ ID 2465> which encodes the amino acid sequence <SEQ ID 2466>. Analysis of this protein sequence reveals the following: TABLE-US-02374 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2619(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10157> which encodes amino acid sequence <SEQ ID 10158> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 812 A DNA sequence (GBSx0861) was identified in S. agalactiae <SEQ ID 2467> which encodes the amino acid sequence <SEQ ID 2468>. This protein is predicted to be terminase large subunit. Analysis of this protein sequence reveals the following: TABLE-US-02375 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2753(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02376 >GP: AAC27181 GB: AF009630 putative terminase subunit [bacteriophage bIL170] Identities = 147/531 (27%), Positives = 261/531 (48%), Gaps = 26/531 (4%) Query: 19 IRICKLTMKSIRRVERYKEQYLFKQEEADKRIEFIEEECSNTKGLAGKLRLALPQKVWLE 78 - I + K K+I++ R ++Y+++ + + IE+IE+ T G K++L QK W E Sbjct: 16 IELNKYMRKTIQKQIRIHKKYIYRYDRVTQAIEWIEDNFYLTTGNLMKIKLHPTQKYWYE 75 Query: 79 TTWGFYHTVEVTKTNPDTLEEYTDYEERRLIHEVPIIVPRGTGKTTLGSAIAEVGQIIDG 138- G+ D ++E + LI+E+ + + RG+GK++L + I+ G Sbjct: 76 LMLGY-----------DMVDEKG--VQVNLINEIFLNLGRGSGKSSLMATRVLNWMILGG 122- Query: 139 EWGADIQLLAYSREQAGYLFNASRAMLSNEESLLHYMREADILRSTKQGILYETTNSLMS 19- 8 ++G + ++AY QA ++F+ R ++L Y E I +STKQG+ + + Sbjct: 123 QYGGESLVIAYDNTQARHVFDQVRNQTEASDTLRVY-NENKIFKSTKQGLEFTAFKTTFK 18- 1 Query: 199 IKTSDYESLDGTNAHYNIFDEVHTYDDDFIKVVNDGSSRKRKNWITWYISTNGTKRDKLF 25- 8 +T+D G N+ NIFDEVHTY +D + VN GS +K+ NW + YI++ G KRD L+ Sbjct: 182 KQTNDTLRAQGGNSSLNIFDEVHTYGEDITESVNKGSRQKQDNWQSIYITSGGLKRDGLY 24- 1 Query: 259 DKYYNIWVDILDDKIINDSVMPWIYQLDDVSEIHDPDMWQKAMPLLGITTEKETIARDIE 31- 8 DK + +++ ND +Y L++ ++ D W A+PL+G + + + E Sbjct: 242 DKLVERFKS--EEEFYNDRSFGLLYMLENHEQVKDKKNWTMALPLIGDVPKWSGVIEEYE 29- 9 Query: 319 MSKNDPAQQAELMAKTFNLPVNNYLAYFSNEECKGWSDKFDESLFVGDDERNARCVIGID 37- 8 +++ DPA Q + +A LP+ + YF+ ++ K +F+ S+F R +GID Sbjct: 300 LAQGDPALQNKFLAFNMGLPMQDTAYYFTPQDTK--LTEFNLSVF-----NKNRTYVGID 35- 2 Query: 379 LSDVNDICSISFMVVRGEERHYLNKKFMPRHTIETLPKELRDKYTEWELSGMLHVHELDY 43- 8 LS + D+ ++SF+ + + F R E L E ++ +TE+ G L + + +Y Sbjct: 353 LSLIGDLTAVSFVCELEGKTYSHTLTFSVRSQYEQLDTEQQELWTEFVDRGELILLDTEY 41- 2 Query: 439 NDQAYIFEELRQFMSDNRILPVAVGYDRYNARELIRLFNDYYGDICHDIPQTVK---SLS 49- 5 + + + F S +GYD L L Y+ D D + ++ S++ Sbjct: 413 INVNDLIPYINDFRSKTGCRLRKIGYDPARYEILKGLIERYFFDKDGDNQRAIRQGFSMN 47- 2 Query: 496 NPLKVYKEKAKMGKIIFDDPVATWNHANVRVKIDANNNIFPNKEKAKEKID 546 + +K+ K K K+I + V W N VKI + + K+ K+KID Sbjct: 473 DYIKLLKSKLVENKLIHNQKVMQWALNNTAVKIGQSGDYMYTKKLEKDKID 523 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 813 A DNA sequence (GBSx0862) was identified in S. agalactiae <SEQ ID 2469> which encodes the amino acid sequence <SEQ ID 2470>. Analysis of this protein sequence reveals the following: TABLE-US-02377 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3319(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02378 >GP: AAB41469 GB: L35061 orfL4 [Bacteriophage phi-41] Identities = 86/374 (22%), Positives = 166/374 (43%), Gaps = 38/374 (10%) Query: 12 FARIFRPNNRKSTRTYLQRSISYWRRNSIYLDNIYNKISTDTAQLRFKHVKITRNPGGVD 71 - F+R N+ + + ++ Y S ++ NI+NKI+ + ++ F HVK ++ G D Sbjct: 10 FSRGKLNNDTQRVTAWQNEAVEY---TSAFVTNIHNKIANEITKVEFNHVKYKKSDVGSD 66 Query: 72 SMVWYEHSDLAEVLTVSPNPLEVPVVFWSNVTRAMLRDGVAVVVPRW--KNGRLVEIWLA 129- +++ SDL EVL S + FW V + +L + P + K G LV++ A Sbjct: 67 TLISMAGSDLDEVLNWSSKGERNSMEFWQKVIKKLLTTRYIDLYPIFDRKTGDLVDLLFA 126- Query: 130 KKTVTWTAESVELMLDDVAVELPLTDVWVFENPKLNVTAQLNQITELIDINLNALTEKLS 18- 9 + E + ++ + N+ T ++D L + KL Sbjct: 127 DNKKEYKPEELVRLISPFYI---------------------NEDTSILDNALAGIQTKLE 16- 5 Query: 190 DGNSSLRGFLKLPT---KAADEHLKQQARDRVDSMLDLAKNGGIAYLEQGEEFQELSKDY 24- 6 G ++G LK+ D+ K +A + +M +++ G+ + E EL KDY Sbjct: 166 QGK--MKGLLKINAFIDTDNDQEFKDKAMLTIKNMQEMSNYNGLTPTDNKTEIVELKKDY 22- 3 Query: 247 STASKEELEFLKSQLYNAHGINEKLFTCDYTEEQYRAYYSSVMKLYQRVYSEEINRKYFT 30- 6 S +K+E++ +KS+L + +NE + ++EQ +Y+S + +E+ K + Sbjct: 224 SVLNKDEIDLIKSELLTGYFMNENILLGTASQEQQIYFYNSTIIPLLIQLEKELTYKLIS 28- 3 Query: 307 KTAR--TQGN----KLLVFFDMADMISFKDLVEGGFKSKYAGLMNSNEFRETYLGLPGYE 36- 0 R +GN +++V + + K+L++ ++ + N+ +G + Sbjct: 284 TNRRRVVKGNLYYERIIVDNQLFKFATLKELIDLYHENINGPIFTQNQLL-VKMGEQPIE 34- 2 Query: 361 GGEVFETNLNAVRI 374 GG+V+ NLNAV + Sbjct: 343 GGDVYIANLNAVAV 356 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 814 A DNA sequence (GBSx0863) was identified in S. agalactiae <SEQ ID 2471> which encodes the amino acid sequence <SEQ ID 2472>. This protein is predicted to be a prohead protease. Analysis of this protein sequence reveals the following: TABLE-US-02379 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3496(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02380 >GP: AAF31089 GB: AF069529 protease [Bacteriophage HK97] Identities = 52/142 (36%), Positives = 73/142 (50%), Gaps = 11/142 (7%) Query: 21 FEAYASTYDNTDREGDVMAKGCFDNTLKSKA-VVPMCLNHDR-NCVIGKHE-LSVDEKGL 77 - FE YAS ++NTD +GD++ G F N L ++ V M NH +GK + L+ DEKGL Sbjct: 26 FEGYASVFNNTDSDGDIILPGAFKNALANQTRKVAMFFNHKTWELPVGKWDSLAEDEKGL 85 Query: 78 RTRSTFNLSDPEAKKTYDLMKMGALDSLSIGFFI--KDYEPIDAKQPYGGWIFKEVE-IF 134- R A M+ G ++ +S+GF + DY I G IFK ++ + Sbjct: 86 YVRGQLTPGHSGAADLKAAMQHGTVEGMSVGFSVAKDDYTIIPT-----GRIFKNIQALR 140- Query: 135 EISVVTVPANPQATVDNIKEFD 156 EISV T PAN QA + +K D Sbjct: 141 EISVCTFPANEQAGIAAMKSVD 162 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 815 A DNA sequence (GBSx0864) was identified in S. agalactiae <SEQ ID 2473> which encodes the amino acid sequence <SEQ ID 2474>. Analysis of this protein sequence reveals the following: TABLE-US-02381 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2247(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10155> which encodes amino acid sequence <SEQ ID 10156> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02382 >GP: AAC27185 GB: AF009630 16 [bacteriophage bIL170] Identities = 70/249 (28%), Positives = 121/249 (48%), Gaps = 23/249 (9%) Query: 51 LEQLKTDAESLVSQATA--IKETIAGLDSDIEETEEELSK-AAKIIK---------EKQK 98 - L +LK + SL SQ +K I L ++E E+ LS+ + +IIK EK K Sbjct: 13 LAELKENNVSLKSQINGFEVKNAIEDLPK-VQELEKTLSENSIEIIKIENELNAQEEKPK 71 Query: 99 GNTPM-DYLKTKAAALDFVRILMDNEGSANSARKAWEANLVEKGV--TNLTKILPEPVLI 155- G M ++++++ A +F +L N G + + AW A L E GV T+ T LP ++ Sbjct: 72 GKAKMTNFIESQNAVTEFFDVLKKNSGKSE-IKNAWNAKLAENGVTITDTTFQLPRKLVE 130- Query: 156 AIQDAFTNYNGILN--HVSKDPRYAVRVALQTQVSQAKGHKAGKTKKDEDFTFLDFTINS 21- 3 +I A N N + HV+ V + + ++A+ HK G+TK ++ T T+ Sbjct: 131 SINTALLNTNPVFKVFHVTNVGALLVSRSFDSS-AEAQVHKDGQTKTEQAATLTIDTLEP 18- 9 Query: 214 ATVY-IKYAFEYSDLKKDTTGAYFNYVMKELAQGFI-RTIERAVVIGDGKSN-SAEDKIT 27- 0 VY ++ E + + +N ++ EL Q + + ++ A+V GDG + + DK Sbjct: 190 VMVYKLQSLAERVKRLQMSYSELYNLIVAELTQAIVNKIVDLALVEGDGSNGFKSIDKEA 24- 9 Query: 271 EIKSIAEET 279 ++K I + T Sbjct: 250 DVKKIKKIT 258 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 816 A DNA sequence (GBSx0865) was identified in S. agalactiae <SEQ ID 2475> which encodes the amino acid sequence <SEQ ID 2476>. Analysis of this protein sequence reveals the following: TABLE-US-02383 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3068(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 817 A DNA sequence (GBSx0866) was identified in S. agalactiae <SEQ ID 2477> which encodes the amino acid sequence <SEQ ID 2478>. Analysis of this protein sequence reveals the following: TABLE-US-02384 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0437(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 818 A DNA sequence (GBSx0867) was identified in S. agalactiae <SEQ ID 2479> which encodes the amino acid sequence <SEQ ID 2480>. Analysis of this protein sequence reveals the following: TABLE-US-02385 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3181(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10153> which encodes amino acid sequence <SEQ ID 10154> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 819 A DNA sequence (GBSx0869) was identified in S. agalactiae <SEQ ID 2481> which encodes the amino acid sequence <SEQ ID 2482>. This protein is predicted to be a major structural protein. Analysis of this protein sequence reveals the following: TABLE-US-02386 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3364(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02387 >GP: AAA74331 GB: L33769 unidentified ORF28; putative [Bacteriophage bIL67] Identities = 55/201 (27%), Positives = 84/201 (41%), Gaps = 18/201 (8%) Query: 9 EVTHGNANGF-YAKIAKTDAGALDLQKPYPFTGLRSTSFETSQESNAYYAD-NVEHVRLQ 66 E+THG G + + + G P GLR ++ QE+ +YA N + + Sbjct: 8 ELTHGLGYGVVFTDLTGSKTGI-------PIAGLRGIETDSKQENKNFYAGFNAPYRTIA 60 Query: 67 GKKSTEGSITTYQIPKQFMIDHLGKKLTNSTPPALIDTGVNTN-FIWGYAETVTDEFGAE 125- G K T+ + +Y +P F LG S L D N + + YAE D+ G Sbjct: 61 GAKDTQIKVKSYDLPDDFATHALG---FGSVQGFLTDDVANYKPYGFAYAERYRDDDGTG 117- Query: 126 IEEFHIWTNVKASAPKGSTSTDETSATPKEIEIPCTASPNNFIVDSEKKPVSEIVWRDDS 18- 5 + + +V+A+ P + DE S T KE E T + +F + +K+ + D Sbjct: 118 YKA-TFYPSVQATTPSDTAEADEESPTGKEYEHEATVTTGDFTLGDKKRLFVKFKVSDTE 17- 6 Query: 186 KGT-VRGK---FDKLFADKSP 202 T GK F KLF D P Sbjct: 177 LATGTSGKALAFKKLFTDLKP 197 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 820 A DNA sequence (GBSx0870) was identified in S. agalactiae <SEQ ID 2483> which encodes the amino acid sequence <SEQ ID 2484>. Analysis of this protein sequence reveals the following:

TABLE-US-02388 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2531(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 821 A DNA sequence (GBSx0871) was identified in S. agalactiae <SEQ ID 2485> which encodes the amino acid sequence <SEQ ID 2486>. Analysis of this protein sequence reveals the following: TABLE-US-02389 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2972(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 822 A DNA sequence (GBSx0872) was identified in S. agalactiae <SEQ ID 2487> which encodes the amino acid sequence <SEQ ID 2488>. Analysis of this protein sequence reveals the following: TABLE-US-02390 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3860(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 823 A DNA sequence (GBSx0873) was identified in S. agalactiae <SEQ ID 2489> which encodes the amino acid sequence <SEQ ID 2490>. Analysis of this protein sequence reveals the following: TABLE-US-02391 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.22 Transmembrane 605-621 (569-631) INTEGRAL Likelihood = -8.12 Transmembrane 583-599 (569-604) ----- Final Results ----- bacterial membrane --- Certainty = 0.6689(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02392 >GP: AAB70053 GB: AF011378 unknown [Bacteriophage skl] Identities = 159/709 (22%), Positives = 285/709 (39%), Gaps = 112/709 (15%) Query: 128 SILNLNKELDNVAKELDIVNQKLELDPDNVELAEQKMKLLGKQSELAGDKVQELKKKQAA 18- 7 S+ +N + + E + L+LDP N + Q K L Q L+ DK +LK++ ++ Sbjct: 21 SLKGVNTAMSGLRGEAKNLRDALKLDPTNTDKMAQLQKNLQTQLGLSRDKATKLKQELSS 80 Query: 188 LGDEK-IGTEEWRQLQNEIGQAEVEVLKIDRAMDILGESSRSATGDI--KEATSYLRADV 24- 4 + G ++W QL ++G AE + +++ + + + S + DI K T + + + Sbjct: 81 VDKSSPAGQKKWLQLTRDLGTAETQANRLEGEIKQVEGAISSGSWDIDAKMDTKGVNSGI 140- Query: 245 MMDVADKAG----------QIGQKMVDAGKMTVDAWSEIDEALDTVTTKTGLTGD----- 28- 9 + +G QIG V A + W + +A+DT L Sbjct: 141 DGMKSRFSGLREIAVGVFRQIGSSAVSAVGNGLKGW--VSDAMDTQKAMISLQNTLKFKG 19- 8 Query: 290 -------ALAELQEIAKDIATG------MPTSFQNAGD----AVGEL------NTQFGLT 32- 6 +Q +AKD + T+F GD AVG+ N FG T Sbjct: 199 NGQDFDYVSKSMQTLAKDTNANTEDTLKLSTTFIGLGDSAKTAVGKTEALVKANQAFGGT 25- 8 Query: 327 GEKLKSASELL--------IKYAEINE-TD--------ISSSAISAKQAIEAYG--LTAE 36- 7 GE+LK + + IN+ TD + S+ + A++ YG +A Sbjct: 259 GEQLKGVVQAYGQMSASGKVSAENINQLTDNNTALGSALKSTVMEMNPALKQYGSFASAS 31- 8 Query: 368 DLGMV----LDNVTKAAQDTGQSVDTIVQKAIDGAPQIKGLGLSFEEGA------ALIGK 41- 7 + G + LD + G T + A D + L L A ++I K Sbjct: 319 EKGAISVEMLDKAMQKLGGAGGGAVTTIGDAWDSFNETLSLALLPTLDALTPIISSIIDK 37- 8 Query: 418 FEKSGVDSSAALSSLSKAAVIYAKD--GKTLTDGLNETVSAIQNSTSET--EALSIASEI 47- 3 G + AL S+ K Y K+ G +G ++S I + T LSI ++ Sbjct: 379 MAGWGESAGKALDSIVK----YVKELWGALEKNGALSSLSKIWDGLKSTFGSVLSIIGQL 43- 4 Query: 474 FGSKAAPRMVDAIQRGAFSFDDLAEAAKSSSGTVSTTFDETLDPIDKLTQYSNQAKEGMA 53- 3 S A +D+ + A + ++ S T++ D I K+ ++ + E Sbjct: 435 IESFAG---IDS------KTGESAGSVENVSKTIANLAKGLADVIKKIADFAKKFSESKG 48- 5 Query: 534 ELGGKLLETVIPALEPLMGMLESSVNWFTSLNETDQ-QTIVILGLVTTAVMMLLGAIAPL 59- 2 + L+T + AL + T+++ + QT + G + AI P Sbjct: 486 AID--TLKTSLVALTAGFVAFKIGSGIITAISAFKKLQTAIQAGTGVMGAFNAVMAINPF 54- 3 Query: 593 VIAIGAIGAPVGIVVAAIV-GAIAVITLIIQAIMNWGAITEWLQSTWDSCAA-------W 64- 4 V +GI +AAIV G + T W + ++L+S WD + W Sbjct: 544 VA--------LGIAIAAIVAGLVYFFTQTETGKKAWASFVDFLKSAWDGIVSFFSGIGQW 59- 5 Query: 645 LSELWTNIVTTATTAWSNFTAWLSGLWSSVVSTGQSLWSSFTSSLSNIFSSLITGAQSLW 70- 4 +++W V A W W SG+ V Q++W+ T+ + ++++++TG Q+ W Sbjct: 596 FADIWNGAVDGAKGIWQGLVDWFSGIVQGV----QNIWNGITTFFTTLWTTVVTGIQTAW 65- 1 Query: 705 SSFTSTLSNLWSGLVSTGSNLFNNLSSTISGIFNGILSTASNIWNSIKS 753 + T + LW G+V+ + +F +SS ++G +N ++T + + KS Sbjct: 652 AGVTGFFTGLWDGIVNVVTTVFTTISSLVTGAYNWFVTTFQPLISFYKS 700 There is also homology to SEQ ID 2492. A related GBS gene <SEQ ID 8663> and protein <SEQ ID 8664> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02393 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -13.98 GvH: Signal Score (-7.5): -2.78 Possible site: 16 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -14.22 threshold: 0.0 INTEGRAL Likelihood = -14.22 Transmembrane 605-621 (569-631) INTEGRAL Likelihood = -8.12 Transmembrane 583-599 (569-604) PERIPHERAL Likelihood = 4.45 539 modified ALOM score: 3.34 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6689 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) The protein has homology with the following sequences in the databases: ##STR00055## ##STR00056## SEQ ID 8664 (GBS58) was expressed in and purified from E. coli as a GST fusion. The purified protein is shown in lane 10 of FIG. 193. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 824 A DNA sequence (GBSx0874) was identified in S. agalactiae <SEQ ID 2493> which encodes the amino acid sequence <SEQ ID 2494>. Analysis of this protein sequence reveals the following: TABLE-US-02394 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2732 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 825 A DNA sequence (GBSx0875) was identified in S. agalactiae <SEQ ID 2495> which encodes the amino acid sequence <SEQ ID 2496>. Analysis of this protein sequence reveals the following: TABLE-US-02395 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2467 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10151> which encodes amino acid sequence <SEQ ID 10152> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10935> which encodes amino acid sequence <SEQ ID 10936> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2497> which encodes the amino acid sequence <SEQ ID 2498>. Analysis of this protein sequence reveals the following: TABLE-US-02396 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2136 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02397 Identities = 55/240 (22%), Positives = 92/240 (37%), Gaps = 20/240 (8%) Query: 4 INELTIDGVKTSSFKCDVLVETRPNVIVSSS--KTALLEHDGISGAVVQSNRHRGLIEKP 61 I ++ ID TSS VL I+S S + +G S + N + I Sbjct: 2 IPKVIIDDFDTSSIPNCVLTGYDVGDILSPSFVENEAYGMNGTSRELESYNESKPTIM-- 59 Query: 62 YHITLIEPSDEEIYRFSALLNREKFW-LENEQEPTIRLWCYKVDSFEIGKDEFGAWVVDV 120- +H++ + + I L + +FW + N ++ Y S +I +W V + Sbjct: 60 WHLSTFDDAVNLINHLDGLSKKIEFWHIPNS------IYYYDCLSVKINAVTMSSWRVTL 113- Query: 121 TFICHPTKFFKTTDIQTLTGNGVLRVQGSALAFPKITVVGQSASETSFTIGNQVIKLEKL 18- 0 +P ++ K + GNG + G+ + PKI V G + + TIG QV++L L Sbjct: 114 KLALYPFRYAKGVSDVVIAGNGNINNAGNVFSEPKIVVEG--TGKGTLTIGKQVMEL-NL 17- 0 Query: 181 SESLVMTNDPDNPSFKTASGKL---IKWAGDFITVDTAKGQNVGVVLGAGITSLKFETVW 23- 7 S + A G + I+ G F + G+ + GIT W Sbjct: 171 SGKATIECKHGQQCVYDAEGNVKNSIRIRGSFFEIQPG---TQGIAVSGGITRTIISPRW 22- 7 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 826 A DNA sequence (GBSx0876) was identified in S. agalactiae <SEQ ID 2499> which encodes the amino acid sequence <SEQ ID 2500>. This protein is predicted to be PblB. Analysis of this protein sequence reveals the following: TABLE-US-02398 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.00 Transmembrane 952-968 (952-968) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02399 >GP: AAG18640 GB: AY007505 PblB [Streptococcus mitis] Identities = 145/542 (26%), Positives = 255/542 (46%), Gaps = 52/542 (9%) Query: 1 MLFLLDANVRTVKWNGIPLHEASSAIVKEETNGDFYLTVRYPITDSGIYQLIKEDMLIKS 60 M++L + N PL+ A + + +E N + LT R+P +D +++ +KE+ +K+ Sbjct: 1 MIYLTNGNT--------PLNAAYADKISQEANSTYQLTFRFPTSDV-LWEKLKEETFLKA 51 Query: 61 PVPVLGAQLFRIKKPIENDDSMDITAYHVSDDIMKRSITPVSVVGQGCAMALSQMVQNAK 120- + G Q F I + + + + A V + I P+S+ + ALS+ + Sbjct: 52 D-DLHGEQDFVIFEVQKKHGYIQVYANQVMTLLNNYVINPISLDRATGSTALSRFAGSI- 109- Query: 121 TGLGDFSFTSDIMDSRTFNTTETETLYSVLMDGKHSIVGTWEGELVRDNFALSIKRSRGA 18- 0 T FSF SDI + TFNT + + D KHSI+G W G+LVR + + + ++ G+ Sbjct: 110 TRYNTFSFFSDIDERHTFNTDSVNAMVAFTKD-KHSILGQWGGDLVRHGYQVRLLKNGGS 16- 8 Query: 181 DRGVVITTHKNLKSYQRTKNSQGVVTRIHARSTFKPDGAE-DEVTLRVSVDSPLINSYPY 23- 9 + + KNL SYQ +++ + TRI ++T K +G + + V VDSPL+N Y Sbjct: 169 ENESLFMYKKNLSSYQHKTSTKSLKTRITFKATVKGEGEKAPDRKFSVVVDSPLVNKYSQ 22- 8 Query: 240 INEKEYENNNAETVED--LRKWAEAKFTNEGIDKVSDAIEIEAYELDGQVVNLGDTVNLK 29- 7 I E E N+ + ++ LRK+ E F D + D++EI+ V + D V+L Sbjct: 229 IYEDVIEVNDQDVKDEVGLRKYGEQYFRTTLCDMLEDSLEIQVEGKSDVPVQIFDIVSLF 28- 8 Query: 298 SRKHSADLYKKAIAYEFNALTEEYISITFDDKPGVGGSGVSSGLSN-VADAILVASATAQ 35- 6 + D+ KK Y ++ + ++ +SI F G SG+S+ LSN V+DA+ + Q Sbjct: 289 HDRFKMDVRKKITKYTYSPMAKKLLSIGF----GQFKSGLSNMLSNAVSDAVKNETQHLQ 34- 4 Query: 357 D---VAVQRAVKNANAAFDAEFGKTKTKINDDIEIAKAKVESFKSELSNRMDNQLLP--- 41- 0 + + +KNA+ AFD + + + D + AKAK E K L+ +D + Sbjct: 345 GQFATQLGKEIKNADLAFDRKKEELVNQFTDGLNAAKAKAEEVKKSLTETIDQRFRDFDS 40- 4 Query: 411 ----------------------LATEAKNLASQAQADLTRKEIELRAELNRQVTSTEAVK 44- 8 LA EAK ++ QA+ + K E + ++ + TS + Sbjct: 405 TGLNEIKQKAEEALQRVGANTLLAQEAKQISEQARQQMDSKFAEYKQSVDGRFTSLSSQL 46- 4 Query: 449 ISLTNLSHNMDIIKQKALNDLRDAETRLKEADSVQQLATKRVEDKLTGLSTKLESFSVGG 50- 8 NL +D + + ++L + E+D +++A + ++L + S +VGG Sbjct: 465 AGKANL---IDFQRVQEKSNLYERIIGSSESDIAEKVARMTLTNQLFQVEVGKYS-AVGG 52- 0 Query: 509 YN 510 N Sbjct: 521 PN 522 Identities = 47/183 (25%), Positives = 83/183 (44%), Gaps = 22/183 (12%) Query: 867 VTTLRVTKGTIPADWSPSPDDLKAYSDTKLEQTANEIKASVTSLDHKTLKQTDITMTSEG 92- 6 +T L +GT W P+P+D +D LE T QT +T+ Sbjct: 667 MTELDFYEGTTDRRWQPAPEDATLETDKTLEAT-----------------QTKLTLLQGS 70- 9 Query: 927 IVLRAGKTSNDVARAIGSYFKVTPDAIALFSSLIKVSGNMLVDGSVTSRKLVTGAVETGH 98- 6 ++ TS A +I S T + I + + I++ G L+D +T+ + G Sbjct: 710 FAIQ-NLTS---AGSIVSQINATNNQILIEAEKIRLKGKTLLD-ELTAIDGYFKRLFVGE 76- 4 Query: 987 VKAGAITGVLLAAEAVTAEKLKVDQAFFNKLMANDAYLKQLFAKSAFITQVQSVTISASQ 10- 46 + ++ ++ +TA+KL +DQA +++D + L AK AFI +++SV +SA+ Sbjct: 765 GTFAKLNAEIIGSKTITADKLIMDQAMARLFVSSDIFTDTLAAKEAFINKLRSVVVSATL 82- 4 Query: 1047 ISG 1049 G Sbjct: 825 FEG 827 A related DNA sequence was identified in S. pyogenes <SEQ ID 2501> which encodes the amino acid sequence <SEQ ID 2502>. Analysis of this protein sequence reveals the following: TABLE-US-02400 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2445 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02401 Identities = 143/552 (25%), Positives = 251/552 (44%), Gaps = 43/552 (7%) Query: 11 TVKWNGIPLHEASSAIVKEETNGDFYLTVRYPITDSGIYQLIKEDMLIKSPVPVLGAQLF 70 - ++K + PL A + +E N D+ L +YP LIK+ +++++ + G+QLF Sbjct: 3 SIKDDNTPLVAAFEDEITQEANSDYKLNFKYPAKHE-YRPLIKKGIILEAD-DLHGSQLF 60 Query: 71 RIKKPIENDDSMDITAYHVSDDIMKRSITPVSVVGQGCAMALSQMVQNAKTGLGDFSFTS 130- RI + + +++ A V+DD+ +I +SV +S++ + K FSF S Sbjct: 61 RIFEITKRHGYINVYANQVADDLNGYAIDTISVDRVQGMTVMSELAGSIKRE-HPFSFFS 119- Query: 131 DIMDSRTFNTTETETLYSVLMDGKHSIVGTWEGELVRDNFALSIKRSRGADRGVVITTHK 19- 0 DI TFN ++ + L +GKHSI+G W GELVR+ + +++ + G D + K Sbjct: 120 DIDGRHTFNQSDVSVM-DALANGKHSIMGQWGGELVRNKYQINLLKKAGKDTETLFMYKK 17- 8 Query: 191 NLKSYQRTKNSQGVVTRIH----------ARSTFKPDG------AEDEVTLRVSVDSPLI 23- 4 NLKSY+ T +G+V+ +H + DG + + T+RVSV+S L Sbjct: 179 NLKSYEETDTIKGLVSILHLVAEVEEEHEVETREASDGNIGHSESPKKKTIRVSVESKLK 23- 8 Query: 235 NSYPYINEK--EYENNNAETVEDLRKWAEAKFTNEGIDKVSDAIEIEAYELDGQVVNLGD 29- 2 +++P I EK + ++ + +T EDL + + F D ++++I+ V L D Sbjct: 239 DTHPIIVEKTIKVQDQDVKTEEDLLAYGKKYFEKTLCDIPGNSLKIDVTNNYEGAVRLFD 29- 8 Query: 293 TVNLKSRKHSADLYKKAIAYEFNALTEEYISITFDDKPGVGGSGVSSGLSNVADAILVAS 35- 2 T + + DL + Y F + SI F G + ++ +SN D + S Sbjct: 299 TAIVFHELYDRDLRMQITGYRFAPMANRLKSIIF----GEIKTNLAKQISNQIDNKVAES 35- 4 Query: 353 ATAQDVA----VQRAVKNANAAFDAEFGKTKTKINDDIEIAKAKVESFKSELSNR-MDNQ 40- 7 D A +Q+ + NAN FD + K + +I D I+ A+A E +E++ + ++ + Sbjct: 355 TAQHDAAFEAKLQKQIDNANRIFDTKEAKLREEIEDGIKKAEANAEVKVAEVNAKVLEAE 41- 4 Query: 408 LLPLATEAK-----NLASQAQADLTRKEIELRAELNRQVTSTEAVKISLTNLSHNMDIIK 46- 2 L A + + + A + D +K E R L + + +L + D + Sbjct: 415 ELAKAVDERLKKFLSDADTKEQDFDKKLEEFRTSLKDLEVDEKQIDDALAKAGFSKDSLA 47- 4 Query: 463 QKALNDLRDAETRLKEADSVQQL-ATKRVEDKLTGLSTKLESFSVGGYNYVIDGGEPKEL 52- 1 +ET A+ V T ++L G + K+ +F GY + GE E Sbjct: 475 DIKAKLEDTSETATVTANIVGSTGGTFYNRNRLDGDTDKVITFE-QGYIDIAHNGEGFE- 53- 2 Query: 522 MANFYGKTYDIN 533 GKTY I+ Sbjct: 533 ----EGKTYTIS 540 A related GBS gene <SEQ ID 8665> and protein <SEQ ID 8666> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02402 Lipop Possible site: -1 Crend: 3 SRCFLG: 0 McG: Length of UR: 11 Peak Value of UR: 1.54 Net Charge of CR: 1 McG: Discrim Score: -3.43 GvH: Signal Score (-7.5): -5.44 Possible site: 58 >>> Seems to have no N-terminal signal sequence Amino Acid Composition: calculated from 1 ALOM program count: 1 value: -0.00 threshold: 0.0 INTEGRAL Likelihood = -0.00 Transmembrane 897-913 (897-913) PERIPHERAL Likelihood = 1.48 932 modified ALOM score: 0.50 icml HYPID: 7 CFP: 0.100 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1001 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00057## A related DNA sequence was identified in S. pyogenes <SEQ ID 9059> which encodes amino acid sequence <SEQ ID 9060>. An alignment of the GAS and GBS sequences follows:

TABLE-US-02403 Score = 87.8 bits (214), Expect = 4e-19 Identities = 88/273 (32%), Positives = 133/273 (48%), Gaps = 47/273 (17%) Query: 370 AINLNSRGVQIAGKNIALDGNTT----VNGAF-------GAKLGEFI--------KLRAD 41- 0 AI L S ++++G N+ +DG+ T V GA GA G + KL+ D Sbjct: 897 AIALFSSLIKVSG-NMLVDGSVTSRKLVTGAVETGHVKAGAITGVLLAAEAVTAEKLKVD 95- 5 Query: 411 QIIGGTIDANKINVINLKASSIVGLDANFIKARISYAIT-DLLEGKVIKARNGAMTIDLQ 46- 9 Q + AN + L A S FI S I+ + G VIKA N AM I + Sbjct: 956 QAFFNKLMANDAYLKQLFAKSA------FITQVQSVTISASQISGGVIKALNNAMEIQMN 10- 09 Query: 470 SGQINHYTNESAMRRIDSSTASQFIKMTKSGFISEIGNMQAAMTVIGSNSDGSENHENKT 52- 9 SGQI +YT+++A++R+ S +QF+K +G +S GN A +TVIGSN G+E+ + Sbjct: 1010 SGQILYYTDQAALKRVLSGYPTQFVKFA-TGTVSGKGN--AGVTVIGSNRYGTESTNDGG 1- 066 Query: 530 FGGIRIWNGKSSYQSTSFVELVGN--RVAIYGNKNRSPWLFDSTTSGYAYLIPQNDRGIK 58- 7 F G+R WNG + ++LVG+ R+A N W + SG + P N Sbjct: 1067 FVGVRAWNG----SNIDSLDLVGDEIRLASSAFDNSDGWDVRTLDSGLK-ITPHN----- 1- 116 Query: 588 HVIGRADRKIDQIHVGDIYV-QGERVAMMLKDL 619 RA + +I VGD+++ +G L+D+ Sbjct: 1117 ----RAAERNSRIEVGDVWILKGNGSYSSLRDI 1145 Score = 31.3 bits (69), Expect = 0.038 Identities = 34/151 (22%), Positives = 62/151 (40%), Gaps = 13/151 (8%) Query: 160 QNADKKLSASYQLGIDGLKATMRSDKIGLQAEIQTTAQGLYQRYDNEIRKLSAKITTTSS 21- 9 Q A K +A++ K + D +A++++ L R DN++ L+ + +S Sbjct: 306 QRAVKNANAAFDAEFGKTKTKINDDIEIAKAKVESFKSELSNRMDNQLLPLATEAKNLAS 36- 5 Query: 220 GTTEAYESKLDGLRAEFTH---SNQGMRVELES--------KISGLQSTQQATARQISQE 26- 8 K LRAE S + +++ L + K L + A R + + Sbjct: 366 QAQADLTRKEIELRAELNRQVTSTEAVKISLTNLSHNMDIIKQKALNDLRDAETR-LKEA 42- 4 Query: 269 ISNREGAVSRVQQGLDSYQRRLQS-AEGNYN 298 S ++ A RV+ L +L+S + G YN Sbjct: 425 DSVQQLATKRVEDKLTGLSTKLESFSVGGYN 455 SEQ ID 8666 (GBS202) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 50 (lane 5; MW 132 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 827 A DNA sequence (GBSx0877) was identified in S. agalactiae <SEQ ID 2503> which encodes the amino acid sequence <SEQ ID 2504>. This protein is predicted to be nuclear/mitotic apparatus protein. Analysis of this protein sequence reveals the following: TABLE-US-02404 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2847 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 828 A DNA sequence (GBSx0879) was identified in S. agalactiae <SEQ ID 2505> which encodes the amino acid sequence <SEQ ID 2506>. Analysis of this protein sequence reveals the following: TABLE-US-02405 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3420 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 829 A DNA sequence (GBSx0880) was identified in S. agalactiae <SEQ ID 2507> which encodes the amino acid sequence <SEQ ID 2508>. Analysis of this protein sequence reveals the following: TABLE-US-02406 Possible site: 13 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.54 Transmembrane 10-26 (2-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.4015 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02407 >GP: CAB07984 GB: Z93946 hypothetical protein [bacteriophage Dp-1] Identities = 67/136 (49%), Positives = 91/136 (66%) Query: 1 MPPWLIDSTVVVAMVTVLGGLFSTIITTSANRKDQLIKHQYEDIKEDLSGLIDKVKTIDH 60 MP WL D+ V+ ++T G+ + ++ K K EDI LS L +V ID Sbjct: 1 MPMWLNDTAVLTTIITACSGVLTVLLNKLFEWKSNKAKSVLEDISTTLSTLKQQVDGIDQ 60 Query: 61 TTTETKKISEITKDGTLKIQRYRLFHDLTKEISQGYTTIEHFRELSILFESYQLLGGNGE 120- TT +++ +DGT KIQRYRL+HDL +E+ GYTT++HFRELSILFESY+ LGGNGE Sbjct: 61 TTVAINHQNDVIQDGTRKIQRYRLYHDLKREVITGYTTLDHFRELSILFESYKNLGGNGE 120- Query: 121 IEALFEKFKQLPIEED 136 +EAL+EK+K+LPI E+ Sbjct: 121 VEALYEKYKKLPIREE 136 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 2508 (GBS118) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 32 (lane 5; MW 42 kDa). GBS118-GST was purified as shown in FIG. 198, lane 8. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 830 A DNA sequence (GBSx0882) was identified in S. agalactiae <SEQ ID 2509> which encodes the amino acid sequence <SEQ ID 2510>. Analysis of this protein sequence reveals the following: TABLE-US-02408 Possible site: 53 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8667> and protein <SEQ ID 8668> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02409 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: 6.58 GvH: Signal Score (-7.5): -0.49 Possible site: 53 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 12.15 threshold: 0.0 PERIPHERAL Likelihood = 12.15 84 modified ALOM score: -2.93 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) SEQ ID 2510 (GBS56) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 8; MW 9.9 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 21 (lane 10; MW 34.9 kDa). GBS56-GST was purified as shown in FIG. 195, lane 7. EXAMPLE 831 A DNA sequence (GBSx0883) was identified in S. agalactiae <SEQ ID 2511> which encodes the amino acid sequence <SEQ ID 2512>. Analysis of this protein sequence reveals the following: TABLE-US-02410 Possible site: 40 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 832 A DNA sequence (GBSx0884) was identified in S. agalactiae <SEQ ID 2513> which encodes the amino acid sequence <SEQ ID 2514>. This protein is predicted to be N-acetylmuramoyl-L-alanine amidase. Analysis of this protein sequence reveals the following: TABLE-US-02411 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0342 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02412 >GP: CAB07986 GB: Z93946 N-acetylmuramoyl-L-alanine amidase [bacteriophage Dp-1] Identities = 96/141 (68%), Positives = 118/141 (83%) Query: 1 MEINTEIAIAWMSARQGKVSYSMDYRDGPNSYDCSSSVYYALRSAGASSAGWAVNTEYMH 60 M ++ E +AWM AR+G+VSYSMD+RDGP+SYDCSSS+YYALRSAGASSAGWAVNTEYMH Sbjct: 1 MGVDIEKGVAWMQARKGRVSYSMDFRDGPDSYDCSSSMYYALRSAGASSAGWAVNTEYMH 60 Query: 61 DWLIKNGYELIAENVDWNAVRGDIAIWGMRGHSSGAGGHVVMFIDPENIIHCNWANNGIT 120- WLI+NGYELI+EN W+A RGDI IWG +G S+GAGGH MFID +NIIHCN+A +GI+ Sbjct: 61 AWLIENGYELISENAPWDAKRGDIFIWGRKGASAGAGGHTGMFIDSDNIIHCNYAYDGIS 120- Query: 121 VNNYNQTAAASGWMYCYVYRL 141 VN++++ +G Y YVYRL Sbjct: 121 VNDHDERWYYAGQPYYYVYRL 141 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8669> and protein <SEQ ID 8670> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02413 RGD motif 81-83 The protein has homology with the following sequences in the databases: ##STR00058## SEQ ID 8670 (GBS302) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 50 (lane 6; MW 55 kDa). The GBS302-His fusion product was purified (FIG. 205, lane 6) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 302), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 833 A DNA sequence (GBSx0885) was identified in S. agalactiae <SEQ ID 2515> which encodes the amino acid sequence <SEQ ID 2516>. Analysis of this protein sequence reveals the following: TABLE-US-02414 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1509 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 834 A DNA sequence (GBSx0886) was identified in S. agalactiae <SEQ ID 2517> which encodes the amino acid sequence <SEQ ID 2518>. Analysis of this protein sequence reveals the following: TABLE-US-02415 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1264 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02416 >GP: CAB13473 GB: Z99112 similar to hypothetical proteins [Bacillus subtilis] Identities = 25/68 (36%), Positives = 41/68 (59%) Query: 4 IENLIIAIVKPLISQPDQLTIKIQDGPEFLEYHLDLDTQDIGRVIGKKGRTITAIRSIVY 63 +E+LI+ IV PL+ PD + + ++ + + L + D G+VIGK+GRT AIR+ V+ Sbjct: 6 LEDLIVHIVTPLVDHPDDIRVIREETDQKIALRLSVHKSDTGKVIGKQGRTAKAIRTAVF 65 Query: 64 SVPTQGKK 71 + Q K Sbjct: 66 AAGVQSSK 73 A related DNA sequence was identified in S. pyogenes <SEQ ID 2519> which encodes the amino acid sequence <SEQ ID 2520>. Analysis of this protein sequence reveals the following: TABLE-US-02417 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1012 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02418 Identities = 72/79 (91%), Positives = 75/79 (94%) Query: 1 MDTIENLIIAIVKPLISQPDQLTIKIQDGPEFLEYHLDLDTQDIGRVIGKKGRTITAIRS 60 MDTIENLIIAIVKPLISQPD LTIKI+D P+FLEYHLDLD QDIGRVIGKKGRTITAIRS Sbjct: 1 MDTIENLIIAIVKPLISQPDNLTIKIEDTPDFLEYHLDLDAQDIGRVIGKKGRTITAIRS 60 Query: 61 IVYSVPTQGKKVRLIIDEK 79 IVYSVPT GKKVRL+IDEK Sbjct: 61 IVYSVPTLGKKVRLVIDEK 79 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 835 A DNA sequence (GBSx0887) was identified in S. agalactiae <SEQ ID 2521> which encodes the amino acid sequence <SEQ ID 2522>. This protein is predicted to be ribosomal protein S116 (rpsP). Analysis of this protein sequence reveals the following: TABLE-US-02419 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3654 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02420 >GP: BAB06202 GB: AP001515 ribosomal protein S16 (BS17) [Bacillus halodurans] Identities = 62/90 (68%), Positives = 73/90 (80%) Query: 1 MAVKIRLTRMGSKKKPFYRINVADSRAPRDGRFIETVGTYNPLVAENQVTIKEERVLEWL 60 MAVKIRL RMGSKK PFYR+ VADSR+PRDGRFIE +GTYNPL +V +KE+R L+W+ Sbjct: 1 MAVKIRLKRMGSKKAPFYRVVVADSRSPRDGRFIEEIGTYNPLTQPAKVELKEDRALDWM 60 Query: 61 SKGAQPSDTVRNLLSKAGVMTKFHDQKFSK 90 KGA+PSDTVRNL SKAG+M K H+ K K Sbjct: 61 LKGAKPSDTVRNLFSKAGLMEKLHNAKNEK 90 A related DNA sequence was identified in S. pyogenes <SEQ ID 2523> which encodes the amino acid sequence <SEQ ID 2524>. Analysis of this protein sequence reveals the following: TABLE-US-02421 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3654(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02422 Identities = 86/90 (95%), Positives = 89/90 (98%) Query: 1 MAVKIRLTRMGSKKKPFYRINVADSRAPRDGRFIETVGTYNPLVAENQVTIKEERVLEWL 60 MAVKIRLTRMGSKKKPFYRINVADSRAPRDGRFIETVGTYNPLVAENQ+TIKE+RVLEWL Sbjct: 1 MAVKIRLTRMGSKKKPFYRINVADSRAPRDGRFIETVGTYNPLVAENQITIKEDRVLEWL 60 Query: 61 SKGAQPSDTVRNLLSKAGVMTKFHDQKFSK 90 SKGAQPSDTVRN+LSKAGVM KFHDQKFSK Sbjct: 61 SKGAQPSDTVRNILSKAGVMAKFHDQKFSK 90 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 836 A DNA sequence (GBSx0888) was identified in S. agalactiae <SEQ ID 2525> which encodes the amino acid sequence <SEQ ID 2526>. Analysis of this protein sequence reveals the following: TABLE-US-02423 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.09 Transmembrane 22-38 (16-42) INTEGRAL Likelihood = -7.64 Transmembrane 382-398 (375-402) INTEGRAL Likelihood = -7.59 Transmembrane 291-307 (284-317) INTEGRAL Likelihood = -4.94 Transmembrane 340-356 (335-366) ----- Final Results ----- bacterial membrane --- Certainty = 0.5437(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02424 >GP: AAC24912 GB: AF012285 YknZ [Bacillus subtilis] Identities = 161/417 (38%), Positives = 241/417 (57%), Gaps = 25/417 (5%) Query: 1 MENWKFALSSILGHKMRAFLTMLGIIIGVASVVLIMALGKGMKDSVTNEITKSQKNLQIY 60 +EN + ALSS+L HKMR+ LTMLGIIIGV SV++++A+G+G + + I+ +++Y Sbjct: 4 LENIRMALSSVLAHKMRSILTMLGIIIGVGSVIVVVAVGQGGEQMLKQSISGPGNTVELY 63 Query: 61 YKTKEDQ-KNEDNFGAQGAFMQGSDTNRKEPIIQESWLKKIAKEVDGVSGYYVTNQTNAP 119- Y +++ + N A+ F + K K ++G+ + + Sbjct: 64 YMPSDEELASNPNAAAESTFTENDI--------------KGLKGIEGIKQVVASTSESMK 109- Query: 120 VAYLEKKAKTVNITGINRTYLGIKKFKIKSGRQFQEEDYNQFSRVILLEEKLAQRLFQTN 17- 9 Y E++ + GIN Y+ + KI+SGR F + D+ +RV ++ +K+A+ LF Sbjct: 110 ARYHEEETDAT-VNGINDGYMNVNSLKIESGRTFTDNDFLAGNRVGIISQKMAKELFDKT 16- 8 Query: 180 EAALNKVVTVKNKSYLVVGVYSDPEAGSGLYGSNSDGNAILTNTQLASEFGAKEAENIYF 23- 9 + L +VV + + ++GV +GL + + N + S FG + N+ Sbjct: 169 -SPLGEVVWINGQPVEIIGVLKKV---TGLLSFDLSEMYVPFN-MMKSSFGTSDFSNVSL 22- 3 Query: 240 HLNDVSQSNRIGKEIGKRLTDISHAKDGYYDNFDMTSIVKSINTQVGIMTGVIGAIAAIS 29- 9 + GKE + + D +H + Y +M I I IMT +IG+IA IS Sbjct: 224 QVESADDIKSAGKEAAQLVND-NHGTEDSYQVMNMEEIAAGIGKVTAIMTTIIGSIAGIS 28- 2 Query: 300 LLVGGIGVMNIMLVSVTERTREIGLRKALGATRRKILAQFLIESMVLTILGGLIGLLLAY 35- 9 LLVGGIGVMNIMLVSVTERTREIG+RK+LGATR +IL QFLIES+VLT++GGL+G+ + Y Sbjct: 283 LLVGGIGVMNIMLVSVTERTREIGIRKSLGATRGQILTQFLIESVVLTLIGGLVGIGIGY 34- 2 Query: 360 GGTMLIANAQDKITPS-VSLNVAIGSLIFSAFIGIIFGLLPANKASKLNPIDALRYE 415 GG L++ PS +S V G ++FS IG+IFG+LPANKA+KL+PI+ALRYE Sbjct: 343 GGAALVSAIAG--WPSLISWQVVCGGVLFSMLIGVIFGMLPANKAAKLDPIEALRYE 397 There is also homology to SEQ ID 1350. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 837 A DNA sequence (GBSx0889) was identified in S. agalactiae <SEQ ID 2527> which encodes the amino acid sequence <SEQ ID 2528>. This protein is predicted to be ABC transporter (ATP-bindingprot). Analysis of this protein sequence reveals the following:

TABLE-US-02425 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4080(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02426 >GP: BAB06841 GB: AP001517 ABC transporter (ATP-binding protein) [Bacillus halodurans] Identities = 131/218 (60%), Positives = 169/218 (77%) Query: 8 LIRLHQIVKSYQNGDQKLQVLKNIDLTVYEGEFLAIMGPSGSGKSTLMNIIGLLDSPTSG 67 +I+L ++ KS++ G + +++L IDL + G+FLAIMGPSGSGKSTLMNIIG LD PTSG Sbjct: 1 MIKLERVTKSFRVGTEMVEILSAIDLEIASGDFLAIMGPSGSGKSTLMNIIGCLDQPTSG 60 Query: 68 DYSLNGKRVEELSQTKLAQVRNKEIGFVFQQFFLLSKLTALQNVELPLIYAGVPPKKRKN 127- Y +GK + S+ ++A++RN+ IGFVFQQF LL +LTALQNVELP++YAG+ K+R Sbjct: 61 RYMFDGKDLTNYSEQEIAKIRNRHIGFVFQQFHLLPRLTALQNVELPMVYAGMKKKERTE 120- Query: 128 LAKQFLDKVELRERMNHLPTELSGGQKQRVAIARALVNSPSIILADEPTGALDTKTGEQI 18- 7 A L++V L ERM +LP LSGGQKQRVAIAR++VN P+IILADEPTGALDTKT E I Sbjct: 121 RAAHALERVGLAERMTYLPNSLSGGQKQRVAIARSIVNEPNIILADEPTGALDTKTSETI 18- 0 Query: 188 MQFLTELNQEGKTIIMVTHEPEIADYATRKIVIRDGEI 225 M+ L LN EG TI +VTHEPEIA+Y + + +RDG+I Sbjct: 181 MELLCSLNNEGTTIALVTHEPEIAEYTQQTVFVRDGQI 218 A related DNA sequence was identified in S. pyogenes <SEQ ID 2529> which encodes the amino acid sequence <SEQ ID 2530>. Analysis of this protein sequence reveals the following: TABLE-US-02427 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1739(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02428 Identities = 182/232 (78%), Positives = 207/232 (88%) Query: 5 RKELIRLHQIVKSYQNGDQKLQVLKNIDLTVYEGEFLAIMGPSGSGKSTLMNIIGLLDSP 64 +K+L++L IVKSYQNGDQ L+VLK I+LTVYEGEFLAIMGPSGSGKSTLMNIIGLLD P Sbjct: 5 KKQLMQLSNIVKSYQNGDQVLKVLKGINLTVYEGEFLAIMGPSGSGKSTLMNIIGLLDRP 64 Query: 65 TSGDYSLNGKRVEELSQTKLAQVRNKEIGFVFQQFFLLSKLTALQNVELPLIYAGVPPKK 124- TSGDY+L+ ++E L+ +LA+VRN EIGFVFQQFFLL+KLTALQNVELPLIYAGV K Sbjct: 65 TSGDYTLHNTKIEILNDRELAKVRNDEIGFVFQQFFLLAKLTALQNVELPLIYAGVNVSK 124- Query: 125 RKNLAKQFLDKVELRERMNHLPTELSGGQKQRVAIARALVNSPSIILADEPTGALDTKTG 18- 4 R+ AKQFL+KV L R+ HLP+ELSGGQKQRVAIARALVN PSIILADEPTGALDTKTG Sbjct: 125 RREQAKQFLEKVGLGRRIKHLPSELSGGQKQRVAIARALVNDPSIILADEPTGALDTKTG 18- 4 Query: 185 EQIMQFLTELNQEGKTIIMVTHEPEIADYATRKIVIRDGEITADTTDSIRID 236 +QIM+ LTELN+EGKTIIMVTHEPEIAD+ATRKI+IRDG+IT DTT S+ ID Sbjct: 185 QQIMELLTELNKEGKTIIMVTHEPEIADFATRKIIIRDGDITTDTTASVVID 236 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 838 A DNA sequence (GBSx0890) was identified in S. agalactiae <SEQ ID 2531> which encodes the amino acid sequence <SEQ ID 2532>. This protein is predicted to be ATP-binding cassette transporter-like protein. Analysis of this protein sequence reveals the following: TABLE-US-02429 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.97 Transmembrane 17-33 (13-39) ----- Final Results ----- bacterial membrane --- Certainty = 0.4588(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9965> which encodes amino acid sequence <SEQ ID 9966> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02430 >GP: AAC24909 GB: AF012285 YknX [Bacillus subtilis] Identities = 104/391 (26%), Positives = 182/391 (45%), Gaps = 21/391 (5%) Query: 13 KKGAIISGLSVALIVVIGGFLWVQSQPNKSAVKTNYKVFNVREGSVSSSTLLTGKAKANQ 72 - KK I G++V + + +G ++ + P + + +V E +SS+ ++ G K + Sbjct: 2 KKVWIGIGIAVIVALFVGINIYRSAAPTSGSAGKEVQTGSVEENEISSTVMVPGTLKFSN 61 Query: 73 EQYVYFDANKGNRATVTVKVGDKITAGQQLVQYDTTTAQAAYDTANRQLNKVARQINNLK 132- EQYV+++A+KG + VK GDK+ G LV Y T Q + + QL + ++ + Sbjct: 62 EQYVFYEADKGTLEDIKVKEGDKVKKGTALVTY--TNEQLSLEKEQNQLTSESNRLQIDQ 119- Query: 133 TTGSLPAMESSDQSSSSSQGQGTQSTSGATNRLQQNYQSQANASYNQQLQDLNDAYADAQ 19- 2 L A++S ++ G+ + R + Q + +L Q Sbjct: 120 IQEKLKALDSKERELEKQVGKKEAEKQIESERTELQMQKKTAEI------ELKQTELQRQ 17- 3 Query: 193 AEVNKAQKALNDTVITSDVSGTVVEVNSDIDPASKTSQV---LVHVATEGKLQVQGTMSE 24- 9 + N+ ++D + S++ GTV+ VN + ASK S + ++H+ L V G +SE Sbjct: 174 SLANR----VSDLEVKSEIEGTVISVNQ--EAASKKSDIQEPVIHIGNPKDLVVSGKLSE 22- 7 Query: 250 YDLANVKKDQAVKIKSKVYPDKEWEGKISYISNYPEAEANNNDSNNGSSAVNYKYKVDIT 30- 9 YD VKK Q V + S V K W+G +S + P+ + + + AV Y +V I Sbjct: 228 YDTLKVKKGQKVTLTSDVIQGKTWKGTVSAVGLVPD-QQESAAAQGTEQAVQYPLQVKIK 28- 6 Query: 310 SPLDALKQGFTVSVEV-VNGDKHLIVPTSSVINKDNKHFVWVYNDSNRKISKVEVKIGKA 36- 8 L K GF + + + K +P+ +V +D++++V+ D K +V+VKIG+ Sbjct: 287 GNLPEGKPGFKFIMNIETDKRKANTLPSKAVKKEDDQYYVYTVKDG--KAKRVDVKIGEV 34- 4 Query: 369 DAKTQEILSGLKAGQIVVTNPSKTFKDGQKI 399 EI GL V+ NPS DG ++ Sbjct: 345 TDDLTEIKEGLTQDDQVILNPSDQVTDGMEV 375 A related DNA sequence was identified in S. pyogenes <SEQ ID 2533> which encodes the amino acid sequence <SEQ ID 2534>. Analysis of this protein sequence reveals the following: TABLE-US-02431 Possible site: 42 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.61 Transmembrane 15-31 (11-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.4843(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02432 >GP: AAC24909 GB: AF012285 YknX [Bacillus subtilis] Identities = 103/380 (27%), Positives = 180/380 (47%), Gaps = 21/380 (5%) Query: 16 ITASVITLVLIITGIVLWKQQRNTLTADIAKEPYSTVSVTEGSIASSTLLSGTVKALSEE 75 - I + +V + GI +++ T + A + T SV E I+S+ ++ GT+K +E+ Sbjct: 6 IGIGIAVIVALFVGINIYRSAAPT--SGSAGKEVQTGSVEENEISSTVMVPGTLKFSNEQ 63 Query: 76 YIYFDANKGNDATVTVKVGDQVTQGQQLVQYNTTTAQSAYDTAVRSLNKIGRQINHLKTY 135- Y++++A+KG + VK GD+V +G LV Y T Q + + + N++ + N L+ Sbjct: 64 YVFYEADKGTLEDIKVKEGDKVKKGTALVTY--TNEQLSLE---KEQNQLTSESNRLQID 118- Query: 136 GVPAVSTETNRDEATGEETTTTVQPSAQ-QNANYKQQLQDLNDAYADAQAEVNKAQIA-- 19- 2 + + E E+ + Q ++ + Q+Q Q E+ + +A Sbjct: 119 QIQEKLKALDSKERELEKQVGKKEAEKQIESERTELQMQKKTAEIELKQTELQRQSLANR 17- 8 Query: 193 LNDTVVISSVSGTVVEVNND-IDPSSKNSQTLVHVATEGQLQVKGTLTEYDLANVKVGQS 25- 1 ++D V S + GTV+ VN + S + ++H+ L V G L+EYD VK GQ Sbjct: 179 VSDLEVKSEIEGTVISVNQEAASKKSDIQEPVIHIGNPKDLVVSGKLSEYDTLKVKKGQK 23- 8 Query: 252 VKIKSKVYSNQEWTGKISYVSNYPTESNAGSTTPAGSTGAGSSTGATYDYKIDIISPLNQ 31- 1 V + S V + W G +S V P + + + G+ Y ++ I L + Sbjct: 239 VTLTSDVIQGKTWKGTVSAVGLVPDQQES-------AAAQGTEQAVQYPLQVKIKGNLPE 29- 1 Query: 312 LKQGFTVSVEVVNEAKQA-LVPLTAVIKKDKKHYVWTYDDATGKAKKVEVTLGNADAOQQ 37- 0 K GF + + + ++A +P AV K+D ++YV+T D GKAK+V+V +G Sbjct: 292 GKPGFKFIMNIETDKRKANTLPSKAVKKEDDQYYVYTVKD--GKAKRVDVKIGEVTDDLT 34- 9 Query: 371 EIHKGVAVGDIVIANPDKNI 390 EI +G+ D VI NP + Sbjct: 350 EIKEGLTQDDQVILNPSDQV 369 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02433 Identities = 234/421 (55%), Positives = 301/421 (70%), Gaps = 19/421 (4%) Query: 3 MSKRQNLGISKKGAIISGLSVALIVVIGGF-LWVQSQPNKSA--VKTNYKVFNVREGSVS 59 MSKR + I+ K +I+ + L+++I G LW Q + +A K Y +V EGS++ Sbjct: 1 MSKRGKIKITTKTKLITASVITLVLIITGIVLWKQQRNTLTADIAKEPYSTVSVTEGSIA 60 Query: 60 SSTLLTGKAKANQEQYVYFDANKGNRATVTVKVGDKITAGQQLVQYDTTTAQAAYDTANR 119- SSTLL+G KA E+Y+YFDANKGN ATVTVKVGD++T GQQLVQY+TTTAQ+AYDTA R Sbjct: 61 SSTLLSGTVKALSEEYIYFDANKGNDATVTVKVGDQVTQGQQLVQYNTTTAQSAYDTAVR 120- Query: 120 QLNKVARQINNLKTTGSLPAMESSDQSSSSSQGQGTQSTSGATNRLQQNYQSQANASYNQ 17- 9 LNK+ RQIN+LKT G +PA+ S++ + + G+ T +T + +Q NA+Y Q Sbjct: 121 SLNKIGRQINHLKTYG-VPAV-STETNRDEATGEETTTTVQPS--------AQQNANYKQ 17- 0 Query: 180 QLQDLNDAYADAQAEVNKAQKALNDTVITSDVSGTVVEVNSDIDPASKTSQVLVHVATEG 23- 9 QLQDLNDAYADAQAEVNKAQ ALNDTV+ S VSGTVVEVN+DIDP+SK SQ LVHVATEG Sbjct: 171 QLQDLNDAYADAQAEVNKAQIALNDTVVISSVSGTVVEVNNDIDPSSKNSQTLVHVATEG 23- 0 Query: 240 KLQVQGTMSEYDLANVKKDQAVKIKSKVYPDKEWEGKISYISNYP-EAEANN-----NDS 29- 3 +LQV+GT++EYDLANVK Q+VKIKSKVY ++EW GKISY+SNYP E+ A + + Sbjct: 231 QLQVKGTLTEYDLANVKVGQSVKIKSKVYSNQEWTGKISYVSNYPTESNAGSTTPAGSTG 29- 0 Query: 294 NNGSSAVNYKYKVDITSPLDALKQGFTVSVEVVNGDKHLIVPTSSVINKDNKHFVWVYND 35- 3 S+ Y YK+DI SPL+ LKQGFTVSVEVVN K +VP ++VI KD KH+VW Y+D Sbjct: 291 AGSSTGATYDYKIDIISPLNQLKQGFTVSVEVVNEAKQALVPLTAVIKKDKKHYVWTYDD 35- 0 Query: 354 SNRKISKVEVKIGKADAKTQEILSGLKAGQIVVTNPSKTFKDGQKIDNIESIDLNSNKKSE 4- 14 + K KVEV +G ADA+ QEI G+ G IV+ NP K K +K++ + SI N+ + + Sbjct: 351 ATGKAKKVEVTLGNADAQQQEIHKGVAVGDIVIANPDKNIKPDKKLEGVISIGTNTKPEKD 4- 11 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 839 A DNA sequence (GBSx0891) was identified in S. agalactiae <SEQ ID 2535> which encodes the amino acid sequence <SEQ ID 2536>. Analysis of this protein sequence reveals the following: TABLE-US-02434 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1832(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 840 A DNA sequence (GBSx0892) was identified in S. agalactiae <SEQ ID 2537> which encodes the amino acid sequence <SEQ ID 2538>. This protein is predicted to be carbamoyl-phosphate synthase, pyrimidine-specific, large chain, putati. Analysis of this protein sequence reveals the following: TABLE-US-02435 Possible site: 59 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.70 Transmembrane 486-502 (486-502) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02436 >GP: CAA91005 GB: Z54240 carbamoyl-phosphate synthase [Lactobacillus plantarum] Identities = 117/417 (28%), Positives = 205/417 (49%), Gaps = 37/417 (8%) Query: 122 FVQVDCLVMRDSLNNCLYVSDLEYIES-NKTTGKSLAIVPSQTLSDAARQTIRDVAFDVC 18- 0 + +++ VMRD+ +N + V ++E + TG S+ P QTL+D Q +RD A + Sbjct: 213 YKEIEFEVMRDAADNAMVVCNMENFDPVGIHTGDSIVYAPVQTLADREVQLLRDAALKII 27- 2 Query: 181 RKANIIGVCYFSFLIDLNSLDYHIISLSSGLSHQSILFETITTYPVLEIATKLTVGYTFS 24- 0 R I G C +D NS +Y+II ++ +S S L T YP+ ++A K+ VG Sbjct: 273 RALKIEGGCNVQLALDPNSFNYYIIEVNPRVSRSSALASKATGYPIAKMAAKIAVGLHLD 33- 2 Query: 241 QLKHSYYPNTSAFLEPQLDYVATV--SFSFEKVDY---------------IFFARNIEQL 28- 3 ++K+ T A EP LDYV + F+K + + RNIE+ Sbjct: 333 EIKNPVTGTTYAEFEPALDYVVCKIPRWPFDKFTHADRRLGTQMKATGEVMAIGRNIEEA 39- 2 Query: 284 FLNLLEASS----HDHFPFLSDISEEDLMFALIQKKENRLAYLLEAFRRGFDLYDLSSVT 33- 9 L + + H L + ++ L LI +++RL YL EA RRG+ + +L+ +T Sbjct: 393 TLKAVRSLEIGVHHVEESTLRSVDDDVLSDKLIHAQDDRLFYLTEAIRRGYQIDELAELT 45- 2 Query: 340 KINPFYLDKCLHIVELYENLNKSQYNVDIYKEAKRYGFSDDYIASSWQISLIDMLEYRKK 39- 9 KIN F+LDK LHI+E+ + L +++ AKR GF+D +A W ++ + ++R Sbjct: 453 KINVFFLDKLLHIIEIEQALRTHTDDIETLTVAKRNGFADQTVADYWHETIDQVRDFRLA 51- 2 Query: 400 HSVAPVLKQVEQSSGVLTGHQIQYFRSYDWHSDYISSGCQKALIM----------VDKGY 44- 9 H +APV K V+ +G Y+ +Y++ ++ I + L++ V+ Y Sbjct: 513 HKLAPVYKMVDTCAGEFASETPYYYGTYEFENESIVTKRPSVLVLGSGPIRIGQGVEFDY 57- 2 Query: 450 SLVKLNELIKQIKQTHLELLIVTNQPLLIEQLNDTS--IIFDTIGIETILTIMGIEE 504 + V +K I++ E +I+ + P + S + F+ + IE +L ++ +E+ Sbjct: 573 ATV---HSVKAIQKAGYEAIIMNSNPETVSTDFSVSDKLYFEPLTIEDVLNVIELEK 626 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 841 A DNA sequence (GBSx0893) was identified in S. agalactiae <SEQ ID 2539> which encodes the amino acid sequence <SEQ ID 2540>. This protein is predicted to be carbamoyl phosphate synthetase small subunit (carA). Analysis of this protein sequence reveals the following: TABLE-US-02437 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2709 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02438 >GP: CAB89872 GB: AJ132624 carbamoyl phosphate synthetase small subunit [Lactococcus lactis] Identities = 188/352 (53%), Positives = 265/352 (74%) Query: 1 MAKKLLILEDGTVFEGLSFGSSLDVTGELVFCTGNTGYQEIITNPSHNGKILVFTSPLIG 60 M+K+LLILEDGT+FEG + G++LDVTGELVF TG TGYQE IT+ S+NG+IL FT P++G Sbjct: 1 MSKRLLILEDGTIFEGEALGANLDVTGELVFNTGMTGYQESITDQSYNGQILTFTYPIVG 60 Query: 61 NYGIHRSYSEAIIPTCLGVVVAEYSRCVSSDTSKMNLDEFLKMKKVPAMSGVDTRYLMQV 120- NYG++R E+I PTC VVV E +R S+ +M+ DEFLK K +P ++GVDTR + ++ Sbjct: 61 NYGVNRDDYESIHPTCKAVVVHEAARRPSNWRMQMSFDEFLKSKNIPGITGVDTRAITKI 120- Query: 121 IKEKGFVKATLAEAGDVLSHLQDQLIATVLPTNNVEQVSTKTAYPSPASGRNIVVLDFGL 18- 0 ++E G +KA+L +A D + H QL ATVLPTN VE ST TAYPSP +GR +VV+DFGL Sbjct: 121 VREHGTMKASLVQARDEVDHQMSQLQATVLPTNQVETSSTATAYPSPNTGRKVVVVDFGL 18- 0 Query: 181 KHSILRELSKRQCDVTVIPYNTSLEGIKNLYPEGIILSNGPGNPEKLQEILNTIKELQKS 24- 0 KHSILRELSKR+C++TV+PYNTS + I + P+G++L+NGPG+P + E + IKE+Q Sbjct: 181 KHSILRELSKRECNLTVVPYNTSAKEILEMEPDGVMLTNGPGDPTDVPEAIEMIKEVQGK 24- 0 Query: 241 VPMLGIGLGHQLIAMANGAEIMRLPVAKKGPNYPMRDIATGRLETVSQFNHFTVNRLNLP 30- 0 +P+ GI LGHQL ++ANGA ++ +G N+ +R++ATGR++ SQ + + V+ NLP Sbjct: 241 IPIFGICLGHQLFSLANGATTYKMKFGHRGFNHAVREVATGRIDFTSQNHGYAVSSENLP 30- 0 Query: 301 HDLLVTHEGLNDQEIVALRHRSFPVMSVQFYPEAAPGPHDVTYFFDEFLEMI 352 DL++TH +ND + +RH+ FP SVQF+P+AAPGPHD +Y FD+F++++ Sbjct: 301 EDLMITHVEINDNSVEGVRHKYFPAFSVQFHPDAAPGPHDASYLFDDFMDLM 352 There is also homology to SEQ ID 2030. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 842 A DNA sequence (GBSx0894) was identified in S. agalactiae <SEQ ID 2541> which encodes the amino acid sequence <SEQ ID 2542>. Analysis of this protein sequence reveals the following: TABLE-US-02439 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3646 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9967> which encodes amino acid sequence <SEQ ID 9968> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02440 >GP: CAB89869 GB: AJ132624 pyrimidine regulatory protein [Lactococcus lactis] Identities = 127/169 (75%), Positives = 147/169 (86%) Query: 13 MKRKEIIDDVTMKRAITRITYEIIERNKNLDNIVLAGIKTRGVFLAKRIQERLKQLENLD 72 - M RKEIID++TMKRAITRITYEIIERNK LD +VL GIKTRGV+LAKRIQERL+QLE L+ Sbjct: 1 MARKEIIDEITMKRAITRITYEIIERNKELDKLVLIGIKTRGVYLAKRIQERLQQLEGLE 60 Query: 73 IPVGELDTKPFRDDMKVEVDTTTMPVDITDKDIILIDDVLYTGRTIRAAIDNLVSLGRPS 132- IP GELDT+PFRDD + + DTT + +DIT KD+IL+DDVLYTGRTIRAAID +V LGRP+ Sbjct: 61 IPFGELDTRPFRDDKQAQEDTTEIDIDITGKDVILVDDVLYTGRTIRAAIDGIVKLGRPA 120- Query: 133 RVSLAVLIDRGHRELPIRADYVGKNIPTSQFEEILVEVMEHDGYDRVSI 181 RV LAVL+DRGHRELPIRADYVGKNIPT EEI+V++ EHDG D + I Sbjct: 121 RVQLAVLVDRGHRELPIRADYVGKNIPTGHDEEIIVQMSEHDGNDSILI 169 A related DNA sequence was identified in S. pyogenes <SEQ ID 2543> which encodes the amino acid sequence <SEQ ID 2544>. Analysis of this protein sequence reveals the following: TABLE-US-02441 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3870 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-02442 Identities = 147/171 (85%), Positives = 158/171 (91%) Query: 13 MKRKEIIDDVTMKRAITRITYEIIERNKNLDNIVLAGIKTRGVFLAKRIQERLKQLENLD 72 - MK KEI+DDVTMKRAITRITYEIIERNK LDN+VLAGIKTRGVFLA+RIQERL QLE LD Sbjct: 1 MKTKEIVDDVTMKRAITRITYEIIERNKQLDNVVLAGIKTRGVFLARRIQERLHQLEGLD 60 Query: 73 IPVGELDTKPFRDDMKVEVDTTTMPVDITDKDIILIDDVLYTGRTIRAAIDNLVSLGRPS 132- +P+GELD KPFRDDM+VE DTT M VDIT KD+ILIDDVLYTGRTIRAAIDNLVSLGRP+ Sbjct: 61 LPIGELDIKPFRDDMRVEEDTTLMSVDITGKDVILIDDVLYTGRTIRAAIDNLVSLGRPA 120- Query: 133 RVSLAVLIDRGHRELPIRADYVGKNIPTSQFEEILVEVMEHDGYDRVSIID 183 RVSLAVL+DRGHRELPIRADYVGKNIPTS EEI+VEV+E DG DRVSIID Sbjct: 121 RVSLAVLVDRGHRELPIRADYVGKNIPTSSVEEIVVEVVEVDGRDRVSIID 171 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 843 A DNA sequence (GBSx0895) was identified in S. agalactiae <SEQ ID 2545> which encodes the amino acid sequence <SEQ ID 2546> (rluD). Analysis of this protein sequence reveals the following: TABLE-US-02443 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0687 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9969> which encodes amino acid sequence <SEQ ID 9970> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02444 >GP: BAB06261 GB: AP001515 unknown conserved protein [Bacillus halodurans] Identities = 178/290 (61%), Positives = 216/290 (74%), Gaps = 2/290 (0%) Query: 17 GVRLDKAL-ADNSELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITFDIPKEEVLDY 75 - G R+DK L A E SR+Q + IK G VL+NG+ K+ Y V+ GD + +P+ EVL+ Sbjct: 15 GERIDKFLTAQGEEWSRTQVQQWIKDGHVLINGRTIKSNYKVETGDTLELFVPEPEVLEV 74 Query: 76 QAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVRPGI 135- ENIP++IIY+D+DVAVVNKP+GMVVHP+ GH++GTLVNALMYH DLSSINGVVRPGI Sbjct: 75 VPENIPIEIIYEDEDVAVVNKPRGMVVHPAPGHTTGTLVNALMYHCNDLSSINGVVRPGI 134- Query: 136 VHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIGRSD 19- 5 VHRIDKDTSGLLM+AKNDRAH+ L +LK K + R Y AIVHGN+P+D G I+APIGR Sbjct: 135 VHRIDKDTSGLLMIAKNDRAHESLVNQLKAKTTERVYQAIVHGNIPHDHGTIDAPIGRDK 19- 4 Query: 196 KDRKKQAVTAK-GKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHPLAGDPV 25- 4 DR+ VT + + A+T F VLERFGD+T VE LETGRTHQIRVH YIG PLAGDP Sbjct: 195 VDRQSMTVTEENSRDAVTHFTVLERFGDFTFVECQLETGRTHQIRVHFKYIGFPLAGDPK 25- 4 Query: 255 YGPRKTLGGKGQFLHAQTLGFTHPSNGENLIFSVEVPEIFQTTLEKLRKN 304 YGP+KTL GQ LHAQ LGF HP GE + F VE+PE + + +L+ N Sbjct: 255 YGPKKTLSIDGQALHAQKLGFEHPRTGEFMRFKVEMPEEMKKLIRQLQNN 304 A related DNA sequence was identified in S. pyogenes <SEQ ID 2547> which encodes the amino acid sequence <SEQ ID 2548>. Analysis of this protein sequence reveals the following: TABLE-US-02445 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2455 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02446 Identities = 239/295 (81%), Positives = 265/295 (89%) Query: 9 MEITIKIAGVRLDKALADNSELSRSQANEEIKKGIVLVNGQVKKAKYTVQEGDRITFDIP 68 MEI + +G RLDKALAD S LSR QAN++IK+G+VLVNGQ KKAKYTVQ GD I F++P Sbjct: 1 MEINVITSGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQKKAKYTVQAGDVICFELP 60 Query: 69 KEEVLDYQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSIN 128- KEEVL+YQA+NIPLDIIY+DD +A++NKPQGMVVHPSAGH SGT+VNALMYHIKDLSSIN Sbjct: 61 KEEVLEYQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSIN 120- Query: 129 GVVRPGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIE 18- 8 GVVRPGIVHRIDKDTSGLLMVAK D AHQ LAEELK KKSLRKYLAIVHGNLPNDRG+IE Sbjct: 121 GVVRPGIVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIE 18- 0 Query: 189 APIGRSDKDRKKQAVTAKGKPAITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 24- 8 APIGRS+KDRKKQAVTAKGK A+TRF VLERFGDY+LVEL LETGRTHQIRVHMAYIGHP Sbjct: 181 APIGRSEKDRKKQAVTAKGKEAVTRFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHP 24- 0 Query: 249 LAGDPVYGPRKTLGGKGQFLHAQTLGFTHPSNGENLIFSVEVPEIFQTTLEKLRK 303 +AGDP+YGPRKTL G GQFLHA+TLG THP G+ +IF+VE PEIFQ L+ LRK Sbjct: 241 VAGDPLYGPRKTLSGHGQFLHAKTLGLTHPMTGKEMIFTVEAPEIFQKVLKLLRK 295 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 844 A DNA sequence (GBSx0896) was identified in S. agalactiae <SEQ ID 2549> which encodes the amino acid sequence <SEQ ID 2550>. Analysis of this protein sequence reveals the following: TABLE-US-02447 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0496 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02448 >GP: AAD53064 GB: AF163833 CpsY [Streptococcus agalactiae] Identities = 105/297 (35%), Positives = 163/297 (54%), Gaps = 4/297 (1%) Query: 1 MNIQQLRYVVAIANSGTFREAAAKLFVSQPSLSVAVRDLETELGFQIFTRTTTGAVLTNQ 60 M IQQL+YV+ I +G+ EAA +L+++QPSLS AVR+LETE+G QIF R G LT Sbjct: 1 MRIQQLQYVIKIVETGSMNEAAKQLYITQPSLSNAVRNLETEMGIQIFIRNPKGITLTKD 60 Query: 61 GMTFYENALEVVKSFDSFEKQFSQSEATEQEFSIASQHYDFLPPLITAFSKCNDNFSY-F 119- GM F A ++++ E+++ + + FS++SQHY F+ A D Y Sbjct: 61 GMEFLSYARQILEQTALLEERYKGDNTSRELFSVSSQHYAFVVNAFVALFNGTDMTQYEL 120- Query: 120 RIFESTTIRILDEVAQGNSEIGIIYINSQNKKGLLQRLDKLGLEFVELIPFKTHIYLGKD 17- 9 + E+ T I+D+V SEIG++++NS N+ L + D L L HI++ K Sbjct: 121 FLRETRTWEIIDDVKNFRSEIGVLFLNSYNRDVLTKLFDDNSLIATTLFTTTPHIFVSKS 18- 0 Query: 180 HPLASKTSLIMTDLEGLPTVRFTQDRDDYRYYSENFVEVLDSSVTYNVTDRATLNGILER 23- 9 +PLA++ L M DLE P + + Q + Y+SE + + + V+DRATL ++ Sbjct: 181 NPLANRKKLSMKDLEDYPYLSYDQGLHNSFYFSEEMMSQIPHPKSIVVSDRATLFNLMIG 24- 0 Query: 240 TQAYATGSGFLDSRSVNG--ITVIPLEDHLDNQMIYIKRKDRNLSQMALKFVAVMEE 294 Y +G L+S+ +NG I IPL+ ++YI+ NLS+M KF+ + E Sbjct: 241 LDGYTVATGILNSK-LNGDEIVAIPLDVDDVIDIVYIRHDKANLSKMGQKFIDYLLE 296 A related DNA sequence was identified in S. pyogenes <SEQ ID 2551> which encodes the amino acid sequence <SEQ ID 2552>. Analysis of this protein sequence reveals the following: TABLE-US-02449 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1252 (Affirmative) < succ> bacterial membrane --- Certainty = 0.000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02450 Identities = 217/296 (73%), Positives = 253/296 (85%) Query: 1 MNIQQLRYVVAIANSGTFREAAAKLFVSQPSLSVAVRDLETELGFQIFTRTTTGAVLTNQ 60 MNIQQLRYVVAIAN+GTFREAA+KLFVSQPSLSV+++DLE ELGFQIF RTT+G VLT+Q Sbjct: 1 MNIQQLRYVVAIANNGTFREAASKLFVSQPSLSVSIKDLEAELGFQIFNRTTSGTVLTSQ 60 Query: 61 GMTFYENALEVVKSFDSFEKQFSQSEATEQEFSIASQHYDFLPPLITAFSKCNDNFSYFR 120- G+ FYE ALEVVKSFDSFEK FSQ++ + EFSIASQHYDFLPPLITAFS+ D FR Sbjct: 61 GLVFYEKALEVVKSFDSFEKTFSQADLDQNEFSIASQHYDFLPPLITAFSQQYDGHRVFR 120- Query: 121 IFESTTIRILDEVAQGNSEIGIIYINSQNKKGLLQRLDKLGLEFVELIPFKTHIYLGKDH 18- 0 IFESTTI+ILDEVAQGNSEIGIIY+N N+KGL QR+DKLGLE+V LIPF THIYL K H Sbjct: 121 IFESTTIQILDEVAQGNSEIGIIYLNVDNQKGLFQRMDKLGLEYVSLIPFTTHIYLSKTH 18- 0 Query: 181 PLASKTSLIMTDLEGLPTVRFTQDRDDYRYYSENFVEVLDSSVTYNVTDRATLNGILERT 24- 0 PLA++ +L + D++GLP VRFTQ+RD+Y YYSENFV+ + YNV+DRATLNGILERT Sbjct: 181 PLANREALYLNDIQGLPAVRFTQERDEYLYYSENFVDTSECPRIYNVSDRATLNGILERT 24- 0 Query: 241 QAYATGSGFLDSRSVNGITVIPLEDHLDNQMIYIKRKDRNLSQMALKFVAVMEEYF 296 A+ATGSGFLD RSVNGI VIPL DH+DNQMIY+KRKD+NLS FV ++++YF Sbjct: 241 NAFATGSGFLDHRSVNGIKVIPLADHIDNQMIYVKRKDKNLSVAGATFVTILKDYF 296 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 845 A DNA sequence (GBSx0897) was identified in S. agalactiae <SEQ ID 2553> which encodes the amino acid sequence <SEQ ID 2554>. This protein is predicted to be 50S ribosomal protein L27 (rpmA). Analysis of this protein sequence reveals the following: TABLE-US-02451 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0976 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02452 >GP: CAB14754 GB: Z99118 ribosomal protein L27 (BL24) [Bacillus subtilis] Identities = 70/90 (77%), Positives = 80/90 (88%) Query: 8 NLQLFAHKKGGGSTSNGRDSQAKRLGAKAADGQTVSGGSILYRQRGTHIYPGANVGRGGD 67 +LQ FA KKG GST NGRDS+AKRLGAK ADGQ V+GGSILYRQRGT IYPG NVGRGGD Sbjct: 5 DLQFFASKKGVGSTKNGRDSEAKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGRGGD 64 Query: 68 DTLFAKVEGVVRFERKGRDKKQVSVYPIAK 97 DTLFAK++G V+FER GRD+K+VSVYP+A+ Sbjct: 65 DTLFAKIDGTVKFERFGRDRKKVSVYPVAQ 94 A related DNA sequence was identified in S. pyogenes <SEQ ID 2555> which encodes the amino acid sequence <SEQ ID 2556>. Analysis of this protein sequence reveals the following: TABLE-US-02453 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0976 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02454 Identities = 95/97 (97%), Positives = 96/97 (98%) Query: 1 MLKMNLANLQLFAHKKGGGSTSNGRDSQAKRLGAKAADGQTVSGGSILYRQRGTHIYPGA 60 MLKMNLANLQLFAHKKGGGSTSNGRDSQAKRLGAKAADGQTVSGGSILYRQRGTHIYPG Sbjct: 1 MLKMNLANLQLFAHKKGGGSTSNGRDSQAKRLGAKAADGQTVSGGSILYRQRGTHIYPGV 60 Query: 61 NVGRGGDDTLFAKVEGVVRFERKGRDKKQVSVYPIAK 97 NVGRGGDDTLFAKVEGVVRFERKGRDKKQVSVYP+AK Sbjct: 61 NVGRGGDDTLFAKVEGVVRFERKGRDKKQVSVYPVAK 97 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 846 A DNA sequence (GBSx0898) was identified in S. agalactiae <SEQ ID 2557> which encodes the amino acid sequence <SEQ ID 2558>. Analysis of this protein sequence reveals the following: TABLE-US-02455 Possible site: 25 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.75 Transmembrane 32-48 (32-48) ----- Final Results ----- bacterial membrane --- Certainty = 0.1298 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02456 >GP: BAB06729 GB: AP001517 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 33/107 (30%), Positives = 63/107 (58%), Gaps = 4/107 (3%) Query: 1 MIKATFTRNQSGYLYSAEISGHAGSGEYGFDVICAAVSTLSINFINSLEALTTCQAQLII 60 MI F RN+ + S +SGHA +G YG D++CA S +++ +N++ AL CQ +L+ Sbjct: 1 MIDVVFERNKQNDIVSFTMSGHADAGPYGQDLVCAGASAVALGTVNAIIAL--CQVELVT 58 Query: 61 N-DVEGGYMKIDL-SSIPQHKEDKVQLLFESYLLGMTNLSKDSSEFV 105 10 + EGG+++ + + + + KVQLL E + + ++++ E + Sbjct: 59 EMENEGGFLRCRVPNDLEETTFEKVQLLLEGMNISLQSIAESYGEHI 105 A related DNA sequence was identified in S. pyogenes <SEQ ID 2559> which encodes the amino acid sequence <SEQ ID 2560>. Analysis of this protein sequence reveals the following: TABLE-US-02457 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.59 Transmembrane 32-48 (32-48) ----- Final Results ----- bacterial membrane --- Certainty = 0.1235 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02458 >GP: BAB06729 GB: AP001517 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 33/109 (30%), Positives = 60/109 (54%), Gaps = 4/109 (3%) Query: 1 MIKAIFTRQKNGQLSSVTLTGHAGSGKHGFDIVCASVSTLAINFVNSLEVLADCQALVDL 60 MI +F R K + S T++GHA +G +G D+VCA S +A+ VN++ L + + ++ Sbjct: 1 MIDVVFERNKQNDIVSFTMSGHADAGPYGQDLVCAGASAVALGTVNAIIALCQVELVTEM 60 Query: 61 NDVEGGYMAITIP---PHDNKEEVQLLFESFLLGMTSLAKDSSKFVNTQ 106 + EGG++ +P E+VQLL E + + S+A+ + + + Sbjct: 61 EN-EGGFLRCRVPNDLEETTFEKVQLLLEGMNISLQSIAESYGEHIQIE 108 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02459 Identities = 67/110 (60%), Positives = 90/110 (80%), Gaps = 2/110 (1%) Query: 1 MIKATFTRNQSGYLYSAEISGHAGSGEYGFDVICAAVSTLSINFINSLEALTTCQAQLII 60 MIKA FTR ++G L S ++GHAGSG++GFD++CA+VSTL+INF+NSLE L CQA + + Sbjct: 1 MIKAIFTRQKNGQLSSVTLTGHAGSGKHGFDIVCASVSTLAINFVNSLEVLADCQALVDL 60 Query: 61 NDVEGGYMKIDLSSIPQHKEDKVQLLFESYLLGMTNLSKDSSEFVSTVVM 110 NDVEGGYM I + P +++VQLLFES+LLGMT+L+KDSS+FV+T V+ Sbjct: 61 NDVEGGYMAITIP--PHDNKEEVQLLFESFLLGMTSLAKDSSKFVNTQVI 108 SEQ ID 2558 (GBS433) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 78 (lane 4; MW 16 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 173 (lane 8; MW 41 kDa). GBS433-GST was purified as shown in FIG. 223, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 847 A DNA sequence (GBSx0899) was identified in S. agalactiae <SEQ ID 2561> which encodes the amino acid sequence <SEQ ID 2562>. This protein is predicted to be ribosomal protein L21 (rplU). Analysis of this protein sequence reveals the following: TABLE-US-02460 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2972 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02461 >GP: CAB14756 GB: Z99118 ribosomal protein L21 (BL20) [Bacillus subtilis] Identities = 67/101 (66%), Positives = 78/101 (76%) Query: 4 YAIIKTGGKQVKVEVGQAIYVEKLDVEAGAEVTFNEVVLVGGETTKVGTPVVEGATVVGT 63 YAIIKTGGKQ+KVE GQ +Y+EKL EAG VTF +V+ VGG+ KVG P VEGATV Sbjct: 2 YAIIKTGGKQIKVEEGQTVYIEKLAAEAGETVTFEDVLFVGGDNVKVGNPTVEGATVTAK 61 Query: 64 VEKQGKQKKVVSYKYKPKKGSHRKQGHRQPYTKVVINAINA 104 VEKQG+ KK+ ++YKPKK H+KQGHRQPYTKV I INA Sbjct: 62 VEKQGRAKKITVFRYKPKKNVHKKQGHRQPYTKVTIEKINA 102 A related DNA sequence was identified in S. pyogenes <SEQ ID 2563> which encodes the amino acid sequence <SEQ ID 2564>. Analysis of this protein sequence reveals the following: TABLE-US-02462 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3026 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02463 Identities = 97/104 (93%), Positives = 101/104 (96%) Query: 1 MSTYAIIKTGGKQVKVEVGQAIYVEKLDVEAGAEVTFNEVVLVGGETTKVGTPVVEGATV 60 MSTYAIIKTGGKQVKVEVGQAIYVEK+D EAGAEVTFNEVVLVGG+ T VGTPVVEGATV Sbjct: 1 MSTYAIIKTGGKQVKVEVGQAIYVEKIDAEAGAEVTFNEVVLVGGDKTVVGTPVVEGATV 60 Query: 61 VGTVEKQGKQKKVVSYKYKPKKGSHRKQGHRQPYTKVVINAINA 104 VGTVEKQGKQKKVV++KYKPKKGSHRKQGHRQPYTKVVINAINA Sbjct: 61 VGTVEKQGKQKKVVTFKYKPKKGSHRKQGHRQPYTKVVINAINA 104 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 848 A DNA sequence (GBSx0900) was identified in S. agalactiae <SEQ ID 2565> which encodes the amino acid sequence <SEQ ID 2566>. Analysis of this protein sequence reveals the following: TABLE-US-02464 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1032 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9369> which encodes amino acid sequence <SEQ ID 9370> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02465 >GP: CAB14809 GB: Z99118 excinuclease ABC (subunit C) [Bacillus subtilis] Identities = 221/373 (59%), Positives = 288/373 (76%) Query: 1 MKSAAMTMEFERAAEYRDLIEAISLLRTKQRVIHQDMKDRDVFGYFVDKGWMCVQVFFVR 60 M AA +EFERA E RD I I KQ++ D+ DRDVF Y DKGWMCVQVFF+R Sbjct: 206 MHEAAENLEFERAKELRDQIAHIESTMEKQKMTMNDLVDRDVFAYAYDKGWMCVQVFFIR 26- 5 Query: 61 NGKLIQRDVNMFPYYNEPEEDFLTYIGQFYQDTKHFLPKEVFIPQDIDAKSVETIVGCKI 120- GKLI+RDV+MFP Y E +E+FLT+IGQFY HFLPKE+ +P ID +E ++ + Sbjct: 266 QGKLIERDVSMFPLYQEADEEFLTFIGQFYSKNNHFLPKEILVPDSIDQSMIEQLLETNV 32- 5 Query: 121 VKPQRGEKKQLVNLAIKNARVSLQQKFDLLEKDIRKTHGAIENLGNLLNIPKPVRIEAFD 18- 0 +P++G KK+L+ LA KNA+++L++KF L+E+D ++ GA++ LG LNI P RI AFD Sbjct: 326 HQPKKGPKKELLMLAHKNAKIALKEKFSLIERDEERSIGAVQKLGEALNIYTPHRIVAFD 38- 5 Query: 181 NSNIQGTSPVAAMVVFVNGKPSKKDYRKFKIKTVIGPDDYASMREVIHRRYSRVLKDGLT 24- 0 NSNIQGT+PV+AM+VF++GKP KK+YRK+KIKTV GPDDY SMREV+ RRY+RVL++ L Sbjct: 386 NSNIQGTNPVSAMIVFIDGKPYKKEYRKYKIKTVTGPDDYGSMREVVRRRYTRVLRENLP 44- 5 Query: 241 PPDLIVIDGGQGQVNIARDVIENQFGLAIPIAGLQKNDKHQTHELLFGDPLEVVELPRNS 30- 0 PDLI+IDGG+GQ+N ARDVIEN+ GL IPIAGL K++KH+T LL GDPLEV L RNS Sbjct: 446 LPDLIIIDGGKGQINAARDVIENELGLDIPIAGLAKDEKHRTSNLLIGDPLEVAYLERNS 50- 5 Query: 301 EEFFLLHRIQDEVHRFAITFHRQLRSKNSFSSKLDGITGLGPKRKQLLMKHFKSLPNIQK 36- 0 +EF+LL RIQDEVHRFAI+FHRQ+R K++F S LD I G+G KRK++L+KHF S+ +++ Sbjct: 506 QEFYLLQRIQDEVHRFAISFHRQIRGKSAFQSVLDDIPGIGEKRKKMLLKHFGSVKKMKE 56- 5 Query: 361 AEIEDIIMCGIPR 373 A +EDI G+P+ Sbjct: 566 ASLEDIKKAGVPQ 578 A related DNA sequence was identified in S. pyogenes <SEQ ID 2567> which encodes the amino acid sequence <SEQ ID 2568>. Analysis of this protein sequence reveals the following:

TABLE-US-02466 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4332 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02467 Identities = 289/385 (75%), Positives = 334/385 (86%) Query: 1 MKSAAMTMEFERAAEYRDLIEAISLLRTKQRVIHQDMKDRDVFGYFVDKGWMCVQVFFVR 60 M +A+ M FERAAEYRDLI I+ +RTKQRV+ +D++DRD+FGY+VDKGWMCVQVFFVR Sbjct: 206 MLAASKEMAFERAAEYRDLISGIATMRTKQRVMSKDLQDRDIFGYYVDKGWMCVQVFFVR 26- 5 Query: 61 NGKLIQRDVNMFPYYNEPEEDFLTYIGQFYQDTKHFLPKEVFIPQDIDAKSVETIVGCKI 120- GKLIQRDVN+FPYY + EEDFLTY+GQFYQD +HF+PKEVFIP+ ID + V IV RI Sbjct: 266 QGKLIQRDVNLFPYYTDAEEDFLTYMGQFYQDKQHFIPKEVFIPEAIDEELVAAIVPTKI 32- 5 Query: 121 VKPQRGEKKQLVNLAIKNARVSLQQKFDLLEKDIRKTHGAIENLGNLLNIPKPVRIEAFD 18- 0 +KP+RGEKKQLV LA KNARVSLQQKFDLLEKDI+KT GAIENLG LL I KPVRIEAFD Sbjct: 326 IKPKRGEKKQLVALATKNARVSLQQKFDLLEKDIKKTSGAIENLGQLLRIDKPVRIEAFD 38- 5 Query: 181 NSNIQGTSPVAAMVVFVNGKPSKKDYRKFKIKTVIGPDDYASMREVIHRRYSRVLKDGLT 24- 0 NSNIQGTSPVAAMVVFV+GKPSKKDYRKFKIKTV+GPDDYASMREV+ RRYSRV K+GL Sbjct: 386 NSNIQGTSPVAAMVVFVDGKPSKKDYRKFKIKTVVGPDDYASMREVLFRRYSRVKKEGLQ 44- 5 Query: 241 PPDLIVIDGGQGQVNIARDVIENQFGLAIPIAGLQKNDKHQTHELLFGDPLEVVELPRNS 30- 0 P+LI++DGG GQVN+A+DVIE Q GL IP+AGLQKNDKHQTH+LLFG+PLEVV LPR S Sbjct: 446 APNLIIVDGGVGQVNVAKDVIEKQLGLTIPVAGLQKNDKHQTHDLLFGNPLEVVPLPRRS 50- 5 Query: 301 EEFFLLHRIQDEVHRFAITFHRQLRSKNSFSSKLDGITGLGPKRKQLLMKHFKSLPNIQK 36- 0 EEFFLLHRIQDEVHRFA+TFHRQ+R KNSFSS LD I+GLGPKRKQLL++HFK++ I Sbjct: 506 EEFFLLHRIQDEVHRFAVTFHRQVRRKNSFSSTLDHISGLGPKRKQLLLRHFKTITAIAS 56- 5 Query: 361 AEIEDIIMCGIPRTVAESLRDSLND 385 A E+I GIP+TV E+++ + D Sbjct: 566 ATSEEIQALGIPKTVVEAIQQQITD 590 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 849 A DNA sequence (GBSx0901) was identified in S. agalactiae <SEQ ID 2569> which encodes the amino acid sequence <SEQ ID 2570>. Analysis of this protein sequence reveals the following: TABLE-US-02468 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2491 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 850 A DNA sequence (GBSx0902) was identified in S. agalactiae <SEQ ID 2571> which encodes the amino acid sequence <SEQ ID 2572>. Analysis of this protein sequence reveals the following: TABLE-US-02469 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3349 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02470 >GP: BAA86651 GB: AB033763 glycerophosphoryl diester phosphodiesterase homologue [Staphylococcus aureus] Identities = 50/202 (24%), Positives = 96/202 (46%), Gaps = 15/202 (7%) Query: 1 MDVIMTKDHKLVVIHDDNLKRLSGMNKDVSKLTLDQVTKIPIHQ---GRFA-SHIPSFTE 56 +DV +TKD +L++IHDD L+R + M+ ++++L D++ +F H+P+F + Sbjct: 36 LDVAITKDEQLIIIHDDYLERTTNMSGEITELNYDEIKDASAGSWFGEKFKDEHLPTFDD 95 Query: 57 FMKTAQSLDQKIMIELKPY-NQNLDIYADEFIKEFKE----LRLSTKHKVMSLNLTLIEK 111- +K A + + +ELK N + +K+ +E L + + + S N+ L++ Sbjct: 96 VVKIANEYNMNLNVELKGITGPNGLALSKSMVKQVEEQLTNLNQNQEVLISSFNVVLVKL 155- Query: 112 VEKKLPQLDTGYLIPL-----HWGTLQNH-NVDFYGIEEFSYNDWIAYLAQEYNKQLYVW 16- 5 E+ +PQ + + W TL ++ N E+ + +E +L VW Sbjct: 156 AEEIMPQYNRAVIFHTTSFREDWRTLLDYCNAKIVNTEDAKLTKAKVKMVKEAGYELNVW 21- 5 Query: 166 TINRDNLMIRYLQSPVNGIITD 187 T+N+ + V+GI TD Sbjct: 216 TVNKPARANQLANWGVDGIFTD 237 A related DNA sequence was identified in S. pyogenes <SEQ ID 2573> which encodes the amino acid sequence <SEQ ID 2574>. Analysis of this protein sequence reveals the following: TABLE-US-02471 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.26 Transmembrane 239-255 (227-260) INTEGRAL Likelihood = -9.45 Transmembrane 80-96 (78-108) INTEGRAL Likelihood = -9.13 Transmembrane 137-153 (131-160) INTEGRAL Likelihood = -4.94 Transmembrane 278-294 (277-295) INTEGRAL Likelihood = -3.56 Transmembrane 36-52 (33-55) INTEGRAL Likelihood = -3.56 Transmembrane 188-204 (185-206) INTEGRAL Likelihood = -3.35 Transmembrane 314-330 (310-331) ----- Final Results ----- bacterial membrane --- Certainty = 0.5904 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02472 >GP: CAB12801 GB: Z99109 similar to glycerophosphodiester phosphodiesterase [Bacillus subtilis] Identities = 67/244 (27%), Positives = 110/244 (44%), Gaps = 14/244 (5%) Query: 344 VIAHRGLVSAGVENSLEALEGAKKAGSDYVELDLILTKDNHFVVSHDNRLKRLAGVNKTI 40- 3 +IAHRG EN++ A + A K +D +ELD+ LTKD VV HD+R+ R + + Sbjct: 3 IIAHRGASGYAPENTIAAFDLAVKMNADMIELDVQLTKDRQIVVIHDDRVDRTTNGSGFV 62 Query: 404 RNLTLKEVEHLTSHQGH---FSGRFVSFDTFYQKAKKLNMPLLIELKPIGTEPGNYVDLF 46- 0 ++ TL+E++ L + + F G + K + LLIELK ++ G ++ Sbjct: 63 KDFTLEELQKLDAGSWYGPAFQGERIPTLEAVLKRYHKKIGLLIELKGHPSQVGIEEEVG 122- Query: 461 LETYHRLGISKDNKVMSLDLEVIEAIKKKNPSITTGYIIPIQFGFFG-------DEFVDF 51- 3 + + S +N V S ++ ++ PSI T I FG F ++ Sbjct: 123 -QLLGQFSFSINNIVQSFQFRSVQRFRELYPSIPTAVITRPNFGMLSRNQMKAFRSFANY 18- 1 Query: 514 YVIEDFSYRSYLSSQAFWNNKEIYVWTINDPKRIEHYLLKPIQGIITDQPALTNQLIKDL 57- 3 I+ + N I+ WT+N+ K + GI+TD P + +IKD Sbjct: 182 VNIKHTRLNRLMIGSINKNGLNIFAWTVNNQKTAAKLQAMGVDGIVTDYP---DFIIKDG 23- 8 Query: 574 KQDN 577 K +N Sbjct: 239 KHEN 242 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02473 Identities = 90/215 (41%), Positives = 136/215 (62%) Query: 1 MDVIMTKDHKLVVIHDDNLKRLSGMNKDVSKLTLDQVTKIPIHQGRFASHIPSFTEFMKT 60 +D+I+TKD+ VV HD+ LKRL+G+NK + LTL +V + HQG F+ SF F + Sbjct: 375 LDLILTKDNHFVVSHDNRLKRLAGVNKTIRNLTLKEVEHLTSHQGHFSGRFVSFDTFYQK 43- 4 Query: 61 AQSLDQKIMIELKPYNQNLDIYADEFIKEFKELRLSTKHKVMSLNLTLIEKVEKKLPQLD 120- A+ L+ ++IELKP Y D F++ + L +S +KVMSL+L +IE ++KK P + Sbjct: 435 AKKLNMPLLIELKPIGTEPGNYVDLFLETYHRLGISKDNKVMSLDLEVIEAIKKKNPSIT 49- 4 Query: 121 TGYLIPLHWGTLQNHNVDFYGIEEFSYNDWIAYLAQEYNKQLYVWTINRDNLMIRYLQSP 18- 0 TGY+IP+ +G + VDFY IE+FSY +++ A NK++YVWTIN + YL P Sbjct: 495 TGYIIPIQFGFFGDEFVDFYVIEDFSYRSYLSSQAFWNNKEIYVWTINDPKRIEHYLLKP 55- 4 Query: 181 VNGIITDELNLFKVINKDIKNSPNYYQRALQLIDS 215 + GIITD+ L + KD+K +Y+ R +++I S Sbjct: 555 IQGIITDQPALTNQLIKDLKQDNSYFSRLVRIISS 589 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 851 A DNA sequence (GBSx0903) was identified in S. agalactiae <SEQ ID 2575> which encodes the amino acid sequence <SEQ ID 2576>. Analysis of this protein sequence reveals the following: TABLE-US-02474 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.02 Transmembrane 84-100 (76-112) INTEGRAL Likelihood = -3.50 Transmembrane 139-155 (139-157) INTEGRAL Likelihood = -2.23 Transmembrane 41-57 (39-59) INTEGRAL Likelihood = -0.96 Transmembrane 179-195 (179-195) ----- Final Results ----- bacterial membrane --- Certainty = 0.7007 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9901> which encodes amino acid sequence <SEQ ID 9902> was also identified. The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 2574. A related GBS gene <SEQ ID 8671> and protein <SEQ ID 8672> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02475 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -3.38 GvH: Signal Score (-7.5): -4.08 Possible site: 53 >>> Seems to have no N-terminal signal sequence ALOM program count: 4 value: -15.02 threshold: 0.0 INTEGRAL Likelihood = -15.02 Transmembrane 84-100 (76-112) INTEGRAL Likelihood = -3.50 Transmembrane 139-155 (139-157) INTEGRAL Likelihood = -2.23 Transmembrane 41-57 (39-59) INTEGRAL Likelihood = -0.96 Transmembrane 179-195 (179-195) PERIPHERAL Likelihood = 2.01 104 modified ALOM score: 3.50 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.7007 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 852 A DNA sequence (GBSx0904) was identified in S. agalactiae <SEQ ID 2577> which encodes the amino acid sequence <SEQ ID 2578>. Analysis of this protein sequence reveals the following: TABLE-US-02476 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4150 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 853 A DNA sequence (GBSx0905) was identified in S. agalactiae <SEQ ID 2579> which encodes the amino acid sequence <SEQ ID 2580>. Analysis of this protein sequence reveals the following: TABLE-US-02477 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 2-18 (2-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 854 A DNA sequence (GBSx0906) was identified in S. agalactiae <SEQ ID 2581> which encodes the amino acid sequence <SEQ ID 2582>. This protein is predicted to be nad(p)h nitroreductase ydgi. Analysis of this protein sequence reveals the following: TABLE-US-02478 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.81 Transmembrane 127-143 (126-143) ----- Final Results ----- bacterial membrane --- Certainty = 0.1723 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02479 >GP: CAC09964 GB: AX033132 unnamed protein product [Bacillus subtilis] Identities = 62/204 (30%), Positives = 106/204 (51%), Gaps = 11/204 (5%) Query: 3 FLELNKKRHAVKHFNDKPVDFKDVRTAI-EIATLAPSANNIQPWKFVVVQ--EKKSALAE 59 F+E+ K R ++++++ K+ T I E AT APS+ N QPW+F+V+ E K LA Sbjct: 7 FMEIMKGRRSIRNYDPAVKISKEEMTEILEEATTAPSSVNAQPWRFLVIDSPEGKEKLAP 66 Query: 60 GLPESNCNQINQAQYVIALFTDTD----LGQRSRKIARIGRRSLPDDLIGYYMETLPPRY 115- L N Q+ + VIA+F D + L + K +G +P ++ + L + Sbjct: 67 -LASFNQTQVTTSSAVIAVFADMNNADYLEEIYSKAVELG--YMPQEVKDRQIAALTAHF 123- Query: 116 ALYSEKQTGEYLSLNAGIVAMNLVLALTDQGISSNMILGFDKAITNDVLEIDK-RFRPEI 17- 4 + E + ++ G+V+M L+L G +N I G+DK + +DK R+ P + Sbjct: 124 EKLPAQVNRETILIDGGLVSMQLMLTARAHGYDTNPIGGYDKENIAETFGLDKERYVPVM 18- 3 Query: 175 LITVGYSDEKVEPSYRLPVDHIIE 198 L+++G + ++ SYRLP+D I E Sbjct: 184 LLSIGKAADEGYASYRLPIDTIAE 207 A related DNA sequence was identified in S. pyogenes <SEQ ID 2583> which encodes the amino acid sequence <SEQ ID 2584>. Analysis of this protein sequence reveals the following: TABLE-US-02480 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.18 Transmembrane 127-143 (126-143) ----- Final Results ----- bacterial membrane --- Certainty = 0.1871 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02481 >GP:CAC09964 GB:AX033132 unnamed protein product [Bacillus subtilis] Identities = 63/204 (30%), Positives = 109/204 (52%), Gaps = 11/204 (5%) Query: 3 FLELNKKRHAIKTFNDQ-PVDYEDLRTAIEIATLAPSANNIQPWKFVVVQ--EKKAELAK 59 F+E+ K R +I+ ++ + E++ +E AT APS+ N QPW+F+V+ E K +LA Sbjct: 7 FMEIMKGRRSIRNYDPAVKISKEEMTEILEEATTAPSSVNAQPWRFLVIDSPEGKEKLA- 65 Query: 60 GLPLA--NKVQVEQAQYVVALFSDTDLALRSRKIARIGVK--SLPDDLIGYYMETLPPRF 115- PLA N+ QV + V+A+F+D + A +I V+ +P ++ + L F Sbjct: 66 --PLASFNQTQVTTSSAVIAVFADMNNADYLEEIYSKAVELGYMPQEVKDRQIAALTAHF 123- Query: 116 AAFNEVQTGEYLAINAGIVAMNLVLSLTDQKIASNIILGFDKSTTNEILDID-PRFRPEL 17- 4 E + I+ G+V+M L+L+ +N I G+DK E +D R+ P + Sbjct: 124 EKLPAQVNRETILIDGGLVSMQLMLTARAHGYDTNPIGGYDKENIAETFGLDKERYVPVM 18- 3 Query: 175 LITVGYSDEKPEPSYRLPVDEVIE 198 L+++G + ++ SYRLP+D + E Sbjct: 184 LLSIGKAADEGYASYRLPIDTIAE 207 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02482 Identities = 157/200 (78%), Positives = 184/200 (91%) Query: 1 MKFLELNKKRHAVKHFNDKPVDFKDVRTAIEIATLAPSANNIQPWKFVVVQEKKSALAEG 60 MKFLELNKKRHA+K FND+PVD++D+RTAIEIATLAPSANNIQPWKFVVVQEKK+ LA+G Sbjct: 1 MKFLELNKKRHAIKTFNDQPVDYEDLRTAIEIATLAPSANNIQPWKFVVVQEKKAELAKG 60 Query: 61 LPESNCNQINQAQYVIALFTDTDLGQRSRKIARIGRRSLPDDLIGYYMETLPPRYALYSE 120- LP +N Q+ QAQYV+ALF+DTDL RSRKIARIG +SLPDDLIGYYMETLPPR+A ++E Sbjct: 61 LPLANKVQVEQAQYVVALFSDTDLALRSRKIARIGVKSLPDDLIGYYMETLPPRFAAFNE 120- Query: 121 KQTGEYLSLNAGIVAMNLVLALTDQGISSNMILGFDKAITNDVLEIDKRFRPEILITVGY 18- 0 QTGEYL++NAGIVAMNLVL+LTDQ I+SN+ILGFDK+ TN++L+ID RFRPE+LITVGY Sbjct: 121 VQTGEYLAINAGIVAMNLVLSLTDQKIASNIILGFDKSTTNEILDIDPRFRPELLITVGY 18- 0 Query: 181 SDEKVEPSYRLPVDHIIEKR 200 SDEK EPSYRLPVD +IE+R Sbjct: 181 SDEKPEPSYRLPVDEVIERR 200 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 855 A DNA sequence (GBSx0907) was identified in S. agalactiae <SEQ ID 2585> which encodes the amino acid sequence <SEQ ID 2586>. Analysis of this protein sequence reveals the following: TABLE-US-02483 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2895 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02484 >GP:AAC45369 GB:U78036 dipeptidase [Lactococcus lactis] Identities = 312/474 (65%), Positives = 370/474 (77%), Gaps = 11/474 (2%) Query: 2 TIDFRAEVDKRKDAIMDDLINLLRINSERDDSQADAEHPFGPGPVKALEFFLEMAERDGY 61 TIDF+AEV+KRKDALM+DL +LLRI+S D ADAE+PFGPGP KAL+ FL++AERDGY Sbjct: 3 TIDFKAEVEKRKDALMEDLFSLLRIDSAMDMEHADAENPFGPGPRKALDAFLKIAERDGY 62 Query: 62 ETKNVDNYAGHFTFGQGE----EELGIFGHLDVVPAGSGWDTDPYEPVIKDNRLYARGSS 117- TKN DNY GHF + G E LGI GHLDVVPAGSGWD++P+EP I++ LYARG+S Sbjct: 63 TTKNYDNYVGHFEYENGANADAEVLGIIGHLDVVPAGSGWDSNPFEPEIRNGNLYARGAS 122- Query: 118 DDKGPTMACYYALKIIKELGLPTSKKVRFVVGTDEESGWGDMDYYFEHVGLPKPDFGFSP 17- 7 DDKGPT+ACYYALKI+KEL LP SKK+RF+VGT+EE+GW DMDYYFEH LP PDFGFSP Sbjct: 123 DDKGPTVACYYALKILKELNLPLSKKIRFIVGTNEETGWADMDYYFEHCELPLPDFGFSP 18- 2 Query: 178 DAEFPIINGEKGNITEYLHFSGENKGAVRLHSFSGGLRENMVPESATARFTSHLDQTTLG 23- 7 DAEFPIINGEKGNITEYLHFSG+N G V LHSF GL ENMVPESATA + D L Sbjct: 183 DAEFPIINGEKGNITEYLHFSGKNAGQVVLHSFKAGLAENMVPESATAVISGAKD---LE 23- 9 Query: 238 ASLADFASKH---NLKAELSVEDEQYTATVYGKSAHGSTPQEGVNGATYLALYLSQFDFE 29- 4 A+L F ++H NL+ +L D + T T+YGKSAHG+ P++G+NGATYL L+L+QFDF Sbjct: 240 AALEKFVAEHASKNLRFDLEEADGKATITLYGKSAHGAMPEKGINGATYLTLFLNQFDFA 29- 9 Query: 295 GPARAFLDVTANIIHEDFSGEKLGVAYEDDCMGPLSMNAGVFQFDETNDDNTIALNFRYP 35- 4 A AF+ V A + ED GEKLG A+ D+ M SMNAGV+ FDE N + IALNFR+P Sbjct: 300 DGAAAFIKVGAEKLLEDHEGEKLGTAFVDELMENTSMNAGVWSFDE-NGEGKIALNFRFP 35- 8 Query: 355 QGTDAKTIQTKLEKLNGVEKVTLSDHEHTPHYVPMDDELVSTLLAVYEKQTGLKGHEQVI 41- 4 QG + +Q L KL+GV +V LS H HTPHYVPM D LVSTL+ VYEK TGLKG+E +I Sbjct: 359 QGNSPERMQEILAKLDGVVEVELSKHLHTPHYVPMSDPLVSTLIDVYEKHTGLKGYETII 41- 8 Query: 415 GGGTFGRLLERGVAYGAMFPGDENTMHQANEYMPLENIFRSAAIYAEAIYELIK 468 GGGTFGRLLERGVAYGAMF G+ ++MHQANE P+ENI+++A IYAEAIYEL K Sbjct: 419 GGGTFGRLLERGVAYGAMFEGEPDSMHQANEMKPVENIYKAAVIYAEAIYELAK 472 A related DNA sequence was identified in S. pyogenes <SEQ ID 2587> which encodes the amino acid sequence <SEQ ID 2588>. Analysis of this protein sequence reveals the following:

TABLE-US-02485 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3107 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02486 Identities = 361/467 (77%), Positives = 403/467 (85%) Query: 2 TIDFRAEVDKRKDALMDDLINLLRINSERDDSQADAEHPFGPGPVKALEFFLEMAERDGY 61 TIDF+AEVDKRK A++ DL++LLRINSERDD AD +HPFGPGPVKALE FL MAERDGY Sbjct: 20 TIDFKAEVDKRKKAMLADLVDLLRINSERDDQLADDKHPFGPGPVKALEHFLAMAERDGY 79 Query: 62 ETKNVDNYAGHFTFGQGEEELGIFGHLDVVPAGSGWDTDPYEPVIKDNRLYARGSSDDKG 121- +T+N+DNYAG F FGQG+E LGIFGHLDVVPAGSGWDTDPYEPVIKD+R+YARGSSDDKG Sbjct: 80 KTRNIDNYAGDFEFGQGDEVLGIFGHLDVVPAGSGWDTDPYEPVIKDDRIYARGSSDDKG 139- Query: 122 PTMACYYALKIIKELGLPTSKKVRFVVGTDEESGWGDMDYYFEHVGLPKPDFGFSPDAEF 18- 1 PTMACYYALKIIKELGLP SKKVRF+VGTDEESGWGDMDYYF H GL FDFGFSPDAEF Sbjct: 140 PTMACYYALKIIKELGLPVSKKVRFIVGTDEESGWGDMDYYFAHNGLKNPDFGFSPDAEF 19- 9 Query: 182 PIINGEKGNITEYLHFSGENKGAVRLHSFSGGLRENMVPESATARFTSHLDQTTLGASLA 24- 1 PIINGEKGNITEYLHF+G+NKGA LH F GGLRENMVPESATA T+ D L A+L Sbjct: 200 PIINGEKGNITEYLHFAGDNKGAFVLHRFQGGLRENMVPESATAVITAPHDLDVLEAALE 25- 9 Query: 242 DFASKHNLKAELSVEDEQYTATVYGKSAHGSTPQEGVNGATYLALYLSQFDFEGPARAFL 30- 1 F S+H +K + D + T+ GKSAHGSTP+ GVNGAT LA +L+QF FEG A+ +L Sbjct: 260 QFLSEHGVKGSMKATDGKIEVTIIGKSAHGSTPEAGVNGATLLAKFLNQFTFEGAAKDYL 31- 9 Query: 302 DVTANIIHEDFSGEKLGVAYEDDCMGPLSMNAGVFQFDETNDDNTIALNFRYPQGTDAKT 36- 1 V ++HEDF+ EKLG+AY DD MG LSMNAGVF FD + DNTIALNFRYP+GTDA T Sbjct: 320 HVAGEVLHEDFAAEKLGLAYTDDRMGALSMNAGVFTFDSQSADNTIALNFRYPKGTDAAT 37- 9 Query: 362 IQTKLEKLNGVERVTLSDHEHTPHYVPMDDELVSTLLAVYEKQTGLKGHEQVIGGGTFGR 42- 1 ++ LEKL G+ KV+LS+HEHTPHYVPMDDELV+TLLAVYEKQTGLKG+EQVIGGGTFGR Sbjct: 380 LKAGLEKLPGLTKVSLSEHEHTPHYVPMDDELVATLLAVYEKQTGLKGYEQVIGGGTFGR 43- 9 Query: 422 LLERGVAYGAMFPGDENTMHQANEYMPLENIFRSAAIYAEAIYELIK 468 LLERGVA+GAMFPGDENTMHQANEYMPLENI+RSAAIYAEAIYELIK Sbjct: 440 LLERGVAFGAMFPGDENTMHQANEYMPLENIYRSAAIYAEAIYELIK 486 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 856 A DNA sequence (GBSx0908) was identified in S. agalactiae <SEQ ID 2589> which encodes the amino acid sequence <SEQ ID 2590>. Analysis of this protein sequence reveals the following: TABLE-US-02487 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5598 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02488 >GP:AAC21888 GB:U32707 H. influenzae predicted coding region HI0220.2 [Haemophilus influenzae Rd] Identities = 123/192 (64%), Positives = 160/192 (83%), Gaps = 1/192 (0%) Query: 1 MTDLEKIIKAIKSDSQNQNYTENGIDPLFAAPKTARINIVGQAPGLKTQEARLYWKDKSG 60 + +L++I +I +D QN+++TE GI PLF+APKTARINIVGQAPGLK +++RLYW DKSG Sbjct: 21 LKNLDEITSSIIADPQNKDFTERGIFPLFSAPKTARINIVGQAPGLKAEQSRLYWNDKSG 80 Query: 61 DRLRQWLGVDEETFYHSGKFAVLPLDFYYPGKGKSGDLSPRKGFAEKWHPLILKEMPNVQ 120- DRLR+WLGVD + FY+SG FAVLP+DFYYPG GKSGDL PR+GFAE+WHP+IL +PN+Q Sbjct: 81 DRLREWLGVDYDYFYNSGIFAVLPMDFYYPGYGKSGDLPPRQGFAERWHPMILGNLPNIQ 140- Query: 121 LTLLVGQYTQKYYLGSSAHKNLTETVKAYKDYLPDYLPLVHPSPRNQIWLKKNPWFEKDL 18- 0 LT+L+GQY QKYYL + N+T TVK Y+ +LP ++PLVHPSPRNQ+W+ KNPWFE+ + Sbjct: 141 LTILIGQYAQKYYLPEN-KDNVTNTVKNYRQFLPHFMPLVHPSPRNQLWVTKNPWFEEQV 19- 9 Query: 181 IVDLQKIVADIL 192 I +LQ +V I+ Sbjct: 200 IPELQILVKQII 211 A related DNA sequence was identified in S. pyogenes <SEQ ID 2591> which encodes the amino acid sequence <SEQ ID 2592>. Analysis of this protein sequence reveals the following: TABLE-US-02489 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3740 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02490 Identities = 122/189 (64%), Positives = 150/189 (78%) Query: 4 LEKIIKAIKSDSQNQNYTENGIDPLFAAPKTARINIVGQAPGLKTQEARLYWKDKSGDRL 63 ++ + KAI +D N +YTE GI PL+ AP+TARI IVGQAPG+ Q +LYW D+SG RL Sbjct: 1 MDDLTKAIMADEANLSYTERGIFPLYDAPQTARIIIVGQAPGIVAQGTKLYWNDRSGIRL 60 Query: 64 RQWLGVDEETFYHSGKFAVLPLDFYYPGKGKSGDLSPRKGFAEKWHPLILKEMPNVQLTL 123- R WLGVD +TFYHSG F ++P+DFYYPGKGKSGDL PR+GFA KWHP + MP V+LT+ Sbjct: 61 RDWLGVDNDTFYHSGLFGIIPMDFYYPGKGKSGDLPPREGFAAKWHPPLRALMPEVELTI 120- Query: 124 LVGQYTQKYYLGSSAHKNLTETVKAYKDYLPDYLPLVHPSPRNQIWLKKNPWFEKDLIVD 18- 3 LVG+Y Q +YLG+ A+K LTETV+ ++DYLPDY PLVHPSPRNQ+WL KNPWFE+DL+ Sbjct: 121 LVGRYAQDFYLGNKAYKTLTETVRHFEDYLPDYFPLVHPSPRNQLWLAKNPWFEQDLLPI 18- 0 Query: 184 LQKIVADIL 192 LQK V IL Sbjct: 181 LQKRVEAIL 189 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 857 A DNA sequence (GBSx0909) was identified in S. agalactiae <SEQ ID 2593> which encodes the amino acid sequence <SEQ ID 2594>. Analysis of this protein sequence reveals the following: TABLE-US-02491 Possible Site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4178 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 858 A DNA sequence (GBSx0910) was identified in S. agalactiae <SEQ ID 2595> which encodes the amino acid sequence <SEQ ID 2596>. Analysis of this protein sequence reveals the following: TABLE-US-02492 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2779 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9899> which encodes amino acid sequence <SEQ ID 9900> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02493 >GP:AAD35886 GB:AE001748 conserved hypothetical protein [Thermotoga maritima] Identities = 36/124 (29%), Positives = 58/124 (46%), Gaps = 3/124 (2%) Query: 19 VPTKELLADYFNRMEFAIGRVEAHVLAHFDYGFRKLNLDVEDLKPFETQLKRIFIKMLSK 78 - +P EL DY R F + RV+ H LAH DY R D K +++I + ++ Sbjct: 98 LPPDELARDYLERTLFVMERVKFHTLAHLDYPARYAKAD---FKANRDLIEKILVFLVKN 154- Query: 79 GLAFELNTKSLYLYGNEKLYRYALEILKQLGCKQYSIGSDGHIPEHFCYEFDRLQGLLKD 138- A E+NT L+ +G + +E+ LG + +IGSD H +H + + LK Sbjct: 155 EKALEINTAGLFKHGKPNPDYWIVEMYYDLGGRVVTIGSDAHESQHIGRGIEEVMRELKK 21- 4 Query: 139 YQID 142 + + Sbjct: 215 FNFE 218 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 859 A DNA sequence (GBSx0911) was identified in S. agalactiae <SEQ ID 2597> which encodes the amino acid sequence <SEQ ID 2598>. This protein is predicted to be alkaline amylopullulanase (pulA). Analysis of this protein sequence reveals the following: TABLE-US-02494 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.08 Transmembrane 1225-1241 (1222-1247) INTEGRAL Likelihood = -2.44 Transmembrane 19-35 (18-36) INTEGRAL Likelihood = -0.11 Transmembrane 1146-1162 (1146-1162) ----- Final Results ----- bacterial membrane --- Certainty = 0.5034 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02495 >GP: AAG33958 GB: AF217414 pullulanase [Streptococcus pneumoniae] Identities = 641/1311 (48%), Positives = 854/1311 (64%), Gaps = 88/1311 (6%) Query: 1 MKRKDLFGDKQTQYTIRKLSVGVASVATGVCIFLHSPQVFAEEVSASPANTAIAESNINQ 60 M++ +K+ Y+IR L G SV G + L A+A I+ Sbjct: 1 MRKTPSHTEKKMVYSIRSLKNGTGSVLIGASLVL----------------LAMATPTISS 44 Query: 61 VDNQQSTNLKDDINSNSETVVTPSDMPDTKQLVSDETDTQKGVTEPDKATSLLEENKG-P 119- ++ +TN + N N+ T+ P + DT + + ++ P A + LE+ + P Sbjct: 45 DESTPTTN--EPNNRNTTTLAQP--LTDT---AAGSGKNESDISSPGNANASLEKTEEKP 97 Query: 120 VSDKNTLDLKVAPSTLQNTPDKTSQAIGAPSPTLKVANQAPRIENGYFRLHLKELPQGHP 17- 9 ++ T A Q D++S+ + SP IE+ YFR+H+K+LP+ + Sbjct: 98 ATEPTTPAASPADPAPQTGQDRSSEPTTSTSPVTTETKAEEPIEDNYFRIHVKKLPEENK 157- Query: 180 VESTGLWIWGDVDQPSSNWPNGAIPMTDAKKDDYGYYVDFKLSEKQRKQISFLINNKAGT 23- 9 ++ GLW W DV++PS NWPNGA+ DAKKDDYGYY+D KL +Q K+ISFLINN AG Sbjct: 158 -DAQGLWTWDDVEKPSENWPNGALSFKDAKKDDYGYYLDVKLKGEQAKKISFLINNTAGK 21- 6 Query: 240 NLSGDHHIPLLRPEMNQVWIDEKYGTHTYQPLKEGYVRINYLSSSSNYDHLSAWLFKDVA 29- 9 NL+GD + L P+MN+ W+D+ Y +Y+P G VR+NY + NYD S W + DV Sbjct: 217 NLTGDKSVEKLVPKMNEAWLDQDYKVFSYEPQPAGTVRVNYYRTDGNYDKKSLWYWGDVK 27- 6 Query: 300 TPSTT-WPDGSNFVNQGLYGRYIDVSLKTNAKEIGFLILDESKTGDAVKVQPNDYVFRDL 35- 8 PS+ WPDG++F G YGRYID+ L A+E GFL+LDESK GD VK++ +Y F DL Sbjct: 277 NPSSAQWPDGTDFTATGKYGRYIDIPLNEAAREFGFLLLDESKQGDDVKIRKENYKFTDL 33- 6 Query: 359 ANHNQIFVKDKDPKVYNNPYYIDQVQLKDAQQIDLTSIQASFTTLDGVDKTEILKELKVT 41- 8 NH+QIF+KD D +Y NPYY+ +++ AQ + +SI++SF+TL G K +ILK +T Sbjct: 337 KNHSQIFLKDDDESIYTNPYYVHDIRMTGAQHVGTSSIESSFSTLVGAKKEDILKHSNIT 39- 6 Query: 419 DKNQNAIQISDITLDTSKSLLIIKGDFNPKQGHFNISYNGNNVMTRQSWEFKDQLYAYSG 47- 8 + N + I+D+ +D + + GDF+ + + +SYN + T+ SW KD+ Y+Y G Sbjct: 397 NHLGNKVTITDVAIDEAGKKVTYSGDFSDTKHPYTVSYNSDQFTTKTSWRLKDETYSYDG 45- 6 Query: 479 NLGAVLNQDGSKVEASLWSPSADSVTMIIYDKDNQNRVVATTPLMKNNKGVWQTILDT-- 53- 6 LGA L ++G +V+ +LWSPSAD V++++YDK++ ++VV T L K +G W+ LD+ Sbjct: 457 KLGADLKEEGKQVDLTLWSPSADKVSVVVYDKNDPDKVVGTVALEKGERGTWKQTLDSTN 51- 6 Query: 537 KLGIKNYTGYYYLYEIKRGKDKVKILDPYAKSLAEWDSNT--VNDDIKTAKAAFVNPSQL 59- 4 KLGI ++TGYYY Y+I+R V LDPYAKSLA W+S+ ++D K AKAAFV+P++L Sbjct: 517 KLGITDFTGYYYQYQIERQGKTVLALDPYAKSLAAWNSDDAKIDDAHKVAKAAFVDPAKL 57- 6 Query: 595 GPQNLSFAKIANFKGRQDAVIYEAHVRDFTSDRSLDGKLKNQFGTFAAFSEKLDYLQKLG 65- 4 GPQ+L++ KI NFK R+DAVIYEAHVRDFTSD ++ L FGTF AF EKLDYL+ LG Sbjct: 577 GPQDLTYGKIHNFKTREDAVIYEAHVRDFTSDPAIAKDLTKPFGTFEAFIEKLDYLKDLG 63- 6 Query: 655 VTHIQLLPVLSYFYVNEMDKSRSTA-YTSSDNNYNWGYDPQSYFALSGMYSEKPKDPSAR 71- 3 VTHIQLLPVLSY++VNE+ + Y SS++NYNWGYDPQ+YF+L+GMYS PK+P R Sbjct: 637 VTHIQLLPVLSYYFVNELKNHEHLSDYASSNSNYNWGYDPQNYFSLTGMYSSDPKNPEKR 69- 6 Query: 714 IAELKQLIHDIHKRGMGVILDVVYNHTAKTYLFEDIEPNYYHFMNEDGSPRESFGGGRLG 77- 3 IAE K LI++IHKRGMG ILDVVYNHTAK +FED+EPNYYHFM+ DG+PR SFGGGRLG Sbjct: 697 IAEFKNLINEIHKRGMGAILDVVYNHTAKVDIFEDLEPNYYHFMDADGTPRTSFGGGRLG 75- 6 Query: 774 TTHAMSRRVLVDSIKYLTSEFKVDGFRFDMMGDHDAAAIELAYKEAKAINPNMIMIGEGW 83- 3 TTH M++R+LVDSIKYL +KVDGFRFDMMGDHDAA+IE AYK A+A+NPN+IM+GEGW Sbjct: 757 TTHHMTKRLLVDSIKYLVDTYKVDGFRFDMMGDHDAASIEEAYKAARALNPNLIMLGEGW 81- 6 Query: 834 RTFQGDQGQPVKPADQDWMKSTDTVGVFSDDIRNSLKSGFPNEGTPAFITGGPQSLQGIF 89- 3 RT+ GD+ P K ADQDWMK TDTV VFSDDIRN+LKSG+PNEG PAFITGG + + IF Sbjct: 817 RTYAGDENMPTKAADQDWMKHTDTVAVFSDDIRNNLKSGYPNEGQPAFITGGKRDVNTIF 87- 6 Query: 894 KNIKAQPGNFEADSPGDVVQYIAAHDNLTLHDVIAKSINKDPKVAEE--EIHRRLRLGNV 95- 1 KN+ AQP NFEADSPGDV+QYIAAHDNLTL D+IA+SI KDP AE EIHRRLRLGN+ Sbjct: 877 KNLIAQPTNFEADSPGDVIQYIAAHDNLTLFDIIAQSIKKDPSKAENYAEIHRRLRLGNL 93- 6 Query: 952 MILTSQGTAFIHSGQEYGRTKRLLNPDYMTKVSDDKLPNKATLIEAVK----EYPYFIHD 10- 07 M+LT+QGT FIHSGQEYGRTK+ NP Y T V++DK+PNK+ L+ +YPYFIHD Sbjct: 937 MVLTAQGTPFIHSGQEYGRTKQFRNPAYRTPVAEDKVPNKSHLLRDKDGNPFDYPYFIHD 99- 6 Query: 1008 SYDSSDAINHFDWAAATDNNKHPISTKTQAYTAGLITLRRSTDAFRKLSKAEIDREVSLI 1- 067 SYDSSDA+N FDW ATD +P + K++ Y GLI LR+STDAFR S +I V LI Sbjct: 997 SYDSSDAVNKFDWTKATDGKAYPENVKSRDYMKGLIALRQSTDAFRLKSLQDIKDRVHLI 10- 56 Query: 1068 TEVGQGDIKEKDLVIAYQTIDSKGDIYAVFVNADSKARNVLLGEKYKHLLKGQVIVDADQ 1- 127 T GQ ++++D+VI YQ GDIYAVFVNAD KAR LG + HL +V+ D +Q Sbjct: 1057 TVPGQNGVEKEDVVIGYQITAPNGDIYAVFVNADEKAREFNLGTAFAHLRNAEVLADENQ 1- 116 Query: 1128 AGIKPISTPRGVHFEKDSLLIDPLTAIVIKVGKVAPS---------------PKEELQAD 1- 172 AG I+ P+G+ + + L ++ LTA V++V + S P+ + +A Sbjct: 1117 AGSVGIANPKGLEWTEKGLKLNALTATVLRVSQNGTSHESTAEEKPDSTPSKPEHQNEAS 1- 176 Query: 1173 YPKTQ----------SFKESKTVEKVNRIANKT---------------SITPVVSKKADS 1- 207 +P Q + ++K + N+ + T S+ V K++ Sbjct: 1177 HPAHQDPAPEARPDSTKPDAKVADAENKPSQATADSQAEQPAQEAQASSVKEAVRKESVE 1- 236 Query: 1208 YLTNE----------ANLPKTGDKSSKILSVVGISILASLLALVGLSLKRNR 1249 + E A LP TG K+ L GIS+LA LL L G LK + Sbjct: 1237 NSSKENISATPDRQAELPNTGIKNENKLLFAGISLLA-LLGL-GFLLKNKK 1285 A related DNA sequence was identified in S. pyogenes <SEQ ID 2599> which encodes the amino acid sequence <SEQ ID 2600>. Analysis of this protein sequence reveals the following: TABLE-US-02496 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.83 Transmembrane 1153-1169 (1148-1171) INTEGRAL Likelihood = -1.97 Transmembrane 29-45 (28-46) ----- Final Results ----- bacterial membrane --- Certainty = 0.5331 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9125> which encodes the amino acid sequence <SEQ ID 9126>. Analysis of this protein sequence reveals the following: TABLE-US-02497 Possible cleavage site: 26 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.533 (Affirmative) < succ> bacterial outside --- Certainty = 0.000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000 (Not Clear) < succ> LPXTG motif: 1133-1137 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02498 Identities = 715/1097 (65%), Positives = 872/1097 (79%), Gaps = 21/1097 (1%) Query: 156 ANQAPRIENGYFRLHLKELPQGHPVESTGLWIWGDVDQPSSNWPNGAIPMTDAKKDDYGY 21- 5 AN A E+ + R+H K LP G + S GLW+WGDVDQPS +WPNGAI MT AKKDDYGY Sbjct: 95 ANPASIAEH-HLRMHFKTLPAGESLGSLGLWVWGDVDQPSKDWPNGAITMTKAKKDDYGY 153- Query: 216 YVDFKLSEKQRKQISFLINNKAGTNLSGDHHIPLLRPEMNQVWIDEKYGTHTYQFLKEGY 27- 5 Y+D L+ K R+Q+S+LINNKAG NLS D HI LL P+MN+VWIDE Y H Y+PLK+GY Sbjct: 154 YLDVPLAAKHRQQVSYLINNKAGENLSKDQHISLLTPKMNEVWIDENYHAHAYRPLKKGY 21- 3 Query: 276 VRINYLSSSSNYDHLSAWLFKDVATPSTTWPDGSNFVNQGLYGRYIDVSLKTNAKEIGFL 33- 5 +RINY + S +YD+L+ W FKDV TP+T WP+G + ++G YG Y+DV LK A EIGFL Sbjct: 214 LRINYHNQSGHYDNLAVWTFKDVKTPTTDWPNGLDLSHKGHYGAYVDVPLKEGANEIGFL 27- 3 Query: 336 ILDESKTGDAVKVQPNDYVFRDLANHNQIFVKDKDPKVYNNPYYIDQVQLKDAQQIDLTS 39- 5 ILD+SKTGDA+KVQP DY+F++L NH Q+FVKD DPKVYNNPYYIDQV LK A+Q Sbjct: 274 ILDKSKTGDAIKVQPKDYLFKELDNHTQVFVKDTDPKVYNNPYYIDQVSLKGAEQTTPNE 33- 3 Query: 396 IQASFTTLDGVDKTEILKELKVTDKNQNAIQISDITLDTSKSLLIIKGDFNPKQGHFNIS 45- 5 I+A FTTLDG+D+ + + +K+TDK + I ++TLD KS++ +KGDF + + ++ Sbjct: 334 IKAIFTTLDGLDEDAVKQNIKITDKAGKTVAIDELTLDRDKSVMTLKGDFKAQGAVYTVT 39- 3 Query: 456 YNGNNVMTRQSWEFKDQLYAYSGNLGAVLNQDGSKVEASLWSPSADSVTMIIYDKDNQNR 51- 5 + + + RQSW+ KD+LYAY G LGA L +DGS V+ +LWSPSAD+V +++YDK +Q R Sbjct: 394 FGEVSQVARQSWQLKDKLYAYDGELGATLAKDGS-VDLALWSPSADTVKVVVYDKQDQTR 45- 2 Query: 516 VVATTPLMKNNKGVWQTIL--DTKLGIKNYTGYYYLYEIKRGKDKVKILDPYAKSLAEWD 57- 3 VV L K++KGVW+ L D+ GI +YTGYYYLYEI RG++KV +LDPYAKSLA W+ Sbjct: 453 VVGQADLTKSDKGVWRAHLTSDSVKGISDYTGYYYLYEITRGQEKVMVLDPYAKSLAAWN 51- 2 Query: 574 SNTVNDDIKTAKAAFVNPSQLGPQNLSFAKIANFKGRQDAVIYEAHVRDFTSDRSLDGKL 63- 3 T DDIKTAKAAF++PS+LGP L FAKI NFK R+DA+IYEAHVRDFTSD++L+GKL Sbjct: 513 DATATDDIKTAKAAFIDPSKLGPTGLDFAKINNFKKREDAIIYEAHVRDFTSDKALEGKL 57- 2 Query: 634 KNQFGTFAAFSEKLDYLQKLGVTHIQLLPVLSYFYVNEMDKSRSTAYTSSDNNYNWGYDP 69- 3 + FGTF+AF E+LDYL+ LGVTH+QLLPVLSYFY NE+DKSRSTAYTSSDNNYNWGYDP Sbjct: 573 THPFGTFSAFVEQLDYLKDLGVTHVQLLPVLSYFYANELDKSRSTAYTSSDNNYNWGYDP 63- 2 Query: 694 QSYFALSGMYSEKPKDPSARIAELKQLIHDIHKRGMGVILDVVYNHTAKTYLFEDIEPNY 75- 3 Q YFALSGMYS P DP+ RIAELK L+++IHKRGMGVI DVVYNHTA+TYLFED+EPNY Sbjct: 633 QHYFALSGMYSANPNDPALRIAELKNLVNEIHKRGMGVIFDVVYNHTARTYLFEDLEPNY 69- 2 Query: 754 YHFMNEDGSPRESFGGGRLGTTHAMSRRVLVDSIKYLTSEFKVDGFRFDMMGDHDAAAIE 81- 3 YHFMN DG+ RESFGGGRLGTTHAMSRR+LVDSI YLT EFKVDGFRFDMMGDHDAAAIE Sbjct: 693 YHFMNADGTARESFGGGRLGTTHAMSRRILVDSITYLTREFKVDGFRFDMMGDHDAAAIE 75- 2 Query: 814 LAYKEAKAINPNMIMIGEGWRTFQGDQGQPVKPADQDWMKSTDTVGVFSDDIRNSLKSGF 87- 3 A+K AKAINPN IMIGEGWRT+QGD+G+ ADQDWMK+T+TVGVFSDDIRN+LKSGF Sbjct: 753 QAFKAAKAINPNTIMIGEGWRTYQGDEGKKEIAADQDWMKATNTVGVFSDDIRNTLKSGF 81- 2 Query: 874 PNEGTPAFITGGPQSLQGIFKNIKAQPGNFEADSPGDVVQYIAAHDNLTLHDVIAKSINK 93- 3 PNEGT AFITGG ++L+G+FK IKAQPGNFEAD+PGDVVQYIAAHDNLTLHDVIAKSINK Sbjct: 813 PNEGTAAFITGGAKNLEGLFKTIKAQPGNFEADAPGDVVQYIAAHDNLTLHDVIAKSINK 87- 2 Query: 934 DPKVAEEEIHRRLRLGNVMILTSQGTAFIHSGQEYGRTKRLLNPDYMTKVSDDKLPNKAT 99- 3 DPKVAEEEIH+R+RLGN MILT+QGTAFIHSGQEYGRTK+LLNPDY TK SDDK+PNKAT Sbjct: 873 DPKVAEEEIHKRIRLGNTMILTAQGTAFIHSGQEYGRTKQLLNPDYKTKASDDKVPNKAT 93- 2 Query: 994 LIEAVKEYPYFIHDSYDSSDAINHFDWAAATDNNKHPISTKTQAYTAGLITLRRSTDAFR 10- 53 LI+AV +YPYFIHDSYDSSDA+NHFDWA ATD+ HPIS +T+AYT GLI LRRSTDAF Sbjct: 933 LIDAVAQYPYFIHDSYDSSDAVNHFDWAKATDSIAHPISNQTKAYTQGLIALRRSTDAFT 99- 2 Query: 1054 KLSKAEIDREVSLITEVGQGDIKEKDLVIAYQTIDSKGDIYAVFVNADSKARNVLLGEKY 1- 113 K +KAE+DR+V+LIT+ GQ I+++DL++ YQT+ S GD YAVFVNAD+K R V+L + Y Sbjct: 993 KATKAEVDRDVTLITQAGQDGIQQEDLIMGYQTVASNGDRYAVFVNADNKTRKVVLPQAY 10- 52 Query: 1114 KHLLKGQVIVDADQAGIKPISTPRGVHFEKDSLLIDPLTAIVIKV-GKVAPSPKEELQAD 1- 172 ++LL QV+VDA+QAG+ I+ P+GV F K+ L I+ LTA+V+KV K A +++ Q D Sbjct: 1053 RYLLGAQVLVDAEQAGVTAIAKPKGVQFTKEGLTIEGLTALVLKVSSKTANPSQQKSQTD 1- 112 Query: 1173 YPKTQSFKESKTVEKVNRIANKTSITPVVSKKADSYLTNEANLPKTGDKSSKILSVVGIS 1- 232 +T++ SK ++K K + T LPKTG+ SSK L GI+ Sbjct: 1113 NHQTKTPDGSKDLDKSLMTRPKRAKT-------------NQKLPKTGEASSKGLLAAGIA 1- 159 Query: 1233 ILASLLALVGLSLKRNR 1249 + LL + L +KR + Sbjct: 1160 L---LLLAISLLMKRQK 1173 A related GBS gene <SEQ ID 8673> and protein <SEQ ID 8674> were also identified. Analysis of this

TABLE-US-02499 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: -0.88 GvH: Signal Score (-7.5): 4.13 Possible site: 41 >>> Seems to have no N-terminal signal sequence ALOM program count: 3 value: -10.08 threshold: 0.0 INTEGRAL Likelihood = -10.08 Transmembrane 1225-1241 (1222-1247) INTEGRAL Likelihood = -2.44 Transmembrane 19-35 (18-36) INTEGRAL Likelihood = -0.11 Transmembrane 1146-1162 (1146-1162) PERIPHERAL Likelihood = 2.44 653 modified ALOM score: 2.52 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5034 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> LPXTG motif: 1081-1085 The protein has homology with the following sequences in the databases: ##STR00059## ##STR00060## SEQ ID 2598 (GBS5) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 3 (lane 7; MW 134 kDa). The His-fusion protein was purified as shown in FIG. 190, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 860 A DNA sequence (GBSx0912) was identified in S. agalactiae <SEQ ID 2601> which encodes the amino acid sequence <SEQ ID 2602>. Analysis of this protein sequence reveals the following: TABLE-US-02500 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.72 Transmembrane 231-247 (228-251) INTEGRAL Likelihood = -8.39 Transmembrane 50-66 (44-68) INTEGRAL Likelihood = -6.74 Transmembrane 23-39 (20-41) INTEGRAL Likelihood = -5.84 Transmembrane 173-189 (168-196) INTEGRAL Likelihood = -4.41 Transmembrane 299-315 (297-318) INTEGRAL Likelihood = -4.14 Transmembrane 115-131 (114-133) INTEGRAL Likelihood = -3.35 Transmembrane 80-96 (79-97) INTEGRAL Likelihood = -0.48 Transmembrane 97-113 (97-113) ----- Final Results ----- bacterial membrane --- Certainty = 0.5288 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8675> which encodes amino acid sequence <SEQ ID 8676> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-02501 SRCFLG: 0 McG: Length of UR: 19 Peak Value of UR: 3.08 Net Charge of CR: 1 McG: Discrim Score: 9.76 GvH: Signal Score (-7.5): -4.57 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 7 value: -10.72 threshold: 0.0 INTEGRAL Likelihood = -10.72 Transmembrane 217-233 (214-237) INTEGRAL Likelihood = -8.39 Transmembrane 36-52 (30-54) INTEGRAL Likelihood = -6.74 Transmembrane 9-25 (6-27) INTEGRAL Likelihood = -5.84 Transmembrane 159-175 (154-182) INTEGRAL Likelihood = -4.14 Transmembrane 101-117 (100-119) INTEGRAL Likelihood = -3.35 Transmembrane 66-82 (65-83) INTEGRAL Likelihood = -0.48 Transmembrane 83-99 (83-99) PERIPHERAL Likelihood = 0.26 136 modified ALOM score: 2.64 icm1 HYPID: 7 CFP: 0.529 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5288 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02502 >GP: BAB08178 GB: AB036768 exfoliative toxin A [Staphylococcus hyicus] Identities = 134/298 (44%), Positives = 197/298 (65%) Query: 22 PLVMAGLVLGLLALGNLLEGYGTYVRYCLGLVALVFWIFLIKGILKNKKESRKELSNPLI 81 - PLV +GLVLGLL LGNLL+ + G++A++ W+ L+ + N + +L++PL+ Sbjct: 7 PLVSSGLVLGLLGLGNLLKDVSLSLNALCGILAILVWLHLLYSMFNNVNHVKNQLNSPLV 66 Query: 82 ASVFTTFFMAGMILSTYILLFRSLGIWVAVLSKGVWWLSFIALIIHMAIFSWKYLRHFSM 141- +SVFTTFFM+G + +TY+ F S ++ L +W L I ++HM IFS KYL+ FS+ Sbjct: 67 SSVFTTFFMSGFLGTTYLNTFFSHISFIHHLITPLWLLCLIGILTHMIIFSHKYLKSFSL 126- Query: 142 ANLFPSWSVLYVGIGVASLTAPISGQFTIGKIVFWYGFIATLVLLPFLFIKAYKIGLPSA 20- 1 N++PSW+VLY+GI +A LTAP+SG F IGK+ YGF+AT ++LP +F + L ++ Sbjct: 127 ENVYPSWTVLYIGIAIAGLTAPVSGYFFIGKLTVIYGFVATCIVLPLVFKRLKTYPLQTS 18- 6 Query: 202 VKPNITTICAPMSLITAGYVNSFVSPNRGLLLLLIVMAQFLYFFILFQVPKLLIGDFTPG 26- 1 +KPN +TICAP SL+ A YV +F + +++L ++++Q YF+I+FQ+PKLL F+P Sbjct: 187 IKPNTSTICAPFSLVAAAYVLAFPEAHDFVVILFLILSQVFYFYIVFQLPKLLREPFSPV 24- 6 Query: 262 FSAFTFPLVISATSLKLSIQHLSLPVDIQGLVHFEIGTTTLIVMIVMVRYIFFLRRTI 319 FSAFTFPLVISAT+LK S+ L P GL+ FE T+IV V YI + + Sbjct: 247 FSAFTFPLVISATALKNSMPILIFPEIWNGLLMFETVLATVIVFRVFFGYIHLFLKPV 304 A related DNA sequence was identified in S. pyogenes <SEQ ID 2603> which encodes the amino acid sequence <SEQ ID 2604>. Analysis of this protein sequence reveals the following: TABLE-US-02503 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.82 Transmembrane 169-185 (163-189) INTEGRAL Likelihood = -8.49 Transmembrane 50-66 (38-69) INTEGRAL Likelihood = -7.86 Transmembrane 228-244 (224-247) INTEGRAL Likelihood = -5.15 Transmembrane 288-304 (284-306) INTEGRAL Likelihood = -3.29 Transmembrane 108-124 (107-126) INTEGRAL Likelihood = -3.29 Transmembrane 140-156 (140-161) INTEGRAL Likelihood = -1.33 Transmembrane 84-100 (84-100) ----- Final Results ----- bacterial membrane --- Certainty = 0.4927 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02504 Identities = 138/305 (45%), Positives = 200/305 (65%), Gaps = 5/305 (1%) Query: 12 RYMMKNWEKPPLVMAGLVLGLLALGNLLEGYGTYVRYCLGLVALVFWIFLIKGILKNKKE 71 - R +MK+ + PPLVM+GL LG L+ GNLL Y + Y L AL + L+ G+++N + Sbjct: 12 RTLMKHLKTPPLVMSGLALGTLSFGNLLATYVSIFNYLGILAALFIYGILLVGMVRNLND 71 Query: 72 SRKELSNPLIASVFTTFFMAGMILSTYILLFRSLGIWVAVLSKGVWWLSFIALIIHMAIF 131- ++ +L PLIASVF TFFM GM+LS+ L G W+ L+ WWL F+ ++ +A + Sbjct: 72 TKMQLRQPLIASVFPTFFMTGMLLSSLFLKVTG-GCWLGFLT---WWLFFLGNLVLIAYY 127- Query: 132 SWKYLRHFSMANLFPSWSVLYVGIGVASLTAPISGQFTIGKIVFWYGFIATLVLLPFLFI 19- 1 ++++ FS N+FPSWSVL+VGI +A+LTAP S QF +G+++FW + T V+LPF+ Sbjct: 128 QYRFVFSFSWDNVFPSWSVLFVGIAMAALTAPASRQFLLGQVIFWVCLLLTAVILPFMAK 18- 7 Query: 192 KAYKIGLPSAVKPNITTICAPMSLITAGYVNSFVSPNRGLLLLLIVMAQFLYFFILFQVP 25- 1 K Y IGL AV PNI+T CAP+SL++A Y+ +F P G+++ L+V +Q LY F++ Q+P Sbjct: 188 KTYGIGLGQAVMPNISTFCAPLSLLSASYLATFPRPQVGMVIFLLVSSQLLYAFVVVQLP 24- 7 Query: 252 KLLIGDFTPGFSAFTFPLVISATSLKLSIQHLSLP-VDIQGLVHFEIGTTTLIVMIVMVR 31- 0 +LL F PGFSAFTFP VISATSLK+++ L + Q L+ E+ T +V V Sbjct: 248 RLLNRPFNPGFSAFTFPFVISATSLKMTLSFLGWQGLGWQVLLLGEVLLATALVTYVYGA 30- 7 Query: 311 YIFFL 315 Y+ FL Sbjct: 308 YLRFL 312 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 861 A DNA sequence (GBSx0913) was identified in S. agalactiae <SEQ ID 2605> which encodes the amino acid sequence <SEQ ID 2606>. Analysis of this protein sequence reveals the following: TABLE-US-02505 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2607> which encodes the amino acid sequence <SEQ ID 2608>. Analysis of this protein sequence reveals the following: TABLE-US-02506 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02507 Identities = 45/57 (78%), Positives = 53/57 (92%) Query: 1 MVKKFAFAKGIATGVVATAATLAGAAFAIKKTIIEPEEEKIAFIEENRKKAARKRVS 57 MVKK+ F KG+ATGV+ATAAT+AGA FA+KKTII+PEEEK AFIEENRKKAAR+RV+ Sbjct: 1 MVKKYQFVKGLATGVLATAATVAGAVFAVKKTIIDPEEEKAAFIEENRKKAARRRVA 57 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 862 A DNA sequence (GBSx0914) was identified in S. agalactiae <SEQ ID 2609> which encodes the amino acid sequence <SEQ ID 2610>. This protein is predicted to be tRNA isopentenylpyrophosphate transferase (miaA). Analysis of this protein sequence reveals the following: TABLE-US-02508 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9897> which encodes amino acid sequence <SEQ ID 9898> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02509 >GP: BAB06085 GB: AP001515 tRNA isopentenylpyrophosphate transferase [Bacillus halodurans] Identities = 139/311 (44%), Positives = 200/311 (63%), Gaps = 21/311 (6%) Query: 7 KIKLIAVVGPTAVGKTALGIELAKTFNGEIISGDSQQVYQKLDIGTAKASKEEQEQAYHH 66 K KL+A+VGPTAVGKT + LAK NGE+ISGDS QVY+ +DIGTAK + EE + HH Sbjct: 2 KEKLVAIVGPTAVGKTKTSVMLAKRLNGEVISGDSMQVYRGMDIGTAKITAEEMDGVPHH 61 Query: 67 LIDVREVNENYSVYDFVKEAKVAIDTIISKGKIPIIVGGTGLYLQSLFEGYHLGGEVNQE 126- LID+++ +E++SV DF A I I +G++P +VGGTGLY+ ++ ++LG E Sbjct: 62 LIDIKDPSESFSVADFQDLATPLITEIHERGRLPFLVGGTGLYVNAVIHQFNLGDIRADE 121- Query: 127 TLMAYREKLE----SLSDEDLFEKLT----EQSIIIPQVNRRRAIRALELAKF------- 17- 1 YR +LE S + L +KL+ + + I N RR IRALE+ K Sbjct: 122 D---YRHELEAFVNSYGVQALHDKLSKIDPKAAAAIHPNNYRRVIRALEIIKLTGKTVTE 17- 8 Query: 172 -GNDLQNSESPYDVLLIGLNDDRQVLYDRINRRVDLMMDNGLLDEAKWLYD-NYPSVQAS 22- 9 + + SPY++++IGL +R VLYDRINRRVD M++ GL+DEAK LYD Q+ Sbjct: 179 QARHEEETPSPYNLVMIGLTMERDVLYDRINRRVDQMVEEGLIDEAKKLYDRGIRDCQSV 23- 8 Query: 230 KGIGYKELFPYFSKQIPLEEAVDKLKQNTRRFAKRQLTWFRNRMNVEFIMVGEENYQQKI 28- 9 + IGYKE++ Y + LEEA+D LK+N+RR+AKRQLTWFRN+ NV + + + ++ +KI Sbjct: 239 QAIGYKEMYDYLDGNVTLEEAIDTLKRNSRRYAKRQLTWFRNKANVTWFDMTDVDFDKKI 29- 8 Query: 290 KRKVSDFLSSK 300 ++ +F++ K Sbjct: 299 -MEIHNFIAGK 308 A related DNA sequence was identified in S. pyogenes <SEQ ID 2611> which encodes the amino acid sequence <SEQ ID 2612>. Analysis of this protein sequence reveals the following: TABLE-US-02510 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02511 Identities = 202/296 (68%), Positives = 250/296 (84%) Query: 5 MRKIKLIAVVGPTAVGKTALGIELAKTFNGEIISGDSQQVYQKLDIGTAKASKEEQEQAY 64 M KIK++ +VGPTAVGKTALGI LAK FNGEIISGDSQQVY++LDIGTAKA++EEQE A Sbjct: 1 MTKIKIVVIVGPTAVGKTALGISLAKAFNGEIISGDSQQVYRQLDIGTAKATQEEQEAAV 60 Query: 65 HHLIDVREVNENYSVYDFVKEAKVAIDTIISKGKIPIIVGGTGLYLQSLFEGYHLGGEVN 124- HHLID+REV E+YS YDFV++A+ +I I+S+GK+PIIVGGTGLYLQSL EGYHLGG+V+ Sbjct: 61 HHLIDIREVTESYSAYDFVQDAQKSISDIVSRGKLPIIVGGTGLYLQSLLEGYHLGGQVD 120- Query: 125 QETLMAYREKLESLSDEDLFEKLTEQSIIIPQVNRRRAIRALELAKFGNDLQNSESPYDV 18- 4 QE + AYR +LE L D DL+E+L +I I QVNRRRAIRALELA+F ++L+N+E+ Y+ Sbjct: 121 QEAVKAYRNELEQLDDHDLYERLQVNNITIEQVNRRRAIRALELAQFADELENAETAYEP 18- 0 Query: 185 LLIGLNDDRQVLYDRINRRVDLMMDNGLLDEAKWLYDNYPSVQASKGIGYKELFPYFSKQ 24- 4 L+IGLNDDRQV+YDRIN+RV+ M++NGLL+EAKWLY++YP+VQAS+GIGYKELFPYF + Sbjct: 181 LIIGLNDDRQVIYDRINQRVNRMIENGLLEEAKWLYEHYPTVQASRGIGYKELFPYFVGE 24- 0 Query: 245 IPLEEAVDKLKQNTRRFARRQLTWFRNRMNVEFIMVGEENYQQKIKRKVSDFLSSK 300 + L EA D+LKQNTRRFAKRQLTWFRNRM V F + +Y Q + +V DFL K Sbjct: 241 MTLAEASDQLKQNTRRFAKRQLTWFRNRMAVSFTAITAPDYPQVVHDRVRDFLGQK 296 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 863 A DNA sequence (GBSx0915) was identified in S. agalactiae <SEQ ID 2613> which encodes the amino acid sequence <SEQ ID 2614>. This protein is predicted to be hflX (hflX). Analysis of this protein sequence reveals the following: TABLE-US-02512 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02513 >GP: BAB06081 GB: AP001515 unknown conserved protein [Bacillus halodurans] Identities = 182/406 (44%), Positives = 254/406 (61%), Gaps = 12/406 (2%) Query: 9 ERVILVGVELQDT--ENFEMSMEELASLAKTAGANVVNHYYQKRDKYDSKSFIGSGKLEE 66 ERV LV +L + E FE S+EEL +L TA V++ QKR+ + ++IG GKL+E Sbjct: 10 ERVFLVACQLPNMTDEQFEASLEELEALTLTAQGTVIDRLTQKREAIEPATYIGRGKLDE 69 Query: 67 IKAIVEADEIDTVVVNNRLTPRQNSNLEAELGVKVIDRMQLILDIFAMRARSHEGKLQVH 126- + +E E D V+VN L+ Q NL LGV+VIDR QLILDIFA RA+S EGKLQV Sbjct: 70 LAIKMEEQEADLVIVNGELSGSQVRNLTNRLGVRVIDRTQLILDIFAGRAKSREGKLQVE 129- Query: 127 LAQLKYMLPRLVGQGIMLSRQAGGIGSRGPGESQLELNRRSIRHQISDIERQLKIVEKNR 18- 6 LAQL Y+LPR+VGQG LSR GGIG+RGPGE++LE +RR IR +++DI++QLK K+R Sbjct: 130 LAQLNYLLPRIVGQGQGLSRLGGGIGTRGPGETKLETDRRHIRKRMADIDKQLKHTVKHR 18- 9 Query: 187 ETVRERRVDSTTFKIGLIGYTNAGKSTIMNVLTDDRQYEANELFATLDATTKQIYLQNQF 24- 6 + R RR + TF+I L+GYTNAGKST++N LT YE + LFATLD T+++ L + Sbjct: 190 DRYRARRERNQTFRIALVGYTNAGKSTLLNRLTASDSYEEDLLFATLDPMTRKMRLPSGM 24- 9 Query: 247 QVTLTDTVGFIQDLPTELVAAFKSTLEESRHVDLLFHVIDASDPNHEEHEKVVMEILKDL 30- 6 +V L+DTVGFI LPT LVAAF+STLEE +H DLL HV+D S + H + V E+L L Sbjct: 250 EVILSDTVGFINQLPTTLVAAFRSTLEEVKHADLLLHVVDRSSEQLQAHMETVSELLHQL 30- 9 Query: 307 DMIDIPRLAIYNKMDVTEQLNATTFP-----NVRIAAKKQGSKDLLRRLIVDEIRHIFDE 36- 1 ++ L +YNK D + N P + ++A K+ LR++I + +F Sbjct: 310 EVDQSQMLVVYNKAD---KPNLPIIPVHQQNGIEMSAHKREDIQRLRQMIERTLVDLFTP 36- 6 Query: 362 FSIRVHQNQAYKLYDLNKIALLDTYTFEEEYE--NITGYISPKQKW 405 + + ++ KL L + ++ ++E+ E + GY+ P W Sbjct: 367 YVTELASDEGNKLAKLRRETIMTEMKWDEDRECYQVKGYVHPNHAW 412 A related DNA sequence was identified in S. pyogenes <SEQ ID 2615> which encodes the amino acid sequence <SEQ ID 2616>. Analysis of this protein sequence reveals the following: TABLE-US-02514 Possible site: 48 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases:

TABLE-US-02515 >GP: BAB06081 GB: AP001515 unknown conserved protein [Bacillus halodurans] Identities = 185/403 (45%), Positives = 246/403 (60%), Gaps = 6/403 (1%) Query: 13 ERVILLGVEL--QTTEHFDMSMTELANLAKTAGVKVMASFSQKRERYDSKTFIGSGKLDE 70 - ERV L+ +L T E F+ S+ EL L TA V+ +QKRE + T+IG GKLDE Sbjct: 10 ERVFLVACQLPNMTDEQFEASLEELEALTLTAQGTVIDRLTQKREAIEPATYIGRGKLDE 69 - Query: 71 IKAIVEADEIDAVIVNNRLTARQNANLEAVLEVKVIDRMQLILDIFAMRARSHEGKLQVH 130- + +E E D VIVN L+ Q NL L V+VIDR QLILDIFA RA+S EGKLQV Sbjct: 70 LAIKMEEQEADLVIVNGELSGSQVRNLTNRLGVRVIDRTQLILDIFAGRAKSREGKLQVE 129- Query: 131 LAQLKYMLPRLVGQGIMLSRQAGGIGSRGPGESQLELNRRSIRHQIADIERQLTQVEKNR 19- 0 LAQL Y+LPR+VGQG LSR GGIG+RGPGE++LE +RR IR ++ADI++QL K+R Sbjct: 130 LAQLNYLLPRIVGQGQGLSRLGGGIGTRGPGETKLETDRRHIRKRMADIDKQLKHTVKHR 18- 9 Query: 191 QTIRDRRVGSDTFKIGLIGYTNAGKSTIMNLLTDDSHYEANELFATLDATTKQLYLENQF 25- 0 R RR + TF+I L+GYTNAGKST++N LT YE + LFATLD T+++ L + Sbjct: 190 DRYRARRERNQTFRIALVGYTNAGKSTLLNRLTASDSYEEDLLFATLDPMTRKMRLPSGM 24- 9 Query: 251 QATLTDTVGFIQDLPTELVAAFKSTLEESKYVDLLLHVIDASDPNHSEQEKVVLNLLKEL 31- 0 + L+DTVGFI LPT LVAAF+STLEE K+ DLLLHV+D S + V LL +L Sbjct: 250 EVILSDTVGFINQLPTTLVAAFRSTLEEVKHADLLLHVVDRSSEQLQAHMETVSELLHQL 30- 9 Query: 311 DMLNIPRLAIYNKVDIAEQ--FTATAFPNIRISARSKDSKILLRRLIIDQIRDQFVPFRI 36- 8 ++ L +YNK D I +SA ++ LR++I + D F P+ Sbjct: 310 EVDQSQMLVVYNKADKPNLPIIPVHQQNGIEMSAHKREDIQRLRQMIERTLVDLFTPYVT 36- 9 Query: 369 KVHQDKAYKLYDLNRVALLDHYTFDQEIE--DISGYISPKQQW 409 ++ D+ KL L R ++ +D++ E + GY+ P W Sbjct: 370 ELASDEGNKLAKLRRETIMTEMKWDEDRECYQVKGYVHPNHAW 412 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02516 Identities = 326/412 (79%), Positives = 375/412 (90%) Query: 1 MIETKEEQERVILVGVELQDTENFEMSMEELASLAKTAGANVVNHYYQKRDKYDSKSFIG 60 MIETK +QERVIL+GVELQ TE+F+MSM ELA+LAKTAG V+ + QKR++YDSK+FIG Sbjct: 5 MIETKRQQERVILLGVELQTTEHFDMSMTELANLAKTAGVKVMASFSQKRERYDSKTFIG 64 Query: 61 SGKLEEIKAIVEADEIDTVVVNNRLTPRQNSNLEAELGVKVIDRMQLILDIFAMRARSHE 120- SGKL+EIKAIVEADEID V+VNNRLT RQN+NLEA L VKVIDRMQLILDIFAMRARSHE Sbjct: 65 SGKLDEIKAIVEADEIDAVIVNNRLTARQNANLEAVLEVKVIDRMQLILDIFAMRARSHE 124- Query: 121 GKLQVHLAQLKYMLPRLVGQGIMLSRQAGGIGSRGPGESQLELNRRSIRHQISDIERQLK 18- 0 GKLQVHLAQLKYMLPRLVGQGIMLSRQAGGIGSRGPGESQLELNRRSIRHQI+DIERQL Sbjct: 125 GKLQVHLAQLKYMLPRLVGQGIMLSRQAGGIGSRGPGESQLELNRRSIRHQIADIERQLT 18- 4 Query: 181 IVEKNRETVRERRVDSTTFKIGLIGYTNAGKSTIMNVLTDDKQYEANELFATLDATTKQI 24- 0 VEKNR+T+R+RRV S TFKIGLIGYTNAGKSTIMN+LTDD YEANELFATLDATTKQ+ Sbjct: 185 QVEKNRQTIRDRRVGSDTFKIGLIGYTNAGKSTIMNLLTDDSHYEANELFATLDATTKQL 24- 4 Query: 241 YLQNQFQVTLTDTVGFIQDLPTELVAAFKSTLEESRHVDLLFHVIDASDPNHEEHEKVVM 30- 0 YL+NQFQ TLTDTVGFIQDLPTELVAAFKSTLEES++VDLL HVIDASDPNH E EKVV+ Sbjct: 245 YLENQFQATLTDTVGFIQDLPTELVAAFKSTLEESKYVDLLLHVIDASDPNHSEQEKVVL 30- 4 Query: 301 EILKDLDMIDIPRLAIYNKMDVTEQLNATTFPNVRIAAKKQGSKDLLRRLIVDEIRHIFD 36- 0 +LK+LDM++IPRLAIYNK+D+ EQ AT FPN+RI+A+ + SK LLRRLI+D+IR F Sbjct: 305 NLLKELDMLNIPRLAIYNKVDIAEQFTATAFPNIRISARSKDSKILLRRLIIDQIRDQFV 36- 4 Query: 361 EFSIRVHQNQAYKLYDLNKIALLDTYTFEEEYENITGYISPKQKWKLEEFYD 412 F I+VHQ++AYKLYDLN++ALLD YTF++E E+I+GYISPKQ+W+L++FY+ Sbjct: 365 PFRIKVHQDKAYKLYDLNRVALLDHYTFDQEIEDISGYISPKQQWRLDDFYE 416 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 864 A DNA sequence (GBSx0916) was identified in S. agalactiae <SEQ ID 2617> which encodes the amino acid sequence <SEQ ID 2618>. Analysis of this protein sequence reveals the following: TABLE-US-02517 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2044 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2619> which encodes the amino acid sequence <SEQ ID 2620>. Analysis of this protein sequence reveals the following: TABLE-US-02518 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3436 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02519 Identities = 124/209 (59%), Positives = 150/209 (71%) Query: 1 MIDYIDLALTYGGFTSLDKVYLEKKLDGLSKQQRLDFITPPPSVINAYFAEIYQKQGPEA 60 M +YIDLA TYGGFTSLD YL L L+ QQ+L FITPPPSVINAYFAEIYQKQ P+A Sbjct: 5 MNNYIDLAKTYGGFTSLDTNYLNHLLASLTDQQKLAFITPPPSVINAYFAEIYQKQSPQA 64 Query: 61 ATDYYFDLSKALGLFPKHLSFDEEKPFIRLNLSGKSFGFAYLNDQEEASVFSEVKEVITP 120- ATDYYF+LSKALGLF SF+EEKPF+RLNLSGK++GFAY NDQE A VFSE E P Sbjct: 65 ATDYYFNLSKALGLFTDQPSFEEEKPFVRLNLSGKAYGFAYQNDQEVALVFSEKAEPKKP 124- Query: 121 QLLLEIAQIFPQYKVYRDRSGIRMAKIDFDETESQNITPETSLLGNVLQLKKDIIKITSF 18- 0 +L E+ QIFPQY VY D+ ++M F++ E ++ITP+ +LL + +L I + F Sbjct: 125 ELFFELTQIFPQYMVYEDKGQLKMQAKQFEQGECEDITPDDTLLSKIYRLANGITMLKGF 18- 4 Query: 181 NQEELLELVKTKSGKYYYSSQGRESVIYI 209 N EEL L +T SG+ YY RE +IYI Sbjct: 185 NVEELWALSQTFSGQKYYDFAQREFMIYI 213 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 865 A DNA sequence (GBSx0917) was identified in S. agalactiae <SEQ ID 2621> which encodes the amino acid sequence <SEQ ID 2622>. Analysis of this protein sequence reveals the following: TABLE-US-02520 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1060 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9895> which encodes amino acid sequence <SEQ ID 9896> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02521 >GP: CAB14316 GB: Z99116 similar to hypothetical proteins [Bacillus subtilis] Identities = 156/309 (50%), Positives = 210/309 (67%), Gaps = 5/309 (1%) Query: 1 MEIQFLGTGAGQPAKARNVSSLVLKLLDEINEVWMFDCGEGTQRQILETTIKPRKVKKIF 60 - ME+ FLGTGAG PAKARNV+S+ LKLL+E VW+FDCGE TQ QIL TTIKPRK++KIF Sbjct: 1 MELLFLGTGAGIPAKARNVTSVALKLLEERRSVWLFDCGEATQHQILHTTIKPRKIEKIF 60 Query: 61 ITHMHGDHVFGLPGFLSSRAFQANEEQTDLDIYGPVGIKSFVMTALRTSGSRLPYRIHFH 120- ITHMHGDHV+GLPG L SR+FQ E++ L +YGP GIK+F+ T+L + + L Y + Sbjct: 61 ITHMHGDHVYGLPGLLGSRSFQGGEDE--LTVYGPKGIKAFIETSLAVTKTHLTYPLAIQ 118- Query: 121 EFDESSLGKIMETDKFTVYAEKLDHTIFCMGYRVVQKDLEGTLDAEALKLAGVPFGPLFG 18- 0 E +E G + E D+F V A + H + GYRV +KD+ G+L A+ LK +P GP++ Sbjct: 119 EIEE---GIVFEDDQFIVTAVSVIHGVEAFGYRVQEKDVPGSLKADVLKEMNIPPGPVYQ 17- 5 Query: 181 KVKNGENVTLEDGREIIAKDYISEPKKGKVITILGDTRKTDASIRLALGADVLVHESTYG 24- 0 K+K GE VTLEDGR I D++ PKKG+ + GDTR +D LA DVLVHE+T+ Sbjct: 176 KIKKGETVTLEDGRIINGNDFLEPPKKGRSVVFSGDTRVSDKLKELARDCDVLVHEATFA 23- 5 Query: 241 KGDERIAKSHGHSTNMQAADIAKQANAKRLLLNHVSARFMGRDCWQMEEDAKTIFSNTHL 30- 0 K D ++A + HST QAA AK+A AK+L+L H+SAR+ G +++++A +F N+ Sbjct: 236 KEDRKLAYDYYHSTTEQAAVTAKEARAKQLILTHISARYQGDASLELQKEAVDVFPNSVA 29- 5 Query: 301 VRDLEEVGI 309 D EV + Sbjct: 296 AYDFLEVNV 304 A related DNA sequence was identified in S. pyogenes <SEQ ID 2623> which encodes the amino acid sequence <SEQ ID 2624>. Analysis of this protein sequence reveals the following: TABLE-US-02522 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2352 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02523 Identities = 253/307 (82%), Positives = 285/307 (92%) Query: 1 MEIQFLGTGAGQPAKARNVSSLVLKLLDEINEVWMFDCGEGTQRQILETTIKPRKVKKIF 60 ME+QFLGTGAGQPAK RNVSSL LKLLDEINEVWMFDCGEGTQRQILETTIKPRK++KIF Sbjct: 1 MELQFLGTGAGQPAKQRNVSSLALKLLDEINEVWMFDCGEGTQRQILETTIKPRKIRKIF 60 Query: 61 ITHMHGDHVFGLPGFLSSRAFQANEEQTDLDIYGPVGIKSFVMTALRTSGSRLPYRIHFH 120- ITH+HGDH+FGLPGFLSSR+FQA+EEQTDLDIYGP+GIK++V+T+L+ SG+R+PY+IHFH Sbjct: 61 ITHLHGDHIFGLPGFLSSRSFQASEEQTDLDIYGPIGIKTYVLTSLKVSGARVPYQIHFH 120- Query: 121 EFDESSLGKIMETDKFTVYAEKLDHTIFCMGYRVVQKDLEGTLDAEALKLAGVPFGPLFG 18- 0 EFD+ SLGKIMETDKF VYAE+L HTIFCMGYRVVQKDLEGTLDAEALK AGVPFGPLFG Sbjct: 121 EFDDKSLGKIMETDKFEVYAERLAHTIFCMGYRVVQKDLEGTLDAEALKAAGVPFGPLFG 18- 0 Query: 181 KVKNGENVTLEDGREIIAKDYISEPKKGKVITILGDTRKTDASIRLALGADVLVHESTYG 24- 0 K+KNG++V LEDGR I AKDYIS PKKGK+ITI+GDTRKT AS++LA ADVLVHESTYG Sbjct: 181 KIKNGQDVELEDGRLICAKDYISAPKKGKIITIIGDTRKTSASVKLAKDADVLVHESTYG 24- 0 Query: 241 KGDERIAKSHGHSTNMQAADIAKQANAKRLLLNHVSARFMGRDCWQMEEDAKTIFSNTHL 30- 0 KGDERIA++HGHSTNMQAA IA +A AKRLLLNHVSARF+GRDC QME+DA TIF N + Sbjct: 241 KGDERIARNHGHSTNMQAAQIAHEAGAKRLLLNHVSARFLGRDCRQMEKDAATIFENVKM 30- 0 Query: 301 VRDLEEV 307 V+DLEEV Sbjct: 301 VQDLEEV 307 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 866 A DNA sequence (GBSx0918) was identified in S. agalactiae <SEQ ID 2625> which encodes the amino acid sequence <SEQ ID 2626>. This protein is predicted to be similar to ketoacyl reductase. Analysis of this protein sequence reveals the following: TABLE-US-02524 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02525 >GP: CAB14310 GB: Z99116 similar to ketoacyl reductase [Bacillus subtilis] Identities = 100/253 (39%), Positives = 152/253 (59%), Gaps = 2/253 (0%) Query: 3 RTILITGASGGLAQAIINQLPQDD-HLIVTGRSREKLEKLYGKRPNTLCLSLDITN-DNA 60 + I ITGASGGL + I + H++++ R ++L ++ K +I D Sbjct: 7 KRIWITGASGGLGERIAYLCAAEGAHVLLSARREDRLIEIKRKITEEWSGQCEIFPLDVG 66 Query: 61 VTNMIEKIYGEFGQIDILINNAGFGSFKEFWDYSDEEVKDMFAVNTFATMSIARQIGHKM 120- I ++ + G ID+LINNAGFG F+ D + +++K MF VN F ++ + + +M Sbjct: 67 RLEDIARVRDQIGSIDVLINNAGFGIFETVLDSTLDDMKAMFDVNVFGLIACTKAVLPQM 126- Query: 121 SLVKSGHIVNIASMAGLIATSKASVYGASKFAVVGFSNALRLELAEKNVYVTSVNPGPIK 18- 0 K GHI+NIAS AG IAT K+S+Y A+K AV+G+SNALR+EL+ +YVT+VNPGPI+ Sbjct: 127 LEQKKGHIINIASQAGKIATPKSSLYSATKHAVLGYSNALRMELSGTGIYVTTVNPGPIQ 18- 6 Query: 181 TGFFAQADPSGDYLASIGRFALTPEKVSKKVVSILGKNKRELNLPFILAFAHKYYSLFPK 24- 0 T FF+ AD GDY ++GR+ L P+ V+ ++ + + KRE+NLP ++ K Y LFP Sbjct: 187 TDFFSIADKGGDYAKNVGRWMLDPDDVAAQITAAIFTKKREINLPRLMNAGTKLYQLFPA 24- 6 Query: 241 TADYFARKVFNYK 253 + A + K Sbjct: 247 LVEKLAGRALMKK 259 A related DNA sequence was identified in S. pyogenes <SEQ ID 2627> which encodes the amino acid sequence <SEQ ID 2628>. Analysis of this protein sequence reveals the following: TABLE-US-02526 Possible site: 18 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02527 >GP: BAB05225 GB: AP001512 oxidoreductase [Bacillus halodurans] Identities = 107/259 (41%), Positives = 156/259 (59%), Gaps = 5/259 (1%) Query: 1 MAQRIIVITGASGGLAQAIVKQLPKEDSLI-LLGRNKERLEHCYQHI----DNKECLELD 55 M ++ I ITGAS GL + + E++++ L R++ERLE+ + + +D Sbjct: 1 MRKKTIFITGASSGLGRQLAIDFSWEETVLCLFARSQERLENVQRIVVENGGEAHIYPVD 60 Query: 56 ITNPVAIEKMVAQIYQRYGRIDVLINNAGYGAFKGFEEFSAQEIADMFQVNTLASIHFAC 115- + +P +I++ A+ G +DVLINNAGYG F+ F + E MF+VN + Sbjct: 61 LADPQSIDRSFAEAISAVGVVDVLINNAGYGVFEPFCDSQMDENERMFRVNVFGLMRATA 120- Query: 116 LIGQKMAEQGQGHLINIVSMAGLIASAKSSIYSATKFALIGFSNALRLELADKGVYVTTV 17- 5 + M EQG GH+INI S AG IA+AKS+IYSATK A++GF+N+LR+EL G++V+ V Sbjct: 121 AVLPTMREQGSGHIINIASQAGKIATAKSAIYSATKHAVLGFTNSLRMELKGTGIHVSAV 18- 0 Query: 176 NPGPIATKFFDQADPSGHYLESVGKFTLQPNQVAKRLVSIIGKNKRELNLPFSLAVTHQF 23- 5 NPGPI T FFDQAD G Y V + L P V++++V + K KRELNLP+ + + Sbjct: 181 NPGPIQTPFFDQADKEGAYTSKVQRIMLDPEDVSEKIVQLTKKPKRELNLPWWMNIGATA 24- 0 Query: 236 YTLFPKLSDYLARKVFNYK 254 Y + P+L + LA K F K Sbjct: 241 YQVAPRLLELLAGKQFRQK 259 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02528 Identities = 155/251 (61%), Positives = 200/251 (78%) Query: 3 RTILITGASGGLAQAIINQLPQDDHLIVTGRSREKLEKLYGKRPNTLCLSLDITNDNAVT 62 R I+ITGASGGLAQAI+ QLP++D LI+ GR++E+LE Y N CL LDITN A+ Sbjct: 4 RIIVITGASGGLAQAIVKQLPKEDSLILLGRNKERLEHCYQHIDNKECLELDITNPVAIE 63 Query: 63 NMIEKIYGEFGQIDILINNAGFGSFKEFWDYSDEEVKDMFAVNTFATMSIARQIGHKMSL 122- M+ +IY +G+ID+LINNAG+G+FK F ++S +E+ DMF VNT A++ A IG KM+ Sbjct: 64 KMVAQIYQRYGRIDVLINNAGYGAFKGFEEFSAQEIADMFQVNTLASIHFACLIGQKMAE 123- Query: 123 VKSGHIVNIASMAGLIATSKASVYGASKFAVVGFSNALRLELAEKNVYVTSVNPGPIKTG 18- 2 GH++NI SMAGLIA++K+S+Y A+KFA++GFSNALRLELA+K VYVT+VNPGPI T Sbjct: 124 QGQGHLINIVSMAGLIASAKSSIYSATKFALIGFSNALRLELADKGVYVTTVNPGPIATK 18- 3 Query: 183 FFAQADPSGDYLASIGRFALTPEKVSKKVVSILGKNKRELNLPFILAFAHKYYSLFPKTA 24- 2 FF QADPSG YL S+G+F L P +V+K++VSI+GKNKRELNLPF LA H++Y+LFPK + Sbjct: 184 FFDQADPSGHYLESVGKFTLQPNQVAKRLVSIIGKNKRELNLPFSLAVTHQFYTLFPKLS 24- 3 Query: 243 DYFARKVFNYK 253 DY ARKVFNYK Sbjct: 244 DYLARKVFNYK 254 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 867 A DNA sequence (GBSx0919) was identified in S. agalactiae <SEQ ID 2629> which encodes the amino acid sequence <SEQ ID 2630>. This protein is predicted to be single-stranded-DNA-specific exonuclease (recJ). Analysis of this protein sequence reveals the following: TABLE-US-02529 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 197-213 (197-213) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02530 >GP: CAB14721 GB: Z99118 similar to single-strand DNA-specific exonuclease [Bacillus subtilis] Identities = 276/772 (35%), Positives = 447/772 (57%), Gaps = 45/772 (5%) Query: 1 MISAKYSWVLNNQKPDAGFFEASKKE-KISEAVASLIYSRGIKTSAELHHFLQTNLENLH 59 M+++K W + Q+PD ++ ++ I+ VASL+ RG T+ FL T + + Sbjct: 1 MLASKMRWEI--QRPDQDKVKSLTEQLHITPLVASLLVKRGFDTAESARLFLHTKDADFY 58 Query: 60 DPYLLNDMDKAVNRIRRAIENNETILVYGDYDADGMTSASIMKEALDMMGAEVQVYLPNR 119- DP+ + M +A +RI++AI E I++YGDYDADG+TS S+M L + A+V Y+P+R Sbjct: 59 DPFEMKGMKEAADRIKQAISQQEKIMIYGDYDADGVTSTSVMLHTLQKLSAQVDFYIPDR 118- Query: 120 FTDGYGPNQSVYKYFIEQQDVSLIITVDNGVAGHEAITYAQNQGVDVVVTDHHSMPADLP 17- 9 F +GYGPN+ ++ I+++ SLIITVD G+A A+ G+DV++TDHH +LP Sbjct: 119 FKEGYGPNEQAFRS-IKERGFSLIITVDTGIAAVHEAKVAKELGLDVIITDHHEPGPELP 17- 7 Query: 180 CAYAIIHPEHPDANYPFPYLAGCGVAFKVACALLETIPTEMLDLVAIGTIADMVSLTDEN 23- 9 AI+HP+ P YPF LAG GVAFK+A ALL +P E+LDL AIGTIAD+V L DEN Sbjct: 178 DVRAIVHPKQPGCTYPFKELAGVGVAFKLAHALLGELPDELLDLAAIGTIADLVPLHDEN 23- 7 Query: 240 RIMVKAGLEVMKDSERIGLQELISLSNIDLKTLNEETIGFKIAPQLNALGRLDDPNPAIE 29- 9 R++ GLE ++ + R+GL+ELI LS D+ NEET+GF++AP+LNA+GR++ +PA+ Sbjct: 238 RLIATLGLERLRRTNRLGLKELIKLSGGDIGEANEETVGFQLAPRLNAVGRIEQADPAVH 29- 7 Query: 300 LLTGFDDEESQAIAQMIDQKNEERKEIVQTIFDQAMQMLDQ---TKPVQVLAKENWHPGV 35- 6 LL D E++ +A IDQ N+ER+++V + D+A++M++Q + V+AK W+PGV Sbjct: 298 LLMSEDSFEAEELAAEIDQLNKERQKMVSKMTDEAIEMVEQQGLDQTAIVVAKAGWNPGV 35- 7 Query: 357 LGIVAGRILERTGQPVIVLNI--EDGIAKGSARSVEALDIFQAFDQHRELFIAFGGHSGA 41- 4 +GIVA ++++R +P IVL I E GIAKGSARS+ ++F++ + R++ FGGH A Sbjct: 358 VGIVASKLVDRFYRPAIVLGIDEEKGIAKGSARSIRGFNLFESLSECRDILPHFGGHPMA 41- 7 Query: 415 AGMTLEESKVGDLSQVLCDYISKKQLDMSQKKTLTIDSELRFDELSLDTVRDFEKLAPFG 47- 4 AGMTL+ V DL L + + +D ++++++++ + L+PFG Sbjct: 418 AGMTLKAEDVPDLRSRLNEIADNTLTEEDFIPVQEVDLVCGVEDITVESIAEMNMLSPFG 47- 7 Query: 475 MDNKKPVFLLKDFKVSQARVMGQNGAHLKLKLEQDGQALDLVAFNMGSQLQEFQQAQHLE 53- 4 M N KP L+++ + R +G N H+K+ + + LD V FN G + + Sbjct: 478 MLNPKPHVLVENAVLEDVRKIGANKTHVKMTIRNESSQLDCVGFNKGELQEGIVPGSRIS 53- 7 Query: 535 LAVTLSVNQWNGATTLQLMLEDARVDGIQLFDIRSK------ASSLPHG----------- 57- 7 + +S+N+WN QLM++DA V QLFD+R K S+LP Sbjct: 538 IVGEMSINEWNNRKKPQLMIKDAAVSEWQLFDLRGKRTWEDTVSALPSAKRAIVSFKEDS 59- 7 Query: 578 ------------VPILSQEEQSKE-------VILLTVPDHPQELKQMTQGKQFDAIYFKN 61- 8 V ++S ++Q+K ++LL P L ++ +GK + IYF Sbjct: 598 TTLLQTEDLRREVHVISSKDQAKAFDLDGAYIVLLDPPPSLDMLARLLEGKAPERIYFIF 65- 7 Query: 619 EIPKNYFISGYGTRDQFASLYKTIYQFPEFDVRYKLKELSSYLHIPDILLIKMIQIFEEL 67- 8 +++F+S + RD F Y + + FDV+ EL+ + + M ++F +L Sbjct: 658 LNHEDHFLSTFPARDHFKWYYAFLLKRGAFDVKKHGSELAKHKGWSVETINFMTKVFFDL 71- 7 Query: 679 HFVTITEGIMTVNKEAEKRDISESQIYQELKETVKFQELMALGTPKEIYDFM 730 FV I G+++V A+KRD+++SQ YQ ++ ++ + + + +E+ +++ Sbjct: 718 GFVKIENGVLSVVSGAKKRDLTDSQTYQAKQQLMELDQKLNYSSAEELKEWL 769 A related DNA sequence was identified in S. pyogenes <SEQ ID 2631> which encodes the amino acid sequence <SEQ ID 2632>. Analysis of this protein sequence reveals the following:

TABLE-US-02531 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 220-236 (220-236) INTEGRAL Likelihood = -0.11 Transmembrane 667-683 (667-683) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02532 Identities = 474/731 (64%), Positives = 594/731 (80%) Query: 1 MISAKYSWVLNNQKPDAGFFEASKKEKISEAVASLIYSRGIKTSAELHHFLQTNLENLHD 60 MI +KYSW + ++KPD GFF+ +K + +++ A LIY RGI+T L FL +L LHD Sbjct: 1 MIKSKYSWKIKDKKPDDGFFKLAKTKGLTQTAAQLIYDRGIRTEEALDEFLTADLSQLHD 60 Query: 61 PYLLNDMDKAVNRIRRAIENNETILVYGDYDADGMTSASIMKEALDMMGAEVQVYLPNRF 120- PYLL+DM KAV RIR+AIE E IL+YGDYDADGMTSASI+KE LDMMGAE VYLPNRF Sbjct: 61 PYLLHDMAKAVPRIRQAIEEGERILIYGDYDADGMTSASIVKETLDMMGAEPLVYLPNRF 120- Query: 121 TDGYGPNQSVYKYFIEQQDVSLIITVDNGVAGHEAITYAQNQGVDVVVTDHHSMPADLPC 18- 0 TDGYGPNQSVYKYFIEQ+ VSLIITVDNGVAGHEAI YAQ Q VDV+VTDHHS+P +LP Sbjct: 121 TDGYGPNQSVYKYFIEQEAVSLIITVDNGVAGHEAIRYAQEQEVDVIVTDHHSLPEELPE 18- 0 Query: 181 AYAIIHPEHPDANYPFPYLAGCGVAFKVACALLETIPTEMLDLVAIGTIADMVSLTDENR 24- 0 A+AIIHPEHPDA+YPF +LAGCGVAFK+A ALLE++PT+ LDLVAIGTIADMVSLT ENR Sbjct: 181 AFAIIHPEHPDADYPFKHLAGCGVAFKLATALLESLPTDCLDLVAIGTIADMVSLTGENR 24- 0 Query: 241 IMVKAGLEVMKDSERIGLQELISLSNIDLKTLNEETIGFKIAPQLNALGRLDDPNPAIEL 30- 0 ++VK GL ++K +ER+GLQEL+SLS IDL+ NE+ IGF+IAPQLNALGRLDDPNPAIEL Sbjct: 241 VLVKNGLAMLKHTERVGLQELMSLSPIDLEHFNEDAIGFQIAPQLNALGRLDDPNPAIEL 30- 0 Query: 301 LTGFDDEESQAIAQMIDQKNEERKEIVQTIFDQAMQMLDQTKPVQVLAKENWHPGVLGIV 36- 0 LTGFDD+E+QAIA MI +KNEERK +VQ IFDQAM M+D KPVQVLA+ WHPGVLGIV Sbjct: 301 LTGFDDQEAQAIALMIKKKNEERKALVQDIFDQAMAMVDPQKPVQVLAQAGWHPGVLGIV 36- 0 Query: 361 AGRILERTGQPVIVLNIEDGIAKGSARSVEALDIFQAFDQHRELFIAFGGHSGAAGMTLE 42- 0 AGRI+E GQ V+VL I++G AKGSARS+EA++IF+A + RELF AFGGH+GAAGMTL Sbjct: 361 AGRIMETIGQTVVVLTIDNGFAKGSARSLEAINIFEALNGKRELFTAFGGHAGAAGMTLP 42- 0 Query: 421 ESKVGDLSQVLCDYISKKQLDMSQKKTLTIDSELRFDELSLDTVRDFEKLAPFGMDNKKP 48- 0 + LS LC ++ ++ LD + K TLTID L D+LSLD ++ +KLAP+GMD++KP Sbjct: 421 VDNLEALSDFLCQFVIERGLDQTAKNTLTIDERLSLDDLSLDILKSLDKLAPYGMDHQKP 48- 0 Query: 481 VFLLKDFKVSQARVMGQNGAHLKLKLEQDGQALDLVAFNMGSQLQEFQQAQHLELAVTLS 54- 0 VF +KD +VSQAR +GQ+ +HLK K+ Q + D++AF GSQLQEF+QA LELAVTLS Sbjct: 481 VFYVKDIRVSQARTIGQDQSHLKFKVSQGKASFDVLAFGQGSQLQEFRQATGLELAVTLS 54- 0 Query: 541 VNQWNGATTLQLMLEDARVDGIQLFDIRSKASSLPHGVPILSQEEQSKEVILLTVPDHPQ 60- 0 VN WNG T+LQ ML DARVDG+QL D+R+K + +P G+P + ++ ++ +++ +P+ + Sbjct: 541 VNHWNGNTSLQFMLVDARVDGVQLLDLRTKTAKVPEGIPTIEEDPNARVILINDIPEDFK 60- 0 Query: 601 ELKQMTQGKQFDAIYFKNEIPKNYFISGYGTRDQFASLYKTIYQFPEFDVRYKLKELSSY 66- 0 + K FDAIYFKN++ Y+++G+G+R+QFA LYKTIYQFPEFD+R+KL ELS Y Sbjct: 601 TWRNQFVHKDFDAIYFKNQMKHPYYLTGFGSREQFAKLYKTIYQFPEFDLRHKLTELSHY 66- 0 Query: 661 LHIPDILLIKMIQIFEELHFVTITEGIMTVNKEAEKRDISESQIYQELKETVKFQELMAL 72- 0 L+I +LLIK+IQIFEEL FVTI +G+MTVN +A+KR+ISES IYQ+LKE VKFQE+MAL Sbjct: 661 LNIEKLLLIKLIQIFEELSFVTIDDGLMTVNPQAQKREISESHIYQDLKELVKFQEIMAL 72- 0 Query: 721 GTPKEIYDFMM 731 +PKE+YD+++ Sbjct: 721 ASPKEMYDYLV 731 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 868 A DNA sequence (GBSx0920) was identified in S. agalactiae <SEQ ID 2633> which encodes the amino acid sequence <SEQ ID 2634>. Analysis of this protein sequence reveals the following: TABLE-US-02533 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4114 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 869 A DNA sequence (GBSx0921) was identified in S. agalactiae <SEQ ID 2635> which encodes the amino acid sequence <SEQ ID 2636>. Analysis of this protein sequence reveals the following: TABLE-US-02534 Possible Site: 42 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.10 Transmembrane 15-31 (14-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.3039 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02535 >GP: AAA88584 GB: M18954 fructosyltransferase [Streptococcus mutans] Identities = 67/219 (30%), Positives = 106/219 (47%), Gaps 31/219 (14%) Query: 1 MRPIVRKKMYKKGKFWVVAGIVT-ILGGSAILGQDVKAEQAEAVTSTISEKTDSSQTISD 59 M VRKKMYKKGKFWVVA I T +L G + V+A++A + T SE + SQ + Sbjct: 1 METKVRKKMYKKGKFWVVATITTAMLTGIGL--SSVQADEANS-TQVSSELAERSQVQEN 57 Query: 60 TSKLTLPVNSSEAMKNSAEPLIKTAFATSVSSNPREIAATPVKTFDASSKVVVKASTAEH 119- T+ SS A +N A KT + S+NP AA V+ D ++KV+ + E Sbjct: 58 TTA------SSSAAENQA----KTEVQETPSTNP---AAATVENTDQTTKVITDNAAVES 104- Query: 120 SANQTN---SNVNQVANDSEVITQQN------STKQLPTVTYSAHVQDIGW----QKSVD 16- 6 A++T + V + A + + Q N +TK+ T + + G +K Sbjct: 105 KASKTKDQAATVTKTAASTPEVGQTNEKDKAKATKEADITTPKNTIDEYGLTEQARKIAT 16- 4 Query: 167 NATVSGTVGQEKQVEAIKLSIKAPEGITG-KLSYKTYVK 204 A ++ + +KQVEA+ + TG +++Y+ + K Sbjct: 165 EAGINLSSLTQKQVEALNKVKLTSDAQTGHQMTYQEFDK 203 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8677> and protein <SEQ ID 8678> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02536 Lipop Possible site: -1 Crend: 5 McG: Discrim Score: 9.08 GvH: Signal Score (-7.5): -3.94 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -5.10 threshold: 0.0 INTEGRAL Likelihood = -5.10 Transmembrane 7-23 (6-25) PERIPHERAL Likelihood = 4.03 694 modified ALOM score: 1.52 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3039 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00061## SEQ ID 8678 (GBS243) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 57 (lane 7; MW 94 kDa). GBS243-His was purified as shown in FIG. 208, lane 10. EXAMPLE 870 A DNA sequence (GBSx0922) was identified in S. agalactiae <SEQ ID 2637> which encodes the amino acid sequence <SEQ ID 2638>. This protein is predicted to be adenine phosphoribosyltransferase (apt). Analysis of this protein sequence reveals the following: TABLE-US-02537 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.86 Transmembrane 61-77 (59-77) INTEGRAL Likelihood = -0.64 Transmembrane 137-153 (137-153) ----- Final Results ----- bacterial membrane --- Certainty = 0.1744 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02538 >GP: AAC46040 GB: U86377 adenine phosphoribosyltransferase; Apt [Bacillus subtilis] Identities = 110/170 (64%), Positives = 135/170 (78%) Query: 1 MDLNNYIASIENYPQEGITFRDISPLMADGKAYSYAVREIVQYAADKDIDMIVGPEARGF 60 MDL Y+ + +YP+EG+ F+DI+ LM G Y YA +IV+YA +K ID++VGPEARGF Sbjct: 1 MDLKQYVTIVPDYPKEGVQFKDITTLMDKGDVYRYATDQIVEYAKEKQIDLVVGPEARGF 60 Query: 61 IVGCPVAYALGIGFAPVRKPGKLPREVISADYEKEYGLDTLTMHADAIKPGQRVLIVDDL 120- I+GCPVAYALG+GFAPVRK GKLPREVI DY EYG D LT+H DAIKPGQRVLI DDL Sbjct: 61 IIGCPVAYALGVGFAPVRKEGKLPREVIKVDYGLEYGKDVLTIHKDAIKPGQRVLITDDL 120- Query: 121 LATGGTVKATIEMIEKLGGVVAGCAFLVELDGLNGRKAIEGYDTKVLMNF 170 LATGGT++ATI+++E+LGGVVAG AFL+EL L+GR +E YD LM + Sbjct: 121 LATGGTIEATIKLVEELGGVVAGIAFLIELSYLDGRNKLEDYDILTLMKY 170 A related DNA sequence was identified in S. pyogenes <SEQ ID 2639> which encodes the amino acid sequence <SEQ ID 2640>. Analysis of this protein sequence reveals the following: TABLE-US-02539 Possible site: 40 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.300 (Affirmative) < succ> bacterial membrane --- Certainty = 0.000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02540 !GB: Z99120 similar to opine catabolism [Bacillus sub . . . 231 1e-59 >GP: CAB15253 GB: Z99120 similar to opine catabolism [Bacillus subtilis] Score = 231 bits (583), Expect = 1e-59 Identities = 138/363 (38%), Positives = 212/363 (58%), Gaps = 11/363 (3%) Query: 5 IIGAGIVGSTAAYYLQQSGQKEVTIFDHGQ-GQATKAAAGIISPWFSKRRNKVWYRMARL 63 I+GAGI+G++ AY+L ++G + VT+ D + GQAT AAAGI+ PW S+RRN+ WY++A+ Sbjct: 6 IVGAGILGASTAYHLAKTGAR-VTVIDRKEPGQATDAAAGIVCPWLSQRRNQDWYQLAKG 64 Query: 64 GADFYQQLINDLKEDGFATDFYQQNGIYVLKKQEEKLRDLYELALARKVESPIIGELAIK 123- GA +Y+ LI+ L++DG + Y++ G + KL + E A R+ ++P IG++ Sbjct: 65 GARYYKDLIHQLEKDGESDTGYKRVGAISIHTDASKLDKMEERAYKRREDAPEIGDITRL 124- Query: 124 NRKELGNDFKGLIGFDNCLYASGAARVEGAALCETLLKAS---GYPVIRQKVTLKQQG-- 17- 8 + E F L ++ SGAARV G ALC +LL A+ G VI+ +L + Sbjct: 125 SASETKKLFPILADGYESVHISGAARVNGRALCRSLLSAAEKRGATVIKGNASLLFENGT 18- 4 Query: 179 -SGYEIAGHYF--DQVILAAGAWLPDLLRPLGYQVDVRPQKGQLLDYDVHHIISDTYPVV 23- 5 +G + F D VI+ AGAW ++L+PLG V QK Q++ +++ + ++PVV Sbjct: 185 VTGVQTDTKQFAADAVIVTAGAWANEILKPLGIHFQVSFQKAQIMHFEMTDADTGSWPVV 24- 4 Query: 236 MPEGEIDLIPFNQGKISVGTSHENDKGY-DLEPDWQVLKKLEMQALTYLPLLKEATQKTC 29- 4 MP + ++ F+ G+I G +HEND G DL ++ +AL P L +A Sbjct: 245 MPPSDQYILSFDNGRIVAGATHENDAGLDDLRVTAGGQHEVLSKALAVAPGLADAAAVET 30- 4 Query: 295 RVGIRAYTSDYSPFYGQVSGLKNLYTASGLGSSGLTVGPLIGYELAQLLLGHEGLLTPSD 35- 4 RVG R +T + P G V ++ LY A+GLG+SGLT+GP +G ELA+L+LG + L S Sbjct: 305 RVGFRPFTPGFLPVVGAVPNVQGLYAANGLGASGLTMGPFLGAELAKLVLGKQTELDLSP 36- 4 Query: 355 YSP 357 Y P Sbjct: 365 YDP 367 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02541 Identities = 150/172 (87%), Positives = 161/172 (93%) Query: 1 MDLNNYIASIENYPQEGITFRDISPLMADGKAYSYAVREIVQYAADKDIDMIVGPEARGF 60 MDL NYIASI++YP+ GITFRDISPLMADGKAYSYA+REI QYA DKDIDM+VGPEARGF Sbjct: 1 MDLTNYIASIKDYPKAGITFRDISPLMADGKAYSYAIREIAQYACDKDIDMVVGPEARGF 60 Query: 61 IVGCPVAYALGIGFAPVRKPGKLPREVISADYEKEYGLDTLTMHADAIKPGQRVLIVDDL 120- I+GCPVA LGIGFAPVRKPGKLPR+V+SADYEKEYGLDTLTMHADAIKPGQRVLIVDDL Sbjct: 61 IIGCPVAVELGIGFAPVRKPGKLPRDVVSADYEKEYGLDTLTMHADAIKPGQRVLIVDDL 120- Query: 121 LATGGTVKATIEMIEKLGGVVAGCAFLVELDGLNGRKAIEGYDTKVLMNFPG 172 LATGGTVKATIEMIEKLGG+VAGCAFL+EL+GLNGR AI YD KVLM FPG Sbjct: 121 LATGGTVKATIEMIEKLGGIVAGCAFLIELEGLNGRHAIRNYDYKVLMQFPG 172 SEQ ID 2638 (GBS419) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 79 (lane 6; MW 22.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 172 (lane 4; MW 47.5 kDa). GBS419-GST was purified as shown in FIG. 219, lane 6-8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 871 A DNA sequence (GBSx0923) was identified in S. agalactiae <SEQ ID 2641> which encodes the amino acid sequence <SEQ ID 2642>. Analysis of this protein sequence reveals the following: TABLE-US-02542 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0847 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02543 >GP: BAA11244 GB: D78182 ORF2 [Streptococcus mutans] Identities = 140/225 (62%), Positives = 178/225 (78%) Query: 1 MTYLEQYQSGQLTLPSALFFHFKSIFKTADDFLVWQFFYLQNTTNLSDLTPSRIATSLDK 60 M++L+ Y+SG L LPSAL FH+K IF ADDFLVWQFFY QNTT + D+ S+IAT++ K Sbjct: 1 MSFLQHYKSGNLVLPSALLFHYKDIFSNADDFLVWQFFYFQNTTKMEDIATSQIATAIGK 60 Query: 61 TVADINRSISNLTSQGLLDVKTIELNHEIEIIFDTSPVFAKLDKLFEEDNQVIIDNKTSD 120- TV ++NRS+SNL SQ LLD+KTIEL+ E E++FD + KLD L ++ + + Sbjct: 61 TVPEVNRSVSNLISQELLDMKTIELDGESEVLFDATLALKKLDDLLTAADETTVSSSKGT 120- Query: 121 SNRLKDLVGDFERELGRLLSPFELEDLQKTLQEDQTDPDIVRAALREAVFNGKTSWNYIN 18- 0 SN LKDLV DFERELGR+LSPFELEDLQKT+ +D+TDPD+VR+ALREAVFNGKT+WNYI Sbjct: 121 SNALKDLVEDFERELGRMLSPFELEDLQKTVSDDKTDPDLVRSALREAVFNGKTNWNYIQ 18- 0 Query: 181 AILRNWRREGLTTLRQIEERKQAREDNQMKDLAISDDFKNAMNLW 225 AILRNWRREG++TLRQ+EER++ RE ++ +SDDF +AMNLW Sbjct: 181 AILRNWRREGISTLRQVEERRKEREQANPANVTVSDDFLSAMNLW 225 A related DNA sequence was identified in S. pyogenes <SEQ ID 2643> which encodes the amino acid sequence <SEQ ID 2644>. Analysis of this protein sequence reveals the following: TABLE-US-02544 Possible site: 57 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02545 >GP: BAA11244 GB: D78182 ORF2 [Streptococcus mutans] Identities = 154/228 (67%), Positives = 188/228 (81%), Gaps = 1/228 (0%) Query: 1 MSFLEHYKSGNLVIPSALLFHYKDLFKSSDDFLVWQFFYLQNTTKRDDLAPSQIAHALGK 60 MSFL+HYKSGNLV+PSALLFHYKD+F ++DDFLVWQFFY QNTTK +D+A SQIA A+GK Sbjct: 1 MSFLQHYKSGNLVLPSALLFHYKDIFSNADDFLVWQFFYFQNTTKMEDIATSQIATAIGK 60 Query: 61 SVADINKIISSLTNQGLLDMRTIELTGEIEIIFDASPVLAKLDQLFVSQTATEIDKQE-T 119- +V ++N+ +S+L +Q LLDM+TIEL GE E++FDA+ L KLD L + T + + T Sbjct: 61 TVPEVNRSVSNLISQELLDMKTIELDGESEVLFDATLALKKLDDLLTAADETTVSSSKGT 120- Query: 120 PNHFKRLVDEFERELGRFLSPFELEDLEKTLRDDKTDPDLIREALKEAVFNGKTNWKYIQ 17- 9 N K LV++FERELGR LSPFELEDL+KT+ DDKTDPDL+R AL+EAVFNGKTNW YIQ Sbjct: 121 SNALKDLVEDFERELGRMLSPFELEDLQKTVSDDKTDPDLVRSALREAVFNGKTNWNYIQ 18- 0 Query: 180 AILRNWRKEGIVNLRQVEERRRVREGEDLSQVTISEDFLSAMNLWSDS 227 AILRNWR+EGI LRQVEERR+ RE + + VT+S+DFLSAMNLWSDS Sbjct: 181 AILRNWRREGISTLRQVEERRKEREQANPANVTVSDDFLSAMNLWSDS 228 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02546 Identities = 144/225 (64%), Positives = 179/225 (79%), Gaps = 1/225 (0%) Query: 1 MTYLEQYQSGQLTLPSALFFHFKSIFKTADDFLVWQFFYLQNTTNLSDLTPSRIATSLDK 60 M++LE Y+SG L +PSAL FH+K +FK++DDFLVWQFFYLQNTT DL PS+IA +L K Sbjct: 1 MSFLEHYKSGNLVIPSALLFHYKDLFKSSDDFLVWQFFYLQNTTKRDDLAPSQIAHALGK 60 Query: 61 TVADINRSISNLTSQGLLDVKTIELNHEIEIIFDTSPVFAKLDKLFEEDNQVIIDNKTSD 120- +VADIN+ IS+LT+QGLLD++TIEL EIEIIFD SPV AKLD+LF ID K Sbjct: 61 SVADINKIISSLTNQGLLDMRTIELTGEIEIIFDASPVLAKLDQLFVSQTATEID-KQET 119- Query: 121 SNRLKDLVGDFERELGRLLSPFELEDLQKTLQEDQTDPDIVRAALREAVFNGKTSWNYIN 18- 0 N K LV +FERELGR LSPFELEDL+KTL++D+TDPD++R AL+EAVFNGKT+W YI Sbjct: 120 PNHFKRLVDEFERELGRFLSPFELEDLEKTLRDDKTDPDLIREALKEAVFNGKTNWKYIQ 17- 9 Query: 181 AILRNWRREGLTTLRQIEERKQAREDNQMKDLAISDDFKNAMNLW 225 AILRNWR+EG+ LRQ+EER++ RE + + IS+DF +AMNLW Sbjct: 180 AILRNWRKEGIVNLRQVEERRRVREGEDLSQVTISEDFLSAMNLW 224 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 872 A DNA sequence (GBSx0924) was identified in S. agalactiae <SEQ ID 2645> which encodes the amino acid sequence <SEQ ID 2646>. Analysis of this protein sequence reveals the following: TABLE-US-02547 Possible site: 47 >> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1617 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-02548 >GP: BAA11245 GB: D78182 ORF3 [Streptococcus mutans] Identities = 134/226 (59%), Positives = 170/226 (74%) Query: 2 DLQLSKRLQKVANYVPKGARLLDVGSDHAYLPIFLLQMGYCDFAIAGEVVNGPYQSALKN 61 ++ LS RLQ+VA++VPKGARLLDVGSDHAYLPI+LL+ G DFA+AGE++ GPY+SA+ N Sbjct: 7 EVSLSHRLQEVASFVPKGARLLDVGSDHAYLPIYLLEQGLIDFAVAGEIIKGPYESAVAN 66 Query: 62 VSEHGLTSKIDVRLANGLSAFEEADNIDTITICGMGGRLIADILNNDIDKLQHVKTLVLQ 121- V+E GL+ +I VRLA+GL+A + D+ID ITICGMGGRLIADIL DKL VK L+LQ Sbjct: 67 VNESGLSGQIAVRLADGLAALNDNDDIDLITICGMGGRLIADILAAGSDKLNSVKQLILQ 126- Query: 122 PNNREDDLRKWLAANDFEIVAEDILTENDKRYEILVVKHGHMNLTAKELRFGPFLLSNNT 18- 1 PNN EDDLR WL ANDF I AE ++ + K YEILVV+ G + L+ K+LRFGPFL + Sbjct: 127 PNNCEDDLRSWLVANDFMIKAEKMVKDRHKYYEILVVEKGKITLSDKDLRFGPFLRQERS 18- 6 Query: 182 TVFKEKWQNELNKLTFALNSIPNSKMEERAILEDKIQDIKEVLDES 227 ++FKE+W+ EL KL AL +P K + L KI+ I+EVL ES Sbjct: 187 SIFKERWRKELAKLELALTRVPAKKKADNMFLSTKIEQIREVLYES 232 A related DNA sequence was identified in S. pyogenes <SEQ ID 2647> which encodes the amino acid sequence <SEQ ID 2648>. Analysis of this protein sequence reveals the following: TABLE-US-02549 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0803 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02550 Identities = 145/224 (64%), Positives = 173/224 (76%) Query: 1 MDLQLSKRLQKVANYVPKGARLLDVGSDHAYLPIFLLQMGYCDFAIAGEVVNGPYQSALK 60 MD QLS RL +VA YVPKG +LLDVGSDHAYLPIFL++ AIAGEVV GPY+SALK Sbjct: 1 MDSQLSNRLAQVAAYVPKGVKLLDVGSDHAYLPIFLVETNQISAAIAGEVVRGPYESALK 60 Query: 61 NVSEHGLTSKIDVRLANGLSAFEEADNIDTITICGMGGRLIADILNNDIDKLQHVKTLVL 120- NV++ GL I VRLANGL+AFEEAD++ ITICGMGGRLIADIL +KLQ ++ LVL Sbjct: 61 NVTQSGLAEHIQVRLANGLAAFEEADDVTAITICGMGGRLIADILEAGKEKLQGIERLVL 120- Query: 121 QPNNREDDLRKWLAANDFEIVAEDILTENDKRYEILVVKHGHMNLTAKELRFGPFLLSNN 18- 0 QPNNREDDLR WL+ N F+IVAE I+ ENDK YEI+V +HG L+A ELRFGP+L Sbjct: 121 QPNNREDDLRAWLSVNAFKIVAETIMAENDKYYEIIVAEHGEKALSATELRFGPYLSQEK 18- 0 Query: 181 TTVFKEKWQNELNKLTFALNSIPNSKMEERAILEDKIQDIKEVL 224 + VFKEKWQ E++KL +AL+ IP K +ER +L KIQ IKEV+ Sbjct: 181 SVVFKEKWQREMDKLAYALSCIPEEKTQERQLLLTKIQQIKEVI 224 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 873 A DNA sequence (GBSx0925) was identified in S. agalactiae <SEQ ID 2649> which encodes the amino acid sequence <SEQ ID 2650>. Analysis of this protein sequence reveals the following: TABLE-US-02551 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3245 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9893> which encodes amino acid sequence <SEQ ID 9894> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02552 >GP: BAA11246 GB: D78182 ORF4 [Streptococcus mutans] Identities = 187/262 (71%), Positives = 224/262 (85%) Query: 2 MKARELIDVYETYCPQELSMEGDISGLQIGSLDKEIKTVMVALDVRETTVAEAIERQVDL 61 MKA ++I YE YCPQ+LS+EGDISGLQIG+LDKEIK +M+ALDVRETTVAEAIE++VDL Sbjct: 1 MKASQIIKRYEAYCPQDLSLEGDISGLQIGTLDKEIKRLMIALDVRETTVAEAIEKKVDL 60 Query: 62 LIVKHAPIFRPLKDLVATPQNKIYIDLLKSDIAVYVSHTNIDIVPNGLNDWFCELLDIQY 121- LIVKHAPIFRPLK+LV T QN IY +L+K DIAVYVSHTNIDIVP+GLNDWFC+LLDI+ Sbjct: 61 LIVKHAPIFRPLKNLVETAQNHIYFNLIKHDIAVYVSHTNIDIVPDGLNDWFCDLLDIKN 120- Query: 122 PDILSETSNGYGIGRIGDIRPQSFEFFAWKIKDVFGLDSVRLVSYDKSNPEIQRVAICGG 18- 1 ILS + + YGIGR+GDI P SFE A K+K +F LDSVRLVSY ++NP I R+AICGG Sbjct: 121 RRILSPSKDDYGIGRVGDISPLSFEDLAKKVKKIFNLDSVRLVSYGENNPLISRIAICGG 18- 0 Query: 182 SGQSFYKEAIAKGADVFVTGDIYYHTAQEMITNGLLAIDPGHHIEVLFVSKIATMIEQWK 24- 1 SGQSFY+EA+ KGA V++TGDIYYHTAQEM+TNGLLA+DPGHHIEVLFV K+A + W Sbjct: 181 SGQSFYQEALTKGAQVYITGDIYYHTAQEMLTNGLLALDPGHHIEVLFVRKLAEKFQTWS 24- 0 Query: 242 LEKGWDISVLESKAPTNPFYHM 263 ++ WDI++LES+ TNPFYH+ Sbjct: 241 CQENWDITILESQVNTNPFYHL 262 A related DNA sequence was identified in S. pyogenes <SEQ ID 2651> which encodes the amino acid sequence <SEQ ID 2652>. Analysis of this protein sequence reveals the following: TABLE-US-02553 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1804 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02554 Identities = 169/262 (64%), Positives = 214/262 (81%) Query: 2 MKARELIDVYETYCPQELSMEGDISGLQIGSLDKEIKTVMVALDVRETTVAEAIERQVDL 61 MKA+ LID YE +CP +LSMEGD+ GLQ+GSLDK+I+ VM+ LD+RE+TVAEAI+ +VDL Sbjct: 3 MKAKTLIDAYEAFCPLDLSMEGDVKGLQMGSLDKDIRKVMITLDIRESTVAEAIKNEVDL 62 Query: 62 LIVKHAPIFRPLKDLVATPQNKIYIDLLKSDIAVYVSHTNIDIVPNGLNDWFCELLDIQY 121- +I KHAPIF+PLKDLV++PQ I +DL+K DI+VYVSHTNIDIVP GLNDWFC+LL+I+ Sbjct: 63 IITKHAPIFKPLKDLVSSPQRDILLDLVKHDISVYVSHTNIDIVPGGLNDWFCDLLEIKE 122- Query: 122 PDILSETSNGYGIGRIGDIRPQSFEFFAWKIKDVFGLDSVRLVSYDKSNPEIQRVAICGG 18- 1 LSET G+GIGRIG ++ Q+ E A K+K VF LD+VRL+ YDK NP I ++AICGG Sbjct: 123 ATYLSETKEGFGIGRIGTVKEQALEELASKVKRVFDLDTVRLIRYDKENPLISKIAICGG 18- 2 Query: 182 SGQSFYKEAIAKGADVFVTGDIYYHTAQEMITNGLLAIDPGHHIEVLFVSKIATMIEQWK 24- 1 SG FY++A+ KGADV++TGDIYYHTAQEM+T GL A+DPGHHIEVLF K+ ++ WK Sbjct: 183 SGGEFYQDAVQKGADVYITGDIYYHTAQEMLTEGLFAVDPGHHIEVLFTEKLKEKLQGWK 24- 2 Query: 242 LEKGWDISVLESKAPTNPFYHM 263 E GWD+S++ SKA TNPF H+ Sbjct: 243 EENGWDVSIISSKASTNPFSHL 264 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 874 A DNA sequence (GBSx0926) was identified in S. agalactiae <SEQ ID 2653> which encodes the amino acid sequence <SEQ ID 2654>. This protein is predicted to be 0. Analysis of this protein sequence reveals the following: TABLE-US-02555 Possible site: 41 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02556 >GP: CAB15253 GB: Z99120 similar to opine catabolism [Bacillus subtilis] Identities = 148/368 (40%), Positives = 211/368 (57%), Gaps = 13/368 (3%) Query: 1 MKKIAIIGAGAVGATLAYYLSKEKDIQVTVFDYGV-GQATKAAAGIISPWFSKRRNKAWY 59 MK I+GAG +GA+ AY+L+K +VTV D GQAT AAAGI+ PW S+RRN+ WY Sbjct: 1 MKSYIIVGAGILGASTAYHLAKT-GARVTVIDRKEPGQATDAAAGIVCPWLSQRRNQDWY 59 Query: 60 RMARLGADFYSKLVTDLQKDGFETKFYQQTGVFLLKKDESQLESLFALADKRRLESPLIG 119- ++A+ GA +Y L+ L+KDG Y++ G + D S+L+ + A KRR ++P IG Sbjct: 60 QLAKGGARYYKDLIHQLEKDGESDTGYKRVGAISIHTDASKLDKMEERAYKRREDAPEIG 119- Query: 120 DLQILNKSEANTHFPEL-DGYEQLLYASGGARVEGADLTRILLEAS---GVNVIKDEVHF 17- 5 D+ L+ SE FP L DGYE ++ SG ARV G L R LL A+ G VIK Sbjct: 120 DITRLSASETKKLFPILADGYES-VHISGAARVNGRALCRSLLSAAEKRGATVIKGNASL 17- 8 Query: 176 -----TITDNGFRVQGIDFDKLVLASGAWLAKILDEHNYQVDVRPQKGQLRDYYFSNINT 23- 0 T+T + D +++ +GAW +IL V QK Q+ + ++ +T Sbjct: 179 LFENGTVTGVQTDTKQFAADAVIVTAGAWANEILKPLGIHFQVSFQKAQIMHFEMTDADT 23- 8 Query: 231 GKYPVVMPEGELDIIPFDNGKVSVGASHENDMAF-DLNIDFKVLDKFEEQAIGYFPQLKK 28- 9 G +PVVMP + I+ FDNG++ GA+HEND DL + + +A+ P L Sbjct: 239 GSWPVVMPPSDQYILSFDNGRIVAGATHENDAGLDDLRVTAGGQHEVLSKALAVAPGLAD 29- 8 Query: 290 ADTTSERVGIRAYTSDFSPFFGPVPCMEGAYAASGLGSTGLTVGPLIGYELCQLILNKEN 34- 9 A RVG R +T F P G VP ++G YAA+GLG++GLT+GP +G EL +L+L K+ Sbjct: 299 AAAVETRVGFRPFTPGFLPVVGAVPNVQGLYAANGLGASGLTMGPFLGAELAKLVLGKQT 35- 8 Query: 350 QLNLEDYD 357 +L+L YD Sbjct: 359 ELDLSPYD 366 A related DNA sequence was identified in S. pyogenes <SEQ ID 2655> which encodes the amino acid sequence <SEQ ID 2656>. Analysis of this protein sequence reveals the following: TABLE-US-02557 Possible site: 40 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02558 Identities = 211/360 (58%), Positives = 262/360 (72%) Query: 3 KIAIIGAGAVGATLAYYLSKEKDIQVTVFDYGVGQATKAAAGIISPWFSKRRNKAWYRMA 62 KIAIIGAG VG+T AYYL + +VT+FD+G GQATKAAAGIISPWFSKRRNK WYRMA Sbjct: 2 KIAIIGAGIVGSTAAYYLQQSGQKEVTIFDHGQGQATKAAAGIISPWFSKRRNKVWYRMA 61 Query: 63 RLGADFYSKLVTDLQKDGFETKFYQQTGVFLLKKDESQLESLFALADKRRLESPLIGDLQ 122- RLGADFY +L+ DL++DGF T FYQQ G+++LKK E +L L+ LA R++ESP+IG+L Sbjct: 62 RLGADFYQQLINDLKEDGFATDFYQQNGIYVLKKQEEKLRDLYELALARKVESPIIGELA 121- Query: 123 ILNKSEANTHFPELDGYEQLLYASGGARVEGADLTRILLEASGVNVIKDEVHFTITDNGF 18- 2 I N+ E F L G++ LYASG ARVEGA L LL+ASG VI+ +V +G+ Sbjct: 122 IKNRKELGNDFKGLIGFDNCLYASGAARVEGAALCETLLKASGYPVIRQKVTLKQQGSGY 18- 1 Query: 183 RVQGIDFDKLVLASGAWLAKILDEHNYQVDVRPQKGQLRDYYFSNINTGKYPVVMPEGEL 24- 2 + G FD+++LA+GAWL +L YQVDVRPQKGQL DY +I + YPVVMPEGE+ Sbjct: 182 EIAGHYFDQVILAAGAWLPDLLRPLGYQVDVRPQKGQLLDYDVHHIISDTYPVVMPEGEI 24- 1 Query: 243 DIIPFDNGKVSVGASHENDMAFDLNIDFKVLDKFEEQAIGYFPQLKKADTTSERVGIRAY 30- 2 D+IPF+ GK+SVG SHEND +DL D++VL K E QA+ Y P LK+A + RVGIRAY Sbjct: 242 DLIPFNQGKISVGTSHENDKGYDLEPDWQVLKKLEMQALTYLPLLKEATQKTCRVGIRAY 30- 1 Query: 303 TSDFSPFFGPVPCMEGAYAASGLGSTGLTVGPLIGYELCQLILNKENQLNLEDYDITKYV 36- 2 TSD+SPF+G V ++ Y ASGLGS+GLTVGPLIGYEL QL+L E L DY Y+ Sbjct: 302 TSDYSPFYGQVSGLKNLYTASGLGSSGLTVGPLIGYELAQLLLGHEGLLTPSDYSPEPYL 36- 1 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8679> and protein <SEQ ID 8680> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02559 Lipop Possible site: -1 Crend: 2 McG: Discrim Score: 4.44 GvH: Signal Score (-7.5): 0.81 Possible site: 41 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 7.32 threshold: 0.0 PERIPHERAL Likelihood = 7.32 153 modified ALOM score: -1.96 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00062## SEQ ID 8680 (GBS290) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 57 (lane 6; MW 22 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 77 (lane 4; MW 47 kDa). GBS290-GST was purified as shown in FIG. 226, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 875 A DNA sequence (GBSx0927) was identified in S. agalactiae <SEQ ID 2657> which encodes the amino acid sequence <SEQ ID 2658>. Analysis of this protein sequence reveals the following: TABLE-US-02560 Possible site: 20 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.18 Transmembrane 38-54 (36-54) ----- Final Results ----- bacterial membrane --- Certainty = 0.1871 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02561 >GP: AAD19913 GB: AF105113 glucose-1-phosphate thymidylyl transferase [Streptococcus pneumoniae] Identities = 262/289 (90%), Positives = 276/289 (94%) Query: 1 MKGIILAGGSGTRLYPLTRAASKQLMPIYDKPMIYYPLSVLMLAGIKEILIISTPQDLPR 60 MKGIILAGGSGTRLYPLTRAASKQLMP+YDKPMIYYPLS LMLAGIK+ILIISTPQDLPR Sbjct: 1 MKGIILAGGSGTRLYPLTRAASKQLMPVYDKPMIYYPLSTLMLAGIKDILIISTPQDLPR 60 Query: 61 FEDMLGDGSELGISLSYAEQPSPDGLAQAFIIGEDFIGDDHVALVLGDNIYHGPGLSAML 120- F+D+L DGSE GI LSYAEQPSPDGLAQAF+IGE+FIGDD VAL+LGDNIYHGPGLS ML Sbjct: 61 FKDLLLDGSEFGIKLSYAEQPSPDGLAQAFLIGEEFIGDDSVALILGDNIYHGPGLSTML 120- Query: 121 QRAASKESGATVFGYQVKDPERFGVVEFDTDMNAISIEEKPAQPKSNYAVTGLYFYDNDV 18- 0 Q+AA KE GATVFGYQVKDPERFGVVEFDTDMNAISIEEKP P+SNYAVTGLYFYDNDV Sbjct: 121 QKAAKKEKGATVFGYQVKDPERFGVVEFDTDMNAISIEEKPEYPRSNYAVTGLYFYDNDV 18- 0 Query: 181 VEIAKNIKPSPRGELEITDVNKAYLDRGDLSVELMGRGFAWLDTGTHESLLEAAQYIETV 24- 0 VEIAK IKPS RGELEITDVNKAYL+RGDLSVELMGRGFAWLDTGTHESLLEA+QYIETV Sbjct: 181 VEIAKQIKPSARGELEITDVNKAYLNRGDLSVELMGRGFAWLDTGTHESLLEASQYIETV 24- 0 Query: 241 QRMQNVQVANLEEIAYRMGYITREQVLELAQPLKKNEYGQYLLRLIGEA 289 QRMQNVQVANLEEI+YRMGYI+RE VLELAQPLKKNEYG+YLLRLIGEA Sbjct: 241 QRMQNVQVANLEEISYRMGYISREDVLELAQPLKKNEYGRYLLRLIGEA 289 A related DNA sequence was identified in S. pyogenes <SEQ ID 2659> which encodes the amino acid sequence <SEQ ID 2660>. Analysis of this protein sequence reveals the following: TABLE-US-02562 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1585 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 207-209 The protein has homology with the following sequences in the databases: TABLE-US-02563 >GP: AAC69538 GB: AF057294 Cps23fO [Streptococcus pneumoniae] Identities = 263/289 (91%), Positives = 276/289 (95%) Query: 1 MKGIILAGGSGTRLYPLTRAASKQLMPIYDKPMIYYPLSTLMLAGIKDVLIISTPQDLPR 60 MKGIILAGGSGTRLYPLTRAASKQLMP+YDKPMIYYPLSTLMLAGI+D+LIISTPQDLPR Sbjct: 1 MKGIILAGGSGTRLYPLTRAASKQLMPVYDKPMIYYPLSTLMLAGIRDILIISTPQDLPR 60 Query: 61 FEELLGDGSEFGISLSYKEQPSPDGLAQAFIIGEEFIGDDRVALILGDNIYHGNGLTKML 120- F+ELL DGSEFGI LSY EQPSPDGLAQAFIIGEEFIGDD VALILGDNIYHG GL+ ML Sbjct: 61 FKELLQDGSEFGIKLSYAEQPSPDGLAQAFIIGEEFIGDDSVALILGDNIYHGPGLSTML 120- Query: 121 QKAAAKEKGATVFGYQVKDPERFGVVEFDENMNAISIEEKPEVPKSHFAVTGLYFYDNDV 18- 0 QKAA KEKGATVFGY VKDPERFGVVEFDENMNAISIEEKPE P+S++AVTGLYFYDNDV Sbjct: 121 QKAAKKEKGATVFGYHVKDPERFGVVEFDENMNAISIEEKPEYPRSNYAVTGLYFYDNDV 18- 0 Query: 181 VEIAKNIKPSARGELEITDVNKAYLERGDLSVELMGRGFAWLDTGTHESLLEAAQYIETV 24- 0 VEIAK+IKPS RGELEITDVNKAYL+RGDLSVELMGRGFAWLDTGTHESLLEA+QYIETV Sbjct: 181 VEIAKSIKPSPRGELEITDVNKAYLDRGDLSVELMGRGFAWLDTGTHESLLEASQYIETV 24- 0 Query: 241 QRLQNAQVANLEEIAYRMGYISKEDVHKLAQSLKKNEYGQYLLRLIGEA 289 QR+QN QVANLEEIAYRMGYIS+EDV LAQSLKKNEYGQYLLRLIGEA Sbjct: 241 QRMQNVQVANLEEIAYRMGYISREDVLALAQSLKKNEYGQYLLRLIGEA 289 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02564 Identities = 257/289 (88%), Positives = 274/289 (93%) Query: 1 MKGIILAGGSGTRLYPLTRAASKQLMPIYDKPMIYYPLSVLMLAGIKEILIISTPQDLPR 60 MKGIILAGGSGTRLYPLTRAASKQLMPIYDKPMIYYPLS LMLAGIK++LIISTPQDLPR Sbjct: 1 MKGIILAGGSGTRLYPLTRAASKQLMPIYDKPMIYYPLSTLMLAGIKDVLIISTPQDLPR 60 Query: 61 FEDMLGDGSELGISLSYAEQPSPDGLAQAFIIGEDFIGDDHVALVLGDNIYHGPGLSAML 120- FE++LGDGSE GISLSY EQPSPDGLAQAFIIGE+FIGDD VAL+LGDNIYHG GL+ ML Sbjct: 61 FEELLGDGSEFGISLSYKEQPSPDGLAQAFIIGEEFIGDDRVALILGDNIYHGNGLTKML 120- Query: 121 QRAASKESGATVFGYQVKDPERFGVVEFDTDMNAISIEEKPAQPKSNYAVTGLYFYDNDV 18- 0 Q+AA+KE GATVFGYQVKDPERFGVVEFD +MNAISIEEKP PKS++AVTGLYFYDNDV Sbjct: 121 QKAAAKEKGATVFGYQVKDPERFGVVEFDENMNAISIEEKPEVPKSHFAVTGLYFYDNDV 18- 0 Query: 181 VEIAKNIKPSPRGELEITDVNKAYLDRGDLSVELMGRGFAWLDTGTHESLLEAAQYIETV 24- 0 VEIAKNIKPS RGELEITDVNKAYL+RGDLSVELMGRGFAWLDTGTHESLLEAAQYIETV Sbjct: 181 VEIAKNIKPSARGELEITDVNKAYLERGDLSVELMGRGFAWLDTGTHESLLEAAQYIETV 24- 0 Query: 241 QRMQNVQVANLEEIAYRMGYITREQVLELAQPLKKNEYGQYLLRLIGEA 289 QR+QN QVANLEEIAYRMGYI++E V +LAQ LKKNEYGQYLLRLIGEA Sbjct: 241 QRLQNAQVANLEEIAYRMGYISKEDVHKLAQSLKKNEYGQYLLRLIGEA 289 There is also homology to SEQ ID 858. SEQ ID 2658 (GBS296) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 43 (lane 5; MW 35.4 kDa). GBS296-His was purified as shown in FIG. 203, lane 7. Based on this analysis, it was predicted that these proteins, and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 876 A DNA sequence (GBSx0929) was identified in S. agalactiae <SEQ ID 2661> which encodes the amino acid sequence <SEQ ID 2662>. Analysis of this protein sequence reveals the following: TABLE-US-02565 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2635 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 877 A DNA sequence (GBSx0930) was identified in S. agalactiae <SEQ ID 2663> which encodes the amino acid sequence <SEQ ID 2664>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following:

TABLE-US-02566 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1868 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2665> which encodes the amino acid sequence <SEQ ID 2666>. Analysis of this protein sequence reveals the following: TABLE-US-02567 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2818 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 29-31 The protein has homology with the following sequences in the databases: TABLE-US-02568 >GP: AAC69539 GB: AF057294 Cps23fP [Streptococcus pneumoniae] Identities = 168/197 (85%), Positives = 183/197 (92%) Query: 1 MTETFFDKPLACREIKEIPGLLEFDIPVRGDNRGWFKENFQKEKMLPIGFPERFFEEGKL 60 MT+ FF K LA R+++ IPG+LEFDIPV GDNRGWFKENFQKEKMLP+GFPE FF EGKL Sbjct: 1 MTDNFFGKTLAARKVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKL 60 Query: 61 QNNVSFSRQHVLRGLHAEPWDKYISVADDGKVLGAWVDLREGETFGNVYQTVIDASKGMF 120- QNNVSFSR++VLRGLHAEPWDKYISVAD GKVLG+WVDLREGETFGN YQTVIDASKG+F Sbjct: 61 QNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGSWVDLREGETFGNTYQTVIDASKGIF 120- Query: 121 VPRGVANGFQVLSETVSYSYLVNDYWALDLKPKYAFVNYADPSLGITWENLAAAEVSEAD 18- 0 VPRGVANGFQVLS+TVSYSYLVNDYWAL+LKPKYAFVNYADPSLGI WEN+A AEVSEAD Sbjct: 121 VPRGVANGFQVLSDTVSYSYLVNDYWALELKPKYAFVNYADPSLGIEWENIAEAEVSEAD 18- 0 Query: 181 KNHPLLSDVKPLKPKDL 197 K+HPLL DVKPLK +DL Sbjct: 181 KHHPLLKDVKPLKKEDL 197 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02569 Identities = 157/197 (79%), Positives = 180/197 (90%) Query: 1 MTEQFFDKELTCRPIEAIPGLLEFDIPVRGDNRGWFKENFQKEKMIPLGFPESFFEADKL 60 MTE FFDK L CR I+ IPGLLEFDIPVRGDNRGWFKENFQKEKM+P+GFPE FFE KL Sbjct: 1 MTETFFDKPLACREIKEIPGLLEFDIPVRGDNRGWFKENFQKEKMLPIGFPERFFEEGKL 60 Query: 61 QNNISFNKKNTLRGLHAEPWDKYVSIADEGRVIGTWVDLREGDSFGNVYQTIIDASKGIF 120- QNN+SF++++ LRGLHAEPWDKY+S+AD+G+V+G WVDLREG++FGNVYQT+IDASKG+F Sbjct: 61 QNNVSFSRQHVLRGLHAEPWDKYISVADDGKVLGAWVDLREGETFGNVYQTVIDASKGMF 120- Query: 121 VPRGVANGFQVLSDKAAYTYLVNDYWALELKPKYAFVNYADPNLGIQWENLEEAEVSEAD 18- 0 VPRGVANGFQVLS+ +Y+YLVNDYWAL+LKPKYAFVNYADP+LGI WENL AEVSEAD Sbjct: 121 VPRGVANGFQVLSETVSYSYLVNDYWALDLKPKYAFVNYADPSLGITWENLAAAEVSEAD 18- 0 Query: 181 KNHPLLKDVKPLKKEDL 197 KNHPLL DVKPLK +DL Sbjct: 181 KNHPLLSDVKPLKPKDL 197 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 878 A DNA sequence (GBSx0931) was identified in S. agalactiae <SEQ ID 2667> which encodes the amino acid sequence <SEQ ID 2668>. Analysis of this protein sequence reveals the following: TABLE-US-02570 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3019 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 879 A DNA sequence (GBSx0932) was identified in S. agalactiae <SEQ ID 2669> which encodes the amino acid sequence <SEQ ID 2670>. Analysis of this protein sequence reveals the following: TABLE-US-02571 Possible site: 37 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 880 A DNA sequence (GBSx0933) was identified in S. agalactiae <SEQ ID 2671> which encodes the amino acid sequence <SEQ ID 2672>. Analysis of this protein sequence reveals the following: TABLE-US-02572 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0957 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9367> which encodes amino acid sequence <SEQ ID 9368> was also identified. The protein is similar to the dTDP-glucose-4,6-dehydratase from S. mutans: TABLE-US-02573 >GP: BAA11249 GB: D78182 dTDP-glucose-4,6-dehydratase [Streptococcus mutans] Identities = 290/310 (93%), Positives = 304/310 (97%) Query: 1 MTYAGNRANIEAILGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPF 60 +TYAGN AN+E ILGDRVELVVGDIAD+ELVDKLAAKADAIVHYAAESHNDNSL DPSPF Sbjct: 39 LTYAGNHANLEEILGDRVELVVGDIADSELVDKLAAKADAIVHYAAESHNDNSLKDPSPF 98 Query: 61 IHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGNGEGPGEKFTAETKYNPS 120- I+TNF+GTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPG+GEGPGEKFTAETKYNPS Sbjct: 99 IYTNFVGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAETKYNPS 158- Query: 121 SPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILAGIKPKLY 18- 0 SPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNIL+GIKPKLY Sbjct: 159 SPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILSGIKPKLY 21- 8 Query: 181 GEGKNVRDWIHTNDHSTGVWAILTKGRIGETYLIGADGEKNNKEVLELILEKMGQPKDAY 24- 0 GEGKNVRDWIHTNDHSTGVWAILTRGRIGETYLIGADGEKNNKEVLELILSKM QPKDAY Sbjct: 219 GEGKNVRDWIHTNDHSTGVWAILTKGRIGETYLIGADGEKNNKEVLELILEKMSQPKDAY 27- 8 Query: 241 DHVTDRAGHDLRYAIDSTKLREELGWEPQFTNFSEGLEETINWYTENQDWWKAEKEAVEA 30- 0 DHVTDRAGHDLRYAIDSTKLREELGW+PQFTNF EGLE+TI WYTE++DWWKAEKEAVEA Sbjct: 279 DHVTDRAGHDLRYAIDSTKLREELGWKPQFTNFEEGLEDTIKWYTEHEDWWKAEKEAVEA 33- 8 Query: 301 NYAKTQEVIN 310 NYAKTQ+++N Sbjct: 339 NYAKTQKILN 348 A related DNA sequence was identified in S. pyogenes <SEQ ID 2673> which encodes the amino acid sequence <SEQ ID 2674>. Analysis of this protein sequence reveals the following: TABLE-US-02574 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1150 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02575 Identities = 300/309 (97%), Positives = 303/309 (97%) Query: 1 MTYAGNRANIEAILGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPF 60 +TYAGNRANIEAILGDRVELVVGDIADAELVDKLAAK DAIVHYAAESHNDNSL DPSPF Sbjct: 37 LTYAGNRANIEAILGDRVELVVGDIADAELVDKLAAKTDAIVHYAAESHNDNSLEDPSPF 96 Query: 61 IHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGNGEGPGEKFTAETKYNPS 120- IHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPG GEGPGEKFTAETKYNPS Sbjct: 97 IHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGQGEGPGEKFTAETKYNPS 156- Query: 121 SPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILAGIKPKLY 18- 0 SPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILAGIKPKLY Sbjct: 157 SPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILAGIKPKLY 21- 6 Query: 181 GEGKNVRDWIHTNDHSTGVWAILTKGRIGETYLIGADGEKNNKEVLELILEKMGQPKDAY 24- 0 GEGKNVRDWIHTNDHSTGVWAILTKGRIGETYLIGADGEKNNKEVLELILEKMGQPKDAY Sbjct: 217 GEGKNVRDWIHTNDHSTGVWAILTKGRIGETYLIGADGEKNNKEVLELILEKMGQPKDAY 27- 6 Query: 241 DHVTDRAGHDLRYAIDSTKLREELGWEPQFTNFSEGLEETINWYTENQDWWKAEKEAVEA 30- 0 DHVTDRAGHDLRYAIDSTKLREELGWEPQFTNFSEGLEETI WYTEN+ WWKAEK+AVEA Sbjct: 277 DHVTDRAGHDLRYAIDSTKLREELGWEPQFTNFSEGLEETIKWYTENETWWKAEKDAVEA 33- 6 Query: 301 NYAKTQEVI 309 YAKTQEVI Sbjct: 337 KYAKTQEVI 345 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 881 A DNA sequence (GBSx0935) was identified in S. agalactiae <SEQ ID 2675> which encodes the amino acid sequence <SEQ ID 2676>. Analysis of this protein sequence reveals the following: TABLE-US-02576 Possible site: 36 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 882 A DNA sequence (GBSx0936) was identified in S. agalactiae <SEQ ID 2677> which encodes the amino acid sequence <SEQ ID 2678>. Analysis of this protein sequence reveals the following: TABLE-US-02577 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -15.55 Transmembrane 13-29 (3-40) ----- Final Results ----- bacterial membrane --- Certainty = 0.7220 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 883 A DNA sequence (GBSx0937) was identified in S. agalactiae <SEQ ID 2679> which encodes the amino acid sequence <SEQ ID 2680>. Analysis of this protein sequence reveals the following: TABLE-US-02578 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2882 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 884 A DNA sequence (GBSx0938) was identified in S. agalactiae <SEQ ID 2681> which encodes the amino acid sequence <SEQ ID 2682>. This protein is predicted to be hyaluronate lyase. Analysis of this protein sequence reveals the following: TABLE-US-02579 Possible site: 30 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2683> which encodes the amino acid sequence <SEQ ID 2684>. Analysis of this protein sequence reveals the following: TABLE-US-02580 Possible site: 46 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9099> which encodes the amino acid sequence <SEQ ID 9100>. Analysis of this protein sequence reveals the following: TABLE-US-02581 Possible cleavage site: 23 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.300 (Affirmative) < succ> bacterial membrane --- Certainty = 0.000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02582 Identities = 359/771 (46%), Positives = 492/771 (63%), Gaps = 50/771 (6%) Query: 307 PNAT--GSTTVKISDKSGKIIKEVPLSVTASTEDNFTKLLDKWNDVTIGNHVYDTNDSNM 36- 4 PN T + T+ +D K+++ +D +T+LLD+WN + GN YD + +M Sbjct: 65 PNNTYFQTQTLTTTDSEKKVVQP-------QQKDYYTELLDQWNSIIAGNDAYDKTNPDM 117- Query: 365 QKLNQKLDETNAKNIEAIKL-----DSNRTFLWKDLDNLNNSAQLTATYRRLEDLAKQIT 41- 9 + K E +A+NI IK NRT+LW+ + + SA +T TYR +E +AKQIT Sbjct: 118 VTFHNKA-EKDAQNI--IKSYQGPDHENRTYLWEHAKDYSASANITKTYRNIEKIAKQIT 17- 4 Query: 420 NPHSTIYKNEKAIRTVKESLAWLHQNFYNVNKDI------EGSANWWDFEIGVPRSITGT 47- 3 NP S Y++ KAI VK+ +A+++++ YN++++ E NWW +EIG PR+I T Sbjct: 175 NPESCYYQDSKAIAIVKDGMAFMYEHAYNLDRENHQTTGKENKENWWVYEIGTPRAINNT 23- 4 Query: 474 LALMYNYFTDAEIKTYTDPIEHFVPDAGFFRKTLVN--PFKALGGNLVDMGRVKIIEGLL 53- 1 L+LMY YFT EI YT PIE FVPD FR N PF+A GNL+DMGRVK+I G+L Sbjct: 235 LSLMYPYFTQEEILKYTAPIEKFVPDPTRFRVRAANFSPFEANSGNLIDMGRVKLISGIL 29- 4 Query: 532 RKDNTIIEKTSHSLKNLFTTATKAEGFYADGSYIDHT-----------NVAYTGAYGNVL 58- 0 RKD+ I T +++ +FT + GFY DGS IDH +AYTGAYGNVL Sbjct: 295 RKDDLEISDTIKAIEKVFTLVDEGNGFYQDGSLIDHVVTNAQSPLYKKGIAYTGAYGNVL 35- 4 Query: 581 IDGLTQLLPIIQETDYKISNQELDMVYKWINQSFLPLIVKGELMDMSRGRSISREAASSH 64- 0 IDGL+QL+PIIQ+T I ++ +Y WIN SF P+IV+GE+MDM+RGRSISR A SH Sbjct: 355 IDGLSQLIPIIQKTKSPIKADKMATIYHWINHSFFPIIVRGEMMDMTRGRSISRFNAQSH 41- 4 Query: 641 AAAVEVLRGFLRLANMSNEERNLDLKSTIKTIITS-NKFYNVFNNLKSYSDIANMNKLLN 69- 9 A +E LR LR+A+MS E L LK+ IKT++T N FYNV++NLK+Y DI M +LL+ Sbjct: 415 VAGIEALRAILRIADMSEEPHRLALKTRIKTLVTQGNAFYNVYDNLKTYHDIKLMKELLS 47- 4 Query: 700 DSTVATKPLKSNLSTFNSMDRLAYYNAEKDFGFALSLHSKRTLNYEGMNDENTRGWYTGD 75- 9 D++V + L S +++FNSMD+LA YN + DF F LS+ S RT NYE MN+EN GW+T D Sbjct: 475 DTSVPVQKLDSYVASFNSMDKLALYNNKHDFAFGLSMFSNRTQNYEAMNNENLHGWFTSD 53- 4 Query: 760 GMFYLYNSDQSHYSNHFWPTVNPYKMAGTTEKDAKREDTTKDFMSKHSKDAKEKTGQVTG 81- 9 GMFYLYN+D HYS ++W TVNPY++ GTTE + K + T + + K ++ G +TG Sbjct: 535 GMFYLYNNDLGHYSENYWATVNPYRLPGTTETEQKPLEGTPE----NIKTNYQQVG-MTG 58- 9 Query: 820 ASD--FVGSVKLNDHFALAAMDFTNWDRTLTAQKGWVILNDKIVFLGSNIKNTNGIGNVS 87- 7 SD FV S KLN+ ALAAM FTNW+++LT KGW IL +KI+F+GSNIKN + Sbjct: 590 LSDDAFVASKKLNNTSALAAMTFTNWNKSLTLNKGWFILGNKIIFVGSNIKNQSS-HKAY 64- 8 Query: 878 TTIDQRKDDSKTPYTTYVNGKTVDLKQASSQQFTDTKSVFLESKEPGRNIGYIFFKNSTI 93- 7 TTI+QRK++ K PY +YVN + VDL FT+TKS+FLES +P +NIGY FFK +T+ Sbjct: 649 TTIEQRKENQKYPYCSYVNNQPVDLNN-QLVDFTNTKSIFLESDDPAQNIGYYFFKPTTL 70- 7 Query: 938 DIERKEQTGTWNSINRTSKNTSI---VSNPFITISQKHDNKGDSYDYMMVPNIDRTSFDK 99- 4 I + QTG W +I K+ VSN FITI Q H GD Y YMM+PN+ R F+ Sbjct: 708 SISKALQTGKWQNIKADDKSPEAIKEVSNTFITIMQNHTQDGDRYAYMMLPNMTRQEFET 76- 7 Query: 995 LANSKEVELLENSSKQQVIYDKNSQTWAVIKHDNQESLINNQFKMNKAGLY 1045 + +++LLEN+ K +YD +SQ VI + + ++ +N ++ G Y Sbjct: 768 YISKLDIDLLENNDKLAAVYDHDSQQMHVIHYGKKATMFSNH-NLSHQGFY 817 SEQ ID 2682 (GBS89) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 6 (lane 3; MW 118 kDa). The His-fusion protein was purified as shown in FIG. 190, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 885 A DNA sequence (GBSx0939) was identified in S. agalactiae <SEQ ID 2685> which encodes the amino acid sequence <SEQ ID 2686>. This protein is predicted to be mutator mutt protein. Analysis of this protein sequence reveals the following: TABLE-US-02583 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3781(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02584 >GP: BAA11250 GB: D78182 MutX [Streptococcus mutans] Identities = 132/160 (82%), Positives = 146/160 (90%), Gaps = 1/160 (0%) Query: 1 MTKLATICYIDNGKELLLLHRNKKENDVHEGKWISVGGKLEAGETPDECAKREILEETHL 60 M KLATICYIDNG+ELLL+HRNKK NDVHEGKWISVGGKLE GE+PDECA+REI EETHL Sbjct: 1 MIKLATICYIDNGRELLLMHRNKKPNDVHEGKWISVGGKLEKGESPDECARREIFEETHL 60 Query: 61 TVKKMDFKGVITFPEFTPGHDWYTYVFKVTDYEGELISDDESREGTLEWVPYDQVLSKPT 120- VK+MDFKG+ITFP+FTPGHDWYTYVFKV D+EG LISD +SREGTLEWVPY+QVL+KPT Sbjct: 61 IVKQMDFKGIITFPDFTPGHDWYTYVFKVRDFEGRLISDKDSREGTLEWVPYNQVLTKPT 120- Query: 121 WQGDYEIFKWILEDVPFFSAKFVYDEHQNLIEKTVNFYEK 160 W+GDYEIFKWILED PFFSAKFVY E Q L++K V FYEK Sbjct: 121 WEGDYEIFKWILEDAPFFSAKFVYQE-QKLVDKHVIFYEK 159 A related DNA sequence was identified in S. pyogenes <SEQ ID 2687> which encodes the amino acid sequence <SEQ ID 2688>. Analysis of this protein sequence reveals the following:

TABLE-US-02585 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3399 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02586 Identities = 131/158 (82%), Positives = 146/158 (91%) Query: 1 MTKLATICYIDNGKELLLLHRNKKENDVHEGKWISVGGKLEAGETPDECAKREILEETHL 60 MT+LATICYIDNG LLLLHRNKKENDVH+GKWISVGGKLEAGETPDECA+REILEETHL Sbjct: 1 MTQLATICYIDNGDSLLLLHRNKKENDVHKGKWISVGGKLEAGETPDECARREILEETHL 60 Query: 61 TVKKMDFKGVITFPEFTPGHDWYTYVFKVTDYEGELISDDESREGTLEWVPYDQVLSKPT 120- TV +M FKG+ITFPEFTPGHDWYTYVFKVT +EG+LISD+ESREGTLEWVPYDQVL KPT Sbjct: 61 TVTEMAFKGIITFPEFTPGHDWYTYVFKVTGFEGDLISDEESREGTLEWVPYDQVLEKPT 120- Query: 121 WQGDYEIFKWILEDVPFFSAKFVYDEHQNLIEKTVNFY 158 W+GDY+IFKWILED FFSAKF YD++ L++K+V FY Sbjct: 121 WEGDYDIFKWILEDRSFFSAKFTYDQNNQLMDKSVTFY 158 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 886 A DNA sequence (GBSx0940) was identified in S. agalactiae <SEQ ID 2689> which encodes the amino acid sequence <SEQ ID 2690>. This protein is predicted to be MutT/nudix family protein. Analysis of this protein sequence reveals the following: TABLE-US-02587 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1901 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02588 >GP: AAF11817 GB: AE002059 MutT/nudix family protein [Deinococcus radiodurans] Identities = 40/135 (29%), Positives = 62/135 (45%), Gaps = 3/135 (2%) Query: 22 FGVRVSALIIENQKLLLIYAPHLDKYY-LPGGALQVGEDSNKAVAREVLEEIGLHSQVGD 80 - F R + + +++ +LL + ++ LPGGA+Q GE S A RE EE GL + V Sbjct: 33 FQTRATLICVQDNRLLTCWDERFPDFFALPGGAVQTGESSAAAAQREWHEETGLRADVTR 92 Query: 81 LAYIIENQFNIKRHHYHSVEFLYFVNLLGQAPESIKEGTHKRHFVWLPIKELTKIDCNPN 140- A +E F+ + H F + V L G+ P ++ + H F WL + L P Sbjct: 93 CA-TLERFFHWEGRERHEFGFFFRVELTGELPATVLDNPHV-FFRWLAVDALDDHTLYPR 150- Query: 141 FLAQDLIEWPGHVVH 155 + Q L G + H Sbjct: 151 CVPQLLRLPAGEIGH 165 A related DNA sequence was identified in S. pyogenes <SEQ ID 2691> which encodes the amino acid sequence <SEQ ID 2692>. Analysis of this protein sequence reveals the following: TABLE-US-02589 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3832 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02590 Identities = 33/80 (41%), Positives = 50/80 (62%), Gaps = 1/80 (1%) Query: 29 LIIENQKLLLIYAPHLDKYYLPGGALQVGEDSNKAVAREVLEEIGLHSQVGDLAYIIENQ 88 - LI+ N K L D+YY GG VGE +++ V RE LEE+G+ ++V LA+++EN Sbjct: 1 LIVRNGKNFLTRDAD-DQYYTIGGTSLVGEKTHETVLRETLEEVGIRAKVNQLAFMVENH 59 Query: 89 FNIKRHHYHSVEFLYFVNLL 108 F+I +H++EF Y V+ L Sbjct: 60 FDIDDVFWHNIEFHYLVSPL 79 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 887 A DNA sequence (GBSx0941) was identified in S. agalactiae <SEQ ID 2693> which encodes the amino acid sequence <SEQ ID 2694>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following: TABLE-US-02591 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.95 Transmembrane 24-40 (17-48) INTEGRAL Likelihood = -11.09 Transmembrane 88-104 (82-112) INTEGRAL Likelihood = -9.39 Transmembrane 294-310 (276-315) INTEGRAL Likelihood = -8.07 Transmembrane 242-258 (236-262) INTEGRAL Likelihood = -7.86 Transmembrane 50-66 (43-74) INTEGRAL Likelihood = -3.13 Transmembrane 337-353 (332-355) INTEGRAL Likelihood = -2.23 Transmembrane 185-201 (182-202) INTEGRAL Likelihood = -1.38 Transmembrane 269-285 (267-285) ----- Final Results ----- bacterial membrane --- Certainty = 0.6180 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2695> which encodes the amino acid sequence <SEQ ID 2696>. Analysis of this protein sequence reveals the following: TABLE-US-02592 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.71 Transmembrane 88-104 (85-112) INTEGRAL Likelihood = -9.29 Transmembrane 24-40 (21-72) INTEGRAL Likelihood = -8.92 Transmembrane 47-63 (41-72) INTEGRAL Likelihood = -7.59 Transmembrane 243-259 (237-266) INTEGRAL Likelihood = -6.10 Transmembrane 181-197 (178-203) INTEGRAL Likelihood = -5.47 Transmembrane 278-294 (273-310) INTEGRAL Likelihood = -3.88 Transmembrane 338-354 (331-368) INTEGRAL Likelihood = -1.59 Transmenbrane 297-313 (297-314) ----- Final Results ----- bacterial membrane --- Certainty = 0.4885 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02593 >GP: AAD00285 GB: U78604 putative membrane protein [Streptococcus mutans] Identities = 244/382 (63%), Positives = 310/382 (80%), Gaps = 3/382 (0%) Query: 12 SLFYKWFLNNQATMALVITLLAFLTIFVFTKISFLFMPVISFFAVIMLPLVISTILYYLT 71 - S F+KWFL+N+ L++ LL FL I VFTKIS +F P++SF AVIMLPLVIS +LYYL Sbjct: 17 SWFFKWFLDNKTVTVLLVLLLVFLDILVFTKISSIFKPLLSFLAVIMLPLVISALLYYLL 76 Query: 72 KPLVDLINHLGPNRTTSIFIVFGLITLLFVWAISGFVPMVQTQLTSFIEDLPKYVGKVNE 131- KP+VD I G +R +I IVF +I L VW I+ F PM+ QLTSFI+ LP YV V+ Sbjct: 77 KPIVDFIEIRGTSRVMAITIVFVIIAGLLVWGIANFFPMLNEQLTSFIKYLPSYVRSVDA 136- Query: 132 EANKLLENEWLVSYKPQLQDMLTHTSQKALDYAQSFSKNAIDWAGNFAGAIARITVAIII 19- 1 + +KLL N+ L S++PQ+++ +T+ SQKA+DYA+ FSK A+ WAGNFA IAR+TVAIII Sbjct: 137 QVSKLLRNDLLASFRPQIENAVTNFSQKAVDYAEPFSKGAVTWAGNFASLIARVTVAIII 19- 6 Query: 192 SPFILFYFLRDSSHMKNGLVNVLPLKLRVPMVRVLGDINKQLSGYVQGQVTVAIVVGFMF 25- 1 SPFI+FY LRDSS MK V+ LP K+R P+ R+LGD+N+QL+GYVQ TVAI+VGFMF Sbjct: 197 SPFIVFYLLRDSSKMKEAFVSYLPTKMRQPIHRILGDVNRQLAGYVQRSSTVAIIVGFMF 25- 6 Query: 252 SIMFSLVGLKYAITFGIIAGFLNMIPYLGSFLAMIPVVIMAMVQGPFMLVKVLVIFMIEQ 31- 1 SIMF+++GL+YA+TFGIIAGFLNMIPYLGSFLA IPV I+A+V+GP +VKV ++F++EQ Sbjct: 257 SIMFTIIGLRYAVTFGIIAGFLNMIPYLGSFLATIPVFILALVEGPVKVVKVALVFIVEQ 31- 6 Query: 312 TIEGRFVAPLVLGNKLSIHPITIMFLLLTAGSMFGVWGVFLVIPIYASVKVVIKELFDWY 37- 1 TIEGRFV+PLVLG+KLSIHPITIMF+LLTAGSMFGVWGVFL IP+YAS+KVV+KE+F+WY Sbjct: 317 TIEGRFVSPLVLGSKLSIHPITIMFILLTAGSMFGVWGVFLGIPVYASIKVVVKEIFEWY 37- 6 Query: 372 KKVSGLYDEEVLVIEEVKDHVK 393 K +SGLY++E E++K VK Sbjct: 377 KPISGLYEKEE---EDIKKDVK 395 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02594 Identities = 243/389 (62%), Positives = 306/389 (78%), Gaps = 2/389 (0%) Query: 6 EKEFKNSLFFKWILNNQAVIALMITFLVFLTIFIFTKISFMFKPVFDFLAVLILPLVISG 65 EK +SLF+KW LNNQA +AL+IT L FLTIF+FTKISF+F PV F AV++LPLVIS Sbjct: 6 EKSRTDSLFYKWFLNNQATMALVITLLAFLTIFVFTKISFLFMPVISFFAVIMLPLVIST 65 Query: 66 LLYYLLKPMVTFLEKRGIKRVTAILSVFTIIILLLIWAMSSFIPMMSNQLRHFMEDLPSY 125- +LYYL KP+V + G R T+I VF +I LL +WA+S F+PM+ QL F+EDLP Y Sbjct: 66 ILYYLTKPLVDLINHLGPNRTTSIFIVFGLITLLFVWAISGFVPMVQTQLTSFIEDLPKY 125- Query: 126 VNKVQMETSSFIDHNPWLKSYKGEISSMLSNISSQAVSYAEKFSKNILDWAGNLASTVAR 18- 5 V KV E + ++ N WL SYK ++ ML++ S +A+ YA+ FSKN +DWAGN A +AR Sbjct: 126 VGKVNEEANKLLE-NEWLVSYKPQLQDMLTHTSQKALDYAQSFSKNAIDWAGNFAGAIAR 18- 4 Query: 186 VTVATIMAPFILFYLLRDSRNMKNGFLMVLPTKLRQPTDRILREMNSQMSGYVQGQIIVA 24- 5 +TVA I++PFILFY LRDS +MKNG + VLP KLR P R+L ++N Q+SGYVQGQ+ VA Sbjct: 185 ITVAIIISPFILFYFLRDSSHMKNGLVNVLPLKLRVPMVRVLGDINKQLSGYVQGQVTVA 24- 4 Query: 246 ITVGVIFSIMYSIIGLRYGVTLGIIAGVLNMVPYLGSFVAQIPVFILALVAGPVMVVKVA 30- 5 I VG +FSIM+S++GL+Y +T GIIAG LNM+PYLGSF+A IPV I+A+V GP M+VKV Sbjct: 245 IVVGFMFSIMFSLVGLKYAITFGIIAGFLNMIPYLGSFLAMIPVVIMAMVQGPFMLVKVL 30- 4 Query: 306 IVFVIEQTLEGRFVSPLVLGNKLSIHPITIMFILLTSGAMFGVWGVFLSIPIYASIKVVV 36- 5 ++F+IEQT+EGRFV+PLVLGNKLSIHPITIMF+LLT+G+MFGVWGVFL IPIYAS+KVV+ Sbjct: 305 VIFMIEQTIEGRFVAPLVLGNKLSIHPITIMFLLLTAGSMFGVWGVFLVIPIYASVKVVI 36- 4 Query: 366 KELFDWYKAVSGLYTVDV-VTEERSEEVK 393 KELFDWYK VSGLY +V V EE + VK Sbjct: 365 KELFDWYKKVSGLYDEEVLVIEEVKDHVK 393 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 888 A DNA sequence (GBSx0942) was identified in S. agalactiae <SEQ ID 2697> which encodes the amino acid sequence <SEQ ID 2698>. Analysis of this protein sequence reveals the following: TABLE-US-02595 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2715 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9891> which encodes amino acid sequence <SEQ ID 9892> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02596 >GP: AAA25160 GB: L16975 ORF1 [Lactococcus lactis] Identities = 132/345 (38%), Positives = 203/345 (58%), Gaps = 3/345 (0%) Query: 79 INLAQIVAEDGDIEQAFLYLDYISEDSQEYVSALLVMADLYDMEGLTDVAREKLLLASKL 138- +NLA+I ++G++++A YL I + + Y++AL+ +ADLY E + A KL A +L Sbjct: 1 VNLAEIAEDNGNLDEALNYLYQIPVNDENYIAALIKIADLYQFEVDFETAISKLEEAREL 60 Query: 139 SDDPLVTFGLAEMNLSLEHYQEAIEGYASLDNREILETTGVSTYQRIGKSYAIMGKFDAA 19- 8 SD PL+TF LAE Y AI YA L R+IL T +S YQRIG SYA +G F+ A Sbjct: 61 SDSPLITFALAESYFEQGDYSAAITEYAKLSERKILHETKISIYQRIGDSYAQLGNFENA 120- Query: 199 IEFLEKAVDIEYDDLTVFELATILYDQEEYQKANLYFKQLDTINPDFAGYEYIYGLSLRE 25- 8 I FLEK+++ + T++++A + + +A FK+L+ ++ +F YE Y +L Sbjct: 121 ISFLEKSLEFDEKPETLYKIALLYGETHNETRAIANFKRLEKMDVEFLNYELAYAQTLEA 18- 0 Query: 259 EHKSEEALRLVQQGIRKNSFDGQLLLLASQLSYELHDVHSSESYLKQAEKVSENQDEIVM 31- 8 + + AL + ++G++KN LL AS++ ++L D ++E YL A + E DE V Sbjct: 181 NQEFKAALEMAKKGMKKNPNAVPLLHFASKICFKLKDKAAAERYLVDALNLPELHDETVF 24- 0 Query: 319 RLSNLYLEEERFEEVLELDN-DNLENILAKWNIAKAHKALEMDDSVD--YYQSLYNDLKD 37- 5 L+NLY EE FE V+ L+ E++LAKW A AHKALE D Y + + +L + Sbjct: 241 LLANLYFNEEDFEAVINLEELLEDEHLLAKWLFAGAHKALENDSEAAALYEELIQTNLSE 30- 0 Query: 376 NPEFLQDYAYILREFGYLDKAQEVGKAYLKLVPDDIEMSEWVNNI 420 NPEFL+DY L+E G + K + + + YL+LVPDD M + ++ Sbjct: 301 NPEFLEDYIDFLKEIGQISKTEPIIEQYLELVPDDENMRNLLTDL 345 A related DNA sequence was identified in S. pyogenes <SEQ ID 2699> which encodes the amino acid sequence <SEQ ID 2700>. Analysis of this protein sequence reveals the following: TABLE-US-02597 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2991 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02598 Identities = 267/409 (65%), Positives = 336/409 (81%), Gaps = 1/409 (0%) Query: 13 MLNSEKMIVSIQNQDLEHANKYFEKALKNDPEEVLLELGAYLESIGFLPQAKRLYDQIRP 72 - MLNSEKMI S+ QDL HA KYF+KALK D + L+LG YLESIGFLP AKR+Y Q+ Sbjct: 7 MLNSEKMIASLDQQDLAHAEKYFQKALKEDDADSLIALGEYLESIGFLPHAKRIYLQLAD 66 Query: 73 NYPEVAINLAQIVAEDGDIEQAFLYLDYISEDSQEYVSALLVMADLYDMEGLTDVAREKL 132- +YPE+ INLAQI AED IE+AFLYLD +S+DS Y+SALLVMADLYDMEGLT+VAREKL Sbjct: 67 DYPELNINLAQIAAEDDAIEEAFLYLDKVSKDSPNYLSALLVMADLYDMEGLTEVAREKL 126- Query: 133 LLASKLSDDPLVTFGLAEMNLSLEHYQEAIEGYASLDNREILETTGVSTYQRIGKSYAIM 19- 2 L A +S +PLV FGLAE+++SL+H++EAI+ YA LDNR+ILE TG+STYQRIG++YA + Sbjct: 127 LQAVGISPEPLVIFGLAEIDMSLQHFKEAIDYYAQLDNRQILELTGISTYQRIGRAYASL 18- 6 Query: 193 GKFDAAIEFLEKAVDIEYDDLTVFELATILYDQEEYQKANLYFKQLDTINPDFAGYEYIY 25- 2 GKF+AAIEFLEKAV IEY+D TVFELAT++YDQE YQKANLYFKQL+TINPD+ GYEY Y Sbjct: 187 GKFEAAIEFLEKAVAIEYEDETVFELATLMYDQENYQKANLYFKQLETINPDYPGYEYGY 24- 6 Query: 253 GLSLREEHKSEEALRLVQQGIRKNSFDGQLLLLASQLSYELHDVHSSESYLKQAEKVSEN 31- 2 LSL EEHK+ EALRLVQQG+RKN+FD QLLLLASQLSYELHD ++E+YL QA++V+ + Sbjct: 247 ALSLHEEHKTSEALRLVQQGLRKNAFDSQLLLLASQLSYELHDRQNAENYLLQAKEVAVD 30- 6 Query: 313 QDEIVMRLSNLYLEEERFEEVLELDNDNLENILAKWNIAKAHKALEMDD-SVDYYQSLYN 37- 1 +EI+MRL LY + ERFEEV+ L+ + ++N+L KW IAKA+ ALE ++ ++ Y + Sbjct: 307 DEEILMRLVTLYFDAERFEEVIALNRETIDNVLTKWTIAKAYHALEQEEVALALYNEISA 36- 6 Query: 372 DLKDNPEFLQDYAYILREFGYLDKAQEVGKAYLKLVPDDIEMSEWVNNI 420 DL +NPEFLQDYAY+LREFG KA ++ AYL+ VPDD+M +++++I Sbjct: 367 DLAENPEFLQDYAYLLREFGQFHKAIQMATAYLRQVPDDVNMQDFLDHI 415 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 889 A DNA sequence (GBSx0943) was identified in S. agalactiae <SEQ ID 2701> which encodes the amino acid sequence <SEQ ID 2702>. This protein is predicted to be alpha-acetolactate synthase (ilvK). Analysis of this protein sequence reveals the following: TABLE-US-02599 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2105 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02600 >GP:CAA01700 GB:A23961 alpha-acetolactate synthase [Lactococcus lactis] Identities = 396/559 (70%), Positives = 466/559 (82%), Gaps 8/559 (1%) Query: 4 SHNQYGADLIVDSLINHDVKYVFGIPGAKIDRVFDTLE-DKGPELIVARHEQNATFMAQA 62 S Q+GA+L+VDSLINH VKYVFGIPGAKIDRVFD LE ++GP+++V RHEQ A FMAQA Sbjct: 2 SEKQFGANLVVDSLINHKVKYVFGIPGAKIDRVFDLLENEEGPQMVVTRHEQGAAFMAQA 61 Query: 63 VGRITGEPGVVIATSGPGISNLATGLVTATDEGDAVLAIGGQVKRGDLLKRAHQSMNNVA 122- VGR+TGEPGVV+ TSGPG+SNLAT L+TAT EGDA+LAIGGQVKR D LKRAHQSM+N Sbjct: 62 VGRLTGEPGVVVVTSGPGVSNLATPLLTATSEGDAILAIGGQVKRSDRLKRAHQSMDNAG 121- Query: 123 MLEPITKYSAEVHDPNTLSETVANAYRLAKSGKPGASFISIPQDVTDSPVSVKAIKPLSA 18- 2 M++ TKYSAEV DPNTLSE++ANAYR+AKSG PGA+F+SIPQDVTD+ VS+KAI+PLS Sbjct: 122 MMQSATKYSAEVLDPNTLSESIANAYRIAKSGHPGATFLSIPQDVTDAEVSIKAIQPLSD 18- 1 Query: 183 PKLGSASVLDINYLAQAINNAVLPVLLLGNGASSEGVTAAVRRLLDAVKLPVVETFQGAG 24- 2 PK+G+AS+ DINYLAQAI NAVLPV+L+G GAS V +++R LL V +PVVETFQGAG Sbjct: 182 PKMGNASIDDINYLAQAIKNAVLPVILVGAGASDAKVASSLRNLLTHVNIPVVETFQGAG 24- 1 Query: 243 IVSRELEDETFFGRVGLFRNQPGDMLLKRADLVIAIGYDPIEYEARNWNAEISARIIVID 30- 2 ++S +LE TF+GR+GLFRNQPGDMLLKR+DLVIA+GYDPIEYEARNWNAEI +RIIVID Sbjct: 242 VISHDLE-HTFYGRIGLFRNQPGDMLLKRSDLVIAVGYDPIEYEARNWNAEIDSRIIVID 30- 0 Query: 303 VEQAEIDTYFQPERELIGDMAHTLDLLLPAIKGYELPEGSKEYLKGLRNNIENVSDVKFD 36- 2 AEIDTY+QPERELIGD+A TLD LLPA++GY++P+G+K+YL GL E +FD Sbjct: 301 NAIAEIDTYYQPERELIGDIAATLDNLLPAVRGYKIPKGTKDYLDGLH---EVAEQHEFD 35- 7 Query: 363 RDSA-HGLVHPLDLIDVLQENTTDDMTVTVDVGSHYIWMARYFKSYEARHLLFSNGMQTL 42- 1 ++ G +HPLDL+ QE DD TVTVDVGS YIWMAR+FKSYE RHLLFSNGMQTL Sbjct: 358 TENTEEGRMHPLDLVSTFQEIVKDDETVTVDVGSLYIWMARHFKSYEPRHLLFSNGMQTL 41- 7 Query: 422 GVALPWAISAALLRPNTKVISVSGDGGFLFSAQSLETAVRLHLPIVHIIWNDGKYNMVEF 48- 1 GVALPWAI+AALLRP KV S SGDGGFLF+ QELETAVRL+LPIV IIWNDG Y+MV+F Sbjct: 418 GVALPWAITAALLRPGKKVYSHSGDGGFLFTGQELETAVRLNLPIVQIIWNDGHYDMVKF 47- 7 Query: 482 QEEMKYGRSSGVDFGPVDFVKYAESFGAKGYRVDSKDSFEETLKQALIDAENGPVLIDVP 54- 1 QEEMKYGRS+ VDFG VD+VKYAE+ AKGYR SK+ E LK I GPV+IDVP Sbjct: 478 QEEMKYGRSAAVDFGYVDYVKYAEAMRAKGYRAHSKEELAEILKS--IPDTTGPVVIDVP 53- 5 Query: 542 IDYKDNVTLGETILPDEFY 560 +DY DN+ L E +LP+EFY Sbjct: 536 LDYSDNIKLAEKLLPEEFY 554 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 890 A DNA sequence (GBSx0944) was identified in S. agalactiae <SEQ ID 2703> which encodes the amino acid sequence <SEQ ID 2704>. This protein is predicted to be alpha-acetolactate decarboxylase (aldC). Analysis of this protein sequence reveals the following: TABLE-US-02601 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3096 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9889> which encodes amino acid sequence <SEQ ID 9890> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-02602 >GP:CAA57941 GB:X82620 alpha-acetolactate decarboxylase [Lactococcus lactis] Identities = 139/239 (58%), Positives = 187/239 (78%), Gaps 3/239 (1%) Query: 16 MSETVKLFQYSTLSSLMAGLYKGSLTIGELLTHGDLGIGTVHMIDGELIVLDGKAYQAIG 75 - MSE +LFQY+TL +LMAGLY+G++TIGELL HGDLGIGT+ IDGELIVLDGKAYQA Sbjct: 1 MSEITQLFQYNTLGALMAGLYEGTMTIGELLKHGDLGIGTLDSIDGELIVLDGKAYQA-- 58 Query: 76 TDGKAEIIQLSDDVTVPYAAVLPHHIQKQFDINAEIDNKDLEEMILKNFEGQNLFKSLKI 135- G I++L+DD+ VPYAAV+PH + F + +K+LE+ I F+GQNLF+S+KI Sbjct: 59 -KGDKTIVELTDDIKVPYAAVVPHQAEVVFKQKFTVSDKELEDRIESYFDGQNLFRSIKI 117- Query: 136 KGTFSRMHVRMIPKSPQHKRFADIASNQPEFTRENVSGTLVGIWTPELFHGVGVKGFHVH 19- 5 G F +MHVRMIP++ +F +++ NQPE+T EN+ GT+VGIWTPE+FHGV V G+H+H Sbjct: 118 TGKFPKMHVRMIPRAKSGTKFVEVSQNQPEYTEENIKGTIVGIWTPEMFHGVSVAGYHLH 17- 7 Query: 196 FISDDLTFGGHVMDYSLTQGKVEIGKVDQLDQCFPTQDQEFLKANFDLQKLREDIDLSE 254- FIS+D TFGGHV+D+ + G VEIG +DQL+Q FP QD++FL A+ D++ L++DID++E Sbjct: 178 FISEDFTFGGHVLDFIIDNGTVEIGAIDQLNQSFPVQDRKFLFADLDIEALKKDIDVAE 236- No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 891 A DNA sequence (GBSx0945) was identified in S. agalactiae <SEQ ID 2705> which encodes the amino acid sequence <SEQ ID 2706>. This protein is predicted to be fibronectin-binding protein-like protein A. Analysis of this protein sequence reveals the following: TABLE-US-02603 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5042 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02604 >GP:CAA46282 GB:X65164 fibronectin-binding protein-like protein A [Streptococcus gordonii] Identities = 392/550 (71%), Positives = 462/550 (83%) Query: 1 MSFDGFFLHHLTNELQEQIEKGRIQKVNQPFDHELVLTIRNNRRNYKLLLSAHPVFGRIQ 60 MSFDGFFLHH+T EL+ ++ GRIQK+NQPF+ ELVL IR+NR++ KLLLSAH VFGR+Q Sbjct: 1 MSFDGFFLHHMTEELRHELVGGRIQKINQPFEQELVLQIRSNRKSLKLLLSAHSVFGRVQ 60 Query: 61 TTEANFQNPQNPNTFTMIMRKYLQGAVIETIQQIENDRILEIVVSNKNEIGDHIKATLVV 120- T+ F+NP PNTF M+MRKYLQGAVIE IQQ+ENDRILEI VSNKNEIGD + TLV+ Sbjct: 61 LTDTTFENPAVPNTFIMVMRKYLQGAVIEAIQQVENDRILEISVSNKNEIGDSVAVTLVI 120- Query: 121 EIMGKHSNIILIDKNEHKIIESIKHVGFSQNSYRTILPGSTYIAPPKTKAINPFDISDQT 18- 0 EIMGKHSNIIL+DK KIIE+IKHVGFSQNSYRTILPGSTY+APP+T ++NPF + D+ Sbjct: 121 EIMGKHSNIILLDKASGKIIEAIKHVGFSQNSYRTILPGSTYVAPPQTGSLNPFTVGDEK 18- 0 Query: 181 LFELLQTNDLSPKNLQQLLQGLGRDTALELSHCLKDNKLNDFRQFFSREYYPSLTEKSFS 24- 0 LFE+LQT ++ PK L Q+ QGLGRDTA ELS L ++L FR FF+ PSLTEKSFS Sbjct: 181 LFEILQTEEIEPKRLLQIFQGLGRDTATELSGRLTTDRLKTFRAFFASPTQPSLTEKSFS 24- 0 Query: 241 AVQFSSSHETFQSLGQLLDYYYQEKAEKDRIAQQASDLIHRVQSELEKNIKKLAKQQDEL 30- 0 A+ FS S +L +LLD +Y++KAE+ R+ QQAS+LI RV++ELEKN KKL KQ+DEL Sbjct: 241 ALVFSDSKTQMSTLSELLDTFYKDKAERYRVNQQASELIRRVENELEKNRKKLGKQEDEL 30- 0 Query: 301 LATENAEEFRQKGELLTTYLSMVPNNQDVVVLDNYYTNQTIEISLDRALTPNQNAQRYFK 36- 0 LATE AEEFRQKGELLTT+L VPN+QD V LDNYYT + I I+LD+ALTPNQNAQRYFK Sbjct: 301 LATEKAEEFRQKGELLTTFLHQVPNDQDQVELDNYYTGEKILITLDKALTPNQNAQRYFK 36- 0 Query: 361 KYQKLKEAVKHLKGIISDTENTITYLESVETSLNHASMEDINDIREELVETGFIKRRAHD 42- 0 +YQKLKEAVKHL +I +T TI YLESVET+L AS+ +I +IREEL++TGFI+RR + Sbjct: 361 RYQKLKEAVKHLTSLIEETRTTILYLESVETALAQASLTEIAEIREELIQTGFIRRRQRE 42- 0 Query: 421 KQHKRKKPEQYLASDGKTIIMVGRNNLQNDELTFKMARKGELWFHAKDIPGSHVLIRDNL 48- 0 K KRKKPE+YLASDG+TII+VGRNNLQNDELTFKMA+K ELWFHAKDIPGSHV+I NL Sbjct: 421 KIQKRKKPEKYLASDGQTIILVGRNNLQNDELTFKMAKKDELWFHAKDIPGSHVVITGNL 48- 0 Query: 481 NPSDEVKTDAAELAAYYSKARLSNLVQVDMIEAKKLNKPSGTKPGFVTYTGQKTLRVTPT 54- 0 PSDEVKTDAAELAAY+SKARLSNLVQVDMIE KKLNKP+G KPGFVTYTGQKTLRVTP Sbjct: 481 QPSDEVKTDAAELAAYFSKARLSNLVQVDMIEIKKLNKPTGGKPGFVTYTGQKTLRVTPD 54- 0 Query: 541 QEKIDSLELK 550 +KI S+K++ Sbjct: 541 ADKIKSMKIQ 550 A related DNA sequence was identified in S. pyogenes <SEQ ID 2707> which encodes the amino acid sequence <SEQ ID 2708>. Analysis of this protein sequence reveals the following: TABLE-US-02605 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5434 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein differs significantly from L28919 in its mid-region: TABLE-US-02606 Query: 223 QHFQGLGRDTAKELAELLTTD F L +T K + ELLTTD Sbjct: 121 PAFSRLRGETPKRIGELLTTD An alignment of the GAS and GBS proteins is shown below. TABLE-US-02607 Identities = 421/549 (76%), Positives = 487/549 (88%) Query: 1 MSFDGFFLHHLTNELQEQIEKGRIQKVNQPFDHELVLTIRNNRRNYKLLLSAHPVFGRIQ 60 MSFDGFFLHHLTNEL+E + GRIQKVNQPF+ ELVLTIRN+R+NYKLLLSAHPVFGR+Q Sbjct: 27 MSFDGFFLHHLTNELKENLLYGRIQKVNQPFERELVLTIRNHRKNYKLLLSAHPVFGRVQ 86 Query: 61 TTEANFQNPQNPNTFTMIMRKYLQGAVIETIQQIENDRILEIVVSNKNEIGDHIKATLVV 120- T+A+FQNFQ PNTFTMIMRKYLQGAVIE ++QI+NDRI+EI VSNKNEIGD I+ATL++ Sbjct: 87 ITQADFQNPQVPNTFTMIMRKYLQGAVIEQLEQIDNDRIIEIKVSNKNEIGDAIQATLII 146- Query: 121 EIMGKHSNIILIDKNEHKIIESIKHVGFSQNSYRTILPGSTYIAPPKTKAINPFDISDQT 18- 0 EIMGKHSNIIL+D+ E+KIIESIKHVGFSQNSYRTILPGSTYI PPKT A+NPF I+D Sbjct: 147 EIMGKHSNIILVDRAENKIIESIKHVGFSQNSYRTILPGSTYIEPPKTAAVNPFTITDVP 20- 6 Query: 181 LFELLQTNDLSPKNLQQLLQGLGRDTALELSHCLKDNKLNDFRQFFSREYYPSLTEKSFS 24- 0 LFE+LQT +L+ K+LQQ QGLGRDTA EL+ L +KL FR+FF+R +LT SF+ Sbjct: 207 LFEILQTQELTVKSLQQHFQGLGRDTAKELAELLTTDKLKRFREFFARPTQANLTTASFA 26- 6 Query: 241 AVQFSSSHETFQSLGQLLDYYYQEKAEKDRIAQQASDLIHRVQSELEKNIKKLAKQQDEL 30- 0 V FS SH TF++L +LD++YQ+KAE+DRI QQASDLIHRVQ+EL+KN KL+KQ+ EL Sbjct: 267 PVLFSDSHATFETLSDMLDHFYQDKAERDRINQQASDLIHRVQTELDKNRNKLSKQEAEL 32- 6 Query: 301 LATENAEEFRQKGELLTTYLSMVPNNQDVVVLDNYYTNQTIEISLDRALTPNQNAQRYFK 36- 0 LATENAE FRQKGELLTTYLS+VPNNQD V+LDNYYT + IEI+LD+ALTPNQNAQRYFK Sbjct: 327 LATENAELFRQKGELLTTYLSLVPNNQDSVILDNYYTGEKIEIALDKALTPNQNAQRYFK 38- 6 Query: 361 KYQKLKEAVKHLKGIISDTENTITYLESVETSLNHASMEDINDIREELVETGFIKRRAHD 42- 0 KYQKLKEAVKHL G+I+DT+ +ITY ESV+ +L+ AS++DI DIREEL + GF+K R D Sbjct: 387 KYQKLKEAVKHLSGLIADTKQSITYFESVDYNLSQASIDDIEDIREELYQAGFLKSRQRD 44- 6 Query: 421 KQHKRKKPEQYLASDGKTIIMVGRNNLQNDELTFKMARKGELWFHAKDIPGSHVLIRDNL 48- 0 K+HKRKKPEQYLASDG TI+MVGRNNLQN+ELTFKMA+KGELWFHAKDIPGSHV+I+DNL Sbjct: 447 KRHKRKKPEQYLASDGTTILMVGRNNLQNEELTFKMAKKGELWFHAKDIPGSHVIIKDNL 50- 6 Query: 481 NPSDEVKTDAAELAAYYSKARLSNLVQVDMIEAKKLNKPSGTKPGFVTYTGQKTLRVTPT 54- 0 +PSDEVKTDAAELAAYYSKARLSNLVQVDMIEAKKL+KPSG KPGFVTYTGQKTLRVTP Sbjct: 507 DPSDEVKTDAAELAAYYSKARLSNLVQVDMIEAKKLHKPSGAKPGFVTYTGQKTLRVTPD 56- 6 Query: 541 QEKIDSLKL 549 Q KI S+KL Sbjct: 567 QAKILSMKL 575 SEQ ID 2706 (GBS81) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 6 (lane 2; MW 64 kDa) and in FIG. 6 (lane 5; MW 64 kDa). The GBS81-His fusion product was purified (FIG. 190, lane 3) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 319), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 892 A DNA sequence (GBSx0946) was identified in S. agalactiae <SEQ ID 2709> which encodes the amino acid sequence <SEQ ID 2710>. Analysis of this protein sequence reveals the following: TABLE-US-02608 Possible site: 53 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.08 Transmembrane 6-22 (1-24) ----- Final Results ----- bacterial membrane --- Certainty = 0.4630 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02609 >GP:AAF94260 GB:AE004191 conserved hypothetical protein [Vibrio cholerae] Identities = 111/295 (37%), Positives = 184/295 (61%), Gaps = 1/295 (0%) Query: 36 QVVKIGILQYVTHDALDAIEKGVEDGLAQEGYK-GKKVKLTVLNAEADQSKIQAMSKQLV 94 - + K+ + Q V H ALDA +G+ DGL +GY+GK ++ A+ + + +++Q V Sbjct: 26 KTAKVAVSQIVEHPALDATRQGLLDGLKAKGYEEGKNLEFDYKTAQGNPAIAVQIARQFV 85 Query: 95 NHHNDILIGIATPSAQGLAASTKDTPIIMGAVSDPLGAKLVTNMKKPTTNVTGLSNVVPT 154- + D+L+GIATP+AQ L ++TK PI+ AV+DP+GAKLV +++P NVTGLS++ P Sbjct: 86 GENPDVLVGIATPTAQALVSATKTIPIVFTAVTDPVGAKLVKQLEQPGKNVTGLSDLSPV 145- Query: 155 KQTVQLIKDITPNIKRIGILYASSEDNSVSQVTEFTKYAQKAGLEVLKYSVPSTNEIKTS 21- 4 +Q V+LIK+I PN+K IG++Y E N+VS + A K G+++++ + + +++++ Sbjct: 146 EQHVELIKEILPNVKSIGVVYNPGEANAVSLMELLKLSAAKHGIKLVEATALKSADVQSA 20- 5 Query: 215 MSVMTKKVDAVFVPQDNTIASAFRTVIVAANQANIPVYSSVDTMVEQGSIASVAQSQYGL 27- 4 + +K D ++ DNT+ASA +IVAANQA PV+ + + VE+G+IAS+ Y + Sbjct: 206 TQAIAEKSDVIYALIDNTVASAIEGMIVAANQAKTPVFGAATSYVERGAIASLGFDYYQI 26- 5 Query: 275 GLETAKQAIKVLRGKPVKDVPVKVIDTGKPSLNLKAAKHLGIKIPKKIMKQAEIT 329 G++TA +L GK + V+V +N AA+ LGI IP+ ++ +A T Sbjct: 266 GVQTADYVAAILEGKEPGSLDVQVAKGSDLVINKTAAEQLGITIPEAVLARATST 320 A related DNA sequence was identified in S. pyogenes <SEQ ID 2711> which encodes the amino acid sequence <SEQ ID 2712>. Analysis of this protein sequence reveals the following: TABLE-US-02610 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.25 Transmembrane 6-22 (1-27) ----- Final Results ----- bacterial membrane --- Certainty = 0.5501 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02611 >GP:AAF94260 GB:AE004191 conserved hypothetical protein [Vibrio cholerae] Identities = 103/304 (33%), Positives = 178/304 (57%), Gaps = 1/304 (0%) Query: 17 VIGSLLSKGVSKENRDLANQQNITIGILQFVTHEALDDIKRGIEDQLK-KQMPQKQNVVI 75 - VI + + G + + + + + Q V H ALD ++G+ D LK K + +N+ Sbjct: 6 VIATAVLAGAALLSSQSIMAKTAKVAVSQIVEHPALDATRQGLLDGLKAKGYEEGKNLEF 65 Query: 76 KVMNAEGDQSKIQTMSRQLVQSGSDIVIGIATPAAQGLAATSKDIPVVMSAVSDPVGSRL 135- A+G+ + ++RQ V D+++GIATP AQ L + +K IP+V +AV+DPVG++L Sbjct: 66 DYKTAQGNPAIAVQIARQFVGENPDVLVGIATPTAQALVSATKTIPIVFTAVTDPVGAKL 125- Query: 136 VMQLDQPEANVTGLSNKVPVKQTIDLMKKLTPHVKTVGILYASNEDNSLSQVKEFRRLAR 19- 5 V QL+QP NVTGLS+ PV+Q ++L+K++ P+VK++G++Y E N++S ++ + A Sbjct: 126 VKQLEQPGKNVTGLSDLSPVEQHVELIKEILPNVKSIGVVYNPGEANAVSLMELLKLSAA 18- 5 Query: 196 KKGYQVISYAVPSTNEVPATMSVMLGKVDAVFIPQDNTIASAFSSVMTTSKAAKIPVYTS 25- 5 K G +++ + +V + + K D ++ DNT+ASA ++ + AK PV+ + Sbjct: 186 KHGIKLVEATALKSADVQSATQAIAEKSDVIYALIDNTVASAIEGMIVAANQAKTPVFGA 24- 5 Query: 256 VDRMVEKGGLAAISQNQYDLGVQTANQVLKLIKGKRVVDVPVKVVDIGQPLINKNVAAEL 31- 5 VE+G +A++ + Y +GVQTA+ V +++GK + V+V +INK A +L Sbjct: 246 ATSYVERGAIASLGFDYYQIGVQTADYVAAILEGKEPGSLDVQVAKGSDLVINKTAAEQL 30- 5 Query: 316 GIAI 319 GI I Sbjct: 306 GITI 309 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02612 Identities = 181/322 (56%), Positives = 252/322 (78%), Gaps = 1/322 (0%) Query: 1 MKNKGLIATLILLTILVVGELFYNK-SEKRLNLSEKQVVKIGILQYVTHDALDAIEKGVE 59 MKNK LIATL++LT++V+G L S++ +L+ +Q + IGILQ+VTH+ALD I++G+E Sbjct: 1 MKNKSLIATLLVLTVIVIGSLLSKGVSKENRDLANQQNITIGILQFVTHEALDDIKRGIE 60 Query: 60 DGLAQEGYKGKKVKLTVLNAEADQSKIQAMSKQLVNHHNDILIGIATPSAQGLAASTKDT 119- D L ++ + + V + V+NAE DQSKIQ MS+QLV +DI+IGIATP+AQGLAA++KD Sbjct: 61 DQLKKQMPQKQNVVIKVMNAEGDQSKIQTMSRQLVQSGSDIVIGIATPAAQGLAATSKDI 120- Query: 120 PIIMGAVSDPLGAKLVTNMKKPTTNVTGLSNVVPTKQTVQLIKDITPNIKRIGILYASSE 17- 9 P++M AVSDP+G++LV + +P NVTGLSN VP KQT+ L+K +TP++K +GILYAS+E Sbjct: 121 PVVMSAVSDPVGSRLVMQLDQPEANVTGLSNKVPVKQTIDLMKKLTPHVKTVGILYASNE 18- 0 Query: 180 DNSVSQVTEFTKYAQKAGLEVLKYSVPSTNEIKTSMSVMTKKVDAVFVPQDNTIASAFRT 23- 9 DNS+SQV EF + A+K G +V+ Y+VPSTNE+ +MSVM KVDAVF+PQDNTIASAF + Sbjct: 181 DNSLSQVKEFRRLARKKGYQVISYAVPSTNEVPATMSVMLGKVDAVFIPQDNTIASAFSS 24- 0 Query: 240 VIVAANQANIPVYSSVDTMVEQGSIASVAQSQYGLGLETAKQAIKVLRGKPVKDVPVKVI 29- 9 V+ + A IPVY+SVD MVE+G +A+++Q+QY LG++TA Q +K+++GK V DVPVKV+ Sbjct: 241 VMTTSKAAKIPVYTSVDRMVEKGGLAAISQNQYDLGVQTANQVLKLIKGKRVVDVPVKVV 30- 0 Query: 300 DTGKPSLNLKAAKHLGIKIPKK 321 D G+P +N A LGI I K+ Sbjct: 301 DIGQPLINKNVAAELGIAIKKE 322 SEQ ID 2710 (GBS254) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 43 (lane 4; MW 27 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 48 (lane 3; MW 59.6 kDa). GBS254-GST was purified as shown in FIG. 203, lane 6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 893 A DNA sequence (GBSx0947) was identified in S. agalactiae <SEQ ID 2713> which encodes the amino acid sequence <SEQ ID 2714>. This protein is predicted to be probable permease of ABC transporter (rbsC). Analysis of this protein sequence reveals the following: TABLE-US-02613 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -15.12 Transmembrane 127-143 (119-151) INTEGRAL Likelihood = -8.81 Transmembrane 206-222 (200-227) INTEGRAL Likelihood = -6.48 Transmembrane 260-276 (258-282) INTEGRAL Likelihood = -5.84 Transmembrane 234-250 (231-257) INTEGRAL Likelihood = -4.78 Transmembrane 55-71 (54-72) INTEGRAL Likelihood = -3.61 Transmembrane 177-193 (176-194) INTEGRAL Likelihood = -3.35 Transmembrane 84-100 (83-102) INTEGRAL Likelihood = -1.91 Transmembrane 10-26 (10-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.7050 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02614 >GP: AAG07224 GB: AE004801 probable permease of ABC transporter [Pseudomonas aeruginosa] Identities = 116/288 (40%), Positives = 185/288 (63%), Gaps = 9/288 (3%) Query: 2 IISSVSQGLLWGILGLGIYLTFRILKFPDMTTEGSFPLGGAVCVTLMNQGVNPILATILG 61 + ++ GL++ ++ LG++++FR+L+FPD+T +GSFPLGGAVC TL+ G +P AT+ Sbjct: 6 LFGALEIGLIFSLVALGVFISFRLLRFPDLTVDGSFPLGGAVCATLIALGWDPYSATLAA 65 Query: 62 MLSGMLAGFVTGLLYTKGKIPTILAGILVMTSCHSIMLMVMKRANLGLNEIQTLKDFLPF 121- +G LAG TGLL K KI +LA IL+M + +SI L +M + N+ L TL L Sbjct: 66 TAAGALAGLATGLLNVKLKIMDLLASILMMIALYSINLRIMGKPNVPLIAEPTLFTLLQP 125- Query: 122 SNDLNLLVLGLIAILLVISA---LIYFLYTRLGQAYIATGDNPDMAKSFGIDTDKMEMLG 17- 8 + + L+ + +VI+A L +F T+ G A ATG NP MA++ G++T M +LG Sbjct: 126 EWLSDYVFRPLLLVFIVIAAKLLLDWFFTTQKGLAIRATGSNPRMARAQGVNTGGMILLG 18- 5 Query: 179 LIVSNGLIALSGALVSQQDGYADVSKGIGVIVIGLASIIIGE-VLYSTGLTLFERLIAIV 23- 7 + +SN L+AL+GAL +Q G AD+S GIG IVIGLA++I+GE +L S L L +A++ Sbjct: 186 MAISNALVALAGALFAQTQGGADISMGIGTIVIGLAAVIVGESILPSRRLIL--ATLAVI 24- 3 Query: 238 VGSILYQFLITAVI---ALGFNTNYLKLFSAIVLGICLMVPVLKTKIL 282 +G+I+Y+F I + +G L L +A+++ + L++P++K ++L Sbjct: 244 LGAIVYRFFIALALNSDFIGLQAQDLNLVTAVLVTVALVIPMMKKRLL 291 A related DNA sequence was identified in S. pyogenes <SEQ ID 2715> which encodes the amino acid sequence <SEQ ID 2716>. Analysis of this protein sequence reveals the following: TABLE-US-02615 Possible site: 55 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.46 Transmembrane 131-147 (125-156) INTEGRAL Likelihood = -8.65 Transmembrane 210-226 (204-230) INTEGRAL Likelihood = -8.17 Transmembrane 265-281 (261-283) INTEGRAL Likelihood = -7.22 Transmembrane 238-254 (233-261) INTEGRAL Likelihood = -3.03 Transmembrane 89-105 (87-107) INTEGRAL Likelihood = -2.60 Transmembrane 63-79 (62-79) INTEGRAL Likelihood = -2.23 Transmembrane 180-196 (180-198) INTEGRAL Likelihood = -2.13 Transmembrane 14-30 (14-30) ----- Final Results ----- bacterial membrane --- Certainty = 0.5182 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02616 >GP: AAG07224 GB: AE004801 probable permease of ABC transporter [Pseudomonas aeruginosa] Identities = 118/285 (41%), Positives = 186/285 (64%), Gaps = 7/285 (2%) Query: 6 IISSVSQGLIWGVLGLGIYLTFRILNFPDMTTEGSFPLGGAVAVTAISLGWNPFLSTLLG 65 + ++ GLI+ ++ LG++++FR+L FPD+T +GSFPLGGAV T I+LGW+P+ +TL Sbjct: 6 LFGALEIGLIFSLVALGVFISFRLLRFPDLTVDGSFPLGGAVCATLIALGWDPYSATLAA 65 Query: 66 MLSGALAGFLTGLLYTKGKNPTLLAGILVMTSCNSIMLMVMGRANLGLHDHKRIQDCLPF 125- +GALAG TGLL K K+ LLA IL+M + SI L +MG+ N+ L + L Sbjct: 66 TAAGALAGLATGLLNVKLKIMDLLASILMMIALYSINLRIMGKPNVPLIAEPTLFTLLQP 125- Query: 126 SIDLNSLLTGLITVVIVIS---VLIYFLYTNLGQAYIATGDNKDMAKSFGINTDWMEVMG 18- 2 + + L+ V IVI+ +L +F T G A ATG N MA++ G+NT M ++G Sbjct: 126 EWLSDYVFRPLLLVFIVIAAKLLLDWFFTTQKGLAIRATGSNPRMARAQGVNTGGMILLG 18- 5 Query: 183 LVVSNSLIALSGALVSQQDGYADVSKGIGVIVIGLASIIVGEVLYSTGLTLLERLIAIVI 24- 2 + +SN+L+AL+GAL +Q G AD+S GIG IVIGLA++IVGE + + +L L A+++ Sbjct: 186 MAISNALVALAGALFAQTQGGADISMGIGTIVIGLAAVIVGESILPSRRLILATL-AVIL 24- 4 Query: 243 GSILYQFLISVVIT---LGFNTSYLKLISALVLALCLMIPVVKER 284 G+I+Y+F I++ + +G L L++A+++ + L+IP++K+R Sbjct: 245 GAIVYRFFIALALNSDFIGLQAQDLNLVTAVLVTVALVIPMMKKR 289 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-02617 Identities = 227/287 (79%), Positives = 259/287 (90%) Query: 1 MIISSVSQGLLWGILGLGIYLTFRILKFPDMTTEGSFPLGGAVCVTLMNQGVNPILATIL 60 MIISSVSQGL+WG+LGLGIYLTFRIL FPDMTTEGSFPLGGAV VT ++ G NP L+T+L Sbjct: 5 MIISSVSQGLIWGVLGLGIYLTFRILNFPDMTTEGSFPLGGAVAVTAISLGWNPFLSTLL 64 Query: 61 GMLSGMLAGFVTGLLYTKGKIPTILAGILVMTSCHSIMLMVMKRANLGLNEIQTLKDFLP 120- GMLSG LAGF+TGLLYTKGK+PT+LAGILVMTSC+SIMLMVM RANLGL++ + ++D LP Sbjct: 65 GMLSGALAGFLTGLLYTKGKMPTLLAGILVMTSCNSIMLMVMGRANLGLHDHKRIQDCLP 124- Query: 121 FSNDLNLLVLGLIAILLVISALIYFLYTRLGQAYIATGDNPDMAKSFGIDTDKMEMLGLI 18- 0 FS DLN L+ GLI +++VIS LIYFLYT LGQAYIATGDN DMAKSFGI+TD ME++GL+ Sbjct: 125 FSIDLNSLLTGLITVVIVISVLIYFLYTNLGQAYIATGDNKDMAKSFGINTDWMEVMGLV 18- 4 Query: 181 VSNGLIALSGALVSQQDGYADVSKGIGVIVIGLASIIIGEVLYSTGLTLFERLIAIVVGS 24- 0 VSN LIALSGALVSQQDGYADVSKGIGVIVIGLASII+GEVLYSTGLTL ERLIAIV+GS Sbjct: 185 VSNSLIALSGALVSQQDGYADVSKGIGVIVIGLASIIVGEVLYSTGLTLLERLIAIVIGS 24- 4 Query: 241 ILYQFLITAVIALGFNTNYLKLFSAIVLGICLMVPVLKTKILKGVRL 287 ILYQFLI+ VI LGFNT+YLKL SA+VL +CLM+PV+K + KGVRL Sbjct: 245 ILYQFLISVVITLGFNTSYLKLISALVLALCLMIPVVKERFFKGVRL 291 A related GBS gene <SEQ ID 8681> and protein <SEQ ID 8682> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02618 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: 4.24 GvH: Signal Score (-7.5): -6.43 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 8 value: -15.12 threshold: 0.0 INTEGRAL Likelihood = -15.12 Transmernbrane 127-143 (119-151) INTEGRAL Likelihood = -7.54 Transmembrane 206-222 (201-225) INTEGRAL Likelihood = -6.48 Tranamembrane 260-276 (258-282) INTEGRAL Likelihood = -5.84 Transmembrane 234-250 (231-257) INTEGRAL Likelihood = -4.78 Transmembrane 55-71 (54-72) INTEGRAL Likelihood = -3.61 Transmembrane 177-193 (176-194) INTEGRAL Likelihood = -3.35 Transmembrane 84-100 (83-102) INTEGRAL Likelihood = -1.91 Transmembrame 10-26 (10-26) PERIPHERAL Likelihood = 4.77 36 modified ALOM score: 3.52 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.7050 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00063## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 894 A DNA sequence (GBSx0948) was identified in S. agalactiae <SEQ ID 2717> which encodes the amino acid sequence <SEQ ID 2718>. This protein is predicted to be ABC transporter (potA). Analysis of this protein sequence reveals the following: TABLE-US-02619 Possible Site: 36 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty= 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9887> which encodes amino acid sequence <SEQ ID 9888> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02620 >GP: AAF86640 GB: AF162694 ABC transporter [Enterococcus gallinarum] Identities = 117/252 (46%), Positives = 167/252 (65%) Query: 19 MVMKIIELKEATVQVSNGLAEMKTILDHVNLSIYEHDFITILGGNGAGKSTLFNVIAGTL 78 - M ++ + + G +L ++L++ DFITI+GGNGAGKSTL N IAGT+ Sbjct: 1 MTTPVLTISDLHQTFEKGTINENHVLRGIDLTMNSGDFITIIGGNGAGKSTLLNSIAGTI 60 Query: 79 MLSSGNIYIMGQDVTNLSAEKRAKYLSRVFQDPKMGTAPRMTVAENLLVAKFRGEKRPLV 138- G I + +++T S +R+K +SRVFQDP+MGTA R+TV ENL +A RG+ R Sbjct: 61 PTEQGKIVLGDKEITRHSVTRRSKEISRVFQDPRMGTAVRLTVEENLALAYKRGQVRGFS 120- Query: 139 PRKIINYTEEFQKLIARTGNGLDRHLETPTGLLSGGQRQALSLLMATLKKPNLLLLDEHT 19- 8 + F++ +AR GL+ L T GLLSGGQRQA++LLMATL++P L+LLDEHT Sbjct: 121 SGVKGKHRAFFKEKLARLNLGLENRLTTEIGLLSGGQRQAITLLMATLQQPKLILLDEHT 18- 0 Query: 199 AALDPRTSVSLMGLTDEFIKQDSLTALMITHHMEDALKYGNRVLVMKDGKIVRDLNQAQR 25- 8 AALDP+TS+++M LTD+ I++ LTA M+TH MEDA++YGNR++++ GKIV D+ +K Sbjct: 181 AALDPKTSMTVMALTDQLIQEQQLTAFMVTHDMEDAIRYGNRLIMLHQGKIVVDITGEEK 24- 0 Query: 259 NKMAIADYYQLF 270 + + D LF Sbjct: 241 QSLTVPDLMALF 252 A related DNA sequence was identified in S. pyogenes <SEQ ID 2719> which encodes the amino acid sequence <SEQ ID 2720>. Analysis of this protein sequence reveals the following: TABLE-US-02621 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2249 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02622 Identities = 186/250 (74%), Positives = 210/250 (83%) Query: 22 KIIELKEATVQVSNGLAEMKTILDHVNLSIYEHDFITILGGNGAGKSTLFNVIAGTLMLS 81 - KIIEL ATV V NG + KTILD+V L+IYEHDF+TILGGNGAGKSTLFNVIAGTL L+ Sbjct: 3 KIIELINATVDVDNGFEDAKTILDNVTLTIYEHDFLTILGGNGAGKSTLFNVIAGTLSLT 62 Query: 82 SGNIYIMGQDVTNLSAEKRAKYLSRVFQDPKMGTAPRMTVAENLLVAKFRGEKRPLVPRK 141- G I I+GQDVT+ AEKRA YLSRVFQD KMGTAPRMTVAENLL+A+ RG KR L RK Sbjct: 63 RGQIRILGQDVTHWPAEKRALYLSRVFQDSKMGTAPRMTVAENLLIARQRGGKRSLASRK 122- Query: 142 IINYTEEFQKLIARTGNGLDRHLETPTGLLSGGQRQALSLLMATLKKPNLLLLDEHTAAL 20- 1 I + F+ L+ RTGNGL++HLETP GLLSGGQRQALSLLMATLKKP LLLLDEHTAAL Sbjct: 123 ITEHLASFEDLVKRTGNGLEKHLETPAGLLSGGQRQALSLLMATLKKPALLLLDEHTAAL 18- 2 Query: 202 DPRTSVSLMGLTDEFIKQDSLTALMITHHMEDALKYGNRVLVMKDGKIVRDLNQAQKNKM 26- 1 DP+TS SLM LTDEF+ +D LTALMITHHMEDAL YGNR++VMKDG I++DLNQ +K ++ Sbjct: 183 DPKTSQSLMQLTDEFVTKDGLTALMITHHMEDALTYGNRLIVMKDGNIIKDLNQMEKEQL 24- 2 Query: 262 AIADYYQLFD 271 I DYYQLFD Sbjct: 243 TITDYYQLFD 252 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 895 A DNA sequence (GBSx0949) was identified in S. agalactiae <SEQ ID 2721> which encodes the amino acid sequence <SEQ ID 2722>. Analysis of this protein sequence reveals the following: TABLE-US-02623 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1930 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 415-417 The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02624 >GP: BAB06117 GB: AP001515 unknown conserved protein [Bacillus halodurans] Identities = 236/549 (42%), Positives = 362/549 (64%), Gaps = 2/549 (0%) Query: 4 IKIMALGGVRENGKNLYVVEVNDSIFVLDAGLKYPENEQLGVDVVIPNLDYLIENKKRVQ 63 I++ ALGGV E GKN+YVVEV+D +FV+DAGL +P++E LGVDVVIP++ YL+EN++RV+ Sbjct: 9 IRVFALGGVGEIGKNMYVVEVDDDLFVIDAGLMFPDDEMLGVDVVIPDISYLVENEERVR 68 Query: 64 GIFLTHGHADAIGALPYIIAEVKAPVFGSPLTIELAKLFVKNSTAVKKFNNFHVIDSETE 123- I LTHGH D IG LPY++ ++ PV+G+ LT+ L + +K + ++ +IDS + Sbjct: 69 AILLTHGHEDHIGGLPYVLQKLNVPVYGTKLTLGLVEEKLKEAGLIRSAK-LKLIDSNSR 127- Query: 124 IEFQDAVISFFKTTHSIPESMGIVIGTKEGNIVYTGDFKFDQAARKYYQTDLARLAEIGR 18- 3 ++ +SFF+T HSIP+S+GI I T +G IV+TGDFKFDQ Q ++ ++A IG Sbjct: 128 LKLGSTPVSFFRTNHSIPDSVGICIQTSQGFIVHTGDFKFDQTPVDGKQAEIGKMAAIGH 18- 7 Query: 184 DGVLALLSDSANATSNEQVASEYEVGDEIKSVIEDAEGRVIVAAVASNLIRIQQVFDAAA 24- 3 GVL LLSDS NA SE EVG I E +GR+IV ASN+ R+QQV AA Sbjct: 188 KGVLCLLSDSTNAERPGMTKSETEVGRGIAEAFEQTKGRIIVTTFASNVHRVQQVIHAAI 24- 7 Query: 244 ENGRRVVLTGFDIENIVRTAIRMKRIHIADENMIIKPKDMTRYEDNELLILETGRMGEPI 30- 3 R++ + G + +V A R+ + D+ + I +++++Y+D + I+ TG GEP+ Sbjct: 248 ATNRKLAVAGRSMVKVVSIAERLGYLEAPDD-LFIDIEEVSKYDDERVAIITTGSQGEPM 30- 6 Query: 304 NGLQKMAIGRHRYVQIKDGDLVFIVTTPSIAKEAVVARVENLIYKAGGSVKLITQNLRVS 36- 3 + L +MA G HR + I + D V I TP E V+ + +L+++ G V + S Sbjct: 307 SALSRMAKGAHRQITITENDTVIIAATPIPGNERSVSTIVDLLHRIGADVIFGHGKVHAS 36- 6 Query: 364 GHANGRELQLLMNLLKPKYLFPIQGEYRDLSAHAGLAQEVGMSADDIYIVKRGDIMVLEK 42- 3 GH + EL+L++NL++PK+ PI GE+R AH LA+ VG+ + I++V +G+++ Sbjct: 367 GNGSAEELKLMLNLMRPKFFVPIHGEFRMQHAHKELAKSVGIREEAIFLVDKGEVVEFRN 42- 6 Query: 424 DGFFHSGSVPAGDVMIDGNAIGDVGNIVLRDRKVLSEDGIFIVVITVSKKEKKIISKARV 48- 3 +G VP+G+V+IDG +GDVGNIVLRDR++LS+DGI +VV+T++K+ I+S + Sbjct: 427 GQGRKAGKVPSGNVLIDGLGVGDVGNIVLRDRRLLSKDGILVVVVTLNKQSGTILSGPNI 48- 6 Query: 484 NTRGFVYVKKSRDILRESAELVNTTVEDYLSKDTFDWGELKGKVRDEVSKFLFDQTKRRP 54- 3 +RGFVYV++S ++ E+ ELV T++ ++++ +W LK VR+ +S+FLF++TKRRP Sbjct: 487 ISRGFVYVRESEKLIEEANELVTETLKKCVTENVNEWSSLKSNVREVLSRFLFEKTKRRP 54- 6 Query: 544 AILPVVMEV 552 ILP++MEV Sbjct: 547 MILPIIMEV 555 A related DNA sequence was identified in S. pyogenes <SEQ ID 2723> which encodes the amino acid sequence <SEQ ID 2724>. Analysis of this protein sequence reveals the following: TABLE-US-02625 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2204 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02626 >GP: BAB06117 GB: AP001515 unknown conserved protein [Bacillus halodurans] Identities = 232/549 (42%), Positives = 360/549 (65%), Gaps = 2/549 (0%) Query: 4 IKMIALGGVREYGKNFYLVEINDSMFILDAGLKYPENEQLGVDLVIPNLDYVIENKGKVQ 63 - I++ ALGGV E GKN Y+VE++D +F++DAGL +P++E LGVD+VIP++ Y++EN+ +V+ Sbjct: 9 IRVFALGGVGEIGKNMYVVEVDDDLFVIDAGLMFPDDEMLGVDVVIPDISYLVENEERVR 68 Query: 64 GIFLSHGHADAIGALPYLLAEVSAPVFGSELTIELAKLFVKSNNSTKKFNNFHVVDSDTE 123- I L+HGH D IG LPY+L +++ PV+G++LT+ L + +K + ++DS++ Sbjct: 69 AILLTHGHEDHIGGLPYVLQKLNVPVYGTKLTLGLVEEKLKEAGLIRSAK-LKLIDSNSR 127- Query: 124 IEFKDGLVSFFRTTHSIPESMGIVIGTDKGNIIYTGDFKFDQAAREGYQTDLLRLAEIGK 18- 3 ++ VSFFRT HSIP+S+GI I T +G I++TGDFKFDQ +G Q ++ ++A IG Sbjct: 128 LKLGSTPVSFFRTNHSIPDSVGICIQTSQGFIVHTGDFKFDQTPVDGKQAEIGKMAAIGH 18- 7 Query: 184 EGVLALLSDSVNATSNDQIASESEVGEEMDSVISDADGRVIVAAVASNLVRIQQVFDSAT 24- 3 +GVL LLSDS NA SE+EVG + GR+IV ASN+ R+QQV +A Sbjct: 188 KGVLCLLSDSTNAERPGMTKSETEVGRGIAEAFEQTKGRIIVTTFASNVHRVQQVIHAAI 24- 7 Query: 244 AHGRRVVLTGTDAENIVRTALRLEKLMITDERLLIKPKDMSKFEDHELIILEAGRMGEPI 30- 3 A R++ + G +V A RL L D+ L I +++SK++D + I+ G GEP+ Sbjct: 248 ATNRKLAVAGRSMVKVVSIAERLGYLEAPDD-LFIDIEEVSKYDDERVAIITTGSQGEPM 30- 6 Query: 304 NSLQKMAAGRHRYVQIKEGDLVYIVTTPSTAKEAMVARVENLIYKAGGSVKLITQNLRVS 36- 3 ++L +MA G HR + I E D V I TP E V+ + +L+++ G V + S Sbjct: 307 SALSRMAKGAHRQITITENDTVIIAATPIPGNERSVSTIVDLLHRIGADVIFGHGKVHAS 36- 6 Query: 364 GHANGRDLQLLMNLLKPQYLFPVQGEYRDLAAHAKLAEEVGIFPENIHILKRGDIMVLND 42- 3 GH + +L+L++NL++P++ P+ GE+R AH +LA+ VGI E I ++ +G+++ + Sbjct: 367 GHGSAEELKLMLNLMRPKFFVPIHGEFRMQHAHKELAKSVGIREEAIFLVDKGEVVEFRN 42- 6 Query: 424 EGFLHEGGVPASDVMIDGNAIGDVGNIVLRDRKVLSEDGIFIVAITVSKKEKRIISKAKV 48- 3 G VP+ +V+IDG +GDVGNIVLRDR++LS+DGI +V +T++K+ I+S + Sbjct: 427 GQGRKAGKVPSGNVLIDGLGVGDVGNIVLRDRRLLSKDGILVVVVTLNKQSGTILSGPNI 48- 6 Query: 484 NTRGFVYVKKSHDILRESAELVNTTVGNYLKKDTFDWGELKGNVRDDLSKFLFEQTKRRP 54- 3 +RGFVYV++S ++ E+ ELV T+ + ++ +W LK NVR+ LS+FLFE+TKRRP Sbjct: 487 ISRGFVYVRESEKLIEEANELVTETLKKCVTENVNEWSSLKSNVREVLSRFLFEKTKRRP 54- 6 Query: 544 AILPVVMEV 552 ILP++MEV Sbjct: 547 MILPIIMEV 555 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02627 Identities = 446/553 (80%), Positives = 513/553 (92%) Query: 1 MSDIKIMALGGVRENGKNLYVVEVNDSIFVLDAGLKYPENEQLGVDVVIPNLDYLIENKK 60 M+DIK++ALGGVRE GKN Y+VE+NDS+F+LDAGLKYPENEQLGVD+VIPNLDY+IENK Sbjct: 1 MTDIKMIALGGVREYGKNFYLVEINDSMFILDAGLKYPENEQLGVDLVIPNLDYVIENKG 60 Query: 61 RVQGIFLTHGHADAIGALPYIIAEVKAPVFGSPLTIELAKLFVKNSTAVKKFNNFHVIDS 120- +VQGIFL+HGHADAIGALPY++AEV APVFGS LTIELAKLFVK++ + KKFNNFHV+DS Sbjct: 61 KVQGIFLSHGHADAIGALPYLLAEVSAPVFGSELTIELAKLFVKSNNSTKKFNNFHVVDS 120- Query: 121 ETEIEFQDAVISFFKTTHSIPESMGIVIGTKEGNIVYTGDFKFDQAARKYYQTDLARLAE 18- 0 +TEIEF+D ++SFF+TTHSIPESMGIVIGT +GNI+YTGDFKFDQAAR+ YQTDL RLAE Sbjct: 121 DTEIEFKDGLVSFFRTTHSIPESMGIVIGTDKGNIIYTGDFKFDQAAREGYQTDLLRLAE 18- 0 Query: 181 IGRDGVLALLSDSANATSNEQVASEYEVGDEIKSVIEDAEGRVIVAAVASNLIRIQQVFD 24- 0 IG++GVLALLSDS NATSN+Q+ASE EVG+E+ SVI DA+GRVIVAAVASNL+RIQQVFD Sbjct: 181 IGKEGVLALLSDSVNATSNDQIASESEVGEEMDSVISDADGRVIVAAVASNLVRIQQVFD 24- 0 Query: 241 AAAENGRRVVLTGFDIENIVRTAIRMKRIHIADENMIIKPKDMTRYEDNELLILETGRMG 30- 0 +A +GRRVVLTG D ENIVRTA+R++++ I DE ++IKPKDM+++ED+EL+ILE GRMG Sbjct: 241 SATAHGRRVVLTGTDAENIVRTALRLEKLMITDERLLIKPKDMSKFEDHELIILEAGRMG 30- 0 Query: 301 EPINGLQKMAIGRHRYVQIKDGDLVFIVTTPSIAKEAVVARVENLIYKAGGSVKLITQNL 36- 0 EPIN LQKMA GRHRYVQIK+GDLV+IVTTPS AKEA+VARVENLIYKAGGSVKLITQNL Sbjct: 301 EPINSLQKMAAGRHRYVQIKEGDLVYIVTTPSTAKEAMVARVENLIYKAGGSVKLITQNL 36- 0 Query: 361 RVSGHANGRELQLLMNLLKPKYLFPIQGEYRDLSAHAGLAQEVGMSADDIYIVKRGDIMV 42- 0 RVSGHANGR+LQLLMNLLKP+YLFP+QGEYRDL+AHA LA+EVG+ ++I+I+KRGDIMV Sbjct: 361 RVSGHANGRDLQLLMNLLKPQYLFPVQGEYRDLAAHAKLAEEVGIFPENIHILKRGDIMV 42- 0 Query: 421 LEKDGFFHSGSVPAGDVMIDGNAIGDVGNIVLRDRKVLSEDGIFIVVITVSKKEKKIISK 48- 0 L +GF H G VPA DVMIDGNAIGDVGNIVLRDRKVLSEDGIFIV ITVSKKEK+IISK Sbjct: 421 LNDEGFLHEGGVPASDVMIDGNAIGDVGNIVLRDRKVLSEDGIFIVAITVSKKEKRIISK 48- 0 Query: 481 ARVNTRGFVYVKKSRDILRESAELVNTTVEDYLSKDTFDWGELKGKVRDEVSKFLFDQTK 54- 0 A+VNTRGFVYVKKS DILRESAELVNTTV +YL KDTFDWGELKG VRD++SKFLF+QTK Sbjct: 481 AKVNTRGFVYVKKSHDILRESAELVNTTVGNYLKKDTFDWGELKGNVRDDLSKFLFEQTK 54- 0 Query: 541 RRPAILPVVMEVR 553 RRPAILPVVMEVR Sbjct: 541 RRPAILPVVMEVR 553 There is also homology to SEQ ID 4910. SEQ ID 2722 (GBS295) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 48 (lane 2; MW 89.4 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 167 (lane 9 & 11; MW 79 kDa--thioredoxin fusion) and in FIG. 238 (lane 3; MW 79 kDa--thioredoxin fusion). Purified Thio-GBS295-His is shown in FIG. 244, lane 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 896 A DNA sequence (GBSx0950) was identified in S. agalactiae <SEQ ID 2725> which encodes the amino acid sequence <SEQ ID 2726>. This protein is predicted to be tributyrin esterase. Analysis of this protein sequence reveals the following: TABLE-US-02628 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9885> which encodes amino acid sequence <SEQ ID 9886> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02629 >GP: AAF62859 GB: AF157484 tributyrin esterase [Lactococcus lactis subsp. lactis] Identities = 154/262 (58%), Positives = 188/262 (70%), Gaps = 4/262 (1%) Query: 21 MAFFNIEYHSKVLGTERQVNVIYPDAFEMSDDKIDDCDIPVLYLLHGMGGNENSWQKRTN 80 - MA NIEY+S+VLG R+VNVIYP++ ++ D DIPVLYLLHGM GNENSW R+ Sbjct: 1 MAVINIEYYSEVLGMNRKVNVIYPESSKVED--FTQTDIPVLYLLHGMSGNENSWIIRSG 58 Query: 81 IERLLRHTNLIVVMPSTDLAWYTNTKYGLDYFDAIAIELPKVLKRFFPNMSDKREKNFIA 140- IERL+RHTNL +VMPSTDL+Y NT YG++YFDAIA ELPKV+ FFPN+S KREKNFIA Sbjct: 59 IERLIRHTNLAIVMPSTDLGFYVNTTYGMNYFDAIAHELPKVINNFFPNLSTKREKNFIA 118- Query: 141 GLSMGGYGAYKIALLTNRFSHAASLSGALSFDFDLLFNNGNNNINYWSGIFGDLNNTDNI 20- 0 GLSMGGYGAY++AL T+ FS+AASLSG L+FD + N N YW GIFG+ Sbjct: 119 GLSMGGYGAYRLALGTDYFSYAASLSGVLTFDG--MEENFKENPAYWGGIFGNWETFKGS 17- 6 Query: 201 ERHSLRRYVESFDMKTKFYAWCGYEDFLFEANEVAIDELRQLGLTIDYFNDHGKHEWYYW 26- 0 + L + K K YAWCG +DFLF NE A EL++LG I Y + G HEWYYW Sbjct: 177 DNEILSLADRKQENKPKLYAWCGKQDFLFPGNEYATAELKKLGFDITYESSDGVHEWYYW 23- 6 Query: 261 NQQLEKVLEWLPVDYVKEERLS 282 Q++E VL+WLP++Y +EERLS Sbjct: 237 TQKIESVLKWLPINYKQEERLS 258 A related DNA sequence was identified in S. pyogenes <SEQ ID 2727> which encodes the amino acid sequence <SEQ ID 2728>. Analysis of this protein sequence reveals the following:

TABLE-US-02630 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2183 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02631 Identities = 172/262 (65%), Positives = 199/262 (75%), Gaps = 1/262 (0%) Query: 21 MAFFNIEYHSKVLGTERQVNVIYPDAFEMSDDKIDDCDIPVLYLLHGMGGNENSWQKRTN 80 - MA IEYHS VLG ER+VNVIYPD E+ D DIPVLYLLHGMGGNENSWQKRT Sbjct: 1 MASIAIEYHSVVLGMERKVNVIYPDQSEIPKKDQGDKDIPVLYLLHGMGGNENSWQKRTA 60 Query: 81 IERLLRHTNLIVVMPSTDLAWYTNTKYGLDYFDAIAIELPKVLKRFFPNMSDKREKNFIA 140- IERLLRHTNLIVVMPSTDL WYT+T YGL+Y+ A++ ELP+VL FFPNM+ KREK F+A Sbjct: 61 IERLLRHTNLIVVMPSTDLGWYTDTAYGLNYYRALSQELPQVLAAFFPNMTQKREKTFVA 120- Query: 141 GLSMGGYGAYKIALLTNRFSHAASLSGALSFDFDLLFNNGNNNINYWSGIFGDLNNTDNI 20- 0 GLSMGGYGA+K AL +NRFS+AAS SGAL F + L + YW G+FG ++ D + Sbjct: 121 GLSMGGYGAFKWALKSNRFSYAASFSGALDFSPETLLEGKLGELAYWQGVFGQFDDPD-L 17- 9 Query: 201 ERHSLRRYVESFDMKTKFYAWCGYEDFLFEANEVAIDELRQLGLTIDYFNDHGKHEWYYW 26- 0 ++H L+ V D KTKFYAWCGYEDFLF NE AI + + GL IDY HGKHEWYYW Sbjct: 180 DKHYLKNMVAESDGKTKFYAWCGYEDFLFATNEKAIADFQAQGLDIDYHKGHGKHEWYYW 23- 9 Query: 261 NQQLEKVLEWLPVDYVKEERLS 282 NQQLE +LEWLP++Y KEERLS Sbjct: 240 NQQLEVLLEWLPINYQKEERLS 261 SEQ ID 2726 (GBS645) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 129 (lanes 8 & 10; MW 60 kDa+lane 9; MW 27 kDa) and in FIG. 186 (lane 4; MW 60 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 129 (lane 12; MW 34.7 kDa), in FIG. 140 (lane 8; MW 35 kDa) and in FIG. 178 (lane 4; MW 35 kDa). Purified GBS645-GST is shown in FIG. 236, lane 11; purified GBS645-His is shown in FIG. 229, lanes 34. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 897 A DNA sequence (GBSx0951) was identified in S. agalactiae <SEQ ID 2729> which encodes the amino acid sequence <SEQ ID 2730>. Analysis of this protein sequence reveals the following: TABLE-US-02632 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.34 Transmembrane 22-38 (18-46) ----- Final Results ----- bacterial membrane --- Certainty = 0.4736 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no-significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2731> which encodes the amino acid sequence <SEQ ID 2732>. Analysis of this protein sequence reveals the following: TABLE-US-02633 Possible site: 52 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.43 Transmembrane 25-41 (20-46) INTEGRAL Likelihood = -2.71 Transmembrane 4-20 (3-20) ----- Final Results ----- bacterial membrane --- Certainty = 0.3972 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-02634 Identities = 31/87 (35%), positives = 50/87 (56%), Gaps = 2/87 (2%) Query: 1 MRTLFRMIFAIPKFIFRLIWNIIWGIFKTVLVIAIILFGLYYYANHSQSEFANQLSDIIQ 60 M+ L +I +PK I ++ W++I G +T+L++ II+ GL YY+NHS S AN++S I Sbjct: 1 MKQLLAIILWLPKLIVKMFWHLIKGFLQTILLVTIIIIGLMYYSNHSDSVLANKIS--IV 58 Query: 61 TGKTFLNFADTNQLKNSFTNLATDNVH 87 T + F Q ++ T + N H Sbjct: 59 TEQVVQIFDILTQKPSAKTRHGSGNSH 85 SEQ ID 2730 (GBS220d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 155 (lane 11-13; MW 50 kDa) and in FIG. 239 (lane 12; MW 50 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 155 (lane 14-16; MW 25.2 kDa) and in FIG. 184 (lane 7; MW 25 kDa). Purified GBS220d-GST is shown in FIG. 246, lanes 3 & 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 898 A DNA sequence (GBSx0953) was identified in S. agalactiae <SEQ ID 2733> which encodes the amino acid sequence <SEQ ID 2734>. This protein is predicted to be unnamed protein product (rpiA). Analysis of this protein sequence reveals the following: TABLE-US-02635 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2538 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02636 >GP: CAB69583 GB: A93589 unnamed protein product [Spinacia oleracea] Identities = 114/232 (49%), Positives = 147/232 (63%), Gaps = 11/232 (4%) Query: 2 DELKKLAGVTAAKYVKNGMIVGLGTGSTAYFFVEEIGRRVKEEGL-QVVGVTTSNRTTEQ 60 D+LKKLA A VK+GM++GLGTGSTA F V IG + L +VG+ TS RT EQ Sbjct: 59 DDLKKLAAEKAVDSVKSGMVLGLGTGSTAAFAVSRIGELLSAGKLTNIVGIPTSKRTAEQ 118- Query: 61 ARGLGIPLKSADDIDVIDVTVDGADEVDPDFNGIKGGGGALLMEKIVATPTKEYIWVVDE 120- A LGIPL DD ID+ +DGADEVDPD N +KG GGALL EK+V + ++I VVD+ Sbjct: 119 AASLGIPLSVLDDHPRIDLAIDGADEVDPDLNLVKGRGGALLREKMVEAASDKFIVVVDD 17- 8 Query: 121 SKLVETLGAFKL--PVEVV----RYGSERLFRVFKSKGYCPSFRETEGDR--FITDMGNY 17- 2 +KLV+ LG +L PVEVV +Y +RL +FK G C + EGD ++TD NY Sbjct: 179 TKLVDGLGGSRLAMPVEVVQFCWKYNLKRLQEIFKELG-CEAKLRMEGDSSPYVTDNSNY 23- 7 Query: 173 IIDLDL-KKIEDPKQLANELDHTVGVVEHGLFNGMVNKVIVAGKNGLDILEK 223 I+DL I+D + E+ GVVEHGLF GM ++VI+AGK G+ + K Sbjct: 238 IVDLYFPTSIKDAEAAGREISALEGVVEHGLFLGMASEVIIAGKTGVSVKTK 289 A related DNA sequence was identified in S. pyogenes <SEQ ID 2735> which encodes the amino acid sequence <SEQ ID 2736>. Analysis of this protein sequence reveals the following: TABLE-US-02637 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1646 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02638 Identities = 166/222 (74%) , Positives = 190/222 (84%) Query: 1 MDELKKLAGVTAAKYVKNGMIVGLGTGSTAYFFVEEIGRRVKEEGLQVVGVTTSNRTTEQ 60 M+ LKK+AGVTAA+YV +GM +GLGTGSTAY+FVEEIGRRVK+EGLQVVGVTTS+ T++Q Sbjct: 1 MEALKKIAGVTAAQYVTDGMTIGLGTGSTAYYFVEEIGRRVKQEGLQVVGVTTSSVTSKQ 60 Query: 61 ARGLGIPLKSADDIDVIDVTVDGADEVDPDFNGIKGGGGALLMEKIVATPTKEYIWVVDE 120- A LGIPLKS DDID ID+TVDGADEVD +FNGIKGGG ALLMEKIVATPTKEYIWVVD Sbjct: 61 AEVLGIPLKSIDDIDSIDLTVDGADEVDKNFNGIKGGGAALLMEKIVATPTKEYIWVVDA 120- Query: 121 SKLVETLGAFKLPVEVVRYGSERLFRVFKSKGYCPSFRETEGDRFITDMGNYIIDLDLKK 18- 0 SK+VE LGAFKLPVEVV+YG++RLFRVF+ GY PSFR R +TDM NYIIDLDL Sbjct: 121 SKMVEHLGAFKLPVEVVQYGADRLFRVFEKAGYKPSFRMKGDSRLVTDMQNYIIDLDLGC 18- 0 Query: 181 IEDPKQLANELDHTVGVVEHGLFNGMVNKVIVAGKNGLDILE 222 I+DP + LD TVGVVEHGLFNGMV+KVIVA K+G+ +LE Sbjct: 181 IKDPVAFGHLLDGTVGVVEHGLFNGMVDKVIVASKDGVTVLE 222 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 899 A DNA sequence (GBSx0954) was identified in S. agalactiae <SEQ ID 2737> which encodes the amino acid sequence <SEQ ID 2738>. This protein is predicted to be phosphopentomutase (deoB). Analysis of this protein sequence reveals the following: TABLE-US-02639 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0546 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02640 >GP: AAC45496 GB: U80410 phosphopentomutase [Lactococcus lactis subsp. cremoris] Identities = 275/408 (67%), Positives = 325/408 (79%), Gaps = 7/408 (1%) Query: 3 QFDRIHLVVLDSVGIGAAPDANDFVNAGVP------DGASDTLGHISKTVGLAVPNMAKI 56 +F RIHLVV+DSVGIGAAPDA+ F N V D SDT+GHIS+ GL VPN+ K+ Sbjct: 4 KFGRIHLVVMDSVGIGAAPDADKFFNHDVETHEAINDVKSDTIGHISEIRGLDVPNLQKL 63 Query: 57 GLGNIPRPQALKTVPAEENPSGYATKLQEVSLGKDTMTGHWEIMGLNITEPFDTFWNGFP 116- G GNIPR LKT+PA + P+ Y TKL+E+S GKDTMTGHWEIMGLNI PF T+ G+P Sbjct: 64 GWGNIPRESPLKTIPAAQKPAAYVTKLEEISKGKDTMTGHWEIMGLNIQTPFPTYPEGYP 123- Query: 117 EDIITKIEDFSGRKVIREANKPYSGTAVIDDFGPRQMETGELIIYTSADPVLQIAAHEDI 17- 6 ED++ KIE+FSGRK+IREANKPYSGTAVI+DFGPRQ+ETGELIIYTSADPVLQIAAHED+ Sbjct: 124 EDLLEKIEEFSGRKIIREANKPYSGTAVIEDFGPRQLETGELIIYTSADPVLQIAAHEDV 18- 3 Query: 177 IPLEELYRICEYARSITMERPALL-GRIIARPYVGEPGNFTRTANRHDYAVSPFEDTVLN 23- 5 I EELY+ICEY RSIT+E ++ GRIIARPYVGE GNF RT R DYA+SPF +TVL Sbjct: 184 ISREELYKICEYVRSITLEGSGIMIGRIIARPYVGEAGNFERTDGRRDYALSPFAETVLE 24- 3 Query: 236 KLDQAGIDTYAVGKINDIFNGSGINHDMGHNKSNSHGIDTLIKTMGLSEFEKGFSFTNLV 29- 5 KL +AGIDTY+VGKI+DIFN G+ +DMGHN ++ G+D L+K M +EF +GFSFTNLV Sbjct: 244 KLYKAGIDTYSVGKISDIFNTVGVKYDMGHNHNDMDGVDRLLKAMTKTEFTEGFSFTNLV 30- 3 Query: 296 DFDALYGHRRDPHGYRDCLHEFDERLPEIISAMRDKDLLLITADHGNDPTYAGTDHTREY 35- 5 DFDA YGHRRD GY + +FD RLPEII AM++ DLL+ITADHGNDP+Y GTDHTREY Sbjct: 304 DFDAKYGHRRDVEGYGKAIEDFDGRLPEIIDAMKEDDLLMITADHGNDPSYVGTDHTREY 36- 3 Query: 356 IPLLAYSPSFTGNGLIPVGHFADISATVADNFGVDTAMIGESFLQDLV 403 IPL+ +S SF ++PVGHFADISAT+A+NF V A GESFL LV Sbjct: 364 IPLVIFSKSFKEPKVLPVGHFADISATIAENFSVKKAQTGESFLDALV 411 A related DNA sequence was identified in S. pyogenes <SEQ ID 2739> which encodes the amino acid sequence <SEQ ID 2740>. Analysis of this protein sequence reveals the following: TABLE-US-02641 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0185(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02642 Identities = 348/402 (86%), Positives = 374/402 (92%) Query: 1 MSQFDRIHLVVLDSVGIGAAPDANDFVNAGVPDGASDTLGHISKTVGLAVPNMAKIGLGN 60 MS+F+RIHLVVLDSVGIGAAPDA+ F NAGV D SDTLGHIS+ GL+VPNMAKIGLGN Sbjct: 1 MSKFNRIHLVVLDSVGIGAAPDADKFFNAGVADTDSDTLGHISEAAGLSVPNMAKIGLGN 60 Query: 61 IPRPQALKTVPAEENPSGYATKLQEVSLGKDTMTGHWEIMGLNITEPFDTFWNGFPEDII 120- I RP LKTVP E+NP+GY TKL+EVSLGKDTMTGHWEIMGLNITEPFDTFWNGFPE+I+ Sbjct: 61 ISRPIPLKTVPTEDNPTGYVTKLEEVSLGKDTMTGHWEIMGLNITEPFDTFWNGFPEEIL 120- Query: 121 TKIEDFSGRKVIREANKPYSGTAVIDDFGPRQMETGELIIYTSADPVLQIAAHEDIIPLE 18- 0 TKIE+FSGRK+IREANKPYSGTAVIDDFGPRQMETGELI+YTSADPVLQIAAHEDIIP+E Sbjct: 121 TKIEEFSGRKIIREANKPYSGTAVIDDFGPRQMETGELIVYTSADPVLQIAAHEDIIPVE 18- 0 Query: 181 ELYRICEYARSITMERPALLGRIIARPYVGEPGNFTRTANRHDYAVSPFEDTVLNKLDQA 24- 0 ELY+ICEYARSIT+ERPALLGRIIARPYVG+PGNFTRTANRHDYAVSPF+DTVLNKL A Sbjct: 181 ELYKICEYARSITLERPALLGRIIARPYVGDPGNFTRTANRHDYAVSPFQDTVLNKLADA 24- 0 Query: 241 GIDTYAVGKINDIFNGSGINHDMGHNKSNSHGIDTLIKTMGLSEFEKGFSFTNLVDFDAL 30- 0 G+ TYAVGKINDIFNGSGI +DMGHNKSNSHGIDTLIKT+ L EF KGFSFTNLVDFDA Sbjct: 241 GVPTYAVGKINDIFNGSGITNDMGHNKSNSHGIDTLIKTLQLPEFTKGFSFTNLVDFDAN 30- 0 Query: 301 YGHRRDPHGYRDCLHEFDERLPEIISAMRDKDLLLITADHGNDPTYAGTDHTREYIPLLA 36- 0 +GHRRDP GYRDCLHEFD RLPEII+ M++ DLLLITADHGNDPTYAGTDHTREYIPLLA Sbjct: 301 FGHRRDPEGYRDCLHEFDNRLPEIIANMKEDDLLLITADHGNDPTYAGTDHTREYIPLLA 36- 0 Query: 361 YSPSFTGNGLIPVGHFADISATVADNFGVDTAMIGESFLQDL 402 YS SFTGNGLIP GHFADISATVA+NFGVDTAMIGESFL L Sbjct: 361 YSVSFTGNGLIPQGHFADISATVAENFGVDTAMIGESFLSHL 402 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 900 A DNA sequence (GBSx0955) was identified in S. agalactiae <SEQ ID 2741> which encodes the amino acid sequence <SEQ ID 2742>. This protein is predicted to be unnamed protein product (mtaP). Analysis of this protein sequence reveals the following: TABLE-US-02643 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.44 Transmembrane 215-231 (215-231) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2743> which encodes the amino acid sequence <SEQ ID 2744>. Analysis of this protein sequence reveals the following: TABLE-US-02644 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.44 Transmembrane 215-231 (215-231) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02645 Identities = 225/269 (83%), Positives = 248/269 (91%) Query: 1 MTLLEKINETRDFLQAKGVTAPEFGLILGSGLGELAEEIENPIVVDYADIPNWGQSTVVG 60 M+L+ KINET+DFL KG+ PEFGLILGSGLGELAEE+EN IV+DYADIPNWG+STVVG Sbjct: 1 MSLMTKINETKDFLVTKGIETPEFGLILGSGLGELAEEVENAIVIDYADIPNWGKSTVVG 60 Query: 61 HAGKLVYGDLSGRKVLALQGRFHFYEGNTMEVVTFPVRIMRALACHSVLVTNAAGGIGYG 120- HAGKLVYGDL+GRKVLALQGRFHFYEGN +EVVTFPVR+M+AL C VLVTNAAGGIGYG Sbjct: 61 HAGKLVYGDLAGRKVLALQGRFHFYEGNPLEVVTFPVRVMKALGCEGVLVTNAAGGIGYG 120- Query: 121 PGTLMLIKDHINMIGTNPLIGENLEEFGPRFPDMSDAYTATYRQKAHQIAEKQNIKLEEG 18- 0 PGTLM I DHINM G NPLIGENL+EFGPRFPDMSDAYT YR KAH++AEK NIKLE+G Sbjct: 121 PGTLMAITDHINMTGNNPLIGENLDEFGPRFPDMSDAYTKVYRNKAHEVAEKMNIKLEDG 18- 0 Query: 181 VYLGVSGPTYETPAEIRAFQTMGAQAVGMSTVPEVIVAAHSGLKVLGISAITNFAAGFQS 24- 0 VY+G++GPTYETPAEIRAF+ +GA AVGMSTVPEVIVAAHSGLKVLGISAITNFAAGFQS Sbjct: 181 VYMGLTGPTYETPAEIRAFKVLGADAVGMSTVPEVIVAAHSGLKVLGISAITNFAAGFQS 24- 0 Query: 241 ELNHEEVVEVTQRIKEDFKGLVKSLVAEL 269 ELNHEEVVEVTQ IKEDFKGLVK+++AEL Sbjct: 241 ELNHEEVVEVTQHIKEDFKGLVKAILAEL 269 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 901 A DNA sequence (GBSx0956) was identified in S. agalactiae <SEQ ID 2745> which encodes the amino acid sequence <SEQ ID 2746>. Analysis of this protein sequence reveals the following: TABLE-US-02646 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.34 Transmembrane 266-282 (263-289) INTEGRAL Likelihood = -8.97 Transmembrane 231-247 (229-253) INTEGRAL Likelihood = -7.70 Transmembrane 356-372 (352-376) INTEGRAL Likelihood = -7.32 Transmembrane 303-319 (297-326) INTEGRAL Likelihood = -5.57 Transmembrane 337-353 (334-355) INTEGRAL Likelihood = -5.57 Transmembrane 391-407 (387-409) INTEGRAL Likelihood = -2.44 Transmembrane 177-193 (177-193) INTEGRAL Likelihood = -1.01 Transmembrane 159-175 (159-175) INTEGRAL Likelihood = -0.43 Transmembrane 198-214 (196-215) ----- Final Results ----- bacterial membrane --- Certainty = 0.4736(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9883> which encodes amino acid sequence <SEQ ID 9884> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02647 >GP: AAD53928 GB: AF179611 chloride channel protein [Zymomonas mobilis] Identities = 121/410 (29%), Positives = 213/410 (51%), Gaps = 19/410 (4%) Query: 14 VKFMIAVLFMTVMAGVGAILMHYVLMFTEWLAFGDSRENTLSLLN------SVTPIKRVL 67 - +++ +A L + + G+G +L+ ++L + +A+G S ++ +S + + +P++R+ Sbjct: 3 IRYGLACLAVGCLTGLGGMLLSWILHAVQHIAYGYSLQHVISEESFLKGSMAASPLRRLE 62 Query: 68 SLTLVSFLASLSWYYLQIKPKQITSIKQQVVFKDFSVKKSPYWLHIGHAFLQLIYVGTGG 127- L + W L+ + SI Q V + P+W I H LQ++ VG G Sbjct: 63 VLVFCGAVVGGGWGLLRHFGSPLVSITQAVAANK---RVMPFWTTIIHVLLQIVTVGLGS 119- Query: 128 PIGKEGAPREFGAINAGKISDLLALKVLDKRLLIISGAAAGLSAVYQVPLASVFFAFETL 18- 7 P+G+E APRE G++ + + L +R+L+ GA AG ++VY VPL+ FA E L Sbjct: 120 PLGREVAPRELGSLIGERFAFWGGLSENQRRILVACGAGAGFASVYNVPLSGALFALEAL 17- 9 Query: 188 ALGISLKNIVTLLASTFGAASIAQLVISTAPLYHISKMSLNSQSLAFMFLIVLCVTPI-- 24- 5 + + ++ L ++ +A +A +++ + +YH+ ++++ + L+ L PI Sbjct: 180 LMTWASPVVIVALLTSALSARMAWILLGNSMVYHVPAWPVDTR----LMLLALLAGPIFG 23- 5 Query: 246 --AISFRYLNQKVTERRIK-NIKILLSLPVVSLIVSVLSIVYPQILGNGNALVQEVFKGT 30- 2 A FR+ +QK+T RIK N ++ L + + +LS+ +P+ILGNG V F Sbjct: 236 IAAHYFRFWSQKITASRIKDNRRLALVAILCFAAIGLLSMWFPEILGNGKGPVSLAFNDN 29- 5 Query: 303 TVSLIA-ILVVLKMIATLSTLYAGAYGGILTPSFSIGACLGFLLASISIPLLPHISIVTS 36- 1 + A L K++A L+AGAYGG+LTP S GA L ++ + LP + I Sbjct: 296 LSGMKAGELFCFKILAVFLALWAGAYGGLLTPGISFGALLAVVIGHLWNMWLPPVPIGAF 35- 5 Query: 362 MLVGAAIFLAITMRAPLTAVGLVISFTGQSVITIVPLTIAVLFATAYDYF 411 ++G A FLA +M+ P+TA+ LVI F ++P+ AV + A F Sbjct: 356 AIIGGAAFLASSMKMPITAMALVIEFARTGHDFLIPIAFAVAGSIAISQF 405 A related DNA sequence was identified in S. pyogenes <SEQ ID 2747> which encodes the amino acid sequence <SEQ ID 2748>. Analysis of this protein sequence reveals the following:

TABLE-US-02648 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.41 Transmembrane 247-263 (245-267) INTEGRAL Likelihood = -5.15 Transmembrane 326-342 (323-345) INTEGRAL Likelihood = -5.04 Transmembrane 411-427 (407-429) INTEGRAL Likelihood = -4.94 Transmembrane 39-55 (34-59) INTEGRAL Likelihood = -4.46 Transmembrane 284-300 (282-307) INTEGRAL Likelihood = -3.45 Transmembrane 380-396 (376-400) INTEGRAL Likelihood = -2.13 Transmembrane 185-201 (184-201) INTEGRAL Likelihood = -2.02 Transmembrane 88-104 (87-105) INTEGRAL Likelihood = -1.12 Transmembrane 350-366 (350-367) ----- Final Results ----- bacterial membrane --- Certainty = 0.3166(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02649 >GP: AAF41386 GB: AE002449 chloride channel protein-related protein [Neisseria meningitidis MC58] Identities = 137/373 (36%), Positives = 201/373 (53%), Gaps = 23/373 (6%) Query: 59 IHLIQSLSFGFSQG----SFSTMIASVPPQRRALSLLFAGLLAGLGWHLLAKKGKDIQSI 114- +H IQ ++G+ SF +A RR L G +AG GW LL + GK I Sbjct: 1 MHFIQHTAYGYGADGVYTSFREGVAQASGMRRVAVLTLCGAVAGSGWWLLKRFGKPQIEI 60 Query: 115 QQIIQDDISFSPW-TQFWHGWLQLTTVSMGAPVGREGASREVAVTLTSLWSQRCNLSKAD 17- 3 + ++ + P+ T +H LQ+ TV +G+P+GRE A RE+ +R L + + Sbjct: 61 KAALKQPLQGLPFLTTVFHVLLQIITVGLGSPLGREVAPREMTAAFAFAGGKRLGLDEGE 120- Query: 174 QKLLLACASGAALGAVYNAPLATILFILEAILNRWSLKNIYAACLTSYVAVETVALLQGR 23- 3 +LL+ACASGA L AVYN PLA+ LFILEA+L W+ + + AA LTS +A + G Sbjct: 121 MRLLIACASGAGLAAVYNVPLASTLFILEAMLGVWTQQAVAAALLTSVIATAVARI--GL 17- 8 Query: 234 HEIQYLMPQQHWTLGT--LIGSVLAGLILSLFAHAYKHLLKHLPKADAKSQWFIPKVLIA 29- 1 ++Q P + T+ T L S + G IL + A ++ + P + IP + Sbjct: 179 GDVQQYHP-ANLTVNTSLLWFSAVIGPILGVAAVFFQRTAQKFPFIKRDNIKIIPLAVCM 23- 7 Query: 292 FSLIAGLSIFFPEILGNGKAG--LLF-FLHEEPH---LSYISWLLVAKAVAISLVFASGA 34- 5 F+LI +S++FPEILGNGKAG L F L + H L+ + WL+V A+A+ GA Sbjct: 238 FALIGVISVWFPEILGNGKAGNQLTFGGLTDWQHSLGLTAVKWLVVLMALAV------GA 29- 1 Query: 346 KGGKIAPSMMLGGASGLLLAILSQYLIPLSLSNTLAIMVGATIFLGVINKIPLAAPVFLV 40- 5 GG I PSMMLG A + P +S+ A +VGA +FLGV K+PL A F++ Sbjct: 292 YGGLITPSMMLGSTIAFAAATAWNSVFP-EMSSESAAIVGAAVFLGVSLKMPLTAIAFIL 35- 0 Query: 406 EITGQSLLMIIPL 418 E+T + +++PL Sbjct: 351 ELTYAPVALLMPL 363 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02650 Identities = 131/415 (31%), Positives = 215/415 (51%), Gaps = 9/415 (2%) Query: 2 LNFKMVSRLYYAVKFMIAVLFMT-VMAGVGAILMHYVLMFTEWLAFGDSRENTLSLLNSV 60 LNF S + + LF+T + AG+ A ++ + + L+FG S+ + +++ SV Sbjct: 22 LNFCYNSLMKRHFLLLTFYLFLTGLTAGLVAFILTKAIHLIQSLSFGFSQGSFSTMIASV 81 Query: 61 TPIKRVLSLTLVSFLASLSWYYLQIKPKQITSIKQQVVFKDFSVKKSPYWLHIGHAFLQL 120- P +R LSL LA L W+ L K K I SI QQ++ D S SP W H +LQL Sbjct: 82 PPQRRALSLLFAGLLAGLGWHLLAKKGKDIQSI-QQIIQDDISF--SP-WTQFWHGWLQL 137- Query: 121 IYVGTGGPIGKEGAPREFGAINAGKISDLLALKVLDKRLLIISGAAAGLSAVYQVPLASV 18- 0 V G P+G+EGA RE S L D++LL+ + A L AVY PLA++ Sbjct: 138 TTVSMGAPVGREGASREVAVTLTSLWSQRCNLSKADQKLLLACASGAALGAVYNAPLATI 19- 7 Query: 181 FFAFETLALGISLKNIVTLLASTFGAASIAQLVISTAPL-YHISKMSLNSQSLAFMFLIV 23- 9 F E + SLKNI +++ A L+ + Y + + +L L Sbjct: 198 LFILEAILNRWSLKNIYAACLTSYVAVETVALLQGRHEIQYLMPQQHWTLGTLIGSVLAG 25- 7 Query: 240 LCVTPIAISFRYLNQKVTERRIKNIKILLSLPVVSLIVSVLSIVYPQILGNGNA-LVQEV 29- 8 L ++ A ++++L + + + K+ + + + +++ LSI +P+ILGNG A L+ + Sbjct: 258 LILSLFAHAYKHLLKHLPKADAKSQWFIPKVLIAFSLIAGLSIFFPEILGNGKAGLLFFL 31- 7 Query: 299 FKGTTVSLIAILVVLKMIATLSTLYAGAYGGILTPSFSIGACLGFLLASISIPLLP-HIS 35- 7 + +S I+ L+V K +A +GA GG + PS +G G LLA +S L+P +S Sbjct: 318 HEEPHLSYISWLLVAKAVAISLVFASGAKGGKIAPSMMLGGASGLLLAILSQYLIPLSLS 37- 7 Query: 358 IVTSMLVGAAIFLAITMRAPLTAVGLVISFTGQSVITIVPLTIA-VLFATAYDYF 411 +++VGA IFL + + PL A ++ TGQS++ I+PL +A ++F +Y ++ Sbjct: 378 NTLAIMVGATIFLGVINKIPLAAPVFLVEITGQSLLMIIPLALANLIFYFSYQFY 432 A related GBS gene <SEQ ID 8683> and protein <SEQ ID 8684> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02651 Lipop: Possible site: -1 Crend: 9 SRCFLG: 0 McG: Length of UR: 19 Peak Value of UR: 2.96 Net Charge of CR: 2 McG: Discrim Score: 9.64 GvH: Signal Score (-7.5): 1.15 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 27 ALOM program count: 9 value: -9.34 threshold: 0.0 INTEGRAL Likelihood = -9.34 Transmembrane 261-277 (258-284) INTEGRAL Likelihood = -8.97 Transmembrane 226-242 (224-248) INTEGRAL Likelihood = -7.70 Transmembrane 351-367 (347-371) INTEGRAL Likelihood = -7.32 Transmembrane 298-314 (292-321) INTEGRAL Likelihood = -5.57 Transmembrane 332-348 (329-350) INTEGRAL Likelihood = -5.57 Transmembrane 386-402 (382-404) INTEGRAL Likelihood = -2.44 Transmembrane 172-188 (172-188) INTEGRAL Likelihood = -1.01 Transmembrane 154-170 (154-170) INTEGRAL Likelihood = -0.43 Transmembrane 193-209 (191-210) PERIPHERAL Likelihood = 1.22 61 modified ALOM score: 2.37 icm1 HYPID: 7 CFP: 0.474 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4736(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00064## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 902 A DNA sequence (GBSx0957) was identified in S. agalactiae <SEQ ID 2749> which encodes the amino acid sequence <SEQ ID 2750>. This protein is predicted to be purine nucleoside phosphorylase fragment (deoD-1). Analysis of this protein sequence reveals the following: TABLE-US-02652 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2384(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02653 >GP: CAC18350 GB: Y17900 putative purine-nucleotide phosphorylase [Streptococcus salivarius] Identities = 200/236 (84%), Positives = 219/236 (92%) Query: 1 MSIHIEAKQGEIADKILLPGDPLRAKFIAENFLEDAVCFNTVRNMFGYTGTYKGHRVSVM 60 MSIHI AKQGEIADKILLPGDPLRAKFIAENFLEDAVCFN VRNMFGYTGTYKG RVSVM Sbjct: 1 MSIHIAAKQGEIADKILLPGDPLRAKFIAENFLEDAVCFNEVRNMFGYTGTYKGERVSVM 60 Query: 61 GTGMGMPSISIYARELIVDYGVKTLIRVGTAGAINPDIHVRELVLAQAAATNSNIIRNDW 120- GTGMGMPSISIYARELIVDYGVK LIRVGTAG++N D+HVRELVLAQAAATNSNIIRNDW Sbjct: 61 GTGMGMPSISIYARELIVDYGVKKLIRVGTAGSLNEDVHVRELVLAQAAATNSNIIRNDW 120- Query: 121 PEFDFPQIADFKLLDKAYHIAKEMDITTHVGSVLSSDVFYSNQPDRNMALGKLGVHAIEM 18- 0 P++DFPQIA+F LLDKAYHIAK +TTHVG+VLSSDVFYSN ++N+ LGK GV A+EM Sbjct: 121 PQYDFPQIANFNLLDKAYHIAKNFGMTTHVGNVLSSDVFYSNYFEKNIELGKWGVKAVEM 18- 0 Query: 181 EAAALYYLAAQHNVNALAMMTISDNLNNPEEDTSAEERQTTFTDMMKVGLETLISE 236 EAAALYYLAAQH V+ALA+MTISD+L NP+EDT+AEERQ TFTDMMKVGLETLI++ Sbjct: 181 EAAALYYLAAQHQVDALAIMTISDSLVNPDEDTTAEERQNTFTDMMKVGLETLIAD 236 A related DNA sequence was identified in S. pyogenes <SEQ ID 2751> which encodes the amino acid sequence <SEQ ID 2752>. Analysis of this protein sequence reveals the following: TABLE-US-02654 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2117(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02655 Identities = 210/235 (89%), Positives = 226/235 (95%) Query: 1 MSIHIEAKQGEIADKILLPGDPLRAKFIAENFLEDAVCFNTVRNMFGYTGTYKGHRVSVM 60 MSIHI AK+G+IADKILLPGDPLRAKFIAENFLEDAVCFN VRNMFGYTGTYKGHRVSVM Sbjct: 1 MSIHISAKKGDIADKILLPGDPLRAKFIAENFLEDAVCFNEVRNMFGYTGTYKGHRVSVM 60 Query: 61 GTGMGMPSISIYARELIVDYGVKTLIRVGTAGAINPDIHVRELVLAQAAATNSNIIRNDW 120- GTGMGMPSISIYARELIVDYGVKTLIRVGTAGAI+P++HVRELVLAQAAATNSNIIRND+ Sbjct: 61 GTGMGMPSISIYARELIVDYGVRTLIRVGTAGAIDPEVHVRELVLAQAAATNSNIIRNDF 120- Query: 121 PEFDFPQIADFKLLDKAYHIAKEMDITTHVGSVLSSDVFYSNQPDRNMALGKLGVHAIEM 18- 0 PEFDFPQIADF LLDKAYHIA+EM +TTHVG+VLSSDVFY+N P+RNMALGKLGV AIEM Sbjct: 121 PEFDFPQIADFGLLDKAYHIAREMGVTTHVGNVLSSDVFYTNMPERNMALGKLGVKAIEM 18- 0 Query: 181 EAAALYYLAAQHNVNALAMMTISDNLNNPEEDTSAEERQTTFTDMMKVGLETLIS 235 EAAALYYLAAQH+V AL +MTISDNLN+P EDT+AEERQTTFTDMMKVGLETLI+ Sbjct: 181 EAAALYYLAAQHHVKALGIMTISDNLNDPTEDTTAEERQTTFTDMMKVGLETLIA 235 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 903 A DNA sequence (GBSx0958) was identified in S. agalactiae <SEQ ID 2753> which encodes the amino acid sequence <SEQ ID 2754>. Analysis of this protein sequence reveals the following: TABLE-US-02656 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1710 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9881> which encodes amino acid sequence <SEQ ID 9882> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2755> which encodes the amino acid sequence <SEQ ID 2756>. Analysis of this protein sequence reveals the following: TABLE-US-02657 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1386 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02658 Identities = 126/253 (49%), Positives = 175/253 (68%), Gaps = 2/253 (0%) Query: 3 IEMTDFSTALKVLVDQYSYHNAFLLLQKHGPLNSDLLFLLEMMKERRELNIDFLFAHQEQ 62 + MT+ T L +L+D Y+Y++AF + + + L+LLEM+KERRELN+ FL H + Sbjct: 1 LPMTNNQT-LDILLDVYAYNHAFRIAKALPNIPKTALYLLEMLKERRELNLAFLAEHAAE 59 Query: 63 VVILQEKYNIKL-LHNPYDLELLANYIMDLEAKVKNGLIIDFVRSVSPILYRLFMILLAQ 121- ++++Y+ L L+ + E +ANYI+DLE KVKNG IIDFVRSVSPILYRLF+ L+ Sbjct: 60 NRTIEDQYHCSLWLNQSLEDEQIANYILDLEVKVKNGAIIDFVRSVSPILYRLFLRLITS 119- Query: 122 EVPHLHDYIHNARDDHYDTWKFKELKESNHPVLLAFSERWHDSRLTSKSLAECLQLTDLD 18- 1 E+P+ YI + ++D YDTW F+ + ES+H V A+ + +T+KSLA+ L LT L Sbjct: 120 EIPNFKAYIFDTKNDQYDTWHFQAMLESDHEVFKAYLSQKQSRNVTTKSLADMLTLTSLP 17- 9 Query: 182 EEVKSTIIQLRQFEKSVRNPLAHLIKPFDEQELYRTTQFSSQAFLDQIIFLAKVIGVEYD 24- 1 +E+K + LR FEK+VRNPLAHLIKPFDE+EL+RTT FSSQAFL+ II LA GV Y Sbjct: 180 QEIKDLVFLLRHFEKAVRNPLAHLIKPFDEEELHRTTHFSSQAFLENIITLATFSGVIYR 23- 9 Query: 242 TVNFHYDTVNKLI 254 F++D +N +I Sbjct: 240 REPFYFDDMNAII 252 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 904 A DNA sequence (GBSx0959) was identified in S. agalactiae <SEQ ID 2757> which encodes the amino acid sequence <SEQ ID 2758>. This protein is predicted to be CpsY protein. Analysis of this protein sequence reveals the following: TABLE-US-02659 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.59 Transmembrane 260-276 (260-276) ----- Final Results ----- bacterial membrane --- Certainty = 0.1235 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9879> which encodes amino acid sequence <SEQ ID 9880> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 2759> which encodes the amino acid sequence <SEQ ID 2760>. Analysis of this protein sequence reveals the following: TABLE-US-02660 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1958 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02661 Identities = 247/301 (82%), Positives = 274/301 (90%) Query: 1 MRIQQLQYVIKIVETGSMNEAAKQLYITQPSLSNAVRNLETEMGIQIFIRNPKGITLTKD 60 MRIQQL Y+IKIVE GSMNEAAKQL+ITQPSLSNAV++LE EMGI IF RNPKGITLTKD Sbjct: 1 MRIQQLHYIIKIVECGSMNEAAKQLFITQPSLSNAVKDLEMEMGITIFNRNPKGITLTKD 60 Query: 61 GMEFLSYARQILEQTALLEERYKGDNTSRELFSVSSQHYAFVVNAFVALFNGTDMTQYEL 120- G+EFLSYARQI+EQT+LLE+RYK NT RELFSVSSQHYAFVVNAFV+L TDMT+YEL Sbjct: 61 GVEFLSYARQIIEQTSLLEDRYKNHNTGRELFSVSSQHYAFVVNAFVSLLKRTDMTRYEL 120- Query: 121 FLRETRTWEIIDDVKNFRSEIGVLFLNSYNRDVLTKLFDDNSLIATTLFTTTPHIFVSKS 18- 0 FLRETRTWEIIDDVKNFRSEIGVLF+N YNRDVLTKLFDDN L A+ LF PHIFVSKS Sbjct: 121 FLRETRTWEIIDDVKNFRSEIGVLFINDYNRDVLTKLFDDNHLTASPLFKAQPHIFVSKS 18- 0 Query: 181 NPLANRKKLNMKDLEDYPYLSYDQGLHNSFYFSEEMMSQIPHPKSIVVSDRATLFNLMIG 24- 0 NPLA + L+M DL D+PYLSYDQG+HNSFYFSEEMMSQ+PH KSIVVSDRATLFNLMIG Sbjct: 181 NPLATKSLLSMDDLRDFPYLSYDQGIHNSFYFSEEMMSQMPHNKSIVVSDRATLFNLMIG 24- 0 Query: 241 LDGYTVATGILNSKLNGDEIVAIPLDVDDVIDIVYIRHDKANLSKMGQKFIDYLLEEVSFN 3- 01 LDGYTVA+GILNS LNGD+IVAIPLDV D IDIV+I+H+KANLSKMG++FI+YLLEEV+F+ Sbjct: 241 LDGYTVASGILNSNLNGDQIVAIPLDVPDEIDIVFIKHEKANLSKMGERFIEYLLEEVTFD 3- 01 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 905 A DNA sequence (GBSx0960) was identified in S. agalactiae <SEQ ID 2761> which encodes the amino acid sequence <SEQ ID 2762>. This protein is predicted to be CpsX protein. Analysis of this protein sequence reveals the following: TABLE-US-02662 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.91 Transmembrane 22-38 (13-42) INTEGRAL Likelihood = -14.65 Transmembrane 52-68 (44-77) INTEGRAL Likelihood = -6.74 Transmembrane 76-92 (73-97) ----- Final Results ----- bacterial membrane --- Certainty = 0.6965 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02663 >GP:AAC44935 GB:U56901 putative transcriptional regulator [Bacillus subtilis] Identities = 120/389 (30%), Positives = 196/389 (49%), Gaps = 17/389 (4%) Query: 2 KIGKKIVLMFTAIVLTTVLALGVYLTSAYTFSTGELSKTFKDFSTSSNKSDAIK-QTRAF 60 KI K+I+L+F A+ L V+ LG Y + E + S+ +++ + + + F Sbjct: 19 KILKRIMLLF-ALALLVVVGLGGYKLYKTINAADESYDALSRGNKSNLRNEVVDMKKKPF 77 Query: 61 SILLMGVDTGSSERASKWEGNSDSMILVTVNPKTKKTTMTSLERDTLTTLSGPKNNEMNG 120- SIL MG++ +++ +G SDS+I+VT++PK K M S+ RDT L+G + G Sbjct: 78 SILFMGIEDYATKGQ---KGRSDSLIVVTLDPKNKTMKMLSIPRDTRVQLAG----DTTG 130- Query: 121 VEAKLNAAYAAGGAQMAIMTVQDLLNITIDNYVQINMQGLIDLVNAVGGITVTNEFDFPI 18- 0 + K+NAAY+ GG + TV++ L I ID YV ++ G D++N VGGI V FDF Sbjct: 131 SKTKINAAYSKGGKDETVETVENFLQIPIDRYVTVDFDGFKDVINEVGGIDVDVPFDFDE 19- 0 Query: 181 SIAENEPEYQATVAPGTHKINGEQALVYARMRYDDPEGDYGRQKRQREVIQKVLKKILAL 24- 0 +E + + G +NGE+AL YARMR D GD+GR RQ++++ ++ ++ + Sbjct: 191 KSDVDESK-RIYFKKGEMHLNGEEALAYARMRKQDKRGDFGRNDRQKQILNALIDRMSSA 24- 9 Query: 241 DSISSYRKILSAVSSNMQTNIEISSRTIPSLLGYRDALRTIKTYQLKGEDATLSDGGSYQ 30- 0 +I+ KI S N++TNI I+ + + I T + G D L +Y Sbjct: 250 SNIAKIDKIAEKASENVETNIRITEGLALQQIYSGFTSKKIDTLSITGSDLYLGPNNTYY 30- 9 Query: 301 IVTSNHLLEIQNRIRTELGLHKVNQLKTNATVYENLYGSTKSQTVNNNYDSSGQAPSYSD 36- 0 LE ++R L H ++ +T T S + + + S+G + Sbjct: 310 FEPDATNLE---KVRKTLQEH-LDYTPDTSTGTSGTEDGTDSSSSSGSTGSTGTTTDGTT 36- 5 Query: 361 SHSSYANYSSGVDTGQSASTDQDSTASSH 389 + SSY+N SS T + ST +T SS+ Sbjct: 366 NGSSYSNDSS---TSSNNSTTNSTTDSSY 391 There is also homology to SEQ ID 2764. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 906 A DNA sequence (GBSx0961) was identified in S. agalactiae <SEQ ID 2765> which encodes the amino acid sequence <SEQ ID 2766>. This protein is predicted to be CpsIaB. Analysis of this protein sequence reveals the following: TABLE-US-02664 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.75 Transmembrane 121-137 (121-137) ----- Final Results ----- bacterial membrane --- Certainty = 0.1298 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9877> which encodes amino acid sequence <SEQ ID 9878> was also identified. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 907 A DNA sequence (GBSx0962) was identified in S. agalactiae <SEQ ID 2767> which encodes the amino acid sequence <SEQ ID 2768>. This protein is predicted to be cpsb protein. Analysis of this protein sequence reveals the following:

TABLE-US-02665 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.02 Transmembrane 182-198 (179-204) INTEGRAL Likelihood = -5.57 Transmembrane 30-46 (24-48) ----- Final Results ----- bacterial membrane --- Certainty = 0.4609(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 10785> and protein <SEQ ID 10786> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02666 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: -8.96 GvH: Signal Score (-7.5): 0.11 Possible site: 35 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -9.02 threshold: 0.0 INTEGRAL Likelihood = -9.02 Transmembrane 182-198 (179-204) INTEGRAL Likelihood = -5.57 Transmembrane 30-46 (24-48) PERIPHERAL Likelihood = 6.21 113 modified ALOM score: 2.30 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4609 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 908 A DNA sequence (GBSx0963) was identified in S. agalactiae <SEQ ID 2769> which encodes the amino acid sequence <SEQ ID 2770>. This protein is predicted to be CpsIaD. Analysis of this protein sequence reveals the following: TABLE-US-02667 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.44 Transmembrane 149-165 (149-166) ----- Final Results ----- bacterial membrane --- Certainty = 0.1977 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 909 A DNA sequence (GBSx0964) was identified in S. agalactiae <SEQ ID 2771> which encodes the amino acid sequence <SEQ ID 2772>. Analysis of this protein sequence reveals the following: TABLE-US-02668 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.26 Transmembrane 276-292 (270-297) INTEGRAL Likelihood = -4.62 Transmembrane 10-26 (9-28) INTEGRAL Likelihood = -4.14 Transmembrane 41-57 (39-58) INTEGRAL Likelihood = -3.24 Transmembrane 100-116 (100-116) INTEGRAL Likelihood = -3.08 Transmembrane 445-461 (443-461) ----- Final Results ----- bacterial membrane --- Certainty = 0.5904 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8687> and protein <SEQ ID 8688> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02669 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 5.69 GvH: Signal Score (-7.5) : -5.63 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 5 value: -12.26 threshold: 0.0 INTEGRAL Likelihood = -12.26 Transmembrane 276-292 (270-297) INTEGRAL Likelihood = -4.62 Transmembrane 10-26 (9-28) INTEGRAL Likelihood = -4.14 Transmembrane 41-57 (39-58) INTEGRAL Likelihood = -3.24 Transmembrane 100-116 (100-116) INTEGRAL Likelihood = -3.08 Transmembrane 445-461 (443-461) PERIPHERAL Likelihood = 2.23 221 modified ALOM score: 2.95 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5904 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 910 A DNA sequence (GBSx0965) was identified in S. agalactiae <SEQ ID 2773> which encodes the amino acid sequence <SEQ ID 2774>. This protein is predicted to be CpsF. Analysis of this protein sequence reveals the following: TABLE-US-02670 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.60 Transmembrane 79-95 (78-95) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 911 A DNA sequence (GBSx0966) was identified in S. agalactiae <SEQ ID 2775> which encodes the amino acid sequence <SEQ ID 2776>. This protein is predicted to be galactosyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-02671 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4634 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 912 A DNA sequence (GBSx0967) was identified in S. agalactiae <SEQ ID 2777> which encodes the amino acid sequence <SEQ ID 2778>. Analysis of this protein sequence reveals the following: TABLE-US-02672 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.47 Transmembrane 59-75 (54-82) INTEGRAL Likelihood = -10.88 Transmembrane 309-325 (307-332) INTEGRAL Likelihood = -8.07 Transmembrane 33-49 (28-53) INTEGRAL Likelihood = -6.48 Transmembrane 195-211 (187-212) INTEGRAL Likelihood = -6.16 Transmembrane 285-301 (283-306) INTEGRAL Likelihood = -4.09 Transmembrane 222-238 (221-240) INTEGRAL Likelihood = -3.50 Transmembrane 78-94 (77-96) INTEGRAL Likelihood = -2.71 Transmembrane 101-117 (99-117) INTEGRAL Likelihood = -2.44 Transmembrane 8-24 (7-25) INTEGRAL Likelihood = -1.59 Transmembrane 147-163 (147-164) INTEGRAL Likelihood = -0.48 Transmembrane 168-184 (168-184) ----- Final Results ----- bacterial membrane --- Certainty = 0.5989 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02673 >GP: CAB43614 GB: AJ239004 polysaccharide polymerase [Streptococcus pneumoniae] Identities = 74/309 (23%), Positives = 137/309 (43%), Gaps = 36/309 (11%) Query: 53 FERRKLV---IIFLLFIATILNLFFVHKVTFILTLIFFLALKDI--SLKKAFSIIIGSRI 107- FE+RK II ++ I T+L + ++ +F+ + I L++ II Sbjct: 61 FEKRKYTLQFIISIILITTLLLYTSIQMQNYVYFTSWFMLIGTIHYDLRRVIKIIFIVS- 119- Query: 108 LGVLLNQIFVKLDLIEIKY-----VNFYRDGQFILRSDLGFGHPNFIHNFFALTIFLYIV 16- 2 L ++ IF+ L + I Y +N R+ + + GF HPN + ++I Sbjct: 120 LSIMFISIFISLLMYIIDYKREILINIRRN-ETVRAFTFGFIHPNKFTIVLSNLCLMFIW 17- 8 Query: 163 LNYKRLKPVVMVLFLTLNYLLYQYTFSRTGYYIVILFIVLIYVTKNSLIKRVFMKLAPYV 22- 2 L RLK + L + Y +T +RT + I+ L+Y+ ++ + ++ Y Sbjct: 179 LIKDRLKYYHVTFCLFIQLFFYFFTQTRTALLVSIVIFALLYI--YMFVENLELRWIGYS 23- 6 Query: 223 QFFLLVFTFLSSTIFFNSN--FVQKLDVLLTGRLHY-AHLQLVDGLTPFGNSFKE----- 27- 4 F + F + + F+ SN F +D +LTGR+ A+ + G T +G + Sbjct: 237 FFCISTFLGVLAFQFYPSNNKFSIFIDNILTGRIKLAAYARTFFGYTFWGQYVDKEIVWD 29- 6 Query: 275 -----TSVLFDNSYSMLLSMYGVVLTMFCMIIY-----YIYSKKIIIIELQLLLFIMSII 32- 4 TS FD+ YS L+S G++ + +++ Y+ +K +I+ LL + M + Sbjct: 297 PIWGLTSFTFDSFYSFLMSNAGIIWLLILSVLFVKLQKYLDNKSLIL----LLAWSMYAV 35- 2 Query: 325 LFTESFYPS 333 T+ +PS Sbjct: 353 TETDLIFPS 361 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 913 A DNA sequence (GBSx0968) was identified in S. agalactiae <SEQ ID 2779> which encodes the amino acid sequence <SEQ ID 2780>. This protein is predicted to be cap8J. Analysis of this protein sequence reveals the following: TABLE-US-02674 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3424 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02675 >GP: CAB43613 GB: AJ239004 cap8J [Streptococcus pneumoniae] Identities = 94/237 (39%), Positives = 135/237 (56%), Gaps = 10/237 (4%) Query: 1 MIPKVIHYCWFGGNPLPDNLKKYIKTWREQCPDYEIIEWNEHNYDVSKNVFMREAYTKKN 60 MIPK IHY WFGG+ PD + K I +W++ PDYEI+EWNE N+D+S + F + AY + Sbjct: 1 MIPKKIHYIWFGGSEKPDVVLKCINSWKKYMPDYEIVEWNEDNFDLSDSQFAKSAYESRK 60 Query: 61 FAYVSDYARLDIIYTYGGFYLDTDVELLKSL-DPLRIHECFLAREISCDVNTGLIIGAVK 119- +A+ SDYAR I+ YGG Y DTDVELLK++ D + H F E +VN GL+ + Sbjct: 61 WAFASDYARFKILSKYGGIYFDTDVELLKTISDDILAHSSFTGFEYIGEVNPGLVYACMP 120- Query: 120 GHHFLKSNMSIYDKS--DLTSLNKTCVEVTTNLLINRGLKNKNIIQKIDDITIYPRNYFN 17- 7 K + Y+++ D+ L T + T+ L+ + N Q ID + IYP +YF Sbjct: 121 DDKIAKYMVQYYEQASFDINHL-VTVNTIITDYLLKNNFQKNNQFQIIDGLAIYPDDYFC 17- 9 Query: 178 PKNLLTGKVDCLTSVTYSIHHYEGSWKSSSFISDSLKIRVRLIIDFLFGYGTYRMLL 234 + +V LT T SIHHY +WK+ +LK +V++I+ + G YR LL Sbjct: 180 GYDQEVKEVR-LTERTISIHHYSATWKTR-----TLKRKVQMIVKTIIGAENYRKLL 230 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 914 A DNA sequence (GBSx0969) was identified in S. agalactiae <SEQ ID 2781> which encodes the amino acid sequence <SEQ ID 2782>. Analysis of this protein sequence reveals the following: TABLE-US-02676 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3897 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02677 >GP: CAA87700 GB: Z47767 WbcL [Yersinia enterocolitica] Identities = 60/207 (28%), Positives = 101/207 (47%), Gaps = 22/207 (10%) Query: 4 IFTPTFNRGYRLSYLYDSLCNQTNKNFIWLIVDDGSEDSTKEIVSNYIKENKVSIVYLYK 63 +FTPTFNR + L Y S+ Q + WLIVDDGS D+T E+V ++ ENK++I Y+Y+ Sbjct: 6 VFTPTFNRAHVLKRCYLSILEQDRDDIEWLIVDDGSTDNTAEVVDSFKIENKLNIKYIYQ 65 Query: 64 RNGGKHSAYNLAMRYMQPSDYHVCVDSDDWLLEDAV------EIIFKDLESLTLSNRYVG 117- N GK +A+N A+ +Y + +DSDD + ++ +F D E + + Sbjct: 66 DNSGKQAAWNKAVENAS-GEYFIGLDSDDAFIAGSINKLLSMNAVFDDKEIIGIR----A 120- Query: 118 LVYPRYSLNQGNNWLNPKILEVNIPDLKYKYHLKIETCIVINNAYLVDFEFPCFEGENFL 17- 7 + +L N +L+ + + + D ++ ++ E L + +P G NF+ Sbjct: 121 ISVSSETLKPNNYYLSNEDKKSSWFD-EFSSGIRGERIDFFKTELLRKYLYPVASGINFI 17- 9 Query: 178 SEEIMYIYLSKKGYFCPQNRKIYCFDY 204 E Y ++K+ YCF Y Sbjct: 180 PEIWFYSTVAKE----------YCFYY 196 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 915 A DNA sequence (GBSx0970) was identified in S. agalactiae <SEQ ID 2783> which encodes the amino acid sequence <SEQ ID 2784>. This protein is predicted to be eps7. Analysis of this protein sequence reveals the following: TABLE-US-02678 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.18 Transmembrane 190-206 (189-206) ----- Final Results ----- bacterial membrane --- Certainty = 0.1871 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02679 >GP: CAB59293 GB: AJ131984 putative galactosyl transferase [Streptococcus pneumoniae] Identities = 101/312 (32%), Positives = 172/312 (54%), Gaps = 4/312 (1%) Query: 3 LISIIVPVYNGEIYIGRCLDSILEQTYQNLEIIIIDDGSSDRTGDICEKYFLEDRRIKYF 62 +IS+IVPVYN Y+ LDS+LEQTY++ E+I+++DGS+D +G+IC++Y I F Sbjct: 1 MISVIVPVYNVADYLRFALDSLLEQTYKDFEVILVNDGSTDNSGEICDEYGKLYDNIHVF 60 Query: 63 YQENRGQSVARNNGVLRCTGDWIAFLDSDDVYLPYSIEVMYNIQKATNADIVLT--SIGN 120- +++N G S ARN G+ + G++I FLDSDD + PY++E++ IQK + DIV T I Sbjct: 61 HKKNGGLSDARNFGLEKSRGEFITFLDSDDYFEPYALELLITIQKKYDVDIVSTKGGITY 120- Query: 121 FNNTYNTSINSQYLKEIKLYTLEVALEEMYYGKTYGVSPLAKLYPRSNLLSNPYPEGKIH 18- 0 ++ Y+ + ++ +K+ T + L +YY VS KLY R +L +P+GKI+ Sbjct: 121 SHDIYSKKLMAEDYLTVKILTNKEFLAAVYYNDEMTVSAWGKLYKR-DLFKTIFPKGKIY 17- 9 Query: 181 EDMDTTFKLISCASKIAVCDIVTAVVYFSDNSTTRTKFNERMLYFFEAIQNNIVFINLNF 24- 0 ED+ + + +A D+ Y S + F++R FF+AI +N I + Sbjct: 180 EDLYVVAERLLNIKTVAHTDLPIYHYYQRQGSIVNSTFSDRQYDFFDAIDHNEAIIKKFY 23- 9 Query: 241 PHNTSLISAVIYNEVFGGIDICGKMIDFKLYDTVDYYRKKYRKYFKTILFNNRISVKEKV 30- 0 + L++A+ V G I + + + + + Y+ ++ N +I +K KV Sbjct: 240 CGDKELLAALNAKRVIGSF-ILSNSAFYNSKNDITKIIRIIKPYYWEVIKNKKIPMKRKV 29- 8 Query: 301 KYILFISSIRYF 312 + +LF+ S Y+ Sbjct: 299 QCVLFLLSPNYY 310 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 916 A DNA sequence (GBSx0971) was identified in S. agalactiae <SEQ ID 2785> which encodes the amino acid sequence <SEQ ID 2786>. This protein is predicted to be galactosyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-02680 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2787> which encodes the amino acid sequence <SEQ ID 2788>. Analysis of this protein sequence reveals the following: TABLE-US-02681 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2065 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02682 Identities = 37/111 (33%), Positives = 61/111 (54%), Gaps = 3/111 (2%) Query: 1 MDKVSIIIPVYNVQSFLNECIESVLAQ-TYSNLEIILVNDGSTDNSGDIC-DYYSEIDGR 58 M KVSII YN ++++ ++S L+Q T +EII+++D STD+S +I Y + G+ Sbjct: 1 MYKVSIICTNYNKAPWISDALDSFLSQVTDFEVEIIVIDDASTDDSREILKSYQKKSSGK 60 Query: 59 I-FVFHKNNGGLSDARNYGISRATGDYIYLLDSDDYLYKEDAIERMVEFSE 108 I +F++ N G++ A G YI D DDY +++ V+ E Sbjct: 61 IKLLFNETNIGITKTWIKACLYAKGKYIARCDGDDYWTDSFKLQKQVDVLE 111 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 917 A DNA sequence (GBSx0972) was identified in S. agalactiae <SEQ ID 2789> which encodes the amino acid sequence <SEQ ID 2790>. This protein is predicted to be CpsK. Analysis of this protein sequence reveals the following: TABLE-US-02683 Possible site: 52 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 918 A DNA sequence (GBSx0973) was identified in S. agalactiae <SEQ ID 2791> which encodes the amino acid sequence <SEQ ID 2792>. Analysis of this protein sequence reveals the following: TABLE-US-02684 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1956 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 919 A DNA sequence (GBSx0974) was identified in S. agalactiae <SEQ ID 2793> which encodes the amino acid sequence <SEQ ID 2794>. This protein is predicted to be capsular polysaccharide. Analysis of this protein sequence reveals the following: TABLE-US-02685 Possible site: 36 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.81 Transmembrane 89-105 (80-112) INTEGRAL Likelihood = -7.01 Transmembrane 439-455 (428-460) INTEGRAL Likelihood = -6.74 Transmembrane 322-338 (317-342) INTEGRAL Likelihood = -4.88 Transmembrane 175-191 (174-195) INTEGRAL Likelihood = -3.45 Transmembrane 146-162 (145-166) INTEGRAL Likelihood = -3.08 Transmembrane 381-397 (375-398) INTEGRAL Likelihood = -2.50 Transmembrane 413-429 (412-430) INTEGRAL Likelihood = -1.91 Transmembrane 206-222 (205-222) INTEGRAL Likelihood = -1.59 Transmembrane 354-370 (354-372) INTEGRAL Likelihood = -1.54 Transmembrane 43-59 (43-61) INTEGRAL Likelihood = -0.22 Transmembrane 252-268 (252-268) ----- Final Results ----- bacterial membrane --- Certainty = 0.4524 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 920 A DNA sequence (GBSx0975) was identified in S. agalactiae <SEQ ID 2795> which encodes the amino acid sequence <SEQ ID 2796>. This protein is predicted to be NeuB. Analysis of this protein sequence reveals the following:

TABLE-US-02686 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2992 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 921 A DNA sequence (GBSx0976) was identified in S. agalactiae <SEQ ID 2797> which encodes the amino acid sequence <SEQ ID 2798>. This protein is predicted to be NeuC. Analysis of this protein sequence reveals the following: TABLE-US-02687 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3150 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 922 A DNA sequence (GBSx0977) was identified in S. agalactiae <SEQ ID 2799> which encodes the amino acid sequence <SEQ ID 2800>. This protein is predicted to be neuD. Analysis of this protein sequence reveals the following: TABLE-US-02688 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> There is homology to SEQ ID 542. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 923 A DNA sequence (GBSx0979) was identified in S. agalactiae <SEQ ID 2801> which encodes the amino acid sequence <SEQ ID 2802>. Analysis of this protein sequence reveals the following: TABLE-US-02689 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2576 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 924 A DNA sequence (GBSx0980) was identified in S. agalactiae <SEQ ID 2803> which encodes the amino acid sequence <SEQ ID 2804>. Analysis of this protein sequence reveals the following: TABLE-US-02690 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1621 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9875> which encodes amino acid sequence <SEQ ID 9876> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 2805> which encodes the amino acid sequence <SEQ ID 2806>. Analysis of this protein sequence reveals the following: TABLE-US-02691 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1066 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02692 Identities = 83/139 (59%), Positives = 111/139 (79%) Query: 6 TETHDHQALIQKLLVSIHYLTLFRDEIILVEKTPSLLGKHFSIAIVQNELGEILSKIEAL 65 TE + HQ LIQKLLVSIHYLTLFRDE+ LVE+TPS+LG F +VQ+ELG+I++ I+ L Sbjct: 4 TEQNSHQILIQKLLVSIHYLTLFRDELKLVERTPSILGGEFPAHLVQSELGDIVAAIDTL 63 Query: 66 SKQKKLIRSIYWYDESSFKVMNKALAIVEEWIKGLDNLLEFCQSQTVFQAILGDERAHVF 125- Q++LI S +WY+ES+FK+MNK L IV+ WIKG+D+L++ CQS+ VFQ I+GD+R VF Sbjct: 64 DMQQRLIESTFWYEESAFKLMNKTLDIVDNWIKGVDHLIDLCQSKEVFQIIIGDKRIRVF 123- Query: 126 GILIDVYTSLNIINTSLKE 144 G+L DV++SL + SLKE Sbjct: 124 GVLSDVFSSLKVSALSLKE 142 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 925 A DNA sequence (GBSx0981) was identified in S. agalactiae <SEQ ID 2807> which encodes the amino acid sequence <SEQ ID 2808>. This protein is predicted to be uracil-DNA glycosylase (ung). Analysis of this protein sequence reveals the following: TABLE-US-02693 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3427 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2809> which encodes the amino acid sequence <SEQ ID 28110>. Analysis of this protein sequence reveals the following: TABLE-US-02694 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4200 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02695 Identities = 160/216 (74%), Positives = 185/216 (85%) Query: 1 MKHSSWHDLIKRELPNHYYNKINTFMDAVYESGIVYPPRDKVFNAIQITPLENVKVVIIG 60 M HS WH+ IK LP HYY +IN F+D Y SG+VYPPR+ VF A+Q+TPLE KV+I+G Sbjct: 1 MAHSIWHEKIKSFLPEHYYGRINHFLDEAYASGLVYPPRENVFKALQVTPLEETKVLILG 60 Query: 61 QDPYHGPQQAQGLSFSVPDNLPAPPSLQNILKELAEDIGSRSHHDLTSWAQQGVLLLNAC 120- QDPYHGP+QAQGLSFSVP+ + APPSL NILKELA+DIG R HHDL++WA QGVLLLNAC Sbjct: 61 QDPYHGPKQAQGLSFSVPEEISAPPSLINILKELADDIGPRDHHDLSTWASQGVLLLNAC 120- Query: 121 LTVPEHQANGHAGLIWEPFTDAVIKVVNQKETPVVFILWGGYARKKKSLIDNPIHHIIES 18- 0 LTVP QANGHAGLIWEPFTDAVIKV+N+K++PVVFILWG YARKKK+ I NP HHIIES Sbjct: 121 LTVPAGQANGHAGLIWEPFTDAVIKVLNEKDSPVVFILWGAYARKKKAFITNPKHHIIES 18- 0 Query: 181 PHPSPLSAYRGFFGSRPFSRTNHFLEEEGINEIDWL 216 PHPSPLS+YRGFFGS+PFSRTN LE+EG+ +DWL Sbjct: 181 PHPSPLSSYRGFFGSKPFSRTNAILEKEGMTGVDWL 216 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 926 A DNA sequence (GBSx0982) was identified in S. agalactiae <SEQ ID 2811> which encodes the amino acid sequence <SEQ ID 2812>. Analysis of this protein sequence reveals the following: TABLE-US-02696 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.15 Transmembrane 147-163 (109-166) INTEGRAL Likelihood = -8.92 Transmembrane 124-140 (109-146) INTEGRAL Likelihood = -6.16 Transmembrane 167-183 (166-186) INTEGRAL Likelihood = -4.67 Transmembrane 3-19 (1-23) INTEGRAL Likelihood = -3.98 Transmembrane 72-88 (64-92) INTEGRAL Likelihood = -1.06 Transmembrane 106-122 (105-122) INTEGRAL Likelihood = -0.90 Transmembrane 54-70 (54-70) ----- Final Results ----- bacterial membrane --- Certainty = 0.5458 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9873> which encodes amino acid sequence <SEQ ID 9874> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02697 >GP: CAA91549 GB: Z67739 unidentified [Streptococcus pneumoniae] Identities = 134/212 (63%), Positives = 168/212 (79%) Query: 1 MNIIIMIIIAYLLGSIQTGLWIGKYFYQVNLRQHGSGNTGTTNTFRILGVKAGIVTLTID 60 M I+++I+AYLLGSI +GLWIG+ F+Q+NLR+HGSGNTGTTNTFRILG KAG+ T ID Sbjct: 1 MITIVLLILAYLLGSIPSGLWIGQVFFQINLREHGSGNTGTTNTFRILGKKAGMATFVID 60 Query: 61 ILKGTLATLIPIILGITTVSPFFIGFFAIIGHTFPIFAQFKGGKAVATSAGVLLGFAPSF 120- KGTLATL+PII + VSP G A+IGHTFPIFA FKGGKAVATSAGV+ GFAP F Sbjct: 61 FFKGTLATLLPIIFHLQGVSPLIFGLLAVIGHTFPIFAGFKGGKAVATSAGVIFGFAPIF 120- Query: 121 FLYLLVIFLLTLYLFSMISLSSITVAVVGILSVLIFPLVGFILTDYDWIFTTVVILMALT 18- 0 LYL +IF LYL SMISLSS+T ++ ++ VL+FPL GFIL++YD++F +++ +A Sbjct: 121 CLYLAIIFFGALYLGSMISLSSVTASIAAVIGVLLFPLFGFILSNYDFLFIAIILALASL 18- 0 Query: 181 IIIRHQDNIKRIRKRQENLVPFGLNLSKQKNK 212 IIIRH+DNI RI+ + ENLVP+GLNL+ Q K Sbjct: 181 IIIRHKDNIARIKNKTENLVPWGLNLTHQDPK 212 A related DNA sequence was identified in S. pyogenes <SEQ ID 2813> which encodes the amino acid sequence <SEQ ID 2814>. Analysis of this protein sequence reveals the following: TABLE-US-02698 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.83 Transmembrane 194-210 (191-216) INTEGRAL Likelihood = -9.77 Transmembrane 146-162 (132-191) INTEGRAL Likelihood = -7.70 Transmembrane 165-181 (163-191) INTEGRAL Likelihood = -5.89 Transmembrane 23-39 (19-47) INTEGRAL Likelihood = -4.83 Transmembrane 95-111 (91-118) ----- Final Results ----- bacterial membrane --- Certainty = 0.5331 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02699 >GP: CAA91549 GB: Z67739 unidentified [Streptococcus pneumoniae] Identities = 138/213 (64%), Positives = 166/213 (77%) Query: 28 MKLLLFITIAYLLGSIPTGLWIGQYFYHINLREHGSGNTGTTNTFRILGVKAGTATLAID 87 - M ++ + +AYLLGSIP+GLWIGQ F+ INLREHGSGNTGTTNTFRILG KAG AT ID Sbjct: 1 MITIVLLILAYLLGSIPSGLWIGQVFFQINLREHGSGNTGTTNTFRILGKKAGMATFVID 60 Query: 88 MFKGTLSILLPIIFGMTSISSIAIGFFAVLGHTFPIFANFKGGKAVATSAGVLLGFAPLY 147- FKGTL+ LLPIIF + +S + G AV+GHTFPIFA FKGGKAVATSAGV+ GFAP++ Sbjct: 61 FFKGTLATLLPIIFHLQGVSPLIFGLLAVIGHTFPIFAGFKGGKAVATSAGVIFGFAPIF 120- Query: 148 LFFLASIFVLVLYLFSMISLASVVSAIVGVLSVLTFPAIHFLLPNYDYFLTFIVILLAFI 20- 7 +LA IF LYL SMISL+SV ++I V+ VL FP F+L NYD+ I++ LA + Sbjct: 121 CLYLAIIFFGALYLGSMISLSSVTASIAAVIGVLLFPLFGFILSNYDFLFIAIILALASL 18- 0 Query: 208 IIIRHKDNISRIKHHTENLIPWGLNLSKQVPPK 240 IIIRHKDNI+RIK+ TENL+PWGLNL+ Q PKK Sbjct: 181 IIIRHKDNIARIKNKTENLVPWGLNLTHQDPKK 213 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02700 Identities = 143/212 (67%), Positives = 174/212 (81%) Query: 1 MNIIIMIIIAYLLGSIQTGLWIGKYFYQVNLRQHGSGNTGTTNTFRILGVKAGIVTLTID 60 M +++ I IAYLLGSI TGLWIG+YFY +NLR+HGSGNTGTTNTFRILGVKAG TL ID Sbjct: 28 MKLLLFITIAYLLGSIPTGLWIGQYFYHINLREHGSGNTGTTNTFRILGVKAGTATLAID 87 Query: 61 ILKGTLATLIPIILGITTVSPFFIGFFAIIGHTFPIFAQFKGGKAVATSAGVLLGFAPSF 120- + KGTL+ L+PII G+T++S IGFFA++GHTFPIFA FKGGKAVATSAGVLLGFAP + Sbjct: 88 MFKGTLSILLPIIFGMTSISSIAIGFFAVLGHTFPIFANFKGGKAVATSAGVLLGFAPLY 147- Query: 121 FLYLLVIFLLTLYLFSMISLSSITVAVVGILSVLIFPLVGFILTDYDWIFTTVVILMALT 18- 0 +L IF+L LYLFSMISL+S+ A+VG+LSVL FP + F+L +YD+ T +VIL+A Sbjct: 148 LFFLASIFVLVLYLFSMISLASVVSAIVGVLSVLTFPAIHFLLPNYDYFLTFIVILLAFI 20- 7 Query: 181 IIIRHQDNIKRIRKRQENLVPFGLNLSKQKNK 212 IIIRH+DNI RI+ ENL+P+GLNLSKQ K Sbjct: 208 IIIRHKDNISRIKHHTENLIPWGLNLSKQVPK 239 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 927 A DNA sequence (GBSx0983) was identified in S. agalactiae <SEQ ID 2815> which encodes the amino acid sequence <SEQ ID 2816>. Analysis of this protein sequence reveals the following: TABLE-US-02701 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 928 A DNA sequence (GBSx0984) was identified in S. agalactiae <SEQ ID 2817> which encodes the amino acid sequence <SEQ ID 2818>. Analysis of this protein sequence reveals the following: TABLE-US-02702 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1585 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9871> which encodes amino acid sequence <SEQ ID 9872> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02703 >GP: CAA91550 GB: Z67739 DNA topoisomerase IV [Streptococcus pneumoniae] (ver 2) Identities = 574/649 (88%), Positives = 617/649 (94%), Gaps = 2/649 (0%) Query: 5 LAKQDITVTNYGDDAIQVLEGLDAVRKRPGMYIGSTDGTGLHHLVWEIVDNAVDEALSGF 64 ++K++I + NY DDAIQVLEGLDAVRKRPGMYIGSTDG GLHHLVWEIVDNAVDEALSGF Sbjct: 1 MSKKEININNYNDDAIQVLEGLDAVRKRPGMYIGSTDGAGLHHLVWEIVDNAVDEALSGF 60 Query: 65 GNRIDVIINKDGSITVTDHGRGMPTGMHAMGKPTVEVIFTVLHAGGKFGQGGYKTSGGLH 124- G+RIDV INKDGS+TV DHGRGMPTGMHAMG PTVEVIFT+LHAGGKFGQGGYKTSGGLH Sbjct: 61 GDRIDVTINKDGSLTVQDHGRGMPTGMHAMGIPTVEVIFTILHAGGKFGQGGYKTSGGLH 120- Query: 125 GVGSSVVNALSSWLEVEIIRDGAIYRQRFENGGKPVTTLKKIGTAPKSKSGTSVSFMPDQ 18- 4 GVGSSVVNALSSWLEVEI RDGA+Y+QRFENGGKPVTTLKKIGTAPKSK+GT V+FMPD Sbjct: 121 GVGSSVVNALSSWLEVEITRDGAVYKQRFENGGKPVTTLKKIGTAPKSKTGTKVTFMPDA 18- 0 Query: 185 SVFSTIDFKFNTIAERLKESAFLLKNVTLTLTDNRSEEAEHLEFHYENGVQDFVEYLNED 24- 4 ++FST DFK+NTI+ERL ESAFLLKNVTL+LTD R++EA +EFHYENGVQDFV YLNED Sbjct: 181 TIFSTTDFKYNTISERLNESAFLLKNVTLSLTDKRTDEA--IEFHYENGVQDFVSYLNED 23- 8 Query: 245 KETLTPIMFFEGEEQEFHIEVALQYNDGFSDNILSFVNNVRTKDGGTHETGLKSAITKSM 30- 4 KE LTP+++FEGE+ F +EVALQYNDGFSDNILSFVNNVRTKDGGTHETGLKSAITK M Sbjct: 239 KEILTPVLYFEGEDNGFQVEVALQYNDGFSDNILSFVNNVRTKDGGTHETGLKSAITKVM 29- 8 Query: 305 NDYARKTGLLKEKDKNLEGSDYREGLSAILSILVPEEHLQFEGQTKDKLGSPLARPIVDG 36- 4 NDYARKTGLLKEKDKNLEGSDYREGL+A+LSILVPEEHLQFEGQTKDKLGSPLARP+VDG Sbjct: 299 NDYARKTGLLKEKDKNLEGSDYREGLAAVLSILVPEEHLQFEGQTKDKLGSPLARPVVDG 35- 8 Query: 365 IVSEKLTYFLMENGDLASNLIRKAIKARDAREAARKARDESRNGKKSKKDKGLLSGKLTP 42- 4 IV++KLT+FLMENG+LASNLIRKAIKARDAREAARKARDESRNGKK+KKDKGLLSGKLTP Sbjct: 359 IVADKLTFFLMENGELASNLIRKAIKARDAREAARKARDESRNGKKNKKDKGLLSGKLTP 41- 8 Query: 425 AQSKNAKKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNTAKAKMADIIKNEEINT 48- 4 AQSKN KNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKV+NTAKAKMADI+KNEEINT Sbjct: 419 AQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINT 47- 8 Query: 485 MHTIGAGVGPDFNLDDINYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEEGHVYIA 544- MI+TIGAGVG DF+++D NYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVE GHVYIA Sbjct: 479 MIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIA 53- 8 Query: 545 LPPLYKMSKGKGKKEIVEYAWTDIELEELRQKFGKGSLLQRYKGLGEMNADQLWETTMNP 60- 4 LPPLYKMSKGKGKKE V YAWTD ELEELR++FGKG+ LQRYKGLGEMNADQLWETTMNP Sbjct: 539 LPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNP 59- 8 Query: 605 ETRTLIRVTIEDLARAERRVNVLMGDKVPPRRQWIEDNVKFTLEENTVF 653 ETRTLIRVTIEDLARAERRVNVLMGDKV PRR+WIEDNVKFTLEE TVF Sbjct: 599 ETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTLEEATVF 647 A related DNA sequence was identified in S. pyogenes <SEQ ID 2819> which encodes the amino acid sequence <SEQ ID 2820>. Analysis of this protein sequence reveals the following: TABLE-US-02704 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1518 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02705 Identities = 560/649 (86%), Positives = 615/649 (94%) Query: 5 LAKQDITVTNYGDDAIQVLEGLDAVRKRPGMYIGSTDGTGLHHLVWEIVDNAVDEALSGF 64 L K++IT+ NY DDAIQVLEGLDAVRKRPGMYIGSTD TGLHHL+WEIVDNAVDEALSGF Sbjct: 2 LTKKEITINNYNDDAIQVLEGLDAVRKRPGMYIGSTDATGLHHLIWEIVDNAVDEALSGF 61 Query: 65 GNRIDVIINKDGSITVTDHGRGMPTGMHAMGKPTVEVIFTVLHAGGKFGQGGYKTSGGLH 124- G+ I V+INKDGS++V D GRGMPTG HAMG PTV+VIFT+LHAGGKFGQGGYKTSGGLH Sbjct: 62 GDDIKVVINKDGSVSVADSGRGMPTGQHAMGIPTVQVIFTILHAGGKFGQGGYKTSGGLH 121- Query: 125 GVGSSVVNALSSWLEVEIIRDGAIYRQRFENGGKPVTTLKKIGTAPKSKSGTSVSFMPDQ 18- 4 GVGSSVVNALS+WLEVEI RDG++YRQRFENGGKPVTTLKK+GTAPKSKSGT V+FMPD Sbjct: 122 GVGSSVVNALSAWLEVEITRDGSVYRQRFENGGKPVTTLKKVGTAPKSKSGTVVTFMPDD 18- 1 Query: 185 SVFSTIDFKFNTIAERLKESAFLLKNVTLTLTDNRSEEAEHLEFHYENGVQDFVEYLNED 24- 4 +FSTIDFKFNTI+ERLKESAFLLKNV ++LTD R ++ EFHYENGVQDFVEYLNED Sbjct: 182 KIFSTIDFKFNTISERLKESAFLLKNVKMSLTDLRGDDPIIEEFHYENGVQDFVEYLNED 24- 1 Query: 245 KETLTPIMFFEGEEQEFHIEVALQYNDGFSDNILSFVNNVRTKDGGTHETGLKSAITRSM 30- 4 KETLTP+++ EG++Q+F +EVALQYNDGFSDNILSFVNNVRTKDGG+HETGLKSAITK+M Sbjct: 242 KETLTPVIYMEGQDQDFQVEVALQYNDGFSDNILSFVNNVRTKDGGSHETGLKSAITKAM 30- 1 Query: 305 NDYARKTGLLKEKDKNLEGSDYREGLSAILSILVPEEHLQFEGQTKDKLGSPLARPIVDG 36- 4 NDYARKT LLKEKDKNLEGSDYREGLSA+LSILVPE+HLQFEGQTKDKLGSPLARPIV+ Sbjct: 302 NDYARKTNLLKEKDKNLEGSDYREGLSAVLSILVPEQHLQFEGQTKDKLGSPLARPIVES 36- 1 Query: 365 IVSEKLTYFLMENGDLASNLIRKAIKARDAREAARKARDESRNGKKSKKDKGLLSGKLTP 42- 4 IVSEKLT+FL+ENG++AS+L+RKAIKARDAREAARKARD+SRNGKK+KKDKGLLSGKLTP Sbjct: 362 IVSEKLTFFLLENGEVASHLVRKAIKARDAREAARKARDDSRNGKKNKKDKGLLSGKLTP 42- 1 Query: 425 AQSKNAKKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNTAKAKMADIIKNEEINT 48- 4 AQSKNAKKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNT KAKMADI+KNEEINT Sbjct: 422 AQSKNAKKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNTEKAKNADILKNEEINT 48- 1 Query: 485 MIHTIGAGVGPDFNLDDINYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEEGHVYIA 54- 4 M++TIGAGVG DFNL+DINYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVE GHVYIA Sbjct: 482 MVYTIGAGVGADFNLEDINYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIA 54- 1 Query: 545 LPPLYKMSKGKGKKEIVEYAWTDIELEELRQKFGKGSLLQRYKGLGEMNADQLWETTMNP 60- 4 LPPLYKMSKGKGK E + YAWTD ELE+LR++FGKG++LQRYKGLGEMNA+QLWETTM+P Sbjct: 542 LPPLYKMSKGKGKTEKIAYAWTDGELEDLRREFGKGAILQRYKGLGEMNANQLWETTMDP 60- 1 Query: 605 ETRTLIRVTIEDLARAERRVNVLMGDKVPPRRQWIEDNVKFTLEENTVF 653 ETRTLIRVTI+DLARAERRV+VLMGDK PRRQWIEDNVKFTLEENTVF Sbjct: 602 ETRTLIRVTIDDLARAERRVSVLMGDKAAPRRQWIEDNVKFTLEENTVF 650 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 929 A DNA sequence (GBSx0985) was identified in S. agalactiae <SEQ ID 2821> which encodes the amino acid sequence <SEQ ID 2822>. Analysis of this protein sequence reveals the following:

TABLE-US-02706 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.80 Transmembrane 378-394 (378-394) ----- Final Results ----- bacterial membrane --- Certainty = 0.1319 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02707 >GP: AAD34369 GB: AF129764 ParC [Streptococcus mitis] Identities = 640/820 (78%), Positives = 722/820 (88%), Gaps = 5/820 (0%) Query: 1 MSNIQNMSLEDIMGERFGRYSKYIIQERALPDIRDGLKPVQRRILYSMNKDGNTFEKGFR 60 MSNIQNMSLEDIMGERFGRYSKYIIQ+RALPDIRDGLKPVQRRILYSMNKDGNTF+K +R Sbjct: 1 MSNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDGNTFDKSYR 60 Query: 61 KSAKSVGNVMGNFHPHGDSSIYDAMVRMSQDWKNRETLIEMHGNNGSMDGDPAAAMRYTE 120- KSAKSVGN+MGNFHPHGDSSIYDAMVRMSQDWKNRE L+EMHGNNGSMDGDP AAMRYTE Sbjct: 61 KSAKSVGNIMGNFHPHGDSSIYDAMVRMSQDWKNREILVEMHGNNGSMDGDPPAAMRYTE 120- Query: 121 ARLSEIAGYLLQDIDKNTVPFAWNFDDTEKEPTVLPAAFPNLLVNGATGISAGYATDIPP 18- 0 ARLSEIAGYLLQDIDK TVPF+WNFDDTEKEPTVLPAAFPNLLVNG+TGISAGYATDTPP Sbjct: 121 ARLSEIAGYLLQDIDKKTVPFSWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPP 18- 0 Query: 181 HNLAEVIDAVVYMIDHPKAKLDKLMEFLPGPDFPTGAIIQGKDEIRKAYETGKGRVAVRS 24- 0 HNLAEVIDA VYMIDHP AK+DKLMEFLPGPDFPTG IIQG+DEI+KAYETGKGRV VRS Sbjct: 181 HNLAEVIDAAVYMIDHPTAKVDKLMEFLPGPDFPTGGIIQGRDEIKKAYETGKGRVVVRS 24- 0 Query: 241 RTAIETLKGGKKQIIVTEIPYEVNKSVLVKRIDDVRVNNKVPGIAEVRDESDRDGLRIAI 30- 0 +T IE LKGGK+QI++TEIPYE+NK+ LVK+IDDVRVN+KV GIAEVRDESDRDGLRIAI Sbjct: 241 KTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNSKVAGIAEVRDESDRDGLRIAI 30- 0 Query: 301 ELKKEADETIVLNYLFKYTDLQVNYNFNMVAIDDYTPKQVGLSRILTSYIAHRREIIIAR 36- 0 ELKK+A+ +VLNYLFKYTDLQ+NYNFNMVAID++TP+QVG+ IL+SYIAHRRE+I+AR Sbjct: 301 ELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILAR 36- 0 Query: 361 SKFDKEKAEKRLHIVEGLIRVLSILDEVIALIRASENKADAKENLKVSYEFSEAQAEAIV 42- 0 S+FDKEKAEKRLHIVEGLIRV+SILDEVIALIRASENKADAKENLKVSY+F+E QAEAIV Sbjct: 361 SRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIV 42- 0 Query: 421 TLQLYRLTNTDIVTLREEEEELRQQITMLKAIISDERTMYNVMKRELREVKKKFANTRRS 48- 0 TLQLYRLTNTD+V L+EEE ELR++I ML AII DERTMYN+MK+ELREVKKKFA R S Sbjct: 421 TLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLS 48- 0 Query: 481 ELQELAETIEIDTASLIIEEDTYVSVTRGGYVKRTSPRSFNASTVDELGKREDDELIFVS 54- 0 L++ A+ IEIDTASLI EEDTYVSVT+ GY+KRTSPRSF AST++E+GKR+DD LIFV Sbjct: 481 SLEDTAKAIEIDTASLIAEEDTYVSVTKAGYIKRTSPRSFAASTLEEIGKRDDDRLIFVQ 54- 0 Query: 541 NAKTTQHLLMFTNLGNLAYRPVHELADIRWKDVGEHLSQNLVNFASNEEIIYAELVDDF- 59- 9 +AKTTQHLLMFT LGN+ YRP+HELADIRWKD+GEHLSQ + NF +NEEI+Y E+VD F Sbjct: 541 SAKTTQHLLMFTTLGNVIYRPIHELADIRWKDIGEHLSQTITNFETNEEILYVEVVDQFD 60- 0 Query: 600 TKETYFAVTSLGQIKRFERQEISPWRTYKSKTAKYAKLKSVEDYVVTVAPIQLEDVILVT 65- 9 TYFA T LGQIKR ER+E +PWRTYKSK+ KYAKLK D +V VAPI+L+DV+L++ Sbjct: 601 DATTYFAATRLGQIKRVERKEFTPWRTYKSKSVKYAKLKDDTDQIVAVAPIKLDDVLLIS 66- 0 Query: 660 YNGYALRFSINDVPVVGSKAAGVKAMNLKDRDHIVSAFIANTTSLYLLTHRGSLKRMAID 71- 9 NGYALRF+I +VPVVG+KAAGVKAMNLK+ D + SAFI NT+S YLLT RGSLKR++ID Sbjct: 661 QNGYALRFNIEEVPVVGAKAAGVKAMNLKEDDTLQSAFICNTSSFYLLTQRGSLKRVSID 72- 0 Query: 720 VIPTTSRANRGLQVLRELKSKPHRVFKAGPVYLEDSSFEFDLFSSVSNHEGDTFVLEIMS 77- 9 IP TSRA RGLQVLRELK+KPHRVF AG V + F DLFS+ T L + S Sbjct: 721 EIPATSRAKRGLQVLRELKNKPHRVFLAGSV--AEQGFVGDLFSTEVEENDQT--LLVQS 77- 6 Query: 780 KTGKVYDVDLSQWSFSERTSNGSFVSDKISDEEVFSVKIK 819 G +Y+ L + SERTSNGSF+SD ISDEEVF +K Sbjct: 777 NKGTIYESRLQDLNLSERTSNGSFISDTISDEEVFDAYLK 816 A related DNA sequence was identified in S. pyogenes <SEQ ID 2823> which encodes the amino acid sequence <SEQ ID 2824>. Analysis of this protein sequence reveals the following: TABLE-US-02708 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.53 Transmembrane 376-392 (376-394) ----- Final Results ----- bacterial membrane --- Certainty = 0.1213 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02709 Identities = 633/819 (77%), Positives = 719/819 (87%) Query: 1 MSNIQNMSLEDIMGERFGRYSKYIIQERALPDIRDGLKPVQRRILYSMNKDGNTFEKGFR 60 MSNIQNMSLEDIMGERFGRYSKYIIQERALPDIRDGLKPVQRRILYSMNKDGNTFEKG+R Sbjct: 3 MSNIQNMSLEDIMGERFGRYSKYIIQERALPDIRDGLKPVQRRILYSMNKDGNTFEKGYR 62 Query: 61 KSAKSVGNVMGNFHPHGDSSIYDAMVRMSQDWKNRETLIEMHGNNGSMDGDPAAAMRYTE 120- KSAKSVGN+MGNFHPHGDSSIYDAMVRMSQDWKNRE L+EMHGNNGSMDGDP AAMRYTE Sbjct: 63 KSAKSVGNIMGNFHPHGDSSIYDAMVRMSQDWKNREILVEMHGNNGSMDGDPPAAMRYTE 122- Query: 121 ARLSEIAGYLLQDIDKNTVPFAWNFDDTEKEPTVLPAAFPNLLVNGATGISAGYATDIPP 18- 0 ARLSEIAGYLLQDI+KNTV FAWNFDDTEKEPTVLPAAFPNLLVNG++GISAGYATDIPP Sbjct: 123 ARLSEIAGYLLQDIEKNTVSFAWNFDDTEKEPTVLPAAFPNLLVNGSSGISAGYATDIPP 18- 2 Query: 181 HNLAEVIDAVVYMIDHPKAKLDKLMEFLPGPDFPTGAIIQGKDEIRKAYETGKGRVAVRS 24- 0 HNL+EVIDAVVYMIDHPKA L+KLMEFLPGPDFPTG IIQG DEI+KAYETGKGRV VRS Sbjct: 183 HNLSEVIDAVVYMIDHPKASLEKLMEFLPGPDFPTGGIIQGADEIKKAYETGKGRVVVRS 24- 2 Query: 241 RTAIETLKGGKKQIIVTEIPYEVNKSVLVKRIDDVRVNNKVPGIAEVRDESDRDGLRIAI 30- 0 RT IE LKGGK+QIIVTEIPYEVNK+VLVK+IDDVRVNNKVPGI EVRDESDR GLRIAI Sbjct: 243 RTEIEELKGGKQQIIVTEIPYEVNKAVLVKKIDDVRVNNKVPGIVEVRDESDRTGLRIAI 30- 2 Query: 301 ELKKEADETIVLNYLFKYTDLQVNYNFNMVAIDDYTPKQVGLSRILTSYIAHRREIIIAR 36- 0 ELKKEAD +LNYL KYTDLQVNYNFNMVAID +TP+QVGL +IL+SYI+HR++III R Sbjct: 303 ELKKEADSQTILNYLLKYTDLQVNYNFNMVAIDHFTPRQVGLQKILSSYISHRKDIIIER 36- 2 Query: 361 SKFDKEKAEKRLHIVEGLIRVLSILDEVIALIRASENKADAKENLKVSYEFSEAQAEAIV 42- 0 SKFDK KAEKRLHIVEGLIRVLSILDE+IALIR+S+NKADAKENLKVSY+FSE QAEAIV Sbjct: 363 SKFDKAKAEKRLHIVEGLIRVLSILDEIIALIRSSDNKADAKENLKVSYDFSEEQAEAIV 42- 2 Query: 421 TLQLYRLTNTDIVTLREEEEELRQQITMLKAIISDERTMYNVMKRELREVKKKFANTRRS 48- 0 TLQLYRLTNTDIVTL+ EE +LR IT L AII DE TMYNVMKRELREVKKKFAN R S Sbjct: 423 TLQLYRLTNTDIVTLQNEENDLRDLITTLSAIIGDEATMYNVMKRELREVKKKFANPRLS 48- 2 Query: 481 ELQELAETIEIDTASLIIEEDTYVSVTRGGYVKRTSPRSFNASTVDELGKREDDELIFVS 54- 0 ELQ ++ IEIDTASLI EE+T+VSVTRGGY+KRTSPRSFNAS+++E+GKR+DDELIFV Sbjct: 483 ELQAESQIIEIDTASLIAEEETFVSVTRGGYLKRTSPRSFNASSLEEVGKRDDDELIFVK 54- 2 Query: 541 NAKTTQHLLMFTNLGNLAYRPVHELADIRWKDVGEHLSQNLVNFASNEEIIYAELVDDFT 60- 0 AKTT+HLL+FT LGN+ YRP+HEL D+RWKD+GEHLSQ + NFA+ EEI+YA++V F Sbjct: 543 QAKTTEHLLLFTTLGNVIYRPIHELTDLRWKDIGEHLSQTISNFATEEEILYADIVTSFD 60- 2 Query: 601 KETYFAVTSLGQIKRFERQEISPWRTYKSKTAKYAKLKSVEDYVVTVAPIQLEDVILVTY 66- 0 + Y AVT G IKRF+R+E+SPWRTYKSK+ KY KLK +D VVT++P+ +ED++LVT Sbjct: 603 QGLYVAVTQNGFIKRFDRKELSPWRTYKSKSTKYVKLKDDKDRVVTLSPVIMEDLLLVTK 66- 2 Query: 661 NGYALRFSINDVPVVGSKAAGVKAMNLKDRDHIVSAFIANTTSLYLLTHRGSLKRMAIDV 72- 0 NGYALRFS +VP+ G K+AGVK +NLK+ D + SAF + S ++LT RGSLKRMA+D Sbjct: 663 NGYALRFSSQEVPIQGLKSAGVKGINLKNDDSLASAFAVTSNSFFVLTQRGSLKRMAVDD 72- 2 Query: 721 IPTTSRANRGLQVLRELKSKPHRVFKAGPVYLEDSSFEFDLFSSVSNHEGDTFVLEIMSK 78- 0 IP TSRANRGL VLRELK+KPHRVF AG V + S+ +FDLF+ + E + +LE++SK Sbjct: 723 IPQTSRANRGLLVLRELKTKPHRVFLAGGVQSDTSAEQFDLFTDIPEEETNQQMLEVISK 78- 2 Query: 781 TGKVYDVDLSQWSFSERTSNGSFVSDKISDEEVFSVKIK 819 TG+ Y++ L S SER SNGSF+SD ISD+EV + + Sbjct: 783 TGQTYEIALETLSLSERISNGSFISDTISDQEVLVARTR 821 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 930 A DNA sequence (GBSx0986) was identified in S. agalactiae <SEQ ID 2825> which encodes the amino acid sequence <SEQ ID 2826>. Analysis of this protein sequence reveals the following: TABLE-US-02710 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3369 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02711 >GP: AAF64593 GB: AF169649 branched-chain aminotransferase IlvE [Lactococcus lactis] Identities = 259/340 (76%), Positives = 294/340 (86%) Query: 1 MTVNLDWDNLGFAYRKLPFRYISHFKDGKWDDGKLTDDATLHISESSPALHYGQQAFEGL 60 M +NLDW+NLGF+YR LPFRYI+ FKDGKW G+LT D LHISESSPALHYGQQ FEGL Sbjct: 1 MAINLDWENLGFSYRNLPFRYIARFKDGKWSAGELTGDNQLHISESSPALHYGQQGFEGL 60 Query: 61 KAYRTKDGSIQLFRPDQNAERLQRTADRLLMPHVPTDKFIAAVKSVVRANEEFVPPYGTG 120- KAYRTKDGSIQLFRPDQNA RLQ+TA RL M V T+ FI AVK VV+AN++FVPPYGTG Sbjct: 61 KAYRTKDGSIQLFRPDQNAARLQKTARRLCMAEVSTEMFIDAVKQVVKANKDFVPPYGTG 120- Query: 121 ATLYIRPLLIGVGDIIGVKPAEEYIFTVFAMPVGSYFKGGLTPTNFIVSKEYDRAAPNGT 18- 0 ATLY+RPLLIGVGD+IGVKPA+EYIF VFAMPVGSYFKGGL P+ F++S+EYDRAAP GT Sbjct: 121 ATLYLRPLLIGVGDVIGVKPADEYIFKVFAMPVGSYFKGGLAPSKFVISREYDRAAPLGT 18- 0 Query: 181 GAAKVGGNYAASLLPGKYAHEKQFSDVIYLDPATHTKIEEVGAANFFGITKDNQFITPLS 24- 0 G AKVGGNYAASL A ++D IYLDP+THTKIEEVGAANFFGIT DN+FITPLS Sbjct: 181 GGAKVGGNYAASLQAEVGAKASGYADAIYLDPSTHTKIEEVGAANFFGITADNEFITPLS 24- 0 Query: 241 PSILPSITKYSLLYLAKERFGMEAIEGDVFVDELDKFTEAGACGTAAVISPIGGIQNGDD 30- 0 PSILPSITKYSLLYLA+ R G++AIEG+V+ +L KF EAGACGTAA+ISPIG I +G+D Sbjct: 241 PSILPSITKYSLLYLAEHRLGLKAIEGEVYAKDLGKFVEAGACGTAAIISPIGRIDDGED 30- 0 Query: 301 FHVFYSETEVGPATRKLYDELVGIQFGDVEAPEGWIYKVD 340 ++F+SETEVGP ++LYDELVGIQFGDVEAPEGWI KVD Sbjct: 301 SYIFHSETEVGPTVKRLYDELVGIQFGDVEAPEGWIVKVD 340 A related DNA sequence was identified in S. pyogenes <SEQ ID 2827> which encodes the amino acid sequence <SEQ ID 2828>. Analysis of this protein sequence reveals the following: TABLE-US-02712 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1208 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02713 Identities = 280/340 (82%), Positives = 308/340 (90%) Query: 1 MTVNLDWDNLGFAYRKLPFRYISHFKDGKWDDGKLTDDATLHISESSPALHYGQQAFEGL 60 MT+ +DWDNLGF Y KLPFRYIS++K+G+WD G+LT+DATLHISES+PALHYGQQAFEGL Sbjct: 16 MTIAIDWDNLGFEYHKLPFRYISYYKNGQWDKGQLTEDATLHISESAPALHYGQQAFEGL 75 Query: 61 KAYRTKDGSIQLFRPDQNAERLQRTADRLLMPHVPTDKFIAAVKSVVRANEEFVPPYGTG 120- KAYRTKDGSIQLFRPD+NA RLQ TADRLLMP V T++FI A K VV+ANE+FVPPYGTG Sbjct: 76 KAYRTKDGSIQLFRPDRNAVRLQATADRLLMPQVSTEQFIDAAKQVVKANEDFVPPYGTG 135- Query: 121 ATLYIRPLLIGVGDIIGVKPAEEYIFTVFAMPVGSYFKGGLTPTNFIVSKEYDRAAPNGT 18- 0 ATLY+RPLLIGVGDIIGVKPAEEYIFT+FAMPVG+YFKGGL PTNFIVS+ +DRAAP GT Sbjct: 136 ATLYLRPLLIGVGDIIGVKPAEEYIFTIFAMPVGNYFKGGLAPTNFIVSEAFDRAAPYGT 19- 5 Query: 181 GAAKVGGNYAASLLPGKYAHEKQFSDVIYLDPATHTKIEEVGAANFFGITKDNQFITPLS 24- 0 GAAKVGGNYA SLLPGK A FSDVIYLDPATHTKIEEVGAANFFGIT +N+F+TPLS Sbjct: 196 GAAKVGGNYAGSLLPGKAAKSAGFSDVIYLDPATHTKIEEVGAANFFGITANNEFVTPLS 25- 5 Query: 241 PSILPSITKYSLLYLAKERFGMEAIEGDVFVDELDKFTEAGACGTAAVISPIGGIQNGDD 30- 0 PSILPSITKYSLL LA+ER GM IEGDV ++ELDKF EAGACGTAAVISPIGGIQ D+ Sbjct: 256 PSILPSITKYSLLQLAEERLGMTVIEGDVPINELDKFVEAGACGTAAVISPIGGIQYKDN 31- 5 Query: 301 FHVFYSETEVGPATRKLYDELVGIQFGDVEAPEGWIYKVD 340 HVFYSETEVGP TR+LYDELVGIQFGD+EAPEGWI KVD Sbjct: 316 LHVFYSETEVGPVTRRLYDELVGIQFGDIEAPEGWIVKVD 355 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 931 A DNA sequence (GBSx0987) was identified in S. agalactiae <SEQ ID 2829> which encodes the amino acid sequence <SEQ ID 2830>. Analysis of this protein sequence reveals the following: TABLE-US-02714 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3459 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9365> which encodes amino acid sequence <SEQ ID 9366> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10915> which encodes amino acid sequence <SEQ ID 10916> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2831> which encodes the amino acid sequence <SEQ ID 2832>. Analysis of this protein sequence reveals the following: TABLE-US-02715 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3043 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02716 Identities = 22/36 (61%), Positives = 30/36 (83%) Query: 4 IVSKKDKKIEIQISDAQVTVNGTKVDGYQLVMEKKL 39 ++SKKDKKIEIQ+ D +V VN TK+DGYQL + K++ Sbjct: 1 VMSKKDKKIEIQLIDHKVMVNETKIDGYQLQIGKRV 36 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 932 A DNA sequence (GBSx0988) was identified in S. agalactiae <SEQ ID 2833> which encodes the amino acid sequence <SEQ ID 2834>. This protein is predicted to be glycyl-tRNA synthetase beta subunit (glyS). Analysis of this protein sequence reveals the following: TABLE-US-02717 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1617 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02718 >GP: CAB73488 GB: AL139077 glycyl-tRNA synthetase beta chain [Campylobacter jejuni] Identities = 33/90 (36%), Positives = 49/90 (53%), Gaps = 2/90 (2%) Query: 3 RAFNLAEKVTHSVLVDSSLFENNQEKALYQAILSLELTEDMHDNLDKLFALSPIINDFFD 62 R N+A K H V D SLF E LY+A + + L+ LFAL P I++FF+ Sbjct: 570 RLANIATKNPHKV--DESLFVQEAESKLYKAFQEKTKANSLQEKLENLFALKPFIDEFFN 62- 7 Query: 63 NTMVMTDDEKMKQNRLAILNSLVAKARTVA 92 M+ +DEK+K NR A++ + A+ +A Sbjct: 628 QVMINAEDEKLKNNRQALVYEIYAEFLKIA 657 There is also homology to SEQ ID 2836. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 933 A DNA sequence (GBSx0989) was identified in S. agalactiae <SEQ ID 2837> which encodes the amino acid sequence <SEQ ID 2838>. Analysis of this protein sequence reveals the following: TABLE-US-02719 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4825 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02720 >GP: CAB13672 GB: Z99113 ynzC [Bacillus subtilis] Identities = 41/72 (56%), Positives = 56/72 (76%) Query: 5 KIARINELSKKKKTVGLTGEEKVEQAKLREEYIEGFRRSVRHHVEGIKLVDDEGNDVTPE 64 KIARINEL+ K K +T EEK EQ KLR+EY++GFR S+++ ++ +K++D EGNDVTPE Sbjct: 6 KIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFRSSMKNTLKSVKIIDPEGNDVTPE 65 Query: 65 KLRQVQREKGLH 76 KL++ QR LH Sbjct: 66 KLKREQRNNKLH 77 A related DNA sequence was identified in S. pyogenes <SEQ ID 2839> which encodes the amino acid sequence <SEQ ID 2840>. Analysis of this protein sequence reveals the following: TABLE-US-02721 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4303 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02722 Identities = 79/85 (92%), Positives = 83/85 (96%) Query: 1 MDPKKIARINELSKKKKTVGLTGEEKVEQAKLREEYIEGFRRSVRHHVEGIKLVDDEGND 60 MDPKKIARINEL+KKKKTVGLTG EKVEQAKLREEYIEG+RRSVRHH+EGIKLVD+EGND Sbjct: 1 MDPKKIARINELAKKKKTVGLTGPEKVEQAKLREEYIEGYRRSVRHHIEGIKLVDEEGND 60 Query: 61 VTPEKLRQVQREKGLHGRSLDDPNS 85 VTPEKLRQVQREKGLHGRSLDDP S Sbjct: 61 VTPEKLRQVQREKGLHGRSLDDPKS 85 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 934 A DNA sequence (GBSx0990) was identified in S. agalactiae <SEQ ID 2841> which encodes the amino acid sequence <SEQ ID 2842>. Analysis of this protein sequence reveals the following:

TABLE-US-02723 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2343 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02724 >GP: AAB69985 GB: U94355 glycerol kinase [Enterococcus casseliflavus] Identities = 381/496 (76%), Positives = 439/496 (87%) Query: 3 SEEKYIMAIDQGTTSSRAIIFNKKGEKIASSQKEFPQIFPQAGWVEHNANQIWNSVQSVI 62 +E+ Y+MAIDQGTTSSRAIIF++ G+KI SSQKEFPQ FP++GWVEHNAN+IWNSVQSVI Sbjct: 2 AEKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVI 61 Query: 63 AGAFIESSIKPGQIEAIGITNQRETTVVWDKKTGLPIYNAIVWQSRQTAPIADQLKQEGH 122- AGAFIES I+P I IGITNQRETTVVWDK TG PI NAIVWQSRQ++PIADQLK +GH Sbjct: 62 AGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGH 121- Query: 123 TNMIHEKTGLVIDAYFSATKVRWILDHVPGAQERAEKGELLFGTIDTWLVWKLTDGLVHV 18- 2 T MIHEKTGLVIDAYFSATKVRW+LD++ GAQE+A+ GELLFGTID+WLVWKLTDG VHV Sbjct: 122 TEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHV 18- 1 Query: 183 TDYSNAARTMLYNIKELKWDDEILELLNIPKAMLPEVKSNSEVYGKTTPFHFYGGEVPIS 24- 2 TDYSNA+RTMLYNI +L+WD EIL+LLNIP +MLPEVKSNSEVYG T +HFYG EVPI+ Sbjct: 182 TDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPIA 24- 1 Query: 243 GMAGDQQAALFGQLAFEPGMVKNTYGTGSFIIMNTGEEMQLSQNNLLTTIGYGINGKVHY 30- 2 GMAGDQQAALFGQ+AFE GM+KNTYGTG+FI+MNTGEE QLS N+LLTTIGYGINGKV+Y Sbjct: 242 GMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYY 30- 1 Query: 303 ALEGSIFIAGSAIQWLRDGLRMIETSSESEGLAQSSTSDDEVYVVPAFTGLGAPYWDSNA 36- 2 ALEGSIF+AGSAIQWLRDGLRMIETS +SE LA + D+EVYVVPAFTGLGAPYWDS A Sbjct: 302 ALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEA 36- 1 Query: 363 RGSVFGLTRGTSKEDFVKATLQSIAYQVRDVIDTMQVDSGIDIQQLRVDGGAAMNNLLMQ 42- 2 RG+VFGLTRGT+KEDFV+ATLQ++AYQ +DVIDTM+ DSGIDI L+VDGGAA N+LLMQ Sbjct: 362 RGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQ 42- 1 Query: 423 FQADILGIDIARAKNLETTALGAAFLAGLSVGYWESMDELKELNATGQLFQATMNESRKE 48- 2 FQADIL ID+ RA NLETTALGAA+LAGL+VG+W+ +DELK + GQ+F M ++ Sbjct: 422 FQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERD 48- 1 Query: 483 KLYKGWRKAVKATQVF 498 LY+GW++AV ATQ F Sbjct: 482 NLYEGWKQAVAATQTF 497 A related DNA sequence was identified in S. pyogenes <SEQ ID 2843> which encodes the amino acid sequence <SEQ ID 2844>. Analysis of this protein sequence reveals the following: TABLE-US-02725 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2282 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02726 Identities = 464/500 (92%), Positives = 484/500 (96%) Query: 3 SEEKYIMAIDQGTTSSRAIIFNKKGEKIASSQKEFPQIFPQAGWVEHNANQIWNSVQSVI 62 S+EKYIMAIDQGTTSSRAIIFN+KGEK++SSQKEFPQIFP AGWVEHNANQIWNSVQSVI Sbjct: 2 SQEKYIMAIDQGTTSSRAIIFNQKGEKVSSSQKEFPQIFPHAGWVEHNANQIWNSVQSVI 61 Query: 63 AGAFIESSIKPGQIEAIGITNQRETTVVWDKKTGLPIYNAIVWQSRQTAPIADQLKQEGH 122- AGAFIESSIKP QIEAIGITNQRETTVVWDKKTG+PIYNAIVWQSRQTAPIA+QLKQ+GH Sbjct: 62 AGAFIESSIKPSQIEAIGITNQRETTVVWDKKTGVPIYNAIVWQSRQTAPIAEQLKQDGH 121- Query: 123 TNMIHEKTGLVIDAYFSATKVRWILDHVPGAQERAEKGELLFGTIDTWLVWKLTDGLVHV 18- 2 T MIHEKTGLVIDAYFSATK+RWILDHVPGAQERAEKGELLFGTIDTWLVWKLTDG VHV Sbjct: 122 TKMIHEKTGLVIDAYFSATKIRWILDHVPGAQERAEKGELLFGTIDTWLVWKLTDGAVHV 18- 1 Query: 183 TDYSNAARTMLYNIKELKWDDEILELLNIPKAMLPEVKSNSEVYGKTTPFHFYGGEVPIS 24- 2 TDYSNAARTMLYNIK+L WDDEILELLNIPK MLPEVKSNSE+YGKT FHFYGGEVPIS Sbjct: 182 TDYSNAARTMLYNIKDLTWDDEILELLNIPKDMLPEVKSNSEIYGKTAAFHFYGGEVPIS 24- 1 Query: 243 GMAGQQAALFGQLAFEPGMVKNTYGTGSFIIMNTGEEMQLSQNNLLTTIGYGINGKVHY 302- GMAGDQQAALFGQLAFEPGMVKNTYGTGSFIIMNTG+EMQLS NNLLTTIGYGINGKVHY Sbjct: 242 GMAGDQQAALFGQLAFEPGMVKNTYGTGSFIIMNTGDEMQLSSNNLLTTIGYGINGKVHY 30- 1 Query: 303 ALEGSIFIAGSAIQWLRDGLRMIETSSESEGLAQSSTSDDEVYVVPAFTGLGAPYWDSNA 36- 2 ALEGSIFIAGSAIQWLRDGL+MIETS ESE A +STSDDEVYVVPAFTGLGAPYWDSNA Sbjct: 302 ALEGSIFIAGSAIQWLRDGLKMIETSPESEQFALASTSDDEVYVVPAFTGLGAPYWDSNA 36- 1 Query: 363 RGSVFGLTRGTSKEDFVKATLQSIAYQVRDVIDTMQVDSGIDIQQLRVDGGAAMNNLLMQ 42- 2 RGSVFGLTRGTSKEDFVKATLQSIAYQVRDVIDTMQVDSGIDIQQLRVDGGAAMNN+LMQ Sbjct: 362 RGSVFGLTRGTSKEDFVKATLQSIAYQVRDVIDTMQVDSGIDIQQLRVDGGAAMNNMLMQ 42- 1 Query: 423 FQADILGIDIARAKNLETTALGAAFLAGLSVGYWESMDELKELNATGQLFQATMNESRKE 48- 2 FQADILGIDIARAKNLETTALGAAFLAGL+VGYWE MD LKELNATGQLF+A+MNESRKE Sbjct: 422 FQADILGIDIARAKNLETTALGAAFLAGLAVGYWEDMDALKELNATGQLFKASMNESRKE 48- 1 Query: 483 KLYKGWRKAVKATQVFAQED 502 KLYKGW++AVKATQVF QE+ Sbjct: 482 KLYKGWKRAVKATQVFTQEE 501 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 935 A DNA sequence (GBSx0992) was identified in S. agalactiae <SEQ ID 2845> which encodes the amino acid sequence <SEQ ID 2846>. Analysis of this protein sequence reveals the following: TABLE-US-02727 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3146 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 936 A DNA sequence (GBSx0993) was identified in S. agalactiae <SEQ ID 2847> which encodes the amino acid sequence <SEQ ID 2848>. This protein is predicted to be alpha-glycerophosphate oxidase (glpD). Analysis of this protein sequence reveals the following: TABLE-US-02728 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.81 Transmembrane 20-36 (20-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.1723 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02729 >GP: AAC34740 GB: U94770 alpha-glycerophosphate oxidase [Streptococcus pneumoniae] Identities = 464/608 (76%), Positives = 539/608 (88%) Query: 1 MEFSRETRRLALQRMQDRTLDLLIIGGGITGAGVALQAAASGLDTGLIEMQDFAEGTSSR 60 MEFS++TR L++++MQ+RTLDLLIIGGGITGAGVALQAAASGL+TGLIEMQDFAEGTSSR Sbjct: 1 MEFSKKTRELSIKKMQERTLDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSR 60 Query: 61 STKLVHGGLRYLKQFDVEVVSDTVSERAVVQQIAPHIPKPDPMLLPVYDEPGSTFSMFRL 120- STKLVHGGLRYLKQFDVEVVSDTVSERAVVQQIAPHIPKPDPMLLPVYDE G+TFS+FRL Sbjct: 61 STKLVHGGLRYLKQFDVEVVSDTVSERAVVQQIAPHIPKPDPMLLPVYDEDGATFSLFRL 120- Query: 121 KVAMDLYDLLAGVTNTPAANKVLSAEDVLKREPDLQKEGLLGGGVYLDFRNNDARLVIEN 18- 0 KVAMDLYDLLAGV+NTP ANKVLS + VL+R+P+L+KEGL+GGGVYLDFRNNDARLVIEN Sbjct: 121 KVAMDLYDLLAGVSNTPTANKVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIEN 18- 0 Query: 181 IKRANRDGAYIASHVKAEDFLFDDNNQIIGVRARDLLTDQVIDIKARLVINTTGPWSDTV 24- 0 IKRAN+DGA IA+HVKAE FLFD++ +I GV ARDLLTDQV +IKARLVINTTGPWSD V Sbjct: 181 IKRANQDGALIANHVKAEGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKV 24- 0 Query: 241 RNFSNEGKQIHQLRPTKGVHLVVDRQKLNISQPVYVDTGLNDGRMIFVLPREDKTYFGTT 30- 0 RN SN+G Q Q+RPTKGVHLVVD K+ +SQPVY DTGL DGRM+FVLPRE+KTYFGTT Sbjct: 241 RNLSNKGTQFSQMRPTKGVHLVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTT 30- 0 Query: 301 DTDYHGDLEHPTVTKEDVDYLLNIVNKRFPEAELTIDDIESSWAGLRPLLSGNSASDYNG 36- 0 DTDY GDLEHP VT+EDVDYLL IVN RFPE+ +TIDDIESSWAGLRPL++GNSASDYNG Sbjct: 301 DTDYTGDLEHPKVTQEDVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNG 36- 0 Query: 361 GNSGKLSDESFEELIDSVKDYIAHKNHREDVEKAISHVESSTSEKELDPSAVSRGSSFER 42- 0 GN+G +SDESF+ LI +V+ Y++ + REDVE A+S +ESSTSEK LDPSAVSRGSS +R Sbjct: 361 GNNGTISDESFDNLIATVESYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDR 42- 0 Query: 421 DDNGLLTLAGGKITDYRKMAEGAMETIINILDKEYNRKFKLINSKTYPVSGGEINPSNVD 48- 0 DDNGLLTLAGGKITDYRKMAEGAME +++IL E++R FKLINSKTYPVSGGE+NP+NVD Sbjct: 421 DDNGLLTLAGGKITDYRKMAEGAMERVVDILKAEFDRSFKLINSKTYPVSGGELNPANVD 48- 0 Query: 481 SEIEAYAQLGTLSGLSIEDARYIANLYGSNAPKLFALTRQITEAEGLSLVETLSLHYAMD 54- 0 SEIEA+AQLG GL ++A Y+ANLYGSNAPK+FAL + +A GLSL +TLSLHYAM Sbjct: 481 SEIEAFAQLGVSRGLDSKEAHYLANLYGSNAPKVFALAHSLEQAPGLSLADTLSLHYAMR 54- 0 Query: 541 YEMALSPTDFFLRRTNHMLFMRDNLDSLIQPVIDEMAKHYQWSDQDKTFYEEELHETLKD 60- 0 E+ALSP DF LRRTNHMLFMRD+LDS+++PV+DEM + Y W++++K Y ++ L + Sbjct: 541 NELALSPVDFLLRRTNHMLFMRDSLDSIVEPVLDEMGRFYDWTEEEKATYRADVEAALAN 60- 0 Query: 601 NDLAALKD 608 NDLA LK+ Sbjct: 601 NDLAELKN 608 There is also homology to SEQ ID 128. SEQ ID 2848 (GBS93) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 7 (lane 7; MW 70.6 kDa). GBS93-His was purified as shown in FIG. 192, lane 4. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 937 A DNA sequence (GBSx0994) was identified in S. agalactiae <SEQ ID 2849> which encodes the amino acid sequence <SEQ ID 2850>. Analysis of this protein sequence reveals the following: TABLE-US-02730 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0965 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 938 A DNA sequence (GBSx0995) was identified in S. agalactiae <SEQ ID 2851> which encodes the amino acid sequence <SEQ ID 2852>. This protein is predicted to be glycerol uptake facilitator protein (glpF). Analysis of this protein sequence reveals the following: TABLE-US-02731 Possible Site: 55 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.43 Transmembrane 220-236 (216-236) INTEGRAL Likelihood = -6.48 Transmembrane 139-155 (136-158) INTEGRAL Likelihood = -3.88 Transmembrane 87-103 (83-107) INTEGRAL Likelihood = -3.03 Transmembrane 164-180 (162-183) ----- Final Results ----- bacterial membrane --- Certainty = 0.3972 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8689> which encodes amino acid sequence <SEQ ID 8690> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-02732 Lipop: Possible site: -1 Crend: 5 SRCFLG: 0 McG: Length of UR: 21 Peak Value of UR: 2.51 Net Charge of CR: -2 McG: Discrim Score: 4.43 GvH: Signal Score (-7.5): -0.139999 Possible site: 50 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 51 ALOM program count: 4 value: -7.43 threshold: 0.0 INTEGRAL Likelihood = -7.43 Transmembrane 215-231 (211-231) INTEGRAL Likelihood = -6.48 Transmembrane 134-150 (131-153) INTEGRAL Likelihood = -3.88 Transmembrane 82-98 (78-102) INTEGRAL Likelihood = -3.03 Transmembrane 159-175 (157-178) PERIPHERAL Likelihood = 4.98 65 modified ALOM score: 1.99 icm1 HYPID: 7 CFP: 0.397 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3972 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02733 >GP: AAA91618 GB: U12567 glycerol uptake facilitator [Streptococcus pneumoniae] Identities = 150/230 (65%), Positives = 194/230 (84%), Gaps 1/230 (0%) Query: 7 DIFGEFLGTALLVLLGNGVVAGVVLPKTKNHNSGWIVITFGWGLAVAIAALVSGNISPAH 66 ++FGEFLGT +L+LLGNGVVAGVVLPKTK+++SGWIVIT G+AVA+A VSG +SPAH Sbjct: 4 ELFGEFLGTLILILLGNGVVAGVVLPKTKSNSSGWIVITMV-GIAVAVAVFVSGKLSPAH 62 Query: 67 LNPAVSLAFAIKGDLAWGTAILYMIAQIIGAMLGSLLVYLQFRPHYEAAENRADILGTFA 126- LNPAV++ A+KG L W + + Y++AQ GAMLG +LV+LQF+PHYEA EN +IL TF+ Sbjct: 63 LNPAVTIGVALKGGLPWASVLPYILAQFAGAMLGQILVWLQFKPHYEAEENAGNILATFS 122- Query: 127 TGPALKDNFSNFLSEVLGTLVLVLTIFAIGKYNMPPGVGTMSVGMLVVGIGLSLGGTTGY 18- 6 TGPA+KD SN +SE+LGT VLVLTIFA+G Y+ G+GT +VG L+VGIGLSLGGTTGY Sbjct: 123 TGPAIKDTVSNLISEILGTFVLVLTIFALGLYDFQAGIGTFAVGTLIVGIGLSLGGTTGY 18- 2 Query: 187 AINPARDFGPRLLHALLPMKNKGDSDWTYSWIPIVGPMVGAILAALIFAM 236 A+NPARD GPR++H++LP+ NKGD DW+Y+WIP+VGP++GA LA L+F++ Sbjct: 183 ALNPARDLGPRIMHSILPIPNKGDGDWSYAWIPVVGPVIGAALAVLVFSL 232 A related DNA sequence was identified in S. pyogenes <SEQ ID 2853> which encodes the amino acid sequence <SEQ ID 2854>. Analysis of this protein sequence reveals the following: TABLE-US-02734 Possible site: 50 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.13 Transmembrane 213-229 (209-232) INTEGRAL Likelihood = -5.52 Transmembrane 137-153 (132-157) INTEGRAL Likelihood = -4.35 Transmembrane 159-175 (155-178) INTEGRAL Likelihood = -1.17 Transmembrane 85-101 (85-101) ----- Final Results ----- bacterial membrane --- Certainty = 0.4652 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02735 >GP: AAA91618 GB: U12567 glycerol uptake facilitator [Streptococcus pneumoniae] Identities = 159/230 (69%), Positives = 196/230 (85%), Gaps = 1/230 (0%) Query: 2 DIFGEFLGTALLVLLGNGVVAGVVLPKTKTHASGWIVIATGWGIAVAVAVFISGKVAPAH 61 ++FGEFLGT +L+LLGNGVVAGVVLPKTK+++SGWIVI T GIAVAVAVF+SGK++PAH Sbjct: 4 ELFGEFLGTLILILLGNGVVAGVVLPKTKSNSSGWIVI-TMVGIAVAVAVFVSGKLSPAH 62 Query: 62 LNPAVSLAFAMSGTIAWSTAIAYSLAQLLGAMVGSTLVFLQFRPHYLAAESQADILGTFA 121- LNPAV++ A+ G + + W++ + Y LAQ GAM+G LV+LQF+PHY A E+ +IL TF+ Sbjct: 63 LNPAVTIGVALKGGLPWASVLPYILAQFAGAMLGQILVWLQFKPHYEAEENAGNILATFS 122- Query: 122 TGPAIRDTSSNLLSEIFGTFVLMLGILAFGLYDMPAGLGTLCVGTLVIGIGLSLGGTTGY 18- 1 TGPAI+DT SNL+SEI GTFVL+L I A GLYD AG+GT VGTL++GIGLSLGGTTGY Sbjct: 123 TGPAIKDTVSNLISEILGTFVLVLTIFALGLYDFQAGIGTFAVGTLIVGIGLSLGGTTGY 18- 2 Query: 182 AINPARDLGPRLVHAILPLNNKGDSDWSYAWIPVVGPIIGAVLAVLLFQV 231 A+NPARDLGPR++H+ILP+ NKGD DWSYAWIPVVGP+IGA LAVL+F + Sbjct: 183 ALNPARDLGPRIMHSILPIPNKGDGDWSYAWIPVVGPVIGAALAVLVFSL 232 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02736 Identities = 169/232 (72%), Positives = 202/232 (86%) Query: 6 MDIFGEFLGTALLVLLGNGVVAGVVLPKTKNHNSGWIVITFGWGLAVAIAALVSGNISPA 65 MDIFGEFLGTALLVLLGNGVVAGVVLPKTK H SGWIVI GWG+AVA+A +SG ++PA Sbjct: 1 MDIFGEFLGTALLVLLGNGVVAGVVLPKTKTHASGWIVIATGWGIAVAVAVFISGKVAPA 60 Query: 66 HLNPAVSLAFAIKGDLAWGTAILYMIAQIIGAMLGSLLVYLQFRPHYEAAENRADILGTF 125- HLNPAVSLAFA+ G +AW TAI Y +AQ++GAM+GS LV+LQFRPHY AAE++ADILGTF Sbjct: 61 HLNPAVSLAFAMSGTIAWSTAIAYSLAQLLGAMVGSTLVFLQFRPHYLAAESQADILGTF 120- Query: 126 ATGPALKDNFSNFLSEVLGTLVLVLTIFAIGKYNMPPGVGTMSVGMLVVGIGLSLGGTTG 18- 5 ATGPA++D SN LSE+ GT VL+L I A G Y+MP G+GT+ VG LV+GIGLSLGGTTG Sbjct: 121 ATGPAIRDTSSNLLSEIFGTFVLMLGILAFGLYDMPAGLGTLCVGTLVIGIGLSLGGTTG 18- 0 Query: 186 YAINPARDFGPRLLHALLPMKNKGDSDWTYSWIPIVGPMVGAILAALIFAMM 237 YAINPARD GPRL+HA+LP+ NKGDSDW+Y+WIP+VGP++GA+LA L+F +M Sbjct: 181 YAINPARDLGPRLVHAILPLNNKGDSDWSYAWIPVVGPIIGAVLAVLLFQVM 232 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 939 A DNA sequence (GBSx0996) was identified in S. agalactiae <SEQ ID 2855> which encodes the amino acid sequence <SEQ ID 2856>. This protein is predicted to be NADH oxidase. Analysis of this protein sequence reveals the following: TABLE-US-02737 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -2.87 Transmembrane 152-168 (152-168) ----- Final Results ----- bacterial membrane --- Certainty = 0.2147 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9523> which encodes amino acid sequence <SEQ ID 9524> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02738 >GP: CAA48728 GB: X68847 NADH oxidase [Enterococcus faecalis] Identities = 105/423 (24%), Positives = 197/423 (45%), Gaps = 15/423 (3%) Query: 10 IVILGASFAGMTCAQKLRQLNPNWDIVLIDKEIHPDYVPNGLNWYYRHEISGLNQAMWQT 69 - +V++G + AG + + + +P ++ + ++ + ++ G+ Y + + Sbjct: 3 VVVVGCTHAGTSAVKSILANHPEAEVTVYERNDNISFLSCGIALYVGGVVKNAADLFYSN 62 Query: 70 EEEQRLQNIRCLFGLKVEKINKEDR-----ELMLSDGSSVYYDQLICAMGSQAESTYIDG 124- EE VE+IN +D+ L +V YD+L+ GS I G Sbjct: 63 PEELASLGATVKMEHNVEEINVDDKTVTAKNLQTGATETVSYDKLVMTTGSWPIIPPIPG 122- Query: 125 ADAQGVLTTKTYATSQNAKQVLDKSHKVAVVGAGIIGLDIAYSLHESGKAVTLLEAQERP 18- 4 DA+ +L K Y+ + + + +V VVG G IG+++ + ESGK VTL++ +R Sbjct: 123 IDAENILLCKNYSQANVIIEKAKDAKRVVVVGGGYIGIELVEAFVESGKQVTLVDGLDRI 18- 2 Query: 185 DFRHTDPDMSLPLLDAMAESKLHFFQNQKVEKITVTREEKLCLRTLTGDTFTVDAVILAV 24- 4 ++ D + L + + ++ + V++ + K+ F D VI+ V Sbjct: 183 LNKYLDKPFTDVLEKELVDRGVNLALGENVQQFVADEQGKVAKVITPSQEFEADMVIMCV 24- 2 Query: 245 NFRPDSRLLTGLVDLSVDNSVVVNDYFQTSDPNIYAIGDLIWSYFKGLNSAYYMPLINQA 30- 4 FRP++ LL VD+ + ++ VN+Y QTS+P+I+A GD ++ + Y+PL A Sbjct: 243 GFRPNTELLKDKVDMLPNGAIEVNEYMQTSNPDIFAAGDSAVVHYNPSQTKNYIPLATNA 30- 2 Query: 305 IRSAQMLAYHLSGHAVPKLKITRATGSKHFGYYRANIGLT---------ELEAGFYEDTV 35- 5 +R ++ +L+ + +G FG+ + G+T ++EA +ED Sbjct: 303 VRQGMLVGRNLTEQKLAYRGTQGTSGLYLFGWKIGSTGVTKESAKLNGLDVEATVFEDNY 36- 2 Query: 356 SVTYFPKEQYDLRIKLIANQKTGHLLGAQLISKENCLATANQLVQAISCDMTDFDLAFQD 41- 5 + P + L ++L+ + T ++G QL+SK + +AN L A+ MT DLA D Sbjct: 363 RPEFMPTTEKVL-MELVYEKGTQRIVGGQLMSKYDITQSANTLSLAVQNKMTVEDLAISD 42- 1 Query: 416 FIY 418 F + Sbjct: 422 FFF 424 A related DNA sequence was identified in S. pyogenes <SEQ ID 2857> which encodes the amino acid sequence <SEQ ID 2858>. Analysis of this protein sequence reveals the following:

TABLE-US-02739 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.35 Transmembrane 155-171 (155-173) ----- Final Results ----- bacterial membrane --- Certainty = 0.2338 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 54-56 The protein has homology with the following sequences in the databases: TABLE-US-02740 >GP: CAA44611 GB: X62755 NADH peroxidase [Enterococcus faecalis] Identities = 111/428 (25%), Positives = 202/428 (46%), Gaps = 24/428 (5%) Query: 10 VIGASFAGLAFVDKYKDLNPDSQIILIDKESCPNYIPNGINQLFRGDIQDLSDAMWGRAC 69 - V+G+S G V++ +L+PD++I +K +++ G+ G ++D++ R Sbjct: 5 VLGSSHGGYEAVEELLNLHPDAEIQWYEKGDFISFLSCGMQLYLEGKVKDVNSV---RYM 61 Query: 70 LAAQIESN--HRFIQAEVLAIEAPSNTLLLKDS-QGRVFEEGYETLVCAMGASPQSHYIE 126- ++ES + F E+ AI+ + + +KD G E Y+L+ + GA P I Sbjct: 62 TGEKMESRGVNVFSNTEITAIQPKEHQVTVKDLVSGEERVENYDKLIISPGAVPFELDIP 121- Query: 127 TSQTNKVLVTKYYEESQASLKLIEASQE-----VLVIGAGLIGLDLAYSLSLQGKRVKLI 18- 1 + + + + Q ++KL + + + V+VIG+G IG++ A + + GK+V +I Sbjct: 122 GKDLDNIYLMR---GRQWAIKLKQKTVDPEVNNVVVIGSGYIGIEAAEAFAKAGKKVTVI 17- 8 Query: 182 EAAERPDFYQTDAELIAPVMAEMSTHHVTFINNKRVTAIHEIEGKVVAHTEQGDTFQGDL 24- 1 + +RP D E + EM +++T + V +E +G+V + + DL Sbjct: 179 DILDRPLGVYLDKEFTDVLTEEMEANNITIATGETVER-YEGDGRVQKVVTDKNAYDADL 23- 7 Query: 242 AILAINFRPNTHLLQGQVACALDKTILVNENLQTSQANIYAIGDMVSLHFGILGMDYYTP 30- 1 ++A+ RPNT L+G + + I +E ++TS+ +++A+GD + + + Sbjct: 238 VVVAVGVRPNTAWLKGTLELHPNGLIKTDEYMRTSEPDVFAVGDATLIKYNPADTEVNIA 29- 7 Query: 302 LINQAMKTGQALALHLAGYPIPPLQTVK-VLGSSHFDYYRASVGVTE-------EEAELY 35- 3 L A K G+ +L P+ P V+ G + FDY AS G+ E +E + Sbjct: 298 LATNARKQGRFAVKNLE-EPVKPFPGVQGSSGLAVFDYKFASTGINEVMAQKLGKETKAV 35- 6 Query: 354 MDTCSYLYQNGDSKNLFWLKLIARKTDGILIGAQLLSKTNALVIANQLGQALALKVTDAD 41- 3 YL K W KL+ ++GAQL+SK + N + A+ K+T D Sbjct: 357 TVVEDYLMDFNPDKQKAWFKLVYDPETTQILGAQLMSKADLTANINAISLAIQAKMTIED 41- 6 Query: 414 LAFQDFLF 421 LA+ DF F Sbjct: 417 LAYADFFF 424 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02741 Identities = 192/440 (43%), Positives = 276/440 (62%), Gaps = 7/440 (1%) Query: 8 KVIVILGASFAGMTCAQKLRQLNPNWDIVLIDKEIHPDYVPNGLNWYYRHEISGLNQAMW 67 K I ++GASFAG+ K + LNP+ I+LIDKE P+Y+PNG+N +R +I L+ AMW Sbjct: 6 KTIHVIGASFAGLAFVDKYKDLNPDSQIILIDKESCPNYIPNGINQLFRGDIQDLSDAMW 65 Query: 68 -QTEEEQRLQNIRCLFGLKVEKINKEDRELMLSDGSSVY----YDQLICAMGSQAESTYI 122- + ++++ +V I L+L D Y+ L+CAMG+ +S YI Sbjct: 66 GRACLAAQIESNHRFIQAEVLAIEAPSNTLLLKDSQGRVFEEGYETLVCAMGASPQSHYI 125- Query: 123 DGADAQGVLTTKTYATSQNAKQVLDKSHKVAVVGAGIIGLDIAYSLHESGKAVTLLEAQE 18- 2 + + VL TK Y SQ + ++++ S +V V+GAG+IGLD+AYSL GK V L+EA E Sbjct: 126 ETSQTNKVLVTKYYEESQASLKLIEASQEVLVIGAGLIGLDLAYSLSLQGKRVKLIEAAE 18- 5 Query: 183 RPDFRHTDPDMSLPLLDAMAESKLHFFQNQKVEKITVTREEKLCLRTLTGDTFTVDAVIL 24- 2 RPDF TD ++ P++ M+ + F N++V I E K+ T GDTF D IL Sbjct: 186 RPDFYQTDAELIAPVMAEMSTHHVTFINNKRVTAIHEI-EGKVVAHTEQGDTFQGDLAIL 24- 4 Query: 243 AVNFRPDSRLLTGLVDLSVDNSVVVNDYFQTSDPNIYAIGDLIWSYFKGLNSAYYMPLIN 30- 2 A+NFRP++ LL G V ++D +++VN+ QTS NIYAIGD++ +F L YY PLIN Sbjct: 245 AINFRPNTHLLQGQVACALDKTILVNENLQTSQANIYAIGDMVSLHFGILGMDYYTPLIN 30- 4 Query: 303 QAIRSAQMLAYHLSGHAVPKLKITRATGSKHFGYYRANIGLTELEAGFYEDTVSVTYFPK 36- 2 QA+++ Q LA HL+G+ +P L+ + GS HF YYRA++G+TE EA Y DT S Y Sbjct: 305 QAMKTGQALALHLAGYPIPPLQTVKVLGSSHFDYYRASVGVTEEEAELYMDTCSYLYQNG 36- 4 Query: 363 EQYDL-RIKLIANQKTGHLLGAQLISKENCLATANQLVQAISCDMTDFDLAFQDFIYTAR 42- 1 + +L +KLIA + G L+GAQL+SK N L ANQL QA++ +TD DLAFQDF++ Sbjct: 365 DSKNLFWLKLIARKTDGILIGAQLLSKTNALVIANQLGQALALKVTDADLAFQDFLFLQG 42- 4 Query: 422 ESEMAYMLHQAAINLYEKRI 441 S++AY LH+A + L+EKR+ Sbjct: 425 HSDLAYHLHEACLKLFEKRL 444 There is also homology to SEQ IDs 1820, 1876, 4666. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 940 A DNA sequence (GBSx0998) was identified in S. agalactiae <SEQ ID 2859> which encodes the amino acid sequence <SEQ ID 2860>. Analysis of this protein sequence reveals the following: TABLE-US-02742 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2980 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 941 A DNA sequence (GBSx0999) was identified in S. agalactiae <SEQ ID 2861> which encodes the amino acid sequence <SEQ ID 2862>. Analysis of this protein sequence reveals the following: TABLE-US-02743 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3548 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 942 A DNA sequence (GBSx1000) was identified in S. agalactiae <SEQ ID 2863> which encodes the amino acid sequence <SEQ ID 2864>. Analysis of this protein sequence reveals the following: TABLE-US-02744 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1685 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9525> which encodes amino acid sequence <SEQ ID 9526> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2865> which encodes the amino acid sequence <SEQ ID 2866>. Analysis of this protein sequence reveals the following: TABLE-US-02745 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3125(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02746 Identities = 179/476 (37%), Positives = 279/476 (58%), Gaps = 5/476 (1%) Query: 1 MRIEALMEKERRVQYRLLSFLRGSPQAIALKLALLETGLSRATFLKYINNLNSYFEQEKV 60 M+IE LM+KERR QYRLL L + + + LK + + LS+ T LKYI+NLN ++ + Sbjct: 21 MKIEDLMDKERRAQYRLLVTLYHAKETLRLKDLMRLSNLSKVTLLKYIDNLNHLCREQGL 80 Query: 61 NCRIVYYKDKLFLEEDYNLSNQEVLKALMKDSIKYTILISLFNQRQFTIVGLSQELMVSE 120- C+++ KD L L+E+ ++++ L+K+S+ Y IL ++ F I LS ELMVSE Sbjct: 81 ACQLLLEKDSLSLKENGQFHWEDLVALLLKESVAYQILTYMYCHEHFNITNLSVELMVSE 140- Query: 121 ATLNRHLAHLNELLAEFDIAISQGKQIGDELQWRYFYYELFKQLWSYDKCQNMIKKLDLD 18- 0 ATLNR LAHLN+LL+EFD+A+SQG+Q+G ELQWRYFY+ELF+ + ++ +LD Sbjct: 141 ATLNRQLAHLNQLLSEFDLALSQGRQLGSELQWRYFYFELFRHTLTRQGIDALVNQLDAS 20- 0 Query: 181 SLILLIERLAQHTLTREAHQNLGLWFSICHHRLLAMEKISDNLKPIVKHYQCNAFYKRLD 24- 0 L LIERL +L+ EA + L +W +I R+ + +D+ N F+KRL+ Sbjct: 201 HLATLIERLIGQSLSAEALEQLLIWLAISQARMSFQKSYNDHFLRDSDFMTSNIFFKRLE 26- 0 Query: 241 AALVLYMSRFALEYREGEVLATFAFLHSQNILPINTMEYIMGFGGPIIDCVTETIIYFKK 30- 0 + L+ Y+ R+ALE+ E + F FLH+ +LPI +M+Y +GFGGPI D ++E + KK Sbjct: 261 SMLLHYLRRYALEFDAFEAKSLFVFLHAYPLLPIASMKYSLGFGGPIADHISEALWLLKK 32- 0 Query: 301 ESILADETSDQVIYQLGQLYSHYYFFKGHILVEQPDLEQTYRLIDHNMRDKLHHISKKII 36- 0 ++ +T +++IY LG +S YFFKG IL + + + Y+L+ + R L I ++ Sbjct: 321 AHVIIHQTKEEIIYGLGIFFSKAYFFKGAILSQPTNSQYLYQLVGEDKRALLRVIINHLV 38- 0 Query: 361 ANVNRIRPLTEDGCSLLTLHLLELLIFSKNSQKMPFRIGLDMTGNAVEQSLLEYRIRQHF 42- 0 +++ D L+ +L LLIFS P +GL + N VE ++ E IR+H Sbjct: 381 LQMDQ----ETDFSQQLSDDILALLIFSIERHHEPLLVGLALGQNKVEAAIAELAIRRHL 43- 6 Query: 421 SGNNSIQVEPYDEGKGFD-MVIYQSHSRPYKAKLTYCLNKGASERELQEIDSLIYD 475 Q+ PYD K +D ++ YQ+ P + Y L + +S EL +++ + D Sbjct: 437 GHRRDFQLMPYDHQKVYDCLITYQTVCLPRQDLPYYRLKQYSSPYELTALEAFLKD 492 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 943 A DNA sequence (GBSx1001) was identified in S. agalactiae <SEQ ID 2867> which encodes the amino acid sequence <SEQ ID 2868>. This protein is predicted to be transketolase (tktA-1). Analysis of this protein sequence reveals the following: TABLE-US-02747 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2084(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9527> which encodes amino acid sequence <SEQ ID 9528> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02748 >GP: BAB06071 GB: AP001515 transketolase [Bacillus halodurans] Identities = 403/661 (60%), Positives = 520/661 (77%), Gaps = 8/661 (1%) Query: 6 IDQLAVNTVRTLSIDAIQAANSGHPGLPMGAAPMAYVLWNKFLNVNPKTSRNWTNRDRFV 65 ++QLAVNT+RTLSID+++ ANSGHPG+PMGAAPMA+ LW KF+N NP + +W NRDRFV Sbjct: 5 VEQLAVNTIRTLSIDSVEKANSGHPGMPMGAAPMAFCLWTKFMNHNP-ANPDWVNRDRFV 63 Query: 66 LSAGHGSALLYSLLHLAGYDLSIDDLKQFRQWGSKTPGHPEVNHTDGVEATTGPLGQGIA 125- LSAGHGS LLYSLLHL GYDLS+++L+ FRQWGSKTPGHPE HT GVEATTGPLGQG+A Sbjct: 64 LSAGHGSMLLYSLLHLTGYDLSLEELQNFRQWGSKTPGHPEYGHTPGVEATTGPLGQGVA 123- Query: 126 NAVGMAMAEAHLAAKFNKPGFDLVDHYTYTLHGDGCLMEGVSQEAASLAGHLKLGKLVLL 18- 5 AVGMAMAE HLAA +N+ G+++VDHYTYT+ GDG LMEGVS EAASLAGHLKLG+++LL Sbjct: 124 MAVGMAMAERHLAATYNRDGYNIVDHYTYTICGDGDLMEGVSAEAASLAGHLKLGRMILL 18- 3 Query: 186 YDSNDISLDGPTSQSFTEDVKGRFESYGWQHILVKDGNDLEAIAAAIEAAKAETDKPTII 24- 5 YDSNDISLDG SF+E V+ RF++YGW + V+DGN+L+ IA AIE AKA+ ++P++I Sbjct: 184 YDSNDISLDGDLHHSFSESVEDRFKAYGWHVVRVEDGNNLDEIAKAIEEAKAD-ERPSLI 24- 2 Query: 246 EVKTIIGFGAEKQGTSSV-HGAPLGAEGITFAKKAYVWEYP-DFTVPAEVADRFASDLQA 30- 3 EVKT IGFG+ +G SV HGAPLGA+ + K+AY W Y +F +P EVA + ++ Sbjct: 243 EVKTTIGFGSPNKGGKSVSHGAPLGADEVKLTKEAYEWTYENEFHIPEEVA-AYYEQVKQ 30- 1 Query: 304 RGAKAEEAWNDLFAKYEVEYPELATEYKEAFAG---QAETVELKAHDLGSSVASRVSSQQ 36- 0 +GA+ EE+WN+LFA+Y+ YPELA++++ A G + ++++G SVA+R SS + Sbjct: 302 QGAEKEESWNELFAQYKKAYPELASQFELAVHGDLPEGWDAVAPSYEVGKSVATRSSSGE 36- 1 Query: 361 AIQQLSTQLPNLWGGSADLSASNNTMVAAETDFQASNYAGRNIWFGVREFAMAAAMNGIA 42- 0 A+ + +P L+GGSADL++SN T++ E +F +Y+GRN+WFGVREFAM AAMNG+A Sbjct: 362 ALNAFAKTVPQLFGGSADLASSNKTLIKGEANFSRDDYSGRNVWFGVREFAMGAAMNGMA 42- 1 Query: 421 LHGGTRVYGGTFFVFSNYLLPAVRMAALQNLPTVYVMTHDSIAVGEDGPTHEPIEQLASV 48- 0 LHGG +V+G TFFVFS+YL PA+R+AAL LP +YV THDSIAVGEDGPTHEP+EQLAS+ Sbjct: 422 LHGGLKVFGATFFVFSDYLRPAIRLAALMQLPVIYVFTHDSIAVGEDGPTHEPVEQLASL 48- 1 Query: 481 RSMPNLNVIRPADGNETNAAWQRAVSETDRPTMLVLTRQNLPVLEGTSELAQEGVNKGAY 54- 0 R+MP L+VIRPADGNE+ AAW+ A+ D+PT LVL+RQNLP LEG + A +GV+KGAY Sbjct: 482 RAMPGLSVIRPADGNESVAAWKLALESKDQPTALVLSRQNLPTLEGAVDRAYDGVSKGAY 54- 1 Query: 541 ILSEAKGELDGIIIATGSEVKLALDTQDKLESEGIHVRVVSMPAQNIFDEQEASYQEQVL 60- 0 +L+ A G D +++A+GSEV LA++ ++ LE EGIH VVSMP+ + F+ Q A Y+E+VL Sbjct: 542 VLAPANGSADLLLLASGSEVSLAVNAKEALEKEGIHAAVVSMPSWDRFEAQSAEYKEEVL 60- 1 Query: 601 PSAVTKRLAIEAGSSFGWGKYVGLNGLTLTIDTWGASAPGNRIFEEYGFTVENAVSLYKEL 6- 61 PS VT RLAIE GSS GW KYVG G + ID +GASAPG RI EE+GFTV++ V+ K L Sbjct: 602 PSDVTARLAIEMGSSLGWAKYVGNQGDVVAIDRFGASAPGERIMEEFGFTVQHVVARAKAL 6- 62 There is also homology to SEQ ID 520. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 944 A DNA sequence (GBSx1002) was identified in S. agalactiae <SEQ ID 2869> which encodes the amino acid sequence <SEQ ID 2870>. Analysis of this protein sequence reveals the following: TABLE-US-02749 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4477(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9529> which encodes amino acid sequence <SEQ ID 9530> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2871> which encodes the amino acid sequence <SEQ ID 2872>. Analysis of this protein sequence reveals the following: TABLE-US-02750 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4581(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02751 Identities = 27/79 (34%), Positives = 45/79 (56%) Query: 3 MKKECRDFYRQIQHTYNDISVREDAVLSSILLSASNGLIKTSDVPRVAYELTQQLENNEI 62 M+K+ + Y I+ Y+ RE+ LS +LL+ASN LIK S+ VAY+L Q ++N + Sbjct: 1 MEKKRQRLYDVIRQAYDYPENRENVALSQLLLAASNRLIKHSNPLLVAYQLNQDVDNYLL 60 Query: 63 EKSFESLATVKELKKSAKK 81 + ++ K+S +K Sbjct: 61 DNDILLPKSLCRFKQSLEK 79 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 945 A DNA sequence (GBSx1003) was identified in S. agalactiae <SEQ ID 2873> which encodes the amino acid sequence <SEQ ID 2874>. This protein is predicted to be ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-02752 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2610(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02753 >GP: CAB49925 GB: AJ248286 ABC transporter, ATP-binding protein [Pyrococcus abyssi] Identities = 96/243 (39%), Positives = 164/243 (66%), Gaps = 2/243 (0%) Query: 1 MIKFEHVSKVYGEKEALSDLTLSVKDGEIFGLIGHNGAGKTTTISILTSIIDATYGQVYI 60 MI E++ K +G KE L ++ +VKDGEI+GL+G NG+GK+TT+ IL+ II G+V + Sbjct: 1 MIIVENLRKRFGGKEVLKGISFTVKDGEIYGLLGPNGSGKSTTMRILSGIITDFEGKVIV 60 Query: 61 DDLLLTEHRDQIKKKIGYVPDSPDIFLNLTAEEYWYFLAKIYDVAPEDIEARITKLVDIF 120- + + + Q+K+ +GYVP++P ++ +LT E++ F+ + + + +E R+ KLV+ F Sbjct: 61 GGVEVAKDPLQVKRIVGYVPETPALYESLTPAEFFSFVGGVRGIPKDILEERVRKLVEAF 120- Query: 121 ELEEQRYNPIESFSHGMRQKVIVIGALLPNPDIWILDEPLTGLDPQASFDLKEMMKEHAK 18- 0 E+++ I + S G +QK+ +I +LL +P + ILDE + GLDP+++ +E++ E + Sbjct: 121 EIKKYMNQLIGTLSFGTKQKISLISSLLHDPKVLILDEAMNGLDPKSARIFRELLYEFKE 18- 0 Query: 181 NGKTVIFSTHVLAVAEQLCDRIGILKQGKLIFVGSLGELKMKYPDKDLETIYLELAGRQA 24- 0 GK+++FSTHVLA+AE +CDR+GI +QG++I G++ ELK ++ LE ++L+L QA Sbjct: 181 EGKSIVFSTHVLALAELICDRVGIIYQGRIIAEGTVEELKEISKEERLEDVFLKLT--QA 23- 8 Query: 241 SRE 243 E Sbjct: 239 KEE 241 A related DNA sequence was identified in S. pyogenes <SEQ ID 2875> which encodes the amino acid sequence <SEQ ID 2876>. Analysis of this protein sequence reveals the following: TABLE-US-02754 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2723(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-02755 Identities = 182/244 (74%), Positives = 215/244 (87%) Query: 1 MIKFEHVSKVYGEKEALSDLTLSVKDGEIFGLIGHNGAGKTTTISILTSIIDATYGQVYI 60 MI+F+HVSK+YG+KEALSDL +++ DGEIFGLIGHNGAGKTTTISILTSII+A+YG+V++ Sbjct: 1 MIEFKHVSKLYGDKEALSDLNVTINDGEIFGLIGHNGAGKTTTISILTSIIEASYGEVFV 60 Query: 61 DDLLLTEHRDQIKKKIGYVPDSPDIFLNLTAEEYWYFLAKIYDVAPEDIEARITKLVDIF 120- D LLTE+R+ IKK+I YVPDSPDIFLNLT EYW FLAKIY V+ ED E R+ +L +F Sbjct: 61 DGQLLTENREAIKKQIAYVPDSPDIFLNLTPNEYWQFLAKIYGVSDEDREERLAQLTTLF 120- Query: 121 ELEEQRYNPIESFSHGMRQKVIVIGALLPNPDIWILDEPLTGLDPQASFDLKEMMKEHAK 18- 0 EL+E+ I+SFSHGMRQKVIVIGAL+ NP+IWILDEPLTGLDPQASFDLKEMMK HA Sbjct: 121 ELKEEVNQTIDSFSHGMRQKVIVIGALVSNPNIWILDEPLTGLDPQASFDLKEMMKAHAA 18- 0 Query: 181 NGKTVIFSTHVLAVAEQLCDRIGILKQGKLIFVGSLGELKMKYPDKDLETIYLELAGRQA 24- 0 +G TV+FSTHVL+VAEQLCDRIGILK+GKLIFVG++ ELK +PDKDLE+IYLELAGR+A Sbjct: 181 SGHTVLFSTHVLSVAEQLCDRIGILKKGKLIFVGTIDELKEHHPDKDLESIYLELAGRKA 24- 0 Query: 241 SREG 244 EG Sbjct: 241 QEEG 244 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 946 A DNA sequence (GBSx1004) was identified in S. agalactiae <SEQ ID 2877> which encodes the amino acid sequence <SEQ ID 2878>. Analysis of this protein sequence reveals the following: TABLE-US-02756 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.43 Transmembrane 504-520 (495-529) INTEGRAL Likelihood = -12.58 Transmembrane 427-443 (400-449) INTEGRAL Likelihood = -10.99 Transmembrane 151-167 (144-179) INTEGRAL Likelihood = -8.44 Transmembrane 194-210 (189-214) INTEGRAL Likelihood = -7.96 Transmembrane 48-64 (46-68) INTEGRAL Likelihood = -7.32 Transmembrane 350-366 (348-378) INTEGRAL Likelihood = -6.69 Transmembrane 475-491 (474-501) INTEGRAL Likelihood = -6.00 Transmembrane 319-335 (318-337) INTEGRAL Likelihood = -5.73 Transmembrane 252-268 (244-271) INTEGRAL Likelihood = -4.78 Transmembrane 125-141 (121-148) INTEGRAL Likelihood = -4.51 Transmembrane 76-92 (71-98) INTEGRAL Likelihood = -3.56 Transmembrane 406-422 (400-426) ----- Final Results ----- bacterial membrane --- Certainty = 0.6371(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 2879> which encodes the amino acid sequence <SEQ ID 2880>. Analysis of this protein sequence reveals the following: TABLE-US-02757 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.33 Transmembrane 167-183 (158-193) INTEGRAL Likelihood = -12.52 Transmembrane 524-540 (508-546) INTEGRAL Likelihood = -10.93 Transmembrane 63-79 (60-84) INTEGRAL Likelihood = -8.39 Transmembrane 421-437 (414-456) INTEGRAL Likelihood = -8.23 Transmembrane 208-224 (203-228) INTEGRAL Likelihood = -8.23 Transmembrane 504-520 (493-521) INTEGRAL Likelihood = -7.59 Transmembrane 139-155 (134-162) INTEGRAL Likelihood = -6.64 Transmembrane 261-277 (257-287) INTEGRAL Likelihood = -4.99 Transmembrane 446-462 (444-464) INTEGRAL Likelihood = -4.25 Transmembrane 369-385 (367-387) INTEGRAL Likelihood = -0.80 Transmembrane 87-103 (87-104) INTEGRAL Likelihood = -0.11 Transmembrane 334-350 (334-350) ----- Final Results ----- bacterial membrane --- Certainty = 0.6731(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9173> which encodes the amino acid sequence <SEQ ID 9174>. Analysis of this protein sequence reveals the following: TABLE-US-02758 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.33 Transmembrane 153-169 (144-179) INTEGRAL Likelihood = -12.52 Transmembrane 510-526 (494-532) INTEGRAL Likelihood = -10.93 Transmembrane 49-65 (46-70) INTEGRAL Likelihood = -8.39 Transmembrane 407-423 (400-442) INTEGRAL Likelihood = -8.23 Transmembrane 194-210 (189-214) INTEGRAL Likelihood = -8.23 Transmembrane 490-506 (479-507) INTEGRAL Likelihood = -7.59 Transmembrane 125-141 (120-148) INTEGRAL Likelihood = -6.64 Transmembrane 247-263 (243-273) INTEGRAL Likelihood = -4.99 Transmembrane 432-448 (430-450) INTEGRAL Likelihood = -4.25 Transmembrane 355-371 (353-373) INTEGRAL Likelihood = -0.80 Transmembrane 73-89 (73-90) INTEGRAL Likelihood = -0.11 Transmembrane 320-336 (320-336) ----- Final Results ----- bacterial membrane --- Certainty = 0.673(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02759 Identities = 255/542 (47%), Positives = 378/542 (69%), Gaps = 12/542 (2%) Query: 1 MNWSRIWELVKINILYSNPQTLSALRKKQEKHPKKEFSAYKSMFRNQLFQILLFSIIYVF 60 MNWS IWEL+KINILYSNPQ+L+ L+K+QEKHPK+ F AYKSM R Q I +F +IY+F Sbjct: 15 MNWSTIWELIKINILYSNPQSLANLKKRQEKHPKENFKAYKSMMRQQALMIAMFLVIYLF 74 Query: 61 LFVSLDFKEYPGYFTFYIGIFTLVSIIYSFIAMYSVFYESDDVKQYAYLPIKSEELYVAK 120- +F+ +DF YPG F+F + +F ++S + +F ++Y++FYES+D+K Y +LP+ SEELY+AK Sbjct: 75 MFIGVDFSHYPGLFSFDVAMFFIMSTLTAFSSLYTIFYESNDLKLYIHLPVTSEELYIAK 134- Query: 121 IFATFGMSVTFLMPILTLMIVAYWRIIGGPLAVLLAIINFAILFLSVTVISLYINSLIGR 18- 0 I ++ GM FLMP+++L+++AYW+++G PL++L+AI+ F +L +S V+++YIN+ +G+ Sbjct: 135 IVSSLGMGAVFLMPLISLLLIAYWQLLGNPLSILVAIVLFLVLLVSSMVLAIYINAWVGK 19- 4 Query: 181 AIIRSANRKLISTILISLATFGAIVPLLFVNMTSQK--MVQGKLQDIAPIPYVRGYYDIV 23- 8 I+RS RKLISTI++ ++TFGA V + +N+++ K M G D IPY +G+YD+V Sbjct: 195 IIVRSRKRKLISTIMMFVSTFGAFVLIFAINISNNKRTMTDGVFTDYPTIPYFKGFYDVV 25- 4 Query: 239 TAPFSMESLLNYYLPLLIILFLIGAIYKWVMPRYYQELLY----GQVKQRK--VHRQIDF 29- 2 APFS +LLN++LPLL+IL ++ I VMP YY+E Y +VKQ K V+R Sbjct: 255 QAPFSTAALLNFWLPLLLILAMVYGIVTKVMPTYYREAFYISNENKVKQTKKPVNRP--- 31- 1 Query: 293 SKRESINKTLVKHHLSSLQNATLLTNTFLMPLLYLAMFIVPILNNGKEIGRFFNENYFGI 35- 2 + +S+ + L KHHL +LQNATLLT T+LMPL+Y+ +FI P L+ G + + +YFG+ Sbjct: 312 HQNQSLAQLLRKHHLLTLQNATLLTQTYLMPLMYVMLFIGPSLSRGTGFFKHISPDYFGV 37- 1 Query: 353 AFLAGILIGSLCVMPASIVGVGISLEKSNFYFIKSLPISFSYFLKHKFVTLITLQLAVPT 41- 2 A L G+ +G +C P S +GVGISLEK NF FIKSLPI+ FL KF L+ LQL VP Sbjct: 372 ALLFGVSLGVMCATPTSFIGVGISLEKDNFTFIKSLPITLKKFLMDKFCLLVGLQLIVPM 43- 1 Query: 413 FIYFLVGFFLLKLSILVLLSFILGLVFMGLIEGQFIYRRDYKHLFLNWQEVTQLFNRGLG 47- 2 IY + G F+L L L+ ++F LG +++G+ +YRRDY+ L L WQ++TQLF RG G Sbjct: 432 VIYLVFGLFVLHLHPLLTIAFCLGYALSLIVQGELMYRRDYRLLDLKWQDMTQLFTRGDG 49- 1 Query: 473 QWLLVGSLFGMMIIGSFL-IGISIFWSMVWNTVAVNIIILIIGLLILSICQYLLLKNFWK 53- 1 QWL +G +FG +I+ L G I +++ + ++I++ + L++L + Q + K FWK Sbjct: 492 QWLTMGLIFGNLIVAGVLGFGAVIIANIIQQPLLISILLSCLILMVLGLAQLWIQKTFWK 55- 1 Query: 532 KL 533 L Sbjct: 552 SL 553 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 947 A DNA sequence (GBSx1005) was identified in S. agalactiae <SEQ ID 2881> which encodes the amino acid sequence <SEQ ID 2882>. Analysis of this protein sequence reveals the following: TABLE-US-02760 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.12 Transmembrane 242-258 (239-265) INTEGRAL Likelihood = -7.64 Transmembrane 430-446 (421-450) INTEGRAL Likelihood = -5.84 Transmembrane 120-136 (113-139) INTEGRAL Likelihood = -5.52 Transmembrane 212-228 (210-232) INTEGRAL Likelihood = -5.20 Transmembrane 287-303 (283-313) INTEGRAL Likelihood = -3.56 Transmembrane 148-164 (143-166) INTEGRAL Likelihood = -0.48 Transmembrane 382-398 (382-398) ----- Final Results ----- bacterial membrane --- Certainty = 0.4248(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02761 >GP: CAB15963 GB: Z99124 phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component [Bacillus subtilis] Identities = 175/447 (39%), Positives = 266/447 (59%), Gaps = 10/447 (2%) Query: 4 EYITLSKNIIKHLGGQNNINNVYHCQTRLRFSLNDPTKVNLEQLKTLKEVKTVVISGGQH 63 +Y LSK+I++ +GG+ N+ V HC TRLRF+L+D K + QL+ L V ISG Q Sbjct: 2 DYDKLSKDILQLVGGEENVQRVIHCMTRLRFNLHDNAKADRSQLEQLPGVMGTNISGEQF 61 Query: 64 QIVIGTHVAKVFEEI---NSLIETNSTTKIEQTKKAKAVSRIIDFVSGTFQPILPALSGA 120- QI+IG V KV++ I ++L + S Q K +S + D +SG F PILPA++GA Sbjct: 62 QIIIGNDVPKVYQAIVRHSNLSDEKSAGSSSQKKNV--LSAVFDVISGVFTPILPAIAGA 119- Query: 121 GMIKALLALLLVFKILTPSSQTYILLNLFADGVFYFLPILIAITAAQKLKANPILALGTV 18- 0 GMIK L+AL + F + SQ +++L DG FYFLP+L+A++AA+K +NP +A Sbjct: 120 GMIKGLVALAVTFGWMAEKSQVHVILTAVGDGAFYFLPLLLAMSAARKFGSNPYVAAAIA 17- 9 Query: 181 VMLLHPNWANLVASGKPVSLFHTIPFTLTNYASSVIPIILIICVQAYIEKYLKQIIPKSL 24- 0 +LHP+ L+ +GKP+S F +P T Y+S+VIPI+L I + +Y+EK++ + SL Sbjct: 180 AAILHPDLTALLGAGKPIS-FIGLPVTAATYSSTVIPILLSIWIASYVEKWIDRFTHASL 23- 8 Query: 241 RLVLVPMLIFLSMGILSFSILGPMGTIAGQYLAVIFTFLSKYASW-APAFLVGAFAPILI 29- 9 +L++VP L + L+ +GP+G I G+YL+ +L +A A FL G F+ ++I Sbjct: 239 KLIVVPTFTLLIVVPLTLITVGPLGAILGEYLSSGVNYLFDHAGLVAMIFLAGTFS-LII 29- 7 Query: 300 MFGVHSGIAALGITQLAKLGVDSIFGPGMLCSNIAQATAGTVVTLITKEKKLKEIAGPAA 35- 9 M G+H + I +A+ G D + P M +N+ QA A V L ++ KK K +A + Sbjct: 298 MTGMHYAFVPIMINNIAQNGHDYLL-PAMFLANMGQAGASFAVFLRSRNKKFKSLALTTS 35- 6 Query: 360 ITAYMGITEPILYGVNLPKRYPLIASLIGGGLGGLYAGIMNAHRFAV-GSSGLPGLFLYI 41- 8 ITA MGITEP +YGVN+ + P A+LIGG GG + G+ + V G++GLP + ++I Sbjct: 357 ITALMGITEPAMYGVNMRLKKPFAAALIGGAAGGAFYGMTGVASYIVGGNAGLPSIPVFI 41- 6 Query: 419 SHTSTHLFITMLIAVIITVSTTAILTF 445 T + I ++IA S +L F Sbjct: 417 GPTFIYAMIGLVIAFAAGTSAAYLLGF 443 There is also homology to SEQ ID 2884. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 948 A DNA sequence (GBSx1006) was identified in S. agalactiae <SEQ ID 2885> which encodes the amino acid sequence <SEQ ID 2886>. This protein is predicted to be gamma-glutamyl kinase (proB). Analysis of this protein sequence reveals the following: TABLE-US-02762 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.11 Transmembrane 160-176 (160-176) ----- Final Results ----- bacterial membrane --- Certainty = 0.1044(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02763 >GP: CAA63147 GB: X92418 gamma-glutamyl kinase [Streptococcus thermophilus] Identities = 200/265 (75%), Positives = 235/265 (88%) Query: 1 MKRHFETTRRIVIKVGTSSLVQTSGKINLSKIDHLAFVISSLMNRGMEVILVSSGAMGFG 60 MKR+F++ +R+VIK+GTSSLV SGKINL KID LAFVISSL N+G+EV+LVSSGAMGFG Sbjct: 1 MKRNFDSVKRLVIKIGTSSLVLPSGKINLEKIDQLAFVISSLHNKGIEVVLVSSGAMGFG 60 Query: 61 LDILKMDKRPQEISQQQAVSSVGQVAMMSLYSQIFSHYQTHVSQILLTRDVVVFPESLQN 120- L++L ++KRP E+ +QQAVSSVGQVAMMSLYSQ+FSHYQT VSQ+LLTRDVV + ESL N Sbjct: 61 LNVLDLEKRPAEVGKQQAVSSVGQVAMMSLYSQVFSHYQTKVSQLLLTRDVVEYSESLAN 120- Query: 121 VTNSFESLLSMGILPIVNENDAVSVDEMDHKTKFGDNDRLSAVVAKITKADLLIMLSDID 18- 0 N+FESL +G++PIVNENDAVSVDEMDH TKFGDNDRLSA+VAK+ ADLLIMLSDID Sbjct: 121 AINAFESLFELGVVPIVNENDAVSVDEMDHATKFGDNDRLSAIVAKVVGADLLIMLSDID 18- 0 Query: 181 GLFDKNPNIYDDAVLRSHVSEITDDIIKSAGGAGSKFGTGGMLSKIKSAQMVFDNNGQMI 24- 0 GLFDKNPN+Y+DA LRS+V EIT++I+ SAGGAGSKFGTGGM+SKIKSAQMVF+N QM+ Sbjct: 181 GLFDKNPNVYEDATLRSYVPEITEEILASAGGAGSKFGTGGMMSKIKSAQMVFENQSQMV 24- 0 Query: 241 LMNGANPRDILKVLDGHNIGTYFAQ 265 LMNG NPRDIL+VL+G IGT F Q Sbjct: 241 LMNGENPRDILRVLEGAKIGTLFKQ 265 A related DNA sequence was identified in S. pyogenes <SEQ ID 2887> which encodes the amino acid sequence <SEQ ID 2888>. Analysis of this protein sequence reveals the following: TABLE-US-02764 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.97 Transmembrane 163-179 (163-179) INTEGRAL Likelihood = -0.06 Transmembrane 124-140 (124-140) ----- Final Results ----- bacterial membrane --- Certainty = 0.1786(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02765 >GP: CAA63147 GB: X92418 gamma-glutamyl kinase [Streptococcus thermophilus] Identities = 212/265 (80%), Positives = 237/265 (89%) Query: 4 MKRQFEDVTRIVIKIGTSSLVLPTGKINLEKIDQLAFVISSLMNKGKEVILVSSGAMGFG 63 MKR F+ V R+VIKIGTSSLVLP+GKINLEKIDQLAFVISSL NKG EV+LVSSGAMGFG Sbjct: 1 MKRNFDSVKRLVIKIGTSSLVLPSGKINLEKIDQLAFVISSLHNKGIEVVLVSSGAMGFG 60 Query: 64 LDILKMEKRPTNLAKQQAVSSVGQVAMMSLYSQIFAYYQTNVSQILLTRDVVVFPESLAN 123- L++L +EKRP + KQQAVSSVGQVAMMSLYSQ+F++YQT VSQ+LLTRDVV + ESLAN Sbjct: 61 LNVLDLEKRPAEVGKQQAVSSVGQVAMMSLYSQVFSHYQTKVSQLLLTRDVVEYSESLAN 120- Query: 124 VTNAFESLISLGIVPIVNENDAVSVDEMDHATKFGDNDRLSAVVAGITKADLLIMLSDID 18- 3 NAFESL LG+VPIVNENDAVSVDEMDHATKFGDNDRLSA+VA + ADLLIMLSDID Sbjct: 121 AINAFESLFELGVVPIVNENDAVSVDEMDHATKFGDNDRLSAIVAKVVGADLLIMLSDID 18- 0 Query: 184 GLFDKNPTIYEDAQLRSHVANITQEIIASAGGAGSKFGTGGMLSKVQSAQMVFENKGQMV 24- 3 GLFDKNP +YEDA LRS+V IT+EI+ASAGGAGSKFGTGGM+SK++SAQMVFEN+ QMV Sbjct: 181 GLFDKNPNVYEDATLRSYVPEITEEILASAGGAGSKFGTGGMMSKIKSAQMVFENQSQMV 24- 0 Query: 244 LMNGANPRDILRVLEGQPLGTWFKQ 268 LMNG NPRDILRVLEG +GT FKQ Sbjct: 241 LMNGENPRDILRVLEGAKIGTLFKQ 265 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02766 Identities = 217/265 (81%), Positives = 242/265 (90%) Query: 1 MKRHFETTRRIVIKVGTSSLVQTSGKINLSKIDHLAFVISSLMNRGMEVILVSSGAMGFG 60 MKR FE RIVIK+GTSSLV +GKINL KID LAFVISSLMN+G EVILVSSGAMGFG Sbjct: 4 MKRQFEDVTRIVIKIGTSSLVLPTGKINLEKIDQLAFVISSLMNKGKEVILVSSGAMGFG 63 Query: 61 LDILKMDKRPQEISQQQAVSSVGQVAMMSLYSQIFSHYQTHVSQILLTRDVVVFPESLQN 120- LDILKM+KRP +++QQAVSSVGQVAMMSLYSQIF++YQT+VSQILLTRDVVVFPESL N Sbjct: 64 LDILKMEKRPTNLAKQQAVSSVGQVAMMSLYSQIFAYYQTNVSQILLTRDVVVFPESLAN 123- Query: 121 VTNSFESLLSMGILPIVNENDAVSVDEMDHKTKFGDNDRLSAVVAKITKADLLIMLSDID 18- 0 VTN+FESL+S+GI+PIVNENDAVSVDEMDH TKFGDNDRLSAVVA ITKADLLIMLSDID Sbjct: 124 VTNAFESLISLGIVPIVNENDAVSVDEMDHATKFGDNDRLSAVVAGITKADLLIMLSDID 18- 3 Query: 181 GLFDKNPNIYDDAVLRSHVSEITDDIIKSAGGAGSKFGTGGMLSKIKSAQMVFDNNGQMI 24- 0 GLFDKNP IY+DA LRSHV+ IT +II SAGGAGSKFGTGGMLSK++SAQMVF+N GQM+ Sbjct: 184 GLFDKNPTIYEDAQLRSHVANITQEIIASAGGAGSKFGTGGMLSKVQSAQMVFENKGQMV 24- 3 Query: 241 LMNGANPRDILKVLDGHNIGTYFAQ 265 LMNGANPRDIL+VL+G +GT+F Q Sbjct: 244 LMNGANPRDILRVLEGQPLGTWFKQ 268 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 949 A DNA sequence (GBSx1007) was identified in S. agalactiae <SEQ ID 2889> which encodes the amino acid sequence <SEQ ID 2890>. This protein is predicted to be unnamed protein product (proA). Analysis of this protein sequence reveals the following: TABLE-US-02767 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3517(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2891> which encodes the amino acid sequence <SEQ ID 2892>. Analysis of this protein sequence reveals the following: TABLE-US-02768 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02769 >GP: CAA63148 GB: X92418 gamma-glutamyl phosphate reductase [Streptococcus thermophilus] Identities = 309/416 (74%), Positives = 355/416 (85%) Query: 1 MTDMRRLGQRAKQASLLIAPLSTQIKNRFLSTLAKALVDDTQTLLAANQKDLANAKEHGI 60 MT + LGQ+AK AS IA LST KN L+ +AKALV ++ + N KD+ANA E+GI Sbjct: 1 MTYVDTLGQQAKVASRQIAKLSTAAKNDLLNQVAKALVAESDYIFTENAKDMANASENGI 60 Query: 61 SDIMMDRLRLTSERIKAIAQGVQQVADLADPIGQVIKGYTNLDGLKILQKRVPLGVIAMI 120- S IM DRL LT +RI IA+GV+QVADL DPIGQV++GYTNLDGLKI+QKRVP+GVIAMI Sbjct: 61 SKIMQDRLLLTEDRIAGIAEGVRQVADLQDPIGQVVRGYTNLDGLKIVQKRVPMGVIAMI 120- Query: 121 FESRPNVSVDAFSLAFKTNNAIILRGGKDALHSNKALVKLIRQSLEKSGITPDAVQLVED 18- 0 FESRPNVS+DAFSLAFKTNNAIILRGG+DA++SNKALV + R++L+ +GIT DAVQ VED Sbjct: 121 FESRPNVSIDAFSLAFKTNNAIILRGGRDAINSNKALVTVARKALKNAGITADAVQFVED 18- 0 Query: 181 PSHAVAEELMQATDYVDVLIPRGGAKLIQTVKEKAKVPVIETGVGNVHIYVDAQADLDIA 24- 0 SH VAEELM AT YVD+LIPRGGA+LIQTVKEKAKVPVIETGVGN HIYVD A+LD+A Sbjct: 181 TSHEVAEELMVATKYVDLLIPRGGARLIQTVKEKAKVPVIETGVGNCHIYVDKYANLDMA 24- 0 Query: 241 TKIVINAKTKRPSVCNAAEGLVIHEAVAARFIPMLEKAINQVQPVEWRADDKALPLFEQA 30- 0 T+IVINAKT+RPSVCNAAE LV+H + F+P LEKAI+++Q VE+RAD++AL L E+A Sbjct: 241 TQIVINAKTQRPSVCNAAESLVVHADIVEEFLPNLEKAISKIQSVEFRADERALKLMEKA 30- 0 Query: 301 VPAKAEDFETEFLDYIMSVKVVSSLEEAISWINQYTSHHSEAIITRDIKAAETFQDLVDA 36- 0 VPA EDF TEFLDYIMSVKVV SL+EAI+WIN YT+ HSEAI+T+DI AE FQD VDA Sbjct: 301 VPASPEDFATEFLDYIMSVKVVDSLDEAINWINTYTTSHSEAIVTQDISRAEQFQDDVDA 36- 0 Query: 361 AAVYVNASTRFTDGFVFGLGAEIGISTQKMHARGPMGLEALTSTKFYINGDGHIRE 416 AAVYVNASTRFTDGFVFGLGAEIGISTQKMHARGPMGLEALTSTKFYING G IRE Sbjct: 361 AAVYVNASTRFTDGFVFGLGAEIGISTQKMHARGPMGLEALTSTKFYINGQGQIRE 416 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-02770 Identities = 307/417 (73%), Positives = 353/417 (84%), Gaps = 1/417 (0%) Query: 1 MTYIEILGQNAKKASQSVARLSTASKNEILRDLARNIVADTETILTENARDVVKAKDNGI 60 MT + LGQ AK+AS +A LST KN L LA+ +V DT+T+L N +D+ AK++GI Sbjct: 1 MTDMRRLGQRAKQASLLIAPLSTQIKNRFLSTLAKALVDDTQTLLAANQKDLANAKEHGI 60 Query: 61 SEIMVDRLRLNKDRIQAIANGIYQVADLADPIGQVVSGYTNLDGLKILKKRVPLGVIAMI 120- S+IM+DRLRL +RI+AIA G+ QVADLADPIGQV+ GYTNLDGLKIL+KRVPLGVIAMI Sbjct: 61 SDIMMDRLRLTSERIKAIAQGVQQVADLADPIGQVIKGYTNLDGLKILQKRVPLGVIAMI 120- Query: 121 FESRPNVSVDAFSLAFKTGNAIILRGGKDAIFSNTALVNCMRQTLQDTGHNPDIVQLVED 18- 0 FESRPNVSVDAFSLAFKT NAIILRGGKDA+ SN ALV +RQ+L+ +G PD VQLVED Sbjct: 121 FESRPNVSVDAFSLAFKTNNAIILRGGKDALHSNKALVKLIRQSLEKSGITPDAVQLVED 18- 0 Query: 181 TSHVVAEELMQATDYVDVLIPRGGAKLIQTVKEKSKIPVIETGVGNVHIYIDEFADLDMA 24- 0 SH VAEELMQATDYVDVLIPRGGAKLIQTVKEK+K+PVIETGVGNVHIY+D ADLD+A Sbjct: 181 PSHAVAEELMQATDYVDVLIPRGGAKLIQTVKEKAKVPVIETGVGNVHIYVDAQADLDIA 24- 0 Query: 241 AKIVINAKTQRPSVCNAAEGLVVHQAIAKGFLSQLEKMLKESNQSVEFRADEEALQLLEN 30- 0 KIVINAKT+RPSVCNAAEGLV+H+A+A F+ LEK + + Q VE+RAD++AL L E Sbjct: 241 TKIVINAKTKRPSVCNAAEGLVIHEAVAARFIPMLEKAINQV-QPVEWRADDKALPLFEQ 29- 9 Query: 301 AVAASESDYATEFLDYIMSVKVVDSFEQAISWINKYSSHHSEAIITNNISRAEIFQDMVD 36- 0 AV A D+ TEFLDYIMSVKVV S E+AISWIN+Y+SHHSEAIIT +I AE FQD+VD Sbjct: 300 AVPAKAEDFETEFLDYIMSVKVVSSLEEAISWINQYTSHHSEAIITRDIKAAETFQDLVD 35- 9 Query: 361 AAAVYVNASTRFTDGFVFGLGAEIGISTQKLHARGPMGLEALTSTKYYINGTGQVRE 417 AAAVYVNASTRFTDGFVFGLGAEIGISTQK+HARGPMGLEALTSTK+YING G +RE Sbjct: 360 AAAVYVNASTRFTDGFVFGLGAEIGISTQKMHARGPMGLEALTSTKFYINGDGHIRE 416 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 950 A DNA sequence (GBSx1008) was identified in S. agalactiae <SEQ ID 2893> which encodes the amino acid sequence <SEQ ID 2894>. Analysis of this protein sequence reveals the following: TABLE-US-02771 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1859(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9531> which encodes amino acid sequence <SEQ ID 9532> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 2895> which encodes the amino acid sequence <SEQ ID 2896>. Analysis of this protein sequence reveals the following: TABLE-US-02772 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0853(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02773 Identities = 259/315 (82%), Positives = 287/315 (90%) Query: 1 MTNDFHHITVLLHETVDMLDIKPDGIYVDATLGGAGHSEYLLSQLGPDGHLYAFDQDQKA 60 MT +FHH+TVLLHETVDMLDIKPDGIYVDATLGG+GHS YLLS+LG +GHLY FDQDQKA Sbjct: 22 MTKEFHHVTVLLHETVDMLDIKPDGIYVDATLGGSGHSAYLLSKLGEEGHLYCFDQDQKA 81 Query: 61 IDNAHIRLKKYVDTGQVTFIKDNFRNLSSNLKALGVSEINGICYDLGVSSPQLDERERGF 120- IDNA + LK Y+D GQVTFIKDNFR+L + L ALGV EI+GI YDLGVSSPQLDERERGF Sbjct: 82 IDNAQVTLKSYIDKGQVTFIKDNFRHLKARLTALGVDEIDGILYDLGVSSPQLDERERGF 141- Query: 121 SYKQDAPLDMRMNREQSLTAYDVVNTYSYHDLVRIFFKYGEDKFSKQIARKIEQVRAEKT 18- 0 SYKQDAPLDMRM+R+ LTAY+VVNTY ++DLV+IFFKYGEDKFSKQIARKIEQ RA K Sbjct: 142 SYKQDAPLDMRMDRQSLLTAYEVVNTYPFNDLVKIFFKYGEDKFSKQIARKIEQARAIKP 20- 1 Query: 181 ISTTTELAEIIKSSKSAKELKKKGHPAKQIFQAIRIEVNDELGAADESIQQAMDLLAVDG 24- 0 I TTTELAE+IK++K AKELKKKGHPAKQIFQAIRIEVNDELGAADESIQ AM+LLA+DG Sbjct: 202 IETTTELAELIKAAKPAKELKKKGHPAKQIFQAIRIEVNDELGAADESIQDAMELLALDG 26- 1 Query: 241 RISVITFHSLEDRLTKQLFKEASTVEVPKGLPFIPDDLQPKMELVNRKPILPSQEELEAN 30- 0 RISVITFHSLEDRLTKQLFKEASTV+VPKGLP IP+D++PK ELV+RKPILPS EL AN Sbjct: 262 RISVITFHSLEDRLTKQLFKEASTVDVPKGLPLIPEDMKPKFELVSRKPILPSHSELTAN 32- 1 Query: 301 NRAHSAKLRVARRIR 315 RAHSAKLRVA++IR Sbjct: 322 KRAHSAKLRVAKKIR 336 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 951 A DNA sequence (GBSx1009) was identified in S. agalactiae <SEQ ID 2897> which encodes the amino acid sequence <SEQ ID 2898>. This protein is predicted to be FtsL. Analysis of this protein sequence reveals the following: TABLE-US-02774 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.92 Transmembrane 30-46 (24-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.4567(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02775 >GP: AAC95455 GB: AF068903 YllD [Streptococcus pneumoniae] Identities = 44/99 (44%) , Positives = 71/99 (71%) Query: 5 KRTEAVTQTLQRHIKTFSRIEKAFYGAIVITAIIMAVGIIYLQSNSLQVKQEVNQLNSKI 64 ++ E Q LQ +K FSR+EKAFY +I +T +I+A+ II++Q+ LQV+ ++ ++N++I Sbjct: 3 EKMEKTGQILQMQLKRFSRVEKAFYFSIAVTTLIVAISIIFMQTKLLQVQNDLTKINAQI 62 Query: 65 NDKQTEFDNAKQEVNELSNRDRITKIAKDAGLTIQNDNI 103 +K+TE D+AKQEVNEL +R+ +IA L + N+NI Sbjct: 63 EEKKTELDDAKQEVNELLRAERLKEIANSHDLQLNNENI 101 A related DNA sequence was identified in S. pyogenes <SEQ ID 2899> which encodes the amino acid sequence <SEQ ID 2900>. Analysis of this protein sequence reveals the following: TABLE-US-02776 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.79 Transmembrane 40-56 (37-58) ----- Final Results ----- bacterial membrane --- Certainty= 0.3314 (Affirmative) < succ> bacterial outside --- Certainty= 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty= 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02777 >GP: AAC95455 GB: AF068903 YllD [Streptococcus pneumoniae] Identities = 45/94 (47%), Positives = 69/94 (72%) Query: 24 LQKRIKTFSRIEKAFYTAIIVTAITMAVSIIYLQSRKLQLQQEITSLNSHISDQKLELNN 83 - LQ ++K FSR+EKAFY +I VT + +A+SII++Q++ LQ+Q ++T +N+ I ++K EL++ Sbjct: 12 LQMQLKRFSRVEKAFYFSIAVTTLIVAISIIFMQTKLLQVQNDLTKINAQIEEKKTELDD 71 Query: 84 AKQEVNELSRRDRIIDIAGKAGLSNRNNNIKKVE 117 AKQEVNEL R +R+ +IA L N NI+ E Sbjct: 72 AKQEVNELLRAERLKEIANSHDLQLNNENIRIAE 105 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02778 Identities = 71/108 (65%), Positives = 87/108 (79%), Gaps = 1/108 (0%) Query: 1 MTNEKRTEAVTQTLQRHIKTFSRIEKAFYGAIVITAIIMAVGIIYLQSNSLQVKQEVNQL 60 MTNEKRT+ VT LQ+ IKTFSRIEKAFY AI++TAI MAV IIYLQS LQ++QE+ L Sbjct: 11 MTNEKRTQVVTNALQKRIKTFSRIEKAFYTAIIVTAITMAVSIIYLQSRKLQLQQEITSL 70 Query: 61 NSKINDKQTEFDNAKQEVNELSNRDRITKIAKDAGLTIQNDNIYRKVD 108 NS I+D++ E +NAKQEVNELS RDRI IA AGL+ +N+NI +KV+ Sbjct: 71 NSHISDQKLELNNAKQEVNELSRRDRIIDIAGKAGLSNRNNNI-KKVE 117 SEQ ID 2898 (GBS82) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 15 (lane 2; 2 bands). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 952 A DNA sequence (GBSx1010) was identified in S. agalactiae <SEQ ID 2901> which encodes the amino acid sequence <SEQ ID 2902>. Analysis of this protein sequence reveals the following: TABLE-US-02779 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1435 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 953 A DNA sequence (GBSx1011) was identified in S. agalactiae <SEQ ID 2903> which encodes the amino acid sequence <SEQ ID 2904>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following: TABLE-US-02780 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.90 Transmembrane 37-53 (30-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.6562 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2905> which encodes the amino acid sequence <SEQ ID 2906>. Analysis of this protein sequence reveals the following: TABLE-US-02781 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.06 Transmembrane 33-49 (24-53) ----- Final Results ----- bacterial membrane --- Certainty = 0.6222 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02782 Identities = 480/753 (63%), Positives = 603/753 (79%), Gaps = 8/753 (1%) Query: 5 KKLKKIFLDYVIHIRDRRSPQKNRERVGQNLMILTIFLFFIFIINFVIIVGTDSKFGVNL 64 KK +K LDYV+ RDRR+P +NR RVGQN+M+LTIF+FFIFIINF+II+GTD KFGV+L Sbjct: 2 KKWQKYVLDYVV--RDRRTPVENRVRVGQNMMLLTIFIFFIFIINFMIIIGTDQKFGVSL 59 Query: 65 SKEAKKVYQQSMTVQAKRGTIYDRNGNPIAEDATTYSLYAIISKNYTTATGQKLYVQPSQ 124- S+ AKKVYQ+++T+QAKRGTIYDRNG IA D+TTYS+YAI+ K++ +A+ +KLYVQPSQ Sbjct: 60 SEGAKKVYQETVTIQAKRGTIYDRNGTAIAVDSTTYSIYAILDKSFVSASDEKLYVQPSQ 119- Query: 125 YEKVASILENKLGMKKNLVLKQLNQKKLFQVSFGSSGSGLSYTKMADIKKTMEKSDIKGI 18- 4 YE VA IL+ LGMKK V+KQL +K LFQVSFG SGSG+SY+ M+ I+K ME + IKGI Sbjct: 120 YETVADILKKHLGMKKTDVIKQLKRKGLFQVSFGPSGSGISYSTMSTIQKAMEDAKIKGI 17- 9 Query: 185 GFSTSPGRIYPNGIFASQFIGF-TLPQDDGDG-KKLVGNTGLEAALNKVLSGTDGKVTYE 24- 2 F+TSPGR+YPNG FAS+FIG +L +D G K LVG TGLEA+ +K+LSG DG +TY+ Sbjct: 180 AFTTSPGRMYPNGTFASEFIGLASLTEDKKTGVKSLVGKTGLEASFDKILSGQDGVITYQ 23- 9 Query: 243 KDRSGNVLLGTATTERRAVNGKDIYTTLSEPIQTVLETQMDVFAEKTKGKFASATVVNAK 30- 2 KDR+G LLGT T ++A++GKDIYTTLSEPIQT LETQMDVF K+ G+ ASAT+VNAK Sbjct: 240 KDRNGTTLLGTGKTVKKAIDGKDIYTTLSEPIQTFLETQMDVFQAKSNGQLASATLVNAK 29- 9 Query: 303 TGEILATSQRPTYNPSTLKGYDKKNLGTYNTLLYDNFFEPGSTMKVMTLASAIDSKHFNS 36- 2 TGEILAT+QRPTYN TLKG + N Y+ L N FEPGSTMKVMTLA+AID K FN Sbjct: 300 TGEILATTQRPTYNADTLKGLENTNYKWYSALHQGN-FEPGSTMKVMTLAAAIDDKVFNP 35- 8 Query: 363 TEVYNSAQ-YKIADAIIRDWDVNEGLSSGSYMTFPQGFAHSSNVGMVTLEQKMGRDKWLN 42- 1 E +++A IADA I+DW +NEG+S+G YM + QGFA SSNVGM LEQKMG KW+N Sbjct: 359 NETFSNANGLTIADATIQDWSINEGISTGQYMNYAQGFAFSSNVGMTKLEQKMGNAKWMN 41- 8 Query: 422 YLSKFKFGYPTRFGMLHESGGLFPSDNEVTIAMSSFGQGIGVTQVQMLRAFTSISNDGVM 48- 1 YL+KF+FG+PTRFG+ E G+FPSDN VT AMS+FGQGI VTQ+QMLRAFT+ISN+G M Sbjct: 419 YLTKFRFGFPTRFGLKDEDAGIFPSDNIVTQAMSAFGQGISVTQIQMLRAFTAISNNGEM 47- 8 Query: 482 LQPQFISSIYDPNTGTSRTARKEVVGKPVSKEAASKTRDYMVTVGTDPYYGTLYA-AGAP 54- 0 L+PQFIS IYDPNT + RTA KE+VGKPVSK+AAS+TR YM+ VGTDP +GTLY+ P Sbjct: 479 LEPQFISQIYDPNTASFRTANKEIVGKPVSKKAASETRQYMIGVGTDPEFGTLYSKTFGP 53- 8 Query: 541 VIQVGNQSVAVKSGTAQIAQEGGGGYLQ-GKNDTINSVVAMVPSENPDFIMYVTIQQPEK 59- 9 +I+VG+ VAVKSGTAQI E G GY G + + SVVAMVP++ PDF+MYVT+ +P+ Sbjct: 539 IIKVGDLPVAVKSGTAQIGSEDGSGYQDGGLTNYVYSVVAMVPADKPDFLMYVTMTKPQH 59- 8 Query: 600 FSITFWKDVVNPVLEQATAMKETILKPGLNDSEHQTKYKLSKIVGENPGHVAEELRRNLV 65- 9 F FW+DVVNPVLE+A M++T+ KP ++D+ QT YKL VG+NPG + ELRRNLV Sbjct: 599 FGPLFWQDVVNPVLEEAYLMQDTLTKPVVSDANRQTTYKLPNFVGKNPGETSSELRRNLV 65- 8 Query: 660 QPIILGNGSKVSKVSKRPGANLAENEQLLVLTNKLTELPDMYGWSKANVEQFAKWTGIKV 71- 9 QP++LG GSK+ KVS +PG L EN+Q+L+L+++ E+PDMYGW+K+NV+ FAKWTGI + Sbjct: 659 QPVVLGTGSKIKKVSHQPGQTLTENQQVLILSDRFVEVPDMYGWTKSNVKTFAKWTGIDI 71- 8 Query: 720 TYKGSTSGKVRKQSIDVGKSINKIKKIKITIGD 752 ++KG+ SG+V KQS+DVGKS+ KIKK+ IT+GD Sbjct: 719 SFKGTDSGRVMKQSVDVGKSLKKIKKMTITLGD 751 A related GBS gene <SEQ ID 8691> and protein <SEQ ID 8692> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02783 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -4.31 GvH: Signal Score (-7.5): -7.07 Possible site: 47 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -13.90 threshold: 0.0 INTEGRAL Likelihood = -13.90 Transmembrane 37-53 (30-60) PERIPHERAL Likelihood = 5.30 450 modified ALOM score: 3.28 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6562 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00065## SEQ ID 8692 (GBS352d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 145 (lane 15 & 16; MW 105.5 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 145 (lane 17 & 18; MW 80.5 kDa), in FIG. 182 (lane 3; MW 80 kDa) and in FIG. 185 (lane 4; MW 105 kDa). Purified GBS352d-GST is shown in lane 5 of FIG. 236. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 954 A DNA sequence (GBSx1012) was identified in S. agalactiae <SEQ ID 2907> which encodes the amino acid sequence <SEQ ID 2908>. Analysis of this protein sequence reveals the following: TABLE-US-02784 Possible site: 36 >>>Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1950 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 955 A DNA sequence (GBSx1013) was identified in S. agalactiae <SEQ ID 2909> which encodes the amino acid sequence <SEQ ID 2910>. This protein is predicted to be unnamed protein product (mraY). Analysis of this protein sequence reveals the following: TABLE-US-02785 Possible site: 18 >> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -15.12 Transmembrane 56-72 (47-76) INTEGRAL Likelihood = -14.70 Transmembrane 203-219 (198-223) INTEGRAL Likelihood = -6.69 Transmembrane 318-334 (315-335) INTEGRAL Likelihood = -6.64 Transmembrane 83-99 (79-103) INTEGRAL Likelihood = -5.52 Transmembrane 179-195 (175-197) INTEGRAL Likelihood = -5.31 Transmembrane 232-248 (230-249) INTEGRAL Likelihood = -3.08 Transmembrane 119-135 (119-137) INTEGRAL Likelihood = -2.87 Transmembrane 151-167 (147-167) INTEGRAL Likelihood = -2.34 Transmembrane 254-270 (254-270) ----- Final Results ----- bacterial membrane --- Certainty = 0.7050 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2911> which encodes the amino acid sequence <SEQ ID 2912>. Analysis of this protein sequence reveals the following: TABLE-US-02786 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.55 Transmembrane 52-68 (48-75) INTEGRAL Likelihood = -9.39 Transmembrane 175-191 (171-194) INTEGRAL Likelihood = -8.12 Transmembrane 30-46 (23-48) INTEGRAL Likelihood = -6.37 Transmembrane 121-137 (119-145) INTEGRAL Likelihood = -6.32 Transmembrane 293-309 (287-309) INTEGRAL Likelihood = -5.31 Transmembrane 204-220 (202-221) INTEGRAL Likelihood = -5.20 Transmembrane 151-167 (150-170) INTEGRAL Likelihood = -4.67 Transmembrane 226-242 (224-244) INTEGRAL Likelihood = -0.11 Transmembrane 91-107 (91-107) ----- Final Results ----- bacterial membrane --- Certainty= 0.4821 (Affirmative) < succ> bacterial outside --- Certainty= 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty= 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02787 >GP: CAB70458 GB: A94911 unnamed protein product [unidentified] Identities = 244/309 (78%), Positives = 273/309 (87%), Gaps = 1/309 (0%) Query: 1 LKKIGGQQMHEDVKQHLAKAGTPTMGGTVFLLVATAVSLLVSLF-SIKNTQSLALISGIL 59 LKKIGGQQMHEDVKQHLAKAGTPTMGGTVFL+VA VSL+S+ S +N+ +L GIL Sbjct: 28 LKKIGGQQMHEDVKQHLAKAGTPTMGGTVFLVVALLVSLIFSIILSKENSGNLGATFGIL 87 Query: 60 SIVVIYGIIGFLDDFLKIFKQINEGLTAKQKLALQLVGGLMFYFLHVSPSGISSINVFGY 119- S+V+IYGIIGFLDDFLKIFKQINEGLT KQK++LQL+ GL+FYF+HV PSG S+IN+FG+ Sbjct: 88 SVVLIYGIIGFLDDFLKIFKQINEGLTPKQKMSLQLIAGLIFYFVHVLPSGTSAINIFGF 147- Query: 120 QLPLGIFYLFFVLFWVVGFSNAVNLTDGIDGLASISVVISLVTYGVIAYVQSQFDVLLLI 17- 9 L +G Y FFVLFWVVGFSNAVNLTDGIDGLASISVVISL+TYG+IAY Q+QFD+LL+I Sbjct: 148 NLEVGYLYAFFVLFWVVGFSNAVNLTDGIDGLASISVVISLITYGIIAYNQTQFDILLII 20- 7 Query: 180 GAMIGALLGFFCFNHKPAKVFMGDVGSLALGAMLAAISIALRQEWTLLIIGIVYVLETSS 23- 9 MIGALLGFF FNHKPAKVFMGDVGSLALGAMLAAISIALRQEWTLL IG VYV ETSS Sbjct: 208 VIMIGALLGFFVFNHKPAKVFMGDVGSLALGAMLAAISIALRQEWTLLFIGFVYVFETSS 26- 7 Query: 240 VMLQVSYFKYTKKKYGEGRRIFRMTPFHHHLELGGLSGKGKKWSEWQVDAFLWGVGSLAS 29- 9 VMLQV+YFKYTKKK C G+RIFRMTPFHHHLELGG+SGKG KWSEW+VDAFLW +G S Sbjct: 268 VMLQVAYFKYTKKKTGVGKRIFRMTPFHHHLELGGVSGKGNKWSEWKVDAFLWAIGIFMS 32- 7 Query: 300 LLVLAILYV 308 + LAILY+ Sbjct: 328 AITLAILYL 336 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-02788 Identities = 244/309 (78%), Positives = 273/309 (87%), Gaps = 1/309 (0%) Query: 28 LKKIGGQQMHEDVKQHLAKAGTPTMGGTVFLIVALLVSLIFSIILSKENSGNLGATFGIL 87 - LKKIGGQQMHEDVKQHLAKAGTPTMGGTVFL+VA VSL+S+ S +N+ +L GIL Sbjct: 1 LKKIGGQQMHEDVKQHLAKAGTPTMGGTVFLLVATAVSLLVSLF-SIKNTQSLALISGIL 59 Query: 88 SVVLIYGIIGFLDDFLKIFKQINEGLTPKQKMSLQLIAGLIFYFVHVLPSGTSAINIFGF 147- S+V+IYGIIGFLDDFLKIFKQINEGLT KQK++LQL+GL+FYF+HV PSG S+IN+FG+ Sbjct: 60 SIVVIYGIIGFLDDFLKIFKQINEGLTAKQKLALQLVGGLMFYFLHVSPSGISSINVFGY 119- Query: 148 YLEVGYLYAFFVLFWVVGFSNAVNLTDGIDGLASISVVISLITYGIIAYNQTQFDILLII 20- 7 L +G Y FFVLFWVVGFSNAVNLTDGIDGLASISVVISL+TYG+IAY Q+QFD+LL+I Sbjct: 120 QLPLGIFYLFFVLFWVVGFSNAVNLTDGIDGLASISVVISLVTYGVIAYVQSQFDVLLLI 17- 9 Query: 208 VIMIGALLGFFVFNHKPAKVFMGDVGSLALGAMLAAISIALRQEWTLLFIGFVYVFETSS 26- 7 MIGALLGFF FNHKPAKVFMGDVGSLALGAMLAAISIALRQEWTLL IG VYV ETSS Sbjct: 180 GAMIGALLGFFCFNHKPAKVFMGDVGSLALGAMLAAISIALRQEWTLLIIGIVYVLETSS 23- 9 Query: 268 VMLQVAYFKYTKKKTGVGKRIFRMTPFHHHLELGGVSGKGNKWSEWKVDAFLWAIGIFMS 32- 7 VMLQV+YFKYTKKK G G+RIFRMTPFHHHLELGG+SGKG KWSEW+VDAFLW +G S Sbjct: 240 VMLQVSYFKYTKKKYGEGRRIFRMTPFHHHLELGGLSGKGKKWSEWQVDAFLWGVGSLAS 29- 9 Query: 328 AITLAILYL 336 + LAILY+ Sbjct: 300 LLVLAILYV 308 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 956 A DNA sequence (GBSx1014) was identified in S. agalactiae <SEQ ID 2913> which encodes the amino acid sequence <SEQ ID 2914>. This protein is predicted to be autoaggregation-mediating protein (deaD). Analysis of this protein sequence reveals the following: TABLE-US-02789 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3018(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02790 >GP:CAB14444 GB:Z99116 similar to ATP-dependent RNA helicase [Bacillus subtilis] Identities = 215/436 (49%), Positives = 310/436 (70%), Gaps = 5/436 (1%) Query: 3 FKDFNFKPYIQRALDELKFVDPTDVQAKLIPVVRSGRDLVGESKTGSGKTHTFLLPIFEK 62 F+ + KP+I A+ L F +PTD+Q +LIP V ++G+S+TG+GKTH +LLP+ K Sbjct: 6 FELYELKPFIIDAVHRLGFYEPTDIQKRLIPAVLKKESVIGQSQTGTGKTHAYLLPLLNK 65 Query: 63 LDESSDDVQVVITAPSRELGTQIYQATKQIAEHSE-QEIRVVNYVGGTDKLRQIEKLKVS 121- +D + D VQVVITAP+REL QIYQ +I + E +IR ++GGTDK + I+KLK+ Sbjct: 66 IDPAKDVVQVVITAPTRELANQIYQEALKITQGEEGSQIRSKCFIGGTDKQKSIDKLKI- 124- Query: 122 QPHIVIGTPGRIYDLVKSGDLAIHKAHTFVVDEADMTLDMGFLDTVDKIAGSLPKDVQIL 18- 1 QPH+V+GTPGRI DL+K L++HKA + V+DEAD+ LDMGFL VD I +P+D+Q+L Sbjct: 125 QPHLVVGTPGRIADLIKEQALSVHKAESLVIDEADLMLDMGFLADVDYIGSRMPEDLQML 18- 4 Query: 182 VFSATIPQKLQPFLKKYLTNPVMEKIKTATVIADTIDNWLLSTKGRDKNAQILELSKLMQ 24- 1 VFSATIP+KL+PFLKKY+ NP ++ V A I++ L+ +K RDK+ + ++ + Sbjct: 185 VFSATIPEKLKPFLKKYMENPKYAHVEPKQVTAAKIEHILIPSKHRDKDKLLFDIMSHLN 24- 4 Query: 242 PYLAMIFVNTKERADELHSYLSSNGLKVAKIHGGIAPRERKRIMNQVKNLEFEYIVATDL 30- 1 PYL ++F NTK AD + YL+ G+K+ +HGG+ PRERK++M Q+ +LEF YI+ATDL Sbjct: 245 PYLGIVFANTKNTADHIAQYLTGKGMKIGLLHGGLTPRERKKVMKQINDLEFTYIIATDL 30- 4 Query: 302 AARGIDIEGVSHVINDAIPQDLSFFVHRVGRTGRNGLSGTAITLYQPSDDSDIRELEKLG 36- 1 AARGIDI+GVSHVIN +P DL F+VHRVGRT R G SG A+T+Y+ +D+ + LEK+G Sbjct: 305 AARGIDIKGVSHVINYELPDDLDFYVHRVGRTARAGSSGQAMTIYELTDEDALVRLEKMG 36- 4 Query: 362 INFIPKVIKNGEFQDTYDRDRRNNREKSYQKLDTEMIGLVKKKKKKIKPGYKKKIQWKVD 42- 1 I F ++ GE++ DR RR R+K+ + D E+ + KK KK+KPGYKKK+ ++++ Sbjct: 365 IEFEYLELEKGEWKKGDDRQRRKKRKKTPNEAD-EIAHRLVKKPKKVKPGYKKKMSYEME 42- 3 Query: 422 EKRRKERRASNRAKGR 437 + ++K+RR N++K R Sbjct: 424 KIKKKQRR--NQSKKR 437 A related DNA sequence was identified in S. pyogenes <SEQ ID 2915> which encodes the amino acid sequence <SEQ ID 2916>. Analysis of this protein sequence reveals the following: TABLE-US-02791 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2315 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02792 Identities = 382/447 (85%), Positives = 420/447 (93%) Query: 1 MSFKDFNFKPYIQRALDELKFVDPTDVQAKLIPVVRSGRDLVGESKTGSGKTHTFLLPIF 60 MSFKD++FK Y+Q+AL+E+ FV+PT+VQ +LIP+V SGRDLVGESKTGSGKTHTFLLPIF Sbjct: 1 MSFKDYHFKQYVQQALEEIGFVNPTEVQKRLIPIVNSGRDLVGESKTGSGKTHTFLLPIF 60 Query: 61 EKLDESSDDVQVVITAPSRELGTQIYQATKQIAEHSEQEIRVVNYVGGTDKLRQIEKLKV 120- EKLDE+ +VQVVITAPSREL TQI+ A KQIA+H ++EIR+ NYVGGTDKLRQIEKLK Sbjct: 61 EKLDEAKAEVQVVITAPSRELATQIFDACKQIAKHFQEEIRLANYVGGTDKLRQIEKLKD 120- Query: 121 SQPHIVIGTPGRIYDLVKSGDLAIHKAHTFVVDEADMTLDMGFLDTVDKIAGSLPKDVQI 18- 0 SQPHIVIGTPGRIYDLVKSGDLAIHKA TFVVDEADMT+DMGFLDTVDKIA SLPK VQI Sbjct: 121 SQPHIVIGTPGRIYDLVKSGDLAIHKATTFVVDEADMTMDMGFLDTVDKIAASLPKSVQI 18- 0 Query: 181 LVFSATIPQKLQPFLKKYLTNPVMEKIKTATVIADTIDNWLLSTKGRDKNAQILELSKLM 24- 0 LVFSATIPQKLQPFLKKYLTNPV+E+IKT TVIADTIDNWL+STKGRDKN Q+LE+ K M Sbjct: 181 LVFSATIPQKLQPFLKKYLTNPVIEQIKTKTVIADTIDNWLVSTKGRDKNGQLLEILKTM 24- 0 Query: 241 QPYLAMIFVNTKERADELHSYLSSNGLKVAKIHGGIAPRERKRIMNQVKNLEFEYIVATD 30- 0 QPY+AM+FVNTKERAD+LH++L++NGLKVAKIHGGI PRERKRIMNQVK L+FEYIVATD Sbjct: 241 QPYMAMLFVNTKERADDLHAFLTANGLKVAKIHGGIPPRERKRIMNQVKKLDFEYIVATD 30- 0 Query: 301 LAARGIDIEGVSHVINDAIPQDLSFFVHRVGRTGRNGLSGTAITLYQPSDDSDIRELEKL 36- 0 LAARGIDIEGVSHVINDAIPQDLSFFVHRVGRTGRNG++GTAITLYQPSDDSDI+ELEK+ Sbjct: 301 LAARGIDIEGVSHVINDAIPQDLSFFVHRVGRTGRNGMAGTAITLYQPSDDSDIKELEKM 36- 0 Query: 361 GINFIPKVIKNGEFQDTYDRDRRNNREKSYQKLDTEMIGLVKKKKKKIKPGYKKKIQWKV 42- 0 GI F PKV+KNGEFQDTYDRDRR NREK+YQKLDTEMIGLVKKKKKK+KPGYKKKIQW V Sbjct: 361 GIAFTPKVLKNGEFQDTYDRDRRQNREKAYQKLDTEMIGLVKKKKKKVKPGYKKKIQWAV 42- 0 Query: 421 DEKRRKERRASNRAKGRAERKAKKQSF 447 DEKRRKERRA NRAKGRAERKAKKQ F Sbjct: 421 DEKRRKERRAENRAKGRAERKAKKQHF 447 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 957 A DNA sequence (GBSx1015) was identified in S. agalactiae <SEQ ID 2917> which encodes the amino acid sequence <SEQ ID 2918>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following: TABLE-US-02793 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> There is also homology to SEQ ID 2920. A related GBS gene <SEQ ID 8693> and protein <SEQ ID 8694> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02794 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 8.85 GvH: Signal Score (-7.5): -1.77 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 8.12 threshold: 0.0 PERIPHERAL Likelihood = 8.12 182 modified ALOM score: -2.12 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00066## SEQ ID 8694 (GBS8) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 2 (lane 5; MW 31 kDa), FIG. 63 (lane 2; MW 31.3 kDa), FIG. 66 (lane 2 & 3; MW 31 kDa), in FIG. 178 (lane 2; MW 31 kDa), in FIG. 179 (lane 3 & 4; MW 31 kDa) and in FIG. 180 (lane 3; MW 31 kDa). It was also expressed in E. coli as a GST-fusion product, with SDS-PAGE shown in FIG. 66 (lanes 4 & 5; MW 56 kDa) and in FIG. 180 (lanes 4 & 5; MW 55 kDa). GBS8-His was purified as shown in FIGS. 189 (lane 7), 211 (lane 3), 228 (lanes 4-5) and 230 (lanes 3-6). Purified GBS8-GST is shown in FIG. 209, lane 6. The GBS8-His fusion product was purified (FIG. 90A) and used to immunise mice (lane 2 product; 12.9 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 90B), FACS (FIG. 90C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 958 A DNA sequence (GBSx1016) was identified in S. agalactiae <SEQ ID 2921> which encodes the amino acid sequence <SEQ ID 2922>. Analysis of this protein sequence reveals the following: TABLE-US-02795 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3991 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 959 A DNA sequence (GBSx1017) was identified in S. agalactiae <SEQ ID 2923> which encodes the amino acid sequence <SEQ ID 2924>. This protein is predicted to be probable amino-acid abc transporter permease protein in idh-deor inter. Analysis of this protein sequence reveals the following: TABLE-US-02796 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.62 Transmembrane 50-66 (41-74) INTEGRAL Likelihood = -0.90 Transmembrane 226-242 (226-242) INTEGRAL Likelihood = -0.53 Transmembrane 80-96 (80-96) ----- Final Results ----- bacterial membrane --- Certainty = 0.5649 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02797 >GP:CAB15985 GB:Z99124 similar to amino acid ABC transporter (permease) [Bacillus subtilis] Identities = 90/224 (40%), Positives = 137/224 (60%), Gaps = 10/224 (4%) Query: 28 WKAVLDAIPSILERLPITLLLTVAGALFGLILALIFAVVKINRVKILYPIQALFVSFLRG 87 - W+ ++ A P++++ LPITL + +A +F +I LI A++ N++ +L+ + L++SF RG Sbjct: 6 WEFMISAFPTLIQALPITLFMAIAAMIFAIIGGLILALITKNKIPVLHQLSKLYISFFRG 65 Query: 88 TPILVQLMLSYYGIPLFLKFLNQKYGFDWNINAIPASVFAITAFAFNEAAYTSETIRAAI 147- P LVQL L YYG+P +++ + A AI + AAY +E RAA+ Sbjct: 66 VPTLVQLFLIYYGLPQLFPEMSK----------MTALTAAIIGLSLKNAAYLAEIFRAAL 115- Query: 148 LSVDQGEIEAARSLGMTSAQVYRRVIIPNAAVVATPTLINTLIGLTKGTSLAFNAGIVEM 20- 7 SVD G++EA S+GMT Q YRR+I+P A A P NT IGL K TSLAF G++EM Sbjct: 116 NSVDDGQLEACLSVGMTKFQAYRRIILPQAIRNAIPATGNTFIGLLKETSLAFTLGVMEM 17- 5 Query: 208 FAQAQIMGGSDYRYFERYISVALVYWAVSFLIEQLGNAIERKMA 251 FAQ ++ + +YFE Y++VA+VYW ++ + L + ER M+ Sbjct: 176 FAQGKMYASGNLKYFETYLAVAIVYWVLTIIYSILQDLFERAMS 219 A related DNA sequence was identified in S. pyogenes <SEQ ID 2925> which encodes the amino acid sequence <SEQ ID 2926>. Analysis of this protein sequence reveals the following: TABLE-US-02798 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.27 Transmembrane 80-96 (74-104) INTEGRAL Likelihood = -1.06 Transmembrane 207-223 (207-223) INTEGRAL Likelihood = -0.90 Transmembrane 110-126 (110-126) ----- Final Results ----- bacterial membrane --- Certainty = 0.3909(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9167> which encodes the amino acid sequence <SEQ ID 9168>. Analysis of this protein sequence reveals the following: TABLE-US-02799 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.27 Transmembrane 50-66 (44-74) INTEGRAL Likelihood = -1.06 Transmembrane 177-193 (177-193) INTEGRAL Likelihood = -0.90 Transmembrane 80-96 (80-96) ----- Final Results ----- bacterial membrane --- Certainty = 0.391(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02800 Identities = 212/267 (79%), Positives = 238/267 (88%) Query: 1 MNQFILTGGWSWYNNLVSQVPAGKLFSWKAVLDAIPSILERLPITLLLTVAGALFGLILA 60 M LT GW++Y+ L+S +P GKLFSW AV DAIP+I++RLPITL LT++GA FGL+LA Sbjct: 31 MTSVFLTSGWAFYDYLISPIPHGKLFSWHAVFDAIPNIIQRLPITLGLTLSGATFGLVLA 90 Query: 61 LIFAVVKINRVKILYPIQALFVSFLRGTPILVQLMLSYYGIPLFLKFLNQKYGFDWNINA 120- LIFA+VKIN+VK+LYPIQA+FVSFLRGTPILVQLML+YYGIPLFLKFLNQKYGFDWN+NA Sbjct: 91 LIFALVKINKVKLLYPIQAIFVSFLRGTPILVQLMLTYYGIPLFLKFLNQKYGFDWNVNA 150- Query: 121 IPASVFAITAFAFNEAAYTSETIRAAILSVDQGEIEAARSLGMTSAQVYRRVIIPNAAVV 18- 0 IPAS+FAITAFAFNEAAY SETIRAAILSVD GEIEAA+SLGMTS QVYRRVIIPNA VV Sbjct: 151 IPASIFAITAFAFNEAAYASETIRAAILSVDTGEIEAAKSLGMTSVQVYRRVIIPNATVV 21- 0 Query: 181 ATPTLINTLIGLTKGTSLAFNAGIVEMFAQAQIMGGSDYRYFERYISVALVYWAVSFLIE 24- 0 A PTLIN LIGLTKGTSLAFNAGIVEMFAQAQI+GGSDYRYFERYISVALVYW++S L+E Sbjct: 211 AIPTLINGLIGLTKGTSLAFNAGIVEMFAQAQILGGSDYRYFERYISVALVYWSISILME 27- 0 Query: 241 QLGNAIERKMAIKAPRHLTDEIPGGVR 267 Q+G IE KMAIKAP +E G +R Sbjct: 271 QVGRLIENKMAIKAPEQARNEKLGELR 297 There is also homology to SEQ ID 4794. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 960 A DNA sequence (GBSx1018) was identified in S. agalactiae <SEQ ID 2927> which encodes the amino acid sequence <SEQ ID 2928>. This protein is predicted to be amino acid ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-02801 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3205(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02802 >GP: AAC00329 GB: AF008220 putative amino acid transporter [Bacillus subtilis] Identities = 121/247 (48%), Positives = 176/247 (70%) Query: 1 MIKLRQLTKSFSGQKVLDKLDLDIEKGQVVALVGASGAGKSTFLRSMNYLEEPDYGTIEI 60 MI+++ + K F VL ++L + KG+VV ++G SG+GK+TFLR +N LE PD G I I Sbjct: 1 MIEIKNIHKQFGIHHVLKGINLTVRKGEVVTIIGPSGSGKTTFLRCLNLLERPDEGIISI 60 Query: 61 DDFKVDFKSISKDDILTLRRKLAMVFQQFNLFERRTALDNVKEGLKIVKKMSDQEATRIA 120- D ++ + SK ++ LR++ AMVFQQ++LF +T ++NV EGL I +KM Q+A +A Sbjct: 61 HDKVINCRFPSKKEVHWLRKQTAMVFQQYHLFAHKTVIENVMEGLTIARKMRKQDAYAVA 120- Query: 121 RDELAKVGLADREKYYPRHLSGGQKQRVALARALAMKPDVLLLDEPTSALDPELVGEVEK 18- 0 +EL KVGL D+ YP LSGGQKQRV +ARALA+ PDVLL DEPT+ALDPELVGEV + Sbjct: 121 ENELRKVGLQDKLNAYPSQLSGGQKQRVGIARALAIHPDVLLFDEPTAALDPELVGEVLE 18- 0 Query: 181 SIADAAKQGQTMVLVSHDMNFVYQVADKVLFLEKGRILESGTPEQLFNHPLEERTKEFFA 24- 0 + + K G TM++V+H+M F +V+D+V+F+++G I+E GTPE++F H ++RT++F Sbjct: 181 VMLEIVKTGATMIVVTHEMEFARRVSDQVVFMDEGVIVEQGTPEEVFRHTKKDRTRQFLR 24- 0 Query: 241 SYNKSYL 247 + YL Sbjct: 241 RVSPEYL 247 A related DNA sequence was identified in S. pyogenes <SEQ ID 2929> which encodes the amino acid sequence <SEQ ID 2930>. Analysis of this protein sequence reveals the following: TABLE-US-02803 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1840(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02804 Identities = 199/247 (80%), Positives = 229/247 (92%) Query: 1 MIKLRQLTKSFSGQKVLDKLDLDIEKGQVVALVGASGAGKSTFLRSMNYLEEPDYGTIEI 60 MI +R L+K+FSGQKVLD L LDIEKGQV+ALVGASGAGKSTFLRS+NYLE+PD G+I I Sbjct: 2 MITIRNLSKTFSGQKVLDSLALDIEKGQVIALVGASGAGKSTFLRSLNYLEKPDSGSISI 61 Query: 61 DDFKVDFKSISKDDILTLRRKLAMVFQQFNLFERRTALDNVKEGLKIVKKMSDQEATRIA 120- DF VDF++I+ + +L LRRKLAMVFQQFNLFERRTAL+NVKSGLK+VKK+SDQEAT++A Sbjct: 62 GDFTVDFETITTEQVLILRRKLAMVFQQFNLFERRTALENVKEGLKVVKKLSDQEATKLA 121- Query: 121 RDELAKVGLADREKYYPRHLSGGQKQRVALARALAMKPDVLLLDEPTSALDPELVGEVEK 18- 0 + ELAKVGLADR+ +YPRHLSGGQKQRVALARALAMKPDVLLLDEPTSALDPELVGEVEK Sbjct: 122 QAELAKVGLADRKHHYPRHLSGGQKQRVALARALAMKPDVLLLDEPTSALDPELVGEVEK 18- 1 Query: 181 SIADAAKQGQTMVLVSHDMNFVYQVADKVLFLEKGRILESGTPEQLFNHPLEERTKEFFA 24- 0 SI DAAK GQTMVLVSHDMNFVYQVAD+VLFL++G+ILE GTPE++F HP +ERTKEFFA Sbjct: 182 SITDAAKSGQTMVLVSHDMNFVYQVADRVLFLDQGKILEQGTPEEVFRHPQKERTKEFFA 24- 1 Query: 241 SYNKSYL 247 SY+K+Y+ Sbjct: 242 SYSKTYI 248 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 961 A DNA sequence (GBSx1019) was identified in S. agalactiae <SEQ ID 2931> which encodes the amino acid sequence <SEQ ID 2932>. Analysis of this protein sequence reveals the following:

TABLE-US-02805 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.831(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02806 >GP: BAB07290 GB: AP001519 thioredoxin reductase (NADPH) [Bacillus halodurans] Identities = 173/302 (57%), Positives = 234/302 (77%) Query: 1 MYDTLIIGSGPGGMTAALYAARSNLKVGLIEQGAPGGQMNNTAEIENYPGYDHISGPELS 60 +YD +I G+GP GMTAA+Y +R+NL ++E+G PGGQM NT ++ENYPG+DHI GPELS Sbjct: 7 VYDVVIAGAGPAGMTAAVYTSRANLSTVMVERGVPGGQMANTEDVENYPGFDHILGPELS 66 Query: 61 MKMYEPLEKFEVEHIYGIVQRVENDGDVKRVITEDESYEAKTVILATGAKNSLLGVPGEE 120- KM+E +KF E+ YG ++ + + GD+K V ++ Y+A+ VI+ATGA+ LGVPGE+ Sbjct: 67 TKMFEHAKKFGAEYAYGDIKEIIDQGDLKLVKAGNKEYKARAVIVATGAEYKKLGVPGEK 126- Query: 121 EYTSRGVSYCAVCDGAFFRDQDLLVVGGGDSAVEEAVFLTQFAKSVTIIHRRDQLRAQKV 18- 0 E + RGVSYCAVCDGAFF+ ++L+VVGGGDSAVEEAV+LT+FA VTIIHRRDQLRAQK+ Sbjct: 127 ELSGRGVSYCAVCDGAFFKGKELVVVGGGDSAVEEAVYLTRFASKVTIIHRRDQLRAQKI 18- 6 Query: 181 LQDRAFANEKIKFVWDSVVKEIKGNEIKVSGVTVENLKTGEISEMTFGGVFIYVGLKPHS 24- 0 LQ RAF N+KI+F+WD VVK+I G + KVS VT+E+ KTGE + GVFIY+G+ P + Sbjct: 187 LQQRAFDNDKIEFIWDHVVKQINGTDGKVSSVTIEHAKTGEQQDFKTDGVFIYIGMLPLN 24- 6 Query: 241 SMVSELGITDETGWVLTDTNMKTSIPGLYAIGDVRQKDLRQIATAVGEGAIAGQGVYNYI 30- 0 V L I ++ G+++T+ M+TS+PG++A GDVR+K LRQI TA G+G++A Q V +YI Sbjct: 247 EAVKNLNILNDEGYIVTNEEMETSVPGIFAAGDVREKSLRQIVTATGDGSLAAQNVQHYI 30- 6 Query: 301 TE 302 E Sbjct: 307 EE 308 A related DNA sequence was identified in S. pyogenes <SEQ ID 2933> which encodes the amino acid sequence <SEQ ID 2934>. Analysis of this protein sequence reveals the following: TABLE-US-02807 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.386(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02808 Identities = 236/300 (78%), Positives = 273/300 (90%) Query: 1 MYDTLIIGSGPGGMTAALYAARSNLKVGLIEQGAPGGQMNNTAEIENYPGYDHISGPELS 60 MYDTLIIGSGP GMTAALYAARSNL V +IEQGAPGGQMNNT +IENYPGYDHISGPEL+ Sbjct: 1 MYDTLIIGSGPAGMTAALYAARSNLSVAIIEQGAPGGQMNNTFDIENYPGYDHISGPELA 60 Query: 61 MKMYEPLEKFEVEHIYGIVQRVENDGDVKRVITEDESYEAKTVILATGAKNSLLGVPGEE 120- MKMYEPLEKF VE+IYGIVQ++EN GD K V+TED SYEAKTVI+ATGAK +LGVPGEE Sbjct: 61 MKMYEPLEKFNVENIYGIVQKIENFGDYKCVLTEDASYEAKTVIIATGAKYRVLGVPGEE 120- Query: 121 EYTSRGVSYCAVCDGAFFRDQDLLVVGGGDSAVEEAVFLTQFAKSVTIIHRRDQLRAQKV 18- 0 YTSRGVSYCAVCDGAFFRDQDLLVVGGGDSAVEEA++LTQFAK VT++HRRDQLRAQK+ Sbjct: 121 YYTSRGVSYCAVCDGAFFRDQDLLVVGGGDSAVEEAIYLTQFAKKVTVVHRRDQLRAQKI 18- 0 Query: 181 LQDRAFANEKIKFVWDSVVKEIKGNEIKVSGVTVENLKTGEISEMTFGGVFIYVGLKPHS 24- 0 LQDRAFAN+K+ F+WDSVVKEI+GN+IKVS V +EN+KTG++++ FGGVFIYVG+ P + Sbjct: 181 LQDRAFANDKVDFIWDSVVKEIQGNDIKVSNVLIENVKTGQVTDHAFGGVFIYVGMNPVT 24- 0 Query: 241 SMVSELGITDETGWVLTDTNMKTSIPGLYAIGDVRQKDLRQIATAVGEGAIAGQGVYNYI 30- 0 MV +L ITD GW++TD +M+TSIPG++AIGDVRQKDLRQI TAVG+GAIAGQGVY+Y+ Sbjct: 241 GMVKDLEITDSEGWIITDDHMRTSIPGIFAIGDVRQKDLRQITTAVGDGAIAGQGVYHYL 30- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 962 A DNA sequence (GBSx1020) was identified in S. agalactiae <SEQ ID 2935> which encodes the amino acid sequence <SEQ ID 2936>. Analysis of this protein sequence reveals the following: TABLE-US-02809 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3626(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02810 >GP: CAB15163 GB: Z99120 similar to nicotinate phosphoribosyltransferase [Bacillus subtilis] Identities = 309/476 (64%), Positives = 384/476 (79%), Gaps = 2/476 (0%) Query: 2 YKDDSLTLHTDLYQINMMQVYFNKGIHNKRAVFEAYFRKVPFENGYAVFAGLERIVRYLE 61 +KDDSL+LHTDLYQINM + Y+ GIH K+A+FE +FR++PFENGYAVFAGLE+ + YLE Sbjct: 6 FKDDSLSLHTDLYQINMAETYWRDGIHEKKAIFELFFRRLPFENGYAVFAGLEKAIEYLE 65 Query: 62 NLSFSDSDLSYLE-ELGYPEEFLDYLKNLKMELTVKSAKEGDLVFANEPLVQIEGPLAQC 120- N F+DSDLSYL+ ELGY E+F++YL+ L ++ S KEG+LVF NEP++++E PL + Sbjct: 66 NFKFTDSDLSYLQDELGYHEDFIEYLRGLSFTGSLYSMKEGELVFNNEPIMRVEAPLVEA 125- Query: 121 QLVETAILNIINYQTLVATKAARIRSVIEDEPLLEFGTRRAQEMDAAIWGTRAAIIGGAN 18- 0 QL+ETA+LNI+NYQTL+ATKAARI+ VI DE LEFGTRRA EMDAA+WG RAA+IGG + Sbjct: 126 QLIETALLNIVNYQTLIATKAARIKGVIGDEVALEFGTRRAHEMDAAMWGARAALIGGFS 18- 5 Query: 181 ATSNVRAGKIFNIPVSGTHAHALVQTYGDDYQAFKAYAETHKDCVFLVDTYDTLRVGVPN 24- 0 ATSNVRAGK FNIPVSGTHAHALVQ Y D+Y AFK YAETHKDCVFLVDTYDTLR G+PN Sbjct: 186 ATSNVRAGKRFNIPVSGTHAHALVQAYRDEYTAFKKYAETHKDCVFLVDTYDTLRSGMPN 24- 5 Query: 241 AIRVAKEMGEKINFLGVRLDSGDLAYLSKKVRQQLDDAGFPNAKIYASNDLDENTILNLK 30- 0 AIRVAKE G++INF+G+RLDSGDLAYLSKK R+ LD+AGF +AK+ AS+DLDE+TI+NLK Sbjct: 246 AIRVAKEFGDRINFIGIRLDSGDLAYLSKKARKMLDEAGFTDAKVIASSDLDEHTIMNLK 30- 5 Query: 301 MQKAKIDVWGVGTKLITAYDQPALGAVYKIVSIETDAGSMRDTIKLSNNAEKVSTPGKKQ 36- 0 Q A+IDVWGVGTKLITAYDQPALGAVYK+V+IE D G M DTIK+S+N EKV+TPG+K+ Sbjct: 306 AQGARIDVWGVGTKLITAYDQPALGAVYKLVAIEED-GKMVDTIKISSNPEKVTTPGRKK 36- 4 Query: 361 VWRITSRAKGKSEGDYITFADTDVTQLDEIEMFHPTYTYINKTVRDFDAVPLLVDIFDKG 42- 0 V+RI +++ SEGDYI D V + MFHP +T+I+K V +F A L IF+KG Sbjct: 365 VYRIINQSNHHSEGDYIALYDEQVNDQKRLRMFHPVHTFISKFVTNFYAKDLHELIFEKG 42- 4 Query: 421 KLVYQLPSLQEIQEYGRKEFDQLWDEYKRVLNPQDYPVDLARDVWQNKMDLIDRIR 476 L YQ P + +IQ+Y + LW+EYKR+ P++YPVDL+ D W NKM I ++ Sbjct: 425 ILCYQNPEISDIQQYVQDNLSLLWEEYKRISKPEEYPVDLSEDCWSNKMQRIHEVK 480 A related DNA sequence was identified in S. pyogenes <SEQ ID 2937> which encodes the amino acid sequence <SEQ ID 2938>. Analysis of this protein sequence reveals the following: TABLE-US-02811 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3192(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02812 Identities = 409/484 (84%), Positives = 446/484 (91%) Query: 1 MYKDDSLTLHTDLYQINMMQVYFNKGIHNKRAVFEAYFRKVPFENGYAVFAGLERIVRYL 60 MYKDDSLTLHTDLYQINMMQVYF +GIHN+ AVFE YFRK PF NGYAVFAGL+R+V YL Sbjct: 1 MYKDDSLTLHTDLYQINMMQVYFEQGIHNRHAVFEVYFRKEPFNNGYAVFAGLQRMVEYL 60 Query: 61 ENLSFSDSDLSYLEELGYPEEFLDYLKNLKMELTVKSAKEGDLVFANEPLVQIEGPLAQC 120- E FS++DL+YLEELGYPE FL YLK L++ELT++SAKEGDLVFANEP+VQ+EGPL QC Sbjct: 61 EQFQFSETDLAYLEELGYPENFLTYLKELRLELTIRSAKEGDLVFANEPIVQVEGPLGQC 120- Query: 121 QLVETAILNIINYQTLVATKAARIRSVIEDEPLLEFGTRRAQEMDAAIWGTRAAIIGGAN 18- 0 QLVETA+LNI+N+QTL+ATKAARIRSVIEDEPLLEFGTRRAQE+DAAIWGTRAA+IGGA+ Sbjct: 121 QLVETALLNIVNFQTLIATKAARIRSVIEDEPLLEFGTRRAQELDAAIWGTRAAMIGGAD 18- 0 Query: 181 ATSNVRAGKIFNIPVSGTHAHALVQTYGDDYQAFKAYAETHKDCVFLVDTYDTLRVGVPN 24- 0 ATSNVRAGK F+IPVSGTHAHALVQ YG+DY AF AYA+THKDCVFLVDTYDTL+VGVP Sbjct: 181 ATSNVRAGKRFDIPVSGTHAHALVQAYGNDYDAFMAYAKTHKDCVFLVDTYDTLKVGVPT 24- 0 Query: 241 AIRVAKEMGEKINFLGVRLDSGDLAYLSKKVRQQLDDAGFPNAKIYASNDLDENTILNLK 30- 0 AIRVAKEMG+KINFLGVRLDSGDLAYLSK VRQQLDDAGF AKIYASNDLDENTILNLK Sbjct: 241 AIRVAKEMGDKINFLGVRLDSGDLAYLSKTVRQQLDDAGFTEAKIYASNDLDENTILNLK 30- 0 Query: 301 MQKAKIDVWGVGTKLITAYDQPALGAVYKIVSIETDAGSMRDTIKLSNNAEKVSTPGKKQ 36- 0 MQKAKIDVWGVGTKLITAYDQPALGAVYKIVSIE + GSMRDTIKLSNNAEKVSTPGKKQ Sbjct: 301 MQKAKIDVWGVGTKLITAYDQPALGAVYKIVSIEQEDGSMRDTIKLSNNAEKVSTPGKKQ 36- 0 Query: 361 VWRITSRAKGKSEGDYITFADTDVTQLDEIEMFHPTYTYINKTVRDFDAVPLLVDIFDKG 42- 0 VWRITSR KGKSEGDYITF D +V +L EIEMFHPTYTYI KTV++FDA+PLLVDIF KG Sbjct: 361 VWRITSREKGKSEGDYITFTDINVNELTEIEMFHPTYTYIKKTVKEFDAIPLLVDIFVKG 42- 0 Query: 421 KLVYQLPSLQEIQEYGRKEFDQLWDEYKRVLNPQDYPVDLARDVWQNKMDLIDRIRKEAL 48- 0 +LVYQLP+L EI+ Y +KEFD+LWDEYKRVLNPQDYPVDLARDVWQNKM LID IRK+A Sbjct: 421 ELVYQLPTLAEIKAYAKKEFDKLWDEYKRVLNPQDYPVDLARDVWQNKMALIDNIRKDAY 48- 0 Query: 481 AKGE 484 K E Sbjct: 481 GKSE 484 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 963 A DNA sequence (GBSx1021) was identified in S. agalactiae <SEQ ID 2939> which encodes the amino acid sequence <SEQ ID 2940>. Analysis of this protein sequence reveals the following: TABLE-US-02813 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2744(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02814 >GP:AAC74810 GB:AE000269 NAD synthetase, prefers NH3 over glutamine [Escherichia coli K12] Identities = 173/274 (63%), Positives = 214/274 (77%), Gaps = 1/274 (0%) Query: 1 MTLQDQIIKELGVKPVINPSQEIRRSVEFLKDYLLKHSFLKTYVLGISGGQDSTLAGRLA 60 MTLQ QIIK LG KP IN +EIRRSV+FLK YL + F+K+ VLGISGGQDSTLAG+L Sbjct: 1 MTLQQQIIKALGAKPQINAEEEIRRSVDFLKSYLQTYPFIKSLVLGISGGQDSTLAGKLC 60 Query: 61 QLAVEELRADTG-ENYQFIAIRLPYGIQADEEDAQKALDFIKPDIALTINIKEAVDGQVR 119- Q+A+ ELR +TG E+ QFIA+RLPYG+QADE+D Q A+ FI+PD LT+NIK AV + Sbjct: 61 QMAINELRLETGNESLQFIAVRLPYGVQADEQDCQDAIAFIQPDRVLTVNIKGAVLASEQ 120- Query: 120 ALNAAGVEITDFNKGNIKARQRMISQYAVAGQYAGAVIGTDHAAENITGFFTKFGDGGAD 17- 9 AL AG+E++DF +GN KAR+RM +QY++AG +G V+GTDHAAE ITGFFTK+GDGG D Sbjct: 121 ALREAGIELSDFVRGNEKARERMKAQYSIAGMTSGVVVGTDHAAEAITGFFTKYGDGGTD 18- 0 Query: 180 LLPLFRLNKSQGKQLLAELGADKALYEKIPTADLEENKPGIADEIALGVTYQEIDAYLEG 23- 9 + PL+RLNK QGKQLLA L + LY+K PTADLE+++P + DE+ALGVTY ID YLEG Sbjct: 181 INPLYRLNKRQGKQLLAALACPEHLYKKAPTADLEDDRPSLPDEVALGVTYDNIDDYLEG 24- 0 Query: 240 KVVSDKSRGIIENWWYKGQHKRHLPITIFDDFWK 273 K V + IENW+ K +HKR PIT+FDDFWK Sbjct: 241 KNVPQQVARTIENWYLKTEHKRRPPITVFDDFWK 274 A related DNA sequence was identified in S. pyogenes <SEQ ID 2941> which encodes the amino acid sequence <SEQ ID 2942>. Analysis of this protein sequence reveals the following: TABLE-US-02815 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3482(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02816 Identities = 213/274 (77%), Positives = 242/274 (87%), Gaps = 1/274 (0%) Query: 1 MTLQDQIIKELGVKPVINPSQEIRRSVEFLKDYLLKHSFLKTYVLGISGGQDSTLAGRLA 60 MTLQ++II++LGVK I+P +EIR++V+FLK YL KHSFLKTYVLGISGGQDSTLAG+LA Sbjct: 15 MTLQEEIIRQLGVKASIDPQEEIRKAVDFLKAYLRKHSFLKTYVLGISGGQDSTLAGKLA 74 Query: 61 QLAVEELRADTGEN-YQFIAIRLPYGIQADEEDAQKALDFIKPDIALTINIKEAVDGQVR 119- Q+A+ ELR + + YQFIA+RLPYG+QADE DAQKAL FI PD LTINIK AVDGQV Sbjct: 75 QMAIAELREEASDQAYQFIAVRLPYGVQADEADAQKALAFIAPDQTLTINIKAAVDGQVE 134- Query: 120 ALNAAGVEITDFNKGNIKARQRMISQYAVAGQYAGAVIGTDHAAENITGFFTKFGDGGAD 17- 9 AL AAGVEI+DFNKGNIKARQRMISQYA+AGQ AGAVIGTDHAAENITGFFTKFGDGGAD Sbjct: 135 ALQAAGVEISDFNKGNIKARQRMISQYAIAGQMAGAVIGTDHAAENITGFFTKFGDGGAD 19- 4 Query: 180 LLPLFRLNKSQGKQLLAELGADKALYEKIPTADLEENKPGIADEIALGVTYQEIDAYLEG 23- 9 +LPLFRLNK QGK LL LGAD ALYEK+PTADLE+ KPG+ADE+ALGVTYQ+ID YLEG Sbjct: 195 ILPLFRLNKRQGKALLKVLGADAALYEKVPTADLEDQKPGLADEVALGVTYQDIDDYLEG 25- 4 Query: 240 KVVSDKSRGIIENWWYKGQHKRHLPITIFDDFWK 273 K++S ++ IE WW+KGQHKRHLPITIFDDFWK Sbjct: 255 KLISKVAQATIEKWWHKGQHKRHLPITIFDDFWK 288 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 964 A DNA sequence (GBSx1022) was identified in S. agalactiae <SEQ ID 2943> which encodes the amino acid sequence <SEQ ID 2944>. Analysis of this protein sequence reveals the following: TABLE-US-02817 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2718(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02818 >GP:CAA82960 GB:Z30315 aminopeptidase C [Streptococcus thermophilus] Identities = 363/444 (81%), Positives = 407/444 (90%) Query: 1 MSKLTQTFTDKLFADYQANTKFSAIENAVTHNGLLKSLETRQSEIENDYVFSIDLTKDEV 60 M+ L+ FT+KLFADY+AN K+ AIENAVTHNGLLKS+ETRQSE+END+VFSIDLTKDEV Sbjct: 1 MTSLSTDFTEKLFADYEANAKYGAIENAVTHNGLLKSIETRQSEVENDFVFSIDLTKDEV 60 Query: 61 SNQKQSGRCWMFAALNTFRHKLISDFKLENFELSQAHTFFWDKYEKSNWFMEQIIATANQ 120- SNQK SGRCWMFAALNTFRHKLISDFKLE+FELSQAHTFFWDKYEKSNWF+EQIIATA+Q Sbjct: 61 SNQKASGRCWMFAALNTFRHKLISDFKLESFELSQAHTFFWDKYEKSNWFLEQIIATADQ 120- Query: 121 ELSSRKVKFLLDVPQQDGGQWDMVVALFEKYGVVPKTVYPESVSSSASRELNQYLNKLLR 18- 0 E+ SRKVKFLLD PQQDGGQWDMVV+LFEKYGVVPK+VYPESV+SS SRELNQYLNKLLR Sbjct: 121 EIGSRKVKFLLDTPQQDGGQWDMVVSLFEKYGVVPKSVYPESVASSNSRELNQYLNKLLR 18- 0 Query: 181 QDAQILRELIAQGADGATVQNKKEELLQEIFNFLAMNLGLPPQSFDFAYRDKDNHYQSDK 24- 0 QDAQILR+LIA GAD A VQ KKEE LQEIFN+LAM LGLPP+ FDFAYRDKD++Y+S+K Sbjct: 181 QDAQILRDLIASGADQAAVQAKKEEFLQEIFNYLAMTLGLPPRQFDFAYRDKDDNYRSEK 24- 0 Query: 241 NITPKAFYQKYVNLDLSDYVSIINAPTVDKPYGQSYTVEMLGNVVGGPAVKYLNLDMKRF 30- 0 ITP+AF++KYV L LSDYVS+INAPT DKPYG+SYTVEMLGNVVG P+V+Y+NL M RF Sbjct: 241 GITPRAFFEKYVGLKLSDYVSVINAPTADKPYGKSYTVEMLGNVVGAPSVRYINLPMDRF 30- 0 Query: 301 KELAIAQMKSGETVWFGSDVGQVSNRQKGILATTTYDFNSSMDIKLSQDKAGRLDYSESL 36- 0 KELAIAQMK+GE+VWFGSDVGQVS+RQKGILAT YDF +SMDI +QDKAGRLDYSESL Sbjct: 301 KELAIAQMKAGESVWFGSDVGQVSDRQKGILATNVYDFTASMDINWTQDKAGRLDYSESL 36- 0 Query: 361 MTHAMVLTGVDLDESGQPLKWKVENSWGEKVGKDGYFVASDAWMDEYTYQIVVRKELLTK 42- 0 MTHAMVLTGVDLD G+P+KWK+ENSWG+KVG+ GYFVASDAWMDEYTYQIVVRK+ LT Sbjct: 361 MTHAMVLTGVDLDADGKPIKWKIENSWGDKVGQKGYFVASDAWMDEYTYQIVVRKDFLTA 42- 0 Query: 421 EELEAYNAEPITLAPWDPMGALAN 444 EEL AY A+P LAPWDPMG+LA+ Sbjct: 421 EELAAYEADPQVLAPWDPMGSLAS 444 A related DNA sequence was identified in S. pyogenes <SEQ ID 2945> which encodes the amino acid sequence <SEQ ID 2946>. Analysis of this protein sequence reveals the following: TABLE-US-02819 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3002(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02820 Identities = 369/443 (83%), Positives = 407/443 (91%) Query: 1 MSKLTQTFTDKLFADYQANTKFSAIENAVTHNGLLKSLETRQSEIENDYVFSIDLTKDEV 60 MS LT+TFT++LFA Y+AN KFSAIENAVTHNGLLKSLETRQSE++ND+VFSIDLTKD+V Sbjct: 1 MSALTETFTEQLFAHYEANAKFSAIENAVTHNGLLKSLETRQSEVDNDFVFSIDLTKDKV 60 Query: 61 SNQKQSGRCWMFAALNTFRHKLISDFKLENFELSQAHTFFWDKYEKSNWFMEQIIATANQ 120- SNQK SGRCWMFAALNTFRHKLI++FKLENFELSQAHTFFWDKYEK+NWFMEQ+IATA+Q Sbjct: 61 SNQKASGRCWMFAALNTFRHKLITEFKLENFELSQAHTFFWDKYEKANWFMEQVIATADQ 120- Query: 121 ELSSRKVKFLLDVPQQDGGQWDMVVALFEKYGVVPKTVYPESVSSSASRELNQYLNKLLR 18- 0 EL+SRKVKFLLDVPQQDGGQWDMVV+LFEKYGVVPK+VYPES+SSS SRELNQYLNKLLR Sbjct: 121 ELTSRKVKFLLDVPQQDGGQWDMVVSLFEKYGVVPKSVYPESISSSNSRELNQYLNKLLR 18- 0 Query: 181 QDAQILRELIAQGADGATVQNKKEELLQEIFNFLAMNLGLPPQSFDFAYRDKDNHYQSDK 24- 0 QDAQILR+LIA GA V+++K ELLQEIFNFLAM LGLPP+FDFAYRDKD+HY +K Sbjct: 181 QDAQILRDLIASGAKADQVEDRKAELLQEIFNFLAMTLGLPPRHFDFAYRDKDDHYHVEK 24- 0 Query: 241 NITPKAFYQKYVNLDLSDYVSIINAPTVDKPYGQSYTVEMLGNVVGGPAVKYLNLDMKRF 30- 0 +TP+AFY K+V L LSDYVS+INAPT DKPYG+SYTVEMLGNVVG V+YLNLDMKRF Sbjct: 241 GLTPQAFYDKFVGLKLSDYVSVINAPTADKPYGKSYTVEMLGNVVGSREVRYLNLDMKRF 30- 0 Query: 301 KELAIAQMKSGETVWFGSDVGQVSNRQKGILATTTYDFNSSMDIKLSQDKAGRLDYSESL 36- 0 KELAI QM++GE+VWFGSDVGQVS+RQKGILAT TYDF +SMDI LSQDKAGRLDYSESL Sbjct: 301 KELAIKQMQAGESVWFGSDVGQVSDRQKGILATNTYDFEASMDINLSQDKAGRLDYSESL 36- 0 Query: 361 MTHAMVLTGVDLDESGQPLKWKVENSWGEKVGKDGYFVASDAWMDEYTYQIVVRKELLTK 42- 0 MTHAMVLTGVDLDE+G+PLKWKVENSWGEKVG GYFVASDAWMDEYTYQIVVRKE LT Sbjct: 361 MTHAMVLTGVDLDETGKPLKWKVENSWGEKVGDKGYFVASDAWMDEYTYQIVVRKEFLTA 42- 0 Query: 421 EELEAYNAEPITLAPWDPMGALA 443 +EL AY EP LAPWDPMGALA Sbjct: 421 DELAAYEKEPQVLAPWDPMGALA 443 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 965 A DNA sequence (GBSx1024) was identified in S. agalactiae <SEQ ID 2947> which encodes the amino acid sequence <SEQ ID 2948>. Analysis of this protein sequence reveals the following:

TABLE-US-02821 Possible site: 36 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9533> which encodes amino acid sequence <SEQ ID 9534> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02822 >GP:AAF17262 GB:AF210752 penicillin-binding protein 1A [Streptococcus pneumoniae] Identities = 412/725 (56%), Positives = 544/725 (74%), Gaps = 14/725 (1%) Query: 4 IKKESVIKLLKYAFGIIMGFIILAIVIGGLLFAYYVSRSPKLTDQALKSVNSSLVYDGNN 63 + K ++++L+KY + +I AIV+GG +F YYVS++P L++ L + SS +YD N Sbjct: 1 MNKPTILRLIKYLSISFLSLVIAAIVLGGGVFFYYVSKAPSLSESKLVATTSSKIYDNKN 60 Query: 64 KLIADLGSEKRESVSADSIPLNLVNAITSIEDKRFFKHRGVDIYRILGAAWHNLVSSNTQ 123- +LIADLGSE+R + A+ IP +LV AI SIED RFF HRG+D RILGA NL S++ Q Sbjct: 61 QLIADLGSERRVNAQANDIPTDLVKAIVSIEDHRFFDHRGIDTIRILGAFLRNLQSNSLQ 120- Query: 124 GGSTLDQQLIKLAYFSTNKSDQTLKRKSQEVWLALQMERKYTKEEILTFYINKVYMGNGN 18- 3 GGSTL QQLIKL YFST+ SDQT+ RK+QE WLA+Q+E+K TK+EILT+YINKVYM NGN Sbjct: 121 GGSTLTQQLIKLTYFSTSTSDQTISRKAQEAWLAIQLEQKATKQEILTYYINKVYMSNGN 18- 0 Query: 184 YGMRTTAKSYFGKDLKELSIAQLALLAGIPQAPTQYDPYKNPESAQTRRNTVLQQMYQDK 24- 3 YGM+T A++Y+GKDL LS+ QLALLAG+PQAP QYDPY +PE+AQ RRN VL +M Sbjct: 181 YGMQTAAQNYYGKDLNNLSLPQLALLAGMPQAPNQYDPYSHPEAAQDRRNLVLSEMKNQG 24- 0 Query: 244 NISKKEYDQAVATPVTDGLKELKQKSTYPKYMDNYLKQVISEVKQKTGKDIFTAGLKVYT 30- 3 IS ++Y++AV TP+TDGL+ LK S YP YMDNYLK+VI++V+++TG ++ T G+ VYT Sbjct: 241 YISAEQYEKAVNTPITDGLQSLKSASNYPAYMDNYLKEVINQVEEETGYNLLTTGMDVYT 30- 0 Query: 304 NINTDAQKQLYDIYNSDTYIAYPNNELQIASTIMDATNGKVIAQLGGRHQNENISFGTNQ 36- 3 N++ +AQK L+DIYN+D Y+AYP++ELQ+ASTI+D +NGKVIAQLG RHQ+ N+SFG NQ Sbjct: 301 NVDQEAQKHLWDIYNTDEYVAYPDDELQVASTIVDVSNGKVIAQLGARHQSSNVSFGINQ 36- 0 Query: 364 SVLTDRDWGSTMKPISAYAPAIDSGVYNSTGQSLNDSVYYWPGTSTQLYDWDRQYMGWMS 42- 3 +V T+RDWGSTMKPI+ YAPA++ GVY+ST ++D Y +PGT T +Y+WDR Y G ++ Sbjct: 361 AVETNRDWGSTMKPITDYAPALEYGVYDSTATIVHDEPYNYPGTDTPVYNWDRGYFGNIT 42- 0 Query: 424 MQTAIQQSRNVPAVRALEAAGLDEAKSFLEKLGIYYPEMNYSNAISSNNSSSDAKYGASS 48- 3 +Q A+QQSRNVPAV L GL+ AK+FL LGI YP ++YSNAISSN + SD KYGASS Sbjct: 421 LQYALQQSRNVPAVETLNKVGLNRAKTFLNGLGIDYPSLHYSNAISSNTTESDKKYGASS 48- 0 Query: 484 EKMAAAYSAFANGGTYYKPQYVNKIEFSDGTNDTYAASGSRAMKETTAYMMTDMLKTVLT 54- 3 EKMAAAY+AFANGGTYYKP Y++K+ FSDG+ ++ G+RAMKETTAYMMTDM+KTVL Sbjct: 481 EKMAAAYAAFANGGTYYKPMYIHKVVFSDGSEKEFSNVGTRAMKETTAYMMTDMMKTVLV 54- 0 Query: 544 FGTGTKAAIPGVAQAGKTGTSNYTEDELAKIEATTGIYNSAVGTMAPDENFVGYTSKYTM 60- 3 +G G A +P + QAGKTGTSNYT++E+ K Y G +APDE FVGYT KY M Sbjct: 541 YGIGRGAYLPWLPQAGKTGTSNYTDEEIEK-------YIKNTGYVAPDEMFVGYTRKYAM 59- 3 Query: 604 AIWTGYKNRLTPLYGSQLDIATEVYRAMMSYLTGGYSA-DWTMPEGLYRSGSYLYINGTT 66- 2 A+WTGY NRLTPL G L +A +VYR+MM+YL+ G + DW +PEGLYR+G +++NG Sbjct: 594 AVWTGYSNRLTPLVGDGLTVAAKVYRSMMTYLSEGSNPEDWNIPEGLYRNGEFVFKNGAR 65- 3 Query: 663 TTGTYSSSVYKNIYQNSGQSSQSSSSTSSEKQKEDKNTANDANSSSPQVETPNNGNATTP 72- 2 +T +SS + S +SS SSS +S+ + + N++ +++P T +TTP Sbjct: 654 ST--WSSFAPQQ--PPSTESSSSSSDSSTSQSNSTTPSTNNSTTTNPNNNTQQSN--TTP 70- 7 Query: 723 NNSNQ 727 + NQ Sbjct: 708 DQQNQ 712 A related DNA sequence was identified in S. pyogenes <SEQ ID 2949> which encodes the amino acid sequence <SEQ ID 2950>. Analysis of this protein sequence reveals the following: TABLE-US-02823 Possible site: 41 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.96 Transmembrane 19-35 (9-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.6583(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02824 >GP:CAA88918 GB:Z49095 penicillin-binding protein 1a [Streptococcus pneumoniae] Identities = 422/712 (59%), Positives = 536/712 (75%), Gaps = 8/712 (1%) Query: 4 IKNPKILKWLKYVLSAILSLIILVIIIGGLLFTFYISSAPKLSEAQLKSTNSSLVYDGNN 63 + P IL+ +KY+ + LSL+I I++GG +F +Y+S AP LSE++L +T SS +YD N Sbjct: 1 MNKPTILRLIKYLSISFLSLVIAAIVLGGGVFFYYVSKAPSLSESKLVATTSSKIYDNKN 60 Query: 64 NLIADLGSEKRENVTADSIPINLVNAITSIEDKRFFNHRGVDLYRIFGAAFHNLTSQTTQ 123- LIADLGSE+R N A+ IP +LV AI SIED RFF+HRG+D RI GA NL S + Q Sbjct: 61 QLIADLGSERRVNAQANDIPTDLVKAIVSIEDHRFFDHRGIDTIRILGAFLRNLQSNSLQ 120- Query: 124 GGSTLDQQLIKLAYFSTNESDQTLKRKAQEVWLALQMERKYTKQEILTFYINKVYMGNGN 18- 3 GGSTL QQLIKL YFST+ SDQT+ RKAQE WLA+Q+E+K TKQEILT+YINKVYM NGN Sbjct: 121 GGSTLTQQLIKLTYFSTSTSDQTISRKAQEAWLAIQLEQKATKQEILTYYINKVYMSNGN 18- 0 Query: 184 YGMLTAAKSYYGKDLKDLSYAQLALLAGIPQAPSQYDPYLHPEAAQNRRNVVLQQMYMEK 24- 3 YGM TAA++YYGKDL +LS QLALLAG+PQAP+QYDPY HPEAAQ+RRN+VL +M + Sbjct: 181 YGMQTAAQNYYGKDLNNLSLPQLALLAGMPQAPNQYDPYSHPEAAQDRRNLVLSEMKNQG 24- 0 Query: 244 HLTKAEYETAIATPVAEGLQSLQQRSTYPKYMDNYLKQVIEEVKKETNKDIFTAGLKVYT 30- 3 +++ +YE A+ TP+ +GLQSL+ S YP YMDNYLK+VI +V++ET ++ T G+ VYT Sbjct: 241 YISAEQYEKAVNTPITDGLQSLKSASNYPAYMDNYLKEVINQVEEETGYNLLTTGMDVYT 30- 0 Query: 304 NIIPDAQQTLYNIYHSGDYVYYPDQDFQVASTIVDVTNGHVIAQLGGRNQDENVSFGTNQ 36- 3 N+ +AQ+ L++IY+S YV YPD D QVAST+VDV+NG VIAQLG R+Q NVSFGTNQ Sbjct: 301 NVDQEAQKHLWDIYNSDQYVSYPDDDLQVASTVVDVSNGKVIAQLGARHQASNVSFGTNQ 36- 0 Query: 364 AVLTDRDWGSTMKPITAYAPAIESGVYTSTAQSTNDSVYYWPGTTTQLFNWDLRYNGWMT 42- 3 AV T+RDWGS+MKPIT YAPA+E GVY STA +D Y +PGT T L+NWD Y G +T Sbjct: 361 AVETNRDWGSSMKPITDYAPALEYGVYDSTASIVHDVPYNYPGTDTPLYNWDHVYFGNIT 42- 0 Query: 424 IQAAIMLSRNVPAVRALEAAGLDYARSFLSSLGINYPEMHYSNAISSNNSSSDKKYGASS 48- 3 IQ A+ SRNV AV L GLD A++FL+ LGI+YP MHY+NAISSN + S+KKYGASS Sbjct: 421 IQYALQQSRNVTAVETLNKVGLDRAKTFLNGLGIDYPSMHYANAISSNTTESNKKYGASS 48- 0 Query: 484 EKMAAAYAAFANGGIYHKPRYVNKVEFSDGTSKTFDEKGKRAMKETTAYMMTDMLKTVLT 54- 3 EKMAAAYAAFANGGIYHKP Y+NK+ FSDG+ K F + G RAMKETTAYMMT+M+KTVLT Sbjct: 481 EKMAAAYAAFANGGIYHKPMYINKIVFSDGSEKEFSDAGTRAMKETTAYMMTEMMKTVLT 54- 0 Query: 544 YGTGTAAAIPGVAQAGKTGTSNYTDEELAKIGEKYGLYPDYVGTLAPDENFVGFTKRYAM 60- 3 YGTG A +P + QAGKTGTSNYTDEE+ K Y G +APDE FVG+T++YAM Sbjct: 541 YGTGRGAYLPWLPQAGKTGTSNYTDEEIEK-------YIKNTGYVAPDEMFVGYTRKYAM 59- 3 Query: 604 AVWTGYKNRLTPVYGSSLEIASDVYRSMMTYLT-NGYSEDWTMPNGLYRSGGFLYLSGTY 66- 2 AVWTGY NRLTP+ G +A VYRSM+TYL+ + DWTMP+GLYR+G F++ +G Sbjct: 594 AVWTGYSNRLTPIIGDGFLVAGKVYRSMITYLSEDDQPGDWTMPDGLYRNGEFVFKNGAR 65- 3 Query: 663 ASNTDYTNSVYNNLYSNNTTTASSQTTSDDTSSSNDTSNSTNTDNNGSHPST 714 ++ + + S+++++ SS + S+ T+ S + S +TN +NN +T Sbjct: 654 STWSSPAPQQPPSTESSSSSSDSSTSQSNSTTPSTNNSTTTNPNNNTQQSNT 705 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02825 Identities = 521/729 (71%), Positives = 621/729 (84%), Gaps = 10/729 (1%) Query: 1 MITIKKESVIKLLKYAFGIIMGFIILAIVIGGLLFAYYVSRSPKLTDQALKSVNSSLVYD 60 +ITIK ++K LKY I+ IIL I+IGGLLF +Y+S +PKL++ LKS NSSLVYD Sbjct: 1 VITIKNPKILKWLKYVLSAILSLIILVIIIGGLLFTFYISSAPKLSEAQLKSTNSSLVYD 60 Query: 61 GNNKLIADLGSEKRESVSADSIPLNLVNAITSIEDKRFFKHRGVDIYRILGAAWHNLVSS 120- GNN LIADLGSEKRE+V+ADSIP+NLVNAITSIEDKRFF HRGVD+YRI GAA+HNL S Sbjct: 61 GNNNLIADLGSEKRENVTADSIPINLVNAITSIEDKRFFNHRGVDLYRIFGAAFHNLTSQ 120- Query: 121 NTQGGSTLDQQLIKLAYFSTNKSDQTLKRKSQEVWLALQMERKYTKEEILTFYINKVYMG 18- 0 TQGGSTLDQQLIKLAYFSTN+SDQTLKRK+QEVWLALQMERKYTK+EILTFYINKVYMG Sbjct: 121 TTQGGSTLDQQLIKLAYFSTNESDQTLKRKAQEVWLALQMERKYTKQEILTFYINKVYMG 18- 0 Query: 181 NGNYGMRTTAKSYFGKDLKELSIAQLALLAGIPQAPTQYDPYKNPESAQTRRNTVLQQMY 24- 0 NGNYGM T AKSY+GKDLK+LS AQLALLAGIPQAP+QYDPY +PE+AQ RRN VLQQMY Sbjct: 181 NGNYGMLTAAKSYYGKDLKDLSYAQLALLAGIPQAPSQYDPYLHPEAAQNRRNVVLQQMY 24- 0 Query: 241 QDKNISKKEYDQAVATPVTDGLKELKQKSTYPKYMDNYLKQVISEVKQKTGKDIFTAGLK 30- 0 +K+++K EY+ A+ATPV +GL+ L+Q+STYPKYMDNYLKQVI EVK++T KDIFTAGLK Sbjct: 241 MEKHLTKAEYETAIATPVAEGLQSLQQRSTYPKYMDNYLKQVIEEVKKETNKDIFTAGLK 30- 0 Query: 301 VYTNINTDAQKQLYDIYNSDTYIAYPNNELQIASTIMDATNGKVIAQLGGRHQNENISFG 36- 0 VYTNI DAQ+ LY+IY+S Y+ YP+ + Q+ASTI+D TNG VIAQLGGR+Q+EN+SFG Sbjct: 301 VYTNIIPDAQQTLYNIYHSGDYVYYPDQDFQVASTIVDVTNGHVIAQLGGRNQDENVSFG 36- 0 Query: 361 TNQSVLTDRDWGSTMKPISAYAPAIDSGVYNSTGQSLNDSVYYWPGTSTQLYDWDRQYMG 42- 0 TNQ+VLTDRDWGSTMKPI+AYAPAI+SGVY ST QS NDSVYYWPGT+TQL++WD +Y G Sbjct: 361 TNQAVLTDRDWGSTMKPITAYAPAIESGVYTSTAQSTNDSVYYWPGTTTQLFNWDLRYNG 42- 0 Query: 421 WMSMQTAIQQSRNVPAVRALEAAGLDEAKSFLEKLGIYYPEMNYSNAISSNNSSSDAKYG 48- 0 WM++Q AI SRNVPAVRALEAAGLD A+SFL LGI YPEM+YSNAISSNNSSSD KYG Sbjct: 421 WMTIQAAIMLSRNVPAVRALEAAGLDYARSFLSSLGINYPEMHYSNAISSNNSSSDKKYG 48- 0 Query: 481 ASSEKMAAAYSAFANGGTYYKPQYVNKIEFSDGTNDTYAASGSRAMKETTAYMMTDMLKT 54- 0 ASSEKMAAAY+AFANGG Y+KP+YVNK+EFSDGT+ T+ G RAMKETTAYMMTDMLKT Sbjct: 481 ASSEKMAAAYAAFANGGIYHKPRYVNKVEFSDGTSKTFDEKGKRAMKETTAYMMTDMLKT 54- 0 Query: 541 VLTFGTGTKAAIPGVAQAGKTGTSNYTEDELAKIEATTGIYNSAVGTMAPDENFVGYTSK 60- 0 VLT+GTGT AAIPGVAQAGKTGTSNYT++ELAKI G+Y VGT+APDENFVG+T + Sbjct: 541 VLTYGTGTAAAIPGVAQAGKTGTSNYTDEELAKIGEKYGLYPDYVGTLAPDENFVGFTKR 60- 0 Query: 601 YTMAIWTGYKNRLTPLYGSQLDIATEVYRAMMSYLTGGYSADWTMPEGLYRSGSYLYING 66- 0 Y MA+WTGYKNRLTP+YGS L+IA++VYR+MM+YLT GYS DWTMP GLYRSG +LY++G Sbjct: 601 YAMAVWTGYKNRLTPVYGSSLEIASDVYRSMMTYLTNGYSEDWTMPNGLYRSGGFLYLSG 66- 0 Query: 661 TTTTGT-YSSSVYKNIYQNSGQSSQSSSSTSSEKQKEDKNTANDANSSSPQVETPNNGNA 71- 9 T + T Y++SVY N+Y N ++++ SS+ +D +++ND ++S+ T NNG+ Sbjct: 661 TYASNTDYTNSVYNNLYSN------NTTTASSQTTSDDTSSSNDTSNST---NTDNNGSH 71- 1 Query: 720 TTPNNSNQT 728 + ++ T Sbjct: 712 PSTDDKKTT 720 A related GBS gene <SEQ ID 8695> and protein <SEQ ID 8696> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02826 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 6.55 GvH: Signal Score (-7.5): -1.98 Possible site: 36 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 4.03 threshold: 0.0 PERIPHERAL Likelihood = 4.03 201 modified ALOM score: -1.31 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00067## SEQ ID 8696 (GBS146) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 23 (lane 4; MW 82 kDa), in FIG. 168 (lane 11-13; MW 96.5 kDa) and in FIG. 238 (lane 8; MW 96.5 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 2; MW 107 kDa). Purified Thio-GBS146-His is shown in FIG. 244, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 966 A DNA sequence (GBSx1025) was identified in S. agalactiae <SEQ ID 2951> which encodes the amino acid sequence <SEQ ID 2952>. Analysis of this protein sequence reveals the following: TABLE-US-02827 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3647(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02828 >GP:AAA26957 GB:M90528 ORF [Streptococcus oralis] Identities = 143/196 (72%), Positives = 165/196 (83%), Gaps = 1/196 (0%) Query: 1 MVNYPHQLIRKTTVTKSKKKKIDFANRGMSFEAAINATNDYYLSHELAVIHKKPTPVQIV 60 MVNYPH++ + + K +FANRGMSFE INATNDYYLSH LAVIHKKPTP+QIV Sbjct: 1 MVNYPHKISSQKRQAPPSQTK-NFANRGMSFEKMINATNDYYLSHGLAVIHKKPTPIQIV 59 Query: 61 KVDYPKRSRAKIVEAYFRQASTTDYSGVYKGYYIDFEAKETRQKTAMPMKNFHAHQIEHM 120- +VDYP+RSRAKIVEAYFRQASTTDYSGVY GYYIDFEAKETRQK A+PMKNFH HQI+HM Sbjct: 60 RVDYPQRSRAKIVEAYFRQASTTDYSGVYDGYYIDFEAKETRQKHAIPMKNFHHHQIQHM 119- Query: 121 ANVLQQKGICFVLLHFSTLKETYLLPANELISFYQIDKGNKSMPIDYIRKNGFFVKESAF 18- 0 VL Q+GICFVLLHF++ +ETYLLPA +LI FY DKG KSMP+ YIR+NG+ ++ AF Sbjct: 120 EQVLAQRGICFVLLHFASQQETYLLPAVDLIRFYHQDKGQKSMPLGYIRENGYRIELGAF 17- 9 Query: 181 PQVPYLDIIEEKLLGG 196 PQ+PYLDII+E LLGG Sbjct: 180 PQIPYLDIIKEHLLGG 195 A related DNA sequence was identified in S. pyogenes <SEQ ID 2953> which encodes the amino acid sequence <SEQ ID 2954>. Analysis of this protein sequence reveals the following: TABLE-US-02829 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5030(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02830 Identities = 166/199 (83%), Positives = 177/199 (88%) Query: 1 MVNYPHQLIRKTTVTKSKKKKIDFANRGMSFEAAINATNDYYLSHELAVIHKKPTPVQIV 60 MVNYPH LIR+ + K+ K+DFANRGMSFEAAINATNDYYLS ++AVIHKKPTPVQIV Sbjct: 1 MVNYPHNLIRQKVSSVQKQNKVDFANRGMSFEAAINATNDYYLSRQIAVIHKKPTPVQIV 60 Query: 61 KVDYPKRSRAKIVEAYFRQASTTDYSGVYKGYYIDFEAKETRQKTAMPMKNFHAHQIEHM 120- KVDYPKRSRAKIVEAYFRQASTTDY GVYKG+Y+DFEAKETRQKTAMPMKNFH HQIEHM Sbjct: 61 KVDYPKRSRAKIVEAYFRQASTTDYCGVYKGHYVDFEAKETRQKTAMPMKNFHLHQIEHM 120- Query: 121 ANVLQQKGICFVLLHFSTLKETYLLPANELISFYQIDKGNKSMPIDYIRKNGFFVKESAF 18- 0 A VL QKGICFVLLHFSTLKETY LPA LISFYQID G+KSMPIDYIRKNGF V AF Sbjct: 121 ACVLHQKGICFVLLHFSTLKETYYLPAQALISFYQIDNGSKSMPIDYIRKNGFKVAFGAF 18- 0 Query: 181 PQVPYLDIIEEKLLGGDYN 199 PQVPYL+IIE+ LGGDYN Sbjct: 181 PQVPYLNIIEQNFLGGDYN 199 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 967 A DNA sequence (GBSx1026) was identified in S. agalactiae <SEQ ID 2955> which encodes the amino acid sequence <SEQ ID 2956>. Analysis of this protein sequence reveals the following: TABLE-US-02831 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3227(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02832 >GP:CAB14136 GB:Z99115 similar to hypothetical proteins from B. subtilis [Bacillus subtilis] Identities = 74/174 (42%), Positives = 97/174 (55%), Gaps = 6/174 (3%) Query: 5 ILVTGYKNFELGIFQDKDPRITIIKKAIDKDFRRFLENGADWFIFMGNLGFEYWALEVAL 64 + +TGYK FELGIF+ D + IKKAI FL+ G +W + G LG E WA E A Sbjct: 4 LAITGYKPFELGIFKQDDKALYYIKKAIKNRLIAFLDEGLEWILISGQLGVELWAAEAAY 63 Query: 65 DLQKEY-DFQIATIFTFENHGQNWNEANKAKL-ALFKQVDF-VKYTFPSYENPGQFKQYN 121- DLQ+EY D ++A I F +NW E NK + A+ Q D+ T YE+P QFKQ N Sbjct: 64 DLQEEYPDLKVAVITPFYEQEKNWKEPNKEQYEAVLAQADYEASLTHRPYESPLQFKQKN 123- Query: 122 HFLINNTQGAYLFYDSENETNLKFLLEMMEKK---EAYDISFLTFDRLNEIYEE 172 F I+ + G L YD E E + K++L EK+ + Y I F+T D L EE Sbjct: 124 QFFIDKSDGLLLLYDPEKEGSPKYMLGTAEKRREQDGYPIYFITMDDLRVTVEE 177 A related DNA sequence was identified in S. pyogenes <SEQ ID 2957> which encodes the amino acid sequence <SEQ ID 2958>. Analysis of this protein sequence reveals the following: TABLE-US-02833 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3041(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02834 Identities = 102/167 (61%), Positives = 127/167 (75%) Query: 3 STILVTGYKNFELGIFQDKDPRITIIKKAIDKDFRRFLENGADWFIFMGNLGFEYWALEV 62 + IL+TGY++FE+GIF KDPR++IIK+AI KD +LENG DWFIF GNLGFE WALEV Sbjct: 2 TAILITGYRSFEIGIFDHKDPRVSIIKQAIRKDLIGYLENGVDWFIFTGNLGFEQWALEV 61 Query: 63 ALDLQKEYDFQIATIFTFENHGQNWNEANKAKLALFKQVDFVKYTFPSYENPGQFKQYNH 122- A +L++EY QIATIF FE HG WNE NK L+ F+ VDFVKY FP+YE P QF QY Sbjct: 62 ANELKEEYPLQIATIFLFETHGDRWNEKNKEVLSQFRAVDFVKYYFPNYEQPTQFSQYYQ 121- Query: 123 FLINNTQGAYLFYDSENETNLKFLLEMMEKKEAYDISFLTFDRLNEI 169 FL+ T+GAY+FYD+ENETNLK+ L+ + Y + LTFDRLN++ Sbjct: 122 FLLEKTEGAYVFYDTENETNLKYFLKKAKDMPHYQLLLLTFDRLNDM 168 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 968 A DNA sequence (GBSx1027) was identified in S. agalactiae <SEQ ID 2959> which encodes the amino acid sequence <SEQ ID 2960>. Analysis of this protein sequence reveals the following:

TABLE-US-02835 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5188(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 969 A DNA sequence (GBSx1028) was identified in S. agalactiae <SEQ ID 2961> which encodes the amino acid sequence <SEQ ID 2962>. This protein is predicted to be cell division protein DivIVA. Analysis of this protein sequence reveals the following: TABLE-US-02836 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2736(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9535> which encodes amino acid sequence <SEQ ID 9536> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02837 >GP:CAB14135 GB:Z99115 YPsB [Bacillus subtilis] Identities = 46/102 (45%), Positives = 69/102 (67%), Gaps = 14/102 (13%) Query: 14 SPKDIFEQDFKVSMRGYDKKEVDVFLDDVIKDYENYLEQIEKLQMENRRLQQALDKKESE 73 - S K+I E++FK +RGY +++VD FLD +IKDYE + ++IE+LQ EN +L++ L+ E Sbjct: 9 SAKEILEKEFKTGVRGYKQEDVDKFLDMIIKDYETFHQEIEELQQENLQLKKQLE----E 64 Query: 74 ASNVRNSGTAMYNQKPIAQSATNFDILKRISRLEKEVFGRQI 115 AS ++P+ + TNFDILKR+S LEK VFG ++ Sbjct: 65 AS----------KKQPVQSNTTNFDILKRLSNLEKHVFGSKL 96 A related DNA sequence was identified in S. pyogenes <SEQ ID 2963> which encodes the amino acid sequence <SEQ ID 2964>. Analysis of this protein sequence reveals the following: TABLE-US-02838 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4466(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02839 Identities = 71/112 (63%), Positives = 85/112 (75%), Gaps = 6/112 (5%) Query: 8 MASIIYSPKDIFEQDFKVSMRGYDKKEVDVFLDDVIKDYENYLEQIEKLQMENRRLQQAL 67 M SIIYSPKDIFEQ+FK SMRG+DKKEVD FLD+VIKDYEN+ QIE L+ EN +AL Sbjct: 1 MTSIIYSPKDIFEQEFKTSMRGFDKKEVDEFLDNVIKDYENFNAQIEALKAEN----EAL 56 Query: 68 DKKESEASNVRNSGTAMYNQKP--IAQSATNFDILKRISRLEKEVFGRQIRE 117 K + +A N ++ +P +AQSATNFDILKRIS+LEKEVFG+QI E Sbjct: 57 KKAKFQARNTVSATVQQPVPQPTRVAQSATNFDILKRISKLEKEVFGKQIIE 108 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 970 A DNA sequence (GBSx1029) was identified in S. agalactiae <SEQ ID 2965> which encodes the amino acid sequence <SEQ ID 2966>. Analysis of this protein sequence reveals the following: TABLE-US-02840 Possible site: 55 >>> Seems to have no N-terminal signal sequence (or aa 1-19) ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0655(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02841 >GP:CAB14134 GB:Z99115 similar to hypothetical proteins [Bacillus subtilis] Identities = 204/382 (53%), Positives = 274/382 (71%), Gaps = 3/382 (0%) Query: 3 ESFKLIATAAAGLEAIVGREIRNLGIDCQVENGRVRFHGDIKTIIETNLWLRAADRIKII 62 + + LIATA G+EA+V +E+R+LG +C+V+NG+V F GD I NLWLR ADRIK+ Sbjct: 2 KKYTLIATAPMGIEAVVAKEVRDLGYECKVDNGKVIFEGDALAICRANLWLRTADRIKVQ 61 Query: 63 VGEFPAPTFEELFQGVYGLDWENYLPLGAKFPIAKAKCVKSKLHNEPSVQAISKKAVAKK 122- V F A TF+ELF+ ++W +++P KFP+ K VKS L + P Q I KKA+ +K Sbjct: 62 VASFKAKTFDELFEKTKAINWRSFIPENGKFPVI-GKSVKSTLASVPDCQRIVKKAIVEK 120- Query: 123 LQKVFHRPEGVPLQENGAEFKIEVSILKDKATVMIDTTGSSLFKRGYRAEKGGAPIKENM 18- 2 L K+ ++E GAE+K+E+S+LKD+A + +D++G+ L KRGYR ++GGAPIKE + Sbjct: 121 L-KLQSGKANDWIEETGAEYKVEISLLKDQALITLDSSGTGLHKRGYRVDQGGAPIKETL 17- 9 Query: 183 AAAIIQLSNWFPDKPLIDPTCGSGTFCIEAAMIGMNIAPGFNRDFAFEAWPWVDQSQVQK 24- 2 AAA++QL+NW PD+P +DP CGSGT IEAA+IG NIAPGFNRDF E W W+ + K Sbjct: 180 AAALVQLTNWTPDRPFVDPFCGSGTIAIEAALIGQNIAPGFNRDFVSEDWEWIGKDLWNK 23- 9 Query: 243 VRDEAESKANYDIDLDISGFDLDGRMVEIARKNAEEAGLGDVIKLKQMRLQDLKTDKING 30- 2 R E E KANYD L I D+D RMV+IA++NAEEAGLGD+I+ KQM+++D T+ G Sbjct: 240 ARLEVEEKANYDQPLTIFASDIDHRMVQIAKENAEEAGLGDLIQFKQMQVKDFTTNLEFG 29- 9 Query: 303 VIISNPPYGERLLDDKAVDILYNEMGQTFAPLKTWSKFILTSDEGFEKKYGSQADKKRKL 36- 2 VI+ NPPYGERL + KAV+ +Y EMGQ F PL TWS ++LTS+E FE+ YG +A KKRKL Sbjct: 300 VIVGNPPYGERLGEKKAVEQMYKEMGQAFEPLDTWSVYMLTSNENFEEAYGRKATKKRKL 35- 9 Query: 363 YNGTLKVDLYQYYGERVRRQVK 384 +NG +K D YQY+ +VR Q K Sbjct: 360 FNGFIKTDYYQYW-SKVRPQRK 380 A related DNA sequence was identified in S. pyogenes <SEQ ID 2967> which encodes the amino acid sequence <SEQ ID 2968>. Analysis of this protein sequence reveals the following: TABLE-US-02842 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0324(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02843 Identities = 317/383 (82%), Positives = 354/383 (91%) Query: 1 MKESFKLIATAAAGLEAIVGREIRNLGIDCQVENGRVRFHGDIKTIIETNLWLRAADRIK 60 MKE+F+L+ATAAAGLEA+VG+E+R LG DCQVENG+V F GD++ I++TNLWLRAADRIK Sbjct: 1 MKETFRLVATAAAGLEAVVGKEVRALGFDCQVENGKVYFEGDVEAIVKTNLWLRAADRIK 60 Query: 61 IIVGEFPAPTFEELFQGVYGLDWENYLPLGAKFPIAKAKCVKSKLHNEPSVQAISKKAVA 120- IIVG+FPA TFEELFQGV+ LDWENYLPLGAKFPI+KAKCVKSKLHNEPSVQAI+KKAV Sbjct: 61 IIVGQFPARTFEELFQGVFALDWENYLPLGAKFPISKAKCVKSKLHNEPSVQAITKKAVV 120- Query: 121 KKLQKVFHRPEGVPLQENGAEFKIEVSILKDKATVMIDTTGSSLFKRGYRAEKGGAPIKE 18- 0 KKLQK FHRPEGVPLQE G+ F IEVSILKD+AT+MIDTTGSSLFKRGYR +KGGAPIKE Sbjct: 121 KKLQKHFHRPEGVPLQEVGSTFNIEVSILKDQATIMIDTTGSSLFKRGYRVQKGGAPIKE 18- 0 Query: 181 NMAAAIIQLSNWFPDKPLIDPTCGSGTFCIEAAMIGMNIAPGFNRDFAFEAWPWVDQSQV 24- 0 NMAAAI+ LSNWFPDKPL+DPTCGSGTFCIEAAMIGMNIAPGFNR FAFE W WVD+ V Sbjct: 181 NMAAAILALSNWFPDKPLVDPTCGSGTFCIEAAMIGMNIAPGFNRSFAFEEWSWVDKDMV 24- 0 Query: 241 QKVRDEAESKANYDIDLDISGFDLDGRMVEIARKNAEEAGLGDVIKLKQMRLQDLKTDKI 30- 0 Q+VRD+AE +ANY+I+LDISGFD+DGRM+EIA+ NAEEAGL DVI KQMRLQD +TDK+ Sbjct: 241 QQVRDDAEQEANYEIELDISGFDIDGRMIEIAKSNAEEAGLSDVITFKQMRLQDFRTDKV 30- 0 Query: 301 NGVIISNPPYGERLLDDKAVDILYNEMGQTFAPLKTWSKFILTSDEGFEKKYGSQADKKR 36- 0 NGV+ISNPPYGERLLDDKAVDILYNEMGQTFAPLKTWSKFILTSDE FE KYG +ADKKR Sbjct: 301 NGVVISNPPYGERLLDDKAVDILYNEMGQTFAPLKTWSKFILTSDELFELKYGQKADKKR 36- 0 Query: 361 KLYNGTLKVDLYQYYGERVRRQV 383 KLYNGTLKVDLYQ+YGERV+R + Sbjct: 361 KLYNGTLKVDLYQFYGERVKRHL 383 SEQ ID 2966 (GBS255) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 43 (lane 7; MW 44 kDa) It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 48 (lane 4; MW 69 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 971 A DNA sequence (GBSx030) was identified in S. agalactiae <SEQ ID 2969> which encodes the amino acid sequence <SEQ ID 2970>. Analysis of this protein sequence reveals the following: TABLE-US-02844 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.02 Transmembrane 171-187 (167-193) ----- Final Results ----- bacterial membrane --- Certainty = 0.7007(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02845 >GP:AAD16120 GB:AF094508 dentin phosphoryn [Homo sapiens] Identities = 71/398 (17%), Positives = 152/398 (37%), Gaps = 16/398 (4%) Query: 16 TDGLEFKDAK-EMTVEEAVRKDSEIKAGITEEDSILDKYIKQHRDEVASQKFETKSSDFA 74 - +D + D+K + + E+ DS+ K+ ++ +S D S S Sbjct: 152 SDSSDSSDSKSDSSKSESDSSDSDSKSDSSDSNSSDSSDNSDSSDSSNSSNSSDSSDSSD 21- 1 Query: 75 NLDTASLDDFIKKQREELSAMLAAEELSKKLDNSVSQEQDTEANAVSPKEESSQEQENSV 134- + D++S D + S + S+ D+S S + D+ ++ S SS ++ Sbjct: 212 SSDSSSSSD--SSNSSDSSDSSDSSNSSESSDSSDSSDSDSSDSSDSSNSNSSDSDSSNS 26- 9 Query: 135 TPVPPLNTEAEPTATEPDSTIADSEEYKSSSKKRGGIVGTLIALILLLIVAIFGYNYFKN 19- 4 + + ++ + + S +DS + SS + + + N + Sbjct: 270 SDSSDSSNSSDSSDSSDSSNSSDSSDSSDSSNSSDSSDSSDSS------DSSDSSNSSDS 32- 3 Query: 195 NNSTNSQTATSQSSSSKATTTSSEEDKKASQNLDNFNKSYANFFVDDKKTQLKNSEFDKL 25- 4 N+S+NS ++ S SS ++ +S D S + D+ N S D +S+ Sbjct: 324 NDSSNSSDSSDSSDSSDSSNSSDSSDSSDSSDSDSSNSS-------DSSNSSDSSDSCNS 37- 6 Query: 255 SELEKKVDALKGTKYYGKVKVKFDSLKRQIDAVKAVNDKFKSPAVVDGKKSEKLEVKDGA 31- 4 S+ D+ G+ + + D+ + N S + + S + D + Sbjct: 377 SDSSDSSDSSDGSDSDSSNRSDSSNSSDSSDSSDSSNSSDSSDSSDSNESSNSSDSSDSS 43- 6 Query: 315 NFDSLDSKTLNTGNASLDSLLHSIVSTGRNQVKQSEEQASSNKVSDTQITEQPNVTNGQS 37- 4 N DS + + S DS S S N S SSN + ++ N ++ + Sbjct: 437 NSSDSDSSDSSNSSDSSDSSNSSDSSESSNSSDNSNSSDSSNSSDSSDSSDSSNSSDSSN 49- 6 Query: 375 SSSAATINNQAAGTASGNLERNRSRVPYNNAAIADTGN 412 SS ++ ++ + +S + + + S +++ +D+ + Sbjct: 497 SSDSSNSSDSSDSNSSDSSDSSXSSDSSDSSDSSDSSD 534 Identities = 64/341 (18%), Positives = 140/341 (40%), Gaps = 35/341 (10%) Query: 59 DEVASQKFETKSSDFANLDTASLDDFIKKQREELS-AMLAAEELSKKLDNSVSQEQDTEA 117- D+ S K ++ SSD + D+++ D + S + +++ S D+S S + D+ Sbjct: 76 DKSDSGKGKSDSSDSDSSDSSNSSDSSDSSDSDSSDSNSSSDSDSSDSDSSDSSDSDSSD 135- Query: 118 NAVSPKEESSQEQENSVTPVPPLNTEAEPTATEPDSTIADSEEYKSSSKKRGGIVGTLIA 17- 7 ++ S S + +S +++++ + +E DS+ +DS+ S S Sbjct: 136 SSNSSDSSDSSDSSDSSDSSDSSDSKSDSSKSESDSSDSDSKSDSSDSN----------- 18- 4 Query: 178 LILLLIVAIFGYNYFKNNNSTNSQTATSQSSSSKATTTSSEEDKKASQNLDNFNKSYANF 23- 7 +++S NS ++ S +SS+ + ++ S + +S + D+ N S ++ Sbjct: 185 ---------------SSDSSDNSDSSDSSNSSNSSDSSDSSDSSDSSSSSDSSNSSDSS- 22- 8 Query: 238 FVDDKKTQLKNSEFDKLSELEKKVDALKGTKYYGKVKVKFDSLKRQIDAVKAVNDKFKSP 29- 7 D +SE S+ D+ + DS D+ + N S Sbjct: 229 ---DSSDSSNSSESSDSSD-SSDSDSSDSSDSSNSNSSDSDS-SNSSDSSDSSNSSDSSD 28- 3 Query: 298 AVVDGKKSEKLEVKDGANFDSLDSKTLNTGNASLDSLLHSIVSTGRNQVKQSEEQASSNK 35- 7 + S+ + D +N S DS + + S DS S + N S+ SS+ Sbjct: 284 SSDSSNSSDSSDSSDSSN--SSDSSDSSDSSDSSDSSNSSDSNDSSNSSDSSDSSDSSDS 34- 1 Query: 358 VSDTQITEQPNVTNGQSSSSAATINNQAAGTASGNLERNRS 398 + + ++ + ++ SS+S+ + N+ + + + + + S Sbjct: 342 SNSSDSSDSSDSSDSDSSNSSDSSNSSDSSDSCNSSDSSDS 382 A related DNA sequence was identified in S. pyogenes <SEQ ID 2971> which encodes the amino acid sequence <SEQ ID 2972>. Analysis of this protein sequence reveals the following: TABLE-US-02846 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.70 Transmembrane 180-196 (175-202) ----- Final Results ----- bacterial membrane --- Certainty = 0.6880(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02847 >GP:AAF15293 GB:AF202180 erythrocyte membrane-associated giant protein antigen 332 [Plasmodium falciparum] Identities = 41/173 (23%), Positives = 87/173 (49%), Gaps = 10/173 (5%) Query: 1 VSEESKEVEVTKESQTLGLNEAKSMTIGEAVRKQSE----IKAGVTKDDSILDKYIKQHR 56 + E + V + KE + GL+ + + ++V +Q+E I + K+ S ++ ++ Sbjct: 78 IEEAEENVWIEKEVEEEGLDNEEVIDEEDSVSEQAEEEVYINEEILKESSDVEDVKVENE 137- Query: 57 ---DEVSSQKFDAKYTELDTASLDNFIKKQREALSKAGLVDDEPVSAESAEQDSTLVEEV 113- +EV+ + + LDN++ ++ E++++ +VD+ P S E E +S ++EE+ Sbjct: 138 LMNEEVNEETQSVAENNEEDKELDNYVVEETESVTEEVVVDEVPNSKEVQEIES-IIEEI 19- 6 Query: 114 AEDLAPMETTAVVTGIPVEATVPVLDLDPSERVIPEPQMTKEEPKRDQFLSED 166 ED + G +E V + D SE ++ E +T+E K++ ++ED Sbjct: 197 VEDGLTTDDLVGQQGSVIEEVVEEVGSD-SEGIVEEASITEEVEKKES-VTED 247 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02848 Identities = 234/506 (46%), Positives = 304/506 (59%), Gaps = 36/506 (7%) Query: 1 MSEDQKHPFFEPKKETDGLEFKDAKEMTVEEAVRKDSEIKAGITEEDSILDKYIKQHRDE 60 +SE+ K E KE+ L +AK MT+ EAVRK SEIKAG+T++DSILDKYIKQHRDE Sbjct: 1 VSEESKE--VEVTKESQTLGLNEAKSMTIGEAVRKQSEIKAGVTKDDSILDKYIKQHRDE 58 Query: 61 VASQKFETKSSDFANLDTASLDDFIKKQREELSAMLAAEELSKKLDNSVSQEQDTEANAV 120- V+SQKF+ K + LDTASLD+FIKKQRE LS A + + ++ S EQD+ Sbjct: 59 VSSQKFDAK---YTELDTASLDNFIKKQREALSK---AGLVDDEPVSAESAEQDSTLVEE 112- Query: 121 SPKEESSQEQENSVTPVPPLNT--------------EAEPTATEP--DSTIADSEEYKSS 16- 4 ++ + E VT +P T E + T EP D +++ + + Sbjct: 113 VAEDLAPMETTAVVTGIPVEATVPVLDLDPSERVIPEPQMTKEEPKRDQFLSEDSHHPAK 17- 2 Query: 165 SKKRGGIVGTLIALILLLIVAIFGYNYFKNNNSTNSQTATSQSSSSKATTTSSEEDKKAS 22- 4 + G + L L+L ++ +FG+N+F +S + S+ + + T S+++ + Sbjct: 173 QNTKKGWLIALFLLLLAILAVVFGWNHFLRQDSGKTTQTASKQTKTSLQTDSAKKATRLK 23- 2 Query: 225 QNLDNFNKSYANFFVDDKKTQLKNSEFDKLSELEKKVDALKGTKYYGKVKVKFDSLKRQI 28- 4 F K Y F+ D K++LKNS F L +LE + AL+G+ YY K K K DSLK+ I Sbjct: 233 AAAKAFEKLYGTFYTDATKSKLKNSAFATLPDLEAALKALEGSAYYDKAKAKVDSLKKAI 29- 2 Query: 285 DAVKAVNDKFKSPAVVDGKKSEKLEVKDGANFDSLDSKTLNTGNASLDSLLHSIVSTGRN 34- 4 A+ AVN KF S VVDG+K EVK ANFD L S TL GNA+LD++L + ++ GR Sbjct: 293 AAITAVNGKFVSDVVVDGEKVSA-EVKADANFDDLSSATLTIGNANLDAVLQASITEGRQ 35- 1 Query: 345 QVKQSEEQASSNKVSDTQITEQPNVTNGQSSSSAATINNQAAGTAS---GNLERNRSRVP 40- 1 Q+ E A K ++ Q Q GQS+S A + G S +L+R+ SRVP Sbjct: 352 QLASKAEAA---KAANEQAV-QDQAAQGQSTSVAPS----GYGLTSYDPASLQRHLSRVP 40- 3 Query: 402 YNNAAIADTGNPAWIFNPGVLEKIVATSQARGYFSGNNYILEPVNIINGNGYYNMFKLDG 46- 1 YN IAD NP+W FNPGVLEKIVATSQARGY SGN YILEPVNIINGNGYYNMFK DG Sbjct: 404 YNQDVIADRANPSWAFNPGVLEKIVATSQARGYISGNQYILEPVNIINGNGYYNMFKPDG 46- 3 Query: 462 TYLFSINAKTGYFVGNAPGRADSLDY 487 TYLFSIN KTGYFVGN G AD+LDY Sbjct: 464 TYLFSINCKTGYFVGNGKGYADALDY 489 SEQ ID 2970 (GBS351) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 73 (lane 2; MW 57 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 81 (lane 5; MW 82 kDa). GBS351-GST was purified as shown in FIG. 216, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 972 A DNA sequence (GBSx1031) was identified in S. agalactiae <SEQ ID 2973> which encodes the amino acid sequence <SEQ ID 2974>. Analysis of this protein sequence reveals the following: TABLE-US-02849 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3169(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2975> which encodes the amino acid sequence <SEQ ID 2976>. Analysis of this protein sequence reveals the following: TABLE-US-02850 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3169(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02851 Identities = 129/160 (80%), Positives = 149/160 (92%) Query: 1 MTKEVVVESFELDHTIVKAPYVRLISEEVGPVGDIITNFDIRLIQPNENAIDTAGLHTIE 60 MTKEV+VESFELDHTIVKAPYVRLISEE GP GD ITNFD+RL+QPN+N+I+TAGLHTIE Sbjct: 1 MTKEVIVESFELDHTIVKAPYVRLISESFGPKGDRITNFDVRLVQPNQNSIETAGLHTIE 60 Query: 61 HLLAKLIRQRINGLIDCSPFGCRTGFHMIMWGKQDATEIAKVIKSSLEAIAGGVTWEDVP 120- HLLAKLIRQRI+G+IDCSPFGCRTGFH+IMWGK +T+IAKVIKSSLE IA G+TWEDVP Sbjct: 61 HLLAKLIRQRIDGMIDCSPFGCRTGFHLIMWGKHSSTDIAKVIKSSLEEIATGITWEDVP 120- Query: 121 GTTIESCGNYKDHSLHSAQEWAKLILSQGISDNAFERHIV 160 GTT+ESCGNYKDHSL +A+EWA+LI+ QGISD+ F RH++ Sbjct: 121 GTTLESCGNYKDHSLFAAKEWAQLIIDQGISDDPFSRHVI 160 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 973 A DNA sequence (GBSx1032) was identified in S. agalactiae <SEQ ID 2977> which encodes the amino acid sequence <SEQ ID 2978>. Analysis of this protein sequence reveals the following:

TABLE-US-02852 Possible site: 32 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02853 >GP:AAF34762 GB:AF228345 unknown [Listeria monocytogenes] Identities = 302/532 (56%), Positives = 400/532 (74%), Gaps = 14/532 (2%) Query: 4 IILAMVCALIGLIIGYVAISMKMKSSKEAAELTLLNAEQDAVDLRGRAEIEAEHIRKAAE 63 I + ++ +L+ LI+G V S+ KSS E+ RG AE+ E +K AE Sbjct: 3 IAITIISSLLFLIVGLVVGSLIFKSS----------TEKKLAAARGTAELIVEDAKKEAE 52 Query: 64 RESKAHQKELLLEAKEEARKYREEIEKEFKSDRQELKQMEARLTDRASSLDRKDENLSNK 123- +KE LLEAKEE + R EIE E + R E ++ E RL R +LDRKD +LS + Sbjct: 53 TT----KKEALLEAKEENHRLRTEIENELRGRRTETQKAENRLLQREENLDRKDTSLSKR 108- Query: 124 EKMLDSKEQSLTDKSRHINEREQEIATLETKKVEELSRIAELSQEEAKDIILADTEKDLA 18- 3 E L+ KE+S++ + + I E+E ++A + + EL RI+ LS+EEAK IIL E++L Sbjct: 109 EATLERKEESISKRQQQIEEKESKLAEMIQAEQTELERISALSKEEAKSIILNQVEEELT 16- 8 Query: 184 HDIATRIKEAEREVKDRSIAKNKDLLAQAMQRLAGEYVTEQTITTVHLPDDNMKGRIIGR 24- 3 HD A +KE+E K+ S+K AK++L+ A+QR A ++V E T++ V LP+D MKGRIIGR Sbjct: 169 HDTAIMVKESENRAKEESDKKAKNILSLAIQRCAADHVAETTVSVVTLPNDEMKGRIIGR 22- 8 Query: 244 EGRNIRTLESLTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLIQDGRIHPARIEELV 30- 3 EGRNIRTLE+LTGID+IIDDTPE V+LSGFDPIRREIAR+ LE L+QDGRIHPARIEE+V Sbjct: 229 EGRNIRTLETLTGIDLIIDDTPEAVILSGFDPIRREIARIALEKLVQDGRIHPARIEEMV 28- 8 Query: 304 EKNRLEMDQRIREYGEAAAYEIGAPNLHPDLIKIMGRLQFRTSYGQNVLRHSVEVGKLAG 36- 3 K+ R E+D+ IRE GE A +E+G ++HPDLIKI+GRL++RTSYGQNVL HS+EV KLAG Sbjct: 289 DKARKEVDEHIREVGEQATFEVGIHSIHPDLIKILGRLRYRTSYGQNVLNHSLEVSKLAG 34- 8 Query: 364 ILAGELGENVDLARRAGFLHDMGKAIDREVEGSHVEIGMEFARKYKEHPIVVNTIASHHG 42- 3 ILAGELGE+V LA+RAG LHD+GKAID E+EGSHVEIG+E A KYKE+ +V+N+IASHHG Sbjct: 349 ILAGELGEDVTLAKRAGLLHDIGKAIDHEIEGSHVEIGVELATKYKENDVVINSIASHHG 40- 8 Query: 424 DVEPDSVIAVIVAAADALSSARPGARNESMENYIKRLRDLEEIANGFEGVQNAFALQAGR 48- 3 D E SVIAV+VAAADALS+ARPGAR+E++ENYI+RL LEEI+ ++GV+ ++A+QAGR Sbjct: 409 DTEATSVIAVLVAAADALSAARPGARSETLENYIRRLEKLEEISESYDGVEKSYAIQAGR 46- 8 Query: 484 EIRIMVQPGKVSDDQVVIMSHKVREKIEQNLDYPGNIKVTVIREMRAVDFAK 535 E+RI+V+P + D ++ +R++IE+ LDYPG+IKVTVIRE RAV++AK Sbjct: 469 EVRIIVEPDTIDDLSSYRLARDIRKRIEEELDYPGHIKVTVIRETRAVEYAK 520 A related DNA sequence was identified in S. pyogenes <SEQ ID 2979> which encodes the amino acid sequence <SEQ ID 2980>. Analysis of this protein sequence reveals the following: TABLE-US-02854 Possible site: 32 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02855 >GP:AAF34762 GB:AF228345 unknown [Listeria monocytogenes] Identities = 299/534 (55%), Positives = 408/534 (75%), Gaps = 14/534 (2%) Query: 2 VNIILLIVSALIGLILGYALISIRLKSAKEAAELTLLNAEQEAVDIRGKAEVDAEHIKKT 61 + I + I+S+L+ LI+G + S+ KS+ E++ RG AE+ I + Sbjct: 1 MTIAITIISSLLFLIVGLVVGSLIFKSS----------TEKKLAAARGTAEL----IVED 46 Query: 62 AKRESKANRKELLLEAKEEARKYREEIEQEFKSERQELKQLETRLAERSLTLDRKDENLS 121- AK+E++ +KE LLEAKEE + R EIE E + R E ++ E RL +R LDRKD +LS Sbjct: 47 AKKEAETTKKEALLEAKEENHRLRTEIENELRGRRTETQKAENRLLQREENLDRKDTSLS 106- Query: 122 SKEKVLDSKEQSLTDKSKHIDERQLQVEKLEEEKKAELEKVAAMTIAEAREVILMETENK 18- 1 +E L+ KE+S++ + + I+E++ ++ ++ + ++ ELE+++A++ EA+ +IL + E + Sbjct: 107 KREATLERKEESISKRQQQIEEKESKLAEMIQAEQTELERISALSKEEAKSIILNQVEEE 16- 6 Query: 182 LTHEIATRIRDAERDIKDRTVKTAKDLLAQAMQRLAGEYVTEQTITSVHLPDDNMKGRII 24- 1 LTH+ A ++++E K+ + K AK++L+ A+QR A ++V E T++ V LP+D MKGRII Sbjct: 167 LTHDTAIMVKESENRAKEESDKKAKNILSLAIQRCAADHVAETTVSVVTLPNDEMKGRII 22- 6 Query: 242 GREGRNIRTLESLTGIDVIIDDTPEVVILSGFDPIRREIARMTLESLIADGRIHPARIEE 30- 1 GREGRNIRTLE+LTGID+IIDDTPE VILSGFDPIRREIAR+ LE L+ DGRIHPARIEE Sbjct: 227 GREGRNIRTLETLTGIDLIIDDTPEAVILSGFDPIRREIARIALEKLVQDGRIHPARIEE 28- 6 Query: 302 LVEKNRLEMDNRIREYGEAAAYEIGAPNLHPDLIKIMGRLQFRTSFGQNVLRHSVEVGKL 36- 1 +V+K R E+D IRE GE A +E+G ++HPDLIKI+GRL++RTS+GQNVL HS+EV KL Sbjct: 287 MVDKARKEVDEHIREVGEQATFEVGIHSIHPDLIKILGRLRYRTSYGQNVLNHSLEVSKL 34- 6 Query: 362 AGILAGELGENVALARRAGFLHDMGKAIDREVEGSHVEIGMEFARKYKEHPVVVNTIASH 42- 1 AGILAGELGE+V LA+RAG LHD+GKAID E+EGSHVEIG+E A KYKE+ VV+N+IASH Sbjct: 347 AGILAGELGEDVTLAKRAGLLHDIGKAIDHEIEGSHVEIGVELATKYKENDVVINSIASH 40- 6 Query: 422 HGDVEPDSVIAVLVAAADALSSARPGARNESMENYIKRLRDLEEIATSFDGVQNSFALQA 48- 1 HGD E SVIAVLVAAADALS+ARPGAR+E++ENYI+RL LEEI+ S+DGV+ S+A+QA Sbjct: 407 HGDTEATSVIAVLVAAADALSAARPGARSETLENYIRRLEKLEEISESYDGVEKSYAIQA 46- 6 Query: 482 GREIRIMVQPEKISDDQVVILSHKVREKIENNLDYPGNIKVTVIREMRAVDYAK 535 GRE+RI+V+P+ I D L+ +R++IE LDYPG+IKVTVIRE RAV+YAK Sbjct: 467 GREVRIIVEPDTIDDLSSYRLARDIRKRIEEELDYPGHIKVTVIRETRAVEYAK 520 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02856 Identities = 451/535 (84%), Positives = 503/535 (93%) Query: 1 MFNIILAMVCALIGLIIGYVAISMKMKSSKEAAELTLLNAEQDAVDLRGKAEIEAEHIRK 60 M NIIL +V ALIGLI+GY IS+++KS+KEAAELTLLNAEQ+AVD+RGKAE++AEHI+K Sbjct: 1 MVNIILLIVSALIGLILGYALISIRLKSAKEAAELTLLNAEQEAVDIRGKAEVDAEHIKK 60 Query: 61 AAERESKAHQKELLLEAKEEARKYREEIEKEFKSDRQELKQMEARLTDRASSLDRKDENL 120- A+RESKA++KELLLEAKEEARKYREEIE+EFKS+RQELKQ+E RL +R+ +LDRKDENL Sbjct: 61 TAKRESKANRKELLLEAKEEARKYREEIEQEFKSERQELKQLETRLAERSLTLDRKDENL 120- Query: 121 SNKEKMLDSKEQSLTDKSRHINEREQEIATLETKKVEELSRIAELSQEEAKDIILADTEK 18- 0 S+KEK+LDSKEQSLTDKS+HI+ER+ ++ LE +K EL ++A ++ EA+++IL +TE Sbjct: 121 SSKEKVLDSKEQSLTDKSKHIDERQLQVEKLEEEKKAELEKVAAMTIAEAREVILMETEN 18- 0 Query: 181 DLAHDIATRIKEAEREVKDRSNKIAKDLLAQAMQRLAGEYVTEQTITTVHLPDDNMKGRI 24- 0 L H+IATRI++AER++KDR+ K AKDLLAQAMQRLAGEYVTEQTIT+VHLPDDNMKGRI Sbjct: 181 KLTHEIATRIRDAERDIKDRTVKTAKDLLAQAMQRLAGEYVTEQTITSVHLPDDNMKGRI 24- 0 Query: 241 IGREGRNIRTLESLTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLIQDGRIHPARIE 30- 0 IGREGRNIRTLESLTGIDVIIDDTPEVV+LSGFDPIRREIARMTLESLI DGRIHPARIE Sbjct: 241 IGREGRNIRTLESLTGIDVIIDDTPEVVILSGFDPIRREIARMTLESLIADGRIHPARIE 30- 0 Query: 301 ELVEKNRLEMDQRIREYGEAAAYEIGAPNLHPDLIKIMGRLQFRTSYGQNVLRHSVEVGK 36- 0 ELVEKNRLEMD RIREYGEAAAYEIGAPNLHPDLIKIMGRLQFRTS+GQNVLRHSVEVGK Sbjct: 301 ELVEKNRLEMDNRIREYGEAAAYEIGAPNLHPDLIKIMGRLQFRTSFGQNVLRHSVEVGK 36- 0 Query: 361 LAGILAGELGENVDLARRAGFLHDMGKAIDREVEGSHVEIGMEFARKYKEHPIVVNTIAS 42- 0 LAGILAGELGENV LARRAGFLHDMGKAIDREVEGSHVEIGMEFARKYKEHP+VVNTIAS Sbjct: 361 LAGILAGELGENVALARRAGFLHDMGKAIDREVEGSHVEIGMEFARKYKEHPVVVNTIAS 42- 0 Query: 421 HHGDVEPDSVIAVIVAAADALSSARPGARNESMENYIKRLRDLEEIANGFEGVQNAFALQ 48- 0 HHGDVEPDSVIAV+VAAADALSSARPGARNESMENYIKRLRDLEEIA F+GVQN+FALQ Sbjct: 421 HHGDVEPDSVIAVLVAAADALSSARPGARNESMENYIKRLRDLEEIATSFDGVQNSFALQ 48- 0 Query: 481 AGREIRIMVQPGKVSDDQVVIMSHKVREKIEQNLDYPGNIKVTVIREMRAVDFAK 535 AGREIRIMVQP K+SDDQVVI+SHKVREKIE NLDYPGNIKVTVIREMRAVD+AK Sbjct: 481 AGREIRIMVQPEKISDDQVVILSHKVREKIENNLDYPGNIKVTVIREMRAVDYAK 535 SEQ ID 2978 (GBS86) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 7 (lane 6; MW 59 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 13 (lane 5; MW 84 kDa). GBS86-GST was purified as shown in FIG. 192, lane 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 974 A DNA sequence (GBSx1033) was identified in S. agalactiae <SEQ ID 2981> which encodes the amino acid sequence <SEQ ID 2982>. Analysis of this protein sequence reveals the following: TABLE-US-02857 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4984(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 975 A DNA sequence (GBSx1034) was identified in S. agalactiae <SEQ ID 2983> which encodes the amino acid sequence <SEQ ID 2984>. Analysis of this protein sequence reveals the following: TABLE-US-02858 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.87 Transmembrane 146-162 (146-162) ----- Final Results ----- bacterial membrane --- Certainty = 0.2147(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8697> which encodes amino acid sequence <SEQ ID 8698> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-02859 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: -10.72 GvH: Signal Score (-7.5): -5.66 Possible site: 29 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -2.87 threshold: 0.0 INTEGRAL Likelihood = -2.87 Transmembrane 138-154 (138-154) PERIPHERAL Likelihood = 3.76 51 modified ALOM score: 1.07 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2147(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02860 >GP:AAG21390 GB:AF302051 ABC transporter ATP binding subunit [Bacillus licheniformis] Identities = 84/218 (38%), Positives = 138/218 (62%), Gaps = 1/218 (0%) Query: 12 DIIKVDHIFKSIGQKTILEDISFSIASNQCVALIGPNGAGKTTLMSTLLGDISISSGSLT 71 - +++ + ++ K+ QKT ++ I FSI + VA++GPNGAGKTT +S +LG + ++G++T Sbjct: 3 NVVSLTNVTKTFRQKTAVDQIDFSIKKGEIVAILGPNGAGKTTTISMILGLLKPTAGNIT 62 Query: 72 IFNLPAHHNRLKYKVAILPQE-NVLPSKFTVRELIDFQRCLFPEVLPMSLILDYLQWSDT 130- +F+ H R++ K+ + QE +V+P E+I+ R +P+ L + +D Sbjct: 63 LFDSMPHEKRVREKIGTMLQEVSVMPGLRCRVEIIELIRSYYPKPLSFQKLRTLTGLTDK 122- Query: 131 HLQQFTETLSGGQKRLLAFVLTLVGKPQLLFLDEPTSGMDTSTRQRFWELIATLKKEGVT 19- 0 L+ E LSGGQKR L F L L G P+L+ DEPT GMD ++R RFW+ + +L ++G T Sbjct: 123 DLKTQAEKLSGGQKRRLGFALALAGDPELMIFDEPTVGMDITSRNRFWQTVQSLAEQGKT 18- 2 Query: 191 IVYSSHYIEEVEHTADRILVLHKGKLLRDTTPLCHEAR 228 I++S+HY++E + A RIL+ GK++ D TPL ++R Sbjct: 183 IIFSTHYLQEADDAAQRILLFKDGKIVADGTPLQIKSR 220 There is also homology to SEQ ID 686. SEQ ID 8698 (GBS350) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 13; MW 28.9 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 81 (lane 4; MW 54 kDa). GBS350-GST was purified as shown in FIG. 226, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 976 A DNA sequence (GBSx1035) was identified in S. agalactiae <SEQ ID 2985> which encodes the amino acid sequence <SEQ ID 2986>. Analysis of this protein sequence reveals the following: TABLE-US-02861 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2913(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 977 A DNA sequence (GBSx1036) was identified in S. agalactiae <SEQ ID 2987> which encodes the amino acid sequence <SEQ ID 2988>. Analysis of this protein sequence reveals the following: TABLE-US-02862 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.51 Transmembrane 222-238 (214-241) INTEGRAL Likelihood = -6.90 Transmembrane 104-120 (101-125) INTEGRAL Likelihood = -5.84 Transmembrane 140-156 (138-159) INTEGRAL Likelihood = -5.20 Transmembrane 19-35 (18-41) INTEGRAL Likelihood = -1.28 Transmembrane 164-180 (164-180) ----- Final Results ----- bacterial membrane --- Certainty = 0.5203(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02863 >GP:CAB69806 GB:AJ243712 YVFS protein [Bacillus cereus] Identities = 73/239 (30%), Positives = 127/239 (52%), Gaps = 4/239 (1%) Query: 9 KMEFLLTKRQLANLIMAIGMPVAFFLFFSGFMGEGLTKAIEAIYVRNYMITMAGFSSLSF 68 K+E L T R + ++ MPV F+ F+ + + +Y+I+MA FS + Sbjct: 4 KIEILRTFRNKLFIFFSLLMPVMFYYIFTNVVQ---VPQNGDAWKAHYLISMATFSIVGT 60 Query: 69 AFFTFPFSMKDDQLSNRMQLLRHSPVPMWQYYLAKIIRILFYYCLAITVVFLTGHILRQV 128- A F+F + ++ LL+ +P+P Y AKII +I V+F+ G ++ V Sbjct: 61 ALFSFGVRLSQERGQGWTHLLKITPLPEGAYLTAKIIAQTVVNAFSILVIFIAGILINHV 120- Query: 129 SMPIEQWMQSFLLLLGGATCFIPFGLLVSYFKNTELMSMVANICYMSLAVLGGMWMPITM 18- 8 + I QW+ + L LL G T F+ G ++ K + + +ANI MSLA++GG+WMPI + Sbjct: 121 ELTIGQWIGAGLWLLLGVTPFLALGTVIGSIKKADAAAGLANILNMSLAIVGGLWMPIEV 18- 0 Query: 189 FPKWLQALSKLTPTYHLTQVILSPFANSFAGF-SLIILIGYGIIMLVIAYLLSQKRHSI 246- FPK L+ + + TPTYH A G+ ++ +L GY +I +V++ + +++ ++ Sbjct: 181 FPKILRTIGEWTPTYHFGSGAWDIVAGKSIGWENIAVLGGYFLIFVVVSIYIRKRQEAV 239- There is also homology to SEQ ID 682 and to SEQ ID 1628. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 978 A DNA sequence (GBSx1037) was identified in S. agalactiae <SEQ ID 2989> which encodes the amino acid sequence <SEQ ID 2990>. This protein is predicted to be histidine kinase. Analysis of this protein sequence reveals the following: TABLE-US-02864 Possible site: 49 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.43 Transmembrane 105-121 (102-124) INTEGRAL Likelihood = -6.95 Transmembrane 130-146 (129-149) ----- Final Results ----- bacterial membrane --- Certainty = 0.3972(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9537> which encodes amino acid sequence <SEQ ID 9538> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02865 >GP:CAB54584 GB:AJ006400 histidine kinase [Streptococcus pneumoniae] Identities = 138/350 (39%), Positives = 212/350 (60%), Gaps = 3/350 (0%) Query: 11 MYFIPLVFLIYPIGGILYYHYPFWTLFFTLAFVGAYLYSVIIRGESKYHMIAWSTMLTYI 70 - M++I L+F+I+PI ++ W L + FV AYL V+ + + W MLTY+ Sbjct: 11 MFWISLIFMIFPILSVVTGWLSAWHLLIDILFVVAYL-GVLTTKSQRLSWLYWGLMLTYV 69 Query: 71 FYMTIFINSGFIWYIYFLSNLLVYRFRDK-LKSFRFISFACTLATVVF-LCFFKASDFGD 128- T F+ +IW+ +FLSNLL Y F + LKS +F VV L F+ + Sbjct: 70 VGNTAFVAVNYIWFFFFLSNLLSYHFSVRSLKSLHVWTFLLAQVLVVGQLLIFQRIEVEF 129- Query: 129 RIMFLIVPIFCIGYMWIAIENRNSEEQREKIAEQNQYINILSAENERNRIGRDLHDSLGH 18- 8 L++ F + + R E+ +E +QN IN+L AENER+RIG+DLHDSLGH Sbjct: 130 LFYLLVILTFVDLMTFGLVRIRIVEDLKEAQVKQNAQINLLLAENERSRIGQDLHDSLGH 18- 9 Query: 189 TFAMMTLKTELALKLLEKRNYDKVQKELSELNHISHQSMSEVRQIVSNLKYRTVVEEIDE 24- 8 TFAM+++KT+LAL+L + Y +V+KEL E++ IS SM+EVR IV NLK RT+ E++ Sbjct: 190 TFAMLSVKTDLALQLFQMEAYPQVEKELKEIHQISKDSMNEVRTIVENLKSRTLTSELET 24- 9 Query: 249 LYRLFQLSNIKLTVVNKLETSQLSPVTQSTITMILKELSNNIVKHAEADSVELSLVRQGA 30- 8 + ++ +++ I++ V N L+ S L+ +ST +MIL EL NI+KHA+A V L L R Sbjct: 250 VKKMLEIAGIEVQVENHLDKSSLTQELESTASMILLELVTNIIKHAKASKVYLKLERTEK 30- 9 Query: 309 TINIEMIDNGCGFTNLDGDELHSIQERLTIVEGTLTILSRSKPTHIQVVL 358 + + + D+GCGF ++ GDELH+++ R+ G ++++S+ PT +QV L Sbjct: 310 ELILTVRDDGCGFASISGDELHTVRNRVFPFSGEVSVISQKHPTEVQVRL 359 There is also homology to SEQ ID 2992. A related GBS gene <SEQ ID 8699> and protein <SEQ ID 8700> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02866 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 10.90 GvH: Signal Score (-7.5): -2.42 Possible site: 49 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 2 value: -7.43 threshold: 0.0 INTEGRAL Likelihood = -7.43 Transmembrane 105-121 (102-124) INTEGRAL Likelihood = -6.95 Transmembrane 130-146 (129-149) PERIPHERAL Likelihood = 0.16 61 modified ALOM score: 1.99 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3972(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 979 A DNA sequence (GBSx1038) was identified in S. agalactiae <SEQ ID 2993> which encodes the amino acid sequence <SEQ ID 2994>. This protein is predicted to be response regulator. Analysis of this protein sequence reveals the following:

TABLE-US-02867 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 49-65 (49-65) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02868 >GP:CAB54585 GB:AJ006400 response regulator [Streptococcus pneumoniae] Identities = 95/153 (62%), Positives = 125/153 (81%), Gaps = 3/153 (1%) Query: 1 MKLLVAEDQSMLRDAMCQLLLMEESVSTIDQAGNGGEAIAILSNKAIDVAILDVEMPILS 60 MK+LVAEDQSMLRDAMCQLL+++ V ++ QA NG EAI +L +++D+AILDVEMP+ + Sbjct: 1 MKVLVAEDQSMLRDAMCQLLMLQPDVESVFQAKNGQEAIQLLEKESVDIAILDVEMPVKT 60 Query: 61 GLDVLEWVRKYQ-NVKVIIVTTFKRSGYFQRAIRSNVDAYVLKDRSVADLMKTIQKVLSG 119- GL+VLEW+R + KV++VTTFKR GYF+RA+++ VDAYVLK+R++ADLM+T+ VL G Sbjct: 61 GLEVLEWIRAEKLETKVVVVTTFKRPGYFERAVKAGVDAYVLKERNIADLMQTLHTVLEG 120- Query: 120 GKEYSPELMENVI--SNPLSEQEIKILSLIAQG 150 KEYSPELME V+ NPL+EQEI +L IAQG Sbjct: 121 RKEYSPELMEVVMMHPNPLTEQEIAVLKGIAQG 153 There is also homology to SEQ ID 2996. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 980 A DNA sequence (GBSx1039) was identified in S. agalactiae <SEQ ID 2997> which encodes the amino acid sequence <SEQ ID 2998>. Analysis of this protein sequence reveals the following: TABLE-US-02869 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.69 Transmembrane 158-174 (145-184) INTEGRAL Likelihood = -4.94 Transmembrane 11-27 (8-31) INTEGRAL Likelihood = -3.93 Transmembrane 74-90 (73-92) INTEGRAL Likelihood = -2.39 Transmembrane 103-119 (102-119) INTEGRAL Likelihood = -1.86 Transmembrane 42-58 (38-59) ----- Final Results ----- bacterial membrane --- Certainty = 0.3675(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02870 >GP:AAB85965 GB:AE000909 unknown [Methanothermobacter thermoautotrophicus] Identities = 46/183 (25%), Positives = 81/183 (44%), Gaps = 11/183 (6%) Query: 5 KERFDTLSDAILAIAMTILVLEI-------KTPATMGDIGDFTRNIGLFIVSFVVVFNFW 57 K+R + L DAI AIAMTILVL I PA I ++ + +SF+++ FW Sbjct: 6 KKRLEGLVDAIFAIAMTILVLGIDVPTGTMSVPAMDAYIMGLASDLYSYCLSFLLLGVFW 65 Query: 58 YERAQNSLDAQKTNDEIIALDIIEHLGICLIPLFTKFMISFENHNFAVMAYGLLTLLVGL 117- + + +K + I ++I+ + + L+P TK ++ + + + L L +GL Sbjct: 66 WVNHMHFEKLEKVDTGFIWINIVWLMVVVLVPFSTKLTGNYGDLVTPNILFHLNMLTIGL 125- Query: 118 TSDIIRIRLASYDLVTIPSELKERVIKVMTTFAIRSVVVRFIIIILAYFLPEVGIFAYLV 17- 7 + I L+ I ++K + ++ + +IL PE AY V Sbjct: 126 LLSMSWIYTQRNGLMDIGENEYRLILKKNLLMPLAAI----LALILTPIAPEYSSTAYAV 18- 1 Query: 178 IPL 180 + L Sbjct: 182 LIL 184 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 981 A DNA sequence (GBSx1040) was identified in S. agalactiae <SEQ ID 2999> which encodes the amino acid sequence <SEQ ID 3000>. This protein is predicted to be guanylate kinase (gmk). Analysis of this protein sequence reveals the following: TABLE-US-02871 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02872 >GP:CAB13441 GB:Z99112 similar to guanylate kinase [Bacillus subtilis] Identities = 121/202 (59%), Positives = 155/202 (75%) Query: 1 MSERGLLIVFSGPSGVGKGTVRQEIFSTPDHKFDYSVSMTTRPQRPGEVDGVDYFFRTRE 60 M ERGLLIV SGPSGVGKGTVRQ IFS D KF+YS+S+TTR R GEV+GVDYFF+TR+ Sbjct: 41 MKERGLLIVLSGPSGVGKGTVRQAIFSQEDTKFEYSISVTTRSPREGEVNGVDYFFKTRD 100- Query: 61 EFEALIKEGQMLEYAEYVGNYYGTPLSYVNETLDKGIDVFLEIEVQGALQVKSKVPDGVF 120- EFE +I + ++LE+AEYVGNYYGTP+ YV +TL G DVFLEIEVQGALQV++ P+G+F Sbjct: 101 EFEQMIADNKLLEWAEYVGNYYGTPVDYVEQTLQDGKDVFLEIEVQGALQVRNAFPEGLF 16- 0 Query: 121 IFLTPPDLEELEERLVGRGTDSPEVIAQRIERAKEEIALMREYDYAVVNDQVSLAAERVK 18- 0 IFL PP L EL+ R+V RGT++ +I R++ AK EI +M YDY V ND V A +++K Sbjct: 161 IFLAPPSLSELKNRIVTRGTETDALIENRMKAAKAEIEMMDAYDYVVENDNVETACDKIK 22- 0 Query: 181 RVIEAEHYRVDRVIGRYTNMVK 202 ++ AEH + +RV RY M++ Sbjct: 221 AIVLAEHLKRERVAPRYKKMLE 242 A related DNA sequence was identified in S. pyogenes <SEQ ID 3001> which encodes the amino acid sequence <SEQ ID 3002>. Analysis of this protein sequence reveals the following: TABLE-US-02873 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02874 >GP:CAB13441 GB:Z99112 similar to guanylate kinase [Bacillus subtilis] Identities = 123/203 (60%), Positives = 157/203 (76%) Query: 1 MSERGLLIVFSGPSGVGKGTVRQEIFSTPDHKFEYSVSMTTRPQRFGEVDGVDYFFRTRE 60 M ERGLLIV SGPSGVGKGTVRQ IFS D KFEYS+S+TTR R GEV+GVDYFF+TR+ Sbjct: 41 MKERGLLIVLSGPSGVGKGTVRQAIFSQEDTKFEYSISVTTRSPREGEVNGVDYFFKTRD 100- Query: 61 EFEELIKTGQMLEYAEYVGNYYGTPLTYVNETLDKGIDVFLEIEVQGALQVKSKVPDGVF 120- EFE++I ++LE+AEYVGNYYGTP+ YV +TL G DVFLEIEVQGALQV++ P+G+F Sbjct: 101 EFEQMIADNKLLEWAEYVGNYYGTPVDYVEQTLQDGKDVFLEIEVQGALQVRNAFPEGLF 16- 0 Query: 121 VFLTPPDLDELEDRLVGRGTDSQEVIAQRIERAKEEIALMREYDYAVVNDEVALAAERVK 18- 0 +FL PP L EL++R+V RGT++ +I R++ AK EI +M YDY V ND V A +++K Sbjct: 161 IFLAPPSLSELKNRIVTRGTETDALIENRMKAAKAEIEMMDAYDYVVENDNVETACDKIK 22- 0 Query: 181 RIIETEHFRVERVIGRYDKMIKI 203 I+ EH + ERV RY KM+++ Sbjct: 221 AIVLAEHLKRERVAPRYKKMLEV 243 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02875 Identities = 186/204 (91%), Positives = 197/204 (96%) Query: 1 MSERGLLIVFSGPSGVGKGTVRQEIFSTPDHKFDYSVSMTTRPQRPGEVDGVDYFFRTRE 60 MSERGLLIVFSGPSGVGKGTVRQEIFSTPDHKF+YSVSMTTRPQRPGEVDGVDYFFRTRE Sbjct: 1 MSERGLLIVFSGPSGVGKGTVRQEIFSTPDHKFEYSVSMTTRPQRPGEVDGVDYFFRTRE 60 Query: 61 EFEALIKEGQMLEYAEYVGNYYGTPLSYVNETLDKGIDVFLEIEVQGALQVKSKVPDGVF 120- EFE LIK GQMLEYAEYVGNYYGTPL+YVNETLDKGIDVFLEIEVQGALQVKSKVPDGVF Sbjct: 61 EFEELIKTGQMLEYAEYVGNYYGTPLTYVNETLDKGIDVFLEIEVQGALQVKSKVPDGVF 120- Query: 121 IFLTPPDLEELEERLVGRGTDSPEVIAQRIERAKEEIALMREYDYAVVNDQVSLAAERVK 18- 0 +FLTPPDL+ELE+RLVGRGTDS EVIAQRIERAKEEIALMREYDYAVVND+V+LAAERVK Sbjct: 121 VFLTPPDLDELEDRLVGRGTDSQEVIAQRIERAKEEIALMREYDYAVVNDEVALAAERVK 18- 0 Query: 181 RVIEAEHYRVDRVIGRYTNMVKET 204 R+IE EH+RV+RVIGRY M+K T Sbjct: 181 RIIETEHFRVERVIGRYDKMIKIT 204 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 982 A DNA sequence (GBSx1041) was identified in S. agalactiae <SEQ ID 3003> which encodes the amino acid sequence <SEQ ID 3004>. Analysis of this protein sequence reveals the following: TABLE-US-02876 Possible site: 30 >>>Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1763 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 3005> which encodes the amino acid sequence <SEQ ID 3006>. Analysis of this protein sequence reveals the following: TABLE-US-02877 Possible site: 35 >>>Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1551 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02878 Identities = 95/105 (90%), Positives = 100/105 (94%), Gaps = 1/105 (0%) Query: 1 MMLKPSIDTLLDKVPSKYSLVILQAKRAHELEAGEKATQDFKSVKSTLRALEEIESGNVV 60 MMLKPSIDTLLDKVPSKYSLVILQAKRAHELEAG TQ+FKSVKSTL+ALEEIESGNVV Sbjct: 1 MMLKPSIDTLLDKVPSKYSLVILQAKRAHELEAGATPTQEFKSVKSTLQALEEIESGNVV 60 Query: 61 IHPDPSAKRASVRARIEAERLAKEEEERKIKEQIAKEK-EDGEKI 104 IHPDPSAKR +VRA+IEAERLAKEEEERKIKEQIAKEK E+GEKI Sbjct: 61 IHPDPSAKREAVRAKIEAERLAKEEEERKIKEQIAKEKEEEGEKI 105 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 983 A DNA sequence (GBSx1043) was identified in S. agalactiae <SEQ ID 3007> which encodes the amino acid sequence <SEQ ID 3008>. Analysis of this protein sequence reveals the following: TABLE-US-02879 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3413(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02880 >GP:CAB13444 GB:Z99112 primosomal replication factor Y (primosomal protein N') [Bacillus subtilis] Identities = 377/807 (46%), Positives = 529/807 (64%), Gaps = 21/807 (2%) Query: 6 AQVIVDIPLMQTDKPFSYAIPKDLEDLVQVGVRVHVPFGRGNRLLQGFVVGFRDDDELET 65 A+VIVD+ D+PF Y IP L+ +++ G+RV VPFG R +QGFV ++ +L Sbjct: 4 AEVIVDVSTKNIDRPFDYKIPDHLKGMIKTGMRVIVPFGP--RKIQGFVTAVKEASDLSG 61 Query: 66 KDIAEV---LDFEPVLNQEQLDLADQMRHTVFSYKISILKSMLPSLLNSQYDKLLL---A 119- K + EV LD PVL +E + L+ + S+KI+ L++MLP+ L ++Y+K L Sbjct: 62 KSVKEVEDLLDLTPVLTEELMILSSWLSDKTLSFKITALQAMLPAALKAKYEKELKIAHG 121- Query: 120 TDTLPSEDREDLFGHKTEIVFSSLSSQDAKKA-GRLIQKGFIEVQYLAKDKKTIKTEKIY 17- 8 D P +R LF +++S + + K R +QKG I+V Y K K + Sbjct: 122 ADLPPQVER--LFSETKTLLYSDIPDHETLKLIQRHVQKGDIDVTYKVAQKTNKKMVRHI 17- 9 Query: 179 KINRTLLEKSQ----IAARAKKRLELKEFLLENPQPGRLTALN----KQFSSPVVNFFRE 23- 0 + N + E ++ ++ +A K+ + FL+ P+ ++ A SS + + Sbjct: 180 QANASKEELAKQAEGLSRQAAKQQAILHFLISEPEGVKIPAAELCKKTDTSSATIKTLIQ 23- 9 Query: 231 EGIIEVIEKEASRSDNYFKGILKTDFLDLNQEQAKVVKIVVDQIGKEQNKPFLLEGITGS 29- 0 +G+++ +E R K KT+ L L EQ + + + + +++K FLL G+TGS Sbjct: 240 KGLLKESYEEVYRDPYQDKMFKKTEPLPLTDEQRAAFEPIRETLDSDEHKVFLLHGVTGS 29- 9 Query: 291 GKTEVYLHIIDNVLKLGKTAIVLVPEISLTPQMTNRFISRFGKQVAIMHSGLSEGEKFDE 35- 0 GKTE+YL I+ VL GK AIVLVPEISLTPQM NRF RFG QVA+MHSGLS GEK+DE Sbjct: 300 GKTEIYLQSIEKVLAKGKEAIVLVPEISLTPQMVNRFKGRFGSQVAVMHSGLSTGEKYDE 35- 9 Query: 351 WRKIKSGQAKVVVGARSAIFAPLENIGAIIIDEEHESTYKQESNPRYHARDVALLRAEYY 41- 0 WRKI + ++VVGARSAIFAP EN+G IIIDEEHES+YKQE PRYHA++VA+ RAE++ Sbjct: 360 WRKIHRKEVRLVVGARSAIFAPFENLGMIIIDEEHESSYKQEEMPRYHAKEVAIKRAEHH 41- 9 Query: 411 KAVLLMGSATPSIESRARASRDVYKFLELKHRANPKARIPQVEIIDFRNFIGQQEVSNFT 47- 0 +++GSATP++ES ARA + VY+ L LKHR N + +P+V ++D R + S F+ Sbjct: 420 SCPVVLGSATPTLESYARAQKGVYELLSLKHRVNHRV-MPEVSLVDMREELRNGNRSMFS 47- 8 Query: 471 SYLLDKIRDRLDKKEQVVLMLNRRGYSSFIMCRDCGYVDQCPNCDISLTLHMATKTMNCH 53- 0 L++K+ + + K EQ VL LN+RGYSSF+MCRDCGYV QCP+CDIS+T H + + CH Sbjct: 479 VELMEKLEETIAKGEQAVLFLNKRGYSSFVMCRDCGYVPQCPHCDISMTYHRYGQRLKCH 53- 8 Query: 531 YCGFEKPIPRTCPNCNSKSISYYGTGTQKAYEELLKVIPDAKILRMDVDTTRQKGGHESI 59- 0 YCG E+P+P TCP C S+ I ++GTGTQ+ EEL KV+P A+++RMDVDTT +KG HE + Sbjct: 539 YCGHEEPVPHTCPECASEHIRFFGTGTQRVEEELTKVLPSARVIRMDVDTTSRKGAHEKL 59- 8 Query: 591 LKRFGNHEADILLGTQMIAKGLDFPNVTLVGVLNADTSLNLPDFRSSERTFQLLTQVAGR 65- 0 L FG +ADILLGTQMIAKGLDFPNVTLVGVL+ADT+L++PDFRS+E+TFQLLTQV+GR Sbjct: 599 LSAFGEGKADILLGTQMIAKGLDFPNVTLVGVLSADTTLHIPDFRSAEKTFQLLTQVSGR 65- 8 Query: 651 AGRAEKEGEVVIQTYNPNHYAIQLAQKQDFEAFYQYEMNIRRQLGYPPYYFTVGLTLSNK 71- 0 AGR EK G V+IQTY P+HY+IQL + D+E FYQ+EM RR+ YPPYY+ +T+SH+ Sbjct: 659 AGRHEKPGHVIIQTYTPSHYSIQLTKTHDYETFYQHEMAHRREQSYPPYYYLALVTVSHE 71- 8 Query: 711 DEEWLIRKSYEVLSLLKQGFSDKVKLLGPTPKPIARTHNLYHYQIIIKYRFEDNLELVLN 77- 0 + + ++ LK K+LGP+ PIAR + Y YQ +IKY+ E L +L Sbjct: 719 EVAKAAVTAEKIAHFLKANCGADTKILGPSASPIARIKDRYRYQCVIKYKQETQLSALLK 77- 8 Query: 771 RLLD-MTQDKENRDLRLAIDHEPQNMM 796 ++L+ ++ E + + ++ID P MM Sbjct: 779 KILEHYKREIEQKHVMISIDMNPYMMM 805 A related DNA sequence was identified in S. pyogenes <SEQ ID 3009> which encodes the amino acid sequence <SEQ ID 3010>. Analysis of this protein sequence reveals the following: TABLE-US-02881 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1396 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02882 Identities = 556/793 (70%), Positives = 659/793 (82%), Gaps = 1/793 (0%) Query: 4 KLAQVIVDIPLMQTDKPFSYAIPKDLEDLVQVGVRVHVPFGRGNRLLQGFVVGFRDDDEL 63 K+A VIVDIPLMQTDKPFSY IPK+L LVQ+G RVHVPFG+GNRLLQGF++GF +D Sbjct: 12 KVAHVIVDIPLMQTDKPFSYGIPKELVSLVQLGSRVHVPFGKGNRLLQGFIIGFGQEDSS 71 Query: 64 ETKDIAEVLDFEPVLNQEQLDLADQMRHTVFSYKISILKSMLPSLLNSQYDKLLLATDTL 123- K I VLD EPVLNQEQL LADQ+R TVFSYKI++LK+M+P+LLNS YDK+L L Sbjct: 72 SLKLIQTVLDPEPVLNQEQLTLADQLRKTVFSYKITLLKAMIPNLLNSNYDKVLRPESGL 131- Query: 124 PSEDREDLFGHKTEIVFSSLSSQDAKKAGRLIQKGFIEVQYLAKDKKTIKTEKIYKINRT 18- 3 DR+ LF K +++S+L + K A + IQ G I V YLAKDKK +KTEK Y ++ Sbjct: 132 KKSDRDFLFEGKPSVLYSTLDREKEKIALKGIQAGHITVSYLAKDKKNLKTEKYYHVDLD 19- 1 Query: 184 LLEKSQIAARAKKRLELKEFLLENPQPGRLTALNKQFSSPVVNFFREEGIIEVIEKEASR 24- 3 L I++RAKKR LK++LL + + +L L + FS VV +F +I + E+ R Sbjct: 192 ALAVHPISSRAKKRQLLKDYLLTHTKEAKLATLYQAFSRDVVAYFVTNHLIRIDERPIDR 25- 1 Query: 244 SDNYFKGILKTDFLDLNQEQAKVVKIVVDQIGKEQNKPFLLEGITGSGKTEVYLHIIDNV 30- 3 S++YF I + FL LN++QA V +V+QIGK +KPFL+EGITGSGKTEVYLHII+ V Sbjct: 252 SESYFDQIKPSSFLTLNEQQASAVTEIVEQIGKP-SKPFLIEGITGSGKTEVYLHIIEAV 31- 0 Query: 304 LKLGKTAIVLVPEISLTPQMTNRFISRFGKQVAIMHSGLSEGEKFDEWRKIKSGQAKVVV 36- 3 LK KTAIVLVPEISLTPQMT+RFISRFGKQVAIMHSGLS+GEKFDEWRKIK+GQAKVVV Sbjct: 311 LKQDKTAIVLVPEISLTPQMTSRFISRFGKQVAIMHSGLSDGEKFDEWRKIKTGQAKVVV 37- 0 Query: 364 GARSAIFAPLENIGAIIIDEEHESTYKQESNPRYHARDVALLRAEYYKAVLLMGSATPSI 42- 3 GARSAIF+PLE IGAIIIDEEHESTYKQESNPRYHAR+VALLRA++++AV++MGSATPSI Sbjct: 371 GARSAIFSPLERIGAIIIDEEHESTYKQESNPRYHAREVALLRAKHHQAVVVMGSATPSI 43- 0 Query: 424 ESRARASRDVYKFLELKHRANPKARIPQVEIIDFRNFIGQQEVSNFTSYLLDKIRDRLDK 48- 3 ESRARAS+ VY F++L RANP A+IP+V I+DFR++IGQQ VSNFT YL+DKI++RL K Sbjct: 431 ESRARASKGVYHFIQLTQRANPLAKIPEVTIVDFRDYIGQQAVSNFTPYLIDKIKERLVK 49- 0 Query: 484 KEQVVLMLNRRGYSSFIMCRDCGYVDQCPNCDISLTLHMATKTMNCHYCGFEKPIPRTCP 54- 3 KEQVVLMLNRRGYSSF+MCRDCGYVD+CPNCDISLTLHM TKTMNCHYCGF+KPIP TCP Sbjct: 491 KEQVVLMLNRRGYSSFVMCRDCGYVDKCPNCDISLTLHMDTKTMNCHYCGFQKPIPITCP 55- 0 Query: 544 NCNSKSISYYGTGTQKAYEELLKVIPDAKILRMDVDTTRQKGGHESILKRFGNHEADILL 60- 3 C+S SI YYGTGTQKA++EL VIP+AKILRMDVDTTR+K H++IL FG EADILL Sbjct: 551 ECHSNSIRYYGTGTQKAFDELQGVIPEAKILRMDVDTTRKKRSHKTILDSFGRQEADILL 61- 0 Query: 604 GTQMIAKGLDFPNVTLVGVLNADTSLNLPDFRSSERTFQLLTQVAGRAGRAEKEGEVVIQ 66- 3 GTQMIAKGLDFPNVTLVGVLNADTSLNLPDFR+SE+TFQLLTQVAGRAGRA K GEV+IQ Sbjct: 611 GTQMIAKGLDFPNVTLVGVLNADTSLNLPDFRASEKTFQLLTQVAGRAGRAHKPGEVLIQ 67- 0 Query: 664 TYNPNHYAIQLAQKQDFEAFYQYEMNIRRQLGYPPYYFTVGLTLSHKDEEWLIRKSYEVL 72- 3 TYNP+HYAIQLA+KQDFEAFY+YEM+IR Q+ YPPYYFTVG+TLSH+ E +++K+Y+V Sbjct: 671 TYNPDHYAIQLAKKQDFEAFYRYEMSIRHQMAYPPYYFTVGITLSHRLEASVVKKAYQVT 73- 0 Query: 724 SLLKQGFSDKVKLLGPTPKPIARTHNLYHYQIIIKYRFEDNLELVLNRLLDMTQDKENRD 78- 3 LLK SD +K+LGPTPKPIARTHNLYHYQI++KYRFEDNLE LNR+LD +Q+ +NR Sbjct: 731 ELLKSHLSDNIKILGPTPKPIARTHNLYHYQILLKYRFEDNLEETLNRILDWSQEADNRH 79- 0 Query: 784 LRLAIDHEPQNMM 796 L+L ID EPQ + Sbjct: 791 LKLIIDCEPQQFL 803 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 984 A DNA sequence (GBSx1044) was identified in S. agalactiae <SEQ ID 3011> which encodes the amino acid sequence <SEQ ID 3012>. This protein is predicted to be methionyl-tRNA formyltransferase (fmt). Analysis of this protein sequence reveals the following:

TABLE-US-02883 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1329 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02884 >GP: CAB13446 GB: Z99112 methionyl-tRNA formyltransferase [Bacillus subtilis] Identities = 155/314 (49%), Positives = 221/314 (70%), Gaps = 7/314 (2%) Query: 1 MTKLLFMGTPDFSATVLKGILADGKYDVLAVVTQPDRAVGRKKEIKMTPVKEVALENNIP 60 MT+++FMGTPDFS VL+ ++ DG Y+V+ VVTQPDR GRKK + PVKE AL + IP Sbjct: 1 MTRIVFMGTPDFSVPVLRTLIEDG-YEVVGVVTQPDRPKGRKKVLTPPPVKEEALRHGIP 59 Query: 61 VYQPEKLSGSPELEQLMTLGADGIVTAAFGQFLPTKLLESVGFA-INVHASLLPKYRGGA 119- V QPEK+ + E+E+++ L D IVTAAFGQ LP +LL+S + INVHASLLP+ RGGA Sbjct: 60 VLQPEKVRLTEEIEKVLALKPDLIVTAAFGQILPKELLDSPKYGCINVHASLLPELRGGA 119- Query: 120 PIHYAIINGEKEAGVTIMEMVAKMDAGDMVSKASVEITDEDNVGTMFDRLAVVGRDLLLD 17- 9 PIHY+I+ G+K+ G+TIM MV K+DAGDM+SK V+I + DNVGT+ D+L+V G LL + Sbjct: 120 PIHYSILQGKKKTGITIMYMVEKLDAGDMISKVEVDIEETDNVGTLHDKLSVAGAKLLSE 17- 9 Query: 180 TLPGYLSGDIKPIPQNEEEVSFSPNISPDEERIDWNKSSRDIFNHVRGMYPWPVAHTLLE 23- 9 T+P ++G I P Q+EE+ +++PNI ++E +DW+++ +++N +RG+ PWPVA+T L Sbjct: 180 TVPNVIAGSISPEKQDEEKATYAPNIKREQELLDWSRTGEELYNQIRGLNPWPVAYTTLN 23- 9 Query: 240 GNRFKLY--EVTMSEGKGSPGQVIAKTKNSLTVATG-DGAIELKSVQPAGKPRMDIKDFL 29- 6 G K++ + + PG V+A K + VATG + A+ L +QPAGK RM +DF+ Sbjct: 240 GQNLKIWASKKIAAPTTAEPGTVVAVEKEGIIVATGNETALLLTELQPAGKKRMKGEDFV 29- 9 Query: 297 NGVGRNLEIGDKFG 310 G ++E GD G Sbjct: 300 RGA--HVEAGDVLG 311 A related DNA sequence was identified in S. pyogenes <SEQ ID 3013> which encodes the amino acid sequence <SEQ ID 3014>. Analysis of this protein sequence reveals the following: TABLE-US-02885 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0730(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02886 Identities = 217/310 (70%), Positives = 266/310 (85%) Query: 1 MTKLLFMGTPDFSATVLKGILADGKYDVLAVVTQPDRAVGRKKEIKMTPVKEVALENNIP 60 M KLLFMGTP FSATVLKG+L + Y++L VVTQPDRAVGRKK+IK+TPVK++ALE+ I Sbjct: 1 MIKLLFMGTPQFSATVLKGLLDNPAYEILGVVTQPDRAVGRKKDIKVTPVKQLALEHGIS 60 Query: 61 VYQPEKLSGSPELEQLMTLGADGIVTAAFGQFLPTKLLESVGFAINVHASLLPKYRGGAP 120- +YQPEKLSGS EL ++M LGADGI+TAAFGQFLPT LL+SV FAINVHASLLPKYRGGAP Sbjct: 61 IYQPEKLSGSQELIEIMGLGADGIITAAFGQFLPTILLDSVSFAINVHASLLPKYRGGAP 120- Query: 121 IHYAIINGEKEAGVTIMEMVAKMDAGDMVSKASVEITDEDNVGTMFDRLAVVGRDLLLDT 18- 0 IHYAI+NG+KEAGVTIMEM+ +MDAGDMV+KAS I + DNVGT+F++LA++GRDLLLD+ Sbjct: 121 IHYAIMNGDKEAGVTIMEMIKEMDAGDMVAKASTPILETDNVGTLFEKLAIIGRDLLLDS 18- 0 Query: 181 LPGYLSGDIKPIPQNEEEVSFSPNISPDEERIDWNKSSRDIFNHVRGMYPWPVAHTLLEG 24- 0 LP YLSG++KPIPQ+ + +FSPNISP+ E++DW S++++FNH+RGM PWPVAHT LEG Sbjct: 181 LPAYLSGELKPIPQDHSQATFSPNISPEHEKLDWTMSNQEVFNHIRGMNPWPVAHTFLEG 24- 0 Query: 241 NRFKLYEVTMSEGKGSPGQVIAKTKNSLTVATGDGAIELKSVQPAGKPRMDIKDFLNGVG 30- 0 R K+YE ++EG+G PGQV+ KTK SL +ATG GA+ L VQPAGKP+M I DFLNG+G Sbjct: 241 QRLKIYEAQLAEGEGLPGQVVVKTKKSLVIATGQGALSLIVVQPAGKPKMSIIDFLNGIG 30- 0 Query: 301 RNLEIGDKFG 310 R LE+GD G Sbjct: 301 RKLEVGDIIG 310 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 985 A DNA sequence (GBSx1045) was identified in S. agalactiae <SEQ ID 3015> which encodes the amino acid sequence <SEQ ID 3016>. This protein is predicted to be sunL protein (sun). Analysis of this protein sequence reveals the following: TABLE-US-02887 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1677(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02888 >GP: CAA10711 GB: AJ132604 sunL protein [Lactococcus lactis] Identities = 222/434 (51%), Positives = 305/434 (70%), Gaps = 15/434 (3%) Query: 7 KSARGLALMTLEEVFDKGAYSNIALNKSLKKSRLSDKDRALVTEIVYGTVARKITLEWYL 66 K+AR AL L ++F AY+NI+L+++L+ S LS D+ VT +VYG V++K LEWY+ Sbjct: 3 KNARQTALDVLNDIFGNDAYANISLDRNLRDSELSTVDKGFVTALVYGVVSKKALLEWYI 62 Query: 67 SHFIVDRDKLELWVYHLLLLSLYQLLYLDNIPDHAIVNDAVTIAKNRGNKKGAEKLINAV 126- + + K W LLLL++YQ+L++D +P A V++AV IAK R + + INAV Sbjct: 63 TPLLKKEPKP--WAKMLLLLTIYQVLFMDKVPISAAVDEAVKIAK-RHDGQATANFINAV 119- Query: 127 LRR-VSSETLPEIASIKRQNKRYSVAYSMPVWLVKKLIDQYGETRALAIMESLFERNKAS 18- 5 LR + SE E + K + YSMP L+ K++ Q+G R I+ESL + + S Sbjct: 120 LRNFMRSEHRNE------EPKDWETKYSMPKLLLDKMVRQFGGKRTGEILESLEKPSHVS 17- 3 Query: 186 LRVTDLSQKQTIKETLNVRDSHIAETALVADSGNFASTSFFQDGLITIQDESSQLVAPTL 24- 5 LR D + E R S + ETAL+ADSGNF+ T FQ G ITIQDE+SQLVAP L Sbjct: 174 LRKIDPTV-----EIAGTRPSLLTETALIADSGNFSITEEFQTGRITIQDETSQLVAPQL 22- 8 Query: 246 KVSGNDQVLDACSAPGGKTSHIASYLTTGAVTALDLYDHKLELVMENAKRLGLSDKIKTK 30- 5 ++ G ++VLDAC+APGGK++H+A YLTTG +TALDLY+HKL+L+ +NA+R ++DKI T+ Sbjct: 229 ELEGTEEVLDACAAPGGKSTHMAQYLTTGHITALDLYEHKLDLINQNAQRQHVADKITTQ 28- 8 Query: 306 KLDASKAHEYFLEDTFDKILVDAPCSGIGLIRRKPDIKYNKANQDFEALQEIQLSILSSV 36- 5 K DA+ +E F + FD+ILVDAPCSGIGLIRRKPDI+Y K + DF LQ+IQL IL+S Sbjct: 289 KADATMIYENFGPEKFDRILVDAPCSGIGLIRRKPDIRYRKESSDFIDLQKIQLEILNSA 34- 8 Query: 366 CQTLRKGGIITYSTCTIFEEENFQVIEKFLENHPNFEQVELSHTQEDIVKRGCISISPEQ 42- 5 ++L+K GI+ YSTCTIF+EENF V+ +FLENHPNFEQVE+S+ + +++K GC+ I+PE Sbjct: 349 SKSLKKSGIMVYSTCTIFDEENFDVVHEFLENHPNFEQVEISNEKPEVIKEGCLFITPEM 40- 8 Query: 426 YHTDGFFIGQVKRI 439 YHTDGFFI + K+I Sbjct: 409 YHTDGFFIAKFKKI 422 A related DNA sequence was identified in S. pyogenes <SEQ ID 3017> which encodes the amino acid sequence <SEQ ID 3018>. Analysis of this protein sequence reveals the following: TABLE-US-02889 Possible site: 42 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02890 >GP:CAA10711 GB:AJ132604 sunL protein [Lactococcus lactis] Identities = 208/433 (48%), Positives = 287/433 (66%), Gaps = 13/433 (3%) Query: 7 KSTRGKALLVIEAIFDQGAYTNIALNQQLSNKALSAKDRALLTEIVYGTVSRKISLEWYL 66 K+ R AL V+ IF AY NI+L++ L + LS D+ +T +VYG VS+K LEWY+ Sbjct: 3 KNARQTALDVLNDIFGNDAYANISLDRNLRDSELSTVDKGFVTALVYGVVSKKALLEWYI 62 Query: 67 AHYVKDRDKLDKWVYYLLMLSLYQLTYLDKLPAHAIVNDAVGIAKNRGNKKGAEKFVNAI 126- +K K W LL+L++YQ+ ++DK+P A V++AV IAK R + + F+NA+ Sbjct: 63 TPLLKKEPK--PWAKMLLLLTIYQVLFMDKVPISAAVDEAVKIAK-RHDGQATANFINAV 119- Query: 127 LRQFTSHPLPDMETIKRRNKYYSVKYSLPVWLVKKLEDQFGSDRSVAIMESLFVRSKASI 18- 6 LR F E K + KYS+P L+ K+ QFG R+ I+ESL S S+ Sbjct: 120 LRNFMRS-----EHRNEEPKDWETKYSMPKLLLDKMVRQFGGKRTGEILESLEKPSHVSL 17- 4 Query: 187 RVTDPLKLEEVAEALDAERSLLSATGLTKASGHFAASDYFTNGDITIQDESSQLVAPTLN 24- 6 R DP E SLL+ T L SG+F+ ++ F G ITIQDE+SQLVAP L Sbjct: 175 RKIDP-----TVEIAGTRPSLLTETALIADSGNFSITEEFQTGRITIQDETSQLVAPQLE 22- 9 Query: 247 IDGDDIILDACSAPGGKTSHIASYLKTGKVIALDLYDHKLELVKENANRLGVADNIETRK 30- 6 ++G + +LDAC+APGGK++H+A YL TG + ALDLY+HKL+L+ +NA R VAD I T+K Sbjct: 230 LEGTEEVLDACAAPGGKSTHMAQYLTTGHITALDLYEHKLDLINQNAQRQHVADKITTQK 28- 9 Query: 307 LDAREVHRHFEKDSFDKILVDAPCSGIGLIRRKPDIKYNKESQGFNALQAIQLEILSSVC 36- 6 DA ++ +F + FD+ILVDAPCSGIGLIRRKPDI+Y KES F LQ IQLEIL+S Sbjct: 290 ADATMIYENFGPEKFDRILVDAPCSGIGLIRRKPDIRYRKESSDFIDLQKIQLEILNSAS 34- 9 Query: 367 QTLRKGGIITYSTCTIFDEENRQVIEAFLQSHPNFEQVKLNHTQADIVKDGYLIITPEQY 42- 6 ++L+K GI+ YSTCTIFDEEN V+ FL++HPNFEQV++++ + +++K+G L ITPE Y Sbjct: 350 KSLKKSGIMVYSTCTIFDEENFDVVHEFLENHPNFEQVEISNEKPEVIKEGCLFITPEMY 40- 9 Query: 427 QTDGFFIGQVRRV 439 TDGFFI + +++ Sbjct: 410 HTDGFFIAKFKKI 422 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02891 Identities = 305/440 (69%), Positives = 370/440 (83%) Query: 1 MANDWKKSARGLALMTLEEVFDKGAYSNIALNKSLKKSRLSDKDRALVTEIVYGTVARKI 60 +A++WKKS RG AL+ +E +FD+GAY+NIALN+ L LS KDRAL+TEIVYGTV+RKI Sbjct: 1 LADNWKKSTRGKALLVIEAIFDQGAYTNIALNQQLSNKALSAKDRALLTEIVYGTVSRKI 60 Query: 61 TLEWYLSHFIVDRDKLELWVYHLLLLSLYQLLYLDNIPDHAIVNDAVTIAKNRGNKKGAE 120- +LEWYL+H++ DRDKL+ WVY+LL+LSLYQL YLD +P HAIVNDAV IAKNRGNKKGAE Sbjct: 61 SLEWYLAHYVKDRDKLDKWVYYLLMLSLYQLTYLDKLPAHAIVNDAVGIAKNRGNKKGAE 120- Query: 121 KLINAVLRRVSSETLPEIASIKRQNKRYSVAYSMPVWLVKKLIDQYGETRALAIMESLFE 18- 0 K +NA+LR+ +S LP++ +IKR+NK YSV YS+PVWLVKKL DQ+G R++AIMESLF Sbjct: 121 KFVNAILRQFTSHPLPDMETIKRRNKYYSVKYSLPVWLVKKLEDQFGSDRSVAIMESLFV 18- 0 Query: 181 RNKASLRVTDLSQKQTIKETLNVRDSHIAETALVADSGNFASTSFFQDGLITIQDESSQL 24- 0 R+KAS+RVTD + + + E L+ S ++ T L SG+FA++ +F +G ITIQDESSQL Sbjct: 181 RSKASIRVTDPLKLEEVAEALDAERSLLSATGLTKASGHFAASDYFTNGDITIQDESSQL 24- 0 Query: 241 VAPTLKVSGNDQVLDACSAPGGKTSHIASYLTTGAVTALDLYDHKLELVMENAKRLGLSD 30- 0 VAPTL + G+D +LDACSAPGGKTSHIASYL TG V ALDLYDHKLELV ENA RLG++D Sbjct: 241 VAPTLNIDGDDIILDACSAPGGKTSHIASYLKTGKVIALDLYDHKLELVKENANRLGVAD 30- 0 Query: 301 KIKTKKLDASKAHEYFLEDTFDKILVDAPCSGIGLIRRKPDIKYNKANQDFEALQEIQLS 36- 0 I+T+KLDA + H +F +D+FDKILVDAPCSGIGLIRRKPDIKYNK +Q F ALQ IQL Sbjct: 301 NIETRKLDAREVHRHFEKDSFDKILVDAPCSGIGLIRRKPDIKYNKESQGFNALQAIQLE 36- 0 Query: 361 ILSSVCQTLRKGGIITYSTCTIFEEENFQVIEKFLENHPNFEQVELSHTQEDIVKRGCIS 42- 0 ILSSVCQTLRKGGIITYSTCTIF+EEN QVIE FL++HPNFEQV+L+HTQ DIVK G + Sbjct: 361 ILSSVCQTLRKGGIITYSTCTIFDEENRQVIEAFLQSHPNFEQVKLNHTQADIVKDGYLI 42- 0 Query: 421 ISPEQYHTDGFFIGQVKRIL 440 I+PEQY TDGFFIGQV+R+L Sbjct: 421 ITPEQYQTDGFFIGQVRRVL 440 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 986 A DNA sequence (GBSx1046) was identified in S. agalactiae <SEQ ID 3019> which encodes the amino acid sequence <SEQ ID 3020>. This protein is predicted to be pppL protein. Analysis of this protein sequence reveals the following: TABLE-US-02892 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5796 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02893 >GP: CAA10712 GB: AJ132604 pppL protein [Lactococcus lactis] Identities = 131/245 (53%), Positives = 177/245 (71%), Gaps = 4/245 (1%) Query: 1 MEISLLTDIGQRRSNNQDFINQFENKAGVPLIILADGMGGHRAGNIASEMTVTDLGSDWA 60 ME S+L+DIG +RS NQD++ + N+AG L +LADGMGGH+AGN+AS++TV DLG W+ Sbjct: 1 MEYSILSDIGSKRSTNQDYVGTYVNRAGYQLFLLADGMGGHKAGNVASKLTVEDLGKLWS 60 Query: 61 ETDF---SELSEIRDWMLVSIETENRKIYELGQSDDYKGMGTTIEAVAIVGDNIIFAHVG 117- ET F + + + W+ + EN I LG+ D+Y+GMGTT+EA+ I G+ I+ AHVG Sbjct: 61 ETFFDAGTPEATLEIWLRNQVRNENENIASLGKLDEYQGMGTTLEALVIKGNTIVSAHVG 120- Query: 118 DSRIGIVRQGEYHLLTSDHSLVNELVKAGQLTEEEAASHPQKNIITQSIGQANPVEPDLG 17- 7 DSR ++R GE + +T+DHSLV ELV AGQ+TEEEA HP KNIIT+S+GQ N V+ D+ Sbjct: 121 DSRTYLMRDGELNKITTDHSLVQELVDAGQITEEEAEVHPNKNIITRSLGQTNEVQADIQ 18- 0 Query: 178 VHLLEEGDYLVVNSDGLTNMLSNADIATVLTQEK-TLDDKNQDLITLANHRGGLDNITVA 23- 6 L+ GD +++NSDGLTNM+S +I VL +E TLD+K++ LI LAN GGLDNITV Sbjct: 181 ALELQAGDIILMNSDGLTNMVSTTEIMEVLEREDLTLDNKSEALIRLANEHGGLDNITVV 24- 0 Query: 237 LVYVE 241 L+ E Sbjct: 241 LIKFE 245 A related DNA sequence was identified in S. pyogenes <SEQ ID 3021> which encodes the amino acid sequence <SEQ ID 3022>. Analysis of this protein sequence reveals the following: TABLE-US-02894 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5301(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02895 Identities = 180/245 (73%), Positives = 220/245 (89%) Query: 1 MEISLLTDIGQRRSNNQDFINQFENKAGVPLIILADGMGGHRAGNIASEMTVTDLGSDWA 60 M+ISL TDIGQ+RSNNQDFIN+F+NK G+ L+ILADGMGGHRAGNIASEMTVTDLG +W Sbjct: 1 MKISLKTDIGQKRSNNQDFINKFDNKKGITLVILADGMGGHRAGNIASEMTVTDLGREWV 60 Query: 61 ETDFSELSEIRDWMLVSIETENRKIYELGQSDDYKGMGTTIEAVAIVGDNIIFAHVGDSR 120- +TDF+ELS+IRDW+ +I++EN++IY+LGQS+D+KGMGTT+EAVA+V + I+AH+GDSR Sbjct: 61 KTDFTELSQIRDWLFETIQSENQRIYDLGQSEDFKGMGTTVEAVALVESSAIYAHIGDSR 120- Query: 121 IGIVRQGEYHLLTSDHSLVNELVKAGQLTEEEAASHPQKNIITQSIGQANPVEPDLGVHL 18- 0 IG+V G Y LLTSDHSLVNELVKAGQ+TEEEAASHPQ+NIITQSIGQA+PVEPDLGV + Sbjct: 121 IGLVHDGHYTLLTSDHSLVNELVKAGQITEEEAASHPQRNIITQSIGQASPVEPDLGVRV 18- 0 Query: 181 LEEGDYLVVNSDGLTNMLSNADIATVLTQEKTLDDKNQDLITLANHRGGLDNITVALVYV 24- 0 LE GDYLV+NSDGLTNM+SN +I T+L + +LD+KNQ++I LAN RGGLDNIT+ALV+ Sbjct: 181 LEPGDYLVINSDGLTNMISNDEIVTILGSKVSLDEKNQEMIDLANLRGGLDNITIALVHN 24- 0 Query: 241 ESEAV 245 ESE V Sbjct: 241 ESEDV 245 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 987 A DNA sequence (GBSx1047) was identified in S. agalactiae <SEQ ID 3023> which encodes the amino acid sequence <SEQ ID 3024>. Analysis of this protein sequence reveals the following: TABLE-US-02896 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.03 Transmembrane 346-362 (340-372) ----- Final Results ----- bacterial membrane --- Certainty = 0.5012(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9539> which encodes amino acid sequence <SEQ ID 9540> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02897 >GP: CAA10713 GB: AJ132604 hypothetical protein [Lactococcus lactis] Identities = 219/380 (57%), Positives = 284/380 (74%), Gaps = 8/380 (2%) Query: 1 MIQIGKLFAGRYRILKSIGRGGMADVYLARDLILDNEEVAIKVLRTNYQTDQIAVARFQR 60 MIQIGK+FA RYRI+K IGRGGMA+VY D L + +VAIKVLR+N++ D IA+ARFQR Sbjct: 1 MIQIGKIFADRYRIIKEIGRGGMANVYQGEDTFLGDRKVAIKVLRSNFENDDIAIARFQR 60 Query: 61 EARAMAELTHPNIVAIRDIGEEDGQQFLVMEYVDGFDLKKYIQDNAPLSNNEVVRIMNEV 120- EA AMAEL+HPNIV I D+GE + QQ++VME+VDG LK+YI NAPL+N+E + I+ E+ Sbjct: 61 EAFAMAELSHPNIVGISDVGEFESQQYIVMEFVDGMTLKQYINQNAPLANDEAIEIITEI 120- Query: 121 LSAMSLAHQKGIVHRDLKPQNILLTKKGTVKVTDFGIAVAFAETSLTQTNSMLGSVHYLS 18- 0 LSAM +AH GI+HRDLKPQN+L++ GTVKVTDFGIA A +ETSLTQTN+M GSVHYLS Sbjct: 121 LSAMDMAHSHGIIHRDLKPQNVLSSSGTVKVTDFGIAKALSETSLTQTNTMFGSVHYLS 180- Query: 181 PEQARGSKATVQSDIYAMGIMLFEMLTGHIPYDGDSAVTIALQHFQKPLPSILAENKSVP 24- 0 PEQARGS ATVQSDIYA+GI+LFE+LTG IP+DGDSAV IAL+HFQ+ +PSI+ N VP Sbjct: 181 PEQARGSNATVQSDIYAIGIILFELLTGQIPFDGDSAVAIALKHFQENIPSIINLNPEVP 24- 0 Query: 241 QALENIVIKATAKKLTDRYKTTYEMGRDLSTALSSTRHREPKLVFN-DTESTKTLPKVTS 29- 9 QALEN+VIKATAK + +RY EM D++T+ S R E KLVFN D + TK +P + Sbjct: 241 QALENVVIKATAKDINNRYADVEEMMTDVATSTSLDRRGEEKLVFNKDHDETKIMP--AN 29- 8 Query: 300 TVSSLTTEQLLRNQKQAKTTEKITPDSASNDKTKSKKKASHRLLGTIMKLFFALCVVGII 35- 9 ++ T+ L+ K+ EK +S++ + K+K K S + G I+ L L V+G Sbjct: 299 LINPYDTKPLI--DKKTDDQEKAQSESSTTENNKNKNKKSKK--GLIISLVVLLLVIGGG 35- 4 Query: 360 VFAYKILVSPTTIRVPDVSN 379 FA+ + +PT ++VP+V+N Sbjct: 355 AFAWAV-STPTNVKVPNVTN 373 A related DNA sequence was identified in S. pyogenes <SEQ ID 3025> which encodes the amino acid sequence <SEQ ID 3026>. Analysis of this protein sequence reveals the following: TABLE-US-02898 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.60 Transmembrane 349-365 (340-370) ----- Final Results ----- bacterial membrane --- Certainty = 0.4439(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02899 >GP:CAA10713 GB:AJ132604 hypothetical protein [Lactococcus lactis] Identities = 209/378 (55%), Positives = 273/378 (71%), Gaps = 8/378 (2%) Query: 1 MIQIGKLFAGRYRILKSIGRGGMADVYLANDLILDNEDVAIKVLRTNYQTDQVAVARFQR 60 MIQIGK+FA RYRI+K IGRGGMA+VY D L + VAIKVLR+N++ D +A+ARFQR Sbjct: 1 MIQIGKIFADRYRIIKEIGRGGMANVYQGEDTFLGDRKVAIKVLRSNFENDDIAIARFQR 60 Query: 61 EARAMAELNHPNIVAIRDIGEEDGQQFLVMEYVDGADLKRYIQNHAPLSNNEVVRIMEEV 120- EA AMAEL+HPNIV I D+GE + QQ++VME+VDG LK+YI +APL+N+E + I+ E+ Sbjct: 61 EAFAMAELSHPNIVGISDVGEFESQQYIVMEFVDGMTLKQYINQNAPLANDEAIEIITEI 120- Query: 121 LSAMTLAHQKGIVHRDLKPQNILLTKEGVVKVTDFGIAVAFAETSLTQTNSMLGSVHYLS 18- 0 LSAM +AH GI+HRDLKPQN+L++ G VKVTDFGIA A +ETSLTQTN+M GSVHYLS Sbjct: 121 LSAMDMAHSHGIIHRDLKPQNVLVSSSGTVKVTDFGIAKALSETSLTQTNTMFGSVHYLS 18- 0 Query: 181 PEQARGSKATIQSDIYAMGIMLFEMLTGHIPYDGDSAVTIALQHFQKPLPSIIEENHNVP 24- 0 PEQARGS AT+QSDIYA+GI+LFE+LTG IP+DGDSAV IAL+HFQ+ +PSII N VP Sbjct: 181 PEQARGSNATVQSDIYAIGIILFELLTGQIPFDGDSAVAIALKHFQENIPSIINLNPEVP 24- 0 Query: 241 QALENVVIRATAKKLSDRYGSTFEMSRDLMTALSYNRSRERKIIF-ENVESTKPLPKVAS 29- 9 QALENVVI+ATAK +++RY EM D+ T+ S +R E K++F ++ + TK +P Sbjct: 241 QALENVVIKATAKDINNRYADVEEMMTDVATSTSLDRRGEEKLVFNKDHDETKIMPANLI 30- 0 Query: 300 GPTASVKLSPPTPTVLTQESRLDQTNQTDALQPPTKKKKSGRFLGTLFKILFSFFIVGVA 35- 9 P + L QE +++ T+ + KK K G + + +L ++G Sbjct: 301 NPYDTKPLIDKKTD--DQEKAQSESSTTENNKNKNKKSKKGLIISLVVLLL----VIGGG 35- 4 Query: 360 LFTYLILTKPTSVKVPNV 377 F + + T PT+VKVPNV Sbjct: 355 AFAWAVST-PTNVKVPNV 371 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-02900 Identities = 390/643 (60%), Positives = 480/643 (73%), Gaps = 29/643 (4%) Query: 1 MIQIGKLFAGRYRILKSIGRGGMADVYLARDLILDNEEVAIKVLRTNYQTDQIAVARFQR 60 MIQIGKLFAGRYRILKSIGRGGMADVYLA DLILDNE+VAIKVLRTNYQTDQ+AVARFQR Sbjct: 1 MIQIGKLFAGRYRILKSIGRGGMADVYLANDLILDNEDVAIKVLRTNYQTDQVAVARFQR 60 Query: 61 EARAMAELTHPNIVAIRDIGEEDGQQFLVMEYVDGFDLKKYIQDNAPLSNNEVVRIMNEV 120- EARAMAEL HPNIVAIRDIGEEDGQQFLVMEYVDG DLK+YIQ++APLSNNEVVRIM EV Sbjct: 61 EARAMAELNHPNIVAIRDIGEEDGQQFLVMEYVDGADLKRYIQNHAPLSNNEVVRIMEEV 120- Query: 121 LSAMSLAHQKGIVHRDLKPQNILLTKKGTVKVTDFGIAVAFAETSLTQTNSMLGSVHYLS 18- 0 LSAM+LAHQKGIVHRDLKPQNILLTK+G VKVTDFGIAVAFAETSLTQTNSMLGSVHYLS Sbjct: 121 LSAMTLAHQKGIVHRDLKPQNILLTKEGVVKVTDFGIAVAFAETSLTQTNSMLGSVHYLS 18- 0 Query: 181 PEQARGSKATVQSDIYAMGIMLFEMLTGHIPYDGDSAVTIALQHFQKPLPSILAENKSVP 24- 0 PEQARGSKAT+QSDIYAMGIMLFEMLTGHIPYDGDSAVTIALQHFQKPLPSI+ EN +VP Sbjct: 181 PEQARGSKATIQSDIYAMGIMLFEMLTGHIPYDGDSAVTIALQHFQKPLPSIIEENHNVP 24- 0 Query: 241 QALENIVIKATAKKLTDRYKTTYEMGRDLSTALSSTRHREPKLVFNDTESTKTLPKVTS- 29- 9 QALEN+VI+ATAKKL+DRY +T+EM RDL TALS R RE K++F + ESTK LPKV S Sbjct: 241 QALENVVIRATAKKLSDRYGSTFEMSRDLMTALSYNRSRERKIIFENVESTKPLPKVASG 30- 0 Query: 300 ----------TVSSLTTEQLLRNQKQAKTTEKITPDSASNDKTKSKKKASHRLLGTIMKL 34- 9 T + LT E L Q T+ + P + KKK S R LGT+ K+ Sbjct: 301 PTASVKLSPPTPTVLTQESRL---DQTNQTDALQPPT--------KKKKSGRFLGTLFKI 34- 9 Query: 350 FFALCVVGIIVFAYKILVSPTTIRVPDVSNKTVAQAKMTLENSGLKVGAIRNIESDSVSE 40- 9 F+ +VG+ +F Y IL PT+++VP+V+ ++ AK L + GLKVG IR IESD+V+E Sbjct: 350 LFSFFIVGVALFTYLILTKPTSVKVPNVAGTSLKVAKQELYDVGLKVGKIRQIESDTVAE 40- 9 Query: 410 GLVVKTDPAAGRSRREGAKVNLYIATPNKSFTLGNYKEHNYKDILKDL-QGKGVKKSLIK 46- 8 G VV+TDP AG ++R+G+ + LY++ NK F + NYK +Y++ + L + GV KS IK Sbjct: 410 GNVVRTDPKAGTAKRQGSSITLYVSIGNKGFDMENYKGLDYQEANNSLIETYGVPKSKIK 46- 9 Query: 469 VKRKINNDYTTGTILAQSLPEGTSFNPDGNKKLTLTVAVNDPMIMPDVTGMTVGEVIETL 52- 8 ++R + N+Y T+++QS G FNP+G K+TL+VAV+D + MP VT + + + TL Sbjct: 470 IERIVTNEYPENTVISQSPSAGDKFNPNGKSKITLSVAVSDTITMPMVTEYSYADAVNTL 52- 9 Query: 529 TDLGLDADNLVFYQMQNGV---YQTVVTPPSSSKIASQDPYYGGEVGLRRGDKVKLYLLG 58- 5 T LG+DA + Y + + + P S + ++ Q PYYG + L ++ LYL Sbjct: 530 TALGIDASRIKAYVPSSSSATGFVPIHSPSSKAIVSGQSPYYGTSLSLSDKGEISLYLYP 58- 9 Query: 586 SKTTNNSSSTPIDSSASSSTGTTTSDSVSSSTDASTSDSSSTS 628 +T ++SSS+ SS SSS ++ +DS + ++ S S +TS Sbjct: 590 EETHSSSSSS---SSTSSSNSSSINDSTAPGSNTELSPSETTS 629 SEQ ID 3024 (GBS297) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 43 (lane 6; MW 75 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 27 (lane 4; MW 100.2 kDa) and in FIG. 159 (lane 24; MW 100 kDa). GBS297-GST was purified as shown in FIG. 223, lane 3. GBS297-His was purified as shown in FIG. 203, lane 8. Based on this analysis; it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 988 A DNA sequence (GBSx1048) was identified in S. agalactiae <SEQ ID 3027> which encodes the amino acid sequence <SEQ ID 3028>. Analysis of this protein sequence reveals the following: TABLE-US-02901 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.91 Transmembrane 60-76 (50-90) INTEGRAL Likelihood = -7.43 Transmembrane 7-23 (3-25) INTEGRAL Likelihood = -5.68 Transmembrane 27-43 (24-46) ----- Final Results ----- bacterial membrane --- Certainty = 0.4163(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02902 >GP: BAB03323 GB: AB035448 hypothetical protein [Staphylococcus aureus] Identities = 53/230 (23%), Positives = 104/230 (45%), Gaps = 14/230 (6%) Query: 5 QFFLLVEAVVLVMGLMKILSDDWTSFIFILAL--ILLALRF-YNNDSRHNFLLTTSLLLL 61 Q ++ A++++ I + F+ +L L +L+ + + Y + R LL+ Sbjct: 9 QMLIIFTALMIIANFYYIFFEK-IGFLLVLLLGCVLVYVGYLYFHKIRGLLAFWIGALLI 67 Query: 62 FLIFMLNPY-IIAAVVFAVLYVLINHFSQVKKKNRYALIQFKNHQLDVKTTRNQWLGTDQ 120- + N Y II VF +L ++ + K K A + +K +W G + Sbjct: 68 AFTLLSNKYTIIILFVFLLLLIVRYLIHKFKPKKVVATDEVMTSPSFIK---QKWFGEQR 124- Query: 121 HESDFYAFEDINIIRISGTDTIDLTNVIVSGQDNVIIIQKVFGDTKVLVPLDVAVKADIS 18- 0 Y +ED+ I G IDLT ++N I+++ + G +V++P++ + ++ Sbjct: 125 TPVYVYKWEDVQIQHGIGDLHIDLTKAANIKENNTIVVRHILGKVQVILPVNYNINLHVA 18- 4 Query: 181 SVYGSVQYFDFEEYDLRNESIKLSQ--EEEYYLLKRVKLVVNTIAGKVEV 228 + YGS Y + + Y + N +I + + + + Y V + V+T G VEV Sbjct: 185 AFYGST-YVNEKSYKVENNNIHIEEMMKPDNY---TVNIYVSTFIGDVEV 230 A related DNA sequence was identified in S. pyogenes <SEQ ID 3029> which encodes the amino acid sequence <SEQ ID 3030>. Analysis of this protein sequence reveals the following: TABLE-US-02903 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.92 Transmembrane 44-60 (36-64) INTEGRAL Likelihood = -8.76 Transmembrane 69-85 (66-105) INTEGRAL Likelihood = -8.70 Transmembrane 24-40 (20-42) INTEGRAL Likelihood = -6.64 Transmembrane 88-104 (85-105) ----- Final Results ----- bacterial membrane --- Certainty = 0.4970(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02904 >GP: BAB03323 GB: AB035448 hypothetical protein [Staphylococcus aureus] Identities = 41/187 (21%), Positives = 85/187 (44%), Gaps = 22/187 (11%) Query: 47 FILILVL--ILLALRF-YNQDSRNNFLLTVSLLFLFLIFMLNPYIIMAVLLGIVYIFINH 103- F+L+L+L +L+ + + Y R + L + + N Y I+ + + ++ + + Sbjct: 33 FLLVLLLGCVLVYVGYLYFHKIRGLLAFWIGALLIAFTLLSNKYTIIILFVFLLLLIV-- 90 Query: 104 FSQVKKKNRFALIRFKEEKIEVNNT--------KHQWIGTANYESDYYCFDDINIIRISG 15- 5 R+ + +FK +K+ + K +W G Y ++D+ I G Sbjct: 91 --------RYLIHKFKPKKVVATDEVMTSPSFIKQKWFGEQRTPVYVYKWEDVQIQHGIG 142- Query: 156 NDTVDLTNVIVTGMDNIIVIRKIFGNTTILVPIDVTVTLDVSSIYGSVDFFRCQQYDLRN 21- 5 + +DLT +N IV+R I G +++P++ + L V++ YGS + + Y + N Sbjct: 143 DLHIDLTKAANIKENNTIVVRHILGKVQVILPVNYNINLHVAAFYGST-YVNEKSYKVEN 20- 1 Query: 216 ESIKFKE 222 +I +E Sbjct: 202 NNIHIEE 208 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02905 Identities = 137/211 (64%), Positives = 175/211 (82%) Query: 1 MKKFQFFLLVEAVVLVMGLMKILSDDWTSFIFILALILLALRFYNNDSRHNFLLTTSLLL 60 MKKFQFFLL+E ++L MG+M IL +D +SFI IL LILLALRFYN DSR+NFLLT SLL Sbjct: 18 MKKFQFFLLIECILLAMGIMTILDNDLSSFILILVLILLALRFYNQDSRNNFLLTVSLLF 77 Query: 61 LFLIFMLNPYIIAAVVFAVLYVLINHFSQVKKKNRYALIQFKNHQLDVKTTRNQWLGTDQ 120- LFLIFMLNPYII AV+ ++Y+ INHFSQVKKKNR+ALI+FK +++V T++QW+GT Sbjct: 78 LFLIFMLNPYIIMAVLLGIVYIFINHFSQVKKKNRFALIRFKEEKIEVNNTKHQWIGTAN 137- Query: 121 HESDFYAFEDINIIRISGTDTIDLTNVIVSGQDNVIIIQKVFGDTKVLVPLDVAVKADIS 18- 0 +ESD+Y F+DINIIRISG DT+DLTNVIV+G DN+I+I+K+FG+T +LVP+DV V D+S Sbjct: 138 YESDYYCFDDINIIRISGNDTVDLTNVIVTGMDNIIVIRKIFGNTTILVPIDVTVTLDVS 19- 7 Query: 181 SVYGSVQYFDFEEYDLRNESIKLSQEEEYYL 211 S+YGSV +F ++YDLRNESIK + + L Sbjct: 198 SIYGSVDFFRCQQYDLRNESIKFKETDNQSL 228 SEQ ID 3028 (GBS66) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 6 (lane 4; MW 25 kDa) and in FIG. 7 (lane 2; MW 24.7 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 989 A DNA sequence (GBSx1049) was identified in S. agalactiae <SEQ ID 3031> which encodes the amino acid sequence <SEQ ID 3032>. This protein is predicted to be histidine kinase (narQ). Analysis of this protein sequence reveals the following: TABLE-US-02906 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.41 Transmembrane 47-63 (40-72) INTEGRAL Likelihood = -9.98 Transmembrane 9-25 (5-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.5564(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02907 >GP: CAB54570 GB: AJ006393 histidine kinase [Streptococcus pneumoniae] Identities = 159/334 (47%), Positives = 239/334 (70%), Gaps = 5/334 (1%) Query: 1 MKKHHYFLAFFYGSVIIFAICFVIIDSLGVNL-VHLYQTSRLWLIEQLIFSIFFLSLAVT 59 MKK Y + + +F +++ L + + L+ + E+ +F + S+++T Sbjct: 1 MKKQAYVIIALTSFLFVFFFSHSLLEILDFDWSIFLHDVEKT---EKFVFLLLVFSMSMT 57 Query: 60 ILLLLTWFLLDDNSKRQINHNLRRILNNQSINVTDDGTEISTNIQRLSKKMNLMTASLQS 119- LL L W +++ S R++ NL+R+L Q + D ++ + + LS K+NL+T +LQ Sbjct: 58 CLLALFWRGIEELSLRKMQANLKRLLAGQEVVQVAD-PDLDASFKSLSGKLNLLTEALQK 116- Query: 120 KENSRILKSQEIVKQERKRIARDLHDTVSQDLFAASMVLSGIAQNVSQLDVDQVGSQLLA 17- 9 EN + + +EI+++ERKRIARDLHDTVSQ+LFAA M+LSGI+Q +LD +++ +QL + Sbjct: 117 AENQSLAQEEEIIEKERKRIARDLHDTVSQELFAAHMILSGISQQALKLDREKMQTQLQS 17- 6 Query: 180 VEEMLQHAQNDLRILLLHLRPVELENKTLSEGFRMILKELTDKSDIEVVYHESILTLPKK 23- 9 V +L+ AQ DLR+LLLHLRPVELE K+L EG +++LKEL DKSD+ V +++ LPKK Sbjct: 177 VTAILETAQKDLRVLLLHLRPVELEQKSLIEGIQILLKELEDKSDLRVSLKQNMTKLPKK 23- 6 Query: 240 IEDNIFRIGQEFISNTLKHSQASRLEVYLNQTENELQLKMIDNGIGFDMDSVYDLSYGLK 29- 9 IE++IFRI QE ISNTL+H+QAS L+VYL QT+ ELQLK++DNGIGF + S+ DLSYGL+ Sbjct: 237 IEEHIFRILQELISNTLRHAQASCLDVYLYQTDVELQLKVVDNGIGFQLGSLDDLSYGLR 29- 6 Query: 300 NIEDRVEDLAGNLQLLSQPGKGVAMDIRLPLVNQ 333 NI++RVED+AG +QLL+ P +G+A+DIR+PL+++ Sbjct: 297 NIKERVEDMAGTVQLLTAPKQGLAVDIRIPLLDK 330 A related DNA sequence was identified in S. pyogenes <SEQ ID 2991> which encodes the amino acid sequence <SEQ ID 2992>. Analysis of this protein sequence reveals the following: TABLE-US-02908 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.22 Transmembrane 49-65 (42-70) INTEGRAL Likelihood = -6.58 Transmembrane 8-24 (5-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.6689(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02909 Identities = 218/337 (64%), Positives = 276/337 (81%), Gaps = 3/337 (0%) Query: 1 MKKHHYFLAFFYGSVIIFAICFVIIDSLGVNLVHLYQTSRLWLIEQLIFSIFFLSLAVTI 60 MKK +Y L + Y ++ I +I FV++D+LG+ +L + LW +E+L FSI L ++VT+ Sbjct: 1 MKKRYYALVWLYSTITILSIVFVVMDNLGITFNYL--RNHLWQVERLGFSILLLIVSVTL 58 Query: 61 LLLLTWFLLDDNSKRQINHNLRRILNNQSINVTDDGTEISTNIQRLSKKMNLMTASLQSK 120- LLLL W ++DDNSKR IN NL+ ILNN+ + + D+ +EI+TN+ RLSKKM+ +TA++Q K Sbjct: 59 LLLLLWIIMDDNSKRNINQNLKYILNNRRLYL-DETSEINTNLSRLSKKMSHLTANMQKK 117- Query: 121 ENSRILKSQEIVKQERKRIARDLHDTVSQDLFAASMVLSGIAQNVSQLDVDQVGSQLLAV 18- 0 E++ IL SQE+VKQERKRIARDLHDTVSQ+LFA+S++LSGI+ ++ QLD Q+ +QL V Sbjct: 118 ESAYILDSQEVVKQERKRIARDLHDTVSQELFASSLILSGISMSLEQLDKTQLQTQLTTV 17- 7 Query: 181 EEMLQHAQNDLRILLLHLRPVELENKTLSEGFRMILKELTDKSDIEVVYHESILTLPKKI 24- 0 E MLQ+AQNDLRILLLHLRP EL N+TLSEG MILKELTDKSDIEV+Y E+I LPK + Sbjct: 178 EAMLQNAQNDLRILLLHLRPTELANRTLSEGLHMILKELTDKSDIEVIYKETIAQLPKTM 23- 7 Query: 241 EDNIFRIGQEFISNTLKHSQASRLEVYLNQTENELQLKMIDNGIGFDMDSVYDLSYGLKN 30- 0 EDN+FRI QEFISNTLRH++ASR+EVYLNQT ELQLKMID+G+GFDMD V DLSYGLKN Sbjct: 238 EDNLFRIAQEFISNTLKHAKASRIEVYLNQTSTELQLKMIDDGVGFDMDQVRDLSYGLKN 29- 7 Query: 301 IEDRVEDLAGNLQLLSQPGKGVAMDIRLPLVNQSEDK 337 IEDRV DLAGNL L+SQ GKGV+MDIRLP+V +D+ Sbjct: 298 IEDRVNDLAGNLHLISQKGKGVSMDIRLPIVKGDDDE 334 A related GBS gene <SEQ ID 8701> and protein <SEQ ID 8702> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-02910 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 14.69 GvH: Signal Score (-7.5): -4.31 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 2 value: -11.41 threshold: 0.0 INTEGRAL Likelihood = -11.41 Transmembrane 47-63 (40-72) INTEGRAL Likelihood = -9.98 Transmembrane 9-25 (5-36) PERIPHERAL Likelihood = 3.61 146 modified ALOM score: 2.78 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5564 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00068## SEQ ID 8702 (GBS31) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 15 (lane 8; MW 64 kDa). It was also expressed as GBS31d in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 151 (lane 8-10; MW 59 kDa) and in FIG. 187 (lane 8; MW 59 kDa). GBS31d was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 151 (lane 11-13; MW 34 kDa) and in FIG. 182 (lane 11; MW 34 kDa). Purified GBS31d-GST is shown in lane 3 of FIG. 237. EXAMPLE 990 A DNA sequence (GBSx1050) was identified in S. agalactiae <SEQ ID 3033> which encodes the amino acid sequence <SEQ ID 3034>. Analysis of this protein sequence reveals the following: TABLE-US-02911 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2706(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02912 >GP: CAB54571 GB: AJ006393 response regulator [Streptococcus pneumoniae] Identities = 154/209 (73%), Positives = 184/209 (87%) Query: 8 IKIVLVDDHEMVRLGLKSFLNLQADVEVIGEASNGLEGIKKALELRPDVVVMDLVMPEMD 67 +KI+LVDDHEMVRLGLKS+ +LQ DVEV+GEASNG +GI ALELRPDV+VMD+VMPEM+ Sbjct: 1 MKILLVDDHEMVRLGLKSYFDLQDDVEVVGEASNGSQGIDLALELRPDVIVMDIVMPEMN 60 Query: 68 GVEATLALLKDWPEAAILVLTSYLDNEKIYPVIEAGAKGYMLKTSSAAEILNAIRKVSRG 127- G++ATLA+LK+WPEA IL++TSYLDNEKI PV++AGAKGYMLKTSSA E+L+A+ KV+ G Sbjct: 61 GIDATLAILKEWPEAKILIVTSYLDNEKIMPVLDAGAKGYMLKTSSADELLHAVSKVAAG 120- Query: 128 EQAIENEVDKKIKAHDKCPALHEGLTARERDILNLLAKGYDNQRIADELFISLKTVKTHV 18- 7 E AIE EV KK++ H LHE LTARERD+L L+AKGY+NQRIAD+LFISLKTVKTHV Sbjct: 121 ELAIEQEVSKKVEYHRNHMELHEELTARERDVLQLIAKGYENQRIADDLFISLKTVKTHV 18- 0 Query: 188 SNILGKLNVADRTQAVVYAFQHHLVPQDD 216 SNIL KL V+DRTQA VYAFQHHLV Q++ Sbjct: 181 SNILAKLEVSDRTQAAVYAFQHHLVGQEE 209 A related DNA sequence was identified in S. pyogenes <SEQ ID 2995> which encodes the amino acid sequence <SEQ ID 2996>. Analysis of this protein sequence reveals the following: TABLE-US-02913 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3094(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02914 Identities = 175/212 (82%), Positives = 192/212 (90%) Query: 5 MDKIKIVLVDDHEMVRLGLKSFLNLQADVEVIGEASNGLEGIKKALELRPDVVVMDLVMP 64 M KIK++LVDDHEMVR+GLKSFLNLQAD++V+GEASNG EG+ AL L+PDV+VMDLVMP Sbjct: 3 MSKIKVILVDDHEMVRMGLKSFLNLQADIDVVGEASNGREGVDLALALKPDVLVMDLVMP 62 Query: 65 EMDGVEATLALLKDWPEAAILVLTSYLDNEKIYPVIEAGAKGYMLKTSSAAEILNAIRKV 124- E+ GVEATL +LK W EA +LVLTSYLDNEKIYPVI+AGAKGYMLKTSSAAEILNAIRKV Sbjct: 63 ELGGVEATLEVLKKWKEAKVLVLTSYLDNEKIYPVIDAGAKGYMLKTSSAAEILNAIRKV 122- Query: 125 SRGEQAIENEVDKKIKAHDKCPALHEGLTARERDILNLLAKGYDNQRIADELFISLKTVK 18- 4 S+GE AIE EVDKKIKAHD+ P LHE LTARE DIL+LLAKGYDNQ IADELFISLKTVK Sbjct: 123 SKGELAIETEVDKKIKAHDQHPDLHEELTAREYDILHLLAKGYDNQTIADELFISLKTVK 18- 2 Query: 185 THVSNILGKLNVADRTQAVVYAFQHHLVPQDD 216 THVSNIL KL V DRTQAVVYAF+HHLVPQDD Sbjct: 183 THVSNILAKLEVGDRTQAVVYAERHHLVPQDD 214 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 991 A DNA sequence (GBSx1051) was identified in S. agalactiae <SEQ ID 3035> which encodes the amino acid sequence <SEQ ID 3036>. Analysis of this protein sequence reveals the following:

TABLE-US-02915 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1688(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02916 >GP: CAB08166 GB: Z94864 putative peptidyl-prolyl cis-trans isomerase [Schizosaccharomyces pombe] Identities = 81/174 (46%), Positives = 109/174 (62%), Gaps = 30/174 (17%) Query: 288 IKTNHGDMTVKLFPDHAPKTVANFIGLAKQGYYDGIIFHRIIPDFMIQGGDPTGTGMGGE 34- 7 ++T+ G + ++L+ +HAPKT NF LAK+GYYDG+IFHR+IPDF+IQGGDPTGTG GG Sbjct: 6 LQTSLGKILIELYTEHAPKTCQNFYTLAKEGYYDGVIFHRVIPDFVIQGGDPTGTGRGGT 65 Query: 348 SIYGESFEDEFSEELYNV-RGALSMANAGPNTNGSQFFIVQNTKIPYAKKELERGGWPTP 40- 6 SIYG+ F+DE +L++ G LSMANAGPNTN SQFFI T P Sbjct: 66 SIYGDKFDDEIHSDLHHTGAGILSMANAGPNTNSSQFFI---TLAP-------------- 108- Query: 407 IAELYAGQGGTPHLDRRHSVFGQLVDQSSFEVLDEIAAVETGSQDKPLEDVVIL 460 TP LD +H++FG++V S V + + T S D+P+E + I+ Sbjct: 109 ----------TPWLDGKHTIFGRVV--SGLSVCKRMGLIRTDSSDRPIEPLKII 150 A related DNA sequence was identified in S. pyogenes <SEQ ID 3037> which encodes the amino acid sequence <SEQ ID 3038>. Analysis of this protein sequence reveals the following: TABLE-US-02917 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2175(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02918 Identities = 381/464 (82%), Positives = 422/464 (90%) Query: 1 MDAKTKYKAKKIKAVFFDIDDTLRVKDTGYMPPSILKVFKALKDKGIVVGIASGRARYGV 60 MDAK KYKAKKIK VFFDIDDTLRVKDTGYMP SI +VFKALI KGI+VGIASGRARYGV Sbjct: 5 MDAKLKYKAKKIKMVFFDIDDTLRVKDTGYMPESIQRVFKALKAKGILVGIASGRARYGV 64 Query: 61 PKEVQDLNADYCVKLNGAYVKDKDKNIIFHRPIPAEYVEQYKKWADTVGIKYGLAGRHEA 120- P+EVQDL+ADYCVKLNGAYVKD K IIF PIPA+ V YKKWAD +GI YG+AGRHEA Sbjct: 65 PQEVQDLHADYCVKLNGAYVKDDAKTIIFQAPIPADVVVAYKKWADDMGIFYGMAGRHEA 124- Query: 121 VLSDRDDLVNDAIDIVYSDLEVNPDFNKEHDIYQMWTFEDKGDSLHLPEPLAEHLRLIRW 18- 0 VLS R+D++++AID VY+ LEV PD+N+ HD+YQMWTFEDKGD L LP LAEHLRL+RW Sbjct: 125 VLSARNDMISNAIDNVYAQLEVCPDYNEYHDVYQMWTFEDKGDGLQLPAELAEHLRLVRW 18- 4 Query: 181 HDHSSDVVLKGTSKALGVSKVVEHLGLKPENILVFGDELNDLELFDYAGLAVAMGVSHPE 24- 0 HD+SSDVVLKGTSKALGVSKVV+HLGLKPENILVFGDELNDLELFDYAG+++AMGVSHP Sbjct: 185 HDNSSDVVLKGTSKALGVSKVVDHLGLKPENILVFGDELNDLELFDYAGISIAMGVSHPL 24- 4 Query: 241 AQKKADFITKKVEEDGILYALEELGLIEKELTFPQVDIENTEGPVAVIKTNHGDMTVKLF 30- 0 Q+KADFITKKVEEDGILYALEELGLI+KEL FPQ+D+ N +GP A IKTNHGDMT+ LF Sbjct: 245 LQEKADFITKKVEEDGILYALEELGLIDKELQFPQLDLPNHKGPKATIKTNHGDMTLVLF 30- 4 Query: 301 PDHAPKTVANFIGLAKQGYYDGIIFHRIIPDFMIQGGDPTGTGMGGESIYGESFEDEFSE 36- 0 PDHAPKTVANF+GLAK+GYYDGIIFHRIIP+FMIQGGDPTGTGM G+SIYGESFEDEFS+ Sbjct: 305 PDHAPKTVANFLGLAKEGYYDGIIFHRIIPEFMIQGGDPTGTGMCGQSIYGESFEDEFSD 36- 4 Query: 361 ELYNVRGALSMANAGPNTNGSQFFIVQNTKIPYAKKELERGGWPTPIAELYAGQGGTPHL 42- 0 ELYN+RGALSMANAGPNTNGSQFFIVQN+KIPYAKKELERGGWP PIA YA GGTPHL Sbjct: 365 ELYNLRGALSMANAGPNTNGSQFFIVQNSKIPYAKKELERGGWPAPIAASYAANGGTPHL 42- 4 Query: 421 DRRHSVFGQLVDQSSFEVLDEIAAVETGSQDKPLEDVVILTIEV 464 DRRH+VFGQLVD++SF+VLD IA VETG+QDKP EDV+I TIEV Sbjct: 425 DRRHTVFGQLVDETSFQVLDLIAGVETGAQDKPKEDVIIETIEV 468 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 992 A DNA sequence (GBSx1052) was identified in S. agalactiae <SEQ ID 3039> which encodes the amino acid sequence <SEQ ID 3040>. This protein is predicted to be ribosomal protein S1 (rpsA). Analysis of this protein sequence reveals the following: TABLE-US-02919 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3126(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02920 >GP:BAB07066 GB:AP001518 polyribonucleotide nucleotidyltransferase (general stress protein 13) [Bacillus halodurans] Identities = 46/120 (38%), Positives = 71/120 (58%), Gaps = 11/120 (9%) Query: 8 KIGDKLKGTVTGIRPYGAFVSLEDGRTGLIHISEIKTGYIDNIYDVLSVGDEVYVQVIDV 67 ++G ++G VTGI+P+GAFV+++D + GL+HISE+ G++ +I DVLSVGDEV V+++ V Sbjct: 5 EVGSIVEGKVTGIKPFGAFVAIDDQKQGLVHISEVAHGFVKDINDVLSVGDEVKVKILSV 64 Query: 68 DEFTQKASLSLRTLEEERHHIQH-----------RHRFSNNRLKIGFKPLEENLPSWVEE 116- DE + K SLS+R +E R GF LE+ L W+++ Sbjct: 65 DEESGKISLSIRATQEAPERPARAPKPRPAGGGGRKPQKGQSQGQGFNTLEDKLKEWLKQ 124- A related DNA sequence was identified in S. pyogenes <SEQ ID 3041> which encodes the amino acid sequence <SEQ ID 3042>. Analysis of this protein sequence reveals the following: TABLE-US-02921 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1832 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02922 Identities = 78/115 (67%), Positives = 100/115 (86%) Query: 7 MKIGDKLKGTVTGIRPYGAFVSLEDGRTGLIHISEIKTGYIDNIYDVLSVGDEVYVQVID 66 MKIGDKL GT+TGI+PYGAFV+LE+G TGLIHISEIKTG+ID+I +L++G++V VQVID Sbjct: 1 MKIGDKLHGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDDIDQLLAIGNQVLVQVID 60 Query: 67 VDEFTQKASLSLRTLEEERHHIQHRHRFSNNRLKIGFKPLEENLPSWVEEGLAYL 121 +DE+++K SLS+RTL EE+ H HRHR+SN+R KIGF+PLEE LP W+EE L +L Sbjct: 61 IDEYSKKPSLSMRTLAEEKQHFFHRHRYSNSRHKIGFRPLEEQLPQWIEESLQFL 115 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 993 A DNA sequence (GBSx1053) was identified in S. agalactiae <SEQ ID 3043> which encodes the amino acid sequence <SEQ ID 3044>. This protein is predicted to be pyruvate formate-lyase 2 activating enzyme (pflA). Analysis of this protein sequence reveals the following: TABLE-US-02923 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2889(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02924 >GP:AAC76934 GB:AE000469 probable pyruvate formate lyase activating enzyme 2 [Escherichia coli K12] Identities = 90/251 (35%), Positives = 142/251 (55%), Gaps = 16/251 (6%) Query: 8 VFNIQHFSIHDGPGIRTTVFLKGCPLRCPWCANPESQKMVPETMR--------------- 52 +FNIQ +S++DG GIRT VF KGCP CPWCANPES +T+R Sbjct: 24 IFNIQRYSLNDGEGIRTVVFFKGCPHLCPWCANPESISGKIQTVRREAKCLHCAKCLRDA 83 Query: 53 -DAITNESVIVGEEKSVDDIIEEVLKDIDFYEESGGGITLSGGEIFAQFEFAKAILKRAK 111- + + +G + S+D + EV+KD F+ SGGG+TLSGGE+ Q EFA L+R + Sbjct: 84 DECPSGAFERIGRDISLDALEREVMKDDIFFRTSGGGVTLSGGEVLMQAEFATRFLQRLR 143- Query: 112 SLGIHTAIETTAYTRHEQFIDLIQYVDFIYTDLKHYNSLKHQEKTMVKNASIIKNIHYAF 17- 1 G+ AIET + + L + D + DLK ++ + ++ + +++N+ Sbjct: 144 LWGVSCAIETAGDAPASKLLPLAKLCDEVLFDLKIMDATQARDVVKMNLPRVLENLRLLV 20- 3 Query: 172 ANGKTIVLRIPVIPNFNDSLEDAEEFACLFDRLDIRQVQLLPFHQFGQNKYQLLNRQYEM 23- 1 + G ++ R+P+IP F S E+ ++ + L+IRQ+ LLPFHQ+G+ KY+LL + + M Sbjct: 204 SEGVNVIPRLPLIPGFTLSRENMQQALDVLIPLNIRQIHLLPFHQYGEPKYRLLGKTWSM 26- 3 Query: 232 EEIAALHPEDL 242 +E+ A D+ Sbjct: 264 KEVPAPSSADV 274 A related DNA sequence was identified in S. pyogenes <SEQ ID 3045> which encodes the amino acid sequence <SEQ ID 3046>. Analysis of this protein sequence reveals the following: TABLE-US-02925 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2209(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02926 Identities = 187/255 (73%), Positives = 220/255 (85%) Query: 4 EKGIVFNIQHFSIHDGPGIRTTVFLKGCPLRCPWCANPESQKMVPETMRDAITNESVIVG 63 ++GIVFNIQHFSIHDGPGIRTTVFLKGCPLRCPWCANPESQ+ PE M + + IVG Sbjct: 3 DRGIVFNIQHFSIHDGPGIRTTVFLKGCPLRCPWCANPESQQKAPEQMLTSDGLNTKIVG 62 Query: 64 EEKSVDDIIEEVLKDIDFYEESGGGITLSGGEIFAQFEFAKAILKRAKSLGIHTAIETTA 123- EEK+VD++IEEVLKD+DFYEESGGG+TLSGGEIFAQF+FA A+LK AK+ G+HTAIETTA Sbjct: 63 EEKTVDEVIEEVLKDLDFYEESGGGMTLSGGEIFAQFDFALALLKAAKAAGLHTAIETTA 122- Query: 124 YTRHEQFIDLIQYVDFIYTDLKHYNSLKHQEKTMVKNASIIKNIHYAFANGKTIVLRIPV 18- 3 + +HEQF+ L+ YVDFIYTDLKHYN L+HQ+ T V+N IIKNIHYAF GK IVLRIPV Sbjct: 123 FAKHEQFVTLVDYVDFIYTDLKHYNQLRHQKVTGVRNDLIIKNIHYAFQAGKEIVLRIPV 18- 2 Query: 184 IPNFNDSLEDAEEFACLFDRLDIRQVQLLPFHQFGQNKYQLLNRQYEMEEIAALHPEDLL 24- 3 IP FNDSL+DA+ F+ LF++L+I QVQLLPFHQFG+NKY+LL R+YEM E+ A HPEDL Sbjct: 183 IPQFNDSLDDAKAFSELFNQLEIDQVQLLPFHQFGENKYKLLGREYEMAEVKAYHPEDLA 24- 2 Query: 244 DYQAIFSKYNIHCYF 258 DYQA+F +NIHCYF Sbjct: 243 DYQAVFLNHNIHCYF 257 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 994 A DNA sequence (GBSx1054) was identified in S. agalactiae <SEQ ID 3047> which encodes the amino acid sequence <SEQ ID 3048>. Analysis of this protein sequence reveals the following: TABLE-US-02927 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1762 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9299> which encodes amino acid sequence <SEQ ID 9300> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02928 >GP:AAC74366 GB:AE000226 putative DEOR-type transcriptional regulator [Escherichia coli K12] Identities = 74/177 (41%), Positives = 113/177 (63%), Gaps = 1/177 (0%) Query: 2 NRLENIISLVSQYQKIDVNTLSELLQVSKVTIRKDLDKLEGKGLLHREHGYAVLNSGDDL 61 +R + I+ +V ++ V L++ VS+VTIR+DL+ LE L R HG+AV DD+ Sbjct: 3 SRQQTILQMVIDQGQVSVTDLAKATGVSEVTIRQDLNTLEKLSYLRRAHGFAVSLDSDDV 62 Query: 62 NVRLSFNHKTKKEIAALAANMVSDNDTILIESGSTCALLAENICQTKRNVTILTNSCFIA 121- R+ N+ K+E+A AA++V +TI IE+GS+ ALLA + + K+NVTI+T S +IA Sbjct: 63 ETRMMSNYTLKRELAEFAASLVQPGETIFIENGSSNALLARTLGEQKKNVTIITVSSYIA 122- Query: 122 NYLREYDSCQIVLLGGEYQSSSQVTVGPLLKKMISLFHVSLAFVGTDGFDPKTRIYG 178 + L++ C+++LLGG YQ S+ VGPL ++ I H S AF+G DG+ P+T G Sbjct: 123 HLLKD-APCEVILLGGVYQKKSESMVGPLTRQCIQQVHFSKAFIGIDGWQPETGFTG 178 A related DNA sequence was identified in S. pyogenes <SEQ ID 3049> which encodes the amino acid sequence <SEQ ID 3050>. Analysis of this protein sequence reveals the following: TABLE-US-02929 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2888 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02930 Identities = 131/171 (76%), Positives = 150/171 (87%) Query: 1 MNRLENIISLVSQYQKIDVNTLSELLQVSKVTIRKDLDKLEGKGLLHREHGYAVLNSGDD 60 MNRLE II LVSQ +KIDVN+LSE L VSKVTIRKDLDKLE KGLL REHGYAVLNSGDD Sbjct: 2 MNRLERIIQLVSQKKKIDVNSLSEQLDVSKVTIRKDLDKLESKGLLRREHGYAVLNSGDD 61 Query: 61 LNVRLSFNHKTKKEIAALAANMVSDNDTILIESGSTCALLAENICQTKRNVTILTNSCFI 120- LNVRLS+N+ K+ IA AA +V DNDTI+IESGSTCALLAE +CQTKRN+ ++TNSCFI Sbjct: 62 LNVRLSYNYNIKRRIAEKAAELVQDNDTIMIESGSTCALLAEVLCQTKRNIKVITNSCFI 121- Query: 121 ANYLREYDSCQIVLLGGEYQSSSQVTVGPLLKKMISLFHVSLAFVGTDGFD 171 ANY+R+Y SCQI+LLGG YQ +S+VTVGPLLK+MISLFHV+ FVGTDGF+ Sbjct: 122 ANYIRQYSSCQIILLGGYYQPNSEVTVGPLLKEMISLFHVNRVFVGTDGFN 172 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 995 A DNA sequence (GBSx1055) was identified in S. agalactiae <SEQ ID 3051> which encodes the amino acid sequence <SEQ ID 3052>. Analysis of this protein sequence reveals the following: TABLE-US-02931 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1672 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02932 >GP:AAG04879 GB:AE004578 probable transcriptional regulator [Pseudomonas aeruginosa] Identities = 20/70 (28%), Positives = 40/70 (56%) Query: 6 GFMGRDLMRSEVAQEMANAADEVIILTDSSKFNQTALVEQLPLSTVSQVITDKHPNSEIA 65 G M + +E+A+ M A ++ ++ DSSK + AL + PLS +++++ D+ P E+ Sbjct: 179 GAMDFSIEEAEIARAMIAQARQLTVIADSSKLGRRALFQVFPLSRINRLVVDRKPTGELW 23- 8 Query: 66 NLFQEAEITI 75 Q+A + + Sbjct: 239 EALQQARVEV 248 There is also homology to SEQ ID 3050. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 996 A DNA sequence (GBSx1056) was identified in S. agalactiae <SEQ ID 3053> which encodes the amino acid sequence <SEQ ID 3054>. This protein is predicted to be transcriptional regulator. Analysis of this protein sequence reveals the following: TABLE-US-02933 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0904 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9541> which encodes amino acid sequence <SEQ ID 9542> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02934 >GP:BAB04499 GB:AP001509 transcriptional regulator [Bacillus halodurans] Identities = 98/309 (31%), Positives = 178/309 (56%), Gaps = 1/309 (0%) Query: 6 ERQKLLAKVAYLYYMEGKSQSEIANELGIYRTTISRMLAKAREEGLVRIEISDFNPEIFQ 65 E ++L+ KVA LYY EG +Q+++A ++G+ R IS++L KA+E+G+V I I D N + Sbjct: 5 EERRLIVKVASLYYFEGWTQAQVAKKIGVSRPVISKLLNKAKEQGIVEIYIKDENIHTVE 64 Query: 66 LESYFKSKYHLKDIEIVSSRKDSDTSEIEKDLAHVAAAMIRKKIKENDKVGIAWGRTLSK 125- LE + KYHLK+ +V + I++ + + + K IK D +GI+WG T+S Sbjct: 65 LEQRLEKKYHLKEAIVVPT-SGLTQDMIKRAIGKATSYYVSKNIKGMDSIGISWGTTVSS 123- Query: 126 VVEAMRPHPVSQVSFVPLAGGPSHINARYHVNTLVYEMSRRFQGSCTFINATLVQENANL 18- 5 V+ ++ +PL GG H N L YE++++ C+++ A + E L Sbjct: 124 FVQEYPYEQHRELKVIPLVGGMGRKFVELHSNLLAYELAKKMNCECSYLYAPAMVEAKEL 18- 3 Query: 186 AKGILTSKYFEGLMDNWEKLDVAIVGVGGKPKSNEQQWLDLLNQDDFQCLDEEAAVGEIT 24- 5 + ++ S+ +++ + +A+VG+G K + + ++ L ++D L + AVG+++ Sbjct: 184 KERLIQSEDIASVLEEGRNVKMAVVGIGSPFKGSTMKVMNYLKEEDIATLKKIGAVGDMS 24- 3 Query: 246 CRFFNHSGDPVNQHLAKRTIGITLEQLQKVPNRIAVAHGNYKAAALLAVLKKGYINHLVT 30- 5 RF++ G P++ L + IGI L++L+++P I V+ G +K ++ A LK GY++ LVT Sbjct: 244 SRFYDALGQPIDHPLNELVIGIDLDELKRIPIVIGVSEGAHKVDSVEAALKGGYLDVLVT 30- 3 Query: 306 DFSTALNIL 314 D STA +++ Sbjct: 304 DDSTAQSLI 312 A related DNA sequence was identified in S. pyogenes <SEQ ID 3055> which encodes the amino acid sequence <SEQ ID 3056>. Analysis of this protein sequence reveals the following: TABLE-US-02935 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2123 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02936 Identities = 165/324 (50%), Positives = 238/324 (72%), Gaps = 1/324 (0%) Query: 3 MKLERQKLLAKVAYLYYMEGKSQSEIANELGIYRTTISRMLAKAREEGLVRIEISDFNPE 62 MK ER++LLAKVAYL+Y++GKSQ+ I+ E+ IYRTT+ RMLAKA+EEG+VRIEI+D++ + Sbjct: 1 MKEERRRLLAKVAYLHYVQGKSQTLISKEMNIYRTTVCRMLAKAKEEGIVRIEIADYDAD 60 Query: 63 IFQLESYFKSKYHLKDIEIVSSRKDSDTSEIEKDLAHVAAAMIRKKIKENDKVGIAWGRT 122- +F LE Y + +Y L+ +++V ++ + + ++A AA + R +K+ DK+G++WG T Sbjct: 61 LFALEEYVRQQYGLEKLDLVPNQVEDTPMDTLTNVAKTAAEVFRHVVKDGDKIGLSWGAT 120- Query: 123 LSKVVEAMRPHPVSQVSFVPLAGGPSHINARYHVNTLVYEMSRRFQGSCTFINATLVQEN 18- 2 LS +++ + P + V PLAGGPSHINA+YHVNTLVY ++R F G+ F+NA ++QE+ Sbjct: 121 LSCLMDELNPKAMKDVFIYPLAGGPSHINAKYHVNTLVYRLARIFHGNSAFMNAMVIQED 18- 0 Query: 183 ANLAKGILTSKYFEGLMDNWEKLDVAIVGVGGKPKSNEQ-QWLDLLNQDDFQCLDEEAAV 24- 1 +LAKGIL SKYF ++ +W++LD+A+VG+GG+P S EQ QW DLL D L E AV Sbjct: 181 KHLAKGILQSKYFNDILTSWDQLDLALVGIGGEPNSLEQSQWRDLLTSSDHDQLKYEKAV 24- 0 Query: 242 GEITCRFFNHSGDPVNQHLAKRTIGITLEQLQKVPNRIAVAHGNYKAAALLAVLKKGYIN 30- 1 GE+ CRFF+ +G PV L RTIGI+LEQL++VP +AVA G +KA A+LA LK G+IN Sbjct: 241 GEVCCRFFDQAGQPVYTGLQDRTIGISLEQLRRVPKTMAVATGKHKAKAILAALKAGFIN 30- 0 Query: 302 HLVTDFSTALNILRLDKDTFVDTI 325 +LVTD T L +L LD+D ++ + Sbjct: 301 YLVTDKETMLAVLALDEDIDLNNV 324 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 997 A DNA sequence (GBSx1057) was identified in S. agalactiae <SEQ ID 3057> which encodes the amino acid sequence <SEQ ID 3058>. This protein is predicted to be PTS enzyme III cel (celC). Analysis of this protein sequence reveals the following:

TABLE-US-02937 Possible site: 55 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9543> which encodes amino acid sequence <SEQ ID 9544> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02938 >GP:AAA23551 GB:M93570 PTS enzyme III cel [Escherichia coli] Identities = 42/102 (41%), Positives = 70/102 (68%) Query: 4 EIIVADQIIMGLILNAGDAKQHIYQALKLAKEGNFAESKIEIELADSALLEAHNLQTQFL 63 E+ ++++MGLI+N+G A+ Y ALK AK+G+FA +K ++ + AL EAH +QT+ + Sbjct: 13 EVEELEEVVMGLIINSGQARSLAYAALKQAKQGDFAAAKAMMDQSRMALNEAHLVQTKLI 72 Query: 64 AQEAGGTRTDISALFIHSQDHLMTSITEINLIKEIIDLRQEL 105 +AG + +S + +H+QDHLMTS+ LI E+I+L ++L Sbjct: 73 EGDAGEGKMKVSLVLVHAQDHLMTSMLARELITELIELHEKL 114 A related DNA sequence was identified in S. pyogenes <SEQ ID 3059> which encodes the amino acid sequence <SEQ ID 3060>. Analysis of this protein sequence reveals the following: TABLE-US-02939 Possible site: 17 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02940 >GP:AAC74806 GB:AE000268 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin [Escherichia coli] Identities = 39/97 (40%), Positives = 66/97 (67%) Query: 7 DQIIMGLILNAGDAKQHIYQALKCAKEDDYATSEKEMALADDALLEAHNLQTQFLAQEAS 66 ++++MGLI+N+G A+ Y ALK AK+ D+A ++ M + AL EAH +QT+ + +A Sbjct: 18 EEVVMGLIINSGQARSLAYAALKQAKQGDFAAAKAMMDQSRMALNEAHLVQTKLIEGDAG 77 Query: 67 GNKSEITALFVHSQDHLMTTITEINLIKEIIDLRKEL 103 K +++ + VH+QDHLMT++ LI E+I+L ++L Sbjct: 78 EGKMKVSLVLVHAQDHLMTSMLARELITELIELHEKL 114 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02941 Identities = 81/103 (78%), Positives = 94/103 (90%) Query: 3 MEIIVADQIIMGLILNAGDAKQHIYQALKLAKEGNFAESKIEIELADSALLEAHNLQTQF 62 M++IV DQIIMGLILNAGDAKQHIYQALK AKE ++A S+ E+ LAD ALLEAHNLQTQF Sbjct: 1 MQVIVPDQIIMGLILNAGDAKQHIYQALKCAKEDDYATSEKEMALADDALLEAHNLQTQF 60 Query: 63 LAQEAGGTRTDISALFIHSQDHLMTSITEINLIKEIIDLRQEL 105 LAQEA G +++I+ALF+HSQDHLMT+ITEINLIKEIIDLR+EL Sbjct: 61 LAQEASGNKSEITALFVHSQDHLMTTITEINLIKEIIDLRKEL 103 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 998 A DNA sequence (GBSx1058) was identified in S. agalactiae <SEQ ID 3061> which encodes the amino acid sequence <SEQ ID 3062>. This protein is predicted to be PTS system, cellobiose-specific IIB component (celA). Analysis of this protein sequence reveals the following: TABLE-US-02942 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02943 >GP: AAF94440 GB: AE004207 PTS system, cellobiose-specific IIB component [Vibrio cholerae] Identities = 46/100 (46%), Positives = 62/100 (62%) Query: 1 MIKIGLFCAAGFSTGMLVNNMKIAADKEGIEAHIEAYSQGKIADYAKDLDVALLGPQVSY 60 M KI L C+AG ST MLV M+ AA+ +GIE I+A S + ++ DV LLGPQV + Sbjct: 1 MKKILLCCSAGMSTSMLVKKMQQAAESKGIECKIDALSVNAFEEAIQEYDVCLLGPQVRF 60 Query: 61 TLDKSKSICDEYGVPIAVIPMADYGMLDGVKVLKLALSLL 100 L++ + DEYG IA I YGM+ G +VL+ AL L+ Sbjct: 61 QLEELRKTADEYGKNIAAISPQAYGMMKGDEVLQQALDLI 100 A related DNA sequence was identified in S. pyogenes <SEQ ID 3063> which encodes the amino acid sequence <SEQ ID 3064>. Analysis of this protein sequence reveals the following: TABLE-US-02944 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02945 >GP: AAF94440 GB: AE004207 PTS system, cellobiose-specific IIB component [Vibrio cholerae] Identities = 43/100 (43%), Positives = 58/100 (58%) Query: 8 MIKIGLFCAAGFSTGMLVNNMKVAAEKKGIDCQIEAYAQGKLADYAPLLDVALLGPQVAY 67 M KI L C+AG ST MLV M+ AAE KGI+C+I+A + + DV LLGPQV + Sbjct: 1 MKKILLCCSAGMSTSMLVKKMQQAAESKGIECKIDALSVNAFEEAIQEYDVCLLGPQVRF 60 Query: 68 TLDKSEAICKDNDIPIAVIPMADYGMLDGNKVLDLALSLV 107 L++ + IA I YGM+ G++VL AL L+ Sbjct: 61 QLEELRKTADEYGKNIAAISPQAYGMMKGDEVLQQALDLI 100 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02946 Identities = 79/101 (78%), Positives = 92/101 (90%) Query: 1 MIKIGLFCAAGFSTGMLVNNMKIAADKEGIEAHIEAYSQGKIADYAKDLDVALLGPQVSY 60 MIKIGLFCAAGFSTGMLVNNMK+AA+K+GI+ IEAY+QGK+ADYA LDVALLGPQV+Y Sbjct: 8 MIKIGLFCAAGFSTGMLVNNMKVAAEKKGIDCQIEAYAQGKLADYAPLLDVALLGPQVAY 67 Query: 61 TLDKSKSICDEYGVPIAVIPMADYGMLDGVKVLKLALSLLE 101 TLDKS++IC + +PIAVIPMADYGMLDG KVL LALSL++ Sbjct: 68 TLDKSEAICKDNDIPIAVIPMADYGMLDGNKVLDLALSLVK 108 SEQ ID 3062 (GBS180) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 39 (lane 4; MW 12.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 41 (lane 2; MW 37.6 kDa). The GBS180-GST fusion product was purified (FIG. 204, lane 8) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 298), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 999 A DNA sequence (GBSx1059) was identified in S. agalactiae <SEQ ID 3065> which encodes the amino acid sequence <SEQ ID 3066>. This protein is predicted to be pts system, cellobiose-specific iic component (celB). Analysis of this protein sequence reveals the following: TABLE-US-02947 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.68 Transmembrane 346-362 (334-374) INTEGRAL Likelihood = -9.77 Transmembrane 182-198 (178-205) INTEGRAL Likelihood = -8.65 Transmembrane 29-45 (27-50) INTEGRAL Likelihood = -6.53 Transmembrane 140-156 (134-161) INTEGRAL Likelihood = -4.78 Transmembrane 292-308 (289-312) INTEGRAL Likelihood = -4.41 Transmembrane 397-413 (395-416) INTEGRAL Likelihood = -2.97 Transmembrane 77-93 (72-93) INTEGRAL Likelihood = -2.97 Transmembrane 228-244 (222-246) ----- Final Results ----- bacterial membrane --- Certainty = 0.5670(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02948 >GP: AAA17390 GB: U07818 cellobiose phosphotransferase enzyme II'' [Bacillus stearothermophilus] Identities = 160/415 (38%), Positives = 251/415 (59%), Gaps = 13/415 (3%) Query: 15 KFVNMRGIIALKDGMLAILPLTVVGSLFLILGQLPFKGLNQAIANVFGPEWTEPFMQVYS 74 - K R + A++DG++ +PL ++GSLFLI+G LP G N+ +A FG W + + Sbjct: 18 KIAEQRHLQAIRDGIILSMPLLIIGSLFLIVGFLPIPGYNEWMAKWFGEHWLDKLLYPVG 77 Query: 75 GTFAIMGLISCFAIAYAYAKNSSVEPLPAGVLSLSSFFILMKSSYIPVKGEA------IA 128- TF IM L+ F +AY A+ V+ L AG +SL++F +L +P E ++ Sbjct: 78 ATFDIMALVVSFGVAYRLAEKYKVDALSAGAISLAAF-LLATPYQVPFTPEGAKETIMVS 136- Query: 129 DAISKVWFGGQGIIGAIIIGLVVGAIYTWFIQHHIVIKMPEQVPQAIAKQFEAMIPAFVI 18- 8 I W G +G+ A+I+ +V IY IQ +IVIK+P+ VP A+A+ F A+IP + Sbjct: 137 GGIPVQWVGSKGLFVAMILAIVSTEIYRKIIQKNIVIKLPDGVPPAVARSFVALIPGAAV 19- 6 Query: 189 FLLSMIVYLIAKVTTGGTFIEMIYDIIQVPLQGLTGSLYGAIGIAFFISFLWWFGVHGQS 24- 8 ++ + LI ++T +F ++ ++ PL L GS++GAI + LW G+HG + Sbjct: 197 LVVVWVARLILEMTPFESFHNIVSVLLNKPLSVLGGSVFGAIVAVLLVQLLWSTGLHGAA 25- 6 Query: 249 VVNGIVTALLLSNLDANKSLLAAN-RLTLDNGAHIVTQQFLDSFLILSGSGITFGLVIAM 30- 7 +V G++ + LS +D N+ + N L N ++TQQF D ++ + GSG T L + M Sbjct: 257 IVGGVMGPIWLSLMDENRMVFQQNPNAELPN---VITQQFFDLWIYIGGSGATLALALTM 31- 3 Query: 308 LFAAKSKQYKALGKVAAFPAIFNVNEPIVFGFPIVMNPVMFLPFILVPVLAALIVYGAIA 36- 7 +F A+S+Q K+LG++A P IFN+NEPI FG PIVMNP++ +PFILVPV+ ++ Y A+A Sbjct: 314 MFRARSRQLKSLGRLAIAPGIFNINEPITFGMPIVMNPLLIIPFILVPVVLVVVSYAAMA 37- 3 Query: 368 VGFMQPFSGVTLPWSTPAIISGFMVGGWQ--GALVQIVILAISTAVYFPFFKIQD 420 G + SGV +PW+TP +ISG++ G + G+++QIV I+ A+Y+PFF I D Sbjct: 374 TGLVAKPSGVAVPWTTPIVISGYLATGGKISGSILQIVNFFIAFAIYYPFFSIWD 428 A related DNA sequence was identified in S. pyogenes <SEQ ID 2215> which encodes the amino acid sequence <SEQ ID 2216>. Analysis of this protein sequence reveals the following: TABLE-US-02949 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.92 Transmembrane 347-363 (335-373) INTEGRAL Likelihood = -7.59 Transmembrane 29-45 (27-50) INTEGRAL Likelihood = -7.38 Transmembrane 182-198 (179-204) INTEGRAL Likelihood = -5.68 Transmembrane 398-414 (395-420) INTEGRAL Likelihood = -4.99 Transmembrane 293-309 (291-314) INTEGRAL Likelihood = -3.61 Transmembrane 140-156 (134-160) INTEGRAL Likelihood = -2.60 Transmembrane 229-245 (229-246) INTEGRAL Likelihood = -0.75 Transmembrane 72-88 (72-88) ----- Final Results ----- bacterial membrane --- Certainty = 0.4567(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02950 Identities = 366/428 (85%), Positives = 402/428 (93%), Gaps = 1/428 (0%) Query: 1 MSKFDSQKIITPIMKFVNMRGIIALKDGMLAILPLTVVGSLFLILGQLPFKGLNQAIANV 60 M+K + Q II PIM FVNMRGIIALKDGMLAILPLTVVGSLFLI GQ+PF+G+N AIA+V Sbjct: 1 MAKMNMQNIIKPIMTFVNMRGIIALKDGMLAILPLTVVGSLFLIAGQIPFQGVNDAIASV 60 Query: 61 FGPEWTEPFMQVYSGTFAIMGLISCFAIAYAYAKNSSVEPLPAGVLSLSSFFILMKSSYI 120- FG +WTEPFMQVY GTFAIMGLISCFAI Y+YAKNS VEPLP+GVLSLS+FFIL++SSY+ Sbjct: 61 FGADWTEPFMQVYHGTFAIMGLISCFAIGYSYAKNSGVEPLPSGVLSLSAFFILLRSSYV 120- Query: 121 PVKGEAIADAISKVWFGGQGIIGAIIIGLVVGAIYTWFIQHHIVIKMPEQVPQAIAKQFE 18- 0 P +GEAI DAISKVWFGGQGIIGAI+IGL VGA+YT FI+ HIVIKMP+QVPQAIAKQFE Sbjct: 121 PAEGEAIGDAISKVWFGGQGIIGAIVIGLTVGAVYTTFIRRHIVIKMPDQVPQAIAKQFE 18- 0 Query: 181 AMIPAFVIFLLSMIVYLIAK-VTTGGTFIEMIYDIIQVPLQGLTGSLYGAIGIAFFISFL 23- 9 AMIPAFVIF LSM+VY+IAK VT GGTFIEMIYD+IQVPLQGLTGSLYGA+GIAFFISFL Sbjct: 181 AMIPAFVIFTLSMLVYIIAKSVTGGGTFIEMIYDVIQVPLQGLTGSLYGALGIAFFISFL 24- 0 Query: 240 WWFGVHGQSVVNGIVTALLLSNLDANKSLLAANRLTLDNGAHIVTQQFLDSFLILSGSGI 29- 9 WWFGVHGQSVVNGIVTALLLSNLDANK+L+AA L+LD GAHIVTQQFLDSFLILSGSGI Sbjct: 241 WWFGVHGQSVVNGIVTALLLSNLDANKALMAAGELSLDKGAHIVTQQFLDSFLILSGSGI 30- 0 Query: 300 TFGLVIAMLFAAKSKQYKALGKVAAFPAIFNVNEPIVFGFPIVMNPVMFLPFILVPVLAA 35- 9 TFGLV+AM+FAAKSKQYKALGKVAAFPA+FNVNEP+VFGFPIVMNPVMFLPFILVPVLAA Sbjct: 301 TFGLVVAMIFAAKSKQYKALGKVAAFPALFNVNEPVVFGFPIVMNPVMFLPFILVPVLAA 36- 0 Query: 360 LIVYGAIAVGFMQPFSGVTLPWSTPAIISGFMVGGWQGALVQIVILAISTAVYFPFFKIQ 41- 9 L VYGAIA+GFMQPF+GVTLPWSTPAIISGFMVGGWQGA+VQI+IL +ST VYFPFFKIQ Sbjct: 361 LTVYGAIAIGFMQPFAGVTLPWSTPAIISGFMVGGWQGAIVQILILIMSTLVYFPFFKIQ 42- 0 Query: 420 DNITYKNE 427 DN+ Y+NE Sbjct: 421 DNMAYQNE 428 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1000 A DNA sequence (GBSx1060) was identified in S. agalactiae <SEQ ID 3067> which encodes the amino acid sequence <SEQ, ID 3068>. This protein is predicted to be formate acetyltransferase 2 (pflB). Analysis of this protein sequence reveals the following: TABLE-US-02951 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5049(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02952 >GP: AAC73910 GB: AE000184 putative formate acetyltransferase [Escherichia coli K12] Identities = 414/805 (51%), Positives = 555/805 (68%), Gaps = 14/805 (1%) Query: 25 LTERMYSYRDKVLD-KKPFIDAERAILVTEAYQKHQEKPNVLKRAYMLQNILEKMTIYID 83 - L++R+ ++++ ++ KP + ERA TE YQ+H +KP ++RA L + L TI+I Sbjct: 9 LSDRIKAHKNALVHIVKPPVCTERAQHYTEMYQQHLDKPIPVRRALALAHHLANRTIWIK 68 Query: 84 DETMIVGNQASSDKDAPIFPEYTLEFVVNELDLFEKRDGDVFYITEETKEQIRNIAPFWE 143- + +I+GNQAS + APIFPEYT+ ++ E+D R G F ++EE K + + P+W Sbjct: 69 HDELIIGNQASEVRAAPIFPEYTVSWIEKEIDDLADRPGAGFAVSEENKRVLHEVCPWWR 128- Query: 144 NNNLRARAGVMLPEEVQVYMETGFFGMEGKMNSGDAHLAVNYQKLLEEGLIGFEKKARKA 20- 3 ++ R M +E + + TG EG M SGDAHLAVN+ LLE+GL G ++ + Sbjct: 129 GQTVQDRCYGMFTDEQKGLLATGIIKAEGNMTSGDAHLAVNFPLLLEKGLDGLREEVAER 18- 8 Query: 204 KADLDLTKPESIDKYHFYDSILITIEAVKTYAERFAILAKKQAKTANAK-RRQELLDIAS 26- 2 ++ ++LT E + F +I I + AV + ERFA LA++ A T + RR ELL +A Sbjct: 189 RSRINLTVLEDLHGEQFLKAIDIVLVAVSEHIERFAALAREMAATETRESRRDELLAMAE 24- 8 Query: 263 ICERVPYYPAETFAEAVQSVWFIQCILQIESNGHSLSYGRFDQYMYPYVKSDLEAGRETE 32- 2 C+ + + P +TF +A+Q +FIQ ILQIESNGHS+S+GR DQY+YPY + D+E + + Sbjct: 249 NCDLIAHQPPQTFWQALQLCYFIQLILQIESNGHSVSFGRMDQYLYPYYRRDVELNQTLD 30- 8 Query: 323 -DSIVERLTNLWIKTITINKVRSQAHTFSSAGSPLYQNVTIGGQTR---HKEDAVNPLSF 37- 8 + +E L + W+K + +NK+RS +H+ +SAGSPLYQNVTIGGQ DAVNPLS+ Sbjct: 309 REHAIEMLHSCWLKLLEVNKIRSGSHSKASAGSPLYQNVTIGGQNLVDGQPMDAVNPLSY 36- 8 Query: 379 LVLKSVAQTHLPQPNLTVRYHANLDKSFMNEAIEVMKLGFGMPAFNNDEIIIPSFIKKGV 43- 8 +L+S + QPNL+VRYHA + F++ ++V++ GFGMPAFNNDEI+IP FIK G+ Sbjct: 369 AILESCGRLRSTQPNLSVRYHAGMSNDFLDACVQVIRCGFGMPAFNNDEIVIPEFIKLGI 42- 8 Query: 439 SEEDAYDYSAIGCVETAVPGKWGYRCTGMSYINFPKVLLITMNDGIDPASGKRFAP---- 49- 4 +DAYDY+AIGC+ETAV GKWGYRCTGMS+INF +V+L + G D SGK F P Sbjct: 429 EPQDAYDYAAIGCIETAVGGKWGYRCTGMSFINFARVMLAALEGGHDATSGKVFLPQEKA 48- 8 Query: 495 -SYGHFTQMTSYKELKEAWDKTLRYLTRMSVIVENAIDISLEREVPDILCSALTDDCIGR 55- 3 S G+F ++ E+ +AWD +RY TR S+ +E +D LE V DILCSAL DDCI R Sbjct: 489 LSAGNFN---NFDEVMDAWDTQIRYYTRKSIEIEYVVDTMLEENVHDILCSALVDDCIER 54- 5 Query: 554 GKHLKEGGAVYDYISGLQVGIANLSDSLAALKKLVFEEKRLTTLEVWQALQSDYAGPRGE 61- 3 K +K+GGA YD++SGLQVGIANL +SLAA+KKLVFE+ + ++ AL D+ G E Sbjct: 546 AKSIKQGGAKYDWVSGLQVGIANLGNSLAAVKKLVFEQGAIGQQQLAAALADDFDGLTHE 60- 5 Query: 614 EIRQMLINEAPKYGNDDDYADSLVRECYDVYVEEIAKYPNTRYGRGPIGGIRYSGTSSIS 67- 3 ++RQ LIN APKYGNDDD D+L+ Y Y++E+ +Y N RYGRGP+GG Y+GTSSIS Sbjct: 606 QLRQRLINGAPKYGNDDDTVDTLLARAYQTYIDELKQYHNPRYGRGPVGGNYYAGTSSIS 66- 5 Query: 674 ANVGQGRGTLATPDGRHAGTPLAEGCSPSHNMDKKGPTSVLKSVSKLPTDEIVGGVLLNQ 73- 3 ANV G T+ATPDGR A TPLAEG SP+ D GPT+V+ SV KLPT I+GGVLLNQ Sbjct: 666 ANVPFGAQTMATPDGRKAHTPLAEGASPASGTDHLGPTAVIGSVGKLPTAAILGGVLLNQ 72- 5 Query: 734 KVNPQTLAKEEDKQKLIALLRTFFNRLHGYHIQYNVVSRETLIDAQKHPEKHRDLIVRVA 79- 3 K+NP TL E DKQKL+ LLRTFF G+HIQYN+VSRETL+DA+KHP+++RDL+VRVA Sbjct: 726 KLNPATLENESDKQKLMILLRTFFEVHKGWHIQYNIVSRETLLDAKKHPDQYRDLVVRVA 78- 5 Query: 794 GYSAFFNVLSKATQDDIIARTEHAL 818 GYSAFF LS QDDIIARTEH L Sbjct: 786 GYSAFFTALSPDAQDDIIARTEHML 810 A related DNA sequence was identified in S. pyogenes <SEQ ID 3069> which encodes the amino acid sequence <SEQ ID 3070>. Analysis of this protein sequence reveals the following: TABLE-US-02953 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4763(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02954 Identities = 694/803 (86%), Positives = 747/803 (92%) Query: 16 QNSQKHFGYLTERMYSYRDKVLDKKPFIDAERAILVTEAYQKHQEKPNVLKRAYMLQNIL 75 - + +FG+LT+RM YR+ VLDKKP+IDAERAIL TEAYQKHQ KP LKRAYMLQ IL Sbjct: 3 ETKSPYFGHLTDRMTHYREAVLDKKPYIDAERAILATEAYQKHQNKPANLKRAYMLQTIL 62 Query: 76 EKMTIYIDDETMIVGNQASSDKDAPIFPEYTLEFVVNELDLFEKRDGDVFYITEETKEQI 135- E MTIYI+DE++I GNQASS+KDAPIFPEYTLEFV+NELDLFEKRDGDVFYITEETK+Q+ Sbjct: 63 ENMTIYIEDESLIAGNQASSNKDAPIFPEYTLEFVLNELDLFEKRDGDVFYITEETKQQL 122- Query: 136 RNIAPFWENNNLRARAGVMLPEEVQVYMETGFFGMEGKMNSGDAHLAVNYQKLLEEGLIG 19- 5 R+IAPFWENNNLRAR GV+LPEEVQVYMETGFFGMEGKMNSGDAHLAVNYQKLLE GL G Sbjct: 123 RDIAPFWENNNLRARCGVLLPEEVQVYMETGFFGMEGKMNSGDAHLAVNYQKLLEHGLKG 18- 2 Query: 196 FEKKARKAKADLDLTKPESIDKYHFYDSILITIEAVKTYAERFAILAKKQAKTANAKRRQ 25- 5 FE++AR AKA LDLT PE+IDKYHFYDS+ I I+AVKTYA+R+A LA++ AKTA +R+ Sbjct: 183 FEERARAAKAALDLTIPENIDKYHFYDSVFIVIDAVKTYAKRYAKLARELAKTAKPERQA 24- 2 Query: 256 ELLDIASICERVPYYPAETFAEAVQSVWFIQCILQIESNGHSLSYGRFDQYMYPYVKSDL 31- 5 ELLDIA IC++VPY PA+TFAEAVQSVWFIQCILQIESNGHSLSYGRFDQYMYPYVK+DL Sbjct: 243 ELLDIARICDKVPYEPAKTFAEAVQSVWFIQCILQIESNGHSLSYGRFDQYMYPYVKADL 30- 2 Query: 316 EAGRETEDSIVERLTNLWIKTITINKVRSQAHTFSSAGSPLYQNVTIGGQTRHKEDAVNP 37- 5 EAGRETED+IVERLTNLWIKT+TINKVRSQAHTFSSAGSPLYQNVTIGGQTR K+DAVNP Sbjct: 303 EAGRETEDTIVERLTNLWIKTLTINKVRSQAHTFSSAGSPLYQNVTIGGQTRDKKDAVNP 36- 2 Query: 376 LSFLVLKSVAQTHLPQPNLTVRYHANLDKSFMNEAIEVMKLGFGMPAFNNDEIIIPSFIK 43- 5 LS+LVL+SVAQT LPQPNLTVRYH LD +FMNE IEVMKLGFGMPA NNDEIIIPSFIK Sbjct: 363 LSYLVLRSVAQTKLPQPNLTVRYHKGLDNTFMNECIEVMKLGFGMPAMNNDEIIIPSFIK 42- 2 Query: 436 KGVSEEDAYDYSAIGCVETAVPGKWGYRCTGMSYINFPKVLLITMNDGIDPASGKRFAPS 49- 5 KGVSEEDAYDYSAIGCVETAVPGKWGYRCTGMSYINFPK+LLITMNDGIDPASGKRFA Sbjct: 423 KGVSEEDAYDYSAIGCVETAVPGKWGYRCTGMSYINFPKILLITMNDGIDPASGKRFAKG 48- 2 Query: 496 YGHFTQMTSYKELKEAWDKTLRYLTRMSVIVENAIDISLEREVPDILCSALTDDCIGRGK 55- 5 +GHF MTSY+ELK AWD TLR +TRMSVIVENAID+ LEREVPDILCSALTDDCIGRGK Sbjct: 483 HGHFKDMTSYEELKAAWDATLREITRMSVIVENAIDLGLEREVPDILCSALTDDCIGRGK 54- 2 Query: 556 HLKEGGAVYDYISGLQVGIANLSDSLAALKKLVFEEKRLTTLEVWQALQSDYAGPRGEEI 61- 5 LKEGGAVYDYISGLQVGIANLSDSLAALKKLVFEE RLT E+W+AL+SD+AG RGE+I Sbjct: 543 TLKEGGAVYDYISGLQVGIANLSDSLAALKKLVFEEGRLTPEELWKALESDFAGERGEDI 60- 2 Query: 616 RQMLINEAPKYGNDDDYADSLVRECYDVYVEEIAKYPNTRYGRGPIGGIRYSGTSSISAN 67- 5 RQMLIN+APKYGNDDDYADSLV E YD Y++EIAKYPNTRYGRGPIGGIRYSGTSSISAN Sbjct: 603 RQMLINDAPKYGNDDDYADSLVVEAYDTYIDEIAKYPNTRYGRGPIGGIRYSGTSSISAN 66- 2 Query: 676 VGQGRGTLATPDGRHAGTPLAEGCSPSHNMDKKGPTSVLKSVSKLPTDEIVGGVLLNQKV 73- 5 VGQG+GTLATPDGRHAGTPLAEGCSP H+MDKKGPTSVLKSV+KLPTDEIVGGVLLNQKV Sbjct: 663 VGQGKGTLATPDGRHAGTPLAEGCSPEHSMDKKGPTSVLKSVAKLPTDEIVGGVLLNQKV 72- 2 Query: 736 NPQTLAKEEDKQKLIALLRTFFNRLHGYHIQYNVVSRETLIDAQKHPEKHRDLIVRVAGY 79- 5 NPQTLAKEEDK KL+ALLRTFFNRLHGYHIQYNVVSRETLIDAQKHPEKHRDLIVRVAGY Sbjct: 723 NPQTLAKEEDKLKLMALLRTFFNRLHGYHIQYNVVSRETLIDAQKHPEKHRDLIVRVAGY 78- 2 Query: 796 SAFFNVLSKATQDDIIARTEHAL 818 SAFFNVLSKATQDDII RTEH L Sbjct: 783 SAFFNVLSKATQDDIIERTEHTL 805 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1001 A DNA sequence (GBSx1061) was identified in S. agalactiae <SEQ ID 3071> which encodes the amino acid sequence <SEQ ID 3072>. Analysis of this protein sequence reveals the following:

TABLE-US-02955 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1024(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02956 >GP: CAA05516 GB: AJ002527 OrfX [Clostridium beijerinckii] Identities = 90/214 (42%), Positives = 131/214 (61%), Gaps = 1/214 (0%) Query: 1 MEFLLDTLNLEAIKKWHHILPLAGVTSNPTIAKKEGDIHFFQRIRDVREIIGREASLHVQ 60 M+ ++D +N+E IK I + GVTSNP+I K G + I+ +RE IG + LHVQ Sbjct: 1 MKLIIDDVNIEKIKDVFSIFQIDGVTSNPSILHKYGKQPYEILIK-IREFIGENSELHVQ 59 Query: 61 VVAKDYQGILDDAAKIRQETDDDIYIKVPVTPDGLAAIKTLKAEGYNITATAIYTSMQGL 120- V+++ +G+L +A KI +E + Y+K+PVT DGL AIK L+ E N+TATAIYT MQ Sbjct: 60 VISESSEGMLKEAHKIIKELGKNTYVKIPVTRDGLKAIKILRKEEINVTATAIYTQMQAY 119- Query: 121 LAISAGADYLAPYFNRMENLDIDATQVIKELAQAIERTGSSSKILAASFKNASQVTKALS 18- 0 LA AGA Y APY NR++NL + QV K++ E+ +++LAASFKN+ QV + Sbjct: 120 LAGKAGAQYAAPYVNRIDNLGANGVQVAKDIHDIFEKNNFKTEVLAASFKNSQQVLELCK 17- 9 Query: 181 QGAQSITAGPDIFESVFAMPSIAKAVNDFADDWK 214 G + T PD+ E + + AV +F D++ Sbjct: 180 YGIGAATISPDVIEGLIKNDCVDVAVENFKKDFE 213 A related DNA sequence was identified in S. pyogenes <SEQ ID 3073> which encodes the amino acid sequence <SEQ ID 3074>. Analysis of this protein sequence reveals the following: TABLE-US-02957 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1090(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02958 Identities = 158/222 (71%), Positives = 194/222 (87%) Query: 1 MEFLLDTLNLEAIKKWHHILPLAGVTSNPTIAKKEGDIHFFQRIRDVREIIGREASLHVQ 60 ME++LDTL+LEAIKKWHHILPLAGVTSNP+IAKKEG+I FF+RIR+VR IIG +AS+HVQ Sbjct: 1 MEYMLDTLDLEAIKKWHHILPLAGVTSNPSIAKKEGEIDFFERIREVRAIIGDKASIHVQ 60 Query: 61 VVAKDYQGILDDAAKIRQETDDDIYIKVPVTPDGLAAIKTLKAEGYNITATAIYTSMQGL 120- V+A+DY+GIL DAA+IR++ D +Y+KVPVT +GLAAIKTLKAEGY+ITATAIYT+ QGL Sbjct: 61 VIAQDYEGILKDAAEIRRQCGDSVYVKVPVTTEGLAAIKTLKAEGYHITATAIYTTFQGL 120- Query: 121 LAISAGADYLAPYFNRMENLDIDATQVIKELAQAIERTGSSSKILAASFKNASQVTKALS 18- 0 LAI AGADYLAPY+NRMENL+ID VI++LA+AI R ++SKILAASFKN +QV K+ + Sbjct: 121 LAIEAGADYLAPYYNRMENLNIDPEAVIEQLAEAINRENANSKILAASFKNVAQVNKSFA 18- 0 Query: 181 QGAQSITAGPDIFESVFAMPSIAKAVNDFADDWKASQHSEHI 222 GAQ+ITAGPD+FE+ FAMPSI KAV+DF DW+A H + I Sbjct: 181 LGAQAITAGPDVFEAGFAMPSIQKAVDDFGKDWEAIHHRKSI 222 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1002 A DNA sequence (GBSx1062) was identified in S. agalactiae <SEQ ID 3075> which encodes the amino acid sequence <SEQ ID 3076>. Analysis of this protein sequence reveals the following: TABLE-US-02959 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3086(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9545> which encodes amino acid sequence <SEQ ID 9546> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02960 >GP: AAA22477 GB: M65289 glycerol dehydrogenase [Bacillus stearothermophilus] Identities = 199/362 (54%), Positives = 271/362 (73%), Gaps = 2/362 (0%) Query: 4 KVFASPSRYIQGKDALFQSIEHIKSLGQTPLILCDDVVYNIVGERFLSYLQD-DLLPHRV 62 +VF SP++Y+QGK+ + + +++ +G +++ D++V+ I G ++ L+ ++ V Sbjct: 5 RVFISPAKYVQGKNVITKIANYLEGIGNKTVVIADEIVWKIAGHTIVNELKKGNIAAEEV 64 Query: 63 SFNGEASDNEINRVVAVAKEKNSDLIIGLGGGKTIDSAKAIADKVNLPVVIAPTVASTDA 122- F+GEAS NE+ R+ +A++ + ++IG+GGGKT+D+AKA+AD+++ +VI PT ASTDA Sbjct: 65 VFSGEASRNEVERIANIARKAEAAIVIGVGGGKTLDTAKAVADELDAYIVIVPTAASTDA 124- Query: 123 PTSALSVIYTDEGAFEKYIFYSKNPDLVLVDTQVIAQAPKRLLASGIADGLATWVEARAV 18- 2 PTSALSVIY+D+G FE Y FY KNPDLVLVDT++IA AP RLLASGIAD LATWVEAR+V Sbjct: 125 PTSALSVIYSDDGVFESYRFYKKNPDLVLVDTKIIANAPPRLLASGIADALATWVEARSV 18- 4 Query: 183 LQKNGIAMAGGRQTLAGVAIAQACERTLFNDSLQALAACDAKVVTKALENVIEANTLLSG 24- 2 ++ G MAGG T+A AIA+ CE+TLF A + AKVVT ALE V+EANTLLSG Sbjct: 185 IKSGGKTMAGGIPTIAAEAIAEKCEQTLFKYGKLAYESVKAKVVTPALEAVVEANTLLSG 24- 4 Query: 243 LGFESAGLAAAHAIHNGFTALSGDIHHLTHGEKVAYGTLTQLFLENRPKEEIDRYINLYQ 30- 2 LGFES GLAAAHAIHNGFTAL G+IHHLTHGEKVA+GTL QL LE ++EI+RYI LY Sbjct: 245 LGFESGGLAAAHAIHNGFTALEGEIHHLTHGEKVAFGTLVQLALEEHSQQEIERYIELYL 30- 4 Query: 303 AIGMPTTLAELHLGDATYEELLKVGQQATIEGETIHEMPFKISAEDVAAALLTVDRYVSN 36- 2 ++ +P TL ++ L DA+ E++LKV + AT EGETIH F ++A+DVA A+ D+Y Sbjct: 305 SLDLPVTLEDIKLKDASREDILKVAKAATAEGETIHN-AFNVTADDVADAIFAADQYAKA 36- 3 Query: 363 HQ 364 ++ Sbjct: 364 YK 365 A related DNA sequence was identified in S. pyogenes <SEQ ID 3077> which encodes the amino acid sequence <SEQ ID 3078>. Analysis of this protein sequence reveals the following: TABLE-US-02961 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.62 Transmembrane 101-117 (98-119) ----- Final Results ----- bacterial membrane --- Certainty = 0.2848(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02962 >GP: AAA22477 GB: M65289 glycerol dehydrogenase [Bacillus stearothermophilus] Identities = 202/357 (56%), Positives = 261/357 (72%), Gaps = 1/357 (0%) Query: 2 KVFASPSRYIQGKNALFTNVKTLKQLGDSPILLCDDVVYGIVGERFESYLIDNGMTPVHV 61 +VF SP++Y+QGKN + L+ +G+ +++ D++V+ I G + L + V Sbjct: 5 RVFISPAKYVQGKNVITKIANYLEGIGNKTVVIADEIVWKIAGHTIVNELKKGNIAAEEV 64 Query: 62 AFNGEASDNEISRVVAIAKENGNDVIIGLGGGKTIDSAKAIADLLAVPVIIAPTIASTDA 121- F+GEAS NE+ R+ IA++ ++IG+GGGKT+D+AKA+AD L ++I PT ASTDA Sbjct: 65 VFSGEASRNEVERIANIARKAEAAIVIGVGGGKTLDTAKAVADELDAYIVIVPTAASTDA 124- Query: 122 PTSALSVIYTDEGAFEKYIFYSKNPDLVLVDTQVICQAPKRLLASGIADGLATWVEARAV 18- 1 PTSALSVIY+D+G FE Y FY KNPDLVLVDT++I AP RLLASGIAD LATWVEAR+V Sbjct: 125 PTSALSVIYSDDGVFESYRFYKKNPDLVLVDTKIIANAPPRLLASGIADALATWVEARSV 18- 4 Query: 182 MQKNGDTMAGGNQTLAGVAIAKACEQTLFADGLKAMASCDRQVVTPALENVIEANTLLSG 24- 1 ++ G TMAGG T+A AIA+ CEQTLF G A S +VVTPALE V+EANTLLSG Sbjct: 185 IKSGGKTMAGGIPTIAAEAIAEKCEQTLFKYGKLAYESVKAKVVTPALEAVVEANTLLSG 24- 4 Query: 242 LGFESAGLAAAHAIHNGFTALTGAIHHLTHGEKVAYGTLTQLFLENRSREEIDRYIDFYQ 30- 1 LGFES GLAAAHAIHNGFTAL G IHHLTHGEKVA+GTL QL LE S++EI+RYI+ Y Sbjct: 245 LGFESGGLAAAHAIHNGFTALEGEIHHLTHGEKVAFGTLVQLALEEHSQQEIERYIELYL 30- 4 Query: 302 AIGMPTTLKEMHLDTATQEDFLKIGRQATMAGETIHQMPFVISPEDVAAALVAVDAY 358 ++ +P TL+++ L A++ED LK+ + AT GETIH F ++ +DVA A+ A D Y Sbjct: 305 SLDLPVTLEDIKLKDASREDILKVAKAATAEGETIHN-AFNVTADDVADAIFAADQY 360 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02963 Identities = 287/361 (79%), Positives = 325/361 (89%), Gaps = 1/361 (0%) Query: 3 MKVFASPSRYIQGKDALFQSIEHIKSLGQTPLILCDDVVYNIVGERFLSYLQDD-LLPHR 61 MKVFASPSRYIQGK+ALF +++ +K LG +P++LCDDVVY IVGERF SYL D+ + P Sbjct: 1 MKVFASPSRYIQGKNALFTNVKTLKQLGDSPILLCDDVVYGIVGERFESYLIDNGMTPVH 60 Query: 62 VSFNGEASDNEINRVVAVAKEKNSDLIIGLGGGKTIDSAKAIADKVNLPVVIAPTVASTD 121- V+FNGEASDNEI+RVVA+AKE +D+IIGLGGGKTIDSAKAIAD + +PV+IAPT+ASTD Sbjct: 61 VAFNGEASDNEISRVVAIAKENGNDVIIGLGGGKTIDSAKAIADLLAVPVIIAPTIASTD 120- Query: 122 APTSALSVIYTDEGAFEKYIFYSKNPDLVLVDTQVIAQAPKRLLASGIADGLATWVEARA 18- 1 APTSALSVIYTDEGAFEKYIFYSKNPDLVLVDTQVI QAPKRLLASGIADGLATWVEARA Sbjct: 121 APTSALSVIYTDEGAFEKYIFYSKNPDLVLVDTQVICQAPKRLLASGIADGLATWVEARA 18- 0 Query: 182 VLQKNGIAMAGGRQTLAGVAIAQACERTLFNDSLQALAACDAKVVTKALENVIEANTLLS 24- 1 V+QKNG MAGG QTLAGVAIA+ACE+TLF D L+A+A+CD +VVT ALENVIEANTLLS Sbjct: 181 VMQKNGDTMAGGNQTLAGVAIAKACEQTLFADGLKAMASCDRQVVTPALENVIEANTLLS 24- 0 Query: 242 GLGFESAGLAAAHAIHNGFTALSGDIHHLTHGEKVAYGTLTQLFLENRPKEEIDRYINLY 30- 1 GLGFESAGLAAAHAIHNGFTAL+G IHHLTHGEKVAYGTLTQLFLENR +EEIDRYI+ Y Sbjct: 241 GLGFESAGLAAAHAIHNGFTALTGAIHHLTHGEKVAYGTLTQLFLENRSREEIDRYIDFY 30- 0 Query: 302 QAIGMPTTLAELHLGDATYEELLKVGQQATIEGETIHEMPFKISAEDVAAALLTVDRYVSN 3- 62 QAIGMPTTL E+HL AT E+ LK+G+QAT+ GETIH+MPF IS EDVAAAL+ VD YV++ Sbjct: 301 QAIGMPTTLKEMHLDTATQEDFLKIGRQATMAGETIHQMPFVISPEDVAAALVAVDAYVTS 3- 61 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1003 A DNA sequence (GBSx1063) was identified in S. agalactiae <SEQ ID 3079> which encodes the amino acid sequence <SEQ ID 3080>. Analysis of this protein sequence reveals the following: TABLE-US-02964 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.75 Transmembrane 262-278 (262-279) ----- Final Results ----- bacterial membrane --- Certainty = 0.1298(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02965 >GP:BAA88310 GB:AB028865 O-acetylserine lyase [Streptococcus suis] Identities = 239/304 (78%), Positives = 273/304 (89%) Query: 4 IYNSITDLIGNTPIIQLHHIVPEGAAEVYVKLESFNPGSSVKDRIALAMIEDAEQKGILK 63 IY +IT L+G TP+I+L++IVPEGAAEVYVKLE+FNPGSSVKDRIALAMIEDAE+ G +K Sbjct: 3 IYQNITQLVGKTPVIKLNNIVPEGAAEVYVKLEAFNPGSSVRDRIALAMIEDAEKAGTIK 62 Query: 64 AGDTIVEPTSGNTGIGLAWVGKAKGYNVIIVMPETMSIERRKIIQAYGAQLVLTPGSEGM 123- GDTIVEPTSGNTGIGLAWVG AKGYNVIIVMPETMS+ERRKIIQAYGA+LVLTPGSEGM Sbjct: 63 PGDTIVEPTSGNTGIGLAWVGAAKGYNVIIVMPETMSVERRKIIQAYGAELVLTPGSEGM 122- Query: 124 KGAIAKAKEISAEQNAWLPLQFNNQANPEIHEKTTGREIIETFGEKGLDAFIAGVGTGGT 18- 3 KGAIAKAKEI+ E+N W+P QF N +NP++HE TTG+EI+E FG GLDAF++GVGTGGT Sbjct: 123 KGAIAKAKEIAEEKNGWVPFQFANPSNPKVHEDTTGQEILEDFGTTGLDAFVSGVGTGGT 18- 2 Query: 184 ITGVSRALKKVNPDVAIYAVEADESAILSGEQPGPHKIQGISAGFIPETLATDSYDHIIR 24- 3 ++GVS LK NPD+AIYAVEADESA+LSGE PGPHKIQGISAGFIP+TL T +YD IIR Sbjct: 183 VSGVSHVLKTANPDIAIYAVEADESAVLSGEAPGPHKIQGISAGFIPDTLDTSAYDGIIR 24- 2 Query: 244 VTSDDAIETGRIIGGLEGFLAGISASAAIYAAIEVAKQLGKGKKVLALLPDNGERYLSTS 30- 3 V SDDA+ TGR IGG EGFL GIS+ AAI+AAIEVAK+LG GKKVLA+LPDNGERYLST+ Sbjct: 243 VKSDDALATGRAIGGKEGFLVGISSGAAIHAAIEVAKELGTGKKVLAILPDNGERYLSTA 30- 2 Query: 304 LYDF 307 LY+F Sbjct: 303 LYEF 306 A related DNA sequence was identified in S. pyogenes <SEQ ID 3081> which encodes the amino acid sequence <SEQ ID 3082>. Analysis of this protein sequence reveals the following: TABLE-US-02966 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.48 Transmembrane 262-278 (262-278) ----- Final Results ----- bacterial membrane --- Certainty = 0.1192(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02967 >GP:BAA88310 GB:AB028865 O-acetylserine lyase [Streptococcus suis] Identities = 235/303 (77%), Positives = 261/303 (85%) Query: 4 IYKTITELVGQTPIIKLNRLIPNEAADVYVKLEAFNPGSSVKDRIALSMIEAAEAEGLIS 63 IY+ IT+LVG+TP+IKLN ++P AA+VYVKLEAFNPGSSVKDRIAL+MIE AE G I Sbjct: 3 IYQNITQLVGKTPVIKLNNIVPEGAAEVYVKLEAFNPGSSVKDRIALAMIEDAEKAGTIK 62 Query: 64 PGDVIIEPTSGNTGIGLAWVGAAKGYRVIIVMPETMSLERRQIIQAYGAELVLTPGAEGM 123- PGD I+EPTSGNTGIGLAWVGAAKGY VIIVMPETMS+ERR+IIQAYGAELVLTPG+EGM Sbjct: 63 PGDTIVEPTSGNTGIGLAWVGAAKGYNVIIVMPETMSVERRKIIQAYGAELVLTPGSEGM 122- Query: 124 KGAIAKAETLAIELGAWMPMQFNNPANPSIHEKTTAQEILEAFKEISLDAFVSGVGTGGT 18- 3 KGAIAEA+ +A E W+P QF NP+NP +HE TT QEILE F LDAFVSGVGTGGT Sbjct: 123 KGAIAKAKEIAEEKNGWVPFQFANPSNPKVHEDTTGQEILEDFGTTGLDAFVSGVGTGGT 18- 2 Query: 184 LSGVSHVLKKANPETVIYAVEAEESAVLSGQEPGPHKIQGISAGFIPNTLDTKAYDQIIR 24- 3 +SGVSHVLK ANP+ IYAVEA+ESAVLSG+ PGPHKIQGISAGFIP+TLDT AYD IIR Sbjct: 183 VSGVSHVLKTANPDIAIYAVEADESAVLSGEAPGPHKIQGISAGFIPDTLDTSAYDGIIR 24- 2 Query: 244 VKSKDALETARLTGAKEGFLVGISSGAALYAAIEVAKQLGKGKHVLTILPDNGERYLSTE 30- 3 VKS DAL T R G KEGFLVGISSGAA++AAIEVAK+LG GK VL ILPDNGERYLST Sbjct: 243 VKSDDALATGRAIGGKEGFLVGISSGAAIHAAIEVAKELGTGKKVLAILPDNGERYLSTA 30- 2 Query: 304 LYD 306 LY+ Sbjct: 303 LYE 305 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02968 Identities = 222/306 (72%), Positives = 263/306 (85%) Query: 1 MSKIYNSITDLIGNTPIIQLHHIVPEGAAEVYVKLESFNPGSSVKDRIALAMIEDAEQKG 60 M+KIY +IT+L+G TPII+L+ ++P AA+VYVKLE+FNPGSSVKDRIAL+MIE AE +G Sbjct: 1 MTKIYKTITELVGQTPIIKLNRLIPNEAADVYVKLEAFNPGSSVKDRIALSMIEAAEAEG 60 Query: 61 ILKAGDTIVEPTSGNTGIGLAWVGKAKGYNVIIVMPETMSIERRKIIQAYGAQLVLTPGS 120- ++ GD I+EPTSGNTGIGLAWVG AKGY VIIVMPETMS+ERR+IIQAYGA+LVLTPG+ Sbjct: 61 LISPGDVIIEPTSGNTGIGLAWVGAAKGYRVIIVMPETMSLERRQIIQAYGAELVLTPGA 120- Query: 121 EGMKGAIAKAKEISAEQNAWLPLQFNNQANPEIHEKTTGREIIETFGEKGLDAFIAGVGT 18- 0 EGMKGAIAKA+ ++E AW+P+QFNN ANP IHEKTT +EI+E F E LDAF++GVGT Sbjct: 121 EGMKGAIAKAETLAIELGAWMPMQFNNPANPSIHEKTTAQEILEAFKEISLDAFVSGVGT 18- 0 Query: 181 GGTITGVSRALKKVNPDVAIYAVEADESAILSGEQPGPHKIQGISAGFIPETLATDSYDH 24- 0 GGT++GVS LKK NP+ IYAVEA+ESA+LSG++PGPHKIQGISAGFIP TL T +YD Sbjct: 181 GGTLSGVSHVLKKANPETVIYAVEAEESAVLSGQEPGPHKIQGISAGFIPNTLDTKAYDQ 24- 0 Query: 241 IIRVTSDDAIETGRIIGGLEGFLAGISASAAIYAAIEVAKQLGKGKKVLALLPDNGERYL 30- 0 IIRV S DA+ET R+ G EGFL GIS+ AA+YAAIEVAKQLGKGK VL +LPDNGERYL Sbjct: 241 IIRVKSKDALETARLTGAKEGFLVGISSGAALYAAIEVAKQLGKGKHVLTILPDNGERYL 30- 0 Query: 301 STSLYD 306 ST LYD Sbjct: 301 STELYD 306 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1004 A DNA sequence (GBSx1064) was identified in S. agalactiae <SEQ ID 3083> which encodes the amino acid sequence <SEQ ID 3084>. Analysis of this protein sequence reveals the following: TABLE-US-02969 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3666(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-02970 >GP: BAB07349 GB: AP001519 unknown conserved protein [Bacillus halodurans] Identities = 96/204 (47%), Positives = 127/204 (62%) Query: 2 NYKTIKSDGIVEEEIKKSRFICHLKRVESEEEGRNYITQIKKAHYKANHSCSAMVIGEKG 61 +Y T+K GI E I+KSRFI HL R SEEE +I QIKK H+ A H+CSA +IGE Sbjct: 4 SYYTVKESGIHEISIQKSRFIAHLSRATSEEEAIQFIEQIKKEHWNATHNCSAYLIGEND 63 Query: 62 DIKRSSDDGEPSGTAGIPMLTVLEKQGLTNVVAVVTRYFGGIKLGAGGLIRAYSGSVANT 121- +++++DDGEPSGTAG+PML VL+K+ L + VAVVTRYFGG+KLGAGGLIRAY +V++ Sbjct: 64 QVQKANDDGEPSGTAGVPMLEVLKKRRLKDTVAVVTRYFGGVKLGAGGLIRAYGSAVSDG 123- Query: 122 IKEIGVVEVKEQIGIRIQLTYPQYQTFDNFLKEHHLQEFETEFLEAVTCKIYVDPKEFEH 18- 1 + IGVVE K I + Y +N L++ H E +LE V + YV E E Sbjct: 124 LNAIGVVERKRMQVIHTSIDYHWLGKVENELRQSHYLLKEISYLENVDVQTYVLEAEVES 18- 3 Query: 182 TITNLTEFYQGKALLTEEGSQIVE 205 +T G+A T + +E Sbjct: 184 YCEWMTNLTNGQAAFTHGAIEYLE 207 A related DNA sequence was identified in S. pyogenes <SEQ ID 3085> which encodes the amino acid sequence <SEQ ID 3086>. Analysis of this protein sequence reveals the following: TABLE-US-02971 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 86-102 (86-102) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9153> which encodes the amino acid sequence <SEQ ID 9154>. Analysis of this protein sequence reveals the following: TABLE-US-02972 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 81-97 (81-97) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02973 Identities = 122/206 (59%), Positives = 153/206 (74%) Query: 2 NYKTIKSDGIVEEEIKKSRFICHLKRVESEEEGRNYITQIKKAHYKANHSCSAMVIGEKG 61 ++KTIK+ G EE IKKSRFICH+KRV +EE+G+N++ IKK HYKANHSC AM+IG Sbjct: 8 HFKTIKASGFFEESIKKSRFICHIKRVSTEEDGKNFVNAIKKEHYKANHSCFAMIIGNNR 67 Query: 62 DIKRSSDDGEPSGTAGIPMLTVLEKQGLTNVVAVVTRYFGGIKLGAGGLIRAYSGSVANT 121- IKRSSDDGEPSGTAGIP+L+VLEKQ LTNVV VVTRYFGGIKLG GGLIRAYS A Sbjct: 68 QIKRSSDDGEPSGTAGIPILSVLEKQCLTNVVVVVTRYFGGIKLGTGGLIRAYSNMTATA 127- Query: 122 IKEIGVVEVKEQIGIRIQLTYPQYQTFDNFLKEHHLQEFETEFLEAVTCKIYVDPKEFEH 18- 1 IK G++EVK+QIG+ I L+YPQYQ + N L + L E ET+F + + +Y D + E+ Sbjct: 128 IKRFGIIEVKQQIGLEITLSYPQYQLYSNLLDQLALTETETKFSDTIKTTLYCDTERVEN 18- 7 Query: 182 TITNLTEFYQGKALLTEEGSQIVEIP 207 I LT +Y G+ + GS+++E P Sbjct: 188 LIDTLTNYYHGQISCEKIGSKVIEFP 213 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1005 A DNA sequence (GBSx1065) was identified in S. agalactiae <SEQ ID 3087> which encodes the amino acid sequence <SEQ ID 3088>. Analysis of this protein sequence reveals the following: TABLE-US-02974 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1421(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02975 >GP: AAC44940 GB: U56901 involved in transformation [Bacillus subtilis] Identities = 160/405 (39%), Positives = 228/405 (55%), Gaps = 20/405 (4%) Query: 35 YICTRCSSSVAKNCQL----PTGNYYCRECIVFGRVTSNENLYYFPQKTFSKTNSLK--W 88 - Y C RC + + YCR C++ GRV+ LY + ++ S S+K W Sbjct: 58 YRCNRCGQTDQRYFSFYHSSGKNKLYCRSCVMMGRVSEEVPLYSWKEENESNWKSIKLTW 117- Query: 89 KGELTPYQNEVSEELLKGISSKENLLVHAVTGAGKTEMIYHSVAKVIDTGGSVCIASPRI 148- G+L+ Q + + L++ IS KE LL+ AV GAGKTEM++ + ++ G VCIA+PR Sbjct: 118 DGKLSSGQQKAANVLIEAISKKEELLIWAVCGAGKTEMLFPGIESALNQGLRVCIATPRT 17- 7 Query: 149 DVCLELYKRLSNDFRCA-ITLMHGESPSYQR-SPLTIATTHQLLKFYHAFDLLIVDEVDA 20- 6 DV LEL RL F+ A I+ ++G S R SPL I+TTHQLL++ A D++I+DEVDA Sbjct: 178 DVVLELAPRLKAAFQGADISALYGGSDDKGRLSPLMISTTHQLLRYKDAIDVMIIDEVDA 23- 7 Query: 207 FPYVDNPILYQGVKQALKENGTSIFLTATSTTELERKVARKELKKLHLARRFHANPLVIP 26- 6 FPY + L V++A K+N T ++L+AT EL+RK +L + + R H PL P Sbjct: 238 FPYSADQTLQFAVQKARKKNSTLVYLSATPPKELKRKALHGQLHSVRIPARHHRKPLPEP 29- 7 Query: 267 EMVWVSGIQKSLQTQKLPPKLYQLINKQRQTRYPLLLFFPHISEGQVFTEILRQAFPMEK 32- 6 VW +K L K+PP + + I + P+ LF P +S IL +A K Sbjct: 298 RFVWCGNWKKKLNRNKIPPAVKRWIEFHVKEGRPVFLFVPSVS-------ILEKAAACFK 35- 0 Query: 327 -----IGFVSSKSTSRLKLVQDFRDNKLSILVSTTILERGVTFPSVDVFVIQANHHLFTK 38- 1 V ++ R + VQ FRD +L +L++TTILERGVT P V V+ A +FT+ Sbjct: 351 GVHCRTASVHAEDKHRKEKVQQFRDGQLDLLITTTILERGVTVPKVQTGVLGAESSIFTE 41- 0 Query: 382 SSLVQISGRVGRALERPEGLLYFLHDGKSKSMHQAIKEIKNMNHI 426 S+LVQI+GR GR E +G + + H GK+KSM A K IK MN + Sbjct: 411 SALVQIAGRTGRHKEYADGDVIYFHFGKTKSMLDARKHIKEMNEL 455 A related DNA sequence was identified in S. pyogenes <SEQ ID 3089> which encodes the amino acid sequence <SEQ ID 3090>. Analysis of this protein sequence reveals the following: TABLE-US-02976 Possible site: 21 >>> Seems to have no N-terminal signal sequence. INTEGRAL Likelihood = -4.09 Transmembrane 304-320 (303-322) ----- Final Results ----- bacterial membrane --- Certainty = 0.2635(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-02977 !GB: U56901 involved in transformation [Bacillus subt . . . 258 1e-67 >GP: AAC44940 GB: U56901 involved in transformation [Bacillus subtilis] Identities = 155/435 (35%), Positives = 249/435 (56%), Gaps = 20/435 (4%) Query: 10 RLLLESQLPDSAKQLAQPLK--------SVVILRGKMICQRCHYQLDEEA-----RLPSG 56 - R LL ++L S + + +K S+ I + + C RC Q D+ Sbjct: 22 RHLLRTELSFSDEMIEWHIKNGYITAENSISINKRRYRCNRCG-QTDQRYFSFYHSSGKN 80 Query: 57 AYYCRFCLVFGRNQSDKLLYAIPPMHFP--KGNYLVWGGQLTAYQEMISQQLLINMQNQK 114- YCR C++ GR + LY+ + K L W G+L++ Q+ + L+ + ++ Sbjct: 81 KLYCRSCVMMGRVSEEVPLYSWKEENESNWKSIKLTWDGKLSSGQQKAANVLIEAISKKE 140- Query: 115 TTLVHAVTGAGKTEMIYAAIEAVINTGGWVCIASPRVDVCVEVATRLSQAFS-CSICLMH 17- 3 L+ AV GAGKTEM++ IE+ +N G VCIA+PR DV +E+A RL AF I ++ Sbjct: 141 ELLIWAVCGAGKTEMLFPGIESALNQGLRVCIATPRTDVVLELAPRLKAAFQGADISALY 20- 0 Query: 174 AESLPYQR-APIIVATTHQLLKFHKAFDLLIIDEVDAFPFVNNIQLHYAASQALKEGGAK 23- 2 S R +P++++TTHQLL++ A D++IIDEVDAFP+ + L +A +A K+ Sbjct: 201 GGSDDKGRLSPLMISTTHQLLRYKDAIDVMIIDEVDAFPYSADQTLQFAVQKARKKNSTL 26- 0 Query: 233 ILLTATSTRTLERKVNKGEVVKLTLARRFHNRPLVIPKFIRSFNLFKMIHRQKLPLKILK 29- 2 + L+AT + L+RK G++ + + R H +PL P+F+ N K ++R K+P + + Sbjct: 261 VYLSATPPKELKRKALNGQLHSVRIPARHHRKPLPEPRFVWCGNWKKKLNRNKIPPAVKR 32- 0 Query: 293 YLKKQRKTGYPLLIFLPTIIMAESVTAILKELLPAEQIACVSSQSQNRKEDITAFRQGKK 35- 2 +++ K G P+ +F+P++ + E A K + + A V ++ ++RKE + FR G+ Sbjct: 321 WIEFHVKEGRPVFLFVPSVSILEKAAACFKGV--HCRTASVHAEDKHRKEKVQQFRDGQL 37- 8 Query: 353 TILITTSILERGVTFPQIDVFVLGSHHRVYSSQSLVQIAGRVGRSIDRPDGTLYFFHEGI 41- 2 +LITT+ILERGVT P++ VLG+ +++ +LVQIAGR GR + DG + +FH G Sbjct: 379 DLLITTTILERGVTVPKVQTGVLGAESSIFTESALVQIAGRTGRHKEYADGDVIYFHFGK 43- 8 Query: 413 SKAMLLARKEIKEMN 427 +K+ML ARK IKEMN Sbjct: 439 TKSMLDARKHIKEMN 453 An alignment of the GAS and GBS proteins is shown below. TABLE-US-02978 Identities = 223/427 (52%), Positives = 299/427 (69%) Query: 1 MENYLGRLWTKAQLSEQLRKIAISLPSFIKKGSDYICTRCSSSVAKNCQLPTGNYYCREC 60 +EN GRL ++QL + +++A L S + IC RC + + +LP+G YYCR C Sbjct: 4 IENSYGRLLLESQLPDSAKQLAQPLKSVVILRGKMICQRCHYQLDEEARLPSGAYYCRFC 63 Query: 61 IVFGRVTSNENLYYFPQKTFSKTNSLKWKGELTPYQNEVSEELLKGISSKENLLVHAVTG 120- +VFGR S++ LY P F K N L W G+LT YQ +S++LL + +++ LVHAVTG Sbjct: 64 LVFGRNQSDKLLYAIPPMHFPKGNYLVWGGQLTAYQEMISQQLLINMQNQKTTLVHAVTG 123- Query: 121 AGKTEMIYHSVAKVIDTGGSVCIASPRIDVCLELYKRLSNDFRCAITLMHGESPSYQRSP 18- 0 AGKTEMIY ++ VI+TGG VCIASPR+DVC+E+ RLS F C+I LMH ES YQR+P Sbjct: 124 AGKTEMIYAAIEAVINTGGWVCIASPRVDVCVEVATRLSQAFSCSICLMHAESLPYQRAP 18- 3 Query: 181 LTIATTHQLLKFYHAFDLLIVDEVDAFPYVDNPILYQGVKQALKENGTSIFLTATSTTEL 24- 0 + +ATTHQLLKF+ AFDLLI+DEVDAFP+V+N L+ QALKE G I LTATST L Sbjct: 184 IIVATTHQLLKFHKAFDLLIIDEVDAFPFVNNIQLHYAASQALKEGGAKILLTATSTRTL 24- 3 Query: 241 ERKVARKELKKLHLARRFHANPLVIPEMVWVSGIQKSLQTQKLPPKLYQLINKQRQTRYP 30- 0 ERKV + E+ KL LARRFH PLVIP+ + + K + QKLP K+ + + KQR+T YP Sbjct: 244 ERKVNKGEVVKLTLARRFHNRPLVIPKFIRSFNLFKMIHRQKLPLKILKYLKKQRKTGYP 30- 3 Query: 301 LLLFFPHISEGQVFTEILRQAFPMEKIGFVSSKSTSRLKLVQDFRDNKLSILVSTTILER 36- 0 LL+F P I + T IL++ P E+I VSS+S +R + + FR K +IL++T+ILER Sbjct: 304 LLIFLPTIIMAESVTAILKELLPAEQIACVSSQSQNRKEDITAFRQGKKTILITTSILER 36- 3 Query: 361 GVTFPSVDVFVIQANHHLFTKSSLVQISGRVGRALERPEGLLYFLHDGKSKSMHQAIKEI 42- 0 GVTFP +DVFV+ ++H +++ SLVQI+GRVGR+++RP+G LYF H+G SK+M A KEI Sbjct: 364 GVTFPQIDVFVLGSHHRVYSSQSLVQIAGRVGRSIDRPDGTLYFFHEGISKAMLLARKEI 42- 3 Query: 421 KNMNHIG 427 K MN+ G Sbjct: 424 KEMNYKG 430 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1006 A DNA sequence (GBSx1066) was identified in S. agalactiae <SEQ ID 3091> which encodes the amino acid sequence <SEQ ID 3092>. This protein is predicted to be comf operon protein 3 (comFC). Analysis of this protein sequence reveals the following: TABLE-US-02979 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0894(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02980 >GP: AAC44942 GB: U56901 involved in transformation [Bacillus subtilis] Identities = 76/230 (33%), Positives = 118/230 (51%), Gaps = 11/230 (4%) Query: 1 MTCLLCHEIDLSQLTFVEUMLLKPKQNVICQTCKGSFEALSREMGCQTCCK-QIPQKQCQ 59 M CLLC +T+ L LLKP +V C +C+ + ++ + C C + Q C+ Sbjct: 1 MICLLCDSQFSQDVTWRALFLLKPDEKV-CYSCRSKLKKITGHI-CPLCGRPQSVHAVCR 58 Query: 60 DCIYWGKKGIEV----NHFSLYRYNEAMKKNFSLFKFQGDYLLKDVFTKEIKAALKKY-- 113- DC W + + + S+Y YN+ MK+ S FKF+GD + + F + + K Sbjct: 59 DCEVWRTRIRDSLLLRQNRSVYTYNDMMKETLSRFKFRGDAEIINAFKSDFSSTFSKVYP 118- Query: 114 -KGYTIVPVPLSHEGYQNRQFNQVIAFLQSANIPYKNILSKKDGGKQSANNKEERLKQVQ 17- 2 K + +VP+PLS E +R FNQ + + P + L + + KQS K ERL Sbjct: 119 DKHFVLVPIPLSKEREEERGFNQAHLLAECLDRPSHHPLIRLNNEKQSKKKKTERLLSEC 17- 8 Query: 173 QFTLKNEAELGDNLLIVDDIYTTGATIAQIRKLLEEKG-IKNIKSFSLAR 221 F KN + G N++++DD+YTTGAT+ + L EKG ++ SF+L R Sbjct: 179 IFDTKNNSAEGMNIILIDDLYTTGATLHFAARCLLEKGKAASVSSFTLIR 228 A related DNA sequence was identified in S. pyogenes <SEQ ID 3093> which encodes the amino acid sequence <SEQ ID 3094>. Analysis of this protein sequence reveals the following: TABLE-US-02981 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0763(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02982 Identities = 100/222 (45%), Positives = 139/222 (62%), Gaps = 2/222 (0%) Query: 1 MTCLLCHEIDLSQLTFVELMLLKPKQNVICQTCKGSFEALSREMGCQTCCKQIPQKQCQD 60 M CLLC +I + ++ E++ L+ + ICQ C+ SF+ + + + C TCC C+D Sbjct: 1 MICLLCQQISQTPISITEIIFLRRISSPICQQCQKSFQKIGKSV-CATCCANSDIIACRD 59 Query: 61 CIYWGKKGIEVNHFSLYRYNEAMKKNFSLFKFQGDYLLKDVFTKEIKAALKKY-KGYTIV 119- C+ W KG VNH SLY YN AMK FS +KFQGDYLL+ VF E+ + KY KGY V Sbjct: 60 CLKWENKGYNVNHRSLYCYNAAMKAYFSQYKFQGDYLLRKVFAVELADVITKYYKGYIPV 119- Query: 120 PVPLSHEGYQNRQFNQVIAFLQSANIPYKNILSKKDGGKQSANNKEERLKQVQQFTLKNE 17- 9 PVP+S ++ RQFNQV A L++AN+ Y ++ K D QS+ K+ERL + +L Sbjct: 120 PVPVSPGCFRERQFNQVSAILEAANVSYLSLFEKLDNTHQSSRTKKERLLVEKSYRLLKV 17- 9 Query: 180 AELGDNLLIVDDIYTTGATIAQIRKLLEEKGIKNIKSFSLAR 221 + + D +LIVDDIYTTG+TI +RK L + +IKS S+AR Sbjct: 180 SNIPDKILIVDDIYTTGSTIIALRKQLAKVANSDIKSLSIAR 221 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1007 A DNA sequence (GBSx1067) was identified in S. agalactiae <SEQ ID 3095> which encodes the amino acid sequence <SEQ ID 3096>. Analysis of this protein sequence reveals the following: TABLE-US-02983 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3889(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02984 >GP: CAB91549 GB: AJ249134 hypothetical protein [Lactococcus lactis] Identities = 107/185 (57%), Positives = 140/185 (74%), Gaps = 3/185 (1%) Query: 1 MIKYSIRGENIEVTEAIREYVETKLSKVEKYFNEAQELDTRVNLKVYREKTAKVEVTILI 60 MIK++IRGEN+EVT+AIR YVE K+ K++KYFN+ E+ VNLKVY EK AKVEVT+ Sbjct: 1 MIKFNIRGENVEVTDAIRAYVEDKIGKLDKYFNDGHEVTAYVNLKVYTEKRAKVEVTLPA 60 Query: 61 DSITLRAEDVSQDMYGSIDLVVDKIERQIRKNKTKIAKKYREKIPASQVFTTEFEAEPDE 120- ++TLRAED SQDMY SID V +K+ERQIRK KT++ +K R +P QVF EF Sbjct: 61 KNVTLRAEDTSQDMYSSIDFVEEKLERQIRKYKTRMNRKPRNAVPTGQVFGDEFAPLDTT 120- Query: 121 EAVSQ---RIVRTKNVNLKPMDVEEALLQMELLGHDFFIYTDAEDNTTNVLYKREDGELG 17- 7 + V++ IVRTK+V LKPMD EEA+LQM++LGHDF+++TDA+ N T+V+Y+R DG G Sbjct: 121 DEVAEDHVDIVRTKHVALKPMDAEEAVLQMDMLGHDFYVFTDADSNGTHVVYRRTDGRYG 18- 0 Query: 178 LIEAK 182 LIE + Sbjct: 181 LIETE 185 A related DNA sequence was identified in S. pyogenes <SEQ ID 3097> which encodes the amino acid sequence <SEQ ID 3098>. Analysis of this protein sequence reveals the following: TABLE-US-02985 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3751(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02986 Identities = 145/182 (79%), Positives = 165/182 (89%) Query: 1 MIKYSIRGENIEVTEAIREYVETKLSKVEKYFNEAQELDTRVNLKVYREKTAKVEVTILI 60 MIK+SIRGENIEVTEAIR+YVE+KL+K+EKYF + QE+D RVNLKVYRE+++KVEVTI + Sbjct: 1 MIKFSIRGENIEVTEAIRDYVESKLTKIEKYFAKDQEIDARVNLKVYRERSSKVEVTIPL 60 Query: 61 DSITLRAEDVSQDMYGSIDLVVDKIERQIRKNKTKIAKKYREKIPASQVFTTEFEAEPDE 20 DS+TLRAEDVSQDMYGSIDLVVDKIERQIRKNKTKIAKK+REK+P QVFTTEFEAE + Sbjct: 61 DSVTLRAEDVSQDMYGSIDLVVDKIERQIRKNKTKIAKKHREKVPTGQVFTTEFEAEEVD 120- Query: 121 EAVSQRIVRTKNVNLKPMDVEEALLQMELLGHDFFIYTDAEDNTTNVLYKREDGELGLIE 18- 0 E ++VRTKNV LKPMDVEEA LQMELLGHDFFIYTD+ED TN+LY+REDG LGLIE Sbjct: 121 EIPEVQVVRTKNVTLKPMDVEEARLQMELLGHDFFIYTDSEDGATNILYRREDGNLGLIE 18- 0 Query: 181 AK 182 AK Sbjct: 181 AK 182 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1008 A DNA sequence (GBSx1068) was identified in S. agalactiae <SEQ ID 3099> which encodes the amino acid sequence <SEQ ID 3100>. Analysis of this protein sequence reveals the following: TABLE-US-02987 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0685(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1009 A DNA sequence (GBSx1077) was identified in S. agalactiae <SEQ ID 3101> which encodes the amino acid sequence <SEQ ID 3102> (sgaT). Analysis of this protein sequence reveals the following: TABLE-US-02988 Possible site: 41 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.95 Transmembrane 99-115 (87-115) INTEGRAL Likelihood = -3.50 Transmembrane 43-59 (42-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.3378(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-02989 >GP:BAB03942 GB:AP001507 unknown conserved protein [Bacillus halodurans] Identities = 47/111 (42%), Positives = 76/111 (68%), Gaps = 5/111 (4%) Query: 1 MAIIYLIVAVFAG--EAYIAKEI---SNGVNGLVYALQLAGQFAAGVFVILAGVRLILGE 55 - M I++L+A+ + A+E+ S + +YA+ +FA G+ V+L GV++ +GE Sbjct: 233 MGILFLVGAIILALKDTQGAQELIAQSGEQSFFIYAIIQSFMFAGGIAVVLLGVKMFIGE 29- 2 Query: 56 IVPAFKGISEKLVPNSKPALDCPIVYPYAPNAVLIGFISKFVGGLVSMIVM 106 +VPAF GI+ KLVP ++PALD P+V+P APNAV++GF+ FVG L+ ++V+ Sbjct: 293 VVPAFNGIATKLVPGARPALDAPVVFPMAPNAVILGFLGAFVGALIWLVVI 343 There is also homology to SEQ ID 516. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1010 A DNA sequence (GBSx1078) was identified in S. agalactiae <SEQ ID 3103> which encodes the amino acid sequence <SEQ ID 3104>. This protein is predicted to be tryptophanyl-tRNA synthetase (trpS). Analysis of this protein sequence reveals the following: TABLE-US-02990 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2156 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02991 >GP:AAC05711 GB:L49336 tryptophanyl-tRNA synthetase [Clostridium longisporum] Identities = 225/340 (66%), Positives = 271/340 (79%), Gaps = 3/340 (0%) Query: 1 MTKPIILTGDRPTGKLHIGHYVGSLKNRVLLQNEGSYTLFVFLADQQALTDHAKDPQTIV 60 - M K IILTGDRPTGKLHIGHYVGSLKNRV LQN G Y F+ +ADQQALTD+A++P+ I Sbjct: 1 MAKEIILTGDRPTGKLHIGHYVGSLKNRVQLQNSGDYRSFIMIADQQALTDNARNPEKIR 60 Query: 61 ESIGNVALDYLAVGLDPNKSTLFIQSQIPELAELSMYYMNLVSLARLERNPTVKTEIAQK 120- S+ VALDYLAVG+DP KST+ +QSQIPEL EL+M+Y+NLV+L+RLERNPTVK EI QK Sbjct: 61 NSLIEVALDYLAVGIDPLKSTILVQSQIPELNELTMHYLNLVTLSRLERNPTVKAEIKQK 120- Query: 121 GFGESIPAGFLVYPVAQAADITAFKANLVPVGTDQKPMIEQTREIVRSFNHAYNCQVLVE 18- 0 F SIPAGFL+YPV+QAADITAFKA VPVG DQ PMIEQ REIVRSFN Y +VLVE Sbjct: 121 NFENSIPAGFLIYPVSQAADITAFKATTVPVGEDQLPMIEQAREIVRSFNTIYGKEVLVE 18- 0 Query: 181 PEGIYPENDAAGRLPGLDGNAKMSKSLNNGIFLADDMDTVKKKVMSMYTDPNHIKVEEPG 24- 0 P+ + P+ GRLPG DG AKMSKS+ N I+LAD+ D +K+KVMSMYTDPNHIKV +PG Sbjct: 181 PKAVIPKG-TIGRLPGTDGKAKMSKSIGNAIYLADEADVIKQKVNSMYTDPNHIKVTDPG 23- 9 Query: 241 QIEGNMVFHYLDVFGRDEDQKEITAMKEHYQKGGLGDVKTKRYLLDILERELSPIRERRL 30- 0 Q+EGN VF YLD F +D + E MK HY +GGLGDVK K++L +IL+ EL PIR RR Sbjct: 240 QVEGNTVFTYLDTFCKDTETLE--EMKAHYSRGGLGDVKVKKFLNEILQAELEPIRNRRK 29- 7 Query: 301 EYAKDMGQVYQMLQKGSEKAQAVAASTLDEVKSAMGLNYF 340 E+ KD+ +VY++L++GSEKA+ VAA TL EV+ +G+ YF Sbjct: 298 EFQKDIPEVYRILKEGSEKAREVAAGTLKEVRETIGIEYF 337 A related DNA sequence was identified in S. pyogenes <SEQ ID 3105> which encodes the amino acid sequence <SEQ ID 3106>. Analysis of this protein sequence reveals the following: TABLE-US-02992 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2737(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02993 Identities = 290/340 (85%), Positives = 316/340 (92%) Query: 1 MTKPIILTGDRPTGKLHIGHYVGSLKNRVLLQNEGSYTLFVFLADQQALTDHAKDPQTIV 60 MTKPIILTGDRPTGKLH+GHYVGSLKNRV LQNE Y +FVFLADQQALTDHAK+ + I Sbjct: 2 MTKPIILTGDRPTGKLHLGHYVGSLKNRVFLQNENKYKMFVFLADQQALTDHAKESELIQ 61 Query: 61 ESIGNVALDYLAVGLDPNKSTLFIQSQIPELAELSMYYMNLVSLARLERNPTVKTEIAQK 120- ESIGNVALDYL+VGLDP +ST+FIQSQIPELAELSMYYMNLVSLARLERNPTVKTEIAQK Sbjct: 62 ESIGNVALDYLSVGLDPKQSTIFIQSQIPELAELSMYYMNLVSLARLERNPTVKTEIAQK 121- Query: 121 GFGESIPAGFLVYPVAQAADITAFKANLVPVGTDQKPMIEQTREIVRSFNHAYNCQVLVE 18- 0 GFGESIP+GFLVYPV+QAADITAFKANLVPVG DQKPMIEQTREIVRSFNH Y+ LVE Sbjct: 122 GFGESIPSGFLVYPVSQAADITAFKANLVPVGNDQKPMIEQTREIVRSFNHTYHTDCLVE 18- 1 Query: 181 PEGIYPENDAAGRLPGLDGNAKMSKSLNNGIFLADDMDTVKKKVMSMYTDPNHIKVEEPG 24- 0 PEGIYPEN+ AGRLPGLDGNAKMSKSL NGI+L+DD DTV+KKVMSMYTDPNHIK+E+PG Sbjct: 182 PEGIYPENEKAGRLPGLDGNAKMSKSLGNGIYLSDDADTVRKKVMSMYTDPNHIKIEDPG 24- 1 Query: 241 QIEGNMVFHYLDVFGRDEDQKEITAMKEHYQKGGLGDVKTKRYLLDILERELSPIRERRL 30- 0 QIEGNMVFHYLD+F R EDQ +I AMKEHYQ GGLGDVKTKRYLLDILEREL+PIRERRL Sbjct: 242 QIEGNMVFHYLDIFARKEDQADIEAMKEHYQIGGLGDVKTKRYLLDILERELAPIRERRL 30- 1 Query: 301 EYAKDMGQVYQMLQKGSEKAQAVAASTLDEVKSAMGLNYF 340 EYAKDMG+V++MLQ+GS+KA+ VAA TL EVKSAMG+NYF Sbjct: 302 EYAKDMGEVFRMLQEGSQKARTVAAKTLSEVKSAMGINYF 341 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1011 A DNA sequence (GBSx1079) was identified in S. agalactiae <SEQ ID 3107> which encodes the amino acid sequence <SEQ ID 3108>. This protein is predicted to be carbamate kinase. Analysis of this protein sequence reveals the following: TABLE-US-02994 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0013(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02995 >GP:CAA04684 GB:AJ001330 carbamate kinase [Lactobacillus sakei] Identities = 199/311 (63%), Positives = 254/311 (80%), Gaps = 3/311 (0%) Query: 6 QKIVVALGGNAILSTDASAKAQQEALINTSKSLVKLIKEGHDVIVTHGNGPQVGNLLLQQ 65 +KIVVALGGNAILSTDASA AQ +A+ T K LV +K+G +I++HGNGPQVGNLL+QQ Sbjct: 4 RKIVVALGGNAILSTDASANAQIKAVKETVKQLVAFVKQGDQLIISHGNGPQVGNLLIQQ 63 Query: 66 AASDSEKNPAMPLDTCVAMTEGSIGFWLQNALNNELQEQGIDKEVATVVTQVIVDEKDQA 125- AASDSEK PAMPLDT AM++G IG+W+QNA N L E+G+ +VAT+VTQ IVD KD+A Sbjct: 64 AASDSEKTPAMPLDTVGAMSQGEIGYWMQNAFNEVLAEEGLALDVATIVTQTIVDAKDEA 123- Query: 126 FTNPTKPIGPFLSEEDAKKQAQ-ETGSKFKEDAGRGWRKVVPSPKPVGIKEASVIRRLVD 18- 4 F NPTKPIGPF SE +AKKQ + F EDAGRGWR+VVPSP+P+GI+EA VI++LV+ Sbjct: 124 FQNPTKPIGPFYSEAEAKKQQSINPEAHFVEDAGRGWRRVVPSPRPIGIQEAPVIQKLVE 18- 3 Query: 185 SGVVVISAGGGGVPVIEDANTKALKGVEAVIDKDFASQTLSELVDADLFIVLTGVDNVFV 24- 4 V+ ISAGGGGVPV ++ N L+GVEAVIDKDFAS+ L+ELV AD+ I+LT VDNV+V Sbjct: 184 GNVITISAGGGGVPVAKEGN--KLRGVEAVIDKDFASEKLAELVGADMLIILTAVDNVYV 24- 1 Query: 245 NFNKPNQEKLEEVTVSQMKQYITENQFAPGSMLPKVEAAIAFVENKPESRAIITSLENID 30- 4 NFNKP+Q+KL V+V++++ YI ++QFA GSMLPK++ AI +V N+P+S+AIITSL+N+ Sbjct: 242 NFNKPDQKKLTNVSVAELEDYIKDDQFAKGSMLPKIQTAIEYVNNRPDSKAIITSLDNVK 30- 1 Query: 305 NVLAQNAGTQI 315 N+LA +AGT I Sbjct: 302 NLLAHDAGTII 312 A related DNA sequence was identified in S. pyogenes <SEQ ID 3109> which encodes the amino acid sequence <SEQ ID 3110>. Analysis of this protein sequence reveals the following: TABLE-US-02996 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0013(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-02997 Identities = 275/312 (88%), Positives = 295/312 (94%) Query: 6 QKIVVALGGNAILSTDASAKAQQEALINTSKSLVKLIKEGHDVIVTHGNGPQVGNLLLQQ 65 QKIVVALGGNAILSTDASAKAQQEALI+TSKSLVKLIKEGH+VIVTHGNGPQVGNLLLQQ Sbjct: 4 QKIVVALGGNAILSTDASAKAQQEALISTSKSLVKLIKEGHEVIVTHGNGPQVGNLLLQQ 63 Query: 66 AASDSEKNPAMPLDTCVAMTEGSIGFWLQNALNNELQEQGIDKEVATVVTQVIVDEKDQA 125- AA+DSEKNPAMPLDTCVAMTEGSIGFWL NAL+NELQ QGI KEVA VVTQVIVD RD A Sbjct: 64 AAADSEKNPAMPLDTCVAMTEGSIGFWLVNALDNELQAQGIQKEVAAVVTQVIVDAKDPA 123- Query: 126 FTNPTKPIGPFLSEEDAKKQAQETGSKFKEDAGRGWRKVVPSPKPVGIKEASVIRRLVDS 18- 5 F NPTKPIGPFL+EEDAKKQ E+G+ FKEDAGRGWRKVVPSPKPVGIKEA+VIR LVDS SbjCt: 124 FENPThPIGPFLTEEDAKKQMAESGASFKEDAGRGWRKVVPSPKPVGIKEANVIRSLVDS 18- 3 Query: 186 GVVVISAGGGGVPVIEDANTKALKGVEAVIDKDFASQTLSELVDADLFIVLTGVDNVFVN 24- 5 GVVV+SAGGGGVPV+EDA +K L GVEAVIDKDFASQTLSELVDADLFIVLTGVDNV+VN SbjCt: 184 GVVVVSAGGGGVPVVEDATSKTLTGVEAVIDKDFASQTLSELVDADLFIVLTGVDNVYVN 24- 3 Query: 246 FNKPNQEKLEEVTVSQMKQYITENQFAPGSMLPKVEAAIAFVENKPESRAIITSLENIDN 30- 5 FNKP+Q KLEEVTVSQMK+YIT++QFAPGSMLPKVEAAIAFVENKP ++AIITSLENIDN Sbjct: 244 FNKPDQAKLEEVTVSQMKEYITQDQFAPGSMLPKVEAAIAFVENKPNAKAIITSLENIDN 30- 3 Query: 306 VLAQNAGTQIVA 317 VL+ NAGTQI+A Sbjct: 304 VLSANAGTQIIA 315 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1012 A DNA sequence (GBSx1080) was identified in S. agalactiae <SEQ ID 3111> which encodes the amino acid sequence <SEQ ID 3112>. This protein is predicted to be permease (potE). Analysis of this protein sequence reveals the following: TABLE-US-02998 Possible site: 52 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.63 Transmembrane 450-466 (441-478) INTEGRAL Likelihood = -8.97 Transmembrane 236-252 (231-259) INTEGRAL Likelihood = -8.70 Transmembrane 283-299 (277-308) INTEGRAL Likelihood = -8.44 Transmembrane 165-181 (153-186) INTEGRAL Likelihood = -7.96 Transmembrane 129-145 (126-151) INTEGRAL Likelihood = -6.16 Transmembrane 396-412 (394-415) INTEGRAL Likelihood = -5.15 Transmembrane 45-61 (38-63) INTEGRAL Likelihood = -4.94 Transmembrane 335-351 (334-352) INTEGRAL Likelihood = -3.72 Transmembrane 13-29 (10-30) INTEGRAL Likelihood = -2.92 Transmembrane 417-433 (417-435) INTEGRAL Likelihood = -1.54 Transmembrane 360-376 (360-376) INTEGRAL Likelihood = -0.53 Transmembrane 207-223 (207-223) ----- Final Results ----- bacterial membrane --- Certainty = 0.6052(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10295> which encodes amino acid sequence <SEQ ID 10296> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-02999 >GP:CAA76779 GB:Y17554 permease [Bacillus licheniformis] Identities = 265/470 (56%), Positives = 347/470 (73%), Gaps = 3/470 (0%) Query: 5 MEKEKKLGLLPLTMLVIGSLIGGGIFDLMQNMSSRAGLVPMLIAWVITAIGMGTFVLSFQ 64 M +EKKLGL L LVIGS+IGGG F+L +M+S AG +LI W+IT +GM SFQ Sbjct: 1 MAEEKKLGLFALIALVIGSMIGGGAFNLASDMASGAGAGAILIGWIITGVGMIALAFSFQ 60 Query: 65 NLSEKRPDLTAGIFSYAKEGFGNFMGFNSAWGYWLSAWLGNVAYAALLFSSLGYFFKFFG 124- NL+ KRPDL GIF+YA+EGFG+FMGFNS WGYW +A LGNVAY LLFS++GYF FG Sbjct: 61 NLTTKRPDLDGGIFTYAREGFGHFMGFNSGWGYWFAALLGNVAYGTLLFSAIGYFIPAFG 120- Query: 125 NGNNIISIIGASIVIWVVHFLILRGVNTAAFINTIVTFAKLVPVIIFLISALLAFKFNIF 18- 4 +G NI SIIGAS+++W VHFLILRGV +AA IN I T +KLVP+ F+I+ + F ++F Sbjct: 121 DGQNIASIIGASVILWCVHFLILRGVQSAAMINLITTISKLVPIFAFIIAIIFVFHLDLF 18- 0 Query: 185 SLDIWGNGLH-QSIFNQVNSTMKTAVWVFIGIEGAVVFSGRAKKIISDIGKASILALFTMI 2- 43 + D WG GL SI QV STM VWVF GIEGAV+FS RAKK SD+GKA+++ L +++ Sbjct: 181 TNDFWGKGLSLGSIGTQVKSTMLVTVWVFTGIEGAVLFSSRAKKSSDVGKATVIGLISVL 24- 0 G Sbjct: 417 FG 418 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03000 Identities = 104/368 (28%), Positives = 162/368 (43%), Gaps = 32/368 (8%) Query: 1 MRYKMEKEKKLGLLPLTMLVIGSLIGGGIFDLMQNMSSRAGLVPMLIAWVI-TAIGMGTF 59 M + ++ K L T+ I ++IG GIF L + + GL P IA + TAI Sbjct: 6 MNEQEREQAKFSLSGATLYGINAVIGSGIFLLPRAIYK--GLGPASIAVMFGTAILTIML 63 Query: 60 VLSFQNLSEKRPDLTAGIFSYAKEGFGNFMGFNSA---WGYWLSAWLGNVAYAALLFSSL 116- + F +S G F Y+K FG+F+GFN W + AW A A +F Sbjct: 64 AVCFAEVSGYFGK-NGGAFQYSKRAFGDFIGFNVGFLGWTVTIFAWAAMAAGFARMFIIT 122- Query: 117 GYFFKFFGNGNNIISIIGASIVIWVVHFLILRGVNTAAFINTIVTFAKLVPVIIFLISAL 17- 6 F+ G +I IG I++ +++ + G+ T+ + T AKL+P++ F L Sbjct: 123 FPAFE----GWHIPLSIGLIILLSLMN---IAGLKTSKIVTITATIAKLIPIVAFCACTL 17- 5 Query: 177 LAFK-----FNIFSLDIWGNGLHQSIFNQVNSTMKTAVWVFIGIEGAVVFSGRAKKHSDI 23- 1 K F F G L +I N TAV++F G G S A + D Sbjct: 176 FFIKNGLPNFTPFVQLEPGTNLLGAISN-------TAVYIFYGFIGFETLSIVAGEMRDP 22- 8 Query: 232 GKASILALFTMISLYVLISVLSLG---IMSRPELANLKTPAM-AYVLEKAVGHWGAILVN 28- 7 K AL IS+ ++ +L +G M ++ P A+V++K +G GA +V+ Sbjct: 229 EKNVPRALLGSISIVSVLYMLIIGGTIAMLGSQIMMTNAPVQDAFV--KMIGPAGAWMVS 28- 6 Query: 288 LGVIISVFGAILAWTLFAAELPYQAAKEGAFPKFFAKENKNKAPINSLLVTNLCVQAFLI 34- 7 +G +IS+ G + ++ A EG P AK+N+N AP+ ++LV+ L+ Sbjct: 287 IGALISITGLNMGESIMVPRYGAAIADEGLLPAAIAKQNQNGAPLVAILVSGAIAIVLLL 34- 6 Query: 348 TFLFTQSA 355 T F A Sbjct: 347 TGSFESLA 354 A further related DNA sequence was identified in S. pyogenes <SEQ ID 9079> which encodes the amino acid sequence <SEQ ID 9080>. Analysis of this protein sequence reveals the following: TABLE-US-03001 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.92 Transmembrane 77-93 (72-100) INTEGRAL Likelihood = -9.29 Transmembrane 279-295 (274-303) INTEGRAL Likelihood = -9.08 Transmembrane 203-219 (199-225) INTEGRAL Likelihood = -8.55 Transmembrane 174-190 (171-197) INTEGRAL Likelihood = -8.33 Tramsmembrane 436-452 (432-455) INTEGRAL Likelihood = -7.32 Transmembrene 329-345 (324-350) INTEGRAL Likelihood = -5.63 Transmembrane 402-418 (396-421) INTEGRAL Likelihood = -4.88 Tramsmembrane 460-476 (456-479) INTEGRAL Likelihood = -4.51 Transmembrane 379-395 (377-401) INTEGRAL Likelihood = -2.81 Transmembrane 48-64 (48-65) INTEGRAL Likelihood = -2.23 Transmembrane 243-259 (243-262) INTEGRAL Likelihood = -0.37 Transmembrane 123-139 (123-139) ----- Final Results ----- bacterial membrane --- Certainty = 0.4970 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS sequences follows: TABLE-US-03002 Score = 62.1 bits (148), Expect = 2e-11 Identities = 59/250 (23%), Positives = 107/250 (42%), Gaps = 12/250 (4%) Query: 143 WGSYLKGLLAN--YNIVLPNALNGTFNL--KNGTYIDILPV-LVMFFVTGIVLMNSKLAL 19- 7 WG +L L N Y +L ++L F I I+ +V++ V ++L A Sbjct: 95 WGYWLSAWLGNVAYAALLFSSLGYFFKFFGNGNNIISIIGASIVIWVVHFLILRGVNTAA 154- Query: 198 RFNSFLVILKFSALALFIFVGIFFIDHNNWSHFAPYGVGQITGGKTGIFAGASVMFFAFL 25- 7 N+ + K + +F+ + N +S +G G + + + F+ Sbjct: 155 FINTIVTFAKLVPVIIFLISALLAFKFNIFS-LDIWGNGLHQSIFNQVNSTMKTAVWVFI 21- 3 Query: 258 GFESISMAVDEVKEPQKTIPKGIILSLIIVTALYIVvTTILTGIV---HYTKLNVPDAVA 31- 4 G E + K+ I K IL+L + +LY++++ + GI+ L P A+A Sbjct: 214 GIEGAVVFSGRAKK-HSDIGKASILALFTMISLYVLISVLSLGIMSRPELANLKTP-AMA 27- 1 Query: 315 FALRNIRLYWAADYVSIVAILTLITVCISMTYALARTIYSISRDGLLPKSLYTLTKKNKV 37- 4 + L +W A V++ I+++ ++ T A Y +++G PK + KNK Sbjct: 272 YVLEKAVGHWGAILVNLGVIISVFGAILAWTLFAAELPYQAAKEGAFPK-FFAKENKNKA 33- 0 Query: 375 PQNATLVTGL 384 P N+ LVT L Sbjct: 331 PINSLLVTNL 340 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1013 A DNA sequence (GBSx1081) was identified in S. agalactiae <SEQ ID 3115> which encodes the amino acid sequence <SEQ ID 3116>. This protein is predicted to be unnamed protein product (argF). Analysis of this protein sequence reveals the following: TABLE-US-03003 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3757(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 3117> which encodes the amino acid sequence <SEQ ID 3118>. Analysis of this protein sequence reveals the following: TABLE-US-03004 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = 0.48 Transmembrane 171-187 (171-188) ----- Final Results ----- bacterial membrane --- Certainty = 0.1192(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03005 >GP:CAB12563 GB:Z99108 similar to metabolite transporter [Bacillus subtilis] Identities = 190/467 (40%), Positives = 284/467 (60%), Gaps = 13/467 (2%) Query: 25 TIFRKK-----KKYSNKTEMQRHFKVIDLVFLGLGSMVGTGIFTVTGIGAAKYAGPALTI 79 - ++FRKK S + R DL LG+G ++GTGIF +TG AA AGPAL I Sbjct: 3 SLFRKKPLETLSAQSKSKSLARTLSAFDLTLLGIGCVIGTGIFVITGTVAATGAGPALII 62 Query: 80 SIIISAIAIGILALFYAEFASRMPSNGGAYSYVYATLGEFPAWLVGWYIIMEFLTAISSV 139- S I++ +A + A YAEF+S +P +G YSY Y TLGE A+L+GW +++E++ A+S+V Sbjct: 63 SFILAGLACALAAFCYAEFSSSIPISGSVYSYSYVTLGELLAFLIGWDLMLEYVIALSAV 122- Query: 140 AVGWGSYLKGLLANYNIVLPNALNGTFNLKNGTYIDILPVLVMFFVTGIVLMNSKLALRF 19- 9 A GW SY + LLA +N+ +P AL G G ++ +++ +T IV K + RF Sbjct: 123 ATGWSSYFQSLLAGFNLHIPAALTGAPGSMAGAVFNLPAAVIILLITAIVSRGVKESTRF 18- 2 Query: 200 NSFLVILKFSALALFIFVGIFFIDHNNWSHFAPYGVGQITGGKTGIFAGASVMFFAFLGF 25- 9 N+ +V++K + + LFI VGI ++ +NWS F P+G+ G+ A+ +FFA+LGF Sbjct: 183 NNVIVLMKIAIILLFIIVGIGYVKPDNWSPFMPFGM-------KGVILSAATVFFAYLGF 23- 5 Query: 260 ESISMAVDEVKEPQKTIPKGIILSLIIVTALYIVVTTILTGIVHYTKLNVPDAVAFALRN 31- 9 +++S A +EVK PQK +P GII +L + T LYI V+ +LTG++ Y KLNV D V+FAL+ Sbjct: 236 DAVSNASEEVKNPQKNMPVGIISALAVCTVLYIAVSLVLTGMMPYAKLNVGDPVSFALKF 29- 5 Query: 320 IRLYWAADYVSIVAILTLITVCISNTYALARTIYSISRDGLLPKSLYTLTKKNKVPQNAT 37- 9 + A +S+ AI+ + TV +++ YA R +++SRDGLLP + K P T Sbjct: 296 VGQDAVAGIISVGAIIGITTVMLALLYAQVRLTFAMSRDGLLPGLFAKVHPSFKTPFRNT 35- 5 Query: 380 LVTGLLAMICAGIFPLSSLAEFVNICTLAYLIILSGAIIKLRRIEGEPKANEFKTPLVPF 43- 9 +TG++A AG L +LA VN+ TLA ++S A+I LR+ E KA+ F+ P VP Sbjct: 356 WLTGIVAAGIAGFINLGTLAHLVNMGTLAAFTVISIAVIVLRKKHPEIKAS-FRVPFVPV 41- 4 Query: 440 LPMLAIIICLSFMSQYKAFTWIAFAIATIIGTLIYLAYGYTHSIENK 486 +P+++ ICL FM TW++F I +GTL+Y Y HS+ NK Sbjct: 415 VPIISAGICLWFMYSLPGVTWLSFVIWIAVGTLVYFLYSRKHSLLNK 461 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03006 Identities = 312/337 (92%), Positives = 324/337 (95%) Query: 1 MTQVFQGRSFLAEKDFSREEFEYLIDFSAHLKDLKKRGVPHHYLEGKNIALLFEKTSTRT 60 MTQVFQGRSFLAEKDF+R E EYLIDFSAHLKDLKKRGVPHHYLEGKNIALLFEKTSTRT Sbjct: 1 MTQVFQGRSFLAEKDFTRAELEYLIDFSAHLKDLKKRGVPHHYLEGKNIALLFEKTSTRT 60 Query: 61 RAAFTTAAIDLGAHPEYLGANDIQLGKKESTEDTAKVLGRMFDGIEFRGFSQRMVEELAE 120- RAAFTTAAIDLGAHPEYLGANDIQLGKKESTEDTAKVLGRMFDGIEFRGFSQRMVEELAE Sbjct: 61 RAAFTTAAIDLGAHPEYLGANDIQLGKKESTEDTAKVLGRMFDGIEFRGFSQRMVEELAE 120- Query: 121 FSGVPVWNGLTDEWHPTQMLADYLTIKENFGKLEGITLVYCGDGRNNVANSLLVAGTLMG 18- 0 FSGVPVWNGLTDEWHPTQMLADY T+KENFGKLEG+TLVYCGDGRNNVANSLLV G ++G Sbjct: 121 FSGVPVWNGLTDEWHPTQMLADYFTVKENFGKLEGLTLVYCGDGRNNVANSLLVTGAILG 18- 0 Query: 181 VNVHIFSPKELFPAEEIVKLAEEYAKESGAHVLVTDNVDEAVKGADVFYTDVWVSMGEED 24- 0 VNVHIFSPKELFP EEIV LAE YAKESGA +L+T++ DEAVKGADV YTDVWVSMGEED Sbjct: 181 VNVHIFSPKELFPEEEIVTLAEGYAKESGARILITEDADEAVKGADVLYTDVWVSMGEED 24- 0 Query: 241 KFKERVELLQPYQVNMELIKKANNDNLIFLHCLPAFHDTNTVYGKDVAEKFGVKEMEVTD 30- 0 KFKERVELLQPYQVNM+L++KA ND LIFLHCLPAFHDTNTVYGKDVAEKFGVKEMEVTD Sbjct: 241 KFKERVELLQPYQVNMDLVQKAGNDKLIFLHCLPAFHDTNTVYGKDVAEKFGVKEMEVTD 30- 0 Query: 301 EVFRSKYARHFDQAENRMHTIKAVMAATLGNLFIPKV 337 EVFRSKYARHFDQAENRMHTIKAVMAATLGNLFIPKV Sbjct: 301 EVFRSKYARHFDQAENRMHTIKAVMAATLGNLFIPKV 337 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1014 A DNA sequence (GBSx1082) was identified in S. agalactiae <SEQ ID 3119> which encodes the amino acid sequence <SEQ ID 3120>. Analysis of this protein sequence reveals the following: TABLE-US-03007 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0456(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10921> which encodes amino acid sequence <SEQ ID 10922> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 3121> which encodes the amino acid sequence <SEQ ID 3122>. Analysis of this protein sequence reveals the following: TABLE-US-03008 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.41 Transmembrane 121-137 (118-140) ----- Final Results ----- bacterial membrane --- Certainty = 0.3166(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03009 Identities = 65/113 (57%), Positives = 83/113 (72%) Query: 31 MEEEFDDNDEQDTIYAVLYDGKQPVSTGRFLPETQTEARLTRIATLKGYRGNGYGTKIII 90 - M ++FD NDE T+YAV+YD QPVSTG+FL ET+ EARLTRI TL Y G GYG K+ Sbjct: 1 MADKFDANDETRTVYAVVYDNDQPVSTGQFLAETKIEARLTRIVTLADYCGCGYGAKVTE 60 Query: 91 ALENYAKENGYHYLTIHAELTAKDFYQTLGYQATGNIYMEDGEACQTLEKYLI 143 ALE Y + G++ LTIH+ELTA+ FY+ LGYQ+ G +EDGE CQ+L K ++ Sbjct: 61 ALETYTRREGFYQLTIHSELTAQTFYENLGYQSYGPKCLEDGEYCQSLAKTIL 113 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1015 A DNA sequence (GBSx1083) was identified in S. agalactiae <SEQ ID 3123> which encodes the amino acid sequence <SEQ ID 3124>. Analysis of this protein sequence reveals the following: TABLE-US-03010 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2160 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 3125> which encodes the amino acid sequence <SEQ ID 3126>. Analysis of this protein sequence reveals the following: TABLE-US-03011 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2730 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03012 Identities = 375/411 (91%), Positives = 395/411 (95%), Gaps = 1/411 (0%) Query: 1 MTQTHPIHVFSEIGKLKKVMLHRPGKEIENLMPDYLERLLFDDIPFLEDAQKEHDAFAQA 60 MT PIHV+SEIGKLKKV+LHRPGKEIENLMPDYLERLLFDDIPFLEDAQKEHDAFAQA Sbjct: 1 MTAQTPIHVYSEIGKLKKVLLHRPGKEIENLMPDYLERLLFDDIPFLEDAQKEHDAFAQA 60 Query: 61 LRNEGVEVLYLENLAAESLTNQEIREQFIDEYIGEANVRGRATKKAIRELLLNIKDNKEL 120- LR+EG+EVLYLE LAAESL EIRE FIDEY+ EAN+RGRATKKAIRELL+ I+DN+EL Sbjct: 61 LRDEGIEVLYLETLAAESLVTPEIREAFIDEYLSEANIRGRATKKAIRELLMAIEDNQEL 120- Query: 121 IEKTMAGIQKSELPEIPSSEKGLTDLVESNYPFAIDPMPNLYFTRDPFATIGNGVSLNHM 18- 0 IEKTMAG+QKSELPEIP+SEKGLTDLVESNYPFAIDPMPNLYFTRDPFATIG GVSLNHM Sbjct: 121 IEKTMAGVQKSELPEIPASEKGLTDLVESNYPFAIDPMPNLYFTRDPFATIGTGVSLNHM 18- 0 Query: 181 FSETRNRETLYGKYIFTHHPEYGG-KVPMVYEREETTRIEGGDELVLSKDVLAVGISQRT 23- 9 FSETRNRETLYGKYIFTHHP YGG KVPMVY+R ETTRIEGGDELVLSKDVLAVGISQRT Sbjct: 181 FSETRNRETLYGKYIFTHHPIYGGGKVPMVYDRNETTRIEGGDELVLSKDVLAVGISQRT 24- 0 Query: 240 DAASIEKLLVNIFKQNLGFKKVLAFEFANNRKFMHLDTVFTMVDYDKFTIHPEIEGDLRV 29- 9 DAASIEKLLVNIFKQNLGFKKVLAFEFANNRKFMHLDTVFTMVDYDKFTIHPEIEGDLRV Sbjct: 241 DAASIEKLLVNIFKQNLGFKKVLAFEFANNRKFMHLDTVFTMVDYDKFTIHPEIEGDLRV 30- 0 Query: 300 YSVTYENQDLHIEEEKGDLADLLAKNLGVEKVELIRCGGDNLVAAGREQWNDGSNTLTIA 35- 9 YSVTY+N++LHI EEKGDLA+LLA NLGVEKV+LIRCGGDNLVAAGREQWNDGSNTLTIA Sbjct: 301 YSVTYDNEELHIVEEKGDLAELLAANLGVEKVDLIRCGGDNLVAAGREQWNDGSNTLTIA 36- 0 Query: 360 PGVVIVYNRNTITNAILESKGLKLIKINGSELVRGRGGPRCMSMPFEREDL 410 PGVV+VYNRNTITNAILESKGLKLIKI+GSELVRGRGGPRCMSMPFERED+ Sbjct: 361 PGVVVVYNRNTITNAILESKGLKLIKIHGSELVRGRGGPRCMSMPFEREDI 411 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1016 A DNA sequence (GBSx1084) was identified in S. agalactiae <SEQ ID 3127> which encodes the amino acid sequence <SEQ ID 3128>. Analysis of this protein sequence reveals the following: TABLE-US-03013 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3162(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8703> which encodes amino acid sequence <SEQ ID 8704> was also identified. This protein has an RGD motif and has homology with the following sequences in the GENPEPT database. TABLE-US-03014 >GP:AAG07568 GB:AE004834 hypothetical protein [Pseudomonas aeruginosa] Identities = 42/132 (31%), Positives = 74/132 (55%), Gaps = 3/132 (2%) Query: 35 IQTYRKAYQTFKTK-KGARSSIEALLKRVNSGNEITSINPLVDIYNAASLRFGLPIGAED 93 - + + +A++ F K + S EAL KR + SI+P+VD+YNA S++F +P+G E+ Sbjct: 63 LAAWAEAFRRFGAKPQRTPCSAEALRKRALRDGGLPSIDPVVDLYNAISVQFAIPVGGEN 122- Query: 94 SDTFRGDLKLTITNGGDEFYLI--GEDFNRPTLSGELAYVDDVGAVCRCFNWRDGKRTMI 151- + G +L + +G + F + GE + GE+ + DD+G CR +NWR G RT + Sbjct: 123 LAAYAGPPRLVVADGSETFDTLKNGEALDESPDPGEVVWRDDLGVTCRRWNWRQGVRTRL 18- 2 Query: 152 TDNTQNAFLVIE 163 + + + ++E Sbjct: 183 DASARRMWFILE 194 A related DNA sequence was identified in S. pyogenes <SEQ ID 3129> which encodes the amino acid sequence <SEQ ID 3130>. Analysis of this protein sequence reveals the following: TABLE-US-03015 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0700(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03016 Identities = 127/199 (63%), Positives = 155/199 (77%) Query: 8 ELKQLLSDSHSLAKKYLQEKEFSQNRVIQTYRKAYQTFKTKKGARSSIEALLKRVNSGNE 67 ++KQLL+DSH LAK YL FS N+V+Q YRKAYQ FKTKKGARSSIEALLKRV++G Sbjct: 36 DVKQLLADSHELAKAYLTADNFSDNQVVQVYRKAYQHFKTKKGARSSIEALLKRVSNGQS 95 Query: 68 ITSINPLVDIYNAASLRFGLPIGAEDSDTFRGDLKLTITNGGDEFYLIGEDFNRPTLSGE 127- I SINPLVDIYNAASLRFGLP GAEDSD+F GDL+LTIT+GGD+FYLIG+ N PTL E Sbjct: 96 IPSINPLVDIYNAASLRFGLPAGAEDSDSFIGDLRLTITDGGDDFYLIGDADNNPTLPNE 155- Query: 128 LAYVDDVGAVCRCFNWRDGKRTMITDNTQNAFLVIELIDNGREIIFKEALDFIATNTNRF 18- 7 L Y DD+GA CRC NWRDG+RTM+T++T+NAFL+IE +D + +EAL FI + + Sbjct: 156 LCYKDDIGAFCRCLNWRDGERTMVTEHTKNAFLIIEALDQEGQNRLQEALKFIEGSAKMY 21- 5 Query: 188 LKAKTQTIILDKEHSEITL 206 L A T +LDK++ + L Sbjct: 216 LHAITSVHVLDKDNPHVPL 234 SEQ ID 8704 (GBS298) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 44 (lane 2; MW 29 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 48 (lane 5; MW 54 kDa). The GBS298-GST fusion product was purified (FIG. 203, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 297), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1017 A DNA sequence (GBSx1085) was identified in S. agalactiae <SEQ ID 3131> which encodes the amino acid sequence <SEQ ID 3132>. Analysis of this protein sequence reveals the following: TABLE-US-03017 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3770(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1018 A DNA sequence (GBSx1086) was identified in S. agalactiae <SEQ ID 3133> which encodes the amino acid sequence <SEQ ID 3134>. Analysis of this protein sequence reveals the following: TABLE-US-03018 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4263(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03019 >GP:CAB95946 GB:Y17554 Crp/Fnr family protein [Bacillus licheniformis] Identities = 85/214 (39%), Positives = 126/214 (58%), Gaps = 14/214 (6%) Query: 11 RQLDDFKHFTIEQFDHIVSHIKHRTALKNHTLFFEGDYREKLFLIQSGHVKIEQSDASGS 70 - R L+D K F I R+ K LF E D RE+++L+ G +K+E+S+ +GS Sbjct: 22 RDLEDMKQF-----------IYWRSYHKGQILFMEDDPRERMYLLLDGFIKLEKSNEAGS 70 Query: 71 FIYTDYVRQGTVFPYGGLFLDDDYHFSAVAITDIEYFSLPMALYEEYSLQNINQMKHLCR 130- YTDYVR T+FP+GGLF D+ YH++A A+TDIE + +PM ++E+ N N + + Sbjct: 71 MFYTDYVRPHTLFPEGGLFRDEHYHYAAEALTDIELYYIPMNIFEDLVRDNKNLLYDILN 130- Query: 131 KYSKLLRVHEIRLRNMVTSSASMRVIQSLATL---LLQVPTERGHLPFPITTIEIANMSG 18- 7 S +L +HE RL+ + S A RV Q++ L L Q + + PIT EIA +SG Sbjct: 131 HLSDILALHEERLKRITLSHAHDRVTQAIYYLTESLGQKESNSTVINCPITAAEIAKISG 19- 0 Query: 188 TTRETVSHVLKELRQKDIVEMKGKKLLYNNKNYF 221 T+RETVS VLK+LR + ++ K+++ N YF Sbjct: 191 TSRETVSAVLKKLRCEGVISQMNKQIMINRPEYF 224 A related DNA sequence was identified in S. pyogenes <SEQ ID 3135> which encodes the amino acid sequence <SEQ ID 3136>. Analysis of this protein sequence reveals the following: TABLE-US-03020 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4478 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03021 Identities = 130/224 (58%), Positives = 180/224 (80%) Query: 1 MITKEQYFYFRQLDDFKHFTIEQFDHIVSHIKHRTALKNHTLFFEGDYREKLFLIQSGHV 60 +I +E Y Y R+L+DF++F+IEQFD IV ++ R A K+H LFFEGD R+KLFL+ SG+ Sbjct: 1 VIRREDYQYLRKLNDFRYFSIEQFDKIVGQMEFRKAKKDHILFFEGDKRDKLFLVTSGYF 60 Query: 61 KIEQSDASGSFIYTDYVRQGTVFPYGGLFLDDDYHFSAVAITDIEYFSLPMALYEEYSLQ 120- K+EQSD SG+F+YTD++R GT+FPYGGLF DD YHFS VA+TD+ YF P+ L+E+YSL+ Sbjct: 61 KVEQSDQSGTFMYTDFIRHGTIFPYGGLFTDDYYHFSVVAMTDVTYFYFPVDLFEDYSLE 120- Query: 121 NINQMKHLCRKYSKLLRVHEIRLRNMVTSSASMRVIQSLATLLLQVPTERGHLPFPITTI 18- 0 N QMKHL K SKLL +HE+R+RN++TSSAS RVIQSLA LL+++ + LPF +TT Sbjct: 121 NRLQMKHLYSKMSKLLELHELRVRNLITSSASSRVIQSLAILLVEMGKDSDTLPFQLTTT 18- 0 Query: 181 EIANMSGTTRETVSHVLKELRQKDIVEMKGKKLLYNNKNYFKKF 224 +IA +SGTTRETVSHVL++L++++++ +KGK L Y +K+YF ++ Sbjct: 181 DIAQISGTTRETVSHVLRDLKKQELITIKGKYLTYLDKDYFLQY 224 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1019 A DNA sequence (GBSx1087) was identified in S. agalactiae <SEQ ID 3137> which encodes the amino acid sequence <SEQ ID 3138>. Analysis of this protein sequence reveals the following: TABLE-US-03022 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1643(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2161> which encodes the amino acid sequence <SEQ ID 2162>. Analysis of this protein sequence reveals the following: TABLE-US-03023 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1201(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03024 Identities = 461/493 (93%), Positives = 478/493 (96%) Query: 2 MSNWDTKFLKKGFTFDDVLLIPAESHVLPNEVDMKTKLADNLTLNIPIITAAMDTVTDSK 61 MSNWDTKFLKKG+TFDDVLLIPAESHVLPNEVD+KTKLADNLTLNIPIITAAMDTVT SK Sbjct: 1 MSNWDTKFLKKGYTFDDVLLIPAESHVLPNEVDLKTKLADNLTLNIPIITAAMDTVTGSK 60 Query: 62 MAIAIARAGGLGIIHKNMSIVDQAEEVRKVKRSENGVIIDPFFLTPDNTVSEAEELMQNY 121- MAIAIARAGGLG+IHKNMSI +QAEEVRKVKRSENGVIIDPFFLTP++ VSEAEELMQ Y Sbjct: 61 MAIAIARAGGLGVIHKNMSITEQAEEVRKVKRSENGVIIDPFFLTPEHKVSEAEELMQRY 120- Query: 122 RISGVPIVETLENRKLVGIITNRDMRFISDYKQLISEHMTSQNLVTAPIGTDLETAERIL 18- 1 RISGVPIVETL NRKLVGIITNRDMRFISDY ISEHMTS++LVTA +GTDLETAERIL Sbjct: 121 RISGVPIVETLANRKLVGIITNRDMRFISDYNAPISEHMTSEHLVTAAVGTDLETAERIL 18- 0 Query: 182 HEHRIEKLPLVDDEGRLSGLITIKDIEKVIEFPKAAKDEFGRLLVAGAVGVTSDTFERAE 24- 1 HEHRIEKLPLVD+ GRLSGLITIKDIEKVIEFP AAKDEFGRLLVA AVGVTSDTFERAE Sbjct: 181 HEHRIEKLPLVDNSGRLSGLITIKDIEKVIEFPHAAKDEFGRLLVAAAVGVTSDTFERAE 24- 0 Query: 242 ALFEAGADAIVIDTAHGHSAGVLRKIAEIRAHFPNRTLIAGNIATAEGARALYDAGVDVV 30- 1 ALFEAGADAIVIDTAHGHSAGVLRKIAEIRAHFPNRTLIAGNIATAEGARALYDAGVDVV Sbjct: 241 ALFEAGADAIVIDTAHGHSAGVLRKIAEIRAHFPNRTLIAGNIATAEGARALYDAGVDVV 30- 0 Query: 302 KVGIGPGSICTTRVVAGVGVPQITAIYDAAAVAREYGKTIIADGGIKYSGDIVKALAAGG 36- 1 KVGIGPGSICTTRVVAGVGVPQ+TAIYDAAAVAREYGKTIIADGGIKYSGDIVKALAAGG Sbjct: 301 KVGIGPGSICTTRVVAGVGVPQVTAIYDAAAVAREYGKTIIADGGIKYSGDIVKALAAGG 36- 0 Query: 362 NAVMLGSMFAGTDEAPGETEIFQGRKFKTYRGMGSIAAMKKGSSDRYFQGSVNEANKLVP 42- 1 NAVMLGSMFAGTDEAPGETEI+QGRKFKTYRGMGSIAAMKKGSSDRYFQGSVNEANKLVP Sbjct: 361 NAVMLGSMFAGTDEAPGETEIYQGRKFKTYRGMGSIAAMKKGSSDRYFQGSVNEANKLVP 42- 0 Query: 422 EGIEGRVAYKGSVADIVFQMLGGIRSGMGYVGAANIKELHDNAQFVEMSGAGLKESHPHD 48- 1 EGIEGRVAYKG+ +DIVFQMLGGIRSGMGYVGA +I+ELH+NAQFVEMSGAGL ESHPHD Sbjct: 421 EGIEGRVAYKGAASDIVFQMLGGIRSGMGYVGAGDIQELHENAQFVEMSGAGLIESHPHD 48- 0 Query: 482 VQITNEAPNYSVH 494 VQITNEAPNYSVH Sbjct: 481 VQITNEAPNYSVH 493 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1020 A DNA sequence (GBSx1089) was identified in S. agalactiae <SEQ ID 3139> which encodes the amino acid sequence <SEQ ID 3140>. This protein is predicted to be MutR. Analysis of this protein sequence reveals the following:

TABLE-US-03025 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1841(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03026 >GP:AAD04237 GB:AF007761 MutR [Streptococcus mutans] Identities = 51/215 (23%), Positives = 102/215 (46%), Gaps = 9/215 (4%) Query: 5 GKILKELREDKGISLSSLAKSAQLSKSTLSRFENGETQIGIDKFIKALQTLEVGVTINEV 64 G++ KELR +G+ L +A+ LS S LS+FENG+T + DK I A+Q + +T +E Sbjct: 9 GELYKELRMARGLKLKDIARD-NLSVSQLSKFENGQTMLAADKLILAIQGIH--MTFSEF 65 Query: 65 SILDSKVKAGTSNTDLEQLTLLESYRDNEDIMRIFSFQKQQSCDRIESNVLKILAKLFIS 124- S ++ + ++L L++ +D + + +I + + + K++ K + Sbjct: 66 SYAFTQYQESDLFKTGKKLVELQTKKDIKGLKKILKDYPDTETYNVYNRLNKLVIKAAVY 125- Query: 125 NLGLNMRLPQDEINLVVTYLNGVTQYNDFYFKVICYFQDILPED--VILNKI----SNMT 17- 8 +L + + +E + +YL + ++ ++ + IL +D V L K + Sbjct: 126 SLDSSFEITNEEKEFLTSYLYAIEEWTEYELYLFGNTLFILSDDDLVFLGKAFVERDKLY 18- 5 Query: 179 KEQLPYSKSLVNLLIKQVIIALEKDSVDKAIVFAD 213 +E + K +LI ++I +E S A F + Sbjct: 186 RELSEHKKRAELVLINLILILVEHHSFYHAQYFIE 220 There is also homology to SEQ ID 628. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1021 A DNA sequence (GBSx1090) was identified in S. agalactiae <SEQ ID 3141> which encodes the amino acid sequence <SEQ ID 3142>. Analysis of this protein sequence reveals the following: TABLE-US-03027 Possible site: 15 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.77 Transmembrane 269-285 (265-287) INTEGRAL Likelihood = -6.90 Transmembrane 33-49 (31-51) INTEGRAL Likelihood = -6.79 Transmembrane 182-198 (176-200) INTEGRAL Likelihood = -6.37 Transmembrane 117-133 (113-135) INTEGRAL Likelihood = -5.57 Transmembrane 240-256 (232-259) INTEGRAL Likelihood = -3.40 Transmembrane 223-239 (220-239) INTEGRAL Likelihood = -0.96 Transmembrane 56-72 (55-72) ----- Final Results ----- bacterial membrane --- Certainty = 0.5310(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 3143> which encodes the amino acid sequence <SEQ ID 3144>. Analysis of this protein sequence reveals the following: TABLE-US-03028 Possible site: 48 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.99 Transmembrane 269-285 (264-286) INTEGRAL Likelihood = -8.76 Transmembrane 117-133 (112-135) INTEGRAL Likelihood = -7.70 Transmembrane 179-195 (174-200) INTEGRAL Likelihood = -4.83 Transmembrane 34-50 (32-52) INTEGRAL Likelihood = -4.46 Transmembrane 213-229 (211-230) INTEGRAL Likelihood = -4.14 Transmembrane 240-256 (232-259) INTEGRAL Likelihood = -0.69 Transmembrane 91-107 (91-108) INTEGRAL Likelihood = -0.32 Transmembrane 4-20 (4-20) ----- Final Results ----- bacterial membrane --- Certainty = 0.5394(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9181> which encodes the amino acid sequence <SEQ ID 9182>. Analysis of this protein sequence reveals the following: TABLE-US-03029 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.99 Transmembrane 259-275 (254-276) INTEGRAL Likelihood = -8.76 Transmembrane 107-123 (102-125) INTEGRAL Likelihood = -7.70 Transmembrane 169-185 (164-190) INTEGRAL Likelihood = -4.83 Transmembrane 24-40 ( 22-42) INTEGRAL Likelihood = -4.46 Transmembrane 203-219 (201-220) INTEGRAL Likelihood = -4.14 Transmembrane 230-246 (222-249) INTEGRAL Likelihood = -0.69 Transmembrane 81-97 ( 81-98) ----- Final Results ----- bacterial membrane --- Certainty = 0.539 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03030 Identities = 200/287 (69%), Positives = 244/287 (84%) Query: 1 MEGLLIALIPMFAWGSIGFVSNKIGGRPNQQTFGMTLGALLFAIIVWLFKQPEMTASLWI 60 +EG+ ALIPMF WGSIGFVSNKIGG+P+QQT GMT GALLF++ VWL +PEMT LW+ Sbjct: 1 LEGIFYALIPMFTWGSIGFVSNKIGGKPSQQTLGMTFGALLFSLAVWLIVRPEMTLQLWL 60 Query: 61 FGILGGILWSVGQNGQFQAMKYMGVSVANPLSSGAQLVGGSLVGALVFHEWTKPIQFILG 120- FGILGG +WS+GQ GQF AM+YMGVSVANPLSSG+QLV GSL+G LVFHEWT+P+QF++G Sbjct: 61 FGILGGFIWSIGQTGQFHAMQYMGVSVANPLSSGSQLVLGSLIGVLVFHEWTRPMQFVVG 120- Query: 121 LTALTLLVIGFYFSSKRDVSEQALATHQEFSKGFATIAYSTVGYISYAVLFNNIMKFDAM 18- 0 AL LL++GFYFSSK+D + + FSKGF + YST+GY+ YAVLFNNIMKF+ + Sbjct: 121 SLALLLLIVGFYFSSKQDDANAQVNHLHNFSKGFRALTYSTIGYVMYAVLFNNIMKFEVL 18- 0 Query: 181 AVILPMAVGMCLGAICFMKFRVNFEAVVVKNMITGLMWGVGNVFMLLAAAKAGLAIAFSF 24- 0 +VILPMAVGM LGAI FM F+++ +V+KN +GL+WG+GN+FMLLAA+KAGLAIAFSF Sbjct: 181 SVILPMAVGMVLGAITFMSFKISIDQYVIKNSVVGLLWGIGNIFMLLAASKAGLAIAFSF 24- 0 Query: 241 SQLGVIISIIGGILFLGETKTKKEQKWVVMGILCFVMGAILLGIVKS 287 SQLG IISI+GGILFLGETKTKKE +WVV GI+CF++GAILLG+VKS Sbjct: 241 SQLGAIISIVGGILFLGETKTKKEMRWVVTGIICFIVGAILLGVVKS 287 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1022 A DNA sequence (GBSx1092) was identified in S. agalactiae <SEQ ID 3145> which encodes the amino acid sequence <SEQ ID 3146>. This protein is predicted to be recf protein (recF). Analysis of this protein sequence reveals the following: TABLE-US-03031 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2653(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 3147> which encodes the amino acid sequence <SEQ ID 3148>. Analysis of this protein sequence reveals the following: TABLE-US-03032 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1677(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03033 Identities = 248/364 (68%), Positives = 300/364 (82%), Gaps = 1/364 (0%) Query: 1 MWIKNISLKHYRNYEEAQVDFSPNLNIFIGRNAQGKTNFLEAIYFLALTRSHRTRSDKEL 60 MWIK + LKHYRNY+ FS LN+FIG NAQGKTNFLEAIYFL+LTRSHRTR+DKEL Sbjct: 1 MWIKELELKHYRNYDHLLASFSSGLNVFIGNNAQGKTNFLEAIYFLSLTRSHRTRADKEL 60 Query: 61 VHFKHHDVQITGEVIRKSGHLNLDIQLSEKGRITKVNHLKQAKLSDYIGAMTVVLFAPED 120- +HF H V +TG++ R SG ++L+I LS+KGR+TK+N LKQAKLSDYIG M VVLFAPED Sbjct: 61 IHFDHSTVSLTGKIQRISGTVDLEINLSDKGRVTKINALKQAKLSDYIGTMMVVLFAPED 120- Query: 121 LQLVKGAPSLRRKFLDIDIGQIKPTYLAELSNYNHVLKQRNTYLKTTNNVDKTFLTVLDE 18- 0 LQLVKGAPSLRRKF+DID+GQIKP YL+ELS+YNHVLKQRN+YLK+ +D FL VLDE Sbjct: 121 LQLVKGAPSLRRKFIDIDLGQIKPVYLSELSHYNHVLKQRNSYLKSAQQIDAAFLAVLDE 18- 0 Query: 181 QLADYGSRVIEHRFDFIQALNDEADKHHYIISTELEHLSIHYKSSIEFTDKSSIREHFLN 24- 0 QLA YG+RV+EHR DFI AL EA+ HH IS LE LS+ Y+SS+ F K++I + FL+ Sbjct: 181 QLASYGARVMEHRIDFINALEKEANTHHQAISNGLESLSLSYQSSVVFDKKTNIYQQFLH 24- 0 Query: 241 QLSKSHSRDIFKKNTSIGPHRDDITFFINDINATFASQGQQRSLILSLKLAEIELIKTVT 30- 0 QL K+H +D F+KNTS+GPHRD++ F+IN +NA FASQGQ RSLILSLK+AE+ L+K +T Sbjct: 241 QLEKNHQKDFFRKNTSVGPHRDELAFYINGMNANFASQGQHRSLILSLKMAEVSLMKALT 30- 0 Query: 301 NDYPILLLDDVMSELDNHRQLKLLEG-IKENVQTFITTTSLEHLSALPDQLKIFNVSDGT 35- 9 D PILLLDDVMSELDN RQ KLLE IKENVQTFITTTSL+HLS LP+ ++IF+V+ GT Sbjct: 301 GDNPILLLDDVMSELDNTRQTKLLETVIKENVQTFITTTSLDHLSQLPEGIRIFHVTKGT 36- 0 Query: 360 ISIN 363 + I+ Sbjct: 361 VQID 364 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1023 A DNA sequence (GBSx1093) was identified in S. agalactiae <SEQ ID 3149> which encodes the amino acid sequence <SEQ ID 3150>. Analysis of this protein sequence reveals the following: TABLE-US-03034 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1807(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03035 >GP: CAA61548 GB: X89367 orf121 [Lactococcus lactis] Identities = 56/116 (48%), Positives = 74/116 (63%), Gaps = 3/116 (2%) Query: 3 YKLFDEYITLQSLLKEIGIIQSGGAIKKFLADNR--VLFNGDLENRRGKKLRLGDIITIP 60 Y LF+EYITL LLKE+G+I +GG K FLA+N + +NG+ ENRRGKKLR GD++ P Sbjct: 4 YILFEEYITLGQLLKELGLISTGGQPKIFLAENEGNIFYNGEAENRRGKKLRDGDLLEFP 63 Query: 61 DQNIEIIIRKPSDQEIEERNIEIAEKQRVSAIVKEMNKNTNKGKSKTSKKPVRFPG 116 ++++ + I+E E AE+ RV AIVK+MN NK K P RFPG Sbjct: 64 TFDLKVTFEQADADAIKEHEAEKAEEARVKAIVKKMNAE-NKTTKPAKKAPPRFPG 118 A related DNA sequence was identified in S. pyogenes <SEQ ID 3151> which encodes the amino acid sequence <SEQ ID 3152>. Analysis of this protein sequence reveals the following: TABLE-US-03036 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0483(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03037 Identities = 74/136 (54%), Positives = 94/136 (68%), Gaps = 20/136 (14%) Query: 1 MDYKLFDEYITLQSLLKEIGIIQSGGAIKKFLADNRVLFNGDLENRRGKKLRLGDIITIP 60 M YKLF E+ITLQ+LLKE+GIIQSGGAIK FLA+ VLFNG+ E RRGKK+R+GD I++P Sbjct: 9 MIYKLFTEFITLQALLKELGIIQSGGAIKGFLAETTVLFNGEDEKRRGKKIRVGDKISLP 68 Query: 61 DQNIEIIIRKPSDQEIEERNIEIAEKQRVSAIVKEMNKNTNKGKSK------TSKK---- 110- DQ++ I I +PS +E E+ E+AEK RV+A+VK+MN+ K SK T+KK Sbjct: 69 DQDLIITIVEPSQEEKEQFAEEMAEKTRVAALVKQMNQANKKTSSKHNNRQSTTKKSLRA 128- Query: 111 ----------PVRFPG 116 PVRFPG Sbjct: 129 TKKTKGKPTAPVRFPG 144 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1024 A DNA sequence (GBSx1094) was identified in S. agalactiae <SEQ ID 3153> which encodes the amino acid sequence <SEQ ID 3154>. Analysis of this protein sequence reveals the following: TABLE-US-03038 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.86 Transmembrane 269-285 (267-285) ----- Final Results ----- bacterial membrane --- Certainty = 0.1744(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 3155> which encodes the amino acid sequence <SEQ ID 3156>. Analysis of this protein sequence reveals the following: TABLE-US-03039 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3008 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03040 Identities = 227/413 (54%), Positives = 309/413 (73%) Query: 1 MKIVEGVSLHLIKNQQFKTNHLTFRFSGDFNNKTVARRSLVAQMLVTANAKYPKVQEFRE 60 MKIV+GV LHLIK +QFKTNN+TFRFSGD N KTVA++ LVAQNL TAN YP V++FRE Sbjct: 1 MKIVQGVQLHLIKTKQFKTNHITFRFSGDLNQKTVAKKVLVAQMLATANECYPTVRQFRE 60 Query: 61 KLASLYGASLSTKISTKGLVHIVDIDIVFVKNTFTLEQENIVEQIITFLEDMLFSPLISL 120- KLA LYGASLST + TKGLVHIVDIDI F+++ + E I++++I FL+D+LFSPL+S+ Sbjct: 61 KLARLYGASLSTNVLTKGLVHIVDIDITFIQDRYACNGEKILDEMIQFLKDILFSPLLSI 120- Query: 121 EQYQTSIFDTEKKNLIQYLEADIEDNFYSSDLALKSLFYNNKTLRLPKYGTASLVESENS 18- 0 QYQ +F+TEK NLI Y+E+D ED+FY S L +K LFY NK L++ +YG+ L+ E + Sbjct: 121 AQYQPKVFETEKNNLINYIESDREDSFYYSSLKVKELFYCNKNLQNSEYGSPELIAKETA 18- 0 Query: 181 FTAYQEFQKMLKEDQLDIFVVGDFDDYRMIQAFNRMAFEPRHKVLAFDYTQTYENITRSQ 24- 0 +T+YQEF KML EDQ+DIF++GDFDDYR++Q ++ + R+K L F + Q NI + Sbjct: 181 YTSYQEFHKMLNEDQIDIFILGDFDDYRVVQLIHQFPLDNRNKNLNFFHLQNSVNIIKES 24- 0 Query: 241 VEDKDVNQSIMQLAYHLPITYKDEDYFALIVFNGLFGAFAHSLLFTEIREKQGLAYTIGS 30- 0 +E + V+QSI+QLAYH P + DY+AL++ NGL G+FAHS LF +IRE++GLAY+IG Sbjct: 241 IEKRAVHQSILQLAYHFPSVFGQRDYYALVLLNGLLGSFAHSRLFIKIREEEGLAYSIGC 30- 0 Query: 301 QFDSFTGLFTIYAGIDKENRERFLKLINKQFNNIKMGRFSSTLLKQTKDILKMNYVLASD 36- 0 +FDS+TGLF IY GID ++R + L+LI ++ N IKMGRFS L+K+T+ +L N +L+ D Sbjct: 301 RFDSYTGLFEIYTGIDSQHRTKTLQLIIQELNAIKMGRFSEQLIKKTRSMLLNNALLSED 36- 0 Query: 361 NPKVIVDHIYHEHYLDQFHTSALFIDKVDDVTKSDIVSVATKLKLQAFYFLEG 413 K I++IY Y+D ++ +I V++V K+DI+ VA LKLQ YFLEG Sbjct: 361 YNKNIIERIYRSSYIDSSYSIKNWIKGVNEVNKADIIKVANLLKLQTVYFLEG 413 SEQ ID 3154 (GBS400) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 76 (lane 2; MW 49.2 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 84 (lane 3; MW 74 kDa) and in FIG. 177 (lane 6; MW 74 kDa). GBS400-GST was purified as shown in FIG. 217, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1025 A DNA sequence (GBSx1095) was identified in S. agalactiae <SEQ ID 3157> which encodes the amino acid sequence <SEQ ID 3158>. Analysis of this protein sequence reveals the following: TABLE-US-03041 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3473 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 3159> which encodes the amino acid sequence <SEQ ID 3160>. Analysis of this protein sequence reveals the following: TABLE-US-03042 Possible site: 45 >>>Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4298 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03043 Identities = 207/424 (48%), Positives = 276/424 (64%), Gaps = 3/424 (0%) Query: 5 KITYQNLQEEVYKLTLESGLNVYLIPKPSFKETVGVLTANFGSLHTKYTRNGCVEHYPAG 64 KI Y N+ E++Y + LE+GL VY I K F E +LT FGSL K T + PAG Sbjct: 6 KINYPNIDEDLYYVKLENGLTVYFIKKIGFLEKTAMLTVGFGSLDNKLTVDDESRDAPAG 65 Query: 65 IAHFLEHKLFELDKGQDAATQFTKYGAESNAFTTFDKTSFYFSTISHITNCLDILLDFVL 124- IAHFLEHKLFE + G D + +FT+ GAE+NAFTTF++TSF+FST S L++L FVL Sbjct: 66 IAHFLEHKLFEDESGGDISLKFTQLGAETNAFTTFNQTSFFFSTASKFQENLELLQYFVL 125- Query: 125 TTNFTEESITKEKDIIKQEIEMYQDDPEYRLYQGVLSNLYPNSPLAFDIAGDYQSISQIT 18- 4 + N T+ES+++EK II QEI+MYQDD +YR Y G+L NL+P + LA DIAG SI +IT Sbjct: 126 SANITDESVSREKKIIGQEIDMYQDDADYRAYSGILQNLFPKTSLANDIAGSKASIQKIT 18- 5 Query: 185 LTDLQENHKDFYQLSNMNLVLVGQFSPQEIITYLQKNSHFTSY--SQNIDRDSISLEPVI 24- 2 L+ +H FYQ +NM+L +VG E +Q+ SY + + D + PVI Sbjct: 186 KILLETHHTYFYQPTNMSLFIVGDIDIDETFLAIQRFQTTLSYPDRKRVTVDPLHYYPVI 24- 5 Query: 243 KNNSCHMTVTKPKLAIGYRKSNHMIHGSYLKEKIGLQLFFAMLLGWTSTINQDWYESGQI 30- 2 K++S M VT KL +G+R + S L +I L+LF +ML+GWTS I YE G+I Sbjct: 246 KSSSVDMDVTTAKLVVGFRGYLTLTQHSLLTYRIALKLFLSMLIGWTSKIYHTLYEDGKI 30- 5 Query: 303 DDSFDIEIEVHPDFECVIISLDTTEPIAFSTQLRLLLKNALQSSDLTESHLKNVKRELYG 36- 2 DDSFD+++E+H +F+ V+ISLDT EPIA S +R L S + T HL +K+E+YG Sbjct: 306 DDSFDVDVEIHHNFQFVLISLDTPEPIAMSNYIRQKLATIKISKEFTNEHLNLLKKEMYG 36- 5 Query: 363 DFLRSLDSIENLAMQFVTYLYDG-KTMYLDLPSIVEELDLEDVITIGKDFLDNADTSDFV 42- 1 DF++SLDSIE+L QF YL D K Y D+P I+E L L+DV+TIGK F + AD SDF Sbjct: 366 DFIQSLDSIEHLTHQFSLYLSDSDKETYFDIPKIIERLTLKDVVTIGKAFFEKADASDFT 42- 5 Query: 422 IFPK 425 +FPK Sbjct: 426 VFPK 429 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1026 A DNA sequence (GBSx1096) was identified in S. agalactiae <SEQ ID 3161> which encodes the amino acid sequence <SEQ ID 3162>. This protein is predicted to be phosphotidylglycerophosphate synthase (pgsA). Analysis of this protein sequence reveals the following:

TABLE-US-03044 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.17 Transmembrane 17-33 (14-39) INTEGRAL Likelihood = -3.77 Transmembrane 92-108 (88-108) INTEGRAL Likelihood = -2.87 Transmembrane 144-160 (142-162) INTEGRAL Likelihood = -1.65 Transmembrane 42-58 (42-59) ----- Final Results ----- bacterial membrane --- Certainty = 0.4270(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10293> which encodes amino acid sequence <SEQ ID 10294> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 3163> which encodes the amino acid sequence <SEQ ID 3164>. Analysis of this protein sequence reveals the following: TABLE-US-03045 Possible site: 48 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.64 Transmembrane 76-92 (72-102) INTEGRAL Likelihood = -5.36 Transmembrane 136-152 (131-164) INTEGRAL Likelihood = -2.34 Transmembrane 98-114 (97-114) ----- Final Results ----- bacterial membrane --- Certainty = 0.3654(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03046 Identities = 145/180 (80%), Positives = 160/180 (88%) Query: 8 MMKKENIPNLLTVVRILMIPLFIVLTSVTTSTTWHIVAAIVFAIASLTDYLDGYLARKWQ 67 M+KKENIPNLLT+VRI MIP F+ +TS + WHI AA++FAIAS TDYLDGYLARKW Sbjct: 1 MIKKSNIPNLLTLVRIAMIPFFLFITSSSNKVGWHIFAAVIFAIASFTDYLDGYLARKWH 60 Query: 68 VVTNFGKFADPLADKMLVMSAFIMLVGLDLAPAWVSAIIICRELAVTGLRLLLVETGGTV 127- V +NFGKFADPLADKMLVMSAFIMLVGL L PAWVSA+IICRELAVTGLRLLLVETGG V Sbjct: 61 VASNFGKFADPLADKMLVMSAFIMLVGLGLVPAWVSAVIICRELAVTGLRLLLVETGGKV 120- Query: 128 LAAAMPGKIKTATQMFAVIFLLVHWMTLGNIMLYIALFFTLYSGYDYFKGAGFLFKDTFK 18- 7 LAAAMPGKIKTATQM ++I LL HW+ LGN++LYIALFFT+YSGYDYFKGA FLFKDTFK Sbjct: 121 LAAAMPGKIKTATQMLSIILLLCHWIFLGNVLLYIALFFTIYSGYDYFKGASFLFKDTFK 18- 0 A related GBS gene <SEQ ID 8705> and protein <SEQ ID 8706> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03047 Lipop Possible site: -1 Crend: 4 SRCFLG: 0 McG: Length of UR: 9 Peak Value of UR: 3.03 Net Charge of CR: 1 McG: Discrim Score: 6.36 GvH: Signal Score (-7.5): -0.400001 Possible site: 48 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 49 ALOM program count: 2 value: -3.77 threshold: 0.0 INTEGRAL Likelihood = -3.77 Transmembrane 85-101 (81-101) INTEGRAL Likelihood = -2.87 Transmembrane 137-153 (135-155) PERIPHERAL Likelihood = 1.27 109 modified ALOM score: 1.25 icm1 HYPID: 7 CFP: 0.251 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2508(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1027 A DNA sequence (GBSx1097) was identified in S. agalactiae <SEQ ID 3165> which encodes the amino acid sequence <SEQ ID 3166>. This protein is predicted to be ABC transporter ATP-binding protein (potA): Analysis of this protein sequence reveals the following: TABLE-US-03048 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1805(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03049 >GP:AAC61484 GB:AF082738 ABC transporter ATP-binding protein [Streptococcus pyogenes] Identities = 201/279 (72%), Positives = 231/279 (82%) Query: 1 MTNIITVNNLFFKYDSNQTHYQLENVSFHVKQGEWLSIIGHNGSGKSTTVRLIDGLLEAE 60 M+ II + + F Y +Q L+ VSFHVKQGEWLSIIGHNGSGKSTT+RLIDGLLE E Sbjct: 18 MSAIIELKKVTFNYHKDQEKPTLDGVSFHVKQGEWLSIIGHNGSGKSTTIRLIDGLLEPE 77 Query: 61 SGQIIIDGQELTEDNVWELRHKIGMVFQNPDNQFVGATVEDDVAFGLENKGIPLKDMKER 120- SG II+DG LT NVWE+RHKIGMVFQNPDNQFVGATVEDDVAFGLENKGI +D+KER Sbjct: 78 SGSIIVDGDLLTITNVWEIRHKIGMVFQNPDNQFVGATVEDDVAFGLENKGIAHEDIKER 137- Query: 121 VDQALDLVGMSEFKMREPARLSGGQKQRVAIAGAVAMRPQVIILDEATSMLDPEGRLELI 18- 0 V+ AL+LVGM FK +EPARLSGGQKQRVAIAGAVAM+P++IILDEATSMLDP+GRLELI Sbjct: 138 VNHALELVGMQNFKEKEPARLSGGQKQRVAIAGAVAMKPKIIILDEATSMLDPKGRLELI 19- 7 Query: 181 RTIRAIRQKYNLTVISITHDLDEVALSDRVIVMKNGKVESTSTPKALFGRGNRLISLGLD 24- 0 +TI+ IR Y LTVISITHDLDEVALSDRV+VMK+G+VESTSTP+ LF RG+ L+ LGLD Sbjct: 198 KTIKNIRDDYQLTVISITHDLDEVALSDRVLVMKDGQVESTSTPEQLFARGDELLQLGLD 25- 7 Query: 241 VPFTSRLMAELAANGLDIGTEYLTEKELEEQLWELNLKM 279 +PFT+ ++ L G I YLTEKELE QL +L KM Sbjct: 258 IPFTTSVVQMLQEEGYPIDYGYLTEKELENQLCQLISKM 296 A related DNA sequence was identified in S. pyogenes <SEQ ID 3167> which encodes the amino acid sequence <SEQ ID 3168>. Analysis of this protein sequence reveals the following: TABLE-US-03050 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2235 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 247-249 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03051 Identities = 200/279 (71%), Positives = 231/279 (82%) Query: 1 MTNIITVNNLFFKYDSNQTHYQLENVSFHVKQGEWLSIIGHNGSGKSTTVRLIDGLLEAE 60 M+ II + + F Y +Q L+ VSFHVKQGEWLSIIGHNGSGKSTT+RLIDGLLE E Sbjct: 18 MSAIIELKKVTFNYHKDQEKPTLDGVSFHVKQGEWLSIIGHNGSGKSTTIRLIDGLLEPE 77 Query: 61 SGQIIIDGQELTEDNVWELRHKIGMVFQNPDNQFVGATVEDDVAFGLENKGIPLKDMKER 120- SG II+DG LT NVWE+RHKIGMVFQNPDNQFVGATVEDDVAFGLENKGI +D+KER Sbjct: 78 SGSIIVDGDLLTITNVWEIRHKIGMVFQNPDNQFVGATVEDDVAFGLENKGIAHEDIKER 137- Query: 121 VDQALDLVGMSEFKMREPARLSGGQKQRVAIAGAVAMRPQVIILDEATSMLDPEGRLELI 18- 0 V+ AL+LVGM FK +EPARLSGGQKQRVAIAGAVAM+P++IILDEATSMLDP+GRLELI Sbjct: 138 VNHALELVGMQNFKEKEPARLSGGQKQRVAIAGAVAMKPKIIILDEATSMLDPKGRLELI 19- 7 Query: 181 RTIRAIRQKYNLTVISITHDLDEVALSDRVIVMKNGKVESTSTPKALFGRGNRLISLGLD 24- 0 +TI+ IR Y LTVISITHDLDEVALSDRV+VMK+G+VESTSTP+ LF RG+ L+ LGLD Sbjct: 198 KTIKNIRDDYQLTVISITHDLDEVALSDRVLVMKDGQVESTSTPEQLFARGDELLQLGLD 25- 7 Query: 241 VPFTSRLMAELAANGLDIGTEYLTEKELEEQLWELNLKM 279 +PFT+ ++ L G + YLTEKELE QL +L KM Sbjct: 258 IPFTTSVVQMLQEEGYPIDYGYLTEKELENQLCQLISKM 296 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1028 A DNA sequence (GBSx1098) was identified in S. agalactiae <SEQ ID 3169> which encodes the amino acid sequence <SEQ ID 3170>. Analysis of this protein sequence reveals the following: TABLE-US-03052 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.27 Transmembrane 154-170 (154-170) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03053 >GP: CAB11922 GB: Z99104 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 141/242 (58%), Positives = 188/242 (77%), Gaps = 1/242 (0%) Query: 16 TPFEGRALFDVNLKIEDASYTAFIGHTGSGKSTIMQLLNGLHIPTKGEVIVDDFSIKAGD 75 - TPFE AL+D+N I++ SY A IGHTGSGKST++Q LNGL PTKG++ + I+AG Sbjct: 3 TPFERLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGK 62 Query: 76 KNKEIKFIRQKVGLVFQFPESQLFEETVLKDVAFGPQNFGISQIEAERLAEEKLRLVGIS 135- KNK++K +R+KVG+VFQFPE QLFEETVLKD++FGP NFG+ + +AE+ A E L+LVG+S Sbjct: 63 KNKDLKKLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLS 122- Query: 136 EDLFDKNPFELSGGQMRRVAIAGILAMEPKVLVLDEPTAGLDPKGRKELMTLFKNLHKKG 19- 5 E+L D++PFELSGGQMRRVAIAG+LAM+P+VLVLDEPTAGLDP+GRKE+M +F LH++G Sbjct: 123 EELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRG 18- 2 Query: 196 -MTIVLVTHLMDDVADYADYVYVLEAGKVTLSGQPKQIFQEVELLESKQLGVPKITKFAQ 25- 4 +T+LVTH M+D A YAD + V+ G + SG P+ +F + E + L +P+ KF + Sbjct: 183 NLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETIKFQR 24- 2 Query: 255 RL 256 L Sbjct: 243 HL 244 A related DNA sequence was identified in S. pyogenes <SEQ ID 3171> which encodes the amino acid sequence <SEQ ID 3172>. Analysis of this protein sequence reveals the following: TABLE-US-03054 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.27 Transmembrane 154-170 (154-170) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03055 >GP: CAB11922 GB: Z99104 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 146/259 (56%), Positives = 187/259 (71%), Gaps = 2/259 (0%) Query: 16 TPFEGRALFNINLDILDGSYTAFIGHTGSGKSTIMQLLNGLHVPTTGIVSVDKQDITNHS 75 - TPFE AL++IN I +GSY A IGHTGSGKST++Q LNGL PT G +S+ I Sbjct: 3 TPFERLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGK 62 Query: 76 KNKEIKSIRKHVGLVFQFPESQLFEETVLKDVAFGPQNFGVSPEEAEALAREKLALVGIS 135- KNK++K +RK VG+VFQFPE QLFEETVLKD++FGP NFGV E+AE ARE L LVG+S Sbjct: 63 KNKDLKKLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLS 122- Query: 136 ENLFEKNPFELSGGQMRRVAIAGILAMQPKVLVLDEPTAGLDPKGRKELMTIFKKLHQSG 19- 5 E L +++PFELSGGQMRRVAIAG+LAM P+VLVLDEPTAGLDP+GRKE+M +F +LHQ G Sbjct: 123 EELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRG 18- 2 Query: 196 -MTIVLVTHLMDDVANYADFVYVLDKGKIILSGKPKTIFQQVSLLEKKQLGVPKVTKLAQ 25- 4 +T +LVTH M+D A YAD + V+ KG I SG P+ +F + + L +P+ K + Sbjct: 183 NLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETIKFQR 24- 2 Query: 255 RL-VDRGIPISSLPITLEE 272 L G+ + +T+E+ Sbjct: 243 HLEAALGVRFNEPMLTIED 261 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03056 Identities = 218/280 (77%), Positives = 241/280 (85%) Query: 1 MGIEFKNVSYTYQAGTPFEGRALFDVNLKIEDASYTAFIGHTGSGKSTIMQLLNGLHIPT 60 M I +NVSYTYQAGTPFEGRALF++NL I D SYTAFIGHTGSGKSTIMQLLNGLH+PT Sbjct: 1 MSINLQNVSYTYQAGTPFEGRALFNINLDILDGSYTAFIGHTGSGKSTIMQLLNGLHVPT 60 Query: 61 KGEVIVDDFSIKAGDKNKEIKFIRQKVGLVFQFPESQLFEETVLKDVAFGPQNFGISQIE 120- G V VD I KNKEIK IR+ VGLVFQFPESQLFEETVLKDVAFGPQNFG+S E Sbjct: 61 TGIVSVDKQDITNHSKNKEIKSIRKHVGLVFQFPESQLFEETVLKDVAFGPQNFGVSPEE 120- Query: 121 AERLAEEKLRLVGISEDLFDKNPFELSGGQMRRVAIAGILAMEPKVLVLDEPTAGLDPKG 18- 0 AE LA EKL LVGISE+LF+KNPFELSGGQMRRVAIAGILAM+PKVLVLDEPTAGLDPKG Sbjct: 121 AEALAREKLALVGISENLFEKNPFELSGGQMRRVAIAGILAMQPKVLVLDEPTAGLDPKG 18- 0 Query: 181 RKELMTLFKNLHKKGMTIVLVTHLMDDVADYADYVYVLEAGKVTLSGQPKQIFQEVELLE 24- 0 RKELMT+FK LH+ GMTIVLVTHLMDDVA+YAD+VYVL+ GK+ LSG+PK IFQ+V LLE Sbjct: 181 RKELMTIFKKLHQSGMTIVLVTHLMDDVANYADFVYVLDKGRIILSGKPKTIFQQVSLLE 24- 0 Query: 241 SKQLGVPKITKFAQRLSHKGLNLPSLPITINEFVEAIKHG 280 KQLGVPK+TK AQRL +G+ + SLPIT+ E E +KHG Sbjct: 241 KKQLGVPKVTKLAQRLVDRGIPISSLPITLEELREVLKHG 280 SEQ ID 3170 (GBS401) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 76 (lane 3; MW 34 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 84 (lane 4; MW 59 kDa). GBS401-GST was purified as shown in FIG. 218, lane 2. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1029 A DNA sequence (GBSx1099) was identified in S. agalactiae <SEQ ID 3173> which encodes the amino acid sequence <SEQ ID 3174>. Analysis of this protein sequence reveals the following: TABLE-US-03057 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.46 Transmembrane 47-63 (25-69) INTEGRAL Likelihood = -8.81 Transmembrane 252-268 (249-269) INTEGRAL Likelihood = -7.91 Transmembrane 116-132 (110-141) INTEGRAL Likelihood = -4.25 Transmembrane 29-45 (25-46) INTEGRAL Likelihood = -2.55 Transmembrane 77-93 (77-95) INTEGRAL Likelihood = -0.43 Transmembrane 199-215 (199-215) ----- Final Results ----- bacterial membrane --- Certainty = 0.5182(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8707> which encodes amino acid sequence <SEQ ID 8708> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-03058 Lipop: Possible site: -1 Crend: 7 SRCFLG: 0 McG: Length of UR: 8 Peak Value of UR: 0.65 Net Charge of CR: 1 McG: Discrim Score: -10.55 GvH: Signal Score (-7.5): 1.45 Possible site: 37 >>> Seems to have no N-terminal signal sequence Amino Acid Composition: calculated from 1 ALOM program count: 6 value: -10.46 threshold: 0.0 INTEGRAL Likelihood = -10.46 Transmembrane 41-57 (19-63) INTEGRAL Likelihood = -8.81 Transmembrane 246-262 (243-263) INTEGRAL Likelihood = -7.91 Transmembrane 110-126 (104-135) INTEGRAL Likelihood = -4.25 Transmembrane 23-39 (19-40) INTEGRAL Likelihood = -2.55 Transmembrane 71-87 (71-89) INTEGRAL Likelihood = -0.43 Transmembrane 193-209 (193-209) PERIPHERAL Likelihood = 0.79 90 modified ALOM score: 2.59 icm1 HYPID: 7 CFP: 0.518 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5182(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03059 >GP:CAB11923 GB:Z99104 ybaF [Bacillus subtilis] Identities = 133/263 (50%), Positives = 191/263 (72%) Query: 7 MDKLILGRYIPGNSLIHKLDPRSKLLAMLLFIIIVFWANNVVTNVIVFIFTLVIVGLSQI 66 MD +I+G+Y+PG SL+H+LDPR+KL+ + LF+ IVF ANNV T ++ +FT+ +V L+++ Sbjct: 2 MDSMIIGKYVPGTSLVHRLDPRTKLITIFLFVCIVFLANNVQTYALLGLFTIGVVSLTRV 61 Query: 67 KFSYFFNGIKPMVGIILFTTLFQMLFAQGGQVIFSFWIFSITSLGLQQAALIFMRFVLII 126- FS+ G+KP++ I+LFT L +L G +IF + GL Q I +RFV +I Sbjct: 62 PFSFLMKGLKPIIWIVLFTFLLHILMTHEGPIIFQIGFSRVYEGGLVQGIFISLRFVYLI 121- Query: 127 FFSTLLTLTTTPLSLADAVESLLKPLEVLRVPAHEIGLMLSLSLRFVPTLMDDTTRIMNA 18- 6 +TLLTLTTTP+ + D +E LL PL+ L++P HE+ LM+S+SLRF+PTLM++T +IM A Sbjct: 122 LITTLLTLTTTPIEITDGMEQLLNPLKKLKLPVHELALMMSISLRFIPTLMEETDKIMKA 18- 1 Query: 187 QRARGVDFGEGNLIHKVKSIIPILIPLFASSFKRADALAIAMEARGYQGGANRSKYRLLK 24- 6 Q ARGVDF G + +VK+I+P+L+PLF S+FKRA+ LA+AMEARGYQGG R+KYR L Sbjct: 182 QMARGVDFTSGPVKERVKAIVPLLVPLFVSAFKRAEELAVAMEARGYQGGEGRTKYRKLV 24- 1 Query: 247 WTVRDTFSILLMLLLGLSLFLLK 269 WT +DT I+ +++L LF L+ Sbjct: 242 WTGKDTSVIVSLIVLAALLFSLR 264 A related DNA sequence was identified in S. pyogenes <SEQ ID 3175> which encodes the amino acid sequence <SEQ ID 3176>. Analysis of this protein sequence reveals the following: TABLE-US-03060 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood =-9.50 Transmembrane 246-262 (243-265) INTEGRAL Likelihood = -9.34 Transmembrane 110-126 (103-135) INTEGRAL Likelihood = -6.69 Transmembrane 41-57 (40-58) INTEGRAL Likelihood = -2.81 Transmembrane 23-39 (21-40) INTEGRAL Likelihood = -1.01 Transmembrane 62-78 (62-78) INTEGRAL Likelihood = -0.27 Transmembrane 193-209 (193-209) ----- Final Results ----- bacterial membrane --- Certainty = 0.4800 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03061 >GP: CAB11923 GB: Z99104 ybaF [Bacillus subtilis] Identities = 138/263 (52%), Positives = 195/263 (73%) Query: 1 MDKLILGRYIPGDSLIHRLDPRSKLLAMIIYIVIIFWANNVVTNLLMLTFTLAVVFLSKI 60 MD +I+G+Y+PG SL+HRLDPR+KL+ + +++ I+F ANNV T L+ FT+ VV L+++ Sbjct: 2 MDSMIIGKYVPGTSLVHRLDPRTKLITIFLFVCIVFLANNVQTYALLGLFTIGVVSLTRV 61 Query: 61 KLSFFLNGVKPMIGIILFTTLFQMFFSQGGKVIFSWWFISITDLGLSQAILIFMRFVLII 120- SF + G+KP+I I+LFT L + + G +IF F + + GL Q I I +RFV +I Sbjct: 62 PFSFLMKGLKPIIWIVLFTFLLHILMTHEGPIIFQIGFSRVYEGGLVQGIFISLRFVYLI 121- Query: 121 FFSTLLTLTTTPLSLSDAVESLLKPLTRFKVPAHEIGLMLSLSLRFVPTLMDDTTRIMNA 18- 0 +TLLTLTTTP+ ++D +E LL PL + K+P HE+ LM+S+SLRF+PTLM++T +IM A Sbjct: 122 LITTLLTLTTTPIEITDGMEQLLNPLKKLKLPVHELALMMSISLRFIPTLMEETDKIMKA 18- 1 Query: 181 QRARGVDFGEGNLIQKVKSIIPILIPLFASSFKRADALAIAMEARGYQGGEGRTKYRQLD 24- 0 Q ARGVDF G + ++VK+I+P+L+PLF S+FKRA+ LA+AMEARGYQGGEGRTKYR+L Sbjct: 182 QMARGVDFTSGPVKERVKAIVPLLVPLFVSAFKRAEELAVAMEARGYQGGEGRTKYRKLV 24- 1 Query: 241 WQLKDSLAIGIVSLLGLLLFFLK 263 W KD+ I + +L LLF L+ Sbjct: 242 WTGKDTSVIVSLIVLAALLFSLR 264 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03062 Identities = 210/263 (79%), Positives = 237/263 (89%) Query: 7 MDKLILGRYIPGNSLIHKLDPRSKLLAMLLFIIIVFWANNVVTNVIVFIFTLVIVGLSQI 66 MDKLILGRYIPG+SLIH+LDPRSKLLAM+++I+I+FWANNVVTN+++ FTL +V LS+I Sbjct: 1 MDKLILGRYIPGDSLIHRLDPRSKLLAMIIYIVIIFWANNVVTNLLMLTFTLAVVFLSKI 60 Query: 67 KFSYFFNGIKPMVGIILFTTLFQMLFAQGGQVIFSFWIFSITSLGLQQAALIFMRFVLII 126- K S+F NG+KPM+GIILFTTLFQM F+QGG+VIFS+W SIT LGL QA LIFMRFVLII Sbjct: 61 KLSFFLNGVKPMIGIILFTTLFQMFFSQGGKVIFSWWFISITDLGLSQAILIFMRFVLII 120- Query: 127 FFSTLLTLTTTPLSLADAVESLLKPLEVLRVPAHEIGLMLSLSLRFVPTLMDDTTRIMNA 18- 6 FFSTLLTLTTTPLSL+DAVESLLKPL +VPAHEIGLMLSLSLRFVPTLMDDTTRIMNA Sbjct: 121 FFSTLLTLTTTPLSLSDAVESLLKPLTRFKVPAHEIGLMLSLSLRFVPTLMDDTTRIMNA 18- 0 Query: 187 QRARGVDFGEGNLIHKVKSIIPILIPLFASSFKRADALAIAMEARGYQGGANRSKYRLLK 24- 6 QRARGVDFGEGNLI KVKSIIPILIPLFASSFKRADALAIAMEARGYQGG R+KYR L Sbjct: 181 QRARGVDFGEGNLIQKVKSIIPILIPLFASSFKRADALAIAMEARGYQGGEGRTKYRQLD 24- 0 Query: 247 WTVRDTFSILLMLLLGLSLFLLK 269 W ++D+ +I ++ LLGL LF LK Sbjct: 241 WQLKDSLAIGIVSLLGLLLFFLK 263 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1030 A DNA sequence (GBSx1101) was identified in S. agalactiae <SEQ ID 3179> which encodes the amino acid sequence <SEQ ID 3180>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following: TABLE-US-03063 Possible site: 45 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.05 Transmembrane 22-38 (16-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.5819 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 3181> which encodes the amino acid sequence <SEQ ID 3182>. Analysis of this protein sequence reveals the following: TABLE-US-03064 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03065 Identities = 116/233 (49%), Positives = 140/233 (59%), Gaps = 39/233 (16%) Query: 9 KLNVKKHHLAYGAITLVALFSCILAVMVIFKSSQVTTESLSKADKVRVAKKSK------- 61 K N+K+ + +G LVAL ILA++ F S T+S +K + ++ K Sbjct: 4 KENLKQRYFNFG---LVALALTILAIIFAFSSKNADTKSYAKKSESKMVTIDKAPKNNHA 60 Query: 62 MTKATSKSKVEDVKQAPKPSQASNEAPKSSSQSTEANSQQQVTASEEAAVEQAVVTENTP 121- +TK SK K + + P P+ ++ AP T +EE V Q VT Sbjct: 61 ITKEESKEKAKSIASEPIPTVENSVAP---------------TVTEEVPVVQQEVT---- 101- Query: 122 ATSQAQQAYAVTETTYRPAQHQTSGQVLSNGNTAGAIGSAAAAQMAAATGVPQSTWEHII 18- 1 Q V+ Y P + VLSNGNTAG +GS AAAQMAAATGVPQSTWEHII Sbjct: 102 -----QTVQQVSSVAYNP-----NNVVLSNGNTAGIVGSQAAAQMAAATGVPQSTWEHII 15- 1 Query: 182 ARESNGNPNVANASGASGLFQTMPGWGSTATVQDQVNSAIKAYRAQGLSAWGY 234 ARESNGNPN ANASGASGLFQTMPGWGSTATV+DQVN+A+KAY AQGLSAWGY Sbjct: 152 ARESNGNPNAANASGASGLFQTMPGWGSTATVEDQVNAALKAYSAQGLSAWGY 204 A related GBS gene <SEQ ID 8713> and protein <SEQ ID 8714> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03066 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 2.48 GvH: Signal Score (-7.5): -3.74 Possible site: 45 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -12.05 threshold: 0.0 INTEGRAL Likelihood = -12.05 Transmembrane 22-38 (16-43) PERIPHERAL Likelihood = 4.29 156 modified ALOM score: 2.91 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5819(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00069## SEQ ID 3180 (GBS25) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 14 (lane 5; MW 25 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 11; MW 50 kDa), FIG. 63 (lane 6; MW 50.3 kDa), FIG. 66 (lane 6; MW 50 kDa) and in FIG. 175 (lane 8 & 9; MW 50 kDa). Purified GBS25-GST is shown in FIG. 9A, FIG. 193 (lane 11) and FIG. 210 (lane 5). The purified GBS25-GST fusion product was used to immunise mice (lane 1+2+3 products; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 95B), FACS (FIG. 95C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1031 A DNA sequence (GBSx1103) was identified in S. agalactiae <SEQ ID 3183> which encodes the amino acid sequence <SEQ ID 3184>. This protein is predicted to be L-serine dehydratase 1 (sdaA-2). Analysis of this protein sequence reveals the following: TABLE-US-03067 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.85 Transmembrane 205-221 (205-221) INTEGRAL Likelihood = -0.59 Transmembrane 171-187 (171-187) INTEGRAL Likelihood = -0.53 Transmembrane 226-242 (226-242) ----- Final Results ----- bacterial membrane --- Certainty = 0.1341(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03068 >GP:CAB13459 GB:Z99112 similar to L-serine dehydratase [Bacillus subtilis] Identities = 176/289 (60%), Positives = 224/289 (76%), Gaps = 1/289 (0%) Query: 1 MFYTIEELVEQANSQHKGNIAELMIQTEIEMTGRSREEIRYIMSRNLEVMKASVIDGLTP 60 MF ++EL+E + + I+++MI E+E+T +++E+I M NL VM+A+V GL Sbjct: 1 MFRNVKELIE-ITKEKQILISDVMIAQEMEVTEKTKEDIFQQMDHNLSVMEAAVQKGLEG 59 Query: 61 SKSISGLTGGDAVKMDQYLQSGKTISDTTILAAVRNAMAVNELNAKKMGLVCATPTAGSAG 12- 0 S +GLTGGDAVK+ Y++SGK++S IL AV A+A NE+NA MG +CATPTAGSAG Sbjct: 60 VTSQTGLTGGDAVKLQAYIRSGKSLSGPLILDAVSKAVATNEVNAAMGTICATPTAGSAG 119- Query: 121 CLPAVISTAIEKLNLTEEEQLDFLFTAGAFGLVIGNNASISGAEGGCQAEVGSASAMAAA 18- 0 +P + EKLN T E+ + FLFTAGAFG V+ NNASISGA GGCQAEVGSAS MAAA Sbjct: 120 VVPGTLFAVKEKLNPTREQMIRFLFTAGAFGFVVANNASISGAAGGCQAEVGSASGMAAA 17- 9 Query: 181 ALVMAGGTPFQASQAIAFVIKNMLGLICDPVAGLVEVPCVKRNALGSSFALVAADMALA 240- A+V AGGTP Q+++A+A +KNMLGL+CDPVAGLVEVPCVKRNA+G+S A++AADMALA Sbjct: 180 AIVEMAGGTPEQSAEAMAITLKNMLGLVCDPVAGLVEVPCVKRNAMGASNAMIAADMALA 23- 9 Query: 241 GIESQIPVDEVIDAMYQVGSSLPTAFRETAEGGLAATPTGRRYSKEIFG 289 GI S+IP DEVIDAMY++G ++PTA RET +GGLAATPTGR K+IFG Sbjct: 240 GITSRIPCDEVIDAMYKIGQTMPTALRETGQGGLAATPTGRELEKKIFG 288 A related DNA sequence was identified in S. pyogenes <SEQ ID 3185> which encodes the amino acid sequence <SEQ ID 3186>. Analysis of this protein sequence reveals the following: TABLE-US-03069 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.12 Transmembrane 196-212 (196-213) INTEGRAL Likelihood = -0.27 Transmembrane 226-242 (226-242) ----- Final Results ----- bacterial membrane --- Certainty = 0.1447 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03070 >GP:CAB13459 GB:Z99112 similar to L-serine dehydratase [Bacillus subtilis] Identities = 173/289 (59%), Positives = 222/289 (75%), Gaps = 1/289 (0%) Query: 1 MFYTIEELVKQADQQFNGNIAELMIATEVEMSGRNREDIIKIMSRNLQVMKAAVTEGLTS 60 MF ++EL++ ++ I+++MIA E+E++ + +EDI + M NL VM+AAV +GL Sbjct: 1 MFRNVKELIEITKEK-QILISDVMIAQEMEVTEKTKEDIFQQMDHNLSVMEAAVQKGLEG 59 Query: 61 TKSISGLTGGDAVKMDNYIKKGNSLSDTTILNAVRNAIAVNELNAKHGLVCATPTAGSAG 120- S +GLTGGDAVK+ YI+G SLS IL+AV A+A NE+NA MG +CATPTAGSAG Sbjct: 60 VTSQTGLTGGDAVKLQAYIRSGKSLSGPLILDAVSKAVATNEVNAAMGTICATPTAGSAG 119- Query: 121 CLPAVLATAIEKLDLSEKEQLEFLFTAGAFGLVIGNNASISGAEGGCQAEVGSAAAMSAA 18- 0 +P L EKL+ + ++ + FLFTAGAFG V+ NNASISGA GGCQAEVGSA+ M+AA Sbjct: 120 VVPGTLFAVKEKLNPTREQMIRFLFTAGAFGFVVANNASISGAAGGCQAEVGSASGMAAA 17- 9 Query: 181 ALVKAAGGTSHQASQAIAFVIKNLLGLVCDPVAGLVEVPCVKRNALGASFALVAADMALA 24- 0 A+V+ AGGT Q+++A+A +KN+LGLVCDPVAGLVEVPCVKRNA+GAS A++AADMALA Sbjct: 180 AIVEMAGGTPEQSAEAMAITLKNMLGLVCDPVAGLVEVPCVKRNAMGASNAMIAAOMALA 23- 9 Query: 241 DIDSQIPVDEVIDAMYQVGSAMPTAFRETAEGGLAATPTGRRYSVEIFG 289 I S+IP DEVIDAMY++G MPTA RET +GGLAATPTGR +IFG Sbjct: 240 GITSRIPCDEVIDAMYKIGQTMPTALRETGQGGLAATPTGRELEKKIFG 288 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03071 Identities = 244/290 (84%), Positives = 273/290 (94%) Query: 1 MFYTIEELVEQANSQHKGNIAELMIQTEIEMTGRSREEIRYIMSRNLEVMKASVIDGLTP 60 MFYTIEELV+QA+ Q GNIAELMI TE+EM+GR+RE+I IMSRNL+VMKA+V +GLT Sbjct: 1 MFYTIEELVKQADQQFNGNIAELMIATEVEMSGRNREDIIKIMSRNLQVMKAAVTEGLTS 60 Query: 61 SKSISGLTGGDAVKMDQYLQSGKTISDTTILAAVRNAMAVNELNAKMGLVCATPTAGSAG 120- +KSISGLTGGDAVKMD Y++ G ++SDTTIL AVRNA+AVNELNAKMGLVCATPTAGSAG Sbjct: 61 TKSISGLTGGDAVKMDNYIKKGNSLSDTTILNAVRNAIAVNELNAKMGLVCATPTAGSAG 120- Query: 121 CLPAVISTAIEKLNLTEEEQLDFLFTAGAFGLVIGNNASISGAEGGCQAEVGSASAMAAA 18- 0 CLPAV++TAIEKL+L+E+EQL+FLFTAGAFGLVIGNNASISGAEGGCQAEVGSA+AM+AA Sbjct: 121 CLPAVLATAIEKLDLSEKEQLEFLFTAGAFGLVIGNNASISGAEGGCQAEVGSAAAMSAA 18- 0 Query: 181 ALVMAAGGTPFQASQAIAFVIKNMLGLICDPVAGLVEVPCVKRNALGSSFALVAADMALA 24- 0 ALV AAGGT QASQAIAFVIKN+LGL+CDPVAGLVEVPCVKRNALG+SFALVAADMALA Sbjct: 181 ALVKAAGGTSHQASQAIAFVIKNLLGLVCDPVAGLVEVPCVKRNALGASFALVAADMALA 24- 0 Query: 241 GIESQIPVDEVIDAMYQVGSSLPTAFRETAEGGLAATPTGRRYSKEIFGE 290 I+SQIPVDEVIDAMYQVGS++PTAFRETAEGGLAATPTGRRYS EIFGE Sbjct: 241 DIDSQIPVDEVIDAMYQVGSAMPTAFRETAEGGLAATPTGRRYSVEIFGE 290 SEQ ID 3184 (GBS358) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 176 (lane 6; MW 35 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1032 A DNA sequence (GBSx1104) was identified in S. agalactiae <SEQ ID 3187> which encodes the amino acid sequence <SEQ ID 3188>. Analysis of this protein sequence reveals the following: TABLE-US-03072 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03073 >GP:BAB06216 GB:AP001515 L-serine dehydratase beta subunit [Bacillus halodurans] Identities = 101/216 (46%), Positives = 156/216 (71%), Gaps = 2/216 (0%) Query: 4 LKFQSVFDIIGPVMIGPSSSHTAGAVRIGKVVHSIFGE-PSEVTFHLYNSFAKTYQGHGT 62 +K+++VFDIIGPVMIGPSSSHTAGA RIG+V ++FG+ P + Y SFA+TY+GHGT Sbjct: 1 MKYRTVFDIIGPVMIGPSSSHTAGAARIGRVARTLFGQQPERCDIYFYGSFAETYKGHGT 60 Query: 63 DKALVAGILGMDTDNPDIKNSLEIAHQKGIKIYWDILKDSNSPHPNTAKITVKNGDRSMS 122- D A+V GIL DT +P I SL++A +KG+++Y+ +++ + HPNTAK+ ++ G+ + Sbjct: 61 DVAIVGGILDFDTFDPRIPRSLQLAKEKGVRVYFHE-EEAITDHPNTAKVVLQKGEDQLE 119- Query: 123 ITGVSIGGGNIQVTELNGFSVSLTMNTPTLIIVHQDIPGMIAKVTDILSDFNINIAQMNV 18- 2 + GVSIGGG I++ ELNGF + L+ N P +++VH D G+IA V+++L+ INI M V Sbjct: 120 VVGVSIGGGKIEIVELNGFHLKLSGNHPAILVVHTDRFGVIASVSNMLAKHEINIGHMEV 17- 9 Query: 183 TRESAGEKAIMIIEVDSRDCQQAVKKIEAIPHLHNV 218 +R+ G++A+M+IEVD ++++E +P++ V Sbjct: 180 SRKEKGKEALMVIEVDQNVDDLLLQELERLPNIVTV 215 A related DNA sequence was identified in S. pyogenes <SEQ ID 3189> which encodes the amino acid sequence <SEQ ID 3190>. Analysis of this protein sequence reveals the following: TABLE-US-03074 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9161> which encodes the amino acid sequence <SEQ ID 9162>. Analysis of this protein sequence reveals the following: TABLE-US-03075 Possible Site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.300(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03076 Identities = 187/223 (83%), Positives = 205/223 (91%), Gaps = 1/223 (0%) Query: 1 MKHLKFQSVFDIIGPVMIGPSSSHTAGAVRIGKVVHSIFGE-PSEVTFHLYNSFAKTYQG 59 M KFQSVFDIIGPVMIGPSSSHTAGAVRIGKVVHSIFG+ P EVTFHLYNSFAKTY+G Sbjct: 3 MNTQKFQSVFDIIGPVMIGPSSSHTAGAVRIGKVVHSIFGDIPDEVTFHLYNSFAKTYRG 62 Query: 60 HGTDKALVAGILGMDTDNPDIKNSLEIAHQKGIKIYWDILKDSNSPHPNTAKITVKNGDR 119- HGTDKALVAGI+GM TDNPDIKNSLEIAHQKGIKIYWDILKDSN+PHPNT KI+VK D+ Sbjct: 63 HGTDKALVAGIMGMGTDNPDIKNSLEIAHQKGIKIYWDILKDSNAPHPNTVKISVKKADK 122- Query: 120 SMSITGVSIGGGNIQVTELNGFSVSLTMNTPTLIIVHQDIPGMIAKVTDILSDFNINIAQ 17- 9 ++S+TGVSIGGGNIQVTELNGFSVSL+MNTPT++ VH+DIPGMIAKVTDILS NINIA Sbjct: 123 TLSVTGVSIGGGNIQVTELNGFSVSLSMNTPTIVTVHKDIPGMIAKVTDILSSNNINIAT 18- 2 Query: 180 MNVTRESAGEKAIMIIEVDSRDCQQAVKKIEAIPHLHNVNFFD 222 MNVTRESAGEKA MIIEVDSR+CQ+A +I IPH++NVNFFD Sbjct: 183 MNVTRESAGEKATMIIEVDSRECQEAANQIAKIPHIYNVNFFD 225 SEQ ID 3188 (GBS151) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 31 (lane 3; MW 50 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 188 (lane 11; MW 25 kDa) and in FIG. 165 (lane 14-16; MW 25.3 kDa). The GBS151-GST fusion product was purified (FIG. 198, lane 3; FIG. 236, lane 8) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 289), which confirmed that the protein is immunoaccessible on GBS bacteria. GBS151L was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 127 (lane 8-10; MW 50 kDa). GBS151L was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 127 (lane 11 & 12; MW 25 kDa), in FIG. 128 (lane 7; MW 25 kDa) and in FIG. 180 (lane 7; MW 25 kDa). Purified GBS151L-His is shown in FIG. 232 (lanes 5 & 6) and in FIG. 240 (lanes 3 & 4). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1033 A DNA sequence (GBSx1105) was identified in S. agalactiae <SEQ ID 3191> which encodes the amino acid sequence <SEQ ID 3192>. This protein is predicted to be tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (trmU). Analysis of this protein sequence reveals the following: TABLE-US-03077 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2208(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10291> which encodes amino acid sequence <SEQ ID 10292> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03078 >GP:BAB04980 GB:AP001511 (5-methylaminomethyl-2-thiouridylate)-methyltran sferase [Bacillus halodurans] Identities = 250/359 (69%), Positives = 292/359 (80%), Gaps = 6/359 (1%) Query: 32 RVVVGMSGGVDSSVTALLLKEQGYDVIGVFMKNWDDTDEFGVCTATEDYKDVAAVADQIG 91 - RVVVGMSGGVDSSVTALLLKEQGYDVIG+FMKNWDDTDE GVCTATEDY+DV V +Q+G Sbjct: 10 RVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDDTDENGVCTATEDYQDVVQVCNQLG 69 Query: 92 IPYYSVNFEKEYWDRVFEYFLAEYRAGRTPNPDVMCNKEIKFKAFLDYAMTLGADYVATG 151- I YY+VNFEKEYWD+VF YFL EY+AGRTPNPDVMCNKEIKFKAFL++A+TLGADYVATG Sbjct: 70 IAYYAVNFEKEYWDKVFTYFLEEYKAGRTPNPDVMCNKEIKFKAFLNHALTLGADYVATG 129- Query: 152 HYAQVTRDENGIVHMLRGADNNKDQTYFLSQLSQEQLQKTLFPLGHLQKPEVRRIAEEAG 21- 1 HYAQV ++ +G ++RG D NKDQTYFL+ LSQ+QL + +FPLGHL+K EVR IAE AG Sbjct: 130 HYAQV-KNVDGQYQLIRGKDPNKDQTYFLNALSQQQLSRVMFPLGHLSKKEVRAIAERAG 18- 8 Query: 212 LATAKKKDSTGICFIGEKNFKDFLGQYLPAQPGRMMTVDGRDMGEHAGLMYYTIGQRGGL 27- 1 LATAKKKDSTGICFIG+++FK+FL YLPAQPG M T+DG G H GLMYYT+GQR GL Sbjct: 189 LATAKKKDSTGICFIGKRDFKEFLSSYLPAQPGEMQTLDGEVKGTHDGLMYYTLGQRQGL 24- 8 Query: 272 GIGGQHGGDNKPWFVVGKDLSKNILYVGQGFYHDSLMSTSLTASEIHFTRDMPNEFKLEC 33- 1 GI GG +PWFV+GK+L KNILYVGQGF+H L S L A ++++ ++ EC Sbjct: 249 GI----GGSGEPWFVIGKNLSKNILYVGQGFHHPGLYSEGLRAIKVNWILRRSSDEPFEC 30- 4 Query: 332 TAKFRYRQPDSKVTVYVKGNQA-RVVFDDLQRAITPGQAVVFYNEQECLGGGMIDQAYR 389- TAKFRYRQPD KVTVY + + A V+F + QRAITPGQAVVFY+ CLGGG ID + Sbjct: 305 TAKFRYRQPDQKVTVYPQSDGAVEVLFAEPQRAITPGQAVVFYDGDVCLGGGTIDHVLK 363- A related DNA sequence was identified in S. pyogenes <SEQ ID 3193> which encodes the amino acid sequence <SEQ ID 3194>. Analysis of this protein sequence reveals the following:

TABLE-US-03079 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1691(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> RGD motif: 331-333 The protein has homology with the following sequences in the databases: TABLE-US-03080 >GP: BAB04980 GB: AP001511 (5-methylaminomethyl-2-thiouridylate)-methyltran sferase [Bacillus halodurans] Identities = 255/359 (71%), Positives = 293/359 (81%), Gaps = 6/359 (1%) Query: 14 RVVVGMSGGVDSSVTALLLKEQGYDVIGVFMKNWDDTDEFGVCTATEDYKDVAAVADKIG 73 - RVVVGMSGGVDSSVTALLLKEQGYDVIG+FMKNWDDTDE GVCTATEDY+DV V +++G Sbjct: 10 RVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDDTDENGHVCTATEDYQDVVQVCNQLG 69- Query: 74 IPYYSVNFEKEYWDRVFEYFLAEYRAGRTPNPDVMCNKEIKFKAFLDYAMTLGADYVATG 133- I YY+VNFEKEYWD+VF YFL EY+AGRTPNPDVMCNKEIKFKAFL++A+TLGADYVATG Sbjct: 70 IAYYAVNFEKEYWDKVFTYFLEEYKAGRTPNDDVMCNKEIKFKAFLNHALTLGADYVATG 129- Query: 134 HYAQVRRDENGTVHMLRGADNGKDQTYFLSQLSQEQLQKTLFPLGHLQKSEVREIAERAG 19- 3 HYAQVK + +G ++RG D KDQTYFL+ LSQ+QL + +FPLGHL+K EVR IAERAG Sbjct: 130 HYAQVK-NVDGQYQLIRGKDPNKDQTYFLNALSQQQLSRVMFPLGHLEKKEVRAIAERAG 18- 8 Query: 194 LATAKKKDSTGICFIGEKNFKQFLSQYLPAQKGRMMTIDGRDMGEHAGLMYYTIGQRGGL 25- 3 LATAKKKDSTGICFIG+++FK+FLS YLPAQ G M T+DG G H GLMYYT+GQR GL Sbjct: 189 LATAKKKDSTGICFIGKRDFKEFLSSYLPAQPGEMTQTLDGEVKGTHDGLMYYTLGQRQGL 2- 48 Query: 254 GIGGQHGGDNQPWFVVGKDLSQNILYVGQGFYHEALMSNSLDASVIHFTREMPEEFTFEC 31- 3 GI GG +PWFV+GK+L +NILYVGQGF+H L S L A +++ + FEC Sbjct: 249 GI----GGSGEPWFVIGKNLEKNILYVGQGFHHPGLYSEGLRAIKVNWILRRESDEPFEC 30- 4 Query: 314 TAKFRYRQPDSHVAVHVRGDKA-EVVFAEPQRAITPGQAVVFYDGKECLGGGMIDMAYK 371- TAKFRYRQPD V V+ + D A EV+FAEPQRAITPGQAVVFYDG CLGGG ID K Sbjct: 305 TAKFRYRQPDQKVTVYPQSDGAVEVLFAEPQRAITPGQAVVFYDGDVCLGGGTIDHVLK 363- An alignment of the GAS and GBS proteins is shown below. TABLE-US-03081 Identities = 332/377 (88%), Positives = 349/377 (92%) Query: 21 GRILMTDNSNIRVVVGMSGGVDSSVTALLLKEQGYDVIGVFMKNWDDTDEFGVCTATEDY 80 - G MTDNS IRVVVGMSGGVDSSVTALLLKEQGYDVIGVFMKNWDDTDEFGVCTATEDY Sbjct: 3 GEFFMTDNSKIRVVVGMSGGVDSSVTALLLKEQGYDVIGVFMKNWDDTDEFGVCTATEDY 62 Query: 81 KDVAAVADQIGIPYYSVNFEKEYWDRVFEYFLAEYRAGRTPNPDVMCNKEIKFKAFLDYA 140- KDVAAVAD+IGIPYYSVNFEKEYWDRVFEYFLAEYRAGRTPNPDVMCNKEIKFKAFLDYA Sbjct: 63 KDVAAVADKIGIPYYSVNFEKEYWDRVFEYFLAEYRAGRTPNPDVMCNKEIKFKAFLDYA 122- Query: 141 MTLGADYVATGHYAQVTRDENGIVHMLRGADNNKDQTYFLSQLSQEQLQKTLFPLGHLQK 20- 0 MTLGADYVATGHYAQV RDENG VHMLRGADN KDQTYFLSQLSQEQLQKTLFPLGHLQK Sbjct: 123 MTLGADYVATGHYAQVKRDENGTVHMLRGADNGKDQTYFLSQLSQEQLQKTLFPLGHLQK 18- 2 Query: 201 PEVRRIAEEAGLATAKKKDSTGICFIGEKNFKDFLGQYLPAQPGRMMTVDGRDMGEHAGL 26- 0 EVR IAE AGLATAKKKDSTGICFIGEKNFK FL QYLPAQ GRMMT+DGRDMGEHAGL Sbjct: 183 SEVREIAERAGLATAKKKDSTGICFIGEKNFKQFLSQYLPAQKGRMMTIDGRDMGEHAGL 24- 2 Query: 261 MYYTIGQRGGLGIGGQHGGDNKPWFVVGKDLSKNILYVGQGFYHDSLMSTSLTASEIHFT 32- 0 MYYTIGQRGGLGIGGQHGGDN+PWFVVGKDLS+NILYVGQGFYH++LMS SL AS IHFT Sbjct: 243 MYYTIGQRGGLGIGGQHGGDNQPWFVVGKDLSQNILYVGQGFYHEALMSNSLDASVIHFT 30- 2 Query: 321 RDMPNEFKLECTAKFRYRQPDSKVTVYVKGNQARVVFDDLQRAITPGQAVVFYNEQECLG 38- 0 R+MP EF ECTAKFRYRQPDS V V+V+G++A VVF + QRAITPGQAVVFY+ +ECLG Sbjct: 303 REMPEEFTFECTAKFRYRQPDSHVAVHVRGDKAEVVFAEPQRAITPGQAVVFYDGKECLG 36- 2 Query: 381 GGMIDQAYRDDKICQYI 397 GGMID AY++ + CQYI Sbjct: 363 GGMIDMAYKNGQPCQYI 379 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1034 A DNA sequence (GBSx1106) was identified in S. agalactiae <SEQ ID 3195> which encodes the amino acid sequence <SEQ ID 3196>. Analysis of this protein sequence reveals the following: TABLE-US-03082 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.84 Transmembrane 141-157 (134-165) INTEGRAL Likelihood = -11.78 Transmembrane 40-56 (36-73) INTEGRAL Likelihood = -4.35 Transmembrane 68-84 (65-86) INTEGRAL Likelihood = -3.50 Transmembrane 180-196 (175-199) ----- Final Results ----- bacterial membrane --- Certainty = 0.6137(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03083 >GP: CAB15390 GB: Z99121 similar to hypothetical proteins [Bacillus subtilis] Identities = 71/202 (35%), Positives = 120/202 (59%), Gaps = 5/202 (2%) Query: 1 MISKFILAFMAFFAIMNPISNLPAFMALVADDDQKISRRIAAKGVLLAFVIIVIFVLSGH 60 M S + F++FA+ NPI N+P F+ L + IA K +L+F I+ F++ GH Sbjct: 2 MFSFIVHVFISLFAVSNPIGNVPIFLTLTEGYTAAERKAIARKAAILSFFILAAFLVFGH 61 Query: 61 LLFNLFGITLAALKISGGILVGIIGYKMINGIHSPTNK-NLEEHKD--DPMNVAVSPLAM 117- L+F LF I + AL+++GGI + I Y ++N S + +EHK+ + +++V+PL++ Sbjct: 62 LIFKLFDINIHALRVAGGIFIFGIAYNLLNAKESHVQSLHHDEHKESKEKADISVTPLSI 121- Query: 118 PLLAGPGTIATAMGLSSG--GLSGKLITILAFAILCVIMYVILISANEITKFLGKNANTI 17- 5 P++AGPGTIAT M LS+G G+ ++ A + + ++ + I+ LGK M + Sbjct: 122 PIIAGPGTIATVMSLSAGHSGIGHYAAVMIGIAAVIALTFLFFHYSAFISSKLGKTEMNV 18- 1 Query: 176 ITKMMGLILMTIGIEMLITGIK 197 IT++MGLIL + + M+ G+K Sbjct: 182 ITRLMGLILAVVAVGMIGAGLK 203 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8715> and protein <SEQ ID 8716> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03084 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 9.79 GvH: Signal Score (-7.5): -1.53 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 4 value: -12.84 threshold: 0.0 INTEGRAL Likelihood = -12.84 Transmembrane 141-157 (134-165) INTEGRAL Likelihood = -11.78 Transmembrane 40-56 (36-73) INTEGRAL Likelihood = -4.35 Transmembrane 68-84 (65-86) INTEGRAL Likelihood = -3.50 Transmembrane 180-196 (175-199) PERIPHERAL Likelihood = 1.27 110 modified ALOM score: 3.07 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6137(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial Cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00070## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1035 A DNA sequence (GBSx1107) was identified in S. agalactiae <SEQ ID 3197> which encodes the amino acid sequence <SEQ ID 3198>. Analysis of this protein sequence reveals the following: TABLE-US-03085 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1747(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10289> which encodes amino acid sequence <SEQ ID 10290> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03086 >GP: AAC45494 GB: U80409 glucose inhibited division protein homolog GidA [Lactococcus lactis subsp. cremoris] Identities = 394/524 (75%), Positives = 458/524 (87%), Gaps = 2/524 (0%) Query: 13 KTLLATINLEMLAFMPCNPSIGGSAKGIVVREIDALGGEMGKNIDKTYIQMKMLNTGKGP 72 - KTLL TINL M+AFMPCNPSIGGSAKGIVVREIDALGGEMG+NIDKTYIQMKMLNTGKGP Sbjct: 12 KTLLMTINLNMVAFMPCNPSIGGSAKGIVVREIDALGGEMGRNIDKTYIQMKMLNTGKGP 71 Query: 73 AVRALRAQADKALYAQTMKQTVEKQENLTLRQAMIDEILVEDGK--VVGVRTATNQKFSA 130- AVRALRAQADK YA +MK TV QENLTLRQ M++E++++D K V+GVRT+T ++ A Sbjct: 72 AVRALRAQADKDEYAASMKNTVSDQENLTLRQGMVEELILDDEKQKVIGVRTSTGTQYGA 131- Query: 131 KSVVITTGTALRGEIILGDLKYSSGPNNSLASVTLADNLRDLGLEIGRFKTGTPPRVKAS 19- 0 K+V+ITTGTALRGEII+G+LKYSSGPNNSL+S+ LADNLR++G EIGRFKTGTPPRV AS Sbjct: 132 KAVIITTGTALRGEIIIGELKYSSGPNNSLSSIGLADNLREIGFEIGRFKTGTPPRVLAS 19- 1 Query: 191 SINYEKTEIQPGDEQPNHFSFMSRDEDYITDQVPCWLTYTNTLSHDIINQNLHRAPMFSG 25- 0 SI+Y+KTEIQPGDE PNHFSFMS DEDY+ DQ+PCWLTYT SH I+ NLHRAP+FSG Sbjct: 192 SIDYDKTEIQPGDEAPNHFSFMSSDEDYLKDQIPCWLTYTTENSHTILRDNLHRAPLFSG 25- 1 Query: 251 IVKGVGPRYCPSIEDKIVRFADKERHQLFLEPEGRYTEEVYVQGLSTSLPEDVQVDLLRS 31- 0 IVKGVGPRYCPSIEDKI RFADK RHQLFLEPEGR TEEVY+ GLSTS+PEDVQ DL++S Sbjct: 252 IVKGVGPRYCPSIEDKITRFADKPRHQLFLEPEGRNTEEVYIGGLSTSMPEDVQFDLVKS 31- 1 Query: 311 IKGLENAEMMRTGYAIEYDIVLPHQLRATLETKVIAGLFTAGQTNGTSGYEEAAGQGLVA 37- 0 I GLENA+MMR GYAIEYD+V+PHQLR TLETK+I+GLFTAGQTNGTSGYEEAAGQGLVA Sbjct: 312 IPGLENAKMMRPGYAIEYDVVMPHQLRPTLETKLISGLFTAGQTNGTSGYEEAAGQGLVA 37- 1 Query: 371 GINAALKVQGKPELILKRSDAYIGVMIDDLVTKGTLEPYRLLTSRAEYRLILRHDNADMR 43- 0 GINAALK+QGKPE ILKRS+AYIGVMIDDLVTKGTLEPYRLLTSRAEYRLILRHDNAD R Sbjct: 372 GINAALKIQGKPEFILKRSEAYIGVMIDDLVTKGTLEPYRLLTSRAEYRLILRHDNADRR 43- 1 Query: 431 LTEIGYEIGLVDEERYAIFKKRQMQFENELERLDSIKLKPVSETNKRIQELGFKPLTDAL 49- 0 LTEIG ++GLV + ++ ++ + QF+ E++RL+S KLKP+ +T +++ +LGF P+ DAL Sbjct: 432 LTEIGRQVGLVSDAQWEHYQAKMAQFDREMKRLNSEKLKPLPDTQEKLGKLGFGPIKDAL 49- 1 Query: 491 TAKEFMRRPQITYAVATDFVGCADEPLDSKVIELLETEIKYEGY 534 T EF++RP++ Y DF+G A E +D V EL+ETEI YEGY Sbjct: 492 TGAEFLKRPEVNYDEVIDFIGQAPEVIDRTVSELIETEITYEGY 535 A related DNA sequence was identified in S. pyogenes <SEQ ID 3199> which encodes the amino acid sequence <SEQ ID 3200>. Analysis of this protein sequence reveals the following: TABLE-US-03087 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1064 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03088 Identities = 530/610 (86%), Positives = 574/610 (93%) Query: 1 MEASLAASRMGCKTLLATINLEMLAFMPCNPSIGGSAKGIVVREIDALGGEMGKNIDKTY 60 +EASLA SRMGCKTLLATINL+MLAFMPCNPSIGGSAKGIVVREIDALGGEMGKNIDKTY Sbjct: 21 VEASLATSRMGCKTLLATINLDMLAFMPCNPSIGGSAKGIVVREIDALGGEMGKNIDKTY 80 Query: 61 IQMKMLNTGKGPAVRALRAQADKALYAQTMKQTVEKQENLTLRQAMIDEILVEDGKVVGV 120- IQMKMLNTGKGPAVRALRAQADK+LYA+ MK TVEKQ NLTLRQ MID+ILVEDG+VVGV Sbjct: 81 IQMKMLNTGKGPAVRALRAQADKSLYAREMKHTVEKQANLTLRQTMIDDILVEDGRVVGV 140- Query: 121 RTATNQKFSAKSVVITTGTALRGEIILGDLKYSSGPNNSLASVTLADNLRDLGLEIGRFK 18- 0 TAT QKF+AK+VV+TTGTALRGEIILG+LKYSSGPNNSLASVTLADNL+ LGLEIGRFK Sbjct: 141 LTATGQKFAAKAVVVTTGTALRGEIILGELKYSSGPNNSLASVTLADNLKKLGLEIGRFK 20- 0 Query: 181 TGTPPRVKASSINYEKTEIQPGDEQPNHFSFMSRDEDYITDQVPCWLTYTNTLSHDIINQ 24- 0 TGTPPRVKASSINY++TEIQPGD++PNHFSFMS+D DY+ DQ+PCWLTYTN SHDIINQ Sbjct: 201 TGTPPRVKASSINYDQTEIQPGDDKPNHFSFMSKDADYLKDQIPCWLTYTNQTSHDIINQ 26- 0 Query: 241 NLHRAPMFSGIVKGVGPRYCPSIEDKIVRFADKERHQLFLEPEGRYTEEVYVQGLSTSLP 30- 0 NL+RAPMFSGIVKGVGPRYCPSIEDKIVRFADKERHQLFLEPEGR TEEVYVQGLSTSLP Sbjct: 261 NLYRAPMFSGIVKGVGPRYCPSIEDKIVRFADKERHQLFLEPEGRDTEEVYVQGLSTSLP 32- 0 Query: 301 EDVQVDLLRSIKGLENAEMMRTGYAIEYDIVLPHQLRATLETKVIAGLFTAGQTNGTSGY 36- 0 EDVQ DL+ SIKGLE AEMMRTGYAIEYDIVLPHQLRATLETK+I+GLFTAGQTNGTSGY Sbjct: 321 EDVQKDLIHSIKGLEKAEMMRTGYAIEYDIVLPHQLRATLETKLISGLFTAGQTNGTSGY 38- 0 Query: 361 EEAAGQGLVAGINAALKVQGKPELILKRSDAYIGVMIDDLVTKGTLEPYRLLTSRAEYRL 42- 0 EEAAGQGL+AGINAALKVQGKPELILKRSDAYIGVMIDDLVTKGTLEPYRLLTSRAEYRL Sbjct: 381 EEAAGQGLIAGINAALKVQGKPELILKRSDAYIGVMIDDLVTKGTLEPYRLLTSRAEYRL 44- 0 Query: 421 ILRHDNADMRLTEIGYEIGLVDEERYAIFKKRQMQFENELERLDSIKLKPVSETNKRIQE 48- 0 ILRHDNADMRLTEIG +IGLVD+ER+ F+ ++ QF+NEL+RL+SIKLKP+ ETN R+Q+ Sbjct: 441 ILRHDNADMRLTEIGRDIGLVDDERWKAFEIKKNQFDNELKRLNSIKLKPIKETNDRVQD 50- 0 Query: 481 LGFKPLTDALTAKEFMRRPQITYAVATDFVGCADEPLDSKVIELLETEIKYEGYIKKALD 54- 0 LGFKPLTDA+TAKEFMRRP+I YA A FVG A E LD+K+IELLETEIKYEGYI+KALD Sbjct: 501 LGFKPLTDAMTAKEFMRRPEIDYATAVSFVGPAAEDLDAKIIELLETEIKYEGYIRKALD 56- 0 Query: 541 QVAKMKRMEEKRIPPHIDWDDIDSIATEARQKFKKINPETLGQASRISGVNPADISILMV 60- 0 QVAKMKRMEEKRIP +IDWD IDSIATEARQKFKKINPET+GQASRISGVNPADISILM+ Sbjct: 561 QVAKMKRMEEKRIPTNIDWDAIDSIATEARQKFKKINPETIGQASRISGVNPADISILMI 62- 0 Query: 601 YLEGRQKGRK 610 YLEG K + Sbjct: 621 YLEGNGKAHR 630 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1036 A DNA sequence (GBSx1108) was identified in S. agalactiae <SEQ ID 3201> which encodes the amino acid sequence <SEQ ID 3202>. Analysis of this protein sequence reveals the following: TABLE-US-03089 Possible site: 44 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03090 >GP:BAB07750 GB:AP001520 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 205/644 (31%), Positives = 362/644 (55%), Gaps = 28/644 (4%) Query: 35 LLLAIFVALSFVVALLYYQ---------------------KITYELSEVEQIELLNDQTE 73 - ++ + VAL F++AL + YQ +I++E + I L+ + Sbjct: 14 VIALLAVALVFLIALSFYQWQLGVIGVLLLLVIAIFSLRARISFERDLEQYISTLSYRVH 73 Query: 74 VSLKSLLEQMPVGVIQFDLETNDIEWFNPYA-ELIFTGDNGHFQSATVKDIITSRRNGTA 132- + + + Q+PVG+I ++ + ++W NPYA E + + +++ + GT Sbjct: 74 KAGEEAVTQLPVGMILYNDQLR-VQWVNPYAAEHLPKAEIDASLEELSPELVRALEEGTD 132- Query: 133 GQSFEYGDNKYSAYLDTETGVFYFFDNFMGNRRNYDSSMLRPVIGIISIDNYDDIMDTML 19- 2 Q + Y + YFFD R + +PV+ I +DNYD++ M Sbjct: 133 EQKIVIEEKTYDCTFKPNERLIYFFDITESERMHQQFEESQPVLTFIYLDNYDEVTQGME 19- 2 Query: 193 EADMSKINAFVTSFISDFTQSKNIFYRRVNMDRYYIFTDYSVLNTLIKDKFDILNEFRKR 25- 2 + S++ + VTS ++ + ++F RR DR+ Y L + K KF IL+E R+ Sbjct: 193 DQVRSRLMSQVTSSLNQWANEHDLFLRRTAADRFIAVMSYGSLLAIEKTKFGILDEIRET 25- 2 Query: 253 AQENHLSLTLSMGISYGDGNHNQIGQIALENLNTALVRGGDQIVVRENDSSKKALYFGGG 31- 2 + + LTLS+G+ YGD + ++GQ+A +L+ AL RGGDQ+ +++ K ++GG Sbjct: 253 TGKEKIPLTLSIGVGYGDLSLRELGQLAQSSLDLALGRGGDQVAIKQKTG--KVRFYGGK 31- 0 Query: 313 AVSTIKRSRTRTRAMMTAISDRLKVVDSVFIVGHRKLDMDALGASVGMQFFASNIVNASY 37- 2 + + KR+R R R + A+ D + D V ++GH+ DMDA+GA++G+ A ++ Sbjct: 311 SNAMEKRTRVRARVISHALRDFVLESDRVIVMGHKNPDMDAVGAAIGILKIAEVNDREAF 37- 0 Query: 373 VVYDPNDMNSDIERAIDYLQEDGET--RLVSVERAFELITQNSLLVMVDHSKTALTLSKE 43- 0 VV DPND+N D+ + ++ ++++ + + ++ E + EL+T+ +LLV+VD K ++ + Sbjct: 371 VVLDPNDVNPDVSKLMEEVEKNEQLWDKFITPEESLELMTEETLLVIVDTHKPSMVIEPR 43- 0 Query: 431 FFNKFADVIVVDHHRRDEDFPKNAVLSFIESGASSASELVTELIQFQQAKDKLSRSQASI 49- 0 + V+V+DHHRR E+F ++ VL ++E ASS +ELVTEL+++Q K K+ +++ Sbjct: 431 LLDYVERVVVLDHHRRGEEFIEDPVLVYMEPYASSTAELVTELLEYQPKKLKMDILESTA 49- 0 Query: 491 LMAGIMLDTRNFASNVTSRTFDVASYLRGLGSNSMAIQKISATDFDEYRLINELILKGER 55- 0 L+AG+++DT++FA +RTFD AS+LR G++++ +QK+ D + Y +L+ + Sbjct: 491 LLAGMIVDTKSFAIRTGARTFDAASFLRSHGADTVLVQKLLKEDLNHYVKRAKLVETAKL 55- 0 Query: 551 IYDNIIVATGEEHKVYSHVIASKAADTMLTMAGIEATFVITKNSSN-IGISARSRNNINV 60- 9 D + +AT E + S ++ ++AADT+LTM G+ A+FVI++ + ISARS ++NV Sbjct: 551 YRDGMAIATAREEEAVSQLLIAQAADTLLTMKGVVASFVISRRHDGVVSISARSLGDVNV 61- 0 Query: 610 QRIMEKLGGGGHFSFAACQIQDKSVKQVRRMLLEIIDEDLRENS 653 Q IME L GGGH + AA Q +D ++++ L E ID+ L S Sbjct: 611 QLIMESLDGGGHLTNAATQFEDATLEEAEAKLKEAIDQYLEGGS 654 A related DNA sequence was identified in S. pyogenes <SEQ ID 3203> which encodes the amino acid sequence <SEQ ID 3204>. Analysis of this protein sequence reveals the following: TABLE-US-03091 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -18.57 Transmembrane 33-49 (6-56) INTEGRAL Likelihood = -10.14 Transmembrane 12-28 (6-32) ----- Final Results ----- bacterial membrane --- Certainty = 0.8429 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03092 >GP:BAB07750 GB:AP001520 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 199/659 {grave over ( )}(30%), Positives = 367/659 (55%), Gaps = 16/659 (2%) Query: 1 MKKF---RFETIHLI-MMGLILFGLLALCVSIMQSKILILLAIFLVLLFVV-ALLWYQKE 55 M KF R+ H+I ++ + L L+AL Q ++ +L + ++ +F + A + ++++ Sbjct: 1 MPKFLLKRWHGYHVIALLAVALVFLIALSFYQWQLGVIGVLLLLVIAIFSLRARISFERD 60 Query: 56 AYQLSDLAHIELLNEQTEDNLKTLLDNMPVGVVQFDQETNAVEWYNPYA-ELIFTTEEGF 114- Q +I L+ + + + +PVG++ ++ + V+W NPYA E + E Sbjct: 61 LEQ-----YISTLSYRVHKAGEEAVTQLPVGMILYNDQLR-VQWVNPYAAEHLPKAEIDA 114- Query: 115 IQNGLIQQIITEKRREDISQTFEVSGNKYTSYIDVSSGIFYFFDSFVGNRQLADASMLRP 17- 4 L +++ Q + Y + + YFFD R +P Sbjct: 115 SLEELSPELVRALEEGTDEQKIVIEEKTYDCTFKPNERLIYFFDITESERMHQQFEESQP 17- 4 Query: 175 VVGIISVDNYDDITDDLSDADTSKINSFVANFIDEFMESKRIFYRRVNMDRYYFFTDFKT 23- 4 V+ I +DNYD++T + D S++ S V + ++++ +F RR DR+ + + Sbjct: 175 VLTFIYLDNYDEVTQGMEDQVRSRLMSQVTSSLNQWANEHDLFLRRTAADRFIAVMSYGS 23- 4 Query: 235 LNDLMDNKFSVLSEEFRKEAQDAQRPLTLSIGISFGEENHSQIGQVALENLNIALVRGGDQ 2- 94 L + KF +L+E R+ + PLTLSIG+ +G+ + ++GQ+A +L++AL RGGDQ Sbjct: 235 LLAIEKTKFGILDEIRETTGKEKIPLTLSIGVGYGDLSLRELGQLAQSSLDLALGRGGDQ 29- 4 Query: 295 IVIRENADHTNPIYFGGGSVSTVKRSRTRTRAMMTAISDRIKMVDNVFIVGHRKLDMDAL 35- 4 + I++ ++GG S + KR+R R R + A+ D + D V ++GH+ DMDA+ Sbjct: 295 VAIKQKTGKVR--FYGGKSNAMEKRTRVRARVISHALRDFVLESDRVIVMGHKNPDMDAV 35- 2 Query: 355 GSAVGMQFFAGNIIENSFAVYNPDEMSPDIERAIERLQADGKT--RLISVSQAMGLVTPR 41- 2 G+A+G+ A +F V +P++++PD+ + +E ++ + + + I+ +++ L+T Sbjct: 353 GAAIGILKIAEVNDREAFVVLDPNDVNPDVSKLMEEVEKNEQLWDKFITPEESLELMTEE 41- 2 Query: 413 SLLVMVDHSKISLTLSKEFYEQFQNVIVVDHHRRDDDFPDNAILTFIESGASSAAELVTE 47- 2 +LLV+VD K S+ + + + V+V+DHHRR ++F ++ +L ++E ASS AELVTE Sbjct: 413 TLLVIVDTHKPSMVIEPRLLDYVERVVVLDHHRRGEEFIEDPVLVYMEPYASSTAELVTE 47- 2 Query: 473 LIQFQNAKKCLNKIQASVLMAGIMLDTKNFSTRVTSRTFDVASYLRSKGSDSVEIQNISA 53- 2 L+++Q K ++ ++++ L+AG+++DTK+F+ R +RTFD AS+LRS G+D+V +Q + Sbjct: 473 LLEYQPKKLKMDILESTALLAGMIVDTKSFAIRTGARTFDAASFLRSHGADTVLVQKLLK 53- 2 Query: 533 TDFEEYKQINEIILQGERLGDSIIVAAGEKNHLYSNVIASKAADTILSMAHVEASFVLVE 59- 2 D Y + +++ + D + +A + S ++ ++AADT+L+M V ASFV+ Sbjct: 533 EDLNHYVKRAKLVETAKLYRDGMAIATAREEEAVSQLLIAQAADTLLTMKGVVASFVISR 59- 2 Query: 593 TASHKIAISARSRSKINVQRVMEKLGGGGHFNLAACQLTDISLPQAKYLLLKTINMTMK 651- ++ISARS +NVQ +ME L GGGH AA Q D +L +A+ L + I+ ++ Sbjct: 593 RHDGVVSISARSLGDVNVQLIMESLDGGGHLTNAATQFEDATLEEAEAKLKEAIDQYLE 651- An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03093 Identities = 428/658 (65%), Positives = 547/658 (83%), Gaps = 1/658 (0%) Query: 1 MKRFRFATVHLVLIGLILFGLLAICVRLFQSYTALLLAIFVALSFVVALLYYQKITYELS 60 MK+FRF T+HL+++GLILFGLLA+CV + QS +LLAIF+ L FVVALL+YQK Y+LS Sbjct: 1 MKKFRFETIHLIMMGLILFGLLALCVSIMQSKILILLAIFLVLLFVVALLWYQKEAYQLS 60 Query: 61 EVEQIELLNDQTEVSLKSLLEQMPVGVIQFDLETNDIEWFNPYAELIFTGDNGHFQSATV 120- ++ IELLN+QTE +LK+LL+ MPVGV+QFD ETN +EW+NPYAELIFT + G Q+ + Sbjct: 61 DLAHIELLNEQTEDNLKTLLDNMPVGVVQFDQETNAVEWYNPYAELIFTTEEGFIQNGLI 120- Query: 121 KDIITSRRNGTAGQSFEYGDNKYSAYLDTETGVFYFFDNFMGNRRNYDSSMLRPVIGIIS 18- 0 + IIT +R Q+FE NKY++Y+D +G+FYFFD+F+GNR+ D+SMLRPV+GIIS Sbjct: 121 QQIITEKRREDISQTFEVSGNKYTSYIDVSSGIFYFFDSFVGNRQLADASMLRPVVGIIS 18- 0 Query: 181 IDNYDDIMDTMLEADMSKINAFVTSFISDFTQSKNIFYRRVNMDRYYIFTDYSVLNTLIK 24- 0 +DNYDDI D + +AD SKIN+FV +FI +F +SK IFYRRVNMDRYY FTD+ LN L+ Sbjct: 181 VDNYDDITDDLSDADTSKINSFVANFIDEFMESKRIFYRRVNMDRYYFFTDFKTLNDLMD 24- 0 Query: 241 DKFDILNEFRKRAQENHLSLTLSMGISYGDGNHNQIGQIALENLNTALVRGGDQIVVREN 30- 0 +KF +L EFRK AQ+ LTLS+GIS+G+ NH+QIGQ+ALENLN ALVRGGDQIV+REN Sbjct: 241 NKFSVLEEFRKEAQDAQRPLTLSIGISFGEENHSQIGQVALENLNIALVRGGDQIVIREN 30- 0 Query: 301 DSSKKALYFGGGAVSTIKRSRTRTRAMMTAISDRLKVVDSVFIVGHRKLDMDALGASVGM 36- 0 +YFGGG+VST+KRSRTRTRAMMTAISDR+K+VD+VFIVGHRKLDMDALG++VGM Sbjct: 301 ADHTNPIYFGGGSVSTVKRSRTRTRAMMTAISDRIKMVDNVFIVGHRKLDMDALGSAVGM 36- 0 Query: 361 QFFASNIVNASYVVYDPNDMNSDIERAIDYLQEDGETRLVSVERAFELITQNSLLVMVDH 42- 0 QFFA NI+ S+ VY+P++M+ DIERAI+ LQ DG+TRL+SV +A L+T SLLVMVDH Sbjct: 361 QFFAGNIIENSFAVYNPDEMSPDIERAIERLQADGKTRLISVSQAMGLVTPRSLLVMVDH 42- 0 Query: 421 SKTALTLSKEFFNKFADVIVVDHHRRDEDFPKNAVLSFIESGASSASELVTELIQFQQAK 48- 0 SK +LTLSKEF+ +F +VIVVDHHRRD+DFP NA+L+FIESGASSA+ELVTELIQFQ AK Sbjct: 421 SKISLTLSKEFYEQFQNVIVVDHHRRDDDFPDNAILTFIESGASSAAELVTELIQFQNAK 48- 0 Query: 481 DKLSRSQASILMAGIMLDTRNFASNVTSRTFDVASYLRGLGSNSMAIQKISATDFDEYRL 54- 0 L++ QAS+LMAGIMLDT+NF++ VTSRTFDVASYLR GS+S+ IQ ISATDF+EY+ Sbjct: 481 KCLNKIQASVLMAGIMLDTKNFSTRVTSRTFDVASYLRSKGSDSVEIQNISATDFEEYKQ 54- 0 Query: 541 INELILKGERIYDNIIVATGEEHKVYSHVIASKAADTMLTMAGIEATFVITKNSSN-IGI 59- 9 INE+IL+GER+ D+IIVA GE++ +YS+VIASKAADT+L+MA +EA+FV+ + +S+ I I Sbjct: 541 INEIILQGERLGDSIIVAAGEKNHLYSNVIASKAADTILSMAHVEASFVLVETASHKIAI 60- 0 Query: 600 SARSRNNINVQRIMEKLGGGGHFSFAACQIQDKSVKQVRRMLLEIIDEDLRENSTVEN 657 SARSR+ INVQR+MEKLGGGGHF+ AACQ+ D S+ Q + +LL+ I+ ++E VE+ Sbjct: 601 SARSRSKINVQRVMEKLGGGGHFNLAACQLTDISLPQAKYLLLKTINMTMKETGEVES 658 A related GBS gene <SEQ ID 8717> and protein <SEQ ID 8718> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03094 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 13.82 GvH: Signal Score (-7.5): -0.890001 Possible site: 44 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 2.97 threshold: 0.0 PERIPHERAL Likelihood = 2.97 574 modified ALOM score: -1.09 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00071## SEQ ID 8718 (GBS10) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 1 (lane 6; MW 98 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 2 (lane 7; MW 73 kDa). The GST-fusion protein was purified as shown in FIG. 189, lane 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1037 A DNA sequence (GBSx1109) was identified in S. agalactiae <SEQ ID 3205> which encodes the amino acid sequence <SEQ ID 3206>. Analysis of this protein sequence reveals the following: TABLE-US-03095 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4643 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03096 >GP:CAA43972 GB:X62002 ribosomal protein L9 [Bacillus stearothermophilus] Identities = 80/149 (53%), Positives = 105/149 (69%), Gaps = 2/149 (1%) Query: 1 MKVIFLQDVKGKGKKGEVKEVPTGYAQNFLLKKNLAKEATTQAIGELKGKQKSEEKAQAE 60 MKVIFL+DVKGKGKKGE+K V GYA NFL K+ LA EAT + L+ +++ E++ AE Sbjct: 1 MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQKEQRQAAE 60 Query: 61 ILAQAKELKTQLESETTRVQFIEKVGPDGRTFGSITAKKIAEELQKQYGIKIDKRHIDLD 120- LA AK+LK QLE T + K G GR FGSIT+K+IAE LQ Q+G+K+DKR I+L Sbjct: 61 ELANAKKLKEQLEKLTVTIP--AKAGEGGRLFGSITSKQIAESLQAQHGLKLDKRKIELA 118- Query: 121 HTIRAIGKVEVPVKLHKQVSSQIKLDIKE 149 IRA+G VPVKLH +V++ +K+ + E Sbjct: 119 DAIRALGYTNVPVKLHPEVTATLKVHVTE 147 A related DNA sequence was identified in S. pyogenes <SEQ ID 3207> which encodes the amino acid sequence <SEQ ID 3208>. Analysis of this protein sequence reveals the following: TABLE-US-03097 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4630 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03098 Identities = 119/150 (79%), Positives = 138/150 (91%) Query: 1 MKVIFLQDVKGKGKKGEVKEVPTGYAQNFLLKKNLAKEATTQAIGELKGKQKSEEKAQAE 60 MKVIFL DVKGKGKKGE+KEVPTGYAQNFL+KKNLAKEAT+Q+IGELKGKQK+EEKAQAE Sbjct: 1 MKVIFLADVKGKGKKGEIKEVPTGYAQNFLIKKNLAKEATSQSIGELKGKQKAEEKAQAE 60 Query: 61 ILAQAKELKTQLESETTRVQFIEKVGPDGRTFGSITAKKIAEELQKQYGIKIDKRHIDLD 120- ILA+A+ +K L+ + TRVQF EKVGPDGRTFGSITAKKI+EELQKQ+G+K+DKRHI LD Sbjct: 61 ILAEAQAVKAVLDEDKTRVQFQEKVGPDGRTFGSITAKKISEELQKQFGVKVDKRHIVLD 120- Query: 121 HTIRAIGKVEVPVKLHKQVSSQIKLDIKEA 150 H IRAIG +EVPVKLHK+V+++IKL I EA Sbjct: 121 HPIRAIGLIEVPVKLHKEVTAEIKLAITEA 150 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1038 A DNA sequence (GBSx1110) was identified in S. agalactiae <SEQ ID 3209> which encodes the amino acid sequence <SEQ ID 3210>. This protein is predicted to be DNA polymerase III delta prime subunit (dnaB). Analysis of this protein sequence reveals the following: TABLE-US-03099 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.43 Transmembrane 204-220 (204-220) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2423> which encodes the amino acid sequence <SEQ ID 2424>. Analysis of this protein sequence reveals the following: TABLE-US-03100 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.27 Transmembrane 210-226 (210-226) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03101 Identities = 397/450 (88%), Positives = 431/450 (95%), Gaps = 1/450 (0%) Query: 3 EVSELRVQPQDLLAEQAVLGSIFISPEKLIMVREFISPDDFYKYSHKVIFRAMITLADRN 62 EV+ELRVQPQDLLAEQ+VLGSIFISP+KLI VREFISPDDFYKY+HK+IFRAMITL+DRN Sbjct: 8 EVAELRVQPQDLLAEQSVLGSIFISPDKLIAVREFISPDDFYKYAHKIIFRAMITLSDRN 67 Query: 63 DAIDAATVRNILDDQGDLQNIGGLGYIVELVNSVPTSANAEFYAKIVSEKAMLRDIISKL 122- DAIDA T+R ILDDQ DLQ+IGGL YIVELVNSVPTSANAE+YAKIV+EKAMLRDII++L Sbjct: 68 DAIDATTIRTILDDQDDLQSIGGLSYIVELVNSVPTSANAEYYAKIVAEKAMLRDIIARL 127- Query: 123 TDTVNMAY-EGNDSDEIIATAEKALVDINEHSNRSGFRKISDVLKVNYENLELRSQQTSD 18- 1 T++VN+AY E +E+IA E+AL+++NEHSNRSGFRKISDVLKVNYE LE RS+QTS+ Sbjct: 128 TESVNLAYDEILKPEEVIAGVERALIELNEHSNRSGFRKISDVLKVNYEALEARSKQTSN 18- 7 Query: 182 VTGLPTGFRDLDRITTGLHPDQLIILAARPAVGKTAFVLNIAQNVGTKQNRPVAIFSLEM 24- 1 VTGLPTGFRDLD+ITTGLHPDOL+ILAARPAVGKTAFVLNIAONVGTKO + VAIFSLEM Sbjct: 188 VTGLPTGFRDLDKITTGLHPDQLVILAARPAVGKTAFVLNIAQNVGTKQKKTVAIFSLEM 24- 7 Query: 242 GAESLVDRMLAAEGMVDSHSLRTGQLTDQDWNNVTIAQGALADAPIYIDDTPGIKITEIR 30- 1 GAESLVDRMLAAEGMVDSHSLRTGQLTDQDWNNVTIAQGALA+APIYIDDTPGIKITEIR Sbjct: 248 GAESLVDRMLAAEGMVDSHSLRTGQLTDQDWNNVTIAQGALAEAPIYIDDTPGIKITEIR 30- 7 Query: 302 ARSRKLSQEVDDGLGLIVIDYLQLISGTRPENRQQEVSEISRQLKILAKELKVPVIALSQ 36- 1 ARSRKLSQEVD GLGLIVIDYLQLI+GT+PENRQQEVS+ISRQLKILAKELKVPVIALSQ Sbjct: 308 ARSRKLSQEVDGGLGLIVIDYLQLITGTKPENRQQEVSDISRQLKILAKELKVPVIALSQ 36- 7 Query: 362 LSRGVEQRQDKRPVLSDIRESGSIEQDADIVAFLYRDDYYRREGEEAEEIVEDNTVEVIL 42- 1 LSRGVEQRQDKRPVLSDIRESGSIEQDADIVAFLYRDDYYR+E ++AEE VEDNT+EVIL Sbjct: 368 LSRGVEQRQDKRPVLSDIRESGSIEQDADIVAFLYRDDYYRKECDDAEEAVEDNTIEVIL 42- 7 Query: 422 EKNRAGARGTVKLMFQKEYNKFSSIAQFEE 451 EKNRAGARGTVKLMFQKEYNKFSSIAQFEE Sbjct: 428 EKNRAGARGTVKLMFQKEYNKFSSIAQFEE 457 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1039 A DNA sequence (GBSx111) was identified in S. agalactiae <SEQ ID 3211> which encodes the amino acid sequence <SEQ ID 3212>. Analysis of this protein sequence reveals the following: TABLE-US-03102 Possible Site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4909(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 3213> which encodes the amino acid sequence <SEQ ID 3214>. Analysis of this protein sequence reveals the following: TABLE-US-03103 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3467(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03104 Identities = 77/90 (85%), Positives = 84/90 (92%) Query: 1 MSDAFADVAKMKKIKEDIKSHEGQMVELTLENGRKREKNKIGRLIEVYPSLFIVEYKDTA 60 MSDAF DVAKMKKIKEDI++HEGQ+VELTLENGRKREKNKIGRLIEVY SLFI+EY D++ Sbjct: 11 MSDAFTDVAKMKKIKEDIRAHEGQLVELTLENGRKREKNKIGRLIEVYSSLFIIEYSDSS 70 Query: 61 AVPGAIDNTYVESYTYSDILTEKTLIRYFD 90 PGAIDN+YVESYTYSDILTEKTLIRY D Sbjct: 71 DTPGAIDNSYVESYTYSDILTEKTLIRYLD 100 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1040 A DNA sequence (GBSx1112) was identified in S. agalactiae <SEQ ID 3215> which encodes the amino acid sequence <SEQ ID 3216>. This protein is predicted to be 30S ribosomal protein S4 (rpsD). Analysis of this protein sequence reveals the following: TABLE-US-03105 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2937(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03106 >GP:AAC00397 GB:AF008220 ribosomal protein S4 [Bacillus subtilis] Identities = 138/201 (68%), Positives = 158/201 (77%), Gaps = 1/201 (0%) Query: 1 MSRYTGPSWKQSRRLGLSLTGTGKELARRNYVPGQHGPNNRSKLSEYGLQLAEKQKLRFS 60 M+RYTGPSWK SRRLG+SL+GTGKEL +R Y PG HGP R KLSEYGLQL EKQKLR Sbjct: 1 MARYTGPSWKLSRRLGISLSGTGKELEKRPYAPGPHGPGQRKKLSEYGLQLQEKQKLRHM 60 Query: 61 YGLGEKQFRNLFVQATKAKEGTLGFNFMVLLERRLDNVVYRLGLATTRRQARQFVNHGHI 120- YG+ E+QFR LF +A K G G NFM+LL+ RLDNVVY+LGLA TRRQARQ VNHGHI Sbjct: 61 YGVNERQFRTLFDKAGKLA-GKHGENFMILLDSRLDNVVYKLGLARTRRQARQLVNHGHI 119- Query: 121 LVDGKRVDIPSYRVTPGQVISVREKSMKVPAILEAVEATLGRPAFVSFDAEKLEGSLTRL 18- 0 LVDG RVDIPSY V PGQ I VREKS + I E+VE P +++FDAEKLEG+ TRL Sbjct: 120 LVDGSRVDIPSYLVKPGQTIGVREKSRNLSIIKESVEVNNFVPEYLTFDAEKLEGTFTRL 17- 9 Query: 181 PERDEINPEINEALVVEFYNK 201 PER E+ PEINEAL+VEFY++ Sbjct: 180 PERSELAPEINEALIVEFYSR 200 A related DNA sequence was identified in S. pyogenes <SEQ ID 3217> which encodes the amino acid sequence <SEQ ID 3218>. Analysis of this protein sequence reveals the following: TABLE-US-03107 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2937(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03108 Identities = 201/203 (99%), Positives = 201/203 (99%) Query: 1 MSRYTGPSWKQSRRLGLSLTGTGKELARRNYVPGQHGPNNRSKLSEYGLQLAEKQKLRFS 60 MSRYTGPSWKQSRRLGLSLTGTGKELARRNYVPGQHGPNNRSKLSEYGLQLAEKQKLRFS Sbjct: 1 MSRYTGPSWKQSRRLGLSLTGTGKELARRNYVPGQHGPNNRSKLSEYGLQLAEKQKLRFS 60 Query: 61 YGLGEKQFRNLFVQATKAKEGTLGFNFMVLLERRLDNVVYRLGLATTRRQARQFVNHGHI 120- YGLGEKQFRNLFVQATK KEGTLGFNFMVLLERRLDNVVYRLGLATTRRQARQFVNHGHI Sbjct: 61 YGLGEKQFRNLFVQATKIKEGTLGFNFMVLLERRLDNVVYRLGLATTRRQARQFVNHGHI 120- Query: 121 LVDGKRVDIPSYRVTPGQVISVREKSMKVPAILEAVEATLGRPAFVSFDAEKLEGSLTRL 18- 0 LVDGKRVDIPSYRV PGOVISVREKSMKVPAILEAVEATLGRPAFVSFDAEKLEGSLTRL Sbjct: 121 LVDGKRVDIPSYRVDPGQVISVREKSMKVPAILEAVEATLGRPAFVSFDAEKLEGSLTRL 18- 0 Query: 181 PERDEINPEINEALVVEFYNKNL 203 PERDEINPEINEALVVEFYNKML Sbjct: 181 PERDEINPEINEALVVEFYNKML 203 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1041 A DNA sequence (GBSx1113) was identified in S. agalactiae <SEQ ID 3219> which encodes the amino acid sequence <SEQ ID 3220>. Analysis of this protein sequence reveals the following: TABLE-US-03109 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4067(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03110 >GP:AAF98302 GB:AF243383 unknown; Orf3 [Lactococcus lactissubsp. lactis] Identities = 46/97 (47%), Positives = 69/97 (70%) Query: 1 MNLNDRLKIEEMEEKYDSFKPRINALVEAIDDFQKHYEDYVKLREFYGSEDWFRLSEQTE 60 M+ D I++ME KYD+F P + L+++++ F Y +Y++LR FYGSE WF E + Sbjct: 1 MDNKDIELIQQMENKYDTFMPVLTNLIDSVEKFNSIYNNYIELRNFYGSEKWFEYMEIEK 60 Query: 61 NNLKCGVLSEDQLFDFIGEHNELVGQFLDNSSQMYRH 97 +KCGVL+EDQLFD I +HNEL+G LD++S+MY++ Sbjct: 61 IPVKCGVLTEDQLFDMISDHNELLGVLLDLTSKMYKN 97 A related DNA sequence was identified in S. pyogenes <SEQ ID 3221> which encodes the amino acid sequence <SEQ ID 3222>. Analysis of this protein sequence reveals the following: TABLE-US-03111 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3465(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03112 Identities = 48/98 (48%), Positives = 74/98 (74%) Query: 1 MNLNDRLKIEEMEEKYDSFKPRINALVEAIDDFQKHYEDYVKLREFYGSEDWFRLSEQTE 60 M D+L +E+ME+ Y++F P++ L+EA+D F++HYE+Y LR FY S++WFRL+ Q Sbjct: 1 MTKQDQLIVEKMEQTYEAFSPKLANLIEALDAFKEHYEEYATLRNFYSSDEWFRLANQPW 60 Query: 61 NNLKCGVLSEDQLFDFIGEHNELVGQFLDMSSQMYRHL 98 +++ CGVLSED LFD IG+HN+L+ LD++ MY+H+ Sbjct: 61 DDIPCGVLSEDLLFDMIGDHNQLLADILDLAPIMYKHN 98 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1042 A DNA sequence (GBSx1114) was identified in S. agalactiae <SEQ ID 3223> which encodes the amino acid sequence <SEQ ID 3224>. Analysis of this protein sequence reveals the following:

TABLE-US-03113 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0965(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03114 >GP:BAB04438 GB:AP001509 transcriptional regulator (TetR/AcrR family) [Bacillus halodurans] Identities = 47/181 (25%), Positives = 95/181 (51%), Gaps = 16/181 (8%) Query: 4 DTRREKTKRAIEAAMITLLKDQSFDEISTINLTKTAGISRSSFYTHYKDKYEMIDQYQQS 63 D R++ T+ ++ +++ L++++ I+ + A I+RS+FY+HY D Y+++ Q + Sbjct: 6 DRRKKYTRMLLKESLMKLMQEKPLSNITIKEICDLADINRSTFYSHYTDLYDLLYQIEDE 65 Query: 64 LFNKV-EYIFDRNQFKKEDAL-----LEIFQFLDRESLFAALLTQNGTKEIQTYILNKLQ 117- + + E + N K E+AL L ++ +RES L ++ G Q K Sbjct: 66 IIKDLSEALSSYNYTKDEEALQMTENLLVYIANNRESC-QTLFSEYGDPSFQ-----KKV 119- Query: 118 LMLSKELPVVNP---DATKSDINRLYYSVYLSHAIFGVYQMWITRGKKESPQQITQVLLSL 1- 75 +ML+ + + P TK DI+ Y S+Y+ + + Q W+ G K+SP+++ ++++ L Sbjct: 120 MMLAHDHVIKTPLVGKHTKPDISE-YVSLYIVNGSIHIVQSWLKNGLKQSPKEMAELIIKL 1- 79 A related DNA sequence was identified in S. pyogenes <SEQ ID 3225> which encodes the amino acid sequence <SEQ ID 3226>. Analysis of this protein sequence reveals the following: TABLE-US-03115 Possible site: 48 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03116 >GP:BAB04438 GB:AP001509 transcriptional regulator (TetR/AcrR family) [Bacillus halodurans] Identities = 47/180 (26%), Positives = 88/180 (48%), Gaps = 18/180 (10%) Query: 4 RKENTKQAILKAMVMLLKTESFDDITTVKLSKRAGISRSSFYTHYKDKYEMIDYYQQTFF 63 RK+ T+ + ++++ L++ + +IT ++ A I+RS+FY+HY D Y+++ + Sbjct: 8 RKKYTRMLLKESLMKLMQEKPLSNITIKEICDLADINRSTFYSHYTDLYDLLYQIEDEII 67 Query: 64 HKLEYIFEKKYQNKEQAFLEVFEFL-----QREQLLSSLLSANGTKEIQAFIINKVRLL- 117- L K++ L++ E L + +L S G Q KV +L Sbjct: 68 KDLSEALSSYNYTKDEEALQMTENLLVYIANNRESCQTLFSEYGDPSFQ----KKVMMLA 123- Query: 118 ----ITTDLQDKFSTEELSQTEKEYQSIYLAHAFFGVCQSWIAKGKKESPQEMTQFVLKM 17- 3 I T L K + ++S EY S+Y+ + + QSW+ G K+SP+EM + ++K+ Sbjct: 124 HDHVIKTPLVGKHTRPDIS----EYVSLYIVNGSIHIVQSWLKNGLKQSPKEMAELIIKL 17- 9 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03117 Identities = 100/179 (55%), Positives = 134/179 (73%), Gaps = 2/179 (1%) Query: 1 MVNDTRREKTKRAIEAAMITLLKDQSWDEISTINLTKTAGISRSSFYTHYKDKYEMIDQY 60 MVN R+E TK+AI AM+ LLK +SFD+I+T+ L+K AGISRSSFYTHYKDKYEMID Y Sbjct: 1 MVN--RKENTKQAILKAMVMLLKTESFDDITTVKLSKRAGISRSSFYTHYKDKYEMIDYY 58 Query: 61 QQSLFNKVEYIFDRNQFKKEDALLEIFQFLDRESLFAALLTQNGTKEIQTYILNKLQLML 120- QQ+ F+K+EYIF++ KE A LE+F+FL RE L ++LL+ NGTKEIQ +I+NK++L++ Sbjct: 59 QQTFFHKLEYIFEKKYQNKEQAFLEVFEFLQREQLLSSLLSANGTKEIQAFIINKVRLLI 118- Query: 121 SKELPVVNPDATKSDINRLYYSVYLSHAIFGVYQMWITRGKKESPQQITQVLLSLLPQT 179- + +L S + Y S+YL+HA FGV Q WI +GKKESPQ++TQ +L +L T Sbjct: 119 TTDLQDKFSTEELSQTEKEYQSIYLAHAFFGVCQSWIAKGKKESPQEMTQFVLKMLTST 177- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1043 A DNA sequence (GBSx1115) was identified in S. agalactiae <SEQ ID 3227> which encodes the amino acid sequence <SEQ ID 3228>. Analysis of this protein sequence reveals the following: TABLE-US-03118 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.35 Transmembrane 790-806 (787-808) INTEGRAL Likelihood = -7.32 Transmembrane 707-723 (703-725) INTEGRAL Likelihood = -7.11 Transmembrane 637-653 (630-659) INTEGRAL Likelihood = -6.32 Transmembrane 678-694 (672-698) INTEGRAL Likelihood = -1.44 Transmembrane 55-71 (55-73) INTEGRAL Likelihood = -0.22 Transmembrane 732-748 (730-748) ----- Final Results ----- bacterial membrane --- Certainty = 0.5140 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10287> which encodes amino acid sequence <SEQ ID 10288> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03119 >GP:CAB12856 GB:Z99109 alternate gene name: yixE~similar to phage infection protein [Bacillus subtilis] Identities = 227/783 (28%), Positives = 387/783 (48%), Gaps = 60/783 (7%) Query: 45 KAIIKSPKLWITMAGVALIPTLYNVIFLSSMWDPYGNTKNLPVAVVNQDKSAKLNGKTIS 104- K I+ S KL I + + +P +Y+ +FL + WDPYG LPV VVNQDK A G+ + Sbjct: 9 KDIVTSKKLLIPIIAILFVPLIYSGVFLKAYWDPYGTVDQLPVVVVNQDKGATYEGERLQ 68 Query: 105 IGKDMEDNLSKNDSLDFHFTT-AKRAEKELEKGHYYMVITFPKDLSRKATTLMTEKPERL 16- 3 IG D+ L N++ D+HF+ ++ K+L YY+V+ P+D S+ A+T++ + P++L Sbjct: 69 IGDDLVKELKDNNNFDWHFSNDLDQSLKDLLNQKYYLVVEIPEDFSKNASTVLDKNPKKL 128- Query: 164 NITYKTTKGRSFVASKMSETAANKLKDEVAESITGTYTESVFKNMGSMKTGINKAADGSQ 22- 3 ++ Y T G ++V + + E A +KLK V++ +T YT+ +F N + G++ A+ G++ Sbjct: 129 DLKYHTNAGSNYVGATIGEKAIDKLKASVSKEVTEQYTKVIFDNFKDIAKGLSDASSGAK 18- 8 Query: 224 ELLNGSNKLQDGSQTLTSNLDVLASSSQTFSGGANKLNSGINLYTDGVGTLSNGLETLSD 28- 3 ++ +G+ ++GS L NL L S+ T S +L G T G+ +L + L D Sbjct: 189 KIDDGTKDAKNGSAQLKENLAKLKESTATISDKTAQLADGAAQVTSGIQSLDSSLGKFQD 24- 8 Query: 284 GVTAYTTGVHKLSEGSQKLDDKSQALV-------EGSEKLTDGLQQLSQATQLKPEQSRT 33- 6 +L+ GS +L K L+ +G+ LT+GL QL+ Q E+ Sbjct: 249 SSNQIYDKSSQLAAGSGELTSKMNELLAGLQNVQKGTPNLTNGLDQLNSKVQEGSEKAAK 30- 8 Query: 337 LQNLSDG--LKNLNQIITNLQSTATTDSDTNSKLFNFLSTIESSTKALMNTAAADKQKQM 39- 4 + + + L L + NL+ + T + +L +F +++++ +A N + + Sbjct: 309 AEKIINALDLTKLETAVNNLEKSETAMKEFKKQLTDFENSLKNRDQAFKN--VINSSDFL 36- 6 Query: 395 TAVQST----SAFKSLTPEQQSQITSAVTGTPTSAE-TIAANISSNIENMKTVLSEASSS 44- 9 TA Q + S K L ++ PT+ + A I S++E++K +++ + Sbjct: 367 TAEQKSQLINSVEKKLPQVDAPDFDQILSQLPTADQLPDIATIKSSLEDVKAQVAQVKAM 42- 6 Query: 450 APSN----NGSQNLQTLSGTANNLVLKAISDLDKIQKLPTATKQLYQGSQTLTKGITDYT 50- 5 + NG++ +Q D I +L ++Y GSQ LT G T T Sbjct: 427 PEATSKLYNGAKTIQ-----------------DAIDRLTEGADKIYNGSQKLTDGQTKLT 46- 9 Query: 506 NAVGQLRKGAVTLDSKSNQLISGTQKASQGAQTLDSKSDQLRDGAGQLASGSDRIADGSN 56- 5 +G+ K + S QL++G S Q+ G +L GS ++ GS+ Sbjct: 470 AGIGEYNKQFAKAKAGSEQLVTG--------------SSQVSGGLFKLLDGSKQVQSGSS 51- 5 Query: 566 KLAGGGHQLTDGLTELSGGVSQLSSSLGKAGDQLSMVSVNKDNANAVSSPVTIKHEDYDS 62- 5 KLA G L GL +L G +LSS L A DQ + + + PV K + S Sbjct: 516 KLADGSASLDTGLGKLLDGTGELSSKLKDAADQTGDIDADDQTYGMFADPVKTKDDAIHS 57- 5 Query: 626 VDTNGVGMAPYMISVALMVVALSANVIFAKALSGKEPANRFSWAKNK---LLINGFIATL 68- 2 V G G+ PY++S+ L V + V+F + P N F W +K +++ G I +L Sbjct: 576 VPNYGTGLTPYILSMGLYVGGIMLTVVFPLKEASGRPRNGFEWFFSKFNVMMLVGIIQSL 63- 5 Query: 683 -AATILFFAVQFIGLKPDYPGKTYFIILLTAWTLMALVTALVGWDNRYGSFLSLLILLFQ 74- 1 AT+L IGL+ + + Y ++T+ +A++ L G F++++IL+ Q Sbjct: 636 IVATVLLLG---IGLEVESTWRFYVFTIITSLAFLAIIQFLATTMGNPGRFIAVIILVLQ 69- 2 Query: 742 LGSSAGTYPIELSPKFFQTIQPFLPMTYSVSGLRETISLTGDVNHQWRMLVIFLVSSMIL 80- 1 LG+S GT+P+EL P F+Q I LPMTYS++G R IS GD + W+M + + ++++ Sbjct: 693 LGASGGTFPLELLPNFYQVIHGALPMTYSINGFRAVIS-NGDFGYMWQMAGVLIGIALVM 75- 1 Query: 802 ALL 804 L Sbjct: 752 IAL 754 A related DNA sequence was identified in S. pyogenes <SEQ ID 2017> which encodes the amino acid sequence <SEQ ID 2018>. Analysis of this protein sequence reveals the following: TABLE-US-03120 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.29 Transmembrane 735-751 (729-754) INTEGRAL Likelihood = -5.79 Transmembrane 582-598 (580-601) INTEGRAL Likelihood = -3.66 Transmembrane 652-668 (650-669) INTEGRAL Likelihood = -2.97 Transmembrane 14-30 (14-34) INTEGRAL Likelihood = -2.66 Transmembrane 623-639 (622-641) ----- Final Results ----- bacterial membrane --- Certainty = 0.4715 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03121 Identities = 360/779 (46%), Positives = 508/779 (64%), Gaps = 32/779 (4%) Query: 40 MLDELKAIIKSPKLWITMAGVALIPTLYNVIFLSSMWDPYGNTKNLPVAVVNQDKSAKLN 99 - ML+ELK +IK+PKL ITM GVAL+P LYN+ FL SMWDPYG +LP+AVVN DK AK Sbjct: 1 MLEELKTLIKNPKLMITMIGVALVPALYNLSFLGSMWDPYGRVNDLPIAVVNHDKPAKRA 60 Query: 100 GKTISIGKDMEDNLSKNDSLDFHFTTAKRAEKELEKGHYYMVITFPKDLSRKATTLMTEK 15- 9 K+++IG DM D +SK+ L++HF +AK+A++ L++G YYMVIT P+DLS++A TL+ + Sbjct: 61 DKSLTIGNDMVDKMSKSKDLEYHFVSAKQAQEGLKEGDYYMVITLPEDLSQRAATLLNPE 120- Query: 160 PERLNITYKTTKGRSFVASKMSETAANKLKDEVAESITGTYTESVFKNMGSMKTGINKAA 21- 9 P++L I Y+T+KG VA+KM ETA KLK+ V+++IT TYT +VF +M +++G+ +A+ Sbjct: 121 PQKLTIRYQTSKCHGMVAAKMGETAMAKLKESVSQNITKTYTSAVFSSMTDLQSGLKEAS 18- 0 Query: 220 DGSQELLNGSNKLQDCSQTLTSNLDVLASSSQTFSGGANKLNSGINLYTDGVGTLSNGLE 27- 9 GSQ L +G+ Q GSQTL++NL L +SQ F G +L SG+ YTDGV + NGL Sbjct: 181 AGSQALASGAKTAQAGSQTLSTNLAALTGASQQFQQGTGRLTSGLTTYTDGVNQVKNGLG 24- 0 Query: 280 TLSDGVTAYTTGVHKLSEGSQKLDDKSQALVEGSEKLTDGLQQLSQATQLKPEQERTLQN 33- 9 TLS + Y GV +LS+G+ +L+ GL QL+QAT L E+ + +Q+ Sbjct: 241 TLSTDIPNYLNGVSRLSQGASQLNQ--------------GLSQLTQATTLSDEKAKGIQS 28- 6 Query: 340 LSDGLKNLNQIITNLQSTATTDSDTN---SKLFNFLSTIESSTKALMNTAAADKQKQNTA 39- 6 L GL LNQ I L + +T N +L N L I + K ++ A + ++++A Sbjct: 287 LIVGLPVLNQGIQQLNTELSTLQPPNLNADELGNSLGAIAQAAKQVIAEETAAQNEELSA 34- 6 Query: 397 VQSTSAFKSLTPEQQSQITSAVTGTPTSAETIAAN-ISSNIENMKTVLSEASSSAPSNNG 45- 5 +Q+TS ++SLT EQQ ++ +A++ + S AA I S+++ + T L S S Sbjct: 347 LQATSVYQSLTAEQQGELAAALSQSDKSQTVSAAQTILSSVQTLSTSLQSLSQEDQSKQL 40- 6 Query: 456 SQNLQTLSGTANNLVLKAISDLDKIQKLPTATKQLYQGSQTLTKGITDYTNAV----GQL 51- 1 Q + ++ AN Q LP A+ L + S L K V QL Sbjct: 407 EQLKEAVAQIANQ----------SNQALPGASSALTELSTGLAKVNGSLNQQVLPGSNQL 45- 6 Query: 512 RKGAVTLDSKSNQLISGTQKASQGAQTLDSKSDQLRDGAGQLASGSDRIADGSNKLAGGG 57- 1 G L+ + + SG K S+GA L SKS +L DG+ QL+ G+ ++ADGS++L+ GG Sbjct: 457 TTGLAQLNRYNTAIGSGVIKLSEGANALSSKSGELLDGSHQLSEGATKLADGSSQLSQGG 51- 6 Query: 572 HQLTDGLTELSGGVSQLSSSLGKAGDQLSMVSVNKDNANAVSSPVTIKHEDYDSVDTNGV 63- 1 HQLT GLTELS G+S L+ SL KA QLS+VSV NA AV+ P+ + +D D V TNG+ Sbjct: 517 HQLTSGLTELSTGLSTLNGSLAKASQQLSLVSVTDKNAKAVAKPLVLNEKDKDGVKTNGI 57- 6 Query: 632 GMAPYMISVALMVVALSANVIFAKALSGKEPANRFSWAKNKLLINGFIATLAATILFFAV 69- 1 GMAPYMI+V+LMVVALS NVIFA +LSG+ +++ WAK K +INGFI+T+ + +L+ A+ Sbjct: 577 GMAPYMIAVSLMVVALSTNVIFANSLSGRPVKDKWDWAKQKFVINGFISTMGSIVLYLAI 63- 6 Query: 692 QFIGLKPDYFGKTYFIILLTAWTLMALVTALVGWDNRYGSFLSLLILLFQLGSSAGTYPI 75- 1 Q +G + Y +T I+L+ WT MALVTALVGWD+RYGSF SL++LL Q+GSS G+YPI Sbjct: 637 QLLGFEARYGMETLGFIMLSGWTFMALVTALVGWDDRYGSFASLVMLLLQVGSSGGSYPI 69- 6 Query: 752 ELSPKFFQTIQPFLPMTYSVSGLRETISLTGDVNHQWRMLVIFLVSSMILALLIYRKQE 810- ELS FFQ + PFLPMTY VSGLR+TISL+G + + ++L FL++ M+LALLIYR ++ Sbjct: 697 ELSGAFFQKLHPFLPMTYVVSGLRQTISLSGHIGVEVKVLTGFLLAFMVLALLIYRPKK 755- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1044 A DNA sequence (GBSx1116) was identified in S. agalactiae <SEQ ID 3229> which encodes the amino acid sequence <SEQ ID 3230>. Analysis of this protein sequence reveals the following: TABLE-US-03122 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2664 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1045 A DNA sequence (GBSx1117) was identified in S. agalactiae <SEQ ID 3231> which encodes the amino acid sequence <SEQ ID 3232>. Analysis of this protein sequence reveals the following: TABLE-US-03123 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.45 Transmembrane 48-64 (45-69) INTEGRAL Likelihood = -1.49 Transmembrane 71-87 (71-87) ----- Final Results ----- bacterial membrane --- Certainty = 0.4779 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9441> which encodes amino acid sequence <SEQ ID 9442> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03124 >GP:AAA25222 GB:M87483 ORF 1 [Lactococcus lactis] Identities = 50/88 (56%), Positives = 66/88 (74%), Gaps = 1/88 (1%) Query: 2 TGKIFSMSKEELSYLPVIKLFKNQGVYNGLIGLFLLYGLYISQNQ-EIVAVFLINVLLVA 60 T ++F+M KEEL V LFKNQG+YNGLIGL L+Y ++ S Q EIV + LI ++LVA Sbjct: 32 TSRVFNMGKEELERSSVQTLFKNQGIYNGLIGLGLIYAIFFSSAQLEIVRLLLIYIILVA 91 Query: 61 IYGALTVDKKILLKQGGLPILALLTFLF 88 +YG+LT +KKI+L QGGL ILAL++ F Sbjct: 92 LYGSLTSNKKIILTQGGLAILALISSFF 119 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8719> and protein <SEQ ID 8720> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03125 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 4.19 GvH: Signal Score (-7.5): -3.99 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 3 value: -9.45 threshold: 0.0 INTSGRAL Likelihood = -9.45 Transmembrane 87-103 (84-108) INTEGRAL Likelihood = -1.49 Transmembrane 110-126 (110-126) INTEGRAL Likelihood = -0.37 Transmembrane 13-29 (13-29) PERIPHERAL Likelihood = 0.47 65 modified ALOM score: 2.39 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4779 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00072## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1046 A DNA sequence (GBSx1118) was identified in S. agalactiae <SEQ ID 3233> which encodes the amino acid sequence <SEQ ID 3234>. Analysis of this protein sequence reveals the following: TABLE-US-03126 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3140 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10285> which encodes amino acid sequence <SEQ ID 10286> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03127 >GP:CAB12447 GB:Z99107 similar to arylesterase [Bacillus subtilis] Identities = 37/91 (40%), Positives = 56/91 (60%) Query: 13 KDGSDIYYRVVGQGQPIVFLHGNSLSSRYFDKQIAYFSKYYQVIVMDSRGHGKSHAKLNT 72 - +D + +YY G G PI+F+HG +S ++F KQ + S YQ I +D RGHG+S L+ Sbjct: 7 EDQTRLYYETHGSGTPILFIHGVLMSGQFFHKQFSVLSANYQCIRLDLRGHGESDKVLHG 66 Query: 73 ISFRQIAVDLKDILVHLEIDKVILVGHSDGA 103 + Q A D+++ L +E+D V+L G S GA Sbjct: 67 HTISQYARDIREFLNANELDHVVLAGWSMGA 97 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1047 A DNA sequence (GBSx1119) was identified in S. agalactiae <SEQ ID 3235> which encodes the amino acid sequence <SEQ ID 3236>. This protein is predicted to be an integral membrane protein. Analysis of this protein sequence reveals the following: TABLE-US-03128 Possible site: 58 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.90 Transmembrane 14-30 (9-41) INTEGRAL Likelihood = -9.71 Transmembrane 451-467 (447-472) INTEGRAL Likelihood = -9.18 Transmembrane 234-250 (229-257) INTEGRAL Likelihood = -8.07 Transmembrane 56-72 (46-77) INTEGRAL Likelihood = -8.01 Transmembrane 490-506 (484-512) INTEGRAL Likelihood = -5.84 Transmembrane 414-430 (412-436) INTEGRAL Likelihood = -4.99 Transmembrane 136-152 (135-159) INTEGRAL Likelihood = -4.14 Transmembrane 213-229 (211-232) INTEGRAL Likelihood = -4.14 Transmembrane 365-381 (364-382) INTEGRAL Likelihood = -2.66 Transmembrane 393-409 (391-412) INTEGRAL Likelihood = -1.06 Transmembrane 168-184 (167-184) INTEGRAL Likelihood = -0.64 Transmembrane 275-291 (275-291) INTEGRAL Likelihood = -0.32 Transmembrane 328-344 (328-345) INTEGRAL Likelihood = -0.27 Transmembrane 821-837 (821-837) ----- Final Results ----- bacterial membrane --- Certainty = 0.6158 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10283> which encodes amino acid sequence <SEQ ID 10284> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-03129 >GP:BAA24464 GB:D85082 YfiX [Bacillus subtilis] Identities = 190/596 (31%), Positives = 324/596 (53%), Gaps = 31/596 (5%) Query: 246 IVSLIPGGLGSFELVLFTGFAAEGLPKETVVAWLLLYRLAYYIIPFFAGIYFFIHYLGSQ 30- 5 ++SL+PGG GSF+L+ G G +E +V ++LYRLAY IPF G++F L Sbjct: 1 MISLVPGGFGSFDLLFLLGMEQLGYHQEAIVTSIVLYRLAYSFIPFILGLFFAAGDLTEN 60 Query: 306 INQRYENVPK-----ELVSTVLQTMVSHLMRILG---AFLIFSTAFFENITYIMWLQKLG 35- 7 +R E P+ E + +L + L+RIL + ++F + + + +L Sbjct: 61 TMKRLETNPRIAPAIETTNVLLVVQRAVLVRILQGSLSLIVFVAGLIVLASVSLPIDRLT 120- Query: 358 LDP-LQEQMLWQFPGLLLGVCFILLARTID--QKVKNAFPIAIIWITLTLFYLNLGHISW 41- 4 + P + L F GL L ILL I+ ++ K ++ +AI + + L ++ Sbjct: 121 VIPHIPRPALLLFNGLSLSSALILLILPIELYKRTKRSYTMAITALVGGFVFSFLKGLNI 18- 0 Query: 415 RLSFWFILLLLGLLVIKPTLYKKQFIYSWEERIKDGIIIVSLMGVLFY----IAGLLFPI 47- 0 F ++++ L+++K ++Q Y+ + I V+L V + IAG ++ Sbjct: 181 SAIFVLPMIIVLLVLLKKQFVREQASYTLGQLI----FAVALFTVALFNYNLIAGFIWDR 23- 6 Query: 471 RAHITGGSIERLHYIIAWEPIALATL----ILTLVYLCLVKILQGKSCQIGDVFNVDRYK 52- 6 + + +++ + I AT+ I+ L +L + ++ IG+ + +R Sbjct: 237 MKKV----LRHEYFVHSTSHITHATIMAIIIVPLFFLIFTVVYHRRTKPIGEKADPERLA 29- 2 Query: 527 KLLQAYGGSSDSGLAFLNDKRLYWYQKNGEDCVAFQFVIVNNKCLIMGEPAGDDTYIREA 58- 6 L GG++ S L FL DKR Y + +G + F + + +++G+P+G Sbjct: 293 AFLNEKGGNALSHLGFLGDKRFY-FSSDGNALLLFGKIA--RRLVVLGDPSGQRESFPLV 34- 9 Query: 587 IESFIDDADKLDYDLVFYSIGQKLTLLLHEYGFDFMKVGEDALVNLETFTLKGNKYKPFR 64- 6 +E F+++A + + ++FY I ++ L H++G++F K+GE+A V+L TFTL G K R Sbjct: 350 LEEFLNEAHQKGFSVLFYQIEREDMALYHDFGYNFFKLGEEAYVDLNTFTLTGKKKAGLR 40- 9 Query: 647 NALNRVEKDGFYFEVVQSPHSQSLLNSLEEISNTWLEGRPEKGFSLGYFNKDYFQQAPIA 70- 6 NR E++ + F V P S L L++IS+ WL + EKGFSLG+F+ Y Q+APIA Sbjct: 410 AINNRFEREEYTFHVDHPPFSDAFLEELKQISDEWLGSKKEKGFSLGFFDPSYLQKAPIA 46- 9 Query: 707 LVKNAEHEVVAFANIMPNYEKSIISIDLMRHDKQKIPNGVMDFLFLSLFSYYQEKGYHYF 76- 6 +KNAE E+VAFAN+MP Y++ IS+DLMR+ + PNG+MD LF+ +F + +E+G F Sbjct: 470 YMKNAEGEIVAFANVMPMYQEGEISVDLMRY-RGDAPNGIMDALFIRMFLWAKEEGCTSF 52- 8 Query: 767 DLGMAPLSGVGRVETSFAKERMAYLVYHFGSHFYSFNGLHKYKKKFTPLWSERYIS 822 ++GMAPL+ VG TSF ER A ++++ + YSF+GL +K+K+ P W +Y++ Sbjct: 529 NMGMAPLANVGTAFTSFWSERFAAVIFNNVRYMYSFSGLRAFKEKYKPEWRGKYLA 584 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8721> and protein <SEQ ID 8722> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03130 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 9.22 GvH: Signal Score (-7.5): -7.66 Possible site: 58 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 14 value: -12.90 threshold: 0.0 INTEGRAL Likelihood = -12.90 Transmembrane 14-30 (9-41) INTEGRAL Likelihood = -9.71 Transmembrane 451-467 (447-472) INTEGRAL Likelihood = -9.18 Transmembrane 234-250 (229-257) INTEGRAL Likelihood = -8.07 Transmembrane 56-72 (46-77) INTEGRAL Likelihood = -8.01 Transmembrane 490-506 (484-512) INTEGRAL Likelihood = -5.84 Tranamembrane 414-430 (412-436) INTEGRAL Likelihood = -4.99 Transmembrane 136-152 (135-159) INTEGRAL Likelihood = -4.14 Transmembrane 213-229 (211-232) INTEGRAL Likelihood = -4.14 Transmembrane 365-381 (364-382) INTEGRAL Likelihood = -2.66 Transmembrane 393-409 (391-412) INTEGRAL Likelihood = -1.06 Transmembrane 168-184 (167-184) INTEGRAL Likelihood = -0.64 Transmembrane 275-291 (275-291) INTEGRAL Likelihood = -0.32 Transmembrane 328-344 (328-345) INTEGRAL Likelihood = -0.27 Transmembrane 821-837 (821-837) PERIPHERAL Likelihood = 1.06 558 modified ALOM score: 3.08 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6158(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00073## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1048 A DNA sequence (GBSx1120) was identified in S. agalactiae <SEQ ID 3237> which encodes the amino acid sequence <SEQ ID 3238>. This protein is predicted to be choline transporter. Analysis of this protein sequence reveals the following: TABLE-US-03131 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.24 Transmembrane 28-44 (22-47) INTEGRAL Likelihood = -8.81 Transmembrane 178-194 (176-204) INTEGRAL Likelihood = -7.22 Transmembrane 81-97 (63-105) INTEGRAL Likelihood = -3.50 Transmembrane 209-225 (206-226) INTEGRAL Likelihood = -3.13 Transmembrane 64-80 (63-80) INTEGRAL Likelihood = -2.44 Transmembrane 156-172 (153-172) INTEGRAL Likelihood = -0.64 Transmembrane 137-153 (137-153) ----- Final Results ----- bacterial membrane --- Certainty = 0.5097(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03132 >GP:AAD45530 GB:AF162656 choline transporter [Streptococcus pneumoniae] Identities = 326/505 (64%), Positives = 409/505 (80%), Gaps = 1/505 (0%) Query: 1 MTTLITTFQERFGDWTQSLIEHLQLSLLTLILATLIAIPLGIIISHYKKISHVVLQITGI 60 MT LI TFQ+RF DW +L +HLQLSLLTL+LA L+AIPL + + +++K++ VLQI GI Sbjct: 1 MTNLIATFQDRFSDWLTALSQHLQLSLLTLLLAILLAIPLAVFLRYHEKLADWVLQIAGI 60 Query: 61 FQTIPSLALLGLFIPFMGIGTVPAVVALIIYALFPILQNTVTVLMQIDANLIEAATAFGM 120- FQTIPSLALLGLFIP MGIGT+PA+ AL+IYA+FPILQNT+T L ID NL EA AFGM Sbjct: 61 FQTIPSLALLGLFIPLMGIGTLPALTALVIYAIFPILQNTITGLKGIDPNLQEAGIAFGM 120- Query: 121 TRWERLKKFELALSMPVIISGIRTASVMIIGTATLASLIGAGGLGSFILLGIDRNNPSLI 18- 0 TRWERLKKFE+ L+MPVI+SGIRTA+V+IIGTATLA+LIGAGGLGSFILLGIDRNN SLI Sbjct: 121 TRWERLKKFEIPLAMPVIMSGIRTAAVLIIGTATLAALIGAGGLGSFILLGIDRNNASLI 18- 0 Query: 181 LIGAISSAVLAIIFSGLIGLLEKARLRTIAVSGILLLAGLGLSYAPKWMPGTNTATITVA 24- 0 LIGA+SSAVLAI F+ L+ ++EKA+LRTI L+ LGLSY+P + + +A Sbjct: 181 LIGALSSAVLAIAFNFLLKVMEKAKLRTIFSGFALVALLLGLSYSPALLVQKEKENLVIA 24- 0 Query: 241 GKLGTEPDILINMYKELIEDQTDIKVKLKPNFGKTTFLYQALKSGDIDLYPEFTGTITSS 30- 0 GK+G EP+IL NMYK LIE+ T + +KPNFGKT+FLY+ALK GDID+YPEFTGT+T S Sbjct: 241 GKIGPEPEILANMYKLLIEENTSMTATVKPNFGKTSFLYEALKKGDIDIYPEFTGTVTES 30- 0 Query: 301 LLKNPPKVSNNPKQVYNLAKNGILKQDKLSLLSPMAYQNTYAVAVKKDYAEANQLKNISD 36- 0 LL+ PKVS+ P+QVY +A++GI KQD L+ L PM+YQNTYAVAV K A+ LK ISD Sbjct: 301 LLQPSPKVSHEPEQVYQVARDGIAKQDHLAYLKPMSYQNTYAVAVPKKIAQEYGLKTISD 36- 0 Query: 361 LKKLD-KLKAGETLEFKDREDGSIGLQKHYGLNLDISTLEPALRYQAINSKDVNIIDAYS 41- 9 LKK++ +LKAGFTLEF DREDG+ GLQ YGLNL+++T+EPALRYQAI S D+ I DAYS Sbjct: 361 LKKVEGQLKAGFTLEFNDREDGNKGLQSMYGLNLNVATIEPALRYQAIQSGDIQITDAYS 42- 0 Query: 420 TDSELIQYQLQILKDDKHLFPPYQGAPLLRQDTIKKYPQVKKALNKLAGHITEKEMQEMN 47- 9 TD+EL +Y LQ+L+DDK LFPPYQGAPL+++ +KK+P++++ LN LAG ITE +M ++N Sbjct: 421 TDAELERYDLQVLEDDKQLFPPYQGAPLMKEALLKKHPELERVLNTLAGKITESQMSQLN 48- 0 Query: 480 YQVAVKHKSAATVAKQYLKAHHIIK 504 YQV V+ KSA VAK++L+ ++K Sbjct: 481 YQVGVEGKSAKQVAKEFLQEQGLLK 505 There is also homology to SEQ ID 636. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1049 A DNA sequence (GBSx1121) was identified in S. agalactiae <SEQ ID 3239> which encodes the amino acid sequence <SEQ ID 3240>. This protein is predicted to be choline transporter (opuBA). Analysis of this protein sequence reveals the following: TABLE-US-03133 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2345(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03134 >GP:AAD45529 GB:AF162655 choline transporter [Streptococcus pneumoniae] Identities = 139/236 (58%), Positives = 178/236 (74%) Query: 1 MISFENVSKSYGDHTIIDNISCHIQRGEFFVLVGASGSGKTTILKMINRLIEPSQGAITL 60 MI ++NV+ Y + ++ +++ I+ GEF VLVG SGSGKTT+LKMINRL+EP+ G I + Sbjct: 1 MIEYKNVALRYTEKDVLRDVNLQIEDGEFMVLVGPSGSGKTTMLKMINRLLEPTDGNIYM 60 Query: 61 DGENITSLDLRQLRLETGYVLQQIALFPNLTVGENIELIPEMKGWSKGDQKKAASDLLDK 120- DG+ I D R+LRL TGYVLQ IALFPNLTV ENI LIPEMKGWSK + K +LL K Sbjct: 61 DGKRIKDYDERELRLSTGYVLQAIALFPNLTVAENIALIPEMKGWSKEEITKKTEELLAK 120- Query: 121 VGLPAKDYFNRYPHELSGGEQQRIGILRAIVAKPKVLLMDEPFSALDPISRRQLQDITKQ 18- 0 VGLP +Y +R P ELSGGEQQR+GI+RA++ +PK+ LMDEPFSALD ISR+QLQ +TK+ Sbjct: 121 VGLPVAEYGHRLPSELSGGEQQRVGIVRAMIGQPKIFLMDEPFSALDAISRKQLQVLTKE 18- 0 Query: 181 LQSELGITLVFVTHDMKEAMRLADRICVIKEGKIVQLDRPEIIQNNPSDQFVRTLF 236 L E G+T +FVTHD EA++LADRI V+++G+I Q+ PE I P+ FV LF Sbjct: 181 LHKEFGMTTIFVTHDTDEALKLADRIAVLQDGEIRQVANPETILKAPATDFVADLF 236 There is also homology to SEQ ID 644. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1050 A DNA sequence (GBSx1122) was identified in S. agalactiae <SEQ ID 3241> which encodes the amino acid sequence <SEQ ID 3242>. This protein is predicted to be two-component response regulator. Analysis of this protein sequence reveals the following: TABLE-US-03135 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.52 Transmembrane 49-65 (46-66) ----- Final Results ----- bacterial membrane --- Certainty = 0.3208(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03136 >GP:BAB06434 GB:AP001516 two-component response regulator [Bacillus halodurans] Identities = 101/305 (33%), Positives = 152/305 (49%), Gaps = 31/305 (10%) Query: 1 MKFYIIDDDPTITMILQDIIE-EDFNNTVVRVNNVSSKAYNELLIADVDIVLIDLLNPIL 59 M F+I DDD T+ IL IIE E V + S L I VDI+LIDLLMP Sbjct: 1 MNFFITDDDVTVRSILAQIIEDEQLGQVVGEAEDGSELDGKRLNIKQVDILLIDLLMPNC 60 Query: 60 DGVTLVQKIYKQRSDLKFIMISQVKDNDLRQEAYKAGIEFEINKPINIIEVKSVVKRVTD 119- DG+ +QKI K K IMISQ++ +L EAY GIE +I KPIN IEV SV+++V + Sbjct: 61 DGLEAIQKI-KPEFKGKIINISQIESKELISEAYLLGIEHYIMKPINKIEVLSVIRKVIN 119- Query: 120 TIEMQKKLNTIQNLLENTPSYQKPITTSNLT----KIRS----ILSYLGITSETAYTDIL 17- 1 +++ L IQ L N P ++ I+S +LS LGI E+ D++ Sbjct: 120 HTRLEQSLYDIQKSLSNVLQGSIPTQVNDQVFHDDSIKSYGQYLLSELGIAGESGSKDLM 17- 9 Query: 172 NICELLLKQELNF-------AQFDFQKELSIDE-----------HQQKIILQRIRRAVKK 21- 3 NI L E + A D ++L+ ++ + K QR+RRAV + Sbjct: 180 NILNFLYTYEKEYSFEKGFPALKDIFEQLASEKLGDAADERDVRREVKAAKQRVRRAVYQ 23- 9 Query: 214 AMINNAHLYIDDFENELTLQYANALFGFQNIHNEAQLIQGK---SMYGGKISLKHFFDEL 27- 0 ++ ++A L + DF N +YA+ F F + ++ ++ + S +I++K F L Sbjct: 240 SLEHVASLGLIDFSNPKFEEYASHFFDFSVVRSKMTELKNETSSSYTSARINVKKFTQAL 29- 9 Query: 271 ILQSK 275 ++K Sbjct: 300 YYEAK 304 There is homology to SEQ ID 460. A related GBS gene <SEQ ID 8723> and protein <SEQ ID 8724> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03137 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -7.05 GvH: Signal Score (-7.5): -6.58 Possible site: 61 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: 5.52 threshold: 0.0 INTEGRAL Likelihood = -5.52 Transmembrane 49-65 (46-66) PERIPHERAL Likelihood = 7.37 155 modified ALOM score: 1.60 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3208(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00074## SEQ ID 8724 (GBS356) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 73 (lane 3; MW 34 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 81 (lane 8; MW 59 kDa). GBS356-GST was purified as shown in FIG. 216, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1051 A DNA sequence (GBSx1123) was identified in S. agalactiae <SEQ ID 3243> which encodes the amino acid sequence <SEQ ID 3244>. Analysis of this protein sequence reveals the following: TABLE-US-03138 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.48 Transmembrane 149-165 (147-172) INTEGRAL Likelihood = -5.20 Transmembrane 37-53 (29-55) INTEGRAL Likelihood = -2.50 Transmembrane 126-142 (126-142) INTEGRAL Likelihood = -2.13 Transmembrane 62-78 (60-78) INTEGRAL Likelihood = -0.64 Transmembrane 314-330 (314-330) INTEGRAL Likelihood = -0.11 Transmembrane 89-105 (89-105) ----- Final Results ----- bacterial membrane --- Certainty = 0.3590(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03139 >GP:BAB06435 GB:AP001516 two-component sensor histidine kinase [Bacillus halodurans] Identities = 118/427 (27%), Positives = 199/427 (45%), Gaps = 25/427 (5%) Query: 10 LERRQRIIISAIAIA-LAAQINISILADGFIMTLSLFILPVFLYFNDDINPILLCLGITF 68 - L + II+S + A +A +IN + + F ++L I +FL F +I+ Sbjct: 7 LSKDYMIILSMLLFAPIAGEINFYPVNETFRVSLGPPIFFLFLLFLRNTAAIVPGFFTAI 66 Query: 69 ASPIFRGIILSIAGEAEIHQIIEFVLTDMAFYICYGITFYTIYWHRSYRNKGTFFFSIII 128- A +FR + ++ + E FY Y + F R + F II Sbjct: 67 AVVVFRVFLDTLHADFYWVDSFEIHYPTFFFYFTYSLLFSLAKVQRFHEQPLIIFLFGII 126- Query: 129 CDYFANLVEISFLIKFNNYTITIFA-TLFAIALLRAFISCAVAYTYSYLSLLLQKD---D 18- 4 + A+ E F+ ++ + + + ++F I L+ S V +S + L + + Sbjct: 127 IEILADTAE--FIAQYFAFGVMVTKDSIFQILLIAFSHSFIVLGVFSMMKLYETRSRELE 18- 4 Query: 185 HERRYYYFMWSTSAVKSEVYFMQKNIIEIENIMKNAYLLDKELSKY---HLPKEYQHLS- 24- 0 +R + + S + E ++K + E+I + L +E+ + H+ + HL Sbjct: 185 IRKRNEHMLLLISNLYEESVHLKKTLQNSEDITSKVFGLYREMKRLQSEHMDQVNPHLEK 24- 4 Query: 241 -----LDISRDVHEVKKDYQNIIKGLGTYFSVKNESTMALKDIFQIVLSYTRS---IIQF 29- 2 L+IS +VHE+KKD Q I GL S NES + +I QI+ R+ Q Sbjct: 245 ISKRLLEISGEVHEIKKDNQRIFAGLSKLIS--NESYVDYIEIGQIIKMIVRTNEKYAQL 30- 2 Query: 293 RHQDIIILENNKCNLIISNYYYLLTIISNIVLNAVEAIDKQKKGTISVHTESLEDFIKIE 35- 2 ++I + + + Y L+II+N+V NAVEAID KG +++ + L ++ Sbjct: 303 LGKEIDFHYSIQGEHPPYHIYTHLSIINNLVANAVEAIDG--KGNLTIRVKALGQTVEFR 36- 0 Query: 353 ISDNGPGIPDKMKHMIFKPGFSTKFDANGDIYRGIGLSHVRILMEEQYQGTITVCPNQ-P 41- 1 I D+GPGIPDK + +IFKPGF++KFD G GIGL++V M ++ GT+ Q Sbjct: 361 IEDDGPGIPDKHRALIFKPGFTSKFDHTGKPSTGIGLTYVHD-MVDKLGGTVVYERGQGG 41- 9 Query: 412 NGTTFTL 418 G+ FT+ Sbjct: 420 KGSVFTI 426 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1052 A DNA sequence (GBSx1124) was identified in S. agalactiae <SEQ ID 3245> which encodes the amino acid sequence <SEQ ID 3246>. This protein is predicted to be ornithine carbamoyltransferase Otc6850 (argF). Analysis of this protein sequence reveals the following: TABLE-US-03140 Possible site: 61 >>>Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.64 Transmembrane 171-187 (171-187) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03141 >GP:CAB75986 GB:AJ272085 ornithine carbamoyltransferase [Staphylococcus aureus] Identities = 264/332 (79%), Positives = 292/332 (87%) Query: 1 MKNLRNRSFLTLLDFSTAEVEFLLKLSEDLKRAKYAGIEQQKLVGKNIALIFEKDSTRTR 60 MKNLRNRSFLTLLDFS EVEFLL LSEDLKRAKY G E+ L KNIAL+FSKDSTRTR Sbjct: 1 MKNLRNRSFLTLLDFSRQEVEFLLTLSEDLKRAKYIGTEKPMLKNKNIALLFEKDSTRTR 60 Query: 61 CAFEVAAHDQGAHVTYLGPTGSQMGKKETSKDTARVLGGMYDGIEYRGFSQETVETLAEF 120- CAFEVAAHDQGA+VTYLGPTGSQMGKKET+KDTARVLGGMYDGIEYRGFSQ TVETLAE+ Sbjct: 61 CAFEVAAHDQGANVTYLGPTGSQMGKKETTKDTARVLGGMYDGIEYRGFSQRTVETLAEY 120- Query: 121 SGVPVWNGLTDADHPTQVLADFLTAKECLHKPYKDIRFTYVGDGRNNVANALMIGASIVG 18- 0 SGVPVWNGLTD DHPTQVLADFLTAKE L K Y DI FTYVGDGRNNVANALM GA+I+G Sbjct: 121 SGVPVWNGLTDEDHPTQVLADFLTAKEVLKKDYADINFTYVGDGRNNVANALMQGAAIMG 18- 0 Query: 181 MTYHLVCPKELEPDPELLSKCQEIAKTTGASIEITADIAEGVRDSDVLYTDVWVSMGSPD 24- 0 M +HLVCPKEL P ELL++C+ IA G +I IT DI +GV+ SDV+YTDVWVSHGEPD Sbjct: 181 MNFHLVCPKELNPTDELLNRCKNIAAENGGNILITDDIDQGVKGSDVIYTDVWVSMGEPD 24- 0 Query: 241 EVWKERIALLEPYRITQEMLNMTENPNVIFEHCLPSFHNIDTKVGYDIYEKYGLKEMSVS 30- 0 EVWKER+ LL+PY++ +EM++ T NPNVIFEHCLPSFHN DTK+G I+EKYG++EMEV+ Sbjct: 241 EVWKERLSLLKPYQVNKEMMDKTGNPNVIFEHCLPSFHNADTKIGQQIFEKYGIREMEVT 30- 0 Query: 301 DSVFEGPHSVVFQEAENRMHTIKAVMVATLGD 332 DEVFE SVVFQSAENRMHTIKAVMVATLG+ Sbjct: 301 DEVFESKASVVFQEAENRMHTIKAVMVATLGE 332 There is also homology to SEQ ID 3118. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1053 A DNA sequence (GBSx1126) was identified in S. agalactiae <SEQ ID 3247> which encodes the amino acid sequence <SEQ ID 3248>. This protein is predicted to be carbamate kinase (b2874). Analysis of this protein sequence reveals the following:

TABLE-US-03142 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.48 Transmembrane 214-230 (214-230) ----- Final Results ----- bacterial membrane --- Certainty = 0.1192 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03143 >GP:CAA66367 GB:X97768 carbamate kinase [Clostridium perfringens] Identities = 162/313 (51%), Positives = 207/313 (65%), Gaps = 7/313 (2%) Query: 3 KIVVALGGNAL-----GNSPEEQLRLVKHTAKSLVALIKKGHEIVVSHGNGPQVGAINLG 57 KIV+ALG NAL S E QL + TA S+ LI+ GHE+ + HGNGPQVG I Sbjct: 2 KIVLALGENALQKDSKDKSAEGQLETCRQTAISVADLIEDGHEVSIVHGNGPQVGQILAS 61 Query: 58 MNFAAESGQGTN-FPFPECGAMSQGYIGYHLQQSLLNELRQEGINKEVATIITQIEVDES 116- + A + G FPF GA S+GYIGYHLQ ++ EL + GI K V TI TQ+ VD++ Sbjct: 62 IELAHQVDNGNPLFPFDVVGAFSEGYIGYHLQNTIREELLKRGIEKSVDTITTQVIVDKN 121- Query: 117 DQAFSAPTKPIGTFYDKETSEKIAIEKGYTFVEDAGRGYRRVVASPEPKKIIEINSIKTL 17- 6 D F+ PTKPIG+FY KE +EK+ +KGYT EDAGRGYRRVVASP+P I+E +IKT+ Sbjct: 122 DPGFTNPTKPIGSFYTKEEAEKLEKDKGYTMKEDAGRGYRRVVASPKPVDIVEKEAIKTM 18- 1 Query: 177 IENDTLVIAGGGGGIPVINKGG-YEGIAAVIDKDKSSALLAGELAADQLIILTAVDYVYT 23- 5 +++ +VIA GGGGIPV+ G EG+ AVIDKD ++ LA L AD L+ILTAVD V Sbjct: 182 VDSGFIVIACGGGGIPVVEDGDRLEGVPAVIDKDFAAEKLAEILDADALLILTAVDRVCV 24- 1 Query: 236 QFGKENQKALTEVNENQMIDYVNQGEFAKGSMLPKVIACMSFLDHNPKGTALITSLNGLE 29- 5 F K +QKAL E+N ++ Y+ +G+FA GSMLPKV AC F+ K A+I SL + Sbjct: 242 NFNKPDQKALKEINLEEVDKYIEEGQFAPGSMLPKVEACKKFVLSGDKKVAIIASLTNAK 30- 1 Query: 296 DALDGKLGTRITK 308 AL G+ GT+I K Sbjct: 302 AALRGESGTKIVK 314 There is also homology to SEQ ID 3110. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1054 A DNA sequence (GBSx1127) was identified in S. agalactiae <SEQ ID 3249> which encodes the amino acid sequence <SEQ ID 3250>. Analysis of this protein sequence reveals the following: TABLE-US-03144 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3558 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1055 A DNA sequence (GBSx1128) was identified in S. agalactiae <SEQ ID 3251> which encodes the amino acid sequence <SEQ ID 3252>. This protein is predicted to be a transmembrane protein (b2298). Analysis of this protein sequence reveals the following: TABLE-US-03145 Possible site: 35 >>>Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -13.11 Transmembrane 413-429 (405-440) INTEGRAL Likelihood = -9.61 Transmembrane 498-514 (489-516) INTEGRAL Likelihood = -9.45 Transmembrane 165-181 (161-185) INTEGRAL Likelihood = -8.07 Transmembrane 127-143 (122-146) INTEGRAL Likelihood = -7.22 Transmembrane 308-324 (306-326) INTEGRAL Likelihood = -5.57 Transmembrane 334-350 (330-357) INTEGRAL Likelihood = -4.51 Transmembrane 194-210 (193-217) INTEGRAL Likelihood = -3.82 Transmembrane 372-388 (371-390) INTEGRAL Likelihood = -1.22 Transmembrane 250-266 (250-268) INTEGRAL Likelihood = -0.80 Transmembrane 468-484 (468-484) INTEGRAL Likelihood = -0.32 Transmembrane 436-452 (436-452) ----- Final Results ----- bacterial membrane --- Certainty = 0.6243 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03146 >GP:AAC22251 GB:U32741 conserved hypothetical transmembrane protein [Haemophilus influenzae Rd] Identities = 303/506 (59%), Positives = 389/506 (75%), Gaps = 6/506 (1%) Query: 10 NKRSKGFRMPGAFTILFILTIFSVLATWWIPAGSYSKLQFDTASSKLVVTDPNGKTVHVP 69 - +K+ K F P AFTILF + I +V TW IP+GSYSKL +++ + VV P Sbjct: 4 SKKKKTFNFPSAFTILFAILILAVGLTWVIPSGSYSKLTYNSTDNVFVVKAYGVDDKTYP 63 Query: 70 ATQTQLDKMNVKIKIKEFTSGAISKPVSVPNTYKRLKQNPAGIGSVTTSMVNGTIEAVDI 129- AT LD +N+KIK+ FT G I KP+++P TY+R++Q+ GI +T SMV GTIEAVD+ Sbjct: 64 ATTDTLDNLNIKIKLSNFTEGVIKKPIAIPGTYQRVEQHHKGIEDITKSMVEGTIEAVDV 123- Query: 130 MVFIMVLGGMIGVVRKSGAFESGLLALTKKTKGREFLLIFLVSLLMVLGGTLCGIEEEAV 18- 9 MVFI VLGGMIGV+ ++G+F +GL+AL KKTKG EF ++F VS+LMVLGGT CGIEEEAV Sbjct: 124 MVFIFVLGGMIGVINRTGSFNAGLMALVKKTKGNEFFIVFCVSVLMVLGGTTCGIEEEAV 18- 3 Query: 190 AFYPILVPIFLAMGYDSIICVGAIFLASSVGTSFSTINPFSSVIASNAAGISFTEGLSWR 24- 9 AFYPILVP+FLA+GYD+I+CVGAIFLA+S+GT+FSTINPFS VIASNAAGI FTEG+ +R Sbjct: 184 AFYPILVPVFLALGYDAIVCVGAIFLAASMGTAFSTINPFSVVIASNAAGIQFTEGIGFR 24- 3 Query: 250 TAGCIAGAIFVVVYLHWYAKKIKANPEFSYSYEDRVEFNAKWGMTTN-HTPSLFTIRQKI 30- 8 G + GA V+ YL+WY KKIKA+P FSY+Y+DR EF ++ + +T F+ R+K+ Sbjct: 244 ALGLVLGATCVIAYLYWYCKKIKADPSFSYTYDDREEFRQRYMKNFDPNTTIPFSARRKL 30- 3 Query: 309 ILSLFVISFPLMVWGVMSQGWWFPTMASSFLAITIIIMFLTATGANGIGERDVVDEFVNG 36- 8 IL+LF ISFP+M+WGVM GWWFP MA+SFLAITIIIMF+ +G+ E+D+++ F G Sbjct: 304 ILTLFCISFPIMIWGVMVGGWWFPQMAASFLAITIIIMFI-----SGLSEKDIMESFTEG 35- 8 Query: 369 ASSLVGVSLIIGLARGINIILSQGYISDTMLYTASKLASHVSGSVFIIVMMFIYFVLGFV 42- 8 AS LVGVSLIIGLARG+N++L QG ISDT+L S + S + GSVFI+ + ++ LG + Sbjct: 359 ASELVGVSLIIGLARGVNLVLEQGMISDTILDYMSNVVSGMPGSVFILGQLVVFIFLGLI 41- 8 Query: 429 VPSSSGLAVLSMPILAPLADTVGIPRSVVVMAYQFGQYAMLFLAPTGLVMATLQMLDMKY 48- 8 VPSSSGLAVLSMPI+APLAD+VGIPR +VV AY +GQYAMLFLAPTGLV+ TLQML + + Sbjct: 419 VPSSSGLAVLSMPIMAPLADSVGIPRDIVVSAYNWGQYAMLFLAPTGLVLVTLQMLQIPF 47- 8 Query: 489 SHWLKFVWPVVLFLLIFGGGLLVLQV 514 W+KFV P++ LL+ G LLV+QV Sbjct: 479 DRWVKFVMPMIGCLLLIGSILLVVQV 504 A related DNA sequence was identified in S. pyogenes <SEQ ID 3253> which encodes the amino acid sequence <SEQ ID 3254>. Analysis of this protein sequence reveals the following: TABLE-US-03147 Possible site: 36 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -13.21 Transmembrane 479-495 (472-496) INTEGRAL Likelihood = -10.24 Transmembrane 261-277 (258-280) INTEGRAL Likelihood = -9.24 Transmembrane 153-169 (142-180) INTEGRAL Likelihood = -7.17 Transmembrane 393-409 (391-411) INTEGRAL Likelihood = -6.00 Transmembrane 81-97 (78-99) INTEGRAL Likelihood = -5.95 Transmembrane 318-334 (314-338) INTEGRAL Likelihood = -3.77 Transmembrane 352-368 (352-369) INTEGRAL Likelihood = -2.66 Transmembrane 120-136 (119-138) INTEGRAL Likelihood = -0.32 Transmembrane 204-220 (204-220) ----- Final Results ----- bacterial membrane --- Certainty = 0.6286 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03148 >GP:AAB94000 GB:AF008219 unknown [Borrelia afzelii] Identities = 174/496 (35%), Positives = 306/496 (61%), Gaps = 37/496 (7%) Query: 10 RIPSSYTVLFIIIAIMAVLTWFIPAGAYETAK---GGG-----VISGTYKTVASNPQGFF 61 - ++PSS+T++F +I + +LT+ IPAG ++ G G +++GTY+T+ P+GF Sbjct: 3 KMPSSFTIIFSLIVFVTILTYVIPAGKFDKEFRQIGDGPKREIIVAGTYQTIDRGPRGFL 62 Query: 62 DILMAPVRGMLGVEGTDGAIQVSFFILMVGGFLGVVNKTGALDTGIASVVRKNKGREKML 121- +M + M +G + A +V F+L+VGG G++ KTGA+D GI S+++K ++K+L Sbjct: 63 HPIMTILTAMS--KGMEHAAEVIIFVLIVGGAYGIIMKTGAIDAGIYSLIKKLGHKDELL 120- Query: 122 IAILIPLFALGGTTYGMGEETMAFYPLLIPVMIAVGFDSIVAVAIILIGSQIGCLASTIN 18- 1 I +L+ +F++GGT GM EET+ FY ++IP+++A+G+D++V VAII +G+ +G +AST+N Sbjct: 121 IPLLMFIFSIGGTVTGMSEETLPFYFVMIPLIVALGYDNVVGVAIIALGAGVGTMASTVN 18- 0 Query: 182 PFATGVAADAAGVSIADGMIWRVIQWVILVGMSIWFVYNYASKIEEDPSKSLVADKEEEH 24- 1 PFATG+A+ A +S+ DG +R++ + I + ++I +V YAS+I++DPSKSLV K+ EH Sbjct: 181 PFATGIASAIASISLQDGFSFRIVLYFISILVAIIYVCVYASRIKKDPSKSLVYSKKNEH 24- 0 Query: 242 KELF-QLQNSGEDLNKRQRNVLTIFTLTFVIMILSLIPWEDFGIKFFTNINTWLTTMPIL 30- 0 + F + + S ED NV TF ++ L+ FG I + ++ L Sbjct: 241 YQYFVKNEISKED------NVQNTLEFTFARKLVLLL----FGFM----ILFLVFSIVQL 28- 6 Query: 301 GGVIGKTMGAFGTWYFPEITMLFIMMGVLVAIVYRMSEEDFFSSFLTGAGEFLGVAMICA 36- 0 G W+ E+TML++ + ++ A + R+ E + + +F+ G+ + A+I Sbjct: 287 G------------WWMQEMTMLYLGVAIISAFICRLGESEMWDAFVKGSESLITAALIIG 33- 4 Query: 361 IARGIQVIMNGGNITATILHLGETSLSGLSSQVFVILAYIFYLPMSFLIPSTSGLAGATM 42- 0 +ARG+ ++ + G+ITAT+L+ L L F+IL I + + F++PS+SG A TM Sbjct: 335 LARGVMIVCDDGLITATMLNAATNFLYNLPRPFFIILNEIIQIFIGFIVPSSSGHASLTM 39- 4 Query: 421 GIMAPLGQFSNVPAHLVITAFQSASGILNMISPTSAIVMGALALGRVDLGTWWKFIGKFI 48- 0 IMAPL F ++ V+ A Q++SG++N+I+PTS ++M L + ++ GTW+KF + Sbjct: 395 PIMAPLADFLSIGRSSVVIAMQTSSGLINLITPTSGVIMAVLGISKLSYGTWFRFVLPLF 45- 4 Query: 481 VMVMLVSVLLLVVATF 496 ++ +S+L+++ + Sbjct: 455 IIEFFISILVIIANVY 470 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03149 Identities = 158/542 (29%), Positives = 274/542 (50%), Gaps = 92/542 (16%) Query: 11 KRSKGFRMPGAFTILFILTIFSVLATWWIPAGSYSKLQFDTASSKLVVTDPNGKTVHVPA 70 - ++ +GFR+P ++T+LFI+ + TW+IPAG+Y +TA Sbjct: 4 EKKRGFRIPSSYTVLFIIIAIMAVLTWFIPAGAY-----ETAKG---------------- 42 Query: 71 TQTQLDKMNVKIKIKEFTSGAISKPVSVPNTYKRLKQNPAGIGSVTTSMVNG------TI 124- G IS TYK + NP G + + V G T Sbjct: 43 ------------------GGVIS------GTYKTVASNPQGFFDILMAPVRGMLGVEGTD 78 Query: 125 EAVDIMVFIMVLGGMIGVVRKSGAFESGLLALTKKTKGREFLLIFLVSLLMVLGGTLCGI 18- 4 A+ + FI+++GG +GVV K+GA ++G+ ++ +K KGRE +LI ++ L LGGT G+ Sbjct: 79 GAIQVSFFILMVGGFLGVVNKTGALDTGIASVVRKNKGREKMLIAILIPLFALGGTTYGM 138- Query: 185 EEEAVAFYPILVPIFLAMGYDSIICVGAIFLASSVGTSFSTINPFSSVIASNAAGISFTE 24- 4 EE +AFYP+L+P+ +A+G+DSI+ V I + S +G STINPF++ +A++AAG+S + Sbjct: 139 GEETMAFYPLLIPVMIAVGFDSIVAVAIILIGSQIGCLASTINPFATGVAADAAGVSIAD 19- 8 Query: 245 GLSWRTAGCIAGAIFVVVYLHWYAKKIKANPEFSYSYEDRVEFNAKWGMTTNHTPSLFTI 30- 4 G+ WR + + +++ YA KI+ +P S D+ E + + N L Sbjct: 199 GMIWRVIQWVILVGMSIWFVYNYASKIEEDPSKSL-VADKEEEHKELFQLQNSGEDL-NK 25- 6 Query: 305 RQKIILSLFVISFPLMV-----W----------------------GVMSQ------GWWF 33- 1 RQ+ +L++F ++F +M+ W GV+ + W+F Sbjct: 257 RQRNVLTIFTLTFVIMILSLIPWEDFGIKFFTNINTWLTTMPILGGVIGKTMGAFGTWYF 31- 6 Query: 332 PTMASSFLAITIIIMFLTATGANGIGERDVVDEFVNGASSLVGVSLIIGLARGINIILSQ 39- 1 P + F+ + +++ + + E D F+ GA +GV++I +ARGI +I++ Sbjct: 317 PEITMLFIMMGVLVAIVYR-----MSEEDFFSSFLTGAGEFLGVAMICAIARGIQVIMNG 37- 1 Query: 392 GYISDTMLYTASKLASHVSGSVFIIVMMFIYFVLGFVVPSSSGLAVLSMPILAPLADTVG 45- 1 G I+ T+L+ S +S VF+I+ Y + F++PS+SGLA +M I+APL Sbjct: 372 GMITATILHLGETSLSGLSSQVFVILAYIFYLPMSFLIPSTSGLAGATMGIMAPLGQFSN 43- 1 Query: 452 IPRSVVVMAYQFGQYAMLFLAPT-GLVMATLQMLDMKYSHWLKFVWPVVLFLLIFGGGLLVL - 512 +P +V+ A+Q + ++PT +VM L + + W KF+ ++ +++ LLV+ Sbjct: 432 VPAHLVITAFQSASGILNMISPTSAIVMGALALGRVDLGTWWKFIGKFIVMVMLVSVLLLVV - 493 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1056 A DNA sequence (GBSx1129) was identified in S. agalactiae <SEQ ID 3255> which encodes the amino acid sequence <SEQ ID 3256>. Analysis of this protein sequence reveals the following: TABLE-US-03150 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.83 Transmembrane 25-41 (18-47) INTEGRAL Likelihood = -10.46 Transmembrane 153-169 (148-176) ----- Final Results ----- bacterial membrane --- Certainty = 0.5331 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03151 >GP:CAB13183 GB:Z99110 similar to two component sensor histidine kinase [YkoG] [Bacillus subtilis] Identities = 119/446 (26%), Positives = 212/446 (46%), Gaps = 18/446 (4%) Query: 17 TQITLWYSSFIFILVIGVLIGSFFISKSIAENKSKKNLEAKAVQMSQALAKGHRYEAFED 76 - T+I L+ S + IL+I V + I S +K L + +++AL Sbjct: 5 TKIHLYTSISLLILLILVHTAVYLIFSSALTSKDAARLADETDNIAEALRAAETEGVALQ 64 Query: 77 GIFYSVYDQNGKV-IYSGFPKGFKRDLDHQHKHKKKLSLFSMEN--------RTFQYVDI 127- + + NG V + +G K + LS S E + F + Sbjct: 65 DMLQAYLPANGMVRVVNGDQKAVMTITKEKAYKDFPLSFHSGETADVRKPDGKLFAEAAV 124- Query: 128 PISGKNQWLRAIRTVDRLDKQLTELLFSLGIVLPLMLIIITVG----GYLILKRTFRPIQ 18- 3 P+ + + +++ V+RL+ E LF L I+L + + G L+ +R PI+ Sbjct: 125 PVIWTDGQVVSLQLVERLENT-EESLFLLKIILIAASAAVCIASFFAGSLLARRIINPIR 18- 3 Query: 184 EITETAQFITQNEDYTKRIITKNNENELTELAAVINTMLASIESSFVREKQFNNDVSHEL 24- 3 + T + I +++++ + + +EL ++ N M ++ + +++QF D SHEL Sbjct: 184 RLMITMKDIQRDKEFKTISLEGQSNDELYQMGLTFNEMAMMLKEHYDKQQQFVQDASHEL 24- 3 Query: 244 RTPVTVILSESEYGKNYAENLSEA-KESFEVIHRQSLSMKKLVEQLLELTKAENPLSIQL 30- 2 +TP+T+I S S K + E +ES E IH +++ MKKL QLL L K+ L + L Sbjct: 244 KTPLTIIESYSSLMKRWGAKKPEVLEESIEAIHSEAVHMKKLTNQLLALAKSHQGLEVDL 30- 3 Query: 303 EPLNFSIMMKQLVSDSSRLLDNTPIHLDSQIEDDLWIIGQQTLLKRLFDNLFSNAIKFTN 36- 2 + ++ I + V + + + I L++ ++ L + + +K+L L NAIK++ Sbjct: 304 KTIDL-IKAARAVMQTLQSVYQRDILLETD-KESLLVKADEERIKQLLTILLDNAIKYSE 36- 1 Query: 363 NHISISLRQSDNQIVFSIKDNGLGISVDDQSKIWNRFYQVDSARTKDSQSGIGLGLSLVK 42- 2 I +S + + S++D G+GI + ++ RFY+ D AR + + G GLGLS+ K Sbjct: 362 KPIEMSAGTRNGRPFLSVRDEGIGIPEEHIPHLFERFYRADEARNRKT-GGTGLGLSIAK 42- 0 Query: 423 QIATIHRAKIWVDSKPDDGSQFTLTF 448 QIA H ++ V SKP G+ T+ F Sbjct: 421 QIADEHGIELSVKSKPGQGTAVTMQF 446 There is also homology to SEQ ID 1178. SEQ ID 3256 (GBS77) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 21 (lane 2; MW 78.5 kDa) and in FIG. 28 (lane 2; MW 78.5 kDa). GBS77-GST was purified as shown in FIG. 195, lane 4. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1057 A DNA sequence (GBSx1130) was identified in S. agalactiae <SEQ ID 3257> which encodes the amino acid sequence <SEQ ID 3258>. This protein is predicted to be CopR protein (tcrA). Analysis of this protein sequence reveals the following: TABLE-US-03152 Possible Site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3963 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03153 >GP:CAC07978 GB:AJ278983 CopR protein [Ralstonia metallidurans] Identities = 102/221 (46%), Positives = 145/221 (65%) Query: 1 MKILVVEDEFDLNRSIVKLLKKQHYSVDSASNGEEALQFVSVAEYDVIILDVMMPKMDGF 60 MK+LVVEDE + + L + + VD +NG + F YD+IILDVM+P +DG+ Sbjct: 1 MKLLVVEDEVKTGEYLRQGLTEAGFVVDLVANGLDGQHFAVNETYDLIILDVMLPDVDGW 60 Query: 61 TFLKLLRNKGSQVSILMLTARDAVEDRIAGLDFGADDYLVKPFEFGELMARIRAMLRRAN 120- L +R G+ V +L LTARD+V DR+ GL+ GADDYLVKPF F EL+AR+R +LRR Sbjct: 61 HILHAIRASGNAVPVLFLTARDSVADRVRGLELGADDYLVKPFAFSELLARVRTLLRRGA 120- Query: 121 RQVSSDDIQIQDITINLSTKQVWRNDNLIDLTAKEYEVLEYLARHRDQVLSRHQIREHVW 18- 0 Q++ D IQ+ D+ ++LS ++ R I LT+KE+ +LE AR R +VL R I VW Sbjct: 121 VQLAMDRIQVADLILDLSRRRASRGGRRITLTSKEFALLELFARRRGEVLPRSLIASQVW 18- 0 Query: 181 DYDYYGESNIIDVLIKNLRRKLDNNRDGSLIKTKRGLGYVI 221 D ++ +SN+IDV I+ LR K+D+ + LI+T RG+GYV+ Sbjct: 181 DMNFDSDSNVIDVAIRRLRAKIDDGFEVKLIQTVRGMGYVL 221 There is also homology to SEQ ID 3260. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1058 A DNA sequence (GBSx1131) was identified in S. agalactiae <SEQ ID 3261> which encodes the amino acid sequence <SEQ ID 3262>. Analysis of this protein sequence reveals the following:

TABLE-US-03154 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.45 Transmembrane 18-34 (16-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.2381 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10281> which encodes amino acid sequence <SEQ ID 10282> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3262 (GBS78) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 4; MW 23.8 kDa). The GBS78-GST fusion product was purified (FIG. 194, lane 4) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 317), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1059 A DNA sequence (GBSx1132) was identified in S. agalactiae <SEQ ID 3263> which encodes the amino acid sequence <SEQ ID 3264>. Analysis of this protein sequence reveals the following: TABLE-US-03155 Possible site: 36 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.04 Transmembrane 15-31 (6-35) INTEGRAL Likelihood = -1.28 Transmembrane 51-67 (51-67) ----- Final Results ----- bacterial membrane --- Certainty = 0.5416 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3264 (GBS79) was expressed in E. coli as a GST-fusion product. GBS79d was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 154 (lane 17 & 18; MW 51 kDa), in FIG. 155 (lane 17; MW 51 kDa) and in FIG. 187 (lane 13; MW 51 kDa). GBS79d was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 155 (lane 24; MW 26 kDa) and in FIG. 183 (lane 5; MW 26 kDa). Purified GBS79d-GST is shown in FIG. 243, lane 2. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1060 A DNA sequence (GBSx1133) was identified in S. agalactiae <SEQ ID 3265> which encodes the amino acid sequence <SEQ ID 3266>. Analysis of this protein sequence reveals the following: TABLE-US-03156 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5326 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10279> which encodes amino acid sequence <SEQ ID 10280> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03157 >GP:AAG20974 GB:AE005164 Vng6349c [Halobacteriurn sp. NRC-1] Identities = 97/358 (27%), Positives = 163/358 (45%), Gaps =20/358 (5%) Query: 35 DPQIIKLTTRANIAIGTYEGFLESIINPMLLISPLLSQEAVLSSKLEGTHATLKDLLNYE 94 - D + A +G G + P +L + LL +EA+ S++++EG L + E Sbjct: 70 DDDFYETLADATFWLGKLSGVSLELDFPPVLYTSLLRKEAMESAEIEGADVDYDALYSLE 129- Query: 95 AGNKVDIERDELHEII------NYRKALFYALENISTINNIDSKGLPLSNRIIKENHKIL 148- D RDE E + R+ L Y I+ +D+ G L+ ++ ++H+ L Sbjct: 130 T-RTFDEGRDEPSETTAAAETKDTREVLNYETAVKEGIDALDA-GEELNVELLHDLHETL 18- 7 Query: 149 LDNV---RGSSKNPGNFKRSQNYIGSVSSISYTPVPAEKTPEYMSNLEQYIHYD-DLDLL 20- 4 L V R + G++K + NY+G + P + M L Y L Sbjct: 188 LTGVPDDRVDTDTIGDYKTNPNYLGD-----FLPPAPGAVEDLMDGLFTYYRTGGSYHPL 24- 2 Query: 205 VQSAIIHAQFEMIHPFEDGNGRIGRLLIPLFLYYQELLSYPTFYMSSYFERDRSLYISHL 26- 4 V A+ H QFE IHP+ DGNGR+GRLLI L LY +LL P Y+S Y R+++ Y+ + Sbjct: 243 VDIALFHYQFETIHPYGDGNGRLGRLLITLQLYDADLLERPNLYLSEYLNRNKTTYVERM 30- 2 Query: 265 SNISKDNNWKDWFEYYLEGVILSAEESTKKAQDILSLYNIMKEQVIPKLNSVSGIQLLDF 32- 4 + W+ W +++EG+ A ES ++ + + L + + K + + QL Sbjct: 303 EGVRFHGEWEAWLSFFIEGIARQAHESVERTRALADLRREYEHEYGGKAYTKN--QLAVT 36- 0 Query: 325 IFSAPIFKAEQVSEHLKISERTTYTLLNKLIDEGYL-STDNAQRNRTYYCPQLLSIVQ 381 +F P ++ V I + T +N+L++EG L RN+ Y ++ I++ Sbjct: 361 LFEQPYITSKTVQRLFDIEQSTASRAINELVNEGILEEVPRHGRNKEYRAREIFEILE 418 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1061 A DNA sequence (GBSx1134) was identified in S. agalactiae <SEQ ID 3267> which encodes the amino acid sequence <SEQ ID 3268>. Analysis of this protein sequence reveals the following: TABLE-US-03158 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4370(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> RGD motif : 46-48 The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3268 (GBS299) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 58 (lane 2; MW 62.2 kDa) and in FIG. 60 (lane 4; MW 62.2 kDa). GBS299-GST was purified as shown in FIG. 207 (lane 4) and FIG. 225 (lanes 2-3). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1062 A DNA sequence (GBSx1135) was identified in S. agalactiae <SEQ ID 3269> which encodes the amino acid sequence <SEQ ID 3270>. Analysis of this protein sequence reveals the following: TABLE-US-03159 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4176(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1063 A DNA sequence (GBSx1136) was identified in S. agalactiae <SEQ ID 3271> which encodes the amino acid sequence <SEQ ID 3272>. Analysis of this protein sequence reveals the following: TABLE-US-03160 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ------ bacterial cytoplasm --- Certainty = 0.1789(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1064 A DNA sequence (GBSx1137) was identified in S. agalactiae <SEQ ID 3273> which encodes the amino acid sequence <SEQ ID 3274>. Analysis of this protein sequence reveals the following: TABLE-US-03161 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3748(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1065 A DNA sequence (GBSx1138) was identified in S. agalactiae <SEQ ID 3275> which encodes the amino acid sequence <SEQ ID 3276>. Analysis of this protein sequence reveals the following: TABLE-US-03162 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1638(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03163 >GP:CAB12294 GB:Z99106 similar to transposon protein [Bacillus subtilis] Identities = 84/291 (28%), Positives = 138/291 (46%), Gaps = 6/291 (2%) Query: 6 MLDYLAVTIKGLAPDDVIEKILILPKDKFVLNEWGINKYQRHYSFSEIKVYFNKDWQSKM 65 M+DY+ V+ K D +IE++L L KD + G Y Y IKV+++ ++ Sbjct: 31 MVDYIRVSFKTHDVDRIIEEVLHLSKDFMTEKQSGFYGYVGTYELDYIKVFYSAPDDNR- 89 Query: 66 GVFIELRGQGCRQYEEYMENNVNNWVTLMKRISECHSNVTRLDIANDIFDDSLSVPLIYS 125- GV IE+ GQGCRQ+E ++E W + + + TR D+A D S+P + Sbjct: 90 GVLIEMSGQGCRQFESFLECRKKTWYDFFQDCMQQGGSFTRFDLAIDDKKTYFSIPELLK 149- Query: 126 YCKKQLCISTAKTFDYHEKSLLENGEKVGEMVTIGVRGTQQW-CVYNKLLEQKLDQELPN 18- 4 +K CIS + D++ L +G G + G + ++ + C Y K EQ +P Sbjct: 150 KAQKGECISRFRKSDFNGSFDLSDGITGGTTIYFGSKKSEAYLCFYEKNYEQAEKYNIPL 20- 9 Query: 185 TPL-SWTRAELRCWQEKANLLAKQIKEGRPLKEIYFEVINGHYRFVSPRDKDSNRWRRKT 24- 3 L W R ELR E+A + + + + L I ++IN + RFV D++ R KT Sbjct: 210 EELGDWNRYELRLKNERAQVAIDALLKTKDLTLIAMQIINNYVRFVD-ADENITREHWKT 26- 8 Query: 244 VKWWNDYLETQEKTVLSVKRTKPTLKRSEKWTEKQVSRTLGKLYVAKAESH 294 +W+D++ + L VK K ++S W + T+ V +A+ H Sbjct: 269 SLFWSDFIGDVGRLPLYVKPQKDFYQKSRNWLRNSCAPTM--KMVLEADEH 317 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1066 A DNA sequence (GBSx1139) was identified in S. agalactiae <SEQ ID 3277> which encodes the amino acid sequence <SEQ ID 3278>. This protein is predicted to be integrase. Analysis of this protein sequence reveals the following: TABLE-US-03164 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1914(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03165 >GP:CAB70622 GB:AJ243106 integrase [Streptococcus thermophilus] Identities = 135/474 (28%), Positives = 233/474 (48%), Gaps = 68/474 (14%) Query: 20 KAGNVLVKFAMRFTHPITKKSHKKYLSTGASKGWFTTKATPSKKLPSGKERLLVSDIKNT 79 - K G + VKF F + +T K ++ LS W+T +KK +GK +L S Sbjct: 19 KTGYIEVKFRTYFNNQLTNK-RREILSD-----WYTIV---NKKDTTGKIKL--SPQIKA 67 Query: 80 QLITQVTQELNKLVDDYIAELMGIKPKKAKKLLTLEEIAKPFDKDGNFYGKAFKAWH--- 136- + ++ ++ NK+ ++ ++ K +TL+E+ + WH Sbjct: 68 IIHKELQEKANKVYEELTRTIL-----LEKSDITLDEV--------------WNEWHNER 108- Query: 137 -ERVKPANNTLKTRVTIYNRYIEPNFDTRMSITKFAFMTDEIQNLIN-----ASSMHMAR 19- 0 ER A TL Y +I + SI K + I+NL++ + +A+ Sbjct: 109 VERQLVAPKTLAGEDGRYRNHITKQIP-KNSILK-NIPSSLIKNLLDNLYPIGNHKRLAQ 16- 6 Query: 191 NLHIYLKMIFDWSVENGQITLTQDPIASNKVKRRVLTKSEEQDK-KREDIAEKYLEASEV 24- 9 + L I+ +++ + I+ Q+P+ + R+ L S+E D+ K+ DI ++YLE+ E+ Sbjct: 167 GVKSDLTSIYKFAILHDYISPDQNPMPYISIGRKGL--SDELDRLKKSDIEDQYLESWEL 22- 4 Query: 250 NHVLRLIESWTNRPDNQLIADVLRMIFLTGMRPSEVLGLNEDMLDFEKKWIKVHWQRASK 30- 9 VL ++ + N+ A + LTGMR EVLGL E+ +DF K V RA+ Sbjct: 225 KEVLSIVRKY-----NEQYARIFEFQALTGMRIGEVLGLKEEAIDFNKNIASVIRTRATH 27- 9 Query: 310 NKSDDMMEALNLDEKERYRADLKTKESVRTIPMSPEVEKILRHYIDRNKFQAQFSPTYQD 36- 9 + + + Y ++K +S R + +S +IL+ I+ N +F+P Y+D Sbjct: 280 GGASE----------DSYEGNVKNLQSYRNVQLSKRAIEILKEEIELNHQHIRFNPDYKD 32- 9 Query: 370 LGYLFTRTYIRAGNRQGSPLYHNELSQFLRGGSSQSAKYNKKAGKPYK---DIDSFLDFG 42- 6 G++FT I + G+PL+++ L+ FL SS++K N+ G P + DID+ L F Sbjct: 330 NGWIFTSKSIHKPDYNGTPLHYSVLNNFL--NSSENGKLNRN-GNPRRAGIDIDNKLSFK 38- 6 Query: 427 RPIHVIPHMFRHSFISIMASEGIDLPTIREFVGHSEDSKEIERVYLHVIKKQKD 480 + H+ H+FRH+ IS +A +G+ L I++ VGHS S+ + +YLH+ KK RD Sbjct: 387 K--HITTHIFRHTHISFLAEQGVPLEAIQDRVGHSRGSR-VTEIYLHITKKTKD 437 A related DNA sequence was identified in S. pyogenes <SEQ ID 3279> which encodes the amino acid sequence <SEQ ID 3280>. Analysis of this protein sequence reveals the following: TABLE-US-03166 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5203(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03167 Identities = 82/357 (22%), Positives = 155/357 (42%), Gaps = 52/357 (14%) Query: 135 WHERVKPANNTLKTRVTIYNRYIEPNFDTRMSITKFAFMTDEIQNLINA--SSMHMARNL 19- 2 W K +T + R + D + I K T +Q++I+ S + Sbjct: 73 WEHHQKSLKSTSVRSLDFRIRELRNLIDPEVMIAKIT--TKYLQSIIDKIPGSYDKRKRA 130- Query: 193 HIYLKMIFDWSVENGQITLTQDPIASNKVKRRVLTKSEEQDKKREDIAEKYLEASEVNHV 25- 2 LK FD+++ +++ +P+ S +++ V T K ED+A+K+LE E+ Sbjct: 131 RQLLKQTFDYAIALEYVSI--NPVISTQLAKPVKTI-----KDFEDVAQKFLSKDELK-- 18- 1 Query: 253 LRLIESWTNRPDNQLIADVLRMIFLTGMRPSEVLGLNEDMLDFEKKWIKVHWQRASKNKS 31- 2 RL++ R + +A + + L G R E L + + + I++H Sbjct: 182 -RLLDEMYRRKGSIKMAYLAEFMSLNGCRIGEALAIQPD--NIKNDIIEIH--------- 22- 9 Query: 313 DDMMEALNLDEKERYRADLKTKESVRTIPMSPEVEKILRHYIDRNKFQAQFSPTYQDLGY 37- 2 ++ + + + KT S R ++ ++I++ + N + +P Y+D+GY Sbjct: 230 -GTLDYTSNGYRNAIKTTPKTNSSWRETLITKREKEIIQDILKINALEKNTNPNYKDNGY 28- 8 Query: 373 LFTRTYIRAGNRQGSPLYNNELSQFLRGGSSQSAKYNKKAGKPYKDIDSFLDFGRPIHVI 43- 2 +F +R G P+ N L+ +R NK+ KP + + Sbjct: 289 IFI-------SRNGVPIQDNALNTSIRAA-------NKRLEKPIQK-----------ELT 32- 3 Query: 433 PHMFRHSFISIMASEGIDLPTIREFVGHSEDSKEIERVYLHVIKKQKDTMRGAVEKL 489 H+FRH+ +S +A + L TI + VGH+ DSK +++Y HV K K+ + + +L Sbjct: 324 SHIFRHTLVSRLAENKVPLKTIMDRVGHA-DSKTTQQIYTHVTHSMKNEVVDILNRL 379 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1067 A DNA sequence (GBSx1140) was identified in S. agalactiae <SEQ ID 3281> which encodes the amino acid sequence <SEQ ID 3282>. Analysis of this protein sequence reveals the following: TABLE-US-03168 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3023(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10277> which encodes amino acid sequence <SEQ ID 10278> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03169 >GP:AAB64982 GB:U43834 Ydr540cp [Saccharomyces cerevisiae] Identities = 88/170 (51%), Positives = 117/170 (68%), Gaps = 3/170 (1%) Query: 36 MRTYSDKNELKEEVLKSYKKYIAEFNDIPEKLKDLRIDEVDRTPAENLAYQVGWTTLILK 95 - MR Y+ K ELKEE+ K Y+KY AEF I E KD +++ VDRTP+ENL+YQ+GW L+L+ Sbjct: 1 MREYTSKKELKEEIEKKYEKYDAEFETISESQKDEKVETVDRTPSENLSYQLGWVNLLLE 60 Query: 96 WESDEQSGLEVKTPTETFKWNQLGELYQHFTETYASLTIKELTAQLNDNVDAIGNMIDSM 155- WE+ E +G V+TP +KWN LG LYQ F + Y +IKE A+L + V+ + I ++ Sbjct: 61 WEAKEIAGYNVETPAPGYKWNNLGGLYQSFYKKYGIYSIKEQRAKLREAVNEVYKWISTL 120- Query: 156 SDEVLFKPHMRNWADSATKNAVWEVYKFIHINTVAPFGTFRTKIRKWKKV 205 SD+ LF+ R W AT A+W VYK+IHINTVAPF FR KIRKWK++ Sbjct: 121 SDDELFQAGNRKW---ATTKAMWPVYKWIHINTVAFFTNFRGKIRKWKRL 167 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1068 A DNA sequence (GBSx1141) was identified in S. agalactiae <SEQ ID 3283> which encodes the amino acid sequence <SEQ ID 3284>. This protein is predicted to be 50S ribosomal protein subunit L33-related protein. Analysis of this protein sequence reveals the following: TABLE-US-03170 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5420(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03171 >GP:AAB66692 GB:U89998 50S ribosomal protein subunit L33 [Lactococcus lactis subsp. cremoris] Identities = 43/49 (87%), Positives = 46/49 (93%) Query: 1 HRVNITLEHKESGERLYLTSKNKRNTPDRLQLKKYSPKLRKHVVFTEVK 49 HRVNITLEHKESGERLYLT KNKRNTPD+L+LKKYS KLRKHV+F EVK Sbjct: 1 MRVNITLEHKESGERLYLTQKNKRNTPDKLELKKYSKKLRKHVIFKEVK 49 A related DNA sequence was identified in S. pyogenes <SEQ ID 3285> which encodes the amino acid sequence <SEQ ID 3286>. Analysis of this protein sequence reveals the following:

TABLE-US-03172 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5394(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03173 Identities = 48/49 (97%), Positives = 48/49 (97%) Query: 1 MRVNITLEHKESGERLYLTSKNKRNTPDRLQLKKYSPKLRKHVVFTEVK 49 MRVNITLEHKESGERLYLTSKNKRNTPDRLQLKKYSPKLRKHV FTEVK Sbjct: 1 MRVNITLEHKESGERLYLTSKNKRNTPDRLQLKKYSPKLRKHVTFTEVK 49 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1069 A DNA sequence (GBSx1142) was identified in S. agalactiae <SEQ ID 3287> which encodes the amino acid sequence <SEQ ID 3288>. This protein is predicted to be 50S ribosomal protein subunit L32-related protein. Analysis of this protein sequence reveals the following: TABLE-US-03174 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3577(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03175 >GP: AAB66691 GB: U89998 50S ribosomal protein subunit L32 [Lactococcus lactis subsp. cremoris] Identities = 44/53 (83%), Positives = 48/53 (90%) Query: 1 MAKPARHTSKAKRNKRRTHYKLTAPSVQFDETTGDYSRSHRVSLKGYYKGRKI 53 MA PARHTS AK+N+RRTHYKLTAP+V FDETTGDY SHRVSLKGYYKGRK+ Sbjct: 1 MAVPARHTSSAKKNRRRTHYKLTAPTVTFDETTGDYRHSHRVSLKGYYKGRKV 53 A related DNA sequence was identified in S. pyogenes <SEQ ID 3289> which encodes the amino acid sequence <SEQ ID 3290>. Analysis of this protein sequence reveals the following: TABLE-US-03176 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5148(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03177 Identities = 38/39 (97%), Positives = 39/39 (99%) Query: 22 LTAPSVQFDETTGDYSRSHRVSLKGYYKGRKIAKANEAK 60 +TAPSVQFDETTGDYSRSHRVSLKGYYKGRKIAKANEAK Sbjct: 1 MTAPSVQFDETTGDYSRSHRVSLKGYYKGRKIAKANEAK 39 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1070 A DNA sequence (GBSx1144) was identified in S. agalactiae <SEQ ID 3291> which encodes the amino acid sequence <SEQ ID 3292>. This protein is predicted to be histidyl-tRNA synthetase (hisS). Analysis of this protein sequence reveals the following: TABLE-US-03178 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4357(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10275> which encodes amino acid sequence <SEQ ID 10276> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03179 >GP: CAA78919 GB: Z17214 histidine--tRNA ligase [Streptococcus equisimilis] Identities = 327/404 (80%), Positives = 361/404 (88%) Query: 32 WQYVENVIRNLFKQYHYDEIRTPMFEHYEVISRSVGDTTDIVTKEMYDFHDKGDRHITLR 91 - WQYVE V R FKQYHY EIRTPMFEHYEVISRSVGDTTDIVTKEMYDF+DKGDRHITLR Sbjct: 1 WQYVEGVARETFKQYHYGEIRTPMFEHYEVISRSVGDTTDIVTKEMYDFYDKGDRHITLR 60 Query: 92 PEGTAPVVRSYVENKLFAPEVQKPTKMYYIGSMFRYERPQAGRLREFHQVGVECFGSNNP 151- PEGTAPVVRSYVENKLFAPEVQKP K+YYIGSMFRYERPQAGRLREFHQ+GVECFGS NP Sbjct: 61 PEGTAPVVRSYVENKLFAPEVQKPVKLYYIGSMFRYERPQAGRLREFHQIGVECFGSANP 120- Query: 152 ATDVETIAMGHHLFEDLGIKNVKLHLNSLGNPESRQAYRQALIDYLTPIREQLSKDSQRR 21- 1 ATDVETIAM +HLFE LGIK V LHLNSLGN SR AYRQALIDYL+P+R+ LSKDSQRR Sbjct: 121 ATDVETIAMAYHLFERLGIKGVTLHLNSLGNAASRAAYRQALIDYLSPMRDTLSKDSQRR 18- 0 Query: 212 LNENPLRVLDSKEPEDKLAVENAPSILDYLDESSQAHFDAVCHMLDALNIPYIIDTNMVR 27- 1 L+ENPLRVLDSKE EDK+AV NAPSILDY DE SQAHFDAV ML+AL IPY+IDTNMVR Sbjct: 181 LDENPLRVLDSKEKEDKIAVANAPSILDYQDEESQAHFDAVRSMLEALAIPYVIDTNMVR 24- 0 Query: 272 GLDYYNHTIFEFITEIEDNELTICAGGRYDGLVSYFGGPETPAFGFGLGLERLLLILDKQ 33- 1 GLDYYNHTIFEFITE++ +ELTICAGGRYDGLV YFGGP TP FGFGLGLERLLLILDKQ Sbjct: 241 GLDYYNHTIFEFITEVDQSELTICAGGRYDGLVEYFGGPATPGFGFGLGLERLLLILDKQ 30- 0 Query: 332 GISLPIENTIDLYIAVLGSEANLAALDLAQSIRHQGFKVERDYLGRKIKAQFKSADTFNA 39- 1 G+ LP+E +D+YIAVLG++AN+AAL L Q+IR QGF VERDYLGRKIKAQFKSADTF A Sbjct: 301 GVELPVEEGLDVYIAVLGADANVAALALTQAIRRQGFTVERDYLGRKIKAQFKSADTFKA 36- 0 Query: 392 KVIMTLGSSEVDSKEVGLKNNQTRQEVKVSFENIKTDFSSVLKQ 435 KV++TLG SE+ + + LK+NQTRQE+ VSF+ I+TDF+S+ + Sbjct: 361 KVVITLGESEIKAGQAVLKHNQTRQEMTVSFDQIQTDFASIFAE 404 A related DNA sequence was identified in S. pyogenes <SEQ ID 3293> which encodes the amino acid sequence <SEQ ID 3294>. Analysis of this protein sequence reveals the following: TABLE-US-03180 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3183(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03181 Identities = 339/424 (79%), Positives = 387/424 (90%) Query: 13 MKLQKPKGTQDILPGESAKWQYVENVIRNLFKQYHYDEIRTPMFEHYEVISRSVGDTTDI 72 - MKLQKPKGTQDILPG++AKWQYVE+V R+ F QY+Y EIRTPMFEHYEVISRSVGDTTDI Sbjct: 1 MKLQKPKGTQDILPGDAAKWQYVESVARDTFSQYNYGEIRTPMFEHYEVISRSVGDTTDI 60 Query: 73 VTKEMYDFHDKGDRHITLRPEGTAPVVRSYVENKLFAPEVQKPTKMYYIGSMFRYERPQA 132- VTKEMYDF+DKGDRHITLRPEGTAPVVRSYVENKLFAPEVQKP K+YYIGSMFRYERPQA Sbjct: 61 VTKEMYDFYDKGDRHITLRPEGTAPVVRSYVENKLFAPEVQKPVKLYYIGSMFRYERPQA 120- Query: 133 GRLREFHQVGVECFGSNNPATDVETIAMGHHLFEDLGIKNVKLHLNSLGNPESRQAYRQA 19- 2 GRLREFHQ+GVECFG+ NPATDVETIAM +HLFE LGIK+V LHLNSLG+PESR AYRQA Sbjct: 121 GRLREFHQIGVECFGAANPATDVETIAMAYHLFEKLGIKDVTLHLNSLGSPESRAAYRQA 18- 0 Query: 193 LIDYLTPIREQLSKDSQRRLNENPLRVLDSKEPEDKLAVENAPSILDYLDESSQAHFDAV 25- 2 LIDYLTP+R+QLSKDSQRRL+ENPLRVLDSKE EDKLAVE APSILDYLDE SQAHF+AV Sbjct: 181 LIDYLTPMRDQLSKDSQRRLDENPLRVLDSKEKEDKLAVEKAPSILDYLDEESQAHFEAV 24- 0 Query: 253 CHMLDALNIPYIIDTNMVRGLDYYNHTIFEFITEIEDNELTICAGGRYDGLVSYFGGPET 31- 2 ML+AL+IPY+IDTNMVRGLDYY+HTIFEFIT +E ++LTICAGGRYD LV YFGGPET Sbjct: 241 KDMLEALDIPYVIDTNMVRGLDYYSHTIFEFITSVEGSDLTICAGGRYDSLVGYFGGPET 30- 0 Query: 313 PAFGFGLGLERLLLILDKQGISLPIENTIDLYIAVLGSEANLAALDLAQSIRHQGFKVER 37- 2 P FGFGLGLERLL+I++KQGI+LPIE +D+Y+AVLG AN AL+L Q+IR QGF ER Sbjct: 301 PGFGFGLGLERLLMIIEKQGITLPIETEMDIYLAVLGDGANSKALELVQAIRRQGFTAER 36- 0 Query: 373 DYLGRKIKAQFKSADTFNAKVIMTLGSSEVDSKEVGLKNNQTRQEVKVSFENIKTDFSSV 43- 2 DYLGRKIKAQFKSADTF AK++MTLG SEV++ + +KNN++RQEV+VSFE++ T+F+++ Sbjct: 361 DYLGRKIKAQFKSADTFKAKLVMTLGESEVEAGKAVIKNNRSRQEVEVSFEDMMTNFANI 42- 0 Query: 433 LKQL 436 +QL Sbjct: 421 SEQL 424 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1071 A DNA sequence (GBSx1145) was identified in S. agalactiae <SEQ ID 3295> which encodes the amino acid sequence <SEQ ID 3296>. This protein is predicted to be aspartyl-tRNA synthetase (aspS). Analysis of this protein sequence reveals the following: TABLE-US-03182 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5124(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10273> which encodes amino acid sequence <SEQ ID 10274> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03183 >GP: CAB14714 GB: Z99118 aspartyl-tRNA synthetase [Bacillus subtilis] Identities = 339/585 (57%), Positives = 432/585 (72%), Gaps = 9/585 (1%) Query: 20 RSMYAGRVRSEHIGTSITLKGWVGRRRDLGGLIFIDLRDREGIMQLVINPEEVSASVMAT 79 R+ Y G + + IG S+TLKGWV +RRDLGGLIFIDLRDR GI+Q+V NP+ VS +A Sbjct: 4 RTYYCGDITEKAIGESVTLKGWVQKRRDLGGLIFIDLRDRTGIVQVVFNPD-VSKEALAI 62 Query: 80 AESLRSEFVIEVSGVVTAREQA--NDNLPTGEVELKVQELSILNTSKTTPFEIKDGIE-A 136- AE +R+E+V+++ G V ARE+ N NL TG +E+ +++LN +KT PF I D E Sbjct: 63 AEGIRNEYVLDIQGKVVAREEGTVNPNLKTGAIEIHADGVNVLNAAKTPPFAISDQAEEV 122- Query: 137 NDDTRMRYRYLDLRRPEMLENFKLRAKVTHSIRNYLDNLEFIDVETPMLTKSTPEGARDY 19- 6 ++D R+++RYLDLRRP M + +LR VT ++R++LD F+D+ETP+LT STPEGARDY Sbjct: 123 SEDVRLKHRYLDLRRPAMFQTMQLRHNVTKAVRSFLDENGFLDIETPILTGSTPEGARDY 18- 2 Query: 197 LVPSRVNQGHFYALPQSPQITKQLLMNAGFDRYYQIVKCFRDEDLRGDRQPEFTQVDLET 25- 6 LVPSRV++G FYALPQSPQ+ KQLLM +G +RYYQI +CFRDEDLR DRQPEFTQ+D+E Sbjct: 183 LVPSRVHEGEFYALPQSPQLFKQLLMVSGIERYYQIARCFRDEDLRADRQPEFTQIDIEM 24- 2 Query: 257 SFLSDQEIQDIVEGMIAKVMKDTKGLEVSLPFPRMAYDDAMNNYGSDKPDTRFDMLLQDL 31- 6 SF+S ++I + E M+AKVM++TKG E+ LP PRM YD+AMN YGSDKPDTRFDMLL D+ Sbjct: 243 SFMSQEDIMSLAEEMMAKVMRETKGEELQLPLPRMTYDEAMNKYGSDKPDTRFDMLLTDV 30- 2 Query: 317 TEIVKEVDFKVFSEA----SVVKAIVVKDKADKYSRKNIDKLTEIAKQYGAKGLAWLKYA 37- 2 ++IVK+ +FKVFS A VVKAI VK A YSRK+ID L A YGAKGLAW+K Sbjct: 303 SDIVKDTEFKVFSSAVANGGVVKAINVKGGAGDYSRKDIDALGAFAANYGAKGLAWVKVE 36- 2 Query: 373 DNTISGPVAKFL-TAIEGRLTEALQLENNDLILFVADSLEVANETLGALRTRIAKELELI 43- 1 + + GP+AKF + +L EAL DL+LF AD EV +LGALR ++ KE LI Sbjct: 363 ADGVKGPIAKFFDEEKQSKLIEALDAAEGDLLLFGADQFEVVAASLGALRLKLGKERGLI 42- 2 Query: 432 DYSKFNFLWVVDWPMFEWSEEEGRYMSAHHPFTLPTAETAHELEGDLAKVRAVAYDIVLN 49- 1 D FNFLWV+DWP+ E EEGR+ +AHHPFT+P E +E ++A AYD+VLN Sbjct: 423 DEKLFNFLWVIDWPLLEHDPEEGRFYAAHHPFTMPVREDLELIETAPEDMKAQAYDLVLN 48- 2 Query: 492 GYELGGGSLRINQKDTQERMFKALGFSAESAQEQFGFLLEAMDYGFPPHGGLAIGLDRFV 55- 1 GYELGGGS+RI +KD QE+MF LGFS E A EQFGFLLEA +YG PPHGG+A+GLDR V Sbjct: 483 GYELGGGSIRIFEKDIQEKMFALLGFSPEEAAEQFGFLLEAFEYGAPPHGGIALGLDRLV 54- 2 Query: 552 MLLAGKDNIREVIAFPKNNKASDPMTQAPSLVSEQQLEELSLTVE 596 MLLAG+ N+R+ IAFPK AS MT+AP VS+ QL+EL L+++ Sbjct: 543 MLLAGRTNLRDTIAFPKTASASCLMTEAPGEVSDAQLDELHLSIK 587 A related DNA sequence was identified in S. pyogenes <SEQ ID 3297> which encodes the amino acid sequence <SEQ ID 3298>. Analysis of this protein sequence reveals the following: TABLE-US-03184 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03185 Identities = 495/582 (85%), Positives = 538/582 (92%) Query: 18 MKRSMYAGRVRSEHIGTSITLKGWVGRRRDLGGLIFIDLRDREGIMQLVINPEEVSASVM 77 - MKRSMYAGRVR EHIGT+ITLKGWV RRRDLGGLIFIDLRDREG+MQLVINPEEVS+ VM Sbjct: 18 MKRSMYAGRVREEHIGTTITLKGWVSRRRDLGGLIFIDLRDREGVMQLVINPEEVSSDVM 77 Query: 78 ATAESLRSEFVIEVSGVVTAREQANDNLPTGEVELKVQELSILNTSKTTPFEIKDGIEAN 137- ATAE LRSE+VIEV G V AR+QAND L TG VELKV L+ILNT+KTTPFEIKD +E + Sbjct: 78 ATAERLRSEYVIEVEGFVEARQQANDKLATGMVELKVSALTILNTAKTTPFEIKDDVEVS 137- Query: 138 DDTRMRYRYLDLRRPEMLENFKLRAKVTHSIRNYLDNLEFIDVETPMLTKSTPEGARDYL 19- 7 DDTR+RYRYLDLRRPEMLENFKLRAKVTHSIRNYLD+LEFIDVETPMLTKSTPEGARDYL Sbjct: 138 DDTRLRYRYLDLRRPEMLENFKLRAKVTHSIRNYLDDLEFIDVETPMLTKSTPEGARDYL 19- 7 Query: 198 VPSRVNQGHFYALPQSPQITKQLLMNAGFDRYYQIVKCFRDEDLRGDRQPEFTQVDLETS 25- 7 VPSRV+QGHFYALPQSPQITKQLLMNAGFDRYYQIVKCFRDEDLRGDRQPEFTQVDLETS Sbjct: 198 VPSRVSQGHFYALPQSPQITKQLLMNAGFDRYYQIVKCFRDEDLRGDRQPEFTQVDLETS 25- 7 Query: 258 FLSDQEIQDIVEGMIAKVMKDTKGLEVSLPFPRMAYDDAMNNYGSDKPDTRFDMLLQDLT 31- 7 FLS+QEIQDIVEGMIAKVMK+TK ++V+LPFPRM+YD AMN+YGSDKPDTRF+MLLQDLT Sbjct: 258 FLSEQEIQDIVEGMIAKVMKETKEIDVTLPFPRMSYDVAMNSYGSDKPDTRFEMLLQDLT 31- 7 Query: 318 EIVKEVDFKVFSEASVVKAIVVKDKADKYSRKNIDKLTEIAKQYGAKGLAWLKYADNTIS 37- 7 VK DFKVFSEA VKAIVVK AD+YSRK+IDKLTE AKQ+GAKGLAW+K D ++ Sbjct: 318 VTVKGNDFKVFSEAPAVKAIVVKGNADRYSRKDIDKLTEFAKQFGAKGLAWVKVTDGQLA 37- 7 Query: 378 GPVAKFLTAIEGRLTEALQLENNDLILFVADSLEVANETLGALRTRIAKELELIDYSKFN 43- 7 GPVAKFLTAIE L+ L+L NDL+LFVAD+LEVAN TLGALR RIAK+L++ID S+FN Sbjct: 378 GPVAKFLTAIETELSSQLKLAENDLVLFVADTLEVANNTLGALRNRIAKDLDMIDQSQFN 43- 7 Query: 438 FLWVVDWPMFEWSEEEGRYMSAHHPFTLPTAETAHELEGDLAKVRAVAYDIVLNGYELGG 49- 7 FLWVVDWPMFEWSEEEGRYMSAHHPFTLPT E+AHELEGDLAKVRA+AYDIVLNGYELGG Sbjct: 438 FLWVVDWPMFEWSEEEGRYMSAHHPFTLPTPESAHELEGDLAKVRAIAYDIVLNGYELGG 49- 7 Query: 498 GSLRINQKDTQERMFKALGFSAESAQEQFGFLLEAMDYGFPPHGGLAIGLDRFVMLLAGK 55- 7 GSLRINQK+ QERMFKALGF+A+ A +QFGFLLEAMDYGFPPHGGLAIGLDRFVMLLAGK Sbjct: 498 GSLRINQKEMQERMFKALGFTADEANDQFGFLLEAMDYGFPPHGGLAIGLDRFVMLLAGK 55- 7 Query: 558 DNIREVIAFPKNNKASDPMTQAPSLVSEQQLEELSLTVESYE 599 DNIREVIAFPKNNKASDPMTQAPSLVSE QLEELSL +ES++ Sbjct: 558 DNIREVIAFPKNNKASDPMTQAPSLVSENQLEELSLQIESHD 599 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1072 A DNA sequence (GBSx1146) was identified in S. agalactiae <SEQ ID 3299> which encodes the amino acid sequence <SEQ ID 3300>. Analysis of this protein sequence reveals the following: TABLE-US-03186 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.44 Transmembrane 186-202 (182-205) INTEGRAL Likelihood = -5.68 Transmembrane 88-104 (86-106) INTEGRAL Likelihood = -3.40 Transmembrane 115-131 (112-132) INTEGRAL Likelihood = -2.13 Transmembrane 141-157 (141-157) INTEGRAL Likelihood = -0.96 Transmembrane 43-59 (43-59) ----- Final Results ----- bacterial membrane --- Certainty = 0.4376(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03187 >GP:CAB12952 GB:Z99109 alternate gene name: yuxA~similar to hypothetical proteins [Bacillus subtilis] Identities = 104/275 (37%), Positives = 181/275 (65%), Gaps = 1/275 (0%) Query: 39 EKISASLLYGILSSVAVNFFFQPGHVYSSGATGLAQVISAVSKHWFSFEIPVALAFYAIN 98 - +K+ ++ +L++ +N F P VY+SG TG+AQ++S+V + F I + +N Sbjct: 7 KKLLIVIIGALLNAAGLNLFLIPADVYASGFTGVAQLLSSVVDQYAPFYISTGTLLFLLN 66 Query: 99 IPLLILSWRKIGHKFTIFTFITVTVSSIFIQLMPQITLTTDPLINAIFGGLIMGAGVGFS 158- IP+ IL W K+G FT+++ ++V ++++F+ ++P+ +L+ D L+NA+FGG+I G+G + Sbjct: 67 IPVGILGWLKVGKSFTVYSILSVALTTLFMGILPETSLSHDILLNAVFGGVISAVGIGLT 126- Query: 159 FKSRISSGGTDIISLTIRKKTGRDVGSISFIINGIILLFAGLLFGWKYALYSMVTIFVSS 21- 8 K S+GG DI+++ + K + VG+ FI+NGII+L AGLL GW+ ALY++VT++V++ Sbjct: 127 LKYGASTGGLDIVAMVLAKWKDKPVGTYFFILNGIIILTAGLLQGWEKALYTLVTLYVTT 18- 6 Query: 219 RVTDAIFTKQKKMQAMIVTSKPYCVIKRIHRDLHRGVTCINDAEGTYNHEKKAVLITILT 27- 8 RV DAI T+ K+ AMIVT K + + I+ + RG+T + A+G + +E+K ++I ++T Sbjct: 187 RVIDAIHTRHMKLTAMIVTKKADEIKEAIYGKMVRGITTV-PAKGAFTNEQKEMMIIVIT 24- 5 Query: 279 REEFSDFKYLMLKADPKAFVSVAENVHIIGRFVDD 313 R E D + ++ + DPKAF ++ + I G F D Sbjct: 246 RYELYDLEKIVKEVDPKAFTNIVQTTGIFGFFRKD 280 A related DNA sequence was identified in S. pyogenes <SEQ ID 3301> which encodes the amino acid sequence <SEQ ID 3302>. Analysis of this protein sequence reveals the following: TABLE-US-03188 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.47 Transmembrane 87-103 (86-106) INTEGRAL Likelihood = -4.94 Transmembrane 185-201 (182-203) INTEGRAL Likelihood = -1.59 Transmembrane 114-130 (113-130) INTEGRAL Likelihood = -1.12 Transmembrane 42-58 (42-58) INTEGRAL Likelihood = -0.32 Transmembrane 140-156 (140-156) ----- Final Results ----- bacterial membrane --- Certainty = 0.3187(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03189 >GP:CAA66894 GB:X98238 orf2 [Lactobacillus sakei] Identities = 105/280 (37%), Positives = 180/280 (63%), Gaps = 7/280 (2%) Query: 37 AEKISASLLYGILSSIAVNFFFQPGHVYSSGATGLAQVFSAL-SHRLLGYDFPIAFAFYL 95 - +++I +++YG L++++VN F P YSSG TG+AQ+ +AL SH LG +A ++ Sbjct: 8 SKRIVIAMVYGFLAAVSVNLFLIPAKTYSSGVTGVAQLLTALVSH--LGGSLSVAALVFI 65 Query: 96 INIPLLILAWYKIGHQFTIFTFITVSMSSFFIQIMPQVT--LTTDPLINAIFGGLVMGMG 153- +N+PLL+LAW+KI HQ+ IF+ + V S F++I+P + T+ A+FGG ++G+G Sbjct: 66 LNVPLLVLAWFKINHQYAIFSIVAVFTSVIFLKIIPVPVQPILTERFAGALFGGALIGLG 125- Query: 154 IGTGLKSRISSGGTDIVSLTLRKRTGKDVGSLSLMVNGAILAFAGILFGWQYALYSMVSI 21- 3 +G ++ S+GGTD++ + + TGK VG+++ ++NG I+ AGI FGW ALYS+V I Sbjct: 126 VGLCFRAGFSTGGTDVIVTLVGRLTGKRVGAVNNVINGMIILAAGIFFGWGAALYSIVEI 18- 5 Query: 214 FVSSRVTDAIFTKQKKMQATIVTSHPERVIHMIHKRLHRGVTSINDAEGTYKHEQKAVLI 27- 3 FVSS + D I+T+Q+K+ TI T PE + + + +H G T + D G Y +++ +V++ Sbjct: 186 FVSSLLMDYIYTQQQKVTVTIFTKQPEALKKRMREFIH-GATEL-DGTGLYTNQETSVIM 24- 3 Query: 274 TILTCEEYPEFKWLMLKTDPQAFVSVAENVRIIGRFVEDD 313 T+++ + K ++ DP AFV++ + +GRF ++ Sbjct: 244 TVVSKYDLTALKLVVQDADPNAFVNIQSTMNLWGRFESNE 283 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03190 Identities = 239/311 (76%), Positives = 274/311 (87%) Query: 4 RRTPLEKKVKYIISVWAKKFGLLHTLKSISREKYAEKISASLLYGILSSVAVNFFFQPGH 63 ++T +KKVKY+IS AKK GLLH L+SISREKYAEKISASLLYGILSS+AVNFFFQPGH Sbjct: 3 KKTTYKKKVKYVISRGAKKVGLLHALRSISREKYAEKISASLLYGILSSIAVNFFFQPGH 62 Query: 64 VYSSGATGLAQVISAVSKHWFSFEIPVALAFYAINIPLLILSWRKIGHKFTIFTFITVTV 123- VYSSGATGLAQV SA+S ++ P+A AFY INIPLLIL+W KIGH+FTIFTFITV++ Sbjct: 63 VYSSGATGLAQVFSALSHRLLGYDFPIAFAFYLINIPLLILAWYKIGHQFTIFTFITVSM 122- Query: 124 SSIFIQLMPQITLTTDPLINAIFGGLIMGAGVGFSFKSRISSGGTDIISLTIRKKTGRDV 18- 3 SS FIQ+MPQ+TLTTDPLINAIFGGL+MG G+G KSRISSGGTDI+SLT+RK+TG+DV Sbjct: 123 SSFFIQIMPQVTLTTDPLINAIFGGLVMGMGIGTGLKSRISSGGTDIVSLTLRKRTGKDV 18- 2 Query: 184 GSISFIINGIILLFAGLLFGWKYALYSMVTIFVSSRVTDAIFTKQKKMQAMIVTSKPYCV 24- 3 GS+S ++NG IL FAG+LFGW+YALYSMV+IFVSSRVTDAIFTKQKKMQA IVTS P V Sbjct: 183 GSLSLMVNGAILAFAGILFGWQYALYSMVSIFVSSRVTDAIFTKQKKMQATIVTSHPERV 24- 2 Query: 244 IKRIHRDLHRGVTCINDAEGTYNHEKKAVLITILTREEFSDFKYLMLKADPKAFVSVAEN 30- 3 I IH+ LHRGVT INDAEGTY HE+KAVLITILT EE+ +FK+LMLK DP+AFVSVAEN Sbjct: 243 IHMIHKRLHRGVTSINDAEGTYKHEQKAVLITILTCEEYPEFKWLMLKTDPQAFVSVAEN 30- 2 Query: 304 VHIIGRFVDDD 314 V IIGRFV+DD Sbjct: 303 VRIIGRFVEDD 313 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1073 A DNA sequence (GBSx1147) was identified in S. agalactiae <SEQ ID 3303> which encodes the amino acid sequence <SEQ ID 3304>. Analysis of this protein sequence reveals the following: TABLE-US-03191 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -3.72 Transmembrane 156-172 (156-174) INTEGRAL Likelihood = -3.03 Transmembrane 112-128 (110-129) INTEGRAL Likelihood = -2.34 Transmembrane 80-96 (79-96) INTEGRAL Likelihood = -1.49 Transmembrane 60-76 (58-76) ----- Final Results ----- bacterial membrane --- Certainty = 0.2487(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03192 >GP:BAB05397 GB:AP001512 unknown conserved protein [Bacillus halodurans] Identities = 113/278 (40%), Positives = 192/278 (68%), Gaps = 1/278 (0%) Query: 7 KTKIKETILIAFGVALYTFGFVKFNMANHLAEGGISGVTLIIHALFGVNPALSSLLLNIP 66 + K K + I G A+++FG V FNM N+LAEGG +G+TLI++ +F +NPA+++L+LNIP Sbjct: 4 RLKWKNIVFILLGSAIFSFGLVYFNMENNLAEGGFTGITLILYFMFQINPAVTNLVLNIP 63 Query: 67 LFILGARILGKKSLLLTIYGTVLMSFFMWFWQQIP-VTVPLKNDMMLVAVAAGILAGTGS 125- + ++G +ILG+ +L+ TI GTV +S F+ +Q+ + +PL +DM L A+ AG+ GTG Sbjct: 64 ILLIGWKILGRVTLIYTIIGTVSVSVFLEMFQRWKFMDIPLHDDMTLAALFAGVFVGTGL 123- Query: 126 GLVFRYGATTGGADIIGRIVEEKSGIKLGQTLLFIDAIVLTSSLVYINLQQMLYTLVASF 18- 5 G+VFR+G TTGG DII ++ G +G+T+ DA+V+ SSL+Y+N ++ +YTL+A F Sbjct: 124 GIVFRFGGTTGGVDIIAKLGFRYLGWSMGKTMFMFDAVVIASSLIYLNYREAMYTLLAVF 18- 3 Query: 186 VFSQVLTNVENGGYTVRGMIIITKESESAAATILHEINRGVTFLRGQGAYSGREHDVLYV 24- 5 + ++V+ ++ Y+ + II++ +E+ A TIL E+ RG T L+G+G+++G E ++LY Sbjct: 184 IAAKVIDFIQQTAYSAKAAFIISEHTEAIADTILKEMERGATTLKGKGSFTGTEKEILYC 24- 3 Query: 246 ALNPSEVRDVKEIMADLDPDAFISVINVDEVISSDFKI 283 + +E+ +K ++ +DP AF++V +V +VI F + Sbjct: 244 VVGRNELIRLKSLVERIDPHAFVTVNDVQDVIGEGFTL 281 A related DNA sequence was identified in S. pyogenes <SEQ ID 3305> which encodes the amino acid sequence <SEQ ID 3306>. Analysis of this protein sequence reveals the following: TABLE-US-03193 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.15 Transmembrane 112-128 (109-130) INTEGRAL Likelihood = -2.34 Transmembrane 156-172 (156-174) INTEGRAL Likelihood = -1.81 Transmembrane 178-194 (177-194) INTEGRAL Likelihood = -1.65 Transmembrane 80-96 (79-96) INTEGRAL Likelihood = -0.37 Transmembrane 60-76 (59-76) ----- Final Results ----- bacterial membrane --- Certainty = 0.3060(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03194 >GP:BAB05397 GB:AP001512 unknown conserved protein [Bacillus halodurans] Identities = 116/276 (42%), Positives = 182/276 (65%), Gaps = 1/276 (0%) Query: 9 KLLKLFLIALGVAIYTFGFVNFNMANALAEGGVAGITLILHAHFGINPAYSSLLFNLPLF 68 K + I LG AI++FG V FNM N LAEGG GITLIL+ F INPA ++L+ N+P+ Sbjct: 6 KWKNIVFILLGSAIFSFGLVYFNMENNLAEGGFTGITLILYFMFQINPAVTNLVLNIPIL 65 Query: 69 ILGAKIFGKRSLALTIYGTVLMSAFIWMWQKVP-IELGLENDMMLVAVVAGLFSGIGSGI 127- ++G KI G+ +L TI GTV +S F+ M+Q+ +++ L +DM L A+ AG+F G G GI Sbjct: 66 LIGWKILGRVTLIYTIIGTVSVSVFLEMFQRWKFMDIPLHDDMTLAALFAGVFVGTGLGI 125- Query: 128 VFRYGATTGGTDIIGRIAEEKFGAKLGQTLLLVDALVLTASLTYVDLKHMLYTLVASFVF 18- 7 VFR+G TTGG DII ++ G +G+T+ + DA+V+ +SL Y++ + +YTL+A F+ Sbjct: 126 VFRFGGTTGGVDIIAKLGFRYLGWSMGKTMFMFDAVVIASSLIYLNYREAMYTLLAVFIA 18- 5 Query: 188 SQMISVVQNGGYTIRGMIIITKHSEAAAQAILTEINRGVTYLKGQGAYSGNDYNIMYVTL 24- 7 +++I +Q Y+ + II++H+EA A IL E+ RG T LKG+G+++G + I+Y + Sbjct: 186 AKVIDFIQQTAYSAKAAFIISEHTEAIADTILKEMERGATTLKGKGSFTGTEKEILYCVV 24- 5 Query: 248 NPTEVREVKRILAGLDPDAFISIIDVDEVISSDFKI 283 E+ +K ++ +DP AF+++ DV +VI F + Sbjct: 246 GRNELIRLKSLVERIDPHAFVTVNDVQDVIGEGFTL 281 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03195 Identities = 206/286 (72%), Positives = 250/286 (87%) Query: 5 DLKTKIKETILIAFGVALYTFGFVKFNMANHLAEGGISGVTLIIHALFGVNPALSSLLLN 64 D TK+ + LIA GVA+YTFGFV FNMAN LAEGG++G+TLI+HA FG+NPA SSLL N Sbjct: 5 DKLTKLLKLFLIALGVAIYTFGFVNFNMANALAEGGVAGITLILHAHFGINPAYSSLLFN 64 Query: 65 IPLFILGARILGKKSLLLTIYGTVLMSFFMWFWQQIPVTVPLKNDMMLVAVAAGILAGTG 124- +PLFILGA+I GK+SL LTIYGTVLMS F+W WQ++P+ + L+NDMMLVAV AG+ +G G Sbjct: 65 LPLFILGAKIFGKRSLALTIYGTVLMSAFIWMWQKVPIELGLENDMMLVAVVAGLFSGIG 124- Query: 125 SGLVFRYGATTGGADIIGRIVEEKSGIKLGQTLLFIDAIVLTSSLVYINLQQMLYTLVAS 18- 4 SG+VFRYGATTGG DIIGRI EEK G KLGQTLL +DA+VLT+SL Y++L+ MLYTLVAS Sbjct: 125 SGIVFRYGATTGGTDIIGRIAEEKFGAKLGQTLLLVDALVLTASLTYVDLKHMLYTLVAS 18- 4 Query: 185 FVFSQVLTNVENGGYTVRGMIIITKESESAAATILHEINRGVTFLRGQGAYSGREHDVLY 24- 4 FVFSQ+++ V+NGGYT+RGMIIITK SE+AA IL EINRGVT+L+GQGAYSG +++++Y Sbjct: 185 FVFSQMISVVQNGGYTIRGMIIITKHSEAAAQAILTEINRGVTYLKGQGAYSGNDYNIMY 24- 4 Query: 245 VALNPSEVRDVKEIMADLDPDAFISVINVDEVISSDFKIRRRNYDK 290 V LNP+EVR+VK I+A LDPDAFIS+I+VDEVISSDFKIRRRNYDK Sbjct: 245 VTLNPTEVREVKRILAGLDPDAFISIIDVDEVISSDFKIRRRNYDK 290 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1074 A DNA sequence (GBSx1148) was identified in S. agalactiae <SEQ ID 3307> which encodes the amino acid sequence <SEQ ID 3308>. This protein is predicted to be BacB protein. Analysis of this protein sequence reveals the following: TABLE-US-03196 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4355(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03197 >GP:BAA11330 GB:D78257 BacB [Enterococcus faecalis] Identities = 27/88 (30%), Positives = 48/88 (53%), Gaps = 1/88 (1%) Query: 1 MPSEKEILDALSKVYSEEVIQADDYFRQAIFELASQLEKEGMN-SLLATKIDSLINQYVL 59 M ++E+LD LSK Y++ I + + +FE A +L N + K+ ++ ++Y+ Sbjct: 1 MDKQQELLDLLSKAYNDPKINEYEGLKDKLFECAKRLTTNETNIGEVCYKLSTINSEYLA 60 Query: 60 THQFDAPKSIFDLSRLVKTKASHYKGTA 87 H F+ PKSI +L + V + Y+G A Sbjct: 61 RHHFEMPKSIIELQKFVTKEGQKYRGWA 88 A related DNA sequence was identified in S. pyogenes <SEQ ID 3309> which encodes the amino acid sequence <SEQ ID 3310>. Analysis of this protein sequence reveals the following: TABLE-US-03198 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2712(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03199 Identities = 99/102 (97%), Positives = 102/102 (99%) Query: 1 MPSEKEILDALSKVYSEEVIQADDYFRQAIFELASQLEKEGMNSLLATKIDSLINQYVLT 60 MPSEKEILDALSKVYSE+VIQADDYFRQAIFELASQLEKEGM+SLLATKIDSLINQY+LT Sbjct: 7 MPSEKEILDALSKVYSEQVIQADDYFRQAIFELASQLEKEGMSSLLATKIDSLINQYILT 66 Query: 61 HQFDAPKSIFDLSRLVKTKASHYKGTAISAIMLGSFLSGGPK 102 HQFDAPKSIFDLSRLVKTKASHYKGTAISAIMLGSFLSGGPK Sbjct: 67 HQFDAPKSIFDLSRLVKTKASHYKGTAISAIMLGSFLSGGPK 108 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1075 A DNA sequence (GBSx1149) was identified in S. agalactiae <SEQ ID 3311> which encodes the amino acid sequence <SEQ ID 3312>. This protein is predicted to be ArgS (argS). Analysis of this protein sequence reveals the following: TABLE-US-03200 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2522(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10271> which encodes amino acid sequence <SEQ ID 10272> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03201 >GP:AAF86984 GB:AF282249 ArgS [Lactococcus lactis subsp. lactis] Identities = 377/566 (66%), Positives = 464/566 (81%), Gaps = 5/566 (0%) Query: 12 MDTKHLIASEIQKVVPD-MEQSTILSLLETPKNSSMGDLAFPAFSLAKTLRKAPQIIASD 70 - MD K L++ + + + I +++E PK+S +GDLAFPAF LAKTLRK+PQIIA + Sbjct: 1 MDEKQLVSQALSAAIDGVLGVEQIAAIIEKPKSSDLGDLAFPAFQLAKTLRKSPQIIAGE 60 Query: 71 IAEQIKSDQFEKVEAVGPYVNFFLDKAAISSQVLKQVLSDGSAYATQNIGEGRNVAIDMS 130- IAE+I + FEKV AVGPYVNFFLDK A +S+V+++VL++G Y NIGEG NV IDMS Sbjct: 61 IAEKIDTKGFEKVIAVGPYVNFFLDKNATASEVIREVLAEGEHYGDANIGEGGNVPIDMS 120- Query: 131 SPNIAKPFSIGHLRSTVIGDSLANIFDKIGYHPVKINHLGDWGKQFGMLIVAYKKWGNEE 19- 0 +PNIAKPFSIGHLRSTVIGDS+A I++K+GY P+KINHLGDWGKQFG+LI AYKK+G+E Sbjct: 121 APNIAKPFSIGHLRSTVIGDSIAKIYEKLGYQPIKINHLGDWGKQFGLLITAYKKYGDEA 18- 0 Query: 191 AVRAHPIDELLKLYVRINAEAETDPSVDEEAREWFRKLEANDPEATELWQWFRDESLLEF 25- 0 + A+PIDELLKLYV+INAEA+ D VDEE R+WF K+E D EA +W+WF D SL+EF Sbjct: 181 TITANPIDELLKLYVKINAEAKEDSEVDEEGRQWFLKMEQGDEEALRIWKWFSDVSLIEF 24- 0 Query: 251 NRLYDQMNVTFDSYNGEAFYNDKMDEVLELLESKNLLVESKGAQVVNLEKYGIEHPALIK 31- 0 NR+Y ++ VTFD + GE+FY+DKMD ++E LE+KNLL ESKGA +V+LEKY + +PALIK Sbjct: 241 NRIYGKLGVTFDHFMGESFYSDKMDAIVEDLENKNLLHESKGALIVDLEKYNL-NPALIK 29- 9 Query: 311 KSDGATLYITRDLAAALYRKRTYDFAKSIYVVGNEQSAHFKQLKAVLKEMDYDWSDDMTH 37- 0 K+DGATLYITRDLA A YRK+T++F KS+YVVG EQ+ HFKQLKAVLKE YDWSDDM H Sbjct: 300 KTDGATLYITRDLATAAYRKKTFNFVKSLYVVGGEQTNHFKQLKAVLKEAGYDWSDDMVH 35- 9 Query: 371 VPFGLVTKGGAKLSTRKGNVILLEPTVAEAINRAASQIEAKNPNLADKDKVAQAVGVGAI 43- 0 VPFG+VT+GG K STRKG+V+ LE + EA++RA QIEAKNPNL +K++VA+ VGVGA+ Sbjct: 360 VPFGMVTQGGKKFSTRKGHVVKLEMALDEAVDRAEKQIEAKNPNLENKEEVAKQVGVGAV 41- 9 Query: 431 KFYDLKTDRTNGYDFDLEAMVSFEGETGPYVQYAHARIQSILRKANFSPSNSDNYSL--N 48- 8 KFYDLKTDR NGYDFDL+ MVSFEGETGPYVQYAHARIQSILRKAN N DN SL + Sbjct: 420 KFYDLKTDRNNGYDFDLDEMVSFEGETGPYVQYAHARIQSILRKAN-RKVNIDNISLVVS 47- 8 Query: 489 DVESWEIIKLIQDFPRIIVRAADNFEPSIIAKFAINLAQCFNKYYAHTRILDEDAEISSR 54- 8 D E+WEI+K +++FP I+ RAADN+EPSIIAK+AI+LAQ FNKYYAH RIL++DA++ R Sbjct: 479 DAEAWEIVKALKEFPNIVKRAADNYEPSIIAKYAISLAQAFNKYYAHVRILEDDAQLDGR 53- 8 Query: 549 LALCYATATVLKESLRLLGVDAPNEM 574 LAL AT+ VLKE+LRLLGV AP M Sbjct: 539 LALISATSIVLKEALRLLGVAAPENM 564 A related DNA sequence was identified in S. pyogenes <SEQ ID 3313> which encodes the amino acid sequence <SEQ ID 3314>. Analysis of this protein sequence reveals the following: TABLE-US-03202 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1734(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03203 Identities = 492/563 (87%), Positives = 526/563 (93%) Query: 12 MDTKHLIASEIQKVVPDMEQSTILSLLETPKNSSMGDLAFPAFSLAKTLRKAPQIIASDI 71 - MDTK LIASEI KVVP++EQ I +LLETPKNS MGDLAFPAFSLAK LRKAPQ+IAS++ Sbjct: 1 MDTKTLIASEIAKVVPELEQDAIFNLLETPKNSDMGDLAFPAFSLAKVLRKAPQMIASEL 60 Query: 72 AEQIKSDQFEKVEAVGPYVNFFLDKAAISSQVLKQVLSDGSAYATQNIGEGRNVAIDMSS 131- AEQI QFEKV AVGPY+NFFLDKA ISSQVL+QV++ GS YA Q+ G+GRNVAIDMSS Sbjct: 61 AEQIDESQFEKVVAVGPYINFFLDKAKISSQVLEQVITAGSDYAQQDEGQGRNVAIDMSS 120- Query: 132 PNIAKPFSIGHLRSTVIGDSLANIFDKIGYHPVKINHLGDWGKQFGMLIVAYKKWGNEEA 19- 1 PNIAKPFSIGHLRSTVIGDSLA+IF K+GY PVKINHLGDWGKQFGMLIVAYKKWG+E A Sbjct: 121 PNIAKPFSIGHLRSTVIGDSLAHIFAKMGYKPVKINHLGDWGKQFGMLIVAYKKWGDEAA 18- 0 Query: 192 VRAHPIDELLKLYVRINAEAETDPSVDEEAREWFRKLEANDPEATELWQWFRDESLLEFN 25- 1 V+AHPIDELLELYVERINAEAETDP+VDEEAREWFRKLE D EATELWQWFRDESLLEFN Sbjct: 181 VQAHPIDELLKLYVRINAEAETDPTVDEEAREWFRKLEDGDKEATELWQWFRDESLLEFN 24- 0 Query: 252 RLYDQMNVTFDSYNGEAFYNDKMDEVLELLESKNLLVESKGAQVVNLEKYGIEHPALIKK 31- 1 RLYDQ++VTFDSYNGEAFYNDKMDEVL+LLE+KNLLVESKGAQVVNLEKYGIEHPALIKK Sbjct: 241 RLYDQLHVTFDSYNGEAFYNDKMDEVLDLLEAKNLLVESKGAQVVNLEKYGIEHPALIKK 30- 0 Query: 312 SDGATLYITRDLAAALYRKRTYDFAKSIYVVGNEQSAHFKQLKAVLKEMDYDWSDDMTHV 37- 1 SDGATLYITRDLAAALYRKRTYDFAKS+YVVGNEQ+AHFKQLKAVLKEM YDWSDDMTHV Sbjct: 301 SDGATLYITRDLAAALYRKRTYDFAKSVYVVGNEQAAHFKQLKAVLKEMGYDWSDDMTHV 36- 0 Query: 372 PFGLVTKGGAKLSTRKGNVILLEPTVAEAINRAASQIEAKNPNLADKDKVAQAVGVGAIK 43- 1 FGLVTKGGAKLSTRKGNVILLEPTVAEAINRAASQIEAKNPNLADK+ VA AVGVGAIK Sbjct: 361 AFGLVTKGGAKLSTRKGNVILLEPTVAEAINRAASQIEAKNPNLADKEAVAHAVGVGAIK 42- 0 Query: 432 FYDLKTDRTNGYDFDLEAMVSFEGETGPYVQYAHARIQSILRKANFSPSNSDNYSLNDVE 49- 1 FYDLKTDR NGYDFDLEAMVSFEGETGPYVQYAHARIQSILRKA+F+PS + YSL D E Sbjct: 421 FYDLKTDRMNGYDFDLEAMVSFEGETGPYVQYAHARIQSILRKADFTPSATTTYSLADAE 48- 0 Query: 492 SWEIIKLIQDFPRIIVRAADNFEPSIIAKFAINLAQCFNKYYAHTRILDEDAEISSRLAL 55- 1 SWEIIKLIQDFPRII R +DNFEPSI+AKFAINLAQ FNKYYAHTRILD+++E +RLAL Sbjct: 481 SWEIIKLIQDFPRIIKRTSDNFEPSIMAKFAINLAQSFNKYYAHTRILDDNSERDNRLAL 54- 0 Query: 552 CYATATVLKESLRLLGVDAPNEM 574 CYATATVLKE+LRLLGVDAPNEM Sbjct: 541 CYATATVLKEALRLLGVDAPNEM 563 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1076 A DNA sequence (GBSx1150) was identified in S. agalactiae <SEQ ID 3315> which encodes the amino acid sequence <SEQ ID 3316>. This protein is predicted to be arginine hydroximate resistance protein (argR). Analysis of this protein sequence reveals the following: TABLE-US-03204 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3252(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10269> which encodes amino acid sequence <SEQ ID 10270> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03205 >GP: AAA88596 GB: M18729 unknown protein [Streptococcus pneumoniae] Identities = 63/141 (44%), Positives = 90/141 (63%) Query: 4 MNKIERQKRIKRLIQSGQIGTQEEIKLHLKNEGIDVTQATLSRDLREIGLLKLRSPEGKL 63 M K +R + IK++I ++ TQ+EI+ L+ + VTQ TLSRDLREIGL K++ + Sbjct: 1 MRKRDRHQLIKKMITEEKLSTQKEIQDRLEAHNVCVTQTTLSRDLREIGLTKVKKNDMVY 60 Query: 64 YYSLSTATSNRFSPALRSYILKVSRASFMLVLNTNLGEASVLANFIDEKGLPEILGTMAG 123- Y ++ L ++ V+RA F LVL+T LGEASVLAN +D ILGT+AG Sbjct: 61 YVLVNETEKIDLVEFLSHHLEGVARAEFTLVLHTKLGEASVLANIVDVNKDEWILGTVAG 120- Query: 124 ADTLLVICQNEDIAKVFEKEL 144 A+TLLVIC+++ +AK+ E L Sbjct: 121 ANTLLVICRDQHVAKLMEDRL 141 A related DNA sequence was identified in S. pyogenes <SEQ ID 3317> which encodes the amino acid sequence <SEQ ID 3318>. Analysis of this protein sequence reveals the following: TABLE-US-03206 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3176(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03207 Identities = 101/145 (69%), Positives = 121/145 (82%) Query: 4 MNKIERQKRIKRLIQSGQIGTQEEIKLHLKNEGIDVTQATLSRDLREIGLLKLRSPEGKL 63 MNK+ERQ++IKR+IQ+ IGTQE+IK HL+ EGI VTQATLSRDLREIGLLKLR +GKL Sbjct: 1 MNKMERQQQIKRIIQAEHIGTQEDIKNHLQKEGIVVTQATLSRDLREIGLLKLRDEQGKL 60 Query: 64 YYSLSTATSNRFSPALRSYILKVSRASFMLVLNTNLGEASVLANFIDEKGLPEILGTMAG 123- YYSLS + FSP +R Y+LKV RA FMLVL+TNLGEA VLAN ID + +ILGT+AG Sbjct: 61 YYSLSEPVATPFSPEVRFYVLKVDRAGFMLVLHTNLGEADVLANLIDNDAIEDILGTIAG 120- Query: 124 ADTLLVICQNEDIAKVFEKELSVGL 148 ADTLLVIC++E+IAK FEK+L+ GL Sbjct: 121 ADTLLVICRDEEIAKRFEKDLAAGL 145 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1077 A DNA sequence (GBSx1151) was identified in S. agalactiae <SEQ ID 3319> which encodes the amino acid sequence <SEQ ID 3320>. This protein is predicted to be DNA mismatch repair protein hexa (mutS). Analysis of this protein sequence reveals the following: TABLE-US-03208 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3570(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03209 >GP: AAA88597 GB: M18729 mismatch repair protein [Streptococcus pneumoniae] Identities = 593/858 (69%), Positives = 698/858 (81%), Gaps = 14/858 (1%) Query: 1 MAKPTISPGMQQYLDIKENYPDAFLLFRMGDFYELFYDDAVKAAQILEISLTSRNKNAEK 60 MA +SPGMQQY+DIK+ YPDAFLLFRMGDFYELFY+DAV AAQILEISLTSRNKNA+ Sbjct: 1 MAIEKLSPGMQQYVDIKKQYPDAFLLFRMGDFYELFYEDAVNAAQILEISLTSRNKNADN 60 Query: 61 PIPMAGVPYHSAQQYIDVLVELGYKVAIAEQMEDPKKAVGVVKREVVQVVTPGTVVESTK 120- PIPMAGVPYHSAQQYIDVL+E GYKVAIAEQMEDPK+AVGVVKREVVQV+TPGTVV+S+K Sbjct: 61 PIPMAGVPYHSAQQYIDVLIEQGYKVAIAEQMEDPKQAVGVVKREVVQVITPGTVVDSSK 120- Query: 121 PDSANNFLVAIDSQDQQTFGLAYMDVSTGEFQATLLTDFESVRSEILNLKAREIVVGYQL 18- 0 PDS NNFLV+ID + Q FGLAYMD+ TG+F T L DF V EI NLKARE+V+GY L Sbjct: 121 PDSQNNFLVSIDREGNQ-FGLAYMDLVTGDFYVTGLLDFTLVCGEIRNLKAREVVLGYDL 17- 9 Query: 181 TDEKNHLLTKQMNLLLSYEDERLNDIHLIDEQLTDLEISAAEKLLQYVHRTQKRELSHLQ 24- 0 ++E+ +L++QMNL+LSYE E D+HL+D +L +E +A+ KLLQYVHRTQ REL+HL+ Sbjct: 180 SEEEEQILSRQMNLVLSYEKESFEDLHLLDLRLATVEQTASSKLLQYVHRTQMRELNHLK 23- 9 Query: 241 KVVHYEIKDYLQMSYATKNSLDLLENARTSKKHGSLYWLLDETKTAMGTRMLRTWIDRPL 30- 0 V+ YEIKD+LQM YATK SLDL+ENAR+ KK GSL+WLLDETKTAMG R+LR+WI RPL Sbjct: 240 PVIRYEIKDFLQMDYATKASLDLVENARSGKKQGSLFWLLDETKTAMGMRLLRSWIHRPL 29- 9 Query: 301 VSMNRIKERQDIIQVFLDYFFERNDLTESLKGVYDIERLASRVSFGKANPKDLLQLGQTL 36- 0 + RI +RQ+++QVFLD+FFER+DLT+SLKGVYDIERLASRVSFGK NPKDLLQL TL Sbjct: 300 IDKERIVQRQEVVQVFLDHFFERSDLTDSLKGVYDIERLASRVSFGKTNPKDLLQLATTL 35- 9 Query: 361 SQIPRIKMILQSFNQPELDIIVNKIDTMPELESLINTAIAPEAQATITEGNIIKSGFDKQ 42- 0 S +PRI+ IL+ QP L ++ ++D +PELESLI+ AIAPEA IT+G II++GFD+ Sbjct: 360 SSVPRIRAILEGMEQPTLAYLIAQLDAIPELESLISAAIAPEAPHVITDGGIIRTGFDET 41- 9 Query: 421 LDNYRTVMREGTGWIADIEAKERAASGIGTLKIDYNKKDGYYFHVTNSNLSLVPEHFFRK 48- 0 LD YR V+REGT WIA+IEAKER SGI TLKIDYNKKDGYYFHVTNS L VP HFFRK Sbjct: 420 LDKYRCVLREGTSWIAEIEAKERENSGISTLKIDYNKKDGYYFHVTNSQLGNVPAHFFRK 47- 9 Query: 481 ATLKNSERYGTAELAKIEGEMLEAREQSSNLEYDIFMRVRAQVESYIKRLQELAKTIATV 54- 0 ATLKNSER+GT ELA+IEG+MLEARE+S+NLEY+IFMR+R +V YI+RLQ LA+ IATV Sbjct: 480 ATLKNSERFGTEELARIEGDMLEAREKSANLEYEIFMRIREEVGKYIQRLQALAQGIATV 53- 9 Query: 541 DVLQSLAVVAENYHYVRPKFNDQHQIKIKNGRHATVEKVMGVQEYIPNSIYFDSQTDIQL 60- 0 DVLQSLAVVAE H +RP+F D QI I+ GRHA VEKVMG Q YIPN+I T IQL Sbjct: 540 DVLQSLAVVAETQHLIRPEFGDDSQIDIRKGRHAVVEKVMGAQTYIPNTIQMAEDTSIQL 59- 9 Query: 601 ITGPNMSGKSTYMRQLALTVIMAQMGGFVSADEVDLPVFDAIFTRIGAADDLISGQSTFM 66- 0 +TGPNMSGKSTYMRQLA+T +MAQ+G +V A+ LP+FDAIFTRIGAADDL+SGQSTFM Sbjct: 600 VTGPNMSGKSTYMRQLAMTAVMAQLGSYVPAESAHLPIFDAIFTRIGAADDLVSGQSTFM 65- 9 Query: 661 VEMMEANQAVKRASDKSLILFDELGRGTATYDGMALAQSIIEYIHDRVRAKTMFATHYHE 72- 0 VEMMEAN A+ A+ SLILFDELGRGTATYDGMALAQSIIEYIH+ + + AKT+FATHYHE Sbjct: 660 VEMMEANNAISHATKNSLILFDELGRGTATYDGMALAQSIIEYIHEHIGAKTLFATHYHE 71- 9 Query: 721 LTDLSEQLTRLVNVHVATLERDGEVTFLHKIESGPADKSYGIHVAKIAGLPIDLLDRATD 78- 0 LT L L LVNVHVATLE+DG+VTFLHKIE GPADKSYGIHVAKIAGLP DLL RA Sbjct: 720 LTSLESSLQHLVNVHVATLEQDGQVTFLHKIEPGPADKSYGIHVAKIAGLPADLLARADK 77- 9 Query: 781 ILSQLEADAVQLIVSPSQEAVTADLNEELDSEKQQGQLSLFEEPSNAGRVIEELEAIDIM 84- 0 IL+QLE + SP T+ + E Q+SLF+ + ++ EL +D+ Sbjct: 780 ILTQLENQGTE---SPPPMRQTSAVTE---------QISLFDR-AEEHPILAELAKLDVY 82- 6 Query: 841 NLTPMQAMNAIFDLKKLL 858 N+TPMQ MN + +LK+ L Sbjct: 827 NMTPMQVMNVLVELKQKL 844 A related DNA sequence was identified in S. pyogenes <SEQ ID 3321> which encodes the amino acid sequence <SEQ ID 3322>. Analysis of this protein sequence reveals the following: TABLE-US-03210 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 532-548 (532-549) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03211 Identities = 661/858 (77%), Positives = 746/858 (86%), Gaps = 7/858 (0%) Query: 1 MAKPTISPGMQQYLDIKENYPDAFLLFRMGDFYELFYDDAVKAAQILEISLTSRNKNAEK 60 MAK ISPGMQQYLDIK++YPDAFLLFRMGDFYELFY+DAVKAAQ+LEI LTSRNKNAE Sbjct: 1 MAKTNISPGMQQYLDIKKDYPDAFLLFRMGDFYELFYEDAVKAAQLLEIGLTSRNKNAEN 60 Query: 61 PIPMAGVPYHSAQQYIDVLVELGYKVAIAEQMEDPKKAVGVVKREVVQVVTPGTVVESTK 120- PIPMAGVP+HSAQQYIDVL+ELGYKVA+AEQMEDPK+AVGVVKREVVQV+TPGTVV+S K Sbjct: 61 PIPMAGVPHHSAQQYIDVLIELGYKVAVAEQMEDPKQAVGVVKREVVQVITPGTVVDSAK 120- Query: 121 PDSANNFLVAIDSQDQQTFGLAYMDVSTGEFQATLLTDFESVRSEILNLKAREIVVGYQL 18- 0 PDSANNFLVA+D D +GLAYMDVSTGEF T L DF SVRSEI NLKA+E+++G+ L Sbjct: 121 PDSANNFLVAVDF-DGCRYGLAYMDVSTGEFCVTDLADFTSVRSEIQNLKAKEVLLGFDL 17- 9 Query: 181 TDEKNHLLTKQMNLLLSYEDERLNDIHLIDEQLTDLEISAAEKLLQYVHRTQKRELSHLQ 24- 0 ++E+ +L KQMNLLLSYE+ D LID QLT +E++AA KLLQYVH+TQ RELSHLQ Sbjct: 180 SEEEQTILVKQMNLLLSYEETVYEDKSLIDGQLTTVELTAAGKLLQYVHKTQMRELSHLQ 23- 9 Query: 241 KVVHYEIKDYLQMSYATKNSLDLLENARTSKKHGSLYWLLDETKTAMGTRMLRTWIDRPL 30- 0 +VHYEIKDYLQMSYATK+SLDL+ENART+KKHGSLYWLLDETKTAMG R+LR+WIDRPL Sbjct: 240 ALVHYEIKDYLQMSYATKSSLDLVENARTNKKHGSLYWLLDETKTAMGMRLLRSWIDRPL 29- 9 Query: 301 VSMNRIKERQDIIQVFLDYFFERNDLTESLKGVYDIERLASRVSFGKANPKDLLQLGQTL 36- 0 VS I ERQ+IIQVFL+ F ER DL+ SLKGVYDIERL+SRVSFGKANPKDLLQLG TL Sbjct: 300 VSKEAILERQEIIQVFLNAFIERTDLSNSLKGVYDIERLSSRVSFGKANPKDLLQLGHTL 35- 9 Query: 361 SQIPRIKMILQSFNQPELDIIVNKIDTMPELESLINTAIAPEAQATITEGNIIKSGFDKQ 42- 0 +Q+P IK IL+SF+ P +D +VN ID++PELE LI TAI P+A ATI+EG+II++GFD++ Sbjct: 360 AQVPYIKAILESFDSPCVDKLVNDIDSLPELEYLIRTAIDPDAPATISEGSIIRNGFDER 41- 9 Query: 421 LDNYRTVMREGTGWIADIEAKERAASGIGTLKIDYNKKDGYYFHVTNSNLSLVPEHFFRK 48- 0 LD+YR VMREGTGWIADIEAKER ASGI LKIDYNKKDGYYFHVTNSNLSLVPEHFFRK Sbjct: 420 LDHYRKVMREGTGWIADIEAKERQASGINNLKIDYNKKDGYYFHVTNSNLSLVPEHFFRK 47- 9 Query: 481 ATLKNSERYGTAELAKIEGEMLEAREQSSNLEYDIFMRVRAQVESYIKRLQELAKTIATV 54- 0 ATLKNSERYGTAELAKIEG+MLEARE+SS+LEYDIFM +RAQVE+YI RLQ+LAK +ATV Sbjct: 480 ATLKNSERYGTAELAKIEGQMLEAREESSSLEYDIFMCIRAQVETYINRLQKLAKILATV 53- 9 Query: 541 DVLQSLAVVAENYHYVRPKFNDQHQIKIKNGRHATVEKVMGVQEYIPNSIYFDSQTDIQL 60- 0 DVLQSLAVVAE HY+RP+FND H I I+ GRHA VEKVMGVQEYIPNSI FD QT IQL Sbjct: 540 DVLQSLAVVAETNHYIRPQFNDNHVITIQEGRHAVVEKVMGVQEYIPNSISFDQQTSIQL 59- 9 Query: 601 ITGPNMSGKSTYMRQLALTVIMAQMGGFVSADEVDLPVFDAIFTRIGAADDLISGQSTFM 66- 0 ITGPNMSGKSTYMRQLALTVIMAQMG FV+AD VDLP+FDAIFTRIGAADDLISGQSTFM Sbjct: 600 ITGPNMSGKSTYMRQLALTVIMAQMGSFVAADHVDLPLFDAIFTRIGAADDLISGQSTFM 65- 9 Query: 661 VEMMEANQAVKRASDKSLILFDELGRGTATYDGMALAQSIIEYIHDRVRAKTMFATHYHE 72- 0 VEMMEANQA+KRASD SLILFDELGRGTATYDGMALAQ+IIEYIHDRV AKT+FATHYHE Sbjct: 660 VEMMEANQAIKRASDNSLILFDELGRGTATYDGMALAQAIIEYIHDRVGAKTIFATHYHE 71- 9 Query: 721 LTDLSEQLTRLVNVHVATLERDGEVTFLHKIESGPADKSYGIHVAKIAGLPIDLLDRATD 78- 0 LTDLS LT LVNVHVATLE+DG+VTFLHKI GPADKSYGIHVAKIAGLP LL RA + Sbjct: 720 LTDLSTNLTSLVNVHVATLEKDGDVTFLHKIAEGPADKSYGIHVAKIAGLPKSLLKRADE 77- 9 Query: 781 ILSQLEADAVQLIVSPSQEAVTADLNEELDSEKQQGQLSLFEEPSNAGRVIEELEAIDIM 84- 0 +L++LE S S E ++ E S +QGQLSLF + A + + LE ID+M Sbjct: 780 VLTRLETQ------SRSTEIISVPSQVESSSAVRQGQLSLFGDEEKAHEIRQALEVIDVM 83- 3 Query: 841 NLTPMQAMNAIFDLKKLL 858 N+TP+QAM +++LKKLL Sbjct: 834 NMTPLQAMTTLYELKKLL 851 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1078 A DNA sequence (GBSx1152) was identified in S. agalactiae <SEQ ID 3323> which encodes the amino acid sequence <SEQ ID 3324>. This protein is predicted to be cold shock protein-related protein. Analysis of this protein sequence reveals the following: TABLE-US-03212 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2095(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03213 >GP: CAB69404 GB: A91080 unnamed protein product [unidentified] Identities = 48/63 (76%), Positives = 56/63 (88%) Query: 1 MTQGTVKWFNSEKGFGFISSETGTDVFAHFSEIKVDGFKTLEEGQKVTFDIQDGQRGPQA 60 MT+GTVKWFN +KGFGFI+SE G DVFAHFS+I+ GFKTL+EGQKVTFD++ GQRGPQA Sbjct: 1 MTKGTVKWFNPDKGFGFITSEDGQDVFAHFSQIQTSGFKTLDEGQKVTFDVEAGQRGPQA 60 Query: 61 TNI 63 NI Sbjct: 61 VNI 63 A related DNA sequence was identified in S. pyogenes <SEQ ID 3325> which encodes the amino acid sequence <SEQ ID 3326>. Analysis of this protein sequence reveals the following: TABLE-US-03214 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2350(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03215 Identities = 49/63 (77%), Positives = 56/63 (88%) Query: 1 MTQGTVKWFNSEKGFGFISSETGTDVFAHFSEIKVDGFKTLEEGQKVTFDIQDGQRGPQA 60 M QGTVKWFN+EKGFGFIS+E G DVFAHFS I+ +GFKTLEEGQKV FD+++GQRGPQA Sbjct: 3 MAQGTVKWFNAEKGFGFISTENGQDVFAHFSAIQTNGFKTLEEGQKVAFDVEEGQRGPQA 62 Query: 61 TNI 63 NI Sbjct: 63 VNI 65 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1079 A DNA sequence (GBSx1153) was identified in S. agalactiae <SEQ ID 3327> which encodes the amino acid sequence <SEQ ID 3328>. Analysis of this protein sequence reveals the following: TABLE-US-03216 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6378(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1080 A DNA sequence (GBSx1154) was identified in S. agalactiae <SEQ ID 3329> which encodes the amino acid sequence <SEQ ID 3330>. This protein is predicted to be DNA mismatch repair protein hexb (mutL). Analysis of this protein sequence reveals the following: TABLE-US-03217 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2242(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10267> which encodes amino acid sequence <SEQ ID 10268> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03218 >GP:AAA88600 GB:M29686 mismatch repair protein [Streptococcus pneumoniae] Identities = 452/657 (68%), Positives = 543/657 (81%), Gaps = 8/657 (1%) Query: 20 LSKIIELPDILANQIAAGEVVERPSSVVKELVENAIDAGSSQITIEVEESGLKKIQITDN 79 - +S IIELP++LANQIAAGEV+ERP+SV KELVENAIDAGSSQI IE+EE+GLKK+QITDN Sbjct: 1 MSHIIELPEMLANQIAAGEVIERPASVCKELVENAIDAGSSQIIIEIEEAGLKKVQITDN 60 Query: 80 GEGMTSEDAVLSLRRHATSKIKSQSDLFRIRTLGFRGEALPSIASISLMTIKTATEQGKQ 139- G G+ ++ L+LRRHATSKIK+Q+DLFRIRTLGFRGEALPSIAS+S++T+ TA + Sbjct: 61 GHGIAHDEVELALRRHATSKIKNQADLFRIRTLGFRGEALPSIASVSVLTLLTAVDGASH 120- Query: 140 GTLLVAKGGNIEKQEVVSSPRGTKILVENLFFNTPARLKYMKSLQSELAHIIDIVNRLSL 19- 9 GT LVA+GG +E+ +SP GTK+ VE+LFFNTPARLKYMKS Q+EL+HIIDIVNRL L Sbjct: 121 GTKLVARGGEVEEVIPATSPVGTKVCVEDLFFNTPARLKYMKSQQAELSHIIDIVNRLGL 18- 0 Query: 200 AHPEVAFTLINDGKEMTKTSGTGDLRQAIAGIYGLNTAKKMIEISNADLDFEISGYVSLP 25- 9 AHPE++F+LI+DGKEMT+T+GTG LRQAIAGIYGL +AKKMIEI N+DLDFEISG+VSLP Sbjct: 181 AHPEISFSLISDGKEMTRTAGTGQLRQAIAGIYGLVSAKKMIEIENSDLDFEISGFVSLP 24- 0 Query: 260 ELTRANRNYITLLINGRYIKNFLLNRSILDGYGSKLMVGRFPIAVIDIQIDPYLADVNVH 31- 9 ELTRANRNYI+L INGRYIKNFLLNR+ILDG+GSKLMVGRFP+AVI I IDPYLADVNVH Sbjct: 241 ELTRANRNYISLFINGRYIKNFLLNRAILDGFGSKLMVGRFPLAVIHIHIDPYLADVNVH 30- 0 Query: 320 PTKQEVRISKERELMSLISTAISESLKQYDLIPDALENLAKTSTRSVDKPIQTSFSLKQP 37- 9 PTKQEVRISKE+ELM+L+S AI+ SLK+ LIPDALENLAK++ R+ +K QT LK+ Sbjct: 301 PTKQEVRISKEKELMTLVSEAIANSLKEQTLIPDALENLAKSTVRNREKVEQTILPLKEN 36- 0 Query: 380 GLYYDRAKNDFFIGADTVSEPIANFTNLDKSDGSVDNDVKNSVNQGATQSPNIKYASRDQ 43- 9 LYY++ + + +E L + K ++++ T+ + +A R Sbjct: 361 TLYYEKTEP----SRPSQTEVADYQVELTDEGQDLTLFAKETLDR-LTKPAKLHFAERKP 41- 5 Query: 440 ADSENFIHSQDYLSSKQSLNKLVEKLDSEESSTFPELEFFGQMHGTYLFAQGNGGLYIID 49- 9 A+ + H + L+ S++K +KL+ EE+S+FPELEFFGQMHGTYLFAQG GLYIID Sbjct: 416 ANYDQLDHPELDLA---SIDKAYDKLEREEASSFPELEFFGQMHGTYLFAQGRDGLYIID 47- 2 Query: 500 QHAAQERVKYEYYREKIGEVDNSLQQLLVPFLFEFSSSDFLQLQEKMSLLQDVGIFLEPY 55- 9 QHAAQERVKYE YRE IG VD S QQLLVP++FEF + D L+L+E+M LL++VG+FL Y Sbjct: 473 QHAAQERVKYEEYRESIGNVDQSQQQLLVPYIFEFPADDALRLKERMPLLEEVGVFLAEY 53- 2 Query: 560 GNNTFILREHPIWMKEEEVESGIYEMCDMLLLTNEVSVKKYRAELAIMMSCKRSIKANHT 61- 9 G N FILREHPIWM EEE+ESGIYEMCDMLLLT EVS+KKYRAELAIMMSCKRSIKANH Sbjct: 533 GENQFILREHPIWMAEEEIESGIYEMCDMLLLTKEVSIKKYRAELAIMMSCKRSIKANHR 59- 2 Query: 620 LDDYSARHLLDQLAQCKNPYNCPHGRPVLVNFTKADMEKMFKRIQENHTSLRDLGKY 676 +DD+SAR LL QL+QC NPYNCPHGRPVLV+FTK+DMEKMF+RIQENHTSLR+LGKY Sbjct: 593 IDDHSARQLLYQLSQCDNPYNCPHGRPVLVHFTKSDMEKMFRRIQENHTSLRELGKY 649 A related DNA sequence was identified in S. pyogenes <SEQ ID 3331> which encodes the amino acid sequence <SEQ ID 3332>. Analysis of this protein sequence reveals the following: TABLE-US-03219 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1854(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03220 Identities = 502/663 (75%), Positives = 574/663 (85%), Gaps = 9/663 (1%) Query: 20 LSKIIELPDILANQIAAGEVVERPSSVVKELVENAIDAGSSQITIEVEESGLKKIQITDN 79 - ++ IIELP++LANQIAAGEVVERP+SVVKELVENAIDA SSQIT+E+EESGLK IQ+TDN Sbjct: 14 MTNIIELPEVLANQIAAGEVVERPASVVKELVENAIDAKSSQITVEIEESGLKMIQVTDN 73 Query: 80 GEGMTSEDAVLSLRRHATSKIKSQSDLFRIRTLGFRGEALPSIASISLMTIKTATEQGKQ 139- GEGM+ ED LSLRRHATSKIKSQSDLFRIRTLGFRGEALPS+ASIS +TIKTAT++ Sbjct: 74 GEGMSHEDLPLSLRRHATSKIKSQSDLFRIRTLGFRGEALPSVASISKITIKTATKEVTH 133- Query: 140 GTLLVAKGGNIEKQEVVSSPRGTKILVENLFFNTPARLKYMKSLQSELAHIIDIVNRLSL 19- 9 G+LL+A GG IE E +S+P GTKI VENLF+NTPARLKYMKSLQ+ELAHI+D+VNRLSL Sbjct: 134 GSLLIATGGEIETLEAISTPTGTKIKVENLFYNTPARLKYMKSLQAELAHIVDVVNRLSL 19- 3 Query: 200 AHPEVAFTLINDGKEMTKTSGTGDLRQAIAGIYGLNTAKKMIEISNADLDFEISGYVSLP 25- 9 AHPEVAFTLI+DG+++T+TSGTGDLRQAIAGIYGLNT KKM+ ISNADLDFE+SGYVSLP Sbjct: 194 AHPEVAFTLISDGRQLTQTSGTGDLRQAIAGIYGLNTTKKMLAISNADLDFEVSGYVSLP 25- 3 Query: 260 ELTRANRNYITLLINGRYIKNFLLNRSILDGYGSKLMVGRFPIAVIDIQIDPYLADVNVH 31- 9 ELTRANRNY+T+L+NGRYIKNFLLNR+ILDGYGSKLMVGRFPI VIDIQIDPYLADVNVH Sbjct: 254 ELTRANRNYMTILVNGRYIKNFLLNRAILDGYGSKLMVGRFPIVVIDIQIDPYLADVNVH 31- 3 Query: 320 PTKQEVRISKERELMSLISTAISESLKQYDLIPDALENLAKTSTRSVDKPIQTSFSLKQP 37- 9 PTKQEVRISKERELM+LISTAISESLK+ DLIPDALENLAK+STR KP QT L+ Sbjct: 314 PTKQEVRISKERELMALISTAISESLKEQDLIPDALENLAKSSTRHFSKPEQTQLPLQSR 37- 3 Query: 380 GLYYDRAKNDFFIGADTVSEPIANFTNLDKSDGSVDNDVKNSV------NQGATQSPNIK 43- 3 GLYYD KNDFF+ VSE I D G+VDN VK ++ K Sbjct: 374 GLYYDPQKNDFFVKESAVSEKI---PETDFYSGAVDNSVKVEKVELLPHSEEVIGPSSVK 43- 0 Query: 434 YASRDQADSENFIHSQDYLSSKQSLNKLVEKLDSEESSTFPELEFFGQMHGTYLFAQGNG 49- 3 +ASR Q H L ++Q L++++ +L++E S FPEL++FGQMHGTYLFAQG Sbjct: 431 HASRPQNTFTETDHPNLDLKNRQKLSQMLTRLENEGQSVFPELDYFGQMHGTYLFAQGKD 49- 0 Query: 494 GLYIIDQHAAQERVKYEYYREKIGEVDNSLQQLLVPFLFEFSSSDFLQLQEKMSLLQDVG 55- 3 GL+IIDQHAAQERVKYEYYR+KIGEVD+SLQQLLVP+LFEFS SDF+ LQEKM+LL +VG Sbjct: 491 GLFIIDQHAAQERVKYEYYRDKIGEVDSSLQQLLVPYLFEFSGSDFINLQEKMALLNEVG 55- 0 Query: 554 IFLEPYGNNTFILREHPIWMKEEEVESGIYEMCDMLLLTNEVSVKKYRAELAIMMSCKRS 61- 3 IFLE YG+NTFILREHPIWMKEEE+ SG+YEMCDMLLLTNEVS+K YRAELAIMMSCKRS Sbjct: 551 IFLEVYGHNTFILREHPIWMKEEEIASGVYEMCDMLLLTNEVSIKTYRAELAIMMSCKRS 61- 0 Query: 614 IKANHTLDDYSARHLLDQLAQCKNPYNCPHGRPVLVNFTKADMEKMFKRIQENHTSLRDLGKY- 676 IKANH+LDDYSAR+LL QLAQC+NPYNCPHGRPVL+NF+KADMEKMF+RIQENHTSLR+LGKY Sbjct: 611 IKANHSLDDYSARNLLLQLAQCQNPYNCPHGRPVLINFSKADMEKMFRRIQENHTSLRELGKY- 673 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1081 A DNA sequence (GBSx1155) was identified in S. agalactiae <SEQ ID 3333> which encodes the amino acid sequence <SEQ ID 3334>. Analysis of this protein sequence reveals the following:

TABLE-US-03221 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3372(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1082 A DNA sequence (GBSx1156) was identified in S. agalactiae <SEQ ID 3335> which encodes the amino acid sequence <SEQ ID 3336>. Analysis of this protein sequence reveals the following: TABLE-US-03222 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.01 Transmembrane 176-192 (170-197) INTEGRAL Likelihood = -8.07 Transmembrane 390-406 (387-412) INTEGRAL Likelihood = -6.10 Transmembrane 271-287 (269-291) INTEGRAL Likelihood = -6.00 Transmembrane 83-99 (82-101) INTEGRAL Likelihood = -4.78 Transmembrane 51-67 (50-71) INTEGRAL Likelihood = -2.92 Transmembrane 303-319 (302-320) INTEGRAL Likelihood = -2.76 Transmembrane 363-379 (362-381) INTEGRAL Likelihood = -2.39 Transmembrane 152-168 (151-169) INTEGRAL Likelihood = -2.02 Transmembrane 325-341 (325-342) INTEGRAL Likelihood = -1.65 Transmembrane 226-242 (226-242) INTEGRAL Likelihood = -0.90 Transmembrane 24-40 (24-40) INTEGRAL Likelihood = -0.27 Transmembrane 111-127 (111-127) ----- Final Results ----- bacterial membrane --- Certainty = 0.6604(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10265> which encodes amino acid sequence <SEQ ID 10266> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03223 >GP:CAA61918 GB:X89779 LmrP integral membrane protein [Lactococcus lactis] Identities = 145/401 (36%), Positives = 236/401 (58%), Gaps = 4/401 (0%) Query: 9 VKEFFALPKQLQLRELLRFISITVGSAIFPFMAMYYVQYFGNLVTGILIIITQLSGFVAT 68 +KEF+ L K LQLR + F+ +F M +YY QY G+ +TGIL+ ++ ++ FVA Sbjct: 1 MKEFWNLDKNLQLRLGIVFLGAFSYGTVFSSMTIYYNQYLGSAITGILLALSAVATFVAG 60 Query: 69 LYGGHLSDAMGRKKVVIIGSLLATIGWAITIAANVPNHITPHLTFVGILIIEIAHQFYFP 128- + G +D GRK V++ G+++ +G A+ IA+N+P H+ P TF+ L+I +F Sbjct: 61 ILAGFFADRNGRKPVMVFGTIIQLLGAALAIASNLPGHVNPWSTFIAFLLISFGYNFVIT 120- Query: 129 AYEAMTIDLTNEQNRRFVYTIGYWLVNIAVMLGSGIAGIFYDHHFFELLIVLLIISAICC 18- 8 A AM ID +N +NR+ V+ + YW N++V+LG+ + + F LL++LL+ + Sbjct: 121 AGNAMIIDASNAENRKVVFMLDYWAQNLSVILGAALGAWLFRPAFEALLVILLLTVLVSF 18- 0 Query: 189 FVVYFKFDET-KPQEGTFKHDKGVLGTFKNYSQVLVDKAFVVYTLGAIGSSVVWLQVDNY 24- 7 F+ F ET KP T K D+ F+ Y VL DK ++++ I ++ + +Q DN+ Sbjct: 181 FLTTFVMTETFKP---TVKVDEKAENIFQAYKTVLQDKTYMIFMGANIATTFIIMQFDNF 23- 7 Query: 248 FSVNLKQNFEVVSILGHTITGAKMLSLAVFTNTLLIVLLMTTINKFIENWPLKRQLILGS 30- 7 V+L +F+ ++ G I G +ML++ + + L+VLLMTT+N+ ++W ++ I GS Sbjct: 238 LPVHLSNSFKTITFWGFEIYGQRMLTIYLILACVLVVLLMTTLNRLTKDWSHQKGFIWGS 29- 7 Query: 308 LICGFGMLFNISLNTFGAILIAMTFFTFGEMIYVPASQVLRAEMMVEGKIGSYSGFLAIA 36- 7 L GM+F+ TF I IA +T GE++Y P+ Q L A++M KIGSY+G AI Sbjct: 298 LFMAIGMIFSFLTTTFTPIFIAGIVYTLGEIVYTPSVQTLGADLMNPEKIGSYNGVAAIK 35- 7 Query: 368 QPVASVLAGAMVSLSYFTGKIGVQITLTIFMLAGLVLILYA 408 P+AS+LAG +VS+S IGV + L + + ++L+L A Sbjct: 358 MPIASILAGLLVSISPMIKAIGVSLVLALTEVLAIILVLVA 398 A related DNA sequence was identified in S. pyogenes <SEQ ID 3337> which encodes the amino acid sequence <SEQ ID 3338>. Analysis of this protein sequence reveals the following: TABLE-US-03224 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.41 Transmembrane 166-182 (161-188) INTEGRAL Likelihood = -7.75 Transmembrane 384-400 (376-403) INTEGRAL Likelihood = -7.64 Transmembrane 266-282 (261-285) INTEGRAL Likelihood = -4.25 Transmembrane 295-311 (291-313) INTEGRAL Likelihood = -2.71 Transmembrane 98-114 (98-115) INTEGRAL Likelihood = -2.23 Transmembrane 355-371 (355-374) INTEGRAL Likelihood = -2.02 Transmembrane 218-234 (218-234) INTEGRAL Likelihood = -1.91 Transmembrane 315-331 (315-331) INTEGRAL Likelihood = -1.22 Transmembrane 75-91 (75-92) INTEGRAL Likelihood = -0.75 Transmembrane 45-61 (45-63) INTEGRAL Likelihood = -0.75 Transmembrane 144-160 (144-161) ----- Final Results ----- bacterial membrane --- Certainty = 0.5564(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03225 >GP:CAA61918 GB:X89779 LmrP integral membrane protein [Lactococcus lactis] Identities = 138/400 (34%), Positives = 223/400 (55%), Gaps = 2/400 (0%) Query: 1 MQEFLNLPKQIQLRQLVRFVTITLGSSIFPFMAMYYTTYFGTFWTGLLMMITSLMGFVGT 60 M+EF NL K +QLR + F+ ++F M +YY Y G+ TG+L+ ++++ FV Sbjct: 1 MKEFWNLDKNLQLRLGIVFLGAFSYGTVFSSMTIYYNQYLGSAITGILLALSAVATFVAG 60 Query: 61 LYGGHLSDALGRKKVIMIGSVGTTLGWFLTILANLPNAAIPWLTFAGILLVEIASSFYGP 120- + G +D GRK V++ G++ LG L I +NLP PW TF LL+ +F Sbjct: 61 ILAGFFADRNGRKPVMVFGTIIQLLGAALAIASNLPGHVNPWSTFIAFLLISFGYNFVIT 120- Query: 121 AYEAMLIDLTDESNRRFVYTINYWFINIAVMFGAGLSGLFYDHHFLALLVALLLVNVLCF 18- 0 A AM+ID ++ NR+ V+ ++YW N++V+ GA L + F ALLV LLL ++ F Sbjct: 121 AGNAMIIDASNAENRKVVFMLDYWAQNLSVILGAALGAWLFRPAFEALLVILLLTVLVSF 18- 0 Query: 181 GVAYYCFDETRPETHAFDHGKGLLASFQNYRQVFHDRAFVLFTLGAIFSGSIWMQMDNYV 24- 0 + + ET T D + FQ Y+ V D+ +++F I + I MQ DN++ Sbjct: 181 FLTTFVMTETFKPTVKVDEKAENI--FQAYKTVLQDKTYMIFMGANIATTFIIMQFDNFL 23- 8 Query: 241 PVHLKLYFQPTAVLGFQVTSSKMLSLMVLTNTLLIVLFMTVVNKLTEKWKLLPQLVVGSL 30- 0 PVHL F+ GF++ +ML++ ++ +L+VL MT +N+LT+ W + GSL Sbjct: 239 PVHLSNSFKTITFWGFEIYGQRMLTIYLILACVLVVLLMTTLNRLTKDWSHQKGFIWGSL 29- 8 Query: 301 LFTLGMLLSFTFTQFYAIWLSVVLLTFGEMINVSASQVLRADMMDHSQIGSYTGFVSMAQ 36- 0 +GM+ SF T F I+++ ++ T GE++ + Q L AD+M+ +IGSY G ++ Sbjct: 299 FMAIGMIFSFLTTTFTPIFIAGIVYTLGEIVYTPSVQTLGADLMNPEKIGSYNGVAAIKM 35- 8 Query: 361 PLGAILASLLVSVSHFTGPLGVQCLFAVIALLGIYFTVVS 400 P+ +ILA LLVS+S +GV + A+ +L I +V+ Sbjct: 359 PIASILAGLLVSISPMIKAIGVSLVLALTEVLAIILVLVA 398 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03226 Identities = 228/406 (56%), Positives = 305/406 (74%) Query: 9 VKEFFALPKQLQLRELLRFISITVGSAIFPFMAMYYVQYFGNLVTGILIIITQLSGFVAT 68 ++EF LPKQ+QLR+L+RF++IT+GS+IFPFMAMYY YFG TG+L++IT L GFV T Sbjct: 1 MQEFLNLPKQIQLRQLVRFVTITLGSSIFPFMAMYYTTYFGTFWTGLLMMITSLMGFVGT 60 Query: 69 LYGGHLSDAMGRKKVVIIGSLLATIGWAITIAANVPNHITPHLTFVGILIIEIAHQFYFP 128- LYGGHLSDA+GRKKV++IGS+ T+GW +TI AN+PN P LTF GIL++EIA FY P Sbjct: 61 LYGGHLSDALGRKKVIMIGSVGTTLGWFLTILANLPNAAIPWLTFAGILLVEIASSFYGP 120- Query: 129 AYEAMTIDLTNEQNRRFVYTIGYWLVNIAVMLGSGIAGIFYDHHFFELLIVLLIISAICC 18- 8 AYEAM IDLT+E NRRFVYTI YW +NIAVM G+G++G+FYDHHF LL+ LL+++ +C Sbjct: 121 AYEAMLIDLTDESNRRFVYTINYWFINIAVMFGAGLSGLFYDHHFLALLVALLLVNVLCF 18- 0 Query: 189 FVVYFKFDETKPQEGTFKHDKGVLGTFKNYSQVLVDKAFVVYTLGAIGSSVVWLQVDNYF 24- 8 V Y+ FDET+P+ F H KG+L +F+NY QV D+AFV++TLGAI S +W+Q+DNY Sbjct: 181 GVAYYCFDETRPETHAFDHGKGLLASFQNYRQVFHDRAFVLFTLGAIFSGSIWMQMDNYV 24- 0 Query: 249 SVNLKQNFEVVSILGHTITGAKMLSLAVFTNTLLIVLLMTTINKFIENWPLKRQLILGSL 30- 8 V+LK F+ ++LG +T +KMLSL V TNTLLIVL MT +NK E W L QL++GSL Sbjct: 241 PVHLKLYFQPTAVLGFQVTSSKMLSLMVLTNTLLIVLFMTVVNKLTEKWKLLPQLVVGSL 30- 0 Query: 309 ICGFGMLFNISLNTFGAILIAMTFFTFGEMIYVPASQVLRAEMMVEGKIGSYSGFLAIAQ 36- 8 + GML + + F AI +++ TFGEMI V ASQVLRA+MM +IGSY+GF+++AQ Sbjct: 301 LFTLGMLLSFTFTQFYAIWLSVVLLTFGEMINVSASQVLRADMMDHSQIGSYTGFVSMAQ 36- 0 Query: 369 PVASVLAGAMVSLSYFTGKIGVQITLTIFMLAGLVLILYATKMKNI 414 P+ ++LA +VS+S+FTG +GVQ + L G+ + + KMK + Sbjct: 361 PLGAILASLLVSVSHFTGPLGVQCLFAVIALLGIYFTVVSAKMKKV 406 A related GBS gene <SEQ ID 8725> and protein <SEQ ID 8726> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03227 Lipop: Possible site: -1 Crend: 8 SRCFLG: 0 McG: Length of UR: 4 Peak Value of UR: 1.73 Net Charge of CR: 1 McG: Discrim Score: -4.26 GvH: Signal Score (-7.5): -2.48 Possible site: 35 >>> Seems to have no N-terminal signal sequence Amino Acid Composition: calculated from 1 ALOM program count: 12 value: -14.01 threshold: 0.0 INTEGRAL Likelihood = -14.01 Transmembrane 168-184 (162-189) INTEGRAL Likelihood = -8.07 Transmembrane 382-398 (379-404) INTEGRAL Likelihood = -6.10 Transmembrane 263-279 (261-283) INTEGRAL Likelihood = -6.00 Transmembrane 75-91 (74-93) INTEGRAL Likelihood = -4.78 Transmembrane 43-59 (42-63) INTEGRAL Likelihood = -2.92 Transmembrane 295-311 (294-312) INTEGRAL Likelihood = -2.76 Transmembrane 355-371 (354-373) INTEGRAL Likelihood = -2.39 Transmembrane 144-160 (143-161) INTEGRAL Likelihood = -2.02 Transmembrane 317-333 (317-334) INTEGRAL Likelihood = -1.65 Transmembrane 218-234 (218-234) INTEGRAL Likelihood = -0.90 Transmembrane 16-32 (16-32) INTEGRAL Likelihood = -0.27 Transmembrane 103-119 (103-119) PERIPHERAL Likelihood = 9.44 239 modified ALOM score: 3.30 icm1 HYPID: 7 CFP: 0.660 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6604(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00075## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1083 A DNA sequence (GBSx1157) was identified in S. agalactiae <SEQ ID 3339> which encodes the amino acid sequence <SEQ ID 3340>. This protein is predicted to be holliday junction DNA helicase (ruvA). Analysis of this protein sequence reveals the following: TABLE-US-03228 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.75 Transmembrane 75-91 (74-91) ----- Final Results ----- bacterial membrane --- Certainty = 0.1702(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03229 >GP:BAB04943 GB:AP001511 holliday junction DNA helicase [Bacillus halodurans] Identities = 86/201 (42%), Positives = 122/201 (59%), Gaps = 6/201 (2%) Query: 1 MYDYIKGKLSKITAKFIVVETAGLGYMIYVANPYSFSGYVNQEVTIYLHQVIRDDAHLLF 60 M DY++G L+ I ++ VVE G+GY +Y NPY F + +TIY Q +R+D L+ Sbjct: 1 MIDYLRGTLTDIDHQYAVVEVHGVGYQVYCPNPYEFEKERDSVITIYTFQYVREDVIRLY 60 Query: 61 GFHTENEKEIFLNLISVSGIGPTTALAIIAVDDNEGLVSAIDNSDIKYLTKFPKIGKKTA 120- GF T+ ++ +F L++VSGIGP ALAI+A E ++ AI+ D +L KFP +GKKTA Sbjct: 61 GFRTKEKRSLFEKLLNVSGIGPKGALAILATGQPEHVIQAIEEEDEAFLVKFPGVGKKTA 120- Query: 121 QQMILDLSGKFVE------ASGESATSRKVSSEQNSNLEEAMEALLALGYKATELKKVKA 17- 4 +Q+ILDL GK E + E ++ N L+EAMEAL ALGY ELKKVK Sbjct: 121 RQIILDLKGKVDELHPGLFSQKEEQPKPHEKNDGNQALDEAMEALKALGYVEKELKKVKP 18- 0 Query: 175 FFEGTNETVEQYIKSSLKMLM 195 E T + YIK +L++++ Sbjct: 181 KLEQETLTTDAYIKKALQLML 201 A related DNA sequence was identified in S. pyogenes <SEQ ID 3341> which encodes the amino acid sequence <SEQ ID 3342>. Analysis of this protein sequence reveals the following: TABLE-US-03230 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.59 Transmembrane 75-91 (74-91) ----- Final Results ----- bacterial membrane --- Certainty = 0.1638(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03231 >GP:BAB04943 GB:AP001511 holliday junction DNA helicase [Bacillus halodurans] Identities = 91/201 (45%), Positives = 128/201 (63%), Gaps = 5/201 (2%) Query: 1 MYDYIKGQLTKITAKYIVVEANGLGYMINVANPYSFTDSVNQLVTIYLHQVIREDAHLLF 60 M DY++G LT I +Y VVE +G+GY + NPY F + ++TIY Q +RED L+ Sbjct: 1 MIDYLRGTLTDIDHQYAVVEVHGVGYQVYCPNPYEFEKERDSVITIYTFQYVREDVIRLY 60 Query: 61 GFHTEDEKDVFLKLISVSGIGPTTALAIVAVDDNEGLVNAIDNSDIKYLMKFPKIGKKTA 120- GF T++++ +F KL++VSGIGP ALAI+A E ++ AI+ D +L+KFP +GKKTA Sbjct: 61 GFRTKEKRSLFEKLLNVSGIGPKGALAILATGQPEHVIQAIEEEDEAFLVKFPGVGKKTA 120- Query: 121 QQMVLDLAGKFVEA-----PQETGHTKARSNKAGNTQLDEAIEALLALGYKAKELKKIRA 17- 5 +Q++LDL GK E Q+ K GN LDEA+EAL ALGY KELKK++ Sbjct: 121 RQIILDLKGKVDELHPGLFSQKEEQPKPHEKNDGNQALDEAMEALKALGYVEKELKKVKP 18- 0 Query: 176 FFEGTSETAEQYIKSALKLLM 196 E + T + YIK AL+L++ Sbjct: 181 KLEQETLTTDAYIKKALQLML 201 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03232 Identities = 153/197 (77%), Positives = 176/197 (88%), Gaps = 1/197 (0%) Query: 1 MYDYIKGKLSKITAKFIVVETAGLGYMIYVANPYSFSGYVNQEVTIYLHQVIRDDAHLLF 60 MYDYIKG+L+KITAK+IVVE GLGYMI VANPYSF+ VNQ VTIYLHQVIR+DAHLLF Sbjct: 1 MYDYIKGQLTKITAKYIVVEANGLGYMINVANPYSFTDSVNQLVTIYLHQVIREDAHLLF 60 Query: 61 GFHTENEKEIFLNLISVSGIGPTTALAIIAVDDNEGLVSAIDNSDIKYLTKFPKIGKKTA 120- GFHTE+EK++FL LISVSGIGPTTALAI+AVDDNEGLV+AIDNSDIKYL KFPKIGKKTA Sbjct: 61 GFHTEDEKDVFLKLISVSGIGPTTALAIVAVDDNEGLVNAIDNSDIKYLMKFPKIGKKTA 120- Query: 121 QQMILDLSGKFVEASGESA-TSRKVSSEQNSNLEEAMEALLALGYKATELKKVKAFFEGT 17- 9 QQM+LDL+GKFVEA E+ T + + N+ L+EA+EALLALGYKA ELKK++AFFEGT Sbjct: 121 QQMVLDLAGKFVEAPQETGHTKARSNKAGNTQLDEAIEALLALGYKAKELKKIRAFFEGT 18- 0 Query: 180 NETVEQYIKSSLKMLMK 196 +ET EQYIKS+LK+LMK Sbjct: 181 SETAEQYIKSALKLLMK 197 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1084 A DNA sequence (GBSx1159) was identified in S. agalactiae <SEQ ID 3343> which encodes the amino acid sequence <SEQ ID 3344>. This protein is predicted to be DNA-3-methyladenine glycosidase I (tag). Analysis of this protein sequence reveals the following: TABLE-US-03233 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2812(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10263> which encodes amino acid sequence <SEQ ID 10264> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03234 >GP:AAC76573 GB:AE000432 3-methyl-adenine DNA glycosylase I, constitutive [Escherichia coli K12] Identities = 87/176 (49%), Positives = 122/176 (68%), Gaps = 1/176 (0%) Query: 5 MKRCSWVNLDNPLYVAYHDKEWGRAVHDDHVLFELLCLETYQSGLSWETVLNKRQEFRQV 64 M+RC WV+ D PLY+AYHD EWG D LFE++CLE Q+GLSW TVL KR+ +R Sbjct: 1 MERCGWVSQD-PLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRAC 59 Query: 65 FHHYNIEKVAAMSDADLEIILQNPRVIRHRLKLFSTRQNARSIILIQKEFGSFDRYIWSF 124- FH ++ KVAAM + D+E ++Q+ +IRHR K+ + NAR+ + +++ F ++WSF Sbjct: 60 FHQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPFVDFVWSF 119- Query: 125 VDNKVQVNSVNNYNDVPASTTLSERLSKDLKKRGFKFVGPTCLYSFIQAAGMVNDH 180 V+++ QV +++P ST+ S+ LSK LKKRGFKFVG T YSF+QA G+VNDH Sbjct: 120 VNHQPQVTQATTLSEIPTSTSASDALSKALKKRGFKFVGTTICYSFMQACGLVNDH 175 A related DNA sequence was identified in S. pyogenes <SEQ ID 3345> which encodes the amino acid sequence <SEQ ID 3346>. Analysis of this protein sequence reveals the following: TABLE-US-03235 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4149(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03236 Identities = 114/184 (61%), Positives = 135/184 (72%) Query: 3 FHMKRCSWVNLDNPLYVAYHDKEWGRAVHDDHVLFELLCLETYQSGLSWETVLNKRQEFR 62 FHMKRCSWV DN LY YHD EWG+ + DD FELLCLE+YQSGLSW TVL KRQ FR Sbjct: 2 FHMKRCSWVPKDNQLYCDYHDLEWGQPLDDDRDFFELLCLESYQSGLSWLTVLKKRQAFR 61 Query: 63 QVFHHYNIEKVAAMSDADLEIILQNPRVIRHRLKLFSTRQNARSIILIQKEFGSFDRYIW 122- VFHHY+I VA + ++ L+NP +IRH+LKL +T NA ++ IQKEFGSF Y+W Sbjct: 62 TVFHHYDIASVATFTSEEMADALENPSIIRHKLKLAATVNNAIAVQKIQKEFGSFSTYLW 121- Query: 123 SFVDNKVQVNSVNNYNDVPASTTLSERLSKDLKKRGFKFVGPTCLYSFIQAAGMVNDHEN 18- 2 +FV K N VN N VPA T LS RL+KDLKKRGFKF+GPT +YSF+QA+G+VNDHE Sbjct: 122 NFVGGKPINNLVNQENLVPAQTELSIRLAKDLKKRGFKFLGPTTVYSFMQASGLVNDHEE 18- 1 Query: 183 ICDF 186 C F Sbjct: 182 ACVF 185 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1085 A DNA sequence (GBSx1160) was identified in S. agalactiae <SEQ ID 3347> which encodes the amino acid sequence <SEQ ID 3348>. This protein is predicted to be competence-damage inducible protein (cinA). Analysis of this protein sequence reveals the following: TABLE-US-03237 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10261> which encodes amino acid sequence <SEQ ID 10262> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03238 >GP:CAA84071 GB:Z34303 CinA protein [Streptococcus pneumoniae] Identities = 194/297 (65%), Positives = 236/297 (79%), Gaps = 1/297 (0%) Query: 1 MVEGSIPLQNLTGLAVGGIVTSKGVQYMVLPGPPSELKPMVMEQVVPILSNNGTKLYSRV 60 +VEG+IPL N TGLAVGG + GV Y+VLPGPPSELKPMV+ Q++P L G+KLYSRV Sbjct: 121 IVEGAIPLPNETGLAVGGKLEVDGVTYVVLPGPPSELKPMVLNQLLPKLMT-GSKLYSRV 17- 9 Query: 61 LRFFGIGESQLVTILEDIIKNQTDPTIAPYAKVGEVTLRLSTKAENQDEADFKLDSLEKE 120- LRFFGIGESQLVTIL D+I NQ DPT+APYAK GEVTLRLSTKA +Q+EA+ LD LE + Sbjct: 180 LRFFGIGESQLVTILADLIDNQIDPTLAPYAKTGEVTLRLSTKASSQEEANQALDILENQ 23- 9 Query: 121 ILALKTLDNRKLKDLLYGYGDNNSMARTVLELLKVQNKTITAAESLTAGLFQSQLAEFSG 18- 0 IL +T + L+D YGYG+ S+A V+E LK Q KTI AAESLTAGLFQ+ +A FSG Sbjct: 240 ILDCQTFEGISLRDFCYGYGEETSLASIVVEELKRQGKTIAAAESLTAGLFQATVANFSG 29- 9 Query: 181 ASQVFNGGFTTYSMEAKSQLLGIPKKKLQEYGVVSHFTAEAMAQQARQLLKADFGIGLTG 24- 0 S +F GGF TYS+E KS++L IP K L+E+GVVS FTA+ MA+QAR ++DFGI LTG Sbjct: 300 VSSIFEGGFVTYSLEEKSRMLDIPAKNLEEHGVVSEFTAQKMAEQARSKTQSDFGISLTG 35- 9 Query: 241 VAGPDELEGYPAGTVFIGIATPEGVSSIKVSIGGKSRSDVRHISTLHAFDLVRRALL 297 VAGPD LEG+P GTVFIG+A +G IKV+IGG+SR+DVRHI+ +HAF+LVR+ALL Sbjct: 360 VAGPDSLEGHPVGTVFIGLAQDQGTEVIKVNIGGRSRADVRHIAVMHAFNLVRKALL 416 A related DNA sequence was identified in S. pyogenes <SEQ ID 3349> which encodes the amino acid sequence <SEQ ID 3350>. Analysis of this protein sequence reveals the following: TABLE-US-03239 Possible site: 22 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.91 Transmembrane 134-150 (134-150) ----- Final Results ----- bacterial membrane --- Certainty = 0.1765(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03240 >GP:CAA84071 GB:Z34303 CinA protein [Streptococcus pneumoniae] Identities = 286/417 (68%), Positives = 336/417 (79%), Gaps = 1/417 (0%) Query: 1 MKAELIAVGTEILTGQIVNTNAQFLSEKMAELGIDVYFQTAVGDNEERLLSVITTASQRS 60 MKAE+IAVGTEILTGQIVNTNAQFLSEK+AE+G+DVYFQTAVGDNE RLLS++ ASQRS Sbjct: 1 MKAEIIAVGTEILTGQIVNTNAQFLSEKLAEIGVDVYFQTAVGDNEVRLLSLLEIASQRS 60 Query: 61 NLVILCGGLGPTKDDLTKQTLAKYLRKDLVYDEQACQKLDDFFAKRKPSSRTPNNERQAQ 120- +LVIL GGLG T+DDLTKQTLAK+L K LV+D QA +KLD FFA R +RTPNNERQAQ Sbjct: 61 SLVILTGGLGATEDDLTKQTLAKFLGKALVFDPQAQEKLDIFFALRPDYARTPNNERQAQ 120- Query: 121 VIEGSIPLPNKTGLAVGGFITVDGISYVVLPGPPSELKPMVNEELVPLLSKQYSTLYSKV 18- 0 ++EG+IPLPN+TGLAVGG + VDG++YVVLPGPPSELKPMV +L+P L S LYS+V Sbjct: 121 IVEGAIPLPNETGLAVGGKLEVDGVTYVVLPGPPSELKPMVLNQLLPKLMTG-SKLYSRV 17- 9 Query: 181 LRFFGIGESQLVTVLSDFIENQTDPTIAPYAKTGEVTLRLSTKTENQALADKKLGQLEAQ 24- 0 LRFFGIGESQLVT+L+D I+NQ DPT+APYAKTGEVTLRLSTK +Q A++ L LE Q Sbjct: 180 LRFFGIGESQLVTILADLIDNQIDPTLAPYAKTGEVTLRLSTKASSQEEANQALDILENQ 23- 9 Query: 241 LLSRKTLEGQPLADVFYGYGEDNSLARETFELLVKYDKTITAAESLTAGLEQSTLASFPG 30- 0 +L +T EG L D YGYGE+ SLA E L + KTI AAESLTAGLFQ+T+A+F G Sbjct: 240 ILDCQTFEGISLRDFCYGYGEETSLASIVVEELKRQGKTIAAAESLTAGLFQATVANFSG 29- 9 Query: 301 ASQVFNGGFVTYSMEEKAKMLGLPLEELKSHGVVSAYTAEGMAEQARLLTGADIGVSLTG 36- 0 S +F GGFVTYS+EEK++ML +P + L+ HGVVS +TA+ MAEQAR T +D G+SLTG Sbjct: 300 VSSIFEGGFVTYSLEEKSRMLDIPAKNLEEHGVVSEFTAQKMAEQARSKTQSDFGISLTG 35- 9 Query: 361 VAGPDMLEEQPAGTVFIGLATQNKVESIKVLISGRSRLDVRYIATLHAFNMVRKTLL 417 VAGPD LE P GTVFIGLA E IKV I GRSR DVR+IA +HAFN+VRK LL Sbjct: 360 VAGPDSLEGHPVGTVFIGLAQDQGTEVIKVNIGGRSRADVRHIAVMHAFNLVRKALL 416 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03241 Identities = 201/299 (67%), Positives = 242/299 (80%) Query: 1 MVEGSIPLQNLTGLAVGGIVTSKGVQYMVLPGPPSELKPMVMEQVVPILSNNGTKLYSRV 60 ++EGSIPL N TGLAVGG +T G+ Y+VLPGPPSELKPMV E++VP+LS + LYS+V Sbjct: 121 VIEGSIPLPNKTGLAVGGFITVDGISYVVLPGPPSELKPMVNEELVPLLSKQYSTLYSKV 18- 0 Query: 61 LRFFGIGESQLVTILEDIIKNQTDPTIAPYAKVGEVTLRLSTKAENQDEADFKLDSLEKE 120- LRFFGIGESQLVT+L D I+NQTDPTIAPYAK GEVTLRLSTK ENQ AD KL LE + Sbjct: 181 LRFFGIGESQLVTVLSDFIENQTDPTIAPYAKTGEVTLRLSTKTENQALADKKLGQLEAQ 24- 0 Query: 121 ILALKTLDNRKLKDLLYGYGDNNSMARTVLELLKVQNKTITAAESLTAGLFQSQLAEFSG 18- 0 +L+ KTL+ + L D+ YGYG++NS+AR ELL +KTITAAESLTAGLFQS LA F G Sbjct: 241 LLSRKTLEGQPLADVFYGYGEDNSLARETFELLVKYDKTITAAESLTAGLFQSTLASFPG 30- 0 Query: 181 ASQVFNGGFTTYSMEAKSQLLGIPKKKLQEYGVVSHFTAEAMAQQARQLLKADFGIGLTG 24- 0 ASQVFNGGF TYSME K+++LG+P ++L+ +GVVS +TAE MA+QAR L AD G+ LTG Sbjct: 301 ASQVFNGGFVTYSMEEKAKMLGLPLEELKSHGVVSAYTAEGMAEQARLLTGADIGVSLTG 36- 0 Query: 241 VAGPDELEGYPAGTVFIGIATPEGVSSIKVSIGGKSRSDVRHISTLHAFDLVRRALLKI 299- VAGPD LE PAGTVFIG+AT V SIKV I G+SR DVR+I+TLHAF++VR+ LLK+ Sbjct: 361 VAGPDMLEEQPAGTVFIGLATQNKVESIKVLISGRSRLDVRYIATLHAFNMVRKTLLKL 419- SEQ ID 3348 (GBS646) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 131 (lane 24; MW 61.6 kDa), in FIG. 134 (lane 3; MW 57.5 kDa+lanes 2 & 4; MW 27 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 131 (lane 5-7; MW 36.6 kDa) and in FIG. 178 (lane 5; MW 37 kDa). GBS646-His was purified as shown in FIG. 229, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1086 A DNA sequence (GBSx1161) was identified in S. agalactiae <SEQ ID 3351> which encodes the amino acid sequence <SEQ ID 3352>. Analysis of this protein sequence reveals the following: TABLE-US-03242 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 148-164 (148-164) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 3353> which encodes the amino acid sequence <SEQ ID 3354>. Analysis of this protein sequence reveals the following: TABLE-US-03243 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 148-164 (148-164) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03244 >GP:AAD04860 GB:AF069745 RecA protein [Streptococcus parasanguinis] Identities = 333/381 (87%), Positives = 356/381 (93%), Gaps = 3/381 (0%) Query: 1 LAKKLKKNEEITKKFGDERRKALDDALKNIEKDFGKGAVMRLGERAEQKVQVMSSGSLAL 60 +AKK KK ++ITKKFGDER KAL+DALK IEKDFGKG++MRLGERAEQKVQVMSSGSLAL Sbjct: 1 MAKKQKKLDDITKKFGDEREKALNDALKLIEKDFGKGSIMRLGERAEQKVQVMSSGSLAL 60 Query: 61 DIALGAGGYPKGRIIEIYGPESSGKTTVALHAVAQAQKEGGIAAFIDAEHALDPAYAAAL 120- DIALGAGGYPKGRIIEIYGPESSGKTTVALHAVAQAQKEGGIAAFIDAEHALDP+YAAAL Sbjct: 61 DIALGAGGYPKGRIIEIYGPESSGKTTVALHAVAQAQKEGGIAAFIDAEHALDPSYAAAL 120- Query: 121 GVNIDELLLSQPDSGEQGLEIAGKLIDSGAVDLVVVDSVAALVPRAEIDGDIGDSHVGLQ 18- 0 GVNIDELLLSQPDSGEQGLEIAGKLIDSGAVDLVVVDSVAALVPRAEIDGDIGDSHVGLQ Sbjct: 121 GVNIDELLLSQPDSGEQGLEIAGKLIDSGAVDLVVVDSVAALVPRAEIDGDIGDSHVGLQ 18- 0 Query: 181 ARMMSQAMRKLSASINKTKTIAIFINQLREKVGVMFGNPETTPGGRALKFYASVRLDVRG 24- 0 ARMMSQAMRKL ASINKTKTIAIFINQLREKVGVMFGNPETTPGGRALKFYASVRLDVRG Sbjct: 181 ARMMSQAMRKLGASINKTKTIAIFINQLREKVGVMFGNPETTPGGRALKFYASVRLDVRG 24- 0 Query: 241 TTQIKGTGDQKDSSIGKETKIKVVKNKVAPPFKVAEVEIMYGEGISRTGELVKIASDLDI 30- 0 TQIKGTGDQKD+++GKETKIKVVKNKVAPPFK A VEIMYGEGISRTGELVKIA+DLDI Sbjct: 241 NTQIKGTGDQKDTNVGKETKIKVVKNKVAPPFKEAMVEIMYGEGISRTGELVKIATDLDI 30- 0 Query: 301 IQKAGAWFSYNGEKIGQGSENAKRYLADHPELFDEIDLKVRVKFGLLEESEEESAMAVAS 36- 0 IQKAGAW+SYNGEKIGQGSENAK++LADHPE+FDEID KVRV FGL+E+ E ++ Sbjct: 301 IQKAGAWYSYNGEKIGQGSENAKKFLADHPEIFDEIDHKVRVHFGLIEKDEAVKSLDKTE 36- 0 Query: 361 EE---TDDLALDLDNGIEIED 378 E +++ LDLD+ IEIED Sbjct: 361 EAAPVVEEVTLDLDDAIEIED 381 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03245 Identities = 339/379 (89%), Positives = 356/379 (93%), Gaps = 1/379 (0%) Query: 1 MAKKTKKAEEITKKFGDERRKALDDALKNIEKDFGKGAVMRLGERAEQKVQVMSSGSLAL 60 +AKK KK EEITKKFGDERRKALDDALKNIEKDFGKGAVMRLGERAEQKVQVMSSGSLAL Sbjct: 1 LAKKLKKNEEITKKFGDERRKALDDALKNIEKDFGKGAVMRLGERAEQKVQVMSSGSLAL 60 Query: 61 DIALGAGGYPKGRIVEIYGPESSGKTTVALHAVAQAQKEGGIAAFIDAEHALDPAYAAAL 120- DIALGAGGYPKGRI+EIYGPESSGKTTVALHAVAQAQKEGGIAAFIDAEHALDPAYAAAL Sbjct: 61 DIALGAGGYPKGRIIEIYGPESSGKTTVALHAVAQAQKEGGIAAFIDAEHALDPAYAAAL 120- Query: 121 GVNIDELLLSQPDSGEQGLEIAGKLIDSGAVDLVVVDSVAALVPRAEIDGDIGDSHVGLQ 18- 0 GVNIDELLLSQPDSGEQGLEIAGKLIDSGAVDLVVVDSVAALVPRAEIDGDIGDSHVGLQ Sbjct: 121 GVNIDELLLSQPDSGEQGLEIAGKLIDSGAVDLVVVDSVAALVPRAEIDGDIGDSHVGLQ 18- 0 Query: 181 ARMMSQAMRKLSASINKTKTIAIFINQLREKVGVMFGNPETTPGGRALKFYSSVRLDVRG 24- 0 ARMMSQAMRKLSASINKTKTIAIFINQLREKVGVMFGNPETTPGGRALKFY+SVRLDVRG Sbjct: 181 ARMMSQAMRKLSASINKTKTIAIFINQLREKVGVMFGNPETTPGGRALKFYASVRLDVRG 24- 0 Query: 241 NTQIKGTGEHKDHNVGKETKIKVVKNKVAPPFREAFVEIMYGEGISRTGELIKIASDLDI 30- 0 TQIKGTG+ KD ++GKETKIKVVKNKVAPPF+ A VEIMYGEGISRTGEL+KIASDLDI Sbjct: 241 TTQIKGTGDQKDSSIGKETKIKVVKNKVAPPFKVAEVEIMYGEGISRTGELVKIASDLDI 30- 0 Query: 301 IQKAGAWYSYNGEKIGQGSENAKKYLADNPAIFDEIDHKVRVHFGMTEDDSPVQSELVEE 36- 0 IQKAGAW+SYNGEKIGQGSENAK+YLAD+P +FDEID KVRV FG+ E +S +S + Sbjct: 301 IQKAGAWFSYNGEKIGQGSENAKRYLADHPELFDEIDLKVRVKFGLLE-ESEEESAMAVA 35- 9 Query: 361 KNEADDLVLDLDNAIEIEE 379 E DDL LDLDN IEIE+ Sbjct: 360 SEETDDLALDLDNGIEIED 378 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1087 A DNA sequence (GBSx1162) was identified in S. agalactiae <SEQ ID 3355> hich encodes the amino acid sequence <SEQ ID 3356>. Analysis of this protein sequence reveals the following: TABLE-US-03246 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2344(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10259> which encodes amino acid sequence <SEQ ID 10260> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03247 >GP: AAG37358 GB: AF028804 NrpR [Lactococcus lactis subsp. cremoris] Identities = 69/132 (52%), Positives = 102/132 (77%) Query: 5 MIKIYTISSCTSCKKAKTWLNAHQLPYKEQNLGKESLTRDEILEILTKTESGIESIVSSK 64 MI IYT SCTSCKKAKTWL+ H +P+ E+NL + L+ EI +IL K + G+E ++SS+ Sbjct: 1 MITIYTAPSCTSCKKAKTWLSYHHIPFNERNLIADPLSTTEISQILQKCDDGVEGLISSR 60 Query: 65 NRYAKALNCNIEELSVNEVIDLIQENPRILKSPILIDDKRLQVGYKEDDIRAFLPRSIRN 124- NR+ K L + E++S+++ I +I ENP+I++ PI++D+KRL VGY E++IRAFLPR++R Sbjct: 61 NRFVKTLGVDFEDISLSQAIKIISENPQIMRRPIIMDEKRLHVGYNEEEIRAFLPRTVRV 120- Query: 125 VENAEARLRAAL 136 +EN ARLR+A+ Sbjct: 121 LENGGARLRSAI 132 A related DNA sequence was identified in S. pyogenes <SEQ ID 3357> which encodes the amino acid sequence <SEQ ID 3358>. Analysis of this protein sequence reveals the following: TABLE-US-03248 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2569(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03249 Identities = 117/132 (88%), Positives = 128/132 (96%) Query: 5 MIKIYTISSCTSCKKAKTWLNAHQLPYKEQNLGKESLTRDEILEILTKTESGIESIVSSK 64 MIKIYTISSCTSCKKAKTWLNAH+L YKEQNLGKE LT++EIL IL+KTE+G+ESIVSSK Sbjct: 1 MIKIYTISSCTSCKKAKTWLNAHKLAYKEQNLGKEPLTKEEILAILSKTENGVESIVSSK 60 Query: 65 NRYAKALNCNIEELSVNEVIDLIQENPRILKSPILIDDKRLQVGYKEDDIRAFLPRSIRN 124- NRYAKAL+C+IEELSV+EVIDLIQ+NPRILKSPILIDDKRLQVGYKEDDIRAFLPRSIRN Sbjct: 61 NRYAKALDCDIEELSVSEVIDLIQDNPRILKSPILIDDKRLQVGYKEDDIRAFLPRSIRN 120- Query: 125 VENAEARLRAAL 136 +EN EARLRAAL Sbjct: 121 IENTEARLRAAL 132 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1088 A DNA sequence (GBSx1163) was identified in S. agalactiae <SEQ ID 3359> which encodes the amino acid sequence <SEQ ID 3360>. Analysis of this protein sequence reveals the following: TABLE-US-03250 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3097(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03251 >GP: BAB04987 GB: AP001511 unknown [Bacillus halodurans] Identities = 49/82 (59%), Positives = 64/82 (77%), Gaps = 1/82 (1%) Query: 1 MGFTDETVRFRLDDSN-KVEISETLTAVYRSLEEKGYNPINQIVGYVLSGDPAYVPRYND 59 M D T++F +++ V++ E L +VY +LEEKGYNPINQIVGY+LSGDPAY+PR+ D Sbjct: 1 MSSMDNTMKFNVNEEPVSVDVQEVLMSVYEALEEKGYNPINQIVGYLLSGDPAYIPRHKD 60 Query: 60 ARNQIRKYERDEIVEELVRYYL 81 AR IRK ERDE++EELV+ YL Sbjct: 61 ARTLIRKLERDELIEELVKSYL 82 A related DNA sequence was identified in S. pyogenes <SEQ ID 3361> which encodes the amino acid sequence <SEQ ID 3362>. Analysis of this protein sequence reveals the following: TABLE-US-03252 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3097(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03253 Identities = 80/88 (90%), Positives = 85/88 (95%) Query: 1 MGFTDETVRFRLDDSNKVEISETLTAVYRSLEEKGYNPINQIVGYVLSGDPAYVPRYNDA 60 MGFTDETVRF+LDD +K +ISETLTAVY SL+EKGYNPINQIVGYVLSGDPAYVPRYNDA Sbjct: 1 MGFTDETVRFKLDDGDKRQISETLTAVYHSLDEKGYNPINQIVGYVLSGDPAYVPRYNDA 60 Query: 61 RNQIRKYERDEIVEELVRYYLQGNGIDL 88 RNQIRKYERDEIVEELVRYYLQGNGID+ Sbjct: 61 RNQIRKYERDEIVEELVRYYLQGNGIDV 88 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1089 A DNA sequence (GBSx1164) was identified in S. agalactiae <SEQ ID 3363> which encodes the amino acid sequence <SEQ ID 3364>. Analysis of this protein sequence reveals the following: TABLE-US-03254 Possible Site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1575(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10257> which encodes amino acid sequence <SEQ ID 10258> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03255 >GP: CAB14698 GB: Z99118 similar to hypothetical proteins [Bacillus subtilis] Identities = 82/138 (59%), Positives = 109/138 (78%), Gaps = 1/138 (0%) Query: 1 MRIMGLDVGSKTVGVAISDPLGFTAQGLEIIKIDEESGNFGFDRLAELVKEYKVDKFVVG 60 MRI+GLD+G+KT+GVA+SD +G+TAQG+E IKI+E G++G RL+EL+K+Y +DK V+G Sbjct: 1 MRILGLDLGTKTLGVALSDEMGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLG 60 Query: 61 LPKNMNNTSGPRVEASQAYGDKITELFNLPVEYQDERLTTVQAERMLVEQADISRGKRKK 120- PKNMN T GPR EASQ + + +N+PV DERLTT+ AE+ML+ AD+SR KRKK Sbjct: 61 FPKNMNGTVGPRGEASQTFAKVLETTYNVPVVLWDERLTTMAAEKMLI-AADVSRQKRKK 119- Query: 121 VIDKLAAQLILQNYLDRM 138 VIDK+AA +ILQ YLD + Sbjct: 120 VIDKMAAVMILQGYLDSL 137 A related DNA sequence was identified in S. pyogenes <SEQ ID 3365> which encodes the amino acid sequence <SEQ ID 3366>. Analysis of this protein sequence reveals the following:

TABLE-US-03256 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1575(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03257 Identities = 114/139 (82%), Positives = 126/139 (90%) Query: 1 MRIMGLDVGSKTVGVAISDPLGFTAQGLEIIKIDEESGNFGFDRLAELVKEYKVDKFVVG 60 MRIMGLDVGSKTVGVAISDPLGFTAQGLEIIKIDEE FGF RL ELVK+Y+V++FV+G Sbjct: 1 MRIMGLDVGSKTVGVAISDPLGFTAQGLEIIKIDEEKAEFGFTRLEELVKQYQVEQFVIG 60 Query: 61 LPKNMNNTSGPRVEASQAYGDKITELFNLPVEYQDERLTTVQAERMLVEQADISRGKRKK 120- LPKNMNNT+GPRV+AS YG+ I LF LPV YQDERLTTV+A+RML+EQADISRGKRKK Sbjct: 61 LPKNMNNTNGPRVDASITYGNHIEHLFGLPVHYQDERLTTVEAKRMLIEQADISRGKRKK 120- Query: 121 VIDKLAAQLILQNYLDRMF 139 VIDKLAAQLILQNYL+R F Sbjct: 121 VIDKLAAQLILQNYLNRNF 139 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1090 A DNA sequence (GBSx1165) was identified in S. agalactiae <SEQ ID 3367> which encodes the amino acid sequence <SEQ ID 3368>. Analysis of this protein sequence reveals the following: TABLE-US-03258 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2631(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03259 >GP: CAB14697 GB: Z99118 yrzB [Bacillus subtilis] Identities = 50/94 (53%), Positives = 65/94 (68%), Gaps = 5/94 (5%) Query: 12 EHQHEVITLVDENGNETLFEILLTIDGREEFGKNYVLLVPAGAEEDEQGEIEIQAYSFTE 71 - EH + IT+VD+ GNE L E+L T + EEFGK+YVL P +++DE E+EI A SFT Sbjct: 2 EHGEKNITIVDDQGNEQLCEVLFTFEN-EEFGKSYVLYYPIESKDDE--EVEILASSFTP 58 Query: 72 NADGTEGDLQPIPEDSDAEWDMIEEVFNSFLDEE 105 N DG G+L PI ++D EWDMIEE N+FL +E Sbjct: 59 NEDGENGELFPI--ETDEEWDMIEETLNTFLADE 90 A related DNA sequence was identified in S. pyogenes <SEQ ID 3369> which encodes the amino acid sequence <SEQ ID 3370>. Analysis of this protein sequence reveals the following: TABLE-US-03260 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3170(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03261 Identities = 90/98 (91%), Positives = 94/98 (95%) Query: 7 HDHNHEHQHEVITLVDENGNETLFEILLTIDGREEFGKNYVLLVPAGAEEDEQGEIEIQA 66 H+H ++HQHEVITLVDE GNETLFEILLTIDGREEFGKNYVLLVPAG+EEDE GEIEIQA Sbjct: 3 HNHENDHQHEVITLVDEQGNETLFEILLTIDGREEFGKNYVLLVPAGSEEDESGEIEIQA 62 Query: 67 YSFTENADGTEGDLQPIPEDSDAEWDMIEEVFNSFLDE 104 YSFTEN DGTEGDLQPIPEDSDAEWDMIEEVFNSFLDE Sbjct: 63 YSFTENEDGTEGDLQPIPEDSDAEWDMIEEVFNSFLDE 100 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1091 A DNA sequence (GBSx1166) was identified in S. agalactiae <SEQ ID 3371> which encodes the amino acid sequence <SEQ ID 3372>. Analysis of this protein sequence reveals the following: TABLE-US-03262 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2059(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1092 A DNA sequence (GBSx1167) was identified in S. agalactiae <SEQ ID 3373> which encodes the amino acid sequence <SEQ ID 3374>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following: TABLE-US-03263 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.18 Transmembrane 314-330 (308-334) INTEGRAL Likelihood = -6.21 Transmembrane 279-295 (274-300) INTEGRAL Likelihood = -6.10 Transmembrane 136-152 (135-157) INTEGRAL Likelihood = -5.31 Transmembrane 232-248 (226-253) INTEGRAL Likelihood = -4.73 Transmembrane 163-179 (162-180) INTEGRAL Likelihood = -3.13 Transmembrane 95-111 (94-119) INTEGRAL Likelihood = -3.03 Transmembrane 386-402 (386-405) INTEGRAL Likelihood = -2.18 Transmembrane 204-220 (204-221) INTEGRAL Likelihood = -2.13 Transmembrane 40-56 (40-57) INTEGRAL Likelihood = -1.70 Transmembrane 186-202 (182-202) ----- Final Results ----- bacterial membrane --- Certainty = 0.4673(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10255> which encodes amino acid sequence <SEQ ID 10256> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 3375> which encodes the amino acid sequence <SEQ ID 3376>. Analysis of this protein sequence reveals the following: TABLE-US-03264 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.38 Transmembrane 315-331 (311-333) INTEGRAL Likelihood = -6.48 Transmembrane 40-56 (37-61) INTEGRAL Likelihood = -6.10 Transmembrane 278-294 (274-298) INTEGRAL Likelihood = -5.57 Transmembrane 392-408 (387-410) INTEGRAL Likelihood = -3.98 Transmembrane 186-202 (184-208) INTEGRAL Likelihood = -3.93 Transmembrane 339-355 (338-356) INTEGRAL Likelihood = -2.97 Transmembrane 235-251 (228-253) INTEGRAL Likelihood = -2.44 Transmembrane 166-182 (166-182) INTEGRAL Likelihood = -2.23 Transmembrane 106-122 (106-125) INTEGRAL Likelihood = -1.81 Transmembrane 83-99 (83-101) ----- Final Results ----- bacterial membrane --- Certainty = 0.3951(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9179> which encodes the amino acid sequence <SEQ ID 9180>. Analysis of this protein sequence reveals the following: TABLE-US-03265 Possible cleavage site: 13 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.38 Transmembrane 243-259 (239-261) INTEGRAL Likelihood = -6.10 Transmembrane 206-222 (202-226) INTEGRAL Likelihood = -5.57 Transmembrane 320-336 (315-338) INTEGRAL Likelihood = -3.98 Transmembrane 114-130 (112-136) INTEGRAL Likelihood = -3.93 Transmembrane 267-283 (266-284) INTEGRAL Likelihood = -2.97 Transmembrane 163-179 (156-181) INTEGRAL Likelihood = -2.44 Transmembrane 94-110 (94-110) INTEGRAL Likelihood = -2.23 Transmembrane 34-50 (34-53) ----- Final Results ----- bacterial membrane --- Certainty = 0.395(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03266 Identities = 200/480 (41%), Positives = 310/480 (63%), Gaps = 1/480 (0%) Query: 40 ILLYSVLSTLLAIANPLLTYFANGLQTQNLYTGLMMTKGQIPYSDVFATGGFLYYVTIAL 99 - +L +S++ + L IA P LT ANGLQ+QNLY G+M+TKGQ+PYS F TGG Y+V IAL Sbjct: 40 LLFFSIIISSLTIAVPFLTDAANGLQSQNLYIGMMLTKGQLPYSAAFTTGGLFYFVIIAL 99 Query: 100 SYLLGSSIWLLIVQFIAYYVSGIYFYKLVYYVAQSEIVSIGMTLIFYIMNIVLGFGGMYP 15- 9 SY LGS++WL+ VQ +Y+SG+Y YKL+ Y+ + V++ ++ +Y++++ LGFGG+YP Sbjct: 100 SYYLGSTLWLVFVQVFCFYLSGLYLYKLINYMTGFQKVALTFSISYYLLSVSLGFGGLYP 15- 9 Query: 160 IQWALPFMLISLWFLIKFCVDNIVDEAFIFYGILAAFSLFIDPQTLIFWLCSFVLLTATN 21- 9 Q A+PF+LIS WFL K+ + DEAFI +G + A ++ IDP TLIFW + V + + N Sbjct: 160 TQLAMPFILISAWFLTKYFACLVKDEAFILFGFVGALAMLIDPSTLIFWSFACVTVFSYN 21- 9 Query: 220 IKQKQSLRGFYQFLCVVFGMILIAYTVGYFMFNLQIISSYIDKAIFYPFTYFARTNHSFL 27- 9 I QK RGFYQ L +FGMIL+ YT GYF+ NLQ+++ Y+ + + YPFT+F N S L Sbjct: 220 ISQKHLARGFYQLLASIFGMILVFYTAGYFILNLQVLNPYLSQTMIYPFTFFKSGNLSLL 27- 9 Query: 280 LSLAIQIVVLLGSGCLFGLWDFIQNRKKASYQIGLNFIACIFIIYAIMAIFSRDFNLYHF 33- 9 LAIQ+ LG G L G+ + I+ K S ++ + + ++AIFS+D+ YH Sbjct: 280 FGLAIQLFFALGLGLLTGMENVIRRFKNNSDRVVKWLFVMVILESILVAIFSQDYRPYHL 33- 9 Query: 340 LPALPFGLLLTSNKITILYQKVIDRRSHRRQY-FSGKSLIVDLFVKKTYYLPLLLVSLSI 39- 8 LP LPFGL+LT+ + Y + + SHRR++ +G ++ +++K+ +YLP+L+V + Sbjct: 340 LPLLPFGLILTAIPVGYQYGIGLGQSSHRRRHGKNGVGRVMNIYLKRHFYLPILIVGTIL 39- 9 Query: 399 GLLVYNTYQNVTLSKERRDISHYLTTKIDRDGKIYVWDKVASIYSQTRLKSASQFVLPHI 45- 8 Y ++ L++ER I+ YL K+++ IYVWD + IY ++ KS SQF P I Sbjct: 400 ICSTYCFISSIPLNQERDHIASYLEQKLNKTQSIYVWDDTSKIYLDSKAKSVSQFSSPDI 45- 9 Query: 459 NTAQKNNEKILKDELLQHGAKYFILNKNEKLPNELKSDIKKHYQEVPLSNITHFVLYRFK 51- 8 NT ++++ KIL+DELL++ A Y ++N+ + LP ++ + +Y+ F++Y+ K Sbjct: 460 NTQKESHRKILEDELLENKAAYIVVNRYKNLPKIIQKVLSTNYKVDKQITTKSFIVYQKK 51- 9 A related GBS gene <SEQ ID 8727> and protein <SEQ ID 8728> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03267 Lipop: Possible site: -1 Crend: 0 SRCFLG: 0 McG: Length of UR: 34 Peak Value of UR: 2.23 Net Charge of CR: 0 McG: Discrim Score: 7.72 GvH: Signal Score (-7.5): -2.21 Possible site: 60 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 61 ALOM program count: 5 value: -9.18 threshold: 0.0 INTEGRAL Likelihood = -9.18 Transmembrane 174-190 (168-194) INTEGRAL Likelihood = -6.21 Transmembrane 139-155 (134-160) INTEGRAL Likelihood = -5.31 Transmembrane 92-108 (86-113) INTEGRAL Likelihood = -3.03 Transmembrane 246-262 (246-265) INTEGRAL Likelihood = -2.18 Transmembrane 64-80 (64-81) PERIPHERAL Likelihood = 3.29 194 modified ALOM score: 2.34 icm1 HYPID: 7 CFP: 0.467 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4673(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00076## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1093 A DNA sequence (GBSx1168) was identified in S. agalactiae <SEQ ID 3377> which encodes the amino acid sequence <SEQ ID 3378>. This protein is predicted to be anaerobic ribonucleotide reductase (nrdD). Analysis of this protein sequence reveals the following: TABLE-US-03268 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3722(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10253> which encodes amino acid sequence <SEQ ID 10254> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03269 >GP:AAD00215 GB:U73336 anaerobic ribonucleotide reductase [Lactococcus lactis subsp. cremoris] Identities = 539/725 (74%), Positives = 616/725 (84%), Gaps = 7/725 (0%) Query: 10 MTESDIKVIKRDGRLVSFDKYKIYTALLKASNKVIKMSPLVEAKLEMIADHVIAEIYNRF 69 - +T +I VIKRDGR V F+ KI+ AL KA+ KV V L + D V++EI++RF Sbjct: 10 VTLEEINVIKRDGRSVKFNSEKIFDALTKAAKKVELTDKSV---LSELTDRVVSEIFSRF 66 Query: 70 KDNIKIYEIQNIVEHKLLEANEYAIAQEYINYRTQRDFERSQATDINFSIGKLINKDQTV 129- +N+KIYEIQ+IVE +LLE+ E A+A+EYI+YR RD R++ATDINF+I KLIN+DQTV Sbjct: 67 SENVKIYEIQSIVEQELLESGETALAEEYISYRANRDLARTKATDINFTIEKLINRDQTV 126- Query: 130 VNENANKDSDVFNTQRDLTAGIVGKSIGLKMLPSHVANAHQKGDIHYHDLDYSPYTPMTN 18- 9 VNENANKDS+VFNTQRDLTAG V K+IGLK+LP HVANAHQKGDIHYHDLDYSP+T M N Sbjct: 127 VNENANKDSNVFNTQRDLTAGAVSKAIGLKLLPPHVANAHQKGDIHYHDLDYSPFTTMAN 18- 6 Query: 190 CCLIDFKGMLANGFKIGNAEVESPKSIQTATAQISQIIANVASSQYGGCTADRIDEFLAP 24- 9 CCLIDFK M NGFK+GNA+V+SPKSIQTATAQ SQIIANVASSQYGGC+ DR DE LAP Sbjct: 187 CCLIDFKNMFENGFKLGNAQVDSPKSIQTATAQASQIIANVASSQYGGCSFDRADEVLAP 24- 6 Query: 250 YAQLNYQKHLKDAKEWVIED-KQEDYARAKTQKDIYDAMQSLEYEINTLFTSNGQTPFTS 30- 8 YA+LNYQKHLKDA++W+ D K+E YAR KT KDIYDAMQSLEYEINTLFTSNGQTPF + Sbjct: 247 YAKLNYQKHLKDAQKWIDGDEKREAYAREKTAKDIYDAMQSLEYEINTLFTSNGQTPFVT 30- 6 Query: 309 LGFGLGTNWFEREIQKAILKIRIQGLGSEHRTAIFPKLIFTLKKGLNLEEDSPNYDIKQL 36- 8 +GFGLG +W+ REIQKAILK+RI GLGSEHRTAIFPKLIFTLK+GLNLE +PNYDIK+L Sbjct: 307 VGFGLGDDWYAREIQKAILKVRIGGLGSEHRTAIFPKLIFTLKRGLNLEVGTPNYDIKEL 36- 6 Query: 369 ALECATKRMYPDVLSYDKIIDLTGSFKAPMGCRSFLQGWRDANGQDVTSGRMNLGVVTVN 42- 8 ALEC+TKRMYPD+LSYDKI++LTGSFKA MGCRSFLQGW+DANG DVT+GR NLGVVTVN Sbjct: 367 ALECSTKRMYPDILSYDKIVELTGSFKASMGCRSFLQGWKDANGNDVTAGRNNLGVVTVN 42- 6 Query: 429 LPRVAMESNGDMDKFWEIFNERMSIARDALVYRVERVKEAIPANAPILYQYGAFGERLGK 48- 8 LPR+A+E+ G+ +KFWEIFNER+ IA DAL +RVER KEA P NAPIL+ GA G RL Sbjct: 427 LPRIALEAAGNKEKFWEIFNERVEIAHDALAFRVERAKEAQPKNAPILFMNGALG-RLDS 48- 5 Query: 489 YDNVDRLFNHRRATVSLGYIGLYEVASVFYGGDWEDNHQAKAFTVDIVRKMKQLCADWSD 54- 8 +VD L+N+ RATVSLGYIGLYEVA+ FYG WE N +AKAFT++IV++M + C DWS Sbjct: 486 EGSVDDLYNNERATVSLGYIGLYEVATTFYGPTWESNPEAKAFTIEIVKRMHEDCEDWSK 54- 5 Query: 549 EYDYHFSVYSTPSESLTDRFCRLDTEKFGIVTDITDKEYYTNSFHYDVRKNPTPFEKLDF 60- 8 YH+SVYSTPSESLTDRFCR+D EKFG V DITDK+YYTNSFHYDVRKNPTPFEKL+F Sbjct: 546 ASGYHYSVYSTPSESLTDRFCRMDKEKFGSVADITDKDYYTNSFHYDVRKNPTPFEKLEF 60- 5 Query: 609 EKIYPETGASGGFIHYCEYPVLQQNPKALEAVWDYAYDRVGYLGTNTPIDKCYQCQFEGD 66- 8 EK YP A+GGFIHYCEYPVLQQNPKALEAVWD+AYDR+GYLGTN PID CY C FEGD Sbjct: 606 EKDYP-VYANGGFIHYCEYPVLQQNPKALEAVWDFAYDRIGYLGTNAPIDHCYACGFEGD 66- 4 Query: 669 FTPTDRGFTCPNCGNSDPKTVDVVKRTCGYLGNPQARPMVNGRHKEISARVKHMNGS-SI 72- 7 FTPT+RGF CP CGN DPKT DVVKRTCGYLGNPQARPMV+GRHKEIS+RVKHMNGS Sbjct: 665 FTPTERGFKCPQCGNDDPKTCDVVKRTCGYLGNPQARPMVHGRHKEISSRVKHMNGSVGA 72- 4 Query: 728 KNQGN 732 N GN Sbjct: 725 LNDGN 729 A related DNA sequence was identified in S. pyogenes <SEQ ID 3379> which encodes the amino acid sequence <SEQ ID 3380>. Analysis of this protein sequence reveals the following: TABLE-US-03270 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2975(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03271 Identities = 641/731 (87%), Positives = 680/731 (92%) Query: 1 MMVLERERFMTESDIKVIKRDGRLVSFDKYKIYTALLKASNKVIKMSPLVEAKLEMIADH 60 M+ LE ++ + DIKVIKRDGRLV+FD KIY+ALLKAS KV +MSPLVEAKLE I+D Sbjct: 1 MVSLEEDKVTVQPDIKVIKRDGRLVNFDSTKIYSALLKASMKVTRMSPLVEAKLEAISDR 60 Query: 61 VIAEIYNRFKDNIKIYEIQNIVEHKLLEANEYAIAQEYINYRTQRDFERSQATDINFSIG 120- +IAEI RF NIKIYEIQNIVEHKLL ANEYAIA+EYINYRTQRDF RSQATDINFSI Sbjct: 61 IIAEIIERFPTNIKIYEIQNIVEHKLLAANEYAIAKEYINYRTQRDFARSQATDINFSID 120- Query: 121 KLINKDQTVVNENANKDSDVFNTQRDLTAGIVGKSIGLKMLPSHVANAHQKGDIHYHDLD 18- 0 KLINKDQTVVNENANKDSDVFNTQRDLTAGIVGKSIGLKMLPSHVANAHQKGDIHYHDLD Sbjct: 121 KLINKDQTVVNENANKDSDVFNTQRDLTAGIVGKSIGLKMLPSHVANAHQKGDIHYHDLD 18- 0 Query: 181 YSPYTPMTNCCLIDFKGMLANGFKIGNAEVESPKSIQTATAQISQIIANVASSQYGGCTA 24- 0 YSPYTPMTNCCLIDFKGMLANGFKIGNAEVESPKSIQTATAQISQIIANVASSQYGGCTA Sbjct: 181 YSPYTPMTNCCLIDFKGMLANGFKIGNAEVESPKSIQTATAQISQIIANVASSQYGGCTA 24- 0 Query: 241 DRIDEFLAPYAQLNYQKHLKDAKEWVIEDKQEDYARAKTQKDIYDAMQSLEYEINTLFTS 30- 0 DRIDEFLAPYA+LN++KH+ DAK+W++E K+E YA KTQKDIYDAMQSLEYEINTLFTS Sbjct: 241 DRIDEFLAPYAELNFKKHMADAKKWIVETKRESYAFEKTQKDIYDAMQSLEYEINTLFTS 30- 0 Query: 301 NGQTPFTSLGFGLGTNWFEREIQKAILKIRIQGLGSEHRTAIFPKLIFTLKKGLNLEEDS 36- 0 NGQTPFTSLGFGLGT+WFEREIQKAIL IRI GLGSEHRTAIFPKLIFT+K+GLNLE DS Sbjct: 301 NGQTPFTSLGFGLGTSWFEREIQKAILTIRINGLGSEHRTAIFPKLIFTVKRGLNLEPDS 36- 0 Query: 361 PNYDIKQLALECATKRMYPDVLSYDKIIDLTGSFKAPMGCRSFLQGWRDANGQDVTSGRM 42- 0 PNYDIK LALECATKRMYPD+LSYDKIIDLTGSFK+PMGCRSFLQGW+D NGQDVTSGRM Sbjct: 361 PNYDIKTLALECATKRMYPDMLSYDKIIDLTGSFKSPMGCRSFLQGWKDENGQDVTSGRM 42- 0 Query: 421 NLGVVTVNLPRVAMESNGDMDKFWEIFNERMSIARDALVYRVERVKEAIPANAPILYQYG 48- 0 NLGVVT+NLPR+AMESNGDMDKFWE+FNERM I++DAL+YRVERV EA PANAPILYQYG Sbjct: 421 NLGVVTLNLPRIAMESNGDMDKFWELFNERMLISKDALIYRVERVTEAKPANAPILYQYG 48- 0 Query: 481 AFGERLGKYDNVDRLFNHRRATVSLGYIGLYEVASVFYGGDWEDNHQAKAFTVDIVRKMK 54- 0 AFG+RL K NV+ LF +RRATVSLGYIGLYEVASVFYGG WE N AKAFT+ IV+ MK Sbjct: 481 AFGKRLEKTGNVNDLFKNRRATVSLGYIGLYEVASVFYGGQWEGNPDAKAFTLSIVKAMK 54- 0 Query: 541 QLCADWSDEYDYHFSVYSTPSESLTDRFCRLDTEKFGIVTDITDKEYYTNSFHYDVRKNP 60- 0 Q C DWSDEY YHFSVYSTPSESLTDRFCRLDTEKFGIVTDITDKEYYTNSFHYDVRK+P Sbjct: 541 QACEDWSDEYGYHFSVYSTPSESLTDRFCRLDTEKFGIVTDITDKEYYTNSFHYDVRKSP 60- 0 Query: 601 TPFEKLDFEKIYPETGASGGFIHYCEYPVLQQNPKALEAVWDYAYDRVGYLGTNTPIDKC 66- 0 TPFEKLDFEK YPE GASGGFIHYCEYPVLQQNPKALEAVWDYAYDRVGYLGTNTPIDKC Sbjct: 601 TPFEKLDFEKDYPEAGASGGFIHYCEYPVLQQNPKALEAVWDYAYDRVGYLGTNTPIDKC 66- 0 Query: 661 YQCQFEGDFTPTDRGFTCPNCGNSDPKTVDVVKRTCGYLGNPQARPMVNGRHKEISARVK 72- 0 Y CQFEGDFTPT+RGFTCPNCGN+DPKTVDVVKRTCGYLGNPQARPMVNGRHKEISARVK Sbjct: 661 YNCQFEGDFTPTERGFTCPNCGNNDPKTVDVVKRTCGYLGNPQARPMVNGRHKEISARVK 72- 0 Query: 721 HMNGSSIKNQG 731 HMNGS+IK G Sbjct: 721 HMNGSTIKYPG 731 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1094 A DNA sequence (GBSx1169) was identified in S. agalactiae <SEQ ID 3381> which encodes the amino acid sequence <SEQ ID 3382>. Analysis of this protein sequence reveals the following:

TABLE-US-03272 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5372(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 3383> which encodes the amino acid sequence <SEQ ID 3384>. Analysis of this protein sequence reveals the following: TABLE-US-03273 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6084(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03274 Identities = 28/47 (59%), Positives = 40/47 (84%), Gaps = 1/47 (2%) Query: 1 MGKYQLDYKGQAQVQKFHEKHSTGENANQKSRLKDLRKQFLEKAKKK 47 MGKYQLDYKG QV++FHEKHS + ++KSR+++L+ +FLEK+KK+ Sbjct: 1 MGKYQLDYKGMQQVERFHEKHSK-KKTDKKSRVQELKARFLEKSKKQ 46 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1095 A DNA sequence (GBSx1170) was identified in S. agalactiae <SEQ ID 3385> which encodes the amino acid sequence <SEQ ID 3386>. Analysis of this protein sequence reveals the following: TABLE-US-03275 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0436(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03276 >GP: CAB95794 GB: AL359949 putative oxidoreductase [Streptomyces coelicolor A3(2)] Identities = 91/299 (30%), Positives = 147/299 (48%), Gaps = 7/299 (2%) Query: 2 LQLGIVGLGGISQKAYLPYMRQVTGVHWHLFTRQKQILEEV--NMLFGSSTAYDSLDSLA 59 +++G +GLG I+QK YLP + + G+ HL TR L V + + + LD+L Sbjct: 1 MKVGCIGLGDIAQKGYLPVLAALPGIELHLQTRTPATLTRVADKLRIPPAQRHADLDALL 60 Query: 60 EHPLDGVFIHVATSAHFDIAKLFLKKGIPVFMDKPLTEDYTSTKALYDLAKDHKTFLMAG 119- LD F+H T+AH +I L+ G+P ++DKPL + ++ L LA++ T L G Sbjct: 61 AQGLDAAFVHAPTAAHPEIVTRLLEAGVPTYVDKPLAYELADSERLVTLAEERGTSLAVG 120- Query: 120 FNRRFAPRIMEMKKVEDKNHIRTFKNAVNAPADFQYKLFDMFIHPLDTALFLTNNVVKRG 17- 9 FNRR AP + + + I KN P D + + D FIH +DT FL V Sbjct: 121 FNRRHAPGYAQCAE-HPRELILMQKNRTGLPEDPRTMILDDFIHVVDTLRFLVPGPVDDV 17- 9 Query: 180 YFVTKRDGNKILQVSVTLETDSEIIEASMNLQSGSRREIIEIESPEVTYSLDDLSNLSVI 23- 9 + +G + V + L D MN SGS EI+E+ + + +L+ VI Sbjct: 180 TVRARTEGGLLHHVVLQLAGDGFTALGVMNRLSGSAEEILEVSGQDTKRQVVNLA--EVI 23- 7 Query: 240 DGFDRRAI-GFGSWASTLEKRGFEPMIDAFIQAITTGVNPISPKSSLLSHFICDQINKA 297- D + + G W +RG E + AF+ A+ +G +S + +L +H +C+++ +A Sbjct: 238 DHKGQPTVRRRGDWVPVARQRGIEQAVLAFLDAVRSG-EVLSARDALATHELCERVVRA 295- A related DNA sequence was identified in S. pyogenes <SEQ ID 3387> which encodes the amino acid sequence <SEQ ID 3388>. Analysis of this protein sequence reveals the following: TABLE-US-03277 Possible site: 57 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03278 >GP: AAF96942 GB: AE004430 oxidoreductase, Gfo/Idh/MocA family [Vibrio cholerae] Identities = 103/304 (33%), Positives = 158/304 (51%), Gaps = 11/304 (3%) Query: 4 LNIGIVGLGAISQKAYLPYMRQLSDITWHLSTRNAAVRQQVGQLFGHAILYSDVKELSKT 63 + I ++GLG I+QKAYLP + Q DI L TRN V + + + +D +++ + Sbjct: 1 MKIAMIGLGDIAQKAYLPVLAQWPDIELVLCTRNPKVLGTLATRYRVSATCTDYRDVLQY 60 Query: 64 NLDGVFIHAATSAHAELASLFLNQGIPVFMDKPIADNYLMTKNLYDLAKENQTFLMAGFN 123- +D V IHAAT H+ LA+ FL+ GIP F+DKP+A + +NLY+LA+++ L GFN Sbjct: 61 GVDAVMIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFN 120- Query: 124 RRFTPRVKK-LSSLSTK-----RKVAVEKNDLNRPGDMTFKLFDFFIHPLDTALFLTEGT 17- 7 RR P + LS L+ + R + EK+ PGD+ +FD FIHPLD+ + Sbjct: 121 RRHIPLYNQHLSELAQQECGALRSLRWEKHRHALPGDIRTFVFDDFIHPLDSVNLSRQCN 18- 0 Query: 178 LLKGHFQYHLEAGLLSQVMVTLMTESMTTTASMNLQSGSRREVMEVQRAEETYHLENLDE 23- 7 L H YH+ GLL+++ V T ASMN Q G E + Y ++ + Sbjct: 181 LDDLHLTYHMSEGLLARLDVQWQTGDTLLHASMNRQFGITTEHVTASYDNVAYLFDSFTQ 24- 0 Query: 238 LSIYKGTEKRVLGFASWDTTLHKRGFETMIDAFLEAISTGVNPVS-PESSLLSHW----I 29- 2 +++ ++ + W L +GF+ M+ +L+ + G P E +L SH I Sbjct: 241 GKMWRDNQESRVALKDWTPMLASKGFDAMVQDWLQVAAAGKLPTHIIERNLASHQLAEAI 30- 0 Query: 293 CQQI 296 CQQI Sbjct: 301 CQQI 304 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03279 Identities = 168/308 (54%), Positives = 223/308 (71%) Query: 1 MLQLGIVGLGGISQKAYLPYMRQVTGVHWHLFTRQKQILEEVNMLFGSSTAYDSLDSLAE 60 ML +GIVGLG ISQKAYLPYMRQ++ + WHL TR + ++V LFG + Y + L++ Sbjct: 3 MLNIGIVGLGAISQKAYLPYMRQLSDITWHLSTRNAAVRQQVGQLFGHAILYSDVKELSK 62 Query: 61 HPLDGVFIHVATSAHFDIAKLFLKKGIPVFMDKPLTEDYTSTKALYDLAKDHKTFLMAGF 120- LDGVFIH ATSAH ++A LFL +GIPVFMDKP+ ++Y TK LYDLAK+++TFLMAGF Sbjct: 63 TNLDGVFIHAATSAHAELASLFLNQGIPVFMDKPIADNYLMTKNLYDLAKENQTFLMAGF 122- Query: 121 NRRFAPRIMEMKKVEDKNHIRTFKNAVNAPADFQYKLFDMFIHPLDTALFLTNNVVKRGY 18- 0 NRRF PR+ ++ + K + KN +N P D +KLFD FIHPLDTALFLT + +G+ Sbjct: 123 NRRFTPRVKKLSSLSTKRKVAVEKNDLNRPGDMTFKLFDFFIHPLDTALFLTEGTLLKGH 18- 2 Query: 181 FVTKRDGNKILQVSVTLETDSEIIEASMNLQSGSRREIIEIESPEVTYSLDDLSNLSVID 24- 0 F + + QV VTL T+S ASMNLQSGSRRE++E++ E TY L++L LS+ Sbjct: 183 FQYHLEAGLLSQVMVTLMTESMTTTASMNLQSGSRREVMEVQRAEETYHLENLDELSIYK 24- 2 Query: 241 GFDRRAIGFGSWASTLEKRGFEPMIDAFIQAITTGVNPISPKSSLLSHFICDQINKANAP 30- 0 G ++R +GF SW +TL KRGFE MIDAF++AI+TGVNP+SP+SSLLSH+IC QI + Sbjct: 243 GTEKRVLGFASWDTTLHKRGFETMIDAFLEAISTGVNPVSPESSLLSHWICQQIADSQLS 30- 2 Query: 301 FGMLNLKI 308 +G L +++ Sbjct: 303 YGELTVEL 310 SEQ ID 3386 (GBS309) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 68 (lane 10; MW 63 kDa). GBS309-GST was purified as shown in FIG. 212, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1096 A DNA sequence (GBSx1171) was identified in S. agalactiae <SEQ ID 3389> which encodes the amino acid sequence <SEQ ID 3390>. Analysis of this protein sequence reveals the following: TABLE-US-03280 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2983(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03281 >GP: BAB04222 GB: AP001508 unknown conserved protein in others [Bacillus halodurans] Identities = 52/129 (40%), Positives = 70/129 (53%), Gaps = 5/129 (3%) Query: 39 FEDWLDHNLNMELGVGVPDNFVPYIQFVSFDNDNNAIGFLNLRLRLNDTLLEKGGHIGYS 98 - FE L + + GV +P N V + IG +N+R LND L +GGHIGY Sbjct: 43 FEHLLKTLKDYQHGVNLPANRVANTTYWLVHEQKRLIGAINIRHTLNDWLHHRGGHIGYG 102- Query: 99 IRPRQRGKGYAKEQLKLGIEQAHLKNINEILVTCHVDNDASKSVILANGGVLEDCLHQ-- 156- IRP +RGKGYA LKLG+E+A + ++L+TC +N S I NGGVL+ + Sbjct: 103 IRPSERGKGYATLMLKLGLEKAAALGLEKVLITCDKENLPSARTIQRNGGVLDSEVVDER 16- 2 Query: 157 ---TERYWI 162 +RYWI Sbjct: 163 GIAIQRYWI 171 A related DNA sequence was identified in S. pyogenes <SEQ ID 3391> which encodes the amino acid sequence <SEQ ID 3392>. Analysis of this protein sequence reveals the following: TABLE-US-03282 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2195(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03283 Identities = 90/164 (54%), Positives = 115/164 (69%), Gaps = 4/164 (2%) Query: 1 MKLRRPVLEDKEEILAMYKEFQKESSSVDG--GFYEPTMHFEDWLDHNLNMELGVGVPDN 58 M++RRP L+DK+ +L+M EF ++ S+ DG F ++E WL+ +L E+G+ Sbjct: 1 MEIRRPTLKDKDAVLSMINEFLEQKSATDGLWHFNVNDFNYETWLEDSLRQEMGLS--SQ 58 Query: 59 FVPYIQFVSFDNDNNAIGFLNLRLRLNDTLLEKGGHIGYSIRPRQRGKGYAKEQLKLGIE 118- VP IQ+V+FD + AIGFLNLRLRLN+ LLEKGGHIGYS+RP QRGKGYAKE LK + Sbjct: 59 GVPAIQYVAFDERSQAIGFLNLRLRLNERLLEKGGHIGYSVRPSQRGKGYAKEMLKQAVS 118- Query: 119 QAHLKNINEILVTCHVDNDASKSVILANGGVLEDCLHQTERYWI 162 A KNI ILVTC N AS++VI+AN G+LED TERYWI Sbjct: 119 YAISKNITTILVTCDETNVASRAVIVANVGILEDSRGGTERYWI 162 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1097 A DNA sequence (GBSx1172) was identified in S. agalactiae <SEQ ID 3393> which encodes the amino acid sequence <SEQ ID 3394>. This protein is predicted to be anaerobic ribonucleotide reductase activator protein (nrdG). Analysis of this protein sequence reveals the following: TABLE-US-03284 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4239(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03285 >GP: AAD00216 GB: U73336 anaerobic ribonucleotide reductase activator protein [Lactococcus lactis subsp. cremoris] Identities = 152/198 (76%), Positives = 176/198 (88%) Query: 8 NTPKPGEWKSEELSHGHIIDYKAFNFVDGEGVRNSLYVAGCMFHCKGCYNTATWSFRAGI 67 N PKPGEW+++ELS +I DYK FNFVDGEGVR SLYV+GCMFHC+GCYN ATWSFR G Sbjct: 2 NNPKPGEWRADELSQNYIADYKPFNFVDGEGVRCSLYVSGCMFHCEGCYNQATWSFRYGR 61 Query: 68 PYTKELEDQIMTDLEQPYVQGLTLLGGEPFLNTGILLPLLQRIRRELPEKDIWSWTGYTW 127- PYTKELED+IM DL +PYVQGLTLLGGEPFLNT L+PLL+RIRRELP+KDIWSWTGYTW Sbjct: 62 PYTKELEDKIMADLAEPYVQGLTLLGGEPFLNTTFLIPLLKRIRRELPDKDIWSWTGYTW 121- Query: 128 EEMMLETQDKLEMLSLIDILVDGRFDQSKRNLMLQFRGSSNQRIIDVQKSLKEGEVVIWE 18- 7 EEMMLET DKLEML L+D+LVDGRF+ SK+NLMLQFRGSSNQRIIDV KS +G+VVIWE Sbjct: 122 EEMMLETDDKLEMLDLLDVLVDGRFELSKKNLMLQFRGSSNQRIIDVPKSRSKGQVVIWE 18- 1 Query: 188 GLNDGDNSYEQVKRDDLL 205 LNDG+N++EQ+ ++ L+ Sbjct: 182 KLNDGENNFEQIHKEKLI 199 A related DNA sequence was identified in S. pyogenes <SEQ ID 3395> which encodes the amino acid sequence <SEQ ID 3396>. Analysis of this protein sequence reveals the following: TABLE-US-03286 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4111(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03287 Identities = 167/202 (82%), Positives = 186/202 (91%) Query: 4 EASWNTPKPGEWKSEELSHGHIIDYKAFNFVDGEGVRNSLYVAGCMFHCKGCYNTATWSF 63 E WN PKP EW++EELS G IIDYKAFNFVDGEGVRNSLYV+GC+FHCKGCYN ATWSF Sbjct: 4 EKCWNNPKPKEWQAEELSQGRIIDYKAFNFVDGEGVRNSLYVSGCLFHCKGCYNAATWSF 63 Query: 64 RAGIPYTKELEDQIMTDLEQPYVQGLTLLGGEPFLNTGILLPLLQRIRRELPEKDIWSWT 123- +AG+PYT+ELE+QIMTDL QPYVQGLTLLGGEPFLNTGIL+PL++RIRRELPEKDIWSWT Sbjct: 64 KAGMPYTQELEEQIMTDLAQPYVQGLTLLGGEPFLNTGILIPLIKRIRRELPEKDIWSWT 123- Query: 124 GYTWEEMMLETQDKLEMLSLIDILVDGRFDQSKRNLMLQFRGSSNQRIIDVQKSLKEGEV 18- 3 GYTWEEMMLET DKLEMLSLIDILVDGRFD +K+NLMLQFRGSSNQRIIDVQKSL EV Sbjct: 124 GYTWEEMMLETPDKLEMLSLIDILVDGRFDITKKNLMLQFRGSSNQRIIDVQKSLAAKEV 18- 3 Query: 184 VIWEGLNDGDNSYEQVKRDDLL 205 +IW+ LNDGD ++EQ+ R+DLL Sbjct: 184 IIWDKLNDGDQTFEQISREDLL 205 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1098 A DNA sequence (GBSx1173) was identified in S. agalactiae <SEQ ID 3397> which encodes the amino acid sequence <SEQ ID 3398>. Analysis of this protein sequence reveals the following: TABLE-US-03288 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.03 Transmembrane 102-118 (101-119) ----- Final Results ----- bacterial membrane --- Certainty = 0.2211(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03289 >GP: AAD24446 GB: AF118389 unknown [Streptococcus suis] Identities = 97/240 (40%), Positives = 151/240 (62%), Gaps = 1/240 (0%) Query: 2 IKILIPTAKEMKV-CQNIAWPKLSAQTKIIIDYFSTLTVSDLEDIYRINTSAARCEAQRW 60 +KI+IP AKE+ +N ++ LS ++K ++D S V + Y++N + A EA RW Sbjct: 1 MKIIIPNAKEVNTNLENASFYLLSDRSKPVLDAISQFDVKKMAAFYKLNEAKAELEADRW 60 Query: 61 QDFKAKQLTLNPAIKLFNGLMYRNIKRHNLSTSEAQFMENSVFITSALYGIIPAMTLISP 120- + Q PA +L++GLMYR + R + + E ++ + V + +ALYG+I ISP Sbjct: 61 YRIRTGQAKTYPAWQLYDGLMYRYMDRRGIDSKEENYLRDHVRVATALYGLIHPFEFISP 120- Query: 121 HRLDFNTKIKINNNSLKVFWRENYDTFMQSDDIMVSLLSNEFETVFSPKERQKLIHLNFI 18- 0 HRLDF +KI N SLK +WR YD + D++++SL S+EFE VFSP+ +++L+ + F+ Sbjct: 121 HRLDFQGSLKIGNQSLKQYWRPYYDQEVGDDELILSLASSEFEQVFSPQIQKRLVKILFM 18- 0 Query: 181 EDRDGQLKTHSTISKKARGKCLTAMMENNCQTLEHLKQLRFDGFCYDNELSDSKQLTFVK 24- 0 E++ GQLK HSTISKK RG+ L+ + +NN Q L ++ + DGF Y S + QLTF++ Sbjct: 181 EEKAGQLKVHSTISKKGRGRLLSWLAKNNIQELSDIQDFKVDGFEYCTSESTANQLTFIR 24- 0 A related GBS nucleic acid sequence <SEQ ID 10941> which encodes amino acid sequence <SEQ ID 10942> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 3399> which encodes the amino acid sequence <SEQ ID 3400>. Analysis of this protein sequence reveals the following: TABLE-US-03290 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3759(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03291 Identities = 114/242 (47%), Positives = 155/242 (63%) Query: 1 MIKILIPTAKEMKVCQNIAWPKLSAQTKIIIDYFSTLTVSDLEDIYRINTSAARCEAQRW 60 M+ LIPTAKEM + + L ++ I+ + +T DL YRI +A+ E QRW Sbjct: 1 MLTFLIPTAKEMTIPKESHPHLLPQDSQAILKIMAAMTTEDLAKSYRIKEESAKKEQQRW 60 Query: 61 QDFKAKQLTLNPAIKLFNGLMYRNIKRHNLSTSEAQFMENSVFITSALYGIIPAMTLISP 120- QD ++Q PA +LFNGLMYR+IKR L+T E ++ V+ITS+ YGIIPA I+ Sbjct: 61 QDMASQQSLAYPAYQLFNGLMYRHIKRDKLTTQEQAYLTQQVYITSSFYGIIPANHPIAE 120- Query: 121 HRLDFNTKIKINNNSLKVFWRENYDTFMQSDDIMVSLLSNEFETVFSPKERQKLIHLNFI 18- 0 HR DF+T+IKI SLK +WR Y+ F + ++SLLS+EF+ VFS +Q I F+ Sbjct: 121 HRHDFHTRIKIEGQSLKSYWRPCYNQFAKEHPQVISLLSSEFDDVFSKDCKQLWISPKFM 18- 0 Query: 181 EDRDGQLKTHSTISKKARGKCLTAMMENNCQTLEHLKQLRFDGFCYDNELSDSKQLTFVKKQ - 242 +++GQ KTHSTISKKARG LTA MENNCQT++ LK L F GF Y +LS + ++KK+ Sbjct: 181 AEKEGQFKTHSTISKKARGAFLTACMENNCQTVDSLKSLVFAGFYYHPDLSTDHEFVYIKKK - 242 SEQ ID 3398 (GBS428) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 80 (lane 6; MW 30.4 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 173 (lane 4; MW 55 kDa). GBS428-GST was purified as shown in FIG. 220, lane 6-7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1099 A DNA sequence (GBSx1174) was identified in S. agalactiae <SEQ ID 3401> which encodes the amino acid sequence <SEQ ID 3402>. Analysis of this protein sequence reveals the following:

TABLE-US-03292 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.59 Transmembrane 3-19 (3-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.1235(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10251> which encodes amino acid sequence <SEQ ID 10252> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03293 >GP: BAB07024 GB: AP001518 unknown conserved protein [Bacillus halodurans] Identities = 86/275 (31%), Positives = 143/275 (51%), Gaps = 6/275 (2%) Query: 17 MSYPYKANHSIESITLKVNDLENLVNFYSDIIGLTVIDKSSTRALLGVNQKIPLIILEKT 76 - M + + N ++ + +KV+DL + FY +IIG V+++S A L N + PL+++E+ Sbjct: 1 MEFHRQPNTFVDLVNIKVSDLSRALTFYQEIIGFQVLERSERSATLTANGRTPLLVIEQP 60 Query: 77 E---LEKHSTYGLYHTAILVPDEYHLSLALNHLLSQHIPLEGGADHGYSNAIYLSDPEGN 133- + ++ T GLYH A+L+P L LNHLL PL+G +DH S AIY +DP+GN Sbjct: 61 DPVIAKQPRTTGLYHFALLLPSRADLGRFLNHLLQSGYPLQGASDHLVSEAIYFADPDGN 120- Query: 134 GIEIYNDKDISMWDIRESGQIIGITERLDIDNLLDSLVNVPNNYKLSEKTSIGHIHLSVK 19- 3 G+E+Y D+ S WD +G++ TE + +NLL + P L +T +GHIHL V Sbjct: 121 GVEVYADRPSSSWD-WSNGEVKMSTEPIHAENLLAEGKDEPWT-ALPPETILGHIHLHVA 17- 8 Query: 194 DAKISSKLYQNVFGLDEKFAIPT-ASWIASGNYHHHLAFNNWAGPNLSKNQEDRPGISLL 25- 2 + + Y G + + A +I++GNYHHH+ N W G E G+ Sbjct: 179 NLFEAETFYIEGLGFNVVARLGNQALFISTGNYHHHIGLNTWNGVGAPTPPENSVGLKWF 23- 8 Query: 253 TIAYNDDNLFRDSLKKAQLYQLTFLEKQDHYYIIE 287 ++ Y + + ++ + + K ++I+ Sbjct: 239 SLTYPSEEVRAKTVNRLETIGFQVERKHGEEWVID 273 A related DNA sequence was identified in S. pyogenes <SEQ ID 3403> which encodes the amino acid sequence <SEQ ID 3404>. Analysis of this protein sequence reveals the following: TABLE-US-03294 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0936(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03295 Identities = 143/282 (50%), Positives = 194/282 (68%) Query: 17 MSYPYKANHSIESITLKVNDLENLVNFYSDIIGLTVIDKSSTRALLGVNQKIPLIILEKT 76 - M YPY + S+ +++L V DL + FY+ IIGL V+ + +T L + K ++ L +T Sbjct: 1 MIYPYNSTISLGTVSLNVTDLAKMTTFYTSIIGLQVLSQDTTSRQLTTDGKTVILELRQT 60 Query: 77 ELEKHSTYGLYHTAILVPDEYHLSLALNHLLSQHIPLEGGADHGYSNAIYLSDPEGNGIE 136- L YGLYHTA LVPD + L L LNH L++ I LEG ADHG+S AIYLSDPEGNGIE Sbjct: 61 PLPGDKAYGLYHTAFLVPDRHSLGLVLNHFLTRSISLEGAADHGHSEAIYLSDPEGNGIE 120- Query: 137 IYNDKDISMWDIRESGQIIGITERLDIDNLLDSLVNVPNNYKLSEKTSIGHIHLSVKDAK 19- 6 IY+DK + WDIR++GQIIG+TE D ++L+ L ++P ++ L++ T I H+HLSVK+A Sbjct: 121 IYHDKAVEHWDIRDNGQIIGVTEPTDTKSILEQLTDIPKHFLLAQDTRIRHVHLSVKNAL 18- 0 Query: 197 ISSKLYQNVFGLDEKFAIPTASWIASGNYHHHLAFNNWAGPNLSKNQEDRPGISLLTIAY 25- 6 SS LYQ VF L +K IP+ASWIASGNY+HHLAFN+W+ P L K+QE PG++ LTI Sbjct: 181 ASSLLYQKVFDLGDKMTIPSASWIASGNYYHHLAFNHWSAPYLKKHQEGAPGLAFLTIHI 24- 0 Query: 257 NDDNLFRDSLKKAQLYQLTFLEKQDHYYIIEDFDGIRIKVVL 298 LF +LKKA+L+ L L++ + ED +GIR+ V+L Sbjct: 241 ETPLLFSATLKKARLHGLAILQEDSSSFTTEDEEGIRVNVIL 282 SEQ ID 3402 (GBS429) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 80 (lane 7; MW 34.2 kDa). GBS429-His was purified as shown in FIG. 214, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1100 A DNA sequence (GBSx1175) was identified in S. agalactiae <SEQ ID 3405> which encodes the amino acid sequence <SEQ ID 3406>. Analysis of this protein sequence reveals the following: TABLE-US-03296 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2362(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10249> which encodes amino acid sequence <SEQ ID 10250> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03297 >GP: AAC21682 GB: U32686 conserved hypothetical protein [Haemophilus influenzae Rd] Identities = 89/261 (34%), Positives = 151/261 (57%), Gaps = 4/261 (1%) Query: 10 MVRLIFSDIDGTLINSNFKVTPKTRQGIKQIVAQGATFVPISARMPEAITPIMEQIGIDS 69 - M + +FSD +GTL+ S ++P+T IK++ A G FVPISAR P I P +Q+ ++ Sbjct: 2 MYKAVFSDFNGTLLTSQHTISPRTVVVIKRLTANGIPFVPISARSPLGILPYWKQLETNN 61 Query: 70 YIISYNGALIQDMQQKTIASHTMDGQVALQVCSYVSKHYSKIAWNVYRYHEWYSCDKENE 129- +++++GALI + + I S ++ + L++ + +++H + N Y ++ ++ D EN+ Sbjct: 62 VLVAFSGALILNQNLEPIYSVQIEPKDILEINTVLAEH-PLLGVNYYTNNDCHARDVENK 120- Query: 130 WVQKEEEIVGLQSKEMSLMELEKQDRIHKLLLMGEPSLMGELENTLKAQYPHLSIAQSAP 18- 9 WV E + ++ + HK+ ++GE + E+E LK ++PHLSI +S Sbjct: 121 WVIYERSVTKIEIHPFDEVATRSP---HKIQIIGEAEEIIEIEVLLKEKFPHLSICRSHA 17- 7 Query: 190 YFIEIMAPGIEKGKSAKTLADYLDISLADSIAFGDNYNDLNLLEIVGKGFVMGNAPKDLQ 24- 9 F+E+M KG + + L DY + + IAFGDN+NDL++LE VG G MGNAP +++ Sbjct: 178 NFLEVMHKSATKGSAVRFLEDYFGVQTNEVIAFGDNFNDLDMLEHVGLGVAMGNAPNEIK 23- 7 Query: 250 ERIGNVTQDNDNDGIYYALVE 270 + VT N+ DG+ L E Sbjct: 238 QAANVVTATNNEDGLALILEE 258 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1101 A DNA sequence (GBSx1176) was identified in S. agalactiae <SEQ ID 3409> which encodes the amino acid sequence <SEQ ID 3410>. Analysis of this protein sequence reveals the following: TABLE-US-03298 Possible site: 19 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03299 >GP: AAG07223 GB: AE004801 hypothetical protein [Pseudomonas aeruginosa] Identities = 103/283 (36%), Positives = 165/283 (57%), Gaps = 1/283 (0%) Query: 33 KHIGILQYVEHPSLTATRKGFIKELAKEGYKDGKNIKIEYKNAQGDQSNIQSISEKLIKD 92 - K + + VEHP+L A R G + L + GY+DGKN+K +Y++AQG+ I+ K I D Sbjct: 31 KSVAVTAIVEHPALDAARDGVKEALQEAGYEDGKNLKWQYQSAQGNTGTAAQIARKFIGD 90 Query: 93 NK-LVLGIATPAAQSLTTVSTETPILFTAVTDPVSAELVKSMKKPEGLATGTSDMSPIKK 151- +++GIATP+AQ+L + PI+F+ VTDPV A L S + TG SDM + K Sbjct: 91 KPDVIVGIATPSAQALVAATKSIPIVFSTVTDPVGAHLTPSWEASGTNVTGVSDMLALDK 150- Query: 152 QVSLLRKVMPKVKRVGIMYTTSERNSEVQVKQAKKIFQEAGIKTSVKGISSTNDVQDTAK 21- 1 Q+ L++KV+P KR+G++Y E NS V VK+ K++ + G+ + DV A+ Sbjct: 151 QIELIKKVVPGAKRIGMVYNPGEANSVVVVKELKELLPKMGLSLVEASAPRSVDVSSAAR 21- 0 Query: 212 SLMSKTEVIFVPTDNIIASSVTLLGNLSKELKVPVVGGSADMVPSGLLFSYGADYEALGR 27- 1 SL+ K + I+ TDN + S+ L + + K+P++ D V G + + G +Y+ +G+ Sbjct: 211 SLVGKVDAIYTNTDNNVVSAYEALVKVGNDAKIPLIASDTDSVKRGAIAALGINYKEMGK 27- 0 Query: 272 QTARQAVKILKGKDVAKVPSEYPQNLKVVVNEDMAKELGIDVS 314 QT R V+ILKG+ ++ E NL++ VN A++ G+ +S Sbjct: 271 QTGRMVVRILKGEKPGEIKPETSDNLQLFVNPGAAQKQGVTLS 313 There is also homology to SEQ ID 2712. SEQ ID 3410 (GBS188) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 39 (lane 2; MW 36.6 kDa). The GBS188-His fusion product was purified (FIG. 204, lane 6) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 247), FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1102 A DNA sequence (GBSx1177) was identified in S. agalactiae <SEQ ID 3411> which encodes the amino acid sequence <SEQ ID 3412>. This protein is predicted to be probable permease of ABC transporter (rbsC). Analysis of this protein sequence reveals the following: TABLE-US-03300 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -16.13 Transmembrane 132-148 (124-160) INTEGRAL Likelihood = -6.42 Transmembrane 241-257 (238-258) INTEGRAL Likelihood = -6.32 Transmembrane 264-280 (260-284) INTEGRAL Likelihood = -6.00 Transmembrane 213-229 (207-235) INTEGRAL Likelihood = -4.67 Transmembrane 58-74 (57-75) INTEGRAL Likelihood = -1.38 Transmembrane 36-52 (36-52) INTEGRAL Likelihood = -0.85 Transmembrane 90-106 (87-106) ----- Final Results ----- bacterial membrane --- Certainty = 0.7453(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03301 >GP: AAG07224 GB: AE004801 probable permease of ABC transporter [Pseudomonas aeruginosa] Identities = 114/285 (40%), Positives = 175/285 (61%), Gaps = 3/285 (1%) Query: 5 ILSGISQGLLWSIMAIGVFITFRILDIADLSAEGAFPMGAAVCALCIVNDINPIVATIAG 64 + + GL++S++A+GVFI+FR+L DL+ +G+FP+G AVCA I +P AT+A Sbjct: 6 LFGALEIGLIFSLVALGVFISFRLLRFPDLTVDGSFPLGGAVCATLIALGWDPYSATLAA 65 Query: 65 MLGGMLAGLVSGFLHTKMKIPALLTGIITLTGLYSINLLVLGRSNVSFALKNTLVTMVTR 124- G LAGL +G L+ K+KI LL I+ + LYSINL ++G+ NV + TL T++ Sbjct: 66 TAAGALAGLATGLLNVKLKIMDLLASILMMIALYSINLRIMGKPNVPLIAEPTLFTLLQP 125- Query: 125 LGLNKLSAVLLIGIVCVGLVILILYLFLNTQLGLALRATGDNEAMGQANSIKVDRMKMLG 18- 4 L+ L+ + V L+L F TQ GLA+RATG N M +A + M +LG Sbjct: 126 EWLSDYVFRPLLLVFIVIAAKLLLDWFFTTQKGLAIRATGSNPRMARAQGVNTGGMILLG 18- 5 Query: 185 YMIGNGLIALSGALLAQNNGYADLNMGVGTIVIGLASIILAEVMIKYLPLGKRLWSIVLG 24- 4 I N L+AL+GAL AQ G AD++MG+GTIVIGLA++I+ E ++ L +++LG Sbjct: 186 MAISNALVALAGALFAQTQGGADISMGIGTIVIGLAAVIVGESILPSRRLILATLAVILG 24- 5 Query: 245 SVLYRMIIVFILTTD---IDAQMIKLVSAILLALILYVPELRAKL 286 +++YR I L +D + AQ + LV+A+L+ + L +P ++ +L Sbjct: 246 AIVYRFFIALALNSDFIGLQAQDLNLVTAVLVTVALVIPMMKKRL 290 There is also homology to SEQ ID 2716. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1103 A DNA sequence (GBSx1178) was identified in S. agalactiae <SEQ ID 3413> which encodes the amino acid sequence <SEQ ID 3414>. This protein is predicted to be ABC transporter. Analysis of this protein sequence reveals the following: TABLE-US-03302 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3798(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03303 >GP: AAF86640 GB: AF162694 ABC transporter [Enterococcus gallinarum] Identities = 171/264 (64%), Positives = 213/264 (79%), Gaps = 1/264 (0%) Query: 3 LLELVNLHKTFEKGTVNENHVLRGLDLTIEDGDFISVIGGNGAGKSTLLNCIAGLIPIDQ 62 +L + +LH+TFEKGT+NENHVLRG+DLT+ GDFI++IGGNGAGKSTLLN IAG IP +Q Sbjct: 5 VLTISDLHQTFEKGTINENHVLRGIDLTMNSGDFITIIGGNGAGKSTLLNSIAGTIPTEQ 64 Query: 63 GAITLDNQSITKDSVEKRSKDISRVFQDPRMGTATNLTIEENMAIAHKRGNKRHIFRQSV 122- G I L ++ IT+ SV +RSK+ISRVFQDPRMGTA LT+EEN+A+A+KRG R F V Sbjct: 65 GKIVLGDKEITRHSVTRRSKEISRVFQDPRMGTAVRLTVEENLALAYKRGQVRG-FSSGV 123- Query: 123 TDDDRQLFKKSLSQLGLGLENRMKTDAAFLSGGQRQALTLAMATLVRPKLLLLDEHTAAL 18- 2 R FK+ L++L LGLENR+ T+ LSGGQRQA+TL MATL +PKL+LLDEHTAAL Sbjct: 124 KGKHRAFFKEKLARLNLGLENRLTTEIGLLSGGQRQAITLLMATLQQPKLILLDEHTAAL 18- 3 Query: 183 DPKTSDMVMELTQKVIEEQRLTALMITHNMEHAIAYGNRLVMLYHGKIVVDVKGEAKRNL 24- 2 DPKTS VM LT ++I+EQ+LTA M+TH+ME AI YGNRL+ML+ GKIVVD+ GE K++L Sbjct: 184 DPKTSMTVMALTDQLIQEQQLTAFMVTHDMEDAIRYGNRLIMLHQGKIVVDITGEEKQSL 24- 3 Query: 243 TVAELMELFHKNSGQQLIDDALVL 266 TV +LM LFH+NSG +L DD L+L Sbjct: 244 TVPDLMALFHQNSGTELKDDQLLL 267 There is also homology to SEQ ID 2720: TABLE-US-03304 Identities = 116/249 (46%), Positives = 166/249 (66%), Gaps = 1/249 (0%) Query: 3 LLELVNLHKTFEKGTVNENHVLRGLDLTIEDGDFISVIGGNGAGKSTLLNCIAGLIPIDQ 62 ++EL+N + G + +L + LTI + DF++++GGNGAGKSTL N IAG + + + Sbjct: 4 IIELINATVDVDNGFEDAKTILDNVTLTIYEHDFLTILGGNGAGKSTLFNVIAGTLSLTR 63 Query: 63 GAITLDNQSITKDSVEKRSKDISRVFQDPRMGTATNLTIEENMAIAHKRGNKRHIFRQSV 122- G I + Q +T EKR+ +SRVFQD +MGTA +T+ EN+ IA +RG KR + + + Sbjct: 64 GQIRILGQDVTHWPAEKRALYLSRVFQDSKMGTAPRMTVAENLLIARQRGGKRSLASRKI 123- Query: 123 TDDDRQLFKKSLSQLGLGLENRMKTDAAFLSGGQRQALTLAMATLVRPKLLLLDEHTAAL 18- 2 T+ F+ + + G GLE ++T A LSGGQRQAL+L MATL +P LLLLDEHTAAL Sbjct: 124 TEHLAS-FEDLVKRTGNGLEKHLETPAGLLSGGQRQALSLLMATLKKPALLLLDEHTAAL 18- 2 Query: 183 DPKTSDMVMELTQKVIEEQRLTALMITHNMEHAIAYGNRLVMLYHGKIVVDVKGEAKRNL 24- 2 DPKTS +M+LT + + + LTALMITH+ME A+ YGNRL+++ G I+ D+ K L Sbjct: 183 DPKTSQSLMQLTDEFVTKDGLTALMITHHMEDALTYGNRLIVMKDGNIIKDLNQMEKEQL 24- 2 Query: 243 TVAELMELF 251 T+ + +LF Sbjct: 243 TITDYYQLF 251 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1104 A DNA sequence (GBSx1179) was identified in S. agalactiae <SEQ ID 3415> which encodes the amino acid sequence <SEQ ID 3416>. This protein is predicted to be mannose-specific phosphotransferase system component IIAB. Analysis of this protein sequence reveals the following: TABLE-US-03305 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3527(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03306 >GP: AAD46485 GB: AF130465 mannose-specific phosphotransferase system component IIAB [Streptococcus salivarius] Identities = 287/336 (85%), Positives = 306/336 (90%), Gaps = 6/336 (1%) Query: 1 MGIGIIIASHGKFAEGIHQSGSMIFGEQEKVQVVTFMPNEGPDDLYGHFNNAIAQFDADD 60 MGIGIIIASHGKFAEGIHQSGSMIFG+QEKVQVVTFMP+EGPDDLY HFN+AIAQFDADD Sbjct: 1 MGIGIIIASHGKFAEGIHQSGSMIFGDQEKVQVVTFMPSEGPDDLYAHFNDAIAQFDADD 60 Query: 61 EVLVLADLWSGSPFNQASRVMGENPERKMAIITGLNLPMLIQAYTERMMDANAGVEQVAA 120- E+LVLADLWSGSPFNQASR+ GENP+RK+AIITGLNLPMLIQAYTERMMDANA EQVAA Sbjct: 61 EILVLADLWSGSPFNQASRIAGENPDRKIAIITGLNLPMLIQAYTERMMDANATAEQVAA 120- Query: 121 NIIKESKEGIKALPEELNPVVEATPVAGVPADVPAEVKQSGSIPEGTVIGDGKLKINLAR 18- 0 NIIKE+K GIKALPEELNP E T A V A P G+IPEGTVIGDGKLKINLAR Sbjct: 121 NIIKEAKGGIKALPEELNPAEETT-AAPVEAAAP-----QGAIPEGTVIGDGKLKINLAR 17- 4 Query: 181 IDTRLLHGQVATAWTPASKANRIIVASDEVSKDELRKQLIKQAAPGGVKANVVPISKLIE 24- 0 +DTRLLHGQVAT WTPASKA+RIIVASD+V+KDELRK+LIKQAAP GVKANVVPI KLI+ Sbjct: 175 LDTRLLHGQVATNWTPASKADRIIVASDDVAKDELRKELIKQAAPNGVKANVVPIQKLID 23- 4 Query: 241 VAKDPRFGNTRALILFETVQDALRAIEGGVEIPELNVGSMAHSTGKTMVNNVLSMDKDDV 30- 0 +KDPRFGNT ALILFETVQDALRAIEGGV I ELNVGSMAHSTGKTMVNNVLSMDKDDV Sbjct: 235 ASKDPRFGNTHALILFETVQDALRAIEGGVPIKELNVGSMAHSTGKTMVNNVLSMDKDDV 29- 4 Query: 301 AAFEKLRDLGVSFDVRKVPNDAKKNLFDLINKANVK 336 A FEKLRDLGV FDVRKVPND+KK+LFDLI KANV+ Sbjct: 295 ACFEKLRDLGVEFDVRKVPNDSKKDLFDLIKKANVQ 330 A related DNA sequence was identified in S. pyogenes <SEQ ID 3417> which encodes the amino acid sequence <SEQ ID 3418>. Analysis of this protein sequence reveals the following: TABLE-US-03307 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3533(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03308 Identities = 288/336 (85%), Positives = 308/336 (90%), Gaps = 6/336 (1%) Query: 1 MGIGIIIASHGKFAEGIHQSGSMIFGEQEKVQVVTFMPNEGPDDLYGHFNNAIAQFDADD 60 MGIGIIIASHGKFAEGIHQSGSMIFGEQEKVQVVTFMPNEGPDDLYGHFNNAI QFDADD Sbjct: 1 MGIGIIIASHGKFAEGIHQSGSMIFGEQEKVQVVTFMPNEGPDDLYGHFNNAIQQFDADD 60 Query: 61 EVLVLADLWSGSPFNQASRVMGENPERKMAIITGLNLPMLIQAYTERMMDANAGVEQVAA 120- E+LVLADLWSGSPFNQASRV GENP+RKMAIITGLNLPMLIQAYTER+MDA AGVEQVAA Sbjct: 61 EILVLADLWSGSPFNQASRVAGENPDRKMAIITGLNLPMLIQAYTERLMDAGAGVEQVAA 120- Query: 121 NIIKESKEGIKALPEELNPVVEATPVAGVPADVPAEVKQSGSIPEGTVIGDGKLKINLAR 18- 0 NIIKESK+GIKALPE+LNPV E V + G+IP GTVIGDGKLKINLAR Sbjct: 121 NIIKESKDGIKALPEDLNPVEETAATEKVVNAL------QGAIPAGTVIGDGKLKINLAR 17- 4 Query: 181 IDTRLLHGQVATAWTPASKANRIIVASDEVSKDELRKQLIKQAAPGGVKANVVPISKLIE 24- 0 +DTRLLHGQVATAWTPASKA+RIIVASDEV++D+LRKQLIKQAAPGGVKANVVPISKLIE Sbjct: 175 VDTRLLHGQVATAWTPASKADRIIVASDEVAQDDLRKQLIKQAAPGGVKANVVPISKLIE 23- 4 Query: 241 VAKDPRFGNTRALILFETVQDALRAIEGGVEIPELNVGSMAHSTGKTMVNNVLSMDKDDV 30- 0 +KDPRFGNT ALILF+T QDALRA+EGGVEI ELNVGSMAHSTGKTMVNNVLSMDK+DV Sbjct: 235 ASKDPRFGNTHALILFQTPQDALRAVEGGVEINELNVGSMAHSTGKTMVNNVLSMDKEDV 29- 4 Query: 301 AAFEKLRDLGVSFDVRKVPNDAKKNLFDLINKANVK 336 A FEKLRDLGV+FDVRKVPND+KKNLF+LI K N+K Sbjct: 295 ATFEKLRDLGVTFDVRKVPNDSKKNLFELIQKTNIK 330 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1105 A DNA sequence (GBSx1180) was identified in S. agalactiae <SEQ ID 3419> which encodes the amino acid sequence <SEQ ID 3420>. Analysis of this protein sequence reveals the following:

TABLE-US-03309 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3873(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03310 >GP: BAB06625 GB: AP001517 unknown conserved protein [Bacillus halodurans] Identities = 89/267 (33%), Positives = 139/267 (51%), Gaps = 3/267 (1%) Query: 3 KKIIAVDLDGTLLHNNNTISDYTADTLRKVQAQGHKVIITTGRPYRMALAHYLRLDLKTP 62 + +IA+DLDGTLL +N TIS T T++K + GH V+I+TGRPYR ++ +Y L L T Sbjct: 4 RHLIALDLDGTLLTDNKTISMKTKQTIQKAREAGHIVVISTGRPYRASIQYYQELQLDTA 63 Query: 63 MINFNGALTHIPEKKWAFERSATIDKKLLLETLNLSDAIQADFIASEYRKNFYITMDNRD 122- ++NFNGA H P+ ++ + + +A I E ++Y+ D Sbjct: 64 IVNFNGAFVHHPKDSSFGTYHHPLELSTARQVIETCEAFDVSNIMVEVIDDYYLRY--YD 121- Query: 123 KINPQLFGVNEITDKMALDVTKITRNPNALLMQTRHKDKYELAKELRQHFNHELEVDSWG 18- 2 ++ Q F + + + K+ +P +L+ + EL L ++ +WG Sbjct: 122 ELFIQTFTEGQGPVEHGNLLKKLRDDPTCVLIHPKDDHVSELRSLLDGAHAEVIDQRTWG 18- 1 Query: 183 GPLNILEFSPKGVNKAYALKHLLKSLNLSQENLIAFGDEHNDTEMLAFAHTGYAMKNANP 24- 2 P N++E G+NKA LK + + +E +IAFGDE ND EM+ +A G AM NA Sbjct: 182 APWNVIEIVKAGMNKAVGLKRIADYYQVPKERIIAFGDEDNDFEMIEYAGKGVAMANAID 24- 1 Query: 243 TLLPYADQQIQWTNEEDGVAKTLEKLL 269 L A+ I +NE+DG+A LE+ L Sbjct: 242 PLKALAN-DITLSNEDDGIAVYLEEAL 267 A related DNA sequence was identified in S. pyogenes <SEQ ID 3421> which encodes the amino acid sequence <SEQ ID 3422>. Analysis of this protein sequence reveals the following: TABLE-US-03311 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4380(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03312 Identities = 188/270 (69%), Positives = 224/270 (82%) Query: 1 MTKKIIAVDLDGTLLHNNNTISDYTADTLRKVQAQGHKVIITTGRPYRMALAHYLRLDLK 60 MTKK+IA+DLDGTLLH++NTIS YT T++ VQ +GH VII+TGRPYRNAL +YL+L+LK Sbjct: 1 MTKKLIAIDLDGTLLHHDNTISTYTQKTIKAVQDKGHHVIISTGRPYRMALGYYLQLNLK 60 Query: 61 TPMINFNGALTHIPEKKWAFERSATIDKKLLLETLNLSDAIQADFIASEYRKNFYITMDN 120- TP+I FNGALTH+PE+KWA+E + T+DK LL L D Q DFIASEYRKN YITM N Sbjct: 61 TPIITFNGALTHMPEQKWAYEHNVTLDKGYLLRLLKYQDDFQMDFIASEYRKNVYITMTN 120- Query: 121 RDKINPQLFGVNEITDKMALDVTKITRNPNALLMQTRHKDKYELAKELRQHFNHELEVDS 18- 0 + I+PQLFGV+EIT MAL++TKITRNPNALLMQT H+DKY LAK +R F E+E+DS Sbjct: 121 PESIDPQLFGVDEITQDMALEITKITRNPNALLMQTHHEDKYALAKNMRACFKDEIEIDS 18- 0 Query: 181 WGGPLNILEFSPKGVNKAYALKHLLKSLNLSQENLIAFGDEHNDTEMLAFAHTGYAMKNA 24- 0 WGGPLNILE S K VNKAYAL +LL N+ +++LIAFGDENNDTEMLAFA TGYAMKNA Sbjct: 181 WGGPLNILEISSKNVNKAYALNYLLGIYNMDKKDLIAFGDEHNDTEMLAFAGTGYAMKNA 24- 0 Query: 241 NPTLLPYADQQIQWTNEEDGVAKTLEKLLL 270 +P LLPYADQQ+ ++NEEDGVAK LE+L L Sbjct: 241 SPVLLPYADQQLNFSNEEDGVAKKLEELFL 270 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1106 A DNA sequence (GBSx1181) was identified in S. agalactiae <SEQ ID 3423> which encodes the amino acid sequence <SEQ ID 3424>. Analysis of this protein sequence reveals the following: TABLE-US-03313 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.38 Transmembrane 96-112 (90-119) INTEGRAL Likelihood = -6.58 Transmembrane 28-44 (27-47) INTEGRAL Likelihood = -6.26 Transmembrane 176-192 (174-193) INTEGRAL Likelihood = -5.26 Transmembrane 127-143 (126-144) INTEGRAL Likelihood = -1.59 Transmembrane 4-20 (3-20) INTEGRAL Likelihood = -0.22 Transmembrane 60-76 (59-78) ----- Final Results ----- bacterial membrane --- Certainty = 0.3951(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1107 A DNA sequence (GBSx1182) was identified in S. agalactiae <SEQ ID 3425> which encodes the amino acid sequence <SEQ ID 3426>. Analysis of this protein sequence reveals the following: TABLE-US-03314 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2025(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1108 A DNA sequence (GBSx1183) was identified in S. agalactiae <SEQ ID 3427> which encodes the amino acid sequence <SEQ ID 3428>. This protein is predicted to be an integral membrane protein. Analysis of this protein sequence reveals the following: TABLE-US-03315 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.41 Transmembrane 180-196 (179-199) INTEGRAL Likelihood = -5.31 Transmembrane 96-112 (94-114) INTEGRAL Likelihood = -2.18 Transmembrane 129-145 (129-145) INTEGRAL Likelihood = -1.33 Transmembrane 37-53 (37-53) ----- Final Results ----- bacterial membrane --- Certainty = 0.3166(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8729> which encodes amino acid sequence <SEQ ID 8730> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-03316 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: 5.85 GvH: Signal Score (-7.5): -2.39 Possible site: 18 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 4 value: -5.41 threshold: 0.0 INTEGRAL Likelihood = -5.41 Transmembrane 176-192 (175-195) INTEGRAL Likelihood = -5.31 Transmembrane 92-108 (90-110) INTEGRAL Likelihood = -2.18 Transmembrane 129-145 (129-145) PERIPHERAL Likelihood = 0.05 57 modified ALOM score: 1.58 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3166(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03317 >GP: AAC65028 GB: AE001188 conserved hypothetical integral membrane protein [Treponema pallidum] Identities = 54/190 (28%), Positives = 93/190 (48%), Gaps = 14/190 (7%) Query: 14 LFFIVISFGIKYYHLQG--PNLIWNMTLALIALDFAYLTSL--FKKKILIGLFALAWFFF 69 - +F +++SFG + L+WN+ LA I + + + F + + L W F Sbjct: 3 VFCLLLSFGRRCVAADNFLSFLVWNLVLAFIPWLISAILHVRRFAVRSVQLFLMLLWLLF 62 Query: 70 YPNTFYMLTDIIHMHFVGDVLYNKTNLILYILYVSSILFGFLSGIESFSVIMRKFRISNI 129- +PN Y+LTDIIH+ L +IL + + + F+S S++ R F I Sbjct: 63 FPNAPYILTDIIHLGKGKSFLLYYDLIILLAYSFTGLFYAFVSLHLIESILARDFHIKRP 122- Query: 130 FLRWGIIGIVSL-VSSFGIHIGRYARLNSWDILTKPQVVINELLAVPSR-----DSFHFI 18- 3 F II + L + +FGI++GR+ R NSWDI+ + +++++ R D++ F+ Sbjct: 123 F----IISVFELYLCAFGIYLGRFLRWNSWDIVLHGRTILSDIGIRVIRPVFYVDTWMFV 17- 8 Query: 184 LGFTFLQVLC 193 F + VLC Sbjct: 179 FFFGTMLVLC 188 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1109 A DNA sequence (GBSx1184) was identified in S. agalactiae <SEQ ID 3429> which encodes the amino acid sequence <SEQ ID 3430>. Analysis of this protein sequence reveals the following: TABLE-US-03318 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.79 Transmembrane 171-187 (166-191) ----- Final Results ----- bacterial membrane --- Certainty = 0.3718(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1110 A DNA sequence (GBSx1185) was identified in S. agalactiae <SEQ ID 3431> which encodes the amino acid sequence <SEQ ID 3432>. Analysis of this protein sequence reveals the following: TABLE-US-03319 Possible site: 29 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.46 Transmembrane 193-209 (191-214) INTEGRAL Likelihood = -10.30 Transmembrane 99-115 (96-119) INTEGRAL Likelihood = -8.17 Transmembrane 454-470 (451-472) INTEGRAL Likelihood = -6.64 Transmembrane 216-232 (212-236) INTEGRAL Likelihood = -6.37 Transmembrane 49-65 (43-68) INTEGRAL Likelihood = -4.88 Transmembrane 362-378 (357-383) INTEGRAL Likelihood = -3.61 Transmembrane 385-401 (385-402) INTEGRAL Likelihood = -2.76 Transmembrane 275-291 (275-291) INTEGRAL Likelihood = -1.70 Transmembrane 18-34 (18-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.5182(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03320 >GP: AAF95422 GB: AE004299 conserved hypothetical protein [Vibrio cholerae] Identities = 193/471 (40%), Positives = 286/471 (59%), Gaps = 42/471 (8%) Query: 1 MEKFFKLKEHGTTIRTEITAGLTTFFAMSYILFVNPAILSQTGMPAQGVFLATIIGAVVA 60 +EK FKL E+GT +RTEI AG+TTF M+YI+FVNPAILS GM VF+AT + A + Sbjct: 2 LEKLFKLSEYGTNVRTEILAGVTTFLTMAYIIFVNPAILSDAGMDRGAVFVATCLAAAIG 61 Query: 61 TSVMAFYANLPYAQAPGMGLNAFFTYTVVFALGYTWQEALAMVFICGLISLIITLTKVRK 120- +M F AN P AQAPGMGLNAFFTY VV +G+TWQ ALA VF G++ ++++L K+R+ Sbjct: 62 CFIMGFIANYPIAQAPGMGLNAFFTYGVVLGMGHTWQVALAAVFCSGVLFILLSLFKIRE 121- Query: 121 MIIESIPTTLKSAITAGIGTFLAYVGIKNAGFLKFSIDPGTYDVVGKGAAKGLATITANS 18- 0 II SIP +L++ I+AGIG FLA++ +KNAG + +P T +V GA L + Sbjct: 122 WIINSIPHSLRTGISAGIGLFLAFIALKNAGIV--VDNPAT--LVSLGAITSLHAV---- 17- 3 Query: 181 SATPGLVSFDNPAILLSLIGLSITIFFIVKGIRGGIILSILTTTLLGILMGVVKLDAINW 24- 0 L+ +G +TI + +G++G ++++IL T LG++G V+ I Sbjct: 174 ---------------LAAVGFFLTIGLVYRGVKGAVMIAILAVTALGLVFGDVQWGGIMS 21- 8 Query: 241 EATNLSASFRDLKQVFGVALGEKGLISLFSNPSRLPSVLMAILAFSLTDIFDTIGTLIGT 30- 0 +++ +F Q+ A+ E G+IS+ + AF D+FDT GTL+G Sbjct: 219 TPPSIAPTF---MQLDFSAVFEIGMISV-------------VFAFLFVDLFDTAGTLVGV 26- 2 Query: 301 GEKVGILATTGDNHESKSLDKALYSDLIGTTFGAICGTSNVTTYVESAAGIGAGGRTGLT 36- 0 K G++ G + L++AL +D T+ GA+ GTSN T+Y+ES +G+ GGRTGLT Sbjct: 263 ATKAGLIEKDG---KIPRLNRALLADSTATSVGALLGTSNTTSYIESVSGVAVGGRTGLT 31- 9 Query: 361 ALVVAGLFAISSFFSPLVSIVPSQATAPILVIVGIMNLSNLKDIKWDDMSEAIPAFFTSL 42- 0 A+VV LF ++ FFSPL ++P+ ATA L V I+M+S L I W D++EA P T L Sbjct: 320 AVVVGILFLLALFFSPLAGMIPAYATAGALFYVAILMMSGLVSIDWRDLTEAAPTVVTCL 37- 9 Query: 421 FMGFTYSITYGIAAGFLTYTLAKVIKGQAKDIHVVLWILDILFILNFISLA 471 M T+SI GI+ GF+ Y K+ G+ + + + +W++ +F++ +I A Sbjct: 380 MMPLTFSIAEGISLGFIAYAAIKLFSGKGRSVSLSVWVMAAIFVIKYILAA 430 A related DNA sequence was identified in S. pyogenes <SEQ ID 3433> which encodes the amino acid sequence <SEQ ID 3434>. Analysis of this protein sequence reveals the following: TABLE-US-03321 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.57 Transmembrane 378-394 (370-419) INTEGRAL Likelihood = -9.29 Transmembrane 202-218 (195-221) INTEGRAL Likelihood = -7.64 Transmembrane 48-64 (46-71) INTEGRAL Likelihood = -7.64 Transmembrane 99-115 (97-118) INTEGRAL Likelihood = -6.90 Transmembrane 225-241 (221-245) INTEGRAL Likelihood = -6.05 Transmembrane 468-484 (465-485) INTEGRAL Likelihood = -4.35 Transmembrane 399-415 (395-419) INTEGRAL Likelihood = -3.24 Transmembrane 425-441 (425-442) INTEGRAL Likelihood = -3.08 Transmembrane 18-34 (18-34) INTEGRAL Likelihood = -2.28 Transmembrane 442-458 (442-460) INTEGRAL Likelihood = -0.00 Transmembrane 282-298 (282-298) ----- Final Results ----- bacterial membrane --- Certainty = 0.5628(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03322 >GP: BAB04327 GB: AP001509 unknown conserved protein [Bacillus halodurans] Identities = 192/485 (39%), Positives = 276/485 (56%), Gaps = 53/485 (10%) Query: 1 MEKFFKLSENGTTVSTEIMAGLTTFFAMSYILFVNPSILGAAGMPSNAVFLATIIAAAIS 60 M+++F E+GTT E +AGLTTF +M+YILFVNP ILG AGM AVF+AT +AAAI Sbjct: 1 MDRYFGFKEHGTTYGRESIAGLTTFLSMAYILFVNPLILGDAGMDVQAVFMATALAAAIG 60 Query: 61 TLIMGLFANVPYALAPGMGLNAFFTYTVVFALRFSWQEALAMVFICGLFNIFITVTKFRK 120- TLIMG+ A P ALAPGMGLNAFF Y+VV + WQ AL VF+ G+ I ITV K R+ Sbjct: 61 TLIMGILAKYPIALAPGMGLNAFFAYSVVIGMGIDWQLALFGVFVSGIIFILITVFKIRE 120- Query: 121 SIIKAIPVSLQHAIGGGIGVFVAYLGFKNANIITFSISAENIVMVNGVEPAKASAKTFAD 18- 0 II AIP L++A GIG+F+A++G KNA I+ Sbjct: 121 VIINAIPAELKNAAAAGIGLFIAFIGLKNAGIVV-------------------------- 15- 4 Query: 181 GLLFVDANGGVVPTISSFTDSGVLLAIFGLLLTTALVIRNFRGAILIGIVATTLVGIPLG 24- 0 ++ ++ + LLA FGL++T ++R +G I G++ T +VG+ G Sbjct: 155 ------SDEATAVSLGHILNGPTLLACFGLIVTVLFMVRGIQGGIFYGMILTAIVGLISG 20- 8 Query: 241 IVDVSNLNFGISHIGEAWTELGTTFLAAFD-GLSSLFSDSSRLPLVFMTIFAFSLSDTFD 29- 9 I+ + I L TF AF+ ++ +FS + + F D FD Sbjct: 209 IITYTG-----GGIVSTPPSLAPTFGQAFNIQMADVFSVQ-----FLIVVLTFLFVDFFD 25- 8 Query: 300 TIGTFIGTGRRTGIFSQDDENALENSIGFSSKMDRALFADAIGTSIGALVGTSNTTTYVE 35- 9 T GT G + G F +D++ + +AL AD+ TSIGA++GTS TT Y+E Sbjct: 259 TAGTLYGVANQAG-FIKDNK---------LPRAGKALLADSSATSIGAILGTSTTTAYIE 30- 8 Query: 360 SAAGIAEGGRTGLTAVSTAVCFLLSILLLPLVGIVPAAATAPALIIVGVMMVSSFLDVNW 41- 9 S+AG+A GGRTG ++ TA F+L++ PL+ +V TA ALI+VG++M SS ++W Sbjct: 309 SSAGVAAGGRTGFASIVTAGLFVLAMFFSPLLSVVTEQVTAAALIVVGILMASSLRFIDW 36- 8 Query: 420 SKFADALPAFFAAFFMALCYSISYGIAAAFIFYCLVKVVEGKTKDIHPIIWGATFLFIVN 47- 9 +K A+P+F M L YSI+ GIA F+FY + +V+G+ K++HPI++ F+F+ Sbjct: 369 TKLEIAIPSFLTVVAMPLTYSIATGIAFGFLFYPITMIVKGRGKEVHPIMYALFFVFLAY 42- 8 Query: 480 FIILT 484 FI L+ Sbjct: 429 FIFLS 433 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03323 Identities = 258/488 (52%), Positives = 336/488 (67%), Gaps = 17/488 (3%) Query: 1 MEKFFKLKEHGTTIRTEITAGLTTFFAMSYILFVNPAILSQTGMPAQGVFLATIIGAVVA 60 MEKFFKL E+GTT+ TEI AGLTTFFAMSYILFVNP+IL GMP+ VFLATII A ++ Sbjct: 1 MEKFFKLSENGTTVSTEIMAGLTTFFAMSYILFVNPSILGAAGMPSNAVFLATIIAAAIS 60 Query: 61 TSVMAFYANLPYAQAPGMGLNAFFTYTVVFALGYTWQEALAMVFICGLISLIITLTKVRK 120- T +M +AN+PYA APGMGLNAFFTYTVVFAL ++WQEALAMVFICGL ++ IT+TK RK Sbjct: 61 TLIMGLFANVPYALAPGMGLNAFFTYTVVFALRFSWQEALAMVFICGLFNIFITVTKFRK 120- Query: 121 MIIESIPTTLKSAITAGIGTFLAYVGIKNAGFLKFSIDPGTYDVV---------GRGAAK 17- 1 II++IP +L+AI GIG F+AY+G KNA + FSI +V K A Sbjct: 121 SIIKAIPVSLQHAIGGGIGVFVAYLGFKNANIITFSISAENIVMVNGVEPAKASAKTFAD 18- 0 Query: 172 GLATITANSSATPGLVSFDNPAILLSLIGLSITIFFIVKGIRGGIILSILTTTLLGILMG 23- 1 GL + AN P + SF + +LL++ GL +T +++ RG I++ I+ TTL+GI +G Sbjct: 181 GLLFVDANGGVVPTISSFTDSGVLLAIFGLLLTTALVIRNFRGAILIGIVATTLVGIPLG 24- 0 Query: 232 VVKLDAINWEATNLSASFRDLKQVFGVALGEKGLISLFSNPSRLPSVLMAILAFSLTDIF 29- 1 +V + +N+ +++ ++ +L F A GL SLFS+ SRLP V M I AFSL+D F Sbjct: 241 IVDVSNLNFGISHIGEAWTELGTTFLAAF--DGLSSLFSDSSRLPLVFMTIFAFSLSDTF 29- 8 Query: 292 DTIGTLIGTGEKVGILATTGDN------HESKSLDKALYSDLIGTTFGAICGTSNVTTYV 34- 5 DTIGT IGTG + GI + +N S +D+AL++D IGT+ GA+ GTSN TTYV Sbjct: 299 DTIGTFIGTGRRTGIFSQDDENALENSIGFSSKMDRALFADAIGTSIGALVGTSNTTTYV 35- 8 Query: 346 ESAAGIGAGGRTGLTALVVAGLFAISSFFSPLVSIVPSQATAPILVIVGIMMLSNLKDIK 40- 5 ESAAGI GGRTGLTA+ A F +S PLV IVP+ ATAP L+IVG+MM+S+ D+ Sbjct: 359 ESAAGIAEGGRTGLTAVSTAVCFLLSILLLPLVGIVPAAATAPALIIVGVMNVSSFLDVN 41- 8 Query: 406 WDDMSEAIPAFFTSLFMGFTYSITYGIAAGFLTYTLAKVIKGQAKDIHVVLWILDILFIL 46- 5 W ++A+PAFF + FM YSI+YGIAA F+ Y L KV++G+ KDIH ++W LFI+ Sbjct: 419 WSKFADALPAFFAAFFMALCYSISYGIAAAFIFYCLVKVVEGKTKDIHPIIWGATFLFIV 47- 8 Query: 466 NFISLAIL 473 NFI L IL Sbjct: 479 NFIILTIL 486 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1111 A DNA sequence (GBSx1186) was identified in S. agalactiae <SEQ ID 3435> which encodes the amino acid sequence <SEQ ID 3436>. Analysis of this protein sequence reveals the following:

TABLE-US-03324 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3221(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03325 >GP: BAB04264 GB: AP001508 unknown conserved protein [Bacillus halodurans] Identities = 68/147 (46%), Positives = 100/147 (67%), Gaps = 1/147 (0%) Query: 27 MFYTQNEEELIALGQKLGTVLKSGDIVLLTGNLGAGKTTLTKGIAKGLDIKQMIKSPTYT 86 - M TQ+ E +A QKL L +GD++ L G+LGAGKT+ TKG+A GL IK+++KSPT+T Sbjct: 5 MMITQSPEATMAFAQKLADKLLAGDVITLEGDLGAGKTSFTKGLALGLGIKRVVKSPTFT 64 Query: 87 IVREYEGRVPLYHLDVYRIGDDPDSIDLDDFLFGQGVTVIEWGELLSDNLINNYLEIVIT 146- I+REY+GR+PLYH+DVYR+ ++ + + D++ G GVTV+EW L+ L L I IT Sbjct: 65 IIREYKGRLPLYHMDVYRLNEEEEDLGFDEYFHGDGVTVVEWASLIEGRLPPVRLAITIT 124- Query: 147 RSNQG-RQVQLEAYGHRAREIIEAIQD 172 + + RQ+ AYG R E+++ + D Sbjct: 125 HAGENERQLSFTAYGERWEEVLKELLD 151 A related DNA sequence was identified in S. pyogenes <SEQ ID 3437> which encodes the amino acid sequence <SEQ ID 3438>. Analysis of this protein sequence reveals the following: TABLE-US-03326 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1202(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03327 Identities = 97/142 (68%), Positives = 122/142 (85%) Query: 27 MFYTQNEEELIALGQKLGTVLKSGDIVLLTGNLGAGKTTLTKGIAKGLDIKQMIKSPTYT 86 - MFY++NE L A G+ LGT L GD+++L+G+LGAGKTTL KGIAKG+ I QMIKSPTYT Sbjct: 1 MFYSENEYTLKAYGETLGTYLSIGDVIVLSGDLGAGKTTLAKGIAKGMGISQMIKSPTYT 60 Query: 87 IVREYEGRVPLYHLDVYRIGDDPDSIDLDDFLFGQGVTVIEWGELLSDNLINNYLEIVIT 146- IVREYEGR+PLYHLD+YR+GDDPDSIDLDDFLFG GVTVIEWGELL + L+ +YL+I IT Sbjct: 61 IVREYEGRLPLYHLDIYRVGDDPDSIDLDDFLFGNGVTVIEWGELLGEGLLQDYLQITIT 120- Query: 147 RSNQGRQVQLEAYGHRAREIIE 168 + ++GRQ+ L A+G R+R+++E Sbjct: 121 KRDKGRQLDLLAHGERSRQLLE 142 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1112 A DNA sequence (GBSx1187) was identified in S. agalactiae <SEQ ID 3439> which encodes the amino acid sequence <SEQ ID 3440>. Analysis of this protein sequence reveals the following: TABLE-US-03328 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1782(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03329 >GP: AAD35662 GB: AE001732 conserved hypothetical protein [Thermotoga maritima] Identities = 56/163 (34%), Positives = 94/163 (57%), Gaps = 1/163 (0%) Query: 24 EASREEASAILEFLNTVTEETDFILHTVSNQLSLSEMETFIENTLMTKNCICLIAKLKNK 83 - EAS +A I+E+L VT ETDF++ +S +I + ++ ++ + Sbjct: 18 EASIWDARRIVEYLKEVTSETDFLITRPDEVYDVSTERNYIRMYRSNPGKLMIVGEINRE 77 Query: 84 VIGLITIISQSDIEIEHVGDLFIAVQKDYWGYGIGHILMEEAIEWASDNDITRRLELSVQ 143- ++ L+T +HVG++ I+V+K YW GIG ++ AIEWA N R++L V Sbjct: 78 IVSLLTFTGFGRKRTKHVGEIGISVKKRYWNIGIGTRMITSAIEWARRNGFI-RIQLEVL 136- Query: 144 GRNERAIHLYQKFGFEIDGLQTRGIKRENGEFLDIYRMSKLID 186 NERAI LY+K GFE++G++ + ++R++G F D+ M+ L+D Sbjct: 137 KSNERAISLYRKLGFELEGIKRKAVRRDDGSFEDVLVMALLLD 179 There is also homology to SEQ ID 1724. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1113 A DNA sequence (GBSx1188) was identified in S. agalactiae <SEQ ID 3441> which encodes the amino acid sequence <SEQ ID 3442>. Analysis of this protein sequence reveals the following: TABLE-US-03330 Possible site: 53 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03331 >GP: CAB15582 GB: Z99122 membrane-bound protein [Bacillus subtilis] Identities = 108/324 (33%), Positives = 178/324 (54%), Gaps = 33/324 (10%) Query: 5 KKITLMFSAIILTTVIALGV--YVASAYNFSTNELSKTFKDFKLAKS--KSHAIEETKPF 60 KK TL+ + + + ++ LG Y ++ + + ++ + +K K +I + PF Sbjct: 8 KKKTLLLTILTIIGLLVLGTGGYAYYLWHKAASTVASIHESIDKSKKRDKEVSINKKDPF 67 Query: 61 SILLMGVDTGSEHRKSKWSGNSDSMILVTINPKTNKTTMTSLERDVLIKLSGPKNNGQTG 120- S+L+MGVD + G +D++I +T+NPKTN T M S+ RD K+ G G Sbjct: 68 SVLIMGVDERDGDK-----GRADTLIYMTVNPKTNTTDMVSIPRDTYTKIIGK------G 116- Query: 121 VEAKLNAAYASGGAEMALMTVQDLLDINVDYFMQINMQGLVDLVNAVGGITVTNKFDFPI 18- 0 K+N +YA GG +M + TV++ LD+ VDYF+++NM+ D+V+ +GGITV + F F Sbjct: 117 TMDKINHSYAFGGTQMTVDTVENFLDVPVDYFVKVNMESFRDVVDTLGGITVNSTFAFSY 17- 6 Query: 181 SIAANEPEYKAVVEPGTHKINGEQALVYSRMRYDDPEGDYGRQKRQREVIQKVLKKILAL 24- 0 + G +NG++AL Y+RMR +DP GD+GRQ RQR+VIQ ++ K + Sbjct: 177 DGYS--------FGKGEITLNGKEALAYTRMRKEDPRGDFGRQDRQRQVIQGIINKGANI 22- 8 Query: 241 NSISSYKKILSAVSNNMQTNIEISSKTIPNL----LAYKDSLEHIKSYQLKGEDATLSDG 29- 6 +SI+ + + V NN++TN+ T N+ YK + +HIK ++LKG T +G Sbjct: 229 SSITKFGDMFKVVENNVKTNL-----TFDNMWDIQSDYKGARKHIKQHELKG-TGTKING 28- 2 Query: 297 GSYQILTKKHLLAVQNRIKKELDK 320 Y + L + +K+ L+K Sbjct: 283 IYYYQADESALSDITKELKESLEK 306 A related DNA sequence was identified in S. pyogenes <SEQ ID 2763> which encodes the amino acid sequence <SEQ ID 2764>. Analysis of this protein sequence reveals the following: TABLE-US-03332 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03333 Identities = 288/436 (66%), Positives = 342/436 (78%), Gaps = 22/436 (5%) Query: 1 MKIWKKITLMFSAIILTTVIALGVYVASAYNFSTNELSKTFKDFKLAKSKSHAIEETKPF 60 MKI KKI LMF+AI+LTTV+ALGVY+ SAY FST ELSKTFKDF + +KS AI++T+ F Sbjct: 1 MKIGKKIVLMFTAIVLTTVLALGVYLTSAYTFSTGELSKTFKDFSTSSNKSDAIKQTRAF 60 Query: 61 SILLMGVDTGSEHRKSKWSGNSDSMILVTINPKTNKTTMTSLERDVLIKLSGPKNNGQTG 120- SILLMGVDTGS R SKW GNSDSMILVT+NPKT KTTMTSLERD L LSGPKNN G Sbjct: 61 SILLMGVDTGSSERASKWEGNSDSMILVTVNPKTKKTTMTSLERDTLTTLSGPKNNEMNG 120- Query: 121 VEAKLNAAYASGGAEMALMTVQDLLDINVDYFMQINMQGLVDLVNAVGGITVTNKFDFPI 18- 0 VEAKLNAAYA+GGA+MA+MTVQDLL+I +D ++QINMQGL+DLVNAVGGITVTN+FDFPI Sbjct: 121 VEAKLNAAYAAGGAQMAIMTVQDLLNITIDNYVQINMQGLIDLVNAVGGITVTNEFDFPI 18- 0 Query: 181 SIAANEPEYKAVVEPGTHKINGEQALVYSRMRYDDPEGDYGRQKRQREVIQKVLKKILAL 24- 0 SIA NEPEY+A V PGTHKINGEQALVY+RMRYDDPEGDYGRQKRQREVIQKVLKKILAL Sbjct: 181 SIAENEPEYQATVAPGTHKINGEQALVYARMRYDDPEGDYGRQKRQREVIQKVLKKILAL 24- 0 Query: 241 NSISSYKKILSAVSNNMQTNIEISSKTIPNLLAYKDSLEHIKSYQLKGEDATLSDGGSYQ 30- 0 +SISSY+KILSAVS+NMQTNIEISS+TIP+LL Y+D+L IK+YQLKGEDATLSDGGSYQ Sbjct: 241 DSISSYRKILSAVSSNMQTNIEISSRTIPSLLGYRDALRTIKTYQLKGEDATLSDGGSYQ 30- 0 Query: 301 ILTKKHLLAVQNRIKKELDKKRSKTLKTSAILYEDYYGTTASNDSSTYSSTQENNYNTT- 35- 9 I+T HLL +QNRI+ EL + LKT+A +YE+ YG ST S T NNY+++ Sbjct: 301 IVTSNHLLEIQNRIRTELGLHKVNQLKTNATVYENLYG-------STKSQTVNNNYDSSG 35- 3 Query: 360 ---PYSEAPPSYSG-----NTTYSSETNQTTHQNYYNSSTPASNYSSNTNTGQADSSGSV 41- 1 YS++ SY+ +T S+ T+Q + + + +TP+S+ S ++ SSGS Sbjct: 354 QAPSYSDSHSSYANYSSGVDTGQSASTDQDSTASSHRPATPSSS-SDALAADESSSSGS- 41- 1 Query: 412 NNHNGAATPNPNTGTQ 427 G+ P N Q Sbjct: 412 ----GSLVPPANINPQ 423 SEQ ID 3442 (GBS54) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 8; MW 48.4 kDa). The GBS54-His fusion product was purified (FIG. 98A; see also FIG. 194, lane 6) and used to immunise mice (lane 1+2 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 98B), FACS (FIG. 98C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1114 A DNA sequence (GBSx1189) was identified in S. agalactiae <SEQ ID 3443> which encodes the amino acid sequence <SEQ ID 3444>. This protein is predicted to be Vesl-1L. Analysis of this protein sequence reveals the following: TABLE-US-03334 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.44 Transmembrane 3-19 (3-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 3445> which encodes the amino acid sequence <SEQ ID 3446>. Analysis of this protein sequence reveals the following: TABLE-US-03335 Possible site: 15 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-03336 Identities = 42/98 (42%), Positives = 64/98 (64%) Query: 1 MKIGRLIALGLVSLGALELYKNRKTIKDSYQNTKNETDSAKLKLERIKNDLAIISQEKEK 60 MK+ +IA+GL+S A + Y+ R TIK+ ++ D+A+L L+ IK +L +I + + Sbjct: 1 MKVKTVIAVGLLSFTAYKAYQKRCTIKELLSISRQAKDAAQLDLDNIKANLDLIHSQGKV 60 Query: 61 IRLISQELNHKFQVFNKDIQPRLEEINQRMAKYQEKDE 98 I+ ISQ+L HK++ FN++ Q L EI RMAKYQE E Sbjct: 61 IQNISQDLAHKWRYFNQETQAHLTEIQNRMAKYQEDSE 98 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1115 A DNA sequence (GBSx1190) was identified in S. agalactiae <SEQ ID 3447> which encodes the amino acid sequence <SEQ ID 3448>. This protein is predicted to be Hit-like protein involved in cell-cycle regulation (hit). Analysis of this protein sequence reveals the following: TABLE-US-03337 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2694(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03338 >GP:BAB04908 GB:AP001511 Hit-like protein involved in cell-cycle regulation [Bacillus halodurans] Identities = 74/137 (54%), Positives = 95/137 (69%), Gaps = 2/137 (1%) Query: 3 NCIFCKIISGEIPSSKVYEDDEVLAFLDITQTTTGHTLLIPKKHVRNVLEMDEKTAQITF 62 NCIFCKII+GEIPS+ VYEDD V AFLDI+Q T GHTL+IPK H RNV E+ E+ A F Sbjct: 6 NCIFCKIIAGEIPSATVYEDDHVYAFLDISQVTKGHTLVIPKVHKRNFELSEEIASSLF 65 Query: 63 ERLPKVARAVQAATKAKGMNIINNNEEIAGQTVFHAHVHLVPRFDESDGIKIHYTTHEPD 122- +PK++RA+ A + GMNI+NNN E AGQTVFH H+HL+PR+ E DG + H Sbjct: 66 AAVPKISRAINDAFQPIGMNIVNNNGEAAGQTVFHYHLHLLPRYGEGDGYGAVWKDHSSQ 125- Query: 123 F--EALAKLAKEIRKEI 137 + + L L+ IR+ + Sbjct: 126 YSGDDLQVLSSSIREHL 142 A related DNA sequence was identified in S. pyogenes <SEQ ID 3449> which encodes the amino acid sequence <SEQ ID 3450>. Analysis of this protein sequence reveals the following: TABLE-US-03339 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0125(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03340 Identities = 97/137 (70%), Positives = 117/137 (84%) Query: 1 MDNCIFCKIISGEIPSSKVYEDDEVLAFLDITQTTTGHTLLIPKKHVRNVLEMDEKTAQI 60 M+NCIFC II G+IPSSKVYED++VLAFLDI+QTT GHTL+IPK+HVRN+LEM +TA Sbjct: 1 MENCIFCSIIQGDIPSSKVYEDEQVLAFLDISQTTKGHTLVIPKQHVRNLLEMTAETASH 60 Query: 61 TFERLPKVARAVQAATKAKGMNIINNNEEIAGQTVFHAHVHLVPRFDESDGIKIHYTTHE 120- F R+PK+ARA+Q+AT A MNIINNNE +AGQTVFHAHVHLVPR++E DGI I YTTHE Sbjct: 61 LFARIPKIARAIQSATGATAMNIINNNEALAGQTVFHAHVHLVPRYNEEDGISIQYTTHE 120- Query: 121 PDFEALAKLAKEIRKEI 137 PDF L KLA++I +E+ Sbjct: 121 PDFPVLEKLARQINQEV 137 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1116 A DNA sequence (GBSx1191) was identified in S. agalactiae <SEQ ID 3451> which encodes the amino acid sequence <SEQ ID 3452>. Analysis of this protein sequence reveals the following: TABLE-US-03341 Possible site: 36 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10923> which encodes amino acid sequence <SEQ ID 10924> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3452 (GBS87) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 8 (lane 3; MW 19.5 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 15 (lane 10; MW 44 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1117 A DNA sequence (GBSx1192) was identified in S. agalactiae <SEQ ID 3453> which encodes the amino acid sequence <SEQ ID 3454>. This protein is predicted to be ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-03342 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.53 Transmembrane 143-159 (141-161) ----- Final Results ----- bacterial membrane --- Certainty = 0.3612(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9563> which encodes amino acid sequence <SEQ ID 9564> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03343 >GP:CAB12844 GB:Z99109 ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 137/242 (56%), Positives = 181/242 (74%) Query: 1 MTMLKIENVTGGYVNIPVLKNISFEVNDGELVGLIGLNGAGKSTTINEIIGILRPYQGDI 60 M++L ++++TGGY PVLKN+SF + ++VGLIGLNGAGKSTTI IIG++ P++G I Sbjct: 1 MSLLSVKDLTGGYTRNPVLKNVSFTLEPNQIVGLIGLNGAGKSTTIRHIIGLMDPHKGSI 60 Query: 61 TIDGISLEADQELYRKKIGFIPETPSLYEELTLREHLETVAMAYDIATDEVMARAQKLLE 120- ++G + D E YR + +IPETP LYEELTL EHLE AMAY ++ + + R LL+ Sbjct: 61 ELNGKTFAEDPEGYRSQFTYIPETPVLYEELTLMEHLELTAMAYGLSKETMEKRLPPLLK 120- Query: 121 MFRLTDKLDWFPMHFSKGMKQKVMIICAFVVSPSLFIVDEPFLGLDPLAISDLINLLAEE 18- 0 FR+ +L WFP HFSKGMKQKVMI+CAF+ P+L+I+DEPFLGLDPLAI+ L+ + E Sbjct: 121 EFRMEKRLKWFPAHFSKGMKQKVMIMCAFLAEPALYIIDEPFLGLDPLAINALLERMNEA 18- 0 Query: 181 KAKGKSILMSTHVLDSAEKMCDRFVILHKGEIRAVGTLEELRAIFGDSNANLNDIYIALT 24- 0 K G S+LMSTH+L +AE+ CD F+ILH GE+RA GTL ELR FG +A L+D+Y+ LT Sbjct: 181 KKGGASVLMSTHILATAERYCDSFIILHNGEVRARGTLSELREQFGMKDAALDDLYLELT 24- 0 Query: 241 KE 242 KE Sbjct: 241 KE 242 A related DNA sequence was identified in S. pyogenes <SEQ ID 3455> which encodes the amino acid sequence <SEQ ID 3456>. Analysis of this protein sequence reveals the following: TABLE-US-03344 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.04 Transmembrane 141-157 (139-158) ----- Final Results ----- bacterial membrane --- Certainty = 0.3017(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases:

TABLE-US-03345 >GP:CAB12844 GB:Z99109 ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 139/241 (57%), Positives = 189/241 (77%) Query: 1 MLNIKNLTGGYHNIPVLNDVSFSVDNGELVGLIGLNGAGKSTTINEIIGFLKPYQGSISI 60 +L++K+LTGGY PVL +VSF+++ ++VGLIGLNGAGKSTTI IIG + P++GSI + Sbjct: 3 LLSVKDLTGGYTRNPVLKNVSFTLEPNQIVGLIGLNGAGKSTTIRHIIGLMDPHKGSIEL 62 Query: 61 DGLTLAENAVAYRQKIGFIPETPSLYEELTLSEHINTVAMAYDIDLEVAQKRAQPFLEMF 120- +G T AE+ YR + +IPETP LYEELTL EH+ AMAY + E +KR P L+ F Sbjct: 63 NGKTFAEDPEGYRSQFTYIPETPVLYEELTLMEHLELTAMAYGLSKETMEKRLPPLLKEF 122- Query: 121 RLTDKLEWFPVNFSKGMKQKVMIICAFVIDPSLFILDEPFLGLDPLAISDLIQTLEVEKA 18- 0 R+ +L+WFP +FSKGMKQKVMI+CAF+ +P+L+I+DEPFLGLDPLAI+ L++ + K Sbjct: 123 RMEKRLKWFPAHFSKGMKQKVMIMCAFLAEPALYIIDEPFLGLDPLAINALLERMNEAKK 18- 2 Query: 181 KGKSILMSTHVLDSAERMCDRFVILHHGQVRAQGTLADLQEAFGDRSASLNDIYLALTKED 2- 41 G S+LMSTH+L +AER CD F+ILH+G+VRA+GTL++L+E FG + A+L+D+YL LTKED Sbjct: 183 GGASVLMSTHILATAERYCDSFIILHNGEVRARGTLSELREQFGMKDAALDDLYLELTKED 2- 43 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03346 Identities = 181/240 (75%), Positives = 208/240 (86%) Query: 3 MLKIENVTGGYVNIPVLKNISFEVNDGELVGLIGLNGAGKSTTINEIIGILRPYQGDITI 62 ML I+N+TGGY NIPVL ++SF V++GELVGLIGLNGAGKSTTINEIIG L+PYQG I+I Sbjct: 1 MLNIKNLTGGYHNIPVLNDVSFSVDNGELVGLIGLNGAGKSTTINEIIGFLKPYQGSISI 60 Query: 63 DGISLEADQELYRKKIGFIPETPSLYEELTLREHLETVAMAYDIATDEVMARAQKLLEMF 122- DG++L + YR+KIGFIPETPSLYEELTL EH+ TVAMAYDI + RAQ LEMF Sbjct: 61 DGLTLAENAVAYRQKIGFIPETPSLYEELTLSEHINTVAMAYDIDLEVAQKRAQPFLEMF 120- Query: 123 RLTDKLDWFPMHFSKGMKQKVMIICAFVVSPSLFIVDEPFLGLDPLAISDLINLLAEEKA 18- 2 RLTDKL+WFP++FSKGMKQKVMIICAFV+ PSLFI+DEPFLGLDPLAISDLI L EKA Sbjct: 121 RLTDKLEWFPVNFSKGMKQKVMIICAFVIDPSLFILDEPFLGLDPLAISDLIQTLEVEKA 18- 0 Query: 183 KGKSILMSTHVLDSAEKMCDRFVILHKGEIRAVGTLEELRAIFGDSNANLNDIYIALTKE 24- 2 KGKSILMSTHVLDSAE+MCDRFVILH G++RA GTL +L+ FGD +A+LNDIY+ALTKE Sbjct: 181 KGKSILMSTHVLDSAERMCDRFVILHHGQVRAQGTLADLQEAFGDRSASLNDIYLALTKE 24- 0 SEQ ID 3454 (GBS353) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 74 (lane 2; MW 30 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 81 (lane 6; MW 55 kDa). GBS353-GST was purified as shown in FIG. 216, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1118 A DNA sequence (GBSx1193) was identified in S. agalactiae <SEQ ID 3457> which encodes the amino acid sequence <SEQ ID 3458>. Analysis of this protein sequence reveals the following: TABLE-US-03347 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1475(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1119 A DNA sequence (GBSx1194) was identified in S. agalactiae <SEQ ID 3459> which encodes the amino acid sequence <SEQ ID 3460>. Analysis of this protein sequence reveals the following: TABLE-US-03348 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.68 Transmembrane 57-73 (50-80) INTEGRAL Likelihood = -8.49 Transmembrane 122-138 (103-152) INTEGRAL Likelihood = -6.58 Transmembrane 319-335 (308-337) INTEGRAL Likelihood = -4.99 Transmembrane 252-268 (249-273) INTEGRAL Likelihood = -4.19 Transmembrane 104-120 (103-121) INTEGRAL Likelihood = -3.50 Transmembrane 231-247 (229-248) INTEGRAL Likelihood = -1.91 Transmembrane 298-314 (298-314) INTEGRAL Likelihood = -1.44 Transmembrane 28-44 (27-44) ----- Final Results ----- bacterial membrane --- Certainty = 0.6074(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03349 >GP:CAB12845 GB:Z99109 ABC transporter (membrane protein) [Bacillus subtilis] Identities = 101/409 (24%), Positives = 187/409 (45%), Gaps = 76/409 (18%) Query: 1 MKKLFNKRRSLFLTQNSKYLRYVFNDHFVLVLMFLSGFLLYQYSQLLKDFPKTHWPIIVI 60 M ++ R + + Y++Y+ NDH V+VL+F YS+ ++D P H+P + Sbjct: 4 MLDIWQSRLQEHIKETRTYMKYMLNDHLVIVLIFFLAGAASWYSKWIRDIP-AHFPSFWV 62 Query: 61 VSIIILMLLAMGGIASYLEPADKQFLLIKEEAIKEIINSAKKRTYI-------------- 106- ++++ ++L + + L+ AD FLL E ++ + A +Y+ Sbjct: 63 MAVLFSLVLTSSYVRTLLKEADLVFLLPLEAKMEPYLKQAFVYSYVSQLFPLIALSIVAM 122- Query: 107 --FWLVIQTLFLVLISPILIKLGL------------------------------------ 12- 8 ++ V LV + + ++L L Sbjct: 123 PLYFAVTPGASLVSYAAVFVQLLLLKAWNQVMEWRTTFQNDRSMKRMDVIIRFAANTLVL 18- 2 Query: 129 -----SVFMITLLIFGLGIIKWLVITYKVKVFYNNQNLNWDAAINHEQERKQSILKFFSL 18- 3 SV+M LL++ + + +L ++ K + W++ I E RKQ + +L Sbjct: 183 YFVFQSVYMYALLVYVIMAVLYLYMSSAAK----RKTFKWESHIESELRRKQRFYRIANL 23- 8 Query: 184 FTNVKGISTSVKRRSFLDGILKLISKTPSRLWTNLFVRAFLRSSDYLGLTIRLVTLNILS 24- 3 FT+V + KRR++LD +L+L+ + + +F RAFLRSSDYLG+ +RL + L Sbjct: 239 FTDVPHLRKQAKRRAYLDFLLRLVPFEQRKTFAYMFTRAFLRSSDYLGILVRLTIVFALI 29- 8 Query: 244 VIFVNETYLALALAFVFN-YLLLFQLLALGHHFDYQYMNQLYPVRLNAKASQLKGFLRVL 30- 2 +++V+ + L A+ VF ++ QLL L HFD+ + +LYPV+ K ++LK + +L Sbjct: 299 IMYVSASPLIAAVLTVFAIFITGIQLLPLFGHFDHLALQELYPVQ---KETKLKSYFSLL 35- 5 Query: 303 SYAVTVIDSI----------LIRELKPVILLIVLMLIVTEYYIPYKIKK 341 A+++ + L L +I VL+ +V Y+ ++KK Sbjct: 356 KTALSIQALLMSVASAYAAGLTGFLYALIGSAVLIFVVLPAYMTTRLKK 404 A related DNA sequence was identified in S. pyogenes <SEQ ID 3461> which encodes the amino acid sequence <SEQ ID 3462>. Analysis of this protein sequence reveals the following: TABLE-US-03350 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.91 Transmembrane 126-142 (119-151) INTEGRAL Likelihood = -9.77 Transmembrane 320-336 (311-339) INTEGRAL Likelihood = -6.37 Transmembrane 59-75 (53-79) INTEGRAL Likelihood = -4.94 Transmembrane 28-44 (22-47) INTEGRAL Likelihood = -4.73 Transmembrane 250-266 (249-273) INTEGRAL Likelihood = -4.04 Transmembrane 231-247 (229-248) INTEGRAL Likelihood = -3.19 Transmembrane 298-314 (295-315) INTEGRAL Likelihood = -2.28 Transmembrane 103-119 (103-119) ----- Final Results ----- bacterial membrane --- Certainty = 0.6965(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03351 >GP:CAB12845 GB:Z99109 ABC transporter (membrane protein) [Bacillus subtilis] Identities = 96/403 (23%), Positives = 173/403 (42%), Gaps = 78/403 (19%) Query: 1 MKALFLKRRQDFQKQQNKYLRYVLNDHFVLVLMFLLGFAMVQYGQLLN----HEPT---- 52 M ++ R Q+ K+ Y++Y+LNDH V+VL+F L A Y + + HFP+ Sbjct: 4 MLDIWQSRLQEHIKETRTYMKYMLNDHLVIVLIFFLAGAASWYSKWIRDIPAHFPSFWVM 63 Query: 53 -------------NHLPIQVCLGILIPLLLSM---------------------------- 71 L + L L+PL M Sbjct: 64 AVLFSLVLTSSYVRTLLKEADLVFLLPLEAKMEPYLKQAFVYSYVSQLFPLIALSIVAMP 123- Query: 72 --------GSIATYLEEADQHFLLPKEEEVISYI------KQAERLSFLLWGTLQTAVLL 117- S+ +Y Q LL +V+ + + +R+ ++ T VL Sbjct: 124 LYFAVTPGASLVSYAAVFVQLLLLKAWNQVMEWRTTFQNDRSMKRMDVIIRFAANTLVLY 18- 3 Query: 118 FLYPIFRRLGLSLFIFIILVLILLALKRVVLSRKTRYFLRGNRLDWAKAVAFESNRKQSI 17- 7 F++ S++++ +LV +++A+ + +S + W + E RKQ Sbjct: 184 FVFQ-------SVYMYALLVYVIMAVLYLYMSSAAKR----KTFKWESHIESELRRKQRF 23- 2 Query: 178 LKFYSLFTTVKGISTKVKERTYLNPLLKLVKQTPSNLWLSLYARAFLRSSDYLGLFLRLM 23- 7 + +LFT V + + K R YL+ LL+LV + ++ RAFLRSSDYLG+ +RL Sbjct: 233 YRIANLFTDVPHLRKQAKRRAYLDFLLRLVPFEQRKTFAYMFTRAFLRSSDYLGILVRLT 29- 2 Query: 238 LLSSLSVFFIHNLYLSVSLALIFN-YLVVFQLLSLYYHYDYHYMTSLYPENSRSKKKNML 29- 6 ++ +L + ++ L ++ +F ++ QLL L+ H+D+ + LYP +K K+ Sbjct: 293 IVFALIIMYVSASPLIAAVLTVFAIFITGIQLLPLFGHFDHLALQELYPVQKETKLKSYF 35- 2 Query: 297 SFLR-GLSFLMLIVNMLCCSSAPKA--LILIVGMVFIACIYLP 336 S L+ LS L++++ +A L ++G + + LP Sbjct: 353 SLLKTALSIQALLMSVASAYAAGLTGFLYALIGSAVLIFVVLP 395 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03352 Identities = 170/344 (49%), Positives = 237/344 (68%) Query: 1 MKKLFNKRRSLFLTQNSKYLRYVFNDHFVLVLHFLSGFLLYQYSQLLKDFPKTHWPIIVI 60 MK LF KRR F Q +KYLRYV NDHFVLVLMFL GF + QY QLL FP H PI V Sbjct: 1 MKALFLKRRQDFQKQQNKYLRYVLNDHFVLVLMFLLGFAMVQYGQLLNHFPTNHLPIQVC 60 Query: 61 VSIIILMLLAMGGIASYLEPADKQFLLIKEEAIKEIINSAKKRTYIFWLVIQTLFLVLIS 120- + I+I +LL+MG IA+YLE AD+ FLL KEE + I A++ +++ W +QT L+ + Sbjct: 61 LGILIPLLLSMGSIATYLEEADQHFLLPKEEEVISYIKQAERLSFLLWGTLQTAVLLFLY 120- Query: 121 PILIKLGLSVFMITLLIFGLGIIKWLVITYKVKVFYNNQNLNWDAAINHEQERKQSILKF 18- 0 PI +LGLS+F+ +L+ L +K +V++ K + F L+W A+ E RKQSILKF Sbjct: 121 PIFRRLGLSLFIFIILVLILLALKRVVLSRKTRYFLRGNRLDWAKAVAFESNRKQSILKF 18- 0 Query: 181 FSLFTNVKGISTSVKRRSFLDGILKLISKTPSRLWTNLFVRAFLRSSDYLGLTIRLVTLN 24- 0 +SLFT VKGIST VK R++L+ +LKL+ +TPS LW +L+ RAFLRSSDYLGL +RL+ L+ Sbjct: 181 YSLFTTVKGISTKVKERTYLNPLLKLVKQTPSNLWLSLYARAFLRSSDYLGLFLRLMLLS 24- 0 Query: 241 ILSVIFVNETYLALALAFVFNYLLLFQLLALGHHFDYQYMNQLYPVRLNAKASQLKGFLR 30- 0 LSV F++ YL+++LA +FNYL++FQLL+L +H+DY YM LYP +K + FLR Sbjct: 241 SLSVFFIHNLYLSVSLALIFNYLVVFQLLSLYYHYDYHYMTSLYPENSRSKKKNMLSFLR 30- 0 Query: 301 VLSYAVTVIDSILIRELKPVILLIVLMLIVTEYYIPYKIKKMID 344 LS+ + +++ + ++LIV M+ + Y+PYK+KK+ID Sbjct: 301 GLSFLMLIVNMLCCSSAPKALILIVGMVFIACIYLPYKLKKIID 344 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1120 A DNA sequence (GBSx1195) was identified in S. agalactiae <SEQ ID 3463> which encodes the amino acid sequence <SEQ ID 3464>. Analysis of this protein sequence reveals the following: TABLE-US-03353 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2821(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03354 >GP:AAC00284 GB:AF008220 YtmP [Bacillus subtilis] Identities = 69/214 (32%), Positives = 121/214 (56%), Gaps = 1/214 (0%) Query: 12 PLRGKSGKAYIGTYPNGERVFVKYNTTPILPALAKEQIAPQLLWARRTSNGDMMSAQEWL 71 - P G +G AY + NG+++F+K N++P L L+ E I P+L+W +R NGD+++AQ W+ Sbjct: 20 PAGGATGDAYYAKH-NGQQLFLKRNSSPFLAVLSAEGIVPKLVWTKRMENGDVITAQHWM 78 Query: 72 DGRTLTKEDMGSKQIIHILLRLHKSRPLVNQLLQLGYKIENPYDLLMDWEKQTPIQIREN 131- GR L +DM + + +L ++H S+ L++ L +LG + NP LL ++ + + Sbjct: 79 TGRELKPKDMSGRPVAELLRKIHTSKALLDMLKRLGKEPLNPGALLSQLKQAVFAVQQSS 138- Query: 132 TYLQSIVTELKRSLPEFRTEVATIVHGDIKHSNWVITTSGLIYLVDWDSVRLTDRMYDVA 19- 1 +Q + L+ L E + H D+ H+NW+++ +YL+DWD + D D+ Sbjct: 139 PLIQEGIKYLEEHLHEVHFGEKVVCHCDVNHNNWLLSEDNQLYLIDWDGAMIADPAMDLG 19- 8 Query: 192 YILSHYIPQKHWKDWLSYYGYKDNEKVWSKIIWY 225 +L HY+ + W+ WLS YG + E + ++ WY Sbjct: 199 PLLYHYVEKPAWESWLSMYGIELTESLRLRMAWY 232 A related DNA sequence was identified in S. pyogenes <SEQ ID 3465> which encodes the amino acid sequence <SEQ ID 3466>. Analysis of this protein sequence reveals the following: TABLE-US-03355 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2686(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03356 Identities = 214/262 (81%), Positives = 242/262 (91%) Query: 1 MTISNQELTLTPLRGKSGKAYIGTYPNGERVFVKYNTTPILPALAKEQIAPQLLWARRTS 60 +T + QELTLTPLRGKSGKAY GTYPNGE VF+K NTTPILPALAKEQIAPQLLWA+R Sbjct: 1 VTTTEQELTLTPLRGKSGKAYKGTYPNGECVFIKLNTTPILPALAKEQIAPQLLWAKRHG 60 Query: 61 NGDMMSAQEWLDGRTLTKEDMGSKQIIHILLRLHKSRPLVNQLLQLGYKIENPYDLLMDW 120- NGDMMSAQEWL+GRTLTKEDM SKQIIHILLRLHKS+ LVNQLLQL YKIENPYDLL+D+ Sbjct: 61 NGDMMSAQEWLNGRTLTKEDMNSKQIIHILLRLHKSKKLVNQLLQLNYKIENPYDLLVDF 120- Query: 121 EKQTPIQIRENTYLQSIVTELKRSLPEFRTEVATIVHGDIKHSNWVITTSGLIYLVDWDS 18- 0 E+ P+QI++N+YLQ+IV ELKRSLPEF++EVATIVHGDIKHSNWVITTSG+I+LVDWDS Sbjct: 121 EQNAPLQIQQNSYLQAIVKELKRSLPEFKSEVATIVHGDIKHSNWVITTSGMIFLVDWDS 18- 0 Query: 181 VRLTDRMYDVAYILSHYIPQKHWKDWLSYYGYKDNEKVWSKIIWYGQFSYLSQIIKCFDK 24- 0 VRLTDRMYDVAY+LSHYIP+ W +WLSYYGYK+N+KV KIIWYGQFS+L+QI+KCFDK Sbjct: 181 VRLTDRMYDVAYLLSHYIPRSRWSEWLSYYGYKNNDKVMQKIIWYGQFSHLTQILKCFDK 24- 0 Query: 241 RDMEHVNQEIYELRKFRELIKK 262 RDMEHVNQEIY LRKFRE+ +K Sbjct: 241 RDMEHVNQEIYALRKFREIFRK 262 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1121 A DNA sequence (GBSx1196) was identified in S. agalactiae <SEQ ID 3467> which encodes the amino acid sequence <SEQ ID 3468>. Analysis of this protein sequence reveals the following: TABLE-US-03357 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4529(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03358 >GP:AAC00285 GB:AF008220 YtmQ [Bacillus subtilis] Identities = 126/211 (59%), Positives = 161/211 (75%) Query: 1 MRVRKRKGAEEHLENNPHYVISNPEEAKGRWHEIFGNNNPIHIEVGSGKGAFITGMAEQN 60 MR+R + A++ L N ISNP + KG+W+ +FGN+NPIHIEVG+GKG FI+GMA+QN Sbjct: 1 MRMRHKPWADDFLAENADIAISNPADYKGKWNTVFGNDNPIHIEVGTGKGQFISGMAKQN 60 Query: 61 PDINYIGIDIQLSVLSYALDKVLDSGAKNIKLLLVDGSSLSNYFDTGEVDLMYLNFSDPW 120- PDINYIGI++ SV+ A+ KV DS A+N+KLL +D +L++ F+ GEV +YLNFSDPW Sbjct: 61 PDINYIGIELFKSVIVTAVQKVKDSEAQNVKLLNIDADTLTDVFEPGEVKRVYLNFSDPW 120- Query: 121 PKKKHEKRRLTYKTFLDTYKDILPEQGEIHFKTDNRGLFEYSLASFSQYGMTLKQVWLDL 18- 0 PKK+HEKRRLTY FL Y++++ + G IHFKTDNRGLFEYSL SFS+YG+ L V LDL Sbjct: 121 PKKRHEKRRLTYSHFLKKYEEVMGKGGSIHFKTDNRGLFEYSLKSFSEYGLLLTYVSLDL 18- 0 Query: 181 HASDYQQNIMTEYERKFSNKGQVIYRVEARF 211 H S+ + NIMTEYE KFS GQ IYR E + Sbjct: 181 HNSNLEGNIMTEYEEKFSALGQPIYRAEVEW 211 A related DNA sequence was identified in S. pyogenes <SEQ ID 3469> which encodes the amino acid sequence <SEQ ID 3470>. Analysis of this protein sequence reveals the following: TABLE-US-03359 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3303(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03360 Identities = 179/211 (84%), Positives = 193/211 (90%) Query: 1 MRVRKRKGAEEHLENNPHYVISNPEEAKGRWHEIFGNNNPIHIEVGSGKGAFITGMAEQN 60 MRVRKRKGAEEHL NNPHYVI NPE+AKGRWH++FGN+ PIHIEVGSGKG FITGMA +N Sbjct: 1 MRVRKRKGAEEHLANNPHYVILNPEDAKGRWHDVFGNDRPIHIEVGSGKGGFITGMALKN 60 Query: 61 PDINYIGIDIQLSVLSYALDKVLDSGAKNIKLLLVDGSSLSNYFDTGEVDLMYLNFSDPW 120- PDINYIGIDIQLSVLSYALDKVL S N+KLL VDGSSL+NYF+ GEVD+MYLNFSDPW Sbjct: 61 PDINYIGIDIQLSVLSYALDKVLASEVPNVKLLRVDGSSLTNYFEDGEVDMMYLNFSDPW 120- Query: 121 PKKKHEKRRLTYKTFLDTYKDILPEQGEIHFKTDNRGLFEYSLASFSQYGMTLKQVWLDL 18- 0 PK KHEKRRLTYK FLDTYK ILPE GEIHFKTDNRGLFEYSLASFSQYGMTL+Q+WLDL Sbjct: 121 PKTKHEKRRLTYKDFLDTYKRILPEHGEIHFKTDNRGLFEYSLASFSQYGMTLRQIWLDL 18- 0 Query: 181 HASDYQQNIMTEYERKFSNKGQVIYRVEARF 211 HAS+Y+ N+MTEYE KFSNKGQVIYRVEA F Sbjct: 181 HASNYEGNVMTEYEEKFSNKGQVIYRVEANF 211 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1122 A DNA sequence (GBSx1197) was identified in S. agalactiae <SEQ ID 3471> which encodes the amino acid sequence <SEQ ID 3472>. Analysis of this protein sequence reveals the following: TABLE-US-03361 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1311(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-03362 >GP:BAB06136 GB:AP001515 unknown conserved protein [Bacillus halodurans] Identities = 61/124 (49%), Positives = 81/124 (65%), Gaps = 2/124 (1%) Query: 2 GGDYVLSILIDKPGGITVEDTAQLTDVVSPLLDTIQPDPFPEQYMLEVSSPGLERPLKTA 61 G D+ L + ID G+ +ED ++++ +S LD + DP + Y LEVSSPG ERPLK Sbjct: 33 GKDWFLRVFIDSETGVDLEDCGKVSERLSEKLD--ETDPIEQAYFLEVSSPGAERPLKRE 90 Query: 62 EALSNAVGSYINVSLYKSIDKVKIFEGDLLSFDGETLTIDYMDKTRHKTVDIPYQTVAKA 121- + L ++G ++V+LY+ ID K EG+L FDGETLTI+ KTR KTV IPY VA A Sbjct: 91 KDLLRSIGKNVHVTLYEPIDGEKALEGELTEFDGETLTIEIKIKTRKKTVTIPYAKVASA 150- Query: 122 RLAV 125 RLAV Sbjct: 151 RLAV 154 A related DNA sequence was identified in S. pyogenes <SEQ ID 3473> which encodes the amino acid sequence <SEQ ID 3474>. Analysis of this protein sequence reveals the following: TABLE-US-03363 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3445(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03364 Identities = 101/127 (79%), Positives = 117/127 (91%) Query: 1 MGGDYVLSILIDKPGGITVEDTAQLTDVVSPLLDTIQPDPFPEQYMLEVSSPGLERPLKT 60 MG DY+LSIL+DK GGITVEDT+ LT+++SPLLDTI PDPFP QYMLEVSSPGLERPLKT Sbjct: 52 MGSDYILSILVDKEGGITVEDTSDLTNIISPLLDTIDPDPFPNQYMLEVSSPGLERPLKT 111- Query: 61 AEALSNAVGSYINVSLYKSIDKVKIFEGDLLSFDGETLTIDYMDKTRHKTVDIPYQTVAK 120- A++L AVGSYINVSLY++IDKVK+F+GDLL+FDGETLTIDY+DKTRHK V+IPYQ VAK Sbjct: 112 ADSLKAAVGSYINVSLYQAIDKVKVFQGDLLAFDGETLTIDYLDKTRHKIVNIPYQAVAK 17- 1 Query: 121 ARLAVKL 127 R+AVKL Sbjct: 172 VRMAVKL 178 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1123 A DNA sequence (GBSx1198) was identified in S. agalactiae <SEQ ID 3475> which encodes the amino acid sequence <SEQ ID 3476>. This protein is predicted to be n utilization substance protein a homolog (nusA). Analysis of this protein sequence reveals the following: TABLE-US-03365 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5069(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9565> which encodes amino acid sequence <SEQ ID 9566> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03366 >GP: CAB13533 GB: Z99112 nusA [Bacillus subtilis] Identities = 164/370 (44%), Positives = 251/370 (67%), Gaps = 15/370 (4%) Query: 4 MSKEMLEAFRILEEEKHINKEDIIDAVTESLKSAYKRRYGQSESCVIEFNEKKADFTVYT 63 MS E+L+A ILE+EK I+KE II+A+ +L SAYKR + Q+++ ++ N + V+ Sbjct: 1 MSSELLDALTILEKEKGISKEIIIEAIEAALISAYKRNFNQAQNVRVDLNRETGSIRVFA 60 Query: 64 VREVVDEVFDSRLEISLKDALAISSAYELGDKIRFEESVTEFGRVAAQSAKQTIMEKMRR 123- ++VVDEV+D RLEIS+++A I Y +GD + E + +FGR+AAQ+AKQ + +++R Sbjct: 61 RKDVVDEVYDQRLEISIEEAQGIHPEYMVGDVVEIEVTPKDFGRIAAQTAKQVVTQRVRE 120- Query: 124 QMREVTFNEYKQHEGEIMTGTVERFDQRFIYVNLGSLEAQLSHQDQIPGESFKSHDMIDV 18- 3 R V ++E+ E +IMTG V+R D +FIYV+LG +EA L +Q+P ES+K HD I V Sbjct: 121 AERGVIYSEFIDREEDIMTGIVQRLDNKFIYVSLGKIEALLPVNEQMPNESYKPHDRIKV 18- 0 Query: 184 YVYKVENNPKGVNVFVSRSHPEFIKRIMEREIPEVFDGTVEIMSVSREAGDRTKVAVRSH 24- 3 Y+ KVE KG ++VSR+HP +KR+ E E+PE++DGTVE+ SV+REAGDR+K++VR+ Sbjct: 181 YITKVEKTTKGPQIYVSRTHPGLLKRLFEIEVPEIYDGTVELKSVAREAGDRSKISVRTD 24- 0 Query: 244 NSNVDAIGTIVGRGGSNIKKVISNFHPKRVDAKTGLEIPVEENIDVIQWVEDPAEFIYNA 30- 3 + +VD +G+ VG G ++ +++ E ID++ W DP EF+ NA Sbjct: 241 DPDVDPVGSCVGPKGQRVQAIVNELK--------------GEKIDIVNWSSDPVEFVANA 28- 6 Query: 304 IAPAEVDMVLFDDEDTKRATVVVPDSKLSLAIGRRGQNVRLAAHLTGYRIDIKSASEYEK 36- 3 ++P++V V+ ++E+ K TV+VPD +LSLAIG+RGQN RLAA LTG++IDIKS ++ + Sbjct: 287 LSPSKVLDVIVNEEE-KATTVIVPDYQLSLAIGKRGQNARLAAKLTGWKIDIKSETDARE 34- 5 Query: 364 MEAQELQTEE 373 + + EE Sbjct: 346 LGIYPRELEE 355 A related DNA sequence was identified in S. pyogenes <SEQ ID 3477> which encodes the amino acid sequence <SEQ ID 3478>. Analysis of this protein sequence reveals the following: TABLE-US-03367 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2074(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03368 Identities = 348/380 (91%), Positives = 361/380 (94%), Gaps = 2/380 (0%) Query: 4 MSKEMLEAFRILEEEKHINKEDIIDAVTESLKSAYKRRYGQSESCVIEFNEKKADFTVYT 63 MSKEMLEAFRILEEEKHI+K DIIDAVTESLKSAYKRRYGQSESCVIEFNEK ADF V+T Sbjct: 12 MSKEMLEAFRILEEEKHIDKADIIDAVTESLKSAYKRRYGQSESCVIEFNEKTADFQVFT 71 Query: 64 VREVVDEVFDSRLEISLKDALAISSAYELGDKIRFEESVTEFGRVAAQSAKQTIMEKMRR 123- VREVV+EVFDSRLEISLKDALAISSAYELGDKIRFEESV EFGRVAAQSAKQTIMEKMRR Sbjct: 72 VREVVEEVFDSRLEISLKDALAISSAYELGDKIRFEESVNEFGRVAAQSAKQTIMEKMRR 131- Query: 124 QMREVTFNEYKQHEGEIMTGTVERFDQRFIYVNLGSLEAQLSHQDQIPGESFKSHDMIDV 18- 3 QMREV FNEYK+HEGEIMTGTVERFDQRFIYVNLGSLEAQLSHQDQIPGE+FKSHD IDV Sbjct: 132 QMREVMFNEYKEHEGEIMTGTVERFDQRFIYVNLGSLEAQLSHQDQIPGETFKSHDRIDV 19- 1 Query: 184 YVYKVENNPKGVNVFVSRSHPEFIKRIMEREIPEVFDGTVEIMSVSREAGDRTKVAVRSH 24- 3 YVYKVENNPKGVNVFVSRSHPEFIKRIME+EIPEVFDGTVEIMSVSREAGDRTKVAVRSH Sbjct: 192 YVYKVENNPKGVNVFVSRSHPEFIKRIMEQEIPEVFDGTVEIMSVSREAGDRTKVAVRSH 25- 1 Query: 244 NSNVDAIGTIVGRGGSNIKKVISNFHPKRVDAKTGLEIPVEENIDVIQWVEDPAEFIYNA 30- 3 N NVDAIGTIVGRGGSNIKKVIS FHPKRVDAKTGLEIPVEENIDVIQWV+DPAEFIYNA Sbjct: 252 NPNVDAIGTIVGRGGSNIKKVISKFHPKRVDAKTGLEIPVEENIDVIQWVDDPAEFIYNA 31- 1 Query: 304 IAPAEVDMVLFDDEDTKRATVVVPDSKLSLAIGRRGQNVRLAAHLTGYRIDIKSASEYEK 36- 3 IAPAEVDMVLFDDED KRATVVVPDSKLSLAIGRRGQNVRLAAHLTGYRIDIKSASEY++ Sbjct: 312 IAPAEVDMVLFDDEDLKRATVVVPDSKLSLAIGRRGQNVRLAAHLTGYRIDIKSASEYDR 37- 1 Query: 364 MEAQELQTEEVAQESEVISD 383 +EA+ + A E V+ D Sbjct: 372 LEAE--KEAATAVEEPVVDD 389 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1124 A DNA sequence (GBSx1199) was identified in S. agalactiae <SEQ ID 3479> which encodes the amino acid sequence <SEQ ID 3480>. Analysis of this protein sequence reveals the following: TABLE-US-03369 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2012(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03370 >GP: CAB13534 GB: Z99112 alternate gene name: ymxB~similar to hypothetical proteins [Bacillus subtilis] Identities = 46/92 (50%), Positives = 67/92 (72%), Gaps = 1/92 (1%) Query: 1 MAKTKKIPLRKSVVSGEVIDKRDLLRIVKNKEGQVFIDPTGKQNGRGAYIKLDNDEAILA 60 M K KKIPLRK VV+GE+ K++L+R+V++KEG++ +DPTGK+NGRGAY+ LD + + A Sbjct: 1 MNKHKKIPLRKCVVTGEMKPKKELIRVVRSKEGEISVDPTGKKNGRGAYLTLDKECILAA 60 Query: 61 KKKRVFDRSFSMEVSDEFYDELLAYVDHKVKR 92 KKK F ++ D+ +DELL + KVK+ Sbjct: 61 KKKNTLQNQFQSQIDDQIFDELLELAE-KVKK 91 A related DNA sequence was identified in S. pyogenes <SEQ ID 3481> which encodes the amino acid sequence <SEQ ID 3482>. Analysis of this protein sequence reveals the following: TABLE-US-03371 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1008(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03372 Identities = 77/98 (78%), Positives = 92/98 (93%) Query: 1 MAKTKKIPLRKSVVSGEVIDKRDLLRIVKNKEGQVFIDPTGKQNGRGAYIKLDNDEAILA 60 M+K KKIPLRKS+VSGE+I KRDLLRIVK K+GQVFIDPTGKQNGRGAYIKLDN EA++A Sbjct: 2 MSKVKKIPLRKSLVSGEIIAKRDLLRIVKTKDGQVFIDPTGKQNGRGAYIKLDNQEALMA 61 Query: 61 KKKRVFDRSFSMEVSDEFYDELLAYVDHKVKRRELGLE 98 KKK+VF+RSFSH++ + FYD+L+AYVDHK+KRRELGL+ Sbjct: 62 KKKQVFNRSFSMDIPESFYDDLIAYVDHKIKRRELGLD 99 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1125 A DNA sequence (GBSx1200) was identified in S. agalactiae <SEQ ID 3483> which encodes the amino acid sequence <SEQ ID 3484>. This protein is predicted to be probable ribosomal protein in infb 5'region. Analysis of this protein sequence reveals the following: TABLE-US-03373 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03374 >GP: BAB06133 GB: AP001515 unknown conserved protein [Bacillus halodurans] Identities = 46/95 (48%), Positives = 65/95 (68%), Gaps = 1/95 (1%) Query: 6 KVLNLIGLAQRAGRLITGEELVIKAIQNQQVSLIFLANDAGPNLTKKVTDKSNYYKTEVS 65 K L+L+GLA RA +L+TGEE V+KA+QN QV+L+ L++DAG + KK+ DK Y+ V Sbjct: 5 KWLSLLGLAARARQLLTGEEQVVKAVQNGQVTLVILSSDAGIHTKKKLLDKCGSYQIPVK 64 Query: 66 TVFSTLELSDALGK-PRKVVAVADAGFSKKMRTLM 99 V + L A+GK R V+ V DAGFS+K+ L+ Sbjct: 65 VVGNRQMLGRAIGKHERVVIGVKDAGFSRKLAALI 99 A related DNA sequence was identified in S. pyogenes <SEQ ID 3485> which encodes the amino acid sequence <SEQ ID 3486>. Analysis of this protein sequence reveals the following: TABLE-US-03375 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1950(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03376 Identities = 75/99 (75%), Positives = 88/99 (88%) Query: 1 MNNSEKVLNLIGLAQRAGRLITGEELVIKAIQNQQVSLIFLANDAGPNLTKKVTDKSNYY 60 + N E++ +LIG AQRAG++I+GEELV+KAIQ+QQV L+FLANDAGPN+TKKVTDKSNYY Sbjct: 1 LTNLERLSSLIGPAQRAGKVISGEELVVKAIQHQQVILVFLANDAGPNVTKKVTDKSNYY 60 Query: 61 KTEVSTVFSTLELSDALGKPRKVVAVADAGFSKKMRTLM 99 EVSTV + LELS ALGKPRKV A+ADAGFSKKMRTLM Sbjct: 61 NVEVSTVLNALELSAALGKPRKVAAIADAGFSKKMRTLM 99 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1126 A DNA sequence (GBSx1201) was identified in S. agalactiae <SEQ ID 3487> which encodes the amino acid sequence <SEQ ID 3488>. Analysis of this protein sequence reveals the following: TABLE-US-03377 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2873(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10959> which encodes amino acid sequence <SEQ ID 10960> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 3489> which encodes the amino acid sequence <SEQ ID 3490>. Analysis of this protein sequence reveals the following: TABLE-US-03378 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2985(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03379 Identities = 735/961 (76%), Positives = 805/961 (83%), Gaps = 42/961 (4%) Query: 1 MSKKRLHEIAKEIGKTSKEVVEQAQSLGLPVKSHASSVEENDATRIVESFS-SSKTKAPT 59 +SKKRLHEIAKEIGK+SKEVVE A+ LGL VKSHASSVEE DA +I+ SFS +SK Sbjct: 1 LSKKRLHEIAKEIGESSKEVVEHAKYLGLDVKSHASSVEEADAKKIISSFSKASKPDVTA 60 Query: 60 NSVQTNQGVKTESKTVETKQGLSDDKPSTQPVAKPKPQSRNFKAEREARAKAEAEKRQHN 119- + + V S TV + G S+ TQ V+KPK SRNFKAEREARAK +A ++Q N Sbjct: 61 SQTVKPKEVAQPSVTVVKETG-SEHVEKTQ-VSKPK--SRNFKAEREARAKEQAARKQAN 116- Query: 120 GD----------HRKNNRHNDTRSDDRR--HQGQKRSNGNR-----------NDNRQ--G 15- 4 G +R+ N H D+R H+ Q +N R +DN Q G Sbjct: 117 GSSHRSQERRGGYRQPNNHQTNEQGDKRITHRSQGDTNDKRIERKASNVSPRHDNHQLVG 17- 6 Query: 155 QQNN----RNKNDGRYADHKQKPQTRPQQPAGNRIDFKARAAALKAEQNAEYSRHSEQRF 21- 0 +N N +GR+ + K++ + PQ + +IDFKARAAALKAEQNAEYSR SE RF Sbjct: 177 DRNRSFAKENHKNGRFTNQKKQGRQEPQSKSP-KIDFKARAAALKAEQNAEYSRQSETRF 23- 5 Query: 211 REEQEAKRQAAKEQELAKAAALKAQEEAQKAKEKLASKPVAKVKEIVNKVAATPSQTADS 27- 0 R +QEAKR A ++ AK AALKAQ E +E A K + + + + + TAD+ Sbjct: 236 RAQQEAKRLAELARQEAKEAALKAQAEEMSHREA-ALKSIEEAETKLKSSNISAKSTADN 29- 4 Query: 271 RRKKQTRSDKSRQFSNENEDGQKQTRNKKNWNNQNQVRNQRNSNWNHNKKNKKGK----T 32- 6 RRKKQ R +K+R+ ++ +++GQK +NKK+WN+QNQVRNQ+NSNWN NKK KKGK T Sbjct: 295 RRKKQARPEKNRELTHHSQEGQK--KNKKSWNSQNQVRNQKNSNWNKNKKTKKGKNVKNT 35- 2 Query: 327 NGAPKPVTERKFHELPKEFEYTEGMTVAEIAKRIKREPAEIVKKLFMMGVMATQNQSLDG 38- 6 N APKPVTERKFHELPKEFEYTEGMTVAEIAKRIKREPAEIVKKLFMMGVMATQNQSLDG Sbjct: 353 NTAPKPVTERKFHELPKEFEYTEGMTVAEIAKRIKREPAEIVKKLFMMGVMATQNQSLDG 41- 2 Query: 387 DTIELLMVDYGIEAHAKVEVDEADIERFFADEDYLNPDNLTERPPVVTIMGHVDHGKTTL 44- 6 DTIELLMVDYGIEA AKVEVD+ADIERFF DE+YLNP+N+ ER PVVTIMGHVDHGKTTL Sbjct: 413 DTIELLMVDYGIEAKAKVEVDDADIERFFEDENYLNPENIVERAPVVTIMGHVDHGKTTL 47- 2 Query: 447 LDTLRNSRVATGEAGGITQHIGAYQIEEAGKKITFLDTPGHAAFTSMRARGASVTDITIL 50- 6 LDTLRNSRVATGEAGGITQHIGAYQIEEAGKKITFLDTPGHAAFTSMRARGASVTDITIL Sbjct: 473 LDTLRNSRVATGEAGGITQHIGAYQIEEAGKKITFLDTPGHAAFTSMRARGASVTDITIL 53- 2 Query: 507 IVAADDGVMPQTVEAINHSKAAGVPIIVAINKIDKPGANPERVISELAEHGVISTAWGGE 56- 6 IVAADDGVMPQT+EAINHSKAAGVPIIVAINKIDKPGANPERVI+ELAE+G+ISTAWGGE Sbjct: 533 IVAADDGVMPQTIEAINHSKAAGVPIIVAINKIDKPGANPERVIAELAEYGIISTAWGGE 59- 2 Query: 567 SEFVEISAKFGKNIQELLETVLLVAEMEELKADADVRAIGTVIEARLDKGKGAVATLLVQ 62- 6 EFVEISAKF KNI ELLETVLLVAE+EELKAD VRAIGTVIEARLDKGKGA+ATLLVQ Sbjct: 593 CEFVEISAKFNKNIDELLETVLLVAEVEELKADPTVRAIGTVIEARLDKGKGAIATLLVQ 65- 2 Query: 627 QGTLNVQDPIVVGNTFGRVRAMTNDLGRRVKVAGPSTPVSITGLNEAPMAGDHFAVYADE 68- 6 QGTL+VQDPIVVGNTFGRVRAM NDLGRRVK A PSTPVSITGLNE PMAGDHFAVYADE Sbjct: 653 QGTLHVQDPIVVGNTFGRVRAMVNDLGRRVKSAEPSTPVSITGLNETPMAGDHFAVYADE 71- 2 Query: 687 KAARAAGEERAKRALLKQRQNTQRVSLENLFDTLKAGEVKSVNVIIKADVQGSVEALAAS 74- 6 KAARAAGEER+KRALLKQRQNTQRVSL+NLFDTLKAGE+K+VNVIIKADVQGSVEALAAS Sbjct: 713 KAARAAGEERSKRALLKQRQNTQRVSLDNLFDTLKAGEIKTVNVIIKADVQGSVEALAAS 77- 2 Query: 747 LLKIDVEGVKVNVVHSAVGAINESDVTLAEASNAVIIGFNVRPTPQARQQADADDVEIRQ 80- 6 L+KI+VEGV+VNVVHSAVGAINESDVTLAEASNAVIIGFNVRPTPQARQQAD DDVEIR Sbjct: 773 LVKIEVEGVRVNVVHSAVGAINESDVTLAEASNAVIIGFNVRPTPQARQQADTDDVEIRL 83- 2 Query: 807 HSIIYKVIEEVEEAMKGKLDPEYQEKILGEAIIRETFKVSKVGTIGGFMVINGKVTRDSS 86- 6 HSIIYKVIEEVEEAMKGKLDP YQEKILGEAIIRETFKVSKVGTIGGFMVINGKVTRDSS Sbjct: 833 HSIIYKVIEEVEEAMKGKLDPVYQEKILGEAIIRETFKVSKVGTIGGFMVINGKVTRDSS 89- 2 Query: 867 VRVIRDGVVIFDGKLASLKHYKDDVKEVGNAQEGGLMIENYNDLKEDDTIEAYIMEEIKRK 9- 27 VRVIRD VVIFDGKLASLKHYKDDVKEVGNAQEGGLMIEN+NDLK DDTIEAYIMEEI RK Sbjct: 893 VRVIRDSVVIFDGKLASLKHYKDDVKEVGNAQEGGLMIENFNDLKVDDTIEAYIMEEIVRK 9- 53 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1127 A DNA sequence (GBSx1202) was identified in S. agalactiae <SEQ ID 3491> which encodes the amino acid sequence <SEQ ID 3492>. This protein is predicted to be ribosome binding factor A (rbfA). Analysis of this protein sequence reveals the following: TABLE-US-03380 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2557(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9567> which encodes amino acid sequence <SEQ ID 9568> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 3493> which encodes the amino acid sequence <SEQ ID 3494>. Analysis of this protein sequence reveals the following: TABLE-US-03381 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4765(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03382 Identities = 93/117 (79%), Positives = 103/117 (87%) Query: 8 LIMANHRIDRVGMEIKREVNEILRLRVNDPRVQDVTITDVQMLGDLSMAKVFYTIHSTLA 67 + MANHRIDRVGMEIKREVN+IL+ +V DPRVQ VTIT+VQM GDLS+AKV+YTI S LA Sbjct: 1 MAMANHRIDRVGMEIKREVNDILQKKVRDPRVQGVTITEVQMQGDLSLAKVYYTIMSDLA 60 Query: 68 SDNQKAQIGLEKATGTIKRELGKNLTMYKIPDLQFVKDESIEYGNKIDEMLRNLDKK 124 SDNQKAQ GLEKATGTIKRELGK LTMYKIPDL F KD SI YGNKID++LR+LD K Sbjct: 61 SDNQKAQTGLEKATGTIKRELGKQLTMYKIPDLVFEKDNSIAYGNKIDQLLRDLDNK 117 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1128 A DNA sequence (GBSx1203) was identified in S. agalactiae <SEQ ID 3495> which encodes the amino acid sequence <SEQ ID 3496>. This protein is predicted to be esterase. Analysis of this protein sequence reveals the following:

TABLE-US-03383 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03384 >GP:AAA79277 GB:M64783 acetyl-hydrolase [Streptomyces hygroscopicus] Identities = 58/220 (26%), Positives = 90/220 (40%), Gaps = 8/220 (3%) Query: 98 WNDNGKANQKTIFYLAGGSYLNNPTPYHISMLKTLSTSLDAKIILPIYPKTPRYTYDYAI 157- W + + +T+ YL GGSY H + L + A ++ Y + P + A+ Sbjct: 58 WVRPARQDGRTLLYLHGGSYALGSPQSHRHLSSALGDAAGAAVLALHYRRPPESPFPAAV 117- Query: 158 PRLVNLYRHFHEKN---ANLTLMGDSAGGGLALGLAHALSHQSGQEAIPQPKNIILLSPW 21- 4 V YR E+ +TL GDSAG GLA+ AL P P + +SPW Sbjct: 118 EDAVAAYRMLLEQGCPPGRVTLAGDSAGAGLAVAALQALR----DAGTPLPAAAVCISPW 17- 3 Query: 215 LDVTMKHPEIPKYEDTDPILSAWGLARVGEIWANGSNNTNHTYVSPKNAPATKLAPITLF 27- 4 D+ + + + +L L R+ E + G+ + H SP + T L P+ + Sbjct: 174 ADLACEGASHTTRKAREILLDTADLRRMAERYLAGT-DPRHPLASPAHGDLTGLPPLLIQ 23- 2 Query: 275 TGTREIFFPDIRDYAAQLQAANHPVNYIAQEGMNHVYPIY 314 G+ E+ D R A PV + M HV+ Y Sbjct: 233 VGSEEVLHDDARALEQAALKAGTPVTFEEWPEMFHVWHWY 272 A related DNA sequence was identified in S. pyogenes <SEQ ID 3497> which encodes the amino acid sequence <SEQ ID 3498>. Analysis of this protein sequence reveals the following: TABLE-US-03385 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03386 Identities = 244/334 (73%), Positives = 280/334 (83%), Gaps = 6/334 (1%) Query: 1 MKPSFKKLLLLFSIITILSIACTPHAKASGRSWKSWFIEQYFWLKRDKSYYKVQDESSFQ 60 +K +K L+ ++ L + TP A AS RSWKSWFIEQYFWLKRDKSYY QD+ SFQ Sbjct: 1 LKHPIRKTLVTLGLLLTLCLP-TPVA-ASSRSWKSWFIEQYFWLKRDKSYYSKQDDPSFQ 58 Query: 61 KYLNASREQSDKGYYLDPNSVNGGLVQERLFDMQVYSWNDNGKANQKTIFYLAGGSYLNN 120- +YL+A REQSDK Y LD N VNG LVQE L+ MQVYSWNDNGK +QKTI YLAGGSYLNN Sbjct: 59 RYLDACREQSDKPYQLDTNLVNGPLVQENLYGMQVYSWNDNGKPDQKTIIYLAGGSYLNN 118- Query: 121 PTPYHISMLKTLSTSLDAKIILPIYPKTPRYTYDYAIPRLVNLYRHFHEKNANLTLMGDS 18- 0 PT YHI+MLKTLSTSLDAKI+LPIYPK PRYTY+Y +P+LVNLY+H++ KN N+ LMGDS Sbjct: 119 PTTYHINMLKTLSTSLDAKIVLPIYPKAPRYTYNYTMPKLVNLYQHYYHKNQNVFLMGDS 17- 8 Query: 181 AGGGLALGLAHALSHQSGQEAIPQPKNIILLSPWLDVTMKHPEIPKYEDTDPILSAWGLA 24- 0 AGGGLALGLAHAL + E++PQPK ++LLSPWLDVTM HPEIP+YED DPILS+WGL Sbjct: 179 AGGGLALGLAHALHN----ESVPQPKQLVLLSPWLDVTMSHPEIPEYEDADPILSSWGLK 23- 4 Query: 241 RVGEIWANGSNNTNHTYVSPKNAPATKLAPITLFTGTREIFFPDIRDYAAQLQAANHPVN 30- 0 RVGE+WA ++NTNH YVSPKN P T L PITLFTGTREIF+PDIRDYAA+L+AANH + Sbjct: 235 RVGELWAYSADNTNHIYVSPKNGPITYLPPITLFTGTREIFYPDIRDYAAKLKAANHNIT 29- 4 Query: 301 YIAQEGMNHVYPIYPIEEAKTAQYQMIDIINKTP 334 +I QEGMNHVYPIYPIEEAKTAQYQ+ID INKTP Sbjct: 295 FITQEGMNHVYPIYPIEEAKTAQYQIIDAINKTP 328 A related GBS gene <SEQ ID 8731> and protein <SEQ ID 8732> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03387 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: 11.88 GvH: Signal Score (-7.5): -1.33 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 4.03 threshold: 0.0 PERIPHERAL Likelihood = 4.03 174 modified ALOM score: -1.31 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00077## SEQ ID 8732 (GBS149) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 23 (lane 6; MW 37 kDa). The GBS149-His fusion product was purified (FIG. 196, lane 6) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 291), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1129 A DNA sequence (GBSx1204) was identified in S. agalactiae <SEQ ID 3499> which encodes the amino acid sequence <SEQ ID 3500>. This protein is predicted to be CopY. Analysis of this protein sequence reveals the following: TABLE-US-03388 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3140(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03389 >GP:AAG10085 GB:AF296446 CopY [Streptococcus mutans] Identities = 67/137 (48%), Positives = 98/137 (70%) Query: 2 TISSAEWEIMRVVWAQQNTTSNEILAVLLEKYDWTPSTVKTLLRRLLDKGYVSREKMGKG 61 +IS+AEWE+MRVVWA+Q T+S+EI+A+L Y W+ ST+KTL+ RL +KGY++ ++ G+ Sbjct: 3 SISNAEWEVMRVVWAKQMTSSSEIIAILSRTYCWSASTIKTLITRLSEKGYLTSQRQGRK 62 Query: 62 FSYSPLIDEDLAMMSEVDSVFQKVCQTKHVAIVRHLLESIPMTEKDRLNLQSSLEAKKGK 121- + YS LI E+ A+ +V VF ++C TKH A++RHL+E PMT D L++ L +KK Sbjct: 63 YIYSSLISEEEALEQQVSEVFSRICVTKHQALIRHLVEETPMTLSDIEKLEALLLSKKAN 122- Query: 122 TLERVACNCIPGQCQCH 138 + V CNCI GQC C+ Sbjct: 123 AVPEVKCNCIVGQCSCY 139 A related DNA sequence was identified in S. pyogenes <SEQ ID 3501> which encodes the amino acid sequence <SEQ ID 3502>. Analysis of this protein sequence reveals the following: TABLE-US-03390 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2331(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03391 Identities = 54/135 (40%), Positives = 84/135 (62%) Query: 3 ISSAEWEIMRVVWAQQNTTSNEILAVLLEKYDWTPSTVKTLLRRLLDKGYVSREKMGKGF 62 IS+AEWE+MRVVWA + S++I+ +L +KY W+ ST+KTL+ RL+ K +++ + G+ + Sbjct: 10 ISAAEWEVMRVVWASGDIKSSDIITILRKKYQWSDSTIKTLIGRLVKKNFLTSYRQGRAY 69 Query: 63 SYSPLIDEDLAMMSEVDSVFQKVCQTKHVAIVRHLLESIPMTEKDRLNLQSSLEAKKGKT 122- Y L+DE L + +V +CQ +H ++ L +PMT ++ Q LE KK Sbjct: 70 IYQALLDETLLQKEALATVLDGICQRQHTRLLLERLYHLPMTLEEIGAFQELLEVKKENA 129- Query: 123 LERVACNCIPGQCQC 137 + V CNC+PGQC C Sbjct: 130 VLEVPCNCLPGQCHC 144 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1130 A DNA sequence (GBSx1206) was identified in S. agalactiae <SEQ ID 3503> which encodes the amino acid sequence <SEQ ID 3504>. This protein is predicted to be CopA. Analysis of this protein sequence reveals the following: TABLE-US-03392 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.82 Transmembrane 382-398 (370-406) INTEGRAL Likelihood = -8.01 Transmembrane 356-372 (344-374) INTEGRAL Likelihood = -2.50 Transmembrane 719-735 (719-738) INTEGRAL Likelihood = -2.28 Transmembrane 202-218 (202-218) INTEGRAL Likelihood = -1.59 Transmembrane 693-709 (691-712) INTEGRAL Likelihood = -1.33 Transmembrane 167-183 (167-183) ----- Final Results ----- bacterial membrane --- Certainty = 0.4927(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03393 >GP:AAG10086 GB:AF296446 CopA [Streptococcus mutans] Identities = 440/740 (59%), Positives = 571/740 (76%), Gaps = 1/740 (0%) Query: 5 KETFLIDGMTCASCALTIEKAVNKLDHVDSAVVNLATEKMTVTFDDTTLSPNVIEECVSE 64 +E FLIDGMTCASCA+ +E AV KLD ++SAVVNL TEKMT+ +D +S + + V+ Sbjct: 3 EEVFLIDGMTCASCAINVENAVKKLDGIESAVVNLTTEKMTIDYDAAKVSEADVTKAVAG 62 Query: 65 SGYEASLFKEETSKSQSERHQLAIEKMWHRFWMSAVATIPLLYISMGPMINLWLPSFLMP 124- +GY A ++ T++SQ +R + + + R +++ TIPL YI+MG M+ L LP+FL P Sbjct: 63 AGYGAKVYDPTTAESQKDREEHKLAGIKKRLLWTSIFTIPLFYIAMGSMVGLPLPNFLAP 122- Query: 125 DKGPLNYGMIQLLLTLPVMYFGRIFYQNGFKALFKRHPNMDSLVAIATTAAFIYSLYGLY 18- 4 PL Y M+ LLLT+PV+ FY NGF++LFK HPNMDSLV++ATTAAF+YSLYG Y Sbjct: 123 SSAPLTYAMVLLLLTIPVIVLSWSFYDNGFRSLFKGHPNMDSLVSLATTAAFLYSLYGTY 18- 2 Query: 185 EILQGDIHYAHQLYFESVAVILTLITLGKYFEILSKGRTSASIEKLLTLSAKEARVIKDG 24- 4 + G H+AH LY+ESVAVILTLITLGKYFE LSKGRTS +I+KL+ LSAKEA +I+DG Sbjct: 183 HVYLGHTHHAHHLYYESVAVILTLITLGKYFETLSKGRTSDAIKKLMHLSAKEATLIRDG 24- 2 Query: 245 EDYMVPLDKVKIGETILVKPGEKIPLDGHVVAGESSIDESMLTGESIPVEKKVGSKVYGA 30- 4 E+ VP+++V+I + ILVKPGEKIP+DG V++G S+IDESMLTGESIP+EK S VY Sbjct: 243 EEIKVPIEQVQIRDQILVKPGEKIPVDGRVLSGHSAIDESMLTGESIPIEKMADSPVYAG 30- 2 Query: 305 SINGQGSLTIFVEKEAGGSLLSQIINLVEAAQTSKAPIANLADKVSGVFVPFVIVIAILS 36- 4 SINGQGSLT EK +LLSQII LVE AQ +KAPIA +ADKVS VFVP +I IAIL+ Sbjct: 303 SINGQGSLTFEAEKVGNETLLSQIIKLVENAQQTKAPIAKIADKVSAVFVPVIITIAILT 36- 2 Query: 365 GLSWYLILGQSFAFSLKIMIAVLVIACPCALGLATPTAIMVASGKAAENGILFKGGEVLE 42- 4 GL WY ++GQ F FS+ I +AVLVIACPCALGLATPTAIMV +G+AAENGIL+K G+VLE Sbjct: 363 GLFWYFVMGQDFTFSMTISVAVLVIACPCALGLATPTAIMVGTGRAAENGILYKRGDVLE 42- 2 Query: 425 KAHHIDTIVFDKTGTLTKGKPEVVAIKTYGGDKEEFLGQVASVEKLSNHPLSQTIVNKAK 48- 4 AH I+TIVFDKTGT+T+GKPEVV +Y D+ + + A++E LS HPLSQ IV+ AK Sbjct: 423 LAHQINTIVFDKTGTITQGKPEVVHQFSY-HDRTDLVQVTAALEALSEHPLSQAIVDYAK 48- 1 Query: 485 EKELPLREVMAFKNILGYGLSATINGKTMLVGNANLMTKNDVNLDLAKADIEIAQEEAQT 54- 4 ++ L V F ++ G GL + +T+LVGN LM + +++L+ A+AD + A + QT Sbjct: 482 KEGTHLLAVDDFTSLTGLGLKGCVADETLLVGNEKLMRQANISLEQAQADFKAATAQGQT 54- 1 Query: 545 VVYVSENGVLSGLITLTDQLKTDSQETVKQLQRLGFNLVLLTGDNKASADAIAQKLGITT 60- 4 ++V+ +G L GLIT+ D++K DS TVK LQ +G + +LTGDN+ +A AIA+++GIT Sbjct: 542 PIFVASDGQLLGLITIADKVKNDSAATVKALQNMGVEVAMLTGDNEETAQAIAKEVGITF 60- 1 Query: 605 VVSEVLPDQKANVILELKEKGGQIAMVGDGINDAPALASSDVGISMSSGTDIAIESADIV 66- 4 V+S+V +K IL+L+ +G ++AMVGDGINDAPALA++D+GISM SGTDIA+ESADIV Sbjct: 602 VISQVFSQEKTQAILDLQAEGKKVAMVGDGINDAPALATADIGISMGSGTDIAMESADIV 66- 1 Query: 665 LMKPELTDLLKAMTISKQTIQIIKENLFWAFFYNVLAIPVAMGVLHLFGGPLLNPMLAGL 72- 4 LMKP + D++KA+ IS+ TI IKENLFWAF YNVL++P+AMGVL+LFGGPLL+PM+AGL Sbjct: 662 LMKPAMLDIIKALKISRVTIINIKENLFWAFIYNVLSVPIAMGVLYLFGGPLLDPMIAGL 72- 1 Query: 725 AMAFSSVSVVLNALRLKVLK 744 AM+FSSVSVVLNALRLKV+K Sbjct: 722 AMSFSSVSVVLNALRLKVVK 741 There is also homology to SEQ ID 3506. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1131 A DNA sequence (GBSx1207) was identified in S. agalactiae <SEQ ID 3507> which encodes the amino acid sequence <SEQ ID 3508>. This protein is predicted to be cation-transporting ATPase, P-type (pacS). Analysis of this protein sequence reveals the following: TABLE-US-03394 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1934(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03395 >GP: AAG10087 GB: AF296446 CopZ [Streptococcus mutans] Identities = 31/67 (46%), Positives = 43/67 (63%) Query: 1 MKHTYRVSGMKCDGCAKTVSDKLSSVIGVDEVNVDLTKNQVVVSGKTFKWLLKRSLKDTK 60 M+ TY + G+KC GCA V+ + S + V++V VDL K +V ++G KW LKR+LK T Sbjct: 1 MEKTYHIDGLKCQGCADNVTKRFSELKKVNDVKVDLDKKEVRITGNPSKWSLKRALKGTN 60 Query: 61 YSLEEEI 67 Y L EI Sbjct: 61 YELGAEI 67 A related DNA sequence was identified in S. pyogenes <SEQ ID 3509> which encodes the amino acid sequence <SEQ ID 3510>. Analysis of this protein sequence reveals the following: TABLE-US-03396 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2997(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03397 Identities = 33/63 (52%), Positives = 48/63 (75%) Query: 1 MKHTYRVSGMKCDGCAKTVSDKLSSVIGVDEVNVDLTKNQVVVSGKTFKWLLKRSLKDTK 60 M+ Y+V+GM CDGCA+TV++KLS+V GV V V+L K + V+G+ +L+KR+LKDTK Sbjct: 1 MEKHYQVTGMTCDGCARTVTEKLSAVPGVQSVQVNLEKGEAKVTGRPLTFLIKRALKDTK 60 Query: 61 YSL 63 + L Sbjct: 61 FEL 63 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1132 A DNA sequence (GBSx1208) was identified in S. agalactiae <SEQ ID 3511> which encodes the amino acid sequence <SEQ ID 3512>. Analysis of this protein sequence reveals the following: TABLE-US-03398 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.59 Transmembrane 67-83 (65-90) INTEGRAL Likelihood = -3.72 Transmembrane 35-51 (31-51) INTEGRAL Likelihood = -3.61 Transmembrane 122-138 (120-139) INTEGRAL Likelihood = -1.59 Transmembrane 154-170 (154-171) ----- Final Results ----- bacterial membrane --- Certainty = 0.4036(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8733> which encodes amino acid sequence <SEQ ID 8734> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-03399 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: 4.09 GvH: Signal Score (-7.5): 3.87 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 4 value: -7.59 threshold: 0.0 INTEGRAL Likelihood = -7.59 Transmembrane 65-81 (63-88) INTEGRAL Likelihood = -3.72 Transmembrane 33-49 (29-49) INTEGRAL Likelihood = -3.61 Transmembrane 120-136 (118-137) INTEGRAL Likelihood = -1.59 Transmembrane 152-168 (152-169) PERIPHERAL Likelihood = 0.85 96 modified ALOM score: 2.02 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4036(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03400 >GP: CAB15351 GB: Z99121 similar to hypothetical proteins [Bacillus subtilis] Identities = 107/192 (55%), Positives = 137/192 (70%) Query: 8 WNILSLVGTVAFASSGAIVAIEEEFDILGLFILGFVTAFGGGAIRNVLIGLPIETLWSQG 67 W +LS++G +AFA SGAIVA+EEE+DILG++ILG VTAFGGGAIRN+LIG+P+ LW QG Sbjct: 3 WELLSVIGIIAFAVSGAIVAMEEEYDILGVYILGIVTAFGGGAIRNLLIGVPVSALWEQG 62 Query: 68 IAFYAAAAAILFIMIFPNLLSGKGRDAEVVSDAIGLAAFSVQGALYATQSHQPLSAVIVA 127- F A +I + +FP LL +SDAIGLAAF++QGALYA + PLSAVIVA Sbjct: 63 AYFQIALLSITIVFLFPKLLLKHWNKWGNLSDAIGLAAFAIQGALYAVKMGHPLSAVIVA 122- Query: 128 AVLTGAGGGIVRDVLAGRKPGVLRSEIYAGWSILVGIILYFKIAKTTTDYYLLVLVVTSL 18- 7 AVLTG+GGGI+RD+LAGRKP VL++EIYA W+ L G+I+ + Y+L V+ Sbjct: 123 AVLTGSGGGIIRDLLAGRKPLVLKAEIYAVWAALGGLIVGLGWLGNSFGLYVLFFVLVVC 18- 2 Query: 188 RMLGYKKQWHLP 199 R+ Y W LP Sbjct: 183 RVCSYMFNWKLP 194 A related DNA sequence was identified in S. pyogenes <SEQ ID 3513> which encodes the amino acid sequence <SEQ ID 3514>. Analysis of this protein sequence reveals the following: TABLE-US-03401 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.15 Transmembrane 70-86 (65-88) INTEGRAL Likelihood = -4.09 Transmembrane 33-49 (29-49) INTEGRAL Likelihood = -2.13 Transmembrane 120-136 (119-137) INTEGRAL Likelihood = -0.43 Transmembrane 173-189 (172-189) ----- Final Results ----- bacterial membrane --- Certainty = 0.3060(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03402 >GP: BAB05428 GB: AP001512 unknown conserved protein [Bacillus halodurans] Identities = 109/195 (55%), Positives = 137/195 (69%) Query: 6 WEILNIIGTIAFALSGAIVAMEEEFDILGIFILGFVTAFGGGAIRNTLIGLPIEALWGQK 65 W++LN+IGTIAFALSG IVAMEE+FD++G++ILGFVTAFGGGAIRN LIG+P+ ALW Q Sbjct: 3 WDVLNVIGTIAFALSGVIVAMEEDFDLMGVYILGFVTAFGGGAIRNLLIGVPVSALWEQG 62 Query: 66 PEFTCAFFAMVLIMLFPKLMARGWVRAAVLTDAIGLAAFSVQGALHAVRLNQPLSAVIVT 125- FT AF M + P L W++ +L DAIGLAAF++QGAL A ++ PLSAVIV Sbjct: 63 TLFTIAFIVMTIAFFLPNLWINHWLKFGLLFDAIGLAAFAIQGALFATSMDHPLSAVIVA 122- Query: 126 AVLTGAGGGVVRDILAGRKPSVLRSEIYAGWSILAAIVLHFKLADSTIECYALVVLLTTL 18- 5 A LTGAGGG+VRD+LA RKP VL EIY GW++LA + + I L++L+ L Sbjct: 123 AALTGAGGGIVRDMLARRKPLVLSKEIYIGWAMLAGAAIGLNIVSGPIGIGFLIILVVFL 18- 2 Query: 186 RMIGNRKKWNLPKIK 200 RM+ W LP K Sbjct: 183 RMLSVHYNWCLPHRK 197 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03403 Identities = 133/200 (66%), Positives = 168/200 (83%) Query: 3 MSIDIWNILSLVGTVAFASSGAIVAIEEEFDILGLFILGFVTAFGGGAIRNVLIGLPIET 62 M+ID+W IL+++GT+AFA SGAIVA+EEEFDILG+FILGFVTAFGGGAIRN LIGLPIE Sbjct: 1 MTIDMWEILNIIGTIAFALSGAIVAMEEEFDILGIFILGFVTAFGGGAIRNTLIGLPIEA 60 Query: 63 LWSQGIAFYAAAAAILFIMIFPNLLSGKGRDAEVVSDAIGLAAFSVQGALYATQSHQPLS 122- LW Q F A A++ IM+FP L++ A V++DAIGLAAFSVQGAL+A + +QPLS Sbjct: 61 LWGQKPEFTCAFFAMVLIMLFPKLMARGWVRAAVLTDAIGLAAFSVQGALHAVRLNQPLS 120- Query: 123 AVIVAAVLTGAGGGIVRDVLAGRKPGVLRSEIYAGWSILVGIILYFKIAKTTTDYYLLVL 18- 2 AVIV AVLTGAGGG+VRD+LAGRKP VLRSEIYAGWSIL I+L+FK+A +T + Y LV+ Sbjct: 121 AVIVTAVLTGAGGGVVRDILAGRKPSVLRSEIYAGWSILAAIVLHFKLADSTIECYALVV 18- 0 Query: 183 VVTSLRMLGYKKQWHLPVVR 202 ++T+LRM+G +K+W+LP ++ Sbjct: 181 LLTTLRMIGNRKKWNLPKIK 200 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1133 A DNA sequence (GBSx1209) was identified in S. agalactiae <SEQ ID 3515> which encodes the amino acid sequence <SEQ ID 3516>. Analysis of this protein sequence reveals the following: TABLE-US-03404 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2805(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9569> which encodes amino acid sequence <SEQ ID 9570> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03405 >GP: CAB94816 GB: AJ245582 hypothetical protein [Streptococcus thermophilus] Identities = 138/238 (57%), Positives = 184/238 (76%) Query: 5 KKMIKLIAIDMDGTLLNDEKKIPKENIQAIKEATQAGIKIVLCTGRPMSGILPYFNELGL 64 + +KLIAIDMDGTLLN +K+IPKENI+AI+EAT AGIKIVLCTGRP SGI+P+F +LGL Sbjct: 3 QNQVKLIAIDMDGTLLNSQKEIPKENIKAIQEATAAGIKIVLCTGRPRSGIVPHFEKLGL 62 Query: 65 TKEEYIIMNNGCSTYSTKDWQLIDSATLTHDELIFLEEVVKEFPNVCLTLTAENTFYAVG 124- ++EE+IIMNNGCSTY TK+W L++S +L+ E+ L + ++FP V LT T E ++Y VG Sbjct: 63 SEEEFIIMNNGCSTYETKNWTLLESESLSRSEMEELLQACEDFPGVALTFTGEKSYYVVG 122- Query: 125 EEVPEIVAYDADLVFTKAKSTSLDALRNQEEIVFQAMYMGLDADVTAFQEAVEEALISKF 18- 4 EVPE+VAYDA VFT+AK+ SL+ + + +++FQAMYM + AFQ AV++ L + Sbjct: 123 NEVPELVAYDAGTVFTEAKARSLEEIFEEGQVIFQAMYMAESEPLDAFQNAVQDRLDQSY 18- 2 Query: 185 SGVRSQDYIYEIMPQGVTKARGLKSLIAKLGLDINQVMAIGDAPNDIELLDLVPNSVA 242 S VRSQ+YI+E+MPQG TKA GLK L KL ++ +Q+MA+GDA ND+E+L V SVA Sbjct: 183 STVRSQEYIFEVMPQGATKASGLKHLAEKLDINRDQIMALGDAANDLEMLQFVGQSVA 240 A related DNA sequence was identified in S. pyogenes <SEQ ID 3517> which encodes the amino acid sequence <SEQ ID 3518>. Analysis of this protein sequence reveals the following: TABLE-US-03406 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1468(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03407 Identities = 152/270 (56%), Positives = 193/270 (71%) Query: 6 KMIKLIAIDMDGTLLNDEKKIPKENIQAIKEATQAGIKIVLCTGRPMSGILPYFNELGLT 65 +MI+LIAID+DGTLLN +K+IPKENI AI+EA Q+G+KIVLCTGRP SG PYF++LGLT Sbjct: 19 RMIQLIAIDLDGTLLNQDKQIPKENITAIQEAAQSGLKIVLCTGRPQSGTRPYFDQLGLT 78 Query: 66 KEEYIIMNNGCSTYSTKDWQLIDSATLTHDELIFLEEVVKEFPNVCLTLTAENTFYAVGE 125- +EE++I+NNGCSTYS+ DWQL S L ++ LEE+ + FP++ LTLT EN + + E Sbjct: 79 QEEFLIINNGCSTYSSPDWQLRHSKMLKVSDIELLEELSQSFPDIYLTLTEENDYLVLEE 138- Query: 126 EVPEIVAYDADLVFTKAKSTSLDALRNQEEIVFQAMYMGLDADVTAFQEAVEEALISKFS 18- 5 EVP++V D DLVFT K SL L + ++FQAMY+G A + AF+ AV L F Sbjct: 139 EVPDLVQEDGDLVFTIVKPVSLAELSDTPRLIFQAMYLGEKAALDAFERAVRNQLSQSFH 19- 8 Query: 186 GVRSQDYIYEIMPQGVTKARGLKSLIAKLGLDINQVMAIGDAPNDIELLDLVPNSVAMGN 24- 5 VRSQD I EI+PQGV+KA LK L+ LGL +QVMAIGDAPNDIE+L VAM N Sbjct: 199 VVRSQDNILEILPQGVSKASALKELVEDLGLTADQVMAIGDAPNDIEMLTYAGLGVAMEN 25- 8 Query: 246 ASDEIKSRCKYITVDNNKAGVAKAIYDYAL 275 AS IK +T+ N+ AGVA+AI +AL Sbjct: 259 ASAAIKPLADKVTLTNDMAGVAQAIRQFAL 288 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1134 A DNA sequence (GBSx1210) was identified in S. agalactiae <SEQ ID 3519> which encodes the amino acid sequence <SEQ ID 3520>. Analysis of this protein sequence reveals the following: TABLE-US-03408 Possible site: 18 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 7-23 (7-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03409 >GP: AAA26954 GB: J04479 DNA polymerase I [Streptococcus pneumoniae] Identities = 655/879 (74%), Positives = 748/879 (84%), Gaps = 4/879 (0%) Query: 3 NKNKLLLIDGSSVAFRAFFALYNQIDRFKNNSGLHTNAIYGFHLMLNHILGRVQPSHILV 62 +K KLLLIDGSSVAFRAFFALY Q+DRFKN +GLHTNAIYGF LML+H+L RV+PSHILV Sbjct: 2 DKKKLLLIDGSSVAFRAFFALYQQLDRFKNAAGLHTNAIYGFQLMLSHLLERVEPSHILV 61 Query: 63 AFDAGKTTFRTEMYADYKGGRAKTPDEFREQFPYIRQQLDVLGIKHYELEHYEADDIIGT 122- AFDAGKTTFRTEMYADYKGGRAKTPDEFREQFP+IR+ LD +GI+HYEL YEADDIIGT Sbjct: 62 AFDAGKTTFRTEMYADYKGGRAKTPDEFREQFPFIRELLDHMGIRHYELAQYEADDIIGT 121- Query: 123 LAKQAEASNEHFDITVVSGDKDLIQLTDTNTVVEISKKGVAEFEEFTPAYLMEKMGITPS 18- 2 L K AE + FDIT+VSGDKDLIQLTD +TVVEISKKGVAEFE FTP YLME+MG+TP+ Sbjct: 122 LDKLAE--QDGFDITIVSGDKDLIQLTDEHTVVEISKKGVAEFEAFTPDYLMEEMGLTPA 17- 9 Query: 183 QFIDLKALMGDKSDNIPGVTKIGEKTGLKLLSEYGSLEGIYENIEAMKQSKMKENLINDK 24- 2 QFIDLKALMGDKSDNIPGVTK+GEKTG+KLL E+GSLEGIYENI+ MK SKMKENLINDK Sbjct: 180 QFIDLKALMGDKSDNIPGVTKVGEKTGIKLLLEHGSLEGIYENIDGMKTSKMKENLINDK 23- 9 Query: 243 EQAFLSKTLATINIASPITIGLEDILYSGPQDIKALSQFYDEMDFKQFKAALGEETSQED 30- 2 EQAFLSKTLATI+ +PI IGLED++YSGP D++ L +FYDEM FKQ K AL ++ Sbjct: 240 EQAFLSKTLATIDTKAPIAIGLEDLVYSGP-DVENLGKFYDEMGFKQLKQALNMSSADVA 29- 8 Query: 303 FEVDFTEVEQLKTEMFSDNDFYYFEMLGDNYHVEDLIGIAWGNSDTIYATSNVSLLQEAL 36- 2 +DFT V+Q+ +M S+ ++FE+ G+NYH ++L+G AW D +YAT + LLQ+ + Sbjct: 299 EGLDFTIVDQISQDMLSEESIFHFELFGENYHTDNLVGFAWSCGDQLYATDKLELLQDPI 35- 8 Query: 363 FKKALSKP-IKTYDFKRSKVLLNRFNIDLPEPAFDTRLAKYLLSTTEDNLVSTIARLYTN 42- 1 FK L K ++ YDFK+ KVLL RF +DL PAFD RLAKYLLST EDN ++TIA LY Sbjct: 359 FKDFLEKTSLRVYDFKKVKVLLQRFGVDLQAPAFDIRLAKYLLSTVEDNEIATIASLYGQ 41- 8 Query: 422 LPLDTDDAVYGKGAKRAIPEKTRFLEHLAKKVKVLVDSEANIMQQLKANEQEELLFEMEQ 48- 1 L D+ YGKG K+AIPE+ +FLEHLA K+ VLV++E ++++L N Q ELL++MEQ Sbjct: 419 TYLVDDETFYGKGVKKAIPEREKFLEHLACKLAVLVETEPILLEKLSENGQLELLYDMEQ 47- 8 Query: 482 PLANVLAKMEIRGIKVKKNTLNEMAIENQKVIETLTQEIYELAGQEFNINSPKQLGKLLF 54- 1 PLA VLAKMEI GI VKK TL EM EN+ VIE LTQEIYELAG+EFN+NSPKQLG LLF Sbjct: 479 PLAFVLAKMEIAGIVVKKETLLEMQAENELVIEKLTQEIYELAGEEFNVNSPKQLGVLLF 53- 8 Query: 542 ETLGLPVEMTKKTKTGYSTAVDVLERLAPISPLVTKILEYRQITKLQSTYIIGLQDYILE 60- 1 E LGLP+E TKKTKTGYSTAVDVLERLAPI+P+V KIL+YRQI K+QSTY+IGLQD+IL Sbjct: 539 EKLGLPLEYTKKTKTGYSTAVDVLERLAPIAPIVKKILDYRQIAKIQSTYVIGLQDWILA 59- 8 Query: 602 DGKIHTRYVQDLTQTGRLSSSDPNLQNIPVRLEQGRLIRKAFVPSEDNAVLLSSDYSQIE 66- 1 DGKIHTRYVQDLTQTGRLSS DPNLQNIP RLEQGRLIRKAFVP +++VLLSSDYSQIE Sbjct: 599 DGKIHTRYVQDLTQTGRLSSVDPNLQNIPARLEQGRLIRKAFVPEWEDSVLLSSDYSQIE 65- 8 Query: 662 LRVLAHISKDEHLIAAFKEGADIHTSTAMRVFGIEKPENVTPNDRRNAKAVNFGIVYGIS 72- 1 LRVLAHISKDEHLI AF+EGADIHTSTAMRVFGIE+P+NVT NDRRNAKAVNFG+VYGIS Sbjct: 659 LRVLAHISKDEHLIKAFQEGADIHTSTAMRVFGIERPDNVTANDRRNAKAVNFGVVYGIS 71- 8 Query: 722 DFGLSHNLGIPRKLAKQYIDTYFERYPGIKNYMETVVREAKDKGYVETLFHRRRSLPDIN 78- 1 DFGLS+NLGI RK AK YIDTYFER+PGIKNYM+ VVREA+DKGYVETLF RRR LPDIN Sbjct: 719 DFGLSNNLGISRKEAKAYIDTYFERFPGIKNYMDEVVREARDKGYVETLFKRRRELPDIN 77- 8 Query: 782 SRNFNIRQFAERTAINSPIQGSAADILKIAMINLDRVLDKGGYKSKMLLQVHDEIVLEVP 84- 1 SRNFNIR FAE TAINSPIQGSAADILKIAMI LD+ L GGY++KMLLQVHDEIVLEVP Sbjct: 779 SRNFNIRGFAEATAINSPIQGSAADILKIAMIQLDKALVAGGYQTKMLLQVHDEIVLEVP 83- 8 Query: 842 NEEIGAIRELVTKTMESAISLSVPLIADENAGETWYEAK 880 E+ +++LV +TME AI LSVPLIADEN G TWYEAK Sbjct: 839 KSELVEMKKLVKQTMEEAIQLSVPLIADENEGATWYEAK 877 A related DNA sequence was identified in S. pyogenes <SEQ ID 3521> which encodes the amino acid sequence <SEQ ID 3522>. Analysis of this protein sequence reveals the following: TABLE-US-03410 Possible site: 18 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 7-23 (7-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03411 Identities = 665/881 (75%), Positives = 761/881 (85%), Gaps = 2/881 (0%) Query: 1 MTNKNKLLLIDGSSVAFRAFFALYNQIDRFKNNSGLHTNAIYGFHLMLNHILGRVQPSHI 60 M NKNKLLLIDGSSVAFRAFFALYNQIDRFKN+SGLHTNAIYGFHLML+H++ RVQP+H+ Sbjct: 1 MENKNKLLLIDGSSVAFRAFFALYNQIDRFKNHSGLHTNAIYGFHLMLDHMMKRVQPTHV 60 Query: 61 LVAFDAGKTTFRTEMYADYKGGRAKTPDEFREQFPYIRQQLDVLGIKHYELEHYEADDII 120- LVAFDAGKTTFRTEMYADYK GRAKTP+EFREQFPYIR+ L LGI +YELEHYEADDII Sbjct: 61 LVAFDAGKTTFRTEMYADYKAGRAKTPEEFREQFPYIREMLTALGIAYYELEHYEADDII 120- Query: 121 GTLAKQAEASNEHFDITVVSGDKDLIQLTDTNTVVEISKKGVAEFEEFTPAYLMEKMGIT 18- 0 GTL K AE + FD+T+VSGDKDLIQLTD NTVVEISKKGVAEFEEFTPAYLMEKMG+T Sbjct: 121 GTLDKMAERTEVPFDVTIVSGDKDLIQLTDENTVVEISKKGVAEFEEFTPAYLMEKMGLT 18- 0 Query: 181 PSQFIDLKALMGDKSDNIPGVTKIGEKTGLKLLSEYGSLEGIYENIEAMKQSKMKENLIN 24- 0 P+QFIDLKALMGDKSDNIPGVTKIGEKTGLKLL E+GSLEGIYE+I+ K SKMKENLIN Sbjct: 181 PNQFIDLKALMGDKSDNIPGVTKIGEKTGLKLLHEFGSLEGIYEHIDGFKTSKMKENLIN 24- 0 Query: 241 DKEQAFLSKTLATINIASPITIGLEDILYSGPQDIKALSQFYDEMDFKQFKAALGEETSQ 30- 0 D++QAFLSKTLATIN ASPITIGL+DI+Y+GP D+ +LSQFYDEMDF Q K L + Q Sbjct: 241 DRDQAFLSKTLATINTASPITIGLDDIVYNGP-DVASLSQFYDEMDFVQLKKGLASQMPQ 29- 9 Query: 301 EDFEV-DFTEVEQLKTEMFSDNDFYYFEMLGDNYHVEDLIGIAWGNSDTIYATSNVSLLQ 35- 9 E V + EV + ++FS D +YFE L DNYH E +IG AWG+ + IYA++++ LL Sbjct: 300 EPVAVISYQEVTNVSADLFSAEDIFYFETLRDNYHREAIIGFAWGHGEQIYASTDLGLLA 35- 9 Query: 360 EALFKKALSKPIKTYDFKRSKVLLNRFNIDLPEPAFDTRLAKYLLSTTEDNLVSTIARLY 41- 9 FK+ KPI TYDFKRSKVLL+ I+L P++D RLA YLLST EDN +STIAR++ Sbjct: 360 TDSFKQVFQKPIATYDFKRSKVLLSHLGIELVAPSYDARLANYLLSTVEDNELSTIARIF 41- 9 Query: 420 TNLPLDTDDAVYGKGAKRAIPEKTRFLEHLAKKVKVLVDSEANIMQQLKANEQEELLFEM 47- 9 T++ L+ DD VYGKGAKRA+P+K LEHLA+KVKVL+DS++ ++ +L A+EQ +L + Sbjct: 420 TDISLEEDDTVYGKGAKRAVPDKDVLLEHLARKVKVLLDSKSQMLDKLTAHEQLDLYQNI 47- 9 Query: 480 EQPLANVLAKMEIRGIKVKKNTLNEMAIENQKVIETLTQEIYELAGQEFNINSPKQLGKL 53- 9 E PLANVLAKMEI GIKV + TL +MA +N+ +IE LTQEIY++AGQEFNINSPKQLG + Sbjct: 480 ELPLANVLAKMEIEGIKVNRATLQDMAEQNKVIIEALTQEIYDMAGQEFNINSPKQLGSI 53- 9 Query: 540 LFETLGLPVEMTKKTKTGYSTAVDVLERLAPISPLVTKILEYRQITKLQSTYIIGLQDYI 59- 9 LFE + LP+EMTKKTKTGYSTAV+VLERLAPI+P+V KIL+YRQITKLQSTY+IGLQDYI Sbjct: 540 LFEKMQLPLEMTKKTKTGYSTAVNVLKRLAPIAPIVAKILDYRQITKLQSTYVIGLQDYI 59- 9 Query: 600 LEDGKIHTRYVQDLTQTGRLSSSDPNLQNIPVRLEQGRLIRKAFVPSEDNAVLLSSDYSQ 65- 9 L DGKIHTRYVQDLTQTGRLSS DPNLQNIP+RLEQGRLIRKAF PS ++AVLLSSDYSQ Sbjct: 600 LADGKIHTRYVQDLTQTGRLSSVDPNLQNIPIRLEQGRLIRKAFTPSHEDAVLLSSDYSQ 65- 9 Query: 660 IELRVLAHISKDEHLIAAFKEGADIHTSTAMRVFGIEKPENVTPNDRRNAKAVNFGIVYG 71- 9 IELRVLAHIS DEHLIAAF EGADIHTSTAMRVFGI++ +VT NDRRNAKAVNFGIVYG Sbjct: 660 IELRVLAHISGDEHLIAAFNEGADIHTSTAMRVFGIDRAADVTANDRRNAKAVNFGIVYG 71- 9 Query: 720 ISDFGLSHNLGIPRKLAKQYIDTYFERYPGIKNYMETVVREAKDKGYVETLFHRRRSLPD 77- 9 ISDFGLS+NLGI RK AK YIDTYFERYPGIK YME VVREAKDKGYVETLF RRR LPD Sbjct: 720 ISDFGLSNNLGITRKQAKSYIDTYFERYPGIKAYMENVVREAKDKGYVETLFKRRRELPD 77- 9 Query: 780 INSRNFNIRQFAERTAINSPIQGSAADILKIAMINLDRVLDKGGYKSKMLLQVHDEIVLE 83- 9 INSRNFN+R FAERTAINSPIQGSAADILKIAMINLD+ L GG+++KMLLQVHDEIVLE Sbjct: 780 INSRNFNVRSFAERTAINSPIQGSAADILKIAMINLDKALQAGGFRAKMLLQVHDEIVLE 83- 9 Query: 840 VPNEEIGAIRELVTKTMESAISLSVPLIADENAGETWYEAK 880 VPN+E+ AI++LV TME+A+ L+VPL DE+ G +WYEAK Sbjct: 840 VPNDELTAIKKLVKDTMEAAVDLAVPLCVDESTGHSWYEAK 880 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1135 A DNA sequence (GBSx1211) was identified in S. agalactiae <SEQ ID 3523> which encodes the amino acid sequence <SEQ ID 3524>. Analysis of this protein sequence reveals the following: TABLE-US-03412 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1880(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9571> which encodes amino acid sequence <SEQ ID 9572> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03413 >GP:BAB05860 GB:AP001514 unknown conserved protein [Bacillus halodurans] Identities = 72/134 (53%), Positives = 94/134 (69%), Gaps = 3/134 (2%) Query: 17 NPSDFMLKNYLTKAKTIAVVGLSDRQETAAYQVSKIMQEAGYQIIPVNPKNAGQKILGQM 76 - NPSD +K L +AK IAVVGLS + +Y VS MQ AGY+IIPVNP ++LG+ Sbjct: 4 NPSDEKIKQILQEAKRIAVVGLSGNPDRTSYMVSAAMQHAGYEIIPVNP--TVDEVLGEK 61 Query: 77 TYASLKDVTEHIDIVNIFRRSEYLPDIAREFLEVDADIFWAQLGLESQEAETILKQAGHK 136- SL+D+ +DIVN+FRRSE+LPD+ARE +E+ A +FWAQLGLE++EA L+Q G Sbjct: 62 AVPSLQDIEGAVDIVNVFRRSEHLPDVARETVEIGAPVFWAQLGLENKEAYDYLQQHGVT 121- Query: 137 QIVMNKCLKVECQK 150 I MN+C+KVE K Sbjct: 122 SI-MNRCIKVEHAK 134 A related DNA sequence was identified in S. pyogenes <SEQ ID 3525> which encodes the amino acid sequence <SEQ ID 3526>. Analysis of this protein sequence reveals the following: TABLE-US-03414 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0837(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03415 Identities = 87/141 (61%), Positives = 114/141 (80%) Query: 11 MVYHFQNPSDFMLKNYLTKAKTIAVVGLSDRQETAAYQVSKIMQEAGYQIIPVNPKNAGQ 70 - ++Y FQNPS+ +LK YL AKTIAVVGLSDR++TAAY V+K MQ Y+IIPVNPK AGQ Sbjct: 1 VIYSFQNPSEDVLKAYLESAKTIAVVGLSDRKDTAAYGVAKFMQAMDYRIIPVNPKLAGQ 60 Query: 71 KILGQMTYASLKDVTEHIDIVNIFRRSEYLPDIAREFLEVDADIFWAQLGLESQEAETIL 130- ILG+ YAS+K + +DIV++FRRSE+LP++AR+FL A +FWAQLGLE+QEA+TIL Sbjct: 61 LILGEKVYASIKAIPFEVDIVDVFRRSEFLPEVARDFLAGQAKVFWAQLGLENQEAQTIL 120- Query: 131 KQAGHKQIVMNKCLKVECQKL 151 + AG + IVMN+CLK++ +L Sbjct: 121 RSAGKEAIVMNRCLKIDYLQL 141 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1136 A DNA sequence (GBSx1212) was identified in S. agalactiae <SEQ ID 3527> which encodes the amino acid sequence <SEQ ID 3528>. Analysis of this protein sequence reveals the following: TABLE-US-03416 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3367(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9573> which encodes amino acid sequence <SEQ ID 9574> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 3529> which encodes the amino acid sequence <SEQ ID 3530>. Analysis of this protein sequence reveals the following: TABLE-US-03417 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4960(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03418 Identities = 113/151 (74%), Positives = 133/151 (87%), Gaps = 1/151 (0%) Query: 7 MDSHSHGHRPLDAYENVLEHLREKRIRITETRKAIISYMVNSREHPSAEKIYNDLLPEYP 66 MD HSH + LDAYENVLEHLREK IRITETRKAIISYM+ S EHPSA+KIY DL P +P Sbjct: 1 MDIHSH-QQALDAYENVLEHLREKHIRITETRKAIISYMIQSTEHPSADKIYRDLQPNFP 59 Query: 67 NMSLATVYNNLKVLVDEGFVTELKLCNYSTTYYDFMGHQHLNIACEDCGKIVDFVDVDLL 126- NMSLATVYNNLKVLVDEGFV+ELK+ N TTYYDFMGHQH+N+ CE CGKI DF+DVD++ Sbjct: 60 NMSLATVYNNLKVLVDEGFVSELKISNDLTTYYDFMGHQHVNVVCEICGKIADFMDVDVM 119- Query: 127 DISREAHQQTGFEVTRVQLVAYGICPECQRK 157 DI++EAH+QTG++VTR+ ++AYGICP+CQ K Sbjct: 120 DIAKEAHEQTGYKVTRIPVIAYGICPDCQAK 150 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1137 A DNA sequence (GBSx1213) was identified in S. agalactiae <SEQ ID 3531> which encodes the amino acid sequence <SEQ ID 3532>. Analysis of this protein sequence reveals the following:

TABLE-US-03419 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.13 Transmembrane 16-32 (14-32) INTEGRAL Likelihood = -1.81 Transmembrane 496-512 (496-515) ----- Final Results ----- bacterial membrane --- Certainty = 0.1850(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03420 >GP:CAA06650 GB:AJ005645 sdrc [Staphylococcus aureus] Identities = 41/146 (28%), Positives = 63/146 (43%), Gaps = 13/146 (8%) Query: 4 SQYNKWSIRRLKVGAASVMIASGSIVALGQSHIVSAD----EMSQPKTTITAPTANTSTN 59 ++ NK+SIR+ VG AS+++ + I L +A+ E++Q K TAP+ N +T Sbjct: 16 NRLNKFSIRKYSVGTASILVGTTLIFGLSGHEAKAAEHTNGELNQSKNETTAPSENKTT- 74 Query: 60 VESSTDKALSKVTTMETSSEMPK--MQNMAKVEKTSDKPMMVATSVRKMMATPTPVAMT- 116- D K T +++ PK M + A V++TS + T T T Sbjct: 75 --KKVDSRQLKDNTQTATADQPKVTMSDSATVKETSSNMQSPQNATANQSTTKTSNVTTN 132- Query: 117 ---KTTSVDEVKKSTDTAFKQTVDVP 139 TT +E KS T K P Sbjct: 133 DKSSTTYSNETDKSNLTQAKDVSTTP 158 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8735> and protein <SEQ ID 8736> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03421 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: -0.92 GvH: Signal Score (-7.5): -2.48 Possible site: 39 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -2.13 threshold: 0.0 INTEGRAL Likelihood = -2.13 Transmembrane 16-32 (14-32) INTEGRAL Likelihood = -1.81 Transmembrane 496-512 (496-515) PERIPHERAL Likelihood = 7.96 402 modified ALOM score: 0.93 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1850(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 485-489 The protein has homology with the following sequences in the databases: TABLE-US-03422 D|5981|5780 leukotoxin > Insert characterized SP|P16462|HLYA_ACTAC LEUKOTOXIN. > Edit characterized GP|141834|gb|AAA21922.1||M27399 leukotoxin (LtA) {Actinobacillus actinomycetemcomitans} Insert characterized Query: 210 VSLNGNTTGKEGQALLDQI|AND---KHSYQATIRVYGAKDGKVDLKNMISPKMVTINIP 26- 6 ++ NG+ + G+A +D +K + KHS + T ++ G +DL + +T P Sbjct: 488 ITRNGDRI-QSGKAYVDYLKKGEELAKHSDKFTKQILDPIKGNIDLSGIKGSTTLTFLNP 54- 6 Query: 267 HITTDMEVKNSLKMAFKEKV-DVPAKYVSAAKAKG-PFLAGVNE--TIPYEAFGGDGMLT 32- 2 +T E + + + E + ++ K + K KG P GV + + A D + Sbjct: 547 LLTAGKEERKTRQSGKYEFITELKVKGRTDWKVKGVPNSNGVYDFSNLIQHAVTRDNKVL 60- 6 Query: 323 RLILKASEGAKWSDNGVDKNSPLL------PLKDLTKGKYFYQVSLNGNTAGKKGQALLD 37- 6 L A+ GAK V S ++ + D +KG+ ++++G A K GQ ++ Sbjct: 607 EARLIANLGAKDDYVFVGSGSTIVNAGDGYDVVDYSKGRTG-ALTIDGRNATKAGQYKVE 66- 5 Query: 377 QIKANGSHTYQATITIYGTKDGKV 400 + +G+ Q T++ TK GKV Sbjct: 666 R-DLSGTQVLQETVSKQETKRGKV 688 SEQ ID 3532 (GBS1) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 1 (lane 3; MW 78 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 2 (lane 3; MW 53 kDa). The His-fusion protein was purified as shown in FIG. 189, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1138 A DNA sequence (GBSx1214) was identified in S. agalactiae <SEQ ID 3533> which encodes the amino acid sequence <SEQ ID 3534>. This protein is predicted to be response regulator (regX3). Analysis of this protein sequence reveals the following: TABLE-US-03423 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3585(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03424 >GP:CAB54578 GB:AJ006397 response regulator [Streptococcus pneumoniae] Identities = 143/228 (62%), Positives = 183/228 (79%), Gaps = 1/228 (0%) Query: 1 MTQKLLLVDDEFEIIDINRRYLEQAGYEVSVAADGIEALKEVDENRFDLIISDIMMPKMD 60 M + +LLVDDE EI DI++RYL QAGY+V VA DG+EAL+ + DLII+D+MMP+MD Sbjct: 1 MGKTILLVDDEVEITDIHQRYLIQAGYQVLVAHDGLEALELFKKKPIDLIITDVMMPRMD 60 Query: 61 GYDFISEVLVREPNQPFLFITAKVSEPDKIYSLSMGADDFISKPFSPRELVLRVKNILRR 120- GYD ISEV P QPFLFITAK SE DKIY LS+GADDFI+KPFSPRELVLRV NILRR Sbjct: 61 GYDLISEVQYLSPEQPFLFITAKTSEQDKIYGLSLGADDFIAKPFSPRELVLRVHNILRR 120- Query: 121 IYGNHQQSEVLTIGDLVIDQKQRLVMVDCNTISLTNKSFDLLWILANHLNRVFSKTELYE 18- 0 ++ ++E++++G+L ++ V + + LT KSF+LLWILA++ RVFSKT+LYE Sbjct: 121 LH-RGGETELISLGNLKMNHSSHEVQIGEEMLDLTVKSFELLWILASNPERVFSKTDLYE 17- 9 Query: 181 RVWGEEFLDDTNTLNVHIHALRNDLAKFSTDNTPTIKTVWGLGYKLEE 228 ++W E+++DDTNTLNVHIHALR +LAK+S+D TPTIKTVWGLGYK+E+ Sbjct: 180 KIWKEDYVDDTNTLNVHIHALRQELAKYSSDQTPTIKTVWGLGYKIEK 227 There is also homology to SEQ ID 1182. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1139 A DNA sequence (GBSx1215) was identified in S. agalactiae <SEQ ID 3535> which encodes the amino acid sequence <SEQ ID 3536>. This protein is predicted to be histidine kinase (resE). Analysis of this protein sequence reveals the following: TABLE-US-03425 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.13 Transmembrane 42-58 (33-65) INTEGRAL Likelihood = -7.54 Transmembrane 7-23 (3-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.4652(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03426 >GP: CAB54579 GB: AJ006397 histidine kinase [Streptococcus pneumoniae] Identities = 190/343 (55%), Positives = 249/343 (72%) Query: 1 MKLKYYIVIGYLISMLITVAGVFFGLNHMLIETRGVYYILSVTIIACIVGGIVNLFLLSS 60 MKLK YI++GY+IS L+T+ VF+ + MLI +Y++L +TI+A +VG ++LFLL Sbjct: 1 MKLKSYILVGYIISTLLTILVVFWAVQKMLIAKGEIYFLLGMTIVASLVGAGISLFLLLP 60 Query: 61 VFTSLKKLKQKMKDISQRCFDTKAQICSPQEFKDLETAFNQMSSELESTFKSLNESEREK 120- VFTSL KLK+ K ++ + F + ++ P EF+ L FN+MS +L+ +F SL ESEREK Sbjct: 61 VFTSLGKLKEHAKRVAAKDFPSNLEVQGPVEFQQLGQTFNEMSHDLQVSFDSLEESEREK 120- Query: 121 TMMIAQLSHDIKTPITSIQSTVEGILDGIISEEEVNYYLNTISRQTNRLNHLVEELSFIT 18- 0 +MIAQLSHDIKTPITSIQ+TVEGILDGII E E +YL TI RQT RLN LVEEL+F+T Sbjct: 121 GLMIAQLSHDIKTPITSIQATVEGILDGIIKESEQAHYLATIGRQTERLNKLVEELNFLT 18- 0 Query: 181 LETMSDTAEPHKEETIYLDKLLIDILSEFQLVFEKENRQVMIDVAPDVSKLSSQYDKLSR 24- 0 L T + E +++I+LDKLLI+ +SEFQ + E+E R V + V P+ +++ Y KLSR Sbjct: 181 LNTARNQVETTSKDSIFLDKLLIECMSEFQFLIEQERRDVHLQVIPESARIEGDYAKLSR 24- 0 Query: 241 ILLNLISNAVKYSDPGSPLTIKAYSNRQDIVIDIIDQGYGIKDEDLASIFNRLYRVESSR 30- 0 IL+NL+ NA KYS PG+ L + A + + I + D+G GI EDL +IF RLYRVE+SR Sbjct: 241 ILVNLVDNAFKYSAPGTKLEVVAKLEKDQLSISVTDEGQGIAPEDLENIFKRLYRVETSR 30- 0 Query: 301 NMKTGGHGLGLYIARQLAHQLNGDILVESQYQKGSKFSLVLKL 343 NMKTGGHGLGL IAR+LAHQL G+I V SQY GS F+LVL L Sbjct: 301 NMKTGGHGLGLAIARELAHQLGGEITVSSQYGLGSTFTLVLNL 343 There is also homology to SEQ ID 1178. A related GBS gene <SEQ ID 8737> and protein <SEQ ID 8738> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03427 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 8.67 GvH: Signal Score (-7.5): -5.75 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 2 value: -9.13 threshold: 0.0 INTEGRAL Likelihood = -9.13 Transmembrane 42-58 (33-65) INTEGRAL Likelihood = -7.54 Transmembrane 7-23 (3-29) PERIPHERAL Likelihood = 3.92 196 modified ALOM score: 2.33 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4652(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00078## SEQ ID 8738 (GBS28) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 14 (lane 3; MW 64 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 85 (lane 5; MW 38.8 kDa) and in FIG. 157 (lane 9-11; MW 39 kDa). GBS28-His was purified as shown in FIG. 221, lane 6-7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1140 A DNA sequence (GBSx1216) was identified in S. agalactiae <SEQ ID 3537> which encodes the amino acid sequence <SEQ ID 3538>. Analysis of this protein sequence reveals the following: TABLE-US-03428 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.70 Transmembrane 125-141 (110-155) INTEGRAL Likelihood = -7.59 Transmembrane 38-54 (36-56) INTEGRAL Likelihood = -6.48 Transmembrane 146-162 (143-174) INTEGRAL Likelihood = -5.57 Transmembrane 72-88 (63-93) INTEGRAL Likelihood = -1.33 Transmembrane 229-245 (227-245) ----- Final Results ----- bacterial membrane --- Certainty = 0.4079(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9575> which encodes amino acid sequence <SEQ ID 9576> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03429 >GP: CAA79984 GB: Z21972 ORF1 [Bacillus megaterium] Identities = 35/119 (29%), Positives = 62/119 (51%), Gaps = 15/119 (12%) Query: 142 SSFRLLLSGNLILAPVLIVVSSLITTKAVIKLV---QQYYSYSISTLVFYTQLESGNYEG 19- 8 +SF+L+ +++ A + + S L+ +IK + QQ++ + YT LE+ Sbjct: 105 TSFKLI-GASILQAIFIFLWSLLLIIPGIIKAIAYSQQFFL--LKDHPEYTVLEA----- 15- 6 Query: 199 PSKVLVASRELMNGNKLRLFLLDLSFIGWQFLTIFSFGLVYIYLLPYQTTARLIFYRNI 257- + S++ M G K + FL+ LSFIGW L +F+ G+ ++L+PY T FY + Sbjct: 157 ----ITESKKRMKGLKWKYFLMHLSFIGWGILCMFTLGIGLLWLIPYAGTTTAAFYEEL 211- A related DNA sequence was identified in S. pyogenes <SEQ ID 3539> which encodes the amino acid sequence <SEQ ID 3540>. Analysis of this protein sequence reveals the following: TABLE-US-03430 Possible site: 54 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.08 Transmembrane 148-164 (143-170) INTEGRAL Likelihood = -8.28 Transmembrane 114-130 (101-141) INTEGRAL Likelihood = -6.69 Transmembrane 60-76 (49-82) INTEGRAL Likelihood = -3.72 Transmembrane 21-37 (21-39) INTEGRAL Likelihood = -2.34 Transmembrane 222-238 (221-239) ----- Final Results ----- bacterial membrane --- Certainty = 0.5034(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03431 >GP: CAA79984 GB: Z21972 ORF1 [Bacillus megaterium] Identities = 63/220 (28%), Positives = 100/220 (44%), Gaps = 31/220 (14%) Query: 62 LGLILSLFILSASFTMI-DVVRHFRQKVSFAESTTAFSKEFFGNLLVLAITKWLFFLIWS 120- + L+L LF+++ F +I +V+ + T + F + +A+ L S Sbjct: 22 VSLMLLLFLINLVFPLIVEVIGSGGFSEWLMQEETPLWSDIFSMVFSIALIP----LTIS 77 Query: 121 LIWFF-------------GLFIFLSGLSAFLVNAKSGSSTVISLIFLLFGAVLSLIGFGI 16- 7 WF+ I+ G ++F + G+S + ++ L+ +L + G Sbjct: 78 TTWFYLNLVREGNPGIPEVFAIYKDGKTSFKL---IGASILQAIFIFLWSLLLIIPG--- 131- Query: 168 YINRYYAYSLSEYLLYDEVKEGTYLGAIAVIETSVAMMKGYKWKLFFLQLSFTGWFLLNI 22- 7 I + AYS +LL D E T L AI S MKG KWK F + LSF GW +L + Sbjct: 132 -IIKAIAYSQQFFLLKDH-PEYTVLEAIT---ESKKRMKGLKWKYFLMHLSFIGWGILCM 18- 6 Query: 228 VTFGLLNIYLLPYFTTANVIFYDQLKKRFKDKDD--PIEG 265 T G+ ++L+PY T FY++L +D DD IEG Sbjct: 187 FTLGIGLLWLIPYAGTTTAAFYEELIVPQEDIDDDQQIEG 226 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03432 Identities = 87/254 (34%), Positives = 137/254 (53%), Gaps = 10/254 (3%) Query: 16 MTNSEIKNEAKTILSNLQGKNQLFLLPILLSIITLYISFYYQYN-----NMTLLDFFVPL 70 - M+ IK +A+ L NL GK LFL+P LL + I + Y ++L + PL Sbjct: 1 MSIKAIKGQARDTLKNLSGKYLLFLIPTLLFMFHFGIEIHQGYVLSSGIEVSLAASYFPL 60 Query: 71 PVYFFYTLFIISVSFVMLDVVKNQKLNVRFSDNTYVFSSHIFWKLLSVLVLKGLILSFFY 130- + +LFI+S SF M+DVV++ + V F+++T FS F LL + + K L + Sbjct: 61 LLGLILSLFILSASFTMIDVVRHFRQKVSFAESTTAFSKEFFGNLLVLAITKWLFFLIWS 120- Query: 131 LLSTFGLLIIISSFRLLL-----SGNLILAPVLIVVSSLITTKAVIKLVQQYYSYSISTL 18- 5 L+ FGL I +S L + +++ + ++ ++++ + +YY+YS+S Sbjct: 121 LIWFFGLFIFLSGLSAFLVNAKSGSSTVISLIFLLFGAVLSLIGFGIYINRYYAYSLSEY 18- 0 Query: 186 VFYTQLESGNYEGPSKVLVASRELMNGNKLRLFLLDLSFIGWQFLTIFSFGLVYIYLLPY 24- 5 + Y +++ G Y G V+ S +M G K +LF L LSF GW L I +FGL+ IYLLPY Sbjct: 181 LLYDEVKEGTYLGAIAVIETSVAMMKGYKWKLFFLQLSFTGWFLLNIVTFGLLNIYLLPY 24- 0 Query: 246 QTTARLIFYRNITK 259 TTA +IFY + K Sbjct: 241 FTTANVIFYDQLKK 254 A related GBS gene <SEQ ID 8739> and protein <SEQ ID 8740> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03433 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: -11.32 GvH: Signal Score (-7.5): -5.39 Possible site: 19 >>> Seems to have no N-terminal signal sequence ALOM program count: 5 value: -7.70 threshold: 0.0 INTEGRAL Likelihood = -7.70 Transmembrane 125-141 (110-155) INTEGRAL Likelihood = -7.59 Transmembrane 38-54 (34-56) INTEGRAL Likelihood = -6.48 Transmembrane 146-162 (143-174) INTEGRAL Likelihood = -5.57 Transmembrane 72-88 (63-93) INTEGRAL Likelihood = -1.33 Transmembrane 229-245 (227-245) PERIPHERAL Likelihood = 0.37 105 modified ALOM score: 2.04 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4079(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00079## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1141 A DNA sequence (GBSx1217) was identified in S. agalactiae <SEQ ID 3541> which encodes the amino acid sequence <SEQ ID 3542>. This protein is predicted to be tRNA-guanine transglycosylase (tgt). Analysis of this protein sequence reveals the following: TABLE-US-03434 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3706(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9577> which encodes amino acid sequence <SEQ ID 9578> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03435 >GP: CAB14731 GB: Z99118 tRNA-guanine transglycosylase [Bacillus subtilis] Identities = 269/377 (71%), Positives = 320/377 (84%) Query: 12 MTDHPIKYRLIKQEKHTGARLGEIITPHGTFPTPMFMPVGTQATVKTQSPEELKEMGSGI 71 - M + PI+Y IK+ K TGARLG++ TPHG+F TP+FMPVGT ATVKT SPEELK M +GI Sbjct: 1 MAEQPIRYEFIKECKQTGARLGKVHTPHGSFETPVFMPVGTLATVKTMSPEELKAMDAGI 60 Query: 72 ILSNTYHLWLRPGDELIAKAGGLHKFMNWDQAILTDSGGFQVYSLADSRNITEEGVTFKN 131- ILSNTYHLWLRPG +++ +AGGLHKFMNWD+AILTDSGGFQV+SL+ RNI EEGV F+N Sbjct: 61 ILSNTYHLWLRPGQDIVKEAGGLHKFMNWDRAILTDSGGFQVFSLSKFRNIEEEGVHFRN 120- Query: 132 HLNGAKMFLSPEKAISIQNNLGSDIMMSFDECPQFYQPYDYVKKSIERTSRWAERGLNAH 19- 1 HLNG K+FLSPEKA+ IQN LGSDIMM+FDECP + YDY+K+S+ERTSRWAER LNAH Sbjct: 121 HLNGDKLFLSPEKAMEIQNALGSDIMMAFDECPPYPAEYDYMKRSVERTSRWAERCLNAH 18- 0 Query: 192 RRPHDQGLFGIVQGAGFEDLRRQSARDLVSMDFPGYSIGGLAVGETHDEMNAVLDFTVPM 25- 1 R +QGLFGIVQG +EDLR QSA+DL+S+DFPGY+IGGL+VGE D MN VL+FT P+ Sbjct: 181 NRQDEQGLFGIVQGGEYEDLRTQSAKDLISLDFPGYAIGGLSVGEPKDVMNRVLEFTTPL 24- 0 Query: 252 LPNDKPRYLMGVGAPDSLIDAVIRGVDMFDCVLPTRIARNGTCNTSQGRLVVKNAKFAED 31- 1 LP DKPRYLBGVG+PD+LID IRGVDMFDCVLPTRIARNGT T++GRL +KNAKF D Sbjct: 241 LPKDKPRYLMGVGSPDALIDGAIRGVDMFDCVLPTRIARNGTVFTAEGRLNMKNAKFERD 30- 0 Query: 312 FTPLDPNCDCYTCKNYTRAYIRHLLKADETFGIRLTSYHNLYFLVNLMKDVRQAIMDDNL 37- 1 F P+D CDCYTCKNYTRAYIRHL++ +ETFG+RLT+YHNL+FL++LM+ VRQAI +D L Sbjct: 301 FRPIDEECDCYTCKNYTRAYIRHLIRCNETFGLRLTTYHNLHFLLHLMEQVRQAIREDRL 36- 0 Query: 372 LEFRQDFMERYGYGMNN 388 +FR++F ERYGY N Sbjct: 361 GDFREEFFERYGYNKPN 377 A related DNA sequence was identified in S. pyogenes <SEQ ID 3543> which encodes the amino acid sequence <SEQ ID 3544>. Analysis of this protein sequence reveals the following:

TABLE-US-03436 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2590(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03437 Identities = 351/380 (92%), Positives = 368/380 (96%) Query: 12 MTDHPIKYRLIKQEKHTGARLGEIITPHGTFPTPMFMPVGTQATVKTQSPEELKEMGSGI 71 - MTD+PIKYRLIK EKHTGARLGEIITPHGTFPTPMFMPVGTQATVKTQSPEELK +GSGI Sbjct: 1 MTDYPIKYRLIKAEKHTGARLGEIITPHGTFPTPMFMPVGTQATVKTQSPEELKAIGSGI 60 Query: 72 ILSNTYHLWLRPGDELIAKAGGLHKFMNWDQAILTDSGGFQVYSLADSRNITEEGVTFKN 131- ILSNTYHLWLRPGDELIA++GGLHKFMNWDQ ILTDSGGFQVYSLADSRNITEEGVTFKN Sbjct: 61 ILSNTYHLWLRPGDELIARSGGLHKFMNWDQPILTDSGGFQVYSLADSRNITEEGVTFKN 120- Query: 132 HLNGAKMFLSPEKAISIQNNLGSDIMMSFDECPQFYQPYDYVKKSIERTSRWAERGLNAH 19- 1 HLNG+KMFLSPEKAISIQNNLGSDIMMSFDECPQFYQPYDYVKKSIERTSRWAERGL AH Sbjct: 121 HLNGSKMFLSPEKAISIQNNLGSDIMMSFDECPQFYQPYDYVKKSIERTSRWAERGLKAH 18- 0 Query: 192 RRPHDQGLFGIVQGAGFEDLRRQSARDLVSMDFPGYSIGGLAVGETHDEMNAVLDFTVPM 25- 1 RRPHDQGLFGIVQGAGFEDLRRQSA DLV+MDFPGYSIGGLAVGE+H+EMNAVLDFT P+ Sbjct: 181 RRPHDQGLFGIVQGAGFEDLRRQSAADLVAMDFPGYSIGGLAVGESHEEMNAVLDETTPL 24- 0 Query: 252 LPNDKPRYLMGVGAPDSLIDAVIRGVDMFDCVLPTRIARNGTCMTSQGRLVVKNAKFAED 31- 1 LP +KPRYLMGVGAPDSLID VIRGVDMFDCVLPTRIARNGTCMTS+GRLV+KNAKFAED Sbjct: 241 LPENKPRYLMGVGAPDSLIDGVIRGVDMFDCVLPTRIARNGTCMTSEGRLVIKNAKFAED 30- 0 Query: 312 FTPLDPNCDCYTCKNYTRAYIRHLLKADETFGIRLTSYHNLYFLVNLMKDVRQAIMDDNL 37- 1 FTPLD +CDCYTC+NY+RAYIRHLLKADETFGIRLTSYHNLYFLVNLMK VRQAIMDDNL Sbjct: 301 FTPLDHDCDCYTCQNYSRAYIRHLLKADETFGIRLTSYHNLYFLVNLMKKVRQAIMDDNL 36- 0 Query: 372 LEFRQDFMERYGYGMNNRNF 391 LEFRQDF+ERYGY +NRNF Sbjct: 361 LEFRQDFLERYGYNKSNRNF 380 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1142 A DNA sequence (GBSx1218) was identified in S. agalactiae <SEQ ID 3545> which encodes the amino acid sequence <SEQ ID 3546>. Analysis of this protein sequence reveals the following: TABLE-US-03438 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2479(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9303> which encodes amino acid sequence <SEQ ID 9304> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10795> which encodes amino acid sequence <SEQ ID 10796> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03439 >GP: CAB16256 GB: Z99164 hypothetical protein [Schizosaccharomyces pombe] Identities = 42/91 (46%), Positives = 62/91 (67%), Gaps = 3/91 (3%) Query: 6 FGIGLDSSSRCYHYHTKLDIVALKCAVCQKYYACYKCHDALEEHCFAA-TKSDETFP-VL 63 +G +D+ +RC+HYH+K D+VAL+C C+K+YAC++CHD L H F K+ P V+ Sbjct: 13 YGKLVDNETRCFHYHSKADVVALRCGQCEKFYACFQCHDELNTHPFLPWRKAKFHIPCVI 72 Query: 64 CGSCRQMLTLKEYK-TGFCPYCRMLFNPNCQ 93 CG+C+ LT++EY+ T C YC FNP C+ Sbjct: 73 CGACKNSLTVEEYRSTVHCKYCNHPFNPKCK 103 A related DNA sequence was identified in S. pyogenes <SEQ ID 3547> which encodes the amino acid sequence <SEQ ID 3548>. Analysis of this protein sequence reveals the following: TABLE-US-03440 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2769(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03441 Identities = 55/93 (59%), Positives = 62/93 (66%) Query: 2 MQEYFGIGLDSSSRCYHYHTKLDIVALKCAVCQKYYACYKCHDALEEHCFAATKSDETFP 61 M + FGI LD RC HYHT LDIV LKCA CQ YYACY CHD L +H F T ET P Sbjct: 1 MTDCFGIDLDQEYRCLHYHTPLDIVGLKCASCQTYYACYHCHDQLTDHAFVPTGHQETSP 60 Query: 62 VLCGSCRQMLTLKEYKTGFCPYCRMLFNPNCQR 94 V+CG CR++L+ EY G CPYC+ FNP C R Sbjct: 61 VICGHCRKLLSRAEYGCGCCPYCQSPFNPACHR 93 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1143 A DNA sequence (GBSx1219) was identified in S. agalactiae <SEQ ID 3549> which encodes the amino acid sequence <SEQ ID 3550>. This protein is predicted to be transport protein. Analysis of this protein sequence reveals the following: TABLE-US-03442 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.45 Transmembrane 300-316 (292-321) INTEGRAL Likelihood = -1.17 Transmembrane 265-281 (265-281) ----- Final Results ----- bacterial membrane --- Certainty = 0.4779(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10113> which encodes amino acid sequence <SEQ ID 10114> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03443 >GP: AAF12002 GB: AE002075 transport protein, putative [Deinococcus radiodurans] Identities = 108/295 (36%), Positives = 174/295 (58%), Gaps = 4/295 (1%) Query: 31 GAWINLVNPSQEESEQVADQFGIDIDDLRAPLDVEETSRISVEDDYTLVIVDVPTYEERN 90 - G WI+ P+ EE +V+ + G+++D L+ PLD +E SR ED L+I+ + Sbjct: 21 GCWIDAAAPTTEELARVSRETGLELDYLKYPLDPDERSRFEREDGQLLIIMQTSYRLAED 80 Query: 91 NKSYYMTIPMGIIVTDNAVITTC-LEHLTLFDHFYRRRVKNFYTFMKTRFVFQLLYRNAE 149- + Y T+P+GI+ TD+ ++T C LE + V+ T K R QL RNA+ Sbjct: 81 SDIPYDTVPLGILHTDHCLVTVCSLEENPVVKDVVSGLVRRVSTVKKNRLTLQLFLRNAQ 140- Query: 150 LYLQALRTIDRQSDKIEAQLESATRNEQLIDMMELEKSIVYLKASLKFNERIVKKLTSST 20- 9 +L +R I+++ D IE ++E+ATRN +L+D+++LEKS+VY LK NE +++++ Sbjct: 141 RFLIDVRQINKRVDAIEDKMENATRNRELLDLLKLEKSLVYFITGLKANEAMMERVKRDR 20- 0 Query: 210 SSLKKYIEDEDLLEDTLIETQQAIEMANIYENVLNAMTETTASIIGNNQNTIMKTLALVT 26- 9 + Y ED +LL+D LIE QAIEMA+I N+L +M AS+I NN N ++K L + T Sbjct: 201 I-FEMYEEDSELLDDVLIENLQAIEMASIASNILTSMAGAFASVINNNVNQVVKVLTVTT 25- 9 Query: 270 MTLDIPTVIFSAYGMNFQNNWMPLNGLAHGFIYVVLLAFLMSSFVVFYFIRKKWF 324 + + IPT++ +GMN + +P + +GF V+ +A ++S + F F R K F Sbjct: 260 ILVAIPTLVSGFFGMNVEG-LPFSDSPYGFWLVMTVAMGIASLLAFLFYRWKVF 312 A related DNA sequence was identified in S. pyogenes <SEQ ID 715> which encodes the amino acid sequence <SEQ ID 716>. Analysis of this protein sequence reveals the following: TABLE-US-03444 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.81 Transmembrane 293-309 (288-311) INTEGRAL Likelihood = -1.28 Transmembrane 255-271 (255-271) ----- Final Results ----- bacterial membrane --- Certainty = 0.4524(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03445 Identities = 272/314 (86%), Positives = 296/314 (93%) Query: 11 MKQMFLSTAIEFKEIETFEPGAWINLVNPSQEESEQVADQFGIDIDDLRAPLDVEETSRI 70 - MKQMFLS+AIEFKEIETFEPGAWI LVNPSQEES ++ADQF IDI DLRAPLDVEETSRI Sbjct: 1 MKQMFLSSAIEFKEIETFEPGAWIKLVNPSQEESMKIADQFNIDISDLRAPLDVEETSRI 60 Query: 71 SVEDDYTLVIVDVPTYEERNNKSYYMTIPMGIIVTDNAVITTCLEHLTLFDHFYRRRVKN 130- +VEDDYTL+IVDVP YEERNNKSYY+T+P+GIIVT+NAVITTCL +TLFDHF+ RRVKN Sbjct: 61 AVEDDYTLIIVDVPIYEERNNKSYYITMPLGIIVTENAVITTCLHDMTLFDHFHNRRVKN 120- Query: 131 FYTFMKTRFVFQLLYRNAELYLQALRTIDRQSDKIEAQLESATRNEQLIDMMELEKSIVY 19- 0 FYTFMKTRFVFQ+LYRNAEL+L ALRTIDRQS+++EAQLE+ATRNE+LIDMMELEKSIVY Sbjct: 121 FYTFMKTRFVFQILYRNAELFLTALRTIDRQSERLEAQLEAATRNEELIDMMELEKSIVY 18- 0 Query: 191 LKASLKFNERIVKKLTSSTSSLKKYIEDEDLLEDTLIETQQAIEMANIYENVLNAMTETT 25- 0 LKASLKFNERIVKKL+SSTSSLKKYIEDEDLLEDTLIETQQAIEMA IYENVLNAMTETT Sbjct: 181 LKASLKFNERIVKKLSSSTSSLKKYIEDEDLLEDTLIETQQAIEMAGIYENVLNAMTETT 24- 0 Query: 251 ASIIGNNQNTIMKTLALVTMTLDIPTVIFSAYGMNFQNNWMPLNGLAHGFIYVVLLAFLM 31- 0 ASII NNQNTIMKTLAL+TM LDIPTVIFSAYGMNFQNNW+PLNGL H F Y+ L+A L+ Sbjct: 241 ASIINNNQNTIMKTLALMTMALDIPTVIFSAYGMNFQNNWLPLNGLEHAFWYITLIAMLL 30- 0 Query: 311 SSFVVFYFIRKKWF 324 SSFVV YFIRKKWF Sbjct: 301 SSFVVIYFIRKKWF 314 SEQ ID 3550 (GBS257) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 44 (lane 3; MW 35 kDa) and in FIG. 169 (lane 9 & 10; MW 50 kDa) and in FIG. 239 (lane 2; MW 50 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 48 (lane 6; MW 60 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1144 A DNA sequence (GBSx1220) was identified in S. agalactiae <SEQ ID 3551> which encodes the amino acid sequence <SEQ ID 3552>. Analysis of this protein sequence reveals the following: TABLE-US-03446 Possible site: 29 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.26 Transmembrane 158-174 (151-182) INTEGRAL Likelihood = -6.37 Transmembrane 93-109 (91-111) INTEGRAL Likelihood = -5.68 Transmembrane 188-204 (184-205) INTEGRAL Likelihood = -0.85 Transmembrane 118-134 (118-134) ----- Final Results ----- bacterial membrane --- Certainty = 0.5904(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 3553> which encodes the amino acid sequence <SEQ ID 3554>. Analysis of this protein sequence reveals the following: TABLE-US-03447 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.95 Transmembrane 92-108 (88-110) INTEGRAL Likelihood = -6.69 Transmembrane 153-169 (151-177) INTEGRAL Likelihood = -2.34 Transmembrane 183-199 (183-200) ----- Final Results ----- bacterial membrane --- Certainty = 0.3781(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-03448 Identities = 135/217 (62%), Positives = 167/217 (76%), Gaps = 1/217 (0%) Query: 1 MTLQDLTKKNQEFVHIATNQLLADGKSDAEIKAILEEHLPEIIDNQKKGITARSLLGAPT 60 M LQ+LTKKNQEF+H ATN+L+ DGKSD +IK ILEE +P I++NQKKG+TAR+LLG PT Sbjct: 1 MELQELTKKNQEFIHTATNKLIQDGKSDEDIKLILEEAIPAILENQKKGVTARNLLGTPT 60 Query: 61 TWAASFTERPEDKARVSVQKNTNPWLMWLDTSLLFLGLVTALNGLMLLFGQSNVNTGLIS 120- WAASF++ P KA KNTNPWLMWLDTSLLF+G+V LNG+M F + TGLIS Sbjct: 61 AWAASFSQDPSQKA-AETDKNTNPWLMWLDTSLLFIGIVALLNGIMTFFNTNATVTGLIS 119- Query: 121 ILTLGFGGGAAMYVTYYYIYRHMGKPKSERPGWLKSFAVLALVMLVWFALFAVVPLLPAT 18- 0 +L LGFGGGA+MY TYY+IYRH+GK KS RP W K A L+L ML+W AL++ LP + Sbjct: 120 LLALGFGGGASMYATYYFIYRHLGKDKSLRPSWFKIIAALSLAMLIWIALYSATAFLPTS 17- 9 Query: 181 INPKLPEVVLFIIALASFGLRFYLQRKYNIQSSMAPV 217 +NP+LP + L II S LR+YLQRKYNIQ++M+PV Sbjct: 180 LNPQLPPLALLIIGGVSLALRYYLQRKYNIQNTMSPV 216 A related GBS gene <SEQ ID 10787> and protein <SEQ ID 10788> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03449 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -9.94 GvH: Signal Score (-7.5): -3.66 Possible site: 29 >>> Seems to have no N-terminal signal sequence ALOM program count: 4 value: -12.26 threshold: 0.0 INTEGRAL Likelihood = -12.26 Transmembrane 158-174 (151-182) INTEGRAL Likelihood = -6.37 Transmembrane 93-109 (91-111) INTEGRAL Likelihood = -5.68 Transmembrane 188-204 (184-205) INTEGRAL Likelihood = -0.85 Transmembrane 118-134 (118-134) PERIPHERAL Likelihood = 8.43 50 modified ALOM score: 2.95 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5904(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1145 A DNA sequence (GBSx1221) was identified in S. agalactiae <SEQ ID 3555> which encodes the amino acid sequence <SEQ ID 3556>. Analysis of this protein sequence reveals the following: TABLE-US-03450 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1348(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1146 A DNA sequence (GBSx1222) was identified in S. agalactiae <SEQ ID 3557> which encodes the amino acid sequence <SEQ ID 3558>. This protein is predicted to be excinuclease ABC (uvrA). Analysis of this protein sequence reveals the following: TABLE-US-03451 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1738(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10111> which encodes amino acid sequence <SEQ ID 10112> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03452 >GP: AAC67271 GB: AF017113 excinuclease ABC subunit A [Bacillus subtilis] Identities = 642/940 (68%), Positives = 785/940 (83%), Gaps = 3/940 (0%) Query: 9 DKLMIRGARAHNLKNISVDIPRDKLVVVTGLSGSGKSSLAFDTIYAEGQRRYVESLSAYA 68 D++ ++GARAHNLKNI V IPRD+LVVVTGLSGSGKSSLAFDTIYAEGQRRYVESLSAYA Sbjct: 4 DRIEVKGARAHNLKNIDVTIPRDQLVVVTGLSGSGKSSLAFDTIYAEGQRRYVESLSAYA 63 Query: 69 RQFLGNMEKPDVDSIDGLSPAISIDQKTTSKNPRSTVGTVTEINDYLRLLYARVGTPYCI 128- RQFLG M+KPDVD+I+GLSPAISIDQKTTS+NPRSTVGTVTEI DYLRLLYARVG P+C Sbjct: 64 RQFLGQMDKPDVDAIEGLSPAISIDQKTTSRNPRSTVGTVTEIYDYLRLLYARVGKPHCP 123- Query: 129 NGHGAITASSVEQIVDKVLALPERTKMQILAPIIRRKKGQHKSTFEKIQKDGYVRVRIDG 18- 8 IT+ ++EQ+VD++L PERTK+Q+LAPI+ +KG H E+I+K GYVRVRIDG Sbjct: 124 EHGIEITSQTIEQMVDRILEYPERTKLQVLAPIVSGRKGAHVKVLEQIRKQGYVRVRIDG 18- 3 Query: 189 DIHDVTEVPELSKSKMHNIDIVVDRLINKEGIRSRLFDSVEAALRLSDGYVVIDTMDGNE 24- 8 ++ ++++ EL K+K H+I++V+DR++ KEG+ +RL DS+E ALRL +G V+ID + E Sbjct: 184 EMAELSDDIELEKNKKHSIEVVIDRIVVKEGVAARLSDSLETALRLGEGRVMIDVIGEEE 24- 3 Query: 249 LLFSEHYSCPECGFTVPELEPRLFSFNAPFGSCPTCDGLGIKLEVDIDLVIPDRSKTLRE 30- 8 L+FSEH++CP CGF++ ELEPRLFSFN+PFG+CPTCDGLG+KLEVD DLVIP++ +L+E Sbjct: 244 LMFSEHHACPHCGFSIGELEPRLFSFNSPFGACPTCDGLGMKLEVDADLVIPNQDLSLKE 30- 3 Query: 309 GALVPWNPISSNYYPTMLEQAMTQFGVDMDTPFEKLSKAEQDLALYGSGEREFHFHYIND 36- 8 A+ PW PISS YYP +LE T +G+DMD P + L K + D LYGSG+ +F Y ND Sbjct: 304 NAVAPWTPISSQYYPQLLEAVCTHYGIDMDVPVKDLPKHQLDKVLYGSGDDLIYFRYEND 36- 3 Query: 369 FGGERNIDLPFEGVVNNINRRYHETNSDYTRNVMREYMNELKCNTCHGYRLNDQALCVRV 42- 8 FG R ++ FEGV+ NI RRY ET SD+ R M +YN++ C TC GYRL +AL V + Sbjct: 364 FGQIREGEIQFEGVLRNIERRYKETGSDFIREQMEQYMSQKSCPTCKGYRLKKEALAVLI 42- 3 Query: 429 GGEEGLNIGQVSDLSIADHLELLETLRLSSNEQLIARPIIKEIHDRLSFLNNVGLNYLNL 48- 8 +G +IG++++LS+AD L + L LS + IA I++EI +RLSFL+ VGL+YL L Sbjct: 424 ---DGRHIGKITELSVADALAFFKDLTLSEKDMQIANLILREIVERLSFLDKVGLDYLTL 48- 0 Query: 489 SRSAGTLSGGESQRIRLATQIGSLSGVLY+LDEPSIGLHQRDNDRLIDSLKKMRDLGNT 548- SR+AGTLSGGE+QRIRLATQIGS LSGVLYVLDEPSIGLHQRDNDRLI +LK MRDLGNT Sbjct: 481 SRAAGTLSGGEAQRIRLATQIGSRLSGVLYILDEPSIGLHQRDNDRLISALKNMRDLGNT 54- 0 Query: 549 LIVVEHDEDTMMAADWLIDVGPGAGAFGGEIVASGTPKQVAKNTKSITGQYLSGKKVIPV 60- 8 LIVVEHDEDTMMAAD+LID+GPGAG GG+++++GTP++V ++ S+TG YLSGKK IP+ Sbjct: 541 LIVVEHDEDTMMAADYLIDIGPGAGIHGGQVISAGTPEEVMEDPNSLTGSYLSGKKFIPL 60- 0 Query: 609 PSERRVGNGRFLEIKGAAENNLQNLDVKFPLGKFIAVTGVSGSGKSTLINSILKKAVAQK 66- 8 P ERR +GR++EIKGA+ENNL+ ++ KFPLG F AVTGVSGSGKSTL+N IL KA+AQK Sbjct: 601 PPERRKPDGRYIEIKGASENNLKKVNAKFPLGTFTAVTGVSGSGKSTLVNEILHKALAQK 66- 0 Query: 669 LNRNSDKPGKYVSLEGIEYVORLIDIDQSPIGRTPRSNPATYTGVFDDIRDLFAQTNEAK 72- 8 L++ KPG + ++G++++D++IDIDQ+PIGRTPRSNPATYTGVFDDIRD+FAQTNEAK Sbjct: 661 LHKAKAKPGSHKEIKGLDHLDKVIDIDQAPIGRTPRSNPATYTGVFDDIRDVFAQTNEAK 72- 0 Query: 729 IRGYKKGRFSFNVKGGRCESCSGDGIIKIEMHFLPDVYVPCEVCHGTRYNSETLEVNYKE 78- 8 +RGYKKGRFSFNVRGGRCE+C GDGIIKIEMHFLPDVYVPCEVCHG RYN ETLEV YK Sbjct: 721 VRGYKKGRFSFNVKGGRCEACRGDGIIKIEMHFLPDVYVPCEVCHGKRYNRETLEVTYKG 78- 0 Query: 789 KNIAQILDNTVNDAVTFFAAIPKIARKLQTIKDVGLGYVTLGQPATTLSGGEAQRMKLAS 84- 8 K+I+ +LDMTV DA++FF IPKI RKLQT+ DVGLGY+TLGQPATTLSGGEAQR+KLAS Sbjct: 781 KSISDVLDMTVEDALSFFENIPKIKRKLQTLYDVGLGYITLGQPATTLSGGEAQRVKLAS 84- 0 Query: 849 ELHKRSTGKSLYILDEPTTGLHADDIARLLKVLDRFVDDGNTVLVIEHNLDVIKTADHII 90- 8 ELHKRSTG++LYILDEPTTGLH DDIARLL VL R VD+G+TVLVIEHNLD+IKTAD+I+ Sbjct: 841 ELHKRSTGRTLYILDEPTTGLHVDDIARLLVVLQRLVDNGDTVLVIEHNLDIIKTADYIV 90- 0 Query: 909 DLGPEGGIGGGQIVAIGTPEEVAENPKSYTGYYLKEKLAR 948 DLGPEGG GGG IVA GTPEE+ E +SYTG YLK + R Sbjct: 901 DLGPEGGAGGGTIVASGTPEEITEVEESYTGRYLKPVIER 940 A related DNA sequence was identified in S. pyogenes <SEQ ID 3559> which encodes the amino acid sequence <SEQ ID 3560>. Analysis of this protein sequence reveals the following:

TABLE-US-03453 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1138(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03454 Identities = 835/940 (88%), Positives = 896/940 (94%) Query: 7 MQDKLMIRGARAHNLKNISVDIPRDKLVVVTGLSGSGKSSLAFDTIYAEGQRRYVESLSA 66 MQ+K++I GARAHNLKNI V+IPRDKLVVVTGLSGSGKSSLAFDTIYAEGQRRYVESLSA Sbjct: 11 MQNKIIIHGARAHNLKNIDVEIPRDKLVVVTGLSGSGKSSLAFDTIYAEGQRRYVESLSA 70 Query: 67 YARQFLGNMEKPDVDSIDGLSPAISIDQKTTSKNPRSTVGTVTEINDYLRLLYARVGTPY 126- YARQFLGNMEKPDVDSIDGLSPAISIDQKTTSKNPRSTVGTVTEINDYLRLLYARVGTPY Sbjct: 71 YARQFLGNMEKPDVDSIDGLSPAISIDQKTTSKNPRSTVGTVTEINDYLRLLYARVGTPY 130- Query: 127 CINGHGAITASSVEQIVDKVLALPERTKMQILAPIIRRKKGQHKSTFEKIQKDGYVRVRI 18- 6 CINGHGAITASS EQIV++VLALPERT+MQILAP++RRKKGQHK+ FEKIQKDGYVRVR+ Sbjct: 131 CINGHGAITASSAEQIVEQVLALPERTRMQILAPVVRRKKGQHKTVFEKIQKDGYVRVRV 19- 0 Query: 187 DGDIHDVTEVPELSKSKMHNIDIVVDRLINKEGIRSRLFDSVEAALRLSDGYVVIDTMDG 24- 6 DGDI DVTEVPELSKSKMHNI++V+DRL+NK+GIRSRLFDSVEAALRL DGY++IDTMDG Sbjct: 191 DGDIFDVTEVPELSKSKMHNIEVVIDRLVNKDGIRSRLFDSVEAALRLGDGYLMIDTMDG 25- 0 Query: 247 NELLFSEHYSCPECGFTVPELEPRLFSFNAPFGSCPTCDGLGIKLEVDIDLVIPDRSKTL 30- 6 NELLFSEHYSCP CGFTVPELEPRLFSFNAPFGSCPTCDGLGIKLEVD+DLV+PD SK+L Sbjct: 251 NELLFSEHYSCPVCGFTVPELEPRLFSFNAPFGSCPTCDGLGIKLEVDLDLVVPDPSKSL 31- 0 Query: 307 REGALVPWNPISSNYYPTMLEQAMTQFGVDMDTPFEKLSKAEQDLALYGSGEREFHFHYI 36- 6 REGAL PWNPISSNYYPTMLEQAM FGVDMDTPFE L++ E+DL LYGSG+REFHFHY+ Sbjct: 311 REGALAPWNPISSNYYPTMLEQAMASFGVDMDTPFEALTEEERDLVLYGSGDREFHFHYV 37- 0 Query: 367 NDFGGERNIDLPFEGVVNNINRRYHETNSDYTRNVMREYMNELKCNTCHGYRLNDQALCV 42- 6 NDFGGERNID+PFEGVV N+NRRYHETNSDYTRNVMR YMNEL C TCHGYRLNDQALCV Sbjct: 371 NDFGGERNIDIPFEGVVTNVNRRYHETNSDYTRNVMRGYMNELTCATCHGYRLNDQALCV 43- 0 Query: 427 RVGGEEGLNIGQVSDLSIADHLELLETLRLSSNEQLIARPIIKEIHDRLSFLNNVGLNYL 48- 6 VGGEEG +IGQ+S+LSIADHL+LLE L L+ NE IA+PI+KEIHDRL+FLNNVGLNYL Sbjct: 431 HVGGEEGTHIGQISELSIADHLQLLEELELTENESTIAKPIVKEIHDRLTFLNNVGLNYL 49- 0 Query: 487 NLSRSAGTLSGGESQRIRLATQIGSNLSGVLYVLDEPSIGLHQRDNDRLIDSLKKMRDLG 54- 6 LSR+AGTLSGGESQRIRLATQIGSNLSGVLY+LDEPSIGLHQRDNDRLI+SLKKMRDLG Sbjct: 491 TLSRAAGTLSGGESQRIRLATQIGSNLSGVLYILDEPSIGLHQRDNDRLIESLKKMRDLG 55- 0 Query: 547 NTLIVVEHDEDTMMAADWLIDVGPGAGAFGGEIVASGTPKQVAKNTKSITGQYLSGKKVI 60- 6 NTLIVVEHDEDTMM ADWLIDVGPGAG FGGEI ASGTPKQVAKN KSITGQYLSGKK I Sbjct: 551 NTLIVVEHDEDTMMQADWLIDVGPGAGEFGGEITASGTPKQVAKNKKSITGQYLSGKKFI 61- 0 Query: 607 PVPSERRVGNGRFLEIKGAAENNLQNLDVKFPLGKFIAVTGVSGSGKSTLINSILKKAVA 66- 6 PVP ERR GNGRF+EIKGAA+NNLQ+LDV+FPLGKFIAVTGVSGSGKSTL+NSILKKAVA Sbjct: 611 PVPLERRSGNGRFIEIKGAAQNNLQSLDVRFPLGKFIAVTGVSGSGKSTLVNSILKKAVA 67- 0 Query: 667 QKLNRNSDKPGKYVSLEGIEYVDRLIDIDQSPIGRTPRSNPATYTGVFDDIRDLFAQTNE 72- 6 QKLNRN+DKPGKY S+ GIE+++RLIDIDQSPIGRTPRSNPATYTGVFDDIRDLFAQTNE Sbjct: 671 QKLNRNADKPGKYHSISGIEHIERLIDIDQSPIGRTPRSNPATYTGVFDDIRDLFAQTNE 73- 0 Query: 727 AKIRGYKKGRFSFNVKGGRCESCSGDGIIKIEMHFLPDVYVPCEVCHGTRYNSETLEVHY 78- 6 AKIRGYKKGRFSFNVKGGRCE+CSGDGIIKIEMHFLPDVYVPCEVCHG RYNSETLEVHY Sbjct: 731 AKIRGYKKGRFSFNVKGGRCEACSGDGIIKIEMHFLPDVYVPCEVCHGRRYNSETLEVHY 79- 0 Query: 787 KEKNIAQILDMTVNDAVTFFAAIPKIARKLQTIKDVGLGYVTLGQPATTLSGGEAQRMKL 84- 6 K KNIA++LDMTV+DA+ FF+AIPKIARK+QTIKDVGLGYVTLGQPATTLSGGEAQRMKL Sbjct: 791 KGKNIAEVLDMTVDDALVFFSAIPKIARKIQTIKDVGLGYVTLGQPATTLSGGEAQRMKL 85- 0 Query: 847 ASELHKRSTGKSLYILDEPTTGLHADDIARLLKVLDRFVDDGNTVLVIEHNLDVIKTADH 90- 6 ASELHKRSTGKSLYILDEPTTGLH DDIARLLKVL+RFVDDGNTVLVIEHNLDVIK+ADH Sbjct: 851 ASELHKRSTGKSLYILDEPTTGLHTDDIARLLKVLERFVDDGNTVLVIEHNLDVIKSADH 91- 0 Query: 907 IIDLGPEGGIGGGQIVAIGTPEEVAENPKSYTGYYLKEKL 946 IIDLGPEGG GGGQIVA GTPEEVA+ +SYTG+YLK KL Sbjct: 911 IIDLGPEGGDGGGQIVATGTPEEVAQVKESYTGHYLKVKL 950 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1147 A DNA sequence (GBSx1223) was identified in S. agalactiae <SEQ ID 3561> which encodes the amino acid sequence <SEQ ID 3562>. Analysis of this protein sequence reveals the following: TABLE-US-03455 Possible site: 60 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.40 Transmembrane 471-487 (463-490) INTEGRAL Likelihood = -9.29 Transmembrane 246-262 (242-264) INTEGRAL Likelihood = -7.27 Transmembrane 183-199 (178-207) INTEGRAL Likelihood = -5.41 Transmembrane 351-367 (349-370) INTEGRAL Likelihood = -4.41 Transmembrane 87-103 (83-107) INTEGRAL Likelihood = -3.24 Transmembrane 375-391 (374-392) INTEGRAL Likelihood = -2.97 Transmembrane 17-33 (16-35) INTEGRAL Likelihood = -2.28 Transmembrane 420-436 (420-438) INTEGRAL Likelihood = -1.97 Transmembrane 320-336 (320-337) INTEGRAL Likelihood = -1.75 Transmembrane 214-230 (214-230) INTEGRAL Likelihood = -1.75 Transmembrane 288-304 (288-304) INTEGRAL Likelihood = -1.70 Transmembrane 110-126 (110-126) INTEGRAL Likelihood = -0.69 Transmembrane 152-168 (151-168) ----- Final Results ----- bacterial membrane --- Certainty = 0.5161(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03456 >GP: CAB12192 GB: Z99106 similar to multidrug resistance protein [Bacillus subtilis] Identities = 198/481 (41%), Positives = 300/481 (62%), Gaps = 24/481 (4%) Query: 9 IHGKPYNRTAMITLLLIATFAGVLNQTSLGTAIPTLMNSFNISLSTAQQATTWFLLANGI 68 I KP+NR+ ++ +LL F +LNQT L TA+P +M FN+ + AQ TT F+L NGI Sbjct: 5 IEQKPFNRSVIVGILLAGAFVAILNQTLLITALPHIMRDFNVDANQAQWLTTSFMLTNGI 64 Query: 69 MIPVSAYLATRFSTKWLYVTSYVVLLIGLLMTTLAPTSNWNLFLVGRIIQAISVGISMPL 128- +IP++A+L +F+++ L +T+ + G ++ AP N+ + L RIIQA GI MPL Sbjct: 65 LIPITAFLIEKFTSRALLITAMSIFTAGTVVGAFAP--NFPVLLTARIIQAAGAGIMMPL 122- Query: 129 MQVVMVNVFPPEQRGAAMGLNGLVVGLAPAIGPTLAGWILKQEFHFAGHDLTWRAIFLLP 18- 8 MQ V + +FP E+RG AMG+ GLV+ APAIGPTL+GW ++ +WR++F + Sbjct: 123 MQTVFLTIFPIEKRGQAMGMVGLVISFAPAIGPTLSGWAVEA--------FSWRSLFYII 17- 4 Query: 189 LLILTVTTILSPFVLKDVVDNKSVKLEVPSLILSIIGFGSFLWGFTNVATYGWGDIGYVI 24- 8 L + IL+ ++K+V + ++++ S+ILS GFG L+GF++V +YGW +I Sbjct: 175 LPFAVIDLILASILMKNVTTLRKTQIDILSVILSTFGFGGLLYGFSSVGSYGWSSSTVLI 23- 4 Query: 249 SPIMVGIIFIALFIHRQLKLETPFLDIRVFKNKQFSVTTAAIALSMMAMMGVEMMLPLYL 30- 8 S ++VG+I + LFI RQ+KL+ P L+ RVF FS+TT L ++G E +LPLY Sbjct: 235 S-LLVGVIALLLFITRQMKLKKPMLEFRVFTFGVFSLTTLLGTLVFALLIGTETILPLYT 29- 3 Query: 309 QNVHGLSALDSGLALLPGALMMGIVSPISGAVYDKVGARRMAMIGFTILGVATLPFVFLT 36- 8 QNV ++A D+GL LLPGA++MG +SPI G ++D+VG R +A+ GF I+ + +LPF+ LT Sbjct: 294 QNVRDVTAFDTGLMLLPGAVVMGFMSPIIGRIFDRVGGRGLAIAGFCIIFLTSLPFMQLT 35- 3 Query: 369 TTTPDHFITLLYAVRMFGIAMVMMPLTASAMSALPPHEAAHGTAANNTARQIASAVVVAL 42- 8 T +I +LY VR+ G AM+MMP+T + ++ALP H HGTA NNT RQ+ ++ AL Sbjct: 354 DHTSLAWIVVLYTVRLLGTAMIMMPVTTAGINALPRHLIPHGTAMNNTIRQVGGSIGTAL 41- 3 Query: 429 LSSVAQNIITNNKPSKDLLTMNPLKYANQMLNASLDGFHVSFAIGFVFAVLGLLVSLFLRK 4- 89 L SV N + + +A+L G + +F + V A++G L+S L+K Sbjct: 414 LVSVMSNQAAH-------------AGTTNVKHAALHGMNAAFIVAAVIALVGFLLSFTLKK 4- 61 There is also homology to SEQ ID 46. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1148 A DNA sequence (GBSx1224) was identified in S. agalactiae <SEQ ID 3563> which encodes the amino acid sequence <SEQ ID 3564>. Analysis of this protein sequence reveals the following: TABLE-US-03457 Possible site: 47 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.81 Transmembrane 8-24 (5-30) INTEGRAL Likelihood = -7.32 Transmembrane 36-52 (31-54) ----- Final Results ----- bacterial membrane --- Certainty = 0.4524(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10109> which encodes amino acid sequence <SEQ ID 10110> was also identified. A related GBS gene <SEQ ID 8743> and protein <SEQ ID 8744> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03458 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 9.52 GvH: Signal Score (-7.5): -3.4 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq ALOM program Count: 1 value: -7.32 threshold: 0.0 INTEGRAL Likelihood = -7.32 Transmembrane 11-27 (6-29) PERIPHERAL Likelihood = 11.19 130 modified ALOM score: 1.96 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3930(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8744 (GBS29) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 7 (lane 2; MW 25.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 15 (lane 6; MW 51 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1149 A DNA sequence (GBSx1225) was identified in S. agalactiae <SEQ ID 3565> which encodes the amino acid sequence <SEQ ID 3566>. This protein is predicted to be aminopeptidase P (pepQ). Analysis of this protein sequence reveals the following: TABLE-US-03459 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0724(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03460 >GP: CAA70068 GB: Y08842 aminopeptidase P [Lactococcus lactis] Identities = 44/126 (34%), Positives = 78/126 (60%) Query: 6 RLTRCQTAISQLSCDALLITNLTNIFYLTGFSGTNATVLISPKHRIFVTDSRYALIAKNT 65 R+ + + + + D+LLIT++ NIFYLTGFSGT TV ++ K IF+TDSRY+ +A+ Sbjct: 2 RIEKLKVKMLTENIDSLLITDMKNIFYLTGFSGTAGTVFLTQKRNIFMTDSRYSEMARGL 61 Query: 66 VREFDIIISREPLAAILKIIRDDALIAIGFETDISYHMYKHMVEVFEDYRLIEAPSVVEK 125- ++ F+II +R+P++ + ++ +++ + FE + Y +K + + L + V + Sbjct: 62 IKNFEIIETRDPISLLTELSASESVKNMAFEETVDYAFFKRLSKAATKLDLFSTSNFVLE 121- Query: 126 LRMIKD 131 LR IKD Sbjct: 122 LRQIKD 127 There is also homology to SEQ ID 3568. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1150 A DNA sequence (GBSx1226) was identified in S. agalactiae <SEQ ID 3569> which encodes the amino acid sequence <SEQ ID 3570>. This protein is predicted to be aminopeptidase P (pepQ-2). Analysis of this protein sequence reveals the following: TABLE-US-03461 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2508(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03462 >GP: CAA70068 GB: Y08842 aminopeptidase P [Lactococcus lactis] Identities = 131/205 (63%), Positives = 163/205 (78%), Gaps = 3/205 (1%) Query: 2 LDFIKPDRTTELQVANFLDFRMRELGATGPSFDFIVASGYRSAMPHGVASQKTIQSGETL 61 L FI+P RT E++VANFLDF+MR+L A+G SF+ IVASG RS++PHGVA+ K IQ G+ + Sbjct: 149 LRFIEPGRT-EIEVANFLDFKMRDLEASGISFETIVASGKRSSLPHGVATSKMIQFGDPV 20- 7 Query: 62 TLDFGCYYQHYVSDMTRTIHIGHVTDQEREIYDIVLKSNQAIIGNVKSGMKRCDYDYLAR 121- T+DFGCYY+HY SDMTRTI +G V D+ R IY+ V K+N+A+I VK+GM YD + R Sbjct: 208 TIDFGCYYEHYASDMTRTIFVGSVDDKMRTIYETVRKANEALIKQVKAGMTYAQYDNIPR 26- 7 Query: 122 QVIENSGYGNHFTHGIGHGMGLDVHEIPYFGKS--EGVIASGMVVTDEPGIYLDNKYGVR 17- 9 +VIE + +G +FTHGIGHG+GLDVHEIPYF +S E + SGMV+TDEPGIYL GVR Sbjct: 268 EVIEKADFGQYFTHGIGHGLGLDVHEIPYFNQSMTENQLRSGMVITDEPGIYLPEFGGVR 32- 7 Query: 180 IEDDLLITETGCEVLTSAPKELIVL 204 IEDDLL+TE GCEVLT APKELIV+ Sbjct: 328 IEDDLLVTENGCEVLTKAPKELIVI 352 A related DNA sequence was identified in S. pyogenes <SEQ ID 3567> which encodes the amino acid sequence <SEQ ID 3568>. Analysis of this protein sequence reveals the following: TABLE-US-03463 Possible Site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1450(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03464 Identities = 145/203 (71%), Positives = 171/203 (83%) Query: 2 LDFIKPDRTTELQVANFLDFRMRELGATGPSFDFIVASGYRSAMPHGVASQKTIQSGETL 61 LDFIKP TTE +ANFLDFRMR+ GA+G SFD IVASGY SAMPHG AS K IQ+ E+L Sbjct: 168 LDFIKPGTTTERDLANFLDFRMRQYGASGTSFDIIVASGYLSAMPHGRASDKVIQNKESL 22- 7 Query: 62 TLDFGCYYQHYVSDMTRTIHIGHVTDQEREIYDIVLKSNQAIIGNVKSGMKRCDYDYLAR 121- T+DFGCYY HYVSDMTRTIHIG VTD+EREIY +VL +N+A+I +GM D+D + R Sbjct: 228 TMDFGCYYNHYVSDMTRTIHIGQVTDEEREIYALVLAANKALIAKASAGMTYSDFDGIPR 28- 7 Query: 122 QVIENSGYGNHFTHGIGHGMGLDVHEIPYFGKSEGVIASGMVVTDEPGIYLDNKYGVRIE 18- 1 Q+I +GYG+ FTHGIGHG+GLD+HE P+FGKSE ++ +GMVVTDEPGIYLDNKYGVRIE Sbjct: 288 QLITEAGYGSRETHGIGHGIGLDIHENPFFGKSEQLLQAGMVVTDEPGIYLDNKYGVRIE 34- 7 Query: 182 DDLLITETGCEVLTSAPKELIVL 204 DDL+IT+TGC+VLT APKELIVL Sbjct: 348 DDLVITKTGCQVLTLAPKELIVL 370 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1151 A DNA sequence (GBSx1227) was identified in S. agalactiae <SEQ ID 3571> which encodes the amino acid sequence <SEQ ID 3572>. This protein is predicted to be yfhC protein (comEB). Analysis of this protein sequence reveals the following: TABLE-US-03465 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1401(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03466 >GP: BAB05053 GB: AP001511 late competence operon required for DNA binding and uptake [Bacillus halodurans] Identities = 78/146 (53%), Positives = 107/146 (72%) Query: 1 MNRLSWEDYFMANAELISKRSTCDRAFVGAVLVKNNRIIATGYNGGVSETDNCNEVGHYM 60 MNR+SW+ YFMA + L++ RSTC R VGA +V++ RIIA GYNG +S +C + G Y+ Sbjct: 1 MNRISWDQYFMAQSHLLALRSTCTRLMVGATIVRDKRIIAGGYNGSISGGPHCIDEGCYV 60 Query: 61 EDGNCIRTVHAEMNALIQCAKEGISTNNTEIYVTHFPCINCTKALLQAGVKKITYKANYR 120- +GHCIRT+HAE+NAL+QCAK G+ T EIYVTHFPC+NCTKA++Q+G+KK+ Y +Y+ Sbjct: 61 VEGHCIRTIHAEVNALLQCAKFGVPTEGAEIYVTHFPCVNCTKAIIQSGIKKVYYATDYK 120- Query: 121 PHPFAIELMEAKGVAYVQHDVPEVTL 146 P+A EL GV Q ++ E+ L Sbjct: 121 NSPYAEELFRDAGVDVEQVELEEMIL 146 A related DNA sequence was identified in S. pyogenes <SEQ ID 3573> which encodes the amino acid sequence <SEQ ID 3574>. Analysis of this protein sequence reveals the following: TABLE-US-03467 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3155(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03468 Identities = 133/146 (91%), Positives = 140/146 (95%) Query: 2 NRLSWEDYFMANAELISKRSTCDRAFVGAVLVKNNRIIATGYNGGVSETDNCNEVGHYME 61 NRLSW+DYFMANAELISKRSTCDRAFVGAVLVK+NRIIATGYNGGVS TDNCNE GHYME Sbjct: 18 NRLSWQDYFMANAELISKRSTCDRAFVGAVLVKDNRIIATGYNGGVSATDNCNEAGHYME 77 Query: 62 DGHCIRTVHAEMNALIQCAKEGISTNNTEIYVTHFPCINCTKALLQAGVKKITYKANYRP 121- DGHCIRTVHAEMNALIQCAKEGIST+ TEIYVTHFPCINCTKALLQAG+ KITYKA+YRP Sbjct: 78 DGHCIRTVHAEMNALIQCAKEGISTDGTEIYVTHFPCINCTKALLQAGITKITYKAHYRP 137- Query: 122 HPFAIELMEAKGVAYVQHDVPEVTLG 147 HPFAIELME KGVAYVQHDVP++ LG Sbjct: 138 HPFAIELMEKKGVAYVQHDVPQIVLG 163 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1152 A DNA sequence (GBSx1228) was identified in S. agalactiae <SEQ ID 3575> which encodes the amino acid sequence <SEQ ID 3576>. Analysis of this protein sequence reveals the following:

TABLE-US-03469 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2454(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1153 A DNA sequence (GBSx1229) was identified in S. agalactiae <SEQ ID 3577> which encodes the amino acid sequence <SEQ ID 3578>. Analysis of this protein sequence reveals the following: TABLE-US-03470 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.65 Transmembrane 4-20 (3-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.1659(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1154 A DNA sequence (GBSx1230) was identified in S. agalactiae <SEQ ID 3579> which encodes the amino acid sequence <SEQ ID 3580>. Analysis of this protein sequence reveals the following: TABLE-US-03471 Possible site: 54 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03472 >GP: BAB04699 GB: AP001510 unknown conserved protein [Bacillus halodurans] Identities = 47/94 (50%), Positives = 65/94 (69%) Query: 2 LLPVGSVVYLIDGNQKLVIVNRGAIVEQEGQEVYFDYLGGIFPEGLNLEQVYYFNQEDID 61 +LP+GS+VYL +G KL+I+NRG I+E G+ FDY G +P+GL ++V+YFN E+ID Sbjct: 1 MLPIGSIVYLKEGTSKLMILNRGPILEANGENKMFDYSGCFYPQGLVPDKVFYFNHENID 60 Query: 62 EVVFEGYHDEEEERVSRLIEKWKNTEGKNLPKGK 95 EVVFEG+ D+EE+R +L WK KGK Sbjct: 61 EVVFEGFQDDEEQRFQKLFHDWKKENKDRYVKGK 94 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1155 A DNA sequence (GBSx1231) was identified in S. agalactiae <SEQ ID 3581> which encodes the amino acid sequence <SEQ ID 3582>. Analysis of this protein sequence reveals the following: TABLE-US-03473 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3560(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1156 A DNA sequence (GBSx1232) was identified in S. agalactiae <SEQ ID 3583> which encodes the amino acid sequence <SEQ ID 3584>. This protein is predicted to be elongation factor p (efp). Analysis of this protein sequence reveals the following: TABLE-US-03474 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3067(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03475 >GP: CAB14376 GB: Z99116 elongation factor P [Bacillus subtilis] Identities = 89/186 (47%), Positives = 120/186 (63%), Gaps = 1/186 (0%) Query: 1 MIEASKLKAGMTFETADGKLIRVLEASHHKPGKGNTIMRMKLRDVRTGSTFDTSYRPEEK 60 MI + + G+T + DG + RV++ H KPGKG +R KLR++RTG+ + ++R BK Sbjct: 1 MISVNDFRTGLTIDV-DGGIWRVVDFQHVKPGKGAAFVRSKLRNLRTGAIQEKTFRAGEK 59 Query: 61 FEQAIIETVPAQYLYKMDDTAYFMNNETYDQYEIPTVNIENELLYILENSEVKIQFYGTE 120- +A IET QYLY D FM+ +Y+Q E+ IE EL Y+LEN V I Y E Sbjct: 60 VAKAQIETKTMQYLYANGDQHVFMDTSSYEQLELSATQIEEELKYLLENMSVHIMNYQDE 119- Query: 121 VIGVQIPTTVELTVAETQPSIKGATVTGSGKPATMETGLVVNVPDFIEAGQKLVINTAEG 18- 0 +G+++P TVEL V ET+P IKG T +G KPA ETGLVVNVP F+ G LV+NT++G Sbjct: 120 TLGIELPNTVELKVVETEPGIKGDTASGGTKPAKTETGLVVNVPFFVNEGDTLVVNTSDG 17- 9 Query: 181 TYVSRA 186 +YVSRA Sbjct: 180 SYVSRA 185 A related DNA sequence was identified in S. pyogenes <SEQ ID 3585> which encodes the amino acid sequence <SEQ ID 3586>. Analysis of this protein sequence reveals the following: TABLE-US-03476 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1813(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03477 Identities = 170/186 (91%), Positives = 180/186 (96%), Gaps = 1/186 (0%) Query: 1 MIEASKLKAGMTFETADGKLIRVLEASHHKPGKGNTIMRMKLRDVRTGSTFDTSYRPEEK 60 MIEASKLKAGMTFE A+GKLIRVLEASHHKPGKGNTIMRMKLRDVRTGSTFDT+YRP+EK Sbjct: 1 MIEASKLKAGMTFE-AEGKLIRVLEASHHKPGKGNTIMRMKLRDVRTGSTFDTTYRPDEK 59 Query: 61 FEQAIIETVPAQYLYKMDDTAYFMNNETYDQYEIPTVNIENELLYILENSEVKIQFYGTE 120- FEQAIIETVPAQYLYKMDDTAYFMN +TYDQYEIP N+E ELLYILENS+VKIQFYG+E Sbjct: 60 FEQAIIETVPAQYLYKMDDTAYFMNTDTYDQYEIPVANVEQELLYILENSDVKIQFYGSE 119- Query: 121 VIGVQIPTTVELTVAETQPSIKGATVTGSGKPATMETGLVVNVPDFIEAGQKLVINTAEG 18- 0 VIGV +PTTVELTVAETQPSIKGATVTGSGKPAT+ETGLVVNVPDFIEAGQKL+INTAEG Sbjct: 120 VIGVTVPTTVELTVAETQPSIKGATVTGSGKPATLETGLVVNVPDFIEAGQKLIINTAEG 17- 9 Query: 181 TYVSRA 186 TYVSRA Sbjct: 180 TYVSRA 185 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1157 A DNA sequence (GBSx1233) was identified in S. agalactiae <SEQ ID 3587> which encodes the amino acid sequence <SEQ ID 3588>. Analysis of this protein sequence reveals the following: TABLE-US-03478 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1508(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03479 >GP: BAB06505 GB: AP001516 unknown conserved protein [Bacillus halodurans] Identities = 42/107 (39%), Positives = 70/107 (65%), Gaps = 4/107 (3%) Query: 5 NLGEIVISPRVLEVITGIAATKVDGVHSLRNK---AVTDSLSKKSLGRGVYLKNEEDDTV 61 +LG + ISP V+EVI GIAA++V+GV ++R V + L K+ G+GV + + D+ + Sbjct: 15 DLGRVEISPEVIEVIAGIAASEVEGVATMRGNFAAGVAEKLGYKNHGKGVKV-DLNDEGI 73 Query: 62 AADIYVYLQYGVNVPAVSIAIQQAVKTAVYDMAEVKISSVNIHVEGI 108 D+ V + YGV+VP V+ IQQ +K A+ M +++ S+N+H+ G+ Sbjct: 74 IVDVSVIILYGVSVPEVAKKIQQNIKQALQTMTAIELQSINVHIVGV 120 A related DNA sequence was identified in S. pyogenes <SEQ ID 3589> which encodes the amino acid sequence <SEQ ID 3590>. Analysis of this protein sequence reveals the following: TABLE-US-03480 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0882(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03481 Identities = 101/129 (78%), Positives = 113/129 (87%) Query: 1 MTTENLGEIVISPRVLEVITGIAATKVDGVHSLRNKAVTDSLSKKSLGRGVYLKNEEDDT 60 MTTE +GEIVISPRVLEVITGIA T+V+GVHSL NK + DS +K SLG+GVYL+ EED + Sbjct: 1 MTTEYIGEIVISPRVLEVITGIATTQVEGVHSLHNKKMADSFNKASLGKGVYLQTEEDGS 60 Query: 61 VAADIYVYLQYGVNVPAVSIAIQQAVKTAVYDMAEVKISSVNIHVEGIVPEKTPKPDLKS 120- V ADIYVYLQYGV VP VS+ IQ+ VK+AVYDMAEV IS+VNIHVEGIV EKTPKPDLKS Sbjct: 61 VTADIYVYLQYGVKVPTVSMNIQKTVKSAVYDMAEVPISAVNIHVEGIVAEKTPKPDLKS 120- Query: 121 LFDEDFLDD 129 LFDEDFLDD Sbjct: 121 LFDEDFLDD 129 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1158 A DNA sequence (GBSx1234) was identified in S. agalactiae <SEQ ID 3591> which encodes the amino acid sequence <SEQ ID 3592>. This protein is predicted to be n utilization substance protein b homolog (nusB). Analysis of this protein sequence reveals the following: TABLE-US-03482 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 48-64 (47-64) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03483 >GP: CAB14363 GB: Z99116 similar to transcription termination [Bacillus subtilis] Identities = 51/129 (39%), Positives = 82/129 (63%), Gaps = 9/129 (6%) Query: 9 RRDLRERAFQTLFSLETGGEFIDAAHFAYGYDKTVSEDKVLEVPIFLLNLVNGVVDHKDE 68 RR RE+A Q LF ++ ++ A + + E+K F LV+GV++H+D+ Sbjct: 3 RRTAREKALQALFQIDVSDIAVNEA-----IEHALDEEKT---DPFFEQLVHGVLEHQDQ 54 Query: 69 LDTLISSHLKSGWSLERLTLVDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETS 128- LD +IS HL + W L+R+ VD+++LRL YE+ Y ++ P V++NE IE+AK++ D+ + Sbjct: 55 LDEMISKHLVN-WKLDRIANVDRAILRLAAYEMAYAEDIPVNVSMNEAIELAKRFGDDKA 113- Query: 129 AKFVNGLLS 137 KFVNG+LS Sbjct: 114 TKFVNGVLS 122 A related DNA sequence was identified in S. pyogenes <SEQ ID 3593> which encodes the amino acid sequence <SEQ ID 3594>. Analysis of this protein sequence reveals the following: TABLE-US-03484 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.75 Transmembrane 53-69 (53-69) ----- Final Results ----- bacterial membrane --- Certainty = 0.1702(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03485 >GP: CAB14363 GB: Z99116 similar to transcription termination [Bacillus subtilis] Identities = 47/134 (35%), Positives = 76/134 (56%), Gaps = 10/134 (7%) Query: 15 RRDLRERAFQALFNIEMGAELLAASQFAYGYDKVTGEDAQVLELPIFLLSLVTGVNNHKE 74 - RR RE+A QALF I++ +++ + D+ + F LV GV H++ Sbjct: 3 RRTAREKALQALFQIDV-SDIAVNEAIEHALDEEKTDP--------FFEQLVHGVLEHQD 53 Query: 75 ELDNLISTHLKKGWSLERLTLTDKTLLRLGLFEIKYFDKTPDRVALNEIIEVVKKYSDET 134- +LD +IS HL W L+R+ D+ +LRL +E+ Y + P V++NE IE+ K++ D+ Sbjct: 54 QLDEMISKHLVN-WKLDRIANVDRAILRLAAYEMAYAEDIPVNVSMNEAIELAKRFGDDK 112- Query: 135 SAKFINGLLSQYVS 148 + KF+NG+LS S Sbjct: 113 ATKFVNGVLSNIKS 126 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03486 Identities = 104/142 (73%), Positives = 125/142 (87%), Gaps = 1/142 (0%) Query: 1 MTSVFKDSRRDLRERAFQTLFSLETGGEFIDAAHFAYGYDKTVSED-KVLEVPIFLLNLV 59 MT+ F++SRRDLRERAFQ LF++E G E + A+ FAYGYDK ED +VLE+PIFLL+LV Sbjct: 7 MTNSFQNSRRDLRERAFQALFNIEMGAELLAASQFAYGYDKVTGEDAQVLELPIFLLSLV 66 Query: 60 NGVVDHKDELDTLISSHLKSGWSLERLTLVDKSLLRLGLYEIKYFDETPDRVALNEIIEI 119- GV +HK+ELD LIS+HLK GWSLERLTL DK+LLRLGL+EIKYFD+TPDRVALNEIIE+ Sbjct: 67 TGVNNHKEELDNLISTHLKKGWSLERLTLTDKTLLRLGLFEIKYFDKTPDRVALNEIIEV 126- Query: 120 AKKYSDETSAKFVNGLLSQFIT 141 KKYSDETSAKF+NGLLSQ+++ Sbjct: 127 VKKYSDETSAKFINGLLSQYVS 148 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1159 A DNA sequence (GBSx1235) was identified in S. agalactiae <SEQ ID 3595> which encodes the amino acid sequence <SEQ ID 3596>. Analysis of this protein sequence reveals the following: TABLE-US-03487 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -2.81 Transmembrane 239-255 (239-255) ----- Final Results ----- bacterial membrane --- Certainty = 0.2126(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03488 >GP: AAC31628 GB: U46902 ScrR [Streptococcus mutans] Identities = 225/320 (70%), Positives = 273/320 (85%) Query: 1 MVAKLTDVAALAGVSPTTVSRVINKKGYLSQKTVTKVNEAMRTLGYKPNNLARSLQGKSA 60 MVAKLTDVA LAGVSPTTVSRVIN+KGYLS+KT+TKV AM+TLGYKPNNLARSLQGKSA Sbjct: 1 MVAKLTDVAKLAGVSPTTVSRVINRKGYLSEKTITKVQAAMKTLGYKPNNLARSLQGKSA 60 Query: 61 KLIGLIFPNIRNIFYAELIEHLEIELFKHGYKTILCNSEKDPIKEKEYLEMLGANQVDGI 120- KLIGLIFPNI +IFY+ELIE+LEIELFKHGYK I+CNS+ +P KE++YLEML ANQVDGI Sbjct: 61 KLIGLIFPNISHIFYSELIEYLEIELFKHGYKAIICNSQNNPDKERDYLEMLEANQVDGI 120- Query: 121 ISSSHNLGIDDYEKVEAPIVAFDRNLAPHIPIVSSDNFFGGKMAAQTLKKHGCQKMIMIT 18- 0 ISSSHNLGIDDYEKV API+AFDRNLAP+IPIVSSDNF GG+MAA+ LKKHGCQ IMI Sbjct: 121 ISSSHNLGIDDYEKVSAPIIAFDRNLAPNIPIVSSDNFEGGRMAAKLLKKHGCQHPIMIA 18- 0 Query: 181 GNDNSDSPTGLRRLGFSYESKESKVITVTNGLSNMRREMELKSIISTHKPDGIFTSDDLT 24- 0 G DNS+SPT LR+LGF ++ + ++ LS +R+EME+K I+ KPDGIF SDD+T Sbjct: 181 GKDNSNSPTALRQLGFKSVFAQAPIFHLSGELSIIRKEMEIKVILQNEKPDGIFLSDDMT 24- 0 Query: 241 ALLVIKLISQLGLSIPEDIKVIGYDGTSFIQDYVPHLTTIKQPIREIAQLMVEILLAKIE 30- 0 A+L +K+ +QL ++IP ++K+IGYDGT F+++Y P+LTTI+QPI++IA L+V+ILL KI+ Sbjct: 241 AILTMKIANQLNITIPHELKIIGYDGTHFVENYYPYLTTIRQPIKDIAHLLVDILLRRID 30- 0 Query: 301 GQKTNKDYILPVSLIPGSSV 320 Q KDYILPV L+ G SV Sbjct: 301 HQDIPKDYILPVGLLSGESV 320 A related DNA sequence was identified in S. pyogenes <SEQ ID 3597> which encodes the amino acid sequence <SEQ ID 3598>. Analysis of this protein sequence reveals the following: TABLE-US-03489 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03490 >GP: AAC31628 GB: U46902 ScrR [Streptococcus mutans] Identities = 226/321 (70%), Positives = 269/321 (83%), Gaps = 1/321 (0%) Query: 1 VVAKLTDVAALAGVSPTTVSRVINKKGYLSQKTVNKVNKAMRELGYKPNNLARSLQGKST 60 +VAKLTDVA LAGVSPTTVSRVIN+KGYLS+KT+ KV AM+ LGYKPNNLARSLQGKS Sbjct: 1 MVAKLTDVAKLAGVSPTTVSRVINRKGYLSEKTITKVQAAMKTLGYKPNNLARSLQGKSA 60 Query: 61 QLIGLIFPNISNIFYAELIEHLEIELFKQGYKTIICNSEHNPVKEREYLEMLAANQVDGI 120- +LIGLIFPNIS+IFY+ELIE+LEIELFK GYK IICNS++NP KER+YLEML ANQVDGI Sbjct: 61 KLIGLIFPNISHIFYSELIEYLEIELFKHGYKAIICNSQNNPDKERDYLEMLEANQVDGI 120- Query: 121 ISSSHNLGIEDYERVEAPIVAFDRNLAPNIPVISSDNFEGGKLAAQTLQKHGCQNIVMIT 18- 0 ISSSHNLGI+DYE+V API+AFDRNLAPNIP++SSDNFEGG++AA+ L+KHGCQ+ +MI Sbjct: 121 ISSSHNLGIDDYEKVSAPIIAFDRNLAPNIPIVSSDNFEGGRMAAKLLKKHGCQHPIMIA 18- 0 Query: 181 GNDNSDSPTGLRQLGFNYQLKRSAEIIKLPNNLSPVRREMEIKSILATRKPDGLFVSDDL 24- 0 G DNS+SPT LRQLGF + A I L LS +R+EMEIK IL KPDG+F+SDD+ Sbjct: 181 GKDNSNSPTALRQLGFK-SVFAQAPIFHLSGELSIIRKEMEIKVILQNEKPDGIFLSDDM 23- 9 Query: 241 TAILIMKVAKQLHITIPEDMKVIGYDGTTFIQQYVPQLATIRQPIDEIAKLSVEILIKKI 30- 0 TAIL MK+A QL+ITIP ++K+IGYDGT F++ Y P L TIRQPI +IA L V+IL+KKI Sbjct: 240 TAILTMKIANQLNITIPHELKIIGYDGTHFVENYYPYLTTIRQPIKDIAHLLVDILLKKI 29- 9 Query: 301 KKEKTSKDYILPITLLPGASI 321 + KDYILP+ LL G S+ Sbjct: 300 DHQDIPKDYILPVGLLSGESV 320 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03491 Identities = 247/321 (76%), Positives = 293/321 (90%), Gaps = 1/321 (0%) Query: 1 MVAKLTDVAALAGVSPTTVSRVINKKGYLSQKTVTKVNEAMRTLGYKPNNLARSLQGKSA 60 +VAKLTDVAALAGVSPTTVSRVINKKGYLSQKTV KVN+AMR LGYKPNNLARSLQGKS Sbjct: 1 VVAKLTDVAALAGVSPTTVSRVINKKGYLSQKTVNKVNKAMRELGYKPNNLARSLQGKST 60 Query: 61 KLIGLIFPNIRNIFYAELIEHLEIELFKHGYKTILCNSEKDPIKEKEYLEMLGANQVDGI 120- +LIGLIFPNI NIFYAELIEHLEIELFK GYKTI+CNSE +P+KE+EYLEML ANQVDGI Sbjct: 61 QLIGLIFPNISNIFYAELIEHLEIELFKQGYKTIICNSEHNPVKEREYLEMLAANQVDGI 120- Query: 121 ISSSHNLGIDDYEKVEAPIVAFDRNLAPHIPIVSSDNFFGGKMAAQTLKKHGCQKMIMIT 18- 0 ISSSHNLGI+DYE+VEAPIVAFDRNLAP+IP++SSDNF GGK+AAQTL+KHGCQ ++MIT Sbjct: 121 ISSSHNLGIEDYERVEAPIVAFDRNLAPNIPVISSDNFEGGKLAAQTLQKHGCQNIVMIT 18- 0 Query: 181 GNDNSDSPTGLRRLGFSYESKES-KVITVTNGLSNMRREMELKSIISTHKPDGIFTSDDL 23- 9 GNDNSDSPTGLR+LGF+Y+ K S ++I + N LS +RREME+KSI++T KPDG+F SDDL Sbjct: 181 GNDNSDSPTGLRQLGFNYQLKRSAEIIKLPNNLSPVRREMEIKSILATRKPDGLFVSDDL 24- 0 Query: 240 TALLVIKLISQLGLSIPEDIKVIGYDGTSFIQDYVPHLTTIKQPIREIAQLMVEILLAKI 29- 9 TA+L++K+ QL ++IPED+KVIGYDGT+FIQ YVP L TI+QPI EIA+L VEIL+KI Sbjct: 241 TAILIMKVAKQLHITIPEDMKVIGYDGTTFIQQYVPQLATIRQPIDEIAKLSVEILIKKI 30- 0 Query: 300 EGQKTNKDYILPVSLIPGSSV 320 + +KT+KDYILP++L+PG+S+ Sbjct: 301 KKEKTSKDYILPITLLPGASI 321 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1160 A DNA sequence (GBSx1236) was identified in S. agalactiae <SEQ ID 3599> which encodes the amino acid sequence <SEQ ID 3600>. This protein is predicted to be sucrose-6-phosphate hydrolase (cscA). Analysis of this protein sequence reveals the following:

TABLE-US-03492 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4775(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03493 >GP: CAA35872 GB: X51507 sucrose-6-phosphate hydrolase [Streptococcus mutans] Identities = 303/479 (63%), Positives = 359/479 (74%), Gaps = 25/479 (5%) Query: 1 MNLPTEIRYRPYDEWTEEDKENIVKNVSKSPWRATYHLEAKTGLLNDPNGFSYFNGKFHL 60 MNLP IRYR Y +WTEE+ ++I NV+ SPW TYH+E KTGLLNDPNGFSYFNGKF+L Sbjct: 1 MNLPQNIRYRRYQDWTEEEIKSIKTNVALSPWHTTYHIEPKTGLLNDPNGFSYFNGKFNL 60 Query: 61 FYQNWPFGAAHGLKQWVHTESDDLVHFKETGIKLKPDHVNDSHGAYSGSALAIDDKLFLF 120- FYQNWPFGAAHGLK W+HTES+DLVHFKETG L PD +DSHGAYSGSA I D+LFLF Sbjct: 61 FYQNWPFGAAHGLKSWIHTESEDLVHFKETGTVLYPDTSHDSHGAYSGSAYEIGDQLFLF 120- Query: 121 YTGNVRDMKWNRDPRQIGAWMTNDGKITKFDKVLISQPNDVTEHFRDPQIFNYDNQFYAV 18- 0 YTGNVRD W R P QIGA+M G I KF VLI QPNDVTEHFRDPQIFNY QFYA+ Sbjct: 121 YTGNVRDENWVRHPLQIGAFMDKKGNIQKFTDVLIKQPNDVTEHFRDPQIFNYKGQFYAI 18- 0 Query: 181 IGAQNSKKCGFIKLYKALNNDIHHWEFVGDLDFGGTGSEYMIECPNIIFVKGKPVLLYSP 24- 0 +GAQ+ LDFGG+ SEYMIECPN++F+ +PVL+YSP Sbjct: 181 VGAQS-------------------------LDFGGSKSEYMIECPNLVFINEQPVLIYSP 21- 5 Query: 241 QGLDKNELDYQNIYPNTYKIGQYFDANSSKIVEPSPIYNLDYGFEAYATQGFNTSDGRAF 30- 0 QGL K+ELDY NIYPNTYK+ Q FD +V+ S I NLD+GFE YATQ+FN DGR Sbjct: 216 QGLSKSELDYHNIYPNTYKVCQSFDTEKPALVDASEIQNLDFGFECYATQAFNAPDGRVY 27- 5 Query: 301 IVSWIGLPDIDYPSDQFDYQGAMSLVKELSIKNGNLYQYPVPAMKNLRQHQAEFKTQLQT 36- 0 VSWIGLPDIDYPSD +DYQGA+SLVKELS+K+G LYQYPV A+++LR + + +T Sbjct: 276 AVSWIGLPDIDYPSDSYDYQGALSLVKELSLKHGKLYQYPVEAVRSLRSEKEAVTYKPET 33- 5 Query: 361 NNTYELELLVPRNDLSSFVLFANPKGQGLSITIDTVKGKVIIDRSQAGQQYATEFGTSRQ 42- 0 NNTYELEL + ++ +LFA+ KG GL+IT+DT G ++IDRS+AG+QYA EFG+ R Sbjct: 336 NNTYELELTFDSSSVNELLLFADNKGNGLAITVDTKMGTILIDRSKAGEQYALEFGSQRS 39- 5 Query: 421 CDIPKDATSINIFIDKSIFEIFINKGEKVFTGRVFPDAEQSGIQLKEGHVHGKYFELKY 479- C I T +NIF+DKSIFEIFINKGEKVFTGRVFP+ +Q+GI +K G G Y+ELKY Sbjct: 396 CSIQAKETVVNIFVDKSIFEIFINKGEKVFTGRVFPNDKQTGIVIKSGKPSGNYYELKY 454- A related DNA sequence was identified in S. pyogenes <SEQ ID 3601> which encodes the amino acid sequence <SEQ ID 3602>. Analysis of this protein sequence reveals the following: TABLE-US-03494 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4629(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03495 Identities = 288/479 (60%), Positives = 367/479 (76%) Query: 1 MNLPTEIRYRPYDEWTEEDKENIVKNVSKSPWRATYHLEAKTGLLNDPNGFSYFNGKFHL 60 M+LP IRYRPY EW+ +D + I + +++SPW + +H+E KTGLLNDPNGFSYFNG++HL Sbjct: 2 MDLPQAIRYRPYKEWSSKDYQAITEKMAQSPWHSQFHVEPKTGLLNDPNGFSYFNGRYHL 61 Query: 61 FYQNWPFGAAHGLKQWVHTESDDLVHFKETGIKLKPDHVNDSHGAYSGSALAIDDKLFLF 120- FYQNWP+GAAHGLKQWVH S DLVHF ET +L PDH +DSHGAYSGSA AIDDKLFLF Sbjct: 62 FYQNWPYGAAHGLKQWVHMTSTDLVHFTETRSRLLPDHAHDSHGAYSGSAYAIDDKLFLF 121- Query: 121 YTGNVRDMKWNRDPRQIGAWMTNDGKITKFDKVLISQPNDVTEHFRDPQIFNYDNQFYAV 18- 0 YTGNVRD W R P Q+GAWM G I+K +VLI QP+DVTEHFRDPQ+F+Y QFYA+ Sbjct: 122 YTGNVRDANWVRTPLQVGAWMDKQGNISKIPQVLIEQPDDVTEHFRDPQLFSYQGQFYAI 18- 1 Query: 181 IGAQNSKKCGFIKLYKALNNDIHHWEFVGDLDFGGTGSEYMIECPNIIFVKGKPVLLYSP 24- 0 IGAQ G IKLYKA++N + +W F+ DLDF +G+EYMIECPN++FV KPVL++SP Sbjct: 182 IGAQGLDGKGKIKLYKAVDNHVDNWRFIADLDFDDSGTEYMIECPNLVFVDDKPVLIFSP 24- 1 Query: 241 QGLDKNELDYQNIYPNTYKIGQYFDANSSKIVEPSPIYNLDYGFEAYATQGFNTSDGRAF 30- 0 QGL K +LDYQNIYPNTYKI + F+ + +++ +NLD+GFEAYATQ F++ DGR Sbjct: 242 QGLAKADLDYQNIYPNTYKIFESFNPETGQLLGGGALQNLDFGFEAYATQAFSSPOGRVL 30- 1 Query: 301 IVSWIGLPDIDYPSDQFDYQGAMSLVKELSIKNGNLYQYPVPAMKNLRQHQAEFKTQLQT 36- 0 VSWIGLPDIDYP+D++DYQGA+SLVKEL IK+G LYQ PV A++NLR F ++ + Sbjct: 302 AVSWIGLPDIDYPTDRYDYQGALSLVKELRIKDGILYQTPVSALQNLRGPAELFHNKIDS 36- 1 Query: 361 NNTYELELLVPRNDLSSFVLFANPKGQGLSITIDTVKGKVIIDRSQAGQQYATEFGTSRQ 42- 0 +N YELEL +P +LFA+ KG GL + +DT KG++ IDRS+AG QYA ++GT R Sbjct: 362 SNCYELELTIPGQKKLDLLLFADQKGNGLRLKVDTTKGQLSIDRSRAGVQYAQDYGTVRS 42- 1 Query: 421 CDIPKDATSINIFIDKSIFEIFINKGEKVFTGRVFPDAEQSGIQLKEGHVHGKYFELKY 479- C IP+ ++N+++D SI EIFIN+G+KV T RVFP Q+GIQ+ EG G Y+E++Y Sbjct: 422 CQIPQGHVTLNVYVDNSILEIFINQGQKVLTSRVFPTHGQTGIQVVEGQAFGHYYEMRY 480- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1161 A DNA sequence (GBSx1237) was identified in S. agalactiae <SEQ ID 3603> which encodes the amino acid sequence <SEQ ID 3604>. Analysis of this protein sequence reveals the following: TABLE-US-03496 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2204(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1162 A DNA sequence (GBSx1238) was identified in S. agalactiae <SEQ ID 3605> which encodes the amino acid sequence <SEQ ID 3606>. Analysis of this protein sequence reveals the following: TABLE-US-03497 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.64 Transmembrane 259-275 (250-283) INTEGRAL Likelihood = -4.41 Transmembrane 113-129 (109-130) INTEGRAL Likelihood = -3.03 Transmembrane 180-196 (180-196) INTEGRAL Likelihood = -3.03 Transmembrane 439-455 (438-456) INTEGRAL Likelihood = -2.81 Transmembrane 298-314 (298-317) INTEGRAL Likelihood = -2.02 Transmembrane 396-412 (395-412) ----- Final Results ----- bacterial membrane --- Certainty = 0.4057(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03498 >GP: AAC99320 GB: AF059741 sucrose-specific PTS permease [Clostridium beijerinckii] Identities = 235/453 (51%), Positives = 312/453 (67%), Gaps = 15/453 (3%) Query: 7 IAKQVINAIGGASNVRSVAHCATRLRVMVKDETVIDKNTVENIEKVQGAFFNSGQYQIIF 66 +AK+++ IGG N++SV HCATRLR+++ D+ I++ +ENI+ V+G FF++ QYQII Sbjct: 6 VAKEILENIGGKENIKSVEHCATRLRLILNDKEKINEKAIENIDGVKGQFFSAAQYQIIL 65 Query: 67 GTGTVNKIYDEVVAQGLPTSSTSDQKAEAAKQGNAFQRAIRTFGDVFVPLLPAIVATGLF 126- GTG VN++YD +V Q T + K EA Q Q+ RTFGDVFVP++P +VATGLF Sbjct: 66 GTGFVNEVYDVIVGQNSDLV-TGNNKEEAYSQMTLIQKISRTFGDVFVPIIPVLVATGLF 124- Query: 127 MGIRGAINNDTVLALFGTTSKAFSSSNFYTYTVVLTDTAFAFFPALISWSAFRVFGGNPV 18- 6 MG+RG + N V + NF +T VLTDTAFAF PAL++WS + FGG PV Sbjct: 125 MGLRGLLTNLGVQM----------NENFVLFTQVLTDTAFAFLPALVAWSTMKKFGGTPV 17- 4 Query: 187 IGLVLGLMMVNSALPNAWAVASGDAHPIKF--FGF-IPVVGYQNSVLPAFFVGLLGAKLE 24- 3 IG+V+GLM+V+ +LPNA+AVA+G A PI G IPVVGYQ SVLPA +G++ AK + Sbjct: 175 IGIVIGLMLVSPSLPNAYAVAAGTATPINLTILGLNIPVVGYQGSVLPALVLGIIAAKTQ 23- 4 Query: 244 KWLHKKIPDVLDLLLVPFLTFTVMSILALFVIGPIFHSVENYVLAGTKFVLNLPLGLSGL 30- 3 K L K +PDVLDL++ PF+T +L L ++GPI H+ E + K + LP GL GL Sbjct: 235 KALKKVVPDVLDLIVTPFITLLFSMVLGLLIVGPIMHNAEQLIFGAIKGFMGLPFGLGGL 29- 4 Query: 304 ILGGVHQIIVVTGVHHIFNLLEAQLIAADGKDPFNAIITAAMTAQAGATLAVGVKTKNKK 36- 3 ++GGVHQ+IVVTGVHH N LE +L+++ GKD FNA+IT + AQ A LAV VKTK+KK Sbjct: 295 VVGGVHQLIVVTGVHHALNALEVELLSSTGKDAFNAMITCGIVAQGAAALAVAVKTKDKK 35- 4 Query: 364 LKALAFPAALSAGLGITEPAIFGVNLRFGKPFIMGLIAGAAGGWLASILKLAGTGFGITI 42- 3 ++L +A+ A LGITEPAIFGVNLRF KPFI G GA GG L+ IL LAGTG GIT Sbjct: 355 KRSLYISSAIPAFLGITEPAIFGVNLRFIKPFIFGCAGGAVGGMLSGILHLAGTGMGITA 41- 4 Query: 424 IPGTLLYLNGQIVKYLIMVIGTTSLAFVLTYMF 456 +PG LLY+N + Y+++ + ++AF LT F Sbjct: 415 LPGMLLYVN-NLGSYILVNVVAIAVAFCLTLFF 446 A related DNA sequence was identified in S. pyogenes <SEQ ID 3607> which encodes the amino acid sequence <SEQ ID 3608>. Analysis of this protein sequence reveals the following: TABLE-US-03499 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.99 Transmembrane 111-127 (108-129) INTEGRAL Likelihood = -4.57 Transmembrane 176-192 (176-193) INTEGRAL Likelihood = -4.35 Transmembrane 436-452 (431-453) INTEGRAL Likelihood = -3.88 Transmembrane 295-311 (293-314) INTEGRAL Likelihood = -3.50 Transmembrane 259-275 (253-277) INTEGRAL Likelihood = -2.07 Transmembrane 405-421 (405-421) INTEGRAL Likelihood = -0.43 Transmembrane 219-235 (219-235) ----- Final Results ----- bacterial membrane --- Certainty = 0.2996(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03500 >GP: AAC99320 GB: AF059741 sucrose-specific PTS permease [Clostridium beijerinckii] Identities = 234/451 (51%), Positives = 312/451 (68%), Gaps = 11/451 (2%) Query: 1 MDNRQIAAEVIEALGGRENVRSVAHCATRLRVMVYDEGKIDKEKAEAIDKVKGAFFNSGQ 60 M + +A E++E +GG+EN++SV HCATRLR+++ D+ KI+++ E ID VKG FF++ Q Sbjct: 1 MKEQIVAKEILENIGGKENIKSVEHCATRLRLILNDKEKINEKAIENIDGVKGQFFSAAQ 60 Query: 61 YQMIFGTGTVNNIYDEVVALGLPTSSTSEQKAEAGKHGNIFQRAIRTFGDVFVPIIPAIV 120- YQ+I GTG VN +YD +V T K EA + Q+ RTFGDVFVPIIP +V Sbjct: 61 YQIILGTGFVNEVYDVIVGQNSDLV-TGNNKEEAYSQMTLIQKISRTFGDVFVPIIPVLV 119- Query: 121 ATGLFMGVRGLVTQPAIMDLFGVHEYGENFLMYTRILTDTAFVYLPALVAWSAFRVFGGN 18- 0 ATGLFMG+RGL+T + + ENF+++T++LTDTAF +LPALVAWS + FGG Sbjct: 120 ATGLFMGLRGLLTNLGV-------QMNENFVLFTQVLTDTAFAFLPALVAWSTMKKFGGT 17- 2 Query: 181 PIIGIVLGLMLVSNELPNAWVVASGGDVK-PLTFFGF-VPVVGYQGTVLPAFFVGLVGAK 23- 8 P+IGIV+GLMLVS LPNA+ VA+G LT G +PVVGYQG+VLPA +G++ AK Sbjct: 173 PVIGIVIGLMLVSPSLPNAYAVAAGTATPINLTILGLNIPVVGYQGSVLPALVLGIIAAK 23- 2 Query: 239 LEKWLHKKVPEALDLLVTPFLTFAIMSTLGLFVIGPVFHSLENLVLAGTQAVLHLPFGIA 29- 8 +K L K VP+ LDL+VTPF+T LGL ++GP+ H+ E L+ + + LPFG+ Sbjct: 233 TQKALKKVVPDVLDLIVTPFITLLFSMVLGLLIVGPIMHNAEQLIFGAIKGFMGLPFGLG 29- 2 Query: 299 GLIVGGIQQLIVVTGIHHIFNFLEAQLIANTGKDPFNAYLTAATAAQAGATLAVAVKTKS 35- 8 GL+VGG+ QLIVVTG+HH N LE +L+++TGKD FNA +T AQ A LAVAVKTK Sbjct: 293 GLVVGGVHQLIVVTGVHHALNALEVELLSSTGKDAFNAMITCGIVAQGAAALAVAVKTKD 35- 2 Query: 359 TKLKGLAFPSTLSALLGITEPAIFGVNLRYPKVFVSGLIGGALGGWVAGLFGIAGTGFGI 41- 8 K + L S + A LGITEPAIFGVNLR+ K F+ G GGA+GG ++G+ +AGTG GI Sbjct: 353 KKKRSLYISSAIPAFLGITEPAIFGVNLRFIKPFIFGCAGGAVGGMLSGILHLAGTGMGI 41- 2 Query: 419 TVLPGTLLYLNGQLLQYLVTMLVGLGVAFAI 449 T LPG LLY+N L Y++ +V + VAF + Sbjct: 413 TALPGMLLYVN-NLGSYILVNVVAIAVAFCL 442 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03501 Identities = 409/618 (66%), Positives = 491/618 (79%), Gaps = 12/618 (1%) Query: 4 NTEIAKQVINAIGGASNVRSVAHCATRLRVMVKDETVIDKNTVENIEKVQGAFFNSGQYQ 63 N +IA +VI A+GG NVRSVAHCATRLRVMV DE IDK E I+KV+GAFFNSGQYQ Sbjct: 3 NRQIAAEVIEALGGRENVRSVAHCATRLRVMVYDEGKIDKEKAEAIDKVKGAFFNSGQYQ 62 Query: 64 IIFGTGTVNKIYDEVVAQGLPTSSTSDQKAEAAKQGNAFQRAIRTFGDVFVPLLPAIVAT 123- +IFGTGTVN IYDEVVA GLPTSSTS+QKAEA K GN FQRAIRTFGDVFVP++PAIVAT Sbjct: 63 MIFGTGTVNNIYDEVVALGLPTSSTSEQKAEAGKHGNIFQRAIRTFGDVFVPIIPAIVAT 122- Query: 124 GLFMGIRGAINNDTVLALFGTTSKAFSSSNFYTYTVVLTDTAFAFFPALISWSAFRVFGG 18- 3 GLFMG+RG + ++ LFG NF YT +LTDTAF + PAL++WSAFRVFGG Sbjct: 123 GLFMGVRGLVTQPAIMDLFGVHEYG---ENFLMYTRILTDTAFVYLPALVAWSAFRVFGG 17- 9 Query: 184 NPVIGLVLGLMMVNSALPNAWAVASG-DAHPIKFFGFIPVVGYQNSVLPAFFVGLLGAKL 24- 2 NP+IG+VLGLM+V++ LPNAW VASG D P+ FFGF+PVVGYQ +VLPAFFVGL+GAKL Sbjct: 180 NPIIGIVLGLMLVSNELPNAWVVASGGDVKPLTFFGFVPVVGYQGTVLPAFFVGLVGAKL 23- 9 Query: 243 EKWLHKKIPDVLDLLLVPFLTFTVMSILALFVIGPIFHSVENYVLAGTKFVLNLPLGLSG 30- 2 EKWLHKK+P+ LDLL+ PFLTF +MS L LFVIGP+FHS+EN VLAGT+ VL+LP G++G Sbjct: 240 EKWLHKKVPEALDLLVTPFLTFAIMSTLGLFVIGPVFHSLENLVLAGTQAVLHLPFGIAG 29- 9 Query: 303 LILGGVHQIIVVTGVHHIFNLLEAQLIAADGKDPFNAIITAAMTAQAGATLAVGVKTKNK 36- 2 LI+GG+ Q+IVVTG+HHIFN LEAQLIA GKDPFNA +TAA AQAGATLAV VKTK+ Sbjct: 300 LIVGGIQQLIVVTGIHHIFNFLEAQLIANTGKDPFNAYLTAATAAQAGATLAVAVKTKST 35- 9 Query: 363 KLKALAFPAALSAGLGITEPAIFGVNLRFGKPFIMGLIAGAAGGWLASILKLAGTGFGIT 42- 2 KLK LAFP+ LSA LGITEPAIFGVNLR+ K F+ GLI GA GGW+A + +AGTGFGIT Sbjct: 360 KLKGLAFPSTLSALLGITEPAIFGVNLRYPKVFVSGLIGGALGGWVAGLFGIAGTGFGIT 41- 9 Query: 423 IIPGTLLYLNGQIVKYLIMVIGTTSLAFVLTYMFGYEDKDEKAVAEVSPLVEETDDDPTI 48- 2 ++PGTLLYLNGQ+++YL+ ++ +AF + Y +GY+D++ + V V++T D P + Sbjct: 420 VLPGTLLYLNGQLLQYLVTMLVGLGVAFAIAYTWGYQDRETLPLPAVE--VDQTADQPAL 47- 7 Query: 483 TQTSQLRAETIVSPLDGQVIALDTVSDPVFSSGIMGDGLAIKPRGNTIYSPVDGFVQIAF 54- 2 + ET+ SPL+G V+ L VSDPVFSSG MG GLAIKP NT+YSPVDG V+I F Sbjct: 478 AE------ETLYSPLNGTVVDLSAVSDPVFSSGAMGQGLAIKPEDNTLYSPVDGKVEIVF 53- 1 Query: 543 ETGHAYGIKSDKGAEILIHIGIDTVTMNGTGFTSKVKADQKVKKGDILGTFDSAKIAEAG 60- 2 ETGHAY I S +GAE+L+HIGIDT +M G GF S V Q VKKGD+LG FD +KIAEAG Sbjct: 532 ETGHAYAITSSQGAEVLLHIGIDTESMAGDGFESLVAVGQAVKKGDLLGHFDPSKIAEAG 59- 1 Query: 603 LDNTAMIIVTNTADFADV 620 LD+T M+IV+N AD+ V Sbjct: 592 LDDTTMMIVSNIADYQSV 609 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1163 A DNA sequence (GBSx1239) was identified in S. agalactiae <SEQ ID 3609> which encodes the amino acid sequence <SEQ ID 3610>. This protein is predicted to be fructokinase. Analysis of this protein sequence reveals the following: TABLE-US-03502 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2436(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03503 >GP: BAA02467 GB: D13175 fructokinase [Streptococcus mutans] Identities = 232/291 (79%), Positives = 257/291 (87%) Query: 1 MTKLYGSIEAGGTKFVCAVGDEELKVVEKMQFPTTTPQETIKKTVDFFKRFEKKLEAVAI 60 M+KLYGSIEAGGTKFVCAVGDE +++EK+QFPTTTP ETI+KTV FFK+FE L +VAI Sbjct: 1 MSKLYGSIEAGGTKFVCAVGDENFQILEKVQFPTTTPYETIEKTVAFFKKFEADLASVAI 60 Query: 61 GSFGPIDIDKKSKTYGYITTTPKLHWANVDLLGLISKDFNVPFYFTTDVNSSAYGEVIAR 120- GSFGPIDID+ S TYGYIT+TPK +WANVD +GLISKDF +PFYFTTDVNSSAYGE IAR Sbjct: 61 GSFGPIDIDQNSDTYGYITSTPKPNWANVDFVGLISKDFKIPFYFTTDVNSSAYGETIAR 120- Query: 121 NNIDSLVYYTIGTGIGAGAIQKGEFIGGTGHTEAGHTYMAMHPQDQANDFKGICPFHNSC 18- 0 +N+ SLVYYTIGTGIGAGAIQ GEFIGG GHTEAGH YMA HP D + F G CPFH C Sbjct: 121 SNVKSLVYYTIGTGIGAGAIQNGEFIGGMGHTEAGHVYMAPHPNDVHHGFVGTCPFHKGC 18- 0 Query: 181 LEGLASGPTLEARTGIRGELIEENSMVWDVQAYYIAQAAIQATVLYRPQVIVFGGGVMAQ 24- 0 LEGLA+GP+LEARTGIRGELIE+NS VWD+QAYYIAQAAIQATVLYRPQVIVFGGGVMAQ Sbjct: 181 LEGLAAGPSLEARTGIRGELIEQNSEVWDIQAYYIAQAAIQATVLYRPQVIVFGGGVMAQ 24- 0 Query: 241 EHMLRRVRQTFATLLNGYLPVPDLSDYIVTPAIEENGSATLGNFALAKKIS 291 EHML RVR+ F +LLN YLPVPD+ DYIVTPA+ ENGSATLGN ALAKKI+ Sbjct: 241 EHMLNRVREKFTSLLNDYLPVPDVKDYIVTPAVAENGSATLGNLALAKKIA 291 A related DNA sequence was identified in S. pyogenes <SEQ ID 3611> which encodes the amino acid sequence <SEQ ID 3612>. Analysis of this protein sequence reveals the following: TABLE-US-03504 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2012(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03505 Identities = 212/293 (72%), Positives = 246/293 (83%) Query: 1 MTKLYGSIEAGGTKFVCAVGDEELKVVEKMQFPTTTPQETIKKTVDFFKRFEKKLEAVAI 60 M KLYGSIEAGGTKFVCAVGDEE VV+K QFPTTTP+ETI +T+ +FK FE L +AI Sbjct: 1 MGKLYGSIEAGGTKFVCAVGDEEFTVVDKTQFPTTTPEETIARTIAYFKAFEADLAGMAI 60 Query: 61 GSFGPIDIDKKSKTYGYITTTPKLHWANVDLLGLISKDFNVPFYFTTDVNSSAYGEVIAR 120- GSFGPIDID S+TYGYITTTPK WANVDLLG +S F +PF TTDVNSSAYGEV+AR Sbjct: 61 GSFGPIDIDPSSETYGYITTTPKSGWANVDLLGQLSAAFKIPFDVTTDVNSSAYGEVLAR 120- Query: 121 NNIDSLVYYTIGTGIGAGAIQKGEFIGGTGHTEAGHTYMAMHPQDQANDFKGICPFHNSC 18- 0 ++SLVYYTIGTGIGAGAIQ G FIGG GHTEAGHTY+ HP D A F G+CPFH C Sbjct: 121 PGVESLVYYTIGTGIGAGAIQHGHFIGGLGHTEAGHTYVMPHPDDMAKGFLGVCPFHKGC 18- 0 Query: 181 LEGLASGPTLEARTGIRGELIEENSMVWDVQAYYIAQAAIQATVLYRPQVIVFGGGVMAQ 24- 0 LEG+A+GP++EARTG+RGE +++ + VWD+QA+YIAQAA+QAT+LYRPQVIVFGGGVMAQ Sbjct: 181 LEGMAAGPSIEARTGVRGERLDQEADVWDIQAFYIAQAALQATMLYRPQVIVFGGGVMAQ 24- 0 Query: 241 EHMLRRVRQTFATLLNGYLPVPDLSDYIVTPAIEENGSATLGNFALAKKISKG 293 EHM+ RV F LL+GYLPVPDL+DYIVTPA+ +NGSATLGNFALAK ++G Sbjct: 241 EHMVLRVHDKFTALLSGYLPVPDLTDYIVTPAVADNGSATLGNFALAKLAAQG 293 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1164 A DNA sequence (GBSx1240) was identified in S. agalactiae <SEQ ID 3613> which encodes the amino acid sequence <SEQ ID 3614>. This protein is predicted to be Mannosephosphate Isomerase (pmi). Analysis of this protein sequence reveals the following: TABLE-US-03506 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4717(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03507 >GP: BAA04021 GB: D16594 Mannosephosphate Isomerase [Streptococcus mutans] Identities = 232/312 (74%), Positives = 262/312 (83%) Query: 1 MSEPLFLEASMHDKIWGGTKLRDEFGYDIPSETTGEYWAISAHPNGVSRVKNGRFKGCFL 60 M PLFL++ MH KIWGG +LR EFGYDIPSETTGEYWAISAHPNGVS VKNG +KG L Sbjct: 1 MEGPLFLQSQMHKKIWGGNRLRKEFGYDIPSETTGEYWAISAHPNGVSVVKNGVYKGVPL 60 Query: 61 DKLYQGEKSLFGNPDDTVFPLLTKILDANDWLSVQVHPDDAYALKHEGELGKTECWYIIS 120- D+LY + LFGN +VFPLLTKILDANDWLSVQVHPD+AYAL+HEGELGKTECWY+IS Sbjct: 61 DELYAEHRELFGNSKSSVFPLLTKILDANDWLSVQVHPDNAYALEHEGELGKTECWYVIS 120- Query: 121 ADEGSEIIYGHNAKTKEELRQMIESGDWEHLLTRIPVKSGDFYYVPSGTMHAIGKGILIL 18- 0 ADEG+EIIYGH AK+KEELRQMI +GDW+HLLT+IPVK+GDF+YVPSGTMHAIG+GI+IL Sbjct: 121 ADEGAEIIYGHEAKSKEELRQMIAAGDWDHLLTKIPVKAGDFFYVPSGTMHAIGRGIMIL 18- 0 Query: 181 ETQQSSDTTYRVYDFDRPDASGKLRDLHIEQSIDVLTIGKPANTVPANMKLKHLSSTLLV 24- 0 ETQQSSDTTYRVYDFDR D G+ R LHIEQSIDVLTIGKPAN PA + L+ L +T+LV Sbjct: 181 ETQQSSDTTYRVYDFDRKDDQGRKRALHIEQSIDVLTIGKPANATPAWLSLQGLETTVLV 24- 0 Query: 241 SNDFFTVYKWEISGVTNFKQFAPYLLVSVLDGAGHITVDNKVYTLKKGDHFILPNDVVKW 30- 0 S+ FFTVYKW+ISG +Q APYLLVSVL G G ITV + Y L+KGDH ILPN + W Sbjct: 241 SSPFFTVYKWQISGSVKMQQTAPYLLVSVLAGQGRITVGLEQYALRKGDHLILPNTIKSW 30- 0 Query: 301 DIDGQLEIIASH 312 DG LEIIASH Sbjct: 301 QFDGDLEIIASH 312 A related DNA sequence was identified in S. pyogenes <SEQ ID 3615> which encodes the amino acid sequence <SEQ ID 3616>. Analysis of this protein sequence reveals the following: TABLE-US-03508 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3714(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03509 Identities = 232/312 (74%), Positives = 264/312 (84%) Query: 1 MSEPLFLEASMHDKIWGGTKLRDEFGYDIPSETTGEYWAISAHPNGVSRVKNGRFKGCFL 60 MSEPLFL+++MHD+IWGGTKLRD F Y+IPS+TTGEYWAISAHPNGVS V NGR++G L Sbjct: 1 MSEPLFLKSTMHDRIWGGTKLRDVFAYNIPSDTTGEYWAISAHPNGVSTVTNGRYQGQPL 60 Query: 61 DKLYQGEKSLFGNPDDTVFPLLTKILDANDWLSVQVHPDDAYALKHEGELGKTECWYIIS 120- + LY E +LFGNP + VFPLLTKILDANDWLSVQVHPDDAY +HEGELGKTECWYIIS Sbjct: 61 NTLYAQEPALFGNPKEEVFPLLTKILDANDWLSVQVHPDDAYGREHEGELGKTECWYIIS 120- Query: 121 ADEGSEIIYGHNAKTKEELRQMIESGDWEHLLTRIPVKSGDFYYVPSGTMHAIGKGILIL 18- 0 A+EGSEI+YGH AK+KE+LR MIE+G W+ LLTR+PVK+GDF+YVPSGTMHAIGKGILIL Sbjct: 121 AEEGSEIVYGHQAKSKEDLRAMIEAGAWDDLLTRVPVKAGDFFYVPSGTMHAIGKGILIL 18- 0 Query: 181 ETQQSSDTTYRVYDFDRPDASGKLRDLHIEQSIDVLTIGKPANTVPANMKLKHLSSTLLV 24- 0 ETQQSSDTTYRVYDFDR D +G LRDLHIE+SIDVLTIGKP N+VPA M L ++ +T LV Sbjct: 181 ETQQSSDTTYRVYDFDRKDVNGNLRDLHIEKSIDVLTIGKPENSVPATMVLDNMVATTLV 24- 0 Query: 241 SNDFFTVYKWEISGVTNFKQFAPYLLVSVLDGAGHITVDNKVYTLKKGDHFILPNDVVKW 30- 0 S FFTVYKW S + + KQ APYLLVSVL G G + VD K Y L+KG HFILPNDV W Sbjct: 241 STPFFTVYKWVTSQMVDMKQAAPYLLVSVLKGQGKLYVDQKAYELEKGMHFILPNDVKSW 30- 0 Query: 301 DIDGQLEIIASH 312 DGQLE+I SH Sbjct: 301 SFDGQLEMIVSH 312 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1165 A DNA sequence (GBSx1241) was identified in S. agalactiae <SEQ ID 3617> which encodes the amino acid sequence <SEQ ID 3618>. This protein is predicted to be preprotein translocase seca subunit (secA). Analysis of this protein sequence reveals the following: TABLE-US-03510 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1102(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10107> which encodes amino acid sequence <SEQ ID 10108> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03511 >GP: AAA50286 GB: L32090 secA [Listerie monocytogenes] Identities = 503/843 (59%), Positives = 643/843 (75%), Gaps = 16/843 (1%) Query: 11 MANILRTVIENDKGELKKLDKIAKKVDSYADHMAALSDEALQAKTPEFKERYQNGETLDQ 70 - MA +L+ + E+ K ++K L++ A ++ + AD AALSD+AL+ KT EFKER Q GETLD Sbjct: 1 MAGLLKKIFESGKKDVKYLERKADEIIALADETAALSDDALREKTVEFKERVQKGETLDD 60 Query: 71 LLPEAFAVVREASKRVLGLYPYHVQIMGGIVLHHGDIPEMRTGEGKTLTATMPVYLNAIS 130- LL EAFAV RE +KR LGLYP+ VQ+MGGIVLH +I EM TGEGKTLTAT+PVYLNA+S Sbjct: 61 LLVEAFAVAREGAKRALGLYPFKVQLMGGIVLHEDNIAEMKTGEGKTLTATLPVYLNALS 120- Query: 131 GLGVHVITVNEYLSTRDATEMGEVYSWLGLSVGINLAAKSPFEKREAYNCDITYSTNAEV 19- 0 G GVHV+TVNEYL+ RDA EMG +Y++LGLSVG+NL A S EKREAY CDITYSTN E+ Sbjct: 121 GEGVHVVTVNEYLAHRDAEEMGVLYNFLGLSVGLNLNALSSTEKREAYACDITYSTNNEL 18- 0 Query: 191 GFDYLRDNMVVRQEDMVQRPLNYALVDEVDSVLIDEARTPLIVSGPVSSEMNQLYTRADM 25- 0 GFDYLRDNMVV +E+MVQRPL +A++DEVDS+L+DEARTPLI+SG + + LY RA+ Sbjct: 181 GFDYLRDNMVVYKEEMVQRPLAFAVIDEVDSILVDEARTPLIISGE-AEKSTILYVRANT 23- 9 Query: 251 FVKTL-NSDDYIIDVPTKTIGLSDTGIDKAENYFHLNNLYDLENVALTHYIDNALRANYI 30- 9 FV+TL +DY +D+ TK++ L++ G+ K ENYF + NL+DLEN + H+I AL+ANY Sbjct: 240 FVRTLTEEEDYTVDIKTKSVQLTEDGMTKGENYFDVENLFDLENTVILHHIAQALKANYT 29- 9 Query: 310 MLLNIDYVVSEEQEILIVDQFTGRTMEGRRFSDGLHQAIEAKESVPIQEESKTSASITYQ 36- 9 M L++DYVV ++ E+LIVDQFTGR M+GRRFS+GLHQA+EAKE V IQ ESKT A+IT+Q Sbjct: 300 MSLDVDYVV-QDDEVLIVDQFTGRIMKGRRFSEGLHQALEAKEGVTIQNESKTMATITFQ 35- 8 Query: 370 NMFRMYHKLAGMTGTGKTEEEEFREIYNMRVIPIPTNRPVQRIDHSDLLYPTLDSKFRAV 42- 9 N FRMY KLAGMTGT KTEEEEFR+IYNMRVI IPTN+ + R D DL+Y T+++KF AV Sbjct: 359 NYFRMYKKLAGMTGTAKTEEEEFRDIYNMRVIEIPTNKVIIRDDRPDLIYTTMEAKFNAV 41- 8 Query: 430 VADVKERYEQGQPVLVGTVAVETSDLISRKLVAAGVPHEVLNAKNHFKEAQIIMNAGQRG 48- 9 V D+ ER+ +GQPVLVGTVA+ +LIS KL G+ H+VLNAK H +EA II +AG+RG Sbjct: 419 VEDIAERHAKGQPVLVGTVAMNI-ELISSKLKRKGIKHDVLNAKQHEREADIIKHAGERG 47- 7 Query: 490 AVTIATNMAGRGTDIKLGEGVRELGGLCVIGTERHESRRIDNQLRGRSGRQGDPGESQFY 54- 9 AV IATNMAGRGTDIKLGEG E GGL VIGTERHESRRIDNQLRGRSGRQGDPG +QFY Sbjct: 478 AVVIATNMAGRGTDIKLGEGTIEAGGLAVIGTERHESRRIDNQLRGRSGRQGDPGVTQFY 53- 7 Query: 550 LSLEDDLMRRFGTDRIKVVLERMNLAEDDTVIKSKMLTRQVESAQRRVEGNNYDTRKQVL 60- 9 LS+ED+LMRRFG+D +K ++ER +AED I+SKM++R VESAQRRVEGNN+D+RKQVL Sbjct: 538 LSMEDELMRRFGSDNMKSMMERFGMAED--AIQSKMVSRAVESAQRRVEGNNFDSRKQVL 59- 5 Query: 610 QYDDVMREQREIIYANRREVITAERDLGPELKGMIKRTIKRAVDAHSRSDKNTAA---EA 66- 6 QYDDV+R+QRE+IY R EVI AE L ++ MI+RT+ V +++ S + A + Sbjct: 596 QYDDVLRQQREVIYKQRYEVINAENSLREIIEQMIQRTVNFIVSSNASSHEPEEAWNLQG 65- 5 Query: 667 IVNFARSALLDEEAITVSELRGLKEAEIKELLYERALAVYEQQIAKLKDPEAIIEFQKVL 72- 6 I+++ + LL E IT+ +L+ +I+ L+ ++ A Y+++ L PE EF+KV+ Sbjct: 656 IIDYVDANLLPEGTITLEDLQNRTSEDIQNLILDKIKAAYDEK-ETLLPPEEFNEFEKVV 71- 4 Query: 727 ILMVVDNQWTEHIDALDQLRNSVGLRGYAQNNPIVEYQSEGFRMFQDMIGSIEFDVTRTL 78- 6 +L VVD +W +HIDA+D LR+ + LR Y Q +P+ EYQSEGF MF+ M+ SI+ DV R + Sbjct: 715 LLRVVDTKWVDHIDAMDHLRDGIHLRAYGQIDPLREYQSEGFEMFEAMVSSIDEDVARYI 77- 4 Query: 787 MKAQIHEQ-ERER-ASQHATTTAEQNISAQHVPMNNESPEYQGIKRNDKCPCGSGMKFKN 84- 4 MKA+I + ERE+ A A AE A+ P+ + Q I RND CPCGSG K+KN Sbjct: 775 MKAEIRQNLEREQVAKGEAINPAEGKPEAKRQPIRKD----QHIGRNDPCPCGSGKKYKN 83- 0 Query: 845 CHG 847 CHG Sbjct: 831 CHG 833 A related DNA sequence was identified in S. pyogenes <SEQ ID 3619> which encodes the amino acid sequence <SEQ ID 3620>. Analysis of this protein sequence reveals the following: TABLE-US-03512 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4443(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03513 Identities = 710/837 (84%), Positives = 777/837 (92%), Gaps = 3/837 (0%) Query: 11 MANILRTVIENDKGELKKLDKIAKKVDSYADHMAALSDEALQAKTPEFKERYQNGETLDQ 70 - MANILR VIENDKGEL+KL+KIAKKV+SYAD MA+LSD LQ KT EFKERYQ GETL+Q Sbjct: 1 MANILRKVIENDKGELRKLEKIAKKVESYADQMASLSDRDLQGKTLEFKERYQKGETLEQ 60 Query: 71 LLPEAFAVVREASKRVLGLYPYHVQIMGGIVLHHGDIPEMRTGEGKTLTATMPVYLNAIS 130- LLPEAFAVVREA+KRVLGL+PY VQIMGGIVLH+GD+PEMRTGEGKTLTATMPVYLNAI+ Sbjct: 61 LLPEAFAVVREAAKRVLGLFPYRVQIMGGIVLHNGDVPEMRTGEGKTLTATMPVYLNAIA 120- Query: 131 GLGVHVITVNEYLSTRDATEMGEVYSWLGLSVGINLAAKSPFEKREAYNCDITYSTNAEV 19- 0 G GVHVITVNEYLSTRDATEMGEVYSWLGLSVGINLAAKSP EKREAYNCDITYSTN+EV Sbjct: 121 GEGVHVITVNEYLSTRDATEMGEVYSWLGLSVGINLAAKSPAEKREAYNCDITYSTNSEV 18- 0 Query: 191 GFDYLRDNMVVRQEDMVQRPLNYALVDEVDSVLIDEARTPLIVSGPVSSEMNQLYTRADM 25- 0 GFDYLRDNMVVRQEDMVQRPLN+ALVDEVDSVLIDEARTPLIVSG VSSE NQLY RADM Sbjct: 181 GFDYLRDNMVVRQEDMVQRPLNFALVDEVDSVLIDEARTPLIVSGAVSSETNQLYIRADM 24- 0 Query: 251 FVKTLNSDDYIIDVPTKTIGLSDTGIDKAENYFHLNNLYDLENVALTHYIDNALRANYIM 31- 0 FVKTL S DY+IDVPTKTIGLSD+GIDKAE+YF+L+NLYD+ENVALTH+IDNALRANYIM Sbjct: 241 FVKTLTSVDYVIDVPTKTIGLSDSGIDKAESYFNLSNLYDIENVALTHFIDNALRANYIM 30- 0 Query: 311 LLNIDYVVSEEQEILIVDQFTGRTMEGRRFSDGLHQAIEAKESVPIQEESKTSASITYQN 37- 0 LL+IDYVVSE+ EILIVDQFTGRTMEGRRFSDGLHQAIEAKE V IQEESKTSASITYQN Sbjct: 301 LLDIDYVVSEDGEILIVDQFTGRTMEGRRFSDGLHQAIEAKEGVRIQEESKTSASITYQN 36- 0 Query: 371 MFRMYHKLAGMTGTGKTEEEEFREIYNMRVIPIPTNRPVQRIDHSDLLYPTLDSKFRAVV 43- 0 MFRMY KLAGMTGT KTEEEEFRE+YNMR+IPIPTNRP+ RIDH+DLLYPTL+SKFRAVV Sbjct: 361 MFRMYKKLAGMTGTAKTEEEEFREVYNMRIIPIPTNRPIARIDHTDLLYPTLESKFRAVV 42- 0 Query: 431 ADVKERYEQGQPVLVGTVAVETSDLISRKLVAAGVPHEVLNAKNHFKEAQIIMNAGQRGA 49- 0 DVK R+ +GQP+LVGTVAVETSDLISRKLV AG+PHEVLNAKNHFKEAQIIMNAGQRGA Sbjct: 421 EDVKTRHAKGQPILVGTVAVETSDLISRKLVEAGIPHEVLNAKNHFKEAQIIMNAGQRGA 48- 0 Query: 491 VTIATNMAGRGTDIKLGEGVRELGGLCVIGTERHESRRIDNQLRGRSGRQGDPGESQFYL 55- 0 VTIATNMAGRGTDIKLGEGVRELGGLCVIGTERHESRRIDNQLRGRSGRQGDPGESQFYL Sbjct: 481 VTIATNMAGRGTDIKLGEGVRELGGLCVIGTERHESRRIDNQLRGRSGRQGDPGESQFYL 54- 0 Query: 551 SLEDDLMRRFGTDRIKVVLERMNLAEDDTVIKSKMLTRQVESAQRRVEGNNYDTRKQVLQ 61- 0 SLEDDLMRRFG+DRIK L+RM L E+DTVIKS ML RQVESAQ+RVEGNNYDTRKQVLQ Sbjct: 541 SLEDDLMRRFGSDRIKAFLDRMKLDEEDTVIKSGMLGRQVESAQKRVEGNNYDTRKQVLQ 60- 0 Query: 611 YDDVMREQREIIYANRREVITAERDLGPELKGMIKRTIKRAVDAHSRSDKNTAAEAIVNF 67- 0 YDDVMREQREIIYANRR+VITA RDLGPE+K MIKRTI RAVDAH+RS++ A +AIV F Sbjct: 601 YDDVMREQREIIYANRRDVITANRDLGPEIKAMIKRTIDRAVDAHARSNRKDAIDAIVTF 66- 0 Query: 671 ARSALLDEEAITVSELRGLKEAEIKELLYERALAVYEQQIAKLKDPEAIIEFQKVLILMV 73- 0 AR++L+ EE I+ ELRGLK+ +IKE LY+RALA+Y+QQ++KL+D EAIIEFQKVLILM+ Sbjct: 661 ARTSLVPEEFISAKELRGLKDDQIKEKLYQRALAIYDQQLSKLRDQEAIIEFQKVLILMI 72- 0 Query: 731 VDNQWTEHIDALDQLRNSVGLRGYAQNNPIVEYQSEGFRMFQDMIGSIEFDVTRTLMKAQ 79- 0 VDN+WTEHIDALDQLRN+VGLRGYAQNNP+VEYQ+EGF+MFQDMIG+IEFDVTRT+MKAQ Sbjct: 721 VDNKWTEHIDALDQLRNAVGLRGYAQNNPVVEYQAEGFKMFQDMIGAIEFDVTRTMMKAQ 78- 0 Query: 791 IHEQERERASQHATTTAEQNISAQHVPMNNESPEYQGIKRNDKCPCGSGMKFKNCHG 847 IHEQERERASQ ATT A QNI +Q ++ P+ ++RN+ CPCGSG KFKNCHG Sbjct: 781 IHEQERERASQRATTAAPQNIQSQQSANTDDLPK---VERNEACPCGSGKKFKNCHG 834 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1166 A DNA sequence (GBSx1242) was identified in S. agalactiae <SEQ ID 3621> which encodes the amino acid sequence <SEQ ID 3622>. This protein is predicted to be phospho-2-dehydro-3-deoxyheptonate aldolase (aroH). Analysis of this protein sequence reveals the following: TABLE-US-03514 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3429(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03515 >GP: AAF40753 GB: AE002387 phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive [Neisseria meningitidis MC58] Identities = 122/348 (35%), Positives = 187/348 (53%), Gaps = 32/348 (9%) Query: 1 MGFHQLSDKINIEILKQKTSLDLEVSQKKLAKE---------EELKNIIKGEDQRFLVIV 51 M H +D I I+ +K+ + + ++KE +E+ +++ G D+R LVI+ Sbjct: 1 MTHHYPTDDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVII 60 Query: 52 GPCSADNPKAVLTYAKRLAKLEAAFKDKMFLVMRVYTAKPRTNGDGYKGLVHHSDKLGVF 111- GPCS +PKA L YA+RL KL +++++ +VMRVY KPRT G+KGL++ G F Sbjct: 61 GPCSIHDPKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTT-VGWKGLINDPHLDGTF 119- Query: 112 ------FQARKMHYDIIRETGLLTADELLYPEMLSVMDDLVSYYAIGARSVEDQGHRFIS 16- 5 QAR + + G+ + E L DL+S+ AIGAR+ E Q HR ++ Sbjct: 120 DINFGLRQARSLLLS-LNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELA 17- 8 Query: 166 SGIDAPVGMKNPTSGNLRVMFNAVYAAQNQQELFYQNKQ-----VRTDGNLLSHVILRGY 22- 0 SG+ PVG KN T GNL++ +A+ AA + K V T GN HVILRG Sbjct: 179 SGLSCPVGFKNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGG 23- 8 Query: 221 HNADYRSIPNYHYENLLETITHYEETDLQNPFIVVDTNHDNSGKQFLEQIRIVKSVLADR 28- 0 PNY E++ E + + +++D +H NS K + Q+ + + + A Sbjct: 239 KE------PNYDAEHVSEAAEQLRAAGVTDK-LMIDCSHANSRKDYTRQMEVAQDIAAQL 29- 1 Query: 281 QWHTKIRNYVRGFLIESYLEDGRQDKPDVFGKSITDPCLGWDKTEMLI 328 + + + G ++ES+L +GRQDKP+V+GKSITD C+GW TE L+ Sbjct: 292 E---QDGGNIMGVMVESHLVEGRQDKPEVYGKSITDACIGWGATEELL 336 A related DNA sequence was identified in S. pyogenes <SEQ ID 3623> which encodes the amino acid sequence <SEQ ID 3624>. Analysis of this protein sequence reveals the following: TABLE-US-03516 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1171(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03517 Identities = 52/233 (22%), Positives = 93/233 (39%), Gaps = 40/233 (17%) Query: 50 IVGPCSADNPKAVLTYAKRLAKLEAAFKDKMFLVMRVYTAKPRTNGDGYKGLVHHSDKLG 109- IVGPCS ++ + A KL + R KPRT+ ++GL Sbjct: 19 IVGPCSIESYDHIRLAASSAKKLGYNY-------FRGGAYKPRTSAASFQGLG------- 64 Query: 110 VFFQARKMHYDIIRETGLLTADELLYPEMLSVMDDLVSYYAIGARSVEDQGHRFISSGID 16- 9 Q + +++ +E GLL+ E++ L D + +GAR++++ S ID Sbjct: 65 --LQGIRYLHEVCQEFGLLSVSEIMSERQLEEAYDYLDVIQVGARNMQNFEFLKTLSHID 122- Query: 170 APVGMKNPTSGNLRVMFNAVYAAQNQQELFYQNKQVRTDGNLLSHVIL--RGYHNADYRS 22- 7 P+ K + A+ Q+ + S++IL RG D Sbjct: 123 KPILFKRGLMATIEEYLGALSYLQDTGK---------------SNIILCERGVRGYD--- 16- 4 Query: 228 IPNYHYENLLETITHYEETDLQNPFIVVDTNHDNSGKQ-FLEQIRIVKSVLAD 279 + + +++ ++TDL I+VD +H + L +I K+V A+ Sbjct: 165 VETRNMLDIMAVPIIQQKTDLP---IIVDVSHSTGRRDLLLPAAKIAKAVGAN 214 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1167 A DNA sequence (GBSx1243) was identified in S. agalactiae <SEQ ID 3625> which encodes the amino acid sequence <SEQ ID 3626>. This protein is predicted to be AcpS (acpS). Analysis of this protein sequence reveals the following: TABLE-US-03518 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3620(Affirmative) < succ> bacterial membrane --- Certainty = 0.00000(Not Clear) < succ> bacterial outside --- Certainty = 0.00000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-03519 >GP: AAG22706 GB: AF276617 acyl carrier protein synthase; AcpS [Streptococcus pneumoniae] Identities = 61/117 (52%), Positives = 90/117 (76%), Gaps = 1/117 (0%) Query: 1 MIVGHGIDLQEIEAITKAYERNQRFAERVLTEQELLLFKGISNPKRQMSFLTGRWAAKEA 60 MIVGHGID++E+ +I A R++ FA+RVLT QE+ F + +RQ+ +L GRW+AKEA Sbjct: 1 MIVGHGIDIEELASIESAVTRHEGFAKRVLTAQEMERFTSLKG-RRQIEYLAGRWSAKEA 59 Query: 61 YSKALGTGIGKVNFHDIEILSDDKGAPLITKEPFNGKSFVSISHSGNYAQASVILEE 117 +SKA+GTGI K+ F D+E+L++++GAP ++ PF+GK ++SISH+ + ASVILEE Sbjct: 60 FSKAMGTGISKLGFQDLEVLNNERGAPYFSQAPFSGKIWLSISHTDQFVTASVILEE 116 A related DNA sequence was identified in S. pyogenes <SEQ ID 3627> which encodes the amino acid sequence <SEQ ID 3628>. Analysis of this protein sequence reveals the following: TABLE-US-03520 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2001(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03521 Identities = 76/119 (63%), Positives = 99/119 (82%), Gaps = 1/119 (0%) Query: 1 MIVGHGIDLQEIEAITKAYERNQRFAERVLTEQELLLFKGISNPKRQMSFLTGRWAAKEA 60 MIVGHGIDLQEI AI K Y+RN RFA+++LTEQEL +F+ KR++++L GRW+ KEA Sbjct: 1 MIVGHGIDLQEISAIEKVYQRNPRFAQKILTEQELAIFESFPY-KRRLNYLAGRWSGKEA 59 Query: 61 YSKALGTGIGKVNFHDIEILSDDKGAPLITKEPFNGKSFVSISHSGNYAQASVILEEEK 119 ++KA+GTGIG++ F DIEIL+D +G P++TK PF G SF+SISHSGNY QASVILE++K Sbjct: 60 FAKAIGTGIGRLTFQDIEILNDVRGCPILTKSPFKGNSFISISHSGNYVQASVILEDKK 118 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1168 A DNA sequence (GBSx1244) was identified in S. agalactiae <SEQ ID 3629> which encodes the amino acid sequence <SEQ ID 3630>. Analysis of this protein sequence reveals the following: TABLE-US-03522 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.24 Transmembrane 78-94 (77-97) ----- Final Results ----- bacterial membrane --- Certainty = 0.2296(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03523 >GP: AAD51027 GB: AF171873 alanine racemase [Streptococcus pneumoniae] Identities = 227/366 (62%), Positives = 270/366 (73%) Query: 1 MISSYHRPTRALIDLEAIANNVKSVQEHIPSDKKTFAVVKANAYGHGAVEVSKYIESIVD 60 M +S HRPT+ALI L AI N++ + HIP AVVKANAYGHGAV V+K I+ VD Sbjct: 1 MKASPHRPTKALIHLGAIRQNIQQMGAHIPQGTLKLAVVKANAYGHGAVAVAKAIQDDVD 60 Query: 61 GFCVSNLDEAIELRQAGIVKMILVLGVVMPEQVILAKNENITLTVASLEWLRLCQTSAVD 120- GFCVSN+DEAIELRQAG+ K IL+LGV E V LAK + TLTVA LEW++ VD Sbjct: 61 GFCVSNIDEAIELRQAGLSKPILILGVSEIEAVALAKEYDFTLTVAGLEWIQALLDKEVD 120- Query: 121 LSGLEVHIKVDSGMGRIGVRQLDEGNKLISELGESGASVKGIFTHFATADEADNCKFNQQ 18- 0 L+GL VH+K+DSGMGRIG R+ E + L + G V+GIFTHFATADE + FN Q Sbjct: 121 LTGLTVHLKIDSGMGRIGFREASEVEQAQDLLQQHGVCVEGIFTHFATADEESDDYFNAQ 18- 0 Query: 181 LTFFKDFISGLDNCPDLVHASNSATSLWHSETIFNAVRLGVVMYGLNPSGTDLDLPYPIN 24- 0 L FK ++ + P+LVHASNSAT+LWH ETIFNAVR+G MYGLNPSG LDLPY + Sbjct: 181 LERFKTILASMKEVPELVHASNSATTLWHVETIFNAVRMGDAMYGLNPSGAVLDLPYDLI 24- 0 Query: 241 PALSLESELVHVKQLHDGSQVGYGATYQVTGDEFVGTVPIGYADGWTRDMQGFSVIVNGE 30- 0 PAL+LES LVHVK + G+ +GYGATYQ ++ + TVPIGYADGWTRDMQ FSV+V+G+ Sbjct: 241 PALTLESALVHVKTVPAGACMGYGATYQADSEQVIATVPIGYADGWTRDMQNFSVLVDGQ 30- 0 Query: 301 LCEIIGRVSMDQMTIRLPQKYTIGTKVTLIGQQGSCNITTTDVAQKRQTINYEVLCLLSD 36- 0 C I+GRVSMDQ+TIRLP+ Y +GTKVTLIG G IT T VA R TINYEV+CLLSD Sbjct: 301 ACPIVGRVSMDQITIRLPKLYPLGTKVTLIGSNGDKEITATQVATYRVTINYEVVCLLSD 36- 0 Query: 361 RIPRYY 366 RIPR Y Sbjct: 361 RIPREY 366 A related DNA sequence was identified in S. pyogenes <SEQ ID 3631> which encodes the amino acid sequence <SEQ ID 3632>. Analysis of this protein sequence reveals the following: TABLE-US-03524 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.34 Transmembrane 82-98 (82-98) ----- Final Results ----- bacterial membrane --- Certainty = 0.1935(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03525 >GP: AAD51027 GB: AF171873 alanine racemase [Streptococcus pneumoniae] Identities = 222/366 (60%), Positives = 273/366 (73%) Query: 1 MISSFHRPTVARVNLQAIKENVASVQKHIPLGVKTYAVVKADAYGHGAVQVSKALLPQVD 60 M +S HRPT A ++L AI++N+ + HIP G AVVKA+AYGHGAV V+KA+ VD Sbjct: 1 MKASPHRPTKALIHLGAIRQNIQQMGAHIPQGTLKLAVVKANAYGHGAVAVAKAIQDDVD 60 Query: 61 GYCVSNLDEALQLRQAGIDKEILILGVLLPNELELAVANAITVTIASLDWIALARLEKKE 120- G+CVSN+DEA++LRQAG+ K ILILGV + LA T+T+A L+WI ++ + Sbjct: 61 GFCVSNIDEAIELRQAGLSKPILILGVSEIEAVALAKEYDFTLTVAGLEWIQALLDKEVD 120- Query: 121 CQGLKVHVKVDSGMGRIGLRSSKEVNLLIDSLKELGADVEGIFTHFATADEADDTKFNQQ 18- 0 GL VH+K+DSGMGRIG R + EV D L++ G VEGIFTHFATADE D FN Q Sbjct: 121 LTGLTVHLKIDSGMGRIGFREASEVEQAQDLLQQHGVCVEGIFTHFATADEESDDYFNAQ 18- 0 Query: 181 LQFFKKLIAGLEDKPRLVHASNSATSIWHSDTIFNAVRLGIVSYGLNPSGSDLSLPFPLQ 24- 0 L+ FK ++A +++ P LVHASNSAT++WH +TIFNAVR+G YGLNPSG+ L LP+ L Sbjct: 181 LERFKTILASMKEVPELVHASNSATTLWHVETIFNAVRMGDAMYGLNPSGAVLDLPYDLI 24- 0 Query: 241 EALSLESSLVHVKMISAGDTVGYGATYTAKKSEYVGTVPIGYADGWTRNMQGFSVLVDGQ 30- 0 AL+LES+LVHVK + AG +GYGATY A + + TVPIGYADGWTR+MQ FSVLVDGQ Sbjct: 241 PALTLESALVHVKTVPAGACMGYGATYQADSEQVIATVPIGYADGWTRDMQNFSVLVDGQ 30- 0 Query: 301 FCEIIGRVSMDQLTIRLPKAYPLGTKVTLIGSNQQKNISTTDIANYRNTINYEVLCLLSD 36- 0 C I+GRVSMDQ+TIRLPK YPLGTKVTLIGSN K I+ T +A YR TINYEV+CLLSD Sbjct: 301 ACPIVGRVSMDQITIRLPKLYPLGTKVTLIGSNGDKEITATQVATYRVTINYEVVCLLSD 36- 0 Query: 361 RIPRIY 366 RIPR Y Sbjct: 361 RIPREY 366 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03526 Identities = 247/366 (67%), Positives = 295/366 (80%) Query: 1 MISSYHRPTRALIDLEAIANNVKSVQEHIPSDKKTFAVVKANAYGHGAVEVSKYIESIVD 60 MISS+HRPT A ++L+AI NV SVQ+HIP KT+AVVKA+AYGHGAV+VSK + VD Sbjct: 1 MISSFHRPTVARVNLQAIKENVASVQKHIPLGVKTYAVVKADAYGHGAVQVSKALLPQVD 60 Query: 61 GFCVSNLDEAIELRQAGIVKMILVLGVVMPEQVILAKNENITLTVASLEWLRLCQTSAVD 120- G+CVSNLDEA++LRQAGI K IL+LGV++P ++ LA IT+T+ASL+W+ L + + Sbjct: 61 GYCVSNLDEALQLRQAGIDKEILILGVLLPNELELAVANAITVTIASLDWIALARLEKKE 120- Query: 121 LSGLEVHIKVDSGMGRIGVRQLDEGNKLISELGESGASVKGIFTHFATADEADNCKFNQQ 18- 0 GL+VH+KVDSGMGRIG+R E N LI L E GA V+GIFTHFATADEAD+ KFNQQ Sbjct: 121 CQGLKVHVKVDSGMGRIGLRSSKEVNLLIDSLKELGADVEGIFTHFATADEADDTKFNQQ 18- 0 Query: 181 LTFFKDFISGLDNCPDLVHASNSATSLWHSETIFNAVRLGVVMYGLNPSGTDLDLPYPIN 24- 0 L FFK I+GL++ P LVHASNSATS+WHS+TIFNAVRLG+V YGLNPSG+DL LP+P+ Sbjct: 181 LQFFKKLIAGLEDKPRLVHASNSATSIWHSDTIFNAVRLGIVSYGLNPSGSDLSLPFPLQ 24- 0 Query: 241 PALSLESELVHVKQLHDGSQVGYGATYQVTGDEFVGTVPIGYADGWTRDMQGFSVIVNGE 30- 0 ALSLES LVHVK + G VGYGATY E+VGTVPIGYADGWTR+MQGFSV+V+G+ Sbjct: 241 EALSLESSLVHVKMISAGDTVGYGATYTAKKSEYVGTVPIGYADGWTRNMQGFSVLVDGQ 30- 0 Query: 301 LCEIIGRVSMDQMTIRLPQKYTIGTKVTLIGQQGSCNITTTDVAQKRQTINYEVLCLLSD 36- 0 CEIIGRVSMDQ+TIRLP+ Y +GTKVTLIG NI+TTD+A R TINYEVLCLLSD Sbjct: 301 FCEIIGRVSMDQLTIRLPKAYPLGTKVTLIGSNQQKNISTTDIANYRNTINYEVLCLLSD 36- 0 Query: 361 RIPRYY 366 RIPR Y Sbjct: 361 RIPRIY 366 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1169 A DNA sequence (GBSx1245) was identified in S. agalactiae <SEQ ID 3633> which encodes the amino acid sequence <SEQ ID 3634>. This protein is predicted to be immunogenic secreted protein precursor. Analysis of this protein sequence reveals the following: TABLE-US-03527 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> There is also homology to SEQ ID 1988. A related GBS gene <SEQ ID 8745> and protein <SEQ ID 8746> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03528 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 8.81 GvH: Signal Score (-7.5): 0.659999 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 1.06 threshold: 0.0 PERIPHERAL Likelihood = 1.06 247 modified ALOM score: -0.71 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) SEQ ID 8746 (GBS98) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 7 (lane 5; MW 80 kDa). GBS98-His was purified as shown in FIG. 192, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1170 A DNA sequence (GBSx1246) was identified in S. agalactiae <SEQ ID 3635> which encodes the amino acid sequence <SEQ ID 3636>. This protein is predicted to be junction specific DNA helicase (mmsA) (recG). Analysis of this protein sequence reveals the following: TABLE-US-03529 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 530-546 (530-546) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03530 >GP: CAA90280 GB: Z49988 MmsA [Streptococcus pneumoniae] Identities = 483/671 (71%), Positives = 568/671 (83%) Query: 1 MLLQSPISNLKGFGPKSAEKFQKLDIYTVEDLLLYYPFRYEDFKSKSVFDLVDGEKAVIT 60 M L P+ L G GPKSAEK+ KL I ++DLLLY+PFRYEDFK+K V +L DGEKAV++ Sbjct: 1 MNLHQPLHVLPGVGPKSAEKYAKLGIENLQDLLLYFPFRYEDFKTKQVLELEDGEKAVLS 60 Query: 61 GLVVTPANVQYYGFKRNRLSFKLRQGEAVLNVSFFNQPYLADKIELGQEVAVFGKWDATK 120- G VVTPA+VQYYGFKRNRL F L+QGE V V+FFNQPYLADKIELG +AVFGKWD K Sbjct: 61 GQVVTPASVQYYGFKRNRLRFSLKQGEVVFAVNFFNQPYLADKIELGATLAVFGKWDRAK 120- Query: 121 SAITGMKVLAQVEDDMQPVYRVAQGISQSTLIKAIKSAFEISAHLELKENLPATLLEKYR 18- 0 +++TGMKVLAQVEDD+QPVYR+AQGISQ++L+K IK+AF+ L ++ENLP +LL+KY+ Sbjct: 121 ASLTGMKVLAQVEDDLQPVYRLAQGISQASLVKVIKTAFDQGLDLLIEENLPQSLLDKYK 18- 0 Query: 181 LMGRSQACLAMHFPKDITEYKQALRRIKFEELFYFQMNLQVLKSENKSETNGLPILYSKH 24- 0 LM R QA AMHFPKD+ EYKQALRRIKF ELFYFQM LQ LKSEN+ + +GL + +S+ Sbjct: 181 LMSRCQAVRAMHFPKDLAEYKQALRRIKFAELFYFQMQLQTLKSENRVQGSGLVLNWSQE 24- 0 Query: 241 AMETKISSLPFILTNAQKRSLDEILSDMSSGAHMNRLLQGDVGSGKTVIAGLSMYAAYTA 30- 0 + +SLPF LT AQ++SL EIL+DM S HMNRLLQGDVGSGKTV+AGL+M+AA TA Sbjct: 241 KVTAVKASLPFALTQAQEKSLQEILTDMKSDHHMNRLLQGDVGSGKTVVAGLAMFAAVTA 30- 0 Query: 301 GFQSALMVPTEILAEQHYISLQELFPDLSIAILTSGMKAAVKRTVLAAIANGSVDMIVGT 36- 0 G+Q+ALMVPTEILAEQH+ SLQ LFP+L +A+LT +KAA KR VL IA G D+I+GT Sbjct: 301 GYQAALMVPTEILAEQHFESLQNLFPNLKLALLTGSLKAAEKREVLETIAKGEADLIIGT 36- 0 Query: 361 HALIQDSVQYHKLGLVITDEQHRFGVKQRRIFREKGENPDVLMMTATPIPRTLAITAFGE 42- 0 HALIQD V+Y +LGL+I DEQHRFGV QRRI REKG+NPDVLMMTATPIPRTLAITAFG+ Sbjct: 361 HALIQDGVEYARLGLIIIDEQHRFGVGQRRILREKGDNPDVLMMTATPIPRTLAITAFGD 42- 0 Query: 421 MDVSIIDELPAGRKPIITRWVKHEQLGTVLEWVKGELQKDAQVYVISPLIEESEALDLKN 48- 0 MDVSIID++PAGRKPI+TRW+KHEQL VL W++GE+QK +Q YVISPLIEESEALDLKN Sbjct: 421 MDVSIIDQMPAGRKPIVTRWIKHEQLPQVLTWLEGEIQKGSQAYVISPLIEESEALDLKN 48- 0 Query: 481 AVALHAELSTYFEGIAKVALVHGRMKNDEKDAIMQDFKDKKSHILVSTTVIEVGVNVPNA 54- 0 A+AL EL+T+F G A+VAL+HGRMK+DEKD IMQDFK++K+ ILVSTTVIEVGVNVPNA Sbjct: 481 AIALSEELTTHFAGKAEVALLHGRMKSDEKDQIMQDFKERKTDILVSTTVIEVGVNVPNA 54- 0 Query: 541 TIMIIMDADRFGLSQLHQLRGRVGRGYKQSYAVLVANPKTDSGKKRMTIMTETTDGFVLA 60- 0 T+MIIMDADRFGLSQLHQLRGRVGRG KQSYAVLVANPKTDSGK RM IMTETT+GFVLA Sbjct: 541 TVMIIMDADRFGLSQLHQLRGRVGRGDKQSYAVLVANPKTDSGKDRMRIMTETTNGFVLA 60- 0 Query: 601 ESDLKMRGSGEIFGTRQSGIPEFQVADIVEDYPILEEARRVASDIVKDNNWKENTEWALI 66- 0 E DLKMRGSGEIFGTRQSG+PEFQVADI+ED+PILEEAR+VAS I W+E+ EW +I Sbjct: 601 EEDLKMRGSGEIFGTRQSGLPEFQVADIIEDFPILEEARKVASYISSIEAWQEDPEWRMI 66- 0 Query: 661 LDNLRQHSDFD 671 +L + D Sbjct: 661 ALHLEKKEHLD 671 A related DNA sequence was identified in S. pyogenes <SEQ ID 3637> which encodes the amino acid sequence <SEQ ID 3638>. Analysis of this protein sequence reveals the following: TABLE-US-03531 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 530-546 (530-546) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03532 Identities = 641/671 (95%), Positives = 655/671 (97%) Query: 1 MLLQSPISNLKGFGPKSAEKFQKLDIYTVEDLLLYYPFRYEDFKSKSVFDLVDGEKAVIT 60 M+L +P+SNLKGFGPKSAEKFQKLDIYTVEDLLLYYPFRYEDFKSKSVFDLVDGEKAVIT Sbjct: 1 MILTAPMSNLKGFGPKSAEKFQKLDIYTVEDLLLYYPFRYEDFKSKSVFDLVDGEKAVIT 60 Query: 61 GLVVTPANVQYYGFKRNRLSFKLRQGEAVLNVSFFNQPYLADKIELGQEVAVFGKWDATK 120- GLVVTPANVQYYGFKRNRLSFKLRQGEAVLNVSFFNQPYLADKIELGQEVAVFGKWDATK Sbjct: 61 GLVVTPANVQYYGFKRNRLSFKLRQGEAVLNVSFFNQPYLADKIELGQEVAVFGKWDATK 120- Query: 121 SAITGMKVLAQVEDDMQPVYRVAQGISQSTLIKAIKSAFEISAHLELKENLPATLLEKYR 18- 0 SAITGMKVLAQVEDDMQPVYRVAQGISQSTLIKAIKSAFEI AHLELKENLPATLLEKYR Sbjct: 121 SAITGMKVLAQVEDDMQPVYRVAQGISQSTLIKAIKSAFEIDAHLELKENLPATLLEKYR 18- 0 Query: 181 LMGRSQACLAMHFPKDITEYKQALRRIKFEELFYFQMNLQVLKSENKSETNGLPILYSKH 24- 0 LMGRSQACLAMHFPKDITEYKQALRRIKFEELFYFQMNLQVLK+ENKSETNGLPILYSK Sbjct: 181 LMGRSQACLAMHFPKDITEYKQALRRIKFEELFYFQMNLQVLKAENKSETNGLPILYSKR 24- 0 Query: 241 AMETKISSLPFILTNAQKRSLDEILSDMSSGAHMNRLLQGDVGSGKTVIAGLSMYAAYTA 30- 0 AMETKISSLPFILTNAQKRSLD+ILSDMSSGAHMNRLLQGDVGSGKTVIAGLSMYAAYTA Sbjct: 241 AMETKISSLPFILTNAQKRSLDDILSDMSSGAHMNRLLQGDVGSGKTVIAGLSMYAAYTA 30- 0 Query: 301 GFQSALMVPTEILAEQHYISLQELFPDLSIAILTSGMKAAVKRTVLAAIANGSVDMIVGT 36- 0 GFQSALMVPTEILAEQHYISLQELFPDLSIAILTSGMKAAVKRTVLAAIANGSVDMIVGT Sbjct: 301 GFQSALMVPTEILAEQHYISLQELFPDLSIAILTSGMKAAVKRTVLAAIANGSVDMIVGT 36- 0 Query: 361 HALIQDSVQYHKLGLVITDEQHRFGVKQRRIFREKGENPDVLMMTATPIPRTLAITAFGE 42- 0 HALIQDSVQYHKLGLVITDEQHRFGVKQRRIFREKGENPDVLMMTATPIPRTLAITAFGE Sbjct: 361 HALIQDSVQYHKLGLVITDEQHRFGVKQRRIFREKGENPDVLMMTATPIPRTLAITAFGE 42- 0 Query: 421 MDVSIIDELPAGRKPIITRWVKHEQLGTVLEWVKGELQKDAQVYVISPLIEESEALDLKN 48- 0 MDVSIIDELPAGRKPI+TRWVKHEQLGTVLEWVKGELQKDAQVYVISPLIEESEALDLKN Sbjct: 421 MDVSIIDELPAGRKPIMTRWVKHEQLGTVLEWVKGELQKDAQVYVISPLIEESEALDLKN 48- 0 Query: 481 AVALHAELSTYFEGIAKVALVHGRMKNDEKDAIMQDFKDKKSHILVSTTVIEVGVNVPNA 54- 0 AVALHAELSTYFEGIAKVALVHGRMKNDEKDAIMQDFKDKKSHILVSTTVIEVGVNVPNA Sbjct: 481 AVALHAELSTYFEGIAKVALVHGRMKNDEKDAIMQDFKDKKSHILVSTTVIEVGVNVPNA 54- 0 Query: 541 TIMIIMDADRFGLSQLHQLRGRVGRGYKQSYAVLVANPKTDSGKKRMTIMTETTDGFVLA 60- 0 TIMIIMDADRFGLSQLHQLRGRVGRGYKQSYAVLVANPKTDSGKKRMTIMTETTDGFVLA Sbjct: 541 TIMIIMDADRFGLSQLHQLRGRVGRGYKQSYAVLVANPKTDSGKKRMTIMTETTDGFVLA 60- 0 Query: 601 ESDLKMRGSGEIFGTRQSGIPEFQVADIVEDYPILEEARRVASDIVKDNNWKENTEWALI 66- 0 ESDLKMRGSGEIFGTRQSGIPEFQVADIVEDYPILEEAR+V++ IV D NW +W L+ Sbjct: 601 ESDLKMRGSGEIFGTRQSGIPEFQVADIVEDYPILEEARKVSAAIVSDPNWIYEKQWQLV 66- 0 Query: 661 LDNLRQHSDFD 671 N+R+ +D Sbjct: 661 AQNIRKKEVYD 671 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1171 A DNA sequence (GBSx1247) was identified in S. agalactiae <SEQ ID 3639> which encodes the amino acid sequence <SEQ ID 3640>. This protein is predicted to be aryl-alcohol dehydrogenase (b1647). Analysis of this protein sequence reveals the following: TABLE-US-03533 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1562(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10105> which encodes amino acid sequence <SEQ ID 10106> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03534 >GP: BAB07646 GB: AP001520 aryl-alcohol dehydrogenase [Bacillus halodurans] Identities = 173/300 (57%), Positives = 224/300 (74%) Query: 7 IGQTGIQATRIALGCMRMSDLKGKQAEEVVGTALDLGINFFDHADIYGGGLSELRFRDAI 66 +G + ++ +A+GCMR++ + K+AE V TAL+ G NFFDHADIYGGG E F DAI Sbjct: 6 LGSSSLEVPVVAVGCMRINAISKKEAERFVQTALEQGANFFDHADIYGGGECEEIFADAI 65 Query: 67 KHLNVNRDKMIIQSKCGIREGYFDFSKEYILSSVDGILERLGTEYLDFLILHRPDVLVEP 126- + R+K+I+QSKCGIREG FDFSKEYIL SVDGIL+RL T+YLD L+LHRPD LVEP Sbjct: 66 QMNEAVREKIILQSKCGIREGRFDFSKEYILQSVDGILQRLKTDYLDVLLLHRPDALVEP 125- Query: 127 EEVAEAFTKLRAEGKVKHFGVSNQNRFQMELLQSYLDEPLAVNQLQLSPAHTPMFDAGLN 18- 6 EEVAEAF L + GKV+HFGVSNQN Q+ELL+ ++ +P+ NQLQLS + M +G+N Sbjct: 126 EEVAEAFDLLESSGKVRHFGVSNQNPMQIELLKKFVRQPIVANQLQLSITNATMISSGIN 18- 5 Query: 187 VNMLNKASIEHDDGIVDYCRLKRVTIQAWSPFQIDLSRGLFVNHPDYKELNETIAKLAKN 24- 6 VNM N+++I D ++DYCRL VTIQ WSPFQ G+F+ + + ELN+ I +LA+ Sbjct: 186 VNMENESAINRDGSVLDYCRLHDVTIQPWSPFQYGFFEGVFLGNDLFPELNKKIDELAEK 24- 5 Query: 247 YNVSSEAIVIAWILRHPAKMQAIVGSMNPSRLKAIDKANDIALTRKEWYDIYRSAGNILP 30- 6 Y VS+ I IAW+LRHPA MQ ++G+MN RLK KA++I LTR+EWY+IYR+AGNILP Sbjct: 246 YEVSNTTIAIAWLLRHPANMQPVIGTMNLKRLKDCCKASEIRLTREEWYEIYRAAGNILP 30- 5 There is also homology to SEQ ID 780. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1172 A DNA sequence (GBSx1248) was identified in S. agalactiae <SEQ ID 3641> which encodes the amino acid sequence <SEQ ID 3642>. This protein is predicted to be shikimate 5-dehydrogenase (aroE) (aroE). Analysis of this protein sequence reveals the following:

TABLE-US-03535 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0988(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03536 >GP: AAC74762 GB: AE000264 putative oxidoreductase [Escherichia coli K12] Identities = 114/279 (40%), Positives = 171/279 (60%), Gaps = 3/279 (1%) Query: 10 LTGLIANPARHSLSPLMWNTSFQEKNMNYAYLTFEVEEGKLTEAVRGVRALGIRGVNVSM 69 - L GL+A P RHSLSP M N + ++ + + Y+ FEV+ A+ G++AL +RG VSM Sbjct: 9 LIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVSM 68 Query: 70 PFKQSVIPLLDDLSPQAKLVGAVNTIVNQGGTGRLVGHMTDGIGCFKALAAQGFSAKNKI 129- P KQ +D+L+P AKLVGA+NTIVN G R G+ TDG G +A+ GF K K Sbjct: 69 PNKQLACEYVDELTPAAKLVGAINTIVNDDGYLR--GYNTDGTGHIRAIKESGFDIKGKT 126- Query: 130 ITIAGIGGSGKAVAVQAAMEGVAEIRLFNRNSSNYDKVIDLSDKIKKQFQIKVVVDYLEN 18- 9 + + G GG+ A+ Q A+EG+ EI+LFNR +DK + + ++ + V V L + Sbjct: 127 MVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLAD 18- 6 Query: 190 KTAFKDAIRTSHFYIDATSLGMRPLDNYSLINDPEILTPNLVVVDLVYKPKETALLRFVR 24- 9 + AF +A+ ++ + T +GM+PL+N SL+ND +L P L+V + VY P T LL+ + Sbjct: 187 QQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQ 24- 6 Query: 250 QNGVKHAYNGLGMLIYQGAEAFQLITNQEMPISSVERVL 288 Q G K +G GML++QGAE F L T ++ P+ V++V+ Sbjct: 247 QAGCK-TIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVM 284 A related DNA sequence was identified in S. pyogenes <SEQ ID 3643> which encodes the amino acid sequence <SEQ ID 3644>. Analysis of this protein sequence reveals the following: TABLE-US-03537 Possible site: 54 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03538 >GP: AAC74762 GB: AE000264 putative oxidoreductase [Escherichia coli] Identities = 132/280 (47%), Positives = 186/280 (66%), Gaps = 3/280 (1%) Query: 11 LVSLLATPIRHSLSPKMHNEAYAKLGLDYAYLAFEVGTEQLADAVQGIRALGIRGSNVSM 70 - L+ L+A PIRHSLSP+M N+A K GL + Y+AFEV + A++G++AL +RG+ VSM Sbjct: 9 LIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVSM 68 Query: 71 PNKEAILPLLDDLSPAAELVGAVNTVVNKDGKGHLVGHITDGIGALRALADEGVSVKNKI 130- PNK+ +D+L+PAA+LVGA+NT+VN DG +L G+ TDG G +RA+ + G +K K Sbjct: 69 PNKQLACEYVDELTPAAKLVGAINTIVNDDG--YLRGYNTDGTGHIRAIKESGFDIKGKT 126- Query: 131 ITLAGVGGAGKAIAVQLAFDGAKEVRLFNRQATRLSSVQKLVTKLNQLTRTKVTLQDLED 19- 0 + L G GGA AI Q A +G KE++LFNR+ ++N+ T VT+ DL D Sbjct: 127 MVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLAD 18- 6 Query: 191 QTAFKEAIRESHLFIDATSVGMKPLENLSLITDPELIRPDLVVFDIVYSPAETKLLAFAR 25- 0 Q AF EA+ + + + T VGMKPLEN SL+ D L+ P L+V + VY+P TKLL A+ Sbjct: 187 QQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQ 24- 6 Query: 251 QHGAQKVINGLGMVLYQGAEAFKLITGQDMPVDAIKPLLG 290 Q G K I+G GM+L+QGAE F L TG+D P++ +K ++G Sbjct: 247 QAGC-KTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMG 285 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03539 Identities = 166/288 (57%), Positives = 221/288 (76%) Query: 4 LNGETLLTGLIANPARHSLSPLMWNTSFQEKNMNYAYLTFEVEEGKLTEAVRGVRALGIR 63 L+G TLL L+A P RHSLSP M N ++ + ++YAYL FEV +L +AV+G+RALGIR Sbjct: 5 LSGHTLLVSLLATPIRHSLSPKMHNEAYAKLGLDYAYLAFEVGTEQLADAVQGIRALGIR 64 Query: 64 GVNVSMPFKQSVIPLLDDLSPQAKLVGAVNTIVNQGGTGRLVGHMTDGIGCFKALAAQGF 123- G NVSMP K++++PLLDDLSP A+LVGAVNT+VN+ G G LVGH+TDGIG +ALA +G Sbjct: 65 GSNVSMPNKEAILPLLDDLSPAAELVGAVNTVVNKDGKGHLVGHITDGIGALRALADEGV 124- Query: 124 SAKNKIITIAGIGGSGKAVAVQAAMEGVAEIRLFNRNSSNYDKVIDLSDKIKKQFQIKVV 18- 3 S KNKIIT+AG+GG+GKA+AVQ A +G E+RLFNR ++ V L K+ + + KV Sbjct: 125 SVKNKIITLAGVGGAGKAIAVQLAFDGAKEVRLFNRQATRLSSVQKLVTKLNQLTRTKVT 18- 4 Query: 184 VDYLENKTAFKDAIRTSHFYIDATSLGMRPLDNYSLINDPEILTPNLVVVDLVYKPKETA 24- 3 + LE++TAFK+AIR SH +IDATS+GM+PL+N SLI DPE++ P+LVV D+VY P ET Sbjct: 185 LQDLEDQTAFKEAIRESHLFIDATSVGMKPLENLSLITDPELIRPDLVVFDIVYSPAETK 24- 4 Query: 244 LLRFVRQNGVKHAYNGLGMLIYQGAEAFQLITNQEMPISSVERVLQTE 291 LL F RQ+G + NGLGM++YQGAEAF+LIT Q+MP+ +++ +L E Sbjct: 245 LLAFARQHGAQKVINGLGMVLYQGAEAFKLITGQDMPVDAIKPLLGDE 292 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1173 A DNA sequence (GBSx1249) was identified in S. agalactiae <SEQ ID 3645> which encodes the amino acid sequence <SEQ ID 3646>. Analysis of this protein sequence reveals the following: TABLE-US-03540 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.16 Transmembrane 57-73 (53-76) ----- Final Results ----- bacterial membrane --- Certainty = 0.3463(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1174 A DNA sequence (GBSx1250) was identified in S. agalactiae <SEQ ID 3647> which encodes the amino acid sequence <SEQ ID 3648>. Analysis of this protein sequence reveals the following: TABLE-US-03541 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2333(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10103> which encodes amino acid sequence <SEQ ID 10104> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03542 >GP: BAB05343 GB: AP001512 L-asparaginase [Bacillus halodurans ] Identities = 158/319 (49%), Positives = 214/319 (66%), Gaps = 4/319 (1%) Query: 1 MKKILVLHTGGTISMNANEKGQVMSSADNPMKYVDLSLDDL-DLTVVDFLNLPSPQITPH 59 MKK+LV+HTGGTI+M+ +EKG V NP+ SL + + V DFLN+PSP +TP Sbjct: 1 MKKVLVIHTGGTIAMHEDEKGGVQPKETNPLFATVESLTSIASIEVDDFLNIPSPHMTPE 60 Query: 60 HMLDIYHYLKQHASN--FDGVVITHGTDTLEETAYFLDTMILPKIPIIITGAMRSTNELG 117- M + LK N FDGVVITHGTDTLEETAY LD ++ ++P+++TGAMRS+NELG Sbjct: 61 LMFQLAERLKSRVGNESFDGVVITHGTDTLEETAYLLDLLLDWEVPVVVTGAMRSSNELG 120- Query: 118 SDGVYNYLSALRVANSTKAADKGVLVVMNDEIHAAKYVTKTHTTNVSTFQTPTHGPLGII 17- 7 +DG +N++SA++ A + +A KGVLVV NDEIH AK VTKTHT+NV+TFQ+P +GP+GI+ Sbjct: 121 ADGPHNFISAVKTAATDEAKGKGVLVVFNDEIHTAKNVTKTHTSNVATFQSPQYGPIGIV 18- 0 Query: 178 MKQDLLFFKATEERVRFDLDKITGTVPIVKAYAGMGDSGIISFLNSQNISGLVIEALGAG 23- 7 K+ + F A + + + I V ++KAYAGM D ++ + I GLVIEA G G Sbjct: 181 TKRGVTFHHAPSYKESYTVSSIDHRVVLLKAYAGM-DGSVVDAIADTGIDGLVIEAFGQG 23- 9 Query: 238 NMPPKAAQEIEELIEQGVPVVLVSRCFNGIAEPVYGYEGGGAKLQESGVMFVKELNAPKA 29- 7 N+PP I+ L + +PVVLVSR +GI + Y YEGGG L++ GV+F LN KA Sbjct: 240 NLPPAVVPSIKRLHQANIPVVLVSRSVSGIVQETYAYEGGGRHLKDLGVIFTNGLNGQKA 29- 9 Query: 298 RLKLLIALNAGLTGQNLKD 316 RLKLL+AL + L++ Sbjct: 300 RLKLLVALELTTDRKKLQE 318 A related DNA sequence was identified in S. pyogenes <SEQ ID 3649> which encodes the amino acid sequence <SEQ ID 3650>. Analysis of this protein sequence reveals the following: TABLE-US-03543 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.28 Transmembrane 245-261 (243-261) ----- Final Results ----- bacterial membrane --- Certainty = 0.1914(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03544 >GP: BAB05343 GB: AP001512 L-asparaginase [Bacillus halodurans] Identities = 158/320 (49%), Positives = 218/320 (67%), Gaps = 5/320 (1%) Query: 1 MKKILVLHTGGTISMQADNSGRVVPNQDNPM-TKIHAAAQDIQLTVSDFLNLPSPHITPH 59 MKK+LV+HTGGTI+M D G V P + NP+ + + + V DFLN+PSPH+TP Sbjct: 1 MKKVLVIHTGGTIAMHEDEKGGVQPKETNPLFATVESLTSIASIEVDDFLNIPSPHMTPE 60 Query: 60 HMLSIYHHIQERT--DVFDGIVITHGTDTLEETAYFLDTMALPTNIPVVLTGAMRSSNEV 117- M + ++ R + FDG+VITHGTDTLEETAY LD + L +PVV+TGAMRSSNE+ Sbjct: 61 LMFQLAERLKSRVGNESFDGVVITHGTDTLEETAYLLDLL-LDWEVPVVVTGAMRSSNEL 119- Query: 118 GSDGIYNYLTALRVASSDKAKEKGVLVVMNDEIHAAKYVTKTHTTNISTFQTPTHGPLGI 17- 7 G+DG +N+++A++ A++D+AK KGVLVV NDEIH AK VTKTHT+N++TFQ+P +GP+GI Sbjct: 120 GADGPHNFISAVKTAATDEAKGKGVLVVFNDEIHTAKNVTKTHTSNVATFQSPQYGPIGI 17- 9 Query: 178 IMKNDLLFFKTAEPRIRFDLRCISGTIPIIKAYAGMGDGSILSLLTPGSIQGLVIEALGA 23- 7 + K + F + + + I + ++KAYAGM DGS++ + I GLVIEA G Sbjct: 180 VTKRGVTFHHAPSYKESYTVSSIDHRVVLLKAYAGM-DGSVVDAIADTGIDGLVIEAFGQ 23- 8 Query: 238 GNVPPLAVGEIEHLIALGIPVILVSRCFNGMAEPVYAYEGGGAMLQEAGVMFVKELNAPK 29- 7 GN+PP V I+ L IPV+LVSR +G+ + YAYEGGG L++ GV+F LN K Sbjct: 239 GNLPPAVVPSIKRLHQANIPVVLVSRSVSGIVQETYAYEGGGRHLKDLGVIFTNGLNGQK 29- 8 Query: 298 ARLKLLIALNAGLTGQELKD 317 ARLKLL+AL ++L++ Sbjct: 299 ARLKLLVALELTTDRKKLQE 318 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03545 Identities = 242/321 (75%), Positives = 275/321 (85%), Gaps = 1/321 (0%) Query: 1 MKKILVLHTGGTISMNANEKGQVMSSADNPMKYVDLSLDDLDLTVVDFLNLPSPQITPHH 60 MKKILVLHTGGTISM A+ G+V+ + DNPM + + D+ LTV DFLNLPSP ITPHH Sbjct: 1 MKKILVLHTGGTISMQADNSGRVVPNQDNPMTKIHAAAQDIQLTVSDFLNLPSPHITPHH 60 Query: 61 MLDIYHYLKQHASNFDGVVITHGTDTLEETAYFLDTMILP-KIPIIITGAMRSTNELGSD 119- ML IYH++++ FDG+VITHGTDTLEETAYFLDTM LP IP+++TGAMRS+NE+GSD Sbjct: 61 MLSIYHHIQERTDVFDGIVITHGTDTLEETAYFLDTMALPTNIPVVLTGAMRSSNEVGSD 120- Query: 120 GVYNYLSALRVANSTKAADKGVLVVMNDEIHAAKYVTKTHTTNVSTFQTPTHGPLGIIMK 17- 9 G+YNYL+ALRVA+S KA +KGVLVVMNDEIHAAKYVTKTHTTN+STFQTPTHGPLGIIMK Sbjct: 121 GIYNYLTALRVASSDKAKEKGVLVVMNDEIHAAKYVTKTHTTNISTFQTPTHGPLGIIMK 18- 0 Query: 180 QDLLFFKATEERVRFDLDKITGTVPIVKAYAGMGDSGIISFLNSQNISGLVIEALGAGNM 23- 9 DLLFFK E R+RFDL I+GT+PI+KAYAGMGD I+S L +I GLVIEALGAGN+ Sbjct: 181 NDLLFFKTAEPRIRFDLRCISGTIPIIKAYAGMGDGSILSLLTPGSIQGLVIEALGAGNV 24- 0 Query: 240 PPKAAQEIEELIEQGVPVVLVSRCFNGIAEPVYGYEGGGAKLQESGVMFVKELNAPKARL 29- 9 PP A EIE LI G+PV+LVSRCFNG+AEPVY YEGGGA LQE+GVMFVKELNAPKARL Sbjct: 241 PPLAVGEIEHLIALGIPVILVSRCFNGMAEPVYAYEGGGAMLQEAGVMFVKELNAPKARL 30- 0 Query: 300 KLLIALNAGLTGQNLKDYIEG 320 KLLIALNAGLTGQ LKDYIEG Sbjct: 301 KLLIALNAGLTGQELKDYIEG 321 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1175 A DNA sequence (GBSx1251) was identified in S. agalactiae <SEQ ID 3651> which encodes the amino acid sequence <SEQ ID 3652>. Analysis of this protein sequence reveals the following: TABLE-US-03546 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4427(Affirmative). < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03547 >GP: CAB85142 GB: AL162757 conserved hypothetical protein [Neisseria meningitidis Z2491] Identities = 87/285 (30%), Positives = 138/285 (47%), Gaps = 35/285 (12%) Query: 4 KAVFFDIDGTLLNDRKNVQKSTIK-AIRNLKDQGILVGLATGRG----PSFVQPFLENLG 58 K VFFDID TL + + ++K A+ L+ +GIL LATGR P V+ + G Sbjct: 11 KIVFFDIDDTLYRKYTDTLRPSVKTAVAALRGKGILTALATGRSLATIPEKVRDMMAETG 70 Query: 59 LDFAVTYNGQYIYSRSEIIYTNQLSKTTVYRLIRYAGARRREISLGTASGLLGSGIIGLG 118- +D VT NGQ+ + + + + R+ + SLG +G G+ Sbjct: 71 MDAVVTINGQFALLHGKTVCEVPMDAGLMGRVCAHLD------SLGMDYAFVGGE--GIA 122- Query: 119 TSRLGQIVSSLVPRKWAKAIERSFKHFIRRIKPQNIDSLMVILREPIYQVVLVATEGE-- 17- 6 S L + V R+ KH I +P+YQ+++ A E E Sbjct: 123 VSALSECVC------------RALKH----IASDFFADKDYFSSKPVYQMLVFAEENEMP 16- 6 Query: 177 --SERIQKQFPRVKLTRSSPYSMDVISEGQSKVKGIERVGQRYGFDLSEVIAFGDSDNDI 23- 4 S+ ++++ +K R ++D++ G SK GI V + G ++++V+AFGD ND+ Sbjct: 167 LWSDIVERE--GLKTVRWHEEAVDLLPAGASKTDGIRSVVEALGLEMADVMAFGDGLNDV 22- 4 Query: 235 EMLSQVGIGVAMGNASQQVRENARYTTADNNDDGISKALAHYGLI 279 EMLS+VG GVAMGN Q +E A+Y ++DG+ + L G+I Sbjct: 225 EMLSEVGFGVAMGNGEQAAKEAAKYVCPGVDEDGVLRGLQDLGVI 269 A related DNA sequence was identified in S. pyogenes <SEQ ID 3653> which encodes the amino acid sequence <SEQ ID 3654>. Analysis of this protein sequence reveals the following: TABLE-US-03548 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6014(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03549 Identities = 320/459 (69%), Positives = 391/459 (84%) Query: 1 MAIKAVFFDIDGTLLNDRKNVQKSTIKAIRNLKDQGILVGLATGRGPSFVQPFLENLGLD 60 + +KAVFFDIDGTLLNDRKN+QK+T KAI+ LK QGI+VGLATGRGP FVQPFLEN GLD Sbjct: 1 LTVKAVFFDIDGTLLNDRKNIQKTTQKAIQQLKKQGIMVGLATGRGPGFVQPFLENFGLD 60 Query: 61 FAVTYNGQYIYSRSEIIYTNQLSKTTVYRLIRYAGARRREISLGTASGLLGSGIIGLGTS 120- FAVTYNGQYI +R +++Y NQL K+ +Y++IRYA ++REISLGTASGL GS II +GTS Sbjct: 61 FAVTYNGQYILTRDKVLYQNQLPKSMIYKVIRYANEKKREISLGTASGLAGSRIIDMGTS 120- Query: 121 RLGQIVSSLVPRKWAKAIERSFKHFIRRIKPQNIDSLMVILREPIYQVVLVATEGESERI 18- 0 GQ++SS VP+ WA+ +E SFKH IRRIKPQ+ +L+ I+REPIYQVVLVA++ E+++I Sbjct: 121 PFGQVISSFVPKSWARTVEGSFKHLIRRIKPQSFRNLVTIMREPIYQVVLVASQAETKKI 18- 0 Query: 181 QKQFPRVKLTRSSPYSMDVISEGQSKVKGIERVGQRYGFDLSEVIAFGDSDNDIEMLSQV 24- 0 Q++FP +K+TRSSPYS+D+IS QSK+KGIER+G+ +GFDLSEV+AFGDSDND+EMLS V Sbjct: 181 QEKFPHIKITRSSPYSLDLISVDQSKIKGIERLGEMFGFDLSEVMAFGDSDNDLEMLSGV 24- 0 Query: 241 GIGVAMGNASQQVRENARYTTADNNDDGISKALAHYGLIQFEIEKTFSSRDENFNKVKSF 30- 0 GIG+AMGNA V++ A +TT NN+DGISKALAHYGLI F+IEK+F SRDENFNKVK F Sbjct: 241 GIGIAMGNAETVVKDGAHFTTDSNNNDGISKALAHYGLIHFDIEKSFKSRDENFNKVKDF 30- 0 Query: 301 HLLMDGETIETPRLYDSKEAGFRSDFKVEEIVEFLYAASQGNQKVFDQSIRNLHLAIDKA 36- 0 H LMD +TIETPR Y EAG+RS FKVEEIVEFLYAAS+G+Q+ F Q+I +LH A+D+A Sbjct: 301 HRLMDSDTIETPRSYTISEAGYRSGFKVEEIVEFLYAASKGDQQQFTQAIFDLHGAVDQA 36- 0 Query: 361 RDKVISKDHPETPLVGEVDALTDLLYLTYGSFVLMGVDPKPLFDTVHEANMGKIFPDGKA 42- 0 +KV +K H ETPL+G+VDAL DLLY TYGSFVLMGVDP+P+F+ VHEANM KIFPDGKA Sbjct: 361 ANKVQAKKHVETPLIGQVDALADLLYFTYGSFVLMGVDPQPIFEAVHEANMAKIFPDGKA 42- 0 Query: 421 HFDPVTHKILKPDDWEEHFAPEPSIRRELDSQIQKSLNR 459 HFDPVTHKI KPD W+E APE +I++ELD Q+QKSL R Sbjct: 421 HFDPVTHKIQKPDYWQERHAPEVAIKKELDKQLQKSLQR 459 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1176 A DNA sequence (GBSx1252) was identified in S. agalactiae <SEQ ID 3655> which encodes the amino acid sequence <SEQ ID 3656>. Analysis of this protein sequence reveals the following: TABLE-US-03550 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1671(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10101> which encodes amino acid sequence <SEQ ID 10102> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03551 >GP: BAB06903 GB: AP001518 unknown conserved protein [Bacillus halodurans] Identities = 61/141 (43%), Positives = 92/141 (64%) Query: 22 YERILVAIDGSTESELAFEKAVNVALRNDSELILTHVIDTRALQSFATFDTYIYEKLEKE 81 - Y ILVA+DGST+++ A KA N A ++L + HVID+R+ + +D + E + Sbjct: 2 YNHILVAVDGSTQAKRALYKAFNYAKEFKADLFICHVIDSRSFATVEQYDRTVVGAAELD 61 Query: 82 AKDVLEEYEKQAREKGADKVRQVIEFGNPKTLLAHDIPEKEKVDLIMVGATGLNTFERFX 141- K +L+ Y ++A + G DKV +++FG+PK ++ I +K +DLI+ GATGLN ERF Sbjct: 62 GKKLLQRYSEEAEKAGVDKVHTILDFGSPKANISKTIAQKYDIDLIITGATGLNAVERFL 121- Query: 142 IGSSSEYILRHAKVDLLIVRD 162 +GS SE + RHAK D+LIVR+ Sbjct: 122 MGSVSESVARHAKCDVLIVRN 142 A related DNA sequence was identified in S. pyogenes <SEQ ID 3657> which encodes the amino acid sequence <SEQ ID 3658>. Analysis of this protein sequence reveals the following:

TABLE-US-03552 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1296(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03553 Identities = 117/156 (75%), Positives = 135/156 (86%) Query: 12 LEEDRLMSQKYERILVAIDGSTESELAFEKAVNVALRNDSELILTHVIDTRALQSFATFD 71 - L+ED MS KY+RILVAIDGS ESELAF K VNVALRND+ L+L HVIDTRALQS ATFD Sbjct: 25 LKEDSSMSLKYKRILVAIDGSYESELAFNKGVNVALRNDATLLLVHVIDTRALQSVATFD 84 Query: 72 TYIYEKLEKEAKDVLEEYEKQAREKGADKVRQVIEFGNPKTLLAHDIPEKEKVDLIMVGA 131- TYIYEKLE+EAKDVL+++EKQA+ G ++Q+IEFGNPK LLAHDIP++E DLIMVGA Sbjct: 85 TYIYEKLEQEAKDVLDDFEKQAQIAGITNIKQIIEFGNPKNLLAHDIPDRENADLIMVGA 144- Query: 132 TGLNTFERFXIGSSSEYILRHAKVDLLIVRDPNKTM 167 TGLNTFER IGSSSEYI+RHAK+DLL+VRD KT+ Sbjct: 145 TGLNTFERLLIGSSSEYIMRHAKIDLLVVRDSTKTL 180 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1177 A DNA sequence (GBSx1253) was identified in S. agalactiae <SEQ ID 3659> which encodes the amino acid sequence <SEQ ID 3660>. This protein is predicted to be aspartate aminotransferase (aspC). Analysis of this protein sequence reveals the following: TABLE-US-03554 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2803(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03555 >GP: AAC21948 GB: U32714 aminotransferase [Haemophilus influenzae Rd] Identities = 142/212 (66%), Positives = 181/212 (84%), Gaps = 1/212 (0%) Query: 1 MKIFDKSMKLEHVAYDIRGPVLEEADRMRANGEKILRLNTGNPAAFGFEAPDEVIRDLIT 60 M++F KS KLEHV YDIRGPV +EA R+ G KIL+LN GNPA FGFEAPDE++ D++ Sbjct: 1 MRLFPKSDKLEHVCYDIRGPVHKEALRLEEEGNKILKLNIGNPAPFGFEAPDEILVDVLR 60 Query: 61 NARESEGYSDSKGIFSARKAVMQYYQLQNI-HVDMDDIYIVNGVSEGISMSMQALLDNDD 119- N ++GY DSKG++SARKA++QYYQ + I ++D+YI NGVSE I+M+MQALL++ D Sbjct: 61 NLPSAQGYCDSKGLYSARKAIVQYYQSKGILGATVNDVYIGNGVSELITMAMQALLNDGD 120- Query: 120 EVLVPMPDYPLWTACVSLAGGNAVHYICDEEANWYPDIDDIKSKITSKTKAIVLINPNNP 17- 9 EVLVPMPDYPLWTA V+L+GG AVHY+CDE+ANW+P IDDIK+K+ +KTKAIV+INPNNP Sbjct: 121 EVLVPMPDYPLWTAAVTLSGGKAVHYLCDEDANWFPTIDDIKAKVNAKTKAIVIINPNNP 18- 0 Query: 180 TGAVYPREILQEIVDIARQNDLIIFSDEVYDR 211 TGAVY +E+LQEIV+IARQN+LIIF+DE+YD+ Sbjct: 181 TGAVYSKELLQEIVEIARQNNLIIFADEIYDK 212 A related DNA sequence was identified in S. pyogenes <SEQ ID 3661> which encodes the amino acid sequence <SEQ ID 3662>. Analysis of this protein sequence reveals the following: TABLE-US-03556 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2936(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03557 Identities = 170/212 (80%), Positives = 193/212 (90%), Gaps = 1/212 (0%) Query: 1 MKIFDKSMKLEHVAYDIRGPVLEEADRMRANGEKILRLNTGNPAAFGFEAPDEVIRDLIT 60 MKI +KS KLEHVAYDIRGPVL+EA+RM A+GEKILRLNTGNPAAFGFEAPDEVIRDLI Sbjct: 13 MKIIEKSSKLEHVAYDIRGPVLDEANRMIASGEKILRLNTGNPAAFGFEAPDEVIRDLIV 72 Query: 61 NARESEGYSDSKGIFSARKAVMQYYQLQNI-HVDMDDIYIVNGVSEGISMSMQALLDNDD 119- NAR SEGYSDSKGIFSARKA+MQY QL+ VD++DIY+ NGVSE IS+S+QALLDN D Sbjct: 73 NARLSEGYSDSKGIFSARKAIMQYCQLKGFPDVDIEDIYLGNGVSELISISLQALLDNGD 132- Query: 120 EVLVPMPDYPLWTACVSLAGGNAVHYICDEEANWYPDIDDIKSKITSKTKAIVLINPNNP 17- 9 EVLVPMPDYPLWTACVSL GG AVHY+CDEEA WYPDI DIKSKITS+TKAIV+INPNNP Sbjct: 133 EVLVPMPDYPLWTACVSLGGGKAVHYLCDEEAGWYPDIADIKSKITSRTKAIVVINPNNP 19- 2 Query: 180 TGAVYPREILQEIVDIARQNDLIIFSDEVYDR 211 TGA+YP+EIL++IV +AR++ LIIF+DE+YDR Sbjct: 193 TGALYPKEILEDIVALAREHQLIIFADEIYDR 224 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1178 A DNA sequence (GBSx1254) was identified in S. agalactiae <SEQ ID 3663> which encodes the amino acid sequence <SEQ ID 3664>. Analysis of this protein sequence reveals the following: TABLE-US-03558 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.75 Transmembrane 38-54 (29-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.6901(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9389> which encodes amino acid sequence <SEQ ID 9390> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 3665> which encodes the amino acid sequence <SEQ ID 3666>. Analysis of this protein sequence reveals the following: TABLE-US-03559 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.97 Transmembrane 35-51 (25-58) ----- Final Results ----- bacterial membrane --- Certainty = 0.7389(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-03560 Identities = 51/87 (58%), Positives = 63/87 (71%), Gaps = 7/87 (8%) Query: 1 MAKKPWEKKVVENNSHRKDKITRTSRGVVSSTPWITAFLSAFFVIVVAILFIVFYTSNRG 60 MAK+PWE+K+V++ + TR SR STPW+TA LS FFVI+VAILFI FYTSN G Sbjct: 1 MAKEPWEEKIVDDTIGTR---TRKSRNAFISTPWLTALLSVFFVIIVAILFIFFYTSNSG 57 Query: 61 EDRAKETSGFYGASSQKVNSSKTKKAS 87 +R ET+GFYGAS+ K KT+KAS Sbjct: 58 SNRQAETNGFYGASTHK----KTRKAS 80 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1179 A DNA sequence (GBSx1255) was identified in S. agalactiae <SEQ ID 3667> which encodes the amino acid sequence <SEQ ID 3668>. Analysis of this protein sequence reveals the following: TABLE-US-03561 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0815(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 3669> which encodes the amino acid sequence <SEQ ID 3670>. Analysis of this protein sequence reveals the following: TABLE-US-03562 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0107(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03563 Identities = 43/64 (67%), Positives = 53/64 (82%) Query: 1 MKVALIPEKCIACGLCQTYSNIFDYQDDGIVKFSDTDNLEKEIPSSDQDTVLAVKSCPTK 60 MKV++IPEKCIACGLCQTYS++FDY D+GIV FS + + I SD+D +LAVKSCPTK Sbjct: 1 MKVSIIPEKCIACGLCQTYSSLFDYHDNGIVTFSSSSETSQSICPSDKDAILAVKSCPTK 60 Query: 61 ALTI 64 ALT+ Sbjct: 61 ALTL 64 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1180 A DNA sequence (GBSx1256) was identified in S. agalactiae <SEQ ID 3671> which encodes the amino acid sequence <SEQ ID 3672>. Analysis of this protein sequence reveals the following: TABLE-US-03564 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.61 Transmembrane 47-63 (41-69) ----- Final Results ----- bacterial membrane --- Certainty = 0.5246(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03565 >GP: AAC36851 GB: L23802 pore-forming peptide [Enterococcus faecalis] Identities = 42/130 (32%), Positives = 63/130 (48%), Gaps = 9/130 (6%) Query: 7 KIRYHWQPELSWAIIYWSIAIAPIFIGLSLLYERTE---IPSQVFVLFAIFIVLVGIGFH 63 K +++WQPEL+ IIYWS +FI L L E I + V V F +F L G Sbjct: 3 KQKFYWQPELASTIIYWSCTFCILFISLILALENNGPYLISNLVMVPFFVFAYL---GIA 59 Query: 64 RYFVIEEDGYLRIVSFNFLRRTKFPIEDIAKIEVTKSSVTIKFNNNHE--RIFYMRKWPK 121- R F + E L + + R+ P+ I K+ + S+ I + E ++F M+K Sbjct: 60 RSFNMTETS-LIVRDVLWFRKKALPLSQIEKVTYNEKSIEIFSSEFKEGSKVFLMKKKTD 118- Query: 122 KYFLDALAIE 131 FL+AL I+ Sbjct: 119 SLFLEALKIK 128 A related DNA sequence was identified in S. pyogenes <SEQ ID 3673> which encodes the amino acid sequence <SEQ ID 3674>. Analysis of this protein sequence reveals the following: TABLE-US-03566 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.87 Transmembrane 47-63 (41-69) INTEGRAL Likelihood = -3.35 Transmembrane 20-36 (18-37) ----- Final Results ----- bacterial membrane --- Certainty = 0.4949(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03567 >GP: AAC36851 GB: L23802 pore-forming peptide [Enterococcus faecalis] Identities = 42/130 (32%), Positives = 70/130 (53%), Gaps = 12/130 (9%) Query: 7 KIRYHWQPELSWSIIYWSIAFAPIFVGLSLLYERTE---IPSRVFILFAIFAVLVGIGLH 63 K +++WQPEL+ +IIYWS F +F+ L L E I + V + F +FA L G+ Sbjct: 3 KQKFYWQPELASTIIYWSCTFCILFISLILALENNGPYLISNLVMVPFFVFAYL---GIA 59 Query: 64 RYF-IIENNGILRIVSFKLFGPRKLLISTITKIEVTKSTLCL---HVEDKSYLFYMRKWP 119- R F + E + I+R V + F + L +S I K+ + ++ + ++ S +F M+K Sbjct: 60 RSFNMTETSLIVRDVLW--FRKKALPLSQIEKVTYNEKSIEIFSSEFKEGSKVFLMKKKT 117- Query: 120 KKYFLDALAV 129 FL+AL + Sbjct: 118 DSLFLEALKI 127 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03568 Identities = 115/162 (70%), Positives = 132/162 (80%), Gaps = 1/162 (0%) Query: 1 MIKLFGKIRYHWQPELSWAIIYWSIAIAPIFIGLSLLYERTEIPSQVFVLFAIFIVLVGI 60 MIKLFGKIRYHWQPELSW+IIYWSIA APIF+GLSLLYERTEIPS+VF+LFAIF VLVGI Sbjct: 1 MIKLFGKIRYHWQPELSWSIIYWSIAFAPIFVGLSLLYERTEIPSRVFILFAIFAVLVGI 60 Query: 61 GFHRYFVIEEDGYLRIVSFNFLRRTKFPIEDIAKIEVTKSSVTIKFNNNHERIFYMRKWP 120- G HRYF+IE +G LRIVSF K I I KIEVTKS++ + + +FYMRKWP Sbjct: 61 GLHRYFIIENNGILRIVSFKLFGPRKLLISTITKIEVTKSTLCLHVEDK-SYLFYMRKWP 119- Query: 121 KKYFLDALAIEPTFKGEVELLDNLIKMDYFECYRYDKKALTK 162 KKYFLDALA+ P F+GEV L DN IK+DYFE Y++DKKALT+ Sbjct: 120 KKYFLDALAVNPYFQGEVILSDNFIKLDYFEVYQHDKKALTR 161 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1181 A DNA sequence (GBSx1257) was identified in S. agalactiae <SEQ ID 3675> which encodes the amino acid sequence <SEQ ID 3676>. This protein is predicted to be peptidase t (pepT). Analysis of this protein sequence reveals the following: TABLE-US-03569 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2913(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03570 >GP: AAA20627 GB: L27596 tripeptidase [Lactococcus lactis] Identities = 274/406 (67%), Positives = 334/406 (81%), Gaps = 4/406 (0%) Query: 1 MSYEKLLERFLTYVKINTRSNPNSTQTPTTQSQVDFALTVLKPEMEAIGLKDVHYLPSNG 60 M YEKLL RFL YVK+NTRS+ NST TP+TQ+ V+FA + +M+A+GLKDVHYL SNG Sbjct: 1 MKYEKLLPRFLEYVKVNTRSDENSTTTPSTQALVEFAHK-MGEDMKALGLKDVHYLESNG 59 Query: 61 YLVGTLPATSDRLRHKIGFISHMDTADFNAENITPQIVDYKGGD--IELGDSGYILSPKD 118- Y++GT+PA +D+ KIG ++H+DTADFNAE + PQI++ G+ I+LGD+ + L PKD Sbjct: 60 YVIGTIPANTDKKVRKIGLLAHLDTADFNAEGVNPQILENYDGESVIQLGDTEFTLDPKD 119- Query: 119 FPNLNNYHGQTLITTDGKTLLGADDKSGIAEIMTAMEYLAS-HPEIEHCEIRVGFGPDEE 17- 7 FPNL NY GQTL+ TDG TLLG+DDKSG+AEIMT +YL + +P+ EH EIRVGFGPDEE Sbjct: 120 FPNLKNYKGQTLVHTDGTTLLGSDDKSGVAEIMTLADYLLNINPDFEHGEIRVGFGPDEE 17- 9 Query: 178 IGIGADKFDVKDFDVDFAYTVDGGPLGELQYETFSAAGLELTFEGRNVHPGTAKNQMINA 23- 7 IG+GADKFDV DFDVDFAYTVDGGPLGELQYETFSAAG + F+G+NVHPGTAKN M+NA Sbjct: 180 IGVGADKFDVADFDVDFAYTVDGGPLGELQYETFSAAGAVIEFQGKNVHPGTAKNMMVNA 23- 9 Query: 238 LQLAMDFHSQLPENERPEQTDGYQGFYHLYDLSGTVDQAKSSYIIRDFEEVDFLKRKHLA 29- 7 LQLA+D+H+ LPE +RPE+T+G +GF+HL L GT ++A++ YIIRD EE F +RK L Sbjct: 240 LQLAIDYHNALPEFDRPEKTEGREGFFHLLKLDGTPEEARAQYIIRDHEEGKFNERKALM 29- 9 Query: 298 QDIADNMNEALQSERVKVKLYDQYYNMKKVIEKDMTPINIAKEVMEELDIKPIIEPIRGG 35- 7 Q+IAD MN L RVK + DQYYNM ++IEKDM+ I+IAK+ ME LDI PIIEPIRGG Sbjct: 300 QEIADKMNAELGQNRVKPVIKDQYYNMAQIIEKDMSIIDIAKKAMENLDIAPIIEPIRGG 35- 9 Query: 358 TDGSKISFMGIPTPNLFAGGENMHGRFEFVSLQTMEKAVDVILGIV 403 TDGSKISFMG+PTPNLFAGGENMHGRFEFVS+QTNEKAVD +L I+ Sbjct: 360 TDGSKISFMGLPTPNLFAGGENMHGRFEFVSVQTMEKAVDTLLEII 405 A related DNA sequence was identified in S. pyogenes <SEQ ID 3677> which encodes the amino acid sequence <SEQ ID 3678>. Analysis of this protein sequence reveals the following: TABLE-US-03571 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2938(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03572 Identities = 305/406 (75%), Positives = 352/406 (86%), Gaps = 1/406 (0%) Query: 1 MSYEKLLERFLTYVKINTRSNPNSTQTPTTQSQVDFALTVLKPEMEAIGLKDVHYLPSNG 60 M Y+ LL+RF+ YVK+NTRS P+S TP+T+SQ FALT+LKPEMEAIGL+DVHY P NG Sbjct: 5 MKYDNLLDRFIKYVKVNTRSVPDSETTPSTESQEAFALTILKPEMEAIGLQDVHYNPVNG 64 Query: 61 YLVGTLPATSDRLRHKIGFISHMDTADFNAENITPQIVD-YKGGDIELGDSGYILSPKDF 119- YL+GTLPA + L KIGFI+HMDTADFNAEN+ PQI+D Y+GGDI LG S Y L PK F Sbjct: 65 YLIGTLPANNPTLTRKIGFIAHMDTADFNAENVNPQIIDNYQGGDITLGSSNYKLDPKAF 124- Query: 120 PNLNNYHGQTLITTDGKTLLGADDKSGIAEIMTAMEYLASHPEIEHCEIRVGFGPDEEIG 17- 9 PNLNNY GQTLITTDG TLLGADDKSGIAEIMTA+E+L S P+IEHC+I+V FGPDEEIG Sbjct: 125 PNLNNYIGQTLITTDGTTLLGADDKSGIAEIMTAIEFLTSQPQIEHCDIKVAFGPDEEIG 18- 4 Query: 180 IGADKFDVKDFDVDFAYTVDGGPLGELQYETFSAAGLELTFEGRNVHPGTAKNQMINALQ 23- 9 +GADKF+V DF+VDFAYT+DGGPLGELQYETFSAA LE+TF GRNVHPGTAK+QMINAL+ Sbjct: 185 VGADKFEVADFEVDFAYTMDGGPLGELQYETFSAAALEVTFLGRNVHPGTAKDQMINALE 24- 4 Query: 240 LAMDFHSQLPENERPEQTDGYQGFYHLYDLSGTVDQAKSSYIIRDFEEVDFLKRKHLAQD 29- 9 LA+DFH +LP +RPE TDGYQGFYHL L+GTV++A++SYIIRDFEE F RK ++ Sbjct: 245 LAIDFHEKLPAKDRPEYTDGYQGFYHLTGLTGTVEEARASYIIRDFEEASFEARKVKVEN 30- 4 Query: 300 IADNMNEALQSERVKVKLYDQYYNMKKVIEKDMTPINIAKEVMEELDIKPIIEPIRGGTD 35- 9 IA +MN L ++RV V+L DQYYNMKKVIEKDMT I +AKEVMEEL IKP+IEPIRGGTD Sbjct: 305 IAQSMNAQLGTKRVLVELNDQYYNMKKVIEKDMTAIELAKEVMEELAIKPVIEPIRGGTD 36- 4 Query: 360 GSKISFMGIPTPNLFAGGENMHGRFEFVSLQTMEKAVDVILGIVAK 405 GSKISFMGIPTPN+FAGGENMHGRFEFVSLQTME+AVDVI+G+V K Sbjct: 365 GSKISFMGIPTPNIFAGGENMHGRFEFVSLQTMERAVDVIIGLVCK 410 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1182 A DNA sequence (GBSx1258) was identified in S. agalactiae <SEQ ID 3679> which encodes the amino acid sequence <SEQ ID 3680>. Analysis of this protein sequence reveals the following: TABLE-US-03573 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.26 Transmembrane 481-497 (477-508) INTEGRAL Likelihood = -9.45 Transmembrane 510-526 (506-534) INTEGRAL Likelihood = -7.96 Transmembrane 316-332 (310-334) INTEGRAL Likelihood = -7.54 Transmembrane 354-370 (351-373) INTEGRAL Likelihood = -7.11 Transmembrane 385-401 (383-409) INTEGRAL Likelihood = -6.58 Transmembrane 215-231 (211-233) INTEGRAL Likelihood = -6.48 Transmembrane 71-87 (69-91) INTEGRAL Likelihood = -6.32 Transmembrane 110-126 (106-133) INTEGRAL Likelihood = -5.10 Transmembrane 446-462 (443-465) INTEGRAL Likelihood = -3.29 Transmembrane 418-434 (418-435) INTEGRAL Likelihood = -2.55 Transmembrane 263-279 (263-279) INTEGRAL Likelihood = -2.02 Transmembrane 142-158 (141-159) INTEGRAL Likelihood = -1.70 Transmembrane 184-200 (184-200) ----- Final Results ----- bacterial membrane --- Certainty = 0.5904(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8747> which encodes amino acid sequence <SEQ ID 8748> was also identified. Analysis of this protein sequence reveals the following:

TABLE-US-03574 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: -10.58 GvH: Signal Score (-7.5): -1.1 Possible site: 32 >>> Seems to have no N-terminal signal sequence ALOM program count: 13 value: -12.26 threshold: 0.0 INTEGRAL Likelihood = -12.26 Transmembrane 470-486 (466-497) INTEGRAL Likelihood = -9.45 Transmembrane 499-515 (495-523) INTEGRAL Likelihood = -7.96 Transmembrane 305-321 (299-323) INTEGRAL Likelihood = -7.54 Transmembrane 343-359 (340-362) INTEGRAL Likelihood = -7.11 Transmembrane 374-390 (372-398) INTEGRAL Likelihood = -6.58 Transmembrane 204-220 (200-222) INTEGRAL Likelihood = -6.48 Transmembrane 60-76 (58-80) INTEGRAL Likelihood = -6.32 Transmembrane 99-115 (95-122) INTEGRAL Likelihood = -5.10 Transmembrane 435-451 (432-454) INTEGRAL Likelihood = -3.29 Transmembrane 407-423 (407-424) INTEGRAL Likelihood = -2.55 Transmembrane 252-268 (252-268) INTEGRAL Likelihood = -2.02 Transmembrane 131-147 (130-148) INTEGRAL Likelihood = -1.70 Transmembrane 173-189 (173-189) PERIPHERAL Likelihood = 1.43 21 modified ALOM score: 2.95 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5904(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03575 >GP: AAC00276 GB: AF008220 YtgP [Bacillus subtilis] Identities = 178/545 (32%), Positives = 302/545 (54%), Gaps 26/545 (4%) Query: 24 QMVKGTAWLTAGNFISRLLGAIYIIPWYAWMGKHAAEANALFGMGYEIYALFLLISTVGI 83 - ++++GT LT G +ISR+LG +Y+IP+ +G A ALF GY Y LFL I+T+G Sbjct: 4 KLLRGTFVLTLGTYISRILGMVYLIPFSIMVG---ATGGALFQYGYNQYTLFLNIATMGF 60 Query: 84 PVAVAKQVSKYNTLGKEEMSIYLVRKILQFMLILGGIFALIMYIGSPLFASLSKGGQE-- 141- P AV+K VSKYN+ G E S +++ + ML+ G I I+Y+ +P+FA +S GG++ Sbjct: 61 PAAVSKFVSKYNSKGDYETSRKMLKAGMSVMLVTGMIAFFILYLSAPMFAEISLGGKDNN 120- Query: 142 ------LVPILRSLTLAVLVFPSMSVLRGFFQGFNNLKPYAISQVAEQIIRVIWMLLTAF 19- 5 +V ++R ++LA+LV P MS++RGFFQG + P A+SQV EQI+R+I++L F Sbjct: 121 GLTIDHVVYVIRMVSLALLVVPIMSLVRGFFQGHQMMGPTAVSQVVEQIVRIIFLLSATF 18- 0 Query: 196 YIMRLGSGDYIAAVTQSTFAAFVGMFASIAVLLYFLW--RYNMLSALIGKTPKHIKLDTK 25- 3 I+++ +G + AV +TFAA +G F + V+LY W R L A++ T L K Sbjct: 181 LILKVFNGGLVIAVGYATFAALIGAFGGL-VVLYIYWNKRKGSLLAMMPNTGPTANLSYK 23- 9 Query: 254 EILIETIKEAIPFIITGAAIQIFKLIDQFSFGNTM--ALFTNYSSEELRVMFAYFSSNPG 31- 1 ++ E A P++ G AI ++ ID +F M A S + L ++ Y Sbjct: 240 KMFFELFSYAAPYVFVGLAIPLYNYIDTNTFNKAMIEAGHQAISQDMLAILTLYVQ---- 29- 5 Query: 312 KVTMILIAVATAIAGVGIPLLTENFVKNDKKAAARLVVNNLQMLLMFLLPAVAGSVILAK 37- 1 K+ MI +++ATA IP +TE+F + K + + +Q +L ++PAV G +L+ Sbjct: 296 KLVMIPVSLATAFGLTLIPTITESFTSGNYKLLNQQINQTMQTILFLIIPAVVGISLLSG 35- 5 Query: 372 PLYTVFYGL----PQGQALGLFVISLIQTIILSIYTVLAPMLQALFENRKAIIYFLYGLV 42- 7 P YT FYG P+ A L S + I+ S++TV A +LQ + + + A++ + G+V Sbjct: 356 PTYTFFYGSESLHPELGANILLWYSPV-AILFSLFTVNAAILQGINKQKFAVVSLVIGVV 41- 4 Query: 428 AKVILQLPSIFLFHAYGPLFSTTVALCIPVILMYLKIHEITGFKRQAIRRTSALVLILTL 48- 7 K++L +P I L A G + + T + ++ ++ I G+ + + + + L+L+L+ Sbjct: 415 IKLVLNVPLIKLMQADGAILATALGYIASLLYGFIMIKRHAGYSYKILVKRTVLMLVLSA 47- 4 Query: 488 LMSFIISMIIWLMNLVI-VPDSRLVSLVYIIVIGAIGLGVYGFMALATHLLDKMIGSRAQ 54- 6 +M + ++ W++ I D ++ + + +++ A+G VY + L K++G R Sbjct: 475 IMGIAVKIVQWVLGFFISYQDGQHQAAIVVVIAAAVGGAVYLYCGYRLGFLQKILGRRLP 53- 4 Query: 547 DLRRK 551 RK Sbjct: 535 GFFRK 539 A related DNA sequence was identified in S. pyogenes <SEQ ID 3681> which encodes the amino acid sequence <SEQ ID 3682>. Analysis of this protein sequence reveals the following: TABLE-US-03576 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.60 Transmembrane 468-484 (466-493) INTEGRAL Likelihood = -8.39 Transmembrane 305-321 (299-323) INTEGRAL Likelihood = -7.75 Transmembrane 343-359 (340-362) INTEGRAL Likelihood = -6.58 Transmembrane 374-390 (373-398) INTEGRAL Likelihood = -4.25 Transmembrane 138-154 (137-157) INTEGRAL Likelihood = -3.45 Transmembrane 100-116 (98-122) INTEGRAL Likelihood = -3.40 Transmembrane 415-431 (410-432) INTEGRAL Likelihood = -3.35 Transmembrane 499-515 (499-519) INTEGRAL Likelihood = -2.60 Transmembrane 433-449 (432-451) INTEGRAL Likelihood = -2.50 Transmembrane 173-189 (173-190) INTEGRAL Likelihood = -0.59 Transmembrane 201-217 (201-220) ----- Final Results ----- bacterial membrane --- Certainty = 0.4439(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03577 >GP: AAC00276 GB: AF008220 YtgP [Bacillus subtilis] Identities = 169/536 (31%), Positives = 295/536 (54%), Gaps = 24/536 (4%) Query: 14 MVQGAAWSTAGNFISRLLGVLYIIPWYIWMGQYAIQANALFNMGYNVYAYFLLISTTGLN 73 - +++G T G +ISR+LG++Y+IP+ I +G ALF GYN Y FL I+T G Sbjct: 5 LLRGTFVLTLGTYISRILGMVYLIPFSIMVGA---TGGALFQYGYNQYTLFLNIATMGFP 61 Query: 74 VAIAKQVAKYNSMGQTEHSYQLIRSTLKLMLGLGLIFSAIMYLGSPLFASLS-GGDDT-- 130- A++K V+KYNS G E S ++++++ + ML G+I I+YL +P+FA +S GG D Sbjct: 62 AAVSKFVSKYNSKGDYETSRKMLKAGMSVMLVTGMIAFFILYLSAPMFAEISLGGKDNNG 121- Query: 131 -----LVPIMHSLSLAVFIFPVMSVIRGIFQGHNNIKPYAVSQIAEQLIRVIWMLLTTFF 18- 5 +V ++ +SLA+ + P+MS++RG FQGH + P AVSQ+ EQ++R+I++L TF Sbjct: 122 LTIDHVVYVIRMVSLALLVVPIMSLVRGFFQGHQMMGPTAVSQVVEQIVRIIFLLSATFL 18- 1 Query: 186 IMKLGSGDYASAVTQSTFAAFIGMVASMGVLGYYLW--KQGLLAAIFSKPDHTVSIDIKG 24- 3 I+K+ +G AV +TFAA IG + VL Y W ++G L A+ T ++ K Sbjct: 182 ILKVFNGGLVIAVGYATFAALIGAFGGLVVL-YIYWNKRKGSLLAMMPNTGPTANLSYKK 24- 0 Query: 244 LLLETLKESIPFIVTGSAIQAFQLIDQWTFVNTMTLFTDYSRSQ--LLVLFGYFNANPAK 30- 1 + E + P++ G AI + ID TF M + SQ L +L Y K Sbjct: 241 MFFELFSYAAPYVFVGLAIPLYNYIDTNTFNKAMIEAGHQAISQDMLAILTLYVQ----K 29- 6 Query: 302 ITMVLIAVAASIGGVGIALLTENYVKKDMKAAARLIINNIEMLVMFLLPALTGAIILARP 36- 1 + M+ +++A + G I +TE++ + K + I ++ ++ ++PA+ G +L+ P Sbjct: 297 LVMIPVSLATAFGLTLIPTITESFTSGNYKLLNQQINQTMQTILFLIIPAVVGISLLSGP 35- 6 Query: 362 LYSVFYGASE---ERAIHLFVAVLFQTLLLALYTLFSPMLQALFENRKAIYYFAYGILIK 41- 8 Y+ FYG+ E ++ + +L +L+T+ + +LQ + + + A+ G++IK Sbjct: 357 TYTFFYGSESLHPELGANILLWYSPVAILFSLFTVNAAILQGINKQKFAVVSLVIGVVIK 41- 6 Query: 419 LVLQIPLIYLLHAYGPLLATTIALVVPIYLMYRRLYQVTHFNRKLLQKRLLLTLIETLLM 47- 8 LVL +PLI L+ A G +LAT + + + + + + ++ K+L KR +L L+ + +M Sbjct: 417 LVLNVPLIKLMQADGAILATALGYIASLLYGFIMIKRHAGYSYKILVKRTVLMLVLSAIM 47- 6 Query: 479 GLVVFVANWLLGYAFK-PTGRLTSLLYLLIIGGLGMTVYTALTLLTHQLDKLIGSK 533 G+ V + W+LG+ G++ + + ++I +G VY L K++G + Sbjct: 477 GIAVKIVQWVLGFFISYQDGQMQAAIVVVIAAAVGGAVYLYCGYRLGFLQKILGRR 532 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03578 dentities = 320/541 (59%), Positives = 431/541 (79%) IQuery: 12 MSQKTTKVSQQEQMVKGTAWLTAGNFISRLLGAIYIIPWYAWMGKHAAEANALFGMGYEI 71- MS + +++Q+E MV+G AW TAGNFISRLLG +YIIPWY WMG++A +ANALF MGY + Sbjct: 1 MSTEKKQLTQEELMVQGAAWSTAGNFISRLLGVLYIIPWYIWMGQYAIQANALFNMGYNV 60 Query: 72 YALFLLISTVGIPVAVAKQVSKYNTLGKEEMSIYLVRKILQFMLILGGIFALIMYIGSPL 131- YA FLLIST G+ VA+AKQV+KYN++G+ E S L+R L+ ML LG IF+ IMY+GSPL Sbjct: 61 YAYFLLISTTGLNVAIAKQVAKYNSMGQTEHSYQLIRSTLKLMLGLGLIFSAIMYLGSPL 120- Query: 132 FASLSKGGQELVPILRSLTLAVLVFPSMSVLRGFFQGFNNLKPYAISQVAEQIIRVIWML 19- 1 FASLS G LVPI+ SL+LAV +FP MSV+RG FQG NN+KPYA+SQ+AEQ+IRVIWML Sbjct: 121 FASLSGGDDTLVPIMHSLSLAVFIFPVMSVIRGIFQGHNNIKPYAVSQIAEQLIRVIWML 18- 0 Query: 192 LTAFYIMRLGSGDYIAAVTQSTFAAFVGMFASIAVLLYFLWRYNMLSALIGKTPKHIKLD 25- 1 LT F+IM+LGSGDY +AVTQSTFAAF+GM AS+ VL Y+LW+ +L+A+ K + +D Sbjct: 181 LTTFFIMKLGSGDYASAVTQSTFAAFIGMVASMGVLGYYLWKQGLLAAIFSKPDHTVSID 24- 0 Query: 252 TKEILIETIKEAIPFIITGAAIQIFKLIDQFSFGNTMALFTNYSSEELRVMFAYFSSNPG 31- 1 K +L+ET+KE+IPFI+TG+AIQ F+LIDQ++F NTM LFT+YS +L V+F YF++NP Sbjct: 241 IKGLLLETLKESIPFIVTGSAIQAFQLIDQWTFVNTMTLFTDYSRSQLLVLFGYFNANPA 30- 0 Query: 312 KVTMILIAVATAIAGVGIPLLTENFVKNDKKAAARLVVNNLQMLLMFLLPAVAGSVILAK 37- 1 K+TM+LIAVA +I GVGI LLTEN+VK D KAAARL++NN++ML+MFLLPA+ G++ILA+ Sbjct: 301 KITMVLIAVAASIGGVGIALLTENYVKKDMKAAARLIINNIEMLVMFLLPALTGAIILAR 36- 0 Query: 372 PLYTVFYGLPQGQALGLFVISLIQTIILSIYTVLAPMLQALFENRKAIIYFLYGLVAKVI 43- 1 PLY+VFYG + +A+ LFV L QT++L++YT+ +PMLQALFENRKAI YF YG++ K++ Sbjct: 361 PLYSVFYGASEERAIHLFVAVLFQTLLLALYTLFSPMLQALFENRKAIYYFAYGILIKLV 42- 0 Query: 432 LQLPSIFLFHAYGPLFSTTVALCIPVILMYLKIHEITGFKRQAIRRTSALVLILTLLMSF 49- 1 LQ+P I+L HAYGPL +TT+AL +P+ LMY +++++T F R+ +++ L LI TLLM Sbjct: 421 LQIPLIYLLHAYGPLLATTIALVVPIYLMYRRLYQVTHFNRKLLQKRLLLTLIETLLMGL 48- 0 Query: 492 IISMIIWLMNLVIVPDSRLVSLVYIIVIGAIGLGVYGFMALATHLLDKMIGSRAQDLRRKL 5- 52 ++ + WL+ P RL SL+Y+++IG +G+ VY + L TH LDK+IGS+A LR+KL Sbjct: 481 VVFVANWLLGYAFKPTGRLTSLLYLLIIGGLGMTVYTALTLLTHQLDKLIGSKASRLRQKL 5- 41 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1183 A DNA sequence (GBSx1259) was identified in S. agalactiae <SEQ ID 3683> which encodes the amino acid sequence <SEQ ID 3684>. Analysis of this protein sequence reveals the following: TABLE-US-03579 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4104(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03580 >GP: BAB06290 GB: AP001515 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate ligase [Bacillus halodurans] Identities = 153/468 (32%), Positives = 237/468 (49%), Gaps = 23/468 (4%) Query: 33 NVTFNALSYDSRQISSDTLFFA-KGATFK-KEYLDSAITAGLSFYVSETDYGADIPVILV 90 - N +++ DSR++ LFF KG T +Y A++ G VSE +PV++V Sbjct: 21 NPDIHSIHMDSREVVEGGLFFCIKGYTVDGHDYAQQAVSNGAVAVVSERPLELSVPVVVV 80 Query: 91 NDIKKAMSLISMSFYNNPQNKLKLLAFTGTKGKTTAAYFAYHMLKVNHR-PAMLSTMNTT 149- D ++AM+ ++ FY P N L+L+ TGT GKTT + +++ + ++ TM T Sbjct: 81 RDSRRAMAQVATKFYGEPTNDLQLIGVTGTNGKTTITHLIEKIMQDQGKMTGLIGTMYTK 140- Query: 150 LDGKSFFKSHLTTPESLDLFRMMATAVENQMTHLIMEVSSQAYLTKRVYGLTFDVGVFLN 20- 9 + G ++ TTPESL L R A ++ +T +MEVSS A + RV G FDV VF N Sbjct: 141 I-GHELKETKNTTPESLVLQRTFADMKKSGVTTAMMEVSSHALQSGRVRGCDFDVAVFSN 19- 9 Query: 210 ISPDHIGPIEHPTFEDYFFHKRLLME------NSNAVVVN----SQMDHFNIVKEQVEYI 25- 9 ++PDH+ H T E Y F K LL V+N + D + QV Sbjct: 200 LTPDHLD--YHGTMERYKFAKGLLFAQLGNTYQGKVAVLNADDPASADFAEMTIAQVVTY 25- 7 Query: 260 PHDFYGDY-SENVITESKAFSFHVKGKLEN-TYDIKLIGKFNQENAIAAGLACLRLGVSI 31- 7 + D+ +ENV S +F + E I LIGKF+ N +AA A GV + Sbjct: 258 GIENEADFQAENVRITSTGTTFELAAFEERMELSIHLIGKFSVYNVLAAAAAAYVSGVPL 31- 7 Query: 318 EDIKNGIAQTT-VPGRMEVLTQTNGAKIFVDYAHNGDSLKKLLAVVEEHQKGDIILVLGA 37- 6 ++IK + + V GR E + + VDYAH DSL+ +L V E KGD+ +V+G Sbjct: 318 QEIKKSLEEVKGVAGRFETVKHDQPFTVIVDYAHTPDSLENVLKTVGELAKGDVRVVVGC 37- 7 Query: 377 PGNKGQSRRKDFGDVINQHPNLQVILTADDPNFEDPLVISQEIASHINRPVTIII-DREE 43- 5 G++ +++R ++ N Q I T+D+P E+P+ I +++ ++I DR+E Sbjct: 378 GGDRDKTKRPVMAEIATTFAN-QAIFTSDNPRSEEPMDILRDMEQGAKGDSYLMIEDRKE 43- 6 Query: 436 AIANASTLTNCKLDAIIIAGKGADAYQIIKGNRDNYSGDLEVAKKYLK 483 AI A L + D I+IAGKG + YQ + ++ D VA++ +K Sbjct: 437 AIFKAIELAK-EDDIIVIAGKGHETYQQFRDRTIDFD-DRIVAQQAIK 482 A related DNA sequence was identified in S. pyogenes <SEQ ID 3685> which encodes the amino acid sequence <SEQ ID 3686>. Analysis of this protein sequence reveals the following: TABLE-US-03581 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4717(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03582 Identities = 350/482 (72%), Positives = 399/482 (82%), Gaps = 1/482 (0%) Query: 1 MITIDKILEILKNDHNFREILFHEHYYYNWTQNVTFNALSYDSRQISSDTLFFAKGATFK 60 MITI+++L+ILK DHNFRE+L + Y+Y++ Q +F LSYDSRQ+ TLFFAKGATFK Sbjct: 1 MITIEQLLDILKKDHNFREVLDADGYHYHY-QGFSFERLSYDSRQVDGKTLFFAKGATFK 59 Query: 61 KEYLDSAITAGLSFYVSETDYGADIPVILVNDIKKAMSLISMSFYNNPQNKLKLLAFTGT 120- +YL AIT GL Y+SE DY IPV+LV DIKKAMSLI+M+FY NPQ KLKLLAFTGT Sbjct: 60 ADYLKEAITNGLQLYISEVDYELGIPVVLVTDIKKAMSLIAMAFYGNPQEKLKLLAFTGT 119- Query: 121 KGKTTAAYFAYHMLKVNHRPAMLSTMNTTLDGKSFFKSHLTTPESLDLFRMMATAVENQM 18- 0 KGKTTAAYFAYHMLK +++PAM STMNTTLDGK+FFKS LTTPESLDLF MMA V N M Sbjct: 120 KGKTTAAYFAYHMLKESYKPAMFSTMNTTLDGKTFFKSQLTTPESLDLFAMMAECVTNGM 17- 9 Query: 181 THLIMEVSSQAYLTKRVYGLTFDVGVFLNISPDHIGPIEHPTFEDYFFHKRLLMENSNAV 24- 0 THLIMEVSSQAYL RVYGLTFDVGVFLNISPDHIGPIEHPTFEDYF+HKRLLMENS AV Sbjct: 180 THLIMEVSSQAYLVDRVYGLTFDVGVFLNISPDHIGPIEHPTFEDYFYHKRLLMENSRAV 23- 9 Query: 241 VVNSQMDHFNIVKEQVEYIPHDFYGDYSENVITESKAFSFHVKGKLENTYDIKLIGKFNQ 30- 0 V+NS MDHF+ + +QV H FYG S+N IT S+AFSF KG+L YDI+LIG FNQ Sbjct: 240 VINSGMDHFSFLADQVADQEHVFYGPLSDNQITTSQAFSFEAKGQLAGHYDIQLIGHFNQ 29- 9 Query: 301 ENAIAAGLACLRLGVSIEDIKNGIAQTTVPGRMEVLTQTNGAKIFVDYAHNGDSLKKLLA 36- 0 ENA+AAGLACLRLG S+ DI+ GIA+T VPGRMEVLT TN AK+FVDYAHNGDSL+KLL+ Sbjct: 300 ENAMAAGLACLRLGASLADIQKGIAKTRVPGRMEVLTMTNHAKVFVDYAHNGDSLEKLLS 35- 9 Query: 361 VVEEHQKGDIILVLGAPGNKGQSRRKDFGDVINQHPNLQVILTADDPNFEDPLVISQEIA 42- 0 VVEEHQ G ++L+LGAPGNKG+SRR DFG VI+QHPNL VILTADDPNFEDP IS+EIA Sbjct: 360 VVEEHQTGKLMLILGAPGNKGESRRADFGRVIHQHPNLTVILTADDPNFEDPEDISKEIA 41- 9 Query: 421 SHINRPVTIIIDREEAIANASTLTNCKLDAIIIAGKGADAYQIIKGNRDNYSGDLEVAKKYL - 482 SHI RPV II DRE+AI A +L DA+IIAGKGADAYQI+KG + Y+GDL +AK YL Sbjct: 420 SHIARPVEIISDREQAIQKAMSLCQGAKDAVIIAGKGADAYQIVKGQQVAYAGDLAIAKHYL - 481 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1184 A DNA sequence (GBSx1260) was identified in S. agalactiae <SEQ ID 3687> which encodes the amino acid sequence <SEQ ID 3688>. Analysis of this protein sequence reveals the following: TABLE-US-03583 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1421(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1185 A DNA sequence (GBSx1261) was identified in S. agalactiae <SEQ ID 3689> which encodes the amino acid sequence <SEQ ID 3690>. This protein is predicted to be FhuA (fepC). Analysis of this protein sequence reveals the following: TABLE-US-03584 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2785(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9975> which encodes amino acid sequence <SEQ ID 9976> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03585 >GP: AAF98153 GB: AF251216 FhuC [Staphylococcus aureus] Identities = 141/259 (54%), Positives = 193/259 (74%) Query: 7 MSHIKAENIIVSYDQKEIINNLSLSILNQKITTIIGANGCGKSTLLKALTRIHKIKDGTI 66 M+ + + + + Y IIN L + I + K+T+IIG NGCGKSTLLKAL+R+ +K+G + Sbjct: 1 MNRLHGQQVKIGYGDNTIINKLDVEIPDGKVTSIIGPNGCGKSTLLKALSRLLAVKEGEV 60 Query: 67 TIDGHDIAHLPTKEIAKKIALLPQVLEATEGITVYELISYGRFPHQKYLGNLTNDDRSKI 126- +DG +I TKEIAKKIA+LPQ E +G+TV EL+SYGRFPHQK G LT +D+ +I Sbjct: 61 FLDGENIHTQSTKEIAKKIAILPQSPEVADGLTVGELVSYGRFPHQKGFGRLTAEDKKEI 120- Query: 127 HWAMEMTNVAQFANRDVDDLSGGQRQKVWIAMALAQDTDTIFLDEPTTYLDMNHQLEVLE 18- 6 WAME+T F +R ++DLSGGQRQ+VWIAMALAQ TD IFLDEPTTYLD+ HQLE+LE Sbjct: 121 DWAMEVTGTDTFRHRSINDLSGGQRQRVWIAMALAQRTDIIFLDEPTTYLDICHQLEILE 18- 0 Query: 187 LLKKLNDETQKTIIMVLHDLNLSARYSDYLVAMKTGKIIYEGSPSQIMTKDIIKDIFKID 24- 6 L++KLN E TI+MVLHD+N +R+SD+L+AMK G II GS ++T++I++ +F ID Sbjct: 181 LVQKLNQEQGCTIVMVLHDINQAIRFSDHLIAMKEGDIIATGSTEDVLTQEILEKVFNID 24- 0 Query: 247 AHIIQDPISKQPVLLSYQL 265 + +DP + +P+L++Y L Sbjct: 241 VVLSKDPKTGKPLLVTYDL 259 A related DNA sequence was identified in S. pyogenes <SEQ ID 1929> which encodes the amino acid sequence <SEQ ID 1930>. Analysis of this protein sequence reveals the following:

TABLE-US-03586 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2970(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03587 Identities = 166/259 (64%), Positives = 208/259 (80%) Query: 7 MSHIKAENIIVSYDQKEIINNLSLSILNQKITTIIGANGCGKSTLLKALTRIHKIKDGTI 66 M+ I AE++ ++Y+Q+ II+ LS I KITTIIGANGCGKS+LLKALTR+ K G + Sbjct: 1 MTTISAEDLTIAYEQRTIIDKLSFYIPEGKITTIIGANGCGKSSLLKALTRLLPPKQGVV 60 Query: 67 TIDGHDIAHLPTKEIAKKIALLPQVLEATEGITVYELISYGRFPHQKYLGNLTNDDRSKI 126- ++G +IA L TKE+AKK+ALLPQV EAT GITVYEL+SYGRFPHQ Y GNL+ D+ I Sbjct: 61 YLNGQNIATLETKEVAKKLALLPQVQEATNGITVYELVSYGRFPHQSYFGNLSPADKKAI 120- Query: 127 HWAMEMTNVAQFANRDVDDLSGGQRQKVWIAMALAQDTDTIFLDEPTTYLDMNHQLEVLE 18- 6 HWAM+ TNV +A++ VD LSGGQRQ+VW+AMALAQ TDTIFLDEPTTYLD+NHQLE+LE Sbjct: 121 HWAMQATNVMAYADQPVDALSGGQRQRVWLAMALAQGTDTIFLDEPTTYLDLNHQLEILE 18- 0 Query: 187 LLKKLNDETQKTIIMVLHDLNLSARYSDYLVAMKTGKIIYEGSPSQIMTKDIIKDIFKID 24- 6 L+K LN + KTI+MVLHDLNLSARYSD+L+AMK GKI Y G+ + +MT II+DIF+I Sbjct: 181 LVKSLNKDAGKTIVMVLHDLNLSARYSDHLIAMKHGKIHYTGTIADVMTSPIIQDIFQIK 24- 0 Query: 247 AHIIQDPISKQPVLLSYQL 265 ++ DPI P++L+YQL Sbjct: 241 PVLVDDPIHNCPIVLTYQL 259 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1186 A DNA sequence (GBSx1262) was identified in S. agalactiae <SEQ ID 3691> which encodes the amino acid sequence <SEQ ID 3692>. This protein is predicted to be ferrichrome ABC transporter. Analysis of this protein sequence reveals the following: TABLE-US-03588 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03589 >GP: BAB07609 GB: AP001520 ferrichrome ABC transporter (ferrichrome-binding protein) [Bacillus halodurans] Identities = 94/301 (31%), Positives = 177/301 (58%), Gaps = 11/301 (3%) Query: 6 IIVLTLLTFFLV---SCGQQTKQESTKTTISK--MPKIEGFTYYGKIPENPKKVINFTYS 60 +++LT+L F L+ +CG T E S+ M E T ++P NP++V+ Sbjct: 7 LLLLTMLLFALLVVAACGSNTDAEQADELESEDGMITYESETGPIEVPANPQRVV--ALG 64 Query: 61 YTGYLLKLGVNVSSYSLDLEKDSPVFGKQLKEAKKLTADDTEAIAAQKPDLIMVFDQDPN 120- +TG +L L VNV K++P + + L++ +++ ++ E I PDLI+ + N Sbjct: 65 FTGNILALDVNVVGVDT-WSKNNPNYEQLLQDVTEVSEENLEQIMELDPDLIIAYSTVQN 123- Query: 121 INTLKKIAPTLVIKYGAQNYLDMMPALGKVFGKEKEANQWVSQWKTKTLAVKKDLHHILK 18- 0 L++IAPT++ Y +YL+ +GK+ KE+EA WV +K + +++ + Sbjct: 124 AEQLQEIAPTVLYTYNNLDYLEQHVEIGKLLNKEEEAQAWVDDFKARAEQAGEEIKEKIG 18- 3 Query: 181 PNTTFTIMDFYDKNIYLYGNNFGRGGELIYDSLGYAAPEKVKKDVFKKGWFTVSQEAIGD 24- 0 + T ++++ ++ +Y++GNN+GRG E++Y ++ A PE+V++ G++ +S EA+ + Sbjct: 184 EDATVSVIETFEDQLYVFGNNWGRGTEILYQTMDLAMPERVEEMALADGYYALSFEALPE 24- 3 Query: 241 YVGDYALVNINKTTKKAASSLKESDVWKNLPAVKKGHIIESNYDVFYFSDPLSLEAQLKSF 3- 0 + GDY +++ N +A +S +E++ ++++PAV+ G + E+N FYF+DPLSLE QL+ F Sbjct: 244 FAGDYIILSKN---DEADNSFQETNTYQSIPAVQNGQVFEANAKEFYFNDPLSLELQLEFF 3- 01 A related DNA sequence was identified in S. pyogenes <SEQ ID 3693> which encodes the amino acid sequence <SEQ ID 3694>. Analysis of this protein sequence reveals the following: TABLE-US-03590 Possible site: 19 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03591 >GP: BAB07609 GB: AP001520 ferrichrome ABC transporter (ferrichrome-binding protein) [Bacillus halodurans] Identities = 112/306 (36%), Positives = 178/306 (57%), Gaps = 3/306 (0%) Query: 2 KKLTLLLTLCLTTITLIACGNQATNHSNTASKSLSPMPQIAGVTYYGDIPKQPKRVVSLA 61 K L LL L + + ACG+ +S M T ++P P+RVV+L Sbjct: 5 KHLLLLTMLLFALLVVAACGSNTDAEQADELESEDGMITYESETGPIEVPANPQRVVALG 64 Query: 62 STYTGYLKKLDMNLVGVTSYDKKNPILAKTVKKAKQVAATDLEAVTTLKPDLIVVGSTEE 121- +TG + LD+N+VGV ++ K NP + ++ +V+ +LE + L PDLI+ ST + Sbjct: 65 --FTGNILALDVNVVGVDTWSKNNPNYEQLLQDVTEVSEENLEQIMELDPDLIIAYSTVQ 122- Query: 122 NIKQLAEIAPVISIEYRKRDYLQVLSDFGRIFNKEDKAKKWLKDWKTKTAAYEKEVKAVT 18- 1 N +QL EIAP + Y DYL+ + G++ NKE++A+ W+ D+K + +E+K Sbjct: 123 NAEQLQEIAPTVLYTYNNLDYLEQHVEIGKLLNKEEEAQAWVDDFKARAEQAGEEIKEKI 18- 2 Query: 182 GDKATFTIMGLYEKDVYLFGKDWGRGGEIIHQAFHYDAPEKVKTEVFKQGYLSLSQEVLP 24- 1 G+ AT +++ +E +Y+FG +WGRG EI++Q PE+V+ GY +LS E LP Sbjct: 183 GEDATVSVIETFEDQLYVFGNNWGRGTEILYQTMDLAMPERVEEMALADGYYALSFEALP 24- 2 Query: 242 DYIGDYVVVAAEDDKTGSALYESKLWQSIPAVKKHHVIKVNANVFYFTDPLSLEYQLETL 30- 1 ++ GDY+++ +++D+ ++ E+ +QSIPAV+ V + NA FYF DPLSLE QLE Sbjct: 243 EFAGDYIIL-SKNDEADNSFQETNTYQSIPAVQNGQVFEANAKEFYFNDPLSLELQLEFF 30- 1 Query: 302 REAILS 307 +E LS Sbjct: 302 KEHFLS 307 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03592 Identities = 140/316 (44%), Positives = 212/316 (66%), Gaps = 12/316 (3%) Query: 1 MKKIGIIV-LTLLTFFLVSCGQQTKQESTKTT--ISKMPKIEGFTYYGKIPENPKKVINF 57 MKK+ +++ L L T L++CG Q S + +S MP+I G TYYG IP+ PK+V++ Sbjct: 1 MKKLTLLLTLCLTTITLIACGNQATNHSNTASKSLSPMPQIAGVTYYGDIPKQPKRVVSL 60 Query: 58 TYSYTGYLLKLGVN---VSSYSLDLEKDSPVFGKQLKEAKKLTADDTEAIAAQKPDLIMV 114- +YTGYL KL +N V+SY +K +P+ K +K+AK++ A D EA+ KPDLI+V Sbjct: 61 ASTYTGYLKKLDMNLVGVTSY----DKKNPILAKTVKKAKQVAATDLEAVTTLKPDLIVV 116- Query: 115 FDQDPNINTLKKIAPTLVIKYGAQNYLDMMPALGKVFGKEKEANQWVSQWKTKTLAVKKD 17- 4 + NI L +IAP + I+Y ++YL ++ G++F KE +A +W+ WKTKT A +K+ Sbjct: 117 GSTEENIKQLAEIAPVISIEYRKRDYLQVLSDFGRIFNKEDKAKKWLKDWKTKTAAYEKE 17- 6 Query: 175 LHHILKPNTTFTIMDFYDKNIYLYGNNFGRGGELIYDSLGYAAPEKVKKDVFKKGWFTVS 23- 4 + + TFTIM Y+K++YL+G ++GRGGE+I+ + Y APEKVK +VFK+G+ ++S Sbjct: 177 VKAVTGDKATFTIMGLYEKDVYLFGKDWGRGGEIIHQAFHYDAPEKVKTEVFKQGYLSLS 23- 6 Query: 235 QEAIGDYVGDYALVNINKTTKKAASSLKESDVWKNLPAVKKGHIIESNYDVFYFSDPLSL 29- 4 QE + DY+GDY +V K S+L ES +W+++PAVKK H+I+ N +VFYF+DPLSL Sbjct: 237 QEVLPDYIGDYVVVAAE--DDKTGSALYESKLWQSIPAVKKHHVIKVNANVFYFTDPLSL 29- 4 Query: 295 EAQLKSFTKAIKENTN 310 E QL++ +AI + N Sbjct: 295 EYQLETLREAILSSEN 310 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1187 A DNA sequence (GBSx1263) was identified in S. agalactiae <SEQ ID 3695> which encodes the amino acid sequence <SEQ ID 3696>. Analysis of this protein sequence reveals the following: TABLE-US-03593 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3431(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1188 A DNA sequence (GBSx1264) was identified in S. agalactiae <SEQ ID 3697> which encodes the amino acid sequence <SEQ ID 3698>. This protein is predicted to be ferrichrome transport permease (permease). Analysis of this protein sequence reveals the following: TABLE-US-03594 Possible site: 39 >>> May be a lipoprotein INTEGRAL Likelihood = -12.74 Transmembrane 129-145 (123-150) INTEGRAL Likelihood = -10.67 Transmembrane 248-264 (240-283) INTEGRAL Likelihood = -10.14 Transmembrane 205-221 (196-228) INTEGRAL Likelihood = -5.95 Transmembrane 319-335 (317-336) INTEGRAL Likelihood = -3.56 Transmembrane 73-89 (73-90) INTEGRAL Likelihood = -3.19 Transmembrane 288-304 (288-304) INTEGRAL Likelihood = -2.76 Transmembrane 266-282 (265-283) INTEGRAL Likelihood = -2.23 Transmembrane 103-119 (101-122) INTEGRAL Likelihood = -1.01 Transmembrane 158-174 (158-174) ----- Final Results ----- bacterial membrane --- Certainty = 0.6095(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03595 >GP: AAF98154 GB: AF251216 FhuB [Staphylococcus aureus] Identities = 116/313 (37%), Positives = 194/313 (61%), Gaps = 3/313 (0%) Query: 26 ILFLIGCYASLRFGAINFKTSDLITVLKNPLKNSNAQDVIFDIRLPRIIAAILVGAAMSQ 85 - ++ LI + S G + S +I + N ++ Q++I +IR+PR IAA++VG A++ Sbjct: 28 MILLITLFISTLIGDAKIQASTIIEAIFNYNPSNQQQNIINEIRIPRNIAAVIVGMALAV 87 Query: 86 AGAIMQGVTRNAIADPGLLGINAGAGLALVVAYAFLGSMHYSTILIVCLLGSVISCLLVF 145- +GAI+QGVTRN +ADP L+G+N+GA AL + YA L + + ++ LG+++ +V Sbjct: 88 SGAIIQGVTRNGLADPALIGLNSGASFALALTYAVLPNTSFLILMFAGFLGAILGGAIVL 147- Query: 146 TLSYTKQKGYHQLRLILAGAMISTLFTSVGQVVTLYFKLNRTVIGWQAGGLSQINWKMLI 20- 5 + +++ G++ +R+ILAGA +S + T++ Q + L F+LN+TV W AGG+S W L Sbjct: 148 MIGRSRRDGFNPMRIILAGAAVSAMLTALSQGIALAFRLNQTVTFWTAGGVSGTTWSHLK 20- 7 Query: 206 IIAPIIILGLLISQLLAHQLTILSLNESVAKALGQKTQLMTAFLLLIVLFLSASSVALIG 26- 5 P+I + L I ++ QLTIL+L ES+AK LGQ ++ L+I + L+ +VA+ G Sbjct: 208 WAIPLIGIALFIILTISKQLTILNLGESLAKGLGQNVTMIRGICLIIAMILAGIAVAIAG 26- 7 Query: 266 TVSFIGLIIPHFIKLFIPKDYRLLLPLIGFSGATFMIWVDLSSRIINPPSETSISSIISI 32- 5 V+F+GL++PH + I DY +LPL G ++ D+ +R + E +IIS Sbjct: 268 QVAFVGLMVPHIARFLIGTDYAKILPLTALLGGILVLVADVIARYL---GEAPVGAIISF 32- 4 Query: 326 VGLPCFLWLIRKG 338 +G+P FL+L++KG Sbjct: 325 IGVPYFLYLVKKG 337 A related DNA sequence was identified in S. pyogenes <SEQ ID 3699> which encodes the amino acid sequence <SEQ ID 3700>. Analysis of this protein sequence reveals the following: TABLE-US-03596 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.09 Transmembrane 256-272 (248-287) INTEGRAL Likelihood = -10.67 Transmembrane 26-42 (23-48) INTEGRAL Likelihood = -6.90 Transmembrane 137-153 (133-157) INTEGRAL Likelihood = -5.10 Transmembrane 167-183 (166-187) INTEGRAL Likelihood = -4.57 Transmembrane 213-229 (210-232) INTEGRAL Likelihood = -2.02 Transmembrane 112-128 (110-131) ----- Final Results ----- bacterial membrane --- Certainty = 0.5437(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03597 >GP: AAF98154 GB: AF251216 FhuB [Staphylococcus aureus] Identities = 99/274 (36%), Positives = 159/274 (57%), Gaps = 1/274 (0%) Query: 34 LSFSLCVAIYCHLRFGAVALSHQDLNSILFG-KQNGHKANVLLAIRLPRLFGATLTGSAL 92 - LS L + ++ G + + +F + + N++ IR+PR A + G AL Sbjct: 26 LSMILLITLFISTLIGDAKIQASTIIEAIFNYNPSNQQQNIINEIRIPRNIAAVIVGMAL 85 Query: 93 AVSGTIMQAITRNPIAEPGLLGINAGAGLALVLAYAFVPHLHYSLIILLSLLGSSLAATL 152- AVSG I+Q +TRN +A+P L+G+N+GA AL L YA +P+ + +++ LG+ L + Sbjct: 86 AVSGAIIQGVTRNGLADPALIGLNSGASFALALTYAVLPNTSFLILMFAGFLGAILGGAI 145- Query: 153 VFGLSYQSGKGYHQLRLVLAGAMVSILLSALGQGITNYYHLANAVIGWQAGGLVGVNWQM 21- 2 V + G++ +R++LAGA VS +L+AL QGI + L V W AGG+ G W Sbjct: 146 VLMIGRSRRDGFNPMRIILAGAAVSAMLTALSQGIALAFRLNQTVTFWTAGGVSGTTWSH 20- 5 Query: 213 IGYIAPLIILSLCLAQLLSYHLTVLSLSESQAKALGQKTNLISAVFMILVLILSSAAVAI 27- 2 + + PLI ++L + +S LT+L+L ES AK LGQ +I + +I+ +IL+ AVAI Sbjct: 206 LKWAIPLIGIALFIILTISKQLTILNLGESLAKGLGQNVTMIRGICLIIAMILAGIAVAI 26- 5 Query: 273 AGSISFIGLVIPHLMKHFTPHHYRYLLPLCAVSG 306 AG ++F+GL++PH+ + Y +LPL A+ G Sbjct: 266 AGQVAFVGLMVPHIARFLIGTDYAKILPLTALLG 299 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03598 Identities = 158/295 (53%), Positives = 214/295 (71%), Gaps 1/295 (0%) Query: 6 KKLVQKNKSNHFWLVFFITLILFLIGCYASLRFGAINFKTSDLITVLKNPLKNSNAQDVI 65 KK KS+ FWLVF + + Y LRFGA+ DL ++L +N + +V+ Sbjct: 16 KKTQIITKSHIFWLVFVLLSFSLCVAIYCHLRFGAVALSHQDLNSILFGK-QNGHKANVL 74 Query: 66 FDIRLPRIIAAILVGAAMSQAGAIMQGVTRNAIADPGLLGINAGAGLALVVAYAFLGSMH 125- IRLPR+ A L G+A++ +G IMQ +TRN IA+PGLLGINAGAGLALV+AYAF+ +H Sbjct: 75 LAIRLPRLFGATLTGSALAVSGTIMQAITRNPIAEPGLLGINAGAGLALVLAYAFVPHLH 134- Query: 126 YSTILIVCLLGSVISCLLVFTLSYTKQKGYHQLRLILAGAMISTLFTSVGQVVTLYFKLN 18- 5 YS I+++ LLGS ++ LVF LSY KGYHQLRL+LAGAM+S L +++GQ +T Y+ L Sbjct: 135 YSLIILLSLLGSSLAATLVFGLSYQSGKGYHQLRLVLAGAMVSILLSALGQGITNYYHLA 19- 4 Query: 186 RTVIGWQAGGLSQINWKMLIIIAPIIILGLLISQLLAHQLTILSLNESVAKALGQKTQLM 24- 5 VIGWQAGGL +NW+M+ IAP+IIL L ++QLL++ LT+LSL+ES AKALGQKT L+ Sbjct: 195 NAVIGWQAGGLVGVNWQMIGYIAPLIILSLCLAQLLSYHLTVLSLSESQAKALGQKTNLI 25- 4 Query: 246 TAFLLLIVLFLSASSVALIGTVSFIGLIIPHFIKLFIPKDYRLLLPLIGFSGATF 300 +A +++VL LS+++VA+ G++SFIGL+IPH +K F P YR LLPL SGA+F Sbjct: 255 SAVFMILVLILSSAAVAIAGSISFIGLVIPHLMKHFTPHHYRYLLPLCAVSGASF 309 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1189 A DNA sequence (GBSx1265) was identified in S. agalactiae <SEQ ID 3701> which encodes the amino acid sequence <SEQ ID 3702>. Analysis of this protein sequence reveals the following: TABLE-US-03599 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1492(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1190 A DNA sequence (GBSx1266) was identified in S. agalactiae <SEQ ID 3703> which encodes the amino acid sequence <SEQ ID 3704>. This protein is predicted to be ferrichrome transport permease (permease). Analysis of this protein sequence reveals the following: TABLE-US-03600 Possible site: 30 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.35 Transmembrane 282-298 (279-309) INTEGRAL Likelihood = -7.06 Transmembrane 120-136 (115-141) INTEGRAL Likelihood = -7.01 Transmembrane 62-78 (61-80) INTEGRAL Likelihood = -6.10 Transmembrane 250-266 (241-272) INTEGRAL Likelihood = -5.52 Transmembrane 196-212 (190-215) INTEGRAL Likelihood = -5.47 Transmembrane 155-171 (151-174) INTEGRAL Likelihood = -4.99 Transmembrane 304-320 (303-322) INTEGRAL Likelihood = -3.35 Transmembrane 91-107 (90-110) ----- Final Results ----- bacterial membrane --- Certainty = 0.5140(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03601 >GP: AAF98155 GB: AF251216 FhuG [Staphylococcus aureus] Identities = 122/334 (36%), Positives = 208/334 (61%), Gaps = 3/334 (0%) Query: 1 MIQKNKAPFVLISSVIILLLLILV---SISLGYANTSVIDVLKLISGKSDDAFLFIITNI 57 MI N LI+ + +LL L SI+ G N V K + G+ D I+ + Sbjct: 1 MISSNNKRRQLIALAVFSILLFLGCTWSITSGEYNIPVERFFKTLIGQGDAIDELILLDF 60 Query: 58 RLPRIIVCIFGGASLGIAGLLLQTLTKNPLADSGILGINAGAGLVIALTIGTFNVSNPTI 117- RLPR+++ I GA+L I+G ++Q++TKNP+A+ GILGINAG G IAL I ++ Sbjct: 61 RLPRMMITILAGAALSISGAIVQSVTKNPIAEPGILGINAGGGFAIALFIAIGKINADNF 120- Query: 118 LYFLPLFAMFGGLVTIFLIYLMSYRRNHNISPTRLIVTGIGISTIISGVMILIISQSNNQ 17- 7 +Y LPL ++ GG+ T +I++ S+ +N ++P +++ G+G+ T + G I I+S+ +++ Sbjct: 121 VYVLPLISILGGITTALIIFIFSFNKNEGVTPASMVLIGVGLQTALYGGSITIMSKFDDK 18- 0 Query: 178 KMDMIVEWLSGKITISSWTTIITFIPILILLWGLAYSRSRHLNIMNLNEQTALALGLHLK 23- 7 + D I W +G I W +I F+P ++++ +S LNI++ + A LG+ L Sbjct: 181 QSDFIAAWFAGNIWGDEWPFVIAFLPWVLIIIPYLLFKSNTLNIIHTGDNIARGLGVRLS 24- 0 Query: 238 KERIYTLMLTSSLAAISVVLIGNITFIGLLAGHLSRRLLGNNHKIILPSCLLIGAIILLV 29- 7 +ER+ + L++ +V + G+I+FIGL+ H+++R++G H++ LP +L+GA +L++ Sbjct: 241 RERLILFFIAVMLSSAAVAVAGSISFIGLMGPHIAKRIVGPRHQLFLPIAILVGACLLVI 30- 0 Query: 298 SDTIGRLLLVGTGIPTGLVVSIIGAPYFLWLMTK 331 +DTIG+++L G+P G+VV+IIGAPYFL+LM K Sbjct: 301 ADTIGKIVLQPGGVPAGIVVAIIGAPYFLYLMYK 334 A related DNA sequence was identified in S. pyogenes <SEQ ID 1939> which encodes the amino acid sequence <SEQ ID 1940>. Analysis of this protein sequence reveals the following: TABLE-US-03602 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.93 Transmembrane 254-270 (252-284) INTEGRAL Likelihood = -10.46 Transmembrane 294-310 (292-320) INTEGRAL Likelihood = -6.74 Transmembrane 25-41 (18-43) INTEGRAL Likelihood = -6.26 Transmembrane 103-119 (102-125) INTEGRAL Likelihood = -3.66 Transmembrane 164-180 (164-186) INTEGRAL Likelihood = -3.03 Transmembrane 209-225 (207-226) INTEGRAL Likelihood = -2.71 Transmembrane 74-90 (74-91) INTEGRAL Likelihood = -2.13 Transmembrane 326-342 (325-343) INTEGRAL Likelihood = -1.97 Transmembrane 135-151 (135-151) ----- Final Results ----- bacterial membrane --- Certainty = 0.5373(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03603 Identities = 153/322 (47%), Positives = 229/322 (70%), Gaps = 1/322 (0%) Query: 11 LISSVIILLLLIL-VSISLGYANTSVIDVLKLISGKSDDAFLFIITNIRLPRIIVCIFGG 69 - L +S+I+LL+ ++ +++SLG ++ S +D++ + GKS A FI+ NIRLPRI+ GG Sbjct: 22 LYTSLILLLVSLMGLALSLGESHLSFLDLVHVFLGKSSHAISFIVINIRLPRILAACLGG 81 Query: 70 ASLGIAGLLLQTLTKNPLADSGILGINAGAGLVIALTIGTFNVSNPTILYFLPLFAMFGG 129- SL ++GLLLQ LT+NPLADSG+LGI GAG+ +A+ + I ++LPLFAM G Sbjct: 82 GSLALSGLLLQRLTRNPLADSGVLGITIGAGISLAIVVSFSFFEQAHISHYLPLFAMLGA 141- Query: 130 LVTIFLIYLMSYRRNHNISPTRLIVTGIGISTIISGVMILIISQSNNQKMDHIVEWLSGK 18- 9 +VT F +Y +S + I PTRLI+TG+ ++T++S +M+ ++ N K+D+++ WLSG+ Sbjct: 142 IVTTFSVYWLSLTKQGQIDPTRLILTGVAVTTMLSSLMVALVGHINRYRVDLVINWLSGQ 20- 1 Query: 190 ITISSWTTIITFIPILILLWGLAYSRSRHLNIMNLNEQTALALGLHLKKERIYTLMLTSS 24- 9 + W T+ P+L+ W L YS++ LNIM L + TA+ LGL L ++R L+L + Sbjct: 202 LIGDDWPTLSVIAPLLLCFWLLTYSQAHFLNIMGLADNTAIGLGLPLNRKRRLILVLAAG 26- 1 Query: 250 LAAISVVLIGNITFIGLLAGHLSRRLLGNNHKIILPSCLLIGAIILLVSDTIGRLLLVGT 30- 9 L A+SV+L+GNI+FIGL+AGH S L+G+NHKI +P +LIG I+LLV+DT+GR+ LVG+ Sbjct: 262 LGALSVLLVGNISFIGLIAGHFSTYLVGSNHKITIPISILIGMILLLVADTVGRVYLVGS 32- 1 Query: 310 GIPTGLVVSIIGAPYFLWLMTK 331 I TG++VS+IGAPYFL+LM K Sbjct: 322 NIQTGILVSLIGAPYFLYLMAK 343 There is also homology to SEQ ID 396. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1191 A DNA sequence (GBSx1267) was identified in S. agalactiae <SEQ ID 3705> which encodes the amino acid sequence <SEQ ID 3706>. Analysis of this protein sequence reveals the following: TABLE-US-03604 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3785(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03605 >GP: AAC05779 GB: AF051356 unknown [Streptococcus mutans] Identities = 49/93 (52%), Positives = 63/93 (67%) Query: 1 MILTFNPGKLERQEFFKELINYLWIHDDVTLRKIKSHFTDYSKIDRLLEEYINHGYILRQ 60 MI +N KL RQ FF +LINYL IHDDVTLR+IK +F D ++R +E+Y+ GY+LR+ Sbjct: 1 MIKIYNGDKLTRQPFFIKLINYLQIHDDVTLRQIKRNFADTEHLERSIEDYVQAGYVLRE 60 Query: 61 NKRYSLNLPFLSSLDGLVLDDLVFIDSDSQIYQ 93 NK Y L +LDGL LD +F+D S IYQ Sbjct: 61 NKHYYNAFELLENLDGLTLDSQIFVDDQSSIYQ 93 A related DNA sequence was identified in S. pyogenes <SEQ ID 3707> which encodes the amino acid sequence <SEQ ID 3708>. Analysis of this protein sequence reveals the following: TABLE-US-03606 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3447 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03607 Identities = 108/212 (50%), Positives = 143/212 (66%) Query: 1 MILTFNPGKLERQEFFKELINYLWIHDDVTLRKIKSHFTDYSKIDRLLEEYINHGYILRQ 60 MI F+ KL RQ FF++LINYL HD V LR+IK F + + ID+ +E Y+ GYI R+ Sbjct: 1 MITVFHSDKLTRQPFFQDLINYLDQHDHVILREIKKAFPNVTGIDKAIESYVQAGYIRRE 60 Query: 61 NKRYSLNLPFLSSLDGLVLDDLVFIDSDSQIYQLLQKRKFVTNLDNPTNHLVFVEETDFE 120- NKRY +NLP +SS L LD ++F+D+ S +Y+ + F T L N TN ++ E+T+ Sbjct: 61 NKRYGINLPLVSSDQQLALDTMLFVDTCSAMYENILAVVFETQLTNQTNRVMIKEKTNIT 120- Query: 121 RNTLTLSNYFYKLTNGYPLSREQKKLYQLLGDVNSEYALKYMSSFILKFLRKDSVKQKRT 18- 0 R+ LTL+NYFY+L G S EQ LY LLGDVN EYALKYM++F+LKF RKD V QKR Sbjct: 121 RDDLTLANYFYRLKRGEKPSAEQMDLYDLLGDVNQEYALKYMTTFLLKFTRKDFVMQKRP 18- 0 Query: 181 VIFIQALELLGYISLNQDTTYRLNAKLDVEAL 212 IF++AL LGY+ + TTY+L LD E+L Sbjct: 181 DIFVEALVTLGYLKQVEPTTYQLLMTLDKESL 212 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1192 A DNA sequence (GBSx1268) was identified in S. agalactiae <SEQ ID 3709> which encodes the amino acid sequence <SEQ ID 3710>. Analysis of this protein sequence reveals the following: TABLE-US-03608 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0824 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03609 >GP: AAB39104 GB: U57759 intrageneric coaggregation-relevant adhesin [Streptococcus gordonii] Identities = 261/311 (83%), Positives = 283/311 (90%) Query: 1 MSKILVFGHQNPDSDAIGSSVAFAYLAKEAWGLDTEAVALGTPNEETAYVLDYFGVQAPR 60 MSKILVFGHQNPDSDAIGSS AFAYLA+EA+GLDTEAVALG PNEETA+VLDYFGV APR Sbjct: 1 MSKILVFGHQNPDSDAIGSSYAFAYLAREAYGLDTEAVALGEPNEETAFVLDYFGVAAPR 60 Query: 61 VVESAKAEGVETVILTDHNEFQQSISDIKDVTVYGVVDHHRVANFETANPLYMRLEPVGS 120- V+ SAKAEG E VILTDHNEFQQS++DI +V VYGVVDHHRVANFETANPLYMRLEPVGS Sbjct: 61 VITSAKAEGAEQVILTDHNEFQQSVADIAEVEVYGVVDHHRVANFETANPLYMRLEPVGS 120- Query: 121 ASSIVYRMFKENGVSVPKELAGLLLSGLISDTLLLKSPTTHASDIPVAKELAELAGVNLE 18- 0 ASSIVYRMFKE+ V+V KE+AGL+LSGLISDTLLLKSPTTH +D +A ELAELAGVNLE Sbjct: 121 ASSIVYRMFKEHSVAVSKEIAGLMLSGLISDTLLLKSPTTHPTDKAIAPELAELAGVNLE 18- 0 Query: 181 EYGLEMLKAGTNLSSKTAAELIDIDAKTFELNGEAVRVAQVNTVDINDILARQEEIEVAI 24- 0 EYGL MLKAGTNL+SK+A ELIDIDAKTFELNG VRVAQVNTVDI ++L RQ EIE AI Sbjct: 181 EYGLAMLKAGTNLASKSAEELIDIDAKTFELNGNNVRVAQVNTVDIAEVLERQAEIEAAI 24- 0 Query: 241 QEAIVTEGYSDFVLMITDIVNSNSEILALGSNMAKVEAAFEFTLENNHAFLAGAVSRKKQ 30- 0 ++AI GYSDFVLMITDI+NSNSEILA+GSNM KVEAAF F LENNHAFLAGAVSRKKQ Sbjct: 241 EKAIADNGYSDFVLMITDIINSNSEILAIGSNMDKVEAAFNFVLENNHAFLAGAVSRKKQ 30- 0 Query: 301 VVPQLTESYNA 311 VVPQLTES+NA Sbjct: 301 VVPQLTESFNA 311 A related DNA sequence was identified in S. pyogenes <SEQ ID 3711> which encodes the amino acid sequence <SEQ ID 3712>. Analysis of this protein sequence reveals the following: TABLE-US-03610 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.02 Transmembrane 141-157 (141-157) ----- Final Results ----- bacterial membrane --- Certainty = 0.1808 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9103> which encodes the amino acid sequence <SEQ ID 9104>. Analysis of this protein sequence reveals the following: TABLE-US-03611 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.02 Transmembrane 139-155 (139-155) ----- Final Results ----- bacterial membrane --- Certainty = 0.181 (Affirmative) < succ> bacterial outside --- Certainty = 0.000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03612 Identities = 253/311 (81%), Positives = 283/311 (90%) Query: 1 MSKILVFGHQNPDSDAIGSSVAFAYLAKEAWGLDTEAVALGTPNEETAYVLDYFGVQAPR 60 MSKILVFGHQNPD+DAI SS AF YL+++A+GLDTE VALGTPNEETA+ LDYFGV+APR Sbjct: 3 MSKILVFGHQNPDTDAIASSYAFDYLSQKAFGLDTEVVALGTPNEETAFALDYFGVEAPR 62 Query: 61 VVESAKAEGVETVILTDHNEFQQSISDIKDVTVYGVVDHHRVANFETANPLYMRLEPVGS 120- VVESAKA+G E VILTDHNEFQQSI+DI++V VYGVVDHHRVANFETANPLYMR+EPVGS Sbjct: 63 VVESAKAQGSEQVILTDHNEFQQSIADIREVEVYGVVDHHRVANFETANPLYMRVEPVGS 122- Query: 121 ASSIVYRMFKENGVSVPKELAGLLLSGLISDTLLLKSPTTHASDIPVAKELAELAGVNLE 18- 0 ASSIVYRMFKENG+ VPK +AG+LLSGLISDTLLLKSPTTH SD VA+ELAELA VNLE Sbjct: 123 ASSIVYRMFKENGIEVPKAIAGMLLSGLISDTLLLKSPTTHVSDHLVAEELAELAEVNLE 18- 2 Query: 181 EYGLEMLKAGTNLSSKTAAELIDIDAKTFELNGEAVRVAQVNTVDINDILARQEEIEVAI 24- 0 +YG+ +LKAGTNL+SK+ ELI IDAKTFELNG AVRVAQVNTVDI ++L RQE IE AI Sbjct: 183 DYGMALLKAGTNLASKSEVELIGIDAKTFELNGNAVRVAQVNTVDIAEVLERQEAIEAAI 24- 2 Query: 241 QEAIVTEGYSDFVLMITDIVNSNSEILALGSNMAKVEAAFEFTLENNHAFLAGAVSRKKQ 30- 0 ++A+ EGYSDFVLMITDIVNSNSEILA+G+NM KVEAAF FTL+NNHAFLAGAVSRKKQ Sbjct: 243 KDAMAAEGYSDFVLMITDIVNSNSEILAIGANMDKVEAAFNFTLDNNHAFLAGAVSRKKQ 30- 2 Query: 301 VVPQLTESYNA 311 VVPQLTES+ A Sbjct: 303 VVPQLTESFGA 313 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1193 A DNA sequence (GBSx1269) was identified in S. agalactiae <SEQ ID 3713> which encodes the amino acid sequence <SEQ ID 3714>. Analysis of this protein sequence reveals the following: TABLE-US-03613 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2769 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03614 >GP: AAC05773 GB: AF051356 pyruvate-formate lyase activating enzyme [Streptococcus mutans] Identities = 184/260 (70%), Positives = 217/260 (82%) Query: 3 EIDYKKVTGMIHSTESFGSVDGPGIRFIIFMQGCKMRCQYCHNPDTWEMETNNSKERTVE 62 ++DY+KVTG+++STESFGSVDGPGIRF++FMQGC+MRCQYCHNPDTW M+ + + ERT Sbjct: 4 KVDYEKVTGLVNSTESFGSVDGPGIRFVVFMQGCQMRCQYCHNPDTWAMKNDRATERTAG 63 Query: 63 DVLKEALRYKHFWGKDGGITVSGGEAMLQIDFITALFIEAKKLGIHTTLDTCGFAYRATP 122- DV KEALR+K FWG GGITVSGGEA LQ+DF+ ALF AK+ GIHTTLDTC +R TP Sbjct: 64 DVFKEALRFKDFWGDTGGITVSGGEATLQMDFLIALFSLAKEKGIHTTLDTCALTFRNTP 123- Query: 123 EYHAILEKLLDVTDLVLLDLKEIDSEQHKIVTRQSNKNILQFARYLSDRGTPVWIRHVLV 18- 2 +Y EKL+ VTDLVLLD+KEI+ +QHKIVT SNK IL ARYLSD G PVWIRHVLV Sbjct: 124 KYLEKYEKLMAVTDLVLLDIKEINPDQHKIVTGHSNKTILACARYLSDIGKPVWIRHVLV 18- 3 Query: 183 PGLTDIDDHLKRLGEFVQTLDNVDKFEVLPYHTMGEFKWRELGIPYPLAGVKPPTPERVK 24- 2 PGLTD D+ L +LGE+V+TL NV +FE+LPYHTMGEFKWRELGIPYPL GVKPPTP+RV+ Sbjct: 184 PGLTDRDEDLIKLGEYVKTLKNVQRFEILPYHTMGEFKWRELGIPYPLEGVKPPTPDRVR 24- 3 Query: 243 NAKDIMKTESYTEYLKRIQN 262 NAK +M TE+Y EY KRI + Sbjct: 244 NAKKLMHTETYEEYKKRINH 263 A related DNA sequence was identified in S. pyogenes <SEQ ID 3715> which encodes the amino acid sequence <SEQ ID 3716>. Analysis of this protein sequence reveals the following: TABLE-US-03615 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4614(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03616 Identities = 223/260 (85%), Positives = 239/260 (91%) Query: 1 MAEIDYKKVTGMIHSTESFGSVDGPGIRFIIFMQGCKMRCQYCHNPDTWEMETNNSKERT 60 M E DY +VTGM+HSTESFGSVDGPGIRFIIF+QGCK+RCQYCHNPDTWEMETNNSK RT Sbjct: 25 MTEKDYGQVTGMVHSTESFGSVDGPGIRFIIFLQGCKLRCQYCHNPDTWEMETNNSKIRT 84 Query: 61 VEDVLKEALRYKHFWGKDGGITVSGGEAMLQIDFITALFIEAKKLGIHTTLDTCGFAYRA 120- V DVLKEAL+YKHFWGK GGITVSGGEAMLQIDFITALFIEAKKLGIHTTLDTCGF YR Sbjct: 85 VNDVLKEALQYKHFWGKKGGITVSGGEAMLQIDFITALFIEAKKLGIHTTLDTCGFTYRP 144- Query: 121 TPEYHAILEKLLDVTDLVLLDLKEIDSEQHKIVTRQSNKNILQFARYLSDRGTPVWIRHV 18- 0 TPEYH +L+ LL VTDL+LLDLKEID +QHKIVTRQ NKNILQFARYLSD+ PVWIRHV Sbjct: 145 TPEYHQVLDNLLAVTDLILLDLKEIDEKQHKIVTRQPNKNILQFARYLSDKQIPVWIRHV 20- 4 Query: 181 LVPGLTDIDDHLKRLGEFVQTLDNVDKFEVLPYHTMGEFKWRELGIPYPLAGVKPPTPER 24- 0 LVPGLTDIDDHL RLGEFV+TL NVDKFEVLPYHTMGEFKWRELGIPY L GVKPPT ER Sbjct: 205 LVPGLTDIDDHLTRLGEFVKTLKNVDKFEVLPYHTMGEFKWRELGIPYQLEGVKPPTKER 26- 4 Query: 241 VKNAKDIMKTESYTEYLKRI 260 V+NAK++M+TESYTEY+ RI Sbjct: 265 VQNAKNLMQTESYTEYMNRI 284 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1194 A DNA sequence (GBSx1270) was identified in S. agalactiae <SEQ ID 3717> which encodes the amino acid sequence <SEQ ID 3718>. Analysis of this protein sequence reveals the following: TABLE-US-03617 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.06 Transmembrane 105-121 (103-126) INTEGRAL Likelihood = -5.57 Transmembrane 137-153 (136-162) ----- Final Results ----- bacterial membrane --- Certainty = 0.3824(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03618 >GP: AAC05772 GB: AF051356 putative hemolysin [Streptococcus mutans] Identities = 347/445 (77%), Positives = 406/445 (90%), Gaps = 1/445 (0%) Query: 1 MQDPGSQSLLLQFVILLILTLFNAFFSASEMALVSLNRSKVEQKAEEGDKRYRRLLDVLE 60 M+DPGSQSL+LQF++LLILTL NAFFSA+EMALVSLNR++VEQKAEEG+K+Y RLL VLE Sbjct: 1 MEDPGSQSLILQFLLLLILTLCNAFFSATEMALVSLNRARVEQKAEEGEKKYIRLLKVLE 60 Query: 61 NPNNFLSTIQVGITFISLLQGASLSASLGHVISGWLGNSATARTAGSIIALIFLTYVSIV 120- NPNNFLSTIQVGIT I+LL GASL+ SLG I+ W GNSATARTAGS+I+L FLTY+SIV Sbjct: 61 NPNNFLSTIQVGITLITLLSGASLADSLGREIAVWFGNSATARTAGSLISLAFLTYISIV 120- Query: 121 LGELYPKRIAMNLKDRLAIVSAPIIIFLGKIVSPFVWLLSASTNLLSRITPMTFDDADEK 18- 0 LGELYPKRIAMNLK+ LA++SAP+IIFLGK+VSPFVWLLS STNLLSR+TPMTFDDADEK Sbjct: 121 LGELYPKRIAMNLKENLAVLSAPVIIFLGKVVSPFVWLLSVSTNLLSRLTPMTFDDADEK 18- 0 Query: 181 MTRDEIEYMLTNSEETLEAEEIEMLQGIFSLDEMMAREVMVPRTDAFMIDINNDAQSNIE 24- 0 MTRDEIEYMLTNSEETL+A+EIEMLQG+FSLDE+MAREVMVPRTDAFM+DIN+D+ I+ Sbjct: 181 MTRDEIEYMLTNSEETLDADEIEMLQGVFSLDELMAREVMVPRTDAFMVDINDDSSDIIQ 24- 0 Query: 241 GILSQNFSRVPVFDDDKDRVVGVLHTKRLLEAGFKTGFDTIDLRKILQEPLFVPETIFVD 30- 0 IL++ FSR+PV+DDDKD+++G++HTK LL AGFK GFD I+LR+ILQEPLFVPETI V+ Sbjct: 241 TILNERFSRIPVYDDDKDKIIGIIHTKNLLNAGFKEGFDHINLRRILQEPLFVPETIVVN 30- 0 Query: 301 DLLKALRNTQNQMAILLDEYGGVAGLVTLEDLLEEIVGEIDDETDTAEQFVREIDENIYI 36- 0 DLL AL+NTQNQMAILLDEYGGVAGLVTLEDLLEEIVGEIDDETD VREI +N YI Sbjct: 301 DLLTALKNTQNQMAILLDEYGGVAGLVTLEDLLEEIVGEIDDETDKTAISVREIADNTYI 36- 0 Query: 361 VLGTMTLNEFNDYFETELESDDVDTIAGYYLTGVGSIPNQEEKVAYEVDSKDKHITLIND 42- 0 VLGTMTLN+FN+YFET+LESD+VDTIAG+YLTGVG+IP+QEEK +EV+S KH+ LIND Sbjct: 361 VLGTMTLNDFNEYFETDLESDNVDTIAGFYLTGVGTIPSQEEKEHFEVESNGKHLELIND 42- 0 Query: 421 KVKDGRITKLKVLLSDIEQ-NIEKD 444 KVKDGR+TKLK+L+S++E+ EKD Sbjct: 421 KVKDGRVTKLKILVSEVEEKEDEKD 445 A related DNA sequence was identified in S. pyogenes <SEQ ID 3719> which encodes the amino acid sequence <SEQ ID 3720>. Analysis of this protein sequence reveals the following: TABLE-US-03619 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.76 Transmembrane 22-38 (16-47) INTEGRAL Likelihood = -5.57 Transmembrane 118-134 (117-138) INTEGRAL Likelihood = -3.19 Transmembrane 150-166 (149-169) ----- Final Results ----- bacterial membrane --- Certainty = 0.4503(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03620 >GP: AAC05772 GB: AF051356 putative hemolysin [Streptococcus mutans] Identities = 343/443 (77%), Positives = 401/443 (90%) Query: 14 MEDPVSQSLVIQFLLLVVLTLLNAFFSASEMALVSLNRSRVEQKAADGDKKYARLLRVLE 73 - MEDP SQSL++QFLLL++LTL NAFFSA+EMALVSLNR+RVEQKA +G+KKY RLL+VLE Sbjct: 1 MEDPGSQSLILQFLLLLILTLCNAFFSATEMALVSLNRARVEQKAEEGEKKYIRLLKVLE 60 Query: 74 EPNHFLSTIQVGITFISLLSGASLSASLGKVISGWLGNSATARTAGTIISLVFLTYVSIV 133- PN+FLSTIQVGIT I+LLSGASL+ SLG+ I+ W GNSATARTAG++ISL FLTY+SIV Sbjct: 61 NPNNFLSTIQVGITLITLLSGASLADSLGREIAVWFGNSATARTAGSLISLAFLTYISIV 120- Query: 134 LGELYPKRIAMNLKDKLAIVSAPIIIGLGRLVSPFVWLLSASTNLLSRLTPMTFDDADEQ 19- 3 LGELYPKRIAMNLK+ LA++SAP+II LG++VSPFVWLLS STNLLSRLTPMTFDDADE+ Sbjct: 121 LGELYPKRIAMNLKENLAVLSAPVIIFLGKVVSPFVWLLSVSTNLLSRLTPMTFDDADEK 18- 0 Query: 194 MTRDEIEYMLSKSEATLDAEEIEMLQGVFSLDEMMAREVMVPRTDAFMIDINDDPLENIQ 25- 3 MTRDEIEYML+ SE TLDA+EIEMLQGVFSLDE+MAREVMVPRTDAFM+DINDD + IQ Sbjct: 181 MTRDEIEYMLTNSEETLDADEIEMLQGVFSLDELMAREVMVPRTDAFMVDINDDSSDIIQ 24- 0 Query: 254 EILKQSFSRIPVYDVDKDKIIGLIHTKRLLESGFRQGFDQINMRKMLQEPLFVPETIFVD 31- 3 IL + FSRIPVYD DKDKIIG+IHTK LL +GF++GFD IN+R++LQEPLFVPETI V+ Sbjct: 241 TILNERFSRIPVYDDDKDKIIGIIHTKNLLNAGFKEGFDHINLRRILQEPLFVPETIVVN 30- 0 Query: 314 DLLRQLRNTQNQMAILLDEYGGVAGLVTLEDLLEEIVGEIDDETDKAEQFVHEIGDNTYI 37- 3 DLL L+NTQNQMAILLDEYGGVAGLVTLEDLLEEIVGEIDDETDK V EI DNTYI Sbjct: 301 DLLTALKNTQNQMAILLDEYGGVAGLVTLEDLLEEIVGEIDDETDKTAISVREIADNTYI 36- 0 Query: 374 VVGTMTLNEFNDYFDTELESDDVDTIAGFYLTGIGTIPSQEQKEAYEIDNKDKHLVLIND 43- 3 V+GTMTLN+FN+YF+T+LESD+VDTIAGFYLTG+GTIPSQE+KE +E+++ KHL LIND Sbjct: 361 VLGTMTLNDFNEYFETDLESDNVDTIAGFYLTGVGTIPSQEEKEHFEVESNGKHLELIND 42- 0 Query: 434 KVKDGRITKLKLILSNIEQIIEE 456 KVKDGR+TKLK+++S +E+ +E Sbjct: 421 KVKDGRVTKLKILVSEVEEKEDE 443 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03621 Identities = 364/444 (81%), Positives = 417/444 (92%) Query: 1 MQDPGSQSLLLQFVILLILTLFNAFFSASEMALVSLNRSKVEQKAEEGDKRYRRLLDVLE 60 M+DP SQSL++QF++L++LTL NAFFSASEMALVSLNRS+VEQKA +GDK+Y RLL VLE Sbjct: 14 MEDPVSQSLVIQFLLLVVLTLLNAFFSASEMALVSLNRSRVEQKAADGDKKYARLLRVLE 73 Query: 61 NPNNFLSTIQVGITFISLLQGASLSASLGHVISGWLGNSATARTAGSIIALIFLTYVSIV 120- PN+FLSTIQVGITFISLL GASLSASLG VISGWLGNSATARTAG+II+L+FLTYVSIV Sbjct: 74 EPNHFLSTIQVGITFISLLSGASLSASLGKVISGWLGNSATARTAGTIISLVFLTYVSIV 133- Query: 121 LGELYPKRIAMNLKDRLAIVSAPIIIFLGKIVSPFVWLLSASTNLLSRITPMTFDDADEK 18- 0 LGELYPKRIAMNLKD+LAIVSAPIII LG++VSPFVWLLSASTNLLSR+TPMTFDDADE+ Sbjct: 134 LGELYPKRIAMNLKDKLAIVSAPIIIGLGRLVSPFVWLLSASTNLLSRLTPMTFDDADEQ 19- 3 Query: 181 MTRDEIEYMLTNSEETLEAEEIEMLQGIFSLDEMMAREVMVPRTDAFMIDINNDAQSNIE 24- 0 MTRDEIEYML+ SE TL+AEEIEMLQG+FSLDEMMAREVMVPRTDAFMIDIN+D NI+ Sbjct: 194 MTRDEIEYMLSKSEATLDAEEIEMLQGVFSLDEMMAREVMVPRTDAFMIDINDDPLENIQ 25- 3 Query: 241 GILSQNFSRVPVFDDDKDRVVGVLHTKRLLEAGFKTGFDTIDLRKILQEPLFVPETIFVD 30- 0 IL Q+FSR+PV+D DKD+++G++HTKRLLE+GF+ GFD I++RK+LQEPLFVPETIFVD Sbjct: 254 EILKQSFSRIPVYDVDKDKIIGLIHTKRLLESGFRQGFDQINMRKMLQEPLFVPETIFVD 31- 3 Query: 301 DLLKALRNTQNQMAILLDEYGGVAGLVTLEDLLEEIVGEIDDETDTAEQFVREIDENIYI 36- 0 DLL+ LRNTQNQMAILLDEYGGVAGLVTLEDLLEEIVGEIDDETD AEQFV EI +N YI Sbjct: 314 DLLRQLRNTQNQMAILLDEYGGVAGLVTLEDLLEEIVGEIDDETDKAEQFVHEIGDNTYI 37- 3 Query: 361 VLGTMTLNEFNDYFETELESDDVDTIAGYYLTGVGSIPNQEEKVAYEVDSKDKHITLIND 42- 0 V+GTMTLNEFNDYF+TELESDDVDTIAG+YLTG+G+IP+QE+K AYE+D+KDKH+ LIND Sbjct: 374 VVGTMTLNEFNDYFDTELESDDVDTIAGFYLTGIGTIPSQEQKEAYEIDNKDKHLVLIND 43- 3 Query: 421 KVKDGRITKLKVLLSDIEQNIEKD 444 KVKDGRITKLK++LS+IEQ IE+D Sbjct: 434 KVKDGRITKLKLILSNIEQIIEED 457 SEQ ID 3718 (GBS70d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 120 (lane 8-10; MW 65 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 120 (lane 11 & 12; MW 44 kDa) and in FIG. 179 (lane 5; MW 35 kDa). GBS70d-His was purified as shown in FIG. 231, lane 9-10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1195 A DNA sequence (GBSx1271) was identified in S. agalactiae <SEQ ID 3721> which encodes the amino acid sequence <SEQ ID 3722>. Analysis of this protein sequence reveals the following: TABLE-US-03622 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1212(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03623 >GP: CAB84230 GB: AL162754 hypothetical protein NMA0960 [Neisseria meningitidis Z2491] Identities = 80/184 (43%), Positives = 119/184 (64%), Gaps = 3/184 (1%) Query: 1 MIKRPIHLSHDFLAEVIDKEAITLDATMGNGNDTVFLAKSSK---KVYAFDIQEEAIAKT 57 ++K + +H L + + + LD T GNG+DT+FLA+++ KV+AFDIQ +A+ T Sbjct: 2 LLKNILPFAHCLLRQALPEGGNALDGTAGNGHDTLFLAQTAGIRGKVWAFDIQPQALNNT 61 Query: 58 KAKLTEQGISNAELILDGHENLEQYVHTPLRAAIFNLGYLPSADKTVITKPHTTIKAIKN 117- + +L E G SN LILDGHENL+QY+ PL AAIFN G+LP DK++ T+ T+I A+ Sbjct: 62 RCRLQEAGYSNVRLILDGHENLKQYIPKPLDAAIFNFGWLPGGDKSLTTRTETSIAALSA 121- Query: 118 VLDILEVGGRLSLMVYYGHDGGKSEKDAVIAFVEQLPQNNFATMLYQPLNQVNTPPFLIM 17- 7 L +L+ G L ++Y GH+ GK E +A+ + + LPQ FA + Y N+ N+PP+L+ Sbjct: 122 ALSLLKENGMLIAVLYPGHENGKQEAEAIEQWAKNLPQEQFAVLRYSFTNRKNSPPYLLA 18- 1 Query: 178 VEKL 181 EKL Sbjct: 182 FEKL 185 A related DNA sequence was identified in S. pyogenes <SEQ ID 3723> which encodes the amino acid sequence <SEQ ID 3724>. Analysis of this protein sequence reveals the following: TABLE-US-03624 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.44 Transmembrane 127-143 (123-143) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9101> which encodes the amino acid sequence <SEQ ID 9102>. Analysis of this protein sequence reveals the following: TABLE-US-03625 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.44 Transmembrane 118-134 (114-134) ----- Final Results ----- bacterial membrane --- Certainty = 0.157(Affirmative) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03626 Identities = 124/184 (67%), Positives = 156/184 (84%) Query: 1 MIKRPIHLSHDFLAEVIDKEAITLDATMGNGNDTVFLAKSSKKVYAFDIQEEAIAKTKAK 60 M+KRPIHLSHDFLAEV+DK ++ +DATMGNGNDT FLA+ +KKVYAFD+QE+AI KT + Sbjct: 10 MLKRPIHLSHDFLAEVVDKSSVVVDATMGNGNDTAFLAQLAKKVYAFDVQEQAIRKTSER 69 Query: 61 LTEQGISNAELILDGHENLEQYVHTPLRAAIFNLGYLPSADKTVITKPHTTIKAIKNVLD 120- L + G+SNAELIL GHE ++QYV P+RAAIFNLGYLPSADK++IT P+TT++A+ +L Sbjct: 70 LAQLGLSNAELILAGHEAVDQYVTEPVRAAIFNLGYLPSADKSIITLPNTTLQALSKLLT 129- Query: 121 ILEVGGRLSLMVYYGHDGGKSEKDAVIAFVEQLPQNNFATMLYQPLNQVNTPPFLIMVEK 18- 0 +L VGGR+++MVYYGHDGG EKDA++ FV+QL Q + MLYQPLNQVNTPPFLIM+EK Sbjct: 130 LLMVGGRIAIMVYYGHDGGSLEKDALLDFVKQLDQRKVSAMLYQPLNQVNTPPFLIMLEK 18- 9 Query: 181 LQSY 184 L + Sbjct: 190 LADF 193 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1196 A DNA sequence (GBSx1272) was identified in S. agalactiae <SEQ ID 3725> which encodes the amino acid sequence <SEQ ID 3726>. Analysis of this protein sequence reveals the following: TABLE-US-03627 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1948 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03628 >GP: AAC00380 GB: AF008220 YtqA [Bacillus subtilis] Identities = 161/302 (53%), Positives = 220/302 (72%), Gaps = 4/302 (1%) Query: 2 KKRYRAINDYYRELFGEKIFKLPIDAGFDCPNRDGTVARGGCTFCTVSGSGDAIVAPEAP 61 +KRY +N + RE FG K+FK+ +D GFDCPNRDGTVA GGCTFC+ +GSGD Sbjct: 13 EKRYHTLNYHLREHFGHKVFKVALDGGFDCPNRDGTVAHGGCTFCSAAGSGDFAGNRTDD 72 Query: 62 IREQFYKEIDFMHRKWPEVNKYLVYFQNFTNTHAKLEIIKERYEQAINEPGVIGINIGTR 121- + QF+ + MH KW + KY+ YFQ FTNTHA +E+++E++E + V+GI+I TR Sbjct: 73 LITQFHDIKNRMHEKWKD-GKYIAYFQAFTNTHAPVEVLREKFESVLALDDVVGISIATR 131- Query: 122 PDCLPDETIYYLAELSERMHVTLELGLQTTYEATSALINRAHSYDLYKKTVKRIRELAPK 18- 1 PDCLPD+ + YLAEL+ER ++ +ELGLQT +E T+ LINRAH ++ Y + V ++R+ Sbjct: 132 PDCLPDDVVDYLAELNERTYLWVELGLQTVHERTALLINRAHDFNCYVEGVNKLRKHG-- 18- 9 Query: 182 VEIVSHLINGLPGETHDMMVENVRRCVTDNDIQGIKLHLLHLMTNTRMQRDYHEGRLRLL 24- 1 + + SH+INGLP E DMM+E + V D D+QGIK+HLLHL+ T M + Y +G+L L Sbjct: 190 IRVCSHIINGLPLEDRDMMMETAK-AVADLDVQGIKIHLLHLLKGTPMVKQYEKGKLEFL 24- 8 Query: 242 SQEDYISIICDQLEIIPKHIVIHRITGDAPRHMLIGPMWSLNKWEVLNAIDKEMEKRQSY 30- 1 SQ+DY+ ++CDQLEIIP +++HRITGD P ++IGPMWS+NKWEVL AI+KE+E R SY Sbjct: 249 SQDDYVQLVCDQLEIIPPEMIVHRITGDGPIELMIGPMWSVNKWEVLGAINKSLENRGSY 30- 8 Query: 302 QG 303 QG Sbjct: 309 QG 310 A related DNA sequence was identified in S. pyogenes <SEQ ID 3727> which encodes the amino acid sequence <SEQ ID 3728>. Analysis of this protein sequence reveals the following: TABLE-US-03629 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2023 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03630 Identities = 260/307 (84%), Positives = 290/307 (93%), Gaps = 1/307 (0%) Query: 1 MKKRYRAINDYYRELFGEKIFKLPIDAGFDCPNRDGTVARGGCTFCTVSGSGDAIVAPEA 60 MKKRY+ +N++YR+LFG K+FK+PIDAGFDCPNRDGTVA GGCTFCTVSGSGDAIVAP+A Sbjct: 7 MKKRYQTLNEHYRQLFGAKMFKVPIDAGFDCPNRDGTVAHGGCTFCTVSGSGDAIVAPDA 66 Query: 61 PIREQFYKEIDFMHRKWPEVNKYLVYFQNFTNTHAKLEIIKERYEQAINEPGVIGINIGT 120- PI+EQFYKEIDFMHRKWP+VN+YLVYFQNFTNTH +++I++RYEQAINEPGV+GINIGT Sbjct: 67 PIKEQFYKEIDFMHRKWPDVNRYLVYFQNFTNTHDTVDVIRDRYEQAINEPGVVGINIGT 26 Query: 121 RPDCLPDETIYYLAELSERMHVTLELGLQTTYEATSALINRAHSYDLYKKTVKRIRELAP 18- 0 RPDCLPD+TI YLAELSERMHVT+ELGLQTTYE TS LINRAHSYDLYK+TV+R+R P Sbjct: 127 RPDCLPDDTIAYLAELSERMHVTVELGLQTTYEETSRLINRAHSYDLYKETVRRLRHY-P 18- 5 Query: 181 KVEIVSHLINGLPGETHDMMVENVRRCVTDNDIQGIKLHLLHLMTNTRMQRDYHEGRLRL 24- 0 + IVSHLINGLP ETHDMM+ENVRRCVTDNDIQGIKLHLLHLMTNTRMQRDYHEGRL+L Sbjct: 186 NINIVSHLINGLPKETHDMMLENVRRCVTDNDIQGIKLHLLHLMTNTRMQRDYHEGRLKL 24- 5 Query: 241 LSQEDYISIICDQLEIIPKHIVIHRITGDAPRHMLIGPMWSLNKWEVLNAIDKEMEKRQS 30- 0 LSQ+DY+SIICDQLEIIPKHIVIHRITGDAPR MLIGPMWSLNKWEVLNAIDKEME+R S Sbjct: 246 LSQKDYVSIICDQLEIIPKHIVIHRITGDAPRDMLIGPMWSLNKWEVLNAIDKEMERRGS 30- 5 Query: 301 YQGCKAE 307 +QGCK + Sbjct: 306 FQGCKVD 312 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1197 A DNA sequence (GBSx1273) was identified in S. agalactiae <SEQ ID 3729> which encodes the amino acid sequence <SEQ ID 3730>. Analysis of this protein sequence reveals the following: TABLE-US-03631 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.82 Transmembrane 10-26 (6-30) INTEGRAL Likelihood = -4.73 Transmembrane 93-109 (87-112) INTEGRAL Likelihood = -4.57 Transmembrane 163-179 (161-181) INTEGRAL Likelihood = -2.97 Transmembrane 189-205 (185-205) INTEGRAL Likelihood = -1.97 Transmembrane 58-74 (58-74) INTEGRAL Likelihood = -0.75 Transmembrane 130-146 (130-146) ----- Final Results ----- bacterial membrane --- Certainty = 0.4927 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03632 >GP: CAA79986 GB: Z21972 ORF2 [Bacillus megaterium] Identities = 62/159 (38%), Positives = 92/159 (56%), Gaps = 3/159 (1%) Query: 34 ISFDQTIQESVRGQLPNLSTRFFKLITVIGNTVSQIAIAIMSVTFCY--LKKWYPQARFI 91 - + FD+ + V+G L T K T IG+T S I ++++ + F Y LK F Sbjct: 34 LKFDEDVISLVQGWESPLLTDIMKFFTYIGSTASLIILSLVILFFLYRILKHRLELVLFT 93 Query: 92 AVNAIISGICILSLKLIFQRVRPTLTHLVFAGGYSFPSGHSMGTFMIFGSIIILLQYYMP 151- AV + S + L +KL FQR RP L L+ GGYSFPSGH+M F ++G + LL ++ Sbjct: 94 AV-MVGSPLLNLMVKLFFQRARPDLHRLIDIGGYSFPSGHAMNAFSLYGILTFLLWRHIT 152- Query: 152 KSIWKLLCQGTLGLLIFLIGLSRIYLGVHFPTDVLAGFI 190 ++L L+I IG+SRIYLGVH+P+D++AG++ Sbjct: 153 ARWARILLILFSMLMILSIGISRIYLGVHYPSDIIAGYL 191 A related DNA sequence was identified in S. pyogenes <SEQ ID 1851> which encodes the amino acid sequence <SEQ ID 1852>. Analysis of this protein sequence reveals the following: TABLE-US-03633 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.30 Transmembrane 154-170 (150-181) INTEGRAL Likelihood = -10.88 Transmembrane 65-81 (58-93) INTEGRAL Likelihood = -8.97 Transmembrane 10-26 (5-31) INTEGRAL Likelihood = -3.77 Transmembrane 86-102 (86-105) INTEGRAL Likelihood = -2.71 Transmembrane 185-201 (183-202) INTEGRAL Likelihood = -1.54 Transmembrane 130-146 (130-148) ----- Final Results ----- bacterial membrane --- Certainty = 0.5522 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03634 Identities = 88/197 (44%), Positives 134/197 (67%), Gaps = 1/197 (0%) Query: 1 MLSRQNSKLIQAFIAIILFFSLGLVIKYWPDTVISFDQTIQESVRGQLPNLSTRFFKLIT 60 M ++Q LI +F A+++F +G +K++P+ + D TIQ +RG LP + T+FF+ +T Sbjct: 2 MTNKQTHFLIASF-ALLIFVIIGYTVKFFPERLALLDNTIQAEIRGNLPIVLTQFFRGVT 60 Query: 61 VIGNTVSQIAIAIMSVTFCYLKKWYPQARFIAVNAIISGICILSLKLIFQRVRPTLTHLV 120- V GN ++Q+ + I+SV + KW +A FI N I+ I +LKL +QR RP + HLV Sbjct: 61 VFGNVMTQVLLVIVSVLVLFFMKWKIEALFILSNGAIAAFLITTLKLFYQRPRPAIEHLV 120- Query: 121 FAGGYSFPSGHSMGTFMIFGSIIILLQYYMPKSIWKLLCQGTLGLLIFLIGLSRIYLGVH 18- 0 +AGGYSFPSGH+MG+ +IFGS++I+ + + + + +LI LIGLSRIYLGVH Sbjct: 121 YAGGYSFPSGHAMGSMLIFGSLLIICYQRLHSKLLQFVTSMIFIILILLIGLSRIYLGVH 18- 0 Query: 181 FPTDVLAGFILAYGILN 197 +P+D+LAGF+L +GIL+ Sbjct: 181 YPSDILAGFVLGFGILH 197 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1198 A DNA sequence (GBSx1274) was identified in S. agalactiae <SEQ ID 3731> which encodes the amino acid sequence <SEQ ID 3732>. Analysis of this protein sequence reveals the following: TABLE-US-03635 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.44 Transmembrane 35-51 (33-59) INTEGRAL Likelihood = -6.53 Transmembrane 193-209 (179-211) INTEGRAL Likelihood = -4.46 Transmembrane 64-80 (60-82) INTEGRAL Likelihood = -4.09 Transmembrane 108-124 (103-128) INTEGRAL Likelihood = -2.71 Transmembrane 150-166 (148-166) INTEGRAL Likelihood = -0.06 Transmembrane 174-190 (174-190) ----- Final Results ----- bacterial membrane --- Certainty = 0.4376 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9977> which encodes amino acid sequence <SEQ ID 9978> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03636 >GP:AAC83944 GB:L47648 putative [Bacillus subtilis] Identities = 53/186 (28%), Positives = 109/186 (58%) Query: 33 RKMVTIAILSALSFVLMMVSFPLIPGAEFLKVDFSILPMLVAFILFDLKSSYGVLLLRSL 92 - +K+V +++LS+++FVLM+++FP ++LK+DFS +P ++A +++ + V ++++ Sbjct: 4 KKLVVVSMLSSIAFVLMLLNFPFPGLPDYLKIDFSDVPAIIAILIYGPLAGIAVEAIKNV 63 Query: 93 LKVILANRGPETFIGLPMNMVALALFLASFAIFWKNRESAKDFIKASLFGTVSLTVSMVA 152- L+ I+ +G N +A LF+ A +K SAK + L GT ++T+ M Sbjct: 64 LQYIIQGSMAGVPVGQVANFIAGTLFILPTAFLFKKLNSAKGLAVSLLLGTAAMTILMSI 123- Query: 153 LNYVFAIPLYAIFANFDIRTFIGVGNYLLTMVIPFNIVEGILISIVFYLTYVACLPILER 21- 2 LNYV +P Y F + + + ++ ++PFN+++GI+I++VF L ++ P +E+ Sbjct: 124 LNYVLILPAYTWFLHSPALSDSALKTAVVAGILPFNMIKGIVITVVFSLIFIKLKPWIEQ 18- 3 Query: 213 YKKTNV 218 + ++ Sbjct: 184 QRSAHI 189 A related DNA sequence was identified in S. pyogenes <SEQ ID 3733> which encodes the amino acid sequence <SEQ ID 3734>. Analysis of this protein sequence reveals the following: TABLE-US-03637 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.48 Transmembrane 82-98 (74-100) INTEGRAL Likelihood = -3.93 Transmembrane 161-177 (152-178) INTEGRAL Likelihood = -3.61 Transmembrane 108-124 (107-126) INTEGRAL Likelihood = -3.61 Transmembrane 33-49 (31-50) ----- Final Results ----- bacterial membrane --- Certainty = 0.3590 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03638 >GP:AAC83944 GB:L47648 putative [Bacillus subtilis] Identities = 46/182 (25%), Positives = 97/182 (53%) Query: 3 KTHKMIMIGILSAISFLLMLVSFAIIPGAAFLKIEFSIIPVLFGLMIMDLKSAYLILLLR 62 K K++++ +LS+I+F+LML++F +LKI+FS +P + ++I + + ++ Sbjct: 2 KVKKLVVVSMLSSIAFVLMLLNFPFPGLPDYLKIDFSDVPAIIAILIYGPLAGIAVEAIK 61 Query: 63 SLLKLFLNNRGVNDFIGLPMNIIAIALFVTAFALVWNRQKTLSQYVFASLLGTGLLTFGM 122- ++L+ + +G N IA LF+ A ++ + + + LLGT +T M Sbjct: 62 NVLQYIIQGSMAGVPVGQVANFIAGTLFILPTAFLFKKLNSAKGLAVSLLLGTAAMTILM 121- Query: 123 VVLNYTFAIPLYAIFANIDIRAYIGVTKYMMTMVIPFNLVEGLIFAITFYFVYIASKPIL 18- 2 +LNY +P Y F + + + ++ ++PFN+++G++ + F ++I KP + Sbjct: 122 SILNYVLILPAYTWFLHSPALSDSALKTAVVAGILPFNMIKGIVITVVFSLIFIKLKPWI 18- 1 Query: 183 ER 184 E+ Sbjct: 182 EQ 183 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03639 Identities = 110/185 (59%), Positives = 144/185 (77%) Query: 29 MTNTRKMVTIAILSALSFVLMMVSFPLIPGAEFLKVDFSILPMLVAFILFDLKSSYGVLL 88 - M+ T KM+ I ILSA+SF+LM+VSF +IPGA FLK++FSI+P+L ++ DLKS+Y +LL Sbjct: 1 MSKTHKMIMIGILSAISFLLMLVSFAIIPGAAFLKIEFSIIPVLFGLMIMDLKSAYLILL 60 Query: 89 LRSLLKVILANRGPETFIGLPMNMVALALFLASFAIFWKNRESAKDFIKASLFGTVSLTV 148- LRSLLK+ L NRG FIGLPMN++A+ALF+ +FA+ W +++ ++ ASL GT LT Sbjct: 61 LRSLLKLFLNNRGVNDFIGLPMNIIAIALFVTAFALVWNRQKTLSQYVFASLLGTGLLTF 120- Query: 149 SMVALNYVFAIPLYAIFANFDIRTFIGVGNYLLTMVIPFNIVEGILISIVFYLTYVACLP 20- 8 MV LNY FAIPLYAIFAN DIR +IGV Y++TMVIPFN+VEG++ +I FY Y+A P Sbjct: 121 GMVVLNYTFAIPLYAIFANIDIRAYIGVTKYMMTMVIPFNLVEGLIFAITFYFVYIASKP 18- 0 Query: 209 ILERY 213 ILERY Sbjct: 181 ILERY 185 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1199 A DNA sequence (GBSx1275) was identified in S. agalactiae <SEQ ID 3735> which encodes the amino acid sequence <SEQ ID 3736>. Analysis of this protein sequence reveals the following: TABLE-US-03640 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -11.04 Transmembrane 278-294 (270-298) ----- Final Results ----- bacterial membrane --- Certainty = 0.5416 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3736 (GBS150) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 23 (lane 7; MW 29.7 kDa) and in FIG. 175 (lane 4 & 5; MW 30 kDa). Purified GBS150-His is shown in FIG. 110A, FIG. 199 (lane 5) and FIG. 227 (lanes 6-7). The purified GBS150-His fusion product was used to immunise mice (lane 1+2 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 110B), FACS (FIG. 110C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1200 A DNA sequence (GBSx1276) was identified in S. agalactiae <SEQ ID 3737> which encodes the amino acid sequence <SEQ ID 3738>. This protein is predicted to be a fimbria-associated protein. Analysis of this protein sequence reveals the following: TABLE-US-03641 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -15.34 Transmembrane 264-280 (257-285) INTEGRAL Likelihood = -7.64 Transmembrane 23-39 (12-41) ----- Final Results ----- bacterial membrane --- Certainty = 0.7135 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03642 >GP:AAC13546 GB:AF019629 putative fimbria-associated protein [Actinomyces naeslundii] Identities = 95/271 (35%), Positives = 139/271 (51%), Gaps = 16/271 (5%) Query: 29 VGLLITSYPFISNWYYNIKANNQVTNFDNQTQKLNTKEINRRFELAKAYNRTLDPSRLSD 88 - +GLL +YP ++W + ++ Q + + E A AYN L + + Sbjct: 1 MGLL--TYPTAASWVSQYNQSKVTADYSAQVDGARP-DAKTQVEQAHAYNDALSAGAVLE 57 Query: 89 PYTE------KEKKGIAEYAHMLEIAE--MIGYIDIPSIKQKLPIYAGTTSSVLEKGAGH 140- K +YA++L+ ++ + IPSI LP+Y GT L KG GH Sbjct: 58 ANNHVPTGAGSSKDSSLQYANILKANNEGLMARLKIPSISLDLPVYHGTADDTLLKGLGH 117- Query: 141 LEGTSLPIGGKSSHTVITAHRGLPKAKLFTDLDKLKKGKIFYIHNIKEVLAYKVDQISVV 20- 0 LEGTSLP+GG+ + +VIT HRGL +A +FT+LDK+K G + EVL Y+V VV Sbjct: 118 LEGTSLPVGGEGTRSVITGHRGLAEATMFTNLDKVKTGDSLIVEVFGEVLTYRVTSTKVV 17- 7 Query: 201 KPDNFSKLLVVKGKDYATLLTCTPYSINSHRLLVRGHRIKYVPPVKEKNYLMKELQTHYK 26- 0 +P+ L V +GKD TL+TCTP IN+HR+L+ G RI Y P K+ K + Sbjct: 178 EPEETEALRVEEGKDLLTLVTCTPLGINTHRILLTGERI-YPTPAKDLAAAGKRPDVPHF 23- 6 Query: 261 LYFLLSILVILILVALLL----YLKRKFKER 287 ++ + + LI+V L L Y + KER Sbjct: 237 PWWAVGLAAGLIVVGLYLWRSGYAAARAKER 267 A related DNA sequence was identified in S. pyogenes <SEQ ID 3739> which encodes the amino acid sequence <SEQ ID 3740>. Analysis of this protein sequence reveals the following: TABLE-US-03643 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.01 Transmembrane 225-241 (220-248) ----- Final Results ----- bacterial membrane --- Certainty = 0.6604 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03644 >GP:AAC13546 GB:AF019629 putative fimbria-associated protein [Actinomyces naeslundii] Identities = 94/250 (37%), Positives = 133/250 (52%), Gaps = 17/250 (6%) Query: 1 VECYRDRQLLSTYHKQVTQKKPSEMEEVWQKAKAYNARLGIQPVPDAF--------SFRD 52 V Y ++ + Y QV +P +V ++A AYN L V +A S +D Sbjct: 13 VSQYNQSKVTADYSAQVDGARPDAKTQV-EQAHAYNDALSAGAVLEANNHVPTGAGSSKD 71 Query: 53 GIHDKNYESLLQIENNDIMGYVEVPSIKVTLPIYHYTTDEVLTKGAGHLFGSALPVGGDG 112- Y ++L+ N +M +++PSI + LP+YH T D+ L KG GHL G++LPVGG+G Sbjct: 72 S--SLQYANILKANNEGLMARLKIPSISLDLPVYHGTADDTLLKGLGHLEGTSLPVGGEG 129- Query: 113 THTVISAHRGLPSAEMFTNLNLVKKGDTFYFRVLNKVLAYKVDQILTVEPDQVTSLSGVM 17- 2 T +VI+ HRGL A MFTNL+ VK GD+ V +VL Y+V VEP++ +L Sbjct: 130 TRSVITGHRGLAEATMFTNLDKVKTGDSLIVEVFGEVLTYRVTSTKVVEPEETEALRVEE 18- 9 Query: 173 GKDYATLVTCTPYGVNTKRLLVRGHRIAYHYKKYQQAKKAMKLVDKSRMWAEVVCAAFGV 23- 2 GKD TLVTCTP G+NT R+L+ G RI Y K + K A G+ Sbjct: 190 GKDLLTLVTCTPLGINTHRILLTGERI------YPTPAKDLAAAGKRPDVPHFPWWAVGL 24- 3 Query: 233 VIAIILVFMY 242 +I+V +Y Sbjct: 244 AAGLIVVGLY 253 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03645 Identities = 93/192 (48%), Positives = 130/192 (67%), Gaps = 2/192 (1%) Query: 52 VTNFDNQTQKLNTKEINRRFELAKAYNRTLDPSRLSDPYTEKEKKGIAEYAHMLEIA--E 109- ++ + Q + E+ ++ AKAYN L + D ++ ++ Y +L+I + Sbjct: 10 LSTYHKQVTQKKPSEMEEVWQKAKAYNARLGIQPVPDAFSFRDGIHDKNYESLLQIENND 69 Query: 110 MIGYIDIPSIKQKLPIYAGTTSSVLEKGAGHLEGTSLPIGGKSSHTVITAHRGLPKAKLF 16- 9 ++GY+++PSIK LPIY TT VL KGAGHL G++LP+GG +HTVI+AHRGLP A++F Sbjct: 70 IMGYVEVPSIKVTLPIYHYTTDEVLTKGAGHLFGSALPVGGDGTHTVISAHRGLPSAEMF 129- Query: 170 TDLDKLKKGKIFYIHNIKEVLAYKVDQISVVKPDNFSKLLVVKGKDYATLLTCTPYSINS 22- 9 T+L+ +KKG FY + +VLAYKVDQI V+PD + L V GKDYATL+TCTPY +N+ Sbjct: 130 TNLNLVKKGDTFYFRVLNKVLAYKVDQILTVEPDQVTSLSGVMGKDYATLVTCTPYGVNT 18- 9 Query: 230 HRLLVRGHRIKY 241 RLLVRGHRI Y Sbjct: 190 KRLLVRGHRIAY 201 SEQ ID 3738 (GBS210) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 50 (lane 3; MW 61 kDa). GBS210d was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 152 (lane 24; MW 54 kDa) and in FIG. 187 (lane 9; MW 54 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 154 (lane 24; MW 28.7 kDa) and in FIG. 182 (lane 13; MW 29 kDa). Purified GBS210d-GST is shown in lane 4 of FIG. 237. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1201 A DNA sequence (GBSx1277) was identified in S. agalactiae <SEQ ID 3741> which encodes the amino acid sequence <SEQ ID 3742>. This protein is predicted to be a fimbria-associated protein. Analysis of this protein sequence reveals the following: TABLE-US-03646 Possible site: 42 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.61 Transmembrane 20-36 (15-40) INTEGRAL Likelihood = -7.27 Transmembrane 259-275 (258-277) ----- Final Results ----- bacterial membrane --- Certainty = 0.5246 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03647 >GP:AAC13546 GB:AF019629 putative fimbria-associated protein [Actinomyces naeslundii] Identities = 76/219 (34%), Positives = 120/219 (54%), Gaps = 12/219 (5%) Query: 28 LSILLYPVVSRFYYTIESNNQTQDFERAAKKLSQKEINRRMALAQAYNDSLN-------N 80 - + +L YP + + + T D+ A ++ + ++ A AYND+L+ N Sbjct: 1 MGLLTYPTAASWVSQYNQSKVTADYS-AQVDGARPDAKTQVEQAHAYNDALSAGAVLEAN 59 Query: 81 VHLEDPYEKKRIQKGVAEYARMLEVSEK--IGTISVPKIGQKLPIFAGSSQEVLSKGAGH 138- H+ P + +YA +L+ + + + + +P I LP++ G++ + L KG GH Sbjct: 60 NHV--PTGAGSSKDSSLQYANILKANNEGLMARLKIPSISLDLPVYHGTADDTLLKGLGH 117- Query: 139 LEGTSLPIGGNSTHTVITAHSGIPDKELFSNLKKLKKGDKFYIQNIKETIAYQVDQIKVV 19- 8 LEGTSLP+GG T +VIT H G+ + +F+NL K+K GD ++ E + Y+V KVV Sbjct: 118 LEGTSLPVGGEGTRSVITGHRGLAEATMFTNLDKVKTGDSLIVEVFGEVLTYRVTSTKVV 17- 7 Query: 199 TPDNFSDLLVVPGHDYATLLTCTPIMINTHRLLVRGHRI 237 P+ L V G D TL+TCTP+ INTHR+L+ G RI Sbjct: 178 EPEETEALRVEEGKDLLTLVTCTPLGINTHRILLTGERI 216 There is also homology to SEQ ID 3740. A related GBS gene <SEQ ID 8749> and protein <SEQ ID 8750> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03648 Lipop Possible site: -1 Crend: 10 McG: Discrim Score: 9.66 GvH: Signal Score (-7.5): -6.53 Possible site: 42 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 2 value: -10.61 threshold: 0.0 INTEGRAL Likelihood = -10.61 Transmembrane 20-36 (15-40) INTEGRAL Likelihood = -7.27 Transmembrane 259-275 (258-277) PERIPHERAL Likelihood = 5.14 216 modified ALOM score: 2.62 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5246 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00080## SEQ ID 8750 (GBS212) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 44 (lane 4; MW 36 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 50 (lane 2; MW 61 kDa). Purified Thio-GBS212-His is shown in FIG. 244, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1202 A DNA sequence (GBSx1278) was identified in S. agalactiae <SEQ ID 3743> which encodes the amino acid sequence <SEQ ID 3744>. Analysis of this protein sequence reveals the following: TABLE-US-03649 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.40 Transmembrane 680-696 (674-699) ----- Final Results ----- bacterial membrane --- Certainty = 0.5161 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03650 >GP:CAA57459 GB:X81869 orf2 [Lactobacillus leichmannii] Identities = 84/325 (25%), Positives = 122/325 (36%), Gaps = 94/325 (28%) Query: 397 VNVVYTLKDKD----------------KTVASVSLTKTSKGTI---DLGNGIKFEVSGNF 43- 7 VNV + +KDKD TV+ LTK++ T+ D G + F+ + Sbjct: 236 VNVPWNIKDKDTFNVVDKPDTGIDIDASTVSIDGLTKSTDYTVNKKDNGYQVVFKTT--- 29- 2 Query: 438 SGKFTGLENKSYMISERVSGYGSAINLENGKVTITNTKDSDNPTPLNPTEPKVETHGKKF 49- 7 S L KS I+ K T+TN D + T +G Sbjct: 293 SAAVQALAGKSLTITY--------------KATLTNNATPDKA--IGNTATLSIGNGTNI 33- 6 Query: 498 VKTNEQGDRL--AGAQFVVKNSAGKYLALKADQSEGQKTLAAKKIALDEAIAAYNKLSAT 55- 5 T G R+ GAQFV K+S + KTLA + L + + N +S Sbjct: 337 TSTPANGPRIYTGGAQFVKKDS------------QSNKTLAGAEFQLVKVDSNGNIVSYA 38- 4 Query: 556 DQKGEKGITAKELIKTKQADYDAAFIEARTAYEWITDKARAITYTSNDQGQFEVTGLADG 61- 5 Q + +Y W A TYTS+ G + GL+ Sbjct: 385 TQASDG------------------------SYTWNDSATEATTYTSDANGLVALKGLSYS 42- 0 Query: 616 -------TYNLEETLAPAGFAKLAGNIKFVVNQGSYITGGNIDYVANSNQKDATRVENKK 66- 8 +Y L E AP G+AKL +KF + QGS+ G+ + + N K+ Sbjct: 421 DKLDSGESYALLEIQAPDGYAKLDSPVKFSITQGSF---GDSNKITIDNTKEG------- 47- 0 Query: 669 VTIPQTGGIGTILFTIIGLSIMLGA 693 +P TGG G +F IG+ IM+ A Sbjct: 471 -LLPSTGGKGIYIFLAIGIVIMIVA 494 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3744 (GBS59) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 7 (lane 8; MW 120 kDa), in FIG. 11 (lane 9; MW 100 kDa) and in FIG. 13 (lane 6; MW 74 kDa). GBS59-His was purified as shown in FIG. 193, lane 2. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1203 A DNA sequence (GBSx1279) was identified in S. agalactiae <SEQ ID 3745> which encodes the amino acid sequence <SEQ ID 3746>. Analysis of this protein sequence reveals the following: TABLE-US-03651 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.13 Transmembrane 870-886 (864-887) ----- Final Results ----- bacterial membrane --- Certainty = 0.2253 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03652 >GP:AAD33086 GB:AF071083 fibronectin-binding protein I [Streptococcus pyogenes] Identities = 58/176 (32%), Positives = 83/176 (46%), Gaps = 19/176 (10%) Query: 6 KFSKILTLSLFCLSQIPLNTNVLGEST---VPENGA--KGKLVVKKTDDQNKPLSKATFV 60 K S +L+L+ F L + + + G S NGA +G +KK D NKPL AT Sbjct: 8 KLSFLLSLTGFILGLLLVFIGLSGVSVGHAETRNGANKQGSFEIKKVDQNNKPLPGATSS 67 Query: 61 LKTTAHPESKIEKVTAELTGEATFDNLIPGDYTLSEETAPEGYKKTNQTWQVKVESNGKT 120- L + + ++ T+ G NL PG YTL EETAP+GY KT++TW V V NG T Sbjct: 68 LTSKDGKGTSVQTFTSNDKGIVDAQNLQPGTYTLKEETAPDGYDKTSRTWTVTVYENGYT 127- Query: 121 TIQNSGDKNSTIGQNQEELDKQYPPTGIYEDTKESYKLEHVKGSVPN--GKSEAKA 174 + + I + +D S +LE+ K SV + GK+E + Sbjct: 128 KLVENPYNGEIISKAGS------------KDVSSSLQLENPKMSVVSKYGKTEVSS 171 Identities = 31/92 (33%), Positives = 49/92 (52%), Gaps = 14/92 (15%) Query: 725 PTITIKNEKKLGEIEFIKVDKDNNKLLLKGATFELQEFNEDYKLYLPIKNNNSKVVTGEN 78- 4 P+IT+ N K++ ++ F K+ DN + L A FEL+ N N+ K+ N Sbjct: 501 PSITVANLKRVAQLRFKKMSTDN--VPLPEAAFELRSSN----------GNSQKLEASSN 54- 8 Query: 785 --GKISYKDLKDGKYQLIEAVSPEDYQKITNK 814 G++ +KDL G Y L E +P+ YQ++T K Sbjct: 549 TQGEVHFKDLTSGTYDLYETKAPKGYQQVTEK 580 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3746 (GBS67) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 7 (lane 10; MW 140 kDa), in FIG. 11 (lane 10; MW 150 kDa) and in FIG. 12 (lane 6; MW 95.3 kDa). GBS67-His was purified as shown in FIG. 192, lane 10. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1204 A DNA sequence (GBSx1280) was identified in S. agalactiae <SEQ ID 3747> which encodes the amino acid sequence <SEQ ID 3748>. This protein is predicted to be Nra. Analysis of this protein sequence reveals the following: TABLE-US-03653 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2020 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9979> which encodes amino acid sequence <SEQ ID 9980> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 3749> which encodes the amino acid sequence <SEQ ID 3750>. Analysis of this protein sequence reveals the following: TABLE-US-03654 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.75 Transmembrane 393-409 (392-409) ----- Final Results ----- bacterial membrane --- Certainty = 0.1702 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03655 Identities = 122/325 (37%), Positives = 186/325 (56%), Gaps = 5/325 (1%) Query: 7 LIENYLEKDILNQIKLLTLCY--DYYPSITLDKSCHQLGLSELLIRKYCHDLTTLFNSQL 64 LIE YLE I ++ +L+ L + Y P + + + GL+ L + YC +L F L Sbjct: 1 LIEKYLESSIESKCQLIVLFFKTSYLP---ITEVAEKTGLTFLQLNHYCEELNAFFPGSL 57 Query: 65 SLNIEKSTIVYQSNGVTREQAFKYIYHQSHVLQLLKFLITNDSGRLPLTYFSEKFGLSCA 124- S+ I+K I Q +E +Y S+VLQLL FLI N S PLT F+ LS + Sbjct: 58 SMTIQKRMISCQFTHPFKETYLYQLYASSNVLQLLAFLIKNGSHSRPLTDFARSHFLSNS 117- Query: 125 TAYRIRKHISPLLEKLGFQIVKNTITGDEYRIRYLIAFLNAQFGIEVYPMSKMDKLLIKR 18- 4 +AYR+R+ + PLL ++ KN I G+EYRIRYLIA L ++FGI+VY +++ DK I Sbjct: 118 SAYRMREALIPLLRNFELKLSKNKIVGEEYRIRYLIALLYSKFGIKVYDLTQQDKNTIHS 17- 7 Query: 185 LLLEHSTTFTASHYFPNTFIFFDTLLSLSWKRINYNVVVPYSSLFTELQNIFIYDTLQYC 24- 4 L ST S + +F F+D LL+LSWKR ++V +P + +F +L+ +F+YD+L+ Sbjct: 178 FLSHSSTHLKTSPWLSESFSFYDILLALSWKRHQFSVTIPQTRIFQQLKKLFVYDSLKKS 23- 7 Query: 245 VKNVIIDSFKINLKKDDIDYIFLAYLTSHNSFSNPNWTEKRIDNVIAIFENYPKFQKLLQ 30- 4 ++I ++N D+DY++L Y+T++NSF++ WT + I +FE F+ LL Sbjct: 238 SHDIIETYCQLNFSAGDLDYLYLIYITANNSFASLQWTPEHIRQYCQLFEENDTFRLLLN 29- 7 Query: 305 PLKDALPLSGSYHDELVKVAIFFSE 329 P+ LP LVK +FFS+ Sbjct: 298 PIITLLPNLKEQKASLVKALMFFSK 322 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1205 A DNA sequence (GBSx1281) was identified in S. agalactiae <SEQ ID 3751> which encodes the amino acid sequence <SEQ ID 3752>. This protein is predicted to be galactosyltransferase. Analysis of this protein sequence reveals the following:

TABLE-US-03656 Possible site: 21 >>> Seems to have no N-terminal signal sequence (or aa 1-22) ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1168 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03657 >GP:AAB99071 GB:U67549 galactosyltransferase isolog [Methanococcus jannaschii] Identities = 108/395 (27%), Positives = 196/395 (49%), Gaps = 28/395 (7%) Query: 4 KVKTVAVFSGYYLPFLGGIERYTDKMTADLVK-RGYRVVIVTTNHGDLPIIDEDKGR--- 59 K+K + +F GYY+P +GG+E + D+ T L + Y + I N +P E + R Sbjct: 3 KIKLI-IFPGYYIPHIGGLETHVDEFTKHLSEDENYDIYIFAPN---IPKYKEFEIRHNN 58 Query: 60 -KIYRLPTKNIVKQRYPIINK-NREYNTLMKYVSDENIDFVICNTRFQLTTLEGLSFAKN 117- K+YR P I+ YP+ N N ++ + + + D V+ TRF TL G FAK Sbjct: 59 VKVYRYPAFEIIPN-YPVPNIFNIKFWRMFFNLYKIDFDIVMTRTRFFSNTLLGFIFAKL 117- Query: 118 HHLPS--IVLDHGSSHFSVNNRFLDFFGAIYEHLLTARVKHYRPDFYAVSKRSVEWLKHF 17- 5 I ++HGS+ + + F + Y+ + + A+SK ++ Sbjct: 118 RFKKKKLIHVEHGSAFVKLESEFKNKLSYFYDKTIGKLIFKKADYVVAISKAVKNFILEN 17- 7 Query: 176 NIEAKGV--IYNSVS----ESLGSDFAGTAYLEKSADDIFITYAGRIIKEKGIELLLEAF 22- 9 + K + IY + ES+G D EK + I + + GR+ K KG+E +++A+ Sbjct: 178 FVNDKDIPIIYRGLEIEKIESIGED---KKIKEKFKNKIKLCFVGRLYKWKGVENIIKAY 23- 4 Query: 230 S--MSQYSENVYLQIAGDGPELAHLKE---KYQSKQINFLGKLNFEQTMSLMAQTDIFVY 28- 4 E + L + G G +L LK+ Y + I F GK++FE+ ++++ +DI+++ Sbjct: 235 VDLPKDLKEKIILIVVGYGEDLERLKKLAGNYLNNGIYFTGKVDFEKAIAIVKASDIYIH 29- 4 Query: 285 PSMYPEGLPTSILEAGLLSSAIIATDRGGTVEVIDSPELGIIMEENT-QSLHESLDLLVK 34- 3 S GL +S+L+A AI+A+ G EV+ GI++++N+ + + + L++ Sbjct: 295 SSYKGGGLSSSLLQAMCCGKAIVASPYEGADEVVIDGYNGILLKDNSPEEIKRGIIKLIE 35- 4 Query: 344 DKALREKLQQNIAKRIKEHFTWEKTVEKLDYIIQK 378 + LR+ +N IKE+F W+K+V++ I ++ Sbjct: 355 NNNLRKIYGENAKNFIKENFNWKKSVKEYKKIFER 389 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3752 (GBS258) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 45 (lane 2; MW 43 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 48 (lane 7; MW 67.9 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1206 A DNA sequence (GBSx1282) was identified in S. agalactiae <SEQ ID 3753> which encodes the amino acid sequence <SEQ ID 3754>. Analysis of this protein sequence reveals the following: TABLE-US-03658 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1182 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03659 >GP:CAB52237 GB:Z98171 EpsQ protein [Streptococcus thermophilus] Identities = 112/278 (40%), Positives = 163/278 (58%), Gaps = 2/278 (0%) Query: 1 MKYLAGIVTFNPNIERLDQNIRAIYPQVSHIYIVDNGSKNKEEISQLVADYNEEGHLTVD 60 M AGIV FNP+I+RL +NI A+ Q +H+Y+VDNGS N +E+ L+ YN+ +++ Sbjct: 1 MDISAGIVLFNPDIKRLKENIDAVIIQCTHLYLVDNGSGNVDEVKGLLNQYNQS-KISIL 59 Query: 61 YLTENKGIAYALNCIGQFAVAQEFDWFLTLDQDSVVLGDLIDNYENYLHLPKVGMLSCLY 120- + EN+GIA ALN + A + FDW LTLDQDSVV +++ +E Y++ VG+L + Sbjct: 60 WNRENQGIAKALNQLTSAAQKEGFDWILTLDQDSVVPSNIVGEFEKYINNSSVGILCPII 119- Query: 121 QDMNRENLVMQEFDYKEIEECITSAALMKTSVFEETSGFAEEMFIDFVDSEMNYRLSEMG 18- 0 D N++ + D EI+ECITS +L+ + E GF E MFID VD ++ YRL + G Sbjct: 120 CDRNKDEEIKINEDCTEIDECITSGSLLNIKAWSEIGGFDERMFIDGVDFDICYRLRQRG 17- 9 Query: 181 YKTYQVNFIGLLHEIGHSSRVKKFGHVFHVLNHSPFRKYYMIRNAIYIIKKYGKKKRYKY 24- 0 YK Y ++ + LLHE+GH + V NHS FRKYY+ RN IY KK Sbjct: 180 YKIYCIHSVVLLHELGHIEYHRFLFWKVLVKNHSAFRKYYIARNIIYTAKKRRSTLLVVK 23- 9 Query: 241 LVFMRNEFVRVLV-AEEQKSKKIVAMIKGLKDGLLMKV 277 + + + +++ EE K KI + +G+ DG KV Sbjct: 240 GLLQEIKLIGIVIFYEEDKLNKIRCICRGIYDGFKGKV 277 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1207 A DNA sequence (GBSx1283) was identified in S. agalactiae <SEQ ID 3755> which encodes the amino acid sequence <SEQ ID 3756>. This protein is predicted to be EpsU protein (rfbX). Analysis of this protein sequence reveals the following: TABLE-US-03660 Possible site: 54 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.44 Transmembrane 357-373 (352-387) INTEGRAL Likelihood = -7.59 Transmembrane 88-104 (79-107) INTEGRAL Likelihood = -7.32 Transmembrane 440-456 (433-465) INTEGRAL Likelihood = -6.48 Transmembrane 246-262 (245-263) INTEGRAL Likelihood = -4.78 Transmembrane 294-310 (290-312) INTEGRAL Likelihood = -3.88 Transmembrane 164-180 (162-183) INTEGRAL Likelihood = -3.56 Transmembrane 144-160 (136-161) INTEGRAL Likelihood = -2.87 Transmembrane 317-333 (316-334) INTEGRAL Likelihood = -2.71 Transmembrane 374-390 (374-393) INTEGRAL Likelihood = -0.96 Transmembrane 44-60 (44-62) INTEGRAL Likelihood = -0.80 Transmembrane 15-31 (15-32) ----- Final Results ----- bacterial membrane --- Certainty = 0.4376 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03661 >GP: CAB52225 GB: Z98171 EpsU protein [Streptococcus thermophilus] Identities = 189/462 (40%), Positives = 313/462 (66%) Query: 1 MKLLKNMFYNTSYQLLTLLLPLVTVPYVSRVLSPQGIGINAYTSSIVMYFTLFGALGISL 60 M+++KN YN YQ+ +++PL+T+PY+SR+L P GIGIN+YT+SIV YF LFG++G+ L Sbjct: 1 MQIVKNYLYNAIYQVFIIIVPLLTIPYLSRILGPSGIGINSYTNSIVQYEVLFGSIGLGL 60 Query: 61 YGNREIAFVQSNKYKRSKIFWELVVLKLASVSIATLLFFGFVLLTNEWQLFYLIQGINLL 120- YGNR+IAFV+ N+ K SK+F+E+ +L+L ++ +A LF F+++ ++ +YL Q I ++ Sbjct: 61 YGNRQIAFVRDNQVKMSKVFYEIFILRLFTICLAYFLFVAFLIINGQYYAYYLSQSIAIV 120- Query: 121 ATATDISWYFIGVEDFKIIVIRNTIVKLITVVLTFLVVKTPDDLALYMFLIAFASLLGNL 18- 0 A A DISW F+G+E+FK+IV+RN IVKL+ + FL VK+ +DL +Y+ + ++L+GNL Sbjct: 121 AAAFDISWAFMGIENFKVIVLRNFIVKLLALFSIFLFVKSYNDLNIYILITVLSTLIGNL 18- 0 Query: 181 TVWHHLKHEIIKIPFSRLDILIHLRPTLMLFLPQITMQIYLSLNKSMLGAMDSVVSAGYF 24- 0 T + L ++K+ + L + HL+ +L++F+PQI +QIY LNK+MLG++DSV S+G+F Sbjct: 181 TFFPSLHRYLVKVNYRELRPIKHLKQSLVMFIPQIALQIYWVLNKTMLGSLDSVTSSGFF 24- 0 Query: 241 DQSDKIIRILFTIVSAIGGVFLPRLSSLFSSGKEKQAKALLLKLVDLSNAISMLMIAGVV 30- 0 DQSDKI++++ IV+A G V LPR+++ F+ + + K + +AIS+ M+ G++ Sbjct: 241 DQSDKIVKLVLAIVTATGTVMLPRVANAFAHREYSKIKEYMYAGFSFVSAISIPMMFGLI 30- 0 Query: 301 GVSSTFAVFFFGKGYEAVGPLMAVESLMIICISYGNALGTQYLLASRRTKAYTMSAVIGL 36- 0 ++ F FF + V P++ +ES+ II I++ NA+G QYLL + + K+YT+S +IG Sbjct: 301 AITPKFVPLFFTSQFSDVIPVLMIESIAIIFIAWSNAIGNQYLLPTNQNKSYTVSVIIGA 36- 0 Query: 361 VANVVLNILLIPILGAMGAIISTVITEFIVSLYQAISLRDVFTFKELTRGMLRYLIAATL 42- 0 + N++LNI LI LGA+GA I+TVI+E V++YQ + L + +YLIA + Sbjct: 361 IVNLMLNIPLIIYLGAVGASIATVISEMSVTVYQLFIIHKQLNLHTLFSDLSKYLIAGLV 42- 0 Query: 421 SGAVLYYINTQMSVSLVNYVIQSLVAVTIYVGIVFITKAPVI 462 +++ I+ S + +++ V + IY+ ++ KA +I Sbjct: 421 MFLIVFKISLLTPTSWIFILLEITVGIIIYIVLLIFLKAEII 462 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1208 A DNA sequence (GBSx1284) was identified in S. agalactiae <SEQ ID 3757> which encodes the amino acid sequence <SEQ ID 3758>. Analysis of this protein sequence reveals the following: TABLE-US-03662 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1742 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1209 A DNA sequence (GBSx1285) was identified in S. agalactiae <SEQ ID 3759> which encodes the amino acid sequence <SEQ ID 3760>. Analysis of this protein sequence reveals the following: TABLE-US-03663 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1210 A DNA sequence (GBSx1286) was identified in S. agalactiae <SEQ ID 3761> which encodes the amino acid sequence <SEQ ID 3762>. Analysis of this protein sequence reveals the following: TABLE-US-03664 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.56 Transmembrane 214-230 (210-236) INTEGRAL Likelihood = -10.03 Transmembrane 364-380 (361-386) INTEGRAL Likelihood = -7.96 Transmembrane 272-288 (271-291) INTEGRAL Likelihood = -6.95 Transmembrane 23-39 (20-41) INTEGRAL Likelihood = -5.57 Transmembrane 191-207 (189-209) INTEGRAL Likelihood = -5.15 Transmembrane 434-450 (425-451) INTEGRAL Likelihood = -4.25 Transmembrane 143-159 (138-162) INTEGRAL Likelihood = -3.13 Transmembrane 167-183 (166-186) INTEGRAL Likelihood = -1.44 Transmembrane 400-416 (400-416) INTEGRAL Likelihood = -1.33 Transmembrane 333-349 (333-349) INTEGRAL Likelihood = -0.80 Transmembrane 232-248 (232-251) ----- Final Results ----- bacterial membrane --- Certainty = 0.5225 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial Cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1211 A DNA sequence (GBSx1287) was identified in S. agalactiae <SEQ ID 3763> which encodes the amino acid sequence <SEQ ID 3764>. This protein is predicted to be rhamnosyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-03665 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1792 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9981> which encodes amino acid sequence <SEQ ID 9982> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03666 >GP: AAF18951 GB: AF155805 Cps9H [Streptococcus suis] Identities = 53/116 (45%), Positives = 75/116 (63%), Gaps = 4/116 (3%) Query: 6 VLMATYNGQGFIHDQLDSIRNQTLRPDYVLMRDDGSTDDTVKVVEDYIKEHRLDGWSITS 65 VLMATYNG FI QLDSIRNQ++ D V++ DD STDDT+K+++DYIK++ LD W ++ Sbjct: 4 VLMATYNGSPFIIKQLDSIRNQSVSADKVIIWDDCSTDDTIKIIKDYIKKYSLDSWVVSQ 63 Query: 66 NDKNLGWRLNFRQLLIDVLAYEVDYVFFSDQDDTWYHHKNKMQVDIMEERQDINLL 121 N N G F L + VFFSDQDD W HK + + I +R++++++ Sbjct: 64 NKSNQGHYQTFINL---TKLVQEGIVFFSDQDDIWDCHKIETMLPIF-DRENVSMV 115 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1212 A DNA sequence (GBSx1288) was identified in S. agalactiae <SEQ ID 3765> which encodes the amino acid sequence <SEQ ID 3766>. This protein is predicted to be rhamnosyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-03667 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1278 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9983> which encodes amino acid sequence <SEQ ID 9984> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03668 >GP: AAF18951 GB: AF155805 Cps9H [Streptococcus suis] Identities = 57/146 (39%), Positives = 81/146 (55%), Gaps = 8/146 (5%) Query: 10 VLMATYNGEIFISEQLDSIRQQTLKPDYVLLRDDCSTDETVNVVNNYIAKHELEGWKIVK 69 - VLMATYNG FI +QLDSIR Q++ D V++ DDCSTD+T+ ++ +YI K+ L+ W + + Sbjct: 4 VLMATYNGSPFIIKQLDSIRNQSVSADKVIIWDDCSTDDTIKIIKDYIKKYSLDSWVVSQ 63 Query: 70 NDKNLGWRLNFRQLLIDVLAYEVDYVFFSDQDDIWYLDKNERQFAIMSDKPQIEVLSADV 129- N N G F L + VFFSDQDDIW K E I D+ + + V Sbjct: 64 NKSNQGHYQTFINL---TKLVQEGIVFFSDQDDIWDCHKIETMLPIF-DRENVSM----V 115- Query: 130 DIKTMSTEASVPHFLTFSSSDRISQY 155 K+ + + + +SDRI+ Y Sbjct: 116 FCKSRLIDENGNIISSPDTSDRINTY 141 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1213 A DNA sequence (GBSx1289) was identified in S. agalactiae <SEQ ID 3767> which encodes the amino acid sequence <SEQ ID 3768>. This protein is predicted to be dTDP-glucose 4-6-dehydratase (galE). Analysis of this protein sequence reveals the following: TABLE-US-03669 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.02 Transmembrane 250-266 (250-266) ----- Final Results ----- bacterial membrane --- Certainty = 0.1808 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9985> which encodes amino acid sequence <SEQ ID 9986> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03670 >GP: CAC14890 GB: AJ295156 d-TDP-glucose dehydratase [Phragmites australis] Identities = 108/327 (33%), Positives = 170/327 (51%), Gaps = 22/327 (6%) Query: 29 ANKGVLISGSNSMLASYMVFLLAYLNETRNYQTQIIATARNIEKARDKFSDLVGKDYFTL 88 - AN +L++G + S++V L N + ++I ++D +G F L Sbjct: 33 ANLRILVTGGAGFIGSHLVDKLM-----ENEKHEVIVADNFFTGSKDNLKKWIGHPRFEL 87 Query: 89 IPYDVEERLEYDGKVDYIIHAASNASPTAILSNPVSIIKANTIGTLNLLDFAKEKTIENF 148- I +DV + L + VD I H A ASP NPV IK N IGTLN+L AK + Sbjct: 88 IRHDVTQPLLVE--VDQIYHLACPASPIFYKHNPVKTIKTNVIGTLNMLGLAK-RVGARI 144- Query: 149 LFLSTREVYGTSIKEVIDEEAYGGFDILATRACYPESKRMAETLLQSYYDQYKVPFTIAR 20- 8 L ST EVYG ++ E +G + + R+CY E KR+AETL+ Y+ Q+ + IAR Sbjct: 145 LLTSTSEVYGDPLEHPQTEAYWGNVNPIGVRSCYDEGKRVAETLMFDYHRQHGIEIRIAR 20- 4 Query: 209 IAHSFGPGMELGNDGRIMNDLLSNVIDGKDIVLKSSGTAERAFCYLADAVSGLFTILLNG 26- 8 I +++GP M + +DGR++++ ++ + G + ++ GT R+FCY+AD V GL L+NG Sbjct: 205 IFNTYGPRMNI-DDGRVVSNFIAQAVRGDPLTVQKPGTQTRSFCYVADMVDGLIK-LMNG 26- 2 Query: 269 EVGQAYNVANEDQPIMIKDLAQKLVDLFSDKNISVVFDIPKTMSAGYSKMGRTR---LTM 32- 5 N+ N + M+ +LA+K+ +L + ++ TM+ R R +T Sbjct: 263 NNTGPINLGNPGEFTML-ELAEKVKELINP-------EVTVTMTENTPDDPRQRKPDITK 31- 4 Query: 326 AKLEALGWKREVSLESGILKTVQAFEE 352 AK E LGW+ +V L G++ F E Sbjct: 315 AK-EVLGWEPKVVLRDGLVLMEDDFRE 340 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1214 A DNA sequence (GBSx1290) was identified in S. agalactiae <SEQ ID 3769> which encodes the amino acid sequence <SEQ ID 3770>. Analysis of this protein sequence reveals the following: TABLE-US-03671 Possible site: 53 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9987> which encodes amino acid sequence <SEQ ID 9988> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-03672 >GP: CAB11866 GB: Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 77/231 (33%), Positives = 131/231 (56%), Gaps = 6/231 (2%) Query: 13 VIFAGGVGRRMNTKGKPKQFLEVHGKPIIVHTIDIFQNTEAIDAVVVVCVSDWLDYMNNL 72 - VI A G G+RM G+ K F+E+ G P+I+HT+ +F + D +++V ++ L Sbjct: 6 VIPAAGQGKRMKA-GRNKLFIELKGDPVIIHTLRVFDSHRQCDKIILVINEQEREHFQQL 64 Query: 73 VERFNLTKVKAVVAGGETGQMSIFKGLEAAEQLATDDAVVLIHDGVRPLINEEVINANIQ 132- + + +VAGG+ Q S++KGL+A +Q + +VL+HDG RP I E I+ I Sbjct: 65 LSDYPFQTSIELVAGGDERQHSVYKGLKAVKQ----EKIVLVHDGARPFIKHEQIDELIA 120- Query: 133 SVKETGSAVTSVRAKETVVLVNDSSKISEVVDRTRSFIAKAPQSFYLSDILSVERDAISK 19- 2 ++TG+A+ +V K+T+ V D ++SE ++R+ + +PQ+F LS ++ +A K Sbjct: 121 EAEQTGAAILAVPVKDTIKRVQDL-QVSETIERSSLWAVQTPQAFRLSLLMKAHAEAERK 17- 9 Query: 193 GITDAIDSSTLMGMYNRELTIVEGPYENIKITTPDDFYMFKALYDARENEQ 243 G D+S + M + +VEG Y NIK+TTPDD +A+ ++ + Sbjct: 180 GFLGTDDASLVEQMEGGSVRVVEGSYTNIKLTTPDDLTSAEAIMESESGNK 230 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3770 (GBS647) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 130 (lane 9 & 10; MW 55.9 kDa+lane 8; MW 27 kDa) and in FIG. 186 (lane 5; MW 56 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 130 (lane 12; MW 31 kDa), in FIG. 140 (lane 9; MW 31 kDa) and in FIG. 178 (lane 6; MW 31 kDa). Purified GBS647-GST is shown in FIG. 243, lane 4; purified GBS647-His is shown in FIG. 229, lane 6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1215 A DNA sequence (GBSx1291) was identified in S. agalactiae <SEQ ID 3771> which encodes the amino acid sequence <SEQ ID 3772>. This protein is predicted to be LicD1. Analysis of this protein sequence reveals the following: TABLE-US-03673 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2647 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9989> which encodes amino acid sequence <SEQ ID 9990> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03674 >GP: AAD37094 GB: AF106539 LicD2 [Streptococcus pneumoniae] Identities = 85/271 (31%) , Positives = 130/271 (47%) , Gaps = 15/271 (5%) Query: 1 MKEMTVSEIREVQLEMLAYIDKVARDNKIEYSLGGGSLLGAMRHKGFIPWDDDIDLMLER 60 M+ + EI+E+QL +L YID+ + + I Y L G++LGA+RHKG IPWDDDID+ L R Sbjct: 1 MQYLEKKEIKEIQLALLDYIDETCKKHDIPYFLSYGTMLGAIRHKGMIPWDDDIDISLYR 60 Query: 61 SQYERLMKALADANNSDFKLLHHSVEKNLW---PFAKLYHTKSMYLSKTDRIHPWTGIFI 117- YERL+K + + N+ +K+L S + + W FA + T ++ T +FI Sbjct: 61 EDYERLLKIIEEENHPRYKVL--SYDTSSWYFHNFASILDTSTVIEDHVKYKRHDTSLFI 118- Query: 118 DIFPLDRLPESAEERQRFFKKVHSAAANLMCTTYPNFASGSRKLYANARLILGLP-RFIA 17- 6 D+FP+DR + + + + + A L G KL RL RF+ Sbjct: 119 DVFPIDRFTDLSIVDKSY---KYVALRQLAYIKKSRAVHGDSKLKDFLRLCSWYALRFVN 17- 5 Query: 177 YHGQAKKRAEIVDQVMETYNNQEVPYMGYTD-SRYRLKEYFPREIFSEYEDVMFENIKTR 23- 5 KK +DQ+++ Y G + +KE FP + F E FE Sbjct: 176 PRYFYKK----IDQLVKNAVTNTPQYEGGVGIGKEGMKEIFPVDTFKELILTEFEGRMLP 23- 1 Query: 236 KIKNEHAYLNQLYGGSYMELPPESKRESHSY 266 K +L Q+Y G YM P + +E +S+ Sbjct: 232 VPKKYDQFLTQMY-GDYMTPPSKEMQEWYSH 261 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1216 A DNA sequence (GBSx1292) was identified in S. agalactiae <SEQ ID 3773> which encodes the amino acid sequence <SEQ ID 3774>. Analysis of this protein sequence reveals the following: TABLE-US-03675 Possible site: 18 >>> May be a lipoprotein INTEGRAL Likelihood = -12.05 Transmembrane 554-570 (547-575) ----- Final Results ----- bacterial membrane --- Certainty = 0.5819 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3774 (GBS182d) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 184 (lane 8; MW 62 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1217 A DNA sequence (GBSx1293) was identified in S. agalactiae <SEQ ID 3775> which encodes the amino acid sequence <SEQ ID 3776>. Analysis of this protein sequence reveals the following: TABLE-US-03676 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4653 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1218 A DNA sequence (GBSx1294) was identified in S. agalactiae <SEQ ID 3777> which encodes the amino acid sequence <SEQ ID 3778>. This protein is predicted to be DOLICHYL-PHOSPHATE MANNOSE SYNTHASE RELATED PROTEIN. Analysis of this protein sequence reveals the following: TABLE-US-03677 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.92 Transmembrane 232-248 (231-248) ----- Final Results ----- bacterial membrane --- Certainty = 0.2168 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9991> which encodes amino acid sequence <SEQ ID 9992> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03678 >GP: AAC35924 GB: AF071085 putative glycosyl transferase [Enterococcus faecalis] Identities = 118/240 (49%), Positives = 152/240 (63%), Gaps = 1/240 (0%) Query: 14 KILLVIPAYNEEGSIAKTVQTIVDFKASRS-LPFELDYIVINDGSTDGTPELLDRLGLNH 72 - K+LL+IPAYNEE +I +T+ +I FK + ELDY+VINDGSTDGT ++L+ +N Sbjct: 2 KVLLIIPAYNEEENILRTIASIETFKQEVTHFQHELDYVVINDGSTDGTKQILEVNQINA 61 Query: 73 IDLVQNLGIGGCVQTGYLYANRNHYDVAVQFDGDGQHDIRSIEDVVMPILNDEADFVIGS 132- I LV NLGIGG VQTGY YA N YDVA QFDGDG HDI S+ ++ P+ F GS Sbjct: 62 IHLVLNLGIGGAVQTGYKYALENEYDVAXQFDGDGXHDIXSLPILLEPLAEGXCXFSXGS 121- Query: 133 RFVDKKHQNFQSTAMRRLGINLISAAIKLTTGHKVYDTTSGYRAANAALIAYLSCHYPVQ 19- 2 RF+ +FQS MRR GI L+S G +Y T G RA N +IA+ + YP Sbjct: 122 RFIPGNXASFQSXKMRRXGIRLLSFCXXXAXGXTIYXVTXGXRAGNRKVIAFFAKRYPTN 18- 1 Query: 193 YPEPESTARILKKGYRLKEVTANMFEREAGTSSISSLKSIFYMTDVLTSIIIAGFIKEDD 25- 2 YPEPES ++KK + + E NM ER G SSI +L S+ YM +V ++I+IA F+KE D Sbjct: 182 YPEPESIVHLIKKRFVIVERPVNMMERLGGVSSIRALASVKYMLEVGSAILIAPFMKEGD 24- 1 A related DNA sequence was identified in S. pyogenes <SEQ ID 3779> which encodes the amino acid sequence <SEQ ID 3780>. Analysis of this protein sequence reveals the following: TABLE-US-03679 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.80 Transmembrane 211-227 (211-227) ----- Final Results ----- bacterial membrane --- Certainty = 0.1319 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03680 >GP: AAC35924 GB: AF071085 putative glycosyl transferase [Enterococcus faecalis] Identities = 104/233 (44%), Positives = 134/233 (56%), Gaps = 9/233 (3%) Query: 1 VKKLIIIPAYNESSNIVNTIRTIESDAPD-------FDYIIIDDCSTDNTLAICQKQGFN 53 +K L+IIPAYNE NI+ TI +IE+ + DY++I+D STD T I + N Sbjct: 1 MKVLLIIPAYNEEENILRTIASIETFKQEVTHFQHELDYVVINDGSTDGTKQILEVNQIN 60 Query: 54 VISLPINLGIGGAVQTGYRYAQRCGYDVAVQVDGDGQHNPCYLEKMVEVLVQSSVNMVIG 113- I L +NLGIGGAVQTGY+YA YDVA Q DGDG H+ L ++E L + G Sbjct: 61 AIHLVLNLGIGGAVQTGYKYALENEYDVAXQFDGDGXHDIXSLPILLEPLAEGXCXFSXG 120- Query: 114 SRFI--TKEGFQSSFARRIGIKYFTWLIALLTGKKITDATSGLRLIDRSLIERFANHYPD 17- 1 SRFI FQS RR GI+ ++ G I T G R +R +I FA YP Sbjct: 121 SRFIPGNXASFQSXKMRRXGIRLLSFCXXXAXGXTIYXVTXGXRAGNRKVIAFFAKRYPT 18- 0 Query: 172 DYPEPETVVDVLVSHFKVKEIPVVMNERQGGVSSISLTKSVYYNIKVTLAILV 224 +YPEPE++V ++ F + E PV M ER GGVSSI SV YM++V AIL+ Sbjct: 181 NYPEPESIVHLIKKRFVIVERPVNMMERLGGVSSIRALASVKYMLEVGSAILI 233 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03681 Identities = 105/231 (45%), Positives = 142/231 (61%), Gaps = 8/231 (3%) Query: 14 KILLVIPAYNEEGSIAKTVQTIVDFKASRSLPFELDYIVINDGSTDGTPELLDRLGLNHI 73 - K L++IPAYNE +I T++TI S + DYI+I+D STD T + + G N I Sbjct: 2 KKLIIIPAYNESSNIVNTIRTI------ESDAPDFDYIIIDDCSTDNTLAICQKQGFNVI 55 Query: 74 DLVQNLGIGGCVQTGYLYANRNHYDVAVQFDGDGQHDIRSIEDVVMPILNDEADFVIGSR 133- L NLGIGG VQTGY YA R YDVAVQ DGDGQH+ +E +V ++ + VIGSR Sbjct: 56 SLPINLGIGGAVQTGYRYAQRCGYDVAVQVDGDGQHNPCYLEKMVEVLVQSSVNMVIGSR 115- Query: 134 FVDKKHQNFQSTAMRRLGINLISAAIKLTTGHKVYDTTSGYRAANAALIAYLSCHYPVQY 19- 3 F+ K + FQS+ RR+GI + I L TG K+ D TSG R + +LI + HYP Y Sbjct: 116 FITK--EGFQSSFARRIGIKYFTWLIALLTGKKITDATSGLRLIDRSLIERFANHYPDDY 17- 3 Query: 194 PEPESTARILKKGYRLKEVTANMFEREAGTSSISSLKSIFYMTDVLTSIII 244 PEPE+ +L +++KE+ M ER+ G SSIS KS++YM V +I++ Sbjct: 174 PEPETVVDVLVSHFKVKEIPVVMNERQGGVSSISLTKSVYYMIKVTLAILV 224 A related GBS gene <SEQ ID 8751> and protein <SEQ ID 8752> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03682 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 0.29 GvH: Signal Score (-7.5): -4.34 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -2.92 threshold: 0.0 INTEGRAL Likelihood = -2.92 Transmembrane 222-238 (221-238) PERIPHERAL Likelihood = 4.40 4 modified ALOM score: 1.08 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2168 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00081## SEQ ID 8752 (GBS355) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 74 (lane 4; MW 27 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 81 (lane 7; MW 52 kDa). GBS355-GST was purified as shown in FIG. 213 (lane 4) and in FIG. 216 (lane 6). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1219 A DNA sequence (GBSx1295) was identified in S. agalactiae <SEQ ID 3781> which encodes the amino acid sequence <SEQ ID 3782>. Analysis of this protein sequence reveals the following: TABLE-US-03683 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.91 Transmembrane 185-201 (185-201) ----- Final Results ----- bacterial membrane --- Certainty = 0.1765 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03684 >GP: BAA32090 GB: AB010970 rhamnosyltransferase [Streptococcus mutans] Identities = 181/315 (57%), Positives = 244/315 (77%), Gaps = 7/315 (2%) Query: 1 MKVNILMATYNGEKFLAQQIESIQKQTFKEWNLLIRDDGSSDKTCDIIRNFTAKDSRIRF 60 MKVNILM+TYNG++F+AQQI+SIQKQTF+ WNLLIRDDGSSD T II +F D+RIRF Sbjct: 1 MKVNILMSTYNGQEFIAQQIQSIQKQTFENWNLLIRDDGSSDGTPKIIADFAKSDARIRF 60 Query: 61 INENEHHNLGVIKSFFTLVNYEVADFYFFSDQDDVWLPEKLSVSLEAAKHKASDVPLLVY 120- IN ++ N GVIK+F+TL+ YE AD+YFFSDQDDVWLP KL ++L + + + + +PL+VY Sbjct: 61 INADKRENFGVIKNFYTLLKYEKADYYFFSDQDDVWLPQKLELTLASVEKENNQIPLMVY 120- Query: 121 TDLKVVNQELNILQDSMIRAQSHHANTTLLPELTENTVTGGTMMINHALAEKW-FTPNDI 17- 9 TDL VV+++L +L DSMI+ QSHHANT+LL ELTENTVTGGTMM+NH LA++W +D+ Sbjct: 121 TDLTVVDRDLQVLHDSMIKTQSHHANTSLLEELTENTVTGGTMMVNHCLAKQWKQCYDDL 18- 0 Query: 180 LMHDWFLALLAASLGEIIYLDLPTQLYRQHDNNVLGARTMDKRFK-ILREGPKSIFTRYW 23- 8 +MHDW+LALLAASLG++IYLD T+LYRQH++NVLGART KR K LR P + +YW Sbjct: 181 IMHDWYLALLAASLGKLIYLDETTELYRQHESNVLGARTWSKRLKNWLR--PHRLVKKYW 23- 8 Query: 239 KLIHDSQKQASLIVDKYGDIMTANDLELIKCFIKIDKQPFMTRLRWLWKYGYSKNQFKHQ 29- 8 L+ SQ+QAS +++ D+ AN +I+ ++ + Q F+ R++WL +YG++KN+ H Sbjct: 239 WLVTSSQQQASHLLEL-DLPAANK-AIIRAYVTLLDQSFLNRIKWLKQYGFAKNRAFHT 295- Query: 299 VVFKWLIATNYYNKR 313 VFK LI T + +R Sbjct: 296 FVFKTLIITKFGYRR 310 A related DNA sequence was identified in S. pyogenes <SEQ ID 817> which encodes the amino acid sequence <SEQ ID 818>. Analysis of this protein sequence reveals the following: TABLE-US-03685 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1980(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03686 Identities = 178/314 (56%), Positives = 232/314 (73%), Gaps = 6/314 (1%) Query: 1 MKVNILMATYNGEKFLAQQIESIQKQTFKEWNLLIRDDGSSDKTCDIIRNFTAKDSRIRF 60 M +NIL++TYNGE+FLA+QI+SIQ+QT +W LLIRDDGS+D T DIIR F +D RI++ Sbjct: 1 MNINILLSTYNGERFLAEQIQSIQRQTVNDWTLLIRDDGSTDGTQDIIRTFVKEDKRIQW 60 Query: 61 INENEHHNLGVIKSFFTLVNYEVADFYFFSDQDDVWLPEKLSVS-LEAAKHKASDVPLLV 119- INE + NLGVIK+F+TL+ ++ AD YFFSDQDD+WL KL V+ LEA KH+ + PLLV Sbjct: 61 INEGQTENLGVIKNFYTLLKHQKADVYFFSDQDDIWLDNKLEVTLLEAQKHEMT-APLLV 119- Query: 120 YTDLKVVNQELNILQDSMIRAQSHHANTTLLPELTENTVTGGTMMINHALAEKWFTPNDI 17- 9 YTDLKVV Q L + DSMI+ QS HANT+LL ELTENTVTGGTMMI HALAE+W T + + Sbjct: 120 YTDLKVVTQHLAVCHDSMIKTQSGHANTSLLQELTENTVTGGTMMITHALAEEWTTCDGL 17- 9 Query: 180 LMHDWFLALLAASLGEIIYLDLPTQLYRQHDNNVLGARTMDKRFKILREGPKSIFTRYWK 23- 9 LMHDW+LALLA+++G+++YLD+PT+LYRQHD NVLGART KR K P + +YW Sbjct: 180 LMHDWYLALLASAIGKLVYLDIPTELYRQHDANVLGARTWSKRMKNWLT-PHHLVNKYWW 23- 8 Query: 240 LIHDSQKQASLIVDKYGDIMTANDLELIKCFIKIDKQPFMTRLRWLWKYGYSKNQFKHQV 29- 9 LI SQEQA L++D + ND EL+ ++ + PF RL L +YG+ KN+ H Sbjct: 239 LITSSQKQAQLLLDL---PLKPNDHELVTAYVSLLDMPFTKRLATLKRYGFRKNRIFHTF 29- 5 Query: 300 VFKWLIATNYYNKR 313 +F+ L+ T + +R Sbjct: 296 IFRSLVVTLFGYRR 309 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1220 A DNA sequence (GBSx1296) was identified in S. agalactiae <SEQ ID 3783> which encodes the amino acid sequence <SEQ ID 3784>. This protein is predicted to be rgpAc. Analysis of this protein sequence reveals the following: TABLE-US-03687 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1881(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9993> which encodes amino acid sequence <SEQ ID 9994> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03688 >GP: BAA32089 GB: AB010970 rgpAc [Streptococcus mutans] Identities = 234/362 (64%), Positives = 284/362 (77%) Query: 33 VSELINHQKSFDIKYHVACLSDKEHHTHFNFADADCFTINPPQLGPARVIAYDIMAINYA 92 - + EL+ +++S + YHVACLS+ + H HF + DCFTI P+LGPARVIAYD+MAI YA Sbjct: 1 MEELVKYKQSQQLTYHVACLSETDQHKHFTYLGVDCFTIKAPKLGPARVIAYDMMAIRYA 60 Query: 93 LDLVKTHDLKEPIFYILGNTIGAFIWHFANKIHKVGGLLYVNPDGLEWKRSKWSRPTQRY 152- L L+K +K PIFYILGNTIGAF+ FA KI ++GG Y+NPDGLEW+RSKWSRP Q Y Sbjct: 61 LKLIKDQKIKHPIFYILGNTIGAFMGPFARKIKRIGGRFYINPDGLEWRRSKWSRPVQAY 120- Query: 153 LKYAEKCMTKNADLIISDNIGIENYIQSTYSNVKTRFIAYGTEINSRKLSSDDPRVKQLF 21- 2 LKYAEKCMTK ADL+ISDN GIE YI+ Y KT FIAYGT+++ L +D +VK + Sbjct: 121 LKYAEKCMTKKADLVISDNTGIEGYIKQMYPWAKTTFIAYGTDLSPSGLLKNDSKVKDFY 18- 0 Query: 213 KKWNIKSKGYYLIVGRFVPENNYETAIREFMASDTKRDLVIICNHQNNPYFEKLSLKTNL 27- 2 KKW IK KGYYLIVGRFVPENNYETAIREFM S ++RDLVIICN++ N YFE L KT Sbjct: 181 KKWAIKDKGYYLIVGRFVPENNYETAIREFMTSSSERDLVIICNYEGNAYFEDLRQKTEF 24- 0 Query: 273 QQDKRVKFVGTLYEKDLLDYVRQQAFAYIHGHEVGGTNPGLLEALANTDLNLVLDVDFNK 33- 2 +DKR+KFVGT+Y++ LL Y+R+QAFAYIHGHEVGGTNPGLLEALA+TDLNLVL +FN Sbjct: 241 DKDKRIKFVGTVYDRPLLTYIREQAFAYIHGHEVGGTNPGLLEALAHTDLNLVLITEFNY 30- 0 Query: 333 SVAGLSSFYWAKKEGDLAKLINDSDQQQDLSTYGDRAKAIIQENYTWKKIVEEYEDLFLN 39- 2 +VA ++ YW + G LA+LIN D+Q++ + YG RAK II YTW+KIVEEYEDLFL+ Sbjct: 301 TVALDAARYWTQDNGSLAQLINQFDKQENFAEYGQRAKEIIVNYYTWEKIVEEYEDLFLH 36- 0 Query: 393 ES 394 ES Sbjct: 361 ES 362 A related DNA sequence was identified in S. pyogenes <SEQ ID 3785> which encodes the amino acid sequence <SEQ ID 3786>. Analysis of this protein sequence reveals the following: TABLE-US-03689 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 95-111 (95-111) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03690 Identities = 250/383 (65%), Positives = 307/383 (79%) Query: 11 MQDVFIIGSRGLPARYGGFETFVSELINHQKSFDIKYHVACLSDKEHHTHFNFADADCFT 70 - MQDVFIIGSRGLPA+YGGFETFV ELI+HQ S +I+YHVACLSD +H HF++ ADCF Sbjct: 1 MQDVFIIGSRGLPAKYGGFETFVEELISHQSSKNIRYHVACLSDTKHKVHFDYKGADCFY 60 Query: 71 INPPQLGPARVIAYDIMAINYALDLVKTHDLKEPIFYILGNTIGAFIWHFANKIHKVGGL 130- +NPP+LGPARVIAYD+MAI YAL H ++ PIFY+LGNT+GAFI F +IH GG Sbjct: 61 LNPPKLGPARVIAYDMMAITYALSYSDQHQIQNPIFYVLGNTVGAFIAPFVKQIHNRGGR 120- Query: 131 LYVNPDGLEWKRSKWSRPTQRYLKYAEKCMTKNADLIISDNIGIENYIQSTYSNVKTRFI 19- 0 ++NPDGLEWKRSKWSRP Q YLK++EK MT+ ADL+ISDNIGI+ Y++ Y KT FI Sbjct: 121 FFINPDGLEWKRSKWSRPVQAYLKFSEKQMTRQADLVISDNIGIDRYLKQVYPWSKTCFI 18- 0 Query: 191 AYGTEINSRKLSSDDPRVKQLFKKWNIKSKGYYLIVGRFVPENNYETAIREFMASDTKRD 25- 0 AYGT+ +L++ D +V+ F+ ++I+ K YYLI+GRFVPENNYETAI+EFMAS TKRD Sbjct: 181 AYGTQTQPSRLATADSKVRAYFQTFDIREKDYYLILGRFVPENNYETAIKEFMASSTKRD 24- 0 Query: 251 LVIICNHQNNPYFEKLSLKTNLQQDKRVKFVGTLYEKDLLDYVRQQAFAYIHGHEVGGTN 31- 0 LVIICNH+ N YF++L +T +D R+KFVGTLY+K+LL Y+R+QA+AYIHGHEVGGTN Sbjct: 241 LVIICNHEGNAYFKQLLAETECDKDPRIKFVGTLYDKELLAYIREQAYAYIHGHEVGGTN 30- 0 Query: 311 PGLLEALANTDLNLVLDVDFNKSVAGLSSFYWAKKEGDLAKLINDSDQQQDLSTYGDRAK 37- 0 PGLLEALA+T+LNLVL VDFN+SVA ++ YW K++G LA+LIN D D G AK Sbjct: 301 PGLLEALAHTNLNLVLGVDFNQSVAKSAALYWTKQKGQLAELINQVDAGFDSDHLGKEAK 36- 0 Query: 371 AIIQENYTWKKIVEEYEDLFLNE 393 AIIQE+YTW+KIV EYE LFLNE Sbjct: 361 AIIQEHYTWEKIVGEYEALFLNE 383 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1221 A DNA sequence (GBSx1297) was identified in S. agalactiae <SEQ ID 3787> which encodes the amino acid sequence <SEQ ID 3788>. This protein is predicted to be dTDP-L-rhamnose synthase. Analysis of this protein sequence reveals the following: TABLE-US-03691 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1059(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03692 >GP: AAD10184 GB: AF026471 Cps2O [Streptococcus pneumoniae] Identities = 258/283 (91%), Positives = 274/283 (96%) Query: 1 MILITGANGQLGSELRHLLDERTQEYVAVDVAEMDITNAEMVDKVFEEVKPSLVYHCAAY 60 MILITGANGQLG+ELR+LLDER +EYVAVDVAEMDIT+AEMV+KVFEEVKP+LVYHCAAY Sbjct: 1 MILITGANGQLGTELRYLLDERNEEYVAVDVAEMDITDAEMVEKVFEEVKPTLVYHCAAY 60 Query: 61 TAVDAAEDEGKELDFAINVTGTENVAKAAAKHDATLVYISTDYVFDGEKPVGQEWEVDDL 120- TAVDAAEDEGKELDFAINVTGT+NVAKA+ KH ATLVYISTDYVFDG+KPVGQEWEVDD Sbjct: 61 TAVDAAEDEGKELDFAINVTGTKNVAKASEKHGATLVYISTDYVFDGKKPVGQEWEVDDR 120- Query: 121 PDPKTEYGRTKRMGEELVEKYTSKFYTIRTAWVFGNYGKNFVFTMQNLAKTHKTLTVVND 18- 0 PDP+TEYGRTKRMGEELVEK+ S FY IRTAWVFGNYGKNFVFTMQNLAKTHKTLTVVND Sbjct: 121 PDPQTEYGRTKRMGEELVEKHVSNFYIIRTAWVFGNYGKNFVFTMQNLAKTHKTLTVVND 18- 0 Query: 181 QHGRPTWTRTLAEFMTYLAENQKDFGYYHLSNDAKEDTTWYDFAVEILKDTDVEVKPVDS 24- 0 Q+GRPTWTRTLAEFMTYLAEN+K+FGYYHLSNDA EDTTWYDFAVEILKDTDVEVKPVDS Sbjct: 181 QYGRPTWTRTLAEFMTYLAENRKEFGYYHLSNDATEDTTWYDFAVEILKDTDVEVKPVDS 24- 0 Query: 241 SQFPAKAKRPLNSTMSLEKAKATGFVIPTWQDALKEFYKQEVK 283 SQFPAKAKRPLNSTMSL KAKATGFVIPTWQDAL+EFYKQEV+ Sbjct: 241 SQFPAKAKRPLNSTMSLAKAKATGFVIPTWQDALQEFYKQEVR 283 A related DNA sequence was identified in S. pyogenes <SEQ ID 3789> which encodes the amino acid sequence <SEQ ID 3790>. Analysis of this protein sequence reveals the following: TABLE-US-03693 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0618(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03694 Identities = 227/284 (79%), Positives = 248/284 (86%) Query: 1 MILITGANGQLGSELRHLLDERTQEYVAVDVAEMDITNAEMVDKVFEEVKPSLVYHCAAY 60 MILITG+NGQLG+ELR+LLDER +YVAVDVAEMDITN + V+ VF +VKP+LVYHCAAY Sbjct: 21 MILITGSNGQLGTELRYLLDERGVDYVAVDVAEMDITNEDKVEAVFAQVKPTLVYHCAAY 80 Query: 61 TAVDAAEDEGKELDFAINVTGTENVAKAAAKHDATLVYISTDYVFDGEKPVGQEWEVDDL 120- TAVDAAEDEGK L+ AINVTG+EN+AKA K+ ATLVYISTDYVFDG KPVGQEW D Sbjct: 81 TAVDAAEDEGKALNEAINVTGSENIAKACGKYGATLVYISTDYVFDGNKPVGQEWVETDH 140- Query: 121 PDPKTEYGRTKRMGEELVEKYTSKFYTIRTAWVFGNYGKNFVFTMQNLAKTHKTLTVVND 18- 0 PDPKTEYGRTKR+GE VE+Y FY IRTAWVFGNYGKNFVFTM+ LA+ H LTVVND Sbjct: 141 PDPKTEYGRTKRLGELAVERYAEHFYIIRTAWVFGNYGKNFVFTMEQLAENHSRLTVVND 20- 0 Query: 181 QHGRPTWTRTLAEFMTYLAENQKDFGYYHLSNDAKEDTTWYDFAVEILKDTDVEVKPVDS 24- 0 QHGRPTWTRTLAEFM YL ENQK FGYYHLSNDAKEDTTWYDFA EILKD VEV PVDS Sbjct: 201 QHGRPTWTRTLAEFMCYLTENQKAFGYYHLSNDAKEDTTWYDFAKEILKDKAVEVVPVDS 26- 0 Query: 241 SQFPAKAKRPLNSTMSLEKAKATGFVIPTWQDALKEFYKQEVKK 284 S FPAKAKRPLNSTM+L+KAKATGFVIPTWQ+ALK FY+Q +KK Sbjct: 261 SAFPAKAKRPLNSTMNLDKAKATGFVIPTWQEALKAFYQQGLKK 304 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1222 A DNA sequence (GBSx1298) was identified in S. agalactiae <SEQ ID 3791> which encodes the amino acid sequence <SEQ ID 3792>. Analysis of this protein sequence reveals the following: TABLE-US-03695 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2554(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03696 >GP:BAA21508 GB:AB000631 unnamed protein product [Streptococcus mutans] Identities = 92/108 (85%), Positives = 100/108 (92%) Query: 5 KQYSEEEVGKIKDRILEALEMVIDPELGIDIVNLGLIYEIRFEDNGRTEIDMTLTTMGCP 64 K Y+ EE+ KIKDRILEALEMVIDPELGIDIVNLGLIY+IRFED+GRTEIDMTLTTMGCP Sbjct: 4 KNYTPEEIAKIKDRILEALEMVIDPELGIDIVNLGLIYDIRFEDSGRTEIDMTLTTMGCP 63 Query: 65 LADLLTDQIHDVMKTVPEVTETEVKLVWYPAWSVDKMSRYARIALGIR 112 LADLLTDQIHD +K VPEV + +VKLVW PAW+VDKMSRYARIALGIR Sbjct: 64 LADLLTDQIHDALKDVPEVLDIDVKLVWSPAWTVDKMSRYARIALGIR 111 A related DNA sequence was identified in S. pyogenes <SEQ ID 3793> which encodes the amino acid sequence <SEQ ID 3794>. Analysis of this protein sequence reveals the following: TABLE-US-03697 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2818(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03698 Identities = 90/112 (80%), Positives = 102/112 (90%) Query: 1 MSEVKQYSEEEVGKIKDRILEALEMVIDPELGIDIVNLGLIYEIRFEDNGRTEIDMTLTT 60 MS+ +Y++++V IK+RILEALE VIDPELGID+VNLGLIYEIRF DNG TEIDMTLTT Sbjct: 1 MSDTPKYTQDQVIAIKNRILEALETVIDPELGIDVVNLGLIYEIRFNDNGYTEIDMTLTT 60 Query: 61 MGCPLADLLTDQIHDVMKTVPEVTETEVKLVWYPAWSVDKMSRYARIALGIR 112 MGCPLADLLTD IHD ++ VPEVT+TEVKLVWYPAW+VDKMSRYARIALGIR Sbjct: 61 MGCPLADLLTDYIHDALQDVPEVTKTEVKLVWYPAWTVDKMSRYARIALGIR 112 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1223 A DNA sequence (GBSx1299) was identified in S. agalactiae <SEQ ID 3795> which encodes the amino acid sequence <SEQ ID 3796>. This protein is predicted to be RNA polymerase sigma factor, sigma-70 family (rpoD). Analysis of this protein sequence reveals the following: TABLE-US-03699 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3157(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to the sigma-42 protein from S. mutans: TABLE-US-03700 >GP:BAA21507 GB:AB000631 sigma 42 protein [Streptococcus mutans] Identities = 345/367 (94%), Positives = 358/367 (97%) Query: 14 EKKGNTTFNVQVADFIRNHKKQGTAIDDEVTEKLVIPFVLDADQIDDLLERLTDGGISIT 73 - +KK ++TFNVQVADFIRNHKK+G A+DDEVTEKLVIPF L+A+QIDDLLERLTDGGISIT Sbjct: 5 KKKTSSTFNVQVADFIRNHKKEGVAVDDEVTEKLVIPFELEAEQIDDLLERLTDGGISIT 64 Query: 74 DKEGNPSTKYVVEGPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTNEEEKELAV 133- D+EGNPSTKY VE KPEELTDEEL+GSNSAKVNDPVRMYLKEIGVVPLLTNEEEKELA+ Sbjct: 65 DREGNPSTKYAVEEIKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLTNEEEKELAI 124- Query: 134 AVAEGDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFK 19- 3 AV GDL AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFK Sbjct: 125 AVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFK 18- 4 Query: 194 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAER 25- 3 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAER Sbjct: 185 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAER 24- 4 Query: 254 MDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDE 31- 3 MDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDE Sbjct: 245 MDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDE 30- 4 Query: 314 VLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSKQ 37- 3 VLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVF+VTRERIRQIEAKALRKLRHPSRSKQ Sbjct: 305 VLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFDVTRERIRQIEAKALRKLRHPSRSKQ 36- 4 Query: 374 LKDFMED 380 L+DF+ED Sbjct: 365 LRDFVED 371 A related DNA sequence was identified in S. pyogenes <SEQ ID 3797> which encodes the amino acid sequence <SEQ ID 3798>. Analysis of this protein sequence reveals the following: TABLE-US-03701 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1788(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03702 Identities = 351/369 (95%), Positives = 364/369 (98%) Query: 12 MAEKKGNTTFNVQVADFIRNHKKQGTAIDDEVTEKLVIPFVLDADQIDDLLERLTDGGIS 71 - M ++K TTFNVQVA+FIR+HKK+GTAIDD+VTEKLVIPF LDADQIDDLLERLTDGGIS Sbjct: 1 MTKQKEITTFNVQVAEFIRHHKKEGTAIDDDVTEKLVIPFALDADQIDDLLERLTDGGIS 60 Query: 72 ITDKEGNPSTKYVVEGPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTNEEEKEL 131- ITDKEGNPS+KY+VE PKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLT+EEEKEL Sbjct: 61 ITDKEGNPSSKYIVEEPKPEELTDEELIGSNSAKVNDPVRMYLKEIGVVPLLTSEEEKEL 120- Query: 132 AVAVAEGDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKG 19- 1 AVAVA+GDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKG Sbjct: 121 AVAVAKGDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKG 18- 0 Query: 192 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIA 25- 1 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIA Sbjct: 181 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIA 24- 0 Query: 252 ERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQL 31- 1 ERM+MTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQL Sbjct: 241 ERMEMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQL 30- 0 Query: 312 DEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRS 37- 1 DEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRS Sbjct: 301 DEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRS 36- 0 Query: 372 KQLKDFMED 380 KQL+DF+ED Sbjct: 361 KQLRDFIED 369 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1224 A DNA sequence (GBSx1300) was identified in S. agalactiae <SEQ ID 3799> which encodes the amino acid sequence <SEQ ID 3800>. Analysis of this protein sequence reveals the following: TABLE-US-03703 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2853(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1225 A DNA sequence (GBSx1301) was identified in S. agalactiae <SEQ ID 3801> which encodes the amino acid sequence <SEQ ID 3802>. Analysis of this protein sequence reveals the following: TABLE-US-03704 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2198(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03705 >GP: BAA03516 GB: D14690 DNA primase [Lactococcus lactis] Identities = 206/398 (51%), Positives = 294/398 (73%), Gaps = 6/398 (1%) Query: 37 LAIDKEKISEIKNSVNIVDVIGEVVGLTKTGRNHLGLCPFHKEKTPSFNVIEDRQFFHCF 96 - +++D E ++++K+ VNI D+I + V L++TG+N++GLCPFH EKTPSFNV ++ F+HCF Sbjct: 2 VSLDTEVVNDLKSKVNIADLISQYVALSRTGKNYIGLCPFHGEKTPSFNVNAEKGFYHCF 61 Query: 97 GCGRSGDVFKFVEDYQHISFLDSVQVLAERSGIPLDTNFKGQVPKKPKANQSLLDIHRVA 156- GCGRSGD +F+++Y + F+D+V+ LA+ +G+ L N +K N L +I+ A Sbjct: 62 GCGRSGDAIEFLKEYNQVGFVDAVKELADFAGVTL--NISDDREEKNNPNAPLFEINNQA 119- Query: 157 SGFYHAYLMTTNDGERARQYLAERGVTEDLIKHFQIGLSPGGQDFLYRRLAKEFDEKTLM 21- 6 + Y+ LM+T GERAR+YL ERG+T+D+IK F IGL+P DF+++ L+ +FDE+ + Sbjct: 120 ARLYNILLMSTELGERARKYLEERGITDDVIKRFNIGLAPEENDFIFKNLSNKFDEEIMA 17- 9 Query: 217 SSGLFNYSENSNQFYDSFNNRIMFPLTNDIGEVIAFSGRVWTQEDIDRKQAKYKNSRATP 27- 6 SGLF++S +N+ +D+F NRIMFP+TN+ G+ I FSGR W QE+ D K AKY N+ AT Sbjct: 180 KSGLFHFS--NNKVFDAFTNRIMFPITNEYGQTIGFSGRKW-QENDDSK-AKYINTSATT 23- 5 Query: 277 IFNKSYELYHLDKARAVINKAHEVYLMEGFMDVIAAYRAGIENVVASMGTALTNEHVRHL 33- 6 IF+KSYEL++LDKA+ I+K HEVYLMEGFMDVIA+Y+AGI NVVASMGTALT +HVR L Sbjct: 236 IFDKSYELWNLDKAKPTISKQHEVYLMEGFMDVIASYKAGINNVVASMGTALTEKHVRRL 29- 5 Query: 337 KRFTKKVVLTYDGDRAGQNAIDKSLELLSDMTVDIVRIPNKMDPDEFLQANSAEDFKQLL 39- 6 K+ KK VL YDGD AGQNAI K+++L+ + V IV++P +DPDE+ + + L+ Sbjct: 296 KQMAKKFVLVYDGDSAGQNAIYKAIDLIGESAVQIVKVPEGLDPDEYSKNYGLKGLSALM 35- 5 Query: 397 ENGRISNTEFYIHYLKPENTDNLQSEIAYVEKIAKLIA 434 E GRI EF I YL+PEN NLQ+++ ++E+I+ +IA Sbjct: 356 ETGRIQPIEFLIDYLRPENLANLQTQLDFIEQISPMIA 393 A related DNA sequence was identified in S. pyogenes <SEQ ID 3803> which encodes the amino acid sequence <SEQ ID 3804>. Analysis of this protein sequence reveals the following: TABLE-US-03706 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3532(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03707 Identities = 378/604 (62%), Positives = 477/604 (78%), Gaps = 2/604 (0%) Query: 28 MGYFCGGHDLAIDKEKISEIKNSVNIVDVIGEVVGLTKTGRNHLGLCPFHKEKTPSFNVI 87 - MG+ GG DLAIDKE IS++KNSVNIVDVIGEVV L+++GR++LGLCPFHKEKTPSFNV+ Sbjct: 1 MGFLWGGDDLAIDKEMISQVKNSVNIVDVIGEVVKLSRSGRHYLGLCPFHKEKTPSFNVV 60 Query: 88 EDRQFFHCFGCGRSGDVFKFVEDYQHISFLDSVQVLAERSGIPLDTNFKGQV--PKKPKA 145- EDRQFFHCFGCG+SGDVFKF+E+Y+ + FL+SVQ++A+++G+ L+ V + Sbjct: 61 EDRQFFHCFGCGKSGDVFKFIEEYRQVPFLESVQIIADKTGMSLNIPPSQAVLASQHKHP 120- Query: 146 NQSLLDIHRVASGFYHAYLMTTNDGERARQYLAERGVTEDLIKHFQIGLSPGGQDFLYRR 20- 5 N +L+ +H A+ FYHA LMTT G+ AR+YL +RG+ + LI+HF IGL+P D+LY+ Sbjct: 121 NHALMTLHEDAAKFYHAVLMTTTIGQEARKYLYQRGLDDQLIEHFNIGLAPDESDYLYQA 18- 0 Query: 206 LAKEFDEKTLMSSGLFNYSENSNQFYDSFNNRIMFPLTNDIGEVIAFSGRVWTQEDIDRK 26- 5 L+K+++E L++SGLF+ S+ SN YD+F NRIMFPL++D G +IAFSGR+WT D++++ Sbjct: 181 LSKKYEEGQLVASGLFHLSDQSNTIYDAFRNRIMFPLSDDRGHIIAFSGRIWTAADMEKR 24- 0 Query: 266 QAKYKNSRATPIFNKSYELYHLDKARAVINKAHEVYLMEGFMDVIAAYRAGIENVVASMG 32- 5 QAKYKNSR T +FNKSYELYHLDKAR VI K HEV+LMEGFMDVIAAYR+G EN VASMG Sbjct: 241 QAKYKNSRGTVLFNKSYELYHLDKARPVIAKTHEVFLMEGFMDVIAAYRSGYENAVASMG 30- 0 Query: 326 TALTNEHVRHLKRFTKKVVLTYDGDRAGQNAIDKSLELLSDMTVDIVRIPNKMDPDEFLQ 38- 5 TALT EHV HLK+ TKKVVL YDGD AGQ+AI KSLELL D V+IVRIPNKMDPDEF+Q Sbjct: 301 TALTQEHVNHLKQVTKKVVLIYDGDDAGQHAIAKSLELLKDFVVEIVRIPNKMDPDEFVQ 36- 0 Query: 386 ANSAEDFKQLLENGRISNTEFYIHYLKPENTDNLQSEIAYVEKIAKLIAKSPSITAQNSY 44- 5 +S E F LL+ RIS+ EF+I YLKP N DNLQS+I YVEK+A LIA+SPSITAQ+SY Sbjct: 361 RHSPEAFADLLKQSRISSVEFFIDYLKPTNVDNLQSQIVYVEKMAPLIAQSPSITAQHSY 42- 0 Query: 446 ITKVAELLPDFDYFQVEQSVNNERLHHRSQQQASSSVQTSATVQLPQTGKLSAITKTEMQ 50- 5 I K+A+LLP+FDYFQVEQSVN R+ R + Q + S V LP L+AI KTE Sbjct: 421 INKIADLLPNFDYFQVEQSVNALRIQDRQKHQGQIAQAVSNLVTLPMPKSLTAIAKTESH 48- 0 Query: 506 LFHRLLNHPYLLNEFRNRDNFYFDTTEIQVLYELLKESGEITSYDLSQESDKVNRTYYII 56- 5 L HRLL+H YLLNEFR+RD+FYFDT+ +++LY+ LK+ G ITSYDLS+ S++VNR YY + Sbjct: 481 LMHRLLHHDYLLNEFRHRDDFYFDTSTLELLYQRLKQQGHITSYDLSEMSEEVNRAYYNV 54- 0 Query: 566 LEEQLPVEVSIGEIEAVEKARDRLLKERDLRKQSQLIRQSSNQGDEEGALAALENLIAQK 62- 5 LEE LP EV++GEI+ + R +LL ERDL KQ + +R+SSN+GD + AL LE+ IAQK Sbjct: 541 LEENLPKEVALGEIDDILSKRAKLLAERDLHKQGKKVRESSNKGDHQAALEVLEHFIAQK 60- 0 Query: 626 RNME 629 R ME Sbjct: 601 RKME 604 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1226 A DNA sequence (GBSx1302) was identified in S. agalactiae <SEQ ID 3805> which encodes the amino acid sequence <SEQ ID 3806>. Analysis of this protein sequence reveals the following:

TABLE-US-03708 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.05 Transmembrane 41-57 (34-58) INTEGRAL Likelihood = -5.79 Transmembrane 93-109 (90-112) ----- Final Results ----- bacterial membrane --- Certainty = 0.3421(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9995> which encodes amino acid sequence <SEQ ID 9996> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03709 >GP: AAC38560 GB: AF029731 large conductance mechanosensitive channel [Staphylococcus aureus] Identities = 64/126 (50%), Positives = 83/126 (65%), Gaps = 8/126 (6%) Query: 23 MIKELKEFLFKGNVLDLAVAVILGAAFNAIITSLVKDVITPLILNPVLKAAGVSNIA-QL 81 - M+KE KEF KGNVLDLA+AV++GAAFN II+SLV+++I PLI K G + A + Sbjct: 1 MLKEFKEFALKGNVLDLAIAVVMGAAFNKIISSLVENIIMPLI----GKIFGSVDFAKEW 56 Query: 82 SWNGVAYGNFLSAVINFLIVGTTLFFIVKAANKVMAKKPAEEEIIEVVEPTQEQLLAEIR 141- S+ G+ YG F+ +VI+F+I+ LF VK AN +M K+ AEE E V LL EIR Sbjct: 57 SFWGIKYGLFIQSVIDFIIIAFALFIFVKIANTLMKKEEAEE---EAVVEENVVLLTEIR 113- Query: 142 DLLANK 147 DLL K Sbjct: 114 DLLREK 119 A related DNA sequence was identified in S. pyogenes <SEQ ID 3807> which encodes the amino acid sequence <SEQ ID 3808>. Analysis of this protein sequence reveals the following: TABLE-US-03710 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.95 Transmembrane 71-87 (67-90) ----- Final Results ----- bacterial membrane --- Certainty = 0.3378(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03711 >GP: CAB15653 GB: Z99122 similar to large conductance mechanosensitive channel protein [Bacillus subtilis] Identities = 61/126 (48%), Positives = 77/126 (60%), Gaps = 7/126 (5%) Query: 1 MVKELKAFLFRGNIIELAVAVIIGGAFGAIVTSFVNDIITPLILNPALKAANVENITQLS 60 M E KAF RGNI++LA+ V+IGGAFG IVTS VNDII PL+ L + ++ Sbjct: 1 MWNEFKAFAMRGNIVDLAIGVVIGGAFGKIVTSLVNDIIMPLV-GLLLGGLDFSGLSFTF 59 Query: 61 WNG-VKYGSFLGAVINFLIIGTSLFFVVKAAEKAMPKKE-----KEAAAPTQEELLTEIR 114- + VKYGSF+ ++NFLII S+F V++ KKE E A QEELL EIR Sbjct: 60 GDAVVKYGSFIQTIVNFLIISFSIFIVIRTLNGLRRKKEAEEEAAEEAVDAQEELLKEIR 119- Query: 115 DLLAQK 120 DLL Q+ Sbjct: 120 DLLKQQ 125 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03712 Identities = 86/125 (68%), Positives = 99/125 (78%), Gaps = 5/125 (4%) Query: 23 MIKELKEFLFKGNVLDLAVAVILGAAFNAIITSLVKDVITPLILNPVLKAAGVSNIAQLS 82 - M+KELK FLF+GN+++LAVAVI+G AF AI+TS V D+ITPLILNP LKAA V NI QLS Sbjct: 1 MVKELKAFLFRGNIIELAVAVIIGGAFGAIVTSFVNDIITPLILNPALKAANVENITQLS 60 Query: 83 WNGVAYGNFLSAVINFLIVGTTLFFIVKAANKVMAKKPAEEEIIEVVEPTQEQLLAEIRD 142- WNGV YG+FL AVINFLI+GT+LFF+VKAA K M KK E PTQE+LL EIRD Sbjct: 61 WNGVKYGSFLGAVINFLIIGTSLFFVVKAAEKAMPKKEK-----EAAAPTQEELLTEIRD 115- Query: 143 LLANK 147 LLA K Sbjct: 116 LLAQK 120 A related GBS gene <SEQ ID 8753> and protein <SEQ ID 8754> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03713 Lipop: Possible site: -1 Crend: 10 SRCFLG: 0 McG: Length of UR: 4 Peak Value of UR: 2.96 Net Charge of CR: 1 McG: Discrim Score: 4.39 GvH: Signal Score (-7.5): -1.79 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 26 ALOM program count: 1 value: -5.79 threshold: 0.0 INTEGRAL Likelihood = -5.79 Transmembrane 71-87 (68-90) PERIPHERAL Likelihood = 1.06 28 modified ALOM score: 1.66 icm1 HYPID: 7 CFP: 0.331 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3314(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00082## SEQ ID 8754 (GBS354) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 74 (lane 3; MW 17 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1227 A DNA sequence (GBSx1303) was identified in S. agalactiae <SEQ ID 3809> which encodes the amino acid sequence <SEQ ID 3810>. This protein is predicted to be 30S ribosomal protein S21-related protein. Analysis of this protein sequence reveals the following: TABLE-US-03714 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6479(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9391> which encodes amino acid sequence <SEQ ID 9392> was also identified. A related GBS nucleic acid sequence <SEQ ID 10799> which encodes amino acid sequence <SEQ ID 10800> was also identified. The protein is similar to the 30S ribosomal protein S21 from Listeria monocytogenes: TABLE-US-03715 >GP: BAA82793 GB: AB023064 30S ribosomal protein S21 [Listeria monocytogenes] Identities = 30/34 (88%), Positives = 34/34 (99%) Query: 1 MTKAGTLQESRKREFYEKPSVKRKRKSEAARKRK 34 ++K+GTLQESRKREFYEKPSVKRK+KSEAARKRK Sbjct: 23 VSKSGTLQESRKREFYEKPSVKRKKKSEAARKRK 56 A related DNA sequence was identified in S. pyogenes <SEQ ID 3811> which encodes the amino acid sequence <SEQ ID 3812>. Analysis of this protein sequence reveals the following: TABLE-US-03716 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4815(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03717 Identities = 35/36 (97%), Positives = 36/36 (99%) Query: 1 MTKAGTLQESRKREFYEKPSVKRKRKSEAARKRKKF 36 +TKAGTLQESRKREFYEKPSVKRKRKSEAARKRKKF Sbjct: 35 VTKAGTLQESRKREFYEKPSVKRKRKSEAARKRKKF 70 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1228 A DNA sequence (GBSx1304) was identified in S. agalactiae <SEQ ID 3813> which encodes the amino acid sequence <SEQ ID 3814>. Analysis of this protein sequence reveals the following: TABLE-US-03718 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.06 Transmembrane 5-21 (3-23) INTEGRAL Likelihood = -2.28 Transmembrane 191-207 (189-207) ----- Final Results ----- bacterial membrane --- Certainty = 0.3824(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8755> and protein <SEQ ID 8756> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03719 Lipop Possible site: -1 Crend: 2 McG: Discrim Score: 8.68 GvH: Signal Score (-7.5): -5.71 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 2 value: -7.06 threshold: 0.0 INTEGRAL Likelihood = -7.06 Transmembrane 5-21 (3-23) INTEGRAL Likelihood = -2.28 Transmembrane 191-207 (189-207) PERIPHERAL Likelihood = 4.35 142 modified ALOM score: 1.91 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3824(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8756 (GBS259) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 45 (lane 4; MW 54 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1229 A DNA sequence (GBSx1305) was identified in S. agalactiae <SEQ ID 3815> which encodes the amino acid sequence <SEQ ID 3816>. Analysis of this protein sequence reveals the following: TABLE-US-03720 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 136-152 (135-152) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03721 >GP: AAD47593 GB: AF140784 Vexp2 [Streptococcus pneumoniae] Identities = 117/212 (55%), Positives = 152/212 (71%) Query: 1 MLELKNIAYRYKGNDNKTLENINYSFQSGVFYTILGNSGSGKTTLLSLMAGLDSPTEGQV 60 +L+L+++ YRYK L INY+F+ G FY+I+G SG+GK+TLLSL+AGLDSP EG + Sbjct: 3 LLQLQDVTYRYKNTAEAVLYQINYNFEPGKFYSIIGESGAGKSTLLSLLAGLDSPVEGSI 62 Query: 61 LFNKKDIKEAGYAQHRKKNIALVFQNYNLLDYLTPLENVQLVKPTADKQLLLDLGLKEDM 120- LF +DI++ GY+ HR +I+LVFQNYNL+DYL+PLEN++LV A K LL+LGL E Sbjct: 63 LFQGEDIRKKGYSYHRMHHISLVFQNYNLIDYLSPLENIRLVNKKASKNTLLELGLDESQ 122- Query: 121 LTRNILRLSGGQQQRVAIARALVVGTPAILLDEPTGNLDFDISRDITMRLKDFAHKEKRC 18- 0 + RN+L+LSGGQQQRVAIAR+LV P IL DEPTGNLD + DI LK A K +C Sbjct: 123 IKRNVLQLSGGQQQRVAIARSLVSEAPVILADEPTGNLDPKTAGDIVELLKSLAQKTGKC 18- 2 Query: 181 VIMVTHSREIAHMADTALQLIGDNLKELSKES 212 VI+VTHS+E+A +D L+L L E S Sbjct: 183 VIVVTHSKEVAQASDITLELKDKKLTETRNTS 214 SEQ ID 3816 (GBS363) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 74 (lane 5; MW 28 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 81 (lane 10; MW 53 kDa). GBS363-GST was purified as shown in FIG. 216, lane 9. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1230 A DNA sequence (GBSx1306) was identified in S. agalactiae <SEQ ID 3817> which encodes the amino acid sequence <SEQ ID 3818>. This protein is predicted to be Vexp3. Analysis of this protein sequence reveals the following: TABLE-US-03722 Possible site: 47 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.97 Transmembrane 71-87 (66-97) INTEGRAL Likelihood = -3.61 Transmembrane 2-18 (1-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.6986(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1231 A DNA sequence (GBSx1307) was identified in S. agalactiae <SEQ ID 3819> which encodes the amino acid sequence <SEQ ID 3820>. This protein is predicted to be Vexp3. Analysis of this protein sequence reveals the following: TABLE-US-03723 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1986(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1232 A DNA sequence (GBSx1308) was identified in S. agalactiae <SEQ ID 3821> which encodes the amino acid sequence <SEQ ID 3822>. This protein is predicted to be Vexp3. Analysis of this protein sequence reveals the following: TABLE-US-03724 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.05 Transmembrane 22-38 (17-39) ----- Final Results ----- bacterial membrane --- Certainty = 0.3421(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03725 >GP: AAD47594 GB: AF140784 Vexp3 [Streptococcus pneumoniae] Identities = 39/153 (25%), Positives = 67/153 (43%), Gaps = 9/153 (5%) Query: 3 LFKRSFLYVSRKKRKSITLFVCLWLVASTLISGIAVKNAGLTA-KKTFSRQTGSILHISS 61 + +F YV+RK KSI +F+ + L+AS + G+++K A A ++TF T S + Sbjct: 1 MLHNAFAYVTRKFFKSIVIFLIILLMASLSLVGLSIKGATAKASQETFKNITNS-FSMQI 59 Query: 62 DSTDLVGDGYGSGEIPEKAIVNIASNPNVKRVNNNLMAYAGLTSEKMVTRPNDKEQYKE- 120- + G G+G I + I I N ++ + A LT ++ P K+ Sbjct: 60 NRRVNQGTPRGAGNIKGEDIKKITENKAIESYVKRINAIGDLTGYDLIETPETKKNLTAD 119- Query: 121 ------QVLQVHGNSYSDTDPKYTAGMISLKGG 147 L + G + S + K+ +G L G Sbjct: 120 RAKRFGSSLMITGVNDSSKEDKFVSGSYKLVEG 152 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1233 A DNA sequence (GBSx1309) was identified in S. agalactiae <SEQ ID 3823> which encodes the amino acid sequence <SEQ ID 3824>. Analysis of this protein sequence reveals the following: TABLE-US-03726 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -15.76 Transmembrane 295-311 (287-317) INTEGRAL Likelihood = -7.59 Transmembrane 49-65 (46-69) INTEGRAL Likelihood = -6.90 Transmembrane 340-356 (339-362) INTEGRAL Likelihood = -5.57 Transmembrane 411-427 (404-430) ----- Final Results ----- bacterial membrane --- Certainty = 0.7305(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9695> which encodes amino acid sequence <SEQ ID 9696> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03727 >GP: CAB12182 GB: Z99106 similar to transporter [Bacillus subtilis] Identities = 95/370 (25%), Positives = 167/370 (44%), Gaps = 41/370 (11%) Query: 109 ESVEASLSIDVGSRLKSVSPYNSS--------KEENQVTLAGYQSTEDLRAFQTKALVLK 16- 0 +++ E+S S D S S + NS + +++ G ST + F + Sbjct: 115 DAIESSSSSDSSSSSSSSNAKNSQGGGQGGPQMVQADLSIEGVISTALVDDFSDGDSKIT 17- 4 Query: 161 KGSHLAADNT--KQVLVPLKLAQKNHLSVGNKLRLGK---ENVT----IAGIYDANSA-- 20- 9 G + + K ++ LA++N LSVG+ + + E+ T I GIY S+ Sbjct: 175 DGRAITKSDVGKKVTVINETLAEENDLSVGDSITIESATDEDTTVKLKIVGIYKTTSSGD 23- 4 Query: 210 -KSKNTFNPNIDNTLIAQATLVRKISKQKGYQTV---AVRLSDKRLVDTVIQNIKQWPLD 26- 5 +++N N N L T + T+ + D + +DT ++ K+ +D Sbjct: 235 DQAQNFSFLNPYNKLYTPYTATAALKGDDYKNTIDSAVYYMDDAKNMDTFVKAAKKTSID 29- 4 Query: 266 FGKLDVQTAKEFYGDSYRNIETLHRLVGRIILIVSLVAMAILVVMLTFWINNRIKETGIL 32- 5 F + T + Y IE + ++ +VS+ IL +++ I R E G+L Sbjct: 295 FDTYTLNTNDQLYQQMVGPIENVASFSKNVVYLVSVAGAVILGLIVMMSIRERKYEMGVL 35- 4 Query: 326 LAIGKTKFEIIGHYLIEVLLVAGAAFTLSIIGGVFLGKTFAAGLLSQV------------ 37- 3 +AIG+ ++++IG +L E+L+VA A L+ + G + LLSQ Sbjct: 355 MAIGEKRWKLIGQFLTEILIVAVIAIGLASVTGNLVANQLGNQLLSQQISSSTDSTQTAS 41- 4 Query: 374 ------NGGVSSQIVQNSSLIIDRIDNLAVSVGVMDVFRLYAQGALICLFAVVLSSYSIL 42- 7 GG+ ++ +SS +D ID+L V+V + D+ L G LI + A +L S S+L Sbjct: 415 GQMPGGGGGNGGKMFGHSSSNVDVIDSLNVAVSMNDMLILGGIGILIAIIATLLPSISVL 47- 4 Query: 428 KLQPKQILSR 437 +L PK IL++ Sbjct: 475 RLHPKTILTK 484 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8757> and protein <SEQ ID 8758> were also identified. Analysis of this protein sequence reveals the following:

TABLE-US-03728 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 1.50 GvH: Signal Score (-7.5): -8.43 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 4 value: -15.76 threshold: 0.0 INTEGRAL Likelihood = -15.76 Transmembrane 295-311 (287-317) INTEGRAL Likelihood = -7.59 Transmewbrane 49-65 (46-69) INTEGRAL Likelihood = -6.90 Transmembrane 340-356 (339-362) INTEGRAL Likelihood = -5.57 Transmembrane 411-427 (404-430) PERIPHERAL Likelihood = 3.45 386 modified ALOM score: 3.65 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.7305(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00083## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1234 A DNA sequence (GBSx1310) was identified in S. agalactiae <SEQ ID 3825> which encodes the amino acid sequence <SEQ ID 3826>. Analysis of this protein sequence reveals the following: TABLE-US-03729 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03730 >GP: CAB11993 GB: Z99105 ybdG [Bacillus subtilis] Identities = 66/224 (29%), Positives = 102/224 (45%), Gaps = 22/224 (9%) Query: 84 IKEYGQKVEVKGKKMNVYTVGEGKVPIVFIPGQGTVTAKHQYHNLISNLSKTHKVVVVEP 143- +K G V+V GKKMNVY G GK VF+ G G ++ L S SK +K+ VV+ Sbjct: 41 LKGKGTVVDVDGKKMNVYQEGSGKDTFVFMSGSGIAAPAYEMKGLYSKFSKENKIAVVDR 100- Query: 144 FGSGLSDVIDQPRNLANITSDIHEALQKVGITGKYVIASHSIGGVYALKYISTYPKEVLG 20- 3 G G S+V R++ + +AL K G Y++ HSI G+ A+ + YPKE+ Sbjct: 101 AGYGYSEVSHDDRDIDTVLEQTRKALMKSGNKPPYILMPHSISGIEAMYWAQKYPKEIKA 16- 0 Query: 204 LIGLDTSTP---------GMEGGKQVDF-------------AAPVLKELPKIPKVSDDIN 24- 1 +I +D P G++ K F +A E+ + ++D+ Sbjct: 161 IIAMDIGLPQQYVTYKLSGVDRLKVRGFHLLTSIGFHRFIPSAVYNPEVIRQSFLTDEEK 22- 0 Query: 242 AQFFAIGHKILNNSNMKEEAKNSSNMINESANYKIPKGIPAMYL 285 + AI K N++M+ E S ++S N PK P + L Sbjct: 221 EIYKAINFKQFFNADMEHELLQSYQNGSKSVNLPAPKETPVLIL 264 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3826 (GBS121) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 24 (lane 9; MW 40 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 31 (lane 6; MW 65 kDa). GBS121-GST was purified as shown in FIG. 198, lane 6. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1235 A DNA sequence (GBSx1311) was identified in S. agalactiae <SEQ ID 3827> which encodes the amino acid sequence <SEQ ID 3828>. Analysis of this protein sequence reveals the following: TABLE-US-03731 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8759> which encodes amino acid sequence <SEQ ID 8760> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-03732 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 3.70 GvH: Signal Score (-7.5): -0.0600004 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 8.01 threshold: 0.0 PERIPHERAL Likelihood = 8.01 167 modified ALOM score: -2.10 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8760 (GBS60) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 7; MW 38.6 kDa). GBS60-His was purified as shown in FIG. 193, lane 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1236 A DNA sequence (GBSx1312) was identified in S. agalactiae <SEQ ID 3829> which encodes the amino acid sequence <SEQ ID 3830>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following: TABLE-US-03733 Possible site: 21 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9693> which encodes amino acid sequence <SEQ ID 9694> was also identified. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8761> and protein <SEQ ID 8762> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03734 Lipop: Possible site: 19 Crend: 5 McG: Discrim Score: 9.85 GvH: Signal Score (-7.5): -0.28 Possible site: 21 >>> May be a lipoprotein ALOM program count: 0 value: 9.07 threshold: 0.0 PERIPHERAL Likelihood = 9.07 99 modified ALOM score: -2.31 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00084## SEQ ID 8762 (GBS21) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 11 (lane 3; MW 31.6 kDa). GBS21-His was purified as shown in FIG. 192, lane 11. GBS21L was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 124 (lane 8-10; MW 66.5 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 124 (lane 11; MW 41.5 kDa) and in FIG. 180 (lane 6; MW 41 kDa). GBS21L-His was purified as shown in FIG. 232 (lanes 3 & 4) Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1237 A DNA sequence (GBSx1313) was identified in S. agalactiae <SEQ ID 3831> which encodes the amino acid sequence <SEQ ID 3832>. This protein is predicted to be endopeptidase 0. Analysis of this protein sequence reveals the following: TABLE-US-03735 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3854(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03736 >GP:AAF67832 GB:AF179267 endopeptidase PepO2 [Lactococcus lactis] Identities = 21/36 (58%), Positives = 26/36 (71%) Query: 1 MRANIPVRNFQEFYDAFGVKKGDSMYLKPEKRLTLW 36 +RANIP N +EFY+ F VK+ D MY PEKRL+W Sbjct: 592 LRANIPPTNLEEFYETFDVKETDQMYRAPEKRLKIW 627 There is also some homology to SEQ ID 2384: TABLE-US-03737 Identities = 13/36 (36%), Positives = 25/36 (69%) Query: 1 MRANIPVRNFQEFYDAFGVKKGDSMYLKPEKRLTLW 36 +R N+ + NF F++ F +K+GD+M+ P+ R+ +W Sbjct: 596 LRTNVTLTNFDAFHETFDIKEGDAMWRAPKDRVIIW 631 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1238 A DNA sequence (GBSx1314) was identified in S. agalactiae <SEQ ID 3833> which encodes the amino acid sequence <SEQ ID 3834>. This protein is predicted to be endopeptidase 0. Analysis of this protein sequence reveals the following: TABLE-US-03738 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3801(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03739 >GP:AAA16168 GB:L18760 endopeptidase [Lactococcus lactis] Identities = 118/268 (44%), Positives = 174/268 (64%), Gaps = 6/268 (2%) Query: 1 MGDYYGKKYFGEAAKKDVEHMAKKIINVYKTRLKNNTWLSENTKAMAIKKLDNMRLMIGY 60 +G +YGKKYFGEAAK DV+ M +I VY+ RL N WLS+ T AI+KLD + IG+ Sbjct: 321 IGLFYGKKYFGEAAKADVKRMVTAMIKVYQVRLSKNEWLSQETAEKAIEKLDAITPFIGF 38- 0 Query: 61 PEDYPDLYRQYQFDSKASFFENNDNYRKLSNKKTFEEFNQSNQREHWQMSANAVNAYNDP 120- P+ P++Y + + S S +E+ + K+ +TFE+F++ + W M A+ VNAY P Sbjct: 381 PDKLPEIYSRLKTTS-GSLYEDALKFDKILTARTFEKFSEDVDKTSWHMPAHMVNAYYSP 43- 9 Query: 121 NTNSIVFPAAIFQSPLYDKTKTVSQNYGAIGAIIGHEISHSFDINGMKYDEKGNLHDWWT 18- 0 ++N+IVFPAAI Q+P Y ++ SQNYG IGA+I HEISH+FD NG ++D++GNL+ WW Sbjct: 440 DSNTIVFPAAILQAPFYSLEQSSSQNYGGIGAVIAHEISHAFDNNGAQFDKEGNLNKWWL 49- 9 Query: 181 KEDLKHYKKKTQAMIDQWDGLKADGGKVDGKLTLAENIADNGGVMASLEALKTEKIQTIK 24- 0 ED + +++K + MI +DG++ + G +GKL ++ENIAD GG+ A+L A K EK +K Sbjct: 500 DEDYEAFEEKQKEMIALFDGVETEAGPANGKLIVSENIADQGGITAALTAAKDEKDVDLK 55- 9 Query: 241 NFLNHGQVFGVKKQPKNKVSPQFSQMFM 268 F + K + K S +F QM + Sbjct: 560 AFFSQW-----AKIWRMKASKEFQQMLL 582 There is also homology to SEQ ID 2384: TABLE-US-03740 Identities = 110/253 (43%), Positives = 161/253 (63%), Gaps = 1/253 (0%) Query: 1 MGDYYGKKYFGEAAKKDVEHMAKKIINVYKTRLKNNTWLSENTKAMAIKKLDNMRLMIGY 60 +G +Y + F AK DVE ++I VYK+RL+ WL+ T+ AI KL+ + IGY Sbjct: 324 LGLWYAGQKFSPEAKADVESKVARMIEVYKSRLETADWLAPATREKAITKLNVITPHIGY 38- 3 Query: 61 PEDYPDLYRQYQFDSKASFFENNDNYRKLSNKKTFEEFNQSNQREHWQMSANAVNAYNDP 120- PE P+ Y + D S EN N K++ T+ ++N+ R W M A+ VNAY D Sbjct: 384 PEKLPETYAKKVIDESLSLVENAQNLAKITIAHTWSKWNKPVDRSEWHMPAHLVNAYYDL 44- 3 Query: 121 NTNSIVFPAAIFQSPLYDKTKTVSQNYGAIGAIIGHEISHSFDINGMKYDEKGNLHDWWT 18- 0 N IVFPAAI Q P Y ++ S NYG IGA+I HEISH+FD NG +DE G+L+DWWT Sbjct: 444 QQNQIVFPAAILQEPFYSLDQSSSANYGGIGAVIAHEISHAFDTNGASFDEHGSLNDWWT 50- 3 Query: 181 KEDLKHYKKKTQAMIDQWDGLKADGGKVDGKLTLAENIADNGGVMASLEALKTEKIQTIK 24- 0 +ED +K++T ++ Q+DGL++ G KV+GKLT++EN+AD GGV +LEA ++E+ + + Sbjct: 504 QEDYAAFKERTDKIVAQFDGLESHGAKVNGKLTVSENVADLGGVACALEAAQSEEDFSAR 56- 3 Query: 241 N-FLNHGQVFGVK 252 + F+N ++ +K Sbjct: 564 DFFINFATIWRMK 576 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1239 A DNA sequence (GBSx1315) was identified in S. agalactiae <SEQ ID 3835> which encodes the amino acid sequence <SEQ ID 3836>. Analysis of this protein sequence reveals the following: TABLE-US-03741 Possible site: 39 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9691> which encodes amino acid sequence <SEQ ID 9692> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03742 >GP:AAC35997 GB:AF019410 endopeptidase O [Lactobacillus helveticus] Identities = 85/315 (26%), Positives = 146/315 (45%), Gaps = 8/315 (2%) Query: 46 NVSPRENLYRAVNDNWLANTKLKQGQTSVNSFSEIEDKLKQLLVSDMAKMASGKIETTN- 104- N P++NLY AVN WL+ ++ QTS +E++ K+++ ++ D A +ASGK + + Sbjct: 20 NAKPQDNLYLAVNSEWLSKAEIPADQTSAGVNTELDIKIEKRMMKDFADIASGKEKMPDI 79 Query: 105 DEQKKMVAYYKQGMDFKTRDKNGLKPLKPVLQKLEAVSSMKDFQSLAHDFVMSGFVLPFG 16- 4 + K +A YK +F RD P++ LQK+ + + F+ A + M + LPF Sbjct: 80 RDFDKAIALYKIAKNFDKRDAEKANPIQNDLQKILDLINFDKFKDNATELFMGPYALPFV 139- Query: 165 LTVETNARDNSQKQLVLRQAPALLESPDQYKKGNKEGEAKLSAYRTSAMALLKQAGKSNI 22- 4 V+ + ++ L L YK E + L ++ LL+ AG Sbjct: 140 FDVDADMKNTDFNVLHFGGPSTFLPDTTTYK--TPEAKKLLDILEKQSINLLEMAGIGKE 19- 7 Query: 225 EDRKLVKQAIAFDRLLSEKTQVDQSKITAESETAAGRYNPESMETVHNYAKEFDFKELIE 28- 4 E R V+ A+AFD+ LS+ K T E A YNP S+ K FD + ++ Sbjct: 198 EARVYVQNALAFDQKLSKVV-----KSTEEWSDYAAIYNPVSLTEFLAKFKSFDMADFLK 25- 2 Query: 285 KLVGPTNKAVNVEDKTYFKQVNDVINSKQLANMKAWMMISMLVDQSDFLGEQNRQAASAF 34- 4 ++ + V V + + +++IN +K WM++ + + +L + R AA F Sbjct: 253 TILPEKVERVIVMEPRFLDHADELINPANFDEIKGWMLVKYINSVAKYLSQDFRAAAFPF 31- 2 Query: 345 KNVASGLTQIESKEK 359 SG ++ S+ K Sbjct: 313 NQAISGTPELPSQIK 327 A related GBS gene <SEQ ID 8763> and protein <SEQ ID 8764> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03743 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 5.41 GvH: Signal Score (-7.5): -1.39 Possible site: 36 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 2.76 threshold: 0.0 PERIPHERAL Likelihood = 2.76 151 modified ALOM score: -1.05 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8764 (GBS12) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 1 (lane 7; MW 65 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 3 (lane 3; MW 39 kDa). The GST-fusion protein was purified as shown in FIG. 189, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1240 A DNA sequence (GBSx1317) was identified in S. agalactiae <SEQ ID 3839> which encodes the amino acid sequence <SEQ ID 3840>. Analysis of this protein sequence reveals the following: TABLE-US-03744 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.75 Transmembrane 301-317 (299-317) ----- Final Results ----- bacterial membrane --- Certainty = 0.1702(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03745 >GP: CAB42180 GB: A67181 unnamed protein product [unidentified] Identities = 245/771 (31%), Positives = 410/771 (52%), Gaps = 80/771 (10%) Query: 22 VRVIVEFNKESILDYATEQKKTVAQLNQADVEKKLQSIKQEQDKVLKNIEKSVHEDSSIIV 81- VRVIV NK + D+ ++ + A + + +E+ +K Q+KV+K +E+ +KV Sbjct: 97 VRVIVSLNKSAAFDHTSKPTGSAASVKK--IEQASDQVKDGQEKVIKQVEE---ITGNKV 151- Query: 82 KR-YDAIINGVALDIQAQEIEKLKTIADVRRVYVSQEYVQTKPLLSSSGQLIGLPEVWNN 140- +R + ++N ++D+ +I+K+K + V+ V + Y P S+ Q+ + +VW Sbjct: 152 RRQFGYLVNAFSIDMDLDDIDKVKDLPQVKNVTPVKVY---HPTDESADQMAQVQDVWQE 20- 8 Query: 141 SQYKGEGTVVAVIDSGVDFKHQALKIKEPNRAKYNKTSIE----KLIHEKNLKGKFYSEK 19- 6 + KGEG V+++ID+G+D HQ LK+ +K+ +E KL H GK+Y+EK Sbjct: 209 QKLKGEGMVISIIDTGIDSSHQDLKLDSGVSTALSKSEVESDKSKLGH-----GKYYTEK 26- 3 Query: 197 VPYGYNYYDYNDNLKDS-YGVMHGMHVTGIVGANDDNQKLYGVAPNAQILAMKVFSDDQQ 25- 5 VPYGYNY D ND + D+ G MHG HV GI GAN ++ GVAP+AQ+LAMKVFS++ + Sbjct: 264 VPYGYNYADKNDQIVDNGCGEMHGQHVAGIAGANG---QVKGVAPDAQLLAMKVFSNNAK 32- 0 Query: 256 NPTTFTDVWLKALDDAILLKADVVNMSLGTPAGFVHEGKDYPELEVIARACKAGIVIAVA 31- 5 N + D + A++D++ L ADV+NMSLG+ + V G P+ + +A+A +AG++ ++ Sbjct: 321 NSGAYDDDIISAIEDSVKLGADVINMSLGSVSSDV--GPSDPQQQAVAKASEAGVINVIS 37- 8 Query: 316 AGNE---GNITDGNTYGVKPLAENYDTALIANPALDDNTLAVASMENLKKHAHVLKFK-- 37- 0 AGN G+ DGN +E + + P + + L VAS EN K +K + Sbjct: 379 AGNSGVAGSTADGNPVNNTGTSE---LSTVGTPGVTPDALTVASAENSKVTTDTVKDELG 43- 5 Query: 371 --------DKKSGTEVTEVINLHVAPNASKTIIGLAVDLGAGAPSELS--KHFDLSGKIA 42- 0 + K +VT + + + K + VD+G G + + K ++ G++A Sbjct: 436 GVTFSSNSELKGAAQVTTQLESNYSVLTKKLKL---VDMGLGGADDYTAEKKAEVKGQLA 49- 2 Query: 421 MLEIPEDNKSNGFLEKVQAITKLNPAAILLYNNAKVKDDLGSQLLVESEAAKFNIARITR 48- 0 +++ + F KV A I++YN+ D L S L + +++ Sbjct: 493 VVK----RGAYTFSAKVANAKAAGAAGIVIYNSE--DDGLLSMSLDDKTFPTLGMSKADG 54- 6 Query: 481 STY----NNIKNNSNKIITILTERQAIDNSLAGQLSSYSSWGPTPDLRLKPEITAPGGHI 53- 6 + ++ + K T L IDNS AG++S ++SWGPTP+L KPEITAPGG I Sbjct: 547 KFWLKQQKKVRASRLKFGTAL-----IDNSRAGKMSDFTSWGPTPELDFKPEITAPGGKI 60- 1 Query: 537 FSTVEDNQYADKSGTSMAAPQVAGAAAVLKQYITDKKIPV--DNAADFIKLLLMNTAQPI 59- 4 +S DN+Y SGTSMA+P VAG+ A++ Q I + + + + F K MNT+ P+ Sbjct: 602 YSLANDNKYQQMSGTSMASPFVAGSEALILQGIKKQGLNLSGEELVQFAKNSAMNTSHPV 66- 1 Query: 595 IN-KQSKDGKTPYFVRQQGSGAMNLAKALVTTVVATVTGTNDNNADGKLELREL-KEKKF 65- 2 + + +K+ +P R+QGSG +N+ A+ TV N +G L+E+ ++ F Sbjct: 662 YDTEHTKEIISP---RRQGSGEINVKDAINNTVEVKAA-----NGNGAAALKEIGRQTTF 71- 3 Query: 653 KARILLRNFGKTNKTYIISSEA--IADPVDEKGFRTQNSEHLVSKKADAVTRKVTVEAGK 71- 0 K + L N GK +TY + + + K +++ +V + T KVTV+ G+ Sbjct: 714 K--VTLTNHGKKAQTYAVDNYGGPYTQATEAKSGEIYDTK-IVKGQLTTETPKVTVQPGE 77- 0 Query: 711 TLAVDLDVDYSDAEALTRNNFLEGYLNLK-DTEGVADLHLPFLGFYGSWTE 760 +VD+ + + R NF+EGY+ + + +L LP++GF+GS+++ Sbjct: 771 --SVDVSFTLTLPYSFQRQNFVEGYVGFEAKDQATPNLVLPYMGFFGSYSQ 819 A related GBS gene <SEQ ID 8767> and protein <SEQ ID 8768> were also identified. Analysis of this protein sequence reveals the following:

TABLE-US-03746 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -8.37 GvH: Signal Score (-7.5): -6.06 Possible site: 15 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -1.75 threshold: 0.0 INTEGRAL Likelihood = -1.75 Transmembrane 301-317 (299-317) PERIPHERAL Likelihood = 1.75 614 modified ALOM score: 0.85 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1702(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00085## ##STR00086## SEQ ID 8768 (GBS362N) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 149 (lane 10; MW 63.5 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 182 (lane 9; MW 38 kDa) and in FIG. 149 (lane 11 & 12; MW 38 kDa). Purified GBS362N is shown in FIG. 235, lanes 3 & 4 GBS362C was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 149 (lane 14-16; MW 91 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 155 (lane 18; MW 66.3 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1241 A DNA sequence (GBSx1318) was identified in S. agalactiae <SEQ ID 3841> which encodes the amino acid sequence <SEQ ID 3842>. Analysis of this protein sequence reveals the following: TABLE-US-03747 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.04 Transmembrane 21-37 (17-38) ----- Final Results ----- bacterial membrane --- Certainty = 0.2614(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03748 >GP: BAA95000 GB: AB042239 PAa [Streptococcus criceti ] Identities = 55/166 (33%), Positives = 81/166 (48%), Gaps = 24/166 (14%) Query: 5 KKTDKFGFRKSKVCRSLCGALLGTVAVVSLATASTEIHADEATTSPTTVTKVPQPVQADT 64 K+ + FGFRKSK+ +SLCGALLGT VVS+ A A++ TTS T+ DT Sbjct: 2 KRKETFGFRKSKISKSLCGALLGTAIVVSV--AGQRALAEDMTTSTTSA--------VDT 51 Query: 65 TALNTSKTHSTQATTTPVEAKENKVVKSETVQSESRV--MPRD-KVVERPETVKASVNS- 120- TA+ ++T + +A + ++ Q+E + MP D E E VK++ + Sbjct: 52 TAVVGTETGNPATNLPEKQADSSSQAEASQAQAEQKTGSMPVDVATTELDEAVKSAAEAG 111- Query: 121 -DVSQPITTTPPTI------NEKTVEIPNLAQDTKKVAPKVTVTPE 159 VSQ T T+------+EK+ EI D K A + +T E Sbjct: 112 VTVSQDETVDKGTVGTSQEADEKSGEI---KADYSKQAETIKITTE 154 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3842 (GBS222) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 44 (lane 6; MW 22 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1242 A DNA sequence (GBSx1319) was identified in S. agalactiae <SEQ ID 3843> which encodes the amino acid sequence <SEQ ID 3844>. This protein is predicted to be CylK. Analysis of this protein sequence reveals the following: TABLE-US-03749 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3738(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1243 A DNA sequence (GBSx1320) was identified in S. agalactiae <SEQ ID 3845> which encodes the amino acid sequence <SEQ ID 3846>. This protein is predicted to be CylJ. Analysis of this protein sequence reveals the following: TABLE-US-03750 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1143(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9689> which encodes amino acid sequence <SEQ ID 9690> was also identified. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1244 A DNA sequence (GBSx1321) was identified in S. agalactiae <SEQ ID 3847> which encodes the amino acid sequence <SEQ ID 3848>. Analysis of this protein sequence reveals the following: TABLE-US-03751 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0913(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1245 A DNA sequence (GBSx1322) was identified in S. agalactiae <SEQ ID 3849> which encodes the amino acid sequence <SEQ ID 3850>. This protein is predicted to be CylI (fabF). Analysis of this protein sequence reveals the following: TABLE-US-03752 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.39 Transmembrane 721-737 (721-738) INTEGRAL Likelihood = -1.97 Transmembrane 326-342 (326-343) INTEGRAL Likelihood = -0.43 Transmembrane 534-550 (534-550) ----- Final Results ----- bacterial membrane --- Certainty = 0.1956(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9687> which encodes amino acid sequence <SEQ ID 9688> was also identified. There is also homology to SEQ ID 3852. A related GBS gene <SEQ ID 8769> and protein <SEQ ID 8770> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03753 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 1.08 GvH: Signal Score (-7.5): -5.97 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 3 value: -2.39 threshold: 0.0 INTEGRAL Likelihood = -2.39 Transmembrane 712-728 (712-729) INTEGRAL Likelihood = -1.97 Transmembrane 317-333 (317-334) PERIPHERAL Likelihood = 3.45 492 modified ALOM score: 0.98 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1956(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8770 (GBS361) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 73 (lane 4; MW 84 kDa). GBS361-His was purified as shown in FIG. 213, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1246 A DNA sequence (GBSx1323) was identified in S. agalactiae <SEQ ID 3853> which encodes the amino acid sequence <SEQ ID 3854>. This protein is predicted to be CylF. Analysis of this protein sequence reveals the following: TABLE-US-03754 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3766(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1247 A DNA sequence (GBSx1324) was identified in S. agalactiae <SEQ ID 3855> which encodes the amino acid sequence <SEQ ID 3856>. This protein is predicted to be CylE. Analysis of this protein sequence reveals the following: TABLE-US-03755 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3498(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1248 A DNA sequence (GBSx1325) was identified in S. agalactiae <SEQ ID 3857> which encodes the amino acid sequence <SEQ ID 3858>. This protein is predicted to be ABC transporter homolog CylB. Analysis of this protein sequence reveals the following: TABLE-US-03756 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.90 Transmembrane 271-287 (263-291) INTEGRAL Likelihood = -10.30 Transmembrane 17-33 (14-43) INTEGRAL Likelihood = -8.60 Transmembrane 114-130 (106-138) INTEGRAL Likelihood = -6.69 Transmembrane 152-168 (149-178) INTEGRAL Likelihood = -1.97 Transmembrane 186-202 (185-202) ----- Final Results ----- bacterial membrane --- Certainty = 0.6562(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9685> which encodes amino acid sequence <SEQ ID 9686> was also identified. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1249 A DNA sequence (GBSx1326) was identified in S. agalactiae <SEQ ID 3859> which encodes the amino acid sequence <SEQ ID 3860>. This protein is predicted to be ABC transporter homolog CylA. Analysis of this protein sequence reveals the following: TABLE-US-03757 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4122(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9683> which encodes amino acid sequence <SEQ ID 9684> was also identified. A further related GBS gene <SEQ ID 8771> and protein <SEQ ID 8772> were also identified. Analysis of this protein sequence reveals homology to membrane protein ABC transporters. A further related DNA sequence was identified in S. pyogenes <SEQ ID 9085> which encodes the amino acid sequence <SEQ ID 9086>. An alignment of the GAS and GBS sequences follows: TABLE-US-03758 Score = 85.4 bits (208), Expect = 1e-18 Identities = 68/271 (25%), Positives = 129/271 (47%), Gaps = 17/271 (6%) Query: 39 KGFTEQHVLKDINFDVYKGDFFGIVGRNGSGKSTLLKIISQIYVPEKGQVT--VDGKMVS 96 - K + L+DIN +G F+G++G NG+GK+TL ++ Q + G + VDGK +S Sbjct: 10 KKYGSFEALRDINLIFEEGKFYGLLGPNGAGKTTLFNLLIQNFKQTSGDIKWEVDGKPLS 69 Query: 97 ----FIELGVGF-----NPELTGRENVYMNGAMLGFTKDEVDDMYNDIVDFAELHHFMNQ 147- + +G+ F + LT EN+ GA+ G +K +V + D+ + ++ Q Sbjct: 70 IKDFYRHIGIVFQSNRLDDNLTVEENLISRGALYGLSKSQVRNRLKDLQTYLDITAIKKQ 129- Query: 148 KLKNYSSGMQVRLAFSVAIKAQGDVLILDEVLAVGDEAFQRKCNDYFME-RKDSGKTTIL 20- 6 K + S G + ++ + A+ Q +L+LDE D +R D + + S T +L Sbjct: 130 KYGSLSGGQKRKVDIARALLPQPSLLLLDEPTTGLDPQSRRDLWDAIAQLNQQSQMTVVL 18- 9 Query: 207 VTHDMGAVKKYCNRAVLIEDGLVKAYGEPFDVANQYSVDNTETA-EDAMNAEKISVSDIA 26- 5 +TH + + C+ ++ +G + G+ Q+S N + + +++S++D Sbjct: 190 ITHYLEEMSA-CDVLNVLIEGNIYYSGDIKSFIEQHSTTNLNVVLKPEKSLDQLSIADFV 24- 8 Query: 266 KDLKVSLISNPRITPNDTITFEVSYEVLKDD 296 K ++S I D I+ E +V+ D+ Sbjct: 249 N--KCQVLSEREIVFKD-ISVEEMMQVISDN 276 There is also homology to SEQ IDs 358, 482, 644, 686, 1832, 2429, 2720, 3882, 4028, 4104, 4280, 5090, 5498, 6034, 6500. SEQ ID 8772 (GBS83) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 20 (lane 2; MW 37.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 21 (lane 5; MW 62.6 kDa) and in FIG. 28 (lane 3; MW 62.6 kDa). GBS83-GST was purified as shown in FIG. 195, lane 6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1250 A DNA sequence (GBSx1327) was identified in S. agalactiae <SEQ ID 3861> which encodes the amino acid sequence <SEQ ID 3862>. This protein is predicted to be acyl carrier protein homolog AcpC. Analysis of this protein sequence reveals the following: TABLE-US-03759 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3451(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1251 A DNA sequence (GBSx1328) was identified in S. agalactiae <SEQ ID 3863> which encodes the amino acid sequence <SEQ ID 3864>. This protein is predicted to be CylG (fabG). Analysis of this protein sequence reveals the following: TABLE-US-03760 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2651(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> There is also homology to SEQ ID 3866. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1252 A DNA sequence (GBSx1329) was identified in S. agalactiae <SEQ ID 3867> which encodes the amino acid sequence <SEQ ID 3868>. This protein is predicted to be CylD. Analysis of this protein sequence reveals the following: TABLE-US-03761 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2030(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1253 A DNA sequence (GBSx1330) was identified in S. agalactiae <SEQ ID 3869> which encodes the amino acid sequence <SEQ ID 3870>. Analysis of this protein sequence reveals the following: TABLE-US-03762 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3219(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1254 A DNA sequence (GBSx1331) was identified in S. agalactiae <SEQ ID 3871> which encodes the amino acid sequence <SEQ ID 3872>. Analysis of this protein sequence reveals the following: TABLE-US-03763 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.97 Transmembrane 231-247 (226-251) INTEGRAL Likelihood = -7.06 Transmembrane 141-157 (134-164) INTEGRAL Likelihood = -2.76 Transmembrane 28-44 (26-44) INTEGRAL Likelihood = -1.38 Transmembrane 123-139 (121-139) INTEGRAL Likelihood = -0.32 Transmembrane 199-215 (199-215) ----- Final Results ----- bacterial membrane --- Certainty = 0.4588(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03764 >GP: CAB88836 GB: AL353832 putative integral membrane transport protein. [Streptomyces coelicolor A3(2)] Identities = 68/264 (25%), Positives = 123/264 (45%), Gaps = 10/264 (3%) Query: 6 RMHFIFIKQYMKQIMEYKIDFFVGVLGVFLTQGLNLLFLNVLFQHIPSLEGWTFQQIAFI 65 R + + +++ M Y+ F + G F L+ + + ++F + +L G++ ++AF+ Sbjct: 34 RAYGLIAGMWIRSTMAYRTSFALTAFGNFAMTALDFVAILLMFSRVDALGGYSLPEVAFL 93 Query: 66 YGFSLLPKGIDHLFFDNLWALGQRLIRKGEFDKYLTRPISPLFHVLVETFQVDALGELLV 125- YG S + G+ L ++ LG+R +R G D L RP L V + F + LG ++ Sbjct: 94 YGLSGVSFGLADLAIGSMERLGRR-VRDGTLDTLLVRPAPVLAQVAADRFALRRLGRVVQ 152- Query: 126 GFILL--STTVSSISWTVPKVLLFIFIIPFATLIYTSLKIATSSIAFWTKQSGAVIYIF- 18- 2 G ++L + V I WT KVLL + I+ ++ +A + F + + V F Sbjct: 153 GLLVLGYALVVVDIDWTAAKVLLLPVALISGAGIFCAVFVAAGAFQFAAQDASEVANAFT 21- 2 Query: 183 YMFNDFAKYPVAIYNNLLRWIISFVIPFAFTAYYPAAYFLQDRNVYFNIGGVI-----LI 23- 7 Y +YP ++ L +FV+P AF + PA+Y L R ++ G + L Sbjct: 213 YGGTTMLQYPPTVFALDLVRGATFVLPLAFVNWLPASYVL-GRPYPLDLPGWVAFTPPLA 27- 1 Query: 238 SLISFMVSLILWHKGVEVYESAGS 261 + ++ + W G+ Y S GS Sbjct: 272 AAACCALAGLAWRAGLRSYRSTGS 295 A related DNA sequence was identified in S. pyogenes <SEQ ID 3873> which encodes the amino acid sequence <SEQ ID 3874>. Analysis of this protein sequence reveals the following:

TABLE-US-03765 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.86 Transmembrane 227-243 (225-251) INTEGRAL Likelihood = -7.22 Transmembrane 141-157 (133-164) INTEGRAL Likelihood = -6.37 Transmembrane 123-139 (114-140) INTEGRAL Likelihood = -2.97 Transmembrane 26-42 (26-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.4545(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03766 >GP: CAB88836 GB: AL353832 putative integral membrane transport protein. [Streptomyces coelicolor A3(2)] Identities = 69/262 (26%), Positives = 125/262 (47%), Gaps = 10/262 (3%) Query: 8 HAIFIKQYLKQIMEYKVDFVVGVLGVFLTQGLNLLFLSVLFQHIPSLEGWTFEQIAFIYG 67 + + +++ M Y+ F + G F L+ + + ++F + +L G++ ++AF+YG Sbjct: 36 YGLIAGMWIRSTMAYRTSFALTAFGNFAMTALDFVAILLMFSRVDALGGYSLPEVAFLYG 95 Query: 68 FCLIPKGIDHLFFDNLWALGQRLVRKGEFDKYLTRPISPLFHVLVETFQVDALGELLVGV 127- + G+ L ++ LG+R VR G D L RP L V + F + LG ++ G+ Sbjct: 96 LSGVSFGLADLAIGSMERLGRR-VRDGTLDTLLVRPAPVLAQVAADRFALRRLGRVVQGL 154- Query: 128 ILL--VTTAGSIVWTLPKVLLFILVIPFATLIYTSLKIATASISFWTKQSGAVIYIF-YM 18- 4 ++L I WT KVLL + + I+ ++ +A + F + + V F Y Sbjct: 155 LVLGYALVVVDIDWTAAKVLLLPVALISGAGIFCAVFVAAGAFQFAAQDASEVANAFTYG 21- 4 Query: 185 FNDFSKYPMSIYHSFLRWLISFIIPFAFTAYYPASYFLTGQHLLFNIGGLV-----VVSL 23- 9 +YP +++ L +F++P AF + PASY L G+ ++ G V + + Sbjct: 215 GTTMLQYPPTVFALDLVRGATFVLPLAFVNWLPASYVL-GRPYPLDLPGWVAFTPPLAAA 27- 3 Query: 240 LVLALSLKLWKWGLDAYESAGS 261 AL+ W+ GL +Y S GS Sbjct: 274 ACCALAGLAWRAGLRSYRSTGS 295 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03767 Identities = 208/261 (79%), Positives = 238/261 (90%) Query: 1 MTKYQRMHFIFIKQYMKQIMEYKIDFFVGVLGVFLTQGLNLLFLNVLFQHIPSLEGWTFQ 60 M K + MH IFIKQY+KQIMEYK+DF VGVLGVFLTQGLNLLFL+VLFQHIPSLEGWTF+ Sbjct: 1 MAKLRCMHAIFIKQYLKQIMEYKVDFVVGVLGVFLTQGLNLLFLSVLFQHIPSLEGWTFE 60 Query: 61 QIAFIYGFSLLPKGIDHLFFDNLWALGQRLIRKGEFDKYLTRPISPLFHVLVETFQVDAL 120- QIAFIYGF L+PKGIDHLFFDNLWALGQRL+RKGEFDKYLTRPISPLFHVLVETFQVDAL Sbjct: 61 QIAFIYGFCLIPKGIDHLFFDNLWALGQRLVRKGEFDKYLTRPISPLFHVLVETFQVDAL 120- Query: 121 GELLVGFILLSTTVSSISWTVPKVLLFIFIIPFATLIYTSLKIATSSIAFWTKQSGAVIY 18- 0 GELLVG ILL TT SI WT+PKVLLFI +IPFATLIYTSLKIAT+SI+FWTKQSGAVIY Sbjct: 121 GELLVGVILLVTTAGSIVWTLPKVLLFILVIPFATLIYTSLKIATASISFWTKQSGAVIY 18- 0 Query: 181 IFYMFNDFAKYPVAIYNNLLRWIISFVIPFAFTAYYPAAYFLQDRNVYFNIGGVILISLI 24- 0 IFYMFNDF+KYP++IY++ LRW+ISF+IPFAFTAYYPA+YFL +++ FNIGG++++SL+ Sbjct: 181 IFYMFNDFSKYPMSIYHSFLRWLISFIIPFAFTAYYPASYFLTGQHLLFNIGGLVVVSLL 24- 0 Query: 241 SFMVSLILWHKGVEVYESAGS 261 +SL LW G++ YESAGS Sbjct: 241 VLALSLKLWKWGLDAYESAGS 261 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1255 A DNA sequence (GBSx1332) was identified in S. agalactiae <SEQ ID 3875> which encodes the amino acid sequence <SEQ ID 3876>. Analysis of this protein sequence reveals the following: TABLE-US-03768 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.60 Transmembrane 147-163 (134-178) INTEGRAL Likelihood = -8.55 Transmembrane 119-135 (114-141) INTEGRAL Likelihood = -7.86 Transmembrane 238-254 (235-260) INTEGRAL Likelihood = -1.70 Transmembrane 215-231 (212-231) INTEGRAL Likelihood = -1.06 Transmembrane 61-77 (61-77) INTEGRAL Likelihood = -0.22 Transmembrane 27-43 (27-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.7241(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03769 >GP: CAB88837 GB: AL353832 putative integral membrane protein. [Streptomyces coelicolor A3(2)] Identities = 60/271 (22%), Positives = 118/271 (43%), Gaps = 13/271 (4%) Query: 6 RRYKPFISTGIQGLITYRVDFILYRIGDVIGAFVAFYLWKAVFDSSSQSLIQGFQLSDMI 65 R Y + G + TYR + + + Y + A++D Q + G+ + + Sbjct: 7 RLYVAVAAGGFRRYATYRAATAAGVFTNTVFGLILVYTYLALWDEKPQ--LGGYDQAQAV 64 Query: 66 LYIIMS-FVTNLLTRTDSSFM--IGDEVKDGSIIMRLLRPVHFAASYLFMEIGSRWLIFL 122- ++ + + L F + + ++ G + + L RP +L ++G L Sbjct: 65 TFVWLGQALLAALAIGGGGFEDELMERIRTGDVAVDLYRPADLQLWWLAADVGRAVFQLL 124- Query: 123 SIGV-PFLLVITGVRLFLGTDLIQAIVLVVFYIISIILAFLINFFFNICFGFSAFVFKNL 18- 1 GV PF+ LF L + + + ++++++LA ++ F SAF + Sbjct: 125 GRGVVPFVFG----SLFFPVALPREVSVWAAFLVAVVLAMVVGFALRYLVALSAFWLLDG 18- 0 Query: 182 WGSNLLKNSLVAFMSGSLIPLTFFPKIVADILGFLPFSSLIYTPVMIIIGKYDGSQIVQA 24- 1 G + F SG L+PL FP ++ D++ LP+SSL+ P +++G+ D + Sbjct: 181 TGVTQMAWLAGLFCSGMLLPLNVFPGVLGDVVRALPWSSLLQGPADVLLGEADP---LGT 23- 7 Query: 242 LLLQIFWLIVMVALSQLIWKKVQLHITIQGG 272 L Q W + ++AL +L+ + +QGG Sbjct: 238 YLFQASWAVALLALGRLVQSAATRRVVVQGG 268 A related DNA sequence was identified in S. pyogenes <SEQ ID 3877> which encodes the amino acid sequence <SEQ ID 3878>. Analysis of this protein sequence reveals the following: TABLE-US-03770 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.18 Transmembrane 252-268 (248-277) INTEGRAL Likelihood = -7.22 Transmembrane 161-177 (151-187) INTEGRAL Likelihood = -6.10 Transmembrane 133-149 (128-160) INTEGRAL Likelihood = -2.81 Transmembrane 213-229 (211-230) ----- Final Results ----- bacterial membrane --- Certainty = 0.4673(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03771 >GP: AAF11144 GB: AE002002 conserved hypothetical protein [Deinococcus radiodurans] Identities = 56/268 (20%), Positives = 113/268 (41%), Gaps = 21/268 (7%) Query: 15 MWSFWKRYRPFLSAGIQELITYRVNFFLYRIGDVMGAFVAYYLWKAVFDSSKQSLINGFT 74 - M +FW++ R + + + YR ++ + + V +W S+ ING+T Sbjct: 1 MTNFWRKVRVLWAVSLASTLEYRAETIIWMLSGTLN-LVMMLVWMTQAKSAPGGQINGYT 59 Query: 75 LSDMTFYIIMSFVTTLLTKSDSSFMIGEEVKDGSIIMRLLRPV-----HFAASYLFMEIG 129- Y + +++ +L + + +++ G++ LL P+ FAA + Sbjct: 60 PQAFAGYFLATWLVSQLLVVWVGWELDYKIRQGTLSPELLHPIDPLWREFAAH--LTDKA 117- Query: 130 FRWIVLMSVGFPFLMVLSGIKVMAGLSILQVLASSCLYLVSLLLAFL---INFYFNICFG 18- 6 FR P ++VL + + A L+ Q + Y L LA L + F + G Sbjct: 118 FR--------LPIMLVL--LLIFAALTGAQFTSQWWAYPAVLGLALLGLCVRFLWEYTLG 16- 7 Query: 187 SSAFVFKNLWGSNLLKNALVAFMSGSLIPLAFFPKMVSIVLSFLPFSSLVYTPVMIVIGK 24- 6 AF ++ + A G PL+F+P + + ++ PF ++ P ++ GK Sbjct: 168 LLAFWTESSSSFGEVLWLFYAAFGGMFAPLSFYPGWLQTLAAWTPFPYMLGLPAALLAGK 22- 7 Query: 247 YSLSQIMVALSLQIFWLLVMVVLSQVIW 274 S ++ + + + WL VM ++ + +W Sbjct: 228 ASGAEALRGAGVLLGWLAVMWLVRRWVW 255 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03772 Identities = 199/268 (74%), Positives = 236/268 (87%) Query: 5 WRRYKPFISTGIQGLITYRVDFILYRIGDVIGAFVAFYLWKAVFDSSSQSLIQGFQLSDM 64 W+RY+PF+S GIQ LITYRV+F LYRIGDV+GAFVA+YLWKAVFDSS QSLI GF LSDM Sbjct: 19 WKRYRPFLSAGIQELITYRVNFFLYRIGDVMGAFVAYYLWKAVFDSSKQSLINGFTLSDM 78 Query: 65 ILYIIMSFVTNLLTRTDSSFMIGDEVKDGSIIMRLLRPVHFAASYLFMEIGSRWLIFLSI 124- YIIMSFVT LLT++DSSFMIG+EVKDGSIIMRLLRPVHFAASYLFMEIG RW++ +S+ Sbjct: 79 TFYIIMSFVTTLLTKSDSSFMIGEEVKDGSIIMRLLRPVHFAASYLFMEIGFRWIVLMSV 138- Query: 125 GVPFLLVITGVRLFLGTDLIQAIVLVVFYIISIILAFLINFFFNICFGFSAFVFKNLWGS 18- 4 G PEL+V++G+++ G ++Q + Y++S++LAFLINF+FNICFG SAFVFKNLWGS Sbjct: 139 GFPFLMVLSGIKVMAGLSILQVLASSCLYLVSLLLAFLINFYFNICFGSSAFVFKNLWGS 19- 8 Query: 185 NLLKNSLVAFMSGSLIPLTFFPKIVADILGFLPFSSLIYTPVMIIIGKYDGSQIVQALLL 24- 4 NLLKN+LVAFMSGSLIPL FFPK+V+ +L FLPFSSL+YTPVMI+IGKY SQI+ AL L Sbjct: 199 NLLKNALVAFMSGSLIPLAFFPKMVSIVLSFLPFSSLVYTPVMIVIGKYSLSQIMVALSL 25- 8 Query: 245 QIFWLIVMVALSQLIWKKVQLHITIQGG 272 QIFWL+VMV LSQ+IWKKVQ H+TIQGG Sbjct: 259 QIFWLLVMVVLSQVIWKKVQYHLTIQGG 286 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1256 A DNA sequence (GBSx1333) was identified in S. agalactiae <SEQ ID 3879> which encodes the amino acid sequence <SEQ ID 3880>. This protein is predicted to be ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-03773 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2013(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9681> which encodes amino acid sequence <SEQ ID 9682> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03774 >GP: AAF09790 GB: AE001882 ABC transporter, ATP-binding protein [Deinococcus radiodurans] Identities = 141/331 (42%), Positives = 201/331 (60%), Gaps = 34/331 (10%) Query: 10 MIEVSHLQKNFIKTVKAPGLKGAFQSFLRPEKHTFEAVKDLTFDVPKGQILGFIGANGAG 69 - MIEV HL K+F + AV+D++F +P G+I+G++G NGAG Sbjct: 46 MIEVRHLCKSFARK---------------------PAVQDISFSIPAGEIVGYLGPNGAG 84 Query: 70 KSTTIKMLTGILKPTSGFCRIDGKLPQENRQNYVKDIGVVFGQRTQLWWDLALQETYTVL 129- KSTTIK+LTG+L P SG R+ G +P + R+ +V +G VFGQRT LWWDL ++E+ +L Sbjct: 85 KSTTIKVLTGLLVPDSGEVRVGGLVPWKQRRQHVARLGAVFGQRTTLWWDLPVRESLELL 144- Query: 130 KEIYDVPDKEFRKRMAFLNEVLELNDFIKDPVRTLSLGQRMRADIAASLLHNPKVLFLDE 18- 9 + +Y VP F + +A E+LEL F+ P R LSLGQRMRAD+AA+LLH+P++LFLDE Sbjct: 145 RHVYRVPAARFAENLAGFTELLELGPFLNTPARALSLGQRMRADLAAALLHDPELLFLDE 20- 4 Query: 190 PTIGLDVSVKDNIRRAITQINQEEETTILLTTHDLSDIEQLCHRIFMIDRGQEIFDGTVS 24- 9 PT+GLDV K+ IR + +N E T+LLTTHDL D+E+L R+ MID G+ +FDG ++ Sbjct: 205 PTVGLDVVAKERIREFVKAVNAERGVTVLLTTHDLGDVERLARRVMMIDTGRLLFDGPLA 26- 4 Query: 250 QLKETFGRMKTL--SFDLRPGQEHISS-SLIGKSEINIKRNDLVLDIQYDSSRYQTADII 30- 6 +L+ +G + L F+ P Q + +L+G+ ++ Y S A I Sbjct: 265 ELQARYGGERELWVEFEKAPAQPALPGLTLLGQDGPRVR---------YGFSGAAAAPIA 31- 5 Query: 307 QQTLADFSVRDLKMTDADIEDIIRRFYRNEL 337 Q T A VRDL + + ++E IRR Y L Sbjct: 316 QVT-ALAPVRDLAVKEPEVEATIRRIYEGNL 345 A related DNA sequence was identified in S. pyogenes <SEQ ID 3881> which encodes the amino acid sequence <SEQ ID 3882>. Analysis of this protein sequence reveals the following: TABLE-US-03775 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3315(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03776 Identities = 272/330 (82%), Positives = 305/330 (92%) Query: 8 MSMIEVSHLQKNFIKTVKAPGLKGAFQSFLRPEKHTFEAVKDLTFDVPKGQILGFIGANG 67 M MIEVSHLQKNF KT+K PGLKGA +SF+ P + FEAVKDL+F+VPKGQILGFIGANG Sbjct: 1 MVMIEVSHLQKNFSKTIKEPGLKGALKSFVHPPREIFEAVKDLSFEVPKGQILGFIGANG 60 Query: 68 AGKSTTIKMLTGILKPTSGFCRIDGKLPQENRQNYVKDIGVVFGQRTQLWWDLALQETYT 127- AGKSTTIKMLTGILKPTSG+CRI+GK+PQ+NRQ YV+DIG VFGQRTQLWWDLALQETY Sbjct: 61 AGKSTTIKMLTGILKPTSGYCRINGKIPQDNRQYYVRDIGAVFGQRTQLWWDLALQETYV 120- Query: 128 VLKEIYDVPDKEFRKRMAFLNEVLELNDFIKDPVRTLSLGQRMRADIAASLLHNPKVLFL 18- 7 VLKEIYDVP+K FRKRM FLNEVL+LN+FIKDPVRTLSLGQRMRADIAASLLHNPKVLFL Sbjct: 121 VLKEIYDVPEKAFRKRMDFLNEVLDLNEFIKDPVRTLSLGQRMRADIAASLLHNPKVLFL 18- 0 Query: 188 DEPTIGLDVSVKDNIRRAITQINQEEETTILLTTHDLSDIEQLCHRIFMIDRGQEIFDGT 24- 7 DEPTIGLDVSVKDNIRRAITQINQEEETTILLTTHDLSDIEQLC RI MID+GQEIFDGT Sbjct: 181 DEPTIGLDVSVKDNIRRAITQINQEEETTILLTTHDLSDIEQLCDRIIMIDKGQEIFDGT 24- 0 Query: 248 VSQLKETFGKMKTLSFDLRPGQEHISSSLIGKSEINIKRNDLVLDIQYDSSRYQTADIIQ 30- 7 V+QLK++FGKMK+LSF+L+PGQE + S +G +I ++R++L LDIQYDSSRYQTADIIQ Sbjct: 241 VTQLKQSFGKMKSLSFELKPGQEQVVSQFMGLPDITVERHELSLDIQYDSSRYQTADIIQ 30- 0 Query: 308 QTLADFSVRDLKMTDADIEDIIRRFYRNEL 337 +T+ADF+VRD+KMTD DIEDI+RRFYR EL Sbjct: 301 KTMADFAVRDVKMTDVDIEDIVRRFYRKEL 330 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1257 A DNA sequence (GBSx1334) was identified in S. agalactiae <SEQ ID 3883> which encodes the amino acid sequence <SEQ ID 3884>. This protein is predicted to be Fmt. Analysis of this protein sequence reveals the following: TABLE-US-03777 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.39 Transmembrane 21-37 (8-39) INTEGRAL Likelihood = -7.75 Transmembrane 360-376 (359-381) ----- Final Results ----- bacterial membrane --- Certainty = 0.4758(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8775> which encodes amino acid sequence <SEQ ID 8776> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-03778 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 8.85 GvH: Signal Score (-7.5): -3.75 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 2 value: -9.39 threshold: 0.0 INTEGRAL Likelihood = -9.39 Transmembrane 21-37 (8-39) INTEGRAL Likelihood = -7.75 Transmembrane 353-369 (352-374) PERIPHERAL Likelihood = 4.24 92 modified ALOM score: 2.38 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4758(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03779 >GP: BAA24012 GB: AB009635 Fmt [Staphylococcus aureus] Identities = 72/279 (25%), Positives = 125/279 (43%), Gaps = 25/279 (8%) Query: 49 LHRFMRKNNVNGMMIVSDNTGKPITISHGINRGEVETDIEN--NKLFPMASLQKLMTGII 106- + ++++ + NG + + +N GK + +S G + E I+N N +F + S QK TG++ Sbjct: 79 IDKYLQSSLFNGSVAIYEN-GK-LKMSKGYGYQDFEKGIKNTPNTMFLIGSAQKFSTGLL 136- Query: 107 IQRLIDQDVLSEDDRLSQFFPQVKGSNSITIHQLLTHTSGLREKGVKVSPYLKNEREQLQ 16- 6 +++L ++ ++ +D +S++ P K S I + L+ H SGL + K S KN + ++ Sbjct: 137 LKQLEEEHKININDPVSKYLPWFKTSKPIPLKDLMLHQSGLYK--YKSSKDYKNLDQAVK 19- 4 Query: 167 FCLKHYNFVNK-KSWYYSNINFSFLTGIATQVTGRTYAELVDDVIKNPLRLDDTQSYQSV 22- 5 K K K Y++ N+ L + +VTG++YAE I +PL+L T Y Sbjct: 195 AIQKRGIDPKKYKKHMYNDGNYLVLAKVIEEVTGKSYAENYYTKIGDPLKLQHTAFYD-- 25- 2 Query: 226 VNHDLVSPMRKNGKLNKINIF----NQVSTAYGAGDFFTTPLNFWVLMRSFSKGYFFPT- 28- 0 + K N + N + YGAG+ + TP + L+ + F Sbjct: 253 -EQPFKKYLAKGYAYNSTGLSFLRPNILDQYYGAGNLYMTPTDMGKLITQIQQYKLFSPK 31- 1 Query: 281 -------DEYTKHQNDAISHYYGGLYMHGRIVNSNGTFF 312 + TK D Y G Y + NG FF Sbjct: 312 ITNPLLHEFGTKQYPD---EYRYGFYAKPTLNRLNGGFF 347 There is also homology to SEQ ID 3886. A related GBS gene <SEQ ID 8773> and protein <SEQ ID 8774> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03780 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: 14.89 GvH: Signal Score (-7.5): -3.75 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -9.39 threshold: 0.0 INTEGRAL Likelihood = -9.39 Transmembrane 14-30 (1-32) PERIPHERAL Likelihood = 4.24 85 modified ALOM score: 2.38 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4758(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00087## SEQ ID 8776 (GBS61) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 33 (lane 3; MW 68 kDa); GBS61-GST was purified as shown in FIG. 195, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1258 A DNA sequence (GBSx1335) was identified in S. agalactiae <SEQ ID 3887> which encodes the amino acid sequence <SEQ ID 3888>. Analysis of this protein sequence reveals the following:

TABLE-US-03781 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2398(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1259 A DNA sequence (GBSx1336) was identified in S. agalactiae <SEQ ID 3889> which encodes the amino acid sequence <SEQ ID 3890>. Analysis of this protein sequence reveals the following: TABLE-US-03782 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.57 Transmembrane 16-32 (13-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.3230(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1260 A DNA sequence (GBSx1337) was identified in S. agalactiae <SEQ ID 3891> which encodes the amino acid sequence <SEQ ID 3892>. Analysis of this protein sequence reveals the following: TABLE-US-03783 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3910(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1261 A DNA sequence (GBSx1338) was identified in S. agalactiae <SEQ ID 3893> which encodes the amino acid sequence <SEQ ID 3894>. Analysis of this protein sequence reveals the following: TABLE-US-03784 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4239(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1262 A DNA sequence (GBSx1339) was identified in S. agalactiae <SEQ ID 3895> which encodes the amino acid sequence <SEQ ID 3896>. Analysis of this protein sequence reveals the following: TABLE-US-03785 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4349(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1263 A DNA sequence (GBSx1340) was identified in S. agalactiae <SEQ ID 3897> which encodes the amino acid sequence <SEQ ID 3898>. Analysis of this protein sequence reveals the following: TABLE-US-03786 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4962(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1264 A DNA sequence (GBSx1341) was identified in S. agalactiae <SEQ ID 3899> which encodes the amino acid sequence <SEQ ID 3900>. Analysis of this protein sequence reveals the following: TABLE-US-03787 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4014(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03788 >GP: AAG38044 GB: AF295925 Orf28 [Streptococcus pneumoniae] Identities = 23/35 (65%), Positives = 28/35 (79%) Query: 9 LIHWEGNSGDKLIEHQTSATGWYYQVDRSFSQPKG 43 L +WEGNSGDKL+E QT AT WYYQ+++ FSQ G Sbjct: 180 LTYWEGNSGDKLLERQTRATEWYYQIEKGFSQTNG 214 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1265 A DNA sequence (GBSx1342) was identified in S. agalactiae <SEQ ID 3901> which encodes the amino acid sequence <SEQ ID 3902>. Analysis of this protein sequence reveals the following: TABLE-US-03789 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2036(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1266 A DNA sequence (GBSx1343) was identified in S. agalactiae <SEQ ID 3903> which encodes the amino acid sequence <SEQ ID 3904>. Analysis of this protein sequence reveals the following: TABLE-US-03790 Possible site: 47 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10933> which encodes amino acid sequence <SEQ ID 10934> was also identified. SEQ ID 3904 (GBS153) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 25 (lane 3; MW 22 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 31 (lane 4; MW 47 kDa). GBS153-GST was purified as shown in FIG. 198, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1267 A DNA sequence (GBSx1344) was identified in S. agalactiae <SEQ ID 3905> which encodes the amino acid sequence <SEQ ID 3906>. Analysis of this protein sequence reveals the following: TABLE-US-03791 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2036(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1268 A DNA sequence (GBSx1345) was identified in S. agalactiae <SEQ ID 3907> which encodes the amino acid sequence <SEQ ID 3908>. Analysis of this protein sequence reveals the following: TABLE-US-03792 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2570(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03793 >GP: CAA59773 GB: X85787 tasA [Streptococcus pneumoniae] Identities = 18/33 (54%), Positives = 28/33 (84%) Query: 2 DVQSDENFAFKIFKVAKAKGLSLDVFDKLVGRF 34 + QSD+N F++FKV+K KG++LD FD+++GRF Sbjct: 320 EYQSDKNPFFEVFKVSKTKGIALDPFDEIIGRF 352 A related DNA sequence was identified in S. pyogenes <SEQ ID 3909> which encodes the amino acid sequence <SEQ ID 3910>. Analysis of this protein sequence reveals the following: TABLE-US-03794 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2405(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03795 Identities = 18/34 (52%), Positives = 25/34 (72%) Query: 1 MDVQSDENFAFKIFKVAKAKGLSLDVFDKLVGRF 34 +DVQSDE+F FK+ KV K+KG+ L+ D+ V F Sbjct: 31 LDVQSDEDFGFKVVKVLKSKGIVLNALDESVCGF 64 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1269 A DNA sequence (GBSx1346) was identified in S. agalactiae <SEQ ID 3911> which encodes the amino acid sequence <SEQ ID 3912>. This protein is predicted to be a fimbria-associated protein. Analysis of this protein sequence reveals the following: TABLE-US-03796 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.17 Transmembrane 169-185 (168-185) ----- Final Results ----- bacterial membrane --- Certainty = 0.1468(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03797 >GP: AAC13546 GB: AF019629 putative fimbria-associated protein [Actinomyces naeslundii] Identities = 53/109 (48%), Positives = 75/109 (68%) Query: 13 IPKINQDLPIYAGSEEDNLQRGVGHLEGISLPIGGASTHAVLSGQRGMPAARLFADLDKM 72 - IP I+ DLP+Y G+ +D L +G+GHLEG SLP+GG T +V++G RG+ A +F +LDK+ Sbjct: 93 IPSISLDLPVYHGTADDTLLKGLGHLEGTSLPVGGEGTRSVITGHRGLAEATMFTNLDKV 152- Query: 73 KKGDYFYVTNLKETLAYQVDRIMVIEPSQLDAVSIEEDKDYVTLLTCTP 121 K GD V E L Y+V V+EP + +A+ +EE KD +TL+TCTP Sbjct: 153 KTGDSLIVEVFGEVLTYRVTSTKVVEPEETEALRVEEGKDLLTLVTCTP 201 There is also homology to SEQ ID 3740 and to SEQ ID 3910. SEQ ID 3912 (GBS194) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 177 (lane 2; MW 24 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1270 A DNA sequence (GBSx1347) was identified in S. agalactiae <SEQ ID 3913> which encodes the amino acid sequence <SEQ ID 3914>. Analysis of this protein sequence reveals the following: TABLE-US-03798 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.15 Transmembrane 880-896 (876-898) INTEGRAL Likelihood = -4.78 Transmembrane 24-40 (23-42) ----- Final Results ----- bacterial membrane --- Certainty = 0.3060(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8777> which encodes amino acid sequence <SEQ ID 8778> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-03799 Lipop: Possible site: -1 Crend: 8 SRCFLG: 0 McG: Length of UR: 20 Peak Value of UR: 2.80 Net Charge of CR: 5 McG: Discrim Score: 10.81 GvH: Signal Score (-7.5): -3.76 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 2 value: -5.15 threshold: 0.0 INTEGRAL Likelihood = -5.15 Transmembrane 867-883 (863-885) INTEGRAL Likelihood = -4.78 Transmembrane 11-27 (10-29) PERIPHERAL Likelihood = 7.58 531 modified ALOM score: 1.53 icm1 HYPID: 7 CFP: 0.306 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3060(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 859-863 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8778 (GBS104) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 27 (lane 5; MW 95 kDa). GBS104-His was purified as shown in FIG. 221, lane 9-10. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1271 A DNA sequence (GBSx1348) was identified in S. agalactiae <SEQ ID 3915> which encodes the amino acid sequence <SEQ ID 3916>. This protein is predicted to be a fimbria-associated protein. Analysis of this protein sequence reveals the following: TABLE-US-03800 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -15.28 Transmembrane 257-273 (252-280) INTEGRAL Likelihood = -7.11 Transmembrane 19-35 (16-39) ----- Final Results ----- bacterial membrane --- Certainty = 0.7114(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03801 >GP: AAC13546 GB: AF019629 putative fimbria-associated protein [Actinomyces naeslundii] Identities = 79/178 (44%), Positives = 112/178 (62%), Gaps = 7/178 (3%) Query: 65 RIALANAYNETLSRNPLL-----IDPFTSKQKEGLREYARMLEVHEQ--IGHVAIPSIGV 117- ++ A+AYN+ LS +L + K+ +YA +L+ + + + + IPSI + Sbjct: 39 QVEQAHAYNDALSAGAVLEANNHVPTGAGSSKDSSLQYANILKANNEGLMARLKIPSISL 98 Query: 118 DIPIYAGTSETVLQKGSGHLEGTSLPVGGLSTHSVLTAHRGLPTARLFTDLNKVKKGQIF 17- 7 D+P+Y GT++ L KG GHLEGTSLPVGG T SV+T HRGL A +FT+L+KVK G Sbjct: 99 DLPVYHGTADDTLLKGLGHLEGTSLPVGGEGTRSVITGHRGLAEATMFTNLDKVKTGDSL 158- Query: 178 YVTNIKETLAYKVVSIKVVDPTALSEVKIVNGKDYITLLTCTPYMINSHRLLVKGERI 235 V E L Y+V S KVV+P +++ GKD +TL+TCTP IN+HR+L+ GERI Sbjct: 159 IVEVFGEVLTYRVTSTKVVEPEETEALRVEEGKDLLTLVTCTPLGINTHRILLTGERI 216 There is also homology to SEQ ID 3740. SEQ ID 3916 (GBS208) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 44 (lane 5; MW 35 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 85 (lane 8; MW 59.7 kDa) and in FIG. 160 (lane 5; MW 60 kDa). GBS208-GST was purified as shown in FIG. 224, lane 7-8. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1272 A DNA sequence (GBSx1349) was identified in S. agalactiae <SEQ ID 3917> which encodes the amino acid sequence <SEQ ID 3918>. This protein is predicted to be a fimbria-associated protein. Analysis of this protein sequence reveals the following: TABLE-US-03802 Possible site: 30 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.13 Transmembrane 265-281 (260-284) ----- Final Results ----- bacterial membrane --- Certainty = 0.4652(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03803 >GP: AAC13546 GB: AF019629 putative fimbria-associated protein [Actinomyces naeslundii] Identities = 96/265 (36%), Positives = 150/265 (56%), Gaps = 10/265 (3%) Query: 41 QASHANINAFKEAVTKIDRVEINRRLELAYAYNASI-AGAKTNGEYPALKDPYSAEQKQA 99 - Q + + + A A R + ++E A+AYN ++ AGA P A + Sbjct: 15 QYNQSKVTADYSAQVDGARPDAKTQVEQAHAYNDALSAGAVLEANNHV---PTGAGSSKD 71 Query: 100 GVVEYARMLEVKEQ--IGHVIIPRINQDIPIYAGSAEENLQRGVGHLEGTSLPVGGESTH 15- 7 ++YA +L+ + + + IP I+ D+P+Y G+A++ L +G+GHLEGTSLPVGGE T Sbjct: 72 SSLQYANILKANNEGLMARLKIPSISLDLPVYHGTADDTLLKGLGHLEGTSLPVGGEGTR 131- Query: 158 AVLTAHRGLPTAKLFTNLDKVTVGDRFYIEHIGGKIAYQVDQIKVIAPDQLEDLYVIQGE 21- 7 +V+T HRGL A +FTNLDKV GD +E G + Y+V KV+ P++ E L V +G+ Sbjct: 132 SVITGHRGLAEATMFTNLDKVKTGDSLIVEVFGEVLTYRVTSTKVVEPEETEALRVEEGK 19- 1 Query: 218 DHVTLLTCTPYMINSHRLLVRGKRI-PYVEKTVQKDSKTFRQQQYLTYAMWVVVGLILLS 27- 6 D +TL+TCTP IN+HR+L+ G+RI P K + K + +A+ + GLI++ Sbjct: 192 DLLTLVTCTPLGINTHRILLTGERIYPTPAKDLAAAGKRPDVPHFPWWAVGLAAGLIVVG 25- 1 Query: 277 LLIW---FKKTKQKKRRKNEKAASQ 298 L +W + + K+R A+Q Sbjct: 252 LYLWRSGYAAARAKERALARARAAQ 276 There is also homology to SEQ ID 3740. SEQ ID 3918 (GBS209) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 50 (lane 4; MW 62 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 85 (lane 3; MW 37.2 kDa). GBS209-His was purified as shown in FIG. 221, lane 8. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1273 A DNA sequence (GBSx1350) was identified in S. agalactiae <SEQ ID 3919> which encodes the amino acid sequence <SEQ ID 3920>. Analysis of this protein sequence reveals the following:

TABLE-US-03804 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.66 Transmembrane 281-297 (276-300) ----- Final Results ----- bacterial membrane --- Certainty = 0.4864(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03805 >GP: BAB04080 GB: AP001508 unknown [Bacillus halodurans] Identities = 45/241 (31%), Positives = 63/141 (43%), Gaps = 20/141 (14%) Query: 153 TGELDLLKVGVDGDTKKPLAGVVFELYEKNGRTPIRVKNGVHSQDIDAAKHLETDSSGHI 21- 2 TG L++ KV D DT + L G F LY+ G IR LET G Sbjct: 1084 TGSLEVTKV--DADTGEVLQGATFTLYDSEGEFAIRT--------------LETGEDGKA 1- 127 Query: 213 RISGLIHGDYVLKEIETQSGYQIGQAETAVTIEKSKTVTVTIENKKVPTPKVPSRGGL-I 27- 1 L++GDY+LKE GY +G +T + VT+EN+K +V + G + + Sbjct: 1128 TFVNLLYGDYLLKEDSAPEGYLVGINDTQRVTIDTVLHEVTVENEKSDINRVSAVGAVQL 1- 187 Query: 272 PKTGEQQAMALVIIGGILIAL 292 K E+ +L G L AL Sbjct: 1188 QKVDEETGESL---QGALFAL 1205 Identities = 64/259 (24%), Positives = 113/259 (42%), Gaps = 48/259 (18%) Query: 16 GTMFGISQT---VLAQETHQLTIVHLEARDIDRPNP----QLEIAPKE-GTPIEGVLYQL 67 - G + GI+ T + H++T+ + E DI+R + QL+ +E G ++G L+ L Sbjct: 1147 GYLVGINDTQRVTIDTVLHEVTVEN-EKSDINRVSAVGAVQLQKVDEETGESLQGALFAL 1- 205 Query: 68 YQLKSTEDGDLLAHWNSLTITELKKQAQQVFEATTNQQGKATFNQLPDGIYYGL----AV 123- Q E +TI E++ + + A + + G F +L + Y L V Sbjct: 1206 QQKVDDE---------FVTIAEMETDEEGIVFAGSLEPGDYQFVELNAPVGYKLDETPVV 1- 256 Query: 124 KAGEKNRNVSAFLVDLSEDKVIYPKIIWSTGELDLLKVGVDGDTKKPLAGVVFELYEKNG 18- 3 E++R + ++L ++ + P G + L+KV D D L G F L + G Sbjct: 1257 FTVEEDRTET---IELQKENHLIP------GSVQLVKVDAD-DAANTLEGAEFTLLDGEG 1- 306 Query: 184 RTPIRVKNGVHSQDIDAAKHLETDSSGHIRISGLIHGDYVLKEIETQSGYQIGQAETAVT 24- 3 V+ G L TD +G + ++ L G+Y E + +GY++ T Sbjct: 1307 NV---VQEG-----------LTTDENGQVVVTDLKPGEYQFVETKAPAGYELEATPIGFT 1- 352 Query: 244 IEKS--KTVTVTIENKKVP 260 IE++ + TV +EN +P Sbjct: 1353 IERNQQEVATVAVENHLIP 1371 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 3920 (GBS52) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 7 (lane 4; MW 30.5 kDa). GBS52-His was purified as shown in FIG. 192, lane 8. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1274 A DNA sequence (GBSx1351) was identified in S. agalactiae <SEQ ID 3921> which encodes the amino acid sequence <SEQ ID 3922>. Analysis of this protein sequence reveals the following: TABLE-US-03806 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.26 Transmembrane 554-570 (551-575) INTEGRAL Likelihood = -0.16 Transmembrane 34-50 (34-50) ----- Final Results ----- bacterial membrane --- Certainty = 0.3506(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8779> which encodes amino acid sequence <SEQ ID 8780> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-03807 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: -5.81 GvH: Signal Score (-7.5): -1.92 Possible site: 37 >>> Seems to have a cleavable N-terminal signal sequence ALOM program count: 2 value: -6.26 threshold: 0.0 INTEGRAL Likelihood = -6.26 Transmembrane 527-543 (524-548) PERIPHERAL Likelihood = 5.36 194 modified ALOM score: 1.75 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3506(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 521-525 The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03808 >GP: CAA57459 GB: X81869 orf2 [Lactobacillus leichmannii] Identities = 140/505 (27%), Positives = 220/505 (42%), Gaps = 94/505 (18%) Query: 102 GEVISNYAKLGDNVKGLQGVQFKRYKVKTDI-----SVDELKKLTTVEAADAKVGTILEE 15- 6 GE+++++ G L GV FK Y V S D + T +DAK L Sbjct: 58 GEIMNDFGGTG-----LNGVTFKAYNVTDHYLSLRKSGDSAQDAVTAIQSDAKDSDNLPS 112- Query: 157 --GVSLPQKTNAQGLVVDAL---------DSKSNVR-YLYVEDLKNSPSNITKAYAVPFV 20- 4 G ++ +T A D + DS N + YL+VE +SP+++T+ A P V Sbjct: 113 YAGSAIATETTATSKGEDGIAAFDNLNLKDSDGNYQTYLFVET--DSPTDVTQQ-AAPIV 16- 9 Query: 205 LELPVANSTGTGFLS-EINIYPKNVVTDEPKTDKDVKKLGQDDAGYTI-----------G 25- 2 L +P+ ++ T ++ +I IYPKNV + P T KD+ + + D T+ G Sbjct: 170 LTMPIYKTSDTSAINHDIQIYPKNVKST-PIT-KDLDEASKKDLAVTLPDGSTIYNAQYG 22- 7 Query: 253 EEFKWFLKSTIPANLGDYEKFEITDKFADGLTYKSVGKIKIGSKTLNRDEHYTIDEPTVD 31- 2 + F + + +P N+ D + F + DK G+ + + L + YT+++ Sbjct: 228 KSFGYNITVNVPWNIKDKDTFNVVDKPDTGI---DIDASTVSIDGLTKSTDYTVNK---- 28- 0 Query: 313 NQNTLKITFKPEKFKEIAELLKGMTLVKNQDALDKATANTDDAAFLEIPVASTINEKAVL 37- 2 N ++ FK + L G +L I +T+ A Sbjct: 281 KDNGYQVVFKTTS--AAVQALAGKSLT--------------------ITYKATLTNNATP 31- 8 Query: 373 GKAIENTFELQYDHTPDKADNPKPSNPPRKPEVHTGGKRFVKKDSTETQTLGGAEFDLLA 43- 2 KAI NT L + + S P P ++TGG +FVKKDS +TL GAEF L+ Sbjct: 319 DKAIGNTATLSIGNGTNIT-----STPANGPRIYTGGAQFVKKDSQSNKTLAGAEFQLVK 37- 3 Query: 433 --SDGTAVKWTDALIKANTNKNYIAGEAVTGQPIKLKSHTDGTFEIKGLAYAVDANAEGT 49- 0 S+G V + + N A EA T S +G +KGL+Y ++ + Sbjct: 374 VDSNGNIVSYATQASDGSYTWNDSATEATT-----YTSDANGLVALKGLSY---SDKLDS 42- 5 Query: 491 AVTYKLKETKAPEGYVIPDKEIEFTVSQTSYNTKPTDITVDSADATPDTIKNNKRPSIPN 55- 0 +Y L E +AP+GY D ++F+++Q S+ D+ TI N K +P+ Sbjct: 426 GESYALLEIQAPDGYAKLDSPVKFSITQGSF-----------GDSNKITIDNTKEGLLPS 47- 4 Query: 551 TGGIGTAIFVAIGAAVMAFAVKGMK 575 TGG G IF+AIG +M A G K Sbjct: 475 TGGKGIYIFLAIGIVIMIVAFGGYK 499 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8780 (GBS80) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 6; MW 56.8 kDa). The GBS80-His fusion product was purified (FIG. 104A; see also FIG. 194, lane 5) and used to immunise mice (lane 1+2 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 104B), FACS (FIG. 104C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS and that it is an effective protective immunogen. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1275 A DNA sequence (GBSx1352) was identified in S. agalactiae <SEQ ID 3923> which encodes the amino acid sequence <SEQ ID 3924>. Analysis of this protein sequence reveals the following: TABLE-US-03809 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4043(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1276 A DNA sequence (GBSx1353) was identified in S. agalactiae <SEQ ID 3925> which encodes the amino acid sequence <SEQ ID 3926>. This protein is predicted to be MsmR. Analysis of this protein sequence reveals the following: TABLE-US-03810 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.01 Transmembrane 75-91 (75-92) ----- Final Results ----- bacterial membrane --- Certainty = 0.1404(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9679> which encodes amino acid sequence <SEQ ID 9680> was also identified. SEQ ID 3926 (GBS360) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 81 (lane 9; MW 74 kDa). GBS360-GST was purified as shown in FIG. 216, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1277 A DNA sequence (GBSx1354) was identified in S. agalactiae <SEQ ID 3927> which encodes the amino acid sequence <SEQ ID 3928>. Analysis of this protein sequence reveals the following: TABLE-US-03811 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1762(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 3929> which encodes the amino acid sequence <SEQ ID 3930>. Analysis of this protein sequence reveals the following: TABLE-US-03812 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1640(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03813 Identities = 93/98 (94%), Positives = 96/98 (97%) Query: 1 MDKIIKSISASGAFRSYVLDSTETVKLAQEKHHTLSSSTVALGRTLIANQILAANQKGDS 60 MDKIIKSI+ SGAFR+YVLDSTETV LAQEKH+TLSSSTVALGRTLIANQILAANQKGDS Sbjct: 1 MDKIIKSIAQSGAFRAYVLDSTETVALAQEKHNTLSSSTVALGRTLIANQILAANQKGDS 60 Query: 61 KITVKVIGDSSFGHIISVADTKGHVKGYIQINTGVDIKK 98 KITVKVIGDSSFGHIISVADTKGHVKGYIQNTGVDIKK Sbjct: 61 KITVKVIGDSSFGHIISVADTKGHVKGYIQNTGVDIKK 98 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1278 A DNA sequence (GBSx1355) was identified in S. agalactiae <SEQ ID 3931> which encodes the amino acid sequence <SEQ ID 3932>. Analysis of this protein sequence reveals the following: TABLE-US-03814 Possible site: 17 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03815 >GP: AAC98436 GB: L29324 unknown [Streptococcus pneumoniae] Identities = 34/48 (70%), Positives = 39/48 (80%) Query: 1 MQEVLIIARENHQVTHEHVSILLTCVQELIVEVNQTQPLSREFREKYM 48 + EV IIA+ NHQVTHEHVSILLTC+QELI EV +T PLS +F KYM Sbjct: 70 VHEVFIIAKTNHQVTHEHVSILLTCIQELIKEVEKTGPLSEDFCNKYM 117 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1279 A DNA sequence (GBSx1356) was identified in S. agalactiae <SEQ ID 3933> which encodes the amino acid sequence <SEQ ID 3934>. This protein is predicted to be TnpA (orfB). Analysis of this protein sequence reveals the following: TABLE-US-03816 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5248(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9907> which encodes amino acid sequence <SEQ ID 9908> was also identified. A further related GBS nucleic acid sequence <SEQ ID 9677> which encodes amino acid sequence <SEQ ID 9678> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10911> which encodes amino acid sequence <SEQ ID 10912> was also identified. There is homology to SEQ ID 1336. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1280 A DNA sequence (GBSx1357) was identified in S. agalactiae <SEQ ID 3935> which encodes the amino acid sequence <SEQ ID 3936>. Analysis of this protein sequence reveals the following: TABLE-US-03817 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4489(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03818 >GP: AAB64982 GB: U43834 Ydr540cp [Saccharomyces cerevisiae] Identities = 93/171 (54%), Positives = 121/171 (70%), Gaps = 3/171 (1%) Query: 1 MRVYENKEELKKEISKTFEKYIMEFNNIPENLKDKRIDEVDRTPAANLSYQVGWTNLVLK 60 MR Y +K+ELK+EI K +EKY EF I E+ KD++++ VDRTP+ NLSYQ+GW NL+L+ Sbjct: 1 MREYTSKKELKEEIEKKYEKYDAEFETISESQKDEKVETVDRTPSENLSYQLGWVNLLLE 60 Query: 61 WEEDERKGLQVKTPSDKFKWNQLGELYQWFTDTYAHLSLQELKAKLNENINSIYAMIDLL 120- WE E G V+TP+ +KWN LG LYQ F Y S++E +AKL E +N +Y I L Sbjct: 61 WEAKEIAGYNVETPAPGYKWNNLGGLYQSFYKKYGIYSIKEQRAKLREAVNEVYKWISTL 120- Query: 121 SEEELFEAHMRKWADEATKTATWEVYKFIHVNTVAPFGTFRTKIRKWKKIV 171 S++ELF+A RKW AT A W VYK+IH+NTVAPF FR KIRKWK++V Sbjct: 121 SDDELFQAGNRKW---ATTKAMWPVYKWIHINTVAPFTNFRGKIRKWKRLV 168 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1281 A DNA sequence (GBSx1358) was identified in S. agalactiae <SEQ ID 3937> which encodes the amino acid sequence <SEQ ID 3938>. Analysis of this protein sequence reveals the following: TABLE-US-03819 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.45 Transmembrance 10-26 (2-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.2381(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8781> which encodes amino acid sequence <SEQ ID 8782> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-03820 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: 8.80 GvH: Signal Score (-7.5): -3.94 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -3.45 threshold: 0.0 INTEGRAL Likelihood = -3.45 Transmembrane 7-23 (2-26) PERIPHERAL Likelihood = 10.40 69 modified ALOM score: 1.19 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2381(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03821 >GP: CAA68889 GB: Y07615 acid phosphatase [Haemophilus influenzae] Identities = 112/245 (45%), Positives = 148/245 (59%), Gaps = 10/245 (4%) Query: 5 MKKVLVSSLLVLGITITLQTVVEAKGPKVAYTQEGMTALSDTNKDKVTTISIDEIQKSLE 64 MK V+ S++ L +T V G YTQ G A + + IS+D+I++SLE Sbjct: 1 MKNVMKLSVIAL---LTAAAVPAMAGKTEPYTQSGTNAREMLQEQAIHWISVDQIKQSLE 57 Query: 65 GKKPITVSFDIDDTLLFSSQYFQYGKEYVTPGSFDFLHKQKEWDLVAKRGDQDSIPKEYA 124- GK PI VSFDIDDT+LFSS F +G++ +PG D+L Q FW+ V D+ SIPK+ A Sbjct: 58 GKAPINVSFDIDDTVLFSSPCFYHGQQKFSPGKHDYLKNQDFWNEVNAGCDKYSIPKQIA 117- Query: 125 KKLIAMHQKRGDKIVFITGRTRGSMYKEGEVDKTAKALAKDFKLDKPIAVNYTGDKPKKP 18- 4 LI MHQ RGD++ F TGRT G+VD L K F + V + G + ++ Sbjct: 118 IDLINMHQARGDQVYFFTGRT------AGKVDGVTPILEKTFNIKNMHPVEFMGSR-ERT 17- 0 Query: 185 YKYDKSYYIKKYGSDIHYGDSDDDIHAAREAGARPIRILRAPNSTNLPLPEAGGYGEEVL 24- 4 KY+K+ I + IHYGDSDDD+ AA+EAG R IR++RA NST P+P GGYGEEVL Sbjct: 171 TKYNKTPAIISHKVSIHYGDSDDDVLAAKEAGVRGIRLMRAANSTYQPMPTLGGYGEEVL 23- 0 Query: 245 ENSAY 249 NS+Y Sbjct: 231 INSSY 235 A related DNA sequence was identified in S. pyogenes <SEQ ID 3939> which encodes the amino acid sequence <SEQ ID 3940>. Analysis of this protein sequence reveals the following:

TABLE-US-03822 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.98 Transmembrane 6-22 (4-25) ----- Final Results ----- bacterial membrane --- Certainty = 0.2593(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03823 >GP: CAA68889 GB: Y07615 acid phosphatase [Haemophilus influenzae] Identities = 105/237 (44%), Positives = 141/237 (59%), Gaps = 10/237 (4%) Query: 9 LFTVSFCGIIALPVEASGPKVPYTQEGITA--ISNQATVKLISIADIASSLEGQKPITVS 66 L ++ A+P A G PYTQ G A + + + IS+ I SLEG+ PI VS Sbjct: 7 LSVIALLTAAAVPAMA-GKTEPYTQSGTNAREMLQEQAIHWISVDQIKQSLEGKAPINVS 65 Query: 67 FDIDDTLLFTSQYFQYGKEYITPGSFDFLHKQKFWDLVAKRGDQDSIPKEYAKQLIAMHQ 126- FDIDDT+LF+S F +G++ +PG D+L Q FW+ V D+ SIPK+ A LI MHQ Sbjct: 66 FDIDDTVLFSSPCFYHGQQKFSPGKHDYLKNQDFWNEVNAGCDKYSIPKQIAIDLINMHQ 125- Query: 127 KRGDKIVFITGRTRGSMYKKGEIDKTAKSLAKDFKLDKPIAINYTGDKAVKPYQYDKTYY 18- 6 RGD++ F TGRT G++D L K F + + + G + + +Y+KT Sbjct: 126 ARGDQVYFFTGRT------AGKVDGVTPILEKTFNIKNMHPVEFMGSRE-RTTKYNKTPA 17- 8 Query: 187 IKKNGSQIHYGDSDEDINAAKEAGARPIRILRAPNSTNLPLPKAGGYGEEVLENSAY 243 I + IHYGDSD+D+ AAKEAG R IR++RA NST P+P GGYGEEVL NS+Y Sbjct: 179 IISHKVSIHYGDSDDDVLAAKEAGVRGIRLMRAANSTYQPMPTLGGYGEEVLINSSY 235 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03824 Identities = 196/245 (80%), Positives = 216/245 (88%), Gaps = 2/245 (0%) Query: 5 MKKVLVSSLLVLGITITLQTVVEAKGPKVAYTQEGMTALSDTNKDKVTTISIDEIQKSLE 64 MKK S L + + VEA GPKV YTQEG+TA+S N+ V ISI +I SLE Sbjct: 1 MKKEFTSILFTVSFCGIIALPVEASGPKVPYTQEGITAIS--NQATVKLISIADIASSLE 58 Query: 65 GKKPITVSFDIDDTLLFSSQYFQYGKEYVTPGSFDFLHKQKFWDLVAKRGDQDSIPKEYA 124- G+KPITVSFDIDDTLLF+SQYFQYGKEY+TPGSFDFLHKQKFWDLVAKRGDQDSIPKEYA Sbjct: 59 GQKPITVSFDIDDTLLFTSQYFQYGKEYITPGSFDFLHKQKFWDLVAKRGDQDSIPKEYA 118- Query: 125 KKLIAMHQKRGDKIVFITGRTRGSMYKEGEVDKTAKALAKDFKLDKPIAVNYTGDKPKKP 18- 4 K+LIAMHQKRGDKIVFITGRTRGSMYK+GE+DKTAK+LAKDFKLDKPIA+NYTGDK KP Sbjct: 119 KQLIAMHQKRGDKIVFITGRTRGSMYKKGEIDKTAKSLAKDFKLDKPIAINYTGDKAVKP 17- 8 Query: 185 YKYDKSYYIKKYGSDIHYGDSDDDIHAAREAGARPIRILRAPNSTNLPLPEAGGYGEEVL 24- 4 Y+YDK+YYIKK GS IHYGDSD+DI+AA+EAGARPIRILRAPNSTNLPLP+AGGYGEEVL Sbjct: 179 YQYDKTYYIKKNGSQIHYGDSDEDINAAKEAGARPIRILRAPNSTNLPLPKAGGYGEEVL 23- 8 Query: 245 ENSAY 249 ENSAY Sbjct: 239 ENSAY 243 SEQ ID 8782 (GBS100) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 5; MW 28 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 33 (lane 2; MW 53 kDa). The GBS100-GST fusion product was purified (FIG. 106A; see also FIG. 197, lane 4) and used to immunise mice (lane 1 product; 9.9 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 106B), FACS (FIG. 106C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1282 A DNA sequence (GBSx1359) was identified in S. agalactiae <SEQ ID 3941> which encodes the amino acid sequence <SEQ ID 3942>. Analysis of this protein sequence reveals the following: TABLE-US-03825 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3288(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1283 A DNA sequence (GBSx1360) was identified in S. agalactiae <SEQ ID 3943> which encodes the amino acid sequence <SEQ ID 3944>. Analysis of this protein sequence reveals the following: TABLE-US-03826 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4004(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9675> which encodes amino acid sequence <SEQ ID 9676> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03827 >GP: BAB04406 GB: AP001509 RNA methyltransferase [Bacillus halodurans] Identities = 198/452 (43%), Positives = 300/452 (65%) Query: 12 KRKIMLHKNDIIETEISDISHEGMGIAKVDGFVFFVENALPGEIIKMRVLKLRKRIGYGK 71 - K++ ++KND++E I D++H+G G+AKVDG+ F+ ALPGE +K +V+K++K G+G+ Sbjct: 3 KQQAPVNKNDVVEVTIEDLTHDGAGVAKVDGYALFIPKALPGERLKAKVVKVKKGYGFGR 62 Query: 72 VEEYLTTSPHRNEGLDYTYLRTGIADLGHLTYEQQLLFKQKQVADNLYKIAHISDVLVEP 131- V + SP R E + + G L H++Y+ QL +KQKQV D L +I I+ V V P Sbjct: 63 VLNMIEASPDRVEAPCPVFNQCGGCQLQHMSYDAQLRYKQKQVQDVLERIGKITAVTVRP 122- Query: 132 TLGMTIPLAYRNKAQVPVRRVDGQLETGFFRKNSHTLVSIEDYLIQEKEIDALINFTRDL 19- 1 T+GM P YRNKAQVPV +G L GF+++ SH ++ +++ +IQ +E D +I ++L Sbjct: 123 TIGMNEPWRYRNKAQVPVGEREGGLIAGFYQERSHRIIDMDECMIQHEENDKVIRQVKEL 18- 2 Query: 192 LRKFDVKPYDEEQQSGLIRNLVVRRGHYTGQLMLVLVTTRPKIFRIDQMIEKLVSAFPSV 25- 1 R+ ++ YDEE+ G +R++V R G TG++M+VL+T ++ +IE++ A P V Sbjct: 183 ARELGIRGYDEEKHRGTLRHVVARYGKNTGEIMVVLITRGEELPHKKTLIERIHKAIPHV 24- 2 Query: 252 VSIMQNINDRNSNVIFGKEFRTLYGSDTIEDQMLGNTYAISAQSFYQVNTEMAEKLYQKA 31- 1 SI+QN+N + +NVIFG + + L+G + I D + +AISA+SFYQVN E + LY +A Sbjct: 243 KSIVQNVNPKRTNVIFGDKTKVLWGEEYIYDTIGDIKFAISARSFYQVNPEQTKVLYDQA 30- 2 Query: 312 IDFSDLNSEDIVIDAYSGIGTIGLSVAKQVKHVYGVEVVEKAVSDAKENATRNGITNSTY 37- 1 ++F++L + VIDAY GIGTI L +A+Q KHVYGVE+V +A+SDAK NA NG N + Sbjct: 303 LEFANLTGSETVIDAYCGIGTISLFLAQQAKHVYGVEIVPEAISDAKRNARLNGFANVQF 36- 2 Query: 372 VADSAENAMAKWLKEGIKPTVIMVDPPRKGLTESFVYSAAQTKADKITYISCNSATMARD 43- 1 AE M W +G++ VI+VDPPRKG E+ + + K D++ Y+SCN AT+ARD Sbjct: 363 AVGDAEKVMPWWYAQGVRADVIVVDPPRKGCDEALLKTILNMKPDRVVYVSCNPATLARD 42- 2 Query: 432 IKLFEELGYHLVKIQPVDLFPMTHHVECVALL 463 +++ E+ GY +QPVD+FP T H+E VA+L Sbjct: 423 LRVLEDGGYETKDVQPVDMFPWTTHIESVAVL 454 A related DNA sequence was identified in S. pyogenes <SEQ ID 3945> which encodes the amino acid sequence <SEQ ID 3946>. Analysis of this protein sequence reveals the following: TABLE-US-03828 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1262(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03829 Identities = 332/454 (73%), Positives = 387/454 (85%) Query: 12 KRKIMLHKNDIIETEISDISHEGMGIAKVDGFVFFVENALPGEIIKMRVLKLRKRIGYGK 71 - KR ML KNDII+ ISD+SHEG G+AK DGFVFFV+NALP E+I MRVLK+ K G+GK Sbjct: 8 KRIRMLKKNDIIQVAISDLSHEGAGVAKHDGFVFFVDNALPEEVIDMRVLKVNKNSGFGK 67 Query: 72 VEEYLTTSPHRNEGLDYTYLRTGIADLGHLTYEQQLLFKQKQVADNLYKIAHISDVLVEP 131- VE Y S RN ++ TYLRTGIADLGHLTYE QL FK+KQV D+LYKIA ISDV VE Sbjct: 68 VEAYHYLSSARNADVNLTYLRTGIADLGHLTYEDQLTFKKKQVQDSLYKIAGISDVTVES 127- Query: 132 TLGMTIPLAYRNKAQVPVRRVDGQLETGFFRKNSHTLVSIEDYLIQEKEIDALINFTRDL 19- 1 T+GMT PLAYRNKAQVPVRRV+GQLETGFFRK+SH L+ I DY IQ+KEID LINFTRDL Sbjct: 128 TIGMTEPLAYRNKAQVPVRRVNGQLETGFFRKHSHDLIPISDYYIQDKEIDRLINFTRDL 18- 7 Query: 192 LRKFDVKPYDEEQQSGLIRNLVVRRGHYTGQLMLVLVTTRPKIFRIDQMIEKLVSAFPSV 25- 1 LR+FD+KPYDE +Q+GL+RN+VVRRGHY+G++MLVLVTTRPK+FR+DQ+IEK+V AFP+V Sbjct: 188 LRRFDIKPYDETEQTGLLRNIVVRRGHYSGEMMLVLVTTRPKVFRVDQVIEKIVEAFPAV 24- 7 Query: 252 VSIMQNINDRNSNVIFGKEFRTLYGSDTIEDQMLGNTYAISAQSFYQVNTEMAEKLYQKA 31- 1 VSI+QNIND+N+N IFGK+F+TLYG DTI D MLGN YAISAQSFYQVNT MAEKLYQ A Sbjct: 248 VSIIQNINDKNTNAIFGKDFKTLYGKDTITDSMLGNNYAISAQSFYQVNTVMAEKLYQTA 30- 7 Query: 312 IDFSDLNSEDIVIDAYSGIGTIGLSVAKQVKHVYGVEVVEKAVSDAKENATRNGITNSTY 37- 1 I FSDL+ +DIVIDAYSGIGTIGLS AK VK VYGVEV+E AV DA++NA NGITN+ + Sbjct: 308 IAFSDLSKDDIVIDAYSGIGTIGLSFAKTVKAVYGVEVIEAAVRDAQQNAALNGITNAYF 36- 7 Query: 372 VADSAENAMAKWLKEGIKPTVIMVDPPRKGLTESFVYSAAQTKADKITYISCNSATMARD 43- 1 VAD+AE+AMA W K+GIKP+VI+VDPPRKGLTESF+ ++ KITY+SCN ATMARD Sbjct: 368 VADTAEHAMATWAKDGIKPSVILVDPPRKGLTESFIQASVAMGPQKITYVSCNPATMARD 42- 7 Query: 432 IKLFEELGYHLVKIQPVDLFPMTHHVECVALLVK 465 IK ++ELGY L K+QPVDLFP THHVECV LL+K Sbjct: 428 IKRYQELGYKLAKVQPVDLFPQTHHVECVVLLIK 461 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1284 A DNA sequence (GBSx1361) was identified in S. agalactiae <SEQ ID 3947> which encodes the amino acid sequence <SEQ ID 3948>. This protein is predicted to be PSR protein. Analysis of this protein sequence reveals the following: TABLE-US-03830 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.15 Transmembrane 135-151 (127-155) ----- Final Results ----- bacterial membrane --- Certainty = 0.5861(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03831 >GP: CAB76822 GB: AJ276232 PSR protein [Enterococcus faecalis] Identities = 143/409 (34%), Positives = 206/409 (49%), Gaps = 56/409 (13%) Query: 48 QRRTESPP--TNSYYEEPYSDSYYQDDDFYSEPQLTSQGLPIYQEERAPKKKKQRARKEK 105- + R E P S E Y DSY +D T G ++ P+ KK + K+K Sbjct: 31 EHREEEPEELAESLQEPVYEDSYTEDSRRSERRHQTDSGGG-NGSDQPPRGKKDKKPKKK 89 Query: 106 QRVKVMAPFPPKAITPPRKKKKFKGFLKFIGIILLIVLSGMVFMFVKGMRDVNNGKSHYS 16- 5 RKK K K F K++ I+L+++ + MF+KG + S Sbjct: 90 -----------------RKKSKTKRFFKWLVILLILLFAYSTVMFLKGKSAAEHDDS-LP 131- Query: 166 PAIIEDFKGKDAVDGT-NILILGSDKRVSERSTDARTDTIMVANVGNKDNKVKMVSFMRD 22- 4 +E F G + +G NILILGSD R + R DTIMV + K K++SFMRD Sbjct: 132 QEKVETFNGVKSSNGAKNILILGSDTRGEDAG---RADTIMVLQLNGPSKKPKLISFMRD 18- 8 Query: 225 LLVNIPNYSTEGYYDMKLNASFNLGEQDNHKGAEYVRQTLKNHFDIDIKYYVMVDFETFA 28- 4 V+IP G K+NA++ G GAE VR+TLK +F++D KYY VDF++F Sbjct: 189 TFVDIP-----GVGPNKINAAYAYG------GAELVRETLKQNFNLDTKYYAKVDFQSFE 23- 7 Query: 285 DAIDTLFPNGVKINAKFGLVGGQSADSVKVPDDLRMKNGVVPSQKIKVGIQYMDGRTLLN 34- 4 +D++FP GVKI+A+ L + D V I+ G Q MDG LL Sbjct: 238 KIVDSMFPKGVKIDAEKSL----NLDGVD----------------IEKGQQVMDGHVLLQ 27- 7 Query: 345 YARFRKDDDGDFGRTQRQQQVMRAIVSQIKDPRRLFTGSAAIGKAYALTSSNLSYSFVLT 40- 4 YARFR D++GDFGR +RQQQVM A++SQ+K+P L ++GK S+++ SF+LT Sbjct: 278 YARFRMDEEGDFGRVRRQQQVMSAVMSQMKNPMTLLRTPESLGKLVGYMSTDVPVSFMLT 33- 7 Query: 405 DGIPILSDAKNGIKQMTIPREGDWVDDYDQYGGQGLTIDFAKYKKILKK 453 +G +L K G++ +++P W Y G L +D K ++K Sbjct: 338 NGPSLLIKGKTGVESLSVPVPDSWNFGESSYAGSILEVDEQKNADAIEK 386 A related DNA sequence was identified in S. pyogenes <SEQ ID 3949> which encodes the amino acid sequence <SEQ ID 3950>. Analysis of this protein sequence reveals the following: TABLE-US-03832 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.96 Transmembrane 159-175 (152-180) ----- Final Results ----- bacterial membrane --- Certainty = 0.4185(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03833 >GP: CAB76822 GB: AJ276232 PSR protein [Enterococcus faecalis] Identities = 140/345 (40%), Positives = 195/345 (55%), Gaps = 41/345 (11%) Query: 140 PRSQK----RKHKKKGCMKWFFNILGLLLMTVLMGLGLMFAKGVFDISTNKANYKPAVSQ 19- 5 PR +K +K +KK K FF L +LL+ + +MF KG + + + V + Sbjct: 78 PRGKKDKKPKKKRKKSKTKRFFKWLVILLILLFAYSTVMFLKGKSAAEHDDSLPQEKV-E 136- Query: 196 AFDGQETQDGT-NILILGSDQRVTQGSTDARTDTIMVVNVGNHAKKIKMVSFMRDTLINI 25- 4 F+G ++ +G NILILGSD T+G R DTIMV+ + +KK K++SFMRDT ++I Sbjct: 137 TFNGVKSSNGAKNILILGSD---TRGEDAGRADTIMVLQLNGPSKKPKLISFMRDTFVDI 19- 3 Query: 255 PGYSYNDNSYDLKLNSAFNLGEQEDHHGAEYVRRALKHNFDIDIKYYVMVDFETFAEAID 31- 4 PG N K+N+A+ G GAE VR LK NF++D KYY VDF++F + +D Sbjct: 194 PGVGPN------KINAAYAYG------GAELVRETLKQNFNLDTKYYAKVDFQSFEKIVD 24- 1 Query: 315 TLFPNGVKIDAKFATVGGVAVDSVEVPDDLRMKNGVVPNQTIEVGEQRMDGRTLLNYARF 37- 4 ++FP GVKIDA+ + + +D V+ IE G+Q MDG LL YARF Sbjct: 242 SMFPKGVKIDAEKS----LNLDGVD----------------IEKGQQVMDGHVLLQYARF 28- 1 Query: 375 RKDDEGDFGRTVRQQQVMSAVMSQIKDPTKLFTGSAAIGKIYALTSTNVSFPFVVKNGVS 43- 4 R D+EGDFGR RQQQVMSAVMSQ+K+P L ++GK+ ST+V F++ NG S Sbjct: 282 RMDEEGDFGRVRRQQQVMSAVMSQMKNPMTLLRTPESLGKLVGYMSTDVPVSFMLTNGPS 34- 1 Query: 435 VLGSGKNGVEHVTIPENGDWVDEYDMYGGQALYIDFDKYQKTLAK 479 +L GK GVE +++P W Y G L +D K + K Sbjct: 342 LLIKGKTGVESLSVPVPDSWNFGESSYAGSILEVDEQKNADAIEK 386 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03834 Identities = 273/486 (56%), Positives = 340/486 (69%), Gaps = 32/486 (6%) Query: 1 MSRNNYGQLNHHEELRYNYLLKNIHYLNEREKMEFQYLHYKKTAVRPQRRTESPPTNSYY 60 M++ G L+HHEELRY YLL+N+ YL+E EK EF +L K R ++ S Sbjct: 1 MTKYPMGGLSHHEELRYFYLLRNLSYLSENEKKEFAFLKSKLEIGRAYAPSKQHYRKSKR 60 Query: 61 EEPY-SDSYY---------QDDDFYSEPQLTSQGLPIYQEERAPKKKKQRARKEKQRVKV 110- +EPY D YY +DDD + GLPIY +E KK K R + Sbjct: 61 QEPYFEDDYYNDYSPNDLLEDDDVNHDSSFVPYGLPIYPKEDRYLNKKT---KLTARRPI 117- Query: 111 MAPFP-----------------PKAITPPRKKKK-FKGFLKFIGIILLIVLSGMVFMFVK 15- 2 AP P P++ KKK K F +G++L+ VL G+ MF K Sbjct: 118 DAPQPIDEDDAFLTESVARCALPRSQKRKHKKKGCMKWFFNILGLLLMTVLMGLGLMFAK 17- 7 Query: 153 GMRDVNNGKSHYSPAIIEDFKGKDAVDGTNILILGSDKRVSERSTDARTDTIMVANVGNK 21- 2 G+ D++ K++Y PA+ + F G++ DGTNILILGSD+RV++ STDARTDTIMV NVGN Sbjct: 178 GVFDISTNKANYKPAVSQAFDGQETQDGTNILILGSDQRVTQGSTDARTDTIMVVNVGNH 23- 7 Query: 213 DNKVKMVSFMRDLLVNIPNYS-TEGYYDMKLNASFNLGEQDNHKGAEYVRQTLKNHFDID 27- 1 K+KMVSFMRD L+NIP YS + YD+KLN++FNLGEQ++H GAEYVR+ LK++FDID Sbjct: 238 AKKIKMVSFMRDTLINIPGYSYNDNSYDLKLNSAFNLGEQEDHHGAEYVRRALKHNFDID 29- 7 Query: 272 IKYYVMVDFETFADAIDTLFPNGVKINAKFGLVGGQSADSVKVPDDLRMKNGVVPSQKIK 33- 1 IKYYVMVDFETFA+AIDTLFPNGVKI+AKF VGG + DSV+VPDDLRMKNGVVP+Q I+ Sbjct: 298 IKYYVMVDFETFAEAIDTLFPNGVKIDAKFATVGGVAVDSVEVPDDLRMKNGVVPNQTIE 35- 7 Query: 332 VGIQYMDGRTLLNYARFRKDDDGDFGRTQRQQQVMRAIVSQIKDPRRLFTGSAAIGKAYA 39- 1 VG Q MDGRTLLNYARFRKDD+GDFGRT RQQQVM A++SQIKDP +LFTGSAAIGK YA Sbjct: 358 VGEQRMDGRTLLNYARFRKDDEGDFGRTVRQQQVMSAVMSQIKDPTKLFTGSAAIGKIYA 41- 7 Query: 392 LTSSNLSYSFVLTDGIPILSDAKNGIKQMTIPREGDWVDDYDQYGGQGLTIDFAKYKKIL 45- 1 LTS+N+S+ FV+ +G+ +L KNG++ +TIP GDWVD+YD YGGQ L IDF KY+K L Sbjct: 418 LTSTNVSFPFVVKNGVSVLGSGKNGVEHVTIPENGDWVDEYDMYGGQALYIDFDKYQKTL 47- 7 Query: 452 KKMGLR 457 K+GLR Sbjct: 478 AKLGLR 483 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1285 A DNA sequence (GBSx1362) was identified in S. agalactiae <SEQ ID 3951> which encodes the amino acid sequence <SEQ ID 3952>. This protein is predicted to be shikimate kinase (aroK). Analysis of this protein sequence reveals the following: TABLE-US-03835 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03836 >GP: CAA55181 GB: X78413 shikimate kinase [Lactococcus lactis] Identities = 65/164 (39%), Positives = 98/164 (59%), Gaps = 8/164 (4%) Query: 1 MPKVLLGFMGVGKTSVANCLENEVIDMDSLIEKHIGMSISRFFTEEGEASFRALESQFLN 60 M +L+GFMG GK++VA L E D+D LIE+ I M I+ FF GEA FR +E++ Sbjct: 1 MSIILIGFMGAGKSTVAKLLAEEFTDLDKLIEEEIEMPIATFFELFGEADFRKIENEVFE 60 Query: 61 ELLKKKNEGLVIASGGGIVLLEENRRLLTLNRHNNIL-LTGSFEVLYHRIKKDEKNRRPL 119- ++K ++IA+GGGI+ E + L L+R + ++ LT F+ L+ RI D +N RP Sbjct: 61 LAVQK---DIIIATGGGII--ENPKNLNVLDRASRVVFLTADFDTLWKRISMDWQNVRP- 114- Query: 120 FLNHSKEEFYDIYQKRMLLYSGLSDMIIDTDYLTPQKIATVIGE 163 L KE +++KRM YS ++D+ ID +P++IA I E Sbjct: 115 -LAQDKEAAQLLFEKRMKDYSLVADLTIDVTDKSPEQIAEQIRE 157 A related DNA sequence was identified in S. pyogenes <SEQ ID 3953> which encodes the amino acid sequence <SEQ ID 3954>. Analysis of this protein sequence reveals the following: TABLE-US-03837 Possible site: 43 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases:

TABLE-US-03838 >GP: CAA55181 GB: X78413 shikimate kinase [Lactococcus lactis] Identities = 63/160 (39%), Positives = 97/160 (60%), Gaps = 5/160 (3%) Query: 1 MTKVLLGFMGVGKTTVSKHLSMHCKDMDAIIEAKIGMSIAAFFEQHGEIAFRTIESQVLK 60 M+ +L+GFMG GK+TV+K L+ D+D +IE +I M IA FFE GE FR IE++V + Sbjct: 1 MSIILIGFMGAGKSTVAKLLAEEFTDLDKLIEEEIEMPIATFFELFGEADFRKIENEVFE 60 Query: 61 DLLFANDNSIIVTGGGVVVLQENRQLLRKNHQHNILLVASFETLYQRLKHDKKSQRPLFL 120- L + II TGGG++ +N +L + + L A F+TL++R+ D ++ RP L Sbjct: 61 --LAVQKDIIIATGGGIIENPKNLNVLDR-ASRVVFLTADFDTLWKRISMDWQNVRP--L 115- Query: 121 KYSKEAFYEFYQQRMVFYEGLSDLVIRVDHRTPEEVANII 160 KEA +++RM Y ++DL I V ++PE++A I Sbjct: 116 AQDKEAAQLLFEKRMKDYSLVADLTIDVTDKSPEQIAEQI 155 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03839 Identities = 88/161 (54%), Positives = 120/161 (73%), Gaps = 1/161 (0%) Query: 1 MPKVLLGFMGVGKTSVANCLENEVIDMDSLIEKHIGMSISRFFTEEGEASFRALESQFLN 60 M KVLLGFMGVGKT+V+ L DMD++IE IGMSI+ FF + GE +FR +ESQ L Sbjct: 1 MTKVLLGFMGVGKTTVSKHLSMHCKDMDAIIEAKIGMSIAAFFEQHGEIAFRTIESQVLK 60 Query: 61 ELLKKKNEGLVIASGGGIVLLEENRRLLTLNRHNNILLTGSFEVLYHRIKKDEKNRRPLF 120- +LL N+ +I +GGG+V+L+ENR+LL N +NILL SFE LY R+K D+K++RPLF Sbjct: 61 DLLFA-NDNSIIVTGGGVVVLQENRQLLRKNHQHNILLVASFETLYQRLKHDKKSQRPLF 119- Query: 121 LNHSKEEFYDIYQKRMLLYSGLSDMIIIDTDYLTPQKIATVI 161 L +SKE FY+ YQ+RM+ Y GLSD++I D+ TP+++A +I Sbjct: 120 LKYSKEAFYEFYQQRMVFYEGLSDLVIRVDHRTPEEVANII 160 SEQ ID 3952 (GBS152) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 25 (lane 2; MW 20 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 37 (lane 2; MW 45.5 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1286 A DNA sequence (GBSx1363) was identified in S. agalactiae <SEQ ID 3955> which encodes the amino acid sequence <SEQ ID 3956>. This protein is predicted to be 3-phosphoshikimate 1-carboxyvinyltransferase (aroA). Analysis of this protein sequence reveals the following: TABLE-US-03840 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.81 Transmembrane 241-257 (240-257) INTEGRAL Likelihood = -0.06 Transmembrane 390-406 (390-406) ----- Final Results ----- bacterial membrane --- Certainty = 0.1723(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9673> which encodes amino acid sequence <SEQ ID 9674> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03841 >GP: AAD45819 GB: AF169483 5-enolpyruvylshikimate-3-phosphate synthase [Streptococcus pneumoniae] Identities = 288/426 (67%), Positives = 347/426 (80%) Query: 5 MKLLTNANTLKGTIRVPGDKSISHRAIIFGSISQGVTRIVDVLRGEDVLSTIEAFKQMGV 64 MKL TN L G IRVPGDKSISHR+IIFGS+++G T++ D+LRGEDVLST++ F+ +GV Sbjct: 1 MKLKTNIRHLHGIIRVPGDKSISHRSIIFGSLAEGETKVYDILRGEDVLSTMQVFRDLGV 60 Query: 65 LIEDDGEIITIYGKGFAGLTQPNNLLDMGNSGTSMRLIAGVLAGQEFEVTMVGDNSLSKR 124- IED +IT+ G G AGL P N L+MGNSGTS+RLI+GVLAG +FEV M GD+SLSKR Sbjct: 61 EIEDKDGVITVQGVGMAGLKAPQNALNMGNSGTSIRLISGVLAGADFEVEMFGDDSLSKR 120- Query: 125 PMDRIALPLSKMGARISGVTNRDLPPLKLQGTKKLKPIFYHLPVASAQVKSALIFAALQT 18- 4 PMDR+ LPL KMG ISG T RDLPPL+L+GTK L+PI Y LP+ASAQVKSAL+FAALQ Sbjct: 121 PMDRVTLPLKKMGVSISGQTERDLPPLRLKGTKNLRPIHYELPIASAQVKSALMFAALQA 18- 0 Query: 185 KGESLIVEKEQTRNHTEDMIRQFGGNLDIKDKEIRLNGGQSLVGQDIRVPGDISSAAFWI 24- 4 KGES+I+EKE TRNHTEDM++QFGGHL + K+I + G Q L GQ + VPGDISSAAFW+ Sbjct: 181 KGESVIIEKEYTRNHTEDMLQQFGGNLSVDGKKITVQGPQKLTGQKVVVPGDISSAAFWL 24- 0 Query: 245 VAGLIIPNSHIILENVGINETRTGILDVVSKMGGKIKLSSVDNQVKSATLTVDYSHLQAT 30- 4 VAGLI PNS ++L+NVGINETRTGI+DV+ MGGK++++ +D KSATL V+ S L+ T Sbjct: 241 VAGLIAPNSRLVLQNVGINETRTGIIDVIRAMGGKLEITEIDPVAKSATLIVESSDLKGT 30- 0 Query: 305 HISGAMIPRLIDELPIIALLATQAQGTTVIADAQELKVKETDRIQVVVESLKQMGADITA 36- 4 I GA+IPRLIDELPIIALLATQAQG TVI DA+ELKVKETDRIQVV ++L MGADIT Sbjct: 301 EICGALIPRLIDELPIIALLATQAQGVTVIKDAEELKVKETDRIQVVADALNSMGADITP 36- 0 Query: 365 TADGMIIRGNTPLHAASLDCHGDHRIGMMIAIAALLVKEGEVDLSGEEAINTSYPNFLEH 42- 4 TADGMII+G + LH A ++ GDHRIGMM AIAALLV +GEV+L EAINTSYP+F + Sbjct: 361 TADGMIIKGKSALHGARVNTFGDHRIGMMTAIAALLVADGEVELDRAEAINTSYPSFFDD 42- 0 Query: 425 LEGLVN 430 LE L++ Sbjct: 421 LESLIH 426 A related DNA sequence was identified in S. pyogenes <SEQ ID 3957> which encodes the amino acid sequence <SEQ ID 3958>. Analysis of this protein sequence reveals the following: TABLE-US-03842 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.18 Transmembrane 240-256 (239-256) ----- Final Results ----- bacterial membrane --- Certainty = 0.1871(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03843 >GP: AAD45819 GB: AF169483 5-enolpyruvylshikimate-3-phosphate synthase [Streptococcus pneumoniae] Identities = 278/426 (65%), Positives = 346/426 (80%) Query: 4 MKLRTNAGPLQGTIQVPGDKSISHRAVILGAVAKGETRVKGLLKGEDVLSTIQAFRNLGV 63 MKL+TN L G I+VPGDKSISHR++I G++A+GET+V +L+GEDVLST+Q FR+LGV Sbjct: 1 MKLKTNIRHLHGIIRVPGDKSISHRSIIFGSLAEGETKVYDILRGEDVLSTMQVFRDLGV 60 Query: 64 RIEEKDDQLVIEGQGFQGLNAPCQTLNMGNSGTSMRLIAGLLAGQPFSVKMIGDESLSKR 123- IE+KD + ++G G GL AP LNMGNSGTS+RLI+G+LAG F V+M GD+SLSKR Sbjct: 61 EIEDKDGVITVQGVGMAGLKAPQNALNMGNSGTSIRLISGVLAGADFEVEMFGDDSLSKR 120- Query: 124 PMDRIVYPLKQMGVEISGETDRQFPPLQLQGNRNLQPITYTLPISSAQVKSAILLAALQA 18- 3 PMDR+ PLK+MGV ISG+T+R PPL+L+G +NL+PI Y LPI+SAQVKSA++ AALQA Sbjct: 121 PMDRVTLPLKKMGVSISGQTERDLPPLRLKGTKNLRPIHYELPIASAQVKSALMFAALQA 18- 0 Query: 184 KGTTQVVEKEITRNHTEEMIQQFGGRLIVDGKRITLVGPQQLTAQEITVPGDISSAAFWL 24- 3 KG + ++EKE TRNHTE+M+QQFGG L VDGK+IT+ GPQ+LT Q++ VPGDISSAAFWL Sbjct: 181 KGESVIIEKEYTRNHTEDMLQQFGGHLSVDGKKITVQGPQKLTGQKVVVPGDISSAAFWL 24- 0 Query: 244 VAGLIIPGSELLLKNVGVNPTRTGILEVVEKMGAQIVYEDMNKKEQVTSIRVVYSNMKGT 30- 3 VAGLI P S L+L+NVG+N TRTGI++V+ MG ++ +++ + ++ V S++KGT Sbjct: 241 VAGLIAPNSRLVLQNVGINETRTGIIDVIRAMGGKLEITEIDPVAKSATLIVESSDLKGT 30- 0 Query: 304 IISGGLIPRLIDELPIIALLATQAQGTTCIKDAQELRVKETDRIQVVTDILNSMGANIKA 36- 3 I G LIPRLIDELPIIALLATQAQG T IKDA+EL+VKETDRIQVV D LNSMGA+I Sbjct: 301 EICGALIPRLIDELPIIALLATQAQGVTVIKDAEELKVKETDRIQVVADALNSMGADITP 36- 0 Query: 364 TADGMIIKGPTVLYGANTSTYGDHRIGMMTAIAALLVKQGQVHLDKEEAIMTSYPTFFKD 42- 3 TADGMIIKG + L+GA +T+GDHRIGMMTAIAALLV G+V LD+ EAI TSYP+FF D Sbjct: 361 TADGMIIKGKSALHGARVNTFGDHRIGMMTAIAALLVADGEVELDRAEAINTSYPSFFDD 42- 0 Query: 424 LERLCH 429 LE L H Sbjct: 421 LESLIH 426 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03844 Identities = 269/424 (63%), Positives = 331/424 (77%) Query: 5 MKLLTNANTLKGTIRVPGDKSISHRAIIFGSISQGVTRIVDVLRGEDVLSTIEAFKQMGV 64 MKL TNA L+GTI+VPGDKSISHRA+I G++++G TR+ +L+GEDVLSTI+AF+ +GV Sbjct: 4 MKLRTNAGPLQGTIQVPGDKSISHRAVILGAVAKGETRVKGLLKGEDVLSTIQAFRNLGV 63 Query: 65 LIEDDGEIITIYGKGFAGLTQPNNLLDMGNSGTSMRLIAGVLAGQEFEVTMVGDNSLSKR 124- IE+ + + I G+GF GL P L+MGNSGTSMRLIAG+LAGQ F V M+GD SLSKR Sbjct: 64 RIEEKDDQLVIEGQGFQGLNAPCQTLNMGNSGTSMRLIAGLLAGQPFSVKMIGDESLSKR 123- Query: 125 PMDRIALPLSKMGARISGVTNRDLPPLKLQGTKKLKPIFYHLPVASAQVKSALIFAALQT 18- 4 PMDRI PL +MG ISG T+R PPL+LQG + L+PI Y LP++SAQVKSA++ AALQ Sbjct: 124 PMDRIVYPLKQMGVEISGETDRQFPPLQLQGNRNLQPITYTLPISSAQVKSAILLAALQA 18- 3 Query: 185 KGESLIVEKEQTRNHTEDMIRQFGGHLDIKDKEIRLNGGQSLVGQDIRVPGDISSAAFWI 24- 4 KG + +VEKE TRNHTE+MI+QFGG L + K I L G Q L Q+I VPGDISSAAFW+ Sbjct: 184 KGTTQVVEKEITRNHTEEMIQQFGGRLIVDGKRITLVGPQQLTAQEITVPGDISSAAFWL 24- 3 Query: 245 VAGLIIPNSHIILENVGINETRTGILDVVSKMGGKIKLSSVDNQVKSATLTVDYSHLQAT 30- 4 VAGLIIP S ++L+NVG+N TRTGIL+VV KMG +I ++ + + ++ V YS+++ T Sbjct: 244 VAGLIIPGSELLLKNVGVNPTRTGILEVVEKMGAQIVYEDMNKKEQVTSIRVVYSNMKGT 30- 3 Query: 305 HISGAMIPRLIDELPIIALLATQAQGTTVIADAQELKVKETDRIQVVVESLKQMGADITA 36- 4 ISG +IPRLIDELPIIALLATQAQGTT I DAQEL+VKETDRIQVV + L MGA+I A Sbjct: 304 IISGGLIPRLIDELPIIALLATQAQGTTCIKDAQELRVKETDRIQVVTDILNSMGANIKA 36- 3 Query: 365 TADGMIIRGNTPLHAASLDCHGDHRIGMMIAIAALLVKEGEVDLSGEEAINTSYPNFLEH 42- 4 TADGMII+G T L+ A+ +GDHRIGMM AIAALLVK+G+V L EEAI TSYP F + Sbjct: 364 TADGMIIKGPTVLYGANTSTYGDHRIGMMTAIAALLVKQGQVHLDKEEAIMTSYPTFFKD 42- 3 Query: 425 LEGL 428 LE L Sbjct: 424 LERL 427 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1287 A DNA sequence (GBSx1364) was identified in S. agalactiae <SEQ ID 3959> which encodes the amino acid sequence <SEQ ID 3960>. Analysis of this protein sequence reveals the following: TABLE-US-03845 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.12 Transmembrane 6-22 (6-22) ----- Final Results ----- bacterial membrane --- Certainty = 0.1447(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03846 >GP: AAF20148 GB: AF208390 actinin-like protein [Entamoeba histolytica] Identities = 62/236 (26%), Positives = 107/236 (45%), Gaps = 38/236 (16%) Query: 144 NYNSTNSSNPESMLFYEKQLKTWLSTH----KNYYLDYK--VTPIYQNNELIPRKIELK- 19- 6 N N + N + + L W+++ N+ D+K V + + +I+ + Sbjct: 116 NANQQKNVNAKEEVVENNALLDWVNSFGLNVSNFSSDWKDGVALVKLTEAVSAGQIKFEQ 17- 5 Query: 197 YVGIDKTGKLLPIFIGNKSTQDQFGI------STVTLENTSPNATIDYLSGKAQN----- 24- 5 + G+D T ++ K +QF I + E P + + Y+S + Sbjct: 176 FSGLDNTQMVIDC---QKLAYEQFKIPILMDVKDLVCERPDPKSIMTYVSVYKERYEQLL 23- 2 Query: 246 TVLSAKEQRKLIAKHEEEKRLAEK-----KVEEEKAAAETQKKL-EEEQARLAAEAQ-RK 29- 8 KE+++ IA+ E+E++ E+ + E+E+ A E Q++L EEQ RLA E Q RK Sbjct: 233 VEKEQKEEQERIAREEQERKQKEEQERLAREEQERLAREEQERLAREEQERLAREEQERK 29- 2 Query: 299 QKEEQARLAAETQKKQETLVQEQTSQGYKRDYRGRWHRPNGQYASKAEIAAAGLQW 354 QKEEQ RLA E Q++++ QE+ +Q +P Q + + AA W Sbjct: 293 QKEEQERLAREEQERKQREEQERLNQ----------QQPTSQQLTFFSVQAAADAW 338 A related DNA sequence was identified in S. pyogenes <SEQ ID 3961> which encodes the amino acid sequence <SEQ ID 3962>. Analysis of this protein sequence reveals the following: TABLE-US-03847 Possible site: 41 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03848 >GP: CAA03161 GB: A49208 unnamed protein product [Streptococcus pyogenes] Identities = 54/222 (24%), Positives = 93/222 (41%), Gaps = 39/222 (17%) Query: 44 HYKNTVSSKLLP--FTANYQLQLGELDNLNRA-----TFSHIQLQDRHETKDVRTKINYD 96 - +YK +S++ P F + +LD L R T ++ ++ + + K N + Sbjct: 76 YYKTLGTSQITPALFPKAGDILYSKLDELGRTRTARGTLTYANVEGSYGVRQSFGK-NQN 134- Query: 97 PVGWHN------YQFPYGDG-SKSSWVMNRGHLVGYQFCGLNDEPRNLVAMTAWLNTGAY 149- P GW Y+ + +G S NR HL+ G + + + A T Sbjct: 135 PAGWTGNPNHVKYKIEWLNGLSYVGDFWNRSHLIADSLGG------DALRVNAVTGTRTQ 18- 8 Query: 150 SGANDSNPEGMLYYENRLDSWLALHPDFWLDYKVTPIYSGNEVVPRQIELQYVGIDSSGE 20- 9 + GM Y E R WL + D +L Y+V PIY+ +E++PR + Sbjct: 189 NVGGRDQKGGMRYTEQRAQEWLEANRDGYLYYEVAPIYNADELIPRAV------------ 23- 6 Query: 210 LLTIRLNSNKESIDENGVTTVILENSAPNINLDYLNGTATPK 251 + + S+ +I+E V++ N+A ++Y NGT T K Sbjct: 237 --VVSMQSSDNTINEK----VLVYNTANGYTINYHNGTPTQK 272 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03849 Identities = 117/245 (47%), Positives = 166/245 (67%), Gaps = 4/245 (1%) Query: 2 KRKQFIKLGIATLLTVISLYTPINLATNHTTENIVTAQEY--KTKENGTLPFKHKRQLVL 59 K+K + + LL++ ++ A T N+ A + T + LPF QL L Sbjct: 5 KQKASLLTAVLLLLSLSITTITVDAARVRTYPNVSHANTHYKNTVSSKLLPFTANYQLQL 64 Query: 60 GELDDKGRATFAHIQLKVKDEPKKKRVKRLKTTPVGWHNFKFYYNDGTQKAWLMSRGRLI 119- GELD+ RATF+HIQL+ + E K R K + PVGWHN++F Y DG++ +W+M+RG L+ Sbjct: 65 GELDNLNRATFSHIQLQDRHETKDVRTK-INYDPVGWHNYQFPYGDGSKSSWVMNRGHLV 123- Query: 120 CHQFSGLNNERKNLVPMTNWLNTGNYNSTNSSNPESMLFYEKQLKTWLSTHKNYYLDYKV 17- 9 +QF GLN+E +NLV MT WLNTG Y+ N SNPE ML+YE +L +WL+ H +++LDYKV Sbjct: 124 GYQFCGLNDEPRNLVAMTAWLNTGAYSGANDSNPEGMLYYENRLDSWLALHPDFWLDYKV 18- 3 Query: 180 TPIYQNNELIPRKIELKYVGIDKTGKLLPIFI-GNKSTQDQFGISTVTLENTSPNATIDY 23- 8 TPIY NE++PR+IEL+YVGID +G+LL I + NK + D+ G++TV LEN++PN +DY Sbjct: 184 TPIYSGNEVVPRQIELQYVGIDSSGELLTIRLNSNKESIDENGVTTVILENSAPNINLDY 24- 3 Query: 239 LSGKA 243 L+G A Sbjct: 244 LNGTA 248 A related DNA sequence was identified in S. pyogenes <SEQ ID 7263> which encodes amino acid sequence <SEQ ID 7264>. An alignment of the GAS and GBS sequences follows: TABLE-US-03850 Score = 58.9 bits (140), Expect = 2e-11 Identities = 34/103 (33%), Positives = 55/103 (53%), Gaps = 1/103 (0%) Query: 1 MPFKTNLKAGILLYAMFMASIFLLVLQVYLSQVTALHKEYQAQTDYVKARLIAEIVYQD- 59 M K LKAGILL A+ +A++F LVLQ YL+++ A ++Y +Q + KA L A++ Y+ Sbjct: 1 MILKKKLKAGILLQAIVLAAVFTLVLQFYLARILATERQYHSQIEASKAYLTAQLAYKTI 60 Query: 60 HRYKASNPVFFKGGQVICRERKERWMLIVKLDQQRQYQFEYLK 102 S +F GG + + V LD+ Y ++ + Sbjct: 61 EGDSISGKCYFTGGYASYLQEGNYLQVKVTLDKGGNYNHKFYR 103 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1288 A DNA sequence (GBSx1365) was identified in S. agalactiae <SEQ ID 3963> which encodes the amino acid sequence <SEQ ID 3964>. This protein is predicted to be enolase (eno). Analysis of this protein sequence reveals the following: TABLE-US-03851 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3025(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03852 >GP: BAA81815 GB: AB029313 enolase [Streptococcus intermedius] Identities = 396/435 (91%), Positives = 414/435 (95%), Gaps = 1/435 (0%) Query: 1 MSIITDVYAREVLDSRGNPTLEVEVYTESGAFGRGMVPSGASTGEHEAVELRDGDKSRYG 60 MSIITDVYAREVLDSRGNPTLEVEVYTESGAFGRGMVPSGASTGEHEAVELRDGDKSRYG Sbjct: 1 MSIITDVYAREVLDSRGNPTLEVEVYTESGAFGRGMVPSGASTGEHEAVELRDGDKSRYG 60 Query: 61 GLGTQKAVDNVNNVIAEAIIGYDVRDQQAIDRAMIALDGTPNKGKLGANAILGVSIAVAR 120- GLGTQKAVDNVNN+IAEA+IGYDVRDQQAIDRAMIALDGTPNKGKLGANAILGVSIAVAR Sbjct: 61 GLGTQKAVDNVNNIIAEAVIGYDVRDQQAIDRAMIALDGTPNKGKLGANAILGVSIAVAR 120- Query: 121 AAADYLEVPLYSYLGGFNTKVLPTPMMNIINGGSHSDAPIAFQEFMIMPVGAPTFKEALR 18- 0 AAADYLE+PLYSYLGGFNTKVLPTPMMNIINGGSHSDAPIAFQEFMI+P GAPTFKEALR Sbjct: 121 AAADYLEIPLYSYLGGFNTKVLPTPMMNIINGGSHSDAPIAFQEFMIVPAGAPTFKEALR 18- 0 Query: 181 WGAEVFHALKKILKERGLETAVGDEGGFAPKFEGTEDGVETILKAIEAAGYEAGENGIMI 24- 0 WGAE+FHALKKILK RGL TAVGDEGGFAP+F+GTEDGVETIL AIEAAGY G++ + + Sbjct: 181 WGAEIFHALKKILKSRGLATAVGDEGGFAPRFDGTEDGVETILAAIEAAGYVPGKD-VFL 23- 9 Query: 241 GFDCASSEFYDAERKVYDYSKFEGEGGAVRTAAEQIDYLEELVNKYPIITIEDGMDENDW 30- 0 GFDCASSEFYD ERKVYDY+KFEGEG AVRTA EQIDYLEELVNKYPIITIEDGMDENDW Sbjct: 240 GFDCASSEFYDKERKVYDYTKFEGEGAAVRTADEQIDYLEELVNKYPIITIEDGMDENDW 29- 9 Query: 301 DGWKALTERLGGRVQLVGDDFFVTNTDYLARGIKEEAANSILIKVNQIGTLTETFEAIEM 36- 0 DGWK LTERLG +VQ VGDDFFVTNT YL +GI E ANSILIKVNQIGTLTETF+AIEM Sbjct: 300 DGWKKLTERLGKKVQPVGDDFFVTNTSYLEKGINEACANSILIKVNQIGTLTETFDAIEM 35- 9 Query: 361 AKEAGYTAVVSHRSGETEDSTIADIAVATNAGQIKTGSLSRTDRIAKYNQLLRIEDQLGE 42- 0 AKEAGYTAVVSHRSGETEDSTIADIAVA NAGQIKTGSLSRTDRIAKYNQLLRIEDQLGE Sbjct: 360 AKEAGYTAVVSHRSGETEDSTIADIAVAANAGQIKTGSLSRTDRIAKYNQLLRIEDQLGE 41- 9 Query: 421 VAQYKGIKSFYNLKK 435 VA+Y+G+KSFYNL K Sbjct: 420 VAEYRGLKSFYNLSK 434 Proteins in the glycolysis/gluconeogenesis pathway have been experimentally detected on the surface of Streptococci. A related DNA sequence was identified in S. pyogenes <SEQ ID 3965> which encodes the amino acid sequence <SEQ ID 3966>. Analysis of this protein sequence reveals the following: TABLE-US-03853 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3025(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03854 >GP: BAA81815 GB: AB029313 enolase [Streptococcus intermedius] Identities = 396/435 (91%), Positives = 415/435 (95%), Gaps = 1/435 (0%) Query: 1 MSIITDVYAREVLDSRGNPTLEVEVYTESGAFGRGMVPSGASTGEHEAVELRDGDKSRYL 60 MSIITDVYAREVLDSRGNPTLEVEVYTESGAFGRGMVPSGASTGEHEAVELRDGDKSRY Sbjct: 1 MSIITDVYAREVLDSRGNPTLEVEVYTESGAFGRGMVPSGASTGEHEAVELRDGDKSRYG 60 Query: 61 GLGTQKAVDNVNNIIAEAIIGYDVRDQQAIDRAMIALDGTPNKGKLGANAILGVSIAVAR 120- GLGTQKAVDNVNNIIAEA+IGYDVRDQQAIDRAMIALDGTPNKGKLGANAILGVSIAVAR Sbjct: 61 GLGTQKAVDNVNNIIAEAVIGYDVRDQQAIDRAMIALDGTPNKGKLGANAILGVSIAVAR 120- Query: 121 AAADYLEVPLYTYLGGFNTKVLPTPMMNIINGGSHSDAPIAFQEFMIMPVGAPTFKEGLR 18- 0 AAADYLE+PLY+YLGGFNTKVLPTPMMNIINGGSHSDAPIAFQEFMI+P GAPTFKE LR Sbjct: 121 AAADYLEIPLYSYLGGFNTKVLPTPMMNIINGGSHSDAPIAFQEFMIVPAGAPTFKEALR 18- 0 Query: 181 WGAEVFHALKKILKERGLVTAVGDEGGFAPKFEGTEDGVETILKAIEAAGYEAGENGIMI 24- 0 WGAE+FHALKKILK RGL TAVGDEGGFAP+F+GTEDGVETIL AIEAAGY G++ + + Sbjct: 181 WGAEIFHALKKILKSRGLATAVGDEGGFAPRFDGTEDGVETILAAIEAAGYVPGKD-VFL 23- 9 Query: 241 GFDCASSEFYDKERKVYDYTKFEGEGAAVRTSAEQVDYLEELVNKYPIITIEDGMDENDW 30- 0 GFDCASSEFYDKERKVYDYTKFEGEGAAVRT+ EQ+DYLEELVNKYPIITIEDGMDENDW Sbjct: 240 GFDCASSEFYDKERKVYDYTKFEGEGAAVRTADEQIDYLEELVNKYPIITIEDGMDENDW 29- 9 Query: 301 DGWKVLTERLGKRVQLVGDDFFVTNTEYLARGIKENAANSILIKVNQIGTLTETFEAIEM 36- 0 DGWK LTERLGK+VQ VGDDFFVTNT YL +GI E ANSILIKVNQIGTLTETF+AIEM Sbjct: 300 DGWKKLTERLGKKVQPVGDDFFVTNTSYLEKGINEACANSILIKVNQIGTLTETFDAIEM 35- 9 Query: 361 AKEAGYTAVVSHRSGETEDSTIADIAVATNAGQIKTGSLSRTDRIAKYNQLLRIEDQLGE 42- 0 AKEAGYTAVVSHRSGETEDSTIADIAVA NAGQIKTGSLSRTDRIAKYNQLLRIEDQLGE Sbjct: 360 AKEAGYTAVVSHRSGETEDSTIADIAVAANAGQIKTGSLSRTDRIAKYNQLLRIEDQLGE 41- 9 Query: 421 VAQYKGIKSFYNLKK 435 VA+Y+G+KSFYNL K Sbjct: 420 VAEYRGLKSFYNLSK 434 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03855 Identities = 421/435 (96%), Positives = 427/435 (97%) Query: 1 MSIITDVYAREVLDSRGNPTLEVEVYTESGAFGRGMVPSGASTGEHEAVELRDGDKSRYG 60 MSIITDVYAREVLDSRGNPTLEVEVYTESGAFGRGMVPSGASTGEHEAVELRDGDKSRY Sbjct: 1 MSIITDVYAREVLDSRGNPTLEVEVYTESGAFGRGMVPSGASTGEHEAVELRDGDKSRYL 60 Query: 61 GLGTQKAVDNVNNVIAEAIIGYDVRDQQAIDRAMIALDGTPNKGKLGANAILGVSIAVAR 120- GLGTQKAVDNVNN+IAEAIIGYDVRDQQAIDRAMIALDGTPNKGKLGANAILGVSIAVAR Sbjct: 61 GLGTQKAVDNVNNIIAEAIIGYDVRDQQAIDRAMIALDGTPNKGKLGANAILGVSIAVAR 120- Query: 121 AAADYLEVPLYSYLGGFNTKVLPTPMMNIINGGSHSDAPIAFQEFMIMPVGAPTFKEALR 18- 0 AAADYLEVPLY+YLGGFNTKVLPTPMMNIINGGSHSDAPIAFQEFMIMPVGAPTFKE LR Sbjct: 121 AAADYLEVPLYTYLGGFNTKVLPTPMMNIINGGSHSDAPIAFQEFMIMPVGAPTFKEGLR 18- 0 Query: 181 WGAEVFHALKKILKERGLETAVGDEGGFAPKFEGTEDGVETILKAIEAAGYEAGENGIMI 24- 0 WGAEVFHALKKILKERGL TAVGDEGGFAPKFEGTEDGVETILKAIEAAGYEAGENGIMI Sbjct: 181 WGAEVFHALKKILKERGLVTAVGDEGGFAPKFEGTEDGVETILKAIEAAGYEAGENGIMI 24- 0 Query: 241 GFDCASSEFYDAERKVYDYSKFEGEGGAVRTAAEQIDYLEELVNKYPIITIEDGMDENDW 30- 0 GFDCASSEFYD ERKVYDY+KFEGEG AVRT+AEQ+DYLEELVNKYPIITIEDGMDENDW Sbjct: 241 GFDCASSEFYDKERKVYDYTKFEGEGAAVRTSAEQVDYLEELVNKYPIITIEDGMDENDW 30- 0 Query: 301 DGWKALTERLGGRVQLVGDDFFVTNTDYLARGIKEEAANSILIKVNQIGTLTETFEAIEM 36- 0 DGWK LTERLG RVQLVGDDFFVTNT+YLARGIKE AANSILIKVNQIGTLTETFEAIEM Sbjct: 301 DGWKVLTERLGKRVQLVGDDFFVTNTEYLARGIKENAANSILIKVNQIGTLTETFEAIEM 36- 0 Query: 361 AKEAGYTAVVSHRSGETEDSTIADIAVATNAGQIKTGSLSRTDRIAKYNQLLRIEDQLGE 42- 0 AKEAGYTAVVSHRSGETEDSTIADIAVATNAGQIKTGSLSRTDRIAKYNQLLRIEDQLGE Sbjct: 361 AKEAGYTAVVSHRSGETEDSTIADIAVATNAGQIKTGSLSRTDRIAKYNQLLRIEDQLGE 42- 0 Query: 421 VAQYKGIKSFYNLKK 435 VAQYKGIKSFYNLKK Sbjct: 421 VAQYKGIKSFYNLKK 435 SEQ ID 3964 (GBS311) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 45 (lane 3; MW 51 kDa). GBS311-His was purified as shown in FIG. 203, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1289 A DNA sequence (GBSx1366) was identified in S. agalactiae <SEQ ID 3967> which encodes the amino acid sequence <SEQ ID 3968>. Analysis of this protein sequence reveals the following: TABLE-US-03856 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1998(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1290 A DNA sequence (GBSx1367) was identified in S. agalactiae <SEQ ID 3969> which encodes the amino acid sequence <SEQ ID 3970>. This protein is predicted to be di-/tripeptide transporter. Analysis of this protein sequence reveals the following: TABLE-US-03857 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.33 Transmembrane 93-109 (87-122) INTEGRAL Likelihood = -9.02 Transmembrane 117-133 (110-141) INTEGRAL Likelihood = -8.44 Transmembrane 333-349 (328-353) INTEGRAL Likelihood = -5.84 Transmembrane 19-35 (17-38) INTEGRAL Likelihood = -3.08 Transmembrane 151-167 (151-167) INTEGRAL Likelihood = -2.55 Transmembrane 264-280 (264-281) INTEGRAL Likelihood = -2.28 Transmembrane 44-60 (44-60) INTEGRAL Likelihood = -2.02 Transmembrane 238-254 (238-255) ----- Final Results ----- bacterial membrane --- Certainty = 0.6731(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9395> which encodes amino acid sequence <SEQ ID 9396> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03858 >GP: CAB12175 GB: Z99106 similar to di-tripeptide ABC transporter (membrane protein) [Bacillus subtilis] Identities = 175/359 (48%), Positives = 254/359 (70%), Gaps = 9/359 (2%) Query: 1 MVGNLYGENDSRRDAGFSIFVFGINLGAFISPIVVGYLGQEVNFHLGFSLAAIGMFFGLL 60 +VG+LY + D RRD+GFSIF GINLG ++P++VG LGQ+ N+HLGF AA+GM GL+ Sbjct: 142 VVGDLYTKEDPRRDSGFSIFYMGINLGGLLAPLIVGTLGQKYNYHLGFGAAAVGMLLGLI 20- 1 Query: 61 QYTLDGKKYLTEESLRPNDPLSPEEKSSLYKKVGLILIGIVIVLILLHLMHMLTIEVIID 120- + L KK L +PLS +KS++ +G+I++ I +++ + +LTI+ ID Sbjct: 202 VFPLTRKKNLGLAGSNVPNPLS--KKSAIGTGIGVIIVAIAVIISVQ--TGVLTIKRFID 25- 7 Query: 121 IFSIIAIAIPIIYFIKILSSKKISSVERSRVWAYIPLFIASILFWSIEEQGSVVLALFAD 18- 0 + SI+ I IP+IYFI + +SKK E+SR+ AY+PLFI +++FW+I+EQG+ +LA++AD Sbjct: 258 LVSILGILIPVIYFIIMFTSKKADKTEKSRLAAYVPLFIGAVMFWAIQEQGATILAVYAD 31- 7 Query: 181 EQTKLYLNFFGHHINFPSSYFQSMNPLFIMLYVPFFAWLWAKWGSKQPSSPKKFAYGLFF 24- 0 E+ +L L F SS+FQS+NPLF++++ P FAWLW K G +QPS+P KF+ G+ Sbjct: 318 ERIRLSLGGF----ELQSSWFQSLNPLFVVIFAPIFAWLWMKLGKRQPSTPVKFSIGIIL 37- 3 Query: 241 AGASFLWMMLPGLLFGVNAKVSPLWLTMSWAIVIVGEMLISPVGLSATSKLAPKAFQAQM 30- 0 AG SF+ M+ P + G A VSPLWL +S+ +V++GE+ +SPVGLS T+KLAP AF AQ Sbjct: 374 AGLSFIIMVFPAMQ-GKEALVSPLWLVLSFLLVVLGELCLSPVGLSVTTKLAPAAFSAQT 43- 2 Query: 301 MSIWFLSNAAAQAINAQIVKLYTPDTQTLYYGVVGGITVVFGFILLFYVPRIEKLMSGV 359- MS+WFL+NAAAQAINAQ+ L+ +T+Y+G +G I++V G ILL P I++ M GV Sbjct: 433 MSMWFLTNAAAQAINAQVAGLFDRIPETMYFGTIGLISIVLGGILLLLSPVIKRAMKGV 491- No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1291 A DNA sequence (GBSx1369) was identified in S. agalactiae <SEQ ID 3971> which encodes the amino acid sequence <SEQ ID 3972>. Analysis of this protein sequence reveals the following: TABLE-US-03859 Possible site: 37 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1292 A DNA sequence (GBSx1370) was identified in S. agalactiae <SEQ ID 3973> which encodes the amino acid sequence <SEQ ID 3974>. Analysis of this protein sequence reveals the following: TABLE-US-03860 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2485(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03861 >GP: AAF61315 GB: U96166 unknown [Streptococcus cristatus] Identities = 181/442 (40%), Positives = 270/442 (60%), Gaps = 2/442 (0%) Query: 1 MINLFDSYTQSSWDLHFSLIKSGYINPTIALNDDGFLPDDVTSPYLYYTGFAKTGAGRPL 60 MI LFD Y Q+S+DL SL +G P + + DDG+L DV SPY Y+TG T GRP+ Sbjct: 1 MICLFDRYDQASFDLLRSLKATGLDCPVVVVQDDGYLSPDVESPYSYFTGDLDTPEGRPI 60 Query: 61 YYNELRVPDTWEIIGFSSGADIVDLGVKKGRIIYANPNHKRLIKEVDWFDEQGRVILKDR 120- Y+N + P WEI + +I+D+G K+ I Y P H+R ++ V+W D +G+V D Sbjct: 61 YFNLVPKPHLWEIRSSNVNGEILDMGKKRANIFYRQPTHERRVRAVEWLDTEGQVRAADI 120- Query: 121 FNKFGFCFAQTFYNADGQAIQTSYYNKDRQEVISENHMTGDYILNDNNQFKVFKSKVEFV 18- 0 +N+ G FAQ Y+ + T Y+++ VI ENH+TGD IL + +FKSK EFV Sbjct: 121 YNRKGRLFAQITYDQTQRPTHTRYFDQSNVVVIMENHLTGDIILTLEGKRHIFKSKQEFV 18- 0 Query: 181 INYLQEAKFNLDRIFYNSLSTPFLVSFYL--NRLESKDVLFWQEPLVDDIPGNMRLLLNN 23- 8 + YLQ ++ DRI YNSL+TPFLV++ L ++DVLFWQEP+ + +PGNM++ + Sbjct: 181 VFYLQYRGYDTDRIIYNSLATPFLVAYALRPKNGRAEDVLFWQEPIGEALPGNMKVAMKM 24- 0 Query: 239 PSPNTKIVIQSYEAYANAMRLLTDEEQKQVSFLGFMYPLKETEKLHNQALILTNSDQIEA 29- 8 P N +I +Q + Y L T EE+ +G++Y + ++ +ALILTNSDQ+E Sbjct: 241 PHRNIRIAVQDRQVYEKIQSLATPEEKVYFHNIGYIYDYQRLNNMNPEALILTNSDQLEQ 30- 0 Query: 299 LESLVTSLPNLTFNIGALTEMSSDLMNFGKYDNVVLYPNITTNQIQYLSNICAFYLDINH 35- 8 +E L+T LPN+ F+IGA+TEMS LM +Y NV LYPNI ++ L C YLDIN Sbjct: 301 IEQLLTQLPNVHFHIGAITEMSGHLMGLNRYPNVSLYPNIRPAKVAELFERCDLYLDINI 36- 0 Query: 359 HNEILSAVRSAFEHQQLIFAFEETSHQIRFVSPKNIFPKKDIFTFISHLQPLIGNKCNIE 41- 8 +EIL+A R+AFE+ LI +F T H RF++ +I+ +++ + +Q + + +E Sbjct: 361 SDEILNACRTAFENNMLILSFTNTCHSRRFIADDHIYAPENVSGMVDKIQSALAHSSEME 42- 0 Query: 419 KALKQQLEDCHVSSSTQYQSVI 440 AL +Q + + +S QY+++I Sbjct: 421 AALTRQKQAANQASLEQYKAII 442 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1293 A DNA sequence (GBSx1371) was identified in S. agalactiae <SEQ ID 3975> which encodes the amino acid sequence <SEQ ID 3976>. Analysis of this protein sequence reveals the following: TABLE-US-03862 Possible site: 22 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.06 Transmembrane 405-421 (404-422) ----- Final Results ----- bacterial membrane --- Certainty = 0.1022(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03863 >GP: BAA94320 GB: AB033763 hypothetical protein [Staphylococcus aureus] Identities = 66/195 (33%), Positives = 99/195 (49%), Gaps = 9/195 (4%) Query: 259 NYYDYQFTNANRFDFFITSTDKQTELLEQQFKQFTNHNPRIITIPVGSID----NLKMPM 31- 4 N Y + F N NR+ I ST +Q + N+ + TIPVG ID NLK Sbjct: 15 NTYKHVFNNLNRYSGIIVSTKQQ----QLDISARINNEIPVHTIPVGYIDEHFTNLKRNN 70 Query: 315 DNRRPYSILTASRLASEKHVDWLVRAVIRIREILPEVTFDIYGSGGEEEKIRNIINAANA 37- 4 + I++ +R + EK ++ + V ++ + P + +YG G EEEK + +I N Sbjct: 71 HSINNNKIISVARYSPEKQLNHQIELVSKLIKEFPNIRLHLYGFGKEEEKYKQLITEYNL 130- Query: 375 TEYIRLMG-HKNLSNVYQNYELYLTASKSEGFGLTLLEAIGAGLPLIGFDVRYGNQTFIK 43- 3 + L G +NLS Q+ + L S EGF L LLE I G+P +G++ +YG I Sbjct: 131 ENNVFLRGFRRNLSAEIQDAYMSLITSNMEGFNLGLLETITEGIPPVGYNSKYGPSELIL 19- 0 Query: 434 DGENGYLIPRFDMDD 448 + ENGYLI + D D+ Sbjct: 191 NNENGYLINKNDKDE 205 SEQ ID 3976 (GBS426) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 80 (lane 4; MW 58.8 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 173 (lane 3; MW 84 kDa). GBS426-GST was purified as shown in FIG. 220, lane 5. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1294 A DNA sequence (GBSx1372) was identified in S. agalactiae <SEQ ID 3977> which encodes the amino acid sequence <SEQ ID 3978>. This protein is predicted to be preprotein translocase seca subunit (secA). Analysis of this protein sequence reveals the following: TABLE-US-03864 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.69 Transmembrane 75-91 (75-91) ----- Final Results ----- bacterial membrane --- Certainty = 0.1277(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03865 >GP: AAC44957 GB: U56901 involved in protein export [Bacillus subtilis] Identities = 336/794 (42%), Positives = 506/794 (63%), Gaps = 29/794 (3%) Query: 5 NSLFSLDKKRLKKLQRTLNTINSLKGQMATLSNEELQAKTTEFRKRLVNGETLDDICAEA 64 N +F K+ L + ++ N I++++G LS++ L+ KT EF++RL G T DD+ EA Sbjct: 6 NKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEA 65 Query: 65 FAVVREADERVLGLFPYDVQVIGGLVLHQGNTAEMKTGEGKTLTATMPLYLNALEGKGAM 124- FAVVREA RV G+FP+ VQ++GG+ LH GN AEMKTGEGKTLT+T+P+YLNAL GKG Sbjct: 66 FAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVH 125- Query: 125 LLTNNSYLAIRDAEEMGKVYRFLGLSVGVGVSDNEEEDRDAATKRAVYSSDIVYSTSSAL 18- 4 ++T N YLA RDAE+MGK++ FLGL+VG+ ++ +++ KR Y++DI YST++ L Sbjct: 126 VVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDE-----KREAYAADITYSTNNEL 18- 0 Query: 185 GFDYLIDNLASSKSQKYMPKLHYAIVDEADAVLLDMAQTPLVISGSPRVQSNLYKIADEL 24- 4 GFDYL DN+ K Q LH+A++DE D++L+D A+TPL+ISG + LY A+ Sbjct: 181 GFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAF 24- 0 Query: 245 ILSFEEQVDYYFDKERQEVWIKNQGVREAERYFRIPHFYKQSNRELVRHLNLSLKAHKLF 30- 4 + + + + DY +D + + V + +G+ +AE+ F I + + + L H+N +LKAH Sbjct: 241 VRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAM 30- 0 Query: 305 ERGKDYVVDDGEIKLLDATNGRVLEGTKLQGGVHQAIEQKEHLNVTPESRAMASITYQNL 36- 4 ++ DYVV+DG++ ++D+ GR+++G + G+HQAIE KE L + ES +A+IT+QN Sbjct: 301 QKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNY 36- 0 Query: 365 FRMFTKLAGMTGTGKTAEKEFIEVYDMEVVRIPTNSPVRRIDYPDKIYTTLPEKIHATIE 42- 4 FRM+ KLAGMTGT KT E+EF +Y+M+VV IPTN PV R D PD IY T+ K A E Sbjct: 361 FRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAE 42- 0 Query: 425 FVKQVHDTGQPILLVAGSVRMSELFSELLLLSGIPHSLLNAQSAVKEAQMIAEAGQKGAV 48- 4 V Q + TGQP+L+ +V SEL S+LL GIPH +LNA++ +EAQ+I EAGQKGAV Sbjct: 421 DVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAV 48- 0 Query: 485 TVATNMAGRGTDIKLGKGVSELGGLAVIGTERMKSQRMDLQLRGRSGRQGDIGFSQFFVS 54- 4 T+ATNMAGRGTDIKLG+GV ELGGLAV+GTER +S+R+D QLRGRSGRQGD G +QF++S Sbjct: 481 TIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLS 54- 0 Query: 545 FEDDLMIESGPKWAQDYFRKNRDKVNPEKPKALGQRRFQKLFQQTQEASDGKGESARSQT 60- 4 ED+LM G + D+ + + + + + +Q+ +G +R Q Sbjct: 541 MEDELMRRFGAERTMAML----DRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQL 59- 6 Query: 605 IEFDSSVQLQREYVYRERNALINGESGHFSPRQIIDTVISSFI-----AYLDGEVEKEEL 65- 9 +++D ++ QRE +Y++R +I+ E + R+I++ +I S + AY E EE Sbjct: 597 LQYDDVLRQQREVIYKQRFEVIDSE----NLREIVENMIKSSLERAIAAYTPREELPEE- 65- 1 Query: 660 IFEVNRFI-FDNMSYNLQGISKEMSL--EEIKNYLFKIADEILREKHNLLGDSFG----- 71- 1 ++++ + N +Y +G ++ + +E L I D I+ K+N + FG Sbjct: 652 -WKLDGLVDLINTTYLDEGALEKSDIFGKEPDEMLELIMDRII-TKYNEKEEQFGKEQMR 70- 9 Query: 712 DFERTAALKAIDEAWIEEVDYLQQLRTVATARQTAQRNPVFEYHKEAYKSYNIMKKEIRE 77- 1 +FE+ L+A+D W++ +D + QLR R AQ NP+ EY E + + M + I + Sbjct: 710 EFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIED 76- 9 Query: 772 QTFRNLLLSEVSFN 785 + + ++ +E+ N Sbjct: 770 EVAKFVMKAEIENN 783 There is also homology to SEQ ID 3620. SEQ ID 3978 (GBS425) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 80 (lane 3; MW 91 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 173 (lane 2; MW 116 kDa). GBS425-GST was purified as shown in FIG. 220, lane 4. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1295 A DNA sequence (GBSx1373) was identified in S. agalactiae <SEQ ID 3979> which encodes the amino acid sequence <SEQ ID 3980>. Analysis of this protein sequence reveals the following: TABLE-US-03866 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3827(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1296 A DNA sequence (GBSx1374) was identified in S. agalactiae <SEQ ID 3981> which encodes the amino acid sequence <SEQ ID 3982>. Analysis of this protein sequence reveals the following:

TABLE-US-03867 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial Cytoplasm --- Certainty = 0.2683(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10001> which encodes amino acid sequence <SEQ ID 10002> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1297 A DNA sequence (GBSx1375) was identified in S. agalactiae <SEQ ID 3983> which encodes the amino acid sequence <SEQ ID 3984>. Analysis of this protein sequence reveals the following: TABLE-US-03868 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5410 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1298 A DNA sequence (GBSx1376) was identified in S. agalactiae <SEQ ID 3985> which encodes the amino acid sequence <SEQ ID 3986>. This protein is predicted to be preprotein translocase secy subunit. Analysis of this protein sequence reveals the following: TABLE-US-03869 Possible site: 59 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.92 Transmembrane 287-303 (278-309) INTEGRAL Likelihood = -9.08 Transmembrane 191-207 (186-210) INTEGRAL Likelihood = -8.44 Transmembrane 104-120 (101-123) INTEGRAL Likelihood = -8.23 Transmembrane 11-27 (9-41) INTEGRAL Likelihood = -3.93 Transmembrane 133-149 (129-150) INTEGRAL Likelihood = -3.19 Transmembrane 347-363 (344-364) INTEGRAL Likelihood = -2.97 Transmembrane 158-174 (155-174) INTEGRAL Likelihood = -1.54 Transmembrane 246-262 (245-262) INTEGRAL Likelihood = -0.90 Transmembrane 372-388 (372-388) INTEGRAL Likelihood = -0.85 Transmembrane 64-80 (64-81) ----- Final Results ----- bacterial membrane --- Certainty = 0.4970 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03870 >GP:AAF30659 GB:AE002122 preprotein translocase [Ureaplasma urealyticum] Identities = 105/422 (24%), Positives = 213/422 (49%), Gaps = 49/422 (11%) Query: 2 KLLYIFEKNIILRKILITFSLIIIFLLGRYVPIPGVLISAYKGQDNNFATLYSTVTGGNL 61 +LL IF+ +L +++T S++I+F +G +P+P + ++ G +F ++ + + GG L Sbjct: 13 QLLMIFKNKKVLVALIVTLSILILFRIGSVIPMPYIKLNGNFGNQGSFFSIINLLGGGGL 72 Query: 62 SQVGVFSLGIGPMMTTMILLRLFT---------IGKYSSGVSQKVQQFRQNVVMLVIAII 112- SQ +F++GIGP +T I+++L + + K +K++ + ++ L +A++ Sbjct: 73 SQFSLFAIGIGPYITAQIIMQLLSSELVPPLAKLSKSGERGRKKIEVITR-IITLPLAVM 131- Query: 113 QGLAITISFQYHNGFSL----------TKLLLATMI--LVTGAYIISWIGNLNAEYGFG- 15- 9 Q + I NGF + L T I +V G YI ++ +L ++ G G Sbjct: 132 QAVIIINLMTRANGFISIVSNAPFAIGSPLFYVTYIFLMVGGTYISLFLADLISKKGVGN 19- 1 Query: 160 GMTILVVVGMLVGQFNNIPLIFELF------QDGYQLAIILFLLWTLVAMYLMITFERSE 21- 3 G+T+L++ G++ FN+ IF + + IL++L+ ++ + ++ S Sbjct: 192 GITLLILTGIVASLFNHFIAIFSNLGSLTSSKVSQIIGFILYILFYIMILIGVVFVNNST 25- 1 Query: 214 YRIPVMRTS-----IHNRLVDDAYMPIKVNASGGMAFMYVYTLLMFPQYIIILLRSIFPT 26- 8 +IPV +T H +L ++PIK+ +G M ++ ++L P + L Sbjct: 252 RKIPVQQTGQALILDHEKL---PFLPIKIMTAGVMPVIFASSVLAIPAQVAEFLDK---Q 30- 5 Query: 269 NPDITSYNDYFSLSSIQGVVIYMILMLVLSVAFTFVNIDPTKISEAMRESGDFIPNYRPG 32- 8 + ++YF + S G+ IY++L+L+ + F++V ++P K++E ++++G FIP + G Sbjct: 306 SMGYYVIHNYFIVDSWTGLAIYVVLILLFTFFFSYVQLNPPKMAEDIKKAGRFIPGVQVG 36- 5 Query: 329 KETQSYLSKICYLFGTFSGFFMAFLGGVPLLFALGNDDLR---------TVSSMTGIFMM 37- 9 +T+ +++K+ Y +AFL +P L AL + T+ T I +M Sbjct: 366 MDTEKHITKVIYRVNWIGAPILAFLACLPHLVALVAKTINHGIPVIQPSTIFGGTSIIIM 42- 5 Query: 380 IT 381 +T Sbjct: 426 VT 427 There is also homology to SEQ ID 3988. A related GBS gene <SEQ ID 8783> and protein <SEQ ID 8784> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03871 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 6.32 GvH: Signal Score (-7.5): -4.07 Possible site: 59 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 10 value: -9.92 threshold: 0.0 INTEGRAL Likelihood = -9.92 Transmembrane 287-303 (278-309) INTEGRAL Likelihood = -9.08 Transmembrane 191-207 (186-210) INTEGRAL Likelihood = -8.44 Transmembrane 104-120 (101-123) INTEGRAL Likelihood = -8.23 Transmembrane 11-27 (9-41) INTEGRAL Likelihood = -3.93 Transmembrane 133-149 (129-150) INTEGRAL Likelihood = -3.19 Transmembrane 347-363 (344-364) INTEGRAL Likelihood = -2.97 Transmembrane 158-174 (155-174) INTEGRAL Likelihood = -1.54 Transmembrane 246-262 (245-262) INTEGRAL Likelihood = -0.90 Transmembrane 372-388 (372-388) INTEGRAL Likelihood = -0.85 Transmembrane 64-80 (64-81) PERIPHERAL Likelihood = -8.65 28 modified ALOM score: 2.48 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4970 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00088## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1299 A DNA sequence (GBSx1377) was identified in S. agalactiae <SEQ ID 3989> which encodes the amino acid sequence <SEQ ID 3990>. Analysis of this protein sequence reveals the following: TABLE-US-03872 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3002 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03873 >GP:AAF61315 GB:U96166 unknown [Streptococcus cristatus] Identities = 30/78 (38%), Positives = 41/78 (52%) Query: 276 ALTVTLTDDIWELEHLLQRCPNTDFHIAAPVYCSDRLKQLVGYPNYYLHEAITEEQFEVL 33- 5 AL +T +D + ++E LL + PN FHI A S L L YPN L+ I + L Sbjct: 289 ALILTNSDQLEQIEQLLTQLPNVHFHIGAITEMSGHLMGLNRYPNVSLYPNIRPAKVAEL 34- 8 Query: 336 LLNSDIYLDINHGEEVWN 353 D+YLDIN +E+ N Sbjct: 349 FERCDLYLDINISDEILN 366 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1300 A DNA sequence (GBSx1378) was identified in S. agalactiae <SEQ ID 3991> which encodes the amino acid sequence <SEQ ID 3992>. This protein is predicted to be eps7. Analysis of this protein sequence reveals the following: TABLE-US-03874 Possible site: 19 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03875 >GP:CAC07458 GB:AX009404 product = eps7 [Streptococcus thermophilus] Identities = 87/232 (37%), Positives = 133/232 (56%), Gaps = 22/232 (9%) Query: 10 VSVIIPVYNAAPYLEGCVNTILGQTYQVFEILLIDDGSTDTSASICDQLSLRDNRIRVFH 69 - +S++IPVYN Y++ C+++IL QT+ EI+L+DDGSTD S ICD S D RI+V H Sbjct: 3 ISIVIPVYNVQDYIKKCLDSILSQTFSDLEIILVDDGSTDLSGRICDYYSENDKRIKVIH 62 Query: 70 IENGGASRARNFGLARISPESQFVTFVDSDDWVKENYLEVLLAQQEKYNADIVISNYYIY 129- NGG S+ARN G+ + S+++TF+DSDD+V +Y+E L + +NADI I+++ Sbjct: 63 TANGGQSEARNVGIKNAT--SEWITFIDSDDYVSSDYIEYLYNLIQVHNADISIASF--- 117- Query: 130 RETEDIFGYYITDKDFV------IEEISAQTAIDRQVHWHLNSSVFIVIWGKLYRRELFD 18- 3 YIT K + + + A+TAI R + LN + +WGK+YR E F+ Sbjct: 118 --------TYITPKKIIKHGNGEVALMDAKTAIRRML---LNEGFDMGVWGKMYRTEYFN 16- 6 Query: 184 TITFPIDKVFEDELVSVLLFIKSKKTILVNGSYYGYRIRPNSIMTSAFSSKR 235 F K+FED L++ +F ++ + Y Y R NS + F+ K+ Sbjct: 167 KYKFVSGKLFEDSLITYQIFSEASTIVFGAKDIYFYVNRKNSTVNGTFNIKK 218 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1301 A DNA sequence (GBSx1379) was identified in S. agalactiae <SEQ ID 3993> which encodes the amino acid sequence <SEQ ID 3994>. Analysis of this protein sequence reveals the following: TABLE-US-03876 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1569 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1302 A DNA sequence (GBSx1380) was identified in S. agalactiae <SEQ ID 3995> which encodes the amino acid sequence <SEQ ID 3996>. Analysis of this protein sequence reveals the following: TABLE-US-03877 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1662 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1303 A DNA sequence (GBSx1381) was identified in S. agalactiae <SEQ ID 3997> which encodes the amino acid sequence <SEQ ID 3998>. This protein is predicted to be a glycosyl transferase (gspA). Analysis of this protein sequence reveals the following: TABLE-US-03878 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2606(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03879 >GP: AAF28363 GB: AF224467 putative glycosyl transferase [Haemophilus ducreyi] Identities = 62/177 (35%), Positives = 105/177 (59%), Gaps = 8/177 (4%) Query: 3 YARYYIPQLIDAEKVLYLDIDTLVVDNLDKLFEIELGDYPIAAILD--GDGIY-----FN 55 + RY+I I+ +KV+YLD D +V +L +L++ ++ +Y +AA+ D + IY FN Sbjct: 89 FFRYFISDFIEQDKVIYLDADIVVNGSLTELYQTDISNYFLAAVKDIISEKIYVNNHIFN 148- Query: 56 SGVMLINSLYWMRYRVTEKLLEITERELDNGIFGDQGVLNLLFDNNWLKLEDKYNAQVGN 115- +G++LIN+ W + +T+ L ++E+ +++ DQ +LNL+F + WLKL YN +G Sbjct: 149 AGMLLINNKKWREHNITQFCLSLSEKYINSLPDADQSILNLIFKDKWLKLNRGYNYLIGT 20- 8 Query: 116 DLGAFYENWQGYFDRNFES-PTIIHYCTHDKPWNTFSSSRFRETWWQYEQLDWNEVF 171 D F Y + E+ P IIHY T KPW ++RFR +W Y +L+W +++ Sbjct: 209 DYLFFKYGKTRYLEDLGETIPLIIHYNTEAKPWLNIFNTRFRNIYWFYYELNWQDIY 265 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1304 A DNA sequence (GBSx1384) was identified in S. agalactiae <SEQ ID 3999> which encodes the amino acid sequence <SEQ ID 4000>. This protein is predicted to be a glycosyl transferase. Analysis of this protein sequence reveals the following: TABLE-US-03880 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1157(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03881 >GP: AAF28363 GB: AF224467 putative glycosyl transferase [Haemophilus ducreyi] Identities = 103/259 (39%), Positives = 156/259 (59%), Gaps = 3/259 (1%) Query: 7 IALAADFGYQEQVKTIIKSICFHNQFIDFYILNDDFPVEWFQMMEYHLSKMDCTISNTKI 66 I LAA+ Y E + T IKSI HN+ I FY+LN D+P EWF ++ L K++ I + K+ Sbjct: 10 IVLAANQSYSEYILTTIKSIYLHNKHIRFYLLNRDYPTEWFDILNNKLRKLNSEIIDIKV 69 Query: 67 FNEEIKHFK-FQKPMPYPTYFRYFIPEVIHEDKVLYLDCDMIITSDLTSIFTLDISKYGV 125- N+ IK+FK + T+FRYFI + I +DKV+YLD D+++ LT ++ DIS Y + Sbjct: 70 TNDTIKNFKTYSHISSDTTFFRYFISDFIEQDKVIYLDADIVVNGSLTELYQTDISNYFL 129- Query: 126 AAVRDDLLEEYDGKEDYFNSGLLLINNIFWREQGISQRLLDYTRENQGALQYHDQDVLND 18- 5 AAV+D + E+ FN+G+LLINN WRE I+Q L + + +L DQ +LN Sbjct: 130 AAVKDIISEKIYVNNHIFNAGMLLINNKKWREHNITQFCLSLSEKYINSLPDADQSILNL 18- 9 Query: 186 VLCDNWLELDETYNYHTGADMLYNLFQQSERQLNRRKDLPKVIHY-TATKPWKYLETSVR 24- 4 + D WL+L+ YNY G D L+ + ++ + + +P +IHY T KPW + + R Sbjct: 190 IFKDKWLKLWRGYNYLIGTDYLFFKYGKTRYLEDLGETIPLIIHYNTEAKPWLNI-FNTR 24- 8 Query: 245 WRDIWWEYNRLEWRDIFTR 263 +R+I+W Y L W+DI+ + Sbjct: 249 FRNIYWFYYELNWQDIYAK 267 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1305 A DNA sequence (GBSx1385) was identified in S. agalactiae <SEQ ID 4001> which encodes the amino acid sequence <SEQ ID 4002>. This protein is predicted to be a glycosyl transferase. Analysis of this protein sequence reveals the following: TABLE-US-03882 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2679(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03883 >GP: AAF28363 GB: AF224467 putative glycosyl transferase [Haemophilus ducreyi] Identities = 94/263 (35%), Positives = 158/263 (59%), Gaps = 4/263 (1%) Query: 2 KKTIVLGADFQYRDQVMTTIKSIVSHNQHLTIYIINTDFPVEWFNILNHSLEQFDCRVKN 61 K IVL A+ Y + ++TTIKSI HN+H+ Y++N D+P EWF+ILN+ L + + + + Sbjct: 7 KMNIVLAANQSYSEYILTTIKSIYLHNKHIRFYLLNRDYPTEWFDILNNKLRKLNSEIID 66 Query: 62 IPISSDVFEGIPTLSHISV-AGFFRWFIPIHLEEEIVLYLDSDVIVRGSLDPLFDINLEE 120- I +++D + T SHIS FFR+FI +E++ V+YLD+D++V GSL L+ ++ Sbjct: 67 IKVTNDTIKNFKTYSHISSDTTFFRYFISDFIEQDKVIYLDADIVVNGSLTELYQTDISN 126- Query: 121 NLLGAVADHFSTLYYGDTAPVSFNSGVMLINNSLWKKEEIYNSLMRIADKG-SAVGVGDQ 17- 9 L AV D S Y + FN+G++LINN W++ I + +++K +++ DQ Sbjct: 127 YFLAAVKDIISEKIYVNNH--IFNAGMLLINNKKWREHNITQFCLSLSEKYINSLPDADQ 18- 4 Query: 180 EYLNILTQNRWIDIGKQYNVQIGQDVNINAYGRPDLYHFYDDCEPVIVHYNSQDKPWNKY 23- 9 LN++ +++W+ + + YN IG D YG+ + P+I+HYN++ KPW Sbjct: 185 SILNLIFKDKWLKLNRGYNYLIGTDYLFFKYGKTRYLEDLGETIPLIIHYNTEAKPWLNI 24- 4 Query: 240 SQSRYRSEWWYYFGLEWSVIYAQ 262 +R+R+ +W+Y+ L W IYA+ Sbjct: 245 FNTRFRNIYWFYYELNWQDIYAK 267 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1306 A DNA sequence (GBSx1386) was identified in S. agalactiae <SEQ ID 4003> which encodes the amino acid sequence <SEQ ID 4004>. Analysis of this protein sequence reveals the following: TABLE-US-03884 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2996(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10003> which encodes amino acid sequence <SEQ ID 10004> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03885 >GP: AAC75095 GB: AE000294 putative Galf transferase [Escherichia coli K12] Identities = 68/286 (23%), Positives = 122/286 (41%), Gaps = 18/286 (6%) Query: 77 STRMDGIIAGLGRGDIVVFQVPTWNSTEFDELFLDKLQAYGARIITFVHDIVPLMFESNF 136- S ++ + GL D+++F P F +L + RI+ +HDI L Sbjct: 50 SVKLSTFLCGLENKDVLIFNFPMAKPFWHILSFFHRLLKE--RIVPLIHDIDELRGGGGS 107- Query: 137 YLLDRVIDMYNRSDVVILPTKAMHDYLIEKGMTTSKVLYQEVWDHPVNIDLPRPEC---Q 19- 3 D V D+VI M YL K M+ K+ +++D+ V+ D+ + Q Sbjct: 108 ---DSV--RLATCDMVISHNPQMTKYL-SKYMSQDKIKDIKIFDYLVSSDVEHRDVTDKQ 16- 1 Query: 194 KVLSFAGDIQRFPFVNDWKENIPLIYYGDGSRLNSEANVHAQGWKDDVELMLSLSKRG-G 25- 2 + + +AG++ R + E +G ++ N G D + ++ G Sbjct: 162 RGVIYAGNLSRHKCSFIYTEGCDFTLFG--VNYENKDNPKYLG-SFDAQSPEKINLPGMQ 21- 8 Query: 253 FGLCWSEDREELVERR---YSRMNASYKLSTFLAAGLPIIANHDISSRDFIKQHGLGFTV 30- 9 FGL W D E Y + N +K S +L+ LP+ + DFI + +G+ V Sbjct: 219 FGLIWDGDSVETCSGAFGDYLKFNNPHKTSLYLSMELPVFIWDKAALADFIVDNRIGYAV 27- 8 Query: 310 ETLEEAVEKINNMEKETYDSYVENVEKIATLLRNGYITKKLLIDAV 355 +++E E +++M ETY EN + I+ +R G + +L + + Sbjct: 279 GSIKEMQEIVDSMTIETYKQISENTKIISQKIRTGSYFRDVLEEVI 324 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1307 A DNA sequence (GBSx1387) was identified in S. agalactiae <SEQ ID 4005> which encodes the amino acid sequence <SEQ ID 4006>. Analysis of this protein sequence reveals the following:

TABLE-US-03886 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3098 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03887 >GP:AAA73093 GB:M76233 [Rabbit smooth muscle myosin light chain kinase mRNA, complete CDS.], gene product [Oryctolagus cuniculus] Identities = 23/63 (36%), Positives = 36/63 (56%) Query: 5 QPAPALQRVRQCQPAPVLQPVPRCQPALALQRVRQCQPAQVLQQVPRCQPAQVLQQVPRC 64 +PA L+ V +PA L+PV +PA L+ V +PA+ L+ V +PA+ L+ V Sbjct: 225 KPAETLKPVGNAKPAETLKPVGNAKPAETLKPVGNAKPAETLKPVGNAKPAETLKAVANA 28- 4 Query: 65 QPA 67 +PA Sbjct: 285 KPA 287 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1308 A DNA sequence (GBSx1388) was identified in S. agalactiae <SEQ ID 4007> which encodes the amino acid sequence <SEQ ID 4008>. Analysis of this protein sequence reveals the following: TABLE-US-03888 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.24 Transmembrane 189-205 (173-245) INTEGRAL Likelihood = -9.24 Transmembrane 213-229 (206-245) INTEGRAL Likelihood = -7.96 Transmembrane 95-111 (83-185) INTEGRAL Likelihood = -7.96 Transmembrane 115-131 (112-185) INTEGRAL Likelihood = -7.96 Transmembrane 135-151 (132-185) INTEGRAL Likelihood = -7.96 Transmembrane 155-171 (152-185) INTEGRAL Likelihood = -6.85 Transmembrane 15-31 (8-45) INTEGRAL Likelihood = -4.09 Transmembrane 39-55 (35-57) INTEGRAL Likelihood = -4.09 Transmembrane 63-79 (59-81) INTEGRAL Likelihood = -2.71 Transmembrane 235-251 (235-251) INTEGRAL Likelihood = -0.11 Transmembrane 253-269 (253-269) ----- Final Results ----- bacterial membrane --- Certainty = 0.4694 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03889 >GP:AAC16164 GB:AF010496 ice nucleation protein [Rhodobacter apsulatus] Identities = 85/286 (29%), Positives = 119/286 (40%), Gaps = 17/286 (5%) Query: 3 ALVLADVDALVETLVLADVVALIEALVLADIEALV----EALVLADIEALVEALVLADID 58 AL A AL T + A ++ L AD+ L +AL A I AL + + A Sbjct: 523 ALSDAQAGALTSTQIGLLSTAAVKGLSTADMAGLTTAEAQALTSAQIAALSSSQIRAMTT 58- 2 Query: 59 ALVEALVLADIEALVEALVL----ADIDALVEALVLADVEALIEALVLALVEALVLADVE 114- A + AL A I+ L + +L ADI AL A + I AL +LV A+ AD+ Sbjct: 583 AQIAALGTAQIKGLTASNILGLETADIVALTTTQAPALSSSQIAALSTSLVAAMETADLA 64- 2 Query: 115 ALIEALVLAL----VEALVLADVEAL----IEALVLALVEALVLADVEALIEALVLALVE 16- 6 L A + AL A A+ I + A ++ L AD+ AL A + + Sbjct: 643 KLSAATFKGFSSTQITALTTAQAGAIGTDQIAQITTAAIKGLESADIAALANATLAKMTT 70- 2 Query: 167 ALVLADVEALIEALVLADVD-ALVLALVEALVLALVEALILAEVEALVLALVEALVLALV 22- 5 A V A + L ++ L A V+AL A + L ++ AL AL V Sbjct: 703 AQVAVLGSAQLTGLTTTQINTVLTTAQVKALGAAALAGLGTDDIVALTTGQAAALSSTQV 76- 2 Query: 226 EALILALVEALVLADVDALMEALVLADVEALMEALVLADVDALVEA 271 AL A + AL AD AL A + + AL +DAL A Sbjct: 763 AALSTAQISALQTADFAALSTAAIKGLSSTQITALSTGQIDALTTA 808 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1309 A DNA sequence (GBSx1389) was identified in S. agalactiae <SEQ ID 4009> which encodes the amino acid sequence <SEQ ID 4010>. Analysis of this protein sequence reveals the following: TABLE-US-03890 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2297 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1310 A DNA sequence (GBSx1390) was identified in S. agalactiae <SEQ ID 4011> which encodes the amino acid sequence <SEQ ID 4012>. This protein is predicted to be fimbriae-associated protein Fap1. Analysis of this protein sequence reveals the following: TABLE-US-03891 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3138 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03892 >GP:BAA97453 GB:AB029393 streptococcal hemagglutinin [Streptococcus gordonii] Identities = 388/968 (40%), Positives = 518/968 (53%), Gaps = 68/968 (7%) Query: 13 VDTKSRVKMHKSEKNWVRTVMSHFNLFKAIKGRATVEADVCIQDVEKEDRLSSGNLTYLK 72 - V+ +R K+ KS K+W+R S F L + +KG +V V +E + G L YLK Sbjct: 13 VERVTRFKLIKSGKHWLRAATSQFGLLRLMKGADISSVEV---KVAEEQSVEKGGLNYLK 69 Query: 73 GILAAGALVGGASLTSR-VYADETPVVQEQSSSVPTLAEQTEVTV--KTTTVQNHQDGTV 129- GI+A GA++GGA +TS VYA+E +++ + LA + E + + T + + Sbjct: 70 GIIATGAVLGGAVVTSSSVYAEEEQALEKVIDTRDVLATRGEAVLSEEAATTLSSEGANP 129- Query: 130 SKNIIDSNSVSMSESASTSTSESVSMSMSGSTLTSVSESVSTSALTSASESISTSASESV 18- 9 +++ D+ S S S SA+ S S S+S+S S S S S S S+S S+SES S S S SV Sbjct: 130 VESLSDTLSASESASAN-SVSTSISISESFSVSASASLSSSSSLSQSSSESASASESLSV 18- 8 Query: 190 SKSTSISEVSNILETQASLTDKGRESFSANQIVTESSLVTDAGKNASVSSLIEITKPKSE 24- 9 S STS S S TQ+S + S S+N + T S V+ +NA V + + +E Sbjct: 189 SASTSQSFSSTTSSTQSSNNESLISSDSSNSLNTNQS-VSARNQNARVRTRRAVAANDTE 24- 7 Query: 250 LQTSKMSNESLITPEKSQVMIASDKTGNESLTPTIRLKSVIQPRSMNLMTLSSEMDLIPL 30- 9 K + + E + ++ T N + ++ N+ ++ L P Sbjct: 248 APQVKSGDYVVYRGESFEYY--AEITDNSGQVNRVVIR--------NVEGGANSTYLSPN 29- 7 Query: 310 EEVSDTEMLGKDVSSELQKVNIALKDNTLSEPGTVKLDSSENLVLNFAFSIASVNEGDVF 36- 9 TE LG+ ++ +Q L+ E ++ + ++ + +A G+ Sbjct: 298 WVKYSTENLGRPGNATVQN---PLRTRIFGEVPLNEIVNEKSYYTRYI--VAWDPSGN-- 35- 0 Query: 370 TVKLSDNLDTQGIGTILKVQDIMDETGQLLATGSYSPLTHNITY--------TWTRYAST 42- 1 ++ DN + G+ + +E Y P ++TY T R A Sbjct: 351 ATQMVDNANRNGLERFVLTVKSQNE--------KYDPAESSVTYVNNLSNLSTSEREAVA 40- 2 Query: 422 LNNIKARVNMPVWPDQRI-------ISKTTSDKQCFTATLNNQVASIE---ERVQYNSPS 47- 1 A N+P P +I ++ T DK T N V ++ S S Sbjct: 403 AAVRAANPNIP--PTAKITVSQNGTVTITYPDKSTDTIPANRVVKDLQISKSNSASQSSS 46- 0 Query: 472 VTEHTNVKTNVRSRIMKLDDERQTETYITQINPEGKEMYFASGLGNLYTIIGSDGTSGSP 53- 1 V+ + T+V + I ++ + + ++ S+ S S Sbjct: 461 VSASQSASTSVSASI---SASMSASVSVSTSASTSASVSASESASTSASVSASESASTS- 51- 6 Query: 532 VNLLNAEVKILKTNSKNLTDSMDQNYDSPEFEDVTSQYSYTNDGSKITIDWKTNSISSTT 59- 1 A V K++S + + S ++ + + S + S + S+S++T Sbjct: 517 -----ASVSASKSSSTSASVSASESASTSASVSASESASTSASVSASESASTSASVSAST 57- 1 Query: 592 SYVVLVKIPKQSGVLYSTVSDINQTYGSKYSYGHTNISGDSDANAEIKL-LSESASTSAS 65- 0 S + ST + ++ + + S ++S A+ + SESASTSAS Sbjct: 572 SASTSASVSASESA--STSASVSASESASTS---ASVSASESASTSASVSASESASTSAS 62- 6 Query: 651 TSASTSASMSASTSASTSASMSASTSASTSASTSASMSASTSASTSASTSASTSASTSAS 71- 0 SAS S+S SAS SAS SAS SAS SAS SASTSAS+SASTSASTSAS SASTSASTSAS Sbjct: 627 VSASESSSTSASVSASESASTSASVSASESASTSASVSASTSASTSASVSASTSASTSAS 68- 6 Query: 711 MSASTSASTSASTSASTSASTSASTSASMSASTSASTSASTSASTSASMSASTSASTSAS 77- 0 +SASTSASTSAS SAS SASTSAS SAS SASTSAS SASTSASTSAS+SASTSASTSAS Sbjct: 687 VSASTSASTSASVSASESASTSASVSASESASTSASVSASTSASTSASVSASTSASTSAS 74- 6 Query: 771 TSASTSASMSASTSASTSASTSASTSASMSASTSASTSASTSASTSASMSASTSASTSAS 83- 0 SAS SAS SAS SASTSASTSAS SAS SASTSAS SAST ASTSAS+SAS SASTSAS Sbjct: 747 VSASESASTSASVSASTSASTSASVSASESASTSASVSASTYASTSASVSASESASTSAS 80- 6 Query: 831 TSASMSASTSASTSASMSASTSASTSASMSASTSASTSASMSASTSASTSASMSASTSAS 89- 0 SAS SASTSAS SAS SASTSAS SAS SASTSAS SAS SASTSAS SAS SASTSAS Sbjct: 807 VSASESASTSASVSASTSASTSASVSASESASTSASVSASESASTSASVSASESASTSAS 86- 6 Query: 891 MSATTSASTSVSTSASTSASTSASTSSSSSVTSNSSKEKVYSALPSTGDQDYSVTATALG 95- 0 +SA+TSASTS S SAS SASTSAS S+S S ++++S SA S +T+ Sbjct: 867 VSASTSASTSASVSASESASTSASVSASESASTSASVSASESASTSASVSASESASTSAS 92- 6 Query: 951 LGLMTGAT 958 + T A+ Sbjct: 927 VSASTSAS 934 There is also homology to SEQ ID 760. SEQ ID 4012 (GBS68) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 33 (lane 4; MW 131.2 kDa). GBS68d was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 153 (lane 14; MW 103 kDa) and in FIG. 239 (lane 13; MW 103 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 152 (lane 17; MW 78 kDa), in FIG. 153 (lane 17; MW>78 kDa) and in FIG. 184 (lane 10; MW 78 kDa). Purified GBS68d-GST is shown in FIG. 246, lane 5. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1311 A DNA sequence (GBSx1391) was identified in S. agalactiae <SEQ ID 4013> which encodes the amino acid sequence <SEQ ID 4014>. This protein is predicted to be RofA. Analysis of this protein sequence reveals the following: TABLE-US-03893 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1738 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10005> which encodes amino acid sequence <SEQ ID 10006> was also identified. There is also homology to SEQ ID 3750. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1312 A DNA sequence (GBSx1392) was identified in S. agalactiae <SEQ ID 4015> which encodes the amino acid sequence <SEQ ID 4016>. This protein is predicted to be Nra. Analysis of this protein sequence reveals the following: TABLE-US-03894 Possible site: 16 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1313 A DNA sequence (GBSx1393) was identified in S. agalactiae <SEQ ID 4017> which encodes the amino acid sequence <SEQ ID 4018>. Analysis of this protein sequence reveals the following: TABLE-US-03895 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3674 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03896 >GP:AAA27020 GB:M80215 uvs402 protein [Streptococcus pneumoniae] Identities = 577/663 (87%), Positives = 633/663 (95%), Gaps = 1/663 (0%) Query: 1 MIDRKDTNRFKLVSKYSPSGDQPQAIETLVDNIEGGEKAQILKGATGTGKTYTMSQVIAQ 60- MI+ N+FKLVSKY PSGDQPQAIE LVDNIEGGEKAQIL GATGTGKTYTMSQVI++ Sbjct: 7 MINHITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISK 66- Query: 61 VNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV 12- 0 VNKPTLVIAHNKTLAGQLYGEFKEFFP+NAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV Sbjct: 67 VNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV 12- 6 Query: 121 NDEIDKLRHSATSSLLERNDVIVVASVSCIYGLGSPKEYADSVVSLRPGQEISRDQLLNN 18- 0 NDEIDKLRHSATS+LLERNDVIVVASVSCIYGLGSPKEYADSVVSLRPG EISRD+LLN+ Sbjct: 127 NDEIDKLRHSATSALLERNDVIVVASVSCIYGLGSPKEYADSVVSLRPGLEISRDKLLND 18- 6 Query: 181 LVDIQFERNDIDFQRGKFRVRGDVVEVFPASRDEHAFRIEFFGDEIDRIREIESLTGRVL 24- 0 LVDIQFERNDIDFQRG+FRVRGDVVE+FPASRDEHAFR+EFFGDEIDRIRE+E+LTG+VL Sbjct: 187 LVDIQFERNDIDFQRGRFRVRGDVVEIFPASRDEHAFRVEFFGDEIDRIREVEALTGQVL 24- 6 Query: 241 GEVEHLAIFPATHFMTNDEHMEEAISKIQAEMENQVELFEKEGKLIEAQRIRQRTEYDIE 30- 0 GEV+HLAIFPATHF+TND+HME AI+KIQAE+E Q+ + FEKEGKL+EAQR++QRTEYDIE Sbjct: 247 GEVDHLAIFPATHFVTNDDHMEVAIAKIQAELEEQLAVFEKEGKLLEAQRLKQRTEYDIE 30- 6 Query: 301 MLREMGYTNGVENYSRHMDGRSEGEPPFTLLDFFPEDFLIMIDESHMTMGQIKGMYNGDR 36- 0 MLREMGYTNGVENYSRHMDGRSEGEPP+TLLDFFP+DFLIMIDESHMTMGQIKGMYNGDR Sbjct: 307 MLREMGYTNGVENYSRHMDGRSEGEPPYTLLDFFPDDFLIMIDESHMTMGQIKGMYNGDR 36- 6 Query: 361 SRKEMLVNYGFRLPSALDNRPLRREEFESHVHQIVYVSATPGDYEMEQTDTVVEQIIRPT 42- 0 SRK+MLVNYGFRLPSALDNRPLRREEFESHVHQIVYVSATPGDYE EQT+TV+EQIIRPT Sbjct: 367 SRKKMLVNYGFRLPSALDNRPLRREEFESHVHQIVYVSATPGDYENEQTETVIEQIIRPT 42- 6 Query: 421 GLLDPEVEVRPSMGQMDDLLGEINLRTEKGERTFITTLTKRMAEDLTDYLKEMGVKVKYM 48- 0 GLLDPEVEVRP+MGQ+DDLLGEIN R EK ERTFITTLTE+MAEDLTDY KEMG+KVKYM Sbjct: 427 GLLDPEVEVRPTMGQIDDLLGEINARVEKNERTFITTLTKKMAEDLTDYFKEMGIKVKYM 48- 6 Query: 481 HSDIKTLERTEIIRDLRLGVFDVLIGINLLREGIDVPEVSLVAILDADKEGFLRNERGLI 54- 0 HSDIKTLERTEIIRDLRLGVFDVL+GINLLREGIDVPEVSLVAILDADKEGFLRNERGLI Sbjct: 487 HSDIKTLERTEIIRDLRLGVFDVLVGINLLREGIDVPEVSLVAILDADKEGFLRNERGLI 54- 6 Query: 541 QTIGRAARNSNGHVIMYADKITDSMQRAMDETARRRRLQMDYNEKHGIVPQTIKKEIRDL 60- 0 QTIGRAARNS GHVIMYAD +T SMQRA+DETARRR++QM YNE+HGIVPQTIKKEIRDL Sbjct: 547 QTIGRAARNSEGHVIMYADTVTQSMQRAIDETARRRKIQMAYNEEHGIVPQTIKKEIRDL 60- 6 Query: 601 IAITKSNDSDKPEKVVDYSSLSKKERQAEIKALQQQMQEAAELLDFELAAQIRDVILELK 66- 0 IA+TK+ ++ +K VD +SL+K+ER+ +K L++QMQEA E+LDFELAAQIRD++LE+K Sbjct: 607 IAVTKAVAKEE-DKEVDINSLNKQERKELVKKLEKQMQEAVEVLDFELAAQIRDMMLEVK 66- 5 Query: 661 AID 663 A+D Sbjct: 666 ALD 668 A related DNA sequence was identified in S. pyogenes <SEQ ID 4019> which encodes the amino acid sequence <SEQ ID 4020>. Analysis of this protein sequence reveals the following: TABLE-US-03897 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4386 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03898 Identities = 570/663 (85%), Positives = 625/663 (93%) Query: 1 MIDRKDTNRFKLVSKYSPSGDQPQAIETLVDNIEGGEKAQILKGATGTGKTYTMSQVIAQ 60- MID++D FKL SKY PSGDQPQAIE+LVDNIEGGEKAQIL GATGTGKTYTMSQVI++ Sbjct: 1 MIDKRDDKPFKLKSKYKPSGDQPQAIESLVDNIEGGEKAQILLGATGTGKTYTMSQVISK 60- Query: 61 VNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV 12- 0 VNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV Sbjct: 61 VNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV 12- 0 Query: 121 NDEIDKLRHSATSSLLERNDVIVVASVSCIYGLGSPKEYADSVVSLRPGQEISRDQLLNN 18- 0 NDEIDKLRHSATSSLLERNDVIVVASVSCIYGLGSPKEYADS VSLRPGQEISRD LLN Sbjct: 121 NDEIDKLRHSATSSLLERNDVIVVASVSCIYGLGSPKEYADSAVSLRPGQEISRDTLLNQ 18- 0 Query: 181 LVDIQFERNDIDFQRGKFRVRGDVVEVFPASRDEHAFRIEFFGDEIDRIREIESLTGRVL 24- 0 LVDIQFERNDIDFQRG FRVRGDVVEVFPASRDEHAFR+EFFGDEIDRI EIESLTG+ + Sbjct: 181 LVDIQFERNDIDFQRGCFRVRGDVVEVFPASRDEHAFRVEFFGDEIDRICEIESLTGKTI 24- 0 Query: 241 GEVEHLAIFPATHFMTNDEHMEEAISKIQAEMENQVELFEKEGKLIEAQRIRQRTEYDIE 30- 0 GEV+HL +FPATHF+TNDEHME++I+KIQAE+ Q++LFS EGKL+EAQR+RQRTEYDIE Sbjct: 241 GEVDHLVLFPATHFVTNDEHMEQSIAKIQAELAEQLQLFESEGKLLEAQRLRQRTEYDIE 30- 0 Query: 301 MLREMGYTNGVENYSRHMDGRSEGEPPFTLLDFFPEDFLIMIDESHMTMGQIKGMYNGDR 36- 0 MLREMGYT+GVENYSRHMDGRS GEPP+TLLDFFPEDFLIMIDESHMTMGQIKGMYNGD+ Sbjct: 301 MLREMGYTSGVENYSRHMDGRSPGEPPYTLLDFFPEDFLIMIDESHMTMGQIKGMYNGDQ 36- 0 Query: 361 SRKEMLVNYGFRLPSALDNRPLRREEFESHVHQIVYVSATPGDYEMEQTDTVVEQIIRPT 42- 0 +RK+MLV+YGFRLPSALDNRPLRREEFESHVHQIVYVSATPG+YEM QT+T++EQIIRPT Sbjct: 361 ARKQMLVDYGFRLPSALDNRPLRREEFESHVHQIVYVSATPGEYEMSQTNTIIEQIIRPT 42- 0 Query: 421 GLLDPEVEVRFSMGQMDDLLGEINLRTEKGERTFITTLTKRMAEDLTDYLKEMGVKVKYM 48- 0 GLLDPE++VR SMGQMDDLLGEIN R + ERTFITTLTK+MAEDLTDYLKEMGVKVKYM Sbjct: 421 GLLDPEIDVRSSMGQMDDLLGEINQRVARDERTFITTLTKKMAEDLTDYLKEMGVKVKYM 48- 0 Query: 481 HSDIKTLERTEIIRDLRLGVFDVLIGINLLREGIDVPEVSLVAILDADKEGFLRNERGLI 54- 0 HSDIKTLERTEIIRDLRLGVFDVLIGINLLREGIDVPEVSLVAILDADKEGFLRNERGLI Sbjct: 481 HSDIKTLERTEIIRDLRLGVFDVLIGINLLREGIDVPEVSLVAILDADKEGFLRNERGLI 54- 0 Query: 541 QTIGRAARNSNGHVIMYADKITDSMQRAMDETARRRRLQMDYNEKHGIVPQTIKKEIRDL 60- 0 QTIGRAARN +GHVIMYADK+TDSMQRA+DETARRR +Q+ YN+ HGIVPQTIKK+IR L Sbjct: 541 QTIGRAARNVDGHVIMYADKMTDSMQRAIDETARRREIQIAYNKAHGIVPQTIKKDIRGL 60- 0 Query: 601 IAITKSNDSDKPEKVVDYSSLSKKERQAEIKALQQQMQEAAELLDFELAAQIRDVILELK 66- 0 I+I+K++ +D ++ +DY S+S+ ER+ I ALQ+QMQEAAELLDFELAAQ+RD+ILELK Sbjct: 601 ISISKTSHNDISKEEMDYESMSRGERKEAINALQKQMQEAAELLDFELAAQMRDLILELK 66- 0 Query: 661 AID 663 +D Sbjct: 661 LMD 663 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1314 A DNA sequence (GBSx1394) was identified in S. agalactiae <SEQ ID 4021> which encodes the amino acid sequence <SEQ ID 4022>. Analysis of this protein sequence reveals the following:

TABLE-US-03899 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.78 Transmembrane 284-300 (274-303) INTEGRAL Likelihood = -10.08 Transmembrane 20-36 (16-53) INTEGRAL Likelihood = -5.52 Transmembrane 117-133 (114-137) INTEGRAL Likelihood = -5.15 Transmembrane 203-219 (201-225) INTEGRAL Likelihood = -3.29 Transmembrane 183-199 (182-200) INTEGRAL Likelihood = -1.54 Transmembrane 74-90 (73-90) INTEGRAL Likelihood = -0.48 Transmembrane 37-53 (37-53) ----- Final Results ----- bacterial membrane --- Certainty = 0.5713 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03900 >Gp:CAA22372 GB:AL034446 putative transmembrane protein [Streptomyces coelicolor A3(2)] Identities = 58/190 (30%), Positives = 96/190 (50%), Gaps = 11/190 (5%) Query: 114 GWS--IGFILFSISVITAYILGGLDFHSYDVSK-ATIFYVVTLLPFWLIQSGTEELLTRG 17- 0 GW IGF LF +VIT G Y+V ++ + L+ F + TEE++ RG Sbjct: 98 GWGTLIGFGLFG-AVITNLFASGY----YEVDGLGSVQGAIGLVGFMAAAAATEEVVFRG 15- 2 Query: 171 WLLPLINHRFHLAVAIGVSSTLFGILHLVNAHVTFLSIVSI-ICSGVLMSLYMIKSGNIW 22- 9 L +I +A+G++ +FG++HL+N T ++I I +G +++ + N+W Sbjct: 153 VLFRIIEEHIGTYLALGLTGLVFGLMHLLNEDATLWGALAIAIEAGFMLAAAYAATRNLW 21- 2 Query: 230 SVAALHGAWNFSQGNLYGIAVSGQKAGASLLHFTVKENAPDWISGGAFGIEGSLISIFVL 28- 9 +H WNF+ G ++ VSG LL T+ + P ++GG FG EGS+ S+ Sbjct: 213 LTIGVHFGWNFAAGGVFSTVVSGNGDSEGLLDATM--SGPKLLTGGDFGPEGSVYSVGFG 27- 0 Query: 290 LAAIIYLLWL 299 + + LWL Sbjct: 271 VLLTLVFLWL 280 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1315 A DNA sequence (GBSx1395) was identified in S. agalactiae <SEQ ID 4023> which encodes the amino acid sequence <SEQ ID 4024>. This protein is predicted to be glutamine-binding periplasmic protein/glutamine transport system perme. Analysis of this protein sequence reveals the following: TABLE-US-03901 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.97 Transmembrane 532-548 (523-553) INTEGRAL Likelihood = -7.38 Transmembrane 700-716 (696-720) INTEGRAL Likelihood = -4.57 Transmembrane 562-578 (558-588) INTEGRAL Likelihood = -0.32 Transmembrane 665-681 (665-681) ----- Final Results ----- bacterial membrane --- Certainty = 0.4588 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03902 >GP:AAF16724 GB:AF141644 putative integral membrane protein [Lactococcus lactis] Identities = 109/195 (55%), Positives = 156/195 (79%), Gaps = 4/195 (2%) Query: 466 KMFNNGLASLKKSGEYDKLVKKYLSTASTSSNDKAAKPVDESTILGLISNNYKQLLSGIG 52- 5 +MFNNGLA+L+ +GEYDK++ KYL++ T + +AK E+T G++ NN++Q+ G+ Sbjct: 1 EMFNNGLANLRANGEYDKIIDKYLAS-DTKTIQSSAK---ENTFFGILQNNWEQIGRGLL 56- Query: 526 TTLSLTLISFAIAMVIGIIFGMMSVSPSNTLRTISMIFVDIVRGIPLMIVAAFIFWGIPN 58- 5 TL L ++SF +AM++GIIFG+ SV+PS LRTI+ I+VD+ R IPL+++ FIF+GIPN Sbjct: 57 VTLELAVLSFILAMIVGIIFGLFSVAPSKILRTIARIYVDLNRSIPLLVLTIFIFYGIPN 11- 6 Query: 586 LIESITGHQSPINDFVAATIALSLNGGAYIAEIVRGGIEAVPSGQMEASRSLGISYGKTM 64- 5 L++ ITGHQSP+N+F A IAL+LN AYIAEIVR G++AVPSGQMEASRSLG++Y +M Sbjct: 117 LLQIITGHQSPLNEFTAGVIALTLNSSAYIAEIVRSGVQAVPSGQMEASRSLGVTYLTSM 17- 6 Query: 646 QKVILPQAVRLMLPN 660 +KVILPQA+++ +P+ Sbjct: 177 RKVILPQAIKITIPS 191 There is also homology to SEQ ID 1198. A further related DNA sequence was identified in S. pyogenes <SEQ ID 9071> which encodes amino acid sequence <SEQ ID 9072>. Analysis of this protein sequence reveals the following: TABLE-US-03903 Possible site: 21 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS sequences follows: TABLE-US-03904 Score = 80.8 bits (196), Expect = 2e-17 Identities = 64/233 (27%), Positives = 113/233 (48%), Gaps = 13/233 (5%) Query: 34 IKKTRKLVVAVSPDYAPFEFKALVNGKDTIVGADVQLAQAIADELDVDLELSPMSFDNVL 93- +K + K+V S +APFE++ NGK G D++L + IA + L++S FD L Sbjct: 268 VKPSYKIVSDSS--FAPFEYQ---NGKGKYTGFDMELIKKIAKQQGFKLDISNPGFDAAL 32- 2 Query: 94 SSLQTGKADLAISGISHTKERAKVYDFSIPYYQAENAIVMRASDAKVTKNISDLNGKKVA 15- 3 +++Q+G+AD I+G + T+ R K++DFS PYY +++++ K+ DL GK V Sbjct: 323 NAVQSGQADGVIAGATITEARQKIFDFSDPYY--TSSVILAVKKGSNVKSYQDLKGKTVG 38- 0 Query: 154 AQKGSIEEGLVKIQLPKANLISLTAMGEA---INELKAGQVYAVTLEAPVAAGFLAQHKD 21- 0 A+ G+ + K N + A EA + + +G + A+ + V A + Q + Sbjct: 381 AKNGTASYTWLSDHADKYN-YHVKAFDEASTMYDSMNSGSIDALMDDEAVLAYAINQGRK 43- 9 Query: 211 LALAPFSLKTSDGDAKAVALPKNSGDLTKAVNKVIAKLDEQERYKSFIAETIA 263 P + S GD + +L K N +A L + Y + + ++ Sbjct: 440 FE-TPIKGEKS-GDIGFAVKKGANPELIKMFNNGLASLKKSGEYDKLVKKYLS 490 Score = 74.5 bits (180), Expect = 1e-15 Identities = 59/215 (27%), Positives = 102/215 (47%), Gaps = 12/215 (5%) Query: 48 YAPFEFKALVNGKDTIVGADVQLAQAIADELDVDLELSPMSFDNVLSSLQTGKADLAISG 10- 7 YAPFEFK + T G DV + +A ++ ++ FD ++++Q+G+AD ++G Sbjct: 36 YAPFEFK---DSDQTYKGIDVDIVNEVAKRAGWNVNMTYPGFDAAVNAVQSGQADALMAG 92- Query: 108 ISHTKERARVYDFSIPYYQAENAIVMRASDAKVTKNISDLNGKKVAAQKGSIEEGLVKIQ 16- 7 + T+ R KV++FS YY + I+ ++ KVT N L GK V + G+ + ++ Sbjct: 93 TTVTEARKKVFNFSDTYYDT-SVILYTKNNNKVT-NYKQLKGKVVGVKNGTAAQSFLEEN 15- 0 Query: 168 LPKANLISLTAMGEAI--NELKAGQVYAVTLEAPVAAGFLAQHKDLALAPFSLKTSDGDA 22- 5 K T + N L +G +YA + PV + Q K A+ +++ + Sbjct: 151 KSKYGYKVKTFDTSDLMNNSLDSGSIYAAMDDQPVVQFAINQGKAYAI---NMEGEAVGS 20- 7 Query: 226 KAVALPKNSG--DLTKAVNKVIAKLDEQERYKSFI 258 A A+ K SG +L K N A++ Y + Sbjct: 208 FAFAVKKGSGHDNLIKEFNTAFAQMKSDGTYNDIM 242 SEQ ID 4024 (GBS154) was expressed in E. coli as a His-fusion product. The purified protein is shown in FIG. 199, lane 6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1316 A DNA sequence (GBSx1396) was identified in S. agalactiae <SEQ ID 4025> which encodes the amino acid sequence <SEQ ID 4026>. This protein is predicted to be amino acid ABC transporter, ATP-binding protein (glnQ). Analysis of this protein sequence reveals the following: TABLE-US-03905 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4183 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03906 >GP:AAB90561 GB:AE001058 glutamine ABC transporter, ATP-binding protein (glnQ) [Archaeoglobus fulgidus] Identities = 147/240 (61%), Positives = 192/240 (79%) Query: 5 KIDVQDLHKSYGQNEVLKGIDAKFYEGDVVCIIGPSGSGKSTFLRTLNLLESITSGKVVV 64- ++++ DLHK +G+ EVLKG+ K +G+VV IIGPSGSGKST LR +N LE TSGK+++ Sbjct: 3 QLEIIDLHKRFGELEVLKGVTMKVEKGEVVVIIGPSGSGKSTLLRCINRLEEPTSGKILL 62- Query: 65 DGFELSNPKTDIDKARENIGMVFQHFNLFPHMSVLENITFAPIELGKESKEAAEKHGMEL 12- 4 DG +++N K DI+K R+ IG+VFQ FNLFPH++ L+N+T API++ K SK AE+ GM L Sbjct: 63 DGVDITNSKIDINKVRQRIGIVFQQFNLFPHLTALQNVTLAPIKIKKMSKREAEELGMRL 12- 2 Query: 125 LEKVGLADKANAKPDSLSGGQKQRVAIARSLAMNPDILLFDEPTSALDPEMVGDVLNVMK 18- 4 LEKVGL DKA+ P LSGGQ+QRVAIAR+LAMNP+++LFDE TSALDPE+V +VL+VMK Sbjct: 123 LEKVGLEDKADYYPAQLSGGQQQRVAIARALAMNPEVMLFDEVTSALDPELVKEVLDVMK 18- 2 Query: 185 DLAEQGMTMLIVTHEMGFARQVANRVIFTDGGRFLEDGTPEQIFDTPQHPRLQDFLNKVL 24- 4 LA GMTM++VTHEMGFAR+V +RVIF DGG +E+G PEQIF P+H R + FL+ + L Sbjct: 183 QLARDGMTMVVVTHEMGFAREVGDRVIFMDGGVIVEEGKPEQIFSNPKHERTRKFLSMIL 24- 2 A related DNA sequence was identified in S. pyogenes <SEQ ID 4027> which encodes the amino acid sequence <SEQ ID 4028>. Analysis of this protein sequence reveals the following: TABLE-US-03907 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4149 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: TABLE-US-03908 >GP: BAB05180 GB: AP001512 ABC transporter (substrate-binding protein) [Bacillus halodurans] Identities = 79/227 (34%), Positives = 126/227 (54%), Gaps = 10/227 (4%) Query: 35 KKTRKLVVAVSPDYAPFEFKALVNGKDTIVGADVQLAQAIADELDVDLELSPMSFDNVLS 94 - +K LV+ S DY P+E + G+ IVG DV +A+ I EL +L++ M F+ ++ Sbjct: 48 EKKSVLVMGTSADYPPYESVDVTTGE--IVGFDVDIAEYITSELGYELKIQDMDFNGIIP 105- Query: 95 SLQTGKADLAISGISHTKERAKVYDFSIPYYQAENAIVMRASDAKVTKNISDLNGKKVAA 154- +LQ G+ D A+SG++ T+ER K DFS YY A+N +V + D ++ DL GK V Sbjct: 106 ALQAGRVDFALSGMTPTEERKKSVDFSDVYYDAQNLVVFKEEDG--LSSVEDLAGKTVGV 16- 3 Query: 155 QKGSI-EEGLVKIQ--LPKANLISLTAMGEAINELKAGQVYAVTLEAPVAAGFLAQHKDL 21- 1 Q SI EE V++Q L + + + E + EL AG+V A+ +E VAAG L + Sbjct: 164 QLASIQEEAAVELQEELDGLTIETRNRVPELVQELLAGRVDALIIEDTVAAGHLEANP-- 22- 1 Query: 212 ALAPFSLKTSDGDAKAVALPKNSGDLTKAVNKVIAKLDEQERYKSFI 258 L F++++ A+A PK+S +LT+ N+ + ++ E + I Sbjct: 222 GLVRFAIESEGETGSAIAFPKDS-ELTEPFNEKLQEMMEDGTMEELI 267 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03909 Identities = 223/246 (90%), Positives = 238/246 (96%) Query: 1 MAELKIDVQDLHKSYGQNEVLKGIDAKFYEGDVVCIIGPSGSGKSTFLRTLNLLESITSG 60 M ELKIDVQDLHKSYGQNEVLKGIDAKFYEGDVVCIIGPSGSGKSTFLRTLNLLE+ITSG Sbjct: 1 MTELKIDVQDLHKSYGQNEVLKGIDAKFYEGDVVCIIGPSGSGKSTFLRTLNLLETITSG 60 Query: 61 KVVVDGFELSNPKTDIDKARENIGMVFQHFNLFPHMSVLENITFAPIELGKESKEAAEKH 120- KV+VDGFELS+PKT+IDKARENIGMVFQHFNLFPHM+VLENI FAP+ELGKESKE A+KH Sbjct: 61 KVMVDGFELSDPKTNIDKARENIGMVFQHFNLFPHMTVLENIIFAPVELGKESKEVAKKH 120- Query: 121 GMELLEKVGLADKANAKPDSLSGGQKQRVAIARSLAMNPDILLFDEPTSALDPEMVGDVL 18- 0 GM LLEKVGL+DKA+A P SLSGGQKQRVAIARSLAMNPDI+LFDEPTSALDPEMVGDVL Sbjct: 121 GMALLEKVGLSDKADAFPGSLSGGQKQRVAIARSLAMNPDIMLFDEPTSALDPEMVGDVL 18- 0 Query: 181 NVMKDLAEQGMTMLIVTHEMGFARQVANRVIFTDGGRFLEDGTPEQIFDTPQHPRLQDFL 24- 0 NVMKDLAEQGMTMLIVTHEMGFARQVANRVIFTDGG+FLEDGTPE+IFD P+HPRL +FL Sbjct: 181 NVMKDLAEQGMTMLIVTHEMGFARQVANRVIFTDGGQFLEDGTPEEIFDHPKHPRLIEFL 24- 0 Query: 241 NKVLNV 246 +KVLNV Sbjct: 241 DKVLNV 246 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1317 A DNA sequence (GBSx1397) was identified in S. agalactiae <SEQ ID 4029> which encodes the amino acid sequence <SEQ ID 4030>. Analysis of this protein sequence reveals the following: TABLE-US-03910 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2311(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4031> which encodes the amino acid sequence <SEQ ID 4032>. Analysis of this protein sequence reveals the following: TABLE-US-03911 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2702(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03912 Identities = 45/51 (88%), Positives = 49/51 (95%) Query: 1 MGDKPISFRDKDGNFVSAADVWNAEKLEELFNTLNPNRKLRLEREKLAKEK 51 MGDKPISF+DKDGNFVSAADVWNAEKLEELFN LNPNR+LRLEREKL K++ Sbjct: 11 MGDKPISFKDKDGNFVSAADVWNAEKLEELFNLLNPNRRLRLEREKLKKDE 61 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1318 A DNA sequence (GBSx1398) was identified in S. agalactiae <SEQ ID 4033> which encodes the amino acid sequence <SEQ ID 4034>. This protein is predicted to be spo0b-associated GTP-binding protein (obg). Analysis of this protein sequence reveals the following: TABLE-US-03913 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2967(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03914 >GP: CAB14752 GB: Z99118 GTPase activity [Bacillus subtilis] Identities = 297/435 (68%), Positives = 345/435 (79%), Gaps = 7/435 (1%) Query: 3 MFLDTAKISVKAGRGGDGMVAFRREKYVPNGGPWGGDGGKGGSVIFKVNEGLRTLMDFRY 62 MF+D K+ VK G GG+GMVAFRREKYVP GGP GGDGGKGG V+F+V+EGLRTLMDFRY Sbjct: 1 MFVDQVKVYVKGGDGGNGMVAFRREKYVPKGGPAGGDGGKGGDVVFEVDEGLRTLMDFRY 60 Query: 63 NRNFKAKAGEKGMTKGMHGRGAEDLIVSLPPGTTVRDATTGKVITDLVEHDQEFVVARGG 122- ++FKA GE GM+K HGR A+D+++ +PPGT V D T +VI DL EH Q V+ARGG Sbjct: 61 KKHFKAIRGEHGMSKNQHGRNADDMVIKVPPGTVVTDDDTKQVIADLTEHGQRAVIARGG 120- Query: 123 RGGRGNIRFATPRNPAPEIAENGEPGEERELQLELKILADVGLVGFPSVGKSTLLSVVSA 18- 2 RGGRGN RFATP NPAP+++ENGEPG+ER + LELK+LADVGLVGFPSVGKSTLLSVVS+ Sbjct: 121 RGGRGNSRFATPANPAPQLSENGEPGKERYIVLELKVLADVGLVGFPSVGKSTLLSVVSS 18- 0 Query: 183 AKPKIGAYHFTTIVPNLGMVRTKSGDSFAMADLPGLIEGASQGVGLGTQFLRHIERTRVI 24- 2 AKPKI YHFTT+VPNLGMV T G SF MADLPGLIEGA QGVGLG QFLRHIERTRVI Sbjct: 181 AKPKIADYHFTTLVPNLGMVETDDGRSFVMADLPGLIEGAHQGVGLGHQFLRHIERTRVI 24- 0 Query: 243 LHVIDMSASEGRDPYDDYVSINNELETYNLRLMERPQIIVANKMDMPDSEENLAAFKEKL 30- 2 +HVIDMS EGRDPYDDY++IN EL YNLRL ERPQIIVANKMDMP++ ENL AFKEKL Sbjct: 241 VHVIDMSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKMDMPEAAENLEAFKEKL 30- 0 Query: 303 AANYDEFDDMPMIFPISSLAHQGLENLMDATAELLANTEEFLLYDETDMQEDEAYYGFNE 36- 2 DD P +FPIS++ +GL L+ A L NT EF LYDE ++ ++ Y Sbjct: 301 T------DDYP-VFPISAVTREGLRELLFEVANQLENTPEFPLYDEEELTQNRVMYTMEN 35- 3 Query: 363 DERPFEITRDDDATWVLYGDKLEKLFVMTNMERDESIMKFARQLRGMGVDEALRERGAKD 42- 2 +E PF ITRD D +VL GD LE+LF MT+ RDES+ +FARQ+RGMGVDEALRERGAKD Sbjct: 354 EEVPFNITRDPDGVFVLSGDSLERLFKMTDFSRDESVKRFARQMRGMGVDEALRERGAKD 41- 3 Query: 423 GDIVRIGNFEFEFVD 437 GDI+R+ FEFEF+D Sbjct: 414 GDIIRLLEFEFEFID 428 A related DNA sequence was identified in S. pyogenes <SEQ ID 4035> which encodes the amino acid sequence <SEQ ID 4036>. Analysis of this protein sequence reveals the following: TABLE-US-03915 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2588(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03916 Identities = 394/437 (90%), Positives = 421/437 (96%) Query: 1 MSMFLDTAKISVKAGRGGDGMVAFRREKYVPNGGPWGGDGGKGGSVIFKVNEGLRTLMDF 60 MSMFLDTAKISV+AGRGGDGMVAFRREKYVPNGGPWGGDGGKGGSVIF+V+EGLRTLMDF Sbjct: 1 MSMFLDTAKISVQAGRGGDGMVAFRREKYVPNGGPWGGDGGKGGSVIFRVDEGLRTLMDF 60 Query: 61 RYNRNFKAKAGEKGMTKGMHGRGAEDLIVSLPPGTTVRDATTGKVITDLVEHDQEFVVAR 120- RYNR FKAK+GEKGMTKGMHGRGAEDLIV +P GTTVRDA TGKVITDLVEH QE V+A+ Sbjct: 61 RYNRKFKAKSGEKGMTKGMHGRGAEDLIVFVPQGTTVRDAETGKVITDLVEHGQEVVIAK 120- Query: 121 GGRGGRGNIRFATPRNPAPEIAENGEPGEERELQLELKILADVGLVGFPSVGKSTLLSVV 18- 0 GGRGGRGNIRFATPRNPAPEIAENGEPGEER+L+LELKILADVGLVGFPSVGKSTLLSVV Sbjct: 121 GGRGGRGNIRFATPRNPAPEIAENGEPGEERQLELELKILADVGLVGFPSVGKSTLLSVV 18- 0 Query: 181 SAAKPKIGAYHFTTIVPNLGMVRTKSGDSFAMADLPGLIEGASQGVGLGTQFLRHIERTR 24- 0 S+AKPKIGAYHFTTIVPNLGMVRTKSGDSFAMADLPGLIEGASQGVGLGTQFLRHIERTR Sbjct: 181 SSAKPKIGAYHFTTIVPNLGMVRTKSGDSFAMADLPGLIEGASQGVGLGTQFLRHIERTR 24- 0 Query: 241 VILHVIDMSASEGRDPYDDYVSINNELETYNLRLMERPQIIVANKMDMPDSEENLAAFKE 30- 0 VILHVIDMSASEGRDPY+DYVSINNELETYNLRLMERPQIIVANKMD+P+++ENL AFK+ Sbjct: 241 VILHVIDMSASEGRDPYEDYVSINNELETYNLRLMERPQIIVANKMDIPEAQENLKAFKK 30- 0 Query: 301 KLAANYDEFDDMPMIFPISSLAHQGLENLMDATAELLANTEEFLLYDETDMQEDEAYYGF 36- 0 KLAA YDEFDD+PMIFPISSLAHQGLENL++ATAELLA T+EFLLYDE+D+ ++EAYYGF Sbjct: 301 KLAAQYDEFDDLPMIFPISSLAHQGLENLLEATAELLAKTDEFLLYDESDLVDEEAYYGF 36- 0 Query: 361 NEDERPFEITRDDDATWVLYGDKLEKLFVMTNMERDESIMKFARQLRGMGVDEALRERGA 42- 0 E E+ FEITRDDDATWVL G+KLE+LFVMTNMERDESIMKFARQLRGMGVDEALRERGA Sbjct: 361 AETEKDFEITRDDDATWVLSGEKLERLFVMTNMERDESIMKFARQLRGMGVDEALRERGA 42- 0 Query: 421 KDGDIVRIGNFEFEFVD 437 KDGD VRIG FEFEFVD Sbjct: 421 KDGDPVRIGKFEFEFVD 437 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1319 A DNA sequence (GBSx1399) was identified in S. agalactiae <SEQ ID 4037> which encodes the amino acid sequence <SEQ ID 4038>. Analysis of this protein sequence reveals the following:

TABLE-US-03917 Possible site: 36 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4039> which encodes the amino acid sequence <SEQ ID 4040>. Analysis of this protein sequence reveals the following: TABLE-US-03918 Possible site: 39 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03919 Identities = 30/42 (71%), Positives = 37/42 (87%) Query: 1 MAFGDNGQRKKTGFEKLTLFVVILMVLVTVGGLVFGAISAIM 42 +AFG+NG RKKT FEK+T+FVVILMVLVTVGGL+ A+S +M Sbjct: 1 VAFGENGPRKKTTFEKVTMFVVILMVLVTVGGLIASALSVLM 42 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1320 A DNA sequence (GBSx1401) was identified in S. agalactiae <SEQ ID 4041> which encodes the amino acid sequence <SEQ ID 4042>. Analysis of this protein sequence reveals the following: TABLE-US-03920 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2484(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03921 >GP: AAD28348 GB: AF102860 aminopeptidase PepS [Streptococcus hermophilus] Identities = 247/413 (59%), Positives = 313/413 (74%) Query: 1 MVLQDFDNLLKKYAQLIISKGLNVQKGHTLALTIDVEQVHLARLLTEAAYEKGASEVIVD 60 MVL +F L+KYA+L+++ G+NVQ GHT+AL+IDVEQ LA LL + AY GA+EVIV Sbjct: 1 MVLPNFKENLEKYAKLLVTNGINVQPGHTVALSIDVEQAELAHLLVKEAYALGAAEVIVQ 60 Query: 61 YTDDFITRQRLLHASDEVLTNVPQYTVDKSLALLNKKASRLVVKSSNPNAFATVDPKRLS 120- ++DD I R+R LHA + VP Y + LL KKASRL V+SS+P+AF V P+RLS Sbjct: 61 WSDDTINRERFLHAEMNRIEEVPAYKKAEMEYLLEKKASRLGVRSSDPDAFNGVAPERLS 120- Query: 121 ETTRATAIALEEQSRAIQANKVSWNVAAAAGREWAALVFPELKTSDQQVDALWDTIFKLN 18- 0 +A A + A Q+NKVSW VAAAAG+EWA VFP + ++ VD LW+ IFK Sbjct: 121 AHAKAIGAAFKPMQVATQSNKVSWTVAAAAGKEWAKKVFPNASSDEEAVDLLWNQIFKTC 18- 0 Query: 181 RIYEDDPIAAWDAHEAKLLEKATRLNQEQFDALHYTAPGTDLTLGMPKNHIWEAAGSLNA 24- 0 R+YE DP+ AW H +L KA LN+ QF ALHYTAPGTDLTLG+PKNH+WE+AG++NA Sbjct: 181 RVYEKDPVRAWKEHADRLDAKARILNEAQFSALHYTAPGTDLTLGLPKNHVWESAGAINA 24- 0 Query: 241 QGETFIANMPTEEIFSAPDYRRADGYVTSTKPLSYAGVIIENMTFTFKDGKIINVTAEKG 30- 0 QGE+F+ NMPTEE+F+APD+RRA GYV+STKPLSY G IIE + TFKDG+I+++TA++G Sbjct: 241 QGESFLPNMPTEEVFTAPDFRRAYGYVSSTKPLSYNGNIIEGIKVTFKDGEIVDITADQG 30- 0 Query: 301 QETVQRLIEENDGARSLGEVALVPHKTPISLSGLIFFNTLFDENASNHLAIGTAYAFNVE 36- 0 ++ ++ L+ N+GAR+LGE ALVP +PIS SG+ FFNTLFDENASNHLAIG AYA +VE Sbjct: 301 EKVMKNLVFNNNGARALGECALVPDSSPISQSGITFFNTLFDENASNHLAIGAAYATSVE 36- 0 Query: 361 GGTEMTSQELDEAGLNRSSTHVDFMIGSEQMDIDGIRADGTAVPIFRNGEWAI 413 GG +MT +EL AGLNRS HVDF+IGS QM+IDGI DG+ VPIFRNG+W I Sbjct: 361 GGADMTEEELKAAGLNRSDVHVDFIIGSNQMNIDGIHHDGSRVPIFRNGDWVI 413 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1321 A DNA sequence (GBSx1403) was identified in S. agalactiae <SEQ ID 4045> which encodes the amino acid sequence <SEQ ID 4046>. Analysis of this protein sequence reveals the following: TABLE-US-03922 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.91 Transmembrane 661-677 (657-680) ----- Final Results ----- bacterial membrane --- Certainty = 0.4163(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8787> which encodes amino acid sequence <SEQ ID 8788> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-03923 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: 6.47 GvH: Signal Score (-7.5): 1.01 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 1 value: -7.91 threshold: 0.0 INTEGRAL Likelihood = -7.91 Transmembrane 658-673 (657-680) PERIPHERAL Likelihood = 4.35 555 modified ALOM score: 2.08 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4163(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty= 0.0000(Not Clear) < succ> LPXTG motif: 647-651 The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03924 >GP: AAF09821 GB: AE001885 6-aminohexanoate-cyclic-dimer hydrolase [Deinococcus radiodurans] Identities = 150/497 (30%), Positives = 233/497 (46%), Gaps = 32/497 (6%) Query: 110 LTEETYKQKDGQDLANMVRSGQVTSEELVNMAYDIIAKENPSLNAVITTRRQEAIEEARK 16- 9 LT Y + D DLA + R G++++E++ A N +LNAV+ + + +AR Sbjct: 45 LTFAEYDRLDALDLAQLFRRGELSAEDMCTAAIHRAQVVNVALNAVVYPLYDQGLAQARA 104- Query: 170 L-------KDTNQPFLGVPLLVKGLGHSIKGGETNNGLIYADGKISTFDSSYVKKYKDLG 22- 2 + PF GVP LVK G + G G +I +D V++++ G Sbjct: 105 TDAARARGEQATGPFAGVPFLVKDFGSRLAGVPHTGGTRAYRDQIPEWDDELVRRWQAAG 16- 4 Query: 223 FIILGQTNFPEYGWRNITDSKLYGLTHNPWDLAHNAGGSSGGSAAAIASGMTPIASGSDA 28- 2 + LG+TN PE+ +T+ +L+G T NPWDL GGSSGGSA+A+A+G+ P+A D Sbjct: 165 LLPLGKTNTPEFALMGVTEPELHGPTRNPWDLGRTPGGSSGGSASAVAAGIVPLAGAGDG 22- 4 Query: 283 GGSIRIPSSWTGLVGLKPTRGLV---SNEKPDSYSTAVHFPLTKSSRDAETLLTYLKKSD 33- 9 GGSIRIP+S GL GLKP+RG V AV LT+S RD+ LL + D Sbjct: 225 GGSIRIPASCCGLFGLKPSRGRVPCGDGVGEPWQGAAVEHVLTRSVRDSAALLDLEQGPD 28- 4 Query: 340 QTLVSV-------------NDLKSLPIAYTLKSPMGTEVSQDAKNAIMDNVTFLRKQGFK 38- 6 + L I ++ P+G V + A+ L G + Sbjct: 285 AGAALFLPSPERPYSEEVGREPGRLRIGFSTAHPLGRSVHPECVAAVQGAARLLESLGHE 34- 4 Query: 387 VTEIDLPIDGRALMRDYSTLAIGMGGAFSTIEKDLKKHGFTKEDVDPITWAVHVIYQNSD 44- 6 V E+ LP DG AL + + L G GA +D DV+ +TW + + ++ Sbjct: 345 VEEVALPWDGPALAQAFLMLYFGETGASLAALRDTLGRPARASDVEAVTWLLGQLGRSYS 40- 4 Query: 447 KAELKKSIMEAQKHMDDYRKAMEKLHKQFPIFLSPTTASLAPLNTDFY----VTEEDKRA 50- 2 A+ A+ + + +AM + H+ + + L+P A+ PL V RA Sbjct: 405 AAD----FAAARASWNVHARAMGRFHQNYDLLLTPVLAT-PPLQIGELQPRGVQAALLRA 45- 9 Query: 503 IYNMENLSQEERIALFNRQWEPMLRRTPFTQIANMTGLPAISIPTYLSESGLPIGTMLMA 56- 2 M+ R + +L + P+TQ+AN+TG PA+S+P + + GLP+G +A Sbjct: 460 AQQMDVSGLLRRSGQVDALATDILEKMPYTQLANLTGQPAMSVPLHWTADGLPVGVQFVA 51- 9 Query: 563 GANYDMVLIKFATFFEK 579 + VL++ A E+ Sbjct: 520 PLAREDVLLRLAGQLEQ 536 There is also homology to SEQ ID 4048. SEQ ID 8788 (GBS173) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 41 (lane 5; MW 96.8 kDa). The GBS173-GST fusion product was purified (FIG. 116A; see also FIG. 201, lane 7) and used to immunise mice (lane 1+2 product; 15 .mu.g/mouse). The resulting antiserum was used for Western blot, FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1322 A DNA sequence (GBSx1404) was identified in S. agalactiae <SEQ ID 4049> which encodes the amino acid sequence <SEQ ID 4050>. This protein is predicted to be ribosomal large subunit pseudouridine synthase B (rsuA). Analysis of this protein sequence reveals the following: TABLE-US-03925 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3674(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03926 >GP: BAB06992 GB: AP001518 16S pseudouridylate synthase [Bacillus halodurans] Identities = 110/236 (46%), Positives = 149/236 (62%), Gaps = 4/236 (1%) Query: 1 MRLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGTLVSYEKF 60 MR+DKFL G GSR VK +LK + V G P V+ + I G V Y+ + Sbjct: 1 MRIDKFLANMGFGSRKDVKKLLKTGAVRVQGQPIKDPSTHVEPESESITVYGEEVEYKPY 60 Query: 61 VYYMLHKPKGVISATDDPSHKTVLDLLDKTARDKAVFPVGRLDIDTTGLLLLTNNGELAH 120- VY M++KPKGVI AT+D H+TV+DLL + R PVGRLD DT GLLL+TN+G+ H Sbjct: 61 VYLMMNKPKGVICATEDLEHETVIDLLGEEERHYEPSPVGRLDKDTVGLLLITNDGKFNH 120- Query: 121 KMLSPKKHVDKCYEVKISGIMTEDDILAFDKGIILKD-FTCLPALLEIVEVNQVKKQSLV 17- 9 ++SPK HV K Y + G +TE+D+ AF G++L D + PA L I+E +S + Sbjct: 121 WLMSPKHHVPKTYRALVEGHVTEEDVGAFSHGVVLDDGYVTKPATLHILEAG---ARSHI 17- 7 Query: 180 KITIKEGKFHQVKRMVAACGKEVLELKRLRMGNLQLDKQLESGQWRRLTIKEIEKL 235 ++ + EGKFHQVKRM A GK VLEL+R+++GNL LD +L G++R LT +EI L Sbjct: 178 ELILTEGKFHQVKRMFQAVGKRVLELERIKIGNLLLDPELARGEYRELTKEEIALL 233 A related DNA sequence was identified in S. pyogenes <SEQ ID 4051> which encodes the amino acid sequence <SEQ ID 4052>. Analysis of this protein sequence reveals the following: TABLE-US-03927 Possible Site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0152(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03928 >GP: AAF09821 GB: AE001885 6-aminohexanoate-cyclic-dimer hydrolase [Deinococcus radiodurans] Identities = 177/485 (36%), Positives = 259/485 (52%), Gaps = 13/485 (2%) Query: 5 DATAMAIAVQTGQTTPLELVTQAIYKAKKLNPTLNAITSERFEAALEEAKQRDFSGL--- 61 DA +A + G+ + ++ T AI++A+ +N LNA+ ++ L +A+ D + Sbjct: 54 DALDLAQLFRRGELSAEDMCTAAIHRAQVVNVALNAVVYPLYDQGLAQARATDAARARGE 113- Query: 62 ----PFAGVPLFLKDLGQELKGHSSTSGSRLFKEYQATKTDLFVKRLEALGFIILGRSNT 117- PFAGVP +KD G L G T G+R +++ D V+R +A G + LG++NT Sbjct: 114 QATGPFAGVPFLVKDFGSRLAGVPHTGGTRAYRDQIPEWDDELVRRWQAAGLLPLGKTNT 17- 3 Query: 118 PEFGFKNISDSSLHGPVNLPRDNTRNAGGSSGGAAALVSSGISALATASDGGGSIRIPAS 17- 7 PEF +++ LHGP P D R GGSSGG+A+ V++GI LA A DGGGSIRIPAS Sbjct: 174 PEFALMGVTEPELHGPTRNPWDLGRTPGGSSGGSASAVAAGIVPLAGAGDGGGSIRIPAS 23- 3 Query: 178 FNGLIGLKPSRGRMPVGPGSYRSWQGASVHFALTKSVRDTRNLLYYLQMEQMESPFPLAT 23- 7 GL GLKPSRGR+P G G WQGA+V LT+SVRD+ LL Q + L + Sbjct: 234 CCGLFGLKPSRGRVPCGDGVGEPWQGAAVEHVLTRSVRDSAALLDLEQGPDAGAALFLPS 29- 3 Query: 238 LTKDSIYQSLQRP--LTIAFYQRLSDGSPVSLDTAKALRQAVTWLREQGHQLVELEEFPV 29- 5 + + + P L I F G V + A++ A L GH++ E+ P Sbjct: 294 PERPYSEEVGREFGRLRIGFSTAHPLGRSVHPECVAAVQGAARLLESLGHEVEEV-ALPW 35- 2 Query: 296 NMTEVIRHYYIMNSVETAAMFADIEDTFGRPMTKDDMETMTWAIYQSGKDIPAWRYSQVL 35- 5 + + + + ++ ET A A + DT GRP D+E +TW + Q G+ A ++ Sbjct: 353 DGPALAQAFLMLYFGETGASLAALRDTLGRPARASDVEAVTWLLGQLGRSYSAADFAAAR 41- 2 Query: 356 QKWDTYSATMASFHETYDLLLTFTTNTPAPKHGELVP---DSKLMANLAQAEIFSSEEQF 41- 2 W+ ++ M FH+ YDLLLT TP + GEL P + L+ Q ++ + Sbjct: 413 ASWNVHARAMGRFHQNYDLLLTPVLATPPLQIGELQPRGVQAALLRAAQQMDVSGLLRRS 47- 2 Query: 413 NLVETMFGKSLAINPYTALPNLTGQPAISLPTYETKEGLSMGIQLIAAKGREDLLLGIAE 47- 2 V+ + L PYT L NLTGQPA+S+P + T +GL +G+Q +A RED+LL +A Sbjct: 473 GQVDALATDILEKMPYTQLANLTGQPAMSVPLHWTADGLPVGVQFVAPLAREDVLLRLAG 53- 2 Query: 473 QFEAA 477 Q E A Sbjct: 533 QLEQA 537 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03929 Identities = 151/240 (62%), Positives = 183/240 (75%) Query: 1 MRLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGTLVSYEKF 60 MRLDKFLV G+G+R+QVKL+LKKK I VN ETS K +DEY+D + Y GT + YE F Sbjct: 2 MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVYESF 61 Query: 61 VYYMLHKPKGVISATDDPSHKTVLDLLDKTARDKAVFPVGRLDIDTTGLLLLTNNGELAH 120- VYY+L+KP G +SAT D TV++LLD TAR KAVFPVGRLD DT GLLLLTNNG+LAH Sbjct: 62 VYYLLNKPSGYVSATQDRQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAH 121- Query: 121 KMLSPKKHVDKCYEVKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSLVK 18- 0 +LSPKKHV K Y K++GIMTE D F +GI LKD CLPA LE++ + ++ SLVK Sbjct: 122 DLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLVK 18- 1 Query: 181 ITIKEGKFHQVKRMVAACGKEVLELKRLRMGNLQLDKQLESGQWRRLTIKEIEKLEKYMQ 24- 0 ITI+EGKFHQVKRMVAACGKEVL+L+RL MG L+LD L G++RRLT +E++ L Y Q Sbjct: 182 ITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQSLAPYCQ 24- 1 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1323 A DNA sequence (GBSx1405) was identified in S. agalactiae <SEQ ID 4053> which encodes the amino acid sequence <SEQ ID 4054>. Analysis of this protein sequence reveals the following: TABLE-US-03930 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2811(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10007> which encodes amino acid sequence <SEQ ID 10008> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03931 >GP:AAA57350 GB:J04483 reductase [Leishmania major] Identities = 129/277 (46%), Positives = 167/277 (59%), Gaps = 3/277 (1%) Query: 26 TLSNTLNIPKIGFGTWQLTEGEEAYKAVTHALKVGYTHIDTAQIYGNEHSVGRAIRDSGL 85 - TLSN + +P+ G G WQ GE AV AL GY HIDTA IY NE SVG +R SG+ Sbjct: 10 TLSNGVKMPQFGLGVWQSPAGEVTENAVNWALCAGYRHIDTAAIYKNEESVGAGLRASGV 69 Query: 86 ARESIFLTTKIWNDKHDYHLAKASIDESLQKLGVDYIDLLLIHWPNPKALRENDAWKAGN 145- RE +F+TTK+WN + Y A+ +ES QKLGVDYIDL LIHWP K + + K Sbjct: 70 PREDVFITTKLWNTEQGYESTLAAFEESRQKLGVDYIDLYLIHWPRGKDILSKEGKKY-- 127- Query: 146 AGTWKAMEEAYKEGKVKAIGVSNFMKHHLEALFETAEIKPMVNQIILAPGCAQEDLVRFC 20- 5 +W+A E+ YKE KV+AIGVSNF HHLE + + PMVNQ+ L P Q DL FC Sbjct: 128 LDSWRAFEQLYKEKKVRAIGVSNFHIHHLEDVLAMCTVTPMVNQVELHPLNNQADLRAFC 18- 7 Query: 206 KGNDILLEAYSPFGTGAIFENESIKAIAEKYGKSVAQVALRWSLDNGFLPLPKSATPKNI 26- 5 I +EA+SP G G + N + AI KY K+ AQV LRW++ + +PKS + I Sbjct: 188 DAKQIKVEAWSPLGQGKLLSNPILSAIGAKYNKTAAQVILRWNIQKNLITIPKSVHRERI 24- 7 Query: 266 EANLDIFDFQLNEDDIATLIQLDSGIK-PKDPDNVSF 301 E N DIFDF+L +D+ ++ L++ + DPD F Sbjct: 248 EENADIFDFELGAEDVMSIDALNTNSRYGPDPDEAQF 284 A related DNA sequence was identified in S. pyogenes <SEQ ID 779> which encodes the amino acid sequence <SEQ ID 780>. Analysis of this protein sequence reveals the following: TABLE-US-03932 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0980(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03933 Identities = 155/282 (54%), Positives = 204/282 (71%), Gaps = 2/282 (0%) Query: 20 IVMETYTLSNTLNIPKIGFGTWQLTEGEEAYKAVTHALKVGYTHIDTAQIYGNEHSVGRA 79 - +++ T +++ IP +GFGT+Q +GEEAY++ A+K GY HIDTA IY NE SVGRA Sbjct: 1 VMVTTVKMTSGYEIPVLGFGTYQAADGEEAYQSTLAAIKAGYRHIDTAAIYKNEESVGRA 60 Query: 80 IRDSGLARESIFLTTKIWNDKHDYHLAKASIDESLQKLGVDYIDLLLIHWPNPKALREND 139- I+DSG+ RE +F+TTK+WND H Y AK ++ SL +LG+DY+DL LIHWPNPKALR + Sbjct: 61 IKDSGVLREDLFITTKLWNDAHSYEGAKDALAASLDRLGLDYVDLYLIHWPNPKALR--N 118- Query: 140 AWKAGNAGTWKAMEEAYKEGKVKAIGVSNFMKHHLEALFETAEIKPMVNQIILAPGCAQE 19- 9 WK NA W+ MEEA + G +K+IGVSNFM HHLEAL ETA+I P +NQI LAPGC Q+ Sbjct: 119 TWKEANAQAWQYMEEAVEAGLIKSIGVSNFMVHHLEALQETAKITPAINQIRLAPGCYQK 17- 8 Query: 200 DLVRFCKGNDILLEAYSPFGTGAIFENESIKAIAEKYGKSVAQVALRWSLDNGFLPLPKS 25- 9 ++V +CK N+ILLEA+SP G G IF+NE+++ +A KY K+VAQVAL WSL GF+PLPKS Sbjct: 179 EVVDYCKANEILLEAWSPLGQGEIFDNETMQQLANKYDKTVAQVALAWSLAEGFIPLPKS 23- 8 Query: 260 ATPKNIEANLDIFDFQLNEDDIATLIQLDSGIKPKDPDNVSF 301 + I+ N+ IFD L ++D T+ L +PD SF Sbjct: 239 VHDERIKENMAIFDVSLTQEDKKTIRYLSGMSAIPNPDTTSF 280 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1324 A DNA sequence (GBSx1406) was identified in S. agalactiae <SEQ ID 4055> which encodes the amino acid sequence <SEQ ID 4056>. Analysis of this protein sequence reveals the following:

TABLE-US-03934 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0633(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10009> which encodes amino acid sequence <SEQ ID 10010> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03935 >GP:CAB12612 GB:Z99108 similar to NAD(P)H-flavin oxidoreductase [Bacillus subtilis] Identities = 106/223 (47%), Positives = 150/223 (66%), Gaps = 8/223 (3%) Query: 29 DIKKQVRRAFDFRMAIRVYN-NNDIPKEDMEYILDTAWLSPSSVGLEGWRFLVLDRQTIA D+K Q+ A++FR A + ++ N + D E+IL+T LSPSS+GLE W+F+V+ Sbjct: 3 DLKTQILDAYNFRHATKEFDPNKKVSDSDFEFILETGRLSPSSLGLEPWKFVVVQNP--- 59 Query: 88 KFRDKLKEVAWGAQYQLDTASHFVLLLAE--KGAYYNADSMINSLIRRGLGDPAALESRI 145- +FR+KL+E WGAQ QL TASHFVL+LA K YNAD + L E + Sbjct: 60 EFREKLREYTWGAQKQLPTASHFVLILARTAKDIKYNADYIKRHLKEVKQMPQDVYEGYL 119- Query: 146 PLYKSFQENDMKI-DSERSLWDWTAKQTYIALGNMMTAAAMIGVDSCPIEGFDYEKVNNI 20- 4 + FQ+ND+ + +S+R+L+DW +KQTYIALGNMMTAAA IGVDSCPIEGF Y+ ++ I Sbjct: 120 SKTEEFQKNDLHLLESDRTLFDWASKQTYIALGNMMTAAAQIGVDSCPIEGFQYDHIHRI 17- 9 Query: 205 LSKEGLIDDKKEAISCMVSFGYRLREPKHSRARKERQEVITWV 247 L +EGL+++ IS MV+FGYR+R+P+ + R ++V+ WV Sbjct: 180 LEEEGLLENGSFDISVMVAFGYRVRDPR-PKTRSAVEDVVKWV 221 A related DNA sequence was identified in S. pyogenes <SEQ ID 4057> which encodes the amino acid sequence <SEQ ID 4058>. Analysis of this protein sequence reveals the following: TABLE-US-03936 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1705(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03937 Identities = 126/222 (56%), Positives = 174/222 (77%), Gaps = 4/222 (1%) Query: 28 EDIKKQVRRAFDFRMAIRVYNNNDIPKEDMEYILDTAWLSPSSVGLEGWRFLVLDRQTIA 87 - + I Q+++A FR A+RVY I ED+ ILD AWLSPSS+GLEGWRF+VLD + I Sbjct: 3 QTIHHQIQQALHFRTAVRVYKEEKISDEDLALILDAAWLSPSSIGLEGWRFVVLDNKPI- 61 Query: 88 KFRDKLKEVAWGAQYQLDTASHFVLLLAEKGAYYNADSMINSLIRRGLGDPAALESRIPL 147- ++++K AWGAQYQL+TASHF+LL+AEK A Y++ ++ NSL+RRG+ + L SR+ L Sbjct: 62 --KEEIKPFAWGAQYQLETASHFILLIAEKHARYDSPAIKNSLLRRGIKEGDGLNSRLKL 119- Query: 148 YKSFQENDMKI-DSERSLWDWTAKQTYIALGNMMTAAAMIGVDSCPIEGFDYEKVNNILS 20- 6 Y+SFQ+ DM + D+ R+L+DWTAKQTYIALGNMM AA++G+D+CPIEGF Y+KVN+IL+ Sbjct: 120 YESFQKEDMDMADNPRALFDWTAKQTYIALGNMMMTAALLGIDTCPIEGFHYDKVNHILA 17- 9 Query: 207 KEGLIDDKKEAISCMVSFGYRLREPKHSRARKERQEVITWVE 248 K +ID +KE I+ M+S GYRLR+PKH++ RK ++EVI+ V+ Sbjct: 180 KHNVIDLEKEGIASMLSLGYRLRDPKHAQVRKPKEEVISVVK 221 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1325 A DNA sequence (GBSx1407) was identified in S. agalactiae <SEQ ID 4059> which encodes the amino acid sequence <SEQ ID 4060>. This protein is predicted to be lactoylglutathione lyase (gloA). Analysis of this protein sequence reveals the following: TABLE-US-03938 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1656(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03939 >GP:AAC21986 GB:U32717 lactoylglutathione lyase (gloA) [Haemophilus influenzae Rd] Identities = 59/131 (45%), Positives = 86/131 (65%), Gaps = 2/131 (1%) Query: 1 MPFLHTCIRVKDLDASIAFYQEALGFKEVRRNDFPENQFTLVYMALEDDPSY-ELELTYN 59 M LHT +RV DLD SI FYQ+ LG + +R ++ PE ++TL ++ ED S E+ELTYN Sbjct: 1 MQILHTMLRVGDLDRSIKFYQDVLGMRLLRTSENPEYKYTLAFLGYEDGESAAEIELTYN 60 Query: 60 YDHEAYDLGNGYGHIAVGVDDLETTYDAHQKAGYSVTKISG-LPGKPNMFYFIQDPDGYK 118- + + Y+ G YGHIA+GVDD+ T +A + +G +VT+ +G + G + F++DPDGYK Sbjct: 61 WGVDKYEHGTAYGHIAIGVDDIYATCEAVRASGGNVTREAGPVKGGSTVIAFVEDPDGYK 120- Query: 119 IEVIRLSQFKA 129 IE I K+ Sbjct: 121 IEFIENKSTKS 131 A related DNA sequence was identified in S. pyogenes <SEQ ID 4061> which encodes the amino acid sequence <SEQ ID 4062>. Analysis of this protein sequence reveals the following: TABLE-US-03940 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1382(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03941 Identities = 80/125 (64%), Positives = 93/125 (74%), Gaps = 1/125 (0%) Query: 1 MPFLHTCIRVKDLDASIAFYQEALGFKEVRRNDFPENQFTLVYMALEDDPSYELELTYNY 60 M LHTCIRVKDLD S+AFY A FKE R DFP++QFTLVY+ALE + SYELELTYNY Sbjct: 1 MKALHTCIRVKDLDQSVAFYTSAFPFKENYRKDFPDSQFTLVYLALEGE-SYELELTYNY 59 Query: 61 DHEAYDLGNGYGHIAVGVDDLETTYDAHQKAGYSVTKISGLPGKPNMFYFIQDPDGYKIE 120- H YDLGNGYGHIA+G + E + H++AG+VT I L K +YFIQDPDGYKIE Sbjct: 60 GHGDYDLGNGYGHIALGSEHFEADHKKHRQAGFPVTDIKELADKSARYYFIQDPDGYKIE 119- Query: 121 VIRLS 125 VI L+ Sbjct: 120 VIDLN 124 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1326 A DNA sequence (GBSx1408) was identified in S. agalactiae <SEQ ID 4063> which encodes the amino acid sequence <SEQ ID 4064>. Analysis of this protein sequence reveals the following: TABLE-US-03942 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.02 Transmembrane 241-257 (229-262) INTEGRAL Likelihood = -4.94 Transmembrane 270-286 (264-287) ----- Final Results ----- bacterial membrane --- Certainty = 0.4609(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03943 >GP:CAB12688 GB:Z99108 stress response protein [Bacillus subtilis] Identities = 139/304 (45%), Positives = 200/304 (65%), Gaps = 3/304 (0%) Query: 3 LLSVIVPCYNEQETVSTFLTEIKKVESEMARYTHFEYIFVNDGSTDRTLELLKKAAKQFD 62 L+S+I+P YNE V +KK E + Y +E F+NDGS D TL+ +K A Sbjct: 5 LISIIIPSYNEGYNVKLIHESLKK-EFKNIHYD-YEIFFINDGSVDDTLQQIKDLAATCS 62 Query: 63 NVHYLSFSRHFGKDAALLAGLEHTTGDFITVMDVDLQDPPTLLPEMYLKLQEGYDIVATR 122- V Y+SFSR+FGK+AA+LAG EH G+ + VMD DLQ P LL E +EGYD V + Sbjct: 63 RVKYISFSRNFGKEAAILAGFEHVQGEAVIVMDADLQHPTYLLKEFIKGYEEGYDQVIAQ 122- Query: 123 RKDRKGEPLIRSLFAKLFYKLINQVSDTKMVDGARDFRLMTKQVVDSILELNEVNRFSKG 18- 2 R +RKG+ +RSL + ++YK IN+ + + DG DFRL+++Q V+++L+L+E NRFSKG Sbjct: 123 R-NRKGDSFVRSLLSSMYYKFINKAVEVDLRDGVGDFRLLSRQAVNALLKLSEGNRFSKG 18- 1 Query: 183 IFSWIGYDVAYISYENRERIAGKTSWSFFNLLKYSLDGFINFSEIPLAIATWIGTLSSVL 24- 2 +F WIG+D + YEN ER G + WSF +L Y +DG ++F+ PL + + G +L Sbjct: 182 LFCWIGFDQKIVFYENVERKNGTSKWSFSSLFNYGMDGVVSFNHKPLRLCFYTGIFILLL 24- 1 Query: 243 SLLAIIFIIIRKLLFGDPVSGWASTVTIVLFMGGIQLLSLGIIGKYISKIFLETKKRPVY 30- 2 S++ II ++ L G V G+ + ++ VLF+GG+QLLSLGIIG+YI +I+ ETKKRP Y Sbjct: 242 SIIYIIATFVKILTNGISVPGYFTIISAVLFLGGVQLLSLGIIGEYIGRIYYETKKRPHY 30- 1 Query: 303 IVKE 306 ++KE Sbjct: 302 LIKE 305 A related DNA sequence was identified in S. pyogenes <SEQ ID 4065> which encodes the amino acid sequence <SEQ ID 4066>. Analysis of this protein sequence reveals the following: TABLE-US-03944 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.55 Transmembrane 256-272 (251-282) INTEGRAL Likelihood = -5.31 Transmembrane 290-306 (284-307) ----- Final Results ----- bacterial membrane --- Certainty = 0.4821(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9113> which encodes the amino acid sequence <SEQ ID 9114>. Analysis of this protein sequence reveals the following: TABLE-US-03945 Possible cleavage site: 36 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.482(Affirmative) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03946 Identities = 207/307 (67%), Positives = 258/307 (83%) Query: 1 MALLSVIVPCYNEQETVSTFLTEIKKVESEMARYTHFEYIFVNDGSTDRTLELLKKAAKQ 60 M LLS+IVPC+NE+ + + E+ ++E+ M FEYIF++DGS D TL +L++ A + Sbjct: 21 MTLLSIIVPCFNEEANILPYFEEMHQLETSMTNQLAFEYIFIDDGSKDNTLGILRELAAR 80 Query: 61 FDNVHYLSFSRHFGKDAALLAGLEHTTGDFITVMDVDLQDPPTLLPEMYLKLQEGYDIVA 120- F NVHYLSFSRHFGK+A LLAGL+ G++ITVMDVDLQDPP LLP MY KL+EGYDIV Sbjct: 81 FPNVHYLSFSRHFGKEAGLLAGLKEAKGNYITVMDVDLQDPPELLPIMYAKLKEGYDIVG 140- Query: 121 TRRKDRKGEPLIRSLFAKLFYKLINQVSDTKMVDGARDFRLMTKQVVDSILELNEVNRFS 18- 0 TRR++R+GEPLIRS+ + LFY LI +SDT+MV+G RD+RLMT+QVVDSILEL EVNRFS Sbjct: 141 TRRQNRQGEPLIRSMCSNLFYGLIKHLSDTEMVNGVRDYRLMTRQVVDSILELGEVNRFS 20- 0 Query: 181 KGIFSWIGYDVAYISYENRERIAGKTSWSFFNLLKYSLDGFINFSEIPLAIATWIGTLSS 24- 0 KGIFSW+GY + Y+S+EN++R GK+ W F+ LL+YSLDGFINFSE+PL IATW GT S Sbjct: 201 KGIFSWVGYRITYLSFENQKRKYGKSRWHFWELLRYSLDGFINFSEMPLTIATWTGTFSF 26- 0 Query: 241 VLSLLAIIFIIIRKLLFGDPVSGWASTVTIVLFMGGIQLLSLGIIGKYISKIFLETKKRP 30- 0 ++S+ AI+FIIIRK+LFGDPVSGWASTV+I+LFMGGIQL +GIIGKYISKIFLETKKRP Sbjct: 261 LISIFAILFIIIRKILFGDPVSGWASTVSIILFMGGIQLFCMGIIGKYISKIFLETKKRP 32- 0 Query: 301 VYIVKEE 307 +YI+KE+ Sbjct: 321 LYIIKEK 327 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1327 A DNA sequence (GBSx1409) was identified in S. agalactiae <SEQ ID 4067> which encodes the amino acid sequence <SEQ ID 4068>. This protein is predicted to be d-serine/d-alanine/glycine transporter (cycA). Analysis of this protein sequence reveals the following: TABLE-US-03947 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.44 Transmembrane 50-66 (50-66) INTEGRAL Likelihood = -1.49 Transmembrane 27-43 (27-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.1977(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03948 >GP:CAA83253 GB:Z31377 potential amino acid permease [Lactobacillus delbrueckii] Identities = 34/55 (61%), Positives = 44/55 (79%) Query: 7 DHTQKSENGMVRGLENRHVQLIAIAGTIGTGLFLGAGRSISLTGPSIVLVYAITG 61 D + ++ +G +R L NRHVQ+IAI GTIGTGLFLGAG +IS TGPS++ +YAI G Sbjct: 5 DRSIENTDGTIRSLSNRHVQMIAIGGTIGTGLFLGAGTTISATGPSVIFIYAIMG 59 A related DNA sequence was identified in S. pyogenes <SEQ ID 4069> which encodes the amino acid sequence <SEQ ID 4070>. Analysis of this protein sequence reveals the following: TABLE-US-03949 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.15 Transmembrane 170-186 (161-190) INTEGRAL Likelihood = -8.44 Transmembrane 256-272 (252-274) INTEGRAL Likelihood = -8.33 Transmembrane 352-368 (347-375) INTEGRAL Likelihood = -7.54 Transmembrane 139-155 (133-160) INTEGRAL Likelihood = -5.73 Transmembrane 420-436 (417-440) INTEGRAL Likelihood = -3.88 Transmembrane 56-72 (54-75) INTEGRAL Likelihood = -3.40 Transmembrane 283-299 (282-300) INTEGRAL Likelihood = -3.29 Transmembrane 440-456 (439-458) INTEGRAL Likelihood = -1.49 Transmembrane 31-47 (31-47) INTEGRAL Likelihood = -1.33 Transmembrane 109-125 (109-127) ----- Final Results ----- bacterial membrane --- Certainty = 0.5458(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03950 >GP:CAB14651 GB:Z99117 amino acid permease [Bacillus subtilis] Identities = 210/454 (46%), Positives = 296/454 (64%), Gaps = 11/454 (2%) Query: 12 DNNELENGMVRGLENRHVQLIAIAGTIGTGLFLGAGRSIALTGPSIIFVYMITGAFMFMM 71 - DN + + RGL+NRH+QL+AI G IGTGLFLG+G+SI GPSI+F Y+ITG F F + Sbjct: 8 DNFGQQQKLSRGLKNRHIQLMAIGGAIGTGLFLGSGKSIHFAGPSILFAYLITGVFCFFI 67 Query: 72 MRAIGEMLYYDPDQHTFINFISKYIGPGWGYFSGLSYWISLIFIGMAEITAVGAYVQFWF 131- +R++GE+L + H+F++F+ Y+G + +G +YW I + MA++TAVG Y Q+W Sbjct: 68 IRSLGELLLSNAGYHSFVDFVRDYLGNMAAFITGWTYWFCWISLAMADLTAVGIYTQYWL 127- Query: 132 PSWPAWLIQLVFLVLLSSINLIAVRVFGETEFWFAMIKILAILALIATAIFMVLTGFETH 19- 1 P P WL L+ L++L +NL V++FGE EFWFA+IK++AILALI T I ++ GF Sbjct: 128 PDVPQWLPGLLALIILLIMNLATVKLFGELEFWFALIKVIAILALIVTGILLIAKGFSAA 18- 7 Query: 192 TGHASLSNIFDHFSMFPNGKLKFFMAFQMVFFAYQAIEFVGITTSETANPRKVLPKAIQE 25- 1 +G ASL+N++ H MFPNG F ++FQMV FA+ IE VG+T ET NP+KV+PKAI + Sbjct: 188 SGPASLNNLWSHGGMFPNGWHGFILSFQMVVFAFVGIELVGLTAGETENPQKVIPKAINQ 24- 7 Query: 252 IPTRIVIFYVGALVSIMAIVPWHQLPVDESPFVMVFKLIGIKWAAALINFVVLTSAASAL 31- 1 IP RI++FYVGAL IM I PW+ L +ESPFV VF +GI AA+LINFVVLTSAASA Sbjct: 248 IPVRILLFYVGALFVIMCIYPWNVLNPNESPFVQVFSAVGIVVAASLINFVVLTSAASAA 30- 7 Query: 312 NSTLYSTGRHLYQIANE--TPNALTNRLKINTLSRQGVPSRAIIASAVVVGISALINILP 36- 9 NS L+ST R +Y +A + P L L+ VPS A+ S++ + I +N L Sbjct: 308 NSALFSTSRMVYSLAKDHHAPGLL------KKLTSSNVPSNALFFSSIAILIGVSLNYLM 36- 1 Query: 370 GVADAFSLITASSSGVYIAIYALTMIAHWKYRQSK--DFMADGYLMPKYKVTTPLTLAFF 42- 7 F+LIT+ S+ +I I+ +T+I H KYR+++ + A+ + MP Y ++ LTLAF Sbjct: 362 -PEQVFTLITSVSTICFIFIWGITVICHLKYRKTRQHEAKANKFKMPFYPLSNYLTLAFL 42- 0 Query: 428 AFVFISLFLQESTYIGAIGATIWIIIFGIYSNVK 461 AF+ + L L T I +W ++ I V+ Sbjct: 421 AFILVILALANDTRIALFVTPVWFVLLIILYKVQ 454 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03951 Identities = 48/62 (77%), Positives = 51/62 (81%) Query: 1 MSKNNNDHTQKSENGMVRGLENRHVQLIAIAGTIGTGLFLGAGRSISLTGPSIVLVYAITGA 62- MS + ENGMVRGLENRHVQLIAIAGTIGTGLFLGAGRSI+LTGPSI+ VY ITGA Sbjct: 5 MSIKEQTDNNELENGMVRGLENRHVQLIAIAGTIGTGLFLGAGRSIALTGPSIIFVYMITGA 66- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1328 A DNA sequence (GBSx1411) was identified in S. agalactiae <SEQ ID 4071> which encodes the amino acid sequence <SEQ ID 4072>. This protein is predicted to be alkylphosphonate uptake protein (phnA). Analysis of this protein sequence reveals the following: TABLE-US-03952 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0965(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03953 >GP: AAC77069 GB: AE000483 orf, hypothetical protein [Escherichia coli K12] Identities = 79/110 (71%), Positives = 91/110 (81%), Gaps = 1/110 (0%) Query: 1 MSLPNCPKCNSEYVYEDGILLVCPECAYEWNPEE-IEEEVGLIVLDSNGTRLSDGDTVTV 59 MSLP+CPKCNSEY YED + +CPECAYEWN E +E LIV D+NG L+DGD+VT+ Sbjct: 1 MSLPHCPKCNSEYTYEDNGMYICPECAYEWNDAEPAQESDELIVKDANGNLLADGDSVTI 60 Query: 60 IKDLKVKGAPKDIKQGTRVKNIRLVDGDHNIDCKIDGFGAMKLKSEFVKK 109 IKDLKVKG+ +K GT+VKNIRLV+GDHNIDCKIDGFG MKLKSEFVKK Sbjct: 61 IKDLKVKGSSSMLKIGTKVKNIRLVEGDHNIDCKIDGFGPMKLKSEFVKK 110 A related DNA sequence was identified in S. pyogenes <SEQ ID 4073> which encodes the amino acid sequence <SEQ ID 4074>. Analysis of this protein sequence reveals the following: TABLE-US-03954 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3428(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03955 Identities = 73/85 (85%), Positives = 79/85 (92%), Gaps = 1/85 (1%) Query: 26 CAYEWNP-EEIEEEVGLIVLDSNGTRLSDGDTVTVIKDLKVKGAPKDIKQGTRVKNIRLV 84 - CA+EW P EE EE GL+VLDSNG RLSDGDT+TV+KDLKVKGAPKD+KQGTRVKNIRLV Sbjct: 2 CAFEWTPGEEATEEEGLVVLDSNGVRLSDGDTITVVKDLKVKGAPKDLKQGTRVKNIRLV 61 Query: 85 DGDHNIDCKIDGFGAMKLKSEFVKK 109 +GDHNIDCKIDGFGAMKLKSEFVKK Sbjct: 62 EGDHNIDCKIDGFGAMKLKSEFVKK 86 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1329 A DNA sequence (GBSx1412) was identified in S. agalactiae <SEQ ID 4075> which encodes the amino acid sequence <SEQ ID 4076>. Analysis of this protein sequence reveals the following:

TABLE-US-03956 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3665(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 500. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1330 A DNA sequence (GBSx1414) was identified in S. agalactiae <SEQ ID 4077> which encodes the amino acid sequence <SEQ ID 4078>. Analysis of this protein sequence reveals the following: TABLE-US-03957 Possible site: 13 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.11 Transmembrane 558-574 (558-574) ----- Final Results ----- bacterial membrane --- Certainty = 0.1044(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03958 >GP: CAB11971 GB: Z99105 L-glutamine-D-fructose-6-phosphate amidotransferase [Bacillus subtilis] Identities = 355/604 (58%), Positives = 445/604 (72%), Gaps = 4/604 (0%) Query: 1 MCGIVGVVGNTNATDILIQGLEKLEYRGYDSAGIFVVGDNKSQLVKSVGRIAEIQAKVGD 60 MCGIVG +G +A +IL++GLEKLEYRGYDSAGI V + + K GRIA+++ V Sbjct: 1 MCGIVGYIGQLDAKEILLKGLEKLEYRGYDSAGIAVANEQGIHVFKEKGRIADLREVVDA 60 Query: 61 SVSGTTGIGHTRWATHGKPTEGNAHPHTSGSGRFVLVHNGVIENYLQIKETYLTKHNLKG 120- +V GIGHTRWATHG+P+ NAHPH S GRF LVHNGVIENY+Q+K+ YL LK Sbjct: 61 NVEAKAGIGHTRWATHGEPSYLNAHPHQSALGRFTLVHNGVIENYVQLKQEYLQDVELKS 120- Query: 121 ETDTEIAIHLVEHFVEEDNLSVLEAFKKALHIIEGSYAFALIDSQDADTIYVAKNKSPLL 18- 0 +TDTE+ + ++E FV L EAF+K L +++GSYA AL D+ + +TI+VAKNKSPLL Sbjct: 121 DTDTEVVVQVIEQFVN-GGLETEEAFRKTLTLLKGSYAIALFDNDNRETIFVAKNKSPLL 17- 9 Query: 181 IGLGNGYNMVCSDAMAMIRETSEYMEIHDKELVIVKKDSVEVQDYDGNVIERGSYTAELD 24- 0 +GLG+ +N+V SDAMAM++ T+EY+E+ DKE+VIV D V +++ DG+VI R SY AELD Sbjct: 180 VGLGDTFNVVASDAMAMLQVTNEYVELMDKEMVIVTDDQVVIKNLDGDVITRASYIAELD 23- 9 Query: 241 LSDIGKGTYPFYMLKEIDEQPTVMRKLISTYANESGDMNVDSDIIKSVQEADRLYILAAG 30- 0 SDI KGTYP YMLKE DEQP VMRK+I TY +E+G ++V DI +V EADR+YI+ G Sbjct: 240 ASDIEKGTYPHYMLKETDEQPVVMRKIIQTYQDENGKLSVPGDIAAAVAEADRIYIIGCG 29- 9 Query: 301 TSYHAGFAAKTMIEKLTDTPVELGVSSEWGYNMPLLSKKPMFILLSQSGETADSRQVLVK 36- 0 TSYHAG K IE + PVE+ V+SE+ YNMPLLSKKP+FI LSQSGETADSR VLV+ Sbjct: 300 TSYHAGLVGKQYIEMWANVPVEVHVASEFSYNMPLLSKKPLFIFLSQSGETADSRAVLVQ 35- 9 Query: 361 ANEMGIPSLTITNVPGSTLSREATYTMLIHAGPEIAVASTKAYTAQVATLAFLAKAVGEA 42- 0 +G +LTITNVPGSTLSREA YT+L+HAGPEIAVASTKAYTAQ+A LA LA + Sbjct: 360 VKALGHKALTITNVPGSTLSREADYTLLLHAGPEIAVASTKAYTAQIAVLAVLASVAADK 41- 9 Query: 421 NGKAEAKDFDLVHELSIVAQSIEATLSEKDVISEKVEQLLISTRNAFYIGRGNDYYVTME 48- 0 NG FDLV EL I A ++EA +KD + + L +RNAF+IGRG DY+V +E Sbjct: 420 NGINIG--FDLVKELGIAANAMEALCDQKDEMEMIAREYLTVSRNAFFIGRGLDYFVCVE 47- 7 Query: 481 AALKLKEISYIQTEGFAAGELKHGTISLIEDNTPVIALISADSTIAAHTRGNIQEVVSRG 54- 0 ALKLKEISYIQ EGFA GELKHGTI+LIE TPV AL + + + RGN++EV +RG Sbjct: 478 GALKLKEISYIQAEGFAGGELKHGTIALIEQGTPVFALATQEH-VNLSIRGNVKEVAARG 53- 6 Query: 541 ANALIIVEEGLEREGDDIIVNKVHPFLSAISMVIPTQLIAYYASLQRGLDVDKPRNLAKA 60- 0 AN II +GL+ D ++ +V+P L+ + V+P QLIAYYA+L RG DVDKPRNLAK+ Sbjct: 537 ANTCIISLKGLDDADDRFVLPEVNPALAPLVSVVPLQLIAYYAALHRGCDVDKPRNLAKS 59- 6 Query: 601 VTVE 604 VTVE Sbjct: 597 VTVE 600 A related DNA sequence was identified in S. pyogenes <SEQ ID 4079> which encodes the amino acid sequence <SEQ ID 4080>. Analysis of this protein sequence reveals the following: TABLE-US-03959 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.06 Transmembrane 558-574 (558-574) ----- Final Results ----- bacterial membrane --- Certainty = 0.1426(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-03960 >GP: CAB11971 GB: Z99105 L-glutamine-D-fructose-6-phosphate amidotransferase [Bacillus subtilis] Identities = 353/604 (58%), Positives = 445/604 (73%), Gaps = 4/604 (0%) Query: 1 MCGIVGVVGNRNATDILMQGLEKLEYRGYDSAGIFVANANQTNLIKSVGRIADLRAKIGI 60 MCGIVG +G +A +IL++GLEKLEYRGYDSAGI VAN ++ K GRIADLR + Sbjct: 1 MCGIVGYIGQLDAKEILLKGLEKLEYRGYDSAGIAVANEQGINVFKEKGRIADLREVVDA 60 Query: 61 DVAGSTGIGHTRWATHGQSTEDNAHPHTSQTGRFVLVHNGVIENYLHIKTEFLAGHDFKG 120- +V GIGHTRWATHG+ + NAHPH S GRF LVHNGVIENY+ +K E+L + K Sbjct: 61 NVEAKAGIGHTRWATHGEPSYLNAHPHQSALGRFTLVHNGVIENYVQLKQEYLQDVELKS 120- Query: 121 QTDTEIAVHLIGKFVEEDKLSVLEAFKKSLSIIEGSYAFALMDSQATDTIYVAKNKSPLL 18- 0 TDTE+ V +I +FV L EAF+K+L++++GSYA AL D+ +TI+VAKNKSPLL Sbjct: 121 DTDTEVVVQVIEQFVNGG-LETEEAFRKTLTLLKGSYAIALFDNDNRETIFVAKNKSPLL 17- 9 Query: 181 IGLGEGYNMVCSDAMAMIRETSEFMEIHDKELVILTKDKVTVTDYDGKELIRDSYTAELD 24- 0 +GLG+ +N+V SDAMAM++ T+E++E+ DKE+VI+T D+V + + DG + R SY AELD Sbjct: 180 VGLGDTFNVVASDAMAMLQVTNEYVELMDKEMVIVTDDQVVIKNLDGDVITRASYIAELD 23- 9 Query: 241 LSDIGKGTYPFYMLKEIDEQPTVMRQLISTYADETGNVQVDPAIITSIQEADRLYILAAG 30- 0 SDI KGTYP YMLKE DEQP VMR++I TY DE G + V I ++ EADR+YI+ G Sbjct: 240 ASDIEKGTYPHYMLKETDEQPVVMRKIIQTYQDENGKLSVPGDIAAAVAEADRIYIIGCG 29- 9 Query: 301 TSYHAGFATKNMLEQLTDTPVELGVASEWGYHMPLLSKKPMFILLSQSGETADSRQVLVK 36- 0 TSYHAG K +E + PVE+ VASE+ Y+MPLLSKKP+FI LSQSGETADSR VLV+ Sbjct: 300 TSYHAGLVGKQYIEMWANVPVEVHVASEFSYNMPLLSKKPLFIFLSQSGETADSRAVLVQ 35- 9 Query: 361 ANAMGIPSLTVTNVPGSTLSREATYTMLIHAGPEIAVASTKAYTAQIAALAFLAKAVGEA 42- 0 A+G +LT+TNVPGSTLSREA YT+L+HAGPEIAVASTKAYTAQIA LA LA + Sbjct: 360 VKALGHKALTITNVPGSTLSREADYTLLLHAGPEIAVASTKAYTAQIAVLAVLASVAADK 41- 9 Query: 421 NGKQEALDFNLVHELSLVAQSIEATLSEKDLVAEKVQALLATTRNAFYIGRGNDYYVAME 48- 0 NG + F+LV EL + A ++EA +KD + + L +RNAF+IGRG DY+V +E Sbjct: 420 NGIN--IGFDLVKELGIAANAMEALCDQKDEMEMIAREYLTVSRNAFFIGRGLDYFVCVE 47- 7 Query: 481 AALKLKEISYIQCEGFAAGELKHGTISLIEEDTPVIALISSSQLVASHTRGNIQEVAARG 54- 0 ALKLKEISYIQ EGFA GELKHGTI+LIE+ TPV AL + + S RGN++EVAARG Sbjct: 478 GALKLKEISYIQAEGFAGGELKHGTIALIEQGTPVFALATQEHVNLS-IRGNVKEVAARG 53- 6 Query: 541 AHVLTVVEEGLDREGDDIIVNKVHPFLAPIAMVIPTQLIAYYASLQRGLDVDKPRNLAKA 60- 0 A+ + +GLD D ++ +V+P LAP+ V+P QLIAYYA+L RG DVDKPRNLAK+ Sbjct: 537 ANTCIISLKGLDDADDRFVLPEVNPALAPLVSVVPLQLIAYYAALHRGCDVDKPRNLAKS 59- 6 Query: 601 VTVE 604 VTVE Sbjct: 597 VTVE 600 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03961 Identities = 500/604 (82%), Positives = 552/604 (90%) Query: 1 MCGIVGVVGNTNATDILIQGLEKLEYRGYDSAGIFVVGDNKSQLVKSVGRIAEIQAKVGD 60 MCGIVGVVGN NATDIL+QGLEKLEYRGYDSAGIFV N++ L+KSVGRIA+++AK+G Sbjct: 1 MCGIVGVVGNRNATDILMQGLEKLEYRGYDSAGIFVANANQTNLIKSVGRIADLRAKIGI 60 Query: 61 SVSGTTGIGHTRWATHGKPTEGNAHPHTSGSGRFVLVHNGVIENYLQIKETYLTKHNLKG 120- V+G+TGIGHTRWATHG+ TE NAHPHTS +GRFVLVHNGVIENYL IK +L H+ KG Sbjct: 61 DVAGSTGIGHTRWATHGQSTEDNAHPHTSQTGRFVLVHNGVIENYLHIKTEFLAGHDFKG 120- Query: 121 ETDTEIAIHLVEHFVEEDNLSVLEAFKKALHIIEGSYAFALIDSQDADTIYVAKNKSPLL 18- 0 +TDTEIA+HL+ FVEED LSVLEAFKK+L IIEGSYAFAL+DSQ DTIYVAKNKSPLL Sbjct: 221 QTDTEIAVHLIGKFVEEDKLSVLEAFKKSLSIIEGSYAFALMDSQATDTIYVAKNKSPLL 18- 0 Query: 181 IGLGNGYNMVCSDAMAMIRETSEYMEIHDKELVIVKKDSVEVQDYDGNVIERGSYTAELD 24- 0 IGLG GYNMVCSDAMAMIRETSE+MEIHDKELVI+ KD V V DYDG + R SYTAELD Sbjct: 181 IGLGEGYNMVCSDAMAMIRETSEFMEIHDKELVILTKDKVTVTDYDGKELIRDSYTAELD 24- 0 Query: 241 LSDIGKGTYPFYMLKEIDEQPTVMRKLISTYANESGDMNVDSDIIKSVQEADRLYILAAG 30- 0 LSDIGKGTYPFYMLKEIDEQPTVMR+LISTYA+E+G++ VD II S+QEADRLYILAAG Sbjct: 241 LSDIGKGTYPFYMLKEIDEQPTVMRQLISTYADETGNVQVDPAIITSIQEADRLYILAAG 30- 0 Query: 301 TSYHAGFAAKTMIEKLTDTPVELGVSSEWGYNMPLLSKKPMFILLSQSGETADSRQVLVK 36- 0 TSYHAGFA K M+E+LTDTPVELGV+SEWGY+MPLLSKKPMFILLSQSGETADSRQVLVK Sbjct: 301 TSYHAGFATKNMLEQLTDTPVELGVASEWGYHMPLLSKKPMFILLSQSGETADSRQVLVK 36- 0 Query: 361 ANEMGIPSLTITNVPGSTLSREATYTMLIHAGPEIAVASTKAYTAQVATLAFLAKAVGEA 42- 0 AN MGIPSLT+TNVPGSTLSREATYTMLIHAGPEIAVASTKAYTAQ+A LAFLAKAVGEA Sbjct: 361 ANAMGIPSLTVTNVPGSTLSREATYTMLIHAGPEIAVASTKAYTAQIAALAFLAKAVGEA 42- 0 Query: 421 NGKAEAKDFDLVHELSIVAQSIEATLSEKDVISEKVEQLLISTRNAFYIGRGNDYYVTME 48- 0 NGK EA DF+LVHELS+VAQSIEATLSEKD+++EKV+ LL +TRNAFYIGRGNDYYV ME Sbjct: 421 NGKQEALDFNLVHELSLVAQSIEATLSEKDLVAEKVQALLATTRNAFYIGRGNDYYVAME 48- 0 Query: 481 AALKLKEISYIQTEGFAAGELKHGTISLIEDNTPVIALISADSTIAAHTRGNIQEVVSRG 54- 0 AALKLKEISYIQ EGFAAGELKHGTISLIE++TPVIALIS+ +A+HTRGNIQEV +RG Sbjct: 481 AALKLKEISYIQCEGFAAGELKHGTISLIEEDTPVIALISSSQLVASHTRGNIQEVAARG 54- 0 Query: 541 ANALIIVEEGLEREGDDIIVNKVHPFLSAISMVIPTQLIAYYASLQRGLDVDKPRNLAKA 60- 0 A+ L +VEEGL+REGDDIIVNKVHPFL+ I+MVIPTQLIAYYASLQRGLDVDKPRNLAKA Sbjct: 541 AHVLTVVEEGLDREGDDIIVNKVHPFLAPIAMVIPTQLIAYYASLQRGLDVDKPRNLAKA 60- 0 Query: 601 VTVE 604 VTVE Sbjct: 601 VTVE 604 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1331 A DNA sequence (GBSx1415) was identified in S. agalactiae <SEQ ID 4081> which encodes the amino acid sequence <SEQ ID 4082>. Analysis of this protein sequence reveals the following: TABLE-US-03962 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9797> which encodes amino acid sequence <SEQ ID 9798> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03963 >GP: AAC44435 GB: U65000 type-I signal peptidase SpsB [Staphylococcus aureus] Identities = 62/185 (33%), Positives = 97/185 (51%), Gaps = 12/185 (6%) Query: 10 VKRDFIRNIILALIAVLILILLRYFVFATFKVHKDATNSYFSNGDVVVVN----RNRTPK 65 - +K++ + II +A +IL ++ F+ + + ++ + +G+ V VN + + Sbjct: 1 MKKELLEWIISIAVAFVILFIVGKFIVTPYTIKGESMDPTLKDGERVAVNIIGYKTGGLE 60 Query: 66 YKDFIVYKVGKIF-YISRVIGEPNQKVRVMDDILYLNDVFKDEPYIEKMKNAYSEKKDGQ 124- + +V+ K Y+ RVIG P KV +D LY+N +DEPY+ N + K G Sbjct: 61 KGNVVVFHANKNDDYVKRVIGVPGDKVEYKNDTLYVNGKKQDEPYL----NYNLKHKQGD 116- Query: 125 MPFTSDFSVETL--TRNKESRVPKGSYLVLNDNRQNKNDSRKFGLIKEKDIRGVITFKVY 18- 2 T F V+ L K + +PKG YLVL DNR+ DSR FGLI E I G ++F+ + Sbjct: 117 Y-ITGTFQVKDLPNANPKSNVIPKGKYLVLGDNREVSKDSRAFGLIDEDQIVGKVSFRFW 17- 5 Query: 183 PLSEF 187 P SEF Sbjct: 176 PFSEF 180 A related DNA sequence was identified in S. pyogenes <SEQ ID 4083> which encodes the amino acid sequence <SEQ ID 4084>. Analysis of this protein sequence reveals the following: TABLE-US-03964 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.22 Transmembrane 10-26 (4-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.6689(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03965 Identities = 99/185 (53%), Positives = 130/185 (69%) Query: 9 MVKRDFIRNIILALIAVLILILLRYFVFATFKVHKDATNSYFSNGDVVVVNRNRTPKYKD 68 MVKRDFIRNI+L LI ++ ILLR FVF+TFKV + N+Y +GD+V + +N PKYKD Sbjct: 1 MVKRDFIRNILLLLIVIIGAILLRIFVFSTFKVSPETANTYLKSGDLVTIKKNIQPKYKD 60 Query: 69 FIVYKVGKIFYISRVIGEPNQKVRVMDDILYLNDVFKDEPYIEKMKNAYSEKKDGQMPFT 128- F+VY+VGK Y+SRVI V MDDI YLN++ + + Y+EKMK Y +T Sbjct: 61 FVVYRVGKKDYVSRVIAVEGDSVTYMDDIFYLNNMVESQAYLEKMKAHYLNHAPFGTLYT 120- Query: 129 SDFSVETLTRNKESRVPKGSYLVLNDNRQNKNDSRKFGLIKEKDIRGVITFKVYPLSEFG 18- 8 DF+V T+T +K +VPKG YL+LNDNR+N NDSR+FGLI I+G++TF+V PLS+FG Sbjct: 121 DDFTVATITADKYQKVPKGKYLLLNDNRKNTNDSRRFGLINASQIKGLVTFRVLPLSDFG 18- 0 Query: 189 FTASE 193 F E Sbjct: 181 FVEVE 185 A related GBS gene <SEQ ID 8789> and protein <SEQ ID 8790> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-03966 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 10.13 GvH: Signal Score (-7.5): 0.45 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 3.82 threshold: 0.0 PERIPHERAL Likelihood = 3.82 69 modified ALOM score: -1.26 *** Reasoning Step: 3 ----- Final Results ----- <\\\\\\\\\\\\\\\\bacterial> outside --- Certainty = 0.3000 (Affirmative) < succ> <\\\\\\\\\\\\\\\bacterial> membrane --- Certainty = 0.0000 (Not Clear) < succ> <\\\\\\\\\\\\\\bacterial> cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00089## SEQ ID 8790 (GBS7) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 1 (lane 4; MW 46 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 2 (lane 4; MW 21 kDa). The GBS7-His fusion product was purified (FIG. 189, lane 6) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 262), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1332 A DNA sequence (GBSx1416) was identified in S. agalactiae <SEQ ID 4085> which encodes the amino acid sequence <SEQ ID 4086>. Analysis of this protein sequence reveals the following: TABLE-US-03967 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- <\\\\\\\\\\\\\\bacterial> cytoplasm --- Certainty = 0.1099 (Affirmative) < succ> <\\\\\\\\\\\\\\\bacterial> membrane --- Certainty = 0.0000 (Not Clear) < succ> <\\\\\\\\\\\\\\\\bacterial> outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9795> which encodes amino acid sequence <SEQ ID 9796> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03968 >GP:AAF25804 GB:AF172173 pyruvate kinase [treptococcus thermophilus] Identities = 413/500 (82%), Positives = 451/500 (89%) Query: 1 MNKRVKIVATLGPAVEFRGGKKFGESGYWGESLDVEASAEKIAQLIKEGANVFRFNFSHG 60 MNKRVKIVATLGPAVE RGGKKFGE GYW E LD +ASA+ IAQLI+EGANVFRFNFSHG Sbjct: 1 MNKRVKIVATLGPAVEIRGGKKFGEDGYWSEKLDPDASAKNIAQLIEEGANVFRFNFSHG 60 Query: 61 DHAEQGARMATVRKAEEIAGQKVGFLLDTKGPEIRTELFEDGADFHSYTTGTKLRVATKQ 120- +HAEQG RM VR AE IAGQKVGFLLDTKGPEIRTELFE A ++Y TG ++R+ATKQ Sbjct: 61 NHAEQGERMDVVRMAESIAGQKVGFLLDTKGPEIRTELFEGDAKEYAYKTGEQIRIATKQ 120- Query: 121 GIKSTPEVIALNVAGGLDIFDDVEVGKQILVDDGKLGLTVFAKDKDTREFEVVVENDGLI 18- 0 G+KST +VIALNVAG LDIFDDVEVGKQ+LVDDGKLGL V KD + REF V VENDG+I Sbjct: 121 GLKSTRDVIALNVAGALDIFDDVEVGKQVLVDDGKLGLRVVDKDAEKREFIVEVENDGII 18- 0 Query: 181 GKQKGVNIPYTKIPFPALAERDNADIRFGLEQGLNFIAISFVRTAKDVNEVRAICEETGN 24- 0 KQKGVNIPYTKIPFPALAERDNADIRFGLEQG+NFIAISFVRTAKDV EVRAICEETGN Sbjct: 181 AKQKGVNIPYTKIPFPALAERDNADIRFGLEQGINFIAISFVRTAKDVQEVRAICEETGN 24- 0 Query: 241 GHVKLFAKIENQQGIDNIDEIIEAADGIMIARGDMGIEVPFEMVPVYQKMIITKVNAAGK 30- 0 GHVKL AKIENQQGIDNIDEIIEAADGIMIARGDMGIEVPFEMVPVYQKMIITKVNAAGK Sbjct: 241 GHVKLLAKIENQQGIDNIDEIIEAADGIMIARGDMGIEVPFEMVPVYQKMIITKVNAAGK 30- 0 Query: 301 AVITATNMLETMTDKPRATRSEVSDVFNAVIDGTDATMLSGESANGKYPVESVRTMATID 36- 0 V+TATNMLETMT+KPRATRSEVSDVFNAVIDGTDATMLSGESANG YPVESVRTMATI Sbjct: 301 IVVTATNMLETMTEKPRATRSEVSDVFNAVIDGTDATMLSGESANGPYPVESVRTMATIH 36- 0 Query: 361 KNAQTLLNEYGRLDSSAFPRNNKTDVIASAVKDATHSMDIKLVVTITETGNTARAISKFR 42- 0 KNAQTLL EYGRL+SS F R++ T+V+ASAVKDAT+SM I+L+V +TE+GNTA I +R Sbjct: 361 KNAQTLLKEYGRLNSSTFDRSSNTEVVASAVKDATNSMHIQLIVALTESGNTASLIDTYR 42- 0 Query: 421 PDADILAVTFDEKVQRSLMINWGVIPVLADKPASTDDMFEVAERVALEAGFVESGDNIVI 48- 0 P+ADI A+TFDE Q+SLM+NWGVIPV+ + P+STDDMFEVAERVALE+G VESGDNIVI Sbjct: 421 PEADIWAITFDELTQKSLMLNWGVIPVVTETPSSTDDMFEVAERVALESGLVESGDNIVI 48- 0 Query: 481 VAGVPVGTGGTNTMRVRTVK 500 VAGVPVG+G TNTMR+RTVK Sbjct: 481 VAGVPVGSGNTNTMRIRTVK 500 A related DNA sequence was identified in S. pyogenes <SEQ ID 4087> which encodes the amino acid sequence <SEQ ID 4088>. Analysis of this protein sequence reveals the following:

TABLE-US-03969 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- <\\\\\\\\\\\\\\bacterial> cytoplasm --- Certainty = 0.0915 (Affirmative) < succ> <\\\\\\\\\\\\\\\bacterial> membrane --- Certainty = 0.0000 (Not Clear) < succ> <\\\\\\\\\\\\\\\\bacterial> outside --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 272-274 The protein has homology with the following sequences in the databases: TABLE-US-03970 >GP:AAF25804 GB:AF172173 pyruvate kinase [Streptococcus thermophilus] Identities = 404/500 (80%), Positives = 457/500 (90%) Query: 1 MNKRVKIVATLGPAVEIRGGKKYGEDGYWAGQLDVEESAKKIAELIEAGANVFRFNFSHG 60 MNKRVKIVATLGPAVEIRGGKK+GEDGYW+ +LD + SAK IA+LIE GANVFRFNFSHG Sbjct: 1 MNKRVKIVATLGPAVEIRGGKKFGEDGYWSEKLDPDASAKNIAQLIEEGANVFRFNFSHG 60 Query: 61 DHKEQGDRMATVRLAEEIARQKVGFLLDTKGPEMRTELFADDAKEFSYVTGEKIRVATTQ 120- +H EQG+RM VR+AE IA QKVGFLLDTKGPE+RTELF DAKE++Y TGE+IR+AT Q Sbjct: 61 NHAEQGERMDVVRMAESIAGQKVGFLLDTKGPEIRTELFEGDAKEYAYKTGEQIRIATKQ 120- Query: 121 GIQSTRDVIALNVAGSLDIYDEVEVGHTILIDDGKLGLKVIDKDIATRQFIVEVENDGII 18- 0 G++STRDVIALNVAG+LDI+D+VEVG +L+DDGKLGL+V+DKD R+FIVEVENDGII Sbjct: 121 GLKSTRDVIALNVAGALDIFDDVEVGKQVLVDDGKLGLRVVDKDAEKREFIVEVENDGII 18- 0 Query: 181 AKQKGVNIPNTKIPFPALAERDNADIRFGLEQGLNFIAISFVRTAKDVEEVREICRETGN 24- 0 AKQKGVNIP TKIPFPALAERDNADIRFGLEQG+NFIAISFVRTAKDV+EVR IC ETGN Sbjct: 181 AKQKGVNIPYTKIPFPALAERDNADIRFGLEQGINFIAISFVRTAKDVQEVRAICEETGN 24- 0 Query: 241 DHVQLFAKIENQQGIDNLDEIIEAADGIMIARGDMGIEVPFEMVPVFQKMIITKVNAAGK 30- 0 HV+L AKIENQQGIDN+DEIIEAADGIMIARGDMGIEVPFEMVPV+QKMIITKVNAAGK Sbjct: 241 GHVKLLAKIENQQGIDNIDEIIEAADGIMIARGDMGIEVPFEMVPVYQKMIITKVNAAGK 30- 0 Query: 301 AVITATNMLETMTEKPRATRSEVSDVFNAVIDGTDATMLSGESANGKYPVESVRTMATID 36- 0 V+TATNMLETMTEKPRATRSEVSDVFNAVIDGTDATMLSGESANG YPVESVRTMATI Sbjct: 301 IVVTATNMLETMTEKPRATRSEVSDVFNAVIDGTDATMLSGESANGPYPVESVRTMATIH 36- 0 Query: 361 RNAQTLLNEYGRLDSSAFPRTNKTDVIASAVKDATHSMDIKLVVTITETGNTARAISKFR 42- 0 +NAQTLL EYGRL+SS F R++ T+V+ASAVKDAT+SM I+L+V +TE+GNTA I +R Sbjct: 361 KNAQTLLKEYGRLNSSTFDRSSNTEVVASAVKDATNSMHIQLIVALTESGNTASLIDTYR 42- 0 Query: 421 PDADILAVTFDEKVQRALMINWGVIPVLAEKPASTDDMFEVAERVAVEAGLVQSGDNIVI 48- 0 P+ADI A+TFDE Q++LM+NWGVIPV+ E P+STDDMFEVAERVA+E+GLV+SGDNIVI Sbjct: 421 PEADIWAITFDELTQKSLMLNWGVIPVVTETPSSTDDMFEVAERVALESGLVESGDNIVI 48- 0 Query: 481 VAGVPVGTGGTNTMRVRTVK 500 VAGVPVG+G TNTMR+RTVK Sbjct: 481 VAGVPVGSGNTNTMRIRTVK 500 An alignment of the GAS and GBS proteins is shown below. TABLE-US-03971 Identities = 440/500 (88%), Positives = 462/500 (92%) Query: 1 MNKRVKIVATLGPAVEFRGGKKFGESGYWGESLDVEASAEKIAQLIKEGANVFRFNFSHG 60 MNKRVKIVATLGPAVE RGGKK+GE GYW LDVE SA+KIA+LI+ GANVFRFNFSHG Sbjct: 1 MNKRVKIVATLGPAVEIRGGKKYGEDGYWAGQLDVEESAKKIAELIEAGANVFRFNFSHG 60 Query: 61 DHAEQGARMATVRKAEEIAGQKVGFLLDTKGPEIRTELFEDGADFHSYTTGTKLRVATKQ 120- DH EQG RMATVR AEEIA QKVGFLLDTKGPE+RTELF D A SY TG K+RVAT Q Sbjct: 61 DHKEQGDRMATVRLAEEIARQKVGFLLDTKGPEMRTELFADDAKEFSYVTGEKIRVATTQ 120- Query: 121 GIKSTFEVIALNVAGGLDIFDDVEVGKQILVDDGKLGLTVFAKDKDTREFEVVVENDGLI 18- 0 GI+ST +VIALNVAG LDI+D+VEVG IL+DDGKLGL V KD TR+F V VENDG+I Sbjct: 121 GIQSTRDVIALNVAGSLDIYDEVEVGHTILIDDGKLGLKVIDKDIATRQFIVEVENDGII 18- 0 Query: 181 GKQKGVNIPYTKIPFPALAERDNADIRFGLEQGLNFIAISFVRTAKDVNEVRAICEETGN 24- 0 KQKGVNIP TKIPFPALAERDNADIRFGLEQGLNFIAISFVRTAKDV EVR IC ETGN Sbjct: 181 AKQKGVNIPNTKIPFPALAERDNADIRFGLEQGLNFIAISFVRTAKDVEEVREICRETGN 24- 0 Query: 241 GHVKLFAKIENQQGIDNIDEIIEAADGIMIARGDMGIEVPFEMVPVYQKMIITKVNAAGK 30- 0 HV+LFAKIENQQGIDN+DEIIEAADGIMIARGDMGIEVPFEMVPV+QKMIITKVNAAGK Sbjct: 241 DHVQLFAKIENQQGIDNLDEIIEAADGIMIARGDMGIEVPFEMVPVFQKMIITKVNAAGK 30- 0 Query: 301 AVITATNMLETMTDKPRATRSEVSDVFNAVIDGTDATMLSGESANGKYPVESVRTMATID 36- 0 AVITATNMLETMT+KPRATRSEVSDVFNAVIDGTDATMLSGESANGKYPVESVRTMATID Sbjct: 301 AVITATNMLETMTEKPRATRSEVSDVFNAVIDGTDATMLSGESANGKYPVESVRTMATID 36- 0 Query: 361 KNAQTLLNEYGRLDSSAFPRNNKTDVIASAVKDATHSMDIKLVVTITETGNTARAISKFR 42- 0 +NAQTLLNEYGRLDSSAFPR NKTDVIASAVKDATHSMDIKLVVTITETGNTARAISKFR Sbjct: 361 RNAQTLLNEYGRLDSSAFPRTNKTDVIASAVKDATHSMDIKLVVTITETGNTARAISKFR 42- 0 Query: 421 PDADILAVTFDEKVQRSLMINWGVIPVLADKPASTDDMFEVAERVALEAGFVESGDNIVI 48- 0 PDADILAVTFDEKVQR+LMINWGVIPVLA+KPASTDDMFEVAERVA+EAG V+SGDNIVI Sbjct: 421 PDADILAVTFDEKVQRALMINWGVIPVLAEKPASTDDMFEVAERVAVEAGLVQSGDNIVI 48- 0 Query: 481 VAGVPVGTGGTNTMRVRTVK 500 VAGVPVGTGGTNTMRVRTVK Sbjct: 481 VAGVPVGTGGTNTMRVRTVK 500 A related GBS gene <SEQ ID 8791> and protein <SEQ ID 8792> were also identified. Analysis of this protein sequence reveals the following: Belongs to Glycolysis/gluconeogenesis pathway. Proteins belonging to this methabolic pathway have been experimentally detected on the surface of Streptococci. The protein has homology with the following sequences in the databases: TABLE-US-03972 >GP|6708108|gb|AAF25804.1|AF172173_2|AF172173 pyruvate kinase [Streptococcus thermophilus] Score = 821 bits (2098), Expect = 0.0 Identities = 412/500 (82%), Positives = 450/500 (89%) Query: 1 MNKRVKIVATLGPAVEFRGGKKFGESGYWGESLDVEASAEKIAQLIKEGANVFRFNFSHG 60 MNKRVKIVATLGPAVE RGGKKFGE GYW E LD +ASA+ IAQLI+EGANVFRFNFSHG Sbjct: 1 MNKRVKIVATLGPAVEIRGGKKFGEDGYWSEKLDPDASAKNIAQLIEEGANVFRFNFSHG 60 Query: 61 DHAEQGARMATVRKAEEIAGQKVGFLLDTKGPEIRTELFEDGADFHSYTTGTKLRVATKQ 120- +HAEQG RM VR AE IAGQKVGFLLDTKGPEIRTELFE A ++Y TG ++R+ATKQ Sbjct: 61 NHAEQGERMDVVRMAESIAGQKVGFLLDTKGPEIRTELFEGDAKEYAYKTGEQIRIATKQ 120- Query: 121 GIKSTPEVIALNVAGGLDIFDDVEVGKQILVDDGKLGLTVFAKDKDTREFEVVVENDGLI 18- 0 G+KST +VIALNVAG LDIFDDVEVGKQ+LVDDGKLGL V KD + REF V VENDG+I Sbjct: 121 GLKSTRDVIALNVAGALDIFDDVEVGKQVLVDDGKLGLRVVDKDAEKREFIVEVENDGII 18- 0 Query: 181 GKQKGVNIPYTKIPFPALAERDNADIRFGLEQGLNFIAISFVRTAKDVNEVRAICEETGX 24- 0 KQKGVNIPYTKIPFPALAERDNADIRFGLEQG+NFIAISFVRTAKDV EVRAICEETG Sbjct: 181 AKQKGVNIPYTKIPFPALAERDNADIRFGLEQGINFIAISFVRTAKDVQEVRAICEETGN 24- 0 Query: 241 GHVKLFAKIENQQGIDNIDEIIEAADGIMIARGDMGIEVPFEMVPVYQKMIITKVNAAGK 30- 0 GHVKL AKIENQQGIDNIDEIIEAADGIMIARGDMGIEVPFEMVPVYQKMIITKVNAAGK Sbjct: 241 GHVKLLAKIENQQGIDNIDEIIEAADGIMIARGDMGIEVPFEMVPVYQKMIITKVNAAGK 30- 0 Query: 301 AVITATNMLETMTDKPRATRSEVSDVFNAVIDGTDATMLSGESANGKYPVESVRTMATID 36- 0 V+TATNMLETMT+KPRATRSEVSDVFNAVIDGTDATMLSGESANG YPVESVRTMATI Sbjct: 301 IVVTATNMLETMTEKPRATRSEVSDVFNAVIDGTDATMLSGESANGPYPVESVRTMATIH 36- 0 Query: 361 KNAQTLLNEYGRLDSSAFPRNNKTDVIASAVKDATHSMDIKLVVTITETGNTARAISKFR 42- 0 KNAQTLL EYGRL+SS F R++ T+V+ASAVKDAT+SM I+L+V +TE+GNTA I +R Sbjct: 361 KNAQTLLKEYGRLNSSTFDRSSNTEVVASAVKDATNSMHIQLIVALTESGNTASLIDTYR 42- 0 Query: 421 PDADILAVTFDEKVQRSLMINWGVIPVLADKPASTDDMFEVAERVALEAGFVESGDNIVI 48- 0 P+ADI A+TFDE Q+SLM+NWGVIPV+ + P+STDDMFEVAERVALE+G VESGDNIVI Sbjct: 421 PEADIWAITFDELTQKSLMLNWGVIPVVTETPSSTDDMFEVAERVALESGLVESGDNIVI 48- 0 Query: 481 VAGVPVGTGGTNTMRVRTVK 500 VAGVPVG+G TNTMR+RTVK Sbjct: 481 VAGVPVGSGNTNTMRIRTVK 500 SEQ ID 8792 (GBS330) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 73 (lane 5; MW 59 kDa). GBS330-His was purified as shown in FIG. 213, lane 6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1333 A DNA sequence (GBSx1417) was identified in S. agalactiae <SEQ ID 4089> which encodes the amino acid sequence <SEQ ID 4090>. Analysis of this protein sequence reveals the following: TABLE-US-03973 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0632(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03974 >GP:AAF25803 GB:AF172173 phosphofructokinase [Streptococcus thermophilus] Identities = 270/337 (80%), Positives = 302/337 (89%), Gaps = 1/337 (0%) Query: 1 MKRIAVLTSGGDAPGMNAAIRAVVRKAISEGMEVYGINQGYYGMVTGDIFPLDANSVGDT 60 MKRIAVLTSGGDAPGMNAA+RAVV KAISEG+EV+GIN+GY GMV GDIF LDA V + Sbjct: 1 MKRIAVLTSGGDAPGMNAAVRAVVLKAISEGIEVFGINRGYAGMVEGDIFKLDAKRVENI 60 Query: 61 INRGGTFLRSARYPEFAELEGQLKGIEQLKKHGIEGVVVIGGDGSYHGAMRLTEHGFPAV 120- ++RGGTFL+SARYPEFA+LEGQLKGIEQLKK+GIEGVVVIGGDGSYHGAMRLTEHGFPAV Sbjct: 61 LSRGGTFLQSARYPEFAQLEGQLKGIEQLKKYGIEGVVVIGGDGSYHGAMRLTEHGFPAV 120- Query: 121 GLPGTIDNDIVGTDYTIGFDTAVATAVENLDRLRDTSASHNRTFVVEVMGRNAGDIALWS 18- 0 GLPGTIDNDIVGTDYTIGFDTAVATA E LD+++DT+ SH RTFVVEVMGRNAGDIALW+ Sbjct: 121 GLPGTIDNDIVGTDYTIGFDTAVATATEALDKIQDTAFSHGRTFVVEVMGRNAGDIALWA 18- 0 Query: 181 GIAAGADQIIVPEEEFNIDEVVSNVRAGYAAG-KHHQIIVLAEGVMSGDEFAKTMKAAGD 23- 9 GIA+GADQIIVPEEE++I+EVV V+ GY +G K H IIVLAEGVM +EFA MK AGD Sbjct: 181 GIASGADQIIVPEEEYDINEVVRKVKEGYESGEKSHHIIVLAEGVMGAEEFAAKMKEAGD 24- 0 Query: 240 DSDLRVTMLGHLLRGGSPTARDRVLASRMGAYAVQLLKEGRGGLAVGVHNEEMVESPILG 29- 9 SDLR TNLGH++RGGSPTARDRVLAS MGA+AV LLKEG GG+AVG+HNE++VESPILG Sbjct: 241 TSDLRATNLGHVIRGGSPTARDRVLASWMGAHAVDLLKEGIGGVAVGIHNEQLVESPILG 30- 0 Query: 300 LAEEGALFSLTDEGKIVVNNPHKADLRLAALNRDLAN 336 AEEGALFSLT++GKI+VNNPHKA L A LNR LAN Sbjct: 301 TAEEGALFSLTEDGKIIVNNPHKARLDFAELNRSLAN 337 Proteins in the glycolysis/gluconeogenesis pathway have been experimentally detected on the surface of Streptococci. A related DNA sequence was identified in S. pyogenes <SEQ ID 4091> which encodes the amino acid sequence <SEQ ID 4092>. Analysis of this protein sequence reveals the following: TABLE-US-03975 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0632(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03976 Identities = 274/336 (81%), Positives = 306/336 (90%), Gaps = 1/336 (0%) Query: 1 MKRIAVLTSGGDAPGMNAAIRAVVRKAISEGMEVYGINQGYYGMVTGDIFPLDANSVGDT 60 MKRIAVLTSGGDAPGMNAAIRAVVRKAISEGMEVYGIN+GY GMV GDIFPL + VGD Sbjct: 1 MKRIAVLTSGGDAPGMNAAIRAVVRKAISEGMEVYGINRGYAGMVDGDIFPLGSKEVGDK 60 Query: 61 INRGGTFLRSARYPEFAELEGQLKGIEQLKKHGIEGVVVIGGDGSYHGAMRLTEHGEPAV 120- I+RGGTFL SARYPEFA+LEGQL GIEQLKKHGIEGVVVIGGDGSYHGAMRLTEHGFPAV Sbjct: 61 ISRGGTFLYSARYPEFAQLEGQLAGIEQLKKHGIEGVVVIGGDGSYHGAMRLTEHGFPAV 120- Query: 121 GLPGTIDNDIVGTDYTIGFDTAVATAVENLDRLRDTSASHNRTFVVEVMGRNAGDIALWS 18- 0 G+PGTIDNDI GTDYTIGFDTAV TAVE +D+LRDTS+SH RTFVVEVMGRNAGDIALW+ Sbjct: 121 GIPGTIDNDIAGTDYTIGFDTAVMTAVEAIDKLRDTSSSHGRTFVVEVMGRNAGDIALWA 18- 0 Query: 181 GIAAGADQIIVPEEEFNIDEVVSNVRAGYA-AGKHHQIIVLAEGVMSGDEFAKTMKAAGD 23- 9 GIA+GADQIIVPEEEF+I++V S ++ + GK+H IIVLAEGVMSG+ FA+ +K AGD Sbjct: 181 GIASGADQIIVPEEEFDIEKVASTIQYDFEHKGKNNHIIVLAEGVMSGEAFAQKLKEAGD 24- 0 Query: 240 DSDLRVTNLGHLLRGGSPTARDRVLASRMGAYAVQLLKEGRGGLAVGVHNEEMVESPILG 29- 9 SDLRVTNLGH+LRGGSPTARDRV+AS MG++AV+LLK+G+GGLAVG+HNEE+VESPILG Sbjct: 241 KSDLRVTNLGHILRGGSPTARDRVIASWMGSHAVELLKDGKGGLAVGIHNEELVESPILG 30- 0 Query: 300 LAEEGALFSLTDEGKIVVNNPHKADLRLAALNRDLA 335 AEEGALFSLT+EGKI+VNNPHKA L AALNR L+ Sbjct: 301 TAEEGALFSLTEEGKIIVNNPHKARLDFAALNRSLS 336 SEQ ID 4090 (GBS313) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 45 (lane 5; MW 41 kDa). GBS313-His was purified as shown in FIG. 204, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1334 A DNA sequence (GBSx1418) was identified in S. agalactiae <SEQ ID 4093> which encodes the amino acid sequence <SEQ ID 4094>. This protein is predicted to be DNA polymerase III alpha subunit (dnaE). Analysis of this protein sequence reveals the following: TABLE-US-03977 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1446(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> There is also homology to SEQ ID 4096. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1335 A DNA sequence (GBSx1419) was identified in S. agalactiae <SEQ ID 4097> which encodes the amino acid sequence <SEQ ID 4098>. This protein is predicted to be YHCF (farR). Analysis of this protein sequence reveals the following: TABLE-US-03978 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3316(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03979 >GP:BAB04102 GB:AP001508 transcriptional regulator (GntR family) [Bacillus halodurans] Identities = 51/116 (43%), Positives = 79/116 (67%) Query: 5 FNEKSPIYSQIAEHIKMQIVSQEIKSGDQLPTVRELAQEAGVNPNTMQRAFTELEREGMV 64 F+ PIY Q+AE +K QIV E++ G++LP+VR++ EA VNPNT+QR + ELE +V Sbjct: 5 FHSSEPIYLQLAERVKRQIVRGELRLGEKLPSVRDMGIEANVNPNTVQRTYRELEGLKIV 64 Query: 65 FSQRTSGRFVTEDNLLIGKIRQQVAKAELATFVNNMKKIGYKLDEITVALDHFIKE 120 S+R G FVTED ++ IR+Q+ + E++ FV M+++GY +EI L+ ++ E Sbjct: 65 ESKRGQGTFVTEDEQVLQAIREQMKETEISHFVQGMREMGYSDNEIQAGLESYLTE 120 A related DNA sequence was identified in S. pyogenes <SEQ ID 4099> which encodes the amino acid sequence <SEQ ID 4100>. Analysis of this protein sequence reveals the following: TABLE-US-03980 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2075(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03981 Identities = 80/120 (66%), Positives = 100/120 (82%) Query: 1 MAWEFNEKSPIYSQIAEHIKMQIVSQEIKSGDQLPTVRELAQEAGVNPNTMQRAFTELER 60 M+W+F EKSPIY+QIA+H+ MQI+SQEIKSGDQLPTVRE A+ AGVNPNTMQRAFTELER Sbjct: 1 MSWKFEEKSPIYAQIAQHVMMQIISQEIKSGDQLPTVREYAEIAGVNPNTMQRAFTELER 60 Query: 61 EGMVFSQRTSGRFVTEDNLLIGKIRQQVAKAELATFVNNMKKIGYKLDEITVALDHFIKE 120- EGMV+SQRT+GRFVT+D LI + R+++A +EL +F+ NM K+G+ EI L F+KE Sbjct: 61 EGMVYSQRTAGRFVTDDQKLIARKRRELAISELESFITNMTKMGFSHTEIIPVLTSFLKE 120- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1336 A DNA sequence (GBSx1420) was identified in S. agalactiae <SEQ ID 4101> which encodes the amino acid sequence <SEQ ID 4102>. This protein is predicted to be ABC transporter, ATP-binding protein (yhcG). Analysis of this protein sequence reveals the following: TABLE-US-03982 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2757(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-03983 >GP: CAB12735 GB: Z99108 similar to glycine betaine/L-proline transport [Bacillus subtilis] Identities = 87/228 (38%), Positives = 150/228 (65%), Gaps = 1/228 (0%) Query: 5 LQLHHVTKKYHKHTAVNDVTVSIPTGKIIGLLGPNGSGKTTIIKMINGLLQPDKGDIVID 64 ++L HV+KKY +HTAVNDV++++ +G+I GL+GPNGSGK+T +KM+ GLL P G + +D Sbjct: 3 IKLEHVSKKYGRHTAVNDVSITLSSGRIYGLIGPNGSGKSTTLKMMAGLLFPTSGFVKVD 62 Query: 65 GYRPSVETKKIISYLPDTSYLQENMKIKDVVTLFEDFYNDFDSKVAYQLFEDLNLNPRER 124- + + E + +YL + + +KD+V ++ + DF ++ Y+L ++ LNP ++ Sbjct: 63 EEQVTREMVRQTAYLTELDMFYPHFTVKDMVNFYQSQFPDFHTEQVYKLLNEMQLNPEKK 122- Query: 125 LKNLSKGNKEKVQLILVMSRKARLYILDEPIGGVDPAARDYILKTIISNYSNDAS-VLIS 18- 3 +K LSKGN+ +++++L ++R+A + +LDEP G+DP RD I+ +++S + V+I+ Sbjct: 123 IKKLSKGNRGRLKIVLALARRADVILLDEPFSGLDPMVRDSIVNSLVSYIDFEQQIVVIA 18- 2 Query: 184 THLISDIEPILDEVIFLKEGEIDLQGNADDLREEHNCSIDALFRERFK 231 TH I +IE +LDEVI L GE Q +D+RE+ S+ F+ + + Sbjct: 183 THEIDEIETLLDEVIILANGEKVAQREVEDIREQEGMSVLQWFKSKME 230 A related DNA sequence was identified in S. pyogenes <SEQ ID 4103> which encodes the amino acid sequence <SEQ ID 4104>. Analysis of this protein sequence reveals the following: TABLE-US-03984 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1983(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-03985 Identities = 171/231 (74%), Positives = 200/231 (86%) Query: 1 MTQLLQLHHVTKKYHKHTAVNDVTVSIPTGKIIGLLGPNGSGKTTIIKMINGLLQPDKGD 60 M LLQLHHV+K Y + A++D+T++IP GKIIGLLGPNGSGKTT+IK+INGLLQP+KG+ Sbjct: 1 MAHLLQLHHVSKSYREKKAIDDLTITIPNGKIIGLLGPNGSGKTTLIKLINGLLQPNKGE 60 Query: 61 IVIDGYRPSVETKKIISYLPDTSYLQENMKIKDVVTLFEDFYNDFDSKVAYQLFEDLNLN 120- IVIDGYRP VETKKIISYLPDT+YL ENM+IKD++ F DFY+DFD A L DL L+ Sbjct: 61 IVIDGYRPCVETKKIISYLPDTTYLNENMRIKDMLEFFSDFYSDFDKSKATSLLRDLELD 120- Query: 121 PRERLKNLSKGNKEKVQLILVMSRKARLYILDEPIGGVDPAARDYILKTIISNYSNDASV 18- 0 P +R K LSKGNKEKVQLILVMSRKARLY+LDEPIGGVDPAARDYILKTII++Y +ASV Sbjct: 121 PEDRFKTLSKGNKEKVQLILVMSRKARLYVLDEPIGGVDPAARDYILKTIINSYCENASV 18- 0 Query: 181 LISTHLISDIEPILDEVIFLKEGEIDLQGNADDLREEHNCSIDALFRERFK 231 +ISTHLISDIEPILDEVIFLK+G + L GNADDLR+E+ SID+LFRE +K Sbjct: 181 IISTHLISDIEPILDEVIFLKQGRLFLSGNADDLRQEYQQSIDSLFRETYK 231 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1337 A DNA sequence (GBSx1421) was identified in S. agalactiae <SEQ ID 4105> which encodes the amino acid sequence <SEQ ID 4106>. Analysis of this protein sequence reveals the following: TABLE-US-03986 Possible site: 48 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -15.39 Transmembrane 120-136 (103-146) INTEGRAL Likelihood = -9.98 Transmembrane 55-71 (47-79) INTEGRAL Likelihood = -9.45 Transmembrane 22-38 (15-43) INTEGRAL Likelihood = -6.05 Transmembrane 192-208 (187-218) INTEGRAL Likelihood = -4.94 Transmembrane 230-246 (228-253) INTEGRAL Likelihood = -4.78 Transmembrane 157-173 (155-175) INTEGRAL Likelihood = -1.44 Transmembrane 103-119 (103-119) ----- Final Results ----- bacterial membrane --- Certainty = 0.7156(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4107> which encodes the amino acid sequence <SEQ ID 4108>. Analysis of this protein sequence reveals the following: TABLE-US-03987 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -11.52 Transmembrane 190-206 (187-215) INTEGRAL Likelihood = -10.67 Transmembrane 121-137 (104-141) INTEGRAL Likelihood = -5.73 Transmembrane 63-79 (59-82) INTEGRAL Likelihood = -4.83 Transmembrane 158-174 (156-181) INTEGRAL Likelihood = -1.38 Transmembrane 232-248 (232-248) INTEGRAL Likelihood = -0.85 Transmembrane 104-120 (104-120) ----- Final Results ----- bacterial membrane --- Certainty = 0.5607(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-03988 Identities = 116/267 (43%), Positives = 165/267 (61%), Gaps = 13/267 (4%) Query: 1 MFGKLLKYELKSVGKWYLTLNAAVLLVSIILGLVLKALG-----GNFSTDTNSTSAQIFT 55 MFGKLLKYE +S+GKWY LNA V+ ++ IL +K G F TN ++ Sbjct: 1 MFGKLLKYEFRSIGKWYFALNAFVIAIAAILSFTIKLFAQSNSDGLFGVLTN----KMLP 56 Query: 56 IILVLLLAMVISGSLLSTLAIIIKRFYSNIFGRQGYLTLTLPVTTNQIICSKLLASLLWS 115- + L L +I+GSLLSTL IIIKRF ++FG +GYLTLTLPV ++QII SKLLAS + S Sbjct: 57 LTLGLTFGSLIAGSLLSTLLIIIKRFSKSVFGWEGYLTLTLPVNSHQIILSKLLASFICS 116- Query: 116 IFNIFIVIIGIILVILPLVGIGQFVVAFPEIYKIISSSNAPLFIAYFFLSYVAGTLLIYL 17- 5 +FN I+ I +VI+P+ I + + F +K+ N +AY LS LLIYL Sbjct: 117 VFNTIILAFAIAIVIVPMFNINELLEGFFNSFKNDYFINMLTVLAYVLLSTFTSILLIYL 17- 6 Query: 176 SIAVGQLFTNKRVLMGIVSYFGISLLITFLTLIIDSIFHIDLFNSHANA-TFSQPVLLY- 23- 3 SI++GQLF+N+R LM ++YF + +LI+ + S HI N+ A++ F++ +Y Sbjct: 177 SISIGQLFSNRRGLMAFIAYFILVILISVAATYVHS--HIFNINTSADSFPFTEQKTIYL 23- 4 Query: 234 NILVSIVEIAIFYMLTHSIIKYKLNIQ 260 IL +E+ +FY+ T+ IIK KLN+Q Sbjct: 235 LILEQFIEMIMFYLATNFIIKNKLNLQ 261 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1338 A DNA sequence (GBSx1422) was identified in S. agalactiae <SEQ ID 4109> which encodes the amino acid sequence <SEQ ID 4110>. Analysis of this protein sequence reveals the following: TABLE-US-03989 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5890(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to ORF24 from S. faecalis. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1339 A DNA sequence (GBSx1423) was identified in S. agalactiae <SEQ ID 4111> which encodes the amino acid sequence <SEQ ID 4112>. Analysis of this protein sequence reveals the following: TABLE-US-03990 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3316(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to ORF23 from S. faecalis. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1340 A DNA sequence (GBSx1424) was identified in S. agalactiae <SEQ ID 4113> which encodes the amino acid sequence <SEQ ID 4114>. Analysis of this protein sequence reveals the following: TABLE-US-03991 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4256(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to ORF22 from S. faecalis. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1341 A DNA sequence (GBSx1425) was identified in S. agalactiae <SEQ ID 4115> which encodes the amino acid sequence <SEQ ID 4116>. Analysis of this protein sequence reveals the following: TABLE-US-03992 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.37 Transmembrane 62-78 (55-84) INTEGRAL Likelihood = -8.44 Transmembrane 19-35 (14-41) ----- Final Results ----- bacterial membrane --- Certainty = 0.6349(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to ORF21 from S. faecalis. A related DNA sequence was identified in S. pyogenes <SEQ ID 4117> which encodes the amino acid sequence <SEQ ID 4118>. Analysis of this protein sequence reveals the following: TABLE-US-03993 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2444 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-03994 Identities = 54/236 (22%), Positives = 95/236 (39%), Gaps = 12/236 (5%) Query: 204 KDGKLRLMKNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKN---- 25- 9 + GK+ ++K+ DK H IAG +G GK Y LT ++L S L I+ DPK Sbjct: 14 QQGKIPVIKHFELNLDKGSHWAIAGNSGSGKPY-ALTYFLSVLKPKSGLIIIDPKFDTPS 72 Query: 260 --ADLADLGSVMANVYYRKEDLLSCIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAH 31- 7 A + + + K D +S + + ++ + + + +L + Sbjct: 73 QWARENKIAVIHPVENHSKSDFVSQVNEQLNQCATLIQKRQAILYDNPNHQFTHLTI--- 129- Query: 318 FLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLGRQAGFFLILACQRPDAKYLGDGIRDQF 37- 7 + DE +A E + A + L QI + LG L L QR D + +R++Q Sbjct: 130 --VIDEVLALSEGVNKNIKEAFFSLLSQIALLGHATKIHLFLGSQRFDHNTIPISVREQL 18- 7 Query: 378 NFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSVISEFYTPLVPKGY 433 N + +G +++ +F + + G G + V + S PL+ Y Sbjct: 188 NVLLQIGNINQKTTQFLFPDLDPEGIVIPTGHGTGIIQVVDNEHSYQVLPLLCPTY 243 SEQ ID 4116 (GBS109d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 121 (lane 8 & 9; MW 71 kDa) and in FIG. 184 (lane 2; MW 71 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 121 (lane 11; MW 46 kDa), FIG. 128 (lane 4; MW 46 kDa) and FIG. 179 (lane 7; MW 46 kDa). GBS109d-His was purified as shown in FIG. 232 (lanes 7 & 8). GBS109d-GST was purified as shown in FIG. 236, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1342 A DNA sequence (GBSx1426) was identified in S. agalactiae <SEQ ID 4119> which encodes the amino acid sequence <SEQ ID 4120>. Analysis of this protein sequence reveals the following: TABLE-US-03995 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1343 A DNA sequence (GBSx1427) was identified in S. agalactiae <SEQ ID 4121> which encodes the amino acid sequence <SEQ ID 4122>. Analysis of this protein sequence reveals the following: TABLE-US-03996 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4469(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9793> which encodes amino acid sequence <SEQ ID 9794> was also identified. The protein is similar to ORF20 from S. faecalis. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1344 A DNA sequence (GBSx1428) was identified in S. agalactiae <SEQ ID 4123> which encodes the amino acid sequence <SEQ ID 4124>. Analysis of this protein sequence reveals the following: TABLE-US-03997 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1367 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1345 A DNA sequence (GBSx1429) was identified in S. agalactiae <SEQ ID 4125> which encodes the amino acid sequence <SEQ ID 4126>. Analysis of this protein sequence reveals the following: TABLE-US-03998 Possible site: 22 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.77 Transmembrane 39-55 (34-64) INTEGRAL Likelihood = -6.32 Transmembrane 16-32 (10-35) ----- Final Results ----- bacterial membrane --- Certainty = 0.5310 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein is similar to ORF19 from S. faecalis. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1346 A DNA sequence (GBSx1430) was identified in S. agalactiae <SEQ ID 4127> which encodes the amino acid sequence <SEQ ID 4128>. This protein is predicted to be antirestriction protein. Analysis of this protein sequence reveals the following: TABLE-US-03999 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2918 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein is similar to ORF18 from S. faecalis. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1347 A DNA sequence (GBSx1431) was identified in S. agalactiae <SEQ ID 4129> which encodes the amino acid sequence <SEQ ID 4130>. Analysis of this protein sequence reveals the following: TABLE-US-04000 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -3.61 Transmembrane 75-91 (72-94) ----- Final Results ----- bacterial membrane --- Certainty = 0.2444 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein is similar to ORF17 from S. faecalis. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8793> and protein <SEQ ID 8794> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04001 Lipop Possible site: -1 Crend: 4 McG: Discrim Score: -7.12 GvH: Signal Score (-7.5): -2.52 Possible site: 43 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -3.61 threshold: 0.0 INTEGRAL Likelihood = -3.61 Transmembrane 37-53 (34-56) PERIPHERAL Likelihood = 3.66 58 modified ALOM score: 1.22 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2444 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00090## SEQ ID 8794 (GBS223) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 44 (lane 7; MW 18 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1348 A DNA sequence (GBSx1432) was identified in S. agalactiae <SEQ ID 4131> which encodes the amino acid sequence <SEQ ID 4132>. Analysis of this protein sequence reveals the following: TABLE-US-04002 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4292 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9791> which encodes amino acid sequence <SEQ ID 9792> was also identified. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1349 A DNA sequence (GBSx1433) was identified in S. agalactiae <SEQ ID 4133> which encodes the amino acid sequence <SEQ ID 4134>. Analysis of this protein sequence reveals the following: TABLE-US-04003 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.21 Transmembrane 350-366 (345-368) INTEGRAL Likelihood = -0.32 Transmembrane 171-187 (171-188) ----- Final Results ----- bacterial membrane --- Certainty = 0.3484 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1350 A DNA sequence (GBSx1434) was identified in S. agalactiae <SEQ ID 4135> which encodes the amino acid sequence <SEQ ID 4136>. Analysis of this protein sequence reveals the following: TABLE-US-04004 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.30 Transmembrane 154-170 (148-177) INTEGRAL Likelihood = -10.30 Transmembrane 21-37 (17-50) INTEGRAL Likelihood = -10.03 Transmembrane 320-336 (316-367) INTEGRAL Likelihood = -7.43 Transmembrane 346-362 (337-367) INTEGRAL Likelihood = -7.01 Transmembrane 186-202 (180-206) INTEGRAL Likelihood = -5.36 Transmembrane 411-427 (404-430) INTEGRAL Likelihood = -1.17 Transmembrane 386-402 (386-402) ----- Final Results ----- bacterial membrane --- Certainty = 0.5118 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1351 A DNA sequence (GBSx1436) was identified in S. agalactiae <SEQ ID 4137> which encodes the amino acid sequence <SEQ ID 4138>. Analysis of this protein sequence reveals the following:

TABLE-US-04005 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6306 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1352 A DNA sequence (GBSx1437) was identified in S. agalactiae <SEQ ID 4139> which encodes the amino acid sequence <SEQ ID 4140>. Analysis of this protein sequence reveals the following: TABLE-US-04006 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2973 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1353 A DNA sequence (GBSx1438) was identified in S. agalactiae <SEQ ID 4141> which encodes the amino acid sequence <SEQ ID 4142>. Analysis of this protein sequence reveals the following: TABLE-US-04007 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3382 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> There is also homology to SEQ ID 4144. A related GBS gene <SEQ ID 8795> and protein <SEQ ID 8796> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04008 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 11.12 GvH: Signal Score (-7.5): 0.27 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 4.19 threshold: 0.0 PERIPHERAL Likelihood = 4.19 69 modified ALOM score: -1.34 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00091## SEQ ID 8796 (GBS155) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 24 (lane 10; MW 38 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 31 (lane 7; MW 62 kDa). The GBS155-GST fusion product was purified (FIG. 111; see also FIG. 198, lane 74) and used to immunise mice (lane 1 product; 20 kg/mouse). The resulting antiserum was used for Western blot, FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1354 A DNA sequence (GBSx1439) was identified in S. agalactiae <SEQ ID 4145> which encodes the amino acid sequence <SEQ ID 4146>. Analysis of this protein sequence reveals the following: TABLE-US-04009 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.60 Transmembrane 37-53 (35-55) ----- Final Results ----- bacterial membrane --- Certainty = 0.4439 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9789> which encodes amino acid sequence <SEQ ID 9790> was also identified. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1355 A DNA sequence (GBSx1440) was identified in S. agalactiae <SEQ ID 4147> which encodes the amino acid sequence <SEQ ID 4148>. Analysis of this protein sequence reveals the following: TABLE-US-04010 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.00 Transmembrane 391-407 (391-407) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9787> which encodes amino acid sequence <SEQ ID 9788> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 4149> which encodes the amino acid sequence <SEQ ID 4150>. Analysis of this protein sequence reveals the following: TABLE-US-04011 Possible Site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2027 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04012 Identities = 183/669 (27%), Positives = 305/669 (45%), Gaps = 63/669 (9%) Query: 7 KIINIGVLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGIT 66 K NIG++AHVDAGKTT TE +LY +G I ++G +G ++ D E++RGITI + T Sbjct: 9 KTRNIGIMAHVDAGKTTTTERILYYTGKIHKIGETHEGASQMDWMEQEQERGITITSAAT 68 Query: 67 SFQWENTKVNIIDTPGHMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMGI 126- + QW+ +VNIIDTPGH+DF EV RSL VLDGA+ ++ ++ GV+ QT ++ + G+ Sbjct: 69 TAQWDGHRVNIIDTPGHVDFTIEVQRSLRVLDGAVTVLDSQSGVEPQTETVWRQATEYGV 128- Query: 127 PTIFFINKIDQNGIDLSTVYQDIKEKLSAEI------------------VIKQKVELYPN 16- 8 P I F NK+D+ G D Q + ++L A +IK K E+Y N Sbjct: 129 PRIVFANKMDKIGADFLYSVQTLHDRLQANAHPIQLPIGAEDDFRGIIDLIKMKAEIYTN 18- 8 Query: 169 MCVTNFTES---EQW------------DTVIEGNDDLLEKYMSGKSLEALELEQEESIRF 21- 3 T+ E E++ + V E ++DL+ KY+ G+ + EL Sbjct: 189 DLGTDILEEDIPEEYLEQAQEYREKLIEAVAETDEDLMMKYLEGEEITNDELIAGIRKAT 24- 8 Query: 214 HNCSLFPVYHGSAKNNIGIDNLIEVI---------------TNKFYSSTHRGPSE----L 25- 4 N FPV GSA N G+ +++ + N + P+ Sbjct: 249 INVEFFPVLCGSAFKNKGVQLMLDAVIAYLPSPLDIPAIKGVNPDTDAEEERPASDEEPF 30- 8 Query: 255 CGNVFKIEYTKKRQRLAYIRLYSGVLHLRDSVRVSEKEKI----KVTEMYTSINGELCKI 31- 0 FKI RL + R+YSGVL+ V + K K ++ +M+ + E I Sbjct: 309 AALAFKIMTDPFVGRLTFFRVYSGVLNSGSYVMNTSKGKRERIGRILQMHANSRQE---I 36- 5 Query: 311 DRAYSGEIVILQN-EFLKLNSVLGDTKLLPQRKKIENPHPLLQTTVEPSKPEQREMLLDA 36- 9 + Y+G+I + L D K + IE P P++Q VEP ++ + A Sbjct: 366 ETVYAGDIAAAVGLKDTTTGDSLTDEKAKVILESIEVPEPVIQLMVEPKSKADQDKMGVA 42- 5 Query: 370 LLEISDSDPLLRYYVDSTTHEIILSFLGKVQMEVISALLQEKYHVEIELKEPTVIYME-- 42- 7 L ++++ DP R + T E +++ +G++ ++V+ ++ ++ VE + P V Y E Sbjct: 426 LQKLAEEDPTFRVETNVETGETVIAGMGELHLDVLVDRMKREFKVEANVGAPQVSYRETF 48- 5 Query: 428 RPLKNAEYTIHIEVPPNPFWASIGLSVSPLPLGSGMQYESSVSLGYLNQSFQNAVMEGIR 48- 7 R A + + + + +P G G ++E+++ G + + F AV +G+ Sbjct: 486 RASTQARGFFKRQSGGKGQFGDVWIEFTPNEEGKGFEFENAIVGGVVPREFIPAVEKGLI 54- 5 Query: 488 YGCEQG-LYGWNVTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQVLKKAGTELLEPYLS 54- 6 G L G+ + D K G Y+ S+ F++ A + L++ K A +LEP + Sbjct: 546 ESMANGVLAGYPMVDVKAKLYDGSYHDVDSSETAFKIAASLALKEAAKSAQPAILEPMML 60- 5 Query: 547 FKIYAPQEYLSRAYNDAPKYCANIVDTQLKNNEVILSGEIPARCIQEYRSDLTFFTNGRS 60- 6 I AP++ L + + N I+ +P + Y + L T GR Sbjct: 606 VTITAPEDNLGDVMGHVTARRGRVDGMEAHGNSQIVRAYVPLAEMFGYATVLRSATQGRG 66- 5 Query: 607 VCLTELKGY 615 + Y Sbjct: 666 TFMMVFDHY 674 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1356 A DNA sequence (GBSx1441) was identified in S. agalactiae <SEQ ID 4151> which encodes the amino acid sequence <SEQ ID 4152>. Analysis of this protein sequence reveals the following: TABLE-US-04013 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2530(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1357 A DNA sequence (GBSx1442) was identified in S. agalactiae <SEQ ID 4153> which encodes the amino acid sequence <SEQ ID 4154>. Analysis of this protein sequence reveals the following: TABLE-US-04014 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1358 A DNA sequence (GBSx1443) was identified in S. agalactiae <SEQ ID 4155> which encodes the amino acid sequence <SEQ ID 4156>. Analysis of this protein sequence reveals the following: TABLE-US-04015 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1630(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1359 A DNA sequence (GBSx1444) was identified in S. agalactiae <SEQ ID 4157> which encodes the amino acid sequence <SEQ ID 4158>. This protein is predicted to be excisionase-related protein. Analysis of this protein sequence reveals the following: TABLE-US-04016 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4481(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to transposon Tn916 from S. faecalis. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1360 A DNA sequence (GBSx1445) was identified in S. agalactiae <SEQ ID 4159> which encodes the amino acid sequence <SEQ ID 4160>. This protein is predicted to be transposase. Analysis of this protein sequence reveals the following: TABLE-US-04017 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4626(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein is similar the Tn1545 integrase from S. pneumoniae and to SEQ ID 578. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1361 A DNA sequence (GBSx1446) was identified in S. agalactiae <SEQ ID 4161> which encodes the amino acid sequence <SEQ ID 4162>. Analysis of this protein sequence reveals the following: TABLE-US-04018 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.72 Transmembrane 18-34 (13-41) INTEGRAL Likelihood = -6.10 Transmembrane 58-74 (55-79) INTEGRAL Likelihood = -5.04 Transmembrane 97-113 (90-116) INTEGRAL Likelihood = -1.81 Transmembrane 78-94 (78-94) INTEGRAL Likelihood = -0.85 Transmembrane 145-161 (145-161) ----- Final Results ----- bacterial membrane --- Certainty = 0.5288(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04019 >GP: AAC74820 GB: AE000270 orf, hypothetical protein [Escherichia coli K12] Identities = 43/174 (24%), Positives = 84/174 (47%), Gaps = 9/174 (5%) Query: 24 LIATLVLVVYLYKL------GILNDSNELKDLVHKYEFWGPMIFIVAQIVQIVFPVIPGG 77 - L A L+ + +Y + +L D L+ L+ + F+G ++I+ I+ + ++PG Sbjct: 24 LFACLIFALVIYAIHAFGLFDLLTDLPHLQTLIRQSGFFGYSLYILLFIIATLL-LLPGS 82 Query: 78 VTTVAGFLIFGPTLGFIYNYIGIIIGSVILFWLVKFYGRKFVLLFM-DQKTFDKYESKLE 136- + +AG ++FGP LG + + I + S F L ++ GR +L ++ TF E + Sbjct: 83 ILVIAGGIVFGPLLGTLLSLIAATLASSCSFLLARWLGRDLLLKYVGHSNTFQAIEKGIA 142- Query: 137 TSGYEKFFIFCMASPISPADIMVMITGLSNMSIKRFVTIIMITKPISIIGYSYL 190 +G + F I P+ P +I GL+ ++ + I +T I+ Y+ + Sbjct: 143 RNGID-FLILTRLIPLFPYNIQNYAYGLTTIAFWPYTLISALTTLPGIVIYTVM 195 A related DNA sequence was identified in S. pyogenes <SEQ ID 4163> which encodes the amino acid sequence <SEQ ID 4164>. Analysis of this protein sequence reveals the following: TABLE-US-04020 Possible site: 43 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.30 Transmembrane 8-24 (6-29) INTEGRAL Likelihood = -0.80 Transmembrane 57-73 (57-73) INTEGRAL Likelihood = -0.00 Transmembrane 86-102 (86-102) ----- Final Results ----- bacterial membrane --- Certainty = 0.2720(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-04021 Identities = 85/114 (74%), Positives = 101/114 (88%) Query: 89 PTLGFIYNYIGIIIGSVILFWLVKFYGRKFVLLFMDQKTFDKYESKLETSGYEKFFIFCM 148- P GFIYNY+GIIIGS+ LF LVK YGRKF+LLF++ KTF KYE +LET GYEK FIFCM Sbjct: 3 PVTGFIYNYVGIIIGSIALFLLVKTYGRKFILLFVNDKTFYKYERRLETPGYEKLFIFCM 62 Query: 149 ASPISPADIMVMITGLSNMSIKRFVTIIMITKPISIIGYSYLWIYGGDILKNFL 202 ASP+SPADIMVMITGL++MS+KRFVTI++ITKPISIIGYSYL+I+G D++ FL Sbjct: 63 ASPVSPADIMVMITGLTDMSLKRFVTILLITKPISIIGYSYLFIFGKDVISWFL 116 There is also homology to SEQ ID 1728. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1362 A DNA sequence (GBSx1447) was identified in S. agalactiae <SEQ ID 4165> which encodes the amino acid sequence <SEQ ID 4166>. This protein is predicted to be chlorAMPhenicol acetyltransferase (cat). Analysis of this protein sequence reveals the following: TABLE-US-04022 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4725(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04023 >GP: AAA86871 GB: U19459 VAT B [Staphylococcus aureus] Identities = 57/130 (43%), Positives = 81/130 (61%), Gaps = 4/130 (3%) Query: 57 IGAFCSIAQNVT--ITGLNHPTDHITTNPFIYYKSRGFINEDRADLIDEKKNGKVIIGND 114- IG FC+IA+ + + G NH + ITT PF G+ + L D G ++GND Sbjct: 65 IGKFCAIAEGIEFIMNGANHRMNSITTYPF-NIMGNGW-EKATPSLEDLPFKGDTVVGND 122- Query: 115 VWIGTNVTILPSVTIGNGAIIGAGSVITKDIPDYAVVAGTPAKIIKYRFSEEEITLLNAS 17- 4 VWIG NVT++P + IG+GAI+ A SV+TKD+P Y ++ G P++IIK RF +E I L Sbjct: 123 VWIGQNVTVMPGIQIGDGAIVAANSVVTKDVPPYRIIGGNPSRIIKKRFEDELIDYLLQI 18- 2 Query: 175 QWWNWSDEAI 184 +WW+WS + I Sbjct: 183 KWWDWSAQKI 192 There is also homology to SEQ ID 1944. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1363 A DNA sequence (GBSx1448) was identified in S. agalactiae <SEQ ID 4167> which encodes the amino acid sequence <SEQ ID 4168>. Analysis of this protein sequence reveals the following: TABLE-US-04024 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2398(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1364 A DNA sequence (GBSx1449) was identified in S. agalactiae <SEQ ID 4169> which encodes the amino acid sequence <SEQ ID 4170>. This protein is predicted to be cation-transporting P-ATPase PacL. Analysis of this protein sequence reveals the following:

TABLE-US-04025 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.18 Transmembrane 873-889 (866-894) INTEGRAL Likelihood = -8.39 Transmembrane 257-273 (251-276) INTEGRAL Likelihood = -5.95 Transmembrane 67-83 (65-88) INTEGRAL Likelihood = -5.41 Transmembrane 282-298 (281-301) INTEGRAL Likelihood = -1.65 Transmembrane 90-106 (89-107) INTEGRAL Likelihood = -0.48 Transmembrane 737-753 (736-753) INTEGRAL Likelihood = -0.00 Transmembrane 898-914 (898-914) ----- Final Results ----- bacterial membrane --- Certainty = 0.4673(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10963> which encodes amino acid sequence <SEQ ID 10964> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04026 >GP: AAB85991 GB: AE000912 cation-transporting P-ATPase PacL [Methanothermobacter thermoautotrophicus] Identities = 409/922 (44%), Positives = 609/922 (65%), Gaps = 22/922 (2%) Query: 10 TNTRFAKEELEEVFEELGTTQGGLSDEEVAVRQKKYGLNLLSEVKQESIILLFLKNFTSL 69 - T T + E+EEV + L T++ GL +E R K +G N L EVK+ +ILLFL N ++ Sbjct: 4 TMTAIYELEVEEVLQRLETSESGLDPQEAEKRLKIHGPNKLEEVKRRPLILLFLSNLYNV 63 Query: 70 MAILLWVGGFVAIVSNSLELGLAIWMVNVINGIFSFIQEYRASQATQALEKMLPSYSRVL 129- +A+LLW+ ++ ++ + +L +AI MV +IN +FSF QEY A +A +AL+ +LP +V+ Sbjct: 64 LALLLWIAAILSFITGNYQLAVAIVMVIIINALFSFWQEYEAEKAAEALKNILPVMVKVI 123- Query: 130 RKGSEEKILSEQLVPGDIVLIEEGDRISADGRLIKTTDLQVNQSALTGESNPIYKDSNVE 18- 9 R E I + +V GDI+++EEGD + AD R++++ +L+V+ SALTGES P+ K S+ Sbjct: 124 RASKEVLIPAADVVHGDIIILEEGDTVPADARILESHNLRVDASALTGESKPVRKVSHPV 18- 3 Query: 190 NDQSKTLIECDNMVFAGTTVSSGSATMVVTAIGMQTQFGQIADLTQGMKSEKSPLQRELD 24- 9 + + I+ +N++FAGT V+SG+ V A G T+F +IA LTQ ++ E SPLQR++ Sbjct: 184 RE-ADNYIDTENILFAGTQVTSGTGRAAVFATGRDTEFSRIATLTQEVREEPSPLQRQIS 24- 2 Query: 250 RLTKQISIISITVGIIFFLAATFFVKEPVSKSFIFALGMIVAFIPEGLLPTVTLSLAMAV 30- 9 + I +++ +G+I FL + V+ P+ +FIFA+G++VA +PEGLLP+VTLSLA + Sbjct: 243 LAARIIGALAVAMGVILFLVNLYIVRLPLETAFIFAIGLMVANVPEGLLPSVTLSLAASA 30- 2 Query: 310 QRMAKEHALVKKLSSVETLGATSVICSDKTGTLTQNEMTVNHLWQNGKSYQVTGLGYAPE 36- 9 ++MA+E+ALVK+LSSVETLG+T++IC+DKTGTLT+ EMTV +W K +VTG GY PE Sbjct: 303 RKMARENALVKRLSSVETLGSTTIICTDKTGTLTRGEMTVRKIWIPHKVIEVTGSGYRPE 36- 2 Query: 370 GQILFEGDNICFGNSDRGDLEKLIRFAHLCSNAQVLPPNDDRSTYTVLGDPTEACLNVLL 42- 9 GQ LF G+ + + D +L+ L+R A C+++ ++ + ++VLGD TE L V Sbjct: 363 GQFLFRGEPV--SHRDMAELKLLMRAATFCNDSALI---HEEGEWSVLGDSTEGALLVAA 41- 7 Query: 430 EKSGINIQENRKFAPRLKELPFDSVRKRMTTIHSLGGDEKDKKISITKGAPKEILDLSDY 48- 9 EK G + + K PR+ ELPFDS RK MT+IH G K+++ KGAPK+I+ LS+ Sbjct: 418 EKLGFDAEAELKAMPRITELPFDSRRKSMTSIHEKSG----KRVAYVKGAPKKIIGLSER 47- 3 Query: 490 VLSDGKVIPLNKEERNKIQLANDTFAKDGLRVLAVSYCDIEGFSKEQWTQENLEQHMVFI 54- 9 + DG+V L+ +E+ +I +D A GLRVLA +Y ++ E +E+ +V + Sbjct: 474 ISVDGRVRALHADEKERIIGIHDEMASKGLRVLAFAYRELPE-DLEVRDPGEVERDLVLV 53- 2 Query: 550 GLIAMSDPPREGVREAIDKCHAASIRIIMVTGDYGLTALSIAKNIGIIRNDDAKVISGLE 60- 9 G+ AM DPPREGV+EA++ C A IRIIM+TGDYGLTA +IA+ IGI+ + ++I G E Sbjct: 533 GMAAMHDPPREGVKEAVEHCKTAGIRIIMITGDYGLTAEAIAREIGIVEG-ECRIIKGKE 59- 1 Query: 610 LSEMTDSQLKKELSGE--VVFARVAPEQKYRVVTILQEMGEVVAVTGDGVNDAPALKKSD 66- 7 L ++ D++L+ L+ E ++FAR PE K R+ ++L++ E+VA+TGDGVNDAPAL+K+D Sbjct: 592 LDKLKDTELRGILARERNLIFARAVPEHKMRIASVLEDSDEIVAMTGDGVNDAPALRKAD 65- 1 Query: 668 IGVAMGVTGTDVAKESADMILTDDHFASIVHAVEEGRAVYQNIKKFLTYIFNSNTPEAVP 72- 7 IGVAMG +GTDVAKE+AD++L DD+FASIV AV EGR VY+NI+KF+TYIF+ T E VP Sbjct: 652 IGVAMG-SGTDVAKEAADIVLADDNFASIVTAVREGRTVYENIRKFITYIFSHETAEIVP 71- 0 Query: 728 SAFFLFSKGFIPLPLTVMQILAVDLGTDMLPALGLGVEPPETDVMNRPPRRLTDRLLDKG 78- 7 F + IPLP+T+MQILA+DLGTD LPAL LG PE+DVM PPR ++RLL++ Sbjct: 711 --FIMMVLFSIPLPITIMQILAIDLGTDTLPALALGRSLPESDVMKLPPRAPSERLLNRE 76- 8 Query: 788 LLIKSFLWYGTIESVLAMGGFFWAHYLRYGNF---TFFVANGIPYREATTMTLGAIIFSQ 84- 4 ++++ +L+ GTIE+ L M +F Y G + A+ Y ATT+ I+ +Q Sbjct: 769 VILRGYLFTGTIEAALIMAAYFLVLY--SGGWLPGQELSASDPLYMRATTVVFAGIVMAQ 82- 6 Query: 845 IGMVMNSRTSYQSIKALSIFGNKLINFGIIMEILAFLVLVYVPLFHNLFNTASLGLSHWL 90- 4 +G +++S+T S + N+ I G++ I L+++Y+P +F TA G+ W Sbjct: 827 LGNLLSSQTLRSSALEAGLLRNRWILAGMVFAISVMLLVIYLPPLQPIFGTAPPGILEWF 88- 6 Query: 905 YLISCPFIMIGLDEVRKLFSSR 926 LI I+ DE+RK R Sbjct: 887 ILILFTPIVFLTDEMRKFIQRR 908 There is also homology to SEQ ID 4172. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1365 A DNA sequence (GBSx1450) was identified in S. agalactiae <SEQ ID 4173> which encodes the amino acid sequence <SEQ ID 4174>. Analysis of this protein sequence reveals the following: TABLE-US-04027 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3740(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04028 >GP: CAB46979 GB: AJ243482 CSRA protein [Enterococcus faecalis] Identities = 85/132 (64%), Positives = 105/132 (79%) Query: 2 KETQEELRQRIGHTAYQVTQNSATEHAFTGKYDDFFEEGIYVDIVSGEVLFSSLDKFQSG 61 K T+EEL+Q + Y VTQ +ATE F+G+YDDF+++GIYVDIVSGE LFSSLDK+ +G Sbjct: 3 KPTEEELKQTLTDLQYAVTQENATERPFSGEYDDFYQDGIYVDIVSGEPLFSSLDKYDAG 62 Query: 62 CGWPAFSKPIENRMVTNHQDHSHGMHRIEVRSRQADSHLGHVFNDGPVDAGGLRYCINSA 121- CGWP+F+KPIE R V D SHGMHR+EVRS++ADSHLGHVF DGP+ GGLRYCIN+A Sbjct: 63 CGWPSFTKPIEKRGVKEKADFSHGMHRVEVRSQEADSHLGHVFTDGPLQEGGLRYCINAA 122- Query: 122 ALDFIPYDQMAK 133 AL F+P + K Sbjct: 123 ALRFVPVADLEK 134 A related DNA sequence was identified in S. pyogenes <SEQ ID 4175> which encodes the amino acid sequence <SEQ ID 4176>. Analysis of this protein sequence reveals the following: TABLE-US-04029 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3692(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04030 Identities = 109/142 (76%), Positives = 126/142 (87%) Query: 3 ETQEELRQRIGHTAYQVTQNSATEHAFTGKYDDFFEEGIYVDIVSGEVLFSSLDKFQSGC 62 ET +EL+QRIG +Y+VTQ++ATE FTG+YD+FFE+GIYVDIVSGEVLFSSLDKF SGC Sbjct: 2 ETSDELKQRIGDLSYEVTQHAATESPFTGEYDNFFEKGIYVDIVSGEVLFSSLDKFNSGC 61 Query: 63 GWPAFSKPIENRMVTNHQDHSHGMHRIEVRSRQADSHLGHVFNDGPVDAGGLRYCINSAA 122- GWPAFSKPIENRMVTNH D S+GM R+EV+SR+A SHLGHVF+DGP +AGGLRYCINSAA Sbjct: 62 GWPAFSKPIENRMVTNHDDSSYGMRRVEVKSREAGSHLGHVFSDGPKEAGGLRYCINSAA 121- Query: 123 LDFIPYDQMAKRGYGDYLSLFD 144 L FIPYDQM K GY +L+LFD Sbjct: 122 LKFIPYDQMEKEGYAQWLTLFD 143 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1366 A DNA sequence (GBSx1451) was identified in S. agalactiae <SEQ ID 4177> which encodes the amino acid sequence <SEQ ID 4178>. Analysis of this protein sequence reveals the following: TABLE-US-04031 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1674(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04032 >GP: BAB05127 GB: AP001511 unknown [Bacillus halodurans] Identities = 48/152 (31%), Positives = 77/152 (50%), Gaps = 1/152 (0%) Query: 1 MIRRAKEKDLPDIAELLKQILMLHHEVRPDIFHTRGSKFSKEQLKEMLIDESKPIFVYES 60 +IR A +D ++A L Q+ H + R DIF + + + + E + V+ Sbjct: 2 IIREATVQDYEEVARLHTQVHEAHVKERGDIFRSNEPTLNPSFFQAAVQGEKSTVLVFVD 61 Query: 61 DEGKVVAHLFLQLQEKRDLPR-KSFKTLYIDDLCIDEEVRGQQIGQKLMDFARQYAKKHG 119- + K+ A+ + L + LP + KT+YI DLC+DE RG IG+ + + Y K H Sbjct: 62 EREKIGAYSVIHLVQTPLLPTMQQRKTVYISDLCVDETRRGGGIGRLIFEAIISYGKAHQ 121- Query: 120 CYNITLNVWNDNQRAVSFYEKLGFKPQQTQME 151 I L+V++ N RA +FY LG + Q+ ME Sbjct: 122 VDAIELDVYDFNDRAKAFYHSLGMRCQKQTME 153 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1367 A DNA sequence (GBSx1452) was identified in S. agalactiae <SEQ ID 4179> which encodes the amino acid sequence <SEQ ID 4180>. Analysis of this protein sequence reveals the following: TABLE-US-04033 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3285(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9785> which encodes amino acid sequence <SEQ ID 9786> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04034 >GP: BAB06554 GB: P001516 unknown conserved protein [Bacillus halodurans] Identities = 108/211 (51%), Positives = 149/211 (70%) Query: 7 EDVILNATENMVHHKLKNDPSGHDWFHIVRVRNLAVELAHKEGANTFICQMAALLHDIID 66 E IL + E V +L ++ SGHDW+HI RV +A + +E + F+ Q+AAL HD+ID Sbjct: 3 EQAILQSAEAWVKKQLMDEYSGHDWYHIRRVTLMAKAIGEQEKVDVFVVQIAALFHDLID 62 Query: 67 DKICQDSKQASYELTQWLYSQDLAIAEVEHILDILENISFKAGTGLTMKTLEGQIVQDAD 126- DK+ D + A +L W+ + + +++H +DI+ ISFK G G ++ T E +VQDAD Sbjct: 63 DKLVDDPETAKQQLIDWMEAAGVPSQKIDHTMDIINTISFKGGHGQSLATREAMVVQDAD 122- Query: 127 RLDAMGAIGIARTMAYSGSKGRLIHDPNLKPRENLTLEEYRNGQDTAIIHFYEKLLKLKD 18- 6 RLDA+GAIGIART AYSG+KG+ I+DP L RE +T+EEYR+G+ TAI HFYEKL KLKD Sbjct: 123 RLDALGAIGIARTFAYSGNKGQPIYDPELPIRETMTVEEYRHGKSTAINHFYEKLFKLKD 18- 2 Query: 187 LMNTKQGKMLAQKRHDFLELYLAEFYAEWNG 217 LMNT+ GK LA++RH F+E ++ F +EWNG Sbjct: 183 LMNTETGKQLAKERHVFMEQFIERFLSEWNG 213 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1368 A DNA sequence (GBSx1453) was identified in S. agalactiae <SEQ ID 4181> which encodes the amino acid sequence <SEQ ID 4182>. Analysis of this protein sequence reveals the following: TABLE-US-04035 Possible site: 21 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04036 !GB: U25448 internalin [Listeria monocytogenes] !GB: U25448 internalin [Listeria monocytogenes] !GB: U25448 internalin [Listeria monocytogenes] !GB: U25448 internalin [Listeria monocytogenes] >GP: AAA69530 GB: U25448 internalin [Listeria monocytogenes] Identities = 78/253 (30%), Positives = 132/253 (51%), Gaps = 2/253 (0%) Query: 531 LKQLWMTNTGITDYSFLDKMPLLEGLDISQNGIKDLSFLTKYKQLSLIAAANNGITSLKP 59- 0 L Q+ +N +TD + L + L + ++ N I D++ L L+ + NN IT + P Sbjct: 26 LTQINFSNNQLTDITPLKDLTKLVDILMNNNQIADITPLANLSNLTGLTLFNNQITDIDP 85 Query: 591 LAELPNLQFLVLSHNNISDLTPLSNLTKLQELYLDHNNVKNLSALSGKKDLKVLDLSNNK 65- 0 L L NL L LS N ISD++ LS LT LQ+L L N V +L L+ L+ LD+S+NK Sbjct: 86 LKNLTNLNRLELSSNTISDISALSGLTSLQQLSLG-NQVTDLKPLANLTTLERLDISSNK 144- Query: 651 SADLSTL-KTTSLETLLLNETNTSNLSFLKQNPKVSNLTINNAKLASLDGIEESDEIVKV 70- 9 +D+S L K T+LE+L+ S+++ L + L++N +L + + + + Sbjct: 145 VSDISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIGTLASLTNLTDL 20- 4 Query: 710 EAEGNQIKSLVLKNKQGSLKFLNVTNNQLTSLEGVNNYTSLETLSVSKNKLESLDIKTPN 76- 9 + NQI +L L L + NQ++++ + T+L L +++N+LE + + Sbjct: 205 DLANNQISNLAPLPGLTKLTELKLGANQISNIXPLAGLTALTNLELNENQLEDISPISNL 26- 4 Query: 770 KTVTNLDFSHNNV 782 K +T L NN+ Sbjct: 265 KNLTYLTLYFNNI 277 Identities = 91/300 (30%), Positives = 141/300 (46%), Gaps = 42/300 (14%) Query: 519 INDMTPVLQFKKLKQLWMTNTGITDYSFLDKMPLLEGLDISQNGIKD---LSFLTKYKQL 57- 5 I D+TP+ L L + N ITD L + L L++S N I D LS LT +QL Sbjct: 58 IADITPLANLSNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQL 117- Query: 576 SLIAAANNGITSLKPLA----------------------ELPNLQFLVLSHNNISDLTPL 61- 3 SL N +T LKPLA +L NL+ L+ ++N ISD+TPL Sbjct: 118 SL----GNQVTDLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPL 17- 3 Query: 614 SNLTKLQELYLDHNNVKNLSALSGKKDLKVLDLSNNKSADLSTLK-TTSLETLLLNETNT 67- 2 LT L EL L+ N +K++ L+ +L LDL+NN+ ++L+ L T L L L Sbjct: 174 GILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLPGLTKLTELKLGANQI 23- 3 Query: 673 SNLSFLKQNPKVSNLTINNAKLASLDGIEESDEIVKVEAEGNQIKSLVLKNKQGSLKFLN 73- 2 SN+ L ++NL +N +L + I + + N I + + L+ L Sbjct: 234 SNIXPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISPVSSLTKLQRLF 29- 3 Query: 733 VTNNQLTSLEGVNNYTSLETLSVSKNKLESLDIKTPNKTVTNLDFSHNNVPTSQLKLNEK 79- 2 NN+++ + +N T++ LS N++ L TP +T + +QL LN++ Sbjct: 294 FYNNKVSDVSSLANLTNINWLSAGHNQISDL---TPLANLTRI---------TQLGLNDQ 34- 1 Identities = 73/253 (28%), Positives = 124/253 (48%), Gaps = 4/253 (1%) Query: 540 GITDYSFLDKMPLLEGLDISQNGIKDLSFLTKYKQLSLIAAANNGITSLKPLAELPNLQF 59- 9 GI L+ + L ++ S N + D++ L +L I NN I + PLA L NL Sbjct: 13 GIKSIDGLEYLNNLTQINFSNNQLTDITPLKDLTKLVDILMNNNQIADITPLANLSNLTG 72 Query: 600 LVLSHNNISDLTPLSNLTKLQELYLDHNNVKNLSALSGKKDLKVLDLSNNKSADLSTLKT 65- 9 L L +N I+D+ PL NLT L L L N + ++SALSG L+ L L N + Sbjct: 73 LTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSLGNQVTDLKPLANL 132- Query: 660 TSLETLLLNETNTSNLSFLKQNPKVSNLTINNAKLASLDGIEESDEIVKVEAEGNQIKSL 71- 9 T+LE L ++ S++S L + + +L N +++ + + + ++ GNQ+K + Sbjct: 133 TTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDI 19- 2 Query: 720 VLKNKQGSLKFLNVTNNQLTSLEGVNNYTSLETLSVSKNKLESLDIKTPNKTVTNLDFSH 77- 9 +L L++ NNQ+++L + T L L + N++ ++ +TNL+ + Sbjct: 193 GTLASLTNLTDLDLANNQISNLAPLPGLTKLTELKLGANQISNIXPLAGLTALTNLELNE 25- 2 Query: 780 NNV----PTSQLK 788 N + P S LK Sbjct: 253 NQLEDISPISNLK 265 Identities = 56/209 (26%), Positives = 115/209 (54%), Gaps = 2/209 (0%) Query: 575 LSLIAAANNGITSLKPLAELPNLQFLVLSHNNISDLTPLSNLTKLQELYLDHNNVKNLSA 63- 4 ++ + A GI S+ L L NL + S+N ++D+TPL +LTKL ++ +++N + +++ Sbjct: 4 VTTLQADRLGIKSIDGLEYLNNLTQINFSNNQLTDITPLKDLTKLVDILMNNNQIADITP 63 Query: 635 LSGKKDLKVLDLSNNKSADLSTLKT-TSLETLLLNETNTSNLSFLKQNPKVSNLTINNAK 69- 3 L+ +L L L NN+ D+ LK T+L L L+ S++S L + L++ N + Sbjct: 64 LANLSNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSLGN-Q 122- Query: 694 LASLDGIEESDEIVKVEAEGNQIKSLVLKNKQGSLKFLNVTNNQLTSLEGVNNYTSLETL 75- 3 + L + + +++ N++ + + K +L+ L TNNQ++ + + T+L+ L Sbjct: 123 VTDLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPLGILTNLDEL 18- 2 Query: 754 SVSKNKLESLDIKTPNKTVTNLDFSHNNV 782 S++ N+L+ + +T+LD ++N + Sbjct: 183 SLNGNQLKDIGTLASLTNLTDLDLANNQI 211 Identities = 61/228 (26%), Positives = 118/228 (51%), Gaps = 3/228 (1%) Query: 483 LATVTKINIGQRTNPFQRFGLSLMPNIEVLGIGFTPINDMTPVLQFKKLKQLWMTNTGIT 54- 2 L ++ ++++G + + L+ + +E L I ++D++ + + L+ L TN I+ Sbjct: 111 LTSLQQLSLGNQVTDLKP--LANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQIS 16- 8 Query: 543 DYSFLDKMPLLEGLDISQNGIKDLSFLTKYKQLSLIAAANNGITSLKPLAELPNLQFLVL 60- 2 D + L + L+ L ++ N +KD+ L L+ + ANN I++L PL L L L L Sbjct: 169 DITPLGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLPGLTKLTELKL 22- 8 Query: 603 SHNNISDLTPLSNLTKLQELYLDHNNVKNLSALSGKKDLKVLDLSNNKSADLSTLKT-TS 66- 1 N IS++ PL+ LT L L L+ N ++++S +S K+L L L N +D+S + + T Sbjct: 229 GANQISNIXPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISPVSSLTK 28- 8 Query: 662 LETLLLNETNTSNLSFLKQNPKVSNLTINNAKLASLDGIEESDEIVKV 709 L+ L S++S L ++ L+ + +++ L + I ++ Sbjct: 289 LQRLFFYNNKVSDVSSLANLTNINWLSAGHNQISDLTPLANLTRITQL 336 Identities = 60/286 (20%), Positives = 129/286 (44%), Gaps = 24/286 (8%) Query: 369 SNKLSDEDQKKLIYLAEKLGLNPNQIEVLTSEDGSIIFKYPHDDHSHTIASKDIEIGKPI 42- 8 +N+++D D K + +L L+ N I +++ G + + + +G + Sbjct: 77 NNQITDIDPLKNLTNLNRLELSSNTISDISALSG-------------LTSLQQLSLGNQV 123- Query: 429 PDGHHDHSHAKDKVGMATLKQIGFDDEIIQDILHADAPTPFPSNETNPEKMRQW--LATV 48- 6 D K + TL+++ + DI T S ++ L + Sbjct: 124 TD-------LKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPLGIL 17- 6 Query: 487 TKIN-IGQRTNPFQRFG-LSLMPNIEVLGIGFTPINDMTPVLQFKKLKQLWMTNTGITDY 54- 4 T ++ + N + G L+ + N+ L + I+++ P+ KL +L + I++ Sbjct: 177 TNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLPGLTKLTELKLGANQISNI 23- 6 Query: 545 SFLDKMPLLEGLDISQNGIKDLSFLTKYKQLSLIAAANNGITSLKPLAELPNLQFLVLSH 60- 4 L + L L++++N ++D+S ++ K L+ + N I+ + P++ L LQ L + Sbjct: 237 XPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISPVSSLTKLQRLFFYN 29- 6 Query: 605 NNISDLTPLSNLTKLQELYLDHNNVKNLSALSGKKDLKVLDLSNNK 650 N +SD++ L+NLT + L HN + +L+ L+ + L L++ + Sbjct: 297 NKVSDVSSLANLTNINWLSAGHNQISDLTPLANLTRITQLGLNDQE 342 A related DNA sequence was identified in S. pyogenes <SEQ ID 4183> which encodes the amino acid sequence <SEQ ID 4184>. Analysis of this protein sequence reveals the following:

TABLE-US-04037 Possible site: 21 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04038 >GP: AAA69530 GB: U25448 internalin [Listeria monocytogenes] Identities = 88/279 (31%), Positives = 149/279 (52%), Gaps = 2/279 (0%) Query: 419 LPNLETLGIGFTPIKDISPVLQFKKLKQLLMTKTGVTDYRFLDNMPQLEGIDISQNNLKD 47- 8 L + TL IK I + L Q+ + +TD L ++ +L I ++ N + D Sbjct: 1 LDXVTTLQADRLGIKSIDGLEYLNNLTQINFSNNQLTDITPLKDLTKLVDILMNNNQIAD 60 Query: 479 ISFLSKYKNLTLVAAADNGIEDIRPLGQLPNLKFLVLSNNKISDLSPLASLHQLQELHID 53- 8 I+ L+ NLT + +N I DI PL L NL L LS+N ISD+S L+ L LQ+L + Sbjct: 61 ITPLANLSNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSL- 119- Query: 539 NNQITDLSPVSHKESLTVVDLSRNADVDLATL-QAPKLETLMVNDTKVSHLDFLKNNPNL 59- 7 NQ+TDL P+++ +L +D+S N D++ L + LE+L+ + ++S + L NL Sbjct: 120 GNQVTDLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPLGILTNL 17- 9 Query: 598 SSLSINRAQLQSLEGIEASSVIVRVEAEGNQIKSLVLKDKQGSLTFLDVTGNQLTSLEGV 65- 7 LS+N QL+ + + + + + ++ NQI +L LT L + NQ++++ + Sbjct: 180 DELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLPGLTKLTELKLGANQISNIXPL 23- 9 Query: 658 NNFTALDILSVSKNQLTNVNLSKPNKTVTNIDISHNNIS 696 TAL L +++NQL +++ K +T + + NNIS Sbjct: 240 AGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNIS 278 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04039 Identities = 346/753 (45%), Positives = 472/753 (61%), Gaps = 63/753 (8%) Query: 187 SRLGNQSNSHYRVNSSK--------IAGLHYPTSNGFLFNGRG-IKGTTPTGILVEHHNH 23- 7 SR G SN + SK +AG+ +PT +GF+ I T GI+V+H H Sbjct: 38 SRKGMTSNKIKPIKKSKKTNKTHKGVAGVDFPTDDGFILTKDSKILSKTDQGIVVDHDGH 97 Query: 238 LHFISFADLRKGGW------GSIADRYQPQKKADSKKQSPSSKKPRTENTLPKDI--KDK 28- 9 HFI +ADL+ + G+ + ++A S+ S + P DI +D Sbjct: 98 SHFIFYADLKGSPFEYLIPKGASLAKPAVAQRAASQGTSKVADPHHHYEFNPADIVAEDA 157- Query: 290 LAYLARE---LHLDI----------------------SRIRVLKTLNGEIGFEYPHDDHT 32- 4 L Y R H + S + T NG G +P D Sbjct: 158 LGYTVRHDDHFHYILKSSLSGQTQAQAKQVATRLPQTSSLVSTATANGIPGLHFPTSDGF 21- 7 Query: 325 HVIMAKDIDLSKPIPNPHHDDEDH-------------HKGHHHD---ESDHKHEEHEHTK 36- 8 + ++K HD H H +D +++ E H+ + Sbjct: 218 QFNGQGIVGVTKDSILVDHDGHLHPISFADLRQGGWAHVADQYDPAKKAEKPAETHQTPE 27- 7 Query: 369 SNKLSDEDQKKLIYLAEKLGLNPNQIEVLTSEDGSIIFKYPHDDHSHTIASKDIEIGKPI 42- 8 ++ E Q+KL YLAEKLG++P+ I+ + ++DG + +YPH DH+H + DIEIGK I Sbjct: 278 LSEREKEYQEKLAYLAEKLGIDPSTIKRVETQDGKLGLEYPHHDHAHVLMLSDIEIGKDI 33- 7 Query: 429 PDGH---HDHSHAKDKVGMATLKQIGFDDEIIQDILHA-DAPTPFPSNETNPEKMRQWLA 48- 4 PD H H K KVGM TL+ +GFD+E+I DI+ DAPTPFPSNE +P M++WLA Sbjct: 338 PDPHAIEHARELEKHKVGMDTLRALGFDEEVILDIVRTHDAPTPFPSNEKDPNMMKEWLA 39- 7 Query: 485 TVTKINIGQRTNPFQRFGLSLMPNIEVLGIGFTPINDMTPVLQFKKLKQLWMTNTGITDY 54- 4 TV K+++G R +P QR GLSL+PN+E LGIGFTPI D++PVLQFKKLKQL MT TG+TDY Sbjct: 398 TVIKLDLGSRKDPLQRKGLSLLPNLETLGIGFTPIKDISPVLQFKKLKQLLMTKTGVTDY 45- 7 Query: 545 SFLDKMPLLEGLDISQNGIKDLSFLTKYKQLSLIAAANNGITSLKPLAELPNLQFLVLSH 60- 4 FLD MP LEG+DISQN +KD+SFL+KYK L+L+AAA+NGI ++PL +LPNL+FLVLS+ Sbjct: 458 RFLDNMPQLEGIDISQNNLKDISFLSKYKNLTLVAAADNGIEDIRPLGQLPNLKFLVLSN 51- 7 Query: 605 NNISDLTPLSNLTKLQELYLDHNNVKNLSALSGKKDLKVLDLSNNKSADLSTLKTTSLET 66- 4 N ISDL+PL++L +LQEL++D+N + +LS +S K+ L V+DLS N DL+TL+ LET Sbjct: 518 NKISDLSPLASLHQLQELHIDNNQITDLSPVSHKESLTVVDLSRNADVDLATLQAPKLET 57- 7 Query: 665 LLLNETNTSNLSFLKQNPKVSNLTINNAKLASLDGIEESDEIVKVEAEGNQIKSLVLKNK 72- 4 L++N+T S+L FLK NP +S+L+IN A+L SL+GIE S IV+VEAEGNQIKSLVLK+K Sbjct: 578 LMVNDTKVSHLDFLKNNPNLSSLSINRAQLQSLEGIEASSVIVRVEAEGNQIKSLVLKDK 63- 7 Query: 725 QGSLKFLNVTNNQLTSLEGVNNYTSLETLSVSKNKLESLDIKTPNKTVTNLDFSHNNVPT 78- 4 QGSL FL+VT NQLTSLEGVNN+T+L+ LSVSKN+L ++++ PNKTVTN+D SHNN+ Sbjct: 638 QGSLTFLDVTGNQLTSLEGVNNFTALDILSVSKNQLTNVNLSKPNKTVTNIDISHNNISL 69- 7 Query: 785 SQLKLNEKNIPEAVAKNFPAVVEGSMVGNGSLAEKAAMASKEDKQVSD-NTNHQKNTEKS 84- 3 + LKLNE++IPEA+AKNFPAV EGSMVGNG+ EKAAMA+K + + + +H N + Sbjct: 698 ADLKLNEQHIPEAIAKNFPAVYEGSMVGNGTAEEKAAMATKAKESAQEASESHDYNHNHT 75- 7 Query: 844 AQANADSKKENPKTHDEHHDHEETDHAHVGHHH 876 + E+ D H+HE+ + A +H Sbjct: 758 YEDEEGHAHEHRDKDDHDHEHEDENEAKDEQNH 790 SEQ ID 4182 (GBS84) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 9; MW 97.6 kDa). GBS84-His was purified as shown in FIG. 194, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1369 A DNA sequence (GBSx1454) was identified in S. agalactiae <SEQ ID 4185> which encodes the amino acid sequence <SEQ ID 4186>. This protein is predicted to be GTP-binding protein lepa (lepA). Analysis of this protein sequence reveals the following: TABLE-US-04040 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1962(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04041 >GP: CAB14493 GB: Z99117 GTP-binding protein [Bacillus subtilis] Identities = 464/603 (76%), Positives = 540/603 (88%) Query: 8 KRQEKIRNFSIIAHIDHGKSTLADRILEKTETVSSREMQAQLLDSMDLERERGITIKLNA 67 +RQ +IRNFSIIAHIDHGKSTLADRILEKT ++ REM+ QLLDSMDLERERGITIKLN+ Sbjct: 9 ERQSRIRNFSIIAHIDHGKSTLADRILEKTSAITQREMKEQLLDSMDLERERGITIKLNS 68 Query: 68 IELNYTAKDGETYIFHLIDTPGHVDFTYEVSRSLAACEGAILVVDAAQGIEAQTLANVYL 127- ++L Y AKDGE YIFHLIDTPGHVDFTYEVSRSLAACEGAILVVDAAQGIEAQTLANVYL Sbjct: 69 VQLKYKAKDGEEYIFHLIDTPGHVDFTYEVSRSLAACEGAILVVDAAQGIEAQTLANVYL 128- Query: 128 ALDNDLEILPVINKIDLPAADPERVRAEVEDVIGLDASEAVLASAKAGIGIEEILEQIVE 18- 7 ALDNDLEILPVINKIDLP+A+PERVR EVEDVIGLDASEAVLASAKAGIGIEEILEQIVE Sbjct: 129 ALDNDLEILPVINKIDLPSAEPERVRQEVEDVIGLDASEAVLASAKAGIGIEEILEQIVE 18- 8 Query: 188 KVPAPTGEVDAPLQALIFDSVYDAYRGVILQVRIVNGMVKPGDKIQMMSNGKTFDVTEVG 24- 7 KVPAPTG+ +APL+ALIFDS+YDAYRGV+ +R+V G VKPG KI+MM+ GK F+VTEVG Sbjct: 189 KVPAPTGDPEAPLKALIFDSLYDAYRGVVAYIRVVEGTVKPGQKIKMMATGKEFEVTEVG 24- 8 Query: 248 IFTPKAVGRDFLATGDVGYIAASIKTVADTRVGDTITLANNPAIEPLHGYKQMNPMVFAG 30- 7 +FTPKA + L GDVG++ ASIK V DTRVGDTIT A NPA E L GY+++NPMV+G Sbjct: 249 VFTPKATPTNELTVGDVGFLTASIKNVGDTRVGDTITSAANPAEEALPGYRKLNPMVYCG 30- 8 Query: 308 LYPIESNKYNDLREALEKLQLNDASLQFEPETSQALGFGFRCGFLGLLHMDVIQERLERE 36- 7 LYPI++ KYNDLREALEKL+LND+SLQ+E ETSQALGFGFRCGFLG+LHM++IQER+ERE Sbjct: 309 LYPIDTAKYNDLREALEKLELNDSSLQYEAETSQALGFGFRCGFLGMLHMEIIQERIERE 36- 8 Query: 368 FNIDLIMTAPSVVYHVNTTDGEMLEVSNPSEFPDPTRVDSIEEPYVKAQIMVPQEFVGAV 42- 7 FNIDLI TAPSV+Y V TDGE + V NPS PDP +++ +EEPYVKA +MVP ++VGAV Sbjct: 369 FNIDLITTAPSVIYDVYMTDGEKVVVDNPSNMPDPQKIERVEEPYVKATMMVPNDYVGAV 42- 8 Query: 428 MELAQRKRGDFVTMDYIDDNRVNVIYQIPLAEIVFDFFDKLKSSTRGYASFDYEISEYRR 48- 7 MEL Q KRG+F+ M Y+D NRV++IY +PLAEIV++FFD+LKSST+GYASFDYE+ Y+ Sbjct: 429 MELCQGKRGNFIDMQYLDANRVSIIYDMPLAEIVYEFFDQLKSSTKGYASFDYELIGYKP 48- 8 Query: 488 SQLXKMDILLNGDKVDALSFIVHKEFAYERGKLIVDKLKKIIPRQQFEVPIQAAIGQKIV 54- 7 S+L KMDI+LNG+K+DALSFIVH+++AYERGK+IV+KLK++IPRQQFEVP+QAAIGQKIV Sbjct: 489 SKLVKMDIMLNGEKIDALSFIVHRDYAYERGKVIVEKLKELIPRQQFEVPVQAAIGQKIV 54- 8 Query: 548 ARSDIKALRKNVLAKCYGGDVSRKRKLLEKQKAGKKRMKAIGSVEVPQEAFLSVLSMDDD 60- 7 ARS IKA+RKNVLAKCYGGD+SRKRKLLEKQK GK+RMK +GSVEVPQSAF++VL MDD Sbjct: 549 ARSTIKAMRKNVLAKCYGGDISRKRKLLEKQKEGKRRMKQVGSVEVPQEAFMAVLKMDDS 60- 8 Query: 608 DKK 610 KK Sbjct: 609 PKK 611 A related GBS sequence was identified <SEQ ID 10775> which encodes the amino acid sequence <SEQ ID 10776>. A further related GBS nucleic acid sequence <SEQ ID 10955> which encodes amino acid sequence <SEQ ID 10956> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 4187> which encodes the amino acid sequence <SEQ ID 4188>. Analysis of this protein sequence reveals the following: TABLE-US-04042 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1829(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04043 >GP: CAB14493 GB: Z99117 GTP-binding protein [Bacillus subtilis] Identities = 463/603 (76%), Positives = 542/603 (89%) Query: 8 KRQEKIRNFSIIAHIDHGKSTLADRILEKTETVSSREMQAQLLDSMDLERERGITIKLNA 67 +RQ +IRNFSIIAHIDHGKSTLADRILEKT ++ REM+ QLLDSMDLERERGITIKLN+ Sbjct: 9 ERQSRIRNFSIIAHIDHGKSTLADRILEKTSAITQREMKEQLLDSMDLERERGITIKLNS 68 Query: 68 IELNYTAKDGETYIFHLIDTPGHVDFTYEVSRSLAACEGAILVVDAAQGIEAQTLANVYL 127- ++L Y AKDGE YIFHLIDTPGHVDFTYEVSRSLAACEGAILVVDAAQGIEAQTLANVYL Sbjct: 69 VQLKYKAKDGEEYIFHLIDTPGHVDFTYEVSRSLAACEGAILVVDAAQGIEAQTLANVYL 128- Query: 128 ALDNDLEILPVINKIDLPAADPERVRHEVEDVIGLDASEAVLASAKAGIGIEEILEQIVE 18- 7 ALDNDLEILPVINKIDLP+A+PERVR EVEDVIGLDASEAVLASAKAGIGIEEILEQIVE Sbjct: 129 ALDNDLEILPVINKIDLPSAEPERVRQEVEDVIGLDASEAVLASAKAGIGIEEILEQIVE 18- 8 Query: 188 KVPAPTGDVDAPLQALIFDSVYDAYRGVILQVRIVNGIVKPGDKIQMMSNGKTFDVTEVG 24- 7 KVPAPTGD +APL+ALIFDS+YDAYRGV+ +R+V G VKPG KI+MM+ GK F+VTEVG Sbjct: 189 KVPAPTGDPEAPLKALIFDSLYDAYRGVVAYIRVVEGTVKPGQKIKMMATGKEFEVTEVG 24- 8 Query: 248 IFTPKAVGRDFLATGDVGYVAASIKTVADTRVGDTVTLANNPAKEALHGYKQMNPMVFAG 30- 7 +FTPKA + L GDVG++ ASIK V DTRVGDT+T A NPA+EAL GY+++NPMV+ G Sbjct: 249 VFTPKATPTNELTVGDVGFLTASIKNVGDTRVGDTITSAANPAEEALPGYRKLNPMVYCG 30- 8 Query: 308 IYPIESNKYNDLREALEKLQLNDASLQFEPETSQALGFGFRCGFLGLLHMDVIQERLERE 36- 7 +YPI++ KYNDLREALEKL+LND+SLQ+E ETSQALGFGFRCGFLG+LHM++IQER+ERE Sbjct: 309 LYPIDTAKYNDLREALEKLELNDSSLQYEAETSQALGFGFRCGFLGMLHMEIIQERIERE 36- 8 Query: 368 FNIDLIMTAPSVVYHVHTTDEDMIEVSNPSEFPDPTRVAFIEEPYVKAQIMVPQEFVGAV 42- 7 FNIDLI TAPSV+Y V+ TD + + V NPS PDP ++ +EEPYVKA +MVP ++VGAV Sbjct: 369 FNIDLITTAPSVIYDVYMTDGEKVVVDNPSNMPDPQKIERVEEPYVKATMMVPNDYVGAV 42- 8 Query: 428 MELSQRKRGDFVTMDYIDDNRVNVIYQIPLAEIVFDFFDKLKSSTRGYASFDYDMSEYRR 48- 7 MEL Q KRG+F+ M Y+D NRV++IY +PLAEIV++FFD+LKSST+GYASFDY++ Y+ Sbjct: 429 MELCQGKRGNFIDMQYLDANRVSIIYDMPLAEIVYEFFDQLKSSTKGYASFDYELIGYKP 48- 8 Query: 488 SQLVKMDILLNGDKVDALSFIVHKEFAYERGKIIVEKLKKIIPRQQFEVPIQAAIGQKIV 54- 7 S+LVKMDI+LNG+K+DALSFIVH+++AYERGK+IVEKLK++IPRQQFEVP+QAAIGQKIV Sbjct: 489 SKLVKMDIMLNGEKIDALSFIVHRDYAYERGKVIVEKLKELIPRQQFEVPVQAAIGQKIV 54- 8 Query: 548 ARSDIKALRKNVLAKCYGGDVSRKRKLLEKQKAGKKRMKAIGSVEVPQEAFLSVLSMDDD 60- 7 ARS IKA+RKNVLAKCYGGD+SRKRKLLEKQK GK+RMK +GSVEVPQEAF++VL MDD Sbjct: 549 ARSTIKAMRKNVLAKCYGGDISRKRKLLEKQKEGKRRMKQVGSVEVPQEAFMAVLKMDDS 60- 8 Query: 608 TKK 610 KK Sbjct: 609 PKK 611 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04044 Identities = 587/610 (96%), Positives = 601/610 (98%) Query: 1 MNIEDLKKRQEKIRNFSIIAHIDHGKSTLADRILEKTETVSSREMQAQLLDSMDLERERG 60 MN +DLKKRQEKIRNFSIIAHIDHGKSTLADRILEKTETVSSREMQAQLLDSMDLERERG Sbjct: 1 MNSQDLKKRQEKIRNFSIIAHIDHGKSTLADRILEKTETVSSREMQAQLLDSMDLERERG 60 Query: 61 ITIKLNAIELNYTAKDGETYIFHLIDTPGHVDFTYEVSRSLAACEGAILVVDAAQGIEAQ 120- ITIKLNAIELNYTAKDGETYIFHLIDTPGHVDFTYEVSRSLAACEGAILVVDAAQGIEAQ Sbjct: 61 ITIKLNAIELNYTAKDGETYIFHLIDTPGHVDFTYEVSRSLAACEGAILVVDAAQGIEAQ 120- Query: 121 TLANVYLALDNDLEILPVINKIDLPAADPERVRAEVEDVIGLDASEAVLASAKAGIGIEE 18- 0 TLANVYLALDNDLEILPVINKIDLPAADPERVR EVEDVIGLDASEAVLASAKAGIGIEE Sbjct: 121 TLANVYLALDNDLEILPVINKIDLPAADPERVRHEVEDVIGLDASEAVLASAKAGIGIEE 18- 0 Query: 181 ILEQIVEKVPAPTGEVDAPLQALIFDSVYDAYRGVILQVRIVNGMVKPGDKIQMMSNGKT 24- 0 ILEQIVEKVPAPTG+VDAPLQALIFDSVYDAYRGVILQVRIVNG+VKPGDKIQMMSNGKT Sbjct: 181 ILEQIVEKVPAPTGDVDAPLQALIFDSVYDAYRGVILQVRIVNGIVKPGDKIQMMSNGKT 24- 0 Query: 241 FDVTEVGIFTPKAVGRDFLATGDVGYIAASIKTVADTRVGDTITLANNPAIEPLHGYKQM 30- 0 FDVTEVGIFTPKAVGRDFLATGDVGY+AASIKTVADTRVGDT+TLANNPA E LHGYKQM Sbjct: 241 FDVTEVGIFTPKAVGRDFLATGDVGYVAASIKTVADTRVGDTVTLANNPAKEALHGYKQM 30- 0 Query: 301 NPMVFAGLYPIESNKYNDLREALEKLQLNDASLQFEPETSQALGFGFRCGFLGLLHMDVI 36- 0 NPMVFAG+YPIESNKYNDLREALEKLQLNDASLQFEPETSQALGFGFRCGFLGLLHMDVI Sbjct: 301 NPMVFAGIYPIESNKYNDLREALEKLQLNDASLQFEPETSQALGFGFRCGFLGLLHMDVI 36- 0 Query: 361 QERLEREFNIDLIMTAPSVVYHVNTTDGEMLEVSNPSEFPDPTRVDSIEEPYVKAQIMVP 42- 0 QERLEREFNIDLIMTAPSVVYHV+TTD +M+EVSNPSEFPDPTRV IEEPYVKAQIMVP Sbjct: 361 QERLEREFNIDLIMTAPSVVYHVHTTDEDMIEVSNPSEFPDPTRVAFIEEPYVKAQIMVP 42- 0 Query: 421 QEFVGAVMELAQRKRGDFVTMDYIDDNRVNVIYQIPLAEIVFDFFDKLKSSTRGYASFDY 48- 0 QEFVGAVMEL+QRKRGDFVTMDYIDDNRVNVIYQIPLAEIVFDFFDKLKSSTRGYASFDY Sbjct: 421 QEFVGAVMELSQRKRGDFVTMDYIDDNRVNVIYQIPLAEIVFDFFDKLKSSTRGYASFDY 48- 0 Query: 481 EISEYRRSQLXKMDILLNGDKVDALSFIVHKEFAYERGKLIVDKLKKIIPRQQFEVPIQA 54- 0 ++SEYRRSQL KMDILLNGDKVDALSFIVHKEFAYERGK+IV+KLKKIIPRQQFEVPIQA Sbjct: 481 DMSEYRRSQLVKMDILLNGDKVDALSFIVHKEFAYERGKIIVEKLKKIIPRQQFEVPIQA 54- 0 Query: 541 AIGQKIVARSDIKALRKNVLAKCYGGDVSRKRKLLEKQKAGKKRMKAIGSVEVPQEAFLS 60- 0 AIGQKIVARSDIKALRKNVLAKCYGGDVSRKRKLLEKQKAGKKRMKAIGSVEVPQEAFLS Sbjct: 541 AIGQKIVARSDIKALRKNVLAKCYGGDVSRKRKLLEKQKAGKKRMKAIGSVEVPQEAFLS 60- 0 Query: 601 VLSMDDDDKK 610 VLSMDDD KK Sbjct: 601 VLSMDDDTKK 610 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1370 A DNA sequence (GBSx1455) was identified in S. agalactiae <SEQ ID 4189> which encodes the amino acid sequence <SEQ ID 4190>. This protein is predicted to be awd gene product (ndk). Analysis of this protein sequence reveals the following: TABLE-US-04045 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2097(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04046 >GP: AAF57188 GB: AE003779 awd gene product [Drosophila melanogaster] Identities = 73/136 (53%), Positives = 100/136 (72%), Gaps = 5/136 (3%) Query: 2 EQTFFMIKPDGVKRGFIGEVISRIERRGFSIDRLEVRYADADILKRHYAELTDRPFFPTL 61 E+TF M+KPDGV+RG +G++I R E++GF + L+ +A ++L++HYA+L+ RPFFP L Sbjct: 25 ERTFIMVKPDGVQRGLVGKIIERFEQKGFKLVALKFTWASKELLEKHYADLSARPFFPGL 84 Query: 62 VDYMTSGPVIIGVISGEEVISTWRTMMGSTNPKDALPGTIRGDFAQAPSPNQATCNIVHG 121- V+YM SGPV+ V G V+ T R M+G+TNP D+LPGTIRGDF Q NI+HG Sbjct: 85 VNYMNSGPVVPMVWEGLNVVKTGRQMLGATNPADSLPGTIRGDFC-----IQVGRNIIHG 139- Query: 122 SDSPESATREIAIWFN 137 SD+ ESA +EIA+WFN Sbjct: 140 SDAVESAEKEIALWFN 155 A related DNA sequence was identified in S. pyogenes <SEQ ID 4191> which encodes the amino acid sequence <SEQ ID 4192>. Analysis of this protein sequence reveals the following: TABLE-US-04047 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2913(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04048 Identities = 30/48 (62%), Positives = 35/48 (72%) Query: 87 MMGSTNPKDALPGTIRGDFAQAPSPNQATCNIVHGSDSPESATREIAI 134 MM TNPKDAL GTIR +FAQAP + N+VHGS S +SA REIA+ Sbjct: 1 MMRVTNPKDALCGTIRENFAQAPGDDGGIFNMVHGSHSRDSARREIAL 48 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1371 A DNA sequence (GBSx1456) was identified in S. agalactiae <SEQ ID 4193> which encodes the amino acid sequence <SEQ ID 4194>. Analysis of this protein sequence reveals the following: TABLE-US-04049 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2734(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4195> which encodes the amino acid sequence <SEQ ID 4196>. Analysis of this protein sequence reveals the following:

TABLE-US-04050 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1985(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04051 Identities = 22/34 (64%), Positives = 26/34 (75%) Query: 28 SFGTIRNSTALKQLTLDSLNLLSFGTIRNSTALK 61 SFGTI+NS ALKQ + +N SFGTI+NS ALK Sbjct: 7 SFGTIQNSIALKQKAQEEINQRSFGTIQNSIALK 40 Identities = 22/34 (64%), Positives = 26/34 (75%) Query: 6 SFGTIRNSTALKLYAKQSPAFRSFGTIRNSTALK 39 SFGTI+NS ALK A++ RSFGTI+NS ALK Sbjct: 7 SFGTIQNSIALKQKAQEEINQRSFGTIQNSIALK 40 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1372 A DNA sequence (GBSx1457) was identified in S. agalactiae <SEQ ID 4197> which encodes the amino acid sequence <SEQ ID 4198>. Analysis of this protein sequence reveals the following: TABLE-US-04052 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1407(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4199> which encodes the amino acid sequence <SEQ ID 4200>. Analysis of this protein sequence reveals the following: TABLE-US-04053 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2055(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04054 Identities = 154/221 (69%), Positives = 187/221 (83%) Query: 1 MIKINFPILDEPLVLSNATILTIEDVSVYSSLVKHFYQYDVDEHLKLFDDKQKSLKATEL 60 ++ +NF +LDEP+ L TIL +EDV V+S +V++ YQY+ D LK FD K K++K +E+ Sbjct: 8 LMNLNFSLLDEPIPLRGGTILVLEDVCVFSKIVQYCYQYEEDSELKFFDHKMKTIKESEI 67 Query: 61 MLVTDILGYDVNSAPILKLIHGDLENQFNEKPEVKSMVEKLAATITELIAFECLENELDL 120- MLVTDILG+DVNS+ ILKLIH DLE+QFNEKPEVKSM++KL ATITELI FECLENELDL Sbjct: 68 MLVTDILGFDVNSSTILKLIHADLESQFNEKPEVKSMIDKLVATITELIVFECLENELDL 127- Query: 121 EYDEIKILELIKALGVKIETQSDTIFEKCFEIIQVYHYLTKKNLLVFVNSGAYLTKDEVI 18- 0 EYDEI ILELIK+LGVK+ETQSDTIFEKC EI+Q++ YLTKK LL+FVNSGA+LTKDEV Sbjct: 128 EYDEITILELIKSLGVKVETQSDTIFEKCLEILQIFKYLTKKKLLIFVNSGAFLTKDEVA 18- 7 Query: 181 KLCEYINLMQKSVLFLEPRRLYDLPQYVIDKDYFLIGENMV 221 L EYI+L +VLFLEPR LYD PQY++D+DYFLI +NMV Sbjct: 188 SLQEYISLTNLTVLFLEPRELYDFPQYILDEDYFLITKNMV 228 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1373 A DNA sequence (GBSx1458) was identified in S. agalactiae <SEQ ID 4201> which encodes the amino acid sequence <SEQ ID 4202>. Analysis of this protein sequence reveals the following: TABLE-US-04055 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0842(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9783> which encodes amino acid sequence <SEQ ID 9784> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04056 >GP: CAB83918 GB: AL162753 hypothetical protein NMA0629 [Neisseria meningitidis Z2491] Identities = 45/104 (43%), Positives = 65/104 (62%), Gaps = 2/104 (1%) Query: 4 RYMRMILMFDMPTETAEERKAYRIFRKFLLSEGFIMHQFSVYSKLLLNNTANNAMIGRLK 63 ++MR+I+ FD+P TA +RKA+ FR+FLL +G+ M Q SVYS+++ + RL Sbjct: 5 KFMRIIVFFDLPVITAAKRKAANQFRQFLLKDGYQMLQLSVYSRIVKGRDSLQKHHNRLC 64 Query: 64 VNNPKKGNITLLTVTEKQFARMVYLHGERNT--SVANSDSRLVF 105 N P++G+I L +TEKQ+A M L GE T NSD L+F Sbjct: 65 ANLPQEGSIRCLEITEKQYAAMKLLLGELKTQEKKVNSDQLLLF 108 A related DNA sequence was identified in S. pyogenes <SEQ ID 4203> which encodes the amino acid sequence <SEQ ID 4204>. Analysis of this protein sequence reveals the following: TABLE-US-04057 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0822(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04058 Identities = 97/112 (86%), Positives = 107/112 (94%) Query: 1 MSYRYMRMILMFDMPTETAEERKAYRKFRKFLLSEGFIMHQFSVYSKLLLNNTANNAMIG 60 MSYRYMRMILMFDMPT+TAEERKAYRKFRKFLLSEGFIMHQFS+YSKLLLNNTANNAMIG Sbjct: 1 MSYRYMRMILMFDMPTDTAEERKAYRKFRKFLLSEGFIMHQFSIYSKLLLNNTANNAMIG 60 Query: 61 RLKVNNPKKGNITLLTVTEKQFARMVYLHGERNTSVANSDSRLVFLGDSYDQ 112 RL+ +NP KGNITLLTVTEKQFARM+YLHGERN +ANSD RLVFLG+++D+ Sbjct: 61 RLREHNPNKGNITLLTVTEKQFARMIYLHGERNNCIANSDERLVFLGEAFDE 112 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1374 A DNA sequence (GBSx1459) was identified in S. agalactiae <SEQ ID 4205> which encodes the amino acid sequence <SEQ ID 4206>. Analysis of this protein sequence reveals the following: TABLE-US-04059 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3185(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04060 >GP: CAB83919 GB: AL162753 hypothetical protein NMA0630 [Neisseria meningitidis Z2491] Identities = 71/224 (31%), Positives = 122/224 (53%) Query: 4 WRTVVVNTHSKLSYKNNHLIFKDSYQTEMIHLSEIDILIMETTDIVLSTMLIKRLVDENI 63 WR++++ KLS + L+ + + ++ + L +I ++I+E + +++ L+ L + Sbjct: 3 WRSLLIQNGGKLSLQRRQLLIQQNGESHTVPLEDIAVIIIENRETLITAPLLSALAEHGA 62 Query: 64 LVIFCDDKRLPTAMLMPYYARHDSSLQLSRQMSWIEDVKADVWTSIIAQKILNQSFYLGE 123- ++ CD++ LP +PY H L Q++ E +K +W I+ QKILNQ+F E Sbjct: 63 TLLTCDEQFLPCGQWLPYAQYHRQLKILKLQLNISEPLKKQLWQHIVRQKILNQAFVADE 122- Query: 124 CSFFEKSQSIMNLYHDLEPFDPSNREGHAARIYFNTLFGNDFSREQDNPINAGLDYGYSL 18- 3 ++ + L ++ D NRE AA +YF LFG F+R +N +NA L+Y Y++ Sbjct: 123 TGNDLAAKRLRTLASEVRSGDTGNREAQAAALYFQALFGEKFTRNDNNAVNAALNYTYAV 18- 2 Query: 184 LLSMFAREVVKCGCMTQFGLKHANQFNQFNLASDIMEPFRPIVD 227 L + AR + G + GL H ++ N FNLA D +EP RP+ D Sbjct: 183 LRAAVARALTLYGWLPALGLFHRSELNPFNLADDFIEPLRPLAD 226 A related DNA sequence was identified in S. pyogenes <SEQ ID 4207> which encodes the amino acid sequence <SEQ ID 4208>. Analysis of this protein sequence reveals the following: TABLE-US-04061 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3185(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04062 Identities = 239/289 (82%), Positives = 271/289 (93%) Query: 1 MAGWRTVVVNTHSKLSYKNNHLIFKDSYQTEMIHLSEIDILIMETTDIVLSTMLIKRLVD 60 MAGWRTVVVNTHSKLSYKNNHLIFKD+Y+TE+IHLSEIDIL++ETTDIVLSTML+KRLVD Sbjct: 1 MAGWRTVVVNTHSKLSYKNNHLIFKDAYKTELIHLSEIDILLLETTDIVLSTMLVKRLVD 60 Query: 61 ENILVIFCDDKRLPTAMLMPYYARHDSSLQLSRQMSWIEDVKADVWTSIIAQKILNQSFY 120- EN+LVIFCDDKRLPTAMLMP+Y RHDSSLQL +QMSW E VK+ VWT+IIAQKILNQS Y Sbjct: 61 ENVLVIFCDDKRLPTAMLMPFYGRHDSSLQLGKQMSWSETVKSQVWTTIIAQKILNQSCY 120- Query: 121 LGECSFFEKSQSIMNLYHDLEPFDPSNREGHAARIYFNTLFGNDFSREQDNPINAGLDYG 18- 0 LG CS+FEKSQSIM+LYH LE FDPSNREGHAARIYFNTLFGNDFSR+ ++PINAGLDYG Sbjct: 121 LGACSYFEKSQSIMDLYHGLENFDPSNREGHAARIYFNTLFGNDFSRDLEHPINAGLDYG 18- 0 Query: 181 YSLLLSMFAREVVKCGCMTQFGLKHANQFNQFNLASDIMEPFRPIVDRIIYENRQSDFVK 24- 0 Y+LLLSMFAREVV GCMTQFGLKHANQFNQFN ASDIMEPFRP+VD+I+YENR F K Sbjct: 181 YTLLLSMFAREVVVSGCMTQFGLKHANQFNQFNFASDIMEPFRPLVDKIVYENRNQPFPK 24- 0 Query: 241 MKRELFSMFSETYSYNGKEMYLSNIVSDYTKKVIKSLNSDGNGIPEFRI 289 +KRELF++FS+T+SYNGKEMYL+NI+SDYTKKV+K+LN++G G+PEFRI Sbjct: 241 IKRELFTLFSDTFSYNGKEMYLTNIISDYTKKVVKALNNEGKGVPEFRI 289 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1375 A DNA sequence (GBSx1460) was identified in S. agalactiae <SEQ ID 4209> which encodes the amino acid sequence <SEQ ID 4210>. Analysis of this protein sequence reveals the following: TABLE-US-04063 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1109(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04064 >GP: CAB73943 GB: AL139078 hyopthetical protein Cj1523c [Campylobacter jejuni] Identities = 165/746 (22%), Positives = 291/746 (38%), Gaps = 115/746 (15%) Query: 318 LSASMIQRYDEHREDLKQLKQFVKASLPEKYQEI--FADSSKDGYAGYIEGKTNQEAFYK 37- 5 L+ S +R + L LK + Y++ F +S Y G + E ++ Sbjct: 50 LARSARKRLARRKARLNHLKHLIANEFKLNYEDYQSFDESLAKAYKGSLISP--YELRFR 107- Query: 376 YLSKLLTKQEDSENFLE--KIKNEDFLRKQRTFDNGSIPHQVHLTELKAIIRRQS----- 42- 8 L++LL+KQ+ + L K + D ++ + G+I + E K + QS Sbjct: 108 ALNELLSKQDFARVILHIAKRRGYDDIKNSDDKEKGAILKAIKQNEEK-LANYQSVGEYL 16- 6 Query: 429 --EYYPFLKENQDRIEKILTFRIPYY-----------IGPLAREKSDFAW-MTRKTDDSI 47- 4 EY+ KEN + + Y + + +++ +F + ++K ++ + Sbjct: 167 YKEYFQKFKENSKEFTNVRNKKESYERCIAQSFLKDELKLIFKKQREFGFSFSKKFEEEV 22- 6 Query: 475 RPWNFEDLVDKEKSAEAFIHRMTNNDFYLPEEKVLPKHSLIYEKFTVYNELTKV--RYKN 53- 2 F +++ + F H + N F+ +EK PK+S + F + + KN Sbjct: 227 LSVAFY-----KRALKDFSHLVGNCSFFT-DEKRAPKNSPLAFMFVALTRIINLLNNLKN 28- 0 Query: 533 EQGETYFFDSNIKQEIFDGVFKEHRKVSK--KKLLDFLAKEYEEFRIVDVIGLDKENKAF 59- 0 +G Y D + + V K K KKLL L+ +YE E + Sbjct: 281 TEGILYTKDD--LNALLNEVLKNGTLTYKQTKKLLG-LSDDYE---------FKGEKGTY 32- 8 Query: 591 NASLGTYHDLEKILDKDFLDNPDNESILEDIVQTLTLFEDREMIKKRLENYKDLFTESQL 65- 0 Y + K L + L D L +I + +TL +D +KK L Y ++Q+ Sbjct: 329 FIEFKKYKEFIKALGEHNLSQDD----LNEIAKDITLIKDEIKLKKALAKYD--LNQNQI 38- 2 Query: 651 KKLYRRHYTGWGRLSAKLINGIRDK--ESQKTILDYLIDDGRSNRNFMQLINDDGLSFKS 70- 8 L + + +S K + + E +K D+ + N IN+D F Sbjct: 383 DSLSKLEFKDHLNISFKALKLVTPLMLEGKK------YDEACNELNLKVAINEDKKDFLP 43- 6 Query: 709 IISKAQAGSHSDNLKEVVGELAGSPAIKKGILQSLKIVDELVKVMGYEPEQIVVEMAREN 76- 8 ++ N P + + I + K+++ L+K G + +I +E+ARE Sbjct: 437 AFNETYYKDEVTN-----------PVVLRAIKEYRKVLNALLKKYG-KVHKINIELAREV 48- 4 Query: 769 QTTNQGR----RNSRQRYKLLDDG---VKNLASDLNG-NILKEYPTDNQALQNERLFLYY 82- 0 + R + + YK D + L +N NILK L L+ Sbjct: 485 GKNHSQRAKIEKEQNENYKAKKDAELECEKLGLKINSKNILK-------------LRLFK 53- 1 Query: 821 LQNGRDMYTGEALDIDNLSQ---YDIDHIIPQAFIKDDSIDNRVLVSSAKNRGKSDDVPS 87- 7 Q Y+GE + I +L +IDHI P + DDS N+VLV + +N+ K + P Sbjct: 532 EQKEFCAYSGEKIKISDLQDEKMLEIDHIYPYSRSFDDSYMNKVLVFTKQNQEKLNQTP- 59- 0 Query: 878 LEIVKDCKVFWKKL--LDAKLMSQRKYDNLTKAERGGLTSDDKARFIQRQLVETRQITKH 93- 5 E + W+K+ L L ++++ L K ++ F R L +TR I + Sbjct: 591 FEAFGNDSAKWQKIEVLAKNLPTKKQKRILDK----NYKDKEQKNFKDRNLNDTRYIARL 64- 6 Query: 936 VARI---------LDERFNNELDSKGRRIRKVKIVTLKSNLVSNFRKEFGFYKIREVNNY 98- 6 V L + N +L+ ++ KV + L S R +GF N+ Sbjct: 647 VLNYTKDYLDFLPLSDDENTKLNDT-QKGSKVHVEAKSGMLTSALRHTWGFSAKDRNNHL 70- 5 Query: 987 HHAHDAYLNAVVAKAILTKYPQLEPE 1012 HHA DA + A +I+ + + E Sbjct: 706 HHAIDAVIIAYANNSIVKAFSDFKKE 731 A related DNA sequence was identified in S. pyogenes <SEQ ID 4211> which encodes the amino acid sequence <SEQ ID 4212>. Analysis of this protein sequence reveals the following: TABLE-US-04065 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0973(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04066 Identities = 881/1380 (63%), Positives = 1088/1380 (78%), Gaps = 22/1380 (1%) Query: 1 MNKPYSIGLDIGTNSVGWSIITDDYKVPAKKMRVLGNTDKEYIKKNLIGALLFDGGNTAA 60 M+K YSIGLDIGTNSVGW++ITD+YKVP+KK +VLGNTD+ IKKNLIGALLFD G TA Sbjct: 1 MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAE 60 Query: 61 DRRLKRTARRRYTRRRNRILYLQEIFAEEMSKVDDSFFHRLEDSFLVEEDKRGSKYPIFA 120- RLKRTARRRYTRR+NRI YLQEIF+ EM+KVDDSFFHRLE+SFLVEEDK+ ++PIF Sbjct: 61 ATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFG 120- Query: 121 TLQEEKDYHEKFSTIYHLRKELADKKEKADLRLIYIALAHIIKFRGHFLIEDDSFDVRNT 18- 0 + +E YHEK+ TIYHLRK+L D +KADLRLIY+ALAH+IKFRGHFLIE D + N+ Sbjct: 121 NIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGD-LNPDNS 17- 9 Query: 181 DISKQYQDFLEIFNTTFENNDLLSQNVDVEAILTDKISKSAKKDRILAQYPNQKSTGIFA 24- 0 D+ K + ++ +N FE N + + VD +AIL+ ++SKS + + ++AQ P +K G+F Sbjct: 180 DVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFG 23- 9 Query: 241 EFLKLIVGNQADFKKYFNLEDKTPLQFAKDSYDEDLENLLGQIGDEFADLFSAAKKLYDS 30- 0 + L +G +FK F+L + LQ +KD+YD+DL+NLL QIGD++ADLF AAK L D+ Sbjct: 240 NLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDA 29- 9 Query: 301 VLLSGILTVIDLSTKAPLSASMIQRYDEHREDLKQLKQFVKASLPEKYQEIFADSSKDGY 36- 0 +LLS IL V TKAPLSASMI+RYDEH +DL LK V+ LPEKY+EIF D SK+GY Sbjct: 300 ILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGY 35- 9 Query: 361 AGYIEGKTNQEAFYKYLSKLLTKQEDSENFLEKIKNEDFLRKQRTFDNGSIPHQVHLTEL 42- 0 AGYI+G +QE FYK++ +L K + +E L K+ ED LRKQRTFDNGSIPHQ+HL EL Sbjct: 360 AGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGEL 41- 9 Query: 421 KAIIRRQSEYYPFLKENQDRIEKILTFRIPYYIGPLAREKSDFAWMTRKTDDSIRPWNFE 48- 0 AI+RRQ ++YPFLK+N+++IEKILTFRIPYY+GPLAR S FAWMTRK++++I PWNFE Sbjct: 420 HAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFE 47- 9 Query: 481 DLVDKEKSAEAFIHRMTNNDFYLPEEKVLPKHSLIYEKFTVYNELTKVRYKNE-QGETYF 53- 9 ++VDK SA++FI RMTN D LP EKVLPKHSL+YE FTVYNELTKV+Y E + F Sbjct: 480 EVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAF 53- 9 Query: 540 FDSNIKQEIFDGVFKEHRKVSKKKLLDFLAKEYEEFRIVDVIGLDKENKAFNASLGTYHD 59- 9 K+ I D +FK +RKV+ K+L + K+ E F V++ G++ FNASLGTYHD Sbjct: 540 LSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDR----FNASLGTYHD 5- 96 Query: 600 LEKIL-DKDFLDNPDNESILEDIVQTLTLFEDREMIKKRLENYKDLFTESQLKKLYRRHY 65- 8 L KI+ DKDFLDN +NE ILEDIV TLTLFEDREMI++RL+ Y LF + +K+L RR Y Sbjct: 597 LLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRY 65- 6 Query: 659 TGWGRLSAKLINGIRDKESQKTILDYLIDDGRSNRNFMQLINDDGLSFKSIISKAQAGSH 71- 8 TGWGRLS KLINGIRDK+S KTILD+L DG +NRNFMQLI+DD L+FK I KAQ Sbjct: 657 TGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQ 71- 6 Query: 719 SDNLKEVVGELAGSPAIKKGILQSLKIVDELVKVMG-YEPEQIVVEMAPENQTTNQGRRN 77- 7 D+L E + LAGSPAIKKGILQ++K+VDELVKVMG ++PE IV+EMARENQTT +G++N Sbjct: 717 GDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKN 77- 6 Query: 778 SRQRYKLLDDGVKNLASDLNGNILKEYPTDNQALQNERLFLYYLQNGRDMYTGEALDIDN 83- 7 SR+R K +++G+K L S ILKE+P +N LQNE+L+LYYLQNGRDMY + LDI+ Sbjct: 777 SRERMKRIEEGIKELGS----QILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINR 83- 2 Query: 838 LSQYDIDHIIPQAFIKDDSIDNRVLVSSAKNRGKSDDVPSLEIVKDCKVFWKKLLDAKLM 89- 7 LS YD+DHI+PQ+F+KDDSIDN+VL S KNRGKSD+VPS E+VK K +W++LL+AKL+ Sbjct: 833 LSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLI 89- 2 Query: 898 SQRKYDNLTKAERGGLTSDDKARFIQRQLVETRQITKHVARILDERFNNELDSKGRRIRK 95- 7 +QRK+DNLTKAERGGL+ DKA FI+RQLVETRQITKHVA+ILD R N + D + IR+ Sbjct: 893 TQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIRE 95- 2 Query: 958 VKIVTLKSNLVSNFRKEFGFYKIREVNNYHHAHDAYLNAVVAKAILTKYPQLEPEFVYGD 10- 17 VK++TLKS LVS+FRK+F FYK+RE+NNYHHAHDAYLNAVV A++ KYP+LE EFVYGD Sbjct: 953 VKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGD 10- 12 Query: 1018 YPKYN-------SYKTRKSATEKLFFYSNIMNFFKTKVTLADGTVVVKDDIEVNNDTGEI 1- 070 Y Y+ S + AT K FFYSNIMNFFKT++TLA+G + + IE N +TGEI Sbjct: 1013 YKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEI 1- 072 Query: 1071 VWDKKKHFATVRKVLSYPQNNIVKKTEIQTGGFSKESILAHGNSDKLIPRKTKDIYLDPK 1- 130 VWDK + FATVRKVLS PQ NIVKKTE+QTGGFSKESIL NSDKLI RK KD DPK Sbjct: 1073 VWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARK-KD--WDPK 1- 129 Query: 1131 KYGGFDSPIVAYSVLVVADIKKGKAQKLKTVTELLGITIMERSRFEKNPSAFLESKGYLN 1- 190 KYGGFDSP VAYSVLVVA ++KGK++KLK+V ELLGITIMERS FEKNP FLE+KGY Sbjct: 1130 KYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKE 1- 189 Query: 1191 IRADKLIILPKYSLFELENGRRRLLASAGELQKGNELALPTQFMKFLYLASRYNESKGKP 1- 250 ++ D +I LPKYSLFELENGR+R+LASAGELQKGNELALP++++ FLYLAS Y + KG P Sbjct: 1190 VKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSP 1- 249 Query: 1251 EEIEKKQEFVNQHVSYFDDILQLINDFSKRVILADANLEKINKLYQDNKENISVDELANN 1- 310 E+ E+KQ FV QH Y D+I++ I++FSKRVILADANL+K+ Y +++ + E A N Sbjct: 1250 EDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDK-PIREQAEN 1- 308 Query: 1311 IINLFTFTSLGAPAAFKFFDKIVDRKRYTSTKEVLNSTLIHQSITGLYETRIDLGKLGED 1- 370 II+LFT T+LGAPAAFK+FD +DRKRYTSTKEVL++TLIHQSITGLYETRIDL +LG D Sbjct: 1309 IIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD 1- 368 SEQ ID 4210 (GBS317) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 27 (lane 2; MW 179.3 kDa) and in FIG. 159 (lane 5 & 6; MW 180 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 27 (lane 3; MW 154.3 kDa) and in FIG. 159 (lane 9 & 10; MW 154 kDa). GBS317-GST was purified as shown in FIG. 224, lane 9-10. GBS317-His was purified as shown in FIG. 222, lane 9. GBS317N was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 149 (lane 24; MW 116 kDa). GBS317C was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 166 (lane 6-8; MW 92 kDa). GBS317dN was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 187 (lane 7; MW 116 kDa). Purified GBS317dN-GST is shown in FIG. 245, lane 8. GBS317C was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 188 (lane 13; MW 92 kDa). Purified GBS317dC-GST is shown in FIG. 245, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1376 A DNA sequence (GBSx1461) was identified in S. agalactiae <SEQ ID 4213> which encodes the amino acid sequence <SEQ ID 4214>. Analysis of this protein sequence reveals the following:

TABLE-US-04067 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -11.94 Transmembrane 132-148 (123-156) INTEGRAL Likelihood = -11.09 Transmembrane 190-206 (183-209) INTEGRAL Likelihood = -4.94 Transmembrane 95-111 (94-115) ----- Final Results ----- bacterial membrane --- Certainty = 0.5776(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related sequence was also identified in GAS <SEQ ID 9133> which encodes the amino acid sequence <SEQ ID 9134>. Analysis of this protein sequence reveals the following: TABLE-US-04068 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.32 Transmembrane 126-142 INTEGRAL Likelihood = -6.90 Transmembrane 178-194 ----- Final Results ----- bacterial membrane --- Certainty = 0.3930(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04069 Identities = 94/204 (46%), Positives = 139/204 (68%) Query: 5 LMKDKLLVVLTWIWIISLATLATIYIAWLIYPIEIQFLKLEKVVYLKAETIYYNFNKLMI 64 +M + ++ +W+W+++LA L TIY WL YP+E+ LKLE+VV++ + I +N+N L+ Sbjct: 4 VMVENTKLLCSWVWLLALAILITIYSTWLWYPLEVDHLKLEQVVFMSKDAILHNYNGLLN 63 Query: 65 YLTHPFISDLNMPSFPSSEDGLKHFADVKYLFTLAHGLFVILTFPVIYFLRRGWKQKSIF 124- YLT+PF++ L +F SS DGLKHFADVK+LF L +F+ L +P + + K K + Sbjct: 64 YLTNPFVTRLEFANFHSSADGLKHFADVKWLFHLTQVVFLGLLYPTLKTFTQRLKTKRFW 123- Query: 125 LYEGFFKIAIMLPIFIVVCAFLLGFDQFFTLFHEVLFPGDSTWQFNPLTDPVIWILPETF 18- 4 L + +A + P+ I + A +GF+ FFTLFH+VLF GDS+W F+PL D VIWILPE F Sbjct: 124 LLQKPLILAALFPLMIGLMASFIGFEHFFTLFHQVLFVGDSSWLFDPLKDSVIWILPEVF 18- 3 Query: 185 FLHCFIIFLLIYETITIILLIIGR 208 FLHCF+ F+++YE I L+ + R Sbjct: 184 FLHCFLFFMIVYEIILWSLVGLAR 207 SEQ ID 4214 (GBS167) was expressed in and purified from E. coli. The purified protein is shown in lanes 5 & 6 of FIG. 223. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1377 A DNA sequence (GBSx1462) was identified in S. agalactiae <SEQ ID 4217> which encodes the amino acid sequence <SEQ ID 4218>. This protein is predicted to be p-nitrophenyl phosphatase (pho2). Analysis of this protein sequence reveals the following: TABLE-US-04070 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3925(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04071 >GP: CAB15219 GB: Z99120 similar to N-acetyl-glucosamine catabolism [Bacillus subtilis] Identities = 121/249 (48%), Positives = 172/249 (68%) Query: 3 YKGYLIDLDGTIYKGKSRIPAGERFIERLQEKGIPYMLVTNNTTRTPESVQEMLRGFNVE 62 YKGYLIDLDGT+Y G +I F+ L+++G+PY+ VTNN++RTP+ V + L F++ Sbjct: 4 YKGYLIDLDGTMYNGTEKIEEACEFVRTLKDRGVPYLFVTNNSSRTPKQVADKLVSFDIP 63 Query: 63 TPLETIYTATMATVDYMNDMNRGKTAYVIGEEGLKKAIADAGYVEDTKNPAYVVVGLDWN 122- E ++T +MAT ++ + + YVIGEEG+++AI + G +N +VVVG+D + Sbjct: 64 ATEEQVFTTSMATAQHIAQQKKDASVYVIGEEGIRQAIEENGLTFGGENADFVVVGIDRS 123- Query: 123 VTYDKLATATLAIQNGALFIGTNPDLNIPTERGLLPGAGSLNALLEAATRIKPVFIGKPN 18- 2 +TY+K A LAI+NGA FI TN D+ IPTERGLLPG GSL ++L +T ++PVFIGKP Sbjct: 124 ITYEKFAVGCLAIRNGARFISTNGDIAIPTERGLLPGNGSLTSVLTVSTGVQPVFIGKPE 18- 3 Query: 183 AIIMNKALEILNIPRNQAVMVGDNYLTDIMAGINNDIDTLLVTTGFTTVEEVPDLPIQPS 24- 2 +IIM +A+ +L ++ +MVGDNY TDIMAGIN +DTLLV TG T E + D +P+ Sbjct: 184 SIIMEQAMRVLGTDVSETLMVGDNYATDIMAGINAGMDTLLVHTGVTKREHMTDDMEKPT 24- 3 Query: 243 YVLASLDEW 251 + + SL EW Sbjct: 244 HAIDSLTEW 252 A related DNA sequence was identified in S. pyogenes <SEQ ID 4219> which encodes the amino acid sequence <SEQ ID 4220>. Analysis of this protein sequence reveals the following: TABLE-US-04072 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.53 Transmembrane 128-144 (128-144) ----- Final Results ----- bacterial membrane --- Certainty = 0.1213(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04073 >GP: CAB15219 GB: Z99120 similar to N-acetyl-glucosamine catabolism [Bacillus subtilis] Identities = 121/250 (48%), Positives = 166/250 (66%), Gaps = 1/250 (0%) Query: 3 YKGYLIDLDGTIYQGKNRIPAGERFIKRLQERGIPYLLVTNNTTRTPEMVQSMLANQFHV 62 YKGYLIDLDGT+Y G +I F++ L++RG+PYL VTNN++RTP+ V L + F + Sbjct: 4 YKGYLIDLDGTMYNGTEKIEEACEFVRTLKDRGVPYLFVTNNSSRTPKQVADKLVS-FDI 62 Query: 63 ETSIETIYTATMATVDYMNDMNRGKTAYVIGETGLKSAIAAAGYVEELENPAYVVVGLDS 122- + E ++T +MAT ++ + + YVIGE G++ AI G EN +VVVG+D Sbjct: 63 PATEEQVFTTSMATAQHIAQQKKDASVYVIGEEGIRQAIEENGLTFGGENADFVVVGIDR 122- Query: 123 QVTYEMLAIATLAIQKGALFIGTNPDLNIPTERGLMPGAGALNALLEAATRVKPVFIGKP 18- 2 +TYE A+ LAI+ GA FI TN D+ IPTERGL+PG G+L ++L +T V+PVFIGKP Sbjct: 123 SITYEKFAVGCLAIRNGARFISTNGDIAIPTERGLLPGNGSLTSVLTVSTGVQPVFIGKP 18- 2 Query: 183 NAIIMNKSLEVLGIQRSEAVMVGDNYLTDIMAGIQNDIATILVTTGFTRPEEVPTLPIQP 24- 2 +IIM +++ VLG SE +MVGDNY TDIMAGI + T+LV TG T+ E + +P Sbjct: 183 ESIIMEQAMRVLGTDVSETLMVGDNYATDIMAGINAGMDTLLVHTGVTKREHMTDDMEKP 24- 2 Query: 243 DHVLSSLDEW 252 H + SL EW Sbjct: 243 THAIDSLTEW 252 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04074 Identities = 207/250 (82%), Positives = 227/250 (90%), Gaps = 1/250 (0%) Query: 3 YKGYLIDLDGTIYKGKSRIPAGERFIERLQEKGIPYMLVTNNTTRTPESVQEMLRG-FNV 61 YKGYLIDLDGTIY+GK+RIPAGERFI+RLQE+GIPY+LVTNNTTRTPE VQ ML F+V Sbjct: 3 YKGYLIDLDGTIYQGKNRIPAGERFIKRLQERGIPYLLVTNNTTRTPEMVQSMLANQFHV 62 Query: 62 ETPLETIYTATMATVDYMNDMNRGKTAYVIGEEGLKKAIADAGYVEDTKNPAYVVVGLDW 121- ET +ETIYTATMATVDYMNDMNRGKTAYVIGE GLK AIA AGYVE+ +NPAYVVVGLD Sbjct: 63 ETSIETIYTATMATVDYMNDMNRGKTAYVIGETGLKSAIAAAGYVEELENPAYVVVGLDS 122- Query: 122 NVTYDKLATATLAIQNGALFIGTNPDLNIPTERGLLPGAGSLNALLEAATRIKPVFIGKP 18- 1 VTY+ LA ATLAIQ GALFIGTNPDLNIPTERGL+PGAG+LNALLEAATR+KPVFIGKP Sbjct: 123 QVTYEMLAIATLAIQKGALFIGTNPDLNIPTERGLMPGAGALNALLEAATRVKPVFIGKP 18- 2 Query: 182 NAIIMNKALEILNIPRNQAVMVGDNYLTDIMAGINNDIDTLLVTTGFTTVEEVPDLPIQP 24- 1 NAIIMNK+LE+L I R++AVMVGDNYLTDIMAGI NDI T+LVTTGFT EEVP LPIQP Sbjct: 183 NAIIMNKSLEVLGIQRSEAVMVGDNYLTDIMAGIQNDIATILVTTGFTRPEEVPTLPIQP 24- 2 Query: 242 SYVLASLDEW 251 +VL+SLDEW Sbjct: 243 DHVLSSLDEW 252 A similar DNA sequence was identified in S. pyogenes <SEQ ID 4215> which encodes amino acid sequence <SEQ ID 4216>. An alignment of the GAS and GBS sequences follows: TABLE-US-04075 Identities = 94/204 (46%), Positives = 139/204 (68%) Query: 4 VMVENTKLLCSWVWLLALAILITIYSTWLWYPLEVDHLKLEQVVFMSKDAILHNYNGLLN 63 +M + ++ +W+W+++LA L TIY WL YP+E+ LKLE+VV++ + I +N+N L+ Sbjct: 5 LMKDKLLVVLTWIWIISLATLATIYIAWLIYPIEIQFLKLEKVVYLKAETIYYNFNKLMI 64 Query: 64 YLTNPFVTRLEFANFHSSADGLKHFADVKWLFHLTQVVFLGLLYPTLKTFTQRLKTKRFW 123- YLT+PF++ L +F SS DGLKHFADVK+LF L +F+ L +P + + K K + Sbjct: 65 YLTHPFISDLNMPSFPSSEDGLKHFADVKYLFTLAHGLFVILTFPVIYFLRRGWKQKSIF 124- Query: 124 LLQKPLILAALFPLMIGLMASFIGFEHFFTLFHQVLFVGDSSWLFDPLKDSVIWILPEVF 18- 3 L + +A + P+ I + A +GF+ FFTLFH+VLF GDS+W F+PL D VIWILPE F Sbjct: 125 LYEGFFKIAIMLPIFIVVCAFLLGFDQFFTLFHEVLFPGDSTWQFNPLTDPVIWILPETF 18- 4 Query: 184 FLHCFLFFMIVYEIILWSLVGLAR 207 FLHCF+ F+++YE I L+ + R Sbjct: 185 FLHCFIIFLLIYETITIILLIIGR 208 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1378 A DNA sequence (GBSx1463) was identified in S. agalactiae <SEQ ID 4221> which encodes the amino acid sequence <SEQ ID 4222>. This protein is predicted to be oleoyl-acyl carrier protein thioesterase. Analysis of this protein sequence reveals the following: TABLE-US-04076 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3332(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04077 >GP:BAB02069 GB:AB026647 acyl carrier protein thioesterase [Arabidopsis thaliana] Identities = 59/248 (23%), Positives = 104/248 (41%), Gaps = 30/248 (12%) Query: 2 GLLYRETYEVPFYESDTNHYMKLPQLLALALQISAKQSLKLGIGDD-----IVFKRYGLV 56 GL Y+E + V YE +N + + L ++ + +G D ++ L+ Sbjct: 81 GLSYKEKFVVRSYEVGSNKTATVETIANLLQEVGCNHAQSVGFSTDGFATTTTMRKLHLI 140- Query: 57 WVVTDYIIDIERLPKHAEKIVIETEAKAHNKLLCYRYFYIYGE-DGQKIITISSAFVLMD 115- WV I+I + P + + IET ++ ++ R + + G+ +S +V+M+ Sbjct: 141 WVTARMHIEIYKYPAWGDVVEIETWCQSEGRIGTRRDWILKDSVTGEVTGRATSKWVMMN 20- 0 Query: 116 FKTRKIHPVLDDITSIY---------------QSQRIKKVIRGPKYHPIGDSKVKQYHVR 16- 0 TR++ V DD+ Y ++ +KK+ PK + R Sbjct: 201 QDTRRLQKVSDDVRDEYLVFCPQEPRLAFPEENNRSLKKI---PKLEDPAQYSMIGLKPR 25- 7 Query: 161 YFDLDMNGHVNNSKYLEWMYDVLDLDFLSSHIPKKIDLKYIKEIQYGTDIKSHWYQDGLV 22- 0 DLDMN HVNN Y+ W+ + + + + +H + I L Y +E Q + D L Sbjct: 258 RADLDMNQHVNNVTYIGWVLESIPQEIVDTHELQVITLDYRRECQQDDVV------DSLT 31- 1 Query: 221 TRHDIIGG 228 T IGG Sbjct: 312 TTTSEIGG 319 A related DNA sequence was identified in S. pyogenes <SEQ ID 4223> which encodes the amino acid sequence <SEQ ID 4224>. Analysis of this protein sequence reveals the following: TABLE-US-04078 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.88 Transmembrane 21-37 (21-38) ----- Final Results ----- bacterial membrane --- Certainty = 0.2550(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04079 >GP:AAB71730 GB:U65643 acyl-ACP thioesterase [Myristica fragrans] Identities = 41/128 (32%), Positives = 67/128 (52%), Gaps = 11/128 (8%) Query: 33 FIFMIKRGGLLVDILAYFALLNPDTRKVATIPEDLVAPFETDFVKKLHRV-----PKMPL 87 - F+ K G +L + + ++N TR+++ IPE++ E FV+ H V K+P Sbjct: 147 FLRDCKTGEILTRATSVWVMMNKRTRRLSKIPEEVRVEIEPYFVE--HGVLDEDSRKLPK 20- 4 Query: 88 LEQS----IDRDYYVRYFDIDMNGHVNNSKYLDWMYDVLGCEFLKTHQPLKMTLKYVKEV 143- L + I R R+ D+D+N HVNN KY+ W+ + + L++H+ MTL+Y KE Sbjct: 205 LNDNTANYIRRGLAPRWSDLDVNQHVNNVKYIGWILESVPSSLLESHELYGMTLEYRKEC 26- 4 Query: 144 SPGGQITS 151 G + S Sbjct: 265 GKDGLLQS 272 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04080 Identities = 62/144 (43%), Positives = 94/144 (65%) Query: 101 GQKIITISSAFVLMDFKTRKIHPVLDDITSIYQSQRIKKVIRGPKYHPIGDSKVKQYHVR 16- 0 G ++ I + F L++ TRK+ + +D+ + +++ +KK+ R PK + S + Y+VR Sbjct: 40 GGLLVDILAYFALLNPDTRKVATIPEDLVAPFETDFVKKLHRVPKMPLLEQSIDRDYYVR 99 Query: 161 YFDLDMNGHVNNSKYLEWMYDVLDLDFLSSHIPKKIDLKYIKEIQYGTDIKSHWYQDGLV 22- 0 YFD+DMNGHVNNSKYL+WMYDVL +FL +H P K+ LKY+KE+ G I S ++ D L Sbjct: 100 YFDIDMNGHVNNSKYLDWMYDVLGCEFLKTHQPLKMTLKYVKEVSPGGQITSSYHLDQLT 15- 9 Query: 221 TRHDIIGGDAIHAQARIEWQEKKE 244 + H I ++AQA IEW+ K+ Sbjct: 160 SYHQITSDGQLNAQAMIEWRAIKQ 183 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1379 A DNA sequence (GBSx1464) was identified in S. agalactiae <SEQ ID 4225> which encodes the amino acid sequence <SEQ ID 4226>. This protein is predicted to be coproporphyrinogen III oxidase. Analysis of this protein sequence reveals the following: TABLE-US-04081 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1484(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04082 >GP:BAB05062 GB:AP001511 coproporphyrinogen III oxidase [Bacillus halodurans] Identities = 173/375 (46%), Positives = 248/375 (66%), Gaps = 5/375 (1%) Query: 5 PTSAYVHIPFCTQICYYCDFSKVFIKNQPVDAYLQALIREFR----SYDITELRTLYIGG 60 P +AY+HIPFC ICYYCDF+K ++KNQPV+ YLQAL E L+TLY+GG Sbjct: 2 PKAAYIHIPFCEHICYYCDFNKFYLKNQPVNEYLQALETEMAMVVAEQPTKSLQTLYVGG 61 Query: 61 GTPTSISAVQLDYLLTELSRDLNLNTLEEFTIEANPGDLTVDKIEVLQKSAVNRVSLGVQ 120- GTPT+++A QL LL + R L L+ LEEFT E NP + +K++VL+ V+R+S+GVQ Sbjct: 62 GTPTALTADQLAQLLASIKRTLPLSDLEEFTFEVNPDSIDEEKLDVLRSYGVDRLSIGVQ 121- Query: 121 TFNDKHLKRIGRSHNEAQIYSTIDALKTAGFQNISIDLIYALPGQTMDDVRSNVAKALSL 18- 0 F LK IGR+H++ + ++ + AGF N+S+DL+ LP QT + + +A +L Sbjct: 122 AFQPLLLKEIGRTHDQKSVEQAVEKSRQAGFANLSLDLMLGLPKQTPEMFAETLKEAFAL 18- 1 Query: 181 NIPHLSLYSLILEHHTVFMNKMRRGKLHLPTEDLEAEMFEYIISEMERNGFEHYEISNFT 24- 0 + HLS YSL +E TVF N+ R+G+L LP ED E +M+ + E E++GF+ YEISNF Sbjct: 182 EVEHLSCYSLKVEAKTVFYNRQRQGRLTLPPEDDEVKMYRQLCYETEKHGFKQYEISNFA 24- 1 Query: 241 KPGFESRHNLMYWDNVEYYGVGAGASGYLDGIRYRNRGPIQHYLKGVSEGNARLSE-EVL 29- 9 K G+ESRHNL+YW+N EYYG GAGA GY+ G+RY N GP+ YL+ + EG + E + Sbjct: 242 KKGYESRHNLVYWNNDEYYGFGAGAHGYVGGVRYMNHGPLPKYLQAMEEGRRPVFESHHV 30- 1 Query: 300 SKNEMMEEELFLGLRKKEGVSIGKFEQKFGTSFEKRYGQIVQELQSDGLLKENNGFIQMT 35- 9 S+ E MEE++FLGLRK+ GV F ++FG S Y + + +L + LL+ + +++T Sbjct: 302 SRVEQMEEQMFLGLRKRSGVEERVFVERFGVSMFSLYEKQIAQLVARCLLERTDDRVRLT 36- 1 Query: 360 KKGLFLGDTVAEKFI 374 +GL LG+ V E+F+ Sbjct: 362 DEGLLLGNEVFEQFL 376 A related DNA sequence was identified in S. pyogenes <SEQ ID 4227> which encodes the amino acid sequence <SEQ ID 4228>. Analysis of this protein sequence reveals the following: TABLE-US-04083 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3202(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04084 Identities = 304/376 (80%), Positives = 343/376 (90%) Query: 1 MLKKPTSAYVHIPFCTQICYYCDFSKVFIKNQPVDAYLQALIREFRSYDITELRTLYIGG 60 M KKPTSAYVHIPFCTQICYYCDFSKVFI+NQPVDAYL+ALI+EF SY I +L+TLYIGG Sbjct: 33 MSKKPTSAYVHIPFCTQICYYCDFSKVFIQNQPVDAYLKALIQEFDSYGIRDLKTLYIGG 92 Query: 61 GTPTSISAVQLDYLLTELSRDLNLNTLEEFTIEANPGDLTVDKIEVLQKSAVNRVSLGVQ 120- GTPT+I+A QL+YLL L R+LNL+ LEEFTIEANPGDLT +KI VLQ+SAVNR+SLGVQ Sbjct: 93 GTPTAITAKQLEYLLNHLERNLNLDDLEEFTIEANPGDLTPEKIAVLQRSAVNRISLGVQ 152- Query: 121 TFNDKHLKRIGRSHNEAQIYSTIDALKTAGFQNISIDLIYALPGQTMDDVRSNVAKALSL 18- 0 TFN+K LK+IGRSHNE QIYSTI LKTAGF NISIDLIYALPGQT+D V+ NVAKAL+L Sbjct: 153 TFNNKQLKQIGRSHNEEQIYSTIANLKTAGFHNISIDLIYALPGQTLDQVKENVAKALAL 21- 2 Query: 181 NIPHLSLYSLILEHHTVFMNKMRRGKLHLPTEDLEAEMFEYIISEMERNGFEHYEISNFT 24- 0 +IPHLSLYSLILEHHTVFMNKMRRGKL+LPTEDLEAEMFEYIISEME NGFEHYEISNFT Sbjct: 213 DIPHLSLYSLILEHHTVFMNKMRRGKLNLPTEDLEAEMFEYIISEMEANGFEHYEISNFT 27- 2 Query: 241 KPGFESRHNLMYWDNVEYYGVGAGASGYLDGIRYRNRGPIQHYLKGVSEGNARLSEEVLS 30- 0 KPGFESRHNLMYWDNVEY+G GAGASGYL+GIRY+NR PIQHYLK V GNARL+EEVL Sbjct: 273 KPGFESRHNLMYWDNVEYFGCGAGASGYLNGIRYQNRVPIQHYLKAVEAGNARLNEEVLR 33- 2 Query: 301 KNEMMEEELFLGLRKKEGVSIGKFEQKFGTSFEKRYGQIVQELQSDGLLKENNGFIQMTK 36- 0 K EMMEEELFLGLRKK GVSI +F++KFG SFE+RYG IV+ELQ+ GLL +++ F++MTK Sbjct: 333 KEEMMEEELFLGLRKKTGVSIQRFQEKFGMSFEERYGNIVRELQNQGLLVKDDAFVRMTK 39- 2 Query: 361 KGLFLGDTVAEKFIVE 376 KGLFLGD+VAE+FI++ Sbjct: 393 KGLFLGDSVAERFILD 408 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1380 A DNA sequence (GBSx1465) was identified in S. agalactiae <SEQ ID 4229> which encodes the amino acid sequence <SEQ ID 4230>. Analysis of this protein sequence reveals the following:

TABLE-US-04085 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3729(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1381 A DNA sequence (GBSx1466) was identified in S. agalactiae <SEQ ID 4231> which encodes the amino acid sequence <SEQ ID 4232>. Analysis of this protein sequence reveals the following: TABLE-US-04086 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2989(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4233> which encodes the amino acid sequence <SEQ ID 4234>. Analysis of this protein sequence reveals the following: TABLE-US-04087 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2993(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04088 Identities = 36/109 (33%), Positives = 58/109 (53%), Gaps = 6/109 (5%) Query: 9 WAKHKYLVLSKSQKIYLDIRQTLKSPNCT---VLDVQSLIDQAVLLEESPSQVTNAYMHI 65 WA KY V++ SQ+ Y +R+ K + VL LI++A + + + AY H+ Sbjct: 13 WAYQKYWVMAHSQQHYNALRELFKGNQWSEEKVLTFHCLIEEAQAIPPTVKSLRTAYQHV 72 Query: 66 WGYFKNKAERQEKEEFLTLLEKYRKTGYQRRKLLAFLKQLLAKYPNSYL 114 WGYFK A ++EK+ F L + + ++L FL+++ A Y SYL Sbjct: 73 WGYFKKVASQEEKDHFKDLDAQLET---KSEEMLCFLQEMTAHYQPSYL 118 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1382 A DNA sequence (GBSx1467) was identified in S. agalactiae <SEQ ID 4235> which encodes the amino acid sequence <SEQ ID 4236>. This protein is predicted to be mrsA (mrsA). Analysis of this protein sequence reveals the following: TABLE-US-04089 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.96 Transmembrane 56-72 (56-72) ----- Final Results ----- bacterial membrane --- Certainty = 0.1383(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04090 >GP:CAB11970 GB:Z99105 similar to phosphoglucomutase (glycolysis) [Bacillus subtilis] Identities = 284/451 (62%), Positives = 353/451 (77%), Gaps = 4/451 (0%) Query: 1 MGKYFGTDGVRGEANVELTPELAFKLGRFGGYVLSQHETDRPRVFVARDTRISGEMLESA 60 MGKYFGTDGVRG AN ELTPELAFK+GRFGGYVL++ + RP+V + RDTRISG MLE A Sbjct: 1 MGKYFGTDGVRGVANSELTPELAFKVGRFGGYVLTK-DKQRPKVLIGRDTRISGHMLEGA 59 Query: 61 LIAGLLSVGIEVYKLGVLATPGVSYLVRTEKASAGVMISASHNPALDNGIKFFGSDGFKL 120- L+AGLLS+G EV +LGV++TPGVSYL + A AGVMISASHNP DNGIKFFG DGFKL Sbjct: 60 LVAGLLSIGAEVMRLGVISTPGVSYLTKAMDAEAGVMISASHNPVQDNGIKFFGGDGFKL 119- Query: 121 DDDRELEIEALLDAKEDTLPRPSAQGLGTLVDYPEGLRKYEKFMESTGI-DLEGMKVALD 17- 9 D++E EIE L+D ED LPRP LG + DY EG +KY +F++ T D G+ VALD Sbjct: 120 SDEQEAEIERLMDEPEDKLPRPVGADLGLVNDYFEGGQKYLQFLKQTADEDFTGIHVALD 17- 9 Query: 180 TANGAATASARNIFLDLNADISVIGDQPDGLNINDGVGSTHPEQLQSLVRENGSDIGLAF 23- 9 ANGA ++ A ++F DL+AD+S +G P+GLNINDGVGSTHPE L + V+E +D+GLAF Sbjct: 180 CANGATSSLATHLFADLDADVSTMGTSPNGLNINDGVGSTHPEALSAFVKEKNADLGLAF 23- 9 Query: 240 DGDSDRLIAVDENGEIVDGDKIMFIIGKYLSDKGQLAQNTIVTTVMSNLGFHKALDREGI 29- 9 DGD DRLIAVDE G IVDGD+IM+I K+L +G+L +T+V+TVMSNLGF+KAL++EGI Sbjct: 240 DGDGDRLIAVDEKGNIVDGDQIMYICSKHLKSEGRLKDDTVVSTVMSNLGFYKALEKEGI 29- 9 Query: 300 HKAITAVGDRYVVEEMRKSGYNLGGEQSGHVIIMDYNTTGDGQLTAIQLTKVMKETGKKL 35- 9 TAVGDRYVVE M+K GYN+GGEQSGH+I +DYNTTGDG L+AI L +K TGK L Sbjct: 300 KSVQTAVGDRYVVEAMKKDGYNVGGEQSGHLIFLDYNTTGDGLLSAIMLMNTLKATGKPL 35- 9 Query: 360 SELASEVTIYPQKLVNIRVENNMKDKAMEVPAIAEIIAKMEEEMDGNGRILVRPSGTEPL 41- 9 SELA+E+ +PQ LVN+RV + K K E + +I+++E+EM+G+GRILVRPSGTEPL Sbjct: 360 SELAAEMQKFPQLLVNVRVTD--KYKVEENEKVKAVISEVEKEMNGDGRILVRPSGTEPL 41- 7 Query: 420 LRVMAEAPTNEAVDYYVDTIADVVRTEIGLD 450 +RVMAEA T E D YV+ I +VVR+E+GL+ Sbjct: 418 VRVMAEAKTKELCDEYVNRIVEVVRSEMGLE 448 A related DNA sequence was identified in S. pyogenes <SEQ ID 4237> which encodes the amino acid sequence <SEQ ID 4238>. Analysis of this protein sequence reveals the following: TABLE-US-04091 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.96 Transmembrane 56-72 (56-72) ----- Final Results ----- bacterial membrane --- Certainty = 0.1383(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04092 >GP:CAB11970 GB:Z99105 similar to phosphoglucomutase (glycolysis) [Bacillus subtilis] Identities = 287/451 (63%), Positives = 346/451 (76%), Gaps = 4/451 (0%) Query: 1 MGKYFGTDGVRGEANVELTPELAFKLGRFGGYVLSQHETERPKVFVARDTRISGEMLESA 60 MGKYFGTDGVRG AN ELTPELAFK+GRFGGYVL++ + +RPKV + RDTRISG MLE A Sbjct: 1 MGKYFGTDGVRGVANSELTPELAFKVGRFGGYVLTK-DKQRPKVLIGRDTRISGHMLEGA 59 Query: 61 LIAGLLSVGIEVYKLGVLATPGVSYLVRTEKASAGVMISASHNPALDNGIKFFGNDGFKL 120- L+AGLLS+G EV +LGV++TPGVSYL + A AGVMISASHNP DNGIKFFG DGFKL Sbjct: 60 LVAGLLSIGAEVMRLGVISTPGVSYLTKAMDAEAGVMISASHNPVQDNGIKFFGGDGFKL 119- Query: 121 ADDQELEIEALLDAPEDTLPRPSAEGLGTLVDYPEGLRKYEKFLVTTGT-DLSGMTVALD 17- 9 +D+QE EIE L+D PED LPRP LG + DY EG +KY +FL T D +G+ VALD Sbjct: 120 SDEQEAEIERLMDEPEDKLPRPVGADLGLVNDYFEGGQKYLQFLKQTADEDFTGIHVALD 17- 9 Query: 180 TANGAASVSARDVFLDLNAEIAVIGEKPNGLNINDGVGSTRPEQLQELVKETGADLGLAF 23- 9 ANGA S A +F DL+A+++ +G PNGLNINDGVGST PE L VKE ADLGLAF Sbjct: 180 CANGATSSLATHLFADLDADVSTMGTSPNGLNINDGVGSTHPEALSAFVKEKNADLGLAF 23- 9 Query: 240 DGDSDRLIAVDETGEIVDGDRIMFIIGKYLSEKGLLAHNTIVTTVMSNLGFHKALDKQGI 29- 9 DGD DRLIAVDE G IVDGD+IM+I K+L +G L +T+V+TVMSNLGF+KAL+K+GI Sbjct: 240 DGDGDRLIAVDEKGNIVDGDQIMYICSKHLKSEGRLKDDTVVSTVMSNLGFYKALEKEGI 29- 9 Query: 300 NKAITAVGDRYVVEEMRSSGYNLGGEQSGHVIIMDYNTTGDGQLTAIQLAKVMKETGKSL 35- 9 TAVGDRYVVE M+ GYN+GGEQSGH+I +DYNTTGDG L+AI L +K TGK L Sbjct: 300 KSVQTAVGDRYVVEAMKKDGYNVGGEQSGHLIFLDYNTTGDGLLSAIMLMNTLKATGKPL 35- 9 Query: 360 SELAAEVTIYPQKLVNIRVENSMKERAMEVPAIANIIAKMEDEMAGNGRILVRPSGTEPL 41- 9 SELAAE+ +PQ LVN+RV + K + E + +I+++E EM G+GRILVRPSGTEPL Sbjct: 360 SELAAEMQKFPQLLVNVRVTD--KYKVEENEKVKAVISEVEKEMNGDGRILVRPSGTEPL 41- 7 Query: 420 LRVMAEAPTDAEVDYYVDTIADVVRTEIGCD 450 +RVMAEA T D YV+ I +VVR+E+G + Sbjct: 418 VRVMAEAKTKELCDEYVNRIVEVVRSEMGLE 448 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04093 Identities = 400/450 (88%), Positives = 429/450 (94%) Query: 1 MGKYFGTDGVRGEANVELTPELAFKLGRFGGYVLSQHETDRPRVFVARDTRISGEMLESA 60 MGKYFGTDGVRGEANVELTPELAFKLGRFGGYVLSQHET+RP+VFVARDTRISGEMLESA Sbjct: 1 MGKYFGTDGVRGEANVELTPELAFKLGRFGGYVLSQHETERPKVFVARDTRISGEMLESA 60 Query: 61 LIAGLLSVGIEVYKLGVLATPGVSYLVRTEKASAGVMISASHNPALDNGIKFFGSDGFKL 120- LIAGLLSVGIEVYKLGVLATPGVSYLVRTEKASAGVMISASHNPALDNGIKFFG+DGFKL Sbjct: 61 LIAGLLSVGIEVYKLGVLATPGVSYLVRTEKASAGVMISASHNPALDNGIKFFGNDGFKL 120- Query: 121 DDDRELEIEALLDAKEDTLPRPSAQGLGTLVDYPEGLRKYEKFMESTGIDLEGMKVALDT 18- 0 DD+ELEIEALLDA EDTLPRPSA+GLGTLVDYPEGLRKYEKF+ +TG DL GM VALDT Sbjct: 121 ADDQELEIEALLDAPEDTLPRPSAEGLGTLVDYPEGLRKYEKFLVTTGTDLSGMTVALDT 18- 0 Query: 181 ANGAATASARNIFLDLNADISVIGDQPDGLNINDGVGSTHPEQLQSLVRENGSDIGLAFD 24- 0 ANGAA+ SAR++FLDLNA+I+VIG++P+GLNINDGVGST PEQLQ LV+E G+D+GLAFD Sbjct: 181 ANGAASVSARDVFLDLNAEIAVIGEKPNGLNINDGVGSTRPEQLQELVKETGADLGLAFD 24- 0 Query: 241 GDSDRLIAVDENGEIVDGDKIMFIIGKYLSDKGQLAQNTIVTTVMSNLGFHKALDREGIH 30- 0 GDSDRLIAVDE GEIVDGD+IMFIIGKYLS+KG LA NTIVTTVMSNLGFHKALD++GI+ Sbjct: 241 GDSDRLIAVDETGEIVDGDRIMFIIGKYLSEKGLLAHNTIVTTVMSNLGFHKALDKQGIN 30- 0 Query: 301 KAITAVGDRYVVEEMRKSGYNLGGEQSGHVIIMDYNTTGDGQLTAIQLTKVMKETGKKLS 36- 0 KAITAVGDRYVVEEMR SGYNLGGEQSGHVIIMDYNTTGDGQLTAIQL KVMKETGK LS Sbjct: 301 KAITAVGDRYVVEEMRSSGYNLGGEQSGHVIIMDYNTTGDGQLTAIQLAKVMKETGKSLS 36- 0 Query: 361 ELASEVTIYPQKLVNIRVENNMKDKAMEVPAIAEIIAKMEEMDGNGRILVRPSGTEPLL 420- ELA+EVTIYPQKLVNIRVEN+MK++AMEVPAIA IIAKME+EM GNGRILVRPSGTEPLL Sbjct: 361 ELAAEVTIYPQKLVNIRVENSMKERAMEVPAIANIIAKMEDEMAGNGRILVRPSGTEPLL 42- 0 Query: 421 RVMAEAPTNEAVDYYVDTIADVVRTEIGLD 450 RVMAEAPT+ VDYYVDTIADVVRTEIG D Sbjct: 421 RVMAEAPTDAEVDYYVDTIADVVRTEIGCD 450 SEQ ID 4236 (GBS402) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 84 (lane 5; MW 78 kDa). GBS402-GST was purified as shown in FIG. 218, lane 3-5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1383 A DNA sequence (GBSx1468) was identified in S. agalactiae <SEQ ID 4239> which encodes the amino acid sequence <SEQ ID 4240>. Analysis of this protein sequence reveals the following: TABLE-US-04094 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04095 >GP:CAB11969 GB:Z99105 ybbR [Bacillus subtilis] Identities = 90/324 (27%), Positives = 167/324 (50%), Gaps = 18/324 (5%) Query: 1 MKKFFTNKFWLGVVSLFLAILLFLTATATSMNHQDNSKIAG-----ASETYTHTLTDVPI 55 M KF N++ + +++L A+LL++ A + N K G S T TLTD+P+ Sbjct: 1 MDKFLNNRWAVKIIALLFALLLYV---AVNSNQAPTPKKPGESFFPTSTTDEATLTDIPV 57 Query: 56 DIKYDSDDYFISGYSYGADVYMS-SVNRVKLDSEINEDTRKFKVVADLTNMKPGTHKVPL 114- YD ++Y ++G +V + S + VK + T+ F++ AD+ ++K GTHKV L Sbjct: 58 KAYYDDENYVVTGVPQTVNVTIKGSTSAVKKARQ----TKNFEIYADMEHLKTGTHKVEL 113- Query: 115 KVVNLPSGVNATVSPTTITVTMGKKKTKEFPV-YGHVNDKQIKAGYAVDKMSVDVSKVKV 17- 3 K N+ G+ +++P+ TVT+ ++ TK FPV + N ++K GY+ ++ V V++ Sbjct: 114 KAKNVSDGLTISINPSVTTVTIQERTTKSFPVEVEYYNKSKMKKGYSPEQPIVSPKNVQI 17- 3 Query: 174 TSDESIIDRIDHVAANIPDDKVLDDDFNKTVTLQAVTADGTVLASIIHPSKATLSVKVKK 23- 3 T +++ID I A++ + D+ K + DG L + PS ++V V Sbjct: 174 TGSKNVIDNISLHKASVNLENA-DETIEKEAKVTVYDKDGNALPVDVEPSVIKITVPVTS 23- 2 Query: 234 LTKTVPINLIPVGQFSDSISKINYKLSQEKAVISGTKEALEAISVIN-AEVDISDVTKNT 29- 2 +K VP + G D +S N +S + + G+++ L+++ I+ +D+S + K++ Sbjct: 233 PSKKVPFKIERTGSLPDGVSIANIESSPSEVTVYGSQDVLDSLEFIDGVSLDLSKINKDS 29- 2 Query: 293 --EKKINLSANNVSVDPAQVTVQL 314 E I L + P++VT+ + Sbjct: 293 DIEADIPLPDGVKKISPSKVTLHI 316 A related DNA sequence was identified in S. pyogenes <SEQ ID 4241> which encodes the amino acid sequence <SEQ ID 4242>. Analysis of this protein sequence reveals the following: TABLE-US-04096 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04097 >GP:CAB11969 GB:Z99105 ybbR [Bacillus subtilis] Identities = 81/322 (25%), Positives = 154/322 (47%), Gaps = 15/322 (4%) Query: 1 MKRFLNSRPWLGMVSVFFAILLFLTAASSNH----NNSSSQIYSPIETYTHSLKDVPIDM 56 M +FLN+R + ++++ FA+LL++ A +SN + T +L D+P+ Sbjct: 1 MDKFLNNRWAVKIIALLFALLLYV-AVNSNQAPTPKKPGESFFPTSTTDEATLTDIPVKA 59 Query: 57 KYDSDKYFISGYSYGAEVYLT-STNRIKLDSEVNNDTRNFKIVADLTHSHPGTVSVNLRV 115- YD + Y ++G V + ST+ +K + T+NF+I AD+ H GT V L+ Sbjct: 60 YYDDENYVVTGVPQTVNVTIKGSTSAVKKARQ----TKNFEIYADMEHLKTGTHKVELKA 115- Query: 116 ENLPSGVTATVSPDKISVTIGKKESKVFPVRGS-VDAKQIANGYEISKIETGVNKVEVTS 17- 4 +N+ G+T +++P +VTI ++ +K FPV + ++ GY + V++T Sbjct: 116 KNVSDGLTISINPSVTTVTIQERTTKSFPVEVEYYNKSKMKKGYSPEQPIVSPKNVQITG 17- 5 Query: 175 DESTIALIDHVVAKLPDDQVLDRNYSSRVTLQAVSADGTILASAIDPAKTNLSVAVKKIT 23- 4 ++ I I A + + D + DG L ++P+ ++V V + Sbjct: 176 SKNVIDNISLHKASVNLENA-DETIEKEAKVTVYDKDGNALPVDVEPSVIKITVPVTSPS 23- 4 Query: 235 KSVPIRVEAVGMMDDSLSDIQYKLSKQTAVISGSREVLEDIDEII-AEVNISDVTKNT-- 29- 1 K VP ++E G + D +S + S + GS++VL+ ++ I +++S + K++ Sbjct: 235 KKVPFKIERTGSLPDGVSIANIESSPSEVTVYGSQDVLDSLEFIDGVSLDLSKINKDSDI 29- 4 Query: 292 SKTVSLSSSQVSIEPSVVTVQL 313 + L I PS VT+ + Sbjct: 295 EADIPLPDGVKKISPSKVTLHI 316 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04098 Identities = 198/319 (62%), Positives = 251/319 (78%), Gaps = 1/319 (0%) Query: 1 MKKFFTNKFWLGVVSLFLAILLFLTATATSMNHQDNSKIAGASETYTHTLTDVPIDIKYD 60 MK+F ++ WLG+VS+F AILLFLTA A+S ++ +S+I ETYTH+L DVPID+KYD Sbjct: 1 MKRFLNSRPWLGMVSVFFAILLFLTA-ASSNHNNSSSQIYSPIETYTHSLKDVPIDMKYD 59 Query: 61 SDDYFISGYSYGADVYMSSVNRVKLDSEINEDTRKFKVVADLTNMKPGTHKVPLKVVNLP 120- SD YFISGYSYGA+VY++S NR+KLDSE+N DTR FK+VADLT+ PGT V L+V NLP Sbjct: 60 SDKYFISGYSYGAEVYLTSTNRIKLDSEVNNDTRNFKIVADLTHSHPGTVSVNLRVENLP 119- Query: 121 SGVNATVSPTTITVTMGKKKTKEFPVYGHVNDKQIKAGYAVDKMSVDVSKVKVTSDESII 18- 0 SGV ATVSP I+VT+GKK++K FPV G V+ KQI GY + K+ V+KV+VTSDES I Sbjct: 120 SGVTATVSPDKISVTIGKKESKVFPVRGSVDAKQIANGYEISKIETGVNKVEVTSDESTI 17- 9 Query: 181 DRIDHVAANIPDDKVLDDDFNKTVTLQAVTADGTVLASIIHPSKATLSVKVKKLTKTVPI 24- 0 IDHV A +PDD+VLD +++ VTLQAV+ADGT+LAS I P+K LSV VKK+TK+VPI Sbjct: 180 ALIDHVVAKLPDDQVLDRNYSSRVTLQAVSADGTILASAIDPAKTNLSVAVKKITKSVPI 23- 9 Query: 241 NLIPVGQFSDSISKINYKLSQEKAVISGTKEALEAISVINAEVDISDVTKNTEKKINLSA 30- 0 + VG DS+S I YKLS++ AVISG++E LE I I AEV+ISDVTKNT K ++LS+ Sbjct: 240 RVEAVGMMDDSLSDIQYKLSKQTAVISGSREVLEDIDEIIAEVNISDVTKNTSKTVSLSS 29- 9 Query: 301 NNVSVDPAQVTVQLTTTKK 319 + VS++P+ VTVQLTTTKK Sbjct: 300 SQVSIEPSVVTVQLTTTKK 318 SEQ ID 4240 (GBS99) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 6; MW 35.7 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 21 (lane 9; MW 60.7 kDa). The GBS99-GST fusion product was purified (FIG. 197, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 293), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1384 A DNA sequence (GBSx1469) was identified in S. agalactiae <SEQ ID 4243> which encodes the amino acid sequence <SEQ ID 4244>. Analysis of this protein sequence reveals the following: TABLE-US-04099 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0503(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1385 A DNA sequence (GBSx1470) was identified in S. agalactiae <SEQ ID 4245> which encodes the amino acid sequence <SEQ ID 4246>. Analysis of this protein sequence reveals the following:

TABLE-US-04100 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.50 Transmembrane 20-36 (18-46) INTEGRAL Likelihood = -7.64 Transmembrane 48-64 (42-68) INTEGRAL Likelihood = -3.40 Transmembrane 80-96 (80-96) ----- Final Results ----- bacterial membrane --- Certainty = 0.4800(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04101 >GP: CAB11968 GB: Z99105 alternate gene name: ybbQ~similar to hypothetical proteins [Bacillus subtilis] Identities = 125/253 (49%), Positives = 186/253 (73%), Gaps = 5/253 (1%) Query: 27 MDIIIVAVLIYKFIKALAGTKIMSLIQGVILFIIIRFVSEWIGLTTITFLMNQIVTYGVI 86 - +DI++V +IYK I + GTK + L++G+++ +++R S+++GL+T+ +LM+Q +T+G + Sbjct: 16 VDILLVWYVIYKLIMVIRGTKAVQLLKGIVVIVLVRMASQYLGLSTLQWLMDQAITWGFL 75 Query: 87 AGVVIFAPEIRTGLEKFGRTPQLFTQRSQLSSDE---KLVDALVKAVAYMSPRKIGALIS 143- A ++IF PE+R LE+ GR F RS +E K ++A+ KA+ YM+ R+IGAL++ Sbjct: 76 AIIIIFQPELRRALEQLGRGR--FFSRSGTPVEEAQQKTIEAITKAINYMAKRRIGALLT 133- Query: 144 IERTQTLQEYIATGIPLDADISSELLINIFIPNTPLHDGAVIVKDKKIATACSYLPLSES 20- 3 IER + +YI TGIPL+A +SSELLINIFIPNTPLHDGAVI+K+ +IA A YLPLSES Sbjct: 134 IERDTGMGDYIETGIPLNAKVSSELLINIFIPNTPLHDGAVIMKNNEIAAAACYLPLSES 19- 3 Query: 204 SSISKEFGTRHRAAIGLSENSDALTVIVSEETGGISVALKGEFLHDLSKDSFEAILRTQL 26- 3 ISKE GTRHRAA+G+SE +D+LT+IVSEETGG+SVA G+ +L++++ + +L + Sbjct: 194 PFISKELGTRHRAAVGISEVTDSLTIIVSEETGGVSVAKNGDLHRELTEEALKEMLEAEF 25- 3 Query: 264 IQNQEENSKLAWY 276 +N + S WY Sbjct: 254 KKNTRDTSSNRWY 266 A related DNA sequence was identified in S. pyogenes <SEQ ID 4247> which encodes the amino acid sequence <SEQ ID 4248>. Analysis of this protein sequence reveals the following: TABLE-US-04102 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.64 Transmembrane 20-36 (19-40) INTEGRAL Likelihood = -6.21 Transmembrane 48-64 (47-68) INTEGRAL Likelihood = -2.07 Transmembrane 76-92 (76-92) ----- Final Results ----- bacterial membrane --- Certainty = 0.3654(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04103 >GP: BAB03984 GB: AP001507 unknown conserved protein [Bacillus halodurans] Identities = 117/255 (45%), Positives = 178/255 (68%), Gaps = 6/255 (2%) Query: 19 PWL-LAVHLLDILIVAYLIYRFIKALTGTKIMSLVQGVIFFLVLRFIAEWIGFTTITYLM 77 - PWL +LDIL+V Y+IY+ I + GT+ + L++G+ L++ I+ + T+ +++ Sbjct: 8 PWLNYLTQILDILVVTYVIYKAIMIIRGTRAVQLLKGITVILIVYAISIFFNLRTLGWIV 67 Query: 78 NQVITYGVIAGVVIFTPEIRAGLEKFGRSTQVFLQKQYVSSESAL---VDALIKSVAYMG 134- NQ ITYG++A ++IF PE+R LE+ GR F + + E + +DA++K+ YMG Sbjct: 68 NQAITYGLLAVIIIFQPELRRALEQLGRGR--FFASRTANEEETMKKTIDAIVKASTYMG 125- Query: 135 PRKIGALIAIEQTQTLQEYIATGIPLNADISSQLLINIFIPNTPLHDGAVIVGQNKIVAA 19- 4 R+IGALI++E+ + +Y+ TGIP+NA+++S+LLIN FIPNTPLHDGAVI+ + I+AA Sbjct: 126 KRRIGALISMERETGMTDYVETGIPMNANLTSELLINTFIPNTPLHDGAVIINNDTILAA 18- 5 Query: 195 CAYLPLSESKAISKEFGTRHRAAIGLSENSDALTIIVSEETGAISVTRKGQFLHDLSTDE 25- 4 YLPLSE+ ISKE GTRHRAA+G+SE +D LTI+VSEETG IS+T+ G+ DL ++ Sbjct: 186 ACYLPLSENPFISKELGTRHRAALGVSEVTDCLTIVVSEETGHISLTKNGELHRDLDEEQ 24- 5 Query: 255 FETVLRTYLMSNSNV 269 ++L L+S + + Sbjct: 246 LRSLLEAELISEAKM 260 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04104 Identities = 201/283 (71%), Positives = 239/283 (84%), Gaps = 2/283 (0%) Query: 1 MDIFSAIDSKFWASIMENPWMILIHLMDIIIVAVLIYKFIKALAGTKIMSLIQGVILFII 60 M+ S+ID KF S+ +PW++ +HL+DI+IVA LIY+FIKAL GTKIMSL+QGVI F++ Sbjct: 1 MNNLSSIDIKFLLSLFADPWLLAVHLLDILIVAYLIYRFIKALTGTKIMSLVQGVIFFLV 60 Query: 61 IRFVSEWIGLTTITFLMNQIVTYGVIAGVVIFAPEIRTGLEKFGRTPQLFTQRSQLSSDE 120- +RF++EWIG TTIT+LMNQ++TYGVIAGVVIF PEIR GLEKFGR+ Q+F Q+ +SS+ Sbjct: 61 LRFIAEWIGFTTITYLMNQVITYGVIAGVVIFTPEIRAGLEKFGRSTQVFLQKQYVSSES 120- Query: 121 KLVDALVKAVAYMSPRKIGALISIERTQTLQEYIATGIPLDADISSELLINIFIPNTPLH 18- 0 LVDAL+K+VAYM PRKIGALI+IE+TQTLQEYIATGIPL+ADISS+LLINIFIPNTPLH Sbjct: 121 ALVDALIKSVAYMGPRKIGALIAIEQTQTLQEYIATGIPLNADISSQLLINIFIPNTPLH 18- 0 Query: 181 DGAVIVKDKKIATACSYLPLSESSSISKEFGTRHRAAIGLSENSDALTVIVSEETGGISV 24- 0 DGAVIV KI AC+YLPLSES +ISKEFGTRHRAAIGLSENSDALT+IVSEETG ISV Sbjct: 181 DGAVIVGQNKIVAACAYLPLSESKAISKEFGTRHRAAIGLSENSDALTIIVSEETGAISV 24- 0 Query: 241 ALKGEFLHDLSKDSFEAILRTQLIQNQEENSKLAWYNQLLRRK 283 KG+FLHDLS D FE +LRT L+ N N L WY ++L K Sbjct: 241 TRKGQFLHDLSTDEFETVLRTYLMSN--SNVTLPWYKKILGGK 281 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1386 A DNA sequence (GBSx1471) was identified in S. agalactiae <SEQ ID 4249> which encodes the amino acid sequence <SEQ ID 4250>. Analysis of this protein sequence reveals the following: TABLE-US-04105 Possible site: 25 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.60 Transmembrane 33-49 (33-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1387 A DNA sequence (GBSx1472) was identified in S. agalactiae <SEQ ID 4251> which encodes the amino acid sequence <SEQ ID 4252>. Analysis of this protein sequence reveals the following: TABLE-US-04106 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1001(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9781> which encodes amino acid sequence <SEQ ID 9782> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04107 >GP: AAC84012 GB: AF080002 UDP-N-acetylmuramyl tripeptide synthetase MurC [Heliobacillus mobilis] Identities = 143/442 (32%), Positives = 229/442 (51%), Gaps = 17/442 (3%) Query: 12 GKSAHYLLSKMGRGST-YPGSLALKFDKDILDTIAKDYE--IVVVTGTNGKTLTTALTVG 68 - GK+A +L + G G T +PG + + IL +A+ + +VVTGTNGKT T+ + Sbjct: 2 GKTAIWLNRRFGHGGTSFPGGIGRRVAPQILTALARQLKRGAMVVTGTNGKTTTSKMLAA 61 Query: 69 ILKEAFGQVVTNPSGANMITGIVSTFLTAKKSKSG--KKIAVLEIDEASLPRITQYIKPS 126- I++++ + N +GAN++ GI + F+ + + ++E+DEA++P++ + ++P Sbjct: 62 IVEKSSLTLTHNRAGANLVGGITTAFIDSATIGGSITSDLGIIEVDEATIPQLVREVQPK 121- Query: 127 LFVFTNIFRDQMDRYGEIYTTYQMILDGAANAP-QATILANGDSPLFNS--KSVTNPVQF 18- 3 V TN FRDQ+DR+GE+ T ++ + P Q+ + N D PL S K V + Sbjct: 122 GVVVTNFFRDQLDRFGELDKTVSLVGEALRLLPVQSIAVLNADDPLVASLGKDFPGRVLY 18- 1 Query: 184 YGFNTDKHEPRLAHYNTEGILCPKCQAILTYRLNTYANLGDYTCPNCDFERPNLDYALTR 24- 3 +G + + R + E C C LTY + LG Y C +C FERP +T Sbjct: 182 FGIDDRSYGAREMLQSAETRFCRLCGHPLTYDWFFFGQLGHYRCSHCGFERPEPKIKVTG 24- 1 Query: 244 LTHLTNTSSGFVIDGQ----QYNINVGGLYNIYNALAAVSVAEYFGVEPSQIKDGFDKSR 29- 9 + S F ++ Q ++ G YNIYNALAA++ A + I+ G R Sbjct: 242 IQLKGEEGSAFTVETPRGTWQLELSTPGFYNIYNALAAIASAIRLDLPEKAIRAGLQGYR 30- 1 Query: 300 AVFGRQETFTIGN-KKCTLVLIKNPVGASQALDMIKLAPYPFSLSVLLNANYADGIDTSW 35- 8 FGR E + + ++ L LIKNP G + + + P L V++N N ADG D SW Sbjct: 302 TNFGRMERIELEDGRRAFLALIKNPTGCDEVIRTLVQNRGPKRLLVIINDNAADGRDISW 36- 1 Query: 359 IWDANFETI--LTMNIPEIFAGGVRHSEIARRLRVTGYDEKRIK-QADKLQDIMTMIEQQ 41- 5 +WDA+FE++ + + +F G+R ++A RL TG + I+ +A+ I + +E Sbjct: 362 LWDADFESLEPVYPELRSVFTSGLRGEDMALRLNYTGIPAESIRYEANVESAIRSALEMT 42- 1 Query: 416 ET-EHAYILATYTAMLEFREIL 436 E E YIL TYTA+LE + L Sbjct: 422 EPGETLYILPTYTALLESKAAL 443 A related DNA sequence was identified in S. pyogenes <SEQ ID 4253> which encodes the amino acid sequence <SEQ ID 4254>. Analysis of this protein sequence reveals the following: TABLE-US-04108 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04109 Identities = 343/446 (76%), Positives = 393/446 (87%) Query: 1 MKINTALGVAAGKSAHYLLSKMGRGSTYPGSLALKFDKDILDTIAKDYEIVVVTGTNGKT 60 MK+ T LG+ AGK+A +L+K+GRGSTYPG LAL DKDIL ++KDY+IVVVTGTNGKT Sbjct: 1 MKMKTLLGIIAGKAAQSILTKLGRGSTYPGRLALACDKDILKDLSKDYDIVVVTGTNGKT 60 Query: 61 LTTALTVGILKEAFGQVVTNPSGANMITGIVSTFLTAKKSKSGKKIAVLEIDEASLPRIT 120- LTTALTVGILKEAFG+++TNPSGANMITGI STFL AKK KS ++IAVLEIDEASLPRIT Sbjct: 61 LTTALTVGILKEAFGEIITNPSGANMITGITSTFLAAKKGKSERQIAVLEIDEASLPRIT 120- Query: 121 QYIKPSLFVFTNIFRDQMDRYGEIYTTYQMILDGAANAPQATILANGDSPLFNSKSVTNP 18- 0 Y+KPSLFV+TNIFRDQMDRYGEIYTTYQMI+DGA NAP+ATILANGDSP+F+SK + NP Sbjct: 121 TYLKPSLFVYTNIFRDQMDRYGEIYTTYQMIVDGARNAPKATILANGDSPIFSSKDIVNP 18- 0 Query: 181 VQFYGFNTDKHEPRLAHYNTEGILCPKCQAILTYRLNTYANLGDYTCPNCDFERPNLDYA 24- 0 VQ+YGF+T KH P+LAHYNTEGILCPKC+ IL YRLNTYANLGD+ C NC F+RP LDY Sbjct: 181 VQYYGFDTAKHAPQLAHYNTEGILCPKCEHILQYRLNTYANLGDFVCLNCQFQRPTLDYQ 24- 0 Query: 241 LTRLTHLTNTSSGFVIDGQQYNINVGGLYNIYNALAAVSVAEYFGVEPSQIKDGFDKSRA 30- 0 LT LT +T+ SS FVIDGQ Y INVGGLYNIYNALAAVSVAE+FGV P +IK GF+KS+A Sbjct: 241 LTELTAITHQSSEFVIDGQNYKINVGGLYNIYNALAAVSVAEFFGVSPEKIKAGFNKSKA 30- 0 Query: 301 VFGRQETFTIGNKKCTLVLIKNPVGASQALDMIKLAPYPFSLSVLLNANYADGIDTSWIW 36- 0 VFGRQETFT+G+K CTL+LIKNPVGASQAL+MI+LA YPFSLSVLLNANYADGIDTSWIW Sbjct: 301 VFGRQETFTVGDKSCTLILIKNPVGASQALEMIQLADYPFSLSVLLNANYADGIDTSWIW 36- 0 Query: 361 DANFETILTMNIPEIFAGGVRHSEIARRLRVTGYDEKRIKQADKLQDIMTMIEQQETEHA 42- 0 DANFE I M I EI AGGVRHSEIARRLRVTG+D+ +IKQA+KL+ I+ IE+QE +HA Sbjct: 361 DANFELITQMPITEINAGGVRHSEIARRLRVTGFDDTKIKQAEKLEQIIETIEKQEAKHA 42- 0 Query: 421 YILATYTAMLEFREILANHNAIRKEM 446 YILATYTAMLEFR +LA+ + + KEM Sbjct: 421 YILATYTAMLEFRSLLADRHVVEKEM 446 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1388 A DNA sequence (GBSx1473) was identified in S. agalactiae <SEQ ID 4255> which encodes the amino acid sequence <SEQ ID 4256>. Analysis of this protein sequence reveals the following: TABLE-US-04110 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3010(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04111 >GP: AAC84011 GB: AF080002 cobyric acid synthase CobQ [Heliobacillus mobilis] Identities = 89/250 (35%), Positives = 129/250 (51%), Gaps = 9/250 (3%) Query: 11 TKDYKYTLNVAHLYGNLLNTYGDNGNILMMKYVGEKLGCQMTFDIVSLEDRFDPNYYQMA 70 - +K TL + HLY +LLN YGD GNI+ ++ E G + SL ++ + + Sbjct: 2 SKTSNRTLTLIHLYPDLLNLYGDRGNIITLRRRCEWRGITLQVHSASLGEKAAFDDADLV 61 Query: 71 FFGGGQDYEQAIVARDLPSKKEDINKFIQNNGV-VLAICGGFQLLGQYYIQANGERIEGI 129- F GGG D EQ ++ +D K G+ +L++CGG+QLLG YY GE + G+ Sbjct: 62 FMGGGSDREQTLLFQDFQQHKGPALVEAAEGGLPLLSVCGGYQLLGLYYRTHTGEEMPGL 121- Query: 130 GVMGHYTLNQNNNRYIGDIKIHNDEFNE--TYYGFENHQGRTFLSEDE--KPLGTVIYGN 18- 5 G+ +T + R IG++ E T GFENH GRTFL +PL V G Sbjct: 122 GLFDAWT-EAGSTRLIGNVVAQAPLLGEQATLVGFENHSGRTFLGSRGGIQPLAQVTAGF 18- 0 Query: 186 GNNKEDGTEGVHYKNVFGSYFHGPILSRNANLAYRLVATALRNKYG---KEIVLPSYEEI 24- 2 GNN +D EG YKN G+Y HGP+L +N LA L++ AL +YG + ++E Sbjct: 181 GNNGDDQGEGAVYKNAVGTYLHGPVLPKNPALADWLLSKALERRYGGGSLSTLQDTWENR 24- 0 Query: 243 LSLEIPEEYG 252 L + + +G Sbjct: 241 AHLSVAQRFG 250 A related DNA sequence was identified in S. pyogenes <SEQ ID 4257> which encodes the amino acid sequence <SEQ ID 4258>. Analysis of this protein sequence reveals the following: TABLE-US-04112 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2586(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04113 Identities = 197/260 (75%), Positives = 224/260 (85%) Query: 1 MTYTSLKSPTTKDYKYTLNVAHLYGNLLNTYGDNGNILMMKYVGEKLGCQMTFDIVSLED 60 MTYTSLKSP +DY Y L +AHLYGNL+NTYGDNGNILM+KYV EKLG ++T DIVS+ D Sbjct: 1 MTYTSLKSPENQDYIYDLTIAHLYGNLMNTYGDNGNILMLKYVAEKLGARVTVDIVSIND 60 Query: 61 RFDPNYYQMAFFGGGQDYEQAIVARDLPSKKEDINKFIQNNGVVLAICGGFQLLGQYYIQ 120- F+ + Y + FFGGGQDYEQ+IVA+DLPSKK + +I NN VVLAICGGFQLLGQYY+Q Sbjct: 61 TFEQDDYDIVFFGGGQDYEQSIVAKDLPSKKAALADYIANNKVVLAICGGFQLLGQYYVQ 120- Query: 121 ANGERIEGIGVMGHYTLNQNNNRYIGDIKIHNDEFNETYYGFENHQGRTFLSEDEKPLGT 18- 0 ANG +I+G+G+MGHYTLNQ+ NR+IGDIKIHNDEFNETYYGFENHQGRTFLS DEKPLG Sbjct: 121 ANGVKIDGLGIMGHYTLNQHQNRFIGDIKIHNDEFNETYYGFENHQGRTFLSGDEKPLGR 18- 0 Query: 181 VIYGNGNNKEDGTEGVHYKNVFGSYFHGPILSRNANLAYRLVATALRNKYGKEIVLPSYE 24- 0 V+YGNGNNKED TEGVHYKNV+GSYFHGPILSRN NLAYRLV TAL+ KYG I LPSY+ Sbjct: 181 VVYGNGNNKEDQTEGVHYKNVYGSYFHGPILSRNVNLAYRLVTTALKKKYGSAISLPSYD 24- 0 Query: 241 EILSLEIPEEYGDVKSKADF 260 +IL EI EEY D+KSKA F Sbjct: 241 DILKQEITEEYADLKSKASF 260 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1389 A DNA sequence (GBSx1474) was identified in S. agalactiae <SEQ ID 4259> which encodes the amino acid sequence <SEQ ID 4260>. Analysis of this protein sequence reveals the following: TABLE-US-04114 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1701(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04115 >GP: BAB04402 GB: AP001509 lipoate-protein ligase [Bacillus halodurans] Identities = 153/316 (48%), Positives = 212/316 (66%), Gaps = 3/316 (0%) Query: 10 DPAYNVALEAYAFQKLTDIDEIFIL-WINEPAIIIGRHQNTIQEINKEFIDKNGIHVVRR 68 - DP N+A+E YA + L DI+E ++L +INEP+IIIGR+QNTI+EIN E+++ NGIHVVRR Sbjct: 11 DPRINLAIEEYALKNL-DINETYLLFYINEPSIIIGRNQNTIEEINTEYVESNGIHVVRR 69 Query: 69 LSGGGAVYHDLNNLNYTIISNNTQEGAFDFQTFSKPVIDTLAKLGVKAEFTGRNDL-EIN 127- LSGGGAVYHD NLN++ I+ + E +FQ F+ PVI LAKLGV AE GRND+ + Sbjct: 70 LSGGGAVYHDHGNLNFSFITKDDGESFSNFQKFTDPVIKALAKLGVTAELKGRNDIIASD 129- Query: 128 GQKFAGNAQAYYKGRMMHHGCLLFDVDMSVLGQALKVSKDKIESKGIKSVRARVTNIVDH 18- 7 G+K +GNAQ KGRM HG LLFD ++ + AL VSKDKIESKGIKS+R+RV NI + Sbjct: 130 GRKISGNAQFSTKGRMFSHGTLLFDSEIDHVVSALNVSKDKIESKGIKSIRSRVANISEF 18- 9 Query: 188 LSDKITVQEFSDAILAQMKEEYPEMDEYVLSDAELSEIQAMRDNQFATWDWTYGKAPEYT 24- 7 L++KI++ +F +L + + + EY L+ + +EI + ++ WDW YGK+P + Sbjct: 190 LTEKISIDQFRSLLLESIFDGQANIQEYKLTADDWAEIHELSKERYQNWDWNYGKSPAFN 24- 9 Query: 248 IERGVRYPAGKITTYANVENSTIKSVKIFGDFFGVKPVDDIEKMLEGVRYDYKDVLAALK 30- 7 ++ R+P G I V+ TI+ KIFGDFFG V D+E L G+RY+ D+ AL Sbjct: 250 LQHSHRFPVGNIDIRLEVKGGTIQQCKIFGDFFGTGDVRDLEDRLVGIRYERADIEQALA 30- 9 Query: 308 TVDTSQYFSRMTPEEI 323 VD YF ++ ++I Sbjct: 310 DVDVKTYFGQVEKDDI 325 A related DNA sequence was identified in S. pyogenes <SEQ ID 4261> which encodes the amino acid sequence <SEQ ID 4262>. Analysis of this protein sequence reveals the following: TABLE-US-04116 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1271(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04117 Identities = 249/328 (75%), Positives = 292/328 (88%) Query: 1 MKYIVNTSNDPAYNVALEAYAFQKLTDIDEIFILWINEPAIIIGRHQNTIQEINKEFIDK 60 MKYIVN S++PA+N+ALEAYAF++L + DE+FILWINEPAIIIG+HQNTIQEINKE+ID+ Sbjct: 1 MKYIVNKSHNPAFNIALEAYAFRELVEEDELFILWINEPAIIIGKHQNTIQEINKEYIDE 60 Query: 61 NGIHVVRRLSGGGAVYHDLNNLNYTIISNNTQEGAFDFQTFSKPVIDTLAKLGVKAEFTG 120- +GIHVVRRLSGGGAVYHDLNNLNYTIISN T EGAFDF+TFS+PVI TLA LGV A FTG Sbjct: 61 HGIHVVRRLSGGGAVYHDLNNLNYTIISNKTAEGAFDFKTFSQPVIATLADLGVTANFTG 120- Query: 121 RNDLEINGQKFAGNAQAYYKGRMMHHGCLLFDVDMSVLGQALKVSKDKIESKGIKSVRAR 18- 0 RND+EI+G+K GNAQAYYKGRMMHHGCLLFDVDM+VLG ALKVSKDKIESKG+KSVRAR Sbjct: 121 RNDIEIDGKKICGNAQAYYKGRMMHHGCLLFDVDMTVLGDALKVSKDKIESKGVKSVRAR 18- 0 Query: 181 VTNIVDHLSDKITVQEFSDAILAQMKEEYPEMDEYVLSDAELSEIQAMRDNQFATWDWTY 24- 0 VTNI++ L +KITV+EFSD ILA+MKE YP+M EYVLS+ EL++I+ QF +WDWTY Sbjct: 181 VTNILNELPEKITVEEFSDKILAKMKETYPDMTEYVLSEDELAKIEQSAKEQFGSWDWTY 24- 0 Query: 241 GKAPEYTIERGVRYPAGKITTYANVENSTIKSVKIFGDFFGVKPVDDIEKMLEGVRYDYK 30- 0 GKAPEYTIER VRYPAGKI+T+ANVENS IK++KI+GDFFG+K V DIE +L G +Y+Y+ Sbjct: 241 GKAPEYTIERNVRYPAGKISTFANVENSIIKNLKIYGDFFGIKDVQDIENLLIGCKYEYR 30- 0 Query: 301 DVLAALKTVDTSQYFSRMTPEEITKAIV 328 DV LKT+DT+QYFSRMT EE+ KAIV Sbjct: 301 DVFERLKTIDTTQYFSRMTVEEVAKAIV 328 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1390 A DNA sequence (GBSx1475) was identified in S. agalactiae <SEQ ID 4263> which encodes the amino acid sequence <SEQ ID 4264>. Analysis of this protein sequence reveals the following:

TABLE-US-04118 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.70 Transmembrane 294-310 (294-312) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04119 >GP:AAA21748 GB:L31844 dihydrolipoamide dehydrogenase [Clostridium magnum] Identities = 229/589 (38%), Positives = 339/589 (56%), Gaps = 25/589 (4%) Query: 1 MAFDVIMPKLGVDMQEGEILEWKKNEGDTVNEGDVLLEIMSDKTNMEIEAEDTGVLLKIV 60 MA V+MPKLG+ M EG ++ WKK EGD V G++L E+ +DK E+E+ D G++ K++ Sbjct: 1 MAKIVVMPKLGLTMTEGTLVTWKKAEGDQVKVGEILFEVSTDKLTNEVESSDEGIVRKLL 60 Query: 61 HQAGDVVPVTEVIAYIGEEGEEVGTSSPSADATITAEDGQSVSGPAAPSQETVAAATPKE 120- GDVV +A IG E++ + +G S +A +T A PK+ Sbjct: 61 VNEGDVVECLNPVAIIGSADEDISSLL----------NGSSEGSGSAEQSDTKA---PKK 107- Query: 121 ELAADEY--DIVVVGGGPAGYYAAIRGAQLGGKIAIVEKTEFGGTCLNVGCIPTKTYLKN 17- 8 E+ A + ++VV+GGGP GY AAIR AQLG K+ ++EK GGTCLNVGCIPTK L + Sbjct: 108 EVEAVKGGDNLVVIGGGPGGYVAAIRAAQLGAKVTLIEKESLGGTCLNVGCIPTKVLLHS 16- 7 Query: 179 AEILDGLKVAAGRGINLASTNYAIDMDKTVAFKNSVVKTLTGGVRGLLKANKVEIFNGLG 23- 8 +++L +K GI++ + ++ K V+K L GV GLL NKV++ G Sbjct: 168 SQLLTEMKEGDKLGIDIEGS-IVVNWKHIQKRKKIVIKKLVSGVSGLLTCNKVKVIKGTA 22- 6 Query: 239 QVNPDKSVVIGDK-----VIKGRNVVLATGSKVSRINIPGIESPLVLTSDDILDLREIPK 29- 3 + ++++ + + N ++ATGS I G + V+ S L L P+ Sbjct: 227 KFESKDTILVTKEDGVAEKVNFDNAIIATGSMPFIPEIEGNKLSGVIDSTGALSLESNPE 28- 6 Query: 294 SLAVMGGGVVGIELGLVWASYGVDVTVIEMADRIIPAMDKEVSLELQKILAKKGMKIKTS 35- 3 S+A++GGGV+G+E ++ S G V++IEM I+P MD+E+S + L + G+ I + Sbjct: 287 SIAIIGGGVIGVEFASIFNSLGCKVSIIEMLPHILPPMDREISEIAKAKLIRDGININNN 34- 6 Query: 354 VGVSEIVEANNQLTLKL--NNGEEVV-ADKALLSIGRVPQMNGLENLEPELEMERGRIKV 41- 0 V+ I + + L + + GEE + +K L+++GR + GL+ + ++ E G I V Sbjct: 347 CKVTRIEQGEDGLKVSFIGDKGEESIDVEKVLIAVGRRSNIEGLDVEKIGVKTEGGSIIV 40- 6 Query: 411 NAYQETSIPGIYAPGDVNGTRMLAHAAYRMGEVAAENALGGNKRKAHLDFTPAAVYTHPE 47- 0 N ET++ GIYA GD G MLAH A G VAAEN +G NK K PA VYT PE Sbjct: 407 NDKMETNVEGIYAIGDCTGKIMLAHVASDQGVVAAENIMGQNK-KMDYKTVPACVYTKPE 46- 5 Query: 471 VAMVGMTEEQAREQYGDILVGKNSFTGNGRAIASNEAHGFVKVIAEPKYKEILGVHIIGP 53- 0 +A VG+TEEQA+E+ D VGK NG+++ NE G +K+I + KY+EILGVHI+GP Sbjct: 466 LASVGLTEEQAKEKGIDYKVGKFQLAANGKSLIMNETGGVIKIITDKKYEEILGVHILGP 52- 5 Query: 531 AAAELINEASTIMENELTVYDVAQSIHGHPTFSEVMYEAFLDVLGEAIH 579 A +LI EA+ + E T+ ++ ++H HPT E M EA L V +AIH Sbjct: 526 RATDLITEAALALRLEATLEEIITTVHAHPTVGEAMKEAALAVNNQAIH 574 A related DNA sequence was identified in S. pyogenes <SEQ ID 1819> which encodes the amino acid sequence <SEQ ID 1820>. Analysis of this protein sequence reveals the following: TABLE-US-04120 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.70 Transmembrane 297-313 (297-315) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04121 Identities = 497/591 (84%), Positives = 538/591 (90%), Gaps = 10/591 (1%) Query: 1 MAFDVIMPKLGVDMQEGEILEWKKNEGDTVNEGDVLLEIMSDKTNMEIEAEDTGVLLKIV 60 MA ++IMPKLGVDMQEGEI+EWKK EGDTVNEGD+LLEIMSDKTNME+EAED+GVLLKI Sbjct: 1 MAVEIIMPKLGVDMQEGEIIEWKKQEGDTVNEGDILLEIMSDKTNMELEAEDSGVLLKIT 60 Query: 61 HQAGDVVPVTEVIAYIGEEGEEVGTSSPSA---DATITAEDGQS--VSGPAAPSQETVAA 115- QAG+ VPVTEVI YIG EGE V SSP+A + T ED ++ + P AP+Q A+ Sbjct: 61 RQAGETVPVTEVIGYIGAEGESVEVSSPAASDVNVARTTEDLEAAGLEVPKAPAQ--AAS 118- Query: 116 ATPKEELAADEYDIVVVGGGPAGYYAAIRGAQLGGKIAIVEKTEFGGTCLNVGCIPTKTY 17- 5 A PK LA DEYDI+VVGGGPAGYYAAIRGAQLGGKIAIVEK+EFGGTCLNVGCIPTKTY Sbjct: 119 AAPKAALADDEYDIIVVGGGPAGYYAAIRGAQLGGKIAIVEKSEFGGTCLNVGCIPTKTY 17- 8 Query: 176 LKNAEILDGLKVAAGRGINLASTNYAIDMDKTVAFKNSVVKTLTGGVRGLLKANKVEIFN 23- 5 LKNAEILDG+K+AAGRGINLASTNY IDMDKTV FKN+VVKTLTGGV+GLLKANKV IFN Sbjct: 179 LKNAEILDGIKIAAGRGINLASTNYTIDMDKTVDFKNTVVKTLTGGVQGLLKANKVTIFN 23- 8 Query: 236 GLGQVNPDKSVVIGDKVIKGRNVVLATGSKVSRINIPGIESPLVLTSDDILDLREIPKSL 29- 5 GLGQVNPDK+V IG + IKGRNV+LATGSKVSRINIPGI+S LVLTSDDILDLRE+PKSL Sbjct: 239 GLGQVNPDKTVTIGSQTIKGRNVILATGSKVSRINIPGIDSKLVLTSDDILDLREMPKSL 29- 8 Query: 296 AVMGGGVVGIELGLVWASYGVDVTVIEMADRIIPAMDKEVSLELQKILAKKGMKIKTSVG 35- 5 AVMGGGVVGIELGLVWASYGVDVTVIEMADRIIPAMDKEVSLELQKIL+KKGMKIKTSVG Sbjct: 299 AVMGGGVVGIELGLVWASYGVDVTVIEMADRIIPAMDKEVSLELQKILSKKGMKIKTSVG 35- 8 Query: 356 VSEIVEANNQLTLKLNNGEEVVADKALLSIGRVPQMNGLENLEPELEMERGRIKVNAYQE 41- 5 VSEIVEANNQLTLKLNNGEEVVA+KALLSIGRV QMNGLENL LEM+R RIKVN YQE Sbjct: 359 VSEIVEANNQLTLKLNNGEEVVAEKALLSIGRVSQMNGLENL--NLEMDRNRIKVNDYQE 41- 6 Query: 416 TSIPGIYAPGDVNGTRMLAHAAYRMGEVAAENALGGN-KRKAHLDFTPAAVYTHPEVAMV 47- 4 TSIPGIYAPGDVNGT+MLAHAAYRMGEVAAENA+ GN RKA+L +TPAAVYTHPEVAMV Sbjct: 417 TSIPGIYAPGDVNGTKMLAHAAYRMGEVAAENAMHGNTTRKANLKYTPAAVYTHPEVAMV 47- 6 Query: 475 GMTEEQAREQYGDILVGKNSFTGNGRAIASNEAHGFVKVIAEPKYKEILGVHIIGPAAAE 53- 4 G+TEEQAREQYGD+L+GKNSFTGNGRAIASNEAHGFVKVIA+ KY EILGVHIIGPAAAE Sbjct: 477 GLTEEQAREQYGDVLIGKNSFTGNGRAIASNEAHGFVKVIADAKYHEILGVHIIGPAAAE 53- 6 Query: 535 LINEASTIMENELTVYDVAQSIHGHPTFSEVMYEAFLDVLGEAIHNPPKRK 585 +INEA+TIME+ELTV ++ SIHGHPTFSEVMYEAF DVLGEAIHNPPKRK Sbjct: 537 MINEAATIMESELTVDELLLSIHGHPTFSEVMYEAFADVLGEAIHNPPKRK 587 SEQ ID 4264 (GBS681) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 165 (lane 2; MW 68.3 kDa) and in FIG. 188 (lane 10; MW 68 kDa). Purified GBS681-His is shown in FIG. 240, lane 5-6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful, antigens for vaccines or diagnostics. EXAMPLE 1391 A DNA sequence (GBSx1476) was identified in S. agalactiae <SEQ ID 4265> which encodes the amino acid sequence <SEQ ID 4266>. This protein is predicted to be dihydrolipoamide acetyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-04122 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4466(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04123 >GP:BAB04497 GB:AP001509 dihydrolipoamide S-acetyltransferase [Bacillus halodurans] Identities = 187/462 (40%), Positives = 266/462 (57%), Gaps = 26/462 (5%) Query: 1 MAVEIIMPKLGVDMQEGEILEWKKQVGDVVNEGDVLLEIMSDKTNMEIEAEDSGVLLKIT 60 MA EI MPKL MQEG +L+W K+ GD V G+ L EIM+DK N+E+EA + G LLK Sbjct: 1 MAKEIFMPKLSSTMQEGTLLQWFKEEGDRVEVGEPLFEIMTDKINIEVEAYEEGTLLKRY 60 Query: 61 HGNGDVVPVTETIGYIGAEGEEVTEASSSENTSVEENATQVTSEPEKVEETSEPSVPAAT 120- +G D +PV IGYIG E V +E E T E T+ P++ Sbjct: 61 YGEDDEIPVNHVIGYIGTPDESVP----TEPPGASEITASSTDEAGDHRTTAVKKAPSSD 116- Query: 121 SGEKVRATPAARKLAREMSIDLALVSGTGANGRVHREDVENFKGAQPRITPLARRIAEDQ 18- 0 E VRATPAAR++A+E IDL V G+G GRV DV FK + TPLA+++AE + Sbjct: 117 R-ENVRATPAARRIAKEKRIDLRQVEGSGPEGRVQAVDVATFKKKGQKATPLAKKVAEVK 17- 5 Query: 181 GVDIAEITGSGIRGKIVKNDVLAAMSPQAAEAPVETKATPTTEEKQLPEGVEVIKMSAMR 24- 0 GV + ++ GSG GK+ + DV A A +PVE K +K+S +R Sbjct: 176 GVALEKVQGSGPYGKVYREDVEHAQ----AASPVEDKGNR-------------VKLSGLR 21- 8 Query: 241 KAISKGMTNSYLTAPSFTLNYDIDMTEMMALRKKLIDPIMAKTGLKVSFTDLIGMAVVKT 30- 0 K ++K M +S +AP T+ +IDM+ + +R +L+ I +TG ++S+T+++ AV Sbjct: 219 KVVAKRMVDSAFSAPHVTITTEIDMSSTIKIRSQLLGMIEQETGYRLSYTEIVMKAVAHA 27- 8 Query: 301 LMKPEHRYLNASLINDAQEIELHNFVNIGIAVGLDDGLIVPVVHNADQMSLSDFVIASKD 36- 0 LM H +NAS + EI H V+IG+AV ++ GL+VPVV + D+ L+ K Sbjct: 279 LMS--HPTINASFFEN--EIVYHEDVHIGLAVAVEGGLVVPVVKHVDKKGLAQLTNECKT 33- 4 Query: 361 VIKKTQEGKLKSAEMSGSTFSITNLGMFGTKTFNPIINQPNSAILGVGATIPTPTVVDGE 42- 0 V ++ +L MSG TF+I+NLGM+ F P+INQP SAILGVG P +DG+ Sbjct: 335 VAMAARDNRLSQEMMSGGTFTISNLGMYAIDVFTPVINQPESAILGVGRIQEKPVGIDGQ 39- 4 Query: 421 IVARPIMAMCLTIDHRIVDGMNGAKFMVDLKNLMENPFGLLI 462 I RP+M L+ DHR++DG A F+ D+K+++E PF LL+ Sbjct: 395 IELRPMMTASLSFDHRVIDGAPAAAFLTDVKSMLEQPFQLLM 436 A related DNA sequence was identified in S. pyogenes <SEQ ID 4267> which encodes the amino acid sequence <SEQ ID 4268>. Analysis of this protein sequence reveals the following: TABLE-US-04124 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4774(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04125 Identities = 354/473 (74%), Positives = 390/473 (81%), Gaps = 15/473 (3%) Query: 1 MAVEIIMPKLGVDMQEGEILEWKKQVGDVVNEGDVLLEIMSDKTNMEIEAEDSGVLLKIT 60 MA EIIMPKLGVDMQEGEI+EWKKQ GD VNEGD+LLEIMSDKTNME+EAEDSGVLLKIT Sbjct: 1 MAFEIIMPKLGVDMQEGEIIEWKKQEGDTVNEGDILLEIMSDKTNMELEAEDSGVLLKIT 60 Query: 61 HGNGDVVPVTETIGYIGAEGEEVTEASSSENTS-----VEENATQVTSEPEKVEETSEPS 115- GD VPVTE IGYIGAEGE V +SSE T+ +A + E V + P Sbjct: 61 RQAGDTVPVTEVIGYIGAEGESVDTIASSEKTTEIPVPASADAGPAVAPKENVASPA-PQ 119- Query: 116 VPAAT----SGEKVRATPAARKLAREMSIDLALVSGTGANGRVHREDVENFKGAQPRITP 17- 1 V A +G KVRATPAARK A EM IDL V GTG GRVH+EDVENFKGAQP+ +P Sbjct: 120 VAATAIPQGNGGKVRATPAARKAAAEMGIDLGQVPGTGPKGRVHKEDVENFKGAQPKASP 17- 9 Query: 172 LARRIAEDQGVDIAEITGSGIRGKIVKNDVLAAMSPQAAEAPVETKATPTTEEK--QLPE 22- 9 LAR+IA D+G+D+A ++G+G GK++K D++A + A P E KA EEK LPE Sbjct: 180 LARKIAADKGIDLATVSGTGFNGKVMKEDIMAILE---AAKPAEAKAPAAKEEKVVDLPE 23- 6 Query: 230 GVEVIKMSAMRKAISKGMTNSYLTAPSFTLNYDIDMTEMMALRKKLIDPIMAKTGLKVSF 28- 9 GVE MSAMRKAISKGMTNSYLTAP+FTLNYDIDMTEM+ALRKKLIDPIMAKTGLKVSF Sbjct: 237 GVEHKPMSAMRKAISKGMTNSYLTAPTFTLNYDIDMTEMIALRKKLIDPIMAKTGLKVSF 29- 6 Query: 290 TDLIGMAVVKTLMKPEHRYLNASLINDAQEIELHNFVNIGIAVGLDDGLIVPVVHNADQM 34- 9 TDLIGMAVVKTLMKPEH Y+NASLINDA +IELH FVN+GIAVGLDDGLIVPV+H A++M Sbjct: 297 TDLIGMAVVKTLMKPEHEYMNASLINDANDIELHRFVNLGIAVGLDDGLIVPVIHGANKM 35- 6 Query: 350 SLSDFVIASKDVIKKTQEGKLKSAEMSGSTFSITNLGMFGTKTFNPIINQPNSAILGVGA 40- 9 LSDFV+ASKDVIKK Q GKLK+AEMSGSTFSITNLGMFGTKTFNPIINQPNSAILGVGA Sbjct: 357 CLSDFVLASKDVIKKAQTGKLKAAEMSGSTFSITNLGMFGTKTFNPIINQPNSAILGVGA 41- 6 Query: 410 TIPTPTVVDGEIVARPIMAMCLTIDHRIVDGMNGAKFMVDLKNLMENPFGLLI 462 TIPTPTVVDGEIV+RPIMAMCLTIDHR+VDGMNGAKFMVDLK LMENPF LLI Sbjct: 417 TIPTPTVVDGEIVSRPIMAMCLTIDHRLVDGMNGAKFMVDLKKLMENPFELLI 469 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1392 A DNA sequence (GBSx1477) was identified in S. agalactiae <SEQ ID 4269> which encodes the amino acid sequence <SEQ ID 4270>. This protein is predicted to be acetoin dehydrogenase (TPP-dependent) beta chain (pdhB). Analysis of this protein sequence reveals the following: TABLE-US-04126 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1267(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9779> which encodes amino acid sequence <SEQ ID 9780> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04127 >GP:BAB04496 GB:AP001509 acetoin dehydrogenase (TPP-dependent) beta chain [Bacillus halodurans] Identities = 189/319 (59%), Positives = 249/319 (77%), Gaps = 1/319 (0%) Query: 11 EAINVAMSEEMRKDEKVFLMGEDVGVYGGDFGTSVGMLEEFGAKRVRDTPISEAAIAGSA 70 - EAI AM+ EMRK+E VF++GED+GVYGG FG + GM+EEFG++RVR+TPISEAAI+G+A Sbjct: 8 EAIREAMTLEMRKNEDVFILGEDIGVYGGAFGVTRGMIEEFGSERVRNTPISEAAISGTA 67 Query: 71 IGAAQTGLRPIVDLTFMDFVTIAMDAIVNQGAKTNYMFGGGLSTPVTFRVASGSGIGSAA 130- IGAA TG+RPI++L F DF+TIAMD +VNQ AK YM+GG P+ R +GSG G+AA Sbjct: 68 IGAALTGMRPILELQFSDFITIAMDNMVNQAAKLRYMYGGKAKVPMVLRTPAGSGTGAAA 127- Query: 131 QHSQSLEAWLTHIPGLKVVAPGTVNESKALLKSSILDNNPVIFLEPKALYGKKEEVNMDP 19- 0 QHSQSLEAW+THIPGLKVV P T ++K LLK++I DNNPVIF E K Y K V + Sbjct: 128 QHSQSLEAWMTHIPGLKVVQPATAYDAKGLLKAAIDDNNPVIFYEHKLCYRTKCHV-PEE 18- 6 Query: 191 DFYIPLGKGDIKREGTDLTIVSYGRMLERVMQAAEEVAEEGINVEVVDPRTLIPLDKELI 25- 0 ++ IPLGK D+KR+GTD+T+V+ M+ + ++AA E+ +EGI+VEV+DPRTL+PLD+E I Sbjct: 187 EYSIPLGKADVKRKGTDVTVVATAVMVHKALEAAVELEKEGISVEVIDPRTLVPLDEETI 24- 6 Query: 251 IDSVKKTGKLILVNDAYKTGGFTGEIATMVAESEAFDYLDHPIVRLASEDVPVPYSRVLE 31- 0 I SVKKT +LI+V++A K GGF GEIA+++AESEAFDYLD PT RL + VP+PY+ LE Sbjct: 247 IRSVKKTSRLIVVHEAVKRGGFGGEIASIIAESEAFDYLDAPIKRLGGKPVPIPYNPTLE 30- 6 Query: 311 QGILPDVAKIKDAIYKVVN 329 + +P V I +A+ + +N Sbjct: 307 RAAIPQVPDIIEAVKETLN 325 A related DNA sequence was identified in S. pyogenes <SEQ ID 4271> which encodes the amino acid sequence <SEQ ID 4272>. Analysis of this protein sequence reveals the following: TABLE-US-04128 Possible site: 18 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.00 Transmembrane 81-97 (81-97) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04129 >GP:BAB04496 GB:AP001509 acetoin dehydrogenase (TPP-dependent) beta chain [Bacillus halodurans] Identities = 187/319 (58%), Positives = 244/319 (75%), Gaps = 1/319 (0%) Query: 11 EAVNLAMTEEMRKDENIFLMGEDVGVYGGDFGTSVGMIEEFGPKRVKDTPISEAAISGAA 70 - EA+ AMT EMRK+E++F++GED+GVYGG FG + GMIEEFG +RV++TPISEAAISG A Sbjct: 8 EAIREAMTLEMRKNEDVFILGEDIGVYGGAFGVTRGMIEEFGSERVRNTPISEAAISGTA 67 Query: 71 IGAAITGLRPIVDVTFMDFLTIMMDAIVNNGAKNNYMFGGGLITPVTFRVASGSGIGSAA 130- IGAA+TG+RPI+++ F DF+TI MD +VN AK YM+GG P+ R +GSG G+AA Sbjct: 68 IGAALTGMRPILELQFSDFITIAMDNMVNQAAKLRYMYGGKAKVPMVLRTPAGSGTGAAA 127- Query: 131 QHSQSLEAWLTHIPGIKVVAPGNANDAKGLLKSAIRDNNIVLFMEPKALYGKKEEVNQDP 19- 0 QHSQSLEAW+THIPG+KVV P A DAKGLLK+AI DNN V+F E K Y K V ++ Sbjct: 128 QHSQSLEAWMTHIPGLKVVQPATAYDAKGLLKAAIDDNNPVIFYEHKLCYRTKCHVPEE- 18- 6 Query: 191 DFYIPLGKGDIKREGTDLTIVSYGRMLERVLQAAEEVAADGINVEVVDPRTLIPLDKELI 25- 0 ++ IPLGK D+KR+GTD+T+V+ M+ + L+AA E+ +GI+VEV+DPRTL+PLD+E I Sbjct: 187 EYSIPLGKADVKRKGTDVTVVATAVMVHKALEAAVELEKEGISVEVIDPRTLVPLDEETI 24- 6 Query: 251 ISSVKKTGKLMLVNDAYKTGGFIGEIATMITESEAFDYLDHPIVRLASEDVPVPYARVLE 31- 0 I SVKKT +L++V++A K GGF GEIA++I ESEAFDYLD PI RL + VP+PY LE Sbjct: 247 IRSVKKTSRLIVVHEAVKRGGFGGEIASIIAESEAFDYLDAPIKRLGGKPVPIPYNPTLE 30- 6 Query: 311 QAILPDVEKIKAAIVKMAN 329 +A +P V I A+ + N Sbjct: 307 RAAIPQVPDIIEAVKETLN 325 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04130 Identities = 286/331 (86%), Positives = 310/331 (93%) Query: 1 MSETKVMALREAINVAMSEEMRKDEKVFLMGEDVGVYGGDFGTSVGMLEEFGAKRVRDTP 60 MSETK+MALREA+N+AM+EEMRKDE +FLMGEDVGVYGGDFGTSVGM+EEFG KRV+DTP Sbjct: 1 MSETKLMALREAVNLAMTEEMRKDENIFLMGEDVGVYGGDFGTSVGDMIEEFGPKRVKDTP 60 Query: 61 ISEAAIAGSAIGAAQTGLRPIVDLTFMDFVTIAMDAIVNQGAKTNYMFGGGLSTPVTFRV 120- ISEAAI+G+AIGAA TGLRPIVD+TFMDF+TI MDAIVN GAK NYMFGGGL TPVTFRV Sbjct: 61 ISEAAISGAAIGAAITGLRPIVDVTFMDFLTIMMDAIVNNGAKNNYMFGGGLITPVTFRV 120- Query: 121 ASGSGIGSAAQHSQSLEAWLTHIPGLKVVAPGTVNESKALLKSSILDNNPVIFLEPKALY 18- 0 ASGSGIGSAAQHSQSLEAWLTHIPG+KVVAPG N++K LLKS+I DNN V+F+EPKALY Sbjct: 121 ASGSGIGSAAQHSQSLEAWLTHIPGIKVVAPGNANDAKGLLISAIRDNNIVLFMEPKALY 18- 0 Query: 181 GKKEEVNMDPDFYIPLGKGDIKREGTDLTIVSYGRMLERVMQAAEEVAEEGINVEVVDPR 24- 0 GKKEEVN DPDFYIPLGKGDIKREGTDLTIVSYGRMLERV+QAAEEVA +GINVEVVDPR Sbjct: 181 GKKEEVNQDPDFYIPLGKGDIKREGTDLTIVSYGRMLERVLQAAEEVAADGINVEVVDPR 24- 0 Query: 241 TLIPLDKELIIDSVKKTGKLILVNDAYKTGGFTGEIATMVAESEAFDYLDHPIVRLASED 30- 0 TLIPLDKELII+SVKKTGKL+LVNDAYKTGGF GEIATM+ ESEAFDYLDHPIVRLASED Sbjct: 241 TLIPLDKELIIESVKKTGKLMLVNDAYKTGGFIGEIATMITESEAFDYLDHPIVRLASED 30- 0 Query: 301 VPVPYSRVLEQGILPDVAKIKDAIYKVVNKG 331 VPVPY+RVLEQ ILPDV KIK AI K+ NKG Sbjct: 301 VPVPYARVLEQAILPDVEKIKAAIVKMANKG 331 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1393 A DNA sequence (GBSx1478) was identified in S. agalactiae <SEQ ID 4273> which encodes the amino acid sequence <SEQ ID 4274>. Analysis of this protein sequence reveals the following:

TABLE-US-04131 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.03 Transmembrane 161-177 (161-178) ----- Final Results ----- bacterial membrane --- Certainty = 0.2211 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9777> which encodes amino acid sequence <SEQ ID 9778> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04132 >GP: BAB04495 GB: AP001509 acetoin dehydrogenase (TPP-dependent) alpha chain [Bacillus halodurans] Identities = 148/317 (46%), Positives = 214/317 (66%), Gaps = 1/317 (0%) Query: 8 LSKEQHLDMFLKMQRIRDVDMKFNKLVRRGFVQGMTHFSVGEEAASVGAIQDLTDSDIIF 67 +++++ +D+F +M IR + K ++ +G + G TH +VG+EA++VG+I L + D + Sbjct: 10 MTEKKLVDLFKQMWLIRYFEEKVDEFFAKGMIHGTTHLAVGQEASAVGSIAVLEERDKLT 69 Query: 68 SNHRGHGQTIAKGIDIGGMFAELAGKATGTSKGRGGSMHLANLERGNYGTNGIVGGGYAL 127- S HRGHG IAKG D+ M AEL G+ TG KG+GGSMH+A++E+GN G NGIVGGG+++ Sbjct: 70 STHRGHGHCIAKGADVNRMMAELFGRETGYCKGKGGSMHIADVERGNLGANGIVGGGFSI 129- Query: 128 AVGAALTQQYEGTDNIVIAFSGDSATNEGSFHESVNLAAVWNLPVIFFIINNRYGISTDI 18- 7 A GAALT + + +V+ F GD A+NEGSFHE+VNLA++W LPV+F NN+YG+S + Sbjct: 130 ATGAALTSKMKKEGYVVLCFFGDGASNEGSFHEAVNLASIWKLPVVFICENNQYGMSGSV 18- 9 Query: 188 TYSTKIPHLYMRADAYGIPGHYVEDGNDLMAVYEKMHEVINYVRSGNGPAIVEVESYRWF 24- 7 I H+ RA YGIPG V DGND+ AV + ++ R G GP IVE ++YRW Sbjct: 190 KEMINIEHISDRAAGYGIPG-MVVDGNDVFAVMNVVGRAVDRARRGEGPTIVEAKTYRWK 24- 8 Query: 248 GHSTADAGVYRTKEEVDSWKAKDPVKRYRAYLIENEIATEEELAAIEAQVIKEVEEGVKF 30- 7 GHS +DA YRT+EE W+ KDP+ R RA L++ I TEES +I+ + +++E+ V+F Sbjct: 249 GHSKSDAKKYRTREEEKEWREKDPIARLRATLVKEGIVTEEEADSIQEEAKQKIEDSVQF 30- 8 Query: 308 AEESPFPDMSVAFEDVF 324 A SP P++ EDV+ Sbjct: 309 ARNSPEPEIESLLEDVY 325 A related DNA sequence was identified in S. pyogenes <SEQ ID 4275> which encodes the amino acid sequence <SEQ ID 4276>. Analysis of this protein sequence reveals the following: TABLE-US-04133 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3502 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04134 Identities = 244/326 (74%), Positives = 278/326 (84%) Query: 1 MEVRMVTLSKEQHLDMFLKMQRIRDVDMKFNKLVRRGFVQGMTHFSVGEEAASVGAIQDL 60 ME MVT+SKEQHLDMFLKM+RIR+ D + NKLVRRGFVQGMTHFSVGEEAA+VGA+ L Sbjct: 1 MEAEMVTVSKEQHLDMFLKMERIREFDSRINKLVRRGFVQGMTHFSVGEEAANVGAVAHL 60 Query: 61 TDSDIIFSNHRGHGQTIAKGIDIGGMFAELAGKATGTSKGRGGSMHLANLEKGNYGTNGI 120- + DIIFSNHRGHGQ+IAK +D+ M AELAGKATG SKGRGGSMHLA+ EKGNYGTNGI Sbjct: 61 SYDDIIFSNHRGHGQSIAKDMDLNKMMAELAGKATGVSKGRGGSMHLADFEKGNYGTNGI 120- Query: 121 VGGGYALAVGAALTQQYEGTDNIVIAFSGDSATNEGSFHESVNLAAVWNLPVIFFIINNR 18- 0 VGGGYALAVGAALTQQY+GT+NI +AFSGD ATNEGSFHESVN+AA W LPVIFFIINNR Sbjct: 121 VGGGYALAVGAALTQQYKGTNNIAVAFSGDGATNEGSFHESVNMAATWKLPVIFFIINNR 18- 0 Query: 181 YGISTDITYSTKIPHLYMRADAYGIPGHYVEDGNDLMAVYEKMHEVINYVRSGNGPAIVE 24- 0 YGIS I +T PHLY RA+AYG+PG Y EDGND+MAVYE M + + +VR GNGPAIVE Sbjct: 181 YGISMSINNATNTPHLYTRAEAYGVPGFYCEDGNDVMAVYETMGKAVEHVRGGNGPAIVE 24- 0 Query: 241 VESYRWFGHSTADAGVYRTKEEVDSWKAKDPVKRYRAYLIENEIATEEELAAIEAQVIKE 30- 0 VESYRWFGHSTADAG YRTKEEVD WK KDP+ +YR YL IAT++EL AI+AQV KE Sbjct: 241 VESYRWFGHSTADAGKYRTKEEVDEWKEKDPMIKYRTYLTSEGIATDDELDAIQAQVKKE 30- 0 Query: 301 VEEGVKFAEESPFPDMSVAFEDVFVD 326 V++ +FA+ SP P++SVAFEDV+VD Sbjct: 301 VDDAYEFAQNSPDPELSVAFEDVWVD 326 A related GBS gene <SEQ ID 8797> and protein <SEQ ID 8798> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04135 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -14.75 GvH: Signal Score (-7.5): -4.24 Possible site: 48 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -3.03 threshold: 0.0 INTEGRAL Likelihood = -3.03 Transmembrane 161-177 (161-178) PERIPHERAL Likelihood = 3.55 117 modified ALOM score: 1.11 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2211 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00092## SEQ ID 8798 (GBS403) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 171 (lane 2; MW 64.4 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 76 (lane 4; MW 39.5 kDa). GBS403-GST was purified as shown in FIG. 218, lane 6. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1394 A DNA sequence (GBSx1479) was identified in S. agalactiae <SEQ ID 4277> which encodes the amino acid sequence <SEQ ID 4278>. This protein is predicted to be ABC transporter. Analysis of this protein sequence reveals the following: TABLE-US-04136 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2464 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9775> which encodes amino acid sequence <SEQ ID 9776> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04137 >GP: CAB12414 GB: Z99107 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 328/643 (51%), Positives = 443/643 (68%), Gaps = 9/643 (1%) Query: 9 MIILQGNKIERSFSGDVLFDNINIQVDQRDRIALVGRNGAGKSTLLKILVGEEAPTKGEI 68 M+ILQ N++ +SF D + +NI ++V RDRIA+VGRNGAGKSTLLKI+ G+ + KGEI Sbjct: 1 MMILQANQLSKSFGADTILNNIKLEVRNRDRIAIVGRNGAGKSTLLKIIAGQLSYEKGEI 60 Query: 69 NKKRDLSLSYLAQDSRFQSENTIFQEMLQVFDSLREVEKRLRELELQMGQVSGSDLEQLM 128- K +D+++ YLAQ + S+ TI +E+L VFD L+ +EK +R +E +M +LE +M Sbjct: 61 IKPKDITMGYLAQHTGLDSKLTIKEELLTVFDHLKAMEKEMRAMEEKMAAADPGELESIM 120- Query: 129 KTYDILSEEFREKGGFTYESDIKAILNGFKFNSDMWEMPISELSGGQNTRLALAKMLLEK 18- 8 KTYD L +EF++KGG+ YE+D++++L+G F+ + LSGGQ TRLAL K+LL + Sbjct: 121 KTYDRLQQEFKDKGGYQYEADVRSVLHGLGFSHFDDSTQVQSLSGGQKTRLALGKLLLTQ 18- 0 Query: 189 PELLVLDEPTNHLDIDTIAWLENYLVNYQGALIIVSHDRYFLDKVATVTYDLTTHSLDRY 24- 8 P+LL+LDEPTNHLDIDT+ WLE+YL Y GA++IVSHDRYFLDKV Y+++ +Y Sbjct: 181 PDLLILDEPTNHLDIDTLTWLEHYLQGYSGAILIVSHDRYFLDKVVNQVYEVSRAESKKY 24- 0 Query: 249 VGNYSKFMDLKAEKIATEEKNFEKQQKEIAKLEDFVQRNIVRASTTKRAQARRKQLEKME 30- 8 GNYS ++D KA + + K +EKQQ EIAKL+DFV RN+RASTTKRAQ+RRKQLE+M+ Sbjct: 241 HGNYSAYLDQKAAQYEKDLKMYEKQQDEIAKLQDFVDRNLARASTTKRAQSRRKQLERMD 30- 0 Query: 309 RLDKPNVEQKSANMTFHAGKVSGNVVLTLENAAIGYEG-VSLSEPIDLDVKKFDAIAIVG 36- 7 + KP ++KSAN F K SGN VL +++ I YE L + + + ++ A+VG Sbjct: 301 VMSKPLGDEKSANFHFDITKQSGNEVLRVQDLTISYENQPPLLTSVSFMLTRGESAALVG 36- 0 Query: 368 PNGIGKSTLIKSLVGQIPFIKGEAKLGANVETGYYDQSQSNLTKTNTVLDELWDAFSTTP 42- 7 PNGIGKSTL+K+L+ + +G G+NV GYYDQ Q+ LT + VLDELWD + P Sbjct: 361 PNGIGKSTLLKTLIDTLKPDQGTISYGSNVSVGYYDQEQAELTSSKRVLDELWDEYPGLP 42- 0 Query: 428 EVEIRNRLGAFLFSGDDVKKSVSMLSGGERARLLLAKLSMENNNFLILDEPTNHLDIDSK 48- 7 E EIR LG FLFSGDDV K V LSGGE+ARL LAKL ++ NFLILDEPTNHLD+DSK Sbjct: 421 EKEIRTCLGNFLFSGDDVLKPVHSLSGGEKARLALAKLMLQKANFLILDEPTNHLDLDSK 48- 0 Query: 488 EVLENALIEFDGTLLFVSHDRYFINRVATKVLEISDKGSTLYLGDYDYYLTKKAELEELA 54- 7 EVLENALI++ GTLLFVSHDRYFINR+AT+VLE+S YLGDYDYY KK E EL Sbjct: 481 EVLENALIDYPGTLLFVSHDRYFINRIATRVLELSSSHIEEYLGDYDYYTEKKTEQLELE 54- 0 Query: 548 RLNEEEVSASKTEIDVTSD----YETQKANQKEFRKITRRVVEIEARLEVLENDENNING 60- 3 ++N++E KT V SD YE +K +K+ R+ RR+ EIE ++ +E + + + Sbjct: 541 KMNQQE-ETDKTPATVKSDSKRSYEEEKEWKKKERQRLRRIEEIETTVQTIEENISRNDE 59- 9 Query: 604 LMLET---NDIGKLSDLQKELESIQEEQLLLMEEWENLNMRLD 643 L+ + D K+ + + E + +E L+ EWE L+ D Sbjct: 600 LLCDPEVYQDHEKVQAIHADNEKLNQELESLLSEWEELSTEED 642 A related DNA sequence was identified in S. pyogenes <SEQ ID 4279> which encodes the amino acid sequence <SEQ ID 4280>. Analysis of this protein sequence reveals the following: TABLE-US-04138 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ---- bacterial cytoplasm --- Certainty = 0.2042 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04139 Identities = 473/635 (74%), Positives = 545/635 (85%), Gaps = 1/635 (0%) Query: 9 MIILQGNKIERSFSGDVLFDNINIQVDQRDRIALVGRNGAGKSTLLKILVGEEAPTKGEI 68 MIILQGNK+ERSFSGDVLF NI++QVD+RDRIALVG NGAGKSTLLK+LVGEE PT GE+ Sbjct: 1 MIILQGNKLERSFSGDVLFQNISLQVDERDRIALVGPNGAGKSTLLKLLVGEETPTSGEV 60 Query: 69 NKKRDLSLSYLAQDSRFQSENTIFQEMLQVFDSLREVEKRLRELELQMGQVSGSDLEQLM 128- N K+DL+LSYLAQ+SRF+S+ TI++EML+VF++LR+ EKRLR++E+ M VSG L +LM Sbjct: 61 NTKKDLTLSYLAQNSRFESDQTIYEEMLKVFEALRQDEKRLRQMEMDMATVSGQVLTRLM 120- Query: 129 KTYDILSEEFREKGGFTYESDIKAILNGFKFNSDMWEMPISELSGGQNTRLALAKMLLEK 18- 8 YD+L+E FR++GGFTYESDIKAILNGFKF+ MW+M I+ELSGGQNTRLALAKMLLEK Sbjct: 121 TDYDLLTEHFRQQGGFTYESDIKAILNGFKFDESMWQMTIAELSGGQNTRLALAKMLLEK 18- 0 Query: 189 PELLVLDEPTNHLDIDTIAWLENYLVNYQGALIIVSHDRYFLDKVATVTYDLTTHSLDRY 24- 8 PELLVLDEPTNHLDI+TIAWLENYL NYQGALIIVSHDRYFLDKVATVT DLT + LDRY Sbjct: 181 PELLVLDEPTNHLDIETIAWLENYLANYQGALIIVSHDRYFLDKVATVTLDLTPNGLDRY 24- 0 Query: 249 VGNYSKFMDLKAEKIATEEKNFEKQQKEIAKLEDFVQRNIVRASTTKRAQARRKQLEKME 30- 8 GNYS+FM LKAEK+ EEK F+KQQKEIAKLEDFVQ+NIVRASTTKRAQARRKQLEK+E Sbjct: 241 SGNYSRFMALKAEKLVAEEKQFDKQQKEIAKLEDFVQKNIVRASTTKRAQARRKQLEKIE 30- 0 Query: 309 RLDKPNVEQKSANMTFHAGKVSGNVVLTLENAAIGYEGVSLSEPIDLDVKKWDAIAIVGP 36- 8 RLDKP +KSA+MTFHA K SGNVVL +E AAIGY LSEPI++D+ K DAIA+VGP Sbjct: 301 RLDKPTGGRKSAHMTFHAEKPSGNVVLRVEEAAIGYGDQVLSEPINVDINKLDAIAVVGP 36- 0 Query: 369 NGIGKSTLIKSLVGQIPFIKGEAKLGANVETGYYDQSQSNLTKTNTVLDELWDAFSTTPE 42- 8 NGIGKSTLIKS++GQ+P +KG+ K GANVETGYYDQ+QS+LT +NTVL+ELW FSTTPE Sbjct: 361 NGIGKSTLIKSIIGQLPLLKGQLKYGANVETGYYDQTQSHLTSSNTVLEELWQDFSTTPE 42- 0 Query: 429 VEIRNRLGAFLFSGDDVKKSVSMLSGGERARLLLAKLSMENNNFLILDEPTNHLDIDSKE 48- 8 V+IRNRLGAFLFSGDDVKKSV+MLSGGE+ARLLLAKLSMENNNFL+LDEPTNHLDIDSKE Sbjct: 421 VDIRNRLGAFLFSGDDVKKSVAMLSGGEKARLLLAKLSMENNNFLVLDEPTNHLDIDSKE 48- 0 Query: 489 VLENALIEFDGTLLFVSHDRYFINRVATKVLEISDKGSTLYLGDYDYYLTKKAELEELAR 54- 8 VLENALI+FDGTLLFVSHDRYFINR+ATKVLEI++ GSTLYLGDYDYYL KKAELEELAR Sbjct: 481 VLENALIDFDGTLLFVSHDRYFINRLATKVLEITENGSTLYLGDYDYYLEKKAELEELAR 54- 0 Query: 549 LNEEEVSASKTEIDVTSDYETQKANQKEFRKITRRVVEIEARLEVLENDENNINGLMLET 60- 8 L E E T DY+ QKANQKE R++TRR EIEARLE +E I M + Sbjct: 541 LAAGETVEETKEASAT-DYQLQKANQKERRRLTRRYEEIEARLETIEERIGAIQEDMHAS 59- 9 Query: 609 NDIGKLSDLQKELESIQEEQLLLMEEWENLNMRLD 643 ND +L QKE + + +EQ LMEEWE + +++ Sbjct: 600 NDTAQLIAWQKEWDQLDQEQEALMEEWETIAEQIE 634 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1395 A DNA sequence (GBSx1480) was identified in S. agalactiae <SEQ ID 4281> which encodes the amino acid sequence <SEQ ID 4282>. This protein is predicted to be thiophene degradation protein F (thdF). Analysis of this protein sequence reveals the following: TABLE-US-04140 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0876(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9773> which encodes amino acid sequence <SEQ ID 9774> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 4283> which encodes the amino acid sequence <SEQ ID 4284>. Analysis of this protein sequence reveals the following: TABLE-US-04141 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0795(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04142 Identities = 384/458 (83%), Positives = 427/458 (92%) Query: 12 MSITKEFDTIAAISTPLGEGAIGIVRISGTDALKIASKIYRGKDLSAIQSHTLNYGHIVD 71 - MSITKEFDTI AISTPLGEGAIGIVR+SGTDAL IA +++GK+L + SHT+NYGHI++ Sbjct: 1 MSITKEFDTITAISTPLGEGAIGIVRLSGTDALAIAQSVFKGKNLEQVASHTINYGHIIN 60 Query: 72 PDKNEILDEVMLGVMLAPKTFTREDVIEINTHGGIAVTNEILQLILRHGARMAEPGEFTK 131- P I+DEVM+ VMLAPRTFTRE+V+EINTHGGIAVTNEILQL++R GARMAEPGEFTK Sbjct: 61 PKTGTIIDEVMVSVMLAPKTFTRENVVEINTHGGIAVTNEILQLLIRQGARMAEPGEFTK 120- Query: 132 RAFLNGRVDLTQAEAVMDLIRAKTDKAMDIAVKQLDGSLKTLINNTRQEILNTLAQVEVN 19- 1 RAFLNGRVDLTQAEAVMD+IRAKTDKAM IAVKQLDGSL LIN+TRQEILNTLAQVEVN Sbjct: 121 RAFLNGRVDLTQAEAVMDIIRAKTDKAMTIAVKQLDGSLSQLINDTRQEILNTLAQVEVN 18- 0 Query: 192 IDYPEYDDVEEMTTTLMREKTQEFQALMENLLRTARRGKILREGLSTAIIGRPNVGKSSL 25- 1 IDYPEYDDVEEMTT L+REKTQEFQ+L+E+LLRTA+RGKILREGLSTAIIGRPNVGKSSL Sbjct: 181 IDYPEYDDVEEMTTALLREKTQEFQSLLESLLRTAKRGKILREGLSTAIIGRPNVGKSSL 24- 0 Query: 252 LNNLLREEKAIVTDIEGTTRDVIEEYVNIKGVPLKLVDTAGIRDTDDIVEKIGVERSKKA 31- 1 LNNLLRE+KAIVTDI GTTRDVIEEYVNIKGVPLKLVDTAGIR+TDD+VE+IGVERSKKA Sbjct: 241 LNNLLREDKAIVTDIAGTTRDVIEEYVNIKGVPLRLVDTAGIRETDDLVEQIGVERSKKA 30- 0 Query: 312 LEEADLVLLVLNSSEPLTLQDRSLLELSKESNRIVLLNKTDLPQKIEVNELPKNVIPISV 37- 1 L+EADLVLLVLN+SE LT QDR+LL LS++SNRI+LLNKTDL QKIE+ +LP + IPISV Sbjct: 301 LQEADLVLLVLNASEKLTDQDRALLNLSQDSNRIILLNKTDLEQKIELEQLPDDYIPISV 36- 0 Query: 372 LENENIDKIEERINDIFFDNAGMVEHDATYLSNARHISLIEKAVDSLKAVNEGLELGMPV 43- 1 L N+NI+ IE+RIN +FFDNAG+VE DATYLSNARHISLIEKAV SL+AVN+GL LGMPV Sbjct: 361 LTNQNINLIEDRINQLFFDNAGLVEQDATYLSNARHISLIEKAVQSLEAVNDGLALGMPV 42- 0 Query: 432 DLLQVDMTRTWEILGEITGDAAPDELITQLFSQFCLGK 469 DLLQVD+TRTWEILGEITGDAAPDELITQLFSQFCLGK Sbjct: 421 DLLQVDLTRTWEILGEITGDAAPDELITQLFSQFCLGK 458 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1396 A DNA sequence (GBSx1481) was identified in S. agalactiae <SEQ ID 4285> which encodes the amino acid sequence <SEQ ID 4286>. Analysis of this protein sequence reveals the following: TABLE-US-04143 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.18 Transmembrane 280-296 (276-299) INTEGRAL Likelihood = -4.83 Transmembrane 249-265 (243-266) ----- Final Results ----- bacterial membrane --- Certainty = 0.4673(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04144 >GP:AAD40365 GB:AF036485 hypothetical protein [Plasmid pNZ4000] Identities = 88/306 (28%), Positives = 149/306 (47%), Gaps = 17/306 (5%) Query: 1 MIVEQKFGNGFTWIN---IEAEQLRTETSEIQAKY-LDSEIITYALDDYERAFMECSHIK 56 MI +K NG WI I AE+ T ++ +Y +D +II Y D+ E I Sbjct: 1 MIKPEKTINGTKWIETIQINAEERAT----LEDQYGIDEDIIEYVTDNDESTNYVYD-IN 55 Query: 57 GKEVLTIIFNTIDLKQKESYYETVPMTFCLSHDRLITVTRSRNSYMLELLQKYLDRNPDV 116- + L I L + Y T P L L T +S + L LD NP+V Sbjct: 56 EDDQLFIFLAPYALDKDALRYITQPFGMLLHKGVLFTFNQSGIPEVNTALYSALD-NPEV 114- Query: 117 -SPKKFLFAALTLITKQYFNVVSKIDREKDILNRQLREQTTNKRLLAMSDLETGSVYLLT 17- 5 S F+ L + + + I ++++ L++ L +T N L+++S L+ +L + Sbjct: 115 KSVDAFILETLFTVVVSFIPISRAITKKRNYLDKMLNRKTKNSDLVSLSYLQQTLTFLSS 17- 4 Query: 176 AANQNALVLEQLDVHPSQRFNSEVEKEQLS---DALIEAHQLVSMTQLNSQVLSQLSSTF 23- 2 A N L +LD P F +++++ D IE Q+ M ++ +QV+ ++ T Sbjct: 175 AVQTN---LSELDRLPKTHFGVGADQDKIDLFEDVQIEGEQVQRMFEIETQVVDRIDHTL 23- 1 Query: 233 NNVLNNNLNENLTGLNIISINLAIIAAITGFFGMNIPLPLTESRSSWLIVIATSVLLWVI 29- 2 N++ NNNLN+ + L I S+ +A+ I+GF+GMN+ LPL + +W++ + SV+L V Sbjct: 232 NSLANNNLNDTMKFLTIWSLTMAVPTIISGFYGMNVKLPLAGMQYAWMLTLGISVVLIVA 29- 1 Query: 293 IAQILK 298 + +LK Sbjct: 292 MLIMLK 297 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1397 A DNA sequence (GBSx1482) was identified in S. agalactiae <SEQ ID 4287> which encodes the amino acid sequence <SEQ ID 4288>. Analysis of this protein sequence reveals the following:

TABLE-US-04145 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1437(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1398 A DNA sequence (GBSx1483) was identified in S. agalactiae <SEQ ID 4289> which encodes the amino acid sequence <SEQ ID 4290>. This protein is predicted to be exonuclease RexA. Analysis of this protein sequence reveals the following: TABLE-US-04146 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3165(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9771> which encodes amino acid sequence <SEQ ID 9772> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04147 >GP:AAC12966 GB:U76424 exonuclease RexA [Lactococcus lactis] Identities = 522/1211 (43%), Positives = 747/1211 (61%), Gaps = 73/1211 (6%) Query: 28 KRTPEQIEAIYTFGNNVLVSASAGSGKTFVMVERILDKLLRGVPIDSLFISTFTVKAAGE 87 - K TPEQ EAI++ G N+LVSASAGSGKTFVM +RI++K+ +G+ ID LFISTFT KAA E Sbjct: 5 KLTPEQNEAIHSSGKNILVSASAGSGKTFVMAQRIVEKVKQGIEIDRLFISTFTRKAASE 64 Query: 88 LKERLEKKINESLKSAESDDLKQFLTQQLVGIQTADIGTMDAFTQKIVNQYGYTLGISPI 147- L+ RLE+ + ++ + + D+ LT L + ADIGTMD+FTQK+ + I P Sbjct: 65 LRMRLERDLKKARQESSDDEEAHRLTLALQNLSNADIGTMDSFTQKLTKANFNRVNIDPN 124- Query: 148 FRILQDKNEQDVIKNEVYADLFSDYMTGKNAAS-----FIKLVKNFSGNRKDSKAFREMV 20- 2 FRIL D+ E D+I+ EV+ L Y++ + + F KL+KNFS +R + F+++V Sbjct: 125 FRILADQTESDLIRQEVFEQLVESYLSADESLNISKDKFEKLIKNFSKDR-NILGFQKVV 18- 3 Query: 203 YKVYAFSQSTDNPKRWMQTVFLKGAQTYTDFEAIPDQEVSSLLNVMQT--TANQLRDLTD 26- 0 Y +Y F+ +T+NP W++ FLKG +TY +++ D +NV + T +L + Sbjct: 184 YTIYRFASATENPISWLENQFLKGFETY---KSLTDLSEDFTVNVKENLLTFFELLEAIS 24- 0 Query: 261 QEDYKQLTAKGVPTANYKKHLKIIENL-VHWSQDFNLLYGKKGLTNLARDITNVIPSGND 31- 9 ++D+ TA L I ++ V S+D L KK + +D+ Sbjct: 241 KKDFVTCTAL---------FLSIDTDIRVGSSKDEALSALKKDFSAQKQDL--------- 28- 2 Query: 320 VTVAGVKYPIFKQLHNRIVGLKHLEVIFKYQGESLFLLELLQSFVLDFSEQYLQEKIQEN 37- 9 V P +L + +KH ++I KYQ ++ + LQ F++DF + YL+ K EN Sbjct: 283 --VGSKSKP--GELRKFVDKIKHGQLIEKYQNQAFEIASDLQKFIIDFYKTYLERKKNEN 33- 8 Query: 380 AFEFSDIAHFAIQILEENHDIRQLYQDKYHEVMVDEYQDNNHTQERMLELLSNGHNRFMV 43- 9 AFE+SDIAHFAI+ILEEN DIR+ ++ Y E+M+DEYQD +HTQERMLELLSNGHN FMV Sbjct: 339 AFEYSDIAHFAIEILEENPDIRENLREHYDEIMIDEYQDTSHTQERMLELLSNGHNLFMV 39- 8 Query: 440 GDIKQSIYRFRQADPQIFNDKYKAYQDNPSQGKLIILKENFRSQSEVLDSTNSVFTHLMD 49- 9 GDIKQSIY FR ADP +F +KYK+Y + +LI LKENFRS+ EVL+ TN +F HLMD Sbjct: 399 GDIKQSIYGFRLADPGLFLEKYKSYDQAENPNQLIRLKENFRSRGEVLNFTNDIFKHLMD 45- 8 Query: 500 EEVGDILYDESHQLKAGS----PRQQERHPNNKTQVLLLDTDEDDIDDSDSQQYDISPAE 55- 5 E++G++ Y + L G+ P + E+ + + +T E++I+DS+ + IS E Sbjct: 459 EKLGEMTYGKEEALVQGNISDYPVEAEKDFYPELLLYKENTSEEEIEDSEVK---ISDGE 51- 5 Query: 556 AKLVAKEIIRLHKEENVPFQDITLLVSSRTRNDGILQTFDRYGIPLVTDGGEQNYLKSVE 61- 5 K A+EI +L E V +DI +LV S++ N+ I Y IP+V D G ++LKS+E Sbjct: 516 IKGAAQEIKKL-IEYGVEPKDIAILVRSKSNNNKIEDILLSYDIPVVLDEGRVDFLKSME 57- 4 Query: 616 VMVMLDTLRSIDNPLNDYALVALLRSPMFGFNEDDLTRIAIQDVK-MAFYHKVKLSYHKE 67- 4 V++MLD LR+IDNPL D +LVA+LRSP+FGFNED+LTRI++Q + + F+ K+ LS KE Sbjct: 575 VLIMLDVLRAIDNPLYDLSLVAMLRSPLFGFNEDELTRISVQGSRDLRFWDKILLSLKKE 63- 4 Query: 675 GHHSDLITPELSSKIDHFMKTFQTWRDFAKWHSLYDLIWKIYNDRFYYDYVGALPKAEQR 73- 4 G + +LI L K+ F + F WR ++ L+WKIY + +Y+DYVGAL E R Sbjct: 635 GKNPELINLSLEQKLKAFNQKFTEWRKLVNKIPIHRLLWKIYTETYYFDYVGALKNGEMR 69- 4 Query: 735 QANLYALALRANQFEKTGFKGLSRFIRMIDKVLENENDLADVEVALPQNAVNLMTIHKSK 79- 4 QANL AL++RA +E +G+KGL +F+R+I+K +E NDLA V + LPQNAV +MT HKSK Sbjct: 695 QANLQALSVRAESYESSGYKGLFKFVRLINKFMEQNNDLASVNIKLPQNAVRVMTFHKSK 75- 4 Query: 795 GLEFKYVFILNIDKKFSMVDITSPLILSRNQGIGIKYVADMRHELEE-EILPAVKVSMET 85- 3 GLEF YVF++N+ +F+ D+ +ILSR G+G+KY+AD++ E + P V MET Sbjct: 755 GLEFDYVFLMNLQSRFNDRDLKEDVILSREHGLGMKYIADLKAEPDVITDFPYALVKMET 81- 4 Query: 854 LPYQLNKRELRLATLSEQMRLLYVAMTRAEKKLYLVGKASQT---KWADHYDLVS-ENNH 90- 9 PY +NK + A LSE+MR+LYVA TRA+KKLYLVGK T + YD + E Sbjct: 815 FPYMVNKDLKQRAALSEEMRVLYVAFTRAKKKLYLVGKIKDTDKKAGLELYDAATLEGKI 87- 4 Query: 910 LPLASRETFVTFQDWLLAVHETYKKQELFYDINFVSLEELTDHHIGMVNPSLPFNPDNK- 96- 8 L R + FQ W+LA+ K L +N + +EL + + PD K Sbjct: 875 LSDKFRNSSRGFQHWILALQNATK---LPMKLNVYTKDELETEKLEFTS-----QPDFKK 92- 6 Query: 969 -VENRQSEDIVRAIS--VLESVEQINQTY--KAAIELPTVRTPSQVKK-IYEPILDIEGV 10- 22 VE + D + + S + E+ + +N Y +AA EL +++TPSQVKK YE L + V Sbjct: 927 LVEESEKFDNIMSFSDEIKEAQKIMNYQYPHQAATELSSIQTPSQVKKRSYEKQLQVGEV 98- 6 Query: 1023 D-VMETITKTSVDFKLPDFSTSKKQDPAALGSAVHELMQRIEMSSHVKMEDIQKALTEVN 1- 081 V E + ++DF DF KK A +GSA H MQ + S + Q L E+ Sbjct: 987 QPVSEFVRVKNLDFS--DFG-PKKITAAEMGSATHSFMQYADF-SQADLFSFQATLDEMG 10- 42 Query: 1082 AETSVKAAIQIEKINYFFQETSLGKYIQEEVEHLHREAPFAMLKEDPESGEKFVVRGIID 1- 141 + +K I I KI F +T G+++ E V+ +EAPF+ML+ D + E+++VRGI D Sbjct: 1043 FDEKIKNQIDITKILTLF-DTEFGQFLSENVDKTVKEAPFSMLRTDEFAKEQYIVRGICD 1- 101 Query: 1142 GYLLLENRIILFDYKTDKFVNP---LELKERYQGQMALYAEALKKSYEIEKIDKYLILLG 1- 198 G++ L ++IILFDYKTD+F N E+KERY+ QM LY+EAL+K+Y + +IDKYLILLG Sbjct: 1102 GFVKLADKIILFDYKTDRFTNVSAISEIKERYKDQMNLYSEALQKAYHVNQIDKYLILLG 1- 161 Query: 1199 G-KQLEVVKMD 1208 G +++ V K+D Sbjct: 1162 GPRKVFVEKID 1172 A related DNA sequence was identified in S. pyogenes <SEQ ID 4291> which encodes the amino acid sequence <SEQ ID 4292>. Analysis of this protein sequence reveals the following: TABLE-US-04148 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04149 >GP:AAC12966 GB:U76424 exonuclease RexA [Lactococcus lactis] Identities = 478/1206 (39%), Positives = 700/1206 (57%), Gaps = 65/1206 (5%) Query: 40 KRTAQQIEAIYTSGQNILVSASAGSGKTFVMVERILDKILRGVSIDRLFISTFTVKAATE 99 - K T +Q EAI++SG+NILVSASAGSGKTFVM +RI++K+ +G+ IDRLFISTFT KAA+E Sbjct: 5 KLTPEQNEAIHSSGKNILVSASAGSGKTFVMAQRIVEKVKQGIEIDRLFISTFTKKAASE 64 Query: 100 LRERIENKLYSQIAQTTDFQMKVYLTEQLQSLCQADIGTMDAFAQKVVSRYGYSIGISSQ 15- 9 LR R+E L +++D + LT LQ+L ADIGTMD+F QK+ + I Sbjct: 65 LRMRLERDLKKARQESSDDEEAHRLTLALQNLSNADIGTMDSFTQKLTKANFNRVNIDPN 124- Query: 160 FRIMQDKAEQDVLKQEVFSKLFNEFMNQKEA-----PVFRALVKNFSGNCKDTSAFRELV 21- 4 FRI+ D+ E D+++QEVF +L +++ E+ F L+KNFS + ++ F+++V Sbjct: 125 FRILADQTESDLIRQEVFEQLVESYLSADESLNISKDKFEKLIKNFSKD-RNILGFQKVV 18- 3 Query: 215 YTCYSFSQSTENPKIWLQENFLSAAKTYQRLEDIPDHDIELLLLAMQDTANQLRDVTDME 27- 4 YT Y F+ +TENP WL+ FL +TY+ L D+ + D + + T +L + + Sbjct: 184 YTIYRFASATENPISWLENQFLKGFETYRSLTDLSE-DFTVNVKENLLTFFELLEAISKK 24- 2 Query: 275 DYGQLTKAG-SRSAKYTKHLTIIEKLSDWVRDFKCLYGKAGLDRLIRDVTGLIPSGNDVT 33- 3 D+ T S + E LS +DF D+ Sbjct: 243 DFVTCTALFLSIDTDIRVGSSKDEALSALKKDFSA-------------------QKQDLV 28- 3 Query: 334 VSKVKYPVFKTLHQKLKQFRHLETILMYQKDCFSLLEQLQDFVLAFSEAYLAVKIQESAF 39- 3 SK K + K+K H + I YQ F + LQ F++ F + YL K E+AF Sbjct: 284 GSKSKPGELRKFVDKIK---HGQLIEKYQNQAFEIASDLQKFIIDFYKTYLERKKNENAF 34- 0 Query: 394 EFSDIAHFAIKILEENTDIRQSYQQHYHEVMVDEYQDNNHMQERLLTLLSNGHNRFMVGD 45- 3 E+SDIAHFAI+ILEEN DIR++ ++HY E+M+DEYQD +H QER+L LLSNGHN FMVGD Sbjct: 341 EYSDIAHFAIEILEENPDIRENLREHYDEIMIDEYQDTSHTQERMLELLSNGHNLFMVGD 40- 0 Query: 454 IKQSIYRFRQADPQIFNQKFRDYQKKPEQGKVILLKENFRSQSEVLNVSNAVFSHLMDES 51- 3 IKQSIY FR ADP +F +K++ Y + ++I LKENFRS+ EVLN +N +F HLMDE Sbjct: 401 IKQSIYGFRLADPGLFLEKYKSYDQAENPNQLIRLKENFRSRGEVLNFTNDIFKHLMDEK 46- 0 Query: 514 VGDVLYDEQHQLIAG--SHAQTVPYLDRRAQLLLYNSDKDDGNAPSDSEGISFSEVTIVA 57- 1 +G++ Y ++ L+ G S D +LLLY + + IS E+ A Sbjct: 461 LGEMTYGKEEALVQGNISDYPVEAEKDFYPELLLYKENTSEEEIEDSEVKISDGEIKGAA 52- 0 Query: 572 KEIIKLHNDKGVPFEDITLLVSSRTRNDIISHTFNQYGIPIATDGGQQNYLKSVEVMVML 63- 1 +EI KL + GV +DI +LV S++ N+ I Y IP+ D G+ ++LKS+EV++ML Sbjct: 521 QEIKKL-IEYGVEPKDIAILVRSKSNNNKIEDILLSYDIPVVLDEGRVDFLKSMEVLIML 57- 9 Query: 632 DTLRTINNPRNDYALVALLRSPMFAFDEDDLARIALQKDNELDKDCLYDKIQRAVIGRGA 69- 1 D LR I+NP D +LVA+LRSP+F F+ED+L RI++Q +L +DKI ++ G Sbjct: 580 DVLRAIDNPLYDLSLVAMLRSPLFGFNEDELTRISVQGSRDLR---FWDKILLSLKKEGK 63- 6 Query: 692 HPELIHDTLLGKLNVFLKTLKSWRRYAKLGSLYDLIWKIFNDRFYFDFVASQAKAEQAQA 75- 1 +PELI+ +L KL F + WR+ ++ L+WKI+ + +YFD+V + E QA Sbjct: 637 NPELINLSLEQKLKAFNQKFTEWRKLVNKIPIHRLLWKIYTETYYFDYVGALKNGEMRQA 69- 6 Query: 752 NLYALALRANQFEKSGYKGLYRFIKMIDKVLETQNDLADVEVATPKQAVNLMTIHKSKGL 81- 1 NL AL++RA +E SGYKGL++F+++I+K +E NDLA V + P+ AV +MT HKSKGL Sbjct: 697 NLQALSVRAESYESSGYKGLFKFVRLINKFMEQNNDLASVNIKLPQNAVRVMTFHKSKGL 75- 6 Query: 812 QFPYVFILNCDKRFSMTDIHKSFILNRQHGIGIKYLADIKGLLGE-TTLNSVKVSMETLP 87- 0 +F YVF++N RF+ D+ + IL+R+HG+G+KY+AD+K T V MET P Sbjct: 757 EFDYVFLMNLQSRFNDRDLKEDVILSREHGLGMKYIADLKAEPDVITDFPYALVKMETFP 81- 6 Query: 871 YQLNKQELRLATLSEEMRLLYVAMTRAEKKVYFIGK---ASKSKSQEITDPKKL-GKLLP 92- 6 Y +NK + A LSEEMR+LYVA TRA+KK+Y +GK K E+ D L GK+L Sbjct: 817 YMVNKDLKQRAALSEEMRVLYVAFTRAKKKLYLVGKIKDTDKKAGLELYDAATLEGKILS 87- 6 Query: 927 LALREQLLTFQDWLLAIADIFSTEDLYFDVRFIEDSDLTQESVGRLQTP---QLLNPDDL 98- 3 R FQ W+LA+ + L + +L E + P +L+ + Sbjct: 877 DKFRNSSRGFQHWILALQ---NATKLPMKLNVYTKDELETEKLEFTSQPDFKKLVEESEK 93- 3 Query: 984 KDNRQSETIARALDMLEAVSQLNANY--EAAIHLPTVRTPSQL-KATYEPLLEPIGVDII 10- 40 DN S + ++ EA +N Y +AA L +++TPSQ+ K +YE L+ V + Sbjct: 934 FDNIMSFSD----EIKEAQKIMNYQYPHQAATELSSIQTPSQVKKRSYEKQLQVGEVQPV 98- 9 Query: 1041 EKSSRSLSDFTLPHFSKKAKVEASHIGSALHQLMQVLPLSKP--INQQTLLDALRGIDSN 1- 098 + R + + F K K+ A+ +GSA H MQ S+ + Q LD + G D Sbjct: 990 SEFVR-VKNLDFSDFGPK-KITAAEMGSATHSFMQYADFSQADLFSFQATLDEM-GFD-- 10- 44 Query: 1099 EEVKTALDLKKIESFFCDTSLGQFFQTYQKHLYREAPFAILKLDPISQEEYVLRGIIDAY 1- 158 E++K +D+ KI + F DT GQF +EAPF++L+ D ++E+Y++RGI D + Sbjct: 1045 EKIKNQIDITKILTLF-DTEFGQFLSENVDKTVKEAPFSMLRTDEFAKEQYIVRGICDGF 1- 103 Query: 1159 FLFDDHIVLVDYKTDKYKQP---IELKKRYQQQLELYAEALTQTYKLPVTKRYLVLMGGG 1- 215 D I+L DYKTD++ E+K+RY+ Q+ LY+EAL + Y + +YL+L+GG Sbjct: 1104 VKLADEIILFDYKTDRFTNVSAISEIKERYKDQMNLYSEALQKAYHVNQIDKYLILLGGP 1- 163 Query: 1216 KPEIVE 1221 + VE Sbjct: 1164 RKVFVE 1169 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04150 Identities = 728/1211 (60%), Positives = 916/1211 (75%), Gaps = 5/1211 (0%) Query: 1 MMTFKPFLNPEDIAVIQTEEKNSDKKQKRTPEQIEAIYTFGNNVLVSASAGSGKTFVMVE 60 +++F PFL+PE I +Q E+ D+ QKRT +QIEAIYT G N+LVSASAGSGKTFVMVE Sbjct: 13 VISFAPFLSPEAIKHLQENERCRDQSQKRTAQQIEAIYTSGQNILVSASAGSGKTFVMVE 72 Query: 61 RILDKLLRGVPIDSLFISTFTVKAAGELKERLEKKINESLKSAESDDLKQFLTQQLVGIQ 120- RILDK+LRGV ID LFISTFTVKAA EL+ER+E K+ + +K +LT+QL + Sbjct: 73 RILDKILRGVSIDRLFISTFTVKAATELRERIENKLYSQIAQTTDFQMKVYLTEQLQSLC 132- Query: 121 TADIGTMDAFTQKIVNQYGYTLGISPIFRILQDKNEQDVIKNEVYADLFSDYMTGKNAAS 18- 0 ADIGTMDAF QK+V++YGY++GIS FRI+QDK EQDV+K EV++ LF+++M K A Sbjct: 133 QADIGTMDAFAQKVVSRYGYSIGISSQFRIMQDKAEQDVLKQEVFSKLFNEFMNQKEAPV 19- 2 Query: 181 FIKLVKNFSGNRKDSKAFREMVYKVYAFSQSTDNPKRWMQTVFLKGAQTYTDFEAIPDQE 24- 0 F LVKNFSGN KD+ AFRE+VY Y+FSQST+NPK W+Q FL A+TY E IPD + Sbjct: 193 FRALVKNFSGNCKDTSAFRELVYTCYSFSQSTENPKIWLQENFLSAAKTYQRLEDIPDHD 25- 2 Query: 241 VSSLLNVMQTTANQLRDLTDQEDYKQLTAKGVPTANYKKHLKIIENLVHWSQDFNLLYGK 30- 0 + LL MQ TANQLRD+TD EDY QLT G +A Y KHL IIE L W +DF LYGK Sbjct: 253 IELLLLAMQDTANQLRDVTDMEDYGQLTKAGSRSAKYTKHLTIIEKLSDWVRDFKCLYGK 31- 2 Query: 301 KGLTNLARDITNVIPSGNDVTVAGVKYPIFKQLHNRIVGLKHLEVIFKYQGESLFLLELL 36- 0 GL L RD+T +IPSGNDVTV+ VKYP+FK LH ++ +HLE I YQ + LLE L Sbjct: 313 AGLDRLIRDVTGLIPSGNDVTVSKVKYPVFKTLHQKLKQFRHLETILMYQKDCFSLLEQL 37- 2 Query: 361 QSFVLDFSEQYLQEKIQENAFEFSDIAHFAIQILEENHDIRQLYQDKYHEVMVDEYQDNN 42- 0 Q FVL FSE YL KIQE+AFEFSDIAHFAI+ILEEN DIRQ YQ YHEVMVDEYQDNN Sbjct: 373 QDFVLAFSEAYLAVKIQESAFEFSDIAHFAIKILEENTDIRQSYQQHYHEVMVDEYQDNN 43- 2 Query: 421 HTQERMLELLSNGHNRFMVGDIKQSIYRFRQADPQIFNDKYKAYQDNPSQGKLIILKENF 48- 0 H QER+L LLSNGHNRFMVGDIKQSIYRFRQADPQIFN K++ YQ P QGK+I+LKENF Sbjct: 433 HMQERLLTLLSNGHNRFMVGDIKQSIYRFRQADPQIFNQKFRDYQKKPEQGKVILLKENF 49- 2 Query: 481 RSQSEVLDSTNSVFTHLMDEEVGDILYDESHQLKAGSPRQQERHPNNKTQVLLLDTDEDD 54- 0 RSQSEVL+ +N+VF+HLMDE VGD+LYDE HQL AGS Q + + + Q+LL ++D+DD Sbjct: 493 RSQSEVLNVSNAVFSHLMDESVGDVLYDEQHQLIAGSHAQTVPYLDRRAQLLLYNSDKDD 55- 2 Query: 541 IDDSDSQQYDISPAEAKLVAKEIIRLHKEENVPFQDITLLVSSRTRNDGILQTFDRYGIP 60- 0 ++ S IS +E +VAKEII+LH ++ VPF+DITLLVSSRTRND I TF++YGIP Sbjct: 553 -GNAPSDSEGISFSEVTIVAKEIIKLHNDKGVPFEDITLLVSSRTRNDIISHTFNQYGIP 61- 1 Query: 601 LVTDGGEQNYLKSVEVMVMLDTLRSIDNPLNDYALVALLRSPMFGFNEDDLTRIAIQD-- 65- 8 + TDGG+QNYLKSVEVMVMLDTLR+I+NP NDYALVALLRSPMF F+EDDL RIA+Q Sbjct: 612 IATDGGQQNYLKSVEVMVMLDTLRTINNPRNDYALVALLRSPMFAFDEDDLARIALQKDN 67- 1 Query: 659 --VKMAFYHKVKLSYHKEGHHSDLITPELSSKIDHFMKTFQTWRDFAKWHSLYDLIWKIY 71- 6 K Y K++ + G H +LI L K++ F+KT ++WR +AK SLYDLIWKI+ Sbjct: 672 ELDKDCLYDKIQRAVIGRGAHPELIHDTLLGKLNVFLKTLKSWRRYAKLGSLYDLIWKIF 73- 1 Query: 717 NDRFYYDYVGALPKAEQRQANLYALALRANQFEKTGFKGLSRFIRMIDKVLENENDLADV 77- 6 NDRFY+D+V + KAEQ QANLYALALRANQFEK+G+KGL RFI+MIDKVLE +NDLADV Sbjct: 732 NDRFYFDFVASQAKAEQAQANLYALALRANQFEKSGYKGLYRFIKMIDKVLETQNDLADV 79- 1 Query: 777 EVALPQNAVNLMTIHKSKGLEFKYVFILNIDKKFSMVDITSPLILSRNQGIGIKYVADMR 83- 6 EVA P+ AVNLMTIHKSKGL+F YVFILN DK+FSM DI IL+R GIGIKY+AD++ Sbjct: 792 EVATPKQAVNLMTIHKSKGLQFPYVFILNCDKRFSMTDIHKSFILNRQHGIGIKYLADIK 85- 1 Query: 837 HELEEEILPAVKVSMETLPYQLNKRELRLATLSEQMRLLYVAMTRAEKKLYLVGKASQTK 89- 6 L E L +VKVSMETLPYQLNK+ELRLATLSE+MRLLYVAMTRAEKK+Y +GKAS++K Sbjct: 852 GLLGETTLNSVKVSMETLPYQLNKQELRLATLSEEMRLLYVAMTRAEKKVYFIGKASKSK 91- 1 Query: 897 WADHYDLVSENNHLPLASRETFVTFQDWLLAVHETYKKQELFYDINFVSLEELTDHHIGM 95- 6 + D LPLA RE +TFQDWLLA+ + + ++L++D+ F+ +LT +G Sbjct: 912 SQEITDPKKLGKLLPLALREQLLTFQDWLLAIADIFSTEDLYFDVRFIEDSDLTQESVGR 97- 1 Query: 957 VNPSLPFNPDNKVENRQSEDIVRAISVLESVEQINQTYKAAIELPTVRTPSQVKKIYEPI 10- 16 + NPD+ +NRQSE I RA+ +LE+V Q+N Y+AAI LPTVRTPSQ+K YEP+ Sbjct: 972 LQTPQLLNPDDLKDNRQSETIARALDMLEAVSQLNANYEAAIHLPTVRTPSQLKATYEPL 10- 31 Query: 1017 LDIEGVDVMETITKTSVDFKLPDFSTSKKQDPAALGSAVHELMQRIEMSSHVKMEDIQKA 1- 076 L+ GVD++E +++ DF LP FS K + + +GSA+H+LMQ + +S + + + A Sbjct: 1032 LEPIGVDIIEKSSRSLSDFTLPHFSKKAKVEASHIGSALHQLMQVLPLSKPINQQTLLDA 1- 091 Query: 1077 LTEVNAETSVKAAIQIEKINYFFQETSLGKYIQEEVEHLHREAPFAMLKEDPESGEKFVV 1- 136 L +++ VK A+ ++KI FF +TSLG++ Q +HL+REAPFA+LK DP S E++V+ Sbjct: 1092 LRGIDSNEEVKTALDLKKIESFFCDTSLGQFFQTYQKHLYREAPFAILKLDPISQEEYVL 1- 151 Query: 1137 RGIIDGYLLLENRIILFDYKTDKFVNPLELKERYQGQMALYAEALKKSYEIEKIDKYLIL 1- 196 RGIID Y L ++ I+L DYKTDK+ P+ELK+RYQ Q+ LYAEAL ++Y++ +YL+L Sbjct: 1152 RGIIDAYFLFDDHIVLVDYKTDKYKQPIELKKRYQQQLELYAEALTQTYKLPVTKRYLVL 1- 211 Query: 1197 LGGKQLEVVKM 1207 +GG + E+V++ Sbjct: 1212 MGGGKPEIVEV 1222 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1399 A DNA sequence (GBSx1484) was identified in S. agalactiae <SEQ ID 4293> which encodes the amino acid sequence <SEQ ID 4294>. This protein is predicted to be exonuclease RexB. Analysis of this protein sequence reveals the following: TABLE-US-04151 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0660(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04152 >GP: AAC12965 GB: U76424 exonuclease RexB [Lactococcus lactis] Identities = 363/1093 (33%), Positives = 604/1093 (55%), Gaps = 67/1093 (6%) Query: 1 MKLLYTDINHDMTEILVNQAAHAAEAGWRIFYIAPNSLSFEKERAVLENLPQ---EASFA 57 M++LYT+I D+TE L+ A E +++YI P+S+SFEKE+ +LE L + A F Sbjct: 1 MEILYTEITQDLTEGLLEIALEELEKNRKVYYIVPSSMSFEKEKEILERLAKGSDTAVFD 60 Query: 58 ITITRFAQLARYFTLNQP-NQKESLNDIGLAMIFYRALASFEDGQLKVFGRLKQDASFIS 116- + +TRF QL YF + K L +GL+M+F R L SF+ ++ ++ L+ A F+ Sbjct: 61 LLVTRFKQLPYYFDKREKATMKTELGTVGLSMLFRRVLRSFKKDEIPLYFSLQDSAGFLE 120- Query: 117 QLVDLYKELQTANLSILELKYLHSPEKFEDLLAIFLVVSDLLREGEYDNQSKIAFFTEQV 17- 6 L+ L EL TANLS+ L ++ + +LA F + EY N S+ FT ++ Sbjct: 121 MLIQLRAELLTANLSVENLPDNPKNQELKKILAKFEAELSV----EYANYSEFGDFTNRL 17- 6 Query: 177 RSGQLDVDLKNTILIVDGFTRFSAEEEALIKSLSSRCQEIIIGAYASQKAYKANFTNGNI 23- 6 G+ D LK+ +I+DG+TRFSAEEE I+S+ + ++G Y+ + + A + I Sbjct: 177 VDGEFDQQLKDVTIIIDGYTRFSAEEELFIESIQEKVARFVVGTYSDENSLTAG--SETI 23- 4 Query: 237 YSAGVDFLRYLATTFQTKPEFILSKWESKSGFEMISK-----NIEGKHDFTNSSHILDDT 29- 1 Y + T F+ K L K S + E+ SK +++ + T+ L Sbjct: 235 YVGTSQMI----TRFRNKFPVELRKIASSAVNEVYSKLTRILDLDSRFVITDEKIELKAE 29- 0 Query: 292 AKDCITIWECINQKDEVEHVARAIRQKLYQGYRYKDILVLLGDVDSYKLQLSKIFEQYDI 35- 1 + IWE NQK E+E VA+ IRQK+ QG +KD VL+GD +Y++ L ++F+ Y+I Sbjct: 291 DEKYFRIWEAENQKVEIERVAKEIRQKIIQGAFFKDFTVLVGDPAAYEITLKEVFDLYEI 35- 0 Query: 352 PYYFGKAETMAAHPLVHFMDSLSRIKRYRFRAEDVLNLFKTGIYGEISQDD--LDYFEAY 40- 9 P+++ + E+M+ HPLV F +SL IK+ +R +DV+NL K+ +Y + + D+ +DYFE Y Sbjct: 351 PFFYAQEESMSQHPLVIFFESLFAIKKNNYRTDDVVNLLKSKVYTDANLDEEVIDYFEYY 41- 0 Query: 410 ISYADIKGPKKFFTDFVVGAKKFDLGRLNTIRQSLL---TPLESFV-KTKKQDGIKTLNQ 46- 5 + I G KKF +F+ ++ + +N +R+ LL +PL+ F+ +K+ G K ++ Sbjct: 411 VQKYKISGRKKFTEEFIE-SEFSQIELVNEMREKLLGSESPLQVFLGNNRKKTGKKWVSD 46- 9 Query: 466 FMFFLTQVGLSDNLSRLVGQMS-ENEQE---KHQEVWKTFTDILEQFQTIFGQEKLNLDE 52- 1 L + N++ +NE + KH++VW+ L +F +F EKL E Sbjct: 470 LQGLLENGNVMTNMNAYFSAAELQNEHQMADKHEQVWQMLISTLNEFLAVFSDEKLKSVE 52- 9 Query: 522 FLSLLNSGMMQAEYRMVPATVDVVTVKSYDLVEPHSNQFVYALGMTQSHFPKIAQNKSLI 58- 1 FL +L +G+ A+YR +PA VDVV VK Y+LVEP +N+++YA+G++Q++FP+I +N +L+ Sbjct: 530 FLDILLAGLKNAKYRQIPANVDVVNVKDYELVEPKTNKYIYAIGLSQTNFPRIKKNSTLL 58- 9 Query: 582 SDIERQLINDANDTDGHFDIMTQENLKKNHFAALSLFNAAKQELVLTIPQLLNESEDQMS 64- 1 SD ER IN D + + + N +KN F LSL N+AK+ LVL++PQ++ + + S Sbjct: 590 SDEERLEINQTTDENQFIEQLNVANYQKNQFTVLSLINSAKESLVLSMPQIMANEQGEFS 64- 9 Query: 642 P-YLVELRDIGVPFNHKGR-QSLKEEADNIGNYKALLSRVVDLYRSAIDKEMTKEE-QTF 69- 8 P + + L+D K + +L E ++IGN +++++ + + R ++ E T E+ + F Sbjct: 650 PVFQLFLKDADEKILQKIQGVNLFESLEHIGNSRSVIAMIGQIERELVESEETSEDKRVF 70- 9 Query: 699 WSVAVRYLRRQLTSKGIEIPIITDSLDTVTVSSDVMTRRFPEDDPLKLSSSALTTFYNNQ 75- 8 WS R L + + + +DTV ++ D + + + D + S S+ FYN + Sbjct: 710 WSSIFRILVKSNADFQKILLDLAKDIDTVNLAPDTLEQIY--GDKIYASVSSFERFYNCE 76- 7 Query: 759 YKYFLQYVLGLEEQDSIHPDMRHHGTYLHRVFEILMKNQGI--ESFEEKLNSAINKTNQE 81- 6 Y+YFL+ L LE ++I + + G + H VFE +MK + E+F+EKL + + ++ Sbjct: 768 YQYFLENTLSLETFENIDINSKIVGNFFHEVFEKVMKETDLSAENFDEKLTLVLQEVDKN 82- 7 Query: 817 DVFKSLYSEDAESRYSLEILEDIARATATILR----QDSQMTVESE-------EERFELM 86- 5 + +++DA +R++ LE+I R TAT+L+ D T+ +E E Sbjct: 828 --YSRYFTQDATARFTWSNLEEIVRQTATVLKATVSTDELKTLLTESSFGLPKSELGNFS 88- 5 Query: 866 IDNTIKINGIIDRIDRLSDGSLGVVDYKSSAQKFDIQKFYNGLSPQLVTYIDAISRDKEV 92- 5 +D+ I + G IDR+D+LS LG +DYKSSA F +Q+ Y+GLS Q +TY+D I K+ Sbjct: 886 VDD-IYLRGRIDRLDQLSTDYLGAIDYKSSAHSFKLQEAYDGLSLQFMTYLDVI---KQA 94- 1 Query: 926 EQKPPIFGAMYLHMQEPRQDLSKIKNLDDLVTKNHQALTYKGLFSEAEKEFLANGKYHL- 98- 4 I+GA+YL + +LS+I L ++ +++ Y+GL E E + G ++ Sbjct: 942 FPNQKIWGALYLQFKNQPINLSEINQLSEIANILKESMRYEGLVLEDAAEQI-KGIENIA 10- 00 Query: 985 --KDSLYSETEIAILQAHNQSLYKKASETIKSGKFLINPYTEDAKTVDGD---------Q 10- 33 K ++Y+E E L N+ Y+ A + +K GK INP + ++ +D Sbjct: 1001 LKKTNIYNEEEFEQLLKLNEEHYRAAGQRLKKGKIAINPIMKRSEGIDQSGNVRGCRYCP 1- 060 Query: 1034 FKSITGFEADRHM 1046 KSI FEA+ HM Sbjct: 1061 LKSICRFEANIHM 1073 A related DNA sequence was identified in S. pyogenes <SEQ ID 4295> which encodes the amino acid sequence <SEQ ID 4296>. Analysis of this protein sequence reveals the following:

TABLE-US-04153 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1891(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04154 Identities = 546/1075 (50%), Positives = 758/1075 (69%), Gaps = 11/1075 (1%) Query: 1 MKLLYTDINHDMTEILVNQAAHAAEAGWRIFYIAPNSLSFEKERAVLENLPQEASFAITI 60 MKL+TY++++ MTEILVN+A AA+ G+R+FYIAPNSLSFEKER VL LP+ +F+I + Sbjct: 1 MKLIYTEMSYSMTEILVNEARKAADQGYRVFYIAPNSLSFEKEREVLTLLPERGTFSIIV 60 Query: 61 TRFAQLARYFTLNQPNQKESLNDIGLAMIFYRALASFEDGQLKVFGRLKQDASFISQLVD 120- TRF Q++RYFT+ K+ L+D LAMIFYRAL + L +GRL+ ++ FI QLV+ Sbjct: 61 TRFVQMSRYFTVESSPSKQHLDDTTLAMIFYRALMQLKPEDLPSYGRLQNNSVFIEQLVE 120- Query: 121 LYKELQTANLSILELKYLHSPEKFEDLLAIFLVVSDLLREGEYDNQSKIAFFTEQVRSGQ 18- 0 LYKEL+ A LS+ +L L P+K EDL+ I + ++ + +Y+ S + F ++ G Sbjct: 121 LYKELKNAQLSVHDLTGLDHPQKQEDLIKIIELAETIMIQQDYNQDSPLQSFARAIKLGL 18- 0 Query: 181 LDVDLKNTILIVDGFTRFSAEEEALIKSLSSRCQEIIIGAYASQKAYKANFTNGNIYSAG 24- 0 L+ L T++++DGF+RFSAEE+ L+ L++ CQE+IIG+Y SQKAY+ +F GNIY A Sbjct: 181 LNNQLSKTVVVIDGFSRFSAEEDYLLSLLNNNCQEVIIGSYVSQKAYQKSFIKGNIYEAS 24- 0 Query: 241 VDFLRYLATTFQTKPEFILSKWESKSGFEMISKNIEGKHDFTNSSHILDDTAKDCITIWE 30- 0 + FL+ LA + KP F S K F +++ E HDF+ L + D ++W+ Sbjct: 241 LHFLQDLAQKYHIKPVFATSNQVFKPAFSRLTQLFEATHDFSQVDWQLQKSDLDHFSLWQ 30- 0 Query: 301 CINQKDEVEHVARAIRQKLYQGYRYKDILVLLGDVDSYKLQLSKIFEQYDIPYYFGKAET 36- 0 C +QK+E+EHVA++IRQKLY+GYRYKDILVLLGD+D+Y+LQ+ IF++++IPYY GKAE Sbjct: 301 CHHQKEEIEHVAKSIRQKLYEGYRYKDILVLLGDMDAYQLQIGPIFDKFEIPYYLGKAEP 36- 0 Query: 361 MAAHPLVHFMDSLSRIKRYRFRAEDVLNLFKTGIYGEISQDDLDYFEAYISYADIKGPKK 42- 0 MAAHPLV F++SL R +RY +R ED+LN+ K+G++G D+D FE Y +ADIKG K Sbjct: 361 MAAHPLVQFIESLERSQRYNWRREDILNMLKSGLFGCFDDSDIDRFEEYTQFADIKGFTK 42- 0 Query: 421 FFTDFVV-GAKKFDLGRLNTIRQSLLTPLESFVKTKKQDGIKTLNQFMFFLTQVGLSDNL 47- 9 F F + ++++ L LN +RQ ++ PL+ K++KQ G +++ + FL ++ L++N+ Sbjct: 421 FSKPFTINSSRQYPLDFLNEMRQDIVLPLQELFKSQKQLGASLVDKLILFLKKIRLAENM 48- 0 Query: 480 SRLVGQMSENEQEKHQEVWKTFTDILEQFQTIFGQEKLNLDEFLSLLNSGMMQAEYRMVP 53- 9 L S+ E EK++EVWK FTDIL F IFGQEKL L + L+L+ +GM A+YR+VP Sbjct: 481 QGLA--QSQLEVEKNEEVWKRFTDILTSFHHIFGQEKLRLSDCLALIKTGMKSAQYRVVP 53- 8 Query: 540 ATVDVVTVKSYDLVEPHSNQFVYALGMTQSHFPKIAQNKSLISDIERQLINDANDTDGHF 59- 9 AT+DVVT+KSYDLV+PHS FVYA+G+TQSHFPK + L+SD ER IN+ + HF Sbjct: 539 ATLDVVTIKSYDLVQPHSKPFVYAIGLTQSHFPKQIHHSGLLSDQERARINEIRNY-RHF 59- 7 Query: 600 DIMTQENLKKNHFAALSLFNAAKQELVLTIPQLLNESEDQMSPYLVELRDIGVPFNHKGR 65- 9 DI + EN KKNH ALSLFNAA +ELVL++ ++NE+ D +SPYL EL + G+P KG+ Sbjct: 598 DIASAENSKKNHQTALSLFNAATKELVLSVSTVINETFDDLSPYLKELINFGLPLLDKGK 65- 7 Query: 660 QSLKEEADNIGNYKALLSRVVDLYRSAIDKEMTKEEQTFWSVAVRYLRRQLTSKGIEIPI 71- 9 L + +IGNYKALLS+++ + R + EM+ +++ FW+V +RYLR+QL + +E+P Sbjct: 658 NYLSYDNSDIGNYKALLSQIIAINRQDL-IEMSDQDKMFWTVVLRYLRKQLRKQQLELPT 71- 6 Query: 720 ITDSLDTVTVSSDVMTRRFPEDDPLKLSSSALTTFYNNQYKYFLQYVLGLEEQDSIHPDM 77- 9 L T +S +V+ FP+ PLKLS++ALT FYNNQY YFL+YVL L + +SIHPD Sbjct: 717 SDYRLSTKPLSKEVIEVCFPKGIPLKLSATALTVFYNNQYNYFLKYVLNLNKTESIHPDS 77- 6 Query: 780 RHHGTYLHRVFEILMKNQGIESFEEKLNSAINKTNQEDVFKSLYSEDAESRYSLEILEDI 83- 9 R HG YLHRVFE LMK+ E F+ KL AI TNQE F+ +Y ++AE+ YSL ILEDI Sbjct: 777 RIHGQYLHRVFERLMKDHTQEPFDNKLKQAIYHTNQESFFQQVYQDNAEAEYSLAILEDI 83- 6 Query: 840 ARATATILRQDSQMTVESEEERFELMIDNTIKINGIIDRIDRLSDGSLGVVDYKSSAQKF 89- 9 R+TA IL+ + + V +E+ F+L + N I ++GIIDRID+LSDGSLG+VDYKSSA +F Sbjct: 837 VRSTAPILQLNQNIQVIDQEKNFQLDMGNEILVHGIIDRIDQLSDGSLGIVDYKSSANQF 89- 6 Query: 900 DIQKFYNGLSPQLVTYIDAISR--DKEVEQKPPIFGAMYLHMQEPRQDLSKIKNLDD-LV 95- 6 DI FYNGLSPQL+TY+ A+ + ++ Q +FGAMYLH+Q+P+ DL K +D+ LV Sbjct: 897 DIGTFYNGLSPQLMTYLAALKQIAPHDINQ---LFGAMYLHLQDPKLDLVTFKQIDNTLV 95- 3 Query: 957 TKNHQALTYKGLFSEAEKEFLANGKYHLKDSLYSETEIAILQAHNQSLYKKASETIKSGK 10- 16 ++ALTYKG+FSE EKE L+ G Y K++LYS E+ L +N+ LY KA++ IK G Sbjct: 954 ESIYKALTYKGIFSEVEKEHLSTGAYQTKNALYSNDELETLLNYNKYLYLKAAKHIKKGH 10- 13 Query: 1017 FLINPYTEDAKTVDGDQFKSITGFEADRHMARARALYKLPAKEKRQGFLTLMQQE 1071 FLINPYT D KTV GDQ K+IT FEAD M +AR L LPAKEK++ FLTLM++E Sbjct: 1014 FLINPYTSDGKTVQGDQLKAITRFEADLDMGQARRLVTLPAKEKKECFLTLMRKE 1068 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1400 A DNA sequence (GBSx1485) was identified in S. agalactiae <SEQ ID 4297> which encodes the amino acid sequence <SEQ ID 4298>. Analysis of this protein sequence reveals the following: TABLE-US-04155 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.80 Transmembrane 51-67 (44-69) ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8799> which encodes amino acid sequence <SEQ ID 8800> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-04156 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -20.62 GvH: Signal Score (-7.5): -6.25 Possible site: 31 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -7.80 threshold: 0.0 INTEGRAL Likelihood = -7.80 Transmembrane 47-63 (40-65) PERIPHERAL Likelihood = 3.34 26 modified ALOM score: 2.06 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04157 >GP:AAC75528 GB:AE000334 orf, hypothetical protein [Escherichia coli K12] Identities = 138/297 (46%), Positives = 193/297 (64%), Gaps = 16/297 (5%) Query: 5 MKIDDLRKSDNVEDRRSSSGGSFSSGGSGLPILQLLLLRGSWKTKLVVLIILLLLG--GG 62 M+ R+SDNVEDRR+SSGG S GG G + S K L++LI++L+ G G Sbjct: 1 MRWQGRRESDNVEDRRNSSGGP-SMGGPGFRL-------PSGKGGLILLIVVLVAGYYGV 52 Query: 63 GLTSIFNDSSSPSSYQSQNVSRSVDNSATREQIDFVNKVLGSTEDFWSQEFQTQGFGNYK 122- LT + ++++S + D +A F + +L +TED W Q+F+ G Y+ Sbjct: 53 DLTGLMTGQPVSQQQSTRSISPNEDEAAK-----FTSVILATTEDTWGQQFEKMG-KTYQ 106- Query: 123 EPKLVLYTNSIQTGCGIGESASGPFYCSADKKIYLDISFYNELSHKYGATGDFAMAYVIA 18- 2 +PKLV+Y +TGCG G+S GPFYC AD +Y+D+SFY+++ K GA GDFA YVIA Sbjct: 107 QPKLVMYRGMTRTGCGAGQSIMGPFYCPADGTVYIDLSFYDDMKDKLGADGDFAQGYVIA 16- 6 Query: 183 HEVGHHIQTELGIMDKYNRMRHGLTKKEANALNVRLELQADYYAGVWAHYIRGKNLLEQG 24- 2 HEVGHH+Q LGI K +++ T+ E N L+VR+ELQAD +AGVW H ++ + +LE G Sbjct: 167 HEVGHHVQKLLGIEPKVRQLQQNATQAEVNRLSVRMELQADCFAGVWGHSMQQQGVLETG 22- 6 Query: 243 DFEEAMNAAHAVGDDTLQKETYGKLVPDSFTHGTAEQRQRWFNKGFQYGDIQHGDTF 299 D EEA+NAA A+GDD LQ+++ G++VPDSFTHGT++QR WF +GF GD +TF Sbjct: 227 DLEEALNAAQAIGDDRLQQQSQGRVVPDSFTHGTSQQRYSWFKRGFDSGDPAQCNTF 283 A related DNA sequence was identified in S. pyogenes <SEQ ID 4299> which encodes the amino acid sequence <SEQ ID 4300>. Analysis of this protein sequence reveals the following: TABLE-US-04158 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.42 Transmembrane 48-64 (41-67) ----- Final Results ----- bacterial membrane --- Certainty = 0.3569(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04159 >GP: AAC75528 GB: AE000334 orf, hypothetical protein [Escherichia coli] Identities = 143/301 (47%), Positives = 195/301 (64%), Gaps = 21/301 (6%) Query: 1 MKTDDLRESQQVEDRRGQSSG-SFGGGGLGGGLLLQLLFSRGGWKTKLVILLLLLVMG-- 57 M+ RES VEDRR S G S GG G +L +GG L++L+++LV G Sbjct: 1 MRWQGRRESDNVEDRRNSSGGPSMGGPGF------RLPSGKGG----LILLIVVLVAGYY 50 Query: 58 GGGLSGVLGGKPSSTNNNAYQSSQVTRTNGDKASQEQVSFVSKVFASTEDYWTKTFREKG 117- G L+G++ G+P S QS++ N D+A++ F S + A+TED W + F + G Sbjct: 51 GVDLTGLMTGQPVSQQ----QSTRSISPNEDEAAK----FTSVILATTEDTWGQQFEKMG 102- Query: 118 LTYHKPTLVLYTGATQTACGRGQASSGPFYCPGDQKVYLDISFYNELSTKYGAKGDFAMA 17- 7 TY +P LV+Y G T+T CG GQ+ GPFYCP D VY+D+SFY+++ K GA GDFA Sbjct: 103 KTYQQPKLVMYRGMTRTGCGAGQSIMGPFYCPADGTVYIDLSFYDDMKDKLGADGDFAQG 16- 2 Query: 178 YVIAHEVGHHIQNELGIMDNYASARQGKSKAKANQLNVKLELQADYYAGAWANYVQGQGL 23- 7 YVIAHEVGHH+Q LGI +Q ++A+ N+L+V++ELQAD +AG W + +Q QG+ Sbjct: 163 YVIAHEVGHHVQKLLGIEPKVRQLQQNATQAEVNRLSVRMELQADCFAGVWGHSMQQQGV 22- 2 Query: 238 LEKGDIEEAMAAAHAVGDDTLQEETYGRTVPDSFTHGTSKQRQRWFDRGYQYGDFEHGDTF 2- 98 LE GD+EEA+ AA A+GDD LQ+++ GR VPDSFTHGTS+QR WF RG+ GD +TF Sbjct: 223 LETGDLEEALNAAQAIGDDRLQQQSQGRVVPDSFTHGTSQQRYSWFKRGFDSGDPAQCNTF 2- 83 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04160 Identities = 191/303 (63%), Positives = 241/303 (79%), Gaps = 5/303 (1%) Query: 5 MKIDDLRKSDNVEDRRSSSGGSFSSGG-SGLPILQLLLLRGSWKTKLVVLIILLLLGGGG 63 MK DDLR+S VEDRR S GSF GG G +LQLL RG WKTKLV+L++LL++GGGG Sbjct: 1 MKTDDLRESQQVEDRRGQSSGSFGGGGLGGGLLLQLLFSRGGWKTKLVILLLLLVMGGGG 60 Query: 64 LTSIFN---DSSSPSSYQSQNVSRSVDNSATREQIDFVNKVLGSTEDFWSQEFQTQGFGN 120- L+ + S++ ++YQS V+R+ + A++EQ+ FV+KV STED+W++ F+ +G Sbjct: 61 LSGVLGGKPSSTNNNAYQSSQVTRTNGDKASQEQVSFVSKVFASTEDYWTKTFREKGL-T 119- Query: 121 YKEPKLVLYTNSIQTGCGIGESASGPFYCSADKKIYLDISFYNELSHKYGATGDFAMAYV 18- 0 Y +P LVLYT + QT CG G+++SGPFYC D+K+YLDISFYNELS KYGA GDFAMAYV Sbjct: 120 YHKPTLVLYTGATQTACGRGQASSGPFYCPGDQKVYLDISFYNELSTKYGAKGDFAMAYV 17- 9 Query: 181 IAHEVGHHIQTELGIMDKYNRMRHGLTKKEANALNVRLELQADYYAGVWAHYIRGKNLLE 24- 0 IAHEVGHHIQ ELGIMD Y R G +K +AN LNV+LELQADYYAG WA+Y++G+ LLE Sbjct: 180 IAHEVGHHIQNELGIMDNYASARQGKSKAKANQLNVKLELQADYYAGAWANYVQGQGLLE 23- 9 Query: 241 QGDFEEAMNAAHAVGDDTLQKETYGKLVPDSFTHGTAEQRQRWFNKGFQYGDIQHGDTFS 30- 0 +GD EEAM AAHAVGDDTLQ+ETYG+ VPDSFTHGT++QRQRWF++G+QYGD +HGDTFS Sbjct: 240 KGDIEEAMAAAHAVGDDTLQEETYGRTVPDSFTHGTSKQRQRWFDRGYQYGDFEHGDTFS 29- 9 Query: 301 VEH 303 + + Sbjct: 300 IPY 302 SEQ ID 8800 (GBS404) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 171 (lane 3; MW 62 kDa). GBS404-GST was purified as shown in FIG. 218, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1401 A DNA sequence (GBSx1486) was identified in S. agalactiae <SEQ ID 4301> which encodes the amino acid sequence <SEQ ID 4302>. This protein is predicted to be phenylalanyl-tRNA synthetase beta chain (pheT). Analysis of this protein sequence reveals the following: TABLE-US-04161 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2617(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04162 >GP: CAB14823 GB: Z99118 phenylalanyl-tRNA synthetase (beta subunit) [Bacillus subtilis] Identities = 376/805 (46%), Positives = 523/805 (64%), Gaps = 6/805 (0%) Query: 1 MLVSYKWLKELVDVD-VTTAELAEKMSTTGIEVEGVETPAEGLSKLVVGHIVSCEDVPDT 59 M VSYKWL++ VD+ + A LAEK++ GIEVEG+E EG+ +V+GH++ E P+ Sbjct: 1 MFVSYKWLEDYVDLKGMDPAVLAEKITRAGIEVEGIEYKGEGIKGVVIGHVLEREQHPNA 60 Query: 60 H-LHLCQVDTGDDELRQVVCGAPNVKTGINVIVAVPGARIADNYKIKKGKIRGMESLGMI 118- L+ C VD G + Q++CGAPNV G V VA GA + N+KIKK K+RG ES GMI Sbjct: 61 DKLNKCLVDIGAEAPVQIICGAPNVDKGQKVAVATVGAVLPGNFKIKKAKLRGEESNGMI 120- Query: 119 CSLQELGLSESIIPKEFSDGIQILPEGAIPGDSIFSYLDLDDEIIELSITPNRADALSMR 17- 8 CSLQELG+ ++ KE+++GI + P A G + L LDD I+EL +TPNRADA++M Sbjct: 121 CSLQELGIESKLVAKEYAEGIFVFPNDAETGSDALAALQLDDAILELGLTPNRADAMNML 18- 0 Query: 179 GVAHEVAAIYGKKVHFEEKNLIEEAERAADKISVVIESDKVLS-YSARIVKNVTVAPSPQ 23- 7 GVA+EVAAI +V + + +E+A+D ISV IE + Y+A+I+KNVT+APSP Sbjct: 181 GVAYEVAAILDTEVKLPQTDYPAASEQASDYISVKIEDQEANPLYTAKIIKNVTIAPSPL 24- 0 Query: 238 WLQNKLMNAGIRPINNVVDVTNYVLLTYGQPMHAFDFDKFDGTTIVARNAENGEKLITLD 29- 7 W+Q KLMNAGIRP NNVVD+TN+VLL YGQP+HAFD+D+F +V R A E ++TLD Sbjct: 241 WMQTKLMNAGIRPHNNVVDITNFVLLEYGQPLHAFDYDRFGSKEVVVRKAAENEMIVTLD 30- 0 Query: 298 GEERDLIADDLVIAVNDQPVALAGVMGGQSTEIGSSSKTVVLEAAVFNGTSIRKTSGRLN 35- 7 +ER L AD LVI + A+AGVMGG +E+ +KT++LEAA FNG +RK S L Sbjct: 301 DQERKLSADHLVITNGTKAQAVAGVMGGAESEVQEDTKTILLEAAYFNGQKVRKASKDLG 36- 0 Query: 358 LRSESSSRFEKGINYDTVSEAMDFAAAMLQELAGGQVLSGQVTEGVLPTEPVEVSTTLGY 41- 7 LRSESS RFEKGI+ V A + AA ++ AGG+VL+G V E L E + + Sbjct: 361 LRSESSVRFEKGIDPARVRLAAERAAQLIHLYAGGEVLAGTVEEDHLTIEANNIHVSADK 42- 0 Query: 418 VNTRLGTELTYTDIEEVFEKLGFAISGSEVKFTVLVPRRRWDIAIQADLVEEIARIYGYE 47- 7 V++ LG ++ ++ ++++LGF + ++ V VP RR DI I+ DL+EE AR+YGY+ Sbjct: 421 VSSVLGLTISKEELISIYKRLGFTVGEADDLLVVTVPSRRGDITIEEDLIEEAARLYGYD 48- 0 Query: 478 KLPTTLPEAGATAGELTSMQRLRRRVRTVAEGAGLSEIITYALTTPEKAVQFSTQATNIT 53- 7 +P+TLPE T G LT Q RR+VR EGAGLS+ ITY+LT +KA F+ + + T Sbjct: 481 NIPSTLPETAGTTGGLTPYQAKRRKVRRFLEGAGLSQAITYSLTNEKKATAFAIEKSLNT 54- 0 Query: 538 ELMWPMTVDRSALRQNVVSGMLDTIAYNVARKNSNLAVYEIGKVFEQTGNPKEDLPTEVE 59- 7 L PM+ +RS LR ++V +LD+++YN+AR+ ++A+YE+G VF ++ P E E Sbjct: 541 VLALPMSEERSILRHSLVPNLLDSVSYNLARQTDSVALYEVGSVF--LTKEEDTKPVETE 59- 8 Query: 598 TFTFALTGLVEEKDFQTKSKPVDFFYAKGIVEALFIKLK-LDVTFVAQKGLASMHPGRTA 65- 6 A+TGL ++ +Q + KPVDFF KGIVE L KL LD Q +HPGRTA Sbjct: 599 RVAGAVTGLWRKQLWQGEKKPVDFFVVKGIVEGLLDKLNVLDSIEFVQSERKQLHPGRTA 65- 8 Query: 657 TILLDGKEIGFVGQVHPQTAKQYDIPETYVAEINLSTIESQMNQALIFEDITKYPSVSRD 71- 6 ILL+G IGF+GQVHP K+ DI ETYV E++L + + L++ I KYPSV+RD Sbjct: 659 NILLNGSLIGFIGQVHPSLEKELDIKETYVFELDLHALLAAETAPLVYTAIPKYPSVTRD 71- 8 Query: 717 IALLLAESVSHHDIVSAIETSGVKRLTAIKLFDVYAGNNIAEGYKSMAYSLTFQNPNDNL 77- 6 IAL+ ++V+ + S I+ +G K L + +FDVY G ++ EG KS+A+SL + NP L Sbjct: 719 IALVTDKTVTSGQLESVIKEAGGKLLKEVTVFDVYEGEHMEEGKKSVAFSLQYVNPEQTL 77- 8 Query: 777 TDEEVAKYMEKITKSLVEKVNAEIR 801 T+EEV K K+ K+L + A +R Sbjct: 779 TEEEVTKAHSKVLKALEDTYQAVLR 803 A related DNA sequence was identified in S. pyogenes <SEQ ID 4303> which encodes the amino acid sequence <SEQ ID 4304>. Analysis of this protein sequence reveals the following:

TABLE-US-04163 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1283(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04164 Identities = 595/801 (74%), Positives = 687/801 (85%) Query: 1 MLVSYKWLKELVDVDVTTAELAEKMSTTGIEVEGVETPAEGLSKLVVGHIVSCEDVPDTH 60 MLVSYKWLKELVD+DVT A LAEKMSTTGIEVEG+E PA+GLSKLVVGH++SCEDVP+TH Sbjct: 6 MLVSYKWLKELVDIDVTPAALAEKMSTTGIEVEGIEVPADGLSKLVVGHVLSCEDVPETH 65 Query: 61 LHLCQVDTGDDELRQVVCGAPNVKTGINVIVAVPGARIADNYKIKKGKIRGMESLGMICS 120- LHLCQVDTGD+ RQ+VCGAPNVK GI VIVAVPGARIADNYKIKKGKIRGMESLGMICS Sbjct: 66 LHLCQVDTGDETPRQIVCGAPNVKAGIKVIVAVPGARIADNYKIKKGKIRGMESLGMICS 125- Query: 121 LQELGLSESIIPKEFSDGIQILPEGAIPGDSIFSYLDLDDEIIELSITPNRADALSMRGV 18- 0 LQELGLS+SIIPKEFSDGIQILPE A+PGD+IF YLDLDD IIELSITPNRADALSMRGV Sbjct: 126 LQELGLSDSIIPKEFSDGIQILPEEAVPGDAIFKYLDLDDHIIELSITPNRADALSMRGV 18- 5 Query: 181 AHEVAAIYGKKVHFEEKNLIEEAERAADKISVVIESDKVLSYSARIVKNVTVAPSPQWLQ 24- 0 AHEVAAIYGK V F +KNL E + ++ I V I SD VL+Y++R+V+NV V PSPQWLQ Sbjct: 186 AHEVAAIYGKSVSFPQKNLQESDKATSEAIEVAIASDNVLTYASRVVENVKVKPSPQWLQ 24- 5 Query: 241 NKLMNAGIRPINNVVDVTNYVLLTYGQPMHAFDFDKFDGTTIVARNAENGEKLITLDGEE 30- 0 N LMNAGIRPINNVVDVTNYVLL +GQPMHAFD+DKF+ IVAR A GE L+TLDGE+ Sbjct: 246 NLLMNAGIRPINNVVDVTNYVLLYFGQPMHAFDYDKFEDHKIVARAARQGESLVTLDGEK 30- 5 Query: 301 RDLIADDLVIAVNDQPVALAGVMGGQSTEIGSSSKTVVLEAAVFNGTSIRKTSGRLNLRS 36- 0 RDL +DLVI V D+PVALAGVMGGQ+TEI ++S+TVVLEAAVF+G SIRKTSGRLNLRS Sbjct: 306 RDLTTEDLVITVADKPVALAGVMGGQATEIDANSQTVVLEAAVFDGKSIRKTSGRLNLRS 36- 5 Query: 361 ESSSRFEKGINYDTVSEAMDFAAAMLQELAGGQVLSGQVTEGVLPTEPVEVSTTLGYVNT 42- 0 ESSSRFEKG+NY TV EA+DFAAAMLQELA GQVLSG V G LPTEPVEVST+L YVN Sbjct: 366 ESSSRFEKGVNYATVLEALDFAAAMLQELAEGQVLSGHVQAGQLPTEPVEVSTSLDYVNV 42- 5 Query: 421 RLGTELTYTDIEEVFEKLGFAISGSEVKFTVLVPRRRWDIAIQADLVEEIARIYGYEKLP 48- 0 RLGTELT+ DI+ +F++LGF ++G E FTV VPRRRWD++I ADLVEEIARIYGY+KLP Sbjct: 426 RLGTELTFADIQRIFDQLGFGLTGDETSFTVAVPRRRWDVSIPADLVEEIARIYGYDKLP 48- 5 Query: 481 TTLPEAGATAGELTSMQRLRRRVRTVAEGAGLSEIITYALTTPEKAVQFSTQATNITELM 54- 0 TTLPEAG TA ELT Q LRR+VR +AEG GL+EII+YALTTPEKAV+F+ +++TELM Sbjct: 486 TTLPEAGGTAAELTPTQALRRKVRGLAEGLGLTEIISYALTTPEKAVEFAVAPSHLTELM 54- 5 Query: 541 WPMTVDRSALRQNVVSGMLDTIAYNVARKNSNLAVYEIGKVFEQTGNPKEDLPTEVETFT 60- 0 WPM+V+RSALRQN+VSGMLDT+AYNVARK SNLA+YEIGK+FEQ NPKEDLP EV F Sbjct: 546 WPMSVERSALRQNMVSGMLDTVAYNVARKQSNLALYEIGKIFEQEANPKEDLPNEVNHFA 60- 5 Query: 601 FALTGLVEEKDFQTKSKPVDFFYAKGIVEALFIKLKLDVTFVAQKGLASMHPGRTATILL 66- 0 FA+ GLV +KDFQT+++ VDF++AKG ++ LF L L V +V K LA+MHPGRTA ILL Sbjct: 606 FAICGLVAQKDFQTQAQAVDFYHAKGNLDTLFANLNLKVQYVPTKDLANMHPGRTALILL 66- 5 Query: 661 DGKEIGFVGQVHPQTAKQYDIPETYVAEINLSTIESQMNQALIFEDITKYPSVSRDIALL 72- 0 D + IGFVGQVHP TAK Y IPETYVAE++++ +E+ + F +ITK+P+++RD+ALL Sbjct: 666 DEQVIGFVGQVHPGTAKAYSIPETYVAELDMAALEAALPSDQTFAEITKFPAMTRDVALL 72- 5 Query: 721 LAESVSHHDIVSAIETSGVKRLTAIKLFDVYAGNNIAEGYKSMAYSLTFQNPNDNLTDEE 78- 0 L VSH IV+AIE++GVKRLT+IKLFDVY G I G KSMAYSLTFQNPNDNLTDEE Sbjct: 726 LDREVSHQAIVTAIESAGVKRLTSIKLFDVYEGATIQAGKKSMAYSLTFQNPNDNLTDEE 78- 5 Query: 781 VAKYMEKITKSLVEKVNAEIR 801 VAKYMEKITK+L E+V AE+R Sbjct: 786 VAKYMEKITKALTEQVGAEVR 806 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1402 A DNA sequence (GBSx1487) was identified in S. agalactiae <SEQ ID 4305> which encodes the amino acid sequence <SEQ ID 4306>. Analysis of this protein sequence reveals the following: TABLE-US-04165 Possible Site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0653(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9769> which encodes amino acid sequence <SEQ ID 9770> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04166 >GP: CAB15205 GB: Z99120 transcriptional regulator [Bacillus subtilis] Identities = 60/169 (35%), Positives = 100/169 (58%) Query: 17 ITFKKVGLDNVNILQNIAIETFRQTFSHDNSEEQLQAFFNESYTLPVLKSEITHAESDTY 76 - + KK +++ LQ ++IETF TF NS E ++A+ ++ L+ E+++ S + Sbjct: 3 VKMKKCSREDLQTLQQLSIETFNDTFKEQNSPENMKAYLESAFNTEQLEKELSNMSSQFF 62 Query: 77 FVYLDTDLVGYLKVNWGSQQTEKDLDKAFEIQRIYLLDAYQGQGIGKATFEFALDLAYKS 136- F+Y D ++ GY+KVN Q+E+ ++ EI+RIY+ +++Q G+GK A+++A + Sbjct: 63 FIYFDHEIAGYVKVNIDDAQSEEMGAESLEIERIYIKNSFQKHGLGKHLLNKAIEIALER 122- Query: 137 GLDWAWLGVWEFNHKAQAFYAKYGFEKFSEHQFSVGDKVDTDWLLRKSL 185 WLGVWE N A AFY K GF + H F +GD+ TD ++ K+L Sbjct: 123 NKKNIWLGVWEKNENAIAFYKKMGFVQTGAHSFYMGDEEQTDLIMAKTL 171 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1403 A DNA sequence (GBSx1488) was identified in S. agalactiae <SEQ ID 4307> which encodes the amino acid sequence <SEQ ID 4308>. This protein is predicted to be phenylalanyl-tRNA synthetase (alpha subunit) (pheS). Analysis of this protein sequence reveals the following: TABLE-US-04167 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3937(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9339> which encodes amino acid sequence <SEQ ID 9340> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04168 >GP: CAB14824 GB: Z99118 phenylalanyl-tRNA synthetase (alpha subunit) [Bacillus subtilis] Identities = 209/338 (61%), Positives = 270/338 (79%), Gaps = 2/338 (0%) Query: 1 MKISTQEKLKEM-TGNHTKELQDLRVQVLGKKGSLTELLKGLKDLSNDLRPVVGKQVNEV 59 +K QE L+++ + K + D+RVQ LGKKG +TE+L+G+ LS + RP +G NEV Sbjct: 5 LKQLEQEALEQVEAASSLKVVNDIRVQYLGKKGPITEVLRGMGKLSAEERPKMGALANEV 64 Query: 60 RDILTKAFEEQAKVVEAAKIQAQLESESVDVTLPGRQMTLGHRHVLTQTSEEIEDIFLGM 119- R+ + A ++ + +E +++ +L +++DVTLPG + +G RH LT EEIED+F+GM Sbjct: 65 RERIANAIADKNEKLEEEEMKQKLAGQTIDVTLPGNPVAVGGRHPLTVVIEEIEDLFIGM 124- Query: 120 GFQVVDGFEVEKDYYNFERMNLPKDHPARDMQDTFYITEEILLRTHTSPVQARTMDQHDF 17- 9 G+ V +G EVE DYYNFE +NLPK+HPARDMQD+FYITEE L+RT TSPVQ RTM++H+ Sbjct: 125 GYTVEEGPEVETDYYNFESLNLPKEHPARDMQDSFYITEETLMRTQTSPVQTRTMEKHE- 18- 3 Query: 180 SKGPLKMISPGRVFRRDTDDATHSHQFHQIEGLVVGENISMGDLKGTLQLISQKMFGAER 23- 9 KGP+K+I PG+V+RRD DDATHSHQF QIEGLVV +NISM DLKGTL+L+++KMFG +R Sbjct: 184 GKGPVKIICPGKVYRRDNDDATHSHQFMQIEGLVVDKNISMSDLKGTLELVAKKMFGQDR 24- 3 Query: 240 KIRLRPSYFPFTEPSVEVDVSCFKCGGKGCNVCKQTGWIEILGAGMVHPSVLEMSGIDSE 29- 9 +IRLRPS+FPFTEPSVEVDV+CFKCGG GC+VCK TGWIEILGAGMVHP+VL+M+G D + Sbjct: 244 EIRLRPSFFPFTEPSVEVDVTCFKCGGNGCSVCKGTGWIEILGAGMVHPNVLKMAGFDPK 30- 3 Query: 300 KYSGFAFGLGQERIAMLRYGINDIRGFYQGDVRFTDQF 337 +Y GFAFG+G ERIAML+YGI+DIR FY DVRF QF Sbjct: 304 EYQGFAFGMGVERIAMLKYGIDDIRHFYTNDVRFISQF 341 A related DNA sequence was identified in S. pyogenes <SEQ ID 4309> which encodes the amino acid sequence <SEQ ID 4310>. Analysis of this protein sequence reveals the following: TABLE-US-04169 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2806(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04170 Identities = 305/337 (90%), Positives = 327/337 (96%) Query: 1 MKISTQEKLKEMTGNHTKELQDLRVQVLGKKGSLTELLKGLKDLSNDLRPVVGKQVNEVR 60 +K T E L+ +TGNHTKELQDLRV VLGKKGSLTELLKGLKDLSNDLRPVVGKQVNEVR Sbjct: 36 LKTKTLETLQSLTGNHTKELQDLRVAVLGKKGSLTELLKGLKDLSNDLRPVVGKQVNEVR 95 Query: 61 DILTKAFEEQAKVVEAAKIQAQLESESVDVTLPGRQMTLGHRHVLTQTSEEIEDIFLGMG 120- D+LTKAFEEQAK+VEAAKIQAQL++ES+DVTLPGRQMTLGHRHVLTQTSEEIEDIFLGMG Sbjct: 96 DLLTKAFEEQAKIVEAAKIQAQLDAESIDVTLPGRQMTLGHRHVLTQTSEEIEDIFLGMG 155- Query: 121 FQVVDGFEVEKDYYNFERMNLPKDHPARDMQDTFYITEEILLRTHTSPVQARTMDQHDFS 18- 0 FQ+VDGFEVEKDYYNFERMNLPKDHPARDMQDTFYITEEILLRTHTSPVQAPT+DQHDFS Sbjct: 156 FQIVDGFEVEKDYYNFERMNLPKDHPARDMQDTFYITEEILLRTHTSPVQARTLDQHDFS 21- 5 Query: 181 KGPLKMISPGRVFRRDTDDATHSHQFHQIEGLVVGENISMGDLKGTLQLISQKMFGAERK 24- 0 KGPLKM+SPGRVFRRDTDDATHSHQFHQIEGLVVG+NISMGDLKGTL++I +KMFG ER Sbjct: 216 KGPLKMVSPGRVFRRDTDDATHSHQFHQIEGLVVGKNISMGDLKGTLEMIIKKMFGDERS 27- 5 Query: 241 IRLRPSYFPFTEPSVEVDVSCFKCGGKGCNVCKQTGWIEILGAGMVHPSVLEMSGIDSEK 30- 0 IRLRPSYFPETEPSVEVDVSCFKCGGKGCNVCK+TGWIEILGAGMVHPSVLEMSG+D+++ Sbjct: 276 IRLRPSYFPFTEPSVEVDVSCFKCGGKGCNVCKKTGWIEILGAGMVHPSVLEMSGVDAKE 33- 5 Query: 301 YSGFAFGLGQERIAMLRYGINDIRGFYQGDVRFTDQF 337 YSGFAFGLGQERIAMLRYGINDIRGFYQGD RF++QF Sbjct: 336 YSGFAFGLGQERIAMLRYGINDIRGFYQGDQRFSEQF 372 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1404 A DNA sequence (GBSx1489) was identified in S. agalactiae <SEQ ID 4311> which encodes the amino acid sequence <SEQ ID 4312>. Analysis of this protein sequence reveals the following: TABLE-US-04171 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2834(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1405 A DNA sequence (GBSx1490) was identified in S. agalactiae <SEQ ID 4313> which encodes the amino acid sequence <SEQ ID 4314>. Analysis of this protein sequence reveals the following: TABLE-US-04172 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2762(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1406 A DNA sequence (GBSx1491) was identified in S. agalactiae <SEQ ID 4315> which encodes the amino acid sequence <SEQ ID 4316>. This protein is predicted to be DNA-entry nuclease. Analysis of this protein sequence reveals the following: TABLE-US-04173 Possible site: 13 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8801> which encodes amino acid sequence <SEQ ID 8802> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-04174 Lipop Possible site: -1 Crend: 5 McG: Discrim Score:10.13 GvH: Signal Score (-7.5): -5.07 Possible site:23 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -6.79 threshold: 0.0 INTEGRAL Likelihood = -6.79 Transmembrane 8-24 (6-27) PERIPHERAL Likelihood = 6.26 258 modified ALOM score: 1.86 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3718(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04175 >GP:CAA38134 GB:X54225 membrane nuclease [Streptococcus pneumoniae] Identities = 154/232 (66%), Positives = 180/232 (77%), Gaps = 1/232 (0%) Query: 41 KNVSGTPSRELSESVLTSNVKKQLGTNIAWNQSGAFIINQNKTDLNAKVSSAPYAINEIK 100- K S PS+ L+ESVLT VK Q+ ++ WN SGAFI+N NKT+L+AKVSS PYA N+ K Sbjct: 43 KQASEAPSQALAESVLTDAVKSQIKGSLEWNGSGAFIVNGNKTNLDAKVSSKPYADNKTK 102- Query: 101 KVNNQIVPTKANALLTKATRQYRNREETGNGRTYWKPAGWHQINGLKGSYNHAVDRGHLI 16- 0 V + VPT ANALL+KATRQY+NR+ETGNG T W P GWHQ+ LKGSY HAVDRGHL+ Sbjct: 103 TVGKETVPTVANALLSKATRQYKNRKETGNGSTSWTPPGWHQVKNLKGSYTHAVDRGHLL 16- 2 Query: 161 GYALVGSLRGFDASTSNPKNIATQAAWANQANSNQSTGQNYYETLVRKALDRHKTVRYRV 22- 0 GYAL+G L GFDASTSNPKNIA Q AWANQA + STGQNYYE+ VRKALD++K VRYRV Sbjct: 163 GYALIGGLDGFDASTSNPKNIAVQTAWANQAQAEYSTGQNYYESKVRKALDQNKRVRYRV 22- 2 Query: 221 TLIY-DRDNLLSSGSHIEAKSSDGSLEFNVFIPNVQSGLLFDYATGKVKQTK 271 TL Y ++L+ S S IEAKSSDG LEFNV +PNVQ GL DY TG+V T+ Sbjct: 223 TLYYASNEDLVPSASQIEAKSSDGELEFNVLVPNVQKGLQLDYRTGEVTVTQ 274 There is also homology to SEQ IDs 368 and 1302. SEQ ID 8802 (GBS285) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 56 (lane 6; MW 32 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 60 (lane 7; MW 57.5 kDa). GBS285-GST was purified as shown in FIG. 208 (lane 7) and FIG. 225 (lane 8). GBS658 was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 134 (lane 8 & 9; MW 27 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1407 A DNA sequence (GBSx1492) was identified in S. agalactiae <SEQ ID 4317> which encodes the amino acid sequence <SEQ ID 4318>. Analysis of this protein sequence reveals the following: TABLE-US-04176 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ----- Final Result ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1408 A DNA sequence (GBSx1493) was identified in S. agalactiae <SEQ ID 4319> which encodes the amino acid sequence <SEQ ID 4320>. This protein is predicted to be UDP-N-acetylglucosamine (murA). Analysis of this protein sequence reveals the following: TABLE-US-04177 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1814(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9767> which encodes amino acid sequence <SEQ ID 9768> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04178 >GP:CAB15693 GB:Z99122 UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Bacillus subtilis] Identities = 248/423 (58%), Positives = 323/423 (75%), Gaps = 5/423 (1%) Query: 5 MDKIIVEGGQTQLQGQVVIEGAKNAVLPLLAATILPSQGKTLLTNVPILSDVFTMNNVVR 64 M+KIIV GGQ +L G V +EGAKNAVLP++AA++L S+ K+++ +VP LSDV+T+N V+R Sbjct: 1 MEKIIVRGGQ-KLNGTVKVEGAKNAVLPVIAASLLASEEKSVICDVPTLSDVYTINEVLR 59 Query: 65 GLDIQVDFNCDKKEILVDASGDILDVAPYEFVSQMRASIVVLGPILARNGHAKVSMPGGC 124- L V F + E+ V+AS + AP+E+V +MRAS++V+GP+LAR GHA+V++PGGC Sbjct: 60 HLGADVHF--ENNEVTVNASYALQTEAPFEYVRKMRASVLVMGPLLARTGHARVALPGGC 117- Query: 125 TIGSRPIDLHLKGLEAMGATITQNGGDITAQAE-KLKGANIYMDFPSVGATQNLMMAATL 18- 3 IGSRPID HLKG EAMGA I G I A+ + +L+GA IY+DFPSVGAT+NL+MAA L Sbjct: 118 AIGSRPIDQHLKGFEAMGAEIKVGNGFIEAEVKGRLQGAKIYLDFPSVGATENLIMAAAL 17- 7 Query: 184 ASGTTTIENAAREPEIVDLAQLLNKMGAKVKGAGTETLTIIGVDALHGTEHDVVQDRIEA 24- 3 A GTTT+EN A+EPEIVDLA +N MG K++GAGT T+ I GV+ LHG +H ++ DRIEA Sbjct: 178 AEGTTTLENVAKEPEIVDLANYINGMGGKIRGAGTGTIKIEGVEKLHGVKHHIIPDRIEA 23- 7 Query: 244 GTFMVAAAMTSGNVLVKDAIWEHNRPLISKLMEMGVEVSEEEDGIRVKADTKKLKPVTVK 30- 3 GTFMVAAA+T GNVLVK A+ EH LI+K+ EMGV + +E +G+RV K+LKP+ +K Sbjct: 238 GTFMVAAAITEGNVLVKGAVPEHLTSLIAKMEEMGVTIKDEGEGLRV-IGPKELKPIDIK 29- 6 Query: 304 TLPHPGFPTDMQAQFTALMAVVNGESTMIETVFENRFQHLEEMRRMGLQTEILRDTAMIH 36- 3 T+PHPGFPTDMQ+Q AL+ +G S + ETVFENRF H EE RRM +I + +I+ Sbjct: 297 TMPHPGFPTDMQSQMMALLLRASGTSMITETVFENRFMHAEEFRRMNGDIKIEGRSVIIN 35- 6 Query: 364 GGRALQGAPVMSTDLRASAALILAGMVAQGQTVVGQLTHLDRGYYQFHEKLAALGANIKR 42- 3 G LQGA V +TDLRA AALILAG+VA+G T V +L HLDRGY FH+KLAALGA+I+R Sbjct: 357 GPVQLQGAEVAATDLRAGAALILAGLVAEGHTRVTELKHLDRGYVDFHQKLAALGADIER 41- 6 Query: 424 VSE 426 V++ Sbjct: 417 VND 419 A related DNA sequence was identified in S. pyogenes <SEQ ID 4321> which encodes the amino acid sequence <SEQ ID 4322>. Analysis of this protein sequence reveals the following:

TABLE-US-04179 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.03 Transmembrane 377-393 (376-394) ----- Final Results ----- bacterial membrane --- Certainty = 0.2211(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04180 >GP: CAB15693 GB: Z99122 UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Bacillus subtilis] Identities = 248/423 (58%), Positives = 318/423 (74%), Gaps = 5/423 (1%) Query: 1 VDKIIIEGGQTRLEGEVVIEGAKNAVLPLLAASILPSKGKTILRNVPILSDVFTMNNVVR 60 ++KII+ GGQ +L G V +EGAKNAVLP++AAS+L S+ K+++ +VP LSDV+T+N V+R Sbjct: 1 MEKIIVRGGQ-KLNGTVKVEGAKNAVLPVIAASLLASEEKSVICDVPTLSDVYTINEVLR 59 Query: 61 GLDIRVDFNEAANEITVDASGHILDEAPYEYVSQMRASIVVLGPILARNGHAKVSMPGGC 120- L V F NE+TV+AS + EAP+EYV +MRAS++V+GP+LAR GHA+V++PGGC Sbjct: 60 HLGADVHFEN--NEVTVNASYALQTEAPFEYVRKMRASVLVMGPLLARTGHARVALPGGC 117- Query: 121 TIGSRPINLHLKGLEAMGATITQKGGDITAQAD-RLQGAMIYMDFPSVGATQNLMMAATL 17- 9 IGSRPI+ HLKG EAMGA I G I A+ RLQGA IY+DFPSVGAT+NL+MAA L Sbjct: 118 AIGSRPIDQHLKGFEAMGAEIKVGNGFIEAEVKGRLQGAKIYLDFPSVGATENLIMAAAL 17- 7 Query: 180 ADGVTTIENAAREPEIVDLAQFLNKMGARIRGAGTETLTITGVTHLRGVEHDVVQDRIEA 23- 9 A+G TT+EN A+EPEIVDLA ++N MG +IRGAGT T+ I GV L GV+H ++ DRIEA Sbjct: 178 AEGTTTLENVAKEPEIVDLANYINGMGGKIRGAGTGTIKIEGVEKLHGVKHHIIPDRIEA 23- 7 Query: 240 GTFMVAAAMTSGNVLIRDAVWEHNRPLISKLMEMGVSVTEEEYGIRVQANTPKLKPVTVK 29- 9 GTFMVAAA+T GNVL++ AV EH LI+K+ EMGV++ +E G+RV +LKP+ +K Sbjct: 238 GTFMVAAAITEGNVLVKGAVPEHLTSLIAKMEEMGVTIKDEGEGLRV-IGPKELKPIDIK 29- 6 Query: 300 TLPHPGFPTDMQAQFTALMAVVNGESTMVETVFENRFQHLEEMRRMGLQSEILRETAMIH 35- 9 T+PHPGFPTDMQ+Q AL+ +G S + ETVFENRF H EE RRM +I + +I+ Sbjct: 297 TMPHPGFPTDMQSQMMALLLRASGTSMITETVFENRFMHAEEFRRMNGDIKIEGRSVIIN 35- 6 Query: 360 GGRQLQGAPVMSTDLRASAALILTGIVAQGVTIVNNLVHLDRGYYQFHEKLAKLGATISR 41- 9 G QLQGA V +TDLRA AALIL G+VA+G T V L HLDRGY FH+KLA LGA I R Sbjct: 357 GPVQLQGAEVAATDLRAGAALILAGLVAEGHTRVTELKHLDRGYVDFHQKLAALGADIER 41- 6 Query: 420 SSE 422 ++ Sbjct: 417 VND 419 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04181 Identities = 363/422 (86%), Positives = 391/422 (92%) Query: 5 MDKIIVEGGQTQLQGQVVIEGAKNAVLPLLAATILPSQGKTLLTNVPILSDVFTMNNVVR 64 +DKII+EGGQT+L+G+VVIEGAKNAVLPLLAA+ILPS+GKT+L NVPILSDVFTMNNVVR Sbjct: 1 VDKIIIEGGQTRLEGEVVIEGAKNAVLPLLAASILPSKGKTILRNVPILSDVFTMNNVVR 60 Query: 65 GLDIQVDFNCDKKEILVDASGDILDVAPYEFVSQMRASIVVLGPILARNGHAKVSMPGGC 124- GLDI+VDFN EI VDASG ILD APYE+VSQMRASIVVLGPILARNGHAKVSMPGGC Sbjct: 61 GLDIRVDFNEAANEITVDASGHILDEAPYEYVSQMRASIVVLGPILARNGHAKVSMPGGC 120- Query: 125 TIGSRPIDLHLKGLEAMGATITQNGGDITAQAEKLKGANIYMDFPSVGATQNLMMAATLA 18- 4 TIGSRPI+LHLKGLEAMGATITQ GGDITAQA++L+GA IYMDFPSVGATQNLMMAATLA Sbjct: 121 TIGSRPINLHLKGLEAMGATITQKGGDITAQADRLQGAMIYMDFPSVGATQNLMMAATLA 18- 0 Query: 185 SGTTTIENAAREPEIVDLAQLLNKMGAKVKGAGTETLTIIGVDALHGTEHDVVQDRIEAG 24- 4 G TTIENAAREPEIVDLAQ LNKMGA+++GAGTETLTI GV L G EHDVVQDRIEAG Sbjct: 181 DGVTTIENAAREPEIVDLAQFLNKMGARIRGAGTETLTITGVTHLRGVEHDVVQDRIEAG 24- 0 Query: 245 TFMVAAAMTSGNVLVKDAIWEHNRPLISKLMEMGVEVSEEEDGIRVKADTKKLKPVTVKT 30- 4 TFMVAAAMTSGNVL++DA+WEHNRPLISKLMEMGV V+EEE GIRV+A+T KLKPVTVKT Sbjct: 241 TFMVAAAMTSGNVLIRDAVWEHNRPLISKLMEMGVSVTEEEYGIRVQANTPKLKPVTVKT 30- 0 Query: 305 LPHPGFPTDMQAQFTALMAVVNGESTMIETVFENRFQHLEEMRRMGLQTEILRDTAMIHG 36- 4 LPHPGFPTDMQAQFTALMAVVNGESTM+ETVFENRFQHLEEMRRMGLQ+EILR+TAMIHG Sbjct: 301 LPHPGFPTDMQAQFTALMAVVNGESTMVETVFENRFQHLEEMRRMGLQSEILRETAMIHG 36- 0 Query: 365 GRALQGAPVMSTDLRASAALILAGMVAQGQTVVGQLTHLDRGYYQFHEKLAALGANIKRVSE - 426 GR LQGAPVMSTDLRASAALIL G+VAQG T+V L HLDRGYYQFHEKLA LGA I RSSE Sbjct: 361 GRQLQGAPVMSTDLRASAALILTGIVAQGVTIVNNLVHLDRGYYQFHEKLAKLGATISRSSE - 422 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1409 A DNA sequence (GBSx1494) was identified in S. agalactiae <SEQ ID 4323> which encodes the amino acid sequence <SEQ ID 4324>. Analysis of this protein sequence reveals the following: TABLE-US-04182 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2096(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04183 >GP: BAA23756 GB: AB009314 proton-translocating ATPase, epsiron subunit [Streptococcus bovis] Identities = 102/138 (73%), Positives = 121/138 (86%), Gaps = 1/138 (0%) Query: 1 MAQLTVQVVTPDGIRYDHHASLITVRTPDGEMGILPGHINLIAPLNVHQMKINRSHQEG- 59 M +TVQVVTPDGIRYDHHA+ I+V+TPDGEMGILP HINLIAPL VH+MKI+R+ Sbjct: 1 MTFMTVQVVTPDGIRYDHHANFISVKTPDGEMGILPEHINLIAPLTVHEMKIHRTDDPNH 60 Query: 60 VDWVAVNGGIIEVNEDQVTIVADSAERARDIDLNRAERAKERAERALEKAQTTQNIDEMR 119- VDWVA+NGGIIE+ ++ VTIVADSAER RDID++RAERAK RAER LE+AQ+T +IDE+R Sbjct: 61 VDWVAINGGIIEIKDNLVTIVADSAERERDIDVSRAERAKIRAERKLEQAQSTHDIDEVR 120- Query: 120 RAEVALRRAINRISVGKK 137 RA+VALRRA+NRISVG K Sbjct: 121 RAQVALRRALNRISVGNK 138 A related DNA sequence was identified in S. pyogenes <SEQ ID 4325> which encodes the amino acid sequence <SEQ ID 4326>. Analysis of this protein sequence reveals the following: TABLE-US-04184 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ---- bacterial cytoplasm --- Certainty = 0.2539(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04185 Identities = 100/138 (72%), Positives = 119/138 (85%), Gaps = 1/138 (0%) Query: 1 MAQLTVQVVTPDGIRYDHHASLITVRTPDGEMGILPGHINLIAPLNVHQMKINRSHQ-EG 59 M Q+TVQVVTPDGI+YDHHA I+V TPDGEMGILP HINLIAPL VH+MKI R + E Sbjct: 1 MTQMTVQVVTPDGIKYDHHAKFISVTTPDGEMGILPNHINLIAPLQVHEMKIRRGGEDEK 60 Query: 60 VDWVAVNGGIIEVNEDQVTIVADSAERARDIDLNRAERAKERAERALEKAQTTQNIDEMR 119- VDW+A+NGGIIE+ ++ VTIVADSAER RDID++RAERAK RAER + +A+TT NIDE+R Sbjct: 61 VDWIAINGGIIEIKDNVVTIVADSAERDRDIDVSRAERAKLRAEREIAQAETTHNIDEVR 120- Query: 120 RAEVALRRAINRISVGKK 137 RA+VALRRA+NRI+V KK Sbjct: 121 RAKVALRRALNRINVSKK 138 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1410 A DNA sequence (GBSx1495) was identified in S. agalactiae <SEQ ID 4327> which encodes the amino acid sequence <SEQ ID 4328>. Analysis of this protein sequence reveals the following: TABLE-US-04186 Possible site: 60 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to the beta subunit of the S. mutans ATPase: TABLE-US-04187 >GP: AAD13383 GB: U31170 ATPase, beta subunit [Streptococcus mutans] Identities = 435/466 (93%), Positives = 455/466 (97%) Query: 1 MSSGKIAQVVGPVVDVVFASGDKLPEINNALIVYKNGDKSQKVVLEVALELGDGLVRTIA 60 MS+GKIAQVVGPVVDV FA+ DKLPEINNAL+VYK+GDKSQ++VLEVALELGDGLVRTIA Sbjct: 1 MSTGKIAQVVGPVVDVAFATDDKLPEINNALVVYKDGDKSQRIVLEVALELGDGLVRTIA 60 Query: 61 MESTDGLTRGLEVLDTGRAISVPVGKDTLGRVFNVLGDAIDLEEPFAEDAERQPIHKKAP 120- MESTDGLTRGLEV DTGRAISVPVGK+TLGRVFNVLGD IDL++PFAEDAERQPIHKKAP Sbjct: 61 MESTDGLTRGLEVFDTGRAISVPVGKETLGRVFNVLGDTIDLDKPFAEDAERQPIHKKAP 120- Query: 121 SFDELSTSSEILETGIKVIDLLAPYLKGGKVGLFGGAGVGKTVLIQELIHNIAQEHGGIS 18- 0 SFD+LSTS+EILETGIKVIDLLAPYLKGGKVGLFGGAGVGKTVLIQELIHNIAQEHGGIS Sbjct: 121 SFDDLSTSTEILETGIKVIDLLAPYLKGGKVGLFGGAGVGKTVLIQELIHNIAQEHGGIS 18- 0 Query: 181 VFTGVGERTREGNDLYWEMKESGVIEKTAMVFGQMNEPPGARMRVALTGLTIAEYFRDVE 24- 0 VFTGVGERTREGNDLYWEMKESGVIEKTAMVFGQMNEPPGARMRVALTGLTIAEYFRDVE Sbjct: 181 VFTGVGERTREGNDLYWEMKESGVIEKTAMVFGQMNEPPGARMRVALTGLTIAEYFRDVE 24- 0 Query: 241 GQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERITSTKKGSVTSI 30- 0 GQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERITSTKKGSVTSI Sbjct: 241 GQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERITSTKKGSVTSI 30- 0 Query: 301 QAIYVPADDYTDPAPATAFAHLDSTTNLERKLTQMGIYPAVDPLASSSRALTPEIVGDEH 36- 0 QAIYVPADDYTDPAPATAFAHLDSTTNLER+LTQMGIYPAVDPLASSSRAL+PEIVG EH Sbjct: 301 QAIYVPADDYTDPAPATAFAHLDSTTNLERRLTQMGIYPAVDPLASSSRALSPEIVGQEH 36- 0 Query: 361 YEVATEVQRVLQRYRELQDIIAILGMDELSDEEKTLVGRARRIQFFLSQNFNVAETFTGQ 42- 0 Y+VATEVQ VLQRYRELQDIIAILGMDELSDEEKTLVGRARRIQFFLSQNFNVAE FTGQ Sbjct: 361 YDVATEVQHVLQRYRELQDIIAILGMDELSDEEKTLVGRARRIQFFLSQNFNVAEQFTGQ 42- 0 Query: 421 PGSYVPVEETVRGFKEILDGKHDQIPEDAFRMVGGIEDVIAKAEKM 466 PGSYVPV ETVRGFKEIL+GK+D++PEDAFR VG IEDV+ KA+KM Sbjct: 421 PGSYVPVAETVRGFKEILEGKYDELPEDAFRSVGAIEDVVEKAKKM 466 A related DNA sequence was identified in S. pyogenes <SEQ ID 4329> which encodes the amino acid sequence <SEQ ID 4330>. Analysis of this protein sequence reveals the following: TABLE-US-04188 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0275(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04189 Identities = 440/468 (94%), Positives = 456/468 (97%) Query: 1 MSSGKIAQVVGPVVDVVFASGDKLPEINNALIVYKNGDKSQKVVLEVALELGDGLVRTIA 60 MSSGKIAQVVGPVVDV+FASGDKLPEINNALIVYK+ DK QK+VLEVALELGDG+VRTIA Sbjct: 1 MSSGKIAQVVGPVVDVMFASGDKLPEINNALIVYKDSDKKQKIVLEVALELGDGMVRTIA 60 Query: 61 MESTDGLTRGLEVLDTGRAISVPVGKDTLGRVFNVLGDAIDLEEPFAEDAERQPIHKKAP 120- MESTDGLTRGLEVLDTGRAISVPVGK+TLGRVFNVLG+IDLEEPFAED +RQPIHKKAP Sbjct: 61 MESTDGLTRGLEVLDTGRAISVPVGKETLGRVFNVLGETIDLEEPFAEDVDRQPIHKKAP 120- Query: 121 SFDELSTSSEILETGIKVIDLLAPYLKGGKVGLFGGAGVGKTVLIQELIHNIAQEHGGIS 18- 0 SFDELSTSSEILETGIKVIDLLAPYLKGGKVGLFGGAGVGKTVLIQELIHNIAQEHGGIS Sbjct: 121 SFDELSTSSEILETGIKVIDLLAPYLKGGKVGLFGGAGVGKTVLIQELIHNIAQEHGGIS 18- 0 Query: 181 VFTGVGERTREGNDLYWEMKESGVIEKTAMVFGQMNEPPGARMRVALTGLTIAEYFRDVE 24- 0 VFTGVGERTREGNDLYWEMKESGVIEKTAMVFGQMNEPPGARMRVALTGLTIAEYFRDVE Sbjct: 181 VFTGVGERTREGNDLYWEMKESGVIEKTAMVFGQMNEPPGARMRVALTGLTIAEYFRDVE 24- 0 Query: 241 GQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERITSTKKGSVTSI 30- 0 GQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERITST+KGSVTSI Sbjct: 241 GQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERITSTQKGSVTSI 30- 0 Query: 301 QAIYVPADDYTDPAPATAFAHLDSTTNLERKLTQMGIYPAVDPLASSSRALTPEIVGDEH 36- 0 QAIYVPADDYTDPAPATAFAHLDSTTNLERKLTQMGIYPAVDPLASSSRAL+PEIVG+EH Sbjct: 301 QAIYVPADDYTDPAPATAFAHLDSTTNLERKLTQMGIYPAVDPLASSSRALSPEIVGEEH 36- 0 Query: 361 YEVATEVQRVLQRYRELQDIIAILGMDELSDEEKTLVGRARRIQFFLSQNFNVAETFTGQ 42- 0 Y VATEVQRVLQRYRELQDIIAILGMDELSDEEKTLVGRARRIQFFLSQNFNVAE FTG Sbjct: 361 YAVATEVQRVLQRYRELQDIIAILGMDELSDEEKTLVGRARRIQFFLSQNFNVAEQFTGL 42- 0 Query: 421 PGSYVPVEETVRGFKEILDGKHDQIPEDAFRMVGGIEDVIAKAEKMNY 468 PGSYVPV +TVRGFKEIL+GK+D++PEDAFR VG IEDVI KAEKM + Sbjct: 421 PGSYVPVADTVRGFKEILEGKYDELPEDAFRSVGPIEDVIKKAEKMGF 468 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1411 A DNA sequence (GBSx1496) was identified in S. agalactiae <SEQ ID 4331> which encodes the amino acid sequence <SEQ ID 4332>. Analysis of this protein sequence reveals the following: TABLE-US-04190 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1889(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04191 >GP: BAA23754 GB: AB009314 proton-translocating ATPase, gamma subunit [Streptococcus bovis] Identities = 252/293 (86%), Positives = 278/293 (94%), Gaps = 2/293 (0%) Query: 1 MAGSLSEIKDKILSTEKTSKITSAMQMVSSAKLVKSEQAARDFQVYASKIRQITTNLLKS 60 MAGSLSEIK KI+ST+KTS IT AMQMVS+AKL KSEQAA+DFQVYASKIRQITT+LLKS Sbjct: 1 MAGSLSEIKGKIISTQKTSHITGAMQMVSAAKLTKSEQAAKDFQVYASKIRQITTDLLKS 60 Query: 61 DLVSGSDNPMLSSRPVKKTGYIVITSDKGLVGGYNSKILKAMMDTITDYHTENDDYAIIS 120- +LV+GS NPML++RPVKKTGYIVITSDKGLVGGYNSKILKAMMD I +YH ++ +YAII+ Sbjct: 61 ELVNGSKNPMLAARPVKKTGYIVITSDKGLVGGYNSKILKAMMDLIEEYH-QDGNYAIIA 119- Query: 121 IGSVGSDFFKARGMNVSFELRGLEDQPSFDQVGKIIAQAVEMYKNELFDELYVCYNHHVN 18- 0 IG +G+DFFKARGMNV FELRGLEDQPSF+QVG IIA++VEMYKNELFDELYVCYNHHVN Sbjct: 120 IGGIGADFFKARGMNVVFELRGLEDQPSFEQVGNIIAKSVEMYKNELFDELYVCYNHHVN 17- 9 Query: 181 SLTSQVRMQQMLPIKELDAEEASEDRVITGFELEPNREVILEQLLPQYTESLIYGAIIDA 24- 0 SLTSQVR+QQMLPI ELDA+EA+E+ V +GFELEPNRE+ILEQLLPQYTESLIYGAI+DA Sbjct: 180 SLTSQVRVQQMLPIAELDADEAAEEGV-SGFELEPNREMILEQLLPQYTESLIYGAIVDA 23- 8 Query: 241 KTAEHAAGMTAMQTATDNAKNVINDLTIQYNRARQAAITQEITEIVAGANALE 293 KTAEHAAGMTAMQTATDNAKNVINDLTIQYNRARQAAITQEITEIVAGANALE Sbjct: 239 KTAEHAAGMTAMQTATDNAKNVINDLTIQYNRARQAAITQEITEIVAGANALE 291 A related DNA sequence was identified in S. pyogenes <SEQ ID 4333> which encodes the amino acid sequence <SEQ ID 4334>. Analysis of this protein sequence reveals the following: TABLE-US-04192 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1969(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04193 Identities = 251/293 (85%), Positives = 275/293 (93%), Gaps = 2/293 (0%) Query: 1 MAGSLSEIKDKILSTEKTSKITSAMQMVSSAKLVKSEQAARDFQVYASKIRQITTNLLKS 60 MAGSLSEIK KI+STEKTSKITSAM+MVSSAKLVKSEQAARDFQ+YASKIRQITT+LLKS Sbjct: 1 MAGSLSEIKAKIISTEKTSKITSAMRMVSSAKLVKSEQAARDFQIYASKIRQITTDLLKS 60 Query: 61 DLVSGSDNPMLSSRPVKKTGYIVITSDKGLVGGYNSKILKAMMDTITDYHTENDDYAIIS 120- +L GSDNPML SRPVKKTGYIVITSDKGLVGGYNSKILK++MD IT+YH + DY IIS Sbjct: 61 ELTIGSDNPMLVSRPVKKTGYIVITSDKGLVGGYNSKILKSVMDMITEYHADG-DYEIIS 119- Query: 121 IGSVGSDFFKARGMNVSFELRGLEDQPSFDQVGKIIAQAVEMYKNELFDELYVCYNHHVN 18- 0 IGSVGSDFFKARGMNV+FELRGL DQPSF+QV +II+Q+V+M+ NE+FDELYVCYNHHVN Sbjct: 120 IGSVGSDFFKARGMNVAFELRGLADQPSFEQVRQIISQSVDMFVNEIFDELYVCYNHHVN 17- 9 Query: 181 SLTSQVRMQQMLPIKELDAEEASEDRVITGFELEPNREVILEQLLPQYTESLIYGAIIDA 24- 0 SLTSQVR+QQMLPI +L A+EA+E+ V TGFELEPNR IL+QLLPQ+TESLIYGAIIDA Sbjct: 180 SLTSQVRVQQMLPISDLVADEAAEEGV-TGFELEPNRHDILDQLLPQFTESLIYGAIIDA 23- 8 Query: 241 KTAEHAAGMTAMQTATDNAKNVINDLTIQYNRARQAAITQEITEIVAGANALE 293 KTAEHAAGMTAMQTATDNAKNVINDLTIQYNRARQAAITQEITEIVAGANALE Sbjct: 239 KTAEHAAGMTAMQTATDNAKNVINDLTIQYNRARQAAITQEITEIVAGANALE 291 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1412 A DNA sequence (GBSx1497) was identified in S. agalactiae <SEQ ID 4335> which encodes the amino acid sequence <SEQ ID 4336>. Analysis of this protein sequence reveals the following: TABLE-US-04194 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1963(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1413 A DNA sequence (GBSx1498) was identified in S. agalactiae <SEQ ID 4337> which encodes the amino acid sequence <SEQ ID 4338>. Analysis of this protein sequence reveals the following:

TABLE-US-04195 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3146(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to the alpha subunit of the proton-translocating ATPase from S. bovis: TABLE-US-04196 >GP: BAA23753 GB: AB009314 proton-translocating ATPase, alpha subunit [Streptococcus bovis] Length = 501 Identities = 482/501 (96%), Positives = 497/501 (98%) Query: 1 MAINAQEISALIKKQIEDFQPNFDVTETGIVTYIGDGIARARGLDNAMSGELLEFSNGAY 60 MAINAQEISALIKKQIE+FQPNFDVTETG+VTYIGDGIARARGLDNAMSGELLEFSNGA+ Sbjct: 1 MAINAQEISALIKKQIENFQPNFDVTETGVVTYIGDGIARARGLDNAMSGELLEFSNGAF 60 Query: 61 GMAQNLESNDVGIIILGDFSEIREGDVVKRTGKIMEVPVGEAMIGRVVNPLGQPVDGLGE 120- GMAQNLESNDVGIIILGDFS IREGD VKRTGKIMEVPVGEA+IGRVVNPLGQPVDGLG+ Sbjct: 61 GMAQNLESNDVGIIILGDFSTIREGDEVKRTGKIMEVPVGEALIGRVVNPLGQPVDGLGD 120- Query: 121 IETTATRPVETPAPGVMQRKSVFEPLQTGLKAIDALVPIGRGQRELIIGDRQTGKTSVAI 18- 0 I+TTATRPVETPAPGVMQRKSV EPLQTGLKAIDALVPIGRGQRELIIGDRQTGKTSVAI Sbjct: 121 IKTTATRPVETPAPGVMQRKSVSEPLQTGLKAIDALVPIGRGQRELIIGDRQTGKTSVAI 18- 0 Query: 181 DAILNQKGQDMICIYVAIGQKESTVRTQVETLRKYGALDYTIVVTASASQPSPLLFIAPY 24- 0 DAILNQKGQDMICIYVAIGQKESTVRTQVETLRKYGALDYTIVVTASASQPSPLL+IAPY Sbjct: 181 DAILNQKGQDMICIYVAIGQKESTVRTQVETLRKYGALDYTIVVTASASQPSPLLYIAPY 24- 0 Query: 241 AGVAMAEEFMYNGKHVLIVYDDLSKQAVAYRELSLLLRRPPGREAYPGDVFYLHSRLLER 30- 0 AGVAMAEEFMYNGKHVLIVYDDLSKQAVAYRELSLLLRRPPGREAYPGDVFYLHSRLLER Sbjct: 241 AGVAMAEEFMYNGKHVLIVYDDLSKQAVAYRELSLLLRRPPGREAYPGDVFYLHSRLLER 30- 0 Query: 301 SAKVSDALGGGSITALPFIETQAGDISAYIATNVISITDGQIFLQENLFNSGIRPAIDAG 36- 0 SAKVSDALGGGSITALPFIETQAGDISAYIATNVISITDGQIFLQENLFNSGIRPAIDAG Sbjct: 301 SAKVSDALGGGSITALPFIETQAGDISAYIATNVISITDGQIFLQENLFNSGIRPAIDAG 36- 0 Query: 361 SSVSRVGGAAQIKAMKRVAGTLRLDLASYRELEAFTQFGSDLDAATQAKLNRGRRTVEVL 42- 0 SSVSRVGG+AQIKAMK+VAGTLRLDLASYRELEAFTQFGSDLDAATQAKLNRGRRTVEVL Sbjct: 361 SSVSRVGGSAQIKAMKKVAGTLRLDLASYRELEAFTQFGSDLDAATQAKLNRGRRTVEVL 42- 0 Query: 421 KQPLHKPLPVEKQVVILYALTHGFLDDVPVNDILAFEEALYDYFDAHYDNLFETIRTTKD 48- 0 KQP+HKPLPVEKQVVILYALTHGFLDDVPVNDILAFEEALYDYFDAHY+++FETIRTTKD Sbjct: 421 KQPVHKPLPVEKQVVILYALTHGFLDDVPVNDILAFEEALYDYFDAHYESIFETIRTTKD 48- 0 Query: 481 LPEEAELDAAIQAFKDQSQFK 501 LPEE+ LDAAIQAFKDQS+FK Sbjct: 481 LPEESVLDAAIQAFKDQSEFK 501 A related DNA sequence was identified in S. pyogenes <SEQ ID 4339> which encodes the amino acid sequence <SEQ ID 4340>. Analysis of this protein sequence reveals the following: TABLE-US-04197 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3654(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04198 Identities = 477/501 (95%), Positives = 490/501 (97%) Query: 1 MAINAQEISALIKKQIEDFQPNFDVTETGIVTYIGDGIARARGLDNAMSGELLEFSNGAY 60 +AINAQEISALIKKQIE+FQPNFDVTETGIVTYIGDGIARARGLDNAMSGELLEF NGAY Sbjct: 1 LAINAQEISALIKKQIENFQPNFDVTETGIVTYIGDGIARARGLDNAMSGELLEFENGAY 60 Query: 61 GMAQNLESNDVGIIILGDFSEIREGDVVKRTGKIMEVPVGEAMIGRVVNPLGQPVDGLGE 120- GMAQNLESNDVGIIILGDFS IREGDVVKRTGKIMEVPVGEA+IGRVVNPLGQPVDGLG+ Sbjct: 61 GMAQNLESNDVGIIILGDFSAIREGDVVKRTGKIMEVPVGEALIGRVVNPLGQPVDGLGD 120- Query: 121 IETTATRPVETPAPGVMQRKSVFEPLQTGLKAIDALVPIGRGQRELIIGDRQTGKTSVAI 18- 0 IETT RPVETPAPGVMQRKSV EPLQTGLKAIDALVPIGRGQRELIIGDRQTGKTSVAI Sbjct: 121 IETTGFRPVETPAPGVMQRKSVSEPLQTGLKAIDALVPIGRGQRELIIGDRQTGKTSVAI 18- 0 Query: 181 DAILNQKGQDMICIYVAIGQKESTVRTQVETLRKYGALDYTIVVTASASQPSPLLFIAPY 24- 0 DAILNQKGQDMICIYVAIGQKESTVRTQVETLR+YGALDYTIVVTASASQPSPLLFIAPY Sbjct: 181 DAILNQKGQDMICIYVAIGQKESTVRTQVETLRRYGALDYTIVVTASASQPSPLLFIAPY 24- 0 Query: 241 AGVAMAEEFMYNGKHVLIVYDDLSKQAVAYRELSLLLRRPPGREAYPGDVFYLHSRLLER 30- 0 AGVAMAEEFMY GKHVLIVYDDLSKQAVAYRELSLLLRRPPGREAYPGDVFYLHSRLLER Sbjct: 241 AGVAMAEEFMYQGKHVLIVYDDLSKQAVAYRELSLLLRRPPGREAYPGDVFYLHSRLLER 30- 0 Query: 301 SAKVSDALGGGSITALPFIETQAGDISAYIATNVISITDGQIFLQENLFNSGIRPAIDAG 36- 0 SAKVSD LGGGSITALPFIETQAGDISAYIATNVISITDGQIFLQENLFNSGIRPAIDAG Sbjct: 301 SAKVSDDLGGGSITALPFIETQAGDISAYIATNVISITDGQIFLQENLFNSGIRPAIDAG 36- 0 Query: 361 SSVSRVGGAAQIKAMKRVAGTLRLDLASYRELEAFTQFGSDLDAATQAKLNRGRRTVEVL 42- 0 SSVSRVGG+AQIKAMK+VAGTLRLDLASYRELEAFTQFGSDLDAATQAKLNRGRRTVE+L Sbjct: 361 SSVSRVGGSAQIKAMKKVAGTLRLDLASYRELEAFTQFGSDLDAATQAKLNRGRRTVEIL 42- 0 Query: 421 KQPLHKPLPVEKQVVILYALTHGFLDDVPVNDILAFEEALYDYFDAHYDNLFETIRTTKD 48- 0 KQPLHKPLPVEKQVVILYALTHGFLDDVPV+DILAFEEALYDYFD HY++LFETIRTTKD Sbjct: 421 KQPLHKPLPVEKQVVILYALTHGFLDDVPVDDILAFEEALYDYFDVHYNDLFETIRTTKD 48- 0 Query: 481 LPEEAELDAAIQAFKDQSQFK 501 LPEEA LDAAI+AFK+ S FK Sbjct: 481 LPEEAALDAAIKAFKEHSNFK 501 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1414 A DNA sequence (GBSx1499) was identified in S. agalactiae <SEQ ID 4341> which encodes the amino acid sequence <SEQ ID 4342>. Analysis of this protein sequence reveals the following: TABLE-US-04199 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1896(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04200 >GP: BAA23752 GB: AB009314 proton-translocating ATPase, delta subunit [Streptococcus bovis] Identities = 98/178 (55%), Positives = 127/178 (71%) Query: 1 MNKKTQALIEQYSKSLVEVAIEHKIVEKIQQEVAALIDIFETSELEGVLSSLAVSHDEKQ 60 M+KKTQAL+EQY+KSLVE+AIE + ++Q E AL+ +FE + L LSSL VS DEK Sbjct: 1 MDKKTQALVEQYAKSLVEIAIEKDSLAELQSETEALLSVFEETNLADFLSSLVVSRDEKV 60 Query: 61 HFVKTLQTSCSTYLVNFLEVIVQNEREALLYPILKSVDQELIKVNGQYPIQITTAVALSP 120- V+ LQ S S Y+ NFLEVI+QNEREA L IL+ V ++ + Q+ I +TTAVAL+ Sbjct: 61 KLVRLLQESSSVYMNNFLEVILQNEREAFLKAILEGVQKDFVIATNQHDIVVTTAVALTD 120- Query: 121 EQKERLFDIAKTKLALPNGQLVEHIDPSIVGGFVVNANNKVIDASVRNQLHQFKMKLK 178 EQKER+ + K + G+LVE+ID SI+GGFV+N NNKVID S+R QL +FKM LK Sbjct: 121 EQKERILALVAEKFGVKAGKLVENIDESILGGFVINVNNKVIDTSIRRQLQEFKMNLK 178 A related DNA sequence was identified in S. pyogenes <SEQ ID 4343> which encodes the amino acid sequence <SEQ ID 4344>. Analysis of this protein sequence reveals the following: TABLE-US-04201 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1668 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04202 Identities = 86/178 (48%), Positives = 125/178 (69%) Query: 1 MNKKTQALIEQYSKSLVEVAIEHKIVEKIQQEVAALIDIFETSELEGVLSSLAVSHDEKQ 60 M KK QALIEQY+KSLVEVA EH ++ +Q +V A+++ F T+ L+ LSS AV H EK Sbjct: 1 MTKKEQALIEQYAKSLVEVASEHHSLDALQADVLAILETFVTTNLDQSLSSQAVPHAEKI 60 Query: 61 HFVKTLQTSCSTYLVNFLEVIVQNEREALLYPILKSVDQELIKVNGQYPIQITTAVALSP 120- + L+ + S Y+ NFL +I+QNEREA LY +L++V E+ V+ QY + +T+++ L+ Sbjct: 61 KLLTLLKGNNSVYMNNFLNLILQNEREAYLYQMLQAVLNEIAIVSNQYDVTVTSSLPLTE 120- Query: 121 EQKERLFDIAKTKLALPNGQLVEHIDPSIVGGFVVNANNKVIDASVRNQLHQFKMKLK 178 EQK R+ + K A+ G+L+E +DPS++GGF+++ NNKVID S+R QL FKM LK Sbjct: 121 EQKSRVRAVVAKKFAVTAGRLIEKVDPSLIGGFIISVNNKVIDTSIRRQLQAFKMNLK 178 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1415 A DNA sequence (GBSx1500) was identified in S. agalactiae <SEQ ID 4345> which encodes the amino acid sequence <SEQ ID 4346>. This protein is predicted to be ATP synthase b chain (atpF). Analysis of this protein sequence reveals the following: TABLE-US-04203 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04204 >GP: AAD13379 GB: U31170 ATPase, b subunit [Streptococcus mutans] Identities = 103/165 (62%), Positives = 130/165 (78%) Query: 1 MSILINSTTIGDIIIVSGSVLLLFILIKTFAWKQITGIFEAREQKIANDIDTAEQARQQA 60 MS LIN T++G+++IV+GS +LL +L+K FAW Q+ IF+ RE+KIA DID AE +RQ A Sbjct: 1 MSTLINGTSLGNLLIVTGSFILLLLLVKKFAWSQLAAIFKTREEKIAKDIDDAENSRQNA 60 Query: 61 EAFATKREEELSNAKTEANQIIDNAKETGLAKGDQIISEAKTEADRLKEKAHQDIAQNKA 120- + KR+ EL+ AK EA QIIDNAKETG A+ +II+EA EA RLK+KA+QDIA +KA Sbjct: 61 QVLENKRQVELNQAKDEAAQIIDNAKETGKAQESKIITEAHEEAGRLKDKANQDIATSKA 120- Query: 121 EALADVKGEVADLTVLLAEKIMVSNLDKEAQSNLIDSYIKKLGDA 165 EAL+ VK +VADL+VLLAEKIM NLDK AQ +LIDSY+ KLGDA Sbjct: 121 EALSSVKADVADLSVLLAEKIMAKNLDKTAQGDLIDSYLDKLGDA 165 A related DNA sequence was identified in S. pyogenes <SEQ ID 4347> which encodes the amino acid sequence <SEQ ID 4348>. Analysis of this protein sequence reveals the following: TABLE-US-04205 Possible site: 32 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04206 >GP: AAD13379 GB: U31170 ATPase, b subunit [Streptococcus mutans] Identities = 88/159 (55%), Positives = 122/159 (76%) Query: 6 GELVGNFILVTGSVIVLLLLIKKFAWGAIESILQTRSQQISRDIDQAEQSRLSAQQLEAK 65 G +GN ++VTGS I+LLLL+KKFAW + +I +TR ++I++DID AE SR +AQ LE K Sbjct: 7 GTSLGNLLIVTGSFILLLLLVKKFAWSQLAAIFKTREEKIAKDIDDAENSRQNAQVLENK 66 Query: 66 SQANLDASRLQASKIISDAKEIGQLQGDKLVAEATDEAKRLKEKALTDIEQSKSDAISAV 125- Q L+ ++ +A++II +AKE G+ Q K++ EA +EA RLK+KA DI SK++A+S+V Sbjct: 67 RQVELNQAKDEAAQIIDNAKETGKAQESKIITEAHEEAGRLKDKANQDIATSKAEALSSV 126- Query: 126 KTEMSDLTVLLAEKIMGANLDKTAQSQLIDSYLDDLGEA 164 K +++DL+VLLAEKIM NLDKTAQ LIDSYLD LG+A Sbjct: 127 KADVADLSVLLAEKIMAKNLDKTAQGDLIDSYLDKLGDA 165 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04207 Identities = 81/156 (51%), Positives = 115/156 (72%) Query: 10 IGDIIIVSGSVLLLFILIKTFAWKQITGIFEAREQKIANDIDTAEQARQQAEAFATKREE 69 - +G+ I+V+GSV++L +LIK FAW I I + R Q+I+ DID AEQ+R A+ K + Sbjct: 9 VGNFILVTGSVIVLLLLIKKFAWGAIESILQTRSQQISRDIDQAEQSRLSAQQLEAKSQA 68 Query: 70 ELSNAKTEANQIIDNAKETGLAKGDQIISEAKTEADRLKEKAHQDIAQNKAEALADVKGE 129- L ++ +A++II +AKE G +GD++++EA EA RLKEKA DI Q+K++A++ VK E Sbjct: 69 NLDASRLQASKIISDAKEIGQLQGDKLVAEATDEAKRLKEKALTDIEQSKSDAISAVKTE 128- Query: 130 VADLTVLLAEKIMVSNLDKEAQSNLIDSYIKKLGDA 165 ++DLTVLLAEKIM +NLDK AQS LIDSY+ LG+A Sbjct: 129 MSDLTVLLAEKIMGANLDKTAQSQLIDSYLDDLGEA 164 SEQ ID 4346 (GBS169) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 34 (lane 6; MW 18 kDa). The GBS169-His fusion product was purified (FIG. 200, lane 11) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 250). These tests confirm that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1416 A DNA sequence (GBSx1501) was identified in S. agalactiae <SEQ ID 4349> which encodes the amino acid sequence <SEQ ID 4350>. Analysis of this protein sequence reveals the following: TABLE-US-04208 Possible site: 29 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.73 Transmembrane 20-36 (14-42) INTEGRAL Likelihood = -5.20 Transmembrane 207-223 (206-228) INTEGRAL Likelihood = -4.35 Transmembrane 78-94 (73-97) INTEGRAL Likelihood = -4.09 Transmembrane 113-129 (113-133) INTEGRAL Likelihood = -2.39 Transmembrane 174-190 (174-190) ----- Final Results ----- bacterial membrane --- Certainty = 0.5692 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04209 >GP: BAA23750 GB: AB009314 proton-translocating ATPase, a subunit [Streptococcus bovis] Identities = 149/238 (62%), Positives = 180/238 (75%) Query: 1 MESTSNPTVSFLGIDFDLTILAMSLLTITIIFILVFWASRKMTIKPKGKQNVLEYVYELV 60 ME++ NPT GI+FDLTILAMSLLT+ I F ++FWA+RKMT+KPKGKQN +EYVYE V Sbjct: 1 METSVNPTAHVFGIEFDLTILAMSLLTVIISFGIIFWATRKMTLKPKGKQNFIEYVYEFV 60 Query: 61 NNTISQNLGHYTKNYSLLMFILFSFVFIANNLGLMTSLKTHEHNFWTSPTANFGVDITLS 120- NTI NLG YT YSLLMF F F+ IANNLGL+ L++ ++NFWTSPT+ VD T S Sbjct: 61 QNTIKPNLGEYTPKYSLLMFTFFFFILIANNLGLLVKLESEDYNFWTSPTSTIMVDCTWS 120- Query: 121 LLVAFICHIEGIRKKGIGGYLKGFLSPTPAMLPMNLLEEVTNVASLALRLFGNIFSGEVV 18- 0 L+VA + H+EG+RKKG+ YLKG+LSP P MLPMN+LE+ TNV SLALRLFGNI++GEVV Sbjct: 121 LIVAIVVHVEGVRKKGVKAYLKGYLSPFPMMLPMNILEQFTNVLSLALRLFGNIYAGEVV 18- 0 Query: 181 TGLLLQLAVLSPFTGPLAFALNIVWTAFSMFIGFIQAYVFIILSSSYIGHKVHGDEEE 238 T L++ S P A ALN+ W AFS FIG IQAYVF ILSS YI K+ DE+E Sbjct: 181 TALIVGFGTKSLIFAPFALALNLAWVAFSAFIGCIQAYVFTILSSKYISEKLPEDEDE 238 A related DNA sequence was identified in S. pyogenes <SEQ ID 4351> which encodes the amino acid sequence <SEQ ID 4352>. Analysis of this protein sequence reveals the following: TABLE-US-04210 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.73 Transmembrane 79-95 (72-97) INTEGRAL Likelihood = -4.35 Transmembrane 115-131 (112-132) INTEGRAL Likelihood = -2.13 Transmembrane 200-216 (197-216) ----- Final Results ----- bacterial membrane --- Certainty = 0.2890 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04211 Identities = 124/239 (51%), Positives = 169/239 (69%), Gaps = 3/239 (1%) Query: 1 MESTSNPTVSFLGIDFDLTILAMSLLTITIIFILVFWASRKMTIKPKGKQNVLEYVYELV 60 ME P + I F+LT+LA+ ++TI I+F VFWASR+M +KP+GKQ LEY+ V Sbjct: 1 MEEAKIPMLKLGPITFNLTLLAVCIVTIAIVFAFVFWASRQMKLKPEGKQTALEYLISFV 60 Query: 61 NNTISQNLGH-YTKNYSLLMFILFSFVFIANNLGLMTSLKT-HEHNFWTSPTANFGVDIT 118- + ++L H K+YSLL+F +F FV +ANNLGL T L+T + +N WTSPTAN D+ Sbjct: 61 DGIGEEHLDHNLQKSYSLLLFTIFLFVAVANNLGLFTKLETVNGYNLWTSPTANLAFDLA 120- Query: 119 LSLLVAFICHIEGIRKKGIGGYLKGFLSPTPAMLPMNLLEEVTNVASLALRLFGNIFSGE 17- 8 LSL + + HIEG+R++G+ +LK +P P M PMNLLEE TN SLA+RLFGNIF+GE Sbjct: 121 LSLFITLMVHIEGVRRRGLVAHLKRLATPWP-MTPMNLLEEFTNFLSLAIRLFGNIFAGE 17- 9 Query: 179 VVTGLLLQLAVLSPFTGPLAFALNIVWTAFSMFIGFIQAYVFIILSSSYIGHKVHGDEE 237- VVTGL++QLA + P+AF +N+ WTAFS+FI IQA+VF L+++Y+G KV+ EE Sbjct: 180 VVTGLIVQLANYRVYWWPIAFLVNMAWTAFSVFISCIQAFVFTKLTATYLGKKVNESEE 238- A related GBS gene <SEQ ID 8803> and protein <SEQ ID 8804> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04212 Lipop: Possible site: -1 Crend: 1 McG: Discrim Score: -3.50 GvH: Signal Score (-7.5): -3.36 Possible site: 29 >>> Seems to have no N-terminal signal sequence ALOM program count: 5 value: -11.73 threshold: 0.0 INTEGRAL Likelihood = -11.73 Transmembrane 20-36 (14-42) INTEGRAL Likelihood = -5.20 Transmembrane 207-223 (206-228) INTEGRAL Likelihood = -4.35 Transmembrane 78-94 (73-97) INTEGRAL Likelihood = -4.09 Transmembrane 113-129 (113-133) INTEGRAL Likelihood = -2.39 Transmembrane 174-190 (174-190) PERIPHERAL Likelihood = 5.30 156 modified ALOM score: 2.85 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5692 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00093## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1417 A DNA sequence (GBSx1502) was identified in S. agalactiae <SEQ ID 4353> which encodes the amino acid sequence <SEQ ID 4354>. This protein is predicted to be ATP synthase c subunit (atpE). Analysis of this protein sequence reveals the following: TABLE-US-04213 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.62 Transmembrane 48-64 (42-65) ----- Final Results ----- bacterial membrane --- Certainty = 0.2848(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-04214 >GP: BAA23749 GB: AB009314 proton-translocating ATPase, c subunit [Streptococcus bovis] Identities = 56/65 (86%), Positives = 59/65 (90%) Query: 1 MNLAILALGFAVMGVSIGEGILVANIAKSAARQPEMFSKLQTLMFTGVAFIEGTFFVLFA 60 +NL ILALG AV+GVS+GEGILVANIAKSAARQPEMFSKLQTLMF GVAFIEGTFFVL A Sbjct: 2 LNLKILALGLAVLGVSLGEGILVANIAKSAARQPEMFSKLQTLMFLGVAFIEGTFFVLLA 61 Query: 61 FTFLV 65 TF V Sbjct: 62 STFFV 66 A related DNA sequence was identified in S. pyogenes <SEQ ID 4355> which encodes the amino acid sequence <SEQ ID 4356>. Analysis of this protein sequence reveals the following: TABLE-US-04215 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.26 Transmembrane 47-63 (41-64) ----- Final Results ----- bacterial membrane --- Certainty = 0.3102(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04216 >GP: AAD00920 GB: AF001955 UncE [Streptococcus sanguinis] Identities = 50/66 (75%), Positives = 58/66 (87%), Gaps = 1/66 (1%) Query: 1 MNPIF-ALALACFGVSLAEGFLMANLFKAASRQPEIIGQLRSLMILGVAFIEGTFFVTLV 59 MN F L ACFGVS+AEG +M+NLFKAASRQPEIIGQLRSL+ILG+AF+EGTFFVTL Sbjct: 1 MNLTFLGLCFACFGVSIAEGLIMSNLFKAASRQPEIIGQLRSLLILGIAFVEGTFFVTLA 60 Query: 60 MAFILK 65 MAF++K Sbjct: 61 MAFVIK 66 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04217 Identities = 33/62 (53%), Positives = 45/62 (72%) Query: 5 ILALGFAVMGVSIGEGILVANIAKSAARQPEMFSKLQTLMFTGVAFIEGTFFVLFAFTFLVR 66- I AL A GVS+ EG L+AN+ K+A+RQPE+ +L++LM GVAFIEGTFFV F+++ Sbjct: 4 IFALALACFGVSLAEGFLMANLFKAASRQPEIIGQLRSLMILGVAFIEGTFFVTLVMAFILK 65- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1418 A DNA sequence (GBSx1503) was identified in S. agalactiae <SEQ ID 4357> which encodes the amino acid sequence <SEQ ID 4358>. Analysis of this protein sequence reveals the following: TABLE-US-04218 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2562(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1419 A DNA sequence (GBSx1504) was identified in S. agalactiae <SEQ ID 4359> which encodes the amino acid sequence <SEQ ID 4360>. This protein is predicted to be bacterial glycogen synthase (glgA). Analysis of this protein sequence reveals the following: TABLE-US-04219 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1574(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04220 >GP: BAA19591 GB: D87026 bacterial glycogen synthase [Bacillus stearothermophilus] Identities = 220/475 (46%), Positives = 312/475 (65%), Gaps = 1/475 (0%) Query: 1 MKIMFVAAEGAPFAKTGGLGDVIGALPKSLSKKGHDVAVVMPYYDMVDQKFGDQIENLMY 60 MK++F +E APFAK+GGL DV GALPK L + G D V++P Y+ + ++ +++ + Sbjct: 1 MKVLFAVSECAPFAKSGGLADVAGALPKELRRLGIDARVMLPKYETIAPEWKKKMKKVAE 60 Query: 61 FYTDVGWRHQYVGVKRLSQDNVTFYFIDNQYYFYRGHVYGDWDDGERFAYFQLAALELME 120- VGWR QY GV+ L D V +YFIDN+YYF R +YG +DDGERFAYF A LE++ Sbjct: 61 LIVPVGWRRQYCGVEELRHDGVIYYFIDNEYYFKRPQLYGHYDDGERFAYFCRAVLEVLP 120- Query: 121 KIDFIPDVLHVHDYHTAMIPFLLKEKYHWIQAYNNIRAVFTIHNIEFQGQFGPEMLGDLF 18- 0 +I F PDV+H HD+HT M+PFLL+E+Y Y ++R VFTIHN++FQG F +L DL Sbjct: 121 EIQFQPDVIHCHDWHTGMVPFLLREQYRHELFYVDMRTVFTIHNLQFQGLFPRGILEDLL 18- 0 Query: 181 GVGAERYEDGTLRWNNCLNWMKAAILYSDRVTTVSPSYANEIKTPEFGKGLDQIMRMEAG 24- 0 + + L + C+++MK A++ SD +TTVSP+Y EI+T +G+ LD ++R Sbjct: 181 NLDGRYFTVDHLEFYGCVSFMKGALVASDLITTVSPTYKEEIQTAYYGERLDGLLRARRD 24- 0 Query: 241 KLSGIVNGIDSDLLNPETDAFLPYHFSKSNLEGKIKNKLALQENLGLPQDKNVPLIGIVS 30- 0 L GI+NGID + NPE D FL +S E K NK ALQ GLP+ +VPLI +V+ Sbjct: 241 DLLGILNGIDDEFYNPEADPFLTATYSVHTRERKQLNKRALQRQFGLPEWDDVPLIAMVT 30- 0 Query: 301 RLTDQKGFDIIASELDNMLQQDIQMVILGTGYHHFEETFSYFASRYPEKLSANITFDLRL 36- 0 R+T QKG D++ M+ +D+Q+V+LGTG FE+ FS A+ YP K+ I F L Sbjct: 301 RMTAQKGLDLVTCVFHEMMSEDMQLVVLGTGDWRFEQFFSQMAAAYPGKVGVYIGFHEPL 36- 0 Query: 361 AQQIYAASDIFMMPSAFEPCGLSQMMAMRYGSLPLVHEVGGLKDTVVAFNQFDGSGTGFS 42- 0 A QIYA +D+F++PS FEPCGLSQM+A+RYG++P+V E GGL DTV ++N+ G GFS Sbjct: 361 AHQIYAGADLFLIPSLFEPCGLSQMIALRYGTIPIVRETGGLNDTVQSYNEITKEGNGFS 42- 0 Query: 421 FNHFSGYWLMQTLKLALEVYNDYPEAWKKLQWQAMSKDFSWDTACVAYEQLYQQL 475 F +F+ + ++ T++ AL Y P W++L +AM D+SW + Y+Q Y+QL Sbjct: 421 FTNFNAHDMLYTIRRALSFYRQ-PSVWEQLTERAMRGDYSWRRSANQYKQAYEQL 474 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1420 A DNA sequence (GBSx1505) was identified in S. agalactiae <SEQ ID 4361> which encodes the amino acid sequence <SEQ ID 4362>. This protein is predicted to be a subunit of ADP-glucose pyrophosphorylase. Analysis of this protein sequence reveals the following: TABLE-US-04221 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3492(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04222 >GP:BAA19590 GB:D87026 subunit of ADP-glucose pyrophosphorylase [Bacillus stearothermophilus] Identities = 59/178 (33%), Positives = 111/178 (62%), Gaps = 1/178 (0%) Query: 37 SAEIYVIDTPWLIEKMEEEAQNNEPRKLRFLLRDLIVESNALAFEYTGYLSNISSIKSYY 96 - S E+Y+++T L++ + + +N+ + ++RD + +EY+GY + I S++ Y+ Sbjct: 157 SLEMYLLETSLLLDLIADY-KNHGYYSIVDVIRDYHRSLSICEYEYSGYAAVIDSVEQYF 21- 5 Query: 97 DANMDMLTPNKFYSLFFSNQKVYTKVKNEEATYFDKQSNVSNSQLASGSIIKGYLDHSIV 156- ++M++L + + LF + +YTKVK+E T + ++ NV S +A+G +I+G +++S++ Sbjct: 216 RSSMELLDRDVWEQLFLPSHPIYTKVKDEPPTKYGREGNVKRSMIANGCVIEGTVENSVL 27- 5 Query: 157 SRNCLLEKGTRVVNSIIFPKVKIGEGATIENTIIDKCVKVASGVTLKGSLDKPLVIPK 214 R+ + KG V NSII K +IG+G ++ IIDK KV GV LKG+ ++P ++ K Sbjct: 276 FRSVKIGKGAVVRNSIIMQKCQIGDGCVLDGVIIDKDAKVEPGVVLKGTKEQPFIVRK 333 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1421 A DNA sequence (GBSx1506) was identified in S. agalactiae <SEQ ID 4363> which encodes the amino acid sequence <SEQ ID 4364>. This protein is predicted to be subunit of ADP-glucose pyrophosphorylase (glgC-1). Analysis of this protein sequence reveals the following: TABLE-US-04223 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq. ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9765> which encodes amino acid sequence <SEQ ID 9766> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04224 >GP:BAA19589 GB:D87026 subunit of ADP-glucose pyrophosphorylase [Bacillus stearothermophilus] Identities = 195/352 (55%), Positives = 259/352 (73%) Query: 7 MKNEMLALILAGGQGTRLGKLTQSIAKPAVQFGGRYRIIDFALSNCANSGINNVGVITQY 66 MK + +A++LAGGQG+RL LT +IAKPAV FGG+YRIIDF LSNC NSGI+ VGV+TQY Sbjct: 1 MKKKCIAMLLAGGQGSRLRSLTTNIAKPAVPFGGKYRIIDFTLSNCTNSGIDTVGVLTQY 60 Query: 67 QPLELNTHIGNGSSWGLDGIDSGVTVLQPYSATEGNRWFQGTSHAIYQNIDYIDRINPEY 126- QPL L+++IG GS+W LD + GVTVL PYS + G +W++GT++A+YQNI+YI++ NP+Y Sbjct: 61 QPLLLHSYIGIGSAWDLDRRNGGVTVLPPYSVSSGVKWYEGTANAVYQNINYIEQYNPDY 120- Query: 127 VLILSGDHIYKMNYDDMLQTHKDNLASLTVAVLDVPLKEASRFGIMNTDSNDRIVEFEEK 18- 6 VL+LSGDHIYKM+Y ML H A +T++V++VP +EASRFGIMNT+ IVEF EK Sbjct: 121 VLVLSGDHIYKMDYQHMLDYHIAKQADVTISVIEVPWEEASRFGIMNTNEEMEIVEFAEK 18- 0 Query: 187 PEHPKSTKASMGIYIFDWKRLRTVLIDGEKNGIDMSDFGKNVIPAYLESGERVYTYNFDG 24- 6 P PKS ASMGIYIF+W L+ L N DFGK+VIP L +R + Y F+G Sbjct: 181 PAEPKSNLASMGIYIFNWPLLKQYLQIDNANPHSSHDFGKDVIPMLLREKKRPFAYPFEG 24- 0 Query: 247 YWKDVGTIESLWEANMEYIGEDNKLHSRDRSWKIYSKNLIAPPNFMTEDANVKDSLVVDG 30- 6 YWKDVGT++SLWEANN+ + E+N+L DRSW+IYS N PP +++ +A V DSLV +G Sbjct: 241 YWKDVGTVKSLWEANMDLLDENNELDLFDRSWRIYSVNPNQPPQYISPEAEVSDSLVNEG 30- 0 Query: 307 CFVAGNVEHSILSTNVQVKPNAIIKDSFVMSGATIGEGAKINRAIIGEDAVI 358 C V G VE S+L V++ A++K+S +M GA + EGA + RAI+ D++I Sbjct: 301 CVVEGTVERSVLFQGVRIGKGAVVKESVIMPGAAVSEGAYVERAIVTPDSII 352 There is also homology to SEQ ID 2660. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1422 A DNA sequence (GBSx1507) was identified in S. agalactiae <SEQ ID 4365> which encodes the amino acid sequence <SEQ ID 4366>. Analysis of this protein sequence reveals the following: TABLE-US-04225 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2844(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04226 >GP:CAA78440 GB:Z14057 1,4-alpha-glucan branching enzyme [Bacillus caldolyticus] Identities = 272/616 (44%), Positives = 371/616 (60%), Gaps = 14/616 (2%) Query: 6 ELYTFGIGENFHLQNYLGVHSENGSFC----FRVWAPNAENVQVIGDFTDWRNRPLQMNK 61 E+Y F G + G H G F VWAP+A V+++G F DW + K Sbjct: 10 EVYLFHEGRLYQSYELFGAHVIRGGGAVGTRFCVWAPHAREVRLVGSFNDWNGTNSPLTK 69 Query: 62 -NQAGVWEANSLDAREGDLYKYLVTRKGGQVVEKIDPMAVYMERRPGTASVIKVLRNKKW 120- N GVW + EG LYKY + G+V+ K DP A Y E RP TAS++ L+ +W Sbjct: 70 VNDEGVWTIVVPENLEGHLYKYEIITPDGRVLLKADPYAFYSELRPHTASIVYDLKGYEW 129- Query: 121 EDGLWMGRRKRLGFQKRPINIYEVHAGSWKKDDFGHPMTFSQLKDYLIPYLVEMNYTHVE 18- 0 D W +++R +P+ IYE+H GSWKK G T+ ++ D LIPY++E +TH+E Sbjct: 130 NDSPWQRKKRRKRIYDQPMVIYELHFGSWKKKPDGRFYTYREMADELIPYVLERGFTHIE 18- 9 Query: 181 FMPLMAHPLDMSWGYQLMGYFAFEHTYGTPEEFQDFVEACHKNNIGVLVDWVPGHFIQND 24- 0 +PL+ HPLD SWGYQ GY++ YGTP +F FV+ CH+ +GV++DWVPGHF ++ Sbjct: 190 LLPLVEHPLDRSWGYQGTGYYSVTSRYGTPHDFMYFVDRCHQAGLGVIIDWVPGHFCKDA 24- 9 Query: 241 DALAYFDGTATYEYQNHDRAHNYRWGALNFDLGKNQVQSFLISSALFWIEHYHIDGIRVD 30- 0 L FDG TYEY N NY WG NFDLGK +V+SFLIS+ALFW+E+YH+DG RVD Sbjct: 250 HGLYMFDGAPTYEYANEKDRENYVWGTANFDLGKPEVRSFLISNALFWLEYYHVDGFRVD 30- 9 Query: 301 AVSNMLYLDYDEGPWEANQFGDNRNLEGYHFLRKLNKVIKERHPNVMMIAEESTASTPIT 36- 0 AV+NMLY ++ +E N FLR+LN+ + PNV MIAE+ST +T Sbjct: 310 AVANMLYWPNNDRLYE--------NPYAVEFLRQLNEAVFAYDPNVWMIAEDSTDWPRVT 36- 1 Query: 361 KDLESGGLGFDFKWNMGWMNDILRFYEEDPLYRQYDFNLVTFSFMYIFNENFVLAFSHDE 42- 0 GGLGF++KWNMGWMND+L++ E P R+Y N V+FS +Y ++ENF+L FSHDE Sbjct: 362 APTYDGGLGFNYKWNMGWMNDMLKYMETPPHERKYAHNQVSFSLLYAYSENFILPFSHDE 42- 1 Query: 421 VVHGKKSMMHKMWGDRYNQFAGLRNLYAYQMCHPGKKLLFMGSEFGQFLEWKYNDQLEWE 48- 0 VVHGKKS+++KM G +FA LR LY Y M HPGKKLLFMGSEF QF EWK+ ++L+W Sbjct: 422 VVHGKKSLLNKMPGSYEEKFAQLRLLYGYMMAHPGKKLLFMGSEFAQFDEWKFAEELDWV 48- 1 Query: 481 NLNDDMNQKMQRYTKQLNQFYKDHKCLWRIDDSFDGLEIIDADNKSETVLSFIRKDDK-G 53- 9 + ++++KM Y KQL YK +K + +D G E ID N +++ SFIR+ K G Sbjct: 482 LFDFELHRKMDEYVKQLIACYKRYKPFYELDHDPRGFEWIDVHNAEQSIFSFIRRGKKEG 54- 1 Query: 540 DLLLCVFNMTPVERPNFTIGVPQAGIYEEVLNTEMEEFGGVWKNHNPVTKTQVATWKDYD 59- 9 D+L+ V N T ++ + VP Y EVLN++ EFGG + + Sbjct: 542 DVLVIVCNFTNQAYDDYKVSVPLLAPYREVLNSDAAEFGGSGHVNGKRLPAFSEPFHGKP 60- 1 Query: 600 HTLSFTLPALGASVWR 615 + + T+P G S+ R Sbjct: 602 YHVRMTIPPFGISILR 617 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1423 A DNA sequence (GBSx1508) was identified in S. agalactiae <SEQ ID 4367> which encodes the amino acid sequence <SEQ ID 4368>. This protein is predicted to be pullulanase (pulA). Analysis of this protein sequence reveals the following: TABLE-US-04227 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3194(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04228 >GP:AAC44685 GB:U67061 pullulanase [Bacteroides thetaiotaomicron] Identities = 223/597 (37%), Positives = 331/597 (55%), Gaps = 55/597 (9%) Query: 139 EYSETKTAFRLWAPTAERVELILYHSTDETASVSKVLSMKRGTAVNYKNHKENTHGVWFT 19- 8 EY+ T F LW+PTA+ V L+LY + E + + M+ G G W Sbjct: 46 EYTPEATKFTLWSPTADEVRLMLYEA-GEGGHAYETVKMQSGE-----------EGTWTA 93 Query: 199 ELEGNYNYQAYTYRVYYRRRTFKITRDPYSIATTANGKRSIVIAPEALTPEGFKISHGKE 25- 8 + + + YT+ V + T + A NGKR+ +I ++ P+G++ + Sbjct: 94 VVSKDLIGKFYTFNVKIDDKWQGDTPGINARAVGVNGKRAAIIDWQSTNPOGWE----SD 149- Query: 259 AKWRLENPNQAVIYEMHVRDFSISETSGVKTDYHGKFKGLHQKGTVNQHGDKTTFDYVQD 31- 8 + L++P +IYEMH RDFS+ TSGVK GK+ L + GT+N T D++ + Sbjct: 150 TRPPLKSPADMIIYEMHHRDFSVDSTSGVKNK--GKYLALTEHGTMNSDKLLTGIDHLIE 20- 7 Query: 319 LGVNYIQLQPIFDHHQTFDDD-GHYAYNWGYDPENYNVPEASFSSNPHEPATRILELKSA 37- 7 LGV ++ L P FD+ + +YNWGYDP+NYNVP+ S++++P++PATR+ E K Sbjct: 208 LGVTHVHLLPSFDYASVDETRLNENSYNWGYDPQNYNVPDGSYATDPYQPATRVKEFKQM 26- 7 Query: 378 IQAYHDAGIGVIMDVVYNHTFSSTDSAFQLTVPDYYYRMNHNGTFQNGSGCGNETASEKE 43- 7 +QA H AGI VIMDVVYNHTF++ +S F+ TVP Y+YR + T NGSGCGNETASE+ Sbjct: 268 VQALHKAGIRVIMDVVYNHTFNTDESNFERTVPGYFYRQKEDKTLANGSGCGNETASERL 32- 7 Query: 438 MCRKYILDSVLYWVKEYNIDGFRFDLMGLHDVETMNIIRNELNKIDPRILVYGEGWDMGA 49- 7 M RK++++SVLYW+KEY++DGFRFDLMG+HD+ETMN IR +N +DP I +YGEGW A Sbjct: 328 MMRKFMVESVLYWIKEYHVDGFRFDLMGIHDIETMNEIRKAVNAVDPTICIYGEGWAAEA 38- 7 Query: 498 GLTPQNK-AKKDNAYQMPGIGFFNDDVRDAV---KGAEIYGEFKKGLVSGNSTEDIVAKG 55- 3 P + A K N Q+PG+ F+D++RD + G + G F G+ G E V G Sbjct: 388 PQYPADSLAMKGNIAQIPGVAVFSDELRDGLCGPVGDKRKGAFLAGIPGG---EMSVKFG 44- 4 Query: 554 ILGSDE-------LVSYI------DPSQVLNYVEAHDNYNLNDLLWELHPNDNEKQHIYR 60- 0 I G+ E V+Y P Q+++YV HD L D L P+ +Q I Sbjct: 445 IAGAIEHPQVQCDSVNYTQKPWAKQPVQMISYVSCHDGLCLVDRLKASMPDITPEQLIRL 50- 4 Query: 601 VEVASAMNLLMQGMAFMQLGQEFLRTKCYPTGDKGQLTQADKERAMNSYNAPDQVNQVNW 66- 0 ++A A+ QG+ F+ G+E +R DK+ NSY +PD VN ++W Sbjct: 505 DKLAQAVVFTSQGIPFIYAGEEIMR---------------DKQGVDNSYKSPDAVNAIDW 54- 9 Query: 661 DNVTFHKSTINFIRKIITLKTNSPYFSYSSFEEIRKHVFVESAQYHSGFISFTVEEH 717 T + +++I L+ + P F ++RKH+ + S I+F +++H Sbjct: 550 RRKTTSADVFMYYKRLIDLRKSHPAFRMGDAGQVRKHLEFLPVE-GSNLIAFRLKDH 605 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1424 A DNA sequence (GBSx1509) was identified in S. agalactiae <SEQ ID 4369> which encodes the amino acid sequence <SEQ ID 4370>. Analysis of this protein sequence reveals the following: TABLE-US-04229 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2368(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04230 >GP:CAB12492 GB:Z99107 similar to hypothetical proteins [Bacillus subtilis] Identities = 151/293 (51%), Positives = 193/293 (65%), Gaps = 5/293 (1%) Query: 5 KKARLIYNPTSGQEIMKKNVAEVLDILEGFGYETSAFQTTPTKNSARDEATRAAQAGFDL 64 K+AR+IYNPTSG+EI KK++A+VL E GYETS TT A A AA FDL Sbjct: 2 KRARIIYNPTSGREIFKKHLAQVLQKFEQAGYETSTHATT-CAGDATHAAKEAALREFDL 60 Query: 65 IVAAGGDGTINEVVNGIAPLKRRPKMAIIPTGTTNDFARALKIPRGNPIEATKLIGKNQI 124- I+AAGGDGTINEVVNG+APL RP + +IP GTTNDFARAL IPR + ++A + Sbjct: 61 IIAAGGDGTINEVVNGLAPLDNRPTLGVIPVGTTNDFARALGIPREDILKAADTVINGVA 120- Query: 125 VKMDIGQAQEDNYFINIAAAGSLTELTYSVPSQLKTTFGYLAYLAKGVELLPRVRKVPVK 18- 4 +DIGQ YFINIA G LTELTY VPS+LKT G LAY KG+E+LP +R V+ Sbjct: 121 RPIDIGQVN-GQYFINIAGGGRLTELTYDVPSKLKTMLGQLAYYLKGMEMLPSLRPTEVE 17- 9 Query: 185 ITHDKGEFIGDASMIFVAITNSVGGFEQIAPDAKLDDGKFTLILVKTANLIEIMHLIRLV 24- 4 I +D F G+ + V +TNSVGGFE++APD+ L+DG F L+++K ANL E + + + Sbjct: 180 IEYDGKLFQGEIMLFLVTLTNSVGGFEKLAPDSSLNDGMFDLMILKKANLAEFIRVATMA 23- 9 Query: 245 LAGGKHINDKRVEYIKTSYLTIEPLSDERMMINLDGEYGGDAPITLANLKNHI 297 L G+HIND+ + Y K + + + E+M +NLDGEYGG P NL HI Sbjct: 240 LR-GEHINDQHIIYTKANRVKVN--VSEKMQLNLDGEYGGMLPGEFVNLYRHI 289 A related DNA sequence was identified in S. pyogenes <SEQ ID 4371> which encodes the amino acid sequence <SEQ ID 4372>. Analysis of this protein sequence reveals the following:

TABLE-US-04231 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2501(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04232 Identities = 272/334 (81%), Positives = 300/334 (89%) Query: 1 MKKQKKARLIYNPTSGQEIMKKNVAEVLDILEGFGYETSAFQTTPTKNSARDEATRAAQA 60 MKKQ +ARLIYNPTSGQE+M+K+V EVLDILEGFGYETSAFQTT KNSA +EA RAA+A Sbjct: 1 MKKQLRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAQKNSALNEARRAAKA 60 Query: 61 GFDLIVAAGGDGTINEVVNGIAPLKRRPKMAIIPTGTTNDFARALKIPRGNPIEATKLIG 120- GFDL++AAGGDGTINEVVNGIAPLK+RPKMAIIPTGTTNDFARALK+PRGNP +A KLIG Sbjct: 61 GFDLLIAAGGDGTINEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIG 120- Query: 121 KNQIVKMDIGQAQEDNYFINIAAAGSLTELTYSVPSQLKTTFGYLAYLAKGVELLPRVRK 18- 0 KNQ ++MDIG+A++D YFINIAAAGSLTELTYSVPSQLKT FGYLAYLAKGVELLPRV Sbjct: 121 KNQTIQMDIGRAKKDTYFINIAAAGSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSN 18- 0 Query: 181 VPVKITHDKGEFIGDASMIFVAITNSVGGFEQIAPDAKLDDGKFTLILVKTANLIEIMHL 24- 0 VPVKITHDKG F G SMIF AITNSVGGFE IAPDAKLDDG FTLIL+KTANL EI+HL Sbjct: 181 VPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIAPDAKLDDGMFTLILIKTANLFEIVHL 24- 0 Query: 241 IRLVLAGGKHINDKRVEYIKTSYLTIEPLSDERMMINLDGEYGGDAPITLANLKNHIRFF 30- 0 +RL+L GGKHI D+RVEYIKTS + IEP +RMMINLDGEYGGDAPITL NLKNHI FF Sbjct: 241 LRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGGDAPITLENLKNHITFF 30- 0 Query: 301 ANTDEISDDALVLDKDELAIEAIAQKFANEVDDL 334 A+TD ISDDALVLD+DEL IE I +KFA+EV+DL Sbjct: 301 ADTDLISDDALVLDQDELEIEEIVKKFAHEVEDL 334 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1425 A DNA sequence (GBSx1510) was identified in S. agalactiae <SEQ ID 4373> which encodes the amino acid sequence <SEQ ID 4374>. This protein is predicted to be DNA ligase (ligA-1) Analysis of this protein sequence reveals the following: TABLE-US-04233 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.27 Transmembrane 363-379 (363-379) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9763> which encodes amino acid sequence <SEQ ID 9764> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04234 >GP: CAB12482 GB: Z99107 similar to DNA ligase [Bacillus subtilis] Identities = 346/657 (52%), Positives = 462/657 (69%), Gaps = 8/657 (1%) Query: 2 ENRMNELVSLLNQYAKEYYTQDNPTVSDSQYDQLYRELVELEKQHPENILPNSPTHRVGG 61 + R EL +N+Y+ EYYT D P+V D++YD+L +EL+ +E++HP+ P+SPT RVGG Sbjct: 7 KQRAEELRRTINKYSYEYYTLDEPSVPDAEYDRLMQELIAIEEEHPDLRTPDSPTQRVGG 66 Query: 62 LVLEGFEKYQHEYPLYSLQDAFSKEELIAFDKRVKAEF-PTAAYMAELKIDGLSVSLTYV 120- VLE F+K H P+ SL +AF+ ++L FD+RV+ AY ELKIDGL+VSL Y Sbjct: 67 AVLEAFQKVTHGTPMLSLGNAFNADDLRDFDRRVRQSVGDDVAYNVELKIDGLAVSLRYE 126- Query: 121 NGVLQVGATRGDGNIGENITENLKRVHDIPLHLDQSLDITVRGECYLPKESFEAINIEKR 18- 0 +G GATRGDG GE+ITENLK + +IPL +++ L I VRGE Y+PK SFEA+N E+ Sbjct: 127 DGYFVRGATRGDGTTGEDITENLKTIRNIPLKMNRELSIEVRGEAYMPKRSFEALNEERI 18- 6 Query: 181 ANGEQEFANPRNAAAGTLRQLNTGIVAKRKLATFLYQEASPTQK--ETQDDVLKELESYG 23- 8 N E+ FANPRNAAAG+LRQL+ I AKR L F+Y A + ETQ L L+ G Sbjct: 187 KNEEEPFANPRNAAAGSLRQLDPKIAAKRNLDIFVYSIAELDEMGVETQSQGLDFLDELG 24- 6 Query: 239 FSVNHHRLISSSMEKIWDFIQTIEKDRVSLPYDIDGIVIKVNSIAMQEELGFTVKAPRWA 29- 8 F N R S+E++ I ++ R LPY+IDGIVIKV+S+ QEELGFT K+PRWA Sbjct: 247 FKTNQERKKCGSIEEVITLIDELQAKRADLPYEIDGIVIKVDSLDQQEELGFTAKSPRWA 30- 6 Query: 299 IAYKFPAEEKEAEILSVDWTVGRTGVVTPTANLTPVQLAGTTVSRATLHNVDYIAEKDIR 35- 8 IAYKFPAEE ++L ++ VGRTGV+TPTA L PV++AGTTVSRA+LHN D I EKDIR Sbjct: 307 IAYKFPAEEVVTKLLDIELNVGRTGVITPTAILEPVKVAGTTVSRASLHNEDLIKEKDIR 36- 6 Query: 359 IGDTVVVYKAGDIIPAVLNVVMSKRNQQEVML-IPKLCPSCGSELVHFEGEVALRCINPL 41- 7 I D VVV KAGDIIP V+NV++ +R +E +P CP CGSELV EGEVALRCINP Sbjct: 367 ILDKVVVKKAGDIIPEVVNVLVDQRTGEEKEFSMPTECPECGSELVRIEGEVALRCINPE 42- 6 Query: 418 CPNQIKERLAHFASRDAMNITGFGPSLVEKLFDAHLIADVADIYRLSIENLLTLDGIKEK 47- 7 CP QI+E L HF SR+AMNI G G ++ +LF+ +L+ +VAD+Y+L+ E ++ L+ + EK Sbjct: 427 CPAQIREGLIHFVSRNAMNIDGLGERVITQLFEENLVRNVADLYKLTKERVIQLERMGEK 48- 6 Query: 478 SATKIYHAIQSSKENSAEKLLFGLGIRHVGSKASRLLLEEFGNLRQLSQASQESIASIDG 53- 7 S + +IQ SKENS E+LLFGLGIR +GSKA++ L F +L L +AS+E + ++D Sbjct: 487 STENLISSIQKSKENSLERLLFGLGIRFIGSKAAKTLAMHFESLENLKKASKEELLAVDE 54- 6 Query: 538 LGGVIAKSLHTFFEKEEVDKLLEELTSYNVNFNYLG----KRVSTDAQLSGLTVVLTGKL 59- 3 +G +A ++ T+F KEE+ +LL EL VN Y G K +D+ +G T+VLTGKL Sbjct: 547 IGEKMADAVITYFHKEEMLELLNELQELGVNTLYKGPKKVKAEDSDSYFAGKTIVLTGKL 60- 6 Query: 594 EKMTRNEAKEKLQNLGAKVTGSVSKKTDLIVAGSDAGSKLTKAQDLGITIQDEDWLL 650 E+++RNEAK +++ LG K+TGSVSK TDL++AG AGSKLTKAQ+L I + +E+ L+ Sbjct: 607 EELSRNEAKAQIEALGGKLTGSVSKNTDLVIAGEAAGSKLTKAQELNIEVWNEEQLM 663 A related DNA sequence was identified in S. pyogenes <SEQ ID 4375> which encodes the amino acid sequence <SEQ ID 4376>. Analysis of this protein sequence reveals the following: TABLE-US-04235 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 363-379 (363-379) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04236 Identities = 472/652 (72%), Positives = 556/652 (84%) Query: 1 MENRMNELVSLLNQYAKEYYTQDNPTVSDSQYDQLYRELVELEKQHPENILPNSPTHRVG 60 M+ R+ EL LLN+Y +YYT+D P+VSDS YD+LYRELV LE+ +PE +L +SPT +VG Sbjct: 1 MKKRIKELTDLLNRYRYDYYTKDAPSVSDSDYDKLYRELVTLEQSYPEYVLQDSPTQQVG 60 Query: 61 GLVLEGFEKYQHEYPLYSLQDAFSKEELIAFDKRVKAEFPTAAYMAELKIDGLSVSLTYV 120- G +L+GFEKY+H+YPL+SLQDAFS+EEL AFDKRVKAEFP A Y+AELKIDGLS+SL+Y Sbjct: 61 GTILKGFEKYRHQYPLFSLQDAFSREELDAFDKRVKAEFPNATYLAELKIDGLSISLSYE 120- Query: 121 NGVLQVGATRGDGNIGENITENLKRVHDIPLHLDQSLDITVRGECYLPKESFEAINIEKR 18- 0 NG LQVGATRGDGNIGENITEN+K++ DIP L + L ITVRGE Y+ ++SF+AIN ++ Sbjct: 121 NGFLQVGATRGDGNIGENITENIKKIKDIPYQLSEPLTITVRGEAYMSRQSFKAINEARQ 18- 0 Query: 181 ANGEQEFANPRNAAAGTLRQLNTGIVAKRKLATFLYQEASPTQKETQDDVLKELESYGFS 24- 0 NGE EFANPRNAAAGTLRQL+T +VAKR+LATFLYQEASPT + Q++VL EL GFS Sbjct: 181 ENGETEFANPRNAAAGTLRQLDTSVVAKRQLATFLYQEASPTARNQQNEVLAELADLGFS 24- 0 Query: 241 VNHHRLISSSMEKIWDFIQTIEKDRVSLPYDIDGIVIKVNSIAMQEELGFTVKAPRWAIA 30- 0 VN + ++SSM++IWDFI+TIE R L YDIDG+VIKVNS+AMQEELGFTVKAPRWAIA Sbjct: 241 VNPYYQLTSSMDEIWDFIKTIEAKRDQLAYDIDGVVIKVNSLAMQEELGFTVKAPRWAIA 30- 0 Query: 301 YKFPAEEKEAEILSVDWTVGRTGVVTPTANLTPVQLAGTTVSRATLHNVDYIAEKDIRIG 36- 0 YKFPAEEKEAEILSVDWTVGRTGVVTPTANLTPVQLAGTTVSRATLHNVDYIAEKDIRIG Sbjct: 301 YKFPAEEKEAEILSVDWTVGRTGVVTPTANLTPVQLAGTTVSRATLHNVDYIAEKDIRIG 36- 0 Query: 361 DTVVVYKAGDIIPAVLNVVMSKRNQQEVMLIPKLCPSCGSELVHFEGEVALRCINPLCPN 42- 0 DTV+VYKAGDIIPAVLNVVMSKRNQQEVMLIPKLCPSCGSELVHFE EVALRCINPLCP+ Sbjct: 361 DTVIVYKAGDIIPAVLNVVMSKRNQQEVMLIPKLCPSCGSELVHFEDEVALRCINPLCPS 42- 0 Query: 421 QIKERLAHFASRDAMNITGFGPSLVEKLFDAHLIADVADIYRLSIENLLTLDGIKEKSAT 48- 0 I+ L HFASRDAMNITG GP++VEKLF A + DVADIY+L+ E+ + LDGIKEKSA Sbjct: 421 LIQRSLEHFASRDAMNITGLGPAIVEKLFLAGFVHDVADIYQLTKEDFMQLDGIKEKSAD 48- 0 Query: 481 KIYHAIQSSKENSAEKLLFGLGIRHVGSKASRLLLEEFGNLRQLSQASQESIASIDGLGG 54- 0 K+ AI++SK NSAEKLLFGLGIRH+GSK SRL+LE +G++ L A +E IA IDGLG Sbjct: 481 KLLAAIEASKSNSAEKLLFGLGIRHIGSKVSRLILEVYGDISALLTAKEEEIARIDGLGS 54- 0 Query: 541 VIAKSLHTFFEKEEVDKLLEELTSYNVNFNYLGKRVSTDAQLSGLTVVLTGKLEKMTRNE 60- 0 IA+SL +FE++ L++EL + VN +Y G++V++DA L GLTVVLTGKL ++ RNE Sbjct: 541 TIAQSLTQYFEQKTAAILVDELKTAGVNMHYSGQKVNSDAALFGLTVVLTGKLNQLNRNE 60- 0 Query: 601 AKEKLQNLGAKVTGSVSKKTDLIVAGSDAGSKLTKAQDLGITIQDEDWLLNL 652 AK+KL+ LGAKVTGSVSKKTDL++AGSDAGSKL KA+ LGI I+DEDWL L Sbjct: 601 AKDKLEALGAKVTGSVSKKTDLVIAGSDAGSKLEKAKSLGIRIEDEDWLRQL 652 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1426 A DNA sequence (GBSx1511) was identified in S. agalactiae <SEQ ID 4377> which encodes the amino acid sequence <SEQ ID 4378>. Analysis of this protein sequence reveals the following: TABLE-US-04237 Possible Site: 32 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.63 Transmembrane 110-126 (108-128) INTEGRAL Likelihood = -2.13 Transmembrane 142-158 (141-159) INTEGRAL Likelihood = -1.12 Transmembrane 75-91 (75-93) ----- Final Results ----- bacterial membrane --- Certainty = 0.3251(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04238 >GP: CAA68244 GB: X99978 citrulline cluster-linked gene [Lactobacillus plantarum] Identities = 56/158 (35%), Positives = 91/158 (57%), Gaps = 8/158 (5%) Query: 13 AIVTAIYIVLTITPPFNAIAYGAYQFRVSEMLNFLAFYHRKYLFAVTLGCMISNLYSFG- 71 - A+V A+Y+VL + P ++A GA QFRVSE LN LA ++RKY++ + G ++ + + G Sbjct: 13 ALVAAMYVVLCLGPAAFSLASGAIQFRVSEGLNHLAVFNRKYIWGIVAGVILFDAFGPGA 72 Query: 72 -MIDVFVGGGSTLLFVYLGTILFKQYQKDYLFNGLINKAFFFFSFFFAASMITVAVELKI 130- +++V GGG +LL + + T L + K L+N A F S F A MIT+ + Sbjct: 73 SLLNVLFGGGQSLLALLVLTWLAPKL-KTVWQRMLLNIALFTVSMFMIALMITM-----M 126- Query: 131 VAGLPLLLTWLTTAVGELASLLVGAVLVDKLSRHVDFT 168 +G+ T+LTTA+ EL + + A ++ L R + F+ Sbjct: 127 SSGVAFWPTYLTTALSELIIMSITAPIMYSLDRVLHFS 164 A related DNA sequence was identified in S. pyogenes <SEQ ID 4379> which encodes the amino acid sequence <SEQ ID 4380>. Analysis of this protein sequence reveals the following: TABLE-US-04239 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.41 Transmembrane 75-91 (70-94) INTEGRAL Likelihood = -3.82 Transmembrane 12-28 (8-28) INTEGRAL Likelihood = -2.28 Transmembrane 141-157 (140-158) INTEGRAL Likelihood = -0.64 Transmembrane 110-126 (110-126) INTEGRAL Likelihood = -0.59 Transmembrane 55-71 (54-73) ----- Final Results ----- bacterial membrane --- Certainty = 0.2763(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04240 Identities = 114/167 (68%), Positives = 137/167 (81%), Gaps = 1/167 (0%) Query: 1 MNTFTTRDYAHMAIVTAIYIVLTITPPFNAIAYGAYQFRVSEMLNFLAFYHRKYLFAVTL 60 M T DY H+ +V A+Y+VLTITPP NAI+YG YQFR+SEM+NFLAFYHRKY+ AVTL Sbjct: 1 MTKLTVHDYVHIGLVAALYVVLTITPPLNAISYGMYQFRISEMMNFLAFYHRKYIIAVTL 60 Query: 61 GCMISNLYSFGMIDVFVGGGSTLLFVYLGTILFKQYQKDYLFNGLINKAFFFFSFFFAAS 120- GCMI+N YSFG+IDVFVGGGSTL+FV LG ILF +YQKDYLFNG+ NKAF +FSFFFA S Sbjct: 61 GCMIANFYSFGLIDVFVGGGSTLIFVTLGVILFSKYQKDYLFNGIFNKAFVYFSFFFATS 120- Query: 121 MITVAVELKIVAGLPLLLTWLTTAVGELASLLVGAVLVDKLSRHVDF 167 M VA+EL G P LLTW TTA+GEL SLL+G++++DKLS+ + F Sbjct: 121 MFNVAIELYFF-GAPFLLTWFTTALGELVSLLIGSLIIDKLSQRISF 166 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1427 A DNA sequence (GBSx1513) was identified in S. agalactiae <SEQ ID 4381> which encodes the amino acid sequence <SEQ ID 4382>. Analysis of this protein sequence reveals the following: TABLE-US-04241 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.20 Transmembrane 255-271 (245-281) INTEGRAL Likelihood = -10.72 Transmembrane 141-157 (132-165) INTEGRAL Likelihood = -8.17 Transmembrane 189-205 (185-208) INTEGRAL Likelihood = -7.01 Transmembrane 36-52 (33-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.5479(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04242 >GP: AAC35915 GB: AF071085 Orfde2 [Enterococcus faecalis] Identities = 83/276 (30%), Positives = 157/276 (56%), Gaps = 3/276 (1%) Query: 17 RPIQVFMRHFQSAEMDLSAIAVAYYLLVTAFPLLVIAANIFPYFHINVSDLLSLMQKNLP 76 - R I+ H +AE+ S++ VAYYLL++ FPLL+ N+ PY I+ + +L + + +P Sbjct: 15 RFIETTQSHMVTAEIGNSSVVVAYYLLLSLFPLLIAVGNVLPYLRIDPNSVLPYIAEAIP 74 Query: 77 KNIYEPASRLAVDAFSKPSTGILGFASLTAFWTMSKSLTSLQKAINKAYGVDQHRDFVIS 136- K++Y+ ++ S G+L ++L AFW+ S+S+ +LQ A+NKA+GV+Q ++F++ Sbjct: 75 KDVYKNLEPAIRSLLTQRSGGLLSVSALAAFWSASQSINALQNAMNKAFGVEQRKNFILV 134- Query: 137 RLVGVGTGLIILFLLTFVLIFSTFSKPVLQIIVNMYDLGDTLTAWLLNLAQPVTFLTIFL 19- 6 R+V L+ + + V++ + +++++ ++ ++ L P+T + + + Sbjct: 135 RVVSFLVILLFMVAIVGVVVILGLGQYIIELLQPIFHYSTSVIDTFQALKWPLTTVVLLV 19- 4 Query: 197 GIGILYFILPNARIRKVRYVIPGTLFSTFVIGFFSNLISQYVLNRVEKMVDIKTFGSVVI 25- 6 + ++Y ++PN ++ +R ++PG +FST S + YV ++ + GS + Sbjct: 195 IMCLIYAVVPNRKL-SLRSILPGAIFSTVGWMLLSQIFGLYVKYFSSRIASYQIIGSFI- 25- 2 Query: 257 FILMLWFIFLAHIMILGAILNASVQEIATGKIESRR 292 ILMLW F A I+ILGAI+NA V E G E ++ Sbjct: 253 -ILMLWLNFAATIIILGAIVNAVVDEYLXGXKEKKQ 287 A related DNA sequence was identified in S. pyogenes <SEQ ID 4383> which encodes the amino acid sequence <SEQ ID 4384>. Analysis of this protein sequence reveals the following: TABLE-US-04243 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.58 Transmembrane 141-157 (132-168) INTEGRAL Likelihood = -12.15 Transmembrane 189-205 (177-210) INTEGRAL Likelihood = -11.68 Transmembrane 256-272 (245-280) INTEGRAL Likelihood = -7.54 Transmembrane 36-52 (33-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.6031(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04244 >GP: CAA68244 GB: X99978 citrulline cluster-linked gene [Lactobacillus plantarum] Identities = 53/170 (31%), Positives = 92/170 (53%), Gaps = 11/170 (6%) Query: 1 MTKLTVHDYVHIGLVAALYVVLTITPPLNAISYGMYQFRISEMMNFLAFYHRKYIIAVTL 60 MT+ + ++ LVAA+YVVL + P +++ G QFR+SE +N LA ++RKYI + Sbjct: 1 MTQSKIRPWIINALVAAMYVVLCLGPAAFSLASGAIQFRVSEGLNHLAVFNRKYIWGIVA 60 Query: 61 GCMIANFYSFG--LIDVFVGGGSTLIFVTLGVILFSKYQKDYLFNGIFNKAFVYFSFFFA 118- G ++ + + G L++V GGG +L+ + + L K + ++ + + + F Sbjct: 61 GVILFDAFGPGASLLNVLFGGGQSLLALLVLTWLAPKLKT------VWQRMLLNIA-LFT 113- Query: 119 TSMFNVA--IELYFFGAPFLLTWFTTALGELVSLLIGSLIIDKLSQRISF 166 SMF +A I + G F T+ TTAL EL+ + I + I+ L + + F Sbjct: 114 VSMFMIALMITMMSSGVAFWPTYLTTALSELIIMSITAPIMYSLDRVLHF 163 !GB: AF071085 Orfde2 [Enterococcus faecalis] 176 2e-43 >GP: AAC35915 GB: AF071085 Orfde2 [Enterococcus faecalis] Identities = 90/271 (33%), Positives = 155/271 (56%), Gaps = 3/271 (1%) Query: 19 IQVFMRHLQSAEMDLSAIAVAYYLILTAFPLIVIAANIFPYLNIDIADLLRLMKQNLPKD 78 - I+ H+ +AE+ S++ VAYYL+L+ FPL++ N+ PYL ID +L + + +PKD Sbjct: 17 IETTQSHMVTAEIGNSSVVVAYYLLLSLFPLLIAVGNVLPYLRIDPNSVLPYIAEAIPKD 76 Query: 79 IFRPASAIVENIFSKPSGSVLGVATLTGLWTMSRSLTSLQKAINKAYGASQHRDFFIGHL 138- +++ + ++ ++ SG +L V+ L W+ S+S+ +LQ A+NKA+G Q ++F + + Sbjct: 77 VYKNLEPAIRSLLTQRSGGLLSVSALAAFWSASQSINALQNAMNKAFGVEQRKNFILVRV 136- Query: 139 VGLLTSLIILFLLAFALIFSIFSKAAIQVLDKHYHLSDNITTIFLLLIQPITVLIIFVGL 19- 8 V L L+ + + ++ + I++L +H S ++ F L P+T +++ V + Sbjct: 137 VSFLVILLFMVAIVGVVVILGLGQYIIELLQPIFHYSTSVIDTFQALKWPLTTVVLLVIM 19- 6 Query: 199 MLLYFLLPNVKIKKIRYILPGTLFTSFVMTFLSNLVGNYVVYNVERMVDIKMFGSVMIFI 25- 8 L+Y ++PN K+ +R ILPG +F++ LS + G YV Y R+ ++ GS I Sbjct: 197 CLIYAVVPNRKL-SLRSILPGAIFSTVGWMLLSQIFGLYVKYFSSRIASYQIIGS--FII 25- 3 Query: 259 IMLWFIFLARILILGAIFNATYQEMSLGKLE 289 +MLW F A I+ILGAI NA E G E Sbjct: 254 LMLWLNFAATIIILGAIVNAVVDEYLXGXKE 284 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04245 Identities = 188/302 (62%), Positives = 244/302 (80%) Query: 1 MKLKKFFEDLLAKLEYRPIQVFMRHFQSAEMDLSAIAVAYYLLVTAFPLLVIAANIFPYF 60 M KK+F+ +L+K +Y PIQVFMRH QSAEMDLSAIAVAYYL++TAFPL+VIAANIFPY Sbjct: 1 MAEKKWFDKVLSKWQYEPIQVFMRHLQSAEMDLSAIAVAYYLILTAFPLIVIAANIFPYL 60 Query: 61 HINVSDLLSLMQKNLPKNIYEPASRLAVDAFSKPSTGILGFASLTAFWTMSKSLTSLQKA 120- +I+++DLL LM++NLPK+I+ PAS + + FSKPS +LG A+LT WTMS+SLTSLQKA Sbjct: 61 NIDIADLLRLMKQNLPKDIFRPASAIVENIFSKPSGSVLGVATLTGLWTMSRSLTSLQKA 120- Query: 121 INKAYGVDQHRDFVISRLVGVGTGLIILFLLTFVLIFSTFSKPVLQIIVNMYDLGDTLTA 18- 0 INKAYG QHRDF I LVG+ T LIILFLL F LIFS FSK +Q++ Y L D +T Sbjct: 121 INKAYGASQHRDFFIGHLVGLLTSLIILFLLAFALIFSIFSKAAIQVLDKHYHLSDNITT 18- 0 Query: 181 WLLNLAQPVTFLTIFLGIGILYFILPNARIRKVRYVIPGTLFSTFVIGFFSNLISQYVLN 24- 0 L L QP+T L IF+G+ +LYF+LPN +I+K+RY++PGTLF++FV+ F SNL+ YV+ Sbjct: 181 IFLLLIQPITVLIIFVGLMLLYFLLPNVKIKKIRYILPGTLFTSFVMTFLSNLVGNYVVY 24- 0 Query: 241 RVEKMVDIKTFGSVVIFILMLWFIFLAHIMILGAILNASVQEIATGKIESRRGDIMSLIQ 30- 0 VE+MVDIK FGSV+IFI+MLWFIFLA I+ILGAI NA+ QE++ GK+E R GD++++++ Sbjct: 241 NVERMVDIKMFGSVMIFIIMLWFIFLARILILGAIFNATYQEMSLGKLEGRSGDMIAILK 30- 0 Query: 301 KS 302 K+ Sbjct: 301 KT 302 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1428 A DNA sequence (GBSx1514) was identified in S. agalactiae <SEQ ID 4385> which encodes the amino acid sequence <SEQ ID 4386>. Analysis of this protein sequence reveals the following:

TABLE-US-04246 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4200(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1429 A DNA sequence (GBSx1515) was identified in S. agalactiae <SEQ ID 4387> which encodes the amino acid sequence <SEQ ID 4388>. This protein is predicted to be methionine aminopeptidase (map). Analysis of this protein sequence reveals the following: TABLE-US-04247 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2342(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9761> which encodes amino acid sequence <SEQ ID 9762> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04248 >GP: AAC35914 GB: AF071085 methionine aminopeptidase A [Enterococcus faecalis] Identities = 101/207 (48%), Positives = 128/207 (61%), Gaps = 31/207 (14%) Query: 1 MITLKSAREIEAMDRAGDFLASIHIGLRDIIKPGVDMWEVEEYVRRRCKEENVLPLQIGV 60 MITLKS REIE MD +G+ LA +H LR IKPG+ W++E +VR + + QIG Sbjct: 1 MITLKSPREIEMMDESGELLADVHRHLRTFIKPGITSWDIEVFVRDFIESHGGVAAQIGY 60 Query: 61 DGAVMDYPYATCCGLNDEVAHAFPRHYTLKQGDLLKVDMVLSEPLDKSIVDVSSLNFDNV 120- +G Y YATCC +NDE+ H FPR LK GDL+KVDM + Sbjct: 61 EG----YKYATCCSINDEICHGFPRKKVLKDGDLIKVDMCVD------------------ 98 Query: 121 AQMKKYTETYSGGLADSCWAYAVGEVSQEVKDLMSVTREAMYIGIEKAVIGNRIGDIGAA 18- 0 G ++DSCW+Y VGE + E+ LM VT++A+Y+GIE+A +GNRIGDIG A Sbjct: 99 ---------LKGAISDSCWSYVVGESTPEIDRLMEVTKKALYLGIEQAQVGNRIGDIGHA 149- Query: 181 IQDYAESRGYGVVRDLVGHGVGPTMHE 207 IQ Y E GYGVVRD VGHG+GPT+HE Sbjct: 150 IQTYVEGEGYGVVRDFVGHGIGPTIHE 176 A related DNA sequence was identified in S. pyogenes <SEQ ID 4389> which encodes the amino acid sequence <SEQ ID 4390>. Analysis of this protein sequence reveals the following: TABLE-US-04249 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2082(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04250 Identities = 256/286 (89%), Positives = 273/286 (94%) Query: 1 MITLKSAREIEAMDRAGDFLASIHIGLRDIIKPGVDMWEVEEYVRRRCKEENVLPLQIGV 60 MITLKSAREIEAMDRAGDFLA IHIGLRDIIKPGVDMWEVE YVRRRCKE+NVLPLQIGV Sbjct: 1 MITLKSAREIEAMDRAGDFLAGIHIGLRDIIKPGVDMWEVEAYVRRRCKEDNVLPLQIGV 60 Query: 61 DGAVMDYPYATCCGLNDEVAHAFPRHYTLKQGDLLKVDMVLSEPLDKSIVDVSSLNFDNV 120- DG +MDYPYATCCGLNDEVAHAFPRHY LK+GDLLKVDMVLSEPLDKSIVDV++L+FDNV Sbjct: 61 DGHMMDYPYATCCGLNDEVAHAFPRHYILKEGDLLKVDMVLSEPLDKSIVDVAALDFDNV 120- Query: 121 AQMKKYTETYSGGLADSCWAYAVGEVSQEVKDLMSVTREAMYIGIEKAVIGNRIGDIGAA 18- 0 +MKK+T +Y+GGLADSCWAYAVG S E+K LM VT+EAMY GIEKAVIGNRIGDIGAA Sbjct: 121 PEMKKWTGSYTGGLADSCWAYAVGTPSDEIKQLMDVTKEAMYRGIEKAVIGNRIGDIGAA 18- 0 Query: 181 IQDYAESRGYGVVRDLVGHGVGPTMHEEPMVPNYGTAGRGLRLREGMVLTIEPMINTGTW 24- 0 +Q+YAES GYGVVRDLVGHGVGPTMHEEPMVPNYGTAGRGLRL+EGMVLT+EPMINTGTW Sbjct: 181 VQEYAESFGYGVVRDLVGHGVGPTMHEEPMVPNYGTAGRGLRLKEGMVLTVEPMINTGTW 24- 0 Query: 241 EIDTDMKTGWAHKTLDGGLSCQYEHQFVITKDGPVILTSQGEERTY 286 EIDTD+KTGWAHKTLDGGLSCQYEHQFVITKDGPVILTSQGEERTY Sbjct: 241 EIDTDIKTGWAHKTLDGGLSCQYEHQFVITKDGPVILTSQGEERTY 286 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1430 A DNA sequence (GBSx1516) was identified in S. agalactiae <SEQ ID 4391> which encodes the amino acid sequence <SEQ ID 4392>. Analysis of this protein sequence reveals the following: TABLE-US-04251 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3473(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9759> which encodes amino acid sequence <SEQ ID 9760> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04252 >GP: BAB06894 GB: AP001518 unknown conserved protein [Bacillus halodurans] Identities = 158/431 (36%), Positives = 270/431 (61%), Gaps = 6/431 (1%) Query: 6 SKHQEILEYLENLAVGKRVSVRSISNHLKVSDGTAYRAIKEAENRGIVETRPRSGTVRVA 65 +KH++IL+Y+ NL VG+++SVR I+ L+VS+GTAYRAIKEAEN+G+V T R GT+R+ Sbjct: 3 TKHEQILQYITNLEVGEKISVRRIAKDLQVSEGTAYRAIKEAENQGLVSTIERVGTIRIE 62 Query: 66 QKAKVNIEKLTYAEIARISDSQVVAGIEGLSKEFSKFSIGAMTHRNIEKYLVQGGLLIVG 125- +K K NIEKLTYAE+ I D QV+ G +GL K ++F IGAM + +Y+ G LLIVG Sbjct: 63 KKQKENIEKLTYAEVVNIVDGQVLGGRDGLHKTLNRFVIGAMKLDAMMRYVEPGNLLIVG 122- Query: 126 DRDEIQHLALQHQNAILVTGGFNVSPSVCRLADKLQIPVMVTHYDTFTVSTMINHTLSNA 18- 5 +R ++ +AL+ A+L+TGGF+ S +LAD+L +PV+ T YDTFTV+TMIN + + Sbjct: 123 NRYQVHQIALEAGAAVLITGGFDTSDEAIKLADELDLPVISTSYDTFTVATMINRAIYDQ 18- 2 Query: 186 KIRTDLKTVEQVYQSQMDYGFLAQDDTVKEFNLLVKQTKNVRFPIVNQANVVVGVVSVQD 24- 5 I+ ++ V+ + D ++ ++ V +++ L ++T + R+P++++ + G+V+ +D Sbjct: 183 LIKKEITLVDDILIPLQDTYYMTTENVVGKWHELNEKTGHSRYPVIDENMKIQGMVAAKD 24- 2 Query: 246 ILGKDKEVKLATVMSKNIIVAKPRMSLANISQKMIFEDLNMMPVVSDDFELLGVITRRQA 30- 5 +L + + VM+KN I R S+A ++ M++E + ++PV+ +L+GV++R+ Sbjct: 243 VLNASRHTPIEKVMTKNPITVSERTSVAAVAHVMVWEGIELLPVIDSHRKLIGVVSRQDV 30- 2 Query: 306 VENLSMSQ-----GTDLYTYSDQILSNLQIEDG-HFSFLVEPAMIDHTGSLTQGVLTEFL 35- 9 ++ L M Q G + L+ + G + + P M + G+++ GV+T + Sbjct: 303 LKALQMIQRQPHVGETIEDLMTNGLNESSSDQGDSYEVEITPQMTNQLGTISHGVMTSLV 36- 2 Query: 360 KEICIRVLTRKHQRSIVVKQMTLYFLQPVQIDEIIMVTPTIISEKRREATLDLELKLENK 41- 9 E RVL + + +VV+ +TLYFL+PVQID + + P ++ R+ +D+E+ E + Sbjct: 363 IESGSRVLRKYKKGDLVVENITLYFLKPVQIDSRLTIRPRVLEIGRKHGKIDVEMYHEGE 42- 2 Query: 420 IIAKAMIAVKI 430 I+ KA+ +I Sbjct: 423 IVGKALFMAQI 433 A related DNA sequence was identified in S. pyogenes <SEQ ID 4393> which encodes the amino acid sequence <SEQ ID 4394>. Analysis of this protein sequence reveals the following: TABLE-US-04253 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3011(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04254 Identities = 267/431 (61%), Positives = 351/431 (80%) Query: 1 MIIVMSKHQEILEYLENLAVGKRVSVRSISNHLKVSDGTAYRAIKEAENRGIVETRPRSG 60 +II+MSKHQ+IL+YLE LA+GK+VSVRSISNHLKVSDGTAYRAIKEAENRGIVET+PRSG Sbjct: 1 VIIIMSKHQDILDYLEKLAIGKKVSVRSISNHLKVSDGTAYRAIKEAENRGIVETKPRSG 60 Query: 61 TVRVAQKAKVNIEKLTYAEIARISDSQVVAGIEGLSKEFSKFSIGAMTHRNIEKYLVQGG 120- TVR+ +K +V I++LTY+EIARISDS+V+AG GL EFS+FSIGAMT +NI +YLV+GG Sbjct: 61 TVRIEKKGRVRIDRLTYSEIARISDSEVLAGHAGLGHEFSRFSIGAMTQQNIRRYLVKGG 120- Query: 121 LLIVGDRDEIQHLALQHQNAILVTGGFNVSPSVCRLADKLQIPVMVTHYDTFTVSTMINH 18- 0 LLIVGDR+ IQ LAL++ NAILVTGGF VS V +A+ +IPVMVTHYDTFTV+TMINH Sbjct: 121 LLIVGDRETIQLLALENHNAILVTGGFPVSKRVIEMANNQRIPVMVTHYDTFTVATMINH 18- 0 Query: 181 TLSNAKIRTDLKTVEQVYQSQMDYGFLAQDDTVKEFNLLVKQTKNVRFPIVNQANVVVGV 24- 0 LSN +I+TDLKTVEQV DYG+L +D +V+EFN L+K+T+ VRFP+++ V+GV Sbjct: 181 ALSNIRIKTDLKTVEQVMIPITDYGYLCEDSSVEEFNTLIKKTRQVRFPVLDYKRKVIGV 24- 0 Query: 241 VSVQDILGKDKEVKLATVMSKNIIVAKPRMSLANISQKMIFEDLNMMPVVSDDFELLGVI 30- 0 VS++D++ + KL VMSKN I A+P SLANISQKMIFEDLNM+PV ++ LLG+I Sbjct: 241 VSMRDVVDQLPTTKLTKVMSKNPITARPNTSLANISQKMIFEDLNMLPVTDEENNLLGMI 30- 0 Query: 301 TRRQAVENLSMSQGTDLYTYSDQILSNLQIEDGHFSFLVEPAMIDHTGSLTQGVLTEFLK 36- 0 TRRQA+ENL Q + YTYS+QILSNL+ ++ +VEP MID G+++ GV++EFLK Sbjct: 301 TRRQAMENLPNHQPNNPYTYSEQILSNLEETVDYYQVVVEPTMIDSAGNMSNGVISEFLK 36- 0 Query: 361 EICIRVLTRKHQRSIVVKQMTLYFLQPVQIDEIIMVTPTIISEKRREATLDLELKLENKI 42- 0 EI IR LT+KHQ++I+++QM +YFL +QI++ + + P II+E RR +T+D+E+ +++++ Sbjct: 361 EISIRALTKKHQKNIIIEQMMVYFLHAIQIEDELKIYPKIITENRRSSTIDIEIFVDDQV 42- 0 Query: 421 IAKAMIAVKIN 431 IAKA+I KIN Sbjct: 421 IAKAIITTKIN 431 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1431 A DNA sequence (GBSx1517) was identified in S. agalactiae <SEQ ID 4395> which encodes the amino acid sequence <SEQ ID 4396>. Analysis of this protein sequence reveals the following: TABLE-US-04255 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2837(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04256 >GP: BAB04556 GB: AP001510 unknown conserved protein [Bacillus halodurans] Identities = 56/185 (30%), Positives = 86/185 (46%), Gaps = 4/185 (2%) Query: 7 MDIWTNLGRFAFIETEHVNLRPVAYTDREAFWRIASKRTNLQFI-FPVQTSKKESDFLLV 65 M+I G +ETE + LR D A + AS +++ + S K+S+ L Sbjct: 1 MEIEDIYGDLPTLETERLRLRKFYKDDAAAIYDYASNEQVTKYVLWETHQSIKDSEAFLA 60 Query: 66 HSFMK---EPLGVWAIEDKVSHKMFGVIRFENIDLSKKTAEIGYFLKESSWGQGIMTECL 122- + K + + WAIE K + +M G + F KTAE+GY L E WGQGIMTE + Sbjct: 61 FALNKYDEKDVSPWAIELKRNERMIGTVDFVWWKPKDKTAELGYVLSEPYWGQGIMTEAV 120- Query: 123 KTLSFFAFREFGMDKLIIVTHKENIASQKVALKAHFKQSRSFKGSDRYTRRIRDYIEFQL 18- 2 L F F ++++ ENI+S +V KA + + + RD+ + + Sbjct: 121 NALVEFGFNNMELERIQAKCFAENISSARVMEKAGLIYEGTHRRAIYVKGAHRDFKVYAI 18- 0 Query: 183 TRGDY 187 R DY Sbjct: 181 IREDY 185 A related DNA sequence was identified in S. pyogenes <SEQ ID 667> which encodes the amino acid sequence <SEQ ID 668>. Analysis of this protein sequence reveals the following: TABLE-US-04257 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1096(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04258 Identities = 94/177 (53%), Positives = 117/177 (65%) Query: 7 MDIWTNLGRFAFIETEHVNLRPVAYTDREAFWRIASKRTNLQFIFPVQTSKKESDFLLVH 66 MDIWT L FAF ET V LRP Y D F+ + + NL ++FP Q +K SD+LLVH Sbjct: 1 MDIWTKLAVFAFFETPKVILRPFRYEDHWDFYSMVNDTKNLYYVFPEQKTKAASDYLLVH 60 Query: 67 SFMKEPLGVWAIEDKVSHKMFGVIRFENIDLSKKTAEIGYFLKESSWGQGIMTECLKTLS 126- SF+K PLG WAIEDK +H++ G IR E+ D + A+IGYFL + WGQGIMTE + L Sbjct: 61 SFIKFPLGQWAIEDKATHQVIGSIRIEHYDAKTRCADIGYFLNYAFWGQGIMTEVVIKLV 120- Query: 127 FFAFREFGMDKLIIVTHKENIASQKVALKAHFKQSRSFKGSDRYTRRIRDYIEFQLT 183 + +F EFG+ L I+TH EN ASQKVA KA F+ FKGSDR T +I Y +QLT Sbjct: 121 YLSFHEFGLKTLRIITHLENKASQKVAKKAGFQLKTCFKGSDRNTHKICIYKMYQLT 177 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1432 A DNA sequence (GBSx1518) was identified in S. agalactiae <SEQ ID 4397> which encodes the amino acid sequence <SEQ ID 4398>. This protein is predicted to be UDP-N-acetylglucosamine-1-carboxyvinyl transferase (murA). Analysis of this protein sequence reveals the following: TABLE-US-04259 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.63 Transmembrane 25-41 (24-42) ----- Final Results ----- bacterial membrane --- Certainty = 0.3251(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04260 >GP: AAF86297 GB: AF072894 UDP-N-acetylglucosamine-1-carboxyvinyl transferase [Listeria monocytogenes] Identities = 240/412 (58%), Positives = 303/412 (73%), Gaps = 2/412 (0%) Query: 3 KIIINGGKQLTGEVAVSGAKNSVVALIPATILADDVVVLDGVPAISDVDSLVDIMETMGA 62 K+II GGK+L G + V GAKNS VALIPA ILA+ VVL+G+P ISDV +L +I+E +G Sbjct: 20 KLIIRGGKKLAGTLQVDGAKNSAVALIPAAILAESEVVLEGLPDISDVHTLYNILEELGG 79 Query: 63 KIKRYGETLEIDPCGVKDIPMPYGKINSLRASYYFYGSLLGRYGQATLGLPGGCDLGPRP 122- ++ +T IDP + +P+P G + LRASYY G++LGR+ +A +GLPGGC LGPRP Sbjct: 80 TVRYDNKTAVIDPTDMISMPLPSGNVKKLRASYYLMGAMLGRFKKAVIGLPGGCYLGPRP 139- Query: 123 IDLHLKAFEAMGASVSYEGDSMRLATNGKPLQGANIYMDTVSVGATINTIIAAAKANGRT 18- 2 ID H+K FEA+GA V+ E ++ L + L+GA IY+D VSVGATIN ++AA +A G+T Sbjct: 140 IDQHIKGFEALGAKVTNEQGAIYLRAD--ELKGARIYLDVVSVGATINIMLAAVRAKGKT 19- 7 Query: 183 VIENAAREPEIIDVATLLNNMGAHIRGAGTDVITIEGVKSLHGTRHQVIPDRIEAGTYIA 24- 2 VIENAA+EPEIIDVATLL NMGA I+GAGTD I I GV+ LHG H +IPDRIEAGT++ Sbjct: 198 VIENAAKEPEIIDVATLLTNMGAIIKGAGTDTIRITGVEHLHGCHHTIIPDRIEAGTFMV 25- 7 Query: 243 MAAAIGRGIKVTNVLYEHLESFIAKLDEMGVRMTVEEDSIFVEEQERLKAVSIKTSPYPG 30- 2 +AAA+G+G+++ NV+ HLE IAKL EMGV M +EED+IFV E E++K V IKT YPG Sbjct: 258 LAAASGKGVRIENVIPTHLEGIIAKLTEMGVPMDIEEDAIFVGEVEKIKKVDIKTYAYPG 31- 7 Query: 303 FATDLQQPLTPLLLTAEGNGSLLDTIYEKRVNHVPELARMGANISTLGGKIVYSGPNQLS 36- 2 F TDLQQPLT LL AEG+ + DTIY R H+ E+ RMG G V +GP QL Sbjct: 318 FPTDLQQPLTALLTRAEGSSVITDTIYPSRFKHIAEIERMGGKFKLEGRSAVINGPVQLQ 37- 7 Query: 363 GAPVKATDLRAGAALVIAGLMAEGRTEITNIEFILRGYSNIIEKLTSLGADI 414 G+ V ATDLRAGAALVIA L+A+G TEI +E I RGYS IIEKL+++GA+I Sbjct: 378 GSKVTATDLRAGAALVIAALLADGETEIHGVEHIERGYSKIIEKLSAIGANI 429 A related DNA sequence was identified in S. pyogenes <SEQ ID 4399> which encodes the amino acid sequence <SEQ ID 4400>. Analysis of this protein sequence reveals the following: TABLE-US-04261 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.70 Transmembrane 25-41 (23-45) ----- Final Results ----- bacterial membrane --- Certainty = 0.4482(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04262 >GP: AAF86297 GB: AF072894 UDP-N-acetylglucosamine-1-carboxyvinyl transferase [Listeris monocytogenes] Identities = 244/412 (59%), Positives = 302/412 (73%), Gaps = 2/412 (0%) Query: 3 KIIINGGKALSGEVAVSGAKNSVVALIPAIILADDIVILDGVPAISDVDSLIEIMELMGA 62 K+II GGK L+G + V GAKNS VALIPA ILA+ V+L+G+P ISDV +LI+E +G Sbjct: 20 KLIIRGGKKLAGTLQVDGAKNSAVALIPAAILAESEVVLEGLPDISDVHTLYNILEELGG 79 Query: 63 TVNYHGDTLEIDPRGVQDIPMPYGRINSLRASYYFYGSLLGRFGQAVVGLPGGCDLGPRP 122- TV Y T IDP + +P+P G + LRASYY G++LGRF +AV+GLPGGC LGPRP Sbjct: 80 TVRYDNKTAVIDPTDMISMPLPSGNVKKLRASYYLMGAMLGRFKKAVIGLPGGCYLGPRP 139- Query: 123 IDLHLKAFEAMGVEVSYEGENMNLSTNGQKIHGAHIYMDTVSVGATINTMVAATKAQGKT 18- 2 ID H+K FEA+G +V+ E + L + ++ GA IY+D VSVGATIN M+AA +A+GKT Sbjct: 140 IDQHIKGFEALGAKVTNEQGAIYLRAD--ELKGARIYLDVVSVGATINIMLAAVRAKGKT 19- 7 Query: 183 VIENAAREPEIIDVATLLNNMGAHIRGAGTDIITIQGVQKLHGTRHQVIPDRIEAGTYIA 24- 2 VIENAA+EPEIIDVATLL NMGA I+GAGTD I I GV+ LHG H +IPDRIEAGT++ Sbjct: 198 VIENAAKEPEIIDVATLLTNMGAIIKGAGTDTIRITGVEHLHGCHHTIIPDRIEAGTFMV 25- 7 Query: 243 LAAAIGKGVKITNVLYEHLESFIAKLEEMGVRMTVEEDAIFVEKQESLKAITIKTSPYPG 30- 2 LAAA GKGV+I NV+ HLE IAKL EMGV M +EEDAIFV + E +K + IKT YPG Sbjct: 258 LAAASGKGVRIENVIPTHLEGIIAKLTEMGVPMDIEEDAIFVGEVEKIKKVDIKTYAYPG 31- 7 Query: 303 FATDLQQPLTPLLLKADGRGTIIDTIYEKRINHVPELMRMGADISVIGGQIVYQGPSRLT 36- 2 F TDLQQPLT LL +A+G I DTIY R H+ E+ RMG + G V GP +L Sbjct: 318 FPTDLQQPLTALLTRAEGSSVITDTIYPSRFKHIAEIERMGGKFKLEGRSAVINGPVQLQ 37- 7 Query: 363 GAQVKATDLRAGAALVTAGLIAEGKTEITNIEFILRGYASIIAKLTALGADI 414 G++V ATDLRAGAALV A L+A+G+TEI +E I RGY+ II KL+A+GA+I Sbjct: 378 GSKVTATDLRAGAALVIAALLADGETEIHGVEHIERGYSKIIEKLSAIGANI 429 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-04263 Identities = 344/419 (82%), Positives = 394/419 (93%) Query: 1 MRKIIINGGKQLTGEVAVSGAKNSVVALIPATILADDVVVLDGVPAISDVDSLVDIMETM 60 MRKIIINGGK L+GEVAVSGAKNSVVALIPA ILADD+V+LDGVPAISDVDSL++IME M Sbjct: 1 MRKIIINGGKALSGEVAVSGAKNSVVALIPAIILADDIVILDGVPAISDVDSLIEIMELM 60 Query: 61 GAKIKRYGETLEIDPCGVKDIPMPYGKINSLRASYYFYGSLLGRYGQATLGLPGGCDLGP 120- GA + +G+TLEIDP GV+DIPMPYGKINSLRASYYFYGSLLGR+GQA +GLPGGCDLGP Sbjct: 61 GATVNYHGDTLEIDPRGVQDIPMPYGKINSLRASYYFYGSLLGRFGQAVVGLPGGCDLGP 120- Query: 121 RPIDLHLKAFEAMGASVSYEGDSMRLATNGKPLQGANIYMDTVSVGATINTIIAAAKANG 18- 0 RPIDLHLKAFEAMG VSYEG++M L+TNG+ + GA+IYMDTVSVGATINT++AA KA G Sbjct: 121 RPIDLHLKAFEAMGVEVSYEGENMNLSTNGQKIHGAHIYMDTVSVGATINTMVAATKAQG 18- 0 Query: 181 RTVIENAAREPEIIDVATLLNNMGAHIRGAGTDVITIEGVKSLHGTRHQVIPDRIEAGTY 24- 0 +TVIENAAREPEIIDVATLLNNMGAHIRGAGTD+ITI+GV+ LHGTRHQVIPDRIEAGTY Sbjct: 181 KTVIENAAREPEIIDVATLLNNMGAHIRGAGTDIITIQGVQKLHGTRHQVIPDRIEAGTY 24- 0 Query: 241 IAMAAAIGRGIKVTNVLYEHLESFIAKLDEMGVRMTVEEDSIFVEEQERLKAVSIKTSPY 30- 0 IA+AAAIG+G+K+TNVLYEHLESFIAKL+EMGVRMTVEED+IFVE+QE LKA++IKTSPY Sbjct: 241 IALAAAIGKGVKITNVLYEHLESFIAKLEEMGVRMTVEEDAIFVEKQESLKAITIKTSPY 30- 0 Query: 301 PGFATDLQQPLTPLLLTAEGNGSLLDTIYEKRVNHVPELARMGANISTLGGKIVYSGPNQ 36- 0 PGFATDLQQPLTPLLL A+G G+++DTIYEKR+NHVPEL RMGA+IS +GG+IVY GP++ Sbjct: 301 PGFATDLQQPLTPLLLKADGRGTIIDTIYEKRINHVPELMRMGADISVIGGQIVYQGPSR 36- 0 Query: 361 LSGAPVKATDLRAGAALVIAGLMAEGRTEITNIEFILRGYSNIIEKLTSLGADIQLVEE 419- L+GA VKATDLRAGAALV AGL+AEG+TEITNIEFILRGY++II KLT+LGADIQL+E+ Sbjct: 361 LTGAQVKATDLRAGAALVTAGLIAEGKTEITNIEFILRGYASIIAKLTALGADIQLIED 419- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1433 A DNA sequence (GBSx1519) was identified in S. agalactiae <SEQ ID 4401> which encodes the amino acid sequence <SEQ ID 4402>. This protein is predicted to be thiamine phosphate pyrophosphorylase (thiE). Analysis of this protein sequence reveals the following: TABLE-US-04264 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0422(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04265 >GP: AAF25544 GB: AF109218 ThiE [Staphylococcus carnosus] Identities = 98/200 (49%), Positives = 140/200 (70%), Gaps = 1/200 (0%) Query: 5 LKLYFVCGTVDCSR-KNILTVVEEALQAGITLFQFREKGFTALQGKEKIAMAKQLQILCK 63 L +YF+CGT D + I V++EAL+ GITL+QFREKG A G++K+A+AK+LQ LCK Sbjct: 7 LNVYFICGTQDIPEGRTIQEVLKEALEGGITLYQFREKGNGAKTGQDKVALAKELQALCK 66 Query: 64 QYQVPFIIDDDIDLVELIDADGLHIGQNDLPVDEARRRLPDKIIGLSVSTMDEYQKSQLS 123- Y VPFI++DD+ L E IDADG+H+GQ+D VD+ R KIIGLS+ ++E S L+ Sbjct: 67 SYNVPFIVNDDVALAEEIDADGIHVGQDDEAVDDFNNRFEGKIIGLSIGNLEELNASDLT 126- Query: 124 VVDYIGIGPFNPTQSKADAKPAVGNRTTKAVREINQDIPIVAIGGITSDFVHDIIESGAD 18- 3 VDYIG+GP T SK DA VG + + +R+ D+PIVAIGGI+ D V ++ ++ AD Sbjct: 127 YVDYIGVGPIFATPSKDDASEPVGPKMIETLRKEVGDLPIVAIGGISLDNVQEVAKTSAD 18- 6 Query: 184 GIAVISAISKANHIVDATRQ 203 G++VISAI+++ H+ + + Sbjct: 187 GVSVISAIARSPHVTETVHK 206 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1434 A DNA sequence (GBSx1520) was identified in S. agalactiae <SEQ ID 4403> which encodes the amino acid sequence <SEQ ID 4404>. This protein is predicted to be hydroxyethylthiazole kinase (b2104). Analysis of this protein sequence reveals the following: TABLE-US-04266 Possible site: 54 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.94 Transmembrane 198-214 (194-217) ----- Final Results ----- bacterial membrane --- Certainty = 0.2975(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8805> which encodes amino acid sequence <SEQ ID 8806> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-04267 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: -2.93 GvH: Signal Score (-7.5): 1.61 Possible site: 39 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -4.94 threshold: 0.0 INTEGRAL Likelihood = -4.94 Transmembrane 183-199 (179-202) PERIPHERAL Likelihood = 2.49 151 modified ALOM score: 1.49 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2975(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04268 >GP: AAF25543 GB: AF109218 ThiM [Staphylococcus carnosus] Identities = 114/253 (45%), Positives = 160/253 (63%), Gaps = 1/253 (0%) Query: 18 LEQLKEVNPLTICITNNVVKNFTANGLLALGASPAMSECIEDLEDLLKVADALLINIGTL 77 - L+Q++ +PL IC TN+VVKNFTANGLL+LGASP MSE ++ ED VA ++LINIGTL Sbjct: 5 LDQIRTEHPLVICYTNDVVKNFTANGLLSLGASPTMSEAPQEAEDFYPVAGSVLINIGTL 64 Query: 78 TKESWQLYQEAIKIANKNQVPVVLDPVAAGASRFRLEVSLDLLKNYSISLLTGNGSEIAA 137- TK E KIAN+ + P+V DPVA GAS++R + LK +++ GN SEI A Sbjct: 65 TKHHEHAMLENAKIANETETPLVFDPVAVGASKYRKDFCKYFLKKIKPTVIKGNASEILA 124- Query: 138 LIGEKQASKGADGGKVADLESIAVKANQVFDVPVVVTGETDAIAVRGEVRLLQNGSPLMP 19- 7 LI + KG D D+ IA KA + + +++TGETD I +V L NGS + Sbjct: 125 LIDDTATMKGTDSADNLDVVDIAEKAYKEYQTAIILTGETDVIVQDNKVVKLSNGSHFLA 18- 4 Query: 198 LVTGTGCLLGAVLAAFIGSSDRSDDLACLTEAMTVYNVAGEIAEKVAKGKGVGSFQVAFL 25- 7 +TG GCLLGAV+ AF+ + + L EA++VYN+A E AE+++ KG G+F F+ Sbjct: 185 KITGAGCLLGAVVGAFL-FRNTHPSIETLIEAVSVYNIAAERAEQLSDSKGPGTFLTQFI 24- 3 Query: 258 DALSQMKSEMIMD 270 DAL ++ S+ + + Sbjct: 244 DALYRIDSDAVAE 256 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8806 (GBS398) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 75 (lane 6; MW 31.8 kDa). The GBS398-His fusion product was purified (FIG. 214, lane 5) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 314), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1435 A DNA sequence (GBSx1521) was identified in S. agalactiae <SEQ ID 4405> which encodes the amino acid sequence <SEQ ID 4406>. This protein is predicted to be ThiD (thiD). Analysis of this protein sequence reveals the following: TABLE-US-04269 Possible site: 44 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04270 >GP: AAF25542 GB: AF109218 ThiD [Staphylococcus carnosus] Identities = 139/258 (53%), Positives = 186/258 (71%), Gaps = 4/258 (1%) Query: 8 LTIAGTDPSGGAGIMADLKTFQARRTYGMAVVTSVVAQNTCGVRGVQHIETAIIDQQLAC 67 LTIAGTDP+GGAG+MADLK+F A YGMA +TS+VAQNT GV+ + +++ + +QL Sbjct: 8 LTIAGTDPTGGAGVMADLKSFHACGVYGMAAITSIVAQNTKGVQHIHNLDITWLKEQLDS 67 Query: 68 VYDDIKPKAVKTGMLAERETISLVASYLKKYPQ-PYVLDPVMVATSGHRLIDSDAVEALK 126- ++DD P+A+KTGM+A +E + L+ SYL+KYP PYV+DPVM+A SG L+D AL+ Sbjct: 68 IFDDELPQAIKTGMIATKEMMELIRSYLEKYPDIPYVIDPVMLAKSGDSLMDDAGKHALQ 127- Query: 127 EDLLPLATIITPNLPEAEVLVGYDLSDEVSIIKAGYDIQKQYSVRNVLIKGGHLD--GLA 18- 4 E LLPLA + TPNLPEAE +VG+ L E +I KAG + + V+IKGGH++ +A Sbjct: 128 EILLPLADVATPNLPEAEEIVGFKLDTEEAIKKAGDIFINEIGSKGVVIKGGHIEDKNIA 18- 7 Query: 185 KDYLFLEKAGLITLSNQRINTIHTHGTGCTFAAVVAAELAKGQSILNAVSTAKSFITSAI 24- 4 KDYLF K+GL ++R +T HTHGTGCTF+AV+ AELAKG++I AV AK FI +I Sbjct: 188 KDYLF-TKDGLEVFESERYDTKHTHGTGCTFSAVITAELAKGKTIYEAVKKAKDFIALSI 24- 6 Query: 245 ETAPELGLGNGPVNHTSY 262 + PE+G G GPVNH +Y Sbjct: 247 KYTPEIGQGRGPVNHFAY 264 There is also homology to SEQ ID 4408. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1436 A DNA sequence (GBSx1522) was identified in S. agalactiae <SEQ ID 4409> which encodes the amino acid sequence <SEQ ID 4410>. This protein is predicted to be TenA (tenA). Analysis of this protein sequence reveals the following: TABLE-US-04271 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2242(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04272 >GP: AAF25541 GB: AF109218 TenA [Staphylococcus carnosus] Identities = 78/213 (36%), Positives = 127/213 (59%), Gaps = 6/213 (2%) Query: 14 IQSIYQDPFIQGIIKGRLDHDVICHYLQADNIYLGKFADIYALCLAKSDNLRDKQFFLEQ 73 - I IYQD FIQ ++KG + + + YL+AD YL +FA+IYAL + +L +F ++Q Sbjct: 15 IDEIYQDHFIQELLKGDIKKEALRQYLRADASYLREFANIYALLIPIMPDLESVRFLVDQ 74 Query: 74 IDFTLNRELADGEGPHQALAAYTNRSYQDIIEKGVWYPSADHYIKHMYFHFY-ENGIAGA 132- I F +N E+ H+ +A Y +Y +I++K VW PS DHYIKHMY++ Y A A Sbjct: 75 IQFIVNGEVE----AHEYMADYIGENYNEIVQKKVWPPSGDHYIKHMYYNVYAHENAAYA 130- Query: 133 LAAMSPCPWIYHQLAKKIIEENQFLNGNPFNNWITFYANDTVEELMENYFRMMDYYAQNL 19- 2 +AAM+PCP++Y +AK+ +++ + W FY N ++ L+E +M+ N+ Sbjct: 131 IAAMAPCPYVYAMIAKRAMKDPNLNKSSILAKWFEFY-NTEMDPLIEVLDDLMNQLTANM 18- 9 Query: 193 SKEKQADLVDAFVKSCQHERRFFQMAINQEKWE 225 S+ ++ ++ + +++S HE FF MA EKW+ Sbjct: 190 SETEKNEVRENYLQSTVHELNFFNMAYTSEKWQ 222 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1437 A DNA sequence (GBSx1523) was identified in S. agalactiae <SEQ ID 4411> which encodes the amino acid sequence <SEQ ID 4412>. Analysis of this protein sequence reveals the following: TABLE-US-04273 Possible site: 35 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.06 Transmembrane 43-59 (36-63) INTEGRAL Likelihood = -2.55 Transmembrane 92-108 (92-112) INTEGRAL Likelihood = -1.49 Transmembrane 135-151 (135-151) INTEGRAL Likelihood = -1.06 Transmembrane 69-85 (69-85) INTEGRAL Likelihood = -0.22 Transmembrane 216-232 (216-232) ----- Final Results ----- bacterial membrane --- Certainty = 0.3824(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04274 >GP: CAA91230 GB: Z56283 orf2 [Lactobacillus helveticus] Identities = 46/215 (21%), Positives = 96/215 (44%), Gaps = 3/215 (1%) Query: 21 AITFLCLLIPTFSFSFTLRLRTSLLFLIIVVTLQCFVKVSLKTWAKVNLISFVMGLSLFL 80 - ++ F+ I + S L T+L+ + + ++ +K + + F+ ++F Sbjct: 4 SLKFILAFIISLEISLKASLTTNLIVIAFALIYLLVTRIKIKELILLIAVPFIASFTIFA 63 Query: 81 GTYFWGKLPHQFVLASLVACRPLIFMNVGLLFHASHSNYDFIESLYQTFKVPSHFAYGIF 140- +++ P + +L + R ++ + + DF SL Q +PS FAYG + Sbjct: 64 TLFWFSPTPDAYYAWNL-STRVYVYTLTIACVTRNTTATDFARSLEQNLHLPSKFAYGVL 122- Query: 141 AVFNLLPLIKLQYQRNRLAFRLKNQVTWALSPRLILSVLLKTIYWVEQLELAMLSKGFEV 20- 0 A N++P +K ++ R + ++ SP L +L + + L M S G+ Sbjct: 123 AAINIIPRMKTAVKQIRTSAMMRGMYLSFWSPVLYFKAILVALNSADNLAQGMESHGYVE 18- 2 Query: 201 GKERTHASTYPVRFRDYSL-LGMSILLSIGM-IFK 233 G++R P+ +D+ + + IL++I + IFK Sbjct: 183 GQKRATIVAIPLTKKDWLIFFTLLILVNISLFIFK 217 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8807> and protein <SEQ ID 8808> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04275 Lipop: Possible Site: -1 Crend: 0 McG: Discrim Score: 4.50 GvH: Signal Score (-7.5): -0.2 Possible site: 35 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 5 value: -7.06 threshold: 0.0 INTEGRAL Likelihood = -7.06 Transmembrane 43-59 (36-63) INTEGRAL Likelihood = -2.55 Transmembrane 92-108 (92-112) INTEGRAL Likelihood = -1.49 Transmembrane 135-151 (135-151) INTEGRAL Likelihood = -1.06 Transmembrane 69-85 (69-85) INTEGRAL Likelihood = -0.22 Transmembrane 216-232 (216-232) PERIPHERAL Likelihood = 2.65 170 modified ALOM score: 1.91 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3824(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1438 A DNA sequence (GBSx1524) was identified in S. agalactiae <SEQ ID 4413> which encodes the amino acid sequence <SEQ ID 4414>. Analysis of this protein sequence reveals the following: TABLE-US-04276 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3007(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04277 >GP: CAA91229 GB: Z56283 orf1 [Lactobacillus helveticus] Identities = 123/424 (29%), Positives = 200/424 (47%), Gaps = 48/424 (11%) Query: 17 LFDEVTFSLNPGERILISGYSGCGKSTLALLLSGL--KESGK--GQVLLNGSLIEPSDVG 72 - L +++ ++ PG +LI G +GCGKSTL +++GL K +GK G++ L+G Sbjct: 12 LINQLNMNIAPGFNLLI-GPTGCGKSTLLKIIAGLYPKYAGKLTGKIDLHGQ-----KAA 65 Query: 73 FLFQNPDLQFCMDTVAHELYFILENLQIEPEQMQDRSEFVLAQVGLKGFQNRLIYTLSQG 132- +FQN QF M T E+ F LENLQI+ + + + + ++ I TLS G Sbjct: 66 MMFQNAAEQFTMTTPREEIIFALENLQIKAKDYDLHIKKAVEFTKIADLLDQKINTLSGG 125- Query: 133 EKQRLALATIFLKSPKLIILDEAFANLDQESASQLLQLVLNYQANNQSMLIVIDHLITYY 19- 2 ++Q +ALA + + +LDE FA+ D + L++ + + ++ +I+ DH++ Y Sbjct: 126 QQQHVALAVLIAMDVDVFLLDEPFASCDPNTRHFLIEKLASLAETGRT-IILSDHVLDDY 18- 4 Query: 193 QDIMDHYFWLEKRLTRVNFDYMLNRLNVFELEKKSHN--------TGDKLLSIKDFQVK- 24- 3 + I DH + E + + N+L F+ K+ H TG + + Q+K Sbjct: 185 EKICDHLYQFEGKTVKELSANEKNKL--FKQNKQFHEQSYSFALPTGTPVFELNKTQIKQ 24- 2 Query: 244 ----LSKNKFISYLDFDLASGERLCLDGPSGVGKSSLFMGLLGLYRTKGK--------KQ 29- 1 L +NK Y G+ + G +GVGK+SLF + + KG + Sbjct: 243 NRLLLKQNKLKIY-------GKTTLITGSNGVGKTSLFKAMTKMIPYKGNFTYLDNEISK 29- 5 Query: 292 FTHRKQIP-ISFLFQNPLDQFIFSTVYDEIFQVCKDSN------KARDILETINLWDKKQ 34- 4 +RK + I+ FQ DQF+ TV DEI KD N K + LE + L Sbjct: 296 IKYRKYLSQIAQFFQKASDQFLTVTVKDEIELSKKDRNNFFTDAKIDEWLEKLQLKQHLD 35- 5 Query: 345 FSPFQLSQGQQRRLAIGSILASDSKLLLLDEPTYGQDAYHANMITTLLLSYCHKNHCGVI 40- 4 + LS GQQ++L I +L + +LL+DEP G D +++ L+ K + Sbjct: 356 QVVYSLSGGQQKKLQILLMLMTKHNVLLIDEPLSGLDHESVDLVLQLMQECQEKLQQTFL 41- 5 Query: 405 FTSH 408 SH Sbjct: 416 IISH 419 Identities = 44/185 (23%), Positives = 83/185 (44%), Gaps = 24/185 (12%) Query: 28 GERILISGYSGCGKSTLALLLSGLKESGKGQVLLNGSLIEP------SDVGFLFQNPDLQ 81 - G+ LI+G +G GK++L ++ + L+ + + S + FQ Q Sbjct: 256 GKTTLITGSNGVGKTSLFKAMTKMIPYKGNFTYLDNEISKIKYRKYLSQIAQFFQKASDQ 13- 5 Query: 82 FCMDTVAHELYFILENLQIEPEQMQDRSEFV--------LAQVGLKGFQNRLIYTLSQGE 133- F TV E+ +DR+ F L ++ LK ++++Y+LS G+ Sbjct: 316 FLTVTVKDEIEL----------SKKDRNNFFTDAKIDEWLEKLQLKQHLDQVVYSLSGGQ 36- 5 Query: 134 KQRLALATIFLKSPKLIILDEAFANLDQESASQLLQLVLNYQANNQSMLIVIDHLITYYQ 19- 3 +++L + + + ++++DE + LD ES +LQL + Q Q ++I H I Sbjct: 366 QKKLQILLMLMTKHNVLLIDEPLSGLDHESVDLVLQLMQECQEKLQQTFLIISHQIDALA 42- 5 Query: 194 DIMDH 198 D D+ Sbjct: 426 DFCDY 430 A related DNA sequence was identified in S. pyogenes <SEQ ID 4415> which encodes the amino acid sequence <SEQ ID 4416>. Analysis of this protein sequence reveals the following: TABLE-US-04278 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3093(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04279 Identities = 120/455 (26%), Positives = 203/455 (44%), Gaps = 47/455 (10%) Query: 1 MLSVEKLACTHGDSHYLFDEV-TFSLNPGERILISGYSGCGKSTLALLLSGLKE---SGK 56 M+S E+L T+ D ++ T + G+ I++ G SG GKST LL+G+ +GK Sbjct: 21 MISAEQLVFTYHDQKNPACQISTCQIASGQFIVLCGPSGSGKSTFLKLLNGIIPDYYAGK 80 Query: 57 GQVLLNGSLIEPS---------DVGFLFQNPDLQFCMDTVAHELYFILENLQIEPEQMQD 107- + L+ + + V +FQNP QF V HEL F EN ++ + + Sbjct: 81 YEGRLDVADCQAGRDSVETFSRSVASVFQNPASQFFYREVQHELVFPCENQGLDAKVIMK 140- Query: 108 RSEFVLAQVGLKGFQNRLIYTLSQGEKQRLALATIFLKSPKLIILDEAFANLDQESASQL 16- 7 R + N+ ++ LS G+KQR+A+AT ++ +++ DE ANLD + + Sbjct: 141 RLWTLAEDFAFAELLNKDMFGLSGGQKQRVAIATAIMQGTNIMLFDEPTANLDSAGIAAV 20- 0 Query: 168 LQLVLNYQANNQSMLIVIDHLITYYQDIMDHYFW-----LEKRLTRVNF---------DY 21- 3 + +A ++ +IV +H + Y D+ D++F+ L +LT N D Sbjct: 201 KAYLTQLKAAGKT-IIVAEHRLHYLMDLADNFFYFKNGRLTDKLTTQNLLALTDEQRQDM 25- 9 Query: 214 MLNRLNVFELE-------KKSHNTGDKLLSIKDFQVKLSKNKFISYLDFDLASGERLCLD 26- 6 L RL++ +L+ + H D L I+ V+ A G + Sbjct: 260 GLRRLDLSDLKPVLAGKIESQHYRPDDSLCIEHLTVRAGSKILRCIEQLSFAVGSISGIT 31- 9 Query: 267 GPSGVGKSSLFMGLLGLYRTKGKKQFTHRKQIPISFLFQNPLDQFIFSTVYDEIF--QVC 32- 4 G +G+GKS L + G+ KK + IP+S + + V ++F V Sbjct: 320 GSNGLGKSQLVYYIAGI--LDDKKATIKFQGIPLSAKQRLSKTSIVLQEVSLQLFAESVS 37- 7 Query: 325 KDSN-------KARDILETINLWDKKQFSPFQLSQGQQRRLAIGSILASDSKLLLLDEPT 37- 7 K+ N + +++E ++L + P LS G+Q+R+ I + L +D +L+ DEP+ Sbjct: 378 KEVNLGHERHPRTTEVIERLSLTTLLERHPASLSGGEQQRVMIAASLLADKDILIFDEPS 43- 7 Query: 378 YGQDAYHANMITTLLLSYCHKNHCGVIFTSHDPHL 412 G D + LL+ H VI SHD L Sbjct: 438 SGLDLLQMKALANLLMQ-LKTQHKVVILISHDEEL 471 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1439 A DNA sequence (GBSx1525) was identified in S. agalactiae <SEQ ID 4417> which encodes the amino acid sequence <SEQ ID 4418>. Analysis of this protein sequence reveals the following:

TABLE-US-04280 Possible site: 42 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.62 Transmembrane 8-24 (1-30) INTEGRAL Likelihood = -8.17 Transmembrane 145-161 (143-163) INTEGRAL Likelihood = -6.32 Transmembrane 66-82 (62-84) INTEGRAL Likelihood = -3.77 Transmembrane 112-128 (111-132) INTEGRAL Likelihood = -2.66 Transmembrane 43-59 (43-59) ----- Final Results ----- bacterial membrane --- Certainty = 0.5649(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04281 >GP: CAB13180 GB: Z99110 ykoE [Bacillus subtilis] Identities = 68/177 (38%), Positives = 117/177 (65%), Gaps = 1/177 (0%) Query: 5 LKDVLLIALLAVVLGVVYFGAGYISNAFVPFVGPIAHEVIYGIWFVAGPMALYILRKPGT 64 +K++++++++++V VVY + N GPIA+E IYGIWF+ +A Y++RKPG Sbjct: 6 VKEIVIMSVISIVFAVVYLLFTHFGNVLAGMFGPIAYEPIYGIWFIVSVIAAYMIRKPGA 65 Query: 65 AIVAELLAALIEVLIGSIYGPSVLVIGTLQGLGSELGFTLFRYHNYKLPAFILSAILTSI 124- A+V+E++AAL+E L+G+ GP V+VIG +QGLG+E F R+ Y LP +L+ + +S+ Sbjct: 66 ALVSEIIAALVECLLGNPSGPMVIVIGIVQGLGAEAVFLATRWKAYSLPVLMLAGMGSSV 125- Query: 125 FSFAWSFYANGLSAFSFSYNILMLIVRTVS-SIIFFLLTKNICDQLHRSGVLNAYGI 180 SF + + +G +A+S Y ++ML++R +S +++ LL K + L +GVLN + Sbjct: 126 ASFIYDLFVSGYAAYSPGYLLIMLVIRLISGALLAGLLGKAVSGSLAYTGVLNGMAL 182 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1440 A DNA sequence (GBSx1526) was identified in S. agalactiae <SEQ ID 4419> which encodes the amino acid sequence <SEQ ID 4420>. Analysis of this protein sequence reveals the following: TABLE-US-04282 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.69 Transmembrane 65-81 (53-95) INTEGRAL Likelihood = -6.37 Transmembrane 34-50 (31-54) INTEGRAL Likelihood = -6.10 Transmembrane 176-192 (169-195) INTEGRAL Likelihood = -3.66 Transmembrane 130-146 (130-151) INTEGRAL Likelihood = -1.97 Transmembrane 3-19 (3-19) INTEGRAL Likelihood = -0.90 Transmembrane 88-104 (88-104) ----- Final Results ----- bacterial membrane --- Certainty = 0.3675(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9757> which encodes amino acid sequence <SEQ ID 9758> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8809> and protein <SEQ ID 8810> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04283 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -4.09 GvH: Signal Score (-7.5): -4.38 Possible site: 47 >>> Seems to have no N-terminal signal sequence ALOM program count: 6 value: -6.69 threshold: 0.0 INTEGRAL Likelihood = -6.69 Transmembrane 65-81 (53-95) INTEGRAL Likelihood = -6.37 Transmembrane 34-50 (31-54) INTEGRAL Likelihood = -6.10 Transmembrane 176-192 (169-195) INTEGRAL Likelihood = -3.66 Transmembrane 130-146 (130-151) INTEGRAL Likelihood = -1.97 Transmembrane 3-19 (3-19) INTEGRAL Likelihood = -0.90 Transmembrane 88-104 (88-104) PERIPHERAL Likelihood = 5.30 158 modified ALOM score: 1.84 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3675(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1441 A DNA sequence (GBSx1527) was identified in S. agalactiae <SEQ ID 4421> which encodes the amino acid sequence <SEQ ID 4422>. Analysis of this protein sequence reveals the following: TABLE-US-04284 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8811> and protein <SEQ ID 8812> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04285 Lipop: Possible site: -1 Crend: 2 McG: Discrim Score: 6.01 GvH: Signal Score (-7.5): 0.45 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 10.66 threshold: 0.0 PERIPHERAL Likelihood = 10.66 80 modified ALOM score: -2.63 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 4422 (GBS19) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 4 (lane 4; MW 24 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 9 (lane 6; MW 46.1 kDa). The GST-fusion protein was purified as shown in FIG. 190, lane 10. EXAMPLE 1442 A DNA sequence (GBSx1528) was identified in S. agalactiae <SEQ ID 4423> which encodes the amino acid sequence <SEQ ID 4424>. Analysis of this protein sequence reveals the following: TABLE-US-04286 Possible site: 30 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8813> which encodes amino acid sequence <SEQ ID 8814> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-04287 Lipop: Possible site: -1 Crend: 6 SRCFLG: 0 McG: Length of UR: 23 Peak Value of UR: 2.61 Net Charge of CR: 3 McG: Discrim Score: 9.08 GvH: Signal Score (-7.5): -0.76 Possible site: 22 >>> Seems, to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 23 ALOM program count: 0 value: 5.14 threshold: 0.0 PERIPHERAL Likelihood = 5.14 365 modified ALOM score: -1.53 *** Reasoning Step: 3 Rule gpo1 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04288 >GP: CAA34476 GB: X16457 precursor polypeptide (AA -26 to 632) [Staphylococcus aureus] Identities = 93/372 (25%), Positives = 160/372 (43%), Gaps = 46/372 (12%) Query: 9 MKKQFLKSAAILSLAVTAVSTSQPVGAIVGKDETKLRQQLGYIDSKKSGKKIDERWGEKI 68 MKKQ + A L++A + + AIV KD +K + + K G + + + KI Sbjct: 1 MKKQIISLGA-LAVASSLFTWDNKADAIVTKDYSK---ESRVNEKSKKGATVSDYYYWKI 56 Query: 69 YNYLSYELIEANEWINRSEFQEPEYRTILSEFKDKIDSIEYYLINLS----NIAKEDAHQ 124- +L + A + + ++ +P Y+ ++ + YL+ + K+ Sbjct: 57 IDSLEAQFTGAIDLLENYKYGDPIYKEAKDRLMTRVLGEDQYLLKKKIDEYELYKKWYKS 116- Query: 125 RNILQSLDKYEKSGIYNLDQGVYNYIYQEISSAKHKFSDGVDKIYRLDSTLFPFSVWYDK 18- 4 N ++ + K +YNL YN I+ + A ++F+ V +I + L F Sbjct: 117 SNKNTNMLTFHKYNLYNLTMNEYNDIFNSLKDAVYQFNKEVKEIEHKNVDLKQF------ 17- 0 Query: 185 HLDNNDNYKDNKDFKEYIALLNEITRKARLGYQIVNNHKD-GEHKDEAEI-LDILIRDIT 24- 2 D ++K KE L++EI Y KD GEH E LD+++ D Sbjct: 171 -----DKDGEDKATKEVYDLVSEIDTLVVTYYA----DKDYGEHAKELRAKLDLILGDTD 22- 1 Query: 243 FVSKDAPGYKYIPNKRIAAKIIEDLDGIINDFFKNTGKDKP-SLEKLKDTEFHKKYLNST 30- 1 K I N+RI ++I+DL+ II+DFF T +++P S+ K T+ + K + Sbjct: 222 NPHK-------ITNERIKKEMIDDLNSIIDDFFMETKQNRPNSITKYDPTKHNFKERSEN 27- 4 Query: 302 EPYSIETNLPSNYKELKEKQIKKLEYGYK-KSSKIY--TSAHYALYSEEIDAAKELLQKV 35- 8 +P N +E K K +K+ + +K K+ K Y T + EE + L KV Sbjct: 275 KP-----NFDKLVEETK-KAVKEADESWKNKTVKKYEETVTKSPVVKEEKKVEEPQLPKV 32- 8 Query: 359 KIAKDNYNEIKS 370 N E+K+ Sbjct: 329 ----GNQQEVKT 336 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8814 (GBS119) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 29 (lane 2; MW 84.3 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 35 (lane 5; 2 bands). The GBS119-GST fusion product was purified (FIG. 109A; see also FIG. 201, lane 6) and used to immunise mice (lane 1+2+3 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot, FACS (FIG. 109B), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1443 A DNA sequence (GBSx1529) was identified in S. agalactiae <SEQ ID 4425> which encodes the amino acid sequence <SEQ ID 4426>. This protein is predicted to be s-adenosylmethionine synthetase (metK). Analysis of this protein sequence reveals the following: TABLE-US-04289 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3609(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04290 >GP: BAB07019 GB: AP001518 S-adenosylmethionine synthetase [Bacillus halodurans] Identities = 266/390 (68%), Positives = 324/390 (82%), Gaps = 1/390 (0%) Query: 4 RKLFTSESVSEGHPDKIADQISDAILDAILEQDPDAHVAAETAVYTGSVHVFGEISTTAY 63 R+LFTSESV+EGHPDKI DQISD+ILD IL++DP+A VA ET+V TG V V GEI+T+ Y Sbjct: 7 RRLFTSESVTEGHPDKICDQISDSILDEILKEDPNARVACETSVTTGLVLVAGEITTSTY 66 Query: 64 VDINRVVRNTIAEIGYDKAEYGFSAESVGVHPSLVEQSPDIAQGVNEALEVR-GSLEQDP 122- VDI +VVR+TI IGY +A+YGF +E+ V S+ EQSPDIAQGVN+ALE R G + Sbjct: 67 VDIPKVVRDTIRNIGYTRAKYGFDSETCAVLTSIDEQSPDIAQGVNQALEAREGQMTDAE 126- Query: 123 LDLIGAGDQGLMFGFAVDETPELMPLPISLAHQLVKKLTDLRKSGELTYLRPDAKSQVTV 18- 2 ++ IGAGDQGLMFG+A +ETPELMPLPISL+H+L ++L++ RK L YLRPD K+QVTV Sbjct: 127 IEAIGAGDQGLMFGYANNETPELMPLPISLSHKLARRLSEARKGEILPYLRPDGKTQVTV 18- 6 Query: 183 EYDENDQPIRVDAVVISTQHDPNVTNDQLHKDVIEKVINEVIPSHYLDDQTKFFINPTGR 24- 2 EYDENDQ +R+D +VISTQH P VT +Q+ D+ + VI V+P +D++TK+FINPTGR Sbjct: 187 EYDENDQSVRIDTIVISTQHHPEVTLEQIESDLKQHVIRSVVPEELIDEETKYFINPTGR 24- 6 Query: 243 FVIGGPQGDSGLTGRKIIVDTYGGYSRHGGGAFSGKDATKVDRSASYAARYIAKNIVAAD 30- 2 FVIGGPQGD+GLTGRKIIVDTYGGY+RHGGGAFSGKD TKVDRS +YAARY+AKNIVAA Sbjct: 247 FVIGGPQGDAGLTGRKIIVDTYGGYARHGGGAFSGKDPTKVDRSGAYAARYVAKNIVAAG 30- 6 Query: 303 LAKKVEVQLAYAIGVAQPVSVRVDTFGTGVIAEADLEAAVRQIFDLRPAGIINMLDLKRP 36- 2 LA K EVQLAYAIGVA+PVS+ +DTFGTG ++EA L VR+ FDLRPAGII MLDL+RP Sbjct: 307 LADKCEVQLAYAIGVAKPVSISIDTFGTGQVSEARLVELVREHFDLRPAGIIKMLDLRRP 36- 6 Query: 363 IYRQTAAYGHMGRTDIDLPWERVDKVQALK 392 IY+QTAAYGH GRTD++LPWE+ DK + L+ Sbjct: 367 IYKQTAAYGHFGRTDVELPWEQTDKAEILR 396 A related DNA sequence was identified in S. pyogenes <SEQ ID 4427> which encodes the amino acid sequence <SEQ ID 4428>. Analysis of this protein sequence reveals the following: TABLE-US-04291 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3389(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04292 Identities = 333/395 (84%), Positives = 361/395 (91%), Gaps = 1/395 (0%) Query: 1 MSERKLFTSESVSEGHPDKIADQISDAILDAILEQDPDAHVAAETAVYTGSVHVFGEIST 60 MSERKLFTSESVSEGHPDKIADQISDAILDAIL +DP+AHVAAET VYTGSVHVFGEIST Sbjct: 1 MSERKLFTSESVSEGHPDKIADQISDAILDAILAEDPEAHVAAETCVYTGSVHVFGEIST 60 Query: 61 TAYVDINRVVRNTIAEIGYDKAEYGFSAESVGVHPSLVEQSPDIAQGVNEALEVRGSLEQ 120- TAY+DINRVVR+TIAEIGY +AEYGFSAESVGVHPSLVEQS DIAQGVNEA E R + Sbjct: 61 TAYIDINRVVRDTIAEIGYTEAEYGFSAESVGVHPSLVEQSGDIAQGVNEAFESREG-DT 119- Query: 121 DPLDLIGAGDQGLMFGFAVDETPELMPLPISLAHQLVKKLTDLRKSGELTYLRPDAKSQV 18- 0 D L IGAGDQGLMFGFA++ETPELMPLPISL+HQLV++L +LRKSGE++YLRPDAKSQV Sbjct: 120 DDLSHIGAGDQGLMFGFAINETPELMPLPISLSHQLVRRLAELRKSGEISYLRPDAKSQV 17- 9 Query: 181 TVEYDENDQPIRVDAVVISTQHDPNVTNDQLHKDVIEKVINEVIPSHYLDDQTKFFINPT 24- 0 TVEYDE+D+P+RVD VVISTQHDP TNDQ+ +DVIEKVI VIP+ YLDD TKFFINPT Sbjct: 180 TVEYDEHDKPVRVDTVVISTQHDPEATNDQIRQDVIEKVIKAVIPADYLDDDTKFFINPT 23- 9 Query: 241 GRFVIGGPQGDSGLTGRKIIVDTYGGYSRHGGGAFSGKDATKVDRSASYAARYIAKNIVA 30- 0 GRFVIGGPQGDSGLTGRKIIVDTYGGYSRHGGGAFSGKDATKVDRSASYAARYIAKN+VA Sbjct: 240 GRFVIGGPQGDSGLTGRKIIVDTYGGYSRHGGGAFSGKDATKVDRSASYAARYIAKNLVA 29- 9 Query: 301 ADLAKKVEVQLAYAIGVAQPVSVRVDTFGTGVIAEADLEAAVRQIFDLRPAGIINMLDLK 36- 0 A L K EVQLAYAIGVAQPVSVRVDTFGT + EA LEAAVRQ+FDLRPAGII MLDLK Sbjct: 300 AGLVTKAEVQLAYAIGVAQPVSVRVDTFGTSTVPEAVLEAAVRQVFDLRPAGIIQMLDLK 35- 9 Query: 361 RPIYRQTAAYGHMGRTDIDLPWERVDKVQALKDFI 395 RPIY+QTAAYGHMGRTDIDLPWER++KV AL + + Sbjct: 360 RPIYKQTAAYGHMGRTDIDLPWERLNKVDALVEAV 394 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1444 A DNA sequence (GBSx1530) was identified in S. agalactiae <SEQ ID 4429> which encodes the amino acid sequence <SEQ ID 4430>. This protein is predicted to be a transcriptional repressor of the biotin operon. Analysis of this protein sequence reveals the following: TABLE-US-04293 Possible site: 24 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 188-204 (188-204) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9755> which encodes amino acid sequence <SEQ ID 9756> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04294 >GP: BAB05404 GB: AP001512 transcriptional repressor of the biotin operon [Bacillus halodurans] Identities = 102/315 (32%), Positives = 169/315 (53%), Gaps = 18/315 (5%) Query: 10 ILSKNNNFISGETMANQLNISRTAIWKGIKTLEELGLEIESVTNKGYRLVSG-DILLPEQ 68 - +L+ ++F+SGE ++ + SRTA+WK I+ L + G E+E+V KGYR+V D + P Sbjct: 9 LLTAGDDFVSGEKISQAIGCSRTAVWKHIEELRKSGYEVEAVQRKGYRIVKRPDQIKPHD 68 Query: 69 LE-----QEIGIKVSLNNNSASTQLDAKMGIESKLKTPHLFLAPNQKKAKGRFDRPFFTS 123- ++ + G +++ ++ASTQ A + K H+ LA Q KGR R +++ Sbjct: 69 IQVVLETERFGREITYLESTASTQTVALKLAQEGAKEGHIVLANEQTSGKGRMGRGWYSP 128- Query: 124 NQGGIYMSLLLQPNVPIEDIKPYTVMVASSAVKAISRLTGITPEIKWVNDIYLDNKKIAG 18- 3 I MS++ +P +P + T++ A + V+AI TG+ +IKW ND+ +D KKI G Sbjct: 129 PGSSISMSIIFRPQLPPQKAPQLTLLTAVAIVRAIKETTGLDSDIKWPNDLLIDGKKIVG 18- 8 Query: 184 ILTEAIASVESGLVTNVIIGLGINFYIKE--FPRALTKRAGSLFTEQ-PTITRNQLITEI 24- 0 ILTE A +S V +VI G+GIN +E F + K A SL ++ I R LI I Sbjct: 189 ILTEMQADQDS--VHSVIQGIGINVNHQEEAFAEEIRKIATSLAIKKGEPIQRAPLIAAI 24- 6 Query: 241 W---NLFFNIPLEDHLK----VYREKSLVLDRTVSFMDGQTMYSGKAIDITDKGYLVVEL 29- 3 LF+++ L+ ++ ++ + + + + G A ITD G L++E Sbjct: 247 LKNIELFYDLYLQHGFSRIKPLWEAHAISIGKRIRARMLNDVKFGVAKGITDDGVLLLED 30- 6 Query: 294 DDGQLKTLRSGEISL 308 DDG+L ++ S +I + Sbjct: 307 DDGKLHSIYSADIEI 321 A related DNA sequence was identified in S. pyogenes <SEQ ID 4431> which encodes the amino acid sequence <SEQ ID 4432>. Analysis of this protein sequence reveals the following:

TABLE-US-04295 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.49 Transmembrane 194-210 (194-211) ----- Final Results ----- bacterial membrane --- Certainty = 0.1595(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04296 >GP: BAB05404 GB: AP001512 transcriptional repressor of the biotin operon [Bacillus halodurans] Identities = 98/315 (31%), Positives = 165/315 (52%), Gaps = 18/315 (5%) Query: 10 LLSQTDDFVSGEYLADQLSISRTSVWKSIKSLENQGIQIDSLKHKGYRMVQG-DILLPKT 68 - LL+ DDFVSGE ++ + SRT+VWK I+ L G ++++++ KGYR+V+ D + P Sbjct: 9 LLTAGDDFVSGEKISQAIGCSRTAVWKHIEELRKSGYEVEAVQRKGYRIVKRPDQIKPHD 68 Query: 69 I-----SQGLGMPVTYTPHSQSTQLDAKQGIEAHNSAPRLYLAPSQEAAKGRLDRQFFSA 123- I ++ G +TY + STQ A + + + LA Q + KGR+ R ++S Sbjct: 69 IQVVLETERFGREITYLESTASTQTVALKLAQEGAKEGHIVLANEQTSGKGRMGRGWYSP 128- Query: 124 STGGIYMSMYLKPNVPYADMPPYTMMVASSIVKAISRLTGIDTEIKWVNDIYLGNMKVAG 18- 3 I MS+ +P +P P T++ A +IV+AI TG+D++IKW ND+ + K+ G Sbjct: 129 PGSSISMSIIFRPQLPPQKAPQLTLLTAVAIVRAIKETTGLDSDIKWPNDLLIDGKKIVG 18- 8 Query: 184 ILTEAITSVETGLITDVIIGVGLNFFVTD--FPEAIAQKAGSLFTEK-PTITRNDLIIDI 24- 0 ILTE + + VI G+G+N + F E I + A SL +K I R LI I Sbjct: 189 ILTE--MQADQDSVHSVIQGIGINVNHQEEAFAEEIRKIATSLAIKKGEPIQRAPLIAAI 24- 6 Query: 241 WK-------LFLSIPVKDHVKVYKEKSLVLNKQVTFIENSQEKRAIAIDLTDQGHLIVQF 29- 3 K L+L +++ ++ + K++ + K +A +TD G L+++ Sbjct: 247 LKNIELFYDLYLQHGFSRIKPLWEAHAISIGKRIRARMLNDVKFGVAKGITDDGVLLLED 30- 6 Query: 294 ENGDLQTLRSGEISL 308 ++G L ++ S +I + Sbjct: 307 DDGKLHSIYSADIEI 321 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04297 Identities = 191/311 (61%), Positives = 257/311 (82%) Query: 1 MKTYEKIYQILSKNNNFISGETMANQLNISRTAIWKGIKTLEELGLEIESVTNKGYRLVS 60 MKT EKIYQ+LS+ ++F+SGE +A+QL+ISRT++WK IK+LE G++I+S+ +KGYR+V Sbjct: 1 MKTSEKIYQLLSQTDDFVSGEYLADQLSISRTSVWKSIKSLENQGIQIDSLKHKGYRMVQ 60 Query: 61 GDILLPEQLEQEIGIKVSLNNNSASTQLDAKMGIESKLKTPHLFLAPNQKKAKGRFDRPF 120- GDILLP+ + Q +G+ V+ +S STQLDAK GIE+ P L+LAP+Q+ AKGR DR F Sbjct: 61 GDILLPKTISQGLGMPVTYTPHSQSTQLDAKQGIEAHNSAPRLYLAPSQEAAKGRLDRQF 120- Query: 121 FTSNQGGIYMSLLLQPNVPIEDIKPYTVMVASSAVKAISRLTGITPEIKWVNDIYLDNKK 18- 0 F+++ GGIYMS+ L+PNVP D+ PYT+MVASS VKAISRLTGI EIKWVNDIYL N K Sbjct: 121 FSASTGGIYMSMYLKPNVPYADMPPYTMMVASSIVKAISRLTGIDTEIKWVNDIYLGNHK 18- 0 Query: 181 IAGILTEAIASVESGLVTNVIIGLGINFYIKEFPRALTKRAGSLFTEQPTITRNQLITEI 24- 0 +AGILTEAI SVE+GL+T+VIIG+G+NF++ +FP A+ ++AGSLFTE+PTITRN LI +I Sbjct: 181 VAGILTEAITSVETGLITDVIIGVGLNFFVTDFPEAIAQKAGSLFTEKPTITRNDLIIDI 24- 0 Query: 241 WNLFFNIPLEDHLKVYREKSLVLDRTVSFMDGQTMYSGKAIDITDKGYLVVELDDGQLKT 30- 0 W LF +IP++DH+KVY+EKSLVL++ V+F++ AID+TD+G+L+V+ ++G L+T Sbjct: 241 WKLFLSIPVKDHVKVYKEKSLVLNKQVTFIENSQEKRAIAIDLTDQGHLIVQFENGDLQT 30- 0 Query: 301 LRSGEISLSSW 311 LRSGEISLSSW Sbjct: 301 LRSGEISLSSW 311 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1445 A DNA sequence (GBSx1531) was identified in S. agalactiae <SEQ ID 4433> which encodes the amino acid sequence <SEQ ID 4434>. Analysis of this protein sequence reveals the following: TABLE-US-04298 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.76 Transmembrane 3-19 (3-20) ----- Final Results ----- bacterial membrane --- Certainty = 0.2105(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1446 A DNA sequence (GBSx1532) was identified in S. agalactiae <SEQ ID 4435> which encodes the amino acid sequence <SEQ ID 4436>. Analysis of this protein sequence reveals the following: TABLE-US-04299 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -2.28 Transmembrane 24-40 (24-40) ----- Final Results ----- bacterial membrane --- Certainty = 0.1914(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4437> which encodes the amino acid sequence <SEQ ID 4438>. Analysis of this protein sequence reveals the following: TABLE-US-04300 Possible site: 49 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -1.91 Transmembrane 58-74 (58-75) ----- Final Results ----- bacterial membrane --- Certainty = 0.1765(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04301 Identities = 37/67 (55%), Positives = 54/67 (80%), Gaps = 3/67 (4%) Query: 1 MTKRQFIFMALLCSFETYFFNQSVMDGSWIFAIFWGVLLLRDLQKVYAISKFTKELIK-- 58 MT RQF+FMA +C+FETYFFN ++ G+++FA+FWG+LL RDL++V+ I++ TK ++K Sbjct: 36 MTIRQFLFMAFVCAFETYFFNDLLLSGNYLFALFWGLLLFRDLRRVHTINQLTKTILKTA 95 Query: 59 -STKKKD 64 S KKKD Sbjct: 96 NSPKKKD 102 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1447 A DNA sequence (GBSx1533) was identified in S. agalactiae <SEQ ID 4439> which encodes the amino acid sequence <SEQ ID 4440>. This protein is predicted to be DNA polymerase III, gamma subunit (dnaZX). Analysis of this protein sequence reveals the following: TABLE-US-04302 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1567(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 4441> which encodes the amino acid sequence <SEQ ID 4442>. Analysis of this protein sequence reveals the following: TABLE-US-04303 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.59 Transmembrane 232-248 (232-249) ----- Final Results ----- bacterial membrane --- Certainty = 0.1235(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04304 Identities = 408/558 (73%), Positives = 473/558 (84%), Gaps = 6/558 (1%) Query: 1 MYQALYRKYRSQTFDEMVGQSVISTTLKQAVSSKKISHAYLFSGPRGTGKTSAAKIFAKA 60 MYQALYRKYRSQTFDEMVGQSVISTTLKQAV S KISHAYLFSGPRGTGKTSAAKIFAKA Sbjct: 1 MYQALYRKYRSQTFDEMVGQSVISTTLKQAVESGKISHAYLFSGPRGTGKTSAAKIFAKA 60 Query: 61 MNCPNQINGEPCNHCDICRDITNGSLEDVIEIDAASNNGVDEIRDIRDKSTYAPSRATYK 120- MNCPNQ++GEPCN CDICRDITNGSLEDVIEIDAASNNGVDEIRDIRDKSTYAPSRATYK Sbjct: 61 MNCPNQVDGEPCNQCDICRDITNGSLEDVIEIDAASNNGVDEIRDIRDKSTYAPSRATYK 120- Query: 121 VYIIDEVHMLSTGAFNALLKTLEEPTENVVFILATTELHKIPATILSRVQRFEFKAIKLL 18- 0 VYIIDEVHMLSTGAFNALLKTLEEPTENVVFILATTELHKIPATILSRVQRFEFKAIK Sbjct: 121 VYIIDEVHMLSTGAFNALLKTLEEPTENVVFILATTELHKIPATILSRVQRFEFKAIKQK 18- 0 Query: 181 AIRDHLAQILDKEAISYDLDALTLVARRAEGGMRDALSILDQALSLAKDNHISLDVAEEI 24- 0 AIR+HLA +LDKE I+Y++DAL L+ARRAEGGMRDALSILDQALSL+ DN +++ +AEEI Sbjct: 181 AIREHLAWVLDKEGIAYEVDALNLIARRAEGGMRDALSILDQALSLSPDNQVAIAIAEEI 24- 0 Query: 241 TGSISLSAIDDYVSNILAHDTTEALAKLEVIFDSGKSMSRFATDLLMYLRDLLVVQAGGE 30- 0 TGSIS+ A+ DYV + T+ALA LE I+DSGKSMSRFATDLL YLRDLLVV+AGG+ Sbjct: 241 TGSISILALGDYVRYVSQEQATQALAALETIYDSGKSMSRFATDLLTYLRDLLVVKAGGD 30- 0 Query: 301 DSHSSDTFIANLNVKQDILFEMIDKVTSVLPEIKNGSHPKVYAEMMTIQLSEMVEKNSS- 35- 9 + S F NL++ D +F+MI VTS LPEIK G+HP++YAEMMTIQL++ + S Sbjct: 301 NQRQSAVFDTNLSLSIDRIFQMITVVTSHLPEIKKGTHPRIYAEMMTIQLAQKEQILSQV 36- 0 Query: 360 NIPADVTAELDSLRRELKSLKNEMSQL-SRADQSSSTQKVKVNNKTFTFKVDRTKILTIM 41- 8 N+ ++ +E+++L+ EL LK ++SQL SR D + + K K KT +++VDR IL IM Sbjct: 361 NLSGELISEIETLKNELAQLKQQLSQLQSRPDSLARSDKTK--PKTTSYRVDRVTILKIM 41- 8 Query: 419 EETVVDSQRSREYLEALKSAWNEILDNITAQDRALLMGSEPVLANSENAILAFDAAFNAE 47- 8 EETV +SQ+SR+YL+ALK+AWNEILDNI+AQDRALLMGSEPVLANSENAILAF+AAFNAE Sbjct: 419 EETVRNSQQSRQYLDALKNAWNEILDNISAQDRALLMGSEPVLANSENAILAFEAAFNAE 47- 8 Query: 479 QAMKRTDLNDIFGNIMSKAAGFSPNILAVPRNDFNQIRSDFAKKMKAQK--TETEPEVNH 53- 6 Q M R +LND+FGNIMSKAAGFSPNILAVPR DF IR +FA++MK+QK + E EV Sbjct: 479 QVMSRNNLNDMFGNIMSKAAGFSPNILAVPRTDFQHIRKEFAQQMKSQKDSVQEEQEVAL 53- 8 Query: 537 QIPEDFSYLAERIAIVED 554 IPE F +L ++I ++D Sbjct: 539 DIPEGFDFLLDKINTIDD 556 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1448 A DNA sequence (GBSx1534) was identified in S. agalactiae <SEQ ID 4443> which encodes the amino acid sequence <SEQ ID 4444>. Analysis of this protein sequence reveals the following: TABLE-US-04305 Possible site: 40 >>> Seems to have no N-terminal signal sequence (or aa 1-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04306 >GP: BAB06927 GB: AP001518 unknown conserved protein [Bacillus halodurans] Identities = 67/143 (46%), Positives = 96/143 (66%) Query: 8 ENYQLLLLQAQALFSDETNALANLSNASAMLNAMLPNSVFTGFYLFDGEELILGPFQGGV 67 E Y L+ Q AL E++A+ANL+NASA+L L + GFYL EL+LGPFQG Sbjct: 13 EKYSLVTKQLAALLEGESDAIANLANASALLYHFLEEVNWVGFYLIKEGELVLGPFQGLP 72 Query: 68 SCVHITLGKGVCGESAQTAKTLIVDDVTKHANYISCDSKAMSEIVVPMFKNGKLLGVLDL 127- +CV I +G+GVCG +A+ +T+ V+DV + +I+CD+ + SEIV+P+F+NG L GVLD+ Sbjct: 73 ACVRIPIGRGVCGTAAKEEQTVRVEDVHQFPGHIACDAASRSEIVIPLFQNGVLYGVLDI 132- Query: 128 DSSLVADYDEIDQEYLEKFVGIL 150 DS + + E +Q LE FV +L Sbjct: 133 DSPSLNRFSEEEQALLESFVDVL 155 A related DNA sequence was identified in S. pyogenes <SEQ ID 4445> which encodes the amino acid sequence <SEQ ID 4446>. Analysis of this protein sequence reveals the following: TABLE-US-04307 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1753(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04308 Identities = 122/164 (74%), Positives = 144/164 (87%) Query: 1 MNKSKKIENYQLLLLQAQALFSDETNALANLSNASAMLNAMLPNSVFTGFYLFDGEELIL 60 MNKSKKIE YQL++ QA+ LF++E+NALANLSNASA+LN LPNSVFTGFYLFDG+ELIL Sbjct: 1 MNKSKKIEQYQLMIAQAKELFANESNALANLSNASALLNMTLPNSVFTGFYLFDGQELIL 60 Query: 61 GPFQGGVSCVHITLGKGVCGESAQTAKTLIVDDVTKHANYISCDSKAMSEIVVPMFKNGK 120- GPFQG VSCVHI LGKGVCGESAQ+ +T+I++DV +HANYISCD+ AMSEIVVPM K G Sbjct: 61 GPFQGRVSCVHIKLGKGVCGESAQSRRTIIINDVKQHANYISCDAAAMSEIVVPMVKEGH 120- Query: 121 LLGVLDLDSSLVADYDEIDQEYLEKFVGILVEHTIWNLDMFGVE 164 L+GVLDLDSSLVADYDE+DQEYLE FV + +E T + +MFGV+ Sbjct: 121 LIGVLDLDSSLVADYDEVDQEYLEAFVDLFLEKTTFTFNMFGVK 164 SEQ ID 4444 (GBS282) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 52 (lane 9; MW 19.8 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 60 (lane 6; MW 44.8 kDa) and in FIG. 63 (lane 7; MW 47 kDa). The GBS282-GST fusion product was purified (FIG. 211, lane 4; see also FIG. 225, lane 6) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 269), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1449 A DNA sequence (GBSx1535) was identified in S. agalactiae <SEQ ID 4447> which encodes the amino acid sequence <SEQ ID 4448>. This protein is predicted to be uridine kinase (udk). Analysis of this protein sequence reveals the following: TABLE-US-04309 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04310 >GP: CAB14675 GB: Z99117 uridine kinase [Bacillus subtilis] Identities = 133/207 (64%), Positives = 167/207 (80%) Query: 1 MRKKPIIIGVTGGSGGGKTSVSRAILSNFPDQKITMIEHDSYYKDQSHLTFEERVKTNYD 60 M K P++IG+ GGSG GKTSV+R+I F I MI+ D YYKDQSHL FEER+ TNYD Sbjct: 1 MGKNPVVIGIAGGSGSGKTSVTRSIYEQFKGHSILMIQQDLYYKDQSHLPFEERLNTNYD 60 Query: 61 HPLAFDTNLMIEQLNELIEGRPVDIPVYDYTKHTRSDRTIRQEPQDVIIVEGILVLEDQR 120- HPLAFD + +IE + +L+ RP++ P+YDY HTRS+ T+ EP+DVII+EGILVLED+R Sbjct: 61 HPLAFDNDYLIEHIQDLLNYRPIEKPIYDYKLHTRSEETVHVEPKDVIILEGILVLEDKR 120- Query: 121 LRDLMDIKLFVDTDDDIRIIRRIKRDMEERDRSLDSIIEQYTEVVKPMYHQFIEPTKRYA 18- 0 LRDLMDIKL+VDTD D+RIIRRI RD+ ER RS+DS+IEQY VV+PM++QF+EPTKRYA Sbjct: 121 LRDLMDIKLYVDTDADLRIIRRIMRDINERGRSIDSVIEQYVSVVRPMHNQFVEPTKRYA 18- 0 Query: 181 DIVIPEGVSNIVAIDLINTKVASILNE 207 DI+IPEG N VAIDL+ TK+ +IL + Sbjct: 181 DIIIPEGGQNHVAIDLMVTKIQTILEQ 207 A related DNA sequence was identified in S. pyogenes <SEQ ID 4449> which encodes the amino acid sequence <SEQ ID 4450>. Analysis of this protein sequence reveals the following: TABLE-US-04311 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9151> which encodes the amino acid sequence <SEQ ID 9152>. Analysis of this protein sequence reveals the following: TABLE-US-04312 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04313 Identities = 173/207 (83%), Positives = 193/207 (92%) Query: 1 MRKKPIIIGVTGGSGGGKTSVSRAILSNFPDQKITMIEHDSYYKDQSHLTFEERVKTNYD 60 M KKPIIIGVTGGSGGGKTSVSRAIL +FP+ +I MI+HDSYYKDQSH++FEERVKTNYD Sbjct: 5 MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYD 64 Query: 61 HPLAFDTNLMIEQLNELIEGRPVDIPVYDYTKHTRSDRTIRQEPQDVIIVEGILVLEDQR 120- HPLAFDT+ MI+QL EL+ GRPVDIP+YDY KHTRS+ T RQ+PQDVIIVEGILVLED+R Sbjct: 65 HPLAFDTDFMIQQLKELLAGRPVDIPIYDYKKHTRSNTTFRQDPQDVIIVEGILVLEDER 124- Query: 121 LRDLMDIKLFVDTDDDIRIIRRIKRDMEERDRSLDSIIEQYTEVVKPMYHQFIEPTKRYA 18- 0 LRDLMDIKLFVDTDDDIRIIRRIKRDM ER RSL+SII+QYT VVKPMYHQFIEP+KRYA Sbjct: 125 LRDLMDIKLFVDTDDDIRIIRRIKRDMMERGRSLESIIDQYTSVVKPMYHQFIEPSKRYA 18- 4 Query: 181 DIVIPEGVSNIVAIDLINTKVASILNE 207 DIVIPEGVSN+VAID+IN+K+ASIL E Sbjct: 185 DIVIPEGVSNVVAIDVINSKIASILGE 211 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1450 A DNA sequence (GBSx1536) was identified in S. agalactiae <SEQ ID 4451> which encodes the amino acid sequence <SEQ ID 4452>. Analysis of this protein sequence reveals the following: TABLE-US-04314 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5083(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-04315 >GP: CAB12572 GB: Z99108 similar to RNA helicase [Bacillus subtilis] Identities = 140/343 (40%), Positives = 202/343 (58%), Gaps = 9/343 (2%) Query: 10 QDKLTQRQFDDLTDIQNKLFQPITDGDNILGISPTGTGKTLAYLFPTLLKLQPK-KSQQL 68 - Q+ F T +Q + Q I DG +++ SPTGTGKTLAY P L +++P+ K Q Sbjct: 16 QENWNASGFQKPTPVQEQAAQLIMDGKDVIAESPTGTGKTLAYALPVLERIKPEQKHPQA 75 Query: 69 LILAPNSELAGQIFDVTKEWAEPLGLTAQLFLSGSSQKRQIERLKKGPEILIGTAGRVFE 128- +ILAP+ EL QIF V ++W L A + G++ K+Q+E+LKK P I++GT GRVFE Sbjct: 76 VILAPSRELVMQIFQVIQDWKAGSELRAASLIGGANVKKQVEKLKKHPHIIVGTPGRVFE 135- Query: 129 LVKLKKIKMMNINTIVLDEFDELLGDSQYHFVDNIINRVPRDQQMIYISATNKLDNS--- 18- 5 L+K KK+KM + TIVLDE D+L+ + II RD+Q++ SAT K + Sbjct: 136 LIKAKKLKMHEVKTIVLDETDQLVLPEHRETMKQIIKTTLRDRQLLCFSATLKKETEDVL 19- 5 Query: 186 -KLADNTITIDLSNQKLDT--IKHYYITVDKRERTDLLRKFSNIPDFRGLVFFNSLSDLG 24- 2 +LA + + K + +KH Y+ D+R++ LL+K S + + LVF + +L Sbjct: 196 RELAQEPEVLKVQRSKAEAGKVKHQYLICDQRDKVKLLQKLSRLEGMQALVFVRDIGNLS 25- 5 Query: 243 ACEERLQFNRASAVSLASDINIKFRKVILEKFKNHDISLLLGTDLVARGIDIDNLEYVIN 30- 2 E+L ++ L S+ R I+ F++ + LLL TD+ ARG+DI+NL YVI+ Sbjct: 256 VYAEKLAYHHVELGVLHSEAKKMERAKIIATFEDGEFPLLLATDIAARGLDIENLPYVIH 31- 5 Query: 303 FDIARDKETYTHRSGRTGRMGKEGCVITFVTHKEELKQLKKYA 345 DI D++ Y HRSGRTGR GKEG V++ VT EE K LKK A Sbjct: 316 ADIP-DEDGYVHRSGRTGRAGKEGNVLSLVTKLEESK-LKKMA 356 A related DNA sequence was identified in S. pyogenes <SEQ ID 4453> which encodes the amino acid sequence <SEQ ID 4454>. Analysis of this protein sequence reveals the following: TABLE-US-04316 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3847(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04317 Identities = 273/358 (76%), Positives = 312/358 (86%) Query: 1 MITKFPDQWQDKLTQRQFDDLTDIQNKLFQPITDGDNILGISPTGTGKTLAYLFPTLLKL 60 MITKFP QWQ+KL Q F LT IQ + FQPI DG N LGISPTGTGKTLAY+FP LL L Sbjct: 12 MITKFPPQWQEKLDQVAFTHLTPIQEQAFQPIVDGKNFLGISPTGTGKTLAYVFPNLLAL 71 Query: 61 QPKKSQQLLILAPNSELAGQIFDVTKEWAEPLGLTAQLFLSGSSQKRQIERLKKGPEILI 120- PKKSQQLLILAPN+ELAGQIF+VTK+WA+PLGLTAQLF+SG+SQKRQIERLKKGPEILI Sbjct: 72 TPKKSQQLLILAPNTELAGQIFEVTKDWAQPLGLTAQLFISGTSQKRQIERLKKGPEILI 131- Query: 121 GTAGRVFELVKLKKIKMMNINTIVLDEFDELLGDSQYHFVDNIINRVPRDQQMIYISATN 18- 0 GT GR+FEL+KLKKIKMM++NTIVLDE+DELLGDSQY FV I + VPRD QM+Y+SATN Sbjct: 132 GTPGRIFELIKLKKIKMMSVNTIVLDEYDELLGDSQYDFVQKISHYVPRDHQMVYMSATN 19- 1 Query: 181 KLDNSKLADNTITIDLSNQKLDTIKHYYITVDKRERTDLLRKFSNIPDFRGLVFFNSLSD 24- 0 K+D + LA NT IDLS Q D I+H+Y+ VDKRERTDLLRKF+NIP FR LVFFNSLSD Sbjct: 192 KVDQTSLAPNTFCIDLSEQTNDAIQHFYLMVDKRERTDLLRKFTNIPHFRALVFFNSLSD 25- 1 Query: 241 LGACEERLQFNRASAVSLASDINIKFRKVILEKFKNHDISLLLGTDLVARGIDIDNLEYV 30- 0 LGA EERLQ+N A+AVSLASDIN+KFRK ILEKFK+H +SLLL TDLVARGIDIDNL+YV Sbjct: 252 LGATEERLQYNGAAAVSLASDINVKFRKTILEKFKSHQLSLLLATDLVARGIDIDNLDYV 31- 1 Query: 301 INFDIARDKETYTHRSGRTGRMGKEGCVITFVTHKEELKQLKKYATVTELVLHNQKLH 358 I+FD+ARDKE YTHR+GRTGRMGK G VITFV+H E+LK+LKK+A V+E+ L NQ+LH Sbjct: 312 IHFDVARDKENYTHRAGRTGRMGKSGIVITFVSHPEDLKKLKKFAKVSEISLKNQQLH 369 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1451 A DNA sequence (GBSx1537) was identified in S. agalactiae <SEQ ID 4455> which encodes the amino acid sequence <SEQ ID 4456>. Analysis of this protein sequence reveals the following: TABLE-US-04318 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.38 Transmembrane 15-31 (13-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1452 A DNA sequence (GBSx1538) was identified in S. agalactiae <SEQ ID 4457> which encodes the amino acid sequence <SEQ ID 4458>. This protein is predicted to be peptidoglycan GlcNAc deacetylase. Analysis of this protein sequence reveals the following: TABLE-US-04319 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.92 Transmembrane 4-20 (1-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.4567 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04320 >GP: CAB96552 GB: AJ251472 peptidoglycan GlcNAc deacetylase [Streptococcus pneumoniae] Identities = 133/431 (30%), Positives = 228/431 (52%), Gaps = 20/431 (4%) Query: 5 IIGIFSLIIIAILAWQGFSFLKHK--EIKLQQAVVEKEIRIAEKTVEVVKRQKTERVLFL 62 +IGI ++ I + + F + K E K++ EK+ +++E + RQ V+ Sbjct: 21 LIGILAISICLLGGFIAFKIYQQKSFEQKIESLKKEKDDQLSEGNQKEHFRQGQAEVIAY 80 Query: 63 EPKGYDKSLSADILKWNQKSFEHKKFYDNQYIILRPQLADSNFANVKKLSIYQILYQKEK 122- P +K +S+ NQ + + DN Q +S V ++ + +Y Sbjct: 81 YPLQGEKVISSVRELINQDVKDKLESKDNLVFYYTEQ-EESGLKGVVNRNVTKQIYDLVA 139- Query: 123 GSMFQKSSRLLRTYLLDQNKKPFELDELLAHNISGFKAILENIAPGTQLK--EHDSNKEF 18- 0 + + L L ++ +PF LD+L + + +++ + + K E D +++ Sbjct: 140 FKIEETEKTSLGKVHLTEDGQPFTLDQLFSDASKAKEQLIKELTSFIEDKKIEQDQSEQI 19- 9 Query: 181 LKTGRVTD----GLDVKDGKLII---------NDLKLPLDKLYNVIDESYLKSSDLDLVS 22- 7 +K D D KD ++I+ ++ LP+ ++VI SYL D L Sbjct: 200 VKNFSDQDLSAWNFDYKDSQIILYPSPVVENLEEIALPVSAFFDVIQSSYLLEKDAALYQ 25- 9 Query: 228 NLKAKAPR--VALTFDDGPNEKTTPKALEILKRYNAKATFFVMGQSAVGHTDILQRMHAE 28- 5 + K + VALTFDDGPN TTP+ LE L +Y+ KATFFV+G++ G+ D+++R+ +E Sbjct: 260 SYFDKKHQKVVALTFDDGPNPATTPQVLETLAKYDIKATFFVLGKNVSGNEDLVKRIKSE 31- 9 Query: 286 GHEIGNHTWDHPNLTKLPAEKIKEEIHKTNDLIMKATGQKPVYLRPPYGATNATVKTVTG 34- 5 GH +GNH+W HP L++L ++ K++I T D++ K G +RPPYGA ++ Sbjct: 320 GHVVGNHSWSHPILSQLSLDEAKKQITDTEDVLTKVLGSSSKLMRPPYGAITDDIRNSLD 37- 9 Query: 346 LKEMLWSVDTEDWKNHNTQAMMTNIKKQLRPGGVILMHDIHQTTIDALPTIMDYLTTQGY 40- 5 L ++W VD+ DWK+ N +++T I+ Q+ G ++LMHDIH T++ALP +++YL QGY Sbjct: 380 LSFIMWDVDSLDWKSKNEASILTEIQHQVANGSIVLMHDIHSPTVNALPRVIEYLKNQGY 43- 9 Query: 406 YFVTVGELYST 416 FVT+ E+ +T Sbjct: 440 TFVTIPEMLNT 450 A related DNA sequence was identified in S. pyogenes <SEQ ID 4459> which encodes the amino acid sequence <SEQ ID 4460>. Analysis of this protein sequence reveals the following: TABLE-US-04321 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.58 Transmembrane 6-22 (1-27) ----- Final Results ----- bacterial membrane --- Certainty = 0.6031 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04322 !GB: AJ251472 peptidoglycan GlcNAc deacetylase [Strep... 239 4e-62 >GP: CAB96552 GB: AJ251472 peptidoglycan GlcNAc deacetylase [Streptococcus pneumoniae] Identities = 136/438 (31%), Positives = 230/438 (52%), Gaps = 23/438 (5%) Query: 3 KLNVILVGLLSILMLSLAI----VFINRWKLNEDSQRIVLAEKKKNTSDLVIKAVKHIKK 58 K +L+ L+ IL +S+ + + ++ Q+I +K+K+ +H ++ Sbjct: 13 KTRHVLLALIGILAISICLLGGFIAFKIYQQKSFEQKIESLKKEKDDQLSEGNQKEHFRQ 72 Query: 59 DQKDYYYFSPIK--QADDFFVDNLPVSLYKKKNSDKELILVRPKLQSSHLRSVNTLTISK 116- Q + + P++ + + + + K S L+ + + S L+ V ++K Sbjct: 73 GQAEVIAYYPLQGEKVISSVRELINQDVKDKLESKDNLVFYYTEQEESGLKGVVNRNVTK 132- Query: 117 IVYQKKFFHLAKKSEKVISTYHVTDDLKPFQVKDLVSGHL---ERIQEEVEKKYPDAGFN 17- 3 +Y F + + + + H+T+D +PF + L S E++ +E+ D Sbjct: 133 QIYDLVAFKIEETEKTSLGKVHLTEDGQPFTLDQLFSDASKAKEQLIKELTSFIEDKKIE 19- 2 Query: 174 SDKYNGLKESNS---LLSDGFEVKSGNLIFD--------KKLTIPLTTLFDVINPDFLAN 22- 2 D+ + ++ S L + F+ K +I +++ +P++ FDVI +L Sbjct: 193 QDQSEQIVKNFSDQDLSAWNFDYKDSQIILYPSPVVENLEEIALPVSAFFDVIQSSYLLE 25- 2 Query: 223 SDRAAYDNYRTYKEQHPKKLVALTFDDGPDPTTTPQVLDILAKYQAKGTFFMIGSKVVNN 28- 2 D A Y +Y K Q K+VALTFDDGP+P TTPQVL+ LAKY K TFF++G V N Sbjct: 253 KDAALYQSYFDKKHQ---KVVALTFDDGPNPATTPQVLETLAKYDIKATFFVLGKNVSGN 30- 9 Query: 283 ENLTKRVSDAGHEIANHTWDHPNLTNLSVSEIQHQVNMTNQAIEKACGKKPRYLRPPYGA 34- 2 E+L KR+ GH + NH+W HP L+ LS+ E + Q+ T + K G + +RPPYGA Sbjct: 310 EDLVKRIKSEGHVVGNHSWSHPILSQLSLDEAKKQITDTEDVLTKVLGSSSKLMRPPYGA 36- 9 Query: 343 TNATVQQSSGLTQMLWTVDTRDWENHSTDGIMTNVKNQLQPGGVVLMHDIHQTTINALPT 40- 2 ++ S L+ ++W VD+ DW++ + I+T +++Q+ G +VLMHDIH T+NALP Sbjct: 370 ITDDIRNSLDLSFIMWDVDSLDWKSKNEASILTEIQHQVANGSIVLMHDIHSPTVNALPR 42- 9 Query: 403 VMEYLKAEGYECVTVSEL 420 V+EYLK +GY VT+ E+ Sbjct: 430 VIEYLKNQGYTFVTIPEM 447 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04323 Identities = 169/420 (40%), Positives = 259/420 (61%), Gaps = 12/420 (2%) Query: 4 LIIGIFSLIIIAILAWQGFSFLKHKEIKLQQAVVEKEIRIAEKTVEVVKRQKTER--VLF 61 +++G+ S+++++ LA + K E + + EK+ ++ ++ VK K ++ + Sbjct: 7 ILVGLLSILMLS-LAIVFINRWKLNEDSQRIVLAEKKKNTSDLVIKAVKHIKKDQKDYYY 65 Query: 62 LEPKGYDKSLSADILKWNQKSFEHKKFYDNQYIILRPQLADSNFANVKKLSIYQILYQKE 121- P D L S KK D + I++RP+L S+ +V L+I +I+YQK+ Sbjct: 66 FSPIKQADDFFVDNLP---VSLYKKKNSDKELILVRPKLQSSHLRSVNTLTISKIVYQKK 122- Query: 122 KGSMFQKSSRLLRTYLLDQNKKPFELDELLAHNISGFKAILENIAPGTQLKEHDSNKEFL 18- 1 + +KS +++ TY + + KPF++ +L++ ++ + +E P N Sbjct: 123 FFHLAKKSEKVISTYHVTDDLKPFQVKDLVSGHLERIQEEVEKKYPDAGFNSDKYNGLKE 18- 2 Query: 182 KTGRVTDGLDVKDGKLIIND-LKLPLDKLYNVIDESYLKSSDLDLVSNL---KAKAPR-- 23- 5 ++DG +VK G LI + L +PL L++VI+ +L +SD N K + P+ Sbjct: 183 SNSLLSDGFEVKSGNLIFDKKLTIPLTTLFDVINPDFLANSDRAAYDNYRTYKEQHPKKL 24- 2 Query: 236 VALTFDDGPNEKTTPKALEILKRYNAKATFFVMGQSAVGHTDILQRMHAEGHEIGNHTWD 29- 5 VALTFDDGP+ TTP+ L+IL +Y AK TFF++G V + ++ +R+ GHEI NHTWD Sbjct: 243 VALTFDDGPDPTTTPQVLDILAKYQAKGTFFMIGSKVVNNENLTKRVSDAGHEIANHTWD 30- 2 Query: 296 HPNLTKLPAEKIKEEIHKTNDLIMKATGQKPVYLRPPYGATNATVKTVTGLKEMLWSVDT 35- 5 HPNLT L +I+ +++ TN I KA G+KP YLRPPYGATNATV+ +GL +MLW+VDT Sbjct: 303 HPNLTNLSVSEIQHQVNMTNQAIEKACGKKPRYLRPPYGATNATVQQSSGLTQMLWTVDT 36- 2 Query: 356 EDWKNHNTQAMMTNIKKQLRPGGVILMHDIHQTTIDALPTIMDYLTTQGYYFVTVGELYS 41- 5 DW+NH+T +MTN+K QL+PGGV+LMHDIHQTTI+ALPT+M+YL +GY VTV ELY+ Sbjct: 363 RDWENHSTDGIMTNVKNQLQPGGVVLMHDIHQTTINALPTVMEYLKAEGYECVTVSELYA 42- 2 GBS281d was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 152 (lane 8-10; MW 71.5 kDa) and in FIG. 187 (lane 10; MW 71 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 152 (lane 12; MW 46.5 kDa) and in FIG. 183 (lane 2; MW 46 kDa). Purified GBS281d-GST is shown in lane 6 of FIG. 237. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1453 A DNA sequence (GBSx1539) was identified in S. agalactiae <SEQ ID 4461> which encodes the amino acid sequence <SEQ ID 4462>. Analysis of this protein sequence reveals the following: TABLE-US-04324 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2488 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 4463> which encodes the amino acid sequence <SEQ ID 4464>. Analysis of this protein sequence reveals the following: TABLE-US-04325 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2799 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04326 Identities = 311/475 (65%), Positives = 389/475 (81%) Query: 1 MTKEYQNYVNGEWKSSVNQIEILSPIDDSSLGFVPAMTREEVDHAMKAGREALPAWAALT 60 + K+Y+N VNGEWK S N+I I +P LG VPAMT+ EVD + ++AL W AL+ Sbjct: 1 LAKQYKNLVNGEWKLSENEITIYAPATGEELGSVPAMTQAEVDAVYASAKKALSDWRALS 60 Query: 61 VYERAQYLHKAADIIERDKEEIATVLAKEISKAYNASVTEVVRTADLIRYAAEEGIRLST 120- ERA YLHKAADI+ RD E+I +L+KE++K + A+V+EV+RTA++I YAAEEG+R+ Sbjct: 61 YVERAAYLHKAADILVRDAEKIGAILSKEVAKGHKAAVSEVIRTAEIINYAAEEGLRMEG 120- Query: 121 SADEGGKMDASTGHKLAVIRRQPVGIVLAIAPYNYPVNLSGSKIAPALIGGNVVMFKPPT 18- 0 EGG +A++ K+A++RR+PVG+VLAI+P+NYPVNL+GSKIAPALI GNVV KPPT Sbjct: 121 EVLEGGSFEAASKKKIAIVRREPVGLVLAISPFNYPVNLAGSKIAPALIAGNVVALKPPT 18- 0 Query: 181 QGSVSGLVLAKAFAEAGLPAGVFNTITGRGSEIGDYIVEHEEVNFINFTGSTPVGKRIGK 24- 0 QGS+SGL+LA+AFAEAG+PAGVFNTITGRGS IGDYIVEHE V+FINFTGSTP+G+ IGK Sbjct: 181 QGSISGLLLAEAFAEAGIPAGVFNTITGRGSVIGDYIVEHEAVSFINFTGSTPIGEGIGK 24- 0 Query: 241 LAGMRPIMLELGGKDAGVVLADADLDNAAKQIVAGAYDYSGQRCTAIKRVLVVEEVADEL 30- 0 LAGMRPIMLELGGKD+ +VL DADL AAK IVAGA+ YSGQRCTA+KRVLV+++VAD+L Sbjct: 241 LAGMRPIMLELGGKDSAIVLEDADLALAAKNIVAGAFGYSGQRCTAVKRVLVMDKVADQL 30- 0 Query: 301 AEKISENVAKLSVGDPFDNATVTPVIDDNSADFIESLVVDARQKGAKELNEFKRDGRLLT 36- 0 A +I V KLSVG P D+A +TP+ID ++ADF+E L+ DA KGA L F R+G L++ Sbjct: 301 AAEIKTLVEKLSVGMPEDDADITPLIDTSAADFVEGLIKDATDKGATALTAFNREGNLIS 36- 0 Query: 361 PGLFDHVTLDMKLAWEEPFGPILPIIRVKDAEEAVAIANKSDFGLQSSVFTRDFQKAFDI 42- 0 P LFDHVT DM+LAWEEPFGP+LPIIRV EEA+ I+N+S++GLQ+S+FT +F KAF I Sbjct: 361 PVLFDHVTTDMRLAWEEPFGPVLPIIRVTTVEEAIKISNESEYGLQASIFTTNFPKAFGI 42- 0 Query: 421 ANKLEVGTVHINNKTGRGPDNFPFLGLKGSGAGVQGIRYSIEAMTNVKSIVFDMK 475 A +LEVGTVH+NNKT RG DNFPFLG K SGAGVQG++YSIEAMT VKS+VFD++ Sbjct: 421 AEQLEVGTVHLNNKTQRGTDNFPFLGAKKSGAGVQGVKYSIEAMTTVKSVVFDIQ 475 A related GBS gene <SEQ ID 8815> and protein <SEQ ID 8816> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04327 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: -15.11 GvH: Signal Score (-7.5): 0.17 Possible site: 57 >>> Seems to have no N-terminal signal sequence ALOM program count: 0 value: 1.22 threshold: 0.0 PERIPHERAL Likelihood = 1.22 187 modified ALOM score: -0.74 *** Reasoning Step: 3 ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2488 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00094## SEQ ID 8816 (GBS127) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 29 (lane 10; MW 55.9 kDa). GBS127-His was purified as shown in FIG. 200, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1454 A DNA sequence (GBSx1540) was identified in S. agalactiae <SEQ ID 4465> which encodes the amino acid sequence <SEQ ID 4466>. Analysis of this protein sequence reveals the following: TABLE-US-04328 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 427-443 (427-443) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04329 >GP: BAA78049 GB: AB027569 phosphoenolpyruvate-protein phosphotransferase [Streptococcus bovis] Identities = 534/577 (92%), Positives = 559/577 (96%) Query: 1 MTEMLKGIAASDGVAVAKAYLLVQPDLSFETVTVEDTNAEEARLDVALQASQDELSVIRE 60 MTEMLKGIAASDGVAVAKAYLLVQPDLSFETVTVEDT+AEEARLD AL+ASQDELS+IRE Sbjct: 1 MTEMLKGIAASDGVAVAKAYLLVQPDLSFETVTVEDTSAEEARLDAALKASQDELSIIRE 60 Query: 61 KAVESLGEEAAAVFDAHLMVLSDPEMINQIKETIRAKQVNAETGLKEVTDMFITIFEGME 120- KAVE+LGEEAAAVFDAHLMVL+DPEMI+QIKETIRAKQ NAE GLKEVTDMFITIFEGME Sbjct: 61 KAVETLGEEAAAVFDAHLMVLADPEMISQIKETIRAKQTNAEAGLKEVTDMFITIFEGME 120- Query: 121 DNPYMQERAADIRDVAKRVLAHLLGVKLPNPATINEESIVIAHDLTPSDTAQLNKQFVKA 18- 0 DNPYMQERAADIRDVAKRVLAHLLG KLPNPATI+EESIVIAHDLTPSDTAQLNKQFVKA Sbjct: 121 DNPYMQERAADIRDVAKRVLAHLLGAKLPNPATIDEESIVIAHDLTPSDTAQLNKQFVKA 18- 0 Query: 181 FVTNIGGRTSHSAIMARTLEIAAVLGTNDITERVQDGQLIAVNGITGEVIIEPTEAQISA 24- 0 FVTNIGGRTSHSAIMARTLEIAAVLGTNDIT RV+DG ++AVNGITGEVII PT+ Q++ Sbjct: 181 FVTNIGGRTSHSAIMARTLEIAAVLGTNDITSRVKDGDIVAVNGITGEVIINPTDEQVAE 24- 0 Query: 241 FKAAGEAYAKQKAEWALLKDAQTVTADGKHFELAANIGTPKDVEGVNENGAEAVGLYRTE 30- 0 FKAAGEAYAKQKAEWALLKDA+TVTADGKHFELAANIGTPKDVEGVN NGAEAVGLYRTE Sbjct: 241 FKAAGEAYAKQKAEWALLKDAKTVTADGKHFELAANIGTPKDVEGVNANGAEAVGLYRTE 30- 0 Query: 301 FLYMDSQDFPTEDEQYEAYKAVLEGMNGKPVVVRTMDIGGDKELPYFDLPKEMNPFLGFR 36- 0 FLYMDSQDFPTEDEQYEAYKAVLEGMNGKPVVVRTMDIGGDKELPY DLPKEMNPFLGFR Sbjct: 301 FLYMDSQDFPTEDEQYEAYKAVLEGMNGKPVVVRTMDIGGDKELPYLDLPKEMNPFLGFR 36- 0 Query: 361 ALRISISETGDAMFRTQIRALLRASVHGQLRIMFPMVALLKEFRAAKAIFEEEKANLLAD 42- 0 ALRISISETG+AMFRTQIRALLRASVHGQLRIMFPMVALLKEFRAAKAIF+EEKANL A+ Sbjct: 361 ALRISISETGNAMFRTQIRALLRASVHGQLRIMFPMVALLKEFRAAKAIFDEEKANLKAE 42- 0 Query: 421 GVAVAEGIEVGIMIEIPAAAMLADQFAKEVDFFSIGTNDLIQYTMAADRMNEQVSYLYQP 48- 0 GVAV++ I+VGIMIEIPAAAMLADQFAKEVDFFSIGTNDLIQYTMAADRMNEQVSYLYQP Sbjct: 421 GVAVSDDIQVGIMIEIPAAAMLADQFAKEVDFFSIGTNDLIQYTMAADRMNEQVSYLYQP 48- 0 Query: 481 YNPSILRLINNVIKAAHAEGKWAGMCGEMAGDQTAVPLLVGMGLDEFSMSATSVLRTRSL 54- 0 YNPSILRLINNVIKAAHAEGKW GMCGEMAGDQ AVPLLV MGLDEFSMSATS+LRTRSL Sbjct: 481 YNPSILRLINNVIKAAHAEGKWVGMCGEMAGDQKAVPLLVEMGLDEFSMSATSILRTRSL 54- 0 Query: 541 MKKLDTAKMEEYANRALSECSTMEEVIELQKEYVDFD 577 MKKLDTAKM+EYANRAL+ECSTMEEV+EL KEYV+ D Sbjct: 541 MKKLDTAKMQEYANRALTECSTMEEVLELSKEYVNVD 577 A related DNA sequence was identified in S. pyogenes <SEQ ID 4467> which encodes the amino acid sequence <SEQ ID 4468>. Analysis of this protein sequence reveals the following:

TABLE-US-04330 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0875(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04331 Identities = 540/577 (93%), Positives = 561/577 (96%) Query: 1 MTEMLKGIAASDGVAVAKAYLLVQPDLSFETVTVEDTNAEEARLDVALQASQDELSVIRE 60 MTEMLKGIAASDGVAVAKAYLLVQPDLSFETVTV DTNAEEARLDVALQA+QDELSVIRE Sbjct: 1 MTEMLKGIAASDGVAVAKAYLLVQPDLSFETVTVADTNAEEARLDVALQAAQDELSVIRE 60 Query: 61 KAVESLGEEAAAVFDAHLMVLSDPEMINQIKETIRAKQVNAETGLKEVTDMFITIFEGME 120- AVESLGEEAAAVFDAHLMVL+DPEMI+Q+KETIRAKQ NAETGLKEVTDMFITIFEGME Sbjct: 61 NAVESLGEEAAAVFDAHLMVLADPEMISQVKETIRAKQTNAETGLKEVTDMFITIFEGME 120- Query: 121 DNPYMQERAADIRDVAKRVLAHLLGVKLPNPATINEESIVIAHDLTPSDTAQLNKQFVKA 18- 0 DNPYMQERAADIRDVAKRVLAHLLGVKLPNPATINEESIVIAHDLTPSDTAQLNKQFVKA Sbjct: 121 DNPYMQERAADIRDVAKRVLAHLLGVKLPNPATINEESIVIAHDLTPSDTAQLNKQFVKA 18- 0 Query: 181 FVTNIGGRTSHSAIMARTLEIAAVLGTNDITERVQDGQLIAVNGITGEVIIEPTEAQISA 24- 0 FVTNIGGRTSHSAIMARTLEIAAVLGTNDIT+RV+DG +IAVNGITGEVII+P+E Q+ A Sbjct: 181 FVTNIGGRTSHSAIMARTLEIAAVLGTNDITKRVKDGDVIAVNGITGEVIIDPSEDQVLA 24- 0 Query: 241 FKAAGEAYAKQKAEWALLKDAQTVTADGKHFELAANIGTPKDVEGVNENGAEAVGLYRTE 30- 0 FK AG AYAKQKAEW+LLKDA T TADGKHFELAANIGTPKDVEGVN+NGAEAVGLYRTE Sbjct: 241 FKEAGAAYAKQKAEWSLLKDAHTETADGKHFELAANIGTPKDVEGVNDNGAEAVGLYRTE 30- 0 Query: 301 FLYMDSQDFPTEDEQYEAYKAVLEGMNGKPVVVRTMDIGGDKELPYFDLPKEMNPFLGFR 36- 0 FLYMDSQDFPTEDEQYEAYKAVLEGMNGKPVVVRTMDIGGDKELPYFDLPKEMNPFLGFR Sbjct: 301 FLYMDSQDFPTEDEQYEAYKAVLEGMNGKPVVVRTMDIGGDKELPYFDLPKEMNPFLGFR 36- 0 Query: 361 ALRISISETGDAMFRTQIRALLRASVHGQLRIMFPMVALLKEFRAAKAIFEEEKANLLAD 42- 0 ALRISISETGDAMFRTQ+RALLRASVHGQLRIMFPMVALLKEFRAAKA+F+EEKANLLA+ Sbjct: 361 ALRISISETGDAMFRTQMRALLRASVHGQLRIMFPMVALLKEFRAAKAVFDEEKANLLAE 42- 0 Query: 421 GVAVAEGIEVGIMIEIPAAAMLADQFAKEVDFFSIGTNDLIQYTMAADRMNEQVSYLYQP 48- 0 GVAVA+ I+VGIMIEIPAAAMLADQFAKEVDFFSIGTNDLIQYTMAADRMNEQVSYLYQP Sbjct: 421 GVAVADDIQVGIMIEIPAAAMLADQFAKEVDFFSIGTNDLIQYTMAADRMNEQVSYLYQP 48- 0 Query: 481 YNPSILRLINNVIKAAHAEGKWAGMCGEMAGDQTAVPLLVGMGLDEFSMSATSVLRTRSL 54- 0 YNPSILRLINNVIKAAHAEGKWAGMCGEMAGDQ AVPLLVGMGLDEFSMSATSVLRTRSL Sbjct: 481 YNPSILRLINNVIKAAHAEGKWAGMCGEMAGDQQAVPLLVGMGLDEFSMSATSVLRTRSL 54- 0 Query: 541 MKKLDTAKMEEYANRALSECSTMEEVIELQKEYVDFD 577 MKKLD+AKMEEYANRAL+ECST EEV+EL KEYV D Sbjct: 541 MKKLDSAKMEEYANRALTECSTAEEVLELSKEYVSED 577 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1455 A DNA sequence (GBSx1541) was identified in S. agalactiae <SEQ ID 4469> which encodes the amino acid sequence <SEQ ID 4470>. Analysis of this protein sequence reveals the following: TABLE-US-04332 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1421(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to a protein from S. bovis: TABLE-US-04333 >GP: BAA78048 GB: AB027569 histidine containing protein [Streptococcus bovis] Identities = 86/87 (98%), Positives = 87/87 (99%) Query: 1 MASKDFHIVAETGIHARPATLLVQTASKFASDITLDYKGKAVNLKSIMGVMSLGVGQGAD 60 MASKDFHIVAETGIHARPATLLVQTASKFASDITLDYKGKAVNLKSIMGVMSLGVGQGAD Sbjct: 1 MASKDFHIVAETGIHARPATLLVQTASKFASDITLDYKGKAVNLKSIMGVMSLGVGQGAD 60 Query: 61 VTISAEGADADDAIAAIEETMTKEGLA 87 VTISAEGADADDA+AAIEETMTKEGLA Sbjct: 61 VTISAEGADADDALAAIEETMTKEGLA 87 A related DNA sequence was identified in S. pyogenes <SEQ ID 4471> which encodes the amino acid sequence <SEQ ID 4472>. Analysis of this protein sequence reveals the following: TABLE-US-04334 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1421(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04335 Identities = 86/87 (98%), Positives = 87/87 (99%) Query: 1 MASKDFHIVAETGIHARPATLLVQTASKFASDITLDYKGKAVNLKSIMGVMSLGVGQGAD 60 MASKDFHIVAETGIHARPATLLVQTASKFASDITLDYKGKAVNLKSIMGVMSLGVGQGAD Sbjct: 1 MASKDFHIVAETGIHARPATLLVQTASKFASDITLDYKGKAVNLKSIMGVMSLGVGQGAD 60 Query: 61 VTISAEGADADDAIAAIEETMTKEGLA 87 VTISAEGADA+DAIAAIEETMTKEGLA Sbjct: 61 VTISAEGADAEDAIAAIEETMTKEGLA 87 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1456 A DNA sequence (GBSx1542) was identified in S. agalactiae <SEQ ID 4473> which encodes the amino acid sequence <SEQ ID 4474>. This protein is predicted to be glutaredoxin-like protein nrdh (b2673). Analysis of this protein sequence reveals the following: TABLE-US-04336 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4532(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04337 >GP: CAA63372 GB: X92690 glutaredoxin-like protein [Lactococcus lactis] Identities = 42/70 (60%), Positives = 53/70 (75%) Query: 4 ITVFSKNNCMQCKMTKKFLDQHGADFEEINIDEKPEKIEYVKNLGFSAAPVIEAGNVVFS 63 +TV+SKNNCMQCKM KK+L +H F EINIDE+PE +E V +GF AAPVI + FS Sbjct: 2 VTVYSKNNCMQCKMVKKWLSEHEIAFNEINIDEQPEFVEKVIEMGFRAAPVITKDDFAFS 61 Query: 64 GFQPSKLKEL 73 GF+PS+L +L Sbjct: 62 GFRPSELAKL 71 A related DNA sequence was identified in S. pyogenes <SEQ ID 4475> which encodes the amino acid sequence <SEQ ID 4476>. Analysis of this protein sequence reveals the following: TABLE-US-04338 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4606(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04339 Identities = 56/71 (78%), Positives = 68/71 (94%) Query: 4 ITVFSKNNCMQCKMTKKFLDQHGADFEEINIDEKPEKIEYVKNLGFSAAPVIEAGNVVFS 63 ITV+SKNNCMQCKMTKKFL+QHG +F+EINIDE PEK++YVK+LGF++APVIEA N+VFS Sbjct: 13 ITVYSKNNCMQCKMTKKFLEQHGVNFQEINIDEHPEKVDYVKSLGFTSAPVIEADNLVFS 72 Query: 64 GFQPSKLKELV 74 GFQP+KLKEL+ Sbjct: 73 GFQPAKLKELI 83 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1457 A DNA sequence (GBSx1543) was identified in S. agalactiae <SEQ ID 4477> which encodes the amino acid sequence <SEQ ID 4478>. This protein is predicted to be ribonucleotide reductase subunit R1E (nrdE). Analysis of this protein sequence reveals the following: TABLE-US-04340 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3676(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04341 >GP: AAD41036 GB: AF112535 ribonucleotide reductase alpha-chain [Corynebacterium glutamicum] Identities = 366/701 (52%), Positives = 488/701 (69%), Gaps = 19/701 (2%) Query: 23 NGQIPLHKDKEALTAFFKENVQPNSKAFDSITDKIAYLLKYDYLEEAFLNKYRPEFIEEL 82 - NG+I KD+EA +F ++V N+ F ++ +KI YL++ Y + L+KY +FI++L Sbjct: 22 NGKIQFEKDREAANQYFLQHVNQNTVFFHNLQEKIDYLVENKYYDPIVLDKYDFQFIKDL 81 Query: 83 STKLFDKKFRFKSFMAAYKFYQQYALKTNDGEYYLESIEDRVLFNALYFADGDEELATDL 142- + + KFRF+SF+ AYK+Y Y LKT DG YLE EDRV AL ADGD LA +L Sbjct: 82 FKRAYGFKFRFQSFLGAYKYYTSYTLKTFDGRRYLERFEDRVCMVALTLADGDRALAENL 141- Query: 143 ALEMISQRYQPATPSFLNAGRSRRGELVSCFLIQVTDDMNAIGRSINSALQLSRIGGGVG 20- 2 E++S R+QPATP+FLN+G+++RGE VSCFL+++ D+M +IGRSINSALQLS+ GGGV Sbjct: 142 VDEIMSGRFQPATPTFLNSGKAQRGEPVSCFLLRIEDNMESIGRSINSALQLSKRGGGVA 20- 1 Query: 203 ISLSNLREAGAPIKGFAGAASGVVPVMKLFEDSFSYSNQLGQRQGAGVVYLDVFHPDIIS 26- 2 + LSNLREAGAPIK +SGV+PVMKL ED+FSY+NQLG RQGAG VYL+ HPDI+S Sbjct: 202 LLLSNLREAGAPIKKIENQSSGVIPVMKLLEDAFSYANQLGARQGAGAVYLNAHHPDILS 26- 1 Query: 263 FLSTKKENADEKVRVKTLSLGITVPDKFYELARNNQEMYLFSPYSIEREYGVPFSYIDIT 32- 2 FL TK+ENADEK+R+KTLSLG+ +PD +ELA+ N +MYLFSPY +ER YG PF+ + IT Sbjct: 262 FLDTKRENADEKIRIKTLSLGVVIPDITFELAKRNDDMYLFSPYDVERIYGKPFADVSIT 32- 1 Query: 323 EKYDELVANPNITKTKINARDLETEISKLQQESGYPYIINIDTANRTNPVDGKIIMSNLC 38- 2 E YDE+V + I KTKINAR ++++Q ESGYPYI+ DT N +NP++G+I SNLC Sbjct: 322 EHYDEMVDDDRIRKTKINARQFFQTLAEIQFESGYPYIMYEDTVNASNPIEGRITHSNLC 38- 1 Query: 383 SEILQVQKPSLINDAQEYLEMGTDISCNLGSTNVLNMMTSPDFGKSIKTMTRALTFVTDS 44- 2 SEILQV PS ND Y E+G DISCNLGS NV M SP+F K+I+T R LT V++ Sbjct: 382 SEILQVSTPSEFNDDLTYAEVGEDISCNLGSLNVAMAMDSPNFEKTIETAIRGLTAVSEQ 44- 1 Query: 443 SNIEAVPTIKNGNAQAHTFGLGAMGLHSYLAKNHIEYGSPESIEFTDIYFMLMNYWTLVE 50- 2 ++I++VP+I+ GN AH GLG M LH Y + H+ YGS E+++FT+ YF + Y L Sbjct: 442 TSIDSVPSIRKGNEAAHAIGLGQMNLHGYFGREHMHYGSEEALDFTNAYFAAVLYQCLRA 50- 1 Query: 503 SNNIARERQTTFVGFEKSKYADGTYFDKYVSGKFVPQSDKVKSLFA--NHFIPEAKDWEN 56- 0 SN IA ER F FE SKYA G YFD + + F P+SDKVK LFA N P +DW Sbjct: 502 SNKIATERGERFKNFENSKYATGEYFDDFDANDFAPKSDKVKELFAKSNIHTPTVEDWAA 56- 1 Query: 561 LRYAVMKDGLYHQNRLAVAPNGSISYINDCSASIHPITQRIEERQEKKIGKIYYPANGLA 62- 0 L+ VM+ GL+++N AV P GSISYIN+ ++SIHPI +IE R+E KIG++YYPA + Sbjct: 562 LKADVMEHGLFNRNLQAVPPTGSISYINNSTSSIHPIASKIEIRKEGKIGRVYYPAPHMD 62- 1 Query: 621 TDTIPYYTSAYDMDMRKVIDVYAAATEHVDQGLSMTLFLRSELPKELYEWKTESKQTTRD 68- 0 D + Y+ AY++ K+ID YA AT++VDQGLS+TLF + TTRD Sbjct: 622 NDNLEYFEDAYEIGYEKIIDTYAVATKYVDQGLSLTLFFK-------------DTATTRD 66- 8 Query: 681 LSILRNYAFNKGVKSIYYI--RTFTDDGSEVGANQCESCVI 719 ++ + YA+ KG+K++YYI R +G+EV + C SC++ Sbjct: 669 INRAQIYAWRKGIKTLYYIRLRQVALEGTEV--DGCVSCML 707 A related DNA sequence was identified in S. pyogenes <SEQ ID 4479> which encodes the amino acid sequence <SEQ ID 4480>. Analysis of this protein sequence reveals the following: TABLE-US-04342 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4241(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04343 Identities = 628/719 (87%), Positives = 682/719 (94%) Query: 1 MSLKNIGDVSYFRLNNEINRPVNGQIPLHKDKEALTAFFKENVQPNSKAFDSITDKIAYL 60 MSLK++GD+SYFRLNNEINRPVNG+IPLHKDKEAL AF ENV PN+ +F SIT+KI YL Sbjct: 1 MSLKDLGDISYFRLNNEINRPVNGKIPLHKDKEALKAFSAENVLPNTMSFTSITEKIEYL 60 Query: 61 LKYDYLEEAFLNKYRPEFIEELSTKLFDKKFRFKSFMAAYKFYQQYALKTNDGEYYLESI 120- + DY+E AF+ KYRPEFI EL + + + FRFKSFMAAYKFYQQYALKTNDGE+YLE++ Sbjct: 61 ISNDYIESAFIQKYRPEFITELDSIIKSENFRFKSFMAAYKFYQQYALKTNDGEHYLENL 120- Query: 121 EDRVLFNALYFADGDEELATDLALEMISQRYQPATPSFLNAGRSRRGELVSCFLIQVTDD 18- 0 EDRVLFNALYFADG E+LA DLA+EMI+QRYQPATPSFLNAGRSRRGELVSCFLIQVTDD Sbjct: 121 EDRVLFNALYFADGQEDLAKDLAVEMINQRYQPATPSFLNAGRSRRGELVSCFLIQVTDD 18- 0 Query: 181 MNAIGRSINSALQLSRIGGGVGISLSNLREAGAPIKGFAGAASGVVPVMKLFEDSFSYSN 24- 0 MN+IGRSINSALQLSRIGGGVGI+LSNLREAGAPIKG+AGAASGVVPVMKLFEDSFSYSN Sbjct: 181 MNSIGRSINSALQLSRIGGGVGITLSNLREAGAPIKGYAGAASGVVPVMKLFEDSFSYSN 24- 0 Query: 241 QLGQRQGAGVVYLDVFHPDIISFLSTKKENADEKVRVKTLSLGITVPDKFYELARNNQEM 30- 0 QLGQRQGAGVVYL+VFHPDII+FLSTKKENADEKVRVKTLSLGITVPDKFYELAR N++M Sbjct: 241 QLGQRQGAGVVYLNVFHPDIIAFLSTKKENADEKVRVKTLSLGITVPDKFYELARKNEDM 30- 0 Query: 301 YLFSPYSIEREYGVPFSYIDITEKYDELVANPNITKTKINARDLETEISKLQQESGYPYI 36- 0 YLFSPY++E+EYG+PF+Y+DIT YDELVANP ITKTKI ARDLETEISKLQQESGYPYI Sbjct: 301 YLFSPYNVEKEYGIPFNYLDITNMYDELVANPKITKTKIKARDLETEISKLQQESGYPYI 36- 0 Query: 361 INIDTANRTNPVDGKIIMSNLCSEILQVQKPSLINDAQEYLEMGTDISCNLGSTNVLNMM 42- 0 INIDTAN+ NP+DGKIIMSNLCSEILQVQ PSLINDAQE++EMGTDISCNLGSTN+LNMM Sbjct: 361 INIDTANKANPIDGKIIMSNLCSEILQVQTPSLINDAQEFVEMGTDISCNLGSTNILNMM 42- 0 Query: 421 TSPDFGKSIKTMTRALTFVTDSSNIEAVPTIKNGNAQAHTFGLGAMGLHSYLAKNHIEYG 48- 0 TSPDFG+SIKTMTRALTFVTDSS+IEAVPTIK+GN+QAHTFGLGAMGLHSYLA++HIEYG Sbjct: 421 TSPDFGRSIKTMTRALTFVTDSSSIEAVPTIKHGNSQAHTFGLGAMGLHSYLAQHHIEYG 48- 0 Query: 481 SPESIEFTDIYFMLMNYWTLVESNNIARERQTTFVGFEKSKYADGTYFDKYVSGKFVPQS 54- 0 SPESIEFTDIYFML+NYWTLVESNNIARERQTTFVGFE SKYA+G+YFDKYV+G FVP+S Sbjct: 481 SPESIEFTDIYFMLLNYWTLVESNNIARERQTTFVGFENSKYANGSYFDKYVTGHFVPKS 54- 0 Query: 541 DKVKSLFANHFIPEAKDWENLRYAVMKDGLYHQNRLAVAPNGSISYINDCSASIHPITQR 60- 0 D VK LF +HFIP+A DWE LR AV KDGLYHQNRLAVAPNGSISYINDCSASIHPITQR Sbjct: 541 DLVKDLFKDHFIPQASDWEALRDAVQKDGLYHQNRLAVAPNGSISYINDCSASIHPITQR 60- 0 Query: 601 IEERQEKKIGKIYYPANGLATDTIPYYTSAYDMDMRKVIDVYAAATEHVDQGLSMTLFLR 66- 0 IEERQEKKIGKIYYPANGL+TDTIPYYTSAYDMDMRKVIDVYAAATEHVDQGLS+TLFLR Sbjct: 601 IEERQEKKIGKIYYPANGLSTDTIPYYTSAYDMDMRKVIDVYAAATEHVDQGLSLTLFLR 66- 0 Query: 661 SELPKELYEWKTESKQTTRDLSILRNYAFNKGVKSIYYIRTFTDDGSEVGANQCESCVI 719- SELP ELYEWKT+SKQTTRDLSILRNYAFNKG+KSIYYIRTFTDDG EVGANQCESCVI Sbjct: 661 SELPMELYEWKTQSKQTTRDLSILRNYAFNKGIKSIYYIRTFTDDGEEVGANQCESCVI 719- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1458 A DNA sequence (GBSx1544) was identified in S. agalactiae <SEQ ID 4481> which encodes the amino acid sequence <SEQ ID 4482>. This protein is predicted to be ribonucleotide reductase subunit R2F (nrdB). Analysis of this protein sequence reveals the following: TABLE-US-04344 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4583(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9753> which encodes amino acid sequence <SEQ ID 9754> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04345 >GP: AAC14561 GB: AF050168 ribonucleoside diphosphate reductase small subunit [Corynebacterium ammoniagenes] Identities = 166/313 (53%), Positives = 215/313 (68%), Gaps = 1/313 (0%) Query: 10 EAINWNEIEDVIDKSTWEKLTEQFWLDTRIPLSNDLDDWRKLSAQEKDLVGKVFGGLTLL 69 - +AINWN I D D W++LT FWL +IP+SND+ W K++ QE+ +VF GLTLL Sbjct: 17 KAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLL 76 Query: 70 DTMQSETGVEAIRADVRTPHEEAVLNNIQFMESVHAKSYSSIFSTLNTKSEIEEIFEWTN 129- DT+Q G ++ DV T HEE V NI FMESVHAKSYS+IF TL + +I E F W+ Sbjct: 77 DTIQGTVGAISLLPDVETMHEEGVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSE 136- Query: 130 NNEFLQEKARIINDIYANGNALQKKVASTYLETFLFYSGFFTPLYYLGNNKLANVAEIIK 18- 9 NE LQ KA+II Y + L+KKVAST LE+FLFYSGF+ P+Y KL N A+II+ Sbjct: 137 ENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIR 19- 6 Query: 190 LIIRDESVHGTYIGYKFQLGFNELPEDEQENFRDWMYDLLYQLYENEEKYTKTLYDGVGW 24- 9 LIIRDESVHG YIGYK+Q G +L E EQE ++ + +DL+Y LYENE +YT+ +YD +GW Sbjct: 197 LIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGW 25- 6 Query: 250 TEEVMTFLRYNANKALMNLGQDPLFPDTANDVNPIVMNGIS-TGTSNHDFFSQVGNGYLL 30- 8 TE+V FLRYNANKAL NLG + LFP V+P +++ +S NHDFFS G+ Y++ Sbjct: 257 TEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLSPNADENHDFFSGSGSSYVI 31- 6 Query: 309 GSVEAMHDDDYNY 321 G E DDD+++ Sbjct: 317 GKAEDTTDDDWDF 329 A related DNA sequence was identified in S. pyogenes <SEQ ID 4483> which encodes the amino acid sequence <SEQ ID 4484>. Analysis of this protein sequence reveals the following: TABLE-US-04346 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4583(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-04347 Identities = 315/319 (98%), Positives = 316/319 (98%) Query: 5 MTTYYEAINWNEIEDVIDKSTWEKLTEQFWLDTRIPLSNDLDDWRKLSAQEKDLVGKVFG 64 MTTYYEAINWNEIEDVIDKSTWEKLTEQFWLDTRIPLSNDLDDWRKLS QEKDLVGKVFG Sbjct: 1 MTTYYEAINWNEIEDVIDKSTWEKLTEQFWLDTRIPLSNDLDDWRKLSLQEKDLVGKVFG 60 Query: 65 GLTLLDTMQSETGVEAIRADVRTPHEEAVLNNIQFMESVHAKSYSSIFSTLNTKSEIEEI 124- GLTLLDTMQSETGVEAIRADVRTPHEEAVLNNIQFMESVHAKSYSSIFSTLNTK EIEEI Sbjct: 61 GLTLLDTMQSETGVEAIRADVRTPHEEAVLNNIQFMESVHAKSYSSIFSTLNTKKEIEEI 120- Query: 125 FEWTNNNEFLQEKARIINDIYANGNALQKKVASTYLETFLFYSGFFTPLYYLGNNKLANV 18- 4 FEWTNNNEFLQEKARIINDIYANG+ALQKKVASTYLETFLFYSGFFTPLYYLGNNKLANV Sbjct: 121 FEWTNNNEFLQEKARIINDIYANGDALQKKVASTYLETFLFYSGFFTPLYYLGNNKLANV 18- 0 Query: 185 AEIIKLIIRDESVHGTYIGYKFQLGFNELPEDEQENFRDWMYDLLYQLYENEEKYTKTLY 24- 4 AEIIKLIIRDESVHGTYIGYKFQLGFNELPEDEQENFRDWMYDLLYQLYENEEKYTKTLY Sbjct: 181 AEIIKLIIRDESVHGTYIGYKFQLGFNELPEDEQENFRDWMYDLLYQLYENEEKYTKTLY 24- 0 Query: 245 DGVGWTEEVMTFLRYNANKALMNLGQDPLFPDTANDVNPIVMNGISTGTSNHDFFSQVGN 30- 4 DGVGWTEEVMTFLRYNANKALMNLGQDPLFPDTANDVNPIVMNGISTGTSNHDFFSQVGN Sbjct: 241 DGVGWTEEVMTFLRYNANKALMNLGQDPLFPDTANDVNPIVMNGISTGTSNHDFFSQVGN 30- 0 Query: 305 GYLLGSVEAMHDDDYNYGL 323 GYLLGSVEAM DDDYNYGL Sbjct: 301 GYLLGSVEAMSDDDYNYGL 319 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1459 A DNA sequence (GBSx1545) was identified in S. agalactiae <SEQ ID 4485> which encodes the amino acid sequence <SEQ ID 4486>. Analysis of this protein sequence reveals the following: TABLE-US-04348 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.27 Transmembrane 50-66 (50-66) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1460 A DNA sequence (GBSx1546) was identified in S. agalactiae <SEQ ID 4487> which encodes the amino acid sequence <SEQ ID 4488>. Analysis of this protein sequence reveals the following: TABLE-US-04349 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.38 Transmembrane 176-192 (168-201) INTEGRAL Likelihood = -4.57 Transmembrane 25-41 (22-42) INTEGRAL Likelihood = -3.88 Transmembrane 94-110 (94-112) INTEGRAL Likelihood = -1.49 Transmembrane 70-86 (70-86) INTEGRAL Likelihood = -1.01 Transmembrane 128-144 (128-144) ----- Final Results ----- bacterial membrane --- Certainty = 0.6753(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9751> which encodes amino acid sequence <SEQ ID 9752> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04350 >GP: CAB15077 GB: Z99119 similar to hypothetical proteins [Bacillus subtilis] Identities = 55/184 (29%), Positives = 98/184 (52%), Gaps = 4/184 (2%) Query: 16 MSKNNNTTCLIETAIFAALAMALSMIP----DFASWFTPSFGAIPLILFALRRGTKYGLF 71 - M+++ LIE AI A A+ L ++ + S IP+ L + R G K GL Sbjct: 1 MNQSKQLVRLIEIAIMTAAAVILDIVSGMFLSMPQGGSVSIMMIPIFLISFRWGVKAGLT 60 Query: 72 AGLIWGLLHFVLSKVYYLSLSQVFIEYILAFISMGLAGVFSAKFKDALSSSSKTKALSLA 131- GL+ GL+ + ++ Q+ ++YI+AF ++G++G F++ + A S +K K + Sbjct: 61 TGLLTGLVQIAIGNLFAQHPVQLLLDYIVAFAAIGISGCFASSVRKAAVSKTKGKLIVSV 120- Query: 132 LSGAILATLVRYVWHYIAGVIFWASYAPKGMSATLYSLSVNGTAGLLTLFFVVISIIILV 19- 1 +S + +L+RY H I+G +F+ S+APKG +YSL+ N T + + I + +L Sbjct: 121 VSAVFIGSLLRYAAHVISGAVFFGSFAPKGTPVWIYSLTYNATYMVPSFIICAIVLCLLF 18- 0 Query: 192 ISYP 195 ++ P Sbjct: 181 MTAP 184 A related DNA sequence was identified in S. pyogenes <SEQ ID 4489> which encodes the amino acid sequence <SEQ ID 4490>. Analysis of this protein sequence reveals the following: TABLE-US-04351 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.34 Transmembrane 162-178 (156-183) INTEGRAL Likelihood = -9.34 Transmembrane 110-126 (107-130) INTEGRAL Likelihood = -1.22 Transmembrane 55-71 (55-71) ----- Final Results ----- bacterial membrane --- Certainty = 0.4736(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04352 >GP: CAB15077 GB: Z99119 similar to hypothetical proteins [Bacillus subtilis] Identities = 55/189 (29%), Positives = 100/189 (52%), Gaps = 10/189 (5%) Query: 1 MSPNTNVKYLIEAAIFAALAMTLSFIPDFAGWF--SPSYGAIALV-----IFSLRRGLKY 53 M+ + + LIE AI A A+ L + +G F P G+++++ + S R G+K Sbjct: 1 MNQSKQLVRLIEIAIMTAAAVILDIV---SGMFLSMPQGGSVSIMMIPIFLISFRWGVKA 57 Query: 54 GMLAGLIWGLLHFVLGKVYYLSMSQVFIEYILAFTSMGLAGSFSDSLIKTLRRQQTFFAV 113- G+ GL+ GL+ +G ++ Q+ ++YI+AF ++G++G F+ S+ K + + Sbjct: 58 GLTTGLLTGLVQIAIGNLFAQHPVQLLLDYIVAFAAIGISGCFASSVRKAAVSKTKGKLI 117- Query: 114 FLAIMASLLAVTVRYLWHFLAGIIFWGSYAPKGMSAVWYSFSVNGTAGVLTFLITCLALM 17- 3 + A + +RY H ++G +F+GS+APKG YS + N T V +F+I + L Sbjct: 118 VSVVSAVFIGSLLRYAAHVISGAVFFGSFAPKGTPVWIYSLTYNATYMVPSFIICAIVLC 17- 7 Query: 174 IALPIHPQL 182 + P+L Sbjct: 178 LLFMTAPRL 186 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04353 Identities = 116/186 (62%), Positives = 138/186 (73%) Query: 16 MSKNNNTTCLIETAIFAALAMALSMIPDFASWFTPSFGAIPLILFALRRGTKYGLFAGLI 75 - MS N N LIE AIFAALAM LS IPDFA WF+PS+GAI L++F+LRRG KYG+ AGLI Sbjct: 1 MSPNTNVKYLIEAAIFAALAMTLSFIPDFAGWFSPSYGAIALVIFSLRRGLKYGMLAGLI 60 Query: 76 WGLLHFVLSKVYYLSLSQVFIEYILAFISMGLAGVFSAKFKDALSSSSKTKALSLALSGA 135- WGLLHFVL KVYYLS+SQVFIEYILAF SMGLAG FS L A+ LA+ + Sbjct: 61 WGLLHFVLGKVYYLSMSQVFIEYILAFTSMGLAGSFSDSLIKTLRRQQTFFAVFLAIMAS 120- Query: 136 ILATLVRYVWHYIAGVIFWASYAPKGMSATLYSLSVNGTAGLLTLFFVVISIIILVISYP 19- 5 +LA VRY+WH++AG+IFW SYAPKGMSA YS SVNGTAG+LT ++++I + +P Sbjct: 121 LLAVTVRYLWHFLAGIIFWGSYAPKGMSAVWYSFSVNGTAGVLTFLITCLALMIALPIHP 18- 0 Query: 196 SFFLPK 201 F PK Sbjct: 181 QLFDPK 186 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1461 A DNA sequence (GBSx1547) was identified in S. agalactiae <SEQ ID 4491> which encodes the amino acid sequence <SEQ ID 4492>. Analysis of this protein sequence reveals the following: TABLE-US-04354 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.43 Transmembrane 206-222 (199-223) INTEGRAL Likelihood = -6.64 Transmembrane 24-40 (19-42) INTEGRAL Likelihood = -6.58 Transmembrane 61-77 (51-78) INTEGRAL Likelihood = -6.58 Transmembrane 134-150 (132-154) INTEGRAL Likelihood = -4.62 Transmembrane 226-242 (224-245) INTEGRAL Likelihood = -3.72 Transmembrane 107-123 (106-125) ----- Final Results ----- bacterial membrane --- Certainty = 0.3972(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9749> which encodes amino acid sequence <SEQ ID 9750> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4493> which encodes the amino acid sequence <SEQ ID 4494>. Analysis of this protein sequence reveals the following: TABLE-US-04355 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.46 Transmembrane 134-150 (131-159) INTEGRAL Likelihood = -7.59 Transmembrane 107-123 (103-128) INTEGRAL Likelihood = -7.48 Transmembrane 225-241 (213-248) INTEGRAL Likelihood = -7.22 Transmembrane 205-221 (199-224) INTEGRAL Likelihood = -3.56 Transmembrane 50-66 (50-73) INTEGRAL Likelihood = -1.28 Transmembrane 16-32 (16-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.5182(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-04356 Identities = 82/253 (32%), Positives = 149/253 (58%), Gaps = 5/253 (1%) Query: 6 IKQSDTTFVRIIKSLLIGGFIGAILGSVGALFIIF--GQDKYLSEI--NIVQYFLWVSRI 61 +K+ +F+R++K L+ G I+G + F+ + G+ +L+ + +++ + ++R+ Sbjct: 1 MKKKKNSFLRLLKMSLLSSLAGGIIGGMVGAFLGYHGGRLDHLTFLKDDVINLIILLNRL 60 Query: 62 VVIITALFSLIYLYQIQKYQKVFFNVDESQ-SEEIYRQINLRHSYGMTFVSISIVLSIVN 120- VV+ S ++L Q++K V+ ++E SE YRQ+N +H+Y M ++++ +LS+ N Sbjct: 61 VVVTDLTLSFVFLTQLKKETAVYNTIEEDDISENGYRQLNKKHAYTMLLIAVASILSMCN 120- Query: 121 TLFNYKLNIFDDSVTLVIPIYDLSLLFVLLGLHIYFLKVYRNIRGIKMTVAPTLKELKNN 18- 0 L L L IP+ D+ LL +++ +K Y IRG + P LKELK+N Sbjct: 121 VLLGLTLTNDSQHAMLAIPLLDILLLLMVIPFQALAMKRYNAIRGTDVPYFPNLKELKHN 18- 0 Query: 181 VLQLDEAELESNYKMCFDIVMNLSGFIFPTIYFVLFFISFVFQKVEIVAIIITTSIHIYI 24- 0 ++ LDEAEL++ +K F+ V++L+G I P++Y +LFF+ +VE+ AI++ I +Y+ Sbjct: 181 IMALDEAELQAYHKTSFESVLSLNGVIIPSLYVILFFVYLFTGQVELTAILVLVLIQLYL 24- 0 Query: 241 LIKSLKAARHFYR 253 L+KS R FYR Sbjct: 241 LVKSATMTRQFYR 253 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1462 A DNA sequence (GBSx1548) was identified in S. agalactiae <SEQ ID 4495> which encodes the amino acid sequence <SEQ ID 4496>. Analysis of this protein sequence reveals the following: TABLE-US-04357 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5172(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1463 A DNA sequence (GBSx1549) was identified in S. agalactiae <SEQ ID 4497> which encodes the amino acid sequence <SEQ ID 4498>. Analysis of this protein sequence reveals the following: TABLE-US-04358 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2059(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04359 >GP: AAC76650 GB: AE000440 UDP-D-glucose: (galactosyl)lipopolysaccharide glucosyltransferase [Escherichia coli K12] Identities = 70/256 (27%), Positives = 121/256 (46%), Gaps = 14/256 (5%) Query: 1 MNLLFSIDDMYVDHFKVMLYSLVRQTKNRKLEIYVLQKT----LLKRHTELIQYTQNLEV 56 +N+ + +D Y+D V + S+V ++ L+ Y++ ++ +L + Q Sbjct: 28 LNVAYGVDANYLDGVGVSITSIVLNNRHINLDFYIIADVYNDGFFQKIAKLAEQNQLRIT 87 Query: 57 GYHPIIVGTEVFAQAPTTDRYPDTIYYRLLAHKFLPETLDRILYLDADMLCLNDWSSLYD 116- Y + T+ P T + +Y+RL A + L TLDR+LYLDAD++C D S L Sbjct: 88 LYR---INTDKLQCLPCTQVWSRAMYFRLFAFQLLGLTLDRLLYLDADVVCKGDISQLLH 144- Query: 117 MELGDQLYAAASHNTDGKFLDYVNKLRLKNVELESSYFNTGVLLMNLPAIRKVVHQQTIL 17- 6 + L A A+ D + + RL + EL YFN+GV+ ++L + L Sbjct: 145 LGLNG---AVAAVVKDVEPMQEKAVSRLSDPELLGQYFNSGVVYLDLKKWADAKLTEKAL 20- 1 Query: 177 DYIMQNRGRLILPDQDILNGLYANLVKPIPDEIYNYDARYSLIYQLKSRNEWDLEWVINH 23- 6 +M PDQD++N L + +P E Y+ Y++ +LK + + + +I Sbjct: 202 SILMSKDNVYKYPDQDVMNVLLKGMTLFLPRE---YNTIYTIKSELKDKTHQNYKKLITE 25- 8 Query: 237 -TVFLHFAGRDKPWKK 251 T+ +H+ G KPW K Sbjct: 259 STLLIHYTGATKPWHK 274 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1464 A DNA sequence (GBSx1550) was identified in S. agalactiae <SEQ ID 4499> which encodes the amino acid sequence <SEQ ID 4500>. Analysis of this protein sequence reveals the following: TABLE-US-04360 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1406(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1465 A DNA sequence (GBSx1551) was identified in S. agalactiae <SEQ ID 4501> which encodes the amino acid sequence <SEQ ID 4502>. Analysis of this protein sequence reveals the following: TABLE-US-04361 Possible site: 54 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.72 Transmembrane 7-23 (1-28) INTEGRAL Likelihood = -4.30 Transmembrane 222-238 (216-238) INTEGRAL Likelihood = -3.66 Transmembrane 151-167 (140-170) INTEGRAL Likelihood = -3.50 Transmembrane 35-51 (34-58) INTEGRAL Likelihood = -3.35 Transmembrane 71-87 (69-88) INTEGRAL Likelihood = -3.29 Transmembrane 113-129 (113-132) INTEGRAL Likelihood = -2.81 Transmembrane 170-186 (168-190) INTEGRAL Likelihood = -2.71 Transmembrane 198-214 (197-217) ----- Final Results ----- bacterial membrane --- Certainty = 0.5288 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04362 >GP: BAB07774 GB: AP001520 unknown conserved protein [Bacillus halodurans] Identities = 84/242 (34%), Positives = 147/242 (60%), Gaps = 16/242 (6%) Query: 1 MVGLGTVINVILIIVGGFVGLFLKNFLKESLQKSLMQAMGVAVLFISISGVLEKMMLVEK 60 MV +GTV+N I++ +GL +KN + E ++ +LMQA+G+A++ + + KM L + Sbjct: 1 MVLIGTVVNGAAIVIAALIGLLVKN-IPERVKTTLMQAIGLAIVLLGV-----KMGLQTE 54 Query: 61 SHLISNHTNMMIITLALGTVLGELLSLDSYIDKFGNYLKQKTGSGNDIKFVEAFVTSTCT 120- LI +I +L +G V+GE+++L+ +D G +++ K G D AFVT+T Sbjct: 55 QFLI------VICSLVIGGVIGEMINLEKRLDHLGRWIESKVGGKKDGSIATAFVTTTLI 108- Query: 121 VCIGAMAVVGSIQDGIAADHSILFAKGMLDMIIIAIMTVSLGKGALFSALPVALLQGSLT 18- 0 +GAMAV+G++ G+ DHS+L K +LD + + T +LG G LFSA+PV L QGS+ Sbjct: 109 YVVGAMAVLGALDSGLRGDHSVLLTKALLDGFLAILFTSTLGIGVLFSAIPVVLYQGSIA 16- 8 Query: 181 IVAF----FMGSLLNPSSLDYLNLVGNMLIFCVGVNLLFNLNIKVINMLPAIILAILWGS 23- 6 + A ++ + L S + ++ G ++I +G+NLL +NI+V N+LP++++ + + Sbjct: 169 LFASQIDQYVPTALMDSFITEMSATGGVMIVAIGLNLLNVVNIRVANLLPSLVIVAVLVT 22- 8 Query: 237 FI 238 F+ Sbjct: 229 FV 230 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1466 A DNA sequence (GBSx1552) was identified in S. agalactiae <SEQ ID 4503> which encodes the amino acid sequence <SEQ ID 4504>. This protein is predicted to be alanyl-tRNA synthetase (alaS). Analysis of this protein sequence reveals the following: TABLE-US-04363 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.41 Transmembrane 805-821 (804-822) ----- Final Results ----- bacterial membrane --- Certainty = 0.2763 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04364 >GP: BAB04986 GB: AP001511 alanyl-tRNA synthetase [Bacillus halodurans] Identities = 482/885 (54%), Positives = 618/885 (69%), Gaps = 27/885 (3%) Query: 1 MKELSSAQIRQMWLDFWKSKGHSVEPSANLVPVNDPTLLWINSGVATLKKYFDGSVIPEN 60 MK L+SAQ+RQM+LDF+K KGH VEPSA+LVP +DP+LLWINSGVATLKKYFDG VIPEN Sbjct: 1 MKYLTSAQVRQMFLDFFKEKGHDVEPSASLVPHDDPSLLWINSGVATLKKYFDGRVIPEN 60 Query: 61 PRITNAQKSIRTNDIENVGKTARHHTMFEMLGNFSIGDYFRDEAIEWGFELLTSPEWFDF 120- PRITNAQKSIRTNDIENVGKTARHHT FEMLGNFSIGDYF++EAIEW +E LTS +W F Sbjct: 61 PRITNAQKSIRTNDIENVGKTARHHTFFEMLGNFSIGDYFKEEAIEWAWEFLTSEKWIGF 120- Query: 121 PKDKLYMTYYPDDKDSYNRWIA-CGVEPSHLVPIEDNFWEIGAGPSGPDTEIFFDRGEDF 17- 9 K+KL +T +P+D ++Y+ W G+ ++ +E NFW+IG GPSGP+TEIF+DRG ++ Sbjct: 121 DKEKLSVTVHPEDDEAYSYWKEKIGIPEERIIRLEGNFWDIGEGPSGPNTEIFYDRGPEY 18- 0 Query: 180 -----DPENIGLRLLAEDIENDRYIEIWNIVLSQFNADPAVPRSEYKELPNKNIDTGAGL 23- 4 DPE L ENDRY+E+WN+V SQFN +P Y LP KNIDTG GL Sbjct: 181 GDQPNDPE------LYPGGENDRYLEVWNLVFSQFNHNPD---GSYTPLPKKNIDTGMGL 23- 1 Query: 235 ERLAAVMQGAKTNFETDLFMPIIREVEKLSGKTYDPDGD-NMSFKVIADHIRALSFAIGD 29- 3 ER+ +V+Q TNFETDLFMPIIR EK+SG Y + ++SFKVIADHIR ++FAIGD Sbjct: 232 ERMVSVIQNVPTNFETDLFMPIIRATEKISGTEYGSHHEADVSFKVIADHIRTVTFAIGD 29- 1 Query: 294 GALPGNEGRGYVLRRLLRRAVMHGRRLGINETFLYKLVPTVGQIMESYYPEVLEKRDFIE 35- 3 GALP NEGRGYVLRRLLRRAV + +++GI+ F+Y+LVP VG IM +YPEV EK FI+ Sbjct: 292 GALPSNEGRGYVLRRLLRRAVRYAKQIGIDRPFMYELVPVVGDIMVDFYPEVKEKAAFIQ 35- 1 Query: 354 KIVKREEETFARTIDAGSGHLDSLLAQLKAEGKDTLEGKDIFKLYDTYGFPVELTEELAE 41- 3 K+VK EEE F T++ G L+ ++ + K+EG T+ G D+F+LYDTYGFPV+LTEE E Sbjct: 352 KVVKTEEERFHETLNEGLSILEKVIDKAKSEGASTISGSDVFRLYDTYGFPVDLTEEYVE 41- 1 Query: 414 DAGYKIDHEGFKSAMKEQQDRARAAVVKGGSMGMQNETLAGIVEESRF-EYDTYSLESSL 47- 2 + G ++D +GF++ M+ Q++RAR A + GSM +Q+E L I +S F Y S E+++ Sbjct: 412 EQGLQVDLDGFEAEMERQRERARTARQQAGSMQVQDEVLGQITVDSTFIGYKQLSTETTI 47- 1 Query: 473 SVIIADNERTEAVSEGQ-ALLVFAQTPFYAEMGGQVADHGVIKNDKGDTVAEVVDVQKAP 53- 1 I+ D + V GQ A ++ +TPFYAE GGQVAD G+I+ G V V DVQKAP Sbjct: 472 ETIVLDKTVADYVGAGQEAKVILKETPFYAESGGQVADKGIIRGANGFAV--VSDVQKAP 52- 9 Query: 532 NGQPLHTVNVL-ASLSVGTNYTLEINKERRLAVEKNHTATHLLHAALHNVIGEHATQAGS 59- 0 NGQ LHTV V +L V + + R + KNHTATHLLH AL +V+GEH QAGS Sbjct: 530 NGQHLHTVIVKEGTLQVNDQVQAIVEETERSGIVKNHTATHLLHRALKDVLGEHVNQAGS 58- 9 Query: 591 LNEEEFLRFDFTHFEAVSNEELRHIEQEVNEQIWNDLTITTTETDVETAKEMGAMALFGE 65- 0 L EE LRFDF+HF V++EE IE+ VNE+IW + + + ++ AK +GAMALFGE Sbjct: 590 LVSEERLRFDFSHFGQVTDEEKEKIERIVNEKIWQAIKVNISTKTLDEAKAIGAMALFGE 64- 9 Query: 651 KYGKVVRVVQIGNYSVELCGGTHLNNSSEIGLFKIVKEEGIGSGTRRIIAVTGRQAFEAY 71- 0 KYG +VRVV++G+YS+ELCGG H+ N+SEIGLFKIV E GIG+G RRI AVTG++AF Sbjct: 650 KYGDIVRVVEVGDYSIELCGGCHVTNTSEIGLFKIVSESGIGAGVRRIEAVTGKEAFLFM 70- 9 Query: 711 RNQEDALKEIAATVKAPQLKDAAAKVQALSDSLRDLQKENVELKEKAAAAAAGDVFKDIQ 77- 0 Q D LKE AATVKA +KD +V+AL +R+LQ+EN L K AG + ++Q Sbjct: 710 AKQLDLLKETAATVKAKNVKDVPVRVEALQQQIRELQRENESLNAKLGNMEAGSLVNEVQ 76- 9 Query: 771 EAKGVRFIASQVDVADAGALRTFADNWKQKDYSDVLVLVAAIGEKVNVLVASKTKDV--- 82- 7 + +GV +A +AD LR+ D KQ+ S V+VL A KVN+ VA TKD+ Sbjct: 770 KIEGVPVLAKAISGADMDGLRSIVDKLKQEIPSVVIVLGTASEGKVNI-VAGVTKDLINK 82- 8 Query: 828 --HAGNMIKGLAPIVAGRGGGKPDMAMAGGSDASKIAELLAAVAE 870 HAG ++K +A G GGG+PDMA AGG K+ + L+ V E Sbjct: 829 GYHAGKLVKEVATRCGGGGGGRPDMAQAGGKQPEKLQDALSFVYE 873 A related DNA sequence was identified in S. pyogenes <SEQ ID 4505> which encodes the amino acid sequence <SEQ ID 4506>. Analysis of this protein sequence reveals the following:

TABLE-US-04365 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.41 Transmembrane 805-821 (804-822) ----- Final Results ----- bacterial membrane --- Certainty = 0.2763 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04366 Identities = 862/870 (99%), Positives = 864/870 (99%) Query: 1 MKELSSAQIRQMWLDFWKSKGHSVEPSANLVPVNDPTLLWINSGVATLKKYFDGSVIPEN 60 MKELSSAQIRQMWLDFWKSKGH VEPSANLVPVNDPTLLWINSGVATLKKYFDGSVIPEN Sbjct: 1 MKELSSAQIRQMWLDFWKSKGHCVEPSANLVPVNDPTLLWINSGVATLKKYFDGSVIPEN 60 Query: 61 PRITNAQKSIRTNDIENVGKTARHHTMFEMLGNFSIGDYFRDEAIEWGFELLTSPEWFDF 120- PRITNAQKSIRTNDIENVGKTARHHTMFEMLGNFSIGDYFRDEAIEWGFELLTSP+WFDF Sbjct: 61 PRITNAQKSIRTNDIENVGKTARHHTMFEMLGNFSIGDYFRDEAIEWGFELLTSPDWFDF 120- Query: 121 PKDKLYMTYYPDDKDSYNRWIACGVEPSHLVPIEDNFWEIGAGPSGPDTEIFFDRGEDFD 18- 0 PKDKLYMTYYPDDKDSYNRWIACGVEPSHLVPIEDNFWEIGAGPSGPDTEIFFDRGEDFD Sbjct: 121 PKDKLYMTYYPDDKDSYNRWIACGVEPSHLVPIEDNFWEIGAGPSGPDTEIFFDRGEDFD 18- 0 Query: 181 PENIGLRLLAEDIENDRYIEIWNIVLSQFNADPAVPRSEYKELPNKNIDTGAGLERLAAV 24- 0 PENIGLRLLAEDIENDRYIEIWNIVLSQFNADPAVPRSEYKELPNKNIDTGAGLERLAAV Sbjct: 181 PENIGLRLLAEDIENDRYIEIWNIVLSQFNADPAVPRSEYKELPNKNIDTGAGLERLAAV 24- 0 Query: 241 MQGAKTNFETDLFMPIIREVEKLSGKTYDPDGDNMSFKVIADHIRALSFAIGDGALPGNE 30- 0 MQGAKTNFETDLFMPIIREVEKLSGKTYDPDGDNMSFKVIADHIRALSFAIGDGALPGNE Sbjct: 241 MQGAKTNFETDLFMPIIREVEKLSGKTYDPDGDNMSFKVIADHIRALSFAIGDGALPGNE 30- 0 Query: 301 GRGYVLRRLLRRAVMHGRRLGINETFLYKLVPTVGQIMESYYPEVLEKRDFIEKIVKREE 36- 0 GRGYVLRRLLRRAVMHGRRLGINETFLYKLVPTVGQIMESYYPEVLEKRDFIEKIVKREE Sbjct: 301 GRGYVLRRLLRRAVMHGRRLGINETFLYKLVPTVGQIMESYYPEVLEKRDFIEKIVKREE 36- 0 Query: 361 ETFARTIDAGSGHLDSLLAQLKAEGKDTLEGKDIFKLYDTYGFPVELTEELAEDAGYKID 42- 0 ETFARTIDAGSGHLDSLLAQLKAEGKDTLEGKDIFKLYDTYGFPVELTEELAEDAGYKID Sbjct: 361 ETFARTIDAGSGHLDSLLAQLKAEGKDTLEGKDIFKLYDTYGFPVELTEELAEDAGYKID 42- 0 Query: 421 HEGFKSAMKEQQDRARAAVVKGGSMGMQNETLAGIVEESRFEYDTYSLESSLSVIIADNE 48- 0 HEGFKSAMKEQQDRARAAVVKGGSMGMQNETLAGIVEESRFEYDTYSLESSLSVIIADNE Sbjct: 421 HEGFKSAMKEQQDRARAAVVKGGSMGMQNETLAGIVEESRFEYDTYSLESSLSVIIADNE 48- 0 Query: 481 RTEAVSEGQALLVFAQTPFYAEMGGQVADHGVIKNDKGDTVAEVVDVQKAPNGQPLHTVN 54- 0 RTEAVSEGQALLVFAQTPFYAEMGGQVAD G IKNDKGDTVAEVVDVQKAFNGQPLHTVN Sbjct: 481 RTEAVSEGQALLVFAQTPFYAEMGGQVADTGRIKNDKGDTVAEVVDVQKAPNGQPLHTVN 54- 0 Query: 541 VLASLSVGTNYTLEINKERRLAVEKNHTATHLLHAALHNVIGEHATQAGSLNEEEFLRFD 60- 0 VLASLSVGTNYTLEINKERRLAVEKNHTATHLLHAALHNVIGEHATQAGSLNEEEFLRFD Sbjct: 541 VLASLSVGTNYTLEINKERRLAVEKNHTATHLLHAALHNVIGEHATQAGSLNEEEFLRFD 60- 0 Query: 601 FTHFEAVSNEELRHIEQEVNEQIWNDLTITTTETDVETAKEMGAMALFGEKYGKVVRVVQ 66- 0 FTHFEAVSNEELRHIEQEVNEQIWN LTITTTETDVETAKEMGAMALFGEKYGKVVRVVQ Sbjct: 601 FTHFEAVSNEELRHIEQEVNEQIWNALTITTTETDVETAKEMGAMALFGEKYGKVVRVVQ 66- 0 Query: 661 IGNYSVELCGGTHLNNSSEIGLFKIVKEEGIGSGTRRIIAVTGRQAFEAYRNQEDALKEI 72- 0 IGNYSVELCGGTHLNNSSEIGLFKIVKEEGIGSGTRRIIAVTGRQAFEAYRNQEDALKEI Sbjct: 661 IGNYSVELCGGTHLNNSSEIGLFKIVKEEGIGSGTRRIIAVTGRQAFEAYRNQEDALKEI 72- 0 Query: 721 AATVRAPQLKDAAAKVQALSDSLRDLQKENVELKEKAAAAAAGDVEKDIQEAKGVRFIAS 78- 0 AATVKAPQLKDAAAKVQALSDSLRDLQKEN ELKEKAAAAAAGDVFKD+QEAKGVRFIAS Sbjct: 721 AATVKAPQLKDAAAKVQALSDSLRDLQKENAELKEKAAAAAAGDVFKDVQEAKGVRFIAS 78- 0 Query: 781 QVDVADAGALRTFADNWKQKDYSDVLVLVAAIGEKVNVLVASKTKDVHAGNMIKGLAPIV 84- 0 QVDVADAGALRTFADNWKQKDYSDVLVLVAAIGEKVNVLVASKTKDVHAGNNIK LAPIV Sbjct: 781 QVDVADAGALRTFADNWKQKDYSDVLVLVAAIGEKVNVLVASKTKDVHAGNMIKELAPIV 84- 0 Query: 841 AGRGGGKPDMAMAGGSDASKIAELLAAVAE 870 AGRGGGKPDMAMAGGSDASKIAELLAAVAE Sbjct: 841 AGRGGGKPDMAMAGGSDASKIAELLAAVAE 870 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1467 A DNA sequence (GBSx1553) was identified in S. agalactiae <SEQ ID 4507> which encodes the amino acid sequence <SEQ ID 4508>. Analysis of this protein sequence reveals the following: TABLE-US-04367 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2974 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9747> which encodes amino acid sequence <SEQ ID 9748> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04368 >GP: CAB15920 GB: Z99123 yxjI [Bacillus subtilis] Identities = 42/144 (29%), Positives = 73/144 (50%), Gaps = 2/144 (1%) Query: 17 IKEKMFSLGGKFTITDLTGLPCYHVEGSLFPLPKTFKVFDEEEHLISQIEKKVLSFLPKF 76 - +K+KMFS F I D + VEG F L + ++ D + IE+K++S LP++ Sbjct: 6 MKQKMFSFKDAFHIYDRDEQETFKVEGRFFSLGDSLQMTDSSGKTLVSIEQKLMSLLPRY 65 Query: 77 NVTLANGNHFTIKKDFSFLKPHYTIEDLDMEVKGNFWDMDFQLLKDNQVIANISQQWFRN 136- +++ + K +F KP + I L+ E+ G+ W +FQL V ++S++W Sbjct: 66 EISIGGKTVCEVTKKVTFSKPKFVISGLNWEIDGDLWRDEFQLTDGENVRMSVSKKWLSW 125- Query: 137 TSTYQVEVYSETYNDLTISLVIAI 160 +Y +++ E D+ I IAI Sbjct: 126 GDSYHLQIAYE--EDVLICTAIAI 147 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1468 A DNA sequence (GBSx1554) was identified in S. agalactiae <SEQ ID 4509> which encodes the amino acid sequence <SEQ ID 4510>. Analysis of this protein sequence reveals the following: TABLE-US-04369 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3833 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04370 >GP: BAA36674 GB: AB016282 ORF17 [bacteriophage phi-105] Identities = 45/133 (33%), Positives = 74/133 (54%), Gaps = 5/133 (3%) Query: 2 KYTYLALFEVDKENGGYNISFPDFHGAFSEADSLNEAIFNAREVLEIYTIMFEDEGKEFP 61 +Y Y ALF+ D + G ++FPD G + +S EA+ A+E + ++ FE +G P Sbjct: 5 RYIYPALFDYDDD--GITVTFPDLPGCITFGNSGGEALTMAKEAMALHLYGFEQDGDIIP 62 Query: 62 KASSFKALASNLASDEDVIQAISVDTELVRERERSKIVNKTVTLPSWLVEVGKENKVNFS 121- +A+ K + A + + I R + V KT+T+P W+ ++ KE+KVN+S Sbjct: 63 EATPSKEIK---AEESQSVVLIETWMPPFRHDMENAAVKKTLTIPRWMDDIAKEHKVNYS 119- Query: 122 QLLQKAIREELQV 134 QLLQ+AI+E L + Sbjct: 120 QLLQEAIKEHLGI 132 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1469 A DNA sequence (GBSx1555) was identified in S. agalactiae <SEQ ID 4511> which encodes the amino acid sequence <SEQ ID 4512>. Analysis of this protein sequence reveals the following: TABLE-US-04371 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1484 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04372 >GP: BAA25696 GB: AB010712 NADH oxidase/alkyl hydroperoxidase reductase [Streptococcus mutans] Identities = 383/509 (75%), Positives = 441/509 (86%) Query: 1 MVLDKEIKAQLAQYLDLLESDIVLQADLGDNDNSQKVKDFLDEIVAMSDRISLESTHLKR 60 M LD EIK QL QYL LLES+IVLQA L D+ NSQKVK+FL EIVAMS ISLE L R Sbjct: 1 MALDAEIKEQLGQYLQLLESEIVLQAQLKDDANSQKVKEFLQEIVAMSPMISLEEKELPR 60 Query: 61 QPSFGIAKKGHESRVIFSGLPMGHEFTSFILALLQVSGRAPKVDEDIIKRIKGIEKTINL 120- PSF IAKKG ES V F+GLP+GHEFTSFILALLQVSGR PKV+ DI+KRI+ +++ ++ Sbjct: 61 TPSFRIAKKGQESGVEFAGLPLGHEFTSFILALLQVSGRPPKVETDIVKRIQAVDEPMHF 120- Query: 121 ETYVSLTCHNCPDVVQAFNIMAVLNPNITHTMIEGGMYQDEVKSKGIMSVPTVYKDQEEF 18- 0 ETYVSLTCHNCPDVVQAFNIM+V+NPNI+HTM+EGGM++DE+++KGIMSVPTVYKD EF Sbjct: 121 ETYVSLTCHNCPDVVQAFNIMSVVNPNISHTMVEGGMFKDEIEAKGIMSVPTVYKDGTEF 18- 0 Query: 181 TSGRATIEQLLEQLDGPLDAEAFADKGVYDVLVIGGGPAGNSAAIYAARKGLKTGILAET 24- 0 TSGRA+IEQLL+ + GPL +AF DKGV+DVLVIGGGPAGNSAAIYAARKG+KTG+LAET Sbjct: 181 TSGRASIEQLLDLIAGPLKEDAFDDKGVFDVLVIGGGPAGNSAAIYAARKGVKTGLLAET 24- 0 Query: 241 FGGQVIETVGIENMIGTLYTEGPKLMAQIEEHTKSYDIDIIKSQLATGIEKKELVEVTLA 30- 0 GGQV+ETVGIENMIGT Y EGP+LMAQ+EEHTKSY +DI+K+ A I+K +LVEV L Sbjct: 241 MGGQVMETVGIENMIGTPYVEGPQLMAQVEEHTKSYSVDIMKAPRAKSIQKTDLVEVELD 30- 0 Query: 301 NGAILQAKTAILALGAKWRNINVPGEEEFRNKGVTYCPHCDGPLFEGKDVAVIGGGNSGM 36- 0 NGA L+AKTA+LALGAKWR INVPGE+EF NKGVTYCPHCDGPLF K VAVIGGGNSG+ Sbjct: 301 NGAHLKAKTAVLALGAKWRKINVPGEKEFFNKGVTYCPHCDGPLFTDKKVAVIGGGNSGL 36- 0 Query: 361 EAALDLAGVTKHVTVLEFLPELKADQVLQERAAKTDNLTILKNVATKDIVGEDHVTGLNY 42- 0 EAA+DLAG+ HV +LEFLPELKAD++LQ+RA DN+TIL NVATK+I+G DHV GL Y Sbjct: 361 EAAIDLAGLASHVYILEFLPELKADKILQDRAEALDNITILTNVATKEIIGNDHVEGLRY 42- 0 Query: 421 TDRDTNEEKHIDLEGVFVQIGLVPSTSWLKDSGIELNERQEIVVDKFGSTNIPGIFAAGD 48- 0 +DR TNEE +DLEGVFVQIGLVPST WLKDSG+ LNE+ EI+V K G+TNIP IFAAGD Sbjct: 421 SDRTTNEEYLLDLEGVFVQIGLVPSTDWLKDSGLALNEKGEIIVAKDGATNIPAIFAAGD 48- 0 Query: 481 CTDAAYKQIIISMGSGATAAIGAFDYLIR 509 CTD+AYKQIIISMGSGATAA+GAFDYLIR Sbjct: 481 CTDSAYKQIIISMGSGATAALGAFDYLIR 509 A related DNA sequence was identified in S. pyogenes <SEQ ID 4513> which encodes the amino acid sequence <SEQ ID 4514>. Analysis of this protein sequence reveals the following: TABLE-US-04373 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0654 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04374 Identities = 419/510 (82%), Positives = 472/510 (92%) Query: 1 MVLDKEIKAQLAQYLDLLESDIVLQADLGDNDNSQKVKDFLDEIVAMSDRISLESTHLKR 60 M L +IK QLAQYL LLE+D+VLQ LGDN+ SQKVKDF++EI AMS+RIS+E+ L R Sbjct: 1 MALSPDIKEQLAQYLTLLEADLVLQVSLGDNEQSQKVKDFVEEIAAMSERISIENITLDR 60 Query: 61 QPSFGIAKKGHESRVIFSGLPMGHEFTSFILALLQVSGRAPKVDEDIIKRIKGIEKTINL 120- QPSF +AKKGH S V+F+GLP+GHE TSFILALLQVSGRAPKVD+D+I RIK I++ ++ Sbjct: 61 QPSFKVAKKGHGSGVVFAGLPLGHELTSFILALLQVSGRAPKVDQDVIDRIKAIDRPLHF 120- Query: 121 ETYVSLTCHNCPDVVQAFNIMAVLNPNITHTMIEGGMYQDEVKSKGIMSVPTVYKDQEEF 18- 0 ETYVSLTCHNCPDVVQA NIM+VLN I+HTM+EGGM+QDEVK+KGIMSVPTV+ D EEF Sbjct: 121 ETYVSLTCHNCPDVVQALNIMSVLNDKISHTMVEGGMFQDEVKAKGIMSVPTVFLDGEEF 18- 0 Query: 181 TSGRATIEQLLEQLDGPLDAEAFADKGVYDVLVIGGGPAGNSAAIYAARKGLKTGILAET 24- 0 TSGRATIEQLLEQ+ GPL EAFADKG+YDVLVIGGGPAGNSAAIYAARKGLKTG+LAET Sbjct: 181 TSGRATIEQLLEQIAGPLSEEAFADKGLYDVLVIGGGPAGNSAAIYAARKGLKTGLLAET 24- 0 Query: 241 FGGQVIETVGIENMIGTLYTEGPKLMAQIEEHTKSYDIDIIKSQLATGIEKKELVEVTLA 30- 0 FGGQV+ETVGIENMIGTLYTEGPKLMA++E HTKSYD+DIIK+QLAT IEKKE +EVTLA Sbjct: 241 FGGQVMETVGIENMIGTLYTEGPKLMAEVEAHTKSYDVDIIKAQLATSIEKKENIEVTLA 30- 0 Query: 301 NGAILQAKTAILALGAKWRNINVPGEEEFRNKGVTYCPHCDGPLFEGKDVAVIGGGNSGM 36- 0 NGA+LQAKTAILALGAKWRNINVPGE+EFRNKGVTYCPHCDGPLFEGKDVAVIGGGNSG+ Sbjct: 301 NGAVLQAKTAILALGAKWRNINVPGEDEFRNKGVTYCPHCDGPLFEGKDVAVIGGGNSGL 36- 0 Query: 361 EAALDLAGVTKHVTVLEFLPELKADQVLQERAAKTDNLTILKNVATKDIVGEDHVTGLNY 42- 0 EAALDLAG+ KHV VLEFLPELKAD+VLQ+RAAKT+N+TI+KNVATKDIVGEDHVTGLNY Sbjct: 361 EAALDLAGLAKHVYVLEFLPELKADKVLQDRAAKTNNMTIIKNVATKDIVGEDHVTGLNY 42- 0 Query: 421 TDRDTNEEKHIDLEGVFVQIGLVPSTSWLKDSGIELNERQEIVVDKFGSTNIPGIFAAGD 48- 0 T+RD+ E+KH+DLEGVFVQIGLVP+T+WLKDSG+ L +R EI+VDK GSTNIPGIFAAGD Sbjct: 421 TERDSGEDKHLDLEGVFVQIGLVPNTAWLKDSGVNLTDRGEIIVDKHGSTNIPGIFAAGD 48- 0 Query: 481 CTDAAYKQIIISMGSGATAAIGAFDYLIRQ 510 CTD+AYKQIIISMGSGATAAIGAFDYLIRQ Sbjct: 481 CTDSAYKQIIISMGSGATAAIGAFDYLIRQ 510 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1470 A DNA sequence (GBSx1556) was identified in S. agalactiae <SEQ ID 4515> which encodes the amino acid sequence <SEQ ID 4516>. Analysis of this protein sequence reveals the following: TABLE-US-04375 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2906 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04376 >GP: BAA25695 GB: AB010712 alkyl hydroperoxidase [Streptococcus mutans] Identities = 167/186 (89%), Positives = 179/186 (95%) Query: 1 MSLVGKEIIEFSAQAYHDGKFITVTNEDVKGKWAVFCFYPADFSFVCPTELGDLQEQYET 60 MSLVGKE++EFSAQAYH G+F+TV NEDVKGKWAVFCFYPADFSFVCPTELGDLQEQY T Sbjct: 1 MSLVGKEMVEFSAQAYHQGEFVTVNNEDVKGKWAVFCFYPADFSFVCPTELGDLQEQYAT 60 Query: 61 LKSLDVEVYSVSTDTHFVHKAWHDDSDVVGTITYPMIGDPSHLISQGFDVLGQDGLAQRG 120- L+SL VEVYSVSTDTHFVHKAWHDDSDVVGTITY MIGDPSH++SQGF+VLG+DGLAQRG Sbjct: 61 LQSLGVEVYSVSTDTHFVHKAWHDDSDVVGTITYTMIGDPSHVLSQGFEVLGEDGLAQRG 120- Query: 121 TFIIDPDGVIQMMEINADGIGRDASTLIDKVRAAQYIRQHTGEVCPAKWKEGAETLTPSL 18- 0 TFI+DPDG+IQMME+NADGIGRDASTLIDKVRAAQYIRQH GEVCPAKWKEGAETL PSL Sbjct: 121 TFIVDPDGIIQMMEVNADGIGRDASTLIDKVRAAQYIRQHPGEVCPAKWKEGAETLKPSL 18- 0 Query: 181 DLVGKI 186 DLVGKI Sbjct: 181 DLVGKI 186 A related DNA sequence was identified in S. pyogenes <SEQ ID 4517> which encodes the amino acid sequence <SEQ ID 4518>. Analysis of this protein sequence reveals the following: TABLE-US-04377 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3022 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04378 Identities = 173/186 (93%), Positives = 181/186 (97%) Query: 1 MSLVGKEIIEFSAQAYHDGKFITVTNEDVKGKWAVFCFYPADFSFVCPTELGDLQEQYET 60 MSL+GKEI EFSAQAYHDGKFITVTNEDVKGKWAVFCFYPADFSFVCPTELGDLQEQYET Sbjct: 1 MSLIGKEIAEFSAQAYHDGKFITVTNEDVKGKWAVFCFYPADFSFVCPTELGDLQEQYET 60 Query: 61 LKSLDVEVYSVSTDTHFVHKAWHDDSDVVGTITYPMIGDPSHLISQGFDVLGQDGLAQRG 120- LKSL VEVYSVSTDTHFVHKAWHDDSDVVGTITYPMIGDPSHLISQ F+VLG+DGLAQRG Sbjct: 61 LKSLGVEVYSVSTDTHFVHKAWHDDSDVVGTITYPMIGDPSHLISQAFEVLGEDGLAQRG 120- Query: 121 TFIIDPDGVIQMMEINADGIGRDASTLIDKVRAAQYIRQHTGEVCPAKWKEGAETLTPSL 18- 0 TFI+DPDG+IQMMEINADGIGRDASTLIDK+ AAQY+R+H GEVCPAKWKEGAETLTPSL Sbjct: 121 TFIVDPDGIIQMMEINADGIGRDASTLIDKIHAAQYVRKHPGEVCPAKWKEGAETLTPSL 18- 0 Query: 181 DLVGKI 186 DLVGKI Sbjct: 181 DLVGKI 186 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1471 A DNA sequence (GBSx1557) was identified in S. agalactiae <SEQ ID 4519> which encodes the amino acid sequence <SEQ ID 4520>. This protein is predicted to be 30S ribosomal protein S2 (rpsB). Analysis of this protein sequence reveals the following:

TABLE-US-04379 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4462 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04380 >GP: CAA50276 GB: X70925 30S ribosomal protein [Pediococcus acidilactici] Identities = 190/260 (73%), Positives 226/260 (86%), Gaps = 4/260 (1%) Query: 1 MAVISMKQLLEAGVHFGHQTRRWNPKMAKYIFTERNGIHVIDLQQTVKLADQAYEFVRDA 60 M+VISMKQLLEAGVHFGHQTRRWNPKM +IFTERNGI++IDLQ+TVKL D AY FV+D Sbjct: 1 MSVISMKQLLEAGVHFGHQTRRWNPKMKPFIFTERNGIYIIDLQKTVKLIDNAYNFVKDV 60 Query: 61 AANDAVILFVGTKKQAAEAVAEEAKRAGQYFINHRWLGGTLTNWGTIQKRIARLKEIKRM 120- AAND V+LFVGTKKQA A+ EEAKRAGQ+++NHRWLGGTLTNW TIQKRI RLK++K+M Sbjct: 61 AANDGVVLFVGTKKQAQTAIEEEAKRAGQFYVNHRWLGGTLTNWNTIQKRIKRLKDLKKM 120- Query: 121 EEEGTFELLPKKEVALLNKQRARLEKFLGGIEDMPRIPDVMYVVDPHKEQIAVKEAKKLG 18- 0 EE+GTF+ LPKKEVALLNKQ+ +LEKFLGGIEDMP IPDV++VVDP KEQIA+KEA+KL Sbjct: 121 EEDGTFDRLPKKEVALLNKQKDKLEKFLGGIEDMPHIPDVLFVVDPRKEQIAIKEAQKLN 18- 0 Query: 181 IPVVAMVDTNADPDDIDVIIPANDDAIRAVKLITSKLADAVIEGRQGEDADV----DFAQ 23- 6 IPVVAMVDTN DPD +DVIIP+NDDAIRAV+LITSK+ADAV+EGRQGED + + A+ Sbjct: 181 IPVVAMVDTNTDPDQVDVIIPSNDDAIRAVRLITSKMADAVVEGRQGEDDEAVQQEEVAE 24- 0 Query: 237 EAQADSIEEIVEVVEGSNND 256 DS+E++ + VE +N+ Sbjct: 241 GVSKDSLEDLKKTVEEGSNE 260 A related DNA sequence was identified in S. pyogenes <SEQ ID 4521> which encodes the amino acid sequence <SEQ ID 4522>. Analysis of this protein sequence reveals the following: TABLE-US-04381 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4462(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04382 Identities = 241/254 (94%), Positives = 248/254 (96%) Query: 1 MAVISMKQLLEAGVHFGHQTRRWNPKMAKYIFTERNGIHVIDLQQTVKLADQAYEFVRDA 60 MAVISMKQLLEAGVHFGHQTRRWNPKMAKYIFTERNGIHVIDLQQTVKLADQAYEFVRDA Sbjct: 1 MAVISMKQLLEAGVHFGHQTRRWNPKMAKYIFTERNGIHVIDLQQTVKLADQAYEFVRDA 60 Query: 61 AANDAVILFVGTKKQAAEAVAEEAKRAGQYFINHRWLGGTLTNWGTIQKRIARLKEIKRM 120- AANDAVILFVGTKKQAAEAVA+EA RAGQYFINHRWLGGTLTNWGTIQKRIARLKEIKRM Sbjct: 61 AANDAVILFVGTKKQAAEAVADEATRAGQYFINHRWLGGTLTNWGTIQKRIARLKEIKRM 120- Query: 121 EEEGTFELLPKKEVALLNKQRARLEKFLGGIEDMPRIPDVMYVVDPHKEQIAVKEAKKLG 18- 0 EEEGTF++LPKKEVALLNKQRARLEKFLGGIEDMPRIPDVMYVVDPHKEQIAVKEAKKLG Sbjct: 121 EEEGTFDVLPKKEVALLNKQRARLEKFLGGIEDMPRIPDVMYVVDPHKEQIAVKEAKKLG 18- 0 Query: 181 IPVVAMVDTNADPDDIDVIIPANDDAIRAVKLITSKLADAVIEGRQGEDADVDFAQEAQA 24- 0 IPVVAMVDTNADPDDID+IIPANDDAIRAVKLIT+KLADA+IEGRQGEDADV F + QA Sbjct: 181 IPVVAMVDTNADPDDIDIIIPANDDAIRAVKLITAKLADAIIEGRQGEDADVAFEADTQA 24- 0 Query: 241 DSIEEIVEVVEGSN 254 DSIEEIVEVVEG N Sbjct: 241 DSIEEIVEVVEGDN 254 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1472 A DNA sequence (GBSx1558) was identified in S. agalactiae <SEQ ID 4523> which encodes the amino acid sequence <SEQ ID 4524>. Analysis of this protein sequence reveals the following: TABLE-US-04383 Possible Site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2648(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04384 >GP: CAB73435 GB: AL139077 elongation factor TS [Campylobacter jejuni] Identities = 169/358 (47%), Positives = 226/358 (62%), Gaps = 19/358 (5%) Query: 1 MAEITAKLVKELREKSGAGVMDAKKALVETDGDLDKAIELLREKGMAKAAKKADRVAAEG 60 M EITA +VKELRE +GAG+MD K AL ET+GD DKA++LLREKG+ KAAKKADR+AAEG Sbjct: 1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG 60 Query: 61 LTGVYV--DGNVAAVIEVNAETDFVAKNDQFVTLVNETAKVIAEGRPSNNEEALALTMPS 118- L V V D A V E+N+ETDFVAKNDQF+ L +T I + EE + T+ + Sbjct: 61 LVSVKVSDDFTSATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTI-N 119- Query: 119 GETLEQAFVTATATIGEKISFRRFALVEKTDEQHFGAYQHNGGRIGVITV-------VEG 17- 1 G E+ + ATIGE + RRFA ++ Y H GR+GV+ V Sbjct: 120 GVKFEEYLKSQIATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVAS 17- 9 Query: 172 GDDALAKQVSMHVAAMKPTVLSYTELDAQFVHDELAQLNHKIEQDNESRAMV---NKPAL 22- 8 L +Q+ MH+AAM+P+ LSY +LD FV +E L ++E++NE R + NKP Sbjct: 180 KSRDLLRQICMHIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEH 23- 9 Query: 229 PFLKYGSKAQLTDEVIAQAEEDIKAELAAEGKPEKIWDKIVPGKMDRFMLDNTKVDQEYT 28- 8 ++ S+ QL+D ++ +AEE IK EL A+GKPEKIWD I+PGKM+ F+ DN+++D + T Sbjct: 240 KIPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLT 29- 9 Query: 289 LLAQVYIMDDSKTVEAYLESV------NAKAVAFVRFEVGEGIEKASNDFEAEVAATM 340 L+ Q Y+MDD KTVE + K V F+ FEVGEG+EK + DF AEVAA + Sbjct: 300 LMGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL 357 A related DNA sequence was identified in S. pyogenes <SEQ ID 4525> which encodes the amino acid sequence <SEQ ID 4526>. Analysis of this protein sequence reveals the following: TABLE-US-04385 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3942(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04386 Identities = 307/344 (89%), Positives = 327/344 (94%) Query: 1 MAEITAKLVKELREKSGAGVMDAKKALVETDGDLDKAIELLREKGMAKAAKKADRVAAEG 60 MAEITAKLVKELREKSGAGVMDAKKALVETDGD+DKA+ELLREKGMAKAAKKADRVAAEG Sbjct: 33 MAEITAKLVKELREKSGAGVMDAKKALVETDGDMDKAVELLREKGMAKAAKKADRVAAEG 92 Query: 61 LTGVYVDGNVAAVIEVNAETDFVAKNDQFVTLVNETAKVIAEGRPSNNEEALALTMPSGE 120- LTGVYV GNVAAV+EVNAETDFVAKN QFV LVN TAKVIAEG+P+NN+EALAL MPSGE Sbjct: 93 LTGVYVHGNVAAVVEVNAETDFVAKNAQFVELVNATAKVIAEGKPANNDEALALVMPSGE 152- Query: 121 TLEQAFVTATATIGEKISFRRFALVEKTDEQHFGAYQHNGGRIGVITVVEGGDDALAKQV 18- 0 TL +A+V ATATIGEKISFRRFAL+EK DEQHFGAYQHNGGRIGVI+VVEGGDDALAKQV Sbjct: 153 TLAEAYVNATATIGEKISFRRFALIEKADEQHFGAYQHNGGRIGVISVVEGGDDALAKQV 21- 2 Query: 181 SMHVAAMKPTVLSYTELDAQFVHDELAQLNHKIEQDNESRAMVNKPALPFLKYGSKAQLT 24- 0 SMH+AAMKPTVLSYTELDAQF+ DELAQLNH IE DNESRAMV+KPALPFLKYGSKAQL+ Sbjct: 213 SMHIAAMKPTVLSYTELDAQFIKDELAQLNHAIELDNESRAMVDKPALPFLKYGSKAQLS 27- 2 Query: 241 DEVIAQAEEDIKAELAAEGKPEKIWDKIVPGKMDRFMLDNTKVDQEYTLLAQVYIMDDSK 30- 0 D+VI AE DIKAELAAEGKPEKIWDKI+PGKMDRFMLDNTKVDQ YTLLAQVYIMDDSK Sbjct: 273 DDVITAAEADIKAELAAEGKPEKIWDKIIPGKMDRFMLDNTKVDQAYTLLAQVYIMDDSK 33- 2 Query: 301 TVEAYLESVNAKAVAFVRFEVGEGIEKASNDFEAEVAATMAAAL 344 TVEAYL+SVNAKA+AF RFEVGEGIEK +NDFE+EVAATMAAAL Sbjct: 333 TVEAYLDSVNAKAIAFARFEVGEGIEKKANDFESEVAATMAAAL 376 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1473 A DNA sequence (GBSx1559) was identified in S. agalactiae <SEQ ID 4527> which encodes the amino acid sequence <SEQ ID 4528>. Analysis of this protein sequence reveals the following: TABLE-US-04387 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1312(Affirmative) < succ> bacterial membrane --- Certainty= 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1474 A DNA sequence (GBSx1560) was identified in S. agalactiae <SEQ ID 4529> which encodes the amino acid sequence <SEQ ID 4530>. Analysis of this protein sequence reveals the following: TABLE-US-04388 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.86 Transmembrane 128-144 (124-152) INTEGRAL Likelihood = -4.57 Transmembrane 35-51 (33-53) INTEGRAL Likelihood = -4.04 Transmembrane 92-108 (87-111) ----- Final Results ----- bacterial membrane --- Certainty= 0.4142(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04389 >GP: BAB04953 GB: AP001511 small multidrug export related protein [Bacillus halodurans] Identities = 47/137 (34%), Positives = 71/137 (51%), Gaps = 5/137 (3%) Query: 12 IPLVELRGAVPFAIANGIPLWEALAIGVVGNMLPVPIIFFFARKVLEWGADKPYTGKFFT 71 - +P+VELRG +P + G+ WEAL G++GN+LP+ I R + W + + + Sbjct: 1 MPIVELRGGIPLGVVLGLSPWEALLFGIIGNLLPIVPILLLFRPISGWMLRFKWYQRLYD 60 Query: 72 WCLKKGHSGGQKLEKVAGEKGLFIALLLFVGIPLPGTGAWTGTLAASLLDWEFKHSVIAV 131- W + +EK I L+LF +PLP TGA++ LAA L F+ + AV Sbjct: 61 WLYNRTMKKSNNVEKFGA-----IGLILFTAVPLPTTGAYSACLAAVLFFIPFRFAFFAV 115- Query: 132 MLGVILAGCIMGTLSII 148 GV++AG +M S I Sbjct: 116 SAGVVIAGIVMTLFSYI 132 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8817> and protein <SEQ ID 8818> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04390 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: 3.98 GvH: Signal Score (-7.5): -2.35 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 3 value: -7.86 threshold: 0.0 INTEGRAL Likelihood = -7.86 Transmembrane 128-144 (124-152) INTEGRAL Likelihood = -4.57 Transmembrane 35-51 (33-53) INTEGRAL Likelihood = -4.04 Transmembrane 92-108 (87-111) PERIPHERAL Likelihood = 12.20 109 modified ALOM score: 2.07 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4142(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 105-109 The protein has homology with the following sequences in the databases: ##STR00095## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1475 A DNA sequence (GBSx1561) was identified in S. agalactiae <SEQ ID 4531> which encodes the amino acid sequence <SEQ ID 4532>. This protein is predicted to be CtsR protein (ctsR). Analysis of this protein sequence reveals the following: TABLE-US-04391 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3672 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04392 >GP: CAB91548 GB: AJ249133 CtsR protein [Lactococcus lactis] Identities = 74/146 (50%), Positives = 103/146 (69%), Gaps = 3/146 (2%) Query: 4 KNTSDNIEEYIKSLLEQSGIAEIKRSNLADTFQVVPSQINYVIKTRFTESRGYVVESKRG 63 KNTSD IE Y++ LLE++ + EIKR++LA+ F VVPSQINYVIKTRFT S+G+ VESKRG Sbjct: 5 KNTSDIIEAYLRQLLEEAQVIEIKRADLANQFDVVPSQINYVIKTRFTASKGFDVESKRG 64 Query: 64 GGGYIRIAKVHFSDQHQLFGNMLSTIGERISEQVFDDLIQLLFDEEIITEREGNLILATS 123- GGGYI+I K +S +H+ + + +S + D++QLLFDE+++TEREGNL+L Sbjct: 65 GGGYIKIVKYQYSARHEFLTALYQKVPANLSSKAAHDIVQLLFDEKVLTEREGNLLLLVI 124- Query: 124 GDDVLGEQASVIRARMLRKLLQRLDR 149 D G + R M++ ++ RLDR Sbjct: 125 TD---GAISPFTRGIMMKSIINRLDR 147 A related DNA sequence was identified in S. pyogenes <SEQ ID 4533> which encodes the amino acid sequence <SEQ ID 4534>. Analysis of this protein sequence reveals the following: TABLE-US-04393 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2514 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04394 Identities = 117/151 (77%), Positives = 131/151 (86%) Query: 1 MAIKNTSDNIEEYIKSLLEQSGIAEIKRSNLADTFQVVPSQINYVIKTRFTESRGYVVES 60 M KNTSD+IEEYIK LL +SGIAEIKRS LAD+FQVVPSQINYVIKTRFTESRGY VES Sbjct: 1 MPTKNTSDSIEEYIKELLAKSGIAEIKRSMLADSFQVVPSQINYVIKTRFTESRGYEVES 60 Query: 61 KRGGGGYIRIAKVHFSDQHQLFGNMLSTIGERISEQVFDDLIQLLFDEEIITEREGNLIL 120- KRGGGGYIRIAKVHFSD+H L GN+++TI + ISEQVF D IQLLFDE ++TEREGN+IL Sbjct: 61 KRGGGGYIRIAKVHFSDKHHLIGNLMATIEDCISEQVFTDSIQLLFDEHLLTEREGNIIL 120- Query: 121 ATSGDDVLGEQASVIRARMLRKLLQRLDRKG 151 A + DDVLG S IRARML +LLQR+DRKG Sbjct: 121 AVASDDVLGTDGSTIRARMLYRLLQRIDRKG 151 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1476 A DNA sequence (GBSx1562) was identified in S. agalactiae <SEQ ID 4535> which encodes the amino acid sequence <SEQ ID 4536>. This protein is predicted to be ClpC (clpB-1). Analysis of this protein sequence reveals the following: TABLE-US-04395 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.34 Transmembrane 32-48 (32-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.1935 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04396 >GP: AAD01783 GB: AF023422 ClpC [Lactococcus lactis] Identities = 401/831 (48%), Positives = 571/831 (68%), Gaps = 52/831 (6%) Query: 4 YSIKLQEVFRLAQFQAARYESHYLESWHLLLAMVLVHDSVAGLTFAEYE---SEVAIEEY 60 Y+ L +F A A +Y+ +ES HLL AM S+A A S++ I+ Sbjct: 8 YTPTLDRIFEKAAEYAHQYQYGTIESAHLLAAMATTSGSIAYSILAGMNVDSSDLLIDLE 67 Query: 61 EAATILALGRAPKEEITNYQFLEQSPALKKILKLAENISIVVGAEDVGTEHVLLAMLVNK 120- + ++ + + R+ L SP ++++ +A +++ AE VGTEH+L A+L + Sbjct: 68 DLSSHVKVKRSE---------LRFSPRAEEVVTVASFLAVHNNAEAVGTEHLLYALLQVE 118- Query: 121 DLLATRILELVGFRGQDDGESVRMVDLRKALERHAGF-TKDDIKAIYELRNPKKAKSGAS 17- 9 D ++L+L + + +V LRK +E+ G ++ KA+ + K AK A Sbjct: 119 DGFGLQLLKL---------QKINIVSLRKEIEKRTGLIVPENKKAVTPMSKRKMAKGVAE 16- 9 Query: 180 FSDMMKPPSTAGDLADFTRDLSQMAVDGEIEPVIGRDKEISRMVQVLSRKTKNNPVLVGD 23- 9 S+ L + DL++ A G+++P+IGR+ E+ R++ +LSR+TKNNPVLVG+ Sbjct: 170 -------NSSTPTLDSVSSDLTEAARSGKLDPMIGREAEVDRLIHILSRRTKNNPVLVGE 22- 2 Query: 240 AGVGKTALAYGLAQRIANGNIPYELRDMRVLELDDMMSVVAGTRFRGDFEERMNQIIADIE 2- 99 GVGK+A+ GLAQRI NG +P L + R++ L+M +VVAGT+FRG+FE+R+ I+ ++ Sbjct: 223 PGVGKSAIIEGLAQRIVNGQVPIGLMNSRIMALNMATVVAGTKFRGEFEDRLTAIVEEVS 28- 2 Query: 300 EDGHIILFIDELHTIMGSGSGIDSTLDAANILKPALARGTLRTVGATTQEEYQKHIEKDA 35- 9 D +I+FIDELHTI+G+G G+DS DAANILKPALARG + VGATT EYQK+IEKD Sbjct: 283 ADPDVIIFIDELHTIIGAGGGMDSVNDAANILKPALARGDFQMVGATTYHEYQKYIEKDE 34- 2 Query: 360 ALSRRFAKVLVEEPNLEDAYEILLGLKPAYEAFHNVTISDEAVMTAVKVAHRYLTSKNLP 41- 9 AL RR A++ V+EP+ ++A IL GL+ +E +H V +D+A+ +AV ++ RY+TS+ LP Sbjct: 343 ALERRLARINVDEPSPDEAIAILQGLREKFEDYHQVKFTDQAIKSAVTLSVRYMTSRKLP 40- 2 Query: 420 DSAIDLLDEASATVQMMIKKNAPSLLT----------EVDQAILDDDMKSA--------- 46- 0 D AIDLLDEA+A V++++K ++ E+ +A++ D+K++ Sbjct: 403 DKAIDLLDEAAARVKILLKTKKQNVFELEKDFVKAQEELAEAVIKLDVKASRIKEKAVEK 46- 2 Query: 461 --SKALKASYKGKKRKPIAVTEDHIMATLSRLSGIPVEKLTQADSKKYLNLEKELHKRVI 51- 8 K K S K +KR+ VT+ ++A S L+G+P+ ++T+++S + +NLEKELHKRV+ Sbjct: 463 ISDKIYKFSIKEEKRQE--VTDQAVIAVASTLTGVPITQMTKSESDRLINLEKELHKRVV 52- 0 Query: 519 GQDDAVTAISRAIRRNQSGIRTGKRPIGSFMFLGPTGVGKTELAKALAEVLFDDESALIR 57- 8 GQ++A++A+SRAIRR +SG+ +RP+GSFMFLGPTGVGKTELAKALA+ +F E +IR Sbjct: 521 GQEEAISAVSRAIRRARSGVADSRRPMGSFMFLGPTGVGKTELAKALADSVFGSEDNMIR 58- 0 Query: 579 FDMSEYMEKFAASHLNGAPPGYVGYDEGGELTEKVRNKPYSVLLFDEVEKAHPDIFNVLL 63- 8 DMSE+MEK + S L GAPPGYVGYDEGG+LTE+VRNKPYSV+L DEVEKAH D+FN++L Sbjct: 581 VDMSEFMEKHSTSRLIGAPPGYVGYDEGGQLTERVRNKPYSVVLLDEVEKAHLDVFNIML 64- 0 Query: 639 QVLDDGVLTDSRGRKVDFSNTIIIMTSNLGATALRDDKTVGFGAKDISHDYTAMQKRIME 69- 8 Q+LDDG +TD++GRKVDF NTIIIMTSNLGATALRDDKTVGFGAK+I+ DY+AMQ RI+E Sbjct: 641 QILDDGFVTDTKGRKVDFRNTIIIMTSNLGATALRDDKTVGFGAKNITADYSAMQSRILE 70- 0 Query: 699 ELKKAYRPEFINRIDEKVVFHSLSQDNMREVVKIMVKPLILALKDKGMDLKFQPSALKHL 75- 8 ELK+ YRPEF+NRIDE +VFHSL + ++VKIM K LI L ++ + +K PSA+K + Sbjct: 701 ELKRHYRPEFLNRIDENIVFHSLESQEIEQIVKIMSKSLIKRLAEQDIHVKLTPSAIKLI 76- 0 Query: 759 AEDGYDIEMGARPLRRTIQTQVEDHLSELLLANQVKEGQVIKIGVSKGKLK 809 AE G+D E GARPLR+ +Q +VED LSE LL+ ++K G I IG S K+K Sbjct: 761 AEVGFDPEYGARPLRKALQKEVEDLLSEQLLSGEIKAGNHISIGASNKKIK 811 A related DNA sequence was identified in S. pyogenes <SEQ ID 4537> which encodes the amino acid sequence <SEQ ID 4538>. Analysis of this protein sequence reveals the following:

TABLE-US-04397 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.75 Transmembrane 32-48 (32-48) ----- Final Results ----- bacterial membrane --- Certainty = 0.1702 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 285-287 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04398 Identities = 618/814 (75%), Positives = 716/814 (87%), Gaps = 1/814 (0%) Query: 1 MSHYSIKLQEVFRLAQFQAARYESHYLESWHLLLAMVLVHDSVAGLTFAEYESEVAIEEY 60 M YS K+Q++FR AQFQAAR++SH LE+WH+LLAMV V +S+A + +EY+++VAIEEY Sbjct: 1 MIMYSTKMQDIFRQAQFQAARFDSHCLETWHVLLAMVAVDNSLANMILSEYDAQVAIEEY 60 Query: 61 EAATILALGRAPKEEITNYQFLEQSPALKKILKLAENISIVVGAEDVGTEHVLLAMLVNK 120- EAA ILA+G+ PKE+++ F QS L +L A+ IS + ++VG+EHVL A+L+N Sbjct: 61 EAAAILAMGKTPKEQLSRVDFRPQSKTLTNLLAFAQAISQITRDQEVGSEHVLFAILLNP 120- Query: 121 DLLATRILELVGFRGQDDGESV-RMVDLRKALERHAGFTKDDIKAIYELRNPKKAKSGAS 17- 9 D++A+R+LE+ G++ +D+G R+ DLRKA+ERHAG++K+ IKAI+ELR PKK K+ + Sbjct: 121 DIMASRLLEIAGYQIKDNGNGQPRLADLRKAIERHAGYSKEMIKAIHELRKPKKTKTQGT 18- 0 Query: 180 FSDMMKPPSTAGDLADFTRDLSQMAVDGEIEPVIGRDKEISRMVQVLSRKTKNNPVLVGD 23- 9 FSDMMKPPSTAG+L+DFTRDL++MA G +E VIGRD+E+SRM+QVLSRKTKNNPVLVGD Sbjct: 181 FSDMMKPPSTAGELSDFTRDLTEMARQGLLESVIGRDQEVSRMIQVLSRKTKNNPVLVGD 24- 0 Query: 240 AGVGKTALAYGLAQRIANGNIPYELRDMRVLELDMMSVVAGTRFRGDFEERMNQIIADIE 29- 9 AGVGRTALAYGLAQRIANG IPYEL++MRVLELDMMSVVAGTRFRGDFEERMNQII DIE Sbjct: 241 AGVGKTALAYGLAQRIANGAIPYELKEMRVLELDMMSVVAGTRFRGDFEERMNQIIDDIE 30- 0 Query: 300 EDGHIILFIDELHTIMGSGSGIDSTLDAANILKPALARGTLRTVGATTQEEYQKHIEKDA 35- 9 DG IILF+DELHTIMGSGSGIDSTLDAANILKPAL+RGTL VGATTQEEYQKHIEKDA Sbjct: 301 ADGQIILFVDELHTIMGSGSGIDSTLDAANILKPALSRGTLHMVGATTQEEYQKHIEKDA 36- 0 Query: 360 ALSRRFAKVLVEEPNLEDAYEILLGLKPAYEAFHNVTISDEAVMTAVKVAHRYLTSKNLP 41- 9 ALSRRFAK+L+EEPN EDAY+IL+GLK +YE +HNV+IS+EAV TAVK+AHRYLTSKNLP Sbjct: 361 ALSRRFAKILIEEPNTEDAYQILMGLKLSYETYHNVSISNEAVKTAVKMAHRYLTSKNLP 42- 0 Query: 420 DSAIDLLDEASATVQMMIKKNAPSLLTEVDQAILDDDMKSASKALKASYKGKKRKPIAVT 47- 9 DSAIDLLDEASA VQ M+KK+AP LT +DQA+++ DMK S+ L KG+ RKP VT Sbjct: 421 DSAIDLLDEASAAVQNMVKKSAPETLTPIDQALINGDMKKVSRLLAKEAKGQMRKPTPVT 48- 0 Query: 480 EDHIMATLSRLSGIPVEKLTQADSKKYLNLEKELHKRVIGQDDAVTAISRAIRRNQSGIR 53- 9 ED I+ATLS+LSGIP+EKLTQADSKKYLNLEKELHKRVIGQD AVTAISRAIRRNQSGIR Sbjct: 481 EDDILATLSKLSGIPLEKLTQADSKKYLNLEKELHKRVIGQDAAVTAISRAIRRNQSGIR 54- 0 Query: 540 TGKRPIGSFMFLGPTGVGKTELAKALAEVLFDDESALIRFDMSEYMEKFAASHLNGAPPG 59- 9 TGKRPIGSFMFLGPTGVGKTELAKALAEVLFDDE+ALIRFDMSEYMEKFAAS LNGAPPG Sbjct: 541 TGKRPIGSFMFLGPTGVGKTELAKALAEVLFDDEAALIRFDMSEYMEKFAASRLNGAPPG 60- 0 Query: 600 YVGYDEGGELTEKVRNKPYSVLLFDEVEKAHPDIFNVLLQVLDDGVLTDSRGRKVDFSNT 65- 9 YVGYDEGGELT+KVRNKPYSVLLFDEVEKAHPDIFNVLLQVLDDG+LTDSRGRKVDFSNT Sbjct: 601 YVGYDEGGELTQKVRNKPYSVLLFDEVEKAHPDIFNVLLQVLDDGILTDSRGRKVDFSNT 66- 0 Query: 660 IIIMTSNLGATALRDDKTVGFGAKDISHDYTAMQKRIMEELKKAYRPEFINRIDEKVVFH 71- 9 IIIMTSNLGATALRDDKTVGFG KDI D+ AM+KRI+EEL+IK YRPEFINRIDEKVVFH Sbjct: 661 IIIMTSNLGATALRDDKTVGFGVKDIHQDHQAMEKRILEELRKTYRPEFINRIDEKVVFH 72- 0 Query: 720 SLSQDNMREVVKIMVKPLILALKDKGMDLKFQPSALKHLAEDGYDIEMGARPLRRTIQTQ 77- 9 SL+QDNMR+VVKIMV+PLI L +KG+ LK QP ALKHL+E GYD MGARPLRRT+QT+ Sbjct: 721 SLTQDNMRDVVKIMVQPLITTLAEKGITLKIQPLALKHLSEVGYDEHMGARPLRRTLQTE 78- 0 Query: 780 VEDHLSELLLANQVKEGQVIKIGVSKGKLKFDIA 813 +ED LSEL+L+ ++ G +KIG+S GKL F IA Sbjct: 781 IEDKLSELILSRELTSGHTLKIGLSHGKLTFHIA 814 A related GBS gene <SEQ ID 8819> and protein <SEQ ID 8820> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04399 Lipop: Possible Site: -1 Crend: 9 McG: Discrim Score: -13.52 GvH: Signal Score (-7.5): -2.1 Possible site: 49 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -2.34 threshold: 0.0 INTEGRAL Likelihood = -2.34 Transmembrane 32-48 (32-49) PERIPHERAL Likelihood = 0.95 112 modified ALOM score: 0.97 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1935 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00096## There is also homology to SEQ ID 258. SEQ ID 8820 (GBS26) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 7 (lane 9; MW 93.3 kDa), in FIG. 167 (lane 16 & 17; MW 108 kDa) and in FIG. 239 (lane 14; MW 108 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 15 (lane 7; MW 18 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1477 A DNA sequence (GBSx1563) was identified in S. agalactiae <SEQ ID 4539> which encodes the amino acid sequence <SEQ ID 4540>. Analysis of this protein sequence reveals the following: TABLE-US-04400 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 4541> which encodes the amino acid sequence <SEQ ID 4542>. Analysis of this protein sequence reveals the following: TABLE-US-04401 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04402 Identities = 178/213 (83%), Positives = 199/213 (92%) Query: 1 MLIVLAGTIGAGKSSLAAALGQHLGTDVFYEAVDNNPVLDLYYQDPQKYAFLLQIFFLNK 60 MLIVLAGTIGAGKSSLAAALG+HLGTDVFYEAVDNNPVLDLYYQDP+KYAFLLQI+FLNK Sbjct: 1 MLIVLAGTIGAGKSSLAAALGEHLGTDVFYEAVDNNPVLDLYYQDPKKYAFLLQIYFLNK 60 Query: 61 RFQSIKEAYKANNNVLDRSIFEDELFLTLNYKNGNVTKTELDIYKELLANMLEELEGMPK 120- RF+SIKEAY+A+NN+LDRSIFEDELFL LNYKNGNVTKTELDIY+ELLANMLEELEGMPK Sbjct: 61 RFKSIKEAYQADNNILDRSIFEDELFLKLNYKNGNVTKTELDIYQELLANMLEELEGMPK 120- Query: 121 KRPDLLVYIDVSFDKMLERIDKRGRSFEQVDSNPELYDYYKQVHSEYPEWYENYDVSPKI 18- 0 KRPDLL+YIDVSFDKMLERI++RGRSFEQVD NP L YY QVH EYP WYE+Y+VSPK+ Sbjct: 121 KRPDLLIYIDVSFDKMLERIERRGRSFEQVDGNPSLEQYYHQVHGEYPTWYEDYEVSPKM 18- 0 Query: 181 RIDGNKLDFVKNPEDLQHVLDTIDSELQKLDLL 213 +IDGN LDFV+NP+DL VL ID++L++L LL Sbjct: 181 KIDGNSLDFVQNPQDLATVLKMIDTKLKELHLL 213 A related GBS gene <SEQ ID 8821> and protein <SEQ ID 8822> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04403 Lipop: Possible Site: -1 Crend: 0 McG: Discrim Score: 3.94 GvH: Signal Score (-7.5): 1.42 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 7.69 threshold: 0.0 PERIPHERAL Likelihood = 7.69 49 modified ALOM score: -2.04 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 4540 (GBS9) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 1 (lane 5; MW 52 kDa) and FIG. 12 (lane 2 & 3; MW 50.3 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 2 (lane 6; MW 27 kDa) and FIG. 3 (lane 2; MW 25 kDa). The GBS9-GST fusion product was purified (FIG. 191, lane 6) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 318), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1478 A DNA sequence (GBSx1564) was identified in S. agalactiae <SEQ ID 4543> which encodes the amino acid sequence <SEQ ID 4544>. Analysis of this protein sequence reveals the following: TABLE-US-04404 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1182(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 4545> which encodes the amino acid sequence <SEQ ID 4546>. Analysis of this protein sequence reveals the following: TABLE-US-04405 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04406 Identities = 281/323 (86%), Positives = 305/323 (93%) Query: 3 QLNSSFMIGKVEIPHRTVLAPMAGITNSAFRTIAKEFGAGLVVMEMISEKGLLYNNEKTL 62 +LNSSF IG VEIPHRTVLAPMAG+TNSAFRTIAKEFGAGLVVMEMISEKGLLYNNEKTL Sbjct: 27 KLNSSFRIGDVEIPHRTVLAPMAGVTNSAFRTIAKEFGAGLVVMEMISEKGLLYNNEKTL 86 Query: 63 HMLHIDENEHPMSIQLFGGDAEGLKRAADFIQSNTKADIVDINMGCPVNKVVKNEAGAKW 122- HMLHIDENEHPMSIQLFGGDAEGLKRAADFIQ+NTKADIVDINMGCPVNKVVKNEAGAKW Sbjct: 87 HMLHIDENEHPMSIQLFGGDAEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKW 146- Query: 123 LRDPEKIYHIVKEVTSVLDIPLTVKMRTGWSDSSNAIENALAAESAGVSALAMHGRTREQ 18- 2 LRDP+KIYHIVKEVTSVLDIPLTVKMRTGW+DSS A+ENALAAESAGVSALAMHGRTREQ Sbjct: 147 LRDPDKIYHIVKEVTSVLDIPLTVKMRTGWADSSLAVENALAAESAGVSALAMHGRTREQ 20- 6 Query: 183 MYTGTCDHETLGKVAKAVTSIPFIANGDIRTVHDAKFMIEEIGADAIMVGRGARSNPYIF 24- 2 MYTGTCDHETL +V+KA+T IPFI NGD+R+V DAKFMIEEIG DA+M+GR A +NPY+F Sbjct: 207 MYTGTCDHETLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLF 26- 6 Query: 243 TQINHFFETGEILFDLPFEKMLDVAEDHLTRLVNLKGETIAVREFRGLAFHYLRGKSGAA 30- 2 TQINHFFETG+ LPDLPF K LD+A+DHL RL+NLKGETIAVREFRGLAPHYLRG +GAA Sbjct: 267 TQINHFFETGQELPDLPFAKKLDIAKDHLKRLINLKGETIAVREFRGLAPHYLRGTAGAA 32- 6 Query: 303 KIRGAVSRAETLAEVQELFAGLR 325 K+RGAVSRAETLAEV+ + F +R Sbjct: 327 KVRGAVSRAETLAEVEAIFETVR 349 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1479 A DNA sequence (GBSx1565) was identified in S. agalactiae <SEQ ID 4547> which encodes the amino acid sequence <SEQ ID 4548>. Analysis of this protein sequence reveals the following: TABLE-US-04407 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2164(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> There is also homology to SEQ ID 3930: TABLE-US-04408 Identities = 235/288 (81%), Positives = 259/288 (89%) Query: 1 MDKIIKSISTSGSFRAYVLDCTSTVRTAQEKHQTLSSSTVALGRTLIANQILAANQKGNS 60 MDKIIKSI+ SG+FRAYVLD TETV AQEKH TLSSSTVALGRTLIANQILAANQKG+S Sbjct: 1 MDKIIKSIAQSGAFRAYVLDSTETVALAQEKHNTLSSSTVALGRTLIANQILAANQKGDS 60 Query: 61 KVTVKVIGDSSFGHIISVADTKGNVKGYIQNTGVDIKKTATGEVLVGPFMGNGHFVVITD 120- K+TVKVIGDSSFGHIISVADTKG+VKGYIQNTGVDIKKTATGEVLVGPFMGNGHFV I D Sbjct: 61 KITVKVIGDSSFGHIISVADTKGHVKGYIQNTGVDIKKTATGEVLVGPFMGNGHFVTIID 120- Query: 121 YATGQPYTSTTPLITGEIGEDFAYYLTESEQTPSAVGLNVLLDDEDKVKVAGGFMLQVLP 18- 0 Y TG PYTSTTPLITGEIGEDFAYYLTESEQTPSA+GLNVLLD+ DKVKVAGGFM+QVLP Sbjct: 121 YGTGNPYTSTTPLITGEIGEDFAYYLTESEQTPSAIGLNVLLDENDKVKVAGGFMVQVLP 18- 0 Query: 181 GASDEEISRYEKRIQEMPSISSLLESENHIESLLSAIYGEDDYKRLSEDSLAFYCDCSKE 24- 0 GAS+EEI+RYEKR+QEMP+IS LL S+NH+++LL AIYG++ YKRLSE+ L+F CDCS+E Sbjct: 181 GASEEEIARYEKRLQEMPAISHLLASKNHVDALLEAIYGDEPYKRLSEEPLSFQCDCSRE 24- 0 Query: 241 RFEAALLTLGTKELQAMKDEDKGVEITCQFCNQTYYFTEEDLEKIIND 288 RFEAAL+TL +LQAM DEDKG EI CQFC Y F E DLE II+D Sbjct: 241 RFEAALMTLPKADLQAMIDEDKGAEIVCQFCGTKYQFNESDLEAIISD 288 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1480 A DNA sequence (GBSx1566) was identified in S. agalactiae <SEQ ID 4549> which encodes the amino acid sequence <SEQ ID 4550>. This protein is predicted to be surface-located membrane protein 1 (Imp1). Analysis of this protein sequence reveals the following: TABLE-US-04409 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4312(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04410 >GP: AAB93480 GB: AF019377 tellurite resistance protein [Rhodobacter sphaeroides] Identities = 64/350 (18%), Positives = 146/350 (41%), Gaps = 7/350 (2%) Query: 44 LTPAQKSAISEKTPALVDTFVGDQNALLDFGQSAVEGVNTTVNHILSEQKKIQIPQVDDL 103- L A E + + V D +++ FG A + T +L++ K + D Sbjct: 34 LASAPPEKAQEIRRRMAELNVSDSQSIIGFGSKAQAELQTISQQMLADVKNKDVGPAGDS 93 Query: 104 LKNANRELNGFIAKYKDATPAELEKKPNLIQKLFKQSKTSLQEFYFDSQNIEQKMDMMAA 16- 3 L+ + GF + ++ +K + ++L ++ F ++++Q++D + Sbjct: 94 LREVVSTIRGF-----SVSEFDVRRKASWWERLLGRT-APFARFVARYEDVQQQIDRITQ 147- Query: 164 NVVKQEDTLARNIVSAEMLIEDNTKSIENLVGVIAFIESSQAEAANRASHLQQEILALDS 22- 3 +++ E L ++I ++L + L IA + A+ R ++ +A Sbjct: 148 SLLTHEHRLLKDIKGLDILYARTLDFYDELALYIAAGDEVLADLDGRVIPAKEAEVAATP 20- 7 Query: 224 QTSEYQIKSNQLARMTEVINTLEQQHPEYVSRLYVAWATTPQMRNLVKVSSDMRQKLGML 28- 3 + + IK+ +L + + LE++ + V + P +R + + + ++ Sbjct: 208 E-GDRMIKAQELRDLRAARDDLERRVHDLKLTRQVTMQSLPSIRLVQENDKALVTRINST 26- 6 Query: 284 RRNTIPTMKLSIAQLGMMQQSVKSGVTADAIVNANNAALQMLAETSKEAIPMLEKTAQSP 34- 3 NT+P + +AQ +Q+S ++ + N L AE ++A ++ K + Sbjct: 267 LVNTVPLWETQLAQAVTIQRSREAAEAVRGASDLTNELLTANAENLQQANKIVRKEMERG 32- 6 Query: 344 TVSIKSVTALAESLVAQNNGIIAAIDKGRKERAQLESAVIKSAETINDSV 393 I++V +L+A N +A D+GR RA E+ + + + D++ Sbjct: 327 VFDIEAVKKANATLIATINESLAIADEGRARRATAETELQRMEAELRDTL 376 A related DNA sequence was identified in S. pyogenes <SEQ ID 4551> which encodes the amino acid sequence <SEQ ID 4552>. Analysis of this protein sequence reveals the following: TABLE-US-04411 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3230(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04412 Identities = 333/413 (80%), Positives = 379/413 (91%) Query: 5 FNFDIDQIADNAITKTDKTTEIISNQTTSQTGQIAFFEKLTPAQKSAISEKTPALVDTFV 64 FNFDIDQIADNA+ KTDKTT+IIS+ T GQI+FFEKL+ Q++AI+ K PALVDTF+ Sbjct: 4 FNFDIDQIADNAVIKTDKTTDIISDLPTDTNGQISFFEKLSADQQTAITAKAPALVDTFL 63 Query: 65 GDQNALLDFGQSAVEGVNTTVNHILSEQKKIQIPQVDDLLKNANRELNGFIAKYKDATPA 124- DQNALLDFGQSAVEGVN TVNHIL+EQKK+QIPQVDDLLK+ NRELNGFIAKYKDATP Sbjct: 64 ADQNALLDFGQSAVEGVNATVNHILAEQKKLQIPQVDDLLKSTNRELNGFIAKYKDATPV 123- Query: 125 ELEKKPNLIQKLFKQSKTSLQEFYFDSQNIEQKMDMMAANVVKQEDTLARNIVSAEMLIE 18- 4 +L+KKPN +QKLFKQS+ +LQEFYFDSQNIEQKMD MAA VVKQEDTLARNIVSAE+LIE Sbjct: 124 DLDKKPNFLQKLFKQSRDTLQEFYFDSQNIEQKMDSMAAAVVKQEDTLARNIVSAELLIE 18- 3 Query: 185 DNTKSIENLVGVIAFIESSQAEAANRASHLQQEILALDSQTSEYQIKSNQLARMTEVINT 24- 4 DNTKSIE+LVGVIAFIE+SQ EA+ RA+ LQ+++ DS T +YQIK++ LAR TEVINT Sbjct: 184 DNTKSIEHLVGVIAFIEASQKEASQRAAALQKDLKTKDSATPDYQIKADLLARTTEVINT 24- 3 Query: 245 LEQQHPEYVSRLYVAWATTPQMRNLVKVSSDMRQKLGMLRRNTIPTMKLSIAQLGMMQQS 30- 4 LEQQH EY+SRLYVAWATTPQMRNLVKVSSDMRQKLGMLRRNTIPTMKLSIAQLGMMQQS Sbjct: 244 LEQQHTEYLSRLYVAWATTPQMRNLVKVSSDMRQKLGMLRRNTIPTMKLSIAQLGMMQQS 30- 3 Query: 305 VKSGVTADAIVNANNAALQMLAETSKEAIPMLEKTAQSPTVSIKSVTALAESLVAQNNGI 36- 4 VKSG+TADAI+NANNAALQMLAETSKEAIP LE++AQ+PT+S+KSVT+LAESLVAQNNGI Sbjct: 304 VKSGMTADAIINANNAALQMLAETSKEAIPALEQSAQNPTLSMKSVTSLAESLVAQNNGI 36- 3 Query: 365 IAAIDKGRKERAQLESAVIKSAETINDSVKIRDKKIVEALLNEGKSTQEKVDE 417 IAAID GRKERAQLESA+I+SAETINDSVK+RD+ IV+ALL+EGK TQ+ +D+ Sbjct: 364 IAAIDHGRKERAQLESAIIRSAETINDSVKLRDQNIVQALLSEGKETQKTIDK 416 SEQ ID 4550 (GBS201) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 5; MW 49 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 54 (lane 3; MW 74.5 kDa) and in FIG. 62 (lane 8 & 9; MW 74.5 kDa). The GBS201-GST fusion product was purified (FIG. 209, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 304), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1481 A DNA sequence (GBSx1567) was identified in S. agalactiae <SEQ ID 4553> which encodes the amino acid sequence <SEQ ID 4554>. This protein is predicted to be rhoptry protein. Analysis of this protein sequence reveals the following:

TABLE-US-04413 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.58 Transmembrane 13-29 (10-31) INTEGRAL Likelihood = -1.54 Transmembrane 33-49 (33-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.3633(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4555> which encodes the amino acid sequence <SEQ ID 4556>. Analysis of this protein sequence reveals the following: TABLE-US-04414 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-04415 Identities = 115/239 (48%), Positives = 162/239 (67%), Gaps = 3/239 (1%) Query: 32 EVIATLLIIGGGYCAYYVYD-KKRLKRFTSNQRIEALKSDIKETDQDIRHLEILKKDNRS 90 - +++ + I G GY + V +KRL + +++E LK+ I+ D+ +R L+ D+ Sbjct: 42 DILPAIAIGGTGYAIFRVRSHQKRLAKAKIAKQLEDLKAKIQLADRKVRLLDTYLADHDD 101- Query: 91 KEYIKLAHQILPQLDLIRNEANQLQKAIEPNIYKRITKKANTFSNEINEQLIKLHASPEL 150- +Y LA Q+LPQL I+ +A L+ ++P IY+RITKKAN ++I QL L + L Sbjct: 102 FQYNVLAQQLLPQLSDIKAKAITLKDQLDPQIYRRITKKANDVESDITLQLETLQIATTL 16- 1 Query: 151 --EPISDQEDEMIRIAPELKPFYHNIQDDHFAILKKIEEADNKAELAAIHQANMKRFTDV 20- 8 +P+ +I APELKP+Y NIQ DH AIL KI+ ADN+ EL A+H ANM+RF D+ Sbjct: 162 NPQPLKTPSPNLINKAPELKPYYDNIQTDHQAILAKIQGADNQEELLALHDANMRRFEDI 22- 1 Query: 209 LAGYIRIKQSPKNFNNAKERLEQALQAIKKFNLDLDETLRQLNESDMKDFDVSLRMMQG 267- L GY++IK+ PKN+ NA RLEQA QAI++F+ DLDETLR+LNESD+KDFD+SLR+MQG Sbjct: 222 LTGYLKIKEEPKNYYNAAARLEQAKQAIQQFDEDLDETLRRLNESDLKDFDISLRIMQG 280- SEQ ID 4554 (GBS265) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 54 (lane 2; MW 56 kDa) and in FIG. 62 (lane 6; MW 56.3 kDa). The GBS265-GST fusion product was purified (FIG. 207, lane 5) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 258A) and FACS (FIG. 258B). These tests confirm that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1482 A DNA sequence (GBSx1568) was identified in S. agalactiae <SEQ ID 4557> which encodes the amino acid sequence <SEQ ID 4558>. This protein is predicted to be glutamate--cysteine ligase (gshA). Analysis of this protein sequence reveals the following: TABLE-US-04416 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.70 Transmembrane 575-591 (575-591) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04417 >GP: AAG08588 GB: AE004933 glutamate--cysteine ligase [Pseudomonas aeruginosa] Identities = 142/468 (30%), Positives 220/468 (46%), Gaps = 62/468 (13%) Query: 12 SHLPIL-QATFGLERESLRIHQPTQRVAQTPHPKTLGSRNYHPYIQTDYSEPQLELITPI 70 - ++LP+L + G+ERE LR+ ++A TPHP+ LGS HP I TDYSE LE ITP Sbjct: 16 ANLPLLTECLHGIERECLRVDSDG-KLALTPHPRALGSTLTHPQITTDYSEALLEFITPT 74 Query: 71 AKDSQEAIRFLKAISDVAGRSINHDEYLWPLSMPPKV-REEDIQIAQLEDA----FEYDY 125- D + + L+ I A ++ EYLW SMP ++ EE I IA+ + +Y Y Sbjct: 75 ETDVADTLGDLERIHRFASSKLD-GEYLWSPSMPCELPDEESIPIARYGSSMIGRLKYVY 133- Query: 126 RKYLEKTYGKLIQSISGIHYNLGLGQELLTSLFELSQAD-NAIDFQNQLYMKLSQNFLRY 18- 4 RK L YGK +Q I+GIHYN L + L L + ++ + D+Q+ Y+ L +NF RY Sbjct: 134 RKGLALRYGKTMQCIAGIHYNFSLPERLWPLLRQAEGSELSERDYQSAAYIALIRNFRRY 19- 3 Query: 185 RWLLTYLYGASPVAEEDFLDQKLNNPVR------------SLRNSHLGYVNHKDIRIS-- 23- 0 WLL YL+GASP + FL + + R SLR S LGY N+ ++ Sbjct: 194 SWLLMYLFGASPALDAGFLRGRPSQLERLDEHTLYLPYATSLRMSDLGYQNNAQAGLTPC 25- 3 Query: 231 YTSLKDYVNDLENAV---------------------KSGQLIAEKEFYSPVRLR-----G 26- 4 Y L+ Y++ L AV + L E E+YS +R + G Sbjct: 254 YNDLQSYIDSLRQAVSTPYPPYEKVGTKQDGEWVQLNTNILQIENEYYSSIRPKRVTYTG 31- 3 Query: 265 SKACRNYLEKGITYLEFRTFDLNPFSPIGITQETVDTVHLFLLALLWIDS---------- 31- 4 + + +G+ Y+E R D+NPF P+GI + + FLL + DS Sbjct: 314 ERPVQALAARGVQYVEVRCLDINPFLPLGIDLDEARFLDAFLLFCAFSDSPLLNGECSDA 37- 3 Query: 315 SSHIDQDIKEANRLN-DLIALSHPLEKLPNQAPVSDLVDAMQSVIQHFNLSPYYQDLLES 37- 3 + + +KE R L P+E + + + +++ + L + Sbjct: 374 TDNFLAVVKEGRRPGLQLQRRGQPVELQVWANELLERIADTAALLDRARGGEAHAAALAA 43- 3 Query: 374 VKRQIQSPELTVAGQLLEMI--EGLSLETFGQRQGQIYHDYAWEAPYA 419 + ++ ELT + Q+L+++ G S E F RQ + + +Y + P A Sbjct: 434 QRAKVADAELTPSAQVLKVMRERGESFEAFSLRQSREHAEYFRQHPLA 481 There is also homology to SEQ ID 4560. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1483 A DNA sequence (GBSx1569) was identified in S. agalactiae <SEQ ID 4561> which encodes the amino acid sequence <SEQ ID 4562>. Analysis of this protein sequence reveals the following: TABLE-US-04418 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1504(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04419 >GP:CAB73814 GB:AL139078 helix-turn-helix containing protein [Campylobacter jejuni] Identities = 107/223 (47%), Positives = 148/223 (65%), Gaps = 7/223 (3%) Query: 1 MDKEKLDYWKTIITFLHNVLGDNYEIVLHVVDENDIYIGELVNSHISGRTISSPLTTFAL 60 MD+ + + + FL VLG+ YEIV HV+ E+ YI + NSHISGR++ SPLT FA Sbjct: 1 MDEGQKQQFIKLTYFLGEVLGEQYEIVFHVITEDGAYIAAIANSHISGRSLDSPLTAFAS 60 Query: 61 DLIKNKVYKEKDFVTNYKAIVSPLNKEVRGSTFFIKNAQNELEGMLCINLDISAYQNIAL 120- +L++NK Y EKDF+ +YKA+V +K +RGSTFFIKN ++L G+LCIN D S +++ Sbjct: 61 ELMQNKKYLEKDFLCDYKALVGK-SKLIRGSTFFIKN-HDKLVGILCINHDTSIMRDLIC 118- Query: 121 DILDLVNL-NVNKILPKSPQKISLPQQEEPVEVLSGNIQDIISEIVDPSLLNQNIHLSQE 17- 9 ++DL + ++ IL IS Q + +E LS +I+DI+ + VD S LN + LS Sbjct: 119 KMIDLEKIGDMGDIL----GNISFSQNDSSIETLSHSIEDILVQSVDSSYLNSDYQLSIT 17- 4 Query: 180 VKVEIVSKLHEKGVFQLKGAVSKVAEVLNISEPSVYRYLKKIE 222 K EI KL+EKG+F +KGAV VA+ L ISEPSVYRYLKK + Sbjct: 175 QKEEIAEKLYEKGIFNIKGAVPIVAKFLKISEPSVYRYLKKFK 217 A related DNA sequence was identified in S. pyogenes <SEQ ID 4563> which encodes the amino acid sequence <SEQ ID 4564>. Analysis of this protein sequence reveals the following: TABLE-US-04420 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1636(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04421 Identities = 169/224 (75%), Positives = 198/224 (87%), Gaps = 3/224 (1%) Query: 1 MDKEKLDYWKTIITFLHNVLGDNYEIVLHVVDENDIYIGELVNSHISGRTISSPLTTFAL 60 MDKE L+YWKT+ITFLH+VLGDNYEI+LHV+D+NDIYIGELVNSHISGR+ SPLTTFAL Sbjct: 1 MDKETLNYWKTVITFLHDVLGDNYEIILHVIDKNDIYIGELVNSHISGRSKQSPLTTFAL 60 Query: 61 DLIKNKVYKEKDFVTNYKAIVSPLNKEVRGSTFFIKNAQNELEGMLCINLDISAYQNIAL 120- DLI NKVYKEKDFVTNYKAIVSP +KEVRGSTFFIK+ + LEGMLCINLDISAYQ +A Sbjct: 61 DLITNKVYKEKDFVTNYKAIVSPQHKEVRGSTFFIKDKKGNLEGMLCINLDISAYQGVAR 120- Query: 121 DILDLVNLNVNKILP--KSPQKISLPQQEEPVEVLSGNIQDIISEIVDPSLLNQNIHLSQ 17- 8 D+L LVNLN+ +P K P+ ++ PQ EE VE+L+ NIQDII +I+DPSLL N+HLSQ Sbjct: 121 DLLKLVNLNLEHFIPTAKEPKTVT-PQPEEAVEILTSNIQDIIGQIIDPSLLRHNVHLSQ 17- 9 Query: 179 EVKVEIVSKLHEKGVFQLKGAVSKVAEVLNISEPSVYRYLKKIE 222 +VK++IV+KL+EKGVFQLKGAVSKVA++L ISEPSVYRYLKKIE Sbjct: 180 DVKIDIVAKLYEKGVFQLKGAVSKVADILCISEPSVYRYLKKIE 223 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1484 A DNA sequence (GBSx1570) was identified in S. agalactiae <SEQ ID 4565> which encodes the amino acid sequence <SEQ ID 4566>. This protein is predicted to be regulatory protein pfoR. Analysis of this protein sequence reveals the following: TABLE-US-04422 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.80 Transmembrane 299-315 (296-325) INTEGRAL Likelihood = -7.54 Transmembrane 172-188 (169-193) INTEGRAL Likelihood = -7.17 Transmembrane 71-87 (66-98) INTEGRAL Likelihood = -4.99 Transmembrane 261-277 (260-278) INTEGRAL Likelihood = -2.81 Transmembrane 128-144 (127-149) INTEGRAL Likelihood = -2.18 Transmembrane 101-117 (101-119) INTEGRAL Likelihood = -0.53 Transmembrane 198-214 (197-214) ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04423 >GP:CAA60239 GB:X86525 pfoS [Clostridium perfringens] Identities = 96/147 (65%), Positives = 122/147 (82%) Query: 100 GTGIIPGFLAGYLVGFLVKWMERNIPGGLDLISIIIIGAPLTRLVAKLLTPLINSTLLTI 15- 9 G GI+PGF+AGYL F++K++E+ IP GLDLI II++GAPL R +A + PL+ +TL I Sbjct: 1 GFGILPGFIAGYLGSFVIKFLEKKIPAGLDLIVIIVLGAPLVRGIAAISNPLVETTLQNI 60 Query: 160 GDILTSGAHSNPILMGIILGGTIVVVATAPLSSMALTAMLGLTGMPMAIGALSVFGSSFM 21- 9 G ++T+ + ++PI+MGIILGG + VVATAPLSSMALTAMLGLTG+PMAIGAL+VFGSSFM Sbjct: 61 GGVITATSTASPIMMGIILGGIVTVVATAPLSSMALTAMLGLTGLPMAIGALAVFGSSFM 120- Query: 220 NGVLFHKLKLGSRKDNIAFAVEPLTQA 246 N V F K+K GS+KD IA A+EPLTQA Sbjct: 121 NLVFFGKMKFGSKKDTIAVAIEPLTQA 147 A related DNA sequence was identified in S. pyogenes <SEQ ID 4567> which encodes the amino acid sequence <SEQ ID 4568>. Analysis of this protein sequence reveals the following: TABLE-US-04424 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.70 Transmembrane 303-319 (296-325) INTEGRAL Likelihood = -7.11 Transmembrane 70-86 (66-98) INTEGRAL Likelihood = -6.53 Transmembrane 172-188 (169-193) INTEGRAL Likelihood = -4.83 Transmembrane 261-277 (260-278) INTEGRAL Likelihood = -2.55 Transmembrane 101-117 (101-119) INTEGRAL Likelihood = -2.28 Transmembrane 124-140 (124-140) INTEGRAL Likelihood = -1.91 Transmembrane 198-214 (197-215) ----- Final Results ----- bacterial membrane --- Certainty = 0.4482(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04425 >GP:CAA60239 GB:X86525 pfoS [Clostridium perfringens] Identities = 95/147 (64%), Positives = 123/147 (63%) Query: 100 GTGIIPGFVAGYVVSFLIKWMEKNIPGGLDLISIIIVGAPLTRFLAQLITPVINSTLLTI 15- 9 G GI+PGF+AGY+ SF+IK++EK IP GLDLI II++GAPL R +A + P++ +TL I Sbjct: 1 GFGILPGFIAGYLGSFVIKFLEKKIPAGLDLIVIIVLGAPLVRGIAAISNPLVETTLQNI 60 Query: 160 GDILTSSANSNPIIMGMILGGTIVVVATAPLSSMALTAMLGLTGIPMAIGALSVFGSSFM 21- 9 G ++T+++ ++PI+MG+ILGG + VVATAPLSSMALTAMLGLTG+PMAIGAL+VFGSSFM Sbjct: 61 GGVITATSTASPIMMGIILGGIVTVVATAPLSSMALTAMLGLTGLPMAIGALAVFGSSFM 120- Query: 220 NGVLFYRLKLGERKDNIAFAIEPLTQA 246 N V F ++K G +KD IA AIEPLTQA Sbjct: 121 NLVFFGKMKFGSKKDTIAVAIEPLTQA 147 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04426 Identities = 302/339 (89%), Positives = 330/339 (97%) Query: 1 MNIIIGTSLLILVLAIFTLFNYKAPYGTKAMGALASAACASFLVEAFQDSFFGKVLGFQF 60 M+IIIGTSLLILVLAIF+LFNYKAP+G KAMGALASAACASFLVEAFQDSFFGKVLGFQF Sbjct: 1 MDIIIGTSLLILVLAIFSLFNYKAPHGAKAMGALASAACASFLVEAFQDSFFGKVLGFQF 60 Query: 61 LSEVGGANGSLSGVAAAILVAIAIGVTPGYAVLIGLSVSGTGIIPGFLAGYLVGFLVKWM 120- LSEVGGANGSLSGVAAAILVAIAIGV+PGYAVLIGLSVSGTGIIPGF+AGY+V FL+KWM Sbjct: 61 LSEVGGANGSLSGVAAAILVAIAIGVSPGYAVLIGLSVSGTGIIPGFVAGYVVSFLIKWM 120- Query: 121 ERNIPGGLDLISIIIIGAPLTRLVAKLLTPLINSTLLTIGDILTSGAHSNPILMGIILGG 18- 0 E+NIPGGLDLISIII+GAPLTR +A+L+TP+INSTLLTIGDILTS A+SNPI+MG+ILGG Sbjct: 121 EKNIPGGLDLISIIIVGAPLTRFLAQLITPVINSTLLTIGDILTSSANSNPIIMGMILGG 18- 0 Query: 181 TIVVVATAPLSSMALTAMLGLTGMPMAIGALSVFGSSFMNGVLFHKLKLGSRKDNIAFAV 24- 0 TIVVVATAPLSSMALTAMLGLTG+PMAIGALSVFGSSFMNGVLF++LKLG RKDNIAFA+ Sbjct: 181 TIVVVATAPLSSMALTAMLGLTGIPMAIGALSVFGSSFMNGVLFYRLKLGERKDNIAFAI 24- 0 Query: 241 EPLTQADVTSANPIPIYVTNFVGGAACGILIALMKLVNDTPGTATPIAGFAVMFAYNPMI 30- 0 EPLTQADVTSANPIPIYVTNFVGGAACG+LIALMKLVNDTPGTATPIAGFAVMFAYNP+ Sbjct: 241 EPLTQADVTSANPIPIYVTNFVGGAACGVLIALMKLVNDTPGTATPIAGFAVMFAYNPVA 30- 0 Query: 301 KVLITALGCIILSLLAGYFGGIVFKDYKLVTKEELQARD 339 KVLITALGCII+SL+ GY GG VFK+Y+LVTK+ELQAR+ Sbjct: 301 KVLITALGCIIISLIVGYIGGSVFKNYRLVTKQELQARN 339 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1485 A DNA sequence (GBSx1571) was identified in S. agalactiae <SEQ ID 4569> which encodes the amino acid sequence <SEQ ID 4570>. This protein is predicted to be adenylosuccinate synthetase (purA). Analysis of this protein sequence reveals the following: TABLE-US-04427 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0560(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04428 >GP: CAB16079 GB: Z99124 adenylosuccinate synthetase [Bacillus subtilis] Identities = 320/427 (74%), Positives = 378/427 (87%) Query: 1 MTSVVVVGTQWGDEGKGKITDFLSADAEVIARYQGGDNAGHTIVIDNKKFKLHLIPSGIF 60 M+SVVVVGTQWGDEGKGKITDFLS +AEVIARYQGG+NAGHTI D +KLHLIPSGIF Sbjct: 1 MSSVVVVGTQWGDEGKGKITDFLSENAEVIARYQGGNNAGHTIKFDGITYKLHLIPSGIF 60 Query: 61 FKEKISVIGNGVVVNPKSLVKELAYLHGEGVTTDNLRISDRAHVILPYHIKLDQLQEDAK 120- +K+K VIGNG+VV+PK+LV ELAYLH V+TDNLRIS+RAHVILPYH+KLD+++E+ K Sbjct: 61 YKDKTCVIGNGMVVDPKALVTELAYLHERNVSTDNLRISNRAHVILPYHLKLDEVEEERK 120- Query: 121 GDNKIGTTIKGIGPAYMDKAARVGIRIADLLDREVFAERLKINLAEKNRLFEKMYDSTPL 18- 0 G NKIGTT KGIGPAYMDKAAR+GIRIADLLDR+ FAE+L+ NL EKNRL EKMY++ Sbjct: 121 GANKIGTTKKGIGPAYMDKAARIGIRIADLLDRDAFAEKLERNLEEKNRLLEKMYETEGF 18- 0 Query: 181 EFDDIFEEYYEYGQQIKQYVTDTSVILNDALDAGKRVLFEGAQGVMLDIDQGTYPFVTSS 24- 0 + +DI +EYYEYGQQIK+YV DTSV+LNDALD G+RVLFEGAQGVMLDIDQGTYPFVTSS Sbjct: 181 KLEDILDEYYEYGQQIKKYVCDTSVVLNDALDEGRRVLFEGAQGVMLDIDQGTYPFVTSS 24- 0 Query: 241 NPVAGGVTIGSGVGPSKINKVVGVCKAYTSRVGDGPFPTELFDEVGDRIREIGKEYGTTT 30- 0 NPVAGGVTIGSGVGP+KI VVGV KAYT+RVGDGPFPTEL DE+GD+IRE+G+EYGTTT Sbjct: 241 NPVAGGVTIGSGVGPTKIKHVVGVSKAYTTRVGDGPFPTELKDEIGDQIREVGREYGTTT 30- 0 Query: 301 GRPRRVGWFDSVVMRHSRRVSGITNLSLNSIDVLSGLDTVKICVAYDLDGKRIDYYPASL 36- 0 GRPRRVGWFDSVV+RH+RRVSGIT+LSLNSIDVL+G++T+KICVAY G+ I+ +PASL Sbjct: 301 GRPRRVGWFDSVVVRHARRVSGITDLSLNSIDVLAGIETLKICVAYRYKGEIIEEFPASL 36- 0 Query: 361 EQLKRCKPIYEELPGWSEDITACRSLDDLPENARNYVRRVGELVGVRISTFSVGPGREQT 42- 0 + L C+P+YEE+PGW+EDIT +SL +LPENAR+Y+ RV +L G+ +S FSVGP R QT Sbjct: 361 KALAECEPVYEEMPGWTEDITGAKSLSELPENARHYLERVSQLTGIPLSIFSVGPDRSQT 42- 0 Query: 421 NILESVW 427 N+L SV+ Sbjct: 421 NVLRSVY 427 A related DNA sequence was identified in S. pyogenes <SEQ ID 4571> which encodes the amino acid sequence <SEQ ID 4572>. Analysis of this protein sequence reveals the following: TABLE-US-04429 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0560(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04430 Identities = 406/430 (94%), Positives = 421/430 (97%) Query: 1 MTSVVVVGTQWGDEGKGKITDFLSADAEVIARYQGGDNAGHTIVIDNKKFKLHLIPSGIF 60 MTSVVVVGTQWGDEGKGKITDFLSADAEVIARYQGGDNAGHTIVID KKFKLHLIPSGIF Sbjct: 1 MTSVVVVGTQWGDEGKGKITDFLSADAEVIARYQGGDNAGHTIVIDGKKFKLHLIPSGIF 60 Query: 61 FKEKISVIGNGVVVNPKSLVKELAYLHGEGVTTDNLRISDRAHVILPYHIKLDQLQEDAK 120- F +KISVIGNGVVVNPKSLVKELAYLH EGVTTDNLRISDRAHVILPYHI+LDQLQEDAK Sbjct: 61 FPQKISVIGNGVVVNPKSLVKELAYLHDEGVTTDNLRISDRAHVILPYHIQLDQLQEDAK 120- Query: 121 GDNKIGTTIKGIGPAYMDKAARVGIRIADLLDREVFAERLKINLAEKNRLFEKMYDSTPL 18- 0 GDNKIGTTIKGIGPAYMDKAARVGIRIADLLD+++FAERL+INLAEKNRLFEKMYDSTPL Sbjct: 121 GDNKIGTTIKGIGPAYMDKAARVGIRIADLLDKDIFAERLRINLAEKNRLFEKMYDSTPL 18- 0 Query: 181 EFDDIFEEYYEYGQQIKQYVTDTSVILNDALDAGKRVLFEGAQGVMLDIDQGTYPFVTSS 24- 0 +FD IFEEYY YGQ+IKQYVTDTSVILNDALDAGKRVLFEGAQGVMLDIDQGTYPFVTSS Sbjct: 181 DFDAIFEEYYAYGQEIKQYVTDTSVILNDALDAGKRVLFEGAQGVMLDIDQGTYPFVTSS 24- 0 Query: 241 NPVAGGVTIGSGVGPSKINKVVGVCKAYTSRVGDGPFPTELFDEVGDRIREIGKEYGTTT 30- 0 NPVAGGVTIGSGVGP+KINKVVGVCKAYTSRVGDGPFPTELFDEVG+RIRE+G EYGTTT Sbjct: 241 NPVAGGVTIGSGVGPNKINKVVGVCKAYTSRVGDGPFPTELFDEVGERIREVGHEYGTTT 30- 0 Query: 301 GRPRRVGWFDSVVMRHSRRVSGITNLSLNSIDVLSGLDTVKICVAYDLDGKRIDYYPASL 36- 0 GRPRRVGWFDSVVMRHSRRVSGITNLSLNSIDVLSGLDTVKICVAYDLDGKRIDYYPA+L Sbjct: 301 GRPRRVGWFDSVVMRHSRRVSGITNLSLNSIDVLSGLDTVKICVAYDLDGKRIDYYPANL 36- 0 Query: 361 EQLKRCKPIYEELPGWSEDITACRSLDDLPENARNYVRRVGELVGVRISTFSVGPGREQT 42- 0 EQLKRCKPIYEELPGW EDIT RSLD+LPENARNYVRRVGELVGVRISTFSVGPGREQT Sbjct: 361 EQLKRCKPIYEELPGWQEDITGVRSLDELPENARNYVRRVGELVGVRISTFSVGPGREQT 42- 0 Query: 421 NILESVWSNI 430 NILESVW++I Sbjct: 421 NILESVWASI 430 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1486 A DNA sequence (GBSx1572) was identified in S. agalactiae <SEQ ID 4573> which encodes the amino acid sequence <SEQ ID 4574>. Analysis of this protein sequence reveals the following:

TABLE-US-04431 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.29 Transmembrane 30-46 (22-55) INTEGRAL Likelihood = -2.97 Transmembrane 110-126 (109-126) INTEGRAL Likelihood = -0.11 Transmembrane 89-105 (89-106) ----- Final Results ----- bacterial membrane --- Certainty = 0.4715(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8823> which encodes amino acid sequence <SEQ ID 8824> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-04432 Lipop Possible site: -1 Crend: 10 SRCFLG: 0 McG: Length of UR: 5 Peak Value of UR: 3.05 Net Charge of CR: 0 McG: Discrim Score: 4.64 GvH: Signal Score (-7.5): -1.66 Possible site: 36 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 37 ALOM program count: 2 value: -2.97 threshold: 0.0 INTEGRAL Likelihood = -2.97 Transmembrane 100-116 (99-116) PERIPHERAL Likelihood = 1.38 56 modified ALOM score: 1.09 icm1 HYPID: 7 CFP: 0.219 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2190(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database and no corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1487 A DNA sequence (GBSx1573) was identified in S. agalactiae <SEQ ID 4575> which encodes the amino acid sequence <SEQ ID 4576>. Analysis of this protein sequence reveals the following: TABLE-US-04433 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0967(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bactarial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1488 A DNA sequence (GBSx1574) was identified in S. agalactiae <SEQ ID 4577> which encodes the amino acid sequence <SEQ ID 4578>. This protein is predicted to be SgaT protein (sgaT). Analysis of this protein sequence reveals the following: TABLE-US-04434 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.80 Transmembrane 441-457 (436-464) INTEGRAL Likelihood = -7.64 Transmembrane 344-360 (339-376) INTEGRAL Likelihood = -6.58 Transmembrane 403-419 (392-422) INTEGRAL Likelihood = -6.48 Transmembrane 237-253 (235-261) INTEGRAL Likelihood = -5.79 Transmembrane 105-121 (99-127) INTEGRAL Likelihood = -5.52 Transmembrane 138-154 (137-155) INTEGRAL Likelihood = -4.78 Transmembrane 18-34 (14-38) INTEGRAL Likelihood = -2.97 Transmembrane 365-381 (365-383) INTEGRAL Likelihood = -0.69 Transmembrane 41-57 (41-57) INTEGRAL Likelihood = -0.16 Transmembrane 160-176 (160-176) ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04435 >GP: AAC77150 GB: AE000491 orf, hypothetical protein [Escherichia coli K12] Identities = 181/451 (40%), Positives = 274/451 (60%), Gaps = 25/451 (5%) Query: 11 FSQNILQNPAFFVGLLVLIGYLLLKKPLHDVFAGFIKATVGYLILNVGAGGLVNTFRPIL 70 - F ++ N +G++ +GY+LL+K + + G IK +G+++L G+G L +TF+P++ Sbjct: 30 FFNQVMTNAPLLLGIVTCLGYILLRKSVSVIIKGTIKTIIGFMLLQAGSGILTSTFKPVV 89 Query: 71 VALAKKFNLEAAVIDPYFGLASANAKLETMG-FISVATTALLIGFGINILLVALRKVTKV 129- +++ + + A+ D Y AS A ++ MG S A+L+ +NI V LR++T + Sbjct: 90 AKMSEVYGINGAISDTY---ASMMATIDRMGDAYSWVGYAVLLALALNICYVLLRRITGI 146- Query: 130 RTLFITGHIMVQQAATISVFVLLLIPQLRNGFGAWAV----GIICGLYWAVSSNMTVEAT 18- 5 RT+ +TGHIM QQA I+V + + G+ W I+ LYW ++SNM + T Sbjct: 147 RTIMLTGHIMFQQAGLIAVTLFIF------GYSMWTTIICTAILVSLYWGITSNMMYKPT 20- 0 Query: 186 QRLTGGGGFAIGHQQQFAIWFVDKVAPFFGKKEENLDNLKLPTFLNIFHDTVVASATLML 24- 5 Q +T G GF+IGHQQQFA W KVAPF GKKEE++++LKLP +LNIFHD +V++A +M Sbjct: 201 QEVTDGCGFSIGHQQQFASWIAYKVAPFLGKKEESVEDLKLPGWLNIFHDNIVSTAIVMT 26- 0 Query: 246 VFFGGILAVLGPDIMSNVKLIGPGAFVPTKQAFFMYILQTSLTFSVYLFILMQGVRMFVT 30- 5 +FFG IL G D + + K + +YILQT +F+V +FI+ QGVRMFV Sbjct: 261 IFFGAILLSFGIDTVQ---------AMAGKVHWTVYILQTGFSFAVAIFIITQGVRMFVA 31- 1 Query: 306 ELTNAFQGISNKLLPGSFPAVDVAASYGFGSSNAVLSGFAFGLIGQLITIALLVVFKNPI 36- 5 EL+ AF GIS +L+PG+ A+D AA Y F + NAV+ GF +G IGQLI + +LV + I Sbjct: 312 ELSEAFNGISQRLIPGAVLAIDCAAIYSF-APNAVVWGFMWGTIGQLIAVGILVACGSSI 37- 0 Query: 366 LIITGFVPVFFDNAAIAVYADKRGGWKAAVALSFISGIIQVALGAVAVGLLGLAGGYHGN 42- 5 LII GF+P+FF NA I V+A+ GGW+AA+ + + G+I++ AV L G++ + G Sbjct: 371 LIIPGFIPMFFSNATIGVFANHFGGWRAALKICLVMGMIEIFGCVWAVKLTGMS-AWMGM 42- 9 Query: 426 IDFEFPWLAFGYIFKYLGIAGYVIVCLFFLA 456 D+ F +GIA ++ + LA Sbjct: 430 ADWSILAPPMMQGFFSIGIAFMAVIIVIALA 460 A related DNA sequence was identified in S. pyogenes <SEQ ID 4579> which encodes the amino acid sequence <SEQ ID 4580>. Analysis of this protein sequence reveals the following: TABLE-US-04436 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.51 Transmembrane 441-457 (435-465) INTEGRAL Likelihood = -7.80 Transmembrane 344-360 (339-376) INTEGRAL Likelihood = -7.64 Transmembrane 238-254 (235-261) INTEGRAL Likelihood = -5.63 Transmembrane 105-121 (100-127) INTEGRAL Likelihood = -5.52 Transmembrane 138-154 (137-155) INTEGRAL Likelihood = -5.20 Transmembrane 400-416 (392-422) INTEGRAL Likelihood = -4.78 Transmembrane 18-34 (14-39) INTEGRAL Likelihood = -2.97 Transmembrane 365-381 (365-383) INTEGRAL Likelihood = -1.49 Transmembrane 160-176 (160-177) INTEGRAL Likelihood = -0.53 Transmembrane 41-57 (41-57) ----- Final Results ----- bacterial membrane --- Certainty = 0.5203(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04437 >GP: AAC77150 GB: AE000491 orf, hypothetical protein [Escherichia coli] Identities = 182/461 (39%), Positives = 279/461 (60%), Gaps = 25/461 (5%) Query: 1 MEMLLAPLNWFSQNILQNPAFFVGLLVLIGYLLLKKPIYEVFAGFVKATVGYLILNVGAG 60 ME+L F ++ N +G++ +GY+LL+K + + G +K +G+++L G+G Sbjct: 20 MEILYNIFTVFFNQVMTNAPLLLGIVTCLGYILLRKSVSVIIKGTIKTIIGFMLLQAGSG 79 Query: 61 GLVTTFRPILVALAKKFELKAAVIDPYFGLAAANTKLEEMG-FISVATTALLIGFGVNIL 119- L +TF+P++ +++ + + A+ D Y + A ++ MG S A+L+ +NI Sbjct: 80 ILTSTFKPVVAKMSEVYGINGAISDTYASMMAT---IDRMGDAYSWVGYAVLLALALNIC 136- Query: 120 LVALRKVTKVRTLFITGHIMVQQAATISVFVLLLIPQFQNAFGAWAV----GIICGLYWA 17- 5 V LR++T +RT+ +TGHIM QQA I+V + + + W I+ LYW Sbjct: 137 YVLLRRITGIRTIMLTGHIMFQQAGLIAVTLFIF------GYSMWTTIICTAILVSLYWG 19- 0 Query: 176 ISSNMTVEATQRLTGGGGFAIGHQQQFAIWFVDKVAPFFGKKEENLDNLKLPTFLNIFHD 23- 5 I+SNM + TQ +T G GF+IGHQQQFA W KVAPF GKKEE++++LKLP +LNIFHD Sbjct: 191 ITSNMMYKPTQEVTDGCGFSIGHQQQFASWIAYKVAPFLGKKEESVEDLKLPGWLNIFHD 25- 0 Query: 236 TVVASATLMLVFFGAILAVLGPDIMSDVDLIGPGAFNPAKQAFFMYILQTSLTFSVYLFI 29- 5 +V++A +M +FFGAIL G D + + K + +YILQT +F+V +FI Sbjct: 251 NIVSTAIVMTIFFGAILLSFGIDTVQAM---------AGKVHWTVYILQTGFSFAVAIFI 30- 1 Query: 296 LMQGVRMFVSELTNAFQGISSKLLPGSFPAVDVAASYGFGSSNAVLSGFAFGLIGQLITI 35- 5 + QGVRMFV+EL+ AF GIS +L+PG+ A+D AA Y F + NAV+ GF +G IGQLI + Sbjct: 302 ITQGVRMFVAELSEAFNGISQRLIPGAVLAIDCAAIYSF-APNAVVWGFMWGTIGQLIAV 36- 0 Query: 356 ALLVIFKNPILIITGFVPVFFDNAAIAVYADKRGGWKAAVALSFISGILQVALGAVAVGL 41- 5 +LV + ILII GF+P+FF NA I V+A+ GGW+AA+ + + G++++ AV L Sbjct: 361 GILVACGSSILIIPGFIPMFFSNATIGVFANHFGGWRAALKICLVMGMIEIFGCVWAVKL 42- 0 Query: 416 LGLTGGYHGNIDLVLPWLPFGYLFKFLGIAGYVLVCIFLLA 456 G++ + G D + P F +GIA ++ + LA Sbjct: 421 TGMS-AWMGMADWSILAPPMMQGFFSIGIAFMAVIIVIALA 460 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04438 Identities = 437/476 (91%), Positives = 457/476 (95%) Query: 1 MENFLAPLNWFSQNILQNPAFFVGLLVLIGYLLLKKPLHDVFAGFIKATVGYLILNVGAG 60 ME LAPLNWFSQNILQNPAFFVGLLVLIGYLLLKKP+++VFAGF+KATVGYLILNVGAG Sbjct: 1 MEMLLAPLNWFSQNILQNPAFFVGLLVLIGYLLLKLPIYEVFAGFVKATVGYLILNVGAG 60 Query: 61 GLVNTFRPILVALAKKFNLEAAVIDPYFGLASANAKLETMGFISVATTALLIGFGINILL 120- GLV TFRPILVALAKKF L+AAVIDPYFGLA+AN KLE MGFISVATTALLIGFG+NILL Sbjct: 61 GLVTTFRPILVALAKKFELKAAVIDPYFGLAAANTKLEEMGFISVATTALLIGFGVNILL 120- Query: 121 VALRKVTKVRTLFITGHIMVQQAATISVFVLLLIPQLRNGFGAWAVGIICGLYWAVSSNM 18- 0 VALRKVTKVRTLFITGHIMVQQAATISVFVLLLIPQ +N FGAWAVGIICGLYWA+SSNM Sbjct: 121 VALRKVTKVRTLFITGHIMVQQAATISVFVLLLIPQFQNAFGAWAVGIICGLYWAISSNM 18- 0 Query: 181 TVEATQRLTGGGGFAIGHQQQFAIWFVDKVAPFFGKKEENLDNLKLPTFLNIFHDTVVAS 24- 0 TVEATQRLTGGGGFAIGHQQQFAIWFVDKVAPFFGKKEENLDNLKLPTFLNIFHDTVVAS Sbjct: 181 TVEATQRLTGGGGFAIGHQQQFAIWFVDKVAPFFGKKEENLDNLKLPTFLNIFHDTVVAS 24- 0 Query: 241 ATLMLVFFGGILAVLGPDIMSNVKLIGPGAFVPTKQAFFMYILQTSLTFSVYLFILMQGV 30- 0 ATLMLVFFG ILAVLGPDIMS+V LIGPGAF P KQAFFMYILQTSLTFSVYLFILMQGV Sbjct: 241 ATLMLVFFGAILAVLGPDIMSDVDLIGPGAFNPAKQAFFMYILQTSLTFSVYLFILMQGV 30- 0 Query: 301 RMFVTELTNAFQGISNKLLPGSFPAVDVAASYGFGSSNAVLSGFAFGLIGQLITIALLVV 36- 0 RMFV+ELTNAFQGIS+KLLPGSFPAVDVAASYGFGSSNAVLSGFAFGLIGQLITIALLV+ Sbjct: 301 RMFVSELTNAFQGISSKLLPGSFPAVDVAASYGFGSSNAVLSGFAFGLIGQLITIALLVI 36- 0 Query: 361 FKNPILIITGFVPVFFDNAAIAVYADKRGGWKAAVALSFISGIIQVALGAVAVGLLGLAG 42- 0 FKNPILIITGFVPVFFDNAAIAVYADKRGGWKAAVALSFISGI+QVALGAVAVGLLGL G Sbjct: 361 FKNPILIITGFVPVFFDNAAIAVYADKRGGWKAAVALSFISGILQVALGAVAVGLLGLTG 42- 0 Query: 421 GYHGNIDFEFPWLAFGYIFKYLGIAGYVIVCLFFLAIPQLQFMKSKDKEAYYRGDA 476 GYHGNID PWL FGY+FK+LGIAGYV+VC+F LAIPQLQF K+KDKEAYYRG+A Sbjct: 421 GYHGNIDLVLPWLPFGYLFKFLGIAGYVLVCIFLLAIPQLQFAKAKDKEAYYRGEA 476 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1489 A DNA sequence (GBSx1575) was identified in S. agalactiae <SEQ ID 4581> which encodes the amino acid sequence <SEQ ID 4582>. Analysis of this protein sequence reveals the following: TABLE-US-04439 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1225(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04440 >GP:AAG34743 GB:AE000033 similar to PTS system:EIIB [Mycoplasma pneumoniae] Identities = 40/89 (44%), Positives = 62/89 (68%), Gaps = 1/89 (1%) Query: 4 VLTACGNGMGSSMVIKMKVENALRQLGVSNFESASCSVGEAKGLAANYDIVVASNHLIHE 63 ++ ACGNGMG+SM+IK+KVE +++LG + A S+G+ KG+ + DI+++S HL E Sbjct: 8 IIAACGNGMGTSMLIKIKVEKIMKELGYTAKVEA-LSMGQTKGMEHSADIIISSIHLTSE 66 Query: 64 LDGRTKGHLVGLDNLMDDNEIKTKLQEIL 92 + K +VG+ NLMD+NEIK L ++L Sbjct: 67 FNPNAKAKIVGVLNLMDENEIKQALSKVL 95 A related DNA sequence was identified in S. pyogenes <SEQ ID 4583> which encodes the amino acid sequence <SEQ ID 4584>. Analysis of this protein sequence reveals the following: TABLE-US-04441 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0977(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04442 Identities = 85/92 (92%), Positives = 90/92 (97%) Query: 1 MVKVLTACGNGMGSSMVIKMKVENALRQLGVSNFESASCSVGEAKGLAANYDIVVASNHL 60 MVKVLTACGNGMGSSMVIKMKVENALRQLGV++ +SASCSVGEAKGLA+ YDIVVASNHL Sbjct: 1 MVKVLTACGNGMGSSMVIKMKVENALRQLGVTDIQSASCSVGEAKGLASGYDIVVASNHL 60 Query: 61 IHELDGRTKGHLVGLDNLMDDNEIKTKLQEIL 92 IHELDGRTKGHLVGLDNLMDDNEIKTKLQE+L Sbjct: 61 IHELDGRTKGHLVGLDNLMDDNEIKTKLQEVL 92 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1490 A DNA sequence (GBSx1576) was identified in S. agalactiae <SEQ ID 4585> which encodes the amino acid sequence <SEQ ID 4586>. This protein is predicted to be a pentitol phosphotransferase enzyme ii, a component (ptxA). Analysis of this protein sequence reveals the following: TABLE-US-04443 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3309(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04444 >GP:AAC77152 GB:AE000491 putative PTS system enzyme II A component [Escherichia coli K12] Identities = 64/150 (42%), Positives = 97/150 (64%), Gaps = 2/150 (1%) Query: 1 MNLKQAFIENDSIRLKLSASDWKEAIKLSIDPLIESGAVDAEYYDAIIESTEEFGPYYIL 60 M L+ + EN SIRL+ A W+EA+K+ +D L+ + V+ YY AI++ E+FGPY+++ Sbjct: 1 MKLRDSLAENKSIRLQAEAETWQEAVKIGVDLLVAADVVEPRYYQAILDGVEQFGPYFVI 60 Query: 61 MPGMAMPHARPEAGVKRDAFSLITLTEPVVF--PDGKEVSVLLALAATSSAIHTSVAIPQ 118- PG+AMPH RPE GVK+ FSL+TL +P+ F D V +L+ +AA + H V I Q Sbjct: 61 APGLAMPHGRPEEGVKKTGFSLVTLKKPLEFNHDDNDPVDILITMAAVDANTHQEVGIMQ 120- Query: 119 IIALFELENSIQRLTECQEAKEVLAMVEES 148 I+ LFE E + RL C+ +EVL +++ + Sbjct: 121 IVNLFEDEENFDRLRACRTEQEVLDLIDRT 150 A related DNA sequence was identified in S. pyogenes <SEQ ID 4587> which encodes the amino acid sequence <SEQ ID 4588>. Analysis of this protein sequence reveals the following: TABLE-US-04445 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2287(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04446 Identities = 113/161 (70%), Positives = 137/161 (84%) Query: 1 MNLKQAFIENDSIRLKLSASDWKEAIKLSIDPLIESGAVDAEYYDAIIESTEEFGPYYIL 60 MNLKQAFI+N+SIRL LSA W+EA++L++ PLI+S AV + YYDAII STE++GPYY+L Sbjct: 1 MNLKQAFIDNNSIRLGLSADTWQEAVRLAVQPLIDSKAVTSAYYDAIIASTEKYGPYYVL 60 Query: 61 MPGMAMPHARPEAGVKRDAFSLITLTEPVVFPDGKEVSVLLALAATSSAIHTSVAIPQII 120- MPGMAMPHA GV R+AF+LITLT+PV F DGKEVSVLL LAAT +IHT+VAIPQI+ Sbjct: 61 MPGMAMPHAEAGLGVNRNAFALITLTKPVTFSDGKEVSVLLTLAATDPSIHTTVAIPQIV 120- Query: 121 ALFELENSIQRLTECQEAKEVLAMVEESKNSPYLEGLDLES 161 ALFEL+N+I+RL CQ KEVL MVEESK+SPYLEG+DL + Sbjct: 121 ALFELDNAIERLVACQSPKEVLEMVEESKDSPYLEGMDLNA 161 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1491 A DNA sequence (GBSx1577) was identified in S. agalactiae <SEQ ID 4589> which encodes the amino acid sequence <SEQ ID 4590>. This protein is predicted to be probable hexulose-6-phosphate synthase. Analysis of this protein sequence reveals the following: TABLE-US-04447 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1584(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-04448 >GP: AAC77153 GB: AE000491 probable hexulose-6-phosphate synthase [Escherichia coli K12] Identities = 108/217 (49%), Positives = 141/217 (64%), Gaps = 3/217 (1%) Query: 5 LPNLQVALDHSDLQGAIKAAVSVGHEVDVIEAGTVCLLQVGSELVEVLRSLFPDKIIVAD 64 LP LQVALD+ + A + + EVD+IE GT+ + G V L++L+P KI++AD Sbjct: 3 LPMLQVALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLAD 62 Query: 65 TKCADAGGTVAKNNAVRGADWMTCICCATIPTMEAALKAIKEERGDRGEIQIELYGDWTY 124- K ADAG +++ ADW+T ICCA I T + AL KE GD +QIEL G WT+ Sbjct: 63 AKIADAGKILSRMCFEANADWVTVICCADINTAKGALDVAKEFNGD---VQIELTGYWTW 119- Query: 125 EQAQQWLDAGISQAIYHQSRDALLAGETWGEKDLNKVKKLIDMGFRVSVTGGLSTDTLQL 18- 4 EQAQQW DAGI Q +YH+SRDA AG WGE D+ +K+L DMGF+V+VTGGL+ + L L Sbjct: 120 EQAQQWRDAGIGQVVYHRSRDAQAAGVAWGEADITAIKRLSDMGFKVTVTGGLALEDLPL 17- 9 Query: 185 FEGVDVFTFIAGRGITEADDPAAAARAFKDEIKRIWG 221 F+G+ + FIAGR I +A P AAR FK I +WG Sbjct: 180 FKGIPIHVFIAGRSIRDAASPVEAARQFKRSIAELWG 216 A related DNA sequence was identified in S. pyogenes <SEQ ID 4591> which encodes the amino acid sequence <SEQ ID 4592>. Analysis of this protein sequence reveals the following: TABLE-US-04449 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1473(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04450 Identities = 206/217 (94%), Positives = 212/217 (96%) Query: 5 LPNLQVALDHSDLQGAIKAAVSVGHEVDVIEAGTVCLLQVGSELVEVLRSLFPDKIIVAD 64 +PNLQVALDHSDLQGA+KAAV+VGHEVDVIEAGTVCLLQVGSELVEVLRSLFP+KIIVAD Sbjct: 4 IPNLQVALDHSDLQGAVKAAVAVGHEVDVIEAGTVCLLQVGSELVEVLRSLFPEKIIVAD 63 Query: 65 TKCADAGGTVAKNNAVRGADWMTCICCATIPTMEAALKAIKEERGDRGEIQIELYGDWTY 124- TKCADAGGTVAKNNA RGADWMTCICCATIPTMEAALKAIKEERGDRGEIQIELYGDWTY Sbjct: 64 TKCADAGGTVAKNNAKRGADWMTCICCATIPTMEAALKAIKEERGDRGEIQIELYGDWTY 123- Query: 125 EQAQQWLDAGISQAIYHQSRDALLAGETWGEKDLNKVKKLIDMGFRVSVTGGLSTDTLQL 18- 4 EQAQ WLDAGISQAIYHQSRDALLAGETWGEKDLNKVK LIDMGFRVSVTGGL DTL+L Sbjct: 124 EQAQLWLDAGISQAIYHQSRDALLAGETWGEKDLNKVKTLIDMGFRVSVTGGLDVDTLRL 18- 3 Query: 185 FEGVDVFTFIAGRGITEADDPAAAARAFKDEIKRIWG 221 FEGVDVFTFIAGRGITEA+DPAAAARAFKDEIKRIWG Sbjct: 184 FEGVDVFTFIAGRGITEAEDPAAAARAFKDEIKRIWG 220 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1492 A DNA sequence (GBSx1578) was identified in S. agalactiae <SEQ ID 4593> which encodes the amino acid sequence <SEQ ID 4594>. Analysis of this protein sequence reveals the following: TABLE-US-04451 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4179(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04452 >GP: AAC22686 GB: U32783 hexulose-6-phosphate isomerase, putative [Haemophilus influenzae Rd] Identities = 143/282 (50%), Positives = 199/282 (69%), Gaps = 3/282 (1%) Query: 5 IGIYEKATPKHFNWLERLQFAKELGFDFVELSIDESDERLARLEWSKEERLELVKAIFET 64 IGIYEKA PK+ W ERL AK GF+F+E+SIDES++RL+RL W+K ER+ L ++I ++ Sbjct: 6 IGIYEKALPKNITWQERLSLAKACGFEFIEMSIDESNDRLSRLNWTKSERIALHQSIIQS 65 Query: 65 GVRVPTITFSGHRRFPMGSNNPEKEARAMDMMKKCIVFAQDIGIRNIQLAGYDVYYEEKS 124- G+ +P++ S HRRFP GS + + ++ ++M+K I + ++GIR IQLAGYDVYYE++ Sbjct: 66 GITIPSMCLSAHRRFPFGSKDKKIRQKSFEIMEKAIDLSVNLGIRTIQLAGYDVYYEKQD 125- Query: 125 PETRARFIKNLRQACTWAEEAQVILSIEIMDDPFMNSIEKYLAVEKEIDSPYLFVYPDTG 18- 4 ET F + + A T A AQV L++EIMD PFM+SI ++ + I+SP+ VYPD G Sbjct: 126 EETIKYFQEGIEFAVTLAASAQVTLAVEIMDTPFMSSISRWKKWDTIINSPWFTVYPDIG 18- 5 Query: 185 NVSAWHNDLWSEFYNGHRSIAALHIKDTYAVTETSKGQFRDVPFGQGCVDWEEMFAVIKK 24- 4 N+SAW+N++ E G I+A+H+KDTY VTETSKGQFRDVPFGQGCVD+ F+++KK Sbjct: 186 NLSAWNNNIEEELTLGIDKISAIHLKDTYPVTETSKGQFRDVPFGQGCVDFVHFFSLLKK 24- 5 Query: 245 TNYNGPFLIEMWSENCETVEETRAAIKEAQDFLYPLMEKTGV 286 NY G FLIEMW+E EE I +A+ ++ MEK G+ Sbjct: 246 LNYRGAFLIEMWTEK---NEEPLLEIIQARKWIVQQMEKAGL 284 A related DNA sequence was identified in S. pyogenes <SEQ ID 4595> which encodes the amino acid sequence <SEQ ID 4596>. Analysis of this protein sequence reveals the following: TABLE-US-04453 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1489(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04454 Identities = 240/286 (83%), Positives = 271/286 (93%) Query: 1 MTRPIGIYEKATPKHFNWLERLQFAKELGFDFVELSIDESDERLARLEWSKEERLELVKA 60 M RPIGIYEKATPK F W ERLQFAK+LGFDFVE+S+DESD RLARLEW+KEERL+LVKA Sbjct: 15 MARPIGIYEKATPKQFTWRERLQFAKDLGFDFVEMSVDESDARLARLEWTKEERLDLVKA 74 Query: 61 IFETGVRVPTITFSGHRRFPMGSNNPEKEARAMDMMKKCIVFAQDIGIRNIQLAGYDVYY 120- I+ETG+R+PTI FSGHRR+P+GSN+P EA+++ +MK+CI AQD+G+R IQLAGYDVYY Sbjct: 75 IYETGIRIPTICFSGHRRYPLGSNDPAIEAKSLKLMKQCIELAQDLGVRTIQLAGYDVYY 134- Query: 121 EEKSPETRARFIKNLRQACTWAEEAQVILSIEIMDDPFMNSIEKYLAVEKEIDSPYLFVY 18- 0 E+KSPETRARFIKNLRQ+C WAEEAQV+LSIEIMDDPF+NSIEKYLAVEKEIDSPYLFVY Sbjct: 135 EKKSPETRARFIKNLRQSCDWAEEAQVMLSIEIMDDPFINSIEKYLAVEKEIDSPYLFVY 19- 4 Query: 181 PDTGNVSAWHNDLWSEFYNGHRSIAALHIKDTYAVTETSKGQFRDVPFGQGCVDWEEMFA 24- 0 PD GNVSAWHNDLWSEFYNGH+SIAALH+KDTYAVTETSKGQFRDVPFGQGCVDW+E+FA Sbjct: 195 PDAGNVSAWHNDLWSEFYNGHKSIAALHLKDTYAVTETSKGQFRDVPFGQGCVDWQELFA 25- 4 Query: 241 VIKKTNYNGPFLIEMWSENCETVEETRAAIKEAQDFLYPLMEKTGV 286 V+KKTNYNGPFLIEMWSENC+TVEET+AAIKEAQDFLYPL+EK G+ Sbjct: 255 VLKKTNYNGPFLIEMWSENCDTVEETKAAIKEAQDFLYPLIEKAGL 300 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1493 A DNA sequence (GBSx1579) was identified in S. agalactiae <SEQ ID 4597> which encodes the amino acid sequence <SEQ ID 4598>. This protein is predicted to be L-ribulose 5-phosphate 4-epimerase. Analysis of this protein sequence reveals the following: TABLE-US-04455 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2559(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04456 >GP: AAD45716 GB: AF160811 L-ribulose 5-phosphate 4-epimerase [Bacillus stearothermophilus] Identities = 143/229 (62%), Positives = 176/229 (76%), Gaps = 2/229 (0%) Query: 5 LQEMRERVCEANKSLPVHSLVKFTWGNVSEVDREAGLIVIKPSGVDYDQLTPENMVVTDL 64 L+E+++ V EAN LP + LV FTWGNVS +DRE GL+VIKPSGV YD+LT ++MVV DL Sbjct: 2 LEELKQAVLEANLQLPQYRLVTFTWGNVSGIDRERGLVVIKPSGVAYDKLTIDDMVVVDL 61 Query: 65 EGNIVEGDLNPSSDLPTHVQLYKAWPEVGGIVHTHSTEAVGWAQAGRDIPFYGTTHADYF 124- GN+VEGDL PSSD PTH+ LYK +P +GGIVHTHST A WAQAG+ IP GTTHADYF Sbjct: 62 TGNVVEGDLKPSSDTPTHLWLYKQFPGIGGIVHTHSTWATVWAQAGKGIPALGTTHADYF 121- Query: 125 YGPVPCARSLSEDEVNTAYEKETGSVIIEEFERRDLDPMAVPGIVVRNHGPFTWGKDPAQ 18- 4 YG +PC R ++ +E+ AYE ETG VI E F R LDP+ +PG++V HGPF WGKDPA Sbjct: 122 YGEIPCTRPMTNEEIQGAYELETGKVITETF--RFLDPLQMPGVLVHGHGPFAWGKDPAN 17- 9 Query: 185 AVYHSVVLEEVAKMNRFTEQINPRVEPAPKYIMDKHYLRKHGPNAYYGQ 233 AV+++VVLEEVAKM T +NP +P + ++D+HYLRKHG NAYYGQ Sbjct: 180 AVHNAVVLEEVAKMAARTYMLNPNAKPISQTLLDRHYLRKHGANAYYGQ 228 A related DNA sequence was identified in S. pyogenes <SEQ ID 4599> which encodes the amino acid sequence <SEQ ID 4600>. Analysis of this protein sequence reveals the following: TABLE-US-04457 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2257(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04458 Identities = 207/234 (88%), Positives = 220/234 (93%) Query: 1 MAKSLQEMRERVCEANKSLPVHSLVKFTWGNVSEVDREAGLIVIKPSGVDYDQLTPENMV 60 MAK+LQEMRERVC ANKSLP H LVKFTWGNVSEV RE G IVIKPSGVDYD LTPENMV Sbjct: 1 MAKNLQEMRERVCAANKSLPQHGLVKFTWGNVSEVCRELGRIVIKPSGVDYDLLTPENMV 60 Query: 61 VTDLEGNIVEGDLNPSSDLPTHVQLYKAWPEVGGIVHTHSTEAVGWAQAGRDIPFYGTTH 120- VTDL+GN+VEGDLNPSSDLPTHV+LYKAWPEVGGIVHTHSTEAVGWAQAGRDIPFYGTTH Sbjct: 61 VTDLDGNVVEGDLNPSSDLPTHVELYKAWPEVGGIVHTHSTEAVGWAQAGRDIPFYGTTH 120- Query: 121 ADYFYGPVPCARSLSEDEVNTAYEKETGSVIIEEFERRDLDPMAVPGIVVRNHGPFTWGK 18- 0 ADYFYGPVPCARSL++ EV+ AYE+ETG+VI+EEF +R LDPMAVPGIVVRNHGPFTWGK Sbjct: 121 ADYFYGPVPCARSLTKAEVDGAYEQETGNVILEEFSKRGLDPMAVPGIVVRNHGPFTWGK 18- 0 Query: 181 DPAQAVYHSVVLEEVAKMNRFTEQINPRVEPAPKYIMDKHYLRKHGPNAYYGQK 234 P QAVYHSVVLEEVA+MNR TEQINPRVEPAP+YIMDKHYLRKHGPNAYYGQK Sbjct: 181 TPEQAVYHSVVLEEVARMNRLTEQINPRVEPAPRYIMDKHYLRKHGPNAYYGQK 234 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1494 A DNA sequence (GBSx1580) was identified in S. agalactiae <SEQ ID 4601> which encodes the amino acid sequence <SEQ ID 4602>. This protein is predicted to be transaldolase (tal). Analysis of this protein sequence reveals the following: TABLE-US-04459 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4232(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10149> which encodes amino acid sequence <SEQ ID 10150> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04460 >GP: AAB98962 GB: U67539 transaldolase [Methanococcus jannaschii] Identities = 124/214 (57%), Positives = 157/214 (72%) Query: 19 MKYFLDTADVSEIRRLNRLGIVDGVTTNPTIISREGRDFKEVINEICQIVDGPVSAEVTG 78 - MK+FLDTA+V EI++ LG+VDGVTTNPT++++EGRDF EV+ EIC+IV+GPVSAEV Sbjct: 1 MKFFLDTANVEEIKKYAELGLVDGVTTNPTLVAKEGRDFYEVVKEICEIVEGPVSAEVIS 60 Query: 79 LTCDEMVTEAREIAKWSPNVVVKIPMTEEGLAAVSQLSKEGIKTNVTLIFTVAQGLSAMK 138- + MV EARE+AK + N+V+KIPMT++G+ AV LS EGIKTNVTL+F+ Q L A K Sbjct: 61 TDAEGMVKEARELAKLADNIVIKIPMTKDGMKAVKILSAEGIKTNVTLVFSPLQALVAAK 120- Query: 139 AGATFISPFVGRLEDIGTDAYALIRDLRHIIDFYGFQSEIIAASIRGLAHVEGVAKCGAH 19- 8 AGAT++SPFVGRL+DIG LI D+ I Y ++E+I AS+R HV AK GA Sbjct: 121 AGATYVSPFVGRLDDIGHVGMKLIEDVVKIYKNYDIKTEVIVASVRHPWHVLEAAKIGAD 18- 0 Query: 199 IATIPDKTFASLFTHPLTDKGIETFLKDWDSFKK 232 IAT+P LF HPLTD G+E FLKDWD + K Sbjct: 181 IATMPPAVMDKLFNHPLTDIGLERFLKDWDEYLK 214 A related DNA sequence was identified in S. pyogenes <SEQ ID 4603> which encodes the amino acid sequence <SEQ ID 4604>. Analysis of this protein sequence reveals the following: TABLE-US-04461 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1902(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04462 Identities = 162/214 (75%), Positives 180/214 (83%) Query: 19 MKYFLDTADVSEIRRLNRLGIVDGVTTNPTIISREGRDFKEVINEICQIVDGPVSAEVTG 78 - MK+FLDTA+V+ I+ +N LG+VDGVTTNPTIISREGRDF+ VI EIC IVDGP+SAEVTG Sbjct: 1 MKFFLDTANVAAIKAINELGVVDGVTTNPTIISREGRDFETVIKEICDIVDGPISAEVTG 60 Query: 79 LTCDEMVTEAREIAKWSPNVVVKIPMTEEGLAAVSQLSKEGIKTNVTLIFTVAQGLSAMK 138- LT D MV EAR IAKW NVVVKIPMT EGL A + LSKEGIKTNVTLIFTV+QGL AMK Sbjct: 61 LTADAMVEEARSIAKWHDNVVVKIPMTTEGLKATNILSKEGIKTNVTLIFTVSQGLMAMK 120- Query: 139 AGATFISPFVGRLEDIGTDAYALIRDLRHIIDFYGFQSEIIAASIRGLAHVEGVAKCGAH 19- 8 AGAT+ISPF+GRLEDIGTDAY LI DLR IID Y FQ+EIIAASIR AHVE VAK GAH Sbjct: 121 AGATYISPFIGRLEDIGTDAYQLISDLREIIDLYDFQAEIIAASIRTTAHVEAVAKLGAH 18- 0 Query: 199 IATIPDKTFASLFTHPLTDKGIETFLKDWDSFKK 232 IATIPD FA + HPLT G++TF++DW SFKK Sbjct: 181 IATIPDPLFAKMTQHPLTTNGLKTFMEDWASFKK 214 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1495 A DNA sequence (GBSx1581) was identified in S. agalactiae <SEQ ID 4605> which encodes the amino acid sequence <SEQ ID 4606>. Analysis of this protein sequence reveals the following: TABLE-US-04463 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1263(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04464 >GP: CAB14129 GB: Z99115 transcriptional regulator (LacI family) [Bacillus subtilis] Identities = 108/331 (32%), Positives = 188/331 (56%), Gaps = 12/331 (3%) Query: 6 TISDIANLVGVSKATVSYYLNGNYKKMSLQTKEKIRLAIKETGYQPSKIAQSLVTKNTRT 65 TI D+A GVSK+TVS Y+NG +S + + I+ AI E Y+PSK+AQ L K ++ Sbjct: 10 TIKDVAECAGVSKSTVSRYINGKIDAISPEKVKNIKKAIAELNYRPSKMAQGLKIKKSKL 69 Query: 66 IGVVIADITNPFISSVMKGIHDTCQQFGYSVNFTNSDNDIDIELENLNRLNQQNVSGIIL 125- IG V+ADITNPF + +G+ + C Q+GYS+ N+DN + E E L +L +V G+IL Sbjct: 70 IGFVVADITNPFSVAAFRGVEEVCDQYGYSIMVCNTDNSPEKEREMLLKLEAHSVEGLIL 129- Query: 126 DSVDPNHSFIETLSNDRL--VMVDRQAKDIKVDTVASDNKESTQIFLEKMQEAGYHDIYF 18- 3 ++ N + + ++ +++DR+ D+K+DTV +DN+ T+ L+K+ GY D+ Sbjct: 130 NATGENKDVLRAFAEQQIPTILIDRKLPDLKLDTVTTDNRWITKEILQKVYSKGYTDVAL 18- 9 Query: 184 VTYPIEGISTRELRYEGFKEVVS-SNPDKLIIITE-DGSTQRILDI------IEHSEQKP 23- 5 T PI IS R R ++E+ S N + L+ + E D + L E EQK Sbjct: 190 FTEPISSISPRAERAAVYQEMASVQNVNGLVRLHEIDVKDKEQLKAELRSFHKEMPEQKK 24- 9 Query: 236 GFLMMNGPTLLNFMKKLNQSTVSYPEDYGLGSYEDLEWMQVLTPNVSCIKQDSYGIGCLA 29- 5 L +NG +L + + + + P+D G+ ++D EW +++ P ++ I Q S+ +G A Sbjct: 250 AILALNGLIMLKIISCMEELGLRIPQDIGIAGFDDTEWYKLIGPGITTIAQPSHDMGRTA 30- 9 Query: 296 AQCLIEKISQGNEPTTARLLEVKNQIVIRQS 326 + ++++I + + +E++ ++++R+S Sbjct: 310 MERVLKRIE--GDKGAPQTIELEAKVIMRKS 338 There is also homology to SEQ ID 2366. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1496 A DNA sequence (GBSx1582) was identified in S. agalactiae <SEQ ID 4607> which encodes the amino acid sequence <SEQ ID 4608>. Analysis of this protein sequence reveals the following: TABLE-US-04465 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1661(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1497 A DNA sequence (GBSx1583) was identified in S. agalactiae <SEQ ID 4609> which encodes the amino acid sequence <SEQ ID 4610>. This protein is predicted to be GLYCERATE DEHYDROGENASE. Analysis of this protein sequence reveals the following: TABLE-US-04466 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04467 >GP: CAB50351 GB: AJ248287 GLYCERATE DEHYDROGENASE [Pyrococcus abyssi] Identities = 123/325 (37%), Positives = 192/325 (58%), Gaps = 8/325 (2%) Query: 1 MDKKKILVTGIVPKEGLRKLMDRFDVTYSED-RPFSRDYVLEHLSEYDGWLLM-GQKGDK 58 M K ++ +T +P+ G+ L F+V ED R R+ +LE + + D + M ++ D+ Sbjct: 1 MSKPRVFITREIPEVGIEMLEKEFEVEVWEDEREIPREILLEKVKDVDALVTMLSERIDR 60 Query: 59 EMIDAGENLQIISLNAVGFDHVDTAYAKEKGIIVSNSPQAVRVPTAEMTFALILAASKRL 118- E+ + L+I++ AVG+D++D A ++GI V+N+P + TA++ FAL+LA ++ L Sbjct: 61 EVFERAPRLRIVANYAVGYDNIDVEEATKRGIYVTNTPGVLTDATADLAFALLLATARHL 120- Query: 119 AFYDSIVRSGEW----IDPSEQRYQGLTLQGSTLGIYGMGRIGLTVANFAKAFGMTVVYN 17- 4 D RSGEW + + + G + G T+GI G GRIG +A A+ F M ++Y Sbjct: 121 VKGDKFTRSGEWKKRGVAWHPKWFLGYDVYGKTIGIIGFGRIGQAIAKRARGFDMRILYY 18- 0 Query: 175 DVYRLPEDKEKELGVTYLEFDQLIKTADVITIHAPALPSTIHKFNKDVFAKMKNRSYLIN 23- 4 R PE EKEL + D+L++ +D + + P T H N++ MK + LIN Sbjct: 181 SRTRKPE-VEKELNAEFKPLDELLRESDFVVLAVPLNKETYHMINEERLKMMKRTAILIN 23- 9 Query: 235 AARGPIVSEEALIEALKEGEIAGAGLDVFENEPQVSEGLRSLDNVIMSPHAGTGTIEGRR 29- 4 ARG ++ +ALI+ALKEG IAGAGLDV+E EP +E L SLDNV+++PH G+ T R Sbjct: 240 VARGKVIDTKALIKALKEGWIAGAGLDVYEEEPYYNEELFSLDNVVLTPHIGSATFGARE 29- 9 Query: 295 TLAEEAADNIIAFFDGK-PQNIVNK 318 +A+ A+N+IAF G+ P +VN+ Sbjct: 300 GMAKLVAENLIAFKRGEVPPTLVNR 324 There is also homology to SEQ ID 124. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1498 A DNA sequence (GBSx1585) was identified in S. agalactiae <SEQ ID 4611> which encodes the amino acid sequence <SEQ ID 4612>. Analysis of this protein sequence reveals the following:

TABLE-US-04468 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1898(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1499 A DNA sequence (GBSx1586) was identified in S. agalactiae <SEQ ID 4613> which encodes the amino acid sequence <SEQ ID 4614>. This protein is predicted to be PTS system, galactitol specific IIC component. Analysis of this protein sequence reveals the following: TABLE-US-04469 Possible site: 25 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.27 Transmembrane 254-270 (245-277) INTEGRAL Likelihood = -9.24 Transmembrane 77-93 (71-100) INTEGRAL Likelihood = -9.24 Transmembrane 367-383 (364-386) INTEGRAL Likelihood = -8.28 Transmembrane 32-48 (26-54) INTEGRAL Likelihood = -7.38 Transmembrane 186-202 (182-215) INTEGRAL Likelihood = -6.26 Transmembrane 158-174 (151-180) INTEGRAL Likelihood = -5.79 Transmembrane 279-295 (276-296) INTEGRAL Likelihood = -1.12 Transmembrane 342-358 (342-359) INTEGRAL Likelihood = -0.00 Transmembrane 308-324 (308-324) ----- Final Results ----- bacterial membrane --- Certainty = 0.6307(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8825> which encodes amino acid sequence <SEQ ID 8826> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-04470 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 8.30 GvH: Signal Score (-7.5): 2.97 Possible site: 58 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 9 value: -13.27 threshold: 0.0 INTEGRAL Likelihood = -13.27 Transmembrane 321-337 (312-344) INTEGRAL Likelihood = -9.24 Transmembrane 144-160 (138-167) INTEGRAL Likelihood = -9.24 Transmembrane 434-450 (431-453) INTEGRAL Likelihood = -8.28 Transmembrane 99-115 (93-121) INTEGRAL Likelihood = -7.38 Transmembrane 253-269 (249-282) INTEGRAL Likelihood = -6.26 Transmembrane 225-241 (218-247) INTEGRAL Likelihood = -5.79 Transmembrane 346-362 (343-363) INTEGRAL Likelihood = -1.12 Transmembrane 409-425 (409-426) INTEGRAL Likelihood = -0.00 Transmembrane 375-391 (375-391) PERIPHERAL Likelihood = 0.69 188 modified ALOM score: 3.15 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6307(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04471 >GP: BAB03909 GB: AP001507 PTS system, galactitol-specific enzyme II, C component [Bacillus halodurans] Identities = 92/347 (26%), positives = 173/347 (49%), Gaps = 15/347 (4%) Query: 1 MVKTTGLHLPIVDIGWQAGSLTAFSSEIGLSFFVFGLLIELGLFLLGITRVFVPSNLWNN 60 MV G+ L ++D+GW A S A++S + GL++ + + + T+ + ++WN Sbjct: 70 MVDRLGVDLNVIDVGWPATSSIAWASVVAAFIIPLGLIVNVIMLVTKTTKT-MNVDIWNF 128- Query: 61 FGYMIWGTMAYAATGNFILSFAFMVFVLLYSLVMSEVLADRWSEYYGVKNATINSIHNIE 120- + Y + Y + + I + V + +L +++ A SE+Y + +I + I Sbjct: 129 WHYTFMAAVVYTVSDSIIQALIAAVMFQIVALKVADWTAPMVSEFYELPGVSIATGSTIS 18- 8 Query: 121 TLIPALILDPLWNLLGVNKVKLNPESLKTKLGIFGEPMTLGFILGVIIGVLGSLRNLASI 18- 0 ++ + + G+ +P++++ + GIFGE + +G ILG IG+L Sbjct: 189 YAPGIWLVKGIQKIPGIKHWNADPDTIQRRFGIFGESIFIGLILGAAIGLLAGYNV---- 24- 4 Query: 181 DTWGGILGFAVALAAVMTIFPLITGVFASAFAPLAEAVERNKKKESQAEQGALDKKRWFI 24- 0 G ++ +A+AAVM + P + + P++E+ K + I Sbjct: 245 ---GEVIEIGMAMAAVMVLMPRMVKILMEGLMPVSESAREWLNKR-------FGDREIHI 29- 4 Query: 241 AVDDGVGFGEPATIIAGLILVPIMVVISLILPGNEALPVVDLIAIPFMIEAMIAVSKGNI 30- 0 +D V G P+ I LILVP+ V++++ILPGN LP DL IPF++ ++ ++GNI Sbjct: 295 GLDAAVLLGHPSVISTALILVPLTVLLAVILPGNALLPFGDLATIPFIVAFIVGAARGNI 35- 4 Query: 301 LKAILNGIIWFSLGLYAASALGPIYTEAVKHFGTALPAGVTLIMSFN 347 + ++L G I +L LY A+ + P++T+ ++ +P G LI S + Sbjct: 355 IHSVLAGAIMIALSLYMATDIAPVFTKMAENSNFNMPEGSALISSID 401 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1500 A DNA sequence (GBSx1587) was identified in S. agalactiae <SEQ ID 4615> which encodes the amino acid sequence <SEQ ID 4616>. Analysis of this protein sequence reveals the following: TABLE-US-04472 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1013(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1501 A DNA sequence (GBSx1588) was identified in S. agalactiae <SEQ ID 4617> which encodes the amino acid sequence <SEQ ID 4618>. Analysis of this protein sequence reveals the following: TABLE-US-04473 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1294(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10147> which encodes amino acid sequence <SEQ ID 10148> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04474 >GP: AAC76604 GB: AE000435 L-xylulose kinase, cryptic [Escherichia coli K12] Identities = 156/496 (31%), Positives = 261/496 (52%), Gaps = 18/496 (3%) Query: 16 YYLSIDYGGTNTKALIFDKLGHQIAVSSFETLKNETQSGHRQVNLVKTWNAITSAIREVI 75 - Y+L +D GG+ KA ++D+ G + V Q G + ++ + W + IR ++ Sbjct: 4 YWLGLDCGGSWLKAGLYDREGREAGVQRLPLCALSPQPGWAERDMAELWQCCMAVIRALL 63 Query: 76 QISKLSPEQISAVACIGHGKGLYLLDNKLEPLEQGILSTDNRAKDLAQYFESK--LDNIW 133- S +S EQI + GKGL+LLD +PL ILS+D RA ++ + ++ + ++ Sbjct: 64 THSGVSGEQIVGIGISAQGKGLFLLDKNDKPLGNAILSSDRRAMEIVRRWQEDGIPEKLY 123- Query: 134 ELTRQHIFPSQSPVILRWLKDYQPETYKSIGAVLSAKDFIRYKLTGKVQQEYGDASGNHW 19- 3 LTRQ ++ +LRWLK+++PE Y IG V+ D++R+ LTG E + S ++ Sbjct: 124 PLTRQTLWTGHPVSLLRWLKEHEPERYAQIGCVMMTHDYLRWCLTGVKGCEESNISESNL 18- 3 Query: 194 INFQTGTYDPAILDFFGIREIENSLPELIDSADLVPGGISSQAAKETGLVEGTPVVGGLF 25- 3 N G YDP + D+ GI EI ++LP ++ SA++ G I++Q A TGL GTPVVGGLF Sbjct: 184 YNMSLGEYDPCLTDWLGIAEINHALPPVVGSAEIC-GEITAQTAALTGLKAGTPVVGGLF 24- 2 Query: 254 DIDACALGSGVLESDTFSVISGTWNINT--YPSLKPAKQDSGLMTSYFPDRRYLLEASSP 31- 1 D+ + AL +G+ + T + + GTW + + L+ + + Y D +++ +SP Sbjct: 243 DVVSTALCAGIEDEFTLNAVMGTWAVTSGITRGLRDGEAHPYVYGRYVNDGEFIVHEASP 30- 2 Query: 312 TSAGNLNFMLKMLMHQEIDNAKSSGGSIYDNLEEFLTHTDATHHGLIFFPFLYGSNTSQD 37- 1 TS+GNL + G +D + + + L F PFLYGSN + Sbjct: 303 TSSGNLEWF-----------TAQWGEISFDEINQAVASLPKAGGDLFFLPFLYGSNAGLE 35- 1 Query: 372 ASACFFGLTTKSTKSQMIRAVYEGIAFAHKQHITDLIKSRGSVPKIIRFSGGATNSPAWM 43- 1 ++ F+G+ T++ +++A+YEG+ F+H H+ + ++ R + +R +GG +S WM Sbjct: 352 MTSGFYGMQAIHTRAHLLQAIYEGVVFSHMTHL-NRMRERFTDVHTLRVTGGPAHSDVWM 41- 0 Query: 432 QMFSDILNFPIETVEGTELGGLGGAILARHALDKI-SLKEAVQDMVRVKAIYKPQLSEVK 49- 0 QM +D+ IE + E G G A+ AR + EA +D+ P ++ + Sbjct: 411 QMLADVSGLRIELPQVEETGCFGAALAARVGTGVYHNFSEAQRDLRHPVRTLLPDMTAHQ 47- 0 Query: 491 GYKKKYHAYQKLLETL 506 Y+KKY YQ L+ L Sbjct: 471 LYQKKYQRYQHLIAAL 486 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1502 A DNA sequence (GBSx1589) was identified in S. agalactiae <SEQ ID 4619> which encodes the amino acid sequence <SEQ ID 4620>. Analysis of this protein sequence reveals the following: TABLE-US-04475 Possible site: 59 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04476 >GP: AAG05648 GB: AE004652 hypothetical protein [Pseudomonas aeruginosa] Identities = 59/235 (25%), Positives = 104/235 (44%), Gaps = 9/235 (3%) Query: 23 QVQLIKLVKDLGFSRFEIRQELLQDPDRELPALKAEADFYDINLYYSANEDLIK-GGKVN 81 - Q + L+ G R E+R+EL P + AL A + +S+ +L + G++N Sbjct: 23 QASFLPLLAMAGAQRVELREELFAGPP-DTEALTAAIQLQGLECVFSSPLELWREDGQLN 81 Query: 82 PYLNKGLKEASQLGAPFIKLNVGQTRNLSKEELEPLKEILKSQTIGIKVENNQDPKAATV 141- P L L+ A GA ++K+++G + +L L L + + VEN+Q P+ + Sbjct: 82 PELEPTLRRAEACGAGWLKVSLGLLPE--QPDLAALGRRLARHGLQLLVENDQTPQGGRI 139- Query: 142 ENCQYFMTLVKELQIPISFVFDTANWAFINQDLYQAVNNLACDTTYLHCKNFIQVAGKPH 20- 1 E + F L + Q+ ++ FD NW + Q +A L Y+HCK I+ Sbjct: 140 EVLERFFRLAERQQLDLAMTFDIGNWRWQEQAADEAALRLGRYVGYVHCKAVIRNRDGKL 19- 9 Query: 202 LSKSLFEGEINLTD-LLKSFSNCEYLALEYPTE----LEILKRDVQRLISISNSQ 251 ++ ++ LL+ F A+EYP + L + +R + L + Q Sbjct: 200 VAVPPSAADLQYWQRLLQHFPEGVARAIEYPLQGDDLLSLSRRHIAALARLGQPQ 254 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1503 A DNA sequence (GBSx1590) was identified in S. agalactiae <SEQ ID 4621> which encodes the amino acid sequence <SEQ ID 4622>. Analysis of this protein sequence reveals the following: TABLE-US-04477 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0430(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04478 >GP: BAB03939 GB: AP001507 unknown conserved protein [Bacillus halodurans] Identities = 136/511 (26%), Positives = 234/511 (45%), Gaps = 29/511 (5%) Query: 4 LDKKSYDLLFYLLKLEEPETVMAIANALNQSRRKVYYHLEKINDALPSDVPQIVSYPRV- 62 LD++S +L LL + + LN SRR VY LEKIN L + V R Sbjct: 3 LDQRSTFILTQLLHARSYLPIQELTQKLNVSRRTVYNDLEKINSWLEEQGLKAVYKVRSQ 62 Query: 63 GILLTEKQKAACRLLLDEVTDYSYVMKSSERLQLSLVSIVVAKDRVTIDRLMQLNDVSRN 122- G++L E+ K L + + Y + ER ++ ++ + + ++ LM VSRN Sbjct: 63 GLILDERAKEEIPTKLRSLKSWHYEYSAQERKAWVVIYLLTRLEPLFLEHLMDRTGVSRN 122- Query: 123 TILNDLNELRSELAEKEYNLQLQSTKCRGYFLDGHPL----SIIQYLYKLLDDIYHNGSS 17- 8 T ++D+ L+ EL ++L L+ + GY + G +++ YL + L Sbjct: 123 TTIDDIKCLKDEL--NNFHLALEFERKDGYTISGDETDKRKALVYYLSQALPQQNWETEL 18- 0 Query: 179 SFIDLFNHKLSQAFGASTYFSKEVLDYFHHYLFISQRSLGKKINSQDGQFMIQILPFILM 23- 8 S I +F L F+ E L + + S++ L KI D L F+L Sbjct: 181 SPIRIF---LRTKRDNGRIFTIEELQKVYDVISESEKVL--KIQYTDDVLHSLSLRFLLF 23- 5 Query: 239 AYRK-----MRLSPEVQTSLNSDFSLVWQRKEYEIAKELADELEENFQLSLDEIEVGLVA 29- 3 R +++ P + L KEYE AK ++ +LE+ F + + EV + Sbjct: 236 MKRVAKGKFIKVHPLEKQVLKGT-------KEYEAAKVMSFKLEQAFGVHYPDEEVLYLT 28- 8 Query: 294 MLMLSFRKDRDN-HLESQ-DYDDMRATLTSFLKELEERYHLHFVHKKDLLRQLLTHCKAL 35- 1 +LS + + N +ES+ + ++ +TS + + ++ + F K+ L + L H K Sbjct: 289 THILSSEINYANGEIESRKESQELTHIVTSMVNDFQKYACVVFEEKELLEKNLFFHIKPA 34- 8 Query: 352 LYRKRYGIFSVNPLTEHIKDKYEELFAITSSSVKLLEKAWQIKLTDDDVAYLTIHLGGEL 41- 1 YR +YG+ N + E IK Y ELF +T V LE+ + D++VA++T+H G + Sbjct: 349 FYRIKYGLEVENNIAESIKTSYPELFLLTRKVVHYLERYVGKSVNDNEVAFITMHFVGWM 40- 8 Query: 412 RNSQQSPNE-LKLVIVSDEGIAIQKLLLKQCQRYLTNSDIEAVFTTEQYQSVSDLMHVDM 47- 0 R P K K +IV G+ + L Q + DI + +Y+ + VD Sbjct: 409 RREGTIPTKRKKALIVCANGVGTSQFLENQLEGLFPAVDIIKTCSIREYEKTP--VEVDF 46- 6 Query: 471 VVSTSDALESRFPMLVVHPVLTDDDIIRLIR 501 ++ST+ E P+ +V+P+LT+ + RL++ Sbjct: 467 IISTTSIPEKNVPIFIVNPILTETEKERLLK 497 A related DNA sequence was identified in S. pyogenes <SEQ ID 4623> which encodes the amino acid sequence <SEQ ID 4624>. Analysis of this protein sequence reveals the following: TABLE-US-04479 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0745(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04480 Identities = 368/548 (67%), Positives = 456/548 (83%) Query: 1 MIILDKKSYDLLFYLLKLEEPETVMAIANALNQSRRKVYYHLEKINDALPSDVPQIVSYP 60 M+ILDKKSYDLL YLLKLE PETVMAI++ALNQSRRKVYY L+KIN ALP V QI+SYP Sbjct: 1 MMILDKKSYDLLSYLLKLETPETVMAISHALNQSRRKVYYQLDKINQALPKGVDQIISYP 60 Query: 61 RVGILLTEKQKAACRLLLDEVTDYSYVMKSSERLQLSLVSIVVAKDRVTIDRLMQLNDVS 120- R+GILLT QKAACRLLL+EVTDY+YVMKS ER +LS + I V+ +RVTID+LMQ+NDVS Sbjct: 61 RLGILLTADQKAACRLLLEEVTDYNYVMKSDERRRLSSIYIAVSTERVTIDKLMQINDVS 120- Query: 121 RNTILNDLNELRSELAEKEYNLQLQSTKCRGYFLDGHPLSIIQYLYKLLDDIYHNGSSSF 18- 0 RNTILNDL ELR EL +K+Y +QL +TK RGY+ HP+++IQYLYKLL D+Y G++SF Sbjct: 121 RNTILNDLTELREELEDKQYKIQLHATKARGYYFGCHPMALIQYLYKLLVDVYQGGNTSF 18- 0 Query: 181 IDLFNHKLSQAFGASTYFSKEVLDYFHHYLFISQRSLGKKINSQDGQFMIQILPFILMAY 24- 0 ID+FN KLS+ G S YFSK++L YFH YLF+SQ SLGK IN+QD QFM+QILPF+L++Y Sbjct: 181 IDIFNRKLSEIQGLSVYFSKDILTYFHEYLFLSQASLGKTINTQDSQFMLQILPFMLLSY 24- 0 Query: 241 RKMRLSPEVQTSLNSDFSLVWQRKEYEIAKELADELEENFQLSLDEIEVGLVAMLMLSFR 30- 0 R MRL E +++L +F L+W+RKEY IA++LA EL NF+L LD+IEV +VAMLMLSFR Sbjct: 241 RNMRLDSETKSALKQEFHLIWKRKEYHIAQDLARELYHNFKLHLDDIEVSMVAMLMLSFR 30- 0 Query: 301 KDRDNHLESQDYDDMRATLTSFLKELEERYHLHFVHKKDLLRQLLTHCKALLYRKRYGIF 36- 0 KD+D+H+ESQDYDDMRAT++ F+ +LE RY LHF HK+DLL++L THCKAL+YRK YGIF Sbjct: 301 KDQDHHVESQDYDDMRATISHFIDQLESRYQLHFTHKQDLLKRLTTHCKALVYRKAYGIF 36- 0 Query: 361 SVNPLTEHIKDKYEELFAITSSSVKLLEKAWQIKLTDDDVAYLTIHLGGELRNSQQSPNK 42- 0 VNPLT+H+K+KYEELFA+T S +LE+ W I LTDDD+AYLTIHLGGELR++ K Sbjct: 361 LVNPLTDHVKEKYEELFAMTQSCATILEQDWTISLTDDDIAYLTIHLGGELRHNNTEQEK 42- 0 Query: 421 LKLVIVSDEGIAIQKLLLKQCQRYLTNSDIEAVFTTEQYQSVSDLMHVDMVVSTSDALES 48- 0 KLVIVSD+GI IQKLL KQCQRYL N IEAVFTTEQYQSV DL+ VDM+V+T+D L++ Sbjct: 421 TKLVIVSDDGIGIQKLLFKQCQRYLANGQIEAVFTTEQYQSVYDLLAVDMIVATTDTLKT 48- 0 Query: 481 RFPMLVVHPVLTDDDIIRLIRFSKKGNCANSNQFTNELEKTIAQYVKEDSERYVLKSKIE 54- 0 + PML+V+P+L+DDDII+LIRFSK+G + ++F+ EL K I VK++S+RY L SKIE Sbjct: 481 KIPMLIVNPILSDDDIIKLIRFSKQGRLSEHSRFSTELTKAIEAVVKDESDRYALVSKIE 54- 0 Query: 541 KLIHQELL 548 KLIH+ELL Sbjct: 541 KLIHRELL 548 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1504 A DNA sequence (GBSx1591) was identified in S. agalactiae <SEQ ID 4625> which encodes the amino acid sequence <SEQ ID 4626>. Analysis of this protein sequence reveals the following: TABLE-US-04481 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2692(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04482 >GP: AAC77149 GB: AE000491 orf, hypothetical protein [Escherichia coli K12] Identities = 211/363 (58%), Positives = 270/363 (74%), Gaps = 9/363 (2%) Query: 1 MPNVKDITRESWILSTFPEWGTWLNEEIEEEVVAEGNFAMWWLGNCGVWIKTPGGANVVM 60 M VK ITRESWILSTFPEWG+WLNEEIE+E VA G FAMWWLG G+W+K+ GG NV + Sbjct: 3 MSKVKSITRESWILSTFPEWGSWLNEEIEQEQVAPGTFAMWWLGCTGIWLKSEGGTNVCV 62 Query: 61 DLWSNRGKSTKKVKDMVRGHQMANMAGVRKLQPNLRAQPMVIDPFAINELDYYLVSHFHS 120- D W GK + M +GHQM MAGV+KLQPNLR P V+DPFAI ++D L +H H+ Sbjct: 63 DFWCGTGKQSHGNPLMKQGHQMQRMAGVKKLQPNLRTTPFVLDPFAIRQIDAVLATHDHN 122- Query: 121 DHIDINTAAAIINNPNLDHVKFVGPYECGEIWKKWGVPEERIIVIKPGESFEFKDIKVTA 18- 0 DHID+N AAA++ N D V F+GP C ++W WGVP+ER IV+KPG+ + KDI++ A Sbjct: 123 DHIDVNVAAAVMQNC-ADDVPFIGPKTCVDLWIGWGVPKERCIVVKPGDVVKVKDIEIHA 18- 1 Query: 181 VESFDRTCLVTLPVDGAEEHDGELAGLAVTDEEMARKAVNYIFETPGGTIYHGADSHFSN 24- 0 +++FDRT L+TLP D + AG V + M +AVNY+F+TPGG++YH DSH+SN Sbjct: 182 LDAFDRTALITLPADQ------KAAG--VLPDGMDDRAVNYLFKTPGGSLYHSGDSHYSN 23- 3 Query: 241 YFAKHGKDYKIDVAINNYGDNPVGIQDKMTSIDLLRMAENLRAKVIIPVHYDIWSNFMAS 30- 0 Y+AKHG +++IDVA+ +YG+NP GI DKMTS D+LRM E L AKV+IP H+DIWSNF A Sbjct: 234 YYAKHGNEHQIDVALGSYGENPRGITDKMTSADMLRMGEALNAKVVIPFHHDIWSNFQAD 29- 3 Query: 301 TDEILQLWKMRKERLQYDFHPFIWEVGGKYTYPQDKDRIEYHHPRGFDDCFEQESNIQFK 36- 0 EI LW+M+K+RL+Y F PFIW+VGGK+T+P DKD EYH+PRGFDDCF E ++ FK Sbjct: 294 PQEIRVLWEMKKDRLKYGFKPFIWQVGGKFTWPLDKDNFEYHYPRGFDDCFTIEPDLPFK 35- 3 Query: 361 ALL 363 + L Sbjct: 354 SFL 356 A related DNA sequence was identified in S. pyogenes <SEQ ID 4627> which encodes the amino acid sequence <SEQ ID 4628>. Analysis of this protein sequence reveals the following:

TABLE-US-04483 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3298(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04484 Identities = 315/363 (86%), Positives = 348/363 (95%) Query: 1 MPNVKDITRESWILSTFPEWGTWLNEEIEEEVVAEGNFAMWWLGNCGVWIKTPGGANVVM 60 M V+DITRESWIL+TFPEWGTWLNEEIE+EVV NFAMWWLGNCG+WIKTPGGANVVM Sbjct: 1 MTKVQDITRESWILNTFPEWGTWLNEEIEQEVVPADNFAMWWLGNCGIWIKTPGGANVVM 60 Query: 61 DLWSNRGKSTKKVKDMVRGHQMANMAGVRKLQPNLRAQPMVIDPFAINELDYYLVSHFHS 120- DLWSNRGK+TK+VKDMVRGHQMANMAG RKLQPNLRAQPMVIDPF INELDYYLVSH+HS Sbjct: 61 DLWSNRGKATKQVKDMVRGHQMANMAGARKLQPNLRAQPMVIDPFMINELDYYLVSHYHS 120- Query: 121 DHIDINTAAAIINNPNLDHVKFVGPYECGEIWKKWGVPEERIIVIKPGESFEFKDIKVTA 18- 0 DHIDINTAAAIINNP L+HVKFVGPYECGE+WK WGVP++RI+++KPG+SFEFKDIK+TA Sbjct: 121 DHIDINTAAAIINNPKLNHVKFVGPYECGEVWKNWGVPKDRIMILKPGDSFEFKDIKITA 18- 0 Query: 181 VESFDRTCLVTLPVDGAEEHDGELAGLAVTDEEMARKAVNYIFETPGGTIYHGADSHFSN 24- 0 VESFDRTCLVTLP+ GA+ DG+LAGLA+TD++MARKAVNYIFETPGGTIYHGADSHFSN Sbjct: 181 VESFDRTCLVTLPIQGADAQDGDLAGLAITDDDMARKAVNYIFETPGGTIYHGADSHFSN 24- 0 Query: 241 YFAKHGKDYKIDVAINNYGDNPVGIQDKMTSIDLLRMAENLRAKVIIPVHYDIWSNFMAS 30- 0 YFAKHG+DY IDV +NNYG+NP+GIQDKMTS+DLLRMAENLRAKV+IPVHYDIWSNFMAS Sbjct: 241 YFAKHGRDYDIDVVLNNYGENPIGIQDKMTSVDLLRMAENLRAKVVIPVHYDIWSNFMAS 30- 0 Query: 301 TDEILQLWKMRKERLQYDFHPFIWEVGGKYTYPQDKDRIEYHHPRGFDDCFEQESNIQFK 36- 0 TDEIL+LWKMRKERLQYDFHPFIWEVGGKYTYPQD++RIEYHHPRGFDDCF ++SNIQFK Sbjct: 301 TDEILELWKMRKERLQYDFHPFIWEVGGKYTYPQDQNRIEYHHPRGFDDCFLEDSNIQFK 36- 0 Query: 361 ALL 363 ALL Sbjct: 361 ALL 363 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1505 A DNA sequence (GBSx1592) was identified in S. agalactiae <SEQ ID 4629> which encodes the amino acid sequence <SEQ ID 4630>. Analysis of this protein sequence reveals the following: TABLE-US-04485 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3988(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10145> which encodes amino acid sequence <SEQ ID 10146> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04486 >GP: BAA18808 GB: D90917 hypothetical protein [Synechocystis sp.] Identities = 358/785 (45%), Positives = 494/785 (62%), Gaps = 15/785 (1%) Query: 22 LEKLDAWWRAANYISAAQMYLKDNPLLRRELVENDLKVHPIGHWGTVPGQNFIYAHLNRA 81 - L ++ +WRAANY++ +YL+DNPLLR L +K +GHWG+ PG +F+Y HLNR Sbjct: 44 LNQMHGFWRAANYLAVGMIYLRDNPLLREPLQPEQIKHRLLGHWGSSPGISFLYTHLNRI 103- Query: 82 INKYDLDMFYIEGPGHGGQVMVSNSYLDGSYTELNPNIEQTEDGFKQLCKIFSFPCGIAS 141- I K+D DM Y+ GPGHG + YL+GSY+ + EDG K+ K FSFP GI S Sbjct: 104 IRKFDQDMLYMVGPGHGAPGFLGPCYLEGSYSRFFAECSEDEDGMKRFFKQFSFPGGIGS 16- 3 Query: 142 HAAPETPGSIHEGGELGYALSHATGAILDNPDVIAATVIGDGEGETGPLMAGWLSNTFIN 20- 1 H PETPGSIHEGGELGY LSHA GA DNP++I + GDGE ETGPL W SN FIN Sbjct: 164 HCTPETPGSIHEGGELGYCLSHAYGAAFDNPNLIVVGLAGDGESETGPLATSWHSNKFIN 22- 3 Query: 202 PVNDGAVLPIFYLNGGKIHNPTIFERKTDEELSQFFEGLGWKPIFADVVELSEDHAAAHA 26- 1 P+ DGAVLP+ +LNG KI+NP++ R + EEL FEG G+ P F + D + H Sbjct: 224 PIRDGAVLPVLHLNGYKINNPSVLSRISHEELKALFEGYGYTPYFVE----GSDPESMHQ 27- 9 Query: 262 LFAEKLDQAIQEIKTIQSEARQKPAEEAIQAKFPVLVARIPKGWTGPKAWEGTPIEGGFR 32- 1 A LD + EI IQ EAR A++ ++P++V R PKGWTGP +G +EG +R Sbjct: 280 AMAATLDHCVSEIHQIQQEARSTGI--AVRPRWPMVVMRTPKGWTGPDYVDGHKVEGFWR 33- 7 Query: 322 AHQVPIPVDAHHMEHVDSLLSWLQSYRPEELFDENGKIVDEIAAISPKGDRRMSMNPITN 38- 1 +HQVP+ + H+ L +W++SY+PEELFDE G + AI+P+GD+R+ P N Sbjct: 338 SHQVPMGGMHENPAHLQQLEAWMRSYKPEELFDEQGTLKPGFKAIAPEGDKRLGSTPYAN 39- 7 Query: 382 AGIV-KAMDTADWKKFALDINVPGQIMAQDMIEFGKYAADLVDANPDNFRIFGPDETKSN 44- 0 G++ + + D++++ +D++ PG I A + G + D++ N NFR+FGPDE SN Sbjct: 398 GGLLRRGLKMPDFRQYGIDVDQPGTIEAPNTAPLGVFLRDVMANNMTNFRLFGPDENSSN 45- 7 Query: 441 RLQEVFTRTSRQWLGRRKPDYDEA--LSPAGRVIDSQLSEHQAEGFLEGYVLTGRHGFFA 49- 8 +L V+ + + W+ + + LSP GRV++ LSEH EG+LE Y+LTGRHGFFA Sbjct: 458 KLHAVYEVSKKFWIAEYLEEDQDGGELSPDGRVME-MLSEHTLEGWLEAYLLTGRHGFFA 51- 6 Query: 499 SYESFLRVVDSMVTQHFKWLRKSKTHTTWRKNYPALNLIAASTVFQQDHNGYTHQDPGIL 55- 8 +YESF V+ SMV QH KWL + H WR + +LN++ STV++QDHNG+THQDPG L Sbjct: 517 TYESFAHVITSMVNQHAKWLDICR-HLNWRADISSLNILMTSTVWRQDHNGFTHQDPGFL 57- 5 Query: 559 THLAEKTPEYIREYLPADTNSLLAVMDKAFKAEDKINLIVTSKHPRPQFYSIAEAEELVA 61- 8 + K+P+ +R YLP D NSLL+V D ++++ IN+IV K Q+ + A Sbjct: 576 DVILNKSPDVVRIYLPPDVNSLLSVADHCLQSKNYINIIVCDKQAHLQYQDMTSAIRNCT 63- 5 Query: 619 EGYKVIDWASNVSLNQEPDVVFAAAGTEPNLEALAAISILHKAFPELKIRFVNVLDILKL 67- 8 +G + +WASN EPDVV AAAG P EALAA ++L + FP L+IRFV+V+D+LKL Sbjct: 636 KGVDIWEWASN-DAGTEPDVVMAAAGDIPTKEALAATAMLRQFFPNLRIRFVSVIDLLKL 69- 4 Query: 679 RHPSQDARGLSDEEFNKVFTTDKPVIFAFHGYEDMIRDIFFSRHNH-NLHTHGYRENGDI 73- 7 + S+ GLSD +F+ +FTTDKP+IF FH Y +I + + R NH NLH GY+E G+I Sbjct: 695 QPESEHPHGLSDRDFDSLFTTDKPIIFNFHAYPWLIHRLTYRRTNHGNLHVRGYKEKGNI 75- 4 Query: 738 TTPFDMRVMSELDRFHLAQDA--ALASLGNKAQAFSDEMNQMVAYHKDYIREHGDDIPEV 79- 5 TP D+ + +++DRF LA D L L + + M +Y EHG D+PE+ Sbjct: 755 NTPMDLAIQNQIDRFSLAIDVIDRLPQLRVAGAHIKEMLKDMQIDCTNYAYEHGIDMPEI 81- 4 Query: 796 QNWKW 800 NW+W Sbjct: 815 VNWRW 819 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1506 A DNA sequence (GBSx1593) was identified in S. agalactiae <SEQ ID 4631> which encodes the amino acid sequence <SEQ ID 4632>. Analysis of this protein sequence reveals the following: TABLE-US-04487 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3509(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04488 >GP: AAF37878 GB: AF234619 OpuAA [Lactococcus lactis] Identities = 274/402 (68%), Positives = 338/402 (83%) Query: 5 LEVKNLTKIFGKKQKAALEMVKQGKSKTEILEKTGATVGVYDASFEIKEGEIFVIMGLSG 64 +++++LTKIFGK+ K AL MV++G+ K EIL+KTGATVGVYD +FEI EGEIFVIMGLSG Sbjct: 5 IKIEHLTKIFGKRIKTALTMVEKGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMGLSG 64 Query: 65 SGKSTLVRMLNRLIDPSSGNIYLDGKDIAKMNVEDLRNIRRHDINMVFQNFGLFPHRTIL 124- SGKSTL+R+LNRLI+P+SG I++D +D+A +N EDL +RR ++MVFQNFGLFPHRTIL Sbjct: 65 SGKSTLLRLLNRLIEPTSGKIFIDNQDVATLNKEDLLQVRRKTMSMVFQNFGLFPHRTIL 124- Query: 125 ENTEFGLEMRGVSKEERTTLAEKALDNAGLLPFKDQYPSQLSGGMQQRVGLARALANSPK 18- 4 ENTE+GLE++ V KEER AEKALDNA LL FKDQYP QLSGGMQQRVGLARALAN P+ Sbjct: 125 ENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALANDPE 18- 4 Query: 185 ILLMDEAFSALDPLIRREMQDELLDLQDTNKQTIIFISHDLNEALRIGDRIALMKDGEIM 24- 4 ILLMDEAFSALDPLIRREMQDELL+LQ ++TIIF+SHDLNEALRIGDRIA+MKDG+IM Sbjct: 185 ILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDGKIM 24- 4 Query: 245 QIGTGEEILTNPANDFVREFVEDVDRSKVLTAQNIMIKPLTTVLEIDGPQVALTRMHREE 30- 4 QIGTGEEILTNPAND+V+ FVEDVDR+KV+TA+NIMI LTT +++DGP VAL +M EE Sbjct: 245 QIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMIPALTTNIDVDGPSVALKKMKTEE 30- 4 Query: 305 VSMLMATNRRRQLLGSLTADAAIEARKKDLPLSEVIDKDVVTVSKDTVITDIMPLIYDSS 36- 4 VS LMA +++RQ G +T++ AI ARK + PL +V+ DV TVSK+ ++ DI+P+IYD+ Sbjct: 305 VSSLMAVDKKRQFRGVVTSEQAIAARKNNQPLKDVMTTDVGTVSKEMLVRDILPIIYDAP 36- 4 Query: 365 APIAVTDDNDRLLGVIIRGRVIEALANVQDETVVESPKETVE 406 P+AV DDN L GV+IRG V+EALA++ DE VE ++ E Sbjct: 365 TPLAVVDDNGFLKGVLIRGSVLEALADIPDEDEVEEIEKEEE 406 A related DNA sequence was identified in S. pyogenes <SEQ ID 4633> which encodes the amino acid sequence <SEQ ID 4634>. Analysis of this protein sequence reveals the following: TABLE-US-04489 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3761(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04490 Identities = 344/395 (87%), Positives = 374/395 (94%) Query: 1 MTNILEVKNLTKIFGKKQKAALEMVKQGKSKTEILEKTGATVGVYDASFEIKEGEIFVIM 60 M ILEVK+L+KIFGKKQKAALEMVK GK+K+EI +KTGATVGVYDASFE+K+GEIFVIM Sbjct: 1 METILEVKHLSKIFGKKQKAALEMVKTGKNKSEIFKKTGATVGVYDASFEVKKGEIFVIM 60 Query: 61 GLSGSGKSTLVRMLNRLIDPSSGNIYLDGKDIAKMNVEDLRNIRRHDINMVFQNFGLFPH 120- GLSGSGKSTLVRMLNRLI+PS+G+I L+GKDI+ M+ + LR +RRHDINMVFQ+F LFPH Sbjct: 61 GLSGSGKSTLVRMLNRLIEPSAGSILLEGKDISTMSADQLREVRRHDINMVFQSFALFPH 120- Query: 121 RTILENTEFGLEMRGVSKEERTTLAEKALDNAGLLPFKDQYPSQLSGGMQQRVGLARALA 18- 0 +TILENTEFGLE+RGV KEER LAEKALDN+GLL FKDQYP+QLSGGMQQRVGLARALA Sbjct: 121 KTILENTEFGLELRGVPKEERQRLAEKALDNSGLLDFKDQYPNQLSGGMQQRVGLARALA 18- 0 Query: 181 NSPKILLMDEAFSALDPLIRREMQDELLDLQDTNKQTIIFISHDLNEALRIGDRIALMKD 24- 0 NSPKILLMDEAFSALDPLIRREMQDELLDLQD+ KQTIIFISHDLNEALRIGDRIALMKD Sbjct: 181 NSPKILLMDEAFSALDPLIRREMQDELLDLQDSMKQTIIFISHDLNEALRIGDRIALMKD 24- 0 Query: 241 GEIMQIGTGEEILTNPANDFVREFVEDVDRSKVLTAQNIMIKPLTTVLEIDGPQVALTRM 30- 0 G+IMQIGTGEEILTNPANDFVREFVEDVDRSKVLTAQNIMIKPLTT +E+DGPQVAL RM Sbjct: 241 GQIMQIGTGEEILTNPANDFVREFVEDVDRSKVLTAQNIMIKPLTTTVELDGPQVALNRM 30- 0 Query: 301 HREEVSMLMATNRRRQLLGSLTADAAIEARKKDLPLSEVIDKDVVTVSKDTVITDIMPLI 36- 0 H EEVSMLMATNRRRQL+GSLTADAAIEARKK LPLSEVID+DV TVSKDT+ITDI+PLI Sbjct: 301 HNEEVSMLMATNRRRQLVGSLTADAAIEARKKGLPLSEVIDRDVRTVSKDTIITDILPLI 36- 0 Query: 361 YDSSAPIAVTDDNDRLLGVIIRGRVIEALANVQDE 395 YDSSAPIAVTDDN+RLLGVIIRGRVIEALAN+ DE Sbjct: 361 YDSSAPIAVTDDNNRLLGVIIRGRVIEALANISDE 395 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1507 A DNA sequence (GBSx1594) was identified in S. agalactiae <SEQ ID 4635> which encodes the amino acid sequence <SEQ ID 4636>. This protein is predicted to be OpuABC (opuAB). Analysis of this protein sequence reveals the following: TABLE-US-04491 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.67 Transmembrane 48-64 (43-72) INTEGRAL Likelihood = -9.24 Transmembrane 101-117 (93-122) INTEGRAL Likelihood = -7.54 Transmembrane 296-312 (290-316) INTEGRAL Likelihood = -6.21 Transmembrane 252-268 (250-273) INTEGRAL Likelihood = -5.57 Transmembrane 141-157 (138-170) INTEGRAL Likelihood = -0.53 Transmembrane 220-236 (220-237) ----- Final Results ----- bacterial membrane --- Certainty = 0.5267(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04492 >GP: AAF37879 GB: AF234619 OpuABC [Lactococcus lactis] Identities = 345/578 (59%), Positives = 429/578 (73%), Gaps = 8/578 (1%) Query: 1 MENLLQHKLPVAPFVESTTNWITKTFSGLFDFIQTIGNALMDWMTKTLLFINPLLFIVLI 60 M +L ++P+A +V S T+WIT TFS FD IQ G LM+ +T L + L I ++ Sbjct: 1 MIDLAIGQVPIANWVSSATDWITSTFSSGFDVIQKSGTVLMNGITGALTAVPFWLMIAVV 60 Query: 61 TIAVFFLAKKKWQLPTFTFIGLLFIYNQGLWEQLINTFNLVLVASLISIIIGVPLGIWMA 120- TI ++ KK P FTFIGL I NQGLW L++T LVL++SL+SIIIGVPLGIWMA Sbjct: 61 TILAILVSGKKIAFPLFTFIGLSLIANQGLWSDLMSTITLVLLSSLLSIIIGVPLGIWMA 120- Query: 121 KSDKVKQVVNPILDFMQTMPAFVYLIPAVAFFGIGMVPGVFASVVFALPPTVRFTNLAIR 18- 0 KSD V ++V PILDFMQTMP FVYLIPAVAFFGIG+VPGVFASV+FALPPTVR TNL IR Sbjct: 121 KSDLVAKIVQPILDFMQTMPGFVYLIPAVAFFGIGVVPGVFASVIFALPPTVRMTNLGIR 18- 0 Query: 181 EIPLELIEASDSFGSTVKQKLFKVELPLAKNTIMAGINQTMMLALSMVVTGSMIGAPGLG 24- 0 ++ EL+EA+DSFGST +QKLFK+E PLAK TIMAG+NQT+MLALSMVV SMIGAPGLG Sbjct: 181 QVSTELVEAADSFGSTARQKLFKLEFPLAKGTIMAGVNQTIMLALSMVVIASMIGAPGLG 24- 0 Query: 241 REVLSALQHADIGTGFVSGLSLVILAIVLDRVSQFFNSKPGEKQAKTSKVKKW---VGLG 29- 7 R VL+A+Q ADIG GFVSG+SLVILAI++DR +Q N P EKQ + VKKW + L Sbjct: 241 RGVLAAVQSADIGKGFVSGISLVILAIIIDRFTQKLNVSPLEKQGNPT-VKKWKRGIALV 29- 9 Query: 298 ALALFILAALGRIVVNMTSGNEAKGQKVKIAYVQWDSEVASTNVIAEVLKSKGYDVELTP 35- 7 +L I+ A M+ G A +KV + Y+ WDSEVAS NV+ + +K G+DV+ T Sbjct: 300 SLLALIIGAFS----GMSFGKTASDKKVDLVYMNWDSEVASINVLTQAMKEHGFDVKTTA 35- 5 Query: 358 LDNAVMWQTVANGNADFTTSAWLPKTHGQYFNKYKNSLDDLGPHVENVKIGLVVPKYMNV 41- 7 LDNAV WQTVANG AD SAWLP TH + KY S+D LGP+++ K+G VVP YMNV Sbjct: 356 LDNAVAWQTVANGQADGMVSAWLPNTHKTQWQKYGKSVDLLGPNLKGAKVGFVVPSYMNV 41- 5 Query: 418 NSIEELSNQADKQITGIEPGAGIMKSAKQSLKDYPNLSSWKLLSASTGAMTTTLGKAIKN 47- 7 NSIE+L+NQA+K ITGIEPGAG+M +++++L Y NL WKL+ +S+GAMT LG+AIK Sbjct: 416 NSIEDLTNQANKTITGIEPGAGVMAASEKTLNSYDNLKDWKLVPSSSGAMTVALGEAIKQ 47- 5 Query: 478 KDQVVITGWSPHWMFAKYDLKYLKDPKKSFGGEEHINTIARKNLKKDMPKVYKIIDKFKW 53- 7 +VITGWSPHWMF KYDLKYL DPK + G E+INTI RK LKK+ P+ YK++DKF W Sbjct: 476 HKDIVITGWSPHWMFNKYDLKYLADPKGTMGTSENINTIVRKGLKKENPEAYKVLDKFNW 53- 5 Query: 538 TKEDMESIMLDMDKGMEPAKAAQKWIKNHKKEVSEWTK 575 T +DME++MLD+ G P +AA+ WIK+H+KEV +W K Sbjct: 536 TTKDMEAVMLDIQNGKTPEEAAKNWIKDHQKEVDKWFK 573 A related DNA sequence was identified in S. pyogenes <SEQ ID 4637> which encodes the amino acid sequence <SEQ ID 4638>. Analysis of this protein sequence reveals the following: TABLE-US-04493 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.86 Transmembrane 101-117 (93-121) INTEGRAL Likelihood = -7.54 Transmembrane 252-268 (250-273) INTEGRAL Likelihood = -6.85 Transmembrane 48-64 (43-70) INTEGRAL Likelihood = -5.57 Transmembrane 141-157 (138-170) INTEGRAL Likelihood = -5.26 Transmembrane 295-311 (289-315) INTEGRAL Likelihood = -0.53 Transmembrane 220-236 (220-237) ----- Final Results ----- bacterial membrane --- Certainty = 0.4545(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04494 >GP: AAF37879 GB: AF234619 OpuABC [Lactococcus lactis] Identities = 340/571 (59%), Positives = 418/571 (72%), Gaps = 8/571 (1%) Query: 8 KLPVAQLVEQLTEWLTKTFSGLFDIMQVVGSFLMDWMTKTLLFIHPLLFIVLVTAGMFFL 67 ++P+A V T+W+T TFS FD++Q G+ LM+ +T L + L I +VT + Sbjct: 8 QVPIANWVSSATDWITSTFSSGFDVIQKSGTVLMNGITGALTAVPFWLMIAVVTILAILV 67 Query: 68 AKKKWPLPTFTLLGLLFIYNQGLWKQLMNTFTLVLVASLISVLIGIPLGIWMAKNATVRQ 127- + KK P FT +GL I NQGLW LM+T TLVL++SL+S++IG+PLGIWMAK+ V + Sbjct: 68 SGKKIAFPLFTFIGLSLIANQGLWSDLMSTITLVLLSSLLSIIIGVPLGIWMAKSDLVAK 127- Query: 128 IVNPILDFMQTMPAFVYLIPAVAFFGIGMVPGVFASVIFALPPTVRFTNLAIRDIPTELI 18- 7 IV PILDFMQTMP FVYLIPAVAFFGIG+VPGVFASVIFALPPTVR TNL IR + TEL+ Sbjct: 128 IVQPILDFMQTMPGFVYLIPAVAFFGIGVVPGVFASVIFALPPTVRMTNLGIRQVSTELV 18- 7 Query: 188 EASDAFGSTGKQKLFKVELPLAKNTIMAGVNQTMMLALSMVVTGSMIGAPGLGREVLSAL 24- 7 EA+D+FGST +QKLFK+E PLAK TIMAGVNQT+MLALSMVV SMIGAPGLGR VL+A+ Sbjct: 188 EAADSFGSTARQKLFKLEFPLAKGTIMAGVNQTIMLALSMVVIASMIGAPGLGRGVLAAV 24- 7 Query: 248 QHADIGSGFVSGLALVILAIVLDRMTQLFNSKPQEKAKAGKTNKW---IGLAALAVFLIA 30- 4 Q ADIG GFVSG++LVILAI++DR TQ N P EK KW I L +L +I Sbjct: 248 QSADIGKGFVSGISLVILAIIIDRFTQKLNVSPLEKQGNPTVKKWKRGIALVSLLALIIG 30- 7 Query: 305 ALGRGIMAMTSGMADKGETVNIAYVQWDSEVASTHVIAEVLKNEGYHVTLTPLDNAVMWQ 36- 4 A M+ G + V++ Y+ WDSEVAS +V+ + +K G+ V T LDNAV WQ Sbjct: 308 AFS----GMSFGKTASDKKVDLVYMNWDSEVASINVLTQAMKEHGFDVKTTALDNAVAWQ 36- 3 Query: 365 TVANGNADFSTSAWLPVTHGQQYQKYKSKLDDLGPNLKGTKLGLAVPKYMTDVNSIEDLS 42- 4 TVANG AD SAWLP TH Q+QKY +D LGPNLKG K+G VP YM +VNSIEDL+ Sbjct: 364 TVANGQADGMVSAWLPNTHKTQWQKYGKSVDLLGPNLKGAKVGFVVPSYM-NVNSIEDLT 42- 2 Query: 425 KQADQKITGIEPGAGIMAAAQKTLKEYHNLSSWELVAASTGAMTTSLDQAIKKKDPIVVT 48- 4 QA++ ITGIEPGAG+MAA++KTL Y NL W+LV +S+GAMT +L +AIK+ IV+T Sbjct: 423 NQANKTITGIEPGAGVMAASEKTLNSYDNLKDWKLVPSSSGAMTVALGEAIKQHKDIVIT 48- 2 Query: 485 AWSPHWMFAKYDLKYLKDPKEIFGSTENINTIARKGLKKELPNVYKIIDKFHWTQKDMEA 54- 4 WSPHWMF KYDLKYL DPK G++ENINTI RKGLKKE P YK++DKF+WT KDMEA Sbjct: 483 GWSPHWMFNKYDLKYLADPKGTMGTSENINTIVRKGLKKENPEAYKVLDKFNWTTKDMEA 54- 2 Query: 545 VMLDINKGMSPEAAAKKWVEANKSKVSSWTK 575 VMLDI G +PE AAK W++ ++ +V W K Sbjct: 543 VMLDIQNGKTPEEAAKNWIKDHQKEVDKWFK 573 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-04495 Identities = 439/576 (76%), Positives = 513/576 (88%), Gaps = 2/576 (0%) Query: 1 MENLLQHKLPVAPFVESTTNWITKTFSGLFDFIQTIGNALMDWMTKTLLFINPLLFIVLI 60 +E +LQ KLPVA VE T W+TKTFSGLFD +Q +G+ LMDWMTKTLLFI+PLLFIVL+ Sbjct: 1 LETILQTKLPVAQLVEQLTEWLTKTFSGLFDIMQVVGSFLMDWMTKTLLFIHPLLFIVLV 60 Query: 61 TIAVFFLAKKKWQLPTFTFIGLLFIYNQGLWEQLINTFNLVLVASLISIIIGVPLGIWMA 120- T +FFLAKKKW LPTFT +GLLFIYNQGLW+QL+NTF LVLVASLIS++IG+PLGIWMA Sbjct: 61 TAGMFFLAKKKWPLPTFTLLGLLFIYNQGLWKQLMNTFTLVLVASLISVLIGIPLGIWMA 120- Query: 121 KSDKVKQVVNPILDFMQTMPAFVYLIPAVAFFGIGMVPGVFASVVFALPPTVRFTNLAIR 18- 0 K+ V+Q+VNPILDFMQTMPAFVYLIPAVAFFGIGMVPGVFASV+FALPPTVRFTNLAIR Sbjct: 121 KNATVRQIVNPILDFMQTMPAFVYLIPAVAFFGIGMVPGVFASVIFALPPTVRFTNLAIR 18- 0 Query: 181 EIPLELIEASDSFGSTVKQKLFKVELPLAKNTIMAGINQTMMLALSMVVTGSMIGAPGLG 24- 0 +IP ELIEASD+FGST KQKLFKVELPLAKNTIMAG+NQTMMLALSMVVTGSMIGAPGLG Sbjct: 181 DIPTELIEASDAFGSTGKQKLFKVELPLAKNTIMAGVNQTMMLALSMVVTGSMIGAPGLG 24- 0 Query: 241 REVLSALQHADIGTGFVSGLSLVILAIVLDRVSQFFNSKPGEKQAKTSKVKKWVGLGALA 30- 0 REVLSALQHADIG+GFVSGL+LVILAIVLDR++Q FNSKP EK AK K KW+GL ALA Sbjct: 241 REVLSALQHADIGSGFVSGLALVILAIVLDRMTQLFNSKPQEK-AKAGKTNKWIGLAALA 29- 9 Query: 301 LFILAALGRIVVNMTSGNEAKGQKVKIAYVQWDSEVASTNVIAEVLKSKGYDVELTPLDN 36- 0 +F++AALGR ++ MTSG KG+ V IAYVQWDSEVAST+VIAEVLK++GY V LTPLDN Sbjct: 300 VFLIAALGRGIMAMTSGMADKGETVNIAYVQWDSEVASTHVIAEVLKNEGYHVTLTPLDN 35- 9 Query: 361 AVMWQTVANGNADFTTSAWLPKTHGQYFNKYKNSLDDLGPHVENVKIGLVVPKYM-NVNS 41- 9 AVMWQTVANGNADF+TSAWLP THGQ + KYK+ LDDLGP+++ K+GL VPKYM +VNS Sbjct: 360 AVMWQTVANGNADFSTSAWLPVTHGQQYQKYKSKLDDLGPNLKGTKLGLAVPKYMTDVNS 41- 9 Query: 420 IEELSNQADKQITGIEPGAGIMKSAKQSLKDYPNLSSWKLLSASTGAMTTTLGKAIKNKD 47- 9 IE+LS QAD++ITGIEPGAGIM +A+++LK+Y NLSSW+L++ASTGAMTT+L +AIK KD Sbjct: 420 IEDLSKQADQKITGIEPGAGIMAAAQKTLKEYHNLSSWELVAASTGAMTTSLDQAIKKKD 47- 9 Query: 480 QVVITGWSPHWMFAKYDLKYLKDPKKSFGGEEHINTIARKNLKKDMPKVYKIIDKFKWTK 53- 9 +V+T WSPHWMFAKYDLKYLKDPK+ FG E+INTIARK LKK++P VYKIIDKF WT+ Sbjct: 480 PIVVTAWSPHWMFAKYDLKYLKDPKEIFGSTENINTIARKGLKKELPNVYKIIDKFHWTQ 53- 9 Query: 540 EDMESIMLDMDKGMEPAKAAQKWIKNHKKEVSEWTK 575 +DME++MLD++KGM P AA+KW++ +K +VS WTK Sbjct: 540 KDMEAVMLDINKGMSPEAAAKKWVEANKSKVSSWTK 575 A related GBS gene <SEQ ID 8827> and protein <SEQ ID 8828> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04496 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: -6.57 GvH: Signal Score (-7.5): -5.37 Possible site: 41 >>> Seems to have no N-terminal signal sequence ALOM program count: 6 value: -10.67 threshold: 0.0 INTEGRAL Likelihood = -10.67 Transmembrane 48-64 (43-72) INTEGRAL Likelihood = -9.24 Transmembrane 101-117 (93-122) INTEGRAL Likelihood = -7.54 Transmembrane 296-312 (290-316) INTEGRAL Likelihood = -6.21 Transmembrane 252-268 (250-273) INTEGRAL Likelihood = -5.57 Transmembrane 141-157 (138-170) INTEGRAL Likelihood = -0.53 Transmembrane 220-236 (220-237) PERIPHERAL Likelihood = 2.44 159 modified ALOM score: 2.63 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5267 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00097## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1508 A DNA sequence (GBSx1596) was identified in S. agalactiae <SEQ ID 4639> which encodes the amino acid sequence <SEQ ID 4640>. This protein is predicted to be a transposase. Analysis of this protein sequence reveals the following: TABLE-US-04497 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.65 Transmembrane 223-239 (223-240) ----- Final Results ----- bacterial membrane --- Certainty = 0.1659 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10057> which encodes amino acid sequence <SEQ ID 10058> was also identified. A related GBS nucleic acid sequence <SEQ ID 10031> which encodes amino acid sequence <SEQ ID 10032> was also identified. A related GBS nucleic acid sequence <SEQ ID 10801> which encodes amino acid sequence <SEQ ID 10802> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04498 >GP: CAA50689 GB: X71844 putative transposase [Clostridium perfringens] Identities = 94/364 (25%), Positives 160/364 (43%), Gaps = 35/364 (9%) Query: 8 KHKHLTLLDRNDIQSGLDRGETFKAIGLNLLKHPTTIAKEVKRN--KQLRESTKDCLDCP 65 K+KHL + +R ++ L G + L + T+ E++R KQ+++ + + Sbjct: 12 KNKHLNMKERMIVEIRLKDGFSAYKNTKELNRPINTVLNEIRRGTTKQIKQGKEFHVYFA 71 Query: 66 LLRKAPYVCNGCPKRRINCGYKKTFYLAKQAQRNYEKLLVESREGIPLNKETFWKIDRVL 125- +A Y N + + N YK ++ K +V+ K W +D + Sbjct: 72 DTGEAVYKKN---RLKSNRKYKLL------ECSDFIKYVVDKV------KNDHWSLDACV 116- Query: 126 SNGVKKGQRIYHILKTNDLEVSSSTVYRHIKKGYLSITPIDLPRAVKFKKRRKSTLPPIP 18- 5 G+ ++ + +S+ T+Y ++ G L I IDLP K + +KST Sbjct: 117 ------GEALHSSRFSPSQIISTKTLYNYVDLGLLPIKNIDLP--AKLHRNKKSTRVRNN 16- 8 Query: 186 KAIKEGRRYEDFIEHM-NQSELNSWLEMDTVIGRIGGK--VLLTFNVAFCNFIFAKLMDS 24- 2 K K G D + N+ E W E+D V+G K VLLT + M S Sbjct: 169 KK-KLGTSISDRPNSIENREEFGHW-EIDCVLGEKSNKDKVLLTLVERKTRYAIISEMSS 22- 6 Query: 243 KTAIETAKHIQVIKRTLYDNKRDFFELFPVILTDNGGEFARVDDIEIDVCGQSQLFFCDP 30- 2 + I K + IK L F E+F I DNG EFA + + E+ +++++F P Sbjct: 227 HSTISVTKALDKIKEFLGSK---FSEVFKSITADNGSEFADLSEFELKT--KTKVYFTHP 28- 1 Query: 303 NRSDQKARIEKNHTLVRDILPKGTSFDNLTQEDINLALSHINSVKRQALNGKTAYELFSF 36- 2 S +K E+++ L+R +PKG + + E I+ + +N++ R+ L+ KT ELF Sbjct: 282 YSSFEKGTNERHNGLIRRFIPKGKRISDYSLETISFIENWMNTLPRKLLDYKTPEELFEI 34- 1 Query: 363 TYGK 366 K Sbjct: 342 HLDK 345 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1509 A DNA sequence (GBSx1597) was identified in S. agalactiae <SEQ ID 4641> which encodes the amino acid sequence <SEQ ID 4642>. Analysis of this protein sequence reveals the following: TABLE-US-04499 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.30 Transmembrane 56-72 (48-79) INTEGRAL Likelihood = -6.85 Transmembrane 11-27 (6-30) INTEGRAL Likelihood = -6.69 Transmembrane 129-145 (126-158) INTEGRAL Likelihood = -6.53 Transmembrane 94-110 (90-117) INTEGRAL Likelihood = -1.54 Transmembrane 216-232 (215-232) INTEGRAL Likelihood = -1.22 Transmembrane 147-163 (147-165) ----- Final Results ----- bacterial membrane --- Certainty = 0.5522 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9431> which encodes amino acid sequence <SEQ ID 9432> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04500 >GP: BAB07666 GB: AP001520 unknown conserved protein [Bacillus halodurans] Identities = 112/224 (50%), Positives = 150/224 (66%), Gaps = 2/224 (0%) Query: 8 IKDILWFIIPSLFGVLLLMTPFKYNGMTTVAVSVISKTINQWINAVFPIHYIILLIIFIS 67 +KD LWF+IPS+ GV L M P + + T+ V+ ++K + ++ P I+L I + Sbjct: 19 LKDYLWFLIPSIIGVGLFMVPIQKDNAITIPVAFLAKQLQGALDDHLPAILTIMLAIVV- 77 Query: 68 CVLALCYRLFRPSFIEKNDLLKEISDITIFWLIIRLIGLALGLMTVLHIGPEMVWGKETG 127- VL+ LF+P+ KN LLK + I WL++R++G MT+L +GPE VW + TG Sbjct: 78 -VLSCVATLFKPNLFMKNGLLKSLFVIHPMWLVVRVLGFIFAFMTLLQLGPEAVWSEGTG 136- Query: 128 GLILFDLIGGLFTIFLAAGFILPFLTEFGLLEFVGVFLTPIMRPFFQLPGRSAVNCVASF 18- 7 L+L+DL+ LFTIFL AG LPFL FGLLE GV L MRP F LPGRS+++C+AS+ Sbjct: 137 ALLLYDLLPLLFTIFLFAGLFLPFLLNFGLLELFGVLLNKFMRPVFTLPGRSSIDCLASW 19- 6 Query: 188 VGDGTIGIALTDKQYVEGYYTSREAATISTTFSAVSITFCLXXL 231 +GDGTIG+ LT+KQY EG+YT REAA ISTTFS VSITF + L Sbjct: 197 MGDGTIGVLLTNKQYEEGFYTQREAAVISTTFSVVSITFSIVVL 240 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1510 A DNA sequence (GBSx1599) was identified in S. agalactiae <SEQ ID 4643> which encodes the amino acid sequence <SEQ ID 4644>. This protein is predicted to be Na/H antiporter homolog (kefB). Analysis of this protein sequence reveals the following: TABLE-US-04501 Possible site: 17 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.14 Transmembrane 176-192 (171-203) INTEGRAL Likelihood = -9.34 Transmembrane 353-369 (348-373) INTEGRAL Likelihood = -9.24 Transmembrane 3-19 (1-26) INTEGRAL Likelihood = -7.17 Transmembrane 145-161 (142-168) INTEGRAL Likelihood = -7.01 Transmembrane 86-102 (81-108) INTEGRAL Likelihood = -6.53 Transmembrane 52-68 (51-72) INTEGRAL Likelihood = -5.79 Transmembrane 24-40 (23-49) INTEGRAL Likelihood = -5.52 Transmembrane 214-230 (209-233) INTEGRAL Likelihood = -4.04 Transmembrane 260-276 (258-278) INTEGRAL Likelihood = -3.66 Transmembrane 287-303 (287-308) INTEGRAL Likelihood = -2.71 Transmembrane 113-129 (112-129) INTEGRAL Likelihood = -2.66 Transmembrane 332-348 (330-349) ----- Final Results ----- bacterial membrane --- Certainty = 0.5055 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04502 >GP: CAA51756 GB: X73329 Na/H antiporter homolog [Lactococcus lactis] Identities = 208/376 (55%), Positives = 285/376 (75%), Gaps = 3/376 (0%) Query: 1 MHIIIQITIILLASVLATLISKRIGIPAVVGQLLVGIIIGPAMLGLVHQNQVLHVLSEIG 60 M+ I+Q+TI+L+AS++ATL S+R+ IPAV+GQ+LVGI+I P++LGLVH VL V+SEIG Sbjct: 1 MNDILQLTIVLIASLIATLASRRLKIPAVIGQMLVGILIAPSVLGLVHSGHVLEVMSEIG 60 Query: 61 VILLMFLAGLEANFDLLKKYLKPSLLVAITGVIVPMALFYFLTRLFGFQINTAIFYGLVF 120- VILLMFLAGLE++ +LKK K S+LVAI GVIVP+ +F + FG+ ++T+ FYG+VF Sbjct: 61 VILLMFLAGLESDLTVLKKNFKASMLVAIGGVIVPLIVFGLVAFSFGYGMSTSFFYGIVF 120- Query: 121 AATSISITVEVLQEYNRVKTDTGAIILGAAVADDVLAVLLLSVFIA--TNGSSSNIGLQI 17- 8 AATS+SITVEVLQEY ++ T G+IILGAAV DD+LAVL+LS+F + GS +++ Q Sbjct: 121 AATSVSITVEVLQEYGKLSTRAGSIILGAAVVDDILAVLILSIFTSFKNGGSGTHLFFQF 18- 0 Query: 179 IIQLLFFVFLFICMKYLVPALFKLIEKVHFFEKYTILAILICFSLSILADKVGMSSIIGS 23- 8 +++LLFF FLF+ K L+P +K ++K+ K TI+A++IC LS+LAD VGMS++IGS Sbjct: 181 LLELLFFAFLFVVHK-LIPRFWKFVQKLPIANKNTIVALIICLGLSLLADSVGMSAVIGS 23- 9 Query: 239 FFAGLAIGQTSFVDKVEHKISLLSYTFFIPIFFASIALPLKFDGMMSHLHTILIFTALAV 29- 8 FFAGLAI QT K+E S + Y FIP+FF IA+ ++FD ++ H IL+FT LA+ Sbjct: 240 FFAGLAISQTEVSHKIEEYTSAIGYVIFIPVFFVLIAISVQFDSLIHHPWIILLFTLLAI 29- 9 Query: 299 LSKLIPGYFVGRGFNFSKLESLTIGGGMVSRGEMALIIVQVGLAAKIISSTTYSELVIVV 35- 8 L+K IP YFVG+ S ES+ IG GM+SRGEMALI+ Q+GL + II+ YSELVIV+ Sbjct: 300 LTKFIPAYFVGKSNKLSTGESMLIGTGMISRGEMALIVAQIGLTSAIITDEVYSELVIVI 35- 9 Query: 359 ILSTIIAPFILKYSFK 374 IL+T++APF++K K Sbjct: 360 ILATVLAPFLIKLVLK 375 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1511 A DNA sequence (GBSx1600) was identified in S. agalactiae <SEQ ID 4645> which encodes the amino acid sequence <SEQ ID 4646>. Analysis of this protein sequence reveals the following: TABLE-US-04503 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04504 >GP: CAB14269 GB: Z99116 ypuA [Bacillus subtilis] Identities = 86/319 (26%), Positives = 147/319 (45%), Gaps = 34/319 (10%) Query: 3 IKKLLFAGLAFILFTLASPAYAASDVQKVIDETYVQPDYVLGYSLNQEQRAQTLQLLNYD 62 +KK+ LA + L P + +D + + V LG L++ + + L +N Sbjct: 1 MKKIWIGMLAAAVLLLMVPKVSLADA--AVGDVIV----TLGADLSESDKQKVLDEMNVP 54 Query: 63 ESRDTKVKTLNTSSYAKIMNIADDASIQLY----SSVKIKKLGSNDTLAVNIVTPENITK 118- ++ T V N + + +A I SS+ I K GS +N+ T NI+ Sbjct: 55 DNATT-VTVTNKEEHEYLGKYISNAQIGSRAISSSSITIAKKGSG----LNVET-HNISG 108- Query: 119 VTEDMYRNAAVTLGIEHATISVAAPIKVTGESALAGIYYSLE-KNGASVSSENKQLAQEE 17- 7 +T++MY NA +T G++ A + V AP +V+G +AL G+ + E + ++S + KQ+A +E Sbjct: 109 ITDEMYLNALMTAGVKDAKVYVTAPFEVSGTAALTGLIKAYEVSSDEAISEDVKQVANQE 16- 8 Query: 178 LSTLSGINAENKGKEGYDADKLNVALTDIKSAVAKGGSDLSKDDIRKIVEETLKNYHLDN 23- 7 L T S + + G E A + IK AK G +K DI K V++ + L+ Sbjct: 169 LVTTSEL-GDKIGNENAAA-----LIAKIKEEFAKNGVPDNKADIEKQVDDAASD--LNV 22- 0 Query: 238 AVTENQINLIVNFAVNLSQSNVIKNSDFTNTLNNLKDNIVSKAGSKFKNINVNFNANKAV 29- 7 +T++Q N +V S N +KN+D + D + KA K + + Sbjct: 221 TLTDSQKNQLV------SLFNKMKNADI--DWGQVSDQL-DKAKDKITKFIESDEGKNFI 27- 1 Query: 298 ESGKGFLANIWQQIVNFFQ 316 + F +IW IV+ F+ Sbjct: 272 QKVIDFFVSIWNAIVSIFK 290 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1512 A repeated DNA sequence (GBSx1602) was identified in S. agalactiae <SEQ ID 4647> which encodes the amino acid sequence <SEQ ID 4648>. Analysis of this protein sequence reveals the following: TABLE-US-04505 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0603 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04506 >GP: CAB15719 GB: Z99122 similar to hypothetical proteins [Bacillus subtilis] Identities = 76/138 (55%), Positives = 91/138 (65%), Gaps = 12/138 (8%) Query: 1 MKLKAVHHIAIIVSDYEKSKDFYVNKLGFEIIRENHRPERHDYKLDLRC-GDIELEIFGN 59 M LK++HHIAII SDYEKSK FYV+KLGF++I+E +R ER YKLDL G +E+F Sbjct: 1 MLLKSIHHIAIICSDYEKSKAFYVHKLGFQVIQETYREERGSYKLDLSLNGSYVIELF-- 58 Query: 60 RLDDPEYETPPQRIGRPNWPREACGLRHLAFYVPDVEAYKVELENLGIFVEPIRYDDYTG 119- + PP+R RP EA GLRHLAF V ++ EL GI EPIR D TG Sbjct: 59 -----SFPDPPERQTRP----EAAGLRHLAFTVGSLDKAVQELHEKGIETEPIRTDPLTG 109- Query: 120 KKMTFFFDPDGLPLELHE 137 K+ TFFFDPD LPLEL+E Sbjct: 110 KRFTFFFDPDQLPLELYE 127 A related DNA sequence was identified in S. pyogenes <SEQ ID 4649> which encodes the amino acid sequence <SEQ ID 4650>. Analysis of this protein sequence reveals the following: TABLE-US-04507 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1205 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04508 Identities = 99/137 (72%), Positives = 116/137 (84%) Query: 1 MKLKAVHHIAIIVSDYEKSKDFYVNKLGFEIIRENHRPERHDYKLDLRCGDIELEIFGNR 60 MKL A+HH+AIIVSDY SKDFYVNKLGFEIIREN+RP++HDYKLDL CG IELEIFG Sbjct: 2 MKLNAIHHVAIIVSDYHLSKDFYVNKLGFEIIRENYRPDKHDYKLDLSCGRIELEIFGKV 61 Query: 61 LDDPEYETPPQRIGRPNWPREACGLRHLAFYVPDVEAYKVELENLGIFVEPIRYDDYTGK 120- DP Y+ PP+R+ P + EACGLRHLAF V ++E+Y +L++LGI VEPIR+DDYTG+ Sbjct: 62 TSDPNYQAPPKRVSEPEFKSEACGLRHLAFRVTNIESYVDDLKSLGIPVEPIRHDDYTGE 121- Query: 121 KMTFFFDPDGLPLELHE 137 KMTFFFDPDGLPLELHE Sbjct: 122 KMTFFFDPDGLPLELHE 138 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1513 A DNA sequence (GBSx1603) was identified in S. agalactiae <SEQ ID 4651> which encodes the amino acid sequence <SEQ ID 4652>. This protein is predicted to be alpha-amylase. Analysis of this protein sequence reveals the following: TABLE-US-04509 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.62 Transmembrane 14-30 (7-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.5649 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04510 >GP: AAG41778 GB: AF213261 sortase [Streptococcus gordonii] Identities = 136/247 (55%), Positives = 174/247 (70%), Gaps = 2/247 (0%) Query: 2 RNKKKSHGFFNFVRWLLVVLLIIVGLALVFNKPIRNAFIAHQSNHYQISRVSKKTIEKNK 61 R KK N + +L V+L++V LAL+FN IRN + +N YQ+S+VSKK IEKNK Sbjct: 6 RRAKKKRSRRNIILNILSVILLLVALALIFNSSIRNMIMVWHTNKYQVSKVSKKEIEKNK 65 Query: 62 KSKTSYDFSSVKSISTESILSAQTKSHNLPVIGGIAIPDVEINLPIFKGLGNTELSYGAG 121- SK S++F V+ +STE++L+AQ K+ LPVIGGIAIP++ +NLPIF GL N L YGAG Sbjct: 66 ASKGSFNFEKVEPLSTEAVLNAQWKAQQLPVIGGIAIPELSLNLPIFNGLENAGLYYGAG 125- Query: 122 TMKENQIMGGPNNYALASHHVFGLTGSSKMLFSPLEHAKKGMKVYLTDKSKVYTYTITEI 18- 1 TMKE Q M G NYALASHHVFG+TG+++MLFSPL+ AK GMK+YLTDK KVYTY+IT + Sbjct: 126 TMKETQEM-GKGNYALASHHVFGITGANEMLFSPLDRAKAGMKIYLTDKEKVYTYSITSV 18- 4 Query: 182 SKVTPEHVEVIDD-TPGKSQLTLVTCTDPEATERIIVHAELEKTGEFSTADESILKAFSK 24- 0 V PE V+V+DD G +++TLVTC D AT R IV LE + + IL F+K Sbjct: 185 ENVEPERVDVVDDAADGTAEVTLVTCEDAAATSRTIVKGVLESETPYKETPKKILNYFNK 24- 4 Query: 241 KYNQINL 247 YNQ+ L Sbjct: 245 SYNQMQL 251 A related DNA sequence was identified in S. pyogenes <SEQ ID 4653> which encodes the amino acid sequence <SEQ ID 4654>. Analysis of this protein sequence reveals the following:

TABLE-US-04511 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.12 Transmembrane 18-34 (13-38) INTEGRAL Likelihood = -0.32 Transmembrane 94-110 (94-110) ----- Final Results ----- bacterial membrane --- Certainty = 0.4248 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04512 >GP: AAA73122 GB: M77279 alpha-amylase [unidentified cloning vector] Identities = 60/122 (49%), Positives = 85/122 (69%) Query: 7 RRKIKSMSWARKLLIAVLLILGLALLFNKPIRNTLIARNSNKYQVTKVSKKQIKKNKEAKS 67 - + K + +W L+ +L I+GLAL+FN IR+ ++ +NS Y V+K+ +KKN ++ Sbjct: 4 KEKKRGKNWLINSLLVLLFIIGLALIFNNQIRSWVVQQNSRSYAVSKLKPADVKKNMARET 64 Query: 68 TFDFQAVEPVSTESVLQAQMAAQQLPVIGGIAIPELGINLPIFKGLGNTELIYGAGTMKEE 12- 7 TFDF +VE +STE+V++AQ + LPVIG IAIP + INLPIFKGL N L+ GAGTMKE+ Sbjct: 65 TFDFDSVESLSTEAVMKAQFENKNLPVIGAIAIPSVEINLPIFKGLSNVALLTGAGTMKED 12- 4 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04513 Identities = 147/245 (60%), Positives = 192/245 (78%) Query: 2 RNKKKSHGFFNFVRWLLVVLLIIVGLALVFNKPIRNAFIAHQSNHYQISRVSKKTIEKNK 61 + K++ ++ R LL+ +L+I+GLAL+FNKPIRN IA SN YQ+++VSKK I+KNK Sbjct: 4 KQKRRKIKSMSWARKLLIAVLLILGLALLFNKPIRNTLIARNSNKYQVTKVSKKQIKKNK 63 Query: 62 KSKTSYDFSSVKSISTESILSAQTKSHNLPVIGGIAIPDVEINLPIFKGLGNTELSYGAG 121- ++K+++DF +V+ +STES+L AQ + LPVIGGIAIP++ INLPIFKGLGNTEL YGAG Sbjct: 64 EAKSTFDFQAVEPVSTESVLQAQMAAQQLPVIGGIAIPELGINLPIFKGLGNTELIYGAG 123- Query: 122 TMKENQIMGGPNNYALASHHVFGLTGSSKMLFSPLEHAKKGMKVYLTDKSKVYTYTITEI 18- 1 TMKE Q+MGG NNY+LASHH+FG+TGSS+MLFSPLE A+ GM +YLTDK K+Y Y I ++ Sbjct: 124 TMKEEQVMGGENNYSLASHHIFGITGSSQMLFSPLERAQNGMSIYLTDKEKIYEYIIKDV 18- 3 Query: 182 SKVTPEHVEVIDDTPGKSQLTLVTCTDPEATERIIVHAELEKTGEFSTADESILKAFSKK 24- 1 V PE V+VIDDT G ++TLVTCTD EATERIIV EL+ +F A +LKAF+ Sbjct: 184 FTVAPERVDVIDDTAGLKEVTLVTCTDIEATERIIVKGELKTEYDFDKAPADVLKAFNHS 24- 3 Query: 242 YNQIN 246 YNQ++ Sbjct: 244 YNQVS 248 SEQ ID 4652 (GBS266) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 1; MW 26 kDa). GBS266-His was purified as shown in FIG. 205, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1514 A DNA sequence (GBSx1604) was identified in S. agalactiae <SEQ ID 4655> which encodes the amino acid sequence <SEQ ID 4656>. Analysis of this protein sequence reveals the following: TABLE-US-04514 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1934 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 4657> which encodes the amino acid sequence <SEQ ID 4658>. Analysis of this protein sequence reveals the following: TABLE-US-04515 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1934 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04516 Identities = 711/819 (86%), Positives = 767/819 (92%) Query: 1 MQDKNLVDVNLTSEMKTSFIDYAMSVIVARALPDVRDGLKPVHRRILYGMNELGVTPDKP 60 MQD+NL+DVNLTSEMKTSFIDYAMSVIVARALPDVRDGLKPVHRRILYGMNELGVTPDKP Sbjct: 1 MQDRNLIDVNLTSEMKTSFIDYAMSVIVARALPDVRDGLKPVHRRILYGMNELGVTPDKP 60 Query: 61 HKKSARITGDVMGKYHPHGDSSIYEAMVRMAQWWSYRHMLVDGHGNFGSMDGDGAAAQRY 120- HKKSARITGDVMGKYHPHGDSSIYEAMVRMAQWWSYRHMLVDGHGNFGSMDGDGAAAQRY Sbjct: 61 HKKSARITGDVMGKYHPHGDSSIYEAMVRMAQWWSYRHMLVDGHGNFGSMDGDGAAAQRY 120- Query: 121 TEARMSKIALEMLRDINKNTVDFQDNYDGSEREPLVLPARFPNLLVNGATGIAVGMATNI 18- 0 TEARMSKIALE+LRDINKNTV+FQDNYDGSEREP+VLPARFPNLLVNGATGIAVGMATNI Sbjct: 121 TEARMSKIALELLRDINKNTVNFQDNYDGSEREPVVLPARFPNLLVNGATGIAVGMATNI 18- 0 Query: 181 PPHNLGESIDAVKLVMDNPDVTTRELMEVIPGPDFPTGALVMGRSGIHRAYETGKGSIVL 24- 0 PPHNL ESIDAVK+VM++PD TTRELMEVIPGPDFPTGALVMGRSGIHRAY+TGKGSIVL Sbjct: 181 PPHNLAESIDAVKMVMEHPDCTTRELMEVIPGPDFPTGALVMGRSGIHRAYDTGKGSIVL 24- 0 Query: 241 RSRTEIETTSNGKERIVVTEFPYGVNKTKVHEHIVRLAQEKRIEGITAVRDESSREGVRF 30- 0 RSRTEIETT G+ERIVVTEFPYGVNKTKVHEHIVRLAQEKR+EGITAVRDESSREGVRF Sbjct: 241 RSRTEIETTQTGRERIVVTEFPYGVNKTKVHEHIVRLAQEKRLEGITAVRDESSREGVRF 30- 0 Query: 301 VIEVRRAASANVILNNLFKLTSLQTNFSFNMLAIEKGVPKILSLRQIIDNYIEHQKEVIV 36- 0 VIE+RR ASA VILNNLFKLTSLQTNFSFNMLAIE GVPKILSLRQIIDNYI HQKEVI+ Sbjct: 301 VIEIRREASATVILNNLFKLTSLQTNFSFNMLAIENGVPKILSLRQIIDNYISHQKEVII 36- 0 Query: 361 RRTQFDKAKAGARAHILEGLLVALDHLDEVITIIRNSETDTIAQAELMSRFELSERQSQA 42- 0 RRT+FDK KA ARAHILEGLL+ALDHLDEVI IIRNSETD IAQ ELMSRF+LSERQSQA Sbjct: 361 RRTRFDKDKAEARAHILEGLLIALDHLDEVIAIIRNSETDVIAQTELMSRFDLSERQSQA 42- 0 Query: 421 ILDMRLRRLTGLERDKIQSEYNDLLALIADLADILAKPERVVTIIKEEMDEVKRKYADAR 48- 0 ILDMRLRRLTGLERDKIQSEY+DLLALIADL+DILAKPER++TIIKEEMDE+KRKYA+ R Sbjct: 421 ILDMRLRRLTGLERDKIQSEYDDLLALIADLSDILAKPERIITIIKEEMDEIKRKYANPR 48- 0 Query: 481 RTELMIGEVLSLEDEDLIEEEDVLITLSNKGYIKRLAQDEFRAQKRGGRGIQGTGVNNDD 54- 0 RTELM+GEVLSLEDEDLIEEEDVLITLSNKGYIKRLAQDEFRAQKRGGRG+QGTGVNNDD Sbjct: 481 RTELMVGEVLSLEDEDLIEEEDVLITLSNKGYIKRLAQDEFRAQKRGGRGVQGTGVNNDD 54- 0 Query: 541 FVRELVSTSTHDTVLFFTNLGRVYRLKAYEIPEYGRTAKGLPIVNLLKLDEGETIQTIIN 60- 0 FVREL+STSTHDT+LFFTN GRVYRLKAYEIPEYGRTAKGLPIVNLLKL++GETIQTIIN Sbjct: 541 FVRELISTSTHDTLLFFTNFGRVYRLKAYEIPEYGRTAKGLPIVNLLKLEDGETIQTIIN 60- 0 Query: 601 ARKEDVANKYFFFTTQQGIVKRTSVSEFSNIRQNGLRAINLKENDELINVLLIDENEDVI 66- 0 ARKE+ A K FFFTT+QGIVKRT VSEF+NIRQNGLRA+ LKE D+LINVLL +D+I Sbjct: 601 ARKEETAGKSFFFTTKQGIVKRTEVSEFNNIRQNGLRALKLKEGDQLINVLLTSGQDDII 66- 0 Query: 661 IGTRTGYSVRFKVNAVRNMGRTATGVRGVLNREGDKVVGASRIVNGQEVLIITEKGYGKR 72- 0 IGT +GYSVRF ++RNMGR+ATGVRGV LRE D+VVGASRI + QEVL+ITE G+GKR Sbjct: 661 IGTHSGYSVRFNEASIRNMGRSATGVRGVKLREDDRVVGASRIQDNQEVLVITENGFGKR 72- 0 Query: 721 TEASEYPTKGRGGKGIKTANITAKNGPLARLVTINGNEDIMVITDTGVIIRTNVANISQT 78- 0 T A++YPTKGRGGKGIKTANIT KNG LA LVT++G EDIMVIT+ GVIIRTNVANISQT Sbjct: 721 TSATDYPTKGRGGKGIKTANITPKNGQLAGLVTVDGTEDIMVITNKGVIIRTNVANISQT 78- 0 Query: 781 GRSTMGVKVMRLDQEAKIVTVALVEQEIEDKSNIEDTKE 819 GR+T+GVK+M+LD +AKIVT LV+ E + I +E Sbjct: 781 GRATLGVKIMKLDADAKIVTFTLVQPEDSSIAEINTDRE 819 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1515 A DNA sequence (GBSx1605) was identified in S. agalactiae <SEQ ID 4659> which encodes the amino acid sequence <SEQ ID 4660>. Analysis of this protein sequence reveals the following: TABLE-US-04517 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04518 >GP: CAA04010 GB: AJ000336 L-lactate dehydrogenase [Streptococcus pneumoniae] Identities = 290/329 (88%), Positives = 313/329 (94%), Gaps = 1/329 (0%) Query: 1 MTATKQHKKVILVGDGAVGSSYAFALVNQGIAQELGIIEIPALFDKAVGDAEDLSHALAF 60 MT+TKQHKKVILVGDGAVGSSYAFALVNQGIAQELGIIEIP L +KAVGDA DLSHALAF Sbjct: 1 MTSTKQHKKVILVGDGAVGSSYAFALVNQGIAQELGIIEIPQLHEKAVGDALDLSHALAF 60 Query: 61 TSPKKIYAATYADCADADLVVITAGAPQKPGETRLDLVGKNLAINKSIVTQVVESGFNGI 120- TSPKKIYAA Y+DCADADLVVITAGAPQKPGETRLDLVGKNLAINKSIVTQVVESGF GI Sbjct: 61 TSPKKIYAAQYSDCADADLVVITAGAPQKPGETRLDLVGKNLAINKSIVTQVVESGFKGI 120- Query: 121 FLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSARFRQALADKIGVDARSVHAYIMGE 18- 0 FLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSARFRQALA+K+ VDARSVHAYIMGE Sbjct: 121 FLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSARFRQALAEKLDVDARSVHAYIMGE 18- 0 Query: 181 HGDSEFAVWSHANVAGVQLEQWLQENRDIDEQGLVDLFISVRDAAYSIINKKGATYYGIA 24- 0 HGDSEFAVWSHAN+AGV LE++L++ +++ E L++LF VRDAAY+IINKKGATYYGIA Sbjct: 181 HGDSEFAVWSHANIAGVNLEEFLKDTQNVQEAELIELFEGVRDAAYTIINKKGATYYGIA 24- 0 Query: 241 VALARITKAILDDENAVLPLSVYQEGQYGDVKDVFIGQPAIVGAHGIVRPVNIPLNDAEL 30- 0 VALARITKAILDDENAVLPLSV+QEGQYG V++VFIGQPA+VGAHGIVRPVNIPLNDAE Sbjct: 241 VALARITKAILDDENAVLPLSVFQEGQYG-VENVFIGQPAVVGAHGIVRPVNIPLNDAET 29- 9 Query: 301 QKMQASAEQLKDIIDEAWKNPEFQEASKN 329 QKMQASA++L+ IIDEAWKNPEFQEASKN Sbjct: 300 QKMQASAKELQAIIDEAWKNPEFQEASKN 328 A related DNA sequence was identified in S. pyogenes <SEQ ID 4661> which encodes the amino acid sequence <SEQ ID 4662>. Analysis of this protein sequence reveals the following: TABLE-US-04519 Possible site: 25 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.17 Transmembrane 106-122 (106-122) ----- Final Results ----- bacterial membrane --- Certainty = 0.1468(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04520 >GP: AAB81558 GB: U60997 L(+)-lactate dehydrogenase [Streptococcus bovis] Identities = 278/329 (84%), Positives = 297/329 (89%), Gaps = 2/329 (0%) Query: 1 MTATKQHKKVILVGDGAVGSSYAFALVTQNIAQELGIIDIFK--EKTQGDAEDLSHALAF 58 MTATKQHKKVILVGDGAVGSSYAFALV Q IAQELGII+I + K GDAEDLSHALAF Sbjct: 1 MTATKQHKKVILVGDGAVGSSYAFALVNQGIAQELGIIEIPQLFNKAVGDAEDLSHALAF 60 Query: 59 TSPKKIYAADYSDCHDADLVVLTAGAPQKPGETRLDLVEKNLRINKEVVTQIVASGFKGI 118- TSPKKIYAA Y DC DADLVV+TAGAPQKPGETRLDLV KNL INK +VT++V SGFKGI Sbjct: 61 TSPKKIYAAKYEDCADADLVVITAGAPQKPGETRLDLVGKNLAINKSIVTEVVKSGFKGI 120- Query: 119 FLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSARFRQALAAKIGVDARSVHAYIMGE 17- 8 FLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSARFRQALA K+ VDARSVHAYIMGE Sbjct: 121 FLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSARFRQALAEKLDVDARSVHAYIMGE 18- 0 Query: 179 HGDSEFAVWSHANVAGVGLYDWLQANRDIDEQGLVDLFISVRDAAYSIINKKGATFYGIA 23- 8 HGDSEFAVWSHANVAGV L +L+ ++++E LV+LF VRDAAYSIINKKGATFYGIA Sbjct: 181 HGDSEFAVWSHANVAGVNLESYLKDVQNVEEAELVELFEGVRDAAYSIINKKGATFYGIA 24- 0 Query: 239 VALARITKAILDDENAVLPLSVFQEGQYEGVEDCYIGQPAIVGAYGIVRPVNIPLNDAEL 29- 8 VALARITKAIL+DENAVLPLSVFQEGQY V DCYIGQPAIVGA+GIVRPVNIPLNDAE Sbjct: 241 VALARITKAILNDENAVLPLSVFQEGQYANVTDCYIGQPAIVGAHGIVRPVNIPLNDAEQ 30- 0 Query: 299 QKMQASANQLKAIIDEAFAKEEFASAAKN 327 QKM+ASA +LKAIIDEAF+KEEFASA KN Sbjct: 301 QKMEASAKELKAIIDEAFSKEEFASACKN 329 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04521 Identities = 286/329 (86%), Positives = 299/329 (89%), Gaps = 2/329 (0%) Query: 1 MTATKQHKKVILVGDGAVGSSYAFALVNQGIAQELGIIEIPALFDKAVGDAEDLSHALAF 60 MTATKQHKKVILVGDGAVGSSYAFALV Q IAQELGII+I +K GDAEDLSHALAF Sbjct: 1 MTATKQHKKVILVGDGAVGSSYAFALVTQNIAQELGIIDI--FKEKTQGDAEDLSHALAF 58 Query: 61 TSPKKIYAATYADCADADLVVITAGAPQKPGETRLDLVGKNLAINKSIVTQVVESGFNGI 120- TSPKKIYAA Y+DC DADLVV+TAGAPQKPGETRLDLV KNL INK +VTQ+V SGF GI Sbjct: 59 TSPKKIYAADYSDCHDADLVVLTAGAPQKPGETRLDLVEKNLRINKEVVTQIVASGFKGI 118- Query: 121 FLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSARFRQALADKIGVDARSVHAYIMGE 18- 0 FLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSARFRQALA KIGVDARSVHAYIMGE Sbjct: 119 FLVAANPVDVLTYSTWKFSGFPKERVIGSGTSLDSARFRQALAAKIGVDARSVHAYIMGE 17- 8 Query: 181 HGDSEFAVWSHANVAGVQLEQWLQENRDIDEQGLVDLFISVRDAAYSIINKKGATYYGIA 24- 0 HGDSEFAVWSHANVAGV L WLQ NRDIDEQGLVDLFISVRDAAYSIINKKGAT+YGIA Sbjct: 179 HGDSEFAVWSHANVAGVGLYDWLQANRDIDEQGLVDLFISVRDAAYSIINKKGATFYGIA 23- 8 Query: 241 VALARITKAILDDENAVLPLSVYQEGQYGDVKDVFIGQPAIVGAHGIVRPVNIPLNDAEL 30- 0 VALARITKAILDDENAVLPLSV+QEGQY V+D +IGQPAIVGA+GIVRPVNIPLNDAEL Sbjct: 239 VALARITKAILDDENAVLPLSVFQEGQYEGVEDCYIGQPAIVGAYGIVRPVNIPLNDAEL 29- 8 Query: 301 QKMQASAEQLKDIIDEAWKNPEFQEASKN 329 QKMQASA QLK IIDEA+ EF A+KN Sbjct: 299 QKMQASANQLKAIIDEAFAKEEFASAAKN 327 SEQ ID 4660 (GBS312) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 7; MW 40 kDa). GBS312-His was purified as shown in FIG. 205, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1516 A DNA sequence (GBSx1606) was identified in S. agalactiae <SEQ ID 4663> which encodes the amino acid sequence <SEQ ID 4664>. This protein is predicted to be NADH oxidase (nox). Analysis of this protein sequence reveals the following: TABLE-US-04522 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1888(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04523 >GP: AAC26485 GB: AF014458 NADH oxidase [Streptococcus pneumoniae] (ver 2) Identities = 363/458 (79%), Positives = 408/458 (88%), Gaps = 3/458 (0%) Query: 1 MSKIVVVGTNHAGTAAIKTMLSNYGEANEIVTFDQNSNISFLGCGMALWIGEQIDGPEGL 60 MSKIVVVG NHAGTA I TML N+G NEIV FDQNSNISFLGCGMALWIGEQIDG EGL Sbjct: 1 MSKIVVVGANHAGTACINTMLDNFGNENEIVVFDQNSNISFLGCGMALWIGEQIDGAEGL 60 Query: 61 FYSDKEQLESMGAKVYMNSPVLNIDYDKKEVTALVDGKEHVESYEKLILATGSQPIIPPI 120- FYSDKE+LE+ GAKVYMNSPVL+IDYD K VTA V+GKEH ESYEKLI ATGS PI+PPI Sbjct: 61 FYSDKEKLEAKGAKVYMNSPVLSIDYDNKVVTAEVEGKEHKESYEKLIFATGSTPILPPI 120- Query: 121 KGVEIQEGSREFKATLENLQFVKLYQNSEEVIEKLAKPG--INRVAVVGAGYIGVELAEA 17- 8 +GVEI +G+REFKATLEN+QFVKLYQN+EEVI KL+ ++R+AVVG GYIGVELAEA Sbjct: 121 EGVEIVKGNREFKATLENVQFVKLYQNAEEVINKLSDKSQHLDRIAVVGGGYIGVELAEA 18- 0 Query: 179 FQRIGKEVTLVDVADTCMGGYYDRDFTDMMSKNLEDHGIRLAFGQAVQAVEGDGKVERLV 23- 8 F+R+GKEV LVD+ DT + GYYD+DFT MM+KNLEDH IRLA GQ V+A+EGDGKVERL+ Sbjct: 181 FERLGKEVVLVDIVDTVLNGYYDKDFTQMMAKNLEDHNIRLALGQTVKAIEGDGKVERLI 24- 0 Query: 239 TDKETFDVDMVILAVGFRPNTELGAGKLDTFRNGAWVVDKKQETSVKDVYAIGDCATIWD 29- 8 TDKE+FDVDMVILAVGFRPNT L GK++ FRNGA++VDKKQETS+ VYA+GDCAT++D Sbjct: 241 TDKESFDVDMVILAVGFRPNTALADGKIELFRNGAFLVDKKQETSIPGVYAVGDCATVYD 30- 0 Query: 299 NSRDDINYIALASNAVRTGIVAAHNACGTELEGAGVQGSNGISIYGLNMVSTGLTLEKAK 35- 8 N+R D +YIALASNAVRTGIV A+NACG ELEG GVQGSNGISIYGL+MVSTGLTLEKAK Sbjct: 301 NARKDTSYIALASNAVRTGIVGAYNACGHELEGIGVQGSNGISIYGLHMVSTGLTLEKAK 36- 0 Query: 359 QAGYNAVETGFNDLQKPEFIKHNNHEVAIKIVYDKDSRVILGCQMVSHE-DVSMGIHMFS 41- 7 AGYNA ETGFNDLQKPEF+KH+NHEVAIKIV+DKDSR ILG QMVSH+ +SMGIHMFS Sbjct: 361 AAGYNATETGFNDLQKPEFMKHDNHEVAIKIVFDKDSREILGAQMVSHDIAISMGIHMFS 42- 0 Query: 418 LAIQEKVTIEKLALTDIFFLPHFNKPYNYITMAALGAK 455 LAIQE VTI+KLALTD+FFLPHFNKPYNYITMAAL A+ Sbjct: 421 LAIQEHVTIDKLALTDLFFLPHFNKPYNYITMAALTAE 458 A related DNA sequence was identified in S. pyogenes <SEQ ID 4665> which encodes the amino acid sequence <SEQ ID 4666>. Analysis of this protein sequence reveals the following: TABLE-US-04524 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2068(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04525 Identities = 362/456 (79%), Positives = 403/456 (87%) Query: 1 MSKIVVVGTNHAGTAAIKTMLSNYGEANEIVTFDQNSNISFLGCGMALWIGEQIDGPEGL 60 MSKIVVVG NHAGTA IKTML+NYG+ANEIV FDQNSNISFLGCGMALWIGEQI GPEGL Sbjct: 1 MSKIVVVGANHAGTACIKTMLTNYGDANEIVVFDQNSNISFLGCGMALWIGEQIAGPEGL 60 Query: 61 FYSDKEQLESMGAKVYMNSPVLNIDYDKKEVTALVDGKEHVESYEKLILATGSQPIIPPI 120- FYSDKE+LES+GAKVYM SPV +IDYD K VTALVDGK HVE+Y+KLI ATGSQPI+PPI Sbjct: 61 FYSDKEELESLGAKVYMESPVQSIDYDAKTVTALVDGKNHVETYDKLIFATGSQPILPPI 120- Query: 121 KGVEIQEGSREFKATLENLQFVKLYQNSEEVIEKLAKPGINRVAVVGAGYIGVELAEAFQ 18- 0 KG EI+EGS EF+ATLENLQFVKLYQNS +VI KL I RVAVVGAGYIGVELAEAFQ Sbjct: 121 KGAEIKEGSLEFEATLENLQFVKLYQNSADVIAKLENKDIKRVAVVGAGYIGVELAEAFQ 18- 0 Query: 181 RIGKEVTLVDVADTCMGGYYDRDFTDMMSKNLEDHGIRLAFGQAVQAVEGDGKVERLVTD 24- 0 R GKEV L+DV DTC+ GYYDRD TD+M+KN+E+HGI+LAFG+ V+ V G+GKVE+++TD Sbjct: 181 RKGKEVVLIDVVDTCLAGYYDRDLTDLMAKNMEEHGIQLAFGETVKEVAGNGKVEKIITD 24- 0 Query: 241 KETFDVDMVILAVGFRPNTELGAGKLDTFRNGAWVVDKKQETSVKDVYAIGDCATIWDNS 30- 0 K +DVDMVILAVGFRPNT LG GK+D FRNGA++V+K+QETS+ VYAIGDCATI+DN+ Sbjct: 241 KNEYDVDMVILAVGFRPNTTLGNGKIDLFRNGAFLVNKRQETSIPGVYAIGDCATIYDNA 30- 0 Query: 301 RDDINYIALASNAVRTGIVAAHNACGTELEGAGVQGSNGISIYGLNMVSTGLTLEKAKQA 36- 0 D NYIALASNAVRTGIVAAHNACGT+LEG GVQGSNGISIYGL+MVSTGLTLEKAK+ Sbjct: 301 TRDTNYIALASNAVRTGIVAAHNACGTDLEGIGVQGSNGISIYGLHMVSTGLTLEKAKRL 36- 0 Query: 361 GYNAVETGFNDLQKPEFIKHNNHEVAIKIVYDKDSRVILGCQMVSHEDVSMGIHMFSLAI 42- 0 G++A T + D QKPEFI+H N V IKIVYDKDSR ILG QM + EDVSMGIHMFSLAI Sbjct: 361 GFDAAVTEYTDNQKPEFIEHGNFPVTIKIVYDKDSRRILGAQMAAREDVSMGIHMFSLAI 42- 0 Query: 421 QEKVTIEKLALTDIFFLPHFNKPYNYITMAALGAKD 456 QE VTIEKLALTDIFFLPHFNKPYNYITMAALGAKD Sbjct: 421 QEGVTIEKLALTDIFFLPHFNKPYNYITMAALGAKD 456 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1517 A DNA sequence (GBSx1607) was identified in S. agalactiae <SEQ ID 4667> which encodes the amino acid sequence <SEQ ID 4668>. Analysis of this protein sequence reveals the following:

TABLE-US-04526 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2319(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1518 A DNA sequence (GBSx1608) was identified in S. agalactiae <SEQ ID 4669> which encodes the amino acid sequence <SEQ ID 4670>. Analysis of this protein sequence reveals the following: TABLE-US-04527 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.75 Transmembrane 160-176 (157-179) INTEGRAL Likelihood = -7.38 Transmembrane 73-89 (70-97) INTEGRAL Likelihood = -5.47 Transmembrane 289-305 (284-312) INTEGRAL Likelihood = -4.09 Transmembrane 107-123 (106-124) INTEGRAL Likelihood = -3.24 Transmembrane 43-59 (43-59) INTEGRAL Likelihood = -1.91 Transmembrane 258-274 (258-275) INTEGRAL Likelihood = -1.33 Transmembrane 234-250 (233-251) INTEGRAL Likelihood = -0.00 Transmembrane 209-225 (209-225) ----- Final Results ----- bacterial membrane --- Certainty = 0.4100(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9805> which encodes amino acid sequence <SEQ ID 9806> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04528 >GP: CAB15146 GB: Z99120 similar to hypothetical proteins [Bacillus subtilis] Identities = 172/318 (54%), Positives = 234/318 (73%) Query: 5 LSLTTIFALLFSSMLIYATPLIFTSIGGTFSERGGIVNVGLEGIMVIGAFSGVVFNLEFA 64 + + I +++ + L+YA PLI T++GG FSER G+VN+GLEG+M+IGAF+ V+FNL F Sbjct: 1 MDIVQILSIIVPATLVYAAPLILTALGGVFSERSGVVNIGLEGLMIIGAFTSVLFNLFFG 60 Query: 65 SVFGDATPWISVLVGGLVGLIFSVIHAVATVNFRADHIISGTVLNLMAPSLAVFLIKVLY 124- G A PW+S+L G +FS+IHA A ++FRAD +SG +N++A +F++K++Y Sbjct: 61 QELGAAAPWLSLLAAMAAGALFSLIHAAAAISFRADQTVSGVAINMLALGATLFIVKLIY 120- Query: 125 NKGQTDNIQESFGKFNFPILSDIPFVGDIFFKGTSLVGYIAILFSFLAWFILYKTRFGLR 18- 4 K QTD I E F K P L DIP +G IFF +AI +F++WFIL+KT FGLR Sbjct: 121 GKAQTDKIPEPFYKTKIPGLGDIPVLGKIFFSDVYYTSILAIALAFISWFILFKTPFGLR 18- 0 Query: 185 LRSVGEHPQAADTLGINVYLMRYSGVLISGFLGGIGGAVYAQSISVNFAATTILGPGFIS 24- 4 +RSVGEHP AADT+GINVY MRY GV+ISG GG+GG VYA +I+++F +TI G GFI+ Sbjct: 181 IRSVGEHPMAADTMGINVYKMRYIGVMISGLFGGLGGGVYASTIALDFTHSTISGQGFIA 24- 0 Query: 245 LAAMIFGKWNPIGAMLASLFFGLSQSLAVIGSHLPLLSNIPTVYLQIAPYVLTIIVLAAF 30- 4 LAA++FGKW+PIGA+ A+LFFG +QSL++IGS LPL +IP VY+ +APY+LTI+ L F Sbjct: 241 LAALVFGKWHPIGALGAALFFGFAQSLSIIGSLLPLFKDIPNVYMLMAPYILTILALTGF 30- 0 Query: 305 FGQAVAPKADGINYIKTK 322 G+A APKA+G+ YIK K Sbjct: 301 IGRADAPKANGVPYIKGK 318 A related DNA sequence was identified in S. pyogenes <SEQ ID 4671> which encodes the amino acid sequence <SEQ ID 4672>. Analysis of this protein sequence reveals the following: TABLE-US-04529 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.92 Transmembrane 73-89 (69-97) INTEGRAL Likelihood = -5.04 Transmembrane 160-176 (158-177) INTEGRAL Likelihood = -4.62 Transmembrane 289-305 (284-312) INTEGRAL Likelihood = -3.98 Transmembrane 234-250 (232-251) INTEGRAL Likelihood = -2.13 Transmembrane 107-123 (106-123) INTEGRAL Likelihood = -2.02 Transmembrane 43-59 (43-59) INTEGRAL Likelihood = -0.53 Transmembrane 258-274 (258-274) ----- Final Results ----- bacterial membrane --- Certainty = 0.4567(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04530 >GP: CAB15146 GB: Z99120 similar to hypothetical proteins [Bacillus subtilis] Identities = 176/318 (55%), Positives = 239/318 (74%) Query: 5 MSLVTIFALLMSSMLIYATPLIFTSIGGTFSERSGVVNVGLEGIMVMGAFSGIVFNLEFA 64 M +V I ++++ + L+YA PLI T++GG FSERSGVVN+GLEG+M++GAF+ ++FNL F Sbjct: 1 MDIVQILSIIVPATLVYAAPLILTALGGVFSERSGVVNIGLEGLMIIGAFTSVLFNLFFG 60 Query: 65 ETFGKATPWIAVLVGGIVGLIFSLIHAVATINFRADHIVSGTVLNLLAPSFAVFLVKAMY 124- + G A PW+++L G +FSLIHA A I+FRAD VSG +N+LA +F+VK +Y Sbjct: 61 QELGAAAPWLSLLAAMAAGALFSLIHAAAAISFRADQTVSGVAINMLALGATLFIVKLIY 120- Query: 125 GKGQTDNIQQSFGKFDFPGLSQIPVIGDIFFKNTSLIGYFAIAFSFFAWFLLYKTRFGLR 18- 4 GK QTD I + F K PGL IPV+G IFF + AIA +F +WF+L+KT FGLR Sbjct: 121 GKAQTDKIPEPFYKTKIPGLGDIPVLGKIFFSDVYYTSILAIALAFISWFILFKTPFGLR 18- 0 Query: 185 LRSVGEHPQAADTLGINVYLMKYYGVMISGFLGGIGGAVYAQSISVNFAVTTILGPGFIA 24- 4 +RSVGEHP AADT+GINVY M+Y GVMISG GG+GG VYA +I+++F +TI G GFIA Sbjct: 181 IRSVGEHPMAADTMGINVYKMRYIGVMISGLFGGLGGGVYASTIALDFTHSTISGQGFIA 24- 0 Query: 245 LAAMIFGKWNPVGAMLSSLFFGLSQSLAVIGAQLPLLEKIPTVYLQIAPYMVTIIILAAF 30- 4 LAA++FGKW+P+GA+ ++LFFG +QSL++IG+ LPL + IP VY+ +APY++TI+ L F Sbjct: 241 LAALVFGKWHPIGALGAALFFGFAQSLSIIGSLLPLFKDIPNVYMLMAPYILTILALTGF 30- 0 Query: 305 FGQAVAPKADGINYIKSK 322 G+A APKA+G+ YIK K Sbjct: 301 IGRADAPKANGVPYIKGK 318 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04531 Identities = 272/322 (84%), Positives = 301/322 (93%) Query: 1 MVSKLSLTTIFALLFSSMLIYATPLIFTSIGGTFSERGGIVNVGLEGIMVIGAFSGVVFN 60 +V+K+SL TIFALL SSMLIYATPLIFTSIGGTFSER G+VNVGLEGIMV+GAFSG+VFN Sbjct: 1 VVNKMSLVTIFALLMSSMLIYATPLIFTSIGGTFSERSGVVNVGLEGIMVMGAFSGIVFN 60 Query: 61 LEFASVFGDATPWISVLVGGLVGLIFSVIHAVATVNFRADHIISGTVLNLMAPSLAVFLI 120- LEFA FG ATPWI+VLVGG+VGLIFS+IHAVAT+NFRADHI+SGTVLNL+APS AVFL+ Sbjct: 61 LEFAETFGKATPWIAVLVGGIVGLIFSLIHAVATINFRADHIVSGTVLNLLAPSFAVFLV 120- Query: 121 KVLYNKGQTDNIQESFGKFNFPILSDIPFVGDIFFKGTSLVGYIAILFSFLAWFILYKTR 18- 0 K +Y KGQTDNIQ+SFGKF+FP LS IP +GDIFFK TSL+GY AI FSF AWF+LYKTR Sbjct: 121 KAMYGKGQTDNIQQSFGKFDFPGLSQIPVIGDIFFKNTSLIGYFAIAFSFFAWFLLYKTR 18- 0 Query: 181 FGLRLRSVGEHPQAADTLGINVYLMRYSGVLISGFLGGIGGAVYAQSISVNFAATTILGP 24- 0 FGLRLRSVGEHPQAADTLGINVYLM+Y GV+ISGFLGGIGGAVYAQSISVNFA TTILGP Sbjct: 181 FGLRLRSVGEHPQAADTLGINVYLMKYYGVMISGFLGGIGGAVYAQSISVNFAVTTILGP 24- 0 Query: 241 GFISLAAMIFGKWNPIGAMLASLFFGLSQSLAVIGSHLPLLSNIPTVYLQIAPYVLTIIV 30- 0 GFI+LAAMIFGKWNP+GAML+SLFFGLSQSLAVIG+ LPLL IPTVYLQIAPY++TII+ Sbjct: 241 GFIALAAMIFGKWNPVGAMLSSLFFGLSQSLAVIGAQLPLLEKIPTVYLQIAPYMVTIII 30- 0 Query: 301 LAAFFGQAVAPKADGINYIKTK 322 LAAFFGQAVAPKADGINYIK+K Sbjct: 301 LAAFFGQAVAPKADGINYIKSK 322 A related GBS gene <SEQ ID 8829> and protein <SEQ ID 8830> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04532 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 8.61 GvH: Signal Score (-7.5): -1.53 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 8 value: -7.75 threshold: 0.0 INTEGRAL Likelihood = -7.75 Transmembrane 160-176 (157-179) INTEGRAL Likelihood = -7.38 Transmembrane 73-89 (70-97) INTEGRAL Likelihood = -5.47 Transmembrane 289-305 (284-312) INTEGRAL Likelihood = -4.09 Transmembrane 107-123 (106-124) INTEGRAL Likelihood = -3.24 Transmembrane 43-59 (43-59) INTEGRAL Likelihood = -1.91 Transmembrane 258-274 (258-275) INTEGRAL Likelihood = -1.33 Transmembrane 234-250 (233-251) INTEGRAL Likelihood = -0.00 Transmembrane 209-225 (209-225) PERIPHERAL Likelihood = 3.34 139 modified ALOM score: 2.05 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4100(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00098## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1519 A DNA sequence (GBSx1609) was identified in S. agalactiae <SEQ ID 4673> which encodes the amino acid sequence <SEQ ID 4674>. This protein is predicted to be ribose/galactose ABC transporter, permease protein (rbsC-1). Analysis of this protein sequence reveals the following: TABLE-US-04533 Possible site: 55 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.59 Transmembrane 205-221 (200-228) INTEGRAL Likelihood = -13.69 Transmembrane 21-37 (13-45) INTEGRAL Likelihood = -7.27 Transmembrane 302-318 (290-321) INTEGRAL Likelihood = -7.17 Transmembrane 115-131 (111-138) INTEGRAL Likelihood = -4.25 Transmembrane 251-267 (250-268) INTEGRAL Likelihood = -2.97 Transmembrane 63-79 (63-80) INTEGRAL Likelihood = -2.87 Transmembrane 333-349 (328-349) ----- Final Results ----- bacterial membrane --- Certainty = 0.6838(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8831> which encodes amino acid sequence <SEQ ID 8832> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-04534 Lipop: Possible Site: -1 Crend: 6 SRCFLG: 0 McG: Length of UR: 24 Peak Value of UR: 3.06 Net Charge of CR: 3 McG: Discrim Score: 12.53 GvH: Signal Score (-7.5): -5.31 Possible site: 46 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 7 value: -14.59 threshold: 0.0 INTEGRAL Likelihood = -14.59 Transmembrane 196-212 (191-219) INTEGRAL Likelihood = -13.69 Transmembrane 12-28 (4-36) INTEGRAL Likelihood = -7.27 Transmembrane 293-309 (281-312) INTEGRAL Likelihood = -7.17 Transmembrane 106-122 (102-129) INTEGRAL Likelihood = -4.25 Transmembrane 242-258 (241-259) INTEGRAL Likelihood = -2.97 Transmembrane 54-70 (54-71) INTEGRAL Likelihood = -2.87 Transmembrane 324-340 (319-340) PERIPHERAL Likelihood = 0.16 133 modified ALOM score: 3.42 icm1 HYPID: 7 CFP: 0.684 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6838(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04535 >GP: CAB15145 GB: Z99120 similar to hypothetical proteins [Bacillus subtilis] Identities = 154/349 (44%), Positives = 220/349 (62%), Gaps = 6/349 (1%) Query: 10 MSKKAQKIAVPLISVVLGIILGAIIMLIFGYDPLWGYEGLFQTAFGSIKNIGEIFRAMGP 69 - M K+ + VPLI+++LG+ GA+IML+ GY GY L+ FG I +GE R + P Sbjct: 1 MVKRLSHLLVPLIAIILGLAAGALIMLVSGYSVASGYSALWNGIFGEIYYVGETIRQITP 60 Query: 70 LILIALGFSVASRAGFFNIGLPGQALSGWIAAGWFALSHPDMPRPAMILCTIIIGIVAGG 129- IL L + A R G FNIG+ GQ L GW AA W + D P + +I AGG Sbjct: 61 YILSGLAVAFAFRTGLFNIGVEGQLLVGWTAAVWVGTAF-DGPAYIHLPLALITAAAAGG 119- Query: 130 ITGAIPGILRAYLGTSEVIVTIMMNYIVLYSGNAIVQRVFPKSIMRTSDSSVYVSANASY 18- 9 + G IPGIL+A EVIVTIMMNYI L+ N I+ V D + + +AS Sbjct: 120 LWGFIPGILKARFYVHEVIVTIMMNYIALHMTNYIISNVLTDH----QDKTGKIHESASL 17- 5 Query: 190 QTDWLSSLTNNSRINIGIFIAIIAVVLVWFLLNKTTLGFEIRSVGLNPNASEYAGMSAKR 24- 9 ++ +L +T+ SR+++GI +A++A V++WF++NK+T GFE+R+VG N +AS+YAGMS ++ Sbjct: 176 RSPFLEQITDYSRLHLGIIVALLAAVIMWFIINKSTKGFELRAVGFNQHASQYAGMSVRK 23- 5 Query: 250 TIILSMIISGAFAGLGGVVEGLGTFENVFVQPSSLAIGFDGMAVSLLAANSPIGILFAAF 30- 9 I+ SM+ISGAFAGL G +EGLGTFE V+ + +GFDG+AV+LL N+ +G++ AA Sbjct: 236 NIMTSMLISGAFAGLAGAMEGLGTFEYAAVKGAFTGVGFDGIAVALLGGNTAVGVVLAAC 29- 5 Query: 310 LFGVLSVGAPGMNI-AGIPPELIKVVTASIIFFVGVHYIIEYVIKPKKQ 357 L G L +GA M I +G+P E++ +V A II FV Y I +V+ K+ Sbjct: 296 LLGGLKIGALNMPIESGVPSEVVDIVIAIIILFVASSYAIRFVMGKLKK 344 A related DNA sequence was identified in S. pyogenes <SEQ ID 2149> which encodes the amino acid sequence <SEQ ID 2150>. Analysis of this protein sequence reveals the following: TABLE-US-04536 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.74 Transmembrane 205-221 (200-228) INTEGRAL Likelihood = -12.42 Transmembrane 21-37 (14-45) INTEGRAL Likelihood = -7.22 Transmembrane 115-131 (111-135) INTEGRAL Likelihood = -4.78 Transmembrane 251-267 (249-269) INTEGRAL Likelihood = -2.50 Transmembrane 70-86 (69-86) INTEGRAL Likelihood = -2.34 Transmembrane 302-318 (300-318) INTEGRAL Likelihood = -1.44 Transmembrane 148-164 (147-165) INTEGRAL Likelihood = -1.33 Transmembrane 326-342 (326-342) ----- Final Results ----- bacterial membrane --- Certainty = 0.6095(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04537 identities = 293/358 (81%), Positives = 333/358 (92%), Gaps = 1/358 (0%) Query: 6 RRREMSKKAQKIAVPLISVVLGIILGAIIMLIFGYDPLWGYEGLFQTAFGSIKNIGEIFR 65 RR+ MSK AQKIAVPLISV+LG +LGAIIM+IFGYDP+WGYEGLFQ AFGS+KNIGEIFR Sbjct: 6 RRKVMSKNAQKIAVPLISVLLGFLLGAIIMVIFGYDPIWGYEGLFQIAFGSVKNIGEIFR 65 Query: 66 AMGPLILIALGFSVASRAGFFNIGLPGQALSGWIAAGWFALSHPDMPRPAMILCTIIIGI 125- +MGPLILIALGF+VASRAGFFN+GL GQAL+GWI+AGWFAL +PDMPRP +IL T +IG+ Sbjct: 66 SMGPLILIALGFTVASRAGFFNVGLSGQALAGWISAGWFALLNPDMPRPLLILMTALIGM 125- Query: 126 VAGGITGAIPGILRAYLGTSEVIVTIMMNYIVLYSGNAIVQRVFPKSIMRTSDSSVYVSA 18- 5 +AGGI GAIPGILRAYLGTSEVIVTIMMNYI+LY GNAIVQR +P+S+ ++ DS++ VS Sbjct: 126 IAGGIAGAIPGILRAYLGTSEVIVTIMMNYIILYVGNAIVQRGYPESVKQSIDSTIQVSD 18- 5 Query: 186 NASYQTDWLSSLTNNSRINIGIFIAIIAVVLVWFLLNKTTLGFEIRSVGLNPNASEYAGM 24- 5 NASYQT WLS+LTNNSRINIGIF AIIA+ L+WFLLNKTTLGFEIRSVGLNP+ASEYAGM Sbjct: 186 NASYQTHWLSALTNNSRINIGIFFAIIAIALIWFLLNKTTLGFEIRSVGLNPHASEYAGM 24- 5 Query: 246 SAKRTIILSMIISGAFAGLGGVVEGLGTFENVFVQPSSLAIGFDGMAVSLLAANSPIGIL 30- 5 S+KRTIILSMIISGA AGLGGVVEGLGTFENVFVQ SSLA+GFDGMAVSLLAANSP+GI Sbjct: 246 SSKRTIILSMIISGALAGLGGVVEGLGTFENVFVQGSSLAVGFDGMAVSLLAANSPLGIF 30- 5 Query: 306 FAAFLFGVLSVGAPGMNIAGIPPELIKVVTASIIFFVGVHYIIE-YVIKPKKQMKGGK 362 F++FLFGVL++GAPGMNIAGIPPEL+KVVTASIIFFVG HY+IE Y+I+PKK +KGGK Sbjct: 306 FSSFLFGVLNIGAPGMNIAGIPPELVKVVTASIIFFVGSHYLIERYIIRPKKLVKGGK 363 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1520 A DNA sequence (GBSx1610) was identified in S. agalactiae <SEQ ID 4675> which encodes the amino acid sequence <SEQ ID 4676>. This protein is predicted to be sugar ABC transporter, ATP-binding protein (mglA). Analysis of this protein sequence reveals the following: TABLE-US-04538 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3851(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9803> which encodes amino acid sequence <SEQ ID 9804> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04539 >GP: CAB15144 GB: Z99120 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 311/497 (62%), Positives = 396/497 (79%), Gaps = 1/497 (0%) Query: 14 VIEMKEITKKFGDFVANDHINLTVEKGEIHALLGENGAGKSTLMNMLAGLLEPTDGQIFI 73 - VIEM I K F VAND+INL V+KGEIHALLGENGAGKSTLMN+L GL +P G+I + Sbjct: 4 VIEMLNIRKAFPGIVANDNINLQVKKGEIHALLGENGAGKSTLMNVLFGLYQPERGEIRV 63 Query: 74 NGQPVTIDSPSKSSQLGIGMVHQHFMLVEAFTVAENIVLGNETTQNGVLDIKTAAKEIKE 133- G+ V I+SP+K++ LGIGMVHQHFMLV+ FTVAENI+LG E + G +D K A +E+++ Sbjct: 64 RGEKVHINSPNKANDLGIGMVHQHFMLVDTFTVAENIILGKEPKKFGRIDRKRAGQEVQD 123- Query: 134 LSEKYGLSVNPNAKISDISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIKELMTIM 19- 3 +S++YGL ++P AK +DISVG QQR EILKTLYRGADILIFDEPTAVLTP EIKELM IM Sbjct: 124 ISDRYGLQIHPEAKAADISVGMQQRAEILKTLYRGADILIFDEPTAVLTPHEIKELMQIM 18- 3 Query: 194 KSLVKEGKSIILITHKLDEIRAVADKVTVIRRGKSIETVPVAGASSQQLAEMMVGRSVSF 25- 3 K+LVKEGKSIILITHKL EI + D+VTVIR+GK I+T+ V + +LA +MVGR VSF Sbjct: 184 KNLVKEGKSIILITHKLKEIMEICDRVTVIRKGKGIKTLDVRDTNQDELASLMVGREVSF 24- 3 Query: 254 RTEKKEANPTDIILSVKDLVVEENRGGVLAVKNLSLDVRAGEIVGIAGIDGNGQSELIQA 31- 3 +TEK+ A P +L++ + V++ R G+ V++LSL V+AGEIVGIAG+DGNGQSELI+A Sbjct: 244 KTEKRAAQPGAEVLAIDGITVKDTR-GIETVRDLSLSVKAGEIVGIAGVDGNGQSELIEA 30- 2 Query: 314 ITGLRKVTSGQIVIKGKDVTKFSSRQITELSVGHVPEDRHRDGLVLDMTMAENLALQTYY 37- 3 +TGLRK SG I + GK + + R+ITE +GH+P+DRH+ GLVLD + EN+ LQ+YY Sbjct: 303 VTGLRKTDSGTITLNGKQIQNLTPRKITESGIGHIPQDRHKHGLVLDFPIGENILLQSYY 36- 2 Query: 374 KEPLSHKGILNFAKIKEYARQLMTEFDVRGAGEHVLARGFSGGNQQKAIIAREVDRDPDL 43- 3 K+P S G+L+ ++ + AR L+TE+DVR E+ AR SGGNQQKAII RE+DR+PDL Sbjct: 363 KKPYSALGVLHKGEMYKKARSLITEYDVRTPDEYTHARALSGGNQQKAIIGREIDRNPDL 42- 2 Query: 434 LIVSQPTRGLDVGAIEYIHKRLIEERDKGKAVLVVSFELDEILNLSDRIAVIHDGKIQGI 49- 3 LI +QPTRGLDVGAIE++HK+LIE+RD GKAVL++SFEL+EI+NLSDRIAVI +G+I Sbjct: 423 LIAAQPTRGLDVGAIEFVHKKLIEQRDAGKAVLLLSFELEEIMNLSDRIAVIFEGRIIAS 48- 2 Query: 494 VKPDQTNKQELGILMAG 510 V P +T +QELG+LMAG Sbjct: 483 VNPQETTEQELGLLMAG 499 Identities = 75/242 (30%), Positives = 128/242 (51%), Gaps = 24/242 (9%) Query: 280 GVLAVKNLSLDVRAGEIVGIAGIDGNGQSELIQAITGLRKVTSGQIVIKGKDVTKFSSRQ 33- 9 G++A N++L V+ GEI + G +G G+S L+ + GL + G+I ++G+ V S + Sbjct: 16 GIVANDNINLQVKKGEIHALLGENGAGKSTLMNVLFGLYQPERGEIRVRGEKVHINSPNK 75 Query: 340 ITELSVGHVPEDRHRDGLVLD-MTMAENLALQTYYKEPLSHKGILNFAKI--KEYARQLM 39- 6 +L +G V H+ +++D T+AEN+ L KEP F +I K +++ Sbjct: 76 ANDLGIGMV----HQHFMLVDTFTVAENIILG---KEPKK------FGRIDRKRAGQEVQ 122- Query: 397 TEFDVRGAGEHVLARG--FSGGNQQKAIIAREVDRDPDLLIVSQPTRGL---DVGAIEYI 45- 1 D G H A+ S G QQ+A I + + R D+LI +PT L ++ + I Sbjct: 123 DISDRYGLQIHPEAKAADISVGMQQRAEILKTLYRGADILIFDEPTAVLTPHEIKELMQI 18- 2 Query: 452 HKRLIEERDKGKAVLVVSFELDEILNLSDRIAVIHDGKIQGIVKPDQTNKQELGILMAGG 51- 1 K L++E GK++++++ +L EI+ + DR+ VI GK + TN+ EL LM G Sbjct: 183 MKNLVKE---GKSIILITHKLKEIMEICDRVTVIRKGKGIKTLDVRDTNQDELASLMVGR 23- 9 Query: 512 KI 513 ++ Sbjct: 240 EV 241 A related DNA sequence was identified in S. pyogenes <SEQ ID 4677> which encodes the amino acid sequence <SEQ ID 4678>. Analysis of this protein sequence reveals the following:

TABLE-US-04540 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3558(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04541 Identities = 431/511 (84%), Positives = 467/511 (91%), Gaps = 1/511 (0%) Query: 10 MTQNVIEMKEITKKFGDFVANDHINLTVEKGEIHALLGENGAGKSTLMNMLAGLLEPTDG 69 - MTQ+VIEM+EITKKFGDFVANDHINL V KGEIHALLGENGAGKSTLMNMLAGLLEPT G Sbjct: 7 MTQHVIEMREITKKFGDFVANDHINLNVRKGEIHALLGENGAGKSTLMNMLAGLLEPTSG 66 Query: 70 QIFINGQPVTIDSPSKSSQLGIGMVHQHFMLVEAFTVAENIVLGNETTQNGVLDIKTAAK 129- +I IN +PV IDSPSKS++LGIGMVHQHFMLVEAFTVAENI+LGNE +NG LD+ A+K Sbjct: 67 EIVINDKPVQIDSPSKSAKLGIGMVHQHFMLVEAFTVAENIILGNEVVKNGCLDLNQASK 126- Query: 130 EIKELSEKYGLSVNPNAKISDISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIKEL 18- 9 +IK LSEKYGL++NP+AK+SDISVGAQQRVEILKTLYRGADILIFDEPTAVLTP+EIKEL Sbjct: 127 DIKVLSEKYGLAINPSAKVSDISVGAQQRVEILKTLYRGADILIFDEPTAVLTPAEIKEL 18- 6 Query: 190 MTIMKSLVKEGKSIILITHKLDEIRAVADKVTVIRRGKSIETVPVAGASSQQLAEMMVGR 24- 9 MTIMK+LVKEGKSIILITHKLDEIRAVAD+VTVIRRGKSIETV VAGA+SQ LAEMMVGR Sbjct: 187 MTIMKNLVKEGKSIILITHKLDEIRAVADRVTVIRRGKSIETVDVAGATSQDLAEMMVGR 24- 6 Query: 250 SVSFRTEKKEANPTDIILSVKDLVVEENRGGVLAVKNLSLDVRAGEIVGIAGIDGNGQSE 30- 9 SVSF T KK A P D++LS+K+L V+ENR GV AVK LSLDVRAGEIVGIAGIDGNGQSE Sbjct: 247 SVSFTTSKKAAEPKDVVLSIKNLEVDENR-GVPAVKGLSLDVRAGEIVGIAGIDGNGQSE 30- 5 Query: 310 LIQAITGLRKVTSGQIVIKGKDVTKFSSRQITELSVGHVPEDRHRDGLVLDMTMAENLAL 36- 9 LIQAITGLRKV SG I+IK +VT SSR+ITELSVGHVPEDRHRDGL+LD+++AEN AL Sbjct: 306 LIQAITGLRKVKSGSIMIKNNEVTHLSSRKITELSVGHVPEDRHRDGLILDLSLAENTAL 36- 5 Query: 370 QTYYKEPLSHKGILNFAKIKEYARQLMTEFDVRGAGEHVLARGFSGGNQQKAIIAREVDR 42- 9 QTYYK+PLS GILN+ KI +YARQLM EFDVRGA E V ARGFSGGNQQKAIIAREVDR Sbjct: 366 QTYYKQPLSQNGILNYTKINDYARQLMKEFDVRGANELVPARGFSGGNQQKAIIAREVDR 42- 5 Query: 430 DPDLLIVSQPTRGLDVGAIEYIHKRLIEERDKGKAVLVVSFELDEILNLSDRIAVIHDGK 48- 9 DPDLLIVSQPTRGLDVGAIEYIHKRLI+ERDKGKAVLVVSFELDEILNLSDRIAVIHDGK Sbjct: 426 DPDLLIVSQPTRGLDVGAIEYIHKRLIKERDKGKAVLVVSFELDEILNLSDRIAVIHDGK 48- 5 Query: 490 IQGIVKPDQTNKQELGILMAGGKIEKEERDV 520 IQGIV P+ TNKQELGILMAGG I KEE V Sbjct: 486 IQGIVSPENTNKQELGILMAGGSIHKEEGHV 516 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1521 A DNA sequence (GBSx1612) was identified in S. agalactiae <SEQ ID 4679> which encodes the amino acid sequence <SEQ ID 4680>. Analysis of this protein sequence reveals the following: TABLE-US-04542 Possible Site: 22 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04543 >GP: CAB15143 GB: Z99120 similar to ABC transporter (lipoprotein) [Bacillus subtilis] Identities = 164/335 (48%), Positives = 224/335 (65%), Gaps = 10/335 (2%) Query: 18 LAACGHRGASKSGGKS-DSLKVAMVTDTGGVDDKSFNQSGWEGMQAWGKKNGLKKGA-GF 75 - L ACG+ S G+ + VAMVTD GGVDDKSFNQS WEG+QA+GK+NGLKKG G+ Sbjct: 11 LGACGNSEKSSGSGEGKNKFSVAMVTDVGGVDDKSFNQSAWEGIQAFGKENGLKKGKNGY 70 Query: 76 DYFQSASESDYATNLDTAVSSGYKLIFGIGFSLHDAIDKAADNNKDVNYVIVDDVIKGKD 135- DY QS S++DY TNL+ + LI+G+G+ + D+I + AD K+ N+ I+D V+ KD Sbjct: 71 DYLQSKSDADYTTNLNKLARENFDLIYGVGYLMEDSISEIADQRKNTNFAIIDAVVD-KD 129- Query: 136 NVASVVFADNESAYLAGIAAAKTTKTKTVGFVGGMESEVITRFEKGFEAGVKSVDKSIKI 19- 5 NVAS+ F + E ++L G+AAA ++K+ +GFVGGMESE+I +FE GF AGV++V+ + Sbjct: 130 NVASITFKEQEGSFLVGVAAALSSKSGKIGFVGGMESELIKKFEVGFRAGVQAVNPKAVV 18- 9 Query: 196 KVDYAGSFGDAAKGKTIAAAQYASGADIVYQVAGGTGAGVFSEAKSRNESLKEADKVWVL 25- 5 +V YAG F A GK A + Y SG D++Y AG TG GVF+EAK+ + + D VWV+ Sbjct: 190 EVKYAGGFDKADVGKATAESMYKSGVDVIYHSAGATGTGVFTEAKNLKKEDPKRD-VWVI 24- 8 Query: 256 GVDRDQAAEGKYTSKDGKASNFVLASSIKEVGKSVELIATKTSKGKFPGGNVTTYGLKDG 31- 5 GVD+DQ AEG+ +G N L S +K+V VE + K S GKFPGG TYGL Sbjct: 249 GVDKDQYAEGQV---EGTDDNVTLTSMVKKVDTVVEDVTKKASDGKFPGGETLTYGLDQD 30- 5 Query: 316 GVDIATT--NLSDDAVKAIKEAKAKIISGDIKVPS 348 GV I+ + NLSDD +KA+ + K KII G +++P+ Sbjct: 306 GVGISPSKQNLSDDVIKAVDKWKKKIIDG-LEIPA 339 A related DNA sequence was identified in S. pyogenes <SEQ ID 861> which encodes the amino acid sequence <SEQ ID 862>. Analysis of this protein sequence reveals the following: TABLE-US-04544 Possible site: 19 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04545 Identities = 275/351 (78%), Positives = 312/351 (88%), Gaps = 3/351 (0%) Query: 1 MNKKIAGIGLASIAVLSLAACGHRGASKSG--GKSDSLKVAMVTDTGGVDDKSFNQSGWE 58 MNKK G+GLAS+AVLSLAACG+RGASK G GK+D LKVAMVTDTGGVDDKSFNQS WE Sbjct: 1 MNKKFIGLGLASVAVLSLAACGNRGASKGGASGKTD-LKVAMVTDTGGVDDKSFNQSAWE 59 Query: 59 GMQAWGKKNGLKKGAGFDYFQSASESDYATNLDTAVSSGYKLIFGIGFSLHDAIDKAADN 118- G+Q+WGK+ GL+KG GFDYFQS SES+YATNLDTAVS GY+LI+GIGF+L DAI KAA + Sbjct: 60 GLQSWGKEMGLQKGTGFDYFQSTSESEYATNLDTAVSGGYQLIYGIGFALKDAIAKAAGD 119- Query: 119 NKDVNYVIVDDVIKGKDNVASVVFADNESAYLAGIAAAKTTKTKTVGFVGGMESEVITRF 17- 8 N+ V +VI+DD+I+GKDNVASV FAD+E+AYLAGIAAAKTTKTKTVGFVGGME VITRF Sbjct: 120 NEGVKFVIIDDIIEGKDNVASVTFADHEAAYLAGIAAAKTTKTKTVGFVGGMEGTVITRF 17- 9 Query: 179 EKGFEAGVKSVDKSIKIKVDYAGSFGDAAKGKTIAAAQYASGADIVYQVAGGTGAGVFSE 23- 8 EKGFEAGVKSVD +I++KVDYAGSFGDAAKGKTIAAAQYA+GAD++YQ AGGTGAGVF+E Sbjct: 180 EKGFEAGVKSVDDTIQVKVDYAGSFGDAAKGKTIAAAQYAAGADVIYQAAGGTGAGVFNE 23- 9 Query: 239 AKSRNESLKEADKVWVLGVDRDQAAEGKYTSKDGKASNFVLASSIKEVGKSVELIATKTS 29- 8 AK+ NE EADKVWV+GVDRDQ EGKYTSKDGK +NFVLASSIKEVGK+V+LI + + Sbjct: 240 AKAINEKRSEADKVWVIGVDRDQKDEGKYTSKDGKEANFVLASSIKEVGKAVQLINKQVA 29- 9 Query: 299 KGKFPGGNVTTYGLKDGGVDIATTNLSDDAVKAIKEAKAKIISGDIKVPSK 349 KFPGG T YGLKDGGV+IATTN+S +AVKAIKEAKAKI SGDIKVP K Sbjct: 300 DKKFPGGKTTVYGLKDGGVEIATTNVSKEAVKAIKEAKAKIKSGDIKVPEK 350 A related DNA sequence was identified in S. pyogenes <SEQ ID 9061> which encodes amino acid sequence <SEQ ID 9062>. Analysis of this protein sequence reveals the following: TABLE-US-04546 Possible site: 17 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS sequences follows: TABLE-US-04547 Score = 414 bits (1052), Expect = e-117 Identities = 196/347 (56%), Positives = 253/347 (72%), Gaps = 2/347 (0%) Query: 1 MNKKVMSLGLVSTALFTLGGCTNNSAKQT--TDNSLKIAMITNQTGIDDKSFNQSAWEGL 58 MNKK+ +GL S A+ +L C + A ++ +SLK+AM+T+ G+DDKSFNQS WEG+ Sbjct: 1 MNKKIAGIGLASIAVLSLAACGHRGASKSGGKSDSLKVAMVTDTGGVDDKSFNQSGWEGM 60 Query: 59 QAWGKENKLEKGKGYDYFQSANESEFTTNLESAVTNGYNLVFGIGFPLHDAVEKVAANNP 118- QAWGK+N L+KG G+DYFQSA+ES++ TNL++AV++GY L+FGIGF LHDA++K A NN Sbjct: 61 QAWGKKNGLKKGAGFDYFQSASESDYATNLDTAVSSGYKLIFGIGFSLHDAIDKAADNNK 120- Query: 119 DNHFAIVDDVIKGQKNVASITFSDHEAAYLAGVXXXXXXXXXQVGFVGGMEGDVVKRFEK 17- 8 D ++ IVDDVIKG+ NVAS+ F+D+E+AYLAG+ VGFVGGME +V+ RFEK Sbjct: 121 DVNYVIVDDVIKGKDNVASVVFADNESAYLAGIAAAKTTKTKTVGFVGGMESEVITRFEK 18- 0 Query: 179 GFEAGVKSVDDTIKVRVAYAGSFXXXXXXXXXXXXXXXEGADVIYHAAGGTGAGVFSEAK 23- 8 GFEAGVKSVD +IK++V YAGSF GAD++Y AGGTGAGVFSEAK Sbjct: 181 GFEAGVKSVDKSIKIKVDYAGSFGDAAKGKTIAAAQYASGADIVYQVAGGTGAGVFSEAK 24- 0 Query: 239 SINEKRKEEDKVWVIGVDRDQSEDGKYTTKDGKSANFVLTSSIKEVGKALVKVAVKTSED 29- 8 S NE KE DKVWV+GVDRDQ+ +GKYT+KDGK++NFVL SSIKEVGK++ +A KTS+ Sbjct: 241 SRNESLKEADKVWVLGVDRDQAAEGKYTSKDGKASNFVLASSIKEVGKSVELIATKTSKG 30- 0 Query: 299 QFPGGQITTFGLKEGGVSLTTDALTQDTXXXXXXXXXXXXXGTITVP 345 +FPGG +TT+GLK+GGV + T L+ D G I VP Sbjct: 301 KFPGGNVTTYGLKDGGVDIATTNLSDDAVKAIKEAKAKIISGDIKVP 347 SEQ ID 4680 (GBS211) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 6; MW 40 kDa). The GBS211-His fusion product was purified (FIG. 205, lane 8) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 259A) and FACS (FIG. 259B). These tests confirm that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1522 A DNA sequence (GBSx1613) was identified in S. agalactiae <SEQ ID 4681> which encodes the amino acid sequence <SEQ ID 4682>. This protein is predicted to be cytidine deaminase (cdd). Analysis of this protein sequence reveals the following: TABLE-US-04548 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2112(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9801> which encodes amino acid sequence <SEQ ID 9802> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04549 >GP: CAB51906 GB: AJ237978 cytidine deaminase [Bacillus psychrophilus] Identities = 66/114 (57%), Positives = 81/114 (70%) Query: 26 KASENAYVPYSKFPVGAALRTAEGKIFTGCNVENISYGLANCAERTAIFKAVSEGYKDFS 85 - KA E AYVPYSKFPVGAAL +G I+ GCN+EN +Y + NCAERTA FKAVS+G + F Sbjct: 12 KAREQAYVPYSKFPVGAALLAEDGTIYHGCNIENSAYSMTNCAERTAFFKAVSDGVRSFK 71 Query: 86 EIAIYGNTEEPISPCGACRQVMVEFFNKNAKVTLIAKNGKTVETTVGELLPYSF 139 +A+ +TE P+SPCGACRQV+ EF N + V L G ETTV +LLP +F Sbjct: 72 ALAVVADTEGPVSPCGACRQVIAEFCNGSMPVYLTNLKGDIEETTVAKLLPGAF 125 A related DNA sequence was identified in S. pyogenes <SEQ ID 4683> which encodes the amino acid sequence <SEQ ID 4684>. Analysis of this protein sequence reveals the following: TABLE-US-04550 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0041(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04551 >GP: CAB15143 GB: Z99120 similar to ABC transporter (lipoprotein) [Bacillus subtilis] Identities = 152/339 (44%), Positives = 223/339 (64%), Gaps = 11/339 (3%) Query: 8 LGLVSTALFTLGGCTNN---SAKQTTDNSLKIAMITNQTGIDDKSFNQSAWEGLQAWGKE 64 + LV A LG C N+ S N +AM+T+ G+DDKSFNQSAWEG+QA+GKE Sbjct: 1 MSLVIAAGTILGACGNSEKSSGSGEGKNKFSVAMVTDVGGVDDKSFNQSAWEGIQAFGKE 60 Query: 65 NKLEKGK-GYDYFQSANESEFTTNLESAVTNGYNLVFGIGFPLHDAVEKVAANNPDNHFA 123- N L+KGK GYDY QS +++++TTNL ++L++G+G+ + D++ ++A + +FA Sbjct: 61 NGLKKGKNGYDYLQSKSDADYTTNLNKLARENFDLIYGVGYLMEDSISEIADQRKNTNFA 120- Query: 124 IVDDVIKGQKNVASITFSDHEAAYLAGVAAAKTTKTKQVGFVGGMEGDVVKRFEKGFEAG 18- 3 I+D V+ + NVASITF + E ++L GVAAA ++K+ ++GFVGGME +++K+FE GF AG Sbjct: 121 IIDAVVD-KDNVASITFKEQEGSFLVGVAAALSSKSGKIGFVGGMESELIKKFEVGFRAG 17- 9 Query: 184 VKSVDDTIKVRVAYAGSFADAAKGKTIAAAQYAEGADVIYHAAGGTGAGVFSEAKSINEK 24- 3 V++V+ V V YAG F A GK A + Y G DVIYH+AG TG GVF+EAK++ ++ Sbjct: 180 VQAVNPKAVVEVKYAGGFDKADVGKATAESMYKSGVDVIYHSAGATGTGVFTEAKNLKKE 23- 9 Query: 244 RKEEDKVWVIGVDRDQSEDGKYTTKDGKSANFVLTSSIKEVGKALVKVAVKTSEDQFPGG 30- 3 + D VWVIGVD+DQ +G+ +G N LTS +K+V + V K S+ +FPGG Sbjct: 240 DPKRD-VWVIGVDKDQYAEGQV---EGTDDNVTLTSMVKKVDTVVEDVTKKASDGKFPGG 29- 5 Query: 304 QITTFGLKEGGVSLTTDA--LTQDTKKAIEAAKKAIIEG 340 + T+GL + GV ++ L+ D KA++ KK II+G Sbjct: 296 ETLTYGLDQDGVGISPSKQNLSDDVIKAVDKWKKKIIDG 334 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04552 Identities = 88/128 (68%), Positives = 107/128 (82%) Query: 15 MGNIELKKLAVKASENAYVPYSKFPVGAALRTAEGKIFTGCNVENISYGLANCAERTAIF 74 - MG +L AV+ASE AYVPYS FPVGAAL+T +G I+TGCN+EN+S+GL NC ERTAIF Sbjct: 1 MGTTDLVSCAVQASEYAYVPYSHFPVGAALKTKDGTIYTGCNIENVSFGLTNCGERTAIF 60 Query: 75 KAVSEGYKDFSEIAIYGNTEEPISPCGACRQVMVEFFNKNAKVTLIAKNGKTVETTVGEL 134- KA+S+G+K+ EIAIYG T +P+SPCGACRQVM EFF+ ++ VTLIARNG+TVE TVG+L Sbjct: 61 KAISDGHKELVEIAIYGETMQPVSPCGACRQVMAEFFDPSSLVTLIAKNGQTVEMTVGDL 120- Query: 135 LPYSFVDL 142 L YSF DL Sbjct: 121 LLYSFTDL 128 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1523 A DNA sequence (GBSx1614) was identified in S. agalactiae <SEQ ID 4685> which encodes the amino acid sequence <SEQ ID 4686>. Analysis of this protein sequence reveals the following: TABLE-US-04553 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2979(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9799> which encodes amino acid sequence <SEQ ID 9800> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04554 >GP: CAB11882 GB: Z99104 alternate gene name: ybaA~similar to hypothetical proteins [Bacillus subtilis] Identities = 90/201 (44%), Positives = 144/201 (70%), Gaps = 5/201 (2%) Query: 1 MANMYYTENPNVEHDIHELNVKLLGESFSFLTDAGVFSKRMIDYGSQVLLNSLHF-EKNK 59 M+ YY+E P+V+ + + +L + F+F +D+GVFSK+ +D+GS++L++S E Sbjct: 1 MSEHYYSEKPSVKSNKQTWSFRLRNKDFTFTSDSGVFSKKEVDFGSRLLIDSFEEPEVEG 60 Query: 60 SLLDLGCGYGPLGISLAK-VQGVKATMVDINTRALELAKKNATRNGVV-VEVFQSNIYEN 117- +LD+GCGYGP+G+SLA + M+D+N RA+EL+ +NA +NG+ V+++QS+++ N Sbjct: 61 GILDVGCGYGPIGLSLASDFKDRTIHMIDVNERAVELSNENAEQNGITNVKIYQSDLFSN 120- Query: 118 I--SKTFDYIISNPPIRAGKQVVHSIIEESICYLNTGGSLTIVIQKKQGAPSAKAKMLDT 17- 5 + ++TF I++NPPIRAGK+VVH+I E+S +L G L IVIQKKQGAPSA K+ + Sbjct: 121 VDSAQTFASILTNPPIRAGKKVVHAIFEKSAEHLKASGELWIVIQKKQGAPSAIEKLEEL 18- 0 Query: 176 FGNCDILKKDKGYYILRSEKV 196 F +++K KGYYI++++KV Sbjct: 181 FDEVSVVQKKKGYYIIKAKKV 201 A related DNA sequence was identified in S. pyogenes <SEQ ID 4687> which encodes the amino acid sequence <SEQ ID 4688>. Analysis of this protein sequence reveals the following: TABLE-US-04555 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4232(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04556 Identities = 139/195 (71%), Positives = 165/195 (84%) Query: 1 MANMYYTENPNVEHDIHELNVKLLGESFSFLTDAGVFSKRMIDYGSQVLLNSLHFEKNKS 60 M MYY ENP+ HDIHE+ V+LL F+FLTD+GVFSK+M+D+GSQVLL +L+F++N+ Sbjct: 12 MTKMYYDENPDSLHDIHEVKVELLNHPFTFLTDSGVFSKKMVDFGSQVLLKTLNFKENER 71 Query: 61 LLDLGCGYGPLGISLAKVQGVKATMVDINTRALELAKKNATRNGVVVEVFQSNIYENISK 120- +LDLGCGYGPLGISLAKVQ V AT+VDIN RAL+LA+KNAT N V V +FQSNIYENIS Sbjct: 72 VLDLGCGYGPLGISLAKVQRVDATLVDINNRALDLARKNATNNQVAVTIFQSNIYENISG 131- Query: 121 TFDYIISNPPIRAGKQVVHSIIEESICYLNTGGSLTIVIQKKQGAPSAKAKMLDTFGNCD 18- 0 F++IISNPPIRAGK+VVHSIIE+SI +L G LTIVIQKKQGAPSAKAKM FGN + Sbjct: 132 HFEHIISNPPIRAGKRVVHSIIEKSIDFLVVNGDLTIVIQKKQGAPSAKAKMATIFGNVE 19- 1 Query: 181 ILKKDKGYYILRSEK 195 IL+KDKGYY+LRS K Sbjct: 192 ILRKDKGYYVLRSIK 206 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1524 A DNA sequence (GBSx1615) was identified in S. agalactiae <SEQ ID 4689> which encodes the amino acid sequence <SEQ ID 4690>. This protein is predicted to be pantothenate kinase (coaA). Analysis of this protein sequence reveals the following:

TABLE-US-04557 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5021(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04558 >GP: BAB06594 GB: AP001516 pantothenate kinase [Bacillus halodurans] Identities = 140/307 (45%), Positives = 203/307 (65%), Gaps = 5/307 (1%) Query: 4 EFINFDRISRENWKDLHQQSQALLTEKELESIKSLNDNINIQDVIDIYLPLINLIQIYKR 63 +F + +SR WK L + S + E+ELE + LN+ I + +V DIY+PL L+ ++ Sbjct: 8 DFFPYTVLSRSQWKSLRKASSLPINEQELEQLVGLNEPITLNEVADIYVPLAELLHVHAT 67 Query: 64 SQENLSFSKAIFLKKENYQRPFIIGISGSVAVGKSTTSRLLQLLISRTFKDSHVELVTTD 123- + + L K F + PFIIG++GSVAVGKSTT+RLLQ L+ + HV+LVTTD Sbjct: 68 AYQRLQQQKRGFFHHGKNRSPFIIGLAGSVAVGKSTTARLLQKLLKAWPEHHHVDLVTTD 127- Query: 124 GFLYPNEKLIQNGILNRKGFPESYDMESLLNFLDTIKNGIT-AKIPIYSHEIYDIVPNQL 18- 2 GFLYPNE L G++++KGFPESYD+ +L+ FL +K G K P+YSH Y+IV Sbjct: 128 GFLYPNETLEARGLMDKKGFPESYDLPALIRFLSDVKAGEPYVKAPVYSHLTYNIVEGDY 18- 7 Query: 183 QTIETPDFLILEGINVFQ-NQQNHRL---YMNDYFDFSIYIDAENKQIEEWYLQRFNSLL 23- 8 Q + PD +I+EGINV Q N++NH + +++D+FDFSIY+DA+ +QI +WY++RF L Sbjct: 188 QVVHEPDIVIVEGINVLQVNKRNHHIPNVFVSDFFDFSIYVDAKEEQILQWYIERFKLLQ 24- 7 Query: 239 QLAEADPSNYYHKFTQIPPHKAMELAKDIWKTINLVNLEKYIEPTRNRADFIIHKGKHHK 29- 8 A DP++Y+H+F + +A + A IWK IN VNL + I PT++RAD ++ KG HH Sbjct: 248 NTAFQDPNSYFHRFRHLSEVEAEQFATSIWKNINGVNLHENILPTKHRADLVLQKGPHHF 30- 7 Query: 299 IDEIYLK 305 IDE+ L+ Sbjct: 308 IDEVKLR 314 A related DNA sequence was identified in S. pyogenes <SEQ ID 4691> which encodes the amino acid sequence <SEQ ID 4692>. Analysis of this protein sequence reveals the following: TABLE-US-04559 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4790(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04560 Identities = 219/306 (71%), Positives = 269/306 (87%) Query: 1 MNNEFINFDRISRENWKDLHQQSQALLTEKELESIKSLNDNINIQDVIDIYLPLINLIQI 60 M+NEFINF++ISRE+WK LHQ+++ALLT++EL+SI SLNDNI+I DVIDIYLPLINLIQ+ Sbjct: 1 MSNEFINFEKISRESWKTLHQKAKALLTQEELKSITSLNDNISINDVIDIYLPLINLIQV 60 Query: 61 YKRSQENLSFSKAIFLKKENYQRPFIIGISGSVAVGKSTTSRLLQLLISRTFKDSHVELV 120- YK +QENLSFSK++FLKK+ RPFIIGISGSVAVGKSTTSRLLQLL+SRT +S VELV Sbjct: 61 YKIAQENLSFSKSLFLKKDIQLRPFIIGISGSVAVGKSTTSRLLQLLLSRTHPNSQVELV 120- Query: 121 TTDGFLYPNEKLIQNGILNRKGFPESYDMESLLNFLDTIKNGITAKIPIYSHEIYDIVPN 18- 0 TTDGFLYPN+ LI+ G+LNRKGFPESY+ME LL+FLD+IKNG TA P+YSH+IYDI+PN Sbjct: 121 TTDGFLYPNQFLIEQGLLNRKGFPESYNMELLLDFLDSIKNGQTAFAPVYSHDIYDIIPN 18- 0 Query: 181 QLQTIETPDFLILEGINVFQNQQNHRLYMNDYFDFSIYIDAENKQIEEWYLQRFNSLLQL 24- 0 Q Q+ PDFLI+EGINVFQNQQN+RLYM+DYFDFSIYIDA++ IE WY++RF S+L+L Sbjct: 181 QKQSFNNPDFLIVEGINVFQNQQNNRLYMSDYFDFSIYIDADSSHIETWYIERFLSILKL 24- 0 Query: 241 AEADPSNYYHKFTQIPPHKAMELAKDIWKTINLVNLEKYIEPTRNRADFIIHKGKHHKID 30- 0 A+ DP NYY ++ Q+P +A+ A+++WKT+NL NLEK+IEPTRNRA+ I+HK HKID Sbjct: 241 AKRDPHNYYAQYAQLPRSEAIAFARNVWKTVNLENLEKFIEPTRNRAELILHKSADHKID 30- 0 Query: 301 EIYLKK 306 EIYLKK Sbjct: 301 EIYLKK 306 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1525 A DNA sequence (GBSx1616) was identified in S. agalactiae <SEQ ID 4693> which encodes the amino acid sequence <SEQ ID 4694>. Analysis of this protein sequence reveals the following: TABLE-US-04561 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3866(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04562 >GP: BAB05058 GB: AP001511 ribosomal protein S20 (BS20) [Bacillus halodurans] Identities = 47/86 (54%), Positives = 59/86 (67%), Gaps = 7/86 (8%) Query: 3 VKTLANIKSAIKRAELNVKQNEKNSAQKSAMRTAIKAFEA---NPSEELYRA----ASSS 55 +K ANIKSAIKR + N K+ +N++ KSA+RTAIK FEA N E +A A+ Sbjct: 1 MKGNANIKSAIKRVKTNEKRRIQNASVKSALRTAIKQFEAKVENNDAEAAKAAFVEATKK 60 Query: 56 IDKAASKGLIHTNKASRDKARLATKL 81 +DKAA+KGLIH N ASR K+RLA KL Sbjct: 61 LDKAANKGLIHKNAASRQKSRLAKKL 86 A related DNA sequence was identified in S. pyogenes <SEQ ID 4695> which encodes the amino acid sequence <SEQ ID 4696>. Analysis of this protein sequence reveals the following: TABLE-US-04563 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3872(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04564 Identities = 76/82 (92%), Positives = 78/82 (94%) Query: 1 MEVKTLANIKSAIKRAELNVKQNEKNSAQKSAMRTAIKAFEANPSEELYRAASSSIDKAA 60 +EVKTLANIKSAIKRAELNVK NEKNSAQKSAMRTAIKAFEANPSEEL+RAASSSIDKA Sbjct: 1 LEVKTLANIKSAIKRAELNVKANEKNSAQKSAMRTAIKAFEANPSEELFRAASSSIDKAE 60 Query: 61 SKGLIHTNKASRDKARLATKLG 82 SKGLIH NKASRDKARLA KLG Sbjct: 61 SKGLIHKNKASRDKARLAAKLG 82 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1526 A DNA sequence (GBSx1617) was identified in S. agalactiae <SEQ ID 4697> which encodes the amino acid sequence <SEQ ID 4698>. Analysis of this protein sequence reveals the following: TABLE-US-04565 Possible Site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.99 Transmembrane 31-47 (25-51) ----- Final Results ----- bacterial membrane --- Certainty = 0.5394(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04566 >GP: AAC35851 GB: AF086736 amino acid-binding protein Abp [Streptococcus uberis] Identities = 169/269 (62%), Positives = 203/269 (74%), Gaps = 2/269 (0%) Query: 29 KNILLTIIFGLFMIILSACGMSNKEMAGIDNWEHYQKEKKITIGFDNTFVPMGFESRSGD 88 - K ILLT + + L ACG S+ A D W+ Y+KEK IT+GFDNTFVPMGF+ SG Sbjct: 4 KKILLTTLALASTLFLVACGKSSA--AKTDQWDTYKKEKSITLGFDNTFVPMGFKDESGK 61 Query: 89 YTGFDIDLANAVFKEYGISVKWQPINWDMKETELNNGNIDLIWNGYSKTAERAKKVAFTN 148- TGFD++LA AVF+EYGI VK+QPINWD+KETEL NG ID+IWNGYS T ER KVAF+ Sbjct: 62 NTGFDVELAKAVFQEYGIKVKFQPINWDLKETELKNGKIDMIWNGYSVTKERQAKVAFST 121- Query: 149 PYMNNHQVIVTKTSSHINSIKDMKGKKLGAQSGSSGFDAFNAKPDILKKFVKGKEAVQYD 20- 8 PYM N QV+VTK SS+I S MKGK LGAQSGSSG+DAF + P +LK VK +A QY+ Sbjct: 122 PYMKNEQVLVTKKSSNITSFAAMKGKVLGAQSGSSGYDAFTSNPKVLKDIVKDNDATQYE 18- 1 Query: 209 TFTQALIDLKNNRIDGLLIDEVYANYYLKQEGNIKAYYFVKTAYQGENFVVGARKVDRRL 26- 8 TF QA IDLKN+RIDGLLID+VYANYYLKQEG + Y VK+ + GE+F VG RK D+ L Sbjct: 182 TFIQAFIDLKNDRIDGLLIDKVYANYYLKQEGELTNYNIVKSEFDGEDFAVGVRKEDKIL 24- 1 Query: 269 IEKINKAFKQLHNKGRFQKISYKWFGEDV 297 ++ IN AF +L+ G+FQ+IS KWFGEDV Sbjct: 242 LKNINSAFTKLYKTGKFQEISQKWFGEDV 270 A related DNA sequence was identified in S. pyogenes <SEQ ID 4699> which encodes the amino acid sequence <SEQ ID 4700>. Analysis of this protein sequence reveals the following: TABLE-US-04567 Possible site: 21 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04568 >GP: AAC35851 GB: AF086736 amino acid-binding protein Abp [Streptococcus uberis] Identities = 176/277 (63%), Positives = 220/277 (78%), Gaps = 1/277 (0%) Query: 1 MIIKKRTVAILAIASSFFLVACQATKSLKSGDAWGVYQKQKSITVGFDNTFVPMGYKDES 60 M +KK + LA+AS+ FLVAC + + K+ D W Y+K+KSIT+GFDNTFVPMG+KDES Sbjct: 1 MNLKKILLTTLALASTLFLVACGKSSAAKT-DQWDTYKKEKSITLGFDNTFVPMGFKDES 59 Query: 61 GRCKGFDIDLAKEVFHQYGLKVNFQAINWDMKEAELNNGKIDVIWNGYSITKERQDKVAF 120- G+ GFD++LAK VF +YG+KV FQ INWD+KE EL NGKID+IWNGYS+TKERQ KVAF Sbjct: 60 GKNTGFDVELAKAVFQEYGIKVKFQPINWDLKETELKNGKIDMIWNGYSVTRERQAKVAF 119- Query: 121 TDSYMRNEQIIVVKKRSDIKTISDMKHKVLGAQSASSGYDSLLRTPKLLKDFIKNKDANQ 18- 0 + YM+NEQ++V KK S+I + + MK KVLGAQS SSGYD+ PK+LKD +K+ DA Q Sbjct: 120 STPYMKNEQVLVTKKSSNITSFAAMKGKVLGAQSGSSGYDAFTSNPKVLKDIVKDNDATQ 17- 9 Query: 181 YETFTQAFIDLKSDRIDGILIDKVYANYYLAKEGQLENYRMIPTTFENEAFSVGLRKEDK 24- 0 YETF QAFIDLK+DRIDG+LIDKVYANYYL +EG+L NY ++ + F+ E F+VG+RKEDK Sbjct: 180 YETFIQAFIDLKNDRIDGLLIDKVYANYYLKQEGELTNYNIVKSEFDGEDFAVGVRKEDK 23- 9 Query: 241 TLQAKINRAFRVLYQNGKFQAISEKWFGDDVATANIK 277 L IN AF LY+ GKFQ IS+KWFG+DVAT N+K Sbjct: 240 ILLKNINSAFTKLYKTGKFQEISQKWFGEDVATENVK 276 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04569 Identities = 151/266 (56%), Positives = 189/266 (70%), Gaps = 4/266 (1%) Query: 32 LLTIIFGLFMIILSACGMSNKEMAGIDNWEHYQKEKKITIGFDNTFVPMGFESRSGDYTG 91 - +L I F++ AC + K + D W YQK+K IT+GFDNTFVPMG++ SG G Sbjct: 10 ILAIASSFFLV---AC-QATKSLKSGDAWGVYQKQKSITVGFDNTFVPMGYKDESGRCKG 65 Query: 92 FDIDLANAVFKEYGISVKWQPINWDMKETELNNGNIDLIWNGYSKTAERAKKVAFTNPYM 151- FDIDLA VF +YG+ V +Q INWDMKE ELNNG ID+IWNGYS T ER KVAFT+ YM Sbjct: 66 FDIDLAKEVFHQYGLKVNFQAINWDMKEAELNNGKIDVIWNGYSITKERQDKVAFTDSYM 125- Query: 152 NNHQVIVTKTSSHINSIKDMKGKKLGAQSGSSGFDAFNAKPDILKKFVKGKEAVQYDTFT 21- 1 N Q+IV K S I +I DMK K LGAQS SSG+D+ P +LK F+K K+A QY+TFT Sbjct: 126 RNEQIIVVKKRSDIKTISDMKHKVLGAQSASSGYDSLLRTPKLLKDFIKNKDANQYETFT 18- 5 Query: 212 QALIDLKNNRIDGLLIDEVYANYYLKQEGNIKAYYFVKTAYQGENFVVGARKVDRRLIEK 27- 1 QA IDLK++RIDG+LID+VYANYYL +EG ++ Y + T ++ E F VG RK D+ L K Sbjct: 186 QAFIDLKSDRIDGILIDKVYANYYLAKEGQLENYRMIPTTFENEAFSVGLRKEDKTLQAK 24- 5 Query: 272 INKAFKQLHNKGRFQKISYKWFGEDV 297 IN+AF+ L+ G+FQ IS KWFG+DV Sbjct: 246 INRAFRVLYQNGKFQAISEKWFGDDV 271 A related GBS gene <SEQ ID 8833> and protein <SEQ ID 8834> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04570 Lipop Possible site: 22 Crend: 4 Sequence Pattern: CGMS SRCFLG: 0 McG: Length of UR: 22 Peak Value of UR: 3.05 Net Charge of CR: 2 McG: Discrim Score: 11.16 GvH: Signal Score (-7.5): -1.96 Possible site: 24 >>> May be a lipoprotein Amino Acid Composition: calculated from 23 ALOM program count: 0 value: 8.96 threshold: 0.0 PERIPHERAL Likelihood = 8.96 68 modified ALOM score: -2.29 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00099## SEQ ID 8834 (GBS225) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 10; MW 32 kDa). The GBS225-His fusion product was purified (FIG. 205, lane 7) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 266), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1527 A DNA sequence (GBSx1618) was identified in S. agalactiae <SEQ ID 4701> which encodes the amino acid sequence <SEQ ID 4702>. This protein is predicted to be arginine ABC transporter, ATP-binding protein (glnQ). Analysis of this protein sequence reveals the following: TABLE-US-04571 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3229(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04572 >GP: AAB49429 GB: U73111 glutamine transport ATP-binding protein GLNQ [Salmonella typhimurium] Identities = 94/210 (44%), Positives = 146/210 (68%), Gaps = 3/210 (1%) Query: 1 MLELKNISKCYGQKEIFKDFNLTVEEGKILSLVGPSGGGKTTLLRMLAGLEKIDSGTIVH 60 M+E KN+SK +G ++ + +L + +G+++ ++GPSG GK+TLLR + LE+I SG ++ Sbjct: 1 MIEFKNVSKHFGPTQVLHNIDLNIRQGEVVVIIGPSGSGKSTLLRCINKLEEITSGDLIV 60 Query: 61 DGKEVS---VDHLETLNLLGFVFQDFQLFPHLTVLDNLILSPVKTMGLSKELAKEKALVL 117- DG +V+ VD G VFQ F LFPHLT L+N++ P++ G+ KE A+++A L Sbjct: 61 DGLKVNDPKVDERLIRQEAGMVFQQFYLFPHLTALENVMFGPLRVRGVKKEEAEKQAKAL 120- Query: 118 LERLGLKDHALVYPFSLSGGQKQRVALARAMMIDPQIIGYDEPTSALDPELRQEVEKLIL 17- 7 L ++GL + A YP LSGGQ+QRVA+ARA+ + P+++ +DEPTSALDPELR EV K++ Sbjct: 121 LAKVGLAERAHHYPSELSGGQQQRVAIARALAVKPKMMLFDEPTSALDPELRHEVLKVMQ 18- 0 Query: 178 QNRETGMTQIVVTHDLQFAESISDTILKIN 207 E GMT ++VTH++ FAE ++ ++ I+ Sbjct: 181 DLAEEGMTMVIVTHEIGFAEKVASRLIFID 210 A related DNA sequence was identified in S. pyogenes <SEQ ID 4703> which encodes the amino acid sequence <SEQ ID 4704>. Analysis of this protein sequence reveals the following: TABLE-US-04573 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2146(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04574 Identities = 164/209 (78%), Positives = 183/209 (87%) Query: 1 MLELKNISKCYGQKEIFKDFNLTVEEGKILSLVGPSGGGKTTLLRMLAGLEKIDSGTIVH 60 MLELKNISK +GQK IF FNLTV++G++LSLVGPS GGKTTLLRMLAGLE IDSG + + Sbjct: 1 MLELKNISKQFGQKTIFDGFNLTVQDGEVLSLVGPSSGGKTTLLRMLAGLESIDSGQVFY 60 Query: 61 DGKEVSVDHLETLNLLGFVFQDFQLFPHLTVLDNLILSPVKTMGLSKELAKEKALVLLER 120- +G++V +DHLE NLLGFVFQDFQLFPHLTVLDNL LSP TMG K AKEKAL LL R Sbjct: 61 NGEDVGIDHLENRNLLGFVFQDFQLFPHLTVLDNLTLSPTITMGKQKADAKEKALDLLAR 120- Query: 121 LGLKDHALVYPFSLSGGQKQRVALARAMMIDPQIIGYDEPTSALDPELRQEVEKLILQNR 18- 0 LGLK+HA VYP+SLSGGQKQRVALARAMMIDPQIIGYDEPTSALDPELRQ VE LI+QNR Sbjct: 121 LGLKEHAQVYPYSLSGGQKQRVALARAMMIDPQIIGYDEPTSALDPELRQTVEALIVQNR 18- 0 Query: 181 ETGMTQIVVTHDLQFAESISDTILKINPK 209 E G+TQIVVTHDL FAE+ISD I+++NPK Sbjct: 181 EMGITQIVVTHDLVFAEAISDRIIRVNPK 209 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1528 A DNA sequence (GBSx1619) was identified in S. agalactiae <SEQ ID 4705> which encodes the amino acid sequence <SEQ ID 4706>. This protein is predicted to be amino acid ABC transporter, permease protein (glnP). Analysis of this protein sequence reveals the following: TABLE-US-04575 Possible site: 16 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.12 Transmembrane 102-118 (96-120) ----- Final Results ----- bacterial membrane --- Certainty = 0.4248(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9341> which encodes amino acid sequence <SEQ ID 9342> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04576 >GP: BAA98402 GB: AP002545 ABC amino acid transporter permease [Chlamydophila pneumoniae J138] Identities = 55/127 (43%), Positives = 83/127 (65%), Gaps = 1/127 (0%) Query: 3 AAIIAFTMNYAAYFAEIFRGGIESIPKGQYEAAKVLKFSKFQTVWYIVLPQVFKIVLPSV 62 A IIA +MN AAY AE RGGI S+ GQ+E+A VL + K+Q YI+ PQVFK +LPS+ Sbjct: 89 AGIIALSMNSAAYLAENIRGGINSLSIGQWESAMVLGYKKYQIFVYIIYPQVFKNILPSL 148- Query: 63 FNETITLVKDSSLVYILGVGDLLLESKTAANRDATLAPMF-IAGGIYLLLIGLLTILSKQ 121- NE ++L+K+SS++ ++GV +L +K +R+ M+ I G+Y L+ + +S+ Sbjct: 149 TNEFVSLIKESSILMVVGVPELTKVTKDIVSRELNPMEMYLICAGLYFLMTSSFSCISRL 20- 8 Query: 122 VEKRFNY 128 EKR +Y Sbjct: 209 SEKRRSY 215 A related DNA sequence was identified in S. pyogenes <SEQ ID 4707> which encodes the amino acid sequence <SEQ ID 4708>. Analysis of this protein sequence reveals the following:

TABLE-US-04577 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.57 Transmembrane 21-37 (7-44) INTEGRAL Likelihood = -10.93 Transmembrane 185-201 (178-206) INTEGRAL Likelihood = -3.29 Transmembrane 63-79 (62-81) ----- Final Results ----- bacterial membrane --- Certainty = 0.5628(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04578 >GP: BAB05181 GB: AP001512 ABC transporter (permease) [Bacillus halodurans] Identities = 86/206 (41%), Positives = 126/206 (60%), Gaps = 1/206 (0%) Query: 4 IQQVLPSLLDGALVTLQVFFIVIILSIPLGAILAFLMKIPFKPLQWFLTLYVWMMRGTPL 63 IQ +P +L+G VTLQ + ++ + LG +LA ++ +WF Y + RGTPL Sbjct: 8 IQPFMPFMLEGVWVTLQFVSVSLLFGLVLGIVLAIFKISKYRLFRWFADFYTSIFRGTPL 67 Query: 64 LLQLIFFYYVLPSVGISFDRMPAAILAFTLNYAAYFAEIFRGGIEAIPKGQYEAAKVLKL 123- +LQL+ Y LP G+ + AA LAF LN AAY +EI R GI+A+ KGQ EAA+ L + Sbjct: 68 ILQLLMIYLALPQFGVDISQFQAAFLAFGLNSAAYVSEIIRAGIQAVDKGQREAAEALGI 127- Query: 124 KPLQTIRYIILPQVFKIVLPSVFNEVINLVKDSSLVYVLGVGDLL-LASKTAANRDATLA 18- 2 + IILPQ + +LP++FNE INL K+S++V V+GV DL+ A T+A L Sbjct: 128 PYRPMMLRIILPQAMRNILPALFNEFINLTKESAIVSVIGVTDLMRRAQITSAETYLYLE 18- 7 Query: 183 PMFIAGLIYLLLIGLVTIISKQVEKR 208 P+ GLIY +L+ +T+I + +E+R Sbjct: 188 PLLFVGLIYYVLVMGLTVIGRLLERR 213 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04579 Identities = 112/130 (86%), Positives = 121/130 (92%) Query: 1 MPAAIIAFTMNYAAYFAEIFRGGIESIPKGQYEAAKVLKFSKFQTVWYIVLPQVFKIVLP 60 MPAAI+AFT+NYAAYFAEIFRGGIE+IPKGQYEAAKVLK QT+ YI+LPQVFKIVLP Sbjct: 84 MPAAILAFTLNYAAYFAEIFRGGIEAIPKGQYEAAKVLKLKPLQTIRYIILPQVFKIVLP 143- Query: 61 SVFNETITLVKDSSLVYILGVGDLLLESKTAANRDATLAPMFIAGGIYLLLIGLLTILSK 120- SVFNE I LVKDSSLVY+LGVGDLLL SKTAANRDATLAPMFIAG IYLLLIGL+TI+SK Sbjct: 144 SVFNEVINLVKDSSLVYVLGVGDLLLASKTAANRDATLAPMFIAGLIYLLLIGLVTIISK 20- 3 Query: 121 QVEKRFNYYK 130 QVEKRFNYY+ Sbjct: 204 QVEKRFNYYQ 213 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1529 A DNA sequence (GBSx1620) was identified in S. agalactiae <SEQ ID 4709> which encodes the amino acid sequence <SEQ ID 4710>. This protein is predicted to be minidiscs. Analysis of this protein sequence reveals the following: TABLE-US-04580 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.66 Transmembrane 44-60 (39-66) INTEGRAL Likelihood = -7.96 Transmembrane 129-145 (123-147) INTEGRAL Likelihood = -5.15 Transmembrane 13-29 (9-33) INTEGRAL Likelihood = -2.39 Transmembrane 94-110 (94-110) ----- Final Results ----- bacterial membrane --- Certainty = 0.4864(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04581 >GP: AAF49688 GB: AE003532 mnd gene product [Drosophila melanogaster] Identities = 48/145 (33%), Positives = 78/145 (53%), Gaps = 8/145 (5%) Query: 7 IKQTYGLMTTIAMIVGVVIGSGIYFKVDDILKFTGGDVFLGMVILVLGSFSIVFGSLSIS 66 +K+ GL+ +A+IVGV++GSGI+ +LKF+ G + +++ VL + G+L + Sbjct: 39 LKKQIGLLDGVAIIVGVIVGSGIFVSPKGVLKFS-GSIGQSLIVWVLSGVLSMVGALCYA 97 Query: 67 ELAIRTSESGGIFSYYEKYVSPALAATLGLFASFLYL-PTLTAIVSWVAAFYTLGE---- 121- EL +SGG ++Y P L A L L+ + L L PT AI + A Y L Sbjct: 98 ELGTMIPKSGGDYAYIGTAFGP-LPAFLYLWVALLILVPTGNAITALTFAIYLLKPFWPS 156- Query: 122 -SSSLESQIILAAVYILALSLMNIF 145 + +E+ +LAA I L+L+N + Sbjct: 157 CDAPIEAVQLLAAAMICVLTLINCY 181 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1530 A DNA sequence (GBSx1621) was identified in S. agalactiae <SEQ ID 4711> which encodes the amino acid sequence <SEQ ID 4712>. Analysis of this protein sequence reveals the following: TABLE-US-04582 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1531 A DNA sequence (GBSx1622) was identified in S. agalactiae <SEQ ID 4713> which encodes the amino acid sequence <SEQ ID 4714>. This protein is predicted to be TRK potassium uptake system protein. Analysis of this protein sequence reveals the following: TABLE-US-04583 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.06 Transmembrane 232-248 (232-248) ----- Final Results ----- bacterial membrane --- Certainty = 0.1022(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8835> which encodes amino acid sequence <SEQ ID 8836> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-04584 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: -4.65 GvH: Signal Score (-7.5): -3.64 Possible site: 27 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -0.06 threshold: 0.0 INTEGRAL Likelihood = -0.06 Transmembrane 228-244 (228-244) PERIPHERAL Likelihood = 1.27 428 modified ALOM score: 0.51 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1022(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04585 >GP: AAB90401 GB: AE001046 TRK potassium uptake system protein (trkA-2) [Archaeoglobus fulgidus] Identities = 136/446 (30%), Positives = 238/446 (52%), Gaps = 12/446 (2%) Query: 5 MRIIVVGGGKVGTALCRSLVAEKHDVVLIEKKENVLKRVTKQHDIMGIVGNGANYKILEQ 64 MRI++ G G+VG L SL A HDV++IEK + +RV++ D++ I GN AN K+L Sbjct: 1 MRIVIAGAGEVGYHLAMSL-APNHDVIIIEKDVSRFERVSEL-DVVAINGNAANMKVLRD 58 Query: 65 AEVKNCDIFIAITDRDEVNMISAVLAKKMGAKETVVRMRNPEYSNPYFKDKNFLGFSSVV 124- A V+ D+F+A+T DEVN++S + AKK+GAK +VR+ NPEY + ++ LG+ ++ Sbjct: 59 AGVERADVFLAVTGNDEVNLLSGLAAKKVGAKNVIVRVENPEYVDRPIVKEHPLGYDVLI 118- Query: 125 NPELLAAQYIANTIEFPNATSVEHFANGRVMLMEFKILEGNKLCHTSMSQIRKKFGNIVI 18- 4 P+L AQ A I P A V F+ G+V ++E +++EG+K +++ + N+VI Sbjct: 119 CPQLSLAQEAARLIGIPGAIEVVTFSGGKVEMIELQVMEGSKADGKAIADLYLP-QNVVI 17- 7 Query: 185 CAIERDGKLIIPDGDATIQVKDKIFVTGNRIEMILFHNYVKNKVVKNLMVIGAGRIAYYL 24- 4 +I R+G + IP GD ++ D++ + ++ + V + + + GAG I Y Sbjct: 178 ASIYRNGHIEIPRGDTVLRAGDRVAIVSKTEDVEMLKGIFGPPVTRRVTIFGAGTIGSYT 23- 7 Query: 245 LNILKNTNTHVKLVELNQEQAEYFSQEFPNVPVVHGDGTAKNILLEESVTSFDAVATLTG 30- 4 IL T VKL+E + E+ E S E V +V GD T L+EE + DAV T Sbjct: 238 AKILAKGMTSVKLIESSMERCEALSGELEGVRIVCGDATDIEFLIEEEIGKSDAVLAATE 29- 7 Query: 305 VDEENIITSMFLESIGIPKNITKVNRTSLLEIIDDKQLSSIITPKRIAVDHVMHFVRGRV 36- 4 DE+N++ S+ +++G I KV + +++ + + + P+ + + V +R Sbjct: 298 SDEKNLLISLLSKNLGARIAIAKVEKREYVKLFEAVGVDVALNPRSVTYNEVSKLLR--- 35- 4 Query: 365 NAQDSNLEAMHHIANDRIETLQFEIKETSKLANRSLASLKLKQNILIAAIIRNNKTIFPT 42- 4 +E + I + + + ++L ++L L L ++ +I AI+R N+ + P Sbjct: 355 ---TMRIETLAEIEGTAVVEV---VVRNTRLVGKALKDLPLPKDAIIGAIVRGNECLIPR 40- 8 Query: 425 GEDVLTVGDRIVVITLLKNITRTSDM 450 G+ + DR++V I + ++ Sbjct: 409 GDTTIEYEDRLLVFAKWDEIEKIEEI 434 Identities = 48/212 (22%), Positives = 99/212 (46%), Gaps = 15/212 (7%) Query: 3 VKMRIIVVGGGKVGTALCRSLVAEKHDVVLIEKKENVLKRVTKQHDIMGIV-GNGANYKI 61 V R+ + G G +G+ + L V LIE + ++ + + + IV G+ + + Sbjct: 221 VTRRVTIFGAGTIGSYTAKILAKGMTSVKLIESSMERCEALSGELEGVRIVCGDATDIEF 28- 0 Query: 62 LEQAEVKNCDIFIAITDRDEVNMISAVLAKKMGAKETVVRMRNPEYSNPYFKDKNFLGFS 121- L + E+ D +A T+ DE N++ ++L+K +GA+ + ++ EY + +G Sbjct: 281 LIEEEIGKSDAVLAATESDEKNLLISLLSKNLGARIAIAKVEKREYVKLF----EAVGVD 33- 6 Query: 122 SVVNPELLAAQYIA---NTIEFPNATSVEHFANGRVMLMEFKILEGNKLCHTSMSQIRKK 17- 8 +NP + ++ T+ +E A V++ +++ G L + + Sbjct: 337 VALNPRSVTYNEVSKLLRTMRIETLAEIEGTAVVEVVVRNTRLV-GKALKDLPLPK---- 39- 1 Query: 179 FGNIVICAIERDGKLIIPDGDATIQVKDKIFV 210 + +I AI R + +IP GD TI+ +D++ V Sbjct: 392 --DAIIGAIVRGNECLIPRGDTTIEYEDRLLV 421 There is also homology to SEQ ID 4716. SEQ ID 8836 (GBS384) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 69 (lane 2; MW 53 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 6; MW 78 kDa). The GBS384-GST fusion product was purified (FIG. 212, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 279), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1532 A DNA sequence (GBSx1623) was identified in S. agalactiae <SEQ ID 4717> which encodes the amino acid sequence <SEQ ID 4718>. Analysis of this protein sequence reveals the following: TABLE-US-04586 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4948(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1533 A DNA sequence (GBSx1624) was identified in S. agalactiae <SEQ ID 4719> which encodes the amino acid sequence <SEQ ID 4720>. Analysis of this protein sequence reveals the following: TABLE-US-04587 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.58 Transmembrane 37-53 (33-61) INTEGRAL Likelihood = -11.57 Transmembrane 183-199 (179-214) INTEGRAL Likelihood = -10.03 Transmembrane 397-413 (392-424) INTEGRAL Likelihood = -6.79 Transmembrane 14-30 (5-31) INTEGRAL Likelihood = -6.42 Transmembrane 71-87 (69-93) INTEGRAL Likelihood = -4.99 Transmembrane 278-294 (274-295) INTEGRAL Likelihood = -4.19 Transmembrane 133-149 (132-152) INTEGRAL Likelihood = -4.09 Transmembrane 327-343 (324-344) INTEGRAL Likelihood = -2.44 Transmembrane 236-252 (234-252) INTEGRAL Likelihood = -0.59 Transmembrane 456-472 (456-472) ----- Final Results ----- bacterial membrane --- Certainty = 0.6031(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10065> which encodes amino acid sequence <SEQ ID 10066> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04588 >GP: AAB90400 GB: AE001046 TRK potassium uptake system protein (trkH) [Archaeoglobus fulgidus] Identities = 166/480 (34%), Positives = 262/480 (54%), Gaps = 10/480 (2%) Query: 1 MNKSMIRFLLSKLLLIEAALLAIPLTVGLIYREP-QSVMMSIVITMIILIILGLLGSLFK 59 MN + +L KLL++ + +PL ++ EP ++ +++++ +LG G + Sbjct: 1 MNLRLTASILGKLLMLFSFSFILPLIAAHVFEEPYHPFLIPAALSLLVGAVLGY-GIKTE 59 Query: 60 PKNYHIYTKEGMLIVALCWILWSFFGALPFVISGQIPNIIDAFFEVSSGFTTTGATILDD 119- + + KE IVAL W+ S FG++P++I G P +DAFFE SGFTTTGA++L Sbjct: 60 SEFDSLRHKESFAIVALIWLFMSIFGSIPYIIFGISP--VDAFFESMSGFTTTGASVLTP 117- Query: 120 VSVLSPALLFWRSFTHLIGGMGVLVFALAIMENSKNSHLEVMRAEVPGPVFGKVVSKLKK 17- 9 L +LL WRS T IGGMG++V LAI N + +AE PG K+ +++ Sbjct: 118 EE-LPKSLLLWRSLTQWIGGMGIIVLFLAIFPNVAKRSTVLFQAEYPGVSLSKLKPRIRD 17- 6 Query: 180 TAQILYLLYLLMFAVFAVILYFAGMPFFDSIIIAMGTAGTGGFAVYNDSIAHYNSPLITN 23- 9 TA LY +YLL+ +LY G+ FD+I T TGG++ +++SIA + + Sbjct: 177 TALSLYKVYLLLTIAEVALLYALGLSLFDAINHTFTTLSTGGYSTHSESIAFFKDVRVEA 23- 6 Query: 240 LVSIGMLIFGVNFNLYYLLLLRKIKAFFGDEELKTYLRIVAIATFMIALNVIGMYDNFRQ 29- 9 +V+ + G NF L Y LL K F + E + Y+ +A+A+ +IA + Y F + Sbjct: 237 VVAFFAFLGGANFALIYFLLSGK-PVIFRNTEFRAYVCFLALASVVIAAVNLDRYSIF-E 29- 4 Query: 300 GLEHIFFEVSAIITTTGFGVTDITRWPLFSQVILLFLMFIGGSAGSTAGGFKVMRSLILA 35- 9 L + F+ +I+TTTGF D W +++IL+ LMFIGGS+GST GG KV+R +L Sbjct: 295 SLRYSIFQAVSIMTTTGFTTADFDAWSDSAKLILVVLMFIGGSSGSTGGGIKVIRIYLLI 35- 4 Query: 360 KIARNQVLSTLYPNRVMSLHINKSVLDKNTQHGVLKYLTIYLAIFMALVLVLTLDTNDFL 41- 9 K A +Q+L P V ++ + K + + +Y+ IF ++++L D + Sbjct: 355 KYAVHQILRAAEPRTVRAVKFEGRAIKKEILDDIAAFFVLYILIFAVSSILVSLSGYDIV 41- 4 Query: 420 VVISAAASCFNNIGP---LLGSNETFSFFSPFSKLLLSFAMIAGRLEIYPVLLMFIPKTW 47- 6 ISA A+ N+GP L G+ E ++ F +K+LL+ M GRLEI+ V+ +FIP W Sbjct: 415 TSISATAATLGNVGPGLGLAGAAENYASFPSLTKILLAVNMWIGRLEIFTVVSLFIPTFW 47- 4 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1534 A DNA sequence (GBSx1625) was identified in S. agalactiae <SEQ ID 4721> which encodes the amino acid sequence <SEQ ID 4722>. Analysis of this protein sequence reveals the following: TABLE-US-04589 Possible site: 22 >>> Seems to have no N-terminal signal sequence (or aa 1-20) ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2870(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04590 >GP: AAD36530 GB: AE001797 conserved hypothetical protein [Thermotoga maritima] Identities = 43/75 (57%), Positives = 57/75 (75%), Gaps = 1/75 (1%) Query: 2 LKSFLIFLVRFYQKNISPAFPASCRYRPTCSTYMIEAIQKHG-LKGVLMGIARILRCHPL 60 +K LI L+RFYQ+ ISP P +CR+ PTCS Y I+A++KHG LKG +G+ RILRC+PL Sbjct: 1 MKKLLIMLIRFYQRYISPLKPPTCRFTPTCSNYFIQALEKHGLLKGTFLGLRRILRCNPL 60 Query: 61 AHGGNDPVPDHFSLR 75 + GG DPVP+ FS + Sbjct: 61 SKGGYDPVPEEFSFK 75 A related DNA sequence was identified in S. pyogenes <SEQ ID 4723> which encodes the amino acid sequence <SEQ ID 4724>. Analysis of this protein sequence reveals the following: TABLE-US-04591 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3639(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04592 Identities = 53/78 (67%), Positives = 60/78 (75%) Query: 1 MLKSFLIFLVRFYQKNISPAFPASCRYRPTCSTYMIEAIQKHGLKGVLMGIARILRCHPL 60 M+K LI V+ YQK ISP P SCRY+PTCS YM+ AI+KHG KG+LMGIARILRCHP Sbjct: 1 MMKKLLIVSVKAYQKYISPLSPPSCRYKPTCSAYMLTAIEKHGTKGILMGIARILRCHPF 60 Query: 61 AHGGNDPVPDHFSLRRNK 78 GG DPVP+ FSL RNK Sbjct: 61 VAGGVDPVPEDFSLMRNK 78 SEQ ID 4722 (GBS233) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 58 (lane 3; MW 35.6 kDa). The GBS233-GST fusion product was purified (FIG. 207, lane 10) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 280), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1535 A DNA sequence (GBSx1626) was identified in S. agalactiae <SEQ ID 4725> which encodes the amino acid sequence <SEQ ID 4726>. This protein is predicted to be ribosomal large subunit pseudouridine synthase B (rluB). Analysis of this protein sequence reveals the following: TABLE-US-04593 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2957(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04594 >GP: BAB05295 GB: AP001512 pseudouridylate synthase [Bacillus halodurans] Identities = 130/239 (54%), Positives = 175/239 (72%), Gaps = 2/239 (0%) Query: 2 RINKYIAHAGIASRRKAEELIKQGMVTINGQVVNELATQVKAG-DLVEIEGSPIYNEEKV 60 R+ K IA AGIASRRKAE+LI +G V +NGQVV EL +V D +E+EG P+ EE V Sbjct: 3 RLQKVIAQAGIASRRKAEQLILEGKVKVNGQVVKELGIKVNPNQDDIEVEGVPVEKEEPV 62 Query: 61 YYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDKM 120- Y+LL KP GVISSV DDKGRK V D L ++++R+YPVGRLD+DT+GLL+LTNDG+F + + Sbjct: 63 YFLLYKPTGVISSVKDDKGRKVVTDFL-EIEQRVYPVGRLDYDTSGLLLLTNDGEFANLL 121- Query: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYTIIKVDHEKNRSVVELT 18- 0 +HPR++I+KVY+A+VKGI T++ L+ L RGV ++ T PA+ ++ VD K ++V+LT Sbjct: 122 MHPRHKIEKVYVAKVKGIPTRDQLKLLARGVKLEDGPTAPAKVKMLSVDRRKQTAIVKLT 18- 1 Query: 181 IHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKKEISQLHNAAINK 239- IHEGRN QV++MFE +G V KL R QF LDL+G+ PG+ R L E+ L A+ K Sbjct: 182 IHEGRNRQVRRMFETIGCEVMKLKREQFAFLDLSGMNPGDVRPLKPIEVKHLRELAVTK 240- A related DNA sequence was identified in S. pyogenes <SEQ ID 4727> which encodes the amino acid sequence <SEQ ID 4728>. Analysis of this protein sequence reveals the following:

TABLE-US-04595 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1587(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04596 Identities = 210/239 (87%), Positives = 228/239 (94%) Query: 1 MRINKYIAHAGIASRRKAEELIKQGMVTINGQVVNELATQVKAGDLVEIEGSPIYNEEKV 60 MRINKYIAHAGIASRRKAEELIKQG+VT+NGQV+ +LAT VK+GD+VEIEGSPIYNEEKV Sbjct: 9 MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV 68 Query: 61 YYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDKM 120- YYLLNKPRG ISSVSDDKGRKTV+DLLPQVKERIYPVGRLDWDT+G+LILTNDGDFTD M Sbjct: 69 YYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM 128- Query: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYTIIKVDHEKNRSVVELT 18- 0 IHPRNEIDKVYLARVKGIATKENLRPLTRG+VIDGKKTKPARY I++V+ +K+RS+VELT Sbjct: 129 IHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKSRSIVELT 18- 8 Query: 181 IHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKKEISQLHNAAINK 239- IHEGRNHQVKKMFE VGLLVDKLSRT+FGT+DL GLRPGEARRLNKKEISQLHN A K Sbjct: 189 IHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKKEISQLHNLANTK 247- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1536 A DNA sequence (GBSx1627) was identified in S. agalactiae <SEQ ID 4729> which encodes the amino acid sequence <SEQ ID 4730>. Analysis of this protein sequence reveals the following: TABLE-US-04597 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1476(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04598 >GP: BAB05280 GB: AP001512 unknown conserved protein [Bacillus halodurans] Identities = 75/180 (41%), Positives = 107/180 (58%), Gaps = 10/180 (5%) Query: 6 SIEALLFVAGEDGLSLRQMAELLSLTPSALIQQLEKLAKRYEEDDDSSLLLLETAQTYKL 65 +IE +LFV G++G++L ++ +LL L+ + LE+L Y D+ L + E A ++L Sbjct: 9 AIEGILFVRGDEGVTLEELCDLLELSTDVVYAALEELRLSYT-DEARGLRIEEVAHAFRL 67 Query: 66 VTKDSYMTLLRDYAKAPINQSLSRASLEVLSIIAYKQPITRIEIDDIRGVNSSGAITRLI 125- TK + A + + LS+A+LE L+IIAY+QPITRIE+D++RGV S AI L Sbjct: 68 STKPELAPYFKKLALSTLQSGLSQAALETLAIIAYRQPITRIEVDEVRGVKSEKAIQTLT 127- Query: 126 AFGLIKEAGKKEVLGRPNLYETTNYFLDYMGINQLDDL------IDASSIELVDEEVSLF 17- 9 + LIKE G+ + GRP LY TT FLD+ G+ L +L ID SSI EE LF Sbjct: 128 SRLLIKEVGRAQGTGRPILYGTTPQFLDHFGLKSLKELPPLPEDIDESSI---GEEADLF 18- 4 A related DNA sequence was identified in S. pyogenes <SEQ ID 4731> which encodes the amino acid sequence <SEQ ID 4732>. Analysis of this protein sequence reveals the following: TABLE-US-04599 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1062(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04600 Identities = 130/179 (72%), Positives = 159/179 (88%) Query: 1 MTYLGSIEALLFVAGEDGLSLRQMAELLSLTPSALIQQLEKLAKRYEEDDDSSLLLLETA 60 MTYL IEALLFVAGE+GLSLR +A +LSLTP+AL QQLEKL+++YE+D SSL L+ETA Sbjct: 1 MTYLSQIEALLFVAGEEGLSLRHLASMLSLTPTALQQQLEKLSQKYEKDQHSSLCLIETA 60 Query: 61 QTYKLVTKDSYMTLLRDYAKAPINQSLSRASLEVLSIIAYKQPITRIEIDDIRGVNSSGA 120- TY+LVTK+ + LLR YAK P+NQSLSRASLEVLSI+AYKQPITRIEIDDIRGVNSSGA Sbjct: 61 NTYRLVTKEGFAELLRAYAKTPMNQSLSRASLEVLSIVAYKQPITRIEIDDIRGVNSSGA 120- Query: 121 ITRLIAFGLIKEAGKKEVLGRPNLYETTNYFLDYMGINQLDDLIDASSIELVDEEVSLF 179- +++L+AF LI+EAGKK+V+GRP+LY TT+YFLDYMGIN LD+LI+ S++E DEE++LF Sbjct: 121 LSKLLAFDLIREAGKKDVVGRPHLYATTDYFLDYMGINHLDELIEVSAVEPADEEIALF 179- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1537 A DNA sequence (GBSx1628) was identified in S. agalactiae <SEQ ID 4733> which encodes the amino acid sequence <SEQ ID 4734>. Analysis of this protein sequence reveals the following: TABLE-US-04601 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1012(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04602 >GP: CAB14254 GB: Z99116 similar to hypothetical proteins [Bacillus subtilis] Identities = 89/246 (36%), Positives = 145/246 (58%), Gaps = 19/246 (7%) Query: 3 IKLKDFEGPLDLLLHLVSKYEVDIYDVPIVEVIEQYLAYIATLQAMRLEVAGEYMLMASQ 62 +K+ FEGPLDLLLHL+++ E+DIYD+P+ ++ EQYL Y+ T++ + L++A EY++MA+ Sbjct: 6 VKIDTFEGPLDLLLHLINRLEIDIYDIPVAKITEQYLLYVHTMRVLELDIASEYLVMAAT 65 Query: 63 LMLIKSRNLLPK----VVESNPI-EDDPEMELLSQLEEYRRFKVLSEELANQHQERAKYF 117- L+ IKSR LLPK + E + E+DP EL+ +L EYR++K +++L + +ER K F Sbjct: 66 LLSIKSRMLLPKQEEELFEDELLEEEDPREELIEKLIEYRKYKDAAKDLKEREEERQKSF 125- Query: 118 SKPKQEVIFEDAILLHDKSVMDLFLTFSQMMSQKQKELSNS------QTVIEKEDYRIED 17- 1 +KP ++ + +S L +T M+ QK L +T I ++D IE Sbjct: 126 TKPPSDL--SEYAKEVKQSEQKLSVTVYDMIGAFQKVLKRKKINRPMETTITRQDIPIEA 18- 3 Query: 172 MMIVIERHFNLKKKTT---LQEVFADCQTKSEMITLFLAMLELIKLHQITVEQDSNFSQV 22- 8 M I +LK + T ++F + K ++ FLA+LEL+K + +EQ+ NFS + Sbjct: 184 RMNEIVH--SLKSRGTRINFMDLF-PYEQKEHLVVTFLAVLELMKNQLVLIEQEHNFSDI 24- 0 Query: 229 ILRKEE 234 + E Sbjct: 241 YITGSE 246 A related DNA sequence was identified in S. pyogenes <SEQ ID 4735> which encodes the amino acid sequence <SEQ ID 4736>. Analysis of this protein sequence reveals the following: TABLE-US-04603 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.61 Transmembrane 199-215 (199-218) ----- Final Results ----- bacterial membrane --- Certainty = 0.2444(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04604 >GP: CAB14254 GB: Z99116 similar to hypothetical proteins [Bacillus subtilis] Identities = 86/239 (35%), Positives = 145/239 (59%), Gaps = 15/239 (6%) Query: 3 IKLKDFEGPLDLLLHLVSQYKVDIYEVPIVEVIEQYLNYIETLQVMKLEVAGDYMLMASQ 62 +K+ FEGPLDLLLHL+++ ++DIY++P+ ++ EQYL Y+ T++V++L++A +Y++MA+ Sbjct: 6 VKIDTFEGPLDLLLHLINRLEIDIYDIPVAKITEQYLLYVHTMRVLELDIASEYLVMAAT 65 Query: 63 LMLIKSRRLLPKVVEHI-------EEDLEQDLLEKIEEYSRFKAVSQALAKQHDQRAKWY 115- L+ IKSR LLPK E + EED ++L+EK+ EY ++K ++ L ++ ++R K + Sbjct: 66 LLSIKSRMLLPKQEEELFEDELLEEEDPREELIEKLIEYRKYKDAAKDLKEREEERQKSF 125- Query: 116 SKPKQELI-FEDAILQEDK----TVMDLFLAFSNIMAAKRAVLKNNHTVIERDDYKIEDM 17- 0 +KP +L + + Q ++ TV D+ AF ++ K+ + + T I R D IE Sbjct: 126 TKPPSDLSEYAKEVKQSEQKLSVTVYDMIGAFQKVLKRKK-INRPMETTITRQDIPIEAR 18- 4 Query: 171 MASIKQRLEKENV-IRLSAIFEECQTLNEVISIFLASLELIKLHVVFVEQLSNFGAIIL 228- M I L+ I +F Q + V++ FLA LEL+K +V +EQ NF I + Sbjct: 185 MNEIVHSLKSRGTRINFMDLFPYEQKEHLVVT-FLAVLELMKNQLVLIEQEHNFSDIYI 242- An alignment of the GAS and GBS proteins is shown below. TABLE-US-04605 Identities = 156/235 (66%), Positives = 191/235 (80%), Gaps = 2/235 (0%) Query: 1 MDIKLKDFEGPLDLLLHLVSKYEVDIYDVPIVEVIEQYLAYIATLQAMRLEVAGEYMLMA 60 MDIKLKDFEGPLDLLLHLVS+Y+VDIY+VPIVEVIEQYL YI TLQ M+LEVAG+YMLMA Sbjct: 1 MDIKLKDFEGPLDLLLHLVSQYKVDIYEVPIVEVIEQYLNYIETLQVMKLEVAGDYMLMA 60 Query: 61 SQLMLIKSRNLLPKVVESNPIEDDPEMELLSQLEEYRRFKVLSEELANQHQERAKYFSKP 120- SQLMLIKSR LLPKVVE IE+D E +LL ++EEY RFK +S+ LA QH +RAK++SKP Sbjct: 61 SQLMLIKSRRLLPKVVEH--IEEDLEQDLLEKIEEYSRFKAVSQALAKQHDQRAKWYSKP 118- Query: 121 KQEVIFEDAILLHDKSVMDLFLTFSQMMSQKQKELSNSQTVIEKEDYRIEDMMIVIERHF 18- 0 KQE+IFEDAIL DK+VMDLFL FS +M+ K+ L N+ TVIE++DY+IEDMM I++ Sbjct: 119 KQELIFEDAILQEDKTVMDLFLAFSNIMAAKRAVLKNNHTVIERDDYKIEDMMASIKQRL 17- 8 Query: 181 NLKKKTTLQEVFADCQTKSEMITLFLAMLELIKLHQITVEQDSNFSQVILRKEEK 235 + L +F +CQT +E+I++FLA LELIKLH + VEQ SNF +ILRKE+K Sbjct: 179 EKENVIRLSAIFEECQTLNEVISIFLASLELIKLHVVFVEQLSNFGAIILRKEKK 233 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1538 A DNA sequence (GBSx1629) was identified in S. agalactiae <SEQ ID 4737> which encodes the amino acid sequence <SEQ ID 4738>. This protein is predicted to be pXO1-18. Analysis of this protein sequence reveals the following: TABLE-US-04606 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.14 Transmembrane 128-144 (127-145) ----- Final Results ----- bacterial membrane --- Certainty = 0.2657(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04607 >GP: BAB05248 GB: AP001512 integrase/recombinase [Bacillus halodurans] Identities = 67/271 (24%), Positives = 117/271 (42%), Gaps = 35/271 (12%) Query: 11 LKTMINDINNFIESKK----LSLNSRKSYHYDLKQFYKII--------GGHVNSEKLALY 58 - ++T+ N++ F+ +K LS N+ +SY DLKQ+ + + ++ E + Y Sbjct: 1 METVNNNLQQFLHFQKVERGLSNNTIQSYGRDLKQYIQYVERVEEIRSARNITRETILHY 60 Query: 59 QQSLSEFKL--TARKRKLSAVNQFLFFLYNRGTLKEFYRL-----QETEKITLAQTKSQI 111- L E T+ R ++A+ F FL + + T+++ A T ++ Sbjct: 61 LYHLREQGRAETSIARAVAAIRSFHQFLLREKLSDSDPTVHVEIPKATKRLPKALTIEEV 120- Query: 112 MDLSNFYQDTDYPSGRLIALLIL--SLGLTPAEIANLKKADFDTTFNILS-IEKSQMKRI 16- 8 L N Q D S R A+L L + G+ +E+ L +D + + + K +RI Sbjct: 121 EALLNSPQGRDPFSLRNKAMLELLYATGMRVSELIGLTLSDIHLSMGFVRCLGKGNKERI 18- 0 Query: 169 LKLPEDLLPFLLESLEEDG----------DLVF-EHNGKPYSRQWFFNQLTDFLNEKN-E 21- 6 + + + + +ES +G D VF H+G+P SRQ F+ L N + Sbjct: 181 IPIGQ-VATEAVESYLANGRGKLMKKQSHDHVFVNHHGRPLSRQGFWKMLKQLAKNVNID 23- 9 Query: 217 QQLTAQLLREQFILKQKENGKTMTELSRLLG 247 + LT LR F ENG + + +LG Sbjct: 240 KPLTPHTLRHSFATHLLENGADLRAVQEMLG 270 A related DNA sequence was identified in S. pyogenes <SEQ ID 4739> which encodes the amino acid sequence <SEQ ID 4740>. Analysis of this protein sequence reveals the following: TABLE-US-04608 Possible site: 20 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.90 Transmembrane 111-127 (110-127) ----- Final Results ----- bacterial membrane --- Certainty = 0.1362(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-04609 Identities = 117/243 (48%), Positives = 167/243 (68%), Gaps = 1/243 (0%) Query: 18 INNFIESKKLSLNSRKSYHYDLKQFYRIIGGHVNSEKLALYQQSLSEFKLTARKRKLSAV 77 - I FI SK LS NS+F+Y YDL+QF ++IG VN +KL LYQ S++ L+A+KRKLS Sbjct: 5 IEPFIASKALSQNSQKAYRYDLQQFCQLIGERVNQDKLLLYQNSIANLSLSAKKRKLSTA 64 Query: 78 NQFLFFLYNRGTLKEFYRLQETEKITLAQTK-SQIMDLSNFYQDTDYPSGRLIALLILSL 136- NQFL++LY L ++RL +T K+ + + + I++ FYQ T + G+LI+LLIL L Sbjct: 65 NQFLYYLYQIKYLNSYFRLTDTMKVMRTEKQQAAIINTDIFYQKTPFVWGQLISLLILEL 124- Query: 137 GLTPAEIANLKKADFDTTFNILSIEKSQMKRILKLPEDLLPFLLESLEEDGDLVFEHNGK 19- 6 GLTP+E+A ++ A+ D F +L+++ + R+L L + L+PFL + L +FEH G Sbjct: 125 GLTPSEVAGIEVANLDLNFQMLTLKTKKGVRVLPLSQILIPFLEQQLVGKEVYLFEHRGI 18- 4 Query: 197 PYSRQWFFNQLTDFLNEKNEQQLTAQLLREQFILKQKENGKTMTELSRLLGLKTPITLER 25- 6 P+SRQWFFN L F+ + LTAQ LREQFILK+K GK++ ELS +LGLK+P+TLE+ Sbjct: 185 PFSRQWFFNHLKTFVRSIGYEGLTAQKLREQFILKEKLAGKSIIELSDILGLKSPMTLEK 24- 4 Query: 257 YYR 259 YY+ Sbjct: 245 YYK 247 SEQ ID 4738 (GBS383) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 68 (lane 7; MW 32 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 5; MW 57.1 kDa). The GBS383-GST fusion product was purified (FIG. 212, lane 8) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 308), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1539 A DNA sequence (GBSx1630) was identified in S. agalactiae <SEQ ID 4741> which encodes the amino acid sequence <SEQ ID 4742>. Analysis of this protein sequence reveals the following: TABLE-US-04610 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2465(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04611 >GP: BAB05201 GB: AP001512 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 38/136 (27%), Positives = 73/136 (52%), Gaps = 1/136 (0%) Query: 7 ESFLLNHLDHYLIPAEDVAIFVDTHNADHVMLLLASNGFSRVPVITKEKKYVGTISISDI 66 ++ + N L +IP E VA ++ +H +L+L +G++ +PV+ + K G IS S I Sbjct: 7 QNIMDNDLKELVIPFEKVAHVHLSNPLEHALLVLIKSGYTAIPVLDEHSKLHGVISKSLI 66 Query: 67 MGYQSKGQLTDWE-MAQTDIVEMVNTKIEPINEAATLTAIMHKIVDYPFLPVISDQNDFR 125- + + + E +A + +++N +I I+ A+ + + + +PF+ ++ D F Sbjct: 67 LDALLGVERIEMERLAHLVVKDVMNPEIPTIHHKASFSRALKVSIAHPFICILDDDGSFL 126- Query: 126 GIITRKSILKAINSLL 141 GI+TR +IL IN L Sbjct: 127 GILTRSTILSFINRQL 142 A related DNA sequence was identified in S. pyogenes <SEQ ID 4743> which encodes the amino acid sequence <SEQ ID 4744>. Analysis of this protein sequence reveals the following: TABLE-US-04612 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3539(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04613 Identities = 119/153 (77%), Positives = 137/153 (88%) Query: 1 MIAKEFESFLLNHLDHYLIPAEDVAIFVDTHNADHVMLLLASNGFSRVPVITKEKKYVGT 60 MIAKEFE+FL++HLD+YLIP +D+AIF+DTHNADHVMLLL SNGFSRVPVIT+EKKYVGT Sbjct: 1 MIAKEFETFLMSHLDNYLIPEQDLAIFIDTHNADHVMLLLVSNGFSRVPVITREKKYVGT 60 Query: 61 ISISDIMGYQSKGQLTDWEMAQTDIVEMVNTKIEPINEAATLTAIMHKIVDYPFLPVISD 120- ISISDIM YQSK QLTDWEM+QTDI EMVNTKIE I+ ++LT IMHK++D+PFLPV+ Sbjct: 61 ISISDIMMYQSKRQLTDWEMSQTDIGEMVNTKIETISITSSLTEIMHKLIDFPFLPVVDR 120- Query: 121 QNDFRGIITRKSILKAINSLLHDFTDEYTITPK 153 N F GIITRKSILKA+NSLLHDFTD+YTI K Sbjct: 121 ANRFVGIITRKSILKAVNSLLHDFTDDYTIIKK 153 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1540 A DNA sequence (GBSx1631) was identified in S. agalactiae <SEQ ID 4745> which encodes the amino acid sequence <SEQ ID 4746>. Analysis of this protein sequence reveals the following: TABLE-US-04614 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4421(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04615 >GP: BAB06785 GB: AP001517 unknown conserved protein [Bacillus halodurans] Identities = 55/169 (32%), Positives = 95/169 (55%), Gaps = 1/169 (0%) Query: 5 KLVVMSDSHGDRDIVKDIKNHYLGKVDAIFHNGDSELPSSDPIWEGIHVVTGNCDYDSGY 64 KL+++SDSHG D +K + + + +VDAI H GDSELP D EG+++V GNCD+ + Sbjct: 2 KLLILSDSHGWSDELKAVADKHRQEVDAIIHCGDSELPRDDRALEGMNIVRGNCDFGVDF 61 Query: 65 PEVLVTKIDNAVIVQTHGHLHQINFTWDKLDLLAQQEDADICLYGHLHRADAWKNGKTIF 124- PE + + + + THGHL+ + ++ L A++ A + +GH H A +++ +F Sbjct: 62 PEDFIKTVGDFNVYVTHGHLYNVKMSYVSLTYRAEEVGAQLVCFGHSHVATSFQENGIVF 121- Query: 125 INPGSVLQPRGPINEKLYAVVTITDSKVLVEYYTRQHQPYPNLTKELSR 173 +NPGS+ PR E+ Y + + D ++ + + R +L + R Sbjct: 122 VNPGSLRLPRNR-KEQTYCLAYVRDDQIELTFLDRDGHEVTDLQRTYLR 169 A related DNA sequence was identified in S. pyogenes <SEQ ID 4747> which encodes the amino acid sequence <SEQ ID 4748>. Analysis of this protein sequence reveals the following:

TABLE-US-04616 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3835(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04617 Identities = 117/173 (67%), Positives = 143/173 (82%) Query: 1 MAIRKLVVMSDSHGDRDIVKDIKNHYLGKVDAIFHNGDSELPSSDPIWEGIHVVTGNCDY 60 MA + ++VMSDSHGDRDIV+ IK+ YLG+VDAIFHNGDSEL SSDPIW GI+VV GNCDY Sbjct: 1 MASKTIIVMSDSHGDRDIVQAIKDKYLGQVDAIFHNGDSELNSSDPIWAGIYVVGGNCDY 60 Query: 61 DSGYPEVLVTKIDNAVIVQTHGHLHQINFTWDKLDLLAQQEDADICLYGHLHRADAWKNG 120- D+GYP+ LVT++ I QTHGHL+ INFTWDKLD AQ+ ADICLYGHLHR AW+ G Sbjct: 61 DTGYPDRLVTQLGTVTIAQTHGHLYHINFTWDKLDYFAQEVVADICLYGHLHRPAAWQVG 120- Query: 121 KTIFINPGSVLQPRGPINEKLYAVVTITDSKVLVEYYTRQHQPYPNLTKELSR 173 +T+F+NPGSV QPRG INEKLYA V +TD+++ V+Y+TR H+ YP+L+KE R Sbjct: 121 QTLFMNPGSVTQPRGEINEKLYARVELTDTQIKVDYFTRDHKLYPSLSKEFKR 173 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1541 A DNA sequence (GBSx1632) was identified in S. agalactiae <SEQ ID 4749> which encodes the amino acid sequence <SEQ ID 4750>. This protein is predicted to be HAM1 family protein. Analysis of this protein sequence reveals the following: TABLE-US-04618 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1218(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04619 >GP: CAB14796 GB: Z99118 similar to hypothetical proteins [Bacillus subtilis] Identities = 96/189 (50%), Positives = 130/189 (67%), Gaps = 1/189 (0%) Query: 128 LIATHNEGKTKEFRELFGKLGLKVENLNDYPDLPEVEETGMTFEENARLKAETISKLTGK 18- 7 +IATHN GK KEF+E+ G V++L + E+EETG TFEENA +KAE ++K K Sbjct: 8 IIATHNPGKVKEFKEILEPRGYDVKSLAEIGFTEEIEETGHTFEENAIMKAEAVAKAVNK 67 Query: 188 MVISDDSGLKVDALGGLPGVWSARFSGPDATDARNNAKLLHELAMVFDKERRSAQFHTTL 24- 7 MVI+DDSGL +D LGG PGV+SAR++G D N K+L EL + +KE+R+A+F L Sbjct: 68 MVIADDSGLSIDNLGGRPGVYSARYAGEQKDDQANIEKVLSELKGI-EKEQRTARFRCAL 126- Query: 248 VVSAPNKESLVVEAEWPGYIGTEPKGENGFGYDPLFIVGEGSRTAAELSAQEKNNLSHRG 30- 7 VS P +E+ VE GYI EP+GE GFGYDP+FIV + +T AEL++ EKN +SHR Sbjct: 127 AVSIPGEETKTVEGHVEGYIAEEPRGEYGFGYDPIFIVKDKDKTMAELTSDEKNKISHRA 18- 6 Query: 308 QAVRKLMEV 316 A++KL ++ Sbjct: 187 DALKKLSKL 195 A related DNA sequence was identified in S. pyogenes <SEQ ID 4751> which encodes the amino acid sequence <SEQ ID 4752>. Analysis of this protein sequence reveals the following: TABLE-US-04620 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2590 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04621 Identities = 214/325 (65%), Positives = 253/325 (77%), Gaps = 5/325 (1%) Query: 1 MTKTIFESKTEGNWFLGSFQAFNYFTCFG-NDESYEAIQDVFHRLLSTLKVE---GLQLH 56 M++ I+E K E NWF+G N + +G + + I D+ + +TL E G + Sbjct: 14 MSEKIYEYKDENNWFIGKMTGHNLISGWGVKHTTIKKIDDLLDGIAATLDWENPKGYDVS 73 Query: 57 VVQMTSDFQLLAFLVDMINQEYSRHIKVTQHKGAILVSEDDQLFLVHLPKEGTSLEKFFD 116- VV+ S L+ F++DMINQE R IKVT H G IL+ E+ +L V+LP+ G S FF Sbjct: 74 VVRHQSPLSLITFIIDMINQETQREIKVTPHAGTILLMENAKLLAVYLPEGGVSTATFF- 132- Query: 117 LKNDNNFGDTILIATHNEGKTKEFRELFGKLGLKVENLNDYPDLPEVEETGMTFEENARL 17- 6 ++ FGD ILIAT NEGKTKEFR LFG+LG +VENLNDYP+LPEV ETG TFEENARL Sbjct: 133 ATSEQGFGDIILIATRNEGKTKEFRNLFGQLGYRVENLNDYPELPEVAETGTTFEENARL 19- 2 Query: 177 KAETISKLTGKMVISDDSGLKVDALGGLPGVWSARFSGPDATDARNNAKLLHELAMVFDK 23- 6 KAETIS+LTGKMV++DDSGLKVDALGGLPGVWSARFSGPDATDA+NNAKLLHELAMVFD+ Sbjct: 193 KAETISRLTGRMVLADDSGLKVDALGGLPGVWSARFSGPDATDAKNNAKLLHELAMVFDQ 25- 2 Query: 237 ERRSAQFHTTLVVSAPNKESLVVEAEWPGYIGTEPKGENGFGYDPLFIVGEGSRTAAELS 29- 6 ++RSAQFHTTLVV+APNK+SLVVEA+WPGYI T+PKGENGFGYDP+FIVGE AAEL Sbjct: 253 KKRSAQFHTTLVVAAPNKDSLVVEADWPGYIATQPKGENGFGYDPVFIVGETGHHAAELE 31- 2 Query: 297 AQEKNNLSHRGQAVRKLMEVFPKWQ 321 A +KN LSHRGQAVRKLMEVFP WQ Sbjct: 313 ADQKNQLSHRGQAVRKLMEVFPAWQ 337 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1542 A DNA sequence (GBSx1633) was identified in S. agalactiae <SEQ ID 4753> which encodes the amino acid sequence <SEQ ID 4754>. This protein is predicted to be glutamate racemase (murI). Analysis of this protein sequence reveals the following: TABLE-US-04622 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.86 Transmembrane 114-130 (114-130) ----- Final Results ----- bacterial membrane --- Certainty = 0.1744 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10067> which encodes amino acid sequence <SEQ ID 10068> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04623 >GP: AAF72713 GB: AF263927 glutamate racemase [Carnobacterium sp. St2] Identities = 160/267 (59%), Positives = 202/267 (74%), Gaps = 3/267 (1%) Query: 27 MDSRPIGFLDSGVGGLTVVKEMFRQLPEEEVIFIGDQARAPYGPRPAQQIREFTWQMVNF 86 - M + IGF+DSGVGGLTVVKE RQLP E + ++GD AR PYGPRP Q+R+FTW+M +F Sbjct: 1 MKKQAIGFIDSGVGGLTVVKEAMRQLPNESIYYVGDTARCPYGPRPEDQVRKFTWEMTHF 60 Query: 87 LLTKNVKMIVIACNTATAVAWQEIKEKLDIPVLGVILPGASAAIKSTNLGKVGIIGTPMT 146- LL KN+KM+VIACNTATA A ++IK+KL IPV+GVILPG+ AAIK+T+ ++G+IGT T Sbjct: 61 LLDKNIKMLVIACNTATAAALKDIKKKLAIPVIGVILPGSRAAIKATHTNRIGVIGTEGT 120- Query: 147 VKSDAYRQKIQALSPNTAVVSLACPKFVPIVESNQMSSSLAKKVVYETLSPLVGK-LDTL 20- 5 VKS+ Y++ I + V SLACPKFVP+VESN+ SS++AKKVV ETL PL + LDTL Sbjct: 121 VKSNQYKKMIHSKDTKALVTSLACPKFVPLVESNEYSSAIAKKVVAETLRPLKNEGLDTL 18- 0 Query: 206 ILGCTHYPLLRPIIQNVMGAEVKLIDSGAETVRDISVLLNYFEINHNWQNKH-GGHHFYT 26- 4 ILGCTHYPLLRPIIQN +G V LIDSGAETV ++S +L+YF + + QNK +FYT Sbjct: 181 ILGCTHYPLLRPIIQNTLGDSVTLIDSGAETVSEVSTILDYFNLAVDSQNKEKAERNFYT 24- 0 Query: 265 TASPKGFKEIAEQWLS-QEINVERIVL 290 T S + F IA +WL ++ VE I L Sbjct: 241 TGSSQMFHAIASEWLQLDDLAVEHITL 267 A related DNA sequence was identified in S. pyogenes <SEQ ID 4755> which encodes the amino acid sequence <SEQ ID 4756>. Analysis of this protein sequence reveals the following: TABLE-US-04624 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.70 Transmembrane 88-104 (86-104) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04625 >GP: AAF72713 GB: AF263927 glutamate racemase [Carnobacterium sp. St2] Identities = 149/267 (55%), Positives = 202/267 (74%), Gaps = 3/267 (1%) Query: 1 MDTRPIGFLDSGVGGLTVVCELIRQLPHEKIVYIGDSARAPYGPRPKKQIKEYTWELVNF 60 M + IGF+DSGVGGLTVV E +RQLP+E I Y+GD+AR PYGPRP+ Q++++TWE+ +F Sbjct: 1 MKKQAIGFIDSGVGGLTVVKEAMRQLPNESIYYVGDTARCPYGPRPEDQVRKFTWEMTHF 60 Query: 61 LLTQNVKMIVFACNTATAVAWEEVKAALDIPVLGVVLPGASAAIKSTTKGQVGVIGTPMT 120- LL +N+KM+V ACNTATA A +++K L IPV+GV+LPG+ AAIK+T ++GVIGT T Sbjct: 61 LLDKNIKMLVIACNTATAAALKDIKKKLAIPVIGVILPGSRAAIKATHTNRIGVIGTEGT 120- Query: 121 VASDIYRKKIQLLAPSIQVRSLACPKFVPIVESNEMCSSIAKKIVYDSLAPLVGK-IDTL 17- 9 V S+ Y+K I V SLACPKFVP+VESNE S+IAKK+V ++L PL + +DTL Sbjct: 121 VKSNQYKKMIHSKDTKALVTSLACPKFVPLVSSNEYSSAIAKKVVAETLRPLKNEGLDTL 18- 0 Query: 180 VLGCTHYPLLRPIIQNVMGPSVKLIDSGAECVRDISVLLNYFDIN-GNYHQKAVEHRFFT 23- 8 +LGCTHYPLLRPIIQN +G SV LIDSGAE V ++S +L+YF++ + +++ E F+T Sbjct: 181 ILGCTHYPLLRPIIQNTLGDSVTLIDSGAETVSEVSTILDYFNLAVDSQNKEKAERNFYT 24- 0 Query: 239 TANPEIFQEIASIWLK-QKINVEHVTL 264 T + ++F IAS WL+ + VEH+TL Sbjct: 241 TGSSQMFHAIASEWLQLDDLAVEHITL 267 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04626 Identities = 195/264 (73%), Positives = 231/264 (86%) Query: 27 MDSRPIGFLDSGVGGLTVVKEMFRQLPEEEVIFIGDQARAPYGPRPAQQIREFTWQMVNF 86 - MD+RPIGFLDSGVGGLTVV E+ RQLP E++++IGD ARAPYGPRP +QI+E+TW++VNF Sbjct: 1 MDTRPIGFLDSGVGGLTVVCELIRQLPHEKIVYIGDSARAPYGPRPKKQIKEYTWELVNF 60 Query: 87 LLTKNVKMIVIACNTATAVAWQEIKEKLDIPVLGVILPGASAAIKSTNLGKVGIIGTPMT 146- LLT+NVKMIV ACNTATAVAW+E+K LDIPVLGV+LPGASAAIKST G+VG+IGTPMT Sbjct: 61 LLTQNVKMIVFACNTATAVAWEEVKAALDIPVLGVVLPGASAAIKSTTKGQVGVIGTPMT 120- Query: 147 VKSDAYRQKIQALSPNTAVVSLACPKFVPIVESNQMSSSLAKKVVYETLSPLVGKLDTLI 20- 6 V SD YR+KIQ L+P+ V SLACPKFVPIVESN+M SS+AKK+VY++L+PLVGK+DTL+ Sbjct: 121 VASDIYRKKIQLLAPSIQVRSLACPKFVPIVESNEMCSSIAKKIVYDSLAPLVGKIDTLV 18- 0 Query: 207 LGCTHYPLLRPIIQNVMGAEVKLIDSGAETVRDISVLLNYFEINHNWQNKHGGHHFYTTA 26- 6 LGCTHYPLLRPIIQNVMG VKLIDSGAE VRDISVLLNYF+IN N+ K H F+TTA Sbjct: 181 LGCTHYPLLRPIIQNVMGPSVKLIDSGAECVRDISVLLNYFDINGNYHQKAVEHRFFTTA 24- 0 Query: 267 SPKGFKEIAEQWLSQEINVERIVL 290 +P+ F+EIA WL Q+INVE + L Sbjct: 241 NPEIFQEIASIWLKQKINVEHVTL 264 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1543 A DNA sequence (GBSx1634) was identified in S. agalactiae <SEQ ID 4757> which encodes the amino acid sequence <SEQ ID 4758>. Analysis of this protein sequence reveals the following: TABLE-US-04627 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.36 Transmembrane 3-19 (1-27) ----- Final Results ----- bacterial membrane --- Certainty = 0.5543 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04628 >GP: CAB13675 GB: Z99113 alternate gene name: yoxG [Bacillus subtilis] Identities = 26/72 (36%), Positives = 42/72 (58%) Query: 1 MSITIWILLIIVALFGGLVGGIFIARKQIEKEIGEHPRLTPDAIREMMSQMGQKPSEAKV 60 M++ + IL+ +VAL G+ G FIARK + + ++P + +R MM QMG KPS+ K+ Sbjct: 1 MTLWVGILVGVVALLIGVALGFFIARKYMMSYLKKNPPINEQMLRMMMMQMGMKPSQKKI 60 Query: 61 QQTYRNIVKHAK 72 Q + + K Sbjct: 61 NQMMKAMNNQTK 72 A related DNA sequence was identified in S. pyogenes <SEQ ID 4759> which encodes the amino acid sequence <SEQ ID 4760>. Analysis of this protein sequence reveals the following: TABLE-US-04629 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.72 Transmembrane 7-23 (1-27) ----- Final Results ----- bacterial membrane --- Certainty = 0.5288(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04630 Identities = 62/79 (78%), Positives = 69/79 (86%) Query: 1 MSITIWILLIIVALFGGLVGGIFIARKQIEKEIGEHPRLTPDAIREMMSQMGQKPSEAKV 60 MS IWILL+IVAL G+ GGIFIARKQIEKEIGEHPRLTP+AIREMMSQMGQKPSEAK+ Sbjct: 1 MSTAIWILLLIVALGVGVFGGIFIARKQIEKEIGEHPRLTPEAIREMMSQMGQKPSEAKI 60 Query: 61 QQTYRNIVKHAKTAIKTKK 79 QQTYRNI+K +K A+ K Sbjct: 61 QQTYRNIIKQSKAAVSKGK 79 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1544 A DNA sequence (GBSx1635) was identified in S. agalactiae <SEQ ID 4761> which encodes the amino acid sequence <SEQ ID 4762>. Analysis of this protein sequence reveals the following: TABLE-US-04631 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.86 Transmembrane 82-98 (79-103) ----- Final Results ----- bacterial membrane --- Certainty = 0.4142(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1545 A DNA sequence (GBSx1636) was identified in S. agalactiae <SEQ ID 4763> which encodes the amino acid sequence <SEQ ID 4764>. Analysis of this protein sequence reveals the following: TABLE-US-04632 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.83 Transmembrane 56-72 (50-105) INTEGRAL Likelihood = -7.27 Transmembrane 27-43 (17-48) INTEGRAL Likelihood = -6.26 Transmembrane 76-92 (73-105) INTEGRAL Likelihood = -4.83 Transmembrane 119-135 (118-141) INTEGRAL Likelihood = -1.65 Transmembrane 160-176 (160-176) ----- Final Results ----- bacterial membrane --- Certainty = 0.5331(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8837> which encodes amino acid sequence <SEQ ID 8838> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4765> which encodes the amino acid sequence <SEQ ID 4766>. Analysis of this protein sequence reveals the following: TABLE-US-04633 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.99 Transmembrane 45-61 (37-94) INTEGRAL Likelihood = -7.06 Transmembrane 74-90 (62-94) INTEGRAL Likelihood = -3.45 Transmembrane 110-126 (108-130) INTEGRAL Likelihood = -2.18 Transmembrane 149-165 (149-165) INTEGRAL Likelihood = -1.91 Transmembrane 21-37 (20-37) ----- Final Results ----- bacterial membrane --- Certainty = 0.5394(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-04634 Identities = 111/173 (64%), Positives = 145/173 (83%) Query: 12 MSKKTTQMVSYTSILVAFAIMIPIIMPAKIIIGPASFTLASHVPLFLSIFISVPVAILVA 71 - M+KK TQ+++YTSILVAFAI+IPIIMP K+IIGPASFTLASHVPLFL+IF+S+PVAILVA Sbjct: 1 MTKKPTQLIAYTSILVAFAILIPIIMPLKLIIGPASFTLASHVPLFLAIFMSIPVAILVA 60 Query: 72 LGTGLGFLLAGFPIVIVLRALSHIGFALIAAFLIKSKPSLLMSKWQTLLFAVAINIIHGL 131- LGT LGFLLAG P++IVLRALSH+ FA++AA+ + KP L+ S + FA IN+IHGL Sbjct: 61 LGTTLGFLLAGLPLIIVLRALSHLLFAILAAWWLSRKPQLMTSAVKCFSFAFFINVINGL 120- Query: 132 LEFITVYIITMTSNSSSTYLWSLFSLIGLGSLLHGLVDFYIALFIWKWMTQKL 184 EF+ VYI+T T+ +S +Y WS+ LIGLGSL+HG++DFY+AL +W+++ + L Sbjct: 121 AEFLVVYILTATTATSMSYFWSMLGLIGLGSLIHGILDFYLALVLWRFLAKNL 173 A related GBS gene <SEQ ID 10789> and protein <SEQ ID 10790> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04635 Lipop: Possible site: -1 Crend: 3 SRCFLG: 0 McG: Length of UR: 24 Peak Value of UR: 3.16 Net Charge of CR: 2 McG: Discrim Score: 12.56 GvH: Signal Score (-7.5): -0.16 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 20 ALOM program count: 5 value: -10.83 threshold: 0.0 INTEGRAL Likelihood = -10.83 Transmembrane 45-61 (39-94) INTEGRAL Likelihood = -6.26 Transmembrane 65-81 (62-94) INTEGRAL Likelihood = -4.83 Transmembrane 108-124 (107-130) INTEGRAL Likelihood = -1.65 Transmembrane 149-165 (149-165) INTEGRAL Likelihood = -0.27 Transmembrane 24-40 (24-40) PERIPHERAL Likelihood = 0.42 86 modified ALOM score: 2.67 icm1 HYPID: 7 CFP: 0.533 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5331(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1546 A DNA sequence (GBSx1637) was identified in S. agalactiae <SEQ ID 4767> which encodes the amino acid sequence <SEQ ID 4768>. This protein is predicted to be transcriptional regulator, biotin repressor family. Analysis of this protein sequence reveals the following:

TABLE-US-04636 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2237(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04637 >GP: CAB14749 GB: Z99118 yrxA [Bacillus subtilis] Identities = 72/165 (43%), Positives = 112/165 (67%), Gaps = 2/165 (1%) Query: 6 RRENILTTLKGTKEAISASTLAKIFSVSRQVIVGDIALLRAQQCDIISTPKGYL-MSSAL 64 RR+ +L LK +K ++ LAK +VSRQVIV DI+LL+A+ II+T +GY+ M +A Sbjct: 12 RRDQLLLWLKESKSPLTGGELAKKANVSRQVIVQDISLLKAKNVPIIATSQGYVYMDAAA 71 Query: 65 STHQFTARLV-CQHGIEQTEEELEIILRYQGIIMNVEVEHPIYGMLTAPLNIQSQKDIDN 123- HQ R++ C HG E+TEEEL++I+ + +V++EHP+YG LTA + + ++K++ + Sbjct: 72 QQHQQAERIIACLHGPERTEEELQLIVDEGVTVKDVKIEHPVYGDLTAAIQVGTRKEVSH 131- Query: 124 FTAKLKVSNAELLSSLTDGLHTHMISCQDQSVFDQICEALKKAGI 168 F K+ +NA LS LTDG+H H ++ D+ DQ C+AL++AGI Sbjct: 132 FIKKINSTNAAYLSQLTDGVHLHTLTAPDEHRIDQACQALEEAGI 176 A related DNA sequence was identified in S. pyogenes <SEQ ID 4769> which encodes the amino acid sequence <SEQ ID 4770>. Analysis of this protein sequence reveals the following: TABLE-US-04638 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2971(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04639 Identities = 109/170 (64%), Positives = 136/170 (79%) Query: 1 MKAQERRENILTTLKGTKEAISASTLAKIFSVSRQVIVGDIALLRAQQCDIISTPKGYLM 60 MKA++RR+ I+ L ++A+SA+ L K+ VSRQVIVGDIALLRAQQ DIISTPKGY+M Sbjct: 1 MKAEDRRQKIIECLNSEQKAVSATRLGKLLGVSRQVIVGDIALLRAQQIDIISTPKGYIM 60 Query: 61 SSALSTHQFTARLVCQHGIEQTEEELEIILRYQGIIMNVEVEHPIYGMLTAPLNIQSQKD 120- S+AL +HQF AR+VCQH +E+T++ELEIIL +QGII VEVEHPIYGM+TAPLNI++ D Sbjct: 61 STALYSHQFCARIVCQHNVEETKKELEIILAHQGIITTVEVEHPIYGMITAPLNIKTHSD 120- Query: 121 IDNFTAKLKVSNAELLSSLTDGLHTHMISCQDQSVFDQICEALKKAGILY 170 + NF +KL S AELLSSLT+GLH+H+ISC Q F I L+ AGILY Sbjct: 121 VTNFMSKLSQSKAELLSSLTEGLHSHLISCPSQEAFLAIKHDLELAGILY 170 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1547 A DNA sequence (GBSx1638) was identified in S. agalactiae <SEQ ID 4771> which encodes the amino acid sequence <SEQ ID 4772>. Analysis of this protein sequence reveals the following: TABLE-US-04640 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.44 Transmembrane 143-159 (138-165) INTEGRAL Likelihood = -8.17 Transmembrane 164-180 (160-184) INTEGRAL Likelihood = -7.17 Transmembrane 56-72 (53-78) INTEGRAL Likelihood = -5.63 Transmembrane 24-40 (21-44) INTEGRAL Likelihood = -4.94 Transmembrane 113-129 (108-131) INTEGRAL Likelihood = -2.39 Transmembrane 86-102 (86-103) INTEGRAL Likelihood = -1.06 Transmembrane 203-219 (203-219) ----- Final Results ----- bacterial membrane --- Certainty = 0.4376(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10069> which encodes amino acid sequence <SEQ ID 10070> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04641 >GP: AAC18360 GB: AF064763 putative membrane spanning protein [Lactococcus lactis subsp. cremoris] Identities = 97/188 (51%), Positives = 133/188 (70%) Query: 38 IMLYMFPQNMIAIMQKMPGLYFGAIILELVLVFVASGAARRNTPAALPLFLIYSALNGFT 97 - IM+ F NM AI+Q I+ LV+V G A +N+ ALP+F+ Y+A GF Sbjct: 1 IMITFFLDNMRAILQSGSLFLLVLWIIPLVMVVSLQGLAMKNSKMALPIFIGYAAFMGFL 60 Query: 98 LSFIIARYTQTTVLQAFITSAAVFFAMALIGAKTKKDLSGMRKALMAALIGILIASLVNL 157- +SF + YT T + AFIT++A+FF +++ G TK++LSGM KAL A+ G+++A L+NL Sbjct: 61 ISFTLLMYTATDITLAFITASAMFFGLSVYGRFTKRNLSGMGKALGVAVWGLIVAMLLNL 120- Query: 158 FIGSGGMSYIISIVCVIIFSGLIAYDNQMIKYVYNSQGGQVADGWAVSMALSLYLDFINL 21- 7 F S G++ +IS+V V+IFSGLIA+DNQ I VYN+ GQV+DGWA+SMALSLYLDFIN+ Sbjct: 121 FFASTGLTILISLVGVVIFSGLIAWDNQKITQVYNAHNGQVSDGWAISMALSLYLDFINM 18- 0 Query: 218 FLNILRLF 225 FL +LRLF Sbjct: 181 FLFLLRLF 188 A related DNA sequence was identified in S. pyogenes <SEQ ID 4773> which encodes the amino acid sequence <SEQ ID 4774>. Analysis of this protein sequence reveals the following: TABLE-US-04642 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.97 Transmembrane 143-159 (138-165) INTEGRAL Likelihood = -5.89 Transmembrane 164-180 (160-184) INTEGRAL Likelihood = -5.68 Transmembrane 56-72 (55-77) INTEGRAL Likelihood = -4.78 Transmembrane 113-129 (110-130) INTEGRAL Likelihood = -2.81 Transmembrane 203-219 (203-222) INTEGRAL Likelihood = -2.76 Transmembrane 24-40 (23-41) INTEGRAL Likelihood = -2.76 Transmembrane 86-102 (86-104) ----- Final Results ----- bacterial membrane --- Certainty = 0.4588(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04643 >GP: AAC18360 GB: AF064763 putative membrane spanning protein [Lactococcus lactis subsp. cremoris] Identities = 90/189 (47%), Positives = 133/189 (69%) Query: 38 LMLYPFRENLISILVNQPMIYYGAAIIELILVFVASSAARKNTPAALPIFLIYSALNGFT 97 - +M+ F +N+ +IL + + II L++V A KN+ ALPIF+ Y+A GF Sbjct: 1 IMITFFLDNMRAILQSGSLFLLVLWIIPLVMVVSLQGLAMKNSKMALPIFIGYAAFMGFL 60 Query: 98 LSFIIVAYAQTTVFQAFLSSAAVFFAMSIIGVKTKRDMSGLRKAMFAALIGVVVASLINL 157- +SF ++ Y T + AF++++A+FF +S+ G TKR++SG+ KA+ A+ G++VA L+NL Sbjct: 61 ISFTLLMYTATDITLAFITASAMFFGLSVYGRFTKRNLSGMGKALGVAVWGLIVAMLLNL 120- Query: 158 FIGSGMMSYVISVISVLIFSGLIASDNQMIKRVYQATNGQVGDGWAVAMALSLYLDFINL 21- 7 F S ++ +IS++ V+IFSGLIA DNQ I +VY A NGQV DGWA++MALSLYLDFIN+ Sbjct: 121 FFASTGLTILISLVGVVIFSGLIAWDNQKITQVYNAHNGQVSDGWAISMALSLYLDFINM 18- 0 Query: 218 FISLLRIFG 226 F+ LLR+FG Sbjct: 181 FLFLLRLFG 189 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04644 Identities = 167/229 (72%), Positives = 202/229 (87%) Query: 1 MNDNVIYTQSDSGLNQFFAKIYGLVGIGVGLSAAVSAIMLYMFPQNMIAIMQKMPGLYFG 60 MND+VIYTQSD GLNQFFAKIY LVG+GVGLSA VS +MLY F +N+I+I+ P +Y+G Sbjct: 1 MNDHVIYTQSDVGLNQFFAKIYSLVGMGVGLSAFVSYLMLYPFRENLISILVNQPMIYYG 60 Query: 61 AIILELVLVFVASGAARRNTPAALPLFLIYSALNGFTLSFIIARYTQTTVLQAFITSAAV 120- A I+EL+LVFVAS AAR+NTPAALP+FLIYSALNGFTLSFII Y QTTV QAF++SAAV Sbjct: 61 AAIIELILVFVASSAARKNTPAALPIFLIYSALNGFTLSFIIVAYAQTTVFQAFLSSAAV 120- Query: 121 FFAMALIGAKTKKDLSGMRKALMAALIGILIASLVNLFIGSGGMSYIISIVCVIIFSGLI 18- 0 FFAM+IG KTK+D+SG+RKA+ AALIG+++ASL+NLFIGSG MSY+IS++ V+IFSGLI Sbjct: 121 FFAMSIIGVKTKRDMSGLRKAMFAALIGVVVASLINLFIGSGMMSYVISVISVLIFSGLI 18- 0 Query: 181 AYDNQMIKYVYNSQGGQVADGWAVSMALSLYLDFINLFLNILRLFARND 229 A DNQMIK VY + GQV DGWAV+MALSLYLDFINLF+++LR+F RND Sbjct: 181 ASDNQMIKRVYQATNGQVGDGWAVAMALSLYLDFINLFISLLRIFGRND 229 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1548 A DNA sequence (GBSx1639) was identified in S. agalactiae <SEQ ID 4775> which encodes the amino acid sequence <SEQ ID 4776>. Analysis of this protein sequence reveals the following: TABLE-US-04645 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2495(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10071> which encodes amino acid sequence <SEQ ID 10072> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4777> which encodes the amino acid sequence <SEQ ID 4778>. Analysis of this protein sequence reveals the following: TABLE-US-04646 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3277(Affirmative) < succ> bacterial membrane Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04647 Identities = 127/163 (77%), Positives = 141/163 (85%) Query: 7 YQDDKDFMDLVGHLIDHPRFQKLEAIVQHHHSTRLEHSINVSYTSYKIAKKFGWDASSTA 66 Y +DK++M+ VGHLI HPRFQKL IVQH HSTRLEHSINVSY+SYK+AK+FGWDA STA Sbjct: 3 YTEDKEYMEHVGHLIAHPRFQKLSHIVQHQHSTRLEHSINVSYSSYKLAKRFGWDAKSTA 62 Query: 67 RGGLLHDFFYYDWRVTKFNKSHAWVHPRIAVRNARKLTDLNAREEDIILKHMWGATIAPP 126- RGGLLHDFFYYDWRVTKFNK HAWVHPRIAVRNA+KLT+LN +EEDIILKHMWGATIA P Sbjct: 63 RGGLLHDFFYYDWRVTKFNKGHAWVHPRIAVRNAKKLTELNKKEEDIILKHMWGATIAFP 122- Query: 127 RYKESYIVTMVDKYWAVREASRPLKRIFKKPIRFSRKFLGSHN 169 RYKESYIVTMVDKYWAV+EA PL++ + RK L SHN Sbjct: 123 RYKESYIVTMVDKYWAVKEAVTPLRQKWSNRRFLRRKTLQSHN 165 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1549 A DNA sequence (GBSx1640) was identified in S. agalactiae <SEQ ID 4779> which encodes the amino acid sequence <SEQ ID 4780>. Analysis of this protein sequence reveals the following: TABLE-US-04648 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.03 Transmembrane 213-229 (212-229) ----- Final Results ----- bacterial membrane --- Certainty = 0.2211(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9413> which encodes amino acid sequence <SEQ ID 9414> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04649 >GP: AB14825 GB: Z99118 similar to rRNA methylase [Bacillus subtilis] Identities = 96/228 (42%), Positives = 143/228 (62%), Gaps = 5/228 (2%) Query: 3 QKKYRKSSYLIEGWHLFEEAEKYGAQFLNIFVT-ETAIDR-LRKPERAIVVTDDVLKELT 60 +++ + +++LIEG HL EEA K I V ET I L + ++++D +T Sbjct: 22 KERTKTNTFLIEGEHLVEEALKSPGIVKEILVKDETRIPSDLETGIQCYMLSEDAFSAVT 81 Query: 61 DSQTPQGIVAEIAFQETRWTDIKKGRFLVLEDVQDPGNLGTMVRTADAANFDAVFLSQKS 120- +++TPQ I A E + +K L+++ VQDPGNLGTM+RTADAA DAV L + Sbjct: 82 ETETPQQIAAVCHMPEEKLATARK--VLLIDAVQDPGNLGTMIRTADAAGLDAVVLGDGT 139- Query: 121 ADLYNQKTLRSMQGSHFHLPVFRVEIEQFVNFCKAEGITMIATTLSEQSVNYKNLPKYDY 18- 0 AD +N KTLRS QGSHFH+PV R + +V+ KAEG+ + T L + Y+ +P+ + Sbjct: 140 ADAFNGKTLRSAQGSHFHIPVVRRNLPSYVDELKAEGVKVYGTAL-QNGAPYQEIPQSES 19- 8 Query: 181 FALIMGNEGQGISKTMTEEADVLAHIEMPGQAESLNVAVAAGVVIFSL 228 FALI+GNEG G+ + E+ D+ ++ + GQAESLNVAVAA ++++ L Sbjct: 199 FALIVGNEGAGVDAALLEKTDLNLYVPLYGQAESLNVAVAAAILVYHL 246 A related DNA sequence was identified in S. pyogenes <SEQ ID 4781> which encodes the amino acid sequence <SEQ ID 4782>. Analysis of this protein sequence reveals the following: TABLE-US-04650 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.97 Transmembrane 229-245 (228-245) ----- Final Results ----- bacterial membrane --- Certainty = 0.2190 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04651 Identities = 141/229 (61%), Positives = 178/229 (77%) Query: 1 MLQKKYRKSSYLIEGWHLFEEAEKYGAQFLNIFVTETAIDRLRKPERAIVVTDDVLKELT 60 +LQKK+RK SYLIEGWHLFEEA+K G F +IFV E ++RL + ++V+ VLKELT Sbjct: 17 LLQKKHRKQSYLIEGWHLFEEAQKSGQVFRHIFVLEEMVERLAGEQELVIVSPQVLKELT 76 Query: 61 DSQTPQGIVAEIAFQETRWTDIKKGRFLVLEDVQDPGNLGTMVRTADAANFDAVFLSQKS 120- DS +PQGIVAE+ + + KG++LVLEDVQDPGNLGT++RTADAA FD VFLS+KS Sbjct: 77 DSPSPQGIVAEVEIPKLAFPSDYKGKYLVLEDVQDPGNLGTIIRTADAARFDGVFLSEKS 136- Query: 121 ADLYNQKTLRSMQGSHFHLPVFRVEIEQFVNFCKAEGITMIATTLSEQSVNYKNLPKYDY 18- 0 AD+YNQKTLRSMQGSHFHLP++R ++ Q + ++ATTLS++SV+YK+L ++ Sbjct: 137 ADIYNQKTLRSMQGSHFHLPIWRTDVYQLCRELQEYETPILATTLSKKSVDYKSLTHHER 19- 6 Query: 181 FALIMGNEGQGISKTMTEEADVLAHIEMPGQAESLNVAVAAGVVIFSLI 229 AL++GNEGQGIS M AD L HI MPGQAESLNVAVAAG++IFSLI Sbjct: 197 LALVLGNEGQGISAEMAALADQLVHITMPGQAESLNVAVAAGILIFSLI 245 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8839> and protein <SEQ ID 8840> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04652 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: -7.98 GvH: Signal Score (-7.5): -3.86 Possible site: 37 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -3.03 threshold: 0.0 INTEGRAL Likelihood = -3.03 Transmembrane 213-229 (212-229) PERIPHERAL Likelihood = 5.14 149 modified ALOM score: 1.11 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2211 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00100## SEQ ID 8840 (GBS430) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 77 (lane 5; MW 29 kDa). GBS430-GST was purified as shown in FIG. 220, lane 8. EXAMPLE 1550 A DNA sequence (GBSx1641) was identified in S. agalactiae <SEQ ID 4783> which encodes the amino acid sequence <SEQ ID 4784>. This protein is predicted to be acylphosphatase (acyP). Analysis of this protein sequence reveals the following: TABLE-US-04653 Possible site: 48 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10073> which encodes amino acid sequence <SEQ ID 10074> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04654 >GP: AAD36630 GB: AE001801 acylphosphatase, putative [Thermotoga maritima] Identities = 35/88 (39%), Positives = 52/88 (58%), Gaps = 3/88 (3%) Query: 24 MKKVHLIVSGRVQGVGFRYATYSLALEIGDIYGRVWNNDDGTVEILAQSTDSNKMTQFIQ 83 - MK + + V G VQGVGFRY T +A +G + G V N DDG+V I A+ D N + +F+ Sbjct: 1 MKALKIRVEGIVQGVGFRYFTRRVAKSLG-VKGYVMNMDDGSVFIHAEG-DENALRRFLN 58 Query: 84 KIRKGPSKWSKVTYVDIKLDNFDDFNDF 111 ++ KGP + VT V ++ + + DF Sbjct: 59 EVAKGPPA-AVVTNVSVEETTPEGYEDF 85 A related DNA sequence was identified in S. pyogenes <SEQ ID 4785> which encodes the amino acid sequence <SEQ ID 4786>. Analysis of this protein sequence reveals the following: TABLE-US-04655 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2433 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04656 Identities = 69/95 (72%), Positives = 85/95 (88%) Query: 19 KRGQVMKKVHLIVSGRVQGVGFRYATYSLALEIGDIYGRVWNNDDGTVEILAQSTDSNKM 78 - K +M+KV LIVSGRVQGVGFRYAT++LAL+IGDIYGRVWNN+DGTVEILAQS DS+K+ Sbjct: 7 KEALLMQKVRLIVSGRVQGVGFRYATHTLALDIGDIYGRVWNNNDGTVEILAQSKDSDKI 66 Query: 79 TQFIQKIRKGPSKWSKVTYVDIKLDNFDDFNDFKM 113 FIQ++RKGPSKW+KVTYVD+ + NF+DF DF++ Sbjct: 67 ATFIQEVRKGPSKWAKVTYVDVTMANFEDFQDFQI 101 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1551 A DNA sequence (GBSx1642) was identified in S. agalactiae <SEQ ID 4787> which encodes the amino acid sequence <SEQ ID 4788>. This protein is predicted to be membrane protein homolog (yidC). Analysis of this protein sequence reveals the following: TABLE-US-04657 Possible site: 16 >>> May be a lipoprotein INTEGRAL Likelihood = -12.52 Transmembrane 60-76 (54-83) INTEGRAL Likelihood = -3.66 Transmembrane 178-194 (177-196) INTEGRAL Likelihood = -2.76 Transmembrane 140-156 (137-157) INTEGRAL Likelihood = -2.60 Transmembrane 216-232 (213-232) ----- Final Results ----- bacterial membrane --- Certainty = 0.6010 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related OBS nucleic acid sequence <SEQ ID 10075> which encodes amino acid sequence <SEQ ID 10076> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-04658 >GP: AAF03934 GB: AF139908 membrane protein homolog [Listeria monocytogenes] Identities = 82/222 (36%), Positives = 133/222 (58%), Gaps = 4/222 (1%) Query: 44 PMANLITYFAQHQGLGFGVAIIIVTVIVRVVILPLGLYQSWKASYQAEKMAYFKPLFEPI 103- P + I + A+ G +G+AIII T+++R +I+PL L + KMA KP + I Sbjct: 3 PFTSFIMFVAKFVGGNYGIAIIITTLLIRALIMPLNLRTAKAQMGMQSKMAVAKPEIDEI 62 Query: 104 NERLRNAKTQEEKLAAQTELMTAQRENGLSMFGGIGCLPLLIQMPFFSAIFFAARYTPGV 16- 3 RL+ A ++EE+ Q E+M + ++ +GCLPLLIQMP A ++A R + + Sbjct: 63 QARLKRATSKEEQATIQKEMMAVYSKYNINPMQ-MGCLPLLIQMPILMAFYYAIRGSSEI 121- Query: 164 SSATFLGLNLGQKSLTLTVIIAILYFVQSWLSMQGVPDEQRQQMKTMMYLMPIMMVFMSI 22- 3 +S TFL NLG + L +I ++Y Q ++SM G EQ++QMK + + PIM++F+S Sbjct: 122 ASHTFLWFNLGSPDMVLAIIAGLVYLAQYFVSMIGYSPEQKKQMKIIGLMSPIMILFVSF 18- 1 Query: 224 SLPASVALYWFIGGIFSIIQQLVT--TYVLK-PKLRRKVEEE 262 + P+++ALYW +GG+F Q L+T Y+ K P+++ +EE Sbjct: 182 TAPSALALYWAVGGLFLAGQTLLTKKLYMNKHPEIKVMEQEE 223 A related DNA sequence was identified in S. pyogenes <SEQ ID 4789> which encodes the amino acid sequence <SEQ ID 4790>. Analysis of this protein sequence reveals the following: TABLE-US-04659 Possible site: 31 >>> May be a lipoprotein INTEGRAL Likelihood = -9.55 Transmembrane 62-78 (54-82) INTEGRAL Likelihood = -2.81 Transmembrane 178-194 (177-195) INTEGRAL Likelihood = -0.90 Transmembrane 216-232 (215-232) ----- Final Results ----- bacterial membrane --- Certainty = 0.4821 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04660 >GP: AAF03934 GB: AF139908 membrane protein homolog [Listeria monocytogenes] Identities = 89/218 (40%), Positives = 132/218 (59%), Gaps = 2/218 (0%) Query: 43 KPMSYFIDYFANNAGLGYGLAIIIVTIIVRTLILPLGLYQSWKASYQSEKMAFLKPVFEP 102- +P + FI + A G YG+AIII T+++R LI+PL L + KMA KP + Sbjct: 2 QPFTSFIMFVAKFVGGNYGIAIIITTLLIRALIMPLNLRTAKAQMGMQSKMAVAKPEIDE 61 Query: 103 INKRIKQANSQEEKMAAQTELMAAQRAHGINPLGGIGCLPLLIQMPFFSAMYFAAQYTKG 16- 2 I R+K+A S+EE+ Q E+MA + INP+ +GCLPLLIQMP A Y+A + + Sbjct: 62 IQARLKRATSKEEQATIQKEMMAVYSKYNINPMQ-MGCLPLLIQMPILMAFYYAIRGSSE 120- Query: 163 VSTSTFMGIDLGSRSLVLTAIIAALYFFQSWLSMMAVSEEQREQMKTMMYTMPIMMIFMS 22- 2 +++ TF+ +LGS +VL I +Y Q ++SM+ S EQ++QMK + PIM++F+S Sbjct: 121 IASHTFLWFNLGSPDMVLAIIAGLVYLAQYFVSMIGYSPEQKKQMKIIGLMSPIMILFVS 18- 0 Query: 223 FSLPAGVGLYWLVGGFFSIIQQLITTYLLKPRLHKQIK 260 F+ P+ + LYW VGG F Q L+T L + H +IK Sbjct: 181 FTAPSALALYWAVGGLFLAGQTLLTKKLYMNK-HPEIK 217 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04661 Identities = 203/309 (65%), Positives = 254/309 (81%), Gaps = 2/309 (0%) Query: 1 MKKTLKRILFSSLSLSMLLLLTGCVSVDKAGKPYGVIWNTLGVPMANLITYFAQHQGLGF 60 +K TL RILFS L+LS+LL LTGCV D G P G+IW LG PM+ I YFA + GLG+ Sbjct: 1 LKLTLNRILFSGLALSILLTLTGCVGRDAHGNPKGMIWEFLGKPMSYFIDYFANNAGLGY 60 Query: 61 GVAIIIVTVIVRVVILPLGLYQSWKASYQAEKMAYFKPLFEPINERLRNAKTQEEKLAAQ 120- G+AIIIVT+IVR +ILPLGLYQSWKASYQ+EKMA+ KP+FEPIN+R++ A +QEEK+AAQ Sbjct: 61 GLAIIIVTIIVRTLILPLGLYQSWKASYQSEKMAFLKPVFEPINKRIKQANSQEEKMAAQ 120- Query: 121 TELMTAQRENGLSMFGGIGCLPLLIQMPFFSAIFFAARYTPGVSSATFLGLNLGQKSLTL 18- 0 TELM AQR +G++ GGIGCLPLLIQMPFFSA++FAA+YT GVS++TF+G++LG +SL L Sbjct: 121 TELMAAQRAHGINPLGGIGCLPLLIQMPFFSAMYFAAQYTKGVSTSTFMGIDLGSRSLVL 18- 0 Query: 181 TVIIAILYFVQSWLSMQGVPDEQRQQMKTMMYLMPIMMVFMSISLPASVALYWFIGGIFS 24- 0 T IIA LYF QSWLSM V +EQR+QMKTMMY MPIMM+FMS SLPA V LYW +GG FS Sbjct: 181 TAIIAALYFFQSWLSMMAVSEEQREQMKTMMYTMPIMMIFMSFSLPAGVGLYWLVGGFFS 24- 0 Query: 241 IIQQLVTTYVLKPKLRRKVEEEYTKNPPKAYKANNARKDVTNSTKATESNQAIITSKKTN 30- 0 IIQQL+TTY+LKP+L ++++EEY KNPPKAY++ ++RKDVT S ++N + K+N Sbjct: 241 IIQQLITTYLLKPRLHKQIKEEYAKNPPKAYQSTSSRKDVTPSQNMEQAN--LPKKIKSN 29- 8 Query: 301 RNAGKQKRR 309 RNAGKQ++R Sbjct: 299 RNAGKQRKR 307 A related GBS gene <SEQ ID 8841> and protein <SEQ ID 8842> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04662 Lipop: Possible site: 23 Crend: 6 McG: Discrim Score: 8.74 GvH: Signal Score (-7.5): -1.47 Possible site: 16 >>> May be a lipoprotein ALOM program count: 4 value: -12.52 threshold: 0.0 INTEGRAL Likelihood = -12.52 Transmembrane 60-76 (54-83) INTEGRAL Likelihood = -3.66 Transmembrane 178-194 (177-196) INTEGRAL Likelihood = -2.76 Transmembrane 140-156 (137-157) INTEGRAL Likelihood = -2.60 Transmembrane 216-232 (213-232) PERIPHERAL Likelihood = 0.74 235 modified ALOM score: 3.00 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6010 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00101## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1552 A DNA sequence (GBSx1644) was identified in S. agalactiae <SEQ ID 4791> which encodes the amino acid sequence <SEQ ID 4792>. This protein is predicted to be amino acid ABC transporter, permease protein. Analysis of this protein sequence reveals the following: TABLE-US-04663 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.98 Transmembrane 32-48 (23-53) INTEGRAL Likelihood = -9.18 Transmembrane 195-211 (189-213) INTEGRAL Likelihood = -8.70 Transmembrane 72-88 (62-93) ----- Final Results ----- bacterial membrane --- Certainty = 0.4991 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04664 >GP: CAB12131 GB: Z99105 similar to amino acid ABC transporter (permease) [Bacillus subtilis] Identities = 116/217 (53%), Positives = 168/217 (76%) Query: 2 INWDAIFNLELAVKAFPSVIQGLPYTIGLSLVGFILGAIVGFFVALMKMSHFRLLRYLAN 61 I W+ IFN +LA+++FP VI+G+ YT+ +S V G ++G F++L +MS LLR+ A Sbjct: 5 IQWEYIFNTKLAIESFPYVIKGIGYTLLISFVSMFAGTVIGLFISLARMSKLALLRWPAK 64 Query: 62 IHISLMRGIPLMVLLFLIYFGLPFIGIQLDAVTASIVGFTMMSSAYISEIIRAALLAVDH 121- ++IS MRG+P++V+LF++YFG P+IGI+ AVTA+++GF++ S+AYI+EI R+A+ +V+ Sbjct: 65 LYISFMRGVPILVILFILYFGFPYIGIEFSAVTAALIGFSLNSAAYIAEINRSAISSVEK 124- Query: 122 GQWEAARALGLKTPTIYRGIIIPQATRIALPSLSNVLLDMVKSSSLTAMITVPDIFNNAK 18- 1 GQWEAA +LGL RGII+PQ+ RIALP L+NVLLD++K+SSL AMITVP++ +AK Sbjct: 125 GQWEAASSLGLSYWQTMRGIILPQSIRIALPPLANVLLDLIKASSLAAMITVPELLQHAK 18- 4 Query: 182 IVGGTYSDYMTAYILVALIYWVICTLYAIIQDWWEKR 218 I+GG DYMT YIL ALIYW IC++ A+ Q+ EK+ Sbjct: 185 IIGGREFDYMTMYILTALIYWAICSIAAVFQNILEKK 221 A related DNA sequence was identified in S. pyogenes <SEQ ID 4793> which encodes the amino acid sequence <SEQ ID 4794>. Analysis of this protein sequence reveals the following: TABLE-US-04665 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.79 Transmembrane 186-202 (184-205) INTEGRAL Likelihood = -5.84 Transmembrane 26-42 (21-43) INTEGRAL Likelihood = -4.78 Transmembrane 57-73 (56-84) INTEGRAL Likelihood = -1.59 Transmembrane 86-102 (86-103) ----- Final Results ----- bacterial membrane --- Certainty = 0.3718 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04666 >GP: CAB12131 GB: Z99105 similar to amino acid ABC transporter (permease) [Bacillus subtilis] Identities = 113/214 (52%), Positives = 157/214 (72%) Query: 1 MINIPLMKDSLGFVLSGLPYTLGISLLSFFTGLFLGLGLALLGRSRQPLIHYLVRAYISI 60 + N L +S +V+ G+ YTL IS +S F G +GL ++L S+ L+ + + YIS Sbjct: 10 IFNTKLAIESFPYVIKGIGYTLLISFVSMFAGTVIGLFISLARMSKLALLRWPAKLYISF 69 Query: 61 MRGVPMIVVLFVLYFGLPYYGLELPALLCAYLGFSMVSAAYISEVFRSSIEAIDKGQWEA 120- MRGVP++V+LF+LYFG PY G+E A+ A +GFS+ SAAYI+E+ RS+I +++KGQWEA Sbjct: 70 MRGVPILVILFILYFGFPYIGIEFSAVTAALIGFSLNSAAYIAEINRSAISSVEKGQWEA 129- Query: 121 AKALGLPYALMVKKIILPQAFRIAVPPLGNVIIDMVKSSSLAAMITVPDIFQNAKIIGGR 18- 0 A +LGL Y ++ IILPQ+ RIA+PPL NV++D++K+SSLAAMITVP++ Q+AKIIGGR Sbjct: 130 ASSLGLSYWQTMRGIILPQSIRIALPPLANVLLDLIKASSLAAMITVPELLQHAKIIGGR 18- 9 Query: 181 EWDYMSMYILVAFIYWLIAFLLERYQEFLENKLA 214 E+DYM+MYIL A IYW I + +Q LE K A Sbjct: 190 EFDYMTMYILTALIYWAICSIAAVFQNILEKKYA 223 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04667 Identities = 110/213 (51%), Positives = 156/213 (72%) Query: 7 IFNLELAVKAFPSVIQGLPYTIGLSLVGFILGAIVGFFVALMKMSHFRLLRYLANIHISL 66 + N+ L + V+ GLPYT+G+SL+ F G +G +AL+ S L+ YL +IS+ Sbjct: 1 MINIPLMKDSLGFVLSGLPYTLGISLLSFFTGLFLGLGLALLGRSRQPLIHYLVRAYISI 60 Query: 67 MRGIPLMVLLFLIYFGLPFIGIQLDAVTASIVGFTMMSSAYISEIIRAALLAVDHGQWEA 126- MRG+P++V+LF++YFGLP+ G++L A+ + +GF+M+S+AYISE+ R+++ A+D GQWEA Sbjct: 61 MRGVPMIVVLFVLYFGLPYYGLELPALLCAYLGFSMVSAAYISEVFRSSIEAIDKGQWEA 120- Query: 127 ARALGLKTPTIYRGIIIPQATRIALPSLSNVLLDMVKSSSLTAMITVPDIFNNAKIVGGT 18- 6 A+ALGL + + II+PQA RIA+P L NV++DMVKSSSL AMITVPDIF NAKI+GG Sbjct: 121 AKALGLPYALMVKKIILPQAFRIAVPPLGNVIIDMVKSSSLAAMITVPDIFQNAKIIGGR 18- 0 Query: 187 YSDYMTAYILVALIYWVICTLYAIIQDWWEKRL 219 DYM+ YILVA IYW+I L Q++ E +L Sbjct: 181 EWDYMSMYILVAFIYWLIAFLLERYQEFLENKL 213 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1553 A DNA sequence (GBSx1645) was identified in S. agalactiae <SEQ ID 4795> which encodes the amino acid sequence <SEQ ID 4796>. Analysis of this protein sequence reveals the following: TABLE-US-04668 Possible site: 18 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04669 >GP: CAB12132 GB: Z99105 similar to amino acid ABC transporter (binding protein) [Bacillus subtilis] Identities = 127/276 (46%), Positives = 183/276 (66%), Gaps = 12/276 (4%) Query: 3 KTILLGLVGLSAMTLAACS--NGQSSKETTWDNIKKDGVLKVATPATLYPTSYYDDHK-- 58 K ++ + LAACS N SK+T W+ IK G + VAT TLYPTSY+D Sbjct: 8 KAVIFSFTMAFFLILAACSGKNEADSKDTGWEQIKDKGKIVVATSGTLYPTSYHDTDSGS 67 Query: 59 -KLTGYEIDMMKAIAKKLKIKVKFVEVGVAESFTSVDSGKVDVAVNNFDTTPERLKKYNF 117- KLTGYE+++++ AK+L +KV+F E+G+ T+V+SG+VD A N+ D T +R +K+ F Sbjct: 68 DKLTGYEVEVVREAAKRLGLKVEFKEMGIDGMLTAVNSGQVDAAANDIDVTKDREEKFAF 127- Query: 118 SQPYKYSVGGMIVRADGSSKITAKDLSDWKGKKAGGGAGTQYMKIAKQQGAEPVIYDNVT 17- 7 S PYKYS G IVR D S I K L D KGKKA G A T YM++A++ GA+ VIYDN T Sbjct: 128 STPYKYSYGTAIVRKDDLSGI--KTLKDLKGKKAAGAATTVYMEVARKYGAKEVIYDNAT 18- 5 Query: 178 NDVYLRDVSTGRTDFIPNDYYTQVIAVKYVTKQYPDIKVKM-GDVKYNPTEQGIVMSKKD 23- 6 N+ YL+DV+ GRTD I NDYY Q +A+ +PD+ + + D+KY P +Q +VM K + Sbjct: 186 NEQYLKDVANGRTDVILNDYYLQTLAL----AAFPDLNITIHPDIKYMPNKQALVMKKSN 24- 1 Query: 237 KSLKTKIDAAIKDMKKDGSLKKISEKYYAGQDLTKE 272 +L+ K++ A+K+M KDGSL K+S++++ D++K+ Sbjct: 242 AALQKKMNEALKEMSKDGSLTKLSKQFFNKADVSKK 277 There is also homology to SEQ ID 1190. SEQ ID 4796 (GBS183) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 26 (lane 2; MW 33 kDa). GBS183-His was purified as shown in FIG. 199, lane 7. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1554 A DNA sequence (GBSx1646) was identified in S. agalactiae <SEQ ID 4797> which encodes the amino acid sequence <SEQ ID 4798>. Analysis of this protein sequence reveals the following: TABLE-US-04670 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1514(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04671 >GP: AAF09821 GB: AE001885 6-aminohexanoate-cyclic-dimer hydrolase [Deinococcus radiodurans] Identities = 178/488 (36%), Positives = 265/488 (53%), Gaps = 17/488 (3%) Query: 5 DATAMVQAIKQHKISSQELVEQAIYKIEEQNVSVNAVVSKQYNEARQAAKYANESNA--- 61 DA + Q ++ ++S++++ AI++ + NV++NAVV Y++ A+ + + A Sbjct: 54 DALDLAQLFRRGELSAEDMCTAAIHRAQVVNVALNAVVYPLYDQGLAQARATDAARARGE 113- Query: 62 ----PFAGVPILLKDLGQNQKGQLSTSGSQLFKHYHAKQTDYLVQSFEKLGFIILGRTNT 117- PFAGVP L+KD G G T G++ ++ + D LV+ ++ G + LG+TNT Sbjct: 114 QATGPFAGVPFLVKDFGSRLAGVPHTGGTRAYRDQIPEWDDELVRRWQAAGLLPLGKTNT 17- 3 Query: 118 PEFGFKNISDGQLHGNVNLPFDHSRNAGGSSGGAAAAVSSGMVPIAGASDGGGSIRIPAS 17- 7 PEF +++ +LHG P+D R GGSSGG+A+AV++G+VP+AGA DGGGSIRIPAS Sbjct: 174 PEFALMGVTEPELHGPTRNPWDLGRTPGGSSGGSASAVAAGIVPLAGAGDGGGSIRIPAS 23- 3 Query: 178 FNGLIGLKPSRGRIPVGPSSYRGWQGASSHFALTKSVRDTKRLLYYLQSYQVES----PF 23- 3 GL GLKPSRGR+P G WQGA+ LT+SVRD+ LL Q + P Sbjct: 234 CCGLFGLKPSRGRVPCGDGVGEPWQGAAVEHVLTRSVRDSAALLDLEQGPDAGAALFLPS 29- 3 Query: 234 PLKKLSKESLFEFSVSKPLKIAVLMDSPLKTKVSSEAKAAIKEAADFLSQKGNHLELVEQ 29- 3 P + S+E E L+I PL V E AA++ AA L G+ +E V Sbjct: 294 PERPYSEEVGRE---PGRLRIGFSTAHPLGRSVHPECVAAVQGAARLLESLGHEVEEVAL 35- 0 Query: 294 PLDGIHSMKTYCMMNSVETAAMFDDIEKSLGRSMEFSDMELMTWAMYQSGQRVLAKDYSK 35- 3 P DG + + M+ ET A + +LGR SD+E +TW + Q G+ A D++ Sbjct: 351 PWDGPALAQAFLMLYFGETGASLAALRDTLGRPARASDVEAVTWLLGQLGRSYSAADFAA 41- 0 Query: 354 LLDSWDQFAATMARFHENYDLILTAATNQPAPFHGQFD---LDETLQKQLRHMGEFSVSE 41- 0 SW+ A M RFH+NYDL+LT P G+ + L + + M + Sbjct: 411 ARASWNVHARAMGRFHQNYDLLLTPVLATPPLQIGELQPRGVQAALLRAAQQMDVSGLLR 47- 0 Query: 411 QQDLIWKMFEDSMAWTPFTHQPNLTGQPSLAIPTHLTKEGLPLGVQLTAAKGREDLLLAV 47- 0 + + + D + P+T NLTGQP++++P H T +GLP+GVQ A RED+LL + Sbjct: 471 RSGQVDALATDILEKMPYTQLANLTGQPAMSVPLHWTADGLPVGVQFVAPLAREDVLLRL 53- 0 Query: 471 AELFEKEK 478 A E+ + Sbjct: 531 AGQLEQAR 538 A related DNA sequence was identified in S. pyogenes <SEQ ID 4047> which encodes the amino acid sequence <SEQ ID 4048>. Analysis of this protein sequence reveals the following: TABLE-US-04672 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty= 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04673 Identities = 277/484 (57%), Positives = 348/484 (71%), Gaps = 2/484 (0%) Query: 1 MVFKDATAMVQAIKQHKISSQELVEQAIYKIEEQNVSVNAVVSKQYNEARQAAKYANESN 60 M ++DATAM A++ + + ELV QAIYK ++ N ++NA+ S+++ A + AK + S Sbjct: 1 MTYQDATAMAIAVQTGQTTPLELVTQAIYKAKKLNPTLNAITSERFEAALEEAKQRDFSG 60 Query: 61 APFAGVPILLKDLGQNQKGQLSTSGSQLFKHYHAKQTDYLVQSFEKLGFIILGRTNTPEF 120- PFAGVP+ LKDLGQ KG STSGS+LFK Y A +TD V+ E LGFIILGR+NTPEF Sbjct: 61 LPFAGVPLFLKDLGQELKGHSSTSGSRLFKEYQATKTDLFVKRLEALGFIILGRSNTPEF 120- Query: 121 GFKNISDGQLHGNVNLPFDHSRNAGGSSGGAAAAVSSGMVPIAGASDGGGSIRIPASFNG 18- 0 GFKNISD LHG VNLP D++RNAGGSSGGAAA VSSG+ +A ASDGGGSIRIPASFNG Sbjct: 121 GFKNISDSSLHGPVNLPRDNTRNAGGSSGGAAALVSSGISALATASDGGGSIRIPASFNG 18- 0 Query: 181 LIGLKPSRGRIPVGPSSYRGWQGASSHFALTKSVRDTKRLLYYLQSYQVESPFPLKKLSK 24- 0 LIGLKPSRGR+PVGP SYR WQGAS HFALTKSVRDT+ LLYYLQ Q+ESPFPL L+K Sbjct: 181 LIGLKPSRGRMPVGPGSYRSWQGASVHFALTKSVRDTRNLLYYLQMEQMESPFPLATLTK 24- 0 Query: 241 ESLFEFSVSKPLKIAVLMDSPLKTKVSSEAKAAIKEAADFLSQKGNHL-ELVEQPLDGIH 29- 9 +S+++ S+ +PL IA + VS + A+++A +L ++G+ L EL E P++ Sbjct: 241 DSIYQ-SLQRPLTIAFYQRLSDGSPVSLDTAKALRQAVTWLREQGHQLVELEEFPVNMTE 29- 9 Query: 300 SMKTYCMMNSVETAAMFDDIEKSLGRSMEFSDMELMTWAMYQSGQRVLAKDYSKLLDSWD 35- 9 ++ Y +MNSVETAAMF DIE + GR M DME MTWA+YQSG+ + A YS++L WD Sbjct: 300 VIRHYYIMNSVETAAMFADIEDTFGRPMTKDDMETMTWAIYQSGKDIPAWRYSQVLQKWD 35- 9 Query: 360 QFAATMARFHENYDLILTAATNQPAPFHGQFDLDETLQKQLRHMGEFSVSEQQDLIWKMF 41- 9 ++ATMA FHE YDL+LT TN PAP HG+ D L L FS EQ +L+ MF Sbjct: 360 TYSATMASFHETYDLLLTFTTNTPAPKHGELVPDSKLMANLAQAEIFSSEEQFNLVETMF 41- 9 Query: 420 EDSMAWTPFTHQPNLTGQPSLAIPTHLTKEGLPLGVQLTAAKGREDLLLAVAELFEKEKQ 47- 9 S+A P+T PNLTGQP++++PT+ TKEGL +G+QL AAKGREDLLL +AE FE Sbjct: 420 GKSLAINPYTALPNLTGQPAISLPTYETKEGLSMGIQLIAAKGREDLLLGIAEQFEAAGL 47- 9 Query: 480 FKGP 483 K P Sbjct: 480 LKIP 483 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1555 A DNA sequence (GBSx1647) was identified in S. agalactiae <SEQ ID 4799> which encodes the amino acid sequence <SEQ ID 4800>. This protein is predicted to be transcription elongation factor (greA). Analysis of this protein sequence reveals the following:

TABLE-US-04674 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5003(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04675 >GP: CAB14674 GB: Z99117 transcription elongation factor [Bacillus subtilis] Identities = 86/154 (55%), Positives = 114/154 (73%), Gaps = 1/154 (0%) Query: 3 EKTYPMTQVEKDQLEKELEELKLVRRPEVVERIKIARSYGDLSENSEYDAAKDEQAFVEG 62 EK +PMT K +LE+ELE LK V+R EVVERIKIARS+GDLSENSEYD+AK+EQAFVEG Sbjct: 4 EKVFPMTAEGKQKLEQELEYLKTVKRKEVVERIKIARSFGDLSENSEYDSAKEEQAFVEG 63 Query: 63 QIQILETKIRYAEIIDSDAVAKDEVAIGKTVLVQEVGTNDKDTYHIVGAAGADIFSGKIS 122- ++ LE IR A+II+ D + V +GKTV E+ D+++Y IVG+A AD F GKIS Sbjct: 64 RVTTLENMIRNAKIIEDDG-GSNVVGLGKTVTFVELPDGDEESYTIVGSAEADPFEGKIS 122- Query: 123 NESPIAHALIGKKTGDLATIESPAGSYQVEIISV 156 N+SPIA +L+GKK + T+++P G V+I+ + Sbjct: 123 NDSPIAKSLLGKKVDEEVTVQTPGGEMLVKIVKI 156 A related DNA sequence was identified in S. pyogenes <SEQ ID 4801> which encodes the amino acid sequence <SEQ ID 4802>. Analysis of this protein sequence reveals the following: TABLE-US-04676 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4434(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04677 Identities = 145/160 (90%), Positives = 149/160 (92%) Query: 1 MAEKTYPMTQVEKDQLEKELEELKLVRRPEVVERIKIARSYGDLSENSEYDAAKDEQAFV 60 MAEKTYPMT EK+QLEKELEELKLVRRPE+VERIKIARSYGDLSENSEYDAAKDEQAFV Sbjct: 17 MAEKTYPMTLTEKEQLEKELEELKLVRRPEIVERIKIARSYGDLSENSEYDAAKDEQAFV 76 Query: 61 EGQIQILETKIRYAEIIDSDAVAKDEVAIGKTVLVQEVGTNDKDTYHIVGAAGADIFSGK 120- EGQI LETKIRYAEIIDSDAVAKDEVAIGKTV+VQEVGT DKDTYHIVGAAGADIFSGK Sbjct: 77 EGQISTLETKIRYAEIIDSDAVAKDEVAIGKTVIVQEVGTTDKDTYHIVGAAGADIFSGK 136- Query: 121 ISNESPIAHALIGKKTGDLATIESPAGSYQVEIISVEKTN 160 ISNESPIA ALIGKKTGD IESPA +Y VEIISVEKTN Sbjct: 137 ISNESPIAQALIGKKTGDKVRIESPAATYDVEIISVEKTN 176 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1556 A DNA sequence (GBSx1648) was identified in S. agalactiae <SEQ ID 4803> which encodes the amino acid sequence <SEQ ID 4804>. This protein is predicted to be aminodeoxychorismate lyase-like protein. Analysis of this protein sequence reveals the following: TABLE-US-04678 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.64 Transmembrane 238-254 (230-260) ----- Final Results ----- bacterial membrane --- Certainty = 0.6456(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04679 >GP: AAF77615 GB: AF151720 aminodeoxychorismate lyase-like protein [Streptococcus thermophilus] Identities = 135/210 (64%), Positives = 171/210 (81%) Query: 373 KTTSTPYKADDFLKLVQDETFIKKMVAKYPNLLGSLPDKSKAIYQLEGYLFPATYNYYKD 43- 2 K +ST K DFLKL++D+ FI KM AKYP LL +LP+ + A Y LEGYLFPATYN + D Sbjct: 5 KHSSTGLKEKDFLKLMKDDAFITKMKAKYPTLLANLPNSTDAKYVLEGYLFPATYNIHDD 64 Query: 433 TTLEGLVEDMISTMNTKMAPYYNTIKAKNMSVNDVLTLSSLVEKEGSTDEDRRKIASVFY 49- 2 TT+E L E+M+ TM+T ++PYY TI + N +VN++LTL+SLVEKEG+TD+DR+ IASVFY Sbjct: 65 TTVESLAEEMLFTMDTHLSPYYATILSSNHNVNEILTLASLVEKEGATDDDRKNIASVFY 124- Query: 493 NRLSAGQALQSNIAILYAMGKLGDKTSLAEDAQINTSIKSPYNIYTNTGLMPGPVDSPSI 55- 2 NRL++ ALQSNIA+LY +GKLG +T+L EDA I+T+I SPYN Y + GLMPGPVDSPS+ Sbjct: 125 NRLNSDMALQSNIAVLYVLGKLGQETTLKEDATIDTNIDSPYNDYVHKGLMPGPVDSPSL 18- 4 Query: 553 SAIEATIKPASTDYLYFVADVKTGNVYYAK 582 SAIEA I P+ST Y+YFVADV TGNVY+A+ Sbjct: 185 SAIEAVINPSSTKYMYFVADVSTGNVYFAE 214 A related DNA sequence was identified in S. pyogenes <SEQ ID 4805> which encodes the amino acid sequence <SEQ ID 4806>. Analysis of this protein sequence reveals the following: TABLE-US-04680 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.91 Transmembrane 161-177 (155-183) ----- Final Results ----- bacterial membrane --- Certainty = 0.4163 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04681 >GP: AAF77615 GB: AF151720 aminodeoxychorismate lyase-like protein [Streptococcus thermophilus] Identities = 135/212 (63%), Positives = 161/212 (75%) Query: 295 KTKKAKTPFNEKDFLDLVTDEAFIQDMVKRYPKLLATIPTKEKAIYRLEGYLFPATYNYY 35- 4 K K + T EKDFL L+ D+AFI M +YP LLA +P A Y LEGYLFPATYN + Sbjct: 3 KGKHSSTGLKEKDFLKLMKDDAFITKMKAKYPTLLANLPNSTDAKYVLEGYLFPATYNIH 62 Query: 355 KETTMRELVEDMLAAMDATLVPYYDKIAASGKTVNEVLTLASLVEKEGSTDDDRRQIASV 41- 4 +TT+ L E+ML MD L PYY I +S VNE+LTLASLVEKEG+TDDDR+ IASV Sbjct: 63 DDTTVESLAEEMLFTMDTHLSPYYATILSSNHNVNEILTLASLVEKEGATDDDRKNIASV 122- Query: 415 FYNRLNSGMALQSNIAILYAMGKLGEKTTLAEDATIDTTINSPYNIYTNTGLMPGPVASS 47- 4 FYNRLNS MALQSNIA+LY +GKLG++TTL EDATIDT I+SPYN Y + GLMPGPV S Sbjct: 123 FYNRLNSDMALQSNIAVLYVLGKLGQETTLKEDATIDTNIDSPYNDYVHKGLMPGPVDSP 18- 2 Query: 475 GVSAIEATLNPASTDYLYFVANVHTGEVYYAK 506 +SAIEA +NP+ST Y+YFVA+V TG VY+A+ Sbjct: 183 SLSAIEAVINPSSTKYMYFVADVSTGNVYFAE 214 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04682 Identities = 310/603 (51%), Positives 403/603 (66%), Gaps = 86/603 (14%) Query: 1 MTEFNDDQHSNHDQKSFKEQILAELEEANRLRKLREEELYQKEQEAKEAARRTAQLMADY 60 +T+F D + Q+SFKEQILAELE+AN++RK +EEEL+ Sbjct: 3 LTDFKDKDQQDQ-QRSFKEQILAELEKANQIRKEKEEELF-------------------- 41 Query: 61 EAQRLKDEREARAKALETKQRLEEQEKARIEAKLLAEAAREEERRQAEQALASQEEQVIN 120- ++ LE +E AR A+L AE R++ A Q+E + + Sbjct: 42 ------------------QKELEAKEAARRTAQLYAEYKRQD---------AFQKESIAH 74 Query: 121 QGMEPSRELDSGSKSSEFRTTENVPDIDLKADKTDVATAVPNQETEEIFLVRATDIPTEG 18- 0 +T ++ +A K V T+ + T + +E Sbjct: 75 NN----------------KTAKH-----FQAIKGAVMTSEALKPT----------LLSEK 103- Query: 181 ENVKLGEISELEPVAKEPIRVEDLSKEEEGIALSAKNKHNKRER---RQKADNVAKRIAR 23- 7 EN L ++ A E +++ + +E + L+ + H+ R + RQ+ + AK+I+ Sbjct: 104 ENSSLKTTNKRVVQANE---LQETASKESQVPLTIEKGHSVRRKLSKRQQTERAAKKIST 16- 0 Query: 238 ILISIIILVLLLTAFVGYRFVDSAIKPVDSNSNKFVQVEIPIGSGNKLIGQILEKAGVIK 29- 7 +LIS II+ LL G +V SA+ PVD NS+ FVQVEIP GSGNKLIGQIL+K G+IK Sbjct: 161 VLISSIIITLLAVTLAGAGYVYSALNPVDKNSDAFVQVEIPSGSGNKLIGQILQKKGLIK 22- 0 Query: 298 SATVFNYYSKFKNYSNFQSGYYNLKKSMTLDQIAAELEKGGTAEPTKPALGKILITEGYT 35- 7 ++TVF++Y+KFKN++NFQSGYYNL+KSM+L++IA+ L++GGTAEPTKP+LGKILI EGYT Sbjct: 221 NSTVFSFYTKFKNFTNFQSGYYNLQKSMSLEEIASALQEGGTAEPTKPSLGKILIPEGYT 28- 0 Query: 358 IKQIAKAIESN-KIDTKTTSTPYKADDFLKLVQDETFIKKMVAKYPNLLGSLPDKSKAIY 41- 6 IKQIAKA+E N K TK TP+ DFL LV DE FI+ MV +YP LL ++P K KAIY Sbjct: 281 IKQIAKAVEHNSKGKTKKAKTPFNEKDFLDLVTDEAFIQDMVKRYPKLLATIPTKEKAIY 34- 0 Query: 417 QLEGYLFPATYNYYKDTTLEGLVEDMISTMNTKMAPYYNTIKAKNMSVNDVLTLSSLVEK 47- 6 +LEGYLFPATYNYYK+TT+ LVEDM++ M+ + PYY+ I A +VN+VLTL+SLVEK Sbjct: 341 RLEGYLFPATYNYYKETTMRELVEDMLAAMDATLVPYYDKIAASGKTVNEVLTLASLVEK 40- 0 Query: 477 EGSTDEDRRKIASVFYNRLSAGQALQSNIAILYAMGKLGDKTSLAEDAQINTSIKSPYNI 53- 6 EGSTD+DRR+IASVFYNRL++G ALQSNIAILYAMGKLG+KT+LAEDA I+T+I SPYNI Sbjct: 401 EGSTDDDRRQIASVFYNRLNSGMALQSNIAILYAMGKLGEKTTLAEDATIDTTINSPYNI 46- 0 Query: 537 YTNTGLMPGPVDSPSISAIEATIKPASTDYLYFVADVKTGNVYYAKDFETHKANVEKYIN 59- 6 YTNTGLMPGPV S +SAIEAT+ PASTDYLYFVA+V TG VYYAK FE H ANVEKY+N Sbjct: 461 YTNTGLMPGPVASSGVSAIEATLNPASTDYLYFVANVHTGEVYYAKTFEEHSANVEKYVN 52- 0 Query: 597 SQI 599 SQI Sbjct: 521 SQI 523 A related GBS gene <SEQ ID 8843> and protein <SEQ ID 8844> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04683 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -17.88 GvH: Signal Score (-7.5): -3.51 Possible site: 58 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -13.64 threshold: 0.0 INTEGRAL Likelihood = -13.64 Transmembrane 238-254 (230-260) PERIPHERAL Likelihood = 5.78 285 modified ALOM score: 3.23 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6456 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00102## SEQ ID 8844 (GBS370) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 64 (lane 6; MW 70 kDa). GBS370-His was purified as shown in FIG. 209, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1557 A DNA sequence (GBSx1649) was identified in S. agalactiae <SEQ ID 4807> which encodes the amino acid sequence <SEQ ID 4808>. Analysis of this protein sequence reveals the following: TABLE-US-04684 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0183 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10077> which encodes amino acid sequence <SEQ ID 10078> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04685 >GP:CAA98889 GB: Z74367 ORF YDR071c [Saccharomyces cerevisiae] Identities = 52/174 (29%), Positives = 81/174 (45%), Gaps 18/174 (10%) Query: 27 MSMIIRNGCLEDLQQVISIEQINFSEAEAASKKAMQERLTIMTDT---FLVAEINGR--- 80 - + M IR +EDL+Q++++E F E AS++ + RL + + EI G+ Sbjct: 10 LHMYIRPLIIEDLKQILNLESQGFPPNERASEEIISFRLINCPELCSGLFIREIEGKEVK 69 Query: 81 ---LAGYIEGPVIKGRYLTDDLFHKVSEFPVRVGGFIGITSLSIHPDFKGQGIGTALLAA 137- L G+I G I Y+T + K+ V IGI S+ I P+++ + + T LL Sbjct: 70 KETLIGHIMGTKIPHEYITIESMGKLQ---VESSNHIGIHSVVIKPEYQKKNLATLLLTD 126- Query: 138 MKDLVVSQE-RDGISLTCHDDLISFYEMNGFKDEGES-----DSKHGGSLWYNM 185 + +QE + I L H+ LI FYE GFK E+ D W +M Sbjct: 127 YIQKLSNQEIGNKIVLIAHEPLIPFYERVGFKIIAENTNVAKDKNFAEQKWIDM 180 A related DNA sequence was identified in S. pyogenes <SEQ ID 4809> which encodes the amino acid sequence <SEQ ID 4810>. Analysis of this protein sequence reveals the following: TABLE-US-04686 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2576(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04687 Identities = 87/159 (54%), Positives = 117/159 (72%), Gaps = 1/159 (0%) Query: 29 MIIRNGCLEDLQQVISIEQINFSEAEAASKKAMQERLTIMTDTFLVAEINGRLAGYIEGP 88 - M+IR DL+ + +IE NFS EA ++ ++E + ++ DTFLVA I+ + GYIEGP Sbjct: 1 MLIRQVQGSDLEVIATIESDNFSPQEATTRAVLEEHIRLIPDTFLVALIDQEIVGYIEGP 60 Query: 89 VIKGRYLTDDLFHKVSEFPVRVGGFIGITSLSIHPDFKGQGIGTALLAAMKDLVVSQERD 148- V+ L D LFH V++ P + GG+I ITSLSI F+ QG+GTALLAA+KDLVV+Q+R Sbjct: 61 VVTTPILEDSLFHGVTKNP-KTGGYIAITSLSIAKHFQQQGVGTALLAALKDLVVAQQRT 119- Query: 149 GISLTCHDDLISFYEMNGFKDEGESDSKHGGSLWYNMIW 187 G+ LTCHD LIS+YEMNGF ++G S+S+HGG+LWY MIW Sbjct: 120 GLILTCHDYLISYYEMNGFINQGISESQHGGTLWYQMIW 158 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1558 A DNA sequence (GBSx1650) was identified in S. agalactiae <SEQ ID 4811> which encodes the amino acid sequence <SEQ ID 4812>. This protein is predicted to be udp-n-acetylmuramate--alanine ligase (murC/ddlA). Analysis of this protein sequence reveals the following: TABLE-US-04688 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -2.60 Transmembrane 272-288 (270-288) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04689 >GP: AAC00294 GB: AF008220 putative UDP-N-acetylmuramate-alanine ligase [Bacillus subtilis] Identities = 238/432 (55%), Positives = 315/432 (72%), Gaps = 3/432 (0%) Query: 5 YHFIGIKGSGMSALALMLHQMGHNVQGSDVDKYYFTQRGLEQAGVTILPFSPNNISEDLE 64 YHF+GIKG+GMS LA +LH G+ VQGSD++K+ FTQ LE+ +TILPFS NI + Sbjct: 4 YHFVGIKGTGMSPLAQILHDNGYTVQGSDIEKFIFTQTALEKRNITILPFSAENIKPGMT 63 Query: 65 IIAGNAFRPDNNEELAYVIEKGYQFKRYHEFLGDFMRQFTSLGVAGAHGKTSTTGLLAHV 124- +IAGNAF PD + E+ + +G RYH+FLGD+M++FTS+ V GAHGKTSTTGLLAHV Sbjct: 64 VIAGNAF-PDTHPEIEKAMSEGIPVIRYHKFLGDYMKKFTSVAVTGAHGKTSTTGLLAHV 122- Query: 125 LKNITDTSFLIGDGTGRGSANANYFVFEADEYERHFMPYHPEYSIITNIDFDHPDYFTGL 18- 4 ++N TSFLIGDGTG+G+ N+ YFVFEA EY RHF+ Y P+Y+I+TNIDFDHPDYF+ + Sbjct: 123 IQNAKPTSFLIGDGTGQGNENSEYFVFEACEYRRHFLSYQPDYAIMTNIDFDHPDYFSSI 18- 2 Query: 185 EDVFNAFNDYAKQVQKGLFIYGEDPKLHEITSEAPIYYYGFEDSNDFIAKDITRTVNGSD 24- 4 +DVF+AF + A QV KG+ G+D L +I + P+ YYG + NDF A++I ++ G+ Sbjct: 183 DDVFDAFQEMALQVNKGIIACGDDEHLPKIHANVPVVYYGTGEENDFQARNIVKSTEGTT 24- 2 Query: 245 FKVFYNQEEIGQFHVPAYGKHNILNATAVIANLYIMGIDMALVAEHLKTFSGVKRRFTEK 30- 4 F VF F++PAYG HN+LN+ AVIA + ID +++ LK+F GVKRRF EK Sbjct: 243 FDVFVRNTFYDTFYIPAYGHHNVLNSLAVIALCHYEEIDSSIIKHALKSFGGVKRRFNEK 30- 2 Query: 305 IIDDTVIIDDFAHHPTEIIATLDAARQKYPSKEIVAIFQPHTFTRTIALLDEFAHALSQA 36- 4 + D V+IDD+AHHPTEI T++AARQKYP +EIVA+FQPHTFTRT LDEFA +LS A Sbjct: 303 QLGDQVLIDDYAHHPTEIKVTIEAARQKYPDREIVAVFQPHTFTRTQQFLDEFAESLSGA 36- 2 Query: 365 DSVYLAQIYGSAREVDNGEVKVEDLAAKIVKHSDLVTVENVSPLLNHDNAVYVFMGAGDI 42- 4 D VYL I+GSARE + G++ + DL KI ++ L+ ++ S L HD AV +FMGAGDI Sbjct: 363 DCVYLCDIFGSARE-NAGKLTIGDLQGRI-HNAKLIEEDDTSVLKAHDKAVLIFMGAGDI 42- 0 Query: 425 QLYERSFEELLA 436 Q Y R++E ++A Sbjct: 421 QKYMRAYENVMA 432 A related DNA sequence was identified in S. pyogenes <SEQ ID 4813> which encodes the amino acid sequence <SEQ ID 4814>. Analysis of this protein sequence reveals the following: TABLE-US-04690 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.57 Transmembrane 271-287 (269-288) ----- Final Results ----- bacterial membrane --- Certainty = 0.2826(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04691 >GP: AAC00294 GB: AF008220 putative UDP-N-acetylmuramate-alanine ligase [Bacillus subtilis] Identities = 236/431 (54%), Positives = 310/431 (71%), Gaps = 2/431 (0%) Query: 5 YHFIGIKGSGMSALALMLHQMGHKVQGSDVEKYYFTQRGLEQAGITILPFSEDNITPDME 64 YHF+GIKG+GMS LA +LH G+ VQGSD+EK+ FTQ LE+ ITILPFS +NI P M Sbjct: 4 YHFVGIKGTGMSPLAQILHDNGYTVQGSDIEKFIFTQTALEKRNITILPFSAENIKPGMT 63 Query: 65 LIVGNAFRENNKEVAYALRHQIPFKRYHDFLGDFMKSFISFAVAGAHGKTSTTGLLSHVL 124- +I GNAF + + E+ A+ IP RYH FLGD+MK F S AV GAHGKTSTTGLL+HV+ Sbjct: 64 VIAGNAFPDTHPEIEKAMSEGIPVIRYHKFLGDYMKKFTSVAVTGAHGKTSTTGLLAHVI 123- Query: 125 KNITDTSYLIGDGTGRGSANAQYFVFESDEYERHFMPYHPEYSIITNIDFDHPDYFTGIA 18- 4 +N TS+LIGDGTG+G+ N++YFVFE+ EY RHF+ Y P+Y+I+TNIDFDHPDYF+ I Sbjct: 124 QNAKPTSFLIGDGTGQGNENSEYFVFEACEYRRHFLSYQPDYAIMTNIDFDHPDYFSSID 18- 3 Query: 185 DVRNAFNDYAKQVKKALFVYGEDDELKKIEAPAPIYYYGFEEGNDFIAYDITRTTNGSDF 24- 4 DV +AF + A QV K + G+D+ L KI A P+ YYG E NDF A +I ++T G+ F Sbjct: 184 DVFDAFQEMALQVNKGIIACGDDEHLPKIHANVPVVYYGTGEENDFQARNIVKSTEGTTF 24- 3 Query: 245 KVKHQGEVIGQFHVPAYGKHNILNATAVIANLFVAGIDMALVADHLKTFSGVKRRFTEKI 30- 4 V + F++PAYG HN+LN+ AVIA ID +++ LK+F GVKRRF EK Sbjct: 244 DVFVRNTFYDTFYIPAYGHHNVLNSLAVIALCHYEEIDSSIIKHALKSFGGVKRRFNEKQ 30- 3 Query: 305 INDTIIIDDFAHHPTEIVATIDAARQKYPSKEIVAIFQPHTFTRTIALLEDFACALNEAD 36- 4 + D ++IDD+AHHPTEI TI+AARQKYP +EIVA+FQPHTFTRT L++FA +L+ AD Sbjct: 304 LGDQVLIDDYAHHPTEIKVTIEAARQKYPDREIVAVFQPHTFTRTQQFLDEFAESLSGAD 36- 3 Query: 365 SVYLAQIYGSAREVDKGEVKVEDLAAKIIKPSQVVTVENVSPLLDHDNAVYVFMGAGDIQ 42- 4 VYL I+GSARE + G++ + DL K I ++++ ++ S L HD AV +FMGAGDIQ Sbjct: 364 CVYLCDIFGSARE-NAGKLTIGDLQGK-IHNAKLIEEDDTSVLKAHDKAVLIFMGAGDIQ 42- 1 Query: 425 LYEHSFEELLA 435 Y ++E ++A Sbjct: 422 KYMRAYENVMA 432 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04692 Identities = 369/443 (83%), Positives = 406/443 (91%), Gaps = 1/443 (0%) Query: 1 MSKTYHFIGIKGSGMSALALMLHQMGHNVQGSDVDKYYFTQRGLEQAGVTILPFSPNNIS 60 MSKTYHFIGIKGSGMSALALMLHQMGH VQGSDV+KYYFTQRGLEQAG+TILPFS +NI+ Sbjct: 1 MSKTYHFIGIKGSGMSALALMLHQMGHKVQGSDVEKYYFTQRGLSQAGITILPFSEDNIT 60 Query: 61 EDLEIIAGNAFRPDNNEELAYVIEKGYQFKRYHEFLGDFMRQFTSLGVAGAHGKTSTTGL 120- D+E+I GNAFR +NN+E+AY + FKRYH+FLGDFM+ F S VAGAHGKTSTTGL Sbjct: 61 PDMELIVGNAFR-ENNKEVAYALRHQIPFKRYHDFLGDFMKSFISFAVAGAHGKTSTTGL 119- Query: 121 LAHVLKNITDTSFLIGDGTGRGSANANYFVFEADEYERHFMPYHPEYSIITNIDFDHPDY 18- 0 L+HVLKNITDTS+LIGDGTGRGSANA YFVFE+DEYERHFMPYHPEYSIITNIDFDHPDY Sbjct: 120 LSHVLKNITDTSYLIGDGTGRGSANAQYFVFESDEYERHFMPYHPEYSIITNIDFDHPDY 17- 9 Query: 181 FTGLEDVFNAFNDYAKQVQKGLFIYGEDPKLHEITSEAPIYYYGFEDSNDFIAKDITRTV 24- 0 FTG+ DV NAFNDYAKQV+K LF+YGED +L +I + APIYYYGFE+ NDFIA DITRT Sbjct: 180 FTGIADVRNAFNDYAKQVKKALFVYGEDDELKKIEAPAPIYYYGFEEGNDFIAYDITRTT 23- 9 Query: 241 NGSDFKVFYNQEEIGQFHVPAYGKHNILNATAVIANLYIMGIDMALVAEHLKTFSGVKRR 30- 0 NGSDFKV + E IGQFHVPAYGKHNILNATAVIANL++ GIDMALVA+HLKTFSGVKRR Sbjct: 240 NGSDFKVKHQGEVIGQFHVPAYGKHNILNATAVIANLFVAGIDMALVADHLKTFSGVKRR 29- 9 Query: 301 FTEKIIDDTVIIDDFAHHPTEIIATLDAARQKYPSKEIVAIFQPHTFTRTIALLDEFAHA 36- 0 FTEKII+DT+IIDDFAHHPTEI+AT+DAARQKYPSKEIVAIFQPHTFTRTIALL++FA A Sbjct: 300 FTEKIINDTIIIDDFAHHPTEIVATIDAARQKYPSKEIVAIFQPHTFTRTIALLEDFACA 35- 9 Query: 361 LSQADSVYLAQIYGSAREVDNGEVKVEDLAAKIVKHSDLVTVENVSPLLNHDNAVYVFMG 42- 0 L++ADSVYLAQIYGSAREVD GEVKVEDLAAKI+K S +VTVENVSPLL+HDNAVYVFMG Sbjct: 360 LNEADSVYLAQIYGSAREVDKGEVKVEDLAAKIIKPSQVVTVENVSPLLDHDNAVYVFMG 41- 9 Query: 421 AGDIQLYERSFEELLANLTKNTQ 443 AGDIQLYE SFEELLANLTKN Q Sbjct: 420 AGDIQLYEHSFEELLANLTKNNQ 442 SEQ ID 4812 (GBS157) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 24 (lane 11; MW 49 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 31 (lane 8; MW 74 kDa), FIG. 33 (lane 8; MW 74 kDa) and FIG. 37 (lane 3; MW 74 kDa). The GBS157-GST fusion product was purified (FIG. 112A; see also FIG. 200, lane 3) and used to immunise mice (lane 1+2 product; 19.5 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 112B), FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. SEQ ID 4812 (GBS157) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 183 (lane 11-13; MW 74 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1559 A DNA sequence (GBSx1651) was identified in S. agalactiae <SEQ ID 4815> which encodes the amino acid sequence <SEQ ID 4816>. Analysis of this protein sequence reveals the following:

TABLE-US-04693 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1980(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4817> which encodes the amino acid sequence <SEQ ID 4818>. Analysis of this protein sequence reveals the following: TABLE-US-04694 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2731(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04695 Identities = 80/201 (39%), Positives = 126/201 (61%), Gaps = 9/201 (4%) Query: 7 RFPLIADDEPVMSPLVKMNLYDNEDLINNIRDFYQEKTYQSMVKSNYEHEEISHPKVIEN 66 +FPL+AD + P +M LY+NEDLI NIR +YQ+K Y + ++ EE + Sbjct: 5 QFPLVADGIAISDPAKQMALYENEDLITNIRGYYQDKEYDDIARN----EEFTAKATSRQ 60 Query: 67 DPVPPQ--SFVKKATELSKSRQEAKRSVREKRQAYYAKQEFKAPSKEAFQQQLKATVPKK 124- P + S +K + ++RQ+AK+ ++EKRQAY AK+ P + + +QQ + P + Sbjct: 61 TPSSKRFCSNDEKHHYVKEARQKAKQDLKEKRQAYLAKEMAYVPKQVSKKQQPADSSPSQ 120- Query: 125 QTQRKVTELSHLSDRLQQESYILAEIPIIFQEPDNTPNP-KTKKNNFDFLKRSQVYNKQD 18- 3 + + TE+S + +L Q++YILAE+P ++EP N P TKKNN+DFLK SQ+YN ++ Sbjct: 121 K--QATTEMSRFTKKLHQDNYILAELPKEYKEPKNLPQQGTTKKNNYDFLKSSQIYNNKE 17- 8 Query: 184 NQFHKERAKAQELNLTRFKDI 204 + +E+ AQELNL+RF+D+ Sbjct: 179 MRQQREKTIAQELNLSRFEDL 199 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1560 A DNA sequence (GBSx1652) was identified in S. agalactiae <SEQ ID 4819> which encodes the amino acid sequence <SEQ ID 4820>. Analysis of this protein sequence reveals the following: TABLE-US-04696 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4959(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1561 A DNA sequence (GBSx1653) was identified in S. agalactiae <SEQ ID 4821> which encodes the amino acid sequence <SEQ ID 4822>. This protein is predicted to be SNF. Analysis of this protein sequence reveals the following: TABLE-US-04697 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 743-759 (743-759) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04698 >GP: CAA67095 GB: X98455 SNF [Bacillus cereus] Identities = 259/678 (38%), Positives = 406/678 (59%), Gaps = 21/678 (3%) Query: 369 QNEILLQMVFDYGNDLTVHNRQELEQLTFASHFKHEEKVFKLLEKYGFAPHFSTSHPAYS 42- 8 +N +L + F YGN + ++ + F K E+++ ++ + FA + ++ Sbjct: 388 KNRLLAGLEFHYGNVVINPLEEDGQPSVFNRDEKKEKEILDIMSESAFAKT-EGGYFMHN 44- 6 Query: 429 AQELYDFYTYMLPQFKKMGTV--SLSAKLESYRLIERPQIDIEAKGSL--LDISFDFSDL 48- 4 + Y+F +++P K + + + + KL ++ P I + K + L FD + Sbjct: 447 EEAEYNFLYHIVPTLKGLVDIYATTAIKLRIHKGDTAPLIRVRRKERIDWLSFRFDIKGI 50- 6 Query: 485 LENDVDQALVALFDNNPYFVNKSGQLVIFD-EETKKVSATLQ--GLRARRAKNGHIELDN 54- 1 E ++ L AL + Y+ +G L+ + +E +++ ++ G+R + + Sbjct: 507 PEAEIKGVLAALEEKRKYYRLANGSLLSLESKEFNEINQFVKESGIRKEFLHGEEVNVPL 56- 6 Query: 542 IAAFQLSELFANQDNVSFSQHFYQLIEDLRHPEKFK--IPGLSVSASLRDYQLTGVRWLS 59- 9 I + + + +S + L+E +++P+K K +P ++ A +R+YQ+ G W+ Sbjct: 567 IRSVKWMNGLHEGNVLSLDESVQDLVESIQNPKKLKFTVPP-TLHAVMREYQVYGFEWMK 62- 5 Query: 600 MLDHYGFAGILADDMGLGKTLQTISFLSTKLT--RDSR--VLILSPSSLIYNWQDEFHKF 65- 5 L +Y F GILADDMGLGKTLQ+I+++ + L R+ + +L++SPSSL+YNW E KF Sbjct: 626 TLAYYRFGGILADDMGLGKTLQSIAYIDSVLPEIREKKLPILVVSPSSLVYNWFSELKKF 68- 5 Query: 656 APDVDVAVAYGSKIRRDEIIAE--RHQVIITSYSSFRQDFETYSEGNYDYLILDEAQVMK 71- 3 AP + +A G++ R +I+ + V+ITSY R+D +Y+ + L LDEAQ K Sbjct: 686 APHIRAVIADGNQTERRKILKDVAEFDVVITSYPLLRRDVRSYARP-FHTLFLDEAQAFK 74- 4 Query: 714 NAQTKIAHSLRSFEVKNCFALSGTPIENKLLEIWSIFQIILPGLLPGKKEFLKLNPKQVA 77- 3 N T+ A ++++ + + F L+GTP+EN L E+WSIF ++ P LLPG+KEF L + +A Sbjct: 745 NPTTQTARAVKTIQAEYRFGLTGTPVENSLEELWSIFHVVFPELLPGRKEFGDLRREDIA 80- 4 Query: 774 RYIKPFVMRRRKEEVLPELPDLIEMNYPNEMTDSQKVIYLAQLRQI-QESIQHSSDADLN 83- 2 +KPFV+RR KE+VL ELPD IE +E+ QK +Y A L ++ +E+++H L Sbjct: 805 NAVKPFVLRRLKEDVLQELPDKIEHLQSSELLPDQKRLYAAYLAKLREETLKHLDKDTLR 86- 4 Query: 833 RRKIEILSGITRLRQICDTPRLFMD-YDGESGKLESLRQLLTQIKENGHRALIFSQFRGM 89- 1 + KI IL+G+TRLRQIC+ P LF+D Y G S KLE L +L + + G R LIFSQF M Sbjct: 865 KNKIRILAGLTRLRQICNHPALFVDDYKGSSAKLEQLLDILEECRSTGKRILIFSQFTKM 92- 4 Query: 892 LDIAEREMVAMGLTTYKITGSTPANERHEMTRAFNAGSKDAFLISLKAGGVGLNLTGADT 95- 1 L I RE+ + + + G+TP+ ER E+ FN G D FLISLKAGG GLNLTGADT Sbjct: 925 LSIIGRELNRQAIPYFYLDGNTPSQERVELCNRFNEGEGDLFLISLKAGGTGLNLTGADT 98- 4 Query: 952 VVLIDLWWNPAVEMQAISRAHRLGQKENVEVYRLITRGTIEEKILEMQETKKHLVTTVLD 10- 11 V+L DLWWNPAVE QA RA+R+GQK V+V +L+ GTIEEK+ E+QE+KKHL+ V++ Sbjct: 985 VILYDLWWNPAVEQQAADRAYRMGQKNTVQVIKLVAHGTIEEKMHELQESKKHLIAEVIE 10- 44 Query: 1012 -GNETHASMSVDDIREIL 1028 G E +S++ ++IR+IL Sbjct: 1045 PGEEKLSSITEEEIRDIL 1062 A related DNA sequence was identified in S. pyogenes <SEQ ID 4823> which encodes the amino acid sequence <SEQ ID 4824>. Analysis of this protein sequence reveals the following: TABLE-US-04699 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3909(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04700 Identities = 674/1031 (65%), Positives = 834/1031 (80%), Gaps = 2/1031 (0%) Query: 1 MSRMIPGRIRNQGIELYEQGLVSLISQEGNLLKAKVGDCQIEYSLVTEETKCSCDFFARK 60 M+R+IPGR+RN+GI+LYEQGLVS +L+ +V Q++Y E+ C CD F K Sbjct: 2 MARLIPGRVRNEGIKLYEQGLVSFQDDNKGILQIEVETYQVQYGADDEDITCQCDTFHMK 61 Query: 61 GYCQHLAALEHFLKNDPEGKAILSKVQVQQESQQETKKKTSFGSVFLDSLIINEDDTIKY 120- YC+H+AA+E+FLKND +GK L ++ Q + ++ TKK TSFGS+FLDSL +NEDD++KY Sbjct: 62 HYCKHIAAVEYFLKNDQKGKLFLKQLTNQTKIKETTKKMTSFGSLFLDSLAMNEDDSVKY 121- Query: 121 QLSAQGEQNPYANDIWWTLKIRRLPDDRSYVIRDIKAFLNTVRKEAYYQIGKQYFETLSL 18- 0 +LSA G ++P+++D WW+LKI RLPDDRSYVIRDIK FL ++KE +YQIGK YFE LS Sbjct: 122 RLSALGSRSPFSSDYWWSLKINRLPDDRSYVIRDIKGFLQLIKKEGFYQIGKNYFEQLSW 18- 1 Query: 181 IQFDETSQELIEFLWRLIPSHSSKIDLEFILPNQGRHLSLTRGFFEEGVTLMNALENFSF 24- 0 +QFD +SQ LIEFLWRL S + K D E I PN RHL L GFFEEG+ + +L +F+F Sbjct: 182 LQFDPSSQALIEFLWRLA-SDTDKGDNENIFPNHARHLRLPSGFFEEGIHYLTSLYDFTF 24- 0 Query: 241 ESDFHQFNHLYFKELEGEDHLYQFKVIVHRQSIELEIKEKDLKPLFANSYLFYRDTFYHL 30- 0 E ++HL+ + LE E LY+FKV VHR+SIEL+I EK+++ LF N YL Y+DTFYHL Sbjct: 241 EGPSQTYHHLFVRSLEAEAGLYEFKVEVHRKSIELQIAEKNVQYLFDNDYLLYQDTFYHL 30- 0 Query: 301 NLKQEKMVTAIRSLPIEGDLAKHIHFDLDDQDKLAAHLLDFKEIGLVDAPRSFSIHDFKV 36- 0 LKQ KMV AIRSLPIE DLAKHIHFDLDD KLAA L DFK+IGLV+AP+SF+I DF+V Sbjct: 301 TLKQRKMVQAIRSLPIEADLAKHIHFDLDDHAKLAASLSDFKQIGLVEAPKSFAIRDFEV 36- 0 Query: 361 NFEFDINSQNEILLQMVFDYGNDLTVHNRQELEQLTFASHFKHEEKVFKLLEKYGFAPHF 42- 0 F+FD+ +++EI Q++FDYGN V ++ LE L FASH K EEK+ + L +GF+P F Sbjct: 361 TFQFDLLNRDEISCQLMFDYGN-YQVSDKASLEALPFASHLKKEEKINRSLLAFGFSPQF 41- 9 Query: 421 STSHPAYSAQELYDFYTYMLPQFKKMGTVSLSAKLESYRLIERPQIDIEAKGSLLDISFD 48- 0 + SA+ELY F+ +P F+++G V+LS +++ ++ E P+I I LLDISFD Sbjct: 420 YSKKRLTSAKELYTFFEETVPCFERLGNVALSTAIQALQVKEMPKIAIRRNQGLLDISFD 47- 9 Query: 481 FSDLLENDVDQALVALFDNNPYFVNKSGQLVIFDEETKKVSATLQGLRARRAKNGHIELD 54- 0 FS ++END+DQA+ ALF NNPYFV+++GQLV+FD+ET+KVS +LQ LRAR+ KNGH++LD Sbjct: 480 FSTIIENDIDQAVTALFQNNPYFVSQTGQLVVFDDETQKVSKSLQELRARQLKNGHLQLD 53- 9 Query: 541 NIAAFQLSELFANQDNVSFSQHFYQLIEDLRHPEKFKIPGLSVSASLRDYQLTGVRWLSM 60- 0 I A Q+S+LF +V FS+ +L L+HPE F I L V A +RDYQ GV+WLSM Sbjct: 540 GIRALQVSKLFEGMTSVHFSKELEELAYHLQHPETFSIKPLPVKAQMRDYQRNGVQWLSM 59- 9 Query: 601 LDHYGFAGILADDMGLGKTLQTISFLSTKLTRDSRVLILSPSSLIYNWQDEFHKFAPDVD 66- 0 L+HYGF GILADDMGLGKTLQT++FL++ L DS+VLILSPSSLIYNW DE KF P +D Sbjct: 600 LNHYGFGGILADDMGLGKTLQTLAFLASHLKSDSKVLILSPSSLIYNWFDECQKFTPQLD 65- 9 Query: 661 VAVAYGSKIRRDEIIAERHQVIITSYSSFRQDFETYSEGNYDYLILDEAQVMKNAQTKIA 72- 0 V V+YG K RD+II E HQ+ ITSYSSFRQDFETY +YDYLILDEAQV+KNAQTKI+ Sbjct: 660 VVVSYGLKQIRDQIIEEGHQITITSYSSFRQDFETYQAFHYDYLILDEAQVIKNAQTKIS 71- 9 Query: 721 HSLRSFEVKNCFALSGTPIENKLLEIWSIFQIILPGLLPGKKEFLKLNPKQVARYIKPFV 78- 0 H LR+F NCFALSGTPIENK+LEIWSIFQI+LPGLLP KKEFLKL +QV+RYIKPFV Sbjct: 720 HCLRAFNTANCFALSGTPIENKMLEIWSIFQIVLPGLLPTKKEFLKLTAEQVSRYIKPFV 77- 9 Query: 781 MRRRKEEVLPELPDLIEMNYPNEMTDSQKVIYLAQLRQIQESIQHSSDADLNRRKIEILS 84- 0 MRR+KE+VLPELPDLIE+NY NEMTD QK IYLAQLRQ+Q+ I++SSD D++R+KIEILS Sbjct: 780 MRRKKEDVLPELPDLIEINYSNEMTDEQKAIYLAQLRQMQDQIRNSSDVDISRQKIEILS 83- 9 Query: 841 GITRLRQICDTPRLFMDYDGESGKLESLRQLLTQIKENGHRALIFSQFRGMLDIAEREMV 90- 0 GITRLRQICDTP LFMDY G+SGKL+SLR LLTQIKENGHRALIFSQFRGMLD+A++EM Sbjct: 840 GITRLRQICDTPSLFMDYQGKSGKLDSLRILLTQIKENGHRALIFSQFRGMLDLAKQEMT 89- 9 Query: 901 AMGLTTYKITGSTPANERHEMTRAFNAGSKDAFLISLKAGGVGLNLTGADTVVLIDLWWN 96- 0 A+GLT+Y++TGSTPANER EMTRAFN GSKDAFLISLKAGGVG+NLTGADTV+LIDLWWN Sbjct: 900 ALGLTSYQMTGSTPANERQEMTRAFNNGSKDAFLISLKAGGVGINLTGADTVILIDLWWN 95- 9 Query: 961 PAVEMQAISRAHRLGQKENVEVYRLITRGTIEEKILEMQETKKHLVTTVLDGNETHASMS 10- 20 PAVEMQAISRA+R+GQKENVEVYRLITRGTIEEKILE+QE+K++LVTTVLDGNE+ ASMS Sbjct: 960 PAVEMQAISRAYRIGQKENVEVYRLITRGTIEEKILELQESKRNLVTTVLDGNESRASMS 10- 19 Query: 1021 VDDIREILGVS 1031 +++I+EILG++ Sbjct: 1020 IEEIKEILGLN 1030 SEQ ID 4822 (GBS369) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 64 (lane 5; MW 120 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 69 (lane 6; MW 142 kDa). The GBS369-GST fusion product was purified (FIG. 215, lane 7) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 303), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1562 A DNA sequence (GBSx1654) was identified in S. agalactiae <SEQ ID 4825> which encodes the amino acid sequence <SEQ ID 4826>. Analysis of this protein sequence reveals the following: TABLE-US-04701 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3391(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. There is also homology to SEQ ID 1034: TABLE-US-04702 Identities = 34/38 (89%), Positives = 37/38 (96%) Query: 1 MEKEAKQIIDLKRNLFKIDVRAQKDEEKVFMRTACQFS 38 +EKEAKQ+IDLKRNLFKIDVRAQKDEEKVFMRTAC+ S Sbjct: 1 LEKEAKQMIDLKRNLFKIDVRAQKDEEKVFMRTACRQS 38 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1563 A DNA sequence (GBSx1656) was identified in S. agalactiae <SEQ ID 4827> which encodes the amino acid sequence <SEQ ID 4828>. This protein is predicted to be phosphoglycerate dehydrogenase (era2). Analysis of this protein sequence reveals the following: TABLE-US-04703 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3709(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04704 >GP: BAA88823 GB: AB016077 phosphoglycerate dehydrogenase [Streptococcus mutans] Identities = 377/436 (86%), Positives = 414/436 (94%) Query: 1 MVLPTVAIVGRPNVGKSTLFNRIAGERISIVEDVEGVTRDRIYTTGEWLNRKFSLIDTGG 60 M LPTVAIVGRPNVGKS LFNRIAGERISIVEDVEGVTRDRIYT EWLNR+FS+IDTGG Sbjct: 1 MALPTVAIVGRPNVGKSALFNRIAGERISIVEDVEGVTRDRIYTKAEWLNRQFSIIDTGG 60 Query: 61 IDDVDAPFMEQIKHQADIAMTEADVIVFVVSGKEGVTDADEYVSRILYKTNKPVILAVNK 120- IDDVDAPFMEQIKHQADIAMTEADVIVFVVS KEG+TDADEYV++ILY+T+KPVILAVNK Sbjct: 61 IDDVDAPFMEQIKHQADIAMTEADVIVFVVSAKEGITDADEYVAKILYRTHKPVILAVNK 120- Query: 121 VDNPEMRNDIYDFYSLGLGDPYPLSSVHGIGTGDILDAIVENLPVEEENENPDIIRFSLI 18- 0 VDNPEMR+ IYDFY+LGLGDPYP+SS HGIGTGD+LDAIV+NLP E + E+ DII+FSLI Sbjct: 121 VDNPEMRSAIYDFYALGLGDPYPVSSAHGIGTGDVLDAIVDNLPAEAQEESSDIIKFSLI 18- 0 Query: 181 GRPNVGKSSLINAILGEDRVIASPVAGTTRDAIDTNFVDSQGQEYTMIDTAGMRKSGKVY 24- 0 GRPNVGKSSLINAILGEDRVIASPVAGTTRDAIDT F D +GQE+TMIDTAGMRKSGKVY Sbjct: 181 GRPNVGKSSLINAILGEDRVIASPVAGTTRDAIDTTFTDEEGQEFTMIDTAGMRKSGKVY 24- 0 Query: 241 ENTEKYSVMRSMRAIDRSDVVLMVINAEEGIREYDKRIAGFAHETGKGIIIVVNKWDTIE 30- 0 ENTEKYSVMR+MRAIDRSD+VLMV+NAEEGIREYDKRIAGFAHE GKGI++VVNKWD I+ Sbjct: 241 ENTEKYSVMRAMRAIDRSDIVLMVLNAEEGIREYDKRIAGFAHEAGKGIVVVVNKWDAIK 30- 0 Query: 301 KDNHTVSQWEADIRDNFQFLSYAPIIFVSAETKQRLHKLPDMIKRISESQNKRIPSAVLN 36- 0 KDN TV+QWE DIRDNFQ++ YAPI+FVSA TKQRLHKLPD+IK++S+SQN RIPS+VLN Sbjct: 301 KDNRTVAQWETDIRDNFQYIPYAPIVFVSAVTKQRLHKLPDVIKQVSQSQNTRIPSSVLN 36- 0 Query: 361 DVIMDAIAINPTPTDKGKRLKIFYATQVAVKPPTFVVFVNEEELMHFSYLRFLENQIREA 42- 0 DV+MDA+AINPTPTDKGKRLKIFYATQV+VKPPTFV+FVNEEELMHFSYLRFLENQIR+A Sbjct: 361 DVVMDAVAINPTPTDKGKRLKIFYATQVSVKPPTFVIFVNEEELMHFSYLRFLENQIRQA 42- 0 Query: 421 FVFEGTPINLIARKRK 436 FVFEGTPI LIARKRK Sbjct: 421 FVFEGTPIRLIARKRK 436 A related DNA sequence was identified in S. pyogenes <SEQ ID 4829> which encodes the amino acid sequence <SEQ ID 4830>. Analysis of this protein sequence reveals the following: TABLE-US-04705 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3463(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-04706 Identities = 403/436 (92%), Positives = 422/436 (96%) Query: 1 MVLPTVAIVGRPNVGKSTLFNRIAGERISIVEDVEGVTRDRIYTTGEWLNRKFSLIDTGG 60 MVLPTVAIVGRPNVGKSTLFNRIAGERISIVEDVEGVTRDRIY TGEWLNR+FSLIDTGG Sbjct: 1 MVLPTVAIVGRPNVGKSTLFNRIAGERISIVEDVEGVTRDRIYATGEWLNRQFSLIDTGG 60 Query: 61 IDDVDAPFMEQIKHQADIAMTEADVIVFVVSGKEGVTDADEYVSRILYKTNKPVILAVNK 120- IDDVDAPFMEQIKHQA IAM EADVIVFVVSGKEGVTDADEYVS+ILY+TN PVILAVNK Sbjct: 61 IDDVDAPFMEQIKHQAQIAMEEADVIVFVVSGKEGVTDADEYVSKILYRTNTPVILAVNK 120- Query: 121 VDNPEMRNDIYDFYSLGLGDPYPLSSVHGIGTGDILDAIVENLPVEEENENPDIIRFSLI 18- 0 VDNPEMRNDIYDFYSLGLGDPYP+SSVHGIGTGD+LDAIVENLPVEE EN DIIRFSLI Sbjct: 121 VDNPEMRNDIYDFYSLGLGDPYPVSSVHGIGTGDVLDAIVENLPVEEAEENDDIIRFSLI 18- 0 Query: 181 GRPNVGKSSLINAILGEDRVIASPVAGTTRDAIDTNFVDSQGQEYTMIDTAGMRKSGKVY 24- 0 GRPNVGKSSLINAILGEDRVIASPVAGTTRDAIDT+F D+ GQE+TMIDTAGMRKSGK+Y Sbjct: 181 GRPNVGKSSLINAILGEDRVIASPVAGTTRDAIDTHFTDADGQEFTMIDTAGMRKSGKIY 24- 0 Query: 241 ENTEKYSVMRSMRAIDRSDVVLMVINAEEGIREYDKRIAGFAHETGKGIIIVVNKWDTIE 30- 0 ENTEKYSVMR+MRAIDRSDVVLMVINAEEGIREYDKRIAGFAHE GKG+IIVVNKWDTI+ Sbjct: 241 ENTEKYSVMRAMRAIDRSDVVLMVINAEEGIREYDKRIAGFAHEAGKGMIIVVNKWDTID 30- 0 Query: 301 KDNHTVSQWEADIRDNFQFLSYAPIIFVSAETKQRLHKLPDMIKRISESQNKRIPSAVLN 36- 0 KDNHTV++WEADIRD FQFL+YAPIIFVSA TKQRL+KLPD+IKRISESQNKRIPSAVLN Sbjct: 301 KDNHTVAKWEADIRDQFQFLTYAPIIFVSALTKQRLNKLPDLIKRISESQNKRIPSAVLN 36- 0 Query: 361 DVIMDAIAINPTPTDKGKRLKIFYATQVAVKPPTFVVFVNEEELMHFSYLRFLENQIREA 42- 0 DVIMDAIAINPTPTDKGKRLKIFYATQV+VKPPTFVVFVNEEELMHFSYLRFLENQIR A Sbjct: 361 DVIMDAIAINPTPTDKGKRLKIFYATQVSVKPPTFVVFVNEEELMHFSYLRFLENQIRAA 42- 0 Query: 421 FVFEGTPINLIARKRK 436 F FEGTPI+LIARKRK Sbjct: 421 FTFEGTPIHLIARKRK 436 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1564 A DNA sequence (GBSx1657) was identified in S. agalactiae <SEQ ID 4831> which encodes the amino acid sequence <SEQ ID 4832>. Analysis of this protein sequence reveals the following: TABLE-US-04707 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2734(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04708 >GP: AAC00359 GB: AF008220 DnaI [Bacillus subtilis] Identities = 105/313 (33%), Positives = 191/313 (60%), Gaps = 17/313 (5%) Query: 1 MKSVGQALENQGRVP--RNTNDELIQMILADAQVAEFIKTHQ--LSQREINISMSKFNQF 56 M+ +G++L+ P + +++ + ++ D V F+K ++ + Q+ I S++K ++ Sbjct: 1 MEPIGRSLQGVTGRPDFQKRLEQMKEKVMKDQDVQAFLKENEEVIDQKMIEKSLNKLYEY 60 Query: 57 LIERQK-----FKNKDSQYIAKGYEPILVMNEGYADVSYLE--TRELIEAQKKQAISDRI 109- IE+ K ++++ + +GY P LV+N D+ Y E + ++ QKKQ + Sbjct: 61 -IEQSKNCSYCSEDENCNNLLEGYHPKLVVNGRSIDIEYYECPVKRKLDQQKKQ--QSLM 117- Query: 110 NLVNLPKSYRNIRMTDFDINNESRMKAMSQLLDFVETYPSYNH-KGLYLYGDMGVGKSYL 16- 8 + + + DI++ SR+ + DF+++Y KGLYLYG GVGK+++ Sbjct: 118 KSMYIQQDLLGATFQQVDISDPSRLAMFQHVTDFLKSYNETGKGKGLYLYGKFGVGKTFM 17- 7 Query: 169 MAAMARELSERKGVSTTLLHFPSFAIDVKNAISSGTVKDEIDAVKSVPILILDDIGAEQA 22- 8 +AA+A EL+E++ S+ +++ P F ++KN++ T++++++ VK+ P+L+LDDIGAE Sbjct: 178 LAAIANELAEKE-YSSMIVYVPEFVRELKNSLQDQTLEEKLNMVKTTPVLMLDDIGAESM 23- 6 Query: 229 TSWVRDEILQVILQHRMLEELPTFFTSNYSFNDLERKWA-NIKGSDETWQAKRVMERVRY 28- 7 TSWVRDE++ +LQHRM ++LPTFF+SN+S ++L+ + + +G E +A R+MER+ Y Sbjct: 237 TSWVRDEVIGTVLQHRMSQQLPTFFSSNFSPDELKHHFTYSQRGEKEEVKAARLMERILY 29- 6 Query: 288 LAIEFHLEGPNRR 300 LA L+G NRR Sbjct: 297 LAAPIRLDGENRR 309 A related DNA sequence was identified in S. pyogenes <SEQ ID 4833> which encodes the amino acid sequence <SEQ ID 4834>. Analysis of this protein sequence reveals the following: TABLE-US-04709 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1944(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04710 Identities = 228/300 (76%), Positives = 264/300 (88%) Query: 1 MKSVGQALENQGRVPRNTNDELIQMILADAQVAEFIKTHQLSQREINISMSKFNQFLIER 60 M+ +G+ + G+ R +D+LIQ ILAD +VA FI H LSQ +IN+S+SKFNQFL+ER Sbjct: 1 MEKIGETMAKLGQNTRVNSDQLIQTILADPEVASFISQHHLSQEQINLSLSKFNQFLVER 60 Query: 61 QKFKNKDSQYIAKGYEPILVMNEGYADVSYLETRELIEAQKKQAISDRINLVNLPKSYRN 120- QK++ KD YIAKGY+PIL MNEGYADVSYLET+EL+EAQK+ AIS+RI LV+LPKSYR+ Sbjct: 61 QKYQLKDPSYIAKGYQPILAMNEGYADVSYLETKELVEAQKQAAISERIQLVSLPKSYRH 120- Query: 121 IRMTDFDINNESRMKAMSQLLDFVETYPSYNHKGLYLYGDMGVGKSYLMAAMARELSERK 18- 0 I ++D D+NN SRM+A S +LDFVE YPS KGLYLYGDMG+GKSYL+AAMA ELSE+K Sbjct: 121 IHLSDIDVNNASRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKK 18- 0 Query: 181 GVSTTLLHFPSFAIDVKNAISSGTVKDEIDAVKSVPILILDDIGAEQATSWVRDEILQVI 24- 0 GVSTTLLHFPSFAIDVKNAIS+G+VK+EIDAVK+VP+LILDDIGAEQATSWVRDE+LQVI Sbjct: 181 GVSTTLLHFPSFAIDVKNAISNGSVKEEIDAVKNVPVLILDDIGAEQATSWVRDEVLQVI 24- 0 Query: 241 LQHRMLEELPTFFTSNYSFNDLERKWANIKGSDETWQAKRVMERVRYLAIEFHLEGPNRR 30- 0 LQ+RMLEELPTFFTSNYSF DLERKWA IKGSDETWQAKRVMERVRYLA EFHLEG NRR Sbjct: 241 LQYRMLEELPTFFTSNYSFADLERKWATIKGSDETWQAKRVMERVRYLAREFHLEGANRR 30- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1565 A DNA sequence (GBSx1658) was identified in S. agalactiae <SEQ ID 4835> which encodes the amino acid sequence <SEQ ID 4836>. Analysis of this protein sequence reveals the following: TABLE-US-04711 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2660(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4837> which encodes the amino acid sequence <SEQ ID 4838>. Analysis of this protein sequence reveals the following: TABLE-US-04712 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2135(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04713 Identities = 217/391 (55%) Positives = 309/391 (78%) Query: 1 MMSPIDEFTYIKQNKIVYDSNSLIQLYFPIMGSDAMALYDYFVHFFDDGIRRHKFSEVLN 60 MM PID FTY+K+NK+ DS +LIQLYFPI+GSDA+++Y YF+HFFDDG++RHKFS++LN Sbjct: 1 MMKPIDTFTYLKRNKVTLDSVTLIQLYFPIIGSDAVSIYQYFIHFFDDGLQRHKFSDILN 60 Query: 61 HLQYGMPRFQDALVMLTALDLLTVYQATGTYLVKLNQAMSNELFLSNPIYRRLLEKRIGE 120- HLQ+GM RF+DAL +LTA++L++VYQ + TYL+ L+Q +S +LF +P Y RLLE++IGE Sbjct: 61 HLQFGMKRFEDALAILTAMELVSVYQLSDTYLITLHQPLSRDLFFQHPAYSRLLEQKIGE 120- Query: 121 VAVAELDMKIPKNARDISKKFTDVFSDLGQPKQEVNRSKNVFDLESFKRLMMRDGLRFNN 18- 0 VAV+EL + +P AR+ISK+F+D+F G + + FDL SF++LM+RDGL+F + Sbjct: 121 VAVSELQVTVPSQARNISKRFSDIFGVQGDLTNVPQKPQKNFDLSSFQQLMVRDGLQFED 18- 0 Query: 181 EKDDVLGIYSVSELYHLNWYDTYQLAKQTAINGMIAPQRMKVQQNEGQHIKDNQSFTNNE 24- 0 + D++ +YS++E Y + W+DTYQ+AK TA+NG I P+R+ ++N+ ++F+ E Sbjct: 181 NQKDIISLYSIAEQYDMTWFDTYQIAKATAVNGKIRPERLLAKKNQSMTKPSKENFSQAE 24- 0 Query: 241 KVILRESKNDSALVFLEKIKRSRKAVTTSGEKTLLEDLAKMNFLDEVINVMVLYTLNKTK 30- 0 ++ILRE+K DSALVFLEKIK++R+A T E+ LL+ LAKMNFLD+VINVMVLYT NKTK Sbjct: 241 QIILREAKQDSALVFLEKIKKARRATITKDERILLQTLAKMNFLDDVINVMVLYTFNKTK 30- 0 Query: 301 SANLNKAYIMKVANDFAFQNVMTAEDAVLKIRDFSDQKVRTKTETKKKQSNVPEWSNPDY 36- 0 SANL K+Y++K+ANDFA+Q V TAE+A++ +R F+D++ R +++ K QSNVP+WSNPDY Sbjct: 301 SANLQKSYVLKMANDFAYQKVSTAEEAIVVLRAFTDRQSRRQSKVKTSQSNVPKWSNPDY 36- 0 Query: 361 KDEVSPEKEIELEQFKTDALKRLERLGKDGE 391 ++ S E++ +L+QFK ALKRLE LGK G+ Sbjct: 361 QETTSQEEQAKLDQFKQAALKRLENLGKGGD 391 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1566 A DNA sequence (GBSx1659) was identified in S. agalactiae <SEQ ID 4839> which encodes the amino acid sequence <SEQ ID 4840>. Analysis of this protein sequence reveals the following: TABLE-US-04714 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4485(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04715 >GP: BAB06865 GB: AP001517 unknown conserved protein [Bacillus halodurans] Identities = 80/150 (53%), Positives = 115/150 (76%) Query: 1 MRCPKCGYNKSSVVDSRQAEEGTTIRRRRECEKCGNRFTTFERLEELPLLVIKKDGTREQ 60 MRCP C +N + V+DSR A EG +IRRRRECE C +RFTTFE +EE+PL+V+KKDGTR++ Sbjct: 1 MRCPACHHNGTRVLDSRPAHEGRSIRRRRECESCNHRFTTFEMIEEVPLIVVKKDGTRQE 60 Query: 61 FSRDKILNGIIQSAQKRPVSSEDIENCILRIERKIRSEYEDEVSSITIGNLVMDELAELD 120- FS DKIL G+I++ +KRPV E +E + +ER++R + ++EV S IG LVM+ LA +D Sbjct: 61 FSSDKILRGLIRACEKRPVPLETLEGIVNEVERELRGQGKNEVDSKEIGELVMERLANVD 120- Query: 121 EITYVRFASVYKSFKDVDEIEELLQQITKR 150 ++ YVRFASVY+ FKD++ + L+++ +R Sbjct: 121 DVAYVRFASVYRQFKDINVFIQELKELMER 150 A related DNA sequence was identified in S. pyogenes <SEQ ID 4841> which encodes the amino acid sequence <SEQ ID 4842>. Analysis of this protein sequence reveals the following: TABLE-US-04716 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4365(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04717 Identities = 131/155 (84%), Positives = 143/155 (91%) Query: 1 MRCPKCGYNKSSVVDSRQAEEGTTIRRRRECEKCGNRFTTFERLEELPLLVIKKDGTREQ 60 +RCPKC Y+KSSVVDSRQAE+G TIRRRRECE+C RFTTFER+EELPLLVIKKDGTREQ Sbjct: 1 VRCPKCNYHKSSVVDSRQAEDGNTIRRRRECEQCHTRFTTFERVEELPLLVIKKDGTREQ 60 Query: 61 FSRDKILNGIIQSAQKRPVSSEDIENCILRIERKIRSEYEDEVSSITIGNLVMDELAELD 120- FSRDKILNG++QSAQKRPVSS DIEN I RIE+++R+ YE+EVSS IGNLVMDELAELD Sbjct: 61 FSRDKILNGVVQSAQKRPVSSTDIENVISRIEQEVRTTYENEVSSTAIGNLVMDELAELD 120- Query: 121 EITYVRFASVYKSFKDVDEIEELLQQITKRVRSKK 155 EITYVRFASVYKSFKDVDEIEELLQQIT RVR KK Sbjct: 121 EITYVRFASVYKSFKDVDEIEELLQQITNRVRGKK 155 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1567 A DNA sequence (GBSx1660) was identified in S. agalactiae <SEQ ID 4843> which encodes the amino acid sequence <SEQ ID 4844>. This protein is predicted to be CsrS (mtrB). Analysis of this protein sequence reveals the following: TABLE-US-04718 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.30 Transmembrane 22-38 (18-43) INTEGRAL Likelihood = -9.66 Transmembrane 189-205 (187-212) ----- Final Results ----- bacterial membrane --- Certainty = 0.5522(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 2109> which encodes the amino acid sequence <SEQ ID 2110>. Analysis of this protein sequence reveals the following: TABLE-US-04719 Possible site: 35 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.32 Transmembrane 196-212 (189-214) ----- Final Results ----- bacterial membrane --- Certainty = 0.3527(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04720 Identities = 248/501 (49%), Positives = 363/501 (71%), Gaps = 4/501 (0%) Query: 1 MKNKKDQFIGVKQPLSKKLSQLVFILFFSLFTVFSVLVYTSATRYVLHREKINVGRSLEK 60 M+N+K + K L K+LS + F+LFF +F+ F+++ Y+S ++L +EK +V +++ Sbjct: 1 MENQKQKQKKYKNSLPKRLSNIFFVLFFCIFSAFTLIAYSSTNYFLLKKEKQSVFQAVNI 60 Query: 61 TRVRLSQANSSLTSDDILEILYNQVFADDIYPHKRQNGIVRTGESIDSILYVNQEMTLYD 120- RVRLS+ +S+ T +++ E+LY ++ + ++R+ I + L NQ++ +Y+ Sbjct: 61 VRVRLSEVDSNFTLENLAEVLYKNDKTHLRIDDRKGSRVIRSERDITNTLDANQDIYVYN 120- Query: 121 VNRKPVFST-LRTGMPTIGKSMGKVIISKVADM-EGFVGTKAIYSQKTGQLLGYVQIFYN 17- 8 ++++ +F+T P + +G+V + D GF T+ +YS +TG+ +GYVQ+F++ Sbjct: 121 IDKQMIFTTDNEESSPGLHGPIGRVYHDHIEDQYRGFSMTQKVYSNRTGKFVGYVQVFHD 18- 0 Query: 179 LGRYYSMRQNIIVFLIMMEVLGTVLALVVINSATKRIVRPVKNLHDLMHQISENPSNLEI 23- 8 LG YY +R ++ +L+++E+ GT LA ++I T+R ++P+ NLH++M ISENP+NL + Sbjct: 181 LGNYYVIRARLLFWLLVVELFGTSLAYLIILITTRRFLKPLHNLHEVMRNISENPNNLNL 24- 0 Query: 239 RSKVRSEDEIGELSRIFDGMLDQLEDYTRRQSQFISDVSHELRTPVAVVKGHIGLLQRWG 29- 8 RS + S DEI ELS IFD MLD+LE +T+ QS+FISDVSHELRTPVA++KGHIGLLQRWG Sbjct: 241 RSDISSGDEIEELSVIFDNMLDKLETHTKLQSRFISDVSHELRTPVAIIKGHIGLLQRWG 30- 0 Query: 299 KDDPEILEESLAAAYHEADRMSLMINDMLNMIRVQGSLELHQDEVTDLSSSISVVIENFR 35- 8 KDD +ILEESL A HEADRM++MINDML+MIRVQGS E HQ+++T L SI V+ NFR Sbjct: 301 KDDSDILEESLTATAHEADRMAIMINDMLDMIRVQGSFEGHQNDMTVLEDSIETVVGNFR 36- 0 Query: 359 ILREDFQFIFENNISDIVWGKIYKIHFEQALMILIDNAIKYSPSYKEVSVVLSVDNDFAT 41- 8 +LREDF F +++ + +IYK HFEQALMILIDNA+KYS K++++ LSV Sbjct: 361 VLREDFIFTWQSENPKTI-ARIYKNHFEQALMILIDNAVKYSRKEKKIAINLSVTGKQEA 41- 9 Query: 419 VV-VKDKGEGISDEDIEFIFDRFYRTDKSRNRESTQAGLGIGLSVFKQIMDAYHLKVDIK 47- 7 +V V+DKGEGIS EDIE IF+RFYRTDKSRNR STQAGLGIGLS+ KQI+D YHL++ ++ Sbjct: 420 IVRVQDKGEGISKEDIEHIFERFYRTDKSRNRTSTQAGLGIGLSILKQIVDGYHLQMKVE 47- 9 Query: 478 SELNQGTEFIVRIPIKKFEET 498 SELN+G+ FI+ IP+ + +E+ Sbjct: 480 SELNEGSVFILHIPLAQSKES 500 A related GBS gene <SEQ ID 8845> and protein <SEQ ID 8846> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04721 Lipop: Possible site: -1 Crend: 5 SRCFLG: 0 McG: Length of UR: 5 Peak Value of UR: 0.74 Net Charge of CR: 2 McG: Discrim Score: -10.19 GvH: Signal Score (-7.5): -3.66 Possible site: 35 >>> Seems to have no N-terminal signal sequence Amino Acid Composition: calculated from 1 ALOM program count: 2 value: -11.30 threshold: 0.0 INTEGRAL Likelihood = -11.30 Transmembrane 22-38 (18-43) INTEGRAL Likelihood = -9.66 Transmembrane 189-205 (187-212) PERIPHERAL Likelihood = 2.86 405 modified ALOM score: 2.76 icml HYPID: 7 CFP: 0.552 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5522(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8846 (GBS321) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 173 (lane 6; MW 84 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 80 (lane 2; MW 58.7 kDa). GBS321-GST was purified as shown in FIG. 220, lane 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1568 A DNA sequence (GBSx1661) was identified in S. agalactiae <SEQ ID 4845> which encodes the amino acid sequence <SEQ ID 4846>. This protein is predicted to be CsrR (trcR). Analysis of this protein sequence reveals the following: TABLE-US-04722 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2649(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 3259> which encodes the amino acid sequence <SEQ ID 3260>. Analysis of this protein sequence reveals the following: TABLE-US-04723 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3226(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04724 Identities = 193/229 (84%), Positives = 211/229 (91%), Gaps = 1/229 (0%) Query: 1 MGKKILIIEDEKNLARFVSLELLHEGYDVVVETNGREGLDTALEKDFDLILLDLMLPEMD 60 M KKILIIEDEKNLARFVSLEL HEGY+V+VE NGREGL+TALEK+FDLILLDLMLPEMD Sbjct: 1 MTKKILIIEDEKNLARFVSLELQHEGYEVIVEVNGREGLETALEKEFDLILLDLMLPEMD 60 Query: 61 GFEITRRLQAEKTTYIMMMTARDSVMDIVAGLDRGADDYIVKPFAIEELLARVRAIFRRQ 120- GFE+TRRLQ EKTTYIMMMTARDS+MD+VAGLDRGADDYIVKPFAIEELLAR+RAIFRRQ Sbjct: 61 GFEVTRRLQTEKTTYIMMMTARDSIMDVVAGLDRGADDYIVKPFAIEELLARIRAIFRRQ 120- Query: 121 EIETKTKEKGDSGSFRDLSLNTHNRSAMRGDEEISLTKREFDLLNVLMTNMNRVMTREEL 18- 0 +IE++ K+ G +RDL LN NRS RGD+EISLTKRE+DLLN+LMTNMNRVMTREEL Sbjct: 121 DIESE-KKVPSQGIYRDLVLNPQNRSVNRGDDEISLTKREYDLLNILMTNMNRVMTREEL 17- 9 Query: 181 LEHVWKYDVAAETNVVDVYIRYLRGKIDIPGRESYIQTVRGMGYVIREK 229 L +VWKYD A ETNVVDVYIRYLRGKIDIPG+ESYIQTVRGMGYVIREK Sbjct: 180 LSNVWKYDEAVETNVVDVYIRYLRGKIDIPGKESYIQTVRGMGYVIREK 228 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1569 A DNA sequence (GBSx1662) was identified in S. agalactiae <SEQ ID 4847> which encodes the amino acid sequence <SEQ ID 4848>. Analysis of this protein sequence reveals the following:

TABLE-US-04725 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3864(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04726 >GP: AAG32547 GB: U12643 YlbN-like hypothetical protein [Streptococcus gordonii] Identities = 91/174 (52%), Positives = 133/174 (76%), Gaps = 3/174 (1%) Query: 3 LTEIKKSPEGLYFDKKIDIKESLMERHSEIMDISDIQVSGHVVYEDGLYLLDYNMAYDIT 62 + EI+K+P+GL F+KK+D+ E L ER++EI+D+ DI SG YEDGLY LDY ++Y IT Sbjct: 4 IQEIRKNPDGLAFEKKLDLAEELKERNAEILDVQDIVASGRAQYEDGLYFLDYELSYTIT 63 Query: 63 LPSSRSMKPVVLSEKQTINEVFIEAENVSTKKELVDQELVLILEEDDINLEESVIDNILL 122- L SSRSM+PV E +NE+F+E V++ +E++DQ+LVL +E +IN+ ESV DNILL Sbjct: 64 LASSRSMEPVERKESYLVNEIFMEDGQVAS-QEMIDQDLVLPIENGEINVAESVADNILL 122- Query: 123 NIPLRVL-AADEVGVEADLSGKNWSLMTEKQYEEKQAKEKEKSNPFAALEGMFD 175 NIPL+VL AA+E G + +G++W +MTE Y++ QA++KE+++PFA L+G+FD Sbjct: 123 NIPLKVLTAAEEAGSDLP-TGRDWQVMTEDDYQKYQAEKKEENSPFAGLQGLFD 175 A related DNA sequence was identified in S. pyogenes <SEQ ID 4849> which encodes the amino acid sequence <SEQ ID 4850>. Analysis of this protein sequence reveals the following: TABLE-US-04727 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3032(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04728 Identities = 86/175 (49%), Positives = 135/175 (77%) Query: 1 MLLTEIKKSPEGLYFDKKIDIKESLMERHSEIMDISDIQVSGHVVYEDGLYLLDYNMAYD 60 + ++EI+K P+GL FD+ D+K L+ER +I+DI ++ G+V Y+ GLYLLDY ++Y+ Sbjct: 3 LAISEIRKHPDGLSFDRLCDVKSMLLERDQQIIDIKAVKAVGNVRYDKGLYLLDYQLSYE 62 Query: 61 ITLPSSRSMKPVVLSEKQTINEVFIEAENVSTKKELVDQELVLILEEDDINLEESVIDNI 120- + LPSSRSM PV LSE Q I E+FIEA +++ KKELV+ LVL+L++D INLEES++DNI Sbjct: 63 VILPSSRSMVPVCLSEVQHIQELFIEATDLADKKELVEDNLVLVLDKDAINLEESIVDNI 122- Query: 121 LLNIPLRVLAADEVGVEADLSGKNWSLMTEKQYEEKQAKEKEKSNPFAALEGMFD 175 LL IP++VL +E + +G+NW+++TE+ Y+ + ++++++NPFA+L+G+FD Sbjct: 123 LLAIPVQVLTEEEKKSKELPAGQNWAVLTEEDYQCLKEEKQKENNPFASLQGLFD 177 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1570 A DNA sequence (GBSx1663) was identified in S. agalactiae <SEQ ID 4851> which encodes the amino acid sequence <SEQ ID 4852>. This protein is predicted to be heat shock protein (htpX). Analysis of this protein sequence reveals the following: TABLE-US-04729 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -11.30 Transmembrane 195-211 (190-221) INTEGRAL Likelihood = -11.09 Transmembrane 43-59 (31-62) INTEGRAL Likelihood = -3.61 Transmembrane 153-169 (153-174) ----- Final Results ----- bacterial membrane --- Certainty = 0.5522(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04730 >GP: AAB70525 GB: AF017421 putative heat shock protein HtpX [Streptococcus gordonii] Identities = 220/297 (74%), Positives = 261/297 (87%), Gaps = 1/297 (0%) Query: 1 MLYQQIASNKRKTVVLLIVFFCLLAAIGAAVGYLVLGSYQFGLVLALIIGVIYAVSMIFQ 60 ML++QIA+NKR+T LL+ FF LLA IGAA GYL + S G+++A IIG+IYA++MIFQ Sbjct: 1 MLFEQIAANKRRTWFLLVAFFALLALIGAAAGYLWMNSPLGGVIIAFIIGLIYAITMIFQ 60 Query: 61 STNVVMSMNNAREVTEDEAPNYFHIVEDMAMIAQIPMPRVFIVEDDSLNAFATGSKPENA 120- ST VVMSMN AR+V+E EAP +HIV+DMAM+AQIPMPRV+IVEDDS NAFATGS PENA Sbjct: 61 STEVVMSMNGARQVSEQEAPELYHIVQDMANVAQIPMPRVYIVEDDSPNAFATGSNPENA 120- Query: 121 AVAATTGLLAVMNREELEGVIGHEVSHIRNYDIRISTIAVALASAVTLISSIGSRMLFYG 18- 0 AVAATTGLL +MNREELEGVIGHEVSHIRNYDIRISTIAVALASA+T+ISS+ RM++YG Sbjct: 121 AVAATTGLLRLMNREELEGVIGHEVSHIRNYDIRISTIAVALASAITMISSVAGRMNWYG 18- 0 Query: 181 GGRRRDDDREDGG-NILVLIFSILSLILAPLAASLVQLAISRQREYLADASSVELTRNPQ 23- 9 GGRRR+D +D G +L+L+FS++++ILAPLAA+LVQLAISRQRE+LADASSVELTRNPQ Sbjct: 181 GGRRRNDRDDDSGLGLLMLVFSLIAIILAPLAATLVQLAISRQREFLADASSVELTRNPQ 24- 0 Query: 240 GMISALEKLDRSEPMGHPVDDASAALYINDPTKKEGLKSLFYTHPPIADRIERLRHM 296 GMI AL+KLD SEPM VDDASAALYI+DP KK GL+ LFYTHPPI++R+ERLR M Sbjct: 241 GMIRALQKLDNSEPMHRHVDDASAALYISDPKKKGGLQKLFYTHPPISERVERLRKM 297 A related DNA sequence was identified in S. pyogenes <SEQ ID 4853> which encodes the amino acid sequence <SEQ ID 4854>. Analysis of this protein sequence reveals the following: TABLE-US-04731 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.77 Transmembrane 197-213 (192-223) INTEGRAL Likelihood = -8.33 Transmembrane 43-59 (33-61) INTEGRAL Likelihood = -3.82 Transmembrane 153-169 (153-174) ----- Final Results ----- bacterial membrane --- Certainty = 0.4906(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04732 >GP: AAB70525 GB: AF017421 putative heat shock protein HtpX [Streptococcus gordonii] Identities = 208/298 (69%), Positives = 257/298 (85%), Gaps = 1/298 (0%) Query: 1 MLYQQISQNKQRTVVLLVGFFALLALIGASAGYLLLDNYAMGLVLALVIGVIYATSMIFQ 60 ML++QI+ NK+RT LLV FFALLALIGA+AGYL +++ G+++A +IG+IYA +MIFQ Sbjct: 1 MLFEQIAANKRRTWFLLVAFFALLALIGAAAGYLWMNSPLGGVIIAFIIGLIYATTMIFQ 60 Query: 61 STSLVMSMNNAREVTEKEAPGFFHIVEDMAMVAQIPMPRVFIIEDPSLNAFATGSSPQNA 120- ST +VMSMN AR+V+E+EAP +HIV+DMAMVAQIPMPRV+I+ED S NAFATGS+P+NA Sbjct: 61 STEVVMSMNGARQVSEQEAPELYHIVQDMAMVAQIPMPRVYIVEDDSPNAFATGSNPENA 120- Query: 121 AVAATTGLLEVMNREELEGVIGHEISHIRNYDIRISTIAVALASAVTVISSIGGRMLWYG 18- 0 AVAATTGLL +MNREELEGVIGHE+SHIRNYDIRISTIAVALASA+T+ISS+ GRM+WYG Sbjct: 121 AVAATTGLLRLMNREELEGVIGHEVSHIRNYDIRISTIAVALASAITMISSVAGRMMWYG 18- 0 Query: 181 GGSRRQRDDGDDDVLRIITLLLSLLSLLLAPLVASLIQLAISRQREYLADASSVELTRNP 24- 0 GG RR+ D DD L ++ L+ SL++++LAPL A+L+QLAISRQRE+LADASSVELTRNP Sbjct: 181 GG-RRRNDRDDDSGLGLLMLVFSLIAIILAPLAATLVQLAISRQREFLADASSVELTRNP 23- 9 Query: 241 QGMIKALEKLQLSQPMKHPVDDASAALYINEPRKKRSFSSLFSTHPPIEERIERLKNM 298 QGMI+AL+KL S+PM VDDASAALYI++P+KK LF THPPI ER+ERL+ M Sbjct: 240 QGMIRALQKLDNSEPMHRHVDDASAALYISDPKKKGGLQKLFYTHPPISERVERLRKM 297 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04733 Identities = 233/298 (78%), Positives = 262/298 (87%), Gaps = 2/298 (0%) Query: 1 MLYQQIASNKRKTVVLLIVFFCLLAAIGAAVGYLVLGSYQFGLVLALIIGVIYAVSMIFQ 60 MLYQQI+ NK++TVVLL+ FF LLA IGA+ GYL+L +Y GLVLAL+IGVIYA SMIFQ Sbjct: 1 MLYQQISQNKQRTVVLLVGFFALLALIGASAGYLLLDNYAMGLVLALVIGVIYATSMIFQ 60 Query: 61 STNVVMSMNNAREVTEDEAPNYFHIVEDMAMIAQIPMPRVFIVEDDSLNAFATGSKPENA 120- ST++VMSMNNAREVTE EAP +FHIVEDMAM+AQIPMPRVFI+ED SLNAFATGS P+NA Sbjct: 61 STSLVMSMNNAREVTEKEAPGFFHIVEDMAMVAQIPMPRVFIIEDPSLNAFATGSSPQNA 120- Query: 121 AVAATTGLLAVMNREELEGVIGHEVSHIRNYDIRISTIAVALASAVTLISSIGSRMLFYG 18- 0 AVAATTGLL VMNREELEGVIGHE+SHIRNYDIRISTIAVALASAVT+ISSIG RML+YG Sbjct: 121 AVAATTGLLEVMNREELEGVIGHEISHIRNYDIRISTIAVALASAVTVISSIGGRMLWYG 18- 0 Query: 181 GG--RRRDDDREDGGNILVLIFSILSLILAPLAASLVQLAISRQREYLADASSVELTRNP 23- 8 GG R+RDD +D I+ L+ S+LSL+LAPL ASL+QLAISRQREYLADASSVELTRNP Sbjct: 181 GGSRRQRDDGDDDVLRIITLLLSLLSLLLAPLVASLIQLAISRQREYLADASSVELTRNP 24- 0 Query: 239 QGMISALEKLDRSEPMGHPVDDASAALYINDPTKKEGLKSLFYTHPPIADRIERLRHM 296 QGMI ALEKL S+PM HPVDDASAALYIN+P KK SLF THPPI +RIERL++M Sbjct: 241 QGMIKALEKLQLSQPMKHPVDDASAALYINEPRKKRSFSSLFSTHPPIEERIERLKNM 298 A related GBS gene <SEQ ID 8847> and protein <SEQ ID 8848> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04734 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 9.61 GvH: Signal Score (-7.5): -0.97 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 3 value: -11.30 threshold: 0.0 INTEGRAL Likelihood = -11.30 Transmembrane 195-211 (190-221) INTEGRAL Likelihood = -11.09 Transmembrane 43-59 (31-62) INTEGRAL Likelihood = -3.61 Transmembrane 153-169 (153-174) PERIPHERAL Likelihood = 5.89 87 modified ALOM score: 2.76 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5522 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00103## SEQ ID 8848 (GBS179) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 175 (lane 11; MW 58 kDa). GBS179-GST was purified as shown in FIG. 227, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1571 A DNA sequence (GBSx1665) was identified in S. agalactiae <SEQ ID 4855> which encodes the amino acid sequence <SEQ ID 4856>. Analysis of this protein sequence reveals the following: TABLE-US-04735 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -15.44 Transmembrane 4-20 (1-27) ----- Final Results ----- bacterial membrane --- Certainty = 0.7177 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04736 >GP: AAG23700 GB: AF017421 LemA-like protein [Streptococcus gordonii] Identities = 124/182 (68%), Positives = 152/182 (83%) Query: 1 MGTMILIAIIALFVIWLIVAYNSLVRSRMHTKESWSQIDVQLKRRNDLIPNLIETVKGYA 60 M +I IA+I + V+++I YNSLVR+RM T+E+WSQIDVQLKRRNDL+PNLIETVKGY Sbjct: 1 MSFIITIAVIVVIVLFVISVYNSLVRARMQTQEAWSQIDVQLKRRNDLLPNLIETVKGYG 60 Query: 61 AYEGKTLEKIAELRAQVAKANTPAEAMTASNELTRQLSSILAVAENYPDLKANNSFVKLQ 120- YE TLEK+ +LRAQVA A++PA+AM AS+ LTRQ+S I AVAE+YPDLKAN +++KLQ Sbjct: 61 KYEQATLEKVTQLRAQVASASSPADAMKASDALTRQISGIFAVAESYPDLKANENYLKLQ 120- Query: 121 EELTNTENKISYSRQLYNTTTSNYNVKLETFPSNIVGKLFGFKPSQFLETPEEEKEVPKV 18- 0 EELTNTENKISYSRQLYN+ NYNVKL+ FPSN++ F F+P+ FL TPEEEK VPKV Sbjct: 121 EELTNTENKISYSRQLYNSVAGNYNVKLQAFPSNVIAGMFAFRPADFLSTPEEEKAVPKV 18- 0 Query: 181 SF 182 F Sbjct: 181 DF 182 A related DNA sequence was identified in S. pyogenes <SEQ ID 4857> which encodes the amino acid sequence <SEQ ID 4858>. Analysis of this protein sequence reveals the following: TABLE-US-04737 Possible site: 15 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04738 >GP: AAC44350 GB: U66186 LemA [Listeria monocytogenes] Identities = 91/181 (50%), Positives = 121/181 (66%), Gaps = 2/181 (1%) Query: 5 LIILVVLGVLALWLMISYNSLVKSRMHTKEAWSQIDVQLKRRNDLIPNLIETVKGYASYE 64 +I + V+ +L L YNSLVK R E W+QIDVQLKRR DLIPNL+ETVKGYA +E Sbjct: 5 IIAIAVVVILVLIYFGLYNSLVKYRNRVDETWAQIDVQLKRRFDLIPNLVETVKGYAKHE 64 Query: 65 QKTFEKITDLRARVAN--ASTPQETMAASNELSKQVTSLFAVAENYPDLKANENFLKLQE 122- ++T ++ + R ++ A Q + A N LS + S+FA+ E YPDLKAN +F++LQ Sbjct: 65 KETLTQVIEARNKMMEVPADNRQGQIEADNMLSGALKSIFALGEAYPDLKANTSFIELQH 124- Query: 123 ELTNTENKISYSRQLYNSTTSNYNLQLESFPSNIAGKLFGFKPSEFLQTPEAEKEVPKVEF 1- 83 ELT TENK++YSRQLYN+T YN +++S P+NI KL F + L PE E+ PKVEF Sbjct: 125 ELTTTENKVAYSRQLYNTTVMTYNTKVQSVPTNIVAKLHNFTERDMLSIPEVERVAPKVEF 1- 85 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04739 Identities = 135/181 (74%), Positives = 165/181 (90%) Query: 4 MILIAIIALFVIWLIVAYNSLVRSRMHTKESWSQIDVQLKRRNDLIPNLIETVKGYAAYE 63 +I++ ++ + +WL+++YNSLV+SRMHTKE+WSQIDVQLKRRNDLIPNLIETVKGYA+YE Sbjct: 5 LIILVVLGVLALWLMISYNSLVKSRMHTKEAWSQIDVQLKRRNDLIPNLIETVKGYASYE 64 Query: 64 GKTLEKIAELRAQVAKANTPAEAMTASNELTRQLSSILAVAENYPDLKANNSFVKLQEEL 123- KT EKI +LRA+VA A+TP E M ASNEL++Q++S+ AVAENYPDLKAN +F+KLQEEL Sbjct: 65 QKTFEKITDLRARVANASTPQETMAASNELSKQVTSLFAVAENYPDLKANENFLKLQEEL 124- Query: 124 TNTENKISYSRQLYNTTTSNYNVKLETFPSNIVGKLFGFKPSQFLETPEEEKEVPKVSFDF 1- 84 TNTENKISYSRQLYN+TTSNYN++LE+FPSNI GKLFGFKPS+FL+TPE EKEVPKV F+F Sbjct: 125 TNTENKISYSRQLYNSTTSNYNLQLESFPSNIAGKLFGFKPSEFLQTPEAEKEVPKVEFNF 1- 85 A related GBS gene <SEQ ID 8849> and protein <SEQ ID 8850> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04740 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: 14.63 GvH: Signal Score (-7.5): -3.19 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -15.44 threshold: 0.0 INTEGRAL Likelihood = -15.44 Transmembrane 4-20 (1-27) PERIPHERAL Likelihood = 8.86 146 modified ALOM score: 3.59 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.7177 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00104## SEQ ID 4856 (GBS42) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 5 (lane 2; MW 21.8 kDa) and in FIG. 168 (lane 5-7; MW 36 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 13 (lane 8; MW 46 kDa). Purified Thio-GBS42-His is shown in FIG. 244, lane 11. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1572 A DNA sequence (GBSx1666) was identified in S. agalactiae <SEQ ID 4859> which encodes the amino acid sequence <SEQ ID 4860>. This protein is predicted to be glucose inhibited division protein b (gidB). Analysis of this protein sequence reveals the following: TABLE-US-04741 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2430 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10079> which encodes amino acid sequence <SEQ ID 10080> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04742 >GP:CAB16137 GB:Z99124 glucose-inhibited division protein [Bacillus subtilis] Identities = 130/239 (54%), Positives = 170/239 (70%), Gaps = 4/239 (1%) Query: 5 MTPQAFYQVLIEHGITLTDKQKKQFETYFRLLVEWNEKINLTAITDKEEVYLKHFYDSIA 64 M + F L E GI+L+ +Q +QFE Y+ +LVEWNEKINLT+IT+K+EVYLKHFYDSI Sbjct: 1 MNIEEFTSGLAEKGISLSPRQLEQFELYYDMLVEWNEKINLTSITEKKEVYLKHFYDSIT 60 Query: 65 PILQGYID-NSPLSILDIGAGAGFPSIPMKILYPEIDITIIDSLNKRINFLNILANELEL 123- Y+D N +I D+GAGAGFPS+P+KI +P + +TI+DSLNKRI FL L+ L+L Sbjct: 61 AAF--YVDFNQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDSLNKRITFLEKLSEALQL 118- Query: 124 SGVHFFHGRAEDFGQDRVFRAKFDIVTARAVAKMQVLAELTIPFLKVNGRLIALKAAAAE 18- 3 F H RAE FGQ + R +DIVTARAVA++ VL+EL +P +K NG +ALKAA+AE Sbjct: 119 ENTTFCHDRAETFGQRKDVRESYDIVTARAVARLSVLSELCLPLVKKNGLFVALKAASAE 17- 8 Query: 184 EELISAEKALKTLFSQVTVNKNYKLP-NGDDRNITIVSKKKETPNKYPRKAGTPNKKPL 241- EEL + +KA+ TL ++ ++KLP DRNI ++ K K TP KYPRK GTPNK P+ Sbjct: 179 EELNAGKKAITTLGGELENIHSFKLPIEESDRNIMVIRKIKNTPKKYPRKPGTPNKSPI 237- A related DNA sequence was identified in S. pyogenes <SEQ ID 4861> which encodes the amino acid sequence <SEQ ID 4862>. Analysis of this protein sequence reveals the following: TABLE-US-04743 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4862 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04744 Identities = 170/237 (71%), Positives = 202/237 (84%) Query: 5 MTPQAFYQVLIEHGITLTDKQKKQFETYFRLLVEWNEKINLTAITDKEEVYLKHFYDSIA 64 MTPQ FY+ L E G +L+ KQK+QF+TYF+ LVEWN KINLTAIT++ EVYLKHFYDSIA Sbjct: 1 MTPQDFYRTLEEDGFSLSSKQKEQFDTYFKSLVEWNTKINLTAITEENEVYLKHFYDSIA 60 Query: 65 PILQGYIDNSPLSILDIGAGAGFPSIPMKILYPEIDITIIDSLNKRINFLNILANELELS 124- PILQG++ N P+ +LDIGAGAGFPS+PMKIL+P +++TIIDSLNKRI+FL +LA EL L Sbjct: 61 PILQGFLANEPIKLLDIGAGAGFPSLPMKILFPNLEVTIIDSLNKRISFLTLLAQELGLE 120- Query: 125 GVHFFHGRAEDFGQDRVFRAKFDIVTARAVAKMQVLAELTIPFLKVNGRLIALKAAAAEE 18- 4 VHFFHGRAEDFGQD+ FR +FD+VTARAVA+MQVL+ELTIPFLK+ G+LIALKA AA++ Sbjct: 121 NVHFFHGRAEDFGQDKAFRGQFDVVTARAVARMQVLSELTIPFLKIGGKLIALKAQAADQ 18- 0 Query: 185 ELISAEKALKTLFSQVTVNKNYKLPNGDDRNITIVSKKKETPNKYPRKAGTPNKKPL 241 EL A+ AL LF +V N +Y+LPNGD R ITIV KKKETPNKYPRKAG PNKKPL Sbjct: 181 ELEEAKNALCLLFGKVIKNHSYQLPNGDSRFITIVEKKKETPNKYPRKAGLPNKKPL 237 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1573 A DNA sequence (GBSx1667) was identified in S. agalactiae <SEQ ID 4863> which encodes the amino acid sequence <SEQ ID 4864>. Analysis of this protein sequence reveals the following:

TABLE-US-04745 Possible site: 13 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1574 A DNA sequence (GBSx1668) was identified in S. agalactiae <SEQ ID 4865> which encodes the amino acid sequence <SEQ ID 4866>. This protein is predicted to be v-type sodium ATP synthase subunit j. Analysis of this protein sequence reveals the following: TABLE-US-04746 Possible site: 45 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.14 Transmembrane 371-387 (362-391) INTEGRAL Likelihood = -7.48 Transmembrane 200-216 (190-217) INTEGRAL Likelihood = -4.94 Transmembrane 425-441 (423-446) INTEGRAL Likelihood = -4.67 Transmembrane 327-343 (325-349) INTEGRAL Likelihood = -3.77 Transmembrane 81-97 (81-98) INTEGRAL Likelihood = -2.66 Transmembrane 140-156 (139-157) INTEGRAL Likelihood = -1.33 Transmembrane 55-71 (53-71) INTEGRAL Likelihood = -0.27 Transmembrane 247-263 (247-263) INTEGRAL Likelihood = -0.11 Transmembrane 165-181 (165-181) ----- Final Results ----- bacterial membrane --- Certainty = 0.5055 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10081> which encodes amino acid sequence <SEQ ID 10082> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04747 >GP:BAA04279 GB:D17462 Na+ -ATPase subunit J [Enterococcus hirae] Identities = 170/461 (36%), Positives = 262/461 (55%), Gaps = 28/461 (6%) Query: 12 KTMSVARKLSISFIAVILLGSILLSLPIFQYANAPKTHYIDHLFTTVSMVCVTGLSVFPI 71 - K +S + ++ F +IL G LL+LP F + TH+ID LFT S VCVTGL+ Sbjct: 10 KRLSPVQLIAAGFFILILFGGSLLTLPFFS-RSGESTHFIDALFTATSAVCVTGLTTLNT 68 Query: 72 SKVYNGWGQIVAILLMQTGGLGLVTLMSLSYYTLRRKMSLNDQTLLQSAITYNSSTDLKK 131- ++ +N GQ + + L++ GGLG + + L + ++K+S + + +L+ A+ + + K Sbjct: 69 AEHWNSAGQFLIMTLIEIGGLGFMMIPILFFAIAKKKISFSMRIVLKEALNLEEMSGVIK 128- Query: 132 YLYMIFKVTLTLEVLAASILAIDFIPRFGLGHGIFNSIFLAVSAFCNAGFDNLEATSLAQ 19- 1 + I K + ++V+ A L++ FIP FG GI+ SIF AVS+FCNAGFD L + LA Sbjct: 129 LMIYILKFAVVIQVIGAVALSVVFIPEFGWAKGIWFSIFHAVSSFCNAGFDLLGDSLLAD 18- 8 Query: 192 FKLNPLVNIIVCFLIISGGLGFAVWKDLIEATIQTSHKGPKLIKTFPKRLSNHSKLVLKT 25- 1 + N + ++V LII+GGLGF VW+D++ + H+ K+++ HSK+ L Sbjct: 189 -QTNVYLIMVVSALIIAGGLGFIVWRDIL-----SYHR--------VKKITLHSKVALSV 23- 4 Query: 252 TTIILLTGTLLSWLLEFGNFRTIANLSLPKQLMVSFFQTVTMRTAGFSTIDYTQTDFATN 31- 1 T ++L+ G +L +L+ N T+ + ++L +FF +VT RTAG+ +IDY Q A Sbjct: 235 TALLLIGGFIL-FLITERNGLTLVKGTFTERLANTFFMSVTPRTAGYYSIDYLQMSHAGL 29- 3 Query: 312 LVYIIQMLIGGAPGGTAGGFKVTVIAILLLLFKAELSGQSQVTFHYRTIPSSIIKQTLSI 37- 1 ++ + M IGG G TAGG K T + ILL+ A G+++ RTI + + L Sbjct: 294 ILTMFLMYIGGTSGSTAGGLKTTTLGILLIQMHAMFKGKTRAEAFGRTIRQAAV---LRA 35- 0 Query: 372 LTFFFII--LISGYLLLLELNPHIDPFS----LFFEASSALATVGVTMNTTNQLTLGGRI 42- 5 LT FF+ L +++L + I S + FE SA TVG+TM T LTL G++ Sbjct: 351 LTLFFVTLSLCVVAIMVLSVTETIPKTSGIEYIAFEVFSAFGTVGLTMGLTPDLTLIGKL 41- 0 Query: 426 VIMFLMFIGRVGPITVLLSILQK---KEKEIHYAETEIILG 463 VI+ LM+IGRVG +TV+LS+L K E Y E I+LG Sbjct: 411 VIISLMYIGRVGIMTVVLSLLVKANRAEANYKYPEESIMLG 451 A related DNA sequence was identified in S. pyogenes <SEQ ID 4867> which encodes the amino acid sequence <SEQ ID 4868>. Analysis of this protein sequence reveals the following: TABLE-US-04748 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.12 Transmembrane 371-387 (364-396) INTEGRAL Likelihood = -7.32 Transmembrane 20-36 (18-42) INTEGRAL Likelihood = -6.53 Transmembrane 425-441 (417-446) INTEGRAL Likelihood = -6.16 Transmembrane 89-105 (81-106) INTEGRAL Likelihood = -5.79 Transmembrane 200-216 (196-223) INTEGRAL Likelihood = -3.35 Transmembrane 140-156 (139-157) INTEGRAL Likelihood = -3.03 Transmembrane 55-71 (53-74) INTEGRAL Likelihood = -3.03 Transmembrane 247-263 (246-264) INTEGRAL Likelihood = -1.12 Transmembrane 393-409 (393-409) INTEGRAL Likelihood = -0.11 Transmembrane 165-181 (165-181) ----- Final Results ----- bacterial membrane --- Certainty = 0.7050 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04749 >GP:BAA04279 GB:D17462 Na+ -ATPase subunit J [Enterococcus hirae] Identities = 168/466 (36%), Positives = 260/466 (55%), Gaps = 26/466 (5%) Query: 6 MKRSFIKSLSVTQRLTFSFAIVILIGTLLLSMPFTHYQNGPNTVYLDHFFNVVSMVCVTG 65 MK+ K LS Q + F I+IL G LL++PF ++G +T ++D F S VCVTG Sbjct: 4 MKKRVRKRLSPVQLIAAGFFILILFGGSLLTLPFFS-RSGESTHFIDALFTATSAVCVTG 62 Query: 66 LSVVPVAEVYNGIGQTIAMALMQIGCLGLVTLIAVSTFAL-KRKMRLSDQTLLQSALNRG 124- L+ + AE +N GQ + M L++IG LG + +I + FA+ K+K+ S + +L+ ALN Sbjct: 63 LTTLNTAEHWNSAGQFLIMTLIEIGGLGFM-MIPILFFAIAKKKISFSMRIVLKEALNLE 121- Query: 125 DSKDLKHYLFFAYKVTFSLEAFAAIVIMIDFIPRFGWKNGIFNSIFLAVSAFCNAGFDNL 18- 4 + + + + K ++ A+ + + FIP FGW GI+ SIF AVS+FCNAGFD L Sbjct: 122 EMSGVIKLMIYILKFAVVIQVIGAVALSVVFIPEFGWAKGIWFSIFHAVSSFCNAGFDLL 18- 1 Query: 185 GSSSLKDFMLNPTLNVIITFLIISGGLGFAVWVDLGVAFKKYFFERPHCYGATFRKLSNQ 24- 4 G S L D N L ++++ LII+GGLGF VW D+ +++ + +K++ Sbjct: 182 GDSLLAD-QTNVYLIMVVSALIIAGGLGFIVWRDI-LSYHR------------VKKITLH 22- 7 Query: 245 SRLVLQTTAVILFLGTFLTWFLEKDNSKTIANFSLHQQLMVSFFQTVTMRTAGFATISYN 30- 4 S++ L TA++L +G F+ + + + N T+ + ++L +FF +VT RTAG+ +I Y Sbjct: 228 SKVALSVTALLL-IGGFILFLITERNGLTLVKGTFTERLANTFFMSVTPRTAGYYSIDYL 28- 6 Query: 305 DTLAPTNILYMIQMVIGGAPGGTAGGIKVTTAAITFLLFKAELSGQSEVTFRNRIIANKT 36- 4 IL M M IGG G TAGG+K TT I + A G++ R I Sbjct: 287 QMSHAGLILTMFLMYIGGTSGSTAGGLKTTTLGILLIQMHAMFKGKTRAEAFGRTIRQAA 34- 6 Query: 365 IKQTMTVLIFFFAVLMIGFILLLSVEPHIAPIP----LLFESISAIATVGVSMDLTPQLS 42- 0 + + +T L F L + I++LSV I + FE SA TVG++M LTP L+ Sbjct: 347 VLRALT-LFFVTLSLCVVAIMVLSVTETIPKTSGIEYIAFEVFSAFGTVGLTMGLTPDLT 40- 5 Query: 421 TAGRLIVIVLMFVGRVGPITVLISLI---QRKEKTIQYATTDILVG 463 G+L++I LM++GRVG +TV++SL+ R E +Y I++G Sbjct: 406 LIGKLVIISLMYIGRVGIMTVVLSLLVKANRAEANYKYPEESIMLG 451 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04750 Identities = 275/462 (59%), Positives = 351/462 (75%), Gaps = 1/462 (0%) Query: 2 GASMKHFFDYKTMSVARKLSISFIAVILLGSILLSLPIFQYANAPKTHYIDHLFTTVSMV 61 G +MK F K++SV ++L+ SF VIL+G++LLS+P Y N P T Y+DH F VSMV Sbjct: 3 GGNMKRSF-IKSLSVTQRLTFSFAIVILIGTLLLSMPFTHYQNGPNTVYLDHFFNVVSMV 61 Query: 62 CVTGLSVFPISKVYNGWGQIVAILLMQTGGLGLVTLMSLSYYTLRRKMSLNDQTLLQSAI 121- CVTGLSV P+++VYNG GQ +A+ LMQ G LGLVTL+++S + L+RKM L+DQTLLQSA+ Sbjct: 62 CVTGLSVVPVAEVYNGIGQTIAMALMQIGCLGLVTLIAVSTFALKRKMRLSDQTLLQSAL 121- Query: 122 TYNSSTDLKKYLYMIFKVTLTLEVLAASILAIDFIPRFGLGHGIFNSIFLAVSAFCNAGF 18- 1 S DLK YL+ +KVT +LE AA ++ IDFIPRFG +GIFNSIFLAVSAFCNAGF Sbjct: 122 NRGDSKDLKHYLFFAYKVTFSLEAFAAIVIMIDFIPRFGWKNGIFNSIFLAVSAFCNAGF 18- 1 Query: 182 DNLEATSLAQFKLNPLVNIIVCFLIISGGLGFAVWKDLIEATIQTSHKGPKLIKTFPKRL 24- 1 DNL ++SL F LNP +N+I+ FLIISGGLGFAVW DL A + + P ++L Sbjct: 182 DNLGSSSLKDFMLNPTLNVIITFLIISGGLGFAVWVDLGVAFKKYFFERPHCYGATFRKL 24- 1 Query: 242 SNHSKLVLKTTTIILLTGTLLSWLLEFGNFRTIANLSLPKQLMVSFFQTVTMRTAGFSTI 30- 1 SN S+LVL+TT +IL GT L+W LE N +TIAN SL +QLMVSFFQTVTMRTAGF+TI Sbjct: 242 SNQSRLVLQTTAVILFLGTFLTWFLEKDNSKTIANFSLHQQLMVSFFQTVTMRTAGFATI 30- 1 Query: 302 DYTQTDFATNLVYIIQMLIGGAPGGTAGGFKVTVIAILLLLFKAELSGQSQVTFHYRTIP 36- 1 Y T TN++Y+IQM+IGGAPGGTAGG KVT AI LLFKAELSGQS+VTF R I Sbjct: 302 SYNDTLAPTNILYMIQMVIGGAPGGTAGGIKVTTAAITFLLFKAELSGQSEVTFRNRIIA 36- 1 Query: 362 SSIIKQTLSILTFFFIILISGYLLLLELNPHIDPFSLFFEASSALATVGVTMNTTNQLTL 42- 1 + IKQT+++L FFF +L+ G++LLL + PHI P L FE+ SA+ATVGV+M+ T QL+ Sbjct: 362 NKTIKQTMTVLIFFFAVLMIGFILLLSVEPHIAPIPLLFESISAIATVGVSMDLTPQLST 42- 1 Query: 422 GGRIVIMFLMFIGRVGPITVLLSILQKKEKEIHYAETEIILG 463 GR++++ LMF+GRVGPITVL+S++Q+KEK I YA T+I++G Sbjct: 422 AGRLIVIVLMFVGRVGPITVLISLIQRKEKTIQYATTDILVG 463 A related GBS gene <SEQ ID 8851> and protein <SEQ ID 8852> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04751 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 0.86 GvH: Signal Score (-7.5): 0.64 Possible site: 45 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 9 value: -10.14 threshold: 0.0 INTEGRAL Likelihood = -10.14 Transmembrane 371-387 (362-391) INTEGRAL Likelihood = -7.48 Transmembrane 200-216 (190-217) INTEGRAL Likelihood = -4.94 Transmembrane 425-441 (423-446) INTEGRAL Likelihood = -4.67 Transmembrane 327-343 (325-349) INTEGRAL Likelihood = -3.77 Transmembrane 81-97 (81-98) INTEGRAL Likelihood = -2.66 Transmembrane 140-156 (139-157) INTEGRAL Likelihood = -1.33 Transmembrane 55-71 (53-71) INTEGRAL Likelihood = -0.27 Transmembrane 247-263 (247-263) INTEGRAL Likelihood = -0.11 Transmembrane 165-181 (165-181) PERIPHERAL Likelihood = 2.49 308 modified ALOM score: 2.53 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5055 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00105## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1575 A DNA sequence (GBSx1669) was identified in S. agalactiae <SEQ ID 4869> which encodes the amino acid sequence <SEQ ID 4870>. This protein is predicted to be TrkA (ktrA). Analysis of this protein sequence reveals the following: TABLE-US-04752 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04753 >GP: AAC46144 GB: AF001974 putative TrkA [Thermoanaerobacter ethanolicus] Identities = 69/177 (38%), Positives = 110/177 (61%), Gaps = 2/177 (1%) Query: 8 VLGLGIFGQTLAQELSNFEQDVIAIDSNPEN--VQAVAEVVTKAAIGDITDLAFLKHIGI 65 V+GLG FG +LA+ L DV+ ID + E VQA+ +VT A D TD LK + + Sbjct: 6 VIGLGSFGISLAKTLYEMGNDVLVIDEDEEEELVQAMNGLVTHAVRADATDENVLKSLRV 65 Query: 66 SDCDTVIIATGNSLESSVLAVMHCKKLGVPQVIAKARNLVYEEVLYEIGADLVISPERES 125- + D I+A G ++ESS++ M K+LGV VIAKA N ++ VLY++GAD V+ PE++ Sbjct: 66 KNFDVAIVAIGKNMESSIMVTMLVKELGVKYVIAKAHNELHARVLYKVGADRVVMPEKDM 125- Query: 126 GQNVAANLMRNKITDVFQIESDISVIEFKIPKSWVGKTVEQLNIRHKFDLNLIGIRK 182 G VA N+ + + D+ + + S+ E + W GKT++++N+R K+ LN++ ++K Sbjct: 126 GIRVARNVFSSNLIDLIEFSKEYSIAEILPIEEWFGKTLKEINVREKYGLNVVAVKK 182 A related DNA sequence was identified in S. pyogenes <SEQ ID 4715> which encodes the amino acid sequence <SEQ ID 4716>. Analysis of this protein sequence reveals the following: TABLE-US-04754 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04755 Identities = 132/221 (59%), positives = 176/221 (78%) Query: 1 MKTKIIGVLGLGIFGQTLAQELSNFEQDVIAIDSNPENVQAVAEVVTKAAIGDITDLAFL 60 +K K +GVLGLGIFG+T+A+ELSNF+QDVIAID +V+ VA++VTKAA+GDITD FL Sbjct: 2 LKRKTVGVLGLGIFGRTVARELSNFDQDVIAIDIRESHVKEVADLVTKAAVGDITDKEFL 61 Query: 61 KHIGISDCDTVIIATGNSLESSVLAVMHCKKLGVPQVIAKARNLVYEEVLYEIGADLVIS 120- +GI CDTV+IA+GN+LESSVLAVMHCKKLGVP +IAKA+N ++EEVLY IGA VI+ Sbjct: 62 LAVGIEHCDTVVIASGNNLESSVLAVMHCKKLGVPTIIAKAKNKIFEEVLYGIGATKVIT 121- Query: 121 PERESGQNVAANLMRNKITDVFQIESDISVIEFKIPKSWVGKTVEQLNIRHKFDLNLIGI 18- 0 PER+SG+ VA+NL+R I + +E IS+IEF IPKSW G+++ +L++R K++LN+IG+ Sbjct: 122 PERDSGKRVASNLLRRHIESIIYLEHGISMIEFVIPKSWEGQSLSELDVRRKYELNVIGM 18- 1 Query: 181 RKAKNKPVDTEVPINSPLEEGIILVAIANSDAFQRYDYLGY 221 R+ + K +DT V PLE I+VAIAN F+++DYLGY Sbjct: 182 RQKEVKTLDTNVKPFEPLEPNTIIVAIANDHTFEKFDYLGY 222 A related GBS gene <SEQ ID 8853> and protein <SEQ ID 8854> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04756 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 5.14 GvH: Signal Score (-7.5): -0.860001 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 1.06 threshold: 0.0 PERIPHERAL Likelihood = 1.06 192 modified ALOM score: -0.71 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) The protein has homology with the following sequences in the databases: ##STR00106## SEQ ID 8854 (GBS57) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 19 (lane 6; MW 26 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 21 (lane 11; MW 51.1 kDa) and in FIG. 183 (lane 9 & 10; MW 51 kDa). The GBS57-GST fusion product was purified (FIG. 99A; see also FIG. 195, lane 8) and used to immunise mice (lane 1 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 99B), FACS (FIG. 99C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1576 A DNA sequence (GBSx1670) was identified in S. agalactiae <SEQ ID 4871> which encodes the amino acid sequence <SEQ ID 4872>. Analysis of this protein sequence reveals the following: TABLE-US-04757 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.62 Transmembrane 73-89 (68-96) INTEGRAL Likelihood = -11.30 Transmembrane 254-270 (248-274) INTEGRAL Likelihood = -4.73 Transmembrane 127-143 (124-144) INTEGRAL Likelihood = -4.19 Transmembrane 50-66 (47-67) INTEGRAL Likelihood = -3.29 Transmembrane 25-41 (25-45) ----- Final Results ----- bacterial membrane --- Certainty = 0.5649 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8855> which encodes amino acid sequence <SEQ ID 8856> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-04758 Lipop Possible site: -1 Crend: 9 McG: Discrim Score: -10.49 GvH: Signal Score (-7.5): -1.14 Possible site: 40 >>> Seems to have no N-terminal signal sequence ALOM program count: 5 value: -11.62 threshold: 0.0 INTEGRAL Likelihood = -11.62 Transmembrane 73-89 (68-96) INTEGRAL Likelihood = -11.30 Transmembrane 254-270 (248-274) INTEGRAL Likelihood = -4.73 Transmembrane 127-143 (124-144) INTEGRAL Likelihood = -4.19 Transmembrane 50-66 (47-67) PERIPHERAL Likelihood = 3.76 201 modified ALOM score: 2.82 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5649 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-04759 >GP: CAB13178 GB: Z99110 ykoC [Bacillus subtilis] Identities = 61/226 (26%), Positives = 108/226 (46%), Gaps = 12/226 (5%) Query: 49 FLIVVSLGSLVLFRLAKIKWQQVSFVMTLVVVFAVLNIIMVYLFAPHYGDKIYGSSSLLL 108- F I++ G L+ + KW + + F +L V+ A K+ + L Sbjct: 36 FYIIIVAGVLLAAGIPLKKW------LLFTIPFLILAFGCVWTAAVF--GKVPTTPDNFL 87 Query: 109 KGIGPYDVTSQELFYLFNLILKYFCTVPLALLFLMTTNPSQFASSL-NQLGLSYKIAYAV 16- 7 GP + S + +L + C L+++F+ TT+P F SL Q LS K+AY V Sbjct: 88 FQAGPISINSDNVSVGISLGFRILCFSALSMMFVFTTDPILFMLSLVQQCRLSPKLAYGV 147- Query: 168 SLTLRYIPDVQEEFYTIRRAQEARGIELSKKSNLVARIKGNLQIVTPLIFSSLERIDTVA 22- 7 R++P +++E I++A + RG + +S ++ +I + PL+ S++ + + A Sbjct: 148 IAGFRFLPLLKDEVQLIQQAHKIRGG--AAESGIINKISALKRYTIPLLASAIRKAERTA 20- 5 Query: 228 TAMELRRFGKNKRRTWYSKQSLEKSDIVLIILALASLFVSLYLIHL 273 AME + F ++ RT+Y S+ + D V L L LF +L+ L Sbjct: 206 LAMESKGFTGSRNRTYYRTLSVNRRDWVFFCLVLL-LFAGSFLVSL 250 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1577 A DNA sequence (GBSx1671) was identified in S. agalactiae <SEQ ID 4873> which encodes the amino acid sequence <SEQ ID 4874>. This protein is predicted to be cobalt ABC transporter, ATP-binding protein (cbiO). Analysis of this protein sequence reveals the following: TABLE-US-04760 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.91 Transmembrane 436-452 (435-452) ----- Final Results ----- bacterial membrane --- Certainty = 0.1765 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04761 >GP: CAB13179 GB: Z99110 similar to cation ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 151/483 (31%), Positives = 248/483 (51%), Gaps = 19/483 (3%) Query: 8 KDFTFQYDVQSEPTLKGINLSIPKGEKVLILGPSGSGKSTLGHCLNGIIPNTHKGQYSGI 67 + +F Y+ +P + I+ + KGE VL+LGPSG GKS+L CLNG+ P G SG Sbjct: 11 EQLSFSYEEDEKPVFQDISFELQKGECVLLLGPSGCGKSSLALCLNGLYPEACDGIQSGH 70 Query: 68 FTINHKNAFDLSIYDK-SHLVSTVLQDPDGQFIGLTVAEDIAFALENDVVAQEEMASIVE 126- + K D + + V QDPD QF LTV ++IAF LEN + +EEM + Sbjct: 71 VFLFQKPVTDAETSETITQHAGVVFQDPDQQFCMLTVEDEIAFGLENLQIPKEEMTEKIN 130- Query: 127 MWAKRLEIAPLLSKRPQDLSGGQKQRVSLAGVLVDDSPILLFDEPLANLDPQSGQDIMAL 18- 6 +L I L K LSGGQKQ+V+LA +L + +++ DEP + LDP S ++ + L Sbjct: 131 AVLGKLRITHLKEKMISTLSGGQKQKVALACILAMEPELIILDEPTSLLDPFSAREFVHL 19- 0 Query: 187 VDRIHQEQDATTIIIEHRLED--VFYERVDRVVLFSDGQIIYNGEPDQLL--KTNFLSEY 24- 2 + + +E+ + ++IEH+L++ + ER +VL G+ +G L + L + Sbjct: 191 MKDLQREKGFSLLVIEHQLDEWAPWIERT--IVLDKSGKKALDGLTKNLFQHEAETLKKL 24- 8 Query: 243 GIREPLYISALKNLGYDFEKQNTMTSIDDFDFSELLIPKMRALDLDKHTDKLLSVQHLSV 30- 2 GI P + L F M + + K +A + +L V LS Sbjct: 249 GIAIPKVCHLQEKLSMPFTLSKEMLFKEPIPAGH--VKKKKA----PSGESVLEVSSLSF 30- 2 Query: 303 SYDLENNTLDDVSFDLYKGQRLAIVGKNGAGKSTLAKALCQFI-PNNATLIYNNEDVSQD 36- 1 + + D+SF L +G A+VG NG GKSTL L + P + ++ ++ + + Sbjct: 303 ARG-QQAIFKDISFSLREGSLTALVGPNGTGKSTLLSVLASLMKPQSGKILLYDQPLQKY 36- 1 Query: 362 SIKERAERIGYVLQNPNQMISQAMVFDEVALGLRLRGFSDNDIESRVYDILKVCGLYQFR 42- 1 KE +R+G+V QNP V+DE+ G + ++ + E + +L+ GL Sbjct: 362 KEKELRKRMGFVFQNPEHQFVTDTVYDELLFGQK----ANAETEKKAQHLLQRFGLAHLA 41- 7 Query: 422 NWPISALSFGQKKRVTIASILILNPEVIILDEPTAGQDMKHYTEMMSFLDKLSCDGHTIV 48- 1 + A+S GQK+R+++A++L+ + +V++LDEPT GQD + E M + ++ +G ++ Sbjct: 418 DHHPFAISQGQKRRLSVATMLMHDVKVLLLDEPTFGQDARTAAECMEMIQRIKAEGTAVL 47- 7 Query: 482 MIT 484 MIT Sbjct: 478 MIT 480 There is also homology to SEQ ID 4416. SEQ ID 4874 (GBS424d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 146 (lane 2 & 4; MW 77 kDa) and in FIG. 239 (lane 10; MW 77 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 146 (lane 5 & 7; MW 52 kDa) and in FIG. 182 (lane 4; MW 52 kDa). Purified GBS424d-His is shown in FIG. 241, lanes 6 & 7. Purified GBS424d-GST is shown in FIG. 246, lane 12. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1578 A DNA sequence (GBSx1672) was identified in S. agalactiae <SEQ ID 4875> which encodes the amino acid sequence <SEQ ID 4876>. Analysis of this protein sequence reveals the following: TABLE-US-04762 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.12 Transmembrane 39-55 (35-63) INTEGRAL Likelihood = -3.98 Transmembrane 72-88 (71-90) INTEGRAL Likelihood = -3.66 Transmembrane 108-124 (106-127) INTEGRAL Likelihood = -2.34 Transmembrane 182-198 (181-198) INTEGRAL Likelihood = -1.44 Transmembrane 141-157 (139-158) ----- Final Results ----- bacterial membrane --- Certainty = 0.4248 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04763 >GP: CAB59830 GB: AJ012388 hypothetical protein [Lactococcus lactis] Identities = 109/182 (59%), Positives = 141/182 (76%) Query: 31 MNTNTIKKVVATGIGAALFIIIGMLVNIPTPIPNTNIQLQYAVLALFAVIYGPGVGFFTG 90 - M N++K VVATGIGAALF+IIG L+NIPTPIPNT+IQLQYAVLALF+ ++GP GF G Sbjct: 1 MKNNSVKIVVATGIGAALFVIIGWLINIPTPIPNTSIQLQYAVLALFSALFGPLAGFLIG 60 Query: 91 FIGHALKDSIQYGSPWWTWVLVSGLLGLMIGFFAKKLAIQLSGMTKKDLLLFNVVQVIAN 120- FIGHALKDS YG+PWWTWVL SGL+GL +GF K+ ++ K+++ FN+VQ +AN Sbjct: 61 FIGHALKDSFLYGAPWWTWVLGSGLMGLFLGFGVKRESLTQGIFGNKEIIRFNIVQFLAN 120- Query: 151 LIGWSVVAPYGDIFFYSEPASKVFAQGFLSSLVNSITIGVGGTLLLLAYAKSRPQKGSLS 21- 0 ++ W ++AP GDI YSEPA+KVF QG ++ LVN++TI V GTLLL YA +R + G+L Sbjct: 121 VVVWGLIAPIGDILVYSEPANKVFTQGVVAGLVNALTIAVAGTLLLKLYAATRTKSGTLD 18- 0 Query: 211 KD 212 K+ Sbjct: 181 KE 182 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8857> and protein <SEQ ID 8858> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04764 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: -5.01 GvH: Signal Score (-7.5): -5.9 Possible site: 50 >>> Seems to have no N-terminal signal sequence ALOM program count: 5 value: -8.12 threshold: 0.0 INTEGRAL Likelihood = -8.12 Transmembrane 31-47 (27-55) INTEGRAL Likelihood = -3.98 Transmembrane 64-80 (63-82) INTEGRAL Likelihood = -3.66 Transmembrane 100-116 (98-119) INTEGRAL Likelihood = -2.34 Transmembrane 174-190 (173-190) INTEGRAL Likelihood = -1.44 Transmembrane 133-149 (131-150) PERIPHERAL Likelihood = 5.78 9 modified ALOM score: 2.12 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4248 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00107## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1579 A DNA sequence (GBSx1673) was identified in S. agalactiae <SEQ ID 4877> which encodes the amino acid sequence <SEQ ID 4878>. Analysis of this protein sequence reveals the following: TABLE-US-04765 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.85 Transmembrane 86-102 (80-106) ----- Final Results ----- bacterial membrane --- Certainty = 0.3739 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1580 A DNA sequence (GBSx1674) was identified in S. agalactiae <SEQ ID 4879> which encodes the amino acid sequence <SEQ ID 4880>. Analysis of this protein sequence reveals the following: TABLE-US-04766 Possible site: 47 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -3.61 Transmembrane 107-123 (96-124) INTEGRAL Likelihood = -1.86 Transmembrane 124-140 (124-142) INTEGRAL Likelihood = -1.38 Transmembrane 83-99 (83-100) INTEGRAL Likelihood = 1.12 Transmembrane 142-158 (142-160) ----- Final Results ----- bacterial membrane --- Certainty = 0.2444 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9415> which encodes amino acid sequence <SEQ ID 9416> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04767 >GP: AAC76124 GB: AE000391 putative transport protein [Escherichia coli K12] Identities = 139/178 (78%), Positives = 159/178 (89%) Query: 1 MVGTMLFVALVVNPIIAFVMMRKNPYPLVLRCLKDSGITAFFTRSSAANIPVNMRLCEDL 60 +VG ML VALVVNP++ + +R+NP+PLVL CL++SG+ AFFTRSSAANIPVNM LCE L Sbjct: 222 LVGCMLLVALVVNPLLVWWKIRRNPFPLVLLCLRESGVYAFFTRSSAANIPVNMALCEKL 28- 1 Query: 61 GLDKDTYSVSIPLGAAINMAGAAITINILTLAAVNTLGITVDFPTAFLLSVVAAVSACGA 120- LD+DTYSVSIPLGA INMAGAAITI +LTLAAVNTLGI VD PTA LLSVVA++ ACGA Sbjct: 282 NLDRDTYSVSIPLGATINMAGAAITITVLTLAAVNTLGIPVDLPTALLLSVVASLCACGA 34- 1 Query: 121 SGVTGGSLLLIPVACSLFGISNDVAMQVVGVGFIVGVIQDSCETALNSSTDVLFTAVA 178 SGV GGSLLLIP+AC++FGISND+AMQVV VGFI+GV+QDSCETALNSSTDVLFTA A Sbjct: 342 SGVAGGSLLLIPLACNMFGISNDIAMQVVAVGFIIGVLQDSCETALNSSTDVLFTAAA 399 A related DNA sequence was identified in S. pyogenes <SEQ ID 4881> which encodes the amino acid sequence <SEQ ID 4882>. Analysis of this protein sequence reveals the following: TABLE-US-04768 Possible site: 58 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.69 Transmembrane 212-228 (202-239) INTEGRAL Likelihood = -7.38 Transmembrane 78-94 (74-108) INTEGRAL Likelihood = -6.53 Transmembrane 179-195 (175-200) INTEGRAL Likelihood = -6.10 Transmembrane 315-331 (312-341) INTEGRAL Likelihood = -5.36 Transmembrane 44-60 (42-61) INTEGRAL Likelihood = -4.41 Transmembrane 13-29 (11-41) INTEGRAL Likelihood = -3.19 Transmembrane 340-356 (333-358) INTEGRAL Likelihood = -3.08 Transmembrane 145-161 (144-162) INTEGRAL Likelihood = -0.90 Transmembrane 358-374 (358-376) ----- Final Results ----- bacterial membrane --- Certainty = 0.6477 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04769 >GP: AAF95950 GB: AE004347 sodium/dicarboxylate symporter [Vibrio cholerae] Identities = 243/385 (63%), Positives = 299/385 (77%), Gaps = 2/385 (0%) Query: 9 VRVSLIKKIGIGVVIGVMLGILAPDLTG-FSILGKLFVGGLKAIAPLLVFALVSQAISHQ 67 VR +L+ +I G+++G + +P+ ++G LFVG LKA+AP+LVF LV+ +I++Q Sbjct: 11 VRGNLVLQILAGILLGAAMATFSPEYAQKVGLIGNLFVGALKAVAPVLVFILVASSIANQ 70 Query: 68 KKGKQTNMTLIIVLYLFGTFASALVAVLTAYLFPLTLVLNTPVNTELSPPQGVAEVFQSL 127- KK + T M I+VLYLFGTF++AL AV+ ++LFP TLVL T +PPQG+AEV +L Sbjct: 71 KKNQHTYMRPIVVLYLFGTFSAALTAVILSFLFPTTLVLATGAEGA-TPPQGIAEVLNTL 129- Query: 128 LLKLVDNPINALATANYIGVLSWAIIFGLALKAASKETKHLIKTAAEVTSQIVVWIINLA 18- 7 L KLVDNP++AL ANYIG+L+W + GLAL +S TK + + + SQIV +II LA Sbjct: 130 LFKLVDNPVSALMNANYIGILAWGVGLGLALHHSSSTTKAVFEDLSHGISQIVRFIIRLA 18- 9 Query: 188 PIGIMSLVFTTISENGVGILSDYAFLILVLVGTMLFVALVVNPLIAVLITRQNPYPLVLR 24- 7 P GI LV +T + G L+ YA L+ VL+G M F+ALVVNP+I R+NP+PLVL+ Sbjct: 190 PFGIFGLVASTFATTGFDALAGYAQLLAVLLGAMAFIALVVNPMIVYYKIRRNPFPLVLQ 24- 9 Query: 248 CLRESGLTAFFTRSSAANIPVNMQLCQKIGLSKDTYSVSIPLGATINMGGAAITINVLTL 30- 7 CLRESG+TAFFTRSSAANIPVNM LC+K+ L +DTYSVSIPLGATINM GAAITI VLTL Sbjct: 250 CLRESGVTAFFTRSSAANIPVNMALCEKLKLDEDTYSVSIPLGATINMAGAAITITVLTL 30- 9 Query: 308 AAVHTFGIPIDELTALLLSVVAAVSACGASGVAGGSLLLIPVACSLFGISNDLAMQVVGV 36- 7 AAVHT GI +D +TALLLSVVAAVSACGASGVAGGSLLLIP+AC LFGISND+AMQVV V Sbjct: 310 AAVHTMGIEVDLMTALLLSVVAAVSACGASGVAGGSLLLIPLACGLFGISNDIAMQVVAV 36- 9 Query: 368 GFIVGVIQDSCETALNSSTDVLFTA 392 GFI+GVIQDS ETALNSSTDVLFTA Sbjct: 370 GFIIGVIQDSAETALNSSTDVLFTA 394 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04770 Identities = 153/186 (82%), Positives = 172/186 (92%) Query: 1 MVGTMLFVALVVNPIIAFVMMRKNPYPLVLRCLKDSGITAFFTRSSAANIPVNMRLCEDL 60 +VGTMLFVALVVNP+IA ++ R+NPYPLVLRCL++SG+TAFFTRSSAANIPVNM+LC+ + Sbjct: 217 LVGTMLFVALVVNPLIAVLITRQNPYPLVLRCLRESGLTAFFTRSSAANIPVNMQLCQKI 27- 6 Query: 61 GLDKDTYSVSIPLGAAINMAGAAITINILTLAAVNTLGITVDFPTAFLLSVVAAVSACGA 120- GL KDTYSVSIPLGA INM GAAITIN+LTLAAV+T GI +DF TA LLSVVAAVSACGA Sbjct: 277 GLSKDTYSVSIPLGATINMGGAAITINVLTLAAVHTFGIPIDFLTALLLSVVAAVSACGA 33- 6 Query: 121 SGVTGGSLLLIPVACSLFGISNDVAMQVVGVGFIVGVIQDSCETALNSSTDVLFTAVAEK 18- 0 SGV GGSLLLIPVACSLFGISND+AMQVVGVGFIVGVIQDSCETALNSSTDVLFTA+AE Sbjct: 337 SGVAGGSLLLIPVACSLFGISNDLAMQVVGVGFIVGVIQDSCETALNSSTDVLFTAIAEN 39- 6 Query: 181 SVFGKK 186 + + +K Sbjct: 397 AFWKRK 402 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1581 A DNA sequence (GBSx1675) was identified in S. agalactiae <SEQ ID 4883> which encodes the amino acid sequence <SEQ ID 4884>. This protein is predicted to be acid phosphatase. Analysis of this protein sequence reveals the following: TABLE-US-04771 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2436 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9427> which encodes amino acid sequence <SEQ ID 9428> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04772 >GP: CAA73175 GB: Y12602 acid phosphatase [Streptococcus equisimilis] Identities = 167/251 (66%), Positives = 209/251 (82%) Query: 7 EQKTKFKNISLSSNKLLAKENTMSVLWYQNSAEAKALYLQGYNVAKMKLDDWLQKPSEKP 66 ++ K ++ S +L + ENTMSVLWYQ +AEAKALYLQGY +A +L + L + ++KP Sbjct: 34 KETVKQTKVTYSDEQLRSNENTMSVLWYQRAAEAKALYLQGYQLATDRLKNQLGQATDKP 93 Query: 67 YSIILDLDETVLDNSPYQAKNIKDGSSFTPESWDKWVQKKSAKAVAGAKEFLKYANEKGI 126- YSI+LD+DETVLDNSPYQAKNI +G+SFTPESWD WVQKK AK VAGAKEFL++A++ G+ Sbjct: 94 YSIVLDIDETVLDNSPYQAKNILEGTSFTPESWDVWVQKKEAKPVAGAKEFLQFADQNGV 153- Query: 127 KIYYVSDRTDAQVDATKENLEKEGIPVQGKDHLLFLKKGMKSKESRRQAVQKDTNLIMLF 18- 6 +IYY+SDR +QVDAT ENL+KEGIPVQG+DHLLFL++G+KSKE+RRQ V++ TNLIMLF Sbjct: 154 QIYYISDRAVSQVDATMENLQKEGIPVQGRDHLLFLEEGVKSKEARRQKVKETTNLIMLF 21- 3 Query: 187 GDNLVDFADFSKSSSTDREQLLTKLQSEFGSKFIVFPNPMYGSWESAIYQGKHLDVQKQL 24- 6 GDNLVDFADFSK S DR LL++LQ EFG +FI+FPNPMYGSWESA+Y+G LD QL Sbjct: 214 GDNLVDFADFSKKSEEDRTALLSELQEEFGRQFIIFPNPMYGSWESAVYKGDKLDASHQL 27- 3 Query: 247 KERQKMLHSYD 257 KER+K L S++ Sbjct: 274 KERRKALESFE 284 A related DNA sequence was identified in S. pyogenes <SEQ ID 4885> which encodes the amino acid sequence <SEQ ID 4886>. Analysis of this protein sequence reveals the following: TABLE-US-04773 Possible site: 25 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04774 >GP:CAA73175 GB:Y12602 acid phosphatase [Streptococcus equisimilis] Identities = 234/284 (82%), Positives = 261/284 (91%) Query: 1 MKSKKVVSVISLTLSLFLVTGCAKVDNNKSVNLKPATKQTYNSYSDDQLRSRENTMSVLW 60 MK+K+V SVISL LSLFLVTGCA++D+ +VN K KQT +YSD+QLRS ENTMSVLW Sbjct: 1 MKTKQVASVISLALSLFLVTGCAQLDHKANVNSKETVKQTKVTYSDEQLRSNENTMSVLW 60 Query: 61 YQRAAETQALYLQGYQLATDRLKEQLNKPTDKPYSIVLDIDETVLDNSPYQAKNVLEGTG 120- YQRAAE +ALYLQGYQLATDRLK QL + TDKPYSIVLDIDETVLDNSPYQAKN+LEGT Sbjct: 61 YQRAAEAKALYLQGYQLATDRLKNQLGQATDKPYSIVLDIDETVLDNSPYQAKNILEGTS 120- Query: 121 FTPESWDYWVQKKEAKPVAGAKDFLQFADQNGVQIYYISDRSTTQVDATMENLQKEGIPV 18- 0 FTPESWD WVQKKEAKPVAGAK+FLQFADQNGVQIYYISDR+ +QVDATMENLQKEGIPV Sbjct: 121 FTPESWDVWVQKKEARPVAGAKEFLQFADQNGVQIYYISDRAVSQVDATMENLQKEGIPV 18- 0 Query: 181 QGRDHLLFLEKGVKSKESRRQKVKETTNVTMLFGDNLLDFADFSKKSQEDRTALLSDLQE 24- 0 QGRDHLLFLE+GVKSKE+RRQKVKETTN+ MLFGDNL+DFADFSKKS+EDRTALLS+LQE Sbjct: 181 QGRDHLLFLEEGVKSKEARRQKVKETTNLIMLFGDNLVDFADFSKKSEEDRTALLSELQE 24- 0 Query: 241 EFGRRFIIFPNPMYGSWEGAIYKGEKLDVLKQLEERRKSLKSFK 284 EFGR+FIIFPNPMYGSWE A+YKG+KLD QL+ERRK+L+SF+ Sbjct: 241 EFGRQFIIFPNPMYGSWESAVYKGDKLDASHQLKERRKALESFE 284 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04775 Identities = 166/247 (67%), Positives = 207/247 (83%) Query: 10 TKFKNISLSSNKLLAKENTMSVLWYQNSAEAKALYLQGYNVAKMKLDDWLQKPSEKPYSI 69 - TK S S ++L ++ENTMSVLWYQ +AE +ALYLQGY +A +L + L KP++KPYSI Sbjct: 37 TKQTYNSYSDDQLRSRENTMSVLWYQRAAETQALYLQGYQLATDRLKEQLNKPTDKPYSI 96 Query: 70 ILDLDETVLDNSPYQAKNIKDGSSFTPESWDKWVQKKSAKAVAGAKEFLKYANEKGIKIY 129- +LD+DETVLDNSPYQAKN+ +G+ FTPESWD WVQKK AK VAGAK+FL++A++ G++IY Sbjct: 97 VLDIDETVLDNSPYQAKNVLEGTGFTPESWDYWVQKKEAKPVAGAKDFLQFADQNGVQIY 156- Query: 130 YVSDRTDAQVDATKENLEKEGIPVQGKDHLLFLKKGMKSKESRRQAVQKDTNLIMLFGDN 18- 9 Y+SDR+ QVDAT ENL+KEGIPVQG+DHLLFL+KG+KSKESRRQ V++ TN+ MLFGDN Sbjct: 157 YISDRSTTQVDATMENLQKEGIPVQGRDHLLFLEKGVKSKESRRQKVKETTNVTMLFGDN 21- 6 Query: 190 LVDFADFSKSSSTDREQLLTKLQSEFGSKFIVFPNPMYGSWESAIYQGKHLDVQKQLKER 24- 9 L+DFADFSK S DR LL+ LQ EFG +FI+FPNPMYGSWE AIY+G+ LDV KQL+ER Sbjct: 217 LLDFADFSKKSQEDRTALLSDLQEEFGRRFIIFPNPMYGSWEGAIYKGEKLDVLKQLEER 27- 6 Query: 250 QKMLHSY 256 +K L S+ Sbjct: 277 RKSLKSF 283 SEQ ID 9428 (GBS661) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 136 (lane 2 & 4; MW 61 kDa+lane 3; MW 27 kDa) and in FIG. 186 (lane 11; MW 61 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 136 (lane 5-7; MW 25 kDa). GBS661-GST was purified as shown in FIG. 237, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1582 A DNA sequence (GBSx1676) was identified in S. agalactiae <SEQ ID 4887> which encodes the amino acid sequence <SEQ ID 4888>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following:

TABLE-US-04776 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3462(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 4889> which encodes the amino acid sequence <SEQ ID 4890>. Analysis of this protein sequence reveals the following: TABLE-US-04777 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3462(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04778 Identities = 395/398 (99%), Positives = 398/398 (99%) Query: 1 MAKLTVKDVDLKGKKVLVRVDFNVPLKDGVITNDNRITAALPTIKYIIEQGGRAILFSHL 60 MAKLTVKDVDLKGKKVLVRVDFNVPLKDGVITNDNRITAALPTIKYIIEQGGRAILFSHL Sbjct: 1 MAKLTVKDVDLKGKKVLVRVDFNVPLKDGVITNDNRITAALPTIKYIIEQGGRAILFSHL 60 Query: 61 GRVKEEADKEGKSLAPVAADLAAKLGQDVVFPGVTRGAKLEEAINALEDGQVLLVENTRF 120- GRVKEEADKEGKSLAPVAADLAAKLGQDVVFPGVTRG+KLEEAINALEDGQVLLVENTRF Sbjct: 61 GRVKEEADKEGKSLAPVAADLAAKLGQDVVFPGVTRGSKLEEAINALEDGQVLLVENTRF 120- Query: 121 EDVDGKKESKNDEELGKYWASLGDGIFVNDAFGTAHRAHASNVGISANVEKAVAGFLLEN 18- 0 EDVDGKKESKNDEELGKYWASLGDGIFVNDAFGTAHRAHASNVGISANVEKAVAGFLLEN Sbjct: 121 EDVDGKKESKNDEELGKYWASLGDGIFVNDAFGTAHRAHASNVGISANVEKAVAGFLLEN 18- 0 Query: 181 EIAYIQEAVETPERPFVAILGGSKVSDKIGVIENLLEKADKVLIGGGMTYTFYKAQGIEI 24- 0 EIAYIQEAVETPERPFVAILGGSKVSDKIGVIENLLEKADKVLIGGGMTYTFYKAQGIEI Sbjct: 181 EIAYIQEAVETPERPFVAILGGSKVSDKIGVIENLLEKADKVLIGGGMTYTFYKAQGIEI 24- 0 Query: 241 GNSLVEEDKLDVAKDLLEKSNGKLILPVDSKEANAFAGYTEVRDTEGEAVSEGFLGLDIG 30- 0 GNSLVEEDKLDVAKDLLEKSNGKLILPVDSKEANAFAGYTEVRDTEGEAVSEGFLGLDIG Sbjct: 241 GNSLVEEDKLDVAKDLLEKSNGKLILPVDSKEANAFAGYTEVRDTEGEAVSEGFLGLDIG 30- 0 Query: 301 PKSIAKFDEALTGAKTVVWNGPMGVFENPDFQAGTIGVMDAIVKQPGVKSIIGGGDSAAA 36- 0 PKSIA+FD+ALTGAKTVVWNGPMGVFENPDFQAGTIGVMDAIVKQPGVKSIIGGGDSAAA Sbjct: 301 PKSIAEFDQALTGAKTVVWNGPMGVFENPDFQAGTIGVMDAIVKQPGVKSIIGGGDSAAA 36- 0 Query: 361 AINLGRADKFSWISTGGGASMELLEGKVLPGLAALTEK 398 AINLGRADKFSWISTGGGASMELLEGKVLPGLAALTEK Sbjct: 361 AINLGRADKFSWISTGGGASMELLEGKVLPGLAALTEK 398 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1583 A DNA sequence (GBSx1677) was identified in S. agalactiae <SEQ ID 4891> which encodes the amino acid sequence <SEQ ID 4892>. Analysis of this protein sequence reveals the following: TABLE-US-04779 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.39 Transmembrane 97-113 (93-118) INTEGRAL Likelihood = -3.66 Transmembrane 25-41 (24-48) INTEGRAL Likelihood = -3.40 Transmembrane 121-137 (121-140) INTEGRAL Likelihood = -3.24 Transmembrane 72-88 (72-88) INTEGRAL Likelihood = -2.07 Transmembrane 143-159 (143-160) ----- Final Results ----- bacterial membrane --- Certainty = 0.4354(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 4893> which encodes the amino acid sequence <SEQ ID 4894>. Analysis of this protein sequence reveals the following: TABLE-US-04780 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.23 Transmembrane 97-113 (93-118) INTEGRAL Likelihood = -7.17 Transmembrane 121-137 (119-140) INTEGRAL Likelihood = -4.19 Transmembrane 25-41 (24-48) INTEGRAL Likelihood = -3.24 Transmembrane 72-88 (72-88) INTEGRAL Likelihood = -2.55 Transmembrane 154-170 (154-170) ----- Final Results ----- bacterial membrane --- Certainty = 0.4291(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-04781 Identities = 155/178 (87%), Positives = 169/178 (94%) Query: 1 MKTLKKLLSNYKFDIKKFKLGMRTFKTGLSVFLVLLVFHLFGWKGLQIGALTAVFSLRED 60 MKTL+KLLSNYKFDIKKFKLGMRT KTGLSVFLVLLVFHLFGWKGLQIGALTAVFSLRED Sbjct: 1 MKTLRKLLSNYKFDIKKFKLGMRTLKTGLSVFLVLLVFHLFGWKGLQIGALTAVFSLRED 60 Query: 61 FDKSVHFGFSRIIGNSIGGLLSLVFFAFNEIFHQAFWVTLLIVPICTMLCIMINVACNNK 120- FDKSVHFGFSRIIGNSIGGLLSLVFFAFNEIFHQAFWVTLLIVPICTMLCIM+NVACNNK Sbjct: 61 FDKSVHFGFSRIIGNSIGGLLSLVFFAFNEIFHQAFWVTLLIVPICTMLCIMVNVACNNK 120- Query: 121 SGIIGGTAALLIITLSIPSGETILYVFARIFETFCGVFIAMMVNTDIEILRKKLKNNK 178 SGIIG AALLIITLSIP+G+T +YV +R+FETFCGVF+A++VNTD+E+++ K N K Sbjct: 121 SGIIGAVAALLIITLSIPTGQTFIYVTSRVFETFCGVFVAILVNTDVELIKNKWFNKK 178 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1584 A DNA sequence (GBSx1678) was identified in S. agalactiae <SEQ ID 4895> which encodes the amino acid sequence <SEQ ID 4896>. This protein is predicted to be regulatory protein glnr (glnR). Analysis of this protein sequence reveals the following: TABLE-US-04782 Possible site: 17 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04783 >GP: BAA00402 GB: D00513 ORF129 [Bacillus cereus] Identities = 59/123 (47%), Positives = 89/123 (71%), Gaps = 5/123 (4%) Query: 4 RELRRTMAVFPIGAVMKLTDLTARQIRYYEDQGLITPERTEGNRRMFSLNDMDRLLEIKD 63 +E RR+ +FPIG VM LT L+ARQIRYYE+ L++P RT+GNRR+FS ND+D+LLEIKD Sbjct: 2 KEDRRSAPLFPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKD 61 Query: 64 FISDGLHISDIKNEYMQRQH-----KSKEKQKSLSDAEVRRLLQDELRNQGRFSSPSQHI 118- + GL+++ IK + +++ K KE+ K +S E+R++L+DEL++ GRF+ S Sbjct: 62 LLDQGLNMAGIKQVLLMKENQTEAVKVKEETKEISKTELRKILRDELQHTGRFNRTSLRQ 121- Query: 119 GNM 121 G++ Sbjct: 122 GDI 124 A related DNA sequence was identified in S. pyogenes <SEQ ID 4897> which encodes the amino acid sequence <SEQ ID 4898>. Analysis of this protein sequence reveals the following: TABLE-US-04784 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04785 >GP: BAA00402 GB: D00513 ORF129 [Bacillus cereus] Identities = 59/122 (48%), Positives = 83/122 (67%), Gaps = 5/122 (4%) Query: 4 KELRRSMAVFPIGTVMTLTDLSARQIRYYEDQGLIKPERTQGNRRMFSLNDMDRLLEIKD 63 KE RRS +FPIG VM LT LSARQIRYYE+ L+ P RT+GNRR+FS ND+D+LLEIKD Sbjct: 2 KEDRRSAPLFPIGIVMDLTQLSARQIRYYEEHNLVSPTRTKGNRRLFSFNDVDKLLEIKD 61 Query: 64 FLSEGLNIAAIKREYVERQG-----KLMQKQKALTDADVRRILHDEMLTQSGFSTPSQHI 118- L +GLN+A IK+ + ++ K+ ++ K ++ ++R+IL DE+ F+ S Sbjct: 62 LLDQGLNMAGIKQVLLMKENQTEAVKVKEETKEISKTELRKILRDELQHTGRFNRTSLRQ 121- Query: 119 GN 120 G+ Sbjct: 122 GD 123 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04786 Identities = 90/123 (73%), Positives = 108/123 (87%) Query: 1 MKERELRRTMAVFPIGAVMKLTDLTARQIRYYEDQGLITPERTEGNRRMFSLNDMDRLLE 60 MKE+ELRR+MAVFPIG VM LTDL+ARQIRYYEDQGLI PERT+GNRRMFSLNDMDRLLE Sbjct: 1 MKEKELRRSMAVFPIGTVMTLTDLSARQIRYYEDQGLIKPERTQGNRRMFSLNDMDRLLE 60 Query: 61 IKDFISDGLHISDIKNEYMQRQHKSKEKQKSLSDAEVRRLLQDELRNQGRFSSPSQHIGN 120- IKDF+S+GL+I+ IK EY++RQ K +KQK+L+DA+VRR+L DE+ Q FS+PSQHIGN Sbjct: 61 IKDFLSEGLNIAAIKREYVERQGKLMQKQKALTDADVRRILHDEMLTQSGFSTPSQHIGN 120- Query: 121 MHL 123 + Sbjct: 121 FRI 123 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1585 A DNA sequence (GBSx1679) was identified in S. agalactiae <SEQ ID 4899> which encodes the amino acid sequence <SEQ ID 4900>. This protein is predicted to be glutamine synthetase (glnA). Analysis of this protein sequence reveals the following: TABLE-US-04787 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2157(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 4901> which encodes the amino acid sequence <SEQ ID 4902>. Analysis of this protein sequence reveals the following: TABLE-US-04788 Possible site: 29 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.00 Transmembrane 347-363 (347-363) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04789 Identities = 392/448 (87%), Positives = 421/448 (93%) Query: 1 MTITAEDIRREVKEKNVTFLRLMFTDILGVMKNVEIPATDEQLDKVLSNKAMFDGSSIEG 60 M IT DIRREVKEKNVTFLRLMFTDI+GVMKNVEIPAT EQLDKVLSNK MFDGSSIEG Sbjct: 1 MAITVADIRREVKEKNVTFLRLMFTDIMGVMKNVEIPATKEQLDKVLSNKVMFDGSSIEG 60 Query: 61 FVRINESDMYLYPDLDTWIVFPWGDENGAVAGLICDIYTAEGEPFAGDPRGNLKRNMKRM 120- FVRINESDMYLYPDLDTWIVFPWGDENGAVAGLICDIYTAEG+PFAGDPRGNLKR +K M Sbjct: 61 FVRINESDMYLYPDLDTWIVFPWGDENGAVAGLICDIYTAEGKPFAGDPRGNLKRALKHM 120- Query: 121 QEMGYKSFNLGPEPEFFLFKMDENGNPTLDVNDKGGYFDLAPTDLADNTRREIVNVLTQM 18- 0 E+GYKSFNLGPEPEFFLFKMD+ GNPTL+VND GGYFDLAP DLADNTRREIVN+LT+M Sbjct: 121 NEIGYKSFNLGPEPEFFLFKMDDKGNPTLEVNDNGGYFDLAPIDLADNTRREIVNILTKM 18- 0 Query: 181 GFEVEASHHEVAVGQHEIDFKYDDVLKACDNIQLFKLVVKTIARKHGLYATFMAKPKFGI 24- 0 GFEVEASHHEVAVGQHEIDFKY DVLKACDNIQ+FKLVVKTIAR+HGLYATFMAKPKFGI Sbjct: 181 GFEVEASHHEVAVGQHEIDFKYADVLKACDNIQIFKLVVKTIAREHGLYATFMAKPKFGI 24- 0 Query: 241 NGSGMHCNMSLFDNEGNNAFFDPEDPRGMQLSEDAYYFLGGLMKHAYNYTAIINPTVNSY 30- 0 GSGMHCNMSLFDN+GNNAF+D D RGMQLSEDAYYFLGGLMKHAYNYTAI NPTVNSY Sbjct: 241 AGSGMHCNMSLFDNQGNNAFYDEADKRGMQLSEDAYYFLGGLMKHAYNYTAITNPTVNSY 30- 0 Query: 301 KRLVPGYEAPVYVAWAGRNRSPLIRVPASRGMGTRLELRSVDPTANPYLALSVLLGSGLE 36- 0 KRLVPGYEAPVYVAWAG NRSPLIRVPASRGMGTRLELRSVDPTANPYLAL+VLL +GL+ Sbjct: 301 KRLVPGYEAPVYVAWAGSNRSPLIRVPASRGMGTRLELRSVDPTANPYLALAVLLEAGLD 36- 0 Query: 361 GIENKIEAPEPIETNIYAMTVEERRQAGIVDLPSTLHNALEALEEDEVVKAALGTHIYTN 42- 0 GI NKIEAPEP+E NIY MT+EER +AGI+DLPSTLHNAL+AL++D+VV+ ALG HIYTN Sbjct: 361 GIINKIEAPEPVEANIYTMTMEERNEAGIIDLPSTLHNALKALQKDDVVQKALGYHIYTN 42- 0 Query: 421 FLDAKRIEWASYATYVSQWEIDNYLDLY 448 FL+AKRIEW+SYAT+VSQWEID+Y+ Y Sbjct: 421 FLEAKRIEWSSYATFVSQWEIDHYIHNY 448 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1586 A DNA sequence (GBSx1680) was identified in S. agalactiae <SEQ ID 4903> which encodes the amino acid sequence <SEQ ID 4904>. This protein is predicted to be SceB precursor. Analysis of this protein sequence reveals the following: TABLE-US-04790 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04791 >GP: CAA66624 GB: X97985 ORF1 [Staphylococcus aureus] Identities = 44/119 (36%), Positives = 66/119 (54%), Gaps = 4/119 (3%) Query: 26 SFASTNADANTYNYAVDVDYLASAEEIAQAHPA-SNTFPLGQCTWGVKE-MATWAGNWWG 83 - S AS + +N + ++ I+ + + SN + GQCT+ V + + G+ WG Sbjct: 117 SGASYSTTSNNVHVTTTAAPSSNGRSISNGYASGSNLYTSGQCTYYVFDRVGGKIGSTWG 17- 6 Query: 84 NGGDWAASAASADYTVGTQPRVGSIVCWTDGSYGHVAYVTAVDPVTNKIQVLESNYAGH 142 N +WA +AAS+ YTV P+VG+I+ T G YGHVAYV V+ ++V E NY GH Sbjct: 177 NASNWANAAASSGYTVNNTPKVGAIMQTTQGYYGHVAYVEGVNS-NGSVRVSEMNY-GH 233- A related DNA sequence was identified in S. pyogenes <SEQ ID 1013> which encodes the amino acid sequence <SEQ ID 1014>. Analysis of this protein sequence reveals the following: TABLE-US-04792 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04793 Identities = 60/115 (52%), Positives = 81/115 (70%), Gaps = 7/115 (6%) Query: 55 AHPASNTFPLGQCTWGVKEMATWAGNWWGNGGDWAASAASADYTVGTQPRVGSIVCWTDG 114- ++ +SNT+P+GQCTWG K +A WAGN WGNGG WA SA +A Y G+ P VG+I W DG Sbjct: 291 SYDSSNTYPVGQCTWGAKSLAPWAGNNWGNGGQWAYSAQAAGYRTGSTPMVGAIAVWNDG 35- 0 Query: 115 SYGHVAYVTAVDPVTNKIQVLESNYAGHQWIDNYRGWFDPQNTVTPGVVSYIYPN 169 YGHVA V V ++ I+V+ESNY+G Q+I ++RGWF+P V++IYP+ Sbjct: 351 GYGHVAVVVEVQSASS-IRVMESNYSGRQYIADHRGWFNPTG------VTFIYPH 398 A related GBS gene <SEQ ID 8859> and protein <SEQ ID 8860> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04794 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 5.85 GvH: Signal Score (-7.5): 3.11 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 6.74 threshold: 0.0 PERIPHERAL Likelihood = 6.74 115 modified ALOM score: -1.85 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00108## SEQ ID 8860 (GBS30) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 8 (lane 2; MW 19.2 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 16 (lane 2; MW 44.2 kDa). GBS30-GST was purified as shown in FIG. 193, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1587 A DNA sequence (GBSx1681) was identified in S. agalactiae <SEQ ID 4905> which encodes the amino acid sequence <SEQ ID 4906>. Analysis of this protein sequence reveals the following: TABLE-US-04795 Possible site: 14 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.93 Transmembrane 2-18 (1-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.2572 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1588 A DNA sequence (GBSx1682) was identified in S. agalactiae <SEQ ID 4907> which encodes the amino acid sequence <SEQ ID 4908>. Analysis of this protein sequence reveals the following:

TABLE-US-04796 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2160 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04797 >GP: BAB06381 GB: AP001516 unknown conserved protein [Bacillus halodurans] Identities = 353/550 (64%), Positives = 443/550 (80%) Query: 6 LKPEEVGVYAIGGLGEIGKNTYGIEYQDEIIIVDAGIKFPEDDLLGIDYVIPDYSYIVEN 65 LK + VYA+GGLGEIGKNTY +++QDEII++DAGIKFPED+LLGIDYVIPDYSY+V+N Sbjct: 4 LKNNQTAVYALGGLGEIGKNTYAVQFQDEIILIDAGIKFPEDELLGIDYVIPDYSYLVKN 63 Query: 66 IDRIKALVITHGHEDHIGGIPFLLKQANLPIYAGPLALALIKGKLEEHGLLRDATLYEIH 125- ++IK L ITHGHEDHIGGIP+LL++ N+PIY G LAL L++GKLEEHGLLR A L++I Sbjct: 64 ENKIKGLFITHGHEDHIGGIPYLLREVNIPIYGGKLALGLLRGKLEEHGLLRKAKLHDIQ 123- Query: 126 ANTELTFKNLSVTFFRTTHSIPEPLGIVIHTPQGKVICTGDFKFDFTPVGEPADLHRMAA 18- 5 + + F SV+FFRTTHSIP+ GIV+ TP G ++ TGDFKFDFTPVGEPA+L +MA Sbjct: 124 EDDIIKFAKTSVSFFRTTHSIPDSYGIVVKTPPGNIVHTGDFKFDFTPVGEPANLTKMAK 18- 3 Query: 186 LGEDGVLCLLSDSTNAEVPTFTNSEKIVGQSIMKIIEGIEGRIIFASFASNIFRLQQAAE 24- 5 +GE+GVLCLLSDSTN+E+P FT SE+ VG+SI I +EGRIIFA+FASNI RLQQA E Sbjct: 184 IGEEGVLCLLSDSTNSEIPEFTMSERKVGESIDHIFRRVEGRIIFATFASNIHRLQQAVE 24- 3 Query: 246 AAVKTGRKIAVFGRSMEKAIVNGIELGYIKVPKGTFIEPSELKNLHASEVLIMCTGSQGE 30- 5 +AV+ GRK+AVFGRSME AI G ELGYIK PK TFIEP++L L +EV+I+CTGSQGE Sbjct: 244 SAVRYGRKVAVFGRSMESAINIGQELGYIKAPKNTFIEPNQLNKLPDNEVMILCTGSQGE 30- 3 Query: 306 SMAALARIANGTHRQVTLQPGDTVIFSSSPIPGNTTSVNKLINTIQEAGVDVIHGKINNI 36- 5 MAAL+R+A GTHRQ+ + PGDTVIFSSSPIPGNT SV+K IN + +AG +VIHG +N+I Sbjct: 304 PMAALSRVAFGTHRQIQIIPGDTVIFSSSPIPGNTLSVSKTINQLYKAGANVIHGSLNDI 36- 3 Query: 366 HTSGHGGQQEQKLMLRLIKPKYFMPVHGEYRMQKVHAGLAVDTGIPKENIFIMENGDVLA 42- 5 HTSGHGGQ+EQKLMLRLIKPKYFMP+HGEYRM K+H LA D G+P EN FIM+NGDVLA Sbjct: 364 HTSGHGGQEEQKLMLRLIKPKYFMPIHGEYRMLKMHTKLAEDCGVPAENCFIMDNGDVLA 42- 3 Query: 426 LTSDSARIAGHFNAQDIYVDGNGIGDIGAAVLRDRHDLSEDGVVLAVATVDFDSKMILAG 48- 5 L D A IAG + +YVDGNGIGDIG VLRDR LSE+G+V+ V +++ + AG Sbjct: 424 LHPDEAGIAGKIPSGSVYVDGNGIGDIGNIVLRDRRILSEEGLVVVVVSLNMKEYKVTAG 48- 3 Query: 486 PDILSRGFIYMRESGDLIRESQHILFNAIRIALKNKDASIQSVNGAIVNALRPFLYEKTE 54- 5 PD++SRGF+YMRESGDLI+E+Q +L N ++ ++ K + I + L PFLY++T+ Sbjct: 484 PDLISRGFVYMRESGDLIQEAQRLLANHLQEVMERKTNQWSEIKNEITDVLGPFLYDRTK 54- 3 Query: 546 REPIIIPMVL 555 R+P+I+P+++ Sbjct: 544 RKPMILPIIM 553 A related DNA sequence was identified in S. pyogenes <SEQ ID 4909> which encodes the amino acid sequence <SEQ ID 4910>. Analysis of this protein sequence reveals the following: TABLE-US-04798 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.11 Transmembrane 468-484 (468-484) ----- Final Results ----- bacterial membrane --- Certainty = 0.1044 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04799 >GP: BAB06381 GB: AP001516 unknown conserved protein [Bacillus halodurans] Identities = 353/550 (64%), Positives = 444/550 (80%) Query: 6 LKPNEVGVFAIGGLGEIGKNTYGIEYQDEIIIVDAGIKFPEDDLLGIDYVIPDYSYIVDN 65 LK N+ V+A+GGLGEIGKNTY +++QDEII++DAGIKFPED+LLGIDYVIPDYSY+V N Sbjct: 4 LKNNQTAVYALGGLGEIGKNTYAVQFQDEIILIDAGIKFPEDELLGIDYVIPDYSYLVKN 63 Query: 66 LDRVKALVITHGHEDHIGGIPFLLKQANIPIYAGPLALALIRGKLEEHGLWREATVYEIN 125- +++K L ITHGHEDHIGGIP+LL++ NIPIY G LAL L+RGKLEEHGL R+A +++I Sbjct: 64 ENKIKGLFITHGHEDHIGGIPYLLREVNIPIYGGKLALGLLRGKLEEHGLLRKAKLHDIQ 123- Query: 126 HNTELTFKNMSVTFFKTTHSIPEPVGIVIHTPQGKIICTGDFKFDFTPVGDPADLQRMAA 18- 5 + + F SV+FF+TTHSIP+ GIV+ TP G I+ TGDFKFDFTPVG+PA+L +MA Sbjct: 124 EDDIIKFAKTSVSFFRTTHSIPDSYGIVVKTPPGNIVHTGDFKFDFTPVGEPANLTKMAK 18- 3 Query: 186 LGEEGVLCLLSDSTNAEIPTFTNSEKVVGQSILKIIEGIHGRIIFASFASNIYRLQQAAE 24- 5 +GEEGVLCLLSDSTN+EIP FT SE+ VG+SI I + GRIIFA+FASNI+RLQQA E Sbjct: 184 IGEEGVLCLLSDSTNSEIPEFTMSERKVGESIDHIFRRVEGRIIFATFASNIHRLQQAVE 24- 3 Query: 246 AAVKTGRKIAVFGRSMEKAIVNGIELGYIKVPKGTFIEPSELKNLHASEVLIMCTGSQGE 30- 5 +AV+ GRK+AVFGRSME AI G ELGYIK PK TFIEP++L L +EV+I+CTGSQGE Sbjct: 244 SAVRYGRKVAVFGRSMESAINIGQELGYIKAPKNTFIEPNQLNKLPDNEVMILCTGSQGE 30- 3 Query: 306 SMAALARIANGTHRQVTLQPGDTVIFSSSPIPGNTTSVNKLINTIQEAGVDVIHGKVNNI 36- 5 MAAL+R+A GTHRQ+ + PGDTVIFSSSPIPGNT SV+K IN + +AG +VIHG +N+I Sbjct: 304 PMAALSRVAFGTHRQIQIIPGDTVIFSSSPIPGNTLSVSKTINQLYKAGANVIHGSLNDI 36- 3 Query: 366 HTSGHGGQQEQKLMLSLIKPKYFMPVHGEYRMQKVHAGLAMDIGIPKENIFIMENGDVLA 42- 5 HTSGHGGQ+EQKLML LIKPKYFMP+HGEYRM K+H LA D G+P EN FIM+NGDVLA Sbjct: 364 HTSGHGGQEEQKLMLRLIKPKYFMPIHGEYRMLKMHTKLAEDCGVPAENCFIMDNGDVLA 42- 3 Query: 426 LTSDSARIAGHFNAQDIYVDGNGIGDIGAAVLRDRRDLSEDGVVLAVATVDFNTQMILAG 48- 5 L D A IAG + +YVDGNGIGDIG VLRDRR LSE+G+V+ V +++ + AG Sbjct: 424 LHPDEAGIAGKIPSGSVYVDGNGIGDIGNIVLRDRRILSEEGLVVVVVSLNMKEYKVTAG 48- 3 Query: 486 PDILSRGFIYMRESGDLIRESQRVLFNAIRIALKNKDASIQSVNGAIVNALRPFLYEKTE 54- 5 PD++SRGF+YMRESGDLI+E+QR+L N ++ ++ K + I + L PFLY++T+ Sbjct: 484 PDLISRGFVYMRESGDLIQEAQRLLANHLQEVMERKTNQWSEIKNEITDVLGPFLYDRTK 54- 3 Query: 546 REPIIIPMVL 555 R+P+I+P+++ Sbjct: 544 RKPMILPIIM 553 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04800 Identities = 523/559 (93%), Positives = 550/559 (97%) Query: 1 MSNINLKPEEVGVYAIGGLGEIGKNTYGIEYQDEIIIVDAGIKFPEDDLLGIDYVIPDYS 60 M+NI+LKP EVGV+AIGGLGEIGKNTYGIEYQDEIIIVDAGIKFPEDDLLGIDYVIPDYS Sbjct: 1 MTNISLKPNEVGVFAIGGLGEIGKNTYGIEYQDEIIIVDAGIKFPEDDLLGIDYVIPDYS 60 Query: 61 YIVENIDRIKALVITHGHEDHIGGIPFLLKQANLPIYAGPLALALIKGKLEEHGLLRDAT 120- YIV+N+DR+KALVITHGHEDHIGGIPFLLKQAN+PIYAGPLALALI+GKLEEHGL R+AT Sbjct: 61 YIVDNLDRVKALVITHGHEDHIGGIPFLLKQANIPIYAGPLALALIRGKLEEHGLWREAT 120- Query: 121 LYEIHANTELTFKNLSVTFFRTTHSIPEPLGIVIHTPQGKVICTGDFKFDFTPVGEPADL 18- 0 +YEI+ NTELTFKN+SVTFF+TTHSIPEP+GIVIHTFQGK+ICTGDFKFDFTPVG+PADL Sbjct: 121 VYEINHNTELTFKNMSVTFFKTTHSIPEPVGIVIHTPQGKIICTGDFKFDFTPVGDPADL 18- 0 Query: 181 HRMAALGEDGVLCLLSDSTNAEVPTFTNSEKIVGQSIMKIIEGIEGRIIFASFASNIFRL 24- 0 RMAALGE+GVLCLLSDSTNAE+PTFTNSEK+VGQSI+KIIEGI GRIIFASFASNI+RL Sbjct: 181 QRMAALGEEGVLCLLSDSTNAEIPTFTNSEKVVGQSILKIIEGIHGRIIFASFASNIYRL 24- 0 Query: 241 QQAAEAAVKTGRKIAVFGRSMEKAIVNGIELGYIKVPKGTFIEPSELKNLHASEVLIMCT 30- 0 QQAAEAAVKTGRKIAVFGRSMEKAIVNGIELGYIKVPKGTFIEPSELKNLHASEVLIMCT Sbjct: 241 QQAAEAAVKTGRKIAVFGRSMEKAIVNGIELGYIKVPKGTFIEPSELKNLHASEVLIMCT 30- 0 Query: 301 GSQGESMAALARIANGTHRQVTLQPGDTVIFSSSPIPGNTTSVNKLINTIQEAGVDVIHG 36- 0 GSQGESMAALARIANGTHRQVTLQPGDTVIFSSSPIPGNTTSVNKLINTIQEAGVDVIHG Sbjct: 301 GSQGESMAALARIANGTHRQVTLQPGDTVIFSSSPIPGNTTSVNKLINTIQEAGVDVIHG 36- 0 Query: 361 KINNIHTSGHGGQQEQKLMLRLIKPKYFMPVHGEYRMQKVHAGLAVDTGIPKENIFIMEN 42- 0 K+NNIHTSGHGGQQEQKLML LIKPKYFMPVHGEYRMQKVHAGLA+D GIPKENIFIMEN Sbjct: 361 KVNNIHTSGHGGQQEQKLMLSLIKPKYFMPVHGEYRMQKVHAGLAMDIGIPKENIFIMEN 42- 0 Query: 421 GDVLALTSDSARIAGHFNAQDIYVDGNGIGDIGAAVLRDRHDLSEDGVVLAVATVDFDSK 48- 0 GDVLALTSDSARIAGHFNAQDIYVDGNGIGDIGAAVLRDR DLSEDGVVLAVATVDF+++ Sbjct: 421 GDVLALTSDSARIAGHFNAQDIYVDGNGIGDIGAAVLRDRRDLSEDGVVLAVATVDFNTQ 48- 0 Query: 481 MILAGPDILSRGFIYMRESGDLIRESQHILFNAIRIALKNKDASIQSVNGAIVNALRPFL 54- 0 MILAGPDILSRGFIYMRESGDLIRESQ +LFNAIRIALKNKDASIQSVNGAIVNALRPFL Sbjct: 481 MILAGPDILSRGFIYMRESGDLIRESQRVLFNAIRIALKNKDASIQSVNGAIVNALRPFL 54- 0 Query: 541 YEKTEREPIIIPMVLTPDK 559 YEKTEREPIIIPMVLTPDK Sbjct: 541 YEKTEREPIIIPMVLTPDK 559 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1589 A DNA sequence (GBSx1683) was identified in S. agalactiae <SEQ ID 4911> which encodes the amino acid sequence <SEQ ID 4912>. Analysis of this protein sequence reveals the following: TABLE-US-04801 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2932(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04802 >GP: CAB13327 GB: Z99111 ykzG [Bacillus subtilis] Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 7/75 (9%) Query: 1 MIYKVFYQETKERNPRREQTKTLYVTIDAANELEGRIAARKLVEENTAYNIEFIELLSDK 60 MIYKVFYQE + P RE+T +LY+ + ++ ++ +K +NIEFI + Sbjct: 1 MIYKVFYQEKADEVPVREKTDSLYIEGVSERDVRTKLKEKK-------FNIEFITPVDGA 53 Query: 61 HLEYEKETGVFELTE 75 LEYE+++ F++ E Sbjct: 54 FLEYEQQSENFKVLE 68 A related DNA sequence was identified in S. pyogenes <SEQ ID 4913> which encodes the amino acid sequence <SEQ ID 4914>. Analysis of this protein sequence reveals the following: TABLE-US-04803 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3428(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04804 Identities = 60/76 (78%), Positives = 70/76 (91%) Query: 1 MIYKVFYQETKERNPRREQTKTLYVTIDAANELEGRIAARKLVEENTAYNIEFIELLSDK 60 MIYKVFYQETK+++PRRE TK LY+ IDA +EL+GRI AR+LVE+NT YN+EFIELLSDK Sbjct: 1 MIYKVFYQETKDQSPRRESTKALYLNIDATDELDGRIKARRLVEDNTYYNVEFIELLSDK 60 Query: 61 HLEYEKETGVFELTEF 76 HL+YEKETGVFELTEF Sbjct: 61 HLDYEKETGVFELTEF 76 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1590 A DNA sequence (GBSx1684) was identified in S. agalactiae <SEQ ID 4915> which encodes the amino acid sequence <SEQ ID 4916>. This protein is predicted to be glycoprotein endopeptidase. Analysis of this protein sequence reveals the following: TABLE-US-04805 Possible site: 13 >>> Seems to have no N-terminal signal sequence (or aa 1-17) ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0430(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04806 >GP: CAA76861 GB: Y17797 hypothetical protein [Enterococcus faecalis] Identities = 94/182 (51%), Positives = 127/182 (69%), Gaps = 6/182 (3%) Query: 2 MKVLAFDTSSKALSVAVLNNMECLATVTINIKKNHSINLMPAIDFLMQSIDLEPQDLDRI 61 +++LA DTS++ LS+AV N + L + T +K+NHS+ LMPAID+LM ++L P +DR Sbjct: 13 VRILAIDTSNQTLSIAVCENQKILGSYTATVKRNHSLTLMPAIDYLMSQLNLAPTAIDRF 72 Query: 62 VVAEGPGSYTGLRVAVATAKMLAYTLKIDLVGVSSLYAL-TNGFSENDLLVPLIDARRNN 120- VVAEGPGSYTGLR+ V TAK LAYTLK +LVG+SSL AL N + L+VPL DARR N Sbjct: 73 VVAEGPGSYTGLRLGVTTAKTLAYTLKKELVGISSLQALAANCVGQTGLIVPLFDARRKN 132- Query: 121 VYVGFYQNGDTV----KPDCHTSLEEVLQEVGNKANVHFVGE-VAAFFDQIKKALPHAKI 17- 5 VY G Y+ D V PD H SL E+L+++ N+ N+ FVGE V F ++I + +PH +I Sbjct: 133 VYAGAYRFVDGVWQNELPDQHISLRELLEQLKNEPNLFFVGEDVEKFTEEIAQIIPHGEI 19- 2 Query: 176 TE 177 + Sbjct: 193 CD 194 A related DNA sequence was identified in S. pyogenes <SEQ ID 4917> which encodes the amino acid sequence <SEQ ID 4918>. Analysis of this protein sequence reveals the following: TABLE-US-04807 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 99-115 (99-115) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9159> which encodes the amino acid sequence <SEQ ID 9160>. Analysis of this protein sequence reveals the following: TABLE-US-04808 Possible site: 25 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 88-104 (88-104) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04809 Identities = 134/232 (57%), Positives = 172/232 (73%), Gaps = 3/232 (1%) Query: 2 MKVLAFDTSSKALSVAVLNNMECLATVTINIKKNHSINLMPAIDFLMQSIDLEPQDLDRI 61 MK LAFDTS+K LS+A+L++ LA +T+NI+K HS++LMPAIDFLM DL+PQDL+RI Sbjct: 12 MKTLAFDTSNKTLSLAILDDETLLADMTLNIQKKHSVSLMPAIDFLMTCTDLKPQDLERI 71 Query: 62 VVAEGPGSYTGLRVAVATAKMLAYTLKIDLVGVSSLYALTNGFSE---NDLLVPLIDARR 118- VVA+GPGSYTGLRVAVATAK LAY+L I LVG+SSLYAL + N L+VPLIDARR Sbjct: 72 VVAKGPGSYTGLRVAVATAKTLAYSLNIALVGISSLYALAASTCKQYPNTLVVPLIDARR 131- Query: 119 NNVYVGFYQNGDTVKPDCHTSLEEVLQEVGNKANVHFVGEVAAFFDQIKKALPHAKITET 17- 8 N YVG+Y+ G +V P H SLE +++++ + + FVGE A F ++I+K LP A + T Sbjct: 132 QNAYVGYYRQGKSVMPQAHASLEVIIEQLVEEGQLIFVGETAPFAEKIQKKLPQAILLPT 19- 1 Query: 179 LPCAVAIGRKGQKMKSVNVDAFVPRYLKRVEAEENWLKNHCETNTEEYIKRV 230 LP A G GQ + NVDAFVP+YLKRVEAEENWLK++ + Y+KR+ Sbjct: 192 LPSAYECGLLGQSLAPENVDAFVPQYLKRVEAEENWLKDNEIKDDSHYVKRI 243 SEQ ID 4916 (GBS69) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 9; MW 28.9 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 20 (lane 4; MW 53.9 kDa). The GBS69-GST fusion product was purified (FIG. 197, lane 6) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 285), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1591 A DNA sequence (GBSx1685) was identified in S. agalactiae <SEQ ID 4919> which encodes the amino acid sequence <SEQ ID 4920>. This protein is predicted to be ribosomal-protein-alanine acetyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-04810 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10137> which encodes amino acid sequence <SEQ ID 10138> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04811 >GP: AAC06803 GB: AE000696 ribosomal-protein-alanine cetyltransferase [Aquifex aeolicus] Identities = 44/141 (31%), Positives = 74/141 (52%), Gaps = 8/141 (5%) Query: 9 LREFEMESSEQALAIWSVLSDVYDKSPWSLSQISEDLKKDSTDYFFVYNDGEVIGFLALQ 68 +RE E E E+ ++ + + + WS +D + + F + DG+V+G++ Sbjct: 4 VREMEREDVER---VYEINRESFTTDAWSRFSFEKDFENKFSRRFVLEEDGKVVGYVIFW 60 Query: 69 QLVGEVEITNIAVKKNYQGKGYAYQLM----SMIADIEVPVFLEVRYSNIVAQKLYERCG 124- + E I A+ Y+GKGY +L+ S + D V L+VR SN+ A LY++ G Sbjct: 61 VVKEEATIMTFAIAPGYRGKGYGEKLLREAISRLGDKVKRVVLDVRKSNLRAINLYKKLG 120- Query: 125 FVVLRKRKNYYHDPIEDAIVM 145 F V+ +RK YY D E+A++M Sbjct: 121 FKVVTERKGYYSDG-ENALLM 140 A related DNA sequence was identified in S. pyogenes <SEQ ID 4921> which encodes the amino acid sequence <SEQ ID 4922>. Analysis of this protein sequence reveals the following: TABLE-US-04812 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3800(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04813 Identities = 65/140 (46%), Positives = 96/140 (68%), Gaps = 1/140 (0%) Query: 9 LREFEMES-SEQALAIWSVLSDVYDKSPWSLSQISEDLKKDSTDYFFVYNDGEVIGFLAL 67 L E M++ EQA I+ +L VY SPW+L Q+ D+++D TDYF +Y+ +++GFLA+ Sbjct: 6 LSESNMKTVEEQAKNIYQLLEMVYGTSPWTLEQVLIDIRRDQTDYFLLYDHDKLLGFLAI 65 Query: 68 QQLVGEVEITNIAVKKNYQGKGYAYQLMSMIADIEVPVFLEVRYSNIVAQKLYERCGFVV 127- Q L GEVE+T IA+ ++Q G A QLM+ + IE +FLEVR SN AQ LY++ GF Sbjct: 66 QDLAGEVEMTQIAILPSHQELGLASQLMTHLDSIESDIFLEVRESNHRAQGLYQKFGFKF 125- Query: 128 LRKRKNYYHDPIEDAIVMRK 147 + KR +YY +PIE A++M++ Sbjct: 126 IGKRPDYYRNPIETALLMKR 145 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1592 A DNA sequence (GBSx1686) was identified in S. agalactiae <SEQ ID 4923> which encodes the amino acid sequence <SEQ ID 4924>. Analysis of this protein sequence reveals the following: TABLE-US-04814 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0334(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1593 A DNA sequence (GBSx1687) was identified in S. agalactiae <SEQ ID 4925> which encodes the amino acid sequence <SEQ ID 4926>. Analysis of this protein sequence reveals the following:

TABLE-US-04815 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.75 Transmembrane 86-102 (86-104) ----- Final Results ----- bacterial membrane --- Certainty = 0.1702(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty= 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04816 >GP: BAB04267 GB: AP001508 glycoprotein endopeptidase [Bacillus halodurans] Identities = 194/331 (58%), Positives = 263/331 (78%), Gaps = 1/331 (0%) Query: 6 ILAVESSCDETSVAILKNDKELLANIIASQVESHKRFGGVVPEVASRHHVEVVTTCFEDA 65 ILA+E+SCDETS A+++N +L+N+++SQ++SHKRFGGVVPE+ASRHHVE +T E+A Sbjct: 12 ILAIETSCDETSAAVIENGTTILSNVVSSQIDSHKRFGGVVPEIASRHHVEQITVIVEEA 71 Query: 66 LQEAGIVASDLDAVAVTYGPGLVGALLVGMAAAKAFAWANKLPLIPINHMAGHLMAARDV 125- + EAG+ +DL AVAVT GPGLVGALL+G+ AAKA A+A++LPLI ++H+AGH+ A R + Sbjct: 72 MHEAGVDFADLAAVAVTEGPGLVGALLIGVNAAKAIAFAHQLPLIGVHHIAGHIYANRLL 131- Query: 126 KELQYPLLALLVSGGHTELVYVSEPGDYKIVGETRDDAVGEAYDKVGRVMGLTYPAGREI 18- 5 KEL++PLLAL+VSGGHTEL+Y+ G+++++GETRDDAVGEAYDKV R +GL YP G I Sbjct: 132 KELEFPLLALVVSGGHTELIYMENHGEFEVIGETRDDAVGEAYDKVARTLGLPYPGGPHI 19- 1 Query: 186 DQLAHKGQDTYHFPRAMIKEDHLEFSFSGLKSAFINLHHNAEQKGEALVLEDLCASFQAA 24- 5 D+LA G+DT FPRA ++ D +FSFSGLKSA IN HNA+Q+GE + ED+ ASFQA+ Sbjct: 192 DRLAVNGEDTLQFPRAWLEPDSFDFSFSGLKSAVINTLHNAKQRGENVQAEDVAASFQAS 25- 1 Query: 246 VLDILLAKTQKALLKYPVKTLVVAGGVAANQGLRERLATDISPD-IDVVIPPLRLCGDNA 30- 4 V+D+L+ KT+KA +Y V+ +++AGGVAAN+GLR L + ID+VIPPL LC DNA Sbjct: 252 VIDVLVTKTKKAAEEYKVRQVLLAGGVAANKGLRTALEEAFFKEPIDLVIPPLSLCTDNA 31- 1 Query: 305 GMIALAAAIEFEKENFASLKLNAKPSLAFES 335 MI AA+I+F+++ FA + LN +PSL E+ Sbjct: 312 AMIGAAASIKFKQQTFAGMDLNGQPSLELEN 342 A related DNA sequence was identified in S. pyogenes <SEQ ID 4927> which encodes the amino acid sequence <SEQ ID 4928>. Analysis of this protein sequence reveals the following: TABLE-US-04817 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.76 Transmembrane 86-102 (85-104) ----- Final Results ----- bacterial membrane --- Certainty = 0.2105(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04818 22 GP: BAB04267 GB: AP001508 glycoprotein endopeptidase [Bacillus halodurans] Identities = 196/330 (59%), Positives = 255/330 (76%), Gaps = 2/330 (0%) Query: 6 ILAVESSCDETSVAILKNESTLLSNVIASQVESHKRFGGVVPEVASRHHVEVITTCFEDA 65 ILA+E+SCDETS A+++N +T+LSNV++SQ++SHKRFGGVVPE+ASRHHVE IT E+A Sbjct: 12 ILAIETSCDETSAAVIENGTTILSNVVSSQIDSHKRFGGVVPEIASRHHVEQITVIVEEA 71 Query: 66 LQEAGISASDLSAVAVTYGPGLVGALLVGLAAAKAFAWANHLPLIPVNHMAGHLMAAREQ 125- + EAG+ +DL+AVAVT GPGLVGALL+G+ AAKA A+A+ LPLI V+H+AGH+ A R Sbjct: 72 MHEAGVDFADLAAVAVTEGPGLVGALLIGVNAAKAIAFAHQLPLIGVHHIAGHIYANRLL 131- Query: 126 KPLVYPLIALLVSGGHTELVYVPEPGDYHIIGETRDDAVGEAYDKVGRVMGLTYPAGREI 18- 5 K L +PL+AL+VSGGHTEL+Y+ G++ +IGETRDDAVGEAYDKV R +GL YP G I Sbjct: 132 KELEFPLLALVVSGGHTELIYMENHGEFEVIGETRDDAVGEAYDKVARTLGLPYPGGPHI 19- 1 Query: 186 DQLAHKGQDTYHFPRAMITEDHLEFSFSGLKSAFINLHHNAKQKGDELILEDLCASFQAA 24- 5 D+LA G+DT FPRA + D +FSFSGLKSA IN HNAKQ+G+ + ED+ ASFQA+ Sbjct: 192 DRLAVNGEDTLQFPRAWLEPDSFDFSFSGLKSAVINTLHNAKQRGENVQAEDVAASFQAS 25- 1 Query: 246 VLDILLAKTKKALSRYPAKMLVVAGGVAANQGLRDRLAQEI--THIEVVIPKLRLCGDNA 30- 3 V+D+L+ KTKKA Y + +++AGGVAAN+GLR L + I++VIP L LC DNA Sbjct: 252 VIDVLVTKTKKAAEEYKVRQVLLAGGVAANKGLRTALEEAFFKEPIDLVIPPLSLCTDNA 31- 1 Query: 304 GMIALAAAIEYDKQHFANMSLNAKPSLAFD 333 MI AA+I++ +Q FA M LN +PSL + Sbjct: 312 AMIGAAASIKFKQQTFAGMDLNGQPSLELE 341 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04819 Identities = 288/334 (86%), Positives = 313/334 (93%), Gaps = 1/334 (0%) Query: 1 MKDRYILAVESSCDETSVAILKNDKELLANIIASQVESHKRFGGVVPEVASRHHVEVVTT 60 M DRYILAVESSCDETSVAILKN+ LL+N+IASQVESHKRFGGVVPEVASRHHVEV+TT Sbjct: 1 MTDRYILAVESSCDETSVAILKNESTLLSNVIASQVESHKRFGGVVPEVASRHHVEVITT 60 Query: 61 CFEDALQEAGIVASDLDAVAVTYGPGLVGALLVGMAAAKAFAWANKLPLIPINHMAGHLM 120- CFEDALQEAGI ASDL AVAVTYGPGLVGALLVG+AAAKAFAWAN LPLIP+NHMAGHLM Sbjct: 61 CFEDALQEAGISASDLSAVAVTYGPGLVGALLVGLAAAKAFAWANHLPLIPVNHMAGHLM 120- Query: 121 AARDVKELQYPLLALLVSGGHTELVYVSEPGDYKIVGETRDDAVGEAYDKVGRVMGLTYP 18- 0 AAR+ K L YPL+ALLVSGGHTELVYV EPGDY I+GETRDDAVGEAYDKVGRVMGLTYP Sbjct: 121 AAREQKPLVYPLIALLVSGGHTELVYVPEPGDYHIIGETRDDAVGEAYDKVGRVMGLTYP 18- 0 Query: 181 AGREIDQLAHKGQDTYHFPRAMIKEDHLEFSFSGLKSAFINLHHNAEQKGEALVLEDLCA 24- 0 AGREIDQLAHKGQDTYHFPRAMI EDHLEFSFSGLKSAFINLHHNA+QKG+ L+LEDLCA Sbjct: 181 AGREIDQLAHKGQDTYHFPRAMITEDHLEFSFSGLKSAFINLHHNAKQKGDELILEDLCA 24- 0 Query: 241 SFQAAVLDILLAKTQKALLKYPVKTLVVAGGVAANQGLRERLATDISPDIDVVIPPLRLC 30- 0 SFQAAVLDILLAKT+KAL +YP K LVVAGGVAANQGLR+RLA +I+ I+VVIP LRLC Sbjct: 241 SFQAAVLDILLAKTKKALSRYPAKMLVVAGGVAANQGLRDRLAQEIT-HIEVVIPKLRLC 29- 9 Query: 301 GDNAGMIALAAAIEFEKENFASLKLNAKPSLAFE 334 GDNAGMIALAAAIE++K++FA++ LNAKPSLAF+ Sbjct: 300 GDNAGMIALAAAIEYDKQHFANMSLNAKPSLAFD 333 SEQ ID 4926 (GBS371) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 64 (lane 7; MW 41 kDa), in FIG. 170 (lane 4 & 5; MW 55 kDa) and in FIG. 239 (lane 6; MW 55 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 69 (lane 7; MW 65 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1594 A DNA sequence (GBSx1688) was identified in S. agalactiae <SEQ ID 4929> which encodes the amino acid sequence <SEQ ID 4930>. Analysis of this protein sequence reveals the following: TABLE-US-04820 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1027(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1595 A DNA sequence (GBSx1689) was identified in S. agalactiae <SEQ ID 4931> which encodes the amino acid sequence <SEQ ID 4932>. Analysis of this protein sequence reveals the following: TABLE-US-04821 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1307(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1596 A DNA sequence (GBSx1690) was identified in S. agalactiae <SEQ ID 4933> which encodes the amino acid sequence <SEQ ID 4934>. This protein is predicted to be L4171-60 protein. Analysis of this protein sequence reveals the following: TABLE-US-04822 Possible site: 36 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10135> which encodes amino acid sequence <SEQ ID 10136> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04823 >GP: AAC24656 GB: AE001274 L4171.5 [Leishmania major] Identities = 118/282 (41%), Positives = 167/282 (58%), Gaps = 4/282 (1%) Query: 2 GGTQTNQVVISSMLASYEGVIAAETGHVSSHEAGAIEFSGHKVLTLPSHNGKLLASEVAT 61 GGTQTN + S L +E VIA + GH+S+HE GAIE +GHKV+T P +GKL ++ Sbjct: 74 GGTQTNLIACSLALRPWEAVIATQLGHISTHETGAIEATGHKVVTAPCPDGKLRVAD--- 130- Query: 62 YIETFYADGNYQHMVFPGMVYISHPTEYGTLYSKAELEELSKICKHYQIPLFIDGARLGY 121- IE+ + +HMV P +VYIS+ TE GT Y+K ELE++S CK + + LF+DGARL Sbjct: 131 -IESALHENRSEHMVIPKLVYISNTTEVGTQYTKQELEDISASCKEHGLYLFLDGARLAS 18- 9 Query: 122 GLAAKDTDVDFPTIAALSDVFYIGGTKMGALAGEAVVFTKKNRPKQFTTIVKQHGALLAK 18- 1 L++ D+ IA L+D+FYIG TK G + GEA++ ++KQ GAL+AK Sbjct: 190 ALSSPVNDLTLADIARLTDMFYIGATKAGGMFGEALIILNDALKPNARHLIKQRGALMAK 24- 9 Query: 182 GRLLGLAFDRFFTDNLYLKIGRHAIDLAEELKIILEEKGYSFYLKSPTNQQFIIVENTKL 24- 1 G LLG+ F+ DNL+ ++G H+ +A LK LE G S +NQ F I+ENT + Sbjct: 250 GWLLGIQFEVLMKDNLFFELGAHSNKMAAILKAGLEACGIRLAWPSASNQLFPILENTMI 30- 9 Query: 242 ADLAKNVAYSFWEKYDDHHTVIRLATSWSTSREDVTALRNVL 283 A+L + E D ++RL TSW+T ++ VL Sbjct: 310 AELNNDFDMYTVEPLKDGTCIMRLCTSWATEEKECHRFVEVL 351 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 4934 (GBS648) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 131 (lane 8-10; MW 60 kDa) and in FIG. 186 (lane 6; MW 60 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 131 (lane 12; MW 35 kDa), in FIG. 140 (lane 10; MW 35 kDa) and in FIG. 178 (lane 7; MW 35 kDa). Purified GBS648-GST is shown in FIG. 243, lane 6; purified GBS648-His is shown in FIG. 229, lane 7. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1597 A DNA sequence (GBSx1691) was identified in S. agalactiae <SEQ ID 4935> which encodes the amino acid sequence <SEQ ID 4936>. Analysis of this protein sequence reveals the following: TABLE-US-04824 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2279(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1598 A DNA sequence (GBSx1692) was identified in S. agalactiae <SEQ ID 4937> which encodes the amino acid sequence <SEQ ID 4938>. This protein is predicted to be ribosomal protein S14 (rpsN). Analysis of this protein sequence reveals the following: TABLE-US-04825 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3848(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04826 >GP: CAB12716 GB: Z99108 similar to ribosomal protein S14 [Bacillus subtilis] Identities = 67/89 (75%), Positives = 76/89 (85%) Query: 1 MAKKSKIAKFQKQQKLVEQYAELRRELKEKGDYEALRKLPKDSNPNRLKNRDLIDGRPHA 60 MAKKSK+AK K+Q+LVEQYA +RRELKEKGDYEAL KLP+DS P RL NR ++ GRP A Sbjct: 1 MAKKSKVAKELKRQQLVEQYAGIRRELKEKGDYEALSKLPRDSAPGRLHNRCMVTGRPRA 60 Query: 61 YMRKFGMSRINFRNLAYKGQIPGIKKASW 89 YMRKF MSRI FR LA+KGQIPG+KKASW Sbjct: 61 YMRKFKMSRIAFRELAHKGQIPGVKKASW 89 A related DNA sequence was identified in S. pyogenes <SEQ ID 4939> which encodes the amino acid sequence <SEQ ID 4940>. Analysis of this protein sequence reveals the following: TABLE-US-04827 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3799(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04828 Identities = 73/89 (82%), Positives = 85/89 (95%) Query: 1 MAKKSKIAKFQKQQKLVEQYAELRRELKEKGDYEALRKLPKDSNPNRLKNRDLIDGRPHA 60 MAKKSKIAK+QKQ +L+EQYA+LRR+LK KGDYE+LRKLP+DSNPNRLKNRD IDGRPHA Sbjct: 1 MAKKSKIAKYQKQLQLIEQYADLRRDLKAKGDYESLRKLPRDSNPNRLKNRDKIDGRPHA 60 Query: 61 YMRKFGMSRINFRNLAYKGQIPGIKKASW 89 YMRKFG+SRINFR+LA+KGQ+PG+ KASW Sbjct: 61 YMRKFGVSRINFRDLAHKGQLPGVTKASW 89 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1599 A DNA sequence (GBSx1693) was identified in S. agalactiae <SEQ ID 4941> which encodes the amino acid sequence <SEQ ID 4942>. Analysis of this protein sequence reveals the following: TABLE-US-04829 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5183(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04830 >GP: CAB95931 GB: AL359989 galactose-1-phosphate uridylyltransferase [Streptomyces coelicolor A3(2)] Identities = 31/105 (29%), Positives = 51/105 (48%), Gaps = 4/105 (3%) Query: 27 DKCPFC--DKSQLGKILDVKDDMIWVENKYPTL--EETYQTLVIESNDHNGDISVYSESK 82 - D+CP C D +L +I D D++ EN++P+L + +V ++DH+ + SE + Sbjct: 68 DQCPLCPSDGERLSEIPDSAYDVVVFENRFPSLAGDSGRCEVVCFTSDHDASFADLSEEQ 127- Query: 83 MRQLLDYLLSKWQLMEESGHYRSVVLYRNFGPLSGGSLRHPHSQI 127 R+LD + + V + N G G +L HPH QI Sbjct: 128 ARLVLDAWTDRTSELSHLPSVEQVFCFENRGAEIGVTLGHPHGQI 172 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1600 A DNA sequence (GBSx1694) was identified in S. agalactiae <SEQ ID 4943> which encodes the amino acid sequence <SEQ ID 4944>. Analysis of this protein sequence reveals the following: TABLE-US-04831 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10133> which encodes amino acid sequence <SEQ ID 10134> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04832 >GP: BAB06998 GB: AP001518 unknown conserved protein [Bacillus halodurans] Identities = 186/410 (45%), Positives = 258/410 (62%), Gaps = 27/410 (6%) Query: 4 YDTIIIGGGPAGMMAAISSNFYGNKTLLIEKNKRLGKKLAGTGGGRCNVTNNGNLDELLA 63 ++ I+IGGGPAG+MA++S+ +G + LL++K +LG+KLA +GGGRCNVTN LDEL+A Sbjct: 2 HEVIVIGGGPAGLMASVSAAEHGARVLLLDKGDKLGRKLAISGGGRCNVTNBMPLDELIA 61 Query: 64 GIPGNGRFLYSVFSQFDNHDIINFFQDNGVTLKEEDHGRMFPTTDKSRTIINALENKIKE 123- IPGNGRF+YS FS F+N DII FF+ G+ LKEED GRMFP +DK+ T++ L +I + Sbjct: 62 HIPGNGRFMYSPFSVFNNEDIIRFFERLGIALKEEDRGRMFPVSDKATTVVQTLLKRIND 121- Query: 124 LGGQIMTDTEVVSVK-KIGDSFYIKTKDTQFASDK-LIVTTGGKSYPSTGSTGFGHDIAR 18- 1 LG + T+T V S++ G ++ K+ + K +IV TGG+S P TGSTG + A+ Sbjct: 122 LGVTVRTNTAVASLEYDDGRIAMVQLKNGERLKTKTVIVATGGQSVPHTGSTGDAYPWAK 18- 1 Query: 182 HFKLEVTDMEAAESPLLTDFP---HKKLQGISLDDVTLSF----EKHIITH--DLLFTHF 23- 2 +T++ E P+ + P KKLQG+SL D+ LS K I TH D++FTHF Sbjct: 182 AAGHTITELYPTEVPITSAEPFIQEKKLQGLSLRDIELSVYAPNGKQIKTHDGDMIFTHF 24- 1 Query: 233 GLSGPAALRISSFVKGGETIY--------LDVLPNISVKEL-EIHFQN---EREKSLKNA 28- 0 GLSGPAALR S +V Y +D+ P I + L + QN E +K+LK Sbjct: 242 GLSGPAALRCSQYVVKALKKYKQPTIEMRIDLRPTIPAEALFQETIQNIKAEPKKALKTV 30- 1 Query: 281 LKILLPERLAEFYAEDL--PEKVKQVSVKD--LEMLIQKLKKLPILVTGKMSLAKSFVTK 33- 6 L+ + PER ++ E L + SV+ + ++Q+LK V G +S+ K+FVT Sbjct: 302 LRGIAPERFLQYIYERLRIDSNLPCASVRHEVIREIVQQLKSFSFHVNGTLSIEKAFVTG 36- 1 Query: 337 GGVDLKEINPKTLESKKVAGLHFAGEVLDINAHTGGFNITSALCTGWVAG 386 GGV +KEI PKT+ SKK AGL F GEVLDI+ +TGG+NIT A TG+ AG Sbjct: 362 GGVSVKEIEPKTMHSKKKAGLFFCGEVLDIHGYTGGYNITCAFSTGYTAG 411 A related DNA sequence was identified in S. pyogenes <SEQ ID 4945> which encodes the amino acid sequence <SEQ ID 4946>. Analysis of this protein sequence reveals the following: TABLE-US-04833 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0448 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04834 Identities = 308/386 (79%), Positives = 344/386 (88%) Query: 1 NKHYDTIIIGGGPAGMMAAISSNFYGNKTLLIEKNKRLGKKLAGTGGGRCNVTNNGNLDE 60 M YDTIIIGGGPAGMMAAISS++YG KTLLIEKN+RLGKKLAGTGGGRCNVTN+GNLD Sbjct: 1 MTQYDTIIIGGGPAGMMAAISSSYYGYKTLLIEKNRRLGKKLAGTGGGRCNVTNSGNLDV 60 Query: 61 LLAGIPGNGRFLYSVFSQFDNHDIINFFQDNGVTLKEEDHGRMFPTTDKSRTIINALENK 120- L+AGIPGNGRFLYSVFSQFDNHDII FF++NGV LKEEDHGRMFPTTDKSRTII+ALE K Sbjct: 61 LMAGIPGNGRFLYSVFSQFDNHDIIAFFEENGVKLKEEDHGRMFPTTDKSRTIIDALEKK 120- Query: 121 IKELGGQIMTDTEVVSVKKIGDSFYIKTKDTQFASDKLIVTTGGKSYPSTGSTGFGHDIA 18- 0 IK LGGQ++T TEVVSVKK D FY+K+ D F KLIVTTGGKSYPSTGSTGFGHDIA Sbjct: 121 IKALGGQVLTSTEVVSVKKQDDLFYLKSADQTFTCQKLIVTTGGKSYPSTGSTGFGHDIA 18- 0 Query: 181 RHFKLEVTDMEAAESPLLTDFPHKKLQGISLDDVTLSFEKHIITHDLLFTHFGLSGPAAL 24- 0 RHFKL VTD+EAAESPLLTDFPHK LQGISLDDVTLS++KH+ITHDLLFTHFGLSGPAAL Sbjct: 181 RHFKLTVTDLEAAESPLLTDFPHKVLQGISLDDVTLSYDKHVITHDLLFTHFGLSGPAAL 24- 0 Query: 241 RISSFVKGGETIYLDVLPNISVKELEIHFQNEREKSLKNALKILLPERLAEFYAEDLPEK 30- 0 R+SSFVKGGE LD LP++S +L + ++R+K++KNALK LLPER+A+F +ED PEK Sbjct: 241 RLSSFVKGGEIAELDFLPHLSTDDLTAYLSDQRDKNIKNALKGLLPERVADFLSEDYPEK 30- 0 Query: 301 VKQVSVKDLEMLIQKLKKLPILVTGKMSLAKSFVTKGGVDLKEINPKTLESKKVAGLHFA 36- 0 VKQ+S K + L+ KLK L I +TGKMSLAKSFVTKGGVDLKEINPKTLESKKV GL+FA Sbjct: 301 VKQLSPKQEKELLDKLKHLQIPITGKMSLAKSFVTKGGVDLKEINPKTLESKKVPGLYFA 36- 0 Query: 361 GEVLDINAHTGGFNITSALCTGWVAG 386 GEVLDINAHTGGFNITSALC+GW+AG Sbjct: 361 GEVLDINAHTGGFNITSALCSGWIAG 386 SEQ ID 4944 (GBS196) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 26 (lane 3; MW 44.5 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 37 (lane 4; MW 69.5 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1601 A DNA sequence (GBSx1695) was identified in S. agalactiae <SEQ ID 4947> which encodes the amino acid sequence <SEQ ID 4948>. Analysis of this protein sequence reveals the following:

TABLE-US-04835 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1550 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10131> which encodes amino acid sequence <SEQ ID 10132> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04836 >GP: CAA73267 GB: Y12736 orfX [Lactococcus lactis subsp. cremoris] Identities = 51/173 (29%), Positives = 87/173 (49%), Gaps = 20/173 (11%) Query: 19 KTVSELAEILGVSRQAMNNRV-KTLPEECVEK---NSKGVTVVNRDGLIKLEEIYKKTIL 74 - KT+ ELA+ LGVS+Q + N++ K E+ V+ V+N G + KKT+ Sbjct: 6 KTIKELADELGVSKQTIRNKIDKDFREKFVQTIKIKGNNTLVINNAGY----SLLKKTLQ 61 Query: 75 EEEPIDEEASRRELLEILVDEKNTEITRLYEQLKAKDIQIASKDEQLHVKDIQIAEKDKQ 134- + + + + + + I L EQL K+ Q++ KD+QL KD QI++ Sbjct: 62 NDTAQTAKTLQNDTAQTKL------ICFLEEQLDKKEQQLSVKDKQLENKDTQISQMQNL 115- Query: 135 LDQQQQLTLTAMEDTQRLQLELNEAKA------EVEEIQEAKEEKIQELEAVK 181 LDQQQ+L L + + + E+NE KA ++++ + E +E+E +K Sbjct: 116 LDQQQRLALQDKKLLEEYKSEINELKALKMPREDMKDGSSIRGEAQEEIERLK 168 A related DNA sequence was identified in S. pyogenes <SEQ ID 4949> which encodes the amino acid sequence <SEQ ID 4950>. Analysis of this protein sequence reveals the following: TABLE-US-04837 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3951 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04838 Identities = 132/194 (68%), Positives = 154/194 (79%), Gaps = 4/194 (2%) Query: 1 MIFFYKKI---STKEEVMTVEKTVSELAEILGVSRQAMNNRVKTLPEECVEKNSKGVTVV 57 M+ F +I S KEE M +EKTVSELA+ILGVSRQA+NNRVK+LPEE ++KN KGVTVV Sbjct: 1 MVLFLIRIFSDSDKEENMGIEKTVSELADILGVSRQAVNNRVKSLPEEDLDKNEKGVTVV 60 Query: 58 NRDGLIKLEEIYKKTILEEEPIDEEASRRELLEILVDEKNTEITRLYEQLKAKDIQIASK 117- R GL+KLEEIYKKTI ++EPI EE +RELLEILVDEKNTEITRLYEQLKAKD Q+ASK Sbjct: 61 KRSGLVKLEEIYKKTIFDDEPISEETKQRELLEILVDEKNTEITRLYEQLKAKDAQLASK 120- Query: 118 DEQLHVKDIQIAEKDKQLDQQQQLTLTAMEDTQRLQLELNEAKAEVEEIQEAKEEKIQEL 17- 7 DEQ+ VKD+QIAEKDKQLDQQQQLT AM D + L+LEL EAKAE + + + E++Q Sbjct: 121 DEQMRVKDVQIAEKDKQLDQQQQLTAKAMADKETLKLELEEAKAEANQAR-LQVEEVQAE 17- 9 Query: 178 EAVKKSFFGRFFNK 191 KK FF R F K Sbjct: 180 VGPKKGFFTRLFAK 193 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1602 A DNA sequence (GBSx1697) was identified in S. agalactiae <SEQ ID 4951> which encodes the amino acid sequence <SEQ ID 4952>. Analysis of this protein sequence reveals the following: TABLE-US-04839 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2157 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04840 >GP: BAB06137 GB: AP001515 DNA polymerase III (alpha subunit) [Bacillus halodurans] Identities = 31/87 (35%), Positives = 52/87 (59%), Gaps = 1/87 (1%) Query: 13 EYIAFDLEFNTVGE-HSNIIQVSAVKYSNHQEIALFDTYVHTKVPLQSFINGLTGITARD 71 - E++ FD+E + ++ II+++AVK N + I F+ + PL + I LTGIT Sbjct: 418 EFVVFDVETTGLSAVYNKIIELAAVKVKNGEIIDREERFADPHEPLTNTIIELTGITDDM 47- 7 Query: 72 IIGAPKIEIVLTDFQSFVGDTPLIGYN 98 + G P++E VL +F +F+GD L+ +N Sbjct: 478 LKGQPEVEQVLNEFHAFIGDAVLVAHN 504 A related DNA sequence was identified in S. pyogenes <SEQ ID 4953> which encodes the amino acid sequence <SEQ ID 4954>. Analysis of this protein sequence reveals the following: TABLE-US-04841 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3427 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04842 Identities = 136/200 (68%), Positives = 159/200 (79%) Query: 3 FLGEIMKQLQEYIAFDLEFNTVGEHSHIIQVSAVKYSNHQEIALFDTYVHTKVPLQSFIN 62 FL E MK L YIAFDLEFNTV + SHIIQVSAVKY +H+E+ FDTYV+T VPLQSFIN Sbjct: 9 FLEENMKHLDTYIAFDLEFNTVNDVSHIIQVSAVKYDHHKEVDSFDTYVYTDVPLQSFIN 68 Query: 63 GLTGITARDIIGAPKIEIVLTDFQSFVGDTPLIGYNGYKSDLPLLVENGLDLTSQYQVDL 122- GLTGIT+ I PK+E V+ F++FVG+ PLIGYN KSDLP+L ENGLDL QYQ+DL Sbjct: 69 GLTGITSDKIAAEPRVEEVMAAFKNFVGELPLIGYNAQKSDLPILAENGLDLRDQYQIDL 128- Query: 123 YDEAFVRRSTDLNGIVNLKLTTVADFLGIKGKAHNSLEDARMTARVYEKFLDLDENKIYL 18- 2 +DEA+ RRS DLNGI NL+L TVA FLGIKG+ HNSLEDARMTA +Y+ FL+ D NK YL Sbjct: 129 FDEAYDRRSADLNGIANLRLQTVATFLGIKGRGHNSLEDARMTAVIYKSFLETDTNKAYL 18- 8 Query: 183 KQQKEVAVDSPFATLGNLFD 202 QQ+EV D+PFA LG+ FD Sbjct: 189 SQQEEVTTDNPFAALGDFFD 208 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1603 A DNA sequence (GBSx1698) was identified in S. agalactiae <SEQ ID 4955> which encodes the amino acid sequence <SEQ ID 4956>. Analysis of this protein sequence reveals the following: TABLE-US-04843 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.10 Transmembrane 143-159 (136-166) INTEGRAL Likelihood = -4.73 Transmembrane 169-185 (168-188) ----- Final Results ----- bacterial membrane --- Certainty = 0.5840 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04844 >GP: CAB42766 GB: AL049841 transcriptional regulator [Streptomyces coelicolor A3(2)] Identities = 46/141 (32%), Positives = 71/141 (49%), Gaps = 11/141 (7%) Query: 5 YSTGDLAKEAGVTVRTVQYYDKRGILSPSELSEGGRRVYSIADLEKLRQIIYLRDLDFSI 64 YS G +A AGVTVRT+ +YD G+L PSE S G R YS ADL++L+QI++ R+L F + Sbjct: 3 YSVGQVAGFAGVTVRTLHHYDDIGLLVPSERSHAGHRRYSDADLDRLQQILFYRELGFPL 62 Query: 65 DNIKNLFTEDNASQILELFLQVQIRELRL--------AIDSKKDKLDKAVNLLKTVEKQD 116- D + L + A L Q ++ R+ A++ + +NL ++ Sbjct: 63 DEVAALLDDPAADPRAHLRRQHELLSARIGKLQKMAAAVEQAMEARSMGINL---TPEEK 119- Query: 117 SKTLGYLSDIVLMEENKRKWG 137 + G EE + +WG Sbjct: 120 FEVFGDFDPDQYEEEVRERWG 140 There is also homology to SEQ ID 1712. SEQ ID 4956 (GBS372) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 69 (lane 8; MW 55 kDa). GBS372-GST was purified as shown in FIG. 215, lane 8. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1604 A DNA sequence (GBSx1699) was identified in S. agalactiae <SEQ ID 4957> which encodes the amino acid sequence <SEQ ID 4958>. This protein is predicted to be cyclopropane-fatty-acyl-phospholipid synthase (mma2). Analysis of this protein sequence reveals the following: TABLE-US-04845 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3145 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04846 >GP: AAD07482 GB: AE000557 cyclopropane fatty acid synthase (cfa) [Helicobacter pylori 26695] Identities = 167/397 (42%), Positives = 254/397 (63%), Gaps = 14/397 (3%) Query: 2 VMDSLIIKQLIKSTFDIPLQVTYPNGNIETYNGSNPHVKLKLNKNFSVSELSKDPSIVLG 61 ++ ++K + K + QV + + ++ +P LK+++ S++ KD S+ + Sbjct: 1 MISKFLLKSMFKQWKNGDYQVVFWDNSVYRNGEHSPKFTLKIHRPLKFSDIKKDMSLTIA 60 Query: 62 EAVMDGDIEIYGSIQELILSAY-RCGDSFLRNSKFSKLIPKQFHDKKHSKSDIQKHYDIG 120- EA MDG I+I GS+ E++ S Y + L +K I K + S+I KHYD+G Sbjct: 61 EAYMDGVIDIEGSMDEVMHSLYLQTNYEHLHKHDNAKAIQKPIKES----SNISKHYDLG 116- Query: 121 NDFYKLWLDDTMTYSCAYFKHENDSLEQAQLNKVHHILNKLNAQPGGKLLDIGCGWGTLI 18- 0 NDFY +WLD+T++YSCAYFK ++D+L AQL K+ H L KL+ +PG KLLDIGCGWG L Sbjct: 117 NDFYSIWLDETLSYSCAYFKKDDDTLHAAQLQKLDHTLKKLHLKPGEKLLDIGCGWGYLS 17- 6 Query: 181 ITAAKEYGLNATGITLSEEQASFITKRIKEEGLENKVTVLIKDYRDI---RETYDYITSV 23- 7 + AA+EYG GIT+S EQ KR++E GLE+KVT+ + +Y+D+ +D + SV Sbjct: 177 VKAAQEYGAEVMGITISSEQYKQANKRVQELGLEDKVTIKLLNYQDLDGRLYRFDKVVSV 23- 6 Query: 238 GMFEHVGKENLSQYFQTISKRLNINGLALIHGITGQVGGNHGSGTNSWINKYIFPGGYIP 29- 7 GMFEHVGK+NL YF+ + + L G+ L+H I G TN+W++KYIFPGGY+P Sbjct: 237 GMFEHVGKDNLPFYFKKVKEVLKRGGMFLLHSILCCFEGK----TNAWVDKYIFPGGYLP 29- 2 Query: 298 RLTENLNHIASAGLQIADLEPLRRHYQKTLELWTKNFHNALPEVQK-THDKRFINMWDLY 35- 6 L E ++ ++ + E LR HY KTL++W NF++ L +V++ ++D+RFI MWDLY Sbjct: 293 SLREVMSVMSECDFHLLMAESLRIHYAKTLDIWRNNFNHNLDQVKRLSYDERFIRMWDLY 35- 2 Query: 357 LQSCAASFESGNIDIFQYLLSKGVSKDTMPMTRDYMY 393 L++CA++F G+ D+FQ LL+ V +T P+T++Y+Y Sbjct: 353 LRTCASAFRVGSADLFQLLLTNSVD-NTFPLTKEYIY 388 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1605 A DNA sequence (GBSx1700) was identified in S. agalactiae <SEQ ID 4959> which encodes the amino acid sequence <SEQ ID 4960>. Analysis of this protein sequence reveals the following: TABLE-US-04847 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4903 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04848 >GP: CAB11796 GB: Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 44/97 (45%), Positives = 60/97 (61%) Query: 1 MMNMQNMMRQAQKLQKQMEQKQADLAASQFTGKSAQELVTVTFTGDKKLISIDYKEAVVD 60 M NMQ MM+Q QK+QK M + Q +LA G + +VTV G K+++ + KE VVD Sbjct: 5 MGNMQKMMKQMQKMQKDMAKAQEELAEKVVEGTAGGGMVTVKANGQKEILDVIIKEEVVD 64 Query: 61 PEDIETLQDMTTQAINDALSQVDDATKKIMGAFAGKM 97 PEDI+ LQD+ A N+AL +VD+ T + MG F M Sbjct: 65 PEDIDMLQDLVLAATNEALKKVDEITNETMGQFTKGM 101 A related DNA sequence was identified in S. pyogenes <SEQ ID 4961> which encodes the amino acid sequence <SEQ ID 4962>. Analysis of this protein sequence reveals the following: TABLE-US-04849 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4451 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04850 Identities = 84/99 (84%), Positives = 94/99 (94%) Query: 1 MMNMQNMMRQAQKLQKQMEQKQADLAASQFTGKSAQELVTVTFTGDKKLISIDYKEAVVD 60 MMNMQNMM+QAQKLQKQMEQKQADLAA QFTGKSAQ+LVT TFTGDKKL+ ID+KEAVVD Sbjct: 1 MMNMQNMMKQAQKLQKQMEQKQADLAAMQFTGKSAQDLVTATFTGDKKLVGIDFKEAVVD 60 Query: 61 PEDIETLQDMTTQAINDALSQVDDATKKIMGAFAGKMPF 99 PED+ETLQDMTTQAINDAL+Q+D+ TKK +GAFAGK+PF Sbjct: 61 PEDVETLQDMTTQAINDALTQIDETTKKTLGAFAGKLPF 99 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1606 A DNA sequence (GBSx1701) was identified in S. agalactiae <SEQ ID 4963> which encodes the amino acid sequence <SEQ ID 4964>. Analysis of this protein sequence reveals the following: TABLE-US-04851 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3963 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1607 A DNA sequence (GBSx1702) was identified in S. agalactiae <SEQ ID 4965> which encodes the amino acid sequence <SEQ ID 4966>. Analysis of this protein sequence reveals the following: TABLE-US-04852 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.76 Transmembrane 21-37 (19-39) ----- Final Results ----- bacterial membrane --- Certainty = 0.2105 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10129> which encodes amino acid sequence <SEQ ID 10130> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1608 A DNA sequence (GBSx1703) was identified in S. agalactiae <SEQ ID 4967> which encodes the amino acid sequence <SEQ ID 4968>. Analysis of this protein sequence reveals the following: TABLE-US-04853 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1783 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1609 A DNA sequence (GBSx1704) was identified in S. agalactiae <SEQ ID 4969> which encodes the amino acid sequence <SEQ ID 4970>. This protein is predicted to be probable 1,4-dihydroxy-2-naphthoate octaprenyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-04854 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.76 Transmembrane 239-255 (219-260) INTEGRAL Likelihood = -8.33 Transmembrane 221-237 (219-238) INTEGRAL Likelihood = -6.74 Transmembrane 91-107 (89-113) INTEGRAL Likelihood = -6.32 Transmembrane 39-55 (35-59) INTEGRAL Likelihood = -3.77 Transmembrane 111-127 (111-132) INTEGRAL Likelihood = -2.97 Transmembrane 144-160 (143-161) INTEGRAL Likelihood = -1.28 Transmembrane 275-291 (275-291) INTEGRAL Likelihood = -0.59 Transmembrane 177-193 (177-193) ----- Final Results ----- bacterial membrane --- Certainty = 0.4503 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-04855 >GP: CAB15875 GB: Z99123 alternate gene name: ipa-6d~similar to quinone biosynthesis [Bacillus subtilis] Identities = 75/290 (25%), Positives = 139/290 (47%), Gaps = 15/290 (5%) Query: 5 IFLELVEMKAKTASVLPFLIGLCFSAYYYNSVHPVYVGLFFVAMFLFNMFVDIWNNYNDY 64 I +L TAS +P L+G + +Y +++ + F +++ + +++N Y D+ Sbjct: 21 ILWQLTRPHTLTASFVPVLLGTVLAMFYVKVDLLLFLAMLFSCLWI-QIATNLFNEYYDF 79 Query: 65 RNAVDL-DYKNDTNIIGRENLSLRQIEVIMASLVITSSMIGLVLVSQVGLPLLWMGLFCF 123- + +D + I R + + I + + + ++G+ + + L +GL Sbjct: 80 KRGLDTAESVGIGGAIVRHGMKPKTILQLALASYGIAILLGVYICASSSWWLALIGLVGM 139- Query: 124 GIGVLYSFGPRPLSSLPLGEVFSGLTMGFMISLICVYLNTYQNFSWDILNLSKIFLISLP 18- 3 IG LY+ GP P++ P GE+FSG+ MG + LI ++ T D +N+ I LIS+P Sbjct: 140 AIGYLYTGGPLPIAYTPFGELFSGICMGSVFVLISFFIQT------DKINMQSI-LISIP 19- 2 Query: 184 NTLWIANLMLANNLCDKEEDEKNHRYTLVHYTGIRGGLLLFAISNSIALLAIVFEFLFGL 24- 3 + + + L+NN+ D EED+K R TL G +G + L A S ++A + +V + G Sbjct: 193 IAILVGAINLSNNIRDIEEDKKGGRKTLAILMGHKGAVTLLAASFAVAYIWVVGLVITGA 25- 2 Query: 244 APVTVLLSLLLIPFIYKQTKLLWQKQVKRETFVCAVRILALGSATQVLTY 293 A + + L +P + K Q ++ I+A+ S Q T+ Sbjct: 253 ASPWLFVVFLSVPKPVQAVKGFVQNEMPMN------MIVAMKSTAQTNTF 296 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1610 A DNA sequence (GBSx1705) was identified in S. agalactiae <SEQ ID 4971> which encodes the amino acid sequence <SEQ ID 4972>. Analysis of this protein sequence reveals the following: TABLE-US-04856 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.22 Transmembrane 155-171 (154-171) ----- Final Results ----- bacterial membrane --- Certainty = 0.1086(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04857 >GP: CAB15200 GB: Z99120 similar to NADH dehydrogenase [Bacillus subtilis] Identities = 178/403 (44%), Positives = 249/403 (61%), Gaps = 7/403 (1%) Query: 3 EILVLGAGYAGLKAVRNLQKQSG--DFHITLVDMNDYHYEATELHEVAAGSQPKEKITFP 60 +I++LGAGY GL V L K G D ITLV+ ++YHYE T +HE +AG+ ++ + Sbjct: 7 KIVILGAGYGGLMTVTRLTKYVGPNDADITLVNKHNYHYETTWMHEASAGTLHHDRCRYQ 66 Query: 61 IKDVINTNKVNFMQDEVLRVDAENKTVTVKNNGELHYDYVVVALGFVSETFGIKGAMENA 120- IKDVIN ++VNF+QD V + + K V + N GEL YDY+V+ LG V ETFGIKG E A Sbjct: 67 IKDVINQSRVNFVQDTVKAIKIDEKKVVLAN-GELQYDYLVIGLGAVPETFGIKGLKEYA 125- Query: 121 LQMTNISQAENIHNHIVNTMKLYRETKDE--NLLKLLVCGAGFTGIELAGAMVDERPKYA 17- 8 + NI+ + + HI Y ++ + L ++V GAGFTGIE G + P+ Sbjct: 126 FPIANINTSRLLREHIELQFATYNTEAEKRPDRLTIVVGGAGFTGIEFLGELAARVPELC 18- 5 Query: 179 ALAGVKPEQIEIICVEAATRILPMFDDELAQYGVNLIKDLGINLMLGSMIKEIKPGEVVY 23- 8 V + IICVEAA +LP FD EL Y V+ +++ G+ +G+ ++E P V Sbjct: 186 KEYDVDRSLVRIICVEAAPTVLPGFDPELVDYAVHYLEENGVEFKIGTAVQECTPEGVRV 24- 5 Query: 239 GTSKEDEELKSITAGTIIWTTGVSGSPVMGESGFDQRRGRVMVNSDLRDPKYDNVYVIGD 29- 8 G K+DEE + I + T++W GV G P++ E+GF+ RGRV VN DLR P +DNV+++GD Sbjct: 246 G--KKDEEPEQIKSQTVVWAAGVRGHPIVEEAGFENMRGRVKVNPDLRAPGHDNVFILGD 30- 3 Query: 299 VSAFMDTESGRPFPTTAQIATRMGAHVAKNLLHQIKGEATEDFSYSPQGTVASVGNTHGL 35- 8 S FM+ ++ RP+P TAQIA + G VAKNL IKG E+F +GTVAS+G + + Sbjct: 304 SSLFMNEDTERPYPPTAQIAMQQGITVAKNLGRLIKGGELEEFKPDIKGTVASLGEHNAV 36- 3 Query: 359 GVVGKTKIKKYPASVMKKIIMNKSLVDMGGLKELLAKGRFDLY 401 GVV K+K PAS MKK+I N+SL +GGL L KG+F + Sbjct: 364 GVVYGRKLKGTPASFMKKVIDNRSLFMIGGLGLTLKKGKFKFF 406 There is also homology to SEQ ID 4666. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1611 A DNA sequence (GBSx1706) was identified in S. agalactiae <SEQ ID 4973> which encodes the amino acid sequence <SEQ ID 4974>. This protein is predicted to be cytochrome d ubiquinol oxidase, subunit I (cydA-1). Analysis of this protein sequence reveals the following: TABLE-US-04858 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.64 Transmembrane 19-35 (15-38) INTEGRAL Likelihood = -5.73 Transmembrane 226-242 (222-244) INTEGRAL Likelihood = -4.94 Transmembrane 130-146 (126-149) INTEGRAL Likelihood = -4.83 Transmembrane 429-445 (422-446) INTEGRAL Likelihood = -3.77 Transmembrane 55-71 (53-74) INTEGRAL Likelihood = -3.56 Transmembrane 342-358 (340-359) INTEGRAL Likelihood = -1.06 Transmembrane 89-105 (89-106) INTEGRAL Likelihood = -0.59 Transmembrane 186-202 (186-202) ----- Final Results ----- bacterial membrane --- Certainty = 0.3654(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04859 >GP: CAB15902 GB: Z99123 cytochrome bd ubiquinol oxidase (subunit I) [Bacillus subtilis] Identities = 246/470 (52%), Positives = 319/470 (67%), Gaps = 12/470 (2%) Query: 6 LARFQFAMTTVFHFFFVPFTIGTCLVVAIMETMYVITKNEEYKKLTKFWGNIMLLSFAVG 65 LAR QFA TT+FHF FVP +IG +VA+MET+Y++ KNE Y K+ KFWG++ L++FAVG Sbjct: 6 LARIQFASTTLFHFLFVPMSIGLVFMVALMETLYLVKKNELYLKMAKFWGHLFLINFAVG 65 Query: 66 VVTGIIQEFQFGMNWSDYSRFVGDIFGAPLAIEALLAFFMESTFLGLWMFTWDNKKISKK 125- VVTGI+QEFQFG+NWSDYSRFVGD+FGAPLAIEALLAFFMES F+GLW+F WD ++ KK Sbjct: 66 VVTGILQEFQFGLNWSDYSRFVGDVFGAPLAIEALLAFFMESIFIGLWIFGWD--RLPKK 123- Query: 126 LHVTFIWLVVFGSLMSAMWILTANSFMQHPVGYEVVNGRAQMTDFLALVKNPQFFYEFTH 18- 5 +H IWLV FG++MS+ WILTANSFMQ PVG+ + NGRA+M DF AL+ NPQ + EF H Sbjct: 124 IHALCIWLVSFGTIMSSFWILTANSFMQEPVGFTIKNGRAEMNDFGALITNPQLWVEFPH 18- 3 Query: 186 VIFGAITMGGTVVAGMSAFRLLKSEQLKDTTVELYKKSVRIGLVVALLGSISVMGVGDLQ 24- 5 VIFGA+ G +AG+SAF+LLK ++ V +K+S ++ ++V L + V G +Q Sbjct: 184 VIFGALATGAFFIAGVSAFKLLKKKE-----VPFFKQSFKLAMIVGLCAGLGVGLSGHMQ 23- 8 Query: 246 MKALIHDQPMKFAAMEGDYEDSGDPAAWSVVAWANEAEHKQVFGIKIPYMLSILSYGKPS 30- 5 + L+ QPMK AA EG +EDSGDPAAW+ A + K IK+PY LS L+Y K S Sbjct: 239 AEHLMESQPMKMAASEGLWEDSGDPAAWTAPATIDTKNEKSSNEIKVPYALSYLAYQKFS 29- 8 Query: 306 GSVKGMDTANKELVAKYGKDNYYPMVNLLFYGFRTMAAMGTAINGVSVLGLFLTRKKKPI 36- 5 GSVKGM T E YGK +Y P V F+ FR M G ++ ++ GL+L R+KK Sbjct: 299 GSVKGMKTLQAEYEKIYGKGDYIPPVKTTFWSFRIMVGAGVVMILAALGGLWLNRRKK-- 35- 6 Query: 366 LYKHKWMLWIVALTTFAPFLANTFGWIVTEQGRYPWTVYGLFKIKDSVSPNVSVASLFVS 42- 5 L KW L I+ PFLAN+ GWI+TE GR PWTV GL SVSPNV+ SL S Sbjct: 357 LENSKWYLRIMIALISFPFLANSAGWIMTEIGRQPWTVMGLMTTAQSVSPNVTAGSLLFS 41- 6 Query: 426 NTVYFLLFGGLAVMMISLTIRELKKGPEYEDEHGHHGAYTSIDPFEEGAY 475 + +++ L +++ L IRE+KKG E+++ HH S DPF + Y Sbjct: 417 IIAFGVMYMILGALLVFLFIREIKKGAEHDN---HHDVPVSTDPFSQEVY 463 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1612 A DNA sequence (GBSx1707) was identified in S. agalactiae <SEQ ID 4975> which encodes the amino acid sequence <SEQ ID 4976>. This protein is predicted to be cytochrome oxidase subunit 11 (cydB-1). Analysis of this protein sequence reveals the following: TABLE-US-04860 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.49 Transmembrane 226-242 (220-250) INTEGRAL Likelihood = -8.12 Transmembrane 254-270 (250-282) INTEGRAL Likelihood = -7.64 Transmembrane 198-214 (196-218) INTEGRAL Likelihood = -6.95 Transmembrane 85-101 (76-103) INTEGRAL Likelihood = -6.74 Transmembrane 6-22 (1-27) INTEGRAL Likelihood = -6.16 Transmembrane 300-316 (298-322) INTEGRAL Likelihood = -5.36 Transmembrane 119-135 (117-143) INTEGRAL Likelihood = -4.04 Transmembrane 159-175 (155-178) ----- Final Results ----- bacterial membrane --- Certainty = 0.6795(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04861 >GP: CAB15901 GB: Z99123 cytochrome bd ubiquinol oxidase (subunit II) [Bacillus subtilis] Identities = 158/331 (47%), Positives = 223/331 (66%), Gaps = 1/331 (0%) Query: 1 MSALQFFWFFLIGLLFSGFFFLEGFDFGVGMAVQTLTHNEHEKDQVVETIGPVWDGNEVW 60 M++L WF L+ +LF GFFFLEGFDFGVGMA + L HNE E+ ++ TIGP WD NEVW Sbjct: 1 MASLHDLWFILVAVLFVGFFFLEGFDFGVGMATRFLGHNELERRVLINTIGPFWDANEVW 60 Query: 61 LLTGGGAMFASFPYWYASLFSGYYLILLTILFGLIIRGVSFEFRHKVPAEK-KQFWNWTL 119- LLTG GA+FA+FP WYA++ SGYY+ + +L L+ RGV+FEFR KV K + W+W + Sbjct: 61 LLTGAGAIFAAFPNWYATMLSGYYIPFVIVLLALMGRGVAFEFRGKVDHLKWVKVWDWVV 120- Query: 120 TIGSAIVPFFFGIMFISLIQGMPLDASGNLSAQFSDYFNIFSLVGGVAMVLLAYLHGLNY 17- 9 GS I PF G++F +L +GMP+DA N+ A SDY N++S++GGV + LL + HGL + Sbjct: 121 FFGSLIPPFVLGVLFTTLFRGMPIDADMNIHAHVSDYINVYSILGGVTVTLLCFQHGLMF 18- 0 Query: 180 IALKTEGPIRERARNYAQLLYWVLYLGLALFAVLLYFKTDFFSNHPIVTTIMVLVIVVLA 23- 9 I L+T G ++ RAR AQ + V+++ + FA L ++TD F+ +T + ++IV+ Sbjct: 181 ITLRTIGDLQNRARKMAQKIMGVVFVAVLAFAALSAYQTDMFTRRGEITIPLAVLIVICF 24- 0 Query: 240 VLAHASTFKGAEMTAFLASGLSLVSVVVLLFQGLFPRVMISSISPKYDLLIQNASSTPYT 29- 9 +LA K + F +G L V ++F LFPRVM+SS+ YDL + NASS Y+ Sbjct: 241 MLAAVFIRKKKDGWTFGMTGAGLALTVGMIFISLFPRVMVSSLHSAYDLTVANASSGDYS 30- 0 Query: 300 LKVMSIVAITLVPFVLAYTAWAYYIFRKRIT 330 LKVMSI A+TL+PFV+ W+YY+FRKR++ Sbjct: 301 LKVMSIAALTLLPFVIGSQIWSYYVFRXRVS 331 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1613 A DNA sequence (GBSx1708) was identified in S. agalactiae <SEQ ID 4977> which encodes the amino acid sequence <SEQ ID 4978>. Analysis of this protein sequence reveals the following: TABLE-US-04862 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1614 A DNA sequence (GBSx1709) was identified in S. agalactiae <SEQ ID 4979> which encodes the amino acid sequence <SEQ ID 4980>. This protein is predicted to be transport ATP-binding protein cydc (cydD). Analysis of this protein sequence reveals the following: TABLE-US-04863 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -16.82 Transmembrane 158-174 (144-182) INTEGRAL Likelihood = -6.48 Transmembrane 15-31 (14-34) INTEGRAL Likelihood = -5.31 Transmembrane 243-259 (238-266) INTEGRAL Likelihood = -2.55 Transmembrane 136-152 (134-152) INTEGRAL Likelihood = -0.48 Transmembrane 263-279 (263-279) ----- Final Results ----- bacterial membrane --- Certainty = 0.7729(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04864 >GP: CAB15900 GB: Z99123 ABC membrane transporter (ATP-binding protein) [Bacillus subtilis] Identities = 279/569 (49%), Positives = 401/569 (70%), Gaps = 6/569 (1%) Query: 2 LDKAVMRLSGIHKLLGLLAGLDVLQAIFIIGQAYYLSLSITGLWEGQKLSSQTVYILLFM 61 + K + R G+ ++L L+ L ++Q II QA +LS ++TGL+ G+ ++S I F+ Sbjct: 1 MGKDLFRYKGMKRILTLITCLTLIQTAAIIMQAEWLSEAVTGLFNGRGITSLLPVIGFFL 60 Query: 62 VSYLGRHVIDYIKNRKLDDFSTAQSSLLRRQLLDKLFDLGPKVVQEQGTGNVVTMALDGV 121- ++++ RH + + + + ++ + LR+ LD+LF LGP+ +++GTG +VT+A++G+ Sbjct: 61 IAFIARHGMTVARQKIVYQYAARTGADLRKSFLDQLFRLGPRFAKKEGTGQMVTLAMEGI 120- Query: 122 SLVENYLRLVLNKMINMSIIPWIILAYIFYLDIESGAILLIVFPLIIIFMIILGYAAQAK 18- 1 S YL L L KM++M+I+P ++ Y+F+ D S IL+ P++IIFMI+LG AQ K Sbjct: 121 SQFRRYLELFLPKMVSMAIVPAAVVIYVFFQDRTSAIILVAAMPILIIFMILLGLVAQRK 18- 0 Query: 182 ADKQYESYQVLSNHFLDSLRGIDTLKYFGLSKRYGKSIYQTSESFRKATMSTLKIGILST 24- 1 AD+Q++SYQ LSNHF+DSLRG++TL++ GLSK + K+I+ SE +RKATMSTL++ LS+ Sbjct: 181 ADRQWKSYQRLSNHFVDSLRGLETLRFLGLSKSHSKNIFYVSERYRKATMSTLRVAFLSS 24- 0 Query: 242 FALDEFTTLSIAIVAVFLGLRLLNEQIYLLPALTILILSPEYFLPVRDFSSDYHATLDGK 30- 1 FALDFFT LS+A VAVFLGLRL++ I L PALT LIL+PEYFLPVR+ +DYHATL+G+ Sbjct: 241 FALDFFTMLSVATVAVFLGLRLIDGDILLGPALTALILAPEYFLPVREVGNDYHATLNGQ 30- 0 Query: 302 NAFQAIQKVLHKTGIKGE-QLVIDDWSKESRLDLENIAIAYDQKRVVEDVTLRFRGHQKV 36- 0 A + IQ++L++ G K E L ++ WS + L L +++ R V D+ L F+G +K+ Sbjct: 301 EAGRTIQEILSQPGFKEETPLQLEAWSDQDELKLSGVSVG----RSVSDIHLSFKGKKKI 35- 6 Query: 361 ALVGVSGSGKSSLINLLSGFLGPDNGSLKVDGREVTNLDQEDWHKQMIYIPQTPYVFEMS 42- 0 ++G SG+GKS+LI++L GFL PD G ++V+G ++L W K ++YIPQ PY+F+ + Sbjct: 357 GIIGASGAGKSTLIDILGGFLEPDGGMIEVNGTSRSHLQDGSWQKNLLYIPQHPYIFDDT 41- 6 Query: 421 LRDNITFYTPNASDEEVVRAIHMVGLDSLLSELPDGLETRIGNGARPLSGGQAQRIALAR 48- 0 L +NI FY P+AS E+ RA GL L++ LPDGLE RIG G R LSGGQAQR+ALAR Sbjct: 417 LGNNIRFYHPSASAEDTTRAAASAGLTELVNNLPDGLEGRIGEGGRALSGGQAQRVALAR 47- 6 Query: 481 AFLDQNRRIMVFDEPTAHLDIETELELKEKMLPLMSDRLVIFATHRLHWLNQMDVIVVME 54- 0 AFL NR I++ DEPTAHLDIETE E+KE ML L D+LV ATHRLHW+ MD I+V++ Sbjct: 477 AFLG-NRPILLLDEPTAHLDIETEYEIKETMLDLFEDKLVFLATHRLHWMLDMDEIIVLD 53- 5 Query: 541 KGRVAEVGSYQELLAKKGYLYQLKHAMGG 569 GRVAE+G++ ELL K G +L A G Sbjct: 536 GGRVAEIGTHNELLEKNGVYTKLVKAQLG 564 A related DNA sequence was identified in S. pyogenes <SEQ ID 4981> which encodes the amino acid sequence <SEQ ID 4982>. Analysis of this protein sequence reveals the following: TABLE-US-04865 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.61 Transmembrane 159-175 (154-190) INTEGRAL Likelihood = -10.03 Transmembrane 70-86 (63-91) INTEGRAL Likelihood = -3.03 Transmembrane 282-298 (282-301) INTEGRAL Likelihood = -1.44 Transmembrane 261-277 (260-278) ----- Final Results ----- bacterial membrane --- Certainty = 0.5246 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04866 >GP: AAC22320 GB: U32749 ATP-binding transport protein (cydD) [Haemophilus influenzae Rd] Identities = 167/544 (30%), Positives = 279/544 (50%), Gaps 15/544 (2%) Query: 46 MISFYLIAKTFSTFILGHAIALGRLAGLLLLLNVVGFVLAILGK---QLQGIASQFARDS 102- + S+ L A F L A+ LG + L L A GK Q AS + Sbjct: 17 VFSYILQAAYFHELSLLSAVILGIVLIAALALR------AFAGKKSVQASYFASTKVKHE 70 Query: 103 LKQSFFEAFIDLDGQFDAHASDADILTLASQGIDSLDTYYGYYL-SLSMRTKWNCTTIMI 16- 1 L+ + + S + I+ +AS+G++ L+ Y+G YL L T Sbjct: 71 LRSLIYRKLASMPLNQVNQQSTSSIIQVASEGVEQLEIYFGRYLPQLFYSLLAPLTLFAF 130- Query: 162 LVFLIYPLAGLVFLGVLPLIPLSIVAMQKRSQPNMSHYWSSYMDVGNLFMDDLKGLNTLY 22- 1 L+F + A ++ L +PLIP+SI+A+ K ++ ++ YWS Y+ +G+ F+D+L+GL TL Sbjct: 131 LIFFSFKTA-IILLICVPLIPMSIIAVNKIAKKLLAKYWSIYVGLGSSFLDNLQGLITLK 18- 9 Query: 222 SYQATERYEQEFSGKAEQFRKATMSLLGFQLQAVGYMDAVMYLGIGLSGFLAVQALATGQ 28- 1 YQ + +AE FRK TM +L QL +V MD + Y G + A+ Q Sbjct: 190 IYQDDAYKAKAMDKEAEHFRKITMKVLTMQLNSVSLMDLLAYGGAAIGILTALLQFQNAQ 24- 9 Query: 282 LSFFNFLFFLLIATEFFTPIREQGYGMHLVMMNTKMADRIFSFLDS-VPARKDNKSKTAI 34- 0 LS + F+L+++EFF P+R G H+ M +D+IF+ LD+ V ++ A Sbjct: 250 LSVLGVILFILLSSEFFIPLRLLGSFFHVAMNGKAASDKIFTLLDTPVETQQSAVDFEAK 30- 9 Query: 341 NFNQIDIQNISLAY-EKKTVLSGVTMTLTKGQLTAIAGVSGQGKTSLAQLLLKRQSATTG 39- 9 N Q++I+++ +Y E+K ++G+ +++ QL+ G SG GK++L LL+ A G Sbjct: 310 NNVQVEIKDLHFSYSEEKPAITGLNLSILPNQLSVFVGKSGCGKSTLVSLLMGFNKAQQG 36- 9 Query: 400 HILFDGLDSDNLSQETINQQVLYVSDQSTLLNRSIYDNLRLA-ANLSKKEILDWIDQHGL 45- 8 ILF+G ++ N+ + + Q+V VS S + ++ +N+ +A + + ++I ++Q L Sbjct: 370 EILFNGQNALNIDRTSFYQKVSLVSHSSYVFKGTLRENMTMAKIDATDEQIYACLEQVNL 42- 9 Query: 459 LSFINWLPDGLDTIVGENGNLLSPGQKQQVICARALLSKRSLYIFDEATSSLDAENERII 51- 8 F+ GLD + G LS GQ Q++ ARALL LYIFDEATS++D E+E II Sbjct: 430 AQFVR-DNGGLDMQLLSRGANLSGGQIQRLALARALLHNAELYIFDEATSNIDVESEEII 48- 8 Query: 519 DNLITRLAKTAIVIVITHKMSRLKGANQVLFLNTGQPACLGKPCDLYRDQPTYRHLVDTQ 57- 8 I + + +++I+H+++ A+ + L+ G+ G +L Q Y + Q Sbjct: 489 LQFIQQFKQQKTIVMISHRLANAVNADCINVLDQGKLIEQGTHKELMEKQGAYAEMFQQQ 54- 8 Query: 579 ARLE 582 LE Sbjct: 549 KDLE 552 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04867 Identities = 143/552 (25%), Positives = 260/552 (46%), Gaps = 12/552 (2%) Query: 1 MLDKAVMRLSGIHKLLGLLAGLDVLQAIFIIGQAYYLSLSITGLWEGQKLSSQTVYILLF 60 +L + R++ LL + A L LQ + + Y ++ + + G ++ + LL Sbjct: 16 LLKRLRERIAPKRYLLYVSAFLSWLQFVMRMISFYLIAKTFSTFILGHAIALGRLAGLLL 75 Query: 61 MVSYLGRHVIDYIKNRKLDDFSTAQSSLLRRQLLDKLFDLGPKVVQEQGTGNVVTMALDG 120- +++ +G V+ + + S L++ + DL + +++T+A G Sbjct: 76 LLNVVG-FVLAILGKQLQGIASQFARDSLKQSFFEAFIDLDGQFDAHASDADILTLASQG 134- Query: 121 VSLVENYLRLVLNKMINMSIIPWIILAYIFYLDIESGAILLIVFPLIIIFMIILGYAAQA 18- 0 + ++ Y L+ + I+ +F + +G + L V PLI + ++ + +Q Sbjct: 135 IDSLDTYYGYYLSLSMRTKWNCTTIMILVFLIYPLAGLVFLGVLPLIPLSIVAMQKRSQP 19- 4 Query: 181 KADKQYESYQVLSNHFLDSLRGIDTLKYFGLSKRYGKSIYQTSESFRKATMSTLKIGILS 24- 0 + SY + N F+D L+G++TL + ++RY + +E FRKATMS L + + Sbjct: 195 NMSHYWSSYMDVGNLFMDDLKGLNTLYSYQATERYEQEFSGKAEQFRKATMSLLGFQLQA 25- 4 Query: 241 TFALDFFTTLSIAIVAVFLGLRLLNEQIYLLPALTILILSPEYFLPVRDFSSDYHATLDG 30- 0 +D L I + L Q+ L L+++ E+F P+R+ H + Sbjct: 255 VGYMDAVMYLGIGLSGFLAVQALATGQLSFFNFLFFLLIATEFFTPIREQGYGMHLVMMN 31- 4 Query: 301 KNAFQAIQKVLNKTGIKGEQLVIDDWSKE----SRLDLENIAIAYDQKRVVEDVTLRFRG 35- 6 I L+ + D+ SK +++D++NI++AY++K V+ VT+ Sbjct: 315 TKMADRIFSFLDSVPARK-----DNKSKTAINFNQIDIQNISLAYEKKTVLSGVTMTLTK 36- 9 Query: 357 HQKVALVGVSGSGKSSLINLLSGFLGPDNGSLKVDGREVTNLDQEDWHKQMIYIPQTPYV 41- 6 Q A+ GVSG GK+SL LL G + DG + NL QE ++Q++Y+ + Sbjct: 370 GQLTAIAGVSGQGKTSLAQLLLKRQSATTGHILFDGLDSDNLSQETINQQVLYVSDQSTL 42- 9 Query: 417 FEMSLRDNITFYTPNASDEEVVRAIHMVGLDSLLSELPDGLETRIGNGARPLSGGQAQRI 47- 6 S+ DN+ N S +E++ I GL S ++ LPDGL+T +G LS GQ Q++ Sbjct: 430 LNRSIYDNLRL-AANLSKKEILDWIDQHGLLSFINWLPDGLDTIVGENGNLLSPGQKQQV 48- 8 Query: 477 ALARAFLDQNRRIMVFDEPTAHLDIETELELKEKMLPLMSDRLVIFATHRLHWLNQMDVI 53- 6 ARA L + R + +FDE T+ LD E E + + L +VI TH++ L + + Sbjct: 489 ICARALLSK-RSLYIFDEATSSLDAENERIIDNLITRLAKTAIVIVITHKMSRLKGANQV 54- 7 Query: 537 VVMEKGRVAEVG 548 + + G+ A +G Sbjct: 548 LFLNTGQPACLG 559 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1615 A DNA sequence (GBSx1710) was identified in S. agalactiae <SEQ ID 4983> which encodes the amino acid sequence <SEQ ID 4984>. This protein is predicted to be transport ATP-binding protein cydd (cydC). Analysis of this protein sequence reveals the following:

TABLE-US-04868 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.84 Transmembrane 260-276 (258-284) INTEGRAL Likelihood = -9.34 Transmembrane 172-188 (147-199) INTEGRAL Likelihood = -6.53 Transmembrane 150-166 (147-171) INTEGRAL Likelihood = -6.05 Transmembrane 31-47 (29-52) INTEGRAL Likelihood = -3.35 Transmembrane 68-84 (67-84) INTEGRAL Likelihood = -1.17 Transmembrane 293-309 (292-310) INTEGRAL Likelihood = -0.69 Transmembrane 494-510 (493-510) ----- Final Results ----- bacterial membrane --- Certainty = 0.6137 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10127> which encodes amino acid sequence <SEQ ID 10128> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04869 >GP: CAB15899 GB: Z99123 ABC membrane transporter (ATP-binding protein) [Bacillus subtilis] Identities = 262/573 (45%), Positives = 389/573 (67%), Gaps = 14/573 (2%) Query: 16 LKTDQWIKPFFKQYKVSLVIALFLGFMTFFSASALMFNSGYLISKSASLPSNILLVYVPI 75 - +K ++WI P+ KQ V+ +FLG +T FSA+ LMF SG+LISK+A+ P NILL+YVPI Sbjct: 1 MKKEEWILPYIKQNARLFVLVIFLGAVTIFSAAFLMFTSGFLISKAATRPENILLIYVPI 60 Query: 76 VLTRAFGIGRPVFRYIERLTSHNWVLRMTSQLRLKLYHSLESNAIFMKRDFRLGDVMGLL 135- V R FGI R V RY+ERL H+ +L++ S +R++LY+ LE A+ ++ FR GD++G+L Sbjct: 61 VAVRTFGIARSVSRYVERLVGHHIILKIVSDMRVRLYNMLEPGALMLRSRFRTGDMLGIL 120- Query: 136 AEDINYLQNLYLRTIFPTIIAWILYSFIIIATGFFSLWFALMMLLYLAIMIFLFPLWSIL 19- 5 +EDI +LQ+ +L+TIFP I A +LY+ +IA GFFS FA+++ LYL +++ LFP+ S+L Sbjct: 121 SEDIEHLQDAFLKTIFPAISALLLYAVSVIALGFFSWPFAILLALYLFVLVVLFPVVSLL 18- 0 Query: 196 ANGARQTREKELKNHLYTDLTDNVLGISDWIFSQRGQEYVALHERSESELMAVQKKIRSF 25- 5 A+ + K +N LY+ LTD V+G+SDW+FS R ++ +E+ E + +++K + F Sbjct: 181 VTRAKNAKLKSGRNVLYSRLTDAVMGVSDWMFSGRRHAFIDAYEKEERDWFELERKKQRF 24- 0 Query: 256 DNRRALIVELVFGFLAILVIIWASNQFIGHRGGEA--NWIAAFVLTVFPLSEAFAGLSAA 31- 3 R + + L +L++ W + Q GE IAAFVL VFPL+EAF LS A Sbjct: 241 TRWRDFAAQCLVAGLILLMLFWTAGQ---QADGELAKTMIAAFVLVVFPLTEAFLPLSDA 29- 7 Query: 314 AQETNKYSDSIHRLN------ELSETYFETTQNQLPNKPYDFSVKNLSFQYKPQEKWVLH 36- 7 E Y DSI R+N E S+T E+ L + + ++++F Y + VLH Sbjct: 298 LGEVPGYQDSIRRMNNVAPQPEASQT--ESGDQILDLQDVTLAFRDVTFSYDNSSQ-VLH 35- 4 Query: 368 HLDLDIKEGEKIAILGRSGSGKSTLASLLRGDLKASQGEITLGDADVSIVGDCISNYIGV 42- 7 + +++GEK+A+LGRSGSGKST +L+ G LK G +TL + +++ D I++ + V Sbjct: 355 NFSFTLRQGEKMALLGRSGSGKSTSLALIEGALKPDSGSVTLNGVETALLKDQIADAVAV 41- 4 Query: 428 IQQAPYLFNTTLLNNIRIGNQDASEEDVWKVLERVGLKEMVTDLSDGLYTMVDEAGLRFS 48- 7 + Q P+LF+T++LNNIR+GN +AS+EDV + ++V L + + L DG +T V E G+RFS Sbjct: 415 LNQKPHLFDTSILNNIRLGNGEASDEDVRRAAKQVKLHDYIESLPDGYHTSVQETGIRFS 47- 4 Query: 488 GGERHRIALARILLKDVPIVILDEPTVGLDPITEQALLRVFMKELEGKTLVWITHHLKGI 54- 7 GGER RIALARILL+D PI+ILDEPTVGLDPITE+ L+ + L+GKT++WITHHL G+ Sbjct: 475 GGERQRIALARILLQDTPIIILDEPTVGLDPITERELMETVFEVLKGKTILWITHHLAGV 53- 4 Query: 548 EHADRILFIENGQLELEGSPQELSQSSQRYRQL 580 E AD+I+F+ENG+ E+EG+ +EL +++RYR+L Sbjct: 535 EAADKIVFLENGKTEMEGTHEELLAANERYRRL 567 A related GBS gene <SEQ ID 8861> and protein <SEQ ID 8862> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04870 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -15.90 GvH: Signal Score (-7.5): 1.97 Possible site: 49 >>> Seems to have no N-terminal signal sequence ALOM program count: 7 value: -12.84 threshold: 0.0 INTEGRAL Likelihood = -12.84 Transmembrane 260-276 (258-284) INTEGRAL Likelihood = -9.34 Transmembrane 172-188 (147-199) INTEGRAL Likelihood = -6.53 Transmembrane 150-166 (147-171) INTEGRAL Likelihood = -6.05 Transmembrane 31-47 (29-52) INTEGRAL Likelihood = -3.35 Transmembrane 68-84 (67-84) INTEGRAL Likelihood = -1.17 Transmembrane 293-309 (292-310) INTEGRAL Likelihood = -0.69 Transmembrane 494-510 (493-510) PERIPHERAL Likelihood = 3.29 412 modified ALOM score: 3.07 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6137 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00109## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1616 A DNA sequence (GBSx1711) was identified in S. agalactiae <SEQ ID 4987> which encodes the amino acid sequence <SEQ ID 4988>. This protein is predicted to be spore germination protein C3 (ispB). Analysis of this protein sequence reveals the following: TABLE-US-04871 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.06 Transmembrane 111-127 (111-128) ----- Final Results ----- bacterial membrane --- Certainty = 0.1426 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04872 >GP: CAB14190 GB: Z99115 heptaprenyl diphosphate synthase component II [Bacillus subtilis] Identities = 101/318 (31%), Positives = 184/318 (57%), Gaps = 5/318 (1%) Query: 8 YPELKKNIDETNQLIQERIQVRNKDIEAALSQLTAAGGKQLRPAFFYLFSQLGNKENQDT 67 Y L +ID + +++ ++ + A L AGGK++RP F L G+ D Sbjct: 35 YSFLNDDIDVIERELEQTVRSDYPLLSEAGLHLLQAGGKRIRPVFVLLSGMFGD---YDI 91 Query: 68 QQLKKIAASLEILHVATLIHDDVIDDSPLRRGNMTIQSKFGKDIAVYTGDLLFTVFFDLI 127- ++K +A +LE++H+A+L+HDDVIDD+ LRRG TI++K+ IA+YTGD + +++ Sbjct: 92 NKIKYVAVTLEMIHMASLVHDDVIDDAELRRGKPTIKAKWDNRIAMYTGDYMLAGSLEMM 151- Query: 128 LESMADTPFMRINAKSMRKILMGELDQMHLRYNQQQGIHHYLRAISGKTAELFKLASKEG 18- 7 + + RI ++++ ++ +GE++Q+ +YN +Q + YLR I KTA L ++ + G Sbjct: 152 TR-INEPKAHRILSQTIVEVCLGEIEQIKDKYNMEQNLRTYLRRIKRKTALLIAVSCQLG 21- 0 Query: 188 AYFGGAEKEVVRLAGHIGFNIGMTFQILDDILDYTADKKTFNKPVLEDLAQGIYSLPLLL 24- 7 A GA++++ + G+ +GM++QI+DDILD+T+ ++ KPV DL QG +LP+L Sbjct: 211 AIASGADEKIHKALYWFGYYVGMSYQIIDDILDFTSTEEELGKPVGGDLLQGNVTLPVLY 27- 0 Query: 248 AIEENPDIFKPILDKKTDMATEDMEKIAYLVVSHRGVDKARHLARKFTEKAISDINKLPQ 30- 7 A+ +NP + + ++ E +E I + ++ + ++ + +KA +N LP+ Sbjct: 271 AL-KNPALKNQLKLINSETTQEQLEPIIEEIKKTDAIEASMAVSEMYLQKAFQKLNTLPR 32- 9 Query: 308 SSAKKQLLQLTNYLLKRK 325 A+ L + Y+ KRK Sbjct: 330 GRARSSLAAIAKYIGKRK 347 There is also homology to SEQ ID 284. An alignment of the GAS and GBS proteins is shown below: TABLE-US-04873 Identities = 65/227 (28%), Positives = 98/227 (42%), Gaps = 9/227 (3%) Query: 43 AGGKQLRPAFFYLFSQLGNKENQDTQQLKKIAASLEILHVATLIHDDV--IDDSPLRRGN 100- +GGK++RP + Q+ +AA+LE++H +LIHDD+ +D+ RRG Sbjct: 36 SGGKRIRPLILLEMIEGFGVSLQNAHF--DLAAALEMIHTGSLIHDDLPAMDNDDYRRGR 93 Query: 101 MTIQSKFGKDIAVYTGDLLFTVFFDLILESM--ADTPFMRINAKSMRKILMGELDQMHLR 15- 8 +T +FG+ A+ GD LF F LI ++ ++ I S+ G + L Sbjct: 94 LTNHKQFGEATAILAGDSLFLDPFGLIAQAELNSEVKVALIQELSLASGTFGMVGGQMLD 153- Query: 159 Y---NQQQGIHHYLRAISGKTAELFKLASKEGAYFGGAEKEVVRLAGHIGFNIGMTFQIL 21- 5 NQ + KT +L K A V + G IG FQI Sbjct: 154 MKGENQALSLPQLSLIHLNKTGKLLAFPFKAAALITEQAMTVRQQLEQAGMLIGHAFQIR 21- 3 Query: 216 DDILDYTADKKTFNKPVLEDLAQGIYSLPLLLAIEENPDIFKPILDK 262 DDILD TA + K +DL + P LL +E + + LD+ Sbjct: 214 DDILDVTASFEDLGKTPKKDLFAEKATYPSLLGLEASYQLLTESLDQ 260 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1617 A DNA sequence (GBSx1712) was identified in S. agalactiae <SEQ ID 4989> which encodes the amino acid sequence <SEQ ID 4990>. Analysis of this protein sequence reveals the following: TABLE-US-04874 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3995 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04875 >GP: AAA25232 GB: M58315 dipeptidyl peptidase IV [Lactococcus lactis] Identities = 385/767 (50%), Positives = 504/767 (65%), Gaps = 21/767 (2%) Query: 1 MRYNQFSYIPTKPNEAFEELKGLGFPLNKKNSDKANLEAFLRHSFLNQTDTDYALSLLIV 60 MR+N FS + +E EL LGF + +K L+ FL S + TD L Sbjct: 1 MRFNHFSIVDKNFDEQLAELDQLGFRWSVFWDEKKILKDFLIQSPSDMTD-------LQA 53 Query: 61 DAKTDALTFFKSNSDLTLENLQWIYLQLLGFIPFVDFKDPKAF-------LQDINFPVSY 113- A+ D + F KS+ +L E I LQLL F+P DF+ KAF L I ++ Sbjct: 54 TAELDVIEFLKSSIELDWEIFWNIALQLLDFVPNFDFEIGKAFEYAKNSNLPQIEAEMTT 113- Query: 114 DNIFQSLHHLLACRGKSGNTLIDQLVADGLLHADNHYHFFNGKSLATFNTNQLIREVVYV 17- 3 +NI + ++LL R K+G L++ V++GLL DNHYHFFN KSLATF+++ L REV++V Sbjct: 114 ENIISAFYYLLCTRRKNGMILVEHWVSEGLLPLDNHYHFFNDKSLATFDSSLLEREVLWV 17- 3 Query: 174 ETSLDTMSSGEHDLVKVNIIRPTTEHTIPTMMTASPYHQGINDPAADQKTYQMEGALAVK 23- 3 E+ +D+ GE+DL+K+ IIRP + +P +MTASPYH GIND A D + M L K Sbjct: 174 ESPVDSEQRGENDLIKIQIIRPKSTEKLPVVMTASPYHLGINDKANDLALHDMNVELEEK 23- 3 Query: 234 QPKHIQVDTKPFKEEVKHPSKLPI-SPATESFTHIDSYSLNDYFLSRGFANIYVSGVGTA 29- 2 I V+ K ++ +LPI A FTH +YSLNDYFL+RGFA+IYV+GVGT Sbjct: 234 TSHEIHVEQKLPQKLSAKAKELPIVDKAPYRFTHGWTYSLNDYFLTRGFASIYVAGVGTR 29- 3 Query: 293 GSTGFMTSGDYQQIQSFKAVIDWLNGKVTAFTSHKRDKQVKANWSNGLVATTGKSYLGTM 35- 2 S GF TSGDYQQI S AVIDWLNG+ A+TS K+ ++KA+W+NG VA TGKSYLGTM Sbjct: 294 SSDGFQTSGDYQQIYSMTAVIDWLNGRARAYTSRKKTHEIKASWANGKVAMTGKSYLGTM 35- 3 Query: 353 STGLATTGVEGLKVIIAEAAISTWYDYYRENGLVCSPGGYPGEDLDVLTELTYSRNLLAG 41- 2 + G ATTGVEGL+VI+AEA IS+WY+YYRENGLV SPGG+PGEDLDVL LTYSRNL Sbjct: 354 AYGAATTGVEGLEVILAEAGISSWYNYYRENGLVRSPGGFPGEDLDVLAALTYSRNLDGA 41- 3 Query: 413 DYIKNNDCYQALLNEQSKAIDRQSGDYNQYWHDRNYLTHVNNVKSRVVYTHGLQDWNVKP 47- 2 D++K N Y+ L E + A+DR+SGDYNQ+WHDRNYL + + VK+ V+ HGLQDWNV P Sbjct: 414 DFLKGNAEYEKRLAEMTAALDRKSGDYNQFWHDRNYLINTDKVKADVLIVHGLQDWNVTP 47- 3 Query: 473 RHVYKVFNALPQTIKKHLFLHQGQHVYMHNWQSIDFRESMNALLSQELLGIDNHFQLEEV 53- 2 Y + ALP+ KH FLH+G H+YM++WQSIDF E++NA +LL D + L V Sbjct: 474 EQAYNFWKALPEGHAKHAFLHRGAHIYMNSWQSIDFSETINAYFVAKLLDRDLNLNLPPV 53- 3 Query: 533 IWQDNTTEQTWQVLDAFGGNHQEQIGLGD---SKKLIDNHYDKEAFDTYCKDFNVFKNDL 58- 9 I Q+N+ +Q W +++ FG N Q ++ LG S DNHYD E F Y KDFNVFK DL Sbjct: 534 ILQENSKDQVWTMMNDFGANTQIKLPLGKTAVSFAQFDNHYDDETFKKYSKDFNVFKKDL 59- 3 Query: 590 FKGNNKTNQITINLPLKKNYLLNGQCKLHLRVKTSDKKAILSAQILDYGPKKRFKDTPTI 64- 9 F+ NK N+ I+L L +NG +L LR+K +D K LSAQILD+G KKR +D + Sbjct: 594 FE--NKANEAVIDLELPSMLTINGPVELELRLKLNDTKGFLSAQILDFGQKKRLEDKARV 65- 1 Query: 650 KFLNSLDNGKNFAREALRELPFTKDHYRVISKGVLNLQNRTDLLTIEAIEPEQWFDIEFS 70- 9 K LD G+NF + L ELP + Y++I+KG NLQN+ +LLT+ ++ ++WF I+F Sbjct: 652 KDFKVLDRGRNFMLDDLVELPLVESPYQLITKGFTNLQNQ-NLLTVSDLKADEWFTIKFE 71- 0 Query: 710 LQPSIYQLSKGDNLRIILYTTDFEHTIRDNASYSITVDLSQSYLTIP 756 LQP+IY L K D LR+ILY+TDFEHT+RDN + +DLSQS L IP Sbjct: 711 LQPTIYHLEKADKLRVILYSTDFEHTVRDNRKVTYEIDLSQSKLIIP 757 A related DNA sequence was identified in S. pyogenes <SEQ ID 4991> which encodes the amino acid sequence <SEQ ID 4992>. Analysis of this protein sequence reveals the following: TABLE-US-04876 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2553(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04877 Identities = 481/758 (63%), Positives = 587/758 (76%), Gaps = 4/758 (0%) Query: 1 MRYNQFSYIPTKPNEAFEELKGLGFPLNKKNSDKANLEAFLRHSFLNQTDTDYALSLLIV 60 MRYNQFSYIPT A EELK LGF L+ + + KA+LE+FLR F + D+DY LS LI Sbjct: 1 MRYNQFSYIPTSLERAAEELKELGFDLDLQKTAKASLESFLRKLFFHYPDSDYPLSHLIA 60 Query: 61 DAKTDALTFEKSNSDLTLENLQWIYLQLLGFIPFVDFKDPKAFLQDINFPVSYDN--IFQ 118- DAL+FF+S +L+ E + LQ+LGFIP VDF + AFL + FP+ +D I + Sbjct: 61 KNDMDALSFFQSEQELSKEVFDLLALQVLGFIPGVDFTEADAFLDKLAFPIHFDETEIIK 120- Query: 119 SLHHLLACRGKSGNTLIDQLVADGLLHADNHYHFFNGKSLATFNTNQLIREVVYVETSLD 17- 8 +HHLLA R KSG TLID LV+ G+L DN YHFFNGKSLATF+T+QLIREVVYVE LD Sbjct: 121 HIHHLLATRCKSGMTLIDDLVSQGMLTMDNDYHFFNGKSLATFDTSQLIREVVYVEAPLD 18- 0 Query: 179 TMSSGEHDLVKVNIIRPTTEHTIPTMMTASPYHQGINDPAADQKTYQMEGALAVKQPKHI 23- 8 T G+ DL+KVNIIRP ++ +PT+MT SPYHQGIN+ A D+K Y+ME L VK+ + I Sbjct: 181 TDQDGQLDLIKVNIIRPQSQKPLPTLMTPSPYHQGINEVANDKKLYRMEKELVVKKRRQI 24- 0 Query: 239 QVDTKPFKEEVKHPSKLPISPATESFTHIDSYSLNDYFLSRGFANIYVSGVGTAGSTGFM 29- 8 V+ + F P KLPI ESF++I+SYSLNDYFL+RGFANIYVSGVGTAGSTGFM Sbjct: 241 TVEDRDFIPLETQPCKLPIGQNLESFSYINSYSLNDYFLARGFANIYVSGVGTAGSTGFM 30- 0 Query: 299 TSGDYQQIQSFKAVIDWLNGKVTAFTSHKRDKQVKANWSNGLVATTGKSYLGTMSTGLAT 35- 8 TSG+Y QI+SFKAVIDWLNG+ TA+TSH + QV+A+W+NGLV TTGKSYLGTMSTGLAT Sbjct: 301 TSGNYAQIESFKAVIDWLNGRATAYTSHSKTHQVRADWANGLVCTTGKSYLGTMSTGLAT 36- 0 Query: 359 TGVEGLKVIIAEAAISTWYDYYRENGLVCSPGGYPGEDLDVLTELTYSRNLLAGDYIKNN 41- 8 TGV+GL +IIAE+AIS+WY+YYRENGLVCSPGGYPGEDLDVLTELTYSRNLLAGDY+++N Sbjct: 361 TGVDGLAMIIAESAISSWYNYYRENGLVCSPGGYPGEDLDVLTELTYSRNLLAGDYLRHN 42- 0 Query: 419 DCYQALLNEQSKAIDRQSGDYNQYWHDRNYLTHVNNVKSRVVYTHGLQDWNVKPRHVYKV 47- 8 D YQ LLN+QS+A+DRQSGDYNQ+WHDRNYL + + +K VVYTHGLQDWNVKPR VY++ Sbjct: 421 DRYQELLNQQSQALDRQSGDYNQFWHDRNYLKNAHQIKCDVVYTHGLQDWNVKPRQVYEI 48- 0 Query: 479 FNALPQTIKKHLFLHQGQHVYMHNWQSIDFRESMNALLSQELLGIDNHFQLEEVIWQDNT 53- 8 FNALP TI KHLFLHQG+HVYMHNWQSIDFRESMNALL Q+LLG+ N F L E+IWQDNT Sbjct: 481 FNALPSTINKHLFLHQGEHVYMHNWQSIDFRESMNALLCQKLLGLANDFSLPEMIWQDNT 54- 0 Query: 539 TEQTWQVLDAFGGNHQEQIGLGDSKKLIDNHYDKEAFDTYCKDFNVFKNDLFKGNNKTNQ 59- 8 Q WQ FG + +++ LG LIDNHY ++ F Y KDF FK LFKG K NQ Sbjct: 541 CPQNWQERKVFGTSTIKELDLGQELLLIDNHYGEDEFKAYGKDFRAFKAALFKG--KANQ 59- 8 Query: 599 ITINLPLKKNYLLNGQCKLHLRVKTSDKKAILSAQILDYGPKKRFKDTPTIKFLNSLDNG 65- 8 I++ L+++ +NG+ L L+VK+S+ K +LSAQILDYG KKR D P +S+DNG Sbjct: 599 ALIDILLEEDLPINGEIVLQLKVKSSENKGLLSAQILDYGKKKRLGDLPIALTQSSIDNG 65- 8 Query: 659 KNFAREALRELPFTKDHYRVISKGVLNLQNRTDLLTIEAIEPEQWFDIEFSLQPSIYQLS 71- 8 +NF+RE L+ELPF +D YRVISKG +NLQNR +L +IE I +W + LQP+IY L Sbjct: 659 QNFSREPLKELPFREDSYRVISKGFMNLQNRNNLSSIETIPNNKWMTVRLPLQPTIYHLE 71- 8 Query: 719 KGDNLRIILYTTDFEHTIRDNASYSITVDLSQSYLTIP 756 KGD LR+ILYTTDFEHT+RDN++Y++T+DLSQS L +P Sbjct: 719 KGDTLRVILYTTDFEHTVRDNSNYALTIDLSQSQLIVP 756 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1618 A DNA sequence (GBSx1713) was identified in S. agalactiae <SEQ ID 4993> which encodes the amino acid sequence <SEQ ID 4994>. This protein is predicted to be PrfA. Analysis of this protein sequence reveals the following: TABLE-US-04878 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3976(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10125> which encodes amino acid sequence <SEQ ID 10126> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-04879 >GP: CAA65740 GB: X97014 PrfA [Listeria seeligeri] Identities = 54/181 (29%), Positives = 95/181 (51%), Gaps = 1/181 (0%) Query: 38 DYTYILKDGIVKQSVLSKYGTEFNLRYVTGLEITSILNTDYSQHMGEPYNVRIESETAHF 97 - +Y L +G+ K + +S+ G NL+Y G I D + +G YN+ + SE A Sbjct: 36 EYCIFLHEGVAKLTSISESGDILNLQYYKGAFIIMTGFIDTEKSLGY-YNLEVVSEQAAA 94 Query: 98 YKVRRSTFLKDINNDIELQGYVKDFYHNRLEKSMKKMQCMLTNGRIGAISTQLYDLSKMF 157- Y ++ S + ++ D++ Y+ D ++ S+ K +NG++G+I Q L+ ++ Sbjct: 95 YIIKISDLKELVSKDLKQLFYIIDTLQKQVSYSLAKFNDFSSNGKVGSICGQFLILAYVY 154- Query: 158 GEERDNGDIYINFVITNEELGKFCGISTGSSVSRILKQLKDDHIIRIEKQHIIITNVEKLK 2- 18 GEE NG +T +ELG GI+ S+VSRI+ +LK +++I + + I N+ LK Sbjct: 155 GEETPNGIKITLEKLTMQELGCSSGIAHSSAVSRIISKLKQENVIEYKDSYFYIKNIAYLK 2- 15 A related DNA sequence was identified in S. pyogenes <SEQ ID 4995> which encodes the amino acid sequence <SEQ ID 4996>. Analysis of this protein sequence reveals the following: TABLE-US-04880 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4088(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04881 Identities = 186/223 (83%), Positives = 203/223 (90%) Query: 1 MEEVMNHQILQNYINSHNLPIIEKDYHKYLTFESLEEDYTYILKDGIVKQSVLSKYGTEF 60 +E+ +NH ILQ YI++HN PIIEK YHKYLTFESLEED+TYILKDGIVKQSVLSKYG EF Sbjct: 17 LEKSVNHHILQRYIDNHNFPIIEKSYHKYLTFESLEEDFTYILKDGIVKQSVLSKYGMEF 76 Query: 61 NLRYVTGLEITSILNTDYSQHMGEPYNVRIESETAHFYKVRRSTFLKDINNDIELQGYVK 120- NLRYVTGLEITS+LNT YS+ MGEPYNVRIESE A FYKVRRS FLKDIN DIELQGYVK Sbjct: 77 NLRYVTGLEITSVLNTGYSKDMGEPYNVRIESEKASFYKVRRSAFLKDINEDIELQGYVK 136- Query: 121 DFYHNRLEKSMKKMQCMLTNGRIGAISTQLYDLSKMFGEERDNGDIYINFVITNEELGKF 18- 0 DFYHNRL+KSMKKMQCMLTNGRIGAISTQ+YDL +FGEE NG I INFVITNEELGKF Sbjct: 137 DFYHNRLQKSMKKMQCMLTNGRIGAISTQIYDLMTLFGEELPNGQILINFVITNEELGKF 19- 6 Query: 181 CGISTGSSVSRILKQLKDDHIIRIEKQHIIITNVEKLKDHIVF 223 CGIST SSVSRILKQLK+ +IIRI+KQHIIITN++KLKD+IVF Sbjct: 197 CGISTASSVSRILKQLKEKNIIRIDKQHIIITNLDKLKDNIVF 239 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1619 A DNA sequence (GBSx1714) was identified in S. agalactiae <SEQ ID 4997> which encodes the amino acid sequence <SEQ ID 4998>. Analysis of this protein sequence reveals the following: TABLE-US-04882 Possible site: 46 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.33 Transmembrane 167-183 (159-193) INTEGRAL Likelihood = -7.96 Transmembrane 18-34 (10-37) INTEGRAL Likelihood = -7.75 Transmembrane 373-389 (369-392) INTEGRAL Likelihood = -5.68 Transmembrane 214-230 (212-234) INTEGRAL Likelihood = -4.78 Transmembrane 243-259 (241-262) INTEGRAL Likelihood = -2.71 Transmembrane 48-64 (47-65) INTEGRAL Likelihood = -2.60 Transmembrane 283-299 (283-300) ----- Final Results ----- bacterial membrane --- Certainty = 0.6731(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04883 >GP: CAB15662 GB: Z99122 similar to antibiotic resistance protein [Bacillus subtilis] Identities = 106/401 (26%), Positives = 199/401 (49%), Gaps = 21/401 (5%) Query: 3 DKLFNKHFIGITILNFIVYMVYYLFTVIIAFIATKELGVSTSQAGLATGIYIVGTLIARL 62 D ++ K FI + ++N V++ +Y F ++ +ELG + SQ GL ++++ +I R Sbjct: 5 DAIWTKDFIMVLLVNLFVFVFFYTFLTVLPIYTLQELGGTESQGGLLISLFLLSAIITRP 64 Query: 63 IFGKQLEVLGRKLVLRGGAIFYLLTTLAYFYMPSIGVMYLVRFLNGFGYGVVSTATNTIV 122- G +E G+K + + L++ Y + + ++ +RF G + +++T T I Sbjct: 65 FSGAIVERFGKKRMAIVSMALFALSSFLYMPIHNFSLLLGLRFFQGIWFSILTTVTGAIA 124- Query: 123 TAYIPADKRGEGINFYGLSTSLAAAIGPFVGTFMLDNLHINFKMVIVLCSILIAIVVLGA 18- 2 IPA +RGEG+ ++ +S +LA AIGPF+G ++ ++F + ++ + +L + Sbjct: 125 ADIIPAKRRGEGLGYFAMSMNLAMAIGPFLGLNLMRV--VSFPVFFTAFALFMVAGLLVS 18- 2 Query: 183 FVFPVKNITLNPEQLAKSKSWTIDSF-----IEKKAIFITIIAFLMGISYASVLGFQKLY 23- 7 F+ V +K T+ F EK A+ I + + Y++V + ++ Sbjct: 183 FLIKVPQ--------SKDSGTTVFRFAFSDMFEKGALKIATVGLFISFCYSTVTSYLSVF 23- 4 Query: 238 TTEINLMTVGAYFFIVYALVITLTRPSMGRLMDAKGDKWVLYPSYLFLTLGLALLGSAMG 29- 7 ++L + YFF+ +A+ + + RP G+L D G V+YPS L ++GL +L Sbjct: 235 AKSVDLSDISGYFFVCFAVTMMIARPFTGKLFDKVGPGIVIYPSILIFSVGLCMLSFTHS 29- 4 Query: 298 SVTYLLSGALIGFGYGTFMSCGQAASIKGVEEHRFNTAMSTYMIGLDLGLGAGPYILGLV 35- 7 + LLSGA+IG GYG+ + C Q +I+ HR A +T+ D G+ G Y+ GL Sbjct: 295 GLMLLLSGAVIGLGYGSIVPCMQTLAIQKSPAHRSGFATATFFTFFDSGIAVGSYVFGL- 35- 3 Query: 358 KDGFLGAGVQSFRELFWIAAIIPVVCGILYFLKSSRQVETK 398 F+ + F ++ A + ++ +LY + E + Sbjct: 354 ---FVASA--GFSAIYLTAGLFVLIALLLYTWSQKKPAEAE 389 A related DNA sequence was identified in S. pyogenes <SEQ ID 4999> which encodes the amino acid sequence <SEQ ID 5000>. Analysis of this protein sequence reveals the following: TABLE-US-04884 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.31 Transmembrane 202-218 (194-225) INTEGRAL Likelihood = -7.80 Transmembrane 53-69 (44-71) INTEGRAL Likelihood = -7.17 Transmembrane 407-423 (404-426) INTEGRAL Likelihood = -5.26 Transmembrane 249-265 (247-269) INTEGRAL Likelihood = -3.77 Transmembrane 279-295 (276-297) INTEGRAL Likelihood = -2.23 Transmembrane 11-27 (10-27) INTEGRAL Likelihood = -2.13 Transmembrane 83-99 (82-99) INTEGRAL Likelihood = -1.91 Transmembrane 312-328 (311-328) ----- Final Results ----- bacterial membrane --- Certainty = 0.5925(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04885 >GP: CAB15662 GB: Z99122 similar to antibiotic resistance protein [Bacillus subtilis] Identities = 110/390 (28%), Positives = 194/390 (49%), Gaps = 11/390 (2%) Query: 38 EKLFNKHFVAITVINFIVYMVYYLFTVIIAFVATRELGAQTSQAGLATGIYILGTLLARL 97 - + ++ K F+ + ++N V++ +Y F ++ +ELG SQ GL +++L ++ R Sbjct: 5 DAIWTKDFIMVLLVNLFVFVFFYTFLTVLPIYTLQELGGTESQGGLLISLFLLSAIITRP 64 Query: 98 IFGKQLEVFGRRLVLRGGAIFYLLTTLAYFYMPTISMMYLVRFLNGFGYGVVSTATNTIV 157- G +E FG++ + + L++ Y + S++ +RF G + +++T T I Sbjct: 65 FSGAIVERFGKKRMAIVSMALFALSSFLYMPIHNFSLLLGLRFFQGIWFSILTTVTGAIA 124- Query: 158 TAYIPARKRGEGINFYGLSTSLAAAIGPFVGTFMLDNLHIDFRMIIVLCSVLIGCVVVGA 21- 7 IPA++RGEG+ ++ +S +LA AIGPF+G ++ + F + ++ + ++ + Sbjct: 125 ADIIPAKRRGEGLGYFAMSMNLAMAIGPFLGLNLMRV--VSFPVFFTAFALFMVAGLLVS 18- 2 Query: 218 FAFPVKNMSLNAEQLAKTKSWTVDSFIEKKALFITAIAFLMGIAYASVLGFQKLYTSEIH 27- 7 F V + + + + EK AL I + + Y++V + ++ + Sbjct: 183 FLIKVPQSKDSGTTVFR---FAFSDMFEKGALKIATVGLFISFCYSTVTSYLSVFAKSVD 23- 9 Query: 278 LTTVGAYFFVVYALIITITRPAMGRLMDAKGDKWVLYPSYLFLAMGLFLLGSVSSGGSYL 33- 7 L+ + YFFV +A+ + I RP G+L D G V+YPS L ++GL +L SG L Sbjct: 240 LSDISGYFFVCFAVTMMIARPFTGKLFDKVGPGIVIYPSILIFSVGLCMLSFTHSGLMLL 29- 9 Query: 338 LSGALIGFGYGTFMSCGQAASIQGVDEHRFNTAMSTYMIGLDLGLGAGPYLLGLIKDLAL 39- 7 LSGA+IG GYG+ + C Q +IQ HR A +T+ D G+ G Y+ GL Sbjct: 300 LSGAVIGLGYGSIVPCMQTLAIQKSPAHRSGFATATFFTFFDSGIAVGSYVFGLF----- 35- 4 Query: 398 GSGVASFRHLFWLAAVIPLICTLLYLLKTK 427 A F ++ A + LI LLY K Sbjct: 355 -VASAGFSAIYLTAGLFVLIALLLYTWSQK 383 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04886 Identities = 328/396 (82%), Positives = 370/396 (92%), Gaps = 1/396 (0%) Query: 1 MEDKLFNKHFIGITILNFIVYMVYYLFTVIIAFIATKELGVSTSQAGLATGIYIVGTLIA 60 ME+KLFNKHF+ IT++NFIVYMVYYLFTVIIAF+AT+ELG TSQAGLATGIYI+GTL+A Sbjct: 36 MEEKLFNKHFVAITVINFIVYNVYYLFTVIIAFVATRELGAQTSQAGLATGIYILGTLLA 95 Query: 61 RLIFGKQLEVLGRKLVLRGGAIFYLLTTLAYFYMPSIGVMYLVRFLNGFGYGVVSTATNT 120- RLIFGKQLEV GR+LVLRGGAIFYLLTTLAYFYMP+I +MYLVRFLNGFGYGVVSTATNT Sbjct: 96 RLIFGKQLEVFGRRLVLRGGAIFYLLTTLAYFYMPTISMMYLVRFLNGFGYGVVSTATNT 155- Query: 121 IVTAYIPADKRGEGINFYGLSTSLAAAIGPFVGTFMLDNLHINFKMVIVLCSILIAIVVL 18- 0 IVTAYIPA KRGEGINFYGLSTSLAAAIGPFVGTFMLDNLHI+F+M+IVLCS+LI VV+ Sbjct: 156 IVTAYIPARKRGEGINFYGLSTSLAAAIGPFVGTFMLDNLHIDFRMIIVLCSVLIGCVVV 21- 5 Query: 181 GAFVFPVKNITLNPEQLAKSKSWTIDSFIEKKAIFITIIAFLMGISYASVLGFQKLYTTE 24- 0 GAF FPVKN++LN EQLAK+KSWT+DSFIEKKA+FIT IAFLMGI+YASVLGFQKLYT+E Sbjct: 216 GAFAFPVKNMSLNAEQLAKTKSWTVDSFIEKKALFITAIAFLMGIAYASVLGFQKLYTSE 27- 5 Query: 241 INLMTVGAYFFIVYALVITLTRPSMGRLMDAKGDKWVLYPSYLFLTLGLALLGSAMGSVT 30- 0 I+L TVGAYFF+VYAL+IT+TRP+MGRLMDAKGDKWVLYPSYLFL +GL LLGS + Sbjct: 276 IHLTTVGAYFFVVYALIITITRPAMGRLMDAKGDKWVLYPSYLFLAMGLFLLGSVSSGGS 33- 5 Query: 301 YLLSGALIGFGYGTFMSCGQAASIKGVEEHRFNTAMSTYMIGLDLGLGAGPYILGLVKDG 36- 0 YLLSGALIGFGYGTEMSCGQAASI+GV+EHRFNTAMSTYMIGLDLGLGAGPY+LGL+KD Sbjct: 336 YLLSGALIGFGYGTFMSCGQAASIQGVDEHRFNTAMSTYMIGLDLGLGAGPYLLGLIKDL 39- 5 Query: 361 FLGAGVQSFRELFWIAAIIPVVCGILYFLKS-SRQV 395 LG+GV SFR LFW+AA+IP++C +LY LK+ +RQV Sbjct: 396 ALGSGVASFRHLFWLAAVIPLICTLLYLLKTKTRQV 431 A related GBS gene <SEQ ID 8863> and protein <SEQ ID 8864> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04887 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 8.26 GvH: Signal Score (-7.5): -5.21 Possible site: 46 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 7 value: -14.33 threshold: 0.0 INTEGRAL Likelihood = -14.33 Transmembrane 167-183 (159-193) INTEGRAL Likelihood = -7.96 Transmembrane 18-34 (10-37) INTEGRAL Likelihood = -7.75 Transmembrane 373-389 (369-392) INTEGRAL Likelihood = -5.68 Transmembrane 214-230 (212-234) INTEGRAL Likelihood = -4.78 Transmembrane 243-259 (241-262) INTEGRAL Likelihood = -2.71 Transmembrane 48-64 (47-65) INTEGRAL Likelihood = -2.60 Transmembrane 283-299 (283-300) PERIPHERAL Likelihood = 0.69 341 modified ALOM score: 3.37 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6731 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00110## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1620 A DNA sequence (GBSx1715) was identified in S. agalactiae <SEQ ID 5001> which encodes the amino acid sequence <SEQ ID 5002>. Analysis of this protein sequence reveals the following: TABLE-US-04888 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0151 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04889 >GP: BAB06903 GB: AP001518 unknown conserved protein [Bacillus halodurans] Identities = 52/143 (36%), Positives = 84/143 (58%) Query: 5 YERILIAIDGSYESELAVEKGINVALRNDAELLLTHVIDAHAYQSEGVFSDYVFDRQEQE 64 Y IL+A+DGS +++ A+ K N A A+L + HVID+ ++ + + V E + Sbjct: 2 YNHILVAVDGSTQAKRALYKAFNYAKEFKADLFICHVIDSRSFATVEQYDRTVVGAAELD 61 Query: 65 SADVLAYFEKLAHSKGLTKIKKITEIGNPKTLLAKDIPIREKADLIMVGATGLNTFERLL 124- +L + + A G+ K+ I + G+PK ++K I + DLI+ GATGLN ER L Sbjct: 62 GKKLLQRYSEEAEKAGVDKVHTILDFGSPKANISKTIAQKYDIDLIITGATGLNAVERFL 121- Query: 125 IGSTSEYILRHSKVDMLVVRDSK 147 +GS SE + RH+K D+L+VR+ + Sbjct: 122 MGSVSESVARHAKCDVLIVRNDQ 144 There is also homology to SEQ ID 3658: TABLE-US-04890 Identities = 105/150 (70%), Positives = 121/150 (80%) Query: 1 MTQKYERILIAIDGSYESELAVEKGINVALRNDAELLLTHVIDAHAYQSEGVFSDYVFDR 60 M+ KY+RIL+AIDGSYESELA KG+NVALRNDA LLL HVID A QS F Y++++ Sbjct: 31 MSLKYKRILVAIDGSYESELAFNKGVNVALRNDATLLLVHVIDTRALQSVATFDTYIYEK 90 Query: 61 QEQESADVLAYFEKLAHSKGLTKIKKITEIGNPKTLLAKDIPIREKADLIMVGATGLNTF 120- EQE+ DVL FEK A G+T IK+I E GNPK LLA DIP RE ADLIMVGATGLNTF Sbjct: 91 LEQEAKDVLDDFEKQAQIAGITNIKQIIEFGNPKNLLAHDIPDRENADLIMVGATGLNTF 150- Query: 121 ERLLIGSTSEYILRHSKVDMLVVRDSKKTL 150 ERLLIGS+SEYI+RH+K+D+LVVRDS KTL Sbjct: 151 ERLLIGSSSEYIMRHAKIDLLVVRDSTKTL 180 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1621 A DNA sequence (GBSx1716) was identified in S. agalactiae <SEQ ID 5003> which encodes the amino acid sequence <SEQ ID 5004>. This protein is predicted to be glycerol uptake facilitator protein (glpF). Analysis of this protein sequence reveals the following: TABLE-US-04891 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.65 Transmembrane 261-277 (257-281) INTEGRAL Likelihood = -5.73 Transmembrane 201-217 (199-222) INTEGRAL Likelihood = -4.51 Transmembrane 92-108 (91-110) INTEGRAL Likelihood = -4.30 Transmembrane 44-60 (42-62) INTEGRAL Likelihood = -2.18 Transmembrane 15-31 (11-31) INTEGRAL Likelihood = -1.54 Transmembrane 150-166 (149-166) ----- Final Results ----- bacterial membrane --- Certainty = 0.4461 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04892 >GP: AAA25231 GB: M58315 putative [Lactococcus lactis] Identities = 183/290 (63%), Positives = 228/290 (78%), Gaps = 10/290 (3%) Query: 2 IEITWTVKYITEFIATAFLIILGNGAVANVDLKGTKGNNSGWIIIAIGYGLGVMMPALMF 61 +++TWTVKYITEF+ TA LII+GNGAVANV+LKGTK + W+II GYGLGVM+PA+ F Sbjct: 1 MDVTWTVKYITEFVGTALLIIMGNGAVANVELKGTKAHAQSWMIIGWGYGLGVMLPAVAF 60 Query: 62 GNVSGNHINPAFTLGLAFSGLFPWAHVGQYILAQILGAMFGQLVVVMVYQPYFVKTENPN 121- GN++ + INPAFTLGLA SGLFPWAHV QYI+AQ+LGAMFGQL+VMVY+PY++KT+NPN Sbjct: 61 GNIT-SQINPAFTLGLAASGLFPWAHVAQYIIAQVLGAMFGQLLIVMVYRPYYLKTQNPN 119- Query: 122 HVLGSFSTISALDDGQKSSRKAAYINGFLNEFVGSFVLFFGALALTKNYFGVE----LVG 17- 7 +LG+FSTI +DD + +R A INGFLNEF+GSFVLFFGA+A T +FG + + Sbjct: 120 AILGTFSTIDNVDDNSEKTRLGATINGFLNEFLGSFVLFFGAVAATNIFFGSQSITWMTN 17- 9 Query: 178 KLVQAGYDQTTAATRISPYVTGSLA-----VAHLGIGFLVMTLVASLGGPTGPALNPARD 23- 2 L G D +++ +V S A +AHL +GFLVM LV +LGGPTGP LNPARD Sbjct: 180 YLKGQGADVSSSDVMNQIWVQASGASASKMIAHLFLGFLVMGLVVALGGPTGPGLNPARD 23- 9 Query: 233 LGPRIVHRLLPKQILGQAKEDSKWWYAWVPVLAPIVASILAVALFKLLYL 282 GPR+VH LLPK +LG+AK SKWWYAWVPVLAPI+AS+ AVALFK++YL Sbjct: 240 FGPRLVHSLLPKSVLGEAKGSSKWWYAWVPVLAPILASLAAVALFKMIYL 289 A related DNA sequence was identified in S. pyogenes <SEQ ID 5005> which encodes the amino acid sequence <SEQ ID 5006>. Analysis of this protein sequence reveals the following: TABLE-US-04893 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.18 Transmembrane 293-309 (288-314) INTEGRAL Likelihood = -7.43 Transmembrane 2-18 (1-20) INTEGRAL Likelihood = -7.38 Transmembrane 233-249 (228-256) INTEGRAL Likelihood = -5.57 Transmembrane 124-140 (123-142) INTEGRAL Likelihood = -2.87 Transmembrane 76-92 (75-93) INTEGRAL Likelihood = -2.18 Transmembrane 47-63 (43-63) INTEGRAL Likelihood = -1.54 Transmembrane 182-198 (181-198) ----- Final Results ----- bacterial membrane --- Certainty = 0.4673 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04894 >GP: AAA25231 GB: M58315 putative [Lactococcus lactis] Identities = 176/290 (60%), Positives = 228/290 (77%), Gaps = 10/290 (3%) Query: 34 MEMTWTVKYITEFIATAFLIILGNGAVANVDLKGTKGHNSGWLVIAFGYGLGVMMPALMF 93 - M++TWTVKYITEF+ TA LII+GNGAVANV+LKGTK H W++I +GYGLGVM+PA+ F Sbjct: 1 MDVTWTVKYITEFVGTALLIIMGNGAVANVELKGTKAHAQSWMIIGWGYGLGVMLPAVAF 60 Query: 94 GNVSGNHINPAFTVGLAVSGLFPWAHVLQYVVAQLLGAIFGQLVVVMVYKPYFMKTENPN 153- GN++ + INPAFT+GLA SGLFPWAHV QY++AQ+LGA+FGQL++VMVY+PY++KT+NPN Sbjct: 61 GNIT-SQINPAFTLGLAASGLFPWAHVAQYIIAQVLGAMFGQLLIVMVYRPYYLKTQNPN 119- Query: 154 HVLGSFSTISSLDNGQKDSHKASYINGFLNEFVGSFVLFFGALALTKNYFGVELVGKLIE 21- 3 +LG+FSTI ++D+ + + + INGFLNEF+GSFVLFFGA+A T +FG + + + Sbjct: 120 AILGTFSTIDNVDDNSEKTRLGATINGFLNEFLGSFVLFFGAVAATNIFFGSQSITWMTN 17- 9 Query: 214 ------AGYDQTTAATQISPYVTGSLA---VAHIGIGFLVMVLVTSLGGPTGPALNPARD 26- 4 A + QI +G+ A +AH+ +GFLVM LV +LGGPTGP LNPARD Sbjct: 180 YLKGQGADVSSSDVMNQIWVQASGASASKMIAHLFLGFLVMGLVVALGGPTGPGLNPARD 23- 9 Query: 265 FGPRLLHHFLPKSVLGQAKGDSKWWYAWVPVVAPILAAIVAVAAFKYLYI 314 FGPRL+H LPKSVLG+AKG SKWWYAWVPV+APILA++ AVA FK +Y+ Sbjct: 240 FGPRLVHSLLPKSVLGEAKGSSKWWYAWVPVLAPILASLAAVALFKMIYL 289 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-04895 Identities = 240/281 (85%), Positives = 267/281 (94%) Query: 2 IEITWTVKYITEFIATAFLIILGNGAVANVDLKGTKGNNSGWIIIAIGYGLGVMMPALMF 61 +E+TWTVKYITEFIATAFLIILGNGAVANVDLKGTKG+NSGW++IA GYGLGVMMPALMF Sbjct: 34 MEMTWTVKYITEFIATAFLIILGNGAVANVDLKGTKGHNSGWLVIAFGYGLGVMMPALMF 93 Query: 62 GNVSGNHINPAFTLGLAFSGLFPWAHVGQYILAQILGAMFGQLVVVMVYQPYFVKTENPN 121- GNVSGNHINPAFT+GLA SGLFPWAHV QY++AQ+LGA+FGQLVVVMVY+PYF+KTENPN Sbjct: 94 GNVSGNHINPAFTVGLAVSGLFPWAHVLQYVVAQLLGAIFGQLVVVMVYKPYFMKTENPN 153- Query: 122 HVLGSFSTISALDDGQKSSRKAAYINGFLNEFVGSFVLFFGALALTKNYFGVELVGKLVQ 18- 1 HVLGSFSTIS+LD+GQK S KA+YINGFLNEFVGSFVLFFGALALTKNYFGVELVGKL++ Sbjct: 154 HVLGSFSTISSLDNGQKDSHKASYINGFLNEFVGSFVLFFGALALTKNYFGVELVGKLIE 21- 3 Query: 182 AGYDQTTAATRISPYVTGSLAVAHLGIGFLVMTLVASLGGPTGPALNPARDLGPRIVHRL 24- 1 AGYDQTTAAT+ISPYVTGSLAVAH+GIGFLVM LV SLGGPTGPALNPARD GPR++H Sbjct: 214 AGYDQTTAATQISPYVTGSLAVAHIGIGFLVMVLVTSLGGPTGPALNPARDFGPRLLHHF 27- 3 Query: 242 LPKQILGQAKEDSKWWYAWVPVLAPIVASILAVALFKLLYL 282 LPK +LGQAK DSKWWYAWVPV+API+A+I+AVA FK LY+ Sbjct: 274 LPKSVLGQAKGDSKWWYAWVPVVAPILAAIVAVAAFKYLYI 314 A related GBS gene <SEQ ID 8865> and protein <SEQ ID 8866> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04896 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 2.81 GvH: Signal Score (-7.5): -3.6 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 6 value: -8.65 threshold: 0.0 INTEGRAL Likelihood = -8.65 Transmembrane 261-277 (257-281) INTEGRAL Likelihood = -5.73 Transmembrane 201-217 (199-222) INTEGRAL Likelihood = -4.51 Transmembrane 92-108 (91-110) INTEGRAL Likelihood = -4.30 Transmembrane 44-60 (42-62) INTEGRAL Likelihood = -2.18 Transmembrane 15-31 (11-31) INTEGRAL Likelihood = -1.54 Transmembrane 150-166 (149-166) PERIPHERAL Likelihood = 2.92 72 modified ALOM score: 2.23 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4461 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00111## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1622 A DNA sequence (GBSx1717) was identified in S. agalactiae <SEQ ID 5007> which encodes the amino acid sequence <SEQ ID 5008>. Analysis of this protein sequence reveals the following: TABLE-US-04897 Possible site: 44 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.70 Transmembrane 266-282 (262-290) INTEGRAL Likelihood = -7.96 Transmembrane 25-41 (24-50) INTEGRAL Likelihood = -6.42 Transmembrane 110-126 (105-140) INTEGRAL Likelihood = -6.26 Transmembrane 194-210 (190-215) INTEGRAL Likelihood = -5.47 Transmembrane 290-306 (289-310) INTEGRAL Likelihood = -4.35 Transmembrane 128-144 (127-147) INTEGRAL Likelihood = -3.29 Transmembrane 157-173 (156-174) INTEGRAL Likelihood = -2.76 Transmembrane 221-237 (221-240) ----- Final Results ----- bacterial membrane --- Certainty = 0.4482 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related sequence was also identified in GAS <SEQ ID 9177> which encodes the amino acid sequence <SEQ ID 9178>. Analysis of this protein sequence reveals the following: TABLE-US-04898 Possible cleavage site: 21 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.77 Transmembrane 139-155 (133-161) INTEGRAL Likelihood = -8.28 Transmembrane 245-261 (240-269) INTEGRAL Likelihood = -7.48 Transmembrane 269-285 (263-289) INTEGRAL Likelihood = -7.06 Transmembrane 97-113 (83-125) INTEGRAL Likelihood = -6.10 Transmembrane 173-189 (169-194) INTEGRAL Likelihood = -1.44 Transmembrane 200-216 (200-217) ----- Final Results ----- bacterial membrane --- Certainty = 0.531 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04899 Identities = 225/301 (74%), Positives = 263/301 (86%) Query: 10 LTVSLFFCRLDIMNETLLLHGIQLILIIAMIITFYQIVRHIRSQKINPFKRFFTGLWIGF 69 - LT +FFC+L MNE L+L IQ +L+ AM+ F+ +V+H++ KINPFKRF+TG WIG Sbjct: 1 LTAKVFFCKLVFMNEMLILRLIQALLVSAMLFIFFMLVKHLKKNKINPFKRFWTGFWIGL 60 Query: 70 VTDALDTLGIGSFATTTTFFKLTKLVEDDRKIPATMTAAHVLPVLLQSLCFIFVVKVEAL 129- +TDALDTLGIGSFATTTT FKLTKLV DDR++P TMT AHVLPVL+QSLCFIFVVKVE L Sbjct: 61 LTDALDTLGIGSFATTTTCFKLTKLVTDDRQLPGTMTVAHVLPVLIQSLCFIFVVKVEVL 120- Query: 130 TLITMAGAAFIGAFVGAKMTKNWHAPTVQRILGTLLITAAIIMLYRMITNPGAGISDSVH 18- 9 TL+ MA AAFIGA+ G +TKNWHAPTVQRILG+LLI AAIIM+ R+I +PG +SD++H Sbjct: 121 TLLAMAAAAFIGAYFGTHITKNWHAPTVQRILGSLLIIAAIIMIIRIIYHPGEHLSDTIH 18- 0 Query: 190 GLHGIWLFVGIGFNFIIGVLMTMGLGNYAPELIFFSLMGLSPAVAMPVMMLDAAMIMTAS 24- 9 GLHGIWLFVGIGFNFI+GVLMTMGLGNYAPELIFFSLMGLSP VAMPVMMLDAAMIMTAS Sbjct: 181 GLHGIWLFVGIGFNFIVGVLMTMGLGNYAPELIFFSLMGLSPTVAMPVMMLDAAMIMTAS 24- 0 Query: 250 STQFIKSGRVNWNGFAGLVTGGILGVIVAVLFLTNLDLNSLKTLVVGIVLFTGAMLIRSSF 3- 10 S+QFIK+ RV+W+GFAG+V+GGI+GV++AV FLTNLD+NSLK LV+ IV FTG MLIRSSF Sbjct: 241 SSQFIKANRVSWDGFAGIVSGGIIGVLLAVFFLTNLDINSLKLLVIAIVFFTGGMLIRSSF 3- 01 A related GBS gene <SEQ ID 8867> and protein <SEQ ID 8868> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04900 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 2.32 GvH: Signal Score (-7.5): -5.59 Possible site: 44 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 8 value: -8.70 threshold: 0.0 INTEGRAL Likelihood = -8.70 Transmembrane 266-282 (262-290) INTEGRAL Likelihood = -7.96 Transmembrane 25-41 (24-50) INTEGRAL Likelihood = -6.42 Transmembrane 110-126 (105-140) INTEGRAL Likelihood = -6.26 Transmembrane 194-210 (190-215) INTEGRAL Likelihood = -5.47 Transmembrane 290-306 (289-310) INTEGRAL Likelihood = -4.35 Transmembrane 128-144 (127-147) INTEGRAL Likelihood = -3.29 Transmembrane 157-173 (156-174) INTEGRAL Likelihood = -2.76 Transmembrane 221-237 (221-240) PERIPHERAL Likelihood = 3.87 67 modified ALOM score: 2.24 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4482 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 5009> which encodes amino acid sequence <SEQ ID 5010>: TABLE-US-04901 Possible site: 33 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.77 Transmembrane 151-167 (145-173) INTEGRAL Likelihood = -9.13 Transmembrane 22-38 (15-42) INTEGRAL Likelihood = -8.28 Transmembrane 257-273 (252-281) INTEGRAL Likelihood = -7.48 Transmembrane 281-297 (275-301) INTEGRAL Likelihood = -7.06 Transmembrane 109-125 (95-137) INTEGRAL Likelihood = -6.10 Transmembrane 185-201 (181-206) INTEGRAL Likelihood = -1.44 Transmembrane 212-228 (212-229) INTEGRAL Likelihood = -0.27 Transmembrane 5-21 (5-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.5310 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS sequences follows: TABLE-US-04902 Score = 405 bits (1029), Expect = e-115 Identities = 198/301 (65%), Positives = 228/301 (74%) Query: 1 LTAKVFFCKLVFMNEMLILRLIQALLVSAMLFIFFMLVKHLKKNKINPFKRFWTGFWIGL 60 LT +FFC+L MNE L+L IQ +L+ AM+ F+ +V+H++ KINPFKRF+TG WIG Sbjct: 10 LTVSLFFCRLDIMNETLLLHGIQLILIIAMIITFYQIVRHIRSQKINPFKRFFTGLWIGF 69 Query: 61 LTDALDTLGIGSFATTTTCFKLTKLVTDDRQLPGTMTVAHVLPVLIQSLCFIFVVKVEVX 120- +TDALDTLGIGSFATTTT FKLTKLV DDR++P TMT AHVLPVL+QSLCFIFVVKVE Sbjct: 70 VTDALDTLGIGSFATTTTFFKLTKLVEDDRKIPATMTAAHVLPVLLQSLCFIFVVKVEAL 129- Query: 121 XXXXXXXXXFIGAYFGTHITKNWHAPTVQRILGSLLXXXXXXXXXXXXYHPGEHLSDTIH 18- 0 FIGA+ G +TKNWHAPTVQRILG+LL +PG +SD++H Sbjct: 130 TLITMAGAAFIGAFVGAMTKNWHAPTVQRILGTLLITAAIIMLYRMITNPGAGISDSVH 189- Query: 181 GLHGIWLFVGIGFNFIVGVLMTMGLGNYAPELIFFSLMGLSPTVAMPVMMLDAAMIMTAS 24- 0 GLHGIWLFVGIGFNFI+GVLMTMGLGNYAPELIFFSLMGLSP VAMPVMMLDAAMIMTAS Sbjct: 190 GLHGIWLFVGIGFNFIIGVLMTMGLGNYAPELIFFSLMGLSPAVAMPVMMLDAAMIMTAS 24- 9 Query: 241 SSQFIKANRVSWDXXXXXXXXXXXXXXXXXFFLTNLDINSLKLLVIAIVFFTGGMLIRSSF 3- 01 S+QFIK+ RV+W+ FLTNLD+NSLK LV+ IV FTG MLIRSSF Sbjct: 250 STQFIKSGRVNWNGFAGLVTGGILGVIVAVLFLTNLDLNSLKTLVVGIVLFTGAMLIRSSF 3- 10 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1623 A DNA sequence (GBSx1718) was identified in S. agalactiae <SEQ ID 5011> which encodes the amino acid sequence <SEQ ID 5012>. This protein is predicted to be C3-degrading proteinase. Analysis of this protein sequence reveals the following: TABLE-US-04903 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2851(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04904 >GP: AAD37110 GB: AF112358 C3-degrading proteinase [Streptococcus pneumoniae] Identities = 92/240 (38%), Positives = 142/240 (58%), Gaps = 11/240 (4%) Query: 12 PVLRVNNRDLNIAFYQESLGFKLISEENAIAVFSAWQNKEASFIIEESPTYRTRAVNGTK 71 - P L+ NNR LN FY E+LG K + EE+A E ++EE+P+ RTR V G K Sbjct: 11 PTLKANNRKLNETFYIETLGMKALLEESAFLSLGDQTGLE-KLVLEEAPSMRTRKVEGRK 69 Query: 72 KLAKIIVKSQDAKDIEKLLANGAQAIQVYQGQNGYAYETVSPEGDLFLLHAEDDLSQLVA 131- KLA++IVK ++ +IE +L+ ++Y+GQNGYA+E SPE DL L+HAEDD++ LV Sbjct: 70 KLARLIVKVENPLEIEGILSKTDSIHRLYKGQNGYAFEIFSPEDDLILIHAEDDIASLVE 129- Query: 132 I-ERPELEKKDDTTGLSNFAFQSISLNVPDAVKAEAFYDKVFAGKFPINLSFKEAQGQDL 19- 0 + E+PE + + LS F S+ L++P + E+F + + + +L F AQGQDL Sbjct: 130 VGEKPEFQTDLASISLSKFEI-SMELHLPTDI--ESFLE---SSEIGASLDFIPAQGQDL 18- 3 Query: 191 QIAPNETWDIEILECCVNEDTNLNDLKSTFESLGLDVYLDSKEKILVISDTSNIEIWISK 25- 0 + TWD+ +L+ VNE ++ L+ FES + ++ EK + D +N+E+W + Sbjct: 184 TVDNTVTWDLSMLKFLVNE-LDIASLRQKFES--TEYFIPKSEKFFLGKDRNNVELWFEE 24- 0 A related DNA sequence was identified in S. pyogenes <SEQ ID 5013> which encodes the amino acid sequence <SEQ ID 5014>. Analysis of this protein sequence reveals the following: TABLE-US-04905 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3267(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04906 Identities = 130/250 (52%), Positives = 177/250 (70%) Query: 1 MTLFHSLTFKHPVLRVNNRDLNIAFYQESLGFKLISEENAIAVFSAWQNKEASFIIEESP 60 MTL ++TFK PVLRVN+RDLNIAFYQ +LG +L+SEENAIA+FS+W + F+IEESP Sbjct: 1 MTLMENITFKTPVLRVNDRDLNIAFYQNNLGLRLVSEENAIAIFSSWGEGQECFVIEESP 60 Query: 61 TYRTRAVNGTKKLAKIIVKSQDAKDIEKLLANGAQAIQVYQGQNGYAYETVSPEGDLFLL 120- + RTRAV G KK+ I++K+ K+IE+LLA+GA +++GQNGYA+ET+SPEGD FLL Sbjct: 61 SVRTRAVEGPKKVNTIVIKTNQPKEIEQLLAHGAHYDALFKGQNGYAFETISPEGDRFLL 120- Query: 121 HAEDDLSQLVAIERPELEKKDDTTGLSNFAFQSISLNVPDAVKAEAFYDKVFAGKFPINL 18- 0 HAE D+ L + P LEK GL+ F F I LNV +++AFY +F+ + PI + Sbjct: 121 HAEQDIKHLQGTDLPSLEKDATFKGLTQFKFDIIVLNVISEERSKAFYRDLFSDQLPITM 18- 0 Query: 181 SFKEAQGQDLQIAPNETWDIEILECCVNEDTNLNDLKSTFESLGLDVYLDSKEKILVISD 24- 0 F + +G DL I P+ WD+EILE V++D ++ LK+T E G VY+D K K+LV+SD Sbjct: 181 DFIQEEGPDLAIDPHIAWDLEILEFQVSKDYDMKVLKATLEEDGHKVYIDKKHKVLVLSD 24- 0 Query: 241 TSNIEIWISK 250 S IE+W +K Sbjct: 241 PSQIEVWFTK 250 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1624 A DNA sequence (GBSx1719) was identified in S. agalactiae <SEQ ID 5015> which encodes the amino acid sequence <SEQ ID 5016>. Analysis of this protein sequence reveals the following: TABLE-US-04907 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2510(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < suec> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04908 >GP: CAC16441 GB: AL450165 putative esterase [Streptomyces coelicolor] Identities = 89/323 (27%), Positives = 143/323 (43%), Gaps = 51/323 (15%) Query: 10 NTVLELIKEQIKDNLYHGASLAIY-ENGEWHEHYLGT-------IDGNEKVKAGLVYDLA 61 - +T+ EL+ E + + GA+ ++ G + GT +DG++ V+DLA Sbjct: 2 STLAELLAEGREQRICSGAAWSVGGPQGPLDRGWTGTRCWDGPPLDGDD------VWDLA 55 Query: 62 SVSKVVGVGTLLAKLVYQGTIDIDKPLRYYYPTFH---HQTLTVRQLATHSSCIDPFIP- 117- SV+K + G ++ LV +G + +D + Y P + LTVRQL H+SGI +P Sbjct: 56 SVTKPIA-GLVVMALVERGALGLDDTVGGYLPDYRGGDKAELTVRQLLAHTSGIPGQVPL 114- Query: 118 NRDQLNATQLKDAINHIKVLEDKSFK--YTDINFLLLGFMLEEVLGDSLDKLFKRYIFTP 17- 5 RD L +A+ + + + Y+ F++LG + E G+ L+ L +R + P Sbjct: 115 YRDHPTRAALLEAVRLLPLTAQPGTRVQYSSQGFIVLGLIAEAAAGEPLEALVERLVCAP 17- 4 Query: 176 FQMKETSFGPRVEAVPTVVGIND---------GIVHDPKAKVLGKHTGSAGLFSTIDDLQ 22- 6 +++T F P V D G VHD A VLG G AGLFST+ D++ Sbjct: 175 LGLRDTVFRPDAGRRARAVATEDCPWRGRRVVGEVHDENAVVLGGVGGHAGLFSTLADME 23- 4 Query: 227 RFSIHYL--------KDDFA-KPLWNNYSLSKSRSLAWD------------IDKDWINHT 26- 5 R + FA + L+ R+LAW + HT Sbjct: 235 RLGAALAAGGRGLLRPETFALMTAAHTDGLALRRALAWQGRDPVGSPAGEVFGPESYGHT 29- 4 Query: 266 GYTGPFIALNYQKQAAAIFLTNR 288 G+TG + ++ + A+ LTNR Sbjct: 295 GFTGTSLWVDPATRRYAVLLTNR 317 A related DNA sequence was identified in S. pyogenes <SEQ ID 3885> which encodes the amino acid sequence <SEQ ID 3886>. Analysis of this protein sequence reveals the following: TABLE-US-04909 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.33 Transmembrane 57-73 (57-74) ----- Final Results ----- bacterial membrane --- Certainty = 0.1532(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04910 Identities = 174/302 (57%), Positives = 229/302 (75%), Gaps = 1/302 (0%) Query: 9 TNTVLELIKEQIKDNLYHGASLAIYENGEWHEHYLGTIDGNEKVKAGLVYDLASVSKVVG 68 T V++ I+ + +Y GASLA++++G W E+++GTIDG V A LVYDLASVSKVVG Sbjct: 6 TLAVIKCIENHLHKKVYKGASLALFQSGRWQEYHIGTIDGRRPVDANLVYDLASVSKVVG 65 Query: 69 VGTLLAKLVYQGTIDIDKPLRYYYPTFHHQTLTVRQLATHSSGIDPFIPNRDQLNATQLK 128- V T+ L+ GT+ +D PL+ YYP+ T+T+RQL TH+SG+DP+IPNRD LNA QL+ Sbjct: 66 VATICNILLNNGTLALDDPLKVYYPSIADATVTIRQLLTHTSGLDPYIPNRDVLNAQQLR 125- Query: 129 DAINHIKVLEDKSFKYTDINFLLLGFMLEEVLGDSLDKLFKRYIFTPFQMKETSFGPRVE 18- 8 A+NH+ E+K+F YTD+NFLLLGFMLEE+ +SLD++F + IFTPF M TSFGPR E Sbjct: 126 KALNHLTQKENKNFYYTDVNFLLLGFMLEELFSESLDQIFDKTIFTPFGMYHTSFGPRPE 18- 5 Query: 189 AVPTVVGINDGIVHDPKAKVLGKHTGSAGLFSTIDDLQRFSIHYLKDDFAKPLWNNYSLS 24- 8 AVPT+ G++DG VHDPKAK+L KH+GSAGLFST+ DL+ FS HYL D F+ LW NYS Sbjct: 186 AVPTLKGVSDGEVHDPKAKILKKHSGSAGLFSTLADLESFSNHYLNDPFSDCLWRNYSQQ 24- 5 Query: 249 K-SRSLAWDIDKDWINHTGYTGPFIALNYQKQAAAIFLTNRTFSYDDRPLWIKKRRHVQE 30- 7 RSL W++D DWI+HTGYTGPF+ LN ++Q AAIFLTNRT+ DD+ W+K+R+ + Sbjct: 246 TIERSLGWNLDGDWISHTGYTGPFLMLNKKEQTAAIFLTNRTYDEDDKSKWLKERQLLYN 30- 5 Query: 308 AI 309 A+ Sbjct: 306 AL 307 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1625 A DNA sequence (GBSx1720) was identified in S. agalactiae <SEQ ID 5017> which encodes the amino acid sequence <SEQ ID 5018>. Analysis of this protein sequence reveals the following: TABLE-US-04911 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0935(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04912 >GP: BAA25177 GB: D21804 FMN-binding protein [Desulfovibrio vulgaris] Identities = 53/124 (42%), Positives = 76/124 (60%), Gaps = 2/124 (1%) Query: 1 MLNHKFLQVLKYEGVVSITSWIELAPHVTNTWNSYLTITDDQRILAPAAGMTHLENDLNN 60 ML F +VLK EGVV+I + E PH+ NTWNSYL + D RI+ P GM E ++ Sbjct: 1 MLPGTFFEVLKNEGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVAR 60 Query: 61 NSKIIMTLGSREVEGRDGYQGTGFRIEGTAKLLEAGSDFEIVKEKYPFLRKVLEVTPINV 120- + +++MTLGSR+V GR+G GTGF I G+A G +FE + ++ + R L +T ++ Sbjct: 61 DERVLMTLGSRKVAGRNG-PGTGFLIRGSAAFRTDGPEFEAI-ARFKWARAALVITVVSA 118- Query: 121 IQLL 124 Q L Sbjct: 119 EQTL 122 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1626 A DNA sequence (GBSx1721) was identified in S. agalactiae <SEQ ID 5019> which encodes the amino acid sequence <SEQ ID 5020>. Analysis of this protein sequence reveals the following:

TABLE-US-04913 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3799(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1627 A DNA sequence (GBSx1722) was identified in S. agalactiae <SEQ ID 5021> which encodes the amino acid sequence <SEQ ID 5022>. Analysis of this protein sequence reveals the following: TABLE-US-04914 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3175(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10123> which encodes amino acid sequence <SEQ ID 10124> was also identified. The protein has homology to a pyruvate formate-lyase from S. mutans: TABLE-US-04915 >GP: BAA09085 GB: D50491 Pyruvate formate-lyase [Streptococcus mutans] Identities = 709/770 (92%), Positives = 750/770 (97%) Query: 7 MATVKTNTDIFEQAWEGFKGVDWKEKASIARFVQANYAPYDGDESFLAGATERSLHIKKV 66 MATVKTNTD+FE+AWEGFKG DWK++ASI+RFVQ NY PYDG ESFLAG TERSLHIKKV Sbjct: 1 MATVKTNTDVFEKAWEGFKGTDWKDRASISRFVQDNYTPYDGGESFLAGPTERSLHIKKV 60 Query: 67 IEETKAHYEETRFPMDTRVASISELPAGFIDKDNELIFGIQNDELFKLNFMPKGGIRMAE 126- +EETKAHYEETRFPMDTR+ SI+++PAG+IDK+NELIFGIQNDELFKLNFMPKGGIRMAE Sbjct: 61 VEETKAHYEETRFPMDTRITSIADIPAGYIDKENELIFGIQNDELFKLNFMPKGGIRMAE 120- Query: 127 TTLKENGYEPDPAVHEIFTKYATTVNDGIFRAYTSNIRRARHAHTVTGLPDAYSRGRIIG 18- 6 T LKE+GYEPDPAVHEIFTKYATTVNDGIFRAYTSNIRRARHAHTVTGLPDAYSRGRIIG Sbjct: 121 TALKEHGYEPDPAVHEIFTKYATTVNDGIFRAYTSNIRRARHAHTVTGLPDAYSRGRIIG 18- 0 Query: 187 VYARLAVYGADYLMQEKVNDWNALNDIDEESIRLREEINLQYQALGEVVKLGDLYGVDVR 24- 6 VYARLA+YGADYLMQEKVNDWN++ +IDEESIRLREEINLQYQALGEVV+LGDLYG+DVR Sbjct: 181 VYARLALYGADYLMQEKVNDWNSIAEIDEESIRLREEINLQYQALGEVVRLGDLYGLDVR 24- 0 Query: 247 KPAMNTKEAIQWVNIAFMAVCRVINGAATSLGRVPIVLDIFAERDLARGTFTESEIQEFV 30- 6 KPAMN KEAIQW+NIAFMAVCRVINGAATSLGRVPIVLDIFAERDLARGTFTESEIQEFV Sbjct: 241 KPAMNVKEAIQWINIAFMAVCRVINGAATSLGRVPIVLDIFAERDLARGTFTESEIQEFV 30- 0 Query: 307 DDFVLKLRTVKFARTKAYDALYSGDPTFITTSMAGMGADGRHRVTKMDYRFLNTLDNIGN 36- 6 DDFV+KLRTVKFARTKAYD LYSGDPTFITTSMAGMGADGRHRVTKMDYRFLNTLDNIGN Sbjct: 301 DDFVMKLRTVKFARTKAYDELYSGDPTFITTSMAGMGADGRHRVTKMDYRFLNTLDNIGN 36- 0 Query: 367 SPEPNLTVLWSDQLPYAFRRYCMSMSHKHSSIQYEGVSTMAKEGYGEMSCISCCVSPLDP 42- 6 +PEPNLTVLWS +LPY+FR YCMSMSHKHSSIQYEGV+TMAKEGYGEMSCISCCVSPLDP Sbjct: 361 APEPNLTVLWSSKLPYSFRHYCMSMSHKHSSIQYEGVTTMAKEGYGEMSCISCCVSPLDP 42- 0 Query: 427 ENEDKRHNLQYFGARVNVMKALLTGLNGGYDDVHKDYKVFDIDPIRDEVLNFDTVKANFE 48- 6 ENED+RHNLQYFGARVNV+KALLTGLNGGYDDVHKDYKVFD++PIRDEVL+F+TVKANFE Sbjct: 421 ENEDRRHNLQYFGARVNVLKALLTGLNGGYDDVHKDYKVFDVEPIRDEVLDFETVKANFE 48- 0 Query: 487 KSLDWLTDTYVDAMNIIHYMTDKYNYEAVQMAFLPSHVRANMGFGICGFANTVDSLSAIK 54- 6 K+LDWLTDTYVDAMNIIHYMTDKYNYEAVQMAFLP+ V+ANMGFGICGF+NTVDSLSAIK Sbjct: 481 KALDWLTDTYVDAMNIIHYMTDKYNYEAVQMAFLPTRVKANMGFGICGFSNTVDSLSAIK 54- 0 Query: 547 YATVKPIRDEDGYIYDYETVGDFPRYGEDDDRVDSIAEWLLEAFHGRLAKHKLYKDAEAT 60- 6 YATVKPIRDEDGYIYDYETVG+FPRYGEDDDRVDSIAEWLLEAFH RLA+HKLYKD+EAT Sbjct: 541 YATVKPIRDEDGYIYDYETVGNFPRYGEDDDRVDSIAEWLLEAFHTRLARHKLYKDSEAT 60- 0 Query: 607 VSLLTITSNVAYSKQTGNSPVHKGVYLNEDGSVNLSKVEFFSPGANPSNKAKGGWLQNLN 66- 6 VSLLTITSNVAYSKQTGNSPVHKGVYLNEDGSVNLSKVEFFSPGANPSNKA GGWLQNLN Sbjct: 601 VSLLTITSNVAYSKQTGNSPVHKGVYLNEDGSVNLSKVEFFSPGANPSNKASGGWLQNLN 66- 0 Query: 667 SLSKLDFAHANDGISLTTQVSPRALGKTFDEQVDNLVTVLDGYFENGGQHVNLNVMDLKD 72- 6 SL KLDFAHANDGISLTTQVSP+ALGKTFDEQV NLVT+LDGYFE GGQHVNLNVMDLKD Sbjct: 661 SLKKLDFAHANDGISLTTQVSPKALGKTFDEQVANLVTILDGYFEGGGQHVNLNVMDLKD 72- 0 Query: 727 VYDKIMNGEDVIVRISGYCVNTKYLTPEQKTELTQRVFHEVLSMDDALTN 776 VYDKIMNGEDVIVRISGYCVNTKYLT EQKTELTQRVFHEVLSMDDA T+ Sbjct: 721 VYDKIMNGEDVIVRISGYCVNTKYLTKEQKTELTQRVFHEVLSMDDAATD 770 A related DNA sequence was identified in S. pyogenes <SEQ ID 5023> which encodes the amino acid sequence <SEQ ID 5024>. Analysis of this protein sequence reveals the following: TABLE-US-04916 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3184(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04917 Identities = 701/773 (90%), Positives = 742/773 (95%), Gaps = 1/773 (0%) Query: 2 FKEKTMATVKTNTDIFEQAWEGFKGVDWKEKASIARFVQANYAPYDGDESFLAGATERSL 61 FKEK MATVKTNTD+FE+AWEGFKG DWKEKAS++RFVQANY PYDGDESFLAGATERSL Sbjct: 5 FKEKFMATVKTNTDVFEKAWEGFKGTDWKEKASVSRFVQANYTPYDGDESFLAGATERSL 64 Query: 62 HIKKVIEETKAHYEETRFPMDTRVASISELPAGFIDKDNELIFGIQNDELFKLNFMPKGG 121- HIKKVIEETKAHYE TRFP DTR SI+++PAGFIDK+NELI+GIQNDELFKLNFMPKGG Sbjct: 65 HIKKVIEETKAHYEATRFPYDTRPTSIADIPAGFIDKENELIYGIQNDELFKLNFMPKGG 124- Query: 122 IRMAETTLKENGYEPDPAVHEIFTKYATTVNDGIFRAYTSNIRRARHAHTVTGLPDAYSR 18- 1 IRMAETTLKENGYEPDPAVHEIFTKY TTVNDGIFRAYTSNIRRARHAHTVTGLPDAYSR Sbjct: 125 IRMAETTLKENGYEPDPAVHEIFTKYVTTVNDGIFRAYTSNIRRARHAHTVTGLPDAYSR 18- 4 Query: 182 GRIIGVYARLAVYGADYLMQEKVNDWNALNDIDEESIRLREEINLQYQALGEVVKLGDLY 24- 1 GRIIGVYARLA+YGADYLMQEKVNDWNA+ +IDEESIRLREE+NLQYQALGEVVKLGDLY Sbjct: 185 GRIIGVYARLALYGADYLMQEKVNDWNAITEIDEESIRLREEVNLQYQALGEVVKLGDLY 24- 4 Query: 242 GVDVRKPAMNTKEAIQWVNIAFMAVCRVINGAATSLGRVPIVLDIFAERDLARGTFTESE 30- 1 GVDVR+PA N KEAIQWVNIAFMAVCRVINGAATSLGRVPIVLDIFAERDLARGTFTESE Sbjct: 245 GVDVRRPAQNVKEAIQWVNIAFMAVCRVINGAATSLGRVPIVLDIFAERDLARGTFTESE 30- 4 Query: 302 IQEFVDDFVLKLRTVKFARTKAYDALYSGDPTFITTSMAGMGADGRHRVTKMDYRFLNTL 36- 1 IQEFVDDFVLKLRTVKF RTKAYDALYSGDPTFITTSMAGMG DGRHRVTKMDYRFLNTL Sbjct: 305 IQEFVDDFVLKLRTVKFGRTKAYDALYSGDPTFITTSMAGMGNDGRHRVTKMDYRFLNTL 36- 4 Query: 362 DNIGNSPEPNLTVLWSDQLPYAFRRYCMSMSHKHSSIQYEGVSTMAKEGYGEMSCISCCV 42- 1 DNIGNSPEPNLTVLW+DQLP FRRYCM MSHKHSSIQYEGV+TMAKEGYGEMSCISCCV Sbjct: 365 DNIGNSPEPNLTVLWTDQLPETFRRYCMKMSHKHSSIQYEGVTTMAKEGYGEMSCISCCV 42- 4 Query: 422 SPLDPENEDKRHNLQYFGARVNVMKALLTGLNGGYDDVHKDYKVFD-IDPIRDEVLNFDT 48- 0 SPLDPENE++RHN+QYFGARVNV+KALLTGLNGGYDDVH+DYKVF+ ++PI EVL +D Sbjct: 425 SPLDPENEEQRHNIQYFGARVNVLKALLTGLNGGYDDVHRDYKVFNVVEPITSEVLEYDE 48- 4 Query: 481 VKANFEKSLDWLTDTYVDAMNIIHYMTDKYNYEAVQMAFLPSHVRANMGFGICGFANTVD 54- 0 V ANFEKSLDWLTDTYVDA+NIIHYMTDKYNYEAVQMAFLP+H RANMGFGICGFANTVD Sbjct: 485 VMANFEKSLDWLTDTYVDALNIIHYMTDKYNYEAVQMAFLPTHQRANMGFGICGFANTVD 54- 4 Query: 541 SLSAIKYATVKPIRDEDGYIYDYETVGDFPRYGEDDDRVDSIAEWLLEAFHGRLAKHKLY 60- 0 +LSAIKYATVK IRDE+GYIYDYE GDFPRYGEDDDRVD IA+WL+EA+H RLA HKLY Sbjct: 545 TLSAIKYATVKTIRDENGYIYDYEVTGDFPRYGEDDDRVDDIAKWLMEAYHTRLASHKLY 60- 4 Query: 601 KDAEATVSLLTITSNVAYSKQTGNSPVHKGVYLNEDGSVNLSKVEFFSPGANPSNKAKGG 66- 0 K+AEA+VSLLTITSNVAYSKQTGNSPVH+GV+LNEDG+VN S+VEFFSPGANPSNKAKGG Sbjct: 605 KNAEASVSLLTITSNVAYSKQTGNSPVHRGVFLNEDGTVNTSQVEFFSPGANPSNKAKGG 66- 4 Query: 661 WLQNLNSLSKLDFAHANDGISLTTQVSPRALGKTFDEQVDNLVTVLDGYFENGGQHVNLN 72- 0 WLQNLNSL+KL+F+HANDGISLTTQVSPRALGKTFDEQVDNLVTVLDGYFENGGQHVNLN Sbjct: 665 WLQNLNSLAKLEFSHANDGISLTTQVSPRALGKTFDEQVDNLVTVLDGYFENGGQHVNLN 72- 4 Query: 721 VMDLKDVYDKIMNGEDVIVRISGYCVNTKYLTPEQKTELTQRVFHEVLSMDDA 773 VMDL DVYDKIMNGEDVIVRISGYCVNTKYLTPEQKTELTQRVFHEVLSMDDA Sbjct: 725 VMDLNDVYDKIMNGEDVIVRISGYCVNTKYLTPEQKTELTQRVFHEVLSMDDA 777 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1628 A DNA sequence (GBSx1723) was identified in S. agalactiae <SEQ ID 5025> which encodes the amino acid sequence <SEQ ID 5026>. This protein is predicted to be DNA-damage inducible protein P (dinP). Analysis of this protein sequence reveals the following: TABLE-US-04918 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10121> which encodes amino acid sequence <SEQ ID 10122> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04919 >GP: AAF95431 GB: AE004300 DNA-damage-inducible protein P [Vibrio cholerae] Identities = 136/349 (38%), Positives = 210/349 (59%), Gaps = 14/349 (4%) Query: 12 INDTSRKIIHIDMDAFFASVEERDNPSLKGKPVIIGSDPRKTGGRGVVSTCNYEARKFGV 71 - + D RKIIH+DMD FFA+VE RDNP+ + + +G ++ RGV+STCNY+ARKFGV Sbjct: 1 MQDRIRKIIHVDMDCFFAAVEMRDNPAYREIALAVGGHEKQ---RGVISTCNYQARKFGV 57 Query: 72 HSAMSSKEAYERCPQAIFISGNYQKYRQVGMEVRDIFKKYTDLVEPMSIDEAYLDVTENK 131- SAM + +A + CPQ + G Y+ V +++ IF++YT L+EP+S+DEAYLDV+E+ Sbjct: 58 RSAMPTAQALKLCPQLHVVPGRMSVYKSVSQQIQTIFQRYTSLIEPLSLDEAYLDVSEST 117- Query: 132 MGIKSAVKLAKMIQYDIWNDVHLTCSAGISYNKFLAKLASDFEKPKGLTLILPDQAQDFL 19- 1 SA +A+ I+ DIW +++LT SAG++ KFLAK+ASD KP GL ++ PD+ Q+ + Sbjct: 118 AYQGSATLIAQAIRRDIWQELNLTASAGVAPIKFLAKVASDLNKPDGLYVVTPDKVQEMV 17- 7 Query: 192 KPLPIEKFHGVGKRSVEKLHALGVYTGEDLLSLSEISLIDMFGRFGYDLYRKARGINASP 25- 1 LP+EK GVGK ++EKLH G+Y G D+ L+ FGR G L++K+ GI+ Sbjct: 178 DSLPLEKIPGVGKVALEKLHQAGLYVGADVRRADYRKLLHQFGRLGASLWKKSHGIDERE 23- 7 Query: 252 VKPDRVRKSIGSEKTYGKLLYNEADIKAEISKNVQRVVASLEKNKKVGKTIV---LKVRY 30- 8 V +R RKS+G E T+ + + + I + + + + + I+ +KV++ Sbjct: 238 VVTERERKSVGVEYTFSQNISTFQECWQVIEQKLYPELDARLSRAHPQRGIIKQGIKVKF 29- 7 Query: 309 ADFETLTKRMTLEEYTQDF--QIIDQVAKAIFDTLEESVFGIRLLGVTV 355 ADF+ T D+ ++++QV + IRLLG++V Sbjct: 298 ADFQQTTIEHVHPALELDYFHELLEQV------LTRQQGREIRLLGLSV 340 A related DNA sequence was identified in S. pyogenes <SEQ ID 5027> which encodes the amino acid sequence <SEQ ID 5028>. Analysis of this protein sequence reveals the following: TABLE-US-04920 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1921(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04921 Identities = 276/363 (76%), Positives = 323/363 (88%) Query: 6 MLIFPLINDTSRKIIHIDMDAFFASVEERDNPSLKGKPVIIGSDPRKTGGRGVVSTCNYE 65 MLIFPLINDTSRKIIHIDMDAFFA+VEERDNP+LKGKPV+IG DPR+TGGRGVVSTCNYE Sbjct: 1 MLIFPLINDTSRKIIHIDMDAFFAAVEERDNPALKGKPVVIGKDPRETGGRGVVSTCNYE 60 Query: 66 ARKFGVHSAMSSKEAYERCPQAIFISGNYQKYRQVGMEVRDIFKKYTDLVEPMSIDEAYL 125- ARK+G+HSAMSSKEAYERCP+AIFISGNY+KYR VG ++R IFK+YTD+VEPMSIDEAYL Sbjct: 61 ARKYGIHSAMSSKEAYERCPKAIFISGNYEKYRTVGDQIRRIFKRYTDVVEPMSIDEAYL 120- Query: 126 DVTENKMGIKSAVKLAKMIQYDIWNDVHLTCSAGISYNKFLAKLASDFEKPKGLTLILPD 18- 5 DVT+NK+GIKSAVK+AK+IQ+DIW +V LTCSAG+SYNKFLAKLASDFEKP GLTL+L + Sbjct: 121 DVTDNKLGIKSAVKIAKLIQHDIWKEVGLTCSAGVSYNKFLAKLASDFEKPHGLTLVLKE 18- 0 Query: 186 QAQDFLKPLPIEKFHGVGKRSVEKLHALGVYTGEDLLSLSEISLIDMFGRFGYDLYRKAR 24- 5 A FL LPIEKFHGVGK+SV+KLH +G+YTG+DLL++ E++LID FGRFG+DLYRKAR Sbjct: 181 DALCFLAKLPIEKFHGVGKKSVKKLHDMGIYTGQDLLAVPEMTLIDHFGRFGFDLYRKAR 24- 0 Query: 246 GINASPVKPDRVRKSIGSEKTYGKLLYNEADIKAEISKNVQRVVASLEKNKKVGKTIVLK 30- 5 GI+ SPVK DR+RKSIGSE+TY KLLY E DIKAEISKNV+RV A L+ +KK+GKTIVLK Sbjct: 241 GISNSPVKYDRIRKSIGSERTYAKLLYQETDIKAEISKNVKRVAALLQDHKKLGKTIVLK 30- 0 Query: 306 VRYADFETLTKRMTLEEYTQDFQIIDQVAKAIFDTLEESVFGIRLLGVTVTTLENEHEAI 36- 5 VRYADF TLTKR+TL E T++ I+QVA IFD+L E+ GIRLLGVT+T LE++ I Sbjct: 301 VRYADFTTLTKRVTLPELTRNAAQIEQVAGDIFDSLSENPAGIRLLGVTMTNLEDKVADI 36- 0 Query: 366 YLD 368 LD Sbjct: 361 SLD 363 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1629 A DNA sequence (GBSx1724) was identified in S. agalactiae <SEQ ID 5029> which encodes the amino acid sequence <SEQ ID 5030>. Analysis of this protein sequence reveals the following: TABLE-US-04922 Possible site: 41 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.11 Transmembrane 70-86 (58-92) INTEGRAL Likelihood = -5.20 Transmembrane 105-121 (100-123) INTEGRAL Likelihood = -4.25 Transmembrane 126-142 (123-144) INTEGRAL Likelihood = -2.71 Transmembrane 18-34 (18-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.6243(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 5031> which encodes the amino acid TABLE-US-04923 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.00 Transmembrane 69-85 (62-93) INTEGRAL Likelihood = -6.85 Transmembrane 16-32 (11-37) INTEGRAL Likelihood = -4.30 Transmembrane 99-115 (96-121) INTEGRAL Likelihood = -3.66 Transmembrane 126-142 (121-143) ----- Final Results ----- bacterial membrane --- Certainty = 0.6201(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-04924 Identities = 57/155 (36%), Positives = 96/155 (61%), Gaps = 5/155 (3%) Query: 1 MVSYEKVRRSLRTATITIIVLNSLSLVFRLFTGISVQLAKTEI-NKGNTGNLPKEHIEAV 59 M+SYEKVR++L+T+TI II+LN L +V L + ++++ N+ L E + + Sbjct: 1 MISYEKVRQALKTSTIAIIILNGLGVVLSLMGFAGIFYLQSQLKNEAFRAQLTTEQLAQL 60 Query: 60 LSATTPFMLFVTALIVLVNIAIVIFCIKNLRAIKRNQTVNYLPYYLGFAITVGLVILGFL 119- S+ TPFM+F++ L VL IAI++FC +NL +K+ TV+Y+PY LG ++V ++ F Sbjct: 61 QSSMTPFMIFLSVLNVLAIIAIIVFCAQNLSKLKQGLTVSYIPYILGLILSVIGLVNQFT 120- Query: 120 TTKAPWAIAINIVFQAIFGLLYFHAYQKAQKLNER 154 TT + + ++ A++G A+ KA+ LNE+ Sbjct: 121 TTMSMVGTILILIQAALYGF----AFYKAKTLNEK 151 SEQ ID 5030 (GBS227) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 119 (lane 5; MW 21.2 kDa). GBS227-His was purified as shown in FIG. 227, lane 8-9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1630 A DNA sequence (GBSx1725) was identified in S. agalactiae <SEQ ID 5033> which encodes the amino acid sequence <SEQ ID 5034>. Analysis of this protein sequence reveals the following: TABLE-US-04925 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1224(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04926 >GP:CAB14706 GB:Z99118 similar to conjugation transfer protein [Bacillus subtilis] Identities = 328/754 (43%), Positives = 484/754 (63%), Gaps = 25/754 (3%) Query: 2 EVFFTGTIERIIFENASNFFKILLLEIEDTDSDFDDVEVIITGTMADVIEGEEYTFWGTL 61 E + GT+ +I+ N +N + +L +++ +T +D V +TG + E E YTF+G + Sbjct: 13 EPYLKGTVNTVIYHNDTNLYTVLKVKVTETSEAIEDKAVSVTGYFPALQEEETYTFYGKI 72 Query: 62 TQHPKYGEQLQSVRYERAKPTSG-GLVKYFSSEQFKGIGKKTAQRIVELYGDNTIDKILE 120- HPK+G Q Q+ +++ PT+ G+++Y SS+ F+GIGKKTA+ IV+ GD+ I+KIL Sbjct: 73 VTHPKFGLQFQAEHFKKEIPTTKEGIIQYLSSDLFEGIGKKTAEEIVKKLGDSAINKILA 132- Query: 121 SPEQLSTISGLSKINREAFIAKLKLNYGTEQVLAKLAEYGLSNRAAIQIFDHYKEESLEV 18- 0 L + LSK + L+ + G EQ++ L ++G + +++I+ Y+ E+LE Sbjct: 133 DASVLYDVPRLSKKKADTLAGALQRHQGLEQIMISLNQFGFGPQLSMKIYQAYESETLEK 19- 2 Query: 181 INENPYQLVEDIQGIGFKIADQLAEQVGIESDSPKRFRAAIIHTLVESSMEQGDTYIEAR 24- 0 I ENPYQLV+D++GIGF AD+L ++G+ + P+R +AAI++TL + + +G TYIE Sbjct: 193 IQENPYQLVKDVEGIGFGKADELGSRMGLSGNHPERVKAAILYTLETTCLSEGHTYIETE 25- 2 Query: 241 TLLEKTITLLEEA-----RQIELDPS---IVAKELTNLIAEDKVQHIGTKIFSNTLFFAE 29- 2 L+ T +LL ++ R E+D + I E +++ ED + + +LF+AE Sbjct: 253 QLIIDTQSLLNQSAREGQRITEMDAANAIIALGENKDIVIEDG------RCYFPSLFYAE 30- 6 Query: 293 EGIKKNLQRILNQP-LDKQLNHKDIDREIRDIQKSLNIHYDNIQEKAIREALLSKVFILT 35- 1 + + K ++ I +Q + Q + + ++++ +++ Y Q++AI++AL S + +LT Sbjct: 307 QNVAKRVKHIASQTEYENQFPESEFLLALGELEERMDVQYAPSQKEAIQKALSSFMLLLT 36- 6 Query: 352 GGPGTGKTTVINGIIEAYSELHHIDLN----KND--IPIVLAAPTGRAARRMNELTGLPS 40- 5 GGPGTGKTTVI GI+E Y ELH + L+ K D PIVLAAPTGRAA+RM+E TGLP+ Sbjct: 367 GGPGTGKTTVIRGIVELYGELHGVSLDPSAYKKDEAFPIVLAAPTGRAAKRMSESTGLPA 42- 6 Query: 406 ATIHRHLGLNGDSDYQSLDDY-LDCSLIIIDEFSMVDTWLAHQLFDALDSHTQVIIVGDS 46- 4 TIHR LG NG + +D ++ L+IIDE SM+D WLAN LF A+ H Q+IIVGD Sbjct: 427 VTIHRLLGWNGAEGFTHTEDQPIEGKLLIIDEASMLDIWLANHLFKAIPDHIQIIIVGDE 48- 6 Query: 465 DQLPSVGPGQVLADLLNINALPHVKLEKIFRQSEESTIVTLANQMRQGFLPEDFTAKKAD 52- 4 DQLPSVGPGQVL DLL +P V+L I+RQ+E S+IV LA+QM+ G LP + TA D Sbjct: 487 DQLPSVGPGQVLRDLLASQVIPTVRLTDIYRQAEGSSIVELAHQMKNGLLPNNLTAPTKD 54- 6 Query: 525 RSYFEASANIIPNMISKIVQSALKSGIEAHEIQILAPMYRGQAGINNLNLIMQNLLNPLK 58- 4 RS+ + I ++ K+V +ALK G A +IQ+LAPMYRG+AGIN LN+++Q++LNP K Sbjct: 547 RSFIRCGGSQIKEVVEKVVANALKKGYTAKDIQVLAPMYRGKAGINELNVMLQDILNPPK 60- 6 Query: 585 D-NNQFTFNDINFRIGDKVLHLVNDTELNVFNGDIGYITDLIPAKYTESKQDEIYMTFDG 64- 3 + + F D+ +R GDK+L LVN E NVFNGDIG IT + AK K+D ++FDG Sbjct: 607 EKRRELKFCDVVYRTGDKILQLVNQPENNVFNGDIGEITSIFYAKENTEKEDMAVVSFDG 66- 6 Query: 644 QEVIYQRKEWLKITLAYAMSIHKSQGSEFQVVILPITRQSGRMLQRNLIYTAITRSKSKL 70- 3 E+ + +K++ + T AY SIHKSQGSEF +V+LP+ + RML+RNL+YTAITR+K L Sbjct: 667 NEMTFTKKDFNQFTHAYCCSIHKSQGSEFPIVVLPVVKGYYRMLRRNLLYTAITRAKKFL 72- 6 Query: 704 ILLGEIGAFDFAVKNEGAK-RNTYLIERFENKQE 736 IL GE A ++ VKN A R T L R + E Sbjct: 727 ILCGEEEALEWGVKNNDATVRQTSLKNRLSVQVE 760 A related DNA sequence was identified in S. pyogenes <SEQ ID 5035> which encodes the amino acid sequence <SEQ ID 5036>. Analysis of this protein sequence reveals the following:

TABLE-US-04927 Possible site: 47 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> RGD motif: 232-234 The protein has homology with the following sequences in the databases: TABLE-US-04928 >GP:CAB14706 GB:Z99118 similar to conjugation transfer protein [Bacillus subtilis] Identities = 318/769 (41%), Positives = 473/769 (61%), Gaps = 29/769 (3%) Query: 7 GTVDRIIFENQANFFKILLLAIEDTDSDIDDFEIIITGTMADIIEGDDYTFWGELTQHPK 66 GTV+ +I+ N N + +L + + +T I+D + +TG + E + YTF+G++ HPK Sbjct: 18 GTVNTVIYHNDTNLYTVLKVKVTETSEAIEDKAVSVTGYFPALQEEETYTFYGKIVTHPK 77 Query: 67 YGQQLKLSRYQKIKPSSS-GLVNYFSSDHFKGIGKKTAEKIIALYGHNTIDHILEDPSKL 125- +G Q + ++K P++ G++ Y SSD F+GIGKKTAE+I+ G + I+ IL D S L Sbjct: 78 FGLQFQAEHFKKEIPTTKEGIIQYLSSDLFEGIGKKTAEEIVKKLGDSAINKILADASVL 137- Query: 126 ETISGLSKANRQAFVAKLKLNYGTEQLIAGLVELGLSNRFALQAFEKYKEEALDLVKENP 18- 5 + LSK L+ + G EQ++ L + G + +++ ++ Y+ E L+ ++ENP Sbjct: 138 YDVPRLSKKKADTLAGALQRHQGLEQIMISLNQFGFGPQLSMKIYQAYESETLEKIQENP 19- 7 Query: 186 YQLVEDLQGFGFKMADALAENLGIESDSPKRFRAALLHCLLEESINRGDTYVQARQLLDF 24- 5 YQLV+D++G GF AD L +G+ + P+R +AA+L+ L ++ G TY++ QL+ Sbjct: 198 YQLVKDVEGIGFGKADELGSRMGLSGNHPERVKAAILYTLETTCLSEGHTYIETEQLIID 25- 7 Query: 246 AITLL-----EDARQVECDPAAVAEQLSE---LIIEGKIKNSDTKLFDASLYFAEEGIAN 29- 7 +LL E R E D A L E ++IE D + + SL++AE+ +A Sbjct: 258 TQSLLNQSAREGQRITEMDAANAIIALGENKDIVIE------DGRCYFPSLFYAEQNVAK 31- 1 Query: 298 NISRLLD-TPLSQSFSHDTIQTTIQAVQKDFAITYDQVQQEAITKALTSKVFLLTGGPGT 35- 6 + + T F + +++ + Y Q+EAI KAL+S + LLTGGPGT Sbjct: 312 RVKHIASQTEYENQFPESEFLLALGELEERMDVQYAPSQKEAIQKALSSPMLLLTGGPGT 37- 1 Query: 357 GKTTVIRGILQAYANLHQIDLD----KKD--LPILLAAPTGRAARRMNELTGLPSATIHR 41- 0 GKTTVIRGI++ Y LH + LD KKD PI+LAAPTGRAA+RM+E TGLP+ TIHR Sbjct: 372 GKTTVIRGIVELYGELHGVSLDPSAYKKDEAFPIVLAAPTGRAAKRMSESTGLPAVTIHR 43- 1 Query: 411 HLGLNGDNDYQAMEDY-LDCDLLIVDEFSMVDTWLANQLLGAINSTTQVIIVGDSDQLPS 46- 9 LG NG + ED ++ LLI+DE SM+D WLAN L AI Q+IIVGD DQLPS Sbjct: 432 LLGWNGAEGFTHTEDQPIEGKLLIIDEASMLDIWLANHLFKAIPDHIQIIIVGDEDQLPS 49- 1 Query: 470 VGPGQVLSDLLKVNSLPQIALQKIFRQSQESTIVNLADQMRRGILAADFRDKKADRSYFE 52- 9 VGPGQVL DLL +P + L I+RQ++ S+IV LA QM+ G+L + DRS+ Sbjct: 492 VGPGQVLRDLLASQVIPTVRLTDIYRQAEGSSIVELAHQMKNGLLPNNLTAPTKDRSFIR 55- 1 Query: 530 AQAAFIPDMIQKIVLSAIKSGIPAEEIQILAPMYKGQAGINHLNQLMQELLN-PLQGQTE 58- 8 + I ++++K+V +A+K G A++IQ+LAPMY+G+AGIN LN ++Q++LN P + + E Sbjct: 552 CGGSQIKEVVEKVVANALKKGYTAKDIQVLAPMYRGKAGINELNVMLQDILNPPKEKRRE 61- 1 Query: 589 FLFNDTHFRKGDKVLHLVNDAQLNVFNGDIGYITDLIPAKYTESKQDELILDFDGSEVTY 64- 8 F D +R GDK+L LVN + NVFNGDIG IT + AK K+D ++ FDG+E+T+ Sbjct: 612 LKFGDVVYRTGDKILQLVNQPENNVFNGDIGEITSIFYAKENTEKEDMAVVSFDGNEMTF 67- 1 Query: 649 PRNEWLKLTLAYAMSIHKSQGSEFQVVILPITRQSGRLLQRNVIYTAITRSKSKLILLGE 70- 8 + ++ + T AY SIHKSQGSEF +V+LP+ + R+L+RN++YTAITR+K LIL GE Sbjct: 672 TKKDFNQFTHAYCCSIHKSQGSEFPIVVLPVVKGYYRMLRRNLLYTAITRAKKFLILCGE 73- 1 Query: 709 YTAFEYAIK-HEGDKRQTYLIERFQEQSDLASSQPNQELKSKEQTSLFS 756 A E+ +K ++ RQT L R Q + + + EL++ ++ FS Sbjct: 732 EEALEWGVKNNDATVRQTSLKNRLSVQVE----EMDAELEALQKELPFS 776 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04929 Identities = 544/816 (66%), Positives = 665/816 (80%), Gaps = 10/816 (1%) Query: 1 MEVFFTGTIERIIFENASNFFKILLLEIEDTDSDFDDVEVIITGTMADVIEGEEYTFWGT 60 ME FTGT++RIIFEN +NFFKILLL IEDTDSD DD E+IITGTMAD+IEG++YTFWG Sbjct: 1 MEYVFTGTVDRIIFENQANFFKILLLAIEDTDSDIDDFEIIITGTMADIIEGDDYTFWGE 60 Query: 61 LTQHPKYGEQLQSVRYERAKPTSGGLVKYFSSEQFKGIGKKTAQRIVELYGDNTIDKILE 120- LTQHPKYG+QL+ RY++ KP+S GLV YFSS+ FKGIGKKTA++I+ LYG NTID ILE Sbjct: 61 LTQHPKYGQQLKLSRYQKIKPSSSGLVNYFSSDHFKGIGKKTAEKIIALYGHNTIDHILE 120- Query: 121 SPEQLSTISGLSKINREAFIAKLKLNYGTEQVLAKLAEYGLSNRAAIQIFDHYKEESLEV 18- 0 P +L TISGLSK NR+AF+AKLKLNYGTEQ++A L E GLSNR A+Q F+ YKEE+L++ Sbjct: 121 DPSKLETISGLSKANRQAFVAKLKLNYGTEQLIAGLVELGLSNRFALQAFEKYKEEALDL 18- 0 Query: 181 INENPYQLVEDIQGIGFKIADQLAEQVGIESDSPKRFRAAIIHTLVESSMEQGDTYIEAR 24- 0 + ENPYQLVED+QG GFK+AD LAE +GIESDSPKRFRAA++H L+E S+ +GDTY++AR Sbjct: 181 VKENPYQLVEDLQGFGFKMADALAENLGIESDSPKRFRAALLHCLLEESINRGDTYVQAR 24- 0 Query: 241 TLLEKTITLLEEARQIELDPSIVAKELTNLIAEDKVQHIGTKIFSNTLFFAEEGIKKNLQ 30- 0 LL+ ITLLE+ARQ+E DP+ VA++L+ LI E K+++ TK+F +L+FAEEGI N+ Sbjct: 241 QLLDFAITLLEDARQVECDPAAVAEQLSELIIEGKIKNSDTKLFDASLYFAEEGIANNIS 30- 0 Query: 301 RILNQPLDKQLNHKDIDREIRDIQKSLNIHYDNIQEKAIREALLSKVFILTGGPGTGKTT 36- 0 R+L+ PL + +H I I+ +QK I YD +Q++AI +AL SKVF+LTGGPGTGKTT Sbjct: 301 RLLDTPLSQSFSHDTIQTTIQAVQKDFAITYDQVQQEAITKALTSKVFLLTGGPGTGKTT 36- 0 Query: 361 VINGIIEAYSELHHIDLNKNDIPIVLAAPTGRAARRMNELTGLPSATIHRHLGLNGDSDY 42- 0 VI GI++AY+ LH IDL+K D+PI+LAAPTGRAARRMNELTGLPSATIHRHLGLNGD+DY Sbjct: 361 VIRGILQAYANLHQIDLDKKDLPILLAAPTGRAARRMNELTGLPSATIHRHLGLNGDNDY 42- 0 Query: 421 QSLDDYLDCSLIIIDEFSMVDTWLANQLFDALDSHTQVIIVGDSDQLPSVGPGQVLADLL 48- 0 Q+++DYLDC L+I+DEFSMVDTWLANQL A++S TQVIIVGDSDQLPSVGPGQVL+DLL Sbjct: 421 QAMEDYLDCDLLIVDEFSMVDTWLANQLLGAINSTTQVIIVGDSDQLPSVGPGQVLSDLL 48- 0 Query: 481 NINALPHVKLEKIFRQSEESTIVTLANQMRQGFLPEDFTAKKADRSYFEASANIIPNMIS 54- 0 +N+LP + L+KIFRQS+ESTIV LA+QMR+G L DF KKADRSYFEA A IP+MI Sbjct: 481 KVNSLPQIALQKIFRQSQESTIVNLADQMRRGILAADFRDKKADRSYFEAQAAFIPDMIQ 54- 0 Query: 541 KIVQSALKSGIEAHEIQILAPMYRGQAGINNLNLIMQNLLNPLKDNNQFTFNDINFRIGD 60- 0 KIV SA+KSGI A EIQILAPMY+GQAGIN+LN +MQ LLNPL+ +F FND +FR GD Sbjct: 541 KIVLSAIKSGIPAEEIQILAPMYKGQAGINHLNQLMQELLNPLQGQTEFLFNDTHFRKGD 60- 0 Query: 601 KVLHLVNDTELNVFNGDIGYITDLIPAKYTESKQDEIYMTFDGQEVIYQRKEWLKITLAY 66- 0 KVLHLVND +LNVFNGDIGYITDLIPAKYTESKQDE+ + FDG EV Y R EWLK+TLAY Sbjct: 601 KVLHLVNDAQLNVFNGDIGYITDLIPAKYTESKQDELILDFDGSEVTYPRNEWLKLTLAY 66- 0 Query: 661 AMSIHKSQGSEFQVVILPITRQSGRMLQRNLIYTAITRSKSKLILLGEIGAFDFAVKNEG 72- 0 AMSIHKSQGSEFQVVILPITRQSGR+LQRN+IYTAITRSKSKLILLGE AF++A+K+EG Sbjct: 661 AMSIHKSQGSEFQVVILPITRQSGRLLQRNVIYTAITRSKSKLILLGEYTAFEYAIKHEG 72- 0 Query: 721 AKRNTYLIERFENKQEIANSQKIEDSSIDQKI----------DNTIINTSIPKTATPIEQ 77- 0 KR TYLIERF+ + ++A+SQ ++ ++ D++ ++S + P E Sbjct: 721 DKRQTYLIERFQEQSDLASSQPNQELKSKEQTSLFSNTATLEDDSQKSSSQSTNSNPTEN 78- 0 Query: 771 TNLSKITYRLTEENYLTIDPMIGINQQDISAIFDSK 806 + +RLT ENY TID MIG+ + DI+ F K Sbjct: 781 SQSDNDDFRLTPENYSTIDSMIGLTESDIALFFQKK 816 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1631 A DNA sequence (GBSx1726) was identified in S. agalactiae <SEQ ID 5037> which encodes the amino acid sequence <SEQ ID 5038>. Analysis of this protein sequence reveals the following: TABLE-US-04930 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.23 Transmembrane 9-25 (7-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.4291(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04931 >GP:AABE9116 GB:U90721 signal peptidase I [Streptococcus pneumoniae] Identities = 120/201 (59%), Positives = 144/201 (70%), Gaps = 9/201 (4%) Query: 2 KEFIKEWGVFILILSLFLLSRIFLWQFVKVDGHSMDPTLADKEQLVVLKQTKINRFDIVV 61 K F+KEWG+F+LILSL LSRIF W V+V+GHSMDPTLAD E L V+K I+RFDIVV Sbjct: 5 KNFLKEWGLFLLILSLLALSRIFFWSNVRVEGHSMDPTLADGEILFVVKHLPIDRFDIVV 64 Query: 62 ANEEEGGQKKKIVKRVIGMPGDVIKYKNDTLTINNKKTEEPYLKEYTKLFKKDKLQEKYS 121- A+EE+G K IVKRVIGMPGD I+Y+ND L IN+K+T+EPYL +Y K FK DKLQ YS Sbjct: 65 AHEEDG--NKDIVKRVIGMPGDTIRYENDKLYINDKETDEPYLADYIKRFKDDKLQSTYS 122- Query: 122 -------YNPLFQDLAQSSTAFTTDSNGSSEFTTVVPKGHYYLVGDDRIVSKDSRAVGPF 17- 4 F+ +AQ + AFT D N ++ F+ VP+G Y L+GDDR+VS DSR VG F Sbjct: 123 GKGFEGNKGTFFRSIAQKAQAFTVDVNYNTNFSFTVPEGEYLLLGDDRLVSSDSRHVGTF 18- 2 Query: 175 KKSTIVGEVKFRFWPIRRFGT 195 K I GE KFRFWPI R GT Sbjct: 183 KAKDITGEAKFRFWPITRIGT 203 A related DNA sequence was identified in S. pyogenes <SEQ ID 5039> which encodes the amino acid sequence <SEQ ID 5040>. Analysis of this protein sequence reveals the following: TABLE-US-04932 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.50 Transmembrane 35-51 (35-51) ----- Final Results ----- bacterial membrane --- Certainty = 0.1999(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9157> which encodes the amino acid sequence <SEQ ID 9158>. Analysis of this protein sequence reveals the following: TABLE-US-04933 Possible site: 43 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.0300(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04934 Identities = 131/197 (66%), Positives = 152/197 (76%) Query: 1 MKEFIKEWGVFILILSLFLLSRIFLWQFVKVDGHSMDPTLADKEQLVVLKQTKINRFDIV 60 MK+FIKEWG F L L LF LSR+FLWQ VKVDGHSMDPTLA E+L+V Q +I+RFDIV Sbjct: 23 MKQFIKEWGPFTLFLILFGLSRLFLWQAVKVDGHSMDPTLAHGERLIVFNQARIDRFDIV 82 Query: 61 VANEEEGGQKKKIVKRVIGMPGDVIKYKNDTLTINNKKTEEPYLKEYTKLFKKDKLQEKY 120- VA EEE GQKK+IVKRVIG+PGD I Y +DTL IN KKT EPYL EY K FK DKLQ+ Y Sbjct: 83 VAQEEENGQKKEIVKRVIGLPGDTISYNDDTLYINGKKTVEPYLAEYLKQFKNDKLQKTY 142- Query: 121 SYNPLFQDLAQSSTAFTTDSNGSSEFTTVVPKGHYYLVGDDRIVSKDSRAVGPFKKSTIV 18- 0 +YN LFQ LA++S AFTT+S G + F VPKG Y L+GDDRIVS+DSR VG FKK ++ Sbjct: 143 AYNTLFQQLAETSDAFTTNSEGQTRFEMSVPKGEYLLLGDDRIVSRDSREVGSFKKENLI 20- 2 Query: 181 GEVKFRFWPIRRFGTIN 197 GEVK RFWP+ + N Sbjct: 203 GEVKARFWPLNKMTVFN 219 SEQ ID 5038 (GBS268) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 54 (lane 4; MW 50.3 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 85 (lane 9; MW 25.3 kDa) and in FIG. 160 (lane 24; MW 25.3 kDa). GBS268-His was purified as shown in FIG. 222, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1632 A DNA sequence (GBSx1727) was identified in S. agalactiae <SEQ ID 5041> which encodes the amino acid sequence <SEQ ID 5042>. This protein is predicted to be ribonuclease HIII (rnhB). Analysis of this protein sequence reveals the following: TABLE-US-04935 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4728(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10119> which encodes amino acid sequence <SEQ ID 10120> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04936 >GP:AAC45437 GB:U93576 ribonuclease HII [Streptococcus pneumoniae] Identities = 176/282 (62%), Positives = 219/282 (77%), Gaps = 13/282 (4%) Query: 16 EKIRTDLAQHHISNNNPYVVFSAKISGATVLLYTSGKLVFQGSNASHIAQKYGF--IEQK 73 - E +T LA + NPY+ + K+ ATV +YTSGK++ QG A A +G+ +EQ Sbjct: 18 EHYQTSLAP----SKNPYIRYFLKLPQATVSIYTSGKILLQGEGAEKYASFFGYQAVEQ- 72 Query: 74 ESCSSESQDIPIIGTDEVGNGSYFGGLAVVASFVTPKDHAYLKKLGVGDSKTLTDQKIKQ 133- + Q++P+IGTDEVGNGSYFGGLAVVA+FVTP H +L+KLGVGDSKTLTDQKI+Q Sbjct: 73 ----TSGQNLPLIGTDEVGNGSYFGGLAVVAAFVTPDQHDFLRKLGVGDSKTLTDQKIRQ 128- Query: 134 IAPLLEKAIPHKALLLSPQKYNQVVSPNNKHNAVSVKVALHNQAIFLLLQDGFEPEKIVI 19- 3 IAP+L++ I H+ALLLSP KYN+V+ +++NAVSVKVALHNQAI+LLLQ G +PEKIVI Sbjct: 129 IAPILKEKIQHQALLLSPSKYNEVIG--DRYNAVSVKVALHNQAIYLLLQKGVQPEKIVI 18- 6 Query: 194 DAFTSSKNYQNYLKNEKNQFKQTITLEEKAENKYLAVAVSSIIARNLFLENLNKLSDDVG 25- 3 DAFTS+KNY YL E N+F I+LEEKAE KYLAVAVSS+IAR+LFLENL L ++G Sbjct: 187 DAFTSAKNYDKYLAQETNRFSNPISLEEKAEGKYLAVAVSSVIARDLFLENLENLGRELG 24- 6 Query: 254 YKLPSGAGHQSDKVASQLLKAYGISSLEHCAKLHFANTKKAQ 295 Y+LPSGAG SDKVASQ+L+AYG+ L CAKLHF NT+KA+ Sbjct: 247 YQLPSGAGTASDKVASQILQAYGMQGLNFCAKLHFKNTEKAK 288 A related DNA sequence was identified in S. pyogenes <SEQ ID 5043> which encodes the amino acid sequence <SEQ ID 5044>. Analysis of this protein sequence reveals the following: TABLE-US-04937 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2148(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04938 Identities = 194/298 (65%), Positives = 240/298 (80%), Gaps = 2/298 (0%) Query: 3 MNTIVMQADKKLQEKIRTDLAQHHISNNNPYVVFSAKISGATVLLYTSGKLVFQGSNASH 62 MNT+V++ D L + ++ LA + IS+ N YV F+AK +G TVLLY SGKLV QG+ A+ Sbjct: 1 MNTLVLKIDAILSKHLKKQLAPYTISSQNTYVAFAAKKNGVTVLLYKSGKLVLQGNGANA 60 Query: 63 IAQKYGFIEQKE--SCSSESQDIPIIGTDEVGNGSYFGGLAVVASFVTPKDHAYLKKLGV 120- +AQ+ K S+ SQDIPIIG+DEVGNGSYFGG+AVVASFV PKDH++LKKLGV Sbjct: 61 LAQELNLPVAKTVFEASNNSQDIPIIGSDEVGNGSYFGGIAVVASFVDPKDHSFLKKLGV 120- Query: 121 GDSKTLTDQKIKQIAPLLEKAIPHKALLLSPQKYNQVVSPNNKHNAVSVKVALHNQAIFL 18- 0 DSK L+D+ I+QIAPLLEK IPH++LLLSP+KYN++V + +NA+S+KVALHNQAIFL Sbjct: 121 DDSKKLSDKTIQQIAPLLEKQIPHQSLLLSPKKYNELVGKSKPYNAISIKVALHNQAIFL 18- 0 Query: 181 LLQDGFEPEKIVIDAFTSSKNYQNYLKNEKNQFKQTITLEEKAENKYLAVAVSSIIARNL 24- 0 LLQ G +P++IVIDAFTS NY+ +LK EKN F +T +EKAE+ YLAVAVSSIIARNL Sbjct: 181 LLQKGIQPKQIVIDAFTSQSNYEKHLKKEKNHFPNPLTFQEKAESHYLAVAVSSIIARNL 24- 0 Query: 241 FLENLNKLSDDVGYKLPSGAGHQSDKVASQLLKAYGISSLEHCAKLHFANTKKAQALL 298 FL+NL++L D+GY+LPSGAG SDKVASQLL AYG+SSLE+ AKLHFANT KAQALL Sbjct: 241 FLDNLDQLGQDLGYQLPSGAGSASDKVASQLLAAYGMSSLEYSAKLHFANTHKAQALL 298 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1633 A DNA sequence (GBSx1728) was identified in S. agalactiae <SEQ ID 5045> which encodes the amino acid sequence <SEQ ID 5046>. This protein is predicted to be heat shock protein 70. Analysis of this protein sequence reveals the following: TABLE-US-04939 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3874(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 5047> which encodes the amino acid sequence <SEQ ID 5048>. Analysis of this protein sequence reveals the following: TABLE-US-04940 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3442(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-04941 Identities = 65/92 (70%), Positives = 76/92 (81%) Query: 11 NRYKFVFGDKPLTLTTDKDNLFMEEIERVATEKYEAIKEKLPNADNETIAILMAINALSV 70 - NRYKF FG+K LTLTTDKDNLFMEE+ERVA EKY+A+K LP AD+ETIAILMAIN LS Sbjct: 5 NRYKFTFGEKTLTLTTDKDNLFMEEVERVAKEKYQALKNHLPEADDETIAILMAINTLST 64 Query: 71 QLSREIDIEKMEDELNKLRSKTISDIKEKVSE 102 QLSREI IEKME E+ LR KT+ ++EK ++ Sbjct: 65 QLSREIAIEKMEAEILDLRQKTLVGLQEKANQ 96 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1634 A DNA sequence (GBSx1729) was identified in S. agalactiae <SEQ ID 5049> which encodes the amino acid sequence <SEQ ID 5050>. Analysis of this protein sequence reveals the following: TABLE-US-04942 Possible site: 48 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.99 Transmembrane 124-140 (114-148) INTEGRAL Likelihood = -5.84 Transmembrane 22-38 (21-40) INTEGRAL Likelihood = -4.88 Transmembrane 2-18 (1-20) INTEGRAL Likelihood = -1.97 Transmembrane 84-100 (84-100) ----- Final Results ----- bacterial membrane --- Certainty = 0.5394(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04943 >GP:BAB06827 GB:AP001517 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 59/182 (32%), Positives = 98/182 (53%), Gaps = 14/182 (7%) Query: 1 MLSLLLLIIVIWHFYIGYSRGIFLQVFYVLMSMVSLMIASQFYQELASQITLWVPYS--N 58 MLS++LL I++ F+IG RG+ LQ+ ++L + + +A ++Y +A+ I LW+PY + Sbjct: 1 MLSVILLFILLCSFFIGKRRGLILQLVHLLGFVAAFFVAYKYYAPVATYIRLWIPYPQFS 60 Query: 59 PVQGVEVYFFKDISKFQLSHVYYAGVAFVFIY----SLSYLVGRLLGVLLHLAPVEHFDS 114- P V + I F +VYY+G+AF ++ L ++VG +L L HL + Sbjct: 61 PDSPVTML----IEAFNFENVYYSGIAFALLFIGTKILLHIVGSMLDFLTHLPILRSV-- 114- Query: 115 LQNNIISGFLAVLVCLLFMSMCLTILATVPMSFVQEKLWNSLFVRFLINDLPFFSQFLVR 17- 4 N + G L + L M + L + A +P+ VQ L SL +F++N PF S+F+ Sbjct: 115 --NGWLGGILGFVEVYLIMFVLLYVGALLPIETVQTHLNQSLVAQFIMNHTPFLSEFIRN 17- 2 Query: 175 TW 176 W Sbjct: 173 LW 174 A related DNA sequence was identified in S. pyogenes <SEQ ID 5051> which encodes the amino acid sequence <SEQ ID 5052>. Analysis of this protein sequence reveals the following: TABLE-US-04944 Possible site: 59 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.17 Transmembrane 124-140 (117-148) INTEGRAL Likelihood = -4.73 Transmembrane 84-100 (78-105) INTEGRAL Likelihood = -0.00 Transmembrane 156-172 (156-172) ----- Final Results ----- bacterial membrane --- Certainty = 0.4270(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04945 >GP:BAB06827 GB:AP001517 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 57/177 (32%), Positives = 98/177 (55%), Gaps = 2/177 (1%) Query: 1 MLSLLIVLILTWNFYIGYSRGIILQSFYVLGALLSLLVANRFYIGLAHKLTLWIPYSNPV 60 MLS++++ IL +F+IG RG+ILQ ++LG + + VA ++Y +A + LWIPY Sbjct: 1 MLSVILLFILLCSFFIGKRRGLILQLVHLLGFVAAFFVAYKYYAPVATYIRLWIPYPQFS 60 Query: 61 EGTSVFFFKSVDIFVLDKVYYAGLAFFIIFLLGYALSRFLGIFVHFLLLNYFDNQWTKCL 120- + V ++ F + VYY+G+AF ++F+ L +G + FL L Sbjct: 61 PDSPVTML--IEAFNFENVYYSGIAFALLFIGTKILLHIVGSMLDFLTHLPILRSVNGWL 118- Query: 121 SGGLAFLVSLLFLNMLLSIFATVPMPFLQHYLHSSFLARLVIEHLPPLTIIIQKLWI 177 G L F+ L + +LL + A +P+ +Q +L+ S +A+ ++ H P L+ I+ LWI Sbjct: 119 GGILGFVEVYLIMFVLLYVGALLPIETVQTHLNQSLVAQFIMNHTPFLSEFIRNLWI 175 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04946 Identities = 87/176 (49%), Positives = 123/176 (69%) Query: 1 MLSLLLLIIVIWHFYIGYSRGIFLQVFYVLMSMVSLMIASQFYQELASQITLWVPYSNPV 60 MLSLL+++I+ W+FYIGYSRGI LQ FYVL +++SL++A++FY LA ++TLW+PYSNPV Sbjct: 1 MLSLLIVLILTWNFYIGYSRGIILQSFYVLGALLSLLVANRFYIGLAHKLTLWIPYSNPV 60 Query: 61 QGVEVYFFKDISKFQLSHVYYAGVAFVFIYSLSYLVGRLLGVLLHLAPVEHFDSLQNNII 120- +G V+FFK + F L VYYAG+AF I+ L Y + R LG+ +H + +FD+ + Sbjct: 61 EGTSVFFFKSVDIFVLDKVYYAGLAFFIIFLLGYALSRFLGIFVHFLLLNYFDNQWTKCL 120- Query: 121 SGFLAVLVCLLFMSMCLTILATVPMSFVQEKLWNSLFVRFLINDLPFFSQFLVRTW 176 SG LA LV LLF++M L+I ATVPM F+Q L +S R +I LP + + + W Sbjct: 121 SGGLAFLVSLLFLNMLLSIFATVPMPFLQHYLHSSFLARLVIEHLPPLTIIIQKLW 176 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1635 A DNA sequence (GBSx1730) was identified in S. agalactiae <SEQ ID 5053> which encodes the amino acid sequence <SEQ ID 5054>. Analysis of this protein sequence reveals the following: TABLE-US-04947 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4176(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10117> which encodes amino acid sequence <SEQ ID 10118> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04948 >GP:CAB14818 GB:Z99118 similar to DNA mismatch repair protein [Bacillus subtilis] Identities = 320/790 (40%), Positives = 466/790 (58%), Gaps = 18/790 (2%) Query: 10 MNNKILEQLEFNKVKELILPYLKTEQSQEELSELEPMTEAPKIEKSFNEISDMEQIFVEH 69 - M K+L LEF+KVKE ++ + + +E L EL+P +I+K +E+ + I Sbjct: 1 MQQKVLSALEFHKVKEQVIGHAASSLGKEMLLELKPSASIDEIKKQLDEVDEASDIIRLR 60 Query: 70 HSFGIVSLSSISESLKRLELSADLNIQELLAIKKVLQSSSDMIHFYSDL--DNVSFQSLD 127- L I +L+R E+ + L+ E I +L + M HF + + D V + Sbjct: 61 GQAPFGGLVDIRGALRRAEIGSVLSPSEFTEISGLLYAVKQMKHFITQMAEDGVDIPLIH 120- Query: 128 RLFENLEQFPNLQGSFQA-INDGGFLEHFASPELERIRRQLTNSERRVRQILQDMLKEKA 18- 6 + E L +L+ + I+D G + AS L IR QL E RVR L+ ML+ + Sbjct: 121 QHAEQLITLSDLERDINSCIDDHGEVLDHASETLRGIRTQLRTLESRVRDRLESMLRSSS 18- 0 Query: 187 --ELLSENLIASRSGRSVLPVKNTYRNRISGVVHDISSSGSTVYIEPRAVVTLNEEITQL 24- 4 ++LS+ ++ R+ R V+PVK YR+ G+VHD SSSG+T++IEP+A+V +N + Q Sbjct: 181 ASKMLSDTIVTIRNDRFVIPVKQEYRSSYGGIVHDTSSSGATLFIEPQAIVDMNNSLQQA 24- 0 Query: 245 RADERHEESRILHAFSDLLRPHVATIRNNAWILGHLDFVRAKYLFMSDNKATIPEISNDS 30- 4 + E+ E RIL ++ + + + +L LDF+ AK + KAT P +++ Sbjct: 241 KVKEKQEIERILRVLTEKTAEYTEELFLDLQVLQTLDFIFAKARYAKAVKATKPIMNDTG 30- 0 Query: 305 TLALINVRHPLL--SNPVANDLHFDQDLTAIVITGPNTGGKTIMLKTLGLAQLMGQSGLP 36- 2 + L RHPLL VAND+ +D + IVITGPNTGGKT+ LKTLGL LM QSGL Sbjct: 301 FIRLKKARHPLLPPDQVVANDIELGRDFSTIVITGPNTGGKTVTLKTLGLLTLMAQSGLH 36- 0 Query: 363 VLADKGSKIAVFNNIFADIGDEQSIEQSLSTFSSHMTHIVSILNEADHNSLVLFDELGAG 42- 2 + AD+GS+ AVF ++FADIGDEQSIEQSLSTFSSHM +IV IL + + NSLVLFDELGAG Sbjct: 361 IPADEGSEAAVFEHVFADIGDEQSIEQSLSTFSSHMVNIVGILEQVNENSLVLFDELGAG 42- 0 Query: 423 TDPQEGASLAMAILEHLRLSNIKTMATTHYPELKAYGIETNFVENASMEFDAETLSPTYR 48- 2 TDPQEGA+LAM+IL+ + +N + +ATTHYPELKAYG V NAS+EFD ETLSPTY+ Sbjct: 421 TDPQEGAALAMSILDDVHRTNARVLATTHYPELKAYGYNREGVMNASVEFDIETLSPTYK 48- 0 Query: 483 FMQGVPGRSNAFEIASRLGLAPFIVKQAK-QMTDSDSDVNRIIEQLEAQTLETRRRLDHI 54- 1 + GVPGRSNAFEI+ RLGL I+ QAK +MT ++V+ +I LE L Sbjct: 481 LLIGVPGRSNAFEISKRLGLPDHIIGQAKSEMTAEHNEVDTMIASLEQSKKRAEEELSET 54- 0 Query: 542 KEVEQENLKFNRAVKKLYNEFSHERDKELEKIYQEAQEIVDMALNESDTILKKL----ND 59- 7 + + +E K ++ +++ E + ++DK LE+ Q+A E V A+ E++ I+ +L + Sbjct: 541 ESIRKEAEKLHKELQQQIIELNSKKDKMLEEAEQQAAEKVKAAMKEAEDIIHELRTIKEE 60- 0 Query: 598 KSQLKPHEIIDAKAQIKKLAPQVDLSKNKVLNKAKKIKAARAPRIGDDIIVTSYGQRGTL 65- 7 K HE+I+AK +++ P + SK K +K R + GD++ V ++GQ+GTL Sbjct: 601 HKSFKDHELINAKKRLEGAMPAFEKSKKPEKPKTQK----RDFKPGDEVKVLTFGQKGTL 65- 6 Query: 658 TSQLKDGRWEAQVGIIKMTLTQDEFTLVRVQEEQKVKSKQINVVKKADSSGPRARLDLRG 71- 7 + W Q+GI+KM + + + ++ E K K K I VK D LDLRG Sbjct: 657 LEKTGGNEWNVQIGILKMKVKEKDLEFIKSAPEPK-KEKMITAVKGKDYH-VSLELDLRG 71- 4 Query: 718 KRYEEAMQELDNFIDQALLNNMGQVDIIHGIGTGVIREGVTKYLRRNKHVKHFAYAPQNA 77- 7 +RYE A+ ++ ++D A+L +V IIHG GTG +R+GV L+ ++ VK + Sbjct: 715 ERYENALSRVEKYLDDAVLAGYPRVSIIHGKGTGALRKGVQDLLKNHRSVKSSRFGEAGE 77- 4 Query: 778 GGSGATIVTL 787 GGSG T+V L Sbjct: 775 GGSGVTVVEL 784 A related DNA sequence was identified in S. pyogenes <SEQ ID 5055> which encodes the amino acid sequence <SEQ ID 5056>. Analysis of this protein sequence reveals the following: TABLE-US-04949 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3843(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04950 Identities = 775/787 (98%), Positives = 781/787 (98%) Query: 2 INLGIMKSMNNKILEQLEFNKVKELILPYLKTEQSQEELSELEPMTEAPKIEKSFNEISD 61 I LGIMKSMNNKILEQLEFNKVKEL+LPYLKTEQSQEEL ELEPMTEAPKIEKSFNEISD Sbjct: 32 IILGIMKSMNNKILEQLEFNKVKELLLPYLKTEQSQEELLELEPMTEAPKIEKSFNEISD 91 Query: 62 MEQIFVEHHSFGIVSLSSISESLKRLELSADLNIQELLAIKKVLQSSSDMIHFYSDLDNV 121- MEQIFVEHHSFGIVSLSSISESLKRLELS DLNIQELLAIKKVLQSSSDMIHFYSDLDNV Sbjct: 92 MEQIFVEHHSFGIVSLSSISESLKRLELSTDLNIQELLAIKKVLQSSSDMIHFYSDLDNV 151- Query: 122 SFQSLDRLFENLEQFPNLQGSFQAINDGGFLEHFASPELERIRRQLTNSERRVRQILQDM 18- 1 SFQSLDRLFENLEQFPNLQGSFQAINDGGFLEHFASPELERIRRQLTNSERRVRQILQDM Sbjct: 152 SFQSLDRLFENLEQFPNLQGSFQAINDGGFLEHFASPELERIRRQLTNSERRVRQILQDM 21- 1 Query: 182 LKEKAELLSENLIASRSGRSVLPVKNTYRNRISGVVHDISSSGSTVYIEPRAVVTLNEEI 24- 1 LKEKAELLSENLIASRSGRSVLPVKNTYRNRISGVVHDISSSGSTVYIEPRAVVTLNEEI Sbjct: 212 LKEKAELLSENLIASRSGRSVLPVKNTYRNRISGVVHDISSSGSTVYIEPRAVVTLNEEI 27- 1 Query: 242 TQLRADERHEESRILHAFSDLLRPHVATIRNNAWILGHLDFVRAKYLFMSDNKATIPEIS 30- 1 TQLRADERHEE RILHAFSDLLRPHVATIRNNAWILGHLDFVRAKYLFMSDNKATIP+IS Sbjct: 272 TQLRADERHEEGRILHAFSDLLRPHVATIRNNAWILGHLDFVRAKYLFMSDNKATIPKIS 33- 1 Query: 302 NDSTLALINVRHPLLSNPVANDLHFDQDLTAIVITGPNTGGKTIMLKTLGLAQLMGQSGL 36- 1 NDSTLALINVRHPLLSNPVANDLHFD DLTAIVITGPNTGGKTIMLKTLGLAQLMGQSGL Sbjct: 332 NDSTLALINVRHPLLSNPVANDLHFDHDLTAIVITGPNTGGKTIMLKTLGLAQLMGQSGL 39- 1 Query: 362 PVLADKGSKIAVFNNIFADIGDEQSIEQSLSTFSSHMTHIVSILNEADHNSLVLFDELGA 42- 1 PVLADKGSKIAVFNNIFADIGDEQSIEQSLSTFSSHMTHIVSILNEADHNSLVLFDELGA Sbjct: 392 PVLADKGSKIAVFNNIFADIGDEQSIEQSLSTFSSHMTHIVSILNEADHNSLVLFDELGA 45- 1 Query: 422 GTDPQEGASLAMAILEHLRLSNIKTMATTHYPELKAYGIETNFVENASMEFDAETLSPTY 48- 1 GTDPQEGASLAMAILEHLRLS+IKTMATTHYPELKAYGIETNFVENASMEFDAETLSPTY Sbjct: 452 GTDPQEGASLAMAILEHLRLSHIKTMATTHYPELKAYGIETNFVENASMEFDAETLSPTY 51- 1 Query: 482 RFMQGVPGRSNAFEIASRLGLAPFIVKQAKQMTDSDSDVNRIIEQLEAQTLETRRRLDHI 54- 1 RFMQGVPGRSNAFEIASRLGLAPFIVKQAKQMTDSDSDVNRIIEQLEAQTLETRRRLDHI Sbjct: 512 RFMQGVPGRSNAFEIASRLGLAPFIVKQAKQMTDSDSDVNRIIEQLEAQTLETRRRLDHI 57- 1 Query: 542 KEVEQENLKFNRAVKKLYNEFSHERDKELEKIYQEAQEIVDMALNESDTILKKLNDKSQL 60- 1 KEVEQENLKFNRAVKKLYNEFSHERDKELEKIYQEAQEIVDMALNESDTILKKLNDKSQL Sbjct: 572 KEVEQENLKFNRAVKKLYNEFSHERDKELEKIYQEAQEIVDMALNESDTILKKLNDKSQL 63- 1 Query: 602 KPHEIIDAKAQIKKLAPQVDLSKNKVLNKAKKIKAARAPRIGDDIIVTSYGQRGTLTSQL 66- 1 KPHEIIDAKAQIKKLAPQVDLSKNKVLNKAKKIKAARAPRIGDDIIVTSYGQRGTLTSQL Sbjct: 632 KPHEIIDAKAQIKKLAPQVDLSKNKVLNKAKKIKAARAPRIGDDIIVTSYGQRGTLTSQL 69- 1 Query: 662 KDGRWEAQVGIIKMTLTQDEFTLVRVQEEQKVKSKQINVVKKADSSGPRARLDLRGKRYE 72- 1 KDGRWEAQVGIIKMTLTQDEF+LVRVQEEQKVK+KQINVVKKAD SGPRARLDLRGKRYE Sbjct: 692 KDGRWEAQVGIIKMTLTQDEFSLVRVQEEQKVKNKQINVVKKADGSGPRARLDLRGKRYE 75- 1 Query: 722 EAMQELDNFIDQALLNNMGQVDIIHGIGTGVIREGVTKYLRRNKHVKHFAYAPQNAGGSG 78- 1 EAMQELD+FIDQALLNNMGQVDIIHGIGTGVIREGVTKYLRRNKHVKHFAYAPQNAGGSG Sbjct: 752 EAMQELDHFIDQALLNNMGQVDIIHGIGTGVIREGVTKYLRRNKHVKHFAYAPQNAGGSG 81- 1 Query: 782 ATIVTLG 788 ATIVTLG Sbjct: 812 ATIVTLG 818 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1636 A DNA sequence (GBSx1731) was identified in S. agalactiae <SEQ ID 5057> which encodes the amino acid sequence <SEQ ID 5058>. This protein is predicted to be thioredoxin (trxA). Analysis of this protein sequence reveals the following: TABLE-US-04951 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2721(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10115> which encodes amino acid sequence <SEQ ID 10116> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04952 >GP:CAB40815 GB:AJ133006 thioredoxin [Listeria monocytogenes] (ver 2) Identities = 64/100 (64%), Positives = 78/100 (78%), Gaps = 1/100 (1%) Query: 15 MALEVTDATFVEETKEGLVLIDFWATWCGPCRMQAPILEQLSQEIDEDELKILKMDVDEN 74 - M E+TDATF +ET EGLVL DFWATWCGPCRM AP+LE++ +E E LKI+KMDVDEN Sbjct: 1 MVKEITDATFEQETSEGLVLTDFWATWCGPCRMVAPVLEEIQEERGE-ALKIVKMDVDEN 59 Query: 75 PETARQFGIMSIPTLMFKKDGEVVKQVAGVHTKDQLKAII 114 PET FG+MSIPTL+ KKDGEVV+ + G K++L +I Sbjct: 60 PETPGSFGVMSIPTLLIKKDGEVVETIIGYRPKEELDEVI 99 A related DNA sequence was identified in S. pyogenes <SEQ ID 5059> which encodes the amino acid sequence <SEQ ID 5060>. Analysis of this protein sequence reveals the following: TABLE-US-04953 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2721(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1637 A DNA sequence (GBSx1732) was identified in S. agalactiae <SEQ ID 5061> which encodes the amino acid sequence <SEQ ID 5062>. Analysis of this protein sequence reveals the following: TABLE-US-04954 Possible site: 33 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.54 Transmembrane 170-186 (167-191) INTEGRAL Likelihood = -5.52 Transmembrane 87-103 (86-107) INTEGRAL Likelihood = -4.62 Transmembrane 105-121 (104-126) ----- Final Results ----- bacterial membrane --- Certainty = 0.4015(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04955 >GP:CAA60798 GB:X87369 ORF3 [Clostridium perfringens] Identities = 27/67 (40%), Positives = 52/67 (77%) Query: 1 MEIGQQIIRYRKQQALSQEELAEKVYVSRQSISNWENDKTYPDIHSLLLLSQIFQVSLDQ 60 M++ +++ RK++ LSQE+LAEK+ +SRQ++S WE+ ++ PD++ L++LS+++ V++D Sbjct: 1 MKLAEKLQLMRKREGLSQEDLAEKLGISRQAVSKWESGQSVPDLNKLIILSELYNVTIDY 60 Query: 61 LIKGDIE 67 L+K E Sbjct: 61 LVKETYE 67 A related DNA sequence was identified in S. pyogenes <SEQ ID 1739> which encodes the amino acid sequence <SEQ ID 1740>. Analysis of this protein sequence reveals the following: TABLE-US-04956 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.86 Transmembrane 173-189 (169-194) INTEGRAL Likelihood = -5.52 Transmembrane 90-106 (89-110) INTEGRAL Likelihood = -4.62 Transmembrane 108-124 (107-129) ----- Final Results ----- bacterial membrane --- Certainty = 0.4545(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04957 Identities = 187/195 (95%), Positives = 191/195 (97%) Query: 1 MEIGQQIIRYRKQQALSQEELAEKVYVSRQSISNWENDKTYPDIHSLLLLSQIFQVSLDQ 60 MEIGQQIIRYRKQQALSQE+LAEKVYVSRQSISNWENDKTYPDIHSLLLLSQIFQVSLDQ Sbjct: 4 MEIGQQIIRYRKQQALSQEKLAEKVYVSRQSISNWENDKTYPDIHSLLLLSQIFQVSLDQ 63 Query: 61 LIKGDIEKMKYTITQVDKKNFERDTKVMVTLMILLMISSYPLVYFLEWLGLGIFVLLSII 120- LIKGDIEKMKYTITQVDKKNF+RDTKVMVTLMILLMISSYPLVYFLEWLGLGIFVLLSII Sbjct: 64 LIKGDIEKMKYTITQVDKKNFKRDTKVMVTLMILLMISSYPLVYFLEWLGLGIFVLLSII 123- Query: 121 TMTYANRVERFKKKYDVQTYKEILAVSSGKLLDEIEKREERAKLPYQKPLIVTVFFLITV 18- 0 TMTYANRVERFKKKYDVQ YKEILAVS+GKLLDEIEKREERA LPYQKPLIVTVFFLITV Sbjct: 124 TMTYANRVERFKKKYDVQPYKEILAVSNGKLLDEIEKREERATLPYQKPLIVTVFFLITV 18- 3 Query: 181 ATFFASRFIFTWLFH 195 A FASRF+FTWLFH Sbjct: 184 AFAFASRFMFTWLFH 198 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1638 A DNA sequence (GBSx1733) was identified in S. agalactiae <SEQ ID 5063> which encodes the amino acid sequence <SEQ ID 5064>. This protein is predicted to be adenine glycosylase (mutY). Analysis of this protein sequence reveals the following: TABLE-US-04958 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2385(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9425> which encodes amino acid sequence <SEQ ID 9426> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-04959 >GP:BAB04650 GB:AP001510 adenine glycosylase [Bacillus halodurans] Identities = 130/331 (39%), Positives = 190/331 (57%), Gaps = 15/331 (4%) Query: 1 MLQQTQVNTVIPYYKRFLEWFPQIKDLADAPEEQLLKAWEGLGYYSRVRNMQKAAQQVMV 60 MLQQT+V+TVIPYY+ F+ FP ++ LA A E+Q+LKAWEGLGYYSR RN+Q A ++V+ Sbjct: 45 MLQQTRVDTVIPYYQAFMRQFPTLETLAYAEEDQVLKAWEGLGYYSRARNLQSAVREVVE 104- Query: 61 DFGGIFPHTYDDIASLKGIGPYTAGAIASISFNLPEPAVDGNVMRVMARLFEVNYDIGDP 120- +GG P T +I+ LKG+GPYTAGAI SI+++ PEPAVDGNVMRV++R+ + DI Sbjct: 105 SYGGEVPSTRKEISKLKGVGPYTAGAILSIAYDQPEPAVDGNVMRVLSRVLYIEEDIAKV 16- 4 Query: 121 KNRKIFQAIMEILIDPDRPGDFNQALMDLGTDIESAKTPRPDESPIRFFNAAYLNGTYSK 18- 0 K R +F++++ LI + P FNQ LM+LG + + +P P+R A+ G + Sbjct: 165 KTRTLFESLLYDLISKENPSFFNQGLMELGALVCTPTSPGCLLCPVRDHCRAFAAGVQEQ 22- 4 Query: 181 YPIKNTKKKPKPMRIQAFVIRNQNGQYLLEKNTKGRLLGGFWSFPIIETSPLSQQLDLFD 24- 0 PIK KKKPK ++ A VIRN+ GQ L+E+ + LL W FP +E L Sbjct: 225 LPIKAKKKKPKAKQLIAAVIRNEKGQVLIERRPEKGLLAKLWQFPNVE---------LES 27- 5 Query: 241 DNQSNPIIWQTQNETFQREYQLKPQWTDNHFPNIKHTFSHQKWTIELIEGVVKAT-DLPN 29- 9 + ++ +E F + + + ++H FSH W I + E VK L + Sbjct: 276 TKNAQQVLGDYIHERFHLDAAV-----GEYVQTVEHVFSHLIWNIRVYEATVKGVPSLND 33- 0 Query: 300 APHLKWVAIEDFSLYPFATPQKKMLETYLKQ 330 WV Y F +K+++ L++ Sbjct: 331 KYEADWVDDRTIENYAFPVSHQKIIQGNLRK 361 A related DNA sequence was identified in S. pyogenes <SEQ ID 5065> which encodes the amino acid sequence <SEQ ID 5066>. Analysis of this protein sequence reveals the following: TABLE-US-04960 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3579(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04961 Identities = 330/333 (99%), Positives = 331/333 (99%) Query: 1 MLQQTQVNTVIPYYKRFLEWFPQIKDLADAPEEQLLKAWEGLGYYSRVRNMQKAAQQVMV 60 MLQQTQVNTVIPYYKRFLEWFPQIKDLADAPEEQLLKAWEGLGYYSRVRNMQKAAQQVMV Sbjct: 52 MLQQTQVNTVIPYYKRFLEWFPQIKDLADAPEEQLLKAWEGLGYYSRVRNMQKAAQQVMV 111- Query: 61 DFGGIFPHTYDDIASLKGIGPYTAGAIASISFNLPEPAVDGNVMRVMARLFEVNYDIGDP 120- DFGGIFPHTYDDIASLKGIGPYTAGAIASISFNLPEPAVDGNVMRVMARLFEVNYDIGDP Sbjct: 112 DFGGIFPHTYDDIASLKGIGPYTAGAIASISFNLPEPAVDGNVMRVMARLFEVNYDIGDP 17- 1 Query: 121 KNRKIFQAIMEILIDPDRPGDFNQALMDLGTDIESAKTPRPDESPIRFFNAAYLNGTYSK 18- 0 KNRKIFQAIMEILIDPDRPGDFNQALMDLGTDIESAKTPRPDESPIRFFNAAYLNGTY K Sbjct: 172 KNRKIFQAIMEILIDPDRPGDFNQALMDLGTDIESAKTPRPDESPIRFFNAAYLNGTYGK 23- 1 Query: 181 YPIKNTKKKPKPMRIQAFVIRNQNGQYLLEKNTKGRLLGGFWSFPIIETSPLSQQLDLFD 24- 0 YPIKN KKKPKPMRIQAFVIRNQNGQYLLEKNTKGRLLGGFWSFPIIETSPLSQQLDLFD Sbjct: 232 YPIKNPKKKPKPMRIQAFVIRNQNGQYLLEKNTKGRLLGGFWSFPIIETSPLSQQLDLFD 29- 1 Query: 241 DNQSNPIIWQTQNETFQREYQLKPQWTDNHFPNIKHTFSHQKWTIELIEGVVKATDLPNA 30- 0 DNQSNPIIWQTQNETF+REYQLKPQWTDNHFPNIKHTFSHQKWTIELIEGVVKATDLPNA Sbjct: 292 DNQSNPIIWQTQNETFEREYQLKPQWTDNHFPNIKHTFSHQKWTIELIEGVVKATDLPNA 35- 1 Query: 301 PHLKWVAIEDFSLYPFATPQKKMLETYLKQKNA 333 PHLKWVAIEDFSLYPFATPQKKMLETYLKQKNA Sbjct: 352 PHLKWVAIEDFSLYPFATPQKKMLETYLKQKNA 384 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1639 A DNA sequence (GBSx1734) was identified in S. agalactiae <SEQ ID 5067> which encodes the amino acid sequence <SEQ ID 5068>. This protein is predicted to be maltose/maltodextrin transport system (malG). Analysis of this protein sequence reveals the following: TABLE-US-04962 Possible site: 52 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.30 Transmembrane 14-30 (5-35) INTEGRAL Likelihood = -6.95 Transmembrane 248-264 (242-267) INTEGRAL Likelihood = -5.15 Transmembrane 75-91 (74-94) INTEGRAL Likelihood = -3.19 Transmembrane 110-126 (110-127) INTEGRAL Likelihood = -2.13 Transmembrane 141-157 (138-157) INTEGRAL Likelihood = -0.32 Transmembrane 188-204 (188-204) ----- Final Results ----- bacterial membrane --- Certainty = 0.5118(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04963 >GP:BAB06643 GB:AP001517 maltose/maltodextrin transport system (permease) [Bacillus halodurans] Identities = 117/281 (41%), Positives = 169/281 (59%), Gaps = 5/281 (1%) Query: 1 MNKK--KRLNLTFVYILLIVLSIMWLFPIVWVVLTSFRGEGSAFVNYFIPKTWTLDNYAK 58 MNKK RL +T +Y+ L+V+ I+ L+P++W V S S F + IP+T + +Y Sbjct: 1 MNKKVKSRLEVTAIYLFLLVMGIVILYPLLWTVGLSLNPGTSLFSSRMIPETISFRHYEW 60 Query: 59 LFTQNTFPFGQWFLNTLFVATCTCILSTLITVAMAYSLSRIKFKHRNGFLKLALVLNMFP 118- LF + QW+ NTL VA+ T + ST + AY+ SR +F R L L+L MFP Sbjct: 61 LFFDPRSNYLQWYKNTLIVASVTSVCSTFLVALTAYAFSRYRFVGRTYGLYGFLLLQMFP 120- Query: 119 GFMSMIAVYYILKALNLDQTLTALIFVY-SAGAALTFYIAKGFFDTIPYSLDESAMIDGA 17- 7 M+M+A+Y +L +NL TL LI +Y + ++ KG+FDTIP LDESA +DGA Sbjct: 121 VLMAMVALYILLNTVNLLDTLLGLILIYVGTSIPMNAFLVKGYFDTIPRELDESAKLDGA 18- 0 Query: 178 TRLDIFLKITLPLSKPIIVYTALIAFMGPWMDFIFAKVILGDATSKYTVAIGLFSMLQQD 23- 7 IF I LPL+KPI+ AL FM P+MDFI ++IL + YT+A+GLF+ + Sbjct: 181 GHFRIFFTIMLPLAKPILAVVALFNFMSPFMDFILPRIIL-RSPENYTLALGLFNFVNDQ 23- 9 Query: 238 TINQWFMSFTAGSVIIAIPITILFMFMQKYYVEGITGGSVK 278 N F F AG+++IAIPI +F+F+Q+Y + G+T G+ K Sbjct: 240 FANN-FTRFAAGAILIAIPIATVFLFLQRYLISGLTTGATK 279 A related DNA sequence was identified in S. pyogenes <SEQ ID 5069> which encodes the amino acid sequence <SEQ ID 5070>. Analysis of this protein sequence reveals the following: TABLE-US-04964 Possible site: 39 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.42 Transmembrane 76-92 (71-97) INTEGRAL Likelihood = -6.05 Transmembrane 248-264 (242-267) INTEGRAL Likelihood = -3.50 Transmembrane 110-126 (110-127) INTEGRAL Likelihood = -1.33 Transmembrane 129-145 (129-145) INTEGRAL Likelihood = -1.33 Transmembrane 188-204 (188-204) ----- Final Results ----- bacterial membrane --- Certainty = 0.3569(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04965 >GP:CAA60006 GB:X86014 cymG [Klebsiella oxytoca] Identities = 119/270 (44%), Positives = 172/270 (63%), Gaps = 7/270 (2%) Query: 11 LVYATLIILSIIWLFPIAWVILTSFRSEGTAYVNYFIPKTFTLNHYINLFTNETFPFGKW 70 - LVY L++ +++ L P+ W +++S + + + F +FTL HY NL T P+ KW Sbjct: 12 LVYLFLLLNALVVLGPVIWTVMSSLKPGNNLFSSGFTEISFTLEHYHNLLTGT--PYLKW 69 Query: 71 FMNTLIVATFTCIISTFITVAIAYSLSRIKFKFRNGFLKLALILNMFPGFMSMIAIYYIL 130- + NT I+AT +IS + A+ SR +FK + L L+L MFP F+SM AIY +L Sbjct: 70 YKNTFILATCNMLISLVVVTITAFIFSRYRFKAKKKILMSILVLQMFPAFLSMTAIYILL 129- Query: 131 KALGLTQTLTALVLVYSSGAALGF--YIAKGFFDTIPYSLDESAMIDGATRMDIFFKITL 18- 8 + L T L+LVY +G+ L F ++ KG+FD IP SLDE+A IDGA + IFF+I L Sbjct: 130 SKMNLIDTYIGLLLVYVTGS-LPFMTWLVKGYFDAIPTSLDEAAKIDGAGHLTIFFEIIL 18- 8 Query: 189 PLAKPIIVYTALLAFMGPWIDFIFAQVILGDATSKYTVAIGLFSMLQPDTINNWFMAFTA 24- 8 PLAKPI+V+ AL++F GPW+DFI +IL + K T+AIG+FS + ++ N F F A Sbjct: 189 PLAKPILVFVALVSFTGPWMDFILPTLIL-RSEDKMTLAIGIFSWISSNSAEN-FTLFAA 24- 6 Query: 249 GSVLIAVPITLLFMFMQKYYVEGITGGSVK 278 G++L+AVPITLLF+ QK+ G+ G+VK Sbjct: 247 GALLVAVPITLLFIVTQKHITTGLVSGAVK 276 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04966 Identities = 227/278 (81%), Positives = 253/278 (90%) Query: 1 MNKKKRLNLTFVYILLIVLSIMWLFPIVWVVLTSFRGEGSAFVNYFIPKTWTLDNYAKLF 60 M K+R L VY LI+LSI+WLFPI WV+LTSFR EG+A+VNYFIPKT+TL++Y LF Sbjct: 1 MKNKRRFQLGLVYATLIILSIIWLFPIAWVILTSFRSEGTAYVNYFIPKTFTLNHYINLF 60 Query: 61 TQNTFPFGQWFLNTLFVATCTCILSTLITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGF 120- T TFPFG+WF+NTL VAT TCI+ST ITVA+AYSLSRIKFK RNGFLKLAL+LNMFPGF Sbjct: 61 TNETFPFGKWFMNTLIVATFTCIISTFITVAIAYSLSRIKFKFRNGFLKLALILNMFPGF 120- Query: 121 MSMIAVYYILKALNLDQTLTALIFVYSAGAALTFYIAKGFFDTIPYSLDESAMIDGATRL 18- 0 MSMIA+YYILKAL L QTLTAL+ VYS+GAAL FYIAKGFFDTIPYSLDESAMIDGATR+ Sbjct: 121 MSMIAIYYILKALGLTQTLTALVLVYSSGAALGFYIAKGFFDTIPYSLDESAMIDGATRM 18- 0 Query: 181 DIFLKITLPLSKPIIVYTALIAFMGPWMDFIFAKVILGDATSKYTVAIGLFSMLQQDTIN 24- 0 DIF KITLPL+KPIIVYTAL+AFMGPW+DFIFA+VILGDATSKYTVAIGLFSMLQ DTIN Sbjct: 181 DIFFKITLPLAKPIIVYTALLAFMGPWIDFIFAQVILGDATSKYTVAIGLFSMLQPDTIN 24- 0 Query: 241 QWFMSFTAGSVIIAIPITILFMFMQKYYVEGITGGSVK 278 WFM+FTAGSV+IA+PIT+LFMFMQKYYVEGITGGSVK Sbjct: 241 NWFMAFTAGSVLIAVPITLLFMFMQKYYVEGITGGSVK 278 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1640 A DNA sequence (GBSx1735) was identified in S. agalactiae <SEQ ID 5071> which encodes the amino acid sequence <SEQ ID 5072>. This protein is predicted to be cymF protein (malF). Analysis of this protein sequence reveals the following: TABLE-US-04967 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.46 Transmembrane 427-443 (417-447) INTEGRAL Likelihood = -10.24 Transmembrane 99-115 (96-121) INTEGRAL Likelihood = -9.39 Transmembrane 166-182 (154-185) INTEGRAL Likelihood = -6.21 Transmembrane 259-275 (257-276) INTEGRAL Likelihood = -6.21 Transmembrane 229-245 (223-247) INTEGRAL Likelihood = -6.10 Transmembrane 44-60 (40-66) INTEGRAL Likelihood = -4.51 Transmembrane 314-330 (312-331) ----- Final Results ----- bacterial membrane --- Certainty = 0.5585 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04968 >GP:CAA60005 GB:X86014 cymF [Klebsiella oxytoca] Identities = 174/428 (40%), Positives = 263/428 (60%), Gaps = 21/428 (4%) Query: 27 SFLIMGLANLKNKQIVKGLLFLISEILFLITFVYQVIPAVKGLISLGTQEQGMTTKTVDG 86 - SFLIMG L + +KG +FL+ +I+ +I+ + ++ A +GLI+LGT Q T G Sbjct: 15 SFLIMGATQLISGHWIKGSVFLLFQIV-VISNINLLLNATQGLITLGTVAQ-----TRSG 68 Query: 87 IKIQVATQGDNSMLMLIFGLASLIFCCVFAYIYWSNIKSAAHLLTLKEEGREIPSFKKDI 146- I GDNS+ ML+ G+ + IF ++YW NIK A + SF + + Sbjct: 69 FDI---VAGDNSIFMLVEGVVAFIFLFFSIFVYWLNIKDAQVCEKCHQ------SFTEQL 119- Query: 147 KSLTDGRFHMTLMSIPLIGVLLFTILPLVYMICLAFTNYDH-NHLPPKSLFDWVGFANFG 20- 5 +++ D RF +++ I + F I+P++ + ++ TNY +H+PPK+L DWVG NF Sbjct: 120 RTIYDNRFATIMLAPAFIACIAFIIMPMIITVLVSLTNYSAPHHIPPKNLVDWVGLKNFI 17- 9 Query: 206 NIFSGRMAS-TFFPVLSWTLIWAVFATVTNFFFGIILALLINTKGLKFKKMWRTIFVITM 26- 4 +F R+ S TF + WT++WA FAT+ FG +LAL + K + KK WR +F++ Sbjct: 180 TLFELRIWSKTFVGIGVWTVLWAFFATLCTCSFGFLLALALENKKIIAKKAWRVVFILPY 23- 9 Query: 265 AVPQFISLLIMRNLLSDAGPVNALLIKWGLISSAHPLPFLSDPVWAKFSIIFVNMWVGIP 32- 4 A+P F++LLI R LL+ GPVN+ L WG+ S + FLSDP+ AK ++I V++WVG P Sbjct: 240 AIPAFVTLLIFRLLLNGIGPVNSTLNSWGIDS----IGFLSDPLIAKMTVIAVSVWVGAP 29- 5 Query: 325 VTMLVATGIIMNLPAEQIEAAEIDGANKFQVFQSITFPQILLIMTPTLIQQFIGNINNFN 38- 4 ML+ TG + N+P + EA+E+DGA+KFQ F+ IT P +L + P+L+ F N NNF Sbjct: 296 YFMLLITGAMTNIPRDLYEASEVDGASKFQQFREITLPMVLHQVAPSLVMTFAHNFNNFG 35- 5 Query: 385 VIYLLTQGGPTNSTYYQAGSTDLLVTWLYNLTVTAADYNLASVVGILIFILSAVFSLLAY 44- 4 IYLLT+GGP N Y AG TD+L+TW+Y LT+ Y +ASV+ I+IF+ ++F++ + Sbjct: 356 AIYLLTEGGPINPEYRFAGHTDILITWIYKLTLDFQQYQIASVISIIIFLFLSIFAIWQF 41- 5 Query: 445 TRTNSYKE 452 R S+KE Sbjct: 416 RRMKSFKE 423 A related DNA sequence was identified in S. pyogenes <SEQ ID 5073> which encodes the amino acid sequence <SEQ ID 5074>. Analysis of this protein sequence reveals the following: TABLE-US-04969 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.93 Transmembrane 98-114 (95-122) INTEGRAL Likelihood = -9.55 Transmembrane 165-181 (152-184) INTEGRAL Likelihood = -9.24 Transmembrane 424-440 (419-443) INTEGRAL Likelihood = -7.91 Transmembrane 43-59 (39-71) INTEGRAL Likelihood = -7.59 Transmembrane 258-274 (256-275) INTEGRAL Likelihood = -6.21 Transmembrane 228-244 (222-246) INTEGRAL Likelihood = -4.09 Transmembrane 311-327 (309-328) ----- Final Results ----- bacterial membrane --- Certainty = 0.5373 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04970 >GP:CAA60005 GB:X86014 cymF [Klebsiella oxytoca] Identities = 179/426 (42%), Positives = 266/426 (62%), Gaps = 19/426 (4%) Query: 26 SSIIMGFANFANKQFIKGILFLISELIFLVAFVSQIIPAIRGLVTLGTQTQGMTTKTIDG 85 - S +IMG + +IKG +FL+ +++ +++ ++ ++ A +GL+TLGT Q T G Sbjct: 15 SFLIMGATQLISGHWIKGSVFLLFQIV-VISNINLLLNATQGLITLGTVAQ-----TRSG 68 Query: 86 INIQVAVDGDNSMLMLIFGLASLIFCLVFAYIYWCNLKSARNLYLFKQKGQKIPSFKEDL 145- +I V GDNS+ ML+ G+ + IF ++YW N+K A+ Q SF E L Sbjct: 69 FDI---VAGDNSIFMLVEGVVAFIFLFFSIFVYWLNIKDAQVCEKCHQ------SFTEQL 119- Query: 146 ATLTNGRFHMTLMAIPLIGVLLFTILPLIYMICLAFTNFDH-NHLPPKSLFDWVGLANFG 20- 4 T+ + RF ++A I + F I+P+I + ++ TN+ +H+PPK+L DWVGL NF Sbjct: 120 RTIYDNRFATIMLAPAFIACIAFIIMPMIITVLVSLTNYSAPHHIPPKNLVDWVGLKNFI 17- 9 Query: 205 NVLSGRM-AGTFFPIFSWTLIWAVFATVTNFFFGIILALLINTKGLKWKKMWRTIFVITI 26- 3 + R+ + TF I WT++WA FAT+ FG +LAL + K + KK WR +F++ Sbjct: 180 TLFELRIWSKTFVGIGVWTVLWAFFATLCTCSFGFLLALALENKKIIAKKAWRVVFILPY 23- 9 Query: 264 AVPQFISLLIMRNLLNDEGPLNALLNKIGLINGSLPFLSDPLWAKFSIIFVNMWIGIPFT 32- 3 A+P F++LLI R LLN GP+N+ LN G+ S+ FLSDPL AK ++I V++W+G P+ Sbjct: 240 AIPAFVTLLIFRLLLNGIGPVNSTLNSWGI--DSIGFLSDPLIAKMTVIAVSVWVGAPYF 29- 7 Query: 324 MLIATGIIMNLPSEQIEAAEIDGASKFQVFKSITFPQILLIMTPNLIQQFIGNINNFNVI 38- 3 ML+ TG + N+P + EA+E+DGASKFQ F+ IT P +L + P+L+ F N NNF I Sbjct: 298 MLLITGAMTNIPRDLYEASEVDGASKFQQFREITLPMVLHQVAPSLVMTFAHNFNNFGAI 35- 7 Query: 384 YLLTGGGPTNSEYYQAGTTDLLVTWLYKLTVTAADYNLASVIGILIFTVSAIFSLLAYTR 44- 3 YLLT GGP N EY AG TD+L+TW+YKLT+ Y +ASVI I+IF +IF++ + R Sbjct: 358 YLLTEGGPINPEYRFAGHTDILITWIYKLTLDFQQYQIASVISIIIFLFLSIFAIWQFRR 41- 7 Query: 444 TASYKE 449 S+KE Sbjct: 418 MKSFKE 423 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04971 Identities = 357/446 (80%), Positives = 404/446 (90%), Gaps = 2/446 (0%) Query: 11 MSLKEVFQKGDLATKLSFLIMGLANLKNKQIVKGLLFLISEILFLITFVYQVIPAVKGLI 70 - +S+ E ++G KLS +IMG AN NKQ +KG+LFLISE++FL+ FV Q+IPA++GL+ Sbjct: 10 ISVIEALKRGSWDIKLSSIIMGFANFANKQFIKGILFLISELIFLVAFVSQIIPAIRGLV 69 Query: 71 SLGTQEQGMTTKTVDGIKIQVATQGDNSMLMLIFGLASLIFCCVFAYIYWSNIKSAAHLL 130- +LGTQ QGMTTKT+DGI IQVA GDNSMLMLIFGLASLIFC VFAYIYW N+KSA +L Sbjct: 70 TLGTQTQGMTTKTIDGINIQVAVDGDNSMLMLIFGLASLIFCLVFAYIYWCNLKSAPNLY 129- Query: 131 TLKEEGREIPSFKKDIKSLTDGRFHMTLMSIPLIGVLLFTILPLVYMICLAFTNYDHNHL 19- 0 K++G++IPSFK+D+ +LT+GRFHMTLM+IPLIGVLLFTILPL+YMICLAFTN+DHNHL Sbjct: 130 LFKQKGQKIPSFKEDLATLTNGRFHMTLMAIPLIGVLLFTILPLIYMICLAFTNFDHNHL 18- 9 Query: 191 PPKSLFDWVGFANFGNIFSGRMASTFFPVLSWTLIWAVFATVTNFFFGIILALLINTKGL 25- 0 PPKSLFDWVG ANFGN+ SGRMA TFFP+ SWTLIWAVFATVTNFFFGIILALLINTKGL Sbjct: 190 PPKSLFDWVGLANFGNVLSGRMAGTFFPIFSWTLIWAVFATVTNFFFGIILALLINTKGL 24- 9 Query: 251 KFKKMWRTIFVITMAVPQFISLLIMRNLLSDAGPVNALLIKWGLISSAHPLPFLSDPVWA 31- 0 K+KKMWRTIFVIT+AVPQFISLLIMRNLL+D GP+NALL K GLI+ + LPFLSDP+WA Sbjct: 250 KWKKMWRTIFVITIAVPQFISLLIMRNLLNDEGPLNALLNKIGLINGS--LPFLSDPLWA 30- 7 Query: 311 KFSIIFVNMWVGIPVTMLVATGIIMNLPAEQIEAAEIDGANKFQVFQSITFPQILLIMTP 37- 0 KFSIIFVNMW+GIP TML+ATGIIMNLP+EQIEAAEIDGA+KFQVF+SITFPQILLIMTP Sbjct: 308 KFSIIFVNMWIGIPFTMLIATGIIMNLPSEQIEAAEIDGASKFQVFKSITFPQILLIMTP 36- 7 Query: 371 TLIQQFIGNINNFNVIYLLTQGGPTNSTYYQAGSTDLLVTWLYNLTVTAADYNLASVVGI 43- 0 LIQQFIGNINNFNVIYLLT GGPTNS YYQAG+TDLLVTWLY LTVTAADYNLASV+GI Sbjct: 368 NLIQQFIGNINNFNVIYLLTGGGPTNSEYYQAGTTDLLVTWLYKLTVTAADYNLASVIGI 42- 7 Query: 431 LIFILSAVFSLLAYTRTNSYKEGAAK 456 LIF +SA+FSLLAYTRT SYKEGAAK Sbjct: 428 LIFTVSAIFSLLAYTRTASYKEGAAK 453 A related GBS gene <SEQ ID 8869> and protein <SEQ ID 8870> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04972 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -12.73 GvH: Signal Score (-7.5): -6.04 Possible site: 36 >>> Seems to have no N-terminal signal sequence ALOM program count: 7 value: -11.46 threshold: 0.0 INTEGRAL Likelihood = -11.46 Transmembrane 427-443 (417-447) INTEGRAL Likelihood = -9.87 Transmembrane 99-115 (96-121) INTEGRAL Likelihood = -9.39 Transmembrane 166-182 (154-185) INTEGRAL Likelihood = -6.21 Transmembrane 259-275 (257-276) INTEGRAL Likelihood = -6.21 Transmembrane 229-245 (223-247) INTEGRAL Likelihood = -6.10 Transmembrane 44-60 (40-66) INTEGRAL Likelihood = -4.51 Transmembrane 314-330 (312-331) PERIPHERAL Likelihood = 0.90 212 modified ALOM score: 2.79 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5585 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00112## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1641 A DNA sequence (GBSx1736) was identified in S. agalactiae <SEQ ID 5075> which encodes the amino acid sequence <SEQ ID 5076>. This protein is predicted to be maltose/maltodextrin-binding protein precursor. Analysis of this protein sequence reveals the following:

TABLE-US-04973 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.98 Transmembrane 25-41 (24-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.2593 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9999> which encodes amino acid sequence <SEQ ID 10000> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04974 >GP:AAA26925 GB:L08611 MalX [Streptococcus pneumoniae] Identities = 117/418 (27%), Positives = 186/418 (43%), Gaps = 43/418 (10%) Query: 15 TKMEKNTWKKLLVSTAALSVVAGGAIAATHSNSVDAASKTTIKLWVPTDSKASYKAIVKK 74 - +K K+T V+ A+L +VA G+ A ++ + ++V K+ + + K Sbjct: 3 SKFMKSTAVLGTVTLASLLLVACGSKTADKPADSGSSEVKELTVYVDEGYKSYIEEVAKA 62 Query: 75 FZKE-NKGVTVKMIESNDSKAQENVKKDPSKAADVFSLPHDQLGQLVESGVIQEIPEQYS 133- ++KE VT+K ++ + ++ DV P+D++G L G + E+ + S Sbjct: 63 YEKEAGVKVTLKTGDALGGLDKLSLDNQSGNVPDVMMAPYDRVGSLGSDGQLSEV--KLS 120- Query: 134 KEIAKNDTKQSLTGAQYKGKTYAFPFGIESQVLYYNKTKLTADDVKSYETITSKGKFGXQ 19- 3 +DT +SL A GK Y P IES V+YYNK L D K++ + + K Sbjct: 121 DGAKTDDTTKSLVTAA-NGKVYGAPAVIESLVMYYNKD-LVKDAPKTFADLENLAKDSKY 17- 8 Query: 194 LKAA-------------NSYVTGPXFLSVGDTLFGKSGEDAKGTNWGNEAGVSVL----- 23- 5 A N Y T G +FG++G+DAK N+ ++ + Sbjct: 179 AFAGEDGKTTAFLADWTNFYYTYGLLAGNGAYVFGQNGKDAKDIGLANDGSIAGINYAKS 23- 8 Query: 236 ---KWIADQKKNDGFVNLTAENTMSKFGDGSVHAFESGPWDYDAAKKAVGEDKIGVAVYP 29- 2 KW + +G NL ++F +G A GPW A K A + GVA P Sbjct: 239 WYEKWPKGMQDTEGAGNLI----QTQFQEGKTAAIIDGPWKAQAFKDA--KVNYGVATIP 29- 2 Query: 293 TMKIGDKEVQQKAFLGVKLYAVNQAPAGSNTKRISASYKLAAYLTNAESQKIQFEKRHIV 35- 2 T+ G + AF G K + + QA K + AS K +L E QK+ ++K + + Sbjct: 293 TLPNGK---EYAAFGGGKAWVIPQA-----VKNLEASQKFVDFLVATEQQKVLYDKTNEI 34- 4 Query: 353 PANSSIQSSDSVQKDELAKAVIEMGSSDKYTTVMPKLSQMSTFWTESAAILSDTYSGK 410 PAN+ +S + DEL AVI+ K T +P +SQMS W + +L D SG+ Sbjct: 345 PANTEARSYAEGKNDELTTAVIK---QFKNTQPLPNISQMSAVWDPAKNMLFDAVSGQ 399 A related DNA sequence was identified in S. pyogenes <SEQ ID 5077> which encodes the amino acid sequence <SEQ ID 5078>. Analysis of this protein sequence reveals the following: TABLE-US-04975 Possible site: 28 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04976 >GP:AAA26925 GB:L08611 MalX [Streptococcus pneumoniae] Identities = 126/423 (29%), Positives = 191/423 (44%), Gaps = 50/423 (11%) Query: 13 SLTLASTLLVGCGSGSKDK--KEAGADSKTIKLWVPTGSKKSYADTIAK-FEKDSGYTVK 69 - ++TLAS LLV CGS + DK ++ K + ++V G KSY + +AK +EK++G V Sbjct: 14 TVTLASLLLVACGSKTADKPADSGSSEVKELTVYVDEG-YKSYIEEVAKAYEKEAGVKVT 72 Query: 70 VVESEDPKAQEKIKKD--ASTAADVFSLPHDQLGQLVESGTIQEVPEKYNKEIAATSTDQ 127- + + +K+ D + DV P+D++G L G + EV K + T + Sbjct: 73 LKTGDALGGLDKLSLDNQSGNVPDVMMAPYDRVGSLGSDGQLSEV--KLSDGAKTDDTTK 130- Query: 128 ALVGAQYKGKTYAFPFGIESQVLFYNKSKLAAEDVTSYD----TITTKATFGGTFKQ--- 18- 0 +LV A GK Y P IES V++YNK + T D +K F G + Sbjct: 131 SLVTAA-NGKVYGAPAVIESLVMYYNKDLVKDAPKTFADLENLAKDSKYAFAGEDGKTTA 18- 9 Query: 181 -----ANTYATGPLFMSVGNTLFGENGEDVKGTNWGNEKGAAVL--------KWIADQAS 22- 7 N Y T L G +FG+NG+D K N+ A + KW Sbjct: 190 FLADWTNFYYTYGLLAGNGAYVFGQNGKDAKDIGLANDGSIAGINYAKSWYEKWPKGMQD 24- 9 Query: 228 NKGFVSLDANNVMSKFGDGSVASFESGPWDYEAAQKAIGKENLGVAIYPKVTIGGETVQQ 28- 7 +G N + ++F +G A+ GPW +A +A K N GVA P + G E Sbjct: 250 TEG----AGNLIQTQFQEGKTAAIIDGPWKAQAFKDA--KVNYGVATIPTLPNGKE---Y 30- 0 Query: 288 KAFLGVKLYAVNQAPAKGDTKRIAASYKLASYLTNAESQENQFKTRNIVPANKEVQSSEA 34- 7 AF G K + + QA K + AS K +L E Q+ + N +PAN E +S Sbjct: 301 AAFGGGKAWVIPQA-----VKNLEASQKFVDFLVATEQQKVLYDKTNEIPANTEARSYAE 35- 5 Query: 348 VQSNELAKTVITMGSSSDYTVVMPKLSQMGTFWTESAAILSDAFNG----KIKENDYLTK 40- 3 +++EL VI + T +P +SQM W + +L DA +G K ND +T Sbjct: 356 GKNDELTTAVIKQFKN---TQPLPNISQMSAVWDPAKNMLFDAVSGQKDAKTAANDAVTL 41- 2 Query: 404 LQQ 406 +++ Sbjct: 413 IKE 415 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04977 Identities = 278/415 (66%), Positives = 334/415 (79%), Gaps = 6/415 (1%) Query: 21 TWKKLLVSTAALSVVAGGAIAATHSNSVD----AASKTTIKLWVPTDSKASYKAIVKKFZ 76 - +W+K++V A+L++ A + S S D A TIKLWVPT SK SY + KF+ Sbjct: 3 SWQKVIVGGASLTL-ASTLLVGCGSGSKDKKEAGADSKTIKLWVPTGSKKSYADTIAKFE 61 Query: 77 KENKGVTVKMIESNDSKAQENVKKDPSKAADVFSLPHDQLGQLVESGVIQEIPEQYSKEI 136- K++ G TVK++ES D KAQE +KKD S AADVFSLPHDQLGQLVESG IQE+PE+Y+KEI Sbjct: 62 KDS-GYTVKVVESEDPKAQEKIKKDASTAADVFSLPHDQLGQLVESGTIQEVPEKYNKEI 120- Query: 137 AKNDTKQSLTGAQYKGKTYAFPFGIESQVLYYNKTKLTADDVKSYETITSKGKFGXQLKA 19- 6 A T Q+L GAQYKGKTYAFPFGIESQVL+YNK+KL A+DV SY+TIT+K FG K Sbjct: 121 AATSTDQALVGAQYKGKTYAFPFGIESQVLFYNKSKLAAEDVTSYDTITTKATFGGTFKQ 18- 0 Query: 197 ANSYVTGPXFLSVGDTLFGKSGEDAKGTNWGNEAGVSVLKWIADQKKNDGFVNLTAENTM 25- 6 AN+Y TGP F+SVG+TLFG++GED KGTNWGNE G +VLKWIADQ N GFV+L A N M Sbjct: 181 ANTYATGPLFMSVGNTLFGENGEDVKGTNWGNEKGAAVLKWIADQASNKGFVSLDANNVM 24- 0 Query: 257 SKFGDGSVHAFESGPWDYDAAKKAVGEDKIGVAVYPTMKIGDKEVQQKAFLGVKLYAVNQ 31- 6 SKFGDGSV +FESGPWDY+AA+KA+G++ +GVA+YP + IG + VQQKAFLGVKLYAVNQ Sbjct: 241 SKFGDGSVASFESGPWDYEAAQKAIGKENLGVAIYPKVTIGGETVQQKAFLGVKLYAVNQ 30- 0 Query: 317 APAGSNTKRISASYKLAAYLTNAESQKIQFEKRHIVPANSSIQSSDSVQKDELAKAVIEM 37- 6 APA +TKRI+ASYKLA+YLTNAESQ+ QF+ R+IVPAN +QSS++VQ +ELAK VI M Sbjct: 301 APAKGDTKRIAASYKLASYLTNAESQENQFKTRNIVPANKEVQSSEAVQSNELAKTVITM 36- 0 Query: 377 GSSDKYTTVMPKLSQMSTFWTESAAILSDTYSGKIKSSDYLKRLKQFDKDIAKTK 431 GSS YT VMPKLSQM TFWTESAAILSD ++GKIK +DYL +L+QFDKDIA TK Sbjct: 361 GSSSDYTVVMPKLSQMGTFWTESAAILSDAFNGKIKENDYLTKLQQFDKDIAATK 415 SEQ ID 5076 (GBS649) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 132 (lane 2 & 3; MW 76 kDa) and in FIG. 186 (lane 7; MW 76 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 132 (lane 7; MW 51 kDa) and in FIG. 178 (lane 8; MW 51 kDa). GBS649-His was purified as shown in FIG. 229, lane 8. Purified GBS649-GST is shown in FIG. 245, lanes 6 &73. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1642 A DNA sequence (GBSx1737) was identified in S. agalactiae <SEQ ID 5079> which encodes the amino acid sequence <SEQ ID 5080>. Analysis of this protein sequence reveals the following: TABLE-US-04978 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2462(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04979 >GP:AAD02112 GB:AF039082 putative maltose operon transcriptional repressor [Lactococcus lactis] Identities = 43/61 (70%), Positives = 49/61 (79%) Query: 2 VTIKDVAAKAGVNPSTVSRVLKDNASISSKTKERVKKAMEELGYVPNVAAQMLASGLTQN 61 VTIKDVA KAGVN STVSRV+KD++ IS KTK +V+KAM ELGY N AAQ+LASG T Sbjct: 3 VTIKDVAKKAGVNASTVSRVIKDSSEISDKTKVKVRKAMHELGYRRNAAAQILASGKTNT 62 Query: 62 I 62 I Sbjct: 63 I 63 A related DNA sequence was identified in S. pyogenes <SEQ ID 5081> which encodes the amino acid sequence <SEQ ID 5082>. Analysis of this protein sequence reveals the following: TABLE-US-04980 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.93 Transmembrane 269-285 (266-287) ----- Final Results ----- bacterial membrane --- Certainty = 0.2572(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04981 Identities = 53/62 (85%), Positives = 57/62 (91%) Query: 1 MVTIKDVAAKAGVNPSTVSRVLKDNASISSKTKERVKKAMEELGYVPNVAAQMLASGLTQ 60 MVTIKDVA KAGVNPSTVSRVLKDN SIS KTKE+V+KAM +LGYVPNVAAQ+LASGLT Sbjct: 26 MVTIKDVAQKAGVNPSTVSRVLKDNRSISMKTKEKVRKAMADLGYVPNVAAQILASGLTH 85 Query: 61 NI 62 NI Sbjct: 86 NI 87 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1643 A DNA sequence (GBSx1738) was identified in S. agalactiae <SEQ ID 5083> which encodes the amino acid sequence <SEQ ID 5084>. Analysis of this protein sequence reveals the following: TABLE-US-04982 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.70 Transmembrane 14-30 (8-34) INTEGRAL Likelihood = -6.90 Transmembrane 66-82 (63-85) INTEGRAL Likelihood = -6.69 Transmembrane 110-126 (105-128) INTEGRAL Likelihood = -3.93 Transmembrane 132-148 (129-149) ----- Final Results ----- bacterial membrane --- Certainty = 0.4079(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9443> which encodes amino acid sequence <SEQ ID 9444> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04983 >GP:AAC67260 GB:AF017113 YvjA [Bacillus subtilis] Identities = 83/227 (36%), Positives = 140/227 (61%) Query: 9 FGWDSAFFIMIINIPLLLLCYFGLGKQTFLKTVYGSWIFPVFIKLTQSVPTLTHNPLLAA 68 +G+++A+ IINIPL + LG + LKT+ GS P+ + LT+ + TH+ LLAA Sbjct: 52 YGFEAAYVQWIINIPLFIAGVILLGGKFGLKTLAGSVFLPLVVFLTRDIQPATHHELLAA 111- Query: 69 LFGGVIVGCGLGIVFWSDSSTGGTGIIIQFLGKYTPISLGQGVILIDGLVTIVGFLAFDS 128- +FGGV +G G+GIV+ STGGT + Q + KY+ +SLG+ + +IDG++ + + F+ Sbjct: 112 IFGGVGIGIGIGIVYLGKGSTGGTALAAQIIHKYSGLSLGKCLAIIDGMIVVTAMIVFNI 17- 1 Query: 129 DTVNFSIIGLITISYIINAIQTGFTTLSTVLIVSQEHQKIKTYINTVADRGVTEIPVKGG 18- 8 + +++++G+ S I+ +Q GF LI++++ Q +K + DRGVT+I GG Sbjct: 172 EQGLYAMLGVYVSSKTIDVVQVGFNRSKMALIITKQEQAVKEAVLQKIDRGVTKISAVGG 23- 1 Query: 189 YSGTNQIMLMTTIAGYEFAKLQEAIAEIDETAFITVTPTSQASGRGF 235 Y+ ++ +LM + EF KL++ + +IDE+AF+ V S+ G GF Sbjct: 232 YTDDDRPILMCVVGQTEFTKLKQIVKQIDESAFVIVADASEVLGEGF 278 A related DNA sequence was identified in S. pyogenes <SEQ ID 5085> which encodes the amino acid sequence <SEQ ID 5086>. Analysis of this protein sequence reveals the following: TABLE-US-04984 Possible site: 57 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.21 Transmembrane 104-120 (101-123) INTEGRAL Likelihood = -3.93 Transmembrane 147-163 (142-167) INTEGRAL Likelihood = -3.29 Transmembrane 169-185 (169-186) ----- Final Results ----- bacterial membrane --- Certainty = 0.3484 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04985 >GP:AAC67260 GB:AF017113 YvjA [Bacillus subtilis] Identities = 106/267 (39%), Positives = 169/267 (62%), Gaps = 1/267 (0%) Query: 7 DLLLVTIGSFITAIGFNTMFVDNHIASGGMVGIAVVIKALFGISPSLFLMASNIPLLLMC 66 D + + IG+ ITA+ FN + N IA+GG+ GI+ ++++ +G + NIPL + Sbjct: 13 DYVYILIGAAITAVSFNVFLLPNKIAAGGVSGISTILQS-YGFEAAYVQWIINIPLFIAG 71 Query: 67 YFFLGKQNFIKTLYGSWIYPIAIRSTNSLPTLTHNQLLAAIFGGIICGIGLGMVFWGNSS 126- LG + +KTL GS P+ + T + TH++LLAAIFGG+ GIG+G+V+ G S Sbjct: 72 VILLGGKFGLKTLAGSVFLPLVVFLTRDIQPATHHELLAAIFGGVGIGIGIGIVYLGKGS 131- Query: 127 TGGTGILTQILHKYSPLSLGVAMTIVDGISVLMGFIALSADDVMYSTIGLFVIGYVISVM 18- 6 TGGT + QI+HKYS LSLG + I+DG+ V+ I + + +Y+ +G++V I V+ Sbjct: 132 TGGTALAAQIIHKYSGLSLGKCLAIIDGMIVVTAMIVFNIEQGLYAMLGVYVSSKTIDVV 19- 1 Query: 187 ENGFDSSKNVMIISKDYQAIREYITTVMDRGVTKLPIRGGYTTSDKIMLMAIVSSHELPT 24- 6 + GF+ SK +II+K QA++E + +DRGVTK+ GGYT D+ +LM +V E Sbjct: 192 QVGFNRSKMALIITKQEQAVKEAVLQKIDRGVTKISAVGGYTDDDRPILMCVVGQTEFTK 25- 1 Query: 247 LQEKILEIDDTAFIVVMPAAQVMGRGF 273 L++ + +ID++AF++V A++V+G GF Sbjct: 252 LKQIVKQIDESAFVIVADASEVLGEGF 278 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04986 Identities = 135/252 (53%), Positives = 190/252 (74%) Query: 1 MAVSFHEVFGWDSAFFIMIINIPLLLLCYFGLGKQTFLKTVYGSWIFPVFIKLTQSVPTL 60 +AV +FG + F+M NIPLLL+CYF LGKQ F+KT+YGSWI+P+ I+ T S+PTL Sbjct: 39 IAVVIKALFGISPSLFLMASNIPLLLMCYFFLGKQNFIKTLYGSWIYPIAIRSTNSLPTL 98 Query: 61 THNPLLAALFGGVIVGCGLGIVFWSDSSTGGTGIIIQFLGKYTPISLGQGVILIDGLVTI 120- THN LLAA+FGG+I G GLG+VFW +SSTGGTGI+ Q L KY+P+SLG + ++DG+ + Sbjct: 99 THNQLLAAIFGGIICGIGLGMVVFWGNSSTGGTGILTQILHKYSPLSLGVAMTIVDGISVL 15- 8 Query: 121 VGFLAFDSDTVMFSIIGLITISYIINAIQTGFTTLSTVLIVSQEHQKIKTYINTVADRGV 18- 0 +GF+A +D VM+S IGL I Y+I+ ++ GF + V+I+S+++Q I+ YI TV DRGV Sbjct: 159 MGFIALSADDVMYSTIGLFVIGYVISVMENGFDSSKNVMIISKDYQAIREYITTVNDRGV 21- 8 Query: 181 TEIPVKGGYSGTNQIMLMTTIAGYEFAKLQEAIAEIDETAFITVTPTSQASGRGFSLQKN 24- 0 T++P++GGY+ +++IMLM ++ +E LQE I EID+TAFI V P +Q GRGFSL K Sbjct: 219 TKLPIRGGYTTSDKIMLMAIVSSHELPTLQEKILEIDDTAFIVVMPAAQVMGRGFSLTKQ 27- 8 Query: 241 HGRLDEDILMPM 252 + R D+D+L+PM Sbjct: 279 YKREDKDVLLPM 290 A related GBS gene <SEQ ID 8871> and protein <SEQ ID 8872> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-04987 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: 1.57 GvH: Signal Score (-7.5): -2.56 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 4 value: -7.70 threshold: 0.0 INTEGRAL Likelihood = -7.70 Transmembrane 14-30 (8-34) INTEGRAL Likelihood = -6.90 Transmembrane 66-82 (63-85) INTEGRAL Likelihood = -6.69 Transmembrane 110-126 (105-128) INTEGRAL Likelihood = -3.93 Transmembrane 132-148 (129-149) PERIPHERAL Likelihood = 3.71 37 modified ALOM score: 2.04 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4079 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00113## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1644 A DNA sequence (GBSx1739) was identified in S. agalactiae <SEQ ID 5087> which encodes the amino acid sequence <SEQ ID 5088>. This protein is predicted to be ABC transporter, ATP-binding protein (b0820). Analysis of this protein sequence reveals the following: TABLE-US-04988 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3122 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04989 >GP:AAC24918 GB:AF012285 YkpA [Bacillus subtilis] Identities = 355/540 (65%), Positives = 451/540 (82%), Gaps = 4/540 (0%) Query: 1 MLTVSDVSLRFSDRKLFDEVNINFTAGNTYGLIGANGAGKSTFLKILAGDIEPTTGHIAL 60 M+ V++VSLRF+DRKLF++VNI FT GN YGLIGANGAGKSTFLK+L+G+IEP TG + + Sbjct: 1 MIAVNNVSLRFADRKLFEDVNIKFTPGNCYGLIGANGAGKSTFLKVLSGEIEPQTGDVHM 60 Query: 61 GPDERLSVLRQNHFDYEDERVIDVVIMGNETLYSIMKERDAIYMKEDFSDEDGVRAAELE 120- P ERL+VL+QNHF+YE+ V+ VVIMG++ LY +M+EKDAIYMK DFSDEDG+RAAELE Sbjct: 61 SPGERLAVLKQNHFEYEEYEVLKVVIMGHKRLYEVMQEKDAIYMKPDFSDEDGIRAAELE 120- Query: 121 GEFAELGGWEAESEASQLLQNLNISEELHYQNMSELANGDKVKVLLAKALFGKPDVLLLD 18- 0 GEFAEL GWEAESEA+ LL+ L ISE+LH + M++L +KVKVLLA+ALFGKPDVLLLD Sbjct: 121 GEFAELNGWEAESEAAILLKGLGISEDLHTKKMADLGGSEKVKVLLAQALFGKPDVLLLD 18- 0 Query: 181 EPTNGLDIQSITWLEDFLIDFENTVIVVSHDRNFLNKVCTHMADLDFGKIKLFVGNYDFW 24- 0 EPTN LD+Q+I WLE+FLI+FENTVIVVSHDRHFLNKVCTH+ADLDF KI+++VGNYDFW Sbjct: 181 SPTNHLDLQAIQWLEEFLINFENTVIVVSHDRHFLNKVCTHIADLDFNKIQIYVGNYDFW 24- 0 Query: 241 KESSELAARLQADRNAKAEEKIKQLQEFVARFSANASKSKQATSRKKMLDKIELEEIVPS 30- 0 ESS+LA +L + N K EE+IKQLQEFVARFSANASKSKQATSRKK+L+KI L++I PS Sbjct: 241 YESSQLALKLSQEANKKKEEQIKQLQEFVARFSANASKSKQATSRKKLLEKITLDDIKPS 30- 0 Query: 301 SRKYPFVNFKAEREMGNDLLTVENLSVTIDGEKILDNISFILRPGDKTALIGQNDIQTTA 36- 0 SR+YP+VNF ERE+GND+L VE L+ TIDG K+LDN+SFI+ DK A G+N++ T Sbjct: 301 SRRYPYVNFTPEREIGNDVLRVEGLTKTIDGVKVLDNVSFINNREDKIAFTGRNELAVTT 36- 0 Query: 361 LIRALMGDIEYE-GTIKWGVTTSRSYLPKDNSRDFASGE-SILEWLRQFASKEEDDNTFL 41- 8 L + + G++E + GT KWGVTTS++Y PKDNS F + ++++WLRQ+ S + +FL Sbjct: 361 LFKIISGEMEADSGTFKWGVTTSQAYFPKDNSEYFEGSDLNLVDWLRQY-SPHDQSESFL 41- 9 Query: 419 RGFLGRMLFSGDEVNKSVNVLSGGEKVRVMLSKLMLLKSNVLVLDDPTNHLDLESISSLN 47- 8 RGFLGRMLFSG+EV+K NVLSGGEKVR MLSK ML +N+L+LD+PTNHLDLESI++LN Sbjct: 420 RGFLGRMLFSGEEVHKKANVLSGGEKVRCMLSKAMLSGANILILDEPTNHLDLESITALN 47- 9 Query: 479 DGLKDFKESIIFASHDHEFIQTLANHIIVLSKNGVIDRIDETYDEFLENTEVQAKVAQLW 53- 8 +GL FK +++F SHDH+F+QT+AN II ++ NG++D+ +YDEFLEN +VQ K+ +L+ Sbjct: 480 NGLISFKGAMLFTSHDHQFVQTIANRIIEITPNGIVDK-QMSYDEFLENADVQKKLTELY 53- 8 A related DNA sequence was identified in S. pyogenes <SEQ ID 5089> which encodes the amino acid sequence <SEQ ID 5090>. Analysis of this protein sequence reveals the following:

TABLE-US-04990 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3124(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-04991 Identities = 497/539 (92%), Positives = 525/539 (97%) Query: 1 MLTVSDVSLRFSDRKLFDEVNINFTAGNTYGLIGANGAGKSTFLKILAGDIEPTTGHIAL 60 +LTVSDVSLRFSDRKLFD+VNI FTAGNTYGLIGANGAGKSTFLKILAGDIEP+TGHI+L Sbjct: 1 LLTVSDVSLRFSDRKLFDDVNIKFTAGNTYGLIGANGAGKSTFLKILAGDIEPSTGHISL 60 Query: 61 GPDERLSVLRQNHFDYEDERVIDVVIMGNETLYSIMKEKDAIYMKEDFSDEDGVRAAELE 120- GPDERLSVLRQNHFDYE+ER IDVVIMGNE LY+IMKEKDAIYMK DFS+EDGVRAAELE Sbjct: 61 GPDERLSVLRQNHFDYEEERAIDVVIMGNEQLYNIMKEKDAIYMKADFSEEDGVRAAELE 120- Query: 121 GEFAELGGWEAESEASQLLQNLNISEELHYQNMSELANGDKVKVLLAKALFGKPDVLLLD 18- 0 G FAELGGWEAESEASQLLQNLNI E+LHYQNMSELANGDKVKVLLAKALFGKFDVLLLD Sbjct: 121 GIFAELGGWEAESEASQLLQNLNIPEDLHYQNMSELANGDKVKVLLAKALFGKPDVLLLD 18- 0 Query: 181 EPTNGLDIQSITWLEDFLIDFENTVIVVSHDRHFLNKVCTHMADLDFGKIKLFVGNYDFW 24- 0 EPTNGLDIQSI+WLEDFLIDFENTVIVVSHDRHFLNKVCTHMADLDFGKIKLFVGNYDFW Sbjct: 181 EPTNGLDIQSISWLEDFLIDFENTVIVVSHDRHFLNKVCTHMADLDFGKIKLFVGNYDFW 24- 0 Query: 241 KESSELAARLQADRNAKAEEKIKQLQEFVARFSANASKSKQATSRKKMLDKIELEEIVPS 30- 0 K+SSELAARLQADRNAKAEEKIK+LQEFVARFSANASKSKQATSRKKMLDKIELEEIVPS Sbjct: 241 KQSSELAARLQADRNAKAEEKIKELQEFVARFSANASKSKQATSRKKMLDKIELEEIVPS 30- 0 Query: 301 SRKYPFVNFKAEREMGNDLLTVENLSVTIDGEKILDNISFILRPGDKTALIGQNDIQTTA 36- 0 SRKYPF+NFKAEREMGND LTVENLSVTIDGEKI+DNISFILRFGDK A+IGQNDIQTTA Sbjct: 301 SRKYPFINFKAEREMGNDFLTVENLSVTIDGEKIIDNISFILRFGDKAAIIGQNDIQTTA 36- 0 Query: 361 LIRALMGDIEYEGTIKWGVTTSRSYLPKDNSRDFASGESILEWLRQFASKEEDDNTFLRG 42- 0 L+RAL DI+YEGTIKWGVTTSRSYLPKDNS+DFA+ ESILSWLRQFASK EDD+TFLRG Sbjct: 361 LMRALADDIDYEGTIKWGVTTSRSYLPKDNSKDFATEESILEWLRQFASKGEDDDTFLRG 42- 0 Query: 421 FLGRMLFSGDEVNKSVNVLSGGEKVRVMLSKLMLLKSNVLVLDDPTNHLDLESISSLNDG 48- 0 FLGRMLFSGDEV KSVNVLSGGEKVRVMLSKLMLLKSNVL+LDDPTNHLDLESISSLNDG Sbjct: 421 FLGRMLFSGDEVKKSVNVLSGGEKVRVMLSKLMLLKSNVLILDDPTNHLDLESISSLNDG 48- 0 Query: 481 LKDFKESIIFASHDHEFIQTLANHIIVLSKNGVIDRIDETYDEFLENTEVQAKVAQLWK 539- +KDFKES+IFASHDHEFIQT+ANHI+V+SKNGVIDRIDETYDEFL+N EVQA+VA+LWK Sbjct: 481 IKDFKESVIFASHDHEFIQTIANHIVVISKNGVIDRIDETYDEFLDNPEVQARVAELWK 539- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1645 A DNA sequence (GBSx1740) was identified in S. agalactiae <SEQ ID 5091> which encodes the amino acid sequence <SEQ ID 5092>. Analysis of this protein sequence reveals the following: TABLE-US-04992 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.71 Transmembrane 14-30 (8-35) INTEGRAL Likelihood = -7.70 Transmembrane 384-400 (382-403) INTEGRAL Likelihood = -7.22 Transmembrane 412-428 (408-433) INTEGRAL Likelihood = -5.73 Transmembrane 163-179 (155-180) INTEGRAL Likelihood = -5.52 Transmembrane 322-338 (320-344) INTEGRAL Likelihood = -5.10 Transmembrane 297-313 (290-314) INTEGRAL Likelihood = -4.41 Transmembrane 360-376 (357-377) INTEGRAL Likelihood = -4.35 Transmembrane 438-454 (437-455) INTEGRAL Likelihood = -4.09 Transmembrane 136-152 (136-153) INTEGRAL Likelihood = -3.35 Transmembrane 110-126 (106-128) INTEGRAL Likelihood = -2.28 Transmembrane 232-248 (232-248) INTEGRAL Likelihood = -1.81 Transmembrane 832-848 (832-848) INTEGRAL Likelihood = -1.12 Transmembrane 200-216 (200-216) ----- Final Results ----- bacterial membrane --- Certainty = 0.4885 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04993 >GP:AAC14608 GB:U95840 transmembrane protein Tmp5 [Lactococcus lactis] Identities = 140/260 (53%), Positives = 182/260 (69%), Gaps = 6/260 (2%) Query: 16 SFLLPFIIIVCILFTKNIYWGSPTTILASDGFHQYVIFNQALRNILH--GSNSLFYTFTS 73 - SF +P I++V + L IYWGS +ILA D +HQYV + RNILH GS YTFTS Sbjct: 14 SFFIPLILMVIVLAMTGIYWGSSRSILAGDAYHQYVAIHSLYRNILHSGGSQGFLYTFTS 73 Query: 74 GLGLNFYALSSYYLGSFLSPIVYFFNLKNMPDAIYLLTICKIGLIGLSMFVTLCKRHCKV 133- GLGLN YA S+YY+GSFL P +FF++K+MPDA+YL TI K GLIGLS FV+ + K+ Sbjct: 74 GLGLNLYAFSAYYMGSFLMPFTFFFDVKSMPDALYLFTIIKFGLIGLSSFVSFKNMYQKL 133- Query: 134 NRVLLLVISTCYSLMSFSISQIEINMWLDVFILIPLVVLGVDQLLWERKPILYFLSLTAL 19- 3 + + +L IST ++LMSF SQ+EI MWLDVFIL+PL++ G+ +L+ ERK LYF+SL L Sbjct: 134 SNLTVLSISTAFALMSFLTSQLEITMWLDVFILLPLIIWGLHRLMDERKRWLYFVSLLIL 19- 3 Query: 194 FIQNYYFGFMTAIFTSLYFIVQITRNTDSKVAFKQFLHFTFLSLLAGMTSSIMILPTYFD 25- 3 FIQNYYFGFM AIF LYF + R T K ++ + L F S LAG+ S IM+LP Y D Sbjct: 194 FIQNYYFGFMVAIFLVLYF---LARMTYEKWSWTKVLDFVVSSTLAGIASLIMLLPMYLD 25- 0 Query: 254 L-TTHGEKLTKVSKMFTENS 272 L + + + L+ +S +FTENS Sbjct: 251 LKSNNSDALSTLSGIFTENS 270 A related DNA sequence was identified in S. pyogenes <SEQ ID 5093> which encodes the amino acid sequence <SEQ ID 5094>. Analysis of this protein sequence reveals the following: TABLE-US-04994 Possible site: 51 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.29 Transmembrane 15-31 (6-35) INTEGRAL Likelihood = -8.81 Transmembrane 201-217 (196-220) INTEGRAL Likelihood = -6.79 Transmembrane 410-426 (402-428) INTEGRAL Likelihood = -6.05 Transmembrane 230-246 (227-252) INTEGRAL Likelihood = -5.57 Transmembrane 161-177 (153-178) INTEGRAL Likelihood = -4.46 Transmembrane 291-307 (290-311) INTEGRAL Likelihood = -3.82 Transmembrane 133-149 (130-151) INTEGRAL Likelihood = -3.77 Transmembrane 380-396 (376-400) INTEGRAL Likelihood = -3.61 Transmembrane 105-121 (103-124) INTEGRAL Likelihood = -3.45 Transmembrane 832-848 (830-848) INTEGRAL Likelihood = -2.66 Transmembrane 436-452 (435-453) INTEGRAL Likelihood = -2.13 Transmembrane 318-334 (314-336) INTEGRAL Likelihood = -1.54 Transmembrane 356-372 (355-372) INTEGRAL Likelihood = -0.27 Transmembrane 80-96 (80-96) ----- Final Results ----- bacterial membrane --- Certainty = 0.4715(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-04995 >GP: AAC14608 GB: U95840 transmembrane protein Tmp5 [Lactococcus lactis] Identities = 134/269 (49%), Positives = 183/269 (67%), Gaps = 8/269 (2%) Query: 5 NKWIIAGLASFLFPLSIIFIILLSMGIYYNSDKTILASDAFHQYVIFAQNFRNIMH--GS 62 NKW + LASF PL ++ I+L GIY+ S ++ILA DA+HQYV +RNI+H GS Sbjct: 7 NKWAL--LASFFIPLILMVIVLAMTGIYWGSSRSILAGDAYHQYVAIHSLYRNILHSGGS 64 Query: 63 DSFFYTFTSGLGINFYALMCYYLGSFFSPLLFFFNLTSMPDAIYLFTLIKFGLIGLAACY 122- F YTFTSGLG+N YA YY+GSF P FFF++ SMPDA+YLFT+IKFGLIGL++ Sbjct: 65 QGFLYTFTSGLGLNLYAFSAYYMGSFLMPFTFFFDVKSMPDALYLFTIIKFGLIGLSSFV 124- Query: 123 SFHRLYPKISAFLMISISVFYSLMSFLTSQMELNSWLDVFILLPLVILGLNKLITENKTR 18- 2 SF +Y K+S ++SIS ++LMSFLTSQ+E+ WLDVFILLPL+I GL++L+ E K Sbjct: 125 SFKNMYQKLSNLTVLSISTAFALMSFLTSQLEITMWLDVFILLPLIIWGLHRLMDERKRW 18- 4 Query: 183 TYYLSISLLFIQNYYFGYMIALFCILYALVCLLRLNDFNKMFIAFVRFTAVSICAALTSA 24- 2 Y++S++ LFIQNYYFG+M+A+F +LY L R+ + + F S A + S Sbjct: 185 LYFVSLLILFIQNYYFGFMVAIFLVLYFLA---RMTYEKWSWTKVLDFVVSSTLAGIASL 24- 1 Query: 243 LVILPTYLDL-STYGENLSPIKQLVTNNA 270 +++LP YLDL S + LS + + T N+ Sbjct: 242 IMLLPMYLDLKSNNSDALSTLSGIFTENS 270 An alignment of the GAS and GBS proteins is shown below. TABLE-US-04996 Identities = 432/836 (51%), Positives = 569/836 (67%), Gaps = 2/836 (0%) Query: 16 SFLLPFIIIVCILFTKNIYWGSPTTILASDGFHQYVIFNQALRNILHGSNSLFYTFTSGL 75 - SFL P II IL + IY+ S TILASD FHQYVIF Q RNI+HGS+S FYTFTSGL Sbjct: 14 SFLFPLSIIFIILLSMGIYYNSDKTILASDAFHQYVIFAQNFRNIMHGSDSFFYTFTSGL 73 Query: 76 GLNFYALSSYYLGSFLSPIVYFFNLKNMPDAIYLLTICKIGLIGLSMFVTLCKRHCKVNR 135- G+NFYAL YYLGSF SP+++FFNL +MPDAIYL T+ K GLIGL+ + + + K++ Sbjct: 74 GINFYALMCYYLGSFFSPLLFFFNLTSMPDAIYLFTLIKFGLIGLAACYSFHRLYPKISA 133- Query: 136 VLLLVISTCYSLMSFSISQIEINMWLDVFILIPLVVLGVDQLLWERKPILYFLSLTALFI 19- 5 L++ IS YSLMSF SQ+E+N WLDVFIL+PLV+LG+++L+ E K Y+LS++ LFI Sbjct: 134 FLMISISVFYSLMSFLTSQMELNSWLDVFILLPLVILGLNKLITENKTRTYYLSISLLFI 19- 3 Query: 196 QNYYFGFMTAIFTSLYFIVQITRNTDSKVAFKQFLHFTFLSLLAGMTSSIMILPTYFDLT 25- 5 QNYYFG+M A+F LY +V + R D F F+ FT +S+ A +TS+++ILPTY DL+ Sbjct: 194 QNYYFGYMIALFCILYALVCLLRLNDFNKMFIAFVRFTAVSICAALTSALVILPTYLDLS 25- 3 Query: 256 THGEKLTKVSKMFTENSWYMDLFAKNMIGAYDTTKFGSIPMIYVGLLPLLLSLLYFTIKE 31- 5 T+GE L+ + ++ T N+W++D+ AK IG YDTTKF ++PMIYVGL PL+LS++YFT++ Sbjct: 254 TYGENLSPIKQLVTNNAWFLDIPAKLSIGVYDTTKFNALPMIYVGLFPLMLSVIYFTLES 31- 3 Query: 316 VPRRTRLAYGFLIIFVIASFYITPLDLFWQGMHAPNMFLHRYSWVLSVLICLLAAECLEY 37- 5 +P + +LA L+ F+I SFY+ PLDLFWQGMH+PNMFLHRY+W S++I LLA E L Sbjct: 314 IPLKIKLANACLLTFIIISFYLQPLDLFWQGMHSPNMFLHRYAWSFSIVILLLACETLSR 37- 3 Query: 376 LDNISWKKILGVNLILVSGFIITFLFKKHYHYLNLELLLLTLTFLSAYIILTISFVSKQI 43- 5 L ++ K + L+ + + F + Y++L L L LL++ L Y I SF + QI Sbjct: 374 LKEVTQIKAGFAFIFLIILTSLPYSFSQQYNFLPLTLFLLSVFLLLGYTISLFSFRNSQI 43- 3 Query: 436 PKLVFYPFLIGFVVLEMTLNTFYQLNSLNDEWIFPSRQGYAKYNHSISKLVRKTERNNST 49- 5 P F++ F +LE LNT+YQL +N EW FPSRQ Y I+ LV +N+ Sbjct: 434 PSTFISAFILIFSLLESGLNTYYQLQGINKEWGFPSRQIYNSQLKDINNLVNSVSKNSQP 49- 3 Query: 496 FFRTERWLGQTGNDSNKYNYNGISQFSSIRNRSSSQVLDRLGFKSDGTNLNLRYQNNTLI 55- 5 FFR ER L QTGNDSMK+NY GISQFSS+RNR SS +LDRLGF+S GTNLNLRYQNNT+I Sbjct: 494 FFRMERLLPQTGNDSMKFNYYGISQFSSVRNRLSSSLLDRLGFQSKGTNLNLRYQNNTII 55- 3 Query: 556 ADSLFGVKYNLTEYPFDKFGFIKKAQDKQTILYKNQFASQLAILTNQVYQDKPFTVNTLD 61- 5 DSL G+KYNL+E P +KFGF K T LY+N ++S LAILT VY+D VNTLD Sbjct: 554 MDSLLGIKYNLSEGPPNKFGFTKLKTSGNTTLYQNHYSSPLAILTRNVYKDVNLNVNTLD 61- 3 Query: 616 NQTTLLNQLSGLKETYFEHLIPNSVSGQTTLNKQVFVK-KNKQGNTEITYNITIPKNSQL 67- 4 NQT LLNQLSG TYF +SG N Q+ + + Q + + Y I IPK+SQL Sbjct: 614 NQTKLLNQLSGKSLTYFNLQPAQLISGANQFNGQISAQASDYQNSVTLNYQINIPKHSQL 67- 3 Query: 675 YVSMPFINFNNEENKIVQISVNNGPFVPNTLDNAYSFFNIGSFAENSRIKVKFQFPHNDQ 73- 4 YVS+P I F+N + K ++I +N F+ T DNAYSFF++G FA+ F FP N Q Sbjct: 674 YVSIPNIIFSNPDAKEMRIQTDNHNFI-YTTDNAYSFFDLGYFADAKVATFSFVFPKNKQ 73- 2 Query: 735 VSFPIPHFYGLKLEAYQKAMTVINKRKVKVRTDHNKVIANYTSPNRSSLFFTIPYDRGWK 79- 4 +SF PHFY L +E+Y +AM I ++ V N VI +Y S + SL FT+PYD+GW Sbjct: 733 ISFKEPHFYSLSIESYLEAMNSIKQKNVHTYAKSNTVITDYNSKTKGSLIFTLPYDKGWS 79- 2 Query: 795 AYQNNKEIKIFKAQKGFMKINIPKGKGKVTLIFIPYGFKFGVGLSITGIVLFTVYY 850 A ++ K + + KAQ GF+ + IPKGKG+V L FIP GFK G+ LS GI+ + + Y Sbjct: 793 AQKDGKNLPVKKAQGGFLSVTIPKGKGRVILTFIPNGFKLGLSLSCVGIIAYMLLY 848 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1646 A DNA sequence (GBSx1741) was identified in S. agalactiae <SEQ ID 5095> which encodes the amino acid sequence <SEQ ID 5096>. Analysis of this protein sequence reveals the following: TABLE-US-04997 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4624(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-04998 >GP: AAC45340 GB: AE000658 ORF1 [Streptococcus pneumoniae] Identities = 111/159 (69%), Positives = 136/159 (84%) Query: 1 MKLKIITVGKLKEKYLKEGVAEYQKRLNRFSKIETIELADEKTPDKASISENQRILDIEG 60 MK+K++TVGKLKEKYLK+G+AEY KR++RF+K E IEL+DEKTPDKAS SENQ+IL+IEG Sbjct: 1 MKIKVVTVGKLKEKYLKDGIAEYSKRISRFAKFEMIELSDEKTPDKASESENQKILEIEG 60 Query: 61 ERILSKIGERDYVIGLAIEGKQLPSESFSHLIDQKMISGYSTITFVIGGSLGLSQKVKKR 120- +RILSKI +RD+VI LAIEGK SE FS +++ I G+ST+TF+IGGSLGLS VK R Sbjct: 61 QRILSKIADRDFVIVLAIEGKTFFSEEFSKQLEETSIKGFSTLTFIIGGSLGLSSSVKNR 120- Query: 121 ADYLMSFGLLTLPHQLMKLVLMEQIYRAFMIRQGTPYHK 159 A+ +SFG LTLPHQLM+LVL+EQIYRAF I+QG PYHK Sbjct: 121 ANLSVSFGRLTLPHQLMRLVLVEQIYRAFTIQQGFPYHK 159 A related DNA sequence was identified in S. pyogenes <SEQ ID 5097> which encodes the amino acid sequence <SEQ ID 5098>. Analysis of this protein sequence reveals the following: TABLE-US-04999 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4462(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05000 Identities = 112/159 (70%), Positives = 133/159 (83%) Query: 1 MKLKIITVGKLKEKYLKEGVAEYQKRLNRFSKIETIELADEKTPDKASISENQRILDIEG 60 MK+K+I VGKLKE+YLK+G++EYQKRL+RF + E IEL DE+TPDKAS ++NQ I+ E Sbjct: 1 MKVKLICVGKLKERYLKDGISEYQKRLSRFCQFEMIELTDERTPDKASFADNQLIMSKEA 60 Query: 61 ERILSKIGERDYVIGLAIEGKQLPSESFSHLIDQKMISGYSTITFVIGGSLGLSQKVKKR 120- +RI KIGERD+VI LAIEGKQ PSE+FS LI + GYSTITF+IGGSLGL +KKR Sbjct: 61 QRIHKKIGERDFVIALAIEGKQFPSETFSELISGVTVKGYSTITFIIGGSLGLDSIIKKR 120- Query: 121 ADYLMSFGLLTLPHQLMKLVLMEQIYRAFMIRQGTPYHK 159 A+ LMSFGLLTLPHQLM+LVL EQIYRAFMI QG+PYHK Sbjct: 121 ANMLMSFGLLTLPHQLMRLVLTEQIYRAFMITQGSPYHK 159 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1647 A DNA sequence (GBSx1742) was identified in S. agalactiae <SEQ ID 5099> which encodes the amino acid sequence <SEQ ID 5100>. Analysis of this protein sequence reveals the following: TABLE-US-05001 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3785(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1648 A DNA sequence (GBSx1743) was identified in S. agalactiae <SEQ ID 5101> which encodes the amino acid sequence <SEQ ID 5102>. This protein is predicted to be a serine protease. Analysis of this protein sequence reveals the following: TABLE-US-05002 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4533(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9445> which encodes amino acid sequence <SEQ ID 9446> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05003 >GP: AAC45334 GB: AF000658 putative serine protease [Streptococcus pneumoniae] Identities = 215/370 (58%), Positives = 278/370 (75%), Gaps = 20/370 (5%) Query: 4 NDNIPNGGVTKTSKVNYNNITPTTKAVKKVQNSVVSVINYKQQESRSDLSDFYSHFFGNQ 63 N++ N +T+T+ Y N TT+AV KV+++VVSVI Y S FGN Sbjct: 46 NNSNNNSTITQTA---YKNENSTTQAVNKVKDAVVSVITYSANRQNS--------VFGND 94 Query: 64 GGNTDKGLQVYGEGSGVIYKKDGKNAYVVTNNHVIDGAKQIEIQLADGSKAVGKLVGSDT 123- +TD ++ EGSGVIYKK+ K AY+VTNNHVI+GA +++I+L+DG+K G++VG+DT Sbjct: 95 DTDTDSQ-RISSEGSGVIYKKNDKEAYIVTNNHVINGASKVDIRLSDGTKVPGEIVGADT 153- Query: 124 YSDLAVVKIPSDKVSNIAEFADSSKLNIGETAIAIGSPLGTEYANSVTQGIVSSLKRTVT 18- 3 +SD+AVVKI S+KV+ +AEF DSSKL +GETAIAIGSPLG+EYAN+VTQGIVSSL R V+ Sbjct: 154 FSDIAVVKISSEKVTTVAEFGDSSKLTVGETAIAIGSPLGSEYANTVTQGIVSSLNRNVS 21- 3 Query: 184 MTNEEGQTVSTNAIQTDAAINPGNSGGALINIEGQVIGINSSKISSTSNQTSGQSSGNSV 24- 3 + +E+GQ +ST AIQTD AINPGNSGG LINI+GQVIGI SSKI++ + G SV Sbjct: 214 LKSEDGQAISTKAIQTDTAINPGNSGGPLINIQGQVIGITSSKIAT--------NGGTSV 26- 5 Query: 244 EGMGFAIPSNDVVKIINQLESNGQVERPALGISMAGLSNLPSDVISKLKIPSNVTNGIVV 30- 3 EG+GFAIP+ND + II QLE NG+V RPALGI M LSN+ + I +L IPSNVT+G++V Sbjct: 266 EGLGFAIPANDAINIIEQLEKNGKVTRPALGIQMVNLSNVSTSDIRRLNIPSNVTSGVIV 32- 5 Query: 304 ASIQSGMPAQGKLKKYDVITKVDDKEVVSPSDLQSLLYGHQVGDSITVTFYRGENKQTVT 36- 3 S+QS MPA G L+KYDVITKVDDKE+ S +DLQS LY H +GD+I +T+YR ++T + Sbjct: 326 RSVQSNMPANGHLEKYDVITKVDDKEIASSTDLQSALYNHSIGDTIKITYYRNGKEETTS 38- 5 Query: 364 IKLTKTSKDL 373 IKL K+S DL Sbjct: 386 IKLNKSSGDL 395 A related DNA sequence was identified in S. pyogenes <SEQ ID 5103> which encodes the amino acid sequence <SEQ ID 5104>. Analysis of this protein sequence reveals the following:

TABLE-US-05004 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.76 Transmembrane 11-27 (6-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.4503(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05005 Identities = 250/375 (66%), Positives = 299/375 (79%), Gaps = 5/375 (1%) Query: 3 HNDNIPNGGVTKTSKVNYNNITPTTKAVKKVQNSVVSVINYKQQESRSDLSDFYSHFFGN 62 H+ + N G TS + +NN T TTKAVK VQN+VVSVINY+ S S LS+ Y+ FG Sbjct: 34 HSPSKINSGKATTSNMVFNNTTNTTKAVKAVQNAVVSVINYQDNPS-SSLSNPYTKLFGE 92 Query: 63 QGG--NTDKGLQVYGEGSGVIYKKDGKNAYVVTNNHVIDGAKQIEIQLADGSKAVGKLVG 120- N D L ++ EGSGVIY+KDG +AYVVTNNHVIDGAK+IEI +ADGSK VG+LVG Sbjct: 93 GRSKENKDAELSIFSEGSGVIYRKDGNSAYVVTNNHVIDGAKRIEILMADGSKVVGELVG 152- Query: 121 SDTYSDLAVVKIPSDKVSNIAEFADSSKLNIGETAIAIGSPLGTEYANSVTQGIVSSLKR 18- 0 +DTYSDLAVVKI SDK+ +AEFADS+KLN+GE AIAIGSPLGT+YANSVTQGIVSSL R Sbjct: 153 ADTYSDLAVVKISSDKIKTVAEFADSTKLNVGEVAIAIGSPLGTQYANSVTQGIVSSLSR 21- 2 Query: 181 TVTMTNEEGQTVSTNAIQTDAAINPGNSGGALINIEGQVIGINSSKISSTSNQTSGQSSG 24- 0 TVT+ NE G+TVSTNAIQTDAAINPGNSGG LINIEGQVIGINSSKISST ++G S Sbjct: 213 TVTLKNENGETVSTNAIQTDAAINPGNSGGPLINIEGQVIGINSSKISSTPTGSNGNS-- 27- 0 Query: 241 NSVEGMGFAIPSNDVVKIINQLESNGQVERPALGISMAGLSNLPSDVISKLKIPSNVTNG 30- 0 +VEG+GFAIPS DV+KII QLE+NG+V RPALGISM L++L ++ +S++ IP++VT G Sbjct: 271 GAVEGIGFAIPSTDVIKIIKQLETNGEVIRPALGISMVNLNDLSTNALSQINIPTSVTGG 33- 0 Query: 301 IVVASIQSGMPAQGKLKKYDVITKVDDKEVVSPSDLQSLLYGHQVGDSITVTFYRGENKQ 36- 0 IVVA ++ GMPA GKL +YDVIT++D K V S SDLQS LYGH + D+I VTFYRG K+ Sbjct: 331 IVVAEVKEGMPASGKLAQYDVITEIDGKTVNSISDLQSSLYGHDINDTIKVTFYRGTTKK 39- 0 Query: 361 TVTIKLTKTSKDLAK 375 IKLTKT++DL K Sbjct: 391 KADIKLTKTTQDLTK 405 A related GBS gene <SEQ ID 8873> and protein <SEQ ID 8874> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05006 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 12.68 GvH: Signal Score (-7.5): -1.33 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 4.56 threshold: 0.0 PERIPHERAL Likelihood = 4.56 301 modified ALOM score: -1.41 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00114## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1649 A DNA sequence (GBSx1744) was identified in S. agalactiae <SEQ ID 5105> which encodes the amino acid sequence <SEQ ID 5106>. This protein is predicted to be SPSpoJ (spo0J). Analysis of this protein sequence reveals the following: TABLE-US-05007 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4152 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05008 >GP:AAC45335 GB:AF000658 SPSpoJ [Streptococcus pneumoniae] Identities = 138/257 (53%), Positives = 188/257 (72%), Gaps = 5/257 (1%) Query: 1 MEYLETININHIAPNPYQPRLEFNTKELEELANSIKINGLIQPIIVRPSAVFGYELVAGE 60 ME E I+I I NPYQPR EF+ ++L+ELA SIK NG+IQPIIVR S V GYE++AGE Sbjct: 1 MEKFEMISITDIQKNPYQPRKEFDREKLDELAQSIKENGVIQPIIVRQSPVIGYEILAGE 60 Query: 61 RRLRAAKLAKLESIPAIIKSYNNDDSMQLAIVENLQRSNLSPIEEAKAYSQLLQKKSMTH 120- RR RA+ LA L SIPA++K ++ + M +I+ENLQR NL+PIEEA+AY L++ K TH Sbjct: 61 RRYRASLLAGLRSIPAVVKQISDQEMMVQSIIENLQRENLNPIEEARAYVSLVE-KGFTH 119- Query: 121 EELAKYMGKSRPYISNTIRLLNLPPLITSAIEEGKLSSGHARALLSLPDASQQKDWYQRI 18- 0 E+A GKSRPYISN+IRLL+LP I S +E GKLS HAR+L+ L + QQ ++QRI Sbjct: 120 AEIADKEGKSRPYISNSIRLLSLPEQILSEVENGKLSQAHARSLVGL-NKEQQDYFFQRI 17- 8 Query: 181 LTEDISVRRLEKLLKQEKKTNHKSLQNKDVFLKHQENELAQFLGSKVKLTINKDGAGNIK 24- 0 + EDISVR+LE LL ++K+ K Q + F++++E +L + LG V++ ++K +G I Sbjct: 179 IEEDISVRKLEALLTEKKQ---KKQQKTNHFIQNEEKQLRKLLGLDVEIKLSKKDSGKII 23- 5 Query: 241 IAFANQEELNRIINTLK 257 I+F+NQEE +RIIN+LK Sbjct: 236 ISFSNQEEYSRIINSLK 252 A related DNA sequence was identified in S. pyogenes <SEQ ID 5107> which encodes the amino acid sequence <SEQ ID 5108>. Analysis of this protein sequence reveals the following: TABLE-US-05009 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1758 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05010 Identities = 146/256 (57%), Positives = 191/256 (74%), Gaps = 1/256 (0%) Query: 2 EYLETININHIAPNPYQPRLEFNTKELEELANSIKINGLIQPIIVRPSAVFGYELVAGER 61 E L + I I NPYQPR++FN +EL++LA SIK NGLIQPIIVR S +FGYELVAGER Sbjct: 14 ELLIDLPIEDIVTNPYQPRIQFNQRELQDLATSIKSNGLIQPIIVRKSDIFGYELVAGER 73 Query: 62 RLRAAKLAKLESIPAIIKSYNNDDSMQLAIVENLQRSNLSPIEEAKAYSQLLQKKSMTHE 121- RL+A+K+A L+ +PAIIK + +SMQ AIVENLQRSNL+ IEEAKAY L++KK MTH+ Sbjct: 74 RLKASKMAGLKKVPAIIKKISTLESMQQAIVENLQRSNLNAIEEAKAYQLLVEKKHMTHD 133- Query: 122 ELAKYMGKSRPYISNTIRLLNLPPLITSAIEEGKLSSGHARALLSLPDASQQKDWYQRIL 18- 1 E+AKYMGKSRPYISNT+RLL LP I AIEEGK+S+GHARALL+L D QQ +I Sbjct: 134 EIAKYMGKSRPYISNTLRLLQLPAPIIKAIEEGKISAGHARALLTLSDDKQQLYLTHKIQ 19- 3 Query: 182 TEDISVRRLEKLLKQEKKTNHKSLQNKDVFLKHQENELAQFLGSKVKLTINKDGAGNIKI 24- 1 E +SVR++E+L+ ++ S + K++F E +LA+ LG V + + + +G ++I Sbjct: 194 NEGLSVRQIEQLV-TSTPSSKLSKKTKNIFATSLEKQLAKSLGLSVNMKLTANHSGYLQI 25- 2 Query: 242 AFANQEELNRIINTLK 257 +F+N +ELNRIIN LK Sbjct: 253 SFSNDDELNRIINKLK 268 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1650 A DNA sequence (GBSx1745) was identified in S. agalactiae <SEQ ID 5109> which encodes the amino acid sequence <SEQ ID 5110>. Analysis of this protein sequence reveals the following: TABLE-US-05011 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 2-18 (1-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10297> which encodes amino acid sequence <SEQ ID 10298> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 5111> which encodes the amino acid sequence <SEQ ID 5112>. Analysis of this protein sequence reveals the following: TABLE-US-05012 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3646 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05013 Identities = 353/455 (77%), Positives = 401/455 (87%), Gaps = 6/455 (1%) Query: 32 MTENEQLFWNRVLELSRSQIAPAAYEFFVLEARLLKIEHQTAVITLDNIEMKKLFWEQNL 91 - MTENEQ+FWNRVLEL++SQ+ A YEFFV +ARLLK++ A I LD +MK+LFWE+NL Sbjct: 1 MTENEQIFWNRVLELAQSQLKQATYEFFVHDARLLKVDKHIATIYLD--QMKELFWEKNL 58 Query: 92 GPVILTAGFEIFNAEITANYV-SNDLHLQETSFS-NYQQSSNEVNTLPIRKIDSNLKEKY 149- VILTAGFE++NA+I+ +YV DL +++ N + +N+LP + S+L KY Sbjct: 59 KDVILTAGFEVYNAQISVDYVFEEDLMIEQNQTKINQKPKQQALNSLPT--VTSDLNSKY 116- Query: 150 TFANFVQGDENRWAVSASIAVADSPGTTYNPLFIWGGPGLGKTHLLNAIGNQVLRDNPNA 20- 9 +F NF+QGDENRWAV+ASIAVA++PGTTYNPLFIWGGPGLGKTHLLNAIGN VL +NPNA Sbjct: 117 SFENFIQGDENRWAVAASIAVANTPGTTYNPLFIWGGPGLGKTHLLNAIGNSVLLENPNA 17- 6 Query: 210 RVLYITAENFINEFVSHIRLDSMEELKEKFRNLDLLLIDDIQSLAKKTLGGTQEEFFNTF 26- 9 R+ YITAENFINEFV HIRLD+M+ELKEKFRNLDLLLIDDIQSLAKKTL GTQEEFFNTF Sbjct: 177 RIKYITAENFINEFVIHIRLDTMDELKEKFRNLDLLLIDDIQSLAKKTLSGTQEEFFNTF 23- 6 Query: 270 NALHTNDKQIVLTSDRNPNQLNDLEERLVTRFSWGLPVNITPPDFETRVAILTNKIQEYP 32- 9 NALH N+KQIVLTSDR P+ LNDLE+RLVTRF WGL VNITPPDFETRVAILTNKIQEY Sbjct: 237 NALHNNNKQIVLTSDRTPDHLNDLEDRLVTRFKWGLTVNITPPDFETRVAILTNKIQEYN 29- 6 Query: 330 YDFPQDTIEYLAGEFDSNVRELEGALKNISLVADFKHAKTITVDIAAEAIRARKNDGPIV 38- 9 + FPQDTIEYLAG+FDSNVR+LEGALK+ISLVA+FK TITVDIAAEAIRARK DGP + Sbjct: 297 FIFPQDTIEYLAGQFDSNVRDLEGALKDISLVANFKQIDTITVDIAAEAIRARKQDGPKM 35- 6 Query: 390 TVIPIEEIQIQVGKFYGVTVKEIKATKRTQDIVLARQVAMYLAREMTDNSLPKIGKEFGG 44- 9 TVIPIEEIQ QVGKFYGVTVKEIKATKRTQ+IVLARQVAM+LAREMTDNSLPKIGKEFGG Sbjct: 357 TVIPIEEIQAQVGKFYGVTVKEIKATKRTQNIVLARQVAMFLAREMTDNSLPKIGKEFGG 41- 6 Query: 450 RDHSTVLHAYNKIKNMVAQDDNLRIEIETIKNKIR 484 RDHSTVLHAYNKIKNM++QD++LRIEIETIKNKI+ Sbjct: 417 RDHSTVLHAYNKIKNMISQDESLRIEIETIKNKIK 451 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1651 A DNA sequence (GBSx1746) was identified in S. agalactiae <SEQ ID 5113> which encodes the amino acid sequence <SEQ ID 5114>. Analysis of this protein sequence reveals the following: TABLE-US-05014 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0556 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05015 >GP:AAC45337 GB:AF000658 beta subunit of DNA polymerase III [Streptococcus pneumoniae] Identities = 278/378 (73%), Positives = 324/378 (85%) Query: 1 MIHFSINKNFFLHALTVTKRAISHKNAIPILSTVKIEVTRDAIILTGSNGQISIENTIPA 60 MIHFSINKN FL AL +TKRAIS KNAIPILSTVKI+VT + + L GSNGQISIEN I Sbjct: 1 MIHFSINKNLFLQALNITKRAISSKNAIPILSTVKIDVTNEGVTLIGSNGQISIENFISQ 60 Query: 61 SNENAGLLVTNPGSILLEAGFFINIISSLPDVTLEFTEIEQHQIVLTSGKSEITLKGKDV 120- NE+AGLL+T+ GSILLEA FFIN++SSLPDVTL+F EIEQ+QIVLTSGKSEITLKGKD Sbjct: 61 KNEDAGLLITSLGSILLEASFFINVVSSLPDVTLDFKEIEQNQIVLTSGKSEITLKGKDS 120- Query: 121 DQYPRLQEMTTDTPLTLETKLLKSIINETAFAASQQESRPILTGVHLVISQNKYFKAVAT 18- 0 +QYPR+QE++ TPL LETKLLK IINETAFAAS QESRPILTGVH V+SQ+K K VAT Sbjct: 121 EQYPRIQEISASTPLILETKLLKKIINETAFAASTQESRPILTGVHFVLSQHKELKTVAT 18- 0 Query: 181 DSHRMSQRTFQLEKSANNFDLVVPSKSLREFSAVFTDDIETVEVFFSDSQMLFRSENISF 24- 0 DSHR+SQ+ LEK++++FD+V+PS+SLREFSAVFTDDIETVE+FF+++Q+LFRSENISF Sbjct: 181 DSHRLSQKKLTLEKNSDDFDVVIPSRSLREFSAVFTDDIETVEIFFANNQILFRSENISF 24- 0 Query: 241 YTRLLEGNYPDTDRLLTNQFETEIIFNTNALRHAMERAYLISNATQNGTVRLEIQNETVS 30- 0 YTRLLEGNYPDTDRL+ F T I FN LR +MERA L+S+ATQNGTV+LEI++ VS Sbjct: 241 YTRLLEGNYPDTDRLIPTDFNTTITFNVVNLRQSMERARLLSSATQNGTVKLEIKDGVVS 30- 0 Query: 301 AHVNSPEVGKVNEELDTVSLKGDSLNISFNPTYLIESLKAVKSETVTIRFISPVRPFTLT 36- 0 AHV+SPEVGKVNEE+DT + G+ L ISFNPTYLI+SLKA+ SE VTI FIS VRPFTL Sbjct: 301 AHVHSPEVGKVNEEIDTDQVTGEDLTISFNPTYLIDSLKALNSEKVTISFISAVRPFTLV 36- 0 Query: 361 PGEDTEDFIQLITPVRTN 378 P + EDF+QLITPVRTN Sbjct: 361 PADTDEDFMQLITPVRTN 378 A related DNA sequence was identified in S. pyogenes <SEQ ID 5115> which encodes the amino acid sequence <SEQ ID 5116>. Analysis of this protein sequence reveals the following: TABLE-US-05016 Possible site: 14 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.70 Transmembrane 67-83 (67-83) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05017 Identities = 295/378 (78%), Positives = 334/378 (88%) Query: 1 MIHFSINKNFFLHALTVTKRAISHKNAIPILSTVKIEVTRDAIILTGSNGQISIENTIPA 60 MI FSIN+ F+HAL TKRAIS KNAIPILS++KIEVT + LTGSNGQISIENTIP Sbjct: 1 MIQFSINRTLFIHALNTTKRAISTKNAIPILSSIKIEVTSTGVTLTGSNGQISIENTIPV 60 Query: 61 SNENAGLLVTNPGSILLEAGFFINIISSLPDVTLEFTEIEQHQIVLTSGKSEITLKGKDV 120- SNENAGLL+T+PG+ILLEA FFINIISSLPD+++ EIEQHQ+VLTSGKSEITLKGKDV Sbjct: 61 SNENAGLLITSPGAILLEASFFINIISSLPDISINVKEIEQHQVVLTSGKSEITLKGKDV 120- Query: 121 DQYPRLQEMTTDTPLTLETKLLKSIINETAFAASQQESRPILTGVHLVISQNKYFKAVAT 18- 0 DQYPRLQE++T+ PL L+TKLLKSII ETAFAAS QESRPILTGVH+V+S +K FKAVAT Sbjct: 121 DQYPRLQEVSTENPLILKTKLLKSIIAETAFAASLQESRPILTGVHIVLSNHKDFKAVAT 18- 0 Query: 181 DSHRMSQRTFQLEKSANNFDLVVPSKSLREFSAVFTDDIETVEVFFSDSQMLFRSENISF 24- 0 DSHRMSQR L+ ++ +FD+V+PSKSLREFSAVFTDDIETVEVFFS SQ+LFRSE+ISF Sbjct: 181 DSHRMSQRLITLDNTSADFDVVIPSKSLREFSAVFTDDIETVEVFFSPSQILFRSEHISF 24- 0 Query: 241 YTRLLEGNYPDTDRLLTNQFETEIIFNTNALRHAMERAYLISNATQNGTVRLEIQNETVS 30- 0 YTRLLEGNYPDTDRLL +FETE++FNT +LRHAMERA+LISNATQNGTV+LEI +S Sbjct: 241 YTRLLEGNYPDTDRLLMTEFETEVVFNTQSLRHAMERAFLISNATQNGTVKLEITQNHIS 30- 0 Query: 301 AHVNSPEVGKVNEELDTVSLKGDSLNISFNPTYLIESLKAVKSETVTIRFISPVRPFTLT 36- 0 AHVNSPEVGKVNE+LD VS G L ISFNPTYLIESLKA+KSETV I F+SPVRPFTLT Sbjct: 301 AHVNSPEVGKVNEDLDIVSQSGSDLTISFNPTYLIESLKAIKSETVKIHFLSPVRPFTLT 36- 0 Query: 361 PGEDTEDFIQLITPVRTN 378 PG++ E FIQLITPVRTN Sbjct: 361 PGDEEESFIQLITPVRTN 378 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1652 A DNA sequence (GBSx1747) was identified in S. agalactiae <SEQ ID 5117> which encodes the amino acid sequence <SEQ ID 5118>. Analysis of this protein sequence reveals the following: TABLE-US-05018 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0857(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10299> which encodes amino acid sequence <SEQ ID 10300> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05019 >GP: AAC00282 GB: AF008220 YtlR [Bacillus subtilis] Identities = 83/298 (27%), Positives = 138/298 (45%), Gaps = 35/298 (11%) Query: 19 YIIANPHAGNKNASTIVGKIQE--LYHTEDISVFYTEQKDDEK--KQVINILRSFKESDH 74 - + I NP AG++N + IQ+ + + F TE + + I+ ++ +K Sbjct: 5 FFIINPTAGHRNGLRVWKSIQKELIKRKVEHRSFLTEHPGHAEVLARQISTIQEYKLK-R 63 Query: 75 LMIIGGDGTLSKVMTYLPQ--HIPCTYYPVGSGNDFARALKIPNL---------KETLTA 123- L++IGGDGT+ +V+ L I ++ P G+ NDF+R I + K LT Sbjct: 64 LIVIGGDGTMHEVVNGLKDVDDIELSFVPAGAYNDFSRGFSIKKIDLIQEIKKVKRPLT- 122- Query: 124 IQTERLKEINCFIYDKGLIL---NSLDLGFAAYVVWKASNSKIKNILNRYRLGKITYIVI 18- 0 +T L +N F+ DK IL N + +GF AYV KA ++ + RL + Y + Sbjct: 123 -RTFHLGSVN-FLQDKSQILYFMNHIGIGFDAYVNKKAMEFPLRRVFLFLRLRFLVYPL- 17- 9 Query: 181 AIKSLLHSSK------VQVLVEGETGQQIKLNDLYFFALANNTYFGGGITIWPKASALTA 23- 4 S LH+S + E ET + +D++F ++N+ ++GGG+ P A+ Sbjct: 180 ---SHLHASATFKPFTLACTTEDETRE---FHDVWFAVVSNHPFYGGGMKAAPLANPREK 23- 3 Query: 235 ELDMVYAKGHTFLKRLSILLSLVFKRHTTSKSIKHQTFKAMTVYFPKNSLIEIDGEIV 292 D+V + FLK+ +L + F +HT + K +T Y DGEI+ Sbjct: 234 TFDIVIVENQPFLKKYWLLCLMAFGKHTKMDGVTMFKAKDITFYTKDKIPFHADGEIM 291 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1653 A DNA sequence (GBSx1748) was identified in S. agalactiae <SEQ ID 5121> which encodes the amino acid sequence <SEQ ID 5122>. Analysis of this protein sequence reveals the following: TABLE-US-05020 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3792(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-05021 >GP: AAC45338 GB: AF000658 ORFX [Streptococcus pneumoniae] Identities = 46/63 (73%), Positives = 57/63 (90%) Query: 1 MYQVGSLVEMKKPHACVIKETGKKANQWKVLRVGADIKIQCTNCQHVIMMSRYDFERKLK 60 MYQVG+ VEMKKPHAC IK TGKKAN+W++ RVGADIKI+C+NC+HV+MM RYDFERK+ Sbjct: 1 MYQVGNFVEMKKPHACTIKSTGKKANRWEITRVGADIKIKCSNCEHVVMMGRYDFERKMN 60 Query: 61 KVL 63 K++ Sbjct: 61 KII 63 A related DNA sequence was identified in S. pyogenes <SEQ ID 5123> which encodes the amino acid sequence <SEQ ID 5124>. Analysis of this protein sequence reveals the following: TABLE-US-05022 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4038(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05023 Identities = 63/65 (96%), Positives = 64/65 (97%) Query: 1 MYQVGSLVEMKKPHACVIKETGKKANQWKVLRVGADIKIQCTNCQHVIMMSRYDFERKLK 60 MYQ+GS VEMKKPHACVIKETGKKANQWKVLRVGADIKIQCTNCQHVIMMSRYDFERKLK Sbjct: 1 MYQIGSFVEMKKPHACVIKETGKKANQWKVLRVGADIKIQCTNCQHVIMMSRYDFERKLK 60 Query: 61 KVLQP 65 KVLQP Sbjct: 61 KVLQP 65 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1654 A DNA sequence (GBSx1749) was identified in S. agalactiae <SEQ ID 5125> which encodes the amino acid sequence <SEQ ID 5126>. Analysis of this protein sequence reveals the following: TABLE-US-05024 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.99 Transmembrane 48-64 (47-66) ----- Final Results ----- bacterial membrane --- Certainty = 0.2996(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1655 A DNA sequence (GBSx1750) was identified in S. agalactiae <SEQ ID 5127> which encodes the amino acid sequence <SEQ ID 5128>. Analysis of this protein sequence reveals the following: TABLE-US-05025 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4171(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1656 A DNA sequence (GBSx1751) was identified in S. agalactiae <SEQ ID 5129> which encodes the amino acid sequence <SEQ ID 5130>. This protein is predicted to be GTP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-05026 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3952(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8875> which encodes amino acid sequence <SEQ ID 8876> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-05027 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: 0.53 GvH: Signal Score (-7.5): -0.13 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 1.48 threshold: 0.0 PERIPHERAL Likelihood = 1.48 195 modified ALOM score: -0.80 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05028 >GP: BAB07770 GB: AP001520 GTP-binding protein [Bacillus halodurans] Identities = 223/329 (67%), Positives = 273/329 (82%), Gaps = 5/329 (1%) Query: 1 MVEVPDERLQKLTELITPKKTVPTTFEFTDIAGIVKGASKGEGLGNKFLANIREVDAIVH 60 +VEVPD RLQKLTEL+ PKKTVPT FEFTDIAGIV+GASKGEGLGN+FL++IR+VDAI H Sbjct: 43 IVEVPDPRLQKLTELVNPKKTVPTAFEFTDIAGIVEGASKGEGLGNQFLSHIRQVDAISH 102- Query: 61 VVRAFDDENVMREQGREDAFVDPIADIDTINLELILADLESINKRYARVEKMARTQKDKE 120- VVR FDDEN+ G VDPI DI INLELILADLES++KR++RV+K+A+T KDKE Sbjct: 103 VVRCFDDENITHVSGS----VDPIRDISVINLELILADLESVDKRFSRVQKLAKT-KDKE 15- 7 Query: 121 SVAEFNVLQKIKPVLEDGKSARTIEFTEEEAKVVKGLFLLTTKPVLYVANVDEDKVADPD 18- 0 +VAE VL+K+K E+ K AR+IEFTEE+ K+VKGL LLT+KPVLYVANV ED V PD Sbjct: 158 AVAELEVLEKLKDAFENEKPARSIEFTEEQQKIVKGLHLLTSKPVLYVANVSEDDVLSPD 21- 7 Query: 181 DIDYVNQIRAFAETENAEVVVISARAEEEISELDDEDKLEFLEAIGLTESGVDKLTRAAY 24- 0 D +V +++AFA EN+EV+V+SA+ EEEI+ELD E+K FLE +G+ ESG+D+L RAAY Sbjct: 218 DNPFVQKVKAFAAEENSEVIVVSAKIEEEIAELDGEEKAMFLEELGIQESGLDQLIRAAY 27- 7 Query: 241 HLLGLGTYFTAGEKEVRAWTFKRGIKAPQAASIIHSDFERGFIRAVTMSYDDLIQYGSEK 30- 0 LLGL TYFTAGE+EVRAWTF++G KAPQAA IIHSDFE+GFIRA T+SY+DL++ GS Sbjct: 278 SLLGLQTYFTAGEQEVRAWTFRKGTKAPQAAGIIHSDFEKGFIRAETVSYNDLVEAGSMA 33- 7 Query: 301 AVKEAGRLREEGKEYIVQDGDIMEFRFNV 329 KE G++R EGKEY+VQDGD++ FRFNV Sbjct: 338 VAKERGKVRLEGKEYVVQDGDVIHFRFNV 366 A related DNA sequence was identified in S. pyogenes <SEQ ID 5131> which encodes the amino acid sequence <SEQ ID 5132>. Analysis of this protein sequence reveals the following: TABLE-US-05029 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05030 >GP: BAB07770 GB: AP001520 GTP-binding protein [Bacillus halodurans] Identities = 259/371 (69%), Positives = 314/371 (83%), Gaps = 5/371 (1%) Query: 1 MALTAGIVGLPNVGKSTLFNAITKAGAEAANYPFATIDPNVGMVEVPDERLQKLTELITP 60 MALT GIVGLPNVGKSTLFNAIT+AGAE+ANYPF TIDPNVG+VEVPD RLQKLTEL+ P Sbjct: 1 MALTTGIVGLPNVGKSTLFNAITQAGAESANYPFCTIDPNVGIVEVPDPRLQKLTELVNP 60 Query: 61 KKTVPTTFEFTDIAGIVKGASRGEGLGNKFLANIREIDAIVHVVRAFDDENVMREQGRED 120- KKTVPT FEFTDIAGIV+GAS+GEGLGN+FL++IR++DAI HVVR FDDEN+ G Sbjct: 61 KKTVPTAFEFTDIAGIVEGASKGEGLGNQFLSHIRQVDAISHVVRCFDDENITHVSGS-- 118- Query: 121 AFVDPIADIDTINLELILADLESINKRYARVEKMARTQKDKESVAEFNVLQKIKPVLEDG 18- 0 VDPI DI INLELILADLES++KR++RV+K+A+T KDKE+VAE VL+K+K E+ Sbjct: 119 --VDPIRDISVINLELILADLESVDKRFSRVQKLAKT-KDKEAVAELEVLEKLKDAFENE 17- 5 Query: 181 KSARTIEFTEDEAKVVKGLFLLTTKPVLYVANVDEDKVANPDGIDYVKQIRDFAATENAE 24- 0 K AR+IEFTE++ K+VKGL LLT+KPVLYVANV ED V +PD +V++++ FAA EN+E Sbjct: 176 KPARSIEFTEEQQKIVKGLHLLTSKPVLYVANVSEDDVLSPDDNPFVQKVKAFAAEENSE 23- 5 Query: 241 VVVISARAEEEISELDDEDKEEFLEAIGLTESGVDKLTRAAYHLLGLGTYFTAGEKEVRA 30- 0 V+V+SA+ EEEI+ELD E+K FLE +G+ ESG+D+L RAAY LLGL TYFTAGE+EVRA Sbjct: 236 VIVVSAKIEEEIAELDGEEKAMFLEELGIQESGLDQLIRAAYSLLGLQTYFTAGEQEVRA 29- 5 Query: 301 WTFKRGIKAPQAAGIIHSDFERGFIRAVTMSYDDLMTYGSEKAVKEAGRLREEGKEYVVQ 36- 0 WTF++G KAPQAAGIIHSDFE+GFIRA T+SY+DL+ GS KE G++R EGKEYVVQ Sbjct: 296 WTFRKGTKAPQAAGIIHSDFEKGFIRAETVSYNDLVEAGSMAVAKERGKVRLEGKEYVVQ 35- 5 Query: 361 DGDIMEFRFNV 371 DGD++ FRFNV Sbjct: 356 DGDVIHFRFNV 366 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05031 Identities = 316/329 (96%), Positives = 322/329 (97%) Query: 1 MVEVPDERLQKLTELITPKKTVPTTFEFTDIAGIVKGASKGEGLGNKFLANIREVDAIVH 60 MVEVPDERLQKLTELITPKKTVPTTFEFTDIAGIVKGAS+GEGLGNKFLANIRE+DAIVH Sbjct: 43 MVEVPDERLQKLTELITPKKTVPTTFEFTDIAGIVKGASRGEGLGNKFLANIREIDAIVH 102- Query: 61 VVRAFDDENVMREQGREDAFVDPIADIDTINLELILADLESINKRYARVEKMARTQKDKE 120- VVRAFDDENVMREQGREDAFVDPIADIDTINLELILADLESINKRYARVEKMARTQKDKE Sbjct: 103 VVRAFDDENVMREQGREDAFVDPIADIDTINLELILADLESINKRYARVEKMARTQKDKE 16- 2 Query: 121 SVAEFNVLQKIKPVLEDGKSARTIEFTEEEAKVVKGLFLLTTKPVLYVANVDEDKVADPD 18- 0 SVAEFNVLQKIKPVLEDGKSARTIEFTE+EAKVVKGLFLLTTKPVLYVANVDEDKVA+PD Sbjct: 163 SVAEFNVLQKIKPVLEDGKSARTIEFTEDEAKVVKGLFLLTTKPVLYVANVDEDKVANPD 22- 2 Query: 181 DIDYVNQIRAFAETENAEVVVISARAEEEISELDDEDKLEFLEAIGLTESGVDKLTRAAY 24- 0 IDYV QIR FA TENAEVVVISARAEEEISELDDEDK EFLEAIGLTESGVDKLTRAAY Sbjct: 223 GIDYVKQIRDFAATENAEVVVISARAEEEISELDDEDKEEFLEAIGLTESGVDKLTRAAY 28- 2 Query: 241 HLLGLGTYFTAGEKEVRAWTFKRGIKAPQAASIIHSDFERGFIRAVTMSYDDLIQYGSEK 30- 0 HLLGLGTYFTAGEKEVRAWTFKRGIKAPQAA IIHSDFERGFIRAVTMSYDDL+ YGSEK Sbjct: 283 HLLGLGTYFTAGEKEVRAWTFKRGIKAPQAAGIIHSDFERGFIRAVTMSYDDLMTYGSEK 34- 2 Query: 301 AVKEAGRLREEGKEYIVQDGDIMEFRFNV 329 AVKEAGRLREEGKEY+VQDGDIMEFRFNV Sbjct: 343 AVKEAGRLREEGKEYVVQDGDIMEFRFNV 371 SEQ ID 8876 (GBS177) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 38 (lane 4; MW 41.2 kDa). The GBS177-His fusion product was purified (FIG. 118A; see also FIG. 202, lane 7) and used to immunise mice (lane 1 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot, FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1657 A DNA sequence (GBSx1752) was identified in S. agalactiae <SEQ ID 5133> which encodes the amino acid sequence <SEQ ID 5134>. This protein is predicted to be stage V sporulation protein C (pth). Analysis of this protein sequence reveals the following: TABLE-US-05032 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2212(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10301> which encodes amino acid sequence <SEQ ID 10302> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05033 >GP: BAB03787 GB: AP001507 stage V sporulation protein C (peptidyl-tRNA hydrolase) [Bacillus halodurans] Identities = 89/187 (47%), Positives = 127/187 (67%), Gaps = 2/187 (1%) Query: 6 VKMIVGLGNPGSKYNDTKHNIGFMAVDRIVKDLDVNFTEDKNFKAEIGSDFINGEKIYFI 65 +K+IVGLGNPG+KY+ T+HN+GF VD + + L++ + K G I+GEKI+ + Sbjct: 1 MKLIVGLGNPGAKYDGTRHNVGFDVVDAVARRLNIEIKQSKA-NGLYGEGRIDGEKIFLL 59 Query: 66 KPTTFMNNSGIAVKALLTYYNISIKDMIIIYDDLDMEVGKIRFRQKGSAGGHNGIKSIIA 125- KP TFMN SG +V+ L YYN+ ++D+++IYDDLD+ VGKIR RQKGSAGGHNG+KS+IA Sbjct: 60 KPQTFMNRSGESVRPFLEYYNMEVEDLLVIYDDLDLPVGKIRLRQKGSAGGHNGMKSLIA 119- Query: 126 HLGTQEFDRIKVGIGRPNGRMTVINHVLGKFDKNDEIMILNTLDKVDNAVNYYLQTNDFQ 18- 5 HLGT +F RI+VG+ RP TV+ HVLG++ ++ I +D A + + F Sbjct: 120 HLGTSDFKRIRVGVDRPAPGETVVQHVLGRYRPEEKDAISEAIDLSAEAAEAFTK-KPFL 17- 8 Query: 186 KTMQKYN 192 + M +N Sbjct: 179 EVMNTFN 185 A related DNA sequence was identified in S. pyogenes <SEQ ID 5135> which encodes the amino acid sequence <SEQ ID 5136>. Analysis of this protein sequence reveals the following: TABLE-US-05034 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2840(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05035 Identities = 148/189 (78%), Positives = 166/189 (87%) Query: 5 MVKMIVGLGNPGSKYNDTKHNIGFMAVDRIVKDLDVNFTEDKNFKAEIGSDFINGEKIYF 64 MVKMIVGLGNPGSKY TKHNIGFMA+D IVK+LDV FT+DKNFKA+IGS FIN EK+YF Sbjct: 16 MVKMIVGLGNPGSKYEKTKHNIGFMAIDNIVKNLDVTFTDDKNFKAQIGSTFINHEKVYF 75 Query: 65 IKPTTFMNNSGIAVKALLTYYNISIKDMIIIYDDLDMEVGKIRFRQKGSAGGHNGIKSII 124- +KPTTFMNNSGIAVKALLTYYNI I D+I+IYDDLDMEV K+R R KGSAGGHNGIKSII Sbjct: 76 VKPTTFMNNSGIAVKALLTYYNIDITDLIVIYDDLDMEVSKLRLRSKGSAGGHNGIKSII 135- Query: 125 AHLGTQEFDRIKVGIGRPNGRMTVINHVLGKFDKNDEIMILNTLDKVDNAVNYYLQTNDF 18- 4 AH+GTQEF+RIKVGIGRP MTVINHV+G+F+ D I I TLD+V NAV +YLQ NDF Sbjct: 136 AHIGTQEFNRIKVGIGRPLKGMTVINHVMGQFNTEDNIAISLTLDRVVNAVKFYLQENDF 19- 5 Query: 185 QKTMQKYNG 193 +KTMQK+NG Sbjct: 196 EKTMQKFNG 204 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1658 A DNA sequence (GBSx1753) was identified in S. agalactiae <SEQ ID 5137> which encodes the amino acid sequence <SEQ ID 5138>. This protein is predicted to be transcription-repair coupling factor (mfd). Analysis of this protein sequence reveals the following: TABLE-US-05036 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2456(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05037 >GP: AAD03810 GB: AF054624 transcription-repair coupling factor [Lactobacillus sakei] Identities = 523/1051 (49%), Positives = 733/1051 (68%), Gaps = 20/1051 (1%) Query: 1 MNIIELFSQNKVVRTWHSGLVTNSRQLVMGFSGASKAIAIASAYEKLSKKIMVVTATQTD 60 M++I + + V++ RQL+ G SG++K + +A+ Y++ + ++++ + Sbjct: 1 MDLISMLGNTQQVQSVLENQKPGVRQLLTGLSGSAKTLFLATIYKQQRQPLLIIESNMFQ 60 Query: 61 SDKLSSDISSLIGEDNVYQFFADDVPAAEFIFSSLDKSISRLSALRFLKDPEKNGVLITS 120- +++++ D+++ + D +Y F ++V AAE SS + R+ L FL +K G+++TS Sbjct: 61 ANQVAEDLANQLNGDQIYTFPVEEVMAAEIAVSSPESRAERVRTLSFLATGKK-GIVVTS 119- Query: 121 ISGLRLLLPNPEVFSKSQYKFEIGQECYLDKLCKNLVNLGYQKVSQVFSPGEFSQRGDIL 18- 0 ++G+R LLP + SQ + E+G E L L +GY + V PGEF+ RGDI+ Sbjct: 120 VAGMRRLLPTVRQWRDSQTQIEMGGEVDPKILGAQLAEMGYHRDKLVGKPGEFAMRGDII 17- 9 Query: 181 DIFEMTQEYPYRLEFFGDEIDGIRQFDIDTQKSLKQLESVQISPADDIILQDADFERAKK 24- 0 DIF + E P R+E F E+D IR F+ DTQ+S++ LESV I PA D++ A E A + Sbjct: 180 DIFPLDTENPVRIELFDTEVDAIRSFEADTQRSIENLESVAIMPATDLLANAAQLEMAGE 23- 9 Query: 241 KLEG-YLVTASEVQ------------RTYLSEVLSTTENHFKHSDIRRFLSIFYEKEWGI 28- 7 L+ Y TA+++ T +S +L+ + ++ F+ Y + Sbjct: 240 ALQADYQQTAAKITAKDDQKALAVNFETPISRLLAGE----RLENLALFVDYLYPDHTSL 29- 5 Query: 288 LDYIPEGTPLFVDDFQKIVDRNAKLDLEIASLLTEDLQQGKSHSSLNYFSDPYKQLRQYQ 34- 7 +DY + DD+ +I + L E A+ T+ L + + D + ++Q Q Sbjct: 296 IDYFKNSGLVVFDDYPRIQETQRVLAEEAANWQTDMLGSRRLLPAQKLLVDVHHLMKQDQ 35- 5 Query: 348 -PATFFSNFHKGLGNLKFDKLHHFTQYGMQEFFNQFPLLVDEINRYKKSGATVLLQVDSQ 40- 6 P + S F KG+G LK D L + +Q+FF+Q PLL E++R++K TV++ V Sbjct: 356 HPHLYLSLFQKGMGKLKLDTLGNMPTRNVQQFFSQMPLLKTEMSRWQKQQQTVVVLVSDA 41- 5 Query: 407 KGLNLLQENLKEYGLDLIISDKNDIVQKESQLIVGHLSNGFYFADEKIVLITEREIYHRR 46- 6 K + + + ++ ++ ++ K +V + Q++ G L NGF D K+V++TE+E+++ Sbjct: 416 KRVKKIDQTFHDFEIEATVTTKTKLVAGQIQIVQGSLQNGFELPDLKLVVLTEKELFNTA 47- 5 Query: 467 VKRKIRRSNISNAERLKDYNELSVGDYVVHNVHGVGKFLGIETIEIQGIHRDYLTIQYQN 52- 6 K+K+RR ++NAERLK Y+EL GDYVVH HG+G+++G+ET+E+ G+H+DY+TI Y++ Sbjct: 476 PKKKVRRQTLANAERLKSYSELKPGDYVVHVNHGIGEYVGMETLEVDGVHQDYITILYRD 53- 5 Query: 527 ADRISIPVEQIELLTKYVSADGKEPKINTLNDGRFKKAKQRVAKQVEDIADDLLKLYAER 58- 6 ++ IPV Q++++ KYVSA+ K PKIN L ++K K +V+ ++EDIADDL++LYA+R Sbjct: 536 NGKLFIPVTQLDMVQKYVSAESKTPKINKLGGAEWQKTKSKVSAKIEDIADDLIELYAQR 59- 5 Query: 587 SQLQGFAFSPDDNMQNDFDNDFAYVETEDQLRSIKEIKQDMEGNRPMDRLLVGDVGFGKT 64- 6 +G+AF DD +Q DF+N FAY ET+DQLRS EIK DME RPMDRLLVGDVGFGKT Sbjct: 596 EAEKGYAFPKDDQLQADFENQFAYPETDDQLRSTAEIKHDMEKVRPMDRLLVGDVGFGKT 65- 5 Query: 647 EVAMRAAFKAVNDHKQVVVLVPTTVLAQQHFENFKERFSNYPVTVDVLSRFRSKKEQTDT 70- 6 EVA+RAAFKAV KQV LVPTT+LAQQH+EN RF+++PV + +LSRF+++KE T T Sbjct: 656 EVALRAAFKAVAAGKQVAFLVPTTILAQQHYENMLARFADFPVELGLLSRFKTRKEVTAT 71- 5 Query: 707 LKRLSKGQVDIIIGTHRLLSQDVVFSDLGLIVIDEEQRFGVKHKEKLKELKTKVDVLTLT 76- 6 LK L KGQVDI+IGTHRLLS+DVVF DLGL+++DEEQRFGVKHKE+LK+LK +VDVLTLT Sbjct: 716 LKGLEKGQVDIVIGTHRLLSKDVVFKDLGLLIVDEEQRFGVKHKERLKQLKAQVDVLTLT 77- 5 Query: 767 ATPIPRTLHMSMLGIRDLSVIETPPTNRYPVQTYVLETNPGLVREAIIREIDRGGQVFYV 82- 6 ATPIPRTLHMSMLG+RDLSVIETPPTNRYP+QTYV+E N G +REAI RE++R GQVFY+ Sbjct: 776 ATPIPRTLHMSMLGVRDLSVIETPPTNRYPIQTYVMEQNAGAMREAIERELERNGQVFYL 83- 5 Query: 827 YNKVDTIDQKVSELQELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGV 88- 6 +N+V I+Q V E+Q LVPEA++G+ HGQM+E QLE + DF+ G YDVLV TTIIETGV Sbjct: 836 HNRVSDIEQTVDEIQALVPEATVGYAHGQMTEAQLEGVIYDFVQGKYDVLVTTTIIETGV 89- 5 Query: 887 DISNVNTLFVENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTEISEKRLDAIKG 94- 6 D+ NVNT+ VE+ADH GLS LYQLRGR+GRS+R+AY Y MY+PDKVLTE+SEKRL AIK Sbjct: 896 DMPNVNTMIVEDADHYGLSQLYQLRGRIGRSSRVAYGYFMYKPDKVLTEVSEKRLQAIKD 95- 5 Query: 947 FTELGSGFKIAMRDLSIRGAGNILGASQSGFIDSVGFEMYSQLLEQAIATKQGKSLIRQK 10- 06 FTELGSGFKIAMRDLSIRGAGN+LG Q GFIDSVGF++YSQ+L +A+A KQGK + K Sbjct: 956 FTELGSGFKIAMRDLSIRGAGNLLGKQQHGFIDSVGFDLYSQMLSEAVAKKQGKK-VAAK 10- 14 Query: 1007 GNAELALQIDAYLPAEYISDERQKIEIYKRI 1037 NAE+ L+++AYLP +YI+D+RQKIEIYKRI Sbjct: 1015 TNAEIDLKLEAYLPDDYINDQRQKIEIYKRI 1045 A related DNA sequence was identified in S. pyogenes <SEQ ID 5139> which encodes the amino acid sequence <SEQ ID 5140>. Analysis of this protein sequence reveals the following:

TABLE-US-05038 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2826(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05039 Identities = 875/1161 (75%), Positives = 1032/1161 (88%) Query: 1 MNIIELFSQNKVVRTWHSGLVTNSRQLVMGFSGASKAIAIASAYEKLSKKIMVVTATQTD 60 M+I+ELFSQNK V++WHSGL T RQLVMG SG+SK +AIASAY KKI+VVT+TQ + Sbjct: 1 MDILELFSQNKKVQSWHSGLTTLGRQLVMGLSGSSKTLAIASAYLDDQKKIVVVTSTQNE 60 Query: 61 SDKLSSDISSLIGEDNVYQFFADDVPAAEFIFSSLDKSISRLSALRFLKDPEKNGVLITS 120- +KL+SD+SSL+ E+ V+QFFADDV AAEFIF+S+DK++SR+ L+FL++P+ GVLI S Sbjct: 61 VEKLASDLSSLLDEELVFQFFADDVAAAEFIFASMDKALSRIETLQFLRNPKSQGVLIVS 120- Query: 121 ISGLRLLLPNPEVFSKSQYKFEIGQECYLDKLCKNLVNLGYQKVSQVFSPGEFSQRGDIL 18- 0 +SGLR+LLPNP+VF+KSQ + +G++ D L K L+ +GYQKVSQV SPGEFS+RGDIL Sbjct: 121 LSGLRILLPNPDVFTKSQIQLTVGEDYDSDTLTKQLMTIGYQKVSQVISPGEFSRRGDIL 18- 0 Query: 181 DIFEMTQEYPYRLEFFGDEIDGIRQFDIDTQKSLKQLESVQISPADDIILQDADFERAKK 24- 0 DI+E+TQE PYRLEFFGD+ID IRQF +TQKS +QLE + I+PA D+I + +DF+R + Sbjct: 181 DIYEITQELPYRLEFFGDDIDSIRQFHPETQKSFEQLEGIFINPASDLIFEVSDFQRGIE 24- 0 Query: 241 KLEGYLVTASEVQRTYLSEVLSTTENHFKHSDIRRFLSIFYEKEWGILDYIPEGTPLFVD 30- 0 +LE L TA + +++YL +VL+ ++N FKH DIR+F S+FYEKEW +LDYIP+GTP+F D Sbjct: 241 QLEKALQTAQDDKKSYLEDVLAVSKNGFKHKDIRKFQSLFYEKEWSLLDYIPKGTPIFFD 30- 0 Query: 301 DFQKIVDRNAKLDLEIASLLTEDLQQGKSHSSLNYFSDPYKQLRQYQPATFFSNFHKGLG 36- 0 DFQK+VD+NA+ DLEIA+LLTEDLQQGK+ S+LNYF+D Y++LR Y+PATFFSNFHKGLG Sbjct: 301 DFQKLVDKNARFDLEIANLLTEDLQQGKALSNLNYFTDNYRELRHYKPATFFSNFHKGLG 36- 0 Query: 361 NLKFDKLHHFTQYGMQEFFNQFPLLVDEINRYKKSGATVLLQVDSQKGLNLLQENLKEYG 42- 0 N+KFD++H TQY MQEFFNQFPLL+DEI RY+K+ TV++QV+SQ L+++ ++Y Sbjct: 361 NIKFDQMHQLTQYAMQEFFNQFPLLIDEIKRYQKNQTTVIVQVESQYAYERLEKSFQDYQ 42- 0 Query: 421 LDLIISDKNDIVQKESQLIVGHLSNGFYFADEKIVLITEREIYHRRVKRKIRRSNISNAE 48- 0 L + N IV +ESQ+++G +S+GFYFADEK+ LITE EIYH+++KR+ RRSNISNAE Sbjct: 421 FRLPLVSANQIVSRESQIVIGAISSGFYFADEKLALITEHEIYHKKIKRRARRSNISNAE 48- 0 Query: 481 RLKDYNELSVGDYVVHNVHGVGKFLGIETIEIQGIHRDYLTIQYQNADRISIPVEQIELL 54- 0 RLKDYNEL+VGDYVVHNVHG+G+FLGIETI+IQGIHRDY+TIQYQN+DRIS+P++QI L Sbjct: 481 RLKDYNELAVGDYVVHNVHGIGRFLGIETIQIQGIHRDYVTIQYQNSDRISLPIDQISSL 54- 0 Query: 541 TKYVSADGKEPKINTLNDGRFKKAKQRVAKQVEDIADDLLKLYAERSQLQGFAFSPDDNM 60- 0 +KYVSADGKEPKIN LNDGRF+K KQ+VA+QVEDIADDLLKLYAERSQ +GF+FSPDD++ Sbjct: 541 SKYVSADGKEPKINKLNDGRFQKTKQKVARQVEDIADDLLKLYAERSQQKGFSFSPDDDL 60- 0 Query: 601 QNDFDNDFAYVETEDQLRSIKEIKQDMEGNRPMDRLLVGDVGFGKTEVAMRAAFKAVNDH 66- 0 Q FD+DFA+VETEDQLRSIKEIK DME +PMDRLLVGDVGFGKTEVAMRAAFKAVNDH Sbjct: 601 QRAFDDDFAFVETEDQLRSIKEIKADMESMQPMDRLLVGDVGFGKTEVAMRAAFKAVNDH 66- 0 Query: 661 KQVVVLVPTTVLAQQHFENFKERFSNYPVTVDVLSRFRSKKEQTDTLKRLSKGQVDIIIG 72- 0 KQV VLVPTTVLAQQH+ENFK RF NYPV VDVLSRFRSKKEQ +TL+R+ KGQ+DIIIG Sbjct: 661 KQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLERVRKGQIDIIIG 72- 0 Query: 721 THRLLSQDVVFSDLGLIVIDEEQRFGVKHKEKLKELKTKVDVLTLTATPIPRTLHMSMLG 78- 0 THRLLS+DVVFSDLGLIVIDEEQRFGVKHKE LKELKTKVDVLTLTATPIPRTLHMSMLG Sbjct: 721 THRLLSKDVVFSDLGLIVIDEEQRFGVKHKETLKELKTKVDVLTLTATPIPRTLHMSMLG 78- 0 Query: 781 IRDLSVIETPPTNRYPVQTYVLETNPGLVREAIIREIDRGGQVFYVYNKVDTIDQKVSEL 84- 0 IRDLSVIETPPTNRYPVQTYVLE NPGLVREAIIRE+DRGGQ+FYVYNKVDTI++KV+EL Sbjct: 781 IRDLSVIETPPTNRYPVQTYVLENNPGLVREAIIREMDRGGQIFYVYNKVDTIEKKVAEL 84- 0 Query: 841 QELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISNVNTLFVENAD 90- 0 QELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISNVNTLF+ENAD Sbjct: 841 QELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISNVNTLFIENAD 90- 0 Query: 901 HMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTEISEKRLDAIKGFTELGSGFKIAMRD 96- 0 HMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTE+SEKRL+AIKGFTELGSGFKIAMRD Sbjct: 901 HMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTEVSEKRLEAIKGFTELGSGFKIAMRD 96- 0 Query: 961 LSIRGAGNILGASQSGFIDSVGFEMYSQLLEQAIATKQGKSLIRQKGNAELALQIDAYLP 10- 20 LSIRGAGNILGASQSGFIDSVGFEMYSQLLEQAIA+KQGK+ +RQKGN E+ LQIDAYLP Sbjct: 961 LSIRGAGNILGASQSGFIDSVGFEMYSQLLEQAIASKQGKTTVRQKGNTEINLQIDAYLP 10- 20 Query: 1021 AEYISDERQKIEIYKRIRELETRADYEALQDELIDRFGEYPDQVAYLLEIGLLKAYLDLA 1- 080 +YI+DERQKI+IYKRIRE+++R DY LQDEL+DRFGEYPDQVAYLLEI LLK Y+D A Sbjct: 1021 DDYIADERQKIDIYKRIREIQSREDYLNLQDELMDRFGEYPDQVAYLLEIALLKHYMDNA 1- 080 Query: 1081 FTELVERKGNEISILFEKASLKYFLTQDYFEALSKTQLKARISETNGKMEVVFNIKHKKN 1- 140 F ELVERK N++ + FE SL YFLTQDYFEALSKT LKA+ISE GK+++VF+++H+K+ Sbjct: 1081 FAELVERKNNQVIVRFEVTSLTYFLTQDYFEALSKTHLKAKISEHQGKIDIVFDVRHQKD 1- 140 Query: 1141 YEIIEELLKFAECFIEIKSRK 1161 Y I+EEL+ F E EIK RK Sbjct: 1141 YRILEELMLFGERLSEIKIRK 1161 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1659 A DNA sequence (GBSx1754) was identified in S. agalactiae <SEQ ID 5141> which encodes the amino acid sequence <SEQ ID 5142>. Analysis of this protein sequence reveals the following: TABLE-US-05040 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4347(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05041 >GP:CA811835 GB:Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 50/84 (59%), Positives = 70/84 (82%) Query: 1 MRLDKYLKVSRIIKRRPVAKEVADKGRVKVNGVLAKSSTDLKLNDQVEIRFGNKLLTVKV 60 - MRLDK+LKVSR+IKRR +AKEVAD+GR+ +NG AK+S+D+K D++ +RFG KL+TV+V Sbjct: 1 MRLDKFLKVSRLIKRRTLAKEVADQGRISINGNQAKASSDVKPGDELTVRFGQKLVTVQV 60 Query: 61 LEMKDSTKKEDAIKMYEIINETRI 84 E+KD+TKKE+A MY I+ E ++ Sbjct: 61 NELKDTTKKEEAANMYTILKEEKL 84 A related DNA sequence was identified in S. pyogenes <SEQ ID 5143> which encodes the amino acid sequence <SEQ ID 5144>. Analysis of this protein sequence reveals the following: TABLE-US-05042 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2963 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05043 Identities = 72/90 (80%), Positives = 85/90 (94%) Query: 1 MRLDKYLKVSRIIKRRPVAKEVADKGRVKVNGVLAKSSTDLKLNDQVEIRFGNKLLTVKV 60 - MRLDKYLKVSR+IKRR VAKEVADKGR+KVNG+LAKSST++KLND +EI FGNKLLTV+V Sbjct: 9 MRLDKYLKVSRLIKRRSVAKEVADKGRIKVNGILAKSSTNIKLNDHIEISFGNKLLTVRV 68 Query: 61 LEMKDSTKKEDAIKMYEIINETRIETDEQA 90 +E+KDSTKKEDA+KMYEII+ETRI +E+A Sbjct: 69 IEIKDSTKKEDALKMYEIISETRITLNEEA 98 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1660 A DNA sequence (GBSx1755) was identified in S. agalactiae <SEQ ID 5145> which encodes the amino acid sequence <SEQ ID 5146>. This protein is predicted to be DivIC homolog. Analysis of this protein sequence reveals the following: TABLE-US-05044 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.12 Transmembrane 34-50 (31-56) ----- Final Results ----- bacterial membrane --- Certainty = 0.4248 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05045 >GP:AAC98903 GB:AF023181 DivIC homolog [Listeria monocytogenes] Identities = 36/119 (30%), Positives = 65/119 (54%), Gaps = 2/119 (1%) Query: 2 SKPNVVQLNNQYINDE-NLKKRYEAEELRRKNRLMGWVLIFVMLLFILPTYNLVKSYRTL 60 - +K V ++ N+YI D +KK + RL +IF ++ +L T K TL Sbjct: 4 AKSKVARIENRYIKDTATMKKTRSRRRIALFRRLAFMAIIFAVVGGLL-TITYTKQVLTL 62 Query: 61 QERRQEVVKLTKDYQTLTNRTENQKLLAKQLKNPDYVQKYARAKYYFSKTGEMIYPLPD 119 +E++++ V++ K + + ++ K+L N DY+ K AR++YY SK GE+I+ +P+ Sbjct: 63 KEKKEKQVQVDKKMVAMKDEQDSLNEQIKKLHNDDYIAKLARSEYYLSKDGEIIFNIPE 121 A related DNA sequence was identified in S. pyogenes <SEQ ID 5147> which encodes the amino acid sequence <SEQ ID 5148>. Analysis of this protein sequence reveals the following: TABLE-US-05046 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.93 Transmembrane 34-50 (32-51) ----- Final Results ----- bacterial membrane --- Certainty = 0.2572 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: TABLE-US-05047 >GP:AAC98903 GB:AF023181 DivIC homolog [Listeria monocytogenes] Identities = 27/116 (23%), Positives = 59/116 (50%) Query: 3 KPSIVQLNNHYIKKENLKKKFEEEESQKRNRFMGWILVSMMFLFILPTYNLVKSYVDFEK 62 - K + ++ N YIK KK R + ++ + + L T K + ++ Sbjct: 5 KSKVARIENRYIKDTATMKKTRSRRRIALFRRLAFMAIIFAVVGGLLTITYTKQVLTLKE 64 Query: 63 QNQQVVKLKKEYNELSESTKKEKQLAERLKDDNFVKKYARAKYYLSREGEMIYPIP 118 + ++ V++ K+ + + + ++L +D+++ K AR++YYLS++GE+I+ IP Sbjct: 65 KKEKQVQVDKKMVAMKDEQDSLNEQIKKLHNDDYIAKLARSEYYLSKDGEIIFNIP 120 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05048 Identities = 73/123 (59%), Positives = 99/123 (80%) Query: 1 MSKPNVVQLNNQYINDENLKKRYEAEELRRKNRLMGWVLIFVMLLFILPTYNLVKSYRTL 60- M KP++VQLNN YI ENLKK++E EE +++NR MGW+L+ +M LFILPTYNLVKSY Sbjct: 1 MKKPSIVQLNNHYIKKENLKKKFEEEESQKRNRFMGWILVSMMFLFILPTYNLVKSYVDF 60- Query: 61 QERRQEVVKLTKDYQTLTNRTENQKLLAKQLKNPDYVQKYARAKYYFSKTGEMIYPLPDL 12- 0 +++ Q+VVKL K+Y L+ T+ +K LA++LK+ ++V+KYARAKYY S+ GEMIYP+P L Sbjct: 61 EKQNQQVVKLKKEYNELSESTKKEKQLAERLKDDNFVKKYARAKYYLSREGEMIYPIPGL 12- 0 Query: 121 LPK 123 LPK Sbjct: 121 LPK 123 SEQ ID 5146 (GBS418) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 172 (lane 3; MW 42 kDa). GBS418-GST was purified as shown in FIG. 219, lane 4-5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1661 A DNA sequence (GBSx1756) was identified in S. agalactiae <SEQ ID 5149> which encodes the amino acid sequence <SEQ ID 5150>. Analysis of this protein sequence reveals the following: TABLE-US-05049 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4355 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1662 A DNA sequence (GBSx1757) was identified in S. agalactiae <SEQ ID 5151> which encodes the amino acid sequence <SEQ ID 5152>. Analysis of this protein sequence reveals the following: TABLE-US-05050 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.52 Transmembrane 4-20 (3-22) ----- Final Results ----- bacterial membrane --- Certainty = 0.3208 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 5153> which encodes the amino acid sequence <SEQ ID 5154>. Analysis of this protein sequence reveals the following: TABLE-US-05051 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-05052 Identities = 205/428 (47%), Positives = 285/428 (65%) Query: 1 MKKVLTFLLCSLYFVSIPAISTEEPLTLSQNRRYALTQTVVDKEMYFDAIPERPTTKIEI 60- M+K+L +L + + +P ISTE+ L S+N Y L Q VV +++ IP P E Sbjct: 1 MRKLLAAMLMTFFLTPLPVISTEKKLIFSKNAVYQLKQDVVQSTQFYNQIPSNPNLYQET 60- Query: 61 SSFQDEALTITGETLVPNTLLSIVSLTINSNGIPVFTLSNGQFIKASREAIFNDLVSKQQ 12- 0 +++D LT+ L N L I SL +N +PVF L++G +++A+R+ I++D+V Q Sbjct: 61 CAYKDSDLTLPAGRLGVNQPLLIKSLVLNKESLPVFELADGTYVEANRQLIYDDIVLNQV 12- 0 Query: 121 SVSLDYWLKPSFVTYEAPYTNGVSEVKNNLKPYSRVHLVEQAETEHGIYYKTDSGFWISV 18- 0 + +W + Y APY G + ++ +VH + A+T HG YY D W S Sbjct: 121 DIDSYFWTQKKLRLYSAPYVLGTQTIPSSFLFAQKVHATQMAQTNHGTYYLIDDKGWASQ 18- 0 Query: 181 EDLSVADNRMAKVQEVLLEKYNKDKYGIYIKQLNTQTVAGINIDRSMYSASIAKLATLYA 24- 0 EDL DNRM KVQE+LL+KYN Y I++KQLNTQT AGIN D+ MY+ASI+KLA LY Sbjct: 181 EDLVQFDNRMLKVQEMLLQKYNNPNYSIFVKQLNTQTSAGINADKKMYAASISKLAPLYI 24- 0 Query: 241 SQEQVKLGKLSLDSKFEYKDNVNQFPNSYDPSGSGKLEKKADHKLYTVKELLEATAKESD 30- 0 Q+Q++ KL + Y +VN F YDP GSGK+ K AD+K Y V++LL+A A++SD Sbjct: 241 VQKQLQKKKLAENKTLTYTKDVNHFYGDYDPLGSGKISKIADNKDYRVEDLLKAVAQQSD 30- 0 Query: 301 NVATNMLGYYVNNQYDSMFQTQVDTISGMHWDMKKRQISPQAAGKMMEAIYYQNGDIVNY 36- 0 NVATN+LGYY+ +QYD F++++ +SG+ WDM++R ++ ++A MMEAIY+Q G I++Y Sbjct: 301 NVATNILGYYLCHQYDKAFRSEIKALSGIDWDMEQRLLTSRSAANMMEAIYHQKGQIISY 36- 0 Query: 361 LSKTDFDNTRIPKNIPVKVAHKIGDAYDYKHDAAIVYAEQPFIMIIFTDKSSYDDITKIA 42- 0 LS T+FD RI KNA V VAHKIGDAYDYKHD AIVY PFI+ IFT+KS+Y+DIT IA Sbjct: 361 LSNTEFDQQRITKNITVPVAHKIGDAYDYKHDVAIVYGNTPFILSIFTNKSTYEDITAIA 42- 0 Query: 421 DDVYQVLK 428 DDVY +LK Sbjct: 421 DDVYGILK 428 SEQ ID 5152 (GBS116) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 38 (lane 3; MW 48.5 kDa). The GBS116-His fusion product was purified (FIG. 202, lane 6) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 316), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1663 A DNA sequence (GBSx1758) was identified in S. agalactiae <SEQ ID 5155> which encodes the amino acid sequence <SEQ ID 5156>. Analysis of this protein sequence reveals the following: TABLE-US-05053 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2260 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05054 >GP:AAD35664 GB:AE001733 conserved hypothetical protein [Thermotoga maritima] Identities = 100/404 (24%), Positives = 181/404 (44%), Gaps = 61/404 (15%) Query: 19 QKVLIAVSGGIDSINLLQFLYQYQKELSISIGIAHINHGQRKESEKEEEYIRQWGQIHDV 78- + VL+AVSGGIDS+ LL L ++ L I I AH++H R+ S ++ E++ + + ++ Sbjct: 6 EHVLVAVSGGIDSMTLLYVLRKFSPLLKIKITAAHLDHRIRESSRRDREFVERICRQWNI 65- Query: 79 PVFISYF--------QGIFSEDRARNHRYNFFSKVMREEGYTALVTAHHADDQAETVFMR 13- 0 PV S G E+ AR RY+F + ++ G + + AHH +D ETV R Sbjct: 66 PVETSEVDVPSLWKDSGKTLEEIAREVRYDFLKRTAKKVGASKIALAHHKNDLLETVVHR 12- 5 Query: 131 ILRGSRLRYLSGIKQVSAFANGQLIRPFLPYKKELLP------NIFHFEDASNASSDYLR 18- 4 ++RG+ L+ I + IRPFL +K+ + N+ + D +N + Y R Sbjct: 126 LIRGTGPLGLACISP----KREEFIRPFLVFKRSEIEEYARKNNVPYVVDETNYNVKYTR 18- 1 Query: 185 NRIRNVYFPALERENNQLKDSLITLSEETECLFTALTDLTRSIEVTNCYDF--------- 23- 5 N IR+ P ++ N ++D++ L T L + + N Y + Sbjct: 182 NFIRHRIVPLMKELNPTVEDAVYRLVSVTHLLRNFVERTVQDFVERNVYFYKDYAVFVEP 24- 1 Query: 236 --LRQTHSVQEFLLQDYISKFPDLQVSKEQFRVILKLIRTKANIDYTIKSGYFLHKDYES 29- 3 L V ++L++ + P+ + KLI T + + SG F+ + + Sbjct: 242 EDLFLFLEVTRWVLKEMYGRVPEYE----------KLIGTLKSKRVELWSGIFVERSFGY 29- 1 Query: 294 FHITKIHPKTDSFKVEKRLELHNIQIFSQYLFSYGKFISQADITIPIYDT---SPIILRR 35- 0 + K FK + R+E+ G + I + + +R Sbjct: 292 VAVGK-----TVFKKKYRVEVK------------GDMLEMEGFKIRVVNNRNDMKFWVRN 33- 4 Query: 351 RKEGDRIFLGNHTKKIRRLFIDEKIT--LKEREEAVIGEQNKEL 392 RKEGDRI + +K++ +FI++K+ ++R ++ E+++ L Sbjct: 335 RKEGDRIIVNGRERKLKDVFIEKKVPTFYRDRVPLLVDEEDRVL 378 A related DNA sequence was identified in S. pyogenes <SEQ ID 5157> which encodes the amino acid sequence <SEQ ID 5158>. Analysis of this protein sequence reveals the following: TABLE-US-05055 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2187 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-05056 Identities = 218/424 (51%), Positives = 290/424 (67%), Gaps = 2/424 (0%) Query: 2 YNTILKDTLSKGLFTAHQKVLIAVSGGIDSINLLQFLYQYQKELSISIGIAHINHGQRKE 61- Y I + +K F H+ VLIAVSGG+DS+NLL FLY +Q +L I IGIAH+NH QR E Sbjct: 4 YQEIFNEIKNKAYFKNHRHVLIAVSGGVDSMNLLHFLYLFQDKLKIRIGIAHVNHKQRSE 63- Query: 62 SEKEEEYIRQWGQIHDVPVFISYFQGIFSEDRARNHRYNFFSKVMREEGYTALVTAHHAD 12- 1 S+ EE Y++ W + HD+P+++S F+GIFSE AR+ RY FF +M + Y+ALVTAHH+D Sbjct: 64 SDSEEAYLKCWAKKHDIPIYVSNFEGIFSEKAARDWRYAFFKSIMLKNNYSALVTAHHSD 12- 3 Query: 122 DQAETVFMRILRGSRLRYLSGIKQVSAFANGQLIRPFLPYKKELLPNIFHFEDASNASSD 18- 1 DQAET+ MR++RGSRLR+LSGIK V FANGQLIRPFL + K+ LP IFHFED+SN Sbjct: 124 DQAETILMRLIRGSRLRHLSGIKSVQPFANGQLIRPFLTFSKKDLPEIFHFEDSSNRELS 18- 3 Query: 182 YLRNRIRNVYFPALERENNQLKDSLITLSEETECLFTALTDLTRSIEVTNCYDFLRQTHS 24- 1 +LRNR+RN Y P L++EN + L L+E LF A +LT I T+ +F Q+ S Sbjct: 184 FLRNRVRNNYLPLLKQENPRFIQGLNQLALENSLLFQAFKELTNHITTTDLTEFNEQSKS 24- 3 Query: 242 VQEFLLQDYISKFPDLQVSKEQFRVILKLIRTKANIDYTIKSGYFLHKDYESFHITKIHP 30- 1 +Q FLLQDY+ FPDL + K QF +L++I+T Y +K Y++ D SF ITKI P Sbjct: 244 IQYFLLQDYLEGFPDLDLKKSQFTQLLQIIQTAKQGYYYLKKDYYIFIDKFSFKITKIVP 30- 3 Query: 302 KTDSFKVEKRLELHNIQIFSQYLFSY--GKFISQADITIPIYDTSPIILRRRKEGDRIFL 35- 9 KT+ K EK LE + + Y FS+ Q ++IP++ S I LR R+ GD I Sbjct: 304 KTELVKEEKMLEYDSNLCYRDYYFSFMPKSNEDQGQVSIPLFSLSSIKLRSRQSGDYISF 36- 3 Query: 360 GNHTKKIRRLFIDEKITLKEREEAVIGEQNKELIFVIVAGRTYLRKPSEHDIMKGKLYIE 41- 9 G+ +KKIRRLFIDEK T+ ER+ A+IGEQ++++IFV++ +TYLRK +HDIM KLYI+ Sbjct: 364 GHFSKKIRRLFIDEKFTIAERQNAIIGEQDEQIIFVLIGNKTYLRKACKHDIMLAKLYID 42- 3 Query: 420 NLEK 423 LEK Sbjct: 424 KLEK 427 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1664 A DNA sequence (GBSx1759) was identified in S. agalactiae <SEQ ID 5159> which encodes the amino acid sequence <SEQ ID 5160>. This protein is predicted to be hypoxanthine-guanine phosphoribosyltransferase (hpt). Analysis of this protein sequence reveals the following: TABLE-US-05057 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 37-53 (37-53) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <suco> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05058 >GP:CAA48876 GB:X69123 hypoxanthine guanine phosphoribosyltransferase [Lactococcus lactis] Identities = 121/179 (67%), Positives = 152/179 (84%), Gaps = 1/179 (0%) Query: 2 LENDIKKVLYSEEDIILKTKELGAKLTADYAGKNPLLVGVLKGSVPFMAELLKHIDTHVE 61- L+ I+KVL SEE+II K+KELG LT +Y GKNPL++G+L+GSVPF+AEL+KHID H+E Sbjct: 6 LDKAIEKVLVSEEEIIEKSKELGEILTKEYEGKNPLVLGILRGSVPFLAELIKHIDCHLE 65- Query: 62 IDFMVVSSYHGGTTSSGEVKILKDVDTNIEGRDVIFIEDIIDTGRTLKYLRDMFKYRQAN 12- 1 DFM VSSYHGGT SSGEVK++ DVDT ++GRD++ +EDIIDTGRTLKYL+++ ++R AN Sbjct: 66 TDFMTVSSYHGGTKSSGEVKLILDVDTAVKGRDILIVEDIIDTGRTLKYLKELLEHRGAN 12- 5 Query: 122 SVKVATLFDKPEGRLVDIDADYVCYDIPNEFIVGFGLDYAENYRNLPYVGVLKEEIYSK 180- VK+ TL DKPEGR+V+I DY + IPNEF+VGFGLDY ENYRNLPYVGVLK E+Y+K Sbjct: 126 -VKIVTLLDKPEGRIVEIKPDYSGFTIPNEFVVGFGLDYEENYRNLPYVGVLKPEVYNK 183- A related DNA sequence was identified in S. pyogenes <SEQ ID 5161> which encodes the amino acid sequence <SEQ ID 5162>. Analysis of this protein sequence reveals the following: TABLE-US-05059 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4095 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05060 Identities = 153/180 (85%), Positives = 171/180 (95%) Query: 1 MLENDIKKVLYSEEDIILKTKELGAKLTADYAGKNPLLVGVLKGSVPFMAELLKHIDTHV 60- MLE DI+K+LYSE DII KTK+LG +LT DY KNPL++GVLKGSVPFMAEL+KHIDTHV Sbjct: 1 MLEQDIQKILYSENDIIRKTKKLGEQLTKDYQEKNPLMIGVLKGSVPFMAELMKHIDTHV 60- Query: 61 EIDFMVVSSYHGGTTSSGEVKILKDVDTNIEGRDVIFIEDIIDTGRTLKYLRDMFKYRQA 12- 0 EIDFMVVSSYHGGT+SSGEVKILKDVDTNIEGRD+I +EDIIDTGRTLKYLRDMFKYR+A Sbjct: 61 EIDFMVVSSYHGGTSSSGEVKILKDVDTNIEGRDIIIVEDIIDTGRTLKYLRDMFKYRKA 12- 0 Query: 121 NSVKVATLFDKPEGRLVDIDADYVCYDIPNEFIVGFGLDYAENYRNLPYVGVLKEEIYSK 18- 0 N++K+ATLFDKPEGR+V I+ADYVCY+IPNEFIVGFGLDYAENYRNLPYVGVLKEE+YSK Sbjct: 121 NTIKIATLFDKPEGRVVKIEADYVCYNIPNEFIVGFGLDYAENYRNLPYVGVLKEEVYSK 18- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1665 A DNA sequence (GBSx1760) was identified in S. agalactiae <SEQ ID 5163> which encodes the amino acid sequence <SEQ ID 5164>. This protein is predicted to be cell division protein FtsH (ftsH). Analysis of this protein sequence reveals the following: TABLE-US-05061 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.11 Transmembrane 139-155 (133-158) INTEGRAL Likelihood = -4.62 Transmembrane 8-24 (7-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.3845 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05062 >GP: AAC16243 GB: AF061748 cell division protein FtsH [Streptococcus pneumoniae] (ver 2) Identities = 490/652 (75%), Positives = 561/652 (85%), Gaps = 5/652 (0%) Query: 5 KNNGFLKNSFIYILLIIAVITTFQYYLKGTSSQ-NQQISYTKLVKQLKAGEIKSISYQPS 63 +NNG +KN F+++L I ++T FQY+ G +S +QQI+YT+LV+++ G +K ++YQP+ Sbjct: 4 QNNGLIKNPFLWLLFIFFLVTGFQYFYSGNNSGGSQQINYTELVQEITDGNVKELTYQPN 63 Query: 64 GGVVEVSGTYKKAKTIKSANSFTFLGGSVATKVTGFNSVILPNDSSIKSLVSAAEENNTN 123- G V+EVSG YK KT K F SV TKV F S ILP D+++ L A ++ Sbjct: 64 GSVIEVSGVYKNPKTSKEGTGIQFFTPSV-TKVEKFTSTILPADTTVSELQKLATDHKAE 122- Query: 124 IQVKHESSSGTWISYIASFLPLVIMIGFFMMMMNQGGGGGARGAMSFGKNKARSSSKDEV 18- 3 + VKHESSSG WI+ + S +P I+ F MM GGG R MSFG++KA++++K+++ Sbjct: 123 VTVKHESSSGIWINLLVSIVPFGILFFFLFSMMGNMGGGNGRNPMSFGRSKAKAANKEDI 18- 2 Query: 184 KVRFSDVAGAEEEKQELIEVVDFLKDPKRYKSLGARIPAGVLLEGPPGTGKTLLAKAVAG 24- 3 KVRFSDVAGAEEEKQEL+EVV+FLKDPKR+ LGARIPAGVLLEGPPGTGKTLLAKAVAG Sbjct: 183 KVRFSDVAGAEEEKQELVEVVEFLKDPKRFTKLGARIPAGVLLEGPPGTGKTLLAKAVAG 24- 2 Query: 244 EAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKAERAIIFIDEIDAVGRRRGAGMGGG 30- 3 EAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKA AIIFIDEIDAVGR+RG G+GGG Sbjct: 243 EAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKAAPAIIFIDEIDAVGRQRGVGLGGG 30- 2 Query: 304 NDEREQTLNQLLIEMDGFEGNESIIVIAATNRSDVLDPALLRPGRFDRKVLVGQPDVKGR 36- 3 NDEREQTLNQLLIEMDGFEGNE IIVIAATNRSDVLDPALLRPGRFDRKVLVG+PDVKGR Sbjct: 303 NDEREQTLNQLLIEMDGFEGNEGIIVIAATNRSDVLDPALLRPGRFDRKVLVGRPDVKGR 36- 2 Query: 364 EAILRVHAKNKPLADNVDLKVVAQQTPGFVGADLENVLNEAALVAARRNKKVIDASDIDE 42- 3 EAIL+VHAKNKPLA++VDLK+VAQQTPGFVGADLENVLNEAALVAARRNK +IDASDIDE Sbjct: 363 EAILKVHAKNKPLAEDVDLKLVAQQTPGFVGADLENVLNEAALVAARRNKSIIDASDIDE 42- 2 Query: 424 AEDRVIAGPSKKDRTISERERAMVAYHEAGHTIVGLILSNARVVHKVTIVPRGRAGGYMI 48- 3 AEDRVIAGPSKKD+T+S++ER +VAYHEAGHTIVGL+LSNARVVHKVTIVPRGRAGGYMI Sbjct: 423 AEDRVIAGPSKKDKTVSQKERELVAYHEAGHTIVGLVLSNARVVHKVTIVPRGRAGGYMI 48- 2 Query: 484 ALPKEDQMLLSKDDMKEQLAGLMGGRVAEEIIFNAQTTGASNDFEQATAMARAMVTEYGM 54- 3 ALPKEDQMLLSK+DMKEQLAGLMGGRVAEEIIFN QTTGASNDFEQAT MARAMVTEYGM Sbjct: 483 ALPKEDQMLLSKEDMKEQLAGLMGGRVAEEIIFNVQTTGASNDFEQATQMARAMVTEYGM 54- 2 Query: 544 SEKLGPVQYEGNHAMMAGQMSPEKSYSAQTAQLIDDEVRHLLNEARNKAADIINENRDTH 60- 3 SEKLGPVQYEGNHAM+ G SP+KS S QTA ID+EVR LLNEARNKAA+II NR+TH Sbjct: 543 SEKLGPVQYEGNHAML-GAQSPQKSISEQTAYEIDEEVRSLLNEARNKAAEIIQSNRETH 60- 1 Query: 604 KLIAEALLKYETLDAAQIKSIFETGKMPETENDEDKARALSYDEIKEKMQEE 655 KLIAEALLKYETLD+ QIK+++ETGKMPE E+++ ALSYDE+K KM +E Sbjct: 602 KLIAEALLKYETLDSTQIKALYETGKMPEAV--EEESHALSYDEVKSKMNDE 651 A related DNA sequence was identified in S. pyogenes <SEQ ID 5165> which encodes the amino acid sequence <SEQ ID 5166>. Analysis of this protein sequence reveals the following: TABLE-US-05063 Possible site: 38 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.38 Transmembrane 138-154 (132-158) ----- Final Results ----- bacterial membrane --- Certainty = 0.3951(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05064 >GP: AAC16243 GB: AF061748 cell division protein FtsH [Streptococcus pneumoniae] (ver 2) Identities = 487/654 (74%), Positives = 565/654 (85%), Gaps = 7/654 (1%) Query: 5 KNNGFVKNSFIYILMIIVVITGFQFYLKGTSTQ-SQQISYSKLIKHLKAGDIKSLSYQPS 63 +NNG +KN F+++L I ++TGFQ++ G ++ SQQI+Y++L++ + G++K L+YQP+ Sbjct: 4 QNNGLIKNPFLWLLFIFFLVTGFQYFYSGNNSGGSQQINYTELVQEITDGNVKELTYQPN 63 Query: 64 GSIIEVKGKYEKPQKVTVNSGLSFLGGRASTQVTEFSSLVLPSDTILKEMTAAADKNGTE 123- GS+IEV G Y+ P+ +G+ F T+V +F+S +LP+DT + E+ A + E Sbjct: 64 GSVIEVSGVYKNPKTSKEGTGIQFFTPSV-TKVEKFTSTILPADTTVSELQKLATDHKAE 122- Query: 124 LTVKQESSSGTWITFLMSFLPIVIFAAFMMMMM-NQGGGGARGAMSFGKNKAKSQSKGNV 18- 2 +TVK ESSSG WI L+S +P I F+ MM N GGG R MSFG++KAK+ +K ++ Sbjct: 123 VTVKHESSSGIWINLLVSIVPFGILFFFLFSMMGNMGGGNGRNPMSFGRSKAKAANKEDI 18- 2 Query: 183 KVRFTDVAGAEEEKQELVEVVDFLKNPKKYKSLGARIPAGVLLEGPPGTGKTLLAKAVAG 24- 2 KVRF+DVAGAEEEKQELVEVV+FLK+PK++ LGARIPAGVLLEGPPGTGKTLLAKAVAG Sbjct: 183 KVRFSDVAGAEEEKQELVEVVEFLKDPKRFTKLGARIPAGVLLEGPPGTGKTLLAKAVAG 24- 2 Query: 243 EAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKAERAIIFIDEIDAVGRRRGAGMGGG 30- 2 EAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKA AIIFIDEIDAVGR+RG G+GGG Sbjct: 243 EAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKAAPAIIFIDEIDAVGRQRGVGLGGG 30- 2 Query: 303 NDEREQTLNQLLIEMDGFEGNENIIVIAATNRSDVLDPALLRPGRFDRKVLVGRPDVKGR 36- 2 NDEREQTLNQLLIEMDGFEGNE IIVIAATNRSDVLDPALLRPGRFDRKVLVGRPDVKGR Sbjct: 303 NDEREQTLNQLLIEMDGFEGNEGIIVIAATNRSDVLDPALLRPGRFDRKVLVGRPDVKGR 36- 2 Query: 363 EAILRVHAKNKPLANDVNLKVVAQQTPGFVGADLENVLNEAALVAARRNKIKIDASDIDE 42- 2 EAIL+VHAKNKPLA DV+LK+VAQQTPGFVGADLENVLNEAALVAARRNK IDASDIDE Sbjct: 363 EAILKVHAKNKPLAEDVDLKLVAQQTPGFVGADLENVLNEAALVAARRNKSIIDASDIDE 42- 2 Query: 423 AEDRVIAGPSKKDRTISQKEREMVAYHEAGHTIVGLVLSNARVVHKVTIVPRGRAGGYMI 48- 2 AEDRVIAGPSKKD+T+SQKERE+VAYHEAGHTIVGLVLSNARVVHKVTIVPRGRAGGYMI Sbjct: 423 AEDRVIAGPSKKDKTVSQKERELVAYHEAGHTIVGLVLSNARVVHKVTIVPRGRAGGYMI 48- 2 Query: 483 ALPKEDQMLLSKEDLKEQLAGLMGGRVAEEIVFNAQTSGASNDFEQATQIARAMVTEYGM 54- 2 ALPKEDQMLLSKED+KEQLAGLMGGRVAEEI+FN QT+GASNDFEQATQ+ARAMVTEYGM Sbjct: 483 ALPKEDQMLLSKEDMKEQLAGLMGGRVAEEIIFNVQTTGASNDFEQATQMARAMVTEYGM 54- 2 Query: 543 SEKLGPVQYEGNHAMMPGQISPEKAYSAQTAQMIDDEVRELLNQARNQAADIINENRDTH 60- 2 SEKLGPVQYEGNHAM+ Q SP+K+ S QTA ID+EVR LLN+ARN+AA+II NR+TH Sbjct: 543 SEKLGPVQYEGNHAMLGAQ-SPQKSISEQTAYEIDEEVRSLLNEARNKAAEIIQSNRETH 60- 1 Query: 603 KLIAEALLKYETLDAAQIKSIYETGKMPVDLETDDNEAHALSYDEIKNKMTESE 656 KLIAEALLKYETLD+ QIK++YETGKMP E + E+HALSYDE+K+KM + + Sbjct: 602 KLIAEALLKYETLDSTQIKALYETGKMP---EAVEEESHALSYDEVKSKMNDEK 652 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05065 Identities = 550/657 (83%), Positives = 612/657 (92%), Gaps = 2/657 (0%) Query: 1 MKNNKNNGFLKNSFIYILLIIAVITTFQYYLKGTSSQNQQISYTKLVKQLKAGEIKSISY 60 MKNNKNNGF+KNSFIYIL+II VIT FQ+YLKGTS+Q+QQISY+KL+K LKAG+IKS+SY Sbjct: 1 MKNNKNNGFVKNSFIYILMIIVVITGFQFYLKGTSTQSQQISYSKLIKHLKAGDIKSLSY 60 Query: 61 QPSGGVVEVSGTYKKAKTIKSANSFTFLGGSVATKVTGFNSVILPNDSSIKSLVSAAEEN 120- QPSG ++EV G Y+K + + + +FLGG +T+VT F+S++LP+D+ +K + +AA++N Sbjct: 61 QPSGSIIEVKGKYEKPQKVTVNSGLSFLGGRASTQVTEFSSLVLPSDTILKEMTAAADKN 120- Query: 121 NTNIQVKHESSSGTWISYIASFLPLVIMIGFFMMMMNQGGGGGARGAMSFGKNKARSSSK 18- 0 T + VK ESSSGTWI+++ SFLP+VI F MMMMNQGGGG ARGAMSFGKNKA+S SK Sbjct: 121 GTELTVKQESSSGTWITFLMSFLPIVIFAAFMMMMMNQGGGG-ARGAMSFGKNKAKSQSK 17- 9 Query: 181 DEVKVRFSDVAGAEEEKQELIEVVDFLKDPKRYKSLGARIPAGVLLEGPPGTGKTLLAKA 24- 0 VKVRF+DVAGAEEEKQEL+EVVDFLK+PK+YKSLGARIPAGVLLEGPPGTGKTLLAKA Sbjct: 180 GNVKVRFTDVAGAEEEKQELVEVVDFLKNPKKYKSLGARIPAGVLLEGPPGTGKTLLAKA 23- 9 Query: 241 VAGEAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKAERAIIFIDEIDAVGRRRGAGM 30- 0 VAGEAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKAERAIIFIDEIDAVGRRRGAGM Sbjct: 240 VAGEAGVPFFSISGSDFVEMFVGVGASRVRSLFEDAKKAERAIIFIDEIDAVGRRRGAGM 29- 9 Query: 301 GGGNDEREQTLNQLLIEMDGFEGNESIIVIAATNRSDVLDPALLRPGRFDRKVLVGQPDV 36- 0 GGGNDEREQTLNQLLIEMDGFEGNE+IIVIAATNRSDVLDPALLRPGRFDRKVLVG+PDV Sbjct: 300 GGGNDEREQTLNQLLIEMDGFEGNENIIVIAATNRSDVLDPALLRPGRFDRKVLVGRPDV 35- 9 Query: 361 KGREAILRVHAKNKPLADNVDLKVVAQQTPGFVGADLENVLNEAALVAARRNKKVIDASD 42- 0 KGREAILRVHAKNKPLA++V+LKVVAQQTPGFVGADLENVLNEAALVAARRNK IDASD Sbjct: 360 KGREAILRVHAKNKPLANDVNLKVVAQQTPGFVGADLENVLNEAALVAARRNKIKIDASD 41- 9 Query: 421 IDEAEDRVIAGPSKKDRTISERERAMVAYHEAGHTIVGLILSNARVVHKVTIVPRGRAGG 48- 0 IDEAEDRVIAGPSKKDRTIS++ER MVAYHEAGHTIVGL+LSNARVVHKVTIVPRGRAGG Sbjct: 420 IDEAEDRVIAGPSKKDRTISQKEREMVAYHEAGHTIVGLVLSNARVVHKVTIVPRGRAGG 47- 9 Query: 481 YMIALPKEDQMLLSKDDMKEQLAGLMGGRVAEEIIFNAQTTGASNDFEQATAMARAMVTE 54- 0 YMIALPKEDQMLLSK+D+KEQLAGLMGGRVAEEI+FNAQT+GASNDFEQAT +ARAMVTE Sbjct: 480 YMIALPKEDQMLLSKEDLKEQLAGLMGGRVAEEIVFNAQTSGASNDFEQATQIARAMVTE 53- 9 Query: 541 YGMSEKLGPVQYEGNHAMMAGQMSPEKSYSAQTAQLIDDEVRHLLNEARNKAADIINENR 60- 0 YGMSEKLGPVQYEGNHAMM GQ+SPEK+YSAQTAQ+IDDEVR LLN+ARN+AADIINENR Sbjct: 540 YGMSEKLGPVQYEGNHAMMPGQISPEKAYSAQTAQMIDDEVRELLNQARNQAADIINENR 59- 9 Query: 601 DTHKLIAEALLKYETLDAAQIKSIFETGKMP-ETENDEDKARALSYDEIKEKMQEED 656 DTHKLIAEALLKYETLDAAQIKSI+ETGKMP + E D+++A ALSYDEIK KM E + Sbjct: 600 DTHKLIAEALLKYETLDAAQIKSIYETGKMPVDLETDDNEAHALSYDEIKNKMTESE 656 SEQ ID 5164 (GBS115) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 35 (lane 8; MW 73 kDa) and in FIG. 39. (lane 3; MW 73.3 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1666 A DNA sequence (GBSx1769) was identified in S. agalactiae <SEQ ID 5167> which encodes the amino acid sequence <SEQ ID 5168>. Analysis of this protein sequence reveals the following: TABLE-US-05066 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2983(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1667 A DNA sequence (GBSx1770) was identified in S. agalactiae <SEQ ID 5169> which encodes the amino acid sequence <SEQ ID 5170>. Analysis of this protein sequence reveals the following: TABLE-US-05067 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2424(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9547> which encodes amino acid sequence <SEQ ID 9548> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05068 >GP: CAB12187 GB: Z99106 similar to homoserine dehydrogenase [Bacillus subtilis] Identities = 223/448 (49%), Positives = 313/448 (69%) Query: 1 MKVVKFGGSSLASSQQLYKVLNIIKSDYTRRFVVVSAPGKRYEEDLKMTDALIQYYQNYI 60 MKVVKFGGSSLAS QL KV +I+ SD R+ VVVSAPGK Y ED K+TD LI + Y+ Sbjct: 1 MKVVKFGGSSLASGAQLDKVFHIVTSDPARKAVVVSAPGKHYAEDTKVTDLLIACAEQYL 60 Query: 61 NGKDIVKDQTWIINRYQEIISDLSLGSTIAEEITRSIEQLASLPIENNQFLYDCFLAAGE 120- + ++ RY I ++L LG +I E+I + L N + D A+GE Sbjct: 61 ATGSAPELAEAVVERYALIANELQLGQSIIEKIRDDLFTLLEGDKSNPEQYLDAVKASGE 120- Query: 121 DNNAKLVATFFNQNDIPARYVHPNEAGIIVTKEPCNARIIPGSYDKIENLCLYNEVLVIP 18- 0 DNNAKL+A +F + A YV+P +AG+ VT EP NA+++P SY + L + +++ P Sbjct: 121 DNNAKLIAAYFRYKGVKAEYVNPKDAGLFVTNEPGNAQVLPESYQNLYRLRERDGLIIFP 18- 0 Query: 181 GFFGVTEDNQICTFSRGGSDITGSLIAAGIKADLYENFTDVDGIFAAHPGVVKNPHAIPE 24- 0 GFFG ++D + TFSR GSDITGS++A G++ADLYENFTDVD +++ +P V+NP I E Sbjct: 181 GFFGFSKDGDVITFSRSGSDITGSILANGLQADLYENFTDVDAVYSVNPSFVENPKEISE 24- 0 Query: 241 LTYKEMRELAYAGFSVLHDEALLPAYRGRIPLVIKNTNNPQQPGTKIVLKHTRSNIAVTG 30- 0 LTY+EMREL+YAGFSV HDEAL+PA+R IP+ IKNTNNP GT++V K +N V G Sbjct: 241 LTYREMRELSYAGFSVFHDEALIPAFRAGIPVQIKNTNNPSAEGTRVVSKRDNTNGPVVG 30- 0 Query: 301 IASDSRFASINVSKYLMNREVGFGRKVLQILEDLNISFEHMPTGIDDLSIVLREKELTPI 36- 0 IASD+ F SI +SKYLMNRE+GFGR+ LQILE+ +++EH+P+GIDD++I+LR+ ++ Sbjct: 301 IASDTGFCSIYISKYLMNREIGFGRRALQILEEHGLTYEHVPSGIDDMTIILRQGQMDAA 36- 0 Query: 361 KEQEILNYLTRKLEVDYVDIQHNLSTIVIVGENMKSQIGVTATATQALSREKINITMISQ 42- 0 E+ ++ + L D V ++H+L+ I++VGE M+ +G TA A +ALS ++NI MI+Q Sbjct: 361 TERSVIKRIEEDLHADEVIVEHHLALIMVVGEAMRHNVGTTARAAKALSEAQVNIEMINQ 42- 0 Query: 421 GSSEVSIMFVINSKDEKRAIKALYETFF 448 GSSEVS+MF + +E++A++ALY+ FF Sbjct: 421 GSSEVSMMFGVKEAEERKAVQALYQEFF 448 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1668 A DNA sequence (GBSx1771) was identified in S. agalactiae <SEQ ID 5171> which encodes the amino acid sequence <SEQ ID 5172>. This protein is predicted to be CbbY family protein. Analysis of this protein sequence reveals the following:

TABLE-US-05069 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2699(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05070 >GP: AAF96016 GB: AE004353 CbbY family protein [Vibrio cholerae] Identities = 59/190 (31%), Positives = 93/190 (48%), Gaps = 10/190 (5%) Query: 4 YKAIIFDMDGVLFDTELFYYKRRERFLKQHGITIDHLPMNFFIGGNMKQVWKSVLGDQYD 63 ++A IFDMDG+L DTE + + G+ IG N K + +L Y Sbjct: 6 FQAAIFDMDGLLLDTERVCMRVFQEACTACGLPFRQEVYLSVIGCNAKTI-NGILSQAYG 64 Query: 64 TWDIDKL----QQDYSRYKEDNPLPYKDLIFQDCKRVIEKLHHKGYLLGLASSSTRHDIM 119- D+ +L +Q Y+ +P+KD + ++E L + + +A+S+ + + Sbjct: 65 E-DLPRLHNEWRQRYNAVVMHEAIPHKDGVIA----LLEWLKARSIPVAVATSTQKEVAL 119- Query: 120 LALESFNLDTYFKVILSGEEFSESKPNPAIYNRAAELLDIPKQQILIVEDSEKGITAGIA 17- 9 + L+ LD YF I +G E ++ KP+P IY AAE L + QQ L EDS GI A +A Sbjct: 120 IKLQLAGLDHYFANITTGCEVTQGKPHPEIYLLAAERLGVEPQQCLAFEDSNNGIKAAMA 17- 9 Query: 180 AGIDVWAIED 189 A + + I D Sbjct: 180 AQMHAFQIPD 189 There is also homology to SEQ ID 448. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1669 A DNA sequence (GBSx1772) was identified in S. agalactiae <SEQ ID 5173> which encodes the amino acid sequence <SEQ ID 5174>. This protein is predicted to be Pseudomonas putida enoyl-CoA hydratase II homologue (b1394). Analysis of this protein sequence reveals the following: TABLE-US-05071 Possible site: 45 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.18 Transmembrane 128-144 (128-145) INTEGRAL Likelihood = -1.06 Transmembrane 154-170 (154-170) ----- Final Results ----- bacterial membrane --- Certainty = 0.1871(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9549> which encodes amino acid sequence <SEQ ID 9550> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 5175> which encodes the amino acid sequence <SEQ ID 5176>. Analysis of this protein sequence reveals the following: TABLE-US-05072 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.08 Transmembrane 110-126 (109-128) ----- Final Results ----- bacterial membrane --- Certainty = 0.2232(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05073 Identities = 150/263 (57%), Positives = 197/263 (74%) Query: 19 LKFENIIYGIDGNVATIMLNRPDISNGFNIPMCQEIIDAIRLVSENKDVMFLVIEAQGPI 78 - ++F++II+ + ++AT+ LNRP++SNGFNIP+CQEI+ A+ V + V FL+I+A G + Sbjct: 1 MQFKHIIFDVVDDLATLTLNRPEVSNGFNIPICQEILVALAEVKRDTSVRFLLIKAVGKV 60 Query: 79 FSIGGDLKVMKAAVESDDISSLTKIAELVNQISYDLLQLEKPVVMCVDGAVAGAAANIAL 138- FS+GGDL M+ AV D++ SL KIAELV +IS+ + L KPV++C DGAVAGAA NIAL Sbjct: 61 FSVGGDLVEMQEAVAKDNVQSLVKIAELVQEISFAIKHLPKPVILCADGAVAGAAFNIAL 120- Query: 139 AADFVIASKKSKFIQAFVGVGLAPDAGGLLLLSKSIGITRAVQLALTGESLSAEKAEALG 19- 8 A DF IAS ++KFIQAFV VGLAPDAGGL LL++++G+ RA L +TGE ++A+K G Sbjct: 121 AVDFCIASTQTKFIQAFVNVGLAPDAGGLFLLTRAVGLNRATHLVMTGEGITADKGLDYG 18- 0 Query: 199 IVYKLCESDKIGKIKDQLLKRLSRHSINSYQAIKSLAWEAAFKDWEQYKKLELQLQESLA 25- 8 VY+ ESDK+ K+ QLLKRL R S NSY +KSL W++ F WE Y K EL +QE LA Sbjct: 181 FVYRTAESDKLDKVCLQLLKRLRRGSSNSYAGMKSLVWQSFFTGWEDYAKAELAIQEELA 24- 0 Query: 259 FKQDFKEGVRAHADRRRPNFLGK 281 FK+DFKEGV A +RRRPNF GK Sbjct: 241 FKEDFKEGVIAFGERRRPNFQGK 263 A related GBS gene <SEQ ID 8877> and protein <SEQ ID 8878> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05074 Lipop: Possible site: -1 Crend: 10 SRCFLG: 0 McG: Length of UR: 9 Peak Value of UR: 1.45 Net Charge of CR: -1 McG: Discrim Score: -5.99 GvH: Signal Score (-7.5): -4.37 Possible site: 27 >>> Seems to have no N-terminal signal sequence Amino Acid Composition: calculated from 1 ALOM program count: 2 value: -2.18 threshold: 0.0 INTEGRAL Likelihood = -2.18 Transmembrane 110-126 (110-127) INTEGRAL Likelihood = -1.06 Transmembrane 136-152 (136-152) PERIPHERAL Likelihood = 1.32 49 modified ALOM score: 0.94 icm1 HYPID: 7 CFP: 0.187 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1871 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00115## SEQ ID 8878 (GBS374) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 64 (lane 8; MW 32 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 71 (lane 2; MW 57 kDa). The GBS374-GST fusion product was purified (FIG. 215, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 307), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1670 A DNA sequence (GBSx1773) was identified in S. agalactiae <SEQ ID 5177> which encodes the amino acid sequence <SEQ ID 5178>. This protein is predicted to be a 16.1 kDa transcriptional regulator. Analysis of this protein sequence reveals the following: TABLE-US-05075 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1738 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05076 >GP: AAD05186 GB: AF110185 unknown [Burkholderia pseudomallei] Identities = 30/102 (29%), Positives = 60/102 (58%) Query: 32 DVSLKEMHTIEIIGKHSEVTPSDVARELMLTLGTVTTSLNKLEKKGYIERKRSSIDRRVV 91 - +++ +++ I ++ + TP +++R+L G++T L++LEKKG++ R RS DRRV+ Sbjct: 39 ELTAQQISVILLLARGYARTPFELSRKLSYDSGSMTRMLDRLEKKGFVVRARSESDRRVI 98 Query: 92 HLSLTKRGRLLDRLHSKFHKSMVSHIIEDLGEEDIKMLTSAL 133 L+LT+RG R + ++ +E +++ +LT L Sbjct: 99 ELALTERGAHAARALPALIATELNAQLEGFSADELALLTDLL 140 A related DNA sequence was identified in S. pyogenes <SEQ ID 5179> which encodes the amino acid sequence <SEQ ID 5180>. Analysis of this protein sequence reveals the following: TABLE-US-05077 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1412 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05078 Identities = 111/144 (77%), Positives = 129/144 (89%) Query: 1 HEYDQINSYLVDIFNRIMIIEEMSLKTSQFSDVSLKEMHTIEIIGKHSEVTPSDVARELM 60 +EYD+I YLVDIFNRI++IEEMSLKTSQFSDVSLKEMHTIEIIGK+ +VTPSD+ARELM Sbjct: 7 LEYDKIYPYLVDIFNRILVIEEMSLKTSQFSDVSLKEMHTIEIIGKYDQVTPSDIARELM 66 Query: 61 LTLGTVTTSLNKLEKKGYIERKRSSIDRRVVHLSLTKRGRLLDRLHSKFHKSMVSHIIED 120- +TLGTVTTSLNKLE KGYI R RS DRRVV+LSLTKRGRLLDRLH+KFHK+MV H+I D Sbjct: 67 VTLGTVTTSLNKLEAKGYIARTRSRSDRRVVYLSLTKRGRLLDRLHAKFHKNMVGHVIAD 126- Query: 121 LGEEDIKMLTSALGNLHKFLEDLV 144 + +E+++ L LGNLH+FLEDLV Sbjct: 127 MSDEEMQALVRGLGNLHQFLEDLV 150 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1671 A DNA sequence (GBSx1774) was identified in S. agalactiae <SEQ ID 5181> which encodes the amino acid sequence <SEQ ID 5182>. This protein is predicted to be 3-oxoacyl-(acyl-carrier-protein) synthase III (fabH-2). Analysis of this protein sequence reveals the following: TABLE-US-05079 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = 1.12 Transmernbrane 103-119 (103-119) ----- Final Results ----- bacterial membrane --- Certainty = 0.1447 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05080 >GP: AAF98271 GB: AF197933 beta-ketoacyl-ACP synthase III [Streptococcus pneumoniae] Identities = 225/324 (69%), Positives = 276/324 (84%), Gaps = 1/324 (0%) Query: 1 MVFAKISQLAHYAPSQIIKNEDLSLIMDTSDDWISSRTGIKQRHISKNETTADLANKVAE 60 M FAKISQ+AHY P Q++ N DL+ IMDT+D+WISSRTGI+QRHIS+ E+T+DLA +VA+ Sbjct: 1 MAFAKISQVAHYVPEQVVTNHDLAQIMDTNDEWISSRTGIRQRHISRTESTSDLATEVAK 60 Query: 61 QLIEKSGYSASQIDFIIVATMTPDSMMPSTAARVQAHIGASNAFAFDLSAACSGFVFALS 120- +L+ K+G + ++DFII+AT+TPDSMMPSTAARVQA+IGA+ AFAFDL+AACSGFVFALS Sbjct: 61 KLMAKAGITGEELDFIILATITPDSMMPSTAARVQANIGANKAFAFDLTAACSGFVFALS 120- Query: 121 TAEKLISSGSYQKGLVIGAETVSKVLDWTDRGTAVLFGDGAGGVLLEASKEKHFLAESLN 18- 0 TAEK I+SG +QKGLVIG+ET+SK +DW+DR TAVLFGDGAGGVLLEAS+++HFLAESLN Sbjct: 121 TAEKFIASGRFQKGLVIGSETLSKAVDWSDRSTAVLFGDGAGGVLLEASEQEHFLAESLN 18- 0 Query: 181 TDGSR-QGLQSSQVGLNSPFSDEVLDDKFLKNDGRAIFDFAIKEVSKSINHLIETSYLEK 23- 9 +DGSR + L GL+SPFSD+ D FLKMDGR +FDFAI++V+KSI I+ S +E Sbjct: 181 SDGSRSECLTYGHSGLHSPFSDQESADSFLKMDGRTVFDFAIRDVAKSIKQTIDESPIEV 24- 0 Query: 240 EDIDYLFLHQANRRILDKMSRKIDIARDKFPENMMDYGNTSAASIPILLSESYENGLLKL 29- 9 D+DYL LHQAN RILDKM+RKI + R K P NMM+YGNTSAASIPILLSE E GL+ L Sbjct: 241 TDLDYLLLHQANDRILDKMARKIGVDRAKLPANMMEYGNTSAASIPILLSECVEQGLIPL 30- 0 Query: 300 DGNQTILLSGFGGGLTWGSLIVKI 323 DG+QT+LLSGFGGGLTWG+LI+ I Sbjct: 301 DGSQTVLLSGFGGGLTWGTLILTI 324 A related DNA sequence was identified in S. pyogenes <SEQ ID 5183> which encodes the amino acid sequence <SEQ ID 5184>. Analysis of this protein sequence reveals the following: TABLE-US-05081 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 103-119 (103-120) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05082 >GP:AAF98271 GB:AF197933 beta-ketoacyl-ACP synthase III [Streptococcus pneumoniae] Identities = 212/324 (65%), Positives = 263/324 (80%) Query: 1 MIFSKISQVAHYVPQQLVTNNDLASIMDTSHEWIFSRTGIAERHISRDEMTSDLAIQVAD 60 M F+KISQVAHYVP+Q+VTN+DLA IMDT+ EWI SRTGI +RHISR E TSDLA +VA Sbjct: 1 MAFAKISQVAHYVPEQVVTNHDLAQIMDTNDEWISSRTGIRQRHISRTESTSDLATEVAK 60 Query: 61 QLLTQSGLKADAIDFIIVATISPDATMPSTAAKVQAAIAATSAFAFDMTAACSGFVFALA 120- +L+ ++G+ + +DFII+ATI+PD+ MPSTAA+VQA I A AFAFD+TAACSGFVFAL+ Sbjct: 61 KLMAKAGITGEELDFIILATITPDSMMPSTAARVQANIGANKAFAFDLTAACSGFVFALS 120- Query: 121 MADKLIASGAYQNGMVIGAETLSKLVNWQDRATAVLFGDGAGGVLLEASKDKHVLAETLH 18- 0 A+K IASG +Q G+VIG+ETLSK V+W DR+TAVLFGDGAGGVLLEAS+ +H LAE+L+ Sbjct: 121 TAEKFIASGRFQKGLVIGSETLSKAVDWSDRSTAVLFGDGAGGVLLEASEQEHFLAESLN 18- 0 Query: 181 TDGARCQSLISGETSLSSPYSIGKKAIATIQMDGRAIFDFAIRDVSKSILTLMAQSDITK 24- 0 +DG+R + L G + L SP+S + A + ++MDGR +FDFAIRDV+KSI + +S I Sbjct: 181 SDGSRSECLTYGHSGLHSPFSDQESADSFLKMDGRTVFDFAIRDVAKSIKQTIDESPIEV 24- 0 Query: 241 DDIDYCLLHQANRRILDKIARKIDVPREKFLENMMRYGNTSAASIPILLSEAVQKGQIRL 30- 0 D+DY LLHQAN RILDK+ARKI V R K NMM YGNTSAASIPILLSE V++G I L Sbjct: 241 TDLDYLLLHQANDRILDKMARKIGVDRAKLPANMMEYGNTSAASIPILLSECVEQGLIPL 30- 0 Query: 301 DGTQKILLSGFGGGLTWGSLIVRI 324 DG+Q +LLSGFGGGLTWG+LI+ I Sbjct: 301 DGSQTVLLSGFGGGLTWGTLILTI 324 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05083 Identities = 216/324 (66%), Positives = 271/324 (82%), Gaps = 1/324 (0%) Query: 1 MVFAKISQLAHYAPSQIIKNEDLSLIMDTSDDWISSRTGIKQRHISKNETTADLANKVAE 60 M+F+KISQ+AHY P Q++ N DL+ IMDTS +WI SRTGI +RHIS++E T+DLA +VA+ Sbjct: 1 MIFSKISQVAHYVPQQLVTNNDLASIMDTSHEWIFSRTGIAERHISRDEMTSDLAIQVAD 60 Query: 61 QLIEKSGYSASQIDFIIVATMTPDSMMPSTAARVQAHIGASNAFAFDLSAACSGFVFALS 120- QL+ +SG A IDFIIVAT++PD+ MPSTAA+VQA I A++AFAFD++AACSGFVFAL+ Sbjct: 61 QLLTQSGLKADAIDFIIVATISPDATMPSTAAKVQAAIAATSAFAFDMTAACSGFVFALA 120- Query: 121 TAEKLISSGSYQKGLVIGAETVSKVLDWTDRGTAVLFGDGAGGVLLEASKEKHFLAESLN 18- 0 A+KLI+SG+YQ G+VIGAET+SK+++W DR TAVLFGDGAGGVLLEASK+KH LAE+L+ Sbjct: 121 MADKLIASGAYQNGMVIGAETLSKLVNWQDRATAVLFGDGAGGVLLEASKDKHVLAETLH 18- 0 Query: 181 TDGSR-QGLQSSQVGLNSPFSDEVLDDKFLKMDGRAIFDFAIKEVSKSINHLIETSYLEK 23- 9 TDG+R Q L S + L+SP+S ++MDGRAIFDFAI++VSKSI L+ S + K Sbjct: 181 TDGARCQSLISGETSLSSPYSIGKKAIATIQMDGRAIFDFAIRDVSKSILTLMAQSDITK 24- 0 Query: 240 EDIDYLFLHQANRRILDKMSRKIDIARDKFPENMMDYGNTSAASIPILLSESYENGLLKL 29- 9 +DIDY LHQANRRILDK++RKID+ R+KF ENMM YGNTSAASIPILLSE+ + G ++L Sbjct: 241 DDIDYCLLHQANRRILDKIARKIDVPREKFLENMMRYGNTSAASIPILLSEAVQKGQIRL 30- 0 Query: 300 DGNQTILLSGFGGGLTWGSLIVKI 323 DG Q ILLSGFGGGLTWGSLIV+I Sbjct: 301 DGTQKILLSGFGGGLTWGSLIVRI 324 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1672 A DNA sequence (GBSx1775) was identified in S. agalactiae <SEQ ID 5185> which encodes the amino acid sequence <SEQ ID 5186>. This protein is predicted to be acyl carrier protein (acpP). Analysis of this protein sequence reveals the following: TABLE-US-05084 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3083(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9551> which encodes amino acid sequence <SEQ ID 9552> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05085 >GP:AAF98272 GB:AF197933 acyl carrier protein [Streptococcus pneumoniae] Identities = 64/74 (86%), Positives = 67/74 (90%) Query: 17 MAVFEKVQEIIVEELGKDAEEVTLNTTFDDLDADSLDVFQVISEIEDAFDIQIETEEGLN 76 - MAVFEKVQEIIVEELGKDA EVTL +TFDDLDADSLD+FQVISEIEDAFDIQIE E L Sbjct: 1 MAVFEKVQEIIVEELGKDASEVTLESTFDDLDADSLDLFQVISEIEDAFDIQIEAENDLK 60 Query: 77 TVGDLVAYVEEKVK 90 TVGDLVAYVEE+ K Sbjct: 61 TVGDLVAYVEEQAK 74 A related DNA sequence was identified in S. pyogenes <SEQ ID 5187> which encodes the amino acid sequence <SEQ ID 5188>. Analysis of this protein sequence reveals the following: TABLE-US-05086 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2995(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05087 Identities = 70/74 (94%), Positives = 71/74 (95%) Query: 17 MAVFEKVQEIIVEELGKDAEEVTLNTTFDDLDADSLDVFQVISEIEDAFDIQIETEEGLN 76 - MAVFEKVQEIIVEELGK+ EEVTL TTFDDLDADSLDVFQVISEIEDAFDIQIETEEGLN Sbjct: 1 MAVFEKVQEIIVEELGKETEEVTLETTFDDLDADSLDVFQVISEIEDAFDIQIETEEGLN 60 Query: 77 TVGDLVAYVEEKVK 90 TVGDLVAYVEEK K Sbjct: 61 TVGDLVAYVEEKSK 74 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1673 A DNA sequence (GBSx1777) was identified in S. agalactiae <SEQ ID 5189> which encodes the amino acid sequence <SEQ ID 5190>. Analysis of this protein sequence reveals the following: TABLE-US-05088 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.27 Transmembrane 156-172 (156-173) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05089 >GP:AAF98273 GB:AF197933 trans-2-enoyl-ACP reductase II [Streptococcus pneumoniae] Identities = 257/318 (80%), Positives = 277/318 (86%), Gaps = 1/318 (0%) Query: 1 MKTRITELLNIKYPIFQGGMAWVADGDLAGAVSKAGGLGIIGGGNAPKEVVKANIDKIKS 60 MKTRITELL I YPIFQGGMAWVADGDLAGAVSKAGGLGIIGGGNAPKEVVKANIDKIKS Sbjct: 1 MKTRITELLKIDYPIFQGGMAWVADGDLAGAVSKAGGLGIIGGGNAPKEVVKANIDKIKS 60 Query: 61 MTDKPFGVNIMLLSPFVDDIVDLVIEEGVKVVTTGAGNPGKYMERFHEAGITVIPVVPSV 120- +TDKPFGVNIMLLSPFV+DIVDLVIEEGVKVVTTGAGNP KYMERFHEAGI VIPVVPSV Sbjct: 61 LTDKPFGVNIMLLSPFVEDIVDLVIEEGVKVVTTGAGNPSKYMERFHEAGIIVIPVVPSV 120- Query: 121 ALAKRMEKLGADAIITEGMEAGGHIGKLTTMTLVRQVVDAVTIPVIAAGGIADGRGAAAG 18- 0 ALAKRMEK+GADA+I EGMEAGGHIGKLTTMTLVRQV A++IPVIAAGGIADG GAAAG Sbjct: 121 ALAKRMEKIGADAVIAEGMEAGGHIGKLTTMTLVRQVATAISIPVIAAGGIADGEGAAAG 18- 0 Query: 181 FMLGADAVQVGTRFVVAKESNAHPNYKAKILKAKDIDTAVSAQVVGHPVRALKNKLVTTY 24- 0 FMLGA+AVQVGTRFVVAKESNAHPNYK KILKA+DIDT +SAQ GH VRA+KN+L + Sbjct: 181 FMLGAEAVQVGTRFVVAKESNAHPNYKEKILKARDIDTTISAQHFGHAVRAIKNQLTRDF 24- 0 Query: 241 SQAEKDYLAGRISINEI-EELGAGALRNAVVDGDVINGSVMAGQIAGLIKSEETCQEILE 29- 9 AEKD EI E++GAGAL AVV GDV GSVMAGQIAGL+ EET +EIL+ Sbjct: 241 ELAEKDAFKQEDPDLEIFEQMGAGALAKAVVHGDVDGGSVMAGQIAGLVSKEETAEEILK 30- 0 Query: 300 DIYSGARQVILSEASRWS 317 D+Y GA + I EASRW+ Sbjct: 301 DLYYGAAKKIQEEASRWT 318 A related DNA sequence was identified in S. pyogenes <SEQ ID 5191> which encodes the amino acid sequence <SEQ ID 5192>. Analysis of this protein sequence reveals the following:

TABLE-US-05090 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.70 Transmembrane 106-122 (106-124) INTEGRAL Likelihood = -0.22 Transmembrane 156-172 (156-173) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05091 >GP:AAF98273 GB:AF197933 trans-2-enoyl-ACP reductase II [Streptococcus pneumoniae] Identities = 252/320 (78%), Positives = 276/320 (85%), Gaps = 1/320 (0%) Query: 1 MKTRITELLNIDYPIFQGGMAWVADGDLAGAVSNAGGLGIIGGGNAPKEVVKANIDRVKA 60 MKTRITELL IDYPIFQGGMAWVADGDLAGAVS AGGLGIIGGGNAPKEVVKANID++K+ Sbjct: 1 MKTRITELLKIDYPIFQGGMAWVADGDLAGAVSKAGGLGIIGGGNAPKEVVKANIDKIKS 60 Query: 61 ITDRPFGVNIMLLSPFADDIVDLVIEEGVKVVTTGAGNPGKYMERLHQAGIIVVPVVPSV 120- +TD+PFGVNIMLLSPF +DIVDLVIEEGVKVVTTGAGNP KYMER H+AGIIV+PVVPSV Sbjct: 61 LTDKPFGVNIMLLSPFVEDIVDLVIEEGVKVVTTGAGNPSKYMERFHEAGIIVIPVVPSV 120- Query: 121 ALAKRMEKLGVDAVIAEGMEAGGHIGKLTTMSLVRQVVEAVSIPVIAAGGIADGHGAAAA 18- 0 ALAKRMEK+G DAVIAEGMEAGGHIGKLTTM+LVRQV A+SIPVIAAGGIADG GAAA Sbjct: 121 ALAKRMEKIGADAVIAEGMEAGGHIGKLTTMTLVRQVATAISIPVIAAGGIADGEGAAAG 18- 0 Query: 181 FMLGAEAVQIGTRFVVAKESNAHQNFKDKILAAKDIDTVISAQVVGHPVRSIKNKLTSAY 24- 0 FMLGAEAVQ+GTRFVVAKESNAH N+K+KIL A+DIDT ISAQ GH VR+IKN+LT + Sbjct: 181 FMLGAEAVQVGTRFVVAKESNAHPNYKEKILKARDIDTTISAQHFGHAVRAIKNQLTRDF 24- 0 Query: 241 AKAEK-AFLIGQKTATDIEEMGAGSLRHAVIEGDVVNGSVMAGQIAGLVRKEESCETILK 29- 9 AEK AF E+MGAG+L AV+ GDV GSVMAGQIAGLV KEE+ E ILK Sbjct: 241 ELAEKDAFKQEDPDLEIFEQMGAGALAKAVVHGDVDGGSVMAGQIAGLVSKEETAEEILK 30- 0 Query: 300 DIYYGAARVIQNEAKRWQSV 319 D+YYGAA+ IQ EA RW V Sbjct: 301 DLYYGAAKKIQEEASRWTGV 320 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05092 Identities = 253/319 (79%), Positives = 291/319 (90%) Query: 1 MKTRITELLNIKYPIFQGGMAWVADGDLAGAVSKAGGLGIIGGGNAPKEVVKANIDKIKS 60- MKTRITELLNI YPIFQGGMAWVADGDLAGAVS AGGLGIIGGGNAPKEVVKANID++K+ Sbjct: 1 MKTRITELLNIDYPIFQGGMAWVADGDLAGAVSNAGGLGIIGGGNAPKEVVKANIDRVKA 60- Query: 61 MTDKPFGVNIMLLSPFVDDIVDLVIEEGVKVVTTGAGNPGKYMERFHEAGITVIPVVPSV 12- 0 +TD+PFGVNIMLLSPF DDIVDLVIEEGVKVVTTGAGNPGKYMER H+AGI V+PVVPSV Sbjct: 61 ITDRPFGVNIMLLSPFADDIVDLVIEEGVKVVTTGAGNPGKYMERLHQAGIIVVPVVPSV 12- 0 Query: 121 ALAKRMEKLGADAIITEGMEAGGHIGKLTTMTLVRQVVDAVTIPVIAAGGIADGRGAAAG 18- 0 ALAKRMEKLG DA+I EGMEAGGHIGKLTTM+LVRQVV+AV+IPVIAAGGIADG GAAA Sbjct: 121 ALAKRMEKLGVDAVIAEGMEAGGHIGKLTTMSLVRQVVEAVSIPVIAAGGIADGHGAAAA 18- 0 Query: 181 FMLGADAVQVGTRFVVAKESNAHPNYKAKILKAKDIDTAVSAQVVGHPVRALKNKLVTTY 24- 0 FMLGA+AVQ+GTRFVVAKESNAH N+K KIL AKDIDT +SAQVVGHPVR++KNKL + Y Sbjct: 181 FMLGAEAVQIGTRFVVAKESNAHQNFKDKILAAKDIDTVISAQVVGHPVRSIKNKLTSAY 24- 0 Query: 241 SQAEKDYLAGRISINEIEELGAGALRNAVVDGDVINGSVMAGQIAGLIKSEETCQEILED 30- 0 ++AEK +L G+ + +IEE+GAG+LR+AV++GDV+NGSVMAGQIAGL++ EE+C+ IL+D Sbjct: 241 AKAEKAFLIGQKTATDIEEMGAGSLRHAVIEGDVVNGSVMAGQIAGLVRKEESCETILKD 30- 0 Query: 301 IYSGARQVILSEASRWSDL 319 IY GA +VI +EA RW + Sbjct: 301 IYYGAARVIQNEAKRWQSV 319 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1674 A DNA sequence (GBSx1778) was identified in S. agalactiae <SEQ ID 5193> which encodes the amino acid sequence <SEQ ID 5194>. This protein is predicted to be MCAT (fabD). Analysis of this protein sequence reveals the following: TABLE-US-05093 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1276 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with a S. pneumoniae sequence: TABLE-US-05094 Identities = 203/306 (66%), Positives = 242/306 (78%), Gaps = 1/306 (0%) Query: 1 MNKVSFLFAGQGAQKLGMARDLYETFPIVKETFDKASHVLGYDLRELIDKDLDKLNQTKY 60- M K +FLFAGQGAQ LGM RD Y+ +PIVKET D+AS VLGYDLR LID + DKLNQT+Y Sbjct: 1 MTKTAFLFAGQGAQYLGMGRDFYDQYPIVKETIDRASQVLGYDLRYLIDTEEDKLNQTRY 60- Query: 61 TQPAILTTSTAIYRLILKEIELRPDMVAGLSLGEYSALVASGAIRFEDAVVLVARRGQLM 12- 0 TQPAIL TS AIYRL L+E +PDMVAGLSLGEYSALVASGA+ FEDAV LVA+RG M Sbjct: 61 TQPAILATSVAIYRL-LQEKGYQPDMVAGLSLGEYSALVASGALDFEDAVALVAKRGAYM 11- 9 Query: 121 EAAAPAGSGKMVAVLNADRQIIEDACKKASQFGIVSPANYNTPKQIVIGGESIAVNAAVE 18- 0 E AAPA SGKMVAVLN ++IE+AC+KAS+ G+V+PANYNTP QIVI GE +AV+ AVE Sbjct: 120 EEAAPADSGKMVAVLNTPVEVIEEACQKASELGVVTPANYNTPAQIVIAGEVVAVDRAVE 17- 9 Query: 181 ELKQQGVKRLIPLNVSGPFHTALLKPASQKLSDVLDKVHFSVSEIPVIGNTEAQIMKKDD 24- 0 L++ G KRLIPL VSGPFHTALL+PASQKL++ L +V FS P++GNTEA +M+K+D Sbjct: 180 LLQEAGAKRLIPLKVSGPFHTALLEPASQKLAETLAQVSFSDFTCPLVGNTEAAVMQKED 23- 9 Query: 241 IKSLLARQVMEPVRFDESIETMKKMGMTQVVEIGPGKVLSGFLKKIDSSLSVHSVEDKIG 30- 0 I LL RQV EPVRF ESI M++ G++ +EIGPGKVLSGF+KKID + + VED+ Sbjct: 240 IAQLLTRQVKEPVRFYESIGVMQEAGISNFIEIGPGKVLSGFVKKIDQTAHLAHVEDQAS 29- 9 Query: 301 FNNLKE 306 L E Sbjct: 300 LVALLE 305 A related DNA sequence was identified in S. pyogenes <SEQ ID 5195> which encodes the amino acid sequence <SEQ ID 5196>. Analysis of this protein sequence reveals the following: TABLE-US-05095 Possible Site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1602 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05096 Identities = 201/299 (67%), Positives = 248/299 (82%), Gaps = 1/299 (0%) Query: 1 MNKVSFLFAGQGAQKLGMARDLYETFPIVKETFDKASHVLGYDLRELIDKDLDKLNQTKY 60- M K +FLFAGQGAQKLGMARD Y+ F IV++TFD+AS VLGYDLR LID D KLNQT Y Sbjct: 3 MTKTAFLFAGQGAQKLGMARDFYDNFAIVRKTFDQASQVLGYDLRRLIDSDELKLNQTSY 62- Query: 61 TQPAILTTSTAIYRLILKEIELRPDMVAGLSLGEYSALVASGAIRFEDAVVLVARRGQLM 12- 0 TQPAILT+S AIYR +L ++PDMVAGLSLGEYSALVASGA+ FED + LVA+RG+LM Sbjct: 63 TQPAILTSSIAIYR-VLGLHHVKPDMVAGLSLGEYSALVASGALSFEDTLSLVAKRGRLM 12- 1 Query: 121 EAAAPAGSGKMVAVLNADRQIIEDACKKASQFGIVSPANYNTPKQIVIGGESIAVNAAVE 18- 0 E AAP GSGKMVAV+N D Q+IE+ C+ A++ G+V+PANYNTP QIVIGG++ AVN AVE Sbjct: 122 EEAAPQGSGKMVAVMNTDVQVIEEVCQIAAKHGVVAPANYNTPSQIVIGGQTDAVNVAVE 18- 1 Query: 181 ELKQQGVKRLIPLNVSGPFHTALLKPASQKLSDVLDKVHFSVSEIPVIGNTEAQIMKKDD 24- 0 LK++GVKRLIPLNVSGPFHTALL+PAS+ L+ L++ +FS + IP++GNTEA IM+KD Sbjct: 182 LLKERGVKRLIPLNVSGPFHTALLEPASRLLAKELERYNFSDFKIPLVGNTEANIMEKDR 24- 1 Query: 241 IKSLLARQVMEPVRFDESIETMKKMGMTQVVEIGPGKVLSGFLKKIDSSLSVHSVEDKI 299- I LLARQVMEPVRF +S+ T+ + G+TQ +E+GPGKVL+GF+KKID +L SVE+ + Sbjct: 242 IPELLARQVMEPVRFYDSVATLVESGITQFIEVGPGKVLTGFVKKIDKNLLCTSVENMV 300- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1675 A DNA sequence (GBSx1779) was identified in S. agalactiae <SEQ ID 5197> which encodes the amino acid sequence <SEQ ID 5198>. This protein is predicted to be beta-ketoacyl-ACP reductase (fabG). Analysis of this protein sequence reveals the following: TABLE-US-05097 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0930 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05098 >GP:AAF98275 GB:AF197933 beta-ketoacyl-ACP reductase [Streptococcus pneumoniae] Identities = 184/243 (75%), Positives = 212/243 (86%) Query: 1 MQLKDKNIFITGSSRGIGLAIAHQFAQLGANIVLNGRSEISEDLIAEFADYGVKVIAISG 60- M+L+ KNIFITGSSRGIGLAIAH+FAQ GANIVLN R ISE+L+AEF++YG+KV+ ISG Sbjct: 1 MKLEHKNIFITGSSRGIGLAIAHKFAQAGANIVLNSRGAISEELLAEFSNYGIKVVPISG 60- Query: 61 DVSSFEDANRMIKEAIASLGSVDVLVNNAGITNDKLMLKMTVEDFESVLKINLTGAFNMT 12- 0 DVS F DA RMI +AIA LGSVDVLVNNAGIT D LMLKMT DFE VLK+NLTGAFNMT Sbjct: 61 DVSDFADAKRMIDQAIAELGSVDVLVNNAGITQDTLMLKMTEADFEKVLKVNLTGAFNMT 12- 0 Query: 121 QSVLKPMTKARQGAIINISSVVGLTGNVGQANYAASKAGLIGFTKSVAREVAARGIRVNA 18- 0 QSVLKPM KAR+GAIIN+SSVVGL GN+GQANYAASKAGLIGFTKSVAREVA+R IRVN Sbjct: 121 QSVLKPMMKAREGAIINMSSVVGLMGNIGQANYAASKAGLIGFTKSVAREVASRNIRVNV 18- 0 Query: 181 IAPGFIESDMTDVIPEKMQEAILAQIPMKRIGKGKEVAQVASFLAEQEYLTGQVIAIDGG 24- 0 IAPG IESDMT ++ +K++EA LAQIPMK G+ ++VA + FLA Q+YLTGQV+AIDGG Sbjct: 181 IAPGMIESDMTAILSDKIKEATLAQIPMKEFGQAEQVADLTVFLAGQDYLTGQVVAIDGG 24- 0 Query: 241 MTM 243 ++M Sbjct: 241 LSM 243 A related DNA sequence was identified in S. pyogenes <SEQ ID 3865> which encodes the amino acid sequence <SEQ ID 3866>. Analysis of this protein sequence reveals the following: TABLE-US-05099 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1088 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05100 Identities = 201/244 (82%), Positives = 220/244 (89%) Query: 1 MQLKDKNIFITGSSRGIGLAIAHQFAQLGANIVLNGRSEISEDLIAEFADYGVKVIAISG 60- M++K KNIFITGS+RGIGLA+AHQFA L ANIVLNGRS ISE+L+A F DYGV V+ ISG Sbjct: 1 MEIKGKNIFITGSTRGIGLAMAHQFASLEANIVLNGRSAISEELVASFTDYGVTVVTISG 60- Query: 61 DVSSFEDANRMIKEAIASLGSVDVLVNNAGITNDKLMLKMTVEDFESVLKINLTGAFNMT 12- 0 DVS +A RM+ EAI SLGS+DVLVNNAGITNDKLMLKMT EDFE VLKINLTGAFNMT Sbjct: 61 DVSEASEAKRMVNEAIESLGSIDVLVNNAGITNDKLMLKMTEEDFERVLKINLTGAFNMT 12- 0 Query: 121 QSVLKPMTKARQGAIINISSVVGLTGNVGQANYAASKAGLIGFTKSVAREVAARGIRVNA 18- 0 QSVLKPM KARQGAIIN+SSVVGLTGN+GQANYAASKAG+IGFTKSVAREVAAR I VNA Sbjct: 121 QSVLKPMIKARQGAIINVSSVVGLTGNIGQANYAASKAGMIGFTKSVAREVAARNICVNA 18- 0 Query: 181 IAPGFIESDMTDVIPEKMQEAILAQIPMKRIGKGKEVAQVASFLAEQEYLTGQVIAIDGG 24- 0 IAPGFIESDMT V+PEKMQE IL+QIPMKRIGK +EVA +ASFL EQ+Y+TGQVIAIDGG Sbjct: 181 IAPGFIESDMTGVLPEKMQEQILSQIPMKRIGKAQEVAHLASFLVEQDYITGQVIAIDGG 24- 0 Query: 241 MTMQ 244 MTMQ Sbjct: 241 MTMQ 244 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1676 A DNA sequence (GBSx1780) was identified in S. agalactiae <SEQ ID 5199> which encodes the amino acid sequence <SEQ ID 5200>. This protein is predicted to be 3-oxoacyl-(acyl-carrier-protein) synthase II (fabF). Analysis of this protein sequence reveals the following: TABLE-US-05101 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 338-354 (338-354) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05102 >GP: AAF98276 GB: AF197933 beta-ketoacyl-ACP synthase II [Streptococcus pneumoniae] Identities = 340/410 (82%), Positives = 375/410 (90%) Query: 1 MTLQRVVVTGYGVTSPIGNTPEEFWNSLKEGNVGIGPITKFDSSDFMVKNAAEIHDFPFD 60 M L RVVVTGYGVTSPIGNTPEEFWNSL G +GIG ITKFD SDF V NAAEI DFPFD Sbjct: 1 MKLNRVVVTGYGVTSPIGNTPEEFWNSLATGKIGIGGITKFDHSDFDVHNAAEIQDFPFD 60 Query: 61 KYFVKKDLNRFDMYSLYALYASSEAIQHANLNLDEIDADRFGVIVASGIGGIQEIEEQVI 120- KYFVKKD NRFD YSLYALYA+ EA+ HANL+++ ++ DRFGVIVASGIGGI+EIE+QV+ Sbjct: 61 KYFVKKDTNRFDNYSLYALYAAQEAVNHANLDVEALNRDRFGVIVASGIGGIKEIEDQVL 120- Query: 121 RLHEKGPKRVKPMTLPKALPNMAAGNVAMRLGAHGVCKSINTACASSNDAIGDAFRNIKF 18- 0 RLHEKGPKRVKPMTLPKALPNMA+GNVAMR GA+GVCKSINTAC+SSNDAIGDAFR+IKF Sbjct: 121 RLHEKGPKRVKPMTLPKALPNMASGNVAMRFGANGVCKSINTACSSSNDAIGDAFRSIKF 18- 0 Query: 181 GIQDIMVVGGAEAAITKFAIAGFQSLTALSTTEDPSRASIPFDKDRNGFIMGEGSGMLVL 24- 0 G QD+M+VGG EA+IT FAIAGFQ+LTALSTTEDP+RASIPFDKDRNGF+MGEGSGMLVL Sbjct: 181 GFQDVMLVGGTEASITPFAIAGFQALTALSTTEDPTRASIPFDKDRNGFVMGEGSGMLVL 24- 0 Query: 241 ESLEHAEKRGATILAEVVGYGNTCDAYHMTSPHPEGLGATKAIQLALVEANIKPEEVNYV 30- 0 ESLEHAEKRGATILAEVVGYGNTCDAYHMTSPHPEG GA KAI+LAL EA I PE+V YV Sbjct: 241 ESLEHAEKRGATILAEVVGYGNTCDAYHMTSPHPEGQGAIKAIKLALEEAEISPEQVAYV 30- 0 Query: 301 NAHGTSTPANEKGESQAIVAALGTDVPVSSTKSFTGHLLGAAGAVEAIATIEAIRHSYVP 36- 0 NAHGTSTPANEKGES AIVA LG +VPVSSTKSFTGHLLGAAGAVEAI TIEA+RH++VP Sbjct: 301 NAHGTSTPANEKGESGAIVAVLGKEVPVSSTKSFTGHLLGAAGAVEAIVTIEAMRHNFVP 36- 0 Query: 361 MTAGTTELSEDITANVIFGQGQDADIRYAISNTFGFGGHNAVLAFKRWED 410 MTAGT+E+S+ I ANV++GQG + +I YAISNTFGFGGHNAVLAFKRWE+ Sbjct: 361 MTAGTSEVSDYIEANVVYGQGLEKEIPYAISNTFGFGGHNAVLAFKRWEN 410 A related DNA sequence was identified in S. pyogenes <SEQ ID 3851> which encodes the amino acid sequence <SEQ ID 3852>. Analysis of this protein sequence reveals the following: TABLE-US-05103 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0890(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05104 Identities = 346/410 (84%), Positives = 377/410 (91%) Query: 1 MTLQRVVVTGYGVTSPIGNTPEEFWNSLKEGNVGIGPITKFDSSDFMVKNAAEIHDFPFD 60 MT +RVVVTGYG+TSPIG+ PE FWN+LK G +GIGPITKFD++D+ VKNAAEI DFPFD Sbjct: 1 MTFKRVVVTGYGLTSPIGHDPETFWNNLKAGQIGIGPITKFDTTDYAVKNAAEIQDFPFD 60 Query: 61 KYFVKKDLNRFDMYSLYALYASSEAIQHANLNLDEIDADRFGVIVASGIGGIQEIEEQVI 120- KYFVKKDLNRFD YSLYALYA+ EAI HA+LN++ +D+DRFGVIVASGIGGI EIEEQVI Sbjct: 61 KYFVKKDLNRFDRYSLYALYAAKEAINHADLNIEMVDSDRFGVIVASGIGGIAEIEEQVI 120- Query: 121 RLHEKGPKRVKPMTLPKALPNMAAGNVAMRLGAHGVCKSINTACASSNDAIGDAFRNIKF 18- 0 RLHEKGPKRVKPMTLPKALPNMAAGNVAM L A GVCKSINTACASSNDAIGDAFR IKF Sbjct: 121 RLHEKGPKRVKPMTLPKALPNMAAGNVAMSLKAQGVCKSINTACASSNDAIGDAFRAIKF 18- 0 Query: 181 GIQDIMVVGGAEAAITKFAIAGFQSLTALSTTEDPSRASIPFDKDRNGFIMGEGSGMLVL 24- 0 G QD+M+VGG+EAAITKFAIAGFQSLTALSTTEDPSR+SIPFDKDRNGFIMGEGSGMLVL Sbjct: 181 GTQDVMIVGGSEAAITKFAIAGFQSLTALSTTEDPSRSSIPFDKDRNGFIMGEGSGMLVL 24- 0 Query: 241 ESLEHAEKRGATILAEVVGYGNTCDAYHMTSPHPEGLGATKAIQLALVEANIKPEEVNYV 30- 0 ESLEHA++RGATILAE+VGYGNTCDAYHMTSP+PEGLGA KAI LAL EA I+ +NYV Sbjct: 241 ESLEHAQERGATILAEIVGYGNTCDAYHMTSPNPEGLGARKAIHLALQEAGIEASAINYV 30- 0 Query: 301 NAHGTSTPANEKGESQAIVAALGTDVPVSSTKSFTGHLLGAAGAVEAIATIEAIRHSYVP 36- 0 NAHGTSTPANEKGESQAIVA LG DVPVSSTKSFTGHLLGAAGA+EAIATIEA+RH+YVP Sbjct: 301 NAHGTSTPANEKGESQAIVAVLGKDVPVSSTKSFTGHLLGAAGAIEAIATIEAMRHNYVP 36- 0 Query: 361 MTAGTTELSEDITANVIFGQGQDADIRYAISNTFGFGGHNAVLAFKRWED 410 MTAGT LSEDI ANVIFG+G++ I YAISNTFGFGGHNAVLAFK WE+ Sbjct: 361 MTAGTQALSEDIEANVIFGEGKETAINYAISNTFGFGGHNAVLAFKCWEE 410 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1677 A DNA sequence (GBSx1781) was identified in S. agalactiae <SEQ ID 5201> which encodes the amino acid sequence <SEQ ID 5202>. Analysis of this protein sequence reveals the following: TABLE-US-05105 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3052(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9553> which encodes amino acid sequence <SEQ ID 9554> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05106 >GP: AAF98277 GB: AF197933 biotin carboxyl carrier protein [Streptococcus pneumoniae] Identities = 103/169 (60%), Positives = 127/169 (74%), Gaps = 11/169 (6%) Query: 19 LDIQEIKDLMTQFDESSLREFSFKTSDGELSFSKNEGKAPLVPTMSPMSHQPEATPTIAT 78 - +++ +IKDLMTQFD+SSLREFS+K EL FSKNE + VP ++ Q P +AT Sbjct: 1 MNLNDIKDLMTQFDQSSLREFSYKNGTDELQFSKNEARP--VPEVAT---QVAPAPVLAT 55 Query: 79 PVSNEAGEQTKQATEVVSEIP---ESTVTVAEGDVVESPLVGVAYLASGPDKPNFVSVGD 135- P + + A V E+P E++V EG++VESPLVGV YLA+GPDKP FV+VGD Sbjct: 56 P--SPVAPTSAPAETVAEEVPAPAEASVAT-EGNLVESPLVGVVYLAAGPDKPAFVTVGD 112- Query: 136 SVKKGQTLMIIEAMKVMNEVPAPHDGVVTEILVANEEVIEFGKGLVRIK 184 SVKKGQTL+IIEAMKVMNE+PAP DGVVTEILV+NEE++EFGKGLVRIK Sbjct: 113 SVKKGQTLVIIEAMKVMNEIPAPKDGVVTEILVSNEEMVEFGKGLVRIK 161 A related DNA sequence was identified in S. pyogenes <SEQ ID 5203> which encodes the amino acid sequence <SEQ ID 5204>. Analysis of this protein sequence reveals the following: TABLE-US-05107 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3132(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-05108 Identities = 107/171 (62%), Positives = 126/171 (73%), Gaps = 10/171 (5%) Query: 19 LDIQEIKDLMTQFDESSLREFSFKTSDGELSFSKNEGKAPLVPTMSPMSHQPEATPT--- 75 - L+IQEIKDLM QFD SSLREF FKT++GEL FSKNE + S+Q A P Sbjct: 1 LNIQEIKDLMAQFDTSSLREFLFKTNEGELIFSKNEQHLN-----ASTSNQEHAVPVPQV 55 Query: 76 --IATPVSNEAGEQTKQATEVVSEIPESTVTVAEGDVVESPLVGVAYLASGPDKPNFVSV 133- + P ++EA V E P++ VAEGD+VESPLVGVAYLA+ PDKP FV+V Sbjct: 56 QLVPNPTASEASSPASVKDVPVEEQPQAESFVAEGDIVESPLVGVAYLAASPDKPPFVAV 115- Query: 134 GDSVKKGQTLMIIEAMKVMNEVPAPHDGVVTEILVANEEVIEFGKGLVRIK 184 GD+VKKGQTL+IIEAMKVMNEVPAP DGV+TEILV+NE+VIEFG+GLVRIK Sbjct: 116 GDTVKKGQTLVIIEAMKVMNEVPAPCDGVITEILVSNEDVIEFGQGLVRIK 166 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1678 A DNA sequence (GBSx1782) was identified in S. agalactiae <SEQ ID 5205> which encodes the amino acid sequence <SEQ ID 5206>. This protein is predicted to be beta-hydroxyacyl-ACP dehydratase (fabZ). Analysis of this protein sequence reveals the following: TABLE-US-05109 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2267(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05110 >GP: AAF98278 GB: AF197933 beta-hydroxyacyl-ACP dehydratase [Streptococcus pneumoniae] Identities = 130/140 (92%), Positives = 135/140 (95%) Query: 1 MIDIKEIREALPHRYPMLLVDRVLEVSEDEIVAIKNVSINEPFFNGHFPEYPVMPGVLIM 60 MIDI+ I+EALPHRYPMLLVDRVLEVSED IVAIKNV+INEPFFNGHFP+YPVMPGV+IM Sbjct: 1 MIDIQGIKEALPHRYPMLLVDRVLEVSEDTIVAIKNVTINEPFFNGHFPQYPVMPGVVIM 60 Query: 61 EALAQTAGVLELSKEENKGKLVFYAGMDKVKFKKQVVPGDQLVMTAKFVKRRGTIAVVEA 120- EALAQTAGVLELSK ENKGKLVFYAGMDKVKFKKQVVPGDQLVMTA FVKRRGTIAVVEA Sbjct: 61 EALAQTAGVLELSKPENKGKLVFYAGMDKVKFKKQVVPGDQLVMTATFVKRRGTIAVVEA 120- Query: 121 IAEVDGKLAASGTLTFAIGN 140 AEVDGKLAASGTLTFAIGN Sbjct: 121 KAEVDGKLAASGTLTFAIGN 140 A related DNA sequence was identified in S. pyogenes <SEQ ID 5207> which encodes the amino acid sequence <SEQ ID 5208>. Analysis of this protein sequence reveals the following: TABLE-US-05111 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1882(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05112 Identities = 127/139 (91%), Positives = 133/139 (95%) Query: 1 MIDIKEIREALPHRYPMLLVDRVLEVSEDEIVAIKNVSINEPFFNGHFPEYPVMPGVLIM 60 M+DI+EI+ ALPHRYPMLLVDRVLEVS+D IVAIKNV+INEPFFNGHFP YPVMPGVLIM Sbjct: 1 MMDIREIQAALPHRYPMLLVDRVLEVSDDHIVAIKNVTINEPFFNGHFPHYPVMPGVLIM 60 Query: 61 EALAQTAGVLELSKEENKGKLVFYAGMDKVKFKKQVVPGDQLVMTAKFIKRRGTIAVVEA 120- EALAQTAGVLELSKEENKGKLVFYAGMDKVKFKKQVVPGDQLVMTA F+KRRGTIAVVEA Sbjct: 61 EALAQTAGVLELSKEENKGKLVFYAGMDKVKFKKQVVPGDQLVMTATFIKRRGTIAVVEA 120- Query: 121 IAEVDGKLAASGTLTFAIG 139 AEVDGKLAASGTLTFA G Sbjct: 121 RAEVDGKLAASGTLTFACG 139 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1679 A DNA sequence (GBSx1783) was identified in S. agalactiae <SEQ ID 5209> which encodes the amino acid sequence <SEQ ID 5210>. This protein is predicted to be acetyl-coenzyme A carboxylase, biotin carboxylase (accC). Analysis of this protein sequence reveals the following: TABLE-US-05113 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1203(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05114 >GP: AAF98279 GB: AF197933 acetyl-CoA carboxylase biotin carboxylase subunit [Streptococcus pneumoniae] Identities = 361/451 (80%), Positives = 405/451 (89%) Query: 1 MFKKILIANRGEIAVRIIRAAREMGISTVAIYSEADKESLHTILADEAICVGPAKSAESY 60 MF+KILIANRGEIAVRIIRAARE+GI+TVA+YS ADKE+LHT+LADEA+C+GP K+ ESY Sbjct: 1 MFRKILIANRGEIAVRIIRAARELGIATVAVYSTADKEALHTLLADEAVCIGPGKATESY 60 Query: 61 LNVNAILSAAIVTGAEAVHPGFGFLSENSKFATMCEEMNLKFIGPSGEVMDKMGDKINAR 120- LN+NA+LSAA++T AEA+HPGFGFLSENSKFATMCEE+ +KFIGPSG VMD MGDKINAR Sbjct: 61 LNINAVLSAAVLTEAEAIHPGFGFLSENSKFATMCEEVGIKFIGPSGHVMDMMGDKINAR 120- Query: 121 TEMIKADVPVIPGSDGQVTSVEEAVSIAEEIGYPLMLKASAGGGGKGIRKVKSADELKPA 18- 0 +MIKA VPVIPGSDG+V + EEA+ +AE+IGYP+MLKASAGGGGKGIRKV+ D+L A Sbjct: 121 AQMIKAGVPVIPGSDGEVHNSEEALIVAEKIGYPVMLKASAGGGGKGIRKVEKPDDLVSA 18- 0 Query: 181 FESASQEALAAFGNGAMYIEKVIYPARHIEVQILGDSFGKIVHLGERDCSLQRNNQKVLE 24- 0 FE+AS EA A +GNGAMYIE+VIYPARHIEVQILGD G ++HLGERDCSLQRNNQKVLE Sbjct: 181 FETASSEAKANYGNGAMYIERVIYPARHIEVQILGDEHGHVIHLGERDCSLQRNNQKVLE 24- 0 Query: 241 ESPSVAIGNTLRQQIGEAAVRAAEAVSYENAGTIEFLLDENSGQFYFMEMNTRVQVEHPV 30- 0 ESPS+AIG TLR +IG AAVRAAE V YENAGTIEFLLDE S FYFMEMNTRVQVEHPV Sbjct: 241 ESPSIAIGKTLRHEIGAAAVRAAEFVGYENAGTIEFLLDEASSNFYFMEMNTRVQVEHPV 30- 0 Query: 301 TEFVTGVDIVKEQIRIAAGIPLSVSQNDIKLTGHAIECRINAENPQFNFAPCPGTINGLH 36- 0 TEFV+GVDIVKEQI IAAG PLSV Q DI L GHAIECRINAENP FNFAP PG I L+ Sbjct: 301 TEFVSGVDIVKEQICIAAGQPLSVKQEDIVLRGHAIECRINAENPAFNFAPSPGKITNLY 36- 0 Query: 361 LPAGGMGLRVDSAVYTGYTIPPYYDSMIAKVIVHGENRFDALMKMQRALYELEIDGIVTN 42- 0 LP+GG+GLRVDSAVY GYTIPPYYDSMIAK+IVHGENRFDALMKMQRALYELEI+G+ TN Sbjct: 361 LPSGGVGLRVDSAVYPGYTIPPYYDSMIAKIIVHGENRFDALMKMQRALYELEIEGVQTN 42- 0 Query: 421 TEFQMDLISDKKVLAGDYDTSFLMEDFLPRY 451 +FQ+DLISD+ V+AGDYDTSFLME FLP+Y Sbjct: 421 ADFQLDLISDRNVIAGDYDTSFLMETFLPKY 451 A related DNA sequence was identified in S. pyogenes <SEQ ID 5211> which encodes the amino acid sequence <SEQ ID 5212>. Analysis of this protein sequence reveals the following: TABLE-US-05115 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1784(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05116 Identities = 369/451 (81%), Positives = 421/451 (92%) Query: 1 MFKKILIANRGEIAVRIIRAAREMGISTVAIYSEADKESLHTILADEAICVGPAKSAESY 60 MFKKILIANRGEIAVRIIRAARE+GISTVA+YSEADKE+LHTILADEAIC+GPA+S ESY Sbjct: 17 MFKKILIANRGEIAVRIIRAARELGISTVAVYSEADKEALHTILADEAICIGPARSKESY 76 Query: 61 LNVNAILSAAIVTGAEAVHPGFGFLSENSKFATMCEEMNLKFIGPSGEVMDKMGDKINAR 120- LN+N++LSAAIVTGA+A+HPGFGFLSENSKFATMCEEMN+KFIGPS VMDKMGDKINAR Sbjct: 77 LNMNSVLSAAIVTGAQAIHPGFGFLSENSKFATMCEEMNIKFIGPSASVMDKMGDKINAR 136- Query: 121 TEMIKADVPVIPGSDGQVTSVEEAVSIAEEIGYPLMLKASAGGGGKGIRKVKSADELKPA 18- 0 +EMIKA VPVIPGSDG+V + +EA++IA +IGYP+MLKASAGGGGKGIRKV++ +L+ A Sbjct: 137 SEMIKAGVPVIPGSDGEVYNAQEALAIANKIGYPVMLKASAGGGGKGIRKVETEADLEAA 19- 6 Query: 181 FESASQEALAAFGNGAMYIEKVIYPARHIEVQILGDSFGKIVHLGERDCSLQRNNQKVLE 24- 0 F +ASQEAL AFGNGAMY+EKVIYPARHIEVQILGD++G I+HLGERDCSLQRNNQKVLE Sbjct: 197 FNAASQEALGAFGNGAMYLEKVIYPARHIEVQILGDAYGNIIHLGERDCSLQRNNQKVLE 25- 6 Query: 241 ESPSVAIGNTLRQQIGEAAVRAAEAVSYENAGTIEFLLDENSGQFYFMEMNTRVQVEHPV 30- 0 ESPS+AIGNTLR ++G+AAVRAAEAV+YENAGTIEFLLDE+S +FYFMEMNTR+QVEHPV Sbjct: 257 ESPSIAIGNTLRHEMGQAAVRAAEAVAYENAGTIEFLLDEDSEKFYFMEMNTRIQVEHPV 31- 6 Query: 301 TEFVTGVDIVKEQIRIAAGIPLSVSQNDIKLTGHAIECRINAENPQFNFAPCPGTINGLH 36- 0 TEFVTGVDIVKEQI+IAAG PL+++Q DI +TGHAIECRINAEN FNFAP PG I L+ Sbjct: 317 TEFVTGVDIVKEQIKIAAGQPLAINQEDITITGHAIECRINAENTAFNFAPSPGKITDLY 37- 6 Query: 361 LPAGGMGLRVDSAVYTGYTIPPYYDSMIAKVIVHGENRFDALMKMQRALYELEIDGIVTN 42- 0 +P+GG+GLRVDSAVY GY IPPYYDSMIAK+IVHG NRFDALMKMQRAL ELEI+GI+TN Sbjct: 377 MPSGGVGLRVDSAVYNGYAIPPYYDSMIAKIIVHGSNRFDALMKMQRALVELEIEGIITN 43- 6 Query: 421 TEFQMDLISDKKVLAGDYDTSFLMEDFLPRY 451 T+FQ+DLISDK+V+AGDYDTSFLME FLP Y Sbjct: 437 TDFQLDLISDKRVIAGDYDTSFLMETFLPHY 467 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1680 A DNA sequence (GBSx1784) was identified in S. agalactiae <SEQ ID 5213> which encodes the amino acid sequence <SEQ ID 5214>. This protein is predicted to be acetyl-CoA carboxylase beta subunit (accD). Analysis of this protein sequence reveals the following: TABLE-US-05117 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3571(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05118 >GP: AAF98280 GB: AF197933 acetyl-CoA carboxylase beta subunit [Streptococcus pneumoniae] Identities = 221/285 (77%), Positives = 248/285 (86%), Gaps = 1/285 (0%) Query: 1 MALFSKKDKYIRISPNKALGSSDKRSLPEVPDELFAKCPSCKHMIYQKDLGLAKICPACS 60 MALFSKKDKYIRI+PN+++ + PEVPDELF++CP CKH IYQKDLG +ICP CS Sbjct: 1 MALFSKKDKYIRINPNRSVREKPQAK-PEVPDELFSQCPGCKHTIYQKDLGSERICPHCS 59 Query: 61 YNFRISAQERLLLTVDEDSFEELFTGIETKDPLNFPNYREKLAATRQKTNLDEAVVTGLA 120- Y FRISAQERL LT+D +F+ELFTGIE+KDPL+FP Y++KLA+ R+KT L EAVVTG A Sbjct: 60 YTFRISAQERLALTIDMGTFKELFTGIESKDPLHFPGYQKKLASMREKTGLHEAVVTGTA 119- Query: 121 KIKGQTTALAIMDSHFIMASMGTVVGEKLTRLFELATEKKLPIVIFTASGGARMQEGIMS 18- 0 IKGQT AL IMDS+FIMASMGTVVGEK+TRLFE AT +KLP+V+FTASGGARMQEGIMS Sbjct: 120 LIKGQTVALGIMDSNFIMASMGTVVGEKITRLFEYATVEKLPVVLFTASGGARMQEGIMS 17- 9 Query: 181 LMQMAKVSAAVKRHSNQGLFYLTILTDPTTGGVTASFAMEGDIILAEPQALVGFAGRRVI 24- 0 LMQMAK+SAAVKRHSN GLFYLTILTDPTTGGVTASFAMEGDIILAEPQ+LVGFAGRRVI Sbjct: 180 LMQMAKISAAVKRHSNAGLFYLTILTDPTTGGVTASFAMEGDIILAEPQSLVGFAGRRVI 23- 9 Query: 241 ETTVREDLPEGFQKAEFLLEHGFVDAIINRTELRDCIAQLIAFHG 285 E TVRE LPE FQKAEFLLEHGFVDAI+ R +L D IA L+ HG Sbjct: 240 ENTVRESLPEDFQKAEFLLEHGFVDAIVKRRDLPDTIASLVRLHG 284 A related DNA sequence was identified in S. pyogenes <SEQ ID 5215> which encodes the amino acid sequence <SEQ ID 5216>. Analysis of this protein sequence reveals the following: TABLE-US-05119 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4092(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05120 Identities = 232/285 (81%), Positives = 253/285 (88%) Query: 1 MALFSKKDKYIRISPNKALGSSDKRSLPEVPDELFAKCPSCKHMIYQKDLGLAKICPACS 60 MALF KKDKYIRI+PN +L S ++PEVPDELFAKCP+CKHMIY+KDLGLAKICP CS Sbjct: 1 MALFRKKDKYIRITPNNSLKGSVSHNVPEVPDELFAKCPACKHMIYKKDLGLAKICPTCS 60 Query: 61 YNFRISAQERLLLTVDEDSFEELFTGIETKDPLNFPNYREKLAATRQKTNLDEAVVTGLA 120- YNFRISAQERL LTVDE SF+ELFT IETKDPL FP Y+EKL ++ T L EAV+TG A Sbjct: 61 YNFRISAQERLTLTVDEGSFQELFTSIETKDPLRFPGYQEKLQKAKETTGLHEAVLTGKA 120- Query: 121 KIKGQTTALAIMDSHFIMASMGTVVGEKLTRLFELATEKKLPIVIFTASGGARMQEGIMS 18- 0 +K Q ALAIMDSHFIMASMGTVVGEK+TRLFELA E+ LP+VIFTASGGARMQEGIMS Sbjct: 121 MVKEQKIALAIMDSHFIMASMGTVVGEKITRLFELAIEENLPVVIFTASGGARMQEGIMS 18- 0 Query: 181 LMQMAKVSAAVKRHSNQGLFYLTILTDPTTGGVTASFAMEGDIILAEPQALVGFAGRRVI 24- 0 LMQMAKVSAAVKRHSN GLFYLTILTDPTTGGVTASFAMEGDIILAEPQ+LVGFAGRRVI Sbjct: 181 LMQMAKVSAAVKRHSNAGLFYLTILTDPTTGGVTASFAMEGDIILAEPQSLVGFAGRRVI 24- 0 Query: 241 ETTVREDLPEGFQKAEFLLEHGFVDAIINRTELRDCIAQLIAFHG 285 ETTVRE+LP+ FQKAEFL +HGFVDAI+ RTELRD IA L+AFHG Sbjct: 241 ETTVRENLPDDFQKAEFLQDHGFVDAIVKRTELRDKIAHLVAFHG 285 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1681 A DNA sequence (GBSx1785) was identified in S. agalactiae <SEQ ID 5217> which encodes the amino acid sequence <SEQ ID 5218>. This protein is predicted to be acetyl-CoA carboxylase alpha subunit (accA). Analysis of this protein sequence reveals the following: TABLE-US-05121 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.22 Transmembrane 149-165 (149-165) ----- Final Results ----- bacterial membrane --- Certainty = 0.1489(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9555> which encodes amino acid sequence <SEQ ID 9556> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05122 >GP: AAF98281 GB: AF197933 acetyl-CoA carboxylase alpha subunit [Streptococcus pneumoniae] Identities = 186/254 (73%), Positives = 222/254 (87%) Query: 13 DVTRILKDARDQGRLTALDYAELIFDNFMELHGDRQFADDKSIIGGLGYLAGRPVTIVGI 72 - ++ +I+++AR+Q RLT LD+A IFD F++LHGDR F DD +++GG+G+L + VT+VGI Sbjct: 2 NIAKIVREAREQSRLTTLDFATGIFDEFIQLHGDRSFRDDGAVVGGIGWLGDQAVTVVGI 61 Query: 73 QKGKNLQDNLDRHFGQPHPEGYRKALRLMKQAEKFGRPVITFINTAGAYPGVGAEERGQG 132- QKGK+LQDNL R+FGQPHPEGYRKALRLMKQAEKFGRPV+TFINTAGAYPGVGAEERGQG Sbjct: 62 QKGKSLQDNLKRNFGQPHPEGYRKALRLMKQAEKFGRPVVTFINTAGAYPGVGAEERGQG 121- Query: 133 EAIARNLLEMSDLKVPIIAIIIGEGGSGGALALAVADKVWMLEHTVYSILSPEGFASILW 19- 2 EAIARNL+EMSDLKVPIIAIIIGEGGSGGALALAVAD+VWMLE+++Y+ILSPEGFASILW Sbjct: 122 EAIARNLMEMSDLKVPIIAIIIGEGGSGGALALAVADRVWMLENSIYAILSPEGFASILW 18- 1 Query: 193 KDGTRTTEAAQLMKMTAGELYHMEVVDKVIPEHGYFSSEIVDMIKTSLISELEVLSQLSL 25- 2 KDGTR EAA+LMK+T+ EL M+VVDKVI E G S E++ +K L +EL LSQ L Sbjct: 182 KDGTRAMEAAELMKITSHELLEMDVVDKVISEIGLSSKELIKSVKKELQTELARLSQKPL 24- 1 Query: 253 EDLLEQRYQRFRKY 266 E+LLE+RYQRFRKY Sbjct: 242 EELLEERYQRFRKY 255 A related DNA sequence was identified in S. pyogenes <SEQ ID 5219> which encodes the amino acid sequence <SEQ ID 5220>. Analysis of this protein sequence reveals the following: TABLE-US-05123 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.22 Transmembrane 139-155 (139-155) ----- Final Results ----- bacterial membrane --- Certainty = 0.1489 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05124 >GP:AAF98281 GB:AF197933 acetyl-CoA carboxylase alpha subunit [Streptococcus pneumoniae] Identities = 189/254 (74%), Positives = 225/254 (88%) Query: 3 DVSRILKEARDQGRLTTLDYANLIFDDFMELHGDRHFSDDGAIVGGLAYLAGQPVTVIGI 62 ++++I++EAR+Q RLTTLD+A IFD+F++LHGDR F DDGA+VGG+ +L Q VTV+GI Sbjct: 2 NIAKIVREAREQSRLTTLDFATGIFDEFIQLHGDRSFRDDGAVVGGIGWLGDQAVTVVGI 61 Query: 63 QKGKNLQDNLARNFGQPNPEGYRKALRLNKQAEKFGRPVVTFINTAGAYPGVGAEERGQG 122- QKGK+LQDNL RNFGQP+PEGYRKALRLMKQAEKfGRPVVTFINThGAYPGVGAEERGQG Sbjct: 62 QKGRSLQDNLKRNFGQPHPEGYRKALRLmKQAEKFGRPVVTFINTAGAYPGVGAEERGQG 121- Query: 123 EAIARNLMEMSDLKVPIIAIIIGEGGSGGALALAVADQVWMLENTMYAVLSPEGFASILW 18- 2 EAIA+NLMEMSDLKVPITAIlIGEGGSGGALALAVAD+VWMLEN++YA+LSPEGFASILW Sbjct: 122 EAIARNLMEMSDLKVPIIAIIIGEGGSGGALALAVADRVWMLENSIYAILSPEGFASILW 18- 1 Query: 183 KDGSRATEAAELMKITAGELYKNGIVDRIIPEHGYFSSEIVDIIKANLIEQITSLQAKPL 24- 2 KDG+RA EAAELMKIT+ EL +N +VD++I E G S E++ +K L ++ L RPL Sbjct: 182 KDGTRANEAAELMKITSHELLEMDVVDKVISEIGLSSKELIKSVKKELQTELARLSQKPL 24- 1 Query: 243 DQLLDERYQRFRKY 256 ++LL+ERYQRFRKY Sbjct: 242 EELLEERYQRFRKY 255 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05125 Identities = 204/254 (80%), Positives = 236/254 (92%) Query: 13 DVTRILKDARDQGRLTALDYAELIFDNFMELHGDRQFADDKSIIGGLGYLAGRPVTIVGI 72 - DV+RILK+ARDQGRLT LDYA LIFD+FNELHGDR F+DD +I+GGL YLAG+PVT++GI Sbjct: 3 DVSRILKEARDQGRLTTLDYANLIFDDFMELHGDRHFSDDGAIVGGLAYLAGQPVTVIGI 62 Query: 73 QKGKNLQDNLDRHFGQPHPEGYRKALRLMKQAEKFGRPVITFINTAGAYPGVGAEERGQG 132- QKGKNLQDNL R+FGQP+PEGYRKALRLMKQAEKFGRPV+TFINTAGAYPGVGAEERGQG Sbjct: 63 QKGKNLQDNLARNFGQPNPEGYRKALRLMKQAEKFGRPVVTFINTAGAYPGVGAEERGQG 122- Query: 133 EAIARNLLEMSDLKVPIIAIIIGEGGSGGALALAVADKVWMLEHTVYSILSPEGFASILW 19- 2 EAIA+NL+EMSDLKVPIIAIIIGEGGSGGALALAVAD+VWMLE+T+Y++LSPEGFASILW Sbjct: 123 EAIAKNLMEMSDLKVPIIAIIIGEGGSGGALALAVADQVWMLENTMYAVLSPEGFASILW 18- 2 Query: 193 KDGTRTTEAAQLMKMTAGELYHMEVVDKVIPEHGYFSSEIVDMIKTSLISELEVLSQLSL 25- 2 KDG+R TEAA+LMK+TAGELY M +VD++IPEHGYFSSEIVD+IK +LI ++ L L Sbjct: 183 KDGSRATEAAELHKITAGELYKMGIVDRIIPEHGYFSSEIVDIIKANLIEQITSLQAKPL 24- 2 Query: 253 EDLLEQRYQRFRKY 266 + LL++RYQRFRKY Sbjct: 243 DQLLDERYQRFRKY 256 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1682 A DNA sequence (GBSx1786) was identified in S. agalactiae <SEQ ID 5221> which encodes the amino acid sequence <SEQ ID 5222>. This protein is predicted to be sakacin A production response regulator. Analysis of this protein sequence reveals the following:

TABLE-US-05126 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3304 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9557> which encodes amino acid sequence <SEQ ID 9558> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05127 >GP:BAA88824 GB:AB016077 sakacin A production response regulator [Streptococcus mutans] Identities = 76/142 (53%), Positives = 99/142 (69%) Query: 36 MQTFKAKGQLARNSFTELSRALEQRNDGFKMQRVSNWANQAQVGRPHFWVYYRKDTDQLD 95 - M K GQ AR FTE+++ L ++ F+M RVSNWANQAQV RPHEW YY++ D D Sbjct: 1 MIALKTLGQSARAEFTEIAKVLALKVSPFEMMRVSNWANQAQVVRPHFWCYYKQPEDNQD 60 Query: 96 DVAVALRVYGVKDSFGVSLEVSFVERQKSDKTLEKQARVLSIPIASPLYFMVQRQGETHR 155- DV +A+R+YG +FG+S+EVSF+ER+KS TL KQ +VL IPIA PLY+ Q + E+HR Sbjct: 61 DVGLAIRLYGNSANFGISVEVSFIERKRSKATLAKQHKVLDIPIAEPLYYFAQEKSESHR 120- Query: 156 EEGNEENRQRLMQEIKSGKVRK 177 G E RQ L Q++G+VRK Sbjct: 121 VSGTEAYRQMLRQKVADGQVRK 142 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1683 A DNA sequence (GBSx1787) was identified in S. agalactiae <SEQ ID 5223> which encodes the amino acid sequence <SEQ ID 5224>. This protein is predicted to be seryl-tRNA synthetase (serS). Analysis of this protein sequence reveals the following: TABLE-US-05128 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1866 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05129 >GP:CAB11789 GB:Z99104 seryl-tRNA synthetase [Bacillus subtilis] Identities = 262/425 (61%), Positives = 322/425 (75%), Gaps = 1/425 (0%) Query: 1 MLDLKRIRTDFDVVAKKLATRGVDQETLTTLKELDIKRRELLIKAEEAKAQRNVASAAIA 6 MLD K +R +F + KL +G D + LD +RREL+ K EE K +RN S +A Sbjct: 1 MLDTKNLRANFQEIKAKLVHKGEDLTDFDKFEALDDRRRELIGKVEELKGKRNEVSQQVA 60 Query: 61 QAKRNKENADEQIAAMQTLSADIKAIDAELADVDANLQSMVTVLPNTPADDVPLGADEDE 120- KR K++AD I M+ + +IK +D EL V+A L +++ +PN P + VP+G ED+ Sbjct: 61 VLKREKKDADHIIKEHREVGEEIKKLDEELRTVEAELDTILLSIPNIPHESVPVGETEDD 120- Query: 121 NVEVRRWGTPREFDFETKAHWDLGESLGILDWERGAKVTGSRFLFYKGLGARLERAIYSF 18- 0 NVEVR+WG F +E K HWD+ + LGILD+ER AKVTGSRF+FYKGLGARLERA+Y+F Sbjct: 121 NVEVRKWGEKPSFAYEPKPHWDIADELGILDFERAAKVTGSRFVFYKGLGARLERALYNF 18- 0 Query: 181 MLDEHAKE-GYTEVIPPYMVNHDSMFGTGQYPKFKEDTFELADSPFVLIPTAEVPLTNYY 23- 9 MLD H E YTEVIPPYMVN SM GTGQ PKF+ED F++ + + LIPTAEVP+TN + Sbjct: 181 MLDLHVDEYNYTEVIPPYMVNRASMTGTGQLPKFEEDAFKIREEDYFLIPTAEVPITNMH 24- 0 Query: 240 RDEIIDGKELPIYFTAMSPSFRSEAGSAGRDTRGLIRLHQFHKVEMVKFAKPEESYQELE 29- 9 RDEI+ G LPI + A S FRSEAGSAGRDTRGLIR HQF+KVE+VKF KPE+SY+ELE Sbjct: 241 RDEILSGDSLPINYAAFSACFRSEAGSAGRDTRGLIRQHQFNKVELVKFVKPEDSYEELE 30- 0 Query: 300 KMTANAENILQKLNLPYRVITLCTGDMGFSAAKTYDLEVWIPAQNTYREISSCSNTEDFQ 35- 9 K+T AE +LQ L LPYRV+++CTGD+GF+AAK YD+SVWIP+Q+TYRSISSCSN E FQ Sbjct: 301 KLTNQAERVLQLLSLPYRVMSMCTGDLGFTAAKKYDISVWIPSQDTYRSISSCSNFSAFQ 36- 0 Query: 360 ARRAQIRYRDSVDGKVRLLHTLNGSGLAVGRTVAAILSNYQNEDGSVTIPSVLRPYMGNI 41- 9 ARRA IR+R E GK +HTLNGSGLAVGRTVAAILSNYQ EDGSV IP+VLRPYMGN Sbjct: 361 ARRANIRFRREAKGKPSHVHTLNGSGLAVGRTVAAILSNYQQEDGSVVIPKVLRPYMGNR 42- 0 Query: 420 DIIKP 424 +++KP Sbjct: 421 EVMKP 425 A related DNA sequence was identified in S. pyogenes <SEQ ID 5225> which encodes the amino acid sequence <SEQ ID 5226>. Analysis of this protein sequence reveals the following: TABLE-US-05130 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2453 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05131 Identities = 357/424 (84%), Positives = 386/424 (90%) Query: 1 MLDLKRIRTDFDVVAKKLATRGVDQETLTTLKELDIKRRELLIKAEEAKAQRNVASAAIA 60 MLDLKRIRTDFD VA KL RGV ++TLT LKELD KRR LL+++EE KA+RN+ASAAIA Sbjct: 1 MLDLKRIRTDFDTVAAKLKNRGVSEDTLTHLKELDEKRRALLVQSEELKAERNIASAAIA 60 Query: 61 QAKRNKENADEQIAAMQTLSADIKAIDASLADVDANLQSMVTVLPNTPADDVPLGADEDE 120- QAKR KE+A +QIA MQ +SADIK ID +L +D + ++TVLPNTP D VP+GADE++ Sbjct: 61 QAKRQKEDATQQIADMQKVSADIKTIDNQLVAIDQQVTDIITVLPNTPHDSVPVGADEED 120- Query: 121 NVEVRRWGTPREFDFETKAHWDLGESLGILDWERGAKVTGSRFLFYKGLGARLERAIYSF 18- 0 NVE+RRWGTPR+FDFE KAHWDLGE L ILDWERGAKVTG+RFLFYK LGARLERA+Y+F Sbjct: 121 NVEIRRWGTPRDFDFEVKAHWDLGEDLDILDWERGAKVTGARFLFYKNLGARLERALYNF 18- 0 Query: 181 MLDEHAKEGYTEVIPPYMVNHDSMFGTGQYPKFKEDTFELADSPFVLIPTAEVPLTNYYR 24- 0 MLDEH KEGY E+I PYMVNHDSMFGTGQYPKFKEDTFELAD+ FVLIPTAEVPLTNYYR Sbjct: 181 MLDSHIKEGYQEIITPYMVNHDSMFGTGQYPKFKEDTFELADTNFVLIPTAEVPLTNYYR 24- 0 Query: 241 DEIIDGKELPIYFTAMSPSFRSEAGSAGRDTRGLIRLHQFHKVEMVKFAKPEESYQELEK 30- 0 EI+DGKELPIYFTANSPSFRSEAGSAGRDTRGLIRLHQFHKVEMVKFAKPEESYQELEK Sbjct: 241 GEILDGKELPIYFTANSPSFRSEAGSAGRDTRGLIRLHQFHKVEMVKFAKPEESYQELEK 30- 0 Query: 301 MTANAENILQKLNLPYRVITLCTGDMGFSAAKTYDLEVWIPAQNTYREISSCSNTEDFQA 36- 0 MTANAENILQKL LPYRVI+LCTGDMGFSAAKTYDLEVWIPAQNTYREISSCSNTEDFQA Sbjct: 301 MTANAENILQKLGLPYRVISLCTGDMGFSAAKTYDLEVWIPAQNTYREISSCSNTEDFQA 36- 0 Query: 361 RRAQIRYRDEVDGKVRLLHTLNGSGLAVGRTVAAILENYQNEDGSVTIPEVLRPYMGNID 42- 0 RRAQIRYRDE DGKV+LLHTLNGSGLAVGRTVAAILENYQNEDGSVTIPEVLRPYMG Sbjct: 361 RRAQIRYRDEADGKVKLLHTLNGSGLAVGRTVAAILENYQNEDGSVTIPEVLRPYMGGET 42- 0 Query: 421 IIKP 424 +I P Sbjct: 421 VISP 424 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1684 A DNA sequence (GBSx1788) was identified in S. agalactiae <SEQ ID 5227> which encodes the amino acid sequence <SEQ ID 5228>. Analysis of this protein sequence reveals the following: TABLE-US-05132 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.36 Transmembrane 313-329 (306-332) INTEGRAL Likelihood = -9.24 Transmembrane 159-175 (155-179) INTEGRAL Likelihood = -4.19 Transmembrane 20-36 (16-37) INTEGRAL Likelihood = -3.29 Transmembrane 271-287 (271-287) INTEGRAL Likelihood = -2.97 Transmembrane 210-226 (209-227) INTEGRAL Likelihood = -2.87 Transmembrane 242-258 (241-258) INTEGRAL Likelihood = -2.13 Transmembrane 52-68 (50-68) ----- Final Results ----- bacterial membrane --- Certainty = 0.5543 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9559> which encodes amino acid sequence <SEQ ID 9560> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05133 >Gp:CAA07406 GB:AJ006986 transmembrane protein [Streptococcus pneumoniae] Identities = 72/330 (21%), Positives = 143/330 (42%), Gaps = 32/330 (9%) Query: 14 RHYGLDLLRIISMFNIVITHVLGKGGLRSSVEGHADSYFIVTWIIQVLVYGAVNCYALIS 73 - R+ LDLL++++ +V+ H GG + + + +Y + ++ VN Y L+ Sbjct: 5 RNINLDLLKVLACVGVVLLHTT-MGGFKETGAWNFLTYLYYLGTYSIPLFFNVNGYLLL- 62 Query: 74 GYVGINSRYRYSKLLSIWAQVFFYTFTITALFAITGHE------VTLLNWRDAFFPIVSG 127- G I Y K+ + V +TF I LF E + L + FF Sbjct: 63 GKREITYSYILQKIKWLLITVSSWTF-IVWLFKRDFTENLIKKIIGSLIQKGYFF----- 116- Query: 128 QYWYITAYFGLLVFMPVINNGLNALTDKQLKQLVLLMFI--IFSILPAVLNNRVPEFSLS 18- 5 Q+W+ A + + +P++ LN+ L L LLM I IF + +L + + + Sbjct: 117 QEWFFGALILIYLCLPILRQFLNS-KRSYLYSLSLLMTIGLIFELSNILLQMPIQTYVIQ 17- 5 Query: 186 KGFEMTWLLILYIIGAYLKRIDL----NIFKTSYLLIIYLLSLVATYAMKFSVGDIW--- 23- 8 TW Y++G Y+ + + + FK ++ LL L++ + F I+ Sbjct: 176 TFRLWTW-FFYYLLGGYIAQFTIEEIESRFKNWMKIVSILLLLISPIILFFIAKTIYHNL 23- 4 Query: 239 ---YWYVSPTLTLGAVSLFILFARASIKPSGFLKKIIVVLAPSTLGVYLCHLHPLIVKYF 29- 5 Y+Y + + + + +F+ ++ + ++ IV L+ T+GV++ +H I+K + Sbjct: 235 FAEYFYDTLFVKVSTLGIFLTILMLTLNEN--RRESIVSLSNQTMGVFI--IHTYIMKVW 29- 0 Query: 296 VRDFAETFVYESIYLYPFLILGAGILIYLL 325 + FV + F + + I++ +L Sbjct: 291 SKVLGFNFVGAYLLFALFTLSVSFIIVGML 320 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1685 A DNA sequence (GBSx1789) was identified in S. agalactiae <SEQ ID 5229> which encodes the amino acid sequence <SEQ ID 5230>. Analysis of this protein sequence reveals the following: TABLE-US-05134 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2752 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9561> which encodes amino acid sequence <SEQ ID 9562> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05135 >GP:AAD46488 GB:AF130465 unknown [Streptococcus salivarius] Identities = 88/112 (78%), Positives = 96/112 (85%) Query: 1 MAQSLNKTVEFQTTGVSYLGNGNKVGKFLVGDQALEFYNDKNVNDYIQIPWTSINQIGAN 60 MAQSLNKTVE TTGVSY+ +G KVGKFL+GD ALEFY D NV YIQIPWTSI QIGAN Sbjct: 1 MAQSLNKTVELHTTGVSYMAIGGKVGKFLIGDVALEFYPDVNVEQYIQIPWTSITQIGAN 60 Query: 61 VSRKKISRHFEVFTDQGKFLFASKDSGTILKHARRHIGDDKVVKLPTLIQTI 112 VS K+ISRHFEV TD+ KFLFASKDSG ILK AR H+G++KVVKLPTLIQTI Sbjct: 61 VSGKRISRHFEVLTDKSKFLFASKDSGKILKIAREHLGNEKVVKLPTLIQTI 112 A related DNA sequence was identified in S. pyogenes <SEQ ID 5231> which encodes the amino acid sequence <SEQ ID 5232>. Analysis of this protein sequence reveals the following: TABLE-US-05136 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3301 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05137 Identities = 87/116 (75%), Positives = 101/116 (87%) Query: 1 MAQSLNKTVEFQTTGVSYLGMGNKVGKFLVGDQALEFYNDKNVNDYIQIPWTSINQIGAN 60 MAQSLN +VE++T VSYLGMG KVG L+GD+ALEFYNDKNVNDYIQIPWT+IN IGAN Sbjct: 1 MAQSLNTSVEYKTKAVSYLGMGGKVGHILLGDKALEFYNDKNVNDYIQIPWTAINHIGAN 60 Query: 61 VSRKKISRHFEVFTDQGKFLFASKDSGTILKHARRHIGDDKVVKLPTLIQTILKIF 116 VSRKK+SRHFE+FTDQGKFLFAS DSG ILK R+HIG++KV+ LPTL+QT + F Sbjct: 61 VSRKKVSRHFEIFTDQGKFLFASGDSGKILKITRQHIGNEKVITLPTLMQTFINKF 116 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1686 A DNA sequence (GBSx1790) was identified in S. agalactiae <SEQ ID 5233> which encodes the amino acid sequence <SEQ ID 5234>. This protein is predicted to be mannose-specific phosphotransferase system component IID (manZ). Analysis of this protein sequence reveals the following: TABLE-US-05138 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.92 Transmembrane 281-297 (279-302) INTEGRAL Likelihood = -4.88 Transmembrane 187-203 (185-205) INTEGRAL Likelihood = -4.35 Transmembrane 260-276 (257-277) INTEGRAL Likelihood = -1.01 Transmembrane 129-145 (129-145) ----- Final Results ----- bacterial membrane --- Certainty = 0.4567 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05139 >GP:AAD46487 GB:AF130465 mannose-specific phosphotransferase system component IID [Streptococcus salivarius] Identities = 247/303 (81%) , Positives = 276/303 (90%) Query: 1 MTEQIKLSKSDRQKVWWRSQFLQGSWNYERNQNMGWAYALIPALKKLYTTKEDRAAALER 60 M E+I+LS++DR+KVWWRSQFLQGSWNYERNQN+GWAY+LIPA+KKLYT KED+AAAL+R Sbjct: 1 MAEKIQLSQADRKKVWWRSQFLQGSWNYERNQNLGWAYSLIPAIKKLYTNKEDQAAALKR 60 Query: 61 HMEFFNTHPYVAAPIIGVTLALEEEKASGTPVEDKAIQGVKIGMMGPLAGIGDPVFWFTV 120- H+EFFNTHPYVAAPI+GVTLALEEEKA+GT +ED AIQGVKIGMNGPLAGIGDPVFWFTV Sbjct: 61 HLEFFNTHPYVAAPIMGVTLALEEEKANGTDIEDAAIQGVKIGMMGPLAGIGDPVFWFTV 120- Query: 121 RPILGALGASLASAGNILGPIIFFVGWNLIRMSFLWYTQELGYKSGKEITKDMSGGILQD 18- 0 RPILGALGASLA AGNI GP+IFF+GWNLIRM+FLWYTQELGYK+G EITKDMSGGIL+D Sbjct: 121 RPILGALGASLAQAGNIAGPLIFFIGWNLIRMAFLWYTQELGYKAGSEITKDMSGGILKD 18- 0 Query: 181 ITKGASILGMFILAVLVKRWVAINFTVDLPKKTLSEGAYINFPKDHVSGQQLHDILGQVQ 24- 0 ITKGASILGMFILAVLV+RWV+I FTV+LP K LS+GAYI +PK +VSG QL ILGQV Sbjct: 181 ITKGASILGMFILAVLVERWVSIVFTVNLPGKVLSKGAYIEWPKGNVSGDQLKTILGQVN 24- 0 Query: 241 SGLSLDKNQFQTLQGQLDSLIPGLAGLLLTFFCNWLLKKKVSPITIIIGLFIVGILARLA 30- 0 LS DK+Q TLQ QLDSLIPGL GLLLTF CNWLLKKKVSPITIIIGL +VGI+A Sbjct: 241 DKLSFDKIQVDTLQKQLDSLIPGLNGLLLTFACNWLLKKKVSPITIIIGLFVVGIVASFF 30- 0 Query: 301 GVM 303 G+M Sbjct: 301 GIM 303 A related DNA sequence was identified in S. pyogenes <SEQ ID 5235> which encodes the amino acid sequence <SEQ ID 5236>. Analysis of this protein sequence reveals the following: TABLE-US-05140 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.39 Transmembrane 284-300 (279-302) INTEGRAL Likelihood = -4.88 Transmembrane 261-277 (257-278) INTEGRAL Likelihood = -4.51 Transmembrane 181-197 (180-198) ----- Final Results ----- bacterial membrane --- Certainty = 0.4354 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05141 >GP:AAD46487 GB:AF130465 mannose-specific phosphotransferase system component IID [Streptococcus salivarius] Identities 239/303 (78%), Positives = 268/303 (87%) Query: 1 MTEQIKLTKSDRQRVWWRSQFLQGSWNYERNQNMGWAYALIPALKKLYTSPEDRAAALER 60 M E+I+L+++DR++VWWRSQFLQGSWNYERNQN+GWAY+LIPA+KKLYT+ ED+AAAL+R Sbjct: 1 MA KIQLSQADRKKVWWRSQFLQGSWNYERNQNLGWAYSLIPAIKKLYTNKEDQAAALKR 60 Query: 61 HMEFFNTHPYVAAPIIGVTLALEEERANGTPIDDKAIQGVKIGMMGPLAGIGDPVFWFTI 120- H+EFFNTHPYVAAPI+GVTLALEEE+ANGT I+D AIQGVKIGMNGPLAGIGDPVFWFT+ Sbjct: 61 HLEFFNTHPYVAAPIMGVTLALEEEKANGTDIEDAAIQGVRIGMMGPLAGIGDPVFWFTV 120- Query: 121 RPILGALGASLASTGNIVGPLLFFFGWNLIRMAFLWYTQEFGYKAGSEITKDMSGGILQD 18- 0 RPILGALGASLA GNI GPL+FF GWNLIRMAFLWYTQE GYKAGSEITKDMSGGIL+D Sbjct: 121 RPILGALGASLAQAGNIAGPLIFFIGWNLIRMAFLWYTQELGYKAGSEITKDHSGGILKD 18- 0 Query: 181 ITKGASILGMFILAVLVQRWVSINFTIDLPGKQLSDGAYVVFPDGAVKGAELKTILANAI 24- 0 ITKGASILGMFILAVLV+RWVSI FT++LPGK LS GAY+ +P G V G +LKTIL Sbjct: 181 ITKGASILGMFILAVLVERWVSIVFTVNLPGKVLSKGAYIEWPKGNVSGDQLKTILGQVN 24- 0 Query: 241 GGMSLDKVQAQTLQGQLDSLIPCLAGLLLTFLCMWLLKKKVSPIAIIIGLFAFGILAHLA 30- 0 +S DK+Q TLQ QLDSLIPGL GLLLTF CMWLLKKKVSPI IIIGLF GI+A Sbjct: 241 DKLSFDKIQVDTLQKQLDSLIPGLHGLLLTFACMWLLKKKVSPITIIIGLFVVGIVASFF 30- 0 Query: 301 GIM 303 GIM Sbjct: 301 GIM 303 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05142 Identities = 255/303 (84%), Positives = 277/303 (91%) Query: 1 MTEQIKLSKSDRQKVWWRSQFLQGSWNYERNQNMGWAYALIPALKKLYTTKEDRAAALER 60 MTEQIKL+KSDRQ+VWWRSQFLQGSWNYERNQNMGWAYALIPALKKLYT+ EDRAAALER Sbjct: 1 MTEQIKLTKSDRQRVWWRSQFLQGSWNYERMQNMGWAYALIPALKKLYTSPEDRAAALER 60 Query: 61 HMEFFNTHPYVAAPIIGVTLALESEKASGTPVEDKAIQGVKIGMMGPLAGIGDPVFWFTV 120- HMEFFNTHPYVAAPIIGVTLALEEE+A+GTP++DKAIQGVKIGMMGPLAGIGDPVFWFT+ Sbjct: 61 HMEFFNTHPYVAAPIIGVTLALEEERANGTPIDDKAIQGVKIGMMGPLAGIGDPVFWFTI 120- Query: 121 RPILGALGASLASAGNILGPIIFFVGWNLIRMSFLWYTQELGYKSGKEITKDMSGGILQD 18- 0 RPILGALGASLAS GNI+GP++FF GWNLIRN+FLWYTQE GYK+G EITKDMSGGILQD Sbjct: 121 RPILGALGASLASTGNIVGPLLFFFGWNLIRNAFLWYTQEFGYKAGSEITKDMSGGILQD 18- 0 Query: 181 ITKGASILGMFILAVLVKRWVAINFTVDLFKKTLSEGAYINFPKDHVSGQQLHDILGQVQ 24- 0 ITKGASILGMFILAVLV+RWV+INFT+DLP K LS+GAY+ FP V G +L IL Sbjct: 181 ITKGASILGMFILAVLVQRWVSINFTIDLPGKQLSDGAYVVFPDGAVKGAELKTILANAI 24- 0 Query: 241 SGLSLDKMQPQTLQGQLDSLIPGLAGLLLTFFCMWLLKKKVSPITIIIGLFIVGILARLA 30- 0 G+SLDK+Q QTLQGQLDSLIPGLAGLLLTF CMWLLKKKVSPI IIIGLF GILA LA Sbjct: 241 GGMSLDKVQAQTLQGQLDSLIPGLAGLLLTFLCMWLLKKKVSPIAIIIGLFAFGILAHLA 30- 0 Query: 301 GVM 303 G+M Sbjct: 301 GIM 303 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1687 A DNA sequence (GBSx1791) was identified in S. agalactiae <SEQ ID 5237> which encodes the amino acid sequence <SEQ ID 5238>. Analysis of this protein sequence reveals the following:

TABLE-US-05143 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2580 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1688 A DNA sequence (GBSx1792) was identified in S. agalactiae <SEQ ID 5239> which encodes the amino acid sequence <SEQ ID 5240>. This protein is predicted to be mannose-specific phosphotransferase system component IIC (manY). Analysis of this protein sequence reveals the following: TABLE-US-05144 Possible site: 39 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.95 Transmembrane 142-158 (137-165) INTEGRAL Likelihood = -2.60 Transmembrane 65-81 (61-81) INTEGRAL Likelihood = -1.97 Transmembrane 103-119 (103-122) ----- Final Results ----- bacterial membrane --- Certainty = 0.3378 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9301> which encodes amino acid sequence <SEQ ID 9302> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05145 >GP:AAD46486 GB:AF130465 mannose-specific phosphotransferase system component IIC [Streptococcus salivarius] Identities = 134/186 (72%), Positives = 154/186 (82%), Gaps = 1/186 (0%) Query: 1 MVKSGDFTQKGINFAFSTAVPLAIAGLFLTMIVRTISTALVHAGDKAASEGNFAAIERFH 60 +VK G+FT +GI A +TA+PLA+AGLFLTM+VRT S ALVHA DKAA GN A +ER H Sbjct: 86 LVKGGNFTTEGIGVATATAIPLAVAGLFLTMLVRTASVALVHAADKAAESGNIAGVERAH 145- Query: 61 FIALLLQGLRIAFPAALLLAIPSSSVQSILEAHPDWLNGGMQVGGANVVAVGYAHVINHN 120- ++ALLLQGLRIA PAALLLAIP+ SVQ L HP WLN GM VGG MVVAVGYAHVIHHH Sbjct: 146 YLALLLQGLRIAVPAALLLAIPAESVQHALGLHPSWLNHGHVVGGGMVVAVGYAMVIHHN 20- 5 Query: 121 ATREVWPFFALGFALAALHQLTLIAMGTIGVAIALIYISLSKHGGSK-GTSHAGSHDPIG 17- 9 ATREVWPFFA+GFA AA++QLTLIA+G IGVAIA IY++LSK GG G +++ GS DPIG Sbjct: 206 ATREVWPFFAIGFAFAAISQLTLIALGAIGVAIAFIYLHLSKQGGGNGGGTSSGSGDPIG 26- 5 Query: 180 DILEDY 185 DILEDY Sbjct: 266 DILEDY 271 A related DNA sequence was identified in S. pyogenes <SEQ ID 5241> which encodes the amino acid sequence <SEQ ID 5242>. Analysis of this protein sequence reveals the following: TABLE-US-05146 Possible Site: 36 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.30 Transmembrane 4-20 (1-28) INTEGRAL Likelihood = -7.64 Transmembrane 226-242 (212-247) INTEGRAL Likelihood = -4.14 Transmembrane 102-118 (101-123) INTEGRAL Likelihood = -3.77 Transmembrane 71-87 (69-87) INTEGRAL Likelihood = -3.40 Transmembrane 150-166 (146-167) INTEGRAL Likelihood = -2.13 Transmembrane 186-202 (186-202) INTEGRAL Likelihood = -0.37 Transmembrane 37-53 (37-53) ----- Final Results ----- bacterial membrane --- Certainty = 0.5522 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05147 >GP:AAD46486 GB:AF130465 mannose-specific phosphotransferase system component IIC [Streptococcus salivarius] Identities = 211/271 (77%), Positives = 237/271 (86%), Gaps = 2/271 (0%) Query: 1 MSDISIISAILVVIIAFFAGLEGILDQFQMHQPLVACTLIGLVTGHLEAGVILGGTLQML 60 MSD+SIISAILVV++AF AGL GILDQFQ HQPLVACTLIG TG+L AG++LGG+LQM+ Sbjct: 1 MSDMSIISAILVVVVAFLAGLEGILDQFQFHQPLVACTLIGAATGNLTAGIMLGGSLQMI 60 Query: 61 ALGWANIGAAVAPDAALASVAAAIIMVKSGDFTQKGITFAYSTAIPLAVAGLFLTMIVRT 120- AL WANIGAAVAPDAALASVAAAII+VK G+FT +GI A +TAIPLAVAGLFLTM+VRT Sbjct: 61 ALAWANIGAAVAPDAALASVAAAIILVKGGNFTTEGIGVATATAIPLAVAGLFLTHLVRT 120- Query: 121 LSTALVHAGDKAAAEGNFAGIERFHFIALLLQGLRIAVPAALLVAVPTSAVQSVLNANPN 18- 0 S ALVHA DKAA GN AG+ER H++ALLLQGLRIAVPAALL+A+P +VQ L MP+ Sbjct: 121 ASVALVHAADKAAESGNIAGVERAHYLALLLQGLRIAVPAALLLAIPAESVQHALGLMPS 18- 0 Query: 181 WLNEGMQIGGAMVVAVGYAMVINMMATREVWPFFALGFALAAISQLTLIAMGVIGVAIAF 24- 0 WLN GM +GG MVVAVGYAMVINMMATREVWPFFA+GFA AAISQLTLIA+G IGVAIAF Sbjct: 181 WLNHGMVVGGGMVVAVGYAMVINMMATREVWPFFAIGFAFAAISQLTLIALGAIGVAIAF 24- 0 Query: 241 IYLNLSKKGG--NGGNAAGSADPIGDILEDY 269 IYLNLSK+GG GG ++GS DPIGDILEDY Sbjct: 241 IYLNLSKQGGGNGGGTSSGSGDPIGDILEDY 271 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05148 Identities = 155/185 (83%), Positives = 173/185 (92%), Gaps = 1/185 (0%) Query: 1 MVKSGDFTQKGINFAFSTAVPLAIAGLFLTMIVRTISTALVHAGDKAASEGNFAAIERFH 60 MVKSGDFTQKGI FA+STA+PLA+AGLFLTMIVRT+STALVHAGDKAA+EGNFA IERFH Sbjct: 86 MVKSGDFTQKGITFAYSTAIPLAVAGLFLTMIVRTLSTALVHAGDKAAAEGNFAGIERFH 145- Query: 61 FIALLLQGLRIAFPAALLLAIPSSSVQSILEAMPDWLNGGMQVGGAMVVAVGYAMVINMM 120- FIALLLQGLRIA PAALL+A+P+S+VQS+L AMP+WLN GMQ+GGAMVVAVGYAMVINMM Sbjct: 146 FIALLLQGLRIAVPAALLVAVPTSAVQSVLNAMPNWLNEGMQIGGANVVAVGYAMVINMM 20- 5 Query: 121 ATREVWPFFALGFALAALNQLTLIAMGTIGVAIALIYISLSKMGGSKGTSNAGSNDPIGD 18- 0 ATREVWPFFALGFALAA++QLTLIAMG IGVAIA IY++LSK GG+ G + AGS DPIGD Sbjct: 206 ATREVWPFFALGFALAAISQLTLIAMGVIGVAIAFIYLNLSKKGGNGGNA-AGSADPIGD 26- 4 Query: 181 ILEDY 185 ILEDY Sbjct: 265 ILEDY 269 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1689 A DNA sequence (GBSx1793) was identified in S. agalactiae <SEQ ID 5243> which encodes the amino acid sequence <SEQ ID 5244>. Analysis of this protein sequence reveals the following: TABLE-US-05149 Possible site: 37 >>> Seems to have a cleavable N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3171 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1690 A DNA sequence (GBSx1794) was identified in S. agalactiae <SEQ ID 5245> which encodes the amino acid sequence <SEQ ID 5246>. This protein is predicted to be pseudouridine synthase (rluC). Analysis of this protein sequence reveals the following: TABLE-US-05150 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2717 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05151 >GP:BAB06566 GB:AP001516 unknown conserved protein [Bacillus halodurans] Identities = 124/281 (44%), Positives = 171/281 (60%), Gaps = 8/281 (2%) Query: 16 LLKSHDVSRGLLAKIKYRGGKIFVNGEEQNAIFLLEIGDVVTIDIPDE-PSHETL-EPVP 73 - L + VS+ LA IK++GG I +NGEE + + D VT+++P E PS + EPVP Sbjct: 24 LREGKHVSKRSLAAIKFKGGTILLNGEEVTVRETVHVNDQVTLELPHEYPSPSMIAEPVP 83 Query: 74 HDLDIIYEDDHFLILNKPFGFASIPSSIH-SNTIANFIKHYYVSNNYANQQVHIVTRLDR 132- D+IYE+DH+L++NKP G +IPS H T+AN + +Y+ A H V RLD+ Sbjct: 84 --FDVIYENDHYLVVNKPAGVPTIPSRDHPQGTLAHGLLNYFQRQKMA-ATFHAVHRLDK 140- Query: 133 DTSGLMLFAKHGYAHARLDKQLQAKAIEKRYYALVSGSGDLADSGDIIAPIARDVDSIIT 19- 2 DTSGL++ AKH AH +L KQ + I++ Y A+V G + + G I APIAR +S+IT Sbjct: 141 DTSGLLIVARHQLAHDQLSKQQRQGNIKRTYMAIVQGEIEQQE-GTITAPIARKEESLIT 19- 9 Query: 193 RRVHESGRYAHTSYQVVARYGDVRLVDIKLHTGRTHQIRVHFAHIGFPLLGDDLYGGRND 25- 2 R V E G+ A T ++V+ R +V ++L TGRTHQIRVHF+++G+PL GDDLYGG Sbjct: 200 REVREDGQLAITHFKVIDRLNQGTIVQVQLETGRTHQIRVHFSYLGYPLFGDDLYGGERR 25- 9 Query: 253 LGINRQALHCHSLSFYDPFMGKINKQTLDLTDDFDSVIMEL 293 GIRQALH L+ + PF T L D +I L Sbjct: 260 -GIERQALHSTELTIHCPFTEVEQTFTEGLPPDMKELIRHL 299 A related DNA sequence was identified in S. pyogenes <SEQ ID 5247> which encodes the amino acid sequence <SEQ ID 5248>. Analysis of this protein sequence reveals the following: TABLE-US-05152 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2786 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05153 Identities = 223/294 (75%), Positives = 251/294 (84%), Gaps = 1/294 (0%) Query: 1 MKFEYVAKERCKVRTLLKSHDVSRGLLAKIKYRGGKIFVNGEEQNAIFLLEIGDVVTIDI 60 M+FE+VA +R KVKTLLKS+DVS+GLLAKIKY+GG I VNG EQNAI+LL++GDVVTIDI Sbjct: 1 MRFEFVADKRIKVKTLLKSYDVSKGLLAKIKYKGGNILVNGIEQNAIYLLQVGDVVTIDI 60 Query: 61 PDEPSHETLEPVPHDLDIIYEDDHFLILNKPFGFASIPSSIHSNTIANFIKHYYVSNNYA 120- P+E E LE +P DLDI++EDDHFL++NKP GFASIPS+IHSNTIANFIK YYV N+Y Sbjct: 61 PNEEPFEKLEAIPFDLDIVHEDDHFLVINKPIGFASIPSAIHSNTIANFIKAYYVDNHYL 120- Query: 121 NQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQAKAIEKRYYALVSGSGDLADSGDII 18- 0 +QQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQ ++IEKRY+ALVSG+G L D GDII Sbjct: 121 DQQVHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQTRSIEKRYFALVSGNGMLPDEGDII 18- 0 Query: 181 APIARDVDSIITRRVHESGKYAHTSYQVVARYGD-VRLVDIRLHTGRTHQIRVHFAHIGF 23- 9 API R DSIITR V GKYA TSY+VVARY + V LVDIKLHTGRTHQIRVHFAHIGF Sbjct: 181 APIGRSKDSIITRAVDPMGKYAKTSYKVVARYSENVHLVDIKLHTGRTHQIRVHFAHIGF 24- 0 Query: 240 PLLGDDLYGGRMDLGINRQALHCHSLSFYDFFMGKINKQTLDLTDDFDSVIMEL 293 PLLGDDLYGGR+DLGI RQALHCH L+F DPF + LTDDFDSVI+ L Sbjct: 241 PLLGDDLYGGRLDLGITRQALHCHYLNFKDPFTES0CSYAIHLTDDFDSVIIGL 294 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1691 A DNA sequence (GBSx1795) was identified in S. agalactiae <SEQ ID 5249> which encodes the amino acid sequence <SEQ ID 5250>. Analysis of this protein sequence reveals the following: TABLE-US-05154 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1521 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9845> which encodes amino acid sequence <SEQ ID 9846> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05155 >GP:CAB13018 GB:Z99110 similar to hypothetical proteins [Bacillus subtilis] Identities = 120/267 (44%), Positives = 174/267 (64%), Gaps = 3/267 (1%) Query: 13 RVAIIANGKYQSKRVASKLFAAFKHDPDFYLSKKDPDIVISIGGDGMLLSAFHMYEKQLD 72 - + A+ + G S + SK+ A+ D D L + +P+IVIS+GGDG LL AFH Y +LD Sbjct: 2 KFAVSSKGDQVSDTLKSKI-QAYLLDFDMELDENEPEIVISVGGDGTLLYAFHRYSDRLD 60 Query: 73 KVRFVGVHTGHLGFYTDYRDFEVDTLINNLKNDKGEQISYPILKVTITL-EDGRVIRARA 131- K FVGVHTGHLGFY D+ E++ L+ + + YP+L+V +T E+ R R A Sbjct: 61 KTAFVGVHTGHLGFYADWVPHEIEKLVLAIAKTPYHTVEYPLLEVIVTYHENEREERYLA 120- Query: 132 LNESTIKRIEKTMVADVVINQVVFERFRGDGILVSTPTGSTAYNKSLGGAVLHPTIEALQ 19- 1 LNE TIK IE ++VADV I +FE FRGDG+ +STP+GSTAYNK+LGGA++HP+I A+Q Sbjct: 121 LNECTIKSIEGSLVADVEIKGQLFETFRGDGLCLSTPSGSTAYNKALGGAIIHPSIRAIQ 18- 0 Query: 192 LTEISSLNNRVYRTLGSSVIIPKKDAIEIVPKRVGVYTISIDNKTVHYKNVTKIEYSIDE 25- 1 L E++S+NNRV+RT+GS +++P I P+ + ++ID+ T+ +K+V I + Sbjct: 181 LAEMASINNRVFRTVGSPLLLPSHHDCMIKPRNEVDFQVTIDHLTLLHKDVKSIRCQVAS 24- 0 Query: 252 KSINFVSTPSHTSFWERVNDAFIGEPE 278 + + F FW+RV D+FIG+ E Sbjct: 241 EKVRFARFRPF-PFWKRVQDSEIGKGE 266 A related sequence was also identified in GAS <SEQ ID 9137> which encodes the amino acid sequence <SEQ ID 9138>. Analysis of this protein sequence reveals the following: TABLE-US-05156 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2190 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 155-157 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05157 Identities = 232/276 (84%), Positives = 257/276 (93%) Query: 1 MMTQMNFTDRATRVAIIANGKYQSRRVASKLFAAFKHDPDFYLSKKDPDIVISIGGDGML 60 +MTQMN+T + RVAIIANGKYQSKRVASKLF+ FK DPDFYLSKK+PDIVISIGGDGML Sbjct: 1 VNTQMNYTGKVKRVAIIANGKYQSKRVASKLFSVFKDDPDFYLSKKNPDIVISIGGDGML 60 Query: 61 LSAFHMYEKQLDKVRFVGVHTGHLGFYTDYRDFEVDTLINNLKNDKGEQISYPILKVTIT 120- LSAFHMYEK+LDKVRFVG+HTGHLGFYTDYRDFEVD LI+NL+ DKGEQISYPILKV IT Sbjct: 61 LSAFHMYEKELDKVRFVGIHTGHLGFYTDYRDFEVDKLIDNLRKDKGEQISYPILKVAIT 120- Query: 121 LEDGRVIRARALNESTIKRIEKTMVADVVINQVVFERFRGDGILVSTPTGSTAYNKSLGG 18- 0 L+DGRV++ARALNE+T+KRIEKTMVADV+IN V FE FRGDGI VSTPTGSTAYNKSLGG Sbjct: 121 LDDGRVVKARALNEATVKRIEKTMVADVIINHVKFESFRGDGISVSTPTGSTAYNKSLGG 18- 0 Query: 181 AVLHPTIEALQLTEISSLNNRVYRTLGSSVIIPKKDAIEIVPKRVGVYTISIDNKTVHYK 24- 0 AVLHPTIEALQLTEISSLNNRV+RTLGSS+IIPKKD IE+VPKR+G+YTISIDNKT K Sbjct: 181 AVLHPTIEALQLTEISSLNNRVFRTLGSSIIIPKKDKIELVPKRLGIYTISIDNKTYQLK 24- 0 Query: 241 NVTKIEYSIDEKSINFVSTPSHTSFWERVNDAFIGE 276 NVTK+EY ID++ I+FVS+PSHTSFWERV DAFIGE Sbjct: 241 NVTKVEYFIDDEKIHFVSSPSHTSFNERVKDAFIGE 276 A related GBS gene <SEQ ID 8879> and protein <SEQ ID 8880> were also identified. Analysis of this protein sequence reveals an RGD motif at residues 159-161. The protein has homology with the following sequences in the databases: ##STR00116## A related DNA sequence was identified in S. pyogenes <SEQ ID 5251> which encodes the amino acid sequence <SEQ ID 5252>. Analysis of this protein sequence reveals the following: TABLE-US-05158 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2190 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS sequences follows: TABLE-US-05159 Score = 481 bits (1224), Expect = e-138 Identities = 233/276 (84%), Positives = 257/276 (92%) Query: 1 VMTQMNYTGKVKRVAIIANGKYQSKRVASKLFSVFKDDPDFYLSKRNPDIVISIGGDGML 60 VMTQMN+T + RVAIIANGKYQSKRVASKLF+ FR DFDFYLSKK+PDIVISIGGDGML Sbjct: 1 VMTQMNFTDRATRVAIIANGKYQSKRVASKLFAAFKHDPDFYLSKKDPDIVISIGGDGML 60 Query: 61 LSAFHMYEKELDKVRFVGIHTGHLGFYTDYRDFEVDKLIDNLRKDKGEQISYPILKVAIT 120- LSAFHMYEK+LDKVRFVG+HTGHLGFYTDYRDFEVD LI+NL+ DKGEQISYPILKV IT Sbjct: 61 LSAFHMYEKQLDKVRFVGVHTGHLGFYTDYRDFEVDTLINNLKNDKGEQISYPILKVTIT 120- Query: 121 LDDGRVVKARALNEATVKRIEKTMVADVIINHVEFESFRGDGISVSTPTGSTAYNKSLGG 18- 0 L+DGRV++ARALNE+T+KRIEKTMVADV+IN V FE FRGDGI VSTPTGSTAYNKSLGG Sbjct: 121 LEDGRVIRARALNESTIKRIEKTMVADVVINQVVFERFRGDGILVSTPTGSTAYNKSLGG 18- 0 Query: 181 AVLHPTIEALQLTEISSLNNRVFRTLGSSIIIPKKDKIELVPKRLGIYTISIDNKTYQLK 24- 0 AVLHPTIEALQLTEISSLNNRV+RTLGSS+IIPKKD IE+VPKR+G+YTISIDNKT K Sbjct: 181 AVLHPTIEALQLTEISSLNNRVYRTLGSSVIIPKKDAIEIVPKRVGVYTISIDNKTVHYK 24- 0 Query: 241 NVTKVEYFIDDEKIHFVSSPSHTSFWERVKDAFIGE 276 NVTK+EY ID++ I+FVS+PSHTSFWERV DAFIGE Sbjct: 241 NVTKIEYSIDEKSINFVSTPSHTSFWERVNDAFIGE 276 SEQ ID 8880 (GBS308) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 57 (lane 4; MW 34 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 77 (lane 3; MW 59 kDa). GBS308-GST was purified as shown in FIG. 226, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1692 A DNA sequence (GBSx1796) was identified in S. agalactiae <SEQ ID 5253> which encodes the amino acid sequence <SEQ ID 5254>. This protein is predicted to be permease. Analysis of this protein sequence reveals the following: TABLE-US-05160 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3653 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05161 >GP:BAB06568 GB:AP001516 GTP pyrophosphokinase [Bacillus halodurans] Identities = 115/208 (55%), Positives = 159/208 (76%), Gaps = 3/208 (1%) Query: 4 DWETFLDPYIQTVGELKIKLRGIRKQFRKQNRHSPIEFVTGRVKSVESIQEKMVLRGISE 63 +W+ FL PY Q V ELK+KL+GIR+Q++K ++H+PIEFVTGRVK + SI +K + + I Sbjct: 3 NWDVFLTPYKQAVEELKVKLKGIREQYQKSSKHTPIEFVTGRVKPISSILDKAIRKNIPL 62 Query: 64 ENLAQDLQDIAGLRIMVQFVDDVDEVLALLRKRHDMTVVQERDYITHMKSSGYRSYHVVV 123- + L + +QD+AGLRI+ QFV+D++ V+ L+R R D +V+ERDY+ K SGYRSYH+V+ Sbjct: 63 DQLEEKMQDLAGLRIVTQFVEDIETVVQLIRSRSDFEIVEERDYVEQKKDSGYRSYHLVL 122- Query: 124 EYPVDTIDGQKKVLAEIQIRTLAMNFWATIEHSLNYKYQGDFPEEIKQRLEKTAKIALEL 18- 3 YPV TI+G+K++L E+QIRTLAMNFWATIEHSLNYKY G+ P IK RL++ A+ A L Sbjct: 123 RYPVQTIEGEKRILVELQIRTLAMNFWATIEHSLNYKYSGEIPLNIKTRLQRAAEAAFRL 18- 2 Query: 184 DEEMRKIREDIREAQLLFDPLNRKLSDG 211 DEEM +IR+++REAQ + + RK G Sbjct: 183 DEEMSQIRDEVREAQQI---ITRKQEQG 207 A related DNA sequence was identified in S. pyogenes <SEQ ID 5255> which encodes the amino acid sequence <SEQ ID 5256>. Analysis of this protein sequence reveals the following:

TABLE-US-05162 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4064 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05163 Identities = 196/223 (87%), Positives = 213/223 (94%) Query: 1 MSMDWETFLDPYIQTVGELKIKLRGIRKQFRKQNRHSPIEFVTGRVKSVESIQEKMVLRG 60 M++DWE FLDPYIQTVGELKIRLRGIRKQ+RKQNR+SPIEFVTGRVKS+ESI+EKM+LRG Sbjct: 1 MTLDWEEFLDPYIQTVGELKIKLRGIRKQYRKQNRYSPIEFVTGRVKSIESIKEKMILRG 60 Query: 61 ISEENLAQDLQDIAGLRIMVQFVDDVDEVLALLRKRHDMTVVQERDYITHMKSSGYRSYH 120- + EEN+AQD+QDIAGLRIMVQFVDDV+EVLALLR+R DMT+V ERDYI +MKSSGYRSYH Sbjct: 61 VIEENIAQDIQDIAGLRIMVQFVDDVEEVLALLRQRQDMTIVYERDYIRNMKSSGYRSYH 120- Query: 121 VVVEYPVDTIDGQKKVLAEIQIRTLAMNFWATIEHSLNYKYQGDFPEEIKQRLEKTAKIA 18- 0 VVVEYPVDTI+GQKKVLAEIQIRTLAMNFWATIEHSLNYKY GDFPEEIK+RLE TAKIA Sbjct: 121 VVVEYPVDTIEGQKKVLAEIQIRTLAMNFWATIEHSLNYKYGGDFPEEIKKRLEVTAKIA 18- 0 Query: 181 LELDEEMRKIREDIREAQLLFDPLNRKLSDGVGNSDDTDEFYR 223 LELDEEMRKIREDIREAQLLFDP+ R LSDGVGNSDDTDE YR Sbjct: 181 LELDEEMRKIREDIREAQLLFDPVTRNLSDGVGNSDDTDELYR 223 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1693 A DNA sequence (GBSx1797) was identified in S. agalactiae <SEQ ID 5257> which encodes the amino acid sequence <SEQ ID 5258>. Analysis of this protein sequence reveals the following: TABLE-US-05164 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2266 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05165 >GP:CAB13015 GB:Z99110 yjbK [Bacillus subtilis] Identities = 63/184 (34%), Positives = 99/184 (53%), Gaps = 10/184 (5%) Query: 4 LEIEYKTLLNKDEFNRLTSLFSHVQP--ITQTNYYFDTETFEMKAHRMSLRIRTLPNRAE 61 +EIE+K +L K EF + S + Q N+YFDT++F +K +LRIR + Sbjct: 5 IEIEFKNMLTKQEFKNIASALQLTEKDFTDQKNHYFDTDSFALKQKHAALRIRRKNGKYV 64 Query: 62 LTLKIPREVGNLEHNHDLT--LEEAKYIVKNGQFPEDTEIASLILEKGVDPTKLAVFGQL 119- LTLK P +VG LE + L+ + A + V G P ++ L +D + FG L Sbjct: 65 LTLKEPADVGLLETHQQLSEVSDLAGFSVPEG--PVKDQLHKL----QIDTDAIQYFGSL 118- Query: 120 TTTRREMETSIGLMALDSNIYADIKDYELELEVKQPKQGKRDFDQFLKENNINFKYAKSK 17- 9 T R E ET GL+ LD + Y + +DYE+E E +G++ F++ L++ +I + K+K Sbjct: 119 ATNRAEKETEKGLIVLDHSRYLNKEDYEIEFEAADWHEGRQAFEKLLQQFSIPQRETKNK 17- 8 Query: 180 VARF 183 + RF Sbjct: 179 ILRF 182 A related DNA sequence was identified in S. pyogenes <SEQ ID 5259> which encodes the amino acid sequence <SEQ ID 5260>. Analysis of this protein sequence reveals the following: TABLE-US-05166 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3470 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05167 Identities = 114/188 (60%), Positives = 139/188 (73%), Gaps = 1/188 (0%) Query: 1 MTHLEIEYKTLLNKDEFNRLTSLFSHVQPITQTNYYFDTETFEMKAHRMSLRIRTLPNRA 60 MT+LEIEYKTLL K+E+NRL S HV P+TQTNYY DT+ F++KA++MSLRIRT N A Sbjct: 1 MTNLEIEYKTLLTKNEYNRLLSQMKHVTPVTQTNYYIDTKAFDLKANKMSLRIRTFVNSA 60 Query: 61 ELTLKIPREVGNLEHNHDLTLEEAKYIVKNGQFPEDTEIASLILEKGVDPTKLAVFGQLT 120- ELTLK+P +VGN E+N L LE+AK ++K+G PE T + +I+ KG+ P+ L FG LT Sbjct: 61 ELTLKVPEKVGNREYNVPLFLEQAKDMIKHGNLPESTAL-DIIISKGIKPSALVTFGNLT 119- Query: 121 TTRREMETSIGLMALDSNIYADIKDYELELEVKQPKQGKRDFDQFLKENNINFKYAKSKV 18- 0 T RRE IG +ALD N+YA+ KDYELELEV QGK DFD FL E +I FKYAKSKV Sbjct: 120 TVRRETVIPIGKLALDYNLYANTKDYELELEVSDALQGKIDFDSFLSEYHITFKYAKSKV 17- 9 Query: 181 ARFSATLK 188 AR TLK Sbjct: 180 ARCINTLK 187 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1694 A DNA sequence (GBSx1798) was identified in S. agalactiae <SEQ ID 5261> which encodes the amino acid sequence <SEQ ID 5262>. Analysis of this protein sequence reveals the following: TABLE-US-05168 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ---- bacterial cytoplasm --- Certainty = 0.1815 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1695 A DNA sequence (GBSx1799) was identified in S. agalactiae <SEQ ID 5263> which encodes the amino acid sequence <SEQ ID 5264>. Analysis of this protein sequence reveals the following: TABLE-US-05169 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0621 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1696 A DNA sequence (GBSx1800) was identified in S. agalactiae <SEQ ID 5265> which encodes the amino acid sequence <SEQ ID 5266>. This protein is predicted to be ribose-phosphate pyrophosphokinase (prsA). Analysis of this protein sequence reveals the following: TABLE-US-05170 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3369 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05171 >GP:CAB11827 GB:Z99104 phosphoribosyl pyrophosphate synthetase [Bacillus subtilis] Identities = 166/319 (52%), Positives = 231/319 (72%), Gaps = 4/319 (1%) Query: 1 MAEQYADKQIKLFSLTANREIAEKISQASGIPLGKMSSRQFSDGEIMINIEETVRGDDIY 60 M+ QY DK +K+FSL +N E+A++I+ G+ LGK S +FSDGE+ INIEE++RG D Y Sbjct: 1 MSNQYGDKNLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCY 60 Query: 61 IIQSTSFPVNDNLWELLIMIDACKRASANTVNIVVPYFGYSRQDRIAASREPITAKLVAN 120- IIQSTS PVN+++ ELLIM+DA KRASA T+NIV+PY+GY+RQDR A SREPITAKL AN Sbjct: 61 IIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFAN 120- Query: 121 MLVKAGVDRVLTLDLHAVQVQGFFDIPVDNLFTVPLFAEHYNQLGLSGEDVVVVSPKNSG 18- 0 +L AG RV+ LDLHA Q+QGFFDIP+D+L VP+ E++ G + ED+V+VSP + G Sbjct: 121 LLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFE--GKNLEDIVIVSPDHGG 17- 8 Query: 181 IKRARSLAEYLDSPIAIIDYAQD-DSEREEGYIIGEVEGKKAIIIDDILNTGKTFAEAAK 23- 9 + RAR LA+ L +PIAIID + + E I+G +EGK AI+IDDI++T T AA Sbjct: 179 VTRARKLADRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAAN 23- 8 Query: 240 ILERGGATEIYAVASHGLFAGGAADILESAPIREIIVTDSV-LSKERIPSNIKYLTASHL 29- 8 L GA E+YA +H + +G A + + ++ I+E++VT+S+ L +E+ K L+ L Sbjct: 239 ALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPL 29- 8 Query: 299 IADAIIRIHERKPLSPLFS 317 +A+AIIR+HE++ +S LFS Sbjct: 299 LAEAIIRVHEQQSVSYLFS 317 A related DNA sequence was identified in S. pyogenes <SEQ ID 5267> which encodes the amino acid sequence <SEQ ID 5268>. Analysis of this protein sequence reveals the following: TABLE-US-05172 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1830 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05173 Identities = 278/324 (85%), Positives = 305/324 (93%) Query: 1 MAEQYADKQIKLFSLTANREIAEKISQASGIPLGKNSSRQFSDGEIMINIEETVRGDDIY 60 M E+YADKQIKLFSLT+N IAEKI++A+GIPLGKMSSRQFS+GEIMINIEETVRGDDIY Sbjct: 1 MTERYADKQIKLFSLTSNLPIAEKIAKAAGIPLGKMSSRQFSNGEIMINIEETVRGDDIY 60 Query: 61 IIQSTSFPVNDNLWELLINIDACKRASANTVNIVVPYFGYSRQDRIAASREPITAKLVAN 120- IIQSTSFPVNDNLWELLIMIDACKRASANTVNIV+PYFGYSRQDR+A REPITAKLVAN Sbjct: 61 IIQSTSFPVNDNLWELLIMIDACKRASANTVNIVLPYFGYSRQDRVAKPREPITAKLVAN 120- Query: 121 MLVKAGVDRVLTLDLHAVQVQGFFDIPVDNLFTVPLFAEHYNQLGLSGEDVVVVSPKNSG 18- 0 ML KAG+DRV+TLDLHAVQVQGFFDIPVDNLFTVPLFAE Y++LGLSG DVVVVSPKNSG Sbjct: 121 MLTKAGIDRVVTLDLHAVQVQGFFDIPVDNLFTVPLFAERYSKLGLSGSDVVVVSPKNSG 18- 0 Query: 181 IKRARSLAEYLDSPIAIIDYAQDDSEREEGYIIGEVEGKKAIIIDDILNTGKTFAEAAKI 24- 0 IKRARSLAEYLDSPIAIIDYAQDDSERE+GYIIG+V GKKAI+IDDILNTGKTFAEAAKI Sbjct: 181 IKRARSLAEYLDSPIAIIDYAQDDSEREQGYIIGDVSGKKAILIDDILNTGKTFAEAAKI 24- 0 Query: 241 LERGGATEIYAVASHGLFAGGAADILESAFIREIIVTDSVLSKERIPSNIKYLTASHLIA 30- 0 LER GAT+ YAVASHGLFAGGAAD+LE+API+EIIVTDSV +K R+P N+ YL+AS LIA Sbjct: 241 LERSGATDTYAVASHGLFAGGAADVLETAPIKEIIVTDSVKTKNRVPENVTYLSASDLIA 30- 0 Query: 301 DAIIRIHERKPLSPLFSYRSDKED 324 +AIIRIHER+PLSPLFSY+ K+ Sbjct: 301 EAIIRIHERRPLSPLFSYQPKGKN 324 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1697 A DNA sequence (GBSx1801) was identified in S. agalactiae <SEQ ID 5269> which encodes the amino acid sequence <SEQ ID 5270>. This protein is predicted to be Fe--S cluster formation protein. Analysis of this protein sequence reveals the following: TABLE-US-05174 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1981 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05175 >GP:BAB04979 GB:AP001511 Fe--S cluster formation protein [Bacillus halodurans] Identities = 174/373 (46%), Positives = 237/373 (62%), Gaps = 6/373 (1%) Query: 3 IYLDNAATTALTPSVIEKMTNVMTSHYGNPSSIHTFGRQANQLLRECRQIIAEYLNVNSR 62 IYLD+AAT+ + P VI+M +GNPSSIH FGR+A Q + E R IA L + Sbjct: 4 IYLDHAATSPVHPEVIQAMLPYYEEQFGNPSSIHQFGRRARQGVDEARGTIARLLQADPS 63 Query: 63 EIIFTSGGTESNNTAIKGYALANQLKGKHIITSEIEHHSVLHTMTYLSSRFGFDITYLKP 122- E IFTSGGTE++N AI GYA ++ KG HIITS++EHH+VLH L E GF++TY+ Sbjct: 64 EFIFTSGGTEADNLAIFGYAYQHRGKGNHIITSQVEHHAVLHACQEL-EHQGFEVTYVPV 122- Query: 123 NH-GQITAKDVQEALRDDTIMVSLMFVNNETGDFLPIQEIGQLLRNHQAVFHVDAVQVFS 18- 1 + G+++ +DV++ALRDDTI+V+LM+ NNE G PI EIG LL++HQAV H DAVQ F Sbjct: 123 DQTGRVSVEDVRQALRDDTILVTLMYGNNEVGTIQPIAEIGALLQDHQAVLHTDAVQAFG 18- 2 Query: 182 KMELDPHSLGIDFLAASAHKFHGPKGVGILYCAPH-HFDSLLHGGDQEEKRRASTENIIG 24- 0 + ++ L +D L+ SAHK +GPKGVG+LY L+GG+QE K+RA TEN+ Sbjct: 183 AISIELDHLPVDMLSVSAHKINGPKGVGLLYVRDGIVLKPALYGGEQERKKRAGTENVAA 24- 2 Query: 241 IAGMSQALTDATTNTLKNWTHISQLRTTFLDAISD--LDFYLNNGQDC-LPHVLNIGFPG 29- 7 I G ++A+ A N + TF D +F+N Q LPH+ N +FPG Sbjct: 243 IIGFAKAVEIAIANREERQKAYFDYCQTFFDQFQQEGVQFVMNGHQTWRLPHIFNVSFPG 30- 2 Query: 298 QNNGLLLTQLDLAGFAVSTGSACTAGTVEPSHVLTSLYGANSPRLNESIRISFSELNTQE 35- 7 + LL LDLAG A S+GSACTAG++EPSHVL +++G++S + + R SF NT+E Sbjct: 303 VHVEALLVNLDLAGIAASSGSACTAGSIEPSHVLVAHHGSDSELVTSGVRFSFGLGNTKE 36- 2 Query: 358 EILELAKTLRKII 370 + AK KI+ Sbjct: 363 HVQWAAKETAKIV 375 A related DNA sequence was identified in S. pyogenes <SEQ ID 5271> which encodes the amino acid sequence <SEQ ID 5272>. Analysis of this protein sequence reveals the following: TABLE-US-05176 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1477 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05177 Identities = 235/370 (63%), Positives = 285/370 (76%) Query: 2 MIYLDNAATTALTPSVIEKMTNVMTSNYGNPSSIHTFGRQANQLLRECRQIIAEYLNVNS 61 M Y DNAATT L+P+VI MT M N+GNPSSIH +GR+AN++LRECRQ IA L + Sbjct: 1 MTYFDNAATTPLSPNVIRAMTAAMQDNFGNPSSIHFYGRRANKILRECRQAIARNLGASE 60 Query: 62 REIIFTSGGTESNNTAIKGYALANQLKGKHIITSEIEHHSVLHTMTYLSERFGWDITYLK 121- ++II TSGGTESMN AIKGYALA+Q KGKH+IT+ IEHHSVLHTM YL ERFGF++TYL Sbjct: 61 QQIIVTSGGTESNNMAIKGYALAHQAKGKHLITTTIEHHSVLHTMAYLEERFGFEVTYLP 120- Query: 122 PNHGQITAKDVQEALRDDTIMVSLMFVHNETGDFLPIQEIGQLLRNHQAVFHVDAVQVFS 18- 1 +GQI D+++ALRDDTI+VS+M+ NNETGD LPI++IG LL++HQA FHVDAVQ Sbjct: 121 CQNGQINLSDLKQALRDDTILVSIMYANNETGDLLPIKDIGNLLKDHQAAFHVDAVQAVG 18- 0 Query: 182 KMELDFHSLGIDFLAASAHKFHGPKGVGILYCAPHHFDSLLHGGDQEEKRRASTENIIGI K+++ P LGIDFL+ASAHKFHGPKG G LY D LLHGGDQE KRRASTEH++GI Sbjct: 181 KLKIIPSELGIDFLSASAHKFHGPKGCGFLYSNGQPIDPLLHGGDQEGKRRASTENMLGI 24- 0 Query: 242 AGMSQALTDATTNTLKNWTHISQLRTTFLDAISDLDFYLNNGQDCLPHVLHIGFPGQNNG 30- 1 GM+QALTDA T ++ HI LR + + L +Y+N G LPHVLNIGF G N Sbjct: 241 IGMAQALTDANTCLDQSTDHIISLRHHLISLLEGLPYYINQGTHYLPHVLNIGFLGYQNT 30- 0 Query: 302 LLLTQLDLAGFAVSTGSACTAGTVEPSHVLTSLYGANSPRLNESIRISFSELNTQEEILE 36- 1 +LLTQLDLAG AVSTGSACTAG V PSHVL + YG +S RL ESIRISFS+ N+ E++ + Sbjct: 301 ILLTQLDLAGIAVSTGSACTAGAVNPSHVLAAYYGDDSSRLKESIRISFSDQNSIEDVNQ 36- 0 Query: 362 LAKTLRKIIG 371 LA+TL+ I+G Sbjct: 361 LAQTLKNILG 370 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1698 A DNA sequence (GBSx1802) was identified in S. agalactiae <SEQ ID 5273> which encodes the amino acid sequence <SEQ ID 5274>. Analysis of this protein sequence reveals the following: TABLE-US-05178 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2753(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05179 >GP:CAB12416 GB:Z99107 ydiH [Bacillus subtilis] Identities = 96/202 (47%), Positives = 140/202 (68%), Gaps = 4/202 (1%) Query: 7 IPKATAKRLSLYYRIFKRFNTDGIEKASSKQIADALGIDSATVRRDFSYFGELGRRGFGY 66 IP+ATAKRL LYYR K + G ++ SS +++DA+ + DSAT+RRDFSYFG LG++G+GY Sbjct: 8 IPQATAKRLPLYYRFLKNLHASGKQRVSSAELSDAVKVDSATIRRDFSYFGALGKKGYGY 67 Query: 67 DVKKLMNFFAEILNDHSTTNVMLVGCGNIGRALLHYRFHDRNKNQISHAFDLDSNDLVGK 126- +V L++FF + L+ T+V+L+G GN+G A LHY F N +ISMAFD++ + + Sbjct: 68 NVDYLLSFFRKTLDQDEMTDVILIGVGNLGTAFLHYNFTKNNNTKISMAFDINESKI--G 125- Query: 127 TTEDGIPVYGISTINDHLIDSDIETAILTVPSTEAQEVADILVKAGIKGILSFSPVHLTL 18- 6 T G+PVY + + H+ D + AILTVP+ AQ + D LV GIKGIL+ F+P L + Sbjct: 126 TEVGGVPVYNLDDLEQHVKDESV--AILTVPAVAAQSITDRLVALGIKGILNFTPARLNV 18- 3 Query: 187 PKDIIVQYVDLTSELQTLLYFM 208 P+ I + ++DL ELQ+L+YF+ Sbjct: 184 PEHIRIHHIDLAVELQSLVYFL 205 A related DNA sequence was identified in S. pyogenes <SEQ ID 5275> which encodes the amino acid sequence <SEQ ID 5276>. Analysis of this protein sequence reveals the following: TABLE-US-05180 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2313 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05181 Identities = 167/210 (79%), Positives = 189/210 (89%) Query: 1 MINDKSIPKATAKRLSLYYRIFRRFNTDGIEKASSKQIADALGIDSATVRRDFSYFGELG 60 +++DKSIPKATAKRLSLYYRIFKRF+ D +EKASSKQIADA+GIDSATVRRDFSYFGELG Sbjct: 1 VVIDKSIPKATAKRLSLYYRIFKRFHADQVEKASSKQIADAMGIDSATVRRDFSYFGELG 60 Query: 61 RRGFGYDVKKLMNFFAEILNDHSTTNVMLVGCGNIGRALLHYRFHDRNKMQISMAFDLDS 120- RRGFGYDV KLMNFFA++LNDHSTTNV+LVGCGNIGRALLHYRFHDRNKMQI+M FD D Sbjct: 61 RRGFGYDVTKLMNEFADLLNDHSTTNVILVGCGNIGRALLHYRFHDRNKMQIAMGFDTDD 120- Query: 121 NDLVGKTTEDGIPVYGISTINDHLIDSDIETAILTVPSTEAQEVADILVKAGIKGILSFS 18- 0 N LVG T D IPV+GIS++ + + ++DIETAILTVPS AQEV D L++AGIKGILSF+ Sbjct: 121 NALVGTKTADNIPVHGISSVKERIANTDIETAILTVPSIHAQEVTDQLIEAGIKGILSWA 18- 0 Query: 181 PVHLTLPKDIIVQYVDLTSELQTLLYFMNQ 210 PVNL +PK +IVQ VDLTSELQTLLYFMNQ Sbjct: 181 PVNLQVPKGVIVQSVDLTSELQTLLYFMNQ 210 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1699 A DNA sequence (GBSx1803) was identified in S. agalactiae <SEQ ID 5277> which encodes the amino acid sequence <SEQ ID 5278>. Analysis of this protein sequence reveals the following:

TABLE-US-05182 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2966 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9847> which encodes amino acid sequence <SEQ ID 9848> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05183 >GP:CAB14764 GB:Z99118 similar to DNA repair protein [Bacillus subtilis] Identities = 90/210 (42%), Positives = 136/210 (63%) Query: 24 PRERLVDLGADRLSNQELLAILLRTGIKEKPVLEISTQILENISSLADWGQLSLQELQSI 83 - PRERL+ +GA+ L+N ELLAILLRTG K + VL++S ++L + L + S++EL SI Sbjct: 19 PRERLLKVGAENLANHELLAILLRTGTKHESVLDLSNRLLRSFDGLRLLKEASVEELSSI 78 Query: 84 KGIGQVKSVEIKAMLELAKRIHKAEYDRKEQILSSEQLARKMNLELGDKKQEHLVAIYMD 143- GIG VK+++I A +EL RIHK + I S E A +M ++ QEH V +Y++ Sbjct: 79 PGIGMVKAIQILAAVELGSRIHKLANEEHFVIRSPEDGANLVMEDMRFLTQEHFVCLYLN 138- Query: 144 TQNRIIEQRTIFIGTVRRSVAEPREILHYACKNMATSLIIIHNHPSGSPKPSESDLSFTK 20- 3 T+N++I +RT+FIG++ S+ PRE+ A K A S I +HNHPSG P PS D+ T+ Sbjct: 139 TKNQVIHKRTVFIGSLNSSIVHPREVFKEAFKRSAASFICVHNHPSGDPTPSREDIEVTR 19- 8 Query: 204 KIKRSCDHLGIVCLDHIIVGKNKYYSFREE 233 ++ + +GI LDH+++G K+ S +E+ Sbjct: 199 RLFECGNLIGIELLDHLVIGDKKFVSLKEK 228 A related DNA sequence was identified in S. pyogenes <SEQ ID 5279> which encodes the amino acid sequence <SEQ ID 5280>. Analysis of this protein sequence reveals the following: TABLE-US-05184 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3307 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05185 Identities = 145/225 (64%), Positives = 182/225 (80%) Query: 12 MYHIELKKEALLPRERLVDLGADRLSNQELLAILLRTGIKEKPVLEISTQILENISSLAD 71 - MY I+ +PRERL+ LGA LSNQELLAILLRTG KEK VLE+S+ +L ++ SLAD Sbjct: 1 MYSIKCDDNKAMPRERLMRLGAESLSNQELLAILLRTGNKEKEVLELSSYLLSHLDSLAD 60 Query: 72 FGQLSLQELQSIKGIGQVKSVEIKAMLELAKRIHKAEYDRKEQILSSEQLARKMMLELGD 131- F ++SLQELQ + GIG+VK++EIKAM+EL RI + + +L+S Q+A KMM LGD Sbjct: 61 FKKMSLQELQHLAGIGKVKAIEIKAMIELVSRILATDKTLTDSVLTSVQVAEKMMAALGD 120- Query: 132 KKQEHLVAIYMDTQNRIIEQRTIFIGTVRRSVAEPREILHYACKNMATSLIIIHNHPSGS 19- 1 KKQEELV +Y+D QNRIIE++TIFIGTVRRS+AEPREIL+YACKNMATSLI+IHNHPSG+ Sbjct: 121 KKQEHLVVLYLDNQNRIIEEKTIFIGTVRRSLAEPREILYYACKNMATSLIVIHNHPSGN 18- 0 Query: 192 PKPSESDLSFTKKIKRSCDHLGIVCLDHIIVGKNKYYSFREEADI 236 +PS +D FT+KIKRSC+ LGI+CLDHIIV YYSFRE++ + Sbjct: 181 IEPSSNDYGFTEKIKRSCEDLGIICLDHIIVSYKDYYSFREKSTL 225 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1700 A DNA sequence (GBSx1804) was identified in S. agalactiae <SEQ ID 5281> which encodes the amino acid sequence <SEQ ID 5282>. This protein is predicted to be a permease. Analysis of this protein sequence reveals the following: TABLE-US-05186 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.86 Transmembrane 258-274 (255-290) INTEGRAL Likelihood = -7.32 Transmembrane 89-105 (79-109) INTEGRAL Likelihood = -4.88 Transmembrane 176-192 (170-194) INTEGRAL Likelihood = -4.78 Transmembrane 339-355 (326-359) INTEGRAL Likelihood = -4.57 Transmembrane 237-253 (236-257) INTEGRAL Likelihood = -3.98 Transmembrane 39-55 (38-59) INTEGRAL Likelihood = -3.40 Transmembrane 292-308 (282-308) INTEGRAL Likelihood = -1.38 Transmembrane 317-333 (317-333) INTEGRAL Likelihood = -0.27 Transmembrane 8-24 (8-24) ----- Final Results ----- bacterial membrane --- Certainty = 0.4142 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05187 >GP:AAC05771 GB:AF051356 putative permease [Streptococcus mutans] Identities = 88/366 (24%), Positives = 175/366 (47%), Gaps = 27/366 (7%) Query: 3 FEKRQVYYVVITFAICYAIQAYW---GAVSNILTTLHKAIF-PFLNGAGIAYIINIVMSV 58 F+ ++++ + + I W G++ N ++ K F PFL+G + YI N+++ Sbjct: 2 FKSSKLFFWTVEILLVTLILFIWRQMGSIFNPFFSVAKTFFLPFLLGGFLYYITNPIVTF 61 Query: 59 YERLYIKLFKGSRLLMAIKRSVSMILSYATFIGLIVWLFSIVIPDLISSLSSLLVIDTGA 118- E + IKR + L +A + L+V+ + +IP+LI+ L+ L+ Sbjct: 62 LENRF-----------KIKRIWGITLIFAVLLSLLVFSITSLIPNLINQLTDLISASQNI 110- Query: 119 LAKLVNNLNENKQISEVLNYMGTDKDLVSTLSGYSQQILKQVLSVLTNLLTSVSSIAATL 17- 8 L + NE K N D+ L ++ + + +VL ++ SVSSI + Sbjct: 111 YVGLQDLFNEWKSNPAFKNI-----DIPVLLKQFNLSYVDILTNVLDSVTVSVSSIVYMI 16- 5 Query: 179 LNVFVSFIFS----IYVLANKEQLGRQFNLLIDTYLGSTGKTFHYVRNILHQRFHGFFVS 23- 4 N + + + Y+L +K+ L +L T L + + + +++ + Sbjct: 166 TNTVMILVLTPVILFYLLKDKDGL---MPMLDRTILKNDRHNISQLLNQMNKTISRYISG 22- 2 Query: 235 QTLEANILGSLTVIGMLIFQFPYALTVGVLVAFTALIPVVGAYIGVTIGFILIATESLTE 29- 4 ++A + +IG I YA ++ T +IP VG Y+G+T + + Sbjct: 223 VAIDAAFIFVFALIGYQIMGVQYAFLFALVAGITNVIPYVGPYLGLTPVVLAYVVSDPKK 28- 2 Query: 295 AFLFVLFLILLQQFEGNVIYPKVVGGSIGLPSMWVLMAITIGGALWGILGNLLAVPVAAT 35- 4 + +++++ LQQ +GN++YP+VVG ++ + + +++ + +GG + G++GML+AVP A Sbjct: 283 MIIAIIYIMTLQQIDGNIVYPRVVGSTMKIHPLTINVLLVLGGNIAGLVGMLVAVPAYAI 34- 2 Query: 355 IYQIVK 360 I +IVK Sbjct: 343 IKEIVK 348 A related DNA sequence was identified in S. pyogenes <SEQ ID 5283> which encodes the amino acid sequence <SEQ ID 5284>. Analysis of this protein sequence reveals the following: TABLE-US-05188 Possible site: 55 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.70 Transmembrane 87-103 (83-116) INTEGRAL Likelihood = -7.27 Transmembrane 178-194 (166-202) INTEGRAL Likelihood = -6.74 Transmembrane 278-294 (256-297) INTEGRAL Likelihood = -5.41 Transmembrane 299-315 (295-321) INTEGRAL Likelihood = -4.46 Transmembrane 14-30 (13-32) INTEGRAL Likelihood = -3.56 Transmembrane 340-356 (333-366) INTEGRAL Likelihood = -3.35 Transmembrane 258-274 (256-277) ----- Final Results ----- bacterial membrane --- Certainty = 0.4482 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05189 >GP:AAC05771 GB:AF051356 putative permease [Streptococcus mutans] Identities = 87/373 (23%), Positives = 168/373 (44%), Gaps = 41/373 (10%) Query: 10 FEKKQVFYLVLTFILCYGILANWRNGTAIVTTIYKTS----LPFFYGAAGAYIVNIVMSA 65 - F+ ++F+ + +L IL WR +I + + LPF G YI N +++ Sbjct: 2 FKSSKLFFWTVEILLVTLILFIWRQMGSIFNPFFSVAKTFFLPFLLGGFLYYITNPIVTF 61 Query: 66 YEKVYVYIFKDWSHVLKVRRGICLLLAYLTFFILITWIISIVIPDLITSISTLTKFDT-- 123- E + K+KR + L + L+ + I+ +IP+LI ++ L Sbjct: 62 LENRF-----------KIKRIWGITLIFAVLLSLLVFSITSLIPNLINQLTDLISASQNI 110- Query: 124 -ITIQEVVNNLEHNKLLARTIQYIGGDGKLTETIANYSQQLLKQFLTVLTNILTSVTVIA 18- 2 + +Q++ N + N I +Q ++ +LTN+L SVTV Sbjct: 111 YVGLQDLFNEWKSNPAFKNI------------DIPVLLKQFNLSYVDILTNVLDSVTVSV 15- 8 Query: 183 SAIINLFISFVFSL--------YVLASKEDLCRQGNTLVDTYTGKYAKRIHYLLELLHQR 23- 4 S+I+ + + V L Y+L K+ L L T I LL +++ Sbjct: 159 SSIVYMITNTVMILVLTPVILFYLLKDKDGLHPM---LDRTILKNDRHNISQLLNQMNKT 21- 5 Query: 235 FHGFFVSQTLEAMILGSLTASGMFILRLPFAGTIGVLVAFTALIPVIGASIGAAIGFILI 29- 4 + ++A + G I+ + +A ++ T +IP +G +G + Sbjct: 216 ISRYISGVAIDAAFIFVFALIGYQIMGVQYAFLFALVAGITNVIPYVGPYLGLTPVVLAY 27- 5 Query: 295 MTQSMSQAIIFIIFLIILQQIEGNFIYPKVVGGSIGLPANWVLMAITIGASLKGIVGHII 35- 4 + + II II+++ LQQI+GN +YP+VVG ++ + + +++ + +G ++ G+VGM++ Sbjct: 276 VVSDPKKMIIAIIYIMTLQQIDGNIVYPRVVGSTMKIHPLTIMVLLVLGGNIAGLVGMLV 33- 5 Query: 355 AVPLAATLYQVIK 367 AVP A + +++K Sbjct: 336 AVPAYAIIKEIVK 348 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05190 Identities = 218/370 (58%), Positives = 291/370 (77%) Query: 1 MKFEKRQVYYVVITFAICYAIQAYWGAVSNILTTLHKAIFPFLMGAGIAYIINIVMSVYE 60 MKFEK+QV+Y+V+TF +CY I A W + I+TT++K PF GA AYI+NIVMS YE Sbjct: 8 MKFEKKQVFYLVLTFILCYGILANWRNGTAIVTTIYKTSLPFFYGAAGAYIVNIVMSAYE 67 Query: 61 RLYIKLFKGSRLLMAIKRSVSMILSYATFIGLIVWLFSIVIPDLISSLSSLLVIDTGALA 120- ++Y+ +FK ++ +KR + ++L+Y TF LI W+ SIVIPDLI+S+S+L DT + Sbjct: 68 KVYVYIFKDWSHVLKVKRGICLLLAYLTPFILITWIISIVIPDLITSISTLTKFDTITIQ 127- Query: 121 KLVNNLNENEQISEVLNYMGTDKDLVSTLSGYSQQILKQVLSVLTNLLTSVSSIAATLLN 18- 0 ++VNNL NK ++ + Y+G D L T++ YSQQ+LKQ L+VLTN+LTSV+ IA+ ++N Sbjct: 128 EVVNNLEHNKLLARTIQYIGGDGKLTETIANYSQQLLKQFLTVLTNILTSVTVIASAIIN 18- 7 Query: 181 VFVSFIFSIYVLANKEQLGRQFNLLIDTYLGSTGKTFHYVRHILHQRFHGFFVSQTLEAM 24- 0 +F+SF+FS+YVLA+KE L RQ N L+DTY G K HY+ +LHQRPHGFFVSQTLEAM Sbjct: 188 LFISFVFSLYVLASKEDLCRQGNTLVDTYTGKYAKRIHYLLELLHQRFHGFFVSQTLEAM 24- 7 Query: 241 ILGSLTVIGMLIFQFPYALTVGVLVAFTALIPVVGAYIGVTIGFILIATESLTEAFLFVL 30- 0 ILGSLT GM I + P+A T+GVLVAFTALIPV+GA IG IGFILI T+S+++A +F++ Sbjct: 248 ILGSLTASGMFILRLPFAGTIGVLVAFTALIPVIGASIGAAIGFILIMTQSMSQAIIFII 30- 7 Query: 301 WLILLQQFEGNVIYPKVVGGSIGLPSMWVLMAITIGGALWGILGMLLAVPVAATIYQIVK 36- 0 FLI+LQQ EGN IYPKVVGGSIGLP+MWVLMAITIG +L GI+GM++AVP+AAT+YQ++K Sbjct: 308 FLIILQQIEGNFIYPKVVGGSIGLPANWVLMAITIGASLKGIVGMIIAVPLAATLYQVIK 36- 7 Query: 361 DHIIKRQTLR 370 D+I KRQ ++ Sbjct: 368 DNIQKRQAIQ 377 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1701 A DNA sequence (GBSx1805) was identified in S. agalactiae <SEQ ID 5285> which encodes the amino acid sequence <SEQ ID 5286>. Analysis of this protein sequence reveals the following: TABLE-US-05191 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1081 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9849> which encodes amino acid sequence <SEQ ID 9850> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05192 >GP:AAA69226 GB:U29579 6-phospho-beta-glucosidase [Escherichia coli] Identities = 290/478 (60%), Positives = 369/478 (76%), Gaps = 2/478 (0%) Query: 2 MVKQVFPKGFLWGGATAANQCEGAYNVDGRGLANVDVVPTGEDRFAIISGQKKNFDFESG 61 M VFP+ FLWGGA AANQ EGA+ +GL VD++P GE R A+ G +K F + Sbjct: 1 MKMSVFPESFLWGGALAAWQSEGAFREGDKGLTTVDMIPHGEHRMAVKLGLEKRFQLRDD 60 Query: 62 YFYPARESIDFYHHYKEDLALLAEMGFKTYRNSIAWTRIFPKGDELYPNEAGLQFYENIF 121- FYP+ E+ DFYH YKED+AL+AEMGFK +R SIAW+R+FP+GDE+ PN+ G+ FY ++F Sbjct: 61 EFYPSHEATDFYHRYKEDIALMAEMGFKVFRTSIAWSRLFPQGDEITPNQQGIAFYRSVF 120- Query: 122 KECRKYGIEPLVTITHFDCPIYLIKHYGGWRSRKNIGFYERLVRALFTRFKGLVKYWLTF 18- 1 +EC+KYGIEPLVT+ HFD P++L+ YG WR+RK++ F+ R R F F GLVKYWLTF Sbjct: 121 EECKKYGIEPLVTLCHFDVPNHLVTEYGSWRNRKLVEFFSRYARTCFEAFDGLVKYWLTF 18- 0 Query: 182 NEINMILHAPFMGAGLYFEDGENQEQIKYQAAHHELVASAIAVKIAHEVDPNNQIGCMLA 24- 1 NEIN++LH+PF GAGL FE+GENQ+Q+KYQAAHH+LVASA+A KIAHEV+P NQ+GCMLA Sbjct: 181 NEINIMLHSPFSGAGLVFEEGENQDQVKYQAAHHQLVASALATKIAHEVNPQNQVGCMLA 24- 0 Query: 242 AGQYYPNTCHPQDYWASMQKNRENYFFIDVQARGKYPNYAKKHFEHLGISIQMTAEDLAL 30- 1 G +YP +C P+D WA+++K+REN FFIDVQARG YP Y+ + F G++I D + Sbjct: 241 GGNFYPYSCKPEDVWAALEKDRENLFFIDVQARGTYPAYSARVFREKGVTINKAPGDDEI 30- 0 Query: 302 LRDYTVDFISFSYYSSRVASGNPTVSEQVQENIFASLKNPYLKSSEWCWQIDPLGLRITL 36- 1 L++ TVDF+SFSYY+SR AS + N+ SL+NPYL+ S+WGW IDPLGLRIT+ Sbjct: 301 LKN-TVDFVSFSYYASRCASAENNANNSSAANVVKSLRNPYLQVSDWGWGIDPLGLRITM 35- 9 Query: 362 NAIWDRYQKPMFIVENGLGAVDIPDENGYVEDDYRIDYLRQHIAANRDAIYVDGVNLIGY 42- 1 N ++DRYQKP+F+VENGLGA D NG + DDYRI YLR+HI AM +AI DG+ L+GY Sbjct: 360 NMNYDRYQKPLFLVENGLGAKDEFAANGEINDDYRISYLREHIRAMGEAI-ADGIPLMGY 41- 8 Query: 422 TTWGCIDLVSAGTGEMEKRYGFIYVDRNNKGEGTLKRYKKKSFYWYKKVIASNGSQIE 479 TTWGCIDLVSA TGEM KRYGF++VDR++ G GTL R +KKSF+WYKKVIASNG +E Sbjct: 419 TTWGCIDLVSASTGEMSKRYGFVFVDRDDAGNGTLTRTRKKSFWWYKKVIASNGEDLE 476 There is also homology to SEQ ID 5288. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1702 A DNA sequence (GBSx1806) was identified in S. agalactiae <SEQ ID 5289> which encodes the amino acid sequence <SEQ ID 5290>. This protein is predicted to be platelet-activating factor acetylhydrolase isoform Ib beta subunit, pu. Analysis of this protein sequence reveals the following: TABLE-US-05193 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5323(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05194 >GP: AAC27974 GB: AF016048 platelet-activating factor acetylhydrolase alpha 2 subunit [Rattus norvegicus] Identities = 43/177 (24%), Positives = 84/177 (47%), Gaps = 9/177 (5%) Query: 28 QEGAIVFTGDSIVEF---FPLKKHLGRDYPLVNRGVAGSDTYWLLENLRTQVWELLPSKV 84 - +E ++F GDS+V+ + + + L +N G+ G T +L L+ E + KV Sbjct: 38 KEPDVLFVGDSMVQLMQQYEIWRELFSPLHALNFGIGGDTTRHVLWRLKNGELENIKPKV 97 Query: 85 FIL-IGTNDIGLGHSQSEIIANITDIIAEIRAESYMTEINILSVLPVSEEDDYIERVKVR 143- ++ +GTN+ ++ E+ I I+ I +I +L +LP E+ + + + + Sbjct: 98 IVVWVGTNNHE--NTAEEVAGGIEAIVQLINTRQPQAKIIVLGLLPRGEKPNPLRQKNAK 155- Query: 144 NNQTIKALNKTLSVISGINYIELYDLLVDEKGQLASSFTKDGLHLTDQAYAKISETI 200 NQ +K +L ++ + +++ V G ++ D LHLT YAKI + + Sbjct: 156 VNQLLKV---SLPKLANVQLLDIDGGFVHSDGAISCHDMFDFLHLTGGGYAKICKPL 209 A related DNA sequence was identified in S. pyogenes <SEQ ID 5291> which encodes the amino acid sequence <SEQ ID 5292>. Analysis of this protein sequence reveals the following: TABLE-US-05195 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5979(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05196 Identities = 92/204 (45%), Positives = 133/204 (65%) Query: 1 MLEVIDKALRDYQMKREQFFEINNQTVQEGAIVFTGDSIVEFFPLKKHLGRDYPLVNRGV 60 MLE++ + LR YQ ++ + NQ +G IVF GDS++EFFPLKK G P++NRG+ Sbjct: 1 MLEIVSEELRHYQEQKLIEYRNKNQLAPKGGIVFAGDSLIEFFPLKKAFGSCLPIINRGI 60 Query: 61 AGSDTYWLLENLRTQVWELLPSKVFILIGTNDIGLGHSQSEIIANITDIIAEIRAESYMT 120- AG D+ WLL + Q+ +L P +F+LIG NDIGLG+ + I+ I ++I++IR+ + Sbjct: 61 AGIDSQWLLRHFSVQITDLEPKHIFLLIGCNDIGLGYDKCHIVKTIVELISQIRSHCVYS 120- Query: 121 EINILSVLPVSEEDDYIERVKVRNNQTIKALNKTLSVISGINYIELYDLLVDEKGQLASS 18- 0 +I +LS+LPVS Y + VK+R N I A+NK L++I + +I L L DEKG L+ Sbjct: 121 QIYLLSLLPVSNNPRYQKTVKIRTNAMIDAINKDLAMIPTVEFINLNTCLKDEKGGLSDE 18- 0 Query: 181 FTKDGLHLTDQAYAKISETIKLYL 204 T DGLHL AYAK++E IK Y+ Sbjct: 181 NTLDGLHLNFPAYAKLAEIIKSYI 204 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1703 A DNA sequence (GBSx1807) was identified in S. agalactiae <SEQ ID 5293> which encodes the amino acid sequence <SEQ ID 5294>. Analysis of this protein sequence reveals the following: TABLE-US-05197 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5226(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9851> which encodes amino acid sequence <SEQ ID 9852> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-05198 >GP: BAA35556 GB: D90723 Hypothetical 30.2 kd protein in idh-deoR intergenic region. [Escherichia coli] Identities = 104/265 (39%), Positives = 154/265 (57%), Gaps = 4/265 (1%) Query: 2 IKLIATDMDGTFLRSDKTYDKARFSSLLTLMEKYDIKFVAASGNLYDQLLLNFLEYPNRI 61 IKLIA DMDGTFL KTY++ RF + M+ I+FV ASGN Y QL+ F E N I sbjct: 4 IKLIAVDMDGTFLSDQKTYNRERFMAQYQQMKAQGIRFVVASGNQYYQLISFFPEIANEI 63 Query: 62 AYVAENGGRVIDQDGTLLKETYLSNDTVAAVLSYLYQNYPETLISLSGEKRSYLERRTPI 121- A+VAENGG V+ + G + LS D A V+ +L PE I G+ +Y ++ Sbjct: 64 AFVAENGGWVVSE-GKDVFNGELSKDAFATVVEHLLTR-PEVEIIACGKNSAYTLKKYDD 121- Query: 122 NRRTELEYYMPNFIYKDHLLPLDDDRYFQMTLWVNENLVSEMLLDISEHFKNHHIRLTSS 18- 1 +T E Y Y D+ L+D +F+ L +++ L+ ++ + E + + + + Sbjct: 122 AMKTVAEMYYHRLEYVDNFDNLEDI-FFKFGLNLSDELIPQVQKALHEAIGDIMVSV-HT 17- 9 Query: 182 GFGCIDVLPADVNKADGIAILLEKWGLKQDQVMVFGDGGNDVEMLRAANISYAMSNAPEE 24- 1 G G ID++ V+KA+G+ L + WG+ +V+VFGDGGND+EMLR A S+AM NA Sbjct: 180 GNGSIDLIIPGVHKANGLRQLQKLWGIDDSEVVVFGDGGNDIEMLRQAGFSFAMENAGSA 23- 9 Query: 242 IKAIAKYQTVSNDQDGVLETIENFL 266 + A AKY+ SN+++GVL+ I+ L Sbjct: 240 VVAAAKYRAGSNNREGVLDVIDKVL 264 There is also homology to SEQ ID 1158. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1704 A DNA sequence (GBSx1808) was identified in S. agalactiae <SEQ ID 5295> which encodes the amino acid sequence <SEQ ID 5296>. This protein is predicted to be transcriptional regulator (AraC/XylSfamily). Analysis of this protein sequence reveals the following: TABLE-US-05199 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4984(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05200 >GP: AAF89977 GB: AF206272 transcriptional regulator [Streptococcus mutans] Identities = 195/287 (67%), Positives = 237/287 (81%) Query: 5 DNLLSHNLEDNRHLLPYEHMHTEVRNGYPDILFHWHPELEISYVHEGTARYHIDYDFFNS 64 D H + + LLPY+ T + NGYPD LFHWHPELEISY++EGTA+YHIDYD+FNS Sbjct: 10 DENFKHEINFDNDLLPYKIYQTTIANGYPDTLFHWHPELEISYIYEGTAQYHIDYDYFNS 69 Query: 65 QSGDIILIRPNGMHSIHPIENKSHITDSIKFHLDLIGYSIVDQVSLRYLQPLQTSSFKFI 124- Q+ DIIL+RPNGMHSIHPI+NK ++ FHLDL+GYS++DQ+SLRYLQPLQ S+FK + Sbjct: 70 QTDDIILVRPNGMHSIHPIKNKMQKAQTLLFHLDLVGYSLLDQISLRYLQPLQNSTFKLV 129- Query: 125 QCIKPSMTGYNDIKNCLFDIFNISKEENRHFELLLKAKLNELLYLLYYHQYVIKKHTDDT 18- 4 CIKP M GY DIKNCLF IF+I + + RHFELLLKAKL EL+YLLY+HQYV++KH+DD Sbjct: 130 PCIKPDMLGYQDIKNCLFAIFDIYQRQGRHFELLLKAKLQELIYLLYFHQYVLRKHSDDM 18- 9 Query: 185 YRKNERIRDLIDYINNNYQQNLTIEFLADYMGYSKTHFMTVFKQHTGTSCTEFIIQVRLN 24- 4 YRKNE+IR+LIDYI+ +YQ+ L+I LAD +GYSKTHFMTVFKQHTGTSCT+FIIQ RL+ Sbjct: 190 YRKNEKIRELIDYIHQHYQEKLSIISLADIIGYSKTHFMTVFKQHTGTSCTDFIIQFRLS 24- 9 Query: 245 KASEHLINSTTAIIDIANSVGFNNLSNFNRQFKRYYHTTPRQYRKQF 291 KA + L+NS I+++A+ VGF NLSNFNRQFKRYY TP QYRKQF Sbjct: 250 KACDLLVNSIKPILEVASEVGFTNLSNFNRQFKRYYQITPSQYRKQF 296 A related DNA sequence was identified in S. pyogenes <SEQ ID 5297> which encodes the amino acid sequence <SEQ ID 5298>. Analysis of this protein sequence reveals the following: TABLE-US-05201 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05202 Identities = 43/169 (25%), Positives = 83/169 (48%), Gaps = 16/169 (9%) Query: 136 DIKNCLFDIFNISKEENRHFELLLKAKLNELLYLLYYHQYV------IKKHTDDTYRKN- 18- 8 D+K+ F +F+ + R F +L K ++ ++ Q + +KK D T + N sbjct: 319 DVKHVSFLLFS---DIYRQFPILDKMTYLSMVKTIHDSQSIDCILRELKKVLDVTNQNNS 37- 5 Query: 189 ------ERIRDLIDYINNNYQQNLTIEFLADYMGYSKTHFMTVFKQHTGTSCTEFIIQVR 24- 2 + + + ID I Y Q LT++ +AD + + + FK T S T+++ VR Sbjct: 376 PEKRYSDLVSETIDCIRKEYHQELTLKAIADRLHVNGVYLGQCFKNETERSFTQYLNHVR 43- 5 Query: 243 LNKASEHLINSTTAIIDIANSVGFNNLSNFNRQFKRYYHTTPRQYRKQF 291 + KA + L+ + +I +IA G+N F +FK+ +P+++R ++ sbjct: 436 IQKAQQLLLYTNQSINEIAYETGYNTNHYFIKMFKKLNGLSPKEFRDRY 484 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1705 A DNA sequence (GBSx1809) was identified in S. agalactiae <SEQ ID 5299> which encodes the amino acid sequence <SEQ ID 5300>. Analysis of this protein sequence reveals the following: TABLE-US-05203 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3705(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1706 A DNA sequence (GBSx1810) was identified in S. agalactiae <SEQ ID 5301> which encodes the amino acid sequence <SEQ ID 5302>. Analysis of this protein sequence reveals the following: TABLE-US-05204 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.25 Transmembrane 59-75 (56-82) INTEGRAL Likelihood = -7.48 Transmembrane 23-39 (12-41) INTEGRAL Likelihood = -6.64 Transmembrane 231-247 (225-255) INTEGRAL Likelihood = -5.15 Transmembrane 335-351 (333-355) INTEGRAL Likelihood = -4.19 Transmembrane 309-325 (305-327) INTEGRAL Likelihood = -4.14 Transmembrane 272-288 (268-292) INTEGRAL Likelihood = -4.04 Transmembrane 402-418 (400-419) INTEGRAL Likelihood = -3.88 Transmembrane 191-207 (190-208) INTEGRAL Likelihood = -2.71 Transmembrane 365-381 (364-381) INTEGRAL Likelihood = -1.86 Transmembrane 165-181 (164-182) ----- Final Results ----- bacterial membrane --- Certainty = 0.5501(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05205 >GP: AAF96429 GB: AE004383 conserved hypothetical protein [Vibrio cholerae] Identities = 142/443 (32%), Positives = 241/443 (54%), Gaps = 20/443 (4%) Query: 6 NEFQFSLESILGFVWRGIVVGLIAGFVVSIFRLAIEKIFLVVMELYKS--AHYQPIILLS 63 N+F ++ ++ ++VG++AG V + F A+ + + KS + P+ L + Sbjct: 21 NQFLSKDKTPFSVLFLSLLVGILAGLVGTYFEQAVHLVSETRTDWLKSEIGSFLPLWLAA 80 Query: 64 ITVTSIIAAVIIGFFI--KSDPDIKGSGIPHVEGELKGMLSPDWFSIVWKKFIAGILAIS 121- +++ +A IG+F+ + P+ GSGIP +EG + GM W+ ++ KF G+ A+ Sbjct: 81 FLISAFLA--FIGYFLVHRFAPEAAGSGIPEIEGAMDGMRPVRWWRVLPVKFFGGMGALG 138- Query: 122 SGLMLGREGPSIQLGAMTGKGIAQYLNASRMEKR-VLIASGAAAGLSAAFNAPIAGLLFV 18- 0 SG++LGREGP++Q+G G+ I+ + R L+A+GAA GL+AAFNAP+AG++FV Sbjct: 139 SGMVLGREGPTVQMGGAVGRMISDIFRVKNEDTRHSLLAAGAAGGLAAAFNAPLAGIMFV 19- 8 Query: 181 VEEIYHHFS-RLVWITALVASLV-ANFVSLNIFGLTPVLALPSELPSLNLNFYWIFLLMG 23- 8 +EE+ F L+ +A++ S V AN V I G V+ +P + + L+ +FLL+G Sbjct: 199 IEEMRPQFRYTLISVRAVIISAVAANIVFRVINGQDAVITMP-QYDAPELSTLGLFLLLG 25- 7 Query: 239 LFLGILGFIYEWVIL----RFHVIYDYLGKLFHLPSHLYGILAVIFILPIGYYFPQLLGG 29- 4 G+ G ++ ++I F + K + L + G + +L Y P+L GG Sbjct: 258 ALFGVFGVLFNYLITLAQDLFVKFHRNDRKRYLLTGSMIGGCFGLLLL---YVPELTGG 313- Query: 295 GNGLIVSLPRSNLSLMMLGLFFLIRFLWSMLSYSSGLPGGIFLPILALGSLAG-AFFAVG 35- 3 G LI ++ +L L F+ R ++L + SG PGGIF P+LALG+L G AF + Sbjct: 314 GISLIPTITNGGYGAGILLLLFVGRIFTTLLCFGSGAPGGIFAPMLALGTLFGYAFGLIA 37- 3 Query: 354 MQYFGIISHQQISLFVVLGMAGYFGAISKAPLTAMILVTEMVGDLKQLMAIGIVTMVSYI 41- 3 +F ++ + +F + GM F A +AP+T ++LV EM + ++ + I ++ + I Sbjct: 374 KMWFPELNIEP-GMFAIAGMGALFAATVRAPITGILLVIEMTNNYHLILPLIITSLGAVI 43- 2 Query: 414 VMDLLKGEPIYEAMLAKMTFNPK 436 LL G+PIY +L + N K Sbjct: 433 FAQLLGGQPIYSQLLHRTLKNQK 455 A related DNA sequence was identified in S. pyogenes <SEQ ID 5303> which encodes the amino acid sequence <SEQ ID 5304>. Analysis of this protein sequence reveals the following: TABLE-US-05206 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.68 Transmembrane 71-87 (66-95) INTEGRAL Likelihood = -9.45 Transmembrane 36-52 (26-56) INTEGRAL Likelihood = -5.63 Transmembrane 346-362 (342-367) INTEGRAL Likelihood = -5.36 Transmembrane 376-392 (375-393) INTEGRAL Likelihood = -5.15 Transmembrane 413-429 (410-432) INTEGRAL Likelihood = -5.10 Transmembrane 321-337 (318-340) INTEGRAL Likelihood = -4.19 Transmembrane 203-219 (202-220) INTEGRAL Likelihood = -4.19 Transmembrane 244-260 (242-265) INTEGRAL Likelihood = -4.19 Transmembrane 284-300 (280-304) INTEGRAL Likelihood = -1.86 Transmembrane 177-193 (176-194) ----- Final Results ----- bacterial membrane --- Certainty = 0.5670(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05207 >GP: AAF96429 GB: AE004383 conserved hypothetical protein [Vibrio cholerae] Identities = 144/442 (32%), Positives = 236/442 (52%), Gaps = 30/442 (6%) Query: 18 NEFTFSNKSIIAYVWRGVVVGIIAGVIVSLFRLLIEVTADWVIEWYRYAHINSLLLLPIL 77 - N+F +K+ + ++ ++VGI+AG++ + F + + ++ +W + + I S L L + Sbjct: 21 NQFLSKDKTPFSVLFLSLLVGILAGLVGTYFEQAVHLVSETRTDWLK-SEIGSFLPLWLA 79 Query: 78 SVSLLAVL-FVGFLV--KSDSDIKGSGIPHVEGELKGLMSPDWWSVLWKKFLGGIMAISM 134- + + A L F+G+ + + + GSGIP +EG + G+ WW VL KF GG+ A+ Sbjct: 80 AFLISAFLAFIGYFLVHRFAPEAAGSGIPEIEGAMDGMRPVRWWRVLPVKFFGGMGALGS 139- Query: 135 GFMLGREGPSIQLGAMSAKGLAKFLKSSRLEKR-VLIASGAAAGLSAAFNAPIAGLLFVV 19- 3 G +LGREGP++Q+G + ++ + + R L+A+GAA GL+AAFNAP+AG++FV+ Sbjct: 140 GMVLGREGPTVQMGGAVGRMISDIFRVKNEDTRHSLLAAGAAGGLAAAFNAPLAGIMFVI 19- 9 Query: 194 EEIYHHFS-RLIWITALVASLV-ANFISLNIFGLKPVLAMSEAMPFLGLNQYWLLLLLGL 25- 1 EE+ F LI + A++ S V AN + I G V+ M + L+ L LLLG Sbjct: 200 EEMRPQFRYTLISVRAVIISAVAANIVFRVINGQDAVITMPQ-YDAPELSTLGLFLLLGA 25- 8 Query: 252 FLGCLGYLYEIVIL-----------NFNKLYVILGSWLHLPDYFYGIIMVFLILPIGYYL 30- 0 G G L+ +I N K Y++ GS + +G++++ Y+ Sbjct: 259 LFGVFGVLFNYLITLAQDLFVKFHRNDRKRYLLTGSMI---GGCFGLLLL--------YV 30- 7 Query: 301 PQLLGGGHGLILSLSNQQLPLMTIFFYFIIRFIVSMFSYGSGLPGGIFLPILTLGALAGL 36- 0 P+L GGG LI +++N + F+ R ++ +GSG PGGIF P+L LG L G Sbjct: 308 PELTGGGISLIPTITNGGYGAGILLLLFVGRIFTTLLCFGSGAPGGIFAPMLALGTLFGY 36- 7 Query: 361 LFGQIASQLGLLNQSFLSLFLILGMAGYFAAISKAPLTGMILVTEMVGDLKPLMAIAVVT 42- 0 FG IA +F I GM FAA +AP+TG++LV EM + ++ + + + Sbjct: 368 AFGLIAKMWFPELNIEPGMFAIAGMGALFAATVRAPITGILLVIEMTNNYHLILPLIITS 42- 7 Query: 421 FVSYLVMDLLNGQPIYEAMLDK 442 + + LL GQPIY +L + Sbjct: 428 LGAVIFAQLLGGQPIYSQLLHR 449 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05208 Identities = 343/510 (67%), Positives = 410/510 (80%) Query: 1 MENHKNEFQFSLESILGFVWRGIVVGLIAGFVVSIFRLAIEKIFLVVMELYKSAHYQPII 60 MENHKNEF FS +SI+ +VWRG+VVG+IAG +VS+FRL IE V+E Y+ AH ++ Sbjct: 13 MENHKNEFTFSNKSIIAYVWRGVVVGIIAGVIVSLFRLLIEVTADWVIEWYRYAHINSLL 72 Query: 61 LLSITVTSIIAAVIIGFFIKSDPDIKGSGIPHVEGELKGMLSPDWFSIVWKKFIAGILAI 120- LL I S++A + +GF +KSD DIKGSGIPHVEGELKG++SPDW++WKKF+ GI+AI Sbjct: 73 LLPILSVSLLAVLFVGFLVKSDSDIKGSGIPHVEGELKGLMSPDWWSVLWKKFLGGIMAI 132- Query: 121 SSGLMLGREGPSIQLGAMTGKGIAQYLNASRMEKRVLIASGAAAGLSAAFNAPIAGLLFV 18- 0 S G MLGREGPSIQLGAM+ KG+A++L +SR+EKRVLIASGAAAGLSAAFNAPIAGLLFV Sbjct: 133 SMGFMLGREGPSIQLGAMSAKGLAKFLKSSRLSKRVLIASGAAAGLSAAFNAPIAGLLFV 19- 2 Query: 181 VEEIYHHFSRLVWITALVASLVANFVSLNIFGLTPVLALPSELPSLNLNFYWIFLLMGLF 24- 0 VEEIYHHFSRL+WITALVASLVANF+SLNIFGL PVLA+ +P L LN YW +LL+GLF Sbjct: 193 VEEIYHHFSRLIWITALVASLVANFISLNIFGLKPVLAMSEAMPFLGLNQYWLLLLLGLF 25- 2 Query: 241 LGILGFIYEWVILRFHVIYDYLGKLFHLPSHLYGILAVIFILPIGYYFPQLLGGGNGLIV 30- 0 LG LG++YE VIL F+ +Y LG HLP + YGI+ V ILPIGYY PQLLGGG+GLI+ Sbjct: 253 LGCLGYLYEIVILNFNKLYVILGSWLHLPDYFYGIIMVFLILPIGYYLPQLLGGGHGLIL 31- Query: 301 SLPRSNLSLMMLGLFFLIRFLWSMLSYSSGLPGGIFLPILALGSLAGAFFAVGMQYFGII 36- 0 SL L LM + +F+IRF+ SM SY SGLPGGIFLPIL LG+LAG F G++ Sbjct: 313 SLSNQQLPLMTIFFYFIIRFIVSMFSYGSGLPGGIFLPILTLGALAGLLFGQIASQLGLL 37- 2 Query: 361 SHQQISLFVVLGMAGYFGAISKAPLTAMILVTEMVGDLKQLMAIGIVTMVSYIVMDLLKG 42- 0 + +SLF++LGMAGYF AISKAPLT MILVTEMVGDLK LMAI +VT VSY+VMDLL G Sbjct: 373 NQSFLSLFLILGMAGYFAAISKAPLTGMILVTEMVGDLKPLMAIAVVTFVSYLVMDLLNG 43- 2 Query: 421 EPIYEAMLAKMTFNPKDKVMTPTLIELTVSDKISGKYVRDLELPENVLITTQIMHKTSAV 48- 0 +PIYEAML KM ++ PTLIELTV DKI+GKYV++L+LPENVLITTQIHH+ S V Sbjct: 433 QPIYEAMLDKMMAKHPTNLVEPTLIELTVGDKIAGKYVKELKLPENVLITTQIHHQKSQV 49- 2 Query: 481 VSGNTILNAGDTIFLVVNESEIKEVREQLM 510 VSGNT L +G TIFLVVNE++ VRE LM Sbjct: 493 VSGNTRLLSGATIFLVVNEADTGFVREVLM 522 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1707 A DNA sequence (GBSx1811) was identified in S. agalactiae <SEQ ID 5305> which encodes the amino acid sequence <SEQ ID 5306>. This protein is predicted to be spermidine/putrescine-binding periplasmic protein precursor (potD-1). Analysis of this protein sequence reveals the following: TABLE-US-05209 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.02 Transmembrane 20-36(14-40) ----- Final Results ----- bacterial membrane --- Certainty = 0.4609(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8881> which encodes amino acid sequence <SEQ ID 8882> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-05210 Lipop: Possible site: -1 Crend: 2 SRCFLG: 0 McG: Length of UR: 22 Peak Value of UR: 4.16 Net Charge of CR: 2 McG: Discrim Score: 18.94 GvH: Signal Score (-7.5): -3.29 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 1 value: -9.02 threshold: 0.0 INTEGRAL Likelihood = -9.02 Transmembrane 7-23 (1-27) PERIPHERAL Likelihood = 6.05 170 modified ALOM score: 2.30 icm1 HYPID: 7 CFP: 0.461 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4609(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05211 >GP: AAF94581 GB: AE004221 spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein [Vibrio cholerae] Identities = 126/327 (38%), Positives = 196/327 (59%), Gaps = 2/327 (0%) Query: 42 SSSTPNSDKLVIYNWGDYIDPALLKKFTKETGIEVQYETFDSNEAMHTKIKQGGTTYDIA 101- +++ +L YNW +YI +L+ FTKETGI+V Y T++SNE+M+ K+K G YD+ Sbjct: 18 TNAMAKDQELYFYNWSEYIPSEVLEDFTKETGIKVIYSTYESNESMYAKLKTQGAGYDLV 77 Query: 102 VPSDYMIDKMIKENLLVKLDHSKIANWDAIGARFKNLSFDPKNKYSIPYFWGTVGIVYN- 16- 0 VPS Y + KM KE +L ++DHSK+++++ + +F N FDP NK+SIPY WG GI N Sbjct: 78 VPSTYFVSKMRKEGMLQEIDHSKLSHFKDLDPNYLNKPFDPGNKFSIPYIWGATGIGINT 137- Query: 161 DQLVKTPPKHWDDLWRPEFRNKIMLVDSAREVIGVGLNSLGYGLNTKNISELKAASKKLD 22- 0 D L K K+W DLW ++ ++ML+D AREV + L+ LGY NT N E+KAA ++L Sbjct: 138 DMLDKKSLKNWGDLWDAKWAGQLMLMDDAREVFHIALSKLGYSPNTTNPKEIKAAYRELK 19- 7 Query: 221 ALTPNVKAIVADEMKGYMIQGDAAIGVTFSGEAREMLDGNKHLHYVVPSEGSNLWFDNIV 28- 0 L PNV +D + G+ ++G+ ++G A + + P +G+ W D+I Sbjct: 198 KLMPNVLVFNSDFPANPYLAGEVSLGMLWNGSAYMARQEGAPIQIIWPEKGTIFWNDSIS 25- 7 Query: 281 IPKTVKHRKEAYAFINFMMEPKNAAQNAEYIGYATPNLKAKALLPADIKNDKAFYPPDKT 34- 0 IP K+ + A+ I+F++ P+NAA+ A IGY TP A LLP + ND + YPP Sbjct: 258 IPAGAKNIEAAHKMIDFLLRPENAAKIALEIGYPTPVKTAHDLLPKEFANDPSIYPPQSV 31- 7 Query: 341 IDHLEVYNNLGQKWLGIYNDLYLQFKM 367 ID+ E + +G+ + +Y++ + + K+ Sbjct: 318 IDNGEWQDEVGEASV-LYDEYFQKLKV 343 A related DNA sequence was identified in S. pyogenes <SEQ ID 5307> which encodes the amino acid sequence <SEQ ID 5308>. Analysis of this protein sequence reveals the following: TABLE-US-05212 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.44 Transmembrane 8-24 (1-27) ----- Final Results ----- bacterial membrane --- Certainty = 0.4376(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases:

TABLE-US-05213 >GP: AAC74207 GB: AE000212 spermidine/putrescine periplasmic transport protein [Escherichia coli] Identities = 134/342 (39%), Positives = 199/342 (58%), Gaps = 3/342 (0%) Query: 17 ILTSLSFILQKKSGSGSQSDKLVIYNWGDYIDPALLKKFTKETGIEVQYETFDSNEAMYT 76 - +L + + L + ++ L YNW +Y+ P LL++FTKETGI+V Y T++SNE MY Sbjct: 8 LLAAGALALGMSAAHADDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYA 67 Query: 77 KIKQ-GGTTYDIAVPSDYTIDKMIKENLLNKLDKSKLVGMDNIGKEFLGKSFDPQNDYSL 135- K+K YD+ VPS Y +DKM KE ++ K+DKSKL N+ + L K FDP NDYS+ Sbjct: 68 KLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSI 127- Query: 136 PYFWGTVGIVYNDQLVD-KAPMHWEDLWRPEYKNSIMLIDGAREMLGVGLTTFGYSVNSK 19- 4 PY WG I N VD K+ W DLW+PEYK S++L D ARE+ + L GYS N+ Sbjct: 128 PYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTT 18- 7 Query: 195 NLEQLQAAERKLQQLTPNVKAIVADEMKGYMIQGDAAIGITFSGEASEMLDSNEHLHYIV 25- 4 + ++++AA +L++L PNV A +D ++G+ +G+ ++G A + + + Sbjct: 188 DPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVW 24- 7 Query: 255 PSEGSNLWFDNLVLPKTMKHEKEAYAFLNFINRPENAAQNAAYIGYATPNKKAKALLPDE 31- 4 P EG W D+L +P K+++ A +NF+ RP+ A Q A IGY TPN A+ LL E Sbjct: 248 PKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPE 30- 7 Query: 315 IKNDPAFYPTDDIIKKLEVYDNLGSRWLGIYNDLYLQFKMYR 356 + ND YP + IK E +++G+ IY + Y + K R Sbjct: 308 VANDKTLYPDAETIKNGEWQNDVGAA-SSIYEEYYQKLKAGR 348 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05214 Identities = 270/357 (75%), Positives = 306/357 (85%) Query: 14 MRRVYSFLGGIVLVILILFGLTTYLEKKSSSTPNSDKLVIYNWGDYIDPALLKKFTKETG 73 - MR++YSFL G++ VI+IL L+ L+KKS S SDKLVIYNWGDYIDPALLKKFTKETG Sbjct: 1 MRKLYSFLAGVLGVIVILTSLSFILQKKSGSGSQSDKLVIYNWGDYIDPALLKKFTKETG 60 Query: 74 IEVQYETFDSNEAMHTKIKQGGTTYDIAVPSDYMIDKMIKENLLVKLDHSKIANWDAIGA 133- IEVQYETFDSNEAM+TKIKQGGTTYDIAVPSDY IDKMIKENLL KLD SK+ D IG Sbjct: 61 IEVQYETFDSNEAMYTKIKQGGTTYDIAVPSDYTIDKMIKENLLNKLDKSKLVGMDNIGK 120- Query: 134 RFKNLSFDPKNKYSIPYFWGTVGIVYNDQLVKTPPKHWDDLWRPEFRNKIMLVDSAREVI 19- 3 F SFDP+N YS+PYFWGTVGIVYNDQLV P HW+DLWRPE++N IML+D ARE++ Sbjct: 121 EFLGKSFDPQNDYSLPYFWGTVGIVYNDQLVDKAPMHWEDLWRPEYKNSIMLIDGAREML 18- 0 Query: 194 GVGLNSLGYGLNTKNISELKAASKKLDALTPNVKAIVADEMKGYMIQGDAAIGVTFSGEA 25- 3 GVGL + GY +N+KN+ +L+AA +KL LTPNVKAIVADEMKGYMIQGDAAIG+TFSGEA Sbjct: 181 GVGLTTFGYSVNSKNLEQLQAAERKLQQLTPNVKAIVADEMKGYMIQGDAAIGITFSGEA 24- 0 Query: 254 REMLDGNKHLHYVVPSEGSNLWFDNIVIPKTVKHRKEAYAFINFMMEPKNAAQNAEYIGY 31- 3 EMLD N+HLHY+VPSEGSNLWFDN+V+PKT+KH KEAYAF+NF+ P+NAAQNA YIGY Sbjct: 241 SEMLDSNEHLHYIVPSEGSNLWFDNLVLPKTMKHEKEAYAFLNFINRPENAAQNAAYIGY 30- 0 Query: 314 ATPNLKAKALLPADIKNDKAFYPPDKTIDHLEVYNNLGQKWLGIYNDLYLQFKMYRK 370 ATPN KAKALLP +IKND AFYP D I LEVY+NLG +WLGIYNDLYLQFKMYRK Sbjct: 301 ATPNKKAKALLPDEIKNDPAFYPTDDIIKKLEVYDNLGSRWLGIYNDLYLQFKMYRK 357 SEQ ID 8882 (GBS135) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 35 (lane 6; MW 40 kDa). GBS135-His was purified as shown in FIG. 201, lane 10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1708 A DNA sequence (GBSx1812) was identified in S. agalactiae <SEQ ID 5309> which encodes the amino acid sequence <SEQ ID 5310>. This protein is predicted to be spermidine/putrescine ABC transporter, permease protein (potC). Analysis of this protein sequence reveals the following: TABLE-US-05215 Possible site: 51 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.05 Transmembrane 17-33 (10-37) INTEGRAL Likelihood = -8.65 Transmembrane 236-252 (232-259) INTEGRAL Likelihood = -7.75 Transmembrane 137-153 (132-158) INTEGRAL Likelihood = -7.17 Transmembrane 63-79 (60-92) INTEGRAL Likelihood = -6.32 Transmembrane 108-124 (107-136) ----- Final Results ----- bacterial membrane --- Certainty = 0.5819(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8883> which encodes amino acid sequence <SEQ ID 8884> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-05216 Lipop: Possible site: -1 Crend: 2 SRCFLG: 0 McG: Length of UR: 26 Peak Value of UR: 3.65 Net Charge of CR: 2 McG: Discrim Score: 16.58 GvH: Signal Score (-7.5): -6.17 Possible site: 43 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 4 value: -12.05 threshold: 0.0 INTEGRAL Likelihood = -12.05 Transmembrane 9-25 (2-29) INTEGRAL Likelihood = -7.75 Transmembrane 129-145 (124-150) INTEGRAL Likelihood = -7.17 Transmembrane 55-71 (52-84) INTEGRAL Likelihood = -6.32 Transmembrane 100-116 (99-128) PERIPHERAL Likelihood = 0.53 174 modified ALOM score: 2.91 icm1 HYPID: 7 CFP: 0.582 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5819(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05217 >GP: AAB91527 GB: AE001165 spermidine/putrescine ABC transporter, permease protein (potC) [Borrelia burgdorferi] Identities = 97/249 (38%), Positives = 159/249 (62%), Gaps = 3/249 (1%) Query: 10 KKFANIYLALVFIILYIPIIYLIFYSFNKGGDMNSFTGFTFSHYGELFQDSRLMLILVQT 69 - + F NI+L L+ +Y+PII LI YSFN G + GF+ Y E+F S++ + T Sbjct: 3 RAFKNIFLFLILSFIYLPIIILIIYSFNSGDSGFIWQGFSLKWYKEIFASSQIKSAIFNT 62 Query: 70 FFLAFLSALLATIIGTFGAIWIYQVRRRH-QTSILSLNNILLVAPDVMIGASFLLVFTVI 128- +A +S+L + +IG GA IY+ + +T +LS+N I ++ PD++ G S + ++ I Sbjct: 63 ILIAIISSLTSVVIGIIGAYAIYKSENKKLKTILLSVNKITIINPDIVTGISLMTFYSAI 122- Query: 129 GLQLGFTSVLLSHVAFSIPIVVLMVLPRLKEMNDDMINASYDLGASTWQMLKEVMLPYLS 18- 8 +QLGF+++L+SH+ FS P VV+++LP+L + ++I+A+ DLGAS Q+ ++ P ++ Sbjct: 123 KMQLGFSTMLISHIIFSTPYVVIIILPKLYSLPKNIIDAAKDLGASEIQIFFNIIYPEIA 18- 2 Query: 189 SGIISGFFMAFTYSLDDFAVTFFVTGNGFSTLSVEIYSRARRGISLEINALSTIVF--LF 24- 6 I +G +AFT S+DDF ++FF TG GF+ LS+ I S +RGI INA+S I+F + Sbjct: 183 GSIATGALIAFTLSIDDFLISFFTTGQGFNNLSILINSLTKRGIKPVINAISAILFFTIL 24- 2 Query: 247 SILLVIGYY 255 S+L +I + Sbjct: 243 SLLFIINKF 251 A related DNA sequence was identified in S. pyogenes <SEQ ID 5311> which encodes the amino acid sequence <SEQ ID 5312>. Analysis of this protein sequence reveals the following: TABLE-US-05218 Possible site: 49 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.17 Transmembrane 9-25 (4-29) INTEGRAL Likelihood = -8.12 Transmembrane 228-244 (224-250) INTEGRAL Likelihood = -7.91 Transmembrane 129-145 (124-150) INTEGRAL Likelihood = -7.06 Transmembrane 62-78 (54-87) INTEGRAL Likelihood = -3.93 Transmembrane 100-116 (99-118) ----- Final Results ----- bacterial membrane --- Certainty = 0.4270(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05219 >GP: AAB91527 GB: AE001165 spermidine/putrescine ABC transporter, permease protein (potC) [Borrelia burgdorferi] Identities = 91/249 (36%), Positives = 154/249 (61%), Gaps = 3/249 (1%) Query: 2 KKFANLYLASVFVLLYIPIFYLIFYSFNKGGDMNGFTGFTLEHYQTMFEDSRLMTILLQT 61 + F N++L + +Y+PI LI YSFN G + GF+L+ Y+ +F S++ + + T Sbjct: 3 RAFKNIFLFLILSFIYLPIIILIIYSFNSGDSGFIWQGFSLKWYKEIFASSQIKSAIFNT 62 Query: 62 FVLAFSSALLATIIGIFGAIFIHHVRGK-YQNAMLSANNVLMVSPDVMIGASFLILFTSL 120- ++A S+L + +IGI GA I+ K + +LS N + +++PD++ G S + ++++ Sbjct: 63 ILIAIISSLTSVVIGIIGAYAIYKSENKKLKTILLSVNKITIINPDIVTGISLMTFYSAI 122- Query: 121 KFQLGMSSVLLSHIAFSIPIVVLMVLPRLKEMNQDMVNAAYDLGANYFQMLKEVMLPYFT 18- 0 K QLG S++L+SHI FS P VV+++LP+L + +++++AA DLGA+ Q+ ++ P Sbjct: 123 KMQLGFSTMLISHIIFSTPYVVIIILPKLYSLPKNIIDAAKDLGASEIQIFFNIIYPEIA 18- 2 Query: 181 PGIIAGYFMAFTYSLDDFAVTFFLTGNSVTTLSVEIYSRARQGISLDINALSTIVFF--F 23- 8 I G +AFT S+DDF ++FF TG LS+ I S ++GI INA+S I+FF Sbjct: 183 GSIATGALIAFTLSIDDFLISFFTTGQGFNNLSILINSLTKRGIKPVINAISAILFFTIL 24- 2 Query: 239 SILLVIGYY 247 S+L +I + Sbjct: 243 SLLFIINKF 251 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05220 Identities = 196/258 (75%), Positives = 231/258 (88%) Query: 9 MKKFANIYLALVFIILYIPIIYLIFYSFNKGGDMNSFTGFTFSHYGELFQDSRLMLILVQ 68 MKKFAN+YLA VF++LYIPI YLIFYSFNKGGDMN FTGFT HY +F+DSRLM IL+Q Sbjct: 1 MKKFANLYLASVFVLLYIPIFYLIFYSFNKGGDMNGFTGFTLEHYQTMFEDSRLMTILLQ 60 Query: 69 TFFLAFLSALLATIIGTFGAIWIYQVRRRHQTSILSLNNILLVAPDVMIGASFLLVFTVI 128- TF LAF SALLATIIG FGAI+I+ VR ++Q ++LS NN+L+V+PDVMIGASFL++FT + Sbjct: 61 TFVLAFSSALLATIIGIFGAIFIHHVRGKYQNAMLSANNVLMVSPDVMIGASFLILFTSL 120- Query: 129 GLQLGFTSVLLSHVAFSIPIVVLMVLPRLKEMNDDMINASYDLGASTWQMLKEVMLPYLS 18- 8 QLG +SVLLSH+AFSIPIVVLMVLPRLKEMN DM+NA+YDLGA+ +QMLKEVMLPY + Sbjct: 121 KFQLGMSSVLLSHIAFSIPIVVLMVLPRLKEMNQDMVNAAYDLGANYFQMLKEVMLPYFT 18- 0 Query: 189 SGIISGFFMAFTYSLDDFAVTFFVTGNGFSTLSVEIYSRARRGISLEINALSTIVFLFSI 24- 8 GII+G+FMAFTYSLDDFAVTFF+TGN +TLSVEIYSRAR+GISL+INALSTIVF FSI Sbjct: 181 PGIIAGYFMAFTYSLDDFAVTFFLTGNSVTTLSVEIYSRARQGISLDINALSTIVFFFSI 24- 0 Query: 249 LLVIGYYYISKEKGEKNA 266 LLVIGYYY+S++K EK+A Sbjct: 241 LLVIGYYYMSQDKEEKHA 258 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1709 A DNA sequence (GBSx1813) was identified in S. agalactiae <SEQ ID 5313> which encodes the amino acid sequence <SEQ ID 5314>. This protein is predicted to be spermidine/putrescine ABC transporter, permease protein (potB). Analysis of this protein sequence reveals the following: TABLE-US-05221 Possible site: 35 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.55 Transmembrane 250-266 (244-269) INTEGRAL Likelihood = -3.93 Transmembrane 148-164 (146-166) INTEGRAL Likelihood = -3.35 Transmembrane 65-81 (64-85) INTEGRAL Likelihood = -1.97 Transmembrane 96-112 (96-115) ----- Final Results ----- bacterial membrane --- Certainty = 0.4821(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9853> which encodes amino acid sequence <SEQ ID 9854> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05222 >GP: AAC22990 GB: U32813 spermidine/putrescine ABC transporter, permease protein (potB) [Haemophilus influenzae Rd] Identities = 90/255 (35%), Positives = 153/255 (59%), Gaps = 11/255 (4%) Query: 21 AWLFLFVLAPVALIAWNSFFDINGH------FTLANYQTFFSSGTYLKMSFNSVLYAGIV 74 - +WL FVL P L+ SF +G T+ NY F+ Y ++ +NS+ +GI Sbjct: 18 SWLIFFVLIPNLLVLAVSFLTRDGSNFYAFPITIENYTNLFNP-LYAQVVWNSLSMSGIA 76 Query: 75 SFITLLISYPAAYLLTKL--KHKQLWLMLVILPTWINLLLKAYAFMGIFGQQGGINAFLT 132- + I LLI YP A++++K+ K++ L L LV+LP W N L++ Y G +G +N L Sbjct: 77 TIICLLIGYPFAFMMSKIHPKYRPLLLFLVVLPFWTNSLIRIYGMKVFLGVKGILNTMLI 136- Query: 133 FIGI--GPKQILFTDFSFLFVAAYIELPFMLLPIFNALDDIDQNLIYASDDLGANAWQTF 19- 0 +GI P +IL T+ + + Y+ LPFM+LP+++A++ +D L+ A+ DLGAN +Q F Sbjct: 137 DMGILSAPIRILNTEIAVIIGLVYLLLPFMILPLYSAIEKLDNRLLEAARDLGANTFQRF 19- 6 Query: 191 QKVIFPLSLNGVRAGVQSVFIPSLSLFMLTRLIGGNRVITLGTAIEQHFLITQNKGMGST 25- 0 +VI PL++ G+ AG V +P++ +F + L+GG +V+ +G I+ FLI++N GS Sbjct: 197 FRVILPLTMPGIIAGCLLVLLPAMGMFYVADLLGGAKVLLVGNVIKSEFLISRNWPFGSA 25- 6 Query: 251 IGVILILVMVAIMWL 265 + + L ++M ++++ Sbjct: 257 VSIGLTVLMALLIFV 271 A related DNA sequence was identified in S. pyogenes <SEQ ID 5315> which encodes the amino acid sequence <SEQ ID 5316>. Analysis of this protein sequence reveals the following: TABLE-US-05223 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.38 Transmembrane 19-35 (11-40) INTEGRAL Likelihood = -6.79 Transmembrane 250-266 (245-268) INTEGRAL Likelihood = -4.83 Transmembrane 65-81 (63-85) INTEGRAL Likelihood = -1.97 Transmembrane 96-112 (96-115) INTEGRAL Likelihood = -1.91 Transmembrane 148-164 (148-165) ----- Final Results ----- bacterial membrane --- Certainty = 0.3951(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05224 >GP: AAC22990 GB: U32813 spermidine/putrescine ABC transporter, permease protein (potB) [Haemophilus influenzae Rd] Identities = 91/262 (34%), Positives = 158/262 (59%), Gaps = 11/262 (4%) Query: 20 FLWILFFVVAPVTLLFYKSFFDIEGR------VTLANYETFFSSWTYLRMSVNSILYAGI 73 - F W++FFV+ P L+ SF +G +T+ NY F+ Y ++ NS+ +GI Sbjct: 17 FSWLIFFVLIPNLLVLAVSFLTRDGSNFYAFPITIENYTNLFNP-LYAQVVWNSLSMSGI 75 Query: 74 ITLVTLLISYPTALFLTRL--KHKQLWLMLIILPTWVNLLLKAYAFMGIFGQQGGINSFL 131- T++ LLI YP A ++++ K++ L L L++LP W N L++ Y G +G +N+ L Sbjct: 76 ATIICLLIGYPFAFMMSKIHPKYRPLLLFLVVLPFWTNSLIRIYGMKVFLGVKGILNTML 135- Query: 132 TFMGI--GPQQILFTDFSFIFVASYIELPFMMLPIFNALDDIDHNVINASRDLGASEFQA 18- 9 MGI P +IL T+ + I Y+ LPFM+LP+++A++ +D+ ++ A+RDLGA+ FQ Sbjct: 136 IDMGILSAPIRILNTEIAVIIGLVYLLLPFMILPLYSAIEKLDNRLLEAARDLGANTFQR 19- 5 Query: 190 FSKVIFPLSLNGVRAGVQSVFIPSLSLFMLTRLIGGNRVITLGTAIEQHFLTTQNWGMGS 24- 9 F +VI PL++ G+ AG V +P++ +F + L+GG +V+ +G I+ FL ++NW GS Sbjct: 196 FFRVILPLTMPGIIAGCLLVLLPAMGMFYVADLLGGAKVLLVGNVIKSEFLISRNWPFGS 25- 5 Query: 250 TIGVVLILTMVAIMWLTKEKSK 271 + + L + M ++++ +K Sbjct: 256 AVSIGLTVLMALLIFVYYRANK 277 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05225 Identities = 215/266 (80%), Positives = 239/266 (89%) Query: 4 RRREMKKTSSLFSIPYMAWLFLFVLAPVALIAWNSFFDINGHFTLANYQTFFSSGTYLKM 63 RR MKKTSSLFSIPY W+ FV+APV L+ + SFFDI G TLANY+TFFSS TYL+M Sbjct: 4 RRSVMKKTSSLFSIPYFLWILFFVVAPVTLLFYKSFFDIEGRVTLANYETFFSSWTYLRM 63 Query: 64 SFNSVLYAGIVSFITLLISYPAAYLLTKLKHKQLWLMLVILPTWINLLLKAYAFMGIFGQ 123- S NS+LYAGI++ +TLLISYP A LT+LKHKQLWLML+ILPTW+NLLLKAYAFMGIFGQ Sbjct: 64 SVNSILYAGIITLVTLLISYPTALFLTRLKHKQLWLMLIILPTWVNLLLKAYAFMGIFGQ 123- Query: 124 QGGINAFLTFIGIGPKQILFTDFSFLFVAAYIELPFMLLPIFNALDDIDQNLIYASDDLG 18- 3 QGGIN+FLTF+GIGP+QILFTDFSF+FVA+YIELPFM+LPIFNALDDID N+I AS DLG Sbjct: 124 QGGINSFLTFMGIGPQQILFTDFSFIFVASYIELPFMMLPIFNALDDIDHNVINASRDLG 18- 3 Query: 184 ANAWQTFQKVIFPLSLNGVRAGVQSVFIPSLSLFMLTRLIGGNRVITLGTAIEQHFLITQ 24- 3 A+ +Q F KVIFPLSLNGVRAGVQSVFIPSLSLFMLTRLIGGNRVITLGTAIEQHFL TQ Sbjct: 184 ASEFQAFSKVIFPLSLNGVRAGVQSVFIPSLSLFMLTRLIGGNRVITLGTAIEQHFLTTQ 24- 3 Query: 244 NKGMGSTIGVILILVMVAIMWLTKER 269 N GMGSTIGV+LIL MVAIMWLTKE+ Sbjct: 244 NWGMGSTIGVVLILTMVAIMWLTKEK 269 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1710 A DNA sequence (GBSx1814) was identified in S. agalactiae <SEQ ID 5317> which encodes the amino acid sequence <SEQ ID 5318>. This protein is predicted to be spermidine/putrescine ABC transporter, ATP-binding protein (potA). Analysis of this protein sequence reveals the following: TABLE-US-05226 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3031(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05227 >GP: AAB91525 GB: AE001165 spermidine/putrescine ABC transporter, ATP-binding protein (potA) [Borrelia burgdorferi] Identities = 166/345 (48%), Positives = 240/345 (69%), Gaps = 1/345 (0%) Query: 1 MTNPIIAFKNVSKVFEDSNTVVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLEAS 60 M N I+ KN+S ++++ L +IN ++++ +F TLLG SG GK+T++ I+ G L Sbjct: 1 MDNCILEIKNLSHYYDNNGNKTLDNINLKIKKNEFITLLGPSGCGKTTLIKILGGFLSQK 60 Query: 61 TGDIYLDGKRINDVPTNKRDVHTVFQNYALFPHMTVFENVAFPLKLKKMDKKEIQKRVQE 120- G+IY K I+ NKR+++TVFQNYALFPHM VF+N++F L++KK K I+++V+ Sbjct: 61 NGEIYFFSKEISKTSPNKREINTVFQNYALFPHMNVFDNISFGLRMKKTPKDIIKEKVKT 120- Query: 121 TLKMVRLEGFEKRAIQKLSGGQRQRVAIARAIINQPKVVLLDEPLSALDLKLRTEMQYEL 18- 0 +L ++ + + R I +LSGGQ+QRVAIARA++ +PK++LLDEPLSALDLK+R EMQ EL Sbjct: 121 SLSLIGMPKYAYRNINELSGGQKQRVAIARAMVMEPKLLLLDEPLSALDLKMRQEMQKEL 18- 0 Query: 181 RELQQRLGITFVFVTHDQEEALAMSDWIFVMNEGEIVQSGTPVDIYDEPINHFVATFIGE 24- 0 +++Q++LGITF++VTHDQEEAL MSD I VMNEG I+Q GTP +IY+EP FVA FIGE Sbjct: 181 KKIQRQLGITFIYVTHDQEEALTMSDRIVVMNEGIILQIGTPEEIYNEPKTKFVADFIGE 24- 0 Query: 241 SNILSGKMIEDYLVEFNGKRFEAVDGGMRPNESVQVVIRPEDLQITLPDEGKLQVKVDTQ 30- 0 SNI G ++ +V G FE +D G E+V +VIRPED+++ +G L + + Sbjct: 241 SNIFDGTYKKELVVSLLGHEFECLDKGFEAEEAVDLVIRPEDVKLLPKGKGHLSGTITSA 30- 0 Query: 301 LFRGVHYEIIAYDDLGNEWMIHSTRKAIEGEVIGLDFTPEDIHIM 345 +F+GVHYE+ N W++ STR GE + + P+DIH+M Sbjct: 301 IFQGVHYEMTLEIQKTN-WIVQSTRLTKVGEEVDIFLEPDDIHVM 344 There is also homology to SEQ ID 1292 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1711 A DNA sequence (GBSx1815) was identified in S. agalactiae <SEQ ID 5319> which encodes the amino acid sequence <SEQ ID 5320>. Analysis of this protein sequence reveals the following:

TABLE-US-05228 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4990(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05229 >GP: BAB06283 GB: AP001515 UDP-N-acetylenolpyruvoylglucosamine reductase [Bacillus halodurans] Identities = 119/286 (41%), Positives = 166/286 (57%), Gaps = 1/286 (0%) Query: 13 DIRFDEPLKKYTYTKVGGPADYLAFPRNRLELSRIVKFANSQNIPWMVLGNASNIIVRDG 72 - ++R +E L +T K+GGPAD P + L +K W V+G SNI+V D Sbjct: 15 EVRVNESLAHHTTWKIGGPADVFVIPNDIEGLKNTMKLIQETGCKWRVIGRGSNILVSDK 74 Query: 73 GIRGFVIMFDK-LSTVTVNGYVIEAEAGANLIETTRIARYHSLTGFEFACGIPGSVGGAV 131- G+RG I DK L + VNG I AG +++ + L G EFA GIPGSVGGAV Sbjct: 75 GLRGVTIKLDKGLDHLEVNGESITVGAGFPVVKLATVISRQGLAGLEFAAGIPGSVGGAV 134- Query: 132 FMNAGAYGGEIAHILLSAQVLTPQGELKTIEARNMQFGYRHSVIQESGDIVISAKFALKP 19- 1 FMNAGA+G +I+ IL A VL P G L+ + M F YR S++Q++ I + A F+L Sbjct: 135 FMNAGAHGSDISQILTKAHVLFPDGTLRWLTNEEMAFSYRTSLLQKNDGICVEAIFSLTR 19- 4 Query: 192 GDHLMITQEMDRLTYLRELKQPLEYPSCGSVFKRPPGHFAGQLISEAHLKGQRIGGVEVS 25- 1 GD I +++ + R QP +P+CGSVF+ P +AGQLI +A LKG +IGG ++S Sbjct: 195 GDKEDIKKKLQKNKDYRRDTQPWNHPTCGSVFRNPLPEYAGQLIEKAGLKGYQIGGAQIS 25- 4 Query: 252 QKHAGFMVNIAEGSAQDYENLIEHVINTVESTSGVHLEPEVRIIGE 297 HA F+VN + A D LI HV +T++ +++E EV +IGE Sbjct: 255 TMHANFIVNTGDAKAADVLALIHHVKDTIQKQYQMNMETEVELIGE 300 A related DNA sequence was identified in S. pyogenes <SEQ ID 5321> which encodes the amino acid sequence <SEQ ID 5322>. Analysis of this protein sequence reveals the following: TABLE-US-05230 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4557(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05231 Identities = 229/292 (78%), Positives = 267/292 (91%) Query: 8 ELEGLDIRFDEPLKKYTYTKVGGPADYLAFPRNRLELSRIVKFANSQNIPWMVLGNASNI 67 EL G+DIR +EPLK YTYTKVGGPAD+LAFPRN ELSRIV +AN +N+PW+VLGNASN+ Sbjct: 4 ELHGIDIRENEPLKHYTYTKVGGPADFLAFPRNHYELSRIVAYANKENMPWLVLGNASNL 63 Query: 68 IVRDGGIRGFVIMFDKLSTVTVNGYVIEAEAGANLIETTRIARYHSLTGFEFACGIPGSV 127- IVRDGGIRGFVIMFDKL+ V +NGY +EAEAGANLIETT+IA++HSLTGFEFACGIPGS+ Sbjct: 64 IVRDGGIRGFVIMFDKLNAVHLNGYTLEAEAGANLIETTKIAKFHSLTGFEFACGIPGSI 123- Query: 128 GGAVFMNAGAYGGEIAHILLSAQVLTPQGELKTIEARNMQFGYRHSVIQESGDIVISAKF 18- 7 GGAVFMNAGAYGGEI+HI LSA+VLTP GE+KTI AR+M FGYRHS IQE+GDIVISAKF Sbjct: 124 GGAVFMNAGAYGGEISHIFLSAKVLTPSGEIKTISARDMAFGYRHSAIQETGDIVISAKF 18- 3 Query: 188 ALKPGDHLMITQEMDRLTYLRELKQPLEYPSCGSVFKRPPGHFAGQLISEAHLKGQRIGG 24- 7 ALKPG++ I+QEM+RL +LR+LKQPLE+PSCGSVFKRPPGHFAGQLI EA+LKG RIGG Sbjct: 184 ALKPGNYDTISQEMNRLNHLRQLKQPLEFPSCGSVFKRPPGHFAGQLIMEANLKGHRIGG 24- 3 Query: 248 VEVSQKHAGFMVNIAEGSAQDYENLIEHVINTVESTSGVHLEPEVRIIGESL 299 VEVS+KH GFM+N+A+G+A+DYE+LI +VI TVE+ SGV LEPEVRIIGE+L Sbjct: 244 VEVSEKHTGFMINVADGTAKDYEDLIAYVIETVENHSGVRLEPEVRIIGENL 295 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1712 A DNA sequence (GBSx1816) was identified in S. agalactiae <SEQ ID 5323> which encodes the amino acid sequence <SEQ ID 5324>. This protein is predicted to be 2-amino-4-hydroxy-6-hydroxymethyldihydropterin pyrophosphokinase/dihyd. Analysis of this protein sequence reveals the following: TABLE-US-05232 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1122(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05233 >GP: BAB03814 GB: AP001507 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase [Bacillus halodurans] Identities = 64/146 (43%), Positives = 94/146 (63%) Query: 5 YLSLGSNIGDRETFLKQALFSIDHLQKTKVAQISAIYETAAWGNTNQEDFFNICCQVETD 64 Y++LGSNIGDR FL++A+ + K V S+IYET G T+Q F N+ +V T Sbjct: 6 YIALGSNIGDRSRFLEEAIQQLAEHDKVTVTCCSSIYETDPVGYTDQSPFLNMVVEVSTS 65 Query: 65 LAPFELLDYCQEIEKCLKRVRHEHWGPRTIDIDILLFGNQVINQEDLVVPHPYMTKRAFV 124- L +LL+ Q+IE+ R RH WGPRT+D+DILL+ + E+L++PHP M +RAFV Sbjct: 66 LPVEQLLEVTQKIERYCGRERHIRWGPRTLDLDILLYDQENREMENLIIPHPRMWERAFV 125- Query: 125 LVPLLEIAPQLSLPNGSKLEDYLEKL 150 L+PL+E+ P + P+G +E + +L Sbjct: 126 LIPLMELNPSIVAPSGKTIEQVVREL 151 A related DNA sequence was identified in S. pyogenes <SEQ ID 5325> which encodes the amino acid sequence <SEQ ID 5326>. Analysis of this protein sequence reveals the following: TABLE-US-05234 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0479 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05235 Identities = 85/156 (54%), Positives = 111/156 (70%), Gaps = 1/156 (0%) Query: 1 MTTVYLSLGSNIGDRETFLKQALFSIDHLQKTKVAQISAIYETAAWGNTNQEDFFNICCQ 60 MT VYLSLG+N+GDR +L++AL ++ L +T++ S+IYET AWG T Q DF N+ CQ Sbjct: 1 MTIVYLSLGTNMGDRAAYLQKALEALADLPQTRLLAQSSIYETTAWGKTGQADFLNMACQ 60 Query: 61 VETDLAPFELLDYCQEIEKCLKRVRHEHWGPRTIDIDILLFGNQVINQEDLVVPHPYMTK 120- ++T L + L Q IE+ L RVRHE WG RTIDIDILLFG +V + ++L VPHPYMT+ Sbjct: 61 LDTQLTAADFLKETQAIEQSLGRVRHEKWGSRTIDIDILLFGEEVYDTKELKVPHPYMTE 120- Query: 121 RAFVLVPLLEIAPQLSLPNGSK-LEDYLEKLNLGEV 155 RAFVL+PLLE+ P L LP K L DYL L+ ++ Sbjct: 121 RAFVLIPLLELQPDLKLPPNHKFLRDYLAALDQSDI 156 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1713 A DNA sequence (GBSx1817) was identified in S. agalactiae <SEQ ID 5327> which encodes the amino acid sequence <SEQ ID 5328>. Analysis of this protein sequence reveals the following: TABLE-US-05236 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2826 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 5329> which encodes the amino acid sequence <SEQ ID 5330>. Analysis of this protein sequence reveals the following: TABLE-US-05237 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3547 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05238 Identities = 75/119 (63%), Positives = 92/119 (77%) Query: 1 MDKIYLNKCRFYGYHGAFSEEQTLGQVFQVDAVLSLDLAKASQTDDLIDTVHYGEVFDCI 60 MDKI L CRFYGYHGAF EEQTLGQ+F VD LS+DL AS +D L DTVHYG VFD + Sbjct: 1 MDKIVLEGCRFYGYHGAFKEEQTLGQIFLVDLELSVDLQAASLSDQLTDTVHYGMVFDSV 60 Query: 61 KNHVENEQYQLIEKLAGVIVEDIFLQFHPVQAITLKITKDNPPINGHYESVGIELERRR 119 + VE E++ LIE+LAG I E +F +F P++AI + I K+NPPI GHY++VGIELER+R Sbjct: 61 RQLVEGEKFILIERLAGAICEQLFNEFPPIEAIKVAIKKENPPIAGHYKAVGIELERQR 119 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1714 A DNA sequence (GBSx1818) was identified in S. agalactiae <SEQ ID 5331> which encodes the amino acid sequence <SEQ ID 5332>. Analysis of this protein sequence reveals the following: TABLE-US-05239 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 5333> which encodes the amino acid sequence <SEQ ID 5334>. Analysis of this protein sequence reveals the following: TABLE-US-05240 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05241 Identities = 181/267 (67%), Positives = 224/267 (83%), Gaps = 1/267 (0%) Query: 1 MKIGQYDITGKACIMGILNVTPDSFSDGGSYTTIDSALNQVGEMLEQGVAIVDIGGESTR 60 MKIG++ I G A IMGILNVTPDSFSDGGSYTT+ AL+ V +M+ G I+D+GGESTR Sbjct: 1 MKIGKFVIEGNAAIMGILNVTPDSFSDGGSYTTVQKALDHVEQMIADGAKIIDVGGESTR 60 Query: 61 PGAVFVTAEEEIKRVVPMIKAIREVYPDLLLSIDTYKTEVAQAALDAGVHILNDVWSGLY 120- PG FV+A +EI RVVP+IKAI+E Y D+L+SIDTYKTE A+AAL+AG ILNDVW+GLY Sbjct: 61 PGCQFVSATDEIDRVVPVIKAIKENY-DILISIDTYKTETARAALEAGADILNDVWAGLY 119- Query: 121 DGKMLSLAAERNVPIILMHNQEEAVYQDIKKEVCEFLLERAERALEAGVSKDNIWIDPGF 18- 0 DG+M +LAAE + PIILMHNQ+E VYQ++ ++VC+FL RA+ AL+AGV K+NIW+DPGF Sbjct: 120 DGQMFALAAEYDAPIILMHNQDEEVYQEVTQDVCDFLGNRAQAALDAGVPKNNIWVDPGF 17- 9 Query: 181 GFAKTEEQNLELLKGLEQVCDLGYPVLFGISRKRTVNYLLGGNREVTERDMGTAALSAWA 24- 0 GFAK+ +QN ELLKGL++VC LGYPVLFGISRKR V+ LLGGN + ERD TAALSA+A Sbjct: 180 GFAKSVQQNTELLKGLDRVCQLGYPVLFGISRKRVVDALLGGNTKAKERDGATAALSAYA 23- 9 Query: 241 IAKGCQIVRVHNVEVNKDIVTVISQLV 267 + KGCQIVRVH+V+ N+DIV V+SQL+ Sbjct: 240 LGKGCQIVRVHDVKANQDIVAVLSQLM 266 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1715 A DNA sequence (GBSx1819) was identified in S. agalactiae <SEQ ID 5335> which encodes the amino acid sequence <SEQ ID 5336>. Analysis of this protein sequence reveals the following: TABLE-US-05242 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2429(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 5337> which encodes the amino acid sequence <SEQ ID 5338>. Analysis of this protein sequence reveals the following: TABLE-US-05243 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1590(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05244 Identities = 151/184 (82%), Positives = 166/184 (90%) Query: 3 NQEKMEKAIYQFLEALGENPNREGLKDTPKRVAKMYIEMFSGLNQDPKEQFTAVFSENHE 62 N+EK E AIYQFLEA+GENPNREGL DTPKRVAKMY EMF GL +DPKE+FTAVF E HE Sbjct: 16 NKEKAEAAIYQFLEAIGENPNREGLLDTPKRVAKMYAEMFLGLGKDPKEEFTAVFKEQHE 75 Query: 63 EVVIVKDIPFYSMCEHHLVPFYGKAHIAYLPNDGRVTGLSKLARAVEVASKRPQLQERLT 122- +VVIVKDI FYS+CEHHLVPFYGKAHIAYLP+DGRVTGLSKLARAVEVASKRPQLQERLT Sbjct: 76 DVVIVKDISFYSICEHHLVPFYGKAHIAYLPSDGRVTGLSKLARAVEVASKRPQLQERLT 135- Query: 123 AQVAQALEDALAPKGIFVMIEAEHMCMTMRGIKKPGSKTITTVARGLYKDDRYERQEILS 18- 2 +Q+A AL +AL PKG VM+EAEHMCMTMRGIKKPGSKTITT ARGLYK+ R ERQE++S Sbjct: 136 SQIADALVEALNPKGTLVMVEAEHMCMTMRGIKKPGSKTITTTARGLYKESRAERQEVIS 19- 5 Query: 183 LIQK 186 L+ K Sbjct: 196 LMTK 199 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1716 A DNA sequence (GBSx1820) was identified in S. agalactiae <SEQ ID 5339> which encodes the amino acid sequence <SEQ ID 5340>. This protein is predicted to be folylpolyglutamate synthase (folC). Analysis of this protein sequence reveals the following: TABLE-US-05245 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2836 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9855> which encodes amino acid sequence <SEQ ID 9856> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05246 >GP: CAB14768 GB: Z99118 folyl-polyglutamate synthetase [Bacillus subtilis] Identities = 154/426 (36%), Positives = 245/426 (57%), Gaps = 17/426 (3%) Query: 3 YQEALEWIHSKLAFGIKPGLERMRWMLEQLGNPQNNLSAIHVVGTNGKGSTTSYLQHIFT 62 YQ+A WIH +L FG+KPGL RM+ ++ +LG+P+ + A HV GTNGKGST ++++ + Sbjct: 5 YQDARSWIHGRLKFGVKPGLGRMKQLMARLGHPEKKIRAFHVAGTNGKGSTVAFIRSMLQ 64 Query: 63 NSGYQVGTFTSPYIVDFRERISIDGQMIPESDFIKLVETVRPVVERLHLETNLEPATEFE 122- +GY VGTFTSPYI+ F ERIS++G I + ++ LV ++P VE L +T TEFE Sbjct: 65 EAGYTVGTFTSPYIITFNERISVNGIPISDEEWTALVNQMKPHVEALD-QTEYGQPTEFE 123- Query: 123 VITVLMFYYFGNSCPVDIVIIEAGMGGYYDSTNMFKALAVTCPSIGLDHQEVLGRTYVDI 18- 2 ++T F YF VD VI E G+GG +DSTN+ + L SIG DH +LG T +I Sbjct: 124 IMTACAFLYFAEFHKVDFVIFETGLGGRFDSTNVVEPLLTVITSIGHDHMNILGNTIEEI 18- 3 Query: 183 AEQKVGVLKKGVPFVYANDRQDVEEVFQIKAKETHSQTYRLHNDFYIKEEE-----NYFN 23- 7 A +K G++K+G+P V A + + +V + +A+ + LH+ I EE F+ Sbjct: 184 AGEKAGIIKEGIPIVTAVTQPEALQVIRHEAERHAAPFQSLHDACVIFNEEALPAGEQFS 24- 3 Query: 238 YIGPQANIDHIQLQMPGHHQVSNASIAI-TTSLLLRDKYPKLTLQTIKDGLEMTKWVGRT 29- 6 + + + I+ + G HQ NA+++I L ++ ++ + ++ GL W GR Sbjct: 244 FKTEEKCYEDIRTSLIGTHQRQNAALSILAAEWLNKENIAHISDEALRSGLVKAAWPGRL 30- 3 Query: 297 ELI--FPNVMIDGAHNNESVDALVQVIK-KYQQKNVHILFAAINTKPIESMLESLSSIA- 35- 2 EL+ P V +DGAHN E V+ L + +K ++ + ++F+A+ KP ++M++L +IA Sbjct: 304 ELVQEHPPVYLDGAHNEEGVEKLAETMKQRFANSRISVVFSALKDKPYQNMIKRLETIAH 36- 3 Query: 353 PVSVTSFDYPK-SINLDKYPKAYTRVSDWKKWLHDI-----NLTSDKDFYVITGSLYFIS 40- 6 + SFD+P+ S+ D Y + W + D+ + + +ITGSLYFIS Sbjct: 364 AIHFASFDFPRASLAKDLYDASEISNKSWSEDPDDVIKFIESKKGSNEIVLITGSLYFIS 42- 3 Query: 407 QVRQEL 412 +R+ L Sbjct: 424 DIRKRL 429 A related DNA sequence was identified in S. pyogenes <SEQ ID 5341> which encodes the amino acid sequence <SEQ ID 5342>. Analysis of this protein sequence reveals the following: TABLE-US-05247 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.28 Transmembrane 12-28 (12-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.1510 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05248 Identities = 230/411 (55%), Positives = 295/411 (70%), Gaps = 1/411 (0%) Query: 1 MTYQEALEWIHSKLAFGIKPGLERMRWMLEQLGNPQNNLSAIHVVGTNGKGSTTSYLQHI 60 MTY+E LEWIH L FGIKPGL+RM W+L QLGNPQ N+ +H+VGTNGKGST ++LQHI Sbjct: 34 MTYEETLEWIHDHLVFGIKPGLKRMLWVLGQLGNPQKNVKGVHIVGTNGKGSTVNHLQHI 93 Query: 61 FTNSGYQVGTFTSPYIVDFRERISIDGQMIPESDFIKLVETVRPVVERLHLETNLEPATE 120- FT +GY+VGTFTSPYI+DF+ERISI+G+MI E D + +RP+ ERL ET+ TE Sbjct: 94 FTTAGYEVGTFTSPYIMDFKERISINGRMISEKDLVIAANRIRPLTERLVQETDFGEVTE 153- Query: 121 FEVITVLMFYYFGNSCPVDIVIIEAGMGGYYDSTNMFKALAVTCPSIGLDHQEVLGRTYV 18- 0 FEVIT++MF YFG+ PVDI IIEAG+GG YDSTN+F+A+ V CPSIGLDHQ +LG TY Sbjct: 154 FEVITLIMFLYFGDMHPVDIAIIEAGLGGLYDSTNVFQAMVVVCPSIGLDHQAILGETYA 21- 3 Query: 181 DIAEQKVGVLKKGVPFVYANDRQDVEEVFQIKAKETHSQTYRLHNDFYIKEEENYFNYIG 24- 0 +IA QK GVL+ G V+A + EVF KA++ + + F + E + + + Sbjct: 214 NIAAQKAGVLEGGETLVFAVENPSAREVFLTKAEQVGASIWEWQEQFQMAENASGYRFTS 27- 3 Query: 241 PQANIDHIQLQMPGHHQVSNASIAITTSLLLRDKYPKLTLQTIKDGLEMTKWVGRTELIF 30- 0 P I I + MPGHHQVSNA++AI T L L+D+YP+LT I++GL + W+GRTEL+ Sbjct: 274 PLGVISDIHIAMPGHHQVSNAALAIMTCLTLQDRYPRLTPDHIREGLANSLWLGRTELLA 33- 3 Query: 301 PNVMIDGAHNNESVDALVQVIK-KYQQKNVHILFAAINTKPIESMLESLSSIAPVSVTSF 35- 9 PN+MIDGAHNNESV ALV V+K Y K +HILF AI+TKPI ML +L I + VTSF Sbjct: 334 PNLMIDGAHNNESVAALVAVLKNNYNDKKLHILFGAIDTKPIADMLVALEQIGDLQVTSF 39- 3 Query: 360 DYPKSINLDKYPKAYTRVSDWKKWLHDINLTSDKDFYVITGSLYFISQVRQ 410 YP + L+KYP+ + RV+D+K +L DF+VITGSLYFIS++RQ Sbjct: 394 HYPNAYPLEKYPERFGRVADFKDFLALRKHAKADDFFVITGSLYFISEIRQ 444 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1717 A DNA sequence (GBSx1821) was identified in S. agalactiae <SEQ ID 5343> which encodes the amino acid sequence <SEQ ID 5344>. This protein is predicted to be rarD. Analysis of this protein sequence reveals the following:

TABLE-US-05249 Possible site: 38 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.31 Transmembrane 130-146 (125-151) INTEGRAL Likelihood = -10.24 Transmembrane 269-285 (262-291) INTEGRAL Likelihood = -7.75 Transmembrane 212-228 (207-233) INTEGRAL Likelihood = -5.52 Transmembrane 80-96 (75-99) INTEGRAL Likelihood = -4.14 Transmembrane 106-122 (104-125) INTEGRAL Likelihood = -3.50 Transmembrane 182-198 (180-204) INTEGRAL Likelihood = -2.44 Transmembrane 40-56 (39-57) INTEGRAL Likelihood = -0.96 Transmembrane 153-169 (152-169) INTEGRAL Likelihood = -0.32 Transmembrane 251-267 (250-267) ----- Final Results ----- bacterial membrane --- Certainty = 0.5925 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05250 >GP: BAB07585 GB: AP001520 unknown conserved protein [Bacillus halodurans] Identities = 109/288 (37%), Positives = 185/288 (63%), Gaps = 6/288 (2%) Query: 7 GIILGLSAYVLWGLLSLYWKLLSGIEAYSTFAYRIIFTVLTMLIYMLVSGRKTVYLKDLK 66 G+I +SAY++WG L LYWKL+ + A A+RI++++ M+I + V + ++++ Sbjct: 8 GVIAAISAYLIWGFLPLYWKLVDEVPASEMLAHRIVWSLGFMVILLAVMKKNRQVMREIL 67 Query: 67 GLVNNKKSFWTMFVASILISINWLVYIFAVTHGHATEASLGYYMMPIISILLSVLVLREH 126- + NKK+ + + VA+ILIS+NW ++I+AV+ EASLGYY+ P+I++LL+++ LRE Sbjct: 68 DTLANKKTAFGITVAAILISMNWFIFIYAVSSDKVIEASLGYYINPLINVLLAIVFLRES 127- Query: 127 LARVVSLAILIAIMGVGILVYQTGHFPLISLTLALSFGFYGLLKKSISLSSDFSMLVESS 18- 6 L++ + L+A GV + G FP ++ LA+SFG YGL+KK +SLS+ S+ +E+ Sbjct: 128 LSKWEVASFLLAAAGVLNITLHYGSFPWVAFALAISFGVYGLIKKVVSLSAWASLTIETL 18- 7 Query: 187 FIAPFALIYIVFF----AKDFLTDYNILQLVLLSLSGIITAVPLLLFAEAIKRAPLNII 241 + PFAL+++++ A F ++ + L+ SG TA+PLLLFA KR ++I Sbjct: 188 IMTPFALLFLLYIPLSGGASAFSLNH-LSTAWLIIASGAATALPLLLFATGAKRISFSLI 24- 6 Query: 242 GFIQYINPTIQLLLALFIFKETIVSGEVIGFIFIWLAILVFSIGQVHT 289 GF+QY+ PTI L+L +F+F+E + + F+ IW +++F+I + T Sbjct: 247 GFLQYLAPTIMLMLGVFLFQEPFSRVQFVSFLLIWTGLIIFTISRSRT 294 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8885> and protein <SEQ ID 8886> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05251 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 5.30 GvH: Signal Score (-7.5): -1.64 Possible site: 38 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 9 value: -12.31 threshold: 0.0 INTEGRAL Likelihood = -12.31 Transmembrane 130-146 (125-151) INTEGRAL Likelihood = -10.24 Transmembrane 269-285 (262-291) INTEGRAL Likelihood = -7.75 Transmembrane 212-228 (207-233) INTEGRAL Likelihood = -5.52 Transmembrane 80-96 (75-99) INTEGRAL Likelihood = -4.14 Transmembrane 106-122 (104-125) INTEGRAL Likelihood = -3.50 Transmembrane 182-198 (180-204) INTEGRAL Likelihood = -2.44 Transmembrane 40-56 (39-57) INTEGRAL Likelihood = -0.96 Transmembrane 153-169 (152-169) INTEGRAL Likelihood = -0.32 Transmembrane 251-267 (250-267) PERIPHERAL Likelihood = 7.96 229 modified ALOM score: 2.96 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5925 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00117## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1718 A DNA sequence (GBSx1822) was identified in S. agalactiae <SEQ ID 5345> which encodes the amino acid sequence <SEQ ID 5346>. Analysis of this protein sequence reveals the following: TABLE-US-05252 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5200 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1719 A DNA sequence (GBSx1823) was identified in S. agalactiae <SEQ ID 5347> which encodes the amino acid sequence <SEQ ID 5348>. Analysis of this protein sequence reveals the following: TABLE-US-05253 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0881(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05254 >GP: AAC44297 GB: U41735 homoserine kinase homolog [Streptococcus pneumoniae] Identities = 188/289 (65%), positives = 232/289 (80%), Gaps = 1/289 (0%) Query: 1 MRIIVPATSANIGPGFDSIGVALSKYLIIEVLEESTEWLVEHNLVN-IPKDHTNLLIQTA 59 M+IIVPATSANIGPGFDS+GVA++KYL IEV EE EWL+EH + IP D NLL+ A Sbjct: 1 MKIIVPATSANIGPGFDSVGVAVTKYLQIEVSEERDEWLIEHQIGKWIPHDERNLLLTIA 60 Query: 60 LHVKSDLAPHRLKMFSDIPLARGLGSSSSVIVAGIELANQLGNLALSQKEKLEIATRLEG 119- L + DL P RLKM SD+PLARGLGSSSSVIVAGIELANQLG L LS EKL++AT++EG Sbjct: 61 LQIVPDLQPRRLKMTSDVPLARGLGSSSSVIVAGIELANQLGQLNLSDHEKLQLATKIEG 120- Query: 120 HPDNVAPAIFGDLVISSIVKNDIKSLEVMFPDSSFIAFIPNYELKTSDSRNVLPQKLSYE 17- 9 HPDNVAPAI+G+LVI+S V+ + ++ FP+ F+A+IPNYEL+T DSR+VLP+KLSY+ Sbjct: 121 HPDNVAPAIYGNLVIASSVEGQVSAIVADFPECDFLAYIPNYELRTRDSRSVLPKKLSYK 18- 0 Query: 180 DAVASSSVANVMVASLLKGDLVTAGWAIERDLFHERYRQPLVKEFEVIKQISTQNGAYAT 23- 9 +AVA+SS+ANV VA+LL GD+VTAG AIE DLFHERYRQ LV+EF +IKQ++ +NGAYAT Sbjct: 181 EAVAASSIANVAVAALLAGDMVTAGQAIEGDLFHERYRQDLVREFAMIKQVTKENGAYAT 24- 0 Query: 240 YLSGAGPTVMVLCSKEKEQAIVTELSKLCLGGQIQVLNIERKGVRVEKR 288 YLSGAGPTVMVL S +K I EL K G++ L ++ +GVRVE + Sbjct: 241 YLSGAGPTVMVLASHDKMPTIKAELEKQPFKGKLHDLRVDTQGVRVEAK 289 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1720 A DNA sequence (GBSx1824) was identified in S. agalactiae <SEQ ID 5349> which encodes the amino acid sequence <SEQ ID 5350>. This protein is predicted to be homoserine dehydrogenase (hom). Analysis of this protein sequence reveals the following: TABLE-US-05255 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9857> which encodes amino acid sequence <SEQ ID 9858> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05256 >GP: CAA65713 GB: X96988 hom [Lactococcus lactis] Identities = 221/432 (51%), Positives = 307/432 (70%), Gaps = 11/432 (2%) Query: 15 MTIKIALLGFGTVAKGIPYLLKENQHKLLSLEGEDIVIDKVLVRDNESRQRFINQGFTYN 74 - M + IA+LGFGTV G+P LL EN+ KL + E+IVI KVL+RDN++ ++ +QGF Y+ Sbjct: 1 MAVNIAILGFGTVGTGLPTLLSENKEKLAKILDEEIVISKVLMRDNKAIEKARSQGFNYD 60 Query: 75 FVTEINTILQDSQIDIVVELMGGIEPAKTYLSQALGFGKHIVTANKDLIALHGKELMDLA 134- FV ++ IL DS+I IVVELMG IEPAKTY++QA+ GK++VTANKDL+A+HG EL LA Sbjct: 61 FVLNLDDILADSEISIVVELMGRIEPAKTYITQAIEAGKNVVTANKDLLAVHGVELRSLA 120- Query: 135 DARGLALFYEGAVAGGIPILRTLSHSFASDKMTRLLGILNGTSNFMLTKMFEEGWSYEQA 19- 4 +AL+YE AVAGGIPILRTL++SF+SDK+T LLGILNGTSNFM+TKM EEGW+Y+++ Sbjct: 121 QKHHVALYYEAAVAGGIPILRTLANSFSSDKITHLLGILNGTSNFMMTKMSEEGWTYDES 18- 0 Query: 195 LKKAQELGYAESDPTNDVEGIDTAYKATILSQFGFGMPIDFDDVNYKGISSIRSEDVEVA 25- 4 L KAQELGYAESDPTNDV+GID +YK ILS+F FGM + DD+ G+ SI+ DVE+A Sbjct: 181 LAKAQELGYAESDPTNDVDGIDASYKLAILSEFAFGMTLAPDDIAKSGLRSIQKTDVEIA 24- 0 Query: 255 QEMGFAIKLVADLRETPTGISVDVSPTLISQKHPLAAVNHVMNAVFIESIGIGQSLFYGP 31- 4 Q+ G+ +KL ++ E +GI +VSPT + + HPLA+VN VMNAVFIES GIG S+FYG Sbjct: 241 QQFGYVLKLTGEINEVDSGIFAEVSPTFLPKSHPLASVNGVMNAVFIESEGIGDSVFYGA 30- 0 Query: 315 GAGQNPTATSVLADIIDISRSIRSQIKIKPMNTYHCPCRLSMQSDIFNEYYLAISLRNAE 37- 4 GAGQ PTATSVLADI+ I + ++ K N Y L+ DI N+YY ++ E Sbjct: 301 GAGQKPTATSVLADIVRIVKRVKDGTIGKSFNEYARSTSLANPHDIENKYYFSV-----E 35- 5 Query: 375 DSDTLGR------YFEQENIGLKNVIEKALGDKQQEIYVLTDEVSQEKITQFIEEFPESG 42- 8 D+ G+ F EN+ + V+++ K+ + +++ ++++ +++ ++ + Sbjct: 356 TPDSTGQLLLLVELFTSENVSFEQVLQQKGNGKRAVVVIISHKINRVQLSAIQDKLNQEK 41- 5 Query: 429 VIQLINVFKVIG 440 +L+N FKV+G Sbjct: 416 DFKLLNRFKVLG 427 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1721 A DNA sequence (GBSx1825) was identified in S. agalactiae <SEQ ID 5351> which encodes the amino acid sequence <SEQ ID 5352>. Analysis of this protein sequence reveals the following: TABLE-US-05257 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4548(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1722 A DNA sequence (GBSx1826) was identified in S. agalactiae <SEQ ID 5353> which encodes the amino acid sequence <SEQ ID 5354>. Analysis of this protein sequence reveals the following: TABLE-US-05258 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.79 Transmembrane 20-36 (14-41) ----- Final Results ----- bacterial membrane --- Certainty = 0.6116(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05259 >GP: CAB15906 GB: Z99123 similar to hypothetical proteins [Bacillus subtilis] Identities = 105/272 (38%), Positives = 149/272 (54%), Gaps = 20/272 (7%) Query: 25 FLLIALIGIFLFFNNRSKQEIKT-----KTNASSHRKIVTSIKKKK-----WIKQKTPVK 74 - FL I L+G L + QE K K ++KK+ WIK + P K Sbjct: 5 FLSIFLLGSCLALAACADQEANAEQPMPKAEQKKPEKKAVQVQKKEDDTSAWIKTEKPAK 64 Query: 75 IPILMYHAVHVMDPSEAASANLIVAPDIFESHIKRLKKEGYYFLAPNEAYRALNENALPE 134- +PILMYH++ ++ +L V FE+H+K L GY L P EA L ++ P Sbjct: 65 LPILMYHSI-------SSGNSLRVPKKEFEAHMKWLHDNGYQTLTPKEASLMLTQDKKPS 117- Query: 135 KKVIWITFDDGNADFYTKAYPILKKYKVKATNNIITGFVQEGRESNLNVQQMLEMKQNGM 19- 4 +K + ITFDDG D Y AYP+LKKY +KAT +I + G + +L +QM EM Q+G+ Sbjct: 118 EKCVLITFDDGYTDNYQDAYPVLKKYGMKATIFMIGKSI--GHKHHLTEEQMKEMAQHGI 17- 5 Query: 195 SFQGHTVTHPNLSLLTPELQTQEMTLSKQFLDQKLSQDTLAIAYPSGRYNPTTLDIASQY 25- 4 S + HT+ H L+ LTP+ Q EM SK+ D Q T I+YP GRYN TL A + Sbjct: 176 SIESHTIDHLELNGLTPQQQQSEMADSKKLFDNMFHQQTTIISYPVGRYNEETLKAAEKT 23- 5 Query: 255 -YKLGLTTNEGVATKDNGLLSLNRIRILPTTS 285 Y++G+TT G A++D G+ +L+R+R+ P S Sbjct: 236 GYQMGVTTEPGAASRDQGMYALHRVRVSPGMS 267 A related DNA sequence was identified in S. pyogenes <SEQ ID 5355> which encodes the amino acid sequence <SEQ ID 5356>. Analysis of this protein sequence reveals the following: TABLE-US-05260 Possible site: 24 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05261 >GP: CAB15906 GB: Z99123 similar to hypothetical proteins [Bacillus subtilis] Identities = 97/240 (40%), Positives = 140/240 (57%), Gaps = 9/240 (3%) Query: 71 KKTHFDSSKSQKKAHSKLTWTKQETPVKIPILMYHAIHVMSPEETANANLIVNPDLFDQQ 130- KR + + QKK W K E P K+PILMYH+I ++ +L V F+ Sbjct: 37 KKPEKKAVQVQKKEDDTSAWIKTEKPAKLPILMYHSI-------SSGNSLRVPKKEFEAH 89 Query: 131 LQKMKDEGYYFLSPEEVYRALSNNELPAKKVVWLTFDDSMIDFYNVAYPILKKYDAKATN 19- 0 ++ + D GY L+P+E L+ ++ P++K V +TFDD D Y AYP+LKKY KAT Sbjct: 90 MKWLHDNGYQTLTPKEASLMLTQDKKPSEKCVLITFDDGYTDNYQDAYPVLKKYGMKATI 149- Query: 191 NVITGLTEMGSAANLTLKQMKEMKQVGMSFQDHTVNHPDLEQASPDVQTTEMKDSKDYLD 25- 0 +I +G +LT +QMKEM Q G+S + HT++H +L +P Q +EM DSK D Sbjct: 150 FMIG--KSIGHKKHHLTEEQMKEMAQHGISIESHTIDHLELNGLTPQQQQSEMADSKKLFD 2- 07 Query: 251 KQLNQNTIAIAYPSGRYNDTTLQIAARLNYKLGVTTNEGIASAANGLLSLNRIRILPNMS 31- 0 +Q T I+YP GRYN+TL+ A + Y++GVTT G AS G+ +L+R+R+ P MS Sbjct: 208 NMFHQQTTIISYPVGRYNEETLKAAEKTGYQMGVTTEPGAASRDQGMYALHRVRVSPGMS 26- 7 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05262 Identities = 153/265 (57%), Positives = 199/265 (74%), Gaps = 4/265 (1%) Query: 33 IFLFFNNRSKQEIKTK---TNASSHRKIVTSIKKKKWIKQKTPVKIPILMYHAVHVMDPS 89 - I LF + ++ ++ TK T+ S + + K W KQ+TPVKIPILMYHA+HVM P Sbjct: 54 ISLFHHKKTAKKETTKLKKTHFDSSKSQKKAHSKLTWTKQETPVKIPILMYHAIHVMSPE 113- Query: 90 EAASANLIVAPDIFESHIKRLKKEGYYFLAPNEAYRALNENALPEKKVIWITFDDGNADF 149- E A+ANLIV PD+F+ ++++K EGYYFL+P E YRAL+ N LP KKV+W+TFDD DF Sbjct: 114 ETANANLIVNPDLFDQQLQKMKDEGYYFLSPEEVYRALSNNELPAKKVVWLTFDDSMIDF 17- 3 Query: 150 YTKAYPILKKYKVKATNNIITGFVQEGRESNLNVQQMLEMKQNGMSFQGHTVTHPNLSLL 20- 9 Y AYPILKKY KATNN+ITG + G +NL ++QM EMKQ GMSFQ HTV HP+L Sbjct: 174 YNVAYPILKKYDAKATNNVITGLTEMGSAANLTLKQMKEMKQVGMSFQDHTVNHPDLEQA 23- 3 Query: 210 TPELQTQEMTLSKQFLDQKLSQDTLAIAYPSGRYNPTTLDIASQY-YKLGLTTNEGVATK 26- 8 +P++QT EM SK +LD++L+Q+T+AIAYPSGRYN TTL IA++ YKLG+TTNEG+A+ Sbjct: 234 SPDVQTTEMKDSKDYLDKQLNQNTIAIAYPSGRYNDTTLQIAARLNYKLGVTTNEGIASA 29- 3 Query: 269 DNGLLSLNRIRILPTTSDDDLIKTI 293 NGLLSLNRIRILP S ++L++T+ Sbjct: 294 ANGLLSLNRIRILPNMSPENLLQTM 318 SEQ ID 5354 (GBS287d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 145 (lane 3 & 4; MW 57 kDa) and in FIG. 185 (lane 2; MW 57 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 145 (lane 6; MW 32 kDa) and in FIG. 181 (lane 5; MW 32 kDa). Purified GBS287d-GST is shown in FIG. 243, lanes 10-11; purified GBS287d-His is shown in FIG. 234, lanes 7-8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1723 A DNA sequence (GBSx1828) was identified in S. agalactiae <SEQ ID 5357> which encodes the amino acid sequence <SEQ ID 5358>. Analysis of this protein sequence reveals the following: TABLE-US-05263 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1724 A DNA sequence (GBSx1829) was identified in S. agalactiae <SEQ ID 5359> which encodes the amino acid sequence <SEQ ID 5360>. Analysis of this protein sequence reveals the following: TABLE-US-05264 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3352(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1725 A DNA sequence (GBSx1830) was identified in S. agalactiae <SEQ ID 5361> which encodes the amino acid sequence <SEQ ID 5362>. This protein is predicted to be glycine betaine transporter BetL (opuD). Analysis of this protein sequence reveals the following: TABLE-US-05265 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.68 Transmembrane 439-455 (435-491) INTEGRAL Likelihood = -12.10 Transmembrane 256-272 (249-281) INTEGRAL Likelihood = -11.30 Transmembrane 464-480 (456-491) INTEGRAL Likelihood = -10.83 Transmembrane 49-65 (44-74) INTEGRAL Likelihood = -10.40 Transmembrane 11-27 (5-34) INTEGRAL Likelihood = -9.98 Transmembrane 396-412 (390-419) INTEGRAL Likelihood = -9.29 Transmembrane 224-240 (220-247) INTEGRAL Likelihood = -7.11 Transmembrane 347-363 (341-366) INTEGRAL Likelihood = -2.87 Transmembrane 143-159 (143-159) INTEGRAL Likelihood = -2.60 Transmembrane 192-208 (191-208) INTEGRAL Likelihood = -1.44 Transmembrane 86-102 (86-105) ----- Final Results ----- bacterial membrane --- Certainty = 0.6074 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-05266 >GP:AAD30266 GB:AF102174 glycine betaine transporter BetL [Listeria monocytogenes] Identities = 277/503 (55%), Positives = 365/503 (72%), Gaps = 1/503 (0%) Query: 4 KHITPVFTGSLIVSLILVLLGIIVPRGFQSWTQILREQVSTNFGWLYLLLVTSILALCVF 63 K +T VF GS + L+ VL G +P F+++T +++ +++NFGW YL++V I+ C+F Sbjct: 2 KKLTNVFWGSGFLVLLAVLFGAFLPEQFETFTNHIQKFLTSNFGWYYLIVVAIIIIFCLF 61 Query: 64 FIMSPLGQIRLGQPHSRPEYSTVSWIAMMFSAGMGIGLVFYGAAEPLSHFAISTPGAPKE 123- ++SP+G IRLG+P P YS SW AM+FSAGMGIGLVF+GAAEPLSH+A+ PG Sbjct: 62 LVLSPIGSIRLGKPGEEPGYSNKSWFAMLFSAGMGIGLVFWGAAEPLSHYAVQAPGGEVG 121- Query: 124 SQTALADAFRFTFFHWGIHAWAVYALVALALAYFGFRKQEKYLLSVTLKPLFGDKTDGWL 18- 3 +Q A+ DA R++FFHWGI AW++YA+VALALAYF FRK L+S TL P+ G G + Sbjct: 122 TQAAMKDALRYSFFHWGISAWSIYAIVALALAYFKFRKNAPGLISATLYPILGKHAKGPI 18- 1 Query: 184 GKIVDITTVVATVIGVATTLGFGAAQINGGLSFLLGVPNNAFVQIVIILITTALFVMSAL 24- 3 G+++DI V ATVIGVATTLG GA QINGGL++L GVPNN VQ II+I T LF++SA+ Sbjct: 182 GQLIDIIAVFATVIGVATTLGLGAQQINGGLTYLFGVPNNFTVQFTIIVIVTILFMLSAM 24- 1 Query: 244 SGLGKGVKILSNLNLILAVALLALVIVLGPTVRIFDTLTESLGSYLQNFFGMSFRAAAFD 30- 3 SGL KG+++LSN+N+ +A LL L ++LGPT+ I + T S G YLQN MSF+ A Sbjct: 242 SGLDKGIQLLSNVNIYVAGVLLVLTLILGPTLFIMNNFTNSFGDYLQNIIQMSFQTAPDA 30- 1 Query: 304 NTKRSWIDNWTIFYWAWWISWSPFVGVFIARISKGRSIREFLTVVLLIPTLLSFVWFAAF 36- 3 R WID+WTIFYWAWW+SWSPFVG+FIARIS+GR+IR+FL V+++P L+S WFA F Sbjct: 302 PDARKWIDSWTIFYWAWWLSWSPFVGIFIARISRGRTIRQFLLGVIVLPALVSVFWFAVF 36- 1 Query: 364 GTLSTQVQQLG-TNLTKFATEEVLFATFNHYTLGWLLSIIAIILIFSFFITSADSATYVL 42- 2 G + V+Q G + L+ ATE+VLF FN + G +LSI+A+ILI FFITSADSAT+VL Sbjct: 362 GGSAIFVEQHGNSGLSSLATEQVLFGVFNEFPGGMMLSIVAMILIAVFFITSADSATFVL 42- 1 Query: 423 ANLTEDGNLNPKNRTKVIWGLVLAVIAIVLLLSGGLLALQNVLIIVALPFSFVMILMMLA 48- 2 M T G+LNP N KV WGL+ A IA VLL +GGL ALQN II A PFS V+ILM+++ Sbjct: 422 GMQTTGGSLNPPNSVKVTWGLLQAGIASVLLYAGGLTALQNASIIAAFPFSIVIILMIVS 48- 1 Query: 483 LLVELFHEKKEMGLSISPDRYPR 505 L V L E++++GL + P + R Sbjct: 482 LFVSLTREQEKLGLYVRPKKSQR 504 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8887> and protein <SEQ ID 8888> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05267 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 15.28 GvH: Signal Score (-7.5): -4.24 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 11 value: -12.68 threshold: 0.0 INTEGRAL Likelihood = -12.68 Transmembrane 439-455 (435-491) INTEGRAL Likelihood = -12.10 Transmembrane 256-272 (249-281) INTEGRAL Likelihood = -11.30 Transmembrane 464-480 (456 491) INTEGRAL Likelihood = -10.83 Transmembrane 49-65 (44-74) INTEGRAL Likelihood = -10.40 Transmembrane 11-27 (5-34) INTEGRAL Likelihood = -9.98 Transmembrane 396-412 (390-419) INTEGRAL Likelihood = -9.29 Transmembrane 224-240 (220-247) INTEGRAL Likelihood = -7.11 Transmembrane 347-363 (341-366) INTEGRAL Likelihood = -2.87 Transmembrane 143-159 (143-159) INTEGRAL Likelihood = -2.60 Transmembrane 192-208 (191-208) INTEGRAL Likelihood = -1.44 Transmembrane 86-102 (86-105) PERIPHERAL Likelihood = 3.50 319 modified ALOM score: 3.04 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6074 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00118## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1726 A DNA sequence (GBSx1831) was identified in S. agalactiae <SEQ ID 5363> which encodes the amino acid sequence <SEQ ID 5364>. This protein is predicted to be succinic semialdehyde dehydrogenase (gabD-1). Analysis of this protein sequence reveals the following: TABLE-US-05268 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2733 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9859> which encodes amino acid sequence <SEQ ID 9860> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05269 >GP:AAD19405 GB:AF102543 succinic semialdehyde dehydrogenase [Zymomonas mobilis] Identities = 229/455 (50%), Positives = 305/455 (66%), Gaps = 5/455 (1%) Query: 10 MAYKTIYPYTNEVLHEFDNISDSDLEQSLDIAHALYKTWRKEDNVEERQNQLHKVADLLR 69 - MAY+++ P T E + ++ + SD ++ S+D A ++K + + ER LHK A++ R Sbjct: 1 MAYESVNPATGETVKKYPDFSDKQVKDSVDRAATVFKNDWSQRTIAERSKVLHKAAEIFR 60 Query: 70 KDRDKYAEVMTKDNGKLFTEAQGEVDLCADIADYYADNGQKFLKPVPLESPNGEAYYLKQ 129- D DKYA++T DMGK EA+GEV+L ADI DYYA NG+KFL P +E G A Sbjct: 61 SDVDKYAKLLTIDNGKKIAEARGEVNLSADILDYYAKNGEKFLAPQKVEEKPG-AVVKAF 119- Query: 130 AVGVLLAVEPWNFPFYQINRVFAPNFIVGNTNLLKHASICPASAQAFEDLVREAGAPEGA 18- 9 +G+LLA+EPWNFP+YQ+ R+ P I GN +L+KH+S P SA AFE ++ EAGAP+G Sbjct: 120 PLGLLLAIEPWNFPYYQLARIAGPYLIAGNALLVKHSSSVPQSAHAFEAVLEEAGAPKGI 17- 9 Query: 190 FKNIFASYDQVSNLISDFRVAGVCLTGSERGGASIAAEAGKNLKKSSMELGGNDAFLILD 24- 9 + N+ AS DQVS +I DPRV GV +TGS GA +AA+AGK KKS MELGG+DAF++LD Sbjct: 180 YTNLDASPDQVSQIIEDPRVRGVTVTGSASVGAELAAKAGKNWKKSVMELGGSDAFIVLD 23- 9 Query: 250 DADFD--LLSKTIFFARLYNAGQVCTSSKRFIVMADKYDE-FVNNVVETFKSAKWGDPND 30- 6 D D L+ K + RL+NAGQV ++KRFI++ K E F + + F++ K GDPMD Sbjct: 240 GVDIDDKLIDKAAY-GRLFNAGQVWCAAKRFIIVGQKRAELFTEKLKQRFEALKIGDPND 29- 8 Query: 307 SETTLAPLSSAGAKDDVLKQIKLAVDHGAEVVFGNDTIDHPGNFVNPTVLTNITKANPIY 36- 6 T L PLSS GA+D V+KQ++ AV +GA++V G I+ G F+ +LT+I + NP Y Sbjct: 299 ESTDLGPLSSVGARDQVVKQVEKAVQNGAKLVCGGKAIEGKGAFMKAGILTDIKRENPAY 35- 8 Query: 367 NQEIFGPVASIYKVDTEEEAIALANDSSYGLGSTVFSSDPEHAKKVAAQIETGMTFINSG 42- 6 +E FGP+A IY V E EAI LANDS YGLG VF+ D E +KVA QIETGM IN Sbjct: 359 FEEFFGPIAQIYAVKDEAEAIELANDSPYGLGGAVFAPDVEQGRKVAEQIETGMVAINKP 41- 8 Query: 427 WTSLPELPFGGIKNSGYGRELSQLGFDAFVNEHLV 461 + PELPFGG+K+SGYGRELS G F+N L+ Sbjct: 419 LWTAPELPFGGVKHSGYGRELSHFGIQEFINWKLI 453 A related DNA sequence was identified in S. pyogenes <SEQ ID 5365> which encodes the amino acid sequence <SEQ ID 5366>. Analysis of this protein sequence reveals the following: TABLE-US-05270 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2887 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05271 Identities = 335/457 (73%), Positives = 397/457 (86%) Query: 9 IMAYRTIYPYTNEVLHEFDNISDSDLEQSLDIAHALYRTWRKEDNVEERQNQLHKVADLL 68 +MAY+TIYPYTNEVLH FDN++D L L+ AH LYK WRKED++EER+ QLH+VA++L Sbjct: 1 VMAYQTIYPYTWEVLHTFDNMTDQGLADVLERAHLLYKKWRKEDHLEERKAQLHQVANIL 60 Query: 69 RKDRDKYAEVMTKDMGKLFTEAQGEVDLCADIADYYADNGQKFLKPVPLESPNGEAYYLK 128- R+DRDKYAE+MTKDMGKLFTEAQGEV+LCADIADYYAD +FL PLE+ +G+AYYLK Sbjct: 61 RRDRDRYAEIMTKDMGKLFTEAQGEVNLCADIADYYADKADEFLMSTPLETDSGQAYYLK 120- Query: 129 QAVGVLLAVEPWNFPFYQIMRVFAPNFIVGNTMLLKHASICPASAQAFEDLVREAGAPEG 18- 8 Q+ GV+LAVEPWNFP+YQIMRVFAPNFIVGN M+LKHASICP SAQ+FE+LV EAGA G Sbjct: 121 QSTGVILAVEPWNFPYYQIMRVFAPNFIVGNPMVLKHASICPRSAQSFEELVLEAGAEAG 18- 0 Query: 189 AFKNIFASYDQVSNLISDPRVAGVCLTGSERGGASIAAEAGKNLKKSSMELGGNDAFLIL 24- 8 + N+F SYDQVS +I+D RV GVCLTGSERGGASIA EAGKNLKK+++ELGG+DAF+IL Sbjct: 181 SITNLFISYDQVSQVIADKRVVGVCLTGSERGGASIAEEAGKNLKKTTLELGGDDAFIIL 24- 0 Query: 249 DDADFDLLSKTIFFARLYNAGQVCTSSKRFIVMADKYDEFVNMVVETFKSAKWGDPMDSE 30- 8 DDAD+D L K ++F+RLYNAGQVCTSSKRFIV+ YD F ++ + FK+AKWGDPMD E Sbjct: 241 DDADWDQLEKVLYFSRLYNAGQVCTSSKRFIVLDKDYDRFKELLTKVFKTAKWGDPMDPE 30- 0 Query: 309 TTLAPLSSAGAKDDVLKQIKLAVDHGAEVVFGNDTIDHPGNFVMPTVLTNITKANPIYNQ 36- 8 TTLAPLSSA AK DVL QIKLA+DHGAE+V+G + IDHPG+FVMPT++ +TK NPIY Q Sbjct: 301 TTLAPLSSAQAKADVLDQIKLALDHGAELVYGGEAIDHPGHFVMPTIIAGLTKDNPIYYQ 36- 0 Query: 369 EIFGPVASIYKVDTEEEAIALANDSSYGLGSTVFSSDPKHAKKVAAQIETGMTFINSGWT 42- 8 EIFGPV IYKV +EEEAI +ANDS+YGLG T+FSS+ EHAK VAA+IETGM+FINSGWT Sbjct: 361 EIFGPVGEIYKVSSEEEAIEVANDSNYGLGGTIFSSNQEHAKAVAAKIETGMSFINSGWT 42- 0 Query: 429 SLPELPFGGIKNSGYGRELSQLGFDAFVNEHLVFTPN 465 SLPELPFGGIK+SGYGRELS+LGF +FVNEHL++ PN Sbjct: 421 SLPELPFGGIKHSGYGRELSELGFTSFVNEHLIYIPN 457 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1727 A DNA sequence (GBSx1832) was identified in S. agalactiae <SEQ ID 5367> which encodes the amino acid sequence <SEQ ID 5368>. Analysis of this protein sequence reveals the following: TABLE-US-05272 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1728 A DNA sequence (GBSx1833) was identified in S. agalactiae <SEQ ID 5369> which encodes the amino acid sequence <SEQ ID 5370>. Analysis of this protein sequence reveals the following: TABLE-US-05273 Possible site: 41 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.91 Transmembrane 94-110 (86-115) INTEGRAL Likelihood = -7.75 Transmembrane 154-170 (150-176) INTEGRAL Likelihood = -7.11 Transmembrane 316-332 (312-339) INTEGRAL Likelihood = -6.16 Transmembrane 258-274 (253-278) INTEGRAL Likelihood = -2.71 Transmembrane 218-234 (217-234) INTEGRAL Likelihood = -1.49 Transmembrane 286-302 (283-302) INTEGRAL Likelihood = -0.96 Transmembrane 73-89 (73-89) INTEGRAL Likelihood = -0.27 Transmembrane 121-137 (121-137) ----- Final Results ----- bacterial membrane --- Certainty = 0.4163 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9861> which encodes amino acid sequence <SEQ ID 9862> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05274 >GP: AAC75219 GB: AE000305 orf, hypothetical protein [Escherichia coli K12] Identities = 102/331 (30%), Positives = 172/331 (51%), Gaps = 26/331 (7%) Query: 12 IPGLILCFIIA-IPSWLLGLYLPLIGAPVF-----AILIGIIVGSFYQNR--QLFNKGIA 63 - IPGL L +I + W G +P + F AIL+G+++G+ + + G+ Sbjct: 17 IPGLALSAVITGVALW---GGSIPAVAGAGFSALTLAILLGMVLGNTIYPHIWKSCDGGVL 74- Query: 64 FTSKYILQTAVVLLGFGLNLMQVMKVGISSLPIIIMTISISLIIAYVL-QKLFKLDKTIA 122- F +Y+L+ ++L GF L Q+ VGIS + I ++T+S + ++A L QK+F LDK + Sbjct: 75 FAKQYLLRLGIILYGFRLTFSQIADVGISGIIIDVLTLSSTFLLACFLGQKVFGLDKHTS 134- Query: 123 TLIGVGSSICGGSAIAATAPVINAKDDEVAQAISVIFLFNILAALIFPTLGNFIG--LSD 18- 0 LIG GSSICG +A+ AT PV+ A+ +V A++ + +F +A ++P + + S Sbjct: 135 WLIGAGSSICGAAAVLATEPVVKAEASKVTVAVATVVIFGTVAIFLYPAIYPLMSQWFSP 19- 4 Query: 181 HGFALFAGTAVNDTSSVTAT--ATAWDAINHSNTLGGATIVKLTRTLAIIPITIVLSIYH 23- 8 F ++ G+ V++ + V A A + DA N A I K+ R + + P I+L+ Sbjct: 195 ETFGIYIGSTVHEVAQVVAAGHAISPDAEN------AAVISKMLRVMMLAPFLILLAA-R 24- 7 Query: 239 MKQTQKEQSVSVTKI-FPKFVLYFILASLLTTIVASLGFSLRIFEPLKVLSKFFIVMAMG 29- 7 +KQ S +KI P F + FI+ ++ + + L L F + MAM Sbjct: 248 VKQLSGANSGEKSKITIPWFAILFIVVAIFNSFHL---LPQSVVNMLVTLDTFLLAMAMA 30- 4 Query: 298 AIGINTNVSKLIKTGGKSILLGAACWLGIII 328 A+G+ T+VS L K G K +L+ + +I+ Sbjct: 305 ALGLTTHVSALKKAGAKPLLMALVLFAWLIV 335 A related DNA sequence was identified in S. pyogenes <SEQ ID 5371> which encodes the amino acid sequence <SEQ ID 5372>. Analysis of this protein sequence reveals the following: TABLE-US-05275 Possible site: 37 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.29 Transmembrane 30-46 (22-50) INTEGRAL Likelihood = -8.12 Transmembrane 314-330 (311-338) INTEGRAL Likelihood = -6.05 Transmembrane 8-24 (7-29) INTEGRAL Likelihood = -6.00 Transmembrane 150-166 (146-172) INTEGRAL Likelihood = -5.57 Transmembrane 257-273 (252-277) INTEGRAL Likelihood = -3.50 Transmembrane 91-107 (87-108) INTEGRAL Likelihood = -2.60 Transmembrane 69-85 (68-87) INTEGRAL Likelihood = -2.55 Transmembrane 289-305 (289-305) ----- Final Results ----- bacterial membrane --- Certainty = 0.4715 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05276 >GP: AAC75219 GB: AE000305 orf, hypothetical protein [Escherichia coli] Identities = 100/329 (30%), Positives = 173/329 (52%), Gaps = 21/329 (6%) Query: 8 LPGLLLCLLLALPAWCLGRLFPIIGAP----VFAILLGMLLA-LFYEHRDKTKEG-ISFT 61 +PGL L ++ A G + + GA AILLGM+L Y H K+ +G + F Sbjct: 17 IPGLALSAVITGVALWGGSIPAVAGAGFSALTLAILLGMVLGNTIYPHIWKSCDGGVLFA 76 Query: 62 SKYILQTAVVLLGFGLNLTQVMAVGMQSLPIIISTIATALLVAYGL-QKWLRLDVNTATL 120- +Y+L+ ++L GF L +Q+ VG+ + I + T+++ L+A L QK LD +T+ L Sbjct: 77 KQYLLRLGIILYGFRLTFSQIADVGISGIIIDVLTLSSTFLLACFLGQKVFGLDKHTSWL 136- Query: 121 VGVGSSICGGSAVAATAPVIKAKDDEVAKAISVIFLFNMLAALLFPSLGQLLG--LSNEG 17- 8 +G GSSICG +AV AT PV+KA+ +V A++ + +F +A L+P++ L+ S E Sbjct: 137 IGAGSSICGAAAVLATEPVVKAEASKVTVAVATVVIFGTVAIFLYPAIYPLMSQWFSPET 19- 6 Query: 179 FAIFAGTAVNDTSSVTATATAWDALHHSNTLDGATIVKLTRTLAILPITLGLSLYRAKKE 23- 8 F I+ G+ V++ + V A A + + A I K+ R + + P + L+ R K+ Sbjct: 197 FGIYIGSTVHEVAQVVAAGHAIS----PDAENAAVISKMLRVMMLAPFLILLAA-RVKQL 25- 1 Query: 239 HDIVTEENFSLRKSFPRFILFFLLASLITTLMTSLGVSADSFHYLKTLSKFFIVMAMAAI 29- 8 + E + + P F + F++ ++ + + + L TL F + MAMAA+ Sbjct: 252 SGANSGEKSKI--TIPWFAILFIVVAIFNSFHL---LPQSVVNMLVTLDTFLLAMAMAAL 30- 6 Query: 299 GLNTNLVKLIKTGGQAILLGAI--CWVAI 325 GL T++ L K G + +L+ + W+ + Sbjct: 307 GLTTHVSALKKAGAKPLLMALVLFAWLIV 335 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05277 Identities = 225/333 (67%), Positives = 277/333 (82%), Gaps = 3/333 (0%) Query: 11 KIPGLILCFIIAIPSWLLGLYLPLIGAPVFAILIGIIVGSFYQNRQLFNKGIAFTSKYIL 70 - K+PGL+LC ++A+P+W LG P+IGAPVFAIL+G+++ FY++R +GI+FTSKYIL Sbjct: 7 KLPGLLLCLLLALPAWCLGRLFPIIGAPVFAILLGMLLALFYEHRDKTKEGISFTSKYIL 66 Query: 71 QTAVVLLGFGLNLMQVMKVGISSLPIIIMTISISLIIAYVLQKLFKLDKTIATLIGVGSS 130- QTAVVLLGFGLNL QVM VG+ SLPIII TI+ +L++AY LQK +LD ATL+GVGSS Sbjct: 67 QTAVVLLGFGLNLTQVMAVGMQSLPIIISTIATALLVAYGLQKWLRLDVNTATLVGVGSS 126- Query: 131 ICGGSAIAATAPVINAKDDEVAQAISVIFLFNILAALIFPTLGNFIGLSDHGFALFAGTA 19- 0 ICGGSA+AATAPVI AKDDEVA+AISVIFLFN+LAAL+FP+LG +GLS+ GFA+FAGTA Sbjct: 127 ICGGSAVAATAPVIKAKDDEVAKAISVIFLFNMLAALLFPSLGQLLGLSNEGFAIFAGTA 18- 6 Query: 191 VNDTSSVTATATAWDAINHSNTLGGATIVKLTRTLAIIPITIVLSIYHMKQTQ---KEQS 24- 7 VNDTSSVTATATAWDA++HSNTL GATIVKLTRTLAI+PIT+ LS+Y K+ E++ Sbjct: 187 VNDTSSVTATATAWDALHHSNTLDGATIVKLTRTLAILPITLGLSLYRAKKEHDIVTEEN 24- 6 Query: 248 VSVTKIFPKFVLYFILASLLTTIVASLGFSLRIFEPLKVLSKFFIVMAMGAIGINTNVSK 30- 7 S+ K FP+F+L+F+LASL+TT++ SLG S F LK LSKFFIVMAM AIG+NTN+ K Sbjct: 247 FSLRKSFPRFILFFLLASLITTLMTSLGVSADSFHYLKTLSKFFIVMAMAAIGLNTNLVK 30- 6 Query: 308 LIKTGGKSILLGAACWLGIIIVSLTMQAILGTW 340 LIKTGG++ILLGA CW+ I +VSL MQ LG W Sbjct: 307 LIKTGGQAILLGAICWVAITLVSLAMQLSLGIW 339 A related GBS gene <SEQ ID 8889> and protein <SEQ ID 8890> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05278 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 22.17 GvH: Signal Score (-7.5): -0.429999 Possible site: 41 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 8 value: -7.91 threshold: 0.0 INTEGRAL Likelihood = -7.91 Transmembrane 94-110 (86-115) INTEGRAL Likelihood = -7.75 Transmembrane 154-170 (150-176) INTEGRAL Likelihood = -7.11 Transmembrane 316-332 (312-339) INTEGRAL Likelihood = -6.16 Transmembrane 258-274 (253-278) INTEGRAL Likelihood = -2.71 Transmembrane 218-234 (217-234) INTEGRAL Likelihood = -1.49 Transmembrane 286-302 (283-302) INTEGRAL Likelihood = -0.96 Transmembrane 73-89 (73-89) INTEGRAL Likelihood = -0.27 Transmembrane 121-137 (121-137) PERIPHERAL Likelihood = 3.29 175 modified ALOM score: 2.08 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4163 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00119## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1729 A DNA sequence (GBSx1834) was identified in S. agalactiae <SEQ ID 5373> which encodes the amino acid sequence <SEQ ID 5374>. Analysis of this protein sequence reveals the following:

TABLE-US-05279 Possible site: 57 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.93 Transmembrane 7-23 (1-27) ----- Final Results ----- bacterial membrane --- Certainty = 0.5373 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 5375> which encodes the amino acid sequence <SEQ ID 5376>. Analysis of this protein sequence reveals the following: TABLE-US-05280 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -16.34 Transmembrane 22-38 (13-42) ----- Final Results ----- bacterial membrane --- Certainty = 0.7538 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-05281 Identities = 56/215 (26%), Positives = 111/215 (51%), Gaps = 5/215 (2%) Query: 7 VFLTVLVLILIVGAGGLYFWNNHQSLEGKWRTVSLEKQVEKEIEQQLGSQAADMGISAAD 66 +F+ ++ LIL+ G+ + N+ S+EG WRT S+++++ + ++L I + Sbjct: 22 LFVFIIFLILLAVLFGVRYRNS--SIEGIWRTTSIDQKLGDDFAKRLTGLHQSPLIDDS- 78 Query: 67 LVKGANMHMNVKNDEAKITVTAQIDEVKFHQAIKTFIDKALEKQLKDQGLTYNDLSEAGK 126- L+ + M + VKN+ ++ + Q++ F + + + L K LK+ L DLS + Sbjct: 79 LLTSSQMILTVKNNNVDLSFSVQVERDIFVKRLAAYHQNELLKTLKENHLVVGDLSSKER 138- Query: 127 KIFDETKITDQQIDQQIDRSFQSAAQAAGGKYNTNTGEMTLPVMDGKVHRLTSVIKV-SH 18- 5 +I + + +++ +D++F+ A GGKYN TG ++ V+ GKV+R+ I + Sbjct: 139 QIIENSMPASHELEMILDQAFEKLASQIGGKYNQKTGHLSAVVLKGKVNRILHTIDIKEE 19- 8 Query: 186 INKKANAFYGNIVKNGEKTAYKKEGSKL-ILGNEK 219 + +F ++ Y + G KL +LG+EK Sbjct: 199 VAAGHTSFSKGLLTPNGYFDYTRFGKKLELLGDEK 233 SEQ ID 5374 (GBS288) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 59 (lane 3; MW 53.7 kDa). GBS288d was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 154 (lane 8-10; MW 26 kDa) and in FIG. 183 (lane 3; MW 26 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 187 (lane 11; MW 51 kDa). Purified GBS288d-GST is shown in lane 8 of FIG. 237. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1730 A DNA sequence (GBSx1835) was identified in S. agalactiae <SEQ ID 5377> which encodes the amino acid sequence <SEQ ID 5378>. Analysis of this protein sequence reveals the following: TABLE-US-05282 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3885 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1731 A DNA sequence (GBSx1836) was identified in S. agalactiae <SEQ ID 5379> which encodes the amino acid sequence <SEQ ID 5380>. Analysis of this protein sequence reveals the following: TABLE-US-05283 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.37 Transmembrane 67-83 (63-89) INTEGRAL Likelihood = -3.72 Transmembrane 139-155 (137-158) INTEGRAL Likelihood = -1.54 Transmembrane 115-131 (114-131) ----- Final Results ----- bacterial membrane --- Certainty = 0.5946 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10905> which encodes amino acid sequence <SEQ ID 10906> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1732 A DNA sequence (GBSx1837) was identified in S. agalactiae <SEQ ID 5381> which encodes the amino acid sequence <SEQ ID 5382>. Analysis of this protein sequence reveals the following: TABLE-US-05284 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4709 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1733 A DNA sequence (GBSx1838) was identified in S. agalactiae <SEQ ID 5383> which encodes the amino acid sequence <SEQ ID 5384>. Analysis of this protein sequence reveals the following: TABLE-US-05285 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2191(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05286 >GP: AAC98427 GB: M63481 20-kDa protein [Streptococcus sanguinis] Identities = 119/163 (73%), Positives = 146/163 (89%) Query: 1 MTTFLGNPVTFTGKQLQVGDIAKDFLLIATDLSQKSLKDFEGKKKVISVVPSIDTGICSK 60 MTTFLGNPVTFTGKQLQVGD A DF L ATDLS+K+L DF GKKKV+S++PSIDTG+CS Sbjct: 1 MTTFLGNPVTFTGKQLQVGDTAHDFSLTATDLSKKTLADFAGKKKVLSIIPSIDTGVCST 60 Query: 61 QTRTFNEELSELDNTVVITVSMDLPFAQKRWCSAEGLDNVILLSDFYDHSFGQEYALLMN 120- QTR FN+ELS+LDNTVVITVS+DLPFAQ +WC+AEG++N ++LSD++DHSFG++YA+L+N Sbjct: 61 QTRRFNQELSDLDNTVVITVSVDLPFAQGKWCAAEGIENAVMLSDYFDHSFGRDYAVLIN 120- Query: 121 EWHLLTRAVLILDEHNKVTYTEYVDNVNSDVDYEAAINAAKIL 163 EWHLL RAVL+LDE+N VTY EYVDN+N++ DY+AAI A K L Sbjct: 121 EWHLLARAVLVLDENNTVTYAEYVDNINTEPDYDAAIAAVKSL 163 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1734 A DNA sequence (GBSx1839) was identified in S. agalactiae <SEQ ID 5385> which encodes the amino acid sequence <SEQ ID 5386>. This protein is predicted to be DNA alkylation repair enzyme. Analysis of this protein sequence reveals the following: TABLE-US-05287 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4729(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05288 >GP: CAB40581 GB: AJ010128 DNA alkylation repair enzyme [Bacillus cereus] Identities = 67/217 (30%), Positives = 119/217 (53%), Gaps = 5/217 (2%) Query: 6 SLERKFKAASDKEVSKQQEAYLRHHFKCYGIKSPERRMLYKELIKAAKRQAKIDWQLLDK 65 +L+ F A + E ++ Y+++HF GI++PERR L K++I+ + D+Q++ + Sbjct: 7 ALQEHFIANQNPEKAEPMARYMKNHFPFLGIQTPERRQLLKDVIQIHTLPDQKDFQVIVR 66 Query: 66 -CWQSDYREYHHFVLDYLLAMSQFLTYNDCSRLEFYARHQQWWDSIDVLTKIF-GNLSLK 123- W RE+ LD + + LE + WWD++D + F GN+ L+ Sbjct: 67 ELWDLPEREFQAAALDMMQKYKMHINETHIPFLEELIVTKSWWDTVDSIVPTFLGNIFLQ 126- Query: 124 DDKVMNL-LSEWSLDQDFWMRRLAIEHQLGFKEKTNTDILSLFILRNTGSQEFFINKAIG 18- 2 ++++ + +W + W++R AI QL +K+K + ++L I + S+EFFI KAIG Sbjct: 127 HPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWVIGQLHSSKEFFIQKAIG 18- 6 Query: 183 WALRDYSKYNKVWVKDFISNHCDELSTLSIREGSKYL 219 W LR+Y+K V +++ N +EL+ LS RE K++ Sbjct: 187 WVLREYAKTKSDVVWEYVQN--NELAPLSRREAIKHI 221 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1735 A DNA sequence (GBSx1841) was identified in S. agalactiae <SEQ ID 5387> which encodes the amino acid sequence <SEQ ID 5388>. Analysis of this protein sequence reveals the following: TABLE-US-05289 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2117(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05290 >GP: CAA81648 GB: Z27121 unknown [Mycoplasma hominis] Identities = 67/281 (23%), Positives = 113/281 (39%), Gaps = 52/281 (18%) Query: 3 FVFDIDGTLCFDGMS--LSKEIQGILERAQIDYGHRVTFATARSYRDTIGILGDKLSLSK 60 F D+DGTL D + + + + +++A + GH V+ T R +R T+ + +KL L+ Sbjct: 14 FAIDLDGTLLADSANGTVHPKTEEAIKKA-VAQGHIVSIITGRPWRSTLPVY-EKLGLNA 71 Query: 61 IIG-LNGATLHENGHLVDSYYLQSDFFSTIISYCHRHQIPYFVD------EVFNYATYQA 113- I+G NGA +H FF I+Y +++ Y + E+ NYA Sbjct: 72 IVGNYNGAHIHNPA---------DPFFIPAITYLDLNEVLYILGDEKVKKEITNYAIEGP 122- Query: 114 SKIPFIAYVDPQ-----------KRGELLEVSKIE----------KPIKMVLYFGDQLGR 15- 2 + + + DP K E + + KI KP VL L R Sbjct: 123 DWVQLM-HRDPNLERVFGFNQATKFRECINLEKIPLKPTGIVFDVKPDTDVLELLTYLKR 18- 1 Query: 153 ADQMLAELNRFGLSSHFFHEFEKCLYINPIAVDKGKATKKLFG------NRFIAFGNDKN 20- 6 L E + + F+ I I +DKGK + + +A G+ N Sbjct: 182 RYGDLGEFSSWSKGEGLSPVFD----ITSIGIDKGKVISLIMRYYNIDIDDTVAMGDSYN 23- 7 Query: 207 DISMFDAAHYSVQVGDFDELTPYANLRVSRESVHEGITTLF 247 D+SM++ A+ V + + L + V +++ EG F Sbjct: 238 DLSMYNVANVCVSPANAEPLIKKMSTVVMKQTNKEGAVGYF 278 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1736 A DNA sequence (GBSx1842) was identified in S. agalactiae <SEQ ID 5389> which encodes the amino acid sequence <SEQ ID 5390>. Analysis of this protein sequence reveals the following: TABLE-US-05291 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2383(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05292 >GP: AAB90005 GB: AE001018 A. fulgidus predicted coding region AF1244 [Archaeoglobus fulgidus] Identities = 22/48 (45%), Positives = 35/48 (72%) Query: 150 GKSIGELNVWHQTGATIVAIEHEGKFIVSPGPFSVIEQGDHIFFVGDE 197 GKSIGEL + +TGAT++A+ + K I+SP P +V+E GD + +G++ Sbjct: 102 GKSIGELGIRSKTGATVIAVLKKEKTIISPSPETVLEPGDKVVVIGEK 149 A related DNA sequence was identified in S. pyogenes <SEQ ID 5391> which encodes the amino acid sequence <SEQ ID 5392>. Analysis of this protein sequence reveals the following: TABLE-US-05293 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2446(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05294 Identities = 163/213 (76%), Positives = 196/213 (91%) Query: 1 MVSEQSEIVTSKYQKIAVAVAQRIANGDYEVGEKLKSRTTIASTFNVSPETARKGLNILA 60 ++S + EI +SKYQKIA++VAQRIANG+YEVGEKLKSRTTIASTFNVSPETARKGLNILA Sbjct: 1 VISPKKEITSSKYQKIAISVAQRIANGEYEVGEKLKSRTTIASTFNVSPETARKGLNILA 60 Query: 61 DLQILTLKHGSGAIILSKEKAIEFLNQYETSHSVAILKGKIRDNIKAQQQEMEELATLVD 120- DL+ILTLKHGSGAI+LSKE+AIEF+NQYE++HS+A+LK KIR+ I Q + ME++A LV+ Sbjct: 61 DLKILTLKHGSGAIVLSKERAIEFINQYESTHSIAVLKEKIRETINDQGKAMEKMAVLVN 120- Query: 121 DFLLQTRAVSKQYPLAPYEIIVSEDSEHLGKSIGELNVWHQTGATIVAIEHEGKFIVSPG 18- 0 DFL+Q+++VSKQYPLAPYEII ++DSEH GESIG LN+WHQTGATIVAIEH G+FIVSPG Sbjct: 121 DFLMQSQSVSKQYPLAPYEIICNQDSEHFGKSIGVLNIWHQTGATIVAIEHAGQFIVSPG 18- 0 Query: 181 PFSVIEQGDHIFFVGDEDVYARMKTYFNLRMGL 213 P+SVIE+GDHI+FVGDE V +RMKT+FNLR GL Sbjct: 181 PYSVIEKGDHIYFVGDESVISRMKTFFNLRKGL 213 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1737 A DNA sequence (GBSx1844) was identified in S. agalactiae <SEQ ID 5393> which encodes the amino acid sequence <SEQ ID 5394>. This protein is predicted to be gls24. Analysis of this protein sequence reveals the following: TABLE-US-05295 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2855(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9361> which encodes amino acid sequence <SEQ ID 9362> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05296 >GP: AAA86383 GB: U23376 putative 20-kDa protein [Lactococcus lactis] Identities = 63/124 (50%), Positives = 84/124 (66%) Query: 1 MSGGFFSNLKNSVVNSDSVTDGVNVEVGTKEVAVDLDIVVEYGKDIPAIVESIKAIVSQN 60 + GGFFSNL ++N+D VT GV+VEVG +VAVDL +V EY K++P I E IK ++ + Sbjct: 55 VEGGFFSNLTGKLINTDDVTTGVDVEVGKTQVAVDLKVVTEYRKNVPDIYEKIKEVIRKE 114- Query: 61 VEVMTHLKVVELNANVVDIKTKAEHEADSVTVQDRVSDAAQATGNFASEQAGKAKAAISS 120- V MT L+VVE+N V DIKTK + + D V++QDRV+ AAQ TG F SEQ K K + Sbjct: 115 VAAMTELEVVEVNVTVTDIKTKEQQKEDDVSIQDRVTSAAQTTGKFTSEQVDKVKDKVED 17- 4 Query: 121 GAEK 124 +K Sbjct: 175 NTDK 178 A related DNA sequence was identified in S. pyogenes <SEQ ID 5395> which encodes the amino acid sequence <SEQ ID 5396>. Analysis of this protein sequence reveals the following: TABLE-US-05297 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2534(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05298 Identities = 94/137 (68%), Positives = 108/137 (78%), Gaps = 8/137 (5%) Query: 1 MSGGFFSNLKNSVVNSDSVTDGVNVEVGTKEVAVDLDIVVEYGKDIPAIVESIKAIVSQN 60 ++GGFFSN+KN++VNS+SVTDGV+VEVG+KEVAVDL I+VEYGKDIPAI ESIKAIVSQN Sbjct: 35 VTGGFFSNIKNNLVNSESVTDGVSVEVGSKEVAVDLAIIVEYGKDIPAIAESIKAIVSQN 94 Query: 61 VEVMTHLKVVELNANVVDIKTKAEHEADSVTVQDRVSDAAQATGNFASEQAGKAKAAISS 120- V+ MTHLKVVE+N NVVDI+TK EHEA SVTVQDRV+ AA +T F SEQ K K IS Sbjct: 95 VDSMTHLKVVEVNVNVVDIRTKEEHEAASVTVQDRVTSAASSTSQFVSEQTEKLKDTISD 154- Query: 121 GAEKTKEAVSNGTEAAK 137 N EAAK Sbjct: 155 --------TVNSDEAAK 163 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1738 A DNA sequence (GBSx1845) was identified in S. agalactiae <SEQ ID 5397> which encodes the amino acid sequence <SEQ ID 5398>. Analysis of this protein sequence reveals the following: TABLE-US-05299 possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3393(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1739 A DNA sequence (GBSx1846) was identified in S. agalactiae <SEQ ID 5399> which encodes the amino acid sequence <SEQ ID 5400>. Analysis of this protein sequence reveals the following:

TABLE-US-05300 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3168(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1740 A DNA sequence (GBSx1847) was identified in S. agalactiae <SEQ ID 5401> which encodes the amino acid sequence <SEQ ID 5402>. This protein is predicted to be gls24. Analysis of this protein sequence reveals the following: TABLE-US-05301 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2718(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05302 >GP: AAA86383 GB: U23376 putative 20-kDa protein [Lactococcus lactis] Identities = 95/157 (60%), Positives = 120/157 (75%) Query: 18 VRGELTFEDKVIEKIVGIAIEHVDGLLAVNGGFFSNLKNSVVNSDSVTDGVNVEVGKKQV 77 - ++G LT+EDKV++KIVG+A+E VDGLL+V GGFFSNL ++N+D VT GV+VEVGK QV Sbjct: 27 IKGALTYEDKVVQKIVGLALESVDGLLSVEGGFFSNLTGKLINTDDVTTGVDVEVGKTQV 86 Query: 78 AVDLDIVAEYQKHVPTIFADIKKVVEAEVKRMTDLEVVEVNVNVVDIKTRAQHEEDSVTL 137- AVDL +V EY+K+VP I+ IK+V+ EV MT+LEVVEVNV V DIKT+ Q +ED V++ Sbjct: 87 AVDLKVVTEYRKNVPDIYEKIKEVIRKEVAAMTELEVVEVNVTVTDIKTKEQQKEDDVSI 146- Query: 138 QDRVTSAAQATGEFASNQVSNVKSAVGSGVDKVEDMK 174 QDRVTSAAQ TG+F S QV VK V DK +K Sbjct: 147 QDRVTSAAQTTGKFTSEQVDKVKDKVEDNTDKEARVK 183 A related DNA sequence was identified in S. pyogenes <SEQ ID 5403> which encodes the amino acid sequence <SEQ ID 5404>. Analysis of this protein sequence reveals the following: TABLE-US-05303 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3896(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05304 Identities = 123/180 (68%), Positives = 158/180 (87%), Gaps = 1/180 (0%) Query: 1 MTETYIKNTTNNSGTTAVRGELTFEDKVIEKIVGIAIEHVDGLLAVNGGFFSNLKNSVVN 60 MTETYIKNT+ + T+A+RG+LT++DKVIEKIVG+A+E+VDGLL VNGGFF+NLK+ +VN Sbjct: 1 MTETYIKNTSKDL-TSAIRGQLTYDDKVIEKIVGLALENVDGLLGVNGGFFANLKDKLVN 59 Query: 61 SDSVTDGVNVEVGKKQVAVDLDIVAEYQKHVPTIFADIKKVVEAEVKRMTDLEVVEVNVN 120- ++SV DGVNVEVGKKQVAVDLDIVAEYQKHVPTI+ IK +VE EVKRMTDL+V+EVNV Sbjct: 60 TESVRDGVNVEVGKKQVAVDLDIVAEYQKHVPTIYDSIKSIVEEEVKRMTDLDVIEVNVK 119- Query: 121 VVDIKTRAQHEEDSVTLQDRVTSAAQATGEFASNQVSNVKSAVGSGVDKVEDMKSEPRVQ 18- 0 VVDIKT+ Q E + V+LQD+V+ A++T EF S+QV NVK++V +GV+K++D K+EPRV+ Sbjct: 120 VVDIKTKEQFEAEKVSLQDKVSDMARSTSEFTSHQVENVKASVDNGVEKLQDQKAEPRVK 17- 9 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1741 A DNA sequence (GBSx1848) was identified in S. agalactiae <SEQ ID 5405> which encodes the amino acid sequence <SEQ ID 5406>. This protein is predicted to be a 6-kDa protein. Analysis of this protein sequence reveals the following: TABLE-US-05305 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.29 Transmembrane 25-41 (23-52) ----- Final Results ----- bacterial membrane --- Certainty = 0.4715 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05306 >GP: AAA86382 GB: U23376 putative 6-kDa protein [Lactococcus lactis] Identities = 27/61 (44%), Positives = 45/61 (73%) Query: 3 EFVRKYRYPLGGAVIGLVLAAMIVTIGFFKTILALVIIVLGAYAGLYVQRTGMLDQFFNK 62 ++ K RYP+ G ++G ++A I TIGF+K IL L +I LG Y GL+++++G++DQF N+ Sbjct: 2 DYFEKNRYPIIGGIVGALIAVCIFTIGFWKMILVLFLIGLGIYIGLFLKKSGIIDQFINR 61 Query: 63 R 63 + Sbjct: 62 K 62 A related DNA sequence was identified in S. pyogenes <SEQ ID 5407> which encodes the amino acid sequence <SEQ ID 5408>. Analysis of this protein sequence reveals the following: TABLE-US-05307 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.73 Transmembrane 11-27 (6-50) INTEGRAL Likelihood = -7.11 Transmembrane 33-49 (27-50) ----- Final Results ----- bacterial membrane --- Certainty = 0.5692 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05308 Identities = 28/61 (45%), Positives = 48/61 (77%) Query: 3 EFVRKYRYPLGGAVIGLVLAAMIVTIGFFKTILALVIIVLGAYAGLYVQRTGMLDQFFNKR 63 - EF K++YP+ G ++GL++A +++ G FKT+LA++ I+LG Y GLY ++TG++DQF N++ Sbjct: 2 EFYEKFKYPIIGGLVGLIIAILLMAFGLFKTLLAIIFIILGIYGGLYAKKTGIIDQFLNRK 62 A related GBS gene <SEQ ID 8891> and protein <SEQ ID 8892> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05309 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 12.56 GvH: Signal Score (-7.5): -1.11 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 1 value: -9.29 threshold: 0.0 INTEGRAL Likelihood = -9.29 Transmembrane 25-41 (23-52) PERIPHERAL Likelihood = 12.25 44 modified ALOM score: 2.36 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4715 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00120## SEQ ID 5406 (GBS14) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 9 (lane 4; MW 33.3 kDa). The GBS14-GST fusion product was purified (FIG. 190, lane 8) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 263), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1742 A DNA sequence (GBSx1849) was identified in S. agalactiae <SEQ ID 5409> which encodes the amino acid sequence <SEQ ID 5410>. Analysis of this protein sequence reveals the following: TABLE-US-05310 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -18.63 Transmembrane 61-77 (51-83) INTEGRAL Likelihood = -7.91 Transmembrane 10-26 (7-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.8451 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 5411> which encodes the amino acid sequence <SEQ ID 5412>. Analysis of this protein sequence reveals the following: TABLE-US-05311 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -16.19 Transmembrane 71-87 (63-93) ----- Final Results ----- bacterial membrane --- Certainty = 0.7474 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-05312 Identities = 87/193 (45%), Positives = 127/193 (65%), Gaps = 4/193 (2%) Query: 1 MSKGLKSLYTLLGLISLTLLGFVAVISKQHIYLP-SFNWLDWDFN-LPSPIDVGMYHYFF 58 MSK LK Y L+GL+ L++ G+V I+ +IYLP S+ WL W + P+ +D + +Y+F Sbjct: 9 MSKLLKISYCLVGLVLLSVFGWVVGITGGYIYLPYSYRWLSWGMDSFPNLLDSALSYYYF 68 Query: 59 WGALVLFVIVLLAILVVLFYPRRYTEYKLA--DKTGKLMLKKSAIEGFVKTEVLKTGLMK 116- W ALVLFVI LA+LV++ YPR YTE +L +K G L+LKKSAIE +V T + GLM Sbjct: 69 WTALVLFVITFLALLVIILYPRIYTEVQLRHKNKKGTLLLKKSAIESYVATAIQTAGLMP 128- Query: 117 SPSVTAHLYKKKVKVDVKGLLTSRTNVPEQLEHIQSDVELGLKEFFGLEKKMNTRVFVKQ 17- 6 +P+VTA LYK+K + VKG L SR V +Q+ ++ +E GL EFFG+ +N +V+VK Sbjct: 129 NPTVTAKLYKRKFNIIVKGRLASRVAVADQISGVKEGIEKGLTEFFGINYPVNFKVYVKD 18- 8 Query: 177 VEEENVGNAKTNK 189 + + + + N+ Sbjct: 189 IADSDRKHITRNR 201 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1743 A DNA sequence (GBSx1850) was identified in S. agalactiae <SEQ ID 5413> which encodes the amino acid sequence <SEQ ID 5414>. Analysis of this protein sequence reveals the following: TABLE-US-05313 Possible site: 17 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.82 Transmembrane 56-72 (52-81) INTEGRAL Likelihood = -6.42 Transmembrane 4-20 (1-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.4927(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05314 >GP: CAB12244 GB: Z99106 similar to hypothetical proteins from B. subtilis [Bacillus subtilis] Identities = 31/76 (40%), Positives = 48/76 (62%) Query: 1 MSLIWSLIVGAIIGAIAGAVTNKGGSMGWIANILAGLVGSFVGQSLLGTWGPKLAGMALI 60 +S + SL+V +IG I A+ G +++AGL+G+++G LLGTWGP LAG A+ Sbjct: 2 LSFLVSLVVAIVIGLIGSAIVGNRLPGGIFGSMIAGLIGAWIGHGLLGTWGPSLAGFAIF 61 Query: 61 PSIVGAIIVVIVTSFV 76 P+I+GA I V + + Sbjct: 62 PAIIGAAIFVFLLGLI 77 A related DNA sequence was identified in S. pyogenes <SEQ ID 5415> which encodes the amino acid sequence <SEQ ID 5416>. Analysis of this protein sequence reveals the following: TABLE-US-05315 Possible site: 55 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.59 Transmembrane 60-76 (56-80) ----- Final Results ----- bacterial membrane --- Certainty = 0.4036(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05316 >GP: CAB12244 GB: Z99106 similar to hypothetical proteins from B. subtilis [Bacillus subtilis] Identities = 28/76 (36%), Positives = 47/76 (61%) Query: 1 MGLIWTLIVGALIGVIAGALTKKGGSMGWIANIAAGLVGSSVGQALLGSWGPSLAGMSLI 60 + + +L+V +IG+I A+ G ++ AGL+G+ +G LLG+WGPSLAG ++ Sbjct: 2 LSFLVSLVVAIVIGLIGSAIVGNRLPGGIFGSMIAGLIGAWIGHGLLGTWGPSLAGFAIF 61 Query: 61 PSVIGAVIVVMITSFV 76 P++IGA I V + + Sbjct: 62 PAIIGAAIFVFLLGLI 77 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05317 Identities = 63/82 (76%), Positives = 74/82 (89%) Query: 1 MSLIWSLIVGAIIGAIAGAVTNKGGSMGWIANILAGLVGSFVGQSLLGTWGPKLAGMALI 60 M LIW+LIVGA+IG IAGA+T KGGSMGWIANI AGLVGS VGQ+LLG+WGP LAGM+LI Sbjct: 1 MGLIWTLIVGALIGVIAGALTKKGGSMGWIANIAAGLVGSSVGQALLGSWGPSLAGMSLI 60 Query: 61 PSIVGAIIVVIVTSFVLGKMNN 82 PS++GA+IVV++TSFVL K NN Sbjct: 61 PSVIGAVIVVMITSFVLNKTNN 82 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1744 A DNA sequence (GBSx1851) was identified in S. agalactiae <SEQ ID 5417> which encodes the amino acid sequence <SEQ ID 5418>. Analysis of this protein sequence reveals the following: TABLE-US-05318 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.82 Transmembrane 88-104 (84-111) INTEGRAL Likelihood = -8.07 Transmembrane 29-45 (27-54) ----- Final Results ----- bacterial membrane --- Certainty = 0.4927(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05319 >GP: CAB12244 GB: Z99106 similar to hypothetical proteins from B. subtilis [Bacillus subtilis] Identities = 29/77 (37%), Positives = 47/77 (60%) Query: 31 IMGLIWSLIVGAIIGAIAGAITNKGGSMGWIANILAGLVGSFVGQSLLGTWGPKLADMAL 90 - ++ + SL+V +IG I AI G +++AGL+G+++G LLGTWGP LA A+ Sbjct: 1 MLSFLVSLVVAIVIGLIGSAIVGNRLPGGIFGSMIAGLIGAWIGHGLLGTWGPSLAGFAI 60 Query: 91 IPSIVGAIIVIIVTSFV 107 P+I+GA I + + + Sbjct: 61 FPAIIGAAIFVFLLGLI 77 There is also homology to SEQ ID 5416: TABLE-US-05320 Identities = 60/79 (75%), Positives = 72/79 (90%) Query: 32 MGLIWSLIVGAIIGAIAGAITNKGGSMGWIANILAGLVGSFVGQSLLGTWGPKLADMALI 91 - MGLIW+LIVGA+IG IAGA+T KGGSMGWIANI AGLVGS VGQ+LLG+WGP LA M+LI Sbjct: 1 MGLIWTLIVGALIGVIAGALTKKGGSMGWIANIAAGLVGSSVGQALLGSWGPSLAGMSLI 60 Query: 92 PSIVGAIIVIIVTSFVLGK 110 PS++GA+IV+++TSFVL K Sbjct: 61 PSVIGAVIVVMITSFVLNK 79 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1745 A DNA sequence (GBSx1852) was identified in S. agalactiae <SEQ ID 5419> which encodes the amino acid sequence <SEQ ID 5420>. This protein is predicted to be ATP-dependent DNA helicase Rep (uvrD). Analysis of this protein sequence reveals the following: TABLE-US-05321 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1364(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9863> which encodes amino acid sequence <SEQ ID 9864> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05322 >GP: AAD51119 GB: AF176554 DNA helicase PcrA [Leuconostoc citreum] Identities = 414/764 (54%), Positives = 537/764 (70%), Gaps = 23/764 (3%) Query: 6 VEMNPLIIGMNDKQAEAVQTTDGPLLIMAGAGSGKTRVLTHRIAYLIDEKYVNPWNILAI 65 + + L GMN+KQAEAVQTT+GPLLIMAGAGSGKTRVLTHRIA+L+ + V PW ILAI Sbjct: 1 MSVETLTNGMNNKQAEAVQTTEGPLLIMAGAGSGKTRVLTHRIAHLVQDLNVFPWRILAI 60 Query: 66 TFTNKAAREMRERAIAL--NPATQDTLIATFHSMCVRILRREADYIGYNRNFTIVDPGEQ 123- TFTNKAAREMRER AL +D ++TFH++ VRILRR+ + IG +NFTI+D Q Sbjct: 61 TFTNKAAREMRERIAALLSEDVARDIWVSTFHALAVRILRRDGEAIGLAKNFTIIDTSAQ 120- Query: 124 RTLMKRIIKQLNLDTKKWNERSILGTISNAKNDLLDEIAYEKQAGDMYTQVIAKCYKAYQ 18- 3 RTLMKR+I LNLDT +++ R+ILG ISNAKND+L Y K A + + + +A+ Y AYQ Sbjct: 121 RTLMKRVINDLNLDTNQYDPRTILGMISNAKNDMLQPRDYAKAADNAFQETVAEVYTAYQ 18- 0 Query: 184 EELRRSEAMDFDDLIMMTLRLFDQNKDVLAYYQQRYQYIHVDEYQDTNHAQYQLVKLLAS 24- 3 EL+RS+++DFDDLIM+T+ LF DVLA YQQ+++Y+HVDEYQDTN AQY +V LLA Sbjct: 181 AELKRSQSVDFDDLIMLTIDLFQSAPDVLARYQQQFEYLHVDEYQDTNDAQYTIVNLLAQ 24- 0 Query: 244 RFKNICVVGDADQSIYGWRGADMQNILDFEKDYPQAKVVLLEENYRSTKKILQAANNVIN 30- 3 R KN+ VVGDADQSIYGWRGA+M NIL+FEKDYP A V+LE+NYRST+ IL AAN VIN Sbjct: 241 RSKNLAVVGDADQSIYGWRGANMNNILNFEKDYPNAHTVMLEQNYRSTQNILDAANAVIN 30- 0 Query: 304 HNKNRRPKKLWTQNDEGEQIVYHRANNEQEEAVFVASTIDNIVREQGKNFKDFAVLYRTN 36- 3 HN R PKKLWT+N +G+QI Y+RA E +EA F+ S I + + + DFAVLYRTN Sbjct: 301 HNNERVPKKLWTENGKGDQITYYRAQTEHDEANFILSNIQQLRETKHMAYSDFAVLYRTN 36- 0 Query: 364 AQSRTIEEALLKSNIPYTMVGGTKFYSRKEIRDVIAYLNILANTSDNISFERIVNEPKRG 42- 3 AQSR IEE+L+K+N+PY+MVGG KFY RKEI D++AY++++ N DN +FER+VNEPKRG Sbjct: 361 AQSRNIEESLVKANMPYSMVGGHKFYERKEILDIMAYMSLITNPDDNAAFERVVNEPKRG 42- 0 Query: 424 VGPGTLEKIRSFAYEQSMSLLDASSNVMMSP-LKGKAAQAVWDLANLILTLRSNLDSLTV 48- 2 +G +L ++R A ++S + A ++ ++P + KAA A ++ LR + L V Sbjct: 421 LGATSLTRLRELANRLNVSYMKAIGSIELAPSITTKAASKFLTFAEMMHNLRQQSEFLNV 48- 0 Query: 483 TEITENLLDKTGYLEALQVQNTLESQARIENIEEFLSVTKNFDDNPEITVEGETGLDRLS 54- 2 TE+TE ++ ++GY + L +N +SQAR+EN+EEFLSVTK FDD + E +D ++ Sbjct: 481 TELTELVMTQSGYRQMLAEKNDPDSQARLENLEEFLSVTKEFDD--KYQPEDPESIDPVT 53- 8 Query: 543 RFLNDLALIADTDDSATETAEVTLMTLHAAKGLEFPVVFLIGMEEGVFPLSRAIEDADEL 60- 2 FL AL++D DD VTLMTLHAAKGLEFPVVFLIG++EG+FPLSRA+ D D L Sbjct: 539 DFLGTTALMSDLDDFEEGDGAVTLMTLHAAKGLEFPVVFLIGLKEGIFPLSRAMMDEDLL 59- 8 Query: 603 EEERRLAYVGITRAEQILFLTNANTRTLFGKTSYNRPTRFIREIDDELIQ--YQGLARPV 66- 0 EEERRLAYVGITRA + LFLTNA +R L+G+T N P+RFI EI EL++ Y GL+R Sbjct: 599 EEERRLAYVGITRAMKKLFLTNAFSRLLYGRTQANEPSRFIAEISPELLETAYSGLSRDK 65- 8 Query: 661 NSSFGVKYSKEQPTQFGQGMSLQQALQARKSNSQSQVTAQLQALN-ANNSHETSWEIGDV 71- 9 + + ++ R + + Q T + N +TSW GD Sbjct: 659 TQKKTLPFDRK---------------MQRATATTYQATPVTKITNGVTGGDQTSWSTGDK 70- 3 Query: 720 ATHKKWGDGTVLEVSGSGKTQELKINFPGIGLKKLLASVAPISK 763 +HKKWG GTV+ VSG QELK+ FP G+K+LLA+ API K Sbjct: 704 VSHKKWGVGTVISVSGRADDQELKVAFPSEGVKQLLAAFAPIQK 747 A related DNA sequence was identified in S. pyogenes <SEQ ID 5421> which encodes the amino acid sequence <SEQ ID 5422>. Analysis of this protein sequence reveals the following: TABLE-US-05323 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0214(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-05324 Identities = 622/772 (80%), Positives = 699/772 (89%), Gaps = 15/772 (1%) Query: 8 MNPLIIGMNDKQAEAVQTTDGPLLIMAGAGSGKTRVLTHRIAYLIDEKYVNPWNILAITF 67 MNPL+ GMND+QA+AVQTT+GPLLIMAGAGSGKTRVLTHRIAYLIDEK+VNPWNILAITF Sbjct: 1 MNPLLNGMNDRQAQAVQTTEGPLLIMAGAGSGKTRVLTHRIAYLIDEKFVNPWNILAITF 60 Query: 68 TNKAAREMRERAIALNPATQDTLIATFHSMCVRILRREADYIGYNRNFTIVDPGEQRTLM 127- TNKAAREM+ERA+ALNPAT+DTLIATFHSMCVRILRREAD+IGYNRNFTIVDPGEQRTLM Sbjct: 61 TNKAAREMKERALALNPATKDTLIATFHSMCVRILRREADHIGYNRNFTIVDPGEQRTLM 120- Query: 128 KRIIKQLNLDTKKWNERSILGTISNAKNDLLDEIAYEKQAGDMYTQVIAKCYKAYQEELR 18- 7 KRI+KQLN+D KKWNERSILGTISNAKNDLLDE YE QA DMY+Q++A+CYKAYQEELR Sbjct: 121 KRILKQLNIDPKKWNERSILGTISNAKNDLLDEKGYEAQAADMYSQIVARCYKAYQEELR 18- 0 Query: 188 RSEAMDFDDLIMMTLRLFDQNKDVLAYYQQRYQYIHVDEYQDTNHAQYQLVKLLASRFKN 24- 7 RSEA+DFDDLIMMTLRLFD N DVLAYYQQRYQYIHVDEYQDTNHAQYQL+KLLASRFKN Sbjct: 181 RSEALDFDDLIMMTLRLFDANPDVLAYYQQRYQYIHVDEYQDTNHAQYQLIKLLASRFKN 24- 0 Query: 248 ICVVGDADQSIYGWRGADMQNILDFEKDYPQAKVVLLEENYRSTKKILQAANNVINHNKN 30- 7 ICVVGDADQSIYGWRGADMQNILDFEKDYP AKVVLLEENYRSTKKILQAAN+VIN+N+N Sbjct: 241 ICVVGDADQSIYGWRGADMQNILDFEKDYPDAKVVLLEENYRSTKKILQAANDVINNNRN 30- 0 Query: 308 RRPKKLWTQNDEGEQIVYHRANNEQEEAVFVASTIDNIVREQGKNFKDFAVLYRTNAQSR 36- 7 RRPKKLWTQN +GEQ+VY+RAN+E++EAVFVASTI N+ +E GKNFKDFAVLYRTNAQSR Sbjct: 301 RRPKKLWTQNADGEQLVYYRANDERDEAVFVASTISNMSQELGKNFKDFAVLYRTNAQSR 36- 0 Query: 368 TIEEALLKSNIPYTMVGGTKFYSRKEIRDVIAYLNILANTSDNISFERIVNEPKRGVGPG 42- 7 TIEEALLKSNIPYTMVGGTKFYSRKEIRD+IAYL I+AN +DNISFERIVNEPKRGVGPG Sbjct: 361 TIEEALLKSNIPYTMVGGTKFYSRKEIRDLIAYLTIVANPADNISFERIVNEPKRGVGPG 42- 0 Query: 428 TLEKIRSFAYEQSMSLLDASSNVMMSPLKGKAAQAVWDLANLILTLRSNLDSLTVTEITE 48- 7 TL+K+R FAYE SLL+A+SN++MSPLKGKAAQA+ DLAN++ LR +LD +++T++ E Sbjct: 421 TLDKLRQFAYESDQSLLEAASNLLMSPLKGKAAQAIMDLANILGQLRQDLDQMSITDLAE 48- 0 Query: 488 NLLDKTGYLEALQVQNTLESQARIENIEEFLSVTKNFDDNPEITVEGETGLDRLSRFLND 54- 7 LL+KTGYL++L++QNTLESQARIENIEEFLSVTKNFD++ E ETG+DRL RFLND Sbjct: 481 ALLEKTGYLDSLRLQNTLESQARIENIEEFLSVTKNFDESSASQEEDETGVDRLGRFLND 54- 0 Query: 548 LALIADTDDSATETAEVTLMTLHAAKGLEFPVVFLIGMEEGVFPLSRAIEDADELEEERR 60- 7 LALIADTDDS E AEVTLMTLHAAKGLEFPVVFLIGMEEGVFPLSRA ED DELEEERR Sbjct: 541 LALIADTDDSQAEAAEVTLMTLHAAKGLEFPVVFLIGMEEGVFPLSRASEDPDELEEERR 60- 0 Query: 608 LAYVGITRAEQILFLTNANTRTLFGKTSYNRPTRFIREIDDELIQYQGLARPVNSSFGVK 66- 7 LAYVGITRAE++LF+TNANTRTLFGK+SYNRPTRF++EI +EL+ Y+GLARP SSFGV+ Sbjct: 601 LAYVGITRAEEVLFMTNANTRTLFGKSSYNRPTRFLKEISEELLSYKGLARPAQSSFGVR 66- 0 Query: 668 YSKEQPTQFGQGMSLQQALQARKSNSQSQVTAQ-LQA-------------LNANNS-HET 71- 2 +S E TQFGQGMSL +ALQARK+ +Q + +AQ +QA +N+S E Sbjct: 661 FSTETHTQFGQGMSLSEALQARKAQAQVRQSAQPMQAHTIPSASTSSVLPFGSNSSVEEV 72- 0 Query: 713 SWEIGDVATHKKWGDGTVLEVSGSGKTQELKINFPGIGLKKLLASVAPISKK 764 +W+IGD+A HKKWGDGTVLEVSGSGKT ELKI FP +GLKKLLASVAPI KK Sbjct: 721 TWQIGDIAHHKKWGDGTVLEVSGSGKTMELKIKFPEVGLKKLLASVAPIEKK 772 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1746 A DNA sequence (GBSx1853) was identified in S. agalactiae <SEQ ID 5423> which encodes the amino acid sequence <SEQ ID 5424>. Analysis of this protein sequence reveals the following: TABLE-US-05325 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4741(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05326 >GP:AAA88579 GB:M14339 unknown [Streptococcus pneumoniae] Identities = 43/57 (75%), Positives = 50/57 (87%) Query: 41 AHGGYLFTLCDQVSGLVAISTGYEAVTLQSNINYLRAGRLDDLLTVIGTCVHNGRTT 97 AHGGYLFTLCDQ+SGLV IS G + VTLQS+INYL+AG+LDD+LT+ G CVH GRTT Sbjct: 1 AHGGYLFTLCDQISGLVVISLGLDGVTLQSSINYLKAGKLDDVLTIKGECVHQGRTT 57 A related DNA sequence was identified in S. pyogenes <SEQ ID 5425> which encodes the amino acid sequence <SEQ ID 5426>. Analysis of this protein sequence reveals the following: TABLE-US-05327 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1210 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05328 Identities = 57/97 (58%), Positives = 74/97 (75%) Query: 2 KFNLEQVKVFENYEIENWEEGQVTLTTKVVDSSLNYYGNAHGGYLFTLCDQVSGLVAIST 61 - + L + +F+NY+IE E+G + L+T+V +++LNYYGNAHGGYLFTLCDQV GLVA +T Sbjct: 7 EMTLNVISIFDNYQIELAEKGHLILSTEVTETALNYYGNAHGGYLFTLCDQVGGLVARTT 66 Query: 62 GYEAVTLQSNINYLRAGRLDDLLTVIGTCVHNGRTTK 98 G E+VTLQ+N NYL+AG D L V G VH GRTT+ Sbjct: 67 GVESVTLQANANYLKAGHKGDKLMVEGRLVHGGRTTQ 103 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1747 A DNA sequence (GBSx1854) was identified in S. agalactiae <SEQ ID 5427> which encodes the amino acid sequence <SEQ ID 5428>. Analysis of this protein sequence reveals the following: TABLE-US-05329 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3187 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1748 A DNA sequence (GBSx1855) was identified in S. agalactiae <SEQ ID 5429> which encodes the amino acid sequence <SEQ ID 5430>. This protein is predicted to be uracil permease (uraA). Analysis of this protein sequence reveals the following: TABLE-US-05330 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.65 Transmembrane 122-138 (117-146) INTEGRAL Likelihood = -8.65 Transmembrane 212-228 (204-233) INTEGRAL Likelihood = -7.32 Transmembrane 60-76 (49-80) INTEGRAL Likelihood = -6.53 Transmembrane 149-165 (145-172) INTEGRAL Likelihood = -6.48 Transmembrane 402-418 (401-420) INTEGRAL Likelihood = -4.04 Transmembrane 422-438 (420-445) INTEGRAL Likelihood = -3.72 Transmembrane 365-381 (364-385) INTEGRAL Likelihood = -3.40 Transmembrane 184-200 (182-202) INTEGRAL Likelihood = -3.08 Transmembrane 346-362 (345-363) INTEGRAL Likelihood = -1.38 Transmembrane 260-276 (260-276) ----- Final Results ----- bacterial membrane --- Certainty = 0.4461 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9865> which encodes amino acid sequence <SEQ ID 9866> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05331 >GP:CAA53697 GB:X76083 uracil permease [Bacillus caldolyticus] Identities = 208/416 (50%), Positives = 291/416 (69%), Gaps = 11/416 (2%) Query: 32 LLDIDEKPELFQGLLLSFQHVFAMFGATILVPLILGMPVSVALFASGCGTLIYQVATKFK 91- +LDI ++P + Q + LS QH+FAMFGATILVP ++G+ S+AL SG GTL + + TK++ Sbjct: 5 VLDIQDRPTVGQWITLSLQHLFAMFGATILVPYLVGLDPSIALLTSGLGTLAFLLITKWQ 64- Query: 92 VPVYLGSSFAYITAMALAMKQMHGDISAAQTGILFVGLIYVVVATVIKFVGNSWVDKILP 15- 1 VP YLGSSFAYI + A + G AA G GL+Y VVA +IK G WV K+LP Sbjct: 65 VPAYLGSSFAYIAPIIAA--KTAGGPGAAMIGSFLAGLVYGVVALIIKKAGYRWVMKLLP 12- 2 Query: 152 PIIIGPMIIVIGLGLANSAVTNA--GFVAKGDWRKMLVAVVTFLIAAFINTKGKGFIKII 20- 9 P+++GP+IIVIGLGLA +AV A G K VA+VT + +G + +I Sbjct: 123 PVVVGPVIIVIGLGLAGTAVGMAMNGPDGKYSLLHFSVALVTLAATIVCSVLARGMLSLI 18- 2 Query: 210 PFLFAIIGGYILSIILGLVDLSPVEKAAWFELPKFYLPFKTGLFHSYKLYFGPEMLAIL- 26- 8 P L I+ GY+ ++ +GLVDLS V A WFE P F +PF Y + E++ ++ Sbjct: 183 PVLVGIVVGYLYALAVGLVDLSKVAAAKWFEWPDFLIPFA-----DYPVRVTWEIVMLMV 23- 7 Query: 269 PISIVTIAENIGDHTVLGQICGRNFLKKPGLNRLLIGDGLATAFSALIGGPAETTYGENT 32- 8 P++IVT++E+IG VL ++ GR+ ++KPGL+R ++GDG AT SAL+GGP +TTYGEN Sbjct: 238 PVAIVTLSEHIGHQLVLSKVVGRDLIQKPGLHRSILGDGTATMISALLGGPPKTTYGENI 29- 7 Query: 329 GVIGMTRIASVTVIRNAAFIAIAFSFFGKFTALISTIPSAVLGGMAILLYGVIASNGLKV 38- 8 GV+ +TR+ SV V+ AA IAIAF F GK TALIS+IP+ V+GG++ILL+G+IAS+GL++ Sbjct: 298 GVLAITRVYSVYVLAGAAVIAIAFGFVGKITALISSIPTPVMGGVSILLFGIIASSGLRM 35- 7 Query: 389 LIENRVNFAEVRNLIIASSMLVLGLGGAVLDLG-ALTLSGTALSAIVGIILNLILP 443 LI++RV+F + RNL+IAS +LV+G+GGAVL + + ++G ALSAIVG++LNLILP Sbjct: 358 LIDSRVDFGQTRNLVIASVILVIGIGGAVLKISDSFQITGMALSAIVGVLLNLILP 413 A related DNA sequence was identified in S. pyogenes <SEQ ID 5431> which encodes the amino acid sequence <SEQ ID 5432>. Analysis of this protein sequence reveals the following: TABLE-US-05332 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.72 Transmembrane 177-193 (171-206) INTEGRAL Likelihood = -8.55 Transmembrane 313-329 (304-339) INTEGRAL Likelihood = -8.17 Transmembrane 154-170 (152-175) INTEGRAL Likelihood = -7.91 Transmembrane 376-392 (374-395) INTEGRAL Likelihood = -7.48 Transmembrane 25-41 (22-43) INTEGRAL Likelihood = -5.84 Transmembrane 120-136 (116-142) INTEGRAL Likelihood = -4.99 Transmembrane 96-112 (90-117) INTEGRAL Likelihood = -3.29 Transnembrane 339-355 (338-360) INTEGRAL Likelihood = -1.91 Transnembrane 396-412 (396-413) ----- Final Results ----- bacterial membrane --- Certainty = 0.5288 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05333 >GP:CAB89870 GB:AJ132624 uracil transporter [Lactococcus lactis] Identities = 294/421 (69%), Positives = 359/421 (84%), Gaps = 5/421 (1%) Query: 3 DVIYDVEEVPKAGMLVGLSFQHLFAMFGATVLVPILVGIDPSVALLSSGLGTLAHLSVTK 62- D+I V+E P A GLSFQHLFAMFG+TVLVPILVGI+P++ALLSSGLGTLAH+SVTK Sbjct: 5 DIILKVDEKPAASQWFGLSFQHLFAMFGSTVLVPILVGINPAIALLSSGLGTLAHMSVTK 64- Query: 63 FKIPAYMGSSFAYIAAMQLLMKTNGIGAVAQGAMTGGLVYLIVALIVKAIGNDWIDNILP 12- 2 FK+PAYMGSSFAYI AM LLMK G+ A+AQGAMTGGLVYLIVALIVK G WID +LP Sbjct: 65 FKVPAYMGSSFAYIGAMTLLMKNGGMPAIAQGAMTGGLVYLIVALIVKFAGKGWIDKVLP 12- 4 Query: 123 PIVVGPIVMVIGLSLASTAVNDVMLKN----GNYNLTYLVIGLVTLLSVIFFNIYGKGIV 17- 8 PIVVGPIVMVIGLSLA TA+ND M + Y+L Y++I L+T+LS++ ++IYGKG + Sbjct: 125 PIVVGPIVMVIGLSLAPTAINDAMYTDVANLKGYSLAYIIIALITVLSIVVYSIYGKGFL 18- 4 Query: 179 AIVPLLLGLLVGYVVALLVGVLTGQEIVDFTNVAQAKWFSIPSVEIPFLTYGVKFYPSAI 23- 8 ++VP+LLG++ GYV A+++G +TG IV FT ++QAKW ++P +EIPF +Y FYPSAI Sbjct: 185 SVVPILLGIITGYVAAMIIGKITGMNIVSFTGISQAKWLTLPPMEIPFASYKWAFYPSAI 24- 4 Query: 239 LTMAPIAFVTMTEHFGHIMVLNSLTKRDYFKDPGLEKTLTGDGFAQIIAGFLGAPPVTSY 29- 8 LTMAPIAFVTMTEHFGHIMVLNSLTK+DYFK+PGLEKTLTGDG AQIIAGF+GAPPVTSY Sbjct: 245 LTMAPIAFVTMTEHFGHIMVLNSLTKKDYFKEPGLEKTLTGDGLAQIIAGFIGAPPVTSY 30- 4 Query: 299 GENIGVMALNKIFSVYVIAGAAVIAALLSFIGKVSALIQSIPTPVIGGISVALFGVIASS 35- 8 GENIGVMA+ KI S+YVIAGAAV+A ++SF+GK++AL+QSIP PVIGG S+ALFGVIA+S Sbjct: 305 GENIGVMAITKIHSIYVIAGAAVLAIVVSFVGKITALLQSIPAPVIGGASIALFGVIAAS 36- 4 Query: 359 GLKILIESKVDMDNKKNLLIASVILVSGIGGLMLQV-NGLQISGVAFSTLLGIILYQVLPE 4- 18 GLKIL+E+KVD D K+NLLI+SV+LV GIGG+++ + LQIS VA +T+LGI+L VLP+ Sbjct: 365 GLKILVENKVDFDIKRNLLISSVVLVIGIGGMIINITQNLQISSVAIATILGIVLNLVLPK 4- 25 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05334 Identities = 186/425 (43%), Positives = 282/425 (65%), Gaps = 17/425 (4%) Query: 30 NLLLDIDEKPELFQGLLLSFQHVFAMFGATILVPLILGMPVSVALFASGCGTLIYQVATK 89- +++ D++E P+ + LSFQH+FAMFGAT+LVP+++G+ SVAL +SG GTL + TK Sbjct: 3 DVIYDVEEVPKAGMLVGLSFQHLFAMFGATVLVPILVGIDPSVALLSSGLGTLAHLSVTK 62- Query: 90 FKVPVYLGSSFAYITAMALAMKQMHGDISAAQTGILFVGLIYVVVATVIKFVGNSWVDKI 14- 9 FK+P Y+GSSFAYI AM L MK I A G + GL+Y++VA ++K +GN W+D I Sbjct: 63 FKIPAYMGSSFAYIAAMQLLMKT--NGIGAVAQGAMTGGLVYLIVALIVKAIGNDWIDNI 12- 0 Query: 150 LPPIIIGPMIIVIGLGLANSAVTNAGFVAKGDWRK--MLVAVVTFLIAAFINTKGKGFIK 20- 7 LPPI++GP+++VIGL LA++AV + + G++ +++ +VT L F N GKG + Sbjct: 121 LPPIVVGPIVMVIGLSLASTAVNDV-MLKNGNYNLTYLVIGLVTLLSVIFFNIYGKGIVA 17- 9 Query: 208 IIPFLFAIIGGYILSIILG------LVDLSPVEKAAWFELPKFYLPFKTGLFHSYKLYFG 26- 1 I+P L ++ GY++++++G +VD + V +A WF +P +PF T Y + F Sbjct: 180 IVPLLLGLLVGYVVALLVGVLTGQEIVDFTNVAQAKWFSIPSVEIPFLT-----YGVKFY 23- 4 Query: 262 PE-MLAILPISIVTIAENIGDHTVLGQICGRNFLKKPGLNRLLIGDGLATAFSALIGGPA 32- 0 P +L +PI +VT +E +G VL + R++ K PGL + L GDG A + +G P Sbjct: 235 PSAILTMAPIAFVTMTEHFGHIMVLNSLTKRDYFKDPGLEKTLTGDGFAQIIAGFLGAPP 29- 4 Query: 321 ETTYGENTGVIGMTRIASVTVIRNAAFIAIAFSFFGKFTALISTIPSAVLGGMAILLYGV 38- 0 T+YGEN GV+ + +I SV VI AA IA SF GK +ALI +IP+ V+GG+++ L+GV Sbjct: 295 VTSYGENIGVMALNKIFSVYVIAGAAVIAALLSFIGKVSALIQSIPTPVIGGISVALFGV 35- 4 Query: 381 IASNGLKVLIENRVNFAEVRNLIIASSMLVLGLGGAVLDLGALTLSGTALSAIVGIILNL 44- 0 IAS+GLK+LIE++V+ +NL+IAS +LV G+GG +L + L +SG A S ++GIIL Sbjct: 355 IASSGLKILIESKVDMDNKKNLLIASVILVSGIGGLMLQVNGLQISGVAFSTLLGIILYQ 41- 4 Query: 441 ILPKE 445 +LP++ Sbjct: 415 VLPEK 419 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1749 A DNA sequence (GBSx1856) was identified in S. agalactiae <SEQ ID 5433> which encodes the amino acid sequence <SEQ ID 5434>. Analysis of this protein sequence reveals the following: TABLE-US-05335 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3863 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1750 A DNA sequence (GBSx1857) was identified in S. agalactiae <SEQ ID 5435> which encodes the amino acid sequence <SEQ ID 5436>. This protein is predicted to be sodium/alanine symporter. Analysis of this protein sequence reveals the following: TABLE-US-05336 Possible site: 22 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.88 Transmembrane 191-207 (184-214) INTEGRAL Likelihood = -8.97 Transmembrane 151-167 (148-171) INTEGRAL Likelihood = -8.39 Transmembrane 217-233 (216-238) INTEGRAL Likelihood = -6.74 Transmembrane 312-328 (310-333) INTEGRAL Likelihood = -6.26 Transmembrane 357-373 (349-376) INTEGRAL Likelihood = -5.10 Transmembrane 424-440 (422-441) INTEGRAL Likelihood = -5.04 Transmembrane 396-412 (390-417) INTEGRAL Likelihood = -0.37 Transmembrane 25-41 (25-41) ----- Final Results ----- bacterial membrane --- Certainty = 0.5352 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9867> which encodes amino acid sequence <SEQ ID 9868> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05337 >GP:AAC22541 GB:U32770 amino acid carrier protein, putative [Haemophilus influenzae Rd] Identities = 255/443 (57%), Positives = 333/443 (74%), Gaps = 4/443 (0%) Query: 11 TLFTHINSFVWGPPLLALLVGTGIYLSFRLGFIQLRQLSRAFKLIFREDNG-QGDISSYA 69- ++ + I+SF+WG PLL LL GTG+YL+ RLGFIQ+R L RA +F++D G +GD+SS+A Sbjct: 5 SILSAIDSFIWGAPLLILLSGTGLYLTLRLGFIQIRYLPRALGYLFKKDKGGKGDVSSFA 64- Query: 70 ALATALAATVGTGNIVGVATAIKSGGPGALFWMWVAAFFGMATKYAEGLLAIKYRTKDTN 12- 9 AL TALAAT+GTGNIVGVATA+++GGPGA+FWMW+ A GMATKYAE LLA+KYR +D N Sbjct: 65 ALCTALAATIGTGNIVGVATAVQAGGPGAIFWMWLVALLGMATKYAECLLAVKYRVRDKN 12- 4 Query: 130 GEISGGPMYYIINGMGQKWKPLAVFFSAAGILVALLGIGTFTQVNAIASSLEHTFKISTR 18- 9 G ++GGPMYYI G+G +W LA F+ G++VA GIGTF QVNAI +++ TF I Sbjct: 125 GFMAGGPMYYIERGLGIRW--LAKLFALFGVMVAFFGIGTFPQVNAITHAMQDTFNIPVL 18- 2 Query: 190 FTSLILAVIVLFIIFGGIKSISKVSEKIVPFMAISYILATLIIIAVNYNKIPHTFQLIFS 24- 9 T++I+ ++V II GG+K I+ S IVPFMAI Y+ +L+II +N K+P LI Sbjct: 183 VTAIIVTLLVGLIILGGVKRIATASSVIVPFMAILYVTTSLVIILLNIEKVPDAILLIID 24- 2 Query: 250 GAFSGTAAIGGFSGAIVKEAIQKGIARGVFSNESGLGSAPIAAAAAKTKEPVEQGLISMT 30- 9 AF AA+GG G V +AIQ G+ARG+FSNESGLGSAPIAAAAA+T+EPV QGLISMT Sbjct: 243 SAFDPQAALGGAVGLTVMKAIQSGVARGIFSNESGLGSAPIAAAAAQTREPVRQGLISMT 30- 2 Query: 310 GTFIDTIVICTLTGIAILVTGKWLEFDLQGAPLTQASFNTVFG-SLGSFALTFCLVLFAF 36- 8 GTF+DTI++CT+TGI +++TG W +L GA +T +F G S+G+ +T L+ FAF Sbjct: 303 GTFLDTIIVCTMTGIVLVLTGAWNNPELAGATVTNYAFAQGLGTSIGATIVTVGLLFFAF 36- 2 Query: 369 TTILGWSYYGERCFEYLFGTKFINAYRIIFVIMVGLGGFLQLDLIWVIADIVNGLMALPN 42- 8 TTILGW YYGERCF YL G + + YR+ ++++VGLG FL L+LIW+IADIVNGLMA PN Sbjct: 363 TTILGWCYYGERCFVYLVGIRGVKLYRLAYIMLVGLGAFLHLNLIWIIADIVNGLMAFPN 42- 2 Query: 429 LIALLALSPIIVKETQKYFSETK 451 LIAL+ L +I++ET+ YF K Sbjct: 423 LIALIGLRKVIIEETKDYFQRLK 445 A related DNA sequence was identified in S. pyogenes <SEQ ID 5437> which encodes the amino acid sequence <SEQ ID 5438>. Analysis of this protein sequence reveals the following:

TABLE-US-05338 Possible site: 45 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.36 Transmembrane 183-199 (175-206) INTEGRAL Likelihood = -7.80 Transmembrane 143-159 (140-163) INTEGRAL Likelihood = -7.11 Transmembrane 209-225 (208-229) INTEGRAL Likelihood = -5.95 Transmembrane 416-432 (413-434) INTEGRAL Likelihood = -5.15 Transmembrane 304-320 (302-324) INTEGRAL Likelihood = -4.46 Transmembrane 387-403 (382-408) INTEGRAL Likelihood = -3.35 Transmembrane 348-364 (345-366) INTEGRAL Likelihood = -1.17 Transmembrane 11-27 (10-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.5543 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05339 >GP:AAF94579 GB:AE004221 sodium/alanine symporter [Vibrio cholerae] Identities = 261/441 (59%), Positives = 328/441 (74%), Gaps = 7/441 (1%) Query: 3 ALVKLIDNLVWGPPLLILLVGTGIYLTSHLGLIQILKLPRAFKLIFSDDEG---HGDISS 59- + ++ +D+LVWGPPLLILLVGTG+Y T LGL+Q +LP A ++F ++ GD+SS Sbjct: 6 SFLQTVDSLVWGPPLLILLVGTGVYFTFRLGLLQFRRLPTALAMVFGREKSSDKQGDVSS 65- Query: 60 FAALATALAATVGTGNIVGVATAIKSGGPGALFWMWVAAFFGMATKYAEGVLAIKYRTKD 11- 9 FAAL TAL+AT+GTGNIVGVATAIK GGPGALFWMW+AA FGMATKYAE +LA+KYR D Sbjct: 66 FAALCTALSATIGTGNIVGVATAIKLGGPGALFWMWLAALFGMATKYAECLLAVKYRQID 12- 5 Query: 120 ANGHISGGPMYYIVNGMGTKWKPLAVLFAGSGILVALFGIGTFAQVNSITSSLGHSFGLS 17- 9 G + GGPMYY+ +G+ +K LAVLFA + VA FGIGTF QVN+I + SFG+ Sbjct: 126 DKGQMVGGPMYYLRDGVSSK--TLAVLFAVFAVGVACFGIGTFPQVNAILDATQISFGVP 18- 3 Query: 180 PQMVSIVLAIFVAAIIFGGIHSISKVAEKVVPFMAIFYILSSLAVIFSHYQQLLPVIRLV 23- 9 + ++VL + VA + GGI SI+KVA KVVP MA+FYI++ L+VI ++ +L + LV Sbjct: 184 REASAVVLTVLVAIVTIGGIQSIAKVAGKVVPAMALFYIIACLSVIVTNADKLADAVELV 24- 3 Query: 240 FQSAFTPTAAIGGFAGSLMKDAIQKGIARGVFSNESGLRSAPIAAAAAKTNEPVEQGLIS 29- 9 SAFT TAA GGF G+ + AIQ GIARGVFSNESGL SAP+AAAAAKT+ VEQGLIS Sbjct: 244 LVSAFTSTAATGGFLGASIMLAIQSGIARGVFSNESGLGSAPMAAAAAKTDSCVEQGLIS 30- 3 Query: 300 MTGTFIDTIIICTLTGLSILVTGQWTGQLEGAPLTQSAFATVFG--NLGTFGLTFSLVLF 35- 7 MTGTF DTIIICT+TGL++++TG W L GA +T AFAT +G ++ L+ F Sbjct: 304 MTGTFFDTIIICTMTGLALILTGAWQSDLSGAAMTTYAFATGLNAQTIGPMLVSIGLMFF 36- 3 Query: 358 AFTTILGWSYYGERCFEFLFGITHLTYFRIVFILMVGLGGFLKLELIWVLADIVNGLMAL 41- 7 AFTTILGW+YYGERC FLFG + ++IVFI ++ G FL L+LIW++ADIVNGLMA+ Sbjct: 364 AFTTILGWNYYGERCMVFLFGTKAVLPYKIVFIGLIASGAFLHLDLIWIIADIVNGLMAI 42- 3 Query: 418 PNLIALLALSPVVILETKHYF 438 PNLI L+AL VV+ ETK YF Sbjct: 424 PNLIGLVALRHVVVEETKQYF 444 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05340 Identities = 323/439 (73%), Positives = 380/439 (85%), Gaps = 1/439 (0%) Query: 9 MLTLFTHINSFVWGPPLLALLVGTGIYLSFRLGFIQLRQLSRAFKLIFREDNGQGDISSY 68- M+ L I++ VWGPPLL LLVGTGIYL+ LG IQ+ + L RAFKLIF +D G GDISS+ Sbjct: 1 MIALVKLIDNLVWGPPLLILLVGTGIYLTSHLGLIQILKLPRAFKLIFSDDEGHGDISSF 60- Query: 69 AALATALAATVGTGNIVGVATAIKSGGPGALFWMWVAAFFGMATKYAEGLLAIKYRTKDT 12- 8 AALATALAATVGTGNIVGVATAIKSGGPGALFWMWVAAFFGMATKYAEG+LAIKYRTKD Sbjct: 61 AALATALAATVGTGNIVGVATAIKSGGPGALFWMWVAAFFGMATKYAEGVLAIKYRTKDA 12- 0 Query: 129 NGEISGGPMYYIINGMGQKWKPLAVFFSAAGILVALLGIGTFTQVNAIASSLEHTFKIST 18- 8 NG ISGGPMYYI+NGMG KWKPLAV F+ +GILVAL GIGTF QVN+I SSL H+F +S Sbjct: 121 NGHISGGPNYYIVNGMGTKWKPLAVLFAGSGILVALFGIGTFAQVNSITSSLGHSFGLSP 18- 0 Query: 189 RFTSLILAVIVLFIIFGGIKSISKVSEKIVPFMAISYILATLIIIAVNYNKIPHTFQLIF 24- 8 + S++LA+ V IIFGGI SISKV+EK+VPFMAI YIL++L +I +Y ++ +L+F Sbjct: 181 QMVSIVLAIFVAAIIFGGIHSISKVAEKVVPFMAIFYILSSLAVIFSHYQQLLPVIRLVF 24- 0 Query: 249 SGAFSGTAAIGGFSGAIVKEAIQKGIARGVFSNESGLGSAPIAAAAAKTKEPVEQGLISM 30- 8 AF+ TAAIGGF+G+++K+AIQKGIARGVFSNESGL SAPIAAAAAKT EPVEQGLISM Sbjct: 241 QSAFTPTAAIGGFAGSLMKDAIQKGIARGVFSNESGLRSAPIAAAAAKTNEPVEQGLISM 30- 0 Query: 309 TGTFIDTIVICTLTGIAILVTGKWLEFDLQGAPLTQASFNTVFGSLGSFALTFCLVLFAF 36- 8 TGTFIDTI+ICTLTG++ILVTG+W L+GAPLTQ++F TVFG+LG+F LTF LVLFAF Sbjct: 301 TGTFIDTIIICTLTGLSILVTGQWTG-QLEGAPLTQSAFATVFGNLGTFGLTFSLVLFAF 35- 9 Query: 369 TTILGWSYYGERCFEYLFGTKFINAYRIIFVIMVGLGGFLQLDLIWVIADIVNGLMALPN 42- 8 TTILGWSYYGERCFE+LFG + +RI+F++MVGLGGFL+L+LIWV+ADIVNGLMALPN Sbjct: 360 TTILGWSYYGERCFEFLFGITHLTYFRIVFILMVGLGGFLKLELIWVLADIVNGLMALPN 41- 9 Query: 429 LIALLALSPIIVKETQKYF 447 LIALLALSP+++ ET+ YF Sbjct: 420 LIALLALSPVVILETKHYF 438 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1751 A DNA sequence (GBSx1858) was identified in S. agalactiae <SEQ ID 5439> which encodes the amino acid sequence <SEQ ID 5440>. Analysis of this protein sequence reveals the following: TABLE-US-05341 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.16 Transmembrane 85-101 (80-108) INTEGRAL Likelihood = -5.36 Transmembrane 118-134 (115-137) INTEGRAL Likelihood = -2.81 Transmembrane 177-193 (177-193) INTEGRAL Likelihood = -0.48 Transmembrane 49-65 (49-65) ----- Final Results ----- bacterial membrane --- Certainty = 0.3463 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05342 >GP:CAB12451 GB:Z99107 alternate gene name: ydxT~similar to cation efflux system membrane protein [Bacillus subtilis] Identities = 118/282 (41%), Positives = 181/282 (63%) Query: 6 ENLQLAKRGPIISIIAYITLAVAKLAAGYWFDATSLVADGFNNLSDILGNVALLIGLHLA 65- + L+ + G ++SI AY+ L+ KL GY F + +L ADG NN +DI+ +VA+LIGL ++ Sbjct: 5 DELKKGESGALVSIAAYLVLSAIKLIIGYLFHSEALTADGLNNTTDIIASVAVLIGLRIS 64- Query: 66 SQPADSNHRFGHWKIEDLASLITSFIMFVVGIQVFIQTVTKIINNTDTNIDPLGAIVGAI 12- 5 +P D +H +GH++ E +ASLI SFIM VVG+QV I + D + A A Sbjct: 65 QKPPDEDHPYGHFRAETIASLIASFIMMVVGLQVLFSAGESIFSAKQETPDMIAAWTAAG 12- 4 Query: 126 SALVMLGVYFYNKQLSQRVKSSALVAASKDNLSDAVTSIGTSIAIIAASLNFPIIDRLAA 18- 5 A++ML VY YNK+L+++VKS AL+AA+ DN SDA SIGT I I+AA + ID + A Sbjct: 125 GAVLMLIVYRYNKRLAKKVKSQALLAAAADNKSDAFVSIGTFIGIVAAQFHLAWIDTVTA 18- 4 Query: 186 IIITYFILKTAYDIFIESAFSLSDGFDDYQLKQYEKAILTIPKISAVKSQRGRTYGSNIY 24- 5 +I I KTA+DIF ES+ SL+DGFD + Y++ I I +S +K + R GS ++ Sbjct: 185 FVIGLLICKTAWDIFKESSHSLTDGFDIKDISAYKQTIEKISGVSRLKDIKARYLGSTVH 24- 4 Query: 246 LDIVLEMNPDLSVFESHAITERVEKLLSDKFSVYDIDIHVEP 287 +D+V+E++ DL++ ESH I +E+ + ++ ++ +H+EP Sbjct: 245 VDVVVEVSADLNITESHDIANEIERRMKEEHAIDYSHVHMEP 286 A related DNA sequence was identified in S. pyogenes <SEQ ID 5441> which encodes the amino acid sequence <SEQ ID 5442>. Analysis of this protein sequence reveals the following: TABLE-US-05343 Possible site: 46 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.01 Transmembrane 121-137 (114-139) INTEGRAL Likelihood = -5.41 Transmembrane 86-102 (84-109) INTEGRAL Likelihood = -5.04 Transmembrane 178-194 (176-197) INTEGRAL Likelihood = -0.69 Transmembrane 50-66 (50-66) INTEGRAL Likelihood = -0.64 Transmembrane 158-174 (158-174) ----- Final Results ----- bacterial membrane --- Certainty = 0.4206 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05344 >GP:CAB12451 GB:Z99107 alternate gene name: ydxT~similar to cation efflux system membrane protein [Bacillus subtilis] Identities = 127/280 (45%), Positives = 187/280 (66%) Query: 9 LKLARKGPIVSIIVYLSLSVAKLLAGYLLNASSLIADGFNNLSDIVGNVALLIGLHLASQ 68- LK G +VSI YL LS KL+ GYL ++ +L ADG NN +DI+ +VA+LIGL ++ + Sbjct: 7 LKKGESGALVSIAAYLVLSAIKLIIGYLFHSEALTADGLNNTTDIIASVAVLIGLRISQK 66- Query: 69 PADANHKFGHWKIEDLSSLVTSFIMFLVGFQVLIHTIKSIFSGQQVDIDPLGAIVGIVSA 12- 8 P D +H +GH++ E ++SL+ SFIM +VG QVL +SIFS +Q D + A A Sbjct: 67 PPDEDHPYGHFRAETIASLIASFIMMVVGLQVLFSAGESIFSAKQETPDMIAAWTAAGGA 12- 6 Query: 129 FVMLGVYVFNKRLSKRVKSSALVAASKDNLADAVTSIGTSIAIIAASLHLPVIDHIAAMI 18- 8 +ML VY +NKRL+K+VKS AL+AA+ DN +DA SIGT I I+AA HL ID + A + Sbjct: 127 VLMLIVYRYNKRLAKKVKSQALLAAAADNKSDAFVSIGTFIGIVAAQFHLAWIDTVTAFV 18- 6 Query: 189 ITFFILKTAFDIFMESSFSLSDGFDSRHLKKYEKAILEIPKIVAVKSQRARTYGSNVYLD 24- 8 I I KTA+DIF ESS SL+DGFD + + Y++ I +I + + K +AR GS V++D Sbjct: 187 IGLLICKTAWDIFKESSHSLTDGFDIKDISAYKQTIEKISGVSRLKDIKARYLGSTVHVD 24- 6 Query: 249 IVLEMNPDLSVYESHSITEKVEQLLSDQFSIYDIDIHVEP 288 +V+E++ DL++ ESH I +E+ + ++ +I +H+EP Sbjct:247 VVVEVSADLNITESHDIANEIERRMKEEHAIDYSHVNMEP 286 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05345 Identities = 274/406 (67%), Positives = 340/406 (83%), Gaps = 4/406 (0%) Query: 7 NLQLAKRGPIISIIAYITLAVAKLAAGYWFDATSLVADGFNNLSDILGNVALLIGLHLAS 66- NL+LA++GPI+SII Y++L+VAKL AGY +A+SL+ADGFNNLSDI+GNVALLIGLHLAS Sbjct: 8 NLKLARKGPIVSIIVYLSLSVAKLLAGYLLNASSLIADGFNNLSDIVGNVALLIGLHLAS 67- Query: 67 QPADSNHRFGHWKIEDLASLITSFIMFVVGIQVFIQTVTKIINNTDTNIDPLGAIVGAIS 12- 6 QPAD+NH+FGHWKIEDL+SL+TSFIMF+VG QV I T+ I + +IDPLGAIVG +S Sbjct: 68 QPADANHKFGHWKIEDLSSLVTSFIMFLVGFQVLIHTIKSIFSGQQVDIDPLGAIVGIVS 12- 7 Query: 127 ALVMLGVYFYNKQLSQRVKSSALVAASKDNLSDAVTSIGTSIAIIAASLNFPIIDRLAAI 18- 6 A VMLGVY +NK+LS+RVKSSALVAASKDNL+DAVTSIGTSIAIIAASL+ P+ID +AA+ Sbjct: 128 AFVMLGVYVFNKRLSKRVKSSALVAASKDNLADAVTSIGTSIAIIAASLHLPVIDHIAAM 18- 7 Query: 187 IITYFILKTAYDIFIESAFSLSDGFDDYQLKQYEKAILTIPKISAVKSQRGRTYGSNIYL 24- 6 IIT+FILKTA+DIF+ES+FSLSDGFD LK+YEKAIL IPKI AVKSQR RTYGSN+YL Sbjct: 188 IITFFILKTAFDIFMESSFSLSDGFDSRHLKKYEKAILEIPKIVAVKSQRARTYGSNVYL 24- 7 Query: 247 DIVLEMNPDLSVFESHAITERVEKLLSDKFSVYDIDIHVEPASIPEDEIFDNVYQKLYKN 30- 6 DIVLEMNPDLSV+ESH+ITE+VE+LLSD+FS+YDIDIHVEPA IPE+EIFDNV +KLY+ Sbjct: 248 DIVLEMNPDLSVYESHSITEKVEQLLSDQFSIYDIDIHVEPAMIPEEEIFDNVAKKLYRY 30- 7 Query: 307 EKIILAKIPGYETFISPDFYMINEKGNIITSDMLTNATNHSLASNFKYFNVKSISQKTKL 36- 6 EK+IL+K+P Y+ +I+ F +I+ G + + N + SNF +F ++SISQKT L Sbjct: 308 EKLILSKVPDYDHYIAKSFQLIDANGQTVNYEQFLNQEIY-YPSNFNHFQIESISQKTML 36- 6 Query: 367 VSYELEGKRHTSIWRRNEKWFLIYHQIT--AKSSPYKTRRYQITSL 410 V+Y+L G + TSIWRR+E W L++HQIT AK + T Y+I + Sbjct: 367 VTYQLNGNQRTSIWRRHESWSLLFHQITPIAKKQLHHT-HYRIVKM 411 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1752 A DNA sequence (GBSx1859) was identified in S. agalactiae <SEQ ID 5443> which encodes the amino acid sequence <SEQ ID 5444>. Analysis of this protein sequence reveals the following: TABLE-US-05346 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.12 Transmembrane 171-187 (161-194) INTEGRAL Likelihood = -6.32 Transmembrane 118-134 (113-138) INTEGRAL Likelihood = -5.89 Transmembrane 59-75 (53-77) INTEGRAL Likelihood = -5.52 Transmembrane 231-247 (226-252) INTEGRAL Likelihood = -3.24 Transmembrane 86-102 (84-103) INTEGRAL Likelihood = -0.32 Transmembrane 31-47 (31-47) ----- Final Results ----- bacterial membrane --- Certainty = 0.4248 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9869> which encodes amino acid sequence <SEQ ID 9870> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05347 >GP:CAB14850 GB:Z99118 similar to hypothetical proteins [Bacillus subtilis] Identities = 80/226 (35%), Positives = 136/226 (59%), Gaps = 1/226 (0%) Query: 27 TNNPIFGIMLTVWAYYIGIRIFRKYPSPAT-TPLLLATILLIAFLKLTHISYKDYYNGGS 85- T +P FGI++++ A+ IG +F+K TPL +A +L IAFLK+ SY DY NGG Sbjct: 4 TMSPYFGIVVSLAAFGIGTFLFKKTKGFFLFTPLFVAMVLGIAFLKIGGFSYADYNNGGE 63- Query: 86 FLTMLITPSTVVLAIPLYRTFHLMKHHIKSISISIILASVINTVFTAIVAKFFGMKYFLA 14- 5 + + P+T+ AIPLY+ +K + I SII S+ + ++AK + + Sbjct: 64 IIKFFLEPATIAFAIPLYKQRDKLKKYWWQIMASIIAGSICSVTIVYLLAKGIHLDSAVM 12- 3 Query: 146 ISLFPKSVTTAMAVGITSKAGGLATITLVVVVITGILTSVLGPIFLKLLRIEDPVAIGLA 20- 5 S+ P++ TTA+A+ ++ GG++ IT V+ ++ LG +FLK+ ++++P++ GLA Sbjct: 124 KSMLPQAATTAIALPLSKGIGGISDITAFAVIFNAVIVYALGALFLKVFKVKNPISKGLA 18- 3 Query: 206 LGGTGHAIGTGQALKYGQVQGAMAGLAIGITGICYVIVSPLVAGLI 251 LG +GHA+G ++ G+V+ AMA +A+ + G+ V+V P+ LI Sbjct: 184 LGTSGHALGVAVGIEMGEVEAAMASIAVVVVGVVTVLVIPVFVQLI 229 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8893> and protein <SEQ ID 8894> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05348 Lipop: Possible site: -1 Crend: 0 SRCFLG: 0 McG: Length of UR: 22 Peak Value of UR: 2.57 Net Charge of CR: 0 McG: Discrim Score: 6.51 GvH: Signal Score (-7.5): -5.91 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 6 value: 8.12 threshold: 0.0 INTEGRAL Likelihood = -8.12 Transmembrane 149-165 (139-172) INTEGRAL Likelihood = -6.32 Transmembrane 96-112 (91-116) INTEGRAL Likelihood = -5.89 Transmembrane 37-53 (31-55) INTEGRAL Likelihood = -5.52 Transmembrane 209-225 (204-230) INTEGRAL Likelihood = -3.24 Transmembrane 64-80 (62-81) INTEGRAL Likelihood = -0.32 Transmembrane 9-25 (9-25) PERIPHERAL Likelihood = 1.06 121 modified ALOM score: 2.12 icm1 HYPID: 7 CFP: 0.425 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4248 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00121## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1753 A DNA sequence (GBSx1860) was identified in S. agalactiae <SEQ ID 5445> which encodes the amino acid sequence <SEQ ID 5446>. Analysis of this protein sequence reveals the following: TABLE-US-05349 Possible site: 28 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05350 >GP:CAA76857 GB:Y17797 hypothetical protein [Enterococcus faecalis] Identities = 44/194 (22%), Positives = 90/194 (45%), Gaps = 13/194 (6%) Query: 21 TACSSSNTQQTSTSKSNVSQHKNIKADHEELRLKFNKVKLGVKANNFKGGTSLAELKQLF 80 - T S ++T++ S+ K + + K D+ +L+ ++K+ +G N+ +GG++ E+K + Sbjct: 60 TNSSKNDTKKESSEKKSEDKSK----DNSDLKATYDKINVGDIMNSSEGGSTEDEVKAIL 115- Query: 81 GGEPNEKFDTPAGNVTLKGYRW-NVDD----ISITIQLLNDSSIVRSISNFKFIRDANIT 135- GEP T ++ W NV SIT+ + + +S+S K + +T Sbjct: 116 -GEPASSSTTDIQGISTTTLSWTNVKGGDLLASITVSFSDGKAASKSVSGLKVAKHDKVT 17- 4 Query: 136 TKDYNSLKNGMSYN--KVKELLGEPDDISQAVSSDKEELQAAWISGIQSSDSDPGINLTF 19- 3 N++ SY+ + ++ LG+P I+ + ++ W+ + D + ++F Sbjct: 175 ADQVNNIATDGSYSEEQARKDLGDPTGITSTNINGEKNDTLIWMKNL-DGDLGATVTVSF 23- 3 Query: 194 ENDKLTNKQQHGLK 207 N +K GLK Sbjct: 234 SNGNAISKSSSGLK 247 A related DNA sequence was identified in S. pyogenes <SEQ ID 5447> which encodes the amino acid sequence <SEQ ID 5448>. Analysis of this protein sequence reveals the following: TABLE-US-05351 Possible site: 21 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05352 >GP:CAA76857 GB:Y17797 hypothetical protein [Enterococcus faecalis] Identities = 34/166 (20%), Positives = 74/166 (44%), Gaps = 8/166 (4%) Query: 47 HQDKRANFEKIKLATVDSSFTGGTSLEELISLFGEPSQHDPKTAGEVTIDAYTWQFDQ-- 10- 4 + D +A ++KI + + +S GG++ +E+ ++ GEP+ ++ +W + Sbjct: 83 NSDLKATYDKINVGDIMNSSEGGSTEDEVKAILGEPASSSTTDIQGISTTTLSWTNVKGG 14- 2 Query: 105 ---VTLTVNLYQNSSIVKTISNFTFARELGLSQKEYQQLQKGMSY--EDVKKILTEPDNY 15- 9 ++TV+ + K++S A+ ++ + + SY E +K L +P Sbjct: 143 DLLASITVSFSDGKAASKSVSGLKVAKHDKVTADQVNNIATDGSYSEEQARKDLGDPTGI 20- 2 Query: 160 SQASSSDHQTLQAIWVSGLKTDTSGANISLVFENNQLTEMSQVGLE 205 + + + + IW+ L D GA +++ F N S GL+ Sbjct: 203 TSTNINGEKNDTLIWMKNLDGDL-GATVTVSFSNGNAISKSSSGLK 247 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05353 Identities = 84/199 (42%), Positives = 126/199 (63%), Gaps = 3/199 (1%) Query: 11 TIVCLSFLG--LTACSSSNTQQTSTSKSNVSQHKNIKADHEELRLKFNKVKLGVKANNFK 68- T++ +SF L ACS++ ++ S S + + +A H++ R F K+KL ++F Sbjct: 8 TLLLISFFTSFLVACSTTKDKEPQPSDSEIITPRLHQAAHQDKRANFEKIKLATVDSSFT 67- Query: 69 GGTSLAELKQLFGGEPNEKFDTPAGNVTLKGYRWNVDDISITIQLLNDSSIVRSISNFKF 12- 8 GGTSL EL LFG EP++ AG VT+ Y W D +++T+ L +SSIV++ISNF F Sbjct: 68 GGTSLEELISLFG-EPSQHDPKTAGEVTIDAYTWQFDQVTLTVNLYQNSSIVKTISNFTF 12- 6 Query: 129 IRDANITTKDYNSLKNGMSYNKVKELLGEPDDISQAVSSDKEELQAAWISGIQSSDSDPG 18- 8 R+ ++ K+Y L+ GMSY VK++L EPD+ SQA SSD + LQA W+SG+++ S Sbjct: 127 ARELGLSQKEYQQLQKGMSYEDVKKILTEPDNYSQASSSDHQTLQAIWVSGLKTDTSGAN 18- 6 Query: 189 INLTFENDKLTNKQQHGLK 207 I+L FEN++LT Q GL Sbjct: 187 ISLVFENNQLTEMSQVGLE 205 SEQ ID 5446 (GBS650) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 178 (lane 9; MW 28 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1754 A DNA sequence (GBSx1861) was identified in S. agalactiae <SEQ ID 5449> which encodes the amino acid sequence <SEQ ID 5450>. This protein is predicted to be ribosomal protein S1 homolog; Sequence specific DNA-binding protein (r. Analysis of this protein sequence reveals the following:

TABLE-US-05354 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2950 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9363> which encodes amino acid sequence <SEQ ID 9364> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05355 >GP:AAA97575 GB:U27517 ribosomal S1 protein [Homo sapiens] Identities = 156/305 (51%), Positives = 214/305 (70%), Gaps = 7/305 (2%) Query: 1 MEARKAWDKLVGREGEVVTVKGTRAVKGGLSVEFEGLRGFIPASMIDTRFVRNTEKFVGQ 60- ++ARKAW+ L EG+ V K AV+GGL V+ G+RGF+PASM+ RFV + +F + Sbjct: 53 LDARKAWENLSFAEGDTVDAKVINAVRGGLIVDVNGVRGFVPASMVAERFVSDLNQFKNK 11- 2 Query: 61 EFDAKIKEVDAAENRFILSRREVVEESAAAARKEVFSNIEVGSVVTGKVARLTSFGAFID 12- 0 + A++ E+D A R ILSR+ V + AA EVFS + VG VV G VARLT FGAF+D Sbjct: 113 DIKAQVIEIDPANARLILSRKAVAAQERAAQLAEVFSKLSVGEVVEGTVARLTDFGAFVD 17- 2 Query: 121 LGGVDGLVHVTELSHERNVSPKSVVTVGEEVEVKVLSIDEEAGRVSLSLKATTPGPWDGV 18- 0 LGGVDGLVHV+E+SH+R +P V+T G++V+VK+L++D E GR+SLS+KAT GPWD Sbjct: 173 LGGVDGLVHVSEISHDRVKNPADVLTKGDKVDVKILALDTEKGRISLSIKATQRGPWDEA 23- 2 Query: 181 EQKLAAGDVIEGKVKRLTDFGAFVEVLPGIDGLVHISQISHKRVENPKDVLSAGQEVTVK 24- 0 ++AAG V+EG VKR+ DFGAFVE+LPGI+GLVH+SQIS+KR+ENP +VL +G +V VK Sbjct: 233 ADQIAAGSVLEGTVKRVKDFGAFVEILPGIEGLVHVSQISNKRIENPSEVLKSGDKVQVK 29- 2 Query: 241 VLEVNSDAERVSLSMKALEERPAQAEGEKEEKRQSRPRRPRRQEKRDYELPETQTGFSMA 30- 0 VL++ ER+SLSMKALEE+P + E R+ R + Y+ + + ++ Sbjct: 293 VLDIKPAEERISLSMKALEEKP------EREDRRGNDGSASRADIAAYK-QQDDSAATLG 34- 5 Query: 301 DLFGD 305 D+FGD Sbjct: 346 DIFGD 350 A related DNA sequence was identified in S. pyogenes <SEQ ID 5451> which encodes the amino acid sequence <SEQ ID 5452>. Analysis of this protein sequence reveals the following: TABLE-US-05356 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3312 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05357 Identities = 284/309 (91%), Positives = 296/309 (94%), Gaps = 1/309 (0%) Query: 1 MEARKAWDKLVGREGEVVTVKGTRAVKGGLSVEFEGLRGFIPASMIDTRFVRNTEKFVGQ 60- +EARKAWDKLVGREGEVVTVKGTRAVKGGLSVEFEGLRGFIPASMIDTRFVRNTEKFVGQ Sbjct: 93 LEARKAWDKLVGREGEVVTVKGTRAVKGGLSVEFEGLRGFIPASMIDTRFVRNTEKFVGQ 15- 2 Query: 61 EFDAKIKEVDAAENRFILSRREVVEESAAAARKEVFSNIEVGSVVTGKVARLTSFGAFID 12- 0 EFDAKIKEVDAAENRFILSRREV+EE+A AR EVFS I G+VVTG VARLTSFGAFID Sbjct: 153 EFDAKIKEVDAAENRFILSRREVIEEAAKEARAEVFSKISEGAVVTGTVARLTSFGAFID 21- 2 Query: 121 LGGVDGLVHVTELSHERNVSPKSVVTVGEEVSVKVLSIDEEAGRVSLSLKATTPGPWDGV 18- 0 LGGVDGLVHVTELSHERNVSPKSVV+VGEEVEVKVLSIDEEAGRVSLSLKATTPGPWDGV Sbjct: 213 LGGVDGLVHVTELSHERNVSPKSVVSVGEEVEVKVLSIDEEAGRVSLSLKATTPGPWDGV 27- 2 Query: 181 EQKLAAGDVIEGKVKRLTDFGAFVEVLPGIDGLVHISQISHKRVENPKDVLSAGQEVTVK 24- 0 EQKLA GDV+EGKVKRLTDFGAFVEVLPGIDGLVHISQISHKRVENPKDVLS GQEVTVK Sbjct: 273 EQKLAQGDVVEGKVKRLTDFGAFVEVLPGIDGLVHISQISHKRVENPKDVLSVGQEVTVK 33- 2 Query: 241 VLEVNSDAERVSLSMKALEERPAQAEGE-KEEKRQSRPRRPRRQEKRDYELPETQTGFSM 29- 9 VLEVN+ ERVSLS+KALEERPAQAEG+ KEEKRQSRPRRP+R+ +RDYELPETQTGFSM Sbjct: 333 VLEVNAADERVSLSIKALEERPAQAEGDNKEEKRQSRPRRPKRESRRDYELPETQTGFSM 39- 2 Query: 300 ADLFGDIEL 308 ADLFGDIEL Sbjct: 393 ADLFGDIEL 401 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1755 A DNA sequence (GBSx1862) was identified in S. agalactiae <SEQ ID 5453> which encodes the amino acid sequence <SEQ ID 5454>. This protein is predicted to be dihydroorotate dehydrogenase a (pyrD). Analysis of this protein sequence reveals the following: TABLE-US-05358 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1708 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05359 >GP:CAB51330 GB:AJ131985 dihydroorotate dehydrogenase [Streptococcus pneumoniae] Identities = 227/310 (73%), Positives = 268/310 (86%) Query: 1 MVSLKTEIAGFSFDNCLMNAAGIYCMTKEELLAIENSEAGSFVTKTGTLEAREGNPQPRY 60- MVS KT+IAGF FDNCLMNAAG+ CMT EEL ++NS AG+FVTKT TL+ R+GNP+PRY Sbjct: 1 MVSTKTQIAGFEFDNCLMNAAGVACMTIEELEEVKNSAAGTFVTKTATLDFRQGNPEPRY 60- Query: 61 ADTDWGSINSMGLPNKGIDYYLDFVTELQDQDNSKNHVLSLVGLSPEETHIILKKVENSS 12- 0 D GSINSMGLPN G+DYYLD++ +LQ++++++ LSLVG+SPEETH ILKKV+ S Sbjct: 61 QDVPLGSINSMGLPNNGLDYYLDYLLDLQEKESNRTFFLSLVGMSPEETHTILKKVQESD 12- 0 Query: 121 YNGLIELNLSCPNVPGKPQIAYDFEMTDLILSEIFSYYQKPLGIKLPPYFDIVHFDQAAT 18- 0 + GL ELNLSCPNVPGKPQIAYDFE TD IL+E+F+Y+ KPLGIKLPPYFDIV+FDQAA Sbjct: 121 FRGLTELNLSCPNVPGKPQIAYDFETTDRILAEVFAYFTKPLGIKLPPYFDIVYFDQAAA 18- 0 Query: 181 IFNKYPLAFINCVNSIGNGLVIDDETVVIKPKNGFGGIGGDFIKPTALANVHAFYKRLNP 24- 0 IFNKYPL F+NCVNSIGNGL I+DE+VVI+PKNGFGGIGG++IKPTALANVHAFY+RLNP Sbjct: 181 IFNKYPLKFVNCVNSIGNGLYIEDESVVIRPKNGFGGIGGEYIKPTALANVHAFYQRLNP 24- 0 Query: 241 SIKIIGTGGVKNGRDAFEHILCGASMVQIGTALQKEGPEIFQRVSRELKEIMADKGYQSL 30- 0 I+IIGTGGV GRDAFEHILCGASMVQ+GT L KEG F R++ ELK IM +KGY+SL Sbjct: 241 QIQIIGTGGVLTGRDAFEHILCGASMVQVGTTLHKEGVSAFDRITNELKAIMVEKGYESL 30- 0 Query: 301 EDFRGQLNYL 310 EDFRG+L Y+ Sbjct: 301 EDFRGKLRYI 310 A related DNA sequence was identified in S. pyogenes <SEQ ID 5455> which encodes the amino acid sequence <SEQ ID 5456>. Analysis of this protein sequence reveals the following: TABLE-US-05360 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2689 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05361 Identities = 239/309 (77%), Positives = 262/309 (84%) Query: 1 MVSLKTEIAGFSFDNCLMNAAGIYCMTKEELLAIENSEAGSFVTKTGTLEAREGNPQPRY 60- MVS T+I FSFDNCLMNAAG+YCMTKEEL+ +E S+A SFVTKTGTLE R GNP+PRY Sbjct: 5 MVSTATQIGHFSFDNCLMNAAGVYCMTKEELMEVEKSQAASFVTKTGTLEVRPGNPEPRY 64- Query: 61 ADTDWGSINSMGLPNKGIDYYLDFVTELQDQDNSKNHVLSLVGLSPEETHIILKKVENSS 12- 0 ADT GSINSMGLPN G YYLDFV++L K H LS+VGLSP ET ILK + S Sbjct: 65 ADTRLGSINSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAIMASD 12- 4 Query: 121 YNGLIELNLSCPNVPGKPQIAYDFEMTDLILSEIFSYYQKPLGIKLPPYFDIVHFDQAAT 18- 0 Y GL+ELNLSCPNVPGKPQIAYDFE TD +L IF+YY KPLGIKLPPYFDIVHFDQAA Sbjct: 125 YEGLVELNLSCPNVPGKPQIAYDFETTDQLLENIFTYYTKPLGIKLPPYFDIVHFDQAAA 18- 4 Query: 181 IFNKYPLAFINCVNSIGNGLVIDDETVVIKPKNGFGGIGGDFIKPTALANVHAFYKRLNP 24- 0 IFNKYPL+F+NCVNSIGNGLVI DE V+IKPKNGFGGIGGD+IKPTALANVHAFYKRL P Sbjct: 185 IFNKYPLSFVNCVNSIGNGLVIKDEQVLIKPKNGFGGIGGDYIKPTALANVHAFYKRLKP 24- 4 Query: 241 SIKIIGTGGVKNGRDAFEHILCGASMVQIGTALQKEGPEIFQRVSRELKEIMADKGYQSL 30- 0 SI IIGTGGVK GRDAFEHILCGASMVQIGTAL +EGP IF+RV++ELK IM +KGYQSL Sbjct: 245 SIHIIGTGGVKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKTIMVEKGYQSL 30- 4 Query: 301 EDFRGQLNY 309 +DFRG L Y Sbjct: 305 DDFRGNLRY 313 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1756 A DNA sequence (GBSx1863) was identified in S. agalactiae <SEQ ID 5457> which encodes the amino acid sequence <SEQ ID 5458>. This protein is predicted to be beta-lactam resistance factor. Analysis of this protein sequence reveals the following: TABLE-US-05362 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4437 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05363 >GP:CAB89121 GB:AJ277485 betalactani resistance factor [Streptococcus pneumoniae] Identities = 238/410 (58%), Positives = 304/410 (74%) Query: 1 MALKELTAKEFESYSGNYDLQSFMQTPEMAKLLKKRGYDITYMGYQIDGKMEIISIVYTI 60- MAL LT +EF++YS +SFMQ+ +M LL+KRG I Y+ + +G++++ ++VY++ Sbjct: 1 MALTTLTKEEFQTYSDQVSSRSFMQSVQMGDLLEKRGARIVYLALKQEGEIQVAALVYSL 60- Query: 61 PMTGGLHMEVNSGPAHSNSKYLKHFYKELQNYAKSQGALELLIKPYDTYQEFTGEGKPKG 12- 0 PM GGLHME+NSGP ++ L FY EL+ YAK G LELL+KPY+TYQ F +G P Sbjct: 61 PMLGGLHMELNSGPIYTQQDALPVFYAELKEYAKQNGVLELLVKPYETYQTFDSQGNPID 12- 0 Query: 121 APNTYLIDDLTSIGYHHDGLHIGYPGGEPDWHYVKNLEGITPQNLLKSFSKKGRPLVKKA 18- 0 A +I DLT +GY DGL GYPGGEPDW Y K+L +T ++LLKSFSKKG+PLVKKA Sbjct: 121 AEKKSIIQDLTDLGYQFDGLTTGYPGGEPDWLYYKDLTELTEKSLLKSFSKKGKPLVKKA 18- 0 Query: 181 MSFGIKIRVLKREELHIFKDITSSTSDRRDYMDKSLDYYQDFYDSFGDKAEFVIATLNFR 24- 0 +FGI+++ LKREEL IFK+IT TS+RR+Y DKSL+YY+ FYD+FG++AEF+IA+LNF Sbjct: 181 ETFGIRLKKLKREELSIFKNITKETSERREYSDKSLEYYEHFYDTFGEQAEFLIASLNFS 24- 0 Query: 241 EYDHNLQLNAKKLEEQITVLDNRHQNNTDSAKYHRQRTELVNQLASLDKRRKEVEPFIQK 30- 0 +Y LQ KLEE + L N S K Q E +Q + + R+ E I+K Sbjct: 241 DYMSKLQGEQSKLEENLDKLRLDLSKNPHSEKKQNQLREYSSQFETFEVRKAEARDLIEK 30- 0 Query: 301 FGNQDVVLAGSLFIYSPKETVYLFSGSYTEFNKFYAPAVLQEYVMQEALKRQSTFYNFLG 36- 0 +G +D+VLAGSLF+Y P+ET YLFSGSYTEFNKFYAPA+LQ+YVM E++KR YNFLG Sbjct: 301 YGEEDIVLAGSLFVYMPQETTYLFSGSYTEFNKFYAPALLQKYVMLESIKRGIPKYNFLG 36- 0 Query: 361 IQGNFDGSDGVLRFKQNFNGYIVRKMGTFRYYPNPLKYKSIQLLKRILRR 410 IQG FDGSDGVLRFKQNFNGYIVRK GTFRY+P+PLKYK+IQLLKKI+ R Sbjct: 361 IQGIFDGSDGVLRFKQNFNGYIVRKAGTFRYHPSPLKYKAIQLLKKIVGR 410 A related DNA sequence was identified in S. pyogenes <SEQ ID 5459> which encodes the amino acid sequence <SEQ ID 5460>. Analysis of this protein sequence reveals the following: TABLE-US-05364 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2652 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05365 Identities = 216/410 (52%), Positives = 291/410 (70%) Query: 1 MALKELTAKEFESYSGNYDLQSFMQTPEMAKLLKKRGYDITYMGYQIDGKMEIISIVYTI 60- MAL E++ ++F+ Y + SF+QT EMA L+ KRG ++G + DG++++ ++V++ Sbjct: 1 MALIEISQEQFDHYCHSLVHHSFIQTSEMASLMAKRGAKPQFLGLEKDGELKVAAMVFSQ 60- Query: 61 PMTGGLHMEVNSGPAHSNSKYLKHFYKELQNYAKSQGALELLIKPYDTYQEFTGEGKPKG 12- 0 + GG ME+N+GP ++ + L+HFY +L++YAK + +EL++KPYD YQ F +G P Sbjct: 61 KVAGGWRMELNAGPNTNHPEELEHFYTQLKDYAKQKDVIELILKPYDNYQSFDTDGIPIS 12- 0 Query: 121 APNTYLIDDLTSIGYHHDGLHIGYPGGEPDWHYVKNLEGITPQNLLKSFSKKGRPLVKKA 18- 0 PNT LI LT++GY HDGL GYP GEP WHYVK LEGI L +SFSKKG+ L+KKA Sbjct: 121 RPNTDLISLLTALGYKHDGLKTGYPEGEPVWHYVKKLEGIDSSRLTRSFSKKGKALIKKA 18- 0 Query: 181 MSFGIKIRVLKREELHIFKDITSSTSDRRDYMDKSLDYYQDFYDSFGDKAEFVIATLNFR 24- 0 +FGIK+R LKR+ELH FK+IT +TSDRRDY+DKSL YYQDFYDSFGD EF++ATLNF Sbjct: 181 NTFGIKLRQLKRDELHHFKEITEATSDRRDYLDKSLSYYQDFYDSFGDSCEFMVATLNFE 24- 0 Query: 241 EYDHNLQLNAKKLEEQITVLDNRHQNNTDSAKYHRQRTELVNQLASLDKRRKEVEPFIQK 30- 0 +Y +NL+ +L I + N S K + EL +Q + R E F+++ Sbjct: 241 DYLNNLKQRQLQLATSINKVKGDLGKNPHSEKKQNRLKELSSQFETWQVRISEALHFLEE 30- 0 Query: 301 FGNQDVVLAGSLFIYSPKETVYLFSGSYTEFNKFYAPAVLQEYVMQEALKRQSTFYNFLG 36- 0 +G +DV LAGSLFIY+ +E VYLFSGSY +FNKFY+PA+LQE+ M +A+ + YNFLG Sbjct: 301 YGTKDVFLAGSLFIYTEQEAVYLFSGSYPKFNKFYSPALLQEHAMLKAIHKGIKQYNFLG 36- 0 Query: 361 IQGNFDGSDGVLRFKQNFNGYIVRKMGTFRYYPNPLKYKSIQLLKKILRR 410 I G FDGSDGVLRFKQNFNG+I++K GTFR YP P+KY I+L KK+L R Sbjct: 361 ITGKFDGSDGVLRFKQNFNGFILQKPGTFRCYPFPIKYHFIRLAKKLLNR 410 A related GBS gene <SEQ ID 8895> and protein <SEQ ID 8896> were also identified. Analysis of this protein sequence reveals the following: Homology to resistance proteins The protein has homology with the following sequences in the databases: ##STR00122## SEQ ID 8896 (GBS198) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 26 (lane 6; MW 48.8 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 85 (lane 6; MW 73.8 kDa). GBS198-GST was purified as shown in FIG. 223, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1757 A DNA sequence (GBSx1864) was identified in S. agalactiae <SEQ ID 5461> which encodes the amino acid sequence <SEQ ID 5462>. This protein is predicted to be MurM protein. Analysis of this protein sequence reveals the following: TABLE-US-05366 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4418 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05367 >GP:CAB89539 GB:AJ250767 MurM protein [Streptococcus pneumoniae] Identities = 204/410 (49%), Positives = 286/410 (69%), Gaps = 17/410 (4%) Query: 1 MYRE---ITAVEHDRFVSESNQTNLLQSSNWPKVKDNWGSQLLGFFDGETQIASASILIK 57- MYR I +E+D+FV E N+LQSS W KVK +W + LG ++GE +A AS+LIK Sbjct: 1 MYRYQIGIPTLEYDQFVKEHELANVLQSSAWEKVKSDWNHERLGVYEGENLLAVASVLIK 60- Query: 58 SLPLGFSMLYIPRGPIMDYSNLDIVTKVLKDLKAFGKKQRALFIKCDPLIYLK--MVNAK 11- 5 SLPLG+ M YIPRGPI+DY + +++ VL+ +K++ + +RA+F+ DP I L +VN Sbjct: 61 SLPLGYKMFYIPRGPILDYMDKELLKFVLQSIKSYARSKRAVFVTFDPSICLSQHLVN-- 11- 8 Query: 116 DFENSPDEKEGLIAIDHLQRAGADWTGRTTDLAHTIQPRFQANLYANQFGLDKMSKKTRQ 17- 5 ++ + E L ++ L + G W+G+TT++ TIQPR QA +Y F DK+SK TRQ Sbjct: 119 --QDKREYPENLAIVEILGQLGVKWSGQTTEMDDTIQPRIQAKIYKENFEEDKLSKSTRQ 17- 6 Query: 176 AIRTSKNKGVDIQFGSHELLEDFAELMKKTEDRKGINLRGIDYYQKLLDTYPNNSYITMA 23- 5 AIRT++NKG++IQ+G ELL+ F+ELMKKTE RK I+LR YY+KLLD + +SYIT+ Sbjct: 177 AIRTARNKGLEIQYGGLELLDSFSELMKKTEKRKEIHLRNEAYYRKLLDNFKEDSYITLT 23- 6 Query: 236 SLDVAKRLEKIEKECQIAQSERIKS--LELNREKKVKQHQGTIDRLNKEIDFLKEAQKAY 29- 3 +LDV+KRL ++E+ Q+A+++ ++ E R KV+ + +RL +EIDFL + Sbjct: 237 NLDVSKRLRELEE--QLAKNKALEEAFTESTRTSKVEAQKKEKERLVEEIDFL-QGYMNM 29- 3 Query: 294 DRDIIPLAATLTLEFGNTSENIYAGMDDYFKSYSAPIYTWFETAQRAFERGNIWQNMGGI 35- 3 ++ IPLAATL+LEFG TS N+YAGMDD FK Y+API TW+ETA+ AFERG +WQN+GG+ Sbjct: 294 EKSNIPLAATLSLEFGTTSVNLYAGMDDDFKRYNAPILTWYETARYAFERGMVWQNLGGV 35- 3 Query: 354 ENDLSGGLYHFKSKFEPIIEEFIGEFNIPVN---RLLYKASNYVYALRRK 400 EN L+GGLYHFK KF P IEE++GEF +P + LL A ++ LRKK Sbjct: 354 ENSLNGGLYHFKEKFNPTIEEYLGEFTMPTHPLYPLLRLALDFRKTLRKK 403 A related DNA sequence was identified in S. pyogenes <SEQ ID 5463> which encodes the amino acid sequence <SEQ ID 5464>. Analysis of this protein sequence reveals the following: TABLE-US-05368 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2239 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05369 Identities = 203/399 (50%), Positives = 274/399 (67%), Gaps = 4/399 (1%) Query: 5 ITAVEHDRFVSESNQTNLLQSSNWPKVKDNWGSQLLGFFDGETQIASASILIKSLPLGFS 64- I+ EHD+FV Q LLQSS W KVKDNW + + F++ Q+A+A+ LI+ LPLGF+ Sbjct: 13 ISPEEHDQFVLAQPQAGLLQSSKWGKVKDNWKHERISFYENGVQVAAAACLIRKLPLGFT 72- Query: 65 MLYIPRGPIMDYSNLDIVTKVLKDLKAFGKKQRALFIKCDPLIYLKMVNAKDFENSPDEK 12- 4 M+YIPRGPIMDY+N +++ V+K LK FGK +RALFIK DP + +K + + S + Sbjct: 73 MIYIPRGPIMDYANFELLDFVIKTLKTFGKSKRALFIKIDPSLVIKQT--LEGKESKEND 13- 0 Query: 125 EGLIAIDHLQRAGADWTGRTTDLAHTIQPRFQANLYANQFGLDKMSKKTRQAIRTSKNKG 18- 4 L I L++ G +W+GRT +L TIQPR QAN+YA F D + KK +Q+IRT+ NEG Sbjct: 131 VTLSIIAFLKKLGVEWSGRTKELEDTIQPRIQANIYAKDFDFDSLPKKAKQSIRTATNKG 19- 0 Query: 185 VDIQFGSHELLEDFAELMKKTEDRKGINLRGIDYYQKLLDTYPNNSYITMASLDVAKRLE 24- 4 V++ G ELL+DF+ LMKKTE+RKGI LRG YYQKLL Y SYITMASLD+ ++ + Sbjct: 191 VNVTIGGSELLDDFSALMKKTENRKGIILRGKSYYQKLLGIYAGQSYITMASLDLPEQKK 25- 0 Query: 245 KIEKECQIAQSERIKSLELNREKKVKQHQGTIDRLNKEIDFLKEAQKAYDRDIIPLAATL 30- 4 + ++ A +E+ + + ++ KV ++Q TI RL K++ L E Q A + IPLAATL Sbjct: 251 LLIQQLDKALAEQARLTDKSKPSKVAENQKTIARLQKDLTILSE-QLATGQTRIPLAATL 30- 9 Query: 305 TLEFGNTSENIYAGMDDYFKSYSAPIYTWFETAQRAFERGNIWQNMGGIENDLSGGLYHF 36- 4 TL +G TSEN+YAGNDD +++Y AP+ TW+ETA+ AF+RG W N+GG+EN GGLYHF Sbjct: 310 TLIYGETSENLYAGMDDDYRNYQAPLLTWYETAKEAFKRGCRWHNLGGVENQQDGGLYHF 36- 9 Query: 365 KSKFEPIIEEFIGEFNIPVNRLLYKASNYVYALRKKRNS 403 K++ P IEEF GEFNIPV L+ + Y LRKK S Sbjct: 370 KARLNPTIEEFAGEFNIPVG-LVSSLAILTYNLRKKLRS 407 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1758 A DNA sequence (GBSx1865) was identified in S. agalactiae <SEQ ID 5465> which encodes the amino acid sequence <SEQ ID 5466>. Analysis of this protein sequence reveals the following:

TABLE-US-05370 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2669 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1759 A DNA sequence (GBSx1866) was identified in S. agalactiae <SEQ ID 5467> which encodes the amino acid sequence <SEQ ID 5468>. This protein is predicted to be beta-lactam resistance factor. Analysis of this protein sequence reveals the following: TABLE-US-05371 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.07 Transmembrane 56-72 (55-74) ----- Final Results ----- bacterial membrane --- Certainty = 0.1829 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9625> which encodes amino acid sequence <SEQ ID 9626> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05372 >GP:CAB89120 GB:AJ277484 beta-lactam resistance factor [Streptococcus pneumoniae] Identities = 166/410 (40%), Positives = 250/410 (60%), Gaps = 10/410 (2%) Query: 6 MYHVTVGISEKEYDAFAIASSQTNLLHSSKWAQVKSNWQNERLGFYKDDQLVAVASILIK 65- MY +GI EYD F N+L SS W +VKSNWQ+E+ G Y++++L+A ASILI+ Sbjct: 1 MYRYQIGIPTLEYDQFVKEHELANVLQSSAWEEVKSNWQHEKFGVYREEKLLATASILIR 60- Query: 66 SLPLGFTMLYIPRGPIMDYSNKELVNFVLKTLKNFGRKKRAVFAKFDPALLLRQYHLKEE 12- 5 +LPLG+ M YIPRGPI+DY +KEL+NF ++++K++ R KRAVF FDP++ L Q + +E Sbjct: 61 TLPLGYKMFYIPRGPILDYGDKELLNFAIQSIKSYARSKRAVFVTFDPSICLSQSLINQE 12- 0 Query: 126 NVAEEIDESRQAIDNLKSAGAQWIGPTKAISETIQPRFQANIYTKANIEENFPKHTKRLI 18- 5 E E+ ID+L+ G +W G T+ + +TIQPR QA IY + E+ K TK+ I Sbjct: 121 KT--EFPENLAIIDSLQQMGVRWSGKTEEMGDTIQPRIQAKIYKENFEEDKLSKSTKQAI 17- 8 Query: 186 KDAKHRGVQIYRANIDDLPKFATVVALTENRKGVALRNENYFHQLMTIYGEDAYLYLAKV 24- 5 + A+++G++I ++ L F+ ++ TE RK + LRNE Y+ +L+ + + AY+ LA+ Sbjct: 179 RTARNKGLEIQYGGLELLDSFSELMKKTEKRKEIHLRNEAYYKKLLDNFKDKAYITLATL 23- 8 Query: 246 NLPKRLAQFKEQLLQIQKDLSETPSHQKSRLTRLNQQEASVKQYILEFQEFSKKYPD--- 30- 2 ++ KR + +EQL + + L ET + + +R +++ Q+ K+ +LE F ++Y D Sbjct: 239 DVSKRSQELEEQLAK-NRALEETFT-ESTRTSKVEAQKKE-KERLLEELTFLQEYIDVGQ 29- 5 Query: 303 -EPVIAGILSIRFGNVLEMLYAGMDDSFRKFYPQYLLNARVFEDAFKNDIVSANLGGVEG 36- 1 +A LS+ FG +YAGMDD F+++ L AF+ ++ NLGGVE Sbjct: 296 ARVPLAATLSLEFGTTSVNIYAGMDDDFKRYNAPILTWYETARYAFERGMIWQNLGGVEN 35- 5 Query: 362 SLNDGLTKFKSNFNPMFEEYIGEFNLAINPLLYKLANLAYTIRKKQRHSH 411 SLN GL FK FNP EEY+GEF + +P LY L LA RK R H Sbjct: 356 SLNGGLYHFKEKFNPTIEEYLGEFTMPTHP-LYPLLRLALDFRKTLRKKH 404 A related DNA sequence was identified in S. pyogenes <SEQ ID 5469> which encodes the amino acid sequence <SEQ ID 5470>. Analysis of this protein sequence reveals the following: TABLE-US-05373 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.32 Transmembrane 59-75 (59-75) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05374 >GP:CAB89120 GB:AJ277484 beta-lactam resistance factor [Streptococcus pneumoniae] Identities = 166/402 (41%), Positives = 255/402 (63%), Gaps = 5/402 (1%) Query: 9 KIGISSEEHDSFVKEHQQISVLQGSDWAKIKNQWQNERIGIYKEEKQVASLSLLIKLLPL 68- +IGI E+D FVKEH+ +VLQ S W ++K+ WQ+E+ G+Y+EEK +A+ S+LI+ LPL Sbjct: 5 QIGIPTLEYDQFVKEHELANVLQSSAWEEVKSNWQHEKFGVYREEKLLATASILIRTLPL 64- Query: 69 GRSIIYIPRGPVMDYLDRDLVAFTMKTLKDYGKTKKALFIKYDPAILLKQYALGQEEEEK 12- 8 G + YIPRGP++DY D++L+ F ++++K Y ++K+A+F+ +DP+I L Q + QE+ E Sbjct: 65 GYKMFYIPRGPILDYGDKELLNFAIQSIKSYARSKRAVFVTFDPSICLSQSLINQEKTEF 12- 4 Query: 129 PLALAAIKNLQEAGVHWTGLTMEIADSIQPRFQANIYTQENLEMQFPKHTRRLIKDAKQR 18- 8 P LA I +LQ+ GV W+G T E+ D+IQPR QA IY + E + K T++ I+ A+ + Sbjct: 125 PENLAIIDSLQQMGVRWSGKTEEMGDTIQPRIQAKIYKENFEEDKLSKSTKQAIRTARNK 18- 4 Query: 189 GVKTYRVSQSELHKFSKIVSLTEKRKNISLRNEAYFQKLMTTYGDKAYLHLAKVNIPQKL 24- 8 G++ L FS+++ TEKRK I LRNEAY++KL+ + DKAY+ LA +++ ++ Sbjct: 185 GLEIQYGGLELLDSFSELMKKTEKRKEIHLRNEAYYKKLLDNFKDKAYITLATLDVSKRS 24- 4 Query: 249 DQYRQQLILINQDITRTQAHQKKRLKKLEDQKASLERYITE---FEGFTDQYPEEVVVAG 30- 5 + +QL N+ + T + R K+E QK ER + E + + D V +A Sbjct: 245 QELEEQLAK-NRALEETFT-ESTRTSKVEAQKKEKERLLEELTFLQEYIDVGQARVPLAA 30- 2 Query: 306 ILSISYGNVMEMLYAGMNDDFKKFYPQYLLYPNVFQDAYQDGIIWANMGGVEGSLDDGLT 36- 5 LS+ +G +YAGM+DDFK++ L + + A++ G+IW N+GGVE SL+ GL Sbjct: 303 TLSLEFGTTSVNIYAGMDDDFKRYNAPILTWYETARYAFERGMIWQNLGGVENSLNGGLY 36- 2 Query: 366 KFKANFAPTIEEFIGEFNLPVSPLYHIANTMYKIRKQLKNKH 407 FK F PTIEE++GEF +P PLY + RK L+ KH Sbjct: 363 HFKEKFNPTIEEYLGEFTMPTHPLYPLLRLALDFRKTLRKKH 404 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05375 Identities = 226/407 (55%), Positives = 318/407 (77%), Gaps = 3/407 (0%) Query: 5 LMYHVTVGISEKEYDAFAIASSQTNLLHSSKWAQVKSNWQNERLGFYKDDQLVAVASILI 64- L ++ +GISE+E+D+F Q ++L S WA++K+ WQNER+G YK+++ VA S+LI Sbjct: 4 LTFYAKIGISEEEHDSFVKEHQQISVLQGSDWAKIKNQWQNERIGIYKEEKQVASLSLLI 63- Query: 65 KSLPLGFTMLYIPRGPIMDYSNKELVNFVLKTLKNFGRKKRAVFAKFDPALLLRQYHLKE 12- 4 K LPLG +++YIPRGP+MDY +++LV F +KTLK++G+ K+A+F K+DPA+LL+QY L + Sbjct: 64 KLLPLGRSIIYIPRGPVMDYLDRDLVAFTMKTLKDYGKTKKALFIKYDPAILLKQYALGQ 12- 3 Query: 125 ENVAEEIDESRQAIDNLKSAGAQWIGPTKAISETIQPRFQANIYTKANIEENFPKHTKRL 18- 4 E EE + AI NL+ AG W G T I+++IQPRFQANIYT+ N+E FPKHT+RL Sbjct: 124 EE--EEKPLALAAIKNLQEAGVHWTGLTMEIADSIQPRFQANIYTQENLEMQFPKHTRRL 18- 1 Query: 185 IKDAKHRGVQIYRANIDDLPKFATVVALTENRKGVALRNENYFHQLMTIYGEDAYLYLAK 24- 4 IKDAK RGV+ YR + +L KF+ +V+LTE RK ++LRNE YF +LMT YG+ AYL+LAK Sbjct: 182 IKDAKQRGVKTYRVSQSELHKFSKIVSLTEKRKNISLRNEAYFQKLMTTYGDKAYLHLAK 24- 1 Query: 245 VNLPKRLAQFKEQLLQIQKDLSETPSHQKSRLTRLNQQEASVKQYILEFQEFSKKYPDEP 30- 4 VN+P++L Q+++QL+ I +D++ T +HQK RL +L Q+AS+++YI EF+ F+ +YP+E Sbjct: 242 VNIPQKLDQYRQQLILINQDITRTQAHQKKRLKKLEDQKASLERYITEFEGFTDQYPEEV 30- 1 Query: 305 VIAGILSIRFGNVLEMLYAGMDDSFRKFYPQYLLNARVFEDAFKNDIVSANLGGVEGSLN 36- 4 V+AGILSI +GNV+EMLYAGM+D F+KFYPQYLL VF+DA+++ I+ AN+GGVEGSL+ Sbjct: 302 VVAGILSISYGNVMEMLYAGMNDDFKKFYPQYLLYPNVFQDAYQDGIIWANMGGVEGSLD 36- 1 Query: 365 DGLTKFKSNFNPMFEEYIGEFNLAINPLLYKLANLAYTIRKKQRHSH 411 DGLTKFK+NF P EE+IGEFNL ++P LY +AN Y IRK+ ++ H Sbjct: 362 DGLTKFKANFAPTIEEFIGEFHLPVSP-LYHIANTMYKIRKQLKNKH 407 SEQ ID 5468 (GBS377) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 65 (lane 4; MW 49 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 71 (lane 4; MW 74 kDa). GBS377-GST was purified as shown in FIG. 212, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1760 A DNA sequence (GBSx1867) was identified in S. agalactiae <SEQ ID 5471> which encodes the amino acid sequence <SEQ ID 5472>. Analysis of this protein sequence reveals the following: TABLE-US-05376 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2073 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9627> which encodes amino acid sequence <SEQ ID 9628> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05377 >GP:AAC76720 GB:AE000446 orf, hypothetical protein [Escherichia coli K12] Identities = 127/269 (47%), Positives = 189/269 (70%), Gaps = 1/269 (0%) Query: 7 SIKLVAVDIDGTLLNSKREITPEVAKAVQEAKSKGVKIVIATGRPIIGVQDLLEELKLNE 66- +IKL+A+D+DGTLL I+P V A+ A+++GV +V+ TGRP GV + L+EL + + Sbjct: 2 AIKLIAIDMDGTLLLPDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKELHMEQ 61- Query: 67 EGDYVITFNGGLVQDTATGDDIIKETLTYEDYLDFELLARKLGVHMHAITKEGIYTANRD 12- 6 GDY IT+NG LVQ A G + + L+Y+DY E L+R++G H HA+ + +YTANRD Sbjct: 62 PGDYCITYNGALVQKAADGSTVAQTALSYDDYRFLEKLSREVGSHFHALDRTTLYTANRD 12- 1 Query: 127 IGKYTIHEVTLVNMPLFYRTPEEMG-DKEIIKLMMIDQPDILDAAIAKIPKKVLDNYTIV 18- 5 I YT+HE + +PL + E+M + + +K+MMID+P ILD AIA+IP++V + YT++ Sbjct: 122 ISYYTVHESFVATIPLVFCEAEKMDPNTQFLKVMMIDEPAILDQAIARIPQEVKEKYTVL 18- 1 Query: 186 KSTPFYLEILPKNVNKGTALLHLAEKMGLTVDQTMAIGDEENDRAMLEVVGNPVVMQNGN 24- 5 KS P++LEIL K VNKGT + LA+ +G+ ++ MAIGD+END AM+E G V M N Sbjct: 182 KSAPYFLEILDKRVNKGTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVAMDNAI 24- 1 Query: 246 PELKKIAKYITKSNEESGVAYALREWVIN 274 P +K++A ++TKSN E GVA+A+ ++V+N Sbjct: 242 PSVKEVANFVTKSNLEDGVAFAIEKYVLN 270 A related DNA sequence was identified in S. pyogenes <SEQ ID 3407> which encodes the amino acid sequence <SEQ ID 3408>. Analysis of this protein sequence reveals the following: TABLE-US-05378 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3474(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05379 Identities = 197/268 (73%), Positives = 235/268 (87%) Query: 7 SIKLVAVDIDGTLLNSKREITPEVAKAVQEAKSKGVKIVIATGRPIIGVQDLLEELKLNE 66 SIKLVAVDIDGTLL R IT +V +AVQEAK++GV +VIATGRPI GV LLE+L+LN Sbjct: 2 SIKLVAVDIDGTLLTDDRRITDDVFQAVQEAKAQGVHVVIATGRPIAGVISLLEQLELNH 61 Query: 67 EGDYVITFNGGLVQDTATGDDIIKETLTYEDYLDFELLARKLGVHMHAITKEGIYTANRD 126- +G++VITFNGGLVQD TG++I+KE +TY+DYL+ E L+RKLGVHMHAITKEGIYTANR+ Sbjct: 62 KGNHVITFNGGLVQDAETGEEIVKELMTYDDYLETEFLSRKLGVHMHAITKEGIYTANRN 121- Query: 127 IGKYTIHEVTLVNMPLFYRTPEEMGDKEIIKLMMIDQPDILDAAIAKIPKKVLDNYTIVK 18- 6 IGKYT+HE TLVNMP+FYRTPEEM +KEIIK+MMID+PD+LDAAI +IP+ D YTIVK Sbjct: 122 IGKYTVHESTLVNMPIFYRTPEEMTNKEIIKMMMIDEPDLLDAAIKQIPQHFFDKYTIVK 18- 1 Query: 187 STPFYLEILPKNVNKGTALLHLAEKMGLTVDQTMAIGDEENDRAMLEVVGNPVVMQNGNP 24- 6 STPFYLE +PK V+KG A+ HLA+K+GL + QTMAIGD ENDRAMLEVV NPVVM+NG P Sbjct: 182 STPFYLEFMPKTVSKGNAIKHLAKKLGLDMSQTMAIGDAENDRAMLEVVANPVVMENGVP 24- 1 Query: 247 ELKKIAKYITKSNEESGVAYALREWVIN 274 ELKKIAKYITKSN +SGVA+A+R+WV+N Sbjct: 242 ELKKIAKYITKSNNDSGVAHAIRKWVLN 269 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1761 A DNA sequence (GBSx1868) was identified in S. agalactiae <SEQ ID 5473> which encodes the amino acid sequence <SEQ ID 5474>. Analysis of this protein sequence reveals the following: TABLE-US-05380 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2360(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05381 >GP: BAB07537 GB: AP001520 unknown conserved protein [Bacillus halodurans] Identities = 211/423 (49%), Positives = 285/423 (66%), Gaps = 5/423 (1%) Query: 3 EKVFRDPVHTYIHVNNQVIYDLINTKEFQRLRRIKQTSTTSFTFHGAEHSRFSHCLGVYE 62 EKVF+DPVH YIHV +++I+ LI TKEFQRLRR++Q TT TFHGAEH+RF+H LGVYE Sbjct: 12 EKVFKDPVHRYIHVRDELIWALIGTKEFQRLRRVRQLGTTFLTFHGAEHTRFNHSLGVYE 71 Query: 63 LARKVTEIFDEHYSDLWNKNESLLTMAAALLHDIGHGAYSHTFERLFNTDHEAYTQEIIT 122- + R++ E+F WN+ E LLT+ AALLHDIGHG +SH+FE++F+TDHE +T+ +I Sbjct: 72 ITRRIIEVFQGR--PYWNEEERLLTLCAALLHDIGHGPFSHSFEKVFDTDHEEWTRRMIV 129- Query: 123 NPTTEINAILRKVAPDFPDKVASVINHSYPNKQVVQLISSQIDCDRMDYLLRDSYYTAAS 18- 2 T EI+ +L K+ DFP KVA VI +YPNK V +ISSQID DRMDYL RD+YYT S Sbjct: 130 GDT-EIHNVLLKMGDDFPQKVADVIEKTYPNKLVTSIISSQIDADRMDYLQRDAYYTGVS 18- 8 Query: 183 YGQFDLTRILRVIRPTDSGIAFARNGMHAVEDYIVSRFQMYMQVYFHPASRAMELLLQNL 24- 2 YG FD+ RILRV+RP + + ++GMHAVEDYI+SR+QMY QVYFHP +R+ E++L + Sbjct: 189 YGHFDMERILRVMPMEDQVVIKQSGMHAVEDYIMSRYQMYWQVYFHPVTRSAEVILSKV 248- Query: 243 LKRARFLFDTHRDFFEQTSPNLIPFFTDQYDLQDYLALDDGVMNTYFQSWMQADDNILAD 30- 2 KR + L++ F+Q + F L DYL LD+ + YFQ W + +D IL+D Sbjct: 249 FKRVKDLYEQGYK-FKQEPKHFYSLFEGNMSLDDYLRLDESITMYYFQIWQEEEDRILSD 30- 7 Query: 303 LANRFINRKVFKSITFEESDKEN-LVKMKELVSQVGFDPDYYTGVHANFDLPYDVYRPEH 36- 1 L RFINR++FK I F + + N ++++L +Q DP+YY V ++ DLPYD YRP Sbjct: 308 LCVRFINRQLFKYIEFNPNLQMNDWPRLQQLFAQAEIDPEYYLVVDSSSDLPYDFYRPGE 36- 7 Query: 362 SNPRTEIQIIQKNGQLAELSSLSPIVKALTGSNYGDQRFYFPKEMLTLDSLFSSTKEEFQ 42- 1 R I +I NG+L ELS S +V+A++G D + YFP + LT S K+E Sbjct: 368 EEERLPIHLIMPNGKLRELSRESDVVEAISGKKRTDHKLYFPMDCLTDQSDHKEIKQEIL 42- 7 Query: 422 SYI 424 S + Sbjct: 428 SLL 430 A related DNA sequence was identified in S. pyogenes <SEQ ID 5475> which encodes the amino acid sequence <SEQ ID 5476>. Analysis of this protein sequence reveals the following: TABLE-US-05382 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2220(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05383 Identities = 321/428 (75%), Positives = 379/428 (88%) Query: 1 MNEKVFRDPVHTYIHVNNQVIYDLINTKEFQRLRRIKQTSTTSFTFHGAEHSRFSHCLGV 60 MNEKVFRDPVH YIH++N +IYDLINTKEFQRLRRIKQ TT+FTFHGAEHSRFSHCLGV Sbjct: 1 MNEKVFRDPVHNYIHIDNPLIYDLINTKEFQRLRRIKQVPTTAFTFHGAEHSRFSHCLGV 60 Query: 61 YELARKVTEIFDEHYSDLWNKNESLLTMAAALLHDIGHGAYSHTFERLFNTDHEAYTQEI 120- YE+AR+VT IF+E Y+D+WNK+ESL+TM AALLHDIGHGAYSHTFE LF+TDHEA+TQEI Sbjct: 61 YEIARRVTAIFEEKYADIWNKDESLVTMTAALLHDIGHGAYSHTFEVLFHTDHEAFTQEI 120- Query: 121 ITNPTTEINAILRKVAPDFPDKVASVINHSYPNKQVVQLISSQIDCDRMDYLLRDSYYTA 18- 0 ITNP TEINAIL + APDFPDKVASVINH+YPNKQVVQLISSQIDCDRMDYLLRDSY++A Sbjct: 121 ITNPETEINAILVRHAPDFPDKVASVINHTYPNKQVVQLISSQIDCDRMDYLLRDSYFSA 18- 0 Query: 181 ASYGQFDLTRILRVIRPTDSGIAFARNGMHAVEDYIVSRFQMYMQVYFHPASRMELLLQ 240- A+YGQFDL RILRVIRP + GI F +GMHAVEDYIVSRFQMYMQVYFHPASRA+EL+LQ Sbjct: 181 ANYGQFDLMRILRVIRPVEDGIVFEHSGMHAVEDYIVSRFQMYMQVYFHPASRAVELILQ 24- 0 Query: 241 NLLKRARFLFDTHRDFFEQTSPNLIPFFTDQYDLQDYLALDDGVMNTYFQSWMQADDNIL 30- 0 NLLKRA+ L+ + +F++T+P LIPFF + +L DY+ALDDGVMNTYFQ WM ++D+IL Sbjct: 241 NLLKRAQHLYPEQQAYFQKTAPGLIPFFEKKANLADYIALDDGVMNTYFQVWMASEDHIL 30- 0 Query: 301 ADLANRFINRKVFKSITFEESDKENLVKMKELVSQVGFDPDYYTGVHANFDLPYDVYRPE 36- 0 +DLA+RFINRK+ KS+TF++ + L ++++LV VGFDPDYYTG+H NFDLPYD+YRPE Sbjct: 301 SDLASRFINRKILKSVTFDQDSQGELERLRQLVESVGFDPDYYTGIHINFDLPYDIYRPE 36- 0 Query: 361 HSNPRTEIQIIQKNGQLAELSSLSPIVKALTGSNYGDQRFYFPKEMLTLDSLFSSTKEEF 42- 0 NPRT+I+++QK+G LAELS LSPIVKALTG+ YGD+RFYFPKEML LD LF+ +KE F Sbjct: 361 LENPRTQIEMMQKDGSLAELSQLSPIVKALTGTTYGDRRFYFPKEMLELDDLFAPSKETF 42- 0 Query: 421 QSYITNEH 428 SYI+N H Sbjct: 421 MSYISNGH 428 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1762 A DNA sequence (GBSx1869) was identified in S. agalactiae <SEQ ID 5477> which encodes the amino acid sequence <SEQ ID 5478>. Analysis of this protein sequence reveals the following: TABLE-US-05384 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4789(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 5479> which encodes the amino acid sequence <SEQ ID 5480>. Analysis of this protein sequence reveals the following: TABLE-US-05385 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3650(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-05386 Identities = 64/127 (50%), Positives = 89/127 (69%) Query: 5 MKLEINNNIQIDNETEMIHEIHDCQFIEKGSYVYLNYINAEGERVVIKANHEELLMTRFS 64 MKL++ N+I+ +ETE+I EIHDC++ EKG Y YL Y N + E+VVIK N +EL M+RFS Sbjct: 1 MKLQLTNHIRFGDETEIIQEIHDCEWREKGGYQYLIYQNTDKEKVVIKYNETELTMSRFS 60 Query: 65 NPKSVMRFHRETPALVNIPTPLGVQHLITETSHYQFDLSQQRLHINYVLKQTETGDCFAN 124- NP+S+M+F L+ +PTP+GVQ +T+TSHY D S Q+L ++Y L Q +T FA+ Sbjct: 61 NPQSIMKFFAGKKVLIALPTPMGVQQFLTDTSHYHLDCSCQKLDLHYHLLQAQTEMLFAS 120- Query: 125 YELRIQW 131 Y L + W Sbjct: 121 YHLELSW 127 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1763 A DNA sequence (GBSx1870) was identified in S. agalactiae <SEQ ID 5481> which encodes the amino acid sequence <SEQ ID 5482>. This protein is predicted to be cation-transporting ATPase PacL (ctpF). Analysis of this protein sequence reveals the following: TABLE-US-05387 Possible site: 14 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.27 Transmembrane 256-272 (246-276) INTEGRAL Likelihood = -9.02 Transmembrane 64-80 (58-85) INTEGRAL Likelihood = -8.49 Transmembrane 833-849 (828-855) INTEGRAL Likelihood = -8.17 Transmembrane 89-105 (81-107) INTEGRAL Likelihood = -7.48 Transmembrane 864-880 (860-884) INTEGRAL Likelihood = -3.29 Transmembrane 287-303 (284-306) INTEGRAL Likelihood = -2.55 Transmembrane 754-770 (753-773) INTEGRAL Likelihood = -0.85 Transmembrane 695-711 (694-711) INTEGRAL Likelihood = -0.75 Transmembrane 793-809 (792-809) ----- Final Results ----- bacterial membrane --- Certainty = 0.6307(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05388 >GP: CAB13439 GB: Z99112 similar to calcium-transporting ATPase [Bacillus subtilis] Identities = 380/888 (42%), Positives = 545/888 (60%), Gaps = 49/888 (5%) Query: 10 FYTQGQEEVLTSLESS-REGLSTTEAKNRLEMYGRNELEEGKKRSLIAKFFDQFKDLMII 68 - F+ GQ ++L + +S ++GL+ E K RL+ +G NEL+EGKK S + FF QFKD M++ Sbjct: 3 FHEMGQTDLLEATNTSMKQGLTEKEVKKRLDKHGPNELQEGKKTSALLLFFAQFKDFMVL 62 Query: 69 ILLVAAALSVITEGMHG-LTDALIILAVVILNAAFGVYQEGQAEAAIEALKDMSSPIARV 127- +LL A +S G G DA+ I+A+V +N G +QE +AE +++ALK++S+P Sbjct: 63 VLLAATLIS----GFLGEYVDAVAIIAIVFVNGILGFFQERRAEQSLQALKELSTPHVMA 118- Query: 128 RRDGHTIEVDSKELVPGDLVMLEAGDVVPADLRLLEAASLKIEEAALTGESVPVEKDISQ 18- 7 R+G ++ SKELVPGD+V +GD + AD+R++EA SL+IEE+ALTGES+PV K + Sbjct: 119 LREGSWTKIPSKELVPGDIVKFTSGDRIGADVRIVEARSLEIEESALTGESIPVVKHADK 17- 8 Query: 188 VVAEDAGIGDRVNMAYQNSNVTYGRGYGVVTNTGMYTEVGKIADMLANADESETPLKQSL 24- 7 + D +GD NMA+ + VT G G GVV TGM T +GKIADML +A TPL++ L Sbjct: 179 LKKPDVSLGDITNMAFMGTIVTRGSGVGVVVGTGMNTAMGKIADMLESAGTLSTPLQRRL 23- 8 Query: 248 VQLSKLLTYLIVIIAVITFLVGIFVRKEGWIEGLMTSVALAVAAIPEGLPAIVTIVLSMG 30- 7 QL K+L + +++ V+ VG+ ++ + V+LAVAAIPEGLPAIVT+ LS+G Sbjct: 239 EQLGKILIVVALLLTVLVVAVGV-IQGHDLYSMFLAGVSLAVAAIPEGLPAIVTVALSLG 29- 7 Query: 308 TKTLAKRNSIVRKLPAVETLGSTEIIASDKTGTLTMNQMTVEKVYT-------------- 35- 3 + + K+ SIVRKLPAVETLG II SDKTGT+T N+MTV V++ Sbjct: 298 VQRMIKQKSIVRKLPAVETLGCASIICSDKTGTMTQNKMTVTHVWSGGKTWRVAGAGYEP 35- 7 Query: 354 NGVLQSSSEEISVDNNTL--------RIMNFSNDTKIDPSGKLIGDPTETALVQFGLDKN 40- 5 G + +EISV+ + + N SN K D L GDPTE AL+ Sbjct: 358 KGSFTLNEKEISVNEHKPLQQMLLFGALCNNSNIEKRDGEYVLDGDPTEGALLTAARKGG 41- 7 Query: 406 FDVREVLKNEPRVAELPFDSDRKLMSTIHKESDGRYFIAVKGAPDQLLKRVTKIEDNGLV 46- 5 F V N + E PFDS RK+M+ I + D + +I KGAPD L++R ++I +G Sbjct: 418 FSKEFVESNYRVIEEFPFDSARKMMTVIVENQDRKRYIITKGAPDVLMQRSSRIYYDGSA 47- 7 Query: 466 RDITAEDKEAILNTNKELAKQALRVLMMAYK--YETQIPSLETDIVESDLVFSGLVGMID 52- 3 + E K + LA QALR + +AY+ + PS+E E DL GL G+ID Sbjct: 478 ALFSNERKAETEAVLRHLASQALRTIAVAYRPIKAGETPSMEQ--AEKDLTMLGLSGIID 53- 5 Query: 524 PERPEAAEAVRVAKEAGIRPIMITGDHQDTAEAIAKRLGIIDANDTEDHVFTGAELNELS 58- 3 P RPE +A++ +EAGI+ +MITGDH +TA+AIAK L ++ + + G LNELS Sbjct: 536 PPRPEVRQAIKECREAGIKTVMITGDHVETAKAIAKDLRLLPKS---GKIMDGKMLNELS 59- 2 Query: 584 DEEFQKVFKQYSVYARVSPEHKVRIVKAWQNDGKVVAMTGDGVNDAPSLKTADIGIGMGI 64- 3 EE V + V+ARVSPEHK++IVKA+Q +G +VAMTGDGVNDAP++K ADIG+ MGI Sbjct: 593 QEELSHVVEDVYVFARVSPEHKLKIVKAYQENGHIVAMTGDGVNDAPAIKQADIGVSMGI 65- 2 Query: 644 TGTEVSKGASDMVLADDNFATIIVAVEEGRKVFSNIQKSIQYLLSANMAEVFTIFFATLL 70- 3 TGT+V+K AS +VL DDNFATI A++EGR ++ NI+K I+YLL++N+ E+ + FA LL Sbjct: 653 TGTDVAKEASSLVLVDDNFATIKSAIKEGRNIYENIRKFIRYLLASNVGEILVMLFAMLL 71- 2 Query: 704 GWDV-LAPVHLLWINLVTDTLPAIALGVEPAEPGVMTHKPRGRQSNFFDGGVMGAIIYQG 76- 2 + L P+ +LW+NLVTD LPA+ALG++ E VM KPR + F + ++ +G Sbjct: 713 ALPLPLVPIQILWVNLVTDGLPAMALGMDQPEGDVMKRKPRHPKEGVFARKLGWKVVSRG 77- 2 Query: 763 ILQTILVLGVYGWALMY---PEHAGYRMIHADALTMAFATLGLIQLVHAFNVKSVYQSIF 81- 9 L I V + + ++Y PE+ Y A T+AFATL L QL+H F+ +S S+F Sbjct: 773 FL--IGVATILAFIIVYHRNPENLAY------AQTIAFATLVLAQLIHVFDCRS-ETSVF 82- 3 Query: 820 TVGAFKNRTFNWSIPVAFILLMVTIVVPGFNKLFHVTHLSSTQWLTVV 867 + F+N ++ + +L++V I P +FH ++ W+ V+ Sbjct: 824 SRNPFQNLYLIGAVLSSILLMLVVIYYPPLQPIFHTVAITPGDWMLVI 871 A related DNA sequence was identified in S. pyogenes <SEQ ID 4171> which encodes the amino acid sequence <SEQ ID 4172>. Analysis of this protein sequence reveals the following: TABLE-US-05389 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.47 Transmembrane 863-879 (856-883) INTEGRAL Likelihood = -10.08 Transmembrane 64-80 (58-86) INTEGRAL Likelihood = -8.97 Transmembrane 256-272 (249-275) INTEGRAL Likelihood = -8.55 Transmembrane 89-105 (81-107) INTEGRAL Likelihood = -5.84 Transmembrane 832-848 (827-850) INTEGRAL Likelihood = -3.13 Transmembrane 287-303 (284-307) INTEGRAL Likelihood = -2.66 Transmembrane 762-778 (761-779) INTEGRAL Likelihood = -0.37 Transmembrane 685-701 (685-701) ----- Final Results ----- bacterial membrane --- Certainty = 0.5989(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05390 Identities = 735/892 (82%), Positives = 813/892 (90%), Gaps = 1/892 (0%) Query: 3 KEQKKSLFYTQGQEEVLTSLESSREGLSTTEAKNRLEMYGRNELEEGKKRSLIAKFFDQF 62 KEQ+ FYTQ +E VL LE+SREGL++ +AK RL YGRNEL+EG+KRSL KF DQF Sbjct: 3 KEQRHEAFYTQSEETVLAQLETSREGLTSAQAKERLAEYGRNELDEGEKRSLFMRFLDQF 62 Query: 63 KDLMIIILLVAAALSVITEGMHGLTDALIILAVVILNAAFGVYQEGQAEAAIEALKDMSS 122- KDLMIIIL+VAA LSV+TEGM GLTDA+IILAVVILNAAFGVYQEGQAEAAIEALK MSS Sbjct: 63 KDLMIIILIVAALLSVLTEGMEGLTDAIIILAVVILNAAFGVYQEGQAEAAIEALKSMSS 122- Query: 123 PIARVRRDGHTIEVDSKELVPGDLVMLEAGDVVPADLRLLEAASLKIEEAALTGESVPVE 18- 2 P+AR+RRDGH E+DSKELVPGD+V+LEAGDVVPADLRLLEA SLKIEEAALTGESVPVE Sbjct: 123 PLARIRRDGHVTEIDSKELVPGDIVLLEAGDVVPADLRLLEANSLKIEEAALTGESVPVE 18- 2 Query: 183 KDISQVVAEDAGIGDRVNMAYQNSNVTYGRGYGVVTNTGMYTEVGKIADMLANADESETP 24- 2 KD+S V+EDAGIGDRVNM YQNSNVTYGRG GV+TNTGMYTEVG IA MLANADE++TP Sbjct: 183 KDLSTAVSEDAGIGDRVNMGYQNSNVTYGRGIGVITNTGMYTEVGHIAGMLANADETDTP 24- 2 Query: 243 LKQSLVQLSKLLTYLIVIIAVITFLVGIFVRKEGWIEGLMTSVALAVAAIPEGLPAIVTI 30- 2 LKQ+L LSK+LTY I++IA +TF VG+F+R + +EGLMTSVALAVAAIPEGLPAIVT+ Sbjct: 243 LKQNLDNLSKILTYAILVIAAVTFAVGVFLRGQHPLEGLMTSVALAVAAIPEGLPAIVTV 30- 2 Query: 303 VLSMGTKTLAKRNSIVRKLPAVETLGSTEIIASDKTGTLTMNQMTVEKVYTNGVLQSSSE 36- 2 VLS+GT+ LAKRN+I+RKLPAVETLGSTEIIASDKTGTLTMNQMTVEKVYTNG LQSSS Sbjct: 303 VLSLGTQVLAKRNAIIRKLPAVETLGSTEIIASDKTGTLTMNQMTVEKVYTNGTLQSSSA 36- 2 Query: 363 EISVDNNTLRIMNFSNDTKIDPSGKLIGDPTETALVQFGLDKNFDVREVLKNEPRVAELP 42- 2 +I+ DN TLR+MNF+NDTK+DPSGKLIGDPTETALV+FGLD NFDVRE + EPRVAELP Sbjct: 363 DIAFDNTTLRVMNFANDTKVDPSGKLIGDPTETALVEFGLDHNFDVREAMVAEPRVAELP 42- 2 Query: 423 FDSDRKLMSTIHKESDGRYFIAVKGAPDQLLKRVTKIEDNGLVRDITAEDKEAILNTNKE 48- 2 FDSDRKLMSTIHK++DG+YFIAVKGAPDQLLKRVT+IE+NG +R IT DK+ IL+TNK Sbjct: 423 FDSDRKLMSTIHKQADGKYFIAVKGAPDQLLKRVTQIEENGQIRPITDADKKTILDTNKS 48- 2 Query: 483 LAKQALRVLMMAYKYETQIPSLETDIVESDLVFSGLVGMIDPERPEAAEAVRVAKEAGIR 54- 2 LAKQALRVLMMAYKY +P+LET+IVE++LVFSGLVGMIDPERPEAA+AV+VAKEAGIR Sbjct: 483 LAKQALRVLMMAYKYSDALPTLETEIVEANLVFSGLVGMIDPERPEAAQAVKVAKEAGIR 54- 2 Query: 543 PIMITGDHQDTAEAIAKRLGIIDANDTEDHVFTGAELNELSDEEFQKVFKQYSVYARVSP 60- 2 PIMITGDHQDTA+AIAKRLGII+ D DHVFTGAELNELSDEEFQKVFKQYSVYARVSP Sbjct: 543 PIMITGDHQDTAKAIAKRLGIIE-EDGVDHVFTGAELNELSDEEFQKVFKQYSVYARVSP 60- 1 Query: 603 EHKVRIVKAWQNDGKVVAMTGDGVNDAPSLKTADIGIGMGITGTEVSKGASDMVLADDNF 66- 2 EHKVRIVKAWQN+GKVVAMTGDGVNDAPSLKTADIGIGMGITGTEVSKGASDMVLADDNF Sbjct: 602 EHKVRIVKAWQNEGKVVAMTGDGVNDAPSLKTADIGIGMGITGTEVSKGASDMVLADDNF 66- 1 Query: 663 ATIIVAVEEGRKVFSNIQKSIQYLLSANMAEVFTIFFATLLGWDVLAPVHLLWINLVTDT 72- 2 ATIIVAVEEGRKVFSNIQK+IQYLLSANMAEVFTIF ATL GWDVL PVHLLWINLVTDT Sbjct: 662 ATIIVAVEEGRKVFSNIQKTIQYLLSANMAEVFTIFLATLFGWDVLQPVHLLWINLVTDT 72- 1 Query: 723 LPAIALGVEPAEPGVMTHKPRGRQSNFFDGGVMGAIIYQGILQTILVLGVYGWALMYPEH 78- 2 LPAIALGVEPAEPGVM HKPRGR+S+FFDGGV AI+YQG QTILVLGVYG+ALM+PEH Sbjct: 722 LPAIALGVEPAEPGVMKHKPRGRKSSFFDGGVKEAILYQGAFQTILVLGVYGFALMFPEH 78- 1 Query: 783 AGYRMIHADALTMAFATLGLIQLVHAFNVKSVYQSIFTVGAFKNRTFNWSIPVAFILLMV 84- 2 Y +HADALTMA+ TLGLIQLVHA+NVKSVYQSIFTVG FKN+ FN+SIPVAF+ LM Sbjct: 782 TSYHDVHADALTMAYVTLGLIQLVHAYNVKSVYQSIFTVGLFKNKLFNYSIPVAFVALMA 84- 1 Query: 843 TIVVPGFNKLFHVTHLSSTQWLTVVIGSLLMVVLTEIVKFIQRKLGQDEKAI 894 T+VVPGFN+ FHVTHL+ TQWL V+IGSLLMVVL E+VK +QR LGQDEKAI Sbjct: 842 TVVVPGFNQFFHVTHLTITQWLVVIIGSLLMVVLVELVKAVQRSLGQDEKAI 893 A related GBS gene <SEQ ID 8897> and protein <SEQ ID 8898> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05391 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: -9.88 GvH: Signal Score (-7.5): -6.96 Possible site: 14 >>> Seems to have no N-terminal signal sequence ALOM program count: 9 value: -13.27 threshold: 0.0 INTEGRAL Likelihood = -13.27 Transmembrane 256-272 (246-276) INTEGRAL Likelihood = -9.02 Transmembrane 64-80 (58-85) INTEGRAL Likelihood = -8.49 Transmembrane 833-849 (828-855) INTEGRAL Likelihood = -8.17 Transmembrane 89-105 (81-107) INTEGRAL Likelihood = -7.48 Transmembrane 864-880 (860-884) INTEGRAL Likelihood = -3.29 Transmembrane 287-303 (284-306) INTEGRAL Likelihood = -2.55 Transmembrane 754-770 (753-773) INTEGRAL Likelihood = -0.85 Transmembrane 695-711 (694-711) INTEGRAL Likelihood = -0.75 Transmembrane 793-809 (792-809) PERIPHERAL Likelihood = 1.06 714 modified ALOM score: 3.15 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6307 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00123## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1764 A DNA sequence (GBSx1871) was identified in S. agalactiae <SEQ ID 5483> which encodes the amino acid sequence <SEQ ID 5484>. Analysis of this protein sequence reveals the following: TABLE-US-05392 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2905 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05393 >GP:CAB48940 GB:AJ248283 hypothetical protein [Pyrococcus abyssi] Identities = 60/221 (27%), Positives = 100/221 (45%), Gaps = 37/221 (16%) Query: 33 KIDHLHIA------GDISNHFTKDTLP-FINNLKKH---IKLSYNLGNHDMLDLTE--TE 80 - KID L I GD+SN+ D + I+ L + L GNHD+ L + Sbjct: 15 KIDVLKIPDIAIQLGDLSNYGEPDIIENLISELVTQLDPVPLLVIPGNHDIYGLNDIFAA 74 Query: 81 IQRLDFQTYR------------FDKKMLLAFHGWYDYSFSNN--RDIKDVEKLKKTFWFD 126- QR + R ++ ++ GWYDYS + KD ++K F F Sbjct: 75 FQRFNKLVKRAGAIPLMEGPLILEEIGIVGVPGWYDYSLAPGYLNMTKDEYEIK-AFGFR 133- Query: 127 RR-----LKRPNNDVTIQASILKRLDEILAKVDSS--NIIIAMHFVPHKQFTMT--HPRF 17- 7 R +K +D + L L++ ++++ S ++I+A+HF P K +P Sbjct: 134 RLEDADYIKSSLSDEELVRWNLNLLEKFISEIRESVNDVILALHFAPFKDSLKYTGNPEI 19- 3 Query: 178 SPFNAFLGSQAYHDLFQKYHIKDVVFGHAHRSFGDVKIGET 218 F+A++GSQ + + +++I +V GH HRS + IG+T Sbjct: 194 DYFSAYMGSQRFGEFALRHNIGLIVHGHTHRSI-EYYIGKT 233 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1765 A DNA sequence (GBSx1872) was identified in S. agalactiae <SEQ ID 5485> which encodes the amino acid sequence <SEQ ID 5486>. Analysis of this protein sequence reveals the following: TABLE-US-05394 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.18 Transmembrane 173-189 (173-189) ----- Final Results ----- bacterial membrane --- Certainty = 0.1871 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05395 >GP:CAB16056 GB:Z99124 fructose-1,6-bisphosphatase [Bacillus subtilis] Identities = 314/642 (48%), Positives = 446/642 (68%), Gaps = 7/642 (1%) Query: 2 SNFYKLLKEKFPRKEDIVTEMINLEAICQLPKGTEYFISDLHGEYDAVDYLLRTGAGSIR 61 S + LL +K+ +E +VTE+INL+AI LPKGTE+F+SDLHGEY A ++LR G+G ++ Sbjct: 33 SKYLDLLAQKYDCEEKVVTEIINLKAILNLPKGTEHFVSDLHGEYQAFQHVLRNGSGRVK 92 Query: 62 AKLLDCFDWQKIVAVDLDDFCILLYYPKEKLAFDKMNLSASAYKTKLW-EMIPLQIQVLK 120- K+ D F I ++D+ L+YYP++KL K + A + + E I I+++ Sbjct: 93 EKIRDIFSGV-IYDREIDELAALVYYPEDKLKLIKHDFDAKEALNEWYKETIHRMIKLVS 151- Query: 121 YFSSKYTKSKVRKQLSGKFAYIIEELLAEIDRNPEKKSYFDTIIEKLFELDQVEDLIIVL 18- 0 Y SSKYT+SK+RK L +FAYI EELL + ++ K+ Y+ II+++ EL Q + LI L Sbjct: 152 YCSSKYTRSKLRKALPAQFAYITEELLYKTEQAGNKEQYYSEIIDQIIELGQADKLITGL 21- 1 Query: 181 SQTIQVLIIDHLHVVGDIYDRGRYPDRILNRLMAFPNLDIQWGNHDVTWMGAASGSYLCN 24- 0 + ++Q L++DHLHVVGDIYDRG PDRI+ L+ + ++DIQWGNHDV W+GA SGS +C+ Sbjct: 212 AYSVQRLVVDHLHVVGDIYDRGPQPDRIMEELINYHSVDIQWGNHDVLWIGAYSGSKVCL 27- 1 Query: 241 VNVIRIAARYNNITLIEDRYGINLRRLVDYSRRYYEPLPSFVPILDGEEMTHPDELDLLN 30- 0 N+IRI ARY+N+ +IED YGINLR L++ + +YY+ P+F P D E DE+ + Sbjct: 272 ANIIRICARYDNLDIIEDVYGINLRPLLNLAEKYYDDNPAFRPKAD--ENRPEDEIKQIT 32- 9 Query: 301 MIQQATAILQFKLEAQLIDRRPEFQMHNRQLINQVNYKDLSISIKEVVHQLKDFNSRCID 36- 0 I QA A++QFKLE+ +I RRP F M R L+ +++Y I++ +QL++ I+ Sbjct: 330 KIHQAIAMIQFKLESPIIKRRPNFNMEERLLLEKIDYDKNEITLNGKTYQLENTCFATIN 38- 9 Query: 361 SKNPSRLTSEEEELLQQLMIAFQTSESLKKHIDFLFEKGSMYLTYNDNLLFHGCIPMHSN 42- 0 + P +L EE E++ +L+ + Q SE L +H++F+ +KGS+YL YN NLL HGCIP+ N Sbjct: 390 PEQPDQLLEEEAEVIDKLLFSVQHSEKLGRHMNFMMKKGSLYLKYNGNLLIHGCIPVDEN 44- 9 Query: 421 GDFKSFKIAGKTYGGRDLLDLFESQIRLAYARPEKHDDLATDIIWYLWCGENSSLFGKNA 48- 0 G+ ++ I K Y GR+LLD+FE +R A+A PE+ DDLATD+ WYLW GE SSLFGK A Sbjct: 450 GNMETMMIEDKPYAGRELLDVFERFLREAFAHPEETDDLATDMAWYLWTGEYSSLFGKRA 50- 9 Query: 481 MTTFERYYVSDKVTHQERKNPYFKLRDKDDICTALLQEFDL-PKFGHIVNGHTPVKEKNG 53- 9 MTTFERY++ +K TH+E+KNPY+ LR+ + C +L EF L P GHI+NGHTPVKE G Sbjct: 510 MTTFERYFIKEKETHKEKKNPYYYLREDEATCRNILAEFGLNPDHGHIINGHTPVKEIEG 56- 9 Query: 540 EQPIKANGKMLVIDGGFAKGYQKNTGLAGYTLIYNSYGIQLISHLPFTSIEEVLSGTNYI 59- 9 E PIKANGKM+VIDGGF+K YQ TG+AGYTL+YNSYG+QL++H F S EVLS + Sbjct: 570 EDPIKANGKMIVIDGGFSKAYQSTTGIAGYTLLYNSYGMQLVAHKHFNSKAEVLSTGTDV 62- 9 Query: 600 IDTKRLVEEAKDRILVKDTTIGQKLTKEIKDLDHL--YRHFQ 639 + KRLV++ +R VK+T +G++L +E+ L+ L YR+ + Sbjct: 630 LTVKRLVDKELERKKVKETNVGEELLQEVAILESLREYRYMK 671 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 5486 (GBS197) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 168 (lane 17 & 18; MW 89 kDa) and in FIG. 169 (lane 2; MW 89 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 37 (lane 6; MW 99 kDa). Purified Thio-GBS197-His is shown in FIG. 244, lane 6. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1766 A DNA sequence (GBSx1873) was identified in S. agalactiae <SEQ ID 5487> which encodes the amino acid sequence <SEQ ID 5488>. Analysis of this protein sequence reveals the following: TABLE-US-05396 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2433 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-05397 >GP:CAB12719 GB:Z99108 alternate gene name: ygaP~similar to hypothetical proteins [Bacillus subtilis] Identities = 176/367 (47%), Positives = 240/367 (64%), Gaps = 6/367 (1%) Query: 3 IKAEIQKLAKEIGISKIGFTTADNFDYLEKSLRASVEEGRNSGFEHKVIEDRIYPERLLE 62 +K E+ + AK IG+ KIGFTTAD FD L+ L G SGFE IE R+ P+ LL Sbjct: 55 LKEELIEYAKSIGVDKIGFTTADTFDSLKDRLILQESLGYLSGFEEPDIEKRVTPKLLLP 114- Query: 63 SAKTIISIGVAYPHKLPQQPQKT-SYKRGKITPNSWGLDYHYVVGEKLDRLSKGIEELCR 121- AK+I++I +AYP ++ P+ T + +RG SWG DYH V+ EKLD L ++ Sbjct: 115 KAKSIVAIALAYPSRMKDAPRSTRTERRGIFCRASWGKDYHDVLREKLDLLEDFLKSKHE 17- 4 Query: 122 DFPLQQKAMVDTGALVDTAVAQRAGIGFIGKNGLVISKEYGSYMFLGELITNLEIEPDKP 18- 1 D ++ K+MVDTG L D AVA+RAGIGF KN ++ + EYGSY++L E+ITN+ EPD P Sbjct: 175 D--IRTKSMVDTGELSDRAVAERAGIGFSAKNCMITTPEYGSYVYLAEMITNIPFEPDVP 23- 2 Query: 182 VDYDCGDCRRCLDACPTSCLIGDGSMNAKRCLSFQTQDKGMMDIEFRKKIKTVIYGCDIC 24- 1 ++ CG C +CLDACPT L+ G +NA+RC+SF TQ KG + EFR KI +YGCD C Sbjct: 233 IEDMCGSCTKCLDACPTGALVNPGQLNAQRCISFLTQTKGFLPDEFRTKIGNRLYGCDTC 29- 2 Query: 242 QICCPYNKGINNPLATEI--DPELAQPELIPFLSLSNGQFKEKFGMIAGSWRGKNILQRN 29- 9 Q CP NKG + L E+ DPE+A+P L P L++SN +FKEKFG ++GSWRGK +QRN Sbjct: 293 QTVCPLNKGKDFHLHPEMEPDPEIAKPLLKPLLAISNREFKEKFGHVSGSWRGKKPIQRN 35- 2 Query: 300 AIIALANAHDKTAVVKLIEIIDKNNNPIHTATAIWALGEIVKKPNDEILEFMSNLTLKDE 35- 9 AI+ALA+ D +A+ +L E++ K+ P+ TA WA+G+I E LE KDE Sbjct: 353 AILALAHFKDASALPELTELMHKDPRPVIRGTAAWAIGKIGDPAYAEELEKALEKE-KDE 41- 1 Query: 360 DSRKELE 366 +++ E+E Sbjct: 412 EAKLEIE 418 A related DNA sequence was identified in S. pyogenes <SEQ ID 5489> which encodes the amino acid sequence <SEQ ID 5490>. Analysis of this protein sequence reveals the following: TABLE-US-05398 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3337(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05399 Identities = 363/374 (97%), Positives = 367/374 (98%) Query: 1 MDIKAEIQKLAKEIGISKIGFTTADNFDYLEKSLRASVEEGRNSGFEHKVIEDRIYPERL 60 M IKAEI+ LAKEIGISKIGFTTADNFDYLEKSLRASVEEGRNSGFEHKVIEDRIY ERL Sbjct: 18 MTIKAEIKALAKEIGISKIGFTTADNFDYLEKSLRASVEEGRNSGFEHKVIEDRIYTERL 77 Query: 61 LESAKTIISIGVAYPHKLPQQPQKTSYKRGKITPNSWGLDYHYVVGEKLDRLSKGIEELC 120- LESAKTIISIGVAYPHKLPQQPQKT YKRGKITP+SWGLDYHYVVGEKLDRLSKGIEELC Sbjct: 78 LESAKTIISIGVAYPHKLPQQPQKTPYKRGKITPSSWGLDYHYVVGEKLDRLSKGIEELC 137- Query: 121 RDFPLQQKAMVDTGALVDTAVAQRAGIGFIGKNGLVISKEYGSYMFLGELITNLEIEPDK 18- 0 RDFPLQQKAMVDTGALVDTAVAQRAGIGFIGKNGLVISKEYGSYMFLGELITNLEIEPDK Sbjct: 138 RDFPLQQKAMVDTGALVDTAVAQRAGIGFIGKNGLVISKEYGSYMFLGELITNLEIEPDK 19- 7 Query: 181 PVDYDCGDCRRCLDACPTSCLIGDGSMNAKRCLSFQTQDKGMMDIEFRKKIKTVIYGCDI 24- 0 PVDYDCGDCRRCLDACPTSCLIGDGSMNAKRCLSFQTQDKGMMDIEFRKKIKTVIYGCDI Sbjct: 198 PVDYDCGDCRRCLDACPTSCLIGDGSMNAKRCLSFQTQDKGMMDIEFRKKIKTVIYGCDI 25- 7 Query: 241 CQICCPYNKGINNPLATEIDPELAQPELIPFLSLSNGQFKEKFGMIAGSWRGKNILQRNA 30- 0 CQICCPYNKGINN ATEIDPELAQPELIPFLSLSNG+FKEKFGMIAGSWRGKNILQRNA Sbjct: 258 CQICCPYNKGINNSPATEIDPELAQPELIPFLSLSNGKFKEKFGMIAGSWRGKNILQRNA 31- 7 Query: 301 IIALANAHDKTAVVKLIEIIDKNNNPIHTATAIWALGEIVKKPNDEILEFMSNLTLKDED 36- 0 IIALANAHDKTAVVKLIEIIDKNNNPIHTATAIWALGEIVKKPNDEIL FMS+LTLKDED Sbjct: 318 IIALANAHDKTAVVKLIEIIDKNNNPIHTATAIWALGEIVKKPNDEILAFMSHLTLKDED 37- 7 Query: 361 SRKELELIRHKWQF 374 SRKELELIRHKWQF Sbjct: 378 SRKELELIRHKWQF 391 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1767 A DNA sequence (GBSx1874) was identified in S. agalactiae <SEQ ID 5491> which encodes the amino acid sequence <SEQ ID 5492>. This protein is predicted to be peptide chain release factor 2, fragment (prfB). Analysis of this protein sequence reveals the following: TABLE-US-05400 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4903(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05401 >GP:AAC67303 GB:AF017113 putative peptide chain release factor RF-2 [Bacillus subtilis] Identities = 194/336 (57%), Positives = 251/336 (73%), Gaps = 2/336 (0%) Query: 2 EEEIALLENQMTEPDFWNDNIAAQKTSQELNELKGKYDTFHNMQELSDETELLLEMLDE- 60 E IA L+ QM +P+FWND AQ E N LK +++ + E +E ++ ++L E Sbjct: 30 EARIAELDEQMADPEFWNDQQKAQTVINEANGLKDYVNSYKKLNESHEELQMTHDLLKEE 89 Query: 61 -DDSLKEELEENLMQLDKIMGAYEMTLLLSEPYDHNNAILEIHPGSGGTEAQDWGDLLLR 119- D L+ ELE+ L L K +E+ LLLSEPYD NNAILE+HPG+GGTE+QDWG +LLR Sbjct: 90 PDTDLQLELEKELKSLTKEFNEFELQLLLSEPYDKNNAILELHPGAGGTESQDWGSMLLR 149- Query: 120 MYTRFGNANGFKVEVLDYQAGDEAGIKSVTLSFEGPNAYGLLKSEMGVHRLVRISPFDSA 17- 9 MYTR+G GFKVE LDY GDEAGIKSVTL +G NAYG LK+E GVHRLVRISPFDS+ Sbjct: 150 MYTRWGERRGFKVETLDYLPGDEAGIKSVTLLIKGHNAYGYLKAEKGVHRLVRISPFDSS 20- 9 Query: 180 KRRHTSFASVEVMPELDDTIEVEVRDDDIKMDTFRSGGAGGQNVNKVSTGVRLTHIPTGI 23- 9 RRHTSF S EVMPE +D I++++R +DIK+DT+R+ GAGGQ+VN + VR+TH+PT + Sbjct: 210 GRRHTSFVSCEVMPEFNDEIDIDIRTEDIKVDTYRASGAGGQHVNTTDSAVRITHLPTNV 26- 9 Query: 240 VVSSTVDRTQYGNRDRAMKMLQAKLYQLEQEKKAQEVDALKGDKKEITWGSQIRSYVFTP 29- 9 VV+ +R+Q NR+RAMKML+AKLYQ E++ E+D ++G++KEI WGSQIRSYVF P Sbjct: 270 VVTCQTERSQIKNRERAMKMLKAKLYQRRIEEQQAELDEIRGEQKEIGWGSQIRSYVFHP 32- 9 Query: 300 YTMVKDHRTNFELAQVDKVMDGEINGFIDAYLKWRI 335 Y+MVKDHRTN E+ V VMDG+I+ FIDAYL+ ++ Sbjct: 330 YSMVKDHRTNTEMGNVQAVMDGDIDTFIDAYLRSKL 365 A related DNA sequence was identified in S. pyogenes <SEQ ID 5493> which encodes the amino acid sequence <SEQ ID 5494>. Analysis of this protein sequence reveals the following: TABLE-US-05402 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4779(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05403 Identities = 334/337 (99%), Positives = 336/337 (99%) Query: 1 MEEEIALLENQMTEPDFWNDNIAAQKTSQELNELKGKYDTFHNMQELSDETELLLEMLDE 60 +EEEIALLEN MTEPDFWNDNIAAQKTSQELNELKGKYDTFHNMQELSDETELLLEMLDE Sbjct: 1 LEEEIALLENHMTEPDFWNDNIAAQKTSQELNELKGKYDTFHNMQELSDETELLLEMLDE 60 Query: 61 DDSLKEELEENLMQLDKIMGAYEMTLLLSEPYDHNNAILEIHPGSGGTEAQDWGDLLLRM 120- DDSLKEELEENLMQLDKIMGAYEMTLLLSEPYDHNNAILEIHPGSGGTEAQDWGDLLLRM Sbjct: 61 DDSLKEELEENLMQLDKIMGAYEMTLLLSEPYDHNNAILEIHPGSGGTEAQDWGDLLLRM 120- Query: 121 YTRFGNANGFKVEVLDYQAGDEAGIKSVTLSFEGPNAYGLLKSEMGVHRLVRISPFDSAK 18- 0 YTRFGNANGFK+EVLDYQAGDEAGIKSVTLSFEGPNAYGLLKSEMGVHRLVRISPFDSAK Sbjct: 121 YTRFGNANGFKIEVLDYQAGDEAGIKSVTLSFEGPNAYGLLKSEMGVHRLVRISPFDSAK 18- 0 Query: 181 RRHTSFASVEVMPELDDTIEVEVRDDDIKMDTFRSGGAGGQNVNKVSTGVRLTHIPTGIV 24- 0 RRHTSFASVEVMPELDDTIEVEVRDDDIKMDTFRSGGAGGQNVNKVSTGVRLTHIPTGIV Sbjct: 181 RRHTSFASVEVMPELDDTIEVEVRDDDIKMDTFRSGGAGGQNVNKVSTGVRLTHIPTGIV 24- 0 Query: 241 VSSTVDRTQYGNRDRAMKMLQAKLYQLEQEKKAQEVDALKGDKKEITWGSQIRSYVFTPY 30- 0 VSSTVDRTQYGNRDRAMKMLQAKLYQLEQEKKAQEVDALKGDKKEITWGSQIRSYVFTPY Sbjct: 241 VSSTVDRTQYGNRDRAMKMLQAKLYQLEQEKKAQEVDALKGDKKEITWGSQIRSYVFTPY 30- 0 Query: 301 TMVKDHRTNFELAQVDKVMDGEINGFIDAYLKWRIED 337 TMVKDHRTNFELAQVDKVMDGEINGFIDAYLKWRIED Sbjct: 301 TMVKDHRTNFELAQVDKVMDGEINGFIDAYLKWRIED 337 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1768 A DNA sequence (GBSx1875) was identified in S. agalactiae <SEQ ID 5495> which encodes the amino acid sequence <SEQ ID 5496>. This protein is predicted to be cell-division ATP-binding protein (ftsE). Analysis of this protein sequence reveals the following: TABLE-US-05404 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3928(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05405 >GP:AAC67262 GB:AF017113 cell division ATP-binding protein [Bacillus subtilis] Identities = 138/228 (60%), Positives = 179/228 (77%) Query: 3 LIEMSGVTKKYRRSTTALRNLNLSIQQGEFVYLVGPSGAGKSSLIRLLYREEKLSSGRLK 62 +IEM V K Y AL ++++I GEFVY+VGPSGAGKS+ I+++YREEK + G++ Sbjct: 1 MIEMKEVYKAYPNGVKALNGISVTIHPGEFVYVVGPSGAGKSTFIKMIYREEKPTKGQIL 60 Query: 63 VGEFNLNKLKRRQIPILRRSIGVVFQDYKLLPTKTVYENVAFAMQVIGAKRRHIKKRVPE 122- + +L +K ++IP +RR IGVVFQD+KLLP TV+ENVAFA++VIG + IKKRV E Sbjct: 61 INHKDLATIKEKEIPFVRRKIGVVFQDFKLLPKLTVFENVAFALEVIGEQPSVIKKRVLE 120- Query: 123 VLELVGLKHKMRSFPTQLSGGEQQRVAIARAIVNNPKLLIADEPTGNLDPEIAWEIMHLL 18- 2 VL+LV LKHK R FP QLSGGEQQRV+IAR+IVNNP ++IADEPTGNLDP+ +WE+M L Sbjct: 121 VLDLVQLKHKARQFPDQLSGGEQQRVSIARSIVNNPDVVIADEPTGNLDPDTSWEVMKTL 18- 0 Query: 183 ERINLQGTTVLMATHNSQIVNTLRHRVIEIEAGSVIRDEEKGEYGYHD 230 E IN +GTTV+MATHN +IVNT++ RVI IE G ++RDE +GBYG +D Sbjct: 181 EEINNRGTTVVMATHNKEIVNTMKKRVIAIEDGIIVRDESRGEYGSYD 228 A related DNA sequence was identified in S. pyogenes <SEQ ID 5497> which encodes the amino acid sequence <SEQ ID 5498>. Analysis of this protein sequence reveals the following: TABLE-US-05406 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3728(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05407 Identities = 191/230 (83%), Positives = 214/230 (93%) Query: 1 MALIEMSGVTKKYRRSTTALRNLNLSIQQGEFVYLVGPSGAGKSSLIRLLYREEKLSSGR 60 MALIEMSGVTKKYRRSTTALR++N+S+ QGEFVYLVGPSGAGKS+ I+LLYREE+L++G+ Sbjct: 1 MALIEMSGVTKKYRRSTTALRDVNVSVNQGEFVYLVGPSGAGKSTFIKLLYREEQLTTGK 60 Query: 61 LKVGEFNLNKLKRRQIPILRRSIGVVFQDYKLLPTKTVYENVAFAMQVIGAKRRHIKKRV 120- L VGEFNL KLK R +PILRR IGVVFQDYKLLP KTV+ENVA+AM+VIG KRRHIKKRV Sbjct: 61 LYVGEFNLTKLKARDVPILRRHIGVVFQDYKLLPRKTVFENVAYAMEVIGEKRRHIKKRV 120- Query: 121 PEVLELVGLKHKMRSFPTQLSGGEQQRVAIARAIVNNPKLLIADEPTGNLDPEIAWEIMH 18- 0 PEVL+LVGLKHKMRSFP+QLSGGEQQRVAIARAIVNNPKLLIADEPTGNLDPEI+WEIM Sbjct: 121 PEVLDLVGLKHKMRSFPSQLSGGEQQRVAIARAIVNNPKLLIADEPTGNLDPEISWEIMQ 18- 0 Query: 181 LLERINLQGTTVLMATHNSQIVNTLRHRVIEIEAGSVIRDEEKGEYGYHD 230 LLERIN+QGTT+LMATHNS IVNT RHRV+ IE G ++RDEEKG+YGY D Sbjct: 181 LLERINVQGTTILMATHNSHIVNTFRHRVVAIEDGRIVRDEEKGDYGYDD 230 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1769 A DNA sequence (GBSx1876) was identified in S. agalactiae <SEQ ID 5499> which encodes the amino acid sequence <SEQ ID 5500>. This protein is predicted to be ftsE protein (ftsX). Analysis of this protein sequence reveals the following: TABLE-US-05408 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.77 Transmembrane 296-312 (291-322) INTEGRAL Likelihood = -9.24 Transmembrane 203-219 (198-228) INTEGRAL Likelihood = -6.16 Transmembrane 49-65 (40-68) INTEGRAL Likelihood = -3.40 Transmembrane 255-271 (252-273) ----- Final Results ----- bacterial membrane --- Certainty = 0.5310(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9629> which encodes amino acid sequence <SEQ ID 9630> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05409 >GP:AAC67264 GB:AF017113 cell division protein [Bacillus subtilis] Identities = 112/311 (36%), Positives = 182/311 (58%), Gaps = 31/311 (9%) Query: 27 RHFWESLKNLKRNFWMTFASVTSVTITLLLVGLFSSVLLNVEKLTTDVSGNFTISAFLNV 86 - RH ES K+L RN WMTFAS+++VT+TL+LVG+F ++LN+ + T+ I +++ Sbjct: 7 RHLRESFKSLGRNTWMTFASISAVTVTLILVGVFLVIMLNLNNMATNAEKQVEIKVLIDL 66 Query: 87 DSTDAQKQVKDKDGKLKDNPDYHKVYDKIKRISGVEKVTYSSKAEQLKEVQKEYGSDVID 146- + D K +D K+ + IK + G++ VT+SSK ++L ++ +G Sbjct: 67 TA----------DQKAQD-----KLQNDIKELKGIQSVTFSSREKELDQLVDSFGDSGKS 111- Query: 147 DTYKDA---LLDVYVVGTSSAKVSKSVSEAIGRIEGV---DYTKEPIDST-KLSNLTDNI 19- 9 T KD L D +VV T+ + +V++ I +++ V Y KE + K+ ++ NI Sbjct: 112 LTMKDQENPLNDAFVVKTTDPHDTPNVAKKIEKMDHVYKVTYGKEEVSRLFKVVGVSRNI 17- 1 Query: 200 RIWGFGGVALLIVL---AIFLISNTIRMSIMSRRTDIEIMRLVGAKNSYIRGPFFFEGAW 25- 6 G+AL+I L A+FLISNTI+++I +RR +IEIM+LVGA N +IR PFF EG Sbjct: 172 ------GIALIIGLVFTAMFLISNTIKITIFARRKEIEIMKLVGATNWFIRWPFFLEGLL 22- 5 Query: 257 VGILGAIVPSLIFYFGYQFVFNKFNPKFETSHVSLYPMDIMVPAIIGGMVIIGIIIGSLG 31- 6 +G+ G+++P + YQ+V PK + S VSL P + V + ++ IG +IG G Sbjct: 226 LGVFGSVIPIALVLSTYQYVIGWVVPKVQGSFVSLLPYNPFVFQVSLVLIAIGAVIGVWG 28- 5 Query: 317 SVLSMRRYLKI 327 S+ S+R++L++ Sbjct: 286 SLTSIRKFLRV 296 A related DNA sequence was identified in S. pyogenes <SEQ ID 5501> which encodes the amino acid sequence <SEQ ID 5502>. Analysis of this protein sequence reveals the following: TABLE-US-05410 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.70 Transmembrane 195-211 (189-219) INTEGRAL Likelihood = -6.74 Transmembrane 39-55 (30-58) INTEGRAL Likelihood = -5.52 Transmembrane 294-310 (288-314) INTEGRAL Likelihood = -1.49 Transmembrane 246-262 (245-263) ----- Final Results ----- bacterial membrane --- Certainty = 0.4079(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05411 >GP:AAC67264 GB:AF017113 cell division protein [Bacillus subtilis] Identities = 117/311 (37%), Positives = 184/311 (58%), Gaps = 19/311 (6%) Query: 11 MIRYFFRHIWESIKNLKRNFWMTFASVSMVAVTLTLVGVFAATLLNIQRVASGVENNVHI 70 - MI+ RH+ ES K+L RN WMTFAS+S V VTL LVGVF +LN+ +A+ E V I Sbjct: 1 MIKILGRHLRESFKSLGRNTWMTFASISAVTVTLILVGVFLVIMLNLNNMATNAEKQVEI 60 Query: 71 NTYLQVDSTDAAKVIQNTAGEPVNNDNYHSVYDKIAQIKGVKKITFSSKDEQLKKLQETL 130- + + + A+ + + ND I ++KG++ +TFSSK+++L +L ++ Sbjct: 61 KVLIDLTADQKAQ-------DKLQND--------IKELKGIQSVTFSSKEKELDQLVDSF 105- Query: 131 GDVWN---MYDQDTNPLQDIYLIETQTPKQVKAITKKIRTIEGVEAADYGGINSDKLFKF 18- 7 GD M DQ+ NPL D ++++T P + KKI ++ V YG +LFK Sbjct: 106 GDSGKSLTMKDQE-NPLNDAFVVKTTDPHDTPNVAKKIEKMDHVYKVTYGKEEVSRLFKV 16- 4 Query: 188 STLIQTWGLIGTAMLLFVAVFLISNTIRMTIMSRKRDIEIMRLVGAKNSYIRGPFFFEGA 24- 7 + + G+ L+F A+FLISNTI++TI +R+++IEIM+LVGA N +IR PFF EG Sbjct: 165 VGVSRNIGIALIIGLVFTAMFLISNTIKITIFARRKEIEIMKLVGATNWFIRWPFFLEGL 22- 4 Query: 248 WVGLLGAVLPSLLIYYGYDLVYKHFAQELQRNNLSMYPLDPYVYYLIGALFVIGIMIGSL 30- 7 +G+ G+V+P L+ Y V ++Q + +S+ P +P+V+ + L IG +IG Sbjct: 225 LLGVFGSVIPIALVLSTYQYVIGWVVPKVQGSFVSLLPYNPFVFQVSLVLIAIGAVIGVW 28- 4 Query: 308 GSVLSMRRYLK 318 GS+ S+R++L+ Sbjct: 285 GSLTSIRKFLR 295 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05412 Identities = 173/318 (54%), Positives = 238/318 (74%), Gaps = 5/318 (1%) Query: 13 MKRRENMVIMIN-FFRHFWESLKNLKRNFWMTFASVTSVTITLLLVGLFSSVLLNVEKLT 71 - MK++E MV MI FFRH WES+KNLKRNFWMTFASV+ V +TL LVG+F++ LLN++++ Sbjct: 2 MKKKEIMVTMIRYFFRHIWESIKNLKRNFWMTFASVSMVAVTLTLVGVFAATLLNIQRVA 61 Query: 72 TDVSGNFTISAFLNVDSTDAQKQVKDKDGKLKDNPDYHKVYDKIKRISGVEKVTYSSKAE 131- + V N I+ +L VDSTDA K +++ G+ +N +YH VYDKI +I GV+K+T+SSK E Sbjct: 62 SGVENNVHINTYLQVDSTDAAKVIQNTAGEPVNNDNYHSVYDKIAQIKGVKKITFSSKDE 121- Query: 132 QLKEVQKEYGSDVID--DTYKDALLDVYVVGTSSAKVSKSVSEAIGRIEGVDYTKEP-ID 18- 8 QLK++Q+ G DV + D + L D+Y++ T + K K++++ I IEGV+ I+ Sbjct: 122 QLKKLQETLG-DVWNMYDQDTNPLQDIYLIETQTPKQVKAITKKIRTIEGVEAADYGGIN 18- 0 Query: 189 STKLSNLTDNIRIWGFGGVALLIVLAIFLISNTIRMSIMSRRTDIEIMRLVGAKNSYIRG 24- 8 S KL + I+ WG G A+L+ +A+FLISNTIRM+IMSR+ DIEIMRLVGAKNSYIRG Sbjct: 181 SDKLFKFSTLIQTWGLIGTAMLLFVAVFLISNTIRMTIMSRKRDIEIMRLVGAKNSYIRG 24- 0 Query: 249 PFFFEGAWVGILGAIVPSLIFYFGYQFVFNKFNPKFETSHVSLYPMDIMVPAIIGGMVII 30- 8 PFFFEGAWVG+LGA++PSL+ Y+GY V+ F + + +++S+YP+D V +IG + +I Sbjct: 241 PFFFEGAWVGLLGAVLPSLLIYYGYDLVYKHFAQELQRNNLSMYPLDPYVYYLIGALFVI 30- 0 Query: 309 GIIIGSLGSVLSMRRYLK 326 GI+IGSLGSVLSMRRYLK Sbjct: 301 GIMIGSLGSVLSMRRYLK 318 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1770 A DNA sequence (GBSx1877) was identified in S. agalactiae <SEQ ID 5503> which encodes the amino acid sequence <SEQ ID 5504>. This protein is predicted to be carboxymethylenebutenolidase-related protein. Analysis of this protein sequence reveals the following:

TABLE-US-05413 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05414 >GP:AAF10898 GB:AE001979 carboxymethylenebutenolidase-related protein [Deinococcus radiodurans] Identities = 65/183 (35%), Positives = 98/183 (53%), Gaps = 3/183 (1%) Query: 56 SKGKVKANIIFYQGALVEEEAYSQLARDLADKGDNTYILKTPLNLPVLSPHRAKTIINQN 115- + +VK ++FY G V +AY L R LA +G T I PL+L + +A+ +I + Sbjct: 100 ASAEVKTLLVFYPGGRVRPQAYEWLGRALAVRGVQTVIPAFPLDLAITGTERAEGLIARY 15- 9 Query: 116 HL-TNVYLAGHSLGGVVASQNAKVAP--VRGLILLASYPSRKSDLSHKNLRVLSITASND 17- 2 V LAGHSLGG VA+Q A + P + GL+LLA+YP+ +L LS+ A D Sbjct: 160 GAGKRVVLAGHSLGGTVAAQYAALRPDKIDGLLLLAAYPAPNVNLHDARFPALSLLAEKD 21- 9 Query: 173 HILNWEKYEEAKKRLPNSSTFRTIVGGNHSRFGNYGHQKGDGKATLSHKSSEKQLATFIS 23- 2 + + +RLP ++ + G HS FG YG Q+GDG T+S +E+++ + Sbjct: 220 GVADAGLVRGGLERLPKNTRLTVLPGAVHSFFGRYGPQQGDGVPTVSRARAEREIVQAVE 27- 9 Query: 233 NFI 235 FI Sbjct: 280 TFI 282 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 5504 (GBS158) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 26 (lane 4; MW 27 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 37 (lane 5; MW 52 kDa). The GBS158-GST fusion product was purified (FIG. 113; see also FIG. 201, lane 4) and used to immunise mice (lane 1+2 product; 14.5 kg/mouse). The resulting antiserum was used for Western blot, FACS, and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1771 A DNA sequence (GBSx1878) was identified in S. agalactiae <SEQ ID 5505> which encodes the amino acid sequence <SEQ ID 5506>. Analysis of this protein sequence reveals the following: TABLE-US-05415 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0281(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05416 >GP:BAB06539 GB:AP001516 unknown conserved protein [Bacillus halodurans] Identities = 83/197 (42%), Positives = 114/197 (57%), Gaps = 4/197 (2%) Query: 35 NTYYLVNDQAV-ILIDPGSNGQEIIAKIKSFEKPLVAILLTHTHYDHIFSLDLVRDTFDN 93 - N Y NDQ I+ DPG +++I ++ + +AILLTH H+DHI +++ VR+TF + Sbjct: 14 NWYIQTNDQGEGIIFDPGGEVEKLITWLRDRQITPLAILLTHAHFDHIGAVEDVRNTF-H 72 Query: 94 PPVYVSEKEAAWLSSPDDNLSGLGRHDDIINVIARPAENFFKLKQPYQLNGFEFTVLPTP 153- PVY+ E E WL P N S L I AR AE+ +Q + F + VL TP Sbjct: 73 IPVYIHENEKEWLIDPQRNGSSLFIPGSSIK--AREAEHLITGEQDLSIGSFSYQVLETP 130- Query: 154 GHSWGGVSFVFHSDELVVTGDALFRETIGRTDLPTSNFEDLITGIRQELFTLPSHYSVHP 21- 3 GHS G +S+ D++V +GDALF +IGRTDLP + + L+ I +L LP +V Sbjct: 131 GHSPGSLSYYAKEDKIVFSGDALFAGSIGRTDLPGGDHQLLLDSIHDKLLELPEDTTVAS 19- 0 Query: 214 GHGMNTTIGHEKNFNPF 230 GHG TTIGHE + NPF Sbjct: 191 GHGPTTTIGHEMDGNPF 207 A related DNA sequence was identified in S. pyogenes <SEQ ID 5507> which encodes the amino acid sequence <SEQ ID 5508>. Analysis of this protein sequence reveals the following: TABLE-US-05417 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0407(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05418 Identities = 217/231 (93%), Positives = 224/231 (96%) Query: 1 MPFIFRHSFFNKVLIFWYTIIMKIYKTINHIAGENTYYLVNDQAVILIDPGSNGQEIIAK 60 +PFIFR+SFFNKVLIFWYTI+MKIYKTINHIAGENTYYLVNDQAVILIDPGSNGQEIIAK Sbjct: 1 LPFIFRYSFFNKVLIFWYTILMKIYKTINHIAGENTYYLVNDQAVILIDPGSNGQEIIAK 60 Query: 61 IKSFEKPLVAILLTHTHYDHIFSLDLVRDTFDNPPVYVSEKEAAWLSSPDDNLSGLGRHD 120- IKSFEKPLVAILLTHTHYDHIFSLDLVRD FD+PPVYVSEKEAAWLSSPDDNLSGLGRHD Sbjct: 61 IKSFEKPLVAILLTHTHYDHIFSLDLVRDAFDHPPVYVSEKEAAWLSSPDDNLSGLGRHD 120- Query: 121 DIINVIARPAENFFKLKQPYQLNGFEFTVLPTPGHSWGGVSFVFHSDELVVTGDALFRET 18- 0 DII VIARPAENFFKLKQPYQLNGFEFTVLPT GHSWGGVSFVFHSDELVVTGDALFRET Sbjct: 121 DIITVIARPAENFFKLKQPYQLNGFEFTVLPTSGHSWGGVSFVFHSDELVVTGDALFRET 18- 0 Query: 181 IGRTDLPTSNFEDLITGIRQELFTLPSHYSVHPGHGMNTTIGHEKNFNPFF 231 IGRTDLPTSNFEDLITGIRQELFTLP+HY V+PGHG +TTI HEKN NPFF Sbjct: 181 IGRTDLPTSNFEDLITGIRQELFTLPNHYRVYPGHGPSTTICHEKNANPFF 231 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1772 A DNA sequence (GBSx1879) was identified in S. agalactiae <SEQ ID 5509> which encodes the amino acid sequence <SEQ ID 5510>. This protein is predicted to be acetoin reductase (fabG). Analysis of this protein sequence reveals the following: TABLE-US-05419 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1596(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9631> which encodes amino acid sequence <SEQ ID 9632> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05420 >GP: AAC48769 GB: U71200 acetoin reductase [Bos taurus] Identities = 162/254 (63%), Positives = 188/254 (73%), Gaps = 2/254 (0%) Query: 12 KVAIVTGAGQGIGFAIAKRLHADGFKIGVLDYNEETAQAAVDKLSPED--AVAVVADVSK 69 - KVA+VTG QGIG AI L ADGF + V D NE ++ + A+AV DVS Sbjct: 4 KVAMVTGGAQGIGEAIVXXLSADGFAVAVADLNEAKSKXVATDIEKNGGTAIAVKLDVSD 63 Query: 70 RDQVFDAFQKVVDTFGDLNVVVNNAGVAPTTPLDTITEEQFEKAFAINVGGTIWGSQAAQ 129- R+ F A ++V + G +V+VNNAG+ PTTP+DTIT E F+K + INV G IWG QAA Sbjct: 64 REGFFAAVKEVAEKLGGFDVLVNNAGLGPTTPIDTITPELFDKVYHINVAGDIWGIQAAV 123- Query: 130 KHFRELGHGGKIINATSQAGCEGNPNLTVYGGTKFAVRGITQTLAKDLASEGITVNAYAP 18- 9 + F++ G+GGKIINATSQAG GNPNL++Y TKFAVR +T A+DLA + ITVNAYAP Sbjct: 124 EQFKKNGNGGKIINATSQAGVVGNPNLSLYSSTKFAVRCLTPVAARDLAEQNITVNAYAP 18- 3 Query: 190 GIVKTPMMFDIAHEVGKNAGKDDEWGMEQFAKDITLKRLSEPEDVANAVGFLAGDDSNYI 24- 9 GIVKTP FDIAHEVGKNAGKDDEWGM+ FAKDI LKRLSEPEDVA AV FLAG DSNYI Sbjct: 184 GIVKTPXXFDIAHEVGKNAGKDDEWGMQTFAKDIALKRLSEPEDVAAAVAFLAGPDSNYI 24- 3 Query: 250 TGQTIVVDGGMVFH 263 TGQTI VDGGM FH Sbjct: 244 TGQTIEVDGGMQFH 257 A related DNA sequence was identified in S. pyogenes <SEQ ID 5511> which encodes the amino acid sequence <SEQ ID 5512>. Analysis of this protein sequence reveals the following: TABLE-US-05421 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1131(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05422 Identities = 209/213 (98%), Positives = 212/213 (99%) Query: 1 MTKEYEVEDMSKVAIVTGAGQGIGFAIAKRLHADGFKIGVLDYNEETAQAAVDKLSPEDA 60 +TK+YEVEDMSKVAIVTGAGQGIGFAIAKRLHADGFKIG+LDYNEETAQAAVDKLSPEDA Sbjct: 1 LTKKYEVEDMSKVAIVTGAGQGIGFAIAKRLHADGFKIGILDYNEETAQAAVDKLSPEDA 60 Query: 61 VAVVADVSKRDQVFDAFQKVVDTFGDLNVVVNNAGVAPTTPLDTITEEQFEKAFAINVGG 120- VAVVADVSKRDQVFDAFQKVVDTFGDLNVVVNNAGVAPTTPLDTITEEQFEKAFAINVGG Sbjct: 61 VAVVADVSKRDQVFDAFQKVVDTFGDLNVVVNNAGVAPTTPLDTITEEQFEKAFAINVGG 120- Query: 121 TIWGSQAAQKHFRELGHGGKIINATSQAGCEGNPNLTVYGGTKFAVRGITQTLAKDLASE 18- 0 TIWGSQAAQKHFRELGHGGKIINATSQAGCEGNPNLTVYGGTKFAVRGITQTLAKDLASE Sbjct: 121 TIWGSQAAQKHFRELGHGGKIINATSQAGCEGNPNLTVYGGTKFAVRGITQTLAKDLASE 18- 0 Query: 181 GITVNAYAPGIVKTPMMFDIAHEVGKNAGKDDE 213 GITVNAYAPGIVKTPMMF IAHEVGKNAGKDDE Sbjct: 181 GITVNAYAPGIVKTPMMFAIAHEVGKNAGKDDE 213 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1773 A DNA sequence (GBSx1880) was identified in S. agalactiae <SEQ ID 5513> which encodes the amino acid sequence <SEQ ID 5514>. This protein is predicted to be ATP-dependent DNA helicase. Analysis of this protein sequence reveals the following: TABLE-US-05423 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3735(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05424 >GP: AAB38451 GB: L47709 22.4% identity with Escherichia coli DNA-damage inducible protein . . . ; putative [Bacillus subtilis] Identities = 132/461 (28%), Positives = 231/461 (49%), Gaps = 22/461 (4%) Query: 21 RKYAVVDLEATGAGPNAS--IIQVGIVIIQGNKIIDSYETDVNPHESLDEHIVHLTGITD 78 - +++ V+D+E TG P IIQ+ V+I+ +I + + +NP++S+ I LTGI++ Sbjct: 4 QRFVVIDVETTGNSPKKGDKIIQIAAVVIENGQITERFSKYINPNKSIPAFIEQLTGISN 63 Query: 79 KQLAKAPDFGQVAHHIYQLIEDCIFVAHNVKFDANLLAEQLFLEGCELRTPRI-DTVELS 137- + + F VA ++QL++ FVAHN+ FD + +L G +L + DTVELS Sbjct: 64 QMVENEQPFEAVAEEVFQLLDGAYFVAHNIHFDLGFVKYELHKAGFQLPDCEVLDTVELS 123- Query: 138 QVFYPCLEKYSLGALAESLNIELTDAHTAIADARATAQLFIKLKAKISSLPKEVLETILT 19- 7 ++ +P E Y L L+E L + H A +DA T +F+++ K+ LP L+ + Sbjct: 124 RIVFPGFEGYKLTELSEELQLRHDQPHRADSDAEVTGLIFLEILEKLRQLPYPTLKQLRR 18- 3 Query: 198 FADNLLFESYLLIEEAYQEADFVNPKEYYFWQGLVLKKEKAVGKPKKLSSDFQ------- 25- 0 + + + + L++ E Y + +++ +A+ +F Sbjct: 184 LSQHFISDLTHLLDMFINENRHTEIPGYTRFSSFSVREPEAIDVRINEDENFSFEIESWE 24- 3 Query: 251 ------VNMALLGMDARPKQVVFADLVKAHFNDQTTTFLEAQPGLGKTYGYLLP--LLDQ 30- 2 ++ + G + R Q++ V F ++ +EA PG+GKT GYL+P L + Sbjct: 244 AGNEKALSELMPGYEKRDGQDMMMMREVADAFANREHALIEAPPGIGKTIGYLIPAALFAK 3- 03 Query: 303 SQKQQIIVSVPTKILQDQIMAKEIKHIQELFHIPCHS--IKGPRNYLKLDAFYKSLQVQD 36- 0 K+ +I+S + +LQ QI+ K++ +Q+LF P + +KG +YL L F + L +D Sbjct: 304 KSKKPVIISTYSTLLQQQILTKDLPIVQDLFPFPVTAAILKGQSHYLCLYKFEQVLHEED 36- 3 Query: 361 RNRLINRFKMQLLVWLTETTTGDLDEIKQKQRLESYFDQLKHDGE-VTQSSLFYDLDFWK 41- 9 N K QLLVWLTET TGD+ E+ + +D+L +D + +S + + F++ Sbjct: 364 DNYDAVLTKAQLLVWLTETNTGDVAELNLPSGGKLLWDRLAYDDDSYKRSRSEHVIGFYE 42- 3 Query: 420 RSYDKVAQSQLVIINHAYFL-ERVQDDKDFAKGKVLVFDEA 459 R+ +S LVI NH+ L + K + + DEA Sbjct: 424 RAKQIAMRSDLVITNHSLLLTDEGSHKKRLPESGTFIIDEA 464 Identities = 63/195 (32%), Positives = 88/195 (44%), Gaps = 16/195 (8%) Query: 629 KVWIDTSMPNILDLSPEQYAYEIAKRLQDIMTLKQPT-LVLLTSKQTMFMVSDYLDKWEI 68- 7 +V I M +I D ++ + A+ ++ + KQP LVL TS + V E+ Sbjct: 720 QVMIPKEMKSIQDTGQPEFIQDTARYIELMAKEKQPKILVLFTSHDMLKKVHQ-----EL 77- 4 Query: 688 KH---------LTQD-KNGLAYNVKKRFDRGESNLLLGTGSFWEGVDFVHRDRLIEVITR 73- 7 KH L Q G + K F +LLGT FWEGVDF + +I R Sbjct: 775 KHNMSASGIQLLAQGITGGSPGKLMKTFKTSNQAILLGTNHFWEGVDFPGDELTTVMIVR 83- 4 Query: 738 LPFDTPKDYFIQKLSQSLTKEGKNFFYDYSLPMTVLKLKQALGRTTRREEQKSAVIILDS 79- 7 LPF +P + K+GKN F SLP VL +Q +GR R K +IILD Sbjct: 835 LPFRSPDHPLHAAKCELARKKGKNPFQTVSLPEAVLTFRQGIGRLLRSAGDKGTIIILDR 89- 4 Query: 798 RLVIKSYGQTIMHSL 812 R+ YG+ + +L Sbjct: 895 RIKTAGYGRLFLDAL 909 A related DNA sequence was identified in S. pyogenes <SEQ ID 5515> which encodes the amino acid sequence <SEQ ID 5516>. Analysis of this protein sequence reveals the following: TABLE-US-05425 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3735(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05426 Identities = 500/835 (59%), Positives = 626/835 (74%), Gaps = 2/835 (0%) Query: 1 MFCFIDIACYNRLTMTQKKLRKYAVVDLEATGAGPNASIIQVGIVIIQGNKIIDSYETDV 60 MFCFIDIACYNRLTMTQKKLRKYAVVDLEATGAGPNASIIQVGIVIIQGNKIIDSYETDV Sbjct: 1 MFCFIDIACYNRLTMTQKKLRKYAVVDLEATGAGPNASIIQVGIVIIQGNKIIDSYETDV 60 Query: 61 NPHESLDEHIVHLTGITDKQLAKAPDFGQVAHHIYQLIEDCIFVAHNVKFDANLLAEQLF 120- NPHESLDEHIVHLTGITDKQLAKAPDFGQVAHHIYQLIEDCIFVAHNVKFDANLLAE LF Sbjct: 61 NPHESLDEHIVHLTGITDKQLAKAPDFGQVAHHIYQLIEDCIFVAHNVKFDANLLAEALF 120- Query: 121 LEGCELRTPRIDTVELSQVFYPCLEKYSLGALAESLNIELTDAHTAIADARATAQLFIKL 18- 0 LEG EL PR+DTVEL+Q+F+P EKY+L L+ LNI+L +AHTAIADARATA LF++L Sbjct: 121 LEGYELTIPRVDTVELAQLFFPRFEKYNLSHLSRQLNIDLAEAHTAIADARATAILFLRL 18- 0 Query: 181 KAKISSLPKEVLETILTFADNLLFESYLLIEEAYQEADFVNPKEYYFWQGLVLKKEKAVG 24- 0 KI SLP E LE++L ++D+LLFE+ ++I+E +A +P +Y + ++L K Sbjct: 181 LQKIESLPIECLESLLVYSDSLLFETAMVIQEGLAKAKPYDPNKYIKIRQILLPKGSKAL 24- 0 Query: 241 KPKKLSSDFQVNMALLGMDARPKQVVFADLVKAHFNDQTTTFLEAQPGLGKTYGYLLPLL 30- 0 KP ++S F +NMALLG++ RPKQ FA L+ ++ +F+EAQ G+GKTYGYLLPLL Sbjct: 241 KPYQISKSFPINMALLGLEERPKQTQFAQLIDEDYHQGVASFIEAQTGIGKTYGYLLPLL 30- 0 Query: 301 DQSQKQQIIVSVPTKILQDQIMAKEIKHIQELFHIPCHSIKGPRNYLKLDAFYKSLQVQD 36- 0 + + QIIVSVPTK+LQDQ+MA E+ IQE FHI CHS+KGP NYLKLD+F SL D Sbjct: 301 AKEDQNQIIVSVPTKLLQDQLMAGEVAAIQEQFHIACHSLKGPANYLKLDSFADSLDQND 36- 0 Query: 361 RNRLINRFKMQLLVWLTETTTGDLDEIKQKQRLESYFDQLKHDGEVTQSSLFYDLDFWKR 42- 0 +NRL+NR+KMQLLVWL ET TGDLDEIKQKQR +YF+QLKHDG++ QSS FYD DFW+ Sbjct: 361 QNRLVNRYKMQLLVWLLETKTGDLDEIKQKQRFAAYFEQLKHDGDIKQSSEFYDYDFWRV 42- 0 Query: 421 SYDKVAQSQLVIINHAYFLERVQDDKDFAKGKVLVFDEAQKLVLGLENFSRGQLDISHQL 48- 0 SY+K ++L+I NHAYFL RVQDDKDFA+ KVLVFDEAQKL+L L+ SR QL+++ L Sbjct: 421 SYEKAKTARLLITNHAYFLHRVQDDKDFARNKVLVFDEAQKLMLQLDQLSRHQLNLTVFL 48- 0 Query: 481 QVIQKIIDSSIPLLQKRLLESISYELSHAVELFYRHNSFEFSETWLKRLKNSINALEVVG 54- 0 Q IQ + + +PLL+KRLLES+S+EL +Y++ + + W R+ L Sbjct: 481 QTIQAKLSNPLPLLEKRLLESLSFELGQVSSDYYQNKEHQLAHDW-SRIAGYAKELTGAD 53- 9 Query: 541 LDELQTFFTATYTNYWFETDKVNEKRLTILRGAREDFLKFSKFLPPTKKTYMISATLQIS 60- 0 ELQ FF + +YW ++K EKR+T L A + F+ F + LP T KTY +SATL IS Sbjct: 540 YQELQAFFATSDGDYWLSSEKQEEKRVTYLNSASKAFIHFQQLLPETVKTYFVSATLTIS 59- 9 Query: 601 PKVYLSDLLGGFSSISTEKIAHEKNANQKVWIDTSMPNILDLSPEQYAYEIAKRLQDIMT 66- 0 +V L+DLL GF I +K +Q V +D P + ++S + Y IAKR++ + Sbjct: 600 SEVTLADLL-GFEEYLYHVIEKDKKQDQLVLVDQEAPIVTEVSDQIYVEAIAKRIESLKQ 65- 8 Query: 661 LKQPTLVLLTSKQTMFMVSDYLDKWEIKHLTQDKNGLAYNVKKRFDRGESNLLLGTGSFW 72- 0 P LVL SK+ + +VSDYLD+W++ HL Q+KNG AYN+KKRFD+GE +LLG GSFW Sbjct: 659 EGYPILVLFNSKKHLLLVSDYLDQWQVPHLAQEKNGTAYNIKKRFDQGEQTILLGLGSFW 71- 8 Query: 721 EGVDFVHRDRLIEVITRLPFDTPKDYFIQKLSQSLTKEGKNFFYDYSLPMTVLKLKQALG 78- 0 EGVDF+ DR+I +I RLPFD P+D+F++K+S L ++GKN F DY LPMT+L+LKQA+G Sbjct: 719 EGVDFIQADRMITLIARLPFDNPEDFFVKKMSHYLLEKGKNPFRDYFLPMTILRLKQAIG 77- 8 Query: 781 RTTRREEQKSAVIILDSRLVIKSYGQTIMHSLGRDFEISKEKINKVLTEMAKFLI 835 RT RR++QKS VIILD RL+ KSYGQ I+ LG++F IS++ + L E FLI Sbjct: 779 RTMRRQDQKSVVIILDRRLLTKSYGQVILEGLGQEFLISQQNFHDCLVETDCFLI 833 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1774 A DNA sequence (GBSx1881) was identified in S. agalactiae <SEQ ID 5517> which encodes the amino acid sequence <SEQ ID 5518>. Analysis of this protein sequence reveals the following: TABLE-US-05427 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2042(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9633> which encodes amino acid sequence <SEQ ID 9634> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05428 >GP: AAF12702 GB: AF035157 aspartate aminotransferase [Lactococcus lactis] Identities = 270/391 (69%), Positives = 314/391 (80%) Query: 7 MTYLSERVLNMEESVTLAAGAKARELRVQGRDILSLTLGEPDFATPKNIQQAAIEAITDG 66 M S+ VL M+ESVTLAA +A+ L+ QGRDI+ LTLG+PDF TPK I QAAIEAI +G Sbjct: 1 MKKCSDFVLKMDESVTLAAANRAKALKAQGRDIIDLTLGQPDFPTPKKIGQAAIEAINNG 60 Query: 67 RASFYTPSSGLPELKSAINAYFERFYGYSLKPNQVVVGTGAKFILYTFFMTVLNPGDEVI 126- +ASFYT + GLPELK A+ Y+ RFY Y ++ N++++ GAKF LY +FM ++P DEVI Sbjct: 61 QASFYTQAGGLPELKKAVQHYWTRFYAYEIQTNEILITAGAKFALYAYFMATVDPLDEVI 120- Query: 127 IPTPYWVSYADQIKMAEGKPVFVTAKEVNHFKVTVEQLEAVRTDKTKVILLNSPSNPTGM 18- 6 IP PYWVSY DQ+KMA G PV V AK+ N+FKVTVEQLE RT KTK++LLNSPSNPTGM Sbjct: 121 IPAPYWVSYVDQVKMAGGNPVIVEAKQENNFKVTVEQLEKARTSKTKILLLNSPSNPTGM 18- 0 Query: 187 IYKAEELEAIGNWAVEHDILILADDIYGRLVYNGNIFTPISSLSESIRNQTIVINGVSKT 24- 6 IY EEL AIG WAV HD+LILADDIY RLVYNG FT ISSLS+ IRN+T VINGVSKT Sbjct: 181 IYSKEELTAIGEWAVAHDLLILADDIYHRLVYNGAEFTAISSLSDEIRNRTTVINGVSKT 24- 0 Query: 247 YAMTGWRVGFAVGNHDIIAAMSKVVSQTTSNLTAVSQYATIEALNGSQESFEKMRLAFEE 30- 6 +AMTGWR+G AVG+ +IIAAM+K+ SQTTSN TAV+QYA IEA + +SFEKM AFEE Sbjct: 241 FAMTGWRIGLAVGDPEIIAAMTKIASQTTSNPTAVAQYAAIEAFEENDKSFEKMHAAFEE 30- 0 Query: 307 RLNIIYPLLCQVPGFEVVKPQGAFYLFPNVTKAMEMKGYTDVTAFTDAILEEVGLALVTG 36- 6 RLN IY L +VPGFE+VKP GAFYLFP VTKAM MKGYTDVT FT AILEE G+ALVTG Sbjct: 301 RLNKIYLQLSEVPGFELVKPNGAFYLFPKVTKAMAMKGYTDVTDFTTAILEEAGVALVTG 36- 0 Query: 367 AGFGAPENVRLSYATDLETLKEAVRRLHVFM 397 AGFG+PENVRLSYAT LETL+ AV RL +M Sbjct: 361 AGFGSPENVRLSYATSLETLEAAVTRLKDWM 391 A related DNA sequence was identified in S. pyogenes <SEQ ID 1005> which encodes the amino acid sequence <SEQ ID 1006>. Analysis of this protein sequence reveals the following:

TABLE-US-05429 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.48 Transmembrane 95-111 (95-113) ----- Final Results ----- bacterial membrane --- Certainty = 0.1192(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05430 Identities = 301/397 (75%), Positives = 343/397 (85%) Query: 7 MTYLSERVLNMEESVTLAAGAKARELRVQGRDILSLTLGEPDFATPKNIQQAAIEAITDG 66 M LS+RVL M+ESVTLAAGA+A+ L+ QGRD+L+LTLGEPDF TPK+IQ AIE+I +G Sbjct: 1 MPKLSKRVLEMKESVTLAAGARAKALKAQGRDVLNLTLGEPDFFTPKHIQDKAIESIQNG 60 Query: 67 RASFYTPSSGLPELKSAINAYFERFYGYSLKPNQVVVGTGAKFILYTFFMTVLNPGDEVI 126- ASFYT +SGLPELK+AI Y + YGY L P+Q+V GTGAKFILY FFM VLNPGD+V+ Sbjct: 61 TASFYTNASGLPELKAAIATYLKNQYGYHLSPDQIVAGTGAKFILYAFFMAVLNPGDQVL 120- Query: 127 IPTPYWVSYADQIKMAEGKPVFVTAKEVNHFKVTVEQLEAVRTDKTKVILLNSPSNPTGM 18- 6 IPTPYWVSY+DQ+KMAEG+P+FV E N FKVTV+QLE RT KTKV+L+NSPSNPTGM Sbjct: 121 IPTPYWVSYSDQVKMAEGQPIFVQGLEENQFKVTVDQLERARTSKTKVVLINSPSNPTGM 18- 0 Query: 187 IYKAEELEAIGNWAVEHDILILADDIYGRLVYNGNIFTPISSLSESIRNQTIVINGVSKT 24- 6 IY AEEL AIG WAV +DILILADDIYG LVYNGN F PIS+LSE+IR QTI +NGV+K+ Sbjct: 181 IYGAEELRAIGEWAVHNDILILADDIYGSLVYNGNQFVPISTLSEAIRRQTITVNGVAKS 24- 0 Query: 247 YAMTGWRVGFAVGNHDIIAAMSKVVSQTTSNLTAVSQYATIEALNGSQESFEKMRLAFEE 30- 6 YAMTGWRVGFA G +II+AMSK++ QTTSNLT VSQYA IEA GSQ S E+MRLAFEE Sbjct: 241 YAMTGWRVGFAAGEPEIISAMSKIIGQTTSNLTTVSQYAAIEAFCGSQSSLEEMRLAFEE 30- 0 Query: 307 RLNIIYPLLCQVPGFEVVKPQGAFYLFPNVTKAMEMKGYTDVTAFTDAILEEVGLALVTG 36- 6 RLNI YPLLCQVPGFEVVKPQGAFY FPNV KAMEM G++DVT+F +AILEEVGLA+V+G Sbjct: 301 RLNITYPLLCQVPGFEVVKPQGAFYFFPNVKKAMEMTGFSDVTSFANAILEEVGLAVVSG 36- 0 Query: 367 AGFGAPENVRLSYATDLETLKEAVRRLHVFMGSNEIN 403 AGFGAPENVRLSYATD+ETLKEAVRRLHVFM SNEIN Sbjct: 361 AGFGAPENVRLSYATDIETLKEAVRRLHVFMESNEIN 397 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1775 A DNA sequence (GBSx1882) was identified in S. agalactiae <SEQ ID 5519> which encodes the amino acid sequence <SEQ ID 5520>. This protein is predicted to be asparaginyl-tRNA synthetase (asnS). Analysis of this protein sequence reveals the following: TABLE-US-05431 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1488(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05432 >GP:BAB05415 GB:AP001512 asparaginyl-tRNA synthetase [Bacillus halodurans] Identities = 252/442 (57%), Positives = 316/442 (71%), Gaps = 15/442 (3%) Query: 7 SIVDVKDYVGQEVTIGAWVANKSGKGKIAFVQLRDGSAFFQGVAFKPNFIEKYGEESGLE 66 +I + YV QEVT+GAW+ANK GKIAF+QLRDG+ F QGV K E G E Sbjct: 4 TIAKIGQYVDQEVTLGAWLANKRSSGKIAFLQLRDGTGFIQGVVVKA--------EVGDE 55 Query: 67 KFDVIKRLNQETSVYVTGIVKEDERSKFGYELDITDLEVIGESHEYPITPKEHGTDFLMD 126- F K L QE+S+YVTGIV++DER+ GYEL +T ++I E+ +YPITPKEHGT+FLMD Sbjct: 56 WFQKAKNLTQESSLYVTGIVRKDERAPSGYELTVTSFDIIHEATDYPITPKEHGTEFLMD 115- Query: 127 NRHLWLRSRKQMAVMQIRNAIIYSTYEFFDQNGFIKFDSPILSENAAEDSTELFETDYFG 18- 6 +RHLW+RSRKQ AV++IRN II +TYEFF +NGF+K D PIL+ +A E +TELF T YF Sbjct: 116 HRHLWIRSRKQHAVLRIRNEIIRATYEFFHENGFVKVDPPILTGSAPEGTTELFHTKYFD 17- 5 Query: 187 KPAFLSQSGQLYLEAGAMALGRVFDFGPVFRAEKSKTRRHLTEFWMMDAEYSFLSHEESL 24- 6 + AFLSQSGQLY+EA A+A GRVF FGP FRAEKSKTRRHL EFWM++ E +F+ EESL Sbjct: 176 EDAFLSQSGQLYMEAAALAFGRVFSFGPTFRAEKSKTRRHLIEFWMIEPEMAFVEFEESL 23- 5 Query: 247 DLQEAYVKALIQGVLDRAPQALDILERDVEALKRYIAEPFKRVSYDDAITLLQEHEADED 30- 6 ++QE YV ++Q VL L L RD L+ I PF R+SYDDAI L E D+ Sbjct: 236 EIQENYVAYIVQSVLKHCAIELKTLGRDTSVLES-IQAPFPRISYDDAIKFLHEKGFDD- 29- 3 Query: 307 TDYEHLEHGDDFGSPHETWISNYFGVPTFVVNYPASFKAFYMKPVPGNPERVLCADLLAP 36- 6 +E GDDFG+PHET I+ +F P F+ +YP S K FYM+P P + VLCADL+AP Sbjct: 294 -----IEWGDDFGAPHETAIAEHFDKPVFITHYPTSLKPFYMEPDPNRDDVVLCADLIAP 34- 8 Query: 367 EGYGEIIGGSMREDDYDALVAKMDELGMDKSEYDFYLDLRKYGSVPHGGFGIGIERMVTF 42- 6 EGYGEIIGGS R DYD L +++E + Y +YLDLRKYGSVPH GFG+G+ER V + Sbjct: 349 EGYGEIIGGSQRISDYDLLKKRLEEHDLSLDAYAWYLDLRKYGSVPHSGFGLGLERTVGW 40- 8 Query: 427 VAGTKHIREAIPFPRMLHRIKP 448 ++G H+RE IPFPR+L+R+ P Sbjct: 409 ISGAGHVRETIPFPRLLNRLYP 430 A related DNA sequence was identified in S. pyogenes <SEQ ID 5521> which encodes the amino acid sequence <SEQ ID 5522>. Analysis of this protein sequence reveals the following: TABLE-US-05433 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1488(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05434 Identities = 443/448 (98%), Positives = 447/448 (98%) Query: 1 MSKKLISIVDVKDYVGQEVTIGAWVANKSGKGKIAFVQLRDGSAFFQGVAFKPNFIEKYG 60 MSKKLISIVDVKDYVGQEVTIGAWVANKSGKGKIAFVQLRDGSAFFQGVAFKPNFIEKYG Sbjct: 1 MSKKLISIVDVKDYVGQEVTIGAWVANKSGKGKIAFVQLRDGSAFFQGVAFKPNFIEKYG 60 Query: 61 EESGLEKFDVIKRLNQETSVYVTGIVKEDERSKFGYELDITDLEVIGESHEYPITPKEHG 120- EESGLEKFDVIKRLNQETSVYVTGIVKEDERSKFGYELDITDLE+IGESHEYPITPKEHG Sbjct: 61 EESGLEKFDVIKRLNQETSVYVTGIVKEDERSKFGYELDITDLEIIGESHEYPITPKEHG 120- Query: 121 TDFLMDNRHLWLRSRKQMAVMQIRNAIIYSTYEFFDQNGFIKFDSPILSENAAEDSTELF 18- 0 TDFLMDNRHLWLRSRKQMAVMQIRNAIIY+TYEFFDQNGFIKFDSPILSENAAEDSTELF Sbjct: 121 TDFLMDNRHLWLRSRKQMAVMQIRNAIIYATYEFFDQNGFIKFDSPILSENAAEDSTELF 18- 0 Query: 181 ETDYFGKPAFLSQSGQLYLEAGAMALGRVFDFGPVFRAEKSKTRRHLTEFWMMDAEYSFL 24- 0 ETDYFGKPAFLSQSGQLYLEAGAMALGRVFDFGPVFRAEKSKTRRHLTEFWMMDAEYSFL Sbjct: 181 ETDYFGKPAFLSQSGQLYLEAGAMALGRVFDFGPVFRAEKSKTRRHLTEFWMMDAEYSFL 24- 0 Query: 241 SHEESLDLQEAYVKALIQGVLDRAPQALDILERDVEALKRYIAEPFKRVSYDDAITLLQE 30- 0 SHEESLDLQEAYVKALIQGVLDRAPQALDILERDVEALKRYI EPFKRVSYDDAITLLQE Sbjct: 241 SHEESLDLQEAYVKALIQGVLDRAPQALDILERDVEALKRYITEPFKRVSYDDAITLLQE 30- 0 Query: 301 HEADEDTDYEHLEHGDDFGSPHETWISNYFGVPTFVVNYPASFKAFYMKPVPGNPERVLC 36- 0 HEADEDTDYEHLEHGDDFGSPHETWISNYFGVPTFVVNYPASFKAFYMKPVPGNPERVLC Sbjct: 301 HEADEDTDYEHLEHGDDFGSPHETWISNYFGVPTFVVNYPASFKAFYMKPVPGNPERVLC 36- 0 Query: 361 ADLLAPEGYGEIIGGSMREDDYDALVAKMDELGMDKSEYDFYLDLRKYGSVPHGGFGIGI 42- 0 ADLLAPEGYGEIIGGSMRED+YDALVAKMDELGMDKSEYDFYLDLRKYGSVPHGGFGIGI Sbjct: 361 ADLLAPEGYGEIIGGSMREDNYDALVAKMDELGMDKSEYDFYLDLRKYGSVPHGGFGIGI 42- 0 Query: 421 ERMVTFVAGTKHIREAIPFPRMLHRIKP 448 ERMVTFVAGTKHIREAIPFPRMLHRI+P Sbjct: 421 ERMVTFVAGTKHIREAIPFPRMLHRIRP 448 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1776 A DNA sequence (GBSx1883) was identified in S. agalactiae <SEQ ID 5523> which encodes the amino acid sequence <SEQ ID 5524>. Analysis of this protein sequence reveals the following: TABLE-US-05435 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.85 Transmembrane 103-119 (102-127) INTEGRAL Likelihood = -5.04 Transmembrane 73-89 (68-93) INTEGRAL Likelihood = -4.19 Transmembrane 31-47 (31-49) INTEGRAL Likelihood = -1.86 Transmembrane 157-173 (157-173) ----- Final Results ----- bacterial membrane --- Certainty = 0.3739(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05436 >GP:AAD40355 GB:AF036485 hypothetical protein [Plasmid pNZ4000] Identities = 39/135 (28%), Positives = 72/135 (52%), Gaps = 4/135 (2%) Query: 3 KSPARLISFISIAIAINLVGANLALFLRLPIYLDTIGTLLIAVILGPWYAASTAFLSALI 62 K A ++ I A+ IN V LA L+LP++L ++GT L +++ GP A + F++ +I Sbjct: 15 KLSAATMTLIPAAVGINYVAKALAEGLKLPVWLGSLGTFLASMLAGPVAGAISGFINNVI 74 Query: 63 NWMTTDIFSLYYSPVAIVVAIITGILIKRNCKPSS--LLWKSLIISLPGTIIASVITVIL 120- +T S Y+ +I + I G+L S+ + ++II++ +I++ + VI Sbjct: 75 YGLTLSPISTVYAITSIGIGIAVGVLHANGWFSSARRVFVSAIIIAIVSAVISTPLNVIF 134- Query: 121 FKGIT--SSGSSIIA 133 + G T + G S+ A Sbjct: 135 WGGQTGIAWGDSLFA 149 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1777 A DNA sequence (GBSx1884) was identified in S. agalactiae <SEQ ID 5525> which encodes the amino acid sequence <SEQ ID 5526>. Analysis of this protein sequence reveals the following: TABLE-US-05437 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1873(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05438 >GP:AAC75223 GB:AE000305 orf, hypothetical protein [Escherichia coli K12] Identities = 97/305 (31%), Positives = 160/305 (51%), Gaps = 10/305 (3%) Query: 1 MNKEKIIIDCDPGIDDTLALMYAIQHPKLEVVAITITAGNSPVELGLKNTFVTLELLNRH 60 M K KII+DCDPG DD +A+M A +HP ++++ ITI AGN ++ L N + L Sbjct: 1 MEKRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKL-EI 59 Query: 61 DIPVYVGDNLPLQREFVSAQDTHGMDGLGENNFTLAQPIIFQEESADC---FLANYFEHK 117- ++PVY G P+ R+ + A + HG GL F +P+ Q ES + Sbjct: 60 NVPVYAGMPQPIMRQQIVADNIHGETGLDGPVF---EPLTRQAESTHAVKYIIDTLMASD 116- Query: 118 NDTSIIALGPLTNIARALQTNPKLGKHCKRFISMGGSFKSHGNCSPVAEYNYWCDPHAAQ 17- 7 D +++ +GPL+NIA A++ P + + + MGG++ + GN +P AE+N + DP AA+ Sbjct: 117 GDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGT-GNFTPSAEFNIFADPEAAR 17- 5 Query: 178 YVFENLDKKIEMVGLDITRHIVLTPNHLSYMERINPDVSSFIQKITKFYFDFHWQYEHII 23- 7 VF + + M+GLD+T V TP+ ++ MER I F ++ + Sbjct: 176 VVFTS-GVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFENYGLA 23- 4 Query: 238 GCVINDPLAIAYFVNENIATGFDSYTDVACH-GIAMGQTIVDQYHFYKKDANSKILTSVN 29- 6 G ++D I Y +N + + Y +V + G G+T+ D+ K AN+K+ +++ Sbjct: 235 GGPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITID 29- 4 Query: 297 TNLFW 301 T+ FW Sbjct: 295 TDWFW 299 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1778 A DNA sequence (GBSx1885) was identified in S. agalactiae <SEQ ID 5527> which encodes the amino acid sequence <SEQ ID 5528>. Analysis of this protein sequence reveals the following: TABLE-US-05439 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1860(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05440 >GP:CAB62728 GB:AL133423 hypothetical protein SC4A7.24c [Streptomyces coelicolor A3(2)] Identities = 36/134 (26%), Positives = 57/134 (41%), Gaps = 7/134 (5%) Query: 1 MLYEVTSSNTQGVDGKVYLSNGKIVETNHPLNHL----PGFNPEELIALAWSTCLNATIK 56 +LY ++ G DG+V +G++ +P + G NPE+L A +S C + Sbjct: 8 VLYTAVATAENGRDGRVATDDGRLDVVVNPPKEMGGNGAGTNPEQLFAAGYSACFQGALG 67 Query: 57 AILEQKGFKDLKSRVDVTCQLMKERQVGKGFYFQVNAVASIEKLSLSDSKLIVNKAHSRC 116- + Q+G S V + K GF V A I + + ++ +V KAH C Sbjct: 68 VVARQEGADISGSTVTAKVGIGKNDD---GFGIIVEISAEIPTVDAATARSLVEKAHQVC 124- Query: 117 PISKLISNAKTINL 130 P SK T+ L Sbjct: 125 PYSKATRGNITVTL 138 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1779 A DNA sequence (GBSx1886) was identified in S. agalactiae <SEQ ID 5529> which encodes the amino acid sequence <SEQ ID 5530>. Analysis of this protein sequence reveals the following: TABLE-US-05441 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0531(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9635> which encodes amino acid sequence <SEQ ID 9636> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05442 >GP:CAB15482 GB:Z99121 similar to hypothetical proteins [Bacillus subtilis] Identities = 164/285 (57%), Positives = 207/285 (72%), Gaps = 2/285 (0%) Query: 6 IKLVIVTGMSGAGKTVAIQSFEDLGYFTIDNMPPTLVPKFLELAAQSGDT-SKIAMVVDM 64 I+LVI+TGMSGAGKTVAIQSFEDLGYF +DN+PP+L+PKFLEL +S SK+A+V+D+ Sbjct: 9 IQLVIITGMSGAGKTVAIQSFEDLGYFCVDNLPPSLLPKFLELMKESNSKMSKVALVMDL 68 Query: 65 RSRLFFREINSILDSLEINDNINFKILFLDATDTELVSRYKETRRSHPLAADGRVLDGIS 124- R R FF + LD + N I +ILFLDA D+ LV+RYKETRRSHPLAA G L+GI+ Sbjct: 69 RGREFFDRLIEALDEMAENPWITPRILFLDAKDSILVTRYKETRRSHPLAATGLPLEGIA 128- Query: 125 LERELLAPLKSMSQNVVDTSELTPRQLRKVISKEFSNQDSQSSFRIEVMSFGFKYGIPLD 18- 4 LERELL LK SQ + DTS++ PR LR+ I K F+ ++ F + VMSFGFKYGIP+D Sbjct: 129 LERELLEELKGRSQIIYDTSDMKPRDLREKIVKHFATNQGET-FTVNVMSFGFKYGIPID 18- 7 Query: 185 ADLVFDVRFLPNPYYKPELRDKTGLDTEVYDYVMSFDESDDFYDHLLALIKPILPGYQNE 24- 4 ADLVFDVRFLPNPYY +R TG D EV YVM ++E+ F + L+ L+ +LP Y+ E Sbjct: 188 ADLVFDVRFLPNPYYIESMRPLTGKDKEVSSYVMKWNETQKFNEKLIDLLSFMLPSYKRE 24- 7 Query: 245 GKSVLTVAIGCTGGQHRSTAFAHRLSEDLKADWTVNESHRDKNKR 289 GKS + +AIGCTGGQHRS A L++ K D+ + +HRD KR Sbjct: 248 GKSQVVIAIGCTGGQHRSVTLAENLADYFKKDYYTHVTHRDIEKR 292 A related DNA sequence was identified in S. pyogenes <SEQ ID 5531> which encodes the amino acid sequence <SEQ ID 5532>. Analysis of this protein sequence reveals the following: TABLE-US-05443 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05444 >GP:CAB15482 GB:Z99121 similar to hypothetical proteins [Bacillus subtilis] Identities = 164/291 (56%), Positives = 213/291 (72%), Gaps = 3/291 (1%) Query: 1 MSDKH-INLVIVTGMSGAGKTVAIQSFEDLGYFTIDNMPPALVPKFLELIEQTNENR-RV 58 +S+ H I LVI+TGMSGAGKTVAIQSFEDLGYF +DN+PP+L+PKFLEL++++N +V Sbjct: 3 VSESHDIQLVIITGMSGAGKTVAIQSFEDLGYFCVDNLPPSLLPKFLELMKESNSKMSKV 62 Query: 59 ALVVDMRSRLFFKEINSTLDSIESNPSIDFRILFLDATDGELVSRYKETRRSHPLAADGR 118- ALV+D+R R FF + LD + NP I RILFLDA D LV+RYKETRRSHPLAA G Sbjct: 63 ALVMDLRGREFFDRLIEALDEMAENPWITPRILFLDAKDSILVTRYKETRRSHPLAATGL 122- Query: 119 VLDGIRLERELLSPLKSMSQHVVDTTKLTPRQLRKTISDQFSEGSNQASFRIEVMSFGFK 17- 8 L+GI LERELL LK SQ + DT+ + PR LR+ I F+ + +F + VMSFGFK Sbjct: 123 PLEGIALERELLEELKGRSQIIYDTSDMKPRDLREKIVKHFATNQGE-TFTVNVMSFGFK 18- 1 Query: 179 YGLPLDADLVFDVRFLPNPYYQVELREKTGLDEDVFNYVMSHPESEVFYKHLLNLIVPIL 23- 8 YG+P+DADLVFDVRFLPNPYY +R TG D++V +YVM E++ F + L++L+ +L Sbjct: 182 YGIPIDADLVFDVRFLPNPYYIESMRPLTGKDKEVSSYVMKWNETQKFNEKLIDLLSFML 24- 1 Query: 239 PAYQKEGKSVLTVAIGCTGGQHRSVAFAHCLAESLATDWSVNESHRDQNRR 289 P+Y++EGKS + +AIGCTGGQHRSV A LA+ D+ + +HRD +R Sbjct: 242 PSYKREGKSQVVIAIGCTGGQHRSVTLAENLADYFKKDYYTHVTHRDIEKR 292 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05445 Identities = 234/296 (79%), Positives = 263/296 (88%) Query: 1 MSDEQIKLVIVTGMSGAGKTVAIQSFEDLGYFTIDNMPPTLVPKFLELAAQSGDTSKIAM 60 MSD+ I LVIVTGMSGAGKTVAIQSFEDLGYFTIDNMPP LVPKFLEL Q+ + ++A+ Sbjct: 1 MSDKHINLVIVTGMSGAGKTVAIQSFEDLGYFTIDNMPPALVPKFLELIEQTNENRRVAL 60 Query: 61 VVDMRSRLFFREINSILDSLEINDNINFKILFLDATDTELVSRYKETRRSHPLAADGRVL 120- VVDMRSRLFF+EINS LDS+E N +I+F+ILFLDATD ELVSRYKETRRSHPLAADGRVL Sbjct: 61 VVDMRSRLFFKEINSTLDSIESNPSIDFRILFLDATDGELVSRYKETRRSHPLAADGRVL 120- Query: 121 DGISLERELLAPLKSMSQNVVDTSELTPRQLRKVISKEFSNQDSQSSFRIEVMSFGFKYG 18- 0 DGI LERELL+PLKSMSQ+VVDT++LTPRQLRK IS +FS +Q+SFRIEVMSFGFKYG Sbjct: 121 DGIRLERELLSPLKSMSQHVVDTTKLTPRQLRKTISDQFSEGSNQASFRIEVMSFGFKYG 18- 0 Query: 181 IPLDADLVFDVRFLPNPYYKPELRDKTGLDTEVYDYVMSFDESDDFYDHLLALIKPILPG 24- 0 +PLDADLVFDVRFLPNPYY+ ELR+KTGLD +V++YVMS ES+ FY HLL LI PILP Sbjct: 181 LPLDADLVFDVRFLPNPYYQVELREKTGLDEDVFNYVMSHPESEVFYKHLLNLIVPILPA 24- 0 Query: 241 YQNEGKSVLTVAIGCTGGQHRSTAFAHRLSEDLKADWTVNESHRDKNKRKETVNRS 296 YQ EGKSVLTVAIGCTGGQHRS AFAH L+E L DW+VNESHRD+N+RKETVNRS Sbjct: 241 YQKEGKSVLTVAIGCTGGQHRSVAFAHCLAESLATDWSVNESHRDQNRRKETVNRS 296 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1780 A DNA sequence (GBSx1887) was identified in S. agalactiae <SEQ ID 5533> which encodes the amino acid sequence <SEQ ID 5534>. Analysis of this protein sequence reveals the following:

TABLE-US-05446 Possible site: 36 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05447 >GP:CAB96620 GB:AJ400630 hypothetical protein [Streptococcus pneumoniae bacteriophage MM1] Identities = 254/321 (79%), Positives = 286/321 (88%), Gaps = 1/321 (0%) Query: 1 MRKPKITVIGGGTGIPVILKSLRLEDVEITAVVTVADDGGSSGELRSVMQ-LTPPGDLRN 59 MRKPKITVIGGGTGIPVILKSLR +DVEI A+VTVADDGGSSGELR MQ LTPPGDLRN Sbjct: 1 MRKPKITVIGGGTGIPVILKSLREKDVEIAAIVTVADDGGSSGELRKNMQQLTPPGDLRN 60 Query: 60 VLVALSDMPKFYEQIFQYRFAEGDGDFAGHPLGNLIIAGVAEMQGSTYNAMQSLTQFFHT 119- VLVA+SDMPKFYE++FQYRF+E G FAGHPLGNLIIAG++EMQGSTYNAMQ L++FFHT Sbjct: 61 VLVAMSDMPKFYEKVFQYRFSEDAGAFAGHPLGNLIIAGLSEMQGSTYNANQLLSKFFHT 120- Query: 120 TGKIYPSSEHPLTLHAVFKDGHEVVGESQIADYKGMIDHVYVTNTYNEETPTASRKVVDA 17- 9 TGKIYPSS+HPLTLHAVF+DG EV GES I D++G+ID+VYVTN N++TP ASR+VV Sbjct: 121 TGKIYPSSDHPLTLHAVFQDGTEVAGESHIVDHRGIIDNVYVTNALNDDTPLASRRVVQT 18- 0 Query: 180 ILESDMIVLGPGSLFTSILPNLVIPEIKQALLETRAEVAYVCNIMTQRGETEHFTDADHV 23- 9 ILESDMIVLGPGSLFTSILPN+VI EI +ALLET+AE+AYVCNIMTQRGETEHFTD+DHV Sbjct: 181 ILESDMIVLGPGSLFTSILPNIVIKEIGRALLETKAEIAYVCNIMTQRGETEHFTDSDHV 24- 0 Query: 240 EVLKRHLGQDAIDTVLVNIEKVPESYMENNHFDEYLVQVEHDFSGLRKHARRVISSNFLK 29- 9 EVL RHLG+ IDTVLVNIEKVP+ YM +N FDEYLVQVEHDF GL K RVISSNFL+ Sbjct: 241 EVLHRHLGRPFIDTVLVNIEKVPQEYMNSNRFDEYLVQVEHDFVGLCKQVSRVISSNFLR 30- 0 Query: 300 LEKGGAFHHGDFVVEELMNLV 320 LE GGAFH GD +V+ELM ++ Sbjct: 301 LENGGAFHDGDLIVDELMRII 321 A related DNA sequence was identified in S. pyogenes <SEQ ID 5535> which encodes the amino acid sequence <SEQ ID 5536>. Analysis of this protein sequence reveals the following: TABLE-US-05448 Possible site: 36 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05449 Identities = 251/320 (78%), Positives = 284/320 (88%) Query: 1 MRKPKITVIGGGTGIPVILKSLRLEDVEITAVVTVADDGGSSGELRSVMQLTPPGDLRNV 60 M+ PK+TVIGGGTGI +ILKSLR E V+ITAVVTVADDGGSSGELR+ MQL PPGDLRNV Sbjct: 1 MKNPKMTVIGGGTGISIILKSLRNEAVDITAVVTVADDGGSSGELRNAMQLAPPGDLRNV 60 Query: 61 LVALSDMPKFYEQIFQYRFAEGDGDFAGHPLGNLIIAGVAEMQGSTYNAMQSLTQFFHTT 120- L+A+SDMPKFYE++FQYRF E DG AGHPLGNLIIAG++EMQGSTYNA+Q LT+FFH T Sbjct: 61 LLAMSDMPKFYERVFQYRFNESDGALAGHPLGNLIIAGISEMQGSTYNAIQILTKFFHIT 120- Query: 121 GKIYPSSEHPLTLHAVFKDGHEVVGESQIADYKGMIDHVYVTNTYNEETPTASRKVVDAI 18- 0 GKIYPSSE LTLHAVFKDGHEV GES IA Y GMIDHVYVTNTYN++ P ASRKVV+AI Sbjct: 121 GKIYPSSEQALTLHAVFKDGHEVAGESSIAKYPGMIDHVYVTNTYNDQKPQASRKVVEAI 18- 0 Query: 181 LESDMIVLGPGSLFTSILPNLVIPEIKQALLETRAEVAYVCNIMTQRGETEHFTDADHVE 24- 0 LESDMIVLGPGSLFTSILPNLVIPEIK+AL +T+AEV Y+CNIMTQ GETE F+DADHV Sbjct: 181 LESDMIVLGPGSLFTSILPNLVIPEIKEALRQTKAEVVYICNIMTQYGETEQFSDADHVA 24- 0 Query: 241 VLKRHLGQDAIDTVLVNIEKVPESYMENNHFDEYLVQVEHDFSGLRKHARRVISSNFLKL 30- 0 VL +HLG+D IDTVLVN+ KVP++YM +N FDEYLVQV+HDF+GL + A+RVISS FL+L Sbjct: 241 VLNQHLGRDLIDTVLVNVAKVPQAYMNSNKFDEYLVQVDHDFAGLCRAAKRVISSYFLRL 30- 0 Query: 301 EKGGAFHHGDFVVEELMNLV 320 E GGAFH G+ VVEELMNLV Sbjct: 301 ENGGAFHDGNLVVEELMNLV 320 SEQ ID 5534 (GBS269) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 49 (lane 12; MW 35 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 54 (lane 5; MW 60.5 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1781 A DNA sequence (GBSx1888) was identified in S. agalactiae <SEQ ID 5537> which encodes the amino acid sequence <SEQ ID 5538>. Analysis of this protein sequence reveals the following: TABLE-US-05450 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2479(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05451 >GP: CAB96619 GB: AJ400630 hypothetical protein [Streptococcus pneumoniae bacteriophage MM1] Identities = 209/303 (68%), Positives = 260/303 (84%) Query: 1 MSFTVKVKEELLGHKSENKMELSAIIKMSGSLGLANHGLNLSITTENAKIARHIYSMLEE 60 MSFTV VKEE+LG ++ ELSAIIKMSGS+GL+ GL LS+ TENAK+ARH+Y Sbjct: 1 MSFTVAVKEEILGQHHLSRHELSAIIKMSGSIGLSTSGLTLSVVTENAKLARHLYESFLH 60 Query: 61 HYHLQPEIKYHQKTNLRKNRVYTVFIEEKVDVILADLKLADAFFGIETGIEHSILDNDEN 120- Y ++ EI++HQ++NLRKNRVYTVF +EKV +L+DL LAD+FFG+ETGI+ +IL ++E Sbjct: 61 FYEIKSEIRHHQRSNLRKNRVYTVFTDEKVQDLLSDLHLADSFFGLETGIDEAILSDEEA 120- Query: 121 GRAYLRGAFLSTGTVREPDSGKYQLEIFSVYLDHAQDLANLMKKFMLDAKVIEHKHGAVT 18- 0 GRAYL GAFL+ G++R+P+SGKYQLEI SVYLDHAQ +A+L+++F+LDAKV+E K GAVT Sbjct: 121 GRAYLCGAFLANGSIRDPESGKYQLEISSVYLDHAQGIASLLQQFLLDAKVLERKKGAVT 18- 0 Query: 181 YLQKAEDIMDFLIVIDAMEARDAFEEIKMIRETRNDINRANNVETANIARTITASMKTIN 24- 0 YLQ+AEDIMDFLIVI AM+ARD FE +K++RETRND+NRANN ETANIART++ASMKTIN Sbjct: 181 YLQRAEDIMDFLIVIGAMQARDDFERVKILRETRNDLNRANNAETANIARTVSASMKTIN 24- 0 Query: 241 NIIKIMDTIGFDALPSDLRQVAQVRVAHPDYSIQQIADSLETPLSKSGVNHRLRKINKIA 30- 0 NI KI D +G + LP DL++VAQ+R+ HPDYSIQQ+ADSL TPL+KSGVNHRLRKINKIA Sbjct: 241 NISKIKDIMGLENLPVDLQEVAQLRIQHPDYSIQQLADSLSTPLTKSGVNHRLRKINKIA 30- 0 Query: 301 DEL 303 DEL Sbjct: 301 DEL 303 A related DNA sequence was identified in S. pyogenes <SEQ ID 5539> which encodes the amino acid sequence <SEQ ID 5540>. Analysis of this protein sequence reveals the following: TABLE-US-05452 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1698(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05453 Identities = 222/303 (73%), Positives = 269/303 (88%) Query: 1 MSFTVKVKEELLGHKSENKMELSAIIKMSGSLGLANHGLNLSITTENAKIARHIYSMLEE 60 MSFT KVKEEL+ + + EL+AIIK+SGSLGLA+ L+LSITTENAKIAR+IYS++E+ Sbjct: 1 MSFTTKVKEELIHLSTGDNNELAAIIKLSGSLGLAHQSLHLSITTENAKIARYIYSLIED 60 Query: 61 HYHLQPEIKYHQKTNLRKNRVYTVFIEEKVDVILADLKLADAFFGIETGIEHSILDNDEN 120- Y + PEI+YHQKTNLRKNRVYTV++E+ V+ ILADLKLAD+FFG+ETGIE +L +D Sbjct: 61 AYVIVPEIRYHQKTNLRKNRVYTVYVEQGVETILADLKLADSFFGLETGIEPQVLSDDNA 120- Query: 121 GRAYLRGAFLSTGTVREPDSGKYQLEIFSVYLDHAQDLANLMKKFMLDAKVIEHKHGAVT 18- 0 GR+YL+GAFL+ G++R+P+SGKYQLEI+SVYLDHAQDLA LM+KFMLDAK IEHK GAVT Sbjct: 121 GRSYLKGAFLAAGSIRDPESGKYQLEIYSVYLDHAQDLAQLMQKFMLDAKTIEHKSGAVT 18- 0 Query: 181 YLQKAEDIMDFLIVIDAMEARDAFEEIKMIRETRNDINRANNVETANIARTITASMKTIN 24- 0 YLQKAEDIMDFLI+I AM ++ FE IK++RE RNDINRANN ETANIA+TI+ASMKTIN Sbjct: 181 YLQKAEDIMDFLIIIGAMSCKEDFEAIKLLREARNDINRANNAETANIAKTISASMKTIN 24- 0 Query: 241 NIIKIMDTIGFDALPSDLRQVAQVRVAHPDYSIQQIADSLETPLSKSGVNHRLRKINKIA 30- 0 NIIKIMDTIG ++LP +L+QVAQ+RV HPDYSIQQ+AD+LE P++KSGVNHRLRKINKIA Sbjct: 241 NIIKIMDTIGLESLPIELQQVAQLRVKHPDYSIQQVADALEFPITKSGVNHRLRKINKIA 30- 0 Query: 301 DEL 303 D+L Sbjct: 301 DDL 303 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1782 A DNA sequence (GBSx1889) was identified in S. agalactiae <SEQ ID 5541> which encodes the amino acid sequence <SEQ ID 5542>. This protein is predicted to be dipeptidase. Analysis of this protein sequence reveals the following: TABLE-US-05454 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3544(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05455 >GP: CAA86210 GB: Z38063 dipeptidase [Lactobacillus helveticus] Identities = 218/473 (46%), Positives = 310/473 (65%), Gaps = 14/473 (2%) Query: 3 CTTILVGKKASYDGSTMIARTEDSVNGDFTPKKLKVMTSKDQPRHYKSVLSNFEVD---L 59 CTTILVGKKAS DGSTMIAR+ED P+ KV+ +DQP+HY SV+S ++D L Sbjct: 6 CTTILVGKKASIDGSTMIARSEDG-GRVIIPEGFKVVNPEDQPKHYTSVISKQKIDDEDL 64 Query: 60 PDNPLPYTSVPDALGKDGIWGEAGINSKNVAMSATETITTNSRVLGADPLVSD---GIGE 116- + PL YTS PD GK+GIWG AGIN+ NVAM+ATETITTNSR+ G DP++ G+GE Sbjct: 65 AETPLRYTSAPDVSGKNGIWGAAGINADNVAMTATETITTNSRIQGVDPILDPSEGGLGE 124- Query: 117 EDILTLVLPYIQSAREGVERLGAILEKYGTYESNGIAFSDTEEIWWLETIGGHHWIARRV 17- 6 ED +TL LPY+ SA +GV+R+G ++EKYGTYE NG+AFSD + IW+LETIGGHHWIARR+ Sbjct: 125 EDFVTLTLPYLHSAFDGVKRVGYLVEKYGTYEMNGMAFSDKDNIWYLETIGGHHWIARRI 18- 4 Query: 177 PDDVYVTNPNQLGIDHFEFNNCDDYMCSSDLKEFIEQYHLDLTYSNEHFNPRYAFGSQRD 23- 6 PDD YV PN+L ID F+F++ +++ +SDLK+ I++YHL+ E +N R+ FGS Sbjct: 185 PDDAYVIAPNRLNIDTFDFDDSENFAAASDLKDLIDEYHLN--PDREGYNMRHIFGSSTI 24- 2 Query: 237 KDRHYNTPRSWAMQRFLNPEIEQDPRSLFIPWCQKPYRKITVEDIKYVLSDHYQDSVYDP 29- 6 KD HYN PR+W + + +P+ P P+ + R I++EDIK+ S HYQD+ YD Sbjct: 243 KDAHYNNPRAWYIHNYFDPDFGGTPADQDQPFICRANRLISIEDIKWAESSHYQDTPYDA 30- 2 Query: 297 YGPEGDAVSRRAFRSVGINRTSQTSILQLRPNKSLETTGVQWLSYGSMPFATMVPLFTQV 35- 6 YG +G ++ FR +GINR +T ILQ+R + E GVQWL++G F +M+P +T V Sbjct: 303 YGDQGTPEQKKTFRPIGINRNFETHILQIRNDVPAEIAGVQWLAFGPNTFNSMLPFYTNV 36- 2 Query: 357 ETVPNYFSNTTKDASTDNFYWTNRLIAALADPHFYQHEADIESYIERTMAQGHAHINGVD 41- 6 T P + T K + + +W N+L A L D ++ + +++ ++++AQ H + D Sbjct: 363 TTTPEAWQTTPK-FNLNKIFWLNKLTAQLGDTNYRVYGELEDAFEQKSLAQCHKIQHETD 42- 1 Query: 417 REVAENKEIDFQQK----NQEMSDYIQKESQELLNRILFDASNLMTNRFSMGD 465 +EV + Q K NQ+MSD + + ELL +++ + LMT ++ + D Sbjct: 422 KEVKNLSGKELQDKLIAANQKMSDTVYNNTVELLGQMVDEGHGLMTLKYDLLD 474 A related DNA sequence was identified in S. pyogenes <SEQ ID 5543> which encodes the amino acid sequence <SEQ ID 5544>. Analysis of this protein sequence reveals the following: TABLE-US-05456 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0514(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05457 Identities = 345/464 (74%), Positives = 407/464 (87%) Query: 2 ACTTILVGKKASYDGSTMIARTEDSVNGDFTPKKLKVMTSKDQPRHYKSVLSNFEVDLPD 61 +CTTILVGKKASYDGSTM+ARTEDS NGDFTPKK+ V+ +DQPRHY+SV S+FE+DLPD Sbjct: 9 SCTTILVGKKASYDGSTMVARTEDSQNGDFTPKKMIVVKPEDQPRHYRSVQSSFEMDLPD 68 Query: 62 NPLPYTSVPDALGKDGIWGEAGINSKNVAMSATETITTNSRVLGADPLVSDGIGEEDILT 121- NP+ YTSVPDALGKDGIW EAG+N NVAMSATETITTNSRVLGADPLV+ GIGEED++T Sbjct: 69 NPMTYTSVPDALGKDGIWAEAGVNEANVAMSATETITTNSRVLGADPLVASGIGEEDMVT 128- Query: 122 LVLPYIQSAREGVERLGAILEKYGTYESNGIAFSDTEEIWWLETIGGHHWIARRVPDDVY 18- 1 LVLPYI+SAREGV RLGAILE YGTYESNG+AFSD +IWWLETIGGHHWIARRVPDD Y Sbjct: 129 LVLPYIRSAREGVLRLGAILEDYGTYESNGVAFSDEHDIWWLETIGGHHWIARRVPDDAY 18- 8 Query: 182 VTNPNQLGIDHFEFNNCDDYMCSSDLKEFIEQYHLDLTYSNEHFNPRYAFGSQRDKDRHY 24- 1 VTNPNQ GIDHFEFNN +DY+CS+DLK+FI+ YHLDLTYS+EHFNPRYAFGSQRDKDR Y Sbjct: 189 VTNPNQFGIDHFEFNNPEDYLCSADLKDFIDTYHLDLTYSHEHFNPRYAFGSQRDKDRQY 24- 8 Query: 242 NTPRSWAMQRFLNPEIEQDPRSLFIPWCQKPYRKITVEDIKYVLSDHYQDSVYDPYGPEG 30- 1 NTPR+W MQ+FLNPEI QDPRS + WCQKPYRKITVED+KYVLS HYQD+ YDPYG EG Sbjct: 249 NTPRAWIMQKFLNPEIVQDPRSFALAWCQKPYRKITVEDVKYVLSSHYQDTGYDPYGSEG 30- 8 Query: 302 DAVSRRAFRSVGINRTSQTSILQLRPNKSLETTGVQWLSYGSMPFATMVPLFTQVETVPN 36- 1 VS++ FR +GINRTSQT+IL +RPNK E +QW++YGSMPF TMVP FTQV+T+P+ Sbjct: 309 TPVSKKVFRPIGINRTSQTAILHIRPNKPQEIAAIQWMAYGSMPFNTMVPFFTQVKTIPD 36- 8 Query: 362 YFSNTTKDASTDNFYWTNRLIAALADPHFYQHEADIESYIERTMAQGHAHINGVDREVAE 42- 1 YF+NT ++ TDNFYWTNRLIAALADPH+ HE D+++Y+E TMA+GHA ++ V+ ++ Sbjct: 369 YFANTYENVFTDNFYWTNRLIAALADPHYNHHETDLDNYLEETMAKGHAMLHAVEVQLLA 42- 8 Query: 422 NKEIDFQQKNQEMSDYIQKESQELLNRILFDASNLMTNRFSMGD 465 + +D +++NQ+MSDY+Q E+Q LLN+ILFDASNLMTNRFS+ D Sbjct: 429 GETVDLEEENQKMSDYVQGETQTLLNKILFDASNLMTNRFSLSD 472 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1783 A DNA sequence (GBSx1890) was identified in S. agalactiae <SEQ ID 5545> which encodes the amino acid sequence <SEQ ID 5546>. Analysis of this protein sequence reveals the following: TABLE-US-05458 Possible site: 15 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05459 >GP:CAA96185 GB:Z71552 AdcA protein [Streptococcus pneumoniae] Identities = 257/429 (59%), Positives = 312/429 (71%), Gaps = 7/429 (1%) Query: 1 MRKKFLLLMSFVAMFAAWQLVQVKQVWADSKLKVVTTFYPVYEFTKNVVGDKADVSMLIK 60- M+K LLL S A+F + Q AD KL +VTTFYPVYEFTK V GD A+V +LI Sbjct: 1 MKKISLLLASLCALFL---VACSNQKQADGKLNIVTTFYPVYEFTKQVAGDTANVELLIG 57- Query: 61 AGTEPHDFEPSTKNIAAIQDSNAFVYMDDNMETWAPKVAKSVKSKKVTTIKGTGDMLLTK 12- 0 AGTEPH++EPS K +A IQD++ FVY ++NMETW PK+ ++ KKV TIK TGDMLL Sbjct: 58 AGTEPHEYEPSAKAVAKIQDADTFVYENENMETWVPKLLDTLDKKKVKTIKATGDMLLLP 11- 7 Query: 121 GVEEEGEEHEGHGHEGHHHELDPHVWLSPERAISVVENIRNKFVKAYPKDAASFNKNADA 18- 0 G EEE +H+ HG EGHHHE DPHVWLSP RAI +VE+IR+ YP +F KNA A Sbjct: 118 GGEEEEGDHD-HGEEGHHHEFDPHVWLSPVRAIKLVEHIRDTLSADYPDKKETFEKNAAA 17- 6 Query: 181 YIAKLKELDKEYKNGLSNAKQKSFVTQHAAFGYMALDYGLNQVPIAGLTPDAEPSSKRLG 24- 0 YI KL+ LDK Y GLS AK+KSFVTQHAAF Y+ALDYGL QV I+GL+PDAEPS+ RL Sbjct: 177 YIEKLQSLDKAYAEGLSQAKEKSFVTQHAAFNYLALDYGLKQVAISGLSPDAEPSAARLA 23- 6 Query: 241 ELAKYIKKYNINYIYFEENASNKVAKTLADEVGVKTAVLSPLEGLSKKEMAAGEDYFSVM 30- 0 EL +Y+KK I YIYFEENAS +A TL+ E GVKT VL+PLE L++++ AGE+Y SVM Sbjct: 237 ELTEYVKKNKIAYIYFEENASQALANTLSKEAGVKTDVLNPLESLTEEDTKAGENYISVM 29- 6 Query: 301 RRNLKVLKKTTDVAGKEVAPEE-DKTKTVETGYFKTKDVKDRKLTDYSGNWQSVYPLLQD 35- 9 +NLK LK+TTD G + PE+ + TKTV+ GYF+ VKDR L+DY+GNWQSVYP L+D Sbjct: 297 EKNLKALKQTTDQEGPAIEPEKAEDTKTVQNGYFEDAAVKDRTLSDYAGNWQSVYPFLED 35- 6 Query: 360 GTLDPVWDYKAKSKKDMTAAEYKKYYTAGYKTDVESIKIDGKKHQMTFVRNGKSQTFTYK 41- 9 GT D V+DYKAK MT AEYK YYT GY+TDV I I + M FV+ G+S+ +TYK Sbjct: 357 GTFDQVFDYKAKLTGKMTQAEYKAYYTKGYQTDVTKINI--TDNTMEFVQGGQSKKYTYK 41- 4 Query: 420 YAGYKILTY 428 Y G KILTY Sbjct: 415 YVGKKILTY 423 A related DNA sequence was identified in S. pyogenes <SEQ ID 5547> which encodes the amino acid sequence <SEQ ID 5548>. Analysis of this protein sequence reveals the following: TABLE-US-05460 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: TABLE-US-05461 >GP:CAA96185 GB:Z71552 AdcA protein [Streptococcus pneumoniae] Identities = 259/438 (59%), Positives = 326/438 (74%), Gaps = 16/438 (3%) Query: 1 MKKKILLMMSLISVFFAWQLTQAKQVLAEGKVKVVTTFYPVYEFTKGVIGNDGDVFMLMK 60- MKK LL+ SL ++F + + Q A+GK+ +VTTFYPVYEFTK V G+ +V +L+ Sbjct: 1 MKKISLLLASLCALFL---VACSNQKQADGKLNIVTTFYPVYEFTKQVAGDTANVELLIG 57- Query: 61 AGTEPHDFEPSTKDIKKIQDADAFVYMDDNMETWVSDVKKSLTSKKVTIVKGTGNMLLVA 12- 0 AGTEPH++EPS K + KIQDAD FVY ++NMETWV + +L KKV +K TG+MLL+ Sbjct: 58 AGTEPHEYEPSAKAVAKIQDADTFVYENENMETWVPKLLDTLDKKKVKTIKATGDMLLLP 11- 7 Query: 121 GAGHDHPHEDADKKHEHNKHSEEGHNHAFDPHVWLSPYRSITVVENIRDSLSKAYPEKAE 18- 0 G E+ + H+H EEGH+H FDPHVWLSP R+I +VE+IRD+LS YP+K E Sbjct: 118 GG------EEEEGDHDHG---EEGHHHEFDPHVWLSPVRAIKLVEHIRDTLSADYPDKKE 16- 8 Query: 181 NFKANAATYIEKLKELDKDYTAALSDAKQKSFVTQHAAFGYMALDYGLNQISINGVTPDA 24- 0 F+ NAA YIEKL+ LDK Y LS AK+KSFVTQHAAF Y+ALDYGL Q++I+G++PDA Sbjct: 169 TFEKNAAAYIEKLQSLDKAYAEGLSQAKEKSFVTQHAAFNYLALDYGLKQVAISGLSPDA 22- 8 Query: 241 EPSAKRIATLSKYVKKYGIKYIYFEENASSKVAKTLAKEAGVKAAVLSPLEGLTEKEMKA 30- 0 EPSA R+A L++YVKK I YIYFEENAS +A TL+KEAGVK VL+PLE LTE++ KA Sbjct: 229 EPSAARLAELTEYVKKNKIAYIYFEENASQALANTLSKEAGVKTDVLNPLESLTEEDTKA 28- 8 Query: 301 GQDYFTVMRKNLETLRLTTDVAGKEILPEK-DTTKTVYNGYFKDKEVKDRQLSDWSGSWQ 35- 9 G++Y +VM KNL+ L+ TTD G I PEK + TKTV NGYF+D VKDR LSD++G+WQ Sbjct: 289 GENYISVMEKNLKALKQTTDQEGPAIEPEKAEDTKTVQNGYFEDAAVKDRTLSDYAGNWQ 34- 8 Query: 360 SVYPYLQDGTLDQVWDYKAKKSKGKMTAAEYKDYYTTGYKTDVEQIKINGKKKTMTFVRN 41- 9 SVYP+L+DGT DQV+DYKAK + GKMT AEYK YYT GY+TDV KIN TM FV+ Sbjct: 349 SVYPFLEDGTFDQVFDYKAKLT-GKMTQAEYKAYYTKGYQTDV--TKINITDNTMEFVQG 40- 5 Query: 420 GEKKTFTYTYAGKEILTY 437 G+ K +TY Y GK+ILTY Sbjct: 406 GQSKKYTYKYVGKKILTY 423 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-05462 Identities = 353/515 (68%), Positives = 422/515 (81%), Gaps = 9/515 (1%) Query: 1 MRKKFLLLMSFVAMFAAWQLVQVKQVWADSKLKVVTTFYPVYEFTKNVVGDKADVSMLIK 60- M+KK LL+MS +++F AWQL Q KQV A+ K+KVVTTFYPVYEFTK V+G+ DV ML+K Sbjct: 1 MKKKILLMMSLISVFFAWQLTQAKQVLAEGKVKVVTTFYPVYEFTKGVIGNDGDVFMLMK 60- Query: 61 AGTEPHDFEPSTKNIAAIQDSNAFVYMDDNMETWAPKVAKSVKSKKVTTIKGTGDMLLTK 12- 0 AGTEPHDFEPSTK+I IQD++AFVYMDDNMETW V KS+ SKKVT +KGTG+MLL Sbjct: 61 AGTEPHDFEPSTKDIKKIQDADAFVYMDDNMETWVSDVKKSLTSKKVTIVKGTGNMLLVA 12- 0 Query: 121 GV--------EEEGEEHEGHGHEGHHHELDPHVWLSPERAISVVENIRNKFVKAYPKDAA 17- 2 G ++ EH H EGH+H DPHVWLSP R+I+VVENIR+ KAYP+ A Sbjct: 121 GAGHDHPHEDADKKHEHNKHSEEGHNHAFDPHVWLSPYRSITVVENIRDSLSKAYPEKAE 18- 0 Query: 173 SFNKNADAYIAKLKELDKEYKNGLSNAKQKSFVTQHAAFGYMALDYGLNQVPIAGLTPDA 23- 2 +F NA YI KLKELDK+Y LS+AKQKSFVTQHAAFGYMALDYGLNQ+ I G+TPDA Sbjct: 181 NFKANAATYIEKLKELDKDYTAALSDAKQKSFVTQHAAFGYMALDYGLNQISINGVTPDA 24- 0 Query: 233 EPSSKRLGELAKYIKKYNINYIYFEENASNKVAKTLADEVGVKTAVLSPLEGLSKKEMAA 29- 2 EPS+KR+ L+KY+KKY I YIYFEENAS+KVAKTLA E GVK AVLSPLEGL++KEM A Sbjct: 241 EPSAKRIATLSKYVKKYGIKYIYFEENASSKVAKTLAKEAGVKAAVLSPLEGLTEKEMKA 30- 0 Query: 293 GEDYFSVMRRNLKVLKKTTDVAGKEVAPEEDKTKTVETGYFKTKDVKDRKLTDYSGNWQS 35- 2 G+DYF+VMR+NL+ L+ TTDVAGKE+ PE+D TKTV GYFK K+VKDR+L+D+SG+WQS Sbjct: 301 GQDYFTVMRKNLETLRLTTDVAGKEILPEKDTTKTVYNGYFKDKEVKDRQLSDWSGSWQS 36- 0 Query: 353 VYPLLQDGTLDPVWDYKA-KSKKDMTAAEYKKYYTAGYKTDVESIKIDGKKHQMTFVRNG 41- 1 VYP LQDGTLD VWDYKA KSK MTAAEYK YYT GYKTDVE IKI+GKK MTFVRNG Sbjct: 361 VYPYLQDGTLDQVWDYKAKKSKGKMTAAEYKDYYTTGYKTDVEQIKINGKKKTMTFVRNG 42- 0 Query: 412 KSQTFTYKYAGYKILTYKKGNRGVRYLFEAKEKDAGQFKYIQFSDHGIKPNKAEHFHIFW 47- 1 ++TFTY YAG +ILTY KGNRGVR++FEAKE DAG+FKY+QFSDH I P KA+HFH++W Sbjct: 421 EKKTFTYTYAGKEILTYPKGNRGVRFMFEAKEADAGEFKYVQFSDHAIAPEKAKHFHLYW 48- 0 Query: 472 GSESQEKLFEEMENWPTYFPAKMSGREVAQDLMSH 506 G +SQEKL +E+E+WPTY+ + +SGRE+AQ++ +H Sbjct: 481 GGDSQEKLHKELEHWPTYYGSDLSGREIAQEINAH 515 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8899> and protein <SEQ ID 8900> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05463 Lipop: Possible site: -1 Crend: 3 SRCFLG: 0 McG: Length of UR: 19 Peak Value of UR: 2.79 Net Charge of CR: 3 McG: Discrim Score: 9.08 GvH: Signal Score (-7.5): 2.59 Possible site: 15 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 16 ALOM program count: 0 value: 7.69 threshold: 0.0 PERIPHERAL Likelihood = 7.69 264 modified ALOM score: -2.04 *** Reasoning Step: 3 Rule gpol ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: TABLE-US-05464 3758895|emb|CAA96185.1||Z71552 AdcA protein {Streptococcus pneumoniae} >PIR|T46756|T46756 Zn-binding lipoprotein adcA [imported] - Streptococcus pneumoniae (fragment) Score = 508 bits (1294), Expect = e-143 Identities = 257/429 (59%), Positives = 312/429 (71%), Gaps = 7/429 (1%) Query: 1 MRKKFLLLMSFVAMFAAWQLVQVKQVWADSKLKVVTTFYPVYEFTKNVVGDKADVSMLIK 60- M+K LLL S A+F + Q AD KL +VTTFYPVYEFTK V GD A+V +LI Sbjct: 1 MKKISLLLASLCALFL---VACSNQKQADGKLNIVTTFYPVYEFTKQVAGDTANVELLIG 57- Query: 61 AGTEPHDFEPSTKNIAAIQDSNAFVYMDDNMETWAPKVAKSVKSKKVTTIKGTGDMLLTK 12- 0 AGTEPH++EPS K +A IQD++ FVY ++NMETW PK+ ++ KKV TIK TGDMLL Sbjct: 58 AGTEPHEYEPSAKAVAKIQDADTFVYENENMETWVPKLLDTLDKKKVKTIKATGDMLLLP 11- 7 Query: 121 GVEEEGEEHEGHGHEGHHHELDPHVWLSPERAISVVENIRNKFVKAYPKDAASFNKNADA 18- 0 G EEE +H+ HG EGHHHE DPHVWLSP RAI +VE+IR+ YP +F KNA A Sbjct: 118 GGEEEEGDHD-HGEEGHHHEFDPHVWLSPVRAIKLVEHIRDTLSADYPDKKETFEKNAAA 17- 6 Query: 181 YIAKLKELDKEYKNGLSNAKQKSFVTQHAAFGYMALDYGLNQVPIAGLTPDAEPSSKRLG 24- 0 YI KL+ LDK Y GLS AK+KSFVTQHAAF Y+ALDYGL QV I+GL+PDAEPS+ RL Sbjct: 177 YIEKLQSLDKAYAEGLSQAKEKSFVTQHAAFNYLALDYGLKQVAISGLSPDAEPSAARLA 23- 6 Query: 241 ELAKYIKKYNINYIYFEENASNKVAKTLADEVGVKTAVLSPLEGLSKKEMAAGEDYFSVM 30- 0 EL +Y+KK I YIYFEENAS +A TL+ E GVKT VL+PLE L++++ AGE+Y SVM Sbjct: 237 ELTEYVKKNKIAYIYFEENASQALANTLSKEAGVKTDVLNPLESLTEEDTKAGENYISVM 29- 6 Query: 301 RRNLKVLKKTTDVAGKEVAPEE-DKTKTVETGYFKTKDVKDRKLTDYSGNWQSVYPLLQD 35- 9 +NLK LK+TTD G + PE+ + TKTV+ GYF+ VKDR L+DY+GNWQSVYP L+D Sbjct: 297 EKNLKALKQTTDQEGPAIEPEKAEDTKTVQNGYFEDAAVKDRTLSDYAGNWQSVYPFLED 35- 6 Query: 360 GTLDPVWDYKAKSKKDMTAAEYKKYYTAGYKTDVESIKIDGKXHQMTFVRNGKSQTFTYK 41- 9 GT D V+DYKAK MT AEYK YYT GY+TDV I I + M FV+ G+S+ +TYK Sbjct: 357 GTFDQVFDYKAKLTGKMTQAEYKAYYTKGYQTDVTKINI--TDNTMEFVQGGQSKKYTYK 41- 4 Query: 420 YAGYKILTY 428 Y G KILTY Sbjct: 415 YVGKKILTY 423 SEQ ID 8900 (GBS325) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 65 (lane 3; MW 58 kDa). The GBS325-His fusion product was purified (FIG. 210, lane 7) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 257A) and FACS (FIG. 257B). These tests confirm that the protein is immunoaccessible on GBS bacteria. EXAMPLE 1784 A DNA sequence (GBSx1891) was identified in S. agalactiae <SEQ ID 5549> which encodes the amino acid sequence <SEQ ID 5550>. This protein is predicted to be ribosomal protein L31 (r131). Analysis of this protein sequence reveals the following: TABLE-US-05465 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1948 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> A related GBS nucleic acid sequence <SEQ ID 9637> which encodes amino acid sequence <SEQ ID 9638> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05466 >GP:AAF80389 GB:AF160251 ribosomal protein L31 [Listeria innocua] Identities = 61/81 (75%), Positives = 71/81 (87%), Gaps = 1/81 (1%) Query: 9 MKKDIHPDYRPVVFLDTTTGYKFLSGSTKSTKETVEFE-GETYPLIRVEISSDSHPFYTG 67 - MK IHP+YRPVVF+DT+T +KFLSGSTKS+ ET+++E G YPL+RVEISSDSHPFYTG Sbjct: 1 MKTGIHPEYRPVVFVDTSTDFKFLSGSTKSSSETIKWEDGNEYPLLRVEISSDSHPFYTG 60 Query: 68 RQKFTQADGRVDRFNKKYGLK 88 +QK ADGRVDRFNKKYGLK Sbjct: 61 KQKHATADGRVDRFNKKYGLK 81 A related DNA sequence was identified in S. pyogenes <SEQ ID 5551> which encodes the amino acid sequence <SEQ ID 5552>. Analysis of this protein sequence reveals the following: TABLE-US-05467 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1910 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05468 Identities = 81/86 (94%), Positives = 86/86 (99%) Query: 9 MKKDIHPDYRPVVFLDTTTGYKFLSGSTKSTKETVEFEGETYPLIRVEISSDSHPFYTGR 68 - M+KDIHPDYRPVVFLDTTTGY+FLSGSTK++KETVEFEGETYPLIRVEISSDSHPFYTGR Sbjct: 1 MRKDIHPDYPRVVFLDTTTGYQFLSGSTKASKETVEFEGETYPLIRVEISSDSHPFYTGR 60 Query: 69 QKFTQADGRVDRFNKKYGLKDANAAQ 94 QKFTQADGRVDRFNKKYGLKDANAA+ Sbjct: 61 QKFTQADGRVDRFNKKYGLKDANAAK 86 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1785 A DNA sequence (GBSx1892) was identified in S. agalactiae <SEQ ID 5553> which encodes the amino acid sequence <SEQ ID 5554>. This protein is predicted to be aspartate aminotransferase (aspC). Analysis of this protein sequence reveals the following: TABLE-US-05469 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1740(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9421> which encodes amino acid sequence <SEQ ID 9422> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05470 >GP: AAC21948 GB: U32714 aminotransferase [Haemophilus influenzae Rd] Identities = 200/323 (61%), Positives = 264/323 (80%), Gaps = 1/323 (0%) Query: 1 MQYYQLQNI-HVDMDDIYIVNGVSEGISMSMQALLDNDDEVLVPMPDYPLWTACVSLAGG 59 +QYYQ + I ++D+YI NGVSE I+M+MQALL++ DEVLVPMPDYPLWTA V+L+GG Sbjct: 82 VQYYQSKGILGATVNDVYIGNGVSELITMAMQALLNDGDEVLVPMPDYPLWTAAVTLSGG 141- Query: 60 NAVHYICDEEANWYPDIDDIKSKITSKTKAIVLINPNNPTGAVYPREILQEIVDIARQND 119- AVHY+CDE+ANW+P IDDIK+K+ +KTKAIV+INPNNPTGAVY +E+LQEIV+IARQN+ Sbjct: 142 KAVHYLCDEDANWFPTIDDIKAKVNAKTKAIVIINPNNPTGAVYSKELLQEIVEIARQNN 20- 1 Query: 120 LIIFSDEVYDRLVMDGMEHIPIASIAEDIFTVTLSGLSKSHRICGFRVGWMVLSGPRQHV 17- 9 LIIF+DE+YD+++ DG H IA++A D+ TVTL+GLSK++R+ GFR GWM+L+GP+ + Sbjct: 202 LIIFADEIYDKILYDGAVHHHIAALAPDLLTVTLNGLSKAYRVAGFRQGWMILNGPKHNA 26- 1 Query: 180 KGYIEGLNMLANMRLCSNVLAQQVIQTSLGGQQSIDSMLLPGGRIYEQRNYIHKAINEIP 23- 9 KGYIEGL+MLA+MRLC+NV Q IQT+LGG QSI+ +LPGGR+ EQRN + I +IP Sbjct: 262 KGYIEGLDMLASMRLCANVPMQHAIQTALGGYQSINEFILPGGRLLEQRNKAYDLITQIP 32- 1 Query: 240 GLSAVKPNAGLYLFPKIDTDMYRIDNDEEFVLNFLKQEKVLLTHGRGFNMNTADHFRIVY 29- 9 G++ VKP +Y+FPKID + I +DE+ VL+ L+QEKVLL HG+GFN ++ DHFRIV Sbjct: 322 GITCVKPMGAMYMFPKIDVKKFNIHSDEKMVLDLLRQEKVLLVHGKGFNWHSPDHFRIVT 38- 1 Query: 300 LPRVDELTELQEKMARFLSQYKR 322 LP V++L E K+ARFLS Y++ Sbjct: 382 LPYVNQLEEAITKLARFLSDYRQ 404 There is also homology to SEQ ID 3662. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1786 A DNA sequence (GBSx1893) was identified in S. agalactiae <SEQ ID 5555> which encodes the amino acid sequence <SEQ ID 5556>. Analysis of this protein sequence reveals the following: TABLE-US-05471 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.02 Transmembrane 164-180 (163-181) ----- Final Results ----- bacterial membrane --- Certainty = 0.1808(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10099> which encodes amino acid sequence <SEQ ID 10100> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05472 >GP: BAB06181 GB: AP001515 transcriptional pleiotropic repressor [Bacillus halodurans] Identities = 129/257 (50%), Positives = 181/257 (70%), Gaps = 3/257 (1%) Query: 23 NLLEKTRKITSILQRSVDSLDAELPYNTMAAQLADIIDCNACIINGGGNLLGYAMKYKTN 82 - +LL + RKI +LQ+S + + MA L D+I N +++ G LLG+A+K + Sbjct: 2 SLLSRMRKINDMLQKSGVQ---HVNFREMAETLRDVISANIFVVSRRGKLLGFAIKQEIE 58 Query: 83 TDRVEEFFETKQFPDYYVKSASRVYDTEANLSVDNDLSIFPVETKENFQDGITTIAPIYG 142- +R+++ E +QFP+ Y +V +T ANL ++++ + FPVE KE F+ G+TTI PI G Sbjct: 59 NERMKKMLEDRQFPEEYTTGLFKVEETSANLDINSEFTAFPVENKELFKTGLTTIVPISG 118- Query: 143 GGMRLGTFIIWRNDKEFSDDDLILVEIASTVVGIQLLNLQTENLEENIRKQTAVTMAINT 20- 2 GG RLGT I+ R + F+DDDLIL E +TVVG+++L+ +T+ +EE R + V MAI++ Sbjct: 119 GGQRLGTLILARLNDSFNDDDLILAEYGATVVGMEILHEKTQEIEEEARSKAVVQMAISS 17- 8 Query: 203 LSYSEMKAVAAILGELDGLEGRLTASVIADRIGITRSVIVNALRKLESAGIIESRSLGMK 26- 2 LSYSE++AV I ELDG EG L AS IADR+GITRSVIVNALRKLESAG+IESRSLGMK Sbjct: 179 LSYSELEAVEHIFEELDGKEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMK 23- 8 Query: 263 GTYLKVINEGIFDKLKE 279 GTY+KV+N+ +L++ Sbjct: 239 GTYIKVLNDKFLVELEK 255 A related DNA sequence was identified in S. pyogenes <SEQ ID 5557> which encodes the amino acid sequence <SEQ ID 5558>. Analysis of this protein sequence reveals the following: TABLE-US-05473 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.64 Transmembrane 144-160 (143-161) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05474 >GP: CAB13490 GB: Z99112 transcriptional regulator [Bacillus subtilis] Identities = 131/255 (51%), Positives = 179/255 (69%), Gaps = 3/255 (1%) Query: 4 LLEKTRKITSILQRSVDSLETELPYNTMASRLADIIDCNACIINGGGTLLGYAMKYKTNT 63 LL+KTR I S+LQ + + + MA L D+ID N +++ G LLGY++ + Sbjct: 3 LLQKTRIINSMLQAAAGK---PVNFKEMAETLRDVIDSNIFVVSRRGKLLGYSINQQIEN 59 Query: 64 DRVEEFFEAKQFPDTYVKAASRVYDTEANLSVENELTIFPVESKDTYPGGLTTIAPIYGG 123- DR+++ E +QFP+ Y K V +T +NL + +E T FPVE++D + GLTTI PI GG Sbjct: 60 DRMKKMLEDRQFPEEYTKNLFNVPETSSNLDINSEYTAFPVENRDLFQAGLTTIVPIIGG 119- Query: 124 GMRLGSLIIWRNDNEFSDDDLILVEISSTVVGIQLLNLQTENLEDTIRKQTAVNMAINTL 18- 3 G RLG+LI+ R ++F+DDDLIL E +TVVG+++L + E +E+ R + V MAI++L Sbjct: 120 GERLGTLILSRLQDQFNDDDLILAEYGATVVGMEILREKAEEIEEEARSKAVVQMAISSL 17- 9 Query: 184 SYSEMKAVAAILGELDGNEGRLTASVIADRIGITRSVIVNALRKLESAGIIESRSLGMKG 24- 3 SYSE++A+ I ELDGNEG L AS IADR+GITRSVIVNALRKLESAG+IESRSLGMKG Sbjct: 180 SYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKG 23- 9 Query: 244 TYLKVINEGIFAKLK 258 TY+KV+N +L+ Sbjct: 240 TYIKVLNNKFLIELE 254 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05475 Identities = 232/260 (89%), Positives = 247/260 (94%) Query: 21 MPNLLEKTRKITSILQRSVDSLDAELPYNTMAAQLADIIDCNACIINGGGNLLGYAMKYK 80 - MPNLLEKTRKITSILQRSVDSL+ ELPYNTMA++LADIIDCNACIINGGG LLGYAMKYK Sbjct: 1 MPNLLEKTRKITSILQRSVDSLETELPYNTMASRLADIIDCNACIINGGGTLLGYAMKYK 60 Query: 81 TNTDRVEEFFETKQFPDYYVKSASRVYDTEANLSVDNDLSIFPVETKENFQDGITTIAPI 140- TNTDRVEEFFE KQFPD YVK+ASRVYDTEANLSV+N+L+IFPVE+K+ + G+TTIAPI Sbjct: 61 TNTDRVEEFFEAKQFPDTYVKAASRVYDTEANLSVENELTIFPVESKDTYPGGLTTIAPI 120- Query: 141 YGGGMRLGTFIIWRNDKEFSDDDLILVEIASTVVGIQLLNLQTENLEENIRKQTAVTMAI 20- 0 YGGGMRLG+ IIWRND EFSDDDLILVEI+STVVGIQLLNLQTENLE+ IRKQTAV MAI Sbjct: 121 YGGGMRLGSLIIWRNDNEFSDDDLILVEISSTVVGIQLLNLQTENLEDTIRKQTAVNMAI 18- 0 Query: 201 NTLSYSEMKAVAAILGELDGLEGRLTASVIADRIGITRSVIVNALRKLESAGIIESRSLG 26- 0 NTLSYSEMKAVAAILGELDG EGRLTASVIADRIGITRSVIVNALRKLESAGIIESRSLG Sbjct: 181 NTLSYSEMKAVAAILGELDGNEGRLTASVIADRIGITRSVIVNALRKLESAGIIESRSLG 24- 0 Query: 261 MKGTYLKVINEGIFDKLKEY 280 MKGTYLKVINEGIF KLKE+ Sbjct: 241 MKGTYLKVINEGIFAKLKEF 260 A related GBS gene <SEQ ID 8901> and protein <SEQ ID 8902> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05476 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: -6.84 GvH: Signal Score (-7.5): -5.37 Possible site: 13 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -2.02 threshold: 0.0 INTEGRAL Likelihood = -2.02 Transmembrane 114-130 (113-131) PERIPHERAL Likelihood = 3.61 179 modified ALOM score: 0.90 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1808(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00124## SEQ ID 8902 (GBS431) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 173 (lane 7; MW 54 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 77 (lane 6; MW 29 kDa). GBS431-GST was purified as shown in FIG. 223, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1787 A DNA sequence (GBSx1894) was identified in S. agalactiae <SEQ ID 5559> which encodes the amino acid sequence <SEQ ID 5560>. This protein is predicted to be isochorismatase. Analysis of this protein sequence reveals the following: TABLE-US-05477 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.81 Transmembrane 126-142 (125-142) ----- Final Results ----- bacterial membrane --- Certainty = 0.2126(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-05478 >GP: CAB15164 GB: Z99120 similar to pyrazinamidase/nicotinamidase [Bacillus subtilis] Identities = 99/181 (54%), Positives = 132/181 (72%) Query: 1 MTKALISIDYTYDFVADDGKLTAGKPAQSIASAIADVTEKAYRSGDYIFFAIDNHDIGDV 60 M KALI IDYT DFVA DGKLT G+P + I AI ++T++ +GDY+ A+D+HD GD Sbjct: 1 MKKALICIDYTNDFVASDGKLTCGEPGRMIEEAIVNLTKEFITNGDYVVLAVDSHDEGDQ 60 Query: 61 FHPESNLFPEHNIKGTSGRNLYGPLGTLYETIKEDSRVFWIDKRHYSAFSGTDLDIRLRE 120- +HPE+ LFP HNIKGT G++LYG L LY+ + + V++++K YSAF+GTDL+++LRE Sbjct: 61 YHPETRLFPPHNIKGTEGKDLYGKLLPLYQKHEHEPNVYYMEKTRYSAFAGTDLELKLRE 120- Query: 121 RRVDTLILTGVLTDICVLHTAIDAYNLGYKIEVPAAAVASLNDSNHQWALNHFKTVLGATI 1- 81 R++ L L GV TDICVLHTA+DAYN G++I V AVAS N H WAL+HF +GA + Sbjct: 121 RQIGELHLAGVCTDICVLHTAVDAYNKGFRIVVHKQAVASFNQEGHAWALSHFANSIGAQV 1- 81 A related DNA sequence was identified in S. pyogenes <SEQ ID 5561> which encodes the amino acid sequence <SEQ ID 5562>. Analysis of this protein sequence reveals the following: TABLE-US-05479 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.60 Transmembrane 126-142 (126-142) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05480 >GP: CAB15164 GB: Z99120 similar to pyrazinamidase/nicotinamidase [Bacillus subtilis] Identities = 90/179 (50%), Positives = 127/179 (70%) Query: 3 RALISIDYTNDFVADDGKLSAGKSAQAIATKIAEVTKTAFDQGDYIFFAIDCHDQNDSWH 62 +ALI IDYTNDFVA DGKL+ G+ + I I +TK GDY+ A+D HD+ D +H Sbjct: 3 KALICIDYTNDFVASDGKLTCGEPGRMIEEAIVNLTKEFITNGDYVVLAVDSHDEGDQYH 62 Query: 63 PESKLFAAHNIKGTTGRHLYGPLAEVYSYMKQHPRVFWIDKRYYSAFSGTDLDIRLRERG 122- PE++LF HNIKGT G+ LYG L +Y + P V++++K YSAF+GTDL+++LRER Sbjct: 63 PETRLFPPHNIKGTEGKDLYGKLLPLYQKHEHEPNVYYMEKTRYSAFAGTDLELKLRERQ 122- Query: 123 ITQLVLTGVLSDICVLHTAIDAYHLGYQLEIVKSAVASLTKESYEWSLAHFEQVLGAKL 181- I +L L GV +DICVLHTA+DAY+ G+++ + K AVAS +E + W+L+HF +GA++ Sbjct: 123 IGELHLAGVCTDICVLHTAVDAYNKGFRIVVHKQAVASFNQEGHAWALSHFANSIGAQV 181- An alignment of the GAS and GBS proteins is shown below. TABLE-US-05481 Identities = 121/180 (67%), Positives = 150/180 (83%) Query: 3 KALISIDYTYDFVADDGKLTAGKPAQSIASAIADVTEKAYRSGDYIFFAIDNHDIGDVFH 62 +ALISIDYT DFVADDGKL+AGK AQ+IA+ IA+VT+ A+ GDYIFFAID HD D +H Sbjct: 3 RALISIDYTNDFVADDGKLSAGKSAQAIATKIAEVTKTAFDQGDYIFFAIDCHDQNDSWH 62 Query: 63 PESNLFPEHNIKGTSGRNLYGPLGTLYETIKEDSRVFWIDKRHYSAFSGTDLDIRLRERR 122- PES LF HNIKGT+GR+LYGPL +Y +K+ RVFWIDKR+YSAFSGTDLDIRLRER Sbjct: 63 PESKLFAAHNIKGTTGRHLYGPLAEVYSYMKQHPRVFWIDKRYYSAFSGTDLDIRLRERG 122- Query: 123 VDTLILTGVLTDICVLHTAIDAYNLGYKIEVPAAAVASLNDSNHQWALNHFKTVLGATIL 18- 2 + L+LTGVL+DICVLHTAIDAY+LGY++E+ +AVASL +++W+L HF+ VLGA ++ Sbjct: 123 ITQLVLTGVLSDICVLHTAIDAYHLGYQLEIVKSAVASLTKESYEWSLAHFEQVLGAKLI 18- 2 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1788 A DNA sequence (GBSx1895) was identified in S. agalactiae <SEQ ID 5563> which encodes the amino acid sequence <SEQ ID 5564>. Analysis of this protein sequence reveals the following: TABLE-US-05482 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1539(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1789 A DNA sequence (GBSx1896) was identified in S. agalactiae <SEQ ID 5565> which encodes the amino acid sequence <SEQ ID 5566>. This protein is predicted to be 3-hydroxyacyl-CoA dehydrogenase (hbd-10). Analysis of this protein sequence reveals the following: TABLE-US-05483 Possible site: 46 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.27 Transmembrane 3-19 (1-19) INTEGRAL Likelihood = -0.11 Transmembrane 277-293 (277-294) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05484 >GP: AAF12219 GB: AE001862 3-hydroxyacyl-CoA dehydrogenase, putative [Deinococcus radiodurans] Identities = 151/321 (47%), Positives = 196/321 (61%), Gaps = 36/321 (11%) Query: 56 NMTIKNLTVAGSGVLGSQIAFQAAYKGMSVTIYDINDEALNKGKERIKKLAKVYQSEIET 115- +M+IK +TV GSGVLGSQIAFQ A+ G V +YDIND A+ K +E + KL YQ +++ Sbjct: 51 SMSIKTVTVCGSGVLGSQIAFQTAFHGFDVHLYDINDAAIAKARETLGKLQARYQQDLKV 110- Query: 116 AKEAYSDKAKSIKYNKNLLPSLDHIFLSKVADSLDLIADLPNQITFSKNLDQAVSDADLV 17- 5 + D +I+F ++ +AV DLV Sbjct: 111 DAQQTGDAFA--------------------------------RISFFTDIAEAVKGVDLV 13- 8 Query: 176 IEAVPETVSIKEDFYKQLAKVAPSKTIFATNSSTLVPSQFADITGRPDKFLAMHFANNIW 23- 5 IEA+PE + IK FY QL +VA TIFATNSSTL+PSQF + TGRP+KFLA+HFAN IW Sbjct: 139 IEAIPENMDIKRKFYNQLGEVADPNTIFATNSSTLLPSQFMEETGRPEKFLALHFANEIW 19- 8 Query: 236 QNNIVEIMGHKGTDDEVIKEALAFSKDIGMVPLHIHKEQPGYILNSILVPFLESALALYY 29- 5 + N EIM TDD V + F+KDIGMV L ++KEQ GYILN++LVP L +AL L Sbjct: 199 KFNTAEIMRTPRTDDAVFDTVVQFAKDIGMVALPMYKEQAGYILNTLLVPLLGAALELVV 25- 8 Query: 296 DKVSDSETIDKTWKLGTGAPMGPLEILDIIGIDTAYNIMKNYSDTNSDPNSLHAHLAKML 35- 5 ++D +T+DKTW + TGAP GP LD+IG+ T YNI N + ++P S A AK + Sbjct: 259 KGIADPQTVDKTWMIATGAPRGPFAFLDVIGLTTPYNI--NMASAETNPGS--AAAAKYI 31- 4 Query: 356 KEEFIDKGRTGKAAGHGFYDY 376 KE +IDKG+ G A G GFY Y Sbjct: 315 KENYIDKGKLGTATGEGFYKY 335 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8903> and protein <SEQ ID 8904> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05485 Lipop: Possible site: -1 Crend: 3 SRCFLG: 0 McG: Length of UR: 20 Peak Value of UR: 1.55 Net Charge of CR: 1 McG: Discrim Score: -0.60 GvH: Signal Score (-7.5): -3.93 Possible site: 21 >>> Seems to have no N-terminal signal sequence Amino Acid Composition: calculated from 1 ALOM program count: 1 value: -0.11 threshold: 0.0 INTEGRAL Likelihood = -0.11 Transmembrane 221-237 (221-238) PERIPHERAL Likelihood = 4.61 6 modified ALOM score: 0.52 icm1 HYPID: 7 CFP: 0.104 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1044(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00125## SEQ ID 8904 (GBS112) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 28 (lane 5; MW 39 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 34 (lane 3; MW 64 kDa). GBS112-GST was purified as shown in FIG. 198, lane 10. EXAMPLE 1790 A DNA sequence (GBSx1897) was identified in S. agalactiae <SEQ ID 5567> which encodes the amino acid sequence <SEQ ID 5568>. Analysis of this protein sequence reveals the following: TABLE-US-05486 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3332(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10097> which encodes amino acid sequence <SEQ ID 10098> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05487 >GP:CAB14467 GB:Z99117 similar to hypothetical proteins [Bacillus subtilis] Identities = 62/169 (36%), Positives = 109/169 (63%), Gaps = 3/169 (1%) Query: 1 MAVLSMLGIIDAKPKVGYFYLGQYHASIGTSHFEKMTVSEIMGIPLTVHQKDSVYDVIVH 60- +A+L+M G ++A+P+VGYFY G+ + +K+ V + IP+ +H+ SVYD I Sbjct: 43 LAILTMSGFLEARPRVGYFYTGKTGTQLLADKLKKLQVKDFQSIPVVIHENVSVYDAICT 10- 2 Query: 61 IFMEDAGCAFILDDDDFLCGVVSRKDLLKISIGGGDLSKMPIGMVMTRMPHVTTVLENES 12- 0 +F+ED G F++D D L GV+SRKDLL+ SIG +L+ +P+ ++MTRMP++T + Sbjct: 103 MFLEDVGTLFVVDRDAVLVGVLSRKDLLRASIGQQELTSVPVHIIMTRMPNITVCRREDY 16- 2 Query: 121 LFAAADKLVSRKVDSLPVVRHDKQYPEKFKVIGKLSKTILASLFLEIRD 169 + A L+ +++D+LPV+ K + F+VIG+++KT + + + + + Sbjct: 163 VMDIAKHLIEKQIDALPVI---KDTDKGFEVIGRVTKTNMTKILVSLSE 208 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1791 A DNA sequence (GBSx1898) was identified in S. agalactiae <SEQ ID 5569> which encodes the amino acid sequence <SEQ ID 5570>. Analysis of this protein sequence reveals the following: TABLE-US-05488 Possible site: 22 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.53 Transmembrane 60-76 (60-76) ----- Final Results ----- bacterial membrane --- Certainty = 0.1213 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05489 >GP:BAB05092 GB:AP001511 unknown conserved protein [Bacillus halodurans] Identities = 126/256 (49%), Positives = 183/256 (71%), Gaps = 1/256 (0%) Query: 7 IFIISDSLGETAKAIAKACLSQFPGHDDWHFQRFSYINSQERLEQVFEEASQKTVFMMFS 66- ++++SDS+GETA+ + KA SQF G +R Y+ +E +++V + A Q + F+ Sbjct: 10 VYVVSDSVGETAELVVKAAASQFSGAGI-EVRRIPYVEDKETVDEVIQLAKQADAIIAFT 68- Query: 67 LVDVALASYAQKRCESEHYAYVDLLTNVIQGISRISGIDPLGEPGILRRLDNDYFKRVES 12- 6 LV + +Y ++ VD++ +++ IS ++ +P EPGI+ RLD DYF++VE+ Sbjct: 69 LVVPGIRTYLLEKATEAKVETVDIIGPMLEKISSLTKEEPRYEPGIVYRLDEDYFRKVEA 12- 8 Query: 127 IEFAVKYDDGRDPRGILQADLVIIGISRTSKTPLSMFLADKNIKVINIPLVPEVPVPKEL 18- 6 IEFAVKYDDGRDPRGI++ADLV+IG+SRTSKTPLS +LA K +KV N+PLVPEV P+EL Sbjct: 129 IEFAVKYDDGRDPRGIVRADLVLIGVSRTSKTPLSQYLAHKRLKVANVPLVPEVEPPEEL 18- 8 Query: 187 RMIDSRRIIGLTNSVDHLNQVRKVRLKSLGLSSTANYASLERILEETRYAEEVMKNLGCP 24- 6 + +++IGL S + LN +R RLK+LGL S ANYA+++RI EE YAE +MK +GCP Sbjct: 189 FKLSPKKVIGLKISPEQLNGIRAERLKTLGLKSQANYANIDRIKEELAYAEGIMKRIGCP 24- 8 Query: 247 IINVSDKAIEETATII 262 +I+VS+KA+EETA +I Sbjct: 249 VIDVSNKAVEETANLI 264 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 5570 (GBS378) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 68 (lane 4; MW 34 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 2; MW 59 kDa). GBS378-GST was purified as shown in FIG. 212, lane 6. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1792 A DNA sequence (GBSx1899) was identified in S. agalactiae <SEQ ID 5571> which encodes the amino acid sequence <SEQ ID 5572>. Analysis of this protein sequence reveals the following: TABLE-US-05490 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3703 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05491 >GP:AAD35361 GB:AE001709 pyruvate, orthophosphate dikinase [Thermotoga maritima] Identities = 494/882 (56%), Positives = 639/882 (72%), Gaps = 9/882 (1%) Query: 1 METKFVYHFD----EGCKEMKELLGGKGANLAEMTSIGLPVPQGFTITTQACNDYYDNAC 56- M K+VY F EG +MK++LGGKGANLAEMT++G+PVP GFTI+ + C YYD+ Sbjct: 1 MAKKYVYFFANGKAEGRADMKDILGGKGANLAEMTNLGIPVPPGFTISAEVCKYYYDHGR 60- Query: 57 HIRESILSQIDQAMAQLEVEQNKQLGSVDDPLLVSVRSGSVFSMPGMMDTVLNLGLNDRS 11- 6 E + Q+++AM +LE K+ G ++PLLVSVRSG+ SMPGMMDTVLNLGLND + Sbjct: 61 TYPEELKEQVEEAMRRLEEVTGKKFGDPNNPLLVSVRSGAAISMPGMMDTVLNLGLNDET 12- 0 Query: 117 VQGLVKKTEDERFAYDSYRRFIQMFADVVTGIPKYKFDTILDRLKTDKCYQDDTELTGSD 17- 6 V+GL K T +ERFAYD+YRRF+QMF DVV IP KF+ L+ LK +K + DTEL D Sbjct: 121 VKGLAKLTNNERFAYDAYRRFLQMFGDVVLKIPHEKFEKALEELKKEKGVKLDTELDAED 18- 0 Query: 177 LKRLVEFYKELYQKEAGEKFPQDPKRQLLLAIEAVFKSWNNPRAKIYRKLNDIPE--TLG 23- 4 LK+LVE YK++Y KE G++FPQDP +QL LAI+AVF SW N RA YR+++ I E LG Sbjct: 181 LKKLVERYKQIY-KEEGKEFPQDPWKQLWLAIDAVFGSWMNERAIKYRQIHGIKEGDLLG 23- 9 Query: 235 TAVNIQAMVFGNMGNNSGTGVAFTRNPSTGAANLFGEYLINAQGEDVVAGIRTPQSISKL 29- 4 TAVNI AMVFGNMG +SGTGVAFTR+P+TG +GE+L NAQGEDVVAGIRTP + +L Sbjct: 240 TAVNIVAMVFGNMGEDSGTGVAFTRDPNTGEKKPYGEFLPNAQGEDVVAGIRTPLKLEEL 29- 9 Query: 295 AEQMPIIYQEFVSVTQKLEAHYRDMQDMEFTIENGNLYMLQTRSGKRTAKAAIKIAVDQV 35- 4 +MP +Y + + + KLE HYRDMQD+EFT+E G LY+LQTR+GKRT++AAI+IAVD V Sbjct: 300 KNRMPEVYNQLLEIMDKLEKHYRDMQDIEFTVERGKLYILQTRNGKRTSQAAIRIAVDMV 35- 9 Query: 355 NEGLISKEEAILRIEPKQLDQLLHPSFDLKSLKKAIILTTGLPASPGAAYGKVYFHAEDV 41- 4 +EGLI+KEEAILR+ P+ ++Q+LHP FD K +A ++ GLPASPGAA GKV F+A+ Sbjct: 360 HEGLITKEEAILRVRPEDVEQVLHPVFDPKEKAQAKVIAKGLPASPGAATGKVVFNAKKA 41- 9 Query: 415 VKEMKKGNPVLLVRQETSPEDIEGMVSANGIITARGGMTSHAAVVARGMGKPCVAGCSQL 47- 4 + K G V+LVR ETSPED+ GM +A GI+T+RGGMTSHAAVVARGMGKP V G + Sbjct: 420 EELGKAGEQVILVRPETSPEDVGGMAAAQGILTSRGGMTSHAAVVARGMGKPAVVGAESI 47- 9 Query: 475 LVDEVRREISIGHQTIKEGEMLSIDGATGNVYIGQV-PMAETSVDRDFEIFMKWVDENRD 53- 3 V +G +KEGE +SIDG TG V +G+V + ++ ++W DE R Sbjct: 480 EVHPEEGYFKVGDVVVKEGEWISIDGTTGEVLLGKVTTIKPQGLEGPVAELLQWADEIRR 53- 9 Query: 534 MMVCSNADNPRDAQKALDFGAEGIGLCRTEHMFFDDERIPVVREMILADEILSRRKALER 59- 3 + V +NAD PRDA+ A FGAEGIGLCRTEHMFF+ +RIP VR MILA R KAL+ Sbjct: 540 LGVRTNADIPRDAEVARKFGAEGIGLCRTEHMFFEKDRIPKVRRMILAKTKEEREKALDE 59- 9 Query: 594 LLSFQRDDFYQIFKVLKGKACTIRLLDPPLHEFLPHDKESIESMARQMGISTLAIEKRIQ 65- 3 LL Q++DF +F+V+KG TIRL+DPPLHEFLP + E I+ +A QMG+S ++ ++ Sbjct: 600 LLPLQKFDFKGLFRVMKGLPVTIRLIDPPLHEFLPQEDEQIKEVAEQMGVSFEELKNVVE 65- 9 Query: 654 TLEEFNPMLGHRGCRLAITYPEIYQMQVRALVQGAI-LAMKEGYEAKPEIMIPLVTAHEE 71- 2 L+E NPMLGHRGCRL ITYPEI MQ +A++ AI L +EG + PEIMIPLV E Sbjct: 660 NLKELNPMLGHRGCRLTITYPEIAVMQTKAIIGAAIELKKEEGIDVIPEIMIPLVGHVNE 71- 9 Query: 713 ISIIRDLIEETIVEESKSKKINLSFPIGTMIETPRACMIADDIAKFADFFSFGTNDLTQM 77- 2 + ++ +I+ET K + L++ IGTMIE PRA + A IA+ A+FFSFGTNDLTQM Sbjct: 720 LRYLKKIIKETADALIKEAGVELTYKIGTMIEVPRAAVTAHQIAEEAEFFSFGTNDLTQM 77- 9 Query: 773 SFGFSRDDAGKFLGEYVDKGLLKKDPFQVLDQKGIGRFIGQAVRLGKEVKPNLKIGICGE 83- 2 +FGFSRDD GKFL EY++KG+L+ DPF+ LD G+G + G+ +P+LK+ G+CGE Sbjct: 780 TFGFSRDDVGKFLPEYLEKGILEHDPFKTLDYDGVGELVRMGKEKGRSTRPDLKVGVCGE 83- 9 Query: 833 HGGEPSSIEFCYQLGLHYVSCSPFRIPIAKLAAAQAKIKQSR 874 HGG+P SI F ++GL YVSCSP+R+P+A+LAAAQA +K + Sbjct: 840 HGGDPRSILFFDKIGLDYVSCSPYRVPVARLAAAQAALKNKK 881 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1793 A DNA sequence (GBSx1900) was identified in S. agalactiae <SEQ ID 5573> which encodes the amino acid sequence <SEQ ID 5574>. This protein is predicted to be glutamyl-tRNA (Gln) amidotransferase subunit C (gatC). Analysis of this protein sequence reveals the following: TABLE-US-05492 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3229 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05493 >GP:BAB04384 GB:AP001509 glutamyl-tRNA (Gln) amidotransferase subunit C [Bacillus halodurans] Identities = 42/94 (44%), Positives = 63/94 (66%) Query: 2 KISEEEVRHVANLSKLRFSDQETKEFASSLSKIVDMIELLNEVDTEGVPVTTTMADRKTV 61 - +IS E+V+HVA+L++L +++E K F L I+ E LNE+DTEGV T+ + D K V Sbjct: 3 RISMEQVKHVAHLARLAITEEEAKLFTEQLGDIIQFAEQLNELDTEGVEPTSHVLDMKNV 62 Query: 62 MREDIAQPGHNRDDLFKNVPQHQDYYIKVPAILE 95 +RED + G +D+ KN P H+D I+VP++LE Sbjct: 63 LREDKPEKGLPVEDVLKNAPDHEDGQIRVPSVLE 96 A related DNA sequence was identified in S. pyogenes <SEQ ID 5575> which encodes the amino acid sequence <SEQ ID 5576>. Analysis of this protein sequence reveals the following: TABLE-US-05494 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3247 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05495 Identities = 72/100 (72%), Positives = 88/100 (88%) Query: 1 MKISEEEVRHVANLSKLRFSDQETKEFASSLSKIVDMIELLNEVDTEGVPVTTTMADRKT 60 - MKISEEEVRHVA LSKL FS+ ET FA++LSKIVDM+ELLNEVDTEGV +TTTMAD+K Sbjct: 5 MKISEEEVRHVAKLSKLSFSESETTTFATTLSKIVDMVELLNEVDTEGVAITTTMADKKN 64 Query: 61 VMREDIAQPGHNRDDLFKNVPQHQDYYIKVPAILEDGGDA 100 VMR+D+A+ G +R LFKNVP+ ++++IKVPAIL+DGGDA Sbjct: 65 VMRQDVAEEGTDRALLFKNVPEKENHFIKVPAILDDGGDA 104 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1794 A DNA sequence (GBSx1900) was identified in S. agalactiae <SEQ ID 5577> which encodes the amino acid sequence <SEQ ID 5578>. Analysis of this protein sequence reveals the following:

TABLE-US-05496 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.64 Transmembrane 7-23 (6-24) ----- Final Results ----- bacterial membrane --- Certainty = 0.4057 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1795 A DNA sequence (GBSx1902) was identified in S. agalactiae <SEQ ID 5579> which encodes the amino acid sequence <SEQ ID 5580>. This protein is predicted to be glutamyl-tRNA amidotransferase, subunit A (gatA). Analysis of this protein sequence reveals the following: TABLE-US-05497 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2855(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05498 >GP:BAB04385 GB:AP001509 glutamyl-tRNA (Gln) amidotransferase subunit A [Bacillus halodurans] Identities = 285/486 (58%), Positives = 367/486 (74%), Gaps = 4/486 (0%) Query: 1 MSFNNQSIDQLHDFLVKKEISATELTKATLEDIHAREQAVGSFITISDEMAIAQAKEID- 59- MS + + +H L +KEIS ++L + I + V +F+ +++E A A AKE+D Sbjct: 1 MSLFDLKLKDVHTKLHEKEISVSDLVDEAYKRIEQVDGQVEAFLALNEEKARAYAKELDA 60- Query: 60 --DKGIDADNVMSGIPLAVKNDISTKGILTTAASKMLYNYEPIFDATAVEKLYAKDMIVI 11- 7 D+ +A ++ GIP+ VKDNI TK + TT +S++L N++PI+DAT V KL + I Sbjct: 61 ALDRS-EARGLLFGIPIGVKDNIVTKNLRTTCSSRILGNFDPIYDATVVHKLREAQAVTI 11- 9 Query: 118 GKANMDEFAMGGSTETSYFKKTNNAWDNSKVPGGSSGGSAAAVASGQVRLSLGSDTGGSI 17- 7 GK NMDEFAMG STE S F+KT N W+ VPGGSSGGSAAAVA+G+V +LGSDTGGSI Sbjct: 120 GKLNMDEFAMGSSTENSAFQKTKNPWNLEYVPGGSSGGSAAAVAAGEVPFTLGSDTGGSI 17- 9 Query: 178 RQPASFNGIVGMKPTYGRVSRFGLFAFGSSLDQIGPMSQTVKENAQLLTVISGHDVRDST 23- 7 RQPA++ G+VG+KPTYGRVSR+GL AF SSLDQIGP+++ V++NA LL ISGHD DST Sbjct: 180 RQPAAYCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRNVEDNAYLLQAISGHDPMDST 23- 9 Query: 238 SSERTVGDFTAKIGQDIQGMKIALPKEYLGEGIAQGVKETIIKAAKHLEKLGAVIEEVSL 29- 7 S+ V D+ + + DI+G+KIA+PKEYLGEG+ + VK++++ A K LE LGA EEVSL Sbjct: 240 SANLDVPDYLSALTGDIKGLKIAVPKEYLGEGVKEEVKOSVLDALKVLEGLGATWEEVSL 29- 9 Query: 298 PHSKYGVAVYYIVASSEASSNLQRFDGIRYGYRTENYKNLDDIYVNTRSEGFGDEVKRRI 35- 7 PHSKY +A YY++ASSEAS+NL RFDG+RYG+R++N NL D+Y TR+EGFGDEVKRRI Sbjct: 300 PHSKYALATYYLLASSEASANLARFDGVRYGFRSDNADNLLDMYKQTRAEGFGDEVKRRI 35- 9 Query: 358 MLGTFSLSSGYYDAYYKKAGQVRSLIIQDFEKVFADYDLILGPTAPTTAFDLDSLNHDPV 41- 7 MLGTF+LSSGYYDAYYKKA QVR+LI QDFEKVF YD+I+GPT PT AF + DP+ Sbjct: 360 MLGTFALSSGYYDAYYKKAQQVRTLIKQDFEKVFEQYDVIIGPTTPTPAFKIGEKTDDPL 41- 9 Query: 418 AMYLADILTIPVNLAGLPGISIPAGFDQGLPVGMQLIGPKFSEETIYQVAAAFEATTDYH 47- 7 MY DILTIPVNLAG+P IS+P GFD GLP+G+Q+IG F E ++Y+VA AFE TDYH Sbjct: 420 TMYANDILTIPVNLAGVPAISVPCGFDNGLPLGLQIIGKNFDEGSVYRVAHAFEQATDYH 47- 9 Query: 478 KQQPKI 483 ++P + Sbjct: 480 TKRPTL 485 A related DNA sequence was identified in S. pyogenes <SEQ ID 5581> which encodes the amino acid sequence <SEQ ID 5582>. Analysis of this protein sequence reveals the following: TABLE-US-05499 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2364(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05500 Identities = 392/487 (80%), Positives = 442/487 (90%) Query: 1 MSFNNQSIDQLHDFLVKKEISATELTKATLEDIHAREQAVGSFITISDEMAIAQAKEIDD 60- MSFN+++I++LHD LV KEISATELT+ATLEDI +RE+AVGSFIT+S+E+A+ QA ID Sbjct: 1 MSFNHKTIEELHDLLVAKEISATELTQATLEDIKSREEAVGSFITVSEEVALKQAAAIDA 60- Query: 61 KGIDADNVMSGIPLAVKDNISTKGILTTAASKMLYNYEPIFDATAVEKLYAKDMIVIGKA 12- 0 KGIDADN+MSGIPLAVKDNISTK ILTTAASKMLYNYEPIF+AT+V YAKDMIVIGK Sbjct: 61 KGIDADNLMSGIPLAVKDNISTKEILTTAASKMLYNYEPIFNATSVANAYAKDMIVIGKT 12- 0 Query: 121 NMDEFAMGGSTETSYFKKTNNAWDHSKVPGGSSGGSAAAVASGQVRLSLGSDTGGSIRQP 18- 0 NMDEFAMGGSTETSYFKKT NAWDH+KVPGGSSGGSA AVASGQVRLSLGSDTGGSIRQP Sbjct: 121 NMDEFAMGGSTETSYFKKTKNAWDHTKVPGGSSGGSATAVASGQVRLSLGSDTGGSIRQP 18- 0 Query: 181 ASFNGIVGMKPTYGRVSRFGLFAFGSSLDQIGPMSQTVKENAQLLTVISGHDVRDSTSSE 24- 0 A+FN +VG+KPTYG VSR+GL AFGSSLDQIGP + TVKENAQLL VI+ DV+D+TS+ Sbjct: 181 AAFNSVVGLKPTYGTVSRYGLIAFGSSLDQIGPFAPTVKENAQLLNVIASSDVKDATSAP 24- 0 Query: 241 RTVGDFTAKIGQDIQGMKIALPKEYLGEGIAQGVKETIIKAAKHLEKLGAVIEEVSLPHS 30- 0 + D+T+KIG+DI+GMKIALPKEYLGEGI +KET++ + K E LGA +EEVSLPHS Sbjct: 241 VRIADYTSKIGRDIKGMKIALPKEYLGEGIDPEIKETVLASVKQFEALGATVEEVSLPHS 30- 0 Query: 301 KYGVAVYYIVASSEASSNLQRFDGIRYGYRTENYKNLDDIYVNTRSEGFGDEVKRRIMLG 36- 0 KYGVAVYYI+ASSEASSNLQRFDGIRYG+R ++ KNLD+IYVNTRS+GFGDEVKRRIMLG Sbjct: 301 KYGVAVYYIIASSEASSNLQRFDGIRYGFRADDAKNLDEIYVNTRSQGFGDEVKRRIMLG 36- 0 Query: 361 TFSLSSGYYDAYYKKAGQVRSLIIQDFEKVFADYDLILGPTAPTTAFDLDSLNHDPVAMY 42- 0 TFSLSSGYYDAY+KKAGQVR+LIIQDF+KVFADYDLILGPT PT AF LD+LNHDPVAMY Sbjct: 361 TFSLSSGYYDAYFKKAGQVRTLIIQDFDKVFADYDLILGPTTPTVAFGLDTLNHDPVAMY 42- 0 Query: 421 LADILTIPVNLAGLPGISIPAGFDQGLPVGMQLIGPKFSEETIYQVAAAFEATTDYHKQQ 48- 0 LAD+LTIPVNLAGLPGISIPAGF GLPVG+QLIGPK++EETIYQ AAAFEA TDYHKQQ Sbjct: 421 LADLLTIPVNLAGLPGISIPAGFVDGLPVGLQLIGPKYAEETIYQAAAAFEAVTDYHKQQ 48- 0 Query: 481 PKIFGGE 487 P IFGG+ Sbjct: 481 PIIFGGD 487 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1796 A DNA sequence (GBSx1903) was identified in S. agalactiae <SEQ ID 5583> which encodes the amino acid sequence <SEQ ID 5584>. This protein is predicted to be glutamyl-tRNAGln amidotransferase subunit B (gatB). Analysis of this protein sequence reveals the following: TABLE-US-05501 Possible site: 27 >>> Seems to have no N-terminal signal sequence ------ Final Results ------ bacterial cytoplasm --- Certainty = 0.3935(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10095> which encodes amino acid sequence <SEQ ID 10096> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05502 >GP:BAB04386 GB:AP001509 glutamyl-tRNA (GLn) amidotransferase subunit B [Bacillus halodurans] Identities = 308/476 (64%), Positives = 361/476 (75%), Gaps = 1/476 (0%) Query: 1 MNFETVIGLEVHVELNTNSKIFSPSSAHFGQEQNANTNVIDWSFPGVLPVMNKGVIDAGI 60- MNFETVIGLSVHVEL T SKIFS S HFG E NANT+VID +PGVLPV+NK ++ + Sbjct: 1 MNFETVIGLEVHVELKTESKIFSASPNHFGAEPNANTSVIDLGYPGVLPVLNKAAVEFAM 60- Query: 61 KAALALNMDIHQNMHFDRKNYFYPDNPKAYQISQFDEPIGYNGWIEIELEDGTRKKIRIE 12- 0 KAA+ALN ++ + FDRKNYFYPDNPKAYQISQFD+PIG NGWIEIE+ DGT+KKI I Sbjct: 61 KAAMALNCEVATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-DGTKKKIGIT 11- 9 Query: 121 RAHLEEDAGKNTHGTDGYSYVDLNRQGVPLIEIVSEADMRSPEEAYAYLTALKEIIQYTG 18- 0 R HLEEDAGK TH +GYS VD NRQG PLIEIVSE D+R+P+EAYAYL LK IIQYTG Sbjct: 120 RLHLEEDAGKLTHSGNGYSLVDFNRQGTPLIEIVSEPDIRTPQEAYAYLEKLKSIIQYTG 17- 9 Query: 181 ISDVKMEEGSMRVDANISLRPYGQEEFGTKAELKNLNSFNNVRKGLIHEEKRQAQVLRSG 24- 0 +SD KMEEGS+R DANISLRP GQEEFGTK ELKNLNSFN VRKGL +EEKRQAQVL SG SbjCt: 180 VSDCKMEEGSLRCDANISLRPVGQEEFGTKTELKNLNSFNFVRKGLFYEEKRQAQVLLSG 23- 9 Query: 241 GQIQQETRRFDETTGETILMRVKEGSSDYRYFPEPDLPLFDISDEWIDQVRLELPEFPQE 30- 0 G+I QETRR+DE +T+LMRVKEGS DYRYFPEPDL I DEW ++R E+PE P Sbjct: 240 GEILQETRRYDEAANKTVLMRVKEGSDDYRYFPEPDLVALHIDDEWKARIRSEIPELPDA 29- 9 Query: 301 RRAKYVSSFGLSSYDASQLTATKATSDFFEKAVAIGGDAKQVSNWLQGEVAQFLNSESKS 36- 0 R+ +YV GL +YDA LT TK SDFFE+ +A G D K SNWL GEV+ +LN+E K Sbjct: 300 RKKRYVEELGLPAYDAMVLTLTKEMSDFFEETIAKGADPKLASNWLMGEVSGYLNAEQKE 35- 9 Query: 361 IEEIGLTPENLVEMIGLIADGTISSKIAKKVFVHLAKNGGSAEEFVKKAGLVQISDPEVL 42- 0 ++E+ LTP+ L +MI LI GTISSKIAKKVF L + GG EE VK GLVQISD L Sbjct: 360 LDEVALTPDGLAKMIQLIEKGTISSKIAKKVFKDLIEKGGDPEEIVKAKGLVQISDEGEL 41- 9 Query: 421 IPIIHQVFADNEAAVIDFKSGKRNADKAFTGYLMKATKGQANPQVALKLLAQELAK 476 + +V +N+ ++ DFK+GK A G +MKATKG+ANP + KLL +E+ K Sbjct: 420 RKYVVEVLDNNQQSIDDFKNGKDRAIGFLVGQIMKATKGKANPPMVNKLLLEEIWK 475 A related DNA sequence was identified in S. pyogenes <SEQ ID 5585> which encodes the amino acid sequence <SEQ ID 5586>. Analysis of this protein sequence reveals the following: TABLE-US-05503 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3935(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05504 Identities = 410/479 (85%), Positives = 447/479 (92%) Query: 1 MNFETVIGLEVHVELNTNSKIFSPSSAHFGQEQNANTNVIDWSFPGVLPVMNKGVIDAGI 60- MNFET+IGLEVHVELNTNSKIFSPSSAHFG++ NANTNVIDWSFPGVLPVMNKGVIDAGI Sbjct: 1 MNFETIIGLEVHVELNTNSKIFSPSSAHFGEDPNANTNVIDWSFPGVLPVMNKGVIDAGI 60- Query: 61 KAALALNMDIHQNMHFDRKNYFYPDNPKAYQISQFDEPIGYNGWIEIELEDGTRKKIRIE 12- 0 KAALALNMDIH+ MHFDRKNYFYPDNPKAYQISQFDEPIGYNGWI+I+LEDG+ KKIRIE Sbjct: 61 KAALALNMDIHKEMHFDRKNYFYPDNPKAYQISQFDEPIGYNGWIDIKLEDGSTKKIRIE 12- 0 Query: 121 RAHLEEDAGKNTHGTDGYSYVDLNRQGVPLIEIVSEADMRSPEEAYAYLTALKEIIQYTG 18- 0 RAHLEEDAGKNTHGTDGYSYVDLNRQGVPLIEIVSEADMRSPEEAYAYLTALKEIIQYTG Sbjct: 121 RAHLEEDAGKNTHGTDGYSYVDLNRQGVPLIEIVSEADMRSPEEAYAYLTALKEIIQYTG 18- 0 Query: 181 ISDVKMEEGSMRVDANISLRPYGQEEFGTKAELKNLNSFNNVRKGLIHEEKRQAQVLRSG 24- 0 ISDVKMEEGSMRVDANISLRPYGQE+FGTK ELKNLNSF+NVRKGL E +RQA++LRSG Sbjct: 181 ISDVKMEEGSMRVDANISLRPYGQEQFGTKTELKNLNSFSNVRKGLEFEVERQAKLLRSG 24- 0 Query: 241 GQIQQETRRFDETTGETILMRVKEGSSDYRYFPEPDLPLFDISDEWIDQVRLELPEFPQE 30- 0 G I+QETRR+DE TILMRVKEG++DYRYFPEPDLPL++I D WID++R +LP+FP + Sbjct: 241 GVIRQETRRYDEANKGTILMRVKEGAADYRYFPEPDLPLYEIDDAWIDEMRAQLPQFPAQ 30- 0 Query: 301 RRAKYVSSFGLSSYDASQLTATKATSDFFEKAVAIGGDAKQVSNWLQGEVAQFLNSESKS 36- 0 RRAKY GLS+YDASQLTATK SDFFE AV++GGDAKQVSNWLQGEVAQFLN+E K+ Sbjct: 301 RRARYEEELGLSAYDASQLTATKVLSDFFETAVSLGGDARQVSNWLQGEVAQFLNAEGKT 36- 0 Query: 361 IEEIGLTPENLVEMIGLIADGTISSKIAKKVFVHLAKNGGSAEEFVKKAGLVQISDPEVL 42- 0 IEEI LTPENLVEMI +IADGTISSK+AKKVFVHLAKNGGSA +V+KAGLVQISDP VL Sbjct: 361 IEEIALTPENLVEMIAIIADGTISSKMAKKVFVHLAKNGGSARAYVEKAGLVQISDPAVL 42- 0 Query: 421 IPIIHQVFADNEAAVIDFKSGKRNADKAFTGYLMKATKGQANPQVALKLLAQELAKLKE 479- +PIIHQVFADNEAAV DFKSGKRNADKAFTG+LMKATKGQANPQVA +LLAQEL KL++ Sbjct: 421 VPIIHQVFADNEAAVADFKSGKRNADKAFTGFLMKATKGQANPQVAQQLLAQELQKLRD 479- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1797 A DNA sequence (GBSx1904) was identified in S. agalactiae <SEQ ID 5587> which encodes the amino acid sequence <SEQ ID 5588>. Analysis of this protein sequence reveals the following: TABLE-US-05505 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.27 Transmembrane 108-124 (105-125) INTEGRAL Likelihood = -7.27 Transmembrane 278-294 (268-301) INTEGRAL Likelihood = -6.05 Transmembrane 191-207 (188-208) INTEGRAL Likelihood = -5.63 Transmembrane 219-235 (215-242) INTEGRAL Likelihood = -3.93 Transmembrane 41-57 (39-58) INTEGRAL Likelihood = -3.88 Transmembrane 132-148 (131-150) INTEGRAL Likelihood = -3.03 Transmembrane 254-270 (253-272) INTEGRAL Likelihood = -3.03 Transmembrane 79-95 (79-95) ----- Final Results ----- bacterial membrane --- Certainty = 0.3909(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10093> which encodes amino acid sequence <SEQ ID 10094> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05506 >GP:CAA04271 GB:AJ000733 hypothetical protein [Bacillus megaterium] Identities = 102/292 (34%), Positives = 169/292 (56%), Gaps = 3/292 (1%) Query: 6 TKKEKGTMMTLAAGLAWGISGISGQYLMSH-GVHVNLLTSLRLLITGIFLLSLARSKQKE 64- +++ G ++ + WG+SG QYL H + L +R+L++G+ LL++A SKQ+ Sbjct: 1 SRRAWGLLLVIIGATMWGVSGTVAQYLFQHKSFNAEWLVVVRMLVSGLLLLAIA-SKQR- 58- Query: 65 HLVAAWKQPKFLKQVLLFSIFGLVLNQYAFLRAIHLTNAGTATVLQYMAPILILSIVCIL 12- 4 ++ A WI + +LLF + G++ QY + AI NA TATVLQY +PI I+ + + Sbjct: 59 NIFAIWKTKEERTSLLLFGVIGMLGVQYTYFAAIEAGNAATATVLQYTSPIFIIGYLAVQ 11- 8 Query: 125 NRQRPTSFEIIAIAMAILGTYMIATHGRLGSLAITPKGLMWGLGSAITYSIYILLPVKLI 18- 4 R+ P E+I++ + I GT+ +AT G L+IT L WG+G+A+T + Y L P +L+ Sbjct: 119 ARKWPVKVEMISVVLVIAGTFFLATSGNFNELSITGWALFWGIGAAVTSAFYTLQPKRLL 17- 8 Query: 185 HEWGSTIVIGSGHFIGGILFSLVTKAWQYPLQINVMSILAYIGIIGIGTIFAYTFFLKGV 24- 4 +W S V+G GM IGG FS + W + +++S+ A + +I GT+ A+ +L+ + Sbjct: 179 AKWSSIEVVGWGMVIGGASFSFIHPPWHIAGEWSLLSLCAVLFVIIFGTLIAFYCYLESL 23- 8 Query: 245 SIVGAVKGSLLASVEPVSSVFLTVLVLGEIFYPIDLLGMLFIFLAVTLISYK 296 + A + +LAS EP+S+ L+VL L F + LG + I V L+S + Sbjct: 239 KHISASEAIVLASREPLSAAALSVLWLHVTFGWTEWLGTILIIATVFLLSQR 290 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1798 A DNA sequence (GBSx1905) was identified in S. agalactiae <SEQ ID 5589> which encodes the amino acid sequence <SEQ ID 5590>. Analysis of this protein sequence reveals the following: TABLE-US-05507 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2103(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10091> which encodes amino acid sequence <SEQ ID 10092> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05508 >GP:CAB14510 GB:Z99117 similar to hypothetical proteins [Bacillus subtilis] Identities = 52/153 (33%), Positives = 88/153 (56%) Query: 17 YRPTFVVEAVYDLRAEDLLRHGIRAVLVDLDNTLIAWNNPDGTAEVRAWLDEMTTADISV 76 - + P V+ ++ + E L ++ ++ DLDNTL+ W+ P+ T + W +EM I V Sbjct: 6 FLPDEFVKNIFHITPERLKERNVKGIITDLDNTLVEWDRPNATPRLIEWFEEMKEHGIKV 65 Query: 77 VVVSNNNHARVERAVSRFGVDFVSRAMKPFTRGINMAIERYGFDRDEVIMVGDQLMTDIR 136- +VSNNN RV+ G+ F+ +A KP + N A+ +++ +++GDQL+TD+ Sbjct: 66 TIVSNNNERRVKLFSEPLGIPFIYKARKPMGKAFNRAVRNMELKKEDCVVIGDQLLTDVL 125- Query: 137 ASHRAGIKSVLVKPIVKSDAWNTKFNRLRERRV 169 +R G ++LV P+ SD +T+FNR ERR+ Sbjct: 126 GGNRNGYHTILVVPVASSDGFITRFNRQVERRI 158 A related DNA sequence was identified in S. pyogenes <SEQ ID 5591> which encodes the amino acid sequence <SEQ ID 5592>. Analysis of this protein sequence reveals the following: TABLE-US-05509 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4252 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05510 Identities = 147/175 (84%), Positives = 158/175 (90%) Query: 12 LSIDDYRPTFVVEAVYDLRAEDLLRHGIRAVLVDLDNTLIAWNNPDGTAEVRAWLDEMTT 71 - +SIDDYRPT++VEA+YDLRA DLLRHGI AVLVDLDNTLIAWNNPDGT EVRAWLDEMT Sbjct: 20 MSIDDYRPTYMVEAIYDLRANDLLRHGITAVLVDLDNTLIAWNNPDGTPEVRAWLDEMTI 79 Query: 72 ADISVVVVSNNNHARVERAVSRFGVDFVSRAMKPFTRGINMAIERYGFDRDEVIMVGDQL 131- ADISVVVVSNN H+RVERAVSRFGVDF+SRA+KPF GI AI RYGFDR+EVIMVGDQL Sbjct: 80 ADISVVVVSNNKHSRVERAVSRFGVDFISRALKPFAYGIEKAIARYGFDRNEVIMVGDQL 139- Query: 132 MTDIRASHRAGIKSVLVKPIVKSDAWNTKFNRLRERRVWKKIEENYGKIVYQKGI 186 MTDIRASHRAGIKSVLVKP+V SDAWNTK NR RERRV K+EE YGK+ YQKGI Sbjct: 140 MTDIRASHRAGIKSVLVKPLVASDAWNTKINRWRERRVMAKLEEKYGKLSYQKGI 194 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1799 A DNA sequence (GBSx1906) was identified in S. agalactiae <SEQ ID 5593> which encodes the amino acid sequence <SEQ ID 5594>. Analysis of this protein sequence reveals the following: TABLE-US-05511 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1091 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05512 >GP:CAB14509 GB:Z99117 similar to hypothetical proteins [Bacillus subtilis] Identities = 220/373 (58%), Positives = 280/373 (74%), Gaps = 8/373 (2%) Query: 1 MEELFCIGCGARIQTENKDAAGYTPRAALEKGLETGELYCQRCFRLRHYNEITDVHITDD 60 ME++ CIGCG IQTE+K GY P A+L K + CQRCFRL++YNEI DV +TDD Sbjct: 1 MEKVVCIGCGVTIQTEDKTGLGYAPPASLTKE----NVICQRCFRLKNYNEIQDVSLTDD 56 Query: 61 EFLKLLHEVGDSDALVVNVIDIFDFNGSIIPGLSRFVAGNDVLLVGNKKDILPKSVKDGK 120- +FL +LH +G++D+LVV ++DIFDFNGS I GL R V GN +LLVGNK DILPKS+K + Sbjct: 57 DFLNILHGIGETDSLVVKIVDIFDFNGSWINGLQRLVGGNPILLVGNKADILPKSLKRER 116- Query: 121 VTQWLTERAHEEGLRPVDVILTSAQNHHAIKDLIDTIEKYRHGQDVYVVGVTNVGKSTLI 18- 0 + QW+ A E GL+PVDV L SA I+++ID IE YR+G+DVYVVG TNVGKST I Sbjct: 117 LIQWMKREAKELGLKPVDVFLVSAGRGQGIREVIDAIEHYRNGKDVYVVGCTNVGKSTFI 17- 6 Query: 181 NAIIREITGSRDVITTSRFPGTTLDKIEIPLDDGSYIFDTPGIIHRHQMAHYLTAKNLKY 24- 0 N II+E++G D+ITTS+FPGTTLD IEIPLDDGS ++DTPGII+ HQMAHY+ K+LK Sbjct: 177 NRIIKEVSGEEDIITTSQFPGTTLDAIEIPLDDGSSLYDTPGIINNHQMAHYVNKKDLKI 23- 6 Query: 241 VSPKKEIKPKTYQLNSEQTLFLAGLARFDFISGQKQGFTAYFDNNLNLHRTKLVGADEFY 30- 0 +SPKKE+KP+T+QLN +QTL+ GLARFD++SG++ F Y N L +HRTKL AD Y Sbjct: 237 LSPKKELKPRTFQLNDQQTLYFGGLARFDYVSGERSPFICYMPNELMIHRTKLENADALY 29- 6 Query: 301 TKHVGKLLTPPTGKEVSDFPKLVRHEFTIKD-KMDIVYSGLGWIRVKSEAENPVVVAAWA 35- 9 KH G+LLTPP E+ +FP+LV H FTIKD K DIV+SGLGW+ V + V A+A Sbjct: 297 EKHAGELLTPPGKDEMDEFPELVAHTFTIKDKKTDIVFSGLGWVTVHDADKK---VTAYA 35- 3 Query: 360 PEGVAVVLRKALI 372 P+GV V +R++LI Sbjct: 354 PKGVHVFVRRSLI 366 A related DNA sequence was identified in S. pyogenes <SEQ ID 5595> which encodes the amino acid sequence <SEQ ID 5596>. Analysis of this protein sequence reveals the following:

TABLE-US-05513 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05514 >GP:CAB14509 GB:Z99117 similar to hypothetical proteins [Bacillus subtilis] Identities = 220/373 (58%), Positives = 286/373 (75%), Gaps = 8/373 (2%) Query: 1 MEELFCIGCGIQIQTEDKEKAGFTPAAALKKGMETGELYCQRCFRLRHYNEITDVHITDD 60 ME++ CIGCG+ IQTEDK G+ P A+L K + CQRCFRL++YNEI DV +TDD Sbjct: 1 MEKVVCIGCGVTIQTEDKTGLGYAPPASLTKE----NVICQRCFRLKNYNEIQDVSLTDD 56 Query: 61 EFLRLLHEVGDSDALVVNVIDIFDFNGSIIPGLSRFISGNDVLLVGNKKDILPKSVKDGK 120- +FL +LH +G++D+LVV ++DIFDFNGS I GL R + GN +LLVGNK DILPKS+K + Sbjct: 57 DFLNILHGIGETDSLVVKIVDIFDFNGSWINGLQRLVGGNPILLVGNKADILPKSLKRER 116- Query: 121 VTQWLTERAHEEGLRPLDVMLTSAQNKYAIKDLIGRINELRNGRDVYVVGVTNVGKSTLI 18- 0 + QW+ A E GL+P+DV L SA I+++I I RNG+DVYVVG TNVGKST I Sbjct: 117 LIQWMKREAKELGLKPVDVFLVSAGRGQGIREVIDAIEHYRNGKDVYVVGCTNVGKSTFI 17- 6 Query: 181 NAIIQEITGNKDVITTSRFPGTTLDKIEIPLDDGTFIFDTPGIIHRHQMAHYLSPKELKI 24- 0 N II+E++G +D+ITTS+FPGTTLD IEIPLDDG+ ++DTPGII+ HQMAHY++ K+LKI Sbjct: 177 NRIIKEVSGEEDIITTSQFPGTTLDAIEIPLDDGSSLYDTPGIINNHQMAHYVNKKDLKI 23- 6 Query: 241 VSPKKEIKPKTYQLNPEQTLFLGGLARFDFINGERQGFTAFFDNQLELHRTKLAGADAFY 30- 0 +SPKKE+KP+T+QLN +QTL+ GGLARFD+++GER F + N+L +HRTKL ADA Y Sbjct: 237 LSPKKELKPRTFQLNDQQTLYFGGLARFDYVSGERSPFICYMPNELMIHRTKLENADALY 29- 6 Query: 301 DKHVGTLLTPPDKKELTAFPKLVRHEFTI-DQKMDIVFSGLGWIRVNGQKDSKAIVAAWA 35- 9 +KH G LLTPP K E+ FP+LV H FTI D+K DIVFSGLGW+ V+ D+ V A+A Sbjct: 297 EKHAGELLTPPGKDEMDEFPELVAHTFTIKDKKTDIVFSGLGWVTVH---DADKKVTAYA 35- 3 Query: 360 PEGVAVIVRKAII 372 P+GV V VR+++I Sbjct: 354 PKGVHVFVRRSLI 366 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05515 Identities = 308/372 (82%), Positives = 343/372 (91%) Query: 1 MEELFCIGCGARIQTENKDAAGYTPRAALEKGLETGELYCQRCFRLRHYNEITDVHITDD 60 MEELFCIGCG +IQTE+K+ AG+TP AAL+KG+ETGELYCQRCFRLRHYNEITDVHITDD Sbjct: 1 MEELFCIGCGIQIQTEDKEKAGFTPAAALKKGMETGELYCQRCFRLRHYNEITDVHITDD 60 Query: 61 EFLKLLHEVGDSDALVVNVIDIFDFNGSIIPGLSRFVAGNDVLLVGNKKDILPKSVKDGK 120- EFL+LLHEVGDSDALVVNVIDIFDFNGSIIPGLSRF++GNDVLLVGNKKDILPKSVKDGK Sbjct: 61 EFLRLLHEVGDSDALVVNVIDIFDFNGSIIPGLSRFISGNDVLLVGNKKDILPKSVKDGR 120- Query: 121 VTQWLTERAHEEGLRPVDVILTSAQNHHAIKDLIDTIEKYRHGQDVYVVGVTNVGKSTLI 18- 0 VTQWLTERAHEEGLRP+DV+LTSAQN +AIKDLI I + R+G+DVYVVGVTNVGKSTLI Sbjct: 121 VTQWLTERAHEEGLRPLDVMLTSAQNKYAIKDLIGRINELRNGRDVYVVGVTNVGKSTLI 18- 0 Query: 181 NAIIREITGSRDVITTSRFPGTTLDKIEIPLDDGSYIFDTPGIIHRHQMAHYLTAKNLKY 24- 0 NAII+EITG++DVITTSRFPGTTLDKIEIPLDDG++IFDTPGIIHRHQMAHYL+ K LK Sbjct: 181 NAIIQEITGNKDVITTSRFPGTTLDKIEIPLDDGTFIFDTPGIIHRHQMAHYLSPKELKI 24- 0 Query: 241 VSPKKEIKPKTYQLNSEQTLFLAGLARFDFISGQKQGFTAYFDNNLNLHRTKLVGADEFY 30- 0 VSPKKEIKPKTYQLN EQTLFL GLARFDFI+G++QGFTA+FDN L LHRTKL GAD FY Sbjct: 241 VSPKKEIKPKTYQLNPEQTLFLGGLARFDFINGERQGFTAFFDNQLELHRTKLAGADAFY 30- 0 Query: 301 TKHVGKLLTPPTGKEVSDFPKLVRHEFTIKDKMDIVYSGLGWIRVKSEAENPVVVAAWAP 36- 0 KHVG LLTPP KE++ FPKLVRHEFTI KMDIV+SGLGWIRV + ++ +VAAWAP Sbjct: 301 DKHVGTLLTPPDKKELTAFPKLVRHEFTIDQKMDIVFSGLGWIRVNGQKDSKAIVAAWAP 36- 0 Query: 361 EGVAVVLRKALI 372 EGVAV++RKA+I Sbjct: 361 EGVAVIVRKAII 372 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1800 A DNA sequence (GBSx1907) was identified in S. agalactiae <SEQ ID 5597> which encodes the amino acid sequence <SEQ ID 5598>. Analysis of this protein sequence reveals the following: TABLE-US-05516 Possible site: 18 >>>Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2948 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05517 >GP:CAB14507 GB:Z99117 similar to dihydrodipicolinate reductase [Bacillus subtilis] Identities = 49/97 (50%), Positives = 67/97 (68%), Gaps = 2/97 (2%) Query: 1 MLTSKQRAFLKSEAHSMKPIIQIGKNGLNDQIKTSVRNALDARELIKVTLLQNTDEDIHD 60 MLT KQ+ FL+S+AH + PI Q+GK G+ND + + AL+ARELIKV++LQN +ED +D Sbjct: 1 MLTGKQKRFLRSKAHHLTPIFQVGKGGVNDNMIKQIAEALEARELIKVSVLQNCEEDKND 60 Query: 61 VAEVLEDEIGCDTVLKIGRILILYKESARKENRKISV 97 VAE L V IG ++LYKES KEN++I + Sbjct: 61 VAEALVKGSRSQLVQTIGNTIVLYKES--KENKQIEL 95 A related DNA sequence was identified in S. pyogenes <SEQ ID 5599> which encodes the amino acid sequence <SEQ ID 5600>. Analysis of this protein sequence reveals the following: TABLE-US-05518 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ---- bacterial cytoplasm --- Certainty = 0.2839 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05519 Identities = 89/102 (87%), Positives = 98/102 (95%) Query: 1 MLTSKQRAFLKSEAHSMKPIIQIGKNGLNDQIKTSVRNALDARELIKVTLLQNTDEDIHD 60 MLTSKQRAFLKSEAHS+KPI+QIGKNGLND IKTS+R ALDARELIKVTLLQNTDEDIH+ Sbjct: 1 MLTSKQRAFLKSEAHSLKPIVQIGKNGLNDHIKTSIRQALDARELIKVTLLQNTDEDIHE 60 Query: 61 VAEVLEDEIGCDTVLKIGRILILYKESARKENRKISVKVKAV 102 VAE+LE+EIGCDTVLKIGRILILYK SA+KENRK+S KVKA+ Sbjct: 61 VAEILEEEIGCDTVLKIGRILILYKVSAKKENRKLSPKVKAI 102 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1801 A DNA sequence (GBSx1908) was identified in S. agalactiae <SEQ ID 5601> which encodes the amino acid sequence <SEQ ID 5602>. Analysis of this protein sequence reveals the following: TABLE-US-05520 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.66 Transmembrane 3-19 (1-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.2062 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10089> which encodes amino acid sequence <SEQ ID 10090> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05521 >GP:CAB14506 GB:Z99117 similar to hypothetical proteins [Bacillus subtilis] Identities = 85/187 (45%), Positives = 134/187 (71%) Query: 38 KQIGIMGGNFNPVHNAHLVVADQVRQQLCLDQVLLMPEFQPPHIDKKETIDEQHRLKMLE 97 - K+IGI GG F+P HN HL++A++V Q LD++ MP PPH ++ D HR++ML+ Sbjct: 2 KKIGIFGGTFDPPHNGHLLMANEVLYQAGLDEIWFMPNQIPPHKQNEDYTDSFHRVEMLK 61 Query: 98 LAIEGIDGLSIEPIEIERKGISYTYDTMKLLIEKNPDVDYYFIIGADMVEYLPKWHRIDE 157- LAI+ +E +E+ER+G SYT+DT+ LL ++ P+ +FIIGADM+EYLPKW+++DE Sbjct: 62 LAIQSNPSFKLELVEMEREGPSYTFDTVSLLKQRYPNDQLFFIIGADMIEYLPKWYKLDE 121- Query: 158 LVKMVQFVGVQRPKYKAGTSYPVIWVDLPLMDISSSMIRQFIKSNRQPNYLLPREVLDYI 21- 7 L+ ++QF+GV+RP + T YP+++ D+P ++SS+MIR+ KS + +YL+P +V Y+ Sbjct: 122 LLNLIQFIGVKRPGFHVETPYPLLFADVPEFEVSSTMIRERFKSKKPTDYLIPDKVKKYV 18- 1 Query: 218 RKEGLYK 224 + GLY+ Sbjct: 182 EENGLYE 188 A related DNA sequence was identified in S. pyogenes <SEQ ID 5603> which encodes the amino acid sequence <SEQ ID 5604>. Analysis of this protein sequence reveals the following: TABLE-US-05522 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4660 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05523 Identities = 172/210 (81%), Positives = 196/210 (92%) Query: 15 MALELLTPFTKVELEEKKRDTNRKQIGIMGGNFNPVHNAHLVVADQVRQQLCLDQVLLMP 74 - MALELLTPFTKVELEE+K+++NRKQIGI+GGNFNP+HNAHLVVADQVRQQL LDQVLLMP Sbjct: 1 MALELLTPFTKVELEEEKKESNRKQIGILGGNFNPIHNAHLVVADQVRQQLGLDQVLLMP 60 Query: 75 EFQPPHIDKKETIDEQHRLKMLELAIEGIDGLSIEPIEIERKGISYTYDTMKLLIEKNPD 134- E +PPH+D KETIDE+HRL+MLELAIE ++GL+IE E+ER+GISYTYDTM L E++PD Sbjct: 61 ECKPPHVDAKETIDEKHRLRMLELAIEDVEGLAIETCELERQGISYTYDTMLYLTEQHPD 120- Query: 135 VDYYFIIGADMVEYLPKWHRIDELVKMVQFVGVQRPKYKAGTSYPVIWVDLPLMDISSSM 19- 4 VD+YFIIGADMV+YLPKWHRIDELVK+VQFVGVQRPKYKAGTSYPVIWVDLPL+DISSSM Sbjct: 121 VDFYFIIGADMVDYLPKWHRIDELVKLVQFVGVQRPKYKAGTSYPVIWVDLPLIDISSSM 18- 0 Query: 195 IRQFIKSNRQPNYLLPREVLDYIRKEGLYK 224 IR FIK RQPNYLLP+ VLDYI +EGLY+ Sbjct: 181 IRDFIKKGRQPNYLLPKRVLDYITQEGLYQ 210 SEQ ID 5602 (GBS651) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 132 (lane 8-10; MW 53.3 kDa) and in FIG. 186 (lane 8; MW 53 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 132 (lane 12; MW 28.4 kDa) and in FIG. 140 (lane 11; MW 20 kDa). Purified GBS651-GST is shown in FIG. 243, lane 4; purified GBS651-His is shown in FIG. 229, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1802 A DNA sequence (GBSx1909) was identified in S. agalactiae <SEQ ID 5605> which encodes the amino acid sequence <SEQ ID 5606>. Analysis of this protein sequence reveals the following: TABLE-US-05524 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4281 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05525 >GP:CAB14505 GB:Z99117 similar to hypothetical proteins [Bacillus subtilis] Identities = 79/180 (43%), Positives = 115/180 (63%) Query: 9 LDRTELLSKVRHMMSDKRFNHVLGVERAAIELAERYGYDKEKAGLAALLHDYAKELSDDE 68 ++R E L+ V+ +++ R+ H +GV AIELAER+G D +KA +AA+ HDYAK +E Sbjct: 1 MNREEALACVKQQLTEHRYIHTVGVMNTAIELAERFGADSKKAEIAAIFHDYAKFRPKEE 60 Query: 69 FLRLIDKYQPDPDLKKWGNNIWHGLVGIYKIQEDLAIKDQDILAAIAKHTVGSAQMSTLD 128- ++I + + L +WH VG Y +Q + ++D+DIL AI HT G M+ L+ Sbjct: 61 MKQIIAREKMPAHLLDHNPELWHAPVGAYLVQREAGVQDEDILDAIRYHTSGRPGMTLLE 120- Query: 129 KIVYVADYIEHNRDFPGVEEARELAKVDLNKAVAYETARTVAFLASKAQPIYPKTIETYN 18- 8 K++YVADYIE NR FPGV+E R+LA+ DLN+A+ T+ FL K QP++P T TYN Sbjct: 121 KVIYVADYIEPNRAFPGVDEVRKLAETDLNQALIQSIKNTMVFLMKKNQPVFPDTFLTYN 18- 0 A related DNA sequence was identified in S. pyogenes <SEQ ID 5607> which encodes the amino acid sequence <SEQ ID 5608>. Analysis of this protein sequence reveals the following: TABLE-US-05526 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2615 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05527 Identities = 130/194 (67%), Positives = 159/194 (81%) Query: 1 MTYKDYTGLDRTELLSKVRHMMSDKRFNHVLGVERAAIELAERYGYDKEKAGLAALLHDY 60 MTY+DY RTELL+K+ MS KRF HVLGVE+AA+ LAE YG + +KAGLAALLHDY Sbjct: 1 MTYEDYLPYSRTELLAKIAEQMSPKRFKHVLGVEKAALSLAECYGCNPDKAGLAALLHDY 60 Query: 61 AKELSDDEFLRLIDKYQPDPDLKKWGNNIWHGLVGIYKIQEDLAIKDQDILAAIAKHTVG 120- AKE D FL LIDKYQ P+L KW NN+WHG+VGIYKIQEDL +KD+DIL AI HTVG Sbjct: 61 AKECPDQVFLDLIDKYQLSPELAKWNNNVWHGMVGIYKIQEDLGLKDKDILRAIEIHTVG 120- Query: 121 SAQMSTLDKIVYVADYIEHNRDFPGVEEARELAKVDLNKAVAYETARTVAFLASKAQPIY 18- 0 +A+M+ LDK++YVADYIE R FP V++AR++AK+DLN+AVAYET TVA+LASKAQPI+ Sbjct: 121 AAEMTLLDKVLYVADYIEEGRIFPLVDDARKIAKLDLNQAVAYETVNTVAYLASKAQPIF 18- 0 Query: 181 PKTIETYNAYIPYL 194 P+T++TYNA+ YL Sbjct: 181 PQTLDTYNAFCSYL 194 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1803 A DNA sequence (GBSx1910) was identified in S. agalactiae <SEQ ID 5609> which encodes the amino acid sequence <SEQ ID 5610>. Analysis of this protein sequence reveals the following: TABLE-US-05528 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.34 Transmembrane 12-28 (10-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.1935 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10087> which encodes amino acid sequence <SEQ ID 10088> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05529 >GP:AAG19496 GB:AE005041 Vng1100c [Halobacterium sp. NRC-1] Identities = 46/175 (26%), Positives = 82/175 (46%), Gaps = 12/175 (6%) Query: 22 ALLLIDIQQGIMDKK--PKHLTNFAVLLDDLLLSAKGSNCEVIWIRHHDKE----LPQGS 75 - AL+L+D QQG D ++ + ++LL + + + + +RH+ E L QG Sbjct: 7 ALVLVDFQQGFADPAWGDRNNPDAEAHAEELLAAWRDAAAPIAHVRHNSTEATSPLRQGE 66 Query: 76 PQWEIWEQRHLVTHHKIIDKTYNSCFKDTHLHDYLQSKHISQLIMMGLQTEYCFDTSVKV 135- P + + K+ N F DT L +L+ + L++ GL T++C T+V++ Sbjct: 67 PGFAYTDGLAPAADEPEFVKSVNGAFVDTALEGWLRDRDTGSLVVCGLTTDHCVSTTVRM 126- Query: 136 AFEYGYDIFIPQGGHLTFDTPTLSGDSIKK---HYENIWHHR--FATMVAKDSLL 185 A G+D+ + + T D TL G+ + H + H R FAT+ ++L Sbjct: 127 ADNRGFDVTLVRDATATHDR-TLDGERLPPSVVHRTALAHLRGEFATLATTATVL 180 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 5610 (GBS652) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 133 (lane 2 & 3; MW 49.7 kDa)+lane 4; MW 27 kDa) and in FIG. 186 (lane 9; MW 50 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 133 (lane 5 & 7; MW 24.8 kDa) and in FIG. 178 (lane 10; MW 25 kDa). Purified GBS652-GST is shown in FIG. 243, lane 9; purified GBS652-His is shown in FIG. 229, lane 10. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1804 A DNA sequence (GBSx1911) was identified in S. agalactiae <SEQ ID 5611> which encodes the amino acid sequence <SEQ ID 5612>. Analysis of this protein sequence reveals the following: TABLE-US-05530 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0945 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05531 >GP:CAB14504 GB:Z99117 similar to hypothetical proteins [Bacillus subtilis] Identities = 55/118 (46%), Positives = 82/118 (68%) Query: 1 MTEKDLLQLVVKAADEKRAEDIVILDLQPVTSVADYFVIMSASNSRQLEAIADNIREQVK 60 - M +K +L++ A D+KRAEDI+ LD++ ++ VADYF+I ++ +Q++AIA I++Q Sbjct: 1 MNQKSILKIAAAACDDKRAEDILALDMEGISLVADYFLICHGNSDKQVQAIAREIKDQAD 60 Query: 61 GNGGDASHLEGDSKAGWVLLDLNSVVVHIFSEDERQHYNLEKLWHEAPLLDAEVFMTE 118 NG +EG +A WVL+DL VVVH+F +DER +YNLEKLW +APL D + M + Sbjct: 61 ENGIQVKKMEGFDEARWVLVDLGDVVVHVFHKDERSYYNLEKLWGDAPLADLDFGMNQ 118 A related DNA sequence was identified in S. pyogenes <SEQ ID 5613> which encodes the amino acid sequence <SEQ ID 5614>. Analysis of this protein sequence reveals the following: TABLE-US-05532 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.69 Transmembrane 91-107 (91-107) ----- Final Results ----- bacterial membrane --- Certainty = 0.1277 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: TABLE-US-05533 >GP:CAB14504 GB:Z99117 similar to hypothetical proteins [Bacillus subtilis] Identities = 55/113 (48%), Positives = 80/113 (70%) Query: 17 MKKEELLKIVVEATEEKRAKDILALDLEGLTSLTDYFVIASATNSRQLEAIADNIREKVK 76 - M ++ +LKI A ++KRA+DILALD+EG++ + DYF+I + +Q++AIA I+++ Sbjct: 1 MNQKSILKIAAAACDDKRAEDILALDMEGISLVADYFLICHGNSDKQVQAIAREIKDQAD 60 Query: 77 EAGGDASHVEGNSQAGWVLLDLTDVVVHLFLEDERYHYNLEKLWHEAPAVALD 129 E G +EG +A WVL+DL DVVVH+F +DER +YNLEKLW +AP LD Sbjct: 61 ENGIQVKKMEGFDEARWVLVDLGDVVVHVFHKDERSYYNLEKLWGDAPLADLD 113 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-05534 Identities = 78/116 (67%), Positives = 100/116 (85%) Query: 1 MTEKDLLQLVVKAADEKRAEDIVILDLQPVTSVADYFVIMSASNSRQLEAIADNIREQVK 60 - M +++LL++VV+A +EKRA+DI+ LDL+ +TS+ DYFVI SA+NSRQLEAIADNIRE+VK Sbjct: 17 MKKEELLKIVVEATEEKRAKDILALDLEGLTSLTDYFVIASATNSRQLEAIADNIREKVK 76 Query: 61 GNGGDASHLSGDSKAGWVLLDLNSVVVHIFSEDERQHYNLEKLWHEAPLLDAEVFM 116 GGDASH+EG+S+AGWVLLDL VVVH+F EDER HYNLEKLWHEAP + + ++ Sbjct: 77 EAGGDASHVEGNSQAGWVLLDLTDVVVHLFLEDERYHYNLEKLWHEAPAVALDAYL 132 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1805 A DNA sequence (GBSx1912) was identified in S. agalactiae <SEQ ID 5615> which encodes the amino acid sequence <SEQ ID 5616>. Analysis of this protein sequence reveals the following: TABLE-US-05535 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2415 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1806 A DNA sequence (GBSx1913) was identified in S. agalactiae <SEQ ID 5617> which encodes the amino acid sequence <SEQ ID 5618>. Analysis of this protein sequence reveals the following: TABLE-US-05536 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1570 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05537 >GP:CAB14503 GB:Z99117 similar to hypothetical proteins [Bacillus subtilis] Identities = 86/242 (35%), Positives = 154/242 (63%), Gaps = 4/242 (1%) Query: 4 YETFAAVYDAVMDDTLYAKWTDFSLRHFPKGKKKLLELACGTGIQSVRFAQAGYAVTGLD 63- Y+ FA+VYD +M Y +WT + P+ K ++L+LACGTG S+R A+ G+ VTG+D Sbjct: 3 YQGFASVYDELMSHAPYDQWTKWIEASLPE-KGRILDLACGTGEISIRLAEKGFEVTGID 61- Query: 64 LSGDMLKLAKKRATSAHQSIQFIEGNMLDLSNV-GKYDLITCYSDSICYMQDEVEVGDVF 12- 2 LS +ML A+++ +S+ Q I F++ +M +++ G++D + DS+ Y++ + +V + F Sbjct: 62 LSEEMLSFAQQKVSSS-QPILFLQQDMREITGFDGQFDAVVICCDSLNYLKTKNDVIETF 12- 0 Query: 123 IEVYKALEENGVFIFDVHSTYQTDKVFPGYSYHENADDFAMVWDTYEDDAPHSIVHELTF 18- 2 V++ L+ G+ +FDVHS+++ +VFP ++ + +D + +W ++ S++H+++F Sbjct: 121 KSVFRVLKPEGILLFDVHSSFKIAEVFPDSTFADQDEDISYIWQSFAGSDELSVIHDMSF 18- 0 Query: 183 FVQEEDGRFTRHDEVHEERTYDILTYDILLEQAGFKDVKVYADFEDKKPTATSARWFFVA 24- 2 FV + + R DE HE+RT+ + Y+ +L+ GF+ +V ADF D +P+A S R FF A Sbjct: 181 FVWNGEA-YDRFDETHEQRTFPVEEYEEMLKNCGFQLHRVTADFTDTEPSAQSERLFFKA 23- 9 Query: 243 HK 244 K Sbjct: 240 QK 241 A related DNA sequence was identified in S. pyogenes <SEQ ID 5619> which encodes the amino acid sequence <SEQ ID 5620>. Analysis of this protein sequence reveals the following: TABLE-US-05538 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Result ----- bacterial cytoplasm --- Certainty = 0.2315 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05539 Identities = 191/243 (78%), Positives = 215/243 (87%), Gaps = 2/243 (0%) Query: 4 YETFAAVYDAVMDDTLYAKWTDFSLRHFPK--GKKKLLELACGTGIQSVRFAQAGYAVTG 61- YE FA+VYDAVMDD+LY WTDFSLRH PK G+ +LLELACGTGIQSVRFAQAG+ VTG Sbjct: 21 YEKFASVYDAVMDDSLYDLWTDFSLRHLPKSKGRNRLLELACGTGIQSVRFAQAGFDVTG 80- Query: 62 LDLSGDMLKLAKKRATSAHQSIQFIEGNMLDLSNVGKYDLITCYSDSICYMQDEVEVGDV 12- 1 LDLS DML +AKKRA SA + I FI+GNMLDLS VG++D +TCYSDSICYMQDEV+VGDV Sbjct: 81 LDLSQDMLAIAKKRAQSAKKKIDFIQGNMLDLSQVGQFDFVTCYSDSICYMQDEVDVGDV 14- 0 Query: 122 FIEVYKALEENGVFIFDVHSTYQTDKVFPGYSYHENADDFAMVWDTYEDDAPHSIVHELT 18- 1 F EVY L +G+FIFDVHSTYQTD+ FPGYSYHENADDFAMVWDTY D+APHS+VHELT Sbjct: 141 FKEVYDVLANDGIFIFDVHSTYQTDECEPGYSYHENADDFAMVWDTYADEAPHSVVHELT 20- 0 Query: 182 FFVQEEDGRFTRHDEVHEERTYDILTYDILLEQAGFKDVKVYADFEDKKPTATSARWFFV 24- 1 FF+QE+DGRF+R DEVHEERTY++LTYDILLEQAGFK KVYADFEDK+PT TS RWFFV Sbjct: 201 FFIQEDDGRFSRFDEVHEERTYELLTYDILLEQAGFKSFKVYADFEDKEPTKTSKRWFFV 26- 0 Query: 242 AHK 244 A+K Sbjct: 261 AYK 263 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1807 A DNA sequence (GBSx1914) was identified in S. agalactiae <SEQ ID 5621> which encodes the amino acid sequence <SEQ ID 5622>. Analysis of this protein sequence reveals the following: TABLE-US-05540 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3538 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05541 >GP:BAB06304 GB:AP001516 unknown conserved protein [Bacillus halodurans] Identities = 129/367 (35%), Positives = 184/367 (49%), Gaps = 45/367 (12%) Query: 1 MTVTGIVAEFNPFHNGHKYLLEQAQ-----GIKVIAMSGNFMQRGEPAIVDKWTRSQMAL 55 M G+V E+NPFHNGH + L +A+ + + MSG F+QRGEPAI+ KW R+ +AL Sbjct: 1 MKAVGVVVEYNPFHNGHLHHLTEARKQAKADVVIAVMSGYFLQRGEPAILPKWERTSLAL 60- Query: 56 ENGADLVIELPFLVSVQSADYFASGAVSILARLGVDNLCFGTEE--MLDYARIGDIYVNK 1- 13 + GADLV+ELP+ S Q A++FA+GAVSILA L D LCFG+EE + + R+ Sbjct: 61 QGGADLVVELPYAFSTQKAEWFATGAVSILAALEADALCFGSEEGTIEPFHRLYHFMAKH 12- 0 Query: 114 KEEMEAFLKKQSD-SLSYPQKMQAMWQEFAGIT--FSGQTPNHILGLAYTKAA--SQNGI 16- 8 + + +K++ D +SYP ++ G PN+ILG Y KA I Sbjct: 121 RLAWDRMIKEELDKGMSYPTATSLAFKRLEGSAEHLDLSRPNNILGFHYVKAIYDLHTSI 18- 0 Query: 169 RLNPIQRQGAGYHSSEKTE-IFASATSLRK--------HQSDRFF------VEKGMPNSD 21- 3 + I R AGYH E ASATS+RK DR + K Sbjct: 181 KAMTIPRIKAGYHDDSLNESSIASATSIRKSLKTKEGWQMVDRVVPSYTTEMLRSFEKET 24- 0 Query: 214 LFLNSPQVVWQDYFSLLKYQIMTHS--DLTQIYQVNEEIANRIKSQIRYVETVDELVDKV 27- 1 FL S W+ F LLKY+++T + L IY+ E + R I + + + K+ Sbjct: 241 TFLPS----WERLFPLLKYRLLTATPEQLHAIYEGEEGLEYRALKTIVSATSFHDWMTKM 29- 6 Query: 272 ATKRYTKARIRRLLTYILINAVESPIPNA----------IHVLGFTQKGQQHLKSVKK-- 31- 9 TKRYT RI+R T++ N + I + I +LG T +GQ +L KK Sbjct: 297 KTKRYTWTRIQRYATHLFTNTTKEEIHSVLPRGTSSLPYIRLLGMTSRGQMYLNGKKKQL 35- 6 Query: 320 SVDIVTR 326 + ++TR Sbjct: 357 TTPVITR 363 A related DNA sequence was identified in S. pyogenes <SEQ ID 5623> which encodes the amino acid sequence <SEQ ID 5624>. Analysis of this protein sequence reveals the following: TABLE-US-05542 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ------ bacterial cytoplasm --- Certainty = 0.3165(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05543 Identities = 221/359 (61%), Positives = 288/359 (79%) Query: 1 MTVTGIVAEFNPFHNGHKYLLEQAQGIKVIAMSGNFMQRGEPAIVDKWTRSQMALENGAD 60- MTVTGI+AEFNPFHNGHKYLLE A+G+K+IAMSGNFMQRGEPA++DKW RS+MAL+NGAD Sbjct: 1 MTVTGIIAEFNPFHNGHKYLLETAEGLKIIAMSGNFMQRGEPALIDKWIRSEMALKNGAD 60- Query: 61 LVIELPFLVSVQSADYFASGAVSILARLGVDNLCFGTEEMLDYARIGDIYVNKKEEMEAF 12- 0 +V+ELPF VSVQSADYFA GA+ IL +LG+ L FGTE ++DY ++ +Y K E+M A+ Sbjct: 61 IVVELPFFVSVQSADYFAQGAIDILCQLGIQQLAFGTENVIDYQKLIKVYEKKSEQMTAY 12- 0 Query: 121 LKKQSDSLSYPQKMQAMWQEFAGITFSGQTPNHILGLAYTKAASQNGIRLNPIQRQGAGY 18- 0 L D+ SYPQK Q MW+ FAG+ FSGQTPNHILGL+Y KA++ I+L PI+RQGA Y Sbjct: 121 LSTLEDTFSYPQKTQKMWEIFAGVKFSGQTPNHILGLSYAKASAGKHIQLCPIKRQGAAY 18- 0 Query: 181 HSSEKTEIFASATSLRKHQSDRFFVEKGMPNSDLFLNSPQVVWQDYFSLLKYQIMTHSDL 24- 0 HS +K + ASA+++R+H +D F+ +PN+ L +N+P + W YFS LKYQI+ HSDL Sbjct: 181 HSKDKNHLLASASAIRQHLNDWDFISHSVPNAGLLINNPHMSWDHYFSFLKYQILNHSDL 24- 0 Query: 241 TQIYQVNEEIANRIKSQIRYVETVDELVDKVATKRYTKARIRRLLTYILINAVESPIPNA 30- 0 T I+QVN+E+A+RIK I+ + +D LVD VATKRYTKAR+RR+LTYIL+NA E +P Sbjct: 241 TSIFQVNDELASRIKKAIKVSQNIDHLVDTVATKRYTKARVRRILTYILVNAKEPTLPKG 30- 0 Query: 301 IHVLGFTQKGQQHLKSVKKSVDIVTRIGSQTWDSLTQRADSVYQMGNANIAEQTWGRIP 359- IH+LGFT KGQ HLK +KKS ++TRIG++TWD +TQ+ADS+YQ+G+ +I EQ++GRIP Sbjct: 301 IHILGFTSKGQAHLKKLKKSRPLITRIGAETWDEMTQKADSIYQLGHQDIPEQSFGRIP 359- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1808 A DNA sequence (GBSx1915) was identified in S. agalactiae <SEQ ID 5625> which encodes the amino acid sequence <SEQ ID 5626>. This protein is predicted to be transcriptional activator tipa. Analysis of this protein sequence reveals the following: TABLE-US-05544 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3117(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05545 >GP:CAB15677 GB:Z99122 transcriptional regulator [Bacillus subtilis] Identities = 91/246 (36%), Positives = 144/246 (57%), Gaps = 14/246 (5%) Query: 4 VKEISHISGISVRTLHYYDEIDLLSPSFVGENGYRYYDDESLIKLQEILLFKELEFPLKK 63- VK+++ ISG+S+RTLH+YD I+LL+PS + + GYR Y D L +LQ+IL FKE+ F L + Sbjct: 5 VKQVAEISGVSIRTLHHYDNIELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDE 64- Query: 64 IKEIMDSPNYDRNQALLDQIRWLELKKQRLEEVIEHAK----SIQRGKNMSD---FTAYN 11- 6 IKE++D PN+DR AL Q L KKQR++E+I+ S+ G+ M+ F + Sbjct: 65 IKEMLDHPNFDRKAALQSQKEILMKKKQRMDEMIQTIDRTLLSVDGGETMNKRDLFAGLS 12- 4 Query: 117 QEELEAFQ----EEARTRWGD--TDSYKEFENSHSKNDFSMISQAMSQIFKDFGQLKELS 17- 0 +++E Q +E R +G + ++ +++S +D+ I I++ + Sbjct: 125 MKDIEEHQQTYADEVRKLYGKEIAEETEKRTSAYSADDWRTIMAEFDSIYRRIAARMKHG 18- 4 Query: 171 PTDEKVQKQVQILQDYITAQFYNCTNDLLASLGIMYIQDERFQKSIDNWGGQGTALFVSK 23- 0 P D ++Q V +D+I Y+CT D+ LG +YI DERF SI+ + G+G A F+ + Sbjct: 185 PDDAEIQAAVGAFRDHICQYHYDCTLDIFRGLGEVYITDERFTDSINQY-GEGLAAFLRE 24- 3 Query: 231 AIDSYC 236 AI YC Sbjct: 244 AIIIYC 249 There is also homology to SEQ ID 1712. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1809 A DNA sequence (GBSx1916) was identified in S. agalactiae <SEQ ID 5627> which encodes the amino acid sequence <SEQ ID 5628>. Analysis of this protein sequence reveals the following: TABLE-US-05546 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2590(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05547 >GP:CAB14597 GB:Z99117 yrkC [Bacillus subtilis] Identities = 56/129 (43%), Positives = 74/129 (56%), Gaps = 7/129 (5%) Query: 2 KGFHGNIEKLTLGNTNFRQVLYTAEHCQLVLMTLPVGGEIGSEIHAENDQFFRFEAGHGK 61- K F NI + T N FR L+T +H Q+ LM+L +G +IG EIH DQF R E G G Sbjct: 59 KPFVVNINRATKQNNTFRTALWTGKHFQVTLMSLGIGEDIGLEIHPNVDQFLRIEQGRGI 11- 8 Query: 62 VVIDGN------EYEVADGDAIIVPAGAEHNVINTSETEMLKLYTIYSPAHHKDGIIRAT 11- 5 V + + + V D AI+VPAG HNVINT T LKLY+IY+P +H G + T Sbjct: 119 VKMGKSKDHLNFQRNVYDDSAIVVPAGTWHNVINTGNTP-LKLYSIYAPPNHPFGTVHET 17- 7 Query: 116 REEAEENEE 124 + +A E+ Sbjct: 178 KADAVAAED 186 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1810 A DNA sequence (GBSx1917) was identified in S. agalactiae <SEQ ID 5629> which encodes the amino acid sequence <SEQ ID 5630>. This protein is predicted to be glycerol uptake facilitator (glpF). Analysis of this protein sequence reveals the following: TABLE-US-05548 Possible site: 61 >>>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.08 Transmembrane 156-172 (153-180) INTEGRAL Likelihood = -6.21 Transmembrane 135-151 (132-155) INTEGRAL Likelihood = -4.09 Transmembrane 86-102 (80-103) INTEGRAL Likelihood = -3.93 Transmembrane 213-229 (212-230) INTEGRAL Likelihood = -3.72 Transmembrane 8-24 (5-28) INTEGRAL Likelihood = -2.76 Transmembrane 38-54 (36-58) ----- Final Results ----- bacterial membrane --- Certainty = 0.4630(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05549 >GP:BAB04811 GB:AP001510 glycerol uptake facilitator [Bacillus halodurans] Identities = 135/230 (58%), Positives = 171/230 (73%) Query: 1 MTQFLGEFLGTFILVLLGDGVVAGNVLSKTKEEGTGWTAIVFGWGIACTVAVYVSGLFSP 60- M+ FLGE +GT IL++LG GVVAG VL TK E GW I WG+A AVY G S Sbjct: 1 MSPFLGEVIGTMILIILGGGVVAGVVLKGTKSENGGWIVITAAWGLAVATAVYCVGQISG 60- Query: 61 AHLNPAVTLAMASIGAISWGQVIPFIIAQMLGAMVAATILWLHYYPHWKETKDSGLILAS 12- 0 AHLNPAVT+ +A +GA W QV +I+AQMLGAM+ AT+++LHYYPH+K T+D G LA Sbjct: 61 AHLNPAVTIGLALVGAFEWSQVAGYIVAQMLGAMIGATLVFLHYYPHFKATEDQGAKLAV 12- 0 Query: 121 FSTGPAIRHTPSNLLGEIIGTAILVITIMAIGPSKVAAGLGPIIVGIVIFAVGFSLDPTT 18- 0 FST PAI+H P+N E++GT +LV+ I+AIG ++ GL P+IVG++I +G SL TT Sbjct: 121 FSTDPAIKHLPANFFSEVLGTFVLVLGILAIGANEFTEGLNPLIVGLLIVVIGLSLGGTT 18- 0 Query: 181 GYAINPARDLGPRLMHAILPIEHKGNSDWSYAWIPVVGPIIGGVLGAILY 230 GYAINPARDLGPR+ H +LPI KG+S+WSYAWIP+VGFIIGG +GA+ Y Sbjct: 181 GYAINPARDLGPRIAHFLLPIPGKGSSNWSYAWIPIVGPIIGGGIGALTY 230 There is also homology to SEQ ID 2854. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1811 A DNA sequence (GBSx1918) was identified in S. agalactiae <SEQ ID 5631> which encodes the amino acid sequence <SEQ ID 5632>. Analysis of this protein sequence reveals the following: TABLE-US-05550 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1694(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05551 >GP: BAB07114 GB: AP001518 unknown conserved protein in others [Bacillus halodurans] Identities = 64/118 (54%), Positives = 85/118 (71%) Query: 5 GIIVVSHSKNIAQGVVDLISEVAKDVSITYVGGTEDGEIGTSFDQVQQIVEQNDKKTLLA 64 GI++ SH +A+G+V L+ E AKDVSITY GGT+D ++G SF+++QQ V N+ L Sbjct: 7 GIVISSHVPALAEGIVTLLKEAAKDVSITYAGGTDDDQVGASFEKIQQAVMDNEADELFV 66 Query: 65 FFDLGSAKMNLELVADFSEKNIIINSVPVVEGAYTAAALLQAGADLDSIQSQLAELTI 122 F+DLGSAKMN+E+V + SEK I + V +VEGAYTAAAL Q GA ++I QL LTI Sbjct: 67 FYDLGSAKMNVEMVMELSEKTIHLMDVALVEGAYTAAALTQGGASFETIMEQLQPLTI 124 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1812 A DNA sequence (GBSx1919) was identified in S. agalactiae <SEQ ID 5633> which encodes the amino acid sequence <SEQ ID 5634>. Analysis of this protein sequence reveals the following: TABLE-US-05552 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4753 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05553 >GP: BAB07115 GB: AP001518 unknown conserved protein in others [Bacillus halodurans] Identities = 98/190 (51%), Positives = 135/190 (70%), Gaps = 2/190 (1%) Query: 3 VKTAIEWMHTFNQKIQSNKDYLSELDTPIGDGDHGGNMARGMTAVIENLDNNEFSSAADV 62 V+ +W+H F++K+Q+N+ YLSELD+ IGDGDHG NMARG+ V L N F S +V Sbjct: 4 VENTTKWLHAFHEKVQANQSYLSELDSAIGDGDHGTNMARGLAEVERKLKENLFESPQEV 63 Query: 63 FKTVSMQLLSKVGGASGPLYGSAFMGITK-AEQSKSTISEALGAGLEMIQKRGKAELNEK 121- K +M L+SK GGASGPLYG+A + ++K I +++ AGL I KRGKA EK Sbjct: 64 LKMAAMALISKTGGASGPLYGTALLEMSKQVANDPQNIGKSIEAGLNGILKRGKATTGEK 123- Query: 122 TMVDVWHGVIEAI-EKNELTEDRIDSLVDATKGMKATKGRASYVGERSVGHIDPGSFSSG 18- 0 TMVD+W V+E++ + +L+++RI V TK MKATKGRASY+GERS+GH+DPG+ SSG Sbjct: 124 TMVDIWKPVVESLMAEQQLSKERIQQFVSETKEMKATKGRASYLGERSLGHLDPGAVSSG 18- 3 Query: 181 LLFKALLEVG 190 LF+A+++ G Sbict: 184 YLFEAMIDGG 193 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1813 A DNA sequence (GBSx1920) was identified in S. agalactiae <SEQ ID 5637> which encodes the amino acid sequence <SEQ ID 5638>. This protein is predicted to be dihydroxyacetone kinase (b1200). Analysis of this protein sequence reveals the following:

TABLE-US-05554 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2080(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05555 >GP: BAB07116 GB: AP001518 dihydroxyacetone kinase [Bacillus halodurans] Identities = 204/329 (62%), Positives = 261/329 (79%) Query: 1 MKKILNQPTDVVTEMLDGLAYVHNDLVHRIEGFDIIARNEEKSGKVALISGGGSGHEPSH 60 MKKILN P +V+ EMLDG Y + LV R+ G +I R E GKVAL+SGGGSGHEPSH Sbjct: 1 MKKILNDPQNVLDEMLDGFVYANGHLVERVAGTGVIRRTYEDKGKVALVSGGGSGHEPSH 60 Query: 61 AGFVGEGMLSAAVCGAVFTSPTPDQVLEAIKEADEGAGVFMVIKNYSGDIMNFEMAQDMA 120- AGFVG+GMLSAAVCG VFTSPTPDQ+ E IK AD+G GV ++IKNY+GD+MNFEMA +MA Sbjct: 61 AGFVGQGMLSAAVCGEVFTSPTPDQIFEGIKAADQGGGVLLIIKNYTGDVMNFEMAGEMA 120- Query: 121 EMEGIEVASVVVDDDIAVEDSLYTQGKRGVAGTILVHKILGHAARHGKSLQEIKAIADEL 18- 0 E EGI V ++V+DDIAVEDS +T G+RGVAGTI+VHKI+G AA G SLQ +K + + + Sbjct: 121 EAEGITVDHIIVNDDIAVEDSSFTAGRRGVAGTIIVHKIVGAAAEAGLSLQSLKVLGETV 18- 0 Query: 181 VPNIHTVGLALSGATVPEVGKPGFVLAEDEIEFGIGIHGEPGYRKEKMQPSKALATELVD 24- 0 + N T+G+++ ATVP VGKPGF L +DE+E+G+GIHGEPGYRKEK++ SK +A EL+ Sbjct: 181 IENTKTIGVSILPATVPAVGKPGFELGDDEMEYGVGIHGEPGYRKEKLKSSKEIAEELIL 24- 0 Query: 241 KLIESFDAKSGEKYGVLINGMGATPLMEQYVFANDVAKLLEDKGIEVNYKKLGNYMTSID 30- 0 KL E+F G+EYGVL+NG+GATPLMEQYVF NDVA L ++G+ + +KK+G++MTSID Sbjct: 241 KLKEAFGWSEGDEYGVLVNGLGATPLMEQYVFMNDVANELTEEGLNIQFKKVGSFMTSID 30- 0 Query: 301 MAGLSLTLIKLENQEWLEALNSDVTTIAW 329 MAG+SLTLIK+ ++WL+ N +V T+ W Sbjct: 301 MAGVSLTLIKIVEEKWLDYWNHEVKTVDW 329 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1814 A DNA sequence (GBSx1921) was identified in S. agalactiae <SEQ ID 5639> which encodes the amino acid sequence <SEQ ID 5640>. Analysis of this protein sequence reveals the following: TABLE-US-05556 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1997(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05557 >GP: BAB07113 GB: AP001518 unknown [Bacillus halodurans] Identities = 59/142 (41%), Positives = 82/142 (57%), Gaps = 5/142 (3%) Query: 1 MTSSLITKKKIAKSFKRLFISQAFDKISVSDIMEDAGIRRQTFYNHFVDKYALLEWIFQT 60 MT+S+ITKK IAK+FK L Q F KISVSDIM A +RRQTFY HF DK+ LL WI++ Sbjct: 1 MTNSIITKKVIAKAFKDLMEVQPFSKISVSDIMNRANMRRQTFYYHFQDKFELLHWIYKQ 60 Query: 61 ELSEQVTDNLDYISGFQLLSELLTFFKMNQEFYIKLFQIEDQNDFSSYFESYCEQLVDKL 120- E E D L Y + L+ +F NQ FY + + QN F+ Y + + L Sbjct: 61 ETKEHSIDFLAYDDIHTIFRHLMHYFYENQTFYQRAMVVNGQNGFTDYLYEHIQTL---Y 117- Query: 121 LSDYSKSNFNQKERVTFINYHS 142 L++ + +QK+R +++S Sbjct: 118 LNEIDRR--SQKDREFISSFYS 137 A related DNA sequence was identified in S. pyogenes <SEQ ID 5641> which encodes the amino acid sequence <SEQ ID 5642>. Analysis of this protein sequence reveals the following: TABLE-US-05558 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2101(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05559 Identities = 31/115 (26%), Positives = 58/115 (49%), Gaps = 6/115 (5%) Query: 7 TKKKIAKSFKRLFISQAFDKISVSDIMEDAGIRRQTFYNHFVDKYALLEWIFQTELSEQV 66 TK + + L Q+F+ ++VSD+ + AGI R TFY H+ DK+ ++ F+ + + + Sbjct: 8 TKAYVKTALTTLLTEQSFETLTVSDLTKKAGINRGTFYLHYTDKFDMMNH-FKNDTLDDL 66 Query: 67 TDNLD----YISGFQLLSELLTFFKMNQEFYIKLFQIEDQNDFSSYFESYCEQLV 117 L+ Y Q+L++ L++ ++EF L I F + +C Q + Sbjct: 67 YRLLNQAEIYTDTRQVLNQTLSYLIEHREFITALATI-SYLKFPQLIKDFCYQFL 120 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1815 A DNA sequence (GBSx1922) was identified in S. agalactiae <SEQ ID 5643> which encodes the amino acid sequence <SEQ ID 5644>. Analysis of this protein sequence reveals the following: TABLE-US-05560 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1974(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1816 A DNA sequence (GBSx1923) was identified in S. agalactiae <SEQ ID 5645> which encodes the amino acid sequence <SEQ ID 5646>. This protein is predicted to be dihydroxyacetone kinase (b1200). Analysis of this protein sequence reveals the following: TABLE-US-05561 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1806(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05562 >GP: BAB07112 GB: AP001518 dihydroxyacetone kinase [Bacillus halodurans] Identities = 141/285 (49%), Positives = 197/285 (68%), Gaps = 1/285 (0%) Query: 45 IPILSGGGSGHEPAHFGYVGEGMLSAAISGPIFVPPCASDILETIRFINRGKGVFVIIKN 104- +PI+SGGGSGHEP H GYVGEGML+AA+ G +FVPP A +L IR +++GKGV +IIKN Sbjct: 46 VPIISGGGSGHEPGHLGYVGEGMLAAAVHGDVFVPPSAQQVLAAIRQMDQGKGVLLIIKN 105- Query: 105 FEADLEEFSQAIEQARQEGIPIKYIVSHDDISVET-SNFKIRHRGVAGTVLLHKIIGQAA 16- 3 F ADL F A QAR EG + +++ +DD+SVE+ ++F+ R RGVAG VL+HKIIG AA Sbjct: 106 FVADLATFLSAEVQARAEGRDVAHVIVNDDVSVESDASFEKRRRGVAGAVLVHKIIGAAA 16- 5 Query: 164 LEGASLDELEQLGLSLTTSMATLGVASKSATILGQHQPVFDIEEGYISFGIGIHGEPGYR 22- 3 EG SL+ L+++G + ++ATLGVA A + + +P F +EEG + FG+GIHGE GYR Sbjct: 166 KEGYSLEALQEIGEQVVKNLATLGVALTHADLPERREPQFLLEEGEVYFGVGIHGEQGYR 22- 5 Query: 224 TMPFVSMEHLANELVNKLKMKLRWQDGEAFILLINNLGGSSKMEELLFTNAVMEFLALDD 28- 3 VS E LA ELVNKLK RW + + +LIN LGG+ +E+ +F N V LA+++ Sbjct: 226 KEKLVSSELLAVELVNKLKSLYRWDKNDQYAVLINGLGGTPLIEQYVFANDVRRLLAIEN 28- 5 Query: 284 LQLPFIKTGHLITSLDMAGLSVTLCRVKDSRWIDYLKHKTDARAW 328 L + F+R G +TSL+M G+S+T+ ++ D +W+ +L D W Sbjct: 286 LHVSFVKVGTQLTSLNMKGISLTMLKICDEQWVKWLYAPVDVAHW 330 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1817 A DNA sequence (GBSx1924) was identified in S. agalactiae <SEQ ID 5647> which encodes the amino acid sequence <SEQ ID 5648>. Analysis of this protein sequence reveals the following: TABLE-US-05563 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3902(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10085> which encodes amino acid sequence <SEQ ID 10086> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05564 >GP: AAC75047 GB: AE000290 orf, hypothetical protein [Escherichia coli K12] Identities = 182/237 (76%), Positives = 201/237 (84%) Query: 20 MGRKWANIVAKKTAKDGANSKVYAKFGVEIYVAAKQGEPDPESNSALKFVLDRAKQAQVP 79 - MGRKWANIVAKKTAKDGA SK+YAKFGVEIY AAKQGEPDPE N++LKFV++RAKQAQVP Sbjct: 1 MGRKWANIVAKKTAKDGATSKIYAKFGVEIYAAAKQGEPDPELNTSLKFVIERAKQAQVP 60 Query: 80 KHVIDKAIDKAKGNTDETFVEGRYEGFGPNGSMIIVDTLTSNVNRTAANVRTAYGKNGGN 139- KHVIDKAIDKAKG DETFV+GRYEGFGPNGSMII +TLTSNVNRT ANVRT + K GGN Sbjct: 61 KHVIDKAIDKAKGGGDETFVQGRYEGFGPNGSMIIAETLTSNVNRTIANVRTIFNKKGGN 120- Query: 140 MGASGSVSYLFDKKGVIVFAGDDADTVFEQLLEADVDVDDVEAEEGTITVYTAPTDLHKG 19- 9 +GA+GSVSY+FD GVIVF G D D +FE LLEA+VDV DV EEG I +YT PTDLHKG Sbjct: 121 IGAAGSVSYMFDNTGVIVFKGTDPDHIFEILLEAEVDVRDVTEEEGNIVIYTEPTDLHKG 18- 0 Query: 200 IQALRDNGVEEFQVTELEMIPQSEVVLEGDDLETFEKLIDALESDDDVQKVYHNVAD 256 I AL+ G+ EF TELEMI QSEV L +DLE FE L+DALE DDDVQKVYHNVA+ Sbjct: 181 IAALKAAGITEFSTTELEMIAQSEVELSPEDLEIFEGLVDALEDDDDVQKVYHNVAN 237 A related DNA sequence was identified in S. pyogenes <SEQ ID 5649> which encodes the amino acid sequence <SEQ ID 5650>. Analysis of this protein sequence reveals the following: TABLE-US-05565 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2926(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05566 Identities = 233/238 (97%), Positives = 236/238 (98%) Query: 20 MGRKWANIVAKKTAKDGANSKVYAKFGVEIYVAAKQGEPDPESNSALKFVLDRAKQAQVP 79 - MGRKWANIVAKKTAKDGA SKVYAKFGVEIYVAAKQGEPDPE N+ALKFV+DRAKQAQVP Sbjct: 1 MGRKWANIVAKKTAKDGATSKVYAKFGVEIYVAAKQGEPDPELNTALKFVIDRAKQAQVP 60 Query: 80 KHVIDKAIDKAKGNTDETFVEGRYEGFGPNGSMIIVDTLTSNVNRTAANVRTAYGKNGGN 139- KHVIDKAIDKAKGNTDETFVEGRYEGFGPNGSMIIVDTLTSNVNRTAANVRTAYGKNGGN Sbjct: 61 KHVIDKAIDKAKGNTDETFVEGRYEGFGPNGSMIIVDTLTSNVNRTAANVRTAYGKNGGN 120- Query: 140 MGASGSVSYLFDKKGVIVFAGDDADTVFEQLLEADVDVDDVEAEEGTITVYTAPTDLHKG 19- 9 MGASGSVSYLFDKKGVIVFAGDDAD+VFEQLLEADVDVDDVEAEEGTITVYTAPTDLHKG Sbjct: 121 MGASGSVSYLFDKKGVIVFAGDDADSVFEQLLEADVDVDDVEAEEGTITVYTAPTDLHKG 18- 0 Query: 200 IQALRDNGVEEFQVTELEMIPQSEVVLEGDDLETFEKLIDALESDDDVQKVYHNVADF 257 IQALRDNGVEEFQVTELEMIPQSEVVLEGDDLETFEKLIDALESDDDVQKVYHNVADF Sbjct: 181 IQALRDNGVEEFQVTELEMIPQSEVVLEGDDLETFEKLIDALESDDDVQKVYHNVADF 238 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1818 A DNA sequence (GBSx1925) was identified in S. agalactiae <SEQ ID 5651> which encodes the amino acid sequence <SEQ ID 5652>. Analysis of this protein sequence reveals the following: TABLE-US-05567 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2507(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1819 A DNA sequence (GBSx1926) was identified in S. agalactiae <SEQ ID 5653> which encodes the amino acid sequence <SEQ ID 5654>. Analysis of this protein sequence reveals the following: TABLE-US-05568 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1523(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05569 >GP: CAA20826 GB: AL031541 hypothetical protein SCI35.37 [Streptomyces coelicolor A3(2)] Identities = 73/178 (41%), Positives = 101/178 (56%), Gaps = 2/178 (1%) Query: 35 VKNAGGLPVILPISEAESAKAYVEMIDKLIISGGQNVLPSYYGEEKIIESDDYSLARDIF 94 - V+ AGGL +LP E A A V +D ++I+GG +V P YG E + + ARD + Sbjct: 37 VQRAGGLAAMLPPDAPEHAAATVARVDGVVIAGGPDVEPVRYGAEPDPRTGPPARARDTW 96 Query: 95 EFALVEEALKQNKPIFAICRGMQLVNVALGGTLNQSIDNHYQEPYIGFAHYLNVEKGSFL 154- E AL+E AL P+ ICRGMQL+NVALGGTL Q I+ H + + H + G+ Sbjct: 97 ELALIEAALAARVPLLGICRGMQLLNVALGGTLVQHIERHAEVVGVFGGHPVRPVPGTLY 156- Query: 155 EGFISGDFKINSLHRQSVKLLAEGLIVSARDPRDGTVEAYESRT-EQCIIGVQWHPEL 211 G + + + + H Q+V L GL+ SA DGTVEA E + ++GVQWHPE+ Sbjct: 157 AGAVPEETFVPTYHHQAVDRLGSGLVASAH-AADGTVEALEMPSGSGWVLGVQWHPEM 213 A related DNA sequence was identified in S. pyogenes <SEQ ID 5655> which encodes the amino acid sequence <SEQ ID 5656>. Analysis of this protein sequence reveals the following: TABLE-US-05570 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1210(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05571 Identities = 111/230 (48%), Positives = 145/230 (62%), Gaps = 3/230 (1%) Query: 2 LTKPIIGITGNEREMSDIPGYYYDSVSRHISEGVKNAGGLPVILPISEAESAKAYVEMID 61- +TKPIIGIT N+R + + + V +GGLP++LPI + +AK YV M+D Sbjct: 1 MTKPIIGITANQRLNMALDNLPWSYAPTGFVQAVTQSGGLPLLLPIGDEAAAKTYVSMVD 60- Query: 62 KLIISGGQNVLPSYYGEEKIIESDDYSLARDIFEFALVEEALKQNKPIFAICRGMQLVNV 12- 1 K+I+ GGQNV P YY EEK DD+S RD FE A+++EA+ KPI ICRG QL+NV Sbjct: 61 KIILIGGQNVDPKYYQEEKAAFDDDFSPERDTFELAIIKEAITLKKPILGICRGTQLMNV 12- 0 Query: 122 ALGGTLNQSIDNHYQE-PYIGFAHYLNVEKGSFLEGFISGDFKINSLHRQSVKLLAEGLI 18- 0 ALGG LNQ ID+H+QE P +H + +E S L INS HRQS+K +A+ L Sbjct: 121 ALGGNLNQHIDSHWQEAPSDFLSHEMIIEPDSILYPIYGHKTLINSFHRQSLKTVAKDLK 18- 0 Query: 181 VSARDPRDGTVEAYESRTEQC-IIGVQWHPELMLH-QIENQTLFGYFVNE 228 V ARDPRDGT+EA S + +GVQWHPEL+ + E+ LF FVN+ Sbjct: 181 VIARDPRDGTIEAVISTNDAIPFLGVQWHPELLQGVRDEDLQLFRLFVND 230 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1820 A DNA sequence (GBSx1927) was identified in S. agalactiae <SEQ ID 5657> which encodes the amino acid sequence <SEQ ID 5658>. Analysis of this protein sequence reveals the following: TABLE-US-05572 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5794(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1821 A DNA sequence (GBSx1928) was identified in S. agalactiae <SEQ ID 5659> which encodes the amino acid sequence <SEQ ID 5660>. Analysis of this protein sequence reveals the following: TABLE-US-05573 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0524(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8905> which encodes amino acid sequence <SEQ ID 8906> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-05574 Lipop: Possible site: 22 Crend: 4 McG: Discrim Score: 8.37 GvH: Signal Score (-7.5): 0.64 Possible site: 21 >>> May be a lipoprotein ALOM program count: 0 value: 6.74 threshold: 0.0 PERIPHERAL Likelihood = 6.74 112 modified ALOM score: -1.85 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) A related DNA sequence was identified in S. pyogenes <SEQ ID 2919> which encodes the amino acid sequence <SEQ ID 2920>. Analysis of this protein sequence reveals the following: TABLE-US-05575 Possible site: 21 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05576 Identities = 120/162 (74%), Positives = 141/162 (86%), Gaps = 5/162 (3%) Query: 6 LAACSSKSHTTKTGK----KEVNFATVGTTAPFSYVKDGKLTGFDIEVAKAVFKGSDNYK 61- LAAC S S T ++G KEV FATVGTTAPFSY K G+LTG+DIEVAKAVFKGSD+YK SbjCt: 20 LAACGS-SKTAESGNQGSSKEVLFATVGTTAPFSYEKGGQLTGYDIEVAKAVFKGSDDYK 78- Query: 62 VTFKKTEWSSVFTGIDSGKFQMGGNNISYSSERSQKYLFSYPIGSTPSVLAVPKNSNIKA 12- 1 V+FKKTEWSS+FTG+DSGK+QMGGNNIS++ ERS KYLFSYPIGSTPSVL VPK+S+IK+ Sbjct: 79 VSFKKTEWSSIFTGLDSGKYQMGGNNISFTKERSAKYLFSYPIGSTPSVLVVPKDSDIKS 13- 8 Query: 122 YNDISGHKTQVVQGTTTAKQLENFNKEHQKNPVTLKYTNENL 163 ++DI GH TQVVQGTT+ QLE+FNK+H NPVTLK+TNEN+ Sbjct: 139 FDDIQGHTTQVVQGTTSVAQLEDFNKKHSONPVTLKFTNENI 180 SEQ ID 8906 (GBS71) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 4; MW 31.8 kDa). GBS71-His was purified as shown in FIG. 196, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1822 A DNA sequence (GBSx1929) was identified in S. agalactiae <SEQ ID 5661> which encodes the amino acid sequence <SEQ ID 5662>. Analysis of this protein sequence reveals the following:

TABLE-US-05577 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ------ bacterial cytoplasm --- Certainty = 0.2179(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. There is also homology to SEQ ID 2920: TABLE-US-05578 Identities = 64/91 (70%), Positives = 78/91 (85%) Query: 1 MSDGKADFKLFDGPTVNAIIRNQGLTNLKTIPLTMRDQPYIYFIFGQDQKDLQKYVNNRL 60- +S+GKADFK+FD PTVNAIIKNQGL NLKTI LT +QP+IYFIF QDQ+ LQ +VN R+ Sbjct: 187 LSEGKADFKIFDAPTVNAIIRNQGLDNLKTIELTSTEQPFIYFIFSQDQEKLQSFVNKRI 24- 6 Query: 61 KQLRKDGTLSKIAKEYLGGDYVPNEKDLVTP 91 K+L DGTLSK+AKE+LGGDYVP++K+L P Sbjct: 247 KELTADGTLSKLAKEHLGGDYVPSDKELKLP 277 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1823 A DNA sequence (GBSx1930) was identified in S. agalactiae <SEQ ID 5663> which encodes the amino acid sequence <SEQ ID 5664>. This protein is predicted to be 28 kDa outer membrane protein (yaeC). Analysis of this protein sequence reveals the following: TABLE-US-05579 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = 1.44 Transmembrane 25-41 (25-42) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05580 >GP:CAB59825 GB:AJ012388 hypothetical protein [Lactococcus lactis] Identities = 110/283 (38%), Positives = 175/283 (60%), Gaps = 13/283 (4%) Query: 22 KLKHIVLGLALTTLLGV----TFSNQEVSASSTSSKVVKVGVMTFSDTEKARWDKIEKLV 77- K ++I++ +A+ L+ + + ++Q +S K VKVG+M+ ++ W + Sbjct: 4 KNRNIIIAVAVLILVALVAFFSLNHQGGVKASAGEKTVKVGIMSGDKQDQEVWKSVANTA 63- Query: 78 GDK--AKIKETEFTDYTQPNQATANKDVDINAFQHYNFLENWNKENKKNLIPLEKTYLAP 13- 5 +K K+KF F+DY QPN+A + D+DINAFQ YN+++ WNK +K +++ + TY+ P Sbjct: 64 KEKYDLKLKFVYFSDYNQPNEALLSGDIDINAFQSYNYVKTWNKAHKSDIVAVGNTYITP 12- 3 Query: 136 IRIYSEKVKSLKKLKKGATIAIPNDATNGSRALYVLQSAGLIKLNVS-GKKVATVANITS 19- 4 + IYS+++ L LK+G+T+AIPNDA+N SRAL+VLQSAGL+KL S K+ + +IT Sbjct: 124 MHIYSKEISKLSDLKEGSTVAIPNDASNESRALFVLQSAGLLKLTTSDSSKLVGLPDITE 18- 3 Query: 195 NKKDINIQELDASQTPRALKDVDAAIINNTYIEQANLKPSDAIFVEKSDKNSKQWINIIA 25- 4 N + +E+DASQTPPAL V +++N Y A+L S+++F+E +K S Q+IN IA Sbjct: 184 NPHQLKFKEVDASQTPRALDSVALSVVNYNYATAASLPKSESVFMEPLNKTSAQYINFIA 24- 3 Query: 255 GRKNWKKQKNAKAIQAILDAYHTDEVKKVIKDTSAD---IPQW 294 K+KN K + + AY + +K IK+ D +P W Sbjct: 244 ---TTSKEKNNKVYKEVAKAYASKATEKAIKEQYPDGGELPAW 283 There is also homology to SEQ ID 2132. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8907> and protein <SEQ ID 8908> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05581 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 7.47 GVH: Signal Score (-7.5): -4.79 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -1.44 threshold: 0.0 INTEGRAL Likelihood = -1.44 Transmembrane 5-21 (5-22) PERIPHERAL Likelihood = 5.20 147 modified ALOM score: 0.79 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00126## SEQ ID 8908 (GBS35) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 11 (lane 2; MW 31.6 kDa). The GBS35-His fusion product was purified (FIG. 96A; see also FIG. 192, lane 6) and used to immunise mice (lane 2 product; 20 kg/mouse). The resulting antiserum was used for Western blot (FIG. 96B), FACS (FIG. 96C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. EXAMPLE 1824 A DNA sequence (GBSx1931) was identified in S. agalactiae <SEQ ID 5665> which encodes the amino acid sequence <SEQ ID 5666>. Analysis of this protein sequence reveals the following: TABLE-US-05582 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3126(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05583 GP:AAF11560 GB:AE002038 ArgE/DapE/Acyl family protein {Deinococcus radiodurans} Identities = 129/419 (30%), Positives = 210/419 (49%), Gaps = 14/419 (3%) Query: 26 LRDLIAIKSIFAQKVGLNDLSSYLGEVFIKAGAEVIIDDSYSAPFIVANFKSSKVDAKRI 85- LR L+A+ S+ AQ L + + + + G V AP ++A + Sbjct: 16 LRALVALPSVSAQGRMLPETADAVAGLLRAEGFGVQQFPGTVAPVLLAEAGEGPFT---L 72- Query: 86 IFYNHYDTVPADEVEQWTEDPFTLSLRYGKMYGRGVDDDKGHITARLSAVKKYLSRHKGE 14- 5 + YNHYD P D +E W PF L+ R G++YGRG DDKG + +RL+AV+ + G Sbjct: 73 LIYNHYDVQPEDPLELWDTPPFELTERGGRLYGRGASDDKGELASRLAAVRA-VREQLGH 13- 1 Query: 146 LPLDITFIVEGAEESASVGLDYYLEKYQEQLQGADLIVWEDGPKNPKGQLEIAGGNKGIV 20- 5 LP+ I +++EG EE S L+ ++ ++ +LQ AD WE G +P+G+ ++ G KG++ Sbjct: 132 LPVKIKWLIEGEEEVGSPTLERFVAEHAAELQ-ADGCWWEFGGISPEGRPILSLGLKGVM 19- 0 Query: 206 TFDLSVSSADVDIHSSFGGVVDSSTWYLIQALNTLRDNKGHILVEGIYDKVIPPTKRELE 26- 5 +L AD D+HSS G V+D+ + L +A+ +LRD +G++ + G YD V + + + Sbjct: 191 CLELRCRVADSDLHSSLGAVIDNPLYCLARAVASLRDEQGNVTIPGFYDDVRAASGADRQ 25- 0 Query: 266 LVEKYSYRSAKALEGAYQLVLPSLADSHKTFLRKLYFEPSIAIEGITSGYQGEGVKTILP 32- 5 + + +A+ + + P + + + P + + G GYQGEG KT+LP Sbjct: 251 AIAQIP-GDGQAVRDTFGVRRP--LATGPAYNERTNLHPVVNVNGWGGGYQGEGSKTVLP 30- 7 Query: 326 AYAKCKAEVRLVPGLTPKGVLDSIQNHLKENGFKDIELT-YTLGEMSYRSDMSAPSILKV 38- 4 K + RLVP P VL ++ HL G DIE+ + R+D P + Sbjct: 308 GAGFVKLDFRLVPDQDPARVLSLLREHLTAQGLSDIEVVELEAHQKPARADAGHPFVQAC 36- 7 Query: 385 VDLAEQFYPEGISLLPTSPGTGPMY-----LVHQALRAPIAAIGIGHANSRDHGVDENV 438- V A + + + P+S +GPM+ L P A+GIG+ R H +EN+ Sbjct: 368 VAAARAAHGQDPIVHPSSGASGPMFPFTGGAGGGGLGIPCVAVGIGNHAGRVHAPNENI 426- There is also homology to SEQ ID 2588. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1825 A DNA sequence (GBSx1932) was identified in S. agalactiae <SEQ ID 5667> which encodes the amino acid sequence <SEQ ID 5668>. This protein is predicted to be amino acid ABC transporter, ATP-binding protein. Analysis of this protein sequence reveals the following: TABLE-US-05584 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5366(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05585 >GP:CAB59828 GB:AJ012388 hypothetical protein [Lactococcus lactis] Identities = 187/338 (55%), Positives = 256/338 (75%), Gaps = 12/338 (3%) Query: 6 IIKLDNIDVTFHQKKREINAVKDVTIHINQGDIYGIVGYSGAGKSTLVRVINLLQEPSAG 65- II+L+N+ V FHQK R + AVK+ T+HI +GDIYG++GYSGAGKSTLVR INLLQ+P+G Sbjct: 4 IIELNNLSVQFHQKGRLVTAVKNATLHIEKGDIYGVIGYSGAGKSTLVRTINLLQKPTEG 63- Query: 66 KITIDDQVIYD--NKVTLTSTQLREQRREIGMIFQHFNLMSQLTAEQNVAFALKHSG--- 12- 0 +I I+ + I+D N V T +LRE R++IGMIFQHFNL+S+ T NVAFAL+HS Sbjct: 64 QIVINGEKIFDSENPVKFTGAKLREFRQKIGMIFQHFNLLSEKTVFNNVAFALQHSQIED 12- 3 Query: 121 -------LSKEAKAAKVAKLLELVGLSDRAQNYPSQLSGGQKQRVAIARALANDPKILIS 17- 3 L+K+ K KV +LL+LV L+D + YP+QLSGGQKQRVAIARALANDP+ILIS Sbjct: 124 KNGKKRYLTKKEKNDKVTELLKLVDLADLSDKYPAQLSGGQKQRVAIARALANDPEILIS 18- 3 Query: 174 DESTSALDPKTTKQILALLQDLNKKLGLTIVLITHEMQIVKDIANRVAVMQNGKLIEEGS 23- 3 DE TSALDPKTT QIL LL+ L++KLG+T+VLITHEMQ+VK+IAN+VAVMQNG++IE+ S Sbjct: 184 DEGTSALDPKTTNQILDLLKSLHEKLGITVVLITHEMQVVKEIANKVAVMQNGEIIEQNS 24- 3 Query: 234 VLDIFSHPRESLTQDFIKIATGIDEAMLKIEQQEVVKNLPVGSKLVQLKYAGHSTDEPLL 29- 3 ++DIF+ P+E+LT+ FI+ + ++ + + + E++ L +L+ L Y+G ++P++ Sbjct: 244 LIDIFAQPKEALTKQFIETTSSVNRFIASLSKTELLAQLADDEELIHLDYSGSELEDPVV 30- 3 Query: 294 NQIYKEFEVTANILYGNIEILDGIPVGEMVVILSGDEE 331 + I K+F+VT NI YGN+E+L G P G +V+ L G E Sbjct: 304 SDITKKFDVTTNIFYGNVELLQGQPFGSLVLTLKGSSE 341 There is also homology to SEQ ID 76. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1826 A DNA sequence (GBSx1933) was identified in S. agalactiae <SEQ ID 5669> which encodes the amino acid sequence <SEQ ID 5670>. This protein is predicted to be ABC transporter, permease protein. Analysis of this protein sequence reveals the following: TABLE-US-05586 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.79 Transmembrane 203-219 (197-225) INTEGRAL Likelihood = -8.86 Transmembrane 73-89 (69-102) INTEGRAL Likelihood = -7.38 Transmembrane 38-54 (35-56) INTEGRAL Likelihood = -1.12 Transmembrane 103-119 (103-119) ----- Final Results ----- bacterial membrane --- Certainty = 0.6116(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10083> which encodes amino acid sequence <SEQ ID 10084> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05587 >GP:CAB59829 GB:AJ012388 hypothetical protein [Lactococcus lactis] Identities = 137/231 (59%), Positives = 171/231 (73%), Gaps = 1/231 (0%) Query: 1 MIEWIQTHLPNVYQMGWEGAYGWQTAIVQTLYMTFWSFLIGGLMGLLGGLFLVLTSPRGV 60- M EW PNV +GW G GW TAIVQTLYMTF S LIGGL+GL+ G+ +V+T+ G+ Sbjct: 1 MAEWFAHTFPNVVYLGWTGETGWWTAIVQTLYMTFISALIGGLLGLIFGIGVVVTAEDGI 60- Query: 61 IANKLVFGVLDKVVSVFRALPFIILLALIAPVTRVIVGTTLGSPAALVPLSLAVFPFFAR 12- 0 N+ +F +LDK+VS+ RA PFIILLA IAP+T+++VGT +G AALVPL+L V PF+AR Sbjct: 61 TPNRPLFWILDKIVSIGRAFPFIILLAAIAPLTKILVGTQIGVTAALVPLALGVAPFYAR 12- 0 Query: 121 QVQVVLAELDGGVIEAAQASGGTLWDII-VVYLREGLPDLIRVSTVTLISLVGETAMAGA 17- 9 QVQ L +D G +EAAQ G DI+ VYLRE L LIRVSTVTLISL+G TAMAGA Sbjct: 121 QVQASLESVDHGKVEAAQTVGADFLDIVFTVYLREELASLIRVSTVTLISLIGLTAMAGA 18- 0 Query: 180 IGAGGLGSVAITKGYNYSRDDITLVATILILLLIFFIQFLGDFLTRRLSHK 230 IGAGGLG+ AI+ GYN +D+T ATILIL+ + +Q +GDFL RR+SH+ Sbjct: 181 IGAGGLGNTAISYGYNRFANDVTWFATILILIFVLLVQLVGDFLARRVSHR 231 A related DNA sequence was identified in S. pyogenes <SEQ ID 5671> which encodes the amino acid sequence <SEQ ID 5672>. Analysis of this protein sequence reveals the following: TABLE-US-05588 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.15 Transmembrane 194-210 (187-215) INTEGRAL Likelihood = -10.67 Transmembrane 28-44 (20-52) INTEGRAL Likelihood = -8.12 Transmembrane 70-86 (62-91) ----- Final Results ----- bacterial membrane --- Certainty = 0.5458(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05589 >GP:CAB59829 GB:AJ012388 hypothetical protein [Lactococcus lactis] Identities = 123/213 (57%), Positives = 153/213 (71%), Gaps = 1/213 (0%) Query: 9 GDAGWGLAIWNTLYMTIVPFIVGGAIGLLLGLLLVLTGPDGVIENKTICWVIDKVTSIFR 68- G+ GW AI TLYMT + ++GG +GL+ G+ +V+T DG+ N+ + W++DK+ SI R Sbjct: 19 GETGWWTAIVQTLYMTFISALIGGLLGLIFGIGVVVTAEDGITPNRPLFWILDKIVSIGR 78- Query: 69 AIPFVILIAILASFTYLLLRTTLGATAALVPLTFATFPFYARQVQVVFSELDKGVIEAAQ 12- 8 A PF+IL+A +A T +L+ T +G TAALVPL PFYARQVQ +D G +EAAQ Sbjct: 79 AFPFIILLAAIAPLTKILVGTQIGVTAALVPLALGVAPFYARQVQASLESVDHGKVEAAQ 13- 8 Query: 129 ASGATFWDIV-KVYLSEGLPDLIRVSTVTLISLVGETAMAGAIGAGGLGNVAISYGYNRF 18- 7 GA F DIV VYL E L LIRVSTVTLISL+G TAMAGAIGAGGLGN AISYGYNRF Sbjct: 139 TVGADFLDIVFTVYLREELASLIRVSTVTLISLIGLTAMAGAIGAGGLGNTAISYGYNRF 19- 8 Query: 188 NNDVTWVATIIILLIIFAIQFIGDSLTRRFSHK 220 NDVTW ATI+IL+ + +Q +GD L RR SH+ Sbjct: 199 ANDVTWFATILILIFVLLVQLVGDFLARRVSHR 231 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05590 Identities = 146/212 (68%), Positives = 172/212 (80%) Query: 19 GAYGWQTAIVQTLYMTFWSFLIGGLMGLLGGLFLVLTSPRGVIANKLVFGVLDKVVSVFR 78- G GW AI TLYMT F++GG +GLL GL LVLT P GVI NK + V+DKV S+FR Sbjct: 9 GDAGWGLAIWNTLYMTIVPFIVGGAIGLLLGLLLVLTGPDGVIENKTICWVIDKVTSIFR 68- Query: 79 ALPFIILLALIAPVTRVIVGTTLGSPAALVPLSLAVFPFFARQVQVVLAELDGGVIEAAQ 13- 8 A+PF+IL+A++A T +++ TTLG+ AALVPL+ A FPF+ARQVQVV +ELD GVIEAAQ Sbjct: 69 AIPFVILIAILASFTYLLLRTTLGATAALVPLTFATFPFYARQVQVVFSELDKGVIEAAQ 12- 8 Query: 139 ASGGTLWDIIVVYLREGLPDLIRVSTVTLISLVGETAMAGAIGAGGLGSVAITKGYNYSR 19- 8 ASG T WDI+ VYL EGLPDLIRVSTVTLISLVGETAMAGAIGAGGLG+VAI+ GYN Sbjct: 129 ASGATFWDIVKVYLSEGLPDLIRVSTVTLISLVGETAMAGAIGAGGLGNVAISYGYNRFN 18- 8 Query: 199 DDITLVATILILLLIFFIQFLGDFLTRRLSHK 230 +D+T VATI+ILL+IF IQF+GD LTRR SHK Sbjct: 189 NDVTWVATIIILLIIFAIQFIGDSLTRRFSHK 220 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1827 A DNA sequence (GBSx1934) was identified in S. agalactiae <SEQ ID 5673> which encodes the amino acid sequence <SEQ ID 5674>. This protein is predicted to be alcohol dehydrogenase, zinc-containing (Zn-dependent). Analysis of this protein sequence reveals the following: TABLE-US-05591 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Liklihood = -2.92 Transmembrane 71-87 (69-87) ----- Final Results ----- bacterial membrane --- Certainly = 0.2168(Affirmative) < succ> bacterial outside --- Certainly = 0.0000(Not clear) < succ> bacterial cytoplasm --- Certainly = 0.0000(Not clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9419> which encodes amino acid sequence <SEQ ID 9420> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05592 >GP:AAE41759 GB:AE002488 alcohol dehydrogenase, zinc-containing [Neisseria meningitidis MC58] Identities = 135/246 (54%), Positives = 186/246 (74%), Gaps = 1/246 (0%) Query: 3 SHCEDGGWILGHLIEGTQAEYVHIPHADGSLYHAPEGVCDDALVMLSDILPTSYEIGVLP 62- SHC +GGWILG++I+GTQAEYV P+AD SL P+ V ++ ++LSD LPT++EIGV Sbjct: 102 SHCRNGGWILGYMIDGTQAEYVRTPYADNSLVPLPDNVNEEIALLLSDALPTAHEIGVQY 16- 1 Query: 63 SHIKPGDTVCIVGAGPIGLSALLTAQFYSPAKIIMVDLSQRRLEASKKFGATHTILSTST 12- 2 +KPGDTV I GAGP+G+SALLTAQ YSPA II+ D+ + RL+ +K+ GATHTI + ++ Sbjct: 162 GDVKPGDTVFIAGAGPVGMSALLTAQLYSPAAIIVCDMDENRLKLAKELGATHTI-NPAS 22- 0 Query: 123 QEVKEEIDKITKGRGVDVVLECVGYPATFDICQNVVSIGGHIANVGVHGKPVEFNLQDLW 18- 2 EV +++ I GVD +E VG PAT+++CQ++V GGHIA VGVHG+ V+F L+ LW Sbjct: 221 GEVSKQVFAIVGEDGVDCAIEAVGIPATWNMCQDIVKPGGHIAVVGVHGQSVDFKLEKLW 28- 0 Query: 183 IKNITLNTGLVNANTTEMLLEVLETGKIDATQLVTHHFKLSEIEEAYKVFKAAEENNTLK 24- 2 IK + + TGLVNANTTEML++ + + +D T+++THHFK SE+E+AY VEK A EN +K Sbjct: 281 IKKLAITTGLVNANTTEMLNKAISSSSVDYTKMLTHHFKFSELEKAYDVFKHAAENQVMK 34- 0 Query: 243 VIIEND 248 V++E D Sbjct: 341 VVLEAD 346 A related DNA sequence was identified in S. pyogenes <SEQ ID 785> which encodes the amino acid sequence <SEQ ID 786>. Analysis of this protein sequence reveals the following: TABLE-US-05593 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.41 Transmembrane 184-200 (183-203) ----- Final Results ----- bacterial membrane --- Certainty = 0.3166(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05594 Identities = 199/250 (79%), Positives = 226/250 (89%) Query: 1 MPSHCEDGGWILGHLIEGTQAEYVHIPHADGSLYHAPEGVCDDALVMLSDILPTSYEIGV 60- + SHC+DGGWILGHLI GTQAEYVHIPHADGSLYHAP+ + D+ALVMLSDILPTSYEIGV Sbjct: 114 LSSHCQDGGWILGHLINGTQAEYVHIPHADGSLYHAPDTIDDEALVMLSDILPTSYEIGV 17- 3 Query: 61 LPSHIKPGDTVCIVGAGPIGLSALLTAQFYSPAKIIMVDLSQKRLEASKKFGATHTILST 12- 0 LPSH+KPGD VCIVGAGP+GL+ALLT QF+SPA IIMVDLSQ RLEA+K FGATHTI S Sbjct: 174 LPSHVKPGDNVCIVGAGPVGLAALLTVQFFSPANIIMVDLSQNRLEAAKTFGATHTICSG 23- 3 Query: 121 STQEVKEEIDKITKGRGVDVVLECVGYPATFDICQNVVSIGGHIANVGVHGKPVEFNLQD 18- 0 S++EVK ID IT GRGVD+ +ECVGYPATFDICQ ++S+GGHIANVGVHGKPV+FNL + Sbjct: 234 SSSEVKAIIDDITNGRGVDISMECVGYPATFDICQKIISVGGHIANVGVHGKPVDFNLDE 29- 3 Query: 181 LWIKNITLNTGLVNANTTEMLLEVLETGKIDATQLVTHHFKLSEIEEAYKVFKAAEENNT 24- 0 LWIKNITLNTGLVNANTTEMLL VL+TGKIDAT+L+THHFKLSE+E+AY+FK A NN Sbjct: 294 LWIKNITLNTGLVNANTTEMLLNVLKTGKIDATRLITHHFKLSEVEKAYETFKHAGANNA 35- 3 Query: 241 LKVIIENDIT 250 LKVII+NDI+ Sbjct: 354 LKVIIDNDIS 363 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1828 A DNA sequence (GBSx1935) was identified in S. agalactiae <SEQ ID 5675> which encodes the amino acid sequence <SEQ ID 5676>. This protein is predicted to be a dehydrogenase fragment. Analysis of this protein sequence reveals the following:

TABLE-US-05595 Possible site: 20 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.46 Transmembrane 47-63 (33-66) ----- Final Results ----- bacterial membrane --- Certainty = 0.5182(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. There is also homology to SEQ ID 786: TABLE-US-05596 Identities = 23/38 (60%), Positives = 28/38 (73%) Query: WRNSNMRAATYLSANELSLTDKAKPQVIKPTDAVVXLV 44 7 ++ NM+AATYLS L L DK KP +IKPTDA+V LV Sbjct: YKKLNMKAATYLSTGNLQLIDKPKPVIIKPTDAIVQLV 47 10 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1829 A DNA sequence (GBSx1936) was identified in S. agalactiae <SEQ ID 5677> which encodes the amino acid sequence <SEQ ID 5678>. Analysis of this protein sequence reveals the following: TABLE-US-05597 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1001(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1830 A DNA sequence (GBSx1937) was identified in S. agalactiae <SEQ ID 5679> which encodes the amino acid sequence <SEQ ID 5680>. This protein is predicted to be branched chain amino acid transport system II carrier protein (brnQ). Analysis of this protein sequence reveals the following: TABLE-US-05598 Possible site: 44 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.66 Transmembrane 158-174 (154-177) INTEGRAL Likelihood = -6.64 Transmembrane 233-249 (231-252) INTEGRAL Likelihood = -5.20 Transmembrane 37-53 (30-57) INTEGRAL Likelihood = -3.98 Transmembrane 90-106 (87-108) INTEGRAL Likelihood = -0.80 Transmembrane 130-146 (130-146) ----- Final Results ----- bacterial membrane --- Certainty = 0.4864(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9417> which encodes amino acid sequence <SEQ ID 9418> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05599 >GP:AAC00400 G8:AF008220 branch-chain amino acid transporter [Bacillus subtilis] Identities = 89/250 (35%), Positives = 139/250 (55%), Gaps = 18/250 (7%) Query: 1 MDALASIAFAIIVIQASKQYGAITKKEITSMALKSGAIATFLLAFIYIFVGRIGATSQSL 60- MDALASI F ++V+ A K G K + + +K+G IA L FIY+ + +GATS + Sbjct: 199 MDALASIVFGVVVVNAVKSKGVTQSKALAAACIKAGVIAALGLTFIYVSLAYLGATSTNA 25- 8 Query: 61 FKFANGSFLLHNTPI-DGGHVLSQSANFYLGIVGQAILGTAIFLACLTTATGLITACAEY 11- 9 P+ +G +LS S+++ G +G +LG AI +ACLTT+ GL+T+C +Y Sbjct: 259 IG-----------PVGEGAKILSASSHYLFGSLGNIVLGAAITVACLTTSIGLVTSCGQY 30- 7 Query: 120 FHKLLPKISHITWATIFTLIAITFYFGGLSEIIRWSLPVLYLLYPLTIVLIFLVFFDQKF 17- 9 F KL+P +S+ TI TL ++ GL++II +S+P+L +YPL IV+I L F D+ F Sbjct: 308 FSKLIPALSYKIVVTIVTLFSLIIANFGLAQIIAFSVPILSAIYPLAIVIIVLSFIDKIF 36- 7 Query: 180 ESSRIVYQTSIAATAVAALYDALSKLGEMTGLFTIPSALTTFFTKVVPLGEYSMGWISFA 23- 9 + R VY + T + ++ D + G G +L F +PL +GW+ Sbjct: 368 KERREVYIACLIGTGLFSILDGIKAAGFSLG------SLDVFLNANLPLYSLGIGWVLPG 42- 1 Query: 240 ICGVLVGLIL 249 I G ++G +L Sbjct: 422 IVGAVIGYVL 431 A related DNA sequence was identified in S. pyogenes <SEQ ID 2233> which encodes the amino acid sequence <SEQ ID 2234>. Analysis of this protein sequence reveals the following: TABLE-US-05600 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.83 Transmembrane 235-251 (228-258) INTEGRAL Likelihood = -8.49 Transmembrane 434-450 (429-454) INTEGRAL Likelihood = -8.12 Transmembrane 359-375 (356-377) INTEGRAL Likelihood = -7.86 Transmembrane 150-166 (144-171) INTEGRAL Likelihood = -6.00 Transmembrane 298-314 (288-316) INTEGRAL Likelihood = -5.95 Transmembrane 42-58 (38-63) INTEGRAL Likelihood = -3.35 Transmembrane 336-352 (335-354) INTEGRAL Likelihood = -2.81 Transmembrane 199-215 (198-218) INTEGRAL Likelihood = -2.18 Transmembrane 120-136 (120-138) INTEGRAL Likelihood = -1.81 Transmembrane 390-406 (390-407) INTEGRAL Likelihood = -1.01 Transmembrane 81-97 (81-97) ----- Final Results ----- bacterial membrane --- Certainty = 0.5331(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05601 Identities = 161/253 (63%), Positives = 197/253 (77%) Query: 1 MDALASIAFAIIVIQASKQYGAITKKEITSMALKSGAIATFLLAFIYIFVGRIGATSQSL 60- MDALAS+ FAI+VI+A+KQ+GA T KE+T + L SGAIA LLA +YIFVGRIGATSQSL Sbjct: 202 MDALASLVFAILVIEATKQFGAKTDKEMTKITLISGAIAILLLALVYIFVGRIGATSQSL 26- 1 Query: 61 FKFANGSFLLHNTPIDGGHVLSQSANFYLGIVGQAILGTAIFLACLTTATGLITACAEYF 12- 0 F F +GSF LH P++GG +LS ++ FYLG +GQA L IFLACLTT+TGLIT+ AEYF Sbjct: 262 FPFIDGSFTLHGNPVNGGQILSHASRFYLGGIGQAFLAVVIFLACLTTSTGLITSSAEYF 32- 1 Query: 121 HKLLPKISHITWATIFTLIAITFYFGGLSEIIRWSLPVLYLLYPLTIVLIFLVFFDQKFE 18- 0 HKL+P +SHI WATIFTL++ FYFGGLS II WS PVL+LLYPLT+ LIFLV + F Sbjct: 322 HKLVPALSHIAWATIFTLLSAFFYFGGLSVIINWSAPVLFLLYPLTVDLIFLVLAQKCFN 38- 1 Query: 181 SSRIVYQTSIAATAVAALYDALSKLGEMTGLFTIPSALTTFFTKVVPLGEYSMGWISFAI 24- 0 + IVY+T+I T + A++DAL L +MTGLF +P A+ TFF K VPLG++SMGWI FA Sbjct: 382 NDPIVYRTTIGLTFIPAIFDALLTLSQMTGLFHLPEAVVTFFQKTVPLGQFSMGWIIFAA 44- 1 Query: 241 CGVLVGLILKKVK 253 G L+GLIL K K Sbjct: 442 IGFLIGLILSKTK 454 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1831 A DNA sequence (GBSx1938) was identified in S. agalactiae <SEQ ID 5681> which encodes the amino acid sequence <SEQ ID 5682>. This protein is predicted to be 30S ribosomal protein S12 (rpsL). Analysis of this protein sequence reveals the following: TABLE-US-05602 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3698(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9429> which encodes amino acid sequence <SEQ ID 9430> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05603 >GP:CAA78825 GB:Z15120 ribosomal protein 512 [Streptococcus pneumoniae] Identities = 64/71 (90%), Positives = 68/71 (95%) Query: 1 MPTINQLVRKPRKSKVEKSDSPALNIGYNSHRKVHTKLSAPQKRGVATRVGTMTPKKPNS 60 - MPTINQLVRKPRKSKVEKS SPALN+GYNSH+KV T +S+PQKRGVATRVGTMTPKKPNS Sbjct: 1 MPTINQLVRKPRKSKVEKSKSPALNVGYNSHKKVQTNVSSPQKRGVATRVGTMTPKKPNS 60 Query: 61 ALRKFARVRLS 71 ALRKFARVRLS Sbjct: 61 ALRKFARVRLS 71 A related DNA sequence was identified in S. pyogenes <SEQ ID 5683> which encodes the amino acid sequence <SEQ ID 5684>. Analysis of this protein sequence reveals the following: TABLE-US-05604 Possible Site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3879(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05605 Identities = 44/48 (91%), Positives = 47/48 (97%) Query: 24 LNIGYNSHRKVHTKLSAPQKRGVATRVGTMTPKKPNSALRRFARVRLS 71 LNIGYNSH+KV TK++APQKRGVATRVGTMTPKKPNSALRRFARVRLS Sbjct: 1 LNIGYNSHKKVQTKMAAPQKRGVATRVGTMTPKKPNSALRKFARVRLS 48 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1832 A DNA sequence (GBSx1939) was identified in S. agalactiae <SEQ ID 5685> which encodes the amino acid sequence <SEQ ID 5686>. This protein is predicted to be purR. Analysis of this protein sequence reveals the following: TABLE-US-05606 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.37 Transmembrane 142-158 (142-159) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05607 >GP:CAA10902 GB:AJ222642 purR [Lactococcus lactis] Identities = 143/269 (53%), Positives = 195/269 (72%), Gaps = 1/269 (0%) Query: 3 LRRSERMVVISNYLINNPYTLTSLNTFASKYGAAKSSISEDIAIIKKAFEQAQIGDIKTV 62- ++R+ER+V +N+LIN+P + +LN + Y AKSSISED+ IK+ FE +G ++T Sbjct: 1 MKRNERLVDFTNFLINHPNQMLNLNELSKHYEVAKSSISEDLVFIKRVFENQGVGLVETF 60- Query: 63 TGASGGVIFTPTIAEAEAKEIVEELRQRLSENDRILPGGYIYLSDLLSTPKMLQSIGRII 12- 2 G+ GGV FTP I + + E+ +E+ + L E +RILPGGYIYLSD+L TP L+ IG+II Sbjct: 61 PGSLGGVRFTPYITDERSLEMSQEIAELLREENRILPGGYIYLSDILGTPSNLRKIGQII 12- 0 Query: 123 ANAYRGQKIDAVMTVATKGVPLANAVANVLDVPFVIVRRDLKITEGSTVSVNYASGSSGR 18- 2 A+ Y +++D VMT+ATKG+P+A +VA +LDVPFVIVRRD K+TEG+T++VNY SGSS R Sbjct: 121 AHEYHEKQVDVVMTIATKGIPIAQSVAEILDVPFVIVRRDPKVTEGATLNVNYMSGSSSR 18- 0 Query: 183 IEKMFLSKRSLKPNSRVLIVDDFLKGGGTVSGMISLLSEFDSTLVGVAVFAENA-QEQRE 24- 1 +E M LSKRSL VLIVDDF+KG GT++GM SL+ EFD L GVAVF E + +R Sbjct: 181 VENMTLSKRSLSIGQNVLIVDDFMKGAGTINGMRSLVHEFDCLLAGVAVFLEGPFKGERL 24- 0 Query: 242 KMAYKSLLRVSEIDVKNNRVSVEAGNIFD 270 YKS+L+V ID+ N + V+ GNIF+ Sbjct: 241 IDDYKSILKVDRIDIANRSIDVQLGNIFN 269 A related DNA sequence was identified in S. pyogenes <SEQ ID 5687> which encodes the amino acid sequence <SEQ ID 5688>. Analysis of this protein sequence reveals the following: TABLE-US-05608 Possible site: 41 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.97 Transmembrane 142-158 (142-160) ----- Final Results ----- bacterial membrane --- Certainty = 0.1786(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05609 >GP:CAA10902 GB:AJ222642 purR [Lactococcus lactis] Identities = 142/269 (52%), Positives = 196/269 (72%), Gaps = 1/269 (0%) Query: 3 LRRSERMVVISNYLINNPYKLTSLNTFATKYEAAKSSISEDIAIIKKAFEEANIGDIDTL 62- ++R+ER+V +N+LIN+P ++ +LN + YE AKSSISED+ IK+ FE +G ++T Sbjct: 1 MKRNERLVDFTNFLINHPNQMLNLNELSKHYEVAKSSISEDLVFIKRVFENQGVGLVETF 60- Query: 63 TGASGGVIFTPSISETEARTIVEDLCQRLSESDRILPGGYIYLSDLLSTPKILQNIGRII 12- 2 G+ GGV FTP I++ + + +++ + L E +RILPGGYIYLSD+L TP L+ IG+II Sbjct: 61 PGSLGGVRFTPYITDERSLEMSQEIAELLREENRILPGGYIYLSDILGTPSNLRKIGQII 12- 0 Query: 123 ANAFKGEKIDAVMTVATKGVPLANAVANILSVPFVIVRRDLKITEGSTVSVNYASASSDR 18- 2 A+ + +++D VMT+ATRG+P+A +VA IL VPFVIVRRD K+TEG+T++VNY S SS R Sbjct: 121 AHEYHEKQVDVVMTIATKGIPIAQSVAEILDVPFVIVRRDPKVTEGATLNVNYMSGSSSR 18- 0 Query: 183 IEKMFLSKRSLKPNSRVLIVDDFLKGGGTITGMISLLTEFDSTLVGVAVFAENA-QSERE 24- 1 +E M LSKRSL VLIVDDF+KG GTI GM SL+ EFD L GVAVF E + ER Sbjct: 181 VENMTLSKRSLSIGQNVLIVDDFMKGAGTINGMRSLVHEFDCLLAGVAVFLEGPFKGERL 24- 0 Query: 242 QMTFKSLLKVSEIDVKNNNVVVEVGNIFD 270 +KS+LKV ID+ N ++ V++GNIF+ Sbjct: 241 IDDYKSILKVDRIDIANRSIDVQLGNIFN 269 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05610 Identities = 234/270 (86%) , Positives = 255/270 (93%) Query: 1 MKLRRSERMVVISNYLINNPYTLTSLNTFASKYGAAKSSISEDIAIIKKAFEQAQIGDIK 60- MKLRRSERMVVISNYLINNPY LTSLNTFA+KY AAKSSISEDIAIIKKAFE+A IGDI Sbjct: 1 MKLRRSERMVVISNYLINNPYKLTSLNTFATKYEAAKSSISEDIAIIKKAFEEANIGDID 60- Query: 61 TVTGASGGVIFTPTIAEAEAKEIVEELRQRLSENDRILPGGYIYLSDLLSTPKMLQSIGR 12- 0 T+TGASGGVIFTP+I+E EA+ IVE+L QRLSE+DRILPGGYIYLSDLLSTPK+LQ+IGR Sbjct: 61 TLTGASGGVIFTPSISETEARTIVEDLCQRLSESDRILPGGYIYLSDLLSTPKILQNIGR 12- 0 Query: 121 IIANAYRGQKIDAVMTVATKGVPLANAVANVLDVPFVIVRRDLKITEGSTVSVNYASGSS 18- 0 IIANA++G+KIDAVMTVATKGVPLANAVAN+L VPFVIVRRDLKITEGSTVSVNYAS SS Sbjct: 121 IIANAFKGEKIDAVMTVATKGVPLANAVANILSVPFVIVRRDLKITEGSTVSVNYASASS 18- 0 Query: 181 GRIEKMFLSKRSLKPNSRVLIVDDFLKGGGTVSGMISLLSEFDSTLVGVAVFAENAQEQR 24- 0 RIEKMFLSKRSLKPNSRVLIVDDFLKGGGT++GMISLL+EFDSTLVGVAVFAENAQ +R Sbjct: 181 DRIEKMFLSKRSLKPNSRVLIVDDFLKGGGTITGMISLLTEFDSTLVGVAVFAENAQSER 24- 0 Query: 241 EKMAYKSLLRVSEIDVKNNRVSVEAGNIFD 270 E+M +KSLL+VSEIDVKNN V VE GNIFD Sbjct: 241 EQMTFKSLLKVSEIDVKNNNVVVEVGNIFD 270 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1833 A DNA sequence (GBSx1940) was identified in S. agalactiae <SEQ ID 5689> which encodes the amino acid sequence <SEQ ID 5690>. This protein is predicted to be cmp-binding-factor 1. Analysis of this protein sequence reveals the following: TABLE-US-05611 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1753(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05612 >GP:AAC44803 GB:U21636 cmp-binding-factor 1 [Staphylococcus aureus] Identities = 140/310 (45%), Positives = 195/310 (62%), Gaps = 6/310 (1%) Query: 3 INQMKKDELFEGFYLIKKASVRKTRAGKDFIAFTFQDDTGEISGNMWDAQTYNVEEFVAG 62- I + + + F+L+ KA T GKD++ QD +GEI W A ++ Sbjct: 4 IENLNPGDSVDHFFLVHKATQGVTAQGKDYMTLHLQDKSGEISAKFWTATKNDMATIKPE 63- Query: 63 KIVHMKGRREVYNGTPQ--VNQITLRNIKDGEPNDPRDFKEKPPINVDNVREYMEQMLFK 12- 0 +IVH+KG Y G Q VNQI L +D + F + P++ ++E + L Sbjct: 64 EIVHVKGDIINYRGNKQMKVNQIRLATTEDQLKTE--QFVDGAPLSPAEIQEEISHYLLD 12- 1 Query: 121 IENATWQRVVRALYRKYNKEFFTYPAAKTNHHAFESGLAYHTATMVRLADSIGDIYPELN 18- 0 IENA QR+ R L +KY + F+TYPAA ++HH F SGL+YH TM+R+A SI DIYP LN Sbjct: 122 IENANLQRITRHLLKKYQERFYTYPAASSHHHNFASGLSYHVLTMLRIAKSICDIYPLLN 18- 1 Query: 181 KSLMFAGIMLHDLAKVIELSGPDNTEYTIRGNLIGHISLIDEELTKILAELNIDDTKEEV 24- 0 KSL+++GI+LHD+ KV ELSGP T YT+ GNL+GHIS+ +E+ + ELNI+ EE+ Sbjct: 182 KSLLYSGIILHDIGKVRELSGPVATSYTVEGNLLGHISIASDEVVEAARELNIEG--EEI 23- 9 Query: 241 TVLRHVILSHHGQLEYGSPVRPRIMEAEIIHMIDNIDANMMMMTTALNRVNEGEMTNRIF 30- 0 +LRH+ILSHHG+LEYGSP P + EAEI+ IDNIDA M M A + ++G+ T++IF Sbjct: 240 MLLRHHILSHHGKLEYGSPKLPYLKEAEILCYIDNIDARMNMFEKAYKKTDKGQFTDKIF 29- 9 Query: 301 AMDNRSFYKP 310 ++NR FY P Sbjct: 300 GLENRRFYNP 309 A related DNA sequence was identified in S. pyogenes <SEQ ID 5691> which encodes the amino acid sequence <SEQ ID 5692>. Analysis of this protein sequence reveals the following: TABLE-US-05613 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1822(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05614 Identities = 275/311 (88%), Positives = 300/311 (96%) Query: 1 MKINQMKKDELFEGFYLIKKAEVRKTRAGKDFIAFTFQDDTGEISGNMWDAQTYNVEEFV 60- MKINQMKKD+LFEGFYLIK AEVRKTRAGKDFI+ TFQDDTGEISGN+WDAQ YNVEEF Sbjct: 1 MKINQMKKDQLFEGFYLIKSAEVRKTRAGKDFISLTFQDDTGEISGNLWDAQPYNVEEFT 60- Query: 61 AGKIVNMKGRREVYNGTPQVNQITLRNIKDGEPNDPRDFKEKPPINVDNVREYMEQMLFK 12- 0 AGK+V MKGRREVYNGTPQVNQITLRN++ GEPNDP+DFKEK P++V VR+Y+EQMLFK Sbjct: 61 AGKVVFMKGRREVYNGTPQVNQITLRNVRPGEPNDPKDFKEKAPVSVTEVRDYLEQMLFK 12- 0 Query: 121 IENATWQRVVRALYRKYNKEFFTYPAAKTNHHAFESGLAYHTATMVRLADSIGDIYPELN 18- 0 IENATWQR+VRALYRKY+KEF+TYPAAKTNHHAFESGLAYHTATMVRLADSIGDIYP+LN Sbjct: 121 IENATWQRIVRALYRKYDKEFYTYPAAKTNHHAFESGLAYHTATMVRLADSIGDIYPDLN 18- 0 Query: 181 KSLMFAGIMLHDLAKVIELSGPDNTEYTIRGNLIGHISLIDEELTKILASLNIDDTKEEV 24- 0 KSL+FAGIMLHDLAKVIEL+GPDNTEYT+RGNLIGHISLI+EE+TK+++EL IDDTKEEV Sbjct: 181 KSLLFAGIMLHDLAKVIELTGPDNTEYTVRGNLIGHISLINEEITKVISELQIDDTKESV 24- 0 Query: 241 TVLRHVILSHHGQLEYGSPVRPRIMEAEIIHMIDNIDANMMMMTTALNRVNEGEMTNRIF 30- 0 VLRHVILSHHGQLEYGSPVRPRIMEAEIIHMIDNIDANMMMMTTAL+RV+EGEMTNRIF Sbjct: 241 IVLRHVILSHHGQLEYGSPVRPRIMEAEIIHMIDNIDANMMMMTTALSRVSEGEMTNRIF 30- 0 Query: 301 AMDNRSFYKPN 311 AMDNRSFYKPN Sbjct: 301 AMDNRSFYKPN 311 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1834 A DNA sequence (GBSx1941) was identified in S. agalactiae <SEQ ID 5693> which encodes the amino acid sequence <SEQ ID 5694>. Analysis of this protein sequence reveals the following:

TABLE-US-05615 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.59 Transmembrane 2-18 (1-22) ----- Final Results ----- bacterial membrane --- Certainty = 0.6838(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 5695> which encodes the amino acid sequence <SEQ ID 5696>. Analysis of this protein sequence reveals the following: TABLE-US-05616 Possible site: 17 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.05 Transmembrane 3-19 (1-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.5819(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05617 Identities = 309/424 (72%), Positives = 370/424 (86%), Gaps = 3/424 (0%) Query: 1 MLVIILIIVLASLTVTIISYQKMTELTKSVEKQLEDNADNLSDQLTYQIEVAQKDQILTL 60- +++ +L++VL L ++ K+ L + + LE NADNLSDQ+TYQ++ A K Q+L L Sbjct: 3 LILFLLVLVLLGLGAYLLF--KVNGLQHQLAQTLEGNADNLSDQMTYQLDTANKQQLLEL 60- Query: 61 TNQLNRMQQEIYQLLTDMRTELNQHLTESRDRSDKRLELINSNLSQSVQKMQDSNEKRLD 12- 0 T +NR Q +YQ LTD+R L++ L++SRDRSDKRLE IN ++QS++ MQ+SNEKRL+ Sbjct: 61 TQLMNRQQAGLYQQLTDIRDVLHRSLSDSRDRSDKRLSKINQQVNQSLKNMQESNEKRLE 12- 0 Query: 121 QMRQTVEEKLEKTLQTRLQTSFETVSRQLESVNQGLGEMKTVAQDVGTLNKVLSNTKTRG 18- 0 +MRQ VEEKLE+TL+ RL SF++VS+QLESVN+GLGEM++VAQDVGTLNKVLSNTKTRG Sbjct: 121 KMRQIVEEKLEETLKNRLHASFDSVSKQLESVNKGLGEMRSVAQDVGTLNKVLSNTKTRG 18- 0 Query: 181 ILGELQLGQIIEDIMTVSQYEREFPTVSGSSERVEYAIKLPGNGQGDYIYLPIDSKFPLE 24- 0 ILGELQLGQIIEDIMT SQYEREF TVSGSSERVEYAIKLPGNGQG YIYLPIDSKFPLE Sbjct: 181 ILGELQLGQIIEDIMTSSQYEREFVTVSGSSERVEYAIKLPGNGQGGYIYLPIDSKFPLE 24- 0 Query: 241 DYYRLEDAYELGDKVQIELYRKSLLASIRKFAKDINNKYLNPPETTNFGIMFLPTEGLYS 30- 0 DYYRLEDAYE+GDK+ IE RK+LLA+I++FAKDI+ KYLNPPETTNFG+MFLPTEGLYS Sbjct: 241 DYYRLEDAYEVGDKLAIEASRKALLAAIKRFAKDIHKKYLNPPETTNFGVMFLPTEGLYS 30- 0 Query: 301 EVVRNATFFDSLRRDENIVVAGPSTLSALLNSLSVGFKTLNIQKNANDISKILGNVKVEF 36- 0 EVVRNA+FFDSLRR+ENIVVAGPSTLSALLNSLSVGFKTLNIQKNA+DISKILGNVK+EF Sbjct: 301 EVVRNASFFDSLRREENIVVAGPSTLSALLNSLSVGFKTLNIQKNADDISKILGNVKLEF 36- 0 Query: 361 GKFGGMLSKAQKQLNTASKSIDSLLTTRTNAIIRVLNTVEEHQDQATTSLLNLPITEEEE 42- 0 KFGG+L+KAQKQ+NTA+ ++D L++TRTNAI+R LNTVE +QDQAT SLLN+P+ EEE Sbjct: 361 DKFGGLLAKAQKQMNTANNTLDQLISTRTNAIVRALNTVETYQDQATKSLLNMPLLEEEN 42- 0 Query: 421 INEN 424 NEN Sbjct: 421 -NEN 423 SEQ ID 5694 (GBS88) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 18 (lane 2; MW 48 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1835 A DNA sequence (GBSx1942) was identified in S. agalactiae <SEQ ID 5697> which encodes the amino acid sequence <SEQ ID 5698>. Analysis of this protein sequence reveals the following: TABLE-US-05618 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2722(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05619 >GP:CAB13453 GB:Z99112 ylos [Bacillus subtilis] Identities = 75/217 (34%), Positives = 109/217 (49%), Gaps = 12/217 (5%) Query: 1 MTKIALFAGG------DLTYFEYDFDYFVGIDRGSLFLLKNGLSLDMAVGDFDSITEDEL 54- M I + AGG DLT + + ++G+D+G++ LL G+ A GDFDSITE E Sbjct: 1 MKTINIVAGGPKNLIPDLTGYTDEHTLWIGVDKGTVTLLDAGIIPVEAFGDFDSITEQER 60- Query: 55 LYIKHYCSNIVSASAEKNDTDTELALKTIFKEFPEAQVTVFGAFGGRIDHMMSNIFLPSD 11- 4 I+ + AEK+ TD +LAL ++ P+ + +FG GGR DH + NI L Sbjct: 61 RRIEKAAPALHVYQAEKDQTDLDLALDWALEKQPDI-IQIFGITGGRADHFLGNIQLLYK 11- 9 Query: 115 RDLEPFMSQIRLKDEQNIVTYLPSGKNQVSRIEGMSYVSFMPESES--TLQISGAKYELN 17- 2 +IRL D+QN + P G+ + + E Y+SF+P SE L ++G KY LN Sbjct: 120 GVKTNI--KIRLIDKQNHIQMFPPGEYDIEKDENKRYISFIPFSEDIHELTLTGFKYPLN 17- 7 Query: 173 KSNY-FKKKMYSSNEFMTSPIEVELKDGYLIIIYSKD 208 + + SNE + S G LI+I S D Sbjct: 178 NCHITLGSTLCISNELIHSRGTFSFAKGILIHIRSTD 214 A related DNA sequence was identified in S. pyogenes <SEQ ID 5699> which encodes the amino acid sequence <SEQ ID 5700>. Analysis of this protein sequence reveals the following: TABLE-US-05620 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2467(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05621 Identities = 130/208 (62%), Positives = 166/208 (79%) Query: 1 MTKIALFAGGDLTYFEYDFDYFVGIDRGSLFLLKNGLSLDMAVGDFDSITEDELLYIKHY 60 M+K+ALFAGGDL+Y DFDYFVGIDRGSLFLL+NGL L+MAVGDFDS+++ IK Sbjct: 1 MSKVALFAGGDLSYISRDFDYFVGIDRGSLFLLENGLPLNMAVGDFDSVSQKAFTDIKEK 60 Query: 61 CSNIVSASAEKNDTDTELALKTIFKEFPEAQVTVFGAFGGRIDHMMSNIFLPSDRDLEPF 120- ++A EKNDTDTELALK +F FPEA+VT+FGAFGGR+DH++SNIFLPSD + PF Sbjct: 61 AELFITAHPEKNDTDTELALKEVFARFPEAEVTIFGAFGGRMDHLLSNIFLPSDPGIAPF 120- Query: 121 MSQIRLKDEQNIVTYLPSGKNQVSRIEGMSYVSFMPESESTLQISGAKYELNKSNYFKKK 18- 0 M+QI L+D+QN++TY P+G++ + + EGM+YV+FM E E+ L I+GAK+EL + N+FKKK Sbjct: 121 MAQIALRDQQNMITYRPAGQHLIHQEEGMTYVAFMAEGEADLTITGAKFELTQDNFFKKK 18- 0 Query: 181 MYSSNEFMTSPIEVELKDGYLIIIYSKD 208 +YSSN F+ PI V L GYLIII SKD Sbjct: 181 IYSSNAFIHQPITVSLPSGYLIIIQSKD 208 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1836 A DNA sequence (GBSx1943) was identified in S. agalactiae <SEQ ID 5701> which encodes the amino acid sequence <SEQ ID 5702>. This protein is predicted to be ribulose-phosphate 3-epimerase (rpe). Analysis of this protein sequence reveals the following: TABLE-US-05622 Possible site: 18 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.59 Transmembrane 124-140 (124-141) ----- Final Results ----- bacterial membrane --- Certainty = 0.1638(Atfirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05623 >GP:BAB0E221 GB:AP001515 unknown conserved protein [Bacillus halodurans] Identities = 113/211 (53%), Positives = 153/211 (71%) Query: 5 KIAPSILAADYANFANELKRIEETTAEYVHIDIMDGQFVPNISFGADVVSSMRKHSKLVF 64- KIAPSIL+AD+AN NE++ +E A+Y+H+D+MDG FVPNI+ G +V ++R + L Sbjct: 3 KIAPSILSADFANLGNEIQDVERGGADYIHVDVMDGHFVPNITIGPLIVDAIRPVTTLPL 62- Query: 65 DCHLMVVDPERYIEAFAQAGADIMTIHVEATKHIHGALQKIKEAGHKAGVVINPGTPVES 12- 4 D HLM+ P+ YI AFA+AGADI+T+HVEA H+H L IKE+G+KAGVV+NP TPV S Sbjct: 63 DVHLMIEQPDGYIPAFAKAGADIITVHVEACPHLHRTLHLIKESGVKAGVVLNPATPVSS 12- 2 Query: 125 LIPILDLVDQILIMTVNPGFGGQAFIPEMMSKVKTVAAWRKEYGHHYDIEVDGGIDNTTI 18- 4 + +L VD +L MTVNPGFGGQ FIP ++ K+K +A+ +KE G ++IEVDGG++ T Sbjct: 123 IQHVLSDVDMVLFMTVNPGFGGQRFIPSVLPKLKELASLKKEQGLTFEIEVDGGVNEETA 18- 2 Query: 185 KAAAEAGANVFVAGSYLFKASDLPAQVETLR 215 K EAGANV VAGS +F D A ++ +R Sbjct: 183 KQCVEAGANVLVAGSAVFNEEDRAAAIKGIR 213 A related DNA sequence was identified in S. pyogenes <SEQ ID 5703> which encodes the amino acid sequence <SEQ ID 5704>. Analysis of this protein sequence reveals the following: TABLE-US-05624 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0072(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05625 Identities = 183/219 (83%), Positives = 198/219 (89%) Query: 1 MSTNKIAPSILAADYANFANELKRIEETTAEYVHIDIMDGQFVPNISFGADVVSSMRKHS 60- MST KIAPSILAADYANFA+EL RIEET AEYVHIDIMDGQFVPNISFGADVV+SMRKHS Sbjct: 1 MSTLKIAPSILAADYANFASELARIEETDAEYVHIDIMDGQFVPNISFGADVVASMRKHS 60- Query: 61 KLVFDCHLMVVDPERYIEAFAQAGADIMTIHVEATKHIHGALQKIKEAGMKAGVVINPGT 12- 0 KLVFDCHLMVVDPERY+EAFAQAGADIMTIH E+T+HIHGALQKIK AGMKAGVVINPGT Sbjct: 61 KLVFDCHLMVVDPERYVEAFAQAGADIMTIHTESTRHIHGALQKIKAAGMKAGVVINPGT 12- 0 Query: 121 PVESLIPILDLVDQILIMTVNPGFGGQAFIPEMMSKVKTVAAWRKEYGHHYDIEVDGGID 18- 0 P +L P+LDLVDQ+LIMTVNPGFGGQAFIPE + KV TVA WR E G +DIEVDGG+D Sbjct: 121 PATALEPLLDLVDQVLIMTVNPGFGGQAFIPECLEKVATVAKWRDEKGLSFDIEVDGGVD 18- 0 Query: 181 NTTIKAAAEAGANVFVAGSYLFKASDLPAQVETLRVALD 219 N TI+A EAGANVFVAGSYLFKASDL +QV+TLR AL+ Sbjct: 181 NKTIRACYEAGANVFVAGSYLFKASDLVSQVQTLRTALN 219 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1837 A DNA sequence (GBSx1944) was identified in S. agalactiae <SEQ ID 5705> which encodes the amino acid sequence <SEQ ID 5706>. Analysis of this protein sequence reveals the following: TABLE-US-05626 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2098(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05627 >GP: CAB13451 GB: Z99112 similar to hypothetical proteins [Bacillus subtilis] Identities = 148/296 (50%), Positives = 202/296 (68%), Gaps = 14/296 (4%) Query: 2 QGRIVKSLAGFYYV----ESDGVVYQTRARGNFRKKGQIPYVGDWVEFSSQDQSEGYILS 57 +G+I+K+L+GFYYV E V Q R RG FRK P VGD+V + +++ EGY++ Sbjct: 3 EGKIIKALSGFYYVLDESEDSDKVIQCRGRGIFRKNKITPLVGDYVVYQAENDKEGYLME 62 Query: 58 IEERKNSLVRPPIVNIDQAVVIMSAKEPDFNANLLDRFLVLLEYKMIQPIIYISKLDLLD 117- I+ER N L+RPPI N+DQAV++ SA +P F+ LLDRFLVL+E IQPII I+K+DL++ Sbjct: 63 IKERTNELIRPPICNVDQAVLVFSAVQPSFSTALLDRFLVLVEANDIQPIICITKMDLIE 122- Query: 118 DLVVIDDIR---EHYQNIGY-VFCYSQEE------LLPLLANKVTVFMGQTGVGKSTLLN 16- 7 D D I+ E Y+NIGY V+ S ++ ++P +K TVF GQ+GVGKS+LLN Sbjct: 123 DQDTEDTIQAYAEDYRNIGYDVYLTSSKDQDSLADIIPHFQDKTTVFAGQSGVGKSSLLN 18- 2 Query: 168 KIAPELKLETGEISGSLGRGRHTTRAVSFYNVHKGKIADTPGFSSLDYEVDNAEDLNESF 22- 7 +PEL L T EIS LGRG+HTTR V + G +ADTPGFSSL++ E+L +F Sbjct: 183 AISPELGLRTNEISEHLGRGKHTTRHVELIHTSGGLVADTPGFSSLEFTDIEEEELGYTF 24- 2 Query: 228 PELRRLSHFCKFRSCTHTHEPKCAVKEALTQGQLWQVRYDNYLQFLSEIESRRETY 283 P++R S CKFR C H EPKCAVK+A+ G+L Q RYD+Y++F++EI+ R+ Y Sbjct: 243 PDIREKSSSCKFRGCLHLKEPKCAVKQAVEDGELKQYRYDHYVEFMTEIKDRKPRY 298 A related DNA sequence was identified in S. pyogenes <SEQ ID 5707> which encodes the amino acid sequence <SEQ ID 5708>. Analysis of this protein sequence reveals the following: TABLE-US-05628 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2290(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05629 Identities = 230/290 (79%), Positives = 257/290 (88%) Query: 1 MQGRIVKSLAGFYYVESDGVVYQTRARGNFRKKGQIPYVGDWVEFSSQDQSEGYILSIEE 60 +QG+I+KSLAGFYYVES+G VYQTRARGNFRK+G+ PYVGD V+FS++D SEGYIL+I Sbjct: 1 LQGKIIKSLAGFYYVESEGQVYQTRARGNFRKRGETPYVGDIVDFSAEDNSEGYILAIHP 60 Query: 61 RKNSLVRPPIVNIDQAVVIMSAKEPDFNANLLDRFLVLLEYKMIQPIIYISKLDLLDDLV 120- RKNSLVRPPIVNIDQAVVIMSAKEP+FN+NLLDRFL+LLE+K I P++YISK+DLLD Sbjct: 61 RKNSLVRPPIVNIDQAVVIMSAKEPEFNSNLLDRFLILLEHKAIHPVVYISKMDLLDSPE 120- Query: 121 VIDDIREHYQNIGYVFCYSQEELLPLLANKVTVFMGQTGVGKSTLLNKIAPELKLETGEI 18- 0 I I YQ IGY F S EELLPLLA+K+TVFMGQTGVGKSTLLN+IAPEL LE GEI Sbjct: 121 EIKAIGRQYQAIGYDFVTSLEELLPLLADKITVFMGQTGVGKSTLLNRIAPELALEIGEI 18- 0 Query: 181 SGSLGRGRHTTRAVSFYNVHKGKIADTPGFSSLDYEVDNAEDLNESFPELRRLSHFCKFR 24- 0 S SLGRGRHTTRAVSFYN H GKIADTPGFSSLDY++ NAEDLNE+FPELRRLSH CKFR Sbjct: 181 SDSLGRGRHTTRAVSFYNTHGGKIADTPGFSSLDYDIANAEDLNEAFPELRRLSHECKFR 24- 0 Query: 241 SCTHTHEPKCAVKEALTQGQLWQVRYDNYLQFLSEIESRRETYKKVIKRK 290 SCTHTHEPKCAVK AL G+LW VRY++YLQFLSEIE+RRETYKKVIKRK Sbjct: 241 SCTHTHEPKCAVKAALETGELWPVRYEHYLQFLSEIENRRETYKKVIKRK 290 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1838 A DNA sequence (GBSx1945) was identified in S. agalactiae <SEQ ID 5709> which encodes the amino acid sequence <SEQ ID 5710>. This protein is predicted to be rRNA. Analysis of this protein sequence reveals the following: TABLE-US-05630 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 259-275 (259-275) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05631 >GP: CAB15937 GB: Z99124 similar to hypothetical proteins [Bacillus subtilis] Identities = 95/278 (34%), Positives = 147/278 (52%), Gaps = 16/278 (5%) Query: 14 SYFACPKCQNPLIKESN-SLKCSDN-HCFDLSKFGYVNLLGGKKVDEHYDKKSFENR-QL 70 - S F CP C + + S SL C++ H FDLS+ GYVN L K V Y + FE R +L Sbjct: 8 SMFRCPLCDSSMDAASGKSLICTERGHTFDLSRHGYVNFLT-KPVKTSYGAELFEARSRL 66 Query: 71 VLENGYYNHILEAISKVLENNSQFH---SVLDIGCGEGFYSRQLVNKHEKTFLAF----D 123- + E G+++ + +AI++++ + H ++LD GCGEG + L A D Sbjct: 67 IGECGFFDPLHDAIAELISHPKSGHEAFTILDSGCGEGSHLNALCGFDYAGKAAIGTGID 126- Query: 124 ISKDSIQLAAKSDQSRLVKWFVSDLANLPIQDSSIDIILDIFSPANYKEFRRVLSDDGIL 18- 3 +SKD I A+K+ + + W V+D+A P D D++L IFSP+NY EF R+L +DG+L Sbjct: 127 LSKDGILKASKAFKDLM--WAVADVARAPFHDRQFDVVLSIFSPSNYAEFHRLLKNDGML 18- 4 Query: 184 VKVVPVAEHVQELREKASQYLKQKDYSNQKILDHFRENFEIISEQKVVQSYNCSQQERQA 24- 3 +KVVP ++++ ELR+ ++ YSN ++ F N ++ QQ Sbjct: 185 IKVVPRSDYLIELRQFLYTDSPRRTYSNTAAVERFTANAAHSRPVRLRYVKTLDQQAIHW 24- 4 Query: 244 FIDMTPLLFSVDKTTIDW---ASISEITVGALIVIGKK 278 + MTPL +S K + ++ITV I+IG K Sbjct: 245 LLKMTPLAWSAPKDRVSLLKEMKSADITVDVDILIGMK 282 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1839 A DNA sequence (GBSx1946) was identified in S. agalactiae <SEQ ID 5711> which encodes the amino acid sequence <SEQ ID 5712>. This protein is predicted to be dimethyladenosine transferase (ksgA). Analysis of this protein sequence reveals the following: TABLE-US-05632 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3257(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05633 >GP: CAB11818 GB: Z99104 dimethyladenosine transferase [Bacillus subtilis] Identities = 157/284 (55%), Positives = 215/284 (75%), Gaps = 2/284 (0%) Query: 3 IADKTVTRAILERHGFTFKKSFGQNFLTDTNILQKIVDTAEIDKGVNVIEIGPGIGALTE 62 IA T+ IL+++GF+FKKS GQNFL DTNIL +IVD AE+ + VIEIGPGIGALTE Sbjct: 5 IATPIRTKEILKKYGFSFKKSLGQNFLIDTNILNRIVDHAEVTEKTGVIEIGPGIGALTE 64 Query: 63 FLAENAAEVMAFEIDDRLIPILADTLARFDNVQVVNQDILKADLQTQIQA-FKNPDLPIK 121- LA+ A +V+AFEID RL+PIL DTL+ ++NV V++QD+LKAD+++ I+ F++ D I Sbjct: 65 QLAKRAKKVVAFEIDQRLLPILKDTLSPYENVTVIHQDVLKADVKSVIEEQFQDCD-EIM 123- Query: 122 VVANLPYYITTPILMHLIESKIPFAEFVVMIQKEVADRISAMPNTKAYGSLSIAVQYYMT 18- 1 VVANLPYY+TTPI+M L+E +P VVM+QKEVA+R++A P++K YGSLSIAVQ+Y Sbjct: 124 VVANLPYYVTTPIIMKLLEEHLPLKGIVVMLQKEVAERMAADPSSKEYGSLSIAVQFYTE 18- 3 Query: 182 AKVSFIVPRTVFVPAPNVDSAILKMVRRDQPVVSVQDEDFFFRVSKVAFVHRRKTLWNNL 24- 1 AK IVP+TVFVP PNVDSA+++++ RD P V V++E FFF++ K +F RRKTL NNL Sbjct: 184 AKTVMIVPKTVFVPQPNVDSAVIRLILRDGPAVDVENESFFFQLIKASFAQRRKTLLNNL 24- 3 Query: 242 TSHFGKSEDTKAKLEKALEIAKIKPSIRGEALSIPDFASLADAL 285 ++ + + K+ +E+ LE I RGE+LSI +FA+L++ L Sbjct: 244 VNNLPEGKAQKSTIEQVLEETNIDGKRRGESLSIEEFAALSNGL 287 A related DNA sequence was identified in S. pyogenes <SEQ ID 5713> which encodes the amino acid sequence <SEQ ID 5714>. Analysis of this protein sequence reveals the following:

TABLE-US-05634 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2420(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05635 Identities = 257/290 (88%), Positives = 275/290 (94%) Query: 1 MRIADKTVTRAILERHGFTFKKSFGQNFLTDTNILQKIVDTAEIDKGVNVIEIGPGIGAL 60 MRIAD +VT+A+L+RHGFTFKKSFGQNFLTDTNILQKIVDTAEID+ VNVIEIGPGIGAL Sbjct: 9 MRIADYSVTKAVLDRHGFTFKKSFGQNFLTDTNILQKIVDTAEIDQNVNVIEIGPGIGAL 68 Query: 61 TEFLAENAAEVMAFEIDDRLIPILADTLARFDNVQVVNQDILKADLQTQIQAFKNPDLPI 120- TEFLAENAAEVMAFEIDDRL+PILADTL FDNVQVVNQDILKADLQTQI+ FKNPDLPI Sbjct: 69 TEFLAENAAEVMAFEIDDRLVPILADTLRDFDNVQVVNQDILKADLQTQIKQFKNPDLPI 128- Query: 121 KVVANLPYYITTPILMHLIESKIPFAEFVVMIQKEVADRISAMPNTKAYGSLSIAVQYYM 18- 0 KVVANLPYYITTPILMHLIESKIPF EFVVM+Q+EVADRISA PNTKAYGSLSIAVQYYM Sbjct: 129 KVVANLPYYITTPILMHLIESKIPFQEFVVMMQREVADRISAEPNTKAYGSLSIAVQYYM 18- 8 Query: 181 TAKVSFIVPRTVFVPAPNVDSAILKMVRRDQPVVSVQDEDFFFRVSKVAFVHRRKTLWNN 24- 0 TAKV+FIVPRTVFVPAPNVDSAILKMVRRDQP++ V+DEDFFFRVS+++FVHRRKTLWNN Sbjct: 189 TAKVAFIVPRTVFVPAPNVDSAILKMVRRDQPLIEVKDEDFFFRVSRLSFVHRRKTLWNN 24- 8 Query: 241 LTSHFGKSEDTKAKLEKALEIAKIKPSIRGEALSIPDFASLADALKEVGI 290 LTSHFGKSED KAKLEK L +A IKPSIRGEALSI DF LADALKEVG+ Sbjct: 249 LTSHFGKSEDIKAKLEKGLALADIKPSIRGEALSIQDFGKLADALKEVGL 298 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1840 A DNA sequence (GBSx1947) was identified in S. agalactiae <SEQ ID 5715> which encodes the amino acid sequence <SEQ ID 5716>. Analysis of this protein sequence reveals the following: TABLE-US-05636 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0736 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1841 A DNA sequence (GBSx1948) was identified in S. agalactiae <SEQ ID 5717> which encodes the amino acid sequence <SEQ ID 5718>. Analysis of this protein sequence reveals the following: TABLE-US-05637 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3031 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05638 >GP:CAB11817 GB:Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 81/179 (45%), Positives = 117/179 (65%), Gaps = 4/179 (2%) Query: 7 IQEVIVVEGKDDTANLRRFYNVDTYETRGSAIDEDDLERIERLHNLRGVIVFTDPDYNGE 66- I+E+IVVEG+DDTA ++ + DT ET GSAID+ +++I RGVI+ TDPD+ GE Sbjct: 3 IKEIIVVEGRDDTARIKLAVDADTIETNGSAIDDHVIDQIRLAQKTRGVIILTDPDFPGE 62- Query: 67 RIRKIIMNAIPTVRHAFLNRDEAKPGSKTKGRSLGVEHASFEDLQKALSKVTQHFDDEDH 12- 6 +IRK I A+P +HAFL + AKP +K R +GVEHAS E ++ L V + + + Sbjct: 63 KIRKTISEAVPGCKHAFLPKHLAKPKNK---RGIGVEHASVESIRACLENVHEEMEAQPS 11- 9 Query: 127 FDITQADLIRWGFITASDSRKRREYLGNQLRIGYSNGKQLLKRLRLFGVTKAEVEECME 185- DI+ DLI G I ++ RRE LG+ L+IGY+NGKQL KRL++F + K++ ++ Sbjct: 120 -DISAEDLIHAGLIGGPAAKCRRERLGDLLKIGYTNGKQLQKRLQMFQIKKSDFMSALD 177- A related DNA sequence was identified in S. pyogenes <SEQ ID 5719> which encodes the amino acid sequence <SEQ ID 5720>. Analysis of this protein sequence reveals the following: TABLE-US-05639 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1474 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05640 Identities = 146/187 (78%), Positives = 165/187 (88%) Query: 1 MMKKIDIQEVIVVEGKDDTANLRRFYNVDTYETRGSAIDEDDLERIERLHNLRGVIVFTD 60- + +KI+IQEV+VVEGKDDTANLRRFY VDTYETRGSAI E+DLERI RL++LRGVIV TD Sbjct: 15 LTEKINIQEVLVVEGKDDTANLRRFYEVDTYETRGSAITEEDLERINRLNDLRGVIVLTD 74- Query: 61 PDYNGERIRKIIMNAIPTVRHAFLNRDEAKPGSKTKGRSLGVEHASFEDLQKALSKVTQH 12- 0 PDYNGERIRK+IM A+PT RHAFLNR+EA P SK+KGRSLGVEHA+FEDLQKAL+ VTQ Sbjct: 75 PDYNGERIRKLIMAAVPTARHAFLNRNEAVPSSKSKGRSLGVEHANFEDLQKALAHVTQQ 13- 4 Query: 121 FDDEDHFDITQADLIRWGFITASDSRKRREYLGNQLRIGYSNGKQLLKRLRLFGVTKAEV 18- 0 +DDE +FDI Q DLIR G + ASDSRKRREYLG +LRIGY+NGKQLLKRL LFG+T AEV Sbjct: 135 YDDESYFDIRQTDLIRLGLLMASDSRKRREYLGEKLRIGYANGKQLLKRLELFGITLAEV 19- 4 Query: 181 EECMEGY 187 EE ME Y Sbjct: 195 EEVMETY 201 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1842 A DNA sequence (GBSx1949) was identified in S. agalactiae <SEQ ID 5721> which encodes the amino acid sequence <SEQ ID 5722>. Analysis of this protein sequence reveals the following: TABLE-US-05641 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4955 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> A related GBS nucleic acid sequence <SEQ ID 10139> which encodes amino acid sequence <SEQ ID 10140> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05642 >GP:CAB11815 GB:Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 115/254 (45%), Positives = 172/254 (67%) Query: 28 IFDTHTHLNVENFEGKIDEEINLASELGVTKMNVVGFDQDTISKSLELSSQYAQVYSTIG 87- +FDTH HLN E ++ ++E I A V ++ VVGFD+ TI++++E+ +Y +Y+ IG Sbjct: 2 LFDTHAHLNAEQYDTDLEEVIERAKAEKVERIVVVGFDRPTITRAMEHIEEYDFIYAAIG 61- Query: 88 WHPTEAGSYDDNIESMIISHLENPKVIALGEIGLDYYWMEDPKDIQIEVFKRQIELSKEY 14- 7 WHP +A + + I + KV+A+GE+GLDY+W + PKDIQ EVF+ QI L+KE Sbjct: 62 WHPVDAIDMTEEDLAWIKELSAHEKVVAIGEMGLDYHWDKSPKDIQKEVFRNQIALAKEV 12- 1 Query: 148 NLPFVVHTRDALEDTYEVIKESGVGPFGGIMHSFSGSLEMAQKFIDLGMMISFSGVVTFK 20- 7 NLP ++H RDA ED ++KE G GGIMH F+GS E+A++ + + +SF G VTFK Sbjct: 122 NLPIIIHNRDATEDVVTILKEEGAEAVGGIMHCFTGSAEVARECMKMNFYLSFGGPVTFK 18- 1 Query: 208 KALDVQEAARELPLDKILVETDAPYLAPVPKRGRENKTAYTRYVVEKIAELRGITVEEVA 26- 7 A +E +E+P D++L+ETD P+L P P RG+ N+ +Y +YV E+IAEL+ +T EE+A Sbjct: 182 NAKKPKEVVKEIPNDRLLIETDCPFLTPHPFRGKRNEPSYVKYVAEQIAELKEMTFEEIA 24- 1 Query: 268 EATYQNAVRIFRLD 281 T +NA R+FR++ Sbjct: 242 SITTENAKRLFRIN 255 A related DNA sequence was identified in S. pyogenes <SEQ ID 5723> which encodes the amino acid sequence <SEQ ID 5724>. Analysis of this protein sequence reveals the following: TABLE-US-05643 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2817 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05644 Identities = 190/258 (73%), Positives = 227/258 (87%) Query: 24 DMIKIFDTHTHLNVENFEGKIDEEINLASELGVTKMNVVGFDQDTISKSLELSSQYAQVY 83- + + IFDTHTHLNV F+G EE+ LA E+GV NVVGFDQ TIS +L L+++YA +Y Sbjct: 38 EKLTIFDTHTHLNVAEFQGHETEELTLAQEMGVAYHNVVGFDQATISGALTLANKYANIY 97- Query: 84 STIGWHPTEAGSYDDNIESMIISHLENPKVIALGEIGLDYYWMEDPKDIQIEVFKRQIEL 14- 3 +TIGWHPTEAGSY + +E I+S L + KVIALGEIGLDYYWMEDPK++QIEVFKRQ++L Sbjct: 98 ATIGWHPTEAGSYSEAVEEAIVSQLSHSKVIALGEIGLDYYWMEDPKEVQIEVFKRQMQL 15- 7 Query: 144 SKEYNLPFVVHTRDALEDTYEVIKESGVGPFGGIMHSFSGSLEMAQKFIDLGMMISFSGV 20- 3 +K+++LPFVVHTRDALEDTYEVIK +GVGP GGIMHS+SGSLEMA++FI+LGMMISFSGV Sbjct: 158 AKDHDLPFVVHTRDALEDTYEVIKAAGVGPRGGIMHSYSGSLEMAERFIELGMMISFSGV 21- 7 Query: 204 VTFKKALDVQEAARELPLDKILVETDAPYLAPVPKRGRENKTAYTRYVVEKIAELRGITV 26- 3 VTFKKALD+QEAA+ LPLDKILVETDAPYL PVPKRG++N TAYTRYVV+KIAELRG+TV Sbjct: 218 VTFKKALDIQEAAQHLPLDKILVETDAPYLTPVPKRGKQNHTAYTRYVVDKIAELRGMTV 27- 7 Query: 264 EEVAEATYQNAVRIFRLD 281 EEVA+AT NA R+F+LD Sbjct: 278 EEVAKATTANAKRVFKLD 295 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1843 A DNA sequence (GBSx1950) was identified in S. agalactiae <SEQ ID 5725> which encodes the amino acid sequence <SEQ ID 5726>. This protein is predicted to be endosome-associated protein. Analysis of this protein sequence reveals the following: TABLE-US-05645 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5142 (Affirmative) <succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1844 A DNA sequence (GBSx1951) was identified in S. agalactiae <SEQ ID 5727> which encodes the amino acid sequence <SEQ ID 5728>. This protein is predicted to be CG17785 gene product. Analysis of this protein sequence reveals the following: TABLE-US-05646 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4730(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1845 A DNA sequence (GBSx1952) was identified in S. agalactiae <SEQ ID 5729> which encodes the amino acid sequence <SEQ ID 5730>. Analysis of this protein sequence reveals the following: TABLE-US-05647 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4032(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05648 >GP: BAB01041 GB: AB022220 gene_id: MLN21.14~unknown protein [Arabidopsis thaliana] Identities = 49/185 (26%), Positives = 85/185 (45%), Gaps = 46/185 (24%) Query: 5 LTDLDRVNIAKQEYELGSQLDTLVKIMSQDKVLPIGKVAHVQ------DGGKETGEQIYT 58 L +D V+ + + ELGS+ + +M+ K+ V+ D K+ Q++ Sbjct: 154 LEGIDSVDSGRVRIELGSRGLMDLCVMASKLAYENAKMNLVEFLDCWNDYQKQMSTQVFV 21- 3 Query: 59 ITPNGTLDKPEDVKEVTVLFKGSTAPFGGDDWKTD----WFKNDIPIASKL---LLKKFG 111- T DK +D + + F+G T PF DDW TD W+ ++P KL L+ G Sbjct: 214 FT-----DKQKDANLIVISFRG-TEPFDADDWGTDFDYSWY--EVPNVGKLHMGFLEAMG 26- 5 Query: 112 ---------------SQSVSHKQGTKQ-----LEQSAH-----LLKEVMNKYPNAKISVY 14- 6 Q+ S ++ +K+ +E+SA+ +LK +++++ NA+ V Sbjct: 266 LGNRDDTTTFHYNLFEQTSSEEENSKKNLLDMVERSAYYAVRVILKRLLSEHENARFVVT 32- 5 Query: 147 GHSLG 151 GHSLG Sbjct: 326 GHSLG 330 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1846 A DNA sequence (GBSx1953) was identified in S. agalactiae <SEQ ID 5731> which encodes the amino acid sequence <SEQ ID 5732>. Analysis of this protein sequence reveals the following: TABLE-US-05649 Possible site: 52 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.97 Transmembrane 12-28 (5-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.4588(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10141> which encodes amino acid sequence <SEQ ID 10142> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8909> and protein <SEQ ID 8910> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05650 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 14.01 GvH: Signal Score (-7.5): -5.55 Possible site: 46 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -8.97 threshold: 0.0 INTEGRAL Likelihood = -8.97 Transmembrane 6-22 (1-27) PERIPHERAL Likelihood = 9.49 84 modified ALOM score: 2.29 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4588(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8910 (GBS32) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 10 (lane 2; MW 15.6 kDa). GBS32-His was purified as shown in FIG. 191, lane 8. EXAMPLE 1847 A DNA sequence (GBSx1954) was identified in S. agalactiae <SEQ ID 5733> which encodes the amino acid sequence <SEQ ID 5734>. This protein is predicted to be extramembranal protein (dltD). Analysis of this protein sequence reveals the following: TABLE-US-05651 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.24 Transmembrane 12-28 (4-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.5097(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05652 >GP: AAC29041 GB: AF050517 unknown [Streptococcus mutans] Identities = 242/421 (57%), Positives = 309/421 (72%), Gaps = 1/421 (0%) Query: 1 MLKRLGKVFGPLVCALLLLVGLYFVFPVSQ-PHHLGKEKNSAVALTKAGFKSRVQKVRAF 59 MLKRL + GP+ CAL+L+ L +P H+ +EKN AVAL+ + FKS +K+RA Sbjct: 1 MLKRLWLILGPVFCALVLVFSLIMFYPAKHLSHNYNEEKNDAVALSPSSFKSTNKKMRAL 60 Query: 60 SDPKANFVPFFGSSEWLRFQAMHPSVLAEAYNRSYIPYLLGQKGAASLTQYYGIQQIKGQ 119- SD + FVPFFGSSEW R D MHPSVLAE YNRSY PYLLGQKG+ SL+ Y+G+QQI Q Sbjct: 61 SDKRHLFVPFFGSSEWQRIDNMHPSVLAERYNRSYRPYLLGQKGSTSLSHYFGMQQIGNQ 120- Query: 120 IKNKKAIYVISPQWFVRKGANKGAFQNYFSNDQTIRFLQNQTGTTYDRYAARRLLKLYPE 17- 9 IKNKKA+YVISPQWFV KG + AFQ YFS++Q FL NQTG+T DRYAA+RLL + P Sbjct: 121 IKNKKAVYVISPQWFVPKGTSPIAFQQYFSSEQLADFLLNQTGSTADRYAAKRLLDIKPS 18- 0 Query: 180 ASMSDLIEKVADGQKLSNKDKQRLKFNDWVFEKTDAIFSYLPLGKTYNQAIMPHVGKLPK 23- 9 +++ +I+K+A G+ L++ D+ L+ +K DA+F L Y + ++PHV KLPK Sbjct: 181 SNLQGMIKKIAAGKTLNSFDRASLRLIKSFLKKEDALFGSLTFSDNYERRVLPHVKKLPK 24- 0 Query: 240 AFSYNHLSRIASQDAKVATRSNQFGIQDRFYQTRIKKHLKKLKGSQRHFNYTKSPEFNDL 29- 9 FSY LS+IAS+D + T++NQF I+D FY RIK LK+LKG Q+ +Y +SPE+NDL Sbjct: 241 HFSYGTLSQIASKDGQRLTKTNQFEINDHFYNKRIKGQLKRLKGFQKQLSYLQSPEYNDL 30- 0 Query: 300 QLVLNEFSKQNTDVLFVIPPVNKKWTDYTGLDQKMYQKSVEKIKHQLQSQGFNHIADLSR 35- 9 QL L + +K T V+FVIPPVN KW +YTGL Q MYQK+VEKIK+QLQSQGF++IADLS+ Sbjct: 301 QLALTQLAKSKTKVIFVIPPVNAKWVEYTGLSQDMYQKTVEKIKYQLQSQGFDNIADLSK 36- 0 Query: 360 DGGKPYFMQDTIHLGWNGWLELDKHINPFLTEENSKPNYHINNKFLKKSWAKYTGRPSDYK 4- 20 +G +PYFMQDTIHLGWNGWL DK +NPFL+++ +P Y INN FL K WA YTG P +K Sbjct: 361 NGDQPYFMQDTIHLGWNGWLAFDKEVNPFLSKKQLQPAYKINNHFLSKKWATYTGNPFQFK 4- 21 A related DNA sequence was identified in S. pyogenes <SEQ ID 5735> which encodes the amino acid sequence <SEQ ID 5736>. Analysis of this protein sequence reveals the following: TABLE-US-05653 Possible site: 41 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.06 Transmembrane 7-23 (1-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.6222(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05654 Identities = 209/410 (50%), Positives = 278/410 (66%) Query: 1 MLKRLGKVFGPLVCALLLLVGLYFVFPVSQPHHLGKEKNSAVALTKAGFKSRVQKVRAFS 60 MLKRL + GPL+ A +L+V F FP H + +EK +AVA+T + FK+ + K +A S Sbjct: 1 MLKRLWLILGPLLIAFVLVVITIFSFPTQLDHSIAQEKANAVAITDSSFKNGLIKRQALS 60 Query: 61 DPKANFVPFFGSSEWLRFDAMHPSVLAEAYNRSYIPYLLGQKGAASLTQYYGIQQIKGQI 120- D FVPFFGSSEW R D+MHPSVLAE Y RSY P+L+G++G+ASL+ YYGIQQI ++ Sbjct: 61 DETCRFVPFFGSSEWSRMDSMHPSVLAERYKRSYRPFLIGKRGSASLSHYYGIQQITNEM 120- Query: 121 KNKKAIYVISPQWFVRKGANKGAFQNYFSNDQTIRFLQNQTGTTYDRYAARRLLKLYPEA 18- 0 + KKAI+V+SPQWF +G N A Q Y SN Q I FL ++AA+RLL+L P Sbjct: 121 QKKKAIFVVSPQWFTAQGINPSAVQMYLSNTQVIEFLLKARTDKESQFAAKRLLELNPGV 18- 0 Query: 181 SMSDLIEKVADGQKLSNKDKQRLKFNDWVFEKTDAIFSYLPLGKTYNQAIMPHVGKLPKA 24- 0 S S+L++KV+ G+ LS D+ LK V + +++FS+L Y + I+P V LPK Sbjct: 181 SKSNLLKKVSKGKSLSRLDRAILKCQHQVALREESLFSFLGKSTNYEKRILPRVKGLPKV 24- 0 Query: 241 FSYNHLSRIASQDAKVATRSNQFGIDDRFYQTRIKKHLKKLKGSQRHFNYTKSPEFNDLQ 30- 0 FSY L+ +A++ ++AT +N+FGI + FY+ RI K Q +++Y SPE+ND Q Sbjct: 241 FSYKQLNALATKRGQLATTNNRFGIKNTFYRKRIAPKYNLYKNFQVNYSYLASPEYNDFQ 30- 0 Query: 301 LVLNEFSKQNTDVLFVIPPVNKKWTDYTGLDQKMYQKSVEKIKHQLQSQGFNHIADLSRD 36- 0 L+L+EF+K+ TDVLFVI PVNK W DYTGL+Q YQ +V KIK QL+SQGF+ IAD S+D Sbjct: 301 LLLSEFAKRKTDVLFVITPVNKAWADYTGLNQDKYQAAVRKIKFQLKSQGFHRIADFSKD 36- 0 Query: 361 GGKPYFMQDTIHLGWNGWLELDKHINPFLTEENSKPNYHINNKFLKKSWA 410 GG+ YFMQDTIHLGWNGWL DK + PFL + PNY +N F K WA Sbjct: 361 GGESYFMQDTIHLGWNGWLAFDKKVQPFLETKQPVPNYKMNPYFYSKIWA 410 A related GBS gene <SEQ ID 8911> and protein <SEQ ID 8912> were also identified. Analysis of this protein sequence reveals the following:

TABLE-US-05655 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: 15.50 GvH: Signal Score (-7.5): -4.52 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -10.24 threshold: 0.0 INTEGRAL Likelihood = -10.24 Transmembrane 12-28 (4-31) PERIPHERAL Likelihood = 8.33 301 modified ALOM score: 2.55 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5097(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00127## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1848 A DNA sequence (GBSx1955) was identified in S. agalactiae <SEQ ID 5737> which encodes the amino acid sequence <SEQ ID 5738>. This protein is predicted to be d-alanyl carrier protein (dltC). Analysis of this protein sequence reveals the following: TABLE-US-05656 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1061 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05657 >GP: AAC05776 GB: AF051356 D-alanyl carrier protein [Streptococcus mutans] Identities = 65/79 (82%), Positives = 74/79 (93%) Query: 1 MDIKSEVLAIIDDLFMEDVSSMMDEDLFDAGVLDSMGTVELIVELESHFNIDIPIAEFGR 60 MDIKSEVL IID+LFMEDVS MMDEDLFDAGVLDSMGTVELIVELE+HF+I +P++EFGR Sbjct: 1 MDIKSEVLKIIDELFMEDVSDMMDEDLFDAGVLDSMGTVELIVELENHFDITVPVSEFGR 60 Query: 61 NDWNTANKIVAGVTELCNA 79 +DWNTANKI+ G+TEL NA Sbjct: 61 DDWNTANKIIEGITELRNA 79 A related DNA sequence was identified in S. pyogenes <SEQ ID 5739> which encodes the amino acid sequence <SEQ ID 5740>. Analysis of this protein sequence reveals the following: TABLE-US-05658 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3976 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05659 Identities = 57/79 (72%), Positives = 65/79 (82%) Query: 1 MDIKSEVLAIIDDLFMEDVSSMMDEDLFDAGVLDSMGTVELIVELESHFNIDIPIAEFGR 60 M I+ V+ + D LFMEDVS MMDEDLFDAGVLDS+GTVELIVELES FNI +PI+EFGR Sbjct: 1 MSIEETVIELFDRLFMEDVSEMMDEDLFDAGVLDSLGTVELIVELESTFNIKVPISEFGR 60 Query: 61 NDWNTANKIVAGVTELCNA 79 +DWNT KIV GV EL +A Sbjct: 61 DDWNTVTKIVQGVEELQHA 79 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1849 A DNA sequence (GBSx1956) was identified in S. agalactiae <SEQ ID 5741> which encodes the amino acid sequence <SEQ ID 5742>. Analysis of this protein sequence reveals the following: TABLE-US-05660 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.55 Transmembrane 93-109 (91-117) INTEGRAL Likelihood = -7.64 Transmembrane 21-37 (19-39) INTEGRAL Likelihood = -6.79 Transmembrane 390-406 (387-410) INTEGRAL Likelihood = -5.20 Transmembrane 41-57 (40-59) INTEGRAL Likelihood = -2.07 Transmembrane 203-219 (200-221) INTEGRAL Likelihood = -1.65 Transmembrane 65-81 (65-81) INTEGRAL Likelihood = -0.75 Transmembrane 125-141 (125-141) ----- Final Results ----- bacterial membrane --- Certainty = 0.4418(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 5743> which encodes the amino acid sequence <SEQ ID 5744>. Analysis of this protein sequence reveals the following: TABLE-US-05661 Possible site: 57 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.14 Transmembrane 387-403 (382-409) INTEGRAL Likelihood = -9.66 Transmembrane 18-34 (15-37) INTEGRAL Likelihood = -5.95 Transmembrane 64-80 (63-81) INTEGRAL Likelihood = -5.63 Transmembrane 92-108 (89-114) INTEGRAL Likelihood = -1.97 Transmembrane 40-56 (40-56) ----- Final Results ----- bacterial membrane --- Certainty = 0.5055 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05662 >GP: AAC05775 GB: AF051356 integral membrane protein [Streptococcus mutans] Identities = 246/413 (59%), Positives = 319/413 (76%) Query: 1 MMMFFSHIPYMEPYGNPIYFVYLILAFLPVIIGIFKQKRLSTYETLVSLVFILFMFGGDH 60 M+ FF ++P++E YGNP YF Y+ILA LP+ IG+F +KR YE VSL+FI+ M G+ Sbjct: 1 MIDFFKNLPHLEAYGNPQYFFYIILAVLPIFIGLFFKKRFPLYEAFVSLIFIVLMLTGEK 60 Query: 61 YQQLVAFLFYLLWQIISVFAYQKYRENANSAGVFYLAIAMALFPLIWVKVAPLTGPSSQT 120- Q+ A FY++WQI V++Y+ YR++ ++ +FYL + M++ PL VK+ P + Q+ Sbjct: 61 SHQIFALFFYIIWQIFCVYSYKFYRKSRDNKWIFYLHVFMSILPLSLVKITPAIWTNQQS 120- Query: 121 LFSFLGISYLTFKSIGMIIEMRDGTLQEVRLPDFIRFMIFFPTFSSGPIDRFRHFQEDYH 18- 0 LF FLGISYLTF+S+GMI+EMRDG L +FIRFM+F PTFSSGPIDRFR F +DY Sbjct: 121 LFGFLGISYLTFRSVGMIMEMRDGVLTSFTFWEFIRFMLFMPTFSSGPIDRFRRFNDDYE 18- 0 Query: 181 KLPERDDYFAMLNKAVMYLMLGFLYKHIISYCLGGILLPLLENKALMVGGYFNKETILVM 24- 0 K+P++D+ ML ++V Y+MLGF YK +++ LG ++LP L+ AL GG+FN T+ VM Sbjct: 181 KIPDKDELLDMLEQSVHYIMLGFFYKFVLAQILGTMILPGLKEMALQKGGWFNWPTLGVM 24- 0 Query: 241 YVYGLNLFFDFAGYSMFAIGISYLLGIRTPENFNMPFLSASLKDFWNRWHMSLSFWFRDY 30- 0 YVYGL+LFFDFAGYSMFAI IS +GI++P NFN PF S LK+FWNRWHMSLSFWFRD+ Sbjct: 241 YVYGLDLFFDFAGYSMFAIAISNFMGIKSPTNFNQPFKSQDLKEFWNRWHMSLSFWFRDF 30- 0 Query: 301 VFMRLVHLLIKHKTFKNRNVTSGVAYLVNMLVMGFWHGLTWYYIAYGLFHGIGLIINDAW 36- 0 VFMRLV +L+K+K FKNRNVTS VAY+VNML+MGFWHG+TWYYI YGLFHG+GL++NDAW Sbjct: 301 VFMRLVKVLVKNKVFKNRNVTSSVAYIVNMLIMGFWHGVTWYYITYGLFHGVGLVLNDAW 36- 0 Query: 361 IRKKKEINRHRKKKGLSPLFQSRAFHVLCIVVTFHVVMFSLLLFSGFLNDLWF 413 +RKKK +N+ RK K LSPL ++ L IV+TF+VVM S L+FSGFLNDLWF Sbjct: 361 LRKKKRLNKERKAKNLSPLPENGWTRALGIVITFNVVMLSFLIFSGFLNDLWF 413 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05663 Identities = 240/416 (57%), Positives = 317/416 (75%), Gaps = 5/416 (1%) Query: 5 FLEKLPHLDVYGNPQYFFYLILAVLPIYIGLFFKKRFALYEIIFSLSFIVMMLTGSTFNQ 64 F +P+++ YGNP YF YLILA LP+ IG+F +KR + YE + SL FI+ M G + Q Sbjct: 4 FFSHIPYMEPYGNPIYFVYLILAFLPVIIGIFKQKRLSTYETLVSLVFILFMFGGDHYQQ 63 Query: 65 LKSLLAYVVGQSLLVFIYKAYRKRFNHTLVFYVTVCLSIFPLFLVKLIPAISEDGHQSLF 124- L + L Y++ Q + VF Y+ YR+ N VFY+ + +++FPL VK+ P ++ Q+LF Sbjct: 64 LVAFLFYLLWQIISVFAYQKYRENANSAGVFYLAIAMALFPLIWVKVAP-LTGPSSQTLF 122- Query: 125 GFLGISYLTFRAVAMIIEMRDGVLKEFTLWEFLRFLLFFPTFSSGPIDRFKRFNEDYINI 18- 4 FLGISYLTF+++ MIIEMRDG L+E L +F+RF++FFPTFSSGPIDRF+ F EDY + Sbjct: 123 SFLGISYLTFKSIGMIIEMRDGTLQEVRLPDFIRFMIFFPTFSSGPIDRFRHFQEDYNKL 18- 2 Query: 185 PDRNELLDMLGQAIHYLMLGFLYKFILAYIFGSLIMPPLKELALEQGGVFNWPTLGVMYA 24- 4 P+R++ ML +A+ YLMLGFLYK I++Y G +++P L+ AL GG FN T+ VMY Sbjct: 183 PERDDYFAMLNKAVMYLMLGFLYKHIISYCLGGILLPLLENKALMVGGYFNKETILVMYV 24- 2 Query: 245 FGFDLFFDFAGYTMFALAISNLMGIKSPINFDKPFKSRDLKEFWNRWHMSLSFWFRDFVF 30- 4 +G +LFFDFAGY+MFA+ IS L+GI++P NF+ PF S LK+FWNRWHMSLSFWFRD+VF Sbjct: 243 YGLNLFFDFAGYSMFAIGISYLLGIRTPENFNMPFLSASLKDFWNRWHMSLSFWFRDYVF 30- 2 Query: 305 MRLVKLLVKNKVFKNRNVTSSVAYIINMLLMGFWHGLTWYYIAYGLFHGIGLVINDAWVR 36- 4 MRLV LL+K+K FKNRNVTS VAY++NML+MGFWHGLTWYYIAYGLFHGIGL+INDAW+R Sbjct: 303 MRLVHLLIKHKTFKNRNVTSGVAYLVNMLVMGFWHGLTWYYIAYGLFHGIGLIINDAWIR 36- 2 Query: 365 KKKNINKERRLAKKPLLP--ENKWTYALGVFITFNVVMFSFLIFSGFLDLLWFPQP 418 KKK IN+ R+ KK L P +++ + L + +TF+VVMFS L+FSGFL+ LWF +P Sbjct: 363 KKKEINRHRK--KKGLSPLFQSRAFHVLCIVVTFHVVMFSLLLFSGFLNDLWFNRP 416 A related GBS gene <SEQ ID 8913> and protein <SEQ ID 8914> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05664 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 3.22 GvH: Signal Score (-7.5): -4.56 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 7 value: -8.55 threshold: 0.0 INTEGRAL Likelihood = -8.55 Transmembrane 93-109 (91-117) INTEGRAL Likelihood = -7.64 Transmembrane 21-37 (19-39) INTEGRAL Likelihood = -6.79 Transmembrane 390-406 (387-410) INTEGRAL Likelihood = -5.20 Transmembrane 41-57 (40-59) INTEGRAL Likelihood = -2.07 Transmembrane 203-219 (200-221) INTEGRAL Likelihood = -1.65 Transmembrane 65-81 (65-81) INTEGRAL Likelihood = -0.75 Transmembrane 125-141 (125-141) PERIPHERAL Likelihood = 1.01 322 modified ALOM score: 2.21 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4418 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00128## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1850 A DNA sequence (GBSx1957) was identified in S. agalactiae <SEQ ID 5745> which encodes the amino acid sequence <SEQ ID 5746>. Analysis of this protein sequence reveals the following: TABLE-US-05665 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2611 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10143> which encodes amino acid sequence <SEQ ID 10144> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05666 >GP: AAC05774 GB: AF051356 D-alanine-D-alanyl carrier protein ligase [Streptococcus mutans] Identities = 404/510 (79%), Positives = 465/510 (90%) Query: 5 IHDMIKTIEHFAETQADFPVYDILGEVHTYGQLKVDSDSLAAHIDSLGLVEKSPVLVFGG 64 I DMI TIE+FA+ QA+FPVY+ILGE+HTYG+LK DSDSLAAH+D L L KSPV+VFGG Sbjct: 6 IKDMIATIENFAQEQAEFPVYNILGEIHTYGELKADSDSLAAHLDQLDLTAKSPVVVFGG 65 Query: 65 QEYEMLATFVALTKSGHAYIPVDQHSALDRIQAIMTVAQPSLIISIGEFPLEVDNVPILD 124- QEY MLA+FVALTKSGHAYIP+D HSAL+RI+AI+ VA+PSL+I++ +FP++ VP++ Sbjct: 66 QEYAMLASFVALTKSGHAYIPIDHHSALERIEAILEVAEPSLVIAVDDFPIDNLQVPVIQ 125- Query: 125 VSQVSAIFEEKTPYEVTHSVKGDDNYYIIFTSGTTGLPKGVQISHDNLLSFTNWMISDDE 18- 4 SQ+ IF++K Y++ H+VKGDD YYIIFTSGTTG PKGVQISHDNLLSFTNWMI+ + Sbjct: 126 YSQLEEIFKQKLSYQINHAVKGDDTYYIIFTSGTTGKPKGVQISHDNLLSFTNWMINAEA 18- 5 Query: 185 FSVPERPQMLAQPPYSFDLSVMYWAPTLAMGGTLFALPKTVVNDFKKLFATINELPIQVW 24- 4 F+ P RPQMLAQPPYSFDLSVMYWAPTLA+GGTLFALPK + DFK+LF TIN+LPI VW Sbjct: 186 FATPHRPQMLAQPPYSFDLSVMYWAPTLALGGTLFALPKEITADFKQLFTTINQLPIGVW 24- 5 Query: 245 TSTPSFADMALLSNDFNSETLPQLTHFYFDGEELTVKTAQKLRQRFPKARIVNAYGPTEA 30- 4 TSTPSF DMA+LS+DFN++ LP LTHFYFDGEELTVKTA+KLRQRFP+ARIVNAYGPTEA Sbjct: 246 TSTPSFVDMAMLSDDFNAQQLPHLTHFYFDGEELTVKTAKKLRQRFPQARIVNAYGPTEA 30- 5 Query: 305 TVALSAVAITDEMLETCKRLPIGYTKDDSPTYVIDEEGHKLPNGEQGEIIIAGPAVSKGY 36- 4 TVALSA+A+TD+MLETCKRLPIGYTK DSPT++IDE GHKL NG+QGEII++GPAVSKGY Sbjct: 306 TVALSALAVTDKMLETCKRLPIGYTKPDSPTFIIDESGHKLANGQQGEIIVSGPAVSKGY 36- 5 Query: 365 LNNPEKTAEAFFQFEGLPAYHTGDLGSMTDEGLLLYGGRMDFQIKFNGYRIELEDVSQNL 42- 4 LNNPE+TA AFF+FEGLPAYHTGDLGSMTDEGLLLYGGRMDFQIKFNGYRIELE+VSQNL Sbjct: 366 LNNPERTAAAFFEFEGLPAYHTGDLGSMTDEGLLLYGGRMDFQIKFNGYRIELEEVSQNL 42- 5 Query: 425 NKSQYVKSAVAVPRYNKDHKVQNLLAYIVLKEGVRDDFERDLDLTKAIKEDLKDIMMDYM 48- 4 NKSQY+ SAVAVPRYNKDHKVQNLLAY+VLK+GV + FER LD+TKAIK DL+D+MMDYM Sbjct: 426 NKSQYIASAVAVPRYNKDHKVQNLLAYVVLKDGVEEQFERALDITKAIKADLQDVMMDYM 48- 5 Query: 485 MPSKFIYREDLPLTPNGKIDIKGLMSEVNK 514 MPSKF+YR+DLPLTPNGKIDIKGLMSEVNK Sbjct: 486 MPSKFLYRKDLPLTPNGKIDIKGLMSEVNK 515 A related DNA sequence was identified in S. pyogenes <SEQ ID 5747> which encodes the amino acid sequence <SEQ ID 5748>. Analysis of this protein sequence reveals the following: TABLE-US-05667 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.28 Transmembrane 92-108 (91-108) INTEGRAL Likelihood = -0.85 Transmembrane 43-59 (41-59) ----- Final Results ----- bacterial membrane --- Certainty = 0.1914 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05668 >GP: AAC05774 GB: AF051356 D-alanine-D-alanyl carrier protein ligase [Streptococcus mutans] Identities = 365/511 (71%), Positives = 438/511 (85%) Query: 2 IKDMIDSIEQFAQTQADFPVYDCLGERRTYGQLKRDSDSIAAFIDSLALLAKSPVLVFGA 61 IKDMI +IE FAQ QA+FPVY+ LGE TYG+LK DSDS+AA +D L L AKSPV+VFG Sbjct: 6 IKDMIATIENFAQEQAEFPVYNILGEIHTYGELKADSDSLAAHLDQLDLTAKSPVVVFGG 65 Query: 62 QTYDMLATFVALTKSGHAYIPVDVHSAPERILAIIEIAKPSLIIAIEEFPLTIEGISLVS 121- Q Y MLA+FVALTKSGHAYIP+D HSA ERI AI+E+A+PSL+IA+++FP+ + ++ Sbjct: 66 QEYAMLASFVALTKSGHAYIPIDHHSALERIEAILEVAEPSLVIAVDDFPIDNLQVPVIQ 125- Query: 122 LSEIESAKLAEMPYERTHSVKGDDNYYIIFTSGTTGQPKGVQISHDNLLSFTNWMIEDAA 18- 1 S++E ++ Y+ H+VKGDD YYIIFTSGTTG+PKGVQISHDNLLSFTNWMI A Sbjct: 126 YSQLEEIFKQKLSYQINHAVKGDDTYYIIFTSGTTGKPKGVQISHDNLLSFTNWMINAEA 18- 5 Query: 182 FDVPKQPQMLAQPPYSFDLSVMYWAPTLALGGTLFALPKELVADFKQLFTTIAQLPVGIW 24- 1 F P +PQMLAQPPYSFDLSVMYWAPTLALGGTLFALPKE+ ADFKQLFTTI QLP+G+W Sbjct: 186 FATPHRPQMLAQPPYSFDLSVMYWAPTLALGGTLFALPKEITADFKQLFTTINQLPIGVW 24- 5 Query: 242 TSTPSFADMAMLSDDFCQAKMPALTHFYFDGEELTVSTARKLFERFPSAKIINAYGPTEA 30- 1 TSTPSF DMAMLSDDF ++P LTHFYFDGEELTV TA+KL +RFP A+I+NAYGPTEA Sbjct: 246 TSTPSFVDMAMLSDDFNAQQLPHLTHFYFDGEELTVKTAKKLRQRFPQARIVNAYGPTEA 30- 5 Query: 302 TVALSAIEITREMVDNYTRLPIGYPKPDSPTYIIDEDGKELSSGEQGEIIVTGPAVSKGY 36- 1 TVALSA+ +T +M++ RLPIGY KPDSPT+IIDE G +L++G+QGEIIV+GPAVSKGY Sbjct: 306 TVALSALAVTDKMLETCKRLPIGYTKPDSPTFIIDESGHKLANGQQGEIIVSGPAVSKGY 36- 5 Query: 362 LNNPEKTAEAFFTFKGQPAYHTGDIGSLTEDNILLYGGRLDFQIKYAGYRIELEDVSQQL 42- 1 LNNPE+TA AFF F+G PAYHTGD+GS+T++ +LLYGGR+DFQIK+ GYRIELE+VSQ L Sbjct: 366 LNNPERTAAAFFEFEGLPAYHTGDLGSMTDEGLLLYGGRMDFQIKFNGYRIELEEVSQNL 42- 5 Query: 422 NQSPMVASAVAVPRYNKEHKVQNLLAYIVVKDGVKERFDRELELTKAIKASVKDHMMSYM 48- 1 N+S+ +ASAVAVPRYNK+HKVQNLLAY+V+KDGV+E+F+R L++TKAIKA ++D MM YM Sbjct: 426 NKSQYIASAVAVPRYNKDHKVQNLLAYVVLKDGVEEQFERALDITKAIKADLQDVMMDYM 48- 5 Query: 482 MPSKFLYRDSLPLTPNGKIDIKTLINEVNNR 512 MPSKFLYR LPLTPNGKIDIK L++EVN + Sbjct: 486 MPSKFLYRKDLPLTPNGKIDIKGLMSEVNKK 516 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05669 Identities = 374/510 (73%), Positives = 439/510 (85%) Query: 4 MIHDMIKTIEHFAETQADFPVYDILGEVHTYGQLKVDSDSLAAHIDSLGLVEKSPVLVFG 63 MI DMI +IE FA+TQADFPVYD LGE TYGQLK DSDS+AA IDSL L+ KSPVLVFG Sbjct: 1 MIKDMIDSIEQFAQTQADFPVYDCLGERRTYGQLKRDSDSIAAFIDSLALLAKSPVLVFG 60 Query: 64 GQEYEMLATFVALTKSGHAYIPVDQHSALDRIQAIMTVAQPSLIISIGEFPLEVDNVPIL 123- Q Y+MLATFVALTKSGHAYIPVD HSA +RI AI+ +A+PSLII+I EFPL ++ + ++ Sbjct: 61 AQTYDMLATFVALTKSGHAYIPVDVHSAPERILAIIEIAKPSLIIAIEEFPLTIEGISLV 120- Query: 124 DVSQVSAIFEEKTPYEVTHSVKGDDNYYIIFTSGTTGLPKGVQISHDNLLSFTNWMISDD 18- 3 +S++ + + PYE THSVKGDDNYYIIFTSGTTG PKGVQISHDNLLSFTNWMI D Sbjct: 121 SLSEIESAKLAEMPYERTHSVKGDDNYYIIFTSGTTGQPKGVQISHDNLLSFTNWMIEDA 18- 0 Query: 184 EFSVPERPQMLAQPPYSFDLSVMYWAPTLAMGGTLFALPKTVVNDFKKLFATINELPIQV 24- 3 F VP++PQMLAQPPYSFDLSVMYWAPTLA+GGTLFALPK +V DFK+LF TI +LP+ + Sbjct: 181 AFDVPKQPQMLAQPPYSFDLSVMYWAPTLALGGTLFALPKELVADFKQLFTTIAQLPVGI 24- 0 Query: 244 WTSTPSFADMALLSNDFNSETLPQLTHFYFDGEELTVKTAQKLRQRFPKARIVNAYGPTE 30- 3 WTSTPSFADMA+LS+DF +P LTHFYFDGEELTV TA+KL +RFP A+I+NAYGPTE Sbjct: 241 WTSTPSFADMAMLSDDFCQAKMPALTHFYFDGEELTVSTARKLFERFPSAKIINAYGPTE 30- 0 Query: 304 ATVALSAVAITDEMLETCKRLPIGYTKDDSPTYVIDEEGHKLPNGEQGEIIIAGPAVSKG 36- 3 ATVALSA+ IT EM++ RLPIGY K DSPTY+IDE+G +L +GEQGEII+ GPAVSKG Sbjct: 301 ATVALSAIEITREMVDNYTRLPIGYPKPDSPTYIIDEDGKELSSGEQGEIIVTGPAVSKG 36- 0 Query: 364 YLNNPEKTAEAFFQFEGLPAYHTGDLGSMTDEGLLLYGGRMDFQIKFNGYRIELEDVSQN 42- 3 YLNNPEKTAEAFF F+G PAYHTGD+GS+T++ +LLYGGR+DFQIK+ GYRIELEDVSQ Sbjct: 361 YLNNPEKTAEAFFTFKGQPAYHTGDIGSLTEDNILLYGGRLDFQIKYAGYRIELEDVSQQ 42- 0 Query: 424 LNKSQYVKSAVAVPRYNKDHKVQNLLAYIVLKEGVRDDFERDLDLTKAIKEDLKDIMMDY 48- 3 LN+S V SAVAVPRYNK+HKVQNLLAYIV+K+GV++ F+R+L+LTKAIK +KD MM Y Sbjct: 421 LNQSPMVASAVAVPRYNKEHKVQNLLAYIVVKDGVKERFDRELELTKAIKASVKDHMMSY 48- 0 Query: 484 MMPSKFIYREDLPLTPNGKIDIKGLMSEVN 513 MMPSKF+YR+ LPLTPNGKIDIK L++EVN Sbjct: 481 MNPSKFLYRDSLPLTPNGKIDIKTLINEVN 510 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1851 A DNA sequence (GBSx1958) was identified in S. agalactiae <SEQ ID 5749> which encodes the amino acid sequence <SEQ ID 5750>. This protein is predicted to be a histidine protein kinase (phoR). Analysis of this protein sequence reveals the following:

TABLE-US-05670 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.64 Transmembrane 9-25 (5-32) INTEGRAL Likelihood = -11.62 Transmembrane 136-152 (132-164) ----- Final Results ----- bacterial membrane --- Certainty = 0.6456 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05671 >GP: CAB54569 GB: AJ006392 histidine kinase [Streptococcus pneumoniae] Identities = 105/416 (25%), Positives = 197/416 (47%), Gaps = 56/416 (13%) Query: 7 KKFVFLTMSILIVVVLFLFAVSNRYNQYWDEYDAYRIVKLVAKNDY---LGIPGDEPIAL 63 + F+F+ + + ++V+ L + NR + + ++ L+A DY L + G I Sbjct: 12 RDFIFILILLGFILVVTLLLLENRRDNIQLKQVNQKVKDLIA-GDYSKVLDMQGGSEITN 70 Query: 64 VTIDNQKMVKIQSNNTDLTNDVIEKSSLKL------LEQGKKSRKWKSFIYSIKE----- 112- +T + + ++ LT + +E+ S +L + G + + I I + Sbjct: 71 ITNNLNDLSEV----IRLTQENLEQESKRLNSILFYMTDGVLATNRRGQIIMINDTAKKQ 126- Query: 113 ---YKDKTYTIAIMDLASYEVPYARRFLILVFT--------IFGFCLLAAVSLYLSR--- 15- 8 K+ +I++L E Y R LI I G L V L R Sbjct: 127 LGLVKEDVLNRSILELLKIEENYELRDLITQSPELLLDSQDINGEYLNLRVRFALIRRES 18- 6 Query: 159 -FIVGPVE-----TEMTREKQ----FVSDASHELKTPIAAIRANVQVLEQ----QIPGNR 20- 4 FI G V TE +E++ FVS+ SHEL+TP+ ++++ ++ L++ + Sbjct: 187 GFISGLVAVLHDTTEQEKEERERRLFVSNVSHELRTPLTSVKSYLEALDEGALCETVAPD 24- 6 Query: 205 YLDHVVSETKRMEFLIEDLLNLSRLDEKRSKVNFKKLNLSVLCQEVLLTYESLAYEEEKC 26- 4 ++ + ET RM ++ DLL+LSR+D S ++ + +N + +L ++ + +E++ Sbjct: 247 FIKVSLDETNRMMRMVTDLLHLSRIDNATSHLDVELINFTAFITFILNRFDKMKGQEKEK 30- 6 Query: 265 LNDTIED----DVWIVGEESQIKQILIILLDNAIRHSLSKSAIQFSLKQARRKAILTISN 32- 0 + + D +W+ + ++ Q++ +L+NAI++S I +K + IL+IS+ Sbjct: 307 KYELVRDYPINSIWMEIDTDKMTQVVDNILNNAIKYSPDGGKITVRMKTTEDQMILSISD 36- 6 Query: 321 PSAIYSKEVMDNLFERFYQAKDDHADSLS---FGLGLSIAKAIVERHKGRIRAYQE 373 K+ + +F+RFY+ D A S + GLGLSIAK I+++HKG I A E Sbjct: 367 HGLGIPKQDLPRIFDRFYRV--DRARSRAQGGTGLGLSIAKEIIKQHKGFIWAKSE 420 A related sequence was also identified in GAS <SEQ ID 9131> which encodes the amino acid sequence <SEQ ID 9132>. Analysis of this protein sequence reveals the following: TABLE-US-05672 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.30 Transmembrane 9-25 (4-33) INTEGRAL Likelihood = -10.35 Transmembrane 161-177 (154-190) PERIPHERAL Likelihood = 4.35 142 ----- Final Results ----- bacterial membrane --- Certainty = 0.5522 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05673 Identities = 94/406 (23%), Positives = 190/406 (46%), Gaps = 31/406 (7%) Query: 1 MFSDLRKKFVFLTMSILIVVVLFLFAVSNRYNQYWDEYDAYRIVKLVAKNDYLGIPGDEP 60 MF+ +R +F+ + + +++ + + N Y + + RI+ L++ N +PG Sbjct: 10 MFNRIRIRFIMIASIAIFIILSSIVGIINTARCYQSQQEINRILHLISSNKGK-LPGTTE 68 Query: 61 IAL-----VTIDNQKMVKIQS-----NNTDLTNDVIEKSSLKLLE------------QGK 98 + ++ D+ + S N L+++ S+L E + K Sbjct: 69 SSKRLGTKLSEDSLSQFRYYSVIFNANGHLLSSNTANISALDREEAQYFARLFAKSGEEK 128- Query: 99 KSRKWKSFIYS--IKEYKDKTYTIAIMDLASYEVPYARRFLILVFTIFG-FCLLAAVSLY 155- S + + +YS I + ++ + I+D Y + V FG F + Sbjct: 129 GSYRHQDSVYSYLITQLPNEEKLVVILDTTFYFRSVGDLLAVSVMLAFGGFIFFVVLVSL 18- 8 Query: 156 LSRFIVGPVETEMTREKQFVSDASHELKTPIAAIRANVQVLEQQIPGNRYLDHVVSETKR 21- 5 S ++ P ++++F+++A HELKTP+A I AN +++E + + + KR Sbjct: 189 FSGMVIKPFVQNYEKQRRFITNAGHELKTPLAIISANNELVELMTGESEWTKSTSDQVKR 24- 8 Query: 216 MEFLIEDLLNLSRLDEKRSKVNFKKLNLSVLCQEVLLTYESLAYEEEKCLNDTIEDDVWI 27- 5 + LI ++ L+RL+E+ V ++ S + Q+ ++SL ++ K + TI+ ++ I Sbjct: 249 LTGLINQMITLARLEEQPDVV-LHMVDFSAIAQDAAEDFKSLVLKDGKRFDLTIQPNIMI 30- 7 Query: 276 VGEESQIKQILIILLDNAIRHSLSKSAIQFSLK---QARRKAILTISNPSAIYSKEVMDN 33- 2 EE + +++ IL+DNA ++ K ++ SL + R++A L +SN Sbjct: 308 KAEEKSLFELVTILVDNANKYCDPKGLVKVSLTTIGRRRKRAKLEVSNTYLEGKSIDYSR 36- 7 Query: 333 LFERFYQAKDDH-ADSLSFGLGLSIAKAIVERHKGRIRAYQEKDQL 377 FERFY+ + H + +G+GLS+A+++V+ KG I + D + Sbjct: 368 FFERFYREDESHNSKEKGYGIGLSMAESMVKLFKGTITVNYKNDAI 413 A related GBS gene <SEQ ID 8915> and protein <SEQ ID 8916> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05674 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: 17.50 GvH: Signal Score (-7.5): -2.9 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 2 value: -13.64 threshold: 0.0 INTEGRAL Likelihood = -13.64 Transmembrane 9-25 (5-32) INTEGRAL Likelihood = -11.62 Transmembrane 136-152 (132-164) PERIPHERAL Likelihood = 2.49 345 modified ALOM score: 3.23 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6456 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00129## SEQ ID 5750 (GBS34) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 15 (lane 9; MW 69 kDa). GBS34-GST was purified as shown in FIG. 193, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1852 A DNA sequence (GBSx1959) was identified in S. agalactiae <SEQ ID 5753> which encodes the amino acid sequence <SEQ ID 5754>. This protein is predicted to be two-component response regulator (regX3). Analysis of this protein sequence reveals the following: TABLE-US-05675 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1986 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05676 >GP: BAB04091 GB: AP001508 two-component response regulator [Bacillus halodurans] Identities = 98/223 (43%), Positives = 145/223 (64%), Gaps = 5/223 (2%) Query: 2 RLLVVEDEKSIAEAIQALLADKGYSVDLAFDGDDGLEYILTGLYDLVLLDIMLPKRSGLS 61 R+L++EDEK IA +Q L +GY D AF G DGLE +DLVLLD+MLP+ SGL Sbjct: 3 RILIIEDEKKIARVLQLELEHEGYETDAAFSGSDGLETFQAHAWDLVLLDVMLPELSGLE 62 Query: 62 VLKRVREAGLETPIIFLTAKSQTYDKVNGLDLGADDYITKPFEADELLARIR--LRTRQS 119- VL+R+R TPII LTA++ DKV+GLDLGA+DYITKPFE +ELLAR+R LRT Q+ Sbjct: 63 VLRRIRMTDPVTPIILLTARNSIPDKVSGLDLGANDYITKPFEIEELLARVRACLRTVQT 122- Query: 120 SLIRANQLRLGNIRLNTDSHELESKESSVKLSNKEFLLMEVFMRNAKQIIPKNQLISKVW 17- 9 + L + +N + +++ +++L+ KEF L+ F++N Q++ + Q+++ VW Sbjct: 123 RERVEDTLMFQELTINEKTRDVQRGNETIELTPKEFELLVFFIKNKGQVLSREQILTNVW 18- 2 Query: 180 GPSDNSEYNQLEVFISFLRKKLRFLKADIEIITTKGFGYSLEE 222 G + N ++V++ +LRKKL +A + T +G GY L+E Sbjct: 183 GFDYYGDTNVIDVYVRYLRKKLSLTEA---LQTVRGVGYRLKE 222 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1853 A DNA sequence (GBSx1960) was identified in S. agalactiae <SEQ ID 5755> which encodes the amino acid sequence <SEQ ID 5756>. This protein is predicted to be 50S ribosomal protein L34-related protein. Analysis of this protein sequence reveals the following: TABLE-US-05677 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5923(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05678 >GP: AAC22660 GB: U32781 ribosomal protein L34 (rpL34) [Haemophilus influenzae Rd] Identities = 32/44 (72%), Positives = 37/44 (83%) Query: 1 MKRTYQPSKIRRQRKHGFRHRMSTKNGRRVLASRRRKGRKVLSA 44 MKRT+QPS ++R R HGFR RM+TKNGR+VLA RR KGRK LSA Sbjct: 1 MKRTFQPSVLKRSRTHGFRARMATKNGRQVLARRRAKGRKSLSA 44 A related DNA sequence was identified in S. pyogenes <SEQ ID 5757> which encodes the amino acid sequence <SEQ ID 5758>. Analysis of this protein sequence reveals the following: TABLE-US-05679 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5385(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05680 Identities = 42/44 (95%), Positives = 44/44 (99%) Query: 1 MKRTYQPSKIRRQRKHGFRHRMSTKNGRRVLASRRRKGRKVLSA 44 +KRTYQPSKIRRQRKHGFRHRMSTKNGRRVLA+RRRKGRKVLSA Sbjct: 1 VKRTYQPSKIRRQRKHGFRHRMSTKNGRRVLAARRRKGRKVLSA 44 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1854 A DNA sequence (GBSx1961) was identified in S. agalactiae <SEQ ID 5759> which encodes the amino acid sequence <SEQ ID 5760>. Analysis of this protein sequence reveals the following: TABLE-US-05681 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.79 Transmembrane 122-138 (115-141) INTEGRAL Likelihood = -4.35 Transmembrane 19-35 (15-40) ----- Final Results ----- bacterial membrane --- Certainty = 0.3314(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05682 >GP: AAF95990 GB: AE004350 conserved hypothetical protein [Vibrio cholerae] Identities = 79/145 (54%), Positives = 117/145 (80%) Query: 1 MKTFVNNASKTVLSLWFGVMPTIMTVGTIALIISVSTPIFKILGTPFLPFLELLGIPEAD 60 +++ + + + + FGV+P +M +GTIAL+I+ T +F +LG PF+PFLELLG+PEA Sbjct: 314 VQSVIGEGIRNAVDMVFGVLPVVMGLGTIALVIAEYTSVFSLLGQPFIPFLELLGVPEAT 37- 3 Query: 61 IASQTMIVGFSDMVVPSIMAAEIHSEMTRFIVATVSIVQLIYMSETGAVILGSKIPINIL 120- AS+T++VGF+DM +P+I+AA I +EMTRF++A +S+ QLIYMSE GA++LGS+IP+NI+ Sbjct: 374 AASKTIVVGFADMFIPAILAASIDNEMTRFVIAAMSVTQLIYMSEVGALLLGSRIPVNIV 43- 3 Query: 121 ELFIIFIERTIISLPIIVLMAHLFF 145 ELF+IFI RT+I+LP+I +AHL F Sbjct: 434 ELFVIFILRTLITLPVIAAVAHLLF 458 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1855 A DNA sequence (GBSx1962) was identified in S. agalactiae <SEQ ID 5761> which encodes the amino acid sequence <SEQ ID 5762>. This protein is predicted to be D,D-carboxypeptidase (dacA-2). Analysis of this protein sequence reveals the following: TABLE-US-05683 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2443(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9485> which encodes amino acid sequence <SEQ ID 9486> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10945> which encodes amino acid sequence <SEQ ID 10946> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05684 >GP: CAA67776 GB: X99400 D,D-carboxypeptidase [Streptococcus pneumoniae] Identities = 193/383 (50%), Positives = 282/383 (73%), Gaps = 6/383 (1%) Query: 1 MAVDLDSGKILYEKDANKPAAIASLTKIMTVYMVYKEIDNGNLKWNTKVNISDYPYQLTR 60 +AV+ ++GKILYEKDA +P IAS+TK++TVY+VY+ ++NG++ +T V+ISDYPYQLT Sbjct: 33 IAVEANTGKILYEKDATQPVEIASITKLITVYLVYEALENGSITLSTPVDISDYPYQLTT 92 Query: 61 ESDASNVPLEKRRYTVKQLVDAAMISSANSAAIALAEHISGTESKFVDKMTAQLEKWGIH 120- S+ASN+P+E R YTV++L++A ++SSANSAAIALAE I+G+E FVD M A+L +WGI Sbjct: 93 NSEASNIPMEARNYTVEELLEATLVSSANSAAIALAEKIAGSEKDFVDMMRAKLLEWGIQ 152- Query: 121 DSHLVNASGLNNSMLGNHIYPKSSQNDENKMSARDIAIVAYHLVNEYPSILKITSKSVAK 18- 0 D+ +VN +GLNN LG++IYP S +++ENK+SA D+AIVA +L+ +YP +L+IT K + Sbjct: 153 DATVVNTTGLNNETLGDNIYPGSKKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSST 21- 2 Query: 181 FDKDIMHSYNYMLPDMPVFRPGITGLKTGTTELAGQSFIATSTESGMRLLTVIMHADKAD 24- 0 F + S NYML MP +R G GLKTGTT+ AG+SF+ T+ E GMR++TV+++AD D Sbjct: 213 FAGMTITSTNYMLEGMPAYRGGFDGLKTGTTDKAGESFVGTTVEKGMRVITVVLNADHQD 27- 2 Query: 241 KDKYARFTATNSLLNYITNTYEPNLVLAKGAAYKGKEASVRDGKEQSVIAVAKNDLKVVQ 30- 0 + YARFTAT+SL++YI++T+ ++ +G AY+ +A V+DGKE +VIAVA D+ +++ Sbjct: 273 NNPYARFTATSSLMDYISSTFTLRKIVQQGDAYQDSKAPVQDGKEDTVIAVAPEDIYLIE 33- 2 Query: 301 KKNITKQNQLKINF---KKELTAPITKKENLGKAYYVDLNKVGKGYLIKE-PSVHLVAKD 35- 6 + + Q+ + F K + AP+ +G Y D + +G+GY+ E PS +VA Sbjct: 333 R--VGNQSSQSVQFTPDSKAIPAPLEAGTVVGHLTYEDKDLIGQGYITTERPSFEMVADK 39- 0 Query: 357 SIERSFFLKVWWNHFVRYVNEKL 379 IE++FFLKVWWN FVR+VNEKL Sbjct: 391 KIEKAFFLFVWWNQFVRFVNEKL 413 A related DNA sequence was identified in S. pyogenes <SEQ ID 5763> which encodes the amino acid sequence <SEQ ID 5764>. Analysis of this protein sequence reveals the following: TABLE-US-05685 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05686 Identities = 176/380 (46%), Positives = 257/380 (67%), Gaps = 3/380 (0%) Query: 1 MAVDLDSGKILYEKDANKPAAIASLTKIMTVYMVYKEIDNGNLKWNTKVNISDYPYQLTR 60 +AVDL+SGK+LYEKDA + +AS++K++T Y+VYEE+ G L W++ V IS+YPY+LT Sbjct: 33 IAVDLESGKVLYEKDAKEVVPVASVSKLLTTYLVYKEVSKGKLNWDSPVTISNYPYELTT 92 Query: 61 ESDASNVPLEKRRYTVKQLVDAAMISSANSAAIALAEHISGTESKFVDKMTAQLEKWGIH 120- SNVPL+KR+YTVK+L+ A ++++ANS AIALAE I GTE KFVDKM QL +WGI Sbjct: 93 NYTISNVPLDKRKYTVKELLSALVVNNANSPAIALAEKIGGTEPKFVDKMKKQLRQWGIS 152- Query: 121 DSHLVNASGLNNSMLGNHIYPKSSQNDENKMSARDIAIVAYHLVNEYPSILKITSKSVAK 18- 0 D+ +VN++GL N LG + YP + +DEN A D+AI+A HL+ E+P +LK++SKS Sbjct: 153 DAKVVNSTGLTNHFLGANTYPNTEPDDENCFCATDLAIIARHLLLEFPEVLKLSSKSSTI 21- 2 Query: 181 FDKDIMHSYNYMLPDMPVFRPGITGLKTGTTELAGQSFIATSTESGMRLLTVIMHADKAD 24- 0 F ++SYNYML MP +R G+ GL G ++ AG SF+ATS E+ MR++TV+++AD++ Sbjct: 213 FAGQTIYSYNYMLKGMPCYREGVDGLFVGYSKKAGASFVATSVENQMRVITVVLNADQSH 27- 2 Query: 241 KDKYARFTATNSLLNYITNTYEPNLVLAKGAAYKGKEASVRDGKEQSVIAVAKNDLKVVQ 30- 0 +D A F TN LL Y+ ++ ++ K V D E++V VA+N L ++ Sbjct: 273 EDDLAIFKTTNQLLQYLLINFQKVQLIENNKPV--KTLYVLDSPEKTVKLVAQNSLFFIK 33- 0 Query: 301 KKNITKQNQLKINFKKE-LTAPITKKENLGKAYYVDLNKVGKGYLIKEPSVHLVAKDSIE 35- 9 + +N + I K + AP++K + LG+A D + +G+GYL PS++L+ + +I Sbjct: 331 PIHTKTKNTVHITKKSSTMIAPLSKGQVLGRATLQDKHLIGQGYLDTPPSINLILQKNIS 39- 0 Query: 360 RSFFLKVWWNHFVRYVNEKL 379 +SFFLKVWWN FVRYVN L Sbjct: 391 KSFFLKVWWNRFVRYVNTSL 410 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1856 A DNA sequence (GBSx1963) was identified in S. agalactiae <SEQ ID 5765> which encodes the amino acid sequence <SEQ ID 5766>. This protein is predicted to be penicillin binding protein 4 (pdp4) (dacA-1). Analysis of this protein sequence reveals the following: TABLE-US-05687 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.58 Transmembrane 368-384 (363-394) ----- Final Results ----- bacterial membrane --- Certainty = 0.6031(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-05688 >GP: CAA60582 GB: X87104 penicillin binding protein 4 [Staphylococcus aureus] Identities = 117/333 (35%), Positives = 188/333 (56%), Gaps = 8/333 (2%) Query: 5 IVSFLCILLSLTCVNSVQAEEHKDIMQITREAGY-DVKDINKPKASIVIDNKGHILWEDN 63 I+ LC+ LS+ + A +Q + GY + +P +++ + G +L++ N Sbjct: 7 IIIILCLTLSIMTPYAQAANSDVTPVQAANQYGYAGLSAAYEPTSAVNVSQTGQLLYQYN 66 Query: 64 ADLERDPASMSKMFTLYLLFEDLAKGKTSLNTTVTATETDQAISKIYEISNNNIHAGVAY 123- D + +PASM+K+ T+YL E + KG+ SL+ TVT T + +S + E+SN ++ G + Sbjct: 67 IDTKWNPASMTKLMTMYLTLEAVNKGQLSLDDTVTMTNKEYIMSTLPELSNTKLYPGQVW 126- Query: 124 PIRELITMTAVPSSNVATIMIANHLSQNNPDAFIKRINETAKKLGMTKTHFYNPSGAVAS 18- 3 I +L+ +T SSN A +++A +S+N D F+ +N AK +GM THF NP+GA S Sbjct: 127 TIADLLQITVSNSSNAAALILAKKVSKNTSD-FVDLMNNKAKAIGMKNTHFVNPTGAENS 18- 5 Query: 184 AFNGLYSPKEYDNNATNVTTARDLSILTYHFLKKYPDILNYTKYPEVKAMVGTPYEETFT 24- 3 ++P +Y + VTTARD +IL H +K+ P IL++T K + T + T+ Sbjct: 186 RLR-TFAPTKYKDQERTVTTARDYAILDLHVIKETPKILDFT-----KQLAPTTHAVTYY 23- 9 Query: 244 TYNYSTPGAKFGLEGVDGLKTGSSPSAAFNALVTAKRQNTRLITVVLGVGDWSDQDGEYY 30- 3 T+N+S GAK L G DGLKTGSS +A +N +T KR R+ V++G GD+ + GE Sbjct: 240 TFNFSLEGAKMSLPGTDGLKTGSSDTANYNHTITTKRGKFRINQVIMGAGDYKNLGGEKQ 29- 9 Query: 304 RHPFVNALVEKGFKDAKNISSKTPVLKAVKPKK 336 R+ NAL+E+ F K + + + + KK Sbjct: 300 RNMMGNALMERSFDQYKYVKILSKGEQRINGKK 332 A related DNA sequence was identified in S. pyogenes <SEQ ID 5767> which encodes the amino acid sequence <SEQ ID 5768>. Analysis of this protein sequence reveals the following: TABLE-US-05689 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -15.18 Transmembrane 371-387 (364-392) ----- Final Results ----- bacterial membrane --- Certainty = 0.7071 (Affirmative) <succ> bacterial outside --- Certainty = 0.0000 (Not Clear) <succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) <succ> The protein has homology with the following sequences in the databases: TABLE-US-05690 >GP: CAA62899 GB: X91786 penicillin-binding protein 4 [Staphylococcus aureus] Identities = 119/328 (36%), Positives = 184/328 (55%), Gaps = 19/328 (5%) Query: 6 ILTIFTFICF--SVMPLVHAEDVMDIT-----RQAGYT-VSEVNRPKSSIVVDANSSDIL 57 +++I +C S+M D+T Q GY +S P S++ V + + +L Sbjct: 4 LISIIIILCLTLSIMTPYAQATNSDVTPVQAANQYGYAGLSAAYEPTSAVNV-SQTGQLL 62 Query: 58 WQDNIDIPRDPASMSKMFTLYILFEELAKGKITMDTTITATPTDQAIANIYEISNNNIVA 117- +Q NID +PASM+K+ T+Y+ E + KG++++D T+T T + ++ + E+SN + Sbjct: 63 YQYNIDTKWNPASMTKLMTMYLTLEAVNKGQLSLDDTVTMTNKEYIMSTLPELSNTKLYP 122- Query: 118 GVAYPIRDLITMTAVPSSNAATVMIANYLSNNDASAFIDRVNATAKQLGMTNTHFSNASG 17- 7 G + I DL+ +T SSNAA +++A +S N S F+D +N AK +GM NTHF N +G Sbjct: 123 GQVWTIADLLQITVSNSSNAAALILAKKVSKN-TSDFVDLMNNKAKAIGMKNTHFVNPTG 18- 1 Query: 178 AAAQAFQGYYNPTKYDLSASNITTARDLSKLLYAFLKKYPEIISFTNKSVVHTMVGTPYE 23- 7 A + + PTKY +TTARD + L +K+ P+I+ FT + T+ T Sbjct: 182 AENSRLR-TFAPTKYKDQERTVTTARDYAILDLHVIKETPKILDFTKQLAPTTLAVT--- 23- 7 Query: 238 EEFHTYNHSLPDNQFGMKGVDGLKTGSSPSAAFNAMITAKRGKTRLITIVMGVGDWSDQN 29- 7 ++T+N SL + + G DGLKTGSS +A +N IT KRGK R+ ++MG GD+ + Sbjct: 238 --YYTFNFSLEGAKMSLPGTDGLKTGSSDTANYNHTITTKRGKFRINQVIMGAGDYKNLG 29- 5 Query: 298 GEFYRHPFVNALTEKGF---KDSKTLSK 322 GE R+ NAL E+ F K K LSK Sbjct: 296 GEKQRNMMGNALMERSFDQYKYVKILSK 323 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05691 Identities = 226/382 (59%), Positives = 289/382 (75%), Gaps = 7/382 (1%) Query: 12 LLSLTCVNSVQAEEHKDIMQITREAGYDVKDINKPKASIVID-NKGHILWEDNADLERDP 70 - + + C + + +D+M ITR+AGY V ++N+PK+SIV+D N ILW+DN D+ RDP Sbjct: 9 IFTFICFSVMPLVHAEDVMDITRQAGYTVSEVNRPKSSIVVDANSSDILWQDNIDIPRDP 68 Query: 71 ASMSKMFTLYLLFEDLAKGKTSLNTTVTATETDQAISKIYEISNNNIHAGVAYPIRELIT 130- ASMSKMFTLY+LFE+LAKGK +++TT+TAT TDQAI+ IYEISNNNI AGVAYPIR+LIT Sbjct: 69 ASMSKMFTLYILFEELAKGKITMDTTITATPTDQAIANIYEISNNNIVAGVAYPIRDLIT 128- Query: 131 MTAVPSSNVATIMIANHLSQNNPDAFIKRINETAKKLGMTKTHFYNPSGAVASAFNGLYS 19- 0 MTAVPSSN AT+MIAN+LS N+ AFI R+N TAK+LGMT THF N SGA A AF G Y+ Sbjct: 129 MTAVPSSNAATVMIANYLSNNDASAFIDRVNATAKQLGMTNTHFSNASGAAAQAFQGYYN 18- 8 Query: 191 PKEYDNNATNVTTARDLSILTYHFLKKYPDILNYTKYPEVKAMVGTPYEETFTTYNYSTP 25- 0 P +YD +A+N+TTARDLS L Y FLKKYP+I+++T V MVGTPYEE F TYN+S P Sbjct: 189 PTKYDLSASNITTARDLSKLLYAFLKKYPEIISFTNKSVVHTMVGTPYEEEFHTYNHSLP 24- 8 Query: 251 GAKFGLEGVDGLKTGSSPSAAFNALVTAKRQNTRLITVVLGVGDWSDQDGEYYRHPFVNA 31- 0 +FG++GVDGLKTGSSPSAAFNA++TAKR TRLIT+V+GVGDWSDQ+GE+YRHPFVNA Sbjct: 249 DNQFGMKGVDGLKTGSSPSAAFNAMITAKRGKTRLITIVMGVGDWSDQNGEFYRHPFVNA 30- 8 Query: 311 LVEKGFKDAKNISSKT-PVLKAVKPKKEVTKTKTKSIQE--QPQTKEQWWTKTDQFIQSH 36- 7 L EKGFKD+K +S K L+ + P+ TK +T S Q+ + K+ + + + F+ + Sbjct: 309 LTEKGFKDSKTLSKKARQKLEKLVPQ---TKKETSSKQQHFKATKKQSYLERVEDFMNHN 36- 5 Query: 368 FVSILIVLGTIAILCLLAGIVL 389 +LI L I LL +V+ Sbjct: 366 HTFLLICLAIFIITILLLSLVV 387 A related GBS gene <SEQ ID 8917> and protein <SEQ ID 8918> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05692 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: -14.02 GvH: Signal Score (-7.5): -2.54 Possible site: 60 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -12.58 threshold: 0.0 INTEGRAL Likelihood = -12.58 Transmembrane 339-355 (334-365) PERIPHERAL Likelihood = 1.38 99 modified ALOM score: 3.02 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6031 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00130## SEQ ID 8918 (GBS379) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 68 (lane 5; MW 44 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 3; MW 68.9 kDa). GBS379-GST was purified as shown in FIG. 212, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1857 A DNA sequence (GBSx1964) was identified in S. agalactiae <SEQ ID 5769> which encodes the amino acid sequence <SEQ ID 5770>. Analysis of this protein sequence reveals the following: TABLE-US-05693 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4039 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05694 >GP: CAB15256 GB: Z99120 similar to hypothetical proteins [Bacillus subtilis] Identities = 316/459 (68%), Positives = 386/459 (83%) Query: 14 DLGEYKFGFHDDVKPIYSTGKGLNEAVIRELSAAKGEPEWMLDFRLKSLETFNKMPMQTW 73 - D+GEYK+GFHD I+ + +GL + ++ E+S K EP+WMLDFRLKSLE F MPM W Sbjct: 7 DIGEYKYGFHDKDVSIFRSERGLTKEIVEEISRMKEEPQWMLDFRLKSLEHFYNMPMPQW 66 Query: 74 GADLSDIDFDDIIYYQKASDKPARDWDDVPEKIKETFERIGIPEAERAYLAGASAQYESE 133- G DL+ ++FD+I YY K S++ R WD+VPE+IK+TF+++GIPEAE+ YLAG SAQYESE Sbjct: 67 GGDLNSLNFDEITYYVKPSERSERSWDEVPEEIKQTFDKLGIPEAEQKYLAGVSAQYESE 126- Query: 134 VVYHNMKEEYDKLGIVFTDTDSALKEYPELFKKYFAKLVPPTDNKLAALNSAVWSGGTFI 19- 3 VVYHNMKE+ + GIVF DTDSALKE ++F++++AK++PPTDNK AALNSAVWSGG+FI Sbjct: 127 VVYHNMKEDLEAQGIVFKDTDSALKENEDIFREHWAKVIPPTDNKFAALNSAVWSGGSFI 18- 6 Query: 194 YVPKGVKVDIPLQTYFRINNENTGQFERTLIIVDEGASVHYVEGCTAPTYSSNSLHAAIV 25- 3 YVPKGVKV+ PLQ YFRIN+EN GQFERTLIIVDE ASVHYVEGCTAP Y++NSLH+A+V Sbjct: 187 YVPKGVKVETPLQAYFRINSENMGQFERTLIIVDEEASVHYVEGCTAPVYTTNSLHSAVV 24- 6 Query: 254 EIFALDGAYMRYTTIQNWSDNVYNLVTKRATAKKDATVEWIDGNLGAKTTMKYPSVYLDG 31- 3 EI G Y RYTTIQNW++NVYNLVTKR +++AT+EWIDGN+G+K TMKYP+ L G Sbjct: 247 EIIVKKGGYCRYTTIQNWANNVYNLVTKRTVCEENATMEWIDGNIGSKLTMKYPACILKG 30- 6 Query: 314 EGARGTMLSIAFANKGQHQDTGAKMIHNAPHTSSSIVSKSIAKGGGKVDYRGQVTFNKDS 37- 3 EGARG LSIA A KGQHQD GAKMIH AP+TSS+IVSKST+K GGKV YRG V F + + Sbjct: 307 EGARGMTLSIALAGKGQHQDAGAKMIHLAPNTSSTIVSKSISKQGGKVTYRGIVHFGRKA 36- 6 Query: 374 KKSVSHIECDTILMDDISKSDTIPFNEIHNSQVALEHEAKVSKISEEQLYYLMSRGLSEA 43- 3 + + S+IECDT++MD+ S SDTIP+NEI N ++LEHEAKVSK+SEEQL+YLMSRG+SE Sbjct: 367 EGARSNIECDTLIMDNKSTSDTIPYNEILNDNISLEHEAKVSKVSEEQLFYLMSRGISEE 42- 6 Query: 434 EATEMIVMGFVEPFTKELPMEYAVELNRLISYEMEGSVG 472 EATEMIVMGF+EPFTKELPMEYAVE+NRLI +EMEGS+G Sbjct: 427 EATEMIVMGFIEPFTKELPMEYAVEMNRLIKFEMEGSIG 465 A related DNA sequence was identified in S. pyogenes <SEQ ID 5771> which encodes the amino acid sequence <SEQ ID 5772>. Analysis of this protein sequence reveals the following: TABLE-US-05695 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3780 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05696 Identities = 445/472 (94%), Positives = 461/472 (97%) Query: 1 MSEINEKVEPQPIDLGEYKFGFHDDVKPIYSTGKGLNEAVIRELSAAKGEPEWMLDFRLK 60 MS+INEKVEP+PIDLG+Y+FGFHDDV+PIYSTGKGL+EAV+RELSAAK EPEWML+FRLK Sbjct: 1 MSDINEKVEPKPIDLGDYQFGFHDDVEPIYSTGKGLSEAVVRELSAAKNEPEWMLEFRLK 60 Query: 61 SLETFNKMPMQTWGADLSDIDFDDIIYYQKASDKPARDWDDVPEKIKETFERIGIPEAER 120- SLETFNKMPMQTWGADLSDI+FDDIIYYQKASDKPAR WDDVPEKIKETF+RIGIPEAER Sbjct: 61 SLETFNKMPMQTWGADLSDINFDDIIYYQKASDKPARSWDDVPEKIKETFDRIGIPEAER 120- Query: 121 AYLAGASAQYESEVVYHNMKEEYDKLGIVFTDTDSALKEYPELFKKYFAKLVPPTDNKLA 18- 0 AYLAGASAQYESEVVYHNMK E++KLGI+FTDTDSALKEYP+LFK+YFAKLVPPTDNKLA Sbjct: 121 AYLAGASAQYESEVVYHNMKGEFEKLGIIFTDTDSALKEYPDLFKQYFAKLVPPTDNKLA 18- 0 Query: 181 ALNSAVWSGGTFIYVPKGVKVDIPLQTYFRINNENTGQFERTLIIVDEGASVHYVEGCTA 24- 0 ALNSA WSGGTFIYVPKGVKVDIPLQTYFRINNENTGQFERTLIIVDEGASVHYVEGCTA Sbjct: 181 ALNSAAWSGGTFIYVPKGVKVDIPLQTYFRINNENTGQFERTLIIVDEGASVHYVEGCTA 24- 0 Query: 241 PTYSSNSLHAAIVEIFALDGAYMRYTTIQNWSDNVYNLVTKRATAKKDATVEWIDGNLGA 30- 0 PTYSSNSLHAAIVEIFALDGAYMRYTTIQNWSDNVYNLVTKRA A DATVEWIDGNLGA Sbjct: 241 PTYSSNSLHAAIVEIFALDGAYMRYTTIQNWSDNVYNLVTKRARALTDATVEWIDGNLGA 30- 0 Query: 301 KTTMKYPSVYLDGEGARGTMLSIAFANKGQHQDTGAKMIHNAPHTSSSIVSKSIAKGGGK 36- 0 KTTMKYPSVYLDG GARGTMLSIAFAN GQHQDTGAKMIHNAPHTSSSIVSKSIAK GGK Sbjct: 301 KTTMKYPSVYLDGPGARGTMLSIAFANAGQHQDTGAKMIHNAPHTSSSIVSKSIAKSGGK 36- 0 Query: 361 VDYRGQVTFNKDSKKSVSHIECDTILMDDISKSDTIPFNEIHNSQVALEHEAKVSKISEE 42- 0 VDYRGQVTFNK SKKSVSHIECDTILMDDISKSDTIPFNEIHNSQVALEHEAKVSKISEE Sbjct: 361 VDYRGQVTFNKQSKKSVSHIECDTILMDDISKSDTIPFNEIHNSQVALEHEAKVSKISEE 42- 0 Query: 421 QLYYLMSRGLSEAEATEMIVMGFVEPFTKELPMEYAVELNRLISYEMEGSVG 472 QLYYLMSRGLSE+EATEMIVMGFVEPFTKELPMEYAVELNRLISYEMEGSVG Sbjct: 421 QLYYLMSRGLSESEATEMIVMGFVEPFTKELPMEYAVELNRLISYEMEGSVG 472 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1858 A DNA sequence (GBSx1965) was identified in S. agalactiae <SEQ ID 5773> which encodes the amino acid sequence <SEQ ID 5774>. This protein is predicted to be nitrogen fixation protein (nifU). Analysis of this protein sequence reveals the following: TABLE-US-05697 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1078 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05698 >GP: CAB15257 GB: Z99120 similar to NifU protein homolog [Bacillus subtilis] Identities = 72/139 (51%), Positives = 92/139 (65%) Query: 4 SKLDNLYMAVVADHSKHPHHHGFLEGVEQVQLNNPTCGDVISLSVKFDGNIISDIAFAGN 63 - + LD LY V+ DH K+P + G L V +NNPTCGD I L++K DG+I+ D F G Sbjct: 5 ANLDTLYRQVIMDHYKNPRNKGVLNDSIVVDMNNPTCGDRIRLTMKLDGDIVEDAKFEGE 64 Query: 64 GCTISTASSSMMTDAVIGKTKEEALQLADVFSKMVQGDQNPKQEKLGDAEFLAGVSKFPQ 123- GC+IS AS+SMMT A+ GK E AL ++ +FS M+QG + LGD E L GVSKFP Sbjct: 65 GCSISMASASMMTQAIKGKDIETALSMSKIFSDMMQGKEYDDSIDLGDIEALQGVSKFPA 124- Query: 124 RIKCATLSWNALRKAIERD 142 RIKCATLSW AL K + ++ Sbjct: 125 RIKCATLSWKALEKGVAKE 143 A related DNA sequence was identified in S. pyogenes <SEQ ID 5775> which encodes the amino acid sequence <SEQ ID 5776>. Analysis of this protein sequence reveals the following: TABLE-US-05699 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1202 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05700 Identities = 114/146 (78%), Positives = 133/146 (91%) Query: 1 MALSKLDNLYMAVVADHSKHPHHHGFLEGVEQVQLNNPTCGDVISLSVKFDGNIISDIAF 60 MALSKL++LYMAVVADHSK PHHHG L+GVE VQLNNPTCGDVISL+VKFD + I DIAF Sbjct: 1 MALSKLNHLYMAVVADHSKRPHHHGQLDGVEAVQLNNPTCGDVISLTVKFDEDKIEDIAF 60 Query: 61 AGNGCTISTASSSMMTDAVIGKTKEEALQLADVFSKMVQGDQNPKQEKLGDAEFLAGVSK 120- AGNGCTISTASSSMMTDAVIGK+KEEAL LAD+FS+MVQG +NP Q++LG+AE LAGV+K Sbjct: 61 AGNGCTISTASSSMMTDAVIGKSKEEALALADIFSEMVQGQENPAQKELGEAELLAGVAK 120- Query: 121 FPQRIKCATLSWNALRKAIERDNQAE 146 FPQRIKC+TL+WNAL++AI+R A+ Sbjct: 121 FPQRIKCSTLAWNALKEAIKRSANAQ 146 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1859 A DNA sequence (GBSx1966) was identified in S. agalactiae <SEQ ID 5777> which encodes the amino acid sequence <SEQ ID 5778>. This protein is predicted to be nitrogen fixation protein (nifS) (b1680). Analysis of this protein sequence reveals the following: TABLE-US-05701 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2453 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05702 >GP: CAB15258 GB: Z99120 similar to NifS protein homolog [Bacillus subtilis] Identities = 240/400 (60%), Positives = 306/400 (76%), Gaps = 5/400 (1%) Query: 9 LKQDFPILNQLVNDEPLIYLDNAATTQKPNQVLEALRDYYQNDNANVHRGVHTLAERATA 68 - +++ FPIL+Q VN L+YLD+AAT+QKP V+E L YY N+NVHRGVHTL RAT Sbjct: 6 IREQFPILHQQVNGHDLVYLDSAATSQKPRAVIETLDKYYNQYNSNVHRGVHTLGTRATD 65 Query: 69 QYENAREKARQFLNAKLSKEILFTRGTTTGLNWVA-KFAESILERGDEVLISIMEHHSNI 127- YE AREK R+F+NAK EI+FT+GTTT LN VA +A + L+ GDEV+I+ MEHH+NI Sbjct: 66 GYEGAREKVRKFINAKSMAEIIFTKGTTTSLNMVALSYARANLKPGDEVVITYMEHHANI 125- Query: 128 IPWQQACERTGAKLVYAYLK-DGSLDLEDFYNKLSSKTKFVSLAHISNVLGCVTPVKAIA 18- 6 IPWQQA + TGA L Y L+ DG++ LED ++S TK V+++H+SNVLG V P+K +A Sbjct: 126 IPWQQAVKATGATLKYIPLQEDGTISLEDVRETVTSNTKIVAVSHVSNVLGTVNPIKEMA 18- 5 Query: 187 ERVHQVGAYMVVDGAQSAPHMAIDVQDLDCDFFALSGHKMLGPTGIGVLYGKESILDKMF 24- 6 + H GA +VVDGAQS PHW IDVQDLDCDFFALS HKM GPTG+GVLYGK+++L+ M Sbjct: 186 KIAHDNGAVIVVDGAQSTPHMKIDVQDLDCDFFALSSHKMCGPTGVGVLYGKKALLENME 24- 5 Query: 247 PVEFGGEMIDFVYEQSATWKELPWKFEAGTPNIAGAIAFGEALDYLTDVGMDEIHQYEQS 30- 6 P EFGGEMIDFV +TWKELPWKFEAGTP IAGAI G A+D+L ++G+DEI ++E Sbjct: 246 PAEFGGEMIDFVGLYESTWKELPWKFEAGTPIIAGAIGLGAAIDFLEEIGLDEISRHEHK 30- 5 Query: 307 LVSYVLPKLQAIDGLTIYGPSDAESHVGVIAFNLEGLHPHDVATAMDYEGVAVRAGHHCA 36- 6 L +Y L + + +DG+T+YGP E G++ FNL+ +HPHDVAT +D EG+AVRAGHHCA Sbjct: 306 LAAYALERFRQLDGVTVYGP---EERAGLVTFNLDDVHPHDVATVLDAEGIAVRAGHHCA 36- 2 Query: 367 QPLINHLGIHSAVRASFYFYNTKEDCDKLVDAIQKTKEFF 406 QPL+ L + + RASFY YNT+E+ DKLV+A+QKTKE+F Sbjct: 363 QPLMKWLDVTATARASFYLYNTEEEIDKLVEALQKTKEYF 402 A related DNA sequence was identified in S. pyogenes <SEQ ID 5779> which encodes the amino acid sequence <SEQ ID 5780>. Analysis of this protein sequence reveals the following: TABLE-US-05703 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3714 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside ---- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05704 Identities = 293/408 (71%), Positives = 349/408 (84%) Query: 3 LLDSYKLKQDFPILNQLVNDEPLIYLDNAATTQKPNQVLEALRDYYQNDNANVHRGVHTL 62 LLD+ +KQDF ILNQ VNDEPL+YLDNAATTQKP VLEAL+ YYQ DNANVHRGVHTL Sbjct: 1 LLDAKDIKQDFQILNQQVNDEPLVYLDNAATTQKPALVLEALQSYYQEDNANVHRGVHTL 60 Query: 63 AERATAQYENAREKARQFLNAKLSKEILFTRGTTTGLNWVAKFAESILERGDEVLISIME 122- AERAT +YE +R++ F++AK SKE+LFTRGTTT LNWVA+FAE +L DEVLISIME Sbjct: 61 AERATLKYEASRQQVADFIHAKSSKEVLFTRGTTTSLNWVARFAEQVLTPEDEVLISIME 120- Query: 123 HHSNIIPWQQACERTGAKLVYAYLKDGSLDLEDFYNKLSSKTKFVSLAHISNVLGCVTPV 18- 2 HH+NIIPWQQAC++TGA+LVY YLKDG LD++D NKL++KT+FVSL H+SNVLGC+ P+ Sbjct: 121 HHANIIPWQQACQKTGARLVYVYLKDGQLDMDDLANKLTTKTRFVSLVHVSNVLGCINPI 18- 0 Query: 183 KAIAERVHQVGAYMVVDGAQSAPHMAIDVQDLDCDFFALSGHKMLGPTGIGVLYGKESIL 24- 2 K IA+ H GAY+VVDGAQS PH+AIDVQDLDCDFFA S HKMLGPTG+GVLYGKE +L Sbjct: 181 KEIAKLAHAKGAYLVVDGAQSVPHLAIDVQDLDCDFFAFSAHKMLGPTGLGVLYGKEELL 24- 0 Query: 243 DKMPPVEFGGEMIDFVYEQSATWKELPWKFEAGTPNIAGAIAFGEALDYLTDVGMDEIHQ 30- 2 +++ P+EFGGEMIDFVYEQ ATWKELPWKFEAGTP+IAGAI A+ YL +GM +IH Sbjct: 241 NQVEPLEFGGEMIDFVYEQEATWKELPWKFEAGTPHIAGAIGLSAAISYLQRLGMADIHA 30- 0 Query: 303 YEQSLVSYVLPKLQAIDGLTIYGPSDAESHVGVIAFNLEGLHPHDVATAMDYEGVAVRAG 36- 2 +E L++YVLPKL+AI+GLTIYGPS + G+I+FNL+ LHPHD+ATA+DYEGVAVRAG Sbjct: 301 HEAELIAYVLPKLEAIEGLTIYGPSQPSARSGLISFNLDDLHPHDLATALDYEGVAVRAG 36- 0 Query: 363 HHCAQPLINHLGIHSAVRASFYFYNTKEDCDKLVDAIQKTKEFFNGTL 410 HHCAQPL+++LG+ + VRASFY YNTK DCD+LV+AI K KEFFNGTL Sbjct: 361 HHCAQPLLSYLGVPATVRASFYIYNTKADCDRLVEAILKAKEFFNGTL 408 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1860 A DNA sequence (GBSx1967) was identified in S. agalactiae <SEQ ID 5781> which encodes the amino acid sequence <SEQ ID 5782>. Analysis of this protein sequence reveals the following:

TABLE-US-05705 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1441 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05706 >GP: BAB07189 GB: AP001518 unknown conserved protein [Bacillus halodurans] Identities = 171/430 (39%), Positives = 267/430 (61%), Gaps = 15/430 (3%) Query: 1 MSKEAILNFLQAKGEPTWLQELRLKAFEKIEELELPVIERVKFHRWNLG--DGTILENDY 58 - + KE + +F A+ EP W +++RLK FE +E LELP ++ K WN D + E Sbjct: 9 IDKEYVQSFSDARNEPQWFKDIRLKGFELVETLELPKPDKTKITSWNFTNFDHKLPEVSP 68 Query: 59 TANVPDFTE---------LGNNPKLVQIGTQTVLEQVPMELIEKGVVFTDFYSALEEIPE 109- A++ + + LVQ V ++ L KGV+FTD +A++E + Sbjct: 69 VASIDELRDEVKGLIGEASDTQNLLVQRDATVVYSKLDEALKAKGVIFTDLLTAVKEHGD 128- Query: 110 VIERYFGK-ARPFEEDRLAAYHTAYFNSGAVLYIPDNVEITQPIEGLFYQDSQSKVPFNK 16- 8 ++E+Y+ K A +E+RL A H A N G +Y+P NVEI P++ +F+ D++ FN Sbjct: 129 LVEKYYMKDAVKVDENRLTALHAALVNGGTFIYVPRNVEIEVPLQSVFWFDTEKAGLFN- 18- 7 Query: 169 HILLIVGKNAKVSYLERFESIGDGTERTSANISVEVIAQAGSQIKFASIDRLGENVTTFI 22- 8 H++++ N+ ++Y+E + S G +E ANI VEV A A +++ F ++D L VTT++ Sbjct: 188 HVIIVAEDNSSITYVENYASFG--SEEAVANIVVEVFAGANAKVSFGAVDNLAAGVTTYV 24- 5 Query: 229 SRRGRHSSDATIDWALGVMNEGNVVADFDSDLIGDGSHANLKVVAASSGRQVQGIDTRVT 28- 8 RR D+ ++WALG MN+GN V++ + L+GD S A+ K V+ G Q Q T++ Sbjct: 246 VRRAHVGRDSRVEWALGQMNDGNTVSENTTHLLGDNSWADTKTVSVGRGEQKQNFTTQIF 30- 5 Query: 289 NYGCNSVGHILQHGVILERGTLTFNGIGHIIKGAKGADAQQESRVLMLSDKARSDANPIL 34- 8 ++G +S G+IL+HGV+ E T FNGI I GA + +Q RVLMLS+KAR DANPIL Sbjct: 306 HNGKHSEGYILKHGVMREAATSIFNGISKIEHGATKSHGEQTERVLMLSEKARGDANPIL 36- 5 Query: 349 LIDENDVTAGHAASIGQVDPEDLYYLMSRGLNQKTAEQLVIRGFLGTVIAEIPVKEVRDE 40- 8 LIDE+DVTAGHAAS+G++DP ++YLMSRG+++ AE+LVI GFL V+ ++P++ V++ Sbjct: 366 LIDEDDVTAGHAASVGKIDPIQMFYLMSRGISRAEAERLVIHGFLAPVVGQLPIESVKER 42- 5 Query: 409 MIAVIDTRLE 418 ++ I+ K++ Sbjct: 426 LVEAIERKVK 435 A related DNA sequence was identified in S. pyogenes <SEQ ID 5783> which encodes the amino acid sequence <SEQ ID 5784>. Analysis of this protein sequence reveals the following: TABLE-US-05707 Possible site: 14 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.80 Transmembrane 387-403 (387-403) ----- Final Results ----- bacterial membrane --- Certainty = 0.1319 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05708 >GP: CAB15259 GB: Z99120 similar to hypothetical proteins [Bacillus subtilis] Identities = 177/428 (41%), Positives = 267/428 (62%), Gaps = 15/428 (3%) Query: 3 KEKLVAFSQAHAEPAWLQERRLAALEAIPNLELPTIERVKFHRWNLGDGT--LTENESLA 60 - +E L +FS+ H EPAWL+ RL ALE +L +P ++ K WN + +NE L+ Sbjct: 11 QEYLKSFSEKHQEPAWLKNLRLQALEQAEDLPMPKPDKTKITNWNFTNFAKHTVDNEPLS 70 - Query: 61 SVPDF-------IAIGDNPKLVQVGTQTVLEQLPMA--LIDKGVVFSDFYTALEEIPEVI 111- S+ D I I + K + V L ++ L DKGV+F+D TA E +++ Sbjct: 71 SLEDLTDEVKALIDIENEDKTLYVQRDQTPAHLSLSQELKDKGVIFTDILTAAREHSDLV 130- Query: 112 EAHFGQ-ALAFDEDKLAAYHTAYFNSAAVLYVPDHLEITTPIEAIFLQDSDSDVPFNKHV 17- 0 E +F + + DE KL A H A N A LYVP ++++ TP++A+++ +S+ FN HV Sbjct: 131 EKYFMKDGVKVDEHKLTALHAALVNGGAFLYVPKNVQVETPVQAVYVHESNDTALFN-HV 18- 9 Query: 171 LVIAGKESKFTYLERFESIGNATQKISANISVEVIAQAGSQIKFSAIDRLGPSVTTYISR 23- 0 L++A S TY+E + S N + NI EVI + + + A+D L VTTY++R Sbjct: 190 LIVAEDHSSVTYVENYISTVNPKDAVF-NIISEVITGDNASVTYGAVDNLSSGVTTYVNR 24- 8 Query: 231 RGRLE-KDANIDWALAVMNEGNVIADFDSDLIGQGSQADLKVVAASSGRQVQGIDTRVTN 28- 9 RG +D+ I+WAL +MN+G+ I++ ++L G G+ D K V G Q + T++ + Sbjct: 249 RGAARGRDSKIEWALGLMNDGDTISENTTNLYGDGTYGDTKTVVVGRGEQTENFTTQIIH 30- 8 Query: 290 YGQRTVGHILQHGVILERGTLTFNGIGHILKDAKGADAQQESRVLMLSDQARADANPILL 34- 9 +G+ + G+IL+HGV+ + + FNGIG I A A+A+QESRVLMLS++AR DANPILL Sbjct: 309 FGKASEGYILKHGVMKDSASSIFNGIGKIEHGASKANAEQESRVLMLSEKARGDANPILL 36- 8 Query: 350 IDENEVTAGHAASIGQVDPEDMYYLMSRGLDQETAERLVIRGFLGAVIAEIPIPSVRQEI 40- 9 IDE++VTAGHAAS+G+VDP +YYLMSRG+ +E AERLVI GFL V+ E+PI V++++ Sbjct: 369 IDEDDVTAGHAASVGRVDPIQLYYLMSRGIPKEEAERLVIYGFLAPVVNELPIEGVKKQL 42- 8 Query: 410 IKVLDEKL 417 + V++ K+ Sbjct: 429 VSVIERKV 436 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05709 Identities = 322/420 (76%), Positives = 368/420 (86%) Query: 1 MSKEAILNFLQAKGEPTWLQELRLKAFEKIEELELPVIERVKFHRWNLGDGTILENDYTA 60 M+KE ++ F QA EP WLQE RL A E I LELP IERVRFHRWNLGDGT+ EN+ A Sbjct: 1 MTKEKLVAFSQAHAEPAWLQERRLAALEAIPNLELPTIERVKFHRWNLGDGTLTENESLA 60 Query: 61 NVPDFTELGNNPKLVQIGTQTVLEQVPMELIEKGVVFTDFYSALEEIPEVIERYFGKARP 120- +VPDF +G+NPKLVQ+GTQTVLEQ+PM LI+KGVVF+DFY+ALEEIPEVIE +FG+A Sbjct: 61 SVPDFIAIGDNPKLVQVGTQTVLEQLPMALIDKGVVFSDFYTALEEIPEVIEAHFGQALA 120- Query: 121 FEEDRLAAYHTAYFNSGAVLYIPDNVEITQPIEGLFYQDSQSKVPFNKHILLIVGKNAKV 18- 0 F+ED+LAAYHTAYFNS AVLY+PD++EIT PIE +F QDS S VPFNKH+L+I GK +K Sbjct: 121 FDEDKLAAYHTAYFNSAAVLYVPDHLEITTPIEAIFLQDSDSDVPFNKHVLVIAGKESKF 18- 0 Query: 181 SYLERFESIGDGTERTSANISVEVIAQAGSQIKFASIDRLGENVTTFISRRGRHSSDATI 24- 0 +YLERFESIG+ T++ SANISVEVIAQAGSQIKF++IDRLG +VTT+ISRRGR DA I Sbjct: 181 TYLERFESIGNATQKISANISVEVIAQAGSQIKFSAIDRLGPSVTTYISRRGRLEKDANI 24- 0 Query: 241 DWALGVMNEGNVVADFDSDLIGDGSHANLKVVAASSGRQVQGIDTRVTNYGCNSVGHILQ 30- 0 DWAL VMNEGNV+ADFDSDLIG GS A+LKVVAASSGRQVQGIDTRVTNYG +VGHILQ Sbjct: 241 DWALAVMNEGNVIADFDSDLIGQGSQADLKVVAASSGRQVQGIDTRVTNYGQRTVGHILQ 30- 0 Query: 301 HGVILERGTLTFNGIGHIIKGAKGADAQQESRVLMLSDKARSDANPILLIDENDVTAGHA 36- 0 HGVILERGTLTFNGIGHI+K AKGADAQQESRVLMLSD+AR+DANPILLIDEN+VTAGHA Sbjct: 301 HGVILERGTLTFNGIGHILKDAKGADAQQESRVLMLSDQARADANPILLIDENEVTAGHA 36- 0 Query: 361 ASIGQVDPEDLYYLMSRGLNQKTAEQLVIRGFLGTVIAEIPVKEVRDEMIAVIDTKLEKR 42- 0 ASIGQVDPED+YYLMSRGL+Q+TAE+LVIRGFLG VIAEIP+ VR E+I V+D KL R Sbjct: 361 ASIGQVDPEDMYYLMSRGLDQETAERLVIRGFLGAVIAEIPIPSVRQEIIKVLDEKLLNR 42- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1861 A DNA sequence (GBSx1968) was identified in S. agalactiae <SEQ ID 5785> which encodes the amino acid sequence <SEQ ID 5786>. This protein is predicted to be ABC transporter, ATP-binding protein, Ycf16 family. Analysis of this protein sequence reveals the following: TABLE-US-05710 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2253(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05711 >GP: CAB15260 GB: Z99120 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 180/250 (72%), Positives = 212/250 (84%) Query: 2 SVLEIKNLHVSIEDKEILKGLNLTLKTGEIAAIMGPNGTGKSTLSAAIMGNPNYEVTAGE 61 S L IK+LHV IE KEILKG+NL +K GE A+MGPNGTGKSTLSAAIMG+P YEVT G Sbjct: 4 STLTIKDLHVEIEGKEILKGVNLEIKGGEFHAVMGPNGTGKSTLSAAIMGHPKYEVTKGS 63 Query: 62 ILFDGEDILELEVDERARLGLFLAMQYPSEVPGITNAEFIRAAMNAGKADDDKISIRQFI 121- I DG+D+LE+EVDERA+ GLFLAMQYPSE+ G+TNA+F+R+A+NA + + D+IS+ +FI Sbjct: 64 ITLDGKDVLEMEVDERAQAGLFLAMQYPSEISGVTNADFLRSAINARREEGDEISLMKFI 123- Query: 122 TKLDEKMELLGMKEEMAERYLNEGFSGGEKKRNEILQLLMLEPKFALLDEIDSGLDIDAL 18- 1 K+DE ME L M EMA+RYLNEGFSGGEKKRNEILQL+M+EPK A+LDEIDSGLDIDAL Sbjct: 124 RKMDENMEFLEMDPEMAQRYLNEGFSGGEKKRNEILQLMMIEPKIAILDEIDSGLDIDAL 18- 3 Query: 182 KVVSKGVNEMRGEGFGAMIITHYQRLLNYITPDKVHVMMDGKVVLSGGPELAVRLEKEGY 24- 1 KVVSKG+H+MR E FG ++ITHYQRLLNYITPD VHVMM G+VV SGG ELA RLE EGY Sbjct: 184 KVVSKGINKMRSENFGCLMITHYQRLLNYITPDVVHVMMQGRVVKSGGAELAQRLEAEGY 24- 3 Query: 242 AQIAEELGLE 251 I +ELG+E Sbjct: 244 DWIKQELGIE 253 A related DNA sequence was identified in S. pyogenes <SEQ ID 5787> which encodes the amino acid sequence <SEQ ID 5788>. Analysis of this protein sequence reveals the following: TABLE-US-05712 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2417(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05713 Identities = 225/255 (88%), Positives = 241/255 (94%) Query: 1 MSVLEIKNLHVSIEDKEILKGLNLTLKTGEIAAIMGPNGTGKSTLSAAIMGNPNYEVTAG 60 MS+LEI NLHVSIE KEILKG+NLTLKTGE+AAIMGPNGTGKSTLSAAIMGNPNYEVT G Sbjct: 1 MSILEINNLHVSIEGKEILKGVNLTLKTGEVAAIMGPNGTGKSTLSAAIMGNPNYEVTQG 60 Query: 61 EILFDGEDILELEVDERARLGLFLAMQYPSEVPGITNAEFIRAAMNAGKADDDKISIRQF 120- +IL DG +IL+LEVDERARLGLFLAMQYPSE+PGITNAEF+RAAMNAGKAD+DKIS+R F Sbjct: 61 QILLDGVNILDLEVDERARLGLFLAMQYPSEIPGITNAEFMRAAMNAGKADEDKISVRDF 120- Query: 121 ITKLDEKMELLGMKEEMAERYLNEGFSGGEKKRNEILQLLMLEPKFALLDEIDSGLDIDA 18- 0 ITKLDEKM LLGMKEEMAERYLNEGFSGGEKKRNEILQLLMLEPKFALLDEIDSGLDIDA Sbjct: 121 ITKLDEKMALLGMKEEMAERYLNEGFSGGEKKRNEILQLLMLEPKFALLDEIDSGLDIDA 18- 0 Query: 181 LKVVSKGVNEMRGEGFGAMIITHYQRLLNYITPDKVHVMMDGKVVLSGGPELAVRLEKEG 24- 0 LKVVSKGVNEMRG+ FGAMIITHYQRLLNYITPD VHVMMDG++VLSG LA RLEKEG Sbjct: 181 LKVVSKGVNEMRGKDFGAMIITHYQRLLNYITPDLVHVMMDGRIVLSGDAALATRLEKEG 24- 0 Query: 241 YAQIAEELGLEYKEE 255 YA IA++LG+EYKEE Sbjct: 241 YAGIAQDLGIEYKEE 255 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1862 A DNA sequence (GBSx1969) was identified in S. agalactiae <SEQ ID 5789> which encodes the amino acid sequence <SEQ ID 5790>. This protein is predicted to be RgpG (rfe). Analysis of this protein sequence reveals the following: TABLE-US-05714 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.10 Transmembrane 312-328 (308-336) INTEGRAL Likelihood = -10.03 Transmembrane 15-31 (6-41) INTEGRAL Likelihood = -9.82 Transmembrane 205-221 (197-226) INTEGRAL Likelihood = -8.60 Transmembrane 335-351 (329-358) INTEGRAL Likelihood = -7.48 Transmembrane 257-273 (255-281) INTEGRAL Likelihood = -5.52 Transmembrane 60-76 (56-79) INTEGRAL Likelihood = -5.31 Transmembrane 151-167 (148-171) INTEGRAL Likelihood = -4.88 Transmembrane 91-107 (90-108) INTEGRAL Likelihood = -4.78 Transmembrane 184-200 (177-203) INTEGRAL Likelihood = -3.13 Transmembrane 119-135 (119-135) INTEGRAL Likelihood = -2.97 Transmembrane 229-245 (229-250) ----- Final Results ----- bacterial membrane --- Certainty = 0.5840(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8919> which encodes amino acid sequence <SEQ ID 8920> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-05715 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 5.18 GvH: Signal Score (-7.5): -6.19 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 9 value: -12.10 threshold: 0.0 INTEGRAL Likelihood = -12.10 Transmembrane 239-255 (235-263) INTEGRAL Likelihood = -9.82 Transmembrane 132-148 (124-153) INTEGRAL Likelihood = -8.60 Transmembrane 262-278 (256-285) INTEGRAL Likelihood = -7.48 Transmembrane 184-200 (182-208) INTEGRAL Likelihood = -5.31 Transmembrane 78-94 (75-98) INTEGRAL Likelihood = -4.88 Transmembrane 18-34 (17-35) INTEGRAL Likelihood = -4.78 Transmembrane 111-127 (104-130) INTEGRAL Likelihood = -3.13 Transmembrane 46-62 (46-62) INTEGRAL Likelihood = -2.97 Transmembrane 156-172 (156-177) PERIPHERAL Likelihood = 12.63 284 modified ALOM score: 2.92 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5840(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05716 >GP: BAA82114 GB: AB022909 RgpG [Streptococcus mutans] Identities = 266/382 (69%), Positives = 317/382 (82%) Query: 10 TIEYIFVLIGAFLLSIILTPIIRVISLKVGAVDKPNARRINKVPMPSSGGLAIFLSFVVT 69 - T++++ VLI L S++LTP++R +L+VGAVD PNARRINKVPMPS+GGLAI +SFV+ Sbjct: 7 TLKFVLVLIATLLTSLVLTPLVRFFALRVGAVDNPNARRINKVPMPSAGGLAIIISFVIA 66 Query: 70 TLFFMPMAASRHFIEVSYFHYILPVIIGGLVVTTTGFIDDIFELRPRYKMLGIIIAAIII 129- TL MPM SYF YILPV++G LV+ TGFIDD++EL P+ K LGI++ A+II Sbjct: 67 TLALMPMILKTQIGGKSYFEYILPVVLGALVIALTGFIDDVYELSPKIKFLGILLGAVII 126- Query: 130 WKFTHFRFDSFKIPIGGPLLEFGPILTFFLTVLWIISITNAINLIDGLDGLVSGVSIISL 18- 9 W FT FRFDSFKIP GGP+L F P L+FFLT+LW+++ITNA+NLIDGLDGLVSGVS+ISL Sbjct: 127 WIFTDFRFDSFKIPFGGPMLHFNPFLSFFLTILWVVAITNAVNLIDGLDGLVSGVSMISL 18- 6 Query: 190 ATMAVVSYFFLPKIDFFLTLTIVILIASIVGFFPYNYHPAIIYLGDAGALFIGFMIGVLS 24- 9 TM +VSYFFL D FLTLTI +LI +I GFFPYNYHPAIIYLGD GALFIGFMI VLS Sbjct: 187 TTMGLVSYFFLYDTDIFLTLTIFVLIFAIAGFFPYNYHPAIIYLGDTGALFIGFMISVLS 24- 6 Query: 250 LQGLKNSTAVAVITPVIILGVPILDTAVAIVRRKLSGKKISEADKMHLHHRLLSMGFTHR 30- 9 LQGLKN+TAVAV+TP+I+LGVPI+DT VAI+RR LSG+K EAD MHLHHRLL+MGFTHR Sbjct: 247 LQGLKNATAVAVVTPIIVLGVPIVDTTVAIIRRTLSGQKFYEADNMHLHHRLLAMGFTHR 30- 6 Query: 310 GAVLVVYGIAIIFSLIALLLNVSSRIGGIFLLLALLLAMEIFIEGLNIWGENRTPLFNLL 36- 9 GAVLVVYGIA+ FSL++LLLNVSSR+GGI L++ + A+EIFIEGL IWG RTPLF LL Sbjct: 307 GAVLVVYGIAMFFSLVSLLLNVSSRLGGILLMIGVAFALEIFIEGLEIWGPKRTPLFRLL 36- 6 Query: 370 KFIGNSDYRQSVIAKYSDKHQK 391 FIGNSDYRQ V+AKY K +K Sbjct: 367 AFIGNSDYRQEVVAKYRRKKKK 388 A related DNA sequence was identified in S. pyogenes <SEQ ID 5791> which encodes the amino acid sequence <SEQ ID 5792>. Analysis of this protein sequence reveals the following: TABLE-US-05717 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.28 Transmembrane 9-25 (1-33) INTEGRAL Likelihood = -8.17 Transmembrane 201-217 (198-221) INTEGRAL Likelihood = -7.64 Transmembrane 308-324 (305-329) INTEGRAL Likelihood = -7.17 Transmembrane 55-71 (51-74) INTEGRAL Likelihood = -7.06 Transmembrane 145-161 (138-170) INTEGRAL Likelihood = -6.58 Transmembrane 260-276 (251-278) INTEGRAL Likelihood = -6.21 Transmembrane 180-196 (172-198) INTEGRAL Likelihood = -5.95 Transmembrane 331-347 (330-353) INTEGRAL Likelihood = -5.68 Transmembrane 87-103 (82-104) INTEGRAL Likelihood = -3.93 Transmembrane 113-129 (112-133) INTEGRAL Likelihood = -2.60 Transmembrane 233-249 (232-250) ----- Final Results ----- bacterial membrane --- Certainty = 0.4312(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05718 >GP: BAA82114 GB: AB022909 RgpG [Streptococcus mutans] Identities = 289/381 (75%), Positives = 334/381 (86%), Gaps = 1/381 (0%) Query: 5 TIDYVLVLIGALLMSLFLTPLVRFLAFRVGAVDNPNARRVNKVPMPTSGGLAIFMSFLVA 64 T+ +VLVLI LL SL LTPLVRF A RVGAVDNPNARR+NKVPMP++GGLAI +SF++A Sbjct: 7 TLKFVLVLIATLLTSLVLTPLVRFFALRVGAVDNPNARRINKVPMPSAGGLAIIISFVIA 66 Query: 65 SLGLIPIASKGAMFFGQTYFSYILPVVIGATVITLTGFLDDLYELSPKLKMFGILIGAVI 124- +L L+P+ K G++YF YILPVV+GA VI LTGF+DD+YELSPK+K GIL+GAVI Sbjct: 67 TLALMPMILK-TQIGGKSYFEYILPVVLGALVIALTGFIDDVYELSPKIKFLGILLGAVI 125- Query: 125 VWAFTDFKFDSFKIPFGGPLLVFGPFLTLFLTVLWIVSITNAINLIDGLDGLVSGVSIIS 18- 4 +W FTDF+FDSFKIPFGGP+L F PFL+ FLT+LW+V+ITNA+NLIDGLDGLVSGVS+IS Sbjct: 126 IWIFTDFRFDSFKIPFGGPMLHFNPFLSFFLTILWVVAITNAVNLIDGLDGLVSGVSMIS 18- 5 Query: 185 LVTMAIVSYFFLPQKDFFLTLTILVLISAIAGFFPYNYHPAMIYLGDTGALFIGFMIGVL 24- 4 L TM +VSYFFL D FLTLTI VLI AIAGFFPYNYHPA+IYLGDTGALFIGFMI VL Sbjct: 186 LTTMGLVSYFFLYDTDIFLTLTIFVLIFAIAGFFPYNYHPAIIYLGDTGALFIGFMISVL 24- 5 Query: 245 SLQGLKNSTAVAVVTPVIILGVPIMDTIVAIIRRSLSGQKFYEPDKMHLHHRLLSMGFTH 30- 4 SLQGLKN+TAVAVVTP+I+LGVPI+DT VAIIRR+LSGQKFYE D MHLHHRLL+MGFTH Sbjct: 246 SLQGLKNATAVAVVTPIIVLGVPIVDTTVAIIRRTLSGQKFYEADNMHLHHRLLAMGFTH 30- 5 Query: 305 RGAVLVVYGITMLFSLISLLLNVSSRIGGVLLMLGLLFGLEVFIEGLEIWGEKRTPLFNL 36- 4 RGAVLVVYGI M FSL+SLLLNVSSR+GG+LLM+G+ F LE+FIEGLEIWG KRTPLF L Sbjct: 306 RGAVLVVYGIAMFFSLVSLLLNVSSRLGGILLMIGVAFALEIFIEGLEIWGPKRTPLFRL 36- 5 Query: 365 LKFIGNSDYRQAMLLKWKEKK 385 L FIGNSDYRQ ++ K++ KK Sbjct: 366 LAFIGNSDYRQEVVAKYRRKK 386 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-05719 Identities = 282/384 (73%), Positives = 334/384 (86%), Gaps = 1/384 (0%) Query: 6 MIPFTIEYIFVLIGAFLLSIILTPIIRVISLKVGAVDKPNARRINKVPMPSSGGLAIFLS 65 M FTI+Y+ VLIGA L+S+ LTP++R ++ +VGAVD PNARR+NKVPMP+SGGLAIF+S Sbjct: 1 MFSFTIDYVLVLIGALLMSLFLTPLVRFLAFRVGAVDNPNARRVNKVPMPTSGGLAIFMS 60 Query: 66 FVVTTLFFMPMAAS-RHFIEVSYFHYILPVIIGGLVVTTTGFIDDIFELRPRYKMLGIII 124- F+V +L +P+A+ F +YF YILPV+IG V+T TGF+DD++EL P+ KM GI+I Sbjct: 61 FLVASLGLIPIASKGAMFFGQTYFSYILPVVIGATVITLTGFLDDLYELSPKLKMFGILI 120- Query: 125 AAIIIWKFTHFRFDSFKIPIGGPLLEFGPILTFFLTVLWIISITNAINLIDGLDGLVSGV 18- 4 A+I+W FT F+FDSFKIP GGPLL FGP LT FLTVLWI+SITNAINLIDGLDGLVSGV Sbjct: 121 GAVIVWAFTDFKFDSFKIPFGGPLLVFGPFLTLFLTVLWIVSITNAINLIDGLDGLVSGV 18- 0 Query: 185 SIISLATMAVVSYFFLPKIDFFLTLTIVILIASIVGFFPYNYHPAIIYLGDAGALFIGFM 24- 4 SIISL TMA+VSYFFLP+ DFFLTLTI++LI++I GFFPYNYHPA+IYLGD GALFIGFM Sbjct: 181 SIISLVTMAIVSYFFLPQKDFFLTLTILVLISAIAGFFPYNYHPAMIYLGDTGALFIGFM 24- 0 Query: 245 IGVLSLQGLKNSTAVAVITPVIILGVPILDTAVAIVRRKLSGKKISEADKMHLHHRLLSM 30- 4 IGVLSLQGLKNSTAVAV+TPVIILGVPI+DT VAI+RR LSG+K E DKMHLHHRLLSM Sbjct: 241 IGVLSLQGLKNSTAVAVVTPVIILGVPIMDTIVAIIRRSLSGQKFYEPDKMHLHHRLLSM 30- 0 Query: 305 GFTHRGAVLVVYGIAIIFSLIALLLNVSSRIGGIFLLLALLLAMEIFIEGLNIWGENRTP 36- 4 GFTHRGAVLVVYGI ++FSLI+LLLNVSSRIGG+ L+L LL +E+FIEGL IWGE RTP Sbjct: 301 GFTHRGAVLVVYGITMLFSLISLLLNVSSRIGGVLLMLGLLFGLEVFIEGLEIWGEKRTP 36- 0 Query: 365 LFNLLKFIGNSDYRQSVIAKYSDK 388 LFNLLKFIGNSDYRQ+++ K+ +K Sbjct: 361 LFNLLKFIGNSDYRQAMLLKWKEK 384 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1863 A DNA sequence (GBSx1970) was identified in S. agalactiae <SEQ ID 5793> which encodes the amino acid sequence <SEQ ID 5794>. This protein is predicted to be negative regulator of genetic competence. Analysis of this protein sequence reveals the following: TABLE-US-05720 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3460(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9483> which encodes amino acid sequence <SEQ ID 9484> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05721 >GP: BAA82113 GB: AB022909 negative regulator of genetic competence [Streptococcus mutans] Identities = 168/248 (67%), Positives = 205/248 (81%), Gaps = 9/248 (3%) Query: 1 MEMKQISETTLKITISMEDLEDRGMELKDFLIPQEKTEEFFYSVMDELDLPENFKNSGML 60 MEMKQISETTLKITISMEDLE+RGMELKDFLIPQEKTEEFFY+VMDELDLPENFK SGML Sbjct: 1 MEMKQISETTLKITISMEDLEERGMELKDFLIPQEKTEEFFYTVMDELDLPENFKGSGML 60 Query: 61 SFRVTPKKDRIDVFVTKSELSKDLNLEELADLGDISKMSPEDFFKTLEQSMLEKGDTDAH 120- SFRVTP+ DRIDVFVTKSE++K+LNLE+L+D DISKMSPEDFF TLE++M EKGD A Sbjct: 61 SFRVTPRNDRIDVFVTKSEINKNLNLEDLSDFDDISKMSPEDFFNTLEETMREKGDAAAL 120- Query: 121 AKLAEIENMMDKATQEVVEENVSEEQPEKEVETIGYVHYVFDFDNIEAVVRFSQTIDFPI 18- 0 KLAEIE ++ TQ+ E+ ++E+ + YVH+V DF NI+ V+ F++T+D+ + Sbjct: 121 DKLAEIEKREEEKTQQ--EKGETKEKRD-------YVHFVLDFPNIQQVISFAKTVDYDV 17- 1 Query: 181 EASELYKNGKGYHMTILLDLENQPSYFANLMYARMLEHANVGTKTRAYLKEHSIQLIHDD 24- 0 EASEL+K YHMT+LL+LE++P Y+A+LM+ARMLEHA GTKTRAYL EH +QLI D Sbjct: 172 EASELFKESDAYHMTVLLNLEDKPDYYADLMFARMLEHAGRGTKTRAYLLEHGVQLIKAD 23- 1 Query: 241 AISKLQMI 248 A+ +LQMI Sbjct: 232 ALQELQMI 239 A related DNA sequence was identified in S. pyogenes <SEQ ID 5795> which encodes the amino acid sequence <SEQ ID 5796>. Analysis of this protein sequence reveals the following: TABLE-US-05722 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3307(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05723 Identities = 171/253 (67%), Positives = 209/253 (82%), Gaps = 2/253 (0%) Query: 1 MEMKQISETTLKITISMEDLEDRGMELKDFLIPQEKTEEFFYSVMDELDLPENFKNSGML 60 MEMKQISETTLKITISM+DLE+RGMELKDFLIPQEKTEEFFYSVMDELDLP+NFK+SGML Sbjct: 3 MEMKQISETTLKITISMDDLEERGMELKDFLIPQEKTEEFFYSVMDELDLPDNFKDSGML 62 Query: 61 SFRVTPKKDRIDVFVTKSELSKDLNLEELADLGDISKMSPEDFFKTLEQSMLEKGDTDAH 120- SFRVTP+KDR+DVFVTKSE++KD+NLE+LA+ GD+S+M+PEDFFK+LEQSM EKGD AH Sbjct: 63 SFRVTPRKDRLDVFVTKSEINKDINLEDLAEFGDMSQMTPEDFFKSLEQSMREKGDVKAH 122- Query: 121 AKLAEIENMMDKATQEVV--EENVSEEQPEKEVETIGYVHYVFDFDNIEAVVRFSQTIDF 17- 8 KL +IE +M+ + + + ++ E E + YVHYV DF I V F++TIDF Sbjct: 123 EKLEKIEEIMEDVVEATLANQSEAADPSTNHESEPLDYVHYVLDFSTITEAVAFAKTIDF 18- 2 Query: 179 PIEASELYKNGKGYHMTILLDLENQPSYFANLMYARMLEHANVGTKTRAYLKEHSIQLIH 23- 8 IEASELYK YHMTILLD++ QPSYFAN+MYAR++EHAN G+KTRAYL+EH +QL+ Sbjct: 183 SIEASELYKGSNCYHMTILLDVQQQPSYFANVMYARLIEHANPGSKTRAYLQEHGLQLML 24- 2 Query: 239 DDAISKLQMIEMG 251 D A+ +LQ IE+G Sbjct: 243 DGAVEQLQKIELG 255 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1864 A DNA sequence (GBSx1971) was identified in S. agalactiae <SEQ ID 5797> which encodes the amino acid sequence <SEQ ID 5798>. This protein is predicted to be BacA (bacA). Analysis of this protein sequence reveals the following: TABLE-US-05724 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.02 Transmembrane 115-131 (111-135) INTEGRAL Likelihood = -8.97 Transmembrane 227-243 (219-247) INTEGRAL Likelihood = -7.86 Transmembrane 48-64 (44-69) INTEGRAL Likelihood = -7.27 Transmembrane 263-279 (260-279) INTEGRAL Likelihood = -7.22 Transmembrane 87-103 (85-107) INTEGRAL Likelihood = -3.50 Transmembrane 2-18 (1-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.4609(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05725 >GP: AAD50462 GB: AF169967 BacA [Flavobacterium johnsoniae] Identities = 101/275 (36%), Positives = 165/275 (59%), Gaps = 22/275 (8%) Query: 7 LKALFLGVVEGVTEWLPVSSTGHLILVQEFMKLNQSKSFVEMFNIVIQLGAIMAVIVIYF 66 L+A+ L V+EG+TE+LPVSSTGH+I+ F + + F ++F IVIQLGAI++V+V+YF Sbjct: 4 LQAIVLAVIEGITEFLPVSSTGHMIIASSFFGIAH-EDFTKLFTIVIQLGAILSVVVLYF 62 Query: 67 KRLNPFQPGKSAREIRLTWQLWLKVVIACIPSILIALPFDNWFEAHFNFMIPIAIALIFY 126- KR FQ T + K+++A IP++++ L ++ + + +A++L+ Sbjct: 63 KRF--FQ----------TLDFYFKLLVAFIPAVVLGLLLSDFIDGLLENPVTVAVSLLIG 110- Query: 127 GFVFI----WVEKRNAHLKPQVTELASMSYKTAFLIGCFQVLSIVPGTSRSGATILGAII 18- 2 G + + W NA Q ++Y A IG FQ ++++PG SRSGA+I+G + Sbjct: 111 GLILLKVDEWFNNPNAAETSQ-----KITYLQALKIGLFQCIAMIPGVSRSGASIVGGMS 16- 5 Query: 183 IGTSRSVAADFTFFLAIPTMFGYSGLKAVKYFLDGNVLSLDQSLILLVASLTAFVVSLYV 24- 2 SR+ AA+F+FFLA+PTM G + K Y+ G LS DQ IL++ ++ AF+V+L Sbjct: 166 QKLSRTTAAEFSFFLAVPTMLGATVKKCYDYYKAGFELSHDQVNILIIGNVVAFIVALLA 22- 5 Query: 243 IRFLTDYVKRHDFTIFGKYRIVLGSLLILYWLVVH 277 I+ ++ ++ F +FG YRI+ G +L+L +H Sbjct: 226 IKTFISFLTKNGFKVFGYYRIIAGIILLLIHFFIH 260 A related DNA sequence was identified in S. pyogenes <SEQ ID 5799> which encodes the amino acid sequence <SEQ ID 5800>. Analysis of this protein sequence reveals the following: TABLE-US-05726 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.30 Transmembrane 225-241 (219-247) INTEGRAL Likelihood = -9.24 Transmembrane 115-131 (109-135) INTEGRAL Likelihood = -7.64 Transmembrane 48-64 (44-69) INTEGRAL Likelihood = -7.43 Transmembrane 87-103 (85-108) INTEGRAL Likelihood = -5.15 Transmembrane 263-279 (262-279) INTEGRAL Likelihood = -3.82 Transmembrane 2-18 (1-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.5522(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05727 >GP: AAD50462 GB: AF169967 BacA [Flavobacterium johnsoniae] Identities = 102/269 (37%), Positives = 169/269 (61%), Gaps = 14/269 (5%) Query: 7 LKAIFFGIIEGITEWLPVSSTGHLILVQEFIRLNQDKAFIEMFNIVIQLGAIIAVMLIYF 66 L+AI +IEGITE+LPVSSTGH+I+ F + + F ++F IVIQLGAI++V+++YF Sbjct: 4 LQAIVLAVIEGITEFLPVSSTGHMIIASSFFGIAHED-FTKLFTIVIQLGAILSVVVLYF 62 Query: 67 ERLNPFQPGKTAREVQLTWQLWLKVVIACIPSILIAVPLDNWFEAHFYFMVPIAIALIVY 126- +R FQ T + K+++A IP++++ + L ++ + V +A++L++ Sbjct: 63 KRF--FQ----------TLDFYFKLLVAFIPAVVLGLLLSDFIDGLLENPVTVAVSLLIG 110- Query: 127 GIAFIWIEKRNAQQEPAVTELARMSYKTAFFIGCFQVLSIVPGTSRSGATILGAIILGTS 18- 6 G+ + +++ A T +++Y A IG FQ ++++PG SRSGA+I+G + S Sbjct: 111 GLILLKVDEWFNNPNAAETS-QKITYLQALKIGLFQCIAMIPGVSRSGASIVGGMSQKLS 16- 9 Query: 187 RTVAADFTFFLAIPTMFGYSGLKAVKFFLDGHHLDFAQVLILLVASLTAFVVSLLAIRFL 24- 6 RT AA+F+FFLA+PTM G + K ++ G L QV IL++ ++ AF+V+LLAI+ Sbjct: 170 RTTAAEFSFFLAVPTMLGATVKKCYDYYKAGFELSHDQVNILIIGNVVAFIVALLAIKTF 22- 9 Query: 247 TDYVKKHDFTIFGKYRIVLGSLLLIYSFF 275 ++ K+ F +FG YRI+ G +LL+ FF Sbjct: 230 ISFLTKNGFKVFGYYRIIAGIILLLIHFF 258 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05728 Identities = 227/272 (83%), Positives = 253/272 (92%) Query: 1 MLIIELLKALFLGVVEGVTEWLPVSSTGHLILVQEFMKLNQSKSFVEMFNIVIQLGAIMA 60 MLIIELLKA+F G++EG+TEWLPVSSTGHLILVQEF++LNQ K+F+EMFNIVIQLGAI+A Sbjct: 1 MLIIELLKAIFFGIIEGITEWLPVSSTGHLILVQEFIRLNQDKAFIEMFNIVIQLGAIIA 60 Query: 61 VIVIYFKRLNPFQPGKSAREIRLTWQLWLKVVIACIPSILIALPFDNWFEAHFNFMIPIA 120- V++IYF+RLNPFQPGK+ARE++LTWQLWLKVVIACIPSILIA+P DNWFEAHF FM+PIA Sbjct: 61 VMLIYFERLNPFQPGKTAREVQLTWQLWLKVVIACIPSILIAVPLDNWFEAHFYFMVPIA 120- Query: 121 IALIFYGFVFIWVEKRNAHLKPQVTELASMSYKTAFLIGCFQVLSIVPGTSRSGATILGA 18- 0 IALI YG FIW+EKRNA +P VTELA MSYKTAF IGCFQVLSIVPGTSRSGATILGA Sbjct: 121 IALIVYGIAFIWIEKRNAQQEPAVTELARMSYKTAFFIGCFQVLSIVPGTSRSGATILGA 18- 0 Query: 181 IIIGTSRSVAADFTFFLAIPTMFGYSGLKAVKYFLDGNVLSLDQSLILLVASLTAFVVSL 24- 0 II+GTSR+VAADFTFFLAIPTMFGYSGLKAVK+FLDG+ L Q LILLVASLTAFVVSL Sbjct: 181 IILGTSRTVAADFTFFLAIPTMFGYSGLKAVKFFLDGHHLDFAQVLILLVASLTAFVVSL 24- 0 Query: 241 YVIRFLTDYVKRHDFTIFGKYRIVLGSLLILY 272 IRFLTDYVK+HDFTIFGKYRIVLGSLL++Y Sbjct: 241 LAIRFLTDYVKKHDFTIFGKYRIVLGSLLLIY 272 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1865 A DNA sequence (GBSx1972) was identified in S. agalactiae <SEQ ID 5801> which encodes the amino acid sequence <SEQ ID 5802>. Analysis of this protein sequence reveals the following: TABLE-US-05729 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.65 Transmembrane 494-510 (488-519) INTEGRAL Likelihood = -8.01 Transmembrane 263-279 (256-288) INTEGRAL Likelihood = -5.95 Transmembrane 25-41 (20-43) INTEGRAL Likelihood = -4.94 Transmembrane 475-491 (473-493) ----- Final Results ----- bacterial membrane --- Certainty = 0.4461(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9481> which encodes amino acid sequence <SEQ ID 9482> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05730 >GP: AAB99606 GB: U67598 M. jannaschii predicted coding region MJ1577 [Methanococcus jannaschii] Identities = 41/172 (23%), Positives = 78/172 (44%), Gaps = 19/172 (11%) Query: 479 LISFVVIIYTLFLNYFTYFCIYLLLFGVILLLNKIIFMMTRKISNGYIVTEDGASRVYQW 53- 8 +IS ++ ++ F+ ++ + ++ ++ II +T G ++ +W Sbjct: 442 VISILLAVFLYFIPKYSQTFNEVFYLSIVFVVQNIILALTPTSLFGRWKANYYKEKL-EW 50- 0 Query: 539 TSFRNMLRDIKSFDRSELESIVLWNRILVYATLFGYADRVEKALR-VNQIDIPERFANID 59- 7 +F+N L ++ + E I +W L+Y T G D+V +A++ +N ++ + I Sbjct: 501 DAFKNFLSNLAMIKKYSPEDISIWKDWLIYGTALGVGDKVVEAMKSLNLSELVADYVIIH 56- 0 Query: 598 SHQFAISVNQSSNHFSTITEDVSHASNFSVNSGGSSGGFSGGGG--GGGGGA 647 S+ ++ + S + ST GS GGF GGG GGGGGA Sbjct: 561 SNYDSMKTSVDSVYSSTT GSGGGFGAGGGFGGGGGGA 597 A related DNA sequence was identified in S. pyogenes <SEQ ID 5803> which encodes the amino acid sequence <SEQ ID 5804>. Analysis of this protein sequence reveals the following: TABLE-US-05731 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.91 Transmembrane 486-502 (483-508) INTEGRAL Likelihood = -5.89 Transmembrane 465-481 (460-483) INTEGRAL Likelihood = -2.18 Transmembrane 244-260 (241-260) ----- Final Results ----- bacterial membrane --- Certainty = 0.4163(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05732 >GP: AAB99606 GB: U67598 M. jannaschii predicted coding region MJ1577 [Methanococcus jannaschii] Identities = 59/263 (22%), Positives = 106/263 (39%), Gaps = 14/263 (5%) Query: 369 FLDMAFGNKVTLPVDQLFSQYHYDADTIKQLKKTYKGKKLEQEVRQSSEQVIKAMKKASA 42- 8 ++ + G K+ + L + Y++D +K L K K + E +S Q K+ K Sbjct: 346 YIKIMNGGKIEILKTDLENLDVYESDVMKFLMKYSKNNVFDPEYIKSLAQKYKSSKDKLK 40- 5 Query: 429 AITNNVLETIKKLNLPDTYRQMTPA--EKRKSNSVQGLGCLLLILNSGLLIYLAIKESGL 48- 6 + + E K + P ++ A E R + L + ++L L ++ Sbjct: 406 KLKD---ELDKIMEYPRYSSKVVNAFLETRGKKIIIALLVISILLAVFLYFIPKYSQTFN 46- 2 Query: 487 ALIYLALMVLTMCLGFYISLKLDQYKKLGIETPEGGVRLHQWQSFKNMIRDIDKFEDVAI 54- 6 + YL+++ + I L L G +W +FKN + ++ + + Sbjct: 463 EVFYLSIVFVVQ----NIILALTPTSLFGRWKANYYKEKLEWDAFKNFLSNLAMIKKYSP 51- 8 Query: 547 EGLVVWNRVLVYATLFGYAKKVERYLKVHRIALPEVYQAVRPGELSMVMYATTPTFVSSL 60- 6 E + +W L+Y T G KV +K ++ + V + Y + T V S+ Sbjct: 519 EDISIWKDWLIYGTALGVGDKVVEAMKSLNLS-----ELVADYVIIHSNYDSMKTSVDSV 57- 3 Query: 607 SSATTSSNFSVSSGGGISGGGGG 629 S+TT S +GGG GGGGG Sbjct: 574 YSSTTGSGGGFGAGGGFGGGGGG 596 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05733 Identities = 241/635 (37%), Positives = 372/635 (57%), Gaps = 18/635 (2%) Query: 22 MKKCFLAICLALSFFMVSVQADEVDYNIPHYEGNLTIHNDNSADFTEKVTYQFDSSYNGQ 81 - MKK + + L S + ++A +VDY+I +YEG L + +N+A F +KVTYQFD+SYNGQ Sbjct: 1 MKKILMTLVLCFSLLGIRIKAADVDYSITNYEGQLLLSKENTARFEQKVTYQFDTSYNGQ 60 Query: 82 YVTLGTAGKLPDNFDINNKPQVEVSINGKVRKVSYQIEDLEDGYRLKVFNGGEAGDTVKV 141- Y++LG G LP F I+ KP+VEV NG+ VS + DL DGYRLK++N G+AGD V V Sbjct: 61 YISLGRTGHLPAGFAIDQKPKVEVYQNGQQVPVSQEFSDLGDGYRLKLYNAGQAGDKVDV 120- Query: 142 NVQWKLKNVLFMHKDVGELNWIPISDWDKTLEKVDFWISTDKKVALSRLWGHLGYL-KTP 20- 0 V W+L ++L ++DV ELNW PISDWDKTLEKV ++T + S LW H GY K P Sbjct: 121 KVIWQLHHLLTAYQDVAELNWTPISDWDKTLEKVSLTVTTPTDIQDSNLWAHRGYYQKKP 18- 0 Query: 201 PKIRQNNNRYHLTAFNVNKRLEFHGYWDRSYF--NLPTNSKNNYKKKIEYQEKMIERHGF 25- 8 +++ N+RY + A NV+ +LE H YWD+ P + + K KI E I R Sbjct: 181 QVLKEGNSRYQINAKNVSGQLELHAYWDKKALLGKEPVDVSTSKKNKIVALETKISRRRT 24- 0 Query: 259 ILSFLLRILLPSFFIIVTLFISIRVFLFRKKVNKYGQFPKEHHLYEAPEDLSPLELTQSI 31- 8 +L L ++P + L+ 1+ +K+ N+Y H YE PEDLSPL LTQ+I Sbjct: 241 LLQLLFGKVIPLVEVGFLLWQLIQFTRLKKQFNRYHLANHTDHSYEVPEDLSPLVLTQAI 30- 0 Query: 319 YSMSFKNFQ---DEEKKTHL---ISQEQLIQSILLDLIDRKVL----NYDDNLLSLANLD 36- 8 Y SF E +K + ++ E L+Q+ LLDLID+KVL L ++ LD Sbjct: 301 YGQSFAYLSPTASESQKLLIPKGVTFEALVQATLLDLIDQKVLLLTKEEGKAYLEISQLD 36- 0 Query: 369 RASDAEIDFIEFAFADSTSLKPDQLFSNYQFSYKETLRELKKQHKASDLQTQMRRRGSNA 42- 8 R +D E F++ AF + +L DQLFS Y + +T+++LKK +K L+ ++R+ Sbjct: 361 RVTDEEAAFLDMAFGNKVTLPVDQLFSQYHYD-ADTIKQLKKTYKGKKLEQEVRQSSEQV 41- 9 Query: 429 LSRITRLTRLISKDNINSLRRKGISSPYRKMSSEESKELSRLKRFSYLSPLISFVVIIYT 48- 8 + + + + I+ + + ++++ + YR+M+ E ++ + ++ L +++ ++IY Sbjct: 420 IKAMKKASAAITNNVLETIKKLNLPDTYRQMTPAEKRKSNSVQGLGCLLLILNSGLLIY- 47- 8 Query: 489 LFLNYFTYFCIYLLLFGVILLLNKIIFMMTRKISNGYIVTEDGASRVYQWTSFRNMLRDI 54- 8 L + IYL L + + L I + + I T +G R++QW SF+NM+RDI Sbjct: 479 LAIKESGLALIYLALMVLTMCLGFYISLKLDQYKKLGIETPEGGVRLHQWQSFKNMIRDI 53- 8 Query: 549 KSFDRSELESIVLWNRILVYATLFGYADRVEKALRVNQIDIPERFANIDSHQFAISVNQS 60- 8 F+ +E +V+WNR+LVYATLFGYA +VE+ L+V++I +PE + + + ++ + + Sbjct: 539 DKFEDVAIEGLVVWNRVLVYATLFGYAKKVERYLKVHRIALPEVYQAVRPGELSMVMYAT 59- 8 Query: 609 SNHFSTITEDVSHASNFSVNSGGSSGGFSGGGGGG 643 + F + + +SNFSV+SG GG SGGGGGG Sbjct: 599 TPTFVSSLSSATTSSNFSVSSG---GGISGGGGGG 630 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8921> and protein <SEQ ID 8922> were also identified. Analysis of this protein sequence reveals the following:

TABLE-US-05734 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 10.29 GvH: Signal Score (-7.5): 3.11 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 3 value: -8.65 threshold: 0.0 INTEGRAL Likelihood = -8.65 Transmembrane 475-491 (469-500) INTEGRAL Likelihood = -8.01 Transmembrane 244-260 (237-269) INTEGRAL Likelihood = -4.94 Transmembrane 456-472 (454-474) PERIPHERAL Likelihood = 2.28 540 modified ALOM score: 2.23 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4461 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no homology with any sequences in the databases. EXAMPLE 1866 A DNA sequence (GBSx1973) was identified in S. agalactiae <SEQ ID 5805> which encodes the amino acid sequence <SEQ ID 5806>. This protein is predicted to be glutamine-binding periplasmic protein/glutamine transport system perme. Analysis of this protein sequence reveals the following: TABLE-US-05735 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.86 Transmembrane 301-317 (295-324) INTEGRAL Likelihood = -6.05 Transmembrane 479-495 (473-496) INTEGRAL Likelihood = -0.59 Transmembrane 369-385 (369-385) ----- Final Results ----- bacterial membrane --- Certainty = 0.4545 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05736 >GP: BAA17584 GB: D90907 glutamine-binding periplasmic protein [Synechocystis sp.] Identities = 147/534 (27%), Positives = 256/534 (47%), Gaps = 75/534 (14%) Query: 4 ILLSLFTALLITFGGMTSIQADEYLRVGMEAAYAPFNWTQNDNTNGAVPIEGTDQYANGY 63 +LL++ LL F ++ + + V E + PF T E T Q G+ Sbjct: 24 VLLAIAIPLLPAFSQVSR----QTIIVATEPTFPPFEMTD----------EATGQLT-GF 68 Query: 64 DVQVAKKLAKKLNKKVVVVKTKWEGLVPALTSGKLDMIIAGMSPTEERKKEINFSKPYYI 123- DV + + + + V + ++G++PAL S + I+ ++ T ER + ++FS PY+ Sbjct: 69 DVDLIQAIGEAAQVTVDIQGYPFDGIIPALQSNTVGAAISAITITPERAQSVSFSSPYFK 128- Query: 124 SEPTLVVNAEGKYTNAKNISDFKNAKVTAQQGVYLYNLIDQINGVKKEVAMGDFNQLRQA 18- 3 S L + + KN+ D + ++ G + + G K + +F+ + A Sbjct: 129 S--VLAIAVQDGNDTIKNLKDLEGKRLAVAIGTTGAMVATNVPGAK----VTNFDSITSA 18- 2 Query: 184 VE---SGVVDAYVSERPDATSAQTANPKLKMIELHQGFKTSDADTNISVGMRKGDNRINQ 24- 0 ++ +G DA +++RP A + L+ +++ + D I++ + INQ Sbjct: 183 LQELVNGNADAVINDRPVLLYA-IKDAGLRNVKISADVGSEDY-YGIAMPLAP-PGEINQ 23- 9 Query: 241 VNQVL-----ESISRDKQIALMDKMIKEQ---------PSV------------KKEKNGK 27- 4 +VL + I A+ +K E+---------PS+ + + N Sbjct: 240 TREVLNQGLFQIIENGTYNAIYEKWFGEKNPPFLPLVAPSLVGKVGTAQSLTERSQANPN 29- 9 Query: 275 PNFFEQMATILKNNGSQFLRGTATTLLISMVGTIVGLFIGLLIGVFRTAPKSDNKLKAAL 33- 4 NF + T+ +N +G+ T+L++ GL G + + A SD Sbjct: 300 DNF---LITLFRN----LFKGSILTVLLTAFSVFFGLIGGTGVAI---ALISD------- 34- 2 Query: 335 QKLLGWLLNIYIEVFRGTPMIVQSMVIYYGTAQAF-----GVSLDRTLAAIFIVSINTGA 38- 9 K L + IY+E FRGTPM+VQ +IY+G F G+++DR AAI +S+N A Sbjct: 343 IKPLQLIFRIYVEFFRGTPMLVQLFIIYFGLPALFKEIGLGITIDRFPAAIIALSLNVAA 40- 2 Query: 390 YMSEIVRGGIFSVDKGQFEAATALGFTHGQTMRKIVLPQVVRNILPATGNEFVINIKDTS 44- 9 Y++EI+RGGI S+D+GQ+EA +LG + QTM++++ PQ R ILP GNEF+ IKDTS Sbjct: 403 YLAEIIRGGIQSIDQGQWEACESLGMSPWQTMKEVIFPQAFRRILPPLGNEFITLIKDTS 46- 2 Query: 450 VLNVISVVELYFSGNTVATQTYQYFQTFTIIAIIYFILTFTVTRILRYIEKRFD 503 + VI EL+ G + TY+ F+ + +A++Y +LT + + +++E D Sbjct: 463 LTAVIGFQELFREGQLIVATTYRAFEVYIAVALVYLLLTTISSFVFKWLENYMD 516 There is also homology to SEQ ID 1194. A related GBS gene <SEQ ID 8923> and protein <SEQ ID 8924> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05737 Lipop: Possible Site: -1 Crend: 2 McG: Discrim Score: 6.23 GvH: Signal Score (-7.5): 0.11 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 3 value: -8.86 threshold: 0.0 INTEGRAL Likelihood = -8.86 Transmembrane 301-317 (295-324) INTEGRAL Likelihood = -6.05 Transmembrane 479-495 (473-496) PERIPHERAL Likelihood = 1.32 441 modified ALOM score: 2.27 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4545 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00131## There is also homology to SEQ ID 5804. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1867 A DNA sequence (GBSx1974) was identified in S. agalactiae <SEQ ID 5807> which encodes the amino acid sequence <SEQ ID 5808>. This protein is predicted to be ATP-binding. Analysis of this protein sequence reveals the following: TABLE-US-05738 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3208 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05739 >GP: CAB73160 GB: AL139076 putative glutamine transport ATP-binding protein [Campylobacter jejuni] Identities = 132/241 (54%), Positives = 178/241 (73%), Gaps = 1/241 (0%) Query: 5 ILEIKHLKKSYGSNEVLKDISLSVNKGEVISIIGSSGSGKSTFLRSINLLEEPSGGEILY 64 ++E+K+L+K YG EVLK+I+ +++KG+VI+IIG SG GKSTFLR IN LE GEIL Sbjct: 1 MIEVKNLQKKYGELEVLKNINTTISKGDVIAIIGPSGGGKSTFLRCINRLELADSGEILI 60 Query: 65 HGHNVLEKGYDLNNYREKLGMVFQSFNLFENLNILENAIVAQTTVLKRERQEAEKIAKEN 124- + N+L+K D+N R+K+ MVFQ FNLF N N++EN + ++EA K AK Sbjct: 61 NKQNILDKEIDINKIRQKVSMVFQHFNLFANKNVMENLCLTPIKTGILSQEEAIKKAKLL 120- Query: 125 LNAVGMTEQYWKAKPKQLSGGQKQRVAIARALSVNPEAILFDEPTSALDPEMVGEVLKTM 18- 4 L VG+ ++ P +LSGGQKQR+AIAR+L +NP+ ILFDEPTSALDPEM+GEVL M Sbjct: 121 LAKVGLADKE-NIMPHKLSGGQKQRIAIARSLMMNPDVILFDEPTSALDPEMIGEVLSIM 17- 9 Query: 185 QDLAKSGLTMIIVTHEMEFAKEVSDRVIFMDKGIIAEQGTPKQLFENPTQERTKEFLQRFL 2- 45 +D+AK GLTM++VTHEM FA+ V++R+ FMDKG IA +PK++FENP+ ER +EFL + L Sbjct: 180 KDVAKEGLTMLVVTHEMGFARNVANRIFFMDKGKIAVDASPKEVFENPSNERLREFLNKVL 2- 40 A related DNA sequence was identified in S. pyogenes <SEQ ID 2157> which encodes the amino acid sequence <SEQ ID 2158>. Analysis of this protein sequence reveals the following: TABLE-US-05740 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1170 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05741 Identities = 212/246 (86%), Positives = 237/246 (96%) Query: 1 MTQAILEIKHLKKSYGSNEVLKDISLSVNKGEVISIIGSSGSGKSTFLRSINLLEEPSGG 60 M+ +I+EIK+LKKSYGSNEVLKDISLSVNKGEVISIIGSSGSGKST LRSINLLEEPS G Sbjct: 24 MSNSIIEIKNLKKSYGSNEVLKDISLSVNKGEVISIIGSSGSGKSTLLRSINLLEEPSAG 83 Query: 61 EILYHGHNVLEKGYDLNNYREKLGMVFQSFNLFENLNILENAIVAQTTVLKRERQEAEKI 120- +IL+HG +VL + Y+L +YREKLGMVFQSFNLFENLN+LENAIVAQTTVLKR+R +AE+I Sbjct: 84 QILFHGEDVLAEHYNLTHYREKLGMVFQSFNLFENLNVLENAIVAQTTVLKRDRAQAEQI 143- Query: 121 AKENLNAVGMTEQYWKAKPKQLSGGQKQRVAIARALSVNPEAILFDEPTSALDPEMVGEV 18- 0 AKENLNAVGMTEQYW+AKPKQLSGGQKQRVAIARALSVNPEA+LFDEPTSALDPEMVGEV Sbjct: 144 AKENLNAVGMTEQYWQAKPKQLSGGQKQRVAIARALSVNPEAMLFDEPTSALDPEMVGEV 20- 3 Query: 181 LKTMQDLAKSGLTMIIVTHEMEFAKEVSDRVIFMDKGIIAEQGTPKQLFENPTQERTKEF 24- 0 LKTMQDLAKSGLTMIIVTHEMEFA++VSDR+IFMDKG+I E+G+P+Q+FENPTQ+RTKEF Sbjct: 204 LKTMQDLAKSGLTMIIVTHEMEFARDVSDRIIFMDKGLITEEGSPQQIFENPTQDRTKEF 26- 3 Query: 241 LQRFLK 246 LQRFLK Sbjct: 264 LQRFLK 269 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1868 A DNA sequence (GBSx1976) was identified in S. agalactiae <SEQ ID 5809> which encodes the amino acid sequence <SEQ ID 5810>. This protein is predicted to be hypersensitive-induced response protein. Analysis of this protein sequence reveals the following: TABLE-US-05742 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -17.94 Transmembrane 4-20 (1-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.8175 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9479> which encodes amino acid sequence <SEQ ID 9480> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05743 >GP: AAF68390 GB: AF236374 hypersensitive-induced response protein [Zea mays] Identities = 127/275 (46%), Positives = 174/275 (63%), Gaps = 1/275 (0%) Query: 19 ITSLYVVKQQTVAIIERFGKYQKTATSGIHIRVPLGIDKIAARVQLRLLQSEIIVETKTK 78 - I L V Q TVAI E FGK+ + G H +IA + LR+ Q ++ ETKTK Sbjct: 4 ILGLVQVDQSTVAIKENFGKFSEVLEPGCHFLPWCIGQQIAGYLSLRVRQLDVRCETKTK 63 Query: 79 DNVFVTLNIATQYRVNENNVTDAYYKLIKPEAQIKSYIEDALRSSVPKLTLDELFEKKDE 138- DNVFVT+ + QYR + +DA+YKL QI+SY+ D +R++VPKL LD+ FE+K+E Sbjct: 64 DNVFVTVVASVQYRALADKASDAFYKLSNTREQIQSYVFDVIRATVPKLGLDDAFEQKNE 123- Query: 139 IALEVQHQVAEEMSTYGYIIVKTLITKVEPDAEVKQSMNEINAAQRKRVAAQELANADKI 19- 8 IA V+ ++ + MSTYGY IV+TLI +EPD VK++MNEINAA R RVAA E A A+KI Sbjct: 124 IAKAVEEELEKMNSTYGYQIVQTLIVDIEPDDRVKRAMNEINAAARMRVAASEKAEAEKI 18- 3 Query: 199 KIVTAAEAEAEKDRLHGVGIAQQRKAIVDGLADSIQELKDANVTLTEEQIMSILLTNQYL 25- 8 + AE EAE L GVGIA+QR+AIVDGL DS+ + T + IM ++L QY Sbjct: 184 LQIKKAEGEAESKYLAGVGIARQRQAIVDGLRDSVLAFSENVPGTTAKDIMDMVLVTQYF 24- 3 Query: 259 DTLNTF-AINGNQTIFLPNNPEGVEDIRTQVLSAL 292 DT+ A + + ++F+P+ P V+D+ Q+ L Sbjct: 244 DTMREIGASSKSSSVFIPHGPGAVKDVSAQIRDGL 278 A related DNA sequence was identified in S. pyogenes <SEQ ID 5811> which encodes the amino acid sequence <SEQ ID 5812>. Analysis of this protein sequence reveals the following: TABLE-US-05744 Possible Site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.06 Transmembrane 5-21 (1-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.6222 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05745 >GP: AAF68390 GB: AF236374 hypersensitive-induced response protein [Zea mays] Identities = 126/273 (46%), Positives = 174/273 (63%), Gaps = 3/273 (1%) Query: 23 LYVVRQQSVAIVERFGRYQKTATSGIHIRLPFGI-DKIAARVQLRLLQSEIIVETKTKDN 81 - L V Q +VAI E FG++ + G H LP+ I +IA + LR+ Q ++ ETKTKDN Sbjct: 7 LVQVDQSTVAIKENFGKFSEVLEPGCHF-LPWCIGQQIAGYLSLRVRQLDVRCETKTKDN 65 Query: 82 VFVTLNVATQYRVNEQNVTDAYYKLMKPESQIKSYIEDALRSSVPKLTLDELFEKKDEIA 141- VFVT+ + QYR +DA+YKL QI+SY+ D +R++VPKL LD+ FE+K+EIA Sbjct: 66 VFVTVVASVQYRALADKASDAFYKLSNTREQIQSYVFDVIRATVPKLGLDDAFEQKNEIA 125- Query: 142 LEVQHQVAEEMSTYGYIIVKTLITKVEPDAEVKQSMNEINAAQRKRVAAQELANADKIKI 20- 1 V+ ++ + MSTYGY IV+TLI +EPD VK++MNEINAA R RVAA E A A+KI Sbjct: 126 KAVEEELEKAMSTYGYQIVQTLIVDIEPDDRVKRAMNEINAAARMRVAASEKAEAEKILQ 18- 5 Query: 202 VTAAEAEAEKDRLHGVGIAQQRKAIVDGLAESIQELKEANISLNEEQIMSILLTNQYLDT 26- 1 + AE EAE L GVGIA+QR+AIVDGL +S+ E + IM ++L QY DT Sbjct: 186 IKKAEGEAESKYLAGVGIARQRQAIVDGLRDSVLAFSENVPGTTAKDIMDMVLVTQYFDT 24- 5 Query: 262 LNTFAAKG-NQTLFLPNTPSGVEDIRTQVLSAL 293 + A + ++F+P+ P V+D+ Q+ L Sbjct: 246 MREIGASSKSSSVFIPHGPGAVKDVSAQIRDGL 278 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05746 Identities = 254/291 (87%), Positives = 278/291 (95%) Query: 5 IILTVILVLVIVLLITSLYVVKQQTVAIIERFGKYQKTATSGIHIRVPLGIDKIAARVQL 64 I + +++++ ++ ++LYVV+QQ+VAI+ERFG+YQKTATSGIHIR+P GIDKIAARVQL Sbjct: 6 IFIAFGVIVILAIVASTLYVVRQQSVAIVERFGRYQKTATSGIHIRLPFGIDKIAARVQL 65 Query: 65 RLLQSEIIVETKTKDNVFVTLNIATQYRVNENNVTDAYYKLIKPEAQIKSYIEDALRSSV 124- RLLQSEIIVETKTKDNVFVTLN+ATQYRVNE NVTDAYYKL+KPE+QIKSYIEDALRSSV Sbjct: 66 RLLQSEIIVETKTKDNVFVTLNVATQYRVNEQNVTDAYYKLMKPESQIKSYIEDALRSSV 125- Query: 125 PKLTLDELFEKKDEIALEVQHQVAEEMSTYGYIIVKTLITKVEPDAEVKQSMNEINAAQR 18- 4 PKLTLDELFEKKDEIALEVQHQVAEEMSTYGYIIVKTLITKVEPDAEVKQSMNEINAAQR Sbjct: 126 PKLTLDELFEKKDEIALEVQHQVAEEMSTYGYIIVKTLITKVEPDAEVKQSMNEINAAQR 18- 5 Query: 185 KRVAAQELANADKIKIVTAAEAEAEKDRLHGVGIAQQRKAIVDGLADSIQELKDANVTLT 24- 4 KRVAAQELANADKIKIVTAAEAEAEKDRLHGVGIAQQRKAIVDGLA+SIQELK+AN++L Sbjct: 186 KRVAAQELANADKIKIVTAAEAEAEKDRLHGVGIAQQRKAIVDGLAESIQELKEANISLN 24- 5 Query: 245 EEQIMSILLTNQYLDTLNTFAINGNQTIFLPNNPEGVEDIRTQVLSALKTR 295 EEQIMSILLTNQYLDTLNTFA GNQT+FLPN P GVEDIRTQVLSALKT+ Sbjct: 246 EEQIMSILLTNQYLDTLNTFAAKGNQTLFLPNTPSGVEDIRTQVLSALKTK 296 SEQ ID 5810 (GBS231) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 55 (lane 7; MW 60.9 kDa). GBS231d was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 155 (lane 5-7; MW 59 kDa) and in FIG. 239 (lane 11; MW 59 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 155 (lane 9; MW 34 kDa) and in FIG. 183 (lane 6; MW 34 kDa). Purified GBS231d-GST is shown in FIG. 246, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1869 A DNA sequence (GBSx1977) was identified in S. agalactiae <SEQ ID 5813> which encodes the amino acid sequence <SEQ ID 5814>. Analysis of this protein sequence reveals the following: TABLE-US-05747 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2305 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9291> which encodes amino acid sequence <SEQ ID 9292> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05748 >GP: CAB13457 GB: Z99112 similar to hypothetical proteins [Bacillus subtilis] Identities = 259/514 (50%), Positives = 350/514 (67%), Gaps = 9/514 (1%) Query: 1 MGMTMENGAKEVSDKPATTVGEVGQILSKGVLMGARGNSGVITSQLFRGFGQSIKDKEEL 60 M ++M +GA+EV +G+VG LSKG+LMGARGNSGVI SQLFRGF ++I+ K+E+ Sbjct: 46 MNLSMTSGAREVEQMDTDDIGKVGSALSKGLLMGARGNSGVILSQLFRGFSKNIETKKEI 105- Query: 61 TGQDLAHAFQNGVEVAYKAVMKPVEGTILTVSRGAATAALKKAEETDDAVEVMRATLKGA 120- + A A Q GV++AYKAVMKPVEGTILTV++ AA A+ AE+ D +M A + A Sbjct: 106 NALEFAAALQAGVDMAYKAVMKPVEGTILTVAKDAAKKAMILAEKETDITALMTAVTEEA 16- 5 Query: 121 KRALAKTPDMLPVLKEVGVVDSGGQGLVFIYEGFLSALTGEYIASEDFKATPATMTEMVN 18- 0 + +L +TP++LPVLKEVGVVDSGG+GL+ +YEGFL++L GE + KA ++ +MV+ Sbjct: 166 EASLNRTPELLPVLKEVGVVDSGGKGLLCVYEGFLASLKGETVPQ---KAVLPSLDDMVS 22- 2 Query: 181 AEHHKAVVGHVATEDIKYGYCTEVMVGLKQGPTYVKEFNYEEFQGYLSNLGDSLLVVNDD 24- 0 AEHHK+ + TEDI++G+CTEVMV L Q +EF+ F+ LS GDSLLV+ D+ Sbjct: 223 AEHHKSAQSMMNTEDIEFGFCTEVMVRLDQTK---REFDEGTFRQDLSQFGDSLLVIADE 27- 9 Query: 241 EIVKVHVHTEDPGLVMQEGLKYGSLVKVKVENMRNQHDA---QMQKVEVEETVKETKEYG 29- 7 + KVH+H E+PG V+ YG L+K+K+ENMR QH + Q K ET + YG Sbjct: 280 SLAKVHIHAEEPGNVLNYAQHYGELIKIKIENMREQHTSIISQESKPADNETPPAKQPYG 33- 9 Query: 298 IIAVVAGDGLAEIFKSQGVDYIISGGQTMNPSTEDIVKAIEKVNARNVIILPNNKNIFMA 35- 7 I+ V G+G+A++FKS G +I GGQTMNPSTEDIV A++ VNA V ILPNN NI MA Sbjct: 340 IVTVAMGEGIADLFKSIGASVVIEGGQTMNPSTEDIVDAVKSVNADTVFILPNNSNIIMA 39- 9 Query: 358 AQSAADVVDIPAAVVETRTVPQGFTSLLAFDPAKSLETNVADMTNSLSDVISGSVTLAVR 41- 7 A AA VVD V+ +TVPQG ++LLAF+P + E N A+M +++ V SG VT +VR Sbjct: 400 ANQAASVVDEQVFVIPAKTVPQGMSALLAFNPDQEAEANEANMLSAIQQVKSGQVTFSVR 45- 9 Query: 418 DTTIDGLEIHENDILGMVDGKILVSTPDMEKALKDTFDKMIDEDSEIVTIYVGEDGKQAL 47- 7 DT IDG +I + D +G+++G I+ ++ + A K +MI ED EIVTI GED Q Sbjct: 460 DTHIDGKDIKKGDFMGILNGTIIGTSENQLSAAKMLLSEMIGEDDEIVTILYGEDASQEE 51- 9 Query: 478 AETLSEYLEETYEDVEVEIHQGDQPVYPYLMSVE 511 AE L +L E YE++EVEIH G QP+Y Y++S E Sbjct: 520 AEQLEAFLSEKYEEIEVEIHNGKQPLYSYIVSAE 553 A related DNA sequence was identified in S. pyogenes <SEQ ID 5635> which encodes the amino acid sequence <SEQ ID 5636>. Analysis of this protein sequence reveals the following: TABLE-US-05749 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1816 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-05750 Identities = 434/511 (84%), Positives = 475/511 (92%) Query: 1 MGMTMENGAKEVSDKPATTVGEVGQILSKGVLMGARGNSGVITSQLFRGFGQSIKDKEEL 60 M MTM+NGAKEV+DKPA+TVGEVGQ+LSKG+LMGARGNSGVITSQLFRGFGQSIK K+EL Sbjct: 44 MSMTMDNGAKEVADKPASTVGEVGQMLSKGLLMGARGNSGVITSQLFRGFGQSIKGKDEL 10- 3 Query: 61 TGQDLAHAFQNGVEVAYKAVMKPVEGTILTVSRGAATAALKKAEETDDAVEVMRATLKGA 12- 0 TG+DLA AFQ GVEVAYKAVMKPVEGTILTVSRGAATAALKKA+ TDDAVEVM+A L GA Sbjct: 104 TGKDLAQAFQVGVEVAYKAVMKPVEGTILTVSRGAATAALKKADLTDDAVEVMQAALDGA 16- 3 Query: 121 KRALAKTPDMLPVLKEVGVVDSGGQGLVFIYEGFLSALTGEYIASEDFKATPATMTEMVN 18- 0 K ALAKTPD+LPVLKEVGVVDSGGQGLVFIYEGFLSAL G+Y+ S DFKATPA M+EM+N Sbjct: 164 KGALAKTPDLLPVLKEVGVVDSGGQGLVFIYEGFLSALNGDYVTSADFKATPANMSEMIN 22- 3 Query: 181 AEHHKAVVGHVATEDIKYGYCTEVMVGLKQGPTYVKEFNYEEFQGYLSNLGDSLLVVNDD 24- 0 AEHHK+VVGHVATEDI YGYCTE+MV LKQGPTYVKEFNY+EFQGYLS LGDSLLVVNDD Sbjct: 224 AEHHKSVVGHVATEDITYGYCTEIMVALKQGPTYVKEFNYDEFQGYLSGLGDSLLVVNDD 28- 3 Query: 241 EIVKVHVHTEDPGLVMQEGLKYGSLVKVKVENMRNQHDAQMQKVEVEETVKETKEYGIIA 30- 0 EIVKVHVHTEDPGLVMQEGLKYGSL+K+KV+NMRNQH+AQ+QK +VE+ E K++G+IA Sbjct: 284 EIVKVHVHTEDPGLVMQEGLKYGSLIKIKVDNMRNQHEAQVQKTDVEKNKAEVKDFGLIA 34- 3 Query: 301 VVAGDGLAEIFKSQGVDYIISGGQTMNPSTEDIVKAIEKVNARNVIILPNNKNIFMAAQS 36- 0 VVAG+GL+EIFK+QGVDY+ISGGQTMNPSTEDIVKAIE VNA+ VIILPNNKNIFMAAQS Sbjct: 344 VVAGEGLSEIFKAQGVDYVISGGQTMNPSTEDIVKAIEAVNAKQVIILPNNKNIFMAAQA 40- 3 Query: 361 AADVVDIPAAVVETRTVPQGFTSLLAFDPAKSLETNVADMTNSLSDVISGSVTLAVRDTT 42- 0 AA+VVDIPAAVV TRTVPQGFTSLLAFDP+KSLE NVADM+ SLSDV+SGSVTLAVRDTT Sbjct: 404 AAEVVDIPAAVVATRTVPQGFTSLLAFDPSKSLEDNVADMSTSLSDVVSGSVTLAVRDTT 46- 3 Query: 421 IDGLEIHENDILGMVDGKILVSTPDMEKALKDTFDKMIDEDSEIVTIYVGEDGKQALAET 48- 0 IDGLEIHEND LGMVDGKI+VS PDME LK F+KMIDEDSEIVTI+VGE+G Q LAE Sbjct: 464 IDGLEIHENDFLGMVDGKIIVSNPDMEATLKAAFEKMIDEDSEIVTIFVGEEGDQDLAEE 52- 3 Query: 481 LSEYLEETYEDVEVEIHQGDQPVYPYLMSVE 511 L+ YL ETYEDVEVEIHQGDQPVYPYLMSVE Sbjct: 524 LAGYLGETYEDVEVEIHQGDQPVYPYLMSVE 554 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1870 A DNA sequence (GBSx1978) was identified in S. agalactiae <SEQ ID 5815> which encodes the amino acid sequence <SEQ ID 5816>. Analysis of this protein sequence reveals the following: TABLE-US-05751 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4771(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1871 A DNA sequence (GBSx1979) was identified in S. agalactiae <SEQ ID 5817> which encodes the amino acid sequence <SEQ ID 5818>. This protein is predicted to be proliferating-cell nucleolar antigen P120. Analysis of this protein sequence reveals the following: TABLE-US-05752 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3774(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9345> which encodes amino acid sequence <SEQ ID 9346> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05753 >GP: AAC74905 GB: AE000278 putative nucleolar proteins [Escherichia coli K12] Identities = 87/229 (37%), Positives = 128/229 (54%), Gaps = 8/229 (3%) Query: 63 GKSIEHTTGLVYSQEPAAQ--IVAQIAEPQEGMKVLDLAAAPGGKTTHLLSYLNNTGLLV 12- 0 G + EH +GL Y QE ++ + A A+ +V+D+AAAPG KTT + + +NN G ++ Sbjct: 89 GSTAEHLSGLFYIQEASSMLPVAALFADGNAPQRVMDVAAAPGSKTTQISARMNNEGAIL 14- 8 Query: 121 SNEISNKRSKILVENVERFGARNVIVTNESSQRLAKCFNSFFDLIVFDGPCSGEGMFRKD 18- 0 +NE S R K+L N+ R G NV +T+ + FD I+ D PCSGEG+ RKD Sbjct: 149 ANEFSASRVKVLHANISRCGISNVALTHFDGRVFGAAVPEMFDAILLDAPCSGEGVVRKD 20- 8 Query: 181 PQAIQYWHKDYPTECAQLQRDILKEAIKMLAHGGILVYSTCTWSPEENEEVVNWLLQEY- 23- 9 P A++ W + E A QR+++ A L GG LVYSTCT + EENE V WL + Y Sbjct: 209 PDALKNWSPESNQEIAATQRELIDSAFHALRPGGTLVYSTCTLNQEENEAVCLWLKETYP 26- 8 Query: 240 ---DYLELVDIPKLNGMVEGINVPQVARMYPHHFQGEGQFVAKLRDTRS 285 ++L L D+ G + + ++P + EG FVA+LR T++ Sbjct: 269 DAVEFLPLGDL--FPGANKALTEEGFLHVFPQIYDCEGFFVARLRKTQA 315 A related DNA sequence was identified in S. pyogenes <SEQ ID 5819> which encodes the amino acid sequence <SEQ ID 5820>. Analysis of this protein sequence reveals the following: TABLE-US-05754 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2316(Affirmative) < succ> bacterial membrane --- Certaimty = 0.0000(Not Clear) < succ> bacterial outside --- Certaimty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05755 Identities = 213/311 (68%), Positives = 254/311 (81%), Gaps = 3/311 (0%) Query: 1 MKLPNEFIEKYQTILKDEAEAFFDSFEQKPISAYRTNPLKEKQLDFPNAIPSTPWGHYGK 60 M LP EFI YQ IL E E F SF Q+P++A+R NPLK + F + IP+T WG+YGK Sbjct: 2 MSLPKEFINTYQAILGKELEDFLASFNQEPVNAFRINPLKNQLKTFEHPIPNTLWGYYGK 61 Query: 61 ISGKSIEHTTGLVYSQEPAAQIVAQIAEPQEGMKVLDLAAAPGGKTTHLLSYLNNTGLLV 12- 0 +SGKS EH +GLVYSQEPAAQ+VAQ+A PQ+G +VLDLAAAPGGK+THLL+YL+NTGLLV Sbjct: 62 LSGKSPEHVSGLVYSQEPAAQMVAQVAAPQKGSRVLDLAAAPGGKSTHLLAYLDNTGLLV 12- 1 Query: 121 SNEISNKRSVILVENVERFGARNVIVTNESSQRLAKCFNSFFDLIVFDGPCSGEGMFRKD 18- 0 SNEIS KRSK+LVEN+ERFGARNV+VTNES+ RLAK F+ +FD IVFDGPCSGEGMFRKD Sbjct: 122 SNEISKKRSKVLVENIERFGARNVVVTNESADRLAKVFSHYFDTIVFDGPCSGEGMFRKD 18- 1 Query: 181 PQAIQYWHKDYPTECAQLQRDILKEAIKMLAHGGILVYSTCTWSPEENEEVVNWLLQEYD 24- 0 P AIQYWH YP ECA+LQ+ IL++A+ ML GG L+YSTCTW+PEENE+VV WLL+ Y Sbjct: 182 PDAIQYWHHGYPAECAKLQKSILEDALAMLKPGGELIYSTCTWAPEENEDVVQWLLETYT 24- 1 Query: 241 YLELVDIPKLNGMVEGINVPQVARMYPHHFQGEGQFVAKLRDTRSKEAQKIKPKAQKIN- 29- 9 +LELVD+PKLNGMV GI +P+ ARMYPH +QGEGQFVAKL+D R +E Q K KA K N Sbjct: 242 FLELVDVPKLNGMVSGIGLPETARMYPHRYQGEGQFVAKLKDKR-QEGQSTKLKAPKSNL 30- 0 Query: 300 -KMQLQLWQQF 309 K QL+LW+ F Sbjct: 301 IKDQLRLWKMF 311 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1872 A DNA sequence (GBSx1980) was identified in S. agalactiae <SEQ ID 5821> which encodes the amino acid sequence <SEQ ID 5822>. Analysis of this protein sequence reveals the following: TABLE-US-05756 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4l11(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05757 >GP: AAC24940 GB: AF012285 unknown [Bacillus subtilis] Identities = 86/240 (35%), Positives = 133/240 (54%), Gaps = 10/240 (4%) Query: 6 DFAKQLVYKAGQFIKSEMQNTFDVEEKSRFDDLVTSLDKKTQKLLIQEIIQHYPDDNILA 65 + AK+ + +AG I M + +E KS +DLVT++DK+T+K I I + +P IL Sbjct: 9 EIAKKWIREAGARITQSMHESLTIETKSNPNDLVTNIDKETEKFFIDRIQETFPGHRILG 68 Query: 66 EE---DBVRSPIAQGNVWVLDPIDGTVNFIVQKDNFAVMLAYYEEGVGQFGIIYDVMADI 12- 2 EE D + S +G VW++DPIDGT+NF+ Q+ NFA+ + +E G G+ G+IYDV+ D Sbjct: 69 EEGQGDKIHS--LEGVVWIIDPIDGTMNFVHQQRNFAISIGIFENGEGKIGLIYDVVHDE 12- 6 Query: 123 LYSGGGHFDVYANDKKIVPFQECPLERCLLGVNSAMYAEN----DCGIAHLASETLGVRI 17- 8 LY Y N+ K+ P +E +E +L +N+ EN +A L G R Sbjct: 127 LYHAFSGRGAYMNETKLAPLKETVIEEAILAINATWVTENRRIDQSVLAPLVKRVRGTRS 18- 6 Query: 179 YGGAGISMAKVMQGKLLAYFSY-IQPWDYAAAKIMGETLGFTLLTLDGEEPNYSTRQKVM 23- 7 YG A + +A V G++ AY + + PWDYAA ++ +G T T++GE + V+ Sbjct: 187 YGSAALELANVAAGRIDAYITMRLAPWDYAAGCVLLNEVGGTYTTIEGEPFTFLENHSVL 24- 6 A related GBS nucleic acid sequence <SEQ ID 10937> which encodes amino acid sequence <SEQ ID 10938> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 5823> which encodes the amino acid sequence <SEQ ID 5824>. Analysis of this protein sequence reveals the following: TABLE-US-05758 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1843(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05759 Identities = 155/253 (61%), Positives = 205/253 (80%) Query: 1 MDAKFDFAKQLVYKAGQFIKSEMQNTFDVEEKSRFDDLVTSLDKKTQKLLIQEIIQHYPD 60 ++ K+ FA+Q++ +AG FIKS+M D++ K++FDDLVT++D++TQ+LL+ I Q YP Sbjct: 8 LETKYAFARQIIKEAGLFIKSKMSEQLDIQVKTQFDDLVTNVDQETQQLLMDRIHQTYPC 67 Query: 61 DNILAEEDBVRSPIAQGNVWVLDPIDGTVNFIVQKDNFAVMLAYYEEGVGQFGIIYDVMA 120- D ILAEE++VR PI QGNVWV+DPIDGTVNFIVQ FAVM+AYYE+G+GQFG+IYDVMA Sbjct: 68 DAILAEENDVRHPINQGNVWVIDPIDGTVNFIVQGSQFAVMIAYYEQGIGQFGLIYDVMA 127- Query: 121 DILYSGGGHFDVYANDKKIVPFQECPLERCLLGVNSAMYAENDCGIAHLASETLGVRIYG 18- 0 D L +GGG F+V N K+ +QE PLER L+G N+ M+A ND +AHL ++TLGVR+YG Sbjct: 128 DQLLAGGGDFEVTLNGDKLPAYQEKPLERSLIGCNAGMFARNDRNLAHLIAKTLGVRVYG 18- 7 Query: 181 GAGISMAKVMQGKLLAYFSYIQPWDYAAAKIMGETLGFTLLTLDGEEPNYSTRQKVMFLP 24- 0 GAGI M KVM+ +LLAYFS+IQPWDYAAAK++G+ LG+ LLT+DG EP++ TRQK+MF+P Sbjct: 188 GAGICMVKVMKQELLAYFSFIQPWDYAAAKVLGDKLGYVLLTIDGYEPDFQTRQKIMFVP 24- 7 Query: 241 KSKLNLIQSYLTK 253 K +L I S+LTK Sbjct: 248 KCQLTRIASFLTK 260 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1873 A DNA sequence (GBSx1981) was identified in S. agalactiae <SEQ ID 5825> which encodes the amino acid sequence <SEQ ID 5826>. Analysis of this protein sequence reveals the following: TABLE-US-05760 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4131(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05761 >GP: AAC24938 GB: AF012285 unknown [Bacillus subtilis] Identities = 33/78 (42%), Positives = 50/78 (63%) Query: 13 YSYPLDPSWNTEDITKVLRFLNQVEHAYENSIKVDDLLDSYKEFKKVVKSKAQEKQIDRE 72 - Y YP++ W TE+ V+ F QVE AYE ++LL +Y+ FK++V KA+EK++ E Sbjct: 3 YQYPMNEDWTTEEAVDVIAFFQQVELAYEKGADREELLKAYRRFKEIVPGKAEEKKLCGE 62 Query: 73 FQRTSGYSTYQAVKAAQQ 90 F+ S YS Y+ VK A++ Sbjct: 63 FEEQSTYSPYRTVKQARE 80 A related DNA sequence was identified in S. pyogenes <SEQ ID 5827> which encodes the amino acid sequence <SEQ ID 5828>. Analysis of this protein sequence reveals the following: TABLE-US-05762 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4442(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05763 Identities = 59/91 (64%), Positives = 70/91 (76%) Query: 9 ISSNYSYPLDPSWNTEDITKVLRFLNQVEHAYENSIKVDDLLDSYKEFKKVVKSKAQEKQ 68 +S NY YPLD SW+TE+I+ VL FLN+VE AYE + LLDSYK +K +VKSKAQEKQ Sbjct: 5 MSGNYYYPLDLSWSTEEISSVLHFLNKVELAYEKKVDAKQLLDSYKTYKTIVKSKAQEKQ 64 Query: 69 IDREFQRTSGYSTYQAVKAAQQQAKGFISLG 99 IDR+FQ+ SGYSTYQ VK A+ KGF SLG Sbjct: 65 IDRDFQKVSGYSTYQVVKKAKAIEKGFFSLG 95 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1874 A DNA sequence (GBSx1982) was identified in S. agalactiae <SEQ ID 5829> which encodes the amino acid sequence <SEQ ID 5830>. Analysis of this protein sequence reveals the following: TABLE-US-05764 Possible site: 18 >>> Seems to have no N-terminal signal sequence (or aa 1-18) ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0952(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05765 >GP: AAF21893 GB: AF103794 unknown [Listeria monocytogenes] Identities = 74/126 (58%), Positives = 101/126 (79%) Query: 1 MITLFLSPSCTSCRKARAWLSKHEVAFEEHNIITSPLNKEELLQILSFTENGTEDIISTR 60 M+TL+ SPSCTSCRK+RAWL +H++ ++E NI + PL+ +E+ +IL TE+GT++IISTR Sbjct: 1 MVTLYTSPSCTSCRKSRAWLEEHDIPYKERNIFSEPLSLDEIKEILRMTEDGTDEIISTR 60 Query: 61 SKVFQKLAIDVDELSTSSLMELISENPSLLRRPIILDKKRMQIGFNEDEIRAFLPRDYRK 120- SK FQKL +D+D L L ELI +NP LLRRPII+D+KR+Q+G+NEDEIR FLPR R Sbjct: 61 SKTFQKLNVDLDSLPLQQLFELIQKNPGLLRRPIIIDEKRLQVGYNEDEIRRFLPRRVRT 120- Query: 121 QELKQA 126 +L++A Sbjct: 121 YQLREA 126 A related DNA sequence was identified in S. pyogenes <SEQ ID 5831> which encodes the amino acid sequence <SEQ ID 5832>. Analysis of this protein sequence reveals the following: TABLE-US-05766 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0511(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05767 Identities = 112/134 (83%), Positives = 127/134 (94%) Query: 1 MITLFLSPSCTSCRKARAWLSKHEVAFEEHNIITSPLNKEELLQILSFTENGTEDIISTR 60 M+TLFLSPSCTSCRKARAWL KHEV F+EHNIITSPL+++EL+ ILSFTENGTEDIISTR Sbjct: 1 MVTLFLSPSCTSCRKARAWLVKHEVDFQEHNIITSPLSRDELMSILSFTENGTEDIISTR 60 Query: 61 SKVFQKLAIDVDELSTSSLMELISENPSLLRRPIILDKKRMQIGFNEDEIRAFLPRDYRK 120- SKVFQKL IDV+ELS S L++LI++NPSLLRRPII+D+KRMQIGFNEDEIRAFL RDYRK Sbjct: 61 SKVFQKLDIDVEELSISDLIDLIAKNPSLLRRPIIMDQKRMQIGFNEDEIRAFLSRDYRK 120- Query: 121 QELKQATIRAEIEG 134 QEL+QATI+AEIEG Sbjct: 121 QELRQATIKAEIEG 134 SEQ ID 5830 (GBS232) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 10; MW 16.8 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 56 (lane 2; MW 42 kDa). GBS232-GST was purified as shown in FIG. 207, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1875 A DNA sequence (GBSx1983) was identified in S. agalactiae <SEQ ID 5833> which encodes the amino acid sequence <SEQ ID 5834>. Analysis of this protein sequence reveals the following: TABLE-US-05768 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 5835> which encodes the amino acid sequence <SEQ ID 5836>. Analysis of this protein sequence reveals the following: TABLE-US-05769 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1768(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05770 Identities = 210/308 (68%), Positives = 252/308 (81%) Query: 1 MKIHYINDYKDIQAKEDCVLVLGYFDGLHLGHKALFDKAKKIATEKNLKIVVLTFNETPR 60 M+I YI DY+DI ++D VL+LGYFDGLH GHKALFDKA+++A ++ LK+VV TF E+P+ Sbjct: 1 MEIEYIKDYRDINQEDDTVLILGYFDGLHRGHKALFDKAREVANKEGLKVVVFTFTESPK 60 Query: 61 LTFARFQPELLLHLTSPEKRSEKFQEYGVDELYLMNFTSHFSKVSSDLFIKKYIYGLRAK 120- L F+RF PELLLH+T P+KR EKF +YGV++LYL++FTS FSKVSSD FI YI L+AK Sbjct: 61 LAFSRFSPELLLHITYPKKRYEKFADYGVNKLYLVDFTSKFSKVSSDHFITHYIKNLKAK 120- Query: 121 AAVVGFDYKFGHNRTSGDYLARNFKGPVYIIDEISEGGEKISSTRIRQLITEGNVEKANQ 18- 0 VVGFDYKFGHNRT DYL RNF+G VY I+EI E KIS+T IR+LI EGNV KAN Sbjct: 121 HIVVGFDYKFGHNRTDSDYLTRNFEGQVYTIEEIKEDHRKISATWIRKLIQEGNVVKANH 18- 0 Query: 181 LLGYEFSTCGMVVHGDARGRTIGFPTANLAPINRTYLPADGVYISNVLINGKYYRAMTSI 24- 0 LLGY+ ST G VVHGDARGRTIGFPTANLAPI+ TYLPADGVY++NV++ K YR+MTS+ Sbjct: 181 LLGYDLSTRGRVVHGDARGRTIGFPTANLAPIDNTYLPADGVYVTNVIVANKIYRSMTSL 24- 0 Query: 241 GKNITFGGTELRLEANIFDFDGDIYGETIEIFWLKRIREMVKFNGIDDLVKQLKKDKEIA 30- 0 GKN+TFGG ELRLE NIFDFD +IYGE IEI WL +IR+M KF GI+DL +L+ DK A Sbjct: 241 GKNVTFGGKELRLEVNIFDFDEEIYGEIIEIVWLDKIRDMEKFEGIEDLTDRLEYDKRTA 30- 0 Query: 301 LNWKKDSQ 308 LNWKKDS+ Sbjct: 301 LNWKKDSK 308 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1876 A DNA sequence (GBSx1984) was identified in S. agalactiae <SEQ ID 5837> which encodes the amino acid sequence <SEQ ID 5838>. This protein is predicted to be tRNA pseudouridine 5S synthase (truB). Analysis of this protein sequence reveals the following:

TABLE-US-05771 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2576(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9817> which encodes amino acid sequence <SEQ ID 9818> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05772 >GP: BAB06129 GB: AP0015l5 tRNA pseudouridine 5S synthase [Bacillus halodurans] Identities = 145/283 (51%), Positives 191/283 (67%), Gaps = 12/283 (4%) Query: 2 ITGIINLKKEAGMTSHDAVFKLRKILHTKKIGHGGTLDPDVVGVLPIAVGKATRVIEYMT 61 +TGI+ L K GMTSHD V KLR++L TKK+GH GTLDPDV GVLP+ +G AT+V +YM+ Sbjct: 3 MTGILPLAKPRGMTSHDCVAKLRRLLKTKKVGHTGTLDPDVYGVLPVCIGHATKVAQYMS 62 Query: 62 ESGKIYEGEITLGYATSTEDSSGEVISRTPLTQSDLSEDVVDHAMKSFTGPITQVPPMYS 12- 1 + K YEGE+T+G++T+TED SG+ + T Q E VVD + +F G I Q+PPMYS Sbjct: 63 DYPKAYEGEVTVGFSTTTEDRSGDTVE-TKTIQQPFVEAVVDQVLATFVGEIKQIPPMYS 12- 1 Query: 122 AVKVNGKKLYEYARSGEEVERPKRQITISEFRRTSPLYFEKGICRFSFYVSCSKGTYVRT 18- 1 AVKV GK+LYEYAR+G VERP+R +TI R S + +E+G+CRF F VSCSKGTYVRT Sbjct: 122 AVKVRGKRLYEYARAGITVERPERTVTIFSLERMSDIVYEEGVCRFRFNVSCSKGTYVRT 18- 1 Query: 182 LAVDLGIKLGYASHMSFLKRTSSAGLSITQSLTLEEINEKYKQ-EDFSFLLPIEYGVLDL 24- 0 LAVD+G LGY +HMS L RT S S+ + T E+ E+ +Q E S LLPIE +LD+ Sbjct: 182 LAVDIGKALGYPAHMSDLVRTKSGPFSLEECFTFTELEERLEQGEGSSLLLPIETAILDI 24- 1 Query: 241 PKVNLTEEDKVEISYGR----------RILLENEADTLAAFYE 273 P+V + +E + +I +G R + NE L A Y+ Sbjct: 242 PRVQVNKEIEEKIRHGAVLPQKWFNHPRFTVYNEEGALLAIYK 284 A related DNA sequence was identified in S. pyogenes <SEQ ID 5839> which encodes the amino acid sequence <SEQ ID 5840>. Analysis of this protein sequence reveals the following: TABLE-US-05773 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2698(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05774 Identities = 201/295 (68%), Positives = 246/295 (83%), Gaps = 2/295 (0%) Query: 1 MITGIINLKKEAGMTSHDAVFKLRKILHTKKIGHGGTLDPDVVGVLPIAVGKATRVIEYM 60 MI GIINLKKEAGMTSHDAVFKLRK+L KKIGHGGTLDPDVVGVLPIAVGKATRVIEYM Sbjct: 1 MINGIINLKKEAGMTSHDAVFKLRKLLQEKKIGHGGTLDPDVVGVLPIAVGKATRVIEYM 60 Query: 61 TESGKIYEGEITLGYATSTEDSSGEVISRTPLTQSDLSEDVVDHAMKSFTGPITQVPPMY 12- 0 TE+GK+YEG++TLGY+T+TED+SGEV++R+ L + L+E++VD M +F G ITQ PPMY Sbjct: 61 TEAGKVYEGQVTLGYSTTTEDASGEVVARSSL-PAVLTEELVDQTMTTFLGKITQTPPMY 11- 9 Query: 121 SAVKVNGKKLYEYARSGEEVERPKRQITISEFRRTSPLYF-EKGICRFSFYVSCSKGTYV 17- 9 SAVKVNG+KLYERAR+GE VERP+R++TIS F RTSPL F E G+CRFSF V+CSKGTYV Sbjct: 120 SAVKVNGRKLYERARAGESVERPRREVTISLFERTSPLNFTEDGLCRFSFKVACSKGTYV 17- 9 Query: 180 RTLAVDLGIKLGYASHMSFLKRTSSAGLSITQSLTLEEINEKYKQEDFSFLLPIEYGVLD 23- 9 RTLAVDLG LG SHMSFL+R++SAGL++ + TL EI + +++ SFLLPIEYGV D Sbjct: 180 RTLAVDLGRALGVESHMSFLQRSASAGLTLETAYTLGEIADMVSKQEMSFLLPIEYGVAD 23- 9 Query: 240 LPKVNLTEEDKVEISYGRRILLENEADTLAAFYENRVIAILEKRGNEFKPHKVLL 294 LPK+ + + + EIS+GRR+ L ++ LAAF+ +VIAILEKR E+KP KVL+ Sbjct: 240 LPKMVIDDTELTEISFGRRLSLPSQEPLLAAFHGEKVIAILEKRDQEYKPKKVLI 294 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1877 A DNA sequence (GBSx1985) was identified in S. agalactiae <SEQ ID 5841> which encodes the amino acid sequence <SEQ ID 5842>. Analysis of this protein sequence reveals the following: TABLE-US-05775 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2776(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9819> which encodes amino acid sequence <SEQ ID 9820> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05776 >GP: CAB12871 GB: Z99109 similar to hypothetical proteins [Bacillus subtilis] Identities = 39/145 (26%), Positives = 68/145 (46%), Gaps = 7/145 (4%) Query: 3 MKIRTATLDDSEKLVPLYQELG----YAISLSEIQSILKVILTHSDYGFLIAEDNGKLLA 58 M IR A D+ + PL+ + A L ++ LK L + + LIAE+NG+ + Sbjct: 1 MNIRQAKTSDAAAIAPLFNQYREFYRQASDLQFAEAFLKARLENHESVILIAEENGEFIG 60 Query 59 FVGYHKLYFFEKSGTYYRILALVVNEKHRRKGIASQLINHVKQLAKTDGSEVLALNSSLK 118- F + + Y + L V R KG +L++ K A +G++ L L + + Sbjct: 61 FTQLYPTFSSVSMKRIYILNDLFVVPHARTKGAGGRLLSAAKDYAGQNGAKCLTLQT--E 11- 8 Query: 119 EYRQEAYHFYENLGFKKVSTGFSYY 143 + ++A YE G+++ TGF +Y Sbjct: 119 HHNRKARSLYEQNGYEE-DTGFVHY 142 A related DNA sequence was identified in S. pyogenes <SEQ ID 5843> which encodes the amino acid sequence <SEQ ID 5844>. Analysis of this protein sequence reveals the following: TABLE-US-05777 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0962(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05778 Identities = 37/126 (29%), Positives = 64/126 (50%), Gaps = 16/126 (12%) Query: 18 PLYQE-----LGYAISLSEIQSILKVILTHSDYGFLIA--EDNGKLLAFVG---YHKLYF 67 P+ QE LGY +SL ++ + ++ + FL +D +LL +V Y LY Sbjct: 11 PMLQEINAKALGYLVSLDLLERQYERLIEDCHHYFLAYADKDTNQLLGYVHAERYETLY- 69 Query: 68 FEKSGTYYRILALVVNEKHRRKGIASQLINHVKQLAKTDGSEVLALNSSLKEYRQEAYHF 12- 7 + +L L V ++R+GI S L+ ++ A+ +G + LNS+ +R+EA+ F Sbjct: 70 ---ASDGLNLLGLAVLPAYQRRGIGSALLRALESQARQEGIAFIRLNSA--SHRKEAHAF 12- 4 Query: 128 YENLGF 133 Y NL + Sbjct: 125 YRNLDY 130 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1878 A DNA sequence (GBSx1986) was identified in S. agalactiae <SEQ ID 5845> which encodes the amino acid sequence <SEQ ID 5846>. Analysis of this protein sequence reveals the following: TABLE-US-05779 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1659(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> RGD motif 28-30 The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05780 >GP: AAF30776 GB: AE002133 conserved hypothetical [Ureaplasma urealyticum] Identities = 106/440 (24%), Positives = 206/440 (46%), Gaps = 65/440 (14%) Query: 13 FAINESEYHQLLEQIRGDAFDKEVSERLEKERLILGEQAKNQLQEVVVE-KDKEIAKLQY 71 - F N+ +Y++L++Q +D LEK+R L E+ KN+ + + KD + K Sbjct: 71 FLANDRDYNELVKQ----RYD------LEKQRDELKEKLKNEGNKAIAHFKDSDEYKNLI 120- Query: 72 KVKQFLIEKDNLLKDNEYQLAEQLNQKDMMLRD--------LENQIDRLRLEHENSLQEA 123- K ++ + + ++ NE +++ ++ L+ L+N I + ++ +N+ + A Sbjct: 121 KAQEKINSLNKTIESNEQSYKKEIENIELKLKSQFDEETKSLKNTIAKQEIKLDNAEKMA 18- 0 Query: 124 LTKVERE-------RDAIQNQLHIQ--------------------EKEKDLALASVKSDY 15- 6 + + +D I + I+ E +K + + ++S Sbjct: 181 IINFKESNEYQKIIKDKIDLDIEIEKLKFAIQAHEDNMKAAKENWESKKIVEIKELESKK 24- 0 Query: 157 EVQLKAANEQVEFYKNFKAQQSTKAVGESLEHYAETEFNKVRHLAFPNAYFEKDNTLSSR 21- 6 + ++ E +E K K+ + K VGE LE + + +F++ + P+ F K N Sbjct: 241 DKEIHKLTESIEQLKREKSS-NVKLVGEELEQWLKNKFDETYSFSCPDMTFTKINEAID- 29- 8 Query: 217 GSKGDFIY------REKDENDLEFL-SIMFEMKNESDDTIKKHKNEDFFKELDKDRREKS 26- 9 G K DF+ +E +D + + S E K E D K KN +K+LD+DR + Sbjct: 299 GKKADFLLEFFDFGKEMSNDDKKLIFSATIEAKTEFFDNQKGTKNSAHYKKLDQDRINQK 35- 8 Query: 270 CEYAVLVTMLEADNDYYNIGIVDVSHKYPKMYVIRPQFFIQLIGILRNAALNTLKYKQEL 32- 9 EYA+LVT LE ++ + ++ ++Y M+ +RPQ+FI L+ ++RN A TLK K Sbjct: 359 SEYAILVTELEPEDHF----VIKKINEYKNMFAVRPQYFIPLVDMIRNFA--TLKAKINS 41- 2 Query: 330 ALMKEQNIDITHFEEDLDIFKNAFAKN-YNSASKNFQKAIDEIDKSIKRMEAV-KAALTT 38- 7 +++ + D EE+LD K N + +K ID+ IK+ E++ ++A Sbjct: 413 QIIRYE--DRAKIEENLDELKKDIVDNTLKYINDKTKKIIDDSKAIIKKAESIEESAEDI 47- 0 Query: 388 SENQLRLANNKLDDVSVKKL 407 +L K+++++++K+ Sbjct: 471 INKKLNTLKKKINELTIRKI 490 A related DNA sequence was identified in S. pyogenes <SEQ ID 5847> which encodes the amino acid sequence <SEQ ID 5848>. Analysis of this protein sequence reveals the following: TABLE-US-05781 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3192(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05782 Identities = 310/445 (69%), Positives = 352/445 (78%), Gaps = 22/445 (4%) Query: 1 MNEIKCPHCGTAFAINESEYHQLLEQIRGDAFDKEVSERLEKERLILGEQAKNQLQEVVV 60 MNEIKCPHC T F INESEY QLLEQ+RG AFD+E+ +RL E +L E+AK+QL EVV Sbjct: 1 MNEIKCPHCHTLFTINESEYSQLLEQVRGQAFDEELKKRLINEIALLEEKAKHQLHEVVA 60 Query: 61 EKDKEIAKLQYKVKQF-----------LIEKDNLL-----------KDNEYQLAEQLNQK 98 +K+ I L +++Q L +KD L+ N +LA QL +K Sbjct: 61 KKETAITSLTNQLEQIEKEQAYLRQEELAKKDQLIASLEAKLDKLASQNALELANQLAEK 120- Query: 99 DMMLRDLENQIDRLRLEHENSLQEALTKVERERDAIQNQLHIQEKEKDLALASVKSDYEV 158- D + L NQ+D+L LE + + Q L +E+ERD I+NQL +Q KE +L+LASV+SDYE Sbjct: 121 DKEVVSLTNQLDKLALEKDATFQSKLATIEKERDGIKNQLALQAKESELSLASVRSDYEA 18- 0 Query: 159 QLKAANEQVEFYKNFKAQQSTKAVGESLEHYAETEFNKVRHLAFPNAYFEKDNTLSSRGS 21- 8 QLKAANEQVEFYKNFKAQQSTKA+GESLE YAETEFNKVR AFPNA F KDN LSSRGS Sbjct: 181 QLKAANEQVEFYKNFKAQQSTKAIGESLELYAETEFNKVRSYAFPNASFVKDNQLSSRGS 24- 0 Query: 219 KGDFIYREKDENDLEFLSIMFEMKNESDDTIKKHKNEDFFKELDKDRREKSCEYAVLVTM 27- 8 KGD+IYRE D N +E LSIMFEMKNE+D T KHKN DFFKELDKDRREK CEYAVLV+M Sbjct: 241 KGDYIYREVDANGVEILSIMFEMKNEADTTKTKHKNSDFFKELDKDRREKDCEYAVLVSM 30- 0 Query: 279 LEADNDYYNTGIVDVSHKYPKMYVIRPQFFIQLIGILRNAALNTLKYKQELALMKEQNID 33- 8 LEADNDYYNTGIVDVSH+Y KMYV+RPQ FIQLIGILRNAALN+L YKQELAL+KEQNID Sbjct: 301 LEADNDYYNTGIVDVSHEYQKMYVVRPQLFIQLIGILRNAALNSLHYKQELALVKEQNID 36- 0 Query: 339 ITHFEEDLDIFKNAFAKNYNSASKNFQKAIDEIDKSIKRMEAVKAALTTSENQLRLANNK 39- 8 ITHFEEDLD FKNAFAKNY SAS NF+KAIDEIDKSIKRME VK LTTSENQLRLANNK Sbjct: 361 ITHFEEDLDQFKNAFAKNYQSASNNFKKAIDEIDKSIKRMEEVKRFLTTSENQLRLANNK 42- 0 Query: 399 LDDVSVKKLTRKNPTMKAKFDALKD 423 L+DVSVKKLTR+NPTM+KF+ALKD Sbjct: 421 LEDVSVKKLTRQNPTMREKFEALKD 445 SEQ ID 5846 (GBS304) was expressed in E. coli as a His-fusion product. The purified protein is shown in FIG. 206, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1879 A DNA sequence (GBSx1987) was identified in S. agalactiae <SEQ ID 5849> which encodes the amino acid sequence <SEQ ID 5850>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following: TABLE-US-05783 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1845(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 5851> which encodes the amino acid sequence <SEQ ID 5852>. Analysis of this protein sequence reveals the following: TABLE-US-05784 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2492(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05785 Identities = 113/180 (62%), Positives = 141/180 (77%) Query: 16 LSELVDCFKGKAVPSKAEAGDIRIINLSDMSPLGIDYHNLRTFQDEQRSLLKYLLQEGDV 75 - L +VDCFKGKAV SK GD+ +INLSDM LGI YH LRTFQ ++R LL+YLL++GDV Sbjct: 18 LGTVVDCFKGKAVSSKVVPGDVGLINLSDMGTLGIQYHQLRTFQMDRRQLLRYLLEDGDV 77 Query: 76 LIASKGTVKKVAIFEEQDYPVVASANITILRPTQHIRGYYLKLFFDSEEGQQALENANKG 135- LIASKGT+KKV +F +Q+ VVAS+NIT+LRP + +RGYY+K F DS GQ L+ A+ G Sbjct: 78 LIASKGTLKKVCVFHKQNRDVVASSNITVLRPQKLLRGYYIKFFLDSPIGQALLDVADHG 137- Query: 136 KAVMNISTKELLNIAIPSIPLFRQDYLIQRYKQGLNDYKRKIARAEQEWERIQNDIRQQL 19- 5 K V+N+STKELL+I IP IPL +QDYLI Y +GL DY RK+ RAEQEWE IQN+I++ L Sbjct: 138 KDVINLSTKELLDIPIPVIPLVKQDYLINHYLRGLTDYHRKLNRAEQEWEYIQNEIQKGL 19- 7 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1880 A DNA sequence (GBSx1988) was identified in S. agalactiae <SEQ ID 5853> which encodes the amino acid sequence <SEQ ID 5854>. Analysis of this protein sequence reveals the following: TABLE-US-05786 Possible site: 15 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.43 Transmembrane 62-78 (55-82) INTEGRAL Likelihood = -2.87 Transmembrane 130-146 (130-150) INTEGRAL Likelihood = -1.28 Transmembrane 37-53 (37-53) ----- Final Results ----- bacterial membrane --- Certainty = 0.3972(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9347> which encodes amino acid sequence <SEQ ID 9348> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05787 >GP: CAA22372 GB: AL034446 putative transmembrane protein [Streptomyces coelicolor A3(2)] Identities = 38/139 (27%), Positives = 64/139 (45%), Gaps = 5/139 (3%) Query: 15 SASVEILCRGWLLPVSATKYSKIVSVSISSIFFGLLHSANNHVSLISIFNLCL-FGLFLS 73 - +A+ E++ RG L + +++ ++ + FGL+H N +L + + G L+ Sbjct: 143 AATEEVVFRGVLFRIIEEHIGTYLALGLTGLVFGLMHLLNEDATLWGALAIAIEAGFMLA 20- 2 Query: 74 LYVILKGNIWGACGIHGAWNCVQGSVFGIEVSGEPMLSNSLVHVKTYGADWISGGKFGVE 133- N+W G+H WN G VF VSG S L+ G ++GG FG E Sbjct: 203 AAYAATRNLWLTIGVHFGWNFAAGGVFSTVVSGNGD-SEGLLDATMSGPKLLTGGDFGPE 26- 1 Query: 134 GSMIT---SIVLIVACYWL 149 GS+ + ++L + WL Sbjct: 262 GSVYSVGFGVLLTLVFLWL 280 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1881 A DNA sequence (GBSx1989) was identified in S. agalactiae <SEQ ID 5855> which encodes the amino acid sequence <SEQ ID 5856>, which is a methylase gene homolog. Analysis of this protein sequence reveals the following: TABLE-US-05788 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2192(Affirmative) < succ> bacterial membrane --- Certainty= 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> RGD motif: 264-266 A related GBS nucleic acid sequence <SEQ ID 9929> which encodes amino acid sequence <SEQ ID 9930> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05789 >GP: BAA87672 GB: AB016260 Hypothetical gene, methylase gene homolog [Agrobacterium tumefaciens] Identities = 358/1238 (28%), Positives = 595/1238 (47%), Gaps = 99/1238 (7%) Query: 1072 KEVARIKGMVDIRNAYQEVIAIQRYYDYDKETFNHLLGKLNRTYDSFVKHYGYLNSAV-- 1- 129 K V I+ ++ IR+A +EV+ Q + L +L + SFV+ +G +N Sbjct: 497 KHVRIIRKLIPIRDAVREVLKAQEL----DRPWKDLQVRLRVAWSSFVRDFGPINHTTVS 55- 2 Query: 1130 -----------------NRNLFDSDDKYSLLASLEDESL--DPSGKSVIYTKSLAFEKAL 1- 170 N F D L+AS+ED L D + I+T E+ + Sbjct: 553 ITEDPESGETRESHRRPNLQPFADDPDCWLVASIEDYDLENDTAKPGAIFT-----ERVI 60- 7 Query: 1171 VRPEKEVKKVHTALDALNSSLADGRGVDFAYMMSIYQVESQMTLIEELGDLIMPDPEKYL 1- 230 P V + +A DAL L + VD ++ + + ++ ELG I DP Sbjct: 608 SPPAPPV--ITSAADALAVVLNERGRVDLDHIAELLHRDPD-DVVAELGSAIFRDP---- 66- 0 Query: 1231 NGELTYVSRQDFLSGDVVTKLEVVDLFVKQDNQDFNWSHYAGLLEAIKPARITLADIDYR 1- 290 + ++ +LSG V KL+V + D ++ L ++P + +DI R Sbjct: 661 -ADGSWQMADAYLSGPVRDKLKVAEAAAALDPV---YNRNVTALAGVQPVDLRPSDITAR 71- 6 Query: 1291 IGSRWIPLAVYGKFAQETFMGKAYELSDQ-EVATVLEVSPIDGVITYQSKFAYTYSNATD 1- 349 +G+ WIP A F +E MG + E+A+ + G + A T TD Sbjct: 717 LGAPWIPAADVVAFVKE-MMGTDIRIHHMPELASWTVEARQLGYLA-----AGTSEWGTD 77- 0 Query: 1350 RSLGVPASRYDSGRKIFENLLNSNQPTITKQVVEGDKKKNVTDVEKTTVLRAKETHLQEL 1- 409 R ++ + LNS P I + +GD ++ V +V T + K +++ Sbjct: 771 RR---------HAGELLSDALNSRVPQIFDTIRDGDSERRVLNVVDTEAAKEKLHKIKDA 82- 1 Query: 1410 FQGFVAKYPEVQQMIEDTYNRLYNRTVSKSYDGSHLTIDGLAQNISLRPHQKNAIQRIVE 1- 469 FQ ++ P+ + YN +N + + G HL + G + L HQK I RI+ Sbjct: 822 FQRWIWSDPDRTDRLARVYNDRFNNIAPRKFSGDHLNLPGASGAFVLYGHQKRGIWRIIS 88- 1 Query: 1470 EKRALLAHEVGSGKTLTMLGAGFKLKELGMVHKPLYVVPSSLTAQEGQEIMKFFPTKKVY 1- 529 LAH VG+GKT+TM + + + LG++ K + VVP AQ +E + +PT ++ Sbjct: 882 SGSTYLAHAVGAGKTMTMAASIMEQRRLGLIAKAMQVVPGHCLAQAAREFLALYPTARIL 94- 1 Query: 1530 VTTKKDFAKAKRKQFVSRIITGDYDAIVIGDSQFEKIPMSREKQVTYINDKLEQLREIKL 1- 589 V + +F+K KR +F+SR T +DAI+I S F I + + I+D+LE + L Sbjct: 942 VADETNFSKDKRARFLSRAATATWDAIIITHSAFRFIGVPAAFESQMIHDELELYETLLL 10- 01 Query: 1590 GSDSDYTV--KEAERSIKGLEHQLEELQKLERDTFIEFENLGIDFLFVDEAHHFKNIRPI 1- 647 + + V K ER +GL+ +LE L +D + +G+D + VDEA F+ + Sbjct: 1002 KVEDEDRVSRKRLERLKEGLQERLEALST-RKDDLLTIAEIGVDQIIVDEAQEFRKLSFA 1- 060 Query: 1648 TGLGNVAGITNTTSKKNVDMEMKVRQVQAEHGDRNVVFATGTPVSNSISELFTMMDYIQP 1- 707 T + + G+ S++ D+ +K R ++ + R +V A+GTP++N++ E+F++ + Sbjct: 1061 TNMSTLKGVDPNGSQRAWDLYVKSRFIETINPGRALVLASGTPITNTLGEMFSVQRLMGH 1- 120 Query: 1708 DVLERYLVSNFDSWVGAFGNIENSMELAPTGDKYQPKKRFKKFVNLPELMRIYKETADI- 1- 766 LE + FD+W FG+ +EL P+G KY+P RF FVN+PEL+ +++ AD+ Sbjct: 1121 AALEERGLHEFDAWASTFGDTTTELELQPSG-KYKPVSRFASFVNVPELIAMFRSFADVV 1- 179 Query: 1767 ---QTSDMLDLP-VPEAKIIAVESELTQAQKYYLEELVKRSDAIKSGS--VDPSRDNMLK 1- 820 + + +P + + V S+ TQA K++ L +R AI+ P D +L Sbjct: 1180 MPADLREYVKVPAISTGRRQIVTSKPTQAFKHHQMVLAERIKAIEERERPPQPGDDILLS 1- 239 Query: 1821 ITGEARKLAIDMRLIDPTYSLSDNQKILQVVDNVERIYRDGAGDK-------------AT 1- 867 + + R AID+RL+D + K+ +V N RI++ AG A Sbjct: 1240 VITDGRHAAIDLRLVDADNDNEPDNKLNNLVSNAFRIWKATAGSVYLRHDSKPFEVPGAA 1- 299 Query: 1868 QMIFSDIGTPK-SKEEGFDVYNELKDLFVDRGIPKEEIAFVHDANTDEKKNSLSRKVNSG 1- 926 QMIFSD+GT K GF Y ++D + G+P EIAF+ D E K L V +G Sbjct: 1300 QMIFSDLGTISVEKTRGFSAYRWIRDELIRLGVPASEIAFMQDFKKSEAKQRLFGDVRAG 1- 359 Query: 1927 EVRILMASTEKGGTGLNVQSRMKAVHYLDVPWRPSDIVQRNGRLIRQGNMHQEVDIYHYI 1- 986 VR L+ S+E GTG+NVQ R+KA+H+LDVPW PS I QR GR++RQGN H EVDI+ Y Sbjct: 1360 RVRFLIGSSETMGTGVNVQLRLKALHHLDVPWLPSQIEQREGRIVRQGNQHDEVDIFAYA 1- 419 Query: 1987 TKGSFDNYLWQTQENKLKYITQIMTSKDPVRSAEDIDE-QTMTASDFKALATGNPYLKLK 2- 045 T+GS D +WQ E K ++I ++ +R EDI E Q + KA+A+G+ L K Sbjct: 1420 TEGSLDATMWQNNERKARFIAAALSGDTSIRRLEDIGEGQANQFAMAKAIASGDQRLMQK 1- 479 Query: 2046 MELENELTVLENQKRAFNRSKDEYRHTISYSEKHLPIMEKRLSQYDKDIAQSLATKSQDE 2- 105 LE ++ LE + A + R + +E+ + + +R+++ +DI + + T +DF Sbjct: 1480 AGLEADIARLERLRAAHIDDQHAVRRQLRDAERDIEVSTRRIAEIGQDITRLVPTTGEDF 1- 539 Query: 2106 VMRFDNQAMDNRAEAGDYLRK-LITYNRSETKEVRTLASFRGFDLKM-TTRGASEPLPET 2- 163 M + R EAG L K ++T + + +AS GF+L+ R + T Sbjct: 1540 TMTVAGKDYSERKEAGRALMKEILTLVQLSPEGEAVIASIGGFELEYHGQRYGKDGYRYT 1- 599 Query: 2164 ISLMIVGDNQYTVALDLK-SDVGTIQRISNAIDHIIDDQEKTQELVKDLKDKLRVAKVEV 2- 222 L G + Y + L + + +G + R+ +A+D ++E+ ++ + D + +L + Sbjct: 1600 TMLKRTGAD-YEIELPVTVTPLGAVSRLEHALDDFDGERERYRQRLGDARRRLASYQSRG 1- 658 Query: 2223 DKVFPKEEDYQLVKAKYDVLAPLVEKEAEIEEIDAALA 2260 + +++ L EK ++ E++ ALA Sbjct: 1659 E------------GSEFAFAGELAEKHRQLAEVETALA 1684 Identities = 99/271 (36%), Positives = 153/271 (55%), Gaps = 10/271 (3%) Query: 607 RDKVETNIVAIRLVKNLEVEHRNASPSEQELLAKYVGWGG--LANEFFD-----DYNPKF 65- 9 +D+ NI AIRL +E R A+ EQE L ++ G+G LAN F ++ + Sbjct: 80 KDRARDNIAAIRLAAEIEASERPATREEQETLIRFTGFGASDLANGVFRRPGELEFRKGW 139- Query: 660 SKEREELKSLVTDKEYSDMKQSSLTAYYTDPSLIRQMWDKLERDGFTGGKILDPSMGTGN 71- 9 + +L+ V + +Y+ + + + A++T ++R +W L+R G+ GG++L+P +GTG Sbjct: 140 DEIGSDLEDAVGETDYASLARCTQYAHFTPEFIVRAIWSGLQRLGWRGGRVLEPGIGTGL 19- 9 Query: 720 FFAAMPKHLREKSELYGVELDTITGAIAKHLHPNSHIEIKGFETVAFNDNSFDLVISNVP 77- 9 F A MP+ LR+ S + GVELD +T I + L P + I F SFDL I N P Sbjct: 200 FPALMPEALRDLSHVTGVELDPVTACIVRLLQPRARILTGDFARTEL-PASFDLAIGNPP 25- 8 Query: 780 FANIRIADNRYDRP--YMIHDYFVKKSLDLLHDGGQVAIISSTGTMDKRTENILQDIRET 83- 7 F++ + +R R +HDYFV +S+DLL G A ++S+GTMDK Q I T Sbjct: 259 FSDRTVRSDRAYRSLGLRLHDYFVARSIDLLKPGAFAAFVTSSGTMDKADSAARQHIATT 31- 8 Query: 838 TEFLGGVRLPDSAFKAIAGTSVTTDMLFFQK 868 + + +RLP+ +F+A AGT V D+LFF+K Sbjct: 319 ADLIAAIRLPEGSFRADAGTDVVVDILFFRK 349 SEQ ID 5856 (GBS327N) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 148 (lane 8-10; MW 140 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 148 (lane 11-13; MW 115 kDa) and in FIG. 182 (lane 8; MW 115 kDa). Purified GBS327N-GST is shown in FIG. 243, lane 5; Purified GBS327N-His is shown in FIG. 235, lane 5. GBS327C was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 148 (lane 14; MW 73 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1882 A DNA sequence (GBSx1990) was identified in S. agalactiae <SEQ ID 5857> which encodes the amino acid sequence <SEQ ID 5858>. Analysis of this protein sequence reveals the following:

TABLE-US-05790 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3656(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1883 A repeated DNA sequence (GBSx1991) was identified in S. agalactiae <SEQ ID 5859> which encodes the amino acid sequence <SEQ ID 5860>. This protein is predicted to be giant membrane protein. Analysis of this protein sequence reveals the following: TABLE-US-05791 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3698(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05792 >GP: AAG19662 GB: AE005054 calcium-binding protein homology; Cbp [Halobacterium sp. NRC-1] Identities = 22/43 (51%), Positives = 29/43 (67%), Gaps = 1/43 (2%) Query: 9 KDSDQDGLTDAQELAL-GTDPQSVDTDGDGQADLEELQSGHSP 50 +D+D DGL+D E+ + GTDP DTDGDG D EL++G P Sbjct: 198 RDTDDDGLSDGVEVRVAGTDPTERDTDGDGVDDAAELRAGSLP 240 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1884 A DNA sequence (GBSx1992) was identified in S. agalactiae <SEQ ID 5861> which encodes the amino acid sequence <SEQ ID 5862>. Analysis of this protein sequence reveals the following: TABLE-US-05793 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.39 Transmembrane 1609-1625 (1609-1625) INTEGRAL Likelihood = -1.81 Transmembrane 30-46 (29-46) ----- Final Results ----- bacterial membrane --- Certainty = 0.1956(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif 1600-1604 The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05794 !GB: X57841 antigen I/II [Streptococcus sobrinus] (v . . . >GP: CAA40973 GB: X57841 antigen I/II [Streptococcus sobrinus] Identities = 419/1436 (29%), Positives = 608/1436 (42%), Gaps = 310/1436 (21%) Query: 23 KSKKYRTLCSVALGTMVTAVVAWGGTVAHADEVTTSV----DTTIQRTE--NPATNLPEA 76 - K K RTL LGT + A A G A A+E +T+ DT + TE NPATNLP+ Sbjct: 23 KVKSGRTLSGALLGTAILASGA--GQKALAEETSTTSTSGGDTAVVGTETGNPATNLPDK 80 Query: 77 QPNP-------------------VSEQTESMASTGQSNGAIAVTVPHDTVT-----QAVE 112- Q NP V T + +S VTV D + + Sbjct: 81 QDNPSSQAETSQAQARQKTGAMSVDVSTSELDEAAKSPQEAGVTVSQDATVNKGTVEPSD 140- Query: 113 EAKAEGVSTVEDSPMDLGNTRSAVET---------------NQQIS-------------K 14- 4 EA + +D + + A E NQ+I+ K Sbjct: 141 EANQKEPEIKDDYSKQAADIQKATEDYKASVAANQAETDRINQEIAAKKAQYEQDLAANK 20- 0 Query: 145 AD-------------------ADTQKQVETINEVTK----TYKADKATYESNKARIEQEN 18- 1 A+ A QK + I + Y A K Y+ AR++ N Sbjct: 201 AEVERSLMRMRKPRPIYEAKLAQNQKDLAAIQQANSDSQAAYAAAKEAYDKEWARVQAAN 26- 0 Query: 182 KELSQAYEGANQTGKETNAWVDTKVNDLKARYADADVTVKEQ-------VVSSGNGTSVL 23- 4 +AYE A N + ++ ++ R A AD K +GN + Sbjct: 261 AAAKKAYEEALAANTAKNDQIKAEIEAIQQRSAKADYEAKLAQYEKDLAAAQAGNAANEA 32- 0 Query: 235 DY----TNYGKAVETIQSTNEQAVADY----LTKKTKADDIVAKNQAIQKENEA------ 28- 0 DY Y + + +Q+ N A Y K I A+N+AIQ+ +A Sbjct: 321 DYQAKKAAYEQELARVQAANAAAKQAYEQALAANSAKNAQITAENEAIQQNAQAKADYEA 38- 0 Query: 281 -------GLANAKADNEAIERRNQAGQAAVDAEN---RAGQAAVDQANQEKQQLVSDRAA 33- 0 LA A++ N A E Q AA + E +A AA QA +++ Q + + A Sbjct: 381 KLAQYQKDLAAAQSGNAANEADYQEKLAAYEKELARVQAANAAAKQAYEQQVQQANAKNA 44- 0 Query: 331 EIEAITKRNKEKEAAARKENEAIDAYNTKEMERYQRDLAEIS------------------ 37- 2 EI + +E+ A A+ + E + +E+ +Y++DLAE Sbjct: 441 EITEANRAIRERNAKAKTDYELKLSKYQEELAQYKKDLAEYPAKLQAYADEQAAIKAALA 50- 0 Query: 373 -----KGEEGYISEALAQALNLNNGEPQAQHGAITRN----------------------- 40- 4 K E+G +SE AQ+L + + EP AQ +T Sbjct: 501 ELEKHKNEDGNLSEPSAQSL-VYDLEPNAQVALVTDGKLLKASALDEAFSHDEKNYNNHL 55- 9 Query: 405 --PDQI----------ISTGDALLGGYSRILDSTGF-----------FVYDMFKTGETLS 44- 1 PD + +++ L G + D G+ F + K G++ + Sbjct: 560 LQPDNLNVTYLEQADDVASSVELFGNFG---DKAGWTTTVSNGAEVKFASVLLKRGQSAT 61- 6 Query: 442 FNYQNLQHARFDGKKISRVTYDITNLVSPAG-----TNAVKLVVPNDPTEGFIAYRNDGN 49- 6 Y NL+++ ++GKKIS+V Y T V P T V L + DPT G A G Sbjct: 617 ATYTNLKNSYYNGKKISKVVYKYT--VDPDSKFQNPTGNVWLFIFTDPTLGVFASAYTGQ 67- 4 Query: 497 GDWRTD---KMEFRVVAKYYLEDGSQVTFSKEKPGVFTHSSLNHNDIGLEYVKDSSGKFV 55- 3 + T K EF +Y EDG+ + F + + +SLN +E KD SG FV Sbjct: 675 NEKDTSIFIKNEF----TFYDEDGNPIDFDN---ALLSVASLNREHNSIEMAKDYSGTFV 72- 7 Query: 554 PINGSTVQVTN--------------EGLARSLGSNRASDLNLPEEWDTTSSRYAYKGAIV 59- 9 I+GS++ N EG + RAS+ WD+ + ++ GA Sbjct: 728 KISGSSIGEKNGMIYATDTLNFKKGEGGSLHTMYTRASEPG--SGWDSADAPNSWYGAGA 78- 5 Query: 600 STVTSGNTY--------TVTFGQGDMPQNVGL--------SYWFALN------------- 63- 0 ++ N Y T +MPQ G + W++LN Sbjct: 786 VRMSGPNNYITLGATSATNVLSLAEMPQVPGKDNTAGKKPNIWYSLNGKIRAVNVPKVTK 84- 5 Query: 631 --TLPVARTVTPYSPKPHVTVEL-----EPIPEPITVTPDIYTPKTFTPEKPVTFT---- 67- 9 P P P V EL EP EP TP P PEKPV T Sbjct: 846 EKPTPPVEPTKPDEPTYEVEKELVDLPVEPKYEP-EPTPPSKNPDQSIPEKPVEPTYEVE 90- 4 Query: 680 ----PKPLDEVVQPSLTLTKVT-------LPVKPIPKELPTPP------------QVPTV 71- 6 P P++ + T + T PV+P + LPTPP VPTV Sbjct: 905 KELEPAPVEPSYEKEPTPPQSTPDQEEPEKPVEPSYQSLPTPPVEPVYETVPGPVSVPTV 96- 4 Query: 717 HYHAYRLTTTSEIMKEVVNSDQANLHEKTVAKDSTVIYPLTVDALSPNRAQTTSLIFEDY 77- 6 YH Y+L + KE+ N D ++ + VAK STV + L L R +TTS + D Sbjct: 965 RYHYYKLAVQPGVTKEIKNQDDLDIDKTLVAKQSTVKFQLKTADLPAGRPETTSFVLMDP 10- 24 Query: 777 LPAGYLFDKETTQKENGNYVLSFDETKNFVTLTAKENLLQEVNKDLTQVYQLTAPKLYGS 83- 6 LP+GY + E T+ + + S+D + VT TA L +N+DLT+ P + G Sbjct: 1025 LPSGYQLNLEATKVASPGFEASYDAMTHTVTFTATAETLAALNQDLTKAVATIYPTVVGQ 1- 084 Query: 837 VQNDGATYSNSYKLLLNKGTTNAYTVTSNVVTVRTPG-----DGETTTLITPDKNNENAD 89- 1 V NDGATY+N++ L++N +AY + SN+V V TPG D + ITP K N+N + Sbjct: 1085 VLNDGATYTNNFTLMVN----DAYGIKSNIVRVTTPGKPNDPDNPSNNYITPHKVNKNEN 1- 140 Query: 892 GVLINDTVVALGTTNHYRLTWDLDQYKGDRSAKETIARGFFFVDDYPEEVLDVVENGTAI 95- 1 GV+I+ V GTTN+Y LTWDLDQYKGD+SAKE I +GFF+VDDYPEE LD+ + + Sbjct: 1141 GVVIDGKSVLAGTTNYYELTWDLDQYKGDKSAKEIIQKGFFYVDDYPEEALDLRTDLIKL 1- 200 Query: 952 TTLDGQKVSGITVKNYASLNEAPKDLQDKLARAKITPTGAFQVFMPDDNQAFYDQYVQTG 10- 11 T +G+ V+G++V +YASL AP +QD L +A I P GAFQVF DD QAFYD YV TG Sbjct: 1201 TDANGKAVTGVSVADYASLEAAPAAVQDMLKKANIIPKGAFQVFTADDPQAFYDAYVVTG 1- 260 Query: 1012 TSLALLTKMTVKDSLYGQTKTYTNKAYQVDFGNGYETKEVTNTLVSPEPKKQ-NLNKDKV 1- 070 T L ++T MTVK + +Y N+AYQ+DFGNGYE+ V N + P+K L D Sbjct: 1261 TDLTIVTPMTVKAEMGKTGGSYENRAYQIDFGNGYESNLVVNNVPKINPEKDVTLTMDPA 1- 320 Query: 1071 D---INGKPMLVGTQNHYTLSWDLDQYRGIKADNSQIAQGFYFVDDYPE-----EALLPD 1- 122 D ++G+ + + +Y L + I AD+++ + F DDY + Sbjct: 1321 DSTNVDGQTIALNQVFNYRLIGGI-----IPADHAEELFEYSFSDDYDQTGDQYTGQYKA 1- 375 Query: 1123 EAAIQFVTSDGKTV-SGITVKSY--SQLLEAPKTLQAAFSKQKIQPKGAFQVFMPE 1175 A + DG + +G + SY +Q+ EA + F + ++ F E Sbjct: 1376 FAKVDLTLKDGTIIKAGTDLTSYTEAQVDEANGQIVVTFKEDFLRSVSVDSAFQAE 1431 Identities = 209/442 (47%), Positives = 280/442 (63%), Gaps = 27/442 (6%) Query: 1198 TVLETMLNSGKSY-ENVAYQVDFGQAYETNTVTNFVPK------------VTPHKSNTNQ 1- 244 TV+ +LN G +Y N V+ ++N V P +TPHK N N+ Sbjct: 1080 TVVGQVLNDGATYTNNFTLMVNDAYGIKSNIVRVTTPGKPNDPDNPSNNYITPHKVNKNE 1- 139 Query: 1245 EGISIDGKTVLPNTVNYYKIVLDYSQYKDMVVTDDVLAKGFYMVDDYPEEALTLNPDGIQ 1- 304 G+ IDGK+VL T NYY++ D QYK +++ KGF+ VDDYPEEAL L D I+ Sbjct: 1140 NGVVIDGKSVLAGTTNYYELTWDLDQYKGDKSAKEIIQKGFFYVDDYPEEALDLRTDLIK 1- 199 Query: 1305 VLDKDGNRVSGISVSTYASLSEAPKVVQDAMAKRQFTPKGAIQVLSSDDPKVFYDTYVKT 1- 364 + D +G V+G+SV+ YASL AP VQD + K PKGA QV ++DDP+ FTD YV T Sbjct: 1200 LTDANGKAVTGVSVADYASLEAAPAAVQDMLKKANIIPKGAFQVFTADDPQAFYDAYVVT 1- 259 Query: 1365 GQTLVVTLPMTVKNELTKTGGQYENTAYQIDFGLAYVTETVVNNVPKLDPQKDVVIDLSH 1- 424 G L + PMTVK E+ KTGG YEN AYQIDFG Y + VVNNVPK++P+KDV + + Sbjct: 1260 GTDLTIVTPMTVKAEMGKTGGSYENRAYQIDFGNGYESNLVVNNVPKINPEKDVTLTMPP 1- 319 Query: 1425 KDA-SLDGKEVALHQTFNYRLVGAMIPSNRATDLFEYGFEDNYDEKHDEYNGVYRSYLMT 1- 483 D+ ++DG+ +AL+Q FNYRL+G +IP++ A +LFEY F D+YD+ D+Y G Y+++ Sbjct: 1320 ADSTNVDGQTIALNQVFNYRLIGGIIPADHAEELFEYSFSDDYDQTGDQYTGQYKAFAKV 1- 379 Query: 1484 DVILKDGSVLKEGTEVTKYTLQQVDTENGLVSISFDKSFLETVSDDSAFQADVYLQMKRI 1- 543 D+ LKDG+++K GT++T YT QVD NG + ++F + FL +VS DSAFQA+VYLQMKRI Sbjct: 1380 DLTLKDGTIIKAGTDLTSYTEAQVDEANGQIVVTFKEDFLRSVSVDSAFQAEVYLQMKRI 1- 439 Query: 1544 AAGQVENTYLHTVNGYVISSNTVVTHTPQPEEPSPNQP--------TPPQPPIETIEPPV 1- 595 A G NTY++TVNG SSNTV T TP+P++PSP P P Q PP Sbjct: 1440 AVGTFANTYVNTVNGITYSSNTVRTSTPEPKQPSPVDPKTTTTVVFQPRQGKAYQPAPPA 1- 499 Query: 1596 PASILPNTGEQES----LLGLI 1613 A LP TG+ + LLGL+ Sbjct: 1500 GAQ-LPATGDSSNAYLPLLGLV 1520 Identities = 100/210 (47%), Positives = 137/210 (64%), Gaps = 4/210 (1%) Query: 1060 PKKQNLNKDKVDINGKPMLVGTQNHYTLSWDLDQYRGIKADNSQIAQGFYFVDDYPEEAL 1- 119 P K N N++ V I+GK +L GT N+Y L+WDLDQY+G K+ I +GF++VDDYPEEAL Sbjct: 1132 PHKVNKNENGVVIDGKSVLAGTTNYYELTWDLDQYKGDKSAKEIIQKGFFYVDDYPEEAL 1- 191 Query: 1120 LPDEAAIQFVTSDGKTVSGITVKSYSQLLEAPKTLQAAFSKQKIQPKGAFQVFMPEDPQA 1- 179 I+ ++GK V+G++V Y+ L AP +Q K I PKGAFQVF +DPQA Sbjct: 1192 DLRTDLIKLTDANGKAVTGVSVADYASLEAAPAAVQDMLKKANIIPKGAFQVFTADDPQA 1- 251 Query: 1180 FFESYVTKGENITIVTPMTVLETMLNSGKSYENVAYQVDFGQAYETNTVTNFVPKVTPHK 1- 239 F+++YV G ++TIVTPMTV M +G SYEN AYQ+DFG YE+N V N VPK+ P K Sbjct: 1252 FYDAYVVTGTDLTIVTPMTVKAEMGKTGGSYENRAYQIDFGNGYESNLVVNNVPKINPEK 1- 311 Query: 1240 SNT----NQEGISIDGKTVLPNTVNYYKIV 1265 T + ++DG+T+ N V Y+++ Sbjct: 1312 DVTLTMDPADSTNVDGQTIALNQVFNYRLI 1341 There is also homology to SEQ ID 598. SEQ ID 5862 (GBS76) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 2; MW 17.4 kDa). The GBS76-His fusion product was purified (FIG. 196, lane 8) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 294), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1885 A DNA sequence (GBSx1993) was identified in S. agalactiae <SEQ ID 5863> which encodes the amino acid sequence <SEQ ID 5864>. This protein is predicted to be abortive infection bacteriophage resistance protein (abiEi). Analysis of this protein sequence reveals the following: TABLE-US-05795 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2765(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9931> which encodes amino acid sequence <SEQ ID 9932> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-05796 >GP: AAB52382 GB: U36837 AbiEi [Lactococcus lactis] Identities = 51/206 (24%), Positives = 90/206 (42%), Gaps = 23/206 (11%) Query: 17 KNNGIVTNKDCKALGIPTIYLTRLEKEGIIFRVEKGIFLTQNGDYDEYYFFQYRFPKAIF 76 - K G + K + GI YL + + + V+KG+++ + D + FQ ++ KA+ Sbjct: 76 KYKGNIIRKIVRDEGISDYYLRKFVLKYNLTEVDKGVYIFPHKKKDSLFIFQQKYSKAVI 135- Query: 77 SYISALYLQQFTDEIPQYFDVTVPRGYRF----------------------NTPPANLNI 114- S+ ++LYLQ D IPQ ++VP Y N N+ I Sbjct: 136 SHETSLYLQDVIDYIPQKIQMSVPEKYNISRIQEPHENRLTSYNYVDINSNNIMDKNIPI 19- 5 Query: 115 HFV-SKEYSELGMTTVPTPMGNNVRVYDFERIICDFVIHREKIDSELFVKTLQSYGNYPK 17- 3 + V +K S + TV + +G +RV R I D + K + E+ + ++ Y Sbjct: 196 NLVRNKSISPTQIETVNSFLGLPLRVTSIARSIVDVLKPSHKAEEEVKEQAIKYYLERFP 25- 5 Query: 174 KNLAKLYEYATKMNTLEKVKQTLEVL 199 N+ +L A N L++++ L +L Sbjct: 256 DNIVRLKRIAKTQNVLKELEYYLILL 281 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1886 A DNA sequence (GBSx1994) was identified in S. agalactiae <SEQ ID 5865> which encodes the amino acid sequence <SEQ ID 5866>. This protein is predicted to be abortive infection bacteriophage resistance protein (abiEii). Analysis of this protein sequence reveals the following: TABLE-US-05797 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.12 Transmembrane 260-276 (259-277) ----- Final Results ----- bacterial membrane --- Certainty = 0.1447(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05798 >GP: AAB52383 GB: U36837 AbiEii [Lactococcus lactis] Identities = 76/276 (27%), Positives = 135/276 (48%), Gaps = 19/276 (6%) Query: 14 SKNTGLTFNSVMTYYFLEVILKKLSQSSYSNHYIFKGGFLLSNVIGVESRSTVDIDFLFH 73 - ++N + + Y E L +LS S Y ++ KGGFL+ + R+T D+D Sbjct: 12 TRNDDIGIENYRIRYATERFLTRLSASQYKEKFVLKGGFLIGVTYNLSQRTTKDLDTALI 71 Query: 74 QITLSEETVKQQLKEIL-ADSEEGISFVIQSITTIKESDDYGGYRATISCQLE--NIKQV 130- +++++ + EI D E+ + F ++ +T+ ++ Y GYRA + N + Sbjct: 72 DFKSDAQSIERVITEICNIDLEDQVLFKLKELTSSQDMRIYPGYRAKLKMMFPDGNTRID 131- Query: 131 IHLDIATGDVVTPQPITYDYKAIFDE-----DNFPIIAYTIETILAEKLQTIYSRNFLNS 18- 5 LDI GD +TP+ IF+E ++AY ETI AEKL+TI +R +N+ Sbjct: 132 FDLDIGVGDRITPEAKKIKIPLIFNEVKGVEKQIEVLAYPKETIQAEKLETILTRGKVNT 19- 1 Query: 186 RSKDFYDVYIL--SKLKKKDIDFNQLKNACQRTFSYRE-TELDFEKIIE-----LLERFK 23- 7 R KD+YD ++L + I F A + T+ +R T+ E++ E L E + Sbjct: 192 RMKDYYDFHLLLTDQENSNSISFYY---AFKNTWEFRNPTQFIDEELFEDWLFILDEILE 24- 8 Query: 238 SDPTQNQQWQNYSKKYSYTKGISLANVLDEMISLIT 273 S + + W NY K +Y K +++ +++ E+ ++ Sbjct: 249 SKELKEKYWPNYIKDRNYAKHLNMDDIISEIKEFVS 284 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1887 A DNA sequence (GBSx1995) was identified in S. agalactiae <SEQ ID 5867> which encodes the amino acid sequence <SEQ ID 5868>. Analysis of this protein sequence reveals the following: TABLE-US-05799 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1137(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1888 A DNA sequence (GBSx1996) was identified in S. agalactiae <SEQ ID 5869> which encodes the amino acid sequence <SEQ ID 5870>. Analysis of this protein sequence reveals the following: TABLE-US-05800 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2782(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainyl = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1889 A DNA sequence (GBSx1997) was identified in S. agalactiae <SEQ ID 5871> which encodes the amino acid sequence <SEQ ID 5872>. Analysis of this protein sequence reveals the following: TABLE-US-05801 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.14 Transmembrane 310-326 (301-334) ----- Final Results ----- bacterial membrane --- Certainty = 0.5055(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05802 >GP: AAG38044 GB: AF295925 Orf28 [Streptococcus pneumonia] Identities = 272/344 (79%), Positives = 307/344 (89%) Query: 568 VYVNPAFYFPKVIQVQTTILPTIGQFGGDEFERAKAIYDYLKSKGATNQAIAAILGNWSV 62- 7 +YVNP FYFPKVIQ+QTTILP IGQFGGDEFERAK IY++LKS+GA+ QAIAAILGNWSV Sbjct: 1 MYVNPQFYFPKVIQLQTTILPAIGQFGGDEFERAKHIYEFLKSQGASPQAIAAILGNWSV 60 Query: 628 ESSINPKRAEGDYLSPPVGATDSSWDDEGWLTLNGPTIYNGRYPNILKRGLGLGQWTDTA 68- 7 ESSINPKRAEGDYL+PPVG WDDE WL + GP IY+G YPNIL RGLGLGQWTDTA Sbjct: 61 ESSINPKRAEGDYLTPPVGVPIPPWDDESWLAIGGPAIYSGAYPNILHRGLGLGQWTDTA 12- 0 Query: 688 DGSRRHTLLLEYAKGKHQKWYDLGLQLDFMLYGDSPYYTNWLKDFFKNSGSPASLAQLFL 74- 7 DGS RHT LL YA+ +++KWYDL LQLDFML+GDSPYY +WLKDFFKN+GS A+LAQLFL Sbjct: 121 DGSTRHTALLNYARTQNKKWYDLDLQLDFMLHGDSPYYQSWKKDFFKNTGSAANLAQLFL 18- 0 Query: 748 IYWEGNSGDKLLERQTRASEWYYQIEKGFSQPNGGTAQSDPKALEAVREDLFENSIPGGG 80- 7 YWEGNSGDKLLERQTRA+EWYYQIEKGFSQ NGG A+SDP++LE VR DL+++S+PGGG Sbjct: 181 TYWEGNSGDKLLERQTRATEWYYQIEKGFSQTNGGQAKSDPQSLEGVRGDLYDHSVPGGG 24- 0 Query: 808 DGMGYAYGQCTWGVAARINQLGLKLKGKNGEKIPIISTMGNGQDWVRTAASLGGETGTSP 86- 7 DGM YAYGQCTWGVAAR+NQLGLKLKG+NGEKI II+TMGNGQDWV T++SLGGETG++P Sbjct: 241 DGMAYAYGQCTWGVAARMNQLGLKLKGRNGEKISIINTMGNGQDWVATSSSLGGETGSTP 30- 0 Query: 868 QEGAILSFAGGGHGTPTEYGHVAFVEKVYPDGSFLISETNYNGN 911 +GAI+SF GG HGTP YGHVAFVEKVT DGSFL+SETNY GN Sbjct: 301 RAGAIVSFVGGTHGTPASYGHVAFVEKVYDDGSFLVSETNYGGN 344 SEQ ID 5872 (GBS74d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 121 (lane 3 & 4; MW 95.5 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 121 (lane 5-7; MW 70.5 kDa) and in FIG. 179 (lane 9; MW 70.5 kDa). GBS74d-His was purified as shown in FIG. 233, lane 7-8. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1890 A DNA sequence (GBSx1998) was identified in S. agalactiae <SEQ ID 5873> which encodes the amino acid sequence <SEQ ID 5874>. This protein is predicted to be TrsE-like protein. Analysis of this protein sequence reveals the following: TABLE-US-05803 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5526(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05804 >GP: AAG38042 GB: AF295925 Orf26 [Streptococcus pneumoniae] Identities = 618/782 (79%), Positives = 712/782 (91%), Gaps = 1/782 (0%) Query: 1 MKKLKHSMKSK-TSSNDKKQKTKTQKQEISPSTVNTLAYQGLFQNGLMQVSPSYFSQTYL 59 MK+ +++K + TS++KK++ K +K+E+ PST NTL+YQ L+QNGLMQV YFSQ+YL Sbjct: 3 MKRKSNTLKKQQTSTTNKKEEVKDKKEEVLPSTANTLSYQALYQNGLMQVKEDYFSQSYL 62 Query: 60 LGDVNYQTVGLDDKGAIVEKYSDLINSLDDKTNFQLTIFNQKVNLEKFRKSILYPLQEDG 11- 9 LGDVNYQTVGL+DKGAI+EKYSDLI SLDD+TNFQLTIFN+++NLEKFR S+LY +EDG Sbjct: 63 LGDVNYQTVGLEDKGAIIEKYSDLIKSLDDQTNFQLTIFNKRLNLEKFRSHVLYEEKEDG 12- 2 Query: 120 FDTYRDELNRMMDANLEAGENNFSAVKFLSFGKSDQTPKLAFRSLSQIGEYFKSGFSEID 17- 9 +D+YR ELNRMM+ NL++GENNFSAVK +SFG+ D PK A+RSLSQIGEYFKSGFSEID Sbjct: 123 YDSYRKELNRMMNQNLDSGENNFSAVKLISFGRKDSNPKQAYRSLSQIGEYFKSGFSEID 18- 2 Query: 180 VSLGLLGGEERVNVLADMLRGENHLPFSYKDLTLSGQSTKHFIAPTYLSFKHKNHIELDD 23- 9 L GEERVN+LADMLRGE+HLPFSY+DLT SGQ+T+HFIAP L FK+KN+++++D Sbjct: 183 ARFESLAGEERVNLLADMLRGEHHLPFSYRDLTRSGQTTRHFIAPNLLDFKNKNYLQIND 24- 2 Query: 240 RLLQIVYVRDYGMELGDKFIRDLMQSDLEVMISLHAKGSTKSETMTKLRTKKTLMESQKI 29- 9 RLLQIVYVRDYGMELGD+FIRDLMQ DLE+++SLHA+ STKS+ M KLRTKKTLMESQKI Sbjct: 243 RLLQIVYVRDYGMELGDQFIRDLMQGDLELIVSLHAQSSTKSDAMKKLRTKKTLMESQKI 30- 2 Query: 300 GEQQKMARTGIYLEKVGHVLENNIDEAEALLQTMTQTGDKLFDTVFLIGVLADTEDQLKQ 35- 9 GEQQK+ARTGIYLEKVGHVLE+NIDEAE LL+TMT+TGDKLF TVFLIGV E++LKQ Sbjct: 303 GEQQKLARTGIYLEKVGHVLESNIDEAEELLKTMTETGDKLFQTVFLIGVFGQDEEELKQ 36- 2 Query: 360 SLDIIKQVAGSNDMIIDNLTYMQEAAFNSLLPFGKNYLEGVSRSLLTSNIAVNAPWTSVD 41- 9 +LD ++QVAGSND++ID L YMQEAAFNSLLPFG ++LEGVSRSLLTSNIAVN+PWTSVD Sbjct: 363 ALDTVQQVAGSNDLMIDKLPYMQEAAFNSLLPFGCDGLEGVSRSLLTSNIAVNSPWTSVD 42- 2 Query: 420 IHDKGGKFYGINQISSNIISIDRGKLNTPSGLILGTSGAGKGMATKHEIISTKLKEADSD 47- 9 + D+ GK+YGINQISSNII+IDR LNTPSGLILGTSGAGKGMATKHEII+TK+KE+ + Sbjct: 423 LQDRSGKYYGINQISSNIITIDRSLLNTPSGLILGTSGAGKGMATKHEIITTKIKESGEN 48- 2 Query: 480 TEIIIVDPENEYSIIGQAFGGESIDIAPDSTTFLNVLELSDENMDEDPVKVKSEFLLSWI 53- 9 TEIIIVDPE EYS+IG+ FGGE IDIAPDS T+LNVL+LS+ENMDEDPVKVKSEFLLS+I Sbjct: 483 TEIIIVDPEAEYSVIGRTFGGEMIDIAPDSETYLNVLDLSEENMDEDPVKVKSEFLLSFI 54- 2 Query: 543 GKLLDRKMDGREKSLIDRVTRLTYKHFDTPSLVEWVFVLSQQPEQEAKDLALDMELYVEG 59- 9 GKLLDRKMDGREKS+IDRVTRLTY+ F PSL EWVFVLSQQPE+EA++LALDMELYVEG Sbjct: 543 GKLLDRKMDGREKSIIDRVTRLTYQSFKEPSLEEWVFVLSQQPEEEAQNLALDMELYVEG 60- 2 Query: 600 SLDIFSHRTNIKTDSHFLIYNVKKLGDELKQIALMVIFDQIWNRVVKNQKLGKKTWIYFD 65- 9 SLDIFSH+TNI+T S+FLIYNVKKLGDELKQIALMV+FDQIWNRVV+NQKLGKKTWIYFD Sbjct: 603 SLDIFSHKTNIQTGSNFLIYNVKKLGDELKQIALMVVFDQIWNRVVRNQKLGKKTWIYFD 66- 2 Query: 660 EMQLLLLDKYASDFFFKLWSRVRKYGAIPTGITQNVETLLLDANGRRIIANSEFMILLKQ 71- 9 E++LLLLDKY SDFFFKLWSRVRKYGA PTGITQNVETLLLD NGRRIIANSEFMILLKQ Sbjct: 663 EIELLLLDKYPSDFFFKLWSRVRKYGASPTGITQNVETLLLDPNGRRIIANSEFMILLKQ 72- 2 Query: 720 AKSDREELVHMLGLSKELEKYLVNPEKGAGLIKAGSTVVPFKNKIPQHTKLFDIMSTDPE 77- 9 AK+DREELV +LGLSKELEKYLVNPEKGAGLIKAGS VVPFKNKIPQ ++LFDIM +DP+ Sbjct: 723 AKNDREELVQLLGLSKELEKYLVNPEKGAGLIKAGSVVVPFKNKIPQGSQLFDIMRSDPD 78- 2 Query: 780 KM 781 KM Sbjct: 783 KM 784 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8925> and protein <SEQ ID 8926> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05805 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -26.26 GvH: Signal Score (-7.5): -3.87 Possible site: 55 >>> Seems to have no N-terminal signal sequence ALOM program count: 0 value: 6.26 threshold: 0.0 PERIPHERAL Likelihood = 6.26 335 modified ALOM score: -1.75 *** Reasoning Step: 3 ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5526(Affirmitive) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) The protein has homology with the following sequences in the databases: ##STR00132## A related GBS gene <SEQ ID 8927> and protein <SEQ ID 8928> were also identified. Analysis of this protein sequence reveals the following: This protein might be involved in vancomycin research The protein has homology with the following sequences in the databases: TABLE-US-05806 >GP|8100663|gb|AAF72347.1|AF192329_8|AF192329 TrsE-like protein {Enterococcus faecalis} Score = 427 bits (1086), Expect = e-118 Identities = 257/785 (32%), Positives = 431/785 (54%), Gaps = 28/785 (3%) Query: 9 DKKQKTKTQKQEIS-----------PSTVN-TLAYQGLFQNGLMQVSPSYFSQTYLLGDV 56 +K + T+ Q++EI++++++++++++P T ++ Y+ ++ +G+ +VSP FS+ D+ Sbjct: 11 EKTKLTRAQRKEIDAVIRKYKGDGRPHTAQQSIPYEVMYPDGVCRVSPGVFSKCIEFADI 70 Query: 57 NYQTVGLDDKGAIVEKYSDLINSLDDKTNFQLTIFNQKVNLEKFRKSILYPLQEDGFDTY 11- 6 +YQ D + AI EK DL N +D + Q + N+KV+ ++ KS Q D FD Sbjct: 71 SYQLAQPDTQTAIFEKLCDLYNYVDASIHIQFSFLNRKVDPVQYAKSFEIAPQGDDFDDI 13- 0 Query: 117 RDELNRMMDANLEAGENNFSAVKFLSFGKSDQTPKLAFRSLSQIGEYFKSGFSEIDVSLG 17- 6 R E ++ L G N K+L+F ++ K A L +IG F + Sbjct: 131 RAEYTGILQKQLANGNNGMVKTKYLTFTIEAESVKAARARLKRIGFDLLGYFKSMGAVAH 19- 0 Query: 177 LLGGEERVNVLADMLRGENHL-PFSYKDLTLSGQSTKHFIAPTYLSFKHKNHIELDDRLL 23- 5 ++ G ER+N+L + + + F +K L++SG STK FIAP+ L F + + + Sbjct: 191 VMDGWERLNLLHGVYHPDGEIFNFDWKWLAPSGLSTKDFIAPSSLCFGNAKTFGMGGKYG 25- 0 Query: 236 QIVYVRDYGMELGDKFIRDLMQSDLEVMISLHAKGSTKSETMTKLRTKKTLMESQKIGEQ 29- 5 + +++ EL D + D + ++ V+++LH + +++ + ++ K T +++ KI EQ Sbjct: 251 AVSFLQILSPELSDMMLADFLNTESGVLVNLHVQAIEQTKAIKTIKRKITDLDAMKIAEQ 31- 0 Query: 296 QKMARTGIYLEKVGHVLENNIDEAEALLQTMTQTGDKLFDTVFLIGVLADTEDQLKQSLD 35- 5 +K R+G ++ + L ++A+ LL + ++LF FL+ +ADT+ +L + Sbjct: 311 KKAVRSGYDMDILPSDLATYGEDAKKLLTKLQTRNERLFQLTFLVLNVADTKQKLNNDVF 37- 0 Query: 356 IIKQVAGSNDMIIDNLTYMQEAAFNSLLPFGKNYLEGVSRSLLTSNIAVNAPWTSVDIHD 41- 5 VA ++ + L Y QE S LP G N ++ + RSL TS++AV P+ + ++ Sbjct: 371 QAAGVAQKHNCPLVRLDYQQEQGLASSLPLGVNQIK-IQRSLTTSSVAVFVPFVTQELFQ 42- 9 Query: 416 KGGK-FYGINQISSNIISIDRGKLNTPSGLILGTSGAGKGMATKHEIISTKLKEADSDTE 47- 4 G +YGIN S N+I +DR + P+ L LGT G+GK M+ K EI+S L D + Sbjct: 430 GGAAMYYGINAKSRNMIMLDRKQARCPNALKLGTPGSGKSMSCKSEIVSVFLTTPD---D 48- 6 Query: 475 IIIVDPENEYSIIGQAFGGESIDIAPDSTTFLNVLELS-DENMDEDPVKVKSEFLLSWIG 53- 3 I I DPE EY + + G+ I ++P S F+N L+++ + + D++P+ +KS+F+LS+ Sbjct: 487 IFISDPEAEYYPLVKRLHGQVIRLSPTSKDFVNPLDINLNYSEDDNPLALKSDFVLSFCE 54- 6 Query: 534 KLLDRK--MDGREKSLIDRVTRLTYKHF-------DTPSLVEWVFVLSQQPEQEAKDLAL 58- 4 ++ K ++ EK++IDR R+ Y+ + + P L + L Q EA +A Sbjct: 547 LVMGGKNGLEAIEKTVIDRAVRVIYRPYLADPRPENMPILSDLHKALLDQHVPEADRVAQ 60- 6 Query: 585 DMELYVEGSLDIFSHRTNIKTDSHFLIYNVKKLGDELKQIALMVIFDQIWNRVVKNQKLG 64- 4 ++LYV GSL++F+HRTN+ + + +++K+LG +LK++ ++++ DQIW RV N+ G Sbjct: 607 ALDLYVSGSLNVFNHRTNVDIGNRLVSFDIKELGKQLKKLGMLIVQDQIWGRVTANRSQG 66- 6 Query: 645 KKTWIYFDEMQLLLLDKYASDFFFKLWSRVRKYGAIPTGITQNVETLLLDANGRRIIANS 70- 4 K TW + DE++LLL ++ + + ++W R RK+G IPTG TQNV+ LL I+ NS Sbjct: 667 KATWYFADEFHLLLKEEQTAAYSAEIWKRFRKWGGIPTGATQNVKDLLSSPEIENILENS 72- 6 Query: 705 EFMILLKQAKSDREELVHMLGLSKELEKYLVNPEKGAGLIKAGSTVVPFKNKIPQHTKLF 76- 4 +F+ LL QA DR+ L L LS E +KY+ N E G GL+ + V+PF N IP +T+L+ Sbjct: 727 DFITLLNQASGDRKILAERLNLSTEQQKYIDNSEPGEGLLIFENVVLPFTNPIPHNTQLY 78- 6 Query: 765 DIMST 769 IM+T Sbjct: 787 KIMTT 791 SEQ ID 8926 (GBS75) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 11; MW 89.8 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 20 (lane 6; MW 114.7 kDa). GBS75-GST was purified as shown in FIG. 197, lane 8. GBS329 was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 77 (lane 8; MW 89 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 174 (lane 2; MW 114 kDa). GBS329-GST was purified as shown in FIG. 220, lanes 9 & 10. EXAMPLE 1891 A DNA sequence (GBSx1999) was identified in S. agalactiae <SEQ ID 5875> which encodes the amino acid sequence <SEQ ID 5876>. Analysis of this protein sequence reveals the following: TABLE-US-05807 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2442(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1892 A DNA sequence (GBSx2000) was identified in S. agalactiae <SEQ ID 5877> which encodes the amino acid sequence <SEQ ID 5878>. This protein is predicted to be DNA-directed RNA polymerase ii largest subunit. Analysis of this protein sequence reveals the following: TABLE-US-05808 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4393(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1893 A DNA sequence (GBSx2001) was identified in S. agalactiae <SEQ ID 5879> which encodes the amino acid sequence <SEQ ID 5880>. Analysis of this protein sequence reveals the following:

TABLE-US-05809 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.92 Transmembrane 256-272 ( 250-277) INTEGRAL Likelihood = -8.28 Transmembrane 216-232 ( 213-244) INTEGRAL Likelihood = -8.12 Transmembrane 151-167 ( 148-191) INTEGRAL Likelihood = -7.27 Transmembrane 57-73 ( 54-80) INTEGRAL Likelihood = -6.74 Transmembrane 93-109 ( 88-111) INTEGRAL Likelihood = -3.50 Transmembrane 172-188 ( 168-191) INTEGRAL Likelihood = -2.76 Transmembrane 113-129 ( 110-130) ----- Final Results ----- bacterial membrane --- Certainty = 0.4970(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05810 >GP: AAG38039 GB: AF295925 Orf23 [Streptococcus pneumoniae] Identities = 71/86 (82%), Positives = 83/86 (95%) Query: 37 VKSLADFNPTVWSYMTAITKGIMQPLGVAILAVVLVLEFSKMAKKIANSGGAMTFEAIAP 96 +KSL+ +NPTVW+YM++ITK +MQPLGVAIL+VVL+LEFSKMAKKIANSGGAMTFEA+AP Sbjct: 1 MKSLSSYNPTVWTYMSSITKSVMQPLGVAILSVVLILEFSKMAKKIANSGGMATFEALAP 60 Query: 97 MIVSYIMVAVVITNTTVIVEAIIAIA 122 M++SYIMVAVVITNTTVIVEAII IA Sbjct: 61 MLISYIMVAVVITNTTVIVEAIIGIA 86 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1894 A DNA sequence (GBSx2002) was identified in S. agalactiae <SEQ ID 5881> which encodes the amino acid sequence <SEQ ID 5882>. Analysis of this protein sequence reveals the following: TABLE-US-05811 Possible site: 25 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.54 Transmembrane 32-48 ( 25-52) INTEGRAL Likelihood = -4.09 Transmembrane 63-79 ( 62-80) ----- Final Results ----- bacterial membrane --- Certainty = 0.4015(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9933> which encodes amino acid sequence <SEQ ID 9934> was also identified. A related GBS nucleic acid sequence <SEQ ID 10777> which encodes amino acid sequence <SEQ ID 10778> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1895 A DNA sequence (GBSx2003) was identified in S. agalactiae <SEQ ID 5883> which encodes the amino acid sequence <SEQ ID 5884>. This protein is predicted to be TrsK-like protein (traK). Analysis of this protein sequence reveals the following: TABLE-US-05812 Possible site: 34 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.38 Transmembrane 66-82 ( 62-85) ----- Final Results ----- bacterial membrane --- Certainty = 0.3951(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05813 >GP: AAG38037 GB: AF295925 Orf21 [Streptococcus pneumoniae] Identities = 343/457 (75%), Positives = 385/457 (84%), Gaps = 24/457 (5%) Query: 142 LIVIGGSGAGKTFRFVKPNLIQLNCSNIVVDPKDHLAEKTGKLFLENGYQVKVLDLVNMT 20- 1 + VIGGSG+GKTFRFVKPNLIQ+N SNIVVDPKDHLAEKTGKLFLE+GYQVKVLDLVNM Sbjct: 1 MAVIGGSGSGKTFRFVKPNLIQMNSSNIVVDPKDHLAEKTGKLFLEHGYQVKVLDLVNMK 60 Query: 202 NSDGFNPFRYVETENDLNRMLTVYFNNTKGNGSRSDPFWDEASMTLVRAIASYLVDFYNP 26- 1 NSDGFNPFRY+ETENDLNRML VYFNNTKG+GSRSDPFWDEASMTLVRA+ASYLVDFYNP Sbjct: 61 NSDGFNPFRYIETENDLNRMLAVYFNNTKGSGSRSDPFWDEASMTLVRALASYLVDFYNP 12- 0 Query: 121 PGS---------------------SKQEQEARRKRGRYPAFSEIGKLIKLLSKGDNQDKS 30- 0 P + K+E E R+KRGR F E + + + KS Sbjct: 121 PKTREQLIEESRLSQKEYQNLLKRQKKEVEERKKRGRLSKFCESQNSLNTYPRVKTR-KS 17- 9 Query: 301 ILEVLFEDYAKKYGHENFTMRNWADFQNYKDKTLDSVIAVTTAKFALFNIQSVIDLTQRD 36- 0 +LE+LFE+YAKKYG ENFTMRNWADFQNYKDKTLDSVIAVTTAKFALFNIQSV+DLT+RD Sbjct: 180 VLEILFENYAKKYGTENFTMRNWADFQNYKDKTLDSVIAVTTAKFALFNIQSVMDLTKRD 23- 9 Query: 361 TMDLKTWGTQKTMVYLVIPDNDTTFRFLSAL-FFSTVFSTLTRQADV-DFKGQLPIHVRS 41- 8 T+D+KTWG +K+MVYLVIPDND+TFRFLSAL FF+ F T + + + + +LP+HVR Sbjct: 240 TLDMKTWGQEKSMVYLVIPDNDSTFRFLSALLFFNPYFQTPNKTSQILMLRVRLPLHVRV 29- 9 Query: 419 YLDEFANVGEIPDFAEQTSTVRSRNMSLVPILQNIAQLQGLYKEKEAWKTILGNCDSLLY 47- 8 YLDEFAN+GEIPDFAEQTSTVRSRNMSLVPILQNIAQLQGLYKEKEAWKTILGNCDSL+Y Sbjct: 300 YLDEFANIGEIPDFAEQTSTVRSRNMSLVPILQNIAQLQGLYKEKEAWKTILGNCDSLVY 35- 9 Query: 479 LGGNDEETFKFMSGLLGKQTVDVRSTSRSFGQTGSSSTSHQKIARDLMTADEVGTMKRDE 53- 8 LGGNDE+TFKFMSGLLGKQT+DVR+TSRSFGQTGS S SHQKIARDLMT DEVG MKR E Sbjct: 360 LGGNDEDTFKFMSGLLGKQTIDVRNTSRSFGQTGSGSLSHQKIARDLMTPDEVGNMKRHE 41- 9 Query: 539 CLVRIAGVPVFRTKKYFPLKHKHWKLLADKETDDRWW 575 CLVRIA +PVF++KKY KH +WK LA++EDT+R W Sbjct: 420 VLCRIANMPVFKSKKYNSTKHPNWKYLANQETDERRW 456 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8929> and protein <SEQ ID 8930> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05814 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: 5.53 GvH: Signal Score (-7.5): -0.78 Possible site: 34 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 1 value: -7.38 threshold: 0.0 INTEGRAL Likelihood = -7.38 Transmembrane 66-82 ( 62-85) PERIPHERAL Likelihood = 1.75 338 modified ALOM score: 1.98 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3951(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00133## SEQ ID 5884 (GBS11d) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 151 (lane 6; MW 61 kDa) and in FIG. 182 (lane 10; MW 61 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 12 (lane 5; MW 91.5 kDa). EXAMPLE 1896 A DNA sequence (GBSx2004) was identified in S. agalactiae <SEQ ID 5885> which encodes the amino acid sequence <SEQ ID 5886>. Analysis of this protein sequence reveals the following: TABLE-US-05815 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4192(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9935> which encodes amino acid sequence <SEQ ID 9936> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1897 A DNA sequence (GBSx2005) was identified in S. agalactiae <SEQ ID 5887> which encodes the amino acid sequence <SEQ ID 5888>. Analysis of this protein sequence reveals the following: TABLE-US-05816 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3391(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1898 A DNA sequence (GBSx2006) was identified in S. agalactiae <SEQ ID 5889> which encodes the amino acid sequence <SEQ ID 5890>. Analysis of this protein sequence reveals the following: TABLE-US-05817 Possible site: 45 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.03 Transmembrane 68-84 ( 64-90) INTEGRAL Likelihood = -7.06 Transmembrane 33-49 ( 27-50) INTEGRAL Likelihood = -5.73 Transmembrane 106-122 ( 105-123) INTEGRAL Likelihood = -4.46 Transmembrane 6-22 ( 3-24) INTEGRAL Likelihood = -2.13 Transmembrane 154-170 ( 154-170) INTEGRAL Likelihood = -0.53 Transmembrane 180-196 ( 180-196) ----- Final Results ----- bacterial membrane --- Certainty = 0.5012(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9937> which encodes amino acid sequence <SEQ ID 9938> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05818 >GP: BAA11325 GB: D78257 ORF8 [Enterococcus faecalis] Identities = 35/102 (34%), Positives = 57/102 (55%), Gaps = 4/102 (3%) Query: 90 TRNQAVLVQVGKQVPPIIFLLFL-VNASILEEIVYRQLLWEKLTF--PFEQIGVTSFLFV 14- 6 T N + L+++ V P++ +L L + A I+EEIV+R + L I ++SFLF Sbjct: 7 TANDSTLIKLFSGVSPVLVVLLLGIAAPIMEEIVFRGGIIGYLVENNALLAILISSFLFG 66 Query: 147 LSHGPNQLGSWLIYSCLGLTLAVVRLKT-DCMTAIALHLLWN 187 + HGP S+ +Y +G+ L+V KT D +I++H L N Sbjct: 67 IIHGPTNFISFGMYFFMGIILSVSYYKTKDLRVSISIHFLNN 108 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8931> and protein <SEQ ID 8932> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05819 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 9.32 GvH: Signal Score (-7.5): -5.41 Possible site: 45 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 6 value: -10.03 threshold: 0.0 INTEGRAL Likelihood = -10.03 Transmembrane 68-84 ( 64-90) INTEGRAL Likelihood = -7.06 Transmembrane 33-49 ( 27-50) INTEGRAL Likelihood = -5.73 Transmembrane 106-122 ( 105-123) INTEGRAL Likelihood = -4.46 Transmembrane 6-22 ( 3-24) INTEGRAL Likelihood = -2.13 Transmembrane 154-170 ( 154-170) INTEGRAL Likelihood = -0.53 Transmembrane 180-196 ( 180-196) PERIPHERAL Likelihood = 1.38 131 modified ALON score: 2.51 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5012(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00134## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1899 A DNA sequence (GBSx2007) was identified in S. agalactiae <SEQ ID 5891> which encodes the amino acid sequence <SEQ ID 5892>. Analysis of this protein sequence reveals the following: TABLE-US-05820 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2490(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9939> which encodes amino acid sequence <SEQ ID 9940> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1900 A DNA sequence (GBSx2008) was identified in S. agalactiae <SEQ ID 5893> which encodes the amino acid sequence <SEQ ID 5894>. Analysis of this protein sequence reveals the following: TABLE-US-05821 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5298(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05822 >GP: AAC98423 GB: L29323 unknown [Streptococcus pneumoniae] Identities = 68/126 (53%), Positives = 88/126 (68%) Query: 1 MNLLHKKSILDCTELEERIHQAETNQLLQKILSLPNFDCDFEVTFEDDYHKEMNDPLFYE 60 M L+K+SILDC ELE +H AE QL ++I +PN+ C+FEVTF DDYHK+ N PLFYE Sbjct: 1 MKALNKESILDCDELETELHDAEIKQLDEQIFLMPNYPCEFEVTFLDDYHKKHNYPLFYE 60 Query: 61 SNLHQISDFMETRDIKNGVDTLLTKDNHLAFRAFGENYSARGKEGILTTLVTVKCFGEGR 12- 0 S L I +F+E++DIKNG D + +L F +G+ Y A GKEGILTT VTVK F E + Sbjct: 61 SYLQNIMEFLESQDIKNGADAFVDDHQNLVFVLYGQGYRAEGKEGILTTQVTVKAFDEDK 12- 0 Query: 121 MPIDMS 126 PI+ + Sbjct: 121 KPINFA 126 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1901 A DNA sequence (GBSx2009) was identified in S. agalactiae <SEQ ID 5895> which encodes the amino acid sequence <SEQ ID 5896>. This protein is predicted to be methyl transferase. Analysis of this protein sequence reveals the following: TABLE-US-05823 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1209(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05824 >GP: AAC98421 GB: L29323 methyl transferase [Streptococcus pneumoniae] Identities = 323/449 (71%), Positives 389/449 (85%), Gaps = 3/449 (0%) Query: 1 MKFLDLFAGIGGFRLGMESQGHKCLGFCEIDKFARTSYKAMFNTEGEIEYHDIKEVTDHD 60 M+F+DLF+GIGGFRLGMES GH+C+GFCEIDKFAR SYK++F TEGEIE+HDI++V+D + Sbjct: 1 MRFIDLFSGIGGFRLGMESVGHECIGFCEIDKFARESYKSIFQTEGEIEFHDIRDVSDDE 60 Query: 61 FRQFRGQVDIICGGFPCQAFSLAFRRLGFEDTRGTLFFEIARAAKQIQPRFLFLENVKGL 12- 0 F++ RG+VD+ICGGFPCQAFS+AGRRLGFEDTRGTLFFEIARAAKQIQPRFLFLENVKGL Sbjct: 61 FKKLRGKVDVICGGFPCQAFSIAGRRLGFEDTRGTLFFEIARAAKQIQPRFLFLENVKGL 12- 0 Query: 121 LNHDEGRTFATILSTLDELGYDVEWQVLNSKDFQVPQNRERVFIIGHSRRYRSRFIFPLR 18- 0 LNHD+GRTF TIL+TLDELG+DVEWQ+LNSKDF VPQNRERVFIIGHSR+ +R FP R Sbjct: 121 LNHDKGRTFTTILTTLDELGFDVEWQMLNSKDFGVPQNRERVFIIGHSRKRGTRLGFPFR 18- 0 Query: 181 RED---SPAHLERLGNINPSKHGLNGEVYLTSGLAPTLTRGKGEGAKIAIPVLTPDRLEK 23- 7 RE +P L+ LGN+NPSK G++G+VY + GLAPTL RGKGEG KIAIP +TPDRL+K Sbjct: 181 REGQATNPETLKILGNLNPSKSGMSGKVYYSEGLAPTLVRGKGEGFKIAIPCMTPDRLDK 24- 0 Query: 238 RQHGRRFKDNQDPMFTLTSQDKHGVVVAGNLPTSFDQTGRVFDISGLSPTLTTMQGGDKV 29- 7 RQ+GRRFKDNQ+PMFTL +QD+HG+VV G+LPTSF +TGRV+ GLSPTLTTMQGGDK+ Sbjct: 241 RQNGRRFKDNQEPMFTLNTQDRHGIVVVGDLPTSFKETGRVYGSEGLSPTLTTMQGGDKI 30- 0 Query: 298 PKILLREELPFLKIKEATKTGYAKATLGDSVNLAYPDSTKRRGRVGKGISNTLTTSDNMG 35- 7 PKIL+ E + FLK++EATK GYA+A +GDS+NL P S RRGRVGKGI+NTLTTS MG Sbjct: 301 PKILIPEPIQFLKVREATKKGYQAQEIGDSINLERPSSQHRRGRVGKGIANTLTTSGQMG 36- 0 Query: 358 VVVAALEYRQDKWYEVTGIVLEGKLYRLRIRRLTPRECFRLQGFPDWAYERAESVSSKSQ 41- 7 VVVA+ E + Y+V G++++G+ YRLRIRR+TP+ECFRLQGFPDWA+E A VSS SQ Sbjct: 361 VVVASYEGEDKQVYQVAGVLIDGQFYRLRIRRITPKECFRLQGFPDWAFEAARKVSSNSQ 42- 0 Query: 418 LYKQAGNSVTVTVIEAIAREFRRTEEEEK 446 LYKQAGNSVTV VI AIA++ + EE+++ Sbjct: 421 LYKQAGNSVTVPVIAAIAKKLKEVEEKDE 449 A related DNA sequence was identified in S. pyogenes <SEQ ID 2435> which encodes the amino acid sequence <SEQ ID 2436>. Analysis of this protein sequence reveals the following: TABLE-US-05825 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1725(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05826 Identities = 60/75 (80%), Positives = 69/75 (92%) Query: 1 MKFLDLFAGIGGFRLGMESQGHKCLGFCEIDKFARTSYKAMFNTEGEIEYHDIKEVTDHD 60 - MKFLDLFAGIGGFRLG+ +Q H+C+GFCEIDKFAR SYKA++ TEGEIE+HDI++VTD D Sbjct: 4 MKFLDLFAGIGGFRLGLINQCHECIGFCEIDKFARQSYKAIYETEGEIEFHDIRQVTDQD 63 Query: 61 FRQFRGQVDIICGGF 75 FRQ RGQVDIICGGF Sbjct: 64 FRQLRGQVDIICGGF 78 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1902 A DNA sequence (GBSx2010) was identified in S. agalactiae <SEQ ID 5897> which encodes the amino acid sequence <SEQ ID 5898>. Analysis of this protein sequence reveals the following: TABLE-US-05827 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.71 Transmembrane 8-24 ( 3-30) ----- Final Results ----- bacterial membrane --- Certainty = 0.4885(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9941> which encodes amino acid sequence <SEQ ID 9942> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 5899> which encodes the amino acid sequence <SEQ ID 5900>. Analysis of this protein sequence reveals the following:

TABLE-US-05828 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.81 Transmembrane 20-36 (19-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.1723(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05829 Identities = 16/33 (48%), Positives = 26/33 (78%) Query: 1 MNKMIWWILGGIYLISIIILIVEIIRAPEMDDH 33 ++KM WW+L G++ + I LI+E+I APEM+D+ Sbjct: 12 VSKMFWWLLLGVWGLRTIWLIIEVITAPEMEDY 44 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1903 A DNA sequence (GBSx2011) was identified in S. agalactiae <SEQ ID 5901> which encodes the amino acid sequence <SEQ ID 5902>. This protein is predicted to be ifn-response binding factor 1 (irebf-1). Analysis of this protein sequence reveals the following: TABLE-US-05830 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4771(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05831 >GP: AAD41248 GB: AF106927 unknown [Streptococcus suis] Identities = 258/272 (94%), Positives = 266/272 (96%) Query: 1 MKRITANQYQTSERYYKLPKILFESERYKDMKLEVKVAYAVLKDRLELSLSKGWIDEDGA 60 MKRITANQYQTSERYYKLPKILFESERYKDMKLEVKVAYAVLKDRLELSLSKGWIDEDGA Sbjct: 1 MKRITANQYQTSERYYKLPKILFESERYKDMKLEVKVAYAVLKDRLELSLSKGWIDEDGA 60 Query: 61 IYLIYSNSNLMALLGCSKSKLLSIKKTLREYGLIDEVQQSSSERGRMANKIYLGELEHEP 120- IYLIYSNSNLMALLGCSKSKLLSIKKTLREYGLIDEVQQSSSE+GRMANKIYLGELEHE Sbjct: 61 IYLIYSNSNLMALLGCSKSKLLSIKKTLREYGLIDEVQQSSSEKGRMANKIYLGELEHET 120- Query: 121 TPVLHTDGASVKKTLGESQRKTGPVLYSAPSETEGSETKYSETEGSDLVMKDEEERQLVD 18- 0 TPVLHTDGASVKKTLG SQRKTGPVL SAPSETEGSETKYSET+GSD +++DEEERQ VD Sbjct: 121 TPVLHTDGASVKKTLGGSQRKTGPVLNSAPSETEGSETKYSETKGSDFLIEDEEERQQVD 18- 0 Query: 181 EKKEENFTSKVDGVTKYDRDYIWGLVHDQLRQTGLSQSASDYAMIYFSDRYQYALEQMRF 24- 0 EK+EENFTSKVDGVT+YDRDYIWGLVHDQLRQTGLSQSASDYAMIYFSDRYQYALE MRF Sbjct: 181 EKQEENFTSKVDGVTRYDRDYIWGLVHDQLRQTGLSQSASDYAMIYFSDRYQYALEHMRF 24- 0 Query: 241 ARSAEVIAEYVFNGVLSEWTKQLRRQEVKGGE 272 ARSAEVIAEYVFNGVLSEWTKQLRRQEVKGG+ Sbjct: 241 ARSAEVIAEYVFNGVLSEWTKQLRRQEVKGGD 272 A related DNA sequence was identified in S. pyogenes <SEQ ID 5903> which encodes the amino acid sequence <SEQ ID 5904>. Analysis of this protein sequence reveals the following: TABLE-US-05832 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5248(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05833 Identities = 84/122 (68%), Positives = 99/122 (80%), Gaps = 2/122 (1%) Query: 145 VLYSAPSETEGSETKYSETEGSDLVMKDEEERQLVD--EKKEENFTSKVDGVTKYDRDYI 20- 2 VL SAPSETE SET+ SET+ S+LV++DEEER+ +K E +FT +VD VTKYD+DYI Sbjct: 1 VLNSAPSETEKSETEGSETKESNLVIEDEEERKECTSVKKTEGHFTRQVDQVTKYDKDYI 60 Query: 203 WGLVHDQLRQTGLSQSASDYAMIYFSDRYQYALEQMRFARSAEVIAEYVFNGVLSEWTKQ 26- 2 W LVH QLR+ GLSQ+ASD M YF +RY YALE +RFAR+AE IAEYVFNGVLSEWTKQ Sbjct: 61 WSLVHSQLREGGLSQAASDLVMSYFEERYAYALEHIRFARTAEAIAEYVFNGVLSEWTKQ 120- Query: 263 LR 264 LR Sbjct: 121 LR 122 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1904 A DNA sequence (GBSx2012) was identified in S. agalactiae <SEQ ID 5905> which encodes the amino acid sequence <SEQ ID 5906>. Analysis of this protein sequence reveals the following: TABLE-US-05834 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4191(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9375> which encodes amino acid sequence <SEQ ID 9376> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1905 A DNA sequence (GBSx2013) was identified in S. agalactiae <SEQ ID 5907> which encodes the amino acid sequence <SEQ ID 5908>. Analysis of this protein sequence reveals the following: TABLE-US-05835 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3723(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1906 A DNA sequence (GBSx2014) was identified in S. agalactiae <SEQ ID 5909> which encodes the amino acid sequence <SEQ ID 5910>. Analysis of this protein sequence reveals the following: TABLE-US-05836 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3053(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1907 A DNA sequence (GBSx2015) was identified in S. agalactiae <SEQ ID 5911> which encodes the amino acid sequence <SEQ ID 5912>. This protein is predicted to be 50S ribosomal protein L7/112 (rplL). Analysis of this protein sequence reveals the following: TABLE-US-05837 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1034(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9943> which encodes amino acid sequence <SEQ ID 9944> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05838 >GP: CAB11881 GB: Z99104 ribosomal protein L12 (BL9) [Bacillus subtilis] Identities = 83/123 (67%), Positives = 95/123 (76%), Gaps = 2/123 (1%) Query: 6 MALNIENIIAEIKEATILELNDLVKAIEEEFGVTAAAPVAAA--AAGGEAAAAKDSFDVE 63 MALNIE IIA +KEAT+LELNDLVKAIEEEFGVTAAAPVA A AA G AA + FD+ Sbjct: 1 MALNIEEIIASVKEATVLELNDLVKAIEEEFGVTAAAPVAVAGGAAAGGAAEEQSEFDLI 60 Query: 64 LTAAGDKKVGVIKVVREITGEGLKEAKAIVDNAPSVIKEGASEAEANEIKEKLEAAGASV 123- L AG +K+ VIKVVREITG GLKEAK +VDN P +KEG ++ EA E+K KLE GASV Sbjct: 61 LAGAGSQKIKVIKVVREITGLGLKEAKELVDNTPRPLKEGIAKEEAEELKAKLEEVGASV 120- Query: 124 TLK 126 +K Sbjct: 121 EVK 123 A related DNA sequence was identified in S. pyogenes <SEQ ID 5913> which encodes the amino acid sequence <SEQ ID 5914>. Analysis of this protein sequence reveals the following: TABLE-US-05839 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1164(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05840 Identities = 104/126 (82%), Positives = 113/126 (89%) Query: 1 MEEITMALNIENIIAEIKEATILELNDLVKAIEEEFGVTAAAPVAAAAAGGEAAAAKDSF 60 +EEITMALNIENIIAEIKEA+ILELNDLVKAIEEEFGVTAAAPVAAAAAGG AAKDSF Sbjct: 1 LEEITMALNIENIIAEIKEASILELNDLVKAIEEEFGVTAAAPVAAAAAGGAEEAAKDSF 60 Query: 61 DVELTAAGDKKVGVIKVVREITGEGLKEAKAIVDNAPSVIKEGASEAEANEIKEKLEAAG 120- DVELT+AGDKKVGVIK VREITG GLKEAK +VD AP+ +KEG + AEA EIK KLE AG Sbjct: 61 DVELTSAGDKKVGVIKAVREITGLGLKEAKGLVDGAPANVKEGVAAAEAEEIKAKLEEAG 120- Query: 121 ASVTLK 126 A++TLK Sbjct: 121 ATITLK 126 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1908 A DNA sequence (GBSx2017) was identified in S. agalactiae <SEQ ID 5915> which encodes the amino acid sequence <SEQ ID 5916>. This protein is predicted to be ribosomal protein L10 (rplJ). Analysis of this protein sequence reveals the following: TABLE-US-05841 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1251(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05842 >GP: CAB11880 GB: Z99104 ribosomal protein L10 (BL5) [Bacillus subtilis] Identities = 96/164 (58%), Positives = 125/164 (75%), Gaps = 1/164 (0%) Query: 14 MSEAIIAKKAEQVELIAEKMKAAASIVVVDSRGLTVEQDTNLRRSLRESDVEFKVIKNSI 73 - MS AI KK VE IA K+K + S ++VD RGL V + T LR+ LRE++VE KV KN++ Sbjct: 1 MSSAIETKKVV-VEEIASKLKESKSTIIVDYRGLNVSEVTELRKQLREANVESKVYKNTM 59 Query: 74 LTRAAEKAGLEDLKELFVGPSAVAESNEDVIAPAKVISDFAKDAEALEIKGGSVDGKFTS 133- RA E+A L L + GP+A+AFS EDV+APAKV++DFAK+ EALEIK G ++GK ++ Sbjct: 60 TRRAVEQAELNGLNDFLTGPNAIAFSTEDVVAPAKVLNDFAKNHEALEIKAGVIEGKVST 119- Query: 134 VEEINALAKLPNKEGMLSMLLSVLQAPVRNVAYAVKAVAEKDEE 177 VEE+ ALA+LP +EG+LSMLLSVL+APVRN+A A KAVAE+ EE Sbjct: 120 VEEVKALAELPPREGLLSMLLSVLKAPVRNLALAAKAVAEQKEE 163 A related DNA sequence was identified in S. pyogenes <SEQ ID 5917> which encodes the amino acid sequence <SEQ ID 5918>. Analysis of this protein sequence reveals the following: TABLE-US-05843 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.47 Transmembrane 7-23 (5-24) ----- Final Results ----- bacterial membrane --- Certainty = 0.3187(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05844 Identities = 149/176 (84%), Positives = 162/176 (91%) Query: 4 SQKIKTEVKLMSEAIIAKKAEQVELIAEKMKAAASIVVVDSRGLTVEQDTNLRRSLRESD 63 S KIKTEVKLMSEAIIAKKAEQVELIAEKMKAAASIV+VDSRGLTV+QDT LRRSLRES Sbjct: 23 SPKIKTEVKLMSEAIIAKKAEQVELIAEKMKAAASIVIVDSRGLTVDQDTVLRRSLRESG 82 Query: 64 VEFKVIKNSILTRAAEKAGLEDLKELFVGPSAVAFSNEDVIAPAKVISDFAKDAEALEIK 123- VEFKVIKNSILTRAAEKAGL++LK++FVGPSAVAFSNEDVIAPAKVI+DF K A+ALEIK Sbjct: 83 VEFKVIKNSILTRAAEKAGLDELKDVFVGPSAVAFSNEDVIAPAKVINDFTKTADALEIK 142- Query: 124 GGSVDGKFTSVEEINALAKLPNKEGMLSMLLSVLQAPVRNVAYAVKAVAEKDEEVA 179 GG+++G +S EEI ALA LPN+EGMLSMLLSVLQAPVRNVAYAVKAVAE E A Sbjct: 143 GGAIEGAVSSKEEIQALATLPNREGMLSMLLSVLQAPVRNVAYAVKAVAENKEGAA 198 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1909 A DNA sequence (GBSx2018) was identified in S. agalactiae <SEQ ID 5919> which encodes the amino acid sequence <SEQ ID 5920>. Analysis of this protein sequence reveals the following: TABLE-US-05845 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.22 Transmembrane 125-141 (106-143) INTEGRAL Likelihood = -1.91 Transmembrane 108-124 (106-124) ----- Final Results ----- bacterial membrane --- Certainty = 0.3888(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10931> which encodes amino acid sequence <SEQ ID 10932> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1910 A DNA sequence (GBSx2019) was identified in S. agalactiae <SEQ ID 5921> which encodes the amino acid sequence <SEQ ID 5922>. This protein is predicted to be Clp-like ATP-dependent protease binding subunit (clpC). Analysis of this protein sequence reveals the following: TABLE-US-05846 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3483(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05847 >GP: AAA68910 GB: L34677 Clp-like ATP-dependent protease binding subunit [Bos taurus] Identities = 437/589 (74%), Positives = 514/589 (87%), Gaps = 5/589 (0%) Query: 10 DPFGN-MDDIFNSLMGNMGGYNSENKRYLINGREVTPEEFSQYRQTGKLPGQELNNQNTP 68 - DPF N MDD+FN LMG M G NSEN+RYLINGREVTPEE++ +RQTGKLPG Q Sbjct: 2 DPFNNDMDDLFNQLMGGMNGVNSENRRYLINGREVTPEEYAAFRQTGKLPGVTDPTQ-AK 60 Query: 69 TNQVSADSVLTKLGTNLTDQARQHLLDPVIGRNKEIQETAEILARRTKNNPVLVGDAGVG 128- T Q DS+L KLG NLT +A++ LDPVIGRNKEIQETAEIL+RRTKNNPVLVGDAGVG Sbjct: 61 TKQPQPDSMLAKLGRNLTQEAKEGKLDPVIGRNKEIQETAEILSRRTKNNPVLVGDAGVG 120- Query: 129 KTAVIEGLAQAIINGDVPAAIKNKEIISIDISSLEAGTQYRGSFEENIQNIIKEVKETGN 18- 8 KTAV+EGLAQAI+ GDVPAAIKNK+IISIDISSLEAGTQYRGSFEEN+Q +I EVK+ GN Sbjct: 121 KTAVVEGLAQAIVAGDVPAAIKNKQIISIDISSLEAGTQYRGSFEENMQKLIDEVKKDGN 18- 0 Query: 189 IILFFDEIHQILGAGSTGGDSGSKGLADILKPALSRGELTVIGATTQDEYRNTILKNAAL 24- 8 +ILFFDEIHQI+GAG+ G SGSKG+ADILKPALSRGE+T+IGATTQDEYRNTILK+AAL Sbjct: 181 VILFFDEIHQIIGAGNAGDASGSKGMADILKPALSRGEVTLIGATTQDEYRNTILKDAAL 24- 0 Query: 249 ARRFNEVKVNAPSAQDTFNILMGIRNLYEQHHNVVLPDSVLKAAVDLSIQYIPQRSLPDK 30- 8 +RRFN+V VNAPS +DTF IL G+R LYE+HHNV LPD VLKAA+D S+QYIPQRSLPDK Sbjct: 241 SRRFNQVTVNAPSKEDTFKILQGLRKLYEKHHNVSLPDEVLKAAIDYSVQYIPQRSLPDK 30- 0 Query: 309 AIDLIDMTAAHLAAQHPVTDLKSLEKEIAEQRDKQEKAVNTEDFEEALKVKTRIEELQNQ 36- 8 AIDLID+TAAHLA++HPV D K++E+EI + KQ++AV ED++ A + K ++ +LQ+Q Sbjct: 301 AIDLIDVTAAHLASKHPVKDAKTIEEEIKKTEAKQQEAVEKEDYQAAQEAKDQVAKLQDQ 36- 0 Query: 369 IDNHTEGQKVTATINDIAMSIERLTGVPVSNMGASDIERLKELGNRLKGKVIGQNDAVEA 42- 8 + +H+E ++V AT +D+A ++ER+TG+PVS MGASDIERLK L RL+GKVIGQ +AVEA Sbjct: 361 LKDHSESERVVATPSDVAAAVERMTGIPVSKMGASDIERLKGLATRLEGKVIGQQEAVEA 42- 0 Query: 429 VARAIRRNRAGFDDGNRPIGSFLFVGPTGVGKTELAKQLAFDMFGSKDAIVRLDMSEYND 48- 8 V+RAIRRNRAGFD+GNRPIGSFLFVGPTGVGKTELAKQLA DMFGS + I+RLDMSEY D Sbjct: 421 VSRAIRRNRAGFDEGNRPIGSFLFVGPTGVGKTELAKQLALDMFGSTNDIIRLDMSEYTD 48- 0 Query: 489 RTAVSKLIGATAGYVGYDDNSNTLTERIRRNPYSIVLLDEIEKADPQVITLLLQVLDDGR 54- 8 RTAVSKLIG TAGYVGYDDNSNTLTE++RR+PYSIVLLDEIEKA+PQVITLLLQVLDDGR Sbjct: 481 RTAVSKLIGTTAGYVGYDDNSNTLTEKVRRHPYSIVLLDEIEKANPQVITLLLQVLDDGR 54- 0 Query: 549 LTDGQGNTINFKNTVIIATSNAGFGNEAFTGDSDKDLKIMERISPYERP 597 LTDGQGNT++FKNT+IIATSNAGF ++A G+ D K+M+++ PYFRP Sbjct: 541 LTDGQGNTVDFKNTIIIATSNAGFSSDAVAGE---DAKLMDKLQPYFRP 586 A related DNA sequence was identified in S. pyogenes <SEQ ID 5923> which encodes the amino acid sequence <SEQ ID 5924>. Analysis of this protein sequence reveals the following: TABLE-US-05848 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2718(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05849 Identities = 551/697 (79%), Positives = 616/697 (88%), Gaps = 3/697 (0%) Query: 5 NFYNRDPFGNMDDIFNSLMGNMGGYNSENKRYLINGREVTPEEFSQYRQTGKLPGQELNN 64 +F +DPF NMDDIFN LM NMGGY SEN RYL+NGRE+TPEEF YRQTG+LP Sbjct: 3 HFSGKDPFVNMDDIFNQLMANMGGYRSENPRYLVNGREITPEEFQHYRQTGQLPVATTKA 62 Query: 65 QNTPTNQVSADSVLTKLGTNLTDQARQHLLDPVIGRNKEIQETAEILARRTKNNPVLVGD 124- N+ ADSVLT+LGTNLT +ARQ LDPVIGRNKEIQ+TAEILARRTKNNPVLVGD Sbjct: 63 TNSQMLTPKADSVLTQLGTNLTQEARQGHLDPVIGRNKEIQDTAEILARRTKNNPVLVGD 122- Query: 125 AGVGKTAVIEGLAQAIINGDVPAAIKNKEIISIDISSLEAGTQYRGSFEENIQNIIKEVK 18- 4 AGVGKTAVIEGLAQAI+NGDVPAAIKNKEI+SIDISSLEAGTQYRGSFEE IQN+I+EVK Sbjct: 123 AGVGKTAVIEGLAQAIVNGDVPAAIKNKEIVSIDISSLEAGTQYRGSFEETIQNLIQEVK 18- 2 Query: 185 ETGNIILFFDEIHQILGAGSTGGDSGSKGLADILKPALSRGELTVIGATTQDEYRNTILK 24- 4 E GNIILFFDEIHQI+GAG+T DSGSKGLADILKPALSRGELT+IGATTQDEYRNTILK Sbjct: 183 EAGNIILFFDEIHQIVGAGATSSDSGSKGLADILKPALSRGELTLIGATTQDEYRNTILK 24- 2 Query: 245 NAALARRFNEVKVNAPSAQDTFNILMGIRNLYEQHHNVVLPDSVLKAAVDLSIQYIPQRS 30- 4 NAALARRFNEVKVNAPSA+DTF+ILMGIRNLYEQHH++ LPD+VLKAAVD SIQYIPQRS Sbjct: 243 NAALARRFNEVKVNAPSAEDTFHILMGIRNLYEQHHHITLPDNVLKAAVDYSIQYIPQRS 30- 2 Query: 305 LPDKAIDLIDMTAAHLAAQHPVTDLKSLEKEIAEQRDKQEKAVNTEDFEEALKVKTRIEE 36- 4 LPDKAIDL+DMTAAHLAAQHPVTDLK+LE EIA+Q++ QEKAV EDFE+AL KTRIE Sbjct: 303 LPDKAIDLLDMTAAHLAAQHPVTDLKTLETEIAKQKESQEKAVAKEDFEKALAAKTRIET 36- 2 Query: 365 LQNQIDNHTEGQKVTATINDIAMSIERLTGVPVSNMGASDIERLKELGNRLKGKVIGQND 42- 4 LQ QI+ H + Q VTAT+NDIA S+ERLTG+PVSNMG +D+ERLK + +RLK VIGQ++ Sbjct: 363 LQKQIEQHNQSQNVTATVNDIAESVERLTGIPVSNMGTNDLERLKGISSRLKSHVIGQDE 42- 2 Query: 425 AVEAVARAIRRNRAGFDDGNRPIGSFLFVGPTGVGKTELAKQLAFDMFGSKDAIVRLDMS 48- 4 AV AVARAIRRNRAGFDDG RPIGSFLFVGPTGVGKTELAKQLA D+FGSKDAI+RLDMS Sbjct: 423 AVAAVARAIRRNRAGFDDGKRPIGSFLFVGPTGVGKTELAKQLALDLFGSKDAIIRLDMS 48- 2 Query: 485 EYNDRTAVSKLIGATAGYVGYDDNSNTLTERIRRNPYSIVLLDEIEKADPQVITLLLQVL 54- 4 EYNDRTAVSKLIG TAGYVGYDDN+NTLTER+RRNPY+IVLLDEIEKADPQ+ITLLLQVL Sbjct: 483 EYNDRTAVSKLIGTTAGYVGYDDNNNTLTERVRRNPYAIVLLDEIEKADPQIITLLLQVL 54- 2 Query: 545 DDGRLTDGQGNTINFKNTVIIATSNAGFGNEAFTGDSDKDLKIMERISPYFRPEFLNRFN 60- 4 DDGRLTDGQGNTINFKNTVIIATSNAGFG + + IM+RI+PYFRPEFLNRFN Sbjct: 543 DDGRLTDGQGNTINFKNTVIIATSNAGFGQQ---DTETSESNIMDRIAPYFRPEFLNRFN 59- 9 Query: 605 GVIEFSHLSKDDLSEIVDLMLDEVNQTIGKKGIDLVVDENVKSHLIELGYDEAMGVRPLR 66- 4 +I+F+HL K+ L EIVDLML EVNQT KKGI L + ++ K+HLI+LGY+ AMG RPLR Sbjct: 600 SIIKFNHLQKESLEEIVDLMLAEVNQTTAKKGISLTITDDAKAHLIDLGYNHAMGARPLR 65- 9 Query: 665 RVIEQEIRDRITDYYLDHTDVKHLKANLQDGQIVISE 701 R+IEQEIRDRITDYYLDH +VK L+A L++GQ+VI + Sbjct: 660 RIIEQEIRDRITDYYLDHPEVKKLQAILKEGQLVIRQ 696 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1911 A DNA sequence (GBSx2020) was identified in S. agalactiae <SEQ ID 5925> which encodes the amino acid sequence <SEQ ID 5926>. Analysis of this protein sequence reveals the following:

TABLE-US-05850 Possible Site: 20 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.78 Transmembrane 8-24 (7-25) ----- Final Results ----- bacterial membrane --- Certainty = 0.2911(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9945> which encodes amino acid sequence <SEQ ID 9946> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05851 >GP: AAC73364 GB: AE000134 putative enzyme [Escherichia coli K12] Identities = 142/307 (46%), Positives = 195/307 (63%), Gaps = 6/307 (1%) Query: 39 KELLESKKTLILHGALGTELESRGCDVSGKLWSAKYLIEDPAAIQTIHEDYIRAGADIVT 98 - + LL+ + L+L GA+ TELE+RGC+++ LWSAK L+E+P I+ +H DY RAGA Sbjct: 8 RALLDKQDILLLDGAMATELEARGCNLADSLWSAKVLVENPELIREVHLDYYRAGAQCAI 67 Query: 99 TSTYQATLQGLAQVGVSESQTEDLIRLTVQLAKAAREQVWKSLTKEEKSERIYPLISGDV 158- T++YQAT G A G+ E+Q++ LI +V+LA+ ARE L + ++ + L++G V Sbjct: 68 TASYQATPAGFAARGLDEAQSKALIGKSVELARKAREAY---LAENPQAGTL--LVAGSV 122- Query: 159 GPYAAFLADGSEYTGLYDIDKQGLKNFHRHRIELLLDEGVDILALETIPNAQEAEALIEL 21- 8 GPY A+LADGSEY G Y + + FHR R+E LLD G D+LA ET+PN E EAL EL Sbjct: 123 GPYGAYLADGSEYRGDYHCSVEAFQAFHRPRVEALLDAGADLLACETLPNFSEIEALAEL 18- 2 Query: 219 LAEDFPQVEAYMSFTSQDGKTISDGSAVADLAKAIDVSPQVVALGINCSSPSLVADFLQA 27- 8 L +P+ A+ SFT +D + +SDG+ + D+ + PQVVALGINC + LQ Sbjct: 183 LTA-YPRARAWFSFTLRDSEHLSDGTPLRDVVALLAGYPQVVALGINCIALENTTAALQH 24- 1 Query: 279 IAEQTNKPLVTYPNSGEVYDGASQSWQSSPDHSHTLLENTSDWQKLGAQVVGGCCRTRPA 33- 8 + T PLV YPNSGE YD S++W +H L + WQ GA+++GGCCRT PA Sbjct: 242 LHGLTVLPLVVYPNSGEHYDAVSKTWHHHGEHCAQLADYLPQWQAAGARLIGGCCRTTPA 30- 1 Query: 339 DIADLSA 345 DIA L A Sbjct: 302 DIAALKA 308 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8933> and protein <SEQ ID 8934> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05852 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: 5.48 GvH: Signal Score (-7.5): -2.64 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -4.78 threshold: 0.0 INTEGRAL Likelihood = -4.78 Transmembrane 8-24 (7-25) PERIPHERAL Likelihood = 2.49 259 modified ALOM score: 1.46 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2911(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00135## SEQ ID 8934 (GBS381) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 68 (lane 6; MW 42 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 4; MW 66.9 kDa). EXAMPLE 1912 A DNA sequence (GBSx2021) was identified in S. agalactiae <SEQ ID 5927> which encodes the amino acid sequence <SEQ ID 5928>. Analysis of this protein sequence reveals the following: TABLE-US-05853 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2996(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1913 A DNA sequence (GBSx2022) was identified in S. agalactiae <SEQ ID 5929> which encodes the amino acid sequence <SEQ ID 5930>. Analysis of this protein sequence reveals the following: TABLE-US-05854 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.62 Transmembrane 176-192 (168-198) INTEGRAL Likelihood = -11.57 Transmembrane 89-105 (80-111) INTEGRAL Likelihood = -10.03 Transmembrane 337-353 (332-359) INTEGRAL Likelihood = -9.87 Transmembrane 292-308 (285-316) INTEGRAL Likelihood = -4.51 Transmembrane 58-74 (52-78) INTEGRAL Likelihood = -3.88 Transmembrane 267-283 (267-286) INTEGRAL Likelihood = -3.08 Transmembrane 125-141 (125-142) INTEGRAL Likelihood = -2.13 Transmembrane 212-228 (212-228) ----- Final Results ----- bacterial membrane --- Certainty = 0.5649(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9377> which encodes amino acid sequence <SEQ ID 9378> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05855 >GP: CAB12034 GB: Z99105 similar to histidine permease [Bacillus subtilis] Identities = 221/384 (57%), Positives = 291/384 (75%), Gaps = 2/384 (0%) Query: 2 PVTGSFHTYATKFISPGTGFTVAWLYWICWTVALGTEFLGAAMLMQRWFPNVPAWAFASF 61 PVTG+FHTYA K+I PGTGFTVAWLYW+ WTVALG+EF A +LMQRWFP+ W +++ Sbjct: 76 PVTGAFHTYAAKYIGPGTGFTVAWLYWLTWTVALGSEFTAAGLLMQRWFPHTSVWMWSAV 135- Query: 62 FALVIFGLNALSVRFFAEAESFFSSIKVIAIIIFIILGLGAMFGLVSFEGQHKAILETHL 121- FAL IF LNA SV+FFAE+E +FSSIKV+AI++FI+LG AMFG++ +G A +++ Sbjct: 136 FALFIFLLNAFSVKFFAESEFWFSSIKVLAIVLFILLGGSAMFGIIPIKGGEAAPMLSNF 19- 5 Query: 122 TANGA-FPNGIVAVVSVMLAVNYAFSGTELIGIAAGETDNPKEAVPRAIKTTIGRLVVFF 18- 0 TA G FPNG V ++ ML+VN+AFSGTELIGIAAGE+ +P + +P+AIKTT+ RL +FF Sbjct: 196 TAEGGLFPNGFVPILMTMLSVNFAFSGTELIGIAAGESVDPDKTIPKAIKTTVWRLSLFF 25- 5 Query: 181 VLTIVVLASLLPMKEAGVSTAPFVDVFDKMGIPFTADIMNFVILTAILSAGNSGLYASSR 24- 0 V TI VL+ L+P+++AGV +PFV VFD++G+P+ ADIMNFVILTAILSA NSGLYASSR Sbjct: 256 VGTIFVLSGLIPIQDAGVIKSPFVAVFDRVGVPYAADIMNFVILTAILSAANSGLYASSR 31- 5 Query: 241 MLWSLANEGMLSKSVVKINKHGVPMRALLLSMAGAVLSLFSSIYAADTVYLALVSIAGFA 30- 0 MLWSL+ E L + K+ G P AL+ SM G +LSL SS++A DTVY+ LVSI+GFA Sbjct: 316 MLWSLSKEKTLHPTFAKLTSKGTPFNALVFSMIGGILSLLSSVFAPDTVYVVLVSISGFA 37- 5 Query: 301 VVVVWLAIPVAQINFRKEFLKE-NQLEDLSYKTPFTPVLPYITIILLLISIVGIAWDSSQ 35- 9 VVVVW+ I +Q FRK +++ N++ DL Y+TP P +P +L L S+VGIA+D +Q Sbjct: 376 VVVVWMGIAASQFMFRKRYIEAGNKVTDLKYRTPLYPFVPIAAFLLCLASVVGIAFDPNQ 43- 5 Query: 360 RAGLYFGVPFIIFCYIYHKLRYKK 383 R LY GVPF+ CY + ++ +K Sbjct: 436 RIALYCGVPFMAICYAIYYVKNRK 459 There is also homology to SEQ ID 4070. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1914 A DNA sequence (GBSx2023) was identified in S. agalactiae <SEQ ID 5931> which encodes the amino acid sequence <SEQ ID 5932>. Analysis of this protein sequence reveals the following: TABLE-US-05856 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2378(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> There is also homology to SEQ ID 5642. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1915 A DNA sequence (GBSx2024) was identified in S. agalactiae <SEQ ID 5933> which encodes the amino acid sequence <SEQ ID 5934>. Analysis of this protein sequence reveals the following: TABLE-US-05857 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4935(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1916 A DNA sequence (GBSx2025) was identified in S. agalactiae <SEQ ID 5935> which encodes the amino acid sequence <SEQ ID 5936>. Analysis of this protein sequence reveals the following: TABLE-US-05858 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0530(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1917 A DNA sequence (GBSx2026) was identified in S. agalactiae <SEQ ID 5937> which encodes the amino acid sequence <SEQ ID 5938>. Analysis of this protein sequence reveals the following: TABLE-US-05859 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0175(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05860 >GP:AAF63739 GB:AF236863 hypothetical GTP-binding protein [Lactococcus lactis] Identities = 142/193 (73%), Positives = 165/193 (84%) Query: 6 LNTHNASILLSAANKSHYPQDDLPEVALAGRSNVGKSSFINTLLGRKNLARTSSKPGKTQ 65 +NT+N +I +SAA+K YP++D PE+ALAGRSNEGKSSFINTLL RKN ARTS +PGKTQ Sbjct: 3 INTNNLTITISAASKKQYPENDWPEIALAGRSNVGKSSFINTLLNRKNFARTSGQPGKTQ 62 Query: 66 LLNFYNIDDKLRFVDVPGYGYAKVSKTERAKWGKMIEEYLVTRDNLRVVVSLVDFRHDPS 125- LLNFYNIDD+L FVDVPGYGYA+VSK ER KWGKMIEEYL TR+NL+ VVSLVD RH+PS Sbjct: 63 LLNFYNIDDQLHFVDVPGYGYARVSKKEREKWGKMIEEYLTTRENLKAVVSLVDIRHEPS 122- Query: 126 ADDIQMYEFLKYYEIPVIIVATKADKIPRGKWNKHESSIKKKLNFDKKDHFIVFSSVDRT 18- 5 DD+ MYEFLKYY IPVI+VATKADK+PRGKWNKHES IKK + FD D FI+FSS D+T Sbjct: 123 EDDLMMYEFLKYYHIPVILVATKADKVPRGKWNKHESIIKKAMKFDSTDDFIIFSSTDKT 18- 2 Query: 186 GLDESWDTILSEL 198 G++E+W IL L Sbjct: 183 GIEEAWTAILKYL 195 A related DNA sequence was identified in S. pyogenes <SEQ ID 5939> which encodes the amino acid sequence <SEQ ID 5940>. Analysis of this protein sequence reveals the following: TABLE-US-05861 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0123(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05862 Identities = 167/196 (85%), Positives = 183/196 (93%) Query: 3 EEFLNTHNASILLSAANKSHYPQDDLPEVALAGRSNVGKSSFINTLLGRKNLARTSSKPG 62 E+ LNTHNASILLSAANKSHYPQDDLPE+ALAGRSNVGKSSFINT+LGRKNLARTSSKPG Sbjct: 4 EQVLNTHNASILLSAANKSHYPQDDLPEIALAGRSNVGKSSFINTILGRKNLARTSSKPG 63 Query: 63 KTQLLNFYNIDDKLRFVDVPGYGYAKVSKTERAKWGKMIEEYLVTRDNLRVVVSLVDFRH 122- KTQLLNF+NIDDKLRFVDVPGYGYAKVSK+ERAKWGKMIEEYL +RDNLR VVSLVD RH Sbjct: 64 KTQLLNFFNIDDKLRFVDVPGYGYAKVSKSERAKWGKMIEEYLTSRDNLRAVVSLVDLRH 123- Query: 123 DPSADDIQMYEFLKYYEIPVIIVATKADKIPRGKWNKHESSIKKKLNFDKKDHFIVFSSV 18- 2 PS +DIQMY+FLKYY+IPVI+VATKADKIPRGKWNKHES +KK LNFDR D FIVFSSV Sbjct: 124 APSKEDIQMYDFLKYYDIPVIVVATKADKIPRGKWNKHESVVKKALNFDKSDTFIVFSSV 18- 3 Query: 183 DRTGLDESWDTILSEL 198 +R G+D+SWD IL ++ Sbjct: 184 ERIGIDDSWDAILEQV 199 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1918 A DNA sequence (GBSx2027) was identified in S. agalactiae <SEQ ID 5941> which encodes the amino acid sequence <SEQ ID 5942>. This protein is predicted to be protease ClpX (clpX). Analysis of this protein sequence reveals the following: TABLE-US-05863 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2389(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9947> which encodes amino acid sequence <SEQ ID 9948> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05864 >GP:AAF63738 GB:AF236863 protease ClpX [Lactococcus lactis] Identities = 305/395 (77%), Positives = 357/395 (90%), Gaps = 1/395 (0%) Query: 18 NVYCSFCGKSQDEVKKIIAGNGVFICNECVALSQEIIKEELAEEVLADLAEVPKPKELLE 77 - N+ CSFCGKSQD+VKK+IAG+ V+ICNEC+ LS I++EEL EE +++ EV PKE+ + Sbjct: 8 NIQCSFCGKSQDDVKKMIAGSDVYICNECIELSTRILEEELKEEQDSEMLEVKTPKEMFD 67 Query: 78 ILNQYVVGQDRAKRALAVAVYNHYKRVSYTESS-DDDVDLQKSNILMIGPTGSGKTFLAQ 136- LN+YV+GQ++AKRALAVAVYNHYKR+++T S +D++LQKSNIL+IGPTGSGKTFLAQ Sbjct: 68 HLNEYVIGQEKAKRALAVAVYNHYKRINFTASKIAEDIELQKSNILLIGPTGSGKTFLAQ 127- Query: 137 TLAKSLNVPFAIADATSLTEAGYVGEDVENILLKLIQAADYNVERAERGIIYVDEIDKIA 19- 6 TLAKSLNVPFAIADATSLTEAGYVGEDVENILLKL+QA+D+N+ERAERGIIY+DEIDKIA Sbjct: 128 TLAKSLNVPFAIADATSLTEAGYVGEDVENILLKLLQASDFNIERAERGIIYIDEIDKIA 18- 7 Query: 197 KKGENVSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPNQEMIQINTKNILFIVGGA 25- 6 KK+ENVSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPNQEMIQI+TKNILFIVGGA Sbjct: 188 KKSENVSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPNQEMIQIDTKNILFIVGGA 24- 7 Query: 257 FDGIEDLVKQRLGEKVIGFGQTSRKIDDNASYMQEIISEDIQKFGLIPEFIGRLPVVAAL 31- 6 FDGIE++VKQRLGEK+IGFG ++K+ D SYMQEII+EDIQKFGLIPEFIGRLP+VAAL Sbjct: 248 FDGIEEIVKQRLGEKIIGFGANNKKLSDEDSYMQEIIAEDIQKFGLIPEFIGRLPIVAAL 30- 7 Query: 317 ELLTAEDLVRILTEPRNALVKQYQTLLSYDGVELEFDQDALLAIADKAIERKTGARGLRS 37- 6 E LT EDL++ILTEP+NAL+KQY+ LL +D VELEF AL+AIA KAIERKTGARGLRS Sbjct: 308 ERLTEEDLIQILTEPKNALIKQYKQLLLFDNVELEFKDGALMAIAKKAIERKTGARGLRS 36- 7 Query: 377 IIEETMLDIMFEIPSQEDVTKVRITKAAVEGTDKP 411 IIEE M+DIMFE+PS E++TKV IT+A V+G +P Sbjct: 368 IIEEVMMDIMFEVPSHEEITKVIITEAVVDGKAEP 402 A related DNA sequence was identified in S. pyogenes <SEQ ID 5943> which encodes the amino acid sequence <SEQ ID 5944>. Analysis of this protein sequence reveals the following: TABLE-US-05865 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2711(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05866 Identities = 378/409 (92%), Positives = 393/409 (95%), Gaps = 1/409 (0%) Query: 9 MAGNRNNDMNVYCSFCGKSQDEVKKIIAGNGVFICNECVALSQEIIKEELAEEVLADLAE 68 MAG+R ND+ VYCSFCGKSQD+VKKIIAGN VFICNECVALSQEIIKEELAEEVLADL E Sbjct: 1 MAGSRTNDIKVYCSFCGKSQDDVKKIIAGNNVFICNECVALSQEIIKEELAEEVLADLTE 60 Query: 69 VPKPKELLEILNQYVVGQDRAKRALAVAVYNHYKRVSYTES-SDDDVDLQKSNILMIGPT 127- VPKPKELL++LNQYVVGQDRAKRAL+VAVYNHYKRVS+TES DDDVDLQKSNILMIGPT Sbjct: 61 VPKPKELLDVLNQYVVGQDRAKRALSVAVYNHYKRVSFTESRDDDDVDLQKSNILMIGPT 120- Query: 128 GSGKTFLAQTLAKSLNVPFAIADATSLTEAGYVGEDVENILLKLIQAADYNVERAERGII 18- 7 GSGKTFLAQTLAKSLNVPFAIADATSLTEAGYVGEDVENILLKLIQAADYNVERAERGII Sbjct: 121 GSGKTFLAQTLAKSLNVPFAIADATSLTEAGYVGEDVENILLKLIQAADYNVERAERGII 18- 0 Query: 188 YVDEIDKIAKKGENVSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPNQEMIQINTK 24- 7 YVDEIDKIAKKGENVSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPNQEMIQI+TK Sbjct: 181 YVDEIDKIAKKGENVSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPNQEMIQIDTK 24- 0 Query: 248 NILFIVGGAFDGIEDLVKQRLGEKVIGFGQTSRKIDDNASYMQEIISEDIQKFGLIPEFI 30- 7 NILFIVGGAFDGIE++VKQRLGEKVIGFGQ SRKIDDNASYMQEIISEDIQKFGLIPEFI Sbjct: 241 NILFIVGGAFDGIEEIVKQRLGEKVIGFGQNSRKIDDNASYMQEIISEDIQKFGLIPEFI 30- 0 Query: 308 GRLPVVAALELLTAEDLVRILTEPRNALVKQYQTLLSYDGVELEFDQDALLAIADKAIER 36- 7 GRLPVVAALE L DL++ILTEPRNALVKQYQ LLSYDGVEL FD++AL AIA+KAIER Sbjct: 301 GRLPVVAALEQLNTSDLIQILTEPRNALVKQYQALLSYDGVELAFDKEALEAIANKAIER 36- 0 Query: 368 KTGARGLRSIIEETMLDIMFEIPSQEDVTKVRITKAAVEGTDKPVLETA 416 KTGARGLRSIIEETMLDIMFEIPSQEDVTKVRITKAAVEG KPVLETA Sbjct: 361 KTGARGLRSIIEETMLDIMFEIPSQEDVTKVRITKAAVEGKSKPVLETA 409 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1919 A DNA sequence (GBSx2028) was identified in S. agalactiae <SEQ ID 5945> which encodes the amino acid sequence <SEQ ID 5946>. Analysis of this protein sequence reveals the following:

TABLE-US-05867 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1920 A DNA sequence (GBSx2029) was identified in S. agalactiae <SEQ ID 5947> which encodes the amino acid sequence <SEQ ID 5948>. Analysis of this protein sequence reveals the following: TABLE-US-05868 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4029(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9949> which encodes amino acid sequence <SEQ ID 9950> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05869 >GP:AAC33872 GB:AF055727 dihydrofolate reductase [Streptococcus pneumoniae] Identities = 83/162 (51%), Positives = 118/162 (72%), Gaps = 1/162 (0%) Query: 25 MTKQIIAIWAEDEDHLIGVNGGLPWRLPKELHHFKETTMGQALLMGRKTFDGMNRRVLPG 84 - MTK+I+AIWA+DE+ LIG LPW LP EL HFKETT+ A+LMGR TFDGM RR+LP Sbjct: 1 MTKKIVAIWAQDEEGLIGKENRLPWHLPAELQHFKETTLNHAILMGRVTFDGMGRRLLPK 60 Query: 85 RETIILTKDEQFQADGVTVLNSVEQVIKWFQEHNKTLFIVGGASIYKAFLPYCEAIIKTK 144- RET+ILT++ + + DGV V+ V+ W+Q+ K L+I+GG I++AF PY + +I T Sbjct: 61 RETLILTRNPEEKIDGVATFQDVQSVLDWYQDQEKNLYIIGGKQIFQAFEPYLDEVIVTH 120- Query: 145 VHGKFKGDTYFP-DVNLSEFKVISRDYFEKDEQNAHAFTVTY 185 +H + +GDTYFP +++LS F+ +S ++ KDE+N + FT+ Y Sbjct: 121 IHARVEGDTYFPEELDLSLFETVSSKFYAKDEKNPYDFTIQY 162 A related DNA sequence was identified in S. pyogenes <SEQ ID 5949> which encodes the amino acid sequence <SEQ ID 5950>. Analysis of this protein sequence reveals the following: TABLE-US-05870 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1214(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05871 Identities = 82/160 (51%), Positives = 119/160 (74%) Query: 25 MTKQIIAIWAEDEDHLIGVNGGLPWRLPKELHHFKETTMGQALLMGRKTFDGMNRRVLPG 84 - MTK+IIAIWAEDE LIG+ G LPW LPKEL HFK+TT+ QA+LMGR TF+GMN + LP Sbjct: 1 MTKEIIAIWAEDEAGLIGIAGKLPWYLPKELEHFKKTTLHQAILMGRVTFEGMNCKRLPQ 60 Query: 85 RETIILTKDEQFQADGVTVLNSVEQVIKWFQEHNKTLFIVGGASIYKAFLPYCEAIIKTK 144- R+T+++T++ +Q D V + S+E+V++W+ +KTL+I+GG + +AF Y + IIKT Sbjct: 61 RQTLVMTRNRDYQVDEVLTMTSIEKVLEWYHAQDKTLYIIGGNKVLEAFNGYFDRIIKTV 120- Query: 145 VHGKFKGDTYFPDVNLSEFKVISRDYFEKDEQNAHAFTVT 184 +H +FKGDTY P+++ S F S+ ++ +D +N + FTVT Sbjct: 121 IHHRFKGDTYRPNLDFSHFTQESQTFYARDAKNPYDFTVT 160 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1921 A DNA sequence (GBSx2030) was identified in S. agalactiae <SEQ ID 5951> which encodes the amino acid sequence <SEQ ID 5952>. Analysis of this protein sequence reveals the following: TABLE-US-05872 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1577(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05873 >GP:AAA25221 GB:M33770 thymidylate synthase (EC 2.1.1.45) [Lactococcus lactis] Identities = 215/280 (76%), Positives = 245/280 (86%), Gaps = 2/280 (0%) Query: 1 MTKADLLFKDNITKIMSEGVFSEQARPRYKNGEMANSKYITGAFAEYDLSKGEFPITTLR 60 MT AD +FK NI I+ GVFSE ARP+YK+G+MANSKY+TG+F YDL KGEFPITTLR Sbjct: 1 MTYADQVFKQNIQNILDNGVFSENARPKYKDGQMANSKYVTGSFVTYDLQKGEFPITTLR 60 Query: 61 PIPIKSAIKEIFWIYQDQTNDLAVLNDKYGVTYWNDWEVGHTGTIGQRYGAVVKKHNIIS 120- PIPIKSAIKE+ WIYQDQT++L+VL +KYGV YW +W +G GTIGQRYGA VKK+NII Sbjct: 61 PIPIKSAIKELMWIYQDQTSELSVLEEKYGVKYWGEWGIGD-GTIGQRYGATVKKYNIIG 119- Query: 121 KLLKQLEDNPWNRRNVISLWDYEAFEETEGLLPCAFQTMFDVRRV-NGELYLDATLTQRS 17- 9 KLL+ L NPWNRRN+I+LW YE FEETEGLLPCAFQTMFDVRR +G++YLDATL QRS Sbjct: 120 KLLEGLAKNPWNRRNIINLWQYEDFEETEGLLPCAFQTMFDVRREKDGQIYLDATLIQRS 17- 9 Query: 180 NDMLVAHHINAMQYVALQMMIAKHFGWRVGKFFYFINNLHIYDNQFEQAQELLKRQPSEC 23- 9 NDMLVAHHINAMQYVALQMMIAKHF W+VGKFFYF+NNLHIYDNQFEQA EL+KR SE Sbjct: 180 NDMLVAHHINAMQYVALQMMIAKHFSWKVGKFFYFVNNLHIYDNQFEQANELMKRTASEK 23- 9 Query: 240 NPKLVLNVPDGTDFFDIKPDDFALVDYDPIKPQLRFDLAI 279 P+LVLNVPDGT+FFDIKP+DF LVDY+P+KPQL+FDLAI Sbjct: 240 EPRLVLNVPDGTNFFDIKPEDFELVDYEPVKPQLKFDLAI 279 A related DNA sequence was identified in S. pyogenes <SEQ ID 5953> which encodes the amino acid sequence <SEQ ID 5954>. Analysis of this protein sequence reveals the following: TABLE-US-05874 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3131(Aftirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05875 Identities = 227/279 (81%), Positives = 251/279 (89%) Query: 1 MTKADLLFKDNITKIMSEGVFSEQARPRYKNGEMANSKYITGAFAEYDLSKGEFPITTLR 60 MTKAD +FK NI KI++EG SEQARP+YK+G A+SKYITGAFAEYDL+KGEFPITTLR Sbjct: 9 MTKADQIFKANIQKIINEGSLSEQARPKYKDGRTAHSKYITGAFAEYDLAKGEFPITTLR 68 Query: 61 PIPIKSAIKEIFWIYQDQTNDLAVLNDKYGVTYWNDWEVGHTGTIGQRYGAVVKKHNIIS 120- PIPIKSAIKE+FWIYQDQ+N L VL KY V YWN+WEV T TIGQRYGAVVKKH+IIS Sbjct: 69 PIPIKSAIKELFWIYQDQSNSLDVLEAKYNVHYWNEWEVDQTRTIGQRYGAVVKKHDIIS 128- Query: 121 KLLKQLEDNPWNRRNVISLWDYEAFEETEGLLPCAFQTMFDVRRVNGELYLDATLTQRSN 18- 0 K+LKQL +NPWNRRNVISLWDYEAFEET+GLLPCAFQ MFDVRRV +LYLDA+LTQRSN Sbjct: 129 KILKQLAENPWNRRNVISLWDYEAFEETKGLLPCAFQIMFDVRRVGEDLYLDASLTQRSN 18- 8 Query: 181 DMLVAHHINAMQYVALQMMIAKHFGWRVGKFFYFINNLHIYDNQFEQAQELLKRQPSECN 24- 0 D+LVAHHINAMQYVALQMMIAKHFGW++GKFFYF+NNLHIYDNQF+QAQELLKRQP Sbjct: 189 DILVAHHINAMQYVALQMMIAKHFGWKIGKFFYFVNNLHIYDNQFDQAQELLKRQPVASQ 24- 8 Query: 241 PKLVLNVPDGTDFFDIKPDDFALVDYDPIKPQLRFDLAI 279 PKLVLNVPD T+FFDIKPDDF L +YDP+KPQL FDLAI Sbjct: 249 PKLVLNVPDRTNFFDIKPDDFELQNYDPVKPQLHFDLAI 287 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1922 A DNA sequence (GBSx2031) was identified in S. agalactiae <SEQ ID 5955> which encodes the amino acid sequence <SEQ ID 5956>. This protein is predicted to be HMG-CoA synthase. Analysis of this protein sequence reveals the following: TABLE-US-05876 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0816(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 5957> which encodes the amino acid sequence <SEQ ID 5958>. Analysis of this protein sequence reveals the following: TABLE-US-05877 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1670(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05878 Identities = 260/385 (67%), Positives = 325/385 (83%) Query: 36 MKIGIDKIGFATSQYVLEMTDLAIARQVDPEKFSKGLLLDSLSITPVTEDIVTLAASAAN 95 - M IGIDKIGFATSQYVL++ DLA+ARQVDP KFS+GLL++S S+ P+TEDI+TLAASAA+ Sbjct: 14 MTIGIDKIGFATSQYVLKLEDLALARQVDPAKFSQGLLIESFSVAPITEDIITLAASAAD 73 Query: 96 DILSDEDKETIDMVIVATESSIDQSKAASVYVHQLLEIQPFARSFEMKEACYSATAALDY 155- IL+DED+ IDMVI+ATESS DQSKA+++YVH L+ IQPFARSFE+K+ACYSATAALDY Sbjct: 74 QILTDEDRAKIDMVILATESSTDQSKASAIYVHHLVGIQPFARSFEVKQACYSATAALDY 133- Query: 156 AKLHVEKHPDSKVLVIASDIAKYGIKSTGESTQGAGSIAMLISQNPSILELKEDHLAQTR 21- 5 AKLHV PDS+VLVIASDIA+YG+ S GESTQG+GSIA+L++ NP IL L ED++AQTR Sbjct: 134 AKLHVASKPDSRVLVIASDIARYGVGSPGESTQGSGSIALLVTANPRILALNEDNVAQTR 19- 3 Query: 216 DIMDFWRPNYSDVPYVNGMFSTKQYLDMLKTTWKVYQKRFNTSLSDYAAFCFHIPFPKLA 27- 5 DIMDFWRPNYS PYV+G++STKQYL+ L+TTW+ YQKR N LSD AA CFHIPFPKLA Sbjct: 194 DIMDFWRPNYSFTPYVDGIYSTKQYLNCLETTWQAYQKRENLQLSDLAAVCFHIPFPKLA 25- 3 Query: 276 LKGFNKILDNNLDEQKKAELQENFEHSITYSKKIGNCYTGSLYLGLLSLLENSQNLKAGD 33- 5 LKG N I+DN + + + +L E F+ SI+YSK+IGN YTGSLYLGLLSLLENS+ L++GD Sbjct: 254 LKGLNNIMDNTVPPEHREKLIEAFQASISYSKQIGNIYTGSLYLGLLSLLENSKVLQSGD 31- 3 Query: 336 QIAFFSYGSGAVAEIFTGQLVDGYQNKLQSDRMDQLNKRQKITVTEYEKLFFEKTILDEN 39- 5 +I FFSYGSGAV+E ++GQLV GY L ++R L++R +++V++YE LF+E+ LD+N Sbjct: 314 KIGFFSYGSGAVSEFYSGQLVAGYDKMLNTNRQALLDQRTRLSVSKYEDLFYEQVQLDDN 37- 3 Query: 396 GNANFNTYRTGTFSLDSICEHQRIY 420 GNANF+ Y TG F+L +I EH+RIY Sbjct: 374 GNANFDIYLTGKFALTAIKEHRRIY 398 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1923 A DNA sequence (GBSx2032) was identified in S. agalactiae <SEQ ID 5959> which encodes the amino acid sequence <SEQ ID 5960>. This protein is predicted to be HMG-CoA reductase (mvaA). Analysis of this protein sequence reveals the following: TABLE-US-05879 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.49 Transmembrane 348-364 (348-364) INTEGRAL Likelihood = -1.33 Transmembrane 53-69 (53-69) ----- Final Results ----- bacterial membrane --- Certainty = 0.1595(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05880 >GP:AAG02454 GB:AF290098 HMG-CoA reductase [Streptococcus pneumoniae] Identities = 266/421 (63%), Positives = 343/421 (81%), Gaps = 3/421 (0%) Query: 3 KISWTGFSKKSPEERIHYLEEQDFLADSSLEIVTNQDLLSLSLANQMAENVIGRIALPFS 62 KISW GFSKKS +ER+ L+ Q L+ + + +S+++A+Q++ENV+G +LP+S Sbjct: 2 KISWNGFSKKSYQERLELLKAQALLSPERQASLEKDEQMSVTVADQLSENVVGTFSLPYS 61 Query: 63 LVPDVLVNGKVYQVPYVTEEPSVVAAASFAAKIIKRSGGFLTTVHNRKMIGQVALYDVQD 122- LVP+VLVNG+ Y VPYVTEEPSVVAAAS+A+KIIKR+GGF VH R+MIGQVALY V + Sbjct: 62 LVPEVLVNGQGYTVPYVTEEPSVVAAASYASKIIKRAGGFTAQVHQRQMIGQVALYQVAN 121- Query: 123 SQHTKESILNQKQQLLEIANAAHPSIVKRGGGACDLTIEI---KEDFLIVYLMVDTKEAM 17- 9 + +E I ++K +LLE+AN A+PSIVKRGGGA DL +E + DFL+VY+ VDT+EAM Sbjct: 122 PKLAQEKIASKKAELLELANQAYPSIVKRGGGARDLHVEQIKGEPDFLVVYIHVDTQEAM 18- 1 Query: 180 GANMVNTMMEALSSPLEDISKGKSLMSILSNYATESLVTATCRVDLRFLSRQKEEAIKLA 23- 9 GANM+NTM+EAL LE++S+G+SLM ILSNYAT+SLVTA+CR+ R+LSRQK++ ++A Sbjct: 182 GANMLNTMLEALKPVLEELSQGQSLMGILSNYATDSLVTASCRIAFRYLSRQKDQGREIA 24- 1 Query: 240 QKMTMASQLAQVDPYRASTHNKGIFNGIDAIVLATGNDWRAIEAGAHTYAVKDGQYRGLS 29- 9 +K+ +ASQ AQ DPYRA+THNKGIFNGIDAI++ATGNDWRAIEAGAH +A +DG+Y+GLS Sbjct: 242 EKIALASQFAQADPYRAATHNKGIFNGIDAILIATGNDWRAIEAGAHAFASRDGRYQGLS 30- 1 Query: 300 RWSYKVDDNCLEGTLTLPMPVATKGGSIGINPSVHLAHDLLGRPNAKELASIILSIGLAQ 35- 9 W+ ++ L G +TLPMPVATKGGSIG+NP V L+HDLLG P+A+ELA II+SIGLAQ Sbjct: 302 CWTLDLEREELVGEMTLPMPVATKGGSIGLNPRVALSHDLLGNPSARELAQIIVSIGLAQ 36- 1 Query: 360 NFAALKALVSTGIQAGHMKLQAKSLALLAGAKEEQISEVVKQLLDSKHMNLETAQKIVNKL 4- 20 NFAALKALVSTGIQ GHMKLQAKSLALLAGA E +++ +V++L+ K NLETAQ+ + L Sbjct: 362 NFAALKALVSTGIQQGHMKLQAKSLALLAGASESEVAPLVERLISDKTFNLETAQRYLENL 4- 22 A related DNA sequence was identified in S. pyogenes <SEQ ID 5961> which encodes the amino acid sequence <SEQ ID 5962>. Analysis of this protein sequence reveals the following: TABLE-US-05881 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3929(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05882 Identities = 257/422 (60%), Positives = 330/422 (77%) Query: 2 TKISWTGFSKKSPEERIHYLEEQDFLADSSLEIVTNQDLLSLSLANQMAENVIGRIALPF 61 T ++W+GFSKK+ EER+ +E+ L +L + LL + ANQM ENV+GR+ALPF Sbjct: 4 TNLNWSGFSKKTFEERLQLIEKFKLLNAENLNQLKTDVLLPIQTANQMTENVLGRLALPF 63 Query: 62 SLVPDVLVNGKVYQVPYVTEEPSVVAAASFAAKIIKRSGGFLTTVHNRKMIGQVALYDVQ 121- S+ PD LVNG YQ+P+VTEEPSVVAAASFAAK+IKRSGGF NR+MIGQ+ LYD+ Sbjct: 64 SIAPDFLVNGSTYQMPFVTEEPSVVAAASFAAKLIKRSGGFKAQTLNRQMIGQIVLYDID 123- Query: 122 DSQHTKESILNQKQQLLEIANAAHPSIVKRGGGACDLTIEIKEDFLIVYLMVDTKEAMGA 18- 1 + K +IL++ ++L+ +AN A+PSIVKRGGGA + +E K +FLI YL VDT+EAMGA Sbjct: 124 QIDNAKAAILHKTKKLIALANKAYPSIVKRGGGARTIHLEEKGEFLIFYLTVDTQEAMGA 18- 3 Query: 182 NMVNTMMEALSSPLEDISKGKSLMSILSNYATESLVTATCRVDLRFLSRQKEEAIKLAQK 24- 1 NMVNTMMEAL L +SKG LM+ILSNYATESLVT +C + +R L K ++++LAQK Sbjct: 184 NMVNTMMEALVPDLTRLSKGHCLMAILSNYATESLVTTSCEIPVRLLDHDKTKSLQLAQK 24- 3 Query: 242 MTMASQLAQVDPYRASTHNKGIFNGIDAIVLATGNDWRAIEAGAHTYAVKDGQYRGLSRW 30- 1 + +AS+LAQVDPYRA+THNKGIFNGIDA+V+ATGNDWRAIEAGAH YA ++G Y+GLS+W Sbjct: 244 IELASRLAQVDPYRATTHNKGIFNGIDAVVIATGNDWRAIEAGAHAYASRNGSYQGLSQW 30- 3 Query: 302 SYKVDDNCLEGTLTLPMPVATKGGSIGINPSVHLAHDLLGRPNAKELASIILSIGLAQNF 36- 1 + D L G +TLPMP+A+KGGSIG+NP+V +AHDLL +P+AK LA +I S+GLAQNF Sbjct: 304 HFDQDKQVLLGQMTLPMPIASKGGSIGLNPTVSIAHDLLNQPDAKTLAQLIASVGLAQNF 36- 3 Query: 362 AALKALVSTGIQAGHMKLQAKSLALLAGAKEEQISEVVKQLLDSKHMNLETAQKIVNKLT 42- 1 AALKAL S+GIQAGHMKL AKSLALLAGA +++I+ +V LL K +NLE A +++L Sbjct: 364 AALKALTSSGIQAGHMKLHAKSLALLAGATQDEIAPLVNALLADKPINLEKAHFYLSQLR 42- 3 Query: 422 KS 423 +S Sbjct: 424 QS 425 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1924 A DNA sequence (GBSx2033) was identified in S. agalactiae <SEQ ID 5963> which encodes the amino acid sequence <SEQ ID 5964>. Analysis of this protein sequence reveals the following: TABLE-US-05883 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2355(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 5965> which encodes the amino acid sequence <SEQ ID 5966>. Analysis of this protein sequence reveals the following: TABLE-US-05884 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2687(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05885 Identities = 76/138 (55%), Positives = 100/138 (72%), Gaps = 2/138 (1%) Query: 7 PKWEELPELDLYLDQVLLYVNQLINPKTITNDKLLTASMINNYVKHNYISKPIKKKYNRR 66 P W++LP+LDLYLDQVLLYVNQ + ++++K LTASMINNYVKH Y++KPIKKKY ++ Sbjct: 7 PYWKDLPDLDLYLDQVLLYVNQCTDFSEVSDNKSLTASMINNYVKHGYVTKPIKKKYQKQ 66 Query: 67 QVARLIVITAFKQVFAIQEISQTLELLTADNHSEEAYNGFAACMNKEE--VHDLPPVVIS 124- Q+ARLI I+ FK VF IQ+IS+ LE L A SE YN F C N++ D+PP+V Sbjct: 67 QLARLIAISLFKTVFPIQDISRVLEELQAQADSESLYNTFVTCWNQKAPIEEDIPPIVQV 126- Query: 125 ACQTLNLYQETQKLVLEL 142 ACQT+ Y +T L+ E+ Sbjct: 127 ACQTVKDYHKTIYLLQEV 144 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1925 A DNA sequence (GBSx2034) was identified in S. agalactiae <SEQ ID 5967> which encodes the amino acid sequence <SEQ ID 5968>. This protein is predicted to be hemolysin iii. Analysis of this protein sequence reveals the following:

TABLE-US-05886 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.08 Transmembrane 142-158 (140-165) INTEGRAL Likelihood = -6.79 Transmembrane 26-42 (19-44) INTEGRAL Likelihood = -5.63 Transmembrane 200-216 (196-217) INTEGRAL Likelihood = -5.41 Transmembrane 104-120 (102-121) INTEGRAL Likelihood = -3.98 Transmembrane 51-67 (49-69) INTEGRAL Likelihood = -1.86 Transmembrane 172-188 (169-188) ----- Final Results ----- bacterial membrane --- Certainty = 0.4630(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9951> which encodes amino acid sequence <SEQ ID 9952> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05887 >GP:CAA58877 GB:X84058 novel hemolytic factor [Bacillus cereus] Identities = 79/204 (38%), Positives = 132/204 (63%), Gaps = 4/204 (1%) Query: 17 EELANSITHAVGALLMLILLPITAVYSHNHFGLQAALGTSIFVTSLFLMFLSSSIYHSMT 76 - EE+AN+ITH +GA+L + L I +++ H A + +++ S+FL++L S++ HS+ Sbjct: 14 EEIANAITHGIGAILSIPALIILIIHASKHGTASAVVAFTVYGVSMFLLYLFSTLLHSIH 73 Query: 77 YNSLQKYVLBMIDHSMIYIAIAGSYTPVALSLIGGWLGYLIIFLQWGITLFGILYKIFAP 136- + ++K + ++DHS IY+ IAG+YTP L + G LG+ ++ + W + + GI++KIF Sbjct: 74 HPKVEK-LFTILDHSAIYLLIAGTYTPFLLITLRGPLGWTLLAIIWTLAIGGIIFKIFFV 132- Query: 137 KINDKFSLVLYLIMGWLVIF-IFPAIITKTGPAFWGLLLAGGICYTIGALFYA-RKRPYD 19- 4 + K S + Y+IMGWL+I I P TG F LLLAGGI Y++GA+F+ K P++ Sbjct: 133 RRFIKASTLCYIIMGWLIIVAIKPLYENLTGHGF-SLLLAGGILYSVGAIFFLWSKLPFN 19- 1 Query: 195 HMIWHLFILLASILQYIGIVYFML 218 H IWHLF+L S + + +++++L Sbjct: 192 HAIWHLFVLGGSAMMFFCVLFYVL 215 A related DNA sequence was identified in S. pyogenes <SEQ ID 5969> which encodes the amino acid sequence <SEQ ID 5970>. Analysis of this protein sequence reveals the following: TABLE-US-05888 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.51 Transmembrane 144-160 (138-163) INTEGRAL Likelihood = -9.87 Transmembrane 49-65 (45-71) INTEGRAL Likelihood = -7.11 Transmembrane 198-214 (193-215) INTEGRAL Likelihood = -6.16 Transmembrane 102-118 (100-120) INTEGRAL Likelihood = -2.97 Transmembrane 20-36 (20-41) INTEGRAL Likelihood = -1.01 Transmembrane 167-183 (167-185) ----- Final Results ----- bacterial membrane --- Certainty = 0.5203(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05889 >GP:CAA58877 GB:X84058 novel hemolytic factor [Bacillus cereus] Identities = 82/204 (40%), Positives = 128/204 (62%), Gaps = 4/204 (1%) Query: 15 EEVANSVTHAIGAFAMLILLPISASYAYQTYDLKAAIGISIFVISLFLMFLSSTIYHSMA 74 - EE+AN++TH IGA + L I +A + A + +++ +S+FL++L ST+ HS+ Sbjct: 14 EEIANAITHGIGAILSIPALIILIIHASKHGTASAVVAFTVYGVSMFLLYLFSTLLHSIH 73 Query: 75 YGSVHKYILRIIDHSMIYIAIAGSYTPVALSLVSGWLGYIIIVLQWGITLFGILYKIFAK 134- + V K + I+DHS IY+ IAG+YTP L + G LG+ ++ + W + + GI++KIF Sbjct: 74 HPKVEK-LFTILDHSAIYLLIAGTYTPFLLITLRGPLGWTLLAIIWTLAIGGIIFKIFFV 132- Query: 135 RINEKFSLMLYIVMGWL-VVFILPVIIQKTSLAFGLLMLFGGLSYTIGAVFYA-KKRPYF 19- 2 R K S + YI+HGWL +V I P+ T F LL L GG+ Y++GA+F+ +K P+ Sbjct: 133 RRFIKASTLCYIIMGWLIIVAIKPLYENLTGHGFSLL-LAGGILYSVGAIFFLWEKLPFN 19- 1 Query: 193 HHIWHLFILLASALQFIAITFFML 216 H IWHLF+L SA+ F + F++L Sbjct: 192 HAIWHLFVLGGSAMMFFCVLFYVL 215 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05890 Identities = 153/213 (71%), Positives = 181/213 (84%) Query: 6 SIKLSPQLSFGEELANSITHAVGALLMLILLPITAVYSHNHFGLQAALGTSIFVTSLFLM 65 + K S LSF EE+ANS+THA+GA MLILLPI+A Y++ + L+AA+G SIEV SLFLM Sbjct: 4 TFKQSLPLSFSEEVANSVTHAIGAFAMLILLPISASYAYQTYDLKAAIGISIFVISLFLM 63 Query: 66 FLSSSIYHSMTYNSLQKYVLRMIDHSMIYIAIAGSYTPVALSLIGGWLGYLIIFLQWGIT 125- FLSS+IYHSM Y S+ KY+LR+IDHSMIYIAIAGSYTPVALSL+ GWLGY+II LQWGIT Sbjct: 64 FLSSTIYHSMAYGSVHKYILRIIDHSMIYIAIAGSYTPVALSLVSGWLGYIIIVLQWGIT 123- Query: 126 LFGILYKIFAPKINDKFSLVLYLIMGWLVIFIFPAIITKTGPAFWGLLLAGGICYTIGAL 18- 5 LFGILYKIFA +IN+KFSL+LY++MGWLV+FI P II KT AF L+L GG+ YTIGA+ Sbjct: 124 LFGILYKIFAKRINEKFSLMLYIVMGWLVVFILPVIIQKTSLAFGLLMLFGGLSYTIGAV 18- 3 Query: 186 FYARKRPYDHMIWHLFILLASILQYIGIVYFML 218 FYA+KRPY HMIWHLFILLAS LQ+I I +FML Sbjct: 184 FYAKKRPYFHMIWHLFILLASALQFIAITFFML 216 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1926 A DNA sequence (GBSx2035) was identified in S. agalactiae <SEQ ID 5971> which encodes the amino acid sequence <SEQ ID 5972>. Analysis of this protein sequence reveals the following: TABLE-US-05891 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3641(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05892 >GP:CAB12492 GB:Z99107 similar to hypothetical proteins [Bacillus subtilis] Identities = 81/302 (26%), Positives = 157/302 (51%), Gaps = 10/302 (3%) Query: 1 MKSAYIFFNPKSGKDEQALAKEVKSYLIEHDFQDDY-VRIITPSSVEEAVALAKKASEDH 59 MK A I +NP SG++ + K+ + +++ Q Y + +A AK+A+ Sbjct: 1 MKRARIIYNPTSGRE---IFKKHLAQVLQKFEQAGYETSTHATTCAGDATHAAREAALRE 57 Query: 60 IDLVIPLGGDGTINKICGGVYAGGAYPTIGLVPAGTVNNFSKALNIPQERNL-ALENLLN 118- DL+I GGDGTIN++ G+ PT+G++P GT N+F++AL IP+E L A + ++N Sbjct: 58 FDLIIAAGGDGTINEVVNGLAPLDNRPTLGVIPVGTTNDFARALGIPREDILKAADTVIN 117- Query: 119 GHVKSVDICKVNDDYMISSLTLGLLADIAANVTSEMKRKLGPFAFLGDAYRILKRNRSYS 17- 8 G + +DI +VN Y I+ G L ++ +V S++K LG A+ +L R Sbjct: 118 GVARPIDIGQVNGQYFINIAGGGRLTELTYDVPSKLKTMLGQLAYYLKGMEMLPSLRPTE 17- 7 Query: 179 ITLAYDNNVRSLRTRLLLITMTNSIAGMPAFSPEATIDDGLFRVYTMEHIHFFKLLLHLR 23- 8 + + YD + L L+T+TNS+ G +P+++++DG+F + ++ + + + Sbjct: 178 VEIEYDGKLFQGEIMLFLVTLTNSVGGFEKLAPDSSLNDGMFDLMILKKANLAEFIRVAT 23- 7 Query: 239 QFRKGDFSQAKEIKHFHTNNLTISTFKRKKSAIPKVRIDGDPGDQLPVKVEVIPKALKFI 29- 8 +G+ + I + N + ++ ++ ++ +DG+ G LP + + + + + Sbjct: 238 MALRGEHINDQHIIYTKANRVKVNVSEKM-----QLNLDGEYGGMLPGEFVNLYRHIHVV 29- 2 Query: 299 IP 300 +P Sbjct: 293 MP 294 A related DNA sequence was identified in S. pyogenes <SEQ ID 5119> which encodes the amino acid sequence <SEQ ID 5120>. Analysis of this protein sequence reveals the following: TABLE-US-05893 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4258(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05894 Identities = 172/300 (57%), Positives = 229/300 (76%) Query: 1 MKSAYIFFNPKSGKDEQALAKEVKSYLIEHDFQDDYVRIITPSSVEEAVALAKKASEDHI 60 MK+ IF+NP SGK E LA++VK Y +H F +D V++ITP ++A LAK+A++D I Sbjct: 1 MKTVRIFYNPNSGKKESQLARQVKDYFCQHGFSEDSVKVITPKDADQAFQLAKQAAKDKI 60 Query: 61 DLVIPLGGDGTINKICGGVYAGGAYPTIGLVPAGTVNNFSKALNIPQERNLALENLLNGH 120- DLVIPLGGDGT+NKI GG+Y GGA+ IGLVP+GTVNNF+KA++IP + AL+ +L G Sbjct: 61 DLVIPLGGDGTLNKIIGGIYEGGAHCLIGLVPSGTVNNFAKAMHIPLQITEALDTILTGQ 120- Query: 121 VKSVDICKVNDDYMISSLTLGLLADIAANVTSEMKRKLGPFAFLGDAYRILKRNRSYSIT 18- 0 +K VDICK N YMISSLTLGLLADIAA+VT+E KR+ GP AFL D+ RILKRNRSY+I+ Sbjct: 121 IKQVDICKANQQYMISSLTLGLLADIAADVTAEEKRRFGPLAFLKDSIRILKRNRSYAIS 18- 0 Query: 181 LAYDNNVRSLRTRLLLITMTNSIAGMPAFSPEATIDDGLFRVYTMEHIHFFKLLLHLRQF 24- 0 L N+ L+T+ LLITMTN+IAG P+FSP A DDG F+VYTM+ + FFK L H+ F Sbjct: 181 LISHNHRIHLKTKFLLITMTNTIAGFPSFSPGAQADDGYFQVYTMKKVSFFKFLWHINDF 24- 0 Query: 241 RRGDFSQAKEIKHFHTNNLTISTFKRKKSAIPKVRIDGDPGDQLPVKVEVIPKALKFIIP 30- 0 ++GDFS+A+EI HF N L++ +K++ +P+ RIDGD D LP+++++IPKA+ I+P Sbjct: 241 KQGDFSKAEEISHFQANTLSLLPQAKKQAILPRTRIDGDKSDYLPIQLDIIPKAVSIIVP 30- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1927 A DNA sequence (GBSx2036) was identified in S. agalactiae <SEQ ID 5973> which encodes the amino acid sequence <SEQ ID 5974>. Analysis of this protein sequence reveals the following: TABLE-US-05895 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3628(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05896 >GP:BAB10885 GB:AB010693 gene_id: K21C13.21~pir| |T04769~strong similarity to unknown protein [Arabidopsis thaliana] Identities = 85/291 (29%), Positives = 150/291 (51%), Gaps = 28/291 (9%) Query: 10 DQEWEVPVESGRYHMIVGSFCPYAQRPQIARQLLGLDKHISISFVDDV------------ 57 - D + + P ESGRYH+ + CP+A R ++ GLD+ I+ S V + Sbjct: 29 DPDSQFPAESGRYHLYISYACPWACRCLSYLKIKGLDEAITFSSVHAIWGRTKETDDHRG 88 Query: 58 ----PSDIGLIFSQPEQVTGAKSLRDIYHLTDPTYQGPYTIPILIDKTDNRIVCKESADL 113- SD L ++P+ + GAKS+R++Y + P Y+G YT+P+L DK +V ES+++ Sbjct: 89 WVFPDSDTELPGAEPDYLNGAKSVRELYEIASPNYEGKYTVPVLWDKKLKTVVNNESSEI 148- Query: 114 LRLFTTDFSDLHQEDAPVLFSQETASLIDNDIKDINKNFQSLMYKLAFLDKQADYDTYSK 17- 3 +R+F T+F+ + + + L+ +I+ + + +YK F KQ Y+ Sbjct: 149 IRMFNTEFNGIAKTPSLDLYPSHLRDVINETNGWVFNGINNGVYKCGFARKQEPYNEAVN 20- 8 Query: 174 EFFTFLDQKEHLLGQRPFLLGDNLSEVDIHFFTPLVRWDIAGRDLLLLNQKALEDYPNIF 23- 3 + + +D+ E +LG++ ++ G+ +E DI F L+R+D N++ L +YPNIF Sbjct: 209 QLYEAVDRCEEVLGKQRYICGNTFTEADIRLFVTLIRFDEVYAVHFKCNKRLLREYPNIF 26- 8 Query: 234 SWAKTLYNDFNLKTLTNPQSIKNNYY-----LGKFGRAVRHHTIVPTGPNM 279 ++ K +Y + + N + IK +YY + FG I+P GPN+ Sbjct: 269 NYIKDIYQIHGMSSTVNMEHIKQHYYGSHPTINPFG-------IIPHGPNI 312 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1928 A DNA sequence (GBSx2037) was identified in S. agalactiae <SEQ ID 5975> which encodes the amino acid sequence <SEQ ID 5976>. Analysis of this protein sequence reveals the following: TABLE-US-05897 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2647(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05898 >GP:BAB07793 GB:AB037666 hypothetical protein [Streptomyces sp. CL190] Identities = 127/331 (38%), Positives = 194/331 (58%), Gaps = 9/331 (2%) Query: 4 RKDDHIKYALKYQSHY---NSFDDIELIHSSLPKYNVNDIDLSTHFAGQSFEFPFYINAM 60 RKDDH++ A++ + + N FDD+ +H +L + D+ L+T FAG S++ P YINAM Sbjct: 6 RKDDHVRLAIEQHNAHSGRNQFDDVSFVHHALAGIDRPDVSLATSFAGISWQVPIYINAM 65 Query: 61 TGGSEKGKAVNHKLAQVAQATGIVMVTGSYSAALKNDE--DDSYPTTDLYPDLKLATNIG 118- TGGSEK +N LA A+ TG+ + +GS +A +K+ D D P+ + NI Sbjct: 66 TGGSEKTGLINRDLATAARETGVPIASGSMNAYIKDPSCADTFRVLRDENPNGFVIANIN 125- Query: 119 LDKPVPAAESTVKAMNPIFLQVHVNVMQELLMPEGEREFHMWRSHLKEYVDNIQCPLILK 17- 8 V A+ + + LQ+H+N QE MPEG+R F W +++ + P+I+K Sbjct: 126 ATTTVDNAQRAIDLIEANALQIHINTAQETPMPEGDRSFASWVPQIEKIAAAVDIPVIVK 18- 5 Query: 179 EVGFGMDLQSIKDAYDIGITTVDISGRGGTSFAYIENQRGR--DRSYLNTWGQTTAQSLI 23- 6 EVG G+ Q+I D+G+ D+SGRGGT FA IEN R D ++L+ WGQ+TA L+ Sbjct: 186 EVGNGLSRQTILLLADLGVQAADVSGRGGTDFARIENGRRELGDYAFLHGWGQSTAACLL 24- 5 Query: 237 NAQSMMDKMDILASGGIRHPLDMVKCLVLGAKAVGLSRTVLELVERYPVDDVIAILNSWK 29- 6 +AQ + + +LASGG+RHPLD+V+ L LGA+AVG S L + VD +I L +W Sbjct: 246 DAQDI--SLPVLASGGVRHPLDVVRALALGARAVGSSAGFLRTLMDDGVDALITKLTTWL 30- 3 Query: 297 EDLRMIMCALNCKKITDLRQVNYILYGQLKE 327 + L + L + DL + + +L+G+L++ Sbjct: 304 DQLAALQTMLGARTPADLTRCDVLLHGELRD 334 A related DNA sequence was identified in S. pyogenes <SEQ ID 5977> which encodes the amino acid sequence <SEQ ID 5978>. Analysis of this protein sequence reveals the following: TABLE-US-05899 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2823(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05900 Identities = 244/329 (74%), Positives = 284/329 (86%) Query: 1 MTNRKDDHIKYALKYQSHYNSFDDIELIHSSLPKYNVNDIDLSTHFAGQSFEFPFYINAM 60 MTNRKDDHIKYALKYQS YN+FDDIELIH SLP Y+++DIDLSTHFAGQ F+FPFYINAM Sbjct: 31 MTNRKDDHIKYALKYQSPYNAFDDIELIHHSLPSYDLSDIDLSTHFAGQDFDFPFYINAM 90 Query: 61 TGGSEKGKAVNHKLAQVAQATGIVMVTGSYSAALKNDEDDSYPTTDLYPDLKLATNIGLD 120- TGGS+KGKAVN KLA+VA ATGIVMVTGSYSAALKN DDSY ++ +LKLATNIGLD Sbjct: 91 TGGSQKGKAVNEKLAKVAAATGIVMVTGSYSAALKNPNDDSYRLHEVADNLKLATNIGLD 150- Query: 121 KPVPAAESTVKAMNPIFLQVHVNVMQELLMPEGEREFHMWRSHLKEYVDNIQCPLILKEV 18- 0 KPV + TV+ M P+FLQVHVNVMQELLMPEGER FH W+ HL EY I P+ILKEV Sbjct: 151 KPVALGQQTVQEMQPLFLQVHVNVMQELLMPEGERVFHTWKKHLAEYASQIPVPVILKEV 21- 0 Query: 181 GFGMDLQSIKDAYDIGITTVDISGRGGTSFAYIENQRGRDRSYLNTWGQTTAQSLINAQS 24- 0 GFGMD+ SIK A+D+GI T DISGRGGTSFAYIENQRG DRSYLN WGQTT Q L+NAQ Sbjct: 211 GFGMDVNSIKLAHDLGIQTFDISGRGGTSFAYIENQRGGDRSYLNDWGQTTVQCLLNAQG 27- 0 Query: 241 MMDKMDILASGGIRHPLDMVKCLVLGAKAVGLSRTVLELVERYPVDDVIAILNSWKEDLR 30- 0 +MD+++ILASGG+RHPLDM+KC VLGA+AVGLSRTVLELVE+YP + VIAI+N WKE+L+ Sbjct: 271 LMDQVEILASGGVRHPLDMIKCFVLGARAVGLSRTVLELVEKYPTERVIAIVNGWKEELK 33- 0 Query: 301 MIMCALNCKKITDLRQVNYILYGQLKEAN 329 +IMCAL+CK I +L+ V+Y+LYG+L++ N Sbjct: 331 IIMCALDCKTIKELKGVDYLLYGRLQQVN 359 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1929 A DNA sequence (GBSx2038) was identified in S. agalactiae <SEQ ID 5979> which encodes the amino acid sequence <SEQ ID 5980>. This protein is predicted to be phosphomevalonate kinase. Analysis of this protein sequence reveals the following: TABLE-US-05901 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0785(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05902 >GP:AAG02457 GB:AF290099 phosphomevalonate kinase [Streptococcus pneumoniae] Identities = 170/330 (51%), Positives = 233/330 (70%), Gaps = 1/330 (0%) Query: 1 MVKVQTGGKLYIAGEYAILYPGQVAILKNVPIYMTALATFADNYSLYSDMFNYTASLQPD 60 - M+ V+T GKLY AGEYAIL PGQ+A++K++PIYM A F+D+Y +YSDMF++ L+P+ Sbjct: 1 MIAVKTCGKLYWAGEYAILEPGQLALIKDIPIYMRAEIAFSDSYRIYSDMFDFAVDLRPN 60 Query: 61 KQYSLIQETILLMEEWLINFGKNIKPIHLEITGKLERYGLKFGIGSSGSVVVLTIKAMAA 120- YSLIQETI LM ++L G+N++P L+I GK+ER G KFG+GSSGSVVVL +KA+ A Sbjct: 61 PDYSLIQETIALMGDFLAVRGQNLRPFSLKICGKMEREGKKFGLGSSGSVVVLVVKALLA 120- Query: 121 LYEIEMPSDLLFKLSAYVLLKRGDNGSMGDIACIAYEHLISYSAFDRRAVSKMIETKPLE 18- 0 LY + + +LLFKL++ VLLKRGDNGSMGD+ACI E L+ Y +FDR+ + +E + L Sbjct: 121 LYNLSVDQNLLFKLTSAVLLKRGDNGSMGDLACIVAEDLVLYQSFDRQKAAAWLEEENLA 18- 0 Query: 181 QVLEAEWGYRITKIQALLEMDFLVGWTMQPSISKEMINIVKSTITQRFLDDTKYQVVQLL 24- 0 VLE +WG+ I++++ LE DFLVGWT + ++S M+ +K I Q FL +K VV L+ Sbjct: 181 TVLERDWGFFISQVKPTLECDFLVGWTKEVAVSSHMVQQIKQNINQNFLSSSKETVVSLV 24- 0 Query: 241 SAFKEGDKEAIKRCLEEISLLLFNLHPSIYTDKLQKLKEASKGLDIVTKSSGSGGGDCGI 30- 0 A ++G E + +E S LL L IYT L++LKEAS+ L V KSSG+GGGDCGI Sbjct: 241 EALEQGKAEKVIEQVEVASKLLEGLSTDIYTPLLRQLKEASQDLQAVAKSSGAGGGDCGI 30- 0 Query: 301 AISFN-KNDNQTLIKRWESAGIELLSKETL 329 A+SF+ ++ TL RW GIELL +E + Sbjct: 301 ALSFDAQSSRNTLKNRWADLGIELLYQERI 330 A related DNA sequence was identified in S. pyogenes <SEQ ID 5981> which encodes the amino acid sequence <SEQ ID 5982>. Analysis of this protein sequence reveals the following:

TABLE-US-05903 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2669(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05904 Identities = 171/325 (52%), Positives = 227/325 (69%), Gaps = 2/325 (0%) Query: 4 VQTGGKLYIAGEYAILYPGQVAILKNVPIYMTALATFADNYSLYSDMFNYTASLQPDKQY 63 VQTGGKLY+ GEYAIL PGQ A++ +P+ MTA + A + L SDMF++ A + PD Y Sbjct: 22 VQTGGKLYLTGEYAILTPGQKALIHFIPLMMTAEISPAAHIQLASDMFSHKAGMTPDASY 81 Query: 64 SLIQETILLMEEWLINFGKNIKPIHLEITGKLERYGLKFGIGSSGSVVVLTIKAMAALYE 123- +LIQ T+ ++L ++P L ITGK+ER G KFGIGSSGSV +LT+KA++A Y+ Sbjct: 82 ALIQATVKTFADYLGQSIDQLEPFSLIITGKMERDGKKFGIGSSGSVTLLTLKALSAYYQ 141- Query: 124 IEMPSDLLFKLSAYVLLKRGDNGSMGDIACIAYEHLISYSAFDRRAVSKMIETKPLEQVL 18- 3 I + +LLFKL+AY LLK+GDNGSMGDIACIAY+ L++Y++FDR VS ++T PL+++L Sbjct: 142 ITLTPELLFKLAAYTLLKQGDNGSMGDIACIAYQTLVAYTSFDREQVSNWLQTMPLKKLL 20- 1 Query: 184 EAEWGYRITKIQALLEMDFLVGWTMQPSISKEMINIVKSTITQRFLDDTKYQVVQ-LLSA 24- 2 +WGY I IQ L DFLVGWT P+IS++MI V ++IT FL T YQ+ Q + A Sbjct: 202 VKDWGYHIQVIQPALPCDFLVGWTKIPAISRQMIQQVTASITPAFL-RTSYQLTQSAMVA 26- 0 Query: 243 FKEGDKEAIKRCLEEISLLLFNLHPSIYTDKLQKLKEASKGLDIVTKSSGSGGGDCGIAI 30- 2 +EG KE +K+ L S LL LHP+IY KL L A + D V KSSGSGGGDCGIA+ Sbjct: 261 LQEGHKEELKKSLAGASHLLKELHPAIYHPKLVTLVAACQKQDAVAKSSGSGGGDCGIAL 32- 0 Query: 303 SFNKNDNQTLIKRWESAGIELLSKE 327 +FN++ TLI +W+ A I LL +E Sbjct: 321 AFNQDARDTLISKWQEADIALLYQE 345 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1930 A DNA sequence (GBSx2039) was identified in S. agalactiae <SEQ ID 5983> which encodes the amino acid sequence <SEQ ID 5984>. Analysis of this protein sequence reveals the following: TABLE-US-05905 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.75 Transmembrane 20-36 (18-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.1720(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1931 A DNA sequence (GBSx2040) was identified in S. agalactiae <SEQ ID 5985> which encodes the amino acid sequence <SEQ ID 5986>. This protein is predicted to be mevalonate diphosphate decarboxylase. Analysis of this protein sequence reveals the following: TABLE-US-05906 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1557(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05907 >GP:AAG02456 GB:AF290099 mevalonate diphosphate decarboxylase [Streptococcus pneumoniae] Identities = 219/312 (70%), Positives = 264/312 (84%) Query: 1 MDGKSISVKSYANIAIIKYWGKADAEKMIPATSSISLTLENMYTETRLTALGKDAKKDEF 60 MD + ++V+SYANIAIIKYWGK ++M+PATSSISLTLENMYTET L+ L + DEF Sbjct: 1 MDREPVTVRSYANIAIIKYWGKKKEKEMVPATSSISLTLENMYTETTLSPLPANVTADEF 60 Query: 61 YISGVLQNDHEHDKMSAILDRFRQNRSGFVKIETTNNMPTAAGLSSSSSGLSALVKACND 120- YI+G LQN+ EH KMS I+DR+R GFV+I+T NNMPTAAGLSSSSSGLSALVKACN Sbjct: 61 YINGQLQNEVEHAKMSKIIDRYRPAGEGFVRIDTQNNMPTAAGLSSSSSGLSALVKACNA 120- Query: 121 FFGTNLSQSQLAQEAKFASGSSSRSFFGPVAAWDKDSGDIYKVHTNLDLAMIMLVLNDKR 18- 0 +F L +SQLAQEAKFASGSSSRSF+GP+ AWDKDSG+IY V T+L LAMIMLVL DK+ Sbjct: 121 YFKLGLDRSQLAQEAKFASGSSSRSFYGPLGAWDKDSGEIYPVETDLKLAMIMLVLEDKK 18- 0 Query: 181 KPISSREGMKICTETSTTFNEWVRQSEQDYQDMLVYLKNNDFQKVGQLTERNALAMHSTT 24- 0 KPISSR+GMK+C ETSTTF++WVRQSE+DYQDML+YLK NDF K+G+LTE+NALAMH+TT Sbjct: 181 KPISSRDGMKLCVETSTTFDDWVRQSEKDYQDMLIYLKENDFAKIGELTEKNALAMHATT 24- 0 Query: 241 KTATPAFSYLTEETYKAMDVVKKLREKGHECYYTMDAGPNVKVLCLRQDLEALAAILEKD 30- 0 KTA+PAFSYLT+ +Y+AM V++LREKG CY+TMDAGPNVKV C +DLE L+ I + Sbjct: 241 KTASPAFSYLTDASYEAMAFVRQLREKGEACYFTMDAGPNVKVFCQEKDLEHLSEIFGQR 30- 0 Query: 301 YRIIVSTTKELA 312 YR+IVS TK+L+ Sbjct: 301 YRLIVSKTKDLS 312 A related DNA sequence was identified in S. pyogenes <SEQ ID 5987> which encodes the amino acid sequence <SEQ ID 5988>. Analysis of this protein sequence reveals the following: TABLE-US-05908 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1271(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05909 Identities = 221/313 (70%), Positives = 258/313 (81%) Query: 1 MDGKSISVKSYANIAIIKYWGKADAEKMIPATSSISLTLENMYTETRLTALGKDAKKDEF 60 +D I+V SYANIAIIKYWGK + KMIP+TSSISLTLENM+T T ++ L A D+F Sbjct: 1 VDPNVITVTSYANIAIIKYWGKENQAKMIPSTSSISLTLENMFTTTSVSFLPDTATSDQF 60 Query: 61 YISGVLQNDHEHDKMSAILDRFRQNRSGFVKIETTNNMPTAAGLSSSSSGLSALVKACND 120- YI+G+LQND EH K+SAI+D+FRQ FVK+ET NNMPTAAGLSSSSSGLSALVKAC+ Sbjct: 61 YINGILQNDEEHTKISAIIDQFRQPGQAFVKMETQNNMPTAAGLSSSSSGLSALVKACDQ 120- Query: 121 FFGTNLSQSQLAQEAKFASGSSSRSFFGPVAAWDKDSGDIYKVHTNLDLAMIMLVLNDKR 18- 0 F T L Q LAQ+AKFASGSSSRSFFGPVAAWDKDSG IYKV T+L +AMIMLVLN + Sbjct: 121 LFDTQLDQKALAQKAKFASGSSSRSFFGPVAAWDKDSGAIYKVETDLKMAMIMLVLNAAK 18- 0 Query: 181 KPISSREGMKICTETSTTFNEWVRQSEQDYQDMLVYLKNNDFQKVGQLTERNALAMHSTT 24- 0 KPISSREGMK+C +TSTTF++WV QS DYQ ML YLK N+F+KVGQLTE NALAMH+TT Sbjct: 181 KPISSREGMKLCRDTSTTFDQWVEQSAIDYQHMLTYLKTNNFEKVGQLTEANALAMHATT 24- 0 Query: 241 KTATPAFSYLTEETYKAMDVVKKLREKGHECYYTMDAGPNVKVLCLRQDLEALAAILEKD 30- 0 KTA P FSYLT+E+Y+AM+ VK+LR++G CY+TMDAGPNVKVLCL +DL LA L K+ Sbjct: 241 KTANPPFSYLTKESYQAMEAVKELRQEGFACYFTMDAGPNVKVLCLEKDLAQLAERLGKN 30- 0 Query: 301 YRIIVSTTKELAD 313 YRIIVS TK+L D Sbjct: 301 YRIIVSKTKDLPD 313 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1932 A DNA sequence (GBSx2041) was identified in S. agalactiae <SEQ ID 5989> which encodes the amino acid sequence <SEQ ID 5990>. Analysis of this protein sequence reveals the following: TABLE-US-05910 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1512(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 5991> which encodes the amino acid sequence <SEQ ID 5992>. Analysis of this protein sequence reveals the following: TABLE-US-05911 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1117(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05912 Identities = 182/290 (62%), Positives = 223/290 (76%) Query: 1 MKEKFGIGKAHSKIILMGEHSVVYGYPAIAIPLKNIEVTCLIEEAPQLIALDMTDPLSTA 60 M E G GKAHSKIIL+GEH+VVYGYPAIA+PL +IEV C I A + + D D LSTA Sbjct: 6 MNENIGYGKAHSKIILIGEHAVVYGYPAIALPLTDIEVVCHIFPADKPLVFDFYDTLSTA 65 Query: 61 IFAALDYLGKTSSKIAYHIESQVPERRGMGSSAAVAIAAIRAVFDYFDEDLEADLLECLV 120- I+A+LDYL + IAY I SQVP++RGMGSSAAV+IAAIRAVF Y E L DLLE LV Sbjct: 66 IYASLDYLQRLQEPIAYEIVSQVPQKRGMGSSAAVSIAAIRAVFSYCQEPLSDDLLEILV 125- Query: 121 NRAEMIAHSNPSGLDAKTCLSENTIKFIRNIGFSTVPMHLNAYLVIADTGIHGHTKEAVD 18- 0 N+AE+IAH+NPSGLDAKTCLS++ IKFIRNIGF T+ + LN YL+IADTGIHGHT+EAV+ Sbjct: 126 NKAEIIAHTNPSGLDAKTCLSDHAIKFIRNIGFETIEIALNGYLIIADTGIHGHTREAVN 18- 5 Query: 181 KVKSSGEAVLPFLKELGYLAEASEDAIHKSDSKQLGSLMTKAHQSLKQLGVSSLEADHLV 24- 0 KV E LP+L +LG L +A E AI++ + +G LMT+AH +LK +GVS +AD LV Sbjct: 186 KVAQFEETNLPYLAKLGALTQALERAINQKNKVAIGQLMTQAHSALKAIGVSISKADQLV 24- 5 Query: 241 EVAISCGALGAKMSGGGLGGCIIALVKEKREAERLSQQLEREGAVNTWTE 290 E A+ GALGAKM+GGGLGGC+IAL K AE++S +L+ EGAVNTW + Sbjct: 246 EAALRAGALGAKMTGGGLGGCMIALADTKDMAEKISHRLKEEGAVNTWIQ 295 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1933 A DNA sequence (GBSx2042) was identified in S. agalactiae <SEQ ID 5993> which encodes the amino acid sequence <SEQ ID 5994>. This protein is predicted to be a histidine protein kinase. Analysis of this protein sequence reveals the following: TABLE-US-05913 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.43 Transmembrane 12-28 (4-33) INTEGRAL Likelihood = -9.29 Transmembrane 163-179 (157-191) ----- Final Results ----- bacterial membrane --- Certainty = 0.6371(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05914 >GP:AAF79919 GB:AF039082 putative histidine protein kinase [Lactococcus lactis] Identities = 78/315 (24%), Positives = 154/315 (48%), Gaps = 33/315 (10%) Query: 101 SDRQIKNYAKRIVSQNSHSGHITYNFSTYSYLLKKVGKNDYLVVFLDTTNQYLDNQRLLQ 16- 0 +++QI N + + +N + + Y + T S + V++ + Q + Sbjct: 84 NEKQI-NTIQTVSVKNPYGDNWHYRYLTTSQFIITNSDGTVTPVYVQIFSNVDQIQDAMS 142- Query: 161 LSIWM---SLVSFIVFMVIVSV-LSGRVILPFVANYEKQRRFITNAGHELKTPLAIISAN 21- 6 ++W+ ++++F + VI+S+ L+ + P +A YEKQ+ F+ NA HEL+TPLAI+ Sbjct: 143 RAMWVIVTTMITFWILSVIISLYLANWTLKPILAAYEKQKEFVENASHELRTPLAILQNR 20- 2 Query: 217 NELV-----EMMSGESEWTKSTNDQIQRLTGLINGMVSLAR------FEEQPDISM---- 26- 1 EL+ + +SE + +++ + L + +++LAR E +P + Sbjct: 203 LELLFQKPTATIIDQSENISESLSEVRNMRLLTSNLLNLARRDSGIKIEPEPTTATYFEN 26- 2 Query: 262 VDLDFSHITKDAAEDFKGPIIKDGKDFIMSIQPGIHVKAEEKSLFELVTLLVDNANKYCD 32- 1 + + +T++A + F G + +G V ++ + +L+T+L DNA KY D Sbjct: 263 IFNSYEMLTENAGKKFSGNLKLEGT-----------VNLDQALIKQLLTILFDNALKYTD 31- 1 Query: 322 PMGTVTVKLSRSSRLRRAKLEVSNTYKNGKDIDYSKFFERFYREDESHNNKKSGYGIGLS 38- 1 G ++V + ++ V++ + D D K F+RF+R D++ +K G G+GLS Sbjct: 312 SEGEISVDVIKNGGF--LTFAVADNGEGISDEDKKKIFDRFFRVDKARTRQKGGLGLGLS 36- 9 Query: 382 IVTSLVHLFKGSIDV 396 + +V + G I V Sbjct: 370 LAKQIVEAYNGKITV 384 A related DNA sequence was identified in S. pyogenes <SEQ ID 5751> which encodes the amino acid sequence <SEQ ID 5752>. Analysis of this protein sequence reveals the following: TABLE-US-05915 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.30 Transmembrane 18-34 (13-42) INTEGRAL Likelihood = -10.35 Transmembrane 170-186 (163-199) ----- Final Results ----- bacterial membrane --- Certainty = 0.5522(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05916 Identities = 233/410 (56%), Positives = 303/410 (73%), Gaps = 1/410 (0%) Query: 1 MFRNLRLRFIGIAALAILVVLFSVVGVLNSANHYQTKNEIYRVLTILADNNGRIPNKLEF 60 MF +R+RFI IA++AI ++L S+VG++N+A YQ++ EI R+L +++ N G++P E Sbjct: 10 MFNRIRIRFIMIASIAIFIILSSIVGIINTARCYQSQQEINRILHLISSNKGKLPGTTES 69 Query: 61 SKELGDDLSTDAIFQFRYFSARTDAKGNVTSFDSRNIFEVSDRQIKNYAKRIVSQNSHSG 120- SK LG LS D++ QFRY+S +A G++ S ++ NI + + + +A+ G Sbjct: 70 SKRLGTKLSEDSLSQFRYYSVIFNANGHLLSSNTANISALDREEAQYFARLFAKSGEEKG 129- Query: 121 HITYNFSTYSYLLKKVGKNDYLVVFLDTTNQYLDNQRLLQLSIWMSLVSFIVFMVIVSVL 18- 0 + S YSYL+ ++ + LVV LDTT + LL +S+ ++ FI F+V+VS+ Sbjct: 130 SYRHQDSVYSYLITQLPNEEKLVVILDTTFYFRSVGDLLAVSVMLAFGGFIFFVVLVSLF 18- 9 Query: 181 SGRVILPFVANYEKQRRFITNAGHELKTPLAIISANNELVEMMSGESEWTKSTNDQIQRL 24- 0 SG VI PFV NYEKQRRFITNAGHELKTPLAIISANNELVE+M+GESEWTKST+DQ++RL Sbjct: 190 SGMVIKPFVQNYEKQRRFITNAGHELKTPLAIISANNELVELMTGESEWTKSTSDQVKRL 24- 9 Query: 241 TGLINGMVSLARFEEQPDISMVDLDFSHITKDAAEDFKGPIIKDGKDFIMSIQPGIHVKA 30- 0 TGLIN M++LAR EEQPD+ + +DFS I +DAAEDFK ++KDGK F ++IQP I +KA Sbjct: 250 TGLINQMITLARLEEQPDVVLHMVDFSAIAQDAAEDFKSLVLKDGKRFDLTIQPNIMIKA 30- 9 Query: 301 EEKSLFELVTLLVDNANKYCDPMGTVTVKLSRSSRLR-RAKLEVSNTYKNGKDIDYSKFF 35- 9 EEKSLFELVT+LVDNANKYCDP G V V L+ R R RAKLEVSNTY GK IDYS+FF Sbjct: 310 EEKSLFELVTILVDNANKYCDPKGLVKVSLTTIGRRRKRAKLEVSNTYLEGKSIDYSRFF 36- 9 Query: 360 ERFYREDESHNNKKSGYGIGLSIVTSLVHLFKGSIDVNYKHDTITFVIYI 409 ERFYREDESHN+K+ GYGIGLS+ S+V LFKG+I VNYK+D I F + I Sbjct: 370 ERFYREDESHNSKEKGYGIGLSMAESMVKLFKGTITVNYKNDAIVFTVVI 419 SEQ ID 5994 (GBS273) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 51 (lane 14; MW 46 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 56 (lane 5; MW 71 kDa). GBS273-GST was purified as shown in FIG. 208, lane 4. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1934 A DNA sequence (GBSx2043) was identified in S. agalactiae <SEQ ID 5995> which encodes the amino acid sequence <SEQ ID 5996>. Analysis of this protein sequence reveals the following: TABLE-US-05917 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2181(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1935 A DNA sequence (GBSx2044) was identified in S. agalactiae <SEQ ID 5997> which encodes the amino acid sequence <SEQ ID 5998>. This protein is predicted to be two-component response regulator (trcR). Analysis of this protein sequence reveals the following: TABLE-US-05918 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2503(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9379> which encodes amino acid sequence <SEQ ID 9380> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05919 >GP:BAB04091 GB:AP001508 two-component response regulator [Bacillus halodurans] Identities = 71/183 (38%), Positives = 120/183 (64%), Gaps = 3/183 (1%) Query: 9 RVLIAEDEEQMSRVLSTAISHQGYVVDVAYDGQTAIDLANQNAYDVMVMDVMMPVKTGIE 68 R+LI EDE++++RVL + H+GY D A+ G ++ +A+D++++DVM+P +G+E Sbjct: 3 RILIIEDEKKIARVLQLELEHEGYETDAAFSGSDGLETFQAHAWDLVLLDVMLPELSGLE 62 Query: 69 AVKEIRQSGNKSHIIMLTAMAEIDDRVTGLDAGADDYLTKPFSLKELLARLRSMSRRLE- 127- ++ IR + + II+LTA I D+V+GLD GA+DY+TKPF ++ELLAR+R+ R ++ Sbjct: 63 VLRRIRMTDPVTPIILLTARNSIPDKVSGLDLGANDYITKPFEIEELLARVRACLRTVQT 122- Query: 128 -DFTPNVLSLGRVTLSVGEQELQCEN-TIRLAGKEAKMLAFFMLNHDKELSTQQLFEHVW 18- 5 + + L +T++ +++Q N TI L KE ++L FF+ N + LS +Q+ +VW Sbjct: 123 RERVEDTLMFQELTINEKTRDVQRGNETIELTPKEFELLVFFIKNKGQVLSREQILTNVW 18- 2 Query: 186 GAD 188 G D Sbjct: 183 GFD 185 A related DNA sequence was identified in S. pyogenes <SEQ ID 5999> which encodes the amino acid sequence <SEQ ID 6000>. Analysis of this protein sequence reveals the following: TABLE-US-05920 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2391(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05921 Identities = 125/185 (67%), Positives = 151/185 (81%) Query: 8 MRVLIAEDEEQMSRVLSTAISHQGYVVDVAYDGQTAIDLANQNAYDVMVMDVMMPVKTGI 67 M++L+AEDE QMS VL+TA++HQGY VDV ++GQ AID A NAYD+M++D+MMP+K+GI Sbjct: 1 MKILLAEDEWQMSNVLTTAMTHQGYDVDVVFNGQEAIDKAKDNAYDIMILDIMMPIKSGI 60 Query: 68 EAVKEIRQSGNKSHIIMLTAMAEIDDRVTGLDAGADDYLTKPFSLKELLARLRSMSRRLE 127- EA+KEIR SGN SHIIMLTAMAEI+DRVTGLDAGADDYLTKPFSLKELLARLRSM RR+E Sbjct: 61 EALKEIRASGNCSHIIMLTAMAEINDRVTGLDAGADDYLTKPFSLKELLARLRSMERRVE 120- Query: 128 DFTPNVLSLGRVTLSVGEQELQCENTIRLAGKEAKMLAFFMLNHDKELSTQQLFEHVWGA 18- 7 FTP VL VTL++ EQEL N IRLA KE K++AF MLN K L T+ L++HVW Sbjct: 121 SFTPQVLQFAGVTLNINEQELSAGNAIRLASKEGKLMAFLMLNQGKYLDTKTLYQHVWSD 18- 0 Query: 188 DKDQE 192 +D + Sbjct: 181 QEDYD 185 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1936 A DNA sequence (GBSx2045) was identified in S. agalactiae <SEQ ID 6001> which encodes the amino acid sequence <SEQ ID 6002>. Analysis of this protein sequence reveals the following:

TABLE-US-05922 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2627(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05923 >GP:BAB05604 GB:AP001513 unknown conserved protein [Bacillus halodurans] Identities = 67/182 (36%), Positives = 111/182 (60%), Gaps = 4/182 (2%) Query: 17 LEDFSQRIQLENDKAKVETGYKLYEHIIGRIKTSDSMIEKCRRKQLPVTVDSALKTIRDS 76 - L++ + +I + + + Y EH+ R+K+ +S++ K +R+ T++S + +RD Sbjct: 29 LQELNTKIDILKQEFQYIHDYNPIEHVSSRVKSPESIVNKIQRRGNDFTLESIRENVRDI 88 Query: 77 IGVRIICGFVNDIYQIIERIKAFDDCRIVVEKDYIQHVKPNGYRSYHVILEIDTPYPDCL 136- G+RI C F +DIY + E++ D +V KDYI++ KPNGYRS H+IL I P + Sbjct: 89 AGIRITCSFESDIYTLSEQLMQQHDISVVETKDYIKNPKPNGYRSLHLILSI----PIFM 144- Query: 137 GNSDGKYYIEIQLRTIAQDSWASLEHQMKYKHDIENPERIVRELKRCADEMASVDLTMQT 19- 6 + Y+E+Q+RTIA D WASLEH++ YK++ PE +++ELK A+ A +D M+ Sbjct: 145 SDRVQDVYVEVQIRTIAMDFWASLEHKIYYKYNKNVPEHLLKELKDAAESAALLDQKMEK 20- 4 Query: 197 IR 198 I+ Sbjct: 205 IQ 206 A related DNA sequence was identified in S. pyogenes <SEQ ID 6003> which encodes the amino acid sequence <SEQ ID 6004>. Analysis of this protein sequence reveals the following: TABLE-US-05924 Possible Site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1057(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05925 Identities = 127/206 (61%), Positives = 162/206 (77%) Query: 3 TNIYGDYGRYLPLILEDFSQRIQLENDKAKVETGYKLYEHIIGRIKTSDSMIEKCRRKQL 62 ++IY + YLPL+L+ + I EN K+K ETG+KLYEH RIK+ SMIEKC+RKQL Sbjct: 11 SSIYSGFEVYLPLVLQTITDVIIAENIKSKKETGFKLYEHFTSRIKSEASMIEKCQRKQL 70 Query: 63 PVTVDSALKTIRDSIGVRIICGFVNDIYQIIERIKAFDDCRIVVEKDYIQHVKPNGYRSY 122- P+T SALK I+DSIG+RIICGF++DIY++++ +K+ + EKDYI + KPNGYRSY Sbjct: 71 PLTSKSALKIIKDSIGIRIICGFIDDIYRMVDLLKSIPGMSVNTEKDYILNAKPNGYRSY 130- Query: 123 HVILEIDTPYPDCLGNSDGKYYIEIQLRTIAQDSWASLEHQMKYKHDIENPERIVRELKR 18- 2 H+ILE++T +PD LG G Y+IE+QLRTIAQDSWASLEHQMKYKH + N E I RELKR Sbjct: 131 HLILELETHFPDILGEKKGCYFIEVQLRTIAQDSWASLEHQMKYKHQVANAEMITRELKR 19- 0 Query: 183 CADEMASVDLTMQTIRQLIESGTKKE 208 CADE+AS D+TMQTIRQLI+ T++E Sbjct: 191 CADELASCDVTMQTIRQLIQETTEEE 216 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1937 A DNA sequence (GBSx2046) was identified in S. agalactiae <SEQ ID 6005> which encodes the amino acid sequence <SEQ ID 6006>. Analysis of this protein sequence reveals the following: TABLE-US-05926 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3250(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05927 >GP:CAA37193 GB:X53013 ORF1 (AA 1-384) [Lactococcus lactis] Identities = 30/55 (54%), Positives = 37/55 (66%) Query: 1 MEFYYKTLKRKFINDADTIFIEQSQFEIFIYIETDHNSSSSHVVLDYQSQKEFEK 55 ME +YKTLKR+ +NDA ++ EIF YIET +N+ H LDYQS K+FEK Sbjct: 327 MESFYKTLKRELINDAHFETRAEATQEIFKYIETYYNTKWMHSGLDYQSPKDFEK 381 A related DNA sequence was identified in S. pyogenes <SEQ ID 6007> which encodes the amino acid sequence <SEQ ID 6008>. Analysis of this protein sequence reveals the following: TABLE-US-05928 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3065(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05929 Identities = 31/59 (52%), Positives = 39/59 (65%) Query: 1 MEFYYKTLKRKFINDADTIFIEQSQFEIFIYIETDHNSSSSHVVLDYQSQKEFEKIITN 59 ME +YKTLKR+ +NDA I+Q+Q EIF Y ET +N H L Y S EFEKI+T+ Sbjct: 13 MEAFYKTLKRELVNDAHFATIKQAQLEIFKYSETYYNPKRLHSALGYLSPVEFEKIVTH 71 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1938 A DNA sequence (GBSx2047) was identified in S. agalactiae <SEQ ID 6009> which encodes the amino acid sequence <SEQ ID 6010>. This protein is predicted to be R5 protein. Analysis of this protein sequence reveals the following: TABLE-US-05930 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.98 Transmembrane 30-46 (29-51) INTEGRAL Likelihood = -2.76 Transmembrane 967-983 (966-985) ----- Final Results ----- bacterial membrane --- Certainty = 0.2593(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8935> which encodes amino acid sequence <SEQ ID 8936> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-05931 Lipop: Possible site: -1 Crend: 8 SRCFLG: 0 McG: Length of UR: 2 Peak Value of UR: 2.44 Net Charge of CR: 2 McG: Discrim Score: 0.78 GvH: Signal Score (-7.5): -0.0599995 Possible site: 39 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 40 ALOM program count: 0 value: 7.37 threshold: 0.0 PERIPHERAL Likelihood = 7.37 194 modified ALOM score: -1.97 *** Reasoning Step: 3 Rule gpo1 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 944-948 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8936 (GBS200) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 29 (lane 3; MW 107.4 kDa), in FIG. 169 (lane 4; MW 122 kDa) and in FIG. 238 (lane 11; MW 122 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 35 (lane 3; MW 132 kDa). Purified Thio-GBS200-His is shown in FIG. 244, lane 9. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1939 A DNA sequence (GBSx2048) was identified in S. agalactiae <SEQ ID 6011> which encodes the amino acid sequence <SEQ ID 6012>. This protein is predicted to be a 16.1 kDa transcriptional regulator. Analysis of this protein sequence reveals the following: TABLE-US-05932 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3919(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9953> which encodes amino acid sequence <SEQ ID 9954> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05933 >GP:CAB16108 GB:Z99124 similar to transcriptional regulator (MarR family) [Bacillus subtilis] Identities = 30/114 (26%), Positives = 59/114 (51%), Gaps = 3/114 (2%) Query: 29 DVEHLAGPQGHLVMYLYKHPDKDMSIKAVEEILHISKSVASNLVKRMEKNGFIAIVPSKT 88 - D++ G +LV +Y++P + + + E++ + ++ A+ +K++E GFI +P + Sbjct: 25 DLDLTRGQYLYLVR-IYENPG--IIQEKLAEMIKVDRTTAARAIKKLEMQGFIQKLPDEQ 81 Query: 89 DKRVKYLYLTHLGKKKATQFEIFLEKLHSTMLAGITKEEIRTTKKVIRTLAKNM 142 +K++K L+ T GKK E L+G T EE T ++ + KN+ Sbjct: 82 NKKIKKLFPTEKGKKVYPLLRREGEHSTEVALSGFTSEEKETISALLHRVRKNI 135 A related DNA sequence was identified in S. pyogenes <SEQ ID 6013> which encodes the amino acid sequence <SEQ ID 6014>. Analysis of this protein sequence reveals the following: TABLE-US-05934 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4175(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05935 Identities = 27/64 (42%), Positives = 46/64 (71%) Query: 3 MENPLQKARILVNQLEKYLDHYAKEYDVEHLAGPQGHLVMYLYKHPDKDMSIKAVEEILH 62 M + R L++Q+E+ D AK+YDVEHLAGPQG+++++L KH ++++ +K +E+ L Sbjct: 1 MSQVIGDLRELIHQIEQISDEIAKKYDVEHLAGPQGYVLVFLAKHQNQEIFVKDIEKQLR 60 Query: 63 ISKS 66 I +S Sbjct: 61 IFQS 64 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1940 A DNA sequence (GBSx2049) was identified in S. agalactiae <SEQ ID 6015> which encodes the amino acid sequence <SEQ ID 6016>. This protein is predicted to be 5'-nucleotidase family protein. Analysis of this protein sequence reveals the following: TABLE-US-05936 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -2.66 Transmembrane 668-684 (665-684) ----- Final Results ----- bacterial membrane --- Certainty = 0.2062(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05937 >GP:CAB12747 GB:Z99108 similar to 5'-nucleotidase [Bacillus subtilis] Identities = 178/535 (33%), Positives = 270/535 (50%), Gaps = 55/535 (10%) Query: 28 DQVGVQVIGVNDFHGALDNTGTANMPDGKVANAGTAAQLD---AYMDDAQKDFKQTNPNG 84 - + V ++++ +ND HG +D ++ DG GT ++D AY+ + + + K Sbjct: 586 EHVPLRILSMNDLHGKIDQQYELDL-DGNGTVDGTFGRMDYAAAYLKEKKAEKKN----- 63- 9 Query: 85 ESIRVQAGDMVGASPANSGLLQDEPTVKNFNAMNVEYGTLGNHEFDEGLAEYNRIVTGKA 144- S+ V AGDM+G S S LLQDEPTV+ + + GT+GNHEFDEG E RI+ G Sbjct: 640 -SLIVHAGDMIGGSSPVSSLLQDEPTVELMEDIGFDVGTVGNHEFDEGTDELLRILNG-G 69- 7 Query: 145 PAPDSNINNITKSYPHEAAKQEIVVANVIDKVNKQIPYNWKPYAIKNIPVNNKSVNVGFI 20- 4 P +++P +V AN ++ +P+ +N + V V FI Sbjct: 698 DHPKGTSGYDGQNFP-------LVCANC------KMKSTGEPFLPAYDIINVEGVPVAFI 74- 4 Query: 205 GIVTKDIPNLVLRKNYEQYEFLDEAETIVKYAKELQAKNVKAIVVLAHVPATSKNDIAEG 26- 4 G+VT+ +V+ + + EF DEA + K A+EL+ K VKAI VLAH+ A + G Sbjct: 745 GVVTQSAAGMVMPEGIKNIEFTDEATAVNKAAEELKKKGVKAIAVLAHMSAEQNGNAITG 80- 4 Query: 265 EAAEMMKKVNQLFPENSVDIVFAGHNHQYTNGLVGKTRIVQALSQGKAYADVRGVLDTDT 32- 4 E+A++ K ++ +D++FA HNHQ NG V IVQA GKA V +D T Sbjct: 805 ESADLANKT-----DSEIDVIFAAHNHQVVNGEVNGKLIVQAFEYGKAIGVVDVEIDKTT 85- 9 Query: 325 QDFIETPSAKVIAVAPGKKTGSADIQAIVDQANTIVKQVTEAKIGTAEVSVMITRSVDQD 38- 4 +D ++ SA+++ V K AI+ + TI + + +G A V + S D D Sbjct: 860 KDIVK-KSAEIVYVDQSKIEPDVSASAILKKYETIAEPIISEVVGEAAVDMEGGYSNDGD 91- 8 Query: 385 NVSPVGSLITEAQLAIARKSWPDIDFAMTNNGGIRADLLIKPDGTITWGAAQAVQPFGNI 44- 4 +P+G+LI + A + DFA+ N GGIR L G ITWG +QPFGN+ Sbjct: 919 --TPLGNLIADGMRAAMK-----TDFALMNGGGIREAL---KKGPITWGDLYNIQPFGNV 96- 8 Query: 445 LQVVEITGRDLYKALNEQYDQKQNFFLQIAGLRYTYTDNKEGGEETPFKVVKAYKSNGEE 50- 4 L +EI G+DL + +N Q I+G +TYT +KE G+ K+ ++G E Sbjct: 969 LTKLEIKGKDLREIINAQISPVFGPDYSISG--FTYTWDKETGKAVDMKM-----ADGTE 10- 21 Query: 505 INPDAKYKLVINDFLFGGGDGFASFRNAKLLGAINP-----DTEVFMAYITDLEK 554 I PDA Y L +N+F+ A ++ LLG NP D E + Y+ ++ Sbjct: 1022 IQPDATYTLTVNNFMATATG--AKYQPIGLLGK-NPVTGPEDLEATVEYVKSFDE 1073 A related DNA sequence was identified in S. pyogenes <SEQ ID 1607> which encodes the amino acid sequence <SEQ ID 1608>. Analysis of this protein sequence reveals the following: TABLE-US-05938 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.67 Transmembrane 662-678 (661-679) INTEGRAL Likelihood = -2.02 Transmembrane 19-35 (18-35) ----- Final Results ----- bacterial membrane --- Certainty = 0.2869(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05939 Identities = 415/688 (60%), Positives = 517/688 (74%), Gaps = 21/688 (3%) Query: 1 MKKKIILKSSVLGLVAGTSIMFSSVFADQVGVQVIGVNDFHGALDNTGTANMPDGKVANA 60 MKK ILKSSVL ++ +++ + V ADQV VQ +GVNDFHGALDNTGTA P GK+ NA Sbjct: 14 MKKYFILKSSVLSILTSFTLLVTDVQADQVDVQFLGVNDFHGALDNTGTAYTPSGKIPNA 73 Query: 61 GTAAQLDAYMDDAQKDFKQTNPNGESIRVQAGDMVGASPANSGLLQDEPTVKNFNAMNVE 120- GTAAQL AYMDDA+ DFKQ N +G SIRVQAGDMVGASPANS LLQDEPTVK FN M E Sbjct: 74 GTAAQLGAYMDDAEIDFKQANQDGTSIRVQAGDMVGASPANSALLQDEPTVKVFNKMKFE 133- Query: 121 YGTLGNHEFDEGLAEYNRIVTGKAPAPDSNINNITKSYPHEAAKQEIVVANVIDKVNKQI 18- 0 YGTLGNHEFDEGL E+NRI+TG+AP P+S IN+ITK Y HEA+ Q IV+ANVIDK K I Sbjct: 134 YGTLGNHEFDEGLDEFNRIMTGQAPDPESTINDITKQYEHEASHQTIVIANVIDKKTKDI 19- 3 Query: 181 PYNWKPYAIKNIPVNNKSVNVGFIGIVTKDIPNLVLRKNYEQYEFLDEAETIVKYAKELQ 24- 0 PY WKPYAIK+I +N+K V +GFIG+VT +IPNLVL++NYE Y+FLD AETI KYAKELQ Sbjct: 194 PYGWKPYAIKDIAINDKIVKIGFIGVVTTEIPNLVLKQNYEHYQFLDVAETIAKYAKELQ 25- 3 Query: 241 AKNVKAIVVLAHVPATSKNDIAEGEAAEMMKKVNQLFPENSVDIVFAGHNHQYTNGLVGK 30- 0 ++V AIVVLAHVPATSK+ + + E A +M+KVNQ++PE+S+DI+FAGHNHQYTNG +GK Sbjct: 254 EQHVHAIVVLAHVPATSKDGVVDHEMATVMEKVNQIYPEHSIDIIFAGHNHQYTNGTIGK 31- 3 Query: 301 TRIVQALSQGKAYADVRGVLDTDTQDFIETPSAKVIAVAPGKKTGSADIQAIVDQANTIV 36- 0 TRIVQALSQGKAYADVRG LDTDT DFI+TPSA V+AVAPG KT ++DI+AI++ AN IV Sbjct: 314 TRIVQALSQGKAYADVRGTLDTDTNDFIKTPSANVVAVAPGIKTENSDIKAIINHANDIV 37- 3 Query: 361 KQVTEAKIGTAEVSVMITRSVDQDNVSPVGSLITEAQLAIARKSWPDIDFAMTNNGGIRA 42- 0 K VTE KIGTA S I+++ + D SPVG+L T AQL IA+K++P +DFAMTNNGGIR+ Sbjct: 374 KTVTERKIGTATNSSTISKTENIDKESPVGNLATTAQLTIAKKTFPTVDFAMTNNGGIRS 43- 3 Query: 421 DLLIKPDGTITWGAAQAVQPFGNILQVVEITGRDLYKALNEQYDQKQNFFLQIAGLRYTY 48- 0 DL++K D TITWGAAQAVQPFGNILQV+++TG+ +Y LN+QYD+ Q +FLQ++GL YTY Sbjct: 434 DLVVKNDRTITWGAAQAVQPFGNILQVIQMTGQHIYDVLNQQYDENQTYFLQMSGLTYTY 49- 3 Query: 481 TDNKEGGEETPFKVVKAYKSNGEEINPDAKYKLVINDFLFGGGDGFASFRNAKLLGAINP 54- 0 TDN +TPFK+VK YK NGEEIN Y +V+NDFL+GGGDGF++F+ AKL+GAIN Sbjct: 494 TDNDPKNSDTPFKIVKVYKDNGEEINLTTTYTVVVNDFLYGGGDGFSAFKKAKLIGAINT 55- 3 Query: 541 DTEVFMAYITDLEKAGKKVSVPNNKPKIYVTMKMVNETITQNDGTHSIIKKLYLDRQGNI 60- 0 DTE F+ YIT+LE +GK V+ K YVT + + T + G HSII K++ +R GN Sbjct: 554 DTEAFITYITNLEASGKTVNATIKGVKNYVTSNLESSTKVNSAGKHSIISKVFRNRDGNT 61- 3 Query: 601 VAQEIVSDTLNQTKSKSTKINPVTTIHKKQLHQFTAINPMRNYGKPSNSTTVKSKQLPKT 66- 0 V+ E++SD L T++ + + T +N T+ S LP T Sbjct: 614 VSSEVISDLLTSTENTNNSLGKKET--------------------TTNKNTISSSTLPIT 65- 3 Query: 661 NSEYGQSFLMSVFG-VGLIGIALNTKKK 687 Y S +M++ + L G+ KK+ Sbjct: 654 GDNYKMSPIMTILALISLGGLNAFIKKR 681 SEQ ID 6016 (GBS328) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 69 (lane 4; MW 73 kDa). The GBS328-His fusion product was purified (FIG. 213, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 268), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1941 A DNA sequence (GBSx2050) was identified in S. agalactiae <SEQ ID 6017> which encodes the amino acid sequence <SEQ ID 6018>. This protein is predicted to be peptide deformylase (def-2). Analysis of this protein sequence reveals the following: TABLE-US-05940 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.70 Transmembrane 55-71 (55-74) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05941 >GP:CAB09662 GB:Z96934 peptide deformylase [Clostridium beijerinckii] Identities = 71/136 (52%), Positives = 96/136 (70%) Query: 1 MIKPIVRDTFFLQQKSQMASRADVSLAKDLQETLHANQNYCVGMAANMIGSLKRVIIINV 60 MIKPIV+D FL QKS+ A++ D+ + DL +TL AN +CVG+AANMIG KR+++ V Sbjct: 1 MIKPIVKDILFLGQKSEEATKNDMVVIDDLIDTLRANLEHCVGLAANMIGVKKRILVFTV 60 Query: 61 GITNLVMFNPVVVAKSDPYETEESCLSLVGCRSTQRYCHITISYRDINWKEQQIKLTDFP 120- G + M NPV++ K PYETEESCLSL+G R T+RY I ++Y D N+ +++ F Sbjct: 61 GNLIVPMINPVILKKEKPYETEESCLSLIGFRKTKRYETIEVTYLDRNFNKKKQVFNGFT 120- Query: 121 AQICQHELDHLEGILI 136 AQI QHE+DH EGI+I Sbjct: 121 AQIIQHEMDHFEGIII 136 A related DNA sequence was identified in S. pyogenes <SEQ ID 6019> which encodes the amino acid sequence <SEQ ID 6020>. Analysis of this protein sequence reveals the following:

TABLE-US-05942 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.61 Transmembrane 55-71 (55-73) ----- Final Results ----- bacterial membrane --- Certainty = 0.2444(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05943 Identities = 77/136 (56%), Positives = 103/136 (75%) Query: 1 MIKPIVRDTFFLQQKSQMASRADVSLAKDLQETLHANQNYCVGMAANMIGSLKRVIIINV 60 MI+ I+ D F LQQK+Q+A + D+ + +DLQ+TL + C+GMAANMIG KR++I+++ Sbjct: 1 MIREIITDHFLLQQKAQVAKKEDLWIGQDLQDTLAFYRQECLGMAANMIGEQKRIVIVSM 60 Query: 61 GITNLVMFNPVVVAKSDPYETEESCLSLVGCRSTQRYCHITISYRDINWKEQQIKLTDFP 120- G +LVMFNPV+V+K Y+T+ESCLSL G R TQRY IT+ Y D NW+ +++ LT Sbjct: 61 GFIDLVMFNPVMVSKKGIYQTKESCLSLSGYRKTQRYDKITVEYLDHNWRPKRLSLTGLT 120- Query: 121 AQICQHELDHLEGILI 136 AQICQHELDHLEGILI Sbjct: 121 AQICQHELDHLEGILI 136 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1942 A DNA sequence (GBSx2051) was identified in S. agalactiae <SEQ ID 6021> which encodes the amino acid sequence <SEQ ID 6022>. Analysis of this protein sequence reveals the following: TABLE-US-05944 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2880(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05945 >GP:BAB05820 GB:AP001514 NADP-specific glutamate dehydrogenase [Bacillus halodurans] Identities = 298/444 (67%), Positives = 362/444 (81%), Gaps = 2/444 (0%) Query: 7 YVASVLEKVKKQNEHEEEFLQAVEEVFESLVPVFDKYPQYIEENLLERLVEPERVISFRV 66 YV V E VK++N +E EF QAV+EVF+SL+PV K+PQY+++ +LER+VEPERVISFRV Sbjct: 16 YVQHVYETVKRRNPNEHEFHQAVKEVFDSLLPVLVKHPQYVKQAILERIVEPERVISFRV 75 Query: 67 PWVDDKGQVQVNRGYRVQFSSAIGPYKGGLRFHPTVTQSIVKFLGFEQIFKNSLTGLPIG 126- PWVDD+G VQVNRG+RVQF+SA+GPYKGGLRFHP+V SI+KFLGFEQIFKN+LTG PIG Sbjct: 76 PWVDDQGNVQVNRGFRVQFNSALGPYKGGLRFHPSVNASIIKFLGFEQIFKNALTGQPIG 135- Query: 127 GGKGGSNFDPKGKSDNEVMRFTQSFMTELQKYIGPDLDVPAGDIGVGGREIGYLYGQYKR 18- 6 GGKGGS+FDPKGKSD E+MRF+QSFM+EL YIGPD+DVPAGDIGVG +EIGY++GQYK+ Sbjct: 136 GGKGGSDFDPKGKSDGEIMRFSQSFMSELSNYIGPDIDVPAGDIGVGAKEIGYMFGQYKK 19- 5 Query: 187 L-NGYQNGVLTGKGLTYGGSLARTEATGYGAVYFAKEMLAARGQDLTGKVALVSGSGNVA 24- 5 + G++ GVLTGKG+ YGGSLAR EATGYG VYF +EM+ G G +VSGSGNV+ Sbjct: 196 MRGGFEAGVLTGKGIGYGGSLARKEATGYGTVYFVEEMIKDHGFSFAGSTVVVSGSGNVS 25- 5 Query: 246 IYATEKLQELGATVVAVSDSSGYVYDPDGIDLETLKQIKEVERARIVKYTEKHPKANFTP 30- 5 IYA EK +LGA VVA SDS GYVYD +GIDL+T+K++KEVER RI +Y +HP A++ Sbjct: 256 IYAMEKAMQLGAKVVACSDSGGYVYDKNGIDLQTVKRLKEVERKRISEYVNEHPHAHYVQ 31- 5 Query: 306 ADQGSIWSIKADLAFPCATQNELDEEDAKLLVENGVLAVTEGANMPSTLGAIKVFQKAGV 36- 5 G IWS+ D+A PCATQNELDE A +L+ NGV AV EGANMPSTL A+ FQ+ GV Sbjct: 316 GCSG-IWSVPCDIALPCATQNELDEAAATMLIANGVKAVGEGANMPSTLQAVHTFQEHGV 37- 4 Query: 366 AFGPAKAANAGGVAVSALEMAQNSSRRAWTFEEVDQELQRIMKTIFVNASEAADEFGDSG 42- 5 F PAKAANAGGV+VSALEMAQNS+R AWTFEEVD +L IMK I+ + +AA+ + SG Sbjct: 375 LFAPAKAANAGGVSVSALEMAQNSTRLAWTFEEVDAKLYEIMKNIYRESIKAAELYEASG 43- 4 Query: 426 NLVLGANIAGFLKVAQAMSAQGIV 449 NLV+GANIAGF+KVA AM + G+V Sbjct: 435 NLVVGANIAGFVKVADAMISHGVV 458 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1943 A DNA sequence (GBSx2052) was identified in S. agalactiae <SEQ ID 6023> which encodes the amino acid sequence <SEQ ID 6024>. Analysis of this protein sequence reveals the following: TABLE-US-05946 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.55 Transmembrane 61-77 (55-87) INTEGRAL Likelihood = -7.70 Transmembrane 177-193 (175-202) INTEGRAL Likelihood = -7.06 Transmembrane 99-115 (95-122) INTEGRAL Likelihood = -5.89 Transmembrane 42-58 (40-60) INTEGRAL Likelihood = -3.08 Transmembrane 160-176 (159-176) INTEGRAL Likelihood = -2.44 Transmembrane 124-140 (122-144) ----- Final Results ----- bacterial membrane --- Certainty = 0.4418(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9955> which encodes amino acid sequence <SEQ ID 9956> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1944 A DNA sequence (GBSx2053) was identified in S. agalactiae <SEQ ID 6025> which encodes the amino acid sequence <SEQ ID 6026>. This protein is predicted to be ABC transporter, ATP-binding protein (msbA). Analysis of this protein sequence reveals the following: TABLE-US-05947 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.72 Transmembrane 152-168 (147-192) INTEGRAL Likelihood = -5.47 Transmembrane 267-283 (264-288) INTEGRAL Likelihood = -4.30 Transmembrane 171-187 (169-192) INTEGRAL Likelihood = -2.13 Transmembrane 67-83 (67-83) INTEGRAL Likelihood = -0.32 Transmembrane 493-509 (493-509) ----- Final Results ----- bacterial membrane --- Certainty = 0.5288(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05948 >GP:CAB69752 GB:AL137187 putative ABC transporter [Streptomyces coelicolor A3(2)] Identities = 269/611 (44%), Positives = 392/611 (64%), Gaps = 31/611 (5%) Query: 9 RLWSYLTRYKATLFLAIFLKVLSSFMSILEPFILGLAITELTANLV--DMAKG------- 59 RL S +ATLF + V+S ++++ P ILG A + A +V DM G Sbjct: 27 RLVSQFRPERATLFTLLACVVVSVGLNVVGPKILGRATDLVFAGIVGRDMPSGATKEQVL 86 Query: 60 --------------------VSGAELNVPYIAGILIIYFFRGVFYELGSYGSNYFMTTVV 99 V G ++ + +L++ L + + V Sbjct: 87 ATMREHGDGNVADMLRSTDFVPGQGIDFGAVGEVLLLALATFAVAGLLMAVATRLVNRAV 146- Query: 100 QKSIRDIRHDLNRKINKVPVSYFDKHQFGDMLGRFTSDVETVSNALQQSFLQIINAFLSI 15- 9 +++ +R D+ K++++P+SYFDK Q G++L R T+D++ + LQQS Q+IN+ L+I Sbjct: 147 NRTMFRLREDVQTKLSRLPLSYFDKRQRGEVLSRATNDIDNIGQTLQQSMGQLINSLLTI 20- 6 Query: 160 ILVVVMVLYLNVPLAMIIIACIPVTYFSAQAILKRSQPYFKEQAKILGELNGFVQEKLTG 21- 9 I V+ M+ Y++ LA++ + +P+++ A + KRSQP F +Q + G+LN ++E TG Sbjct: 207 IGVLAMMFYVSWILALVALVTVPLSFVVATRVGKRSQPQFVQQWRSTGQLNAHIEEMYTG 26- 6 Query: 220 FNIIKLYGREEASSQEFRDITDNLRHVGFKASFISGIMMPVLNSISDFIYLIIAFVGGLQ 27- 9 ++K++GR+E S+++F + D L GFKA F SGIM P++ +S+ Y+++A VGGL+ Sbjct: 267 HALVKVFGRQEESAKQFASQNDALYEAGFKAQFNSGIMQPLMMCVSNLNYVLVAVVGGLR 32- 6 Query: 280 VIAGTLTIGNMQAFVQYVWQISQPVQTITQLAGVLQSAKSSLERIFEVLD-EEEEANQVT 33- 8 V +G L+IG++QAF+QY Q S P+ + +A ++QS +S ER+FE+LD EE+ A+ + Sbjct: 327 VASGQLSIGDVQAFIQYSRQFSMPLTQVASMANLVQSGVASAERVFELLDAEEQSADPIP 38- 6 Query: 339 EKLSHDLTGQVSFHGVDFHYSPDKPLIRDFNLDVEPGQMIAIVGPTGAGKTTLINLLMRF 39- 8 DL G+V V F Y P+KPLI D +L VEPG +AIVGPTGAGKTTL+NLLMRF Sbjct: 387 GARPEDLRGRVELEHVSFRYDPEKPLIEDLSLKVEPGHTVAIVGPTGAGKTTLVNLLMRF 44- 6 Query: 399 YDVSEGAITVDGHDIRHLSRQDFRQQFGMVLQDAWLYEGTIKENLRFG-NLEASDEDIVA 45- 7 Y+VS G IT+DG DI +SR + R GMVLQD WL+ GTI EN+ +G + E + +I Sbjct: 447 YEVSGGRITLDGVDIAKMSRDELRAGIGMVLQDTWLFGGTIAENIAYGASREVTRGEIEE 50- 6 Query: 458 AAKAANVDHFIRTLPGGYNMVMNQESSNISLGQKQLLTIARALLADPKILILDEATSSVD 51- 7 AA+AA+ D F+RTLP GY+ V++ E + +S G+KQL+TIARA L+DP IL+LDEATSSVD Sbjct: 507 AARAAHADRFVRTLPDGYDTVIDDEGTGVSAGEKQLITIARAFLSDPVILVLDEATSSVD 56- 6 Query: 518 TRLELLIQKAMKKLMEGRTSFVIAHRLSTIQEADNILVLKDGQIIEQGNHQKLLADKGFY 57- 7 TR E+LIQKAM KL GRTSFVIAHRLSTI++AD ILV++DG I+EQG H +LL G Y Sbjct: 567 TRTEVLIQKAMAKLAHGRTSFVIAHRLSTIRDADTILVMEDGAIVEQGAHTELLTADGAY 62- 6 Query: 578 YELYNSQFSNS 588 LY +QF+ + Sbjct: 627 ARLYKAQFAEA 637 There is also homology to SEQ IDs 160 and 6546. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1945 A DNA sequence (GBSx2054) was identified in S. agalactiae <SEQ ID 6027> which encodes the amino acid sequence <SEQ ID 6028>. Analysis of this protein sequence reveals the following: TABLE-US-05949 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.88 Transmembrane 242-258 (235-263) INTEGRAL Likelihood = -9.82 Transmembrane 159-175 (129-177) INTEGRAL Likelihood = -9.71 Transmembrane 52-68 (49-77) INTEGRAL Likelihood = -8.49 Transmembrane 134-150 (129-158) INTEGRAL Likelihood = -1.17 Transmembrane 272-288 (272-289) ----- Final Results ----- bacterial membrane --- Certainty = 0.5352(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05950 >GP: CAB69751 GB: AL137187 putative ABC transporter [Streptomyces coelicolor A3(2)] Identities = 226/565 (40%), Positives = 342/565 (60%), Gaps = 1/565 (0%) Query: 6 SYLKRYPNWLWLDLLGAMLFVTVILGMPTALAGMIDNGVTKGDRTGVYLWTFIMFIFVVL 65 +YL+ Y + L + L L +PT A +ID GV KGD + + +M + Sbjct: 8 TYLRPYKKPIALLVALQFLQTCASLYLPTLNAHIIDEGVVKGDSGYILSYGALMIGISLA 67 Query: 66 GIIGRITMAYASSRLTTTMIRDMRNDMYAKLQEYSHHEYEQIGVSSLVTRMTSDTFVLMQ 125- ++ I + +R + RD+R ++ ++Q +S E G SL+TR T+D + Sbjct: 68 QVVCNIGAVFYGARTAAALGRDVRGAVFDRVQSFSAREVGHFGAPSLITRTTNDVQQVQM 127- Query: 126 FAEMSLRLGLVTPMVMIFSVVMILITSPSLAWLVAVAMPLLVGVILYVAIKTKPLSERQQ 18- 5 A M+ L + P++ + +VM L L+ ++ +P+L + + K +PL + Q Sbjct: 128 LALMTFTLMVSAPIMCVGGIVMALGLDVPLSGVLLGVVPVLAICVTLIVRKLRPLFRKMQ 18- 7 Query: 186 TMLDKINQYVRENLTGLRVVRAFARENFQSQKFQVANQRYTDTSTGLFKLTGLTEPLFVQ 24- 5 LD +N+ +RE +TG RV+RAF R+ ++ Q+F+ AN T+ + G L L P+ + Sbjct: 188 VRLDTVNRVLREQITGNRVIRAFVRDEYEQQRFRKANTELTEVALGTGNLLALMFPVVMT 24- 7 Query: 246 IIIAMIVAIVWFALDPLQRGAIKIGDLVAFIEYSFHALFSFLLFANLFTMYPRMVVSSHR 30- 5 ++ +A+VWF + G ++IGDL AF+ Y + S ++ +F M PR V + R Sbjct: 248 VVNLSSIAVVWFGAHRIDSGGMQIGDLTAFLAYLMQIVMSVMMATFMFMMVPRAEVCAER 30- 7 Query: 306 IREVMDMPISINPNTEGVTDTKLKGHLEFDNVTFAYPGETESPVLHDISFKAKPGETIAF 36- 5 I+EV++ S+ P VT+ + GHLE F YPG E PVL I A+PGET A Sbjct: 308 IQEVLETESSVVPPVAPVTELRRHGHLEIREAGFRYPG-AEEPVLRHIDLVARPGETTAV 36- 6 Query: 366 IGSTGSGKSSLVNLIPRFYDVTLGKILVDGVDVRDYNLKSLRQKIGFIPQKALLFTGTIG 42- 5 IGSTGSGKS+L+ L+PR +D T G++LV+GVDVR + K+L + + +PQK LF GT+ Sbjct: 367 IGSTGSGKSTLLGLVPRLFDATDGEVLVNGVDVRTVDPKTLAKVVSLVPQKPYLFAGTVA 42- 6 Query: 426 ENLKYGKADATIDDLRQAVDISQAKEFIESHQEAFETHLAEGGSNLSGGQKQRLSIARAV 48- 5 NL+YG DAT ++L A+ ++QAKEF+ + + +A+GG+N+SGGQ+QRL+IAR + Sbjct: 427 TNLRYGNPDATDEELWHALAVAQAKEFVSELEGGLDAPIAQGGTNVSGGQRQRLAIARTL 48- 6 Query: 486 VKDPDLYIFDDSFSALDYKTDATLRARLKEVTGDSTVLIVAQRVGTIMDADQIIVLDEGE 54- 5 V+ P++Y+FDDSFSALDY TDA LRA L + T ++TV+IVAQRV TI DAD+I+VLDEG Sbjct: 487 VQRPEIYLFDDSFSALDYATDAALRAELAQETAEATVVIVAQRVATIRDADRIVVLDEGR 54- 6 Query: 546 IVGRGTHAQLIENNAIYREIAESQL 570 +VG G H +L+ +N YREI SQL Sbjct: 547 VVGVGRHHELMADNETYREIVLSQL 571 A related DNA sequence was identified in S. pyogenes <SEQ ID 4985> which encodes the amino acid sequence <SEQ ID 4986>. Analysis of this protein sequence reveals the following: TABLE-US-05951 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -16.24 Transmembrane 155-171 (145-176) INTEGRAL Likelihood = -7.48 Transmembrane 130-146 (122-150) INTEGRAL Likelihood = -5.04 Transmembrane 13-29 (12-30) INTEGRAL Likelihood = -5.04 Transmembrane 56-72 (52-75) INTEGRAL Likelihood = -4.14 Transmembrane 239-255 (238-259) INTEGRAL Likelihood = -1.70 Transmembrane 269-285 (269-288) ----- Final Results ----- bacterial membrane --- Certainty = 0.7496(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05952 Identities = 175/511 (34%), Positives = 296/511 (57%), Gaps = 3/511 (0%) Query: 59 MFIFVVLGIIGRITMAYASSRLTTTMIRDMRNDMYAKLQEYSHHEYEQIGVSSLVTRMTS 118- + I +LG++ ++++ + DMR + K+Q++S+ E +LV R+T+ Sbjct: 56 LLIIALLGLMSGAINTVLAAKIAQGVSADMREKTFRKIQDFSYANIEAFNAGNLVVRLTN 115- Query: 119 DTFVLMQFAEMSLRLGLVTPMVMIFSVVMILITSPSLAWLVAVAMPLLVGVILYVAIKTK 17- 8 D + M ++ P++ I + +M + T P L W++ V + L+ ++ V + Sbjct: 116 DINQIQSLVMMMFQILFRLPILFIGAFIMAVQTFPQLWWVIVVMVILIALIMGLVMRQMG 17- 5 Query: 179 PLSERQQTMLDKINQYVRENLTGLRVVRAFARENFQSQKFQVANQRYTDTSTGLFKLTGL 23- 8 P + Q ++DKIN+ +ENL G+RVV++F +E Q KF+ + + + L Sbjct: 176 PRFGKFQRLMDKINRIAKENLRGVRVVKSFVQEQQQYTKFKETSNDLLALNLSIGYGFSL 23- 5 Query: 239 TEPLFVQIIIAMIVAIVWFALDPLQRGAIKIGDLVAFIEYSFHALFSFLLFANLFTMYPR 29- 8 +P + + + + ++ IG++ +F+ Y +FS ++ ++ R Sbjct: 236 MQPALMLVSYLAVYVSINVVSTMVETDPTVIGNIASFMTYMMQIMFSIIVVGSMGMQVSR 29- 5 Query: 299 MVVSSHRIREVMDMPISINPNTEGVTDTKLKGHLEFDNVTFAYPGETESPVLHDISFKAK 35- 8 VS RIR+++ ++ E + + G + FD+V+F YP + E P L ISF + Sbjct: 296 AFVSMARIRQILSTEPAMTFENE--KEETISGSIVFDDVSFTYPNDDE-PTLKHISFAIE 35- 2 Query: 359 PGETIAFIGSTGSGKSSLVNLIPRFYDVTLGKILVDGVDVRDYNLKSLRQKIGFIPQKAL 41- 8 PG+ + +G+TGSGKS+L LIPR +D G+IL+ G ++ + +LRQ + + QKA+ Sbjct: 353 PGQMVGIVGATGSGKSTLAQLIPRLFDPQDGQILLGGKPIKTLSQTTLRQSVSIVLQKAI 41- 2 Query: 419 LFTGTIGENLKYGKADATIDDLRQAVDISQAKEFIESHQEAFETHLAEGGSNLSGGQKQR 47- 8 LF+GTI +NL+ G A A ID +++A I+QAKEFI+ +E+ + E GSNLSGGQKQR Sbjct: 413 LFSGTIADNLRQGSAKADIDAMQKAAQIAQAKEFIDRMDSRYESQVEERGSNLSGGQKQR 47- 2 Query: 479 LSIARAVVKDPDLYIFDDSFSALDYKTDATLRARLKEVTGDSTVLIVAQRVGTIMDADQI 53- 8 LSIAR V+ P + I DDS SALD K++ ++ L +T +IVAQ++ +++ AD+I Sbjct: 473 LSIARGVINHPKILILDDSTSALDAKSEKRVQEALSHKLEGTTTVIVAQKISSVVKADKI 53- 2 Query: 539 IVLDEGEIVGRGTHAQLIENNAIYREIAESQ 569 +VLD+G+++G GTHA+L+ NNAIYREI E+Q Sbjct: 533 LVLDQGQLIGEGTHAELVANNAIYREIYETQ 563 There is also homology to SEQ IDs 72 and 6552. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1946 A DNA sequence (GBSx2055) was identified in S. agalactiae <SEQ ID 6029> which encodes the amino acid sequence <SEQ ID 6030>. Analysis of this protein sequence reveals the following: TABLE-US-05953 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2391(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05954 >GP:CAA51784 GB:X73368 ORF 18.3 [Salmonella typhimurium] Identities = 58/162 (35%), Positives = 92/162 (55%), Gaps = 8/162 (4%) Query: 1 MIIRPIIKNDDQAVAQLIRQSLRAYDL--DKPDTAYSDPHLDHLTSYYEKIEKSGFFVIE 58 + +R I D+ A+A++IRQ Y L DK T +DP+LD L Y + + ++V+E Sbjct: 9 LTVRRITTADNAAIARVIRQVSAEYGLTADKGYTV-ADPNLDELYQVYSQ-PGAAYWVVE 66 Query: 59 ERDEIIGCGGFGPLKNL---IAEMQKVYIAERFRGKGLATDLVKMIEVEARKIGYRQLYL 115- + ++G GG PL I E+QK+Y RG+GLA L M AR+ G+++ YL Sbjct: 67 QNGCVVGGGGVAPLSCSEPDICELQKMYFLPVIRGQGLAKKLALMALDHAREQGFKRCYL 126- Query: 116 ETASTLSRATAVYKHMGYCALSQPIANDQGHTAMDIWMIKDL 157 ET + L A A+Y+ +G+ +S+P+ GH ++ M+KDL Sbjct: 127 ETTAFLREAIALYERLGFEHISEPL-GCTGHVDCEVRMLKDL 167 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1947 A DNA sequence (GBSx2056) was identified in S. agalactiae <SEQ ID 6031> which encodes the amino acid sequence <SEQ ID 6032>. This protein is predicted to be ABC transporter. Analysis of this protein sequence reveals the following: TABLE-US-05955 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1738(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-05956 >GP:CAB12566 GB:Z99108 similar to ABC transporter (ATP binding protein) [Bacillus subtilis] Identities = 269/625 (43%), Positives = 397/625 (63%), Gaps = 11/625 (1%) Query: 1 MSDFLVDGLTKSVGDKTVFSNVSFIIHSLDRIGIIGVNGTGKTTLLDVISGELGFDGDRS 60 MS + L K+ GDKT+F ++SF I +RIG+IG NGTGK+TLL VI+G + Sbjct: 1 MSILKAENLYKTYGDKTLFDHISFHIEENERIGLIGPNGTGKSTLLKVIAGLESIE--EG 58 Query: 61 PFSSANDYKIAYLKQEPDFDDSQTILDTVLSSDLREMALIKEYELLLNHY-----EESKQ 115- + + ++ +L Q+P+ QT+L+ + S + M ++EYE L E +Q Sbjct: 59 EITKSGSVQVEFLHQDPELPAGQTVLEHIYSGESAVMKTLREYEKALYELGKDPENEQRQ 118- Query: 116 SRLEKVMAEMDSLDAWSIESEVKTVLSKLGITDLQLSVGELSGGLRRRVQLAQVLLNDAD 17- 5 L A+MD+ +AW + KTVLSKLG+ D+ V ELSGG ++RV +A+ L+ AD Sbjct: 119 KHLLAAQAKMDANNAWDANTLAKTVLSKLGVNDVTKPVNELSGGQKKRVAIAKNLIQPAD 17- 8 Query: 176 LLLLDEPTNHLDIDTIAWLTNFLKNSKKTVLFITHDRYFLDNVATRIFELDKAQITEYQG 23- 5 LL+LDEPTNHLD +TI WL +L V+ +THDRYFL+ V RI+EL++ + Y+G Sbjct: 179 LLILDEPTNHLDNETIEWLEGYLSQYPGAVMLVTHDRYFLNRVTNRIYELERGSLYTYKG 23- 8 Query: 236 NYQDYVRLRAEQDERDAASLHKKKQLYKQELAWMRTQPQARATKQQARINRFQNLKNDLH 29- 5 NY+ ++ RAE++ + K++ L ++ELAW+R +AR+TKQ+ARI+R + LK Sbjct: 239 NYEVFLEKRAEREAQAEQKETKRQNLLRRELAWLRRGAKARSTKQKARIDRVETLKEQTG 29- 8 Query: 296 QTSDTSDLEMTFETSRIGKKVINFENVSFSYPDKSILKDFNLLIQNKDRIGIVGDNGVGK 35- 5 S S L+ + R+GK+VI ENV +Y + ++ FN L+ +RIGI+G NG+GK Sbjct: 299 PQSSGS-LDFAIGSHRLGKQVIEAENVMIAYDGRMLVDRFNELVIPGERIGIIGPNGIGK 35- 7 Query: 356 STLLNLIVQDLQPDSGNVSIGETIRVGYFSQQLHNMDGSKRVINYLQEVADEVKTSVGTT 41- 5 +TLLN + PD G+++IG+T+R+GY++Q M+G +VI+Y++E A+ VKT+ G Sbjct: 358 TTLLNALAGRHTPDGGDITIGQTVRIGYYTQDHSEMNGELKVIDYIKETAEVVKTADGDM 41- 7 Query: 416 SVTE-LLEQFLFPRSTHGTQIAKLSGGEKKRLYLLKILIEKPNVLLLDEPTNDLDIATLT 47- 4 E +LE+FLFPRS T I KLSGGEK+RLYLL++L+++PNVL LDEPTNDLD TL+ Sbjct: 418 ITAEQMLERFLFPRSMQQTYIRKLSGGEKRRLYLLQVLMQEPNVLFLDEPTNDLDTETLS 47- 7 Query: 475 VLENFLQGFGGPVITVSHDRYFLDKVANKIIAFEDND-IREFFGNYTDYLDEKAFNEQNN 53- 3 VLE+++ F G VITVSHDRYFLD+V +++I FE N I F G+Y+DY++E + Sbjct: 478 VLEDYIDQFPGVVITVSHDRYFLDRVVDRLIVFEGNGVISRFQGSYSDYMEESKAKKAAP 53- 7 Query: 534 EVISKKESTKTSREKQSRKRMSYFEKQEWATIEDDIMILENTITRIENDMQTCGSDFTRL 59- 3 + + +E T + K+ RK++SY ++ EW IED I LE ++E D+ GSDF ++ Sbjct: 538 KP-AAEEKTAEAEPKKKRKKLSYKDQLEWDGIEDKIAQLEEKHEQLEADIAAAGSDFGKI 59- 6 Query: 594 SDLQKELDAKNEALLEKYDRYEYLS 618 +L E E L DR+ LS Sbjct: 597 QELMAEQAKTAEELEAAMDRWTELS 621 A related DNA sequence was identified in S. pyogenes <SEQ ID 6033> which encodes the amino acid sequence <SEQ ID 6034>. Analysis of this protein sequence reveals the following: TABLE-US-05957 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2591(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05958 Identities = 467/624 (74%), Positives = 535/624 (84%), Gaps = 3/624 (0%) Query: 1 MSDFLVDGLTKSVGDKTVFSNVSFIIHSLDRIGIIGVNGTGKTTLLDVISGELGFDGDRS 60 MS FLV+ LTK+VGDKTVF ++SFIIH DRIGIIGVNGTGKTTLLDV+SG LGFDGD S Sbjct: 1 MSHFLVEKLTKTVGDKTVFQDISFIIHDFDRIGIIGVNGTGKTTLLDVLSGRLGFDGDHS 60 Query: 61 PFSSANDYKIAYLKQEPDFDDSQTILDTVLSSDLREMALIKEYELLLNHYEESKQSRLEK 120- PFS ANDYKIAYL Q+P+F+D+ ++LDTVLS+D++ + LI++YELL+ +Y E KQ LE Sbjct: 61 PFSKANDYKIAYLTQDPEFNDAASVLDTVLSADVKAIQLIRQYELLMANYTEDKQESLES 120- Query: 121 VMAEMDSLDAWSIESEVKTVLSKLGITDLQLSVGELSGGLRRRVQLAQVLLNDADLLLLD 18- 0 +M+EMD LDAWSIES+VKTVLSKLGITDL+ VG+LSGG+RRRVQLAQVLL ADLLLLD Sbjct: 121 LMSEMDRLDAWSIESDVKTVLSKLGITDLEQKVGDLSGGMRRRVQLAQVLLGAADLLLLD 18- 0 Query: 181 EPTNHLDIDTIAWLTNFLKNSKKTVLFITHDRYFLDNVATRIFELDKAQITEYQGNYQDY 24- 0 EPTNHLDIDTIAWLT +LK +KKTVLFITHDRYFLD+VATRIFELDKA +TEYQGNYQDY Sbjct: 181 EPTNHLDIDTIAWLTTYLKTAKKTVLFITHDRYFLDHVATRIFELDKAGLTEYQGNYQDY 24- 0 Query: 241 VRLRAEQDERDAASLHKKKQLYKQELAWMRTQPQARATKQQARINRFQNLKNDLHQTSDT 30- 0 VRL+AEQDERDAA+LHKKKQLYKQELAWMRTQPQARATKQQARINRF +LK ++HQ S Sbjct: 241 VRLKAEQDERDAANLHKKKQLYKQELAWMRTQPQARATKQQARINRFSDLKKEVHQDSSA 30- 0 Query: 301 SDLEMTFETSRIGKKVINFENVSFSYPDKSILKDFNLLIQNKDRIGIVGDNGVGKSTLLN 36- 0 LEMTFETSRIGKKVI+FE++SF+Y D+ ++KDFNL+IQNKDRIGIVGDNGVGKSTLLN Sbjct: 301 DKLEMTFETSRIGKKVIHFEDLSFAYGDRQLIKDFNLIIQNKDRIGIVGDNGVGKSTLLN 36- 0 Query: 361 LIVQDLQPDSGNVSIGETIRVGYFSQQLHNMDGSKRVINYLQEVADEVKTSVGTTSVTEL 42- 0 +I DL+P SG + IG+TIRVGYFSQQL +MD +KRVINYLQEVADEVKTSVGTTS++EL Sbjct: 361 IINGDLKPTSGKLDIGDTIRVGYFSQQLKDMDETKRVINYLQEVADEVKTSVGTTSISEL 42- 0 Query: 421 LEQFLFPRSTHGTQIAKLSGGEKKRLYLLKILIEKPNVLLLDEPTNDLDIATLTVLENFL 48- 0 LEQFLFPRS+HGT IAKLSGGEKKRLYLLK+LIEKPNVLLLDEPTNDLDIATL VLENFL Sbjct: 421 LEQFLFPRSSHGTLIAKLSGGEKKRLYLLKLLIEKPNVLLLDEPTNDLDIATLKVLENFL 48- 0 Query: 481 QGFGGPVITVSHDRYFLDKVANKIIAFEDNDIREFFGNYTDYLDEKAFNEQNNEVISKKE 54- 0 F GPVITVSHDRYFLDKVA KI+AFE+ DIR F+GNY+DYLDEK F ++ E K Sbjct: 481 ANFAGPVITVSHDRYFLDKVATKILAFEEGDIRVFYGNYSDYLDEKVFEKETVEADLAKT 54- 0 Query: 541 STKTS---REKQSRKRMSYFEKQEWATIEDDIMILENTITRIENDMQTCGSDFTRLSDLQ 59- 7 + +K+ RKRMSY EKQEWA IED I +E I IEN M T SD+ +L+ LQ Sbjct: 541 TVTEEVPLPQKEERKRMSYLEKQEWAQIEDKIATIEANIEEIENQMLTVVSDYGQLAQLQ 60- 0 Query: 598 KELDAKNEALLEKYDRYEYLSELD 621 KELD +N LL Y+R+EYLS LD Sbjct: 601 KELDQRNNDLLLAYERFEYLSGLD 624 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1948 A DNA sequence (GBSx2057) was identified in S. agalactiae <SEQ ID 6035> which encodes the amino acid sequence <SEQ ID 6036>. This protein is predicted to be poly(a) polymerase (papS). Analysis of this protein sequence reveals the following: TABLE-US-05959 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2658(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9957> which encodes amino acid sequence <SEQ ID 9958> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05960 >GP: AAB38446 GB: L47709 poly(A) polymerase [Bacillus subtilis] Identities = 157/395 (39%), Positives = 235/395 (58%), Gaps = 14/395 (3%) Query: 11 FQKALPILKKIKKAGYEAYFVGGSVRDVLLDRPIHDVDIATSSYPEETKQIFKRTVDVGI 70 - F KALP+L+ + +AG++AYFVGG+VRD + R I DVDIAT + P++ +++F+RTVDVG Sbjct: 5 FIKALPVLRILIEAGHQAYFVGGAVRDSYMKRTIGDVDIATDAAPDQVERLFQRTVDVGK 64 Query: 71 EHGTVLVLEKGGEYEITTFRTEEVYVDYRRPSQVNFVRSLEEDLKRRDFTVNAFALNEDG 130- EHGT++VL + YE+TTFRTE YVD+RRPS+V F+ SLEEDLKRRD T+NA A+ DG Sbjct: 65 EHGTIIVLWEDETYEVTTFRTESDYVDFRRPSEVQFISSLEEDLKRRDLTINAMAMTADG 124- Query: 131 EVIDLFHGLDDLDNHLLRAVGLASERFNEDALRIMRGLRFSASLNFDIETTTFEAMKKHA 19- 0 +V+D F G D+D ++R VG +RF EDALR++R +RF + L F + T EA+ K Sbjct: 125 KVLDYFGGKKDIDQKVIRTVGKPEDRFQEDALRMLRAVRFMSQLGFTLSPETEEAIAKEK 18- 4 Query: 191 SLLEKISVERSFIEFDKLLLAPYWRKGMLALIDSHAFNYLPCLKNRELQLSAFLSQLDKD 25- 0 SLL +SVER IEF+KLL R+ + LI + + LP ++ L +S + Sbjct: 185 SLLSHVSVERKTIEFEKLLQGRASRQALQTLIQTRLYEELPGFYHKRENL---ISTSEFP 24- 1 Query: 251 FLFETS-EQAWASLILSMEV--EHTKTFLKKWKTSTHFQKDVEHIVDVYRIREQMGLTKE 30- 7 F TS E+ WA+L++++ + + FLK WK K+ HI D + L Sbjct: 242 FFSLTSREELWAALLINLGIVLKDAPLFLKAWKLPGKVIKEAIHIADTF----GQSLDAM 29- 7 Query: 308 HLYRYGKTIIKQAEGIRKAR-GLMVDFEKIEQLD---SELAIHDRHEIVVNGGTLIKKLG 36- 3 +YR GK + A I + R +D +K++ + L I ++ + G L+ Sbjct: 298 TMYRAGKKALLSAAKISQLRQNEKLDEKKLKDIQYAYQNLPIKSLKDLDITGKDLLALRN 35- 7 Query: 364 IKPGPQMGDIISQIELAIVLGQLINEEEAILHFVK 398 G + + + IE A+V G+L N+++ I ++K Sbjct: 358 RPAGKWVSEELQWIEQAVVTGKLSNQKKHIEEWLK 392 A related DNA sequence was identified in S. pyogenes <SEQ ID 6037> which encodes the amino acid sequence <SEQ ID 6038>. Analysis of this protein sequence reveals the following: TABLE-US-05961 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2023(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05962 Identities = 256/400 (64%), Positives = 312/400 (78%) Query: 2 MRLNYLPSEFQKALPILKKIKKAGYEAYFVGGSVRDVLLDRPIHDVDIATSSYPEETKQI 61 M+L +PSEFQKALPIL KIK+AGYEAYFVGGSVRDVLL+RPIHDVDIATSSYPEETK I Sbjct: 1 MKLMTMPSEFQKALPILTKIKEAGYEAYFVGGSVRDVLLERPIHDVDIATSSYPEETKAI 60 Query: 62 FKRTVDVGIEHGTVLVLEKGGEYEITTFRTEEVYVDYRRPSQVNFVRSLEEDLKRRDFTV 121- F RTVDVGIEHGTVLVLE GGEYEITTFRTE++YVDYRRPSQV+FVRSLEEDLKRRDFTV Sbjct: 61 FNRTVDVGIEHGTVLVLENGGEYEITTFRTEDIYVDYRRPSQVSFVRSLEEDLKRRDFTV 120- Query: 122 NAFALNEDGEVIDLFHGLDDLDNHLLRAVGLASERFNEDALRIMRGLRFSASLNFDIETT 18- 1 NA AL+E+G+VID F GL DL LRAVG A ERF EDALRIMRG RF+ASL+FDIE Sbjct: 121 NALALDENGQVIDKFRGLIDLKQKRLRAVGKAEERFEEDALRIMRGFRFAASLDFDIEAI 18- 0 Query: 182 TFEAMKKHASLLEKISVERSFIEFDKLLLAPYWRKGMLALIDSHAFNYLPCLKNRELQLS 24- 1 TFEAM+ H+ LLEKISVERSF EFDKLL+AP+WRKG+ A+I A++YLP LK +E L+ Sbjct: 181 TFEAMRSHSPLLEKISVERSFTEFDKLLMAPHWRKGISAMIACQAYDYLPGLKQQEAGLN 24- 0 Query: 242 AFLSQLDKDFLFETSEQAWASLILSMEVEHTKTFLKKWKTSTHFQKDVEHIVDVYRIREQ 30- 1 + L +F F QAWA +++S+ +E K+FLK WKTS FQ+ V ++ +YRIR++ Sbjct: 241 HLIVSLKDNFTFSDYHQAWAYVMISLAIEDPKSFLKAWKTSNDFQRYVTKLIALYRIRQE 30- 0 Query: 302 MGLTKEHLYRYGKTIIKQAEGIRKARGLMVDFEKIEQLDSELAIHDRHEIVVNGGTLIKK 36- 1 K +Y+YGK + E +RKA+ L VD ++I LD L IHD+H+IV+NG LIK Sbjct: 301 RSFEKLDIYQYGKKMASLVEDLRKAQSLSVDMDRINTLDQALVIHDKHDIVLNGSHLIKD 36- 0 Query: 362 LGIKPGPQMGDIISQIELAIVLGQLINEEEAILHFVKQYL 401 G+K GPQ+G ++ ++ELAIV G+L N+ I FV++ L Sbjct: 361 FGMKSGPQLGLMLEKVELAIVEGRLDNDFTTIEAFVREEL 400 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1949 A DNA sequence (GBSx2058) was identified in S. agalactiae <SEQ ID 6039> which encodes the amino acid sequence <SEQ ID 6040>. Analysis of this protein sequence reveals the following: TABLE-US-05963 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2939(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05964 >GP: BAB07346 GB: AP001519 unknown conserved protein [Bacillus halodurans] Identities = 94/274 (34%), Positives = 153/274 (55%), Gaps = 2/274 (0%) Query: 2 KLALITDTSAYLPEAIENHEDVYVLDIPIIIDGKTYIEGQNLTLDQYYDKLAASKELPKT 61 K+A++TD++AYL V V+ + ++ + Y E L+ +Y+KL ++LP T Sbjct: 3 KIAIVTDSTAYLGPKRAKELGVIVVPLSVVFGEEAYQEEVELSSADFYEKLKHEEKLPTT 62 Query: 62 SQPSLAELDDLLCQLEKEGYTHVLGLFIAAGISGFWQNIQFLIEEHPNLTIAFPDTKITS 121- SQP++ + +L KEG+ V+ + +++ ISG +Q+ + + D+ I+ Sbjct: 63 SQPAVGLFVETFERLAKEGFEVVISIHLSSKISGTYQSALTAGSMVEGIEVIGYDSGISC 122- Query: 122 APQGNLVRNALMCSREGMDFDVIVNKIQSQIEKIEGFIVVNDLNHLVKGGRLSNGSAIIG 18- 1 PQ N V A +EG D I++ + ++ VV+DL+HL +GGRL+ ++G Sbjct: 123 EPQANFVAEAAKLVKEGADPQTIIDHLDEVKKRTNALFVVHDLSHLHRGGRLNAAQLVVG 18- 2 Query: 182 NLLSIKPVLHFNEEGKIVVYEKVRTEKKALKRLAEI-VKEMTADGEYDIAIIHSRAQDKA 24- 0 +LL IKP+LHF E+G IV EKVRTEKKA R+ E+ +E ++ +IH+ D A Sbjct: 183 SLLKIKPILHF-EDGSIVPLEKVRTEKKAWARVKELFAEEASSASSVKATVIHANRLDGA 24- 1 Query: 241 EQLYNLLAKAGLKDDLEIVSFGGVIATHLGEGAV 274 E+L + + D+ I FG VI THLGEG++ Sbjct: 242 EKLADEIRSQFSHVDVSISHFGPVIGTHLGEGSI 275 A related DNA sequence was identified in S. pyogenes <SEQ ID 6041> which encodes the amino acid sequence <SEQ ID 6042>. Analysis of this protein sequence reveals the following: TABLE-US-05965 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3379(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05966 Identities = 181/281 (64%), Positives = 233/281 (82%) Query: 1 MKLALITDTSAYLPEAIENHEDVYVLDIPIIIDGKTYIEGQNLTLDQYYDKLAASKELPK 60 MKLA+ITD++A LP ++ + ++ LDIP+IID +TY EG+NL++D +Y K+A S+ LPK Sbjct: 1 MKLAVITDSTATLPTDLKQDKAIFSLDIPVIIDDETYFEGRNLSIDDFYQKMADSQNLPK 60 Query: 61 TSQPSLAELDDLLCQLEKEGYTHVLGLFIAAGISGFWQNIQFLIEEHPNLTIAFPDTKIT 120- TSQPSL+ELD+LL L +GYTHV+GLF+A GISGFWQNIQFL EEHP + +AFPD+KIT Sbjct: 61 TSQPSLSELDNLLGLLSSKGYTHVIGLFLAGGISGFWQNIQFLAEEHPEIEMAFPDSKIT 120- Query: 121 SAPQGNLVRNALMCSREGMDFDVIVNKIQSQIEKIEGFIVVNDLNHLVKGGRLSNGSAII 18- 0 SAP G++V+N L SR+GM F I+NK+Q QI+ FI+V+DLNHLVKGGRLSNGSA++ Sbjct: 121 SAPLGSMVKNVLDWSRQGMTFQAILNKLQEQIDGTTAFIMVDDLNHLVKGGRLSNGSALL 18- 0 Query: 181 GNLLSIKPVLHFNEEGKIVVYEKVRTEKKALKRLAEIVKEMTADGEYDIAIIHSRAQDKA 24- 0 GNLLSIKP+L F+EEGKIVVYEKVRTEKKA+KRL EI+ ++ ADG+Y++ IIHS+AQDKA Sbjct: 181 GNLLSIKPILRFDEEGKIVVYEKVRTEKKAMKRLVEILNDLIADGQYNVFIIHSKAQDKA 24- 0 Query: 241 EQLYNLLAKAGLKDDLEIVSFGGVIATHLGEGAVAFGITPK 281 + L LL +G + D+E V FG VIATHLGEGA+AFG+TP+ Sbjct: 241 DYLKRLLQDSGYQYDIEEVHFGAVIATHLGEGAIAFGVTPR 281 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1950 A DNA sequence (GBSx2059) was identified in S. agalactiae <SEQ ID 6043> which encodes the amino acid sequence <SEQ ID 6044>. Analysis of this protein sequence reveals the following: TABLE-US-05967 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.59 Transmembrane 51-67 (50-67) ----- Final Results ----- bacterial membrane --- Certainty = 0.1638(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 6045> which encodes the amino acid sequence <SEQ ID 6046>. Analysis of this protein sequence reveals the following: TABLE-US-05968 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.19 Transmembrane 50-66 (49-67) ----- Final Results ----- bacterial membrane --- Certainty = 0.2275(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-05969 Identities = 94/126 (74%), Positives = 115/126 (90%) Query: 1 MEVIREQEFVNQYHYDARNLEWEEENGTPKTNFEVTFQLANRDEAAKVTSIVAVLQFVIV 60 M+++RE+EFVNQYHYDARNLEWE+ENGTP+TNFEVTFQL ++DE K T IV+VLQFVIV Sbjct: 1 MQLVREKEFVNQYHYDARNLEWEKENGTPETNFEVTFQLIDKDEQQKETVIVSVLQFVIV 60 Query: 61 RDEFVISGVISQMAHIQGRLINEPSEFSQDEVENLAAPLLEIVKRLTYEVTEIALDRPGV 120- ++EFVISGVISQM I RL+++PSEF+Q+EVE+LAAPLL++VKRLTYEVTEIALDRPG+ Sbjct: 61 KEEFVISGVISQMVRILDRLVDKPSEFTQEEVESLAAPLLDMVKRLTYEVTEIALDRPGI 120- Query: 121 TLEFNS 126 LEF + Sbjct: 121 HLEFKN 126 SEQ ID 6044 (GBS416) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 79 (lane 4; MW 17.5 kDa). GBS416-His was purified as shown in FIG. 214, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1951 A DNA sequence (GBSx2060) was identified in S. agalactiae <SEQ ID 6047> which encodes the amino acid sequence <SEQ ID 6048>. Analysis of this protein sequence reveals the following: TABLE-US-05970 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3875(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1952 A DNA sequence (GBSx2061) was identified in S. agalactiae <SEQ ID 6049> which encodes the amino acid sequence <SEQ ID 6050>. Analysis of this protein sequence reveals the following: TABLE-US-05971 Possible site: 17 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1953 A DNA sequence (GBSx2062) was identified in S. agalactiae <SEQ ID 6051> which encodes the amino acid sequence <SEQ ID 6052>. This protein is predicted to be PTS system, fructose-specific enzyme II, BC component (fruA-1). Analysis of this protein sequence reveals the following:

TABLE-US-05972 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.56 Transmembrane 630-646 (618-653) INTEGRAL Likelihood = -7.43 Transmembrane 307-323 (303-331) INTEGRAL Likelihood = -7.01 Transmembrane 415-431 (412-435) INTEGRAL Likelihood = -7.01 Transmembrane 448-464 (444-474) INTEGRAL Likelihood = -3.72 Transmembrane 595-611 (591-612) INTEGRAL Likelihood = -3.61 Transmembrane 530-546 (529-553) INTEGRAL Likelihood = -2.39 Transmembrane 350-366 (350-371) INTEGRAL Likelihood = -1.70 Transmembrane 486-502 (486-506) INTEGRAL Likelihood = -1.49 Transmembrane 376-392 (376-392) ----- Final Results ----- bacterial membrane --- Certainty = 0.5225(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9959> which encodes amino acid sequence <SEQ ID 9960> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05973 >GP: BAB04547 GB: AP001510 PTS system, fructose-specific enzyme II, BC component [Bacillus halodurans] Identities = 320/659 (48%), Positives = 438/659 (65%), Gaps = 46/659 (6%) Query: 1 MKIQDLLKKEVMIMDLKATSKEAAIDEMITKLVDTGVVTNFAIFKDGIMKREAQTSTGLG 60 +KI LLKK+ M+++L+A SKEA IDE++ L G + + FK I++RE+Q++TG+G Sbjct: 2 LKISELLKKDTMVLNLRAASKEAVIDELVRTLDKAGRLNDAQAFKRAILERESQSTTGVG 61 Query: 61 DGIAMPHSKNAAVKEATVLFAKSASGVDYEALDGQPTDLFFMIAAPDGANDTHLAALAEL 120- +GIA+PH+K AAVK+ + F +S +G+DYE+LDGQP+ LFFMIAA +GAN+ HL L+ L Sbjct: 62 EGIAIPHAKTAAVKQPAIAFGRSDAGIDYESLDGQPSHLFFMIAASEGANNEHLETLSRL 121- Query: 121 SKYLLKEGFADQLRQAKTPDDIIATFDSNSISQETVAPQTVQSTSKGSDYIVAVTACTTG 18- 0 S +L+ E F L +A++ D+I+A D +E + +G + ++AVT C TG Sbjct: 122 STFLMDETFRSTLMKAQSEDEILAAID----KKEAETAGEAEEKQEGYE-LLAVTGCPTG 17- 6 Query: 181 IAHTYMAEEALKKKAAEMGVGIKVETNGASGVGNKLTSSDIARAKGVIIAADKAVEMDRF 24- 0 IAHTYMA + LK KA E+GV IKVETNG+ GV N+LT +I+ AK +I+AAD VEMDRF Sbjct: 177 IAHTYMAADNLKSKAQELGVSIKVETNGSGGVKNRLTDEEISAAKAIIVAADTKVEMDRF 23- 6 Query: 241 DGKPLVSRPVADGIKKSEDLINIILDNKAQTYHAKNQNDKQSGESDGKSGLGS---AFYK 29- 7 GKP++ PV DGI++ ++LI+ L KA Y + Q+ DG +G G FYK Sbjct: 237 HGKPVIQVPVTDGIRRPKELIDQALAGKAPVY----EGGAQASGEDGSAGGGRPKLGFYK 29- 2 Query: 298 HLMGGVSQMLPFVIGGGIMIAIAFLFDNILGVPKDQLSNLGSYHEIAALFKNIGGA-AFA 35- 6 HLM GVS MLPFV+GGGI+IAI+F+F P D SYH A + IGG AF Sbjct: 293 HLMNGVSNMLPFVVGGGILIAISFMFGIKAFDPSDP-----SYHPFAEMLMTIGGGNAFG 34- 7 Query: 357 FMLPVLAGYIAYSIAEKPGLVAGFVAGSIASSGLAFGKVPFAEGGKATLALAGVPSGFLG 41- 6 M+PVLA +IA SIA++PG AG + G IAS+G A GFLG Sbjct: 348 LMIPVLAAFIAMSIADRPGFAAGMIGGLIASTGEA---------------------GFLG 38- 6 Query: 417 ALVGGFLAGGVILLLRKLLSGLPKSLEGIKSILLYPLLGVLITGFLMLLVNIPMAAINTA 47- 6 L+ GFLAG V L ++K+L+ LP++L+GIK+IL YP+ + ITG +ML++ P+AA NT Sbjct: 387 GLIAGFLAGYVALGVKKVLANLPQTLDGIKTILFYPVFNIFITGMIMLVIVGPLAAFNTG 44- 6 Query: 477 LNTFLQGLSGSSAVLMGLLVGGMMAVDMGGPVNKAAYVFGTGTLAATVANGGSVVMAAVM 53- 6 L +L + ++ V++G+++GGMMAVDMGGP+NKAA+ FG + A G AAVM Sbjct: 447 LQDWLGSMGTANMVILGVILGGMMAVDMGGPINKAAFTFGIAMIDA----GNFGPHAAVM 50- 2 Query: 537 AGGMVPPLAVFVATLLFKDKFNNEERQSGLTNIVMGLSFITEGAIPFGAADPARAIPSFI 59- 6 AGGMVPPL + +AT LFK KF +ER++G TN ++G SFITEGAIPF AADP R IPS I Sbjct: 503 AGGMVPPLGIALATTLFKKKFTKQEREAGKTNYILGASFITEGAIPFAAADPGRVIPSII 56- 2 Query: 597 VGSALTGALVGLAGIKLMAPHGGIFVI---ALTSNPLLYILFILIGAVVSGVLFGLFRK 652- VGSA G L L + L APHGG FVI + +NPLLY++ I+ G++V+ +L G ++K Sbjct: 563 VGSAFAGGLTALFNVTLSAPHGGAFVIFIGNIVNNPLLYLVAIIAGSIVTALLLGFWKK 621- A related DNA sequence was identified in S. pyogenes <SEQ ID 6053> which encodes the amino acid sequence <SEQ ID 6054>. Analysis of this protein sequence reveals the following: TABLE-US-05974 Possible site: 18 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.77 Transmembrane 624-640 (612-646) INTEGRAL Likelihood = -7.59 Transmembrane 301-317 (297-321) INTEGRAL Likelihood = -6.85 Transmembrane 442-458 (439-468) INTEGRAL Likelihood = -5.95 Transmembrane 409-425 (406-426) INTEGRAL Likelihood = -3.61 Transmembrane 524-540 (523-547) INTEGRAL Likelihood = -2.50 Transmembrane 337-353 (337-353) INTEGRAL Likelihood = -2.44 Transmembrane 589-605 (589-605) INTEGRAL Likelihood = -1.70 Transmembrane 480-496 (480-500) INTEGRAL Likelihood = -1.44 Transmembrane 370-386 (370-386) ----- Final Results ----- bacterial membrane --- Certainty = 0.5310(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05975 >GP: BAB04547 GB: AP001510 PTS system, fructose-specific enzyme II, BC component [Bacillus halodurans] Identities = 322/659 (48%), Positives = 431/659 (64%), Gaps = 48/659 (7%) Query: 1 MKIQDLLRKDIMILDLQAISKEVAIDEMITKLVEKDIVHDFDVFKKSIMTREEQTSTGLG 60 +KI +LL+KD M+L+L+A SKE IDE++ L + ++D FK++I+ RE Q++TG+G Sbjct: 2 LKISELLKKDTMVLNLRAASKEAVIDELVRTLDKAGRLNDAQAFKRAILERESQSTTGVG 61 Query: 61 DGIAMPHSKNIVVDKPAVLFAKSNKGVDYKALDGQPTDLFFMIAAPQGANDTHLAALAEL 120- +GIA+PH+K V +PA+ F +S+ G+DY++LDGQP+ LFFMIAA +GAN+ HL L+ L Sbjct: 62 EGIAIPHAKTAAVKQPAIAFGRSDAGIDYESLDGQPSHLFFMIAASEGANNEHLETLSRL 121- Query: 121 SQYLLKDGFADKLRAAATPEAVIAVFD--EASTAKEEVVAPTSGQDFIVAVTACPTGIAH 17- 8 S +L+ + F L A + + ++A D EA TA E + ++AVT CPTGIAH Sbjct: 122 STFLMDETFRSTLMKAQSEDEILAAIDKKEAETAGEAEEKQEGYE--LLAVTGCPTGIAH 17- 9 Query: 179 TYMAEEALKKQAAEMGVAIKVETNGASGVANRLTAEDIQRAKGVIVAADKAVEMDRFDGK 23- 8 TYMA + LK +A E+GV+IKVETNG+ GV NRLT E+I AK +IVAAD VEMDRF GK Sbjct: 180 TYMAADNLKSKAQELGVSIKVETNGSGGVKNRLTDEEISAAKAIIVAADTKVEMDRFHGK 23- 9 Query: 239 QFIARPVADGIKKSQELISLILNNEGNTYHAKNGKSETAVSTEKTSLGG-----AFYKHL 29- 3 I PV DGI++ +ELI L + Y + S E S GG FYKHL Sbjct: 240 PVIQVPVTDGIRRPKELIDQALAGKAPVY-----EGGAQASGEDGSAGGGRPKLGFYKHL 29- 4 Query: 294 MGGVSQMLPFVIGGGIMIALAFLLDNMLGVPNDQLGSLGSYHEIAAIFMNIGGA-AFSFM 35- 2 M GVS MLPFV+GGGI+IA++F+ P+D SYH A + M IGG AF M Sbjct: 295 MNGVSNMLPFVVGGGILIAISFMFGIKAFDPSDP-----SYHPFAEMLMTIGGGNAFGLM 34- 9 Query: 353 LPVLAGYIAYSIAEKPGLVAGFVAGAIASNGLAFGKVPFAAGGEVSLGLTGVPSGFLGAL 41- 2 +PVLA +IA SIA++PG AG + G IAS G A GFLG L Sbjct: 350 IPVLAAFIAMSIADRPGFAAGMIGGLIASTGEA---------------------GFLGGL 38- 8 Query: 413 VGGFLAGGVILALRKLLAGLPRSLEGVKSILLYPLLGVLVTGFLMLFVNIPMAAINTALN 47- 2 + GFLAG V L ++K+LA LP++L+G+K+IL YP+ + +TG +ML + P+AA NT L Sbjct: 389 IAGFLAGYVALGVKKVLANLPQTLDGIKTILFYPVFNIFITGMIMLVIVGPLAAFNTGLQ 44- 8 Query: 473 DFLQGLSGSSAVLMGLLVGGMMAVDMGGPVNKAAYVFGTGTLAATVANGGSVVMAAVMAG 53- 2 D+L + ++ V++G+++GGMMAVDMGGP+NKAA+ FG + A G AAVMAG Sbjct: 449 DWLGSMGTANMVILGVILGGMMAVDMGGPINKAAFTFGIAMIDA----GNFGPHAAVMAG 50- 4 Query: 533 GMVPPLAVFVATLLFKDKFTKEERESGLTNIVMGLSFITEGAIPFGAADPARAIPSFIAG 59- 2 GMVPPL + +AT LFK KFTK+ERE+G TN ++G SFITEGAIPF AADP R IPS I G Sbjct: 505 GMVPPLGIALATTLFKKKFTKQEREAGKTNYILGASFITEGAIPFAAADPGRVIPSIIVG 56- 4 Query: 593 SALTGALVGLAGIKLMAPHGGIFVI---ALTSNPILYLVFVVIGALVSGILFGALRKKA 648- SA G L L + L APHGG FVI + +NP+LYLV ++ G++V+ +L G +K A Sbjct: 565 SAFAGGLTALFNVTLSAPHGGAFVIFIGNIVNNPLLYLVAIIAGSIVTALLLGFWKKDA 623- An alignment of the GAS and GBS proteins is shown below. TABLE-US-05976 Identities = 526/652 (80%), Positives = 581/652 (88%), Gaps = 6/652 (0%) Query: 1 MKIQDLLKKEVMIMDLKATSKEAAIDEMITKLVDTGVVTNFAIFKDGIMKREAQTSTGLG 60 MKIQDLL+K++MI+DL+A SKE AIDEMITKLV+ +V +F +FK IM RE QTSTGLG Sbjct: 1 MKIQDLLRKDIMILDLQAISKEVAIDEMITKLVEKDIVHDFDVFKKSIMTREEQTSTGLG 60 Query: 61 DGIAMPHSKNAAVKEATVLFAKSASGVDYEALDGQPTDLFFMIAAPDGANDTHLAALAEL 120- DGIAMPHSKN V + VLFAKS GVDY+ALDGQPTDLFFMIAAP GANDTHLAALAEL Sbjct: 61 DGIAMPHSKNIVVDKPAVLFAKSNKGVDYKALDGQPTDLFFMIAAPQGANDTHLAALAEL 120- Query: 121 SKYLLKEGFADQLRQAKTPDDIIATFDSNSISQETVAPQTVQSTSKGSDYIVAVTACTTG 18- 0 S+YLLK+GFAD+LR A TP+ +IA FD S ++E V T G D+IVAVTAC TG Sbjct: 121 SQYLLKDGFADKLRAAATPEAVIAVFDEASTAKEEVVAPT-----SGQDFIVAVTACPTG 17- 5 Query: 181 IAHTYMAEEALKKKAAEMGVGIKVETNGASGVGNKLTSSDIARAKGVIIAADKAVEMDRF 24- 0 IAHTYMAEEALKK+AAEMGV IKVETNGASGV N+LT+ DI RAKGVI+AADKAVEMDRF Sbjct: 176 IAHTYMAEEALKKQAAEMGVAIKVETNGASGVANRLTAEDIQRAKGVIVAADKAVEMDRF 23- 5 Query: 241 DGKPLVSRPVADGIKKSEDLINIILDNKAQTYHAKNQNDKQSGESDGKSGLGSAFYKHLM 30- 0 DGK ++RPVADGIKKS++LI++IL+N+ TYHAKN ++ S K+ LG AFYKHLM Sbjct: 236 DGKQFIARPVADGIKKSQELISLILNNEGNTYHAKN-GKSETAVSTEKTSLGGAFYKHLM 29- 4 Query: 301 GGVSQMLPFVIGGGIMIAIAFLFDNILGVPKDQLSNLGSYHEIAALFKNIGGAAFAFMLP 36- 0 GGVSQMLPFVIGGGIMIA+AFL DN+LGVP DQL +LGSYHEIAA+F NIGGAAF+FMLP Sbjct: 295 GGVSQMLPFVIGGGIMIALAFLLDNMLGVPNDQLGSLGSYHEIAAIFMNIGGAAFSFMLP 35- 4 Query: 361 VLAGYIAYSIAEKPGLVAGFVAGSIASSGLAFGKVPFAEGGKATLALAGVPSGFLGALVG 42- 0 VLAGYIAYSIAEKPGLVAGFVAG+IAS+GLAFGKVPFA GG+ +L L GVPSGFLGALVG Sbjct: 355 VLAGYIAYSIAEKPGLVAGFVAGAIASNGLAFGKVPFAAGGEVSLGLTGVPSGFLGALVG 41- 4 Query: 421 GFLAGGVILLLRKLLSGLPKSLEGIKSILLYPLLGVLITGFLMLLVNIPMAAINTALNTF 48- 0 GFLAGGVIL LRKLL+GLP+SLEG+KSILLYPLLGVL+TGFLML VNIPMAAINTALN F Sbjct: 415 GFLAGGVILALRKLLAGLPRSLEGVKSILLYPLLGVLVTGFLMLFVNIPMAAINTALNDF 47- 4 Query: 481 LQGLSGSSAVLMGLLVGGMMAVDMGGPVNKAAYVFGTGTLAATVANGGSVVMAAVMAGGM 54- 0 LQGLSGSSAVLMGLLVGGMMAVDMGGPVNKAAYVFGTGTLAATVANGGSVVMAAVMAGGM Sbjct: 475 LQGLSGSSAVLMGLLVGGMMAVDMGGPVNKAAYVFGTGTLAATVANGGSVVMAAVMAGGM 53- 4 Query: 541 VPPLAVFVATLLFKDKFNNEERQSGLTNIVMGLSFITEGAIPFGAADPARAIPSFIVGSA 60- 0 VPPLAVFVATLLFKDKF EER+SGLTNIVMGLSFITEGAIPFGAADPARAIPSFI GSA Sbjct: 535 VPPLAVFVATLLFKDKFTKEERESGLTNIVMGLSFITEGAIPFGAADPARAIPSFIAGSA 59- 4 Query: 601 LTGALVGLAGIKLMAPHGGIFVIALTSNPLLYILFILIGAVVSGVLFGLFRK 652 LTGALVGLAGIKLMAPHGGIFVIALTSNP+LY++F++IGA+VSG+LFG RK Sbjct: 595 LTGALVGLAGIKLMAPHGGIFVIALTSNPILYLVFVVIGALVSGILFGALRK 646 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1954 A DNA sequence (GBSx2063) was identified in S. agalactiae <SEQ ID 6055> which encodes the amino acid sequence <SEQ ID 6056>. Analysis of this protein sequence reveals the following: TABLE-US-05977 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1532(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05978 >GP: AAC24914 GB: AF012285 fructose-1-phosphate kinase [Bacillus subtilis] Identities = 146/303 (48%), Positives = 197/303 (64%) Query: 1 MIYTVTLNPSIDFIVRLDTLLLGSVNRMTSDDKYVGGKGINVSRILKRLKIDNTATGFIG 60 MIYTVTLNPS+D+IV ++ +G +NR + D KY GGKGINVSR+LKR + + A GF+G Sbjct: 1 MIYTVTLNPSVDYIVHVEDFTVGGLNRSSYDTKYPGGKGINVSRLLKRHHVASKALGFVG 60 Query: 61 GFTGHFVEDGLVLEGIKTDFVSVNEDTRINVKVKAKIETEINGGGPRITNEQLHRLEKLL 120- GFTG +++ L E ++T F V DTRINVK+K ETEING GP I++E + Sbjct: 61 GFTGEYIKTFLREENLETAFSEVKGDTRINVKLKTGDETEINGQGPTISDEDFKAFLEQF 120- Query: 121 SRLTPEDTVVFAGSAPASLGNKVYNTLIPIAKKTGAEVVCDFEGQTLLDALAYQPLLVKP 18- 0 L D VV AGS P+SL + Y + K+ A VV D G+ LL A +P L+KP Sbjct: 121 QSLQEGDIVVLAGSIPSSLPHDTYEKIAEACKQQNARVVLDISGEALLKATEMKPFLMKP 18- 0 Query: 181 NNHELADIFGVELEGLPDIEKYAHKILDKGAKNVIVSMAGDGALLVTPEASYFAKPIKGE 24- 0 N+HEL ++FG + + + Y K++++GA++VIVSMAGDGALL T EA YFA KG+ Sbjct: 181 NHHELGEMFGTAITSVEEAVPYGKKLVEQGAEHVIVSMAGDGALLFTNEAVYFANVPKGK 24- 0 Query: 241 VKNSVGAGDSMVAGFTGEFVKSKNPVEALKWGVACGTATTFSDDLATAEFIQDIYNKVEV 30- 0 + NSVGAGDS+VAGF K EA + GV G+AT FS++L T EF+Q + +V+V Sbjct: 241 LVNSVGAGDSVVAGFLAGISKQLPLEEAFRLGVTSGSATAFSEELGTEEFVQQLLPEVKV 30- 0 Query: 301 EKL 303 +L Sbjct: 301 TRL 303 A related DNA sequence was identified in S. pyogenes <SEQ ID 6057> which encodes the amino acid sequence <SEQ ID 6058>. Analysis of this protein sequence reveals the following: TABLE-US-05979 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1738(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05980 Identities = 222/302 (73%), Positives = 261/302 (85%) Query: 1 MIYTVTLNPSIDFIVRLDTLLLGSVNRMTSDDKYVGGKGINVSRILKRLKIDNTATGFIG 60 MIYTVTLNPSIDFIVR+D + LGSVNRM SDDK+ GGKGINVSRIL+RL I +TATGF+G Sbjct: 1 MIYTVTLNPSIDFIVRIDQINLGSVNRMASDDKFAGGKGINVSRILQRLDIASTATGFLG 60 Query: 61 GFTGHFVEDGLVLEGIKTDFVSVNEDTRINVKVKAKIETEINGGGPRITNEQLHRLEKLL 120- GFTG F+E+ L EG+KTDFV ++DTRINVK+K++ ETE+NG GP I+ EQL L+ L Sbjct: 61 GFTGRFIEESLSAEGVKTDFVKGDQDTRINVKIKSQEETELNGQGPIISQEQLEDLKTKL 120- Query: 121 SRLTPEDTVVFAGSAPASLGNKVYNTLIPIAKKTGAEVVCDFEGQTLLDALAYQPLLVKP 18- 0 S+LT EDTVVFAGSAPA+LGN VY L+P+ +++GA+VVCDFEGQTL+DALAY PLLVKP Sbjct: 121 SQLTAEDTVVFAGSAPANLGNAVYKELLPLVRQSGAQVVCDFEGQTLIDALAYNPLLVKP 18- 0 Query: 181 NNHELADIFGVELEGLPDIEKYAHKILDKGAKNVIVSMAGDGALLVTPEASYFAKPIKGE 24- 0 NNHEL IFG L L D+E YA ++L+ GA+NVI+SMAGDGALLVT EA+YFAKPIKGE Sbjct: 181 NNHELEAIFGTILTSLDDVETYARRLLEMGAQNVIISMAGDGALLVTKEATYFAKPIKGE 24- 0 Query: 241 VKNSVGAGDSMVAGFTGEFVKSKNPVEALKWGVACGTATTFSDDLATAEFIQDIYNKVEV 30- 0 VKNSVGAGDSMVAGFTGEF+KS+NP+EALKWGVACGTAT FSDDLAT FI++ Y+KVEV Sbjct: 241 VKNSVGAGDSMVAGFTGEFMKSQNPIEALKWGVACGTATAFSDDLATIAFIKETYHKVEV 30- 0 Query: 301 EK 302 EK Sbjct: 301 EK 302 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1955 A DNA sequence (GBSx2064) was identified in S. agalactiae <SEQ ID 6059> which encodes the amino acid sequence <SEQ ID 6060>. Analysis of this protein sequence reveals the following: TABLE-US-05981 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2769(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9961> which encodes amino acid sequence <SEQ ID 9962> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05982 >GP: AAC24913 GB: AF012285 FruR [Bacillus subtilis] Identities = 97/247 (39%), Positives = 148/247 (59%), Gaps = 4/247 (1%) Query: 23 MLKSKRKEIILSRLEQNKSVTLDELTSILETSESTVRRDLDELESAGFLKRVHGGAELPY 82 - ML +R ++I+ ++E++ V + EL ++ SEST+RRDL LE GFLKRVHGGA Sbjct: 1 MLTPERHQLIIDQIEKHDVVKIQELINLTNASESTIRRDLSTLEERGFLKRVHGGAAKLS 60 Query: 83 SLGQELSNQEKAIKNVQKKLDIARQTAKLIAKQDVIFIDAGTTTELLIDFLPH-EQLTVV 141- + E EK+ KN+ KL IA + A L+ + D I++DAGTTT +IDF+ + + VV Sbjct: 61 DIRLEPDMLEKSSKNLHDKLKIAEKAASLLEEGDCIYLDAGTTTLHMIDFMDKTKDIVVV 120- Query: 142 TNSIHHAAKLVDRGIKTIIIGGAVKHSTDASIGQVAINQIRQITVDKAFLGMNGID-EVY 20- 0 TN + H L+ + I ++GG VKH T A IG ++ + Q DK+FLG NG+ E Sbjct: 121 TNGVMHIDALIRKEISFYLLGGYVKHRTGAIIGGASLVAMDQYRFDKSFLGTNGVHTEAG 18- 0 Query: 201 LTTPDLEEAAIKEAIINNSQQTFILMDSSKIGQVTFAKVKEINDINLVTNKTDSELMTII 26- 0 TTPD +EA +K+ I ++ ++L D SK G+++F+ I D ++T TD+E +T Sbjct: 181 FTTPDPDEALLKQKAIKQAKHAYVLADPSKFGEISFSAFAGIGDATIIT--TDAEELTFD 23- 8 Query: 261 KEKMKVI 267 + K + Sbjct: 239 NYQEKTV 245 A related DNA sequence was identified in S. pyogenes <SEQ ID 6061> which encodes the amino acid sequence <SEQ ID 6062>. Analysis of this protein sequence reveals the following: TABLE-US-05983 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2604(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05984 Identities = 135/237 (56%), Positives = 184/237 (76%) Query: 33 LSRLEQNKSVTLDELTSILETSESTVRRDLDELESAGFLKRVHGGAELPYSLGQELSNQE 92 - ++++ + V+L++L +L +SEST+RRDL ELE G L RVHGGAEL +SL +ELSNQE Sbjct: 1 MAKITEENYVSLEDLMQLLNSSESTIRRDLGELEQEGRLHRVHGGAELFHSLQEELSNQE 60 Query: 93 KAIKNVQKKLDIARQTAKLIAKQDVIFIDAGTTTELLIDFLPHEQLTVVTNSIHHAAKLV 152- K++KN K IA++ ++LI DVIFIDAGTTTE L+ FL + LTVVTNSIHHAA+LV Sbjct: 61 KSVKNSHIKKAIAQRASQLIYDNDVIFIDAGTTTEFLLPFLQAKNLTVVTNSIHHAARLV 120- Query: 153 DRGIKTIIIGGAVKHSTDASIGQVAINQIRQITVDKAFLGMNGIDEVYLTTPDLEEAAIK 21- 2 + I+TII+GG VK +TDASIG VA+ QIRQ+ DKAFLGMNG+D+ YLTTPD+EEA IK Sbjct: 121 ELSIETIIVGGYVKQTTDASIGNVALEQIRQMNFDKAFLGMNGVDDSYLTTPDNEEAVIK 18- 0 Query: 213 EAIINNSQQTFILMDSSKIGQVTFAKVKEINDINLVTNKTDSELMTIIKEKMKVIQV 269 +A+++N++ +IL+D +KIGQV+F KV IND+ ++T + ++ IKEK KVI++ Sbjct: 181 KAVLSNAKLAYILVDGTKIGQVSFVKVAPINDVTIITLGGSASILKQIKEKAKVIEL 237 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1956 A DNA sequence (GBSx2065) was identified in S. agalactiae <SEQ ID 6063> which encodes the amino acid sequence <SEQ ID 6064>. This protein is predicted to be beta-lactam resistance factor. Analysis of this protein sequence reveals the following:

TABLE-US-05985 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5777(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05986 >GP: CAB89121 GB: AJ277485 beta-lactam resistance factor [Streptococcus pneumoniae] Identities = 215/410 (52%), Positives = 283/410 (68%) Query: 1 MTLRELTIEEFKEHSGNYDSQSFLQTPEMAKLLEKRGYDVRYLGYQVENKLEIISLSYIM 60 M L LT EEF+ +S S+SF+Q+ +M LLEKRG + YL + E ++++ +L Y + Sbjct: 1 MALTTLTKEEFQTYSDQVSSRSFMQSVQMGDLLEKRGARIVYLALKQEGEIQVAALVYSL 60 Query: 61 PVTGGFQMKIDSGPVHSNSKYLKQFYKALQGYAKSNGVLELIVEPYDDYQLFTSSGVPSN 120- P+ GG M+++SGP+++ L FY L+ YAK NGVLEL+V+PY+ YQ F S G P + Sbjct: 61 PMLGGLHMELNSGPIYTQQDALPVFYAELKEYAKQNGVLELLVKPYETYQTFDSQGNPID 120- Query: 121 QGNDNLIEDFTSSGYHHDGLTTGFTGKYLSWHYVKNLEGVTSETLLSSFSKTGRALVKKA 18- 0 ++I+D T GY DGLTTG+ G W Y K+L +T ++LL SFSK G+ LVKKA Sbjct: 121 AEKKSIIQDLTDLGYQFDGLTTGYPGGEPDWLYYKDLTELTEKSLLKSFSKKGKPLVKKA 18- 0 Query: 181 MSFGIKVRVLKRDELHLFKEITTSTSNRRDYMDKSLDYYQDFYDSFEGKAEFVIATLNFR 24- 0 +FGI+++ LKR+EL +FK IT TS RR+Y DKSL+YY+ FYD+F +AEF+IA+LNF Sbjct: 181 ETFGIRLKKLKREELSIFKNITKETSERREYSDKSLEYYEHFYDTFGEQAEFLIASLNFS 24- 0 Query: 241 EYDHNLQIKAEALENKLKLLDERFRENADSPKYHRQRSEIINQLASFETRRQEVQSFIQK 30- 0 +3 LQ + LE L L +N S K Q E +Q +FE R+ E + I+K Sbjct: 241 DYMSKLQGEQSKLEENLDKLRLDLSKNPHSEKKQNQLREYSSQFETFEVRKAEARDLIEK 30- 0 Query: 301 YDNQDVVLAGSLFVYSLKETVYFFSGSYTEFNKFYAPAVLQEYVMQEALKRGSTFYNLLG 36- 0 Y +D+VLAGSLFVY +ET Y FSGSYTEFNKFYAPA+LQ+YVM E++KRG YN LG Sbjct: 301 YGEEDIVLAGSLFVYMPQETTYLFSGSYTEFNKFYAPALLQKYVMLESIKRGIPKYNFLG 36- 0 Query: 361 IQGTFDGSDSILRFKQNFNGCIIRKMGTFNYYPSPFKYKGIQLLKKVLKR 410 IQG FDGSD +LRFKQNFNG I+RK GTF Y+PSP KYK IQLLKK++ R Sbjct: 361 IQGIFDGSDGVLRFKQNFNGYIVRKAGTFRYHPSPLKYKAIQLLKKIVGR 410 There is also homology to SEQ ID 5460. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1957 A DNA sequence (GBSx2066) was identified in S. agalactiae <SEQ ID 6065> which encodes the amino acid sequence <SEQ ID 6066>. This protein is predicted to be cell wall protein, 40 kDa (sr 5' region). Analysis of this protein sequence reveals the following: TABLE-US-05987 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.45 Transmembrane 25-41 (23-42) ----- Final Results ----- bacterial membrane --- Certainty = 0.2381(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9963> which encodes amino acid sequence <SEQ ID 9964> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05988 !GB: AF278686 choline binding protein D; CbpD [Strept . . . !GB: AF278686 choline binding protein D; CbpD [trept . . . >GP: AAF87768 GB: AF278686 choline binding protein D; CbpD [Streptococcus pneumoniae] Identities = 63/230 (27%), Positives = 108/230 (46%), Gaps = 34/230 (14%) Query: 324 WTEQGGQDDIKWYTAVTTGDG------NYKVAVSFADHKNEKGLYNIHLYYQEASGTLVG 37- 7 W+ G + W + V GD-------NY S+ + +++++ G VG Sbjct: 123 WSTAGTYGHVAWVSNVM-GDQISIEEYNYGYTESYNKRVIKANTMTGFIHFKDLDGGSVG 18- 1 Query: 378 VTGTKVTVAGTNSSQEPIENGLAKTGVYNIIGSTEVKNEAKISSQTQFTLEKGDKINYDQ 43- 7 + + + GT+ + + +K E S G+K++YDQ Sbjct: 182 NSQSSTSTGGTHYFKT----------------KSAIKTEPLASGTVIDYYYPGEKVHYDQ 22- 5 Query: 438 VLTADGYQWISYKSYSGVRRYIPVKKLTTSSEKAKDEATKPTSYPNLPKTG-TYTFTKTV 49- 6 +L DGY+W+SY +Y+G RY+ ++ + + P L TG T+ F Sbjct: 226 ILEKDGYKWLSYTAYNGSYRYVQLEAVNKN----------PLGNSVLSSTGGTHYFKTKS 27- 5 Query: 497 DVKSQPKVSSPVEFNFQKGEKIHYDQVLVVDGHQWISYKSYSGIRRYIEI 546 +K++P VS+ V + GEK+HYDQ+L DG++W+SY +Y+G RRYI++ Sbjct: 276 AIKTEPLVSATVIDYYYPGEKVHYDQILEKDGYKWLSYTAYNGSRRYIQL 325 Identities = 49/161 (30%), Positives = 85/161 (52%), Gaps = 14/161 (8%) Query: 116 GNYVYSKETEVKNTPSKSAPVAFYAKKGDKVFYDQVFNKDNVKWISYKSFCGVRRYAAIE 17- 5 G + + ++ +K P S V Y G+KV YDQ+ KD KW+SY ++ G RY +E Sbjct: 191 GTHYFKTKSAIKTEPLASGTVIDYYYPGEKVHYDQILEKDGYKWLSYTAYNGSYRYVQLE 25- 0 Query: 176 SLDPSGGSETKAPTPVTNSGSNNQEKIATQGNYTFSHKVEVKNEAKVASPTQFTLDKGDR 23- 5 +++ + P+ NS + +T G + F K +K E V++ G++ Sbjct: 251 AVNKN---------PLGNSVLS-----STGGTHYFKTKSAIKTEPLVSATVIDYYYPGEK 29- 6 Query: 236 IFYDQILTIEGNQWLSYKSFNGVRRFVLLGKASSVEKTEDK 276 + YDQIL +G +WLSY ++NG RR++ L +S + +++ Sbjct: 297 VHYDQILEKDGYKWLSYTAYNGSRRYIQLEGVTSSQNYQNQ 337 Identities = 52/192 (27%), Positives = 90/192 (46%), Gaps = 3/192 (6%) Query: 295 ISNETTTGFDILITNIKDDNGIAAVKVPVWTEQGGQDDIKWYTAVTTGDGNYKVAVSFAD 35- 4 I T TGF + KD +G + T GG K +A+ T + + Sbjct: 161 IKANTMTGF----IHFKDLDGGSVGNSQSSTSTGGTHYFKTKSAIKTEPLASGTVIDYY- 21- 5 Query: 355 HKNEKGLYNIHLY---YQEASGTLVGVTGTKVTVAGTNSSQEPIENGLAKT--GVYNIIG 40- 9 + EK Y+ L Y+ S T + V + N + P+ N + + G + Sbjct: 216 YPGEKVHYDQILEKDGYKWLSYTAYNGSYRYVQLEAVNKN--PLGNSVLSSTGGTHYFKT 27- 3 Query: 410 STEVKNEAKISSQTQFTLEKGDKINYDQVLTADGYQWISYKSYSGVRRYIPVKKLTTSSE 46- 9 + +K E +S+ G+K++YDQ+L DGY+W+SY +Y+G RRYI ++ + TSS+ Sbjct: 274 KSAIKTEPLVSATVIDYYYPGEKVHYDQILEKDGYKWLSYTAYNGSRRYIQLEGV-TSSQ 33- 2 Query: 470 KAKDEATKPTSY 481 ++++ +SY Sbjct: 333 NYQNQSGNISSY 344 Identities = 33/113 (29%), Positives = 56/113 (49%), Gaps = 2/113 (1%) Query: 91 NTATKDITTPLVETKPMVEKTLPEQGNYVYSK-ETEVKNTPSKSAPVAFYAKKGDKVFYD 149- N + + + V P+ L G Y K ++ +K P SA V Y G+KV YD Sbjct: 241 NGSYRYVQLEAVNKNPLGNSVLSSTGGTHYFKTKSAIKTEPLVSATVIDYYYPGEKVHYD 30- 0 Query: 150 QVFNKDNVKWISYKSFCGVRRYAAIESLDPSGGSETKAPTPVTNSGSNNQEKI 202 Q+ KD KW+SY ++ G RRY +E + S + ++ +++ GS++ + Sbjct: 301 QILEKDGYKWLSYTAYNGSRRYIQLEGVTSSQNYQNQSGN-ISSYGSHSSSTV 352 A related GBS gene <SEQ ID 8937> and protein <SEQ ID 8938> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-05989 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -6.74 GvH: Signal Score (-7.5): 1.26 Possible site: 42 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -3.45 threshold: 0.0 INTEGRAL Likelihood = -3.45 Transmembrane 22-39 (23-42) PERIPHERAL Likelihood = 6.26 371 modified ALOM score: 1.19 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2381(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) The protein has homology with the following sequences in the databases: ##STR00136## A related DNA sequence was identified in S. pyogenes <SEQ ID 6067> which encodes the amino acid sequence <SEQ ID 6068>. Analysis of this protein sequence reveals the following: TABLE-US-05990 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-05991 >GP: AAF87768 GB: AF278686 choline binding protein D; CbpD [Streptococcus pneumoniae] Identities = 93/217 (42%), Positives = 136/217 (61%), Gaps = 18/217 (8%) Query: 42 GDNYPSKWKKGNG-IDSWNMYIRQCTSFAAFRLSSANGFQLPKGYGNACTWGHIAKNQGY 100- GD+YP+ +K G+ ID W MY RQCTSF AFRLS+ NGF++P YGNA WGH A+ +GY Sbjct: 51 GDDYPAYYKNGSQEIDQWRMYSRQCTSFVAFRLSNVNGFEIPAAYGNANEWGHRARREGY 110- Query: 101 PVNKTPSIGAIAWFDKNAYQSNAAYGHVAWVADIRGDTVTIEEYNYNAGQGPERYHKRQI 16- 0 V+ TP+IG+I W + YGHVAWV+++ GD + IEEYNY E Y+KR I Sbjct: 111 RVDNTPTIGSITW------STAGTYGHVAWVSNVMGDQIEIEEYNYGY---TESYNKRVI 16- 1 Query: 161 PKSQVSGYIHFKDLSSQTSHSYPRQLKHISQASFDPSGTYHFTTRLPVKGQTSIDSPDLA 22- 0 + ++G+IHFKDL + + SQ+S GT++F T+ +K + + Sbjct: 162 KANTMTGFIHFRDLDGGSVGN--------SQSSTSTGGTHYFKTKSAIKTEPLASGTVID 21- 3 Query: 221 YYEAGQSVYYDKVVTAGGYTWLSYLSFSGNRRYIPIK 257 YY G+ V+YD+++ GY WLSY +++G+RY+ ++ Sbjct: 214 YYYPGEKVHYDQILEKDGYKWLSYTAYNGSYRYVQLE 250 An alignment of the GAS and GBS proteins is shown below. TABLE-US-05992 Identities = 34/94 (36%), Positives = 52/94 (55%) Query: 453 SGVRRYIPVKKLTTSSEKAKDSATKPTSYPNLPKTGTYTFTKTVDVKSQPKVSSPVEFNF 51- 2 S V YI K L++ + + K S + +GTY FT + VK Q + SP + Sbjct: 163 SQVSGYIHFKDLSSQTSHSYPRQLKHISQASFDPSGTYHFTTRLPVKGQTSIDSPDLAYY 22- 2 Query: 513 QKGEKIHYDQVLVVDGHQWISYKSYSGIRRYIEI 546 + G+ ++YD+V+ G+ W+SY S+SG RRYI I Sbjct: 223 EAGQSVYYDKVVTAGGYTWLSYLSFSGNRRYIPI 256 Identities = 30/78 (38%), Positives = 45/78 (57%), Gaps = 2/78 (2%) Query: 402 TGVYNIIGSTEVKNEAKISSQTQFTLEKGDKINYDQVLTADGYQWISYKSYSGVRRYIPV 46- 1 +G Y+ VK + I S E G + YD+V+TA GY W+SY S+SG RRYIP+ Sbjct: 197 SGTYHFTTRLPVKGQTSIDSPDLAYYEAGQSVYYDKVVTAGGYTWLSYLSFSGNRRYIPI 25- 6 Query: 462 KKLTTSSEKAKDEATKPT 479 K+ + +++ TKP+ Sbjct: 257 KS--PAQSVVQNDNTKPS 272 Identities = 27/94 (28%), Positives = 47/94 (49%) Query: 198 NQEKIATQGNYTFSHKVEVKNEAKVASPTQFTLDKGDRIFYDQILTIEGNQWLSYKSFNG 25- 7 +Q G Y F+ ++ VK + + SP + G ++YD+++T G WLSY SF+G Sbjct: 190 SQASFDPSGTYHFTTRLPVKGQTSIDSPDLAYYEAGQSVYYDKVVTAGGYTWLSYLSFSG 24- 9 Query: 258 VRRFVLLGKASSVEKTEDKEKVSPQPQARITKTG 291 RR++ + + + D K S + +T G Sbjct: 250 NRRYIPIKEPAQSVVQNDNTKPSIKVGDTVTFPG 283 Identities = 23/73 (31%), Positives = 35/73 (47%) Query: 103 ETKPMVEKTLPEQGNYVYSKETEVKNTPSKSAPVAFYAKKGDKVFYDQVFNKDNVKWISY 16- 2 + K + + + G Y ++ VK S +P Y + G V+YD+V W+SY Sbjct: 185 QLKHISQASFDPSGTYHFTTRLPVKGQTSIDSPDLAYYEAGQSVYYDKVVTAGGYTWLSY 24- 4 Query: 163 KSFCGVRRYAAIE 175 SF G RRY I+ Sbjct: 245 LSFSGNRRYIPIK 257 SEQ ID 8938 (GBS91) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 18 (lane 7; MW 63 kDa). The GBS91-His fusion product was purified (FIG. 195, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 283), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1958 A DNA sequence (GBSx2067) was identified in S. agalactiae <SEQ ID 6069> which encodes the amino acid sequence <SEQ ID 6070>. This protein is predicted to be thiamine biosynthesis protein. Analysis of this protein sequence reveals the following: TABLE-US-05993 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0984(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05994 >GP: CAB49673 GB: AJ248285 PROBABLE 2-DEHYDROPANTOATE 2-REDUCTASE (EC 1.1.1.169) [Pyrococcus abyssi] Identities = 85/301 (28%), Positives = 150/301 (49%), Gaps = 7/301 (2%) Query: 1 MLVYIAGSGAMGCRFGYQISKTNHDVILLDNWADHIMAIKENGLKVTGDTEDLVKLPIMK 60 M +YI G+GA+G FG ++ DV+L+ H+ AI E GLK+G + VK+ Sbjct: 1 MKIYILGAGAIGSLFGGLLANAGEDVLLIGR-DPHVSAINEKGLKIVGIKDLNVKVEATT 59 Query: 61 PTDATEEADLIILFTKAMQLPNMLQDIKKIIGKKTKVLCLLNGLGHEDVIRQYIPEHNIL 120- E+ DLI+L TK+ L+ + I+ K + VL + NG+G+ED I ++ + Sbjct: 60 RVPE-EKPDLIVLATKSYSTIEALKSARHIV-KGSWVLSIQNGIGNEDKIIEF--GGKAI 115- Query: 121 MGVTVWTAGLKGPGHAHLEGVGSVNLQSIDPNNQEAGHRVTELLNEAKLQATYDENVLPN 18- 0 G+T A ++ PG G G + ++ +V ++ N A ++ EN++ Sbjct: 116 GGITTNGAMVEAPGVIKWTGKGVTIIGLYPQGREKFIEKVADVFNSADIETHVSENIISW 17- 5 Query: 181 IWRKACVNGTMNSTCALLDCTIGQLFASEDGVNMVHEIIHEFVTVGKAEGVELDEEEITK 24- 0 IW KA VN +N LL+ + ++ ++M E++ E V G+E D + Sbjct: 176 IWAKAIVNSAINPIGTLLEVKNKVIRENDFLLSMAMEVVKEGCRVALQNGIEFDVPPMDL 23- 5 Query: 241 YVMDTSVKAAHHYPSMHQDLVQNQRLTEIDFLNGAVNKKGENLGIDTPYCRLITQLIHTKE 3- 01 + T + +Y SM QD+ + ++ TE+D++NG + + + + ++ P L+ LI KE Sbjct: 236 F-FQTLEQTRENYNSMLQDIWRGKK-TEVDYINGKIVEYAKAVNLEAPMNLLLWGLIKGKE 2- 94 A related DNA sequence was identified in S. pyogenes <SEQ ID 6071> which encodes the amino acid sequence <SEQ ID 6072>. Analysis of this protein sequence reveals the following: TABLE-US-05995 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1392(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-05996 Identities = 262/307 (85%), Positives = 288/307 (93%) Query: 1 MLVYIAGSGAMGCRFGYQISKTNHDVILLDNWADHIMAIKENGLKVTGDTEDLVKLPIMK 60 MLVYIAGSGAMGCRFGYQISKTN+DVILLDNW DHI AIKENGL VTGD E+ VKLPIMK Sbjct: 1 MLVYIAGSGAMGCRFGYQISKTNNDVILLDNWEDHINAIKENGLVVTGDVEETVKLPIMK 60 Query: 61 PTDATEEADLIILFTKAMQLPNMLQDIKKIIGKKTKVLCLLNGLGHEDVIRQYIPEHNIL 120- PT+AT+EADLIILFTKAMQLP MLQDIK IIGK+TKVLCLLNGLGHEDVIRQYIPEHNIL Sbjct: 61 PTEATQEADLIILFTKAMQLPQMLQDIKGIIGKETKVLCLLNGLGHEDVIRQYIPEHNIL 120- Query: 121 MGVTVWTAGLKGPGHAHLEGVGSVNLQSIDPNNQEAGHRVTELLNEAKLQATYDENVLPN 18- 0 MGVTVWTAGL+GPG AHL+GVG++NLQS+DP+NQEAGH+V +LLNEA L ATYDENV+PN Sbjct: 121 MGVTVWTAGLEGPGRAHLQGVGALNLQSMDPSNQEAGHQVADLLNEANLNATYDENVVPN 18- 0 Query: 181 IWRKACVNGTMNSTCALLDCTIGQLFASEDGVNMVHEIIHEFVTVGKAEGVELDEEEITK 24- 0 IWRKACVNGTMNSTCALLDCTIG+LFASEDG+ MV EIIHEFV VG+AEGVEL+EEEIT+ Sbjct: 181 IWRKACVNGTMNSTCALLDCTIGELFASEDGLKMVKEIIHEFVIVGQAEGVELNEEEITQ 24- 0 Query: 241 YVMDTSVKAAHHYPSMHQDLVQNQRLTEIDFLNGAVNKKGENLGIDTPYCRLITQLIHTK 30- 0 YVMDTSVKAAHHYPSMHQDLVQN RLTEIDF+NGAVN KGE LGI+TPYCR+IT+L+H K Sbjct: 241 YVMDTSVKAAHHYPSMHQDLVQNHRLTEIDFINGAVNTKGEKLGINTPYCRMITELVHAK 30- 0 Query: 301 ENVLSIK 307 E VL+I+ Sbjct: 301 EAVLNIQ 307 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1959 A DNA sequence (GBSx2068) was identified in S. agalactiae <SEQ ID 6073> which encodes the amino acid sequence <SEQ ID 6074>. Analysis of this protein sequence reveals the following: TABLE-US-05997 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.03 Transmembrane 61-77 (61-78) INTEGRAL Likelihood = -1.33 Transmembrane 80-96 (79-96) ----- Final Results ----- bacterial membrane --- Certainty = 0.2211(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1960 A DNA sequence (GBSx2069) was identified in S. agalactiae <SEQ ID 6075> which encodes the amino acid sequence <SEQ ID 6076>. This protein is predicted to be regulatory protein (pfoS/R). Analysis of this protein sequence reveals the following: TABLE-US-05998 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.82 Transmembrane 317-333 (304-335) INTEGRAL Likelihood = -7.64 Transmembrane 187-203 (183-217) INTEGRAL Likelihood = -5.26 Transmembrane 24-40 (18-44) INTEGRAL Likelihood = -5.04 Transmembrane 143-159 (139-161) INTEGRAL Likelihood = -2.34 Transmembrane 116-132 (115-136) INTEGRAL Likelihood = -2.13 Transmembrane 55-71 (55-71) INTEGRAL Likelihood = -0.96 Transmembrane 268-284 (268-284) ----- Final Results ----- bacterial membrane --- Certainty = 0.4927(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-05999 >GP: AAC65034 GB: AE001189 regulatory protein (pfoS/R) [Treponema pallidum] Identities = 138/358 (38%), Positives = 220/358 (60%), Gaps = 18/358 (5%) Query: 2 TNTVTPKETAGSFINKVLGGTATAIVVALIPNAILATFLKPFLSYG-LAAEFLHIVQVFQ 60 T +++P++ F+ K+L G++ IV+ L+P AI + L A H+V Q Sbjct: 3 TQSLSPRQ----FMMKILNGSSAGIVIGLVPPAIAGELFRALAPLSPLFAALYHVVLPIQ 58 Query: 61 FFTPIMAGFLIGQQFKFTPMQQLAVGGAAYIGSGAWAYTEVIQKGVATGSFQLRGIGDLI 120- F P + G L+G QF + + + + I SG + G++ + GIGD+I Sbjct: 59 FSVPALIGTLVGLQFHCSAPEVATLAFVSVIASG--------NVTLQNGAWLITGIGDVI 110- Query: 121 NMMLTAALAVLAVKWFGNKFGSLTIILLPIIIGTGVGYLGWKLLPYVSYVTTLIGQGINS 18- 0 N+ML +ALA++ V+ K GSLTII LP+I+ G +G LPYV +T +G+ I + Sbjct: 111 NVMLISALAIILVRALRGKLGSLTIIALPVIVAVVAGGVGSFSLPYVKMITLFVGRVIAT 17- 0 Query: 181 FTTLQPIAMSILIAMAFSMLIVSPISTVAIGLAIGLNGMSASAASMGVASTTAVLVWATM 24- 0 F LQP+ MSIL++M+FS++I+SP+S+VA+G+A+GL G+++ AA++GV+S L+ TM Sbjct: 171 FIALQPLLMSILLSMSFSLIIISPVSSVAVGIAVGLTGLASGAANIGVSSCAMTLIVGTM 23- 0 Query: 241 KANKSGVPIAIALGAMKMMMPNFLKHPVMAIPMLMTATVSSLTVPLFKLVGTPASSGFGL 30- 0 + NK GVP+A+ GAMKM+MPN++++P++ IP+L+ V + LF L GTPAS+GFG Sbjct: 231 RVNKIGVPLAMFAGAMKMLMPNWIRYPILNIPLLLNGLVCGVLAWLFNLQGTPASAGFGF 29- 0 Query: 301 VGAVGPIASFE--AGASML---IVILSWLVIPFAVGFVSHKICKDILKLYKDDIFVFE 353 +G VGPI ++ A M+ I+ L + V+ F ++ I D LKLY+ ++F+ E Sbjct: 291 IGLVGPINAYRLMAYTPMVRAGILFLVYFVLSFLAAYLIDFILVDRLKLYRRELFIPE 348 There is also homology to SEQ ID 1280. A related GBS gene <SEQ ID 8939> and protein <SEQ ID 8940> were also identified. Analysis of this protein sequence reveals the following:

TABLE-US-06000 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -7.24 GvH: Signal Score (-7.5): -2.94 Possible site: 49 >>> Seems to have no N-terminal signal sequence ALOM program count: 7 value: -9.82 threshold: 0.0 INTEGRAL Likelihood = -9.82 Transmembrane 317-333 (304-335) INTEGRAL Likelihood = -7.64 Transmembrane 187-203 (183-217) INTEGRAL Likelihood = -6.37 Transmembrane 143-159 (136-161) INTEGRAL Likelihood = -5.26 Transmembrane 24-40 (18-44) INTEGRAL Likelihood = -2.34 Transmembrane 116-132 (115-136) INTEGRAL Likelihood = -2.13 Tramsmembrane 55-71 (55-71) INTEGRAL Likelihood = -0.96 Transmembrane 268-284 (268-284) PERIPHERAL Likelihood = 0.69 205 modified ALOM score: 2.46 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4927(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00137## There is also homology to SEQ ID 1276 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1961 A DNA sequence (GBSx2070) was identified in S. agalactiae <SEQ ID 6077> which encodes the amino acid sequence <SEQ ID 6078>. Analysis of this protein sequence reveals the following: TABLE-US-06001 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06002 >GP: BAB07127 GB: AP001518 thioredoxin reductase [Bacillus halodurans] Identities = 163/325 (50%), Positives = 222/325 (68%), Gaps = 3/325 (0%) Query: 5 IYDITIVGGGPVGLFAAFYAGLRGVSVKIIESLSELGGQPAILYPEKKIYDIPGYPVITG 64 +YDITI+GGGP GLFAAFY G+R VKIIES+ +LGGQ A LYPEK IYD+ G+P + Sbjct: 7 LYDITIIGGGPTGLFAAFYGGMRQAKVKIIESMPQLGGQLAALYPEKYIYDVAGFPKVKA 66 Query: 65 RELIDKHIEQLERFKDSIEICLKEEVLSFEK-VDDVFTIQTDKDQHLSRAIVFACGNGAF 123- ++L++ Q E+F +I L++ V + K DD FTI+TDK+ H S+AI+ G GAF Sbjct: 67 QDLVNDLKRQAEQFNPTI--ALEQSVQNVTKETDDTFTIKTDKETHYSKAIIITAGAGAF 124- Query: 124 APRLLGLENEENYADNNLFYNVTKLEQFAGKHVVICGGGDSAVDWANELDKIAASVAIVH 18- 3 PR L +E + Y NL Y V L +AGK+V+I GGGDSAVDWA L+ +A +V ++H Sbjct: 125 QPRRLEVEGAKQYEGKNLQYFVNDLNAYAGKNVLISGGGDSAVDWALMLEPVAKNVTLIH 18- 4 Query: 184 RRDAFRAHEHSVDILKASGVRILTPYVPIGLNGDSQRVSSLVVQKVKGDEVIELPLDNLI 24- 3 RRD FRAHEHSV++L+ S V ILTP+ L+GD +++ + +Q+VKGD V L +D +I Sbjct: 185 RRDKFRAHEHSVELLQKSSVNILTPFAISELSGDGEKIHHVTIQEVKGDAVETLDVDEVI 24- 4 Query: 244 VSFGFSTSNKNLRYWNLDYKRSSINVSSLFETTQEGVYAIGDAANYPGKVELIATGYGEA 30- 3 V+FGF +S ++ W L+ +++SI V++ ET G+YA GD YPGKV+LIATG+GEA Sbjct: 245 VNFGFVSSLGPIKGWGLEIEKNSIVVNTKMETNIPGIYAAGDICTYPGKVKLIATGFGEA 30- 4 Query: 304 PVAINQAINYIYPDRDNRVVHSTSL 328 P A+N A +I P HSTSL Sbjct: 305 PTAVNNAKAFIDPTARVFPGHSTSL 329 A related DNA sequence was identified in S. pyogenes <SEQ ID 6079> which encodes the amino acid sequence <SEQ ID 6080>. Analysis of this protein sequence reveals the following: TABLE-US-06003 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.37 Transmembrane 8-24 (8-24) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06004 >GP: CAB15201 GB: Z99120 similar to thioredoxin reductase [Bacillus subtilis] Identities = 173/328 (52%), Positives = 223/328 (67%), Gaps = 4/328 (1%) Query: 4 KAYDITIIGGGPIGLFAAFYAGLRGVTVKIIESLSELGGQPAILYPEKMIYDIPAYPSLT 63 K YDITIIGGGP+GLF AFY G+R +VKIIESL +LGGQ + LYPEK IYD+ +P + Sbjct: 6 KVYDITIIGGGPVGLFTAFYGGMRQASVKIIESLPQLGGQLSALYPEKYIYDVAGFPKIR 65 Query: 64 GVELTENLIKQLSRFEDRTTICLKEEVLTFDKVKGG-FSIRTNKAEHFSKAIIIACGNGA 122- EL NL +Q+++F+ TICL++ V + +K G F + K K I GNGA Sbjct: 66 AQELINNLKEQMAKFDQ--TICLEQAVESVEKQADGVFKLVQMKKPTTLKRSCITAGNGA 123- Query: 123 FAPRTLGLESEENFADHNLFYNVHQLDQFAGQKVVICGGGDSAVDWALALEDIAESVTVV 18- 2 F PR L LE+ E + NL Y V L +FAG++V I GGGDSAVDWAL LE IA+ V+++ Sbjct: 124 FKPRKLELENAEQYEGKNLHYFVDDLQKFAGRRVAILGGGDSAVDWALMLEPIAKEVSII 18- 3 Query: 183 HRRDAFRAHEHSVELLKASTVNLLTPYVPKALKGIGNLAEKLVIQKVKEDEVLELELDSL 24- 2 HRRD FRAHEHSVE L AS VN+LTP+VP L G + E+LV+++VK D LE+D L Sbjct: 184 HRRDKFRAHEHSVENLHASKVNVLTPFVPAELIGEDKI-EQLVLEEVKGDRKEILEIDDL 24- 2 Query: 243 IVSFGFSTSNKNLKNWNLDYKRSSITVSPLFQTSQEGIFAIGDAAAYNGKVDLIATGFGE 30- 2 IV++GF +S +KNW LD +++SI V +T+ EG FA GD Y GKV+LIA+GFGE Sbjct: 243 IVNYGFVSSLGPIKNWGLDIEKNSIVVKSTMETNIEGFFAAGDICTYEGKVNLIASGFGE 30- 2 Query: 303 APTAVNQAINYIYPDRDNRVVHSTSLID 330 APTAVN A Y+ P + +HSTSL + Sbjct: 303 APTAVNNAKAYMDPKARVQPLHSTSLFE 330 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06005 Identities = 242/324 (74%), Positives = 279/324 (85%) Query: 6 YDITIVGGGPVGLFAAFYAGLRGVSVKIIESLSELGGQPAILYPEKKIYDIPGYPVITGR 65 YDITI+GGGP+GLFAAFYAGLRGV+VKIIESLSELGGQPAILYPEK IYDIP YP +TG Sbjct: 6 YDITIIGGGPIGLFAAFYAGLRGVTVKIIESLSELGGQPAILYPEKMIYDIPAYPSLTGV 65 Query: 66 ELIDKHIEQLERFKDSIEICLKEEVLSFEKVDDVFTIQTDKDQHLSRAIVFACGNGAFAP 125- EL + I+QL RF+D ICLKEEVL+F+KV F+I+T+K +H S+AI+ ACGNGAFAP Sbjct: 66 ELTENLIKQLSRFEDRTTICLKEEVLTFDKVKGGFSIRTNKAEHFSKAIIIACGNGAFAP 125- Query: 126 RLLGLENEENYADNNLFYNVTKLEQFAGKHVVICGGGDSAVDWANELDKIAASVAIVHRR 18- 5 R LGLE+EEN+AD+NLFYNV +L+QFAG+ VVICGGGDSAVDWA L+ IA SV +VHRR Sbjct: 126 RTLGLESEENFADHNLFYNVHQLDQFAGQKVVICGGGDSAVDWALALEDIAESVTVVHRR 18- 5 Query: 186 DAFRAHEHSVDILKASGVRILTPYVPIGLNGDSQRVSSLVVQKVKGDEVIELPLDNLIVS 24- 5 DAFRAHEHSV++LKAS V +LTPYVP L G LV+QKVK DEV+EL LD+LIVS Sbjct: 186 DAFRAHEHSVELLKASTVNLLTPYVPKALKGIGNLAEKLVIQKVKEDEVLELELDSLIVS 24- 5 Query: 246 FGFSTSNKNLRYWNLDYKRSSINVSSLFETTQEGVYAIGDAANYPGKVELIATGYGEAPV 30- 5 FGFSTSNKNL+ WNLDYKRSSI VS LF+T+QEG++AIGDAA Y GKV+LIATG+GEAP Sbjct: 246 FGFSTSNKNLKNWNLDYKRSSITVSPLFQTSQEGIFAIGDAAAYNGKVDLIATGFGEAPT 30- 5 Query: 306 AINQAINYIYPDRDNRVVHSTSLI 329 A+NQAINYIYPDRDNRVVHSTSLI Sbjct: 306 AVNQAINYIYPDRDNRVVHSTSLI 329 SEQ ID 6078 (GBS178) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 38 (lane 5; MW 37.4 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 41 (lane 8; MW 62.4 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1962 A DNA sequence (GBSx2071) was identified in S. agalactiae <SEQ ID 6081> which encodes the amino acid sequence <SEQ ID 6082>. This protein is predicted to be tRNA methyltransferase (trnD). Analysis of this protein sequence reveals the following: TABLE-US-06006 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1496(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06007 >GP: BAB06198 GB: AP001515 tRNA methyltransferase [Bacillus halodurans] Identities = 144/246 (58%), Positives = 186/246 (75%), Gaps = 6/246 (2%) Query: 2 MKIDILTLFPEMFAPLEHS-IVGKAKERGLLEINYHNFRENAE-KSRHVDDEPYGGGQGM 59 MKID LTLFPEMF + HS I+ +A+ERG + NFRE +E K + VDD PYGGG GM Sbjct: 1 MKIDFLTLFPEMFQGVLHSSILKQAQERGAVSFRVVNFREYSENKHKKVDDYPYGGGAGM 60 Query: 60 LLRAQPIFDTIDKIDAQKA---RVILLDPAGRTFDQDFAEELSKEDELIFICGHYEGYDE 116- +L QP+FD ++ + + + RVIL+ P G TF Q AEEL++ + LI +CGHYEGYDE Sbjct: 61 VLSPQPLFDAVEDLTKKSSSTPRVILMCPQGETFTQRKAEELAQAEHLILLCGHYEGYDE 120- Query: 117 RIKS-LVTDEVSLGDFVLTGGELAAMTMVDATVRLIPEVIGKETSHQDDSFSSGLLEYPQ 17- 5 RI+S LVTDE+S+GD+VLTGGEL AM + D+ RL+P V+G ETS Q DSFS+GLLEYPQ Sbjct: 121 RIRSYLVTDELSIGDYVLTGGELGAMVIADSVTRLLPAVLGNETSAQTDSFSTGLLEYPQ 18- 0 Query: 176 YTRPYDYLGMTVPDVLMSGHHENIRKWRLEQSLRKTLERRPDLLENYAMTDEERLILEKI 23- 5 YTRP D+ G VPDVL+SGHH+NI +WR EQSL++TLERRPDLLE +T+EE+ +L+ I Sbjct: 181 YTRPADFRGWKVPDVLLSGHHQNIERWRKEQSLKRTLERRPDLLEGRKLTEEEQELLDSI 24- 0 Query: 236 KTEIER 241 + + E+ Sbjct: 241 RKQQEK 246 A related DNA sequence was identified in S. pyogenes <SEQ ID 6083> which encodes the amino acid sequence <SEQ ID 6084>. Analysis of this protein sequence reveals the following: TABLE-US-06008 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2705(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06009 Identities = 195/240 (81%), Positives = 224/240 (93%) Query: 2 MKIDILTLFPEMFAPLEHSIVGKAKERGLLEINYHNFRENAEKSRHVDDEPYGGGQGMLL 61 MKIDILTLFPEMFAPLEHSIVGKAKE+GLL+I+YHNFR+ AEK+RHVDDEPYGGGQGMLL Sbjct: 1 MKIDILTLFPEMFAPLEHSIVGKAKEKGLLDIHYHNFRDYAEKARHVDDEPYGGGQGMLL 60 Query: 62 RAQPIFDTIDKIDAQKARVILLDPAGRTFDQDFAEELSKEDELIFICGHYEGYDERIKSL 121- RAQPIFDTI++I+A+K R+ILLDPAG+ F Q +AEEL+ E+ELIFICGHYEGYDERIK+L Sbjct: 61 RAQPIFDTIEQIEAKKPRIILLDPAGKPFTQAYAEELALEEELIFICGHYEGYDERIKTL 120- Query: 122 VTDEVSLGDFVLTGGELAAMTMVDATVRLIPEVIGKETSHQDDSFSSGLLEYPQYTRPYD 18- 1 VTDE+SLGDFVLTGGELAAMTMVDATVRLIP+V+GKE+SHQDDSFSSGLLEYPQYTRPYD Sbjct: 121 VTDEISLGDFVLTGGELAAMTMVDATVRLIPQVLGKESSHQDDSFSSGLLEYPQYTRPYD 18- 0 Query: 182 YLGMTVPDVLMSGHHENIRKWRLEQSLRKTLERRPDLLENYAMTDEERLILEKIKTEIER 24- 1 Y GMTVPDVLMSGHHE IR WRLE+SL+KT RRPDLLE+Y ++EER +L+KIK +++ Sbjct: 181 YRGMTVPDVLMSGHHERIRLWRLEESLKKTYLRRPDLLEHYNFSEEERKLLDKIKEALDQ 24- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1963 A DNA sequence (GBSx2072) was identified in S. agalactiae <SEQ ID 6085> which encodes the amino acid sequence <SEQ ID 6086>. This protein is predicted to be 16S rRNA processing protein. Analysis of this protein sequence reveals the following: TABLE-US-06010 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.71 Transmembrane 32-48 (32-52) ----- Final Results ----- bacterial membrane --- Certainty = 0.2084(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9381> which encodes amino acid sequence <SEQ ID 9382> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06011 >GP: CAB13475 GB: Z99112 similar to hypothetical proteins [Bacillus subtilis] Identities = 88/174 (50%), Positives = 128/174 (72%), Gaps = 1/174 (0%) Query: 54 VTMEYFNVGKIVNTQGLQGEMRVLSVTDFVEERFKKGQVLALFDEKNQFVMDIEIASHRK 113- +T +FNVGKIVNT G++GE+RV+S TDF EER+K G L LF + +++ + +HR Sbjct: 1 MTKRWFNVGKIVNTHGIKGEVRVISKTDFAEERYKPGNTLYLFMDGRNEPVEVTVNTHRL 60 Query: 114 QKNFDIIKFKGMYHINDIEKYKGFTLKVAEDQLSDLKDGEFYYHEIIGLDVYEGE-ELIG 17- 2 K F +++FK ++N++E+ K +KV E++L +L +GEFY+HEIIG +V+ E ELIG Sbjct: 61 HKQFHLLQFKERQNLNEVEELKNAIIKVPEEELGELNEGEFYFHEIIGCEVFTEEGELIG 120- Query: 173 KIKEILQPGANDVWVVERHGKRDLLLPYIPPVVLEVDLSNQRVQVELMEGLDDE 226 K+KEIL PGANDVWV+ R GK+D L+PYI VV +D+ +++++ELMEGL DE Sbjct: 121 KVKEILTPGANDVWVIGRKGKKDALIPYIESVVKHIDVREKKIEIELMEGLIDE 174 A related DNA sequence was identified in S. pyogenes <SEQ ID 6087> which encodes the amino acid sequence <SEQ ID 6088>. Analysis of this protein sequence reveals the following: TABLE-US-06012 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2787(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06013 Identities = 133/172 (77%), Positives = 153/172 (88%) Query: 56 MEYFNVGKIVNTQGLQGEMRVLSVTDFVEERFKKGQVLALFDEKNQFVMDIEIASHRKQK 115- MEYFNVGKIVNTQGLQGEMRVLSV+DF EERFKKG LALFD+K++FV ++ I SHRKQK Sbjct: 1 MEYFNVGKIVNTQGLQGEMRVLSVSDFAEERFKKGSQLALFDDKDRFVQEVTIVSHRKQK 60 Query: 116 NFDIIKFKGMYHINDIEKYKGFTLKVAEDQLSDLKDGEFYYHEIIGLDVYEGEELIGKIK 17- 5 +FDIIKFK MYHIN IEKYKG+TLKV++D DL++GEFYYH+IIG+ VYE + LIG +K Sbjct: 61 HFDIIKFKDMYHINAIEKYKGYTLKVSKDNQGDLQEGEFYYHQIIGMAVYEKDVLIGHVK 120- Query: 176 EILQPGANDVWVVERHGKRDLLLPYIPPVVLEVDLSNQRVQVELMEGLDDED 227 EILQPGANDVW+V+R GKRDLLLPYIPPVVL VD+ N+RV VELMEGLDDED Sbjct: 121 EILQPGANDVWIVKRQGKRDLLLPYIPPVVLNVDVPNKRVDVELMEGLDDED 172 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1964 A DNA sequence (GBSx2073) was identified in S. agalactiae <SEQ ID 6089> which encodes the amino acid sequence <SEQ ID 6090>. This protein is predicted to be similar to E. coli ykfc (11). Analysis of this protein sequence reveals the following: TABLE-US-06014 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3488(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9909> which encodes amino acid sequence <SEQ ID 9910> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06015 >GP: AAC38715 GB: AF030367 maturase-related protein [Streptococcus pneumoniae] Identities = 366/425 (86%), Positives = 396/425 (93%) Query: 12 MSELLDKILSRNNMLEAYKQVKSNKGSAGINGVTIEQMDDYLHQNWRETKQLIKERSYKP 71 - MS+LLDKILSR NMLEAY QVKSNKGSAGI+G+TIE+MD+YL QNWR TK+LIK+R YKP Sbjct: 1 MSKLLDKILSRENMLEAYNQVKSNKGSAGIDGMTIEEMDNYLRQNWRLTKELIKQRKYKP 60 Query: 72 QPVLRVEIPKPNGGVRNLGIPTAMDRMIQQAIVQVLSPLCEKHFSEYSYGFRPNRSCETA 131- QPVL+VEIPKP+GG+R LGIPT MDRMIQQAIVQV+SP+CE HFS+ SYGFRPNRSCE A Sbjct: 61 QPVLKVEIPKPDGGIRQLGIPTVMDRMIQQAIVQVMSPICEPHFSDTSYGFRPNRSCEKA 120- Query: 132 IVQLLEYLNDGYEWIVDIDLEKFFDTVPQDRLMSLVHNIIQDGDTESLIRKYLHSGVVIN 19- 1 I++LLEYLNDGYEWIVDIDLEKFFDTVPQDRLMSLVHNII+DGDTESLIRKYLHSGV+IN Sbjct: 121 IMKLLEYLNDGYEWIVDIDLEKFFDTVPQDRLMSLVHNIIEDGDTESLIRKYLHSGVIIN 18- 0 Query: 192 GQRHKTLVGTPQGGNLSPLLSNIMLNELDKGLEKRGLRFVRYADDCVITVGSEAAAKRVM 25- 1 GQR+KTLVGTPQGGNLSPLLSNIMLNELDK LEKRGLRFVRYADDCVITVGSEAAAKRVM Sbjct: 181 GQRYKTLVGTPQGGNLSPLLSNIMLNELDKELEKRGLRFVRYADDCVITVGSEAAAKRVM 24- 0 Query: 252 HSVSSYIEKRLGLKVNMTKTKIVRPNKLKYLGFGFWKSPKGWKCRPHQDSVQSFKRKLKQ 31- 1 +SVS +IEKRLGLKVNMTKTKI RP +LKYLGFGFWKS GWK RPHQDSV+ FK KLK+ Sbjct: 241 YSVSRFIEKRLGLKVNMTKTKITRPRELKYLGFGFWKSSDGWKSRPHQDSVRRFKLKLKK 30- 0 Query: 312 LTMRKWSIDLITRIERLNWVIRGWINYFSLGNMKSIMTQIDERLRTRIRVIIWKQWKKKA 37- 1 LT RKWSIDL RIE+LN IRGWINYFSLGNMKSI+ IDERLRTR+R+IIWKQWKKK+ Sbjct: 301 LTQRKWSIDLTRRIEQLNLSIRGWINYFSLGNMKSIVASIDERLRTRLRMIIWKQWKKKS 36- 0 Query: 372 KRLWGLLKLGVARWIADKVSGWGDHYQLVAQKSVLKRAISKPALAKRGLVSCLDYYLERH 43- 1 +RLWGLLKLGV +WIADKVSGWGDHYQLVAQKSVLKRAISKP L KRGLVSCLDYYLERH Sbjct: 361 RRLWGLLKLGVPKWIADKVSGWGDHYQLVAQKSVLKRAISKPVLEKRGLVSCLDYYLERH 42- 0 Query: 432 ALKVS 436 ALKVS Sbjct: 421 ALKVS 425 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1965 A DNA sequence (GBSx2074) was identified in S. agalactiae <SEQ ID 6091> which encodes the amino acid sequence <SEQ ID 6092>. Analysis of this protein sequence reveals the following:

TABLE-US-06016 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.37 Transmembrane 7-23 (7-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 821> which encodes the amino acid sequence <SEQ ID 822>. Analysis of this protein sequence reveals the following: TABLE-US-06017 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.87 Transmembrane 1157-1173 (1157-1174) ----- Final Results ----- bacterial membrane --- Certainty = 0.2147(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06018 Identities = 1031/1064 (96%), Positives = 1042/1064 (97%) Query: 1 MRKKQKLPFDKLAIALISTSILLNAQSDIKANTVTEDTPATEQAVEPPQPIAVSEESPSS 60 +RKKQKLPFDKLAIAL+STSILLNAQSDIKANTVTEDTPATEQAVE PQP AVSEE+PSS Sbjct: 1 LRKKQKLPFDKLAIALMSTSILLNAQSDIKANTVTEDTPATEQAVETPQPTAVSEEAPSS 60 Query: 61 KETKTSQTPSDVGETVADDANDLAPQAPAKTADTPATSKATIRDLNDPSHVKTLQEKAGK 120- KETKT QTP D ET+ADDANDLAPQAPAKTADTPATSKATIRDLNDPS VKTLQEKAGK Sbjct: 61 KETKTPQTPDDAEETIADDANDLAPQAPAKTADTPATSKATIRDLNDPSQVKTLQEKAGK 120- Query: 121 GVGTVVAVIDAGFDKNHEAWRLTDKTKARYQSKENLEKAKKEHGITYGEWVNDKVAYYHD 18- 0 G GTVVAVIDAGFDKNHEAWRLTDKTKARYQSKE+LEKAKKEHGITYGEWVNDKVAYYHD Sbjct: 121 GAGTVVAVIDAGFDKNHEAWRLTDKTKARYQSKEDLEKAKKEHGITYGEWVNDKVAYYHD 18- 0 Query: 181 YSKDGKNAVDQEHGTHVSGILSGNAPSEMKEPYRLEGAMPEAQLLLMRVEIVNGLADYAR 24- 0 YSKDGK AVDQEHGTHVSGILSGNAPSE KEPYRLEGAMPEAQLLLMRVEIVNGLADYAR Sbjct: 181 YSKDGKTAVDQEHGTHVSGILSGNAPSETKEPYRLEGAMPEAQLLLMRVEIVNGLADYAR 24- 0 Query: 241 NYAQAIRDAVNLGAKVINMSFGNAALAYANLPDETKKAFDYAKSKGVSIVTSAGNDSSFG 30- 0 NYAQAI DAVNLGAKVINMSFGNAALAYANLPDETKKAFDYAKSKGVSIVTSAGNDSSFG Sbjct: 241 NYAQAIIDAVNLGAKVINMSFGNAALAYANLPDETKKAFDYAKSKGVSIVTSAGNDSSFG 30- 0 Query: 301 GKPRLPLADHPDYGVVGTPAAADSTLTVASYSPDKQLTETATVKTDDHQDKEMPVLSTNR 36- 0 GK RLPLADHPDYGVVGTPAAADSTLTVASYSPDKQLTETATVKT D QDKEMPVLSTNR Sbjct: 301 GKTRLPLADHPDYGVVGTPAAADSTLTVASYSPDKQLTETATVKTADQQDKEMPVLSTNR 36- 0 Query: 361 FEPNKAYDYAYANRGTKEDDFKDVEGKIALIERGDIDFKDKIANAKKAGAVGVLIYDNQD 42- 0 FEPNKAYDYAYANRG KEDDFKDV+GKIALIERGDIDFKDKIANAKKAGAVGVLIYDNQD Sbjct: 361 FEPNKAYDYAYANRGMKEDDFKDVKGKIALIERGDIDFKDKIANAKKAGAVGVLIYDNQD 42- 0 Query: 421 KGFPIELPNVDQMPAAFISRRDGLLLKDNPQKTITFNATPKVLPTASGTKLSRFSSWGLT 48- 0 KGFPIELPNVDQMPAAFISR+DGLLLK+NPQKTITFNATPKVLPTASGTKLSRFSSWGLT Sbjct: 421 KGFPIELPNVDQMPAAFISRKDGLLLKENPQKTITFNATPKVLPTASGTKLSRFSSWGLT 48- 0 Query: 481 ADGNIKPDIAAPGQDILSSVANNKYAKLSGTSMSAPLVAGIMGLLQKQYETQYPDMTPSE 54- 0 ADGNIKPDIAAPGQDILSSVANNKYAKLSGTSMSAPLVAGIMGLLQKQYETQYPDMTPSE Sbjct: 481 ADGNIKPDIAAPGQDILSSVANNKYAKLSGTSMSAPLVAGIMGLLQKQYETQYPDMTPSE 54- 0 Query: 541 RLDLAKKVLMSSATALYDEDEKAYFSPRQQGAGAVDAKKASAATMYVTDKDNTSSKVHLN 60- 0 RLDLAKKVLMSSATALYDEDEKAYFSPRQQGAGAVDAKKASAATMYVTDKDNTSSKVHLN Sbjct: 541 RLDLAKKVLMSSATALYDEDEKAYFSPRQQGAGAVDAKKASAATMYVTDKDNTSSKVHLN 60- 0 Query: 601 NVSDKFEVTVTVHNKSDKPQELYYQVTVQTDKVDGKHFALAPKALYETSWQKITIPANSS 66- 0 NVSDKFEVTVTVHNKSDKPQELYYQ TVQTDKVDGK FALAPKALYETSWQKITIPANSS Sbjct: 601 NVSDKFEVTVTVHNKSDKPQELYYQATVQTDKVDGKLFALAPKALYETSWQKITIPANSS 66- 0 Query: 661 KQVTVPIDASRFSKDLLAQMKNGYFLEGFVRFKQDPTKEELMSIPYIGFRGDFGNLSALE 72- 0 KQVT+PID S+FSKDLLA MKNGYFLEGFVRFKQDPTKEELMSIPYIGFRGDFGNLSALE Sbjct: 661 KQVTIPIDVSQFSKDLLAPMKNGYFLEGFVRFKQDPTKEELMSIPYIGFRGDFGNLSALE 72- 0 Query: 721 KPIYDSKDGSSYYHEANSDAKDQLDGDGLQFYALKNNFTALTTESNPWTIIKAVKEGVEN 78- 0 KPIYDSKDGSSYYHEANSDAKDQLDGDGLQFYALKNNFTALTTESNPWTIIKAVKEGVEN Sbjct: 721 KPIYDSKDGSSYYHEANSDAKDQLDGDGLQFYALKNNFTALTTESNPWTIIKAVKEGVEN 78- 0 Query: 781 IEDIESSEITETIFAGTFAKQDDDSHYYIHRHANGKPYAAISPNGDGNRDYVQFQGTFLR 84- 0 IEDIESSEITETIFAGTFAKQDDDSHYYIHRHANGKPYAAISPNGDGNRDYVQFQGTFLR Sbjct: 781 IEDIESSEITETIFAGTFAKQDDDSHYYIHRHANGKPYAAISPNGDGNRDYVQFQGTFLR 84- 0 Query: 841 NAKNLVAEVLDKEGNVVWTSEVTEQVVKNYNNDLASTLGSTRFEKTRWDGKNKDGKVVAN 90- 0 NAKNLVAEVLDKEGNVVWTSEVTEQVVKNYNNDLASTLGSTRFEKTRWDGK+KDGKVVAN Sbjct: 841 NAKNLVAEVLDKEGNVVWTSEVTEQVVKNYNNDLASTLGSTRFEKTRWDGKDKDGKVVAN 90- 0 Query: 901 GTYTYRVRYTPISSGAKEQHTDFDVIVDNTTPEVATSATFSTEDSRLTLASKPKTSQPVY 96- 0 GTYTYRVRYTPISSGAKEQHTDFDVIVDNTTPEVATSATFSTED RLTLASKPKTSQPVY Sbjct: 901 GTYTYRVRYTPISSGAKEQHTDFDVIVDNTTPEVATSATFSTEDRRLTLASKPKTSQPVY 96- 0 Query: 961 RERIAYTYMDEDLPTTEYISPNEDGTFTLPEEAETMEGATVPLKMSDFTYVVEDMAGNIT 10- 20 RERIAYTYMDEDLPTTEYISPNEDGTFTLPEEAETMEGATVPLKMSDFTYVVEDMAGNIT Sbjct: 961 RERIAYTYMDEDLPTTEYISPNEDGTFTLPEEAETMEGATVPLKMSDFTYVVEDMAGNIT 10- 20 Query: 1021 YTPVTKLLEGHSNKPEQDGSDQAPDKKPEAKPEQDGSGQTPDKK 1064 YTPVTKLLEGHSNKPEQDGSDQAPDKKPE KPEQDGSGQ PDKK Sbjct: 1021 YTPVTKLLEGHSNKPEQDGSDQAPDKKPETKPEQDGSGQAPDKK 1064 A related GBS gene <SEQ ID 8941> and protein <SEQ ID 8942> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06019 Lipop Possible site: -1 Crend: 10 McG: Discrim Score: 5.69 GvH: Signal Score (-7.5): -3.33 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -0.37 threshold: 0.0 INTEGRAL Likelihood = -0.37 Transmembrane 7-23 (7-23) PERIPHERAL Likelihood = 2.81 508 modified ALOM score: 0.57 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 8942 (GBS276) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 46 (lane 2; MW 123 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 60 (lane 5; MW 46.5 kDa). The GBS276-His fusion product was purified (FIG. 206, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 296), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1966 A DNA sequence (GBSx2075) was identified in S. agalactiae <SEQ ID 6093> which encodes the amino acid sequence <SEQ ID 6094>. Analysis of this protein sequence reveals the following: TABLE-US-06020 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4286(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1967 A DNA sequence (GBSx2076) was identified in S. agalactiae <SEQ ID 6095> which encodes the amino acid sequence <SEQ ID 6096>. Analysis of this protein sequence reveals the following: TABLE-US-06021 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.15 Transmembrane 19-35 (11-39) ----- Final Results ----- bacterial membrane --- Certainty = 0.5458(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9911> which encodes amino acid sequence <SEQ ID 9912> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 6096 (GBS654) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 142 (lane 8 & 10; MW 51.2 kDa+lane 9; MW 27 kDa). Purified GBS654-GST is shown in FIG. 245, lane 11. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1968 A DNA sequence (GBSx2077) was identified in S. agalactiae <SEQ ID 6097> which encodes the amino acid sequence <SEQ ID 6098>. Analysis of this protein sequence reveals the following: TABLE-US-06022 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4174(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9913> which encodes amino acid sequence <SEQ ID 9914> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06023 >GP: AAF27324 GB: AF178424 unknown [Lactococcus lactis] Identities = 26/75 (34%), Positives = 45/75 (59%), Gaps = 4/75 (5%) Query: 11 MAFEPKNSELTKVLKES-LDEEKKEIFSSEMNIRDFERTKQYQFTLQPSVRKKIDRLSKE 69 - MAF+ + ++ VL S L + K E+ I E K Y FTL+PSV++ +++L+++ Sbjct: 1 MAFDVDDKKVKTVLSNSSLAKSKVEL---PKKIESEENKKSYSFTLEPSVKEGLEKLAEK 57 Query: 70 KGYRSASSFINDFFK 84 + Y++ S F+ND K Sbjct: 58 QNYKNTSQFLNDLIK 72 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1969 A DNA sequence (GBSx2078) was identified in S. agalactiae <SEQ ID 6099> which encodes the amino acid sequence <SEQ ID 6100>. This protein is predicted to be ParA. Analysis of this protein sequence reveals the following: TABLE-US-06024 Possible site: 45 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06025 >GP: AAF27325 GB: AF178424 ParA [Lactococcus lactis] Identities = 49/104 (47%), Positives = 72/104 (69%) Query: 22 LSERLEEFKTEAFDFKTRASYVTAKLFFLGNMIKHNTNSSKELIRSLKNDKSVLAMIPHK 81 - L ERL+ FK E D +TR +Y+TA +F+GN I+HNT SS+E + DK +AMIP K Sbjct: 157 LIERLQNFKDEVIDARTRETYITAIPYFVGNRIRHNTKSSREFSEKISQDKGTIAMIPEK 21- 6 Query: 82 ELFNRSTLDKKSLSYMMSDKELYSRDSKFFKEIDFTFRKITDKL 125 ELFNRSTLD L M DK++++ + F+++++F F +IT+K+ Sbjct: 217 ELFNRSTLDGVPLVEMEKDKDVFNSNKVFYEKLNFAFNEITNKI 260 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1970 A DNA sequence (GBSx2079) was identified in S. agalactiae <SEQ ID 6101> which encodes the amino acid sequence <SEQ ID 6102>. This protein is predicted to be transposase (orfA). Analysis of this protein sequence reveals the following: TABLE-US-06026 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2830(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1971 A DNA sequence (GBSx2080) was identified in S. agalactiae <SEQ ID 6103> which encodes the amino acid sequence <SEQ ID 6104>. This protein is predicted to be transposase (orfB). Analysis of this protein sequence reveals the following: TABLE-US-06027 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2618(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06028 >GP: CAB90834 GB: AJ250837 putative transposase [Streptococcus dysgalactiae] Identities = 242/259 (93%), Positives = 249/259 (95%) Query: 1 MCRWLNMPHSSYYYQAVESVSETEFEETIKRIFLDSESRYGSRKIKICLNNEGITLSRRR 60 MCRWLN+P SSYYY+AVE VSE E EE+IK IFL+S++RYGSRKIKICLNNEGITLSRRR Sbjct: 1 MCRWLNIPRSSYYYKAVEPVSEAELEESIKAIFLESKARYGSRKIKICLNNEGITLSRRR 60 Query: 61 IRRIMKRLNLVSVYQKATFKPHSRGKNEAPIPNHLDRQFKQERPLQALVTDLTYVRVGNR 120- IRRIMKRLNLVSVYQKATFKPHSRGKNEAPIPNHLDRQFK ERPLQALVTDLTYVRVGNR Sbjct: 61 IRRIMKRLNLVSVYQKATFKPHSRGKNEAPIPNHLDRQFKPERPLQALVTDLTYVRVGNR 120- Query: 121 WAYVCLIIDLYNREIIGLSLGWHKTAELVKQAIQSIPYALTKVKMFHSDRXKEFDNQLID 18- 0 WAYVCLIIDLYNREIIGLSLGWHKTAELVKQAIQSIPY LTKVKMFHSDR KEF+NQLID Sbjct: 121 WAYVCLIIDLYNREIIGLSLGWHKTAELVKQAIQSIPYPLTKVKMFHSDRGKEFNNQLID 18- 0 Query: 181 EILEAFGITRSLSQAGCPYDNAVAESTYRAFKIEFVYQETFQLLEELALKTKDYVHWWNY 24- 0 EILEAFGITRSLSQAGCPYDNAVAESTYRAFKIEFVYQETFQ LEELALKTK YVHWWNY Sbjct: 181 EILEAFGITRSLSQAGCPYDNAVAESTYRAFKIEFVYQETFQSLEELALKTKAYVHWWNY 24- 0 Query: 241 HRIHGSLNYQTPMTKRLIA 259 HRIHGSLNYQTPMTKRLIA Sbjct: 241 HRIHGSLNYQTPMTKRLIA 259 There is also homology to SEQ ID 32. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1972 A DNA sequence (GBSx2081) was identified in S. agalactiae <SEQ ID 6105> which encodes the amino acid sequence <SEQ ID 6106>. Analysis of this protein sequence reveals the following: TABLE-US-06029 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3325(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1973 A DNA sequence (GBSx2082) was identified in S. agalactiae <SEQ ID 6107> which encodes the amino acid sequence <SEQ ID 6108>. Analysis of this protein sequence reveals the following: TABLE-US-06030 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4442(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9917> which encodes amino acid sequence <SEQ ID 9918> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06031 >GP: AAD44095 GB: AF115103 orf359 gp [Streptococcus thermophilus bacteriophage Sfi21] Identities = 92/357 (25%), Positives = 162/357 (44%), Gaps = 33/357 (9%) Query: 45 RKNQYGKTFETMKEAYDELVRIKYEFANKVSLENYNMTFENYMNKIYLRAYKQK-VQSVT 103- RK + F T EA ++ + + V+++ ++T +Y K + YK+ V +T Sbjct: 24 RKPKTKGGFRTKSEAIKAAAEMELKLQDNVNVDE-DITLYDYF-KQWCEVYKKPTVSKIT 81 Query: 104 YKTALPHHKLFIQYFGLKPLKAITPRDCEAFRLHIIENYSENYAKNLWSRF----KACMG 15- 9 YK + + +FG K LK+IT + + ++ +Y++ +A++ RF KAC+ Sbjct: 82 YKAYINSQRKIELFFGDKKLKSITATEYQ----RVLNSYAKTHAQDTVERFNVHVKACIE 137- Query: 160 YAERLGYISNMPCKALD---NPRGKHPETPFWTYAEFQTFIKSFDLHDYEELQRFTAIWL 21- 6 A GYI CK +G+ ET F E++ I ++ + E + A+++ Sbjct: 138 MAVHEGYIKRNFCKFAKINAKNKGRDIETKFLEVEEYERLI--YETSKHPEYASYAALYI 19- 5 Query: 217 YYMTGVRVSEGLSLCWEDIDFDKKFLKVHTTLEKDENGNWYRKDQTKTPAGERLIELDDI 27- 6 TG+R +E L L +DI D L V+ T + N + TKT + R I LDD Sbjct: 196 IAKTGIRFAECLGLTVDDIKRDTGMLSVNKTWDYKNNTGFM---PTKTKSSIREIPLDDE 25- 2 Query: 277 TIEVLQVWRKNQFANQDTDFIISRFGDPFCKSTICRIIKRKAQQVGVPVITGKGLRHSHA 33- 6 I + +Q D I+ + T+ +I+ R+ + LRH++A Sbjct: 253 FINFI-----DQLPPTDDGRILPSLSNNAVNKTLRKIVGRE--------VRVHSLRHTYA 29- 9 Query: 337 SYLINVLKKDILYVARRMGHADKSTTLNTYSHWFNALDKTVSEEITQNIKSAGLDSI 393 SYLI D++ V++ +GH + + TL Y+H E+I Q G +++ Sbjct: 300 SYLI-AHDIDLISVSQVLGHENLNITLEVYAHQLQEQKSRNDEKIKQMWTECGRNAL 355 A related DNA sequence was identified in S. pyogenes <SEQ ID 6109> which encodes the amino acid sequence <SEQ ID 6110>. Analysis of this protein sequence reveals the following: TABLE-US-06032 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5549(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06033 Identities = 111/127 (87%), Positives = 119/127 (93%) Query: 242 LKVHTTLEKDENGNWYRKDQTKTPAGERLIELDDITIEVLQVWRKNQFANQDTDFIISRF 30- 1 LKVHTTLEKDENGNWYRKDQTKTPAGERLIELDD+TI VL+ WR+NQ N DTDFIISRF Sbjct: 1 LKVHTTLEKDENGNWYRKDQTKTPAGERLIELDDVTIVVLENWRRNQVVNTDTDFIISRF 60 Query: 302 GDPFCKSTICRIIKRKAQQVGVPVITGKGLRHSHASYLINVLKKDILYVARRMGHADKST 36- 1 G+PFCKSTICR+IK KAQ +GVPVITGKGLRHS+ASYLINVLKKDILYVA+ MGHADKST Sbjct: 61 GEPFCKSTICRVIKHKAQSIGVPVITGKGLRHSYASYLINVLKKDILYVAKCMGHADKST 120- Query: 362 TLNTYSH 368 TLNTYSH Sbjct: 121 TLNTYSH 127 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1974 A DNA sequence (GBSx2083) was identified in S. agalactiae <SEQ ID 6111> which encodes the amino acid sequence <SEQ ID 6112>. Analysis of this protein sequence reveals the following:

TABLE-US-06034 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3299(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1975 A DNA sequence (GBSx2084) was identified in S. agalactiae <SEQ ID 6113> which encodes the amino acid sequence <SEQ ID 6114>. This protein is predicted to be repressor protein-related protein. Analysis of this protein sequence reveals the following: TABLE-US-06035 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2721(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9919> which encodes amino acid sequence <SEQ ID 9920> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06036 >GP: AAC98432 GB: L29324 repressor protein [Streptococcus pneumoniae] Identities = 38/65 (58%), Positives = 52/65 (79%), Gaps = 1/65 (1%) Query: 2 MYRRLRDLREDNDFTQKYVAEK-LSFTHSAYSKIERGERILSADVIIKLSNLYNVSTDYL 60 M +R+RDLRED+D TQ+YVA+ L+ T SAYSK+E G R++S D +IKL++ YNVS DYL Sbjct: 1 MLKRIRDLREDDDLTQEYVAKTILNCTRSAYSKMESGTRLISIDDLIKLADFYNVSLDYL 60 Query: 61 LGQTD 65 +G+ D Sbjct: 61 VGRVD 65 There is also homology to SEQ ID 582. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1976 A DNA sequence (GBSx2085) was identified in S. agalactiae <SEQ ID 6115> which encodes the amino acid sequence <SEQ ID 6116>. This protein is predicted to be relaxase. Analysis of this protein sequence reveals the following: TABLE-US-06037 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3160(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06038 >GP:AAC98434 GB:L29324 relaxase [Streptococcus pneumoniae] Identities = 223/417 (53%), Positives = 310/417 (73%), Gaps = 5/417 (1%) Query: 1 MVITKHYAVHGKKYRRQLIKYILDPKKTRNLSLISDFGMSNYLDFPDYVELVRMYQNNFL 60 MVITKH+A+HGR YR +LIKYIL+P KT+NL+L+SDFGM NYLDFP Y ELVKMY +NFL Sbjct: 1 MVITKHFAIHGKNYRSKLIKYILNPSKTKNLTLVSDFGMRNYLDFPSYKELVKMYNDNFL 60 Query: 61 SNDQLYDSRFDRQEKKQQKIHAHHIIQSFSPEDKLSPEEINRIGYETIRELIGGQYKFIV 120- SND LY+ R DRQE Q+KIH+HHIIQSFSP+D L+PE+INRIGYE KEL GG+++FIV Sbjct: 61 SNDTLYEFRHDRQEVNQRRIHSHHIIQSFSPDDHLTPEQINRIGYEAARELTGGRFRFIV 120- Query: 121 ATHVDQDHCHNHIIINSINSQSQKKLLWDYALERNLQMISDRISKVAGAKIIPPKRYSHR 18- 0 ATHVD+ H HNHII+NSI+ S KK WDY E NL+M+SDR+SK+AGAKII RYSHR Sbjct: 121 ATHVDKGHIHNHIILNSIDQNSDKKFLWDYKAEHNLRMVSDRLSKIAGAKII-ENRYSHR 17- 9 Query: 181 DYEVYRRSNHKYELKQRLFFLMEHSIDFNDFMQKAEQLNVKIDFSRKHSRFFMTDRNMKQ 24- 0 YEVYR++N+KYE+KQR++FL+E+S +F D +KA+ L++KIDF KH +FMTD NMRQ Sbjct: 180 QYEVYRKTNYKYEIKQRVYFLIENSKNFEDLKKKAKALHLKIDFRHKHVTYFMTDSNMRQ 23- 9 Query: 241 VIQGDKLNKREPYSKEYFQRYFAKKKIELILEFLLLRSNSFDDLVEKARLLGLELRSKKK 30- 0 V++ KL++++PY++ YF++ F +++I ILEFLL + + ++L+++A + GL++ K+K Sbjct: 240 VVRDSKLSRKQPYNETYFEKKFVQREIINILEFLLPKMKNMNELIQRAEVFGLKIIPKEK 29- 9 Query: 301 TIDFVLSDGKSCISIPNKSLRKKNLYDTTYFDSYFKEHDVFEVLHNNEVKIEFEKFETQQ 36- 0 +F DG I + + L K NLY +YF YF + VL N + + + + + Sbjct: 300 HVLFEF-DG---IKLAEQELVRSNLYSVSYFQDYFNNKNETFVLDNKNLVELYNEEKIIK 35- 5 Query: 361 LSEILTVEEITEAYETYKTKRDAVHEFEVEITEEQIEKIVLDGLFVKVWMGIGQEGL 417 E+ + E + ++Y+ +K RDAVHEFEVE+ QIE++V G+++KV GI ++ L Sbjct: 356 EKELPSEEMVWKSYQDFKRNRDAVHEFEVELNLNQIEEVVEHGIYIRVQFGIDKKDL 412 A related DNA sequence was identified in S. pyogenes <SEQ ID 6117> which encodes the amino acid sequence <SEQ ID 6118>. Analysis of this protein sequence reveals the following: TABLE-US-06039 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3114(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06040 Identities = 103/218 (47%), Positives = 170/218 (77%) Query: 393 EEQIEKIVLDGLFVKVWMGIGQEGLIFIPNHQLNILEQENKKQYQVFIRETSSYFIYHKE 45- 2 E QIE+++ + +++KV + Q GLIFIPN+QL+I ++EN K+Y+V+IRET+ +FIY+KE Sbjct: 2 EHQIERLIAEDIYIKVSFSVKQSGLIFIPNYQLDIRKEENHKKYKVYIRETAQFFIYNKE 61 Query: 453 DSEMNRFMKGRDLIRQLTFDNKSLPYKRRISLVSLQQKIEEINLLMTLNIQNKSFLELKD 51- 2 SE+NR+M+G +LI QLT D+KS+P +RR ++ +L++KIEEI+LL+ L+ +NK + ++KD Sbjct: 62 ASELNRYMRGHELICQLTNDSKSIPKRRRQTIDTLKKKIEEISLLIELDTENKPYQDIKD 121- Query: 513 ELVGDIAQLDIELTNLQDKNTTLNKMAEVVVNLQSDNQDTKQLAKYECSKMNLSQNVTIG 57- 2 ++V D+AQLD+ +T LQD LNK+AEV++NL +++ + ++LA+Y+ +KMNL+ + I Sbjct: 122 DIVKDMAQLDLTITELQDHIAHLNKVAEVLLNLNNNDIENRRLARYDYAKMNLTAAIKIE 18- 1 Query: 573 QIESEIEMIQNQLDNKIEEYENAVRKLDEYVRVLNMDK 610 ++E EIE QN+L+ I+EYE VR+L+++ +L+ K Sbjct: 182 EVEKEIETSQNELNISIDEYEYLVRRLEKFGEILSDSK 219 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1977 A DNA sequence (GBSx2086) was identified in S. agalactiae <SEQ ID 6119> which encodes the amino acid sequence <SEQ ID 6120>. Analysis of this protein sequence reveals the following: TABLE-US-06041 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4006(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06042 >GP: AAC98436 GB: L29324 unknown [Streptococcus pneumoniae] Identities = 53/115 (46%), Positives = 77/115 (66%), Gaps = 2/115 (1%) Query: 5 VREIRKEVNFSIEEYQQIQNFMEQEGYEQFSPFARGKLLKIDHQPSQQLEEWIKYLQHQK 64 +R IRK+ + E +QI + M ++G + FS F R LL D Q +Q+E+W + QK Sbjct: 5 IRSIRKQFRLTETEEKQILDLMREKGDDNFSDFLRKSLLLSDGQ--KQMEKWFNLWKKQK 62 Query: 65 VEQIYRDVHEILVLAKLSQSVTMEHLEIILTCIKDLMKEIEVTIPLSYSFKDKYM 119 +EQI RDVHE+ ++AK + VT EH+ I+LTCI++L+KE+E T PLS F +KYM Sbjct: 63 LEQISRDVHEVFIIAKTNHQVTHEHVSILLTCIQELIKEVEKTGPLSEDFCNKYM 117 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1978 A DNA sequence (GBSx2087) was identified in S. agalactiae <SEQ ID 6121> which encodes the amino acid sequence <SEQ ID 6122>. This protein is predicted to be TnpA. Analysis of this protein sequence reveals the following: TABLE-US-06043 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2935(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06044 >GP: AAC82523 GB: AF027768 TnpA [Serratia marcescens] Identities = 176/413 (42%), Positives = 243/413 (58%), Gaps = 18/413 (4%) Query: 26 MMFKVEAVGPPERCPECGFD-KLYKHSSRNQLIMDLPIRLKRVGLHLNRRRYKCRECGST 84 - M F+V+ V P C ECG + + R+ DLPI KRV L + RRRY CR C +T Sbjct: 1 MHFQVD-VPDPIACEECGVQGEFVRFGKRDVPYRDLPIHGKRVTLWVVRRRYTCRACRTT 59 Query: 85 IS------VDEKRSMTKRLLKSIQEQSMSKTFVEVAESVGVDEKTIRNVFKDYVALKERE 138- VD R MT RL + ++++S + + VA G+DEKT+R++F R Sbjct: 60 FRPQLPEMVDGFR-MTLRLHEYVEKESFNHPYTFVAAQTGLDEKTVRDIFNARAEFLGRW 118- Query: 139 YQFETPKWLGIDEIHIIRRPRLVLTNIERRTIYDIKPNRNKETVIQRLSEISDRTYIEYV 19- 8 ++FETP+ LGIDE+++ +R R +LTNIE RT+ D+ R ++ V L ++ DR +E V Sbjct: 119 HRFETPRILGIDELYLNKRYRCILTNIEERTLLDLLATRRQDVVTNYLMKLKDRQKVEIV 17- 8 Query: 199 TMDMWKPYKDAVNTILPQAKVVVDKFHVVRMANQALDNVRKSLKAHMSQKERRTLMRERF 25- 8 +MDMW PY+ AV +LPQA++VVDKFHVVRMAN AL+ VRK L+ + + RTL +R Sbjct: 179 SMDMWNPYRAAVKAVLPQARIVVDKFHVVRMANDALERVRKGLRKELKPSQSRTLKGDRK 23- 8 Query: 259 ILLKRKHDLNERESFLLDTWLGNLPALKEAYELKEEFYWIWDTPDPDEGHLRYSQWRHRC 31- 8 ILLKR H++++RE +++TW G P L AYE KE FY IWD + +W Sbjct: 239 ILLKRAHEVSDRERLIMETWTGAFPQLLAAYEHKERFYGIWDATTRLQAEAALDEW-IAT 29- 7 Query: 319 MSSNSKDAYKDLVRAVDNWHVEIFNYF--DKRLTNAYTESINSIIRQVERMGRGYSFDAL 37- 6 + K+ + DLVRAV NW E YF D +TNAYTESIN + + R GRGYSF+ + Sbjct: 298 IPKGQKEVWSDLVRAVGNWREETMTYFETDMPVTNAYTESINRLAKDKNREGRGYSFEVM 35- 7 Query: 377 RAKILFNEKLHKKRKPRFNSSAFNKAMLYDTFNWYEVNDHDITDNLGVDFSTL 429 RA++L+ K HKK+ P S F K + Y + D N GVD ST+ Sbjct: 358 RARMLYTTK-HKKKAPTAKVSPFYKKTI-----GYGLPDFAEELNYGVDLSTI 404 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1979 A DNA sequence (GBSx2088) was identified in S. agalactiae <SEQ ID 6123> which encodes the amino acid sequence <SEQ ID 6124>. This protein is predicted to be mercuric reductase. Analysis of this protein sequence reveals the following: TABLE-US-06045 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2115(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06046 >GP: CAA70224 GB: Y09024 mercuric reductase [Bacillus cereus] Identities = 412/546 (75%), Positives = 484/546 (88%) Query: 1 MNKFKVNISGMTCTGCEKHVESALEKIGAKNIESSYRRGEAVFELPDDIEVESAIKAIDE 60 M K++V++ GMTCTGCE+HV ALE +GA IE +RRGEAVFELP+ + VE+A KAI + Sbjct: 1 MKKYRVDVQGMTCTGCEEHVAVALENMGATGIEVDFRRGEAVFELPNALGVETAKKAISD 60 Query: 61 ANYQAGEIEEVSSLENVALINEDNYDLLIIGSGAAAFSSAIKAIEYGAKVGMIERGTVGG 120- A YQ G+ EEV S E V L NE +YD +IIGSG AAFSSAI+A++YGAKV MIERGT+GG Sbjct: 61 AKYQPGKAEEVQSQEMVQLGNEGDYDYIIIGSGGAAFSSAIEAVKYGAKVAMIERGTIGG 120- Query: 121 TCVNIGCVPSKTLLRAGEINHLSKDNPFIGLQTSAGEVDLASLITQKDKLVSELRNQKYM 18- 0 TCVNIGCVPSKTLLBAGEINHL+K+NPF+GL TSAGEVDLA LI QK++LV+ELRN KY+ Sbjct: 121 TCVNIGCVPSKTLLRAGEINHLAKNNPFVGLHTSAGEVDLAPLIKQKNELVTELRNSKYV 18- 0 Query: 181 DLIDEYNFDLIKGEAKFVDASTVEVNGTKLSAKRFLIATGASPSLPQISGLEKMDYLTST 24- 0 DLID+Y F+LI+GEAKFVD TVEVNG +SAKRFLIATGASP+ P I GL ++DYLTST Sbjct: 181 DLIDDYGFELIEGEAKFVDEKTVEVNGAPISAKRFLIATGASPAKPNIPGLNEVDYLTST 24- 0 Query: 241 TLLELKKIPKRLTVIGSGYIGMELGQLFHHLGSEITLMQRSERLLKEYDPEISESVEKAL 30- 0 +LLELKK+PKRL VIGSGYIGMELGQLFH+LGSE+TL+QRSERLLKEYDPEISESVEK+L Sbjct: 241 SLLELKKVPKRLVVIGSGYIGMELGQLFHNLGSEVTLIQRSERLLKEYDPEISESVEKSL 30- 0 Query: 301 IEQGINLVKGATFERVEQSGEIKRVYVTVNGSREVIESDQLLVATGRKPNTDSLNLSAAG 36- 0 +EQGINLVKGAT+ER+EQ+G+IK+V+V VNG + +IE+DQLLVATGR PNT +LNL AAG Sbjct: 301 VEQGINLVKGATYERIEQNGDIKKVHVEVNGKKRIIEADQLLVATGRTPNTATLNLRAAG 36- 0 Query: 361 VETGKNNEILINDFGQTSNEKIYAAGDVTLGPQFVYVAAYEGGIITDNAIGGLNKIKDLS 42- 0 VE G EI+I+D+ +T+N +IYAAGDVTLGPQFVYVAAY+GG+ NAIGGLNKK++L Sbjct: 361 VEIGSRGEIIIDDYSRTTNTRIYAAGDVTLGPQFVYVAAYQGGVAAPNAIGGLNKKLNLE 42- 0 Query: 421 VVPAVTFTNPTVATVGLTEEQAKEKGYDVKTSVLPLDAVPRAIVNRETTGVFKLVADAET 48- 0 VVP VTFT P +ATVGLTE+QAKE GY+VKTSVLPLDAVPRA+VNRETTGVFKLVAD++T Sbjct: 421 VVPGVTFTAPAIATVGLTEQQAKENGYEVKTSVLPLDAVPRALVNRETTGVFKLVADSKT 48- 0 Query: 481 LKVLGVHIVSENAGDVIYAASLAVKFGLTIEDLTETLAPYLTMAEGLKLVALTFDKDISK 54- 0 +KVLG H+V+ENAGDVIYAA+LAVKFGLT++D+ ETLAPYLTMAEGLKL ALTFDKDISK Sbjct: 481 MKVLGAHVVAENAGDVIYAATLAVKFGLTVDDIRETLAPYLTMAEGLKLAALTFDKDISK 54- 0 Query: 541 LSCCAG 546 LSCCAG Sbjct: 541 LSCCAG 546 There is also homology to SEQ ID 1820. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1980 A DNA sequence (GBSx2089) was identified in S. agalactiae <SEQ ID 6125> which encodes the amino acid sequence <SEQ ID 6126>. This protein is predicted to be regulatory protein. Analysis of this protein sequence reveals the following: TABLE-US-06047 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4529(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06048 >GP: AAA83973 GB: AF138877 mercury resistance operon negative regulator MerR1 [Bacillus sp. RC607] Identities = 83/129 (64%), Positives = 104/129 (80%) Query: 1 MIYRISEFADKCGVNKETIRYYERKNLLQEPHRTEAGYRIYSYDDVKRVGFIKRIQEFGF 60 M +RI E ADKCGVNKETIRYYER L+ EP RTE GYR+YS V R+ FIKR+QE GF Sbjct: 1 MKFRIGELADKCGVNKETIRYYERLGLIPEPERTEKGYRMYSQQTVDRLHFIKRMQELGF 60 Query: 61 SLSEIYKLLGVVDKDEVRCQDMFEFVSKKQKEVQKQIEDLKRIETMLDDLKQRCPDEKKL 120- +L+EI KLLGVVD+DE +C+DM++F K +++Q++IEDLKRIE ML DLK+RCP+ K + Sbjct: 61 TLNEIDKLLGVVDRDEAKCRDMYDFTILKIEDIQRKIEDLKRIERMLMDLKERCPENKDI 120- Query: 121 HSCPIIETL 129 + CPIIETL Sbjct: 121 YECPIIETL 129 There is also homology to SEQ ID 1712. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1981 A DNA sequence (GBSx2090) was identified in S. agalactiae <SEQ ID 6127> which encodes the amino acid sequence <SEQ ID 6128>. Analysis of this protein sequence reveals the following: TABLE-US-06049 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.86 Transmembrane 80-96 (78-100) ----- Final Results ----- bacterial membrane --- Certainty = 0.4142(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8943> and protein <SEQ ID 8944> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06050 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -13.52 GvH: Signal Score (-7.5): -6.14 Possible site: 44 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -7.86 threshold: 0.0 INTEGRAL Likelihood = -7.86 Transmembrane 80-96 (78-100) PERIPHERAL Likelihood = 1.80 136 modified ALOM score: 2.07 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4142(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00138## SEQ ID 8944 (GBS415) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 79 (lane 3; MW 21.2 kDa). EXAMPLE 1982 A DNA sequence (GBSx2092) was identified in S. agalactiae <SEQ ID 6129> which encodes the amino acid sequence <SEQ ID 6130>. Analysis of this protein sequence reveals the following: TABLE-US-06051 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3402(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1983 A DNA sequence (GBSx2093) was identified in S. agalactiae <SEQ ID 6131> which encodes the amino acid sequence <SEQ ID 6132>. This protein is predicted to be ATPase. Analysis of this protein sequence reveals the following: TABLE-US-06052 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.08 Transmembrane 324-340 (317-343) INTEGRAL Likelihood = -5.73 Transmembrane 662-678 (660-690) INTEGRAL Likelihood = -5.41 Transmembrane 350-366 (346-378) INTEGRAL Likelihood = -3.40 Transmembrane 94-110 (93-110) INTEGRAL Likelihood = -2.87 Transmembrane 681-697 (680-699) INTEGRAL Likelihood = -1.38 Transmembrane 148-164 (148-164) ----- Final Results ----- bacterial membrane --- Certainty = 0.5034(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-06053 >GP: AAA22858 GB: M90750 cadmium-efflux ATPase [Bacillus firmus] Identities = 486/725 (67%), Positives = 584/725 (80%), Gaps = 18/725 (2%) Query: 1 MSRGKAKQSEKEMKAYRVQGFTCTNCAAIFENNVKELPGVQDAKVNFGASKVYVKGTTTI 60 MS KA SE+EMKAYRVQGFTC NCA FE NVK+L GV+DAKVNFGASK+ V G TI Sbjct: 1 MSDQKAITSEQEMKAYRVQGFTCANCAGKFEKNVKQLSGVEDAKVNFGASKIAVYGNATI 60 Query: 61 EELEKAGAFENLKIRDEKEQRVGGE-----------PFWKQKENIKVYISALLLVVSWFL 109- EELEKAGAFENLK+ EK R + PF+K K + +Y S LL+ + Sbjct: 61 EELEKAGAFSNLKVTPEKSARQASQEVKEDTKEDKVPFYK-KHSTLLYAS-LLITFGYLS 118- Query: 110 GEQYGEEHVLPTIGYAASILIGGYSLFIKGLKNLRRLNFDMNTLMTIAIIGAAIIGEWGE 16- 9 GEE+++ T+ + AS+ IGG SLF GL+NL R FDM TLMT+A+IG AIIGEW E Sbjct: 119 SYVNGEENIVTTLLFLASMFIGGLSLFKVGLQNLLRFEFDMKTLMTVAVIGGAIIGEWAE 17- 8 Query: 170 GATVVILFAISEALERYSMDKARQSIESLMDIAPKEALIRRGNEEMMIHVDEIQVGDIMI 22- 9 A VVILFAISEALER+SMD+ARQSI SLMDIAPKEAL++R +E+MIHVD+I VGDIMI Sbjct: 179 VAIVVILFAISEALERFSMDRARQSIRSLMDIAPKEALVKRNGQEIMIHVDDIAVGDIMI 23- 8 Query: 230 VKPGQKLAMDGIVVKGTSTLNQAAITGESVPVTKITNDEVFAGTLNEEGLLEVKVTKRVE 28- 9 VKPGQK+AMDG+VV G S +NQ AITGESVPV K ++EVFAGTLNEEGLLEV++TK VE Sbjct: 239 VKPGQKIAMDGVVVSGYSAVNQTAITGESVPVEKTVDNEVFAGTLNEEGLLEVEITKLVE 29- 8 Query: 290 DTTLSKIIHLVEEAQAERAPSQAFVDKFAKYYTPAIVILALLIAVVPPL-FGGDWSQWIY 34- 8 DTT+SKIIHLVEEAQ ERAPSQAFVDKFAKYYTP I+I+A L+A+VPPL F G W WIY Sbjct: 299 DTTISKIIHLVEEAQGERAPSQAFVDKFAKYYTPIIMIIATLVAIVPPLFFDGSWETWIY 35- 8 Query: 349 QGLAVLVVGCPCALVVSTPVAVVTAIGNAAKNGVLIKGGIHLEAAGHLKAIAFDKTGTLT 40- 8 QGLAVLVVGCPCALV+STP+++V+AIGNAAK GVL+KGG++LE G LKAIAFDKTGTLT Sbjct: 359 QGLAVLVVGCPCALVISTPISIVSAIGNAAKKGVLVKGGVYLEEMGALKAIAFDKTGTLT 41- 8 Query: 409 KGIPAVTD--IVTYGRNENELITITSAIEKGSQHPLASAIMRKAEENGLKFNEVTVEDFQ 46- 6 KG+PAVTD ++ NE EL++I +A+E SQHPLASAIM+KAEE + +++V VEDF Sbjct: 419 KGVPAVTDYNVLNKQINEKELLSIITALEYRSQHPLASAIMKKAEEENITYSDVQVEDFS 47- 8 Query: 467 SITGKGVKAKINNEMYYVGSQNLFEE-LHGSISSDKKEKIADMQTQGKTVMVLGTEKEIL 52- 5 SITGKG+K +N YY+GS LF+E L D ++ + +Q QGKT M++GTEKEIL Sbjct: 479 SITGKGIKGIVNGTTYYIGSPKLFKELLTNDFDKDLEQNVTTLQNQGRTAMIIGTEKEIL 53- 8 Query: 526 SFIAVADEMRESSKEVIGKLNNMGI-ETVMLTGDNQRTATAIGKQVGVSDIKADLLPEDK 58- 4 + IAVADE+RESSKE++ KL+ +GI +T+MLTGDN+ TA AIG QVGVSDI+A+L+P+DK Sbjct: 539 AVIAVADEVRESSKEILQKLHQLGIKKTIMLTGDNKGTANAIGGQVGVSDIEAELMPQDK 59- 8 Query: 585 LNFIKELREKHQSVGMVGDGVNDAPALAASTVGVAMGGAGTDTALETADIALMSDDLSKL 64- 4 L+FIK+LR ++ +V MVGDGVNDAPALAASTVG+AMGGAGTDTALETAD+ALM DDL KL Sbjct: 599 LDFIKQLRSEYGNVAMVGDGVNDAPALAASTVGIAMGGAGTDTALETADVALMGDDLRKL 65- 8 Query: 645 PYTIKLSRKALAIIKQNITFSLAIKLVALLLVMPGWLTLWIAIFADMGATLLVTLNSLRL 70- 4 P T+KLSRK L IIK NITF++AIK +A LLV+PGWLTLWIAI +DMGATLLV LN LRL Sbjct: 659 PSTVKLSRKTLNIIKANITFAIAIKFIASLLVIPGWLTLWIAILSDMGATLLVALNGLRL 71- 8 Query: 705 LKIKE 709 +++KE Sbjct: 719 MRVKE 723 There is also homology to SEQ ID 3506. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1984 A DNA sequence (GBSx2094) was identified in S. agalactiae <SEQ ID 6133> which encodes the amino acid sequence <SEQ ID 6134>. Analysis of this protein sequence reveals the following: TABLE-US-06054 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0779(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1985 A DNA sequence (GBSx2095) was identified in S. agalactiae <SEQ ID 6135> which encodes the amino acid sequence <SEQ ID 6136>. Analysis of this protein sequence reveals the following: TABLE-US-06055 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.92 Transmembrane 123-139 (115-145) INTEGRAL Likelihood = -6.74 Transmembrane 172-188 (167-190) INTEGRAL Likelihood = -1.81 Transmembrane 80-96 (80-96) ----- Final Results ----- bacterial membrane --- Certainty = 0.4567(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9923> which encodes amino acid sequence <SEQ ID 9924> was also identified. The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 4216. A related GBS gene <SEQ ID 8945> and protein <SEQ ID 8946> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06056 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -6.41 GvH: Signal Score (-7.5): -2.23 Possible site: 58 >>> Seems to have no N-terminal signal sequence ALOM program count: 3 value: -8.92 threshold: 0.0 INTEGRAL Likelihood = -8.92 Transmembrane 123-139 (115-145) INTEGRAL Likelihood = -6.74 Transmembrane 172-188 (167-190) INTEGRAL Likelihood = -1.81 Transmembrane 80-96 (80-96) PERIPHERAL Likelihood = -2.92 46 modified ALOM score: 2.28 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4567(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1986 A DNA sequence (GBSx2096) was identified in S. agalactiae <SEQ ID 6137> which encodes the amino acid sequence <SEQ ID 6138>. This protein is predicted to be histidine rich P type ATPase (HRA-1) (copB). Analysis of this protein sequence reveals the following: TABLE-US-06057 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.37 Transmembrane 318-334 (307-345) INTEGRAL Likelihood = -5.84 Transmembrane 347-363 (335-364) INTEGRAL Likelihood = -5.15 Transmembrane 88-104 (86-112) INTEGRAL Likelihood = -5.04 Transmembrane 651-667 (649-669) INTEGRAL Likelihood = -4.30 Transmembrane 156-172 (155-173) INTEGRAL Likelihood = -4.30 Transmembrane 669-685 (668-690) INTEGRAL Likelihood = -3.03 Transmembrane 62-78 (60-80) ----- Final Results ----- bacterial membrane --- Certainty = 0.6349(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06058 >GP: AAA62113 GB: U16658 histidine rich P type ATPase [Escherichia coli] Identities = 598/731 (81%), Positives = 651/731 (88%), Gaps = 36/731 (4%) Query: 1 MRNNKKHSSHSHHNHGDIDHSKHDHNEMEHSQMDHS------------------------ 36 MRNNK+HSSHSHHNHGD++HSKHDHNEMEHSQMDHS Sbjct: 1 MRNNKQHSSHSHHNHGDMEHSKHDHNEMEHSQMDHSAMGHCAMGGHAHHHHGDMDHSKHD 60 Query: 37 ------------NMDHSEMDHGAMGGHAHHHHGSFKEIFLKSLPLGIAILLITPMMDIQL 84 MD+SEMDHGAMGGHAHHHHGSFK+IFLKSLPLGIAILLITP+M IQL Sbjct: 61 HNEMKHSQMDHSKMDYSEMDHGAMGGHAHHHHGSFKDIFLKSLPLGIAILLITPLMGIQL 120- Query: 85 PFQIIFPYADVVAAVLATILYIFGGKPFYMGAKDEFNSKAPGMMSLITLGITVSYAYSVY 144- PFQIIFPYADVVAAVLATILYIFGGKPF MGAKDEFNSK PGMMSLITLGITVSYAYSVY Sbjct: 121 PFQIIFPYADVVAAVLATILYIFGGKPFLMGAKDEFNSKVPGMMSLITLGITVSYAYSVY 18- 0 Query: 145 AVAARYVTGEHVMDFFFEFTTLILIMLLGHWIEMKALGEAGDAQKALAELVPKDAHVVLE 20- 4 AVAARYVTGE VMDFFFEFTTLILIMLLGHWIEMKALGEAG+AQKALAELVPKDAHVVLE Sbjct: 181 AVAARYVTGEPVMDFFFEFTTLILIMLLGHWIEMKALGEAGNAQKALAELVPKDAHVVLE 24- 0 Query: 205 DDSIETRPVSELQIGDVIRVQAGENVPADGIIIRGESRVNEALVTGESKPIEKKTGDEVI 26- 4 DDSIETRPV++LQ+GD+IRVQAGENVPADG I RGESRVNEALVTGESKPIEK GDEVI Sbjct: 241 DDSIETRPVADLQVGDLIRVQAGENVPADGTIQRGESRVNEALVTGESKPIEKNPGDEVI 30- 0 Query: 265 GGSTNGGGVLYVEIKQTGDQSFISQVQTLISQAQSQPSRAENVAQKVASWLFYIAVVVAL 32- 4 GGSTNG GVLYVEIKQTGD+SFISQVQTLISQAQSQPSRAEN+AQKVA WLFYIAV+ AL Sbjct: 301 GGSTNGDGVLYVEIKQTGOKSFISQVQTLISQAQSQPSRAENLAQKVAGWLFYIAVIAAL 36- 0 Query: 325 IALLIWTIIADLPTAVIFTVTALVIACPHALGLAIPLVVSRSTSLGASRGLLVKNREALE 38- 4 IAL+IW +IAD+PTAVIFTVT LVIACPHALGLAIPLV +RSTSLGASRGLLVK+R+ALE Sbjct: 361 IALVIWMVIADVPTAVIFTVTTLVIACPHALGLAIPLVTARSTSLGASRGLLVKDRDALE 42- 0 Query: 385 LTTKADVMVLDKTGTLTTGEFKVLDVTVLSDKYSEEEITGLLAGIEAGSSHPIAQSIVNH 44- 4 LTT ADVMVLDKTGTLTTGEFKVLDV + +DKY+++EI LL+GIE GSSHPIAQSI+++ Sbjct: 421 LTTNADVMVLDKTGTLTTGEFKVLDVELFNDKYTKDEIVALLSGIEGGSSHPIAQSIISY 48- 0 Query: 445 AEAKGIKSVSFDSIEIVSGAGIEGEANGHHYQLISQKAYGKALRMDIPKGATLSILVENN 50- 4 AE +GI+ VSFDSI+++SGAG+EG+ANGH YQLISQKAYG+ L MDIPKGAT+S+LVEN+ Sbjct: 481 AEQQGIRPVSFDSIDVMSGAGVEGQANGHRYQLISQKAYGRNLDMDIPKGATISVLVEND 54- 0 Query: 505 EAIGAVALGDELKETSRNLIEVLKKYGIEPLMATGDNEEAAQGVAEVLGIQYQANQSPED 56- 4 EAIGAVALGDELK TS++LI+ LKK I+P+MATGDNE+AAQG AE+LGI Y ANQSP+D Sbjct: 541 EAIGAVALGDELKPTSKDLIQALKKNKIQPIMATGDNEKAAQGAAEILGIDYLANQSPQD 60- 0 Query: 565 KYKLVESMRNQNKTVIMVGDGVNDAPSLALADVGIAIGAGTQVALDSADIILTQSDPGDI 62- 4 KY+LVE +K + K VIMVGDGVNDAPSLALADVGIAIGAGTQVALDSADIILTQ PGDI Sbjct: 601 KYELVEKLKAEGKKVIMVGDGVNDAPSLALADVGIAIGAGTQVALDSADIILTQYSPGDI 66- 0 Query: 625 ESFIELANKTTRKMKQNLVWGAGYNFIAIPIAAGLLAPIGITLGPAFGAVLMSLSTVIVA 68- 4 SFIELA KTTRKMK+NLVWGAGYNFIAIPIAAG+LAPIGITL PA AVLMSLSTVIVA Sbjct: 661 ASFIELAQKTTRKMKENLVWGAGYNFIAIPIAAGILAPIGITLSPAVAAVLMSLSTVIVA 72- 0 Query: 685 INAMTLKLEPK 695 INAMTLKLEPK Sbjct: 721 INAMTLKLEPK 731 There is also homology to SEQ ID 3506. A related GBS gene <SEQ ID 8947> and protein <SEQ ID 8948> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06059 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: -19.12 GvH: Signal Score (-7.5): -3.71 Possible site: 27 >>> Seems to have no N-terminal signal sequence ALOM program count: 7 value: -13.37 threshold: 0.0 INTEGRAL Likelihood = 13.37 Transmembrane 291-307 (280-318) INTEGRAL Likelihood = -5.84 Transmembrane 320-336 (308-337) INTEGRAL Likelihood = -5.15 Transmembrane 61-77 (59-85) INTEGRAL Likelihood = -5.04 Transmembrane 624-640 (622-642) INTEGRAL Likelihood = -4.30 Transmembrane 129-145 (128-146) INTEGRAL Likelihood = -4.30 Transmembrane 642-658 (641-663) INTEGRAL Likelihood = -3.03 Transmembrane 35-51 (33-53) PERIPHERAL Likelihood = 0.74 103 modified ALOM score: 3.17 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6349(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00139## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1987 A DNA sequence (GBSx2097) was identified in S. agalactiae <SEQ ID 6139> which encodes the amino acid sequence <SEQ ID 6140>. This protein is predicted to be CopA. Analysis of this protein sequence reveals the following: TABLE-US-06060 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2197(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06061 >GP: CAA40599 GB: X57326 ORF-1 [Thiobacillus ferrooxidans] Identities = 26/65 (40%), Positives = 40/65 (61%), Gaps = 2/65 (3%) Query: 1 MKQEILL--DGVKCAGCANTVQERFSAIEGVESVEVDLATKKAVLESQTEIDTETLNAAL 58 M Q+I L G+ CA CA++V++ I G++S +V LAT +A + Q+ I TE L AA+ Sbjct: 1 MSQKIFLRITGMTCAHCAHSVEKALLGIHGIDSAQVSLATNQAEVFLQSSIPTEALLAAV 60 Query: 59 AETNY 63 + Y Sbjct: 61 TQAGY 65 There is also homology to SEQ ID 3510. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1988 A DNA sequence (GBSx2098) was identified in S. agalactiae <SEQ ID 6141> which encodes the amino acid sequence <SEQ ID 6142>. Analysis of this protein sequence reveals the following: TABLE-US-06062 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3220(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1989 A DNA sequence (GBSx2099) was identified in S. agalactiae <SEQ ID 6143> which encodes the amino acid sequence <SEQ ID 6144>. This protein is predicted to be heavy-metal transporting P-type ATPase (b0484). Analysis of this protein sequence reveals the following: TABLE-US-06063 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.09 Transmembrane 131-147 (130-150) ----- Final Results ----- bacterial membrane --- Certainty = 0.2635(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06064 >GP: AAB01764 GB: U42410 heavy-metal transporting P-type ATPase [Proteus mirabilis] Identities = 98/153 (64%), Positives = 123/153 (80%) Query: 2 KAVKALRRRGVEVIMITGDNKRTAKAIAKQVGIDSVLSEVLPEDKAEEVKKLQEAGKKVA 61 +A+KAL G++V MITGDNK TAKAIAKQ+GID +++EVLP+ K +K+L + G KVA Sbjct: 649 EAIKALHALGLKVAMITGDNKATAKAIAKQLGIDEIVAEVLPDGKVAALKQLSQKGDKVA 70- 8 Query: 62 MVGDGINDAPALAQANVGIAVGSGTDVAIESADIVLMRNDLTAVLTTIDLSHATLRNIKQ 121- VGDGINDAPALAQA+VG+A+G+GTDVAIE+AD+VLM DL V+ I LS AT+RNIKQ Sbjct: 709 FVGDGINDAPALAQADVGLAIGTGTDVAIEAADVVLMSGDLRGVVDAIALSQATIRNIKQ 76- 8 Query: 122 NLFWAFAYNLVGIPVAMGLLYIFGGLLMSPMLA 154 NLFW FAYN + IPVA G+LY G+L+SP+ A Sbjct: 769 NLFWTFAYNALLIPVAAGMLYPINGMLLSPIFA 801 A related DNA sequence was identified in S. pyogenes <SEQ ID 3505> which encodes the amino acid sequence <SEQ ID 3506>. Analysis of this protein sequence reveals the following: TABLE-US-06065 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.83 Transmembrane 328-344 (314-348) INTEGRAL Likelihood =-7.01 Transmembrane 354-370 (347-377) INTEGRAL Likelihood =-3.24 Transmembrane 101-117 (100-117) INTEGRAL Likelihood =-2.97 Transmembrane 165-181 (165-185) INTEGRAL Likelihood =-2.34 Transmembrane 665-681 (662-684) INTEGRAL Likelihood =-2.18 Transmembrane 67-83 (66-83) INTEGRAL Likelihood =-0.64 Transmembrane 491-507 (490-508) INTEGRAL Likelihood =-0.59 Transmembrane 691-707 (691-707) INTEGRAL Likelihood =-0.43 Transmembrane 140-156 (139-156) ----- Final Results ----- bacterial membrane --- Certainty = 0.5331(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06066 Identities = 92/152 (60%), Positives = 123/152 (80%) Query: 4 VKALRRRGVEVIMITGDNKRTAKAIAKQVGIDSVLSEVLPEDKAEEVKKLQEAGKKVAMV 63 V+AL + G+ IM+TGD+ TAKAIA QVGI V+S+VLP+ KA + L+ G+KVAMV Sbjct: 544 VEALHQLGIHTIMLTGDHDATAKAIASQVGITDVISQVLPDQKAGVIADLRSQGRKVAMV 60- 3 Query: 64 GDGINDAPALAQANVGIAVGSGTDVAIESADIVLMRNDLTAVLTTIDLSHATLRNIKQNL 123- GDGINDAPALA A++GIA+GSGTD+AIESAD++LM+ D+ ++ + LS T+R +K+NL Sbjct: 604 GDGINDAPALAVADIGIAMGSGTDIAIESADVILMKPDMLDLVKAMSLSRVTMRIVKENL 66- 3 Query: 124 FWAFAYNLVGIPVAMGLLYIFGGLLMSPMLAG 155 FWAF YN++ IPVAMGLL++FGG L++PMLAG Sbjct: 664 FWAFIYNVLMIPVAMGLLHLFGGPLLNPMLAG 695 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1990 A DNA sequence (GBSx2100) was identified in S. agalactiae <SEQ ID 6145> which encodes the amino acid sequence <SEQ ID 6146>. This protein is predicted to be CopY. Analysis of this protein sequence reveals the following: TABLE-US-06067 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2067(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-06068 >GP: AAG10085 GB: AF296446 CopY [Streptococcus mutans] Identities = 63/139 (45%), Positives = 96/139 (68%) Query: 8 TSITDAEWEVMRVVWANDLVTSKTVISVLKEKMDWTESTIKTILGRLVEKGVLNTEQEGR 67 TSI++AEWEVMRVVWA + +S +I++L W+ STIKT++ RL EKG L ++++GR Sbjct: 2 TSISNAEWEVMRVVWAKQMTSSSEIIAILSRTYCWSASTIKTLITRLSEKGYLTSQRQGR 61 Query: 68 KFIYTANIVEKEAVRDFAEDIFNRICKKKVGNVIGSIIEDHVLSFDDIDRLEKILEIKKS 127- K+IY++ I E+EA+ ++F+RIC K +I ++E+ ++ DI++LE +L KK+ Sbjct: 62 KYIYSSLISEEEALEQQVSEVFSRICVTKHQALIRHLVEETPMTLSDIEKLEALLLSKKA 121- Query: 128 FAVEEVDCQCTEGQCDCHE 146 AV EV C C GQC C+E Sbjct: 122 NAVPEVKCNCIVGQCSCYE 140 There is also homology to SEQ ID 3502. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1991 A DNA sequence (GBSx2101) was identified in S. agalactiae <SEQ ID 6147> which encodes the amino acid sequence <SEQ ID 6148>. Analysis of this protein sequence reveals the following: TABLE-US-06069 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2829(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1992 A DNA sequence (GBSx2102) was identified in S. agalactiae <SEQ ID 6149> which encodes the amino acid sequence <SEQ ID 6150>. This protein is predicted to be DS RF protein. Analysis of this protein sequence reveals the following: TABLE-US-06070 Possible site: 57 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -13.21 Transmembrane 142-158 (136-169) INTEGRAL Likelihood = -3.45 Transmembrane 70-86 (66-88) INTEGRAL Likelihood = -3.13 Transmembrane 178-194 (176-195) ----- Final Results ----- bacterial membrane --- Certainty = 0.6286(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06071 >GP: AAA26611 GB: L10909 putative [Staphylococcus aureus] Identities = 98/204 (48%), Positives = 148/204 (72%), Gaps = 3/204 (1%) Query: 4 TIISAIGVYISTSIDYLIVLIILFAQLSQNKQKWHIYAGQYLGTGLLVGASLVAAY-VVN 62 TI++A VY++T IDYL++LI+LF+Q+ + + K HI+ GQY+GT +++GASL+ A VVN Sbjct: 18 TILTATAVYVATGIDYLVILILLFSQVKKGQVK-HIWIGQYIGTAIVIGASLLVAQGVVN 76 Query: 63 FVPEAWMVGLLGLIPIYLGIRFAIVGEGEEEEEEEIIERLEQSKANQLFWTVTLLTIASG 122- +P+ W++GLLGL+P+YLG++ I GE E+E+E I+ K NQLF T+ + +AS Sbjct: 77 LIPQQWVIGLLGLLPLYLGVKIWIKGE-EDEDESSILSLFSSGKFNQLFLTMIFIVLASS 135- Query: 123 GDNLGIYIPYFASLDWSQTLVVLLVFAIGIIIFCELSWVLSSIPLISETIEKYQRIIVPL 18- 2 D+ IYIPYF +L S+ +V +VF I + + C +S+ L+S ISETIEKY+R IVP+ Sbjct: 136 ADDFSIYIPYFTTLSMSEIFIVTIVFLIMVGVLCYVSYRLASFDFISETIEKYERWIVPI 19- 5 Query: 183 VFIPLGLYIMYESGTIETFLNFIL 206 VFI LG+YI++E+GT ++F+L Sbjct: 196 VFIGLGIYILFENGTSNALISFLL 219 A related DNA sequence was identified in S. pyogenes <SEQ ID 6151> which encodes the amino acid sequence <SEQ ID 6152>. Analysis of this protein sequence reveals the following: TABLE-US-06072 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.16 Transmembrane 143-159 (135-165) INTEGRAL Likelihood = -9.13 Transmembrane 49-65 (43-71) INTEGRAL Likelihood = -7.17 Transmembrane 73-89 (72-94) INTEGRAL Likelihood = -6.00 Transmembrane 13-29 (9-33) INTEGRAL Likelihood = -2.71 Transmembrane 180-196 (179-197) INTEGRAL Likelihood = -0.59 Transmembrane 112-128 (109-128) ----- Final Results ----- bacterial membrane --- Certainty = 0.6265(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06073 >GP: AAF42284 GB: AE002544 cadmium resistance protein [Neisseria meningitidis MC58] Identities = 201/208 (96%), Positives = 205/208 (97%) Query: 1 MRCFMIQNVVTSIILYSGTAVDLLIILMLFFAKRKSRKDIINIYLGQFLGSVSLILLSLL 60 MRCFMIQNVVTSIILYSGTAVDLLIILMLFFAKRKSRKDIINIYLGQFLGSVSLILLSLL Sbjct: 1 MRCFMIQNVVTSIILYSGTAVDLLIILMLFFAKRKSRKDIINIYLGQFLGSVSLILLSLL 60 Query: 61 FAFVLDYIPSKEILGLLGLIPIFLGLKVLLLGDSDGEAIAKEGLSKDNKNLIFLVAMITF 120- FAFVLDYIPSKEILGLLGLIPI LG+KVLLLGDSDGEAIAKEGL KDNKNLIFLVAMITF Sbjct: 61 FAFVLDYIPSKEILGLLGLIPILLGIKVLLLGDSDGEAIAKEGLRKDNKNLIFLVAMITF 120- Query: 121 ASCGADNIGVFVPYFTTLNLANLIVALLTFLVMIYLLVFSAQKLAQVPSVGETLEKYSRW 18- 0 ASCGADNIGVFVPYFTTLNLANLIVALLTFLVMIYLLVFSAQKLAQVPSVGETLEKYSRW Sbjct: 121 ASCGADNIGVFVPYFTTLNLANLIVALLTFLVMIYLLVFSAQKLAQVPSVGETLEKYSRW 18- 0 Query: 181 FIAVVYLGLGMYILIENNSFDMLWAVLG 208 F+AVVYLGLG+YIL+ENNSFDMLW VLG Sbjct: 181 FVAVVYLGLGIYILVENNSFDMLWTVLG 208 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06074 Identities = 71/200 (35%), Positives = 130/200 (64%), Gaps = 4/200 (2%) Query: 1 MGQTIISAIGVYISTSIDYLIVLIILFAQLSQNKQKWHIYAGQYLGTGLLVGASLVAAYV 60 M Q ++++I +Y T++D LI+L++ FA+ K +IY GQ+LG+ L+ SL+ A+V Sbjct: 5 MIQNVVTSIILYSGTAVDLLIILMLFFAKRKSRKDIINIYLGQFLGSVSLILLSLLFAFV 64 Query: 61 VNFVPEAWMVGLLGLIPIYLGIRFAIVGEGEEEEEEEIIERLEQSKANQLFWTVTLLTIA 120- ++++P ++GLLGLIPI+LG++ ++G+ + E + E L + N +F V ++T A Sbjct: 65 LDYIPSKEILGLLGLIPIFLGLKVLLLGDSDGEAIAK--EGLSKDNKNLIF-LVAMITFA 121- Query: 121 S-GGDNLGIYIPYFASLDWSQTLVVLLVFAIGIIIFCELSWVLSSIPLISETIEKYQRII 17- 9 S G DN+G+++PYF +L+ + +V LL F + I + + L+ +P + ET+EKY R Sbjct: 122 SCGADNIGVFVPYFTTLNLANLIVALLTFLVMIYLLVFSAQKLAQVPSVGETLEKYSRWF 18- 1 Query: 180 VPLVFIPLGLYIMYESGTIE 199 + +V++ LG+YI+ E+ + + Sbjct: 182 IAVVYLGLGMYILIENNSFD 201 SEQ ID 6150 (GBS174) was expressed in and purified from E. coli. The purified protein is shown in lane 7 of FIG. 223. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 1993 A DNA sequence (GBSx2103) was identified in S. agalactiae <SEQ ID 6153> which encodes the amino acid sequence <SEQ ID 6154>. This protein is predicted to be Pgm. Analysis of this protein sequence reveals the following: TABLE-US-06075 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4324(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06076 >GP: CAB96418 GB: AJ243290 phosphoglucomutase [Streptococcus thermophilus] Identities = 65/76 (85%), Positives = 71/76 (92%) Query: 1 MTYTENLQKWLDFEQLPDYLRQELLSMDEKTKEDAFYTNLEFGTAGMRGYIGAGTNRINI 60 M+YTEN QKWLDF +LP YLR EL+SMDEKTKEDAFYTNLEFGTAGMRG IGAGTNRINI Sbjct: 1 MSYTENYQKWLDFAELPAYLRDELVSMDEKTKEDAFYTNLEFGTAGMRGLIGAGTNRINI 60 Query: 61 YVVRQATEGLAKLIET 76 YVVRQATEGLA+LI++ Sbjct: 61 YVVRQATEGLAQLIDS 76 A related DNA sequence was identified in S. pyogenes <SEQ ID 6155> which encodes the amino acid sequence <SEQ ID 6156>. Analysis of this protein sequence reveals the following: TABLE-US-06077 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial Cytoplasm --- Certainty = 0.4324(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06078 Identities = 75/76 (98%), Positives = 75/76 (98%) Query: 1 MTYTENLQKWLDFEQLPDYLRQELLSMDEKTKEDAFYTNLEFGTAGMRGYIGAGTNRINI 60 MTYTEN QKWLDFEQLPDYLRQELLSMDEKTKEDAFYTNLEFGTAGMRGYIGAGTNRINI Sbjct: 1 MTYTENFQKWLDFEQLPDYLRQELLSMDEKTKEDAFYTNLEFGTAGMRGYIGAGTNRINI 60 Query: 61 YVVRQATEGLAKLIET 76 YVVRQATEGLAKLIET Sbjct: 61 YVVRQATEGLAKLIET 76 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1994 A DNA sequence (GBSx2104) was identified in S. agalactiae <SEQ ID 6157> which encodes the amino acid sequence <SEQ ID 6158>. This protein is predicted to be a membrane protein. Analysis of this protein sequence reveals the following: TABLE-US-06079 Possible site: 53 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.21 Transmembrane 94-110 ( 93-115) INTEGRAL Likelihood = -4.14 Transmembrane 172-188 ( 166-188) INTEGRAL Likelihood = -1.97 Transmembrane 130-146 ( 129-149) INTEGRAL Likelihood = -0.16 Transmembrane 62-78 ( 62-79) ----- Final Results ----- bacterial membrane --- Certainty = 0.3484(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06080 >GP:CAA80247 GB:Z22520 membrane protein [Bacillus acidopullulyticus] Identities = 47/185 (25%), Positives = 80/185 (42%), Gaps = 23/185 (12%) Query: 1 MKKKNKSSNIAIIAIFFAIMLVIHFLSSFIFSFWLVPIKPTLMHIPVIIASIAYGPRIGA 60 MKK +I I + A+ +++ T+MHIP II I GP +G Sbjct: 1 MKKSLTVRDIVIAGVLGAVAILLGVTRLGYIPVPTAAGNATIMHIPAIIGGIMQGPVVGL 60 Query: 61 TLGALMGGISVANSSIVLLPTSYLFSPFVENGNFYSLIIALVPRILIGIIPYFVYKLLHN 120- +GA+ G S N+++ L F +++++PR+ IG++ +VY + Sbjct: 61 IVGAIFGISSFLNATVPL---------------FKDPLVSILPRLFIGVVAWLVYIGIRR 105- Query: 121 R---FGLAISGAIGSLTNTVFVLSGIFIFFSSTYNGNIKLMLAGIISSNSLAEMVIAAII 17- 7 + + +S IG+LTNT VL+ F + +A +N L E V+ I+ Sbjct: 106 KSEYVAVGLSAFIGTLTNTALVLA--MAVFRHYLTAGVAWTVA---ITNGLPEAVVGTIV 16- 0 Query: 178 VYLTV 182 V Sbjct: 161 TLAVV 165 A related DNA sequence was identified in S. pyogenes <SEQ ID 6159> which encodes the amino acid sequence <SEQ ID 6160>. Analysis of this protein sequence reveals the following: TABLE-US-06081 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.97 Transmembrane 18-34 ( 10-41) INTEGRAL Likelihood = -7.43 Transmembrane 170-186 ( 160-191) INTEGRAL Likelihood = -5.63 Transmembrane 96-112 ( 94-117) INTEGRAL Likelihood = -4.67 Transmembrane 140-156 ( 131-158) INTEGRAL Likelihood = -3.66 Transmembrane 64-80 ( 63-84) INTEGRAL Likelihood = -0.22 Transmembrane 39-55 ( 39-55) ----- Final Results ----- bacterial membrane --- Certainty = 0.4588(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06082 >GP:0AA80247 GB:Z22520 membrane protein [Bacillus acidopullulyticus] Identities = 47/193 (24%), Positives = 86/193 (44%), Gaps = 28/193 (14%) Query: 8 RKSADISRIAIFFAIMLVIHFVSSLVFNIWPIPI---KPTLVHIPVIIASVLYGPRIGAI 64 +KS + I I + V + P+P T++HIP II ++ GP +G I Sbjct: 2 KKSLTVRDIVIAGVLGAVAILLGVTRLGYIPVPTAAGNATIMHIPAIIGGIMQGPVVGLI 61 Query: 65 LGGLMGIISVITNTIILLPTNYLFSPFVDHGTFASLIIAIIPRILIGITPYYCYKLIPNQ 124- +G + GI S + T+ L F +++I+PR+ IG+ + Y I + Sbjct: 62 VGAIFGISSFLNATVPL---------------FKDPLVSILPRLFIGVVAWLVYIGIRRK 106- Query: 125 FGLIVSGI---IGSLTNTIFVLS-GIFIFFATVFDGNIKALLTAIISSNAIVEMIISAII 18- 0 + G+ IG+LTNT VL+ +F + T + + +N + E ++ I+ Sbjct: 107 SEYVAVGLSAFIGTLTNTALVLAMAVFRHYLTA------GVAWTVAITNGLPEAVVGTIV 16- 0 Query: 181 TFVLIPTLSRLKR 193 T ++ ++ R Sbjct: 161 TLAVVLAWKQIGR 173 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06083 Identities = 121/184 (65%), Positives = 157/184 (84%) Query: 6 KSSNIAIIAIFFAIMLVIHFLSSFIFSFWLVPIKPTLMHIPVIIASIAYGPRIGATLGAL 65 KS++I+ IAIFFAIMLVIHF+SS +F+ W +PIKPTL+HIPVIIAS+ YGPRIGA LG L Sbjct: 9 KSADISRIAIFFAIMLVIHFVSSLVFNIWPIPIKPTLVHIPVIIASVLYGPRIGAILGGL 68 Query: 66 MGGISVANSSIVLLPTSYLFSPFVENGNFYSLIIALVPRILIGIIPYFVYKLLHNRFGLA 125- MG ISV ++I+LLPT+YLFSPFV++G F SLIIA++PRILIGI PY+ YKL+ N+FGL Sbjct: 69 MGIISVITNTIILLPTNYLFSPFVDHGTFASLIIAIIPRILIGITPYYCYKLIPNQFGLI 128- Query: 126 ISGAIGSLTNTVFVLSGIFIFFSSTYNGNIKLMLAGIISSNSLAEMVIAAIIVYLTVPRI 18- 5 +SG IGSLTNT+FVLSGIFIFF++ ++GNIK +L IISSN++ EM+I+AII ++ +P + Sbjct: 129 VSGIIGSLTNTIFVLSGIFIFFATVFDGNIKALLTAIISSNAIVEMIISAIITFVLIPTL 18- 8 Query: 186 LNIK 189 +K Sbjct: 189 SRLK 192 A related GBS gene <SEQ ID 8949> and protein <SEQ ID 8950> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06084 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: 13.42 GvH: Signal Score (-7.5): -1.93 Possible site: 53 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 2 value: -6.21 threshold: 0.0 INTEGRAL Likelihood = -6.21 Transmembrane 94-110 ( 93-115) INTEGRAL Likelihood = -0.16 Transmembrane 62-78 ( 62-79) PERIPHERAL Likelihood = 1.70 123 modified ALOM score: 1.74 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3484(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00140## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1995 A DNA sequence (GBSx2105) was identified in S. agalactiae <SEQ ID 6161> which encodes the amino acid sequence <SEQ ID 6162>. Analysis of this protein sequence reveals the following: TABLE-US-06085 Possible site: 18 >>> Seems to have no Nterminal signal sequence (or aa 1-18) ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0165(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06086 >GP:AAC44502 GB:E148885 DNA/pantothenate metabolism flavoprotein [i Streptococcus mutans] Identities = 101/145 (69%), Positives = 122/145 (83%) Query: 1 MIKRITLAVTGSISAYKAADLTSQLTKIGYDVHIIMTQAATEFITPLTLQVLSKNPIHLD 60 M K+I LAV+GSI+AYKAADL+ QLTK+GY V++ MT AA +FI PLTLQVLSKNP++ + Sbjct: 1 MTKKILLAVSGSIAAYKAADLSHQLTKLGYHVNVFMTNAAKQFIPPLTLQVLSKNPVYSN 60 Query: 61 VMDEHNPKIINHIELAKRTDLFIVAPASANTIAHLAYGFADNIVTSVALANPDETPKLIA 120- VM E +P++INNI LAK+ DLF++ PASANT+AHLA+GFADNIVTSVALA+P E PK A Sbjct: 61 VMKEDDPQVINHIALAKQADLFLLPPASANTLAHLAHGFADNIVTSVALALPLEVPKFFA 120- Query: 121 PAMNTKMYHNTITQRNIDILKKIGY 145 PANNTKMY N ITQ NI +LKK GY Sbjct: 121 PANNTKNYENPITQSNITLLKKWGY 145 A related DNA sequence was identified in S. pyogenes <SEQ ID 6163> which encodes the amino acid sequence <SEQ ID 6164>. Analysis of this protein sequence reveals the following: TABLE-US-06087 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0076(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06088 Identities = 146/178 (82%), Positives = 155/178 (87%) Query: 1 MIKRITLAVTGSISAYKAADLTSQLTKIGYDVHIIMTQAATEFITPLTLQVLSKNPIHLD 60 M K ITLAV+GSISAYKAADLTSQLTKIGYDVHIIMTQAAT+FITPLTLQVLSKN IHLD Sbjct: 1 MTKHITLAVSGSISAYKAADLTSQLTKIGYDVHIIMTQAATQFITPLTLQVLSKNAIHLD 60 Query: 61 VMDEHNPKIINHIELAKRTDLFIVAPASANTIAHLAYGFADNIVTSVALAMPDETPKLIA 120- VMDEH+PK+INHIELAKRTDLFIVAPASANTIAHLAYGFADN+VTSVALA+P TPKLIA Sbjct: 61 VMDEHDPKVINHIELAKRTDLFIVAPASANTIAHLAYGFADNLVTSVALALPATTPKLIA 120- Query: 121 PAMNTKMYHNTITQRNIDILKKIGYQEIEPRISLLACGDTGQGALADISTILKCIQEV 178 PAMNTKMY N ITQ NI L IG+ EI P+ SLLACGD G GALADI IL I + Sbjct: 121 PAMNTKMYQNPITQENIKRLSTIGFTEIPPKSSLLACGDKGPGALADIDVILATIDTI 178 SEQ ID 6162 (GBS236) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 52 (lane 5; MW 21.6 kDa). Purified GBS236-GST is shown in FIG. 208 (lane 6) and in FIG. 225 (lanes 4-5). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1996 A DNA sequence (GBSx2106) was identified in S. agalactiae <SEQ ID 6165> which encodes the amino acid sequence <SEQ ID 6166>. This protein is predicted to be pantothenate metabolism flavoprotein homolog (dfp). Analysis of this protein sequence reveals the following: TABLE-US-06089 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2325(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9835> which encodes amino acid sequence <SEQ ID 9836> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-06090 >GP: AAG39941 GB: AF301375 MTW1216 [Methanothermobacter wolfeii prophage psiM100] Identities = 71/229 (31%), Positives = 117/229 (51%), Gaps = 27/229 (11%) Query: 6 MKILITSGGTTEKIDTVRSITNHATGTLGKIIAEKYLREGHQVTLVTTKNAVKPESATNL 65 +++L++ GGT E ID VR ITN ++G +G +A + +G VTLV V + + L Sbjct: 172 LRVLVSLGGTLEPIDPVRVITNRSSGRMGLAVAREAYIQGADVTLVA--GTVSVDIPSQL 22- 9 Query: 66 STFEIEDVDSLIKTLKPLVKEHDILIHSMAVSDYTPVYMADFEKVKSSDHLDTFLRKDNH 125- T E + + + L+ EHD+ + + AVSD+ PVY Sbjct: 230 RTVRAETAHEMAEAVAELIGEHDVFVSAAAVSDFRPVYS--------------------- 26- 8 Query: 126 EGKISSESEYQVLFLKKTPKVISLVKKWNPQITLVGFKLLVNVTKENLFKVARHSLIKNK 18- 5 E KISS+SE L LK PK+I + ++ NP+ +VGFK V++E L AR + + Sbjct: 269 EEKISSDSEI-TLRLKPNPKIIRMARETNPEAFIVGFKAEHGVSEEELIAAARKQIEDSV 32- 7 Query: 186 ATFILANDL-IDITSKHHIAYLLDHDNVYKATT--KEDIAQLIYEKVKK 231 A ++AND+ ++ + ++ + V + T KE++A LI ++ K Sbjct: 328 ADMVVANDVSVEGFGSENNRAIIVSEGVTELPTMKKEELAGLIIGEIMK 376 A related DNA sequence was identified in S. pyogenes <SEQ ID 6167> which encodes the amino acid sequence <SEQ ID 6168>. Analysis of this protein sequence reveals the following: TABLE-US-06091 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1737(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06092 Identities = 142/230 (61%), Positives = 170/230 (73%) Query: 4 MAMKILITSGGTTEKIDTVRSITNHATGTLGKIIAEKYLREGHQVTLVTTKNAVKPESAT 63 M MK++ITSGGTTE ID VR ITNH+TG LGK+I E++L+ H VTLVTTK A KP Sbjct: 1 MTMKLIITSGGTTEPIDAVRGITNHSTGQLGKLITERFLQYHHDVTLVTTKTATKPLPNK 60 Query: 64 NLSTFEIEDVDSLIKTLKPLVKEHDILIHSMAVSDYTPVYMADFEKVKSSDHLDTFLRKD 123- L E+E V+ L+ LK V HDILIHSMAVSDYTPVYM D E+V +D+L+ FL + Sbjct: 61 RLRIIEVETVNDLMAALKDQVPHHDILIHSMAVSDYTPVYMTDLEQVSQADNLNCFLCEH 120- Query: 124 NHEGKISSESEYQVLFLKKTPKVISLVKKWNPQITLVGFKLLVNVTKENLFKVARHSLIK 18- 3 N E KISS S+YQVLFLKKTPKVIS VK+WNP I LVGFKLLVNV +E L KVAR SL K Sbjct: 121 NSEPKISSASDYQVLFLKKTPKVISYVKQWNPNIKLVGFKLLVNVPQEELIKVARASLAK 18- 0 Query: 184 NKATFILANDLIDITSKHHIAYLLDHDNVYKATTKEDIAQLIYEKVKKYD 233 N A +ILANDL+DI + H A L+ ++ V A TKE IA L+YE++ K+D Sbjct: 181 NHADYILANDLVDIQTGMHKALLISNNEVASADTKEAIADLLYERMTKHD 230 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1997 A DNA sequence (GBSx2107) was identified in S. agalactiae <SEQ ID 6169> which encodes the amino acid sequence <SEQ ID 6170>. Analysis of this protein sequence reveals the following: TABLE-US-06093 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.22 Transmembrane 117-133 (117-133) ----- Final Results ----- bacterial membrane --- Certainty = 0.1086(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9833> which encodes amino acid sequence <SEQ ID 9834> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06094 >GP: BAB07541 GB: AP001520 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 94/221 (42%), Positives = 133/221 (59%), Gaps = 2/221 (0%) Query: 52 AEKPFIWTEVFLREINRSNQEIILHIWPMTKTVILGMLDRELPHLELAKKEIISRGYEPV 111- A + F + + I +S L W TV+LG+ D LP ++ + + ++ + Sbjct: 27 ALQSFAYDDTLCTSIGKSQSPPTLRAWVHHNTVVLGIQDSRLPQIKAGIEALKGFQHDVI 86 Query: 112 VRNFGGLAVVADEGILNFSLVIPDVFERKLSISDGYLIMVDFIRSIFSDFYQPIEHFEVE 17- 1 VRN GGLAVV D GILN SLV+ + E+ SI DGY +M + I S+F D + IE E+ Sbjct: 87 VRNSGGLAVVLDSGILNLSLVLKE--EKGFSIDDGYELMYELICSMFQDHREQIEAREIV 144- Query: 172 TSYCPGKFDLSINGKKFAGLAQRRIKNGIAVSIYLSVCGDQKGRSQMISDFYKIGLGDTG 23- 1 SYCPG +DLSI+GKKFAG++QRRI+ G+AV IYL V G R++MI FY + Sbjct: 145 GSYCPGSYDLSIDGKKFAGISQRRIRGGVAVQIYLCVSGSGAERAKMIRTFYDKAVAGQP 20- 4 Query: 232 SPIAYPNVDPEIMANLSDLLDCPMTVEDVIDRMLISLKQVG 272 + YP + PE MA+LS+LL P V DV+ + L++L+Q G Sbjct: 205 TKFVYPRIKPETMASLSELLGQPHNVSDVLLKALMTLQQHG 245 A related DNA sequence was identified in S. pyogenes <SEQ ID 6171> which encodes the amino acid sequence <SEQ ID 6172>. Analysis of this protein sequence reveals the following: TABLE-US-06095 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.22 Transmembrane 95-111 (95-111) ----- Final Results ----- bacterial membrane --- Certainty = 0.1086(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06096 >GP: BAB07541 GB: AP001520 unknown conserved protein in B. subtilis [Bacillus halodurans] Identities = 97/228 (42%), Positives = 138/228 (59%), Gaps = 2/228 (0%) Query: 30 ALSPFVWTEVFLKTINQEPNQLILHIWPMTRTVILGMLDRQLPYFELAKTEIGNNGYVPV 89 - AL F + + +I + + L W TV+LG+ D +LP + + + + Sbjct: 27 ALQSFAYDDTLCTSIGKSQSPPTLRAWVHHNTVVLGIQDSRLPQIKAGIEALKGFQHDVI 86 Query: 90 TRNIGGLAVVADDGILNFSLVIPDHFSESISISNAYLIMVDVIRESFSDYYQRIEYHEIK 149- RN GGLAVV D GILN SLV+ + + SI + Y +M ++I F D+ ++IE EI Sbjct: 87 VRNSGGLAVVLDSGILNLSLVLKEE--KGFSIDDGYELMYELICSMFQDHREQIEAREIV 144- Query: 150 NSYCPGNFDLSIAGRKFAGIAQRRIKKGIVVSIYLSVCGDQAARGQLIKDFYEAGTQGEV 20- 9 SYCPG++DLSI G+KFAGI+QRRI+ G+ V IYL V G A R ++I+ FY+ G+ Sbjct: 145 GSYCPGSYDLSIDGKKFAGISQRRIRGGVAVQIYLCVSGSGAERAKMIRTFYDKAVAGQP 20- 4 Query: 210 TKVNYPQIDPECMATLSELLETPFTVAEVLERLRLTLRQLGFSLTEKS 257 TK YP+I PE MA+LSELL P V++VL + +TL+Q G SL +S Sbjct: 205 TKFVYPRIKPETMASLSELLGQPHNVSDVLLKALMTLQQHGASLLTES 252 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06097 Identities = 155/275 (56%), Positives = 199/275 (72%), Gaps = 8/275 (2%) Query: 32 QDLAQLPVSIFKDYVTDAQDAEKPFIWTEVFLREINRSNQEIILHIWPMTKTVILGMLDR 91 - +DLA LP+ ++ D A PF+WTEVFL+ IN+ ++ILHIWPNT+TVILGMLDR Sbjct: 10 RDLASLPIFVYGDGNKKVPGALSPFVWTEVFLKTINQEPNQLILHIWPMTRTVILGMLDR 69 Query: 92 ELPHLELAKKEIISRGYEPVVRNFGGLAVVADEGILNFSLVIPDVFERKLSISDGYLIMV 151- +LP+ ELAK EI + GY PV RN GGLAVVAD+GILNFSLVIPD F +SIS+ YLIMV Sbjct: 70 QLPYFELAKTEIGNNGYVPVTRNIGGLAVVADDGILNFSLVIPDHFSESISISNAYLIMV 129- Query: 152 DFIRSIFSDFYQPIEHFEVETSYCPGKFDLSINGKKFAGLAQRRIKNGIAVSIYLSVCGD 21- 1 D IR FSD+YQ IE+ E++ SYCPG FDLSI G+KFAG+AQRRIK GI VSIYLSVCGD Sbjct: 130 DVIRESFSDYYQRIEYHEIKNSYCPGNFDLSIAGRKFAGIAQRRIKKGIVVSIYLSVCGD 18- 9 Query: 212 QKGRSQMISDFYKIGLGDTGSPIAYPNVDPEIMANLSDLLDGPMTVEDVIDRMLISLKQV 27- 1 Q R Q+I DFY+ G + + YP +DPE MA LS+LL+ P TV +V++R+ ++L+Q+ Sbjct: 190 QAARGQLIKDFYSAGTQGEVTKVNYPQIDPECMATLSELLETPFTVAEVLERLRLTLRQL 24- 9 Query: 272 GFN------DRLLNIRPDLVAEFNRFQAKSMANKG 300 GF+ D+ L+ D V + R Q + + +G Sbjct: 250 GFSLTEKSPDQALLTNFDAV--YERMQLEVVRKEG 282 A related GBS gene <SEQ ID 8951> and protein <SEQ ID 8952> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06098 Lipop: Possible site: = -1 Crend: 10 McG: Discrim Score: 16.85 GvH: Signal Score (-7.5): -5.07 Possible site: 49 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -0.22 threshold: 0.0 INTEGRAL Likelihood = -0.22 Transmembrane 117-133 ( 117-133) PERIPHERAL Likelihood = 0.47 73 modified ALOM score: 0.54 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1086(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00141## SEQ ID 8952 (GBS390) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 73 (lane 7; MW 37 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 82 (lane 3; MW 62 kDa). GBS390-GST was purified as shown in FIG. 216, lane 12. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1998 A DNA sequence (GBSx2108) was identified in S. agalactiae <SEQ ID 6173> which encodes the amino acid sequence <SEQ ID 6174>. This protein is predicted to be probable trimethylamine dehydrogenase (nemA). Analysis of this protein sequence reveals the following: TABLE-US-06099 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm ---- Certainty = 0.2218(Affirmative) < succ> bacterial membrane ---- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06100 >GP:CAA83700 GB:Z33015 similar to trimethylamine DH [Mycoplasma capricolum] Identities = 162/311 (52%), Positives = 219/311 (70%), Gaps = 1/311 (0%) Query: 3 NVQGNLFRPLTLPNGLSLENRFVLSPMVTNSSTSEGFVTDDDIAYAVRRAKSAPLQITGA 62 N LF P L NG LENRFVLSPM + +T +G +TD + Y RR+ SAPLQITG Sbjct: 2 NKYEKLFEPFYL-NGWKLENRFVLSPMTLSLATLDGKITDKEADYVKRRSHSAPLQITGG 60 Query: 63 AYITEYGQLFEYGFSVSKDEDIPGLTKLAKANKSKGAKAVLQLTHAGRFSSHTLARHGYV 122- Y E+GQLFEYG S D+DIP LT+L + MK+ +LQL HAG+WS +L ++GY+ Sbjct: 61 VYFDEFGQLFEYGISAKSDDDIPSLTRLYQEMKTDSNCVILQLAHAGKFSKTSLKKYGYL 120- Query: 123 YGPSPMQLQSPYPHQVKELTHKDILRIIDEYVQATRRAIQAGFDGVEISSAQRLLIQTFF 18- 2 YGPS + +P H+V EL + I +II +Y AT R I+AGF+G+EIS AQRLLIQTFF Sbjct: 121 YGPSYEKNNTPIEHEVLELPKEKIKQIIQDYKDATLRVIKAGFNGIEISMAQRLLIQTFF 18- 0 Query: 183 STFSNQRKOEYGPQTLTNRCRLGLEVFKAVQKVIREEAESDFILGFRATPEETRGSQIGY 24- 2 S N+R DEY NR R LEV KA+++VI + A +FI GFRATPEET G +GY Sbjct: 181 SQIIMKRTDEYSATNFENRSRFCLEVVKAIREVIDKYAPKNFIFGFRATPEETYGDILGY 24- 0 Query: 243 SIEEFMEFLEKILAIAQVDYLAIASWGHDVFRNTIRSEGVYKGQLVNQVIFEHFGDRVPI 30- 2 +IE+F++ ++KI+ I ++ YLAIASWGMD++ N +RS YKGQLVN+VI++ + +++PI Sbjct: 241 TIEDFIQLVDKIIEIGKISYLAIASWGHDIYLMKVRSMTKYKGQLVNKVIYDIYKNKLPI 30- 0 Query: 303 MATGGINSASK 313 +++GGIN+ +K Sbjct: 301 ISSGGINTPTK 311 A related DNA sequence was identified in S. pyogenes <SEQ ID 6175> which encodes the amino acid sequence <SEQ ID 6176>. Analysis of this protein sequence reveals the following: TABLE-US-06101 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3055(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06102 Identities = 265/390 (67%), Positives = 321/390 (81%) Query: 8 LFRPLTLPNGLSLENRFVLSPMVTNSSTSEGFVTDDDIAYAVRRAKSAPLQITGAAYITE 67 LE PLTLPNG L+NRFVLSPMVTNSST +G+VT DD++YA+RRA SAPLQITGAAY+ Sbjct: 8 LFEPLTLPNGSQLDNRFVLSPMVTNSSTKDGYVTQDDVSYALRRAASAPLQITGAAYVDP 67 Query: 68 YGQLFEYGFSVSKDEDIPGLTKLAKAMKSKGAKAVLQLTHAGRESSHTLARHGYVYGPSP 127- YGQLFEYGFSV+KD DI GL +LA+AMK+KGAKAVLQLTHAGRF+SH L ++G+VYGPS Sbjct: 68 YGQLFEYGFSVTKDADISGLKELAQAMKAKGAKAVLQLTHAGRFASHALTKYGFVYGPSY 127- Query: 128 MQLQSPYPHQVKELTHKDILRIIDEYVQATRRAIQAGFDGVEISSAQRLLIQTFFSTFSN 18- 7 MQL+SP PH+VK LT + I +I Y QATRRAIQAGFDGVE+SSAQRLLIQTFFSTFSN Sbjct: 128 MQLRSPQPHEVKPLTGQQIEELIAAYAQATRRAIQAGFDGVEVSSAQRLLIQTFFSTFSN 18- 7 Query: 188 QRKDEYGPQTLTNRCRLGLEVFKAVQKVIREEAESDFILGFRATPEETRGSQIGYSIEEF 24- 7 +R D YG QTL HR +L L V +AVQ+VI++EA FI GFRATPEETRG+ IGYSI+EF Sbjct: 188 KRTDSYGCQTLFNRSKLTLAVLQAVQQVIKQEAPDGFIFGFRATPEETRGNDIGYSIDEF 24- 7 Query: 248 MEFLEKILAIAQVDYLAIASWGHDVFRNTIRSEGVYKGQLVNQVIFEHFGDRVPIMATGG 30- 7 ++ ++ +L +A++DYLAIASWG VFRNT+RS G Y G+ VNQV+ ++ +++P+MATGG Sbjct: 248 LQLMDWVLNVAKLDYLAIASWGRHVFRNTVRSPGPYYGRRVNQVVRDYLRHKLPVMATGG 30- 7 Query: 308 INSASKVFEALQHAHMIGASTPLVVDPEFLQKIKAKCSDQINLRIKVSDLEGLAIPKASF 36- 7 +N+ K EAL HA IG STP VVDPEF KIK C + I+LRI+ +DL+ LAIP+ASF Sbjct: 308 MNTPDKAIEALAHADFIGVSTPFVVDPEFAHKIKEGCEESIHLRIRPADLKSLAIPQASF 36- 7 Query: 368 KDIVPLMDYGESLPKEAREVFRELRSNYRE 397 KDIVPLMDYGESLPKE+R +FR L NY+E Sbjct: 368 KDIVPLMDYGESLPKESRTLFRSLTHNYKE 397 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 1999 A DNA sequence (GBSx2109) was identified in S. agalactiae <SEQ ID 6177> which encodes the amino acid sequence <SEQ ID 6178>. Analysis of this protein sequence reveals the following: TABLE-US-06103 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3748(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06104 >GP:BAB04594 GB:AP001510 unknown conserved protein [Bacillus halodurans] Identities = 121/333 (36%), Positives = 192/333 (57%), Gaps = 12/333 (3%) Query: 1 MKLSVLDYGLIDYGKTASDAIQETILLSQEAERLGYHQFWVAEHHGVKAFSISNPELMIM 60 MKLSVLD I YG A +A+++T L++ E LGYH+FWV+EHH +S+PE++I Sbjct: 1 MKLSVLDQSPIAYGSNAKEALRQTTELAKVTEALGYHRFWVSEHHDASTLAGSSPEVLIA 60 Query: 61 HLANQTKSIKIGSGGINPLHYSSFKLAETLKTLSTCHPNRVSIGLGNSLGTVKVSNALRS 120- HLA TK I++GSGG+M HYS++K+AE K LE HP R+ +GLG + G + ++ Sbjct: 61 HLAAHTKKIRLGSGGVMLPHYSAYKVAENFKLLEALHPGRIDVGLGRAPGGMPIAKMALQ 120- Query: 121 LHK---AHDYEEVLEELKSWLIDESSSKEPL----VQPTLSSFPDLYVLGSGQKSAYLAA 17- 3 K HY ++++ +L D+ + P + + PD+++LGS SA +AA Sbjct: 121 EGKEQNIHKYPLQVKDVIGYLQDDLPTDHRFHGLKATPLIDTVPDVWLLGSSGGSANVAA 18- 0 Query: 174 KLGLGFTFGVFPFMDKDPLTEAKKLSSLYYHQFEEYYPNKSPNLMVAAFVVIADTSEEAE 23- 3 + G GF F F++ + +A + Y F+ P VA FV+ ADT E+A+ Sbjct: 181 ENGTGFAFA--HFINGEGGVQAVE---SYRETFQPSALFDRPQTSVAIFVICADTDEQAD 23- 5 Query: 234 NIAKTLDIWMLGNKDFNFATFPTIEEANHYQLTPEQKAKIKSNRDRMIVGDPKQVKESL 293- IA +LD+ ++ ++ P+IE A Y +P ++A+I+ NR RMIVG PK V++ L Sbjct: 236 QIASSLDLSLIMLENGQLSKGTPSIESALSYPYSPFERARIRENRKRMIVGSPKAVRQQL 29- 5 Query: 294 DALVNASQAEELLLIPLVPGLDQRIKSLKLLSQ 326 L A + EE++++ + + RI+S +LL + Sbjct: 296 VELARAYETEEVIVVTITHREEDRIRSYELLGE 328 A related DNA sequence was identified in S. pyogenes <SEQ ID 6179> which encodes the amino acid sequence <SEQ ID 6180>. Analysis of this protein sequence reveals the following: TABLE-US-06105 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.60 Transmembrane 212-228 ( 210-229) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial Cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06106 Identities = 173/329 (52%), Positives = 241/329 (72%), Gaps = 1/329 (0%) Query: 1 MKLSVLDYGLIDYGKTASDAIQETILLSQEAERLGYHQFWVAEHHGVKAFSISNPELMIM 60 MK+S+LDYG+ID KT +A+ ET L+Q A++LG+H+FWVAEHH + AF+IS+PEL++M Sbjct: 1 MKVSILDYGVIDKEKTPQEALLETRCLAQVADKLGFHRFWVAEHHNIYAFAISSPELLMM 60 Query: 61 HLANQTKSIKIGSGGIMPLHYSSFKLAETLKTLETCHPNRVSIGLGNSLGTVKVSNALRS 120- HLA+ TK I+IGSGGIMPLHYSSFK+AE + TLE HPNR+ +G+GNSLGT V AL S Sbjct: 61 HLADHTKQIRIGSGGIMPLHYSSFKIAEWIMTLEALHPNRIDLGIGNSLGTTLVQRALSS 120- Query: 121 LHKAHDYEEVLEELKSWLIDESSSKEPL-VQPTLSSFPDLYVLGSGQKSAYLAAKLGLGF 17- 9 +H Y +V+ EL +L + S P+ V P +++P ++ L + ++A LA +LGLG+ Sbjct: 121 IHCKDSYSQVVTELYQYLNPDHLSPLPIFVNPRGNTYPQIWTLSNSLETAELAGQLGLGY 18- 0 Query: 180 TFGVFPFMDKDPLTEAKKLSSLYYHQFEEYYPNKSPNLMVAAFVVIADTSEEAENIAKTL 23- 9 TFG+FP++ KDP+TEAK++S+ Y F K P L++A F+V++DT E+AE +AK L Sbjct: 181 TFGIFPYIPKDPITEAKRVSAHYRKAFRPSKLLKIPKLILAVFIVLSDTDEKAEALAKPL 24- 0 Query: 240 DIWMLGNKDFNEFATFPTIEEANHYQLTPEQKAKIKSNRDRMIVGDPKQVKESLDALVNA 29- 9 DIWMLG +DFNEF T+P +EEA +Y LT +Q+ I +NR RM++G P VK+ LD L+ A Sbjct: 241 DIWMLGQQDFNEFKTYPDVEEARNYHLTEKQREAIAANRSRMVIGSPHTVKKQLDRLIEA 30- 0 Query: 300 SQAEELLLIPLVPGLDQRIKSLKLLSQLY 328 QA+ELL IPLVP R ++L+LL+ LY Sbjct: 301 CQADELLAIPLVPEFANRQRTLELLADLY 329 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2000 A DNA sequence (GBSx2110) was identified in S. agalactiae <SEQ ID 6181> which encodes the amino acid sequence <SEQ ID 6182>. Analysis of this protein sequence reveals the following: TABLE-US-06107 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2384(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06108 >GP: AAF81345 GB: AC007767 Identical to a glycine cleavage system H-protein precursor from Arabidopsis thaliana gb|P25855. It contains a glycine cleavage H-protein domain PF|01597. ESTs gb|R90208, gb|AI Identities = 30/91 (32%), Positives = 53/91 (57%), Gaps = 1/91 (1%) Query: 18 TISLTPELQDDLGTVGYVEFTD-DANLEVDDVILNIEASKTVMAILSPLTGKVVKVNTAA 76 - TI +T QD LG V +VE + ++++ + +E+ K ILSP++G+V++VNT Sbjct: 59 TIGITDHAQDHLGEVVFVELPEANSSVSKEKSFGAVESVKATSEILSPISGEVIEVNTKL 118- Query: 77 SQEPTLLNSEKADENWLVVLTEVDYAAFEAL 107 ++ P L+NS ++ W++ + A EAL Sbjct: 119 TESPGLINSSPYEDGWMIKVKPSSPAELEAL 149 A related DNA sequence was identified in S. pyogenes <SEQ ID 6183> which encodes the amino acid sequence <SEQ ID 6184>. Analysis of this protein sequence reveals the following:

TABLE-US-06109 Possible Site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3544(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06110 Identities = 80/110 (72%), Positives = 98/110 (88%) Query: 1 MKKIANYLLIEKNEELYTISLTPELQDDLGTVGYVEFTDDANLEVDDVILNIEASKTVMA 60 MKKIANYLLIEK ++ YTIS+TPELQDD+GT+GY EFTD+ +L VDD+ILN+EASKTVM+ Sbjct: 1 MKKIANYLLIEKTDDRYTISMTPELQDDIGTIGYAEFTDNDHLAVDDIILNLEASKTVMS 60 Query: 61 ILSPLTGKVVKVNTAASQEPTLLNSEKADENWLVVLTEVDYAAFEALENA 110 +LSPL G VV+ N AA+ PTLLNSEKA+ENW+VVLT+VD AAF+ALE+A Sbjct: 61 VLSPLAGAVVERNEAATLTPTLLNSEKAEENWIVVLTDVDQAAFDALEDA 110 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2001 A DNA sequence (GBSx2111) was identified in S. agalactiae <SEQ ID 6185> which encodes the amino acid sequence <SEQ ID 6186>. This protein is predicted to be LRP16 (b1045). Analysis of this protein sequence reveals the following: TABLE-US-06111 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0608(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06112 >GP: AAF15294 GB: AF202922 LRP16 [Homo sapiens] Identities = 73/171 (42%), Positives = 98/171 (56%), Gaps = 13/171 (7%) Query: 88 DICLLQVDAIVNAANSKLLGCFIPNHHCIDNQIHTFAGSRLRLACHQLMTQQGRMEAVGQ 147- DI L+VDAIVNAANS LLG +D IH AG L C L + + G+ Sbjct: 78 DITKLEVDAIVNAANSSLLG-----GGGVDGCIHRAAGPLLTDECRTLQSCK-----TGK 127- Query: 148 AKLTESYHLPCKYVIHTVGPYVKVDQKPSRIREDLLKSSYKSCLQLAVRANLKTIVFPCI 20- 7 AK+T Y LP KYVIHTVGP + S+ E L+S Y S L L + L+++ FPCI Sbjct: 128 AKITGGYRLPAKYVIHTVGPIAYGEPSASQAAE--LRSCYLSSLDLLLEHRLRSVAFPCI 18- 5 Query: 208 STGEFGFPNQRAAELAVQAILEWQRENQHKL-YIIFNTFTPKDQDIYQKLL 257 STG FG+P + AAE+ + + EW +++ K+ +I F KD+DIY+ L Sbjct: 186 STGVFGYPCEAAAEIVLATLREWLEQHKDKVDRLIICVFLEKDEDIYRSRL 236 A related DNA sequence was identified in S. pyogenes <SEQ ID 6187> which encodes the amino acid sequence <SEQ ID 6188>. Analysis of this protein sequence reveals the following: TABLE-US-06113 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1992(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06114 Identities = 139/266 (52%), Positives = 178/266 (66%), Gaps = 6/266 (2%) Query: 1 MPNQKQLLLAMIEYLQSEKLTDVDDL----RTTDLQTVWRGLVNQQDPQNISQEYLSLED 56 MP+ LL MI LQ+E+LT T Q +WR L+NQ+ +S++YL+LED Sbjct: 1 MPSSFDLLGEMIGLLQTEQLTSSWACPLPNALTKRQDLWRALINQRPALPLSKDYLNLED 60 Query: 57 RYLSHWWNTQKVKTIDVCHQTVYSNVFTYHGDICLLQVDAIVNAANSKLLGCFIPNHHCI 116- YL W + ++ C +T Y+++F YHGDI L VDAIVNAANS+LLGCF PNH CI Sbjct: 61 AYLDDWRASFVPVSVKDCQKTNYTSLFLYHGDIRYLAVDAIVNAANSELLGCFSPNHGCI 120- Query: 117 DNQIHTFAGSRLRLACHQLMTQQGRMEAVGQAKLTESYHLPCKYVIHTVGPYVKVDQKPS 17- 6 DN IHTFAGSRLRLAC +MT+QGR EA+GQAKLT +YHLP Y+IHTVGP + S Sbjct: 121 DNAIHTFAGSRLRLACQAIMTEQGRKEAIGQAKLTSAYHLPASYIIHTVGPRITKGHHVS 18- 0 Query: 177 RIREDLLKSSYKSCLQLAVRANLKTIVFPCISTGEFGFPNQRAAELAVQAILEWQRENQH 23- 6 IR DLL Y+S L LAV+A L ++ F ISTGEFGFP + AA++A++ +L+WQ E+ Sbjct: 181 PIRADLLARCYRSSLDLAVKAGLTSLAFCSISTGEFGFPKKEAAQIAIKTVLKWQAEHPE 24- 0 Query: 237 K--LYIIFNTFTPKDQDIYQKLLLKE 260 L IFNTFT +D+ +Y L KE Sbjct: 241 SKTLTTIFNTFTSEDKALYDTYLQKE 266 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2002 A DNA sequence (GBSx2112) was identified in S. agalactiae <SEQ ID 6189> which encodes the amino acid sequence <SEQ ID 6190>. Analysis of this protein sequence reveals the following: TABLE-US-06115 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2171(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 6191> which encodes the amino acid sequence <SEQ ID 6192>. Analysis of this protein sequence reveals the following: TABLE-US-06116 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2477(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06117 Identities = 218/284 (76%), Positives = 250/284 (87%) Query: 4 WKTLEKTNHSQSEILSQLIEESDAIVVGIGAGMSAADGFTYIGPRFEEAFPDFIAKYQLL 63 W T + N +Q+E L+QLI+E+DA+VVGIGAGMSAADGFTYIG RFE AFPDFIAKYQ L Sbjct: 4 WTTYPQKNLTQAEQLAQLIKEADALVVGIGAGMSAADGFTYIGSRFETAFPDFIAKYQFL 63 Query: 64 DMLQASLYDFEDWEEYWAFQSRFVALNYLDQPVGQAYLDLKDILAKKEYHIITTNADNAF 123- DMLQASL+DFEDW+EYWAFQSRFVALNYLDQPVGQ+YLDLK+IL K+YHIITTNADNAF Sbjct: 64 DMLQASLFDFEDWQEYWAFQSRFVALNYLDQPVGQSYLDLKEILGTKDYHIITTNADNAF 123- Query: 124 AVADYNLEKVFHIQGEYGLWQCSQHCHQQTYRNDQAIRQMIAQQKDMKIPSNLIPKCPKC 18- 3 VA Y+ +FHIQGEYGLWQCSQHCHQQTY++D IRQMIA+QK+MK+P LIP CP+C Sbjct: 124 WVAGYDPHNIFHIQGEYGLWQCSQHCHQQTYKDDTVIRQMIAEQKNMKVPGQLIPHCPEC 18- 3 Query: 184 DQPFEINKRNEEKGMVEDADFHAQRQRYENFLSQHQNDKVLYLEIGVGHTTPQFIKHPFW 24- 3 + PFEINKRNEEKGMVEDADFHAQ+ RYE FLS+H+ KVLYLEIGVGHTTPQFIKHPFW Sbjct: 184 EAPFEINKRNEEKGMVEDADFHAQKARYEAFLSEHKEGKVLYLEIGVGHTTPQFIKHPFW 24- 3 Query: 244 RFVSLNENSLFVTLNHKHYRIPQKIRSRSVQLTQHIAELIAEAK 287 + VS N N+LFVTLNHKHYRIP IR +S++LT+HIA+LI+ K Sbjct: 244 KRVSENPNALFVTLNHKHYRIPLSIRRQSLELTEHIAQLISATK 287 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2003 A DNA sequence (GBSx2113) was identified in S. agalactiae <SEQ ID 6193> which encodes the amino acid sequence <SEQ ID 6194>. Analysis of this protein sequence reveals the following: TABLE-US-06118 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1086(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06119 >GP: CAB12865 GB: Z99109 similar to lipoate-protein ligase [Bacillus subtilis] Identities = 130/331 (39%), Positives = 206/331 (61%), Gaps = 5/331 (1%) Query: 9 NGKRITDGAIALAMQVYILQNVFLDDDILFPYYCDPKVEIGKFQNAVIETNQEYLKEHDI 68 + + I D I LA++ Y ++++ + L Y P + IGK QN + E N +Y++E+ I Sbjct: 5 DNQNINDPRINLAIEEYCVKHLDPEQQYLLFYVNQPSIIIGKNQNTIEEINTKYVEENGI 64 Query: 69 PVVRRDTGGGAVYVDSGAVNICYLMKDHGQ-FGDFKRAYEPAIKALKTLGASSVEMRERN 127- VVRR +GGGAVY D G +N ++ KD G F +FK+ EP I+AL LG + E+ RN Sbjct: 65 IVVRRLSGGGAVYHDLGNLNFSFITKDDGDSFHNFKKFTEPVIQALHQLGVEA-ELSGRN 123- Query: 128 DLVIDGKKVSGAAMTIVNGRIYGGYSLLLDVDVDAMEKVLNPNRKKIESKGIKSVRSRVG 18- 7 D+V+DG+K+SG A GRI+ +L+ D D + L + KIESKGIKS+RSRV Sbjct: 124 DIVVDGRKISGNAQFATKGRIFSHGTLMFDSAIDHVVSALKVKKDKIESKGIKSIRSRVA 18- 3 Query: 188 DIRSHLSEDYRHITTDQFKDLMVCQLLHIDHIDQAKRYHLTEKDWAAIDALADEKYKNWD 24- 7 +I L + +TT++F+ ++ + + + + Y LTEKDW I ++ E+Y+NWD Sbjct: 184 NISEFLDDK---MTTEEFRSHLLRHIFNTNDVGNVPEYKLTEKDWETIHQISKERYQNWD 24- 0 Query: 248 WNYGNSPQYSYHRDARFPSGTYDFHLEIEKGIITNCRIYGDFFSSKDISDIENLLIGCPM 30- 7 WNYG SP+++ + R+P G+ D HLE++KG I +C+I+GDFF D+S+IENLL+G Sbjct: 241 WNYGRSPRFNLNHSKRYPVGSIDLHLEVKKGKIEDCKIFGDFFGVGDVSEIENLLVGKQY 30- 0 Query: 308 KEELVLEKLSTLSLEDYFGQTSPEEIKAVLF 338 + ++ + L ++L+ YFG + E+ +++ Sbjct: 301 ERSVIADVLEGVNLKHYFGNITKEDFLDLIY 331 A related DNA sequence was identified in S. pyogenes <SEQ ID 6195> which encodes the amino acid sequence <SEQ ID 6196>. Analysis of this protein sequence reveals the following: TABLE-US-06120 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial Cytoplasm --- Certainty = 0.0939(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06121 Identities = 248/339 (73%), Positives = 283/339 (83%) Query: 1 MYLIEPIRNGKRITDGAIALAMQVYILQNVFLDDDILFPYYCDPKVEIGKFQNAVIETNQ 60 MYLIEPIRNGKRITDGA+ALAMQVY+ +N+FLDDDILFPYYCDPKVEIGKFQNAV+ETNQ Sbjct: 1 MYLIEPIRNGKRITDGAVALAMQVYVQENLFLDDDILFPYYCDPKVEIGKFQNAVVETNQ 60 Query: 61 EYLKEHDIPVVRRDTGGGAVYVDSGAVNICYLMKDHGQFGDFKRAYEPAIKALKTLGASS 120- EYLKEH IPVVRRDTGGGAVYVDSGAVNICYL+ D+G FGDFKR Y+PAI+AL LGA+ Sbjct: 61 EYLKEHHIPVVRRDTGGGAVYVDSGAVNICYLINDNGIFGDFKRTYQPAIEALHHLGATE 120- Query: 121 VEMRERNDLVIDGKKVSGAAMTIVNGRIYGGYSLLLDVDFDAMEKVLNPNRKKIESKGIK 18- 0 VEM RNDLVIDGKKVSGAAMTI NGR+YGGYSLLLDVDF+AMEK L PNRKKIESKGI+ Sbjct: 121 VEMSGRNDLVIDGKKVSGAAMTIANGRVYGGYSLLLDVDFEAMEKALKPNRKKIESKGIR 18- 0 Query: 181 SVRSRVGDIRSHLSEDYRHITTDQFKDLMVCQLLHIDHIDQAKRYHLTEKDWAAIDALAD 24- 0 SVRSRVG+IR HL+ Y+ IT ++FKDLMVCQLL I+ I QAKRY LTEKDW IDAL + Sbjct: 181 SVRSRVGNIREHLAPQYQGITIEEFKDLMVCQLLQIETISQAKRYDLTEKDWQQIDALTE 24- 0 Query: 241 EKYKNWDWNYGNSPQYSYHRDARFPSGTYDFHLEIEKGIITNCRIYGDFFSSKDISDIEN 30- 0 KY NW+WNYGN+PQY YHRD RF GT D HL+I+KG I CRIYGDFF DI+++E Sbjct: 241 RKYHNWEWNYGNAPQYRYHRDGRFTGGTVDIHLDIKKGYIAACRIYGDFFGKADIAELEG 30- 0 Query: 301 LLIGCPMKEELVLEKLSTLSLEDYFGQTSPEEIKAVLFS 339 LIG M++E VL L+ + L Y G + EE+ ++FS Sbjct: 301 HLIGTRMEKEDVLATLNAIDLAPYLGAITAEELGDLIFS 339 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2004 A DNA sequence (GBSx2114) was identified in S. agalactiae <SEQ ID 6197> which encodes the amino acid sequence <SEQ ID 6198>. Analysis of this protein sequence reveals the following: TABLE-US-06122 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.49 Transmembrane 196-212 (196-212) ----- Final Results ----- bacterial membrane --- Certainty = 0.1595(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06123 >GP: AAB49329 GB: U39612 formyl-tetrahydrofolate synthetase [Streptococcus mutans] Identities = 432/556 (77%), Positives = 493/556 (87%) Query: 1 MKTDIEIAQSVALKPIAEIVEQVGIGFDDIELYGKYKAKLSFDKIEAVKSQKVGKLILVT 60 MKTDIEIAQSV L+PI +V+++GI FDD+ELYGKYKAKL+FDKI+AV+ GKL+LVT Sbjct: 1 MKTDIEIAQSVDLRPITNVVKKLGIDFDDLELYGKYKAKLTFDKIKAVEENAPGKLVLVT 60 Query: 61 AINPTPAGEGKSTMSIGLADALNKIGKKTMIALREPSLGPVMGIKGGAAGGGYAQVLPME 120- AINPTPAGEGKST++IGLADALNKIGKKTMIA+REPSLGPVMGIKGGAAGGGYAQVLPME Sbjct: 61 AINPTPAGEGKSTITIGLADALNKIGKKTMIAIREPSLGPVMGIKGGAAGGGYAQVLPME 120- Query: 121 DINLHFTGDMHAITTANNALSALLDNHIHQGNELDIDQRRVIWKRVVDLNDRALRQVIVG 18- 0 DINLHFTGDMHAITTANNALSAL+DNH+HQGNEL IDQRR+IWKRVVDLNDRALR V VG Sbjct: 121 DINLHFTGDMHAITTANNALSALIDNHLHQGNELGIDQRRIIWKRVVDLNDRALRHVTVG 18- 0 Query: 181 LGSPVNGIPREDGFDITVASEIMAILCLATDLSDLKKRLSNIVVAYSRNRKPIYVKDLKI 24- 0 LGSP+NGIPRSDGFDITVASEIMAILCLAT++ DLK+RL+NIV+ Y +R P+YV+DL++ Sbjct: 181 LGSPINGIPREDGFDITVASEIMAILCLATNVEDLKERLANIVIGYRFDRSPVYVRDLEV 24- 0 Query: 241 EGALTLILKDTIKPNLVQTIYGTPALVHGGPFANIAHGCNSVLATSTALRLADYVVTEAG 30- 0 +GAL LILK+ IKPNLVQTIYGTPA VHGGPFANIAHGCNSVLATSTALRLADY +TEAG Sbjct: 241 QGALALILKEAIKPNLVQTIYGTPAFVHGGPFANIAHGCNSVLATSTALRLADYTITEAG 30- 0 Query: 301 FGADLGAEKFLDIKTPNLPTSPDAIVIVATLRALKMHGGVSKEDLSQENVEAVKRGFTNL 36- 0 FGADLGAEKFLDIK PNLPTSPDA+VIVAT+RALKH+GGV+K+ L+QENVEAVK GF NL Sbjct: 301 FGADLGAEKFLDIKAPNLPTSPDAVVIVATIRALKMNGGVAKDALNQENVEAVKAGFANL 36- 0 Query: 361 ERHVNNMRQYGVPVVVAINQFTADTESEIATLKTLCSNIDVAVELASVWEDGADGGLELA 42- 0 RHV NMR+YGVPVVVAIN+F DT EIA L+ LC+ IDV VELASVW +GADGG++LA Sbjct: 361 ARHVENMRKYGVPVVVAINEFITDTNDEIAVLRNLCAAIDVPVELASVWANGADGGVDLA 42- 0 Query: 421 QTVANVIETQSSNYKRLYNDEDTIEEKIKKIVTKIYGGNKVHFGPKAQIQLKEFSDNGWD 48- 0 T+ N IE S+YKRLY++ ++EEK+ +I +IY +KV F KA+ Q+ + NGWD Sbjct: 421 NTLINTIENNPSHYKRLYDNNLSVEEKVTEIAKEIYRADKVIFEKKAKTQIAQIVKNGWD 48- 0 Query: 481 KMPICMAKTQYSFSDNPNLLGAPTDFDITVREFVPKTGAGFIVALTGDVLTMPGLPKKPA 54- 0 +PICMAKTQYSFSD+P LLGAPT FDIT+RE VPK GAGFIVALTGDV+TMPGLPKKPA Sbjct: 481 NLPICMAKTQYSFSDDPKLLGAPTGFDITIRELVPKLGAGFIVALTGDVMTMPGLPKKPA 54- 0 Query: 541 ALNMDVLEDGTAIGLF 556 ALNMDV DGTA+GLF Sbjct: 541 ALNMDVAADGTALGLF 556 A related DNA sequence was identified in S. pyogenes <SEQ ID 6199> which encodes the amino acid sequence <SEQ ID 6200>. Analysis of this protein sequence reveals the following: TABLE-US-06124 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.49 Transmembrane 196-212 (196-212) ----- Final Results ----- bacterial membrane --- Certainty = 0.1595(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06125 >GP: AAB49329 GB: U39612 formyl-tetrahydrofolate synthetase [Streptococcus mutans] Identities = 432/556 (77%), Positives = 490/556 (87%) Query: 1 MKSDIEIAQSVALQPITDIVKKVGIDGDDIELYGKYKAKLSFEKMKAVEANEPGKLILVT 60 MK+DIEIAQSV L+PIT++VKK+GID DD+ELYGKYKAKL+F+K+KAVE N PGKL+LVT Sbjct: 1 MKTDIEIAQSVDLRPITNVVKKLGIDFDDLELYGKYKAKLTFDKIKAVEENAPGKLVLVT 60 Query: 61 AINPTPAGEGKSTMSIGLADALNQMGKKTMLALREPSLGPVMGIKGGAAGGGYAQVLPME 120- AINPTPAGEGKST++IGLADALN++GKKTM+A+REPSLGPVMGIKGGAAGGGYAQVLPME Sbjct: 61 AINPTPAGEGKSTITIGLADALNKIGKKTMIAIREPSLGPVMGIKGGAAGGGYAQVLPME 120- Query: 121 DINLHFTGDMHAITTANNALSALIDNHLQQGNDLGIDPRRIIWKRVLDLNDRALRQVIVG 18- 0 DINLHFTGDMHAITTANNALSALIDNHL QGN+LGID RRIIWKRV+DLNDRALR V VG Sbjct: 121 DINLHFTGDMHAITTANNALSALIDNHLHQGNELGIDQRRIIWKRVVDLNDRALRHVTVG 18- 0 Query: 181 LGSPVNGVPREDGFDITVASEINAILCLATDLKDLKKRLADIVVAYTYDRKPVYVRDLKV 24- 0 LGSP+NG+PREDGFDITVASEIMAILCLAT+++DLK+RLA+IV+ Y +DR PVYVRDL+V Sbjct: 181 LGSPINGIPREDGFDITVASEINAILCLATNVEDLKERLANIVIGYRFDRSPVYVRDLEV 24- 0 Query: 241 EGALTLILKDAIKPNLVQTIYGTPALIHGGPFANIANGCNSVLATSTALRLADYTVTEAG 30- 0 +GAL LILK+AIKPNLVQTIYGTPA +HGGPFANIAHGCNSVLATSTALRLADYT+TEAG Sbjct: 241 QGALALILKEAIKPNLVQTIYGTPAFVNGGPFANIAHGCNSVLATSTALRLADYTITEAG 30- 0 Query: 301 FGADLGAEKFLNIKVPNLPKAPDAIVIVATLRALKMHGGVAKSDLAAENCEAVRLGFANL 36- 0 FGADLGAEKFL+IK PNLP +PDA+VIVAT+RALKN+GGVAK L EN EAV+ GFANL Sbjct: 301 FGADLGAEKFLDIKAPNLPTSPDAVVIVATIRALKMNGGVAKDALNQENVEAVKAGFANL 36- 0 Query: 361 KRHVENMRQFKVPVVVAINEFVADTEAEIATLKALCEEIKVPVELASVWANGAEGGLALA 42- 0 RHVENMR++ VPVVVAINEF+ DT EIA L+ LC I VPVELASVWANGA+GG+ LA Sbjct: 361 ARHVENMRKYGVPVVVAINEFITDTNDEIAVLRNLCAAIDVPVELASVWANGADGGVDLA 42- 0 Query: 421 KTVVRVIDQEAADYKRLYSDEDTLEEKVINIVTQIYGGKAVQFGPKAKTQLKQFAEFGWD 48- 0 T++ I+ + YKRLY + ++EEKV I +IY V F KAKTQ+ Q + GWD Sbjct: 421 NTLINTIENNPSHYKRLYDNNLSVEEKVTEIAKEIYRADKVIFEKKAKTQIAQIVKNGWD 48- 0 Query: 481 KLPVCMAKTQYSFSDNPSLLGAPTDFDITIREFVPKTGAGFIVGLTGDVMTMPGLPKVPA 54- 0 LP+CMAKTQYSFSD+P LLGAPT FDITIRE VPK GAGFIV LTGDVMTMPGLPK PA Sbjct: 481 NLPICMAKTQYSFSDDPKLLGAPTGFDITIRELVPKLGAGFIVALTGDVMTMPGLPKKPA 54- 0 Query: 541 AMAMDVAENGTALGLF 556 A+ MDVA +GTALGLF Sbjct: 541 ALNMDVAADGTALGLF 556 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06126 Identities = 452/556 (81%), Positives = 513/556 (91%) Query: 1 MKTDIEIAQSVALKPIAEIVEQVGIGFDDIELYGKYKAKLSFDKIEAVKSQKVGKLILVT 60 MK+DIEIAQSVAL+PI +IV++VGI DDIELYGKYKAKLSF+K++AV++ + GKLILVT Sbjct: 1 MKSOIEIAQSVALQPITDIVKKVGIDGDDIELYGKYKAKLSFERNKAVEANEPGKLILVT 60 Query: 61 AINPTPAGEGKSTMSIGLADALNKICKKTMIALREPSLGPVNGIKGGAAGGGYAQVLPME 120- AINPTPAGEGKSTMSIGLADALN++GKKTM+ALREPSLGPVNGIKGGAAGGGYAQVLPME Sbjct: 61 AINPTPAGEGKSTMSIGLADALNQMGKKTMLALREPSLGPVNGIKGGAAGGGYAQVLPNE 120- Query: 121 DINLHFTGDMHAITTANNALSALLDNNIHQGNELDIDQRRVIWKRVVDLNDRALRQVIVG 18- 0 DINLHFTGDMHAITTANNALSAL+DNH+ QGN+L ID RR+IWKRV+DLNDRALRQVIVG Sbjct: 121 DINLHFTGDMHAITTANNALSALIDNNLQQGNDLGIDPRRIIWKRVLDLNDRALRQVIVG 18- 0 Query: 181 LGSPVNGIPREDGFDITVASEIMAILCLATDLSDLKKRLSNIVVAYSRNRKPIYVKDLKI 24- 0 LGSPVNG+PREDGFDITVASEIMAILCLATDL DLKKRL++IVVAY+ +RKP+YV+DLK+ Sbjct: 181 LGSPVNGVPREDGFDITVASEINAILCLATDLKDLKKRLADIVVAYTYDRKPVYVRDLKV 24- 0 Query: 241 EGALTLILKDTIKPNLVQTIYGTPALVHGGPFANIAHGCNSVLATSTALRLADYVVTEAG 30- 0 EGALTLILKD IKPNLVQTIYGTPAL+HGGPFANIANGCNSVLATSTALRLADY VTEAG Sbjct: 241 EGALTLILKDAIKPNLVQTIYGTPALINGGPFANIAHGCNSVLATSTALRLADYTVTEAG 30- 0 Query: 301 FGADLGAEKFLDIKTPNLPTSFDAIVIVATLRALKMHGGVSKEDLSQENVEAVKRGFTNL 36- 0 FGADLGAEKFL+IK PNLP +PDAIVIVATLRALKMHGGV+E DL+ EN EAV+ GF NL Sbjct: 301 FGADLGAEKFLNIKVPNLPKAPOAIVIVATLRALKMHGGVAKSDLAAENCEAVRLGFANL 36- 0 Query: 361 ERHVNNMRQYGVPVVVAINQFTADTESEIATLKTLCSNIDVAVELASVWEDGADGGLELA 42- 0 +RHV NNRQ+VPVVVAIN+F ADTE+EIATLK LC I V VELASVW +GA+GGL LA Sbjct: 361 KRHVENMRQFKVPVVVAINEFVADTEAEIATLKALCEEIKVPVELASVWANGAEGGLALA 42- 0 Query: 421 QTVANVIETQSSNYKRLYNDEDTIEEKIKKIVTKIYGGNKVNFGPKAQIQLKEFSDNGWD 48- 0 +TV VI+ ++++YKRLY+DEDT+EEK+ IVT+IYGG V FGPKA+ QLK+F++ GWD Sbjct: 421 KTVVRVIDQEAADYKRLYSDEDTLEEKVINIVTQIYGGKAVQFGPKAKTQLRQFAEFGWD 48- 0 Query: 481 KHPICMAKTQYSFSDNPNLLGAPTDFOITVREFVPKTGAGFIVALTGDVLTMPGLPKKPA 54- 0 K+P+CMAKTQYSFSDNP+LLGAPTDFDIT+REFVPKTGAGFIV LTGDV+TNPGLPK PA Sbjct: 481 KLPVCMAKTQYSFSDNPSLLGAPTDFDITIREFVPKTGAGFIVGLTGDVMTNPGLPKVPA 54- 0 Query: 541 ALNMDVLEDGTAIGLF 556 A+ MDV E+GTA+GLF Sbjct: 541 AMAMDVAENGTALGLF 556 A related DNA sequence was identified in S. pyogenes <SEQ ID 9057> which encodes amino acid sequence <SEQ ID 9058>. Analysis of this protein sequence reveals the following:

TABLE-US-06127 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.49 Transmembrane 516-532 ( 516-533) ----- Final Results ----- bacterial membrane --- Certainty = 0.1595(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS sequences follows: TABLE-US-06128 Score = 604 bits (1540), Expect e-174 Identities = 304/555 (54%), Positives = 389/555 (69%), Gaps = 2/555 (0%) Query: 4 SDIEIANSVTMEPISKVADQLGIDKEALCLYGKYKAKIDARQLVALKNKPDGKLILVTAI 63 +DIEIA SV ++PI+++ +Q+GI + + LYGKYKAK+ ++ A+K++ GKLILVTAI Sbjct: 3 TDIEIAQSVALKPIAEIVEQVGIGF00IELYGKYKAKLSFDKIEAVKSQKVGKLILVTAI 62 Query: 64 SPTPAGEGKTTTSVGLVDALSAIGKKAVIALREPSLXXXXXXXXXXXXXXXXXXXPMEDI 123- +PTPAGEGK+T S+GL DAL+ IGKK +IALREPSL PMEDI Sbjct: 63 NPTPAGEGKSTNSIGLADALNKIGKKTMIALREPSLGPVNGIKGGAAGGGYAQVLPMEDI 122- Query: 124 NLNFTGDFHAIGVANNLLAALIDNHIHHGNSLGIDSRRITWKRVVDMNDRQLRHIVDGLQ 18- 3 NLHFTGD HAI ANN L+AL+DNHIH GN L ID RR+ WKRVVD+NDR LE ++ GL Sbjct: 123 NLHFTGDNHAITTANNALSALLDNHIHQGNELDIDQRRVIWKRVVDLNDRALRQVIVGLG 18- 2 Query: 184 GKVNGIPREDGYDITVASEIMAILCLSENISDLKARLEKIIIGYNYQGEPVTXXXXXXXX 24- 3 VNGIPREDG+DITVASEIMAILCL+ ++SDLK RL I++ Y+ +P+ Sbjct: 183 SPVNGIPREDGFDITVASEIMAILCLATDLSDLKKRLSNIVVAYSRNRKPIYVKDLKIEG 24- 2 Query: 244 XXXXXXXXXIHPNLVQTLEHTPALIHGGPFANIAHGCNSVLATKLALKYGDYAVTEAGFG 30- 3 I PNLVQT+ TPAL+HGGPFANIAHGCNSVLAT AL+ DY VTEAGFG Sbjct: 243 ALTLILKDTIKPNLVQTIYGTPALVHGGPFANIAHGCNSVLATSTALRLADYVVTEAGFG 30- 2 Query: 304 ADLGAEKFTDIKCRNSGLRPAAVVLVATIRALKNHGGVPKADLATENVQAVVDGLPNLDK 36- 3 ADLGAEKF+DIK P A+V+VAT+RALKNHGGV K DL+ ENV+AV G NL++ Sbjct: 303 ADLGAEKFLDIKTPNLPTSPDAIVIVATLRALKNHGGVSKEDLSQENVEAVKRGFTNLER 36- 2 Query: 364 HLANIQDVYGLPVVVAINKFPLDTDAELQAVYDACDKRGVDVVISDVWANGGAGGRELAE 42- 3 H+N++ YG+PVVVAIN+F DT++E+ + C V V ++ VW +G GG ELA+ Sbjct: 363 HVNNMRQ-YGVPVVVAINQFTADTESEIATLKTLCSNIDVAVELASVWEDGADGGLELAQ 42- 1 Query: 424 KVVTLAE-QDNQFRFVYEEDDSIETKLTKIVTKVYGGKGINLSSAAKRELADLERLGFGN 48- 2 V + E Q + ++ +Y ++D+IE K+ KIVTK+YGG ++ A+ +L + G+ Sbjct: 422 TVANVIETQSSNYKRLYNDEDTIEEKIKKIVTKIYGGNKVNFGPKAQIQLKEFSDNGWDK 48- 1 Query: 483 YPICMAKTQYSFSDDAKKLGAPTDFTVTISNLKVSAGAGFIVALTGAINTMPGLPKVPAS 54- 2 PICMAKTQYSFSD+ LGAPTDF +T+ GAGFIVALTG ++TMPGLPK PA+ Sbjct: 482 NPICMAKTQYSFSDNPNLLGAPTDFDITVREFVPKTGAGFIVALTGDVLTMPGLPKKPAA 54- 1 Query: 543 ETIDIDEEGNITGLW 557 +D+ E+G GLF Sbjct: 542 LNMDVLEDGTAIGLF 556 SEQ ID 6198 (GBS131) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 29 (lane 6; MW 64.8 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 35 (lane 4; MW 90 kDa). GBS131-GST was purified as shown in FIG. 201, lane 5. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2005 A DNA sequence (GBSx2115) was identified in S. agalactiae <SEQ ID 6201> which encodes the amino acid sequence <SEQ ID 6202>. Analysis of this protein sequence reveals the following: TABLE-US-06129 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.03 Transmembrane 34-50 ( 29-56) INTEGRAL Likelihood = - 7.70 Transmembrane 90-106 ( 84 - 110) INTEGRAL Likelihood = - 1.97 Transmembrane 62-78 ( 62 - 78) INTEGRAL Likelihood = - 0.69 Transmembrane 275-291 ( 275 - 291) ----- Final Results ----- bacterial membrane --- Certainty = 0.5012(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06130 >GP:AAA88609 GB:M37842 unknown protein [Streptococcus mutans] Identities = 243/373 (65%), Positives = 302/373 (80%), Gaps = 1/373 (0%) Query: 71 IGAVLYLVNSEMDALSRVTWLILVMIAPLLGAMFLMYTKFDWGYRGLKQRLETLI0ESQI 130- IG+VLYLVNS+MD LS +TWL++++ P+LG +FL+YTK OWGYR LK ++ + Sbjct: 2 IGSVLYLVNSQMDTLSIITWLLVILPFPILGTLFLIYTKQDWGYRELKSLIKKSTQAIIP 61 Query: 131 YLEDDPETLNQLKSSTSTTYHLVQYFEKAHGNFPVYRNTOVTFLPTGEAFFEK4KEELLK 19- 0 Y + D L +LR S + TY+L QY ++ G FPVY+NT VT+ P G++ FE+MK++LLK Sbjct: 62 YFQYOQRILYKLKESHARTYNLAQYLHRS-GGFPVYKNTKVTYFPNGQSKFEEMKKQLLK 120- Query: 191 AKKYIFLEFFIIDEGIMWGEILSILEQKVEEGVEVRILYDGMIEITKLSFDYTKRLEKIG 25- 0 A+K+IFLE+FII EG+MWGEILSILEQKV+EGVEVR++YDGM+E++LSFDY KRLEKIG Sbjct: 121 ASKFIFLEYFIIAEGLMWGEILSILEQKVQEGVEVRVMYDGMLELSTLSFDYAKRLEKIG 18- 0 Query: 251 IKAKAFSPISPFISTYYNYRDHRKIVVIDGVVGMTGGVNLADEYINHIELFGHWKDSGIM 31- 0 IKAK FSPI+PF+STYYNYROHRKI+VID V GG+NLAOEYIN IE FG+WKD+ +M Sbjct: 181 IKAKVFSPITPFVSTYYNYRDHRKILVIDNKVAFNGGINLADEYINQIERFGYWKDTAVM 24- 0 Query: 311 LKGKAVDSFLLLFLQMWSITEEKMLVAPYLGVHDDLVENEGYVIPYGDSPLDTDKVGENV 37- 0 L+G+ V SF L+FLQMWS T + APYL + + GYVIPY DSPLD +KVGENV Sbjct: 241 LEGEGVASFTLMFLQMWSTTNKOYEFAPYLTQNFHEIVANGYVIPYSDSPLDHEKVGENV 30- 0 Query: 371 YIDILNHAREYVYIMTPYLILDSELEHAIQFAAERGVDVRIIMPGIPDKPIPYALAKTYY 43- 0 YIDILN AR+YVYIMTPYLILDSE+EHA+QFAAERGVDV+IIMPGIPDK +P+ALAK Y+ Sbjct: 301 YIDILNQARDYVYIMTPYLILOSEMEHALQFAAERGVOVKIIMPGIPDKKVPFALAKRYF 36- 0 Query: 431 QALTKSGVKIYEY 443 AL +GVKIYE+ Sbjct: 361 PALLDAGVKIYEF 373 A related DNA sequence was identified in S. pyogenes <SEQ ID 6203> which encodes the amino acid sequence <SEQ ID 6204>. Analysis of this protein sequence reveals the following: TABLE-US-06131 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.86 Transmembrane 84-100 ( 81-104) INTEGRAL Likelihood = -8.33 Transmembrane 28-44 ( 23-49) INTEGRAL Likelihood = -6.74 Transmembrane 56-72 ( 53-74) ----- Final Results ----- bacterial membrane --- Certainty = 0.4545(Affirmative) < succ> bacterial outside --- Certainty = 20.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06132 >GP:AAA23240 GB:J02911 formtyltetrahydrofolate synthetase (FTHFS) (ttg start codon) (EC 6.3.4.3) [Moorella thermoacetica] Identities = 350/557 (62%), Positives = 438/557 (77%), Gaps = 2/557 (0%) Query: 2 VLSDIEIANSVTMEPISKVADQLGIDKEALCLYGKYKAKIDARQLVALKNKPDGELILVT 61 V SDIEIA + M+P+ ++A LGI ++ + LYGEYKAKI LK+KPDGKLILVT Sbjct: 4 VPSDIEIAQAAKMKPVMELARGLGIQEDEVELYGKYKAKISLDVYRRLKDKPDGKLILVT 63 Query: 62 AISPTPAGEGKTTTSVGLVDALSAIGKKAVIALREPSLGPVFGVKGGAAGGGHAQVVPME 121- AI+PTPAGEGKTTTSVGL DAL+ +GK+ ++ LREPSLGP FG+KGGAAGGG+AQVVPME Sbjct: 64 AITPTPAGEGKTTTSVGLTDALARLGKRVMVCLREPSLGPSFGIKGGAAGGGYAQVVPME 123- Query: 122 DINLHFTGDFHAIGVANNLLAALIDNHIHHGNSLGIDSRRITWKRVVDMNDRQLRHIVDG 18- 1 DINLHFTGD HA+ A+NLLAA++DNH+ GM L ID R ITW+RV+D+NDR LR+IV G Sbjct: 124 DINLHFTGDIHAVTYAHNLLAAMVDNHLQQGMVLNIDPRTITWRRVIDLNDRALRNIVIG 18- 3 Query: 182 LQGKVNGIPREDGYDITVASEIMAILCLSEMISDLKARLEKIIIGYNYQGEPVTAKDLKA 24- 1 L GK NG+PRE G+DI+VASE+MA LCL+ ++ DLK R +I++GY Y G+PVTA DL+A Sbjct: 184 LGGKANGVPRETGFDISVASEVMACLCLASDLMDLKERFSRIVVGYTYDGKPVTAGDLEA 24- 3 Query: 242 GGALAALLKDAIHPNLVQTLEHTPALIHGGPFANIAHGCNSVLATKLALKYGDYAVTEAG 30- 1 G++A L+KDAI PNLVQTLE+TPA IHGGPFANIAHGCNS++ATK ALK DY VTEAG Sbjct: 244 QGSMALLMKDAIKPNLVQTLEMTPAFIHGGPFANIAHGCNSIIATKTALKLADYVVTEAG 30- 3 Query: 302 FGADLGAEKFIDIKCRNSGLRPAAVVLVATIRALKMHGGVPKA0LATENVQAVVDGLPNL 36- 1 FGADLGAEKF D+KCR +G +P A V+VAT+RALKMHGGVPK+DLATEN++A++G NL Sbjct: 304 FGADLGAEKFYDVKCRYAGFKPDATVIVATVRALKMNGGVPKSDLATENLEALREGFANL 36- 3 Query: 362 DKHLANIQDVYGLPVVVAINKFPLDTDAELQAVYDACDKRGVOVVISDVWANGGAGGREL 42- 1 +KH+ NI +G+P VVAIN FP DT+AEL +Y+ C K G +V +S+VWA GG GG EL Sbjct: 364 EKHIENI-GKFGVPAVVAINAFPTDTEAELNLLYELCAKAGAEVALSEVWAKGGEGGLEL 42- 2 Query: 422 AEKVV-TLAEQDNQFRFVYEEDOSIETKLTKIVTKVYGGKGINLSSAAKRELADLERLGF 48- 0 A KV+ TL + + F +Y D SI+ K+ KI T++YG G+N ++ A + + E LG+ Sbjct: 423 ARKVLQTLESRPSNFNVLYNLDLSIKDKIAKIATEIYGADGVNYTAEADKAIQRYESLGY 48- 2 Query: 481 GNYPICNAKTQYSFSDDAKKLGAPTDFTVTISNLKVSAGAGFIVALTGAIMTMPGLPKVP 54- 0 GN P+ MAKTQYSFSDD KLG P +FT+T+ +++SAG IV +TGAIMTMPGLPK P Sbjct: 483 GNLPVVMAKTQYSFSDDNTKLGRPRNFTITVREVRLSAGGRLIVPITGAIMTNPGLPKRP 54- 2 Query: 541 ASETIDIDEEGNITGLF 557 A+ IDID +G ITGLF Sbjct: 543 AACNIDIDADGVITGLF 559 >GB:M37842unknown protein [Streptococcus mutans] (v . . . 517 e-145 >GP:AAA88609 GB:M37842 unknown protein .upsilon.Streptococcus mutans] Identities = 246/370 (66%), Positives = 303/370 (81%), Gaps = 1/370 (0%) Query: 68 VLYLVNSDMOAISRMTWLILINIAPLLGSLFLIYTKLDWGYRGLKQRINHLVDLSAPYLS 127- VLYLVNS MD +S +TWL++I+ P+LG+LFLIYTK DWGYR LK I PY Sbjct: 5 VLYLVNSQMOTLSIITWLLVILPFPILGTLFLIYTKQDWGYRELKSLIKKSTQAIKPYFQ 64 Query: 128 DDDAILEVLKDSTSTTYHLVQYLERSRGNFPIYNNTRVTYFPTGETFFDSLKEQLFLAKK 18- 7 D IL LK+S + TY+L QYL RS G FP+Y NT+VTYFP G++ F+ +K+QL A+K Sbjct: 65 YDQRILYKLKESHARTYNLAQYLHRS-GGFPVYKNTKVTYFPNGQSKFEEMKKQLLKAEK 123- Query: 188 YIFLEFFIIAEOQMWGSILSILEKKVSEGVEVRVLFDGMNELSTLSSOYAKRLEQIGIKA 24- 7 +IFLE+FIIAEG MWOEILSILE+KV EGVEVRV++DGM ELSTLS DYAKRLE+IGIKA Sbjct: 124 FIFLEYFIIAEGLMWGEILSILEQKVQEGVEVRVMYDGMLELSTLSFDYAKRLEKIGIKA 18- 3 Query: 248 KSFLPISPFISTYYNYRDHRKIVVIDGEVSFTGGINLADEYINEVERFGHWKDAGLMLEG 30- 7 K F PI+PF+STYYNYRDHRKI+VID +V+F GGINLADEYIN++ERFF+WKD +MLEG Sbjct: 184 KVFSPITPFVSTYYNYRDHRKILVIDNKVAFNGGINLADEYINQIERFGYWKDTAVMLEG 24- 3 Query: 308 EATDSFLILFLQMWSITEKELIIDPYLSDHSLKLPSDGYVIPYGDSPLDTDKIGKNVYID 36- 7 E SF ++FLQMWS T K+ PYL+ + ++ ++GYVIPY DSPLD +K+G+NVYID Sbjct: 244 EGVASFTLMFLQMWSTTNKDYEFAPYLTQNFNEIVANGYVIPYSDSPLDNEKVGENVYID 30- 3 Query: 368 ILNHAKEYVYIMTPYLILDSEMENALRFASERGVDIRIINPGVPDRGVPYALAKTYYKAL 42- 7 ILN A++YVYIMTPYLILDSEMEHAL+FA+ERGVD++IINPG+PDK VP+ALAK Y+ AL Sbjct: 304 ILNQARDYVYIMTPYLILDSEMEHALQFAAERGVDVKIINPGIPDKKVPFALAKRYFPAL 36- 3 Query: 428 MSSGVKIYEY 437 + +GVKIYE+ Sbjct: 364 LDAGVKIYEF 373 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06133 Identities = 362/524 (69%), Positives = 437/524 (83%) Query: 8 LISNKVKIVRLLNKSKKSLLRGIFSRTTVIAILLILQLLFLLASYSWLEQYRVWLATVEH 67 +I K K+ LL+K K LRGIFSRTT+I +L+ILQL+FL SY+W+EQYRVW+ +E Sbjct: 2 IIKKKAKVKYLLHKGKHGFLRGIFSRTTIIVLLIILQLVFLFQSYAWMEQYRVWITILES 61 Query: 68 ILTIGAVLYLVNSEMDALSRVTWLILVMIAPLLGAMFLMYTKFDWGYRGLKQRLETLIDE 127- + I VLYLVNS+MDA+SR+TWLIL+MIAPLLG++FL+YTK DWGYRGLKQR+ L+D Sbjct: 62 VFAITIVLYLVNSDMDAISRMTWLILIMIAPLLGSLFLIYTKLDWGYRGLKQRINHLVDL 121- Query: 128 SQIYLEDDPETLNQLKSSTSTTYHLVQYFEKANGNFPVYRNTDVTFLPTGEAFFEKMKEE 18- 7 S YL DD L LK STSTTYHLVQY E++ GNFP+Y NT VT+ PTGE FF+ +KE+ Sbjct: 122 SAPYLSDDDAILEVLKDSTSTTYNLVQYLERSRGNFPIYNNTRVTYFPTGETFFDSLKEQ 18- 1 Query: 188 LLKAKKYIFLEFFIIDEGIMWGEILSILEQKVEEGVEVRILYDGMISITKLSFDYTKRLE 24- 7 L AKKYIFLEFFII EG MWGEILSILE+KV EGVEVR+L+DGM E++ LS DY ERLE Sbjct: 182 LFLAKKYIFLEFFIIAEGQNWGEILSILEKKVSEGVEVRVLFDGMNELSTLSSDYAKRLE 24- 1 Query: 248 KIGIKAKAFSPISPFISTYYNYRDHRKIVVIDGVVGMTGGVNLADEYINHIELFGHWKDS 30- 7 +IGIKAK+F PISPFISTYYNYRDHRKIVVIDG V TGG+NLADEYIN +E FGHWKD+ Sbjct: 242 QIGIKAKSFLPISPFISTYYNYRDHRKIVVIDGEVSFTGGINLADEYINEVERFGHWKDA 30- 1 Query: 308 GIMLKGKAVDSFLLLFLQMWSITEEKMLVAPYLGVHDDLVENEGYVIPYGDSPLDTDKVG 36- 7 G+ML+G+A DSFL+LFLQMWSITS+++++ PYL H + ++GYVIPYGDSPLDTDK+G Sbjct: 302 GLMLEG.about.ATDSFLILFLQMWSITEKELIIDPYLSDHSLKLPSDGYVIPYGDSPLDTD- KIG 361 Query: 368 ENVYIDILNHAREYVYIMTPYLILDSELEHAIQFAAERGVDVRIIMPGIPDKPIPYALAK 42- 7 +NVYIDILNHA+EYVYIMTPYLILDSE+EHA++FA+ERGVD+RIIMPG+PDK +PYALAK Sbjct: 362 KNVYIDILNHAKEYVYIMTPYLILDSEMEHALRFASERGVDIRIIMPGVPDKGVPYALAK 42- 1 Query: 428 TYYQALTKSGVKIYEYTLGFVHSKIFLSDNTRAVVGTINLDYRSLYHHFECAVYLYKVDA 48- 7 TYY+AL SGVKIYEY GFVHSK+F+SDNTKAVVGTINLDYRSLYHHFECA YLY+V Sbjct: 422 TYYKALMSSGVKIYEYQPGFVHSKVFISDNTKAVVGTINLDYRSLYHHFECATYLYRVSV 48- 1 Query: 488 IQDIYRDYMDTLNKSRLVSLKDINNIPKFQKVIGIVTKTIAPLL 531 I DI D+ + +S L++ + P +QK+IG++ + IAPLL Sbjct: 482 IADIVNDFNEAQKQSLLMTSDHLTQRPWYQKLIGLLVRIIAPLL 525 A related GBS gene <SEQ ID 8953> and protein <SEQ ID 8954> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06134 Lipop Possible site: -1 Crend: 6 McG: Discrim Score: -8.80 GvH: Signal Score (-7.5): -1.94 Possible site: 53 >>> Seems to have no N-terminal signal sequence ALOM program count: 4 value: -10.03 threshold: 0.0 INTEGRAL Likelihood = -10.03 Transmembrane 34-50 ( 29-56) INTEGRAL Likelihood = -7.70 Transmembrane 90-106 ( 84-110) INTEGRAL Likelihood = -1.97 Transmembrane 62-78 ( 62-78) PERIPHERAL Likelihood = -1.22 199 modified ALOM score: 2.51 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5012(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00142## SEQ ID 8954 (GBS277d) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 150 (lane 18; MW 51 kDa), in FIG. 151 (lane 17 & 18; MW 51 kDa) and in FIG. 182 (lane 12; MW 51 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 151 (lane 15 & 16; MW 76 kDa) and in FIG. 58 (lane 5; MW 87 kDa). GBS277d-His was purified as shown in FIG. 235, lane 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2006 A DNA sequence (GBSx2116) was identified in S. agalactiae <SEQ ID 6205> which encodes the amino acid sequence <SEQ ID 6206>. This protein is predicted to be aspartate-semialdehyde dehydrogenase. Analysis of this protein sequence reveals the following: TABLE-US-06135 Possible site: 42 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9831> which encodes amino acid sequence <SEQ ID 9832> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06136 >GP: AAA26850 GB: J02667 aspartate beta-semialdehyde dehydrogenase (EC 1.2.1.11) [Streptococcus mutans] Identities = 261/357 (73%), Positives = 304/357 (85%), Gaps = 1/357 (0%) Query: 1 MGYTVAIVGATGAVGTQMIRQLEQSNLPIEQVKLLSSSRSAGKILHFKDEAIRVEETTKE 60 MGYTVAIVGATGAVGT+MI+QLEQS LP+++V+LLSSSRSAGK+L +KD+ + VE TTK+ Sbjct: 1 MGYTVAIVGATGAVGTRMIQQLEQSTLPVDKVRLLSSSRSAGKVLQYKDQDVTVELTTKD 60 Query: 61 SFYDVDIALFSAGGSISAKFAPYAVKSGAVVVDNTSYFRQNPDVPLVVPEVNAHAMIGHN 120- SF VDIALFSAGGS+SAKFAPYAVK+GAVVVDNTS+FRQNPDVPLVVPEVNA+AM HN Sbjct: 61 SFEAVDIALFSAGGSVSAKFAPYAVKAGAVVVDNTSHFRQNPDVPLVVPEVNAYAMDAHN 120- Query: 121 GIIACPNCSTIQMMIALEPIRQKWGIERVIVSTYQAVSGSGARAVEETKEQLRQVLNDNL 18- 0 GIIACPNCSTIQMM+ALEPIRQKWG+ RVIVSTYQAVSG+G A+ ET ++++V+ND + Sbjct: 121 GIIACPNCSTIQMMVALEPIRQKWGLSRVIVSTYQAVSGAGQSAINETVREIKEVVNDGV 18- 0 Query: 181 SPDQLIATVLPCSSDQKHYPIAFNALPQIDIFTDNDYTYEEMKMTLETKKIMEDATIKVS 24- 0 P + A + P D+KHYPIAFNAL QID+FTDNDYTYEEMKMT ETKKIME+ + VS Sbjct: 181 DPKAVHADIFPSGGDKKHYPIAFNALAQIDVFTDNDYTYEEMKMTNETKKIMEEPELPVS 24- 0 Query: 241 ATCVRIPVLSGHSESIYIETKELASISEIKKAIANFPGAVLQDLPSQQIYPQAINAVGHR 30- 0 A CVR+P+L HSE++YIETK++A I E+K AIA FPGAVL+D QIYPQA NAVG R Sbjct: 241 AHCVRVPILFSHSEAVYIETKDVAPIEEVKAAIAAFPGAVLEDDIKHQIYPQAANAVGSR 30- 0 Query: 301 ETFVGRIRKDLDQENGVHMWVVSDNLLKGAAWNSVQIAETLHKNGLVKPAKELKFEL 357 TFVGRIRKDLD ENG+HMWVVSDNLLKGAAWNS+ A LH+ GLV+ ELKFEL Sbjct: 301 -TFVGRIRKDLDIENGIHMWVVSDNLLKGAAWNSIITANRLHERGLVRSTSELKFEL 356 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2007 A DNA sequence (GBSx2117) was identified in S. agalactiae <SEQ ID 6207> which encodes the amino acid sequence <SEQ ID 6208>. Analysis of this protein sequence reveals the following:

TABLE-US-06137 Possible site: 22 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.66 Transmembrane 33-49 (33-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.2062(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 500. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2008 A DNA sequence (GBSx2119) was identified in S. agalactiae <SEQ ID 6209> which encodes the amino acid sequence <SEQ ID 6210>. Analysis of this protein sequence reveals the following: TABLE-US-06138 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3853(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2009 A DNA sequence (GBSx2120) was identified in S. agalactiae <SEQ ID 6211> which encodes the amino acid sequence <SEQ ID 6212>. This protein is predicted to be unnamed protein product (clpP). Analysis of this protein sequence reveals the following: TABLE-US-06139 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3883(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10061> which encodes amino acid sequence <SEQ ID 10062> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 6213> which encodes the amino acid sequence <SEQ ID 6214>. Analysis of this protein sequence reveals the following: TABLE-US-06140 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2682(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06141 Identities = 175/196 (89%), Positives = 187/196 (95%) Query: 5 MIPVVIEQTSRGERSYDIYSRLLKDRIIMLTGQVEDNMANSIIAQLLFLDAQDNTKDIYL 64 MIPVVIEQTSRGERSYDIYSRLLKDRIIMLTG VEDNMANS+IAQLLFLDAQDNTKDIYL Sbjct: 1 MIPVVIEQTSRGERSYDIYSRLLKDRIIMLTGPVEDNMANSVIAQLLFLDAQDNTKDIYL 60 Query: 65 YVNTPGGSVSAGLAIVDTMNFIKSDVQTIVMGMAASMGTIIASSGAKGKRFMLPNAEYMI 124- YVNTPGGSVSAGLAIVDTMNFIK+DVQTIVMGMAASMGT+IASSG KGKRFMLPNAEYMI Sbjct: 61 YVNTPGGSVSAGLAIVDTMNFIKADVQTIVMGMAASMGTVIASSGTKGKRFMLPNAEYMI 120- Query: 125 HQPMGGTGGGTQQSDMAIAAEHLLKTRHTLEKILADNSGQSIEKVHDDAERDRWMSAQET 18- 4 HQPMGGTGGGTQQ+DMAIAAEHLLKTRH LEKILA N+G++I+++H DAERD WMSA+ET Sbjct: 121 HQPMGGTGGGTQQTDMAIAAEHLLKTRHRLEKILAQNAGKTIKQIHKDAERDYWMSAEET 18- 0 Query: 185 LDYGFIDAIMENNNLQ 200 L YGFID IMENN L+ Sbjct: 181 LAYGFIDEIMENNELK 196 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2010 A DNA sequence (GBSx2121) was identified in S. agalactiae <SEQ ID 6215> which encodes the amino acid sequence <SEQ ID 6216>. This protein is predicted to be uracil phosphoribosyltransferase (upp). Analysis of this protein sequence reveals the following: TABLE-US-06142 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.43 Transmembrane 127-143 (127-144) INTEGRAL Likelihood = -0.06 Transmembrane 72-88 (72-89) INTEGRAL Likelihood = -0.06 Transmembrane 154-170 (154-170) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10063> which encodes amino acid sequence <SEQ ID 10064> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06143 >GP: AAA26890 GB: L07793 uracil phosphoribosyltransferase [Streptococcus salivarius] Identities = 192/209 (91%), Positives 202/209 (95%) Query: 1 MGKFQVISHPLIQHKLSILRRTTTSTKDFRELVDEIAMLMGYEVSRDLPLEDVEIQTPVA 60 MGKFQVISHPLIQHKLSILRR TSTKDFRELV+EIAMLMGYEVSRDLPLE+VEIQTP+ Sbjct: 1 MGKFQVISHPLIQHKLSILRREDTSTKDFRELVNEIAMLMGYEVSRDLPLEEVEIQTPIT 60 Query: 61 TTVQKQLAGKKLAIVPILRAGIGMVDGFLSLVPAAKVGHIGMYRDEETFQPVEYLVKLPE 120- TVQKQL+GKKLAIVPILRAGIGMVDGFLSLVPAAKVGHIGMYRDEET +PVEYLVKLPE Sbjct: 61 KTVQKQLSGKKLAIVPILRAGIGMVDGFLSLVPAAKVGHIGMYRDEETLEPVEYLVKLPE 120- Query: 121 DIDQRQIFVVDPMLATGGSAILAVDSLKKRGAASIKFVCLVAAPEGVAALQEAHPDVDIY 18- 0 DIDQRQIFVVDPMLATGGSAILAVDSLKKRGAA+IKFVCLVAAPEGV LQ+AHPD+DIY Sbjct: 121 DIDQRQIFVVDPMLATGGSAILAVDSLKKRGAANIKFVCLVAAPEGVKKLQDAHPDIDIY 18- 0 Query: 181 TAALDEKLNEHGYIVPGLGDAGDRLFGTK 209 TA+LDEKLNE+GYIVPGLGDAGDRLFGTK Sbjct: 181 TASLDEKLNENGYIVPGLGDAGDRLFGTK 209 A related DNA sequence was identified in S. pyogenes <SEQ ID 6217> which encodes the amino acid sequence <SEQ ID 6218>. Analysis of this protein sequence reveals the following: TABLE-US-06144 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.59 Transmembrane 72-88 (72-89) INTEGRAL Likelihood = -0.22 Transmembrane 127-143 (127-144) ----- Final Results ----- bacterial membrane --- Certainty = 0.1235(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to uracil phosphoribosyltransferase from S. salivarius: TABLE-US-06145 >GP: AAA26890 GB: L07793 uracil phosphoribosyltransferase [Streptococcus salivarius] Identities = 191/209 (91%), Positives = 205/209 (97%) Query: 1 MGKCQVISHPLIQHKLSILRRQTTSTKDFRELVNEIAMLMGYEVSRDLPLEDVDIQTPVS 60 MGK QVISHPLIQHKLSILRR+ TSTKDFRELVNEIAMLMGYEVSRDLPLE+V+IQTP++ Sbjct: 1 MGKFQVISHPLIQHKLSILRREDTSTKDFRELVNEIAMLMGYEVSRDLPLEEVEIQTPIT 60 Query: 61 KTVQKQLAGKKLAIVPILRAGIGMVDGLLSLVPAAKVGHIGMYRNEETLEPVEYLVKLPE 120- KTVQKQL+GKKLAIVPILRAGIGMVDG LSLVPAAKVGHIGMYR+EETLEPVEYLVKLPE Sbjct: 61 KTVQKQLSGKKLAIVPILRAGIGMVDGFLSLVPAAKVGHIGMYRDEETLEPVEYLVKLPE 120- Query: 121 DINQRQIFLVDPMLATGGSAILAVDSLKKRGAANIKFVCLVAAPEGVKKLQEAHPDIDIF 18- 0 DI+QRQIF+VDPMLATGGSAILAVDSLKKRGAANIKFVCLVAAPEGVKKLQ+AHPDIDI+ Sbjct: 121 DIDQRQIFVVDPMLATGGSAILAVDSLKKRGAANIKFVCLVAAPEGVKKLQDAHPDIDIY 18- 0 Query: 181 TAALDDHLNEHGYIVPGLGDAGDRLFGTK 209 TA+LD+ LNE+GYIVPGLGDAGDRLFGTK Sbjct: 181 TASLDEKLNENGYIVPGLGDAGDRLFGTK 209 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06146 Identities = 190/209 (90%), Positives = 201/209 (95%) Query: 1 MGKFQVISHPLIQHKLSILRRTTTSTKDFRELVDEIAMLMGYEVSRDLPLEDVEIQTPVA 60 MGK QVISHPLIQHKLSILRR TTSTKDFRELV+EIAMLMGYEVSRDLPLEDV+IQTPV+ Sbjct: 1 MGKCQVISHPLIQHKLSILRRQTTSTKDFRELVNEIAMLMGYEVSRDLPLEDVDIQTPVS 60 Query: 61 TTVQKQLAGKKLAIVPILRAGIGMVDGFLSLVPAAKVGHIGMYRDEETFQPVEYLVKLPE 120- TVQKQLAGKKLAIVPILRAGIGMVDG LSLVPAAKVGHIGMYR+EET +PVEYLVKLPE Sbjct: 61 KTVQKQLAGKKLAIVPILRAGIGMVDGLLSLVPAAKVGHIGMYRNEETLEPVEYLVKLPE 120- Query: 121 DIDQRQIFVVDPMLATGGSAILAVDSLKKRGAASIKFVCLVAAPEGVAALQEAHPDVDIY 18- 0 DI+QRQIF+VDPMLATGGSAILAVDSLKKRGAA+IKFVCLVAAPEGV LQEAHPD+DI+ Sbjct: 121 DINQRQIFLVDPMLATGGSAILAVDSLKKRGAANIKFVCLVAAPEGVKKLQEAHPDIDIF 18- 0 Query: 181 TAALDEKLNEHGYIVPGLGDAGDRLFGTK 209 TAALD+ LNEHGYIVPGLGDAGDRLFGTK Sbjct: 181 TAALDDHLNEHGYIVPGLGDAGDRLFGTK 209 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2011 A DNA sequence (GBSx2122) was identified in S. agalactiae <SEQ ID 6219> which encodes the amino acid sequence <SEQ ID 6220>. This protein is predicted to be hemolysin (patB). Analysis of this protein sequence reveals the following: TABLE-US-06147 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.29 Transmembrane 88-104 (86-106) ----- Final Results ----- bacterial membrane --- Certainty = 0.2317(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06148 >GP: CAB15133 GB: Z99120 aminotransferase [Bacillus subtilis] Identities = 130/381 (34%), Positives = 221/381 (57%), Gaps = 4/381 (1%) Query: 5 DFTSLPERFSSNTIKWKAVQK---DQEILPLWIADMDFPIFPEMSEAIEDFSHQMVFGYD 61 +F ER + ++KW + + LP+W+ADNDF ++EA+++ +FGY Sbjct: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 Query: 62 SPKDSLYQAISNWEVQEHGYQFDKKSLLLIDGVVPAISVAIQAFTKEGDAVLINTPVYPP 121- +P A+ W HG++ + +S+ GVV A+S+A+QAFT+ GD V++ PVY P Sbjct: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121- Query: 122 FARTIKYNNRHLVSNSLLNNNQYFEIDFKQLEKDIIENNVKLYIFCSPHNPGGRVWTKGE 18- 1 F ++ N RH++ N LL + + IDF+ LE + + +V L+I C+PHNP GR W++ + Sbjct: 122 FYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRED 18- 1 Query: 182 IQKIGDICKRYNVILVSDEIHQDLVLFDNVHHSFNTVDSSFKELSVILSSATKTFNIAGT 24- 1 + K+G++C + V +VSDEIH DL+L+ + H F ++ F ++SV ++ +KTFNIAG Sbjct: 182 LLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNIAGL 24- 1 Query: 242 KNSFAIIENEKLRSDFKKRQIANNQQEISSLGLLATEVAFTKEKQWLKALKMELEGSIEY 30- 1 + S II + R+ F N +++ + A E A++K WL L +E ++ Sbjct: 242 QASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIEKNMNE 30- 1 Query: 302 LYEQL-TQKTNIKVMKPEGTYLVWLDFSAYNLTHLEIQEKLRYDAKLILNDGLTFGKEGK 36- 0 L T+ +K+MKP+ +YL+WLDFSAY L+ E+Q+++ K+IL G +G G+ Sbjct: 302 AEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPGGE 36- 1 Query: 361 KHARINVAAPRSVIEEAVLRL 381 R+N + +++ + R+ Sbjct: 362 GFMRLNAGCSLATLQDGLRRI 382 There is also homology to SEQ ID 1006. SEQ ID 6220 (GBS392) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 75 (lane 2; MW 46.4 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 83 (lane 5; MW 71 kDa). GBS392-GST was purified as shown in FIG. 217, lane 4. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2012 A DNA sequence (GBSx2123) was identified in S. agalactiae <SEQ ID 6221> which encodes the amino acid sequence <SEQ ID 6222>. This protein is predicted to be rRNA methylase, SpoU family (cspR). Analysis of this protein sequence reveals the following: TABLE-US-06149 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1436(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06150 >GP: AAB02738 GB: U58864 CspR [Bacillus subtilis] Identities = 84/155 (54%), Positives = 120/155 (77%), Gaps = 3/155 (1%) Query: 19 HIVLFEPQIPANTGNIARTCAATNAPLHIIRPMGFPIDDKKMKRAGLDYWDKLDVSFYDG 78 - H+VL++P+IPANTGNIARTCAATN LH+IRP+GF DDK +KRAGLDYW+ ++V ++D Sbjct: 4 HVVLYQPEIPANTGNIARTCAATNTTLHLIRPLGFSTDDKMLKRAGLDYWEFVNVVYHDS 63 Query: 79 LEE-FMLSCRGKVHLISKFADKVYSDENYND-DQDHYFMFGREDKGLPETFMREHAEKAL 136- LEE F +GK I+KF + ++ +Y D D+D++F+FGRE GLP+ ++ + ++ L Sbjct: 64 LEELFEAYKKGKFFFITKFGQQPHTSFDYTDLDEDYFFVFGRETSGLPKDLIQNNMDRCL 123- Query: 137 RIPMNDEHVRSLNVSNTVCMIVYEALRQQSFPNLE 171 R+PM EHVRSLN+SNT ++VYEALRQQ++ +L+ Sbjct: 124 RLPMT-EHVRSLNLSNTAAILVYEALRQQNYRDLK 157 A related DNA sequence was identified in S. pyogenes <SEQ ID 6223> which encodes the amino acid sequence <SEQ ID 6224>. Analysis of this protein sequence reveals the following: TABLE-US-06151 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2236(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06152 Identities = 135/182 (74%), Positives = 150/182 (82%) Query: 1 MNIETLTQKNHRSDSGRNHIVLFEPQIPANTGNIARTCAATNAPLHIIRPMGFPIDDKKM 60 M + L KN + RNHIVLF+PQIP NTGNIARTCAATNAPLHII+PMGFPIDD+KM Sbjct: 13 MTTKELINKNDKVKKARNHIVLFQPQIPQNTGNIARTCAATNAPLHIIKPMGFPIDDRKM 72 Query: 61 KRAGLDYWDKLDVSFYDGLEEFMLSCRGKVHLISKFADKVYSDENYNDDQDHYFMFGRED 120- KRAGLDYWDKL++ FYD LE+F+ C G++HLISKFA YS Y D HYF+FGRED Sbjct: 73 KRAGLDYWDKLELHFYDHLEQFINQCHGQLHLISKFAVNNYSQATYADGDSHYFLFGRED 132- Query: 121 KGLPETFMREHAEKALRIPMNDEHVRSLNVSNTVCMIVYEALRQQSFPNLELSHTYENDK 18- 0 GLPE FMREHAEKALRIPMNDSHVRSLNVSNTVCM++YEALRQQ F LEL HTYE+DK Sbjct: 133 TGLPEDFMREHAEKALRIPMNDEHVRSLNVSNTVCMVIYEALRQQGFQGLELKHTYEHDK 19- 2 Query: 181 LK 182 LK Sbjct: 193 LK 194 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2013 A DNA sequence (GBSx2124) was identified in S. agalactiae <SEQ ID 6225> which encodes the amino acid sequence <SEQ ID 6226>. Analysis of this protein sequence reveals the following: TABLE-US-06153 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.79 Transmembrane 82-98 (69-100) INTEGRAL Likelihood = -6.48 Transmembrane 27-43 (24-47) INTEGRAL Likelihood = -5.52 Transmembrane 132-148 (126-151) INTEGRAL Likelihood = -5.10 Transmembrane 162-178 (161-185) ----- Final Results ----- bacterial membrane --- Certainty = 0.3718(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9411> which encodes amino acid sequence <SEQ ID 9412> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06154 >GP: CAB13143 GB: Z99110 similar to amino acid permease [Bacillus subtilis] Identities = 46/143 (32%), Positives = 81/143 (56%), Gaps = 1/143 (0%) Query: 3 FAYDGWTIFVNIAPEVKNPKKNLPLAFVIGPALILLSYLAFFYGLTQILGASFIMTTGND 62 FAYDGW + + E+KNP+K LP A G ++ Y+ + L IL A+ I+T G + Sbjct: 203 FAYDGWILLAALGGEMKNPEKLLPRAMTGGLLIVTAIYIFINFALLHILSANEIVTLGEN 26- 2 Query: 63 AINYAANIIFGPSVGRLLSFIVILSVLGVANGLLLGTMRLPQAFAERGWIK-SERMANIN 121- A + AA ++FG G+L+S +I+S+ G NG +L R+ A AER + +E++++++ Sbjct: 263 ATSTAATMLFGSIGGKLISVGIIVSIFGCLNGKVLSFPRVSFAMAERKQLPFAEKLSHVH 32- 2 Query: 122 LKYQMSLPASLTVTAVAIFWLFV 144 ++ A A+A+ + + Sbjct: 323 PSFRTPWIAISFQIALALIMNLI 345 There is also homology to SEQ ID 3114. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2014 A DNA sequence (GBSx2125) was identified in S. agalactiae <SEQ ID 6227> which encodes the amino acid sequence <SEQ ID 6228>. Analysis of this protein sequence reveals the following: TABLE-US-06155 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1849(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9439> which encodes amino acid sequence <SEQ ID 9440> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06156 >GP: AAD23454 GB: AF117741 cochaperonin GroES [Streptococcus pneumoniae] Identities = 31/52 (59%), Positives = 42/52 (80%) Query: 2 GDGIRTLTGELVAPSVAEGDTVLVENGAGLEVKDGNEKVTVVRESDIVAVVK 53 G G+RTL G+LVAPSV GD VLVE AGL+VKDG+EK +V E++I+A+++ Sbjct: 42 GQGVRTLNGDLVAPSVKTGDRVLVEAHAGLDVKDGDEKYIIVGEANILAIIE 93 A related DNA sequence was identified in S. pyogenes <SEQ ID 6229> which encodes the amino acid sequence <SEQ ID 6230>. Analysis of this protein sequence reveals the following: TABLE-US-06157 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3290(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-06158 Identities = 29/49 (59%), Positives = 39/49 (79%) Query: 4 GIRTLTGELVAPSVAEGDTVLVENGAGLEVKDGNEKVTVVRESDIVAVV 52 G+RT+TG+ V PSV+ G VLVENG LEV +EKV+++RESDI+A+V Sbjct: 60 GVRTITGDSVLPSVSVGQEVLVENGHDLEVTVDDEKVSIIRESDIIAIV 108 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2015 A DNA sequence (GBSx2126) was identified in S. agalactiae <SEQ ID 6231> which encodes the amino acid sequence <SEQ ID 6232>. Analysis of this protein sequence reveals the following: TABLE-US-06159 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1272(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06160 >GP: AAD23455 GB: AF117741 chaperonin GroEL [Streptococcus pneumoniae] Identities = 472/539 (87%), Positives = 513/539 (94%), Gaps = 1/539 (0%) Query: 1 MAKDIKFSADARSAMVRGVDILADTVKVTLGPKGRNVVLEKAFGSPLITNDGVTIAKEIE 60 M+K+IKFS+DARSAMVRGVDILADTVKVTLGPK RNVVLEK+FGSPLITNDGVTIAKEIE Sbjct: 1 MSKEIKFSSDARSAMVRGVDILADTVKVTLGPKDRNVVLEKSFGSPLITNDGVTIAKEIE 60 Query: 61 LEDHFENMGAKLVSEVASKTNDIAGDGTTTATVLTQAIVREGLKNVTAGANPIGIRRGIE 120- LEDHFENMGAKLVSE+ASKTNDIAGDGTTTATVLTQAIVREG+KNVTAGANPIGIRRGIE Sbjct: 61 LEDHFENMGAKLVSEIASKTNDIAGDGTTTATVLTQAIVREGIKNVTAGANPIGIRRGIE 120- Query: 121 TAVSAAVEELKEIAQPVSGKEAIAQVAAVSSRSEKVGEYISEAMERVGNDGVITIEESRG 18- 0 TAV+AAVE LK A PV+ KEAI+QVAAVSSRSEKVGEYISEAME+VG DGVITIEESRG Sbjct: 121 TAVAAAVEALKNNAIPVANKEAISQVAAVSSRSEKVGEYISEAMEKVGKDGVITIEESRG 18- 0 Query: 181 METELEVVEGMQFDRGYLSQYMVTDNEKNVSELENPYILITDKKISNIQEILPLLEEVLK 24- 0 METELEVVEGMQFDRGYLSQYMVTD+EKMV++LENPYILITDKKISNIQEILPLLE +L+ Sbjct: 181 METELEVVEGMQFDRGYLSQYMVTDSEKMVADLENPYILITDKKISNIQEILPLLESILQ 24- 0 Query: 241 TNRPLLIIADDVDGEALPTLVLNKIRGTFNVVAVKAPGFGDRRKAMLEDIAILTGGTVVT 30- 0 +NRPLLIIADDVDGEALPTLVLNKIRGTFNVVAVKAPGFGDRRKAMLEDIAILTGGTV+T Sbjct: 241 SNRPLLIIADDVDGEALPTLVLNKIRGTFNVVAVKAPGFGDRRKAMLEDIAILTGGTVIT 30- 0 Query: 301 EDLGLDLKDATMQVLGQSAKVTVDKDSTVIVEGAGDSSAIANRVAIIKSQMEATTSDFDR 36- 0 EDLGL+LKDAT++ LGQ+A+VTVDKDSTVIVEGAG+ AI++RVA+IKSQ+E TTS+FDR Sbjct: 301 EDLGLELKDATIEALGQAARVTVDKDSTVIVEGAGNPEAISHRVAVIKSQIETTTSEFDR 36- 0 Query: 361 EKLQERLAKLAGGVAVIKVGAATETELKEMKLRIEDALNATRAAVEEGIVSGGGTALVNV 42- 0 EKLQERLAKL+GGVAVIKVGAATETELKEMKLRIEDALNATRAAVEEGIV+GGGTAL NV Sbjct: 361 EKLQERLAKLSGGVAVIKVGAATETELKEMKLRIEDALNATRAAVEEGIVAGGGTALANV 42- 0 Query: 421 IEKVAALKLNGDEETGRNIVLRALEEPVRQIAYNAGYEGSVIIERLKQSEIGTGFNAANG 48- 0 I A L+L GDE TGRNIVLRALEEPVRQIA+NAG+EGS++I+RLK +E+G GFNAA G Sbjct: 421 IPAEATLELTGDEATGRNIVLRALEEPVRQIAHNAGFEGSIVIDRLKNAELGIGFNAATG 48- 0 Query: 481 EWVDMVTTGIIDPVKVTRSALQNAASVASLILTTEAVVANKPEPEAPTAPAMDPSMMGG 539- EWV+M+ GIIDPVKV+RSALQNAASVASLILTTEAVVANKPEP AP APAMDPSMMGG Sbjct: 481 EWVNMIDQGIIDPVKVSRSALQNAASVASLILTTEAVVANKPEPVAP-APAMDPSMMGG 538- A related DNA sequence was identified in S. pyogenes <SEQ ID 6233> which encodes the amino acid sequence <SEQ ID 6234>. Analysis of this protein sequence reveals the following: TABLE-US-06161 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1070(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06162 Identities = 491/543 (90%), Positives = 515/543 (94%), Gaps = 3/543 (0%) Query: 1 MAKDIKFSADARSAMVRGVDILADTVKVTLGPKGRNVVLEKAFGSPLITNDGVTIAKEIE 60 MAKDIKFSADAR+AMVRGVD+LADTVKVTLGPKGRNVVLEKAFGSPLITNDGVTIAKEIE Sbjct: 3 MAKDIKFSADARAAMVRGVDMLADTVKVTLGPKGRNVVLEKAFGSPLITNDGVTIAKEIE 62 Query: 61 LEDHFENMGAKLVSEVASKTNDIAGDGTTTATVLTQAIVREGLKNVTAGANPIGIRRGIE 120- LEDHFENMGAKLVSEVASKTNDIAGDGTTTATVLTQAIV EGLKNVTAGANPIGIRRGIE Sbjct: 63 LEDHFENMGAKLVSEVASKTNDIAGDGTTTATVLTQAIVHEGLKNVTAGANPIGIRRGIE 122- Query: 121 TAVSAAVEELKEIAQPVSGKEAIAQVAAVSSRSEKVGEYISEAMERVGNDGVITIEESRG 18- 0 TA + AVE LK IAQPVSGKEAIAQVAAVSSRSEKVGEYISEAMERVGNDGVITIEESRG Sbjct: 123 TATATAVEALKAIAQPVSGKEAIAQVAAVSSRSEKVGEYISEAMERVGNDGVITIEESRG 18- 2 Query: 181 METELEVVEGMQFDRGYLSQYMVTDNEKMVSELENPYILITDKKISNIQEILPLLEEVLK 24- 0 METELEVVEGMQFDRGYLSQYMVTDNEKMV++LENP+ILITDKK+SNIQ+ILPLLEEVLK Sbjct: 183 METELEVVEGMQFDRGYLSQYMVTDNEKMVADLENPFILITDKKVSNIQDILPLLEEVLK 24- 2 Query: 241 TNRPLLIIADDVDGEALPTLVLNKIRGTFNVVAVKAPGFGDRRKAMLEDIAILTGGTVVT 30- 0 TNRPLLIIADDVDGEALPTLVLNKIRGTFNVVAVKAPGFGDRRKAMLEDIAILTGGTV+T Sbjct: 243 TNRPLLIIADDVDGEALPTLVLNKIRGTFNVVAVKAPGFGDRRKAMLEDIAILTGGTVIT 30- 2 Query: 301 EDLGLDLKDATMQVLGQSAKVTVDKDSTVIVEGAGDSSAIANRVAIIKSQMEATTSDFDR 36- 0 EDLGL+LKDATM LGQ+AK+TVDKDSTVIVEG+G S AIANR+A+IKSQ+E TTSDFDR Sbjct: 303 EDLGLELKDATMTALGQAAKITVDKDSTVIVEGSGSSEAIANRIALIKSQLETTTSDFDR 36- 2 Query: 361 EKLQERLAKLAGGVAVIKVGAATETELKEMKLRIEDALNATRAAVEEGIVSGGGTALVNV 42- 0 EKLQERLAKLAGGVAVIKVGA TET LKEMKLRIEDALNATRAAVEEGIV+GGGTAL+ V Sbjct: 363 EKLQERLAKLAGGVAVIKVGAPTETALKEMKLRIEDALNATRAAVEEGIVAGGGTALITV 42- 2 Query: 421 IEKVAALKLNGDEETGRNIVLRALEEPVRQIAYNAGYEGSVIIERLKQSEIGTGFNAANG 48- 0 IEKVAAL+L GD+ TGRNIVLRALEEPVRQIA NAGYEGSV+I++LK S GTGFNAA G Sbjct: 423 IEKVAALELEGDDATGRNIVLRALEEPVRQIALNAGYEGSVVIDKLKNSPAGTGFNAATG 48- 2 Query: 481 EWVDMVTTGIIDPVKVTRSALQNAASVASLILTTEAVVANKPEP--EAPTAPA-MDPSMM 53- 7 EWVDM+ TGIIDPVKVTRSALQNAASVASLILTTEAVVANKPEP AP PA MDP MM Sbjct: 483 EWVDMIKTGIIDPVKVTRSALQNAASVASLILTTEAVVANKPEPATPAPAMPAGMDPGMM 54- 2 Query: 538 GGF 540 GGF Sbjct: 543 GGF 545 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2016 A DNA sequence (GBSx2127) was identified in S. agalactiae <SEQ ID 6235> which encodes the amino acid sequence <SEQ ID 6236>. Analysis of this protein sequence reveals the following: TABLE-US-06163 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3216(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10247> which encodes amino acid sequence <SEQ ID 10248> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06164 >GP: BAB06113 GB: AP001515 transcriptional regulator (GntR family) [Bacillus halodurans] Identities = 50/171 (29%), Positives = 86/171 (50%), Gaps = 17/171 (9%) Query: 21 HVQVYNKIFNMIQDGTYSPGMQLPSEPELAGQLNVSRATLRKSLALLQEDHLVKNIRGKG 80 - ++QV +K+ + ++ G Y G +LPSE EL+ QL VSRATLR++L LL+E+ +V G G Sbjct: 10 YLQVIDKLKHDMEAGVYEEGEKLPSEFELSKQLGVSRATLREALRLLEEEGVVVRRHGVG 69 Query: 81 NFIRENSSNLSENGYENRQHPIKTCLTSKITEVELE--------FRVEVPAEAITASLKQ 132- F+ ++ L G E +T I ++E +++E + Sbjct: 70 TFV--HTKPLFSAGIEELY-----SVTDMIRHADMEPGTIFLSSYQIEATDDDKRRFQTD 122- Query: 133 ETPVVVIADRWYHTDDGPLAYTLSFIPIELISDAEISLHDTKQLLNFIEEG 183 +++ +R D P+ Y L +P ELI + S+H+ +L+ +E G Sbjct: 123 NLDQLMMIERVRTADGVPIVYCLDKLPAELI--GQHSVHEINSILDHLESG 171 A related DNA sequence was identified in S. pyogenes <SEQ ID 6237> which encodes the amino acid sequence <SEQ ID 6238>. Analysis of this protein sequence reveals the following: TABLE-US-06165 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2297(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06166 Identities = 154/244 (63%), Positives = 189/244 (77%) Query: 7 MPKNELNNKLNKLKHVQVYNKIFNMIQDGTYSPGMQLPSEPELAGQLNVSRATLRKSLAL 66 M N+L KL KLKHVQVYN IF +IQDGTYSPGMQLPSEPELA QLNVSR TLRKSLAL Sbjct: 1 MSTNDLTKKLKKLKHVQVYNTIFQLIQDGTYSPGMQLPSEPELARQLNVSRMTLRKSLAL 60 Query: 67 LQEDHLVKNIRGKGNFIRENSSNLSENGYENRQHPIKTCLTSKITEVELEFRVEVPAEAI 126- LQEDHL+KNIRGKGNFI + G+E QHPI L+S IT+VELE+R+EVP AI Sbjct: 61 LQEDHLIKNIRGKGNFILKTPETKYHQGFEYLQHPIYASLSSDITKVELEYRIEVPTVAI 120- Query: 127 TASLKQETPVVVIADRWYHTDDGPLAYTLSFIPIELISDAEISLHDTKQLLNFIEEGIYQ 18- 6 TASLKQETPVV+I DRWYH+ + +AY+LSFIPIE+IS I+L+ + LL F+EE IY+ Sbjct: 121 TASLKQETPVVIIVDRWYHSQNKAIAYSLSFIPIEVISKYAINLNQEEPLLTFLEEKIYE 18- 0 Query: 187 EGISSHSQSHLGYATSGNFSATKYTLSDHGQFILIQETIFKQEKILMCNKHYVPIEHFEL 24- 6 G +SHS + +GY +GN++ATKYTLS++ FILIQET++ + IL+ KHYVP + F+L Sbjct: 181 SGKASHSCNQIGYTKTGNYTATKYTLSENSAFILIQETLYNGKDILVSTKHYVPADLFDL 24- 0 Query: 247 SITS 250 + S Sbjct: 241 KVQS 244 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2017 A DNA sequence (GBSx2128) was identified in S. agalactiae <SEQ ID 6239> which encodes the amino acid sequence <SEQ ID 6240>. This protein is predicted to be purine nucleoside phosphorylase (udp-1). Analysis of this protein sequence reveals the following: TABLE-US-06167 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3910(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06168 >GP: AAC65977 GB: AE001270 uridine phosphorylase (udp) [Treponema pallidum] Identities = 145/246 (58%), Positives = 171/246 (68%) Query: 11 QYHLQIRPGDVGRYVIMPGDPKRCAKIAEHFDNAVLVADSREYVTYTGTLNGEKVSVTST 70 - +YH+ ++ D+G YVI+PGDP R KIA+HF + V +REYVTYTGTL VSV ST Sbjct: 10 EYHIGLKASDIGHYVILPGDPARSEKIAQHFSHPHKVGHNREYVTYTGTLCETPVSVMST 69 Query: 71 GIGGPSASIAMEELKLCGADTFIRVGTCGGIDLDVKGGDIVIATGAIRMEGTSKEYAPIE 130- GIGGPS +I +EEL GA TFIRVGT GG+ D+ G +VIATGAIR EGTSKEYAP+E Sbjct: 70 GIGGPSTAIGVEELIHLGAHTFIRVGTSGGMQPDILAGTVVIATGAIRFEGTSKEYAPVE 129- Query: 131 FPAVADLEVTNALVNAAKKLGYTSHAGVVQCKDAFYGQHEPERMPVSYELLNKWEAWKRL 19- 0 FPAV D VT AL +AA+ + GVVQCKD FYGQH P MPV EL KW AW Sbjct: 130 FPAVPDFTVTAALKHAAEDVQVRHALGVVQCKDNFYGQHSPHTMPVHAELTQKWHAWIAC 18- 9 Query: 191 GTKASEMESAALFVAASHLGVRCGSDFLVVGNQERNALGMDNPMAHDTEAAIQVAVEALR 25- 0 T ASEMESAALFV S VR G+ LV+GNQ R A G+++ HDTE AI+VAVEA++ Sbjct: 190 NTLASEMESAALFVLGSVRRVRTGAVLLVIGNQTRRAQGLEDIQVHDTENAIRVAVEAVK 24- 9 Query: 251 TLIEND 256 LI D Sbjct: 250 LLITQD 255 A related DNA sequence was identified in S. pyogenes <SEQ ID 6241> which encodes the amino acid sequence <SEQ ID 6242>. Analysis of this protein sequence reveals the following: TABLE-US-06169 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3910(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06170 Identities = 259/259 (100%), Positives = 259/259 (100%) Query: 1 MQNYSGEVGLQYHLQIRPGDVGRYVIMPGDPKRCAKIAEHFDNAVLVADSREYVTYTGTL 60 MQNYSGEVGLQYHLQIRPGDVGRYVIMPGDPKRCAKIAENFDNAVLVADSREYVTYTGTL Sbjct: 1 MQNYSGEVGLQYHLQIRPGDVGRYVIMPGDPKRCAKIAEHFDNAVLVADSREYVTYTGTL 60 Query: 61 NGEKVSVTSTGIGGPSASIAMEELKLCGADTFIRVGTCGGIDLDVKGGDIVIATGAIRME 120- NGEKVSVTSTGIGGPSASIAMEELKLCGADTFIRVGTCGGIDLDVKGGDIVIATGAIRME Sbjct: 61 NGEKVSVTSTGIGGPSASIAMEELKLCGADTFIRVGTCGGIDLDVKGGDIVIATGAIRME 120- Query: 121 GTSKEYAPIEFPAVADLEVTNALVNAAKKLGYTSHAGVVQCRDAFYGQHEPERMPVSYEL 18- 0 GTSKEYAPIEFPAVADLEVTNALVNAAKKLGYTSHAGVVQCKDAFYGQHEPERMPVSYEL Sbjct: 121 GTSKEYAPIEFPAVADLEVTNALVNAAKKLGYTSHAGVVQCKDAFYGQHEPERMPVSYEL 18- 0 Query: 181 LNKWEAWKRLGTKASEMESAALFVAASHLGVRCGSDFLVVGNQSRNALGMDNPMAHDTEA 24- 0 LNKWEAWKRLGTKASEMESAALFVAASHLGVRCGSDFLVVGNQERNALGMDNPMAHDTEA Sbjct: 181 LNKWEAWKRLGTKASEMESAALFVAASHLGVRCGSDFLVVGNQERNALGMDNPMAHDTEA 24- 0 Query: 241 AIQVAVEALRTLIENDKSQ 259 AIQVAVEALRTLIENDKSQ Sbjct: 241 AIQVAVEALRTLIENDKSQ 259 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2018 A DNA sequence (GBSx2129) was identified in S. agalactiae <SEQ ID 6243> which encodes the amino acid sequence <SEQ ID 6244>. This protein is predicted to be nucleoside transporter. Analysis of this protein sequence reveals the following: TABLE-US-06171 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.45 Transmembrane 35-51 (30-57) INTEGRAL Likelihood = -9.29 Transmembrane 8-24 (1-28) INTEGRAL Likelihood = -8.07 Transmembrane 388-404 (379-404) INTEGRAL Likelihood = -7.27 Transmembrane 104-120 (100-127) INTEGRAL Likelihood = -6.58 Transmembrane 259-275 (255-284) INTEGRAL Likelihood = -4.35 Transmembrane 172-188 (171-190) INTEGRAL Likelihood = -3.50 Transmembrane 200-216 (199-221) INTEGRAL Likelihood = -2.18 Tranamembrane 352-368 (352-371) ----- Final Results ----- bacterial membrane --- Certainty = 0.4779(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10245> which encodes amino acid sequence <SEQ ID 10246> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06172 >GP:BAB05165 GB:AP001512 nucleoside transporter [Bacillus halodurans] Identities = 160/405 (39%), Positives = 256/405 (62%), Gaps = 8/405 (1%) Query: 5 MQFIYSIIGILLVLGIVYAISFNRKSVSLSLIGKALIVQFIIALILVRIPLGQQVVSVVS 64 M ++ ++GI++V I +A S NR+++ I L +Q + A+I+++IP GQ ++ ++ Sbjct: 1 MNILWGLLGIVVVFLIAFAFSTNRRAIKPRTILGGLAIQLLFAIIVLKIPAGQALLESLT 60 Query: 65 TGVTKVINCGQAGLNFVFGSLADSGAKTGFIFAIQTLGNIVFLSALVSLLYYVGILGFVV 124- V+ I+ G++FVFG + G+ GF+FAI L ++F SAL+S+LYY+GI+ FV+ Sbjct: 61 NVVLNIISYANEGIDFVFGGFFEEGSGVGFVFAINVLSVVIFFSALISILYYLGIMQFVI 120- Query: 125 KWIGKGVGKIMKSSEVESFVAVANMFLGQTDSPILVSKYLGRMTDSEIMVVLVSGMGSMS 18- 4 K IG + ++ +S+ ES A AN+F+GQT++P++V YL +MT SE+ V+ G+ S++ Sbjct: 121 KIIGGALSWLLGTSKAESMSAAANIFVGQTEAPLVVKPYLPKNTQSELFAVMTGGLASVA 18- 0 Query: 185 VSILGGYIALGIPMEYLLIASTMVPIGSILIAKILLPQTEPVQKI-DDIKMDNKGNNANV 24- 3 S+L GY LG+P++YLL AS M +++AK+++P+TE DD K+ +N+ Sbjct: 181 GSVLIGYSLLGVPLQYLLAASFMAAPAGLIMAKMIMPETEKTTDAEDDFKLAKDEESTNL 24- 0 Query: 244 IDAIAEGASTGAQMAFSIGASLIAFVGLVSLINMMLSGLG-------IRLEQIFSYVFAP 29- 6 IDA A GASTG + +I A L+AFV L++LIN +L +G + LE I YVFAP Sbjct: 241 IDAAANGASTGLMLVLNIAANLLAFVALIALINGILGWIGGLFGASQLSLELILGYVFAP 30- 0 Query: 297 FGFLMGFDHKNILLEGNLLGSKLILNEFVSFQQLGDLIKSLDYRTALVATISLCGFANLS 35- 6 F++G L G+ +G KL++NEFV++ I++L + +V + +LCGFAN S Sbjct: 301 LAFVIGIPWAEALQAGSYIGQKLVVNEFVAYLSFAPEIENLSDKAVMVISFALCGFANFS 36- 0 Query: 357 SLGICVSGIAVLCPEKRGTLARLVFRANIGGIAVSMLSAFIVGIV 401 SLGI + G+ L P +R +ARL RA++ G S+LSA I G++ Sbjct: 361 SLGILLGGLGKLAPSRRPDIARLGLRAILAGTLASLLSASIAGML 405 A related DNA sequence was identified in S. pyogenes <SEQ ID 6245> which encodes the amino acid sequence <SEQ ID 6246>. Analysis of this protein sequence reveals the following: TABLE-US-06173 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.45 Transmembrane 35-51 (30-57) INTEGRAL Likelihood = -9.29 Transmembrane 8-24 (1-28) INTEGRAL Likelihood = -8.07 Transmembrane 388-404 (379-404) INTEGRAL Likelihood = -7.27 Transmembrane 104-120 (100-127) INTEGRAL Likelihood = -6.58 Transmembrane 259-275 (255-284) INTEGRAL Likelihood = -4.35 Transmembrane 172-188 (171-190) INTEGRAL Likelihood = -3.50 Transmembrane 200-216 (199-221) INTEGRAL Likelihood = -2.18 Tranamembrane 352-368 (352-371) ----- Final Results ----- bacterial membrane --- Certainty = 0.4779(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06174 >GP:BAB05165 GB:AP001512 nucleoside transporter [Bacillus halodurans] Identities = 160/405 (39%), Positives = 257/405 (62%), Gaps = 8/405 (1%) Query: 5 MQFIYSIIGILLVLGIVYAISFNRKSVSLSLIGKALIVQFIIALILVRIPLGQQIVSVVS 64 M ++ ++GI++V I +A S NR+++ I L +Q + A+I+++IP GQ ++ ++ Sbjct: 1 MNILWGLLGIVVVFLIAFAFSTNRRAIKPRTILGGLAIQLLFAIIVLKIPAGQALLESLT 60 Query: 65 TGVTSVINCGQAGLNFVFGSLADSGAKTGFIFAIQTLGNIVFLSALVSLLYYVGILGFVV 124- V ++I+ G++FVFG + G+ GF+FAI L ++F SAL+S+LYY+GI+ FV+ Sbjct: 61 NVVLNIISYANEGIDFVFGGFFEEGSGVGFVFAINVLSVVIFFSALISILYYLGIMQFVI 120- Query: 125 KWIGKGVGKIMKSSEVESFVAVANHFLGQTDSPILVSKYLGRNTDSEIMVVLVSGMGSMS 18- 4 K IG + +++S+ES A AN+F+GQT++P++V YL +MT SE+ V+ G+S++ Sbjct: 121 KIIGGALSWLLGTSKAESMSAAANIFVGQTEAPLVVKPYLPKMTQSELFAVMTGGLASVA 18- 0 Query: 185 VSILGGYIALGIPMEYLLIASTMVPIGSILIAKILLPQTEPVQKI-DDIKMDNKGNNANV 24- 3 S+L GY LG+P++YLL AS M +++AK+++P+TE DD K+ + N+ Sbjct: 181 GSVLIGYSLLGVPLQYLLAASFMAAPAGLIMAKMIMPETEKTTDAEDDFKLAKDEESTNL 24- 0 Query: 244 IDAIAEGASTGAQMAFSIGASLIAFVGLVSLINMNLSGLG-------IRLEQIFSYVFAP 29- 6 IDA A GASTG + +I A L+AFV L++LIN +L +G + LE I YVFAP Sbjct: 241 IDAAANGASTGLMLVLNIAAMLLAFVALIALINGILGWIGGLFGASQLSLELILGYVFAP 30- 0 Query: 297 EGFLMGFDHKNILLEGNLLGSKLILNEFVSFQQLGHLIKSLDYRTALVATISLCGFANLS 35- 6 F++G L G+ +G KL++NEFV++ I++L + +V + +LCGFAN S Sbjct: 301 LAFVIGIPWAEALQAGSYIGQKLVVNEFVAYLSFAPEIENLSOKAVMVISFALCGFANFS 36- 0 Query: 357 SLGICVSGIAVLCPEKRSTLARLVFRAMIGGIAVSMLSAFIVGIV 401 SLGI + G+ L P +R +ARL RA++ G S+LSA I G++ Sbjct: 361 SLGILLGGLGKLAPSRRPDIARLGLRAILAGTLASLLSASIAGML 405 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-06175 Identities = 399/404 (98%), Positives = 401/404 (98%) Query: 1 MEVIMQFIYSIIGILLVLGIVYAISFNRKSVSLSLIGKALIVQFIIALILVRIPLGQQVV 60 +EVIMQFIYSIIGILLVLGIVYAISFNRKSVSLSLIGKALIVQFIIALILVRIPLGQQ+V Sbjct: 1 LEVIMQFIYSIIGILLVLGIVYAISFNRKSVSLSLIGKALIVQFIIALILVRIPLGQQIV 60 Query: 61 SVVSTGVTKVINCGQAGLNFVFGSLADSGAKTGFIFAIQTLGNIVFLSALVSLLYYVGIL 120- SVVSTGVT VINCGQAGLNFVFGSLADSGAKTGFIFAIQTLGNIVFLSALVSLLYYVGIL Sbjct: 61 SVVSTGVTSVINCGQAGLNFVFGSLADSGAKTGFIFAIQTLGNIVFLSALVSLLYYVGIL 120- Query: 121 GFVVKWIGKGVGKIMKSSEVESFVAVANMFLGQTDSPILVSKYLGRMTDSEIMVVLVSGN 18- 0 GFVVKWIGKGVGKIMKSSEVESFVAVANMFLGQTDSPILVSKYLGRMTDSEIMVVLVSGM Sbjct: 121 GFVVKWIGKGVGKIMKSSEVESFVAVANMFLGQTDSPILVSRYLGRMTDSEIMVVLVSGM 18- 0 Query: 181 GSMSVSILGGYIALGIPMEYLLIASTMVPIGSILIAKILLPQTEPVQKIDDIKMDNKGNN 24- 0 GSMSVSILGGYIALGIPMEYLLIASTMVPIGSILIAKILLPQTEPVQKIDDIKMDNKGNN Sbjct: 181 GSMSVSILGGYIALGIPMEYLLIASTMVPIGSILIAKILLPQTEPVQKIDDIKMDNKGNN 24- 0 Query: 241 ANVIDAIAEGASTGAQMAFSIGASLIAFVGLVSLINMMLSGLGIRLEQIFSYVFAPFGFL 30- 0 ANVIDAIAEGASTGAQMAFSIGASLIAFVGLVSLINMMLSGLGIRLEQIFSYVFAPFGFL Sbjct: 241 ANVIDAIAEGASTGAQMAFSIGASLIAFVGLVSLINMMLSGLGIRLEQIFSYVFAPFGFL 30- 0 Query: 301 MGFDHKNILLEGNLLGSKLILNEFVSFQQLGDLIKSLDYRTALVATISLCGFANLSSLGI 36- 0 MGFDHKNILLEGNLLGSKLILNEFVSFQQLG LIKSLDYRTALVATISLCGFANLSSLGI Sbjct: 301 MGFDHKNILLEGNLLGSKLILNEFVSFQQLGHLIKSLDYRTALVATISLCGFANLSSLGI 36- 0 Query: 361 CVSGIAVLCPEKRGTLARLVFRAMIGGIAVSMLSAFIVGIVTLF 404 CVSGIAVLCPEKR TLARLVFRAMIGGIAVSMLSAFIVGIVTLF Sbjct: 361 CVSGIAVLCPEKRSTLARLVFRAMIGGIAVSMLSAFIVGIVTLF 404 A related GBS gene <SEQ ID 8955> and protein <SEQ ID 8956> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06176 Lipop: Possible site: -1 Crend: 1 McG: Discrim Score: 13.83 GvH: Signal Score (-7.5): -2.63 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 8 value: 9.45 threshold: 0.0 INTEGRAL Likelihood = -9.45 Transmembrane 35-51 (30-57) INTEGRAL Likelihood = -9.29 Transmembrane 8-24 (1-28) INTEGRAL Likelihood = -8.07 Transmembrane 388-404 (379-404) INTEGRAL Likelihood = -7.27 Transmembrane 104-120 (100-127) INTEGRAL Likelihood = -6.58 Transmembrane 259-275 (255-284) INTEGRAL Likelihood = -4.35 Transmembrane 172-188 (171-190) INTEGRAL Likelihood = -3.50 Transmembrane 200-216 (199-221) INTEGRAL Likelihood = -2.18 Tranamembrane 352-368 (352-371) PERIPHERAL Likelihood = 3.82 286 modified ALON score: 2.39 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4779(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00143## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2019 A DNA sequence (GBSx2130) was identified in S. agalactiae <SEQ ID 6247> which encodes the amino acid sequence <SEQ ID 6248>. This protein is predicted to be deoxyribose-phosphate aldolase (deoC). Analysis of this protein sequence reveals the following: TABLE-US-06177 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2196(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06178 >GP:CAA81646 GB:Z27121 deoxyribose aldolase [Mycoplasma hominis] Identities = 99/199 (49%), Positives = 140/199 (69%), Gaps = 1/199 (0%) Query: 5 DILKTVDHTLLATTATWPEIQTILDDAMAYETASACIPASYVKKAAEYVSGK-LAICTVI 63 ++ K +DHT L+ +AT +I ++ +A+ Y+ S CI SYVK A E + + +CTVI Sbjct: 3 ELNKYIDHTNLSPSATSKDIDKLIQEAIKYDFKSVCIAPSYVKYAKEALKNSDVLVCTVI 62 Query: 64 GFPNGYSTTAAKVFECQDAIKNGADEIDMVINLTDVKNGDFDTVEEEIRQIKAACQDHIL 123- GFP GY+ T+ KV+E + A+++GADEIDMVIN+ K+G ++ V EI+ IK AC L Sbjct: 63 GFPLGYNATSVKVYETKIAVEHGADEIDMVINVGRFKDGQYEYVLNEIKAIKEACNGKTL 122- Query: 124 KVIVETCQLTKEELIELCGVVTRSGADFIKTSTGFSTAGATFEDVEVMAKYVGEGVKIKA 18- 3 KVIVET LTK ELI++ +V +SGADFIKTSTGFS GA+FED++ M + G+ + IKA Sbjct: 123 KVIVETALLTKAELIKITELVMQSGADFIKTSTGFSYRGASFEDIQTMKETCGDKLLIKA 18- 2 Query: 184 AGGISSLSDAEKFIALGAS 202 +GGI +L DA++ I LGA+ Sbjct: 183 SGGIKNLADAQEMIRLGAN 201 A related DNA sequence was identified in S. pyogenes <SEQ ID 6249> which encodes the amino acid sequence <SEQ ID 6250>. Analysis of this protein sequence reveals the following: TABLE-US-06179 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2196(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06180 Identities = 211/223 (94%), Positives = 217/223 (96%) Query: 1 MEVKDILKTVDHTLLATTATWPEIQTILDDAMAYETASACIPASYVKKAAEYVSGKLAIC 60 +EVKDILKTVDHTLLATTATWPEIQTILDDAMAYETASACIPASYVKKAAEYVSGKLAIC Sbjct: 1 VEVKDILKTVDHTLLATTATWPEIQTILDDAMAYETASACIPASYVKKAAEYVSGKLAIC 60 Query: 61 TVIGFPNGYSTTAAKVFECQDAIKNGADEIDMVINLTDVKNGDFDTVEEEIRQIKAACQD 120- TVIGFPNGYSTTAAKVFECQDAI+NGADEIDMVINLTDVKNGDFDTVEEEIRQIKA CQD Sbjct: 61 TVIGFPNGYSTTAAKVFECQDAIQNGADEIDMVINLTDVKNGDFDTVEEEIRQIKAKCQD 120- Query: 121 HILKVIVETCQLTKEELIELCGVVTRSGADFIKTSTGFSTAGATFEDVEVMAKYVGEGVK 18- 0 HILKVIVETCQLTKEELIELCGVVTRSGADFIKTSTGFSTAGATFEDVEVMAKYVGEGVK Sbjct: 121 HILKVIVETCQLTKEELIELCGVVTRSGADFIKTSTGFSTAGATFEDVEVMAKYVGEGVK 18- 0 Query: 181 IKAAGGISSLEDAEKFIALGASRLGTSRIIKIVKNQKVEEGTY 223 IKAAGGISSLEDA+ FIALGASRLGTSRIIKIVKN+ + +Y Sbjct: 181 IKAAGGISSLEDAKTFIALGASRLGTSRIIKIVKNEATKTDSY 223 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2020 A DNA sequence (GBSx2131) was identified in S. agalactiae <SEQ ID 6251> which encodes the amino acid sequence <SEQ ID 6252>. This protein is predicted to be phosphopentomutase (deoB). Analysis of this protein sequence reveals the following: TABLE-US-06181 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0546(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06182 >GP:AAC45496 GB:U80410 phosphopentomutase [Lactococcus lactis subsp. cremoris] Identities = 275/408 (67%), Positives = 325/408 (79%), Gaps = 7/408 (1%) Query: 3 QFDRIHLVVLDSVGIGAAPDANDFVNAGVP------DGASDTLGHISKTVGLAVPNMAKI 56 +F RIHLVV+DSVGIGAAFDA+ F N V D SDT+GHIS+ GL VPN+ K+ Sbjct: 4 KFGRIHLVVMDSVGIGAAPDADKFFNHDVETHEAINDVKSDTIGHISEIRGLDVPNLQKL 63 Query: 57 GLGNIPRPQALKTVPAEENPSGYATKLQEVSLGKDTMTGMWEIMGLNITEPFDTFWNGFP 116- G GNIPR LKT+PA + P+ Y TKL+E+S GKDTMTGHWEIMGLNI PF T+ G+P Sbjct: 64 GWGNIPRESPLKTIPAAQKPAAYVTKLEEISKGKDTMTGHWEIMGLNIQTPFPTYPEGYP 123- Query: 117 EDIITKIEDFSGRKVIREANKPYSGTAVIDDFGPRQMETGELIIYTSADPVLQIAAHEDI 17- 6 ED++ KIE+FSGRK+IREANKPYSGTAVI+DFGPRQ+ETGELIIYTSADPVLQIAAHED+ Sbjct: 124 EDLLEKIEEFSGRKIIREANKPYSGTAVIEDFGPRQLETGELIIYTSADPVLQIAAHEDV 18- 3 Query: 177 IPLEELYRICEYARSITMERPALL-GRIIARPYVGEPGNFTRTANRHDYAVSPFEDTVLN 23- 5 I EELY+ICEY RSIT+E ++ GRIIARPYVGE GNF RT R DYA+SPF +TVL Sbjct: 184 ISREELYKICEYVRSITLEGSGIMIGRIIARPYVGEAGNFERTDGRRDYALSPFAETVLE 24- 3 Query: 236 KLDQAGIDTYAVGKINDIFNGSGINHDMGHNKSNSHGIDTLIKTMGLSEFEKGFSFTNLV 29- 5 KL +AGIDTY+VGKI+DIFN G+ +DMGHN ++ G+D L+K M +EF +GFSFTNLV Sbjct: 244 KLYKAGIDTYSVGKISDIFNTVGVKYDMGHNHNDMDGVDRLLKAMTKTEFTEGFSFTNLV 30- 3 Query: 296 DFDALYGHRRDPHGYRDCLHEFDERLPEIISAMRDKDLLLITADHGNDPTYAGTDHTREY 35- 5 DFDA YGHRRD GY + +FD RLPEII AM++ DLL+ITADHGNDP+Y GTDHTREY Sbjct: 304 DFDAKYGHRRDVEGYGKAIEDFDGRLPEIIDAMKEDDLLMITADHGNDPSYVGTDHTREY 36- 3 Query: 356 IPLLAYSPSFTGNGLIPVGHFADISATVADNFGVDTAMIGESFLQDLV 403 IPL+ +S SF ++PVGHFADISAT+A+NF V A GESFL LV Sbjct: 364 IPLVIFSKSFKEPKVLPVGHFADISATIAENFSVKKAQTGESFLDALV 411 There is also homology to SEQ ID 2740: TABLE-US-06183 Identities = 348/402 (86%), Positives = 374/402 (92%) Query: 1 MSQFDRIHLVVLDSVGIGAAPDANDFVNAGVPDGASDTLGHISKTVGLAVPNMAKIGLGN 60 MS+F+RIHLVVLDSVGIGAAPDA+ F NAGV D SDTLGHIS+ GL+VPNMAKIGLGN Sbjct: 1 MSKFNRIHLVVLDSVGIGAAPDADKFFNAGVADTDSDTLGHISEAAGLSVPNMAKIGLGN 60 Query: 61 IPRPQALKTVPAEENPSGYATKLQEVSLGKDTMTGHWEIMGLNITEPFDTFWNGFPEDII 120- I RP LKTVP E+NP+GY TKL+EVSLGKDTMTGHWEIMGLNITEPFDTFWNGFPE+I+ Sbjct: 61 ISRPIPLKTVPTEDNPTGYVTKLEEVSLGKDTMTGHWEIMGLNITEPFDTFWNGFPEEIL 120- Query: 121 TKIEDFSGRKVIREANKPYSGTAVIDDFGPRQMETGELIIYTSADPVLQIAAHEDIIPLE 18- 0 TKIE+FSGRK+IREANKPYSGTAVIDDFGPRQMETGELI+YTSADPVLQIAAHEDIIP+E Sbjct: 121 TKIEEFSGRKIIREANKPYSGTAVIDDFGPRQMETGELIVYTSADPVLQIAAHEDIIPVE 18- 0 Query: 181 ELYRICEYARSITMERPALLGRIIARPYVGEPGNFTRTANRHDYAVSPFEDTVLNKLDQA 24- 0 ELY+ICEYARSIT+ERPALLGRIIARPYVG+PGNFTRTANRHDYAVSPF+DTVLNKL A Sbjct: 181 ELYKICEYARSITLERPALLGRIIARPYVGDPGNFTRTANRHDYAVSPFQDTVLNKLADA 24- 0 Query: 241 GIDTYAVGKINDIFNGSGINHDMGHNKSNSHGIDTLIKTMGLSEFEKGFSFTNLVDFDAL 30- 0 G+ TYAVGKINDIFNGSGI +DMGHNKSNSHGIDTLIKT+ L EF KGFSFTNLVDFDA Sbjct: 241 GVPTYAVGKINDIFNGSGITNDMGHNKSNSHGIDTLIKTLQLPEFTKGFSFTNLVDFDAN 30- 0 Query: 301 YGHRRDPHGYRDCLHEFDERLPEIISAMRDKDLLLITADHGNDPTYAGTDHTREYIPLLA 36- 0 +GHRRDP GYRDCLHEFD RLPEII+ M++ DLLLITADHGNDPTYAGTDHTREYIPLLA Sbjct: 301 FGHRRDPEGYRDCLHEFDNRLPEIIANMKEDDLLLITADHGNDPTYAGTDHTREYIPLLA 36- 0 Query: 361 YSPSFTGNGLIPVGHFADISATVADNFGVDTAMIGESFLQDL 402 YS SFTGNGLIP GHFADISATVA+NFGVDTANIGESFL L Sbjct: 361 YSVSFTGNGLIPQGHFADISATVAENFGVDTAMIGESFLSHL 402 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2021 A DNA sequence (GBSx2132) was identified in S. agalactiae <SEQ ID 6253> which encodes the amino acid sequence <SEQ ID 6254>. Analysis of this protein sequence reveals the following: TABLE-US-06184 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.05 Transmembrane 9-25 (4-35) ----- Final Results ----- bacterial membrane --- Certainty = 0.5819(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 6255> which encodes the amino acid sequence <SEQ ID 6256>. Analysis of this protein sequence reveals the following: TABLE-US-06185 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.57 Transmembrane 41-57 (38-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.3230(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9143> which encodes the amino acid sequence <SEQ ID 9144>. Analysis of this protein sequence reveals the following: TABLE-US-06186 Possible cleavage site: 49 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.57 Transmembrane 13-29 (10-32) ----- Final Results ----- bacterial membrane --- Certainty = 0.323(Affirmative) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06187 Identities = 276/544 (50%), Positives = 368/544 (66%), Gaps = 5/544 (0%) Query: 5 FKKKVVKVCLVIFGIVLVSLLSLGFFYFSKGQVLSRFVAARSRTSGQAFDNIKEYMVWSD 64 F K +K +I L L G FY+SK ++ ++ ARS SG F+NIK Y+VW D Sbjct: 33 FHHKKLKQITIIAATSLFLFLIGGAFYYSKNHCINAYLKARSAQSGPVFENIKAYLVWDD 92 Query: 65 TGESITNDEANYANFEPLSKSEARKLGQEIKEGNKNDSMYLKRVGSRLGIFPDYRIANKP 124- T E ITNDEA Y F S+ E R+ Q++K +++ ++ +K VG R IFPDYRIA KP Sbjct: 93 TNEQITNDEAMYTKFRRYSQKELRQKKQDLKAASQDSAVQVKSVGRRFWIFPDYRIAIKP 152- Query: 125 MSLTLKTNVPKLDVLLNQKKVATSNSDHFSVTVERLPRTHYTASLEGTSDGKEIKLKKDY 18- 4 M LT+KTNVP+ DVLLNQKKVA S+S+ FSV ++RLP YTAS+ G +G+ IK+ K Y Sbjct: 153 NDLTIKTNVPQADVLLNQKKVAVSDSEQFSVKLDRLPTAEYTASIRGKHNGRNIKVNKSY 21- 2 Query: 185 DGKNQTIDLSVAFKSFTVTSNLMDGNLYFGDNRIAKLKDGSHSVENYPVTDGSKAYIKKV 24- 4 DG N +DLSV+F++F VTSN G+LYF DN I LKDG VE+YPVT+ ++AY+K Sbjct: 213 DGDNPVLDLSVSFRTFLVTSNAKQGDLYFDDNHIGTLKDGQLQVEDYPVTENAQAYMKTT 27- 2 Query: 245 FNDGEITSHKQKLISIADNQTIKLDVDGLLNEKEAGQKLITAFNQLILYVSTGQDPQTLG 30- 4 F DGE+ S K L + + T+++ V LL E +AG+ L++AF+QL+ Y+STGQD L Sbjct: 273 FPDGELRSQKYALADVEEGATLEILVTDLLEEDKAGELLVSAFDQLMHYLSTGQDSSNLR 33- 2 Query: 305 TVFEKGAENDFYKGLKEGIKAKFVTDNRKASHFTIPNIVLNKMTQVGKESYQVNFAADYD 36- 4 +VFE G+ N FY+GLKESIKAKF TD RKAS IP+I+L MTQVGK +Y ++F A Y+ Sbjct: 333 SVFEAGSSNAFYRGLKESIKAKFQTDTRKASRLNIPSILLTTMTQVGKTTYVLDFTATYE 39- 2 Query: 365 FNYDKSTDPDKKTYGHIIQNLTGNFIMKKSGNSYLISNDGKKDITVAKETNKVKADPVSI 42- 4 F YDKSTDP++ T GHI Q+LTG +KK G YLIS G K+ITV KE N++KA S+ Sbjct: 393 FLYDKSTDPEQHTSGHINQDLTGKVTVKKVGQHYLISQSGSKNITVVKEDNQLKAP--SV 45- 0 Query: 425 FPENLVGSWKESVEDGTVTMTFDKDGKVTQK-KVYKDSKSKESNHSAKVTKLEDKGNGLY 48- 3 FPE+++G+W G+ ++ M+ DG +T K + K ++SKE+ +AK++K+EDKGNG Y Sbjct: 451 FPESILGTWTGQANGLSIHMSLASDGTITTKVEDQKGNRSKET-RTAKISKVEDKGNGFY 50- 9 Query: 484 LYQYESGTDTTTFV-TGGIGGLKVKYAYGIKIEGNKIIPVIWQTSSDGEFDYHKPLLSKP 54- 2 LY + G+D + V GG+GG VKYAYG KI G PV+WQ + EFDY KPL Sbjct: 510 LYTPDPGSDISALVPEGGLGGANVKYAYGFKISGKTASPVVWQAALTHSFDYTKPLSGVT 56- 9 Query: 543 LTKQ 546 L KQ Sbjct: 570 LQKQ 573 A related DNA sequence was identified in S. pyogenes <SEQ ID 9065> which encodes amino acid sequence <SEQ ID 9066>. An alignment of the GAS and GBS sequences follows: TABLE-US-06188 Score = 47.3 bits (110), Expect = 4e-07 Identities = 65/303 (21%), Positives = 119/303 (38%), Gaps = 18/303 (5%) Query: 153 FYILGIGTSISIVVALTRFVKEISLNFKEIKKLANKMGIEVLSENENYSQII---EFDDI 20- 9 +YIL + T I+ +V + +S F +KKL KM + +QI EF D+ Sbjct: 37 YYILSV-TIIACIVGGIVNLFLLSSVFTSLKKLKQKMKDISQRCFDTKAQICSPQEFKDL 95 Query: 210 LRTLHIKGDNLKSLIEREILEKQDLSFQIAALSHDIKTPXXXXXXXXXXXXXXXXXXXQE 26- 9 + L+S + +++ + IA LSHDIKTP + Sbjct: 96 ETAFNQMSSELESTFKSLNESEREKTMMIAQLSHDIKTPITSIQSTVEGILDGIISEEEV 155- Query: 270 GYIVSMNNSISVFEGYFNSLISYTRML--------SEDRSVKLILVEELLSELHFEVDDL 32- 1 Y + N+IS N L+ + +E + I +++LL ++ E + Sbjct: 156 NYYL---NTISRQTNRLNHLVEELSFITLETMSDTAEPHKEETIYLDKLLIDILSEFQLV 21- 2 Query: 322 LNINNIEFSICNRLIITSFYGDEENLIRALSNLLVNAIRFMPVLDKKIEVILSESGEQIH 38- 1 N + I ++ + L R L NL+ NA ++ + + + + I Sbjct: 213 FEKENRQVMIDVAPDVSKLSSQYDKLSRILLNLISNAXKYSDP-GSPLTIKAYSNRQDIV 27- 1 Query: 382 FEIWNNGERFSDSTLKKGDKLFYTEDYSRGNK--HYGIGLAFVKGVAIKHGGNLQLNNPA 43- 9 +I + G D L Y + SR K +G+GL + +A + G++ + + Sbjct: 272 IDIIDQGYGIKDEDLASIFNRLYRVESSRNMKTGGHGLGLYIARQLAHQLNGDILVESQY 33- 1 Query: 440 RGG 442 + G Sbjct: 332 QKG 334 A related sequence was also identified in GAS <SEQ ID 9135> which encodes the amino acid sequence <SEQ ID 9136>. Analysis of this protein sequence reveals the following: TABLE-US-06189 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -3.56 Transmembrane 145-161 (145-164) ----- Final Results ----- bacterial membrane --- Certainty = 0.2423(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 6254 (GBS280) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 52 (lane 8; MW 63.7 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 58 (lane 7; MW 88.7 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2022 A DNA sequence (GBSx2133) was identified in S. agalactiae <SEQ ID 6257> which encodes the amino acid sequence <SEQ ID 6258>. This protein is predicted to be ribosomal large subunit pseudouridine synthase D (rluC). Analysis of this protein sequence reveals the following:

TABLE-US-06190 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.62 Transmembrane 2-18 (1-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.2848(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06191 >GP:CAB12749 GB:Z99108 similar to hypothetical proteins [Bacillus subtilis] Identities = 97/251 (38%), Positives = 147/251 (57%), Gaps = 15/251 (5%) Query: 86 KHVLINNEFINWQTVVQENDTITLIFDDEDYFTKKIPLGRAELIDCLYEDEHLIIVNKPE 145- + + +N+E + +V++ D + + + + + G +D L+ED H++I+NKP Sbjct: 43 QQIKVNHESVLNNMIVKKGDRVFIDLQESEASSVIPEYGE---LDILFEDNHMLIINKPA 99 Query: 146 GMKTHGNQPHEIALLNHVSAY----SGQTCYV--VHRLDMETSGAVLFAKNPFILPLINQ 19- 9 G+ TH N+ + L ++ AY +G+TC V VHRLD +TSGA++FAK+ +++Q Sbjct: 100 GIATHPNEDGQTGTLANLIAYHYQINGETCKVRHVHRLDQDTSGAIVFAKHRLAHAILDQ 15- 9 Query: 200 RLERKEIWREYWALVEGKFSPKHQVLRDKIGRNR-HDRRKRIIDSKNGQHAMTIIDVL-- 25- 6 +LE+K + R Y A+ EGK K + IGR+R H R+R+ S GQ A+T V+ Sbjct: 160 QLEKKTLKRTYTAIAEGKLRTKKGTINPPIGRDRSHPTRRRV--SPGGQTAVTHFKVMAS 21- 7 Query: 257 KYIQNSSLIKCRLETGRTHQIRVHLSHHGHPLIGDPLYNPSSN-NERLMLHAHRLTLSHP 31- 5 + SL++ LETGRTHQIRVHL+ GHPL GD LY S R LHA+++ HP Sbjct: 218 NAKERLSLVELELETGRTHQIRVHLASLGHPLTGDSLYGGGSKLLNRQALHANKVQAVHP 27- 7 Query: 316 LTCETISVEAP 326 +T E I EAP Sbjct: 278 ITDELIVAEAP 288 A related DNA sequence was identified in S. pyogenes <SEQ ID 6259> which encodes the amino acid sequence <SEQ ID 6260>. Analysis of this protein sequence reveals the following: TABLE-US-06192 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4198(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06193 Identities = 172/278 (61%), Positives = 212/278 (75%), Gaps = 2/278 (0%) Query: 63 TVKELLEDYFLIPRKIRHFLRVKKHVLINNEFINWQTVVQENDTITLIFDDEDYPTKKIP 122- TVK LLE+ LIPRKIRNFLR KKHVLIN +NWQ+ V+ D + L FD EDYP K I Sbjct: 2 TVKALLEEQLLIPRKIRHFLRTKKHVLINGHSVNWQSCVKYGDQVKLFFDHEDYPSKIIV 61 Query: 123 LGRAELIDCLYEDEHLIIVNKPEGMKTHGNQPNEIALLNHVSAYSGQTCYVVHRLDMETS 18- 2 +G+AE + CLYEDEH+IIVNKPEGMKTHGN P E+ALLNHVSAY+GQTCYVVHRLD ETS Sbjct: 62 MGQAEKVTCLYEDEHIIIVNKPEGMKTHGNDPTELALLNHVSAYTGQTCYVVNRLDKETS 121- Query: 183 GAVLFAKNPFILPLINQRLERKEIWREYWALVEGKFSPKNQVLRDKIGRNRHDRRKRIID 24- 2 GA+LFAK PFILP++N+ LE+++I REY ALV G IGR+RHDRRKR++D Sbjct: 122 GAILFAKTPFILPILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRVVD 18- 1 Query: 243 SKNGQNANTIIDVLK-YIQNSSLIKCRLETGRTHQIRVHLSHHGHPLIGDPLY-NPSSNN 30- 0 NG+ A+T + ++K + + +SL+ C+L+TGRTHQIRVHL+H GH L GDPLY N + Sbjct: 182 PINGKKAITEVTLVKNFHKTASLLTCQLQTGRTHQIRVHLAHQGHVLFGDPLYSNGKKDC 24- 1 Query: 301 ERLMLHANRLTLSHPLTCETISVEAPSSTFEKILNNYK 338 RLMLHA++L L HPLT E I V+A S+TF++LN K Sbjct: 242 ARLMLHAYQLRLKHPLTQEDICVQAKSATFDAVLNAQK 279 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2023 A DNA sequence (GBSx2134) was identified in S. agalactiae <SEQ ID 6261> which encodes the amino acid sequence <SEQ ID 6262>. Analysis of this protein sequence reveals the following: TABLE-US-06194 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.02 Transmembrane 98-114 (93-119) ----- Final Results ----- bacterial membrane --- Certainty = 0.4609(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06195 >GP:AAF04735 GB:AF101780 penicillin-binding protein 2a [Streptococcus pneumoniae] Identities = 424/773 (54%), Positives = 555/773 (70%), Gaps = 47/773 (6%) Query: 2 KLFDKFIDLFRVOEDNDEMTRKNEQETREETSNLDGEEVYDIDDITRPSKSQYQRGIRHQ 61 KLF+KF+ LF+ +ETS L+ + I R S+S Sbjct: 5 KLFEKFLSLFK-----------------KETSELEDSD----STILRRSRS--------- 34 Query: 62 KENAKSRPEWLQKVDRYLPSPKNPIRRFWRRYRIGKLLFIALMAFILIFGSYLFYLSKTA 121- DR + PIR+FWRRY + K++ I ++ L+ G YLF ++K+ Sbjct: 35 --------------DRKKLAQVGPIRKFWRRYHLTKIILILGLSAGLLVGIYLFAVAKST 80 Query: 122 TVSDLQSALKTTTTIYDKNKEYAGKLSGQKGTYVELNAISDHLKNAVIATEDRTFYSNNG 18- 1 V+DLQ+ALKT T I+D+ ++ AG LSGQKGTYVEL IS +L+NAVIATEDR+FY+N+G Sbjct: 81 NVNDLQNALKTRTLIFDREEKEAGALSGQKGTYVELTDISKNLQNAVIATEORSFYKNDG 140- Query: 182 VNFKRFFLAVATLGKFGGGSTITQQLAKNAYLSQDQTIKRKAREFFLALELTKKYSKAEI 24- 1 +N+ RFFLA+ T G+ GGGSTITQQLAKNAYLSQDQT++RKA+EFFLALEL+KKYSK +I Sbjct: 141 INYGRFFLAIVTAGRSGGGSTITQQLAKNAYLSQDQTVERRAKEFFLALELSKKYSKSQI 20- 0 Query: 242 LTMYLNNSYFGNGVWGVEDASRKYFGTSAANLTVDEAATLAGMLKGPEVYNPYYSVENAT 30- 1 LTMYLNN+YFGNGVWGVEDAS+KYFG SA+ +++D+AATLAGMLKGPE+YNP SVE++T Sbjct: 201 LTMYLNNAYFGNGVWGVEDASKKYFGVSASEVSLDQAATLAGMLKGPELYNPLNSVEDST 26- 0 Query: 302 NRRDTVLAAMVDAGKLTKSQAKEAASIGMKNRLADTYAGKINDYRYPSYFDAVVNSAIDT 36- 1 NRRDTVL MV AG + K+Q EAA + M ++L D Y GKI+DYRYPSYFDAVVNEA+ Sbjct: 261 NRRDTVLQNMVAAGYIDKNQSTSAAEVDMTSQLHDKYEGKISDYRYPSYFDAVVNSAVSK 32- 0 Query: 362 YGISEKDIVNNGYKIYTALDQNYQSGMQKTFDDTSLFPVSDYDGQSAQGASVALDPKTGG 42- 1 Y ++E++IVNNGY+IYT LDQNYQ+ MQ +++TSLFP ++ DG AQ SVAL+PKTGG Sbjct: 321 YNLTSEEIVNNGYRIYTELDQNYQANMQIVYENTSLFPRAE-DGTFAQSGSVALEPKTGG 37- 9 Query: 422 VRGLVGRVQSTKDAQFRSFNYATQSKRSPASTIKPLVVYSPAIASGWSIDKELPNKVQDF 48- 1 VRG+VG+V FR+FNYATQSKRSP STIKPLVVY+PA+ +GW+++K+L N + Sbjct: 380 VRGVVGQVADNDKTGFRNFNYATQSKRSPGSTIKPLVVYTPAVEAGWALNKQLDNHTMQY 43- 9 Query: 482 HGYKPSNYGGIET-ESIPMYQALANSYNIPAVYTLDKLGINKAFTYGRKFGLNMSSANKE 54- 0 YK NY GI+T +PMYQ+LA S N+PAV T++ LG++KAF G KFGLNM ++ Sbjct: 440 DSYKVDNYAGIKTSREVPMYQSLAESLNLPAVATVNDLGVDKAFEAGEKFGLNMEKVDRV 49- 9 Query: 541 LGVALGGSVTTNPLEMAQAYSTFANDGIMHRANLITRIETANGKLVKQFTDKPKRVISRS 60- 0 LGVALG V TNPL+MAQAY+ FAN+G+M AH I+RIE A+G+++ + KRVI +S Sbjct: 500 LGVALGSGVETNPLQNAQAYAAFANEGLMPEAHFISRIENASGQVIASHKNSQKRVIDKS 55- 9 Query: 601 VASKMTSMMLGTFSNGTAINANVYGYTMAGKTGTTSTDFNPNLSGDQWVVGYTPDVVISQ 66- 0 VA KMTSMNLGTF+NGT I+++ Y MAGKTGTTE FNP + DQWV+GYTPDVVIS Sbjct: 560 VADKMTSMMLGTFTNGTGISSSPADYVMAGKTGTTEAVFNPEYTSDQWVIGYTPDVVISH 61- 9 Query: 661 WVGFKNTDKHHYLTDSSAGTASNIFSTQASYILPYTKGSSFTHIENAYFQNGIGSVYNAQ W+GF TD++HYL S++ A+++F A+ ILPYT GS+FT +ENAY QNGI + Sbjct: 620 WLGFPTTDENNYLAGSTSNGAAHVFRNIANTILPYTPGSTFT-VENAYKQNGIAPANTKR 67- 8 Query: 721 DASNTTNQESRSIINDLKDSASKAAQDISRAVEDSNFQEKVKDAWNSLKDYFR 773 N ++ ++D++ A + SRA+ D+ +EK + W+S+ +FR Sbjct: 679 QVQTNDNSQTDDNLSDIRGRAQSLVDEASRAISDAKIKEKAQTIWDSIVNLWR 731 A related DNA sequence was identified in S. pyogenes <SEQ ID 6263> which encodes the amino acid sequence <SEQ ID 6264>. Analysis of this protein sequence reveals the following: TABLE-US-06196 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.96 Transmembrane 104-120 (99-124) ----- Final Results ----- bacterial membrane --- Certainty = 0.4185(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06197 >GP:AAF04735 GB:AF101780 penicillin-binding protein 2a [Streptococcus pneumoniae] Identities = 414/730 (56%), Positives = 539/730 (73%), Gaps = 17/730 (2%) Query: 50 TKNSEQDPATALQRSRAYEGSPKSRPAWLQKLEAVLPSPQRPIRRFWRRYHIGKLLMILI 109- T E +T L+RSR+ +KL V PIR+EWRRYH+ K+++IL Sbjct: 18 TSELEDSDSTILRRSRSDR----------KKLAQV-----GPIRKFWRRYHLTKIILILG 62 Query: 110 GTLVLLLGSYLFYLSKTAKVSDLQDALKATTVIYDHKGEYAGSLSGQKGSYVELNAISDD 16- 9 + LL+G YLF ++K+ V+DLQ+ALK T+I+D + + AG+LSGQKG+YVEL IS + Sbjct: 63 LSAGLLVGIYLFAVAKSTNVNDLQNALKTRTLIFDREEKEAGALSGQKGTYVELTDISKN 122- Query: 170 LENAVIATEDRTFYSNSGINLKRFLLAVVTAGRFGGGSTITQQLAKNAYLSQDQTIKRKA 22- 9 L+NAVIATEDR+FY N GIN RF LA+VTAGRGGG STITQQLAKNAYLSQDQT++RKA Sbjct: 123 LQNAVIATEDRSFYKNDGINYGRFFLAIVTAGRSGGGSTITQQLAKNAYLSQDQTVERKA 18- 2 Query: 230 REFFLALELTKKYSKKDILTMYLNNSYFGNGVWGVEDASQKYFGTTAANLTLDEAATLAG 28- 9 +EFFLALEL+KKYSK+ ILTMYLNN+YFGNGVWGVEDAS+KYFG +A+ ++LD+AATLAG Sbjct: 183 KEFFLALELSKKYSKEQILTNYLNNAYFGNGVWGVEDASKKYFGVSASEVSLDQAATLAG 24- 2 Query: 290 MLKGPEIYNPYHSLRNATHRRDTVLGAMVDAKKITQTKAQQARAVGLKNRLADTYVGKTD 34- 9 MLKGPE+YNP +S++++T+RRDTVL MV A I + + +A V + ++L D Y GK Sbjct: 243 NLKGPSLYNPLNSVEDSTNRRDTVLQNMVAAGYIDKNQETEAAEVDMTSQLHDKYEGKIS 30- 2 Query: 350 DYKYPSYFDAVISEAIATYGLSEKDIVNNGYKVYTELDQNYQTGMQTTFNNDELFPVSAY 40- 9 DY+YPSYFDAV++EA++ Y L+E++IVNNGY++YTELDQNYQ MQ + N LFP A Sbjct: 303 DYRYPSYFDAVVNEAVSKYNLTEEEIVNNGYRIYTELDQNYQANMQIVYENTSLFP-RAE 36- 1 Query: 410 DGSSAQAASVALDPKTGGVRGLIGRVNSSENPTFRSFNYATQAKRSPASTIKPLVVYAPA 46- 9 DG+AQ+ SVAL+PKTGGVRG++G+V ++ FR+FNYATQ+KRSP STIKPLVVY PA Sbjct: 362 DGTFAQSGSVALEPKTGGVRGVVGQVADNDKTGFRNFNYATQSKRSPGSTIKPLVVYTPA 42- 1 Query: 470 VASGWSIEKELPNTVQDFDGYQPHNY-GNYESEDVPMYQALANSYNIPAVSTLNDIGIDK 52- 8 V +GW++ K+L N +D Y+ NY G S +VPMYQ+LA S N+PAV+T+ND+G+DK Sbjct: 422 VEAGWALNKQLDNHTMQYDSYKVDNYAGIKTSREVPMYQSLAESLNLPAVATVNDLGVDK 48- 1 Query: 529 AFTYGKTFGLDMSSAKKELGVALGGSVTTNPLEMAQAYAAFANNGVIHPAHLINRIENAR 58- 8 AF G+ FGL+M + LGVALG V TNPL+MAQAYAAFAN G++ AH I+RIENA Sbjct: 482 AFEAGEKFGLNMEKVDRVLGVALGSGVETNPLQMAQAYAAFANEGLMPEAHFISRIENAS 54- 1 Query: 589 GEVLKTFTDKAKRVVSQSVADKMTAMNLGTFSNGTAVNANVYGYTLAGKTGTTETNFNPD 64- 8 G+V+ + + KRV+ +SVADKT+MMLGTF+NGT ++++ Y +AGKTGTTE FNP+ Sbjct: 542 GQVIASHKNSQKRVIDKSVADKMTSMMLGTFTNGTGISSSPADYVMAGKTGTTEAVFNPE 60- 1 Query: 649 LAGDQWVIGYTPDVVISQWVGFNQTDENHYLTDSSAGTASAIFSTQASYILPYTKGSQFH 70- 8 DQWVIGYTPDVVIS W+GF TDENHYL S++ A+ +F A+ ILPYT GS F Sbjct: 602 YTSDQWVIGYTPDVVISHWLGFPTTDENHYLAGSTSNGAAHVFRNIANTILPYTPGSTFT 66- 1 Query: 709 VDNAYAQNGISAVYGVNETGNQSGVDTQSIIDGLRKSAQEASQSLSKAVDQSGLRDKAQS 76- 8 V+NAY QNGI+ + T + +R AQ S+A+ + +++KAQ+ Sbjct: 662 VENAYKQNGIAPANTKRQVQTNDNSQTDDNLSDIRGRAQSLVDEASRAISDAKIKEKAQT 72- 1 Query: 769 IWKEIVDYFR 778 IW IV+ FR Sbjct: 722 IWDSIVNLFR 731 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06198 Identities = 530/715 (74%), Positives = 623/715 (87%), Gaps = 1/715 (0%) Query: 59 RHQKENAKSRPEWLQKVDRYLPSPKNPIRRFWRRYRIGKLLFIALMAFILIFGSYLFYLS 118- R + + KSRP WLQK++ LPSP+ PIRRFWRRY IGKLL I + +L+ GSYLFYLS Sbjct: 65 RAYEGSPKSRPAWLQKLEAVLFSPQRPIRRFWRRYHIGKLLMILIGTLVLLLGSYLFYLS 124- Query: 119 KTATVSDLQSALKTTTTIYDKNKEYAGKLSGQKGTYVELNAISDHLKNAVIATEDRTFYE 17- 8 KTA VSDLQ ALK TT IYD EYAG LSGQKG+YVELNAISD L+NAVIATEDRTFY Sbjct: 125 KTAKVSDLQDALKATTVIYDHKGEYAGSLSGQKGSYVELNAISDDLENAVIATEDRTFYS 18- 4 Query: 179 NNGVNFKRFFLAVATLGKFGGGSTITQQLAKNAYLSQDQTIKRKAREFFLALELTKKYSK 23- 8 N+G+N KRF LAV T G+FGGGSTITQQLAKNAYLSQDQTIKRKAREFFLALELTKKYSK Sbjct: 185 NSGINLKRFLLAVVTAGRFGGGSTITQQLAKNAYLSQDQTIKRKAREFFLALSLTKKYSK 24- 4 Query: 239 AEILTMYLNNSYFGNGVWGVEDASRKYFGTSAANLTVDEAATLAGNLKGPEVYNPYYSVE 29- 8 +ILTMYLNNSYFGNGVWGVEDAS+KYFGT+AANLT+DEAATLAGNLKGPE+YNPY+S++ Sbjct: 245 KDILTMYLNNSYFGNGVWGVEDASQKYFGTTAANLTLDEAATLAGNLKGPEIYNPYHSLK 30- 4 Query: 299 NATNRRDTVLAAMVDAGKLTKSQAKEAASIGMKNRLADTYAGKINDYRYPSYFDAVVNEA 35- 8 NAT+RRDTVL AMVDA K+T+++A++A ++G+KNRLADTY GK +DY+YFSYFDAV++EA Sbjct: 305 NATHRRDTVLGANVDAKKITQTKAQQARAVGLKNRLADTYVGKTDDYKYPSYFDAVISEA 36- 4 Query: 359 IDTYGISEKDIVNNGYKIYTALDQNYQSGMQKTFDDTSLFPVSDYDGQSAQGASVALDPK 41- 8 I TYG+SEKDIVNNGYK+YT LDQNYQ+GMQ TF++ LFPVS YDG SAQ ASVALDPK Sbjct: 365 IATYGLSSKDIVNNGYKVYTELDQNYQTGMQTTFNNDELFPVSAYDGSSAQAASVALDPK 42- 4 Query: 419 TGGVRGLVGRVQSTKDAQFRSFNYATQSKRSPASTIKPLVVYSPAIASGWSIDKELPNKV 47- 8 TGGVRGL+GRV S+++ERSFNYATQ+KRSPASTIKPLVVY+PA+ASGWSI+KELPN V Sbjct: 425 TGGVRGLIGRVNSSENPTFRSFNYATQAKRSPASTIKPLVVYAPAVASGWSIEKSLPNTV 48- 4 Query: 479 QDFHGYKPSNYGGIETESIPHYQALANSYNIPAVYTLDKLGINKAFTYGRKFGLNMSSAN 53- 8 QDF GY+P NYG E+E +PNYQALANSYNIPAV TL+ +GI+KAFTYG+ FGL+MSSA Sbjct: 485 QDFDGYQPHNYGNYESEDVPNYQALANSYNIPAVSTLNDIGIDKAFTYGKTFGLDMSSAK 54- 4 Query: 539 KELGVALGGSVTTNPLEMAQAYSTFANDGIMHRAHLITRIETANGKLVKQFTDKFKRVIS 59- 8 KELGVALGGSVTTNPLEMAQAY+ FAN+G++H AHLI RIE A G+++K FTDK KRV+S Sbjct: 545 KELGVALGGSVTTNPLEMAQAYAAFANNGVIHPAHLINRIENARGEVLKTFTDKAKRVVS 60- 4 Query: 599 RSVASKMTSMMLGTFSNGTAINANVYGYTNAGKTGTTETDFNPNLSGDQWVVGYTPDVVI 65- 8 +SVA KMT+MNLGTFSNGTA+NANVYGYT+AGKTGTTET+FNP+L+GDQWV+GYTPDVVI Sbjct: 605 QSVADKMTAMNLGTFSNGTAVNANVYGYTLAGKTGTTETNFNPDLAGDQWVIGYTPDVVI 66- 4 Query: 659 SQWVGFKNTDKHHYLTDSSAGTASNIFSTQASYILPYTKGSSFTHIENAYFQNGIGSVYN 71- 8 SQWVGF TD++HYLTDSSAGTAS IFSTQASYILPYTKGS F H++NAY QNGI +VY Sbjct: 665 SQWVGFNQTDENNYLTDSSAGTASAIFSTQASYILPYTKGSQF-HVDNAYAQNGISAVYG 72- 3 Query: 719 AQDASNTTNQESRSIINDLKDSASKAAQDISRAVEDSNFQEKVKDAWNSLKDYFR 773 + N + +++SII+ L+ SA +A+Q +S+AV+ S ++K + W +DYFR Sbjct: 724 VNETGNQSGVDTQSIIDGLRKSAQEASQSLSKAVDQSGLRDKAQSIWKEIVDYFR 778 SEQ ID 6262 (GBS397d) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 153 (lane 13; MW 76 kDa) and in FIG. 184 (lane 9; MW 76 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2024 A DNA sequence (GBSx2135) was identified in S. agalactiae <SEQ ID 6265> which encodes the amino acid sequence <SEQ ID 6266>. This protein is predicted to be M-like protein. Analysis of this protein sequence reveals the following: TABLE-US-06199 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.56 Transmembrane 609-625 (599-628) INTEGRAL Likelihood = -0.00 Transmembrane 19-35 (19-35) ----- Final Results ----- bacterial membrane --- Certainty = 0.5225(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06200 >GP:CAB91647 GB:AJ130830 cell wall protein, putative [Zea mays] Identities = 106/182 (58%), Positives = 123/182 (67%), Gaps = 8/182 (4%) Query: 396 KSDKKPDVKPEAKPEAK--PDVKPEAKPDVKPEAKPDVKPEAKPDVKPEAKPDV--KPEA 45- 1 K + KP+ KPE KPE K P KPE KP+ KPE KP+ KPE KP KPE KP+ KPE Sbjct: 116 KPEPKPEPKPEPKPKPKIKPKPKPEPKPEPKPSHKPEPKPEPKPKPKPEPKPEPQPKPEP 17- 5 Query: 452 KPDVKPKAKPDVKPEA--KPDVKPDVKPDVKPEA--KPEDKPDVKPDVKPEAKPDVKPEA 50- 7 KP+ KP+ KP+ KPE KP+ KP+ KP+ KPE KPE KP+ KP+ KPE KP+ KPE Sbjct: 176 KPEPKPEPKPEPKPEPQPKPEPKPEPKPEPKPEPQPKPEPKPEPKPEPKPEPKPEPKPEP 23- 5 Query: 508 KPEAKPEAKPEAKPEAKPEAKPDVKPEAKPDVKPEAKPKAKPEAKSEAKPEAKLEAKPEA 56- 7 KPE KPE +PE KPE KPE KP P+ +P KPE KPE KPE K E KPE K E KPE Sbjct: 236 KPEPKPEPRPEPKPEPKPEPKPKPDPKPEPQPKPEPKPEPKPEPKPEPKPEPKPEPKPEP 29- 5 Query: 568 KP 569 KP Sbjct: 296 KP 297 There is also homology to SEQ ID 822. A related GBS gene <SEQ ID 8957> and protein <SEQ ID 8958> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06201 Lipop: Possible Site: -1 Crend: 8 McG: Discrim Score: -5.20 GvH: Signal Score (-7.5): 3.07 Possible site: 27 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -10.56 threshold: 0.0 INTEGRAL Likelihood = -10.56 Transmembrane 609-625 (599-628) INTEGRAL Likelihood = -0.00 Transmembrane 19-35 (19-35) PERIPHERAL Likelihood = 8.54 139 modified ALOM score: 2.61 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5225(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 596-600 The protein has homology with the following sequences in the databases: ##STR00144## SEQ ID 6266 (GBS3) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 3 (lane 5; MW 65 kDa). The GBS3-His fusion product was purified (FIG. 189, lane 8) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 261), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2025 A DNA sequence (GBSx2136) was identified in S. agalactiae <SEQ ID 6267> which encodes the amino acid sequence <SEQ ID 6268>. This protein is predicted to be transcription antitermination protein nusg (nusG). Analysis of this protein sequence reveals the following: TABLE-US-06202 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3203(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-06203 >GP:CAA53738 GB:X76134 nusG [Staphylococcus carnosus] Identities = 90/175 (51%), Positives = 118/175 (67%), Gaps = 2/175 (1%) Query: 7 KGWFVLQTYSGYENKVKENLLQRAQTYNMLDNILRVEIPTQTVNVEKNGKTKEIEENRFP 66 K W+ + TYSGYENKVK+NL +R ++ NM + I RV IP + K+GK K++ + FP Sbjct: 8 KRWYAVHTYSGYENKVKKNLEKRVESMNMTEQIFRVVIPEEEETQVKDGKAKKLTKKTFP 67 Query: 67 GYVLVEMVMTDEAWFVVRNTPNVTGFVGSHGNRSKPTPLLEEEIRSILISMGQTVDVFDT 126- GYVLVE+VMTDE+W+VVRNTP VTGFVGS G SKP PLL +E+R IL MG D Sbjct: 68 GYVLVELVMTDESWYVVRNTPGVTGFVGSAGAGSKPNPLLPDEVRFILKQMGMKEKTIDV 127- Query: 127 NIKEGDVVQIIDGAFIGQEGRVVEIENNKVKL--MINMFGSETQAELELYQVAEL 179 ++ G+ V+I G F Q G V EIE +K KL +++MFG ET E+E Q+ +L Sbjct: 128 EVEVGEQVRIKSGPFANQVGEVQEIEADKFKLTVLVDMFGRETPVEVEFDQIEKL 182 A related DNA sequence was identified in S. pyogenes <SEQ ID 6269> which encodes the amino acid sequence <SEQ ID 6270>. Analysis of this protein sequence reveals the following: TABLE-US-06204 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3874(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06205 Identities = 170/179 (94%), Positives = 178/179 (98%) Query: 1 MLDSFDKGWFVLQTYSGYENKVKENLLQPAQTYNMLDNILRVEIPTQTVNVEKNGKTKEI 60 MLDSFDKGWFVLQTYSGYENKVKENLLQRAQTYNMLDNILRVEIPTQTVNVEKNG+TKEI Sbjct: 6 MLDSEDRGWFVLQTYSGYENKVKENLLQRAQTYNMLDNILRVEIPTQTVNVEKNGQTKEI 65 Query: 61 EENRFPGYVLVEMVMTDEAWFVVRNTPNVTGFVGSHGNRSKFTPLLEEEIRSILISMGQT 120- EENRFPGYVLVEMVMTDEAWFVVRNTPNVTGFVGSHGNRSKPTPLLEEEIR+IL+SMGQT Sbjct: 66 EENRFPGYVLVEMVMTDEAWFVVRNTPNVTGFVGSHGNRSKPTPLLEEEIRAILLSMGQT 125- Query: 121 VDVFDTNIKEGDVVQIIDGAFIGQEGRVVEIENNKVKLMINMFGSETQAELELYQVAEL 179- +DVFDTNIKEGDVVQIIDGAF+GQEGRVVEIENNKVKLM+NMFGSET AE+ELYQ+AEL Sbjct: 126 IDVFDTNIKEGDVVQIIDGAFMGQEGRVVEIENNKVKLMLNMFGSETVAEVELYQIAEL 184- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2026 A DNA sequence (GBSx2137) was identified in S. agalactiae <SEQ ID 6271> which encodes the amino acid sequence <SEQ ID 6272>. This protein is predicted to be a glycosyl transferase. Analysis of this protein sequence reveals the following: TABLE-US-06206 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1558(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06207 >GP:AAF28363 GB:AF224467 putative glycosyl transferase [Haemophilus ducreyi] Identities = 98/259 (37%), Positives = 155/259 (59%), Gaps = 10/259 (3%) Query: 5 VALAVDSNYLDRALVTIKSICVYNRNITFYLFNQDTPVEWVRNINRKLEPLGSKLINVKI 64 + LA + +Y + L TIKSI ++N++I FYL N+D P EW +N KL L S++I++K+ Sbjct: 10 IVLAANQSYSEYILTTIKSIYLHNKHIRFYLLNRDYPTEWFDILNNKLRKLNSEIIDIKV 69 Query: 65 YNYDIAHLTTFLTVS---TWFRLFLADYIPSSRVLYLDSDIIVNTNLDYLFELDFKGYYL 121- N I + T+ +S---T+FR F++D+I +V+YLD+DI+VN +L L++ D Y+L Sbjct: 70 TNDTIKNFKTYSHISSDTTFFRYFISDFISQDKVIYLDADIVVNGSLTELYQTDISNYFL 129- Query: 122 AAVKDPHKNE----EGGFNAGNLLANLELWREDGLTKTLLKTAEELHRVVKTGDQSILNI 17- 7 AAVKD + FNAGMLL N + WRE +T+ L +E+ + DQSILN+ Sbjct: 130 AAVKDIISEKIYVNNHIFNAGNLLINNKKWREHNITQFCLSLSEKYINSLPDADQSILNL 18- 9 Query: 178 VCHNRWLSLNKTWNF--QTYDVVSRYNHRSYLYLNIENRTPNIIHFLTSDKPWNENSVAR 23- 5 + ++WL LN++N+ T + +Y YL ++ P IIN+ T KPW R Sbjct: 190 IFKDKWLKLNRGYNYLIGTDYLFFKYGKTRYLE-DLGETIPLIIHYNTEAKPWLNIFNTR 24- 8 Query: 236 FRELWWYYFQLDFCQLTGK 254 FR ++W+Y++L++ + K Sbjct: 249 FRNIYWFYYELNWQDIYAK 267 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2027 A DNA sequence (GBSx2138) was identified in S. agalactiae <SEQ ID 6273> which encodes the amino acid sequence <SEQ ID 6274>. Analysis of this protein sequence reveals the following: TABLE-US-06208 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0417(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2028 A DNA sequence (GBSx2139) was identified in S. agalactiae <SEQ ID 6275> which encodes the amino acid sequence <SEQ ID 6276>. Analysis of this protein sequence reveals the following: TABLE-US-06209 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.60 Transmembrane 306-322 (306-322) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06210 >GP:AAF28363 GB:AF224467 putative glycosyl transferase [Haemophilus ducreyi] Identities = 88/259 (33%), Positives = 156/259 (59%), Gaps = 11/259 (4%) Query: 7 VVLAGDYSYIRQIETTLKSLCVYHENLSIFIFNQDIPQEWFLAMKDRVGQTGNQIQDVKL 66 +VLA + SY I TT+KS+ ++++++ ++ N+D P EWF + +++ + ++I D+K+ Sbjct: 10 IVLAANQSYSEYILTTIKSIYLHNKHIRFYLLNRDYPTEWFDILNNKLRKLNSEIIDIKV 69 Query: 67 FHDHLSPKWENKKLNHINY-MTYARYFIPQYISADTVLYLDSDLVVTTNLDNLFQISLDN 125- +D + K +HI+ T+ RYFI +I D V+YLD+D+VV +L L+Q + N Sbjct: 70 TNDTIK---NFKTYSHISSDTTFFRYFISDFIEQDKVIYLDADIVVNGSLTELYQTDISN 126- Query: 126 AYLAAVP-----ALFGLGYGFNAGVNVINNQRWRQENMTIKLIEKNQKEIENANEGDQTI 18- 0 +LAAV ++ + FNAG+++INN++WR+ N+T + ++K I + + DQ+I Sbjct: 127 YFLAAVKDIISEKIYVNNHIFNAGMLLINNKKWREHNITQFCLSLSEKYINSLPDADQSI 18- 6 Query: 181 LNRNFENQVIYLDDTYNFQIGFD-MGAAIDGHKFIFDIPITPLPKIIHYISGIKPWQTLS 23- 9 LN +F+++ + L+ YN+ IG D + +++ D+ T +P IIHY + KPW + Sbjct: 187 LNLIFKDKWLKLNRGYNYLIGTDYLFFKYGKTRYLEDLGET-IPLIIHYNTEAKPWLNIF 24- 5 Query: 240 NMRLRSVWWHYNLLEWSSI 258 N R R ++W Y L W I Sbjct: 246 NTRFRNIYWFYYELNWQDI 264 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 6276 (GBS395) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 75 (lane 5; MW 47.4 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 83 (lane 8; MW 72 kDa) and in FIG. 177 (lane 5; MW 72 kDa). GBS395-GST was purified as shown in FIG. 217, lane 7. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2029 A DNA sequence (GBSx2140) was identified in S. agalactiae <SEQ ID 6277> which encodes the amino acid sequence <SEQ ID 6278>. Analysis of this protein sequence reveals the following: TABLE-US-06211 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial Cytoplasm --- Certainty = 0.1633(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2030 A DNA sequence (GBSx2141) was identified in S. agalactiae <SEQ ID 6279> which encodes the amino acid sequence <SEQ ID 6280>. Analysis of this protein sequence reveals the following: TABLE-US-06212 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 36-52 (36-52) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10243> which encodes amino acid sequence <SEQ ID 10244> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06213 >GP:AAC77330 GB:AE000508 orf, hypothetical protein [Escherichia coli K12] Identities = 75/260 (28%), Positives = 123/260 (46%), Gaps = 22/260 (8%) Query: 6 VGLVLEGGGMRGLYTAGVLDAFLDAGIK-IDGIVSVSAGALFGVNFVSRQRERALRYNKK 64 + LV EGGG RG++TAGVLD F+A D + SAGA F+ Q A + + Sbjct: 25 IALVCEGGGQRGIFTAGVLDEFMRAQFNPFDLYLGTSAGAQNLSAFICNQPGYARKVIMR 84 Query: 65 YLSHPKYMSLRSWFRTGNFVNKDF----TYYEVPMKLD----VFDDEAFKKSSIDFYVVA 116- Y + ++ + R GN ++ D+ T ++P+++D +FD S FY+ A Sbjct: 85 YTTKREFFDPLRFVRGGNLIDLDWLVEATASQMPLQMDTAARLFD------SGKSFYMCA 138- Query: 117 TEMTSGKPEYFKIDSVFEQMEILRASSALPVVSKM-VDWQGKKYLDGGLSDSIPVDFARG 17- 5 P YF + + ++++RASSA+P + V +G YLDGG+SD+IPV A Sbjct: 139 CRQDDYAPNYF-LPTKQNWLDVIRASSAIPGFYRSGVSLEGINYLDGGISDAIPVKEAAR 19- 7 Query: 176 LGFDKLIVVMTRPLNYQKKPSSGR-----LYKTLYRKYPNFVKTASNRYQQYNNSLEKVM 23- 0 G L+V+ T P P + L + + N V+ Y+ +EK Sbjct: 198 QGAKTLVVIRTVPSQMYYTPQWFKRMERWLGDSSLQPLVNLVQHHETSYRDIQQFISKPP 25- 7 Query: 231 SLEKTGDLFAIRPSKSLVIG 250 + +++ +P S+ +G Sbjct: 258 GKLRIFEIYPPKPLHSIALG 277 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8959> and protein <SEQ ID 8960> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06214 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -5.16 GvH: Signal Score (-7.5): -2.17 Possible site: 44 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -0.16 threshold: 0.0 INTEGRAL Likelihood = -0.16 Transmembrane 36-52 (36-52) PERIPHERAL Likelihood = 4.14 18 modified ALOM score: 0.53 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00145## SEQ ID 8960 (GBS394) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 75 (lane 4; MW 34.7 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 83 (lane 7; MW 60 kDa). GBS394-GST was purified as shown in FIG. 217, lane 6. EXAMPLE 2031 A DNA sequence (GBSx2142) was identified in S. agalactiae <SEQ ID 6281> which encodes the amino acid sequence <SEQ ID 6282>. Analysis of this protein sequence reveals the following: TABLE-US-06215 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3004(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2032 A DNA sequence (GBSx2143) was identified in S. agalactiae <SEQ ID 6283> which encodes the amino acid sequence <SEQ ID 6284>. This protein is predicted to be transporter protein. Analysis of this protein sequence reveals the following: TABLE-US-06216 Possible site: 49 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.85 Transmembrane 373-389 (370-395) INTEGRAL Likelihood = -6.74 Transmembrane 168-184 (162-187) INTEGRAL Likelihood = -6.32 Transmembrane 259-275 (257-280) INTEGRAL Likelihood = -4.78 Transmembrane 286-302 (285-306) INTEGRAL Likelihood = -3.19 Transmembrane 55-71 (54-71) INTEGRAL Likelihood = -2.97 Transmembrane 84-100 (79-101) INTEGRAL Likelihood = -2.87 Transmembrane 311-327 (310-328) INTEGRAL Likelihood = -1.44 Transmembrane 355-371 (355-371) INTEGRAL Likelihood = -0.64 Transmembrane 108-124 (108-125) ----- Final Results ----- bacterial membrane --- Certainty = 0.3739(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06217 >GP:AAC22759 GB:U32790 transporter protein [Haemophilus influenzae Rd] Identities = 139/391 (35%), Positives = 221/391 (55%), Gaps = 4/391 (1%) Query: 6 INKNNWRALIAAIVASGTDDLNIMFLAFSMSTIITDLHLSAAQAGWIGTITNLGMLVGGL 65 +N W+ALI + V G D +++ L F +S I DL+L+ AQ G + T T +G + GG+ Sbjct: 5 VNSYGWKALIGSAVGYGMDGFDLLILGFMLSAISADLNLTPAQGGSLVTWTLIGAVFGGI 64 Query: 66 IFGLLADRYNKFKVFKWTILIFSIATGLVFFTTNLSYLYIMRFIAGIGVGGEYGIAIAIM 125- +FG L+D+Y + +V WTIL+F++ TGL L I R IAGIG+GGE+GI +A+ Sbjct: 65 LFGALSDKYGRVRVLTWTILLFAVFTGLCAIAQGYWDLLIYRTIAGIGLGGEFGIGMALA 124- Query: 126 AGIVPTNKMGRISSLNGIAGQVGSISSALLAGWLAPALGWRGLFLFGLLPIVLVLWMQFA 18- 5 A P + +S + QVG + +ALL L P +GWRG+FL G+ P + +++ Sbjct: 125 AEAWPARHRAKAASYVALGWQVGVLGAALLTPLLLPHIGWRGMFLVGIFPAFVAWFLRSH 18- 4 Query: 186 VDDKDILDQYNTDADDEPLDI----SIKALFDTPVLATQSLALMVMTTVQIAGYFGMMNW 24- 1 + + +I Q T + S + L + SL ++V+T+VQ GY+G+M W Sbjct: 185 LHEPEIFTQKQTALSTQSSFTDKLRSFQLLIKDKATSKISLGIVVLTSVQNFGYYGIMIW 24- 4 Query: 242 LPTIIQTNLNVSVKNSSLWMIATILGMCLGMLVFGQLLDKFGPRLVYGCFLLSSAICVYL 30- 1 LP + L S+ S LW T+ GM G+ +FGQL D+ G + + F L + I + + Sbjct: 245 LPNFLSKQLGFSLTKSGLWTAVTVCGMMAGIWIFGQLADRIGRKPSFLLFQLGAVISIVV 30- 4 Query: 302 FQFATTMPSMIIGGAVVGFFVNGMFAGYGAMITRLYPHHIRSTANNLILNVGRAIGGFSS 36- 1 + T M++ GA +G FVNGM GYGA++ YP R+TA N++ N+GRA+GGF Sbjct: 305 YSQLTDPDIMLLAGAFLGMFVNGMLGGYGALMAEAYPTEARATAQNVLFNIGRAVGGFGP 36- 4 Query: 362 VIIGMILDVSNVSMVMLFLASLYIVSFLSML 392 V++G ++ + + LA +Y++ L+ + Sbjct: 365 VVVGSVVLAYSFQTAIALLAIIYVIDMLATI 395 A related DNA sequence was identified in S. pyogenes <SEQ ID 2377> which encodes the amino acid sequence <SEQ ID 2378>. Analysis of this protein sequence reveals the following: TABLE-US-06218 Possible site: 39 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.92 Transmembrane 168-184 (162-188) INTEGRAL Likelihood = -5.41 Transmembrane 286-302 (285-306) INTEGRAL Likelihood = -5.15 Transmembrane 372-388 (362-394) INTEGRAL Likelihood = -3.45 Transmembrane 259-275 (257-276) INTEGRAL Likelihood = -2.87 Transmembrane 311-327 (306-328) INTEGRAL Likelihood = -2.81 Transmembrane 55-71 (51-71) INTEGRAL Likelihood = -0.48 Transmembrane 108-124 (108-125) INTEGRAL Likelihood = -0.37 Transmembrane 84-100 (84-100) ----- Final Results ----- bacterial membrane --- Certainty = 0.4567(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06219 Identities = 306/402 (76%), Positives = 354/402 (87%) Query: 1 MSPLNINKNNWRALIAAIVASGTDDLNIMFLAFSMSTIITDLHLSAAQAGWIGTITNLGN 60 MS L+++ N RAL+AAI ASGTDDLN+MFLAFSMS+I+TDL LS Q GWI TITNLGM Sbjct: 1 MSTLSLDTTNKRALVAAIAASGTDDLNVMFLAFSMSSIMTDLGLSGTQGGWIATITNLGM 60 Query: 61 LVGGLIFGLLADRYNKFKVFKWTILIFSIATGLVFFTTNLSYLYIMRFIAGIGVGGSYGI 120- LVGGL+FGLLADR++KFKVFKWTIL+FS+ATGL++FT +L YLY+MRFIAGIGVGGEYG+ Sbjct: 61 LVGGLLFGLLADRHHKFKVFKWTILLFSVATGLIYFTQSLPYLYLMRFIAGIGVGGEYGV 120- Query: 121 AIAIMAGIVPTNKMGRISSLNGIAGQVGSISSALLAGWLAPALGWRGLFLFGLLPIVLVL 18- 0 AIAIMAGIVP KMGR+SSLNGIAGQ+GSISSALLAGWLAP+LGWRGLFLFGLLPI+LV+ Sbjct: 121 AIAIMAGIVPPEKMGRMSSLNGIAGQLGSISSALLAGWLAPSLGWRGLFLFGLLPILLVI 18- 0 Query: 181 WMQFAVDDKDILDQYNTDADDEPLDISIKALFDTPVLATQSLALMVMTTVQIAGYFGMMN 24- 0 WM A+DD+ I D Y + ++ I I LF T L Q+LALMVMTTVQIAGYFGMMN Sbjct: 181 WMTLAIDDQKIWDHYGQEEEECSQPIKINELFKTKSLTAQTLALMVMTTVQIAGYFGMMN 24- 0 Query: 241 WLPTIIQTNLNVSVKNSSLWMIATILGMCLGMLVFGQLLDKFGPRLVYGCFLLSSAICVY 30- 0 WLPTIIQT+LN+SVK+SSLWM+ATI+GMCLGML FGQLLD FGPRL+Y FLL+S+ICVY Sbjct: 241 WLPTIIQTSLNLSVKSSSLWMVATIVGMCLGMLYFGQLLDCFGPRLIYSLFLLASSICVY 30- 0 Query: 301 LFQFATTMPSMIIGGAVVGFFVNGMFAGYGAMITRLYPHHIRSTANNLILNVGRAIGGFS 36- 0 LFQFA +M SM+IGGA+VGFFVNGMFAGYGAMITRLYPHHIRSTANN+ILNVGRA+GGFS Sbjct: 301 LFQFANSMASMVIGGAIVGFFVNGMFAGYGAMITRLYPHHIRSTANNVILNVGRALGGFS 36- 0 Query: 361 SVIIGMILDVSNVSMVMLFLASLYIVSFLSMLSIKQLKRQKY 402 SV IG ILD S +SMVM+FLASLY++SF +M SI QLK ++Y Sbjct: 361 SVAIGSILDASGISMVMIFLASLYVISFGAMWSIGQLKAERY 402 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2033 A DNA sequence (GBSx2144) was identified in S. agalactiae <SEQ ID 6285> which encodes the amino acid sequence <SEQ ID 6286>. This protein is predicted to be leucyl-tRNA synthetase (leuS). Analysis of this protein sequence reveals the following:

TABLE-US-06220 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3481(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10241> which encodes amino acid sequence <SEQ ID 10242> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06221 >GP:AAC00259 GB:AF008220 leucine tRNA synthetase [Bacillus subtilis] Identities = 569/835 (68%), Positives = 666/835 (79%), Gaps = 42/835 (5%) Query: 10 YNHKEIEPKWQAFWADNHTFKTGTDASKPKFYALDMFPYPSGAGLHVGHPEGYTATDILS 69 - + HKETE KWQ +W +N TF T + K KFYALDMFPYPSGAGLHVGHPEGYTATDILS Sbjct: 3 FQHKEIEKKWQTYWLENKTFATLDNNEKQKFYALDMFPYPSGAGLHVGHPEGYTATDILS 62 Query: 70 RFKRAQGHNVLHPMGWDAFGLPAEQYAMDTGNDPAEFTAENIANFKRQINALGFSYDWDR 129- R KR QG++VLHPMGWDAFGLPAEQYA+DTGNDPA FT +NI NF+RQI ALGFSYDWDR Sbjct: 63 RMKRMQGYDVLHPMGWDAFGLPAEQYALDTGNDPAVFTKQNIDNFRRQIQALGFSYDWDR 122- Query: 130 EVNTTDPNYYKWTQWIFTKLYEKGLAYEAEVPVNWVEELGTAIANEEVLPDGTSERGGYP 18- 9 E+NTTDP YYKWTQWIF KLYEKGLAY EVPVNW LGT +ANEEV+ DG SERGG+P Sbjct: 123 EINTTDPEYYKWTQWIFLKLYEKGLAYVDEVPVNWCPALGTVLANEEVI-DGKSERGGHP 18- 1 Query: 190 VVRKPMRQWMLKITAYAERLLEDLEEVDWPESIKDMQRNWIGKSTGANVTFKVKDTDKDF 24- 9 V R+PM+QWMLKITAYA+RLLEDLEE+DWPESIKDMQRNWIG+S GA+V F + D F Sbjct: 182 VERRPMKQWMLKITAYADRLLEDLEELDWPESIKDMQRNWIGRSEGAHVHFAIDGHDDSF 24- 1 Query: 250 TVFTTRPDTLFGATYAVLAPEHALVDAITTADQAEAVAEYKRQASLKSDLARTDLAKEKT 30- 9 TVFTTRPDTLFGATY VLAPEHALV+ ITTA+Q EAV Y ++ KSDL RTDLAK KT Sbjct: 242 TVFTTRPDTLFGATYTVLAPEHALVENITTAEQKEAVEAYIKEIQSKSDLERTDLAKTKT 30- 1 Query: 310 GVWTGAYAINPVNGKEIPVWIADYVLASYGTGAIMAVPAHDERDWEFAKQFNLDIIPVLE 36- 9 GV+TGAYAINPVNG+++P+WIADYVLASYGTGA+MAVP HDERD+EFAK F L + V++ Sbjct: 302 GVFTGAYAINPVNGEKLPIWIADYVLASYGTGAVMAVPGHDERDFEFAKTFGLPVKEVVK 36- 1 Query: 370 GGNVEEAAFTEDGLHINSDFLDGLDKAAAIAKMVEWLEAEGVGNEKVTYRLRDWLFSRQR 42- 9 GGNVEEAA+T DG H+NSDFL+GL K AI K++ WLE G +KVTYRLRDWLFSRQR Sbjct: 362 GGNVEEAAYTGDGEHVNSDFLNGLHKQEAIEKVIAWLEETKNGEKKVTYRLRDWLFSRQR 42- 1 Query: 430 YWGEPIPIIHWEDGTSTAVPESELPLVLPVTKDIRPSGTGESPLANLTDWLEVT-REDGV 48- 8 YWGEPIP+IHWEDGTSTAVPE ELPL+LP T +I+PSGTGESPLAN+ +W+EVT E G Sbjct: 422 YWGEPIPVIHWEDGTSTAVPEEELPLILPKTDEIKPSGTGESPLANIKEWVEVTDPETGK 48- 1 Query: 489 KGRRETNTMPQWAGSSWYYLRYIDPHNTEKLADEELLKQWLPVDIYVGGAEHAVLHLLYA 54- 8 KGRRETNTMPQWAGS WY+LRYIDPHN ++LA E L++WLPVD+Y+GGAEHAVLHLLYA Sbjct: 482 KGRRETNTMPQWAGSCWYFLRYIDPHNPDQLASPEKLEKWLPVDMYIGGAEHAVLHLLYA 54- 1 Query: 549 RFWHKVLYDLGVVPTKEPFQKLFNQGMILGTSYRDSRGALVATDKVEKRDGSFFHVETGE 60- 8 RFWHK LYD+GVVPTKEPFQKL+NQGMILG E E Sbjct: 542 RFWHKFLYDIGVVPTKEPFQKLYNQGMILG--------------------------ENNE 57- 5 Query: 609 ELEQAPAKMSKSLKNVVNPDDVVEQYGADTLRVYEMFMGPLDASIAWSEEGLEGSRKFLD 66- 8 KMSKS NVVNPD++V +GADTLR+YEMFMGPLDASIAWSE GL+G+R+FLD Sbjct: 576 -------KMSKSKGNVVNPDEIVASHGADTLRLYEMFMGPLDASIAWSESGLDGARRFLD 62- 8 Query: 669 RVYRLI------TTKEITEENSGALDKVYNETVKAVTEQVDQMKFNTAIAQLMVFVNAAN 72- 2 RV+RL +I E L++VY+ETV VT+ + ++FNT I+QLMVF+N A Sbjct: 629 RVWRLFIEDSGELNGKIVEGAGETLERVYHETVMKVTDHYEGLRFNTGISQLMVFINEAY 68- 8 Query: 723 KEDKLFSDYAKGFVQLIAPFAPHLGEELWQVLTASGQSISYVPWPSYDESKLVENEIEIV 78- 2 K +L +Y +GFV+L++P APHL EELW+ L SG +I+Y WP YDE+KLV++E+EIV Sbjct: 689 KATELPKEYMEGFVKLLSPVAPHLAEELWEKLGHSG-TIAYEAWPVYDETKLVDDEVEIV 74- 7 Query: 783 VQIKGKVKAKLVVAKDLSREELQDLALANEKVQAEIAGKDIIKVIAVPNKLVNIV 837 VQ+ GKVKAKL V D ++E+L+ LA A+EKV+ ++ GK I K+IAVP KLVNIV Sbjct: 748 VQLNGKVKAKLQVPADATKEQLEQLAQADEKVKEQLEGKTIRKIIAVPGKLVNIV 802 A related DNA sequence was identified in S. pyogenes <SEQ ID 6287> which encodes the amino acid sequence <SEQ ID 6288>. Analysis of this protein sequence reveals the following: TABLE-US-06222 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4358(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06223 Identities = 815/833 (97%), Positives = 827/833 (98%) Query: 7 MTFYNHKEIEPKWQAFWADNHTFKTGTDASKPKFYALDMFPYPSGAGLHVGHPEGYTATD 66 MTFY+H IEPKWQAFWADNHTFKTGTDASKPKFYALDMFPYPSGAGLHVGHPEGYTATD Sbjct: 1 MTFYDHTAIEPKWQAFWADNHTFKTGTDASKPKFYALDMFPYPSGAGLHVGHPEGYTATD 60 Query: 67 ILSRFKRAQGHNVLHPMGWDAFGLPAEQYAMDTGNDPAEFTAENIANFKRQINALGFSYD 126- ILSRFKRAQGHN+LHPMGWDAFGLPAEQYAMDTGNDPAEFTAENIANFKRQINALGFSYD Sbjct: 61 ILSRFKRAQGHNILHPMGWDAFGLPAEQYAMDTGNDPAEFTAENIANFKRQINALGFSYD 120- Query: 127 WDREVNTTDPNYYKWTQWIFTKLYEKGLAYEAEVPVNWVEELGTAIANEEVLPDGTSERG 18- 6 WDREVNTTDPNYYKWTQWIFTKLYEKGLAYEAEVPVNWVEELGTAIANEEVLPDGTSERG Sbjct: 121 WDREVNTTDPNYYKWTQWIFTKLYEKGLAYEAEVPVNWVEELGTAIANEEVLPDGTSERG 18- 0 Query: 187 GYPVVRKPMRQWMLKITAYAERLLEDLEEVDWPESIKDMQRNWIGKSTGANVTFKVKDTD 24- 6 GYPVVRKPMRQWMLKITAYAERLLEDLEEVDWPESIKDMQRNWIGKSTGANVTFKVKDTD Sbjct: 181 GYPVVRKPMRQWMLKITAYAERLLEDLEEVDWPESIKDMQRNWIGKSTGANVTFKVKDTD 24- 0 Query: 247 KDFTVFTTRPDTLFGATYAVLAPEHALVDAITTADQAEAVAEYKRQASLKSDLARTDLAK 30- 6 KDFTVETTRPDTLFGATYAVLAPEHALVDAITTADQAEAVA+YKRQASLKSDLARTDLAK Sbjct: 241 KDFTVFTTRPDTLFGATYAVLAPEHALVDAITTADQAEAVAKYKRQASLKSDLARTDLAK 30- 0 Query: 307 EKTGVWTGAYAINPVNGKEIPVWIADYVLASYGTGAIMAVPAHDERDWEFARQFNLDIIP 36- 6 EKTGVWTGAYAINPVNG E+PVWIADYVLASYGTGAIMAVPAHDERDWEFAKQF LDIIP Sbjct: 301 EKTGVWTGAYAINPVNGNEMPVWIADYVLASYGTGAIMAVPAHDERDWEFAKQFKLDIIP 36- 0 Query: 367 VLEGGNVEEAAFTEDGLHINSDFLDGLDKAAAIAKMVEWLEAEGVGNEKVTYRLRDWLFS 42- 6 VLEGGNVEEAAFTEDGLHINS FLDGLDKA+AIAKMVEWLEAEGVGNEKVTYRLRDWLFS Sbjct: 361 VLEGGNVEEAAFTEDGLHINSGFLDGLDKASAIAKMVEWLEAEGVGNEKVTYRLRDWLFS 42- 0 Query: 427 RQRYWGEPIPIIHWEDGTSTAVPESELPLVLPVTKDIRPSGTGESPLANLTDWLEVTRED 48- 6 RQRYWGEPIPIIHWEDGTSTAVPESELPLVLPVTKDIRPSGTGESPLAN+TDWLEVTRED Sbjct: 421 RQRYWGEPIPIIHWEDGTSTAVPESELPLVLPVTKDIRPSGTGESPLANVTDWLEVTRED 48- 0 Query: 487 GVKGRRETNTMPQWAGSSWYYLRYIDPHNTEKLADEELLKQWLPVDIYVGGAEHAVLHLL 54- 6 GVKGRRETNTMPQWAGSSWYYLRYIDPHNTEKLADEELLKQWLPVDIYVGGAEHAVLHLL Sbjct: 481 GVKGRRETNTMPQWAGSSWYYLRYIDPHNTEKLADEELLKQWLPVDIYVGGAEHAVLHLL 54- 0 Query: 547 YARFWHKVLYDLGVVPTKEPFQKLFNQGMILGTSYRDSRGALVATDKVEKRDGSFFHVET 60- 6 YARFWHKVLYDLGVVPTKEPFQKLFNQGMILGTSYRDSRGALVATDKVEKRDGSFFHVET Sbjct: 541 YARFWHKVLYDLGVVPTKEPFQKLFNQGMILGTSYRDSRGALVATDKVEKRDGSFFHVET 60- 0 Query: 607 GEELEQAPAKMSKSLKNVVNPDDVVEQYGADTLRVYEMFMGPLDASIAWSEEGLEGSRKF 66- 6 GEELEQAPAKMSKSLKNVVNPDDVVEQYGADTLRVYEMFMGPLDASIAWSEEGLEGSRKF Sbjct: 601 GEELEQAPAKMSKSLKNVVNPDDVVEQYGADTLRVYEMFMGPLDASIAWSEEGLEGSRKF 66- 0 Query: 667 LDRVYRLITTKEITEENSGALDKVYNETVKAVTEQVDQMKFNTAIAQLMVFVNAANKEDK 72- 6 LDRVYRLITTKEITEENSGALDKVYNETVKAVTEQVDQMKFNTAIAQLMVFVNAANKEDK Sbjct: 661 LDRVYRLITTKEITEENSGALDKVYNETVKAVTEQVDQMKFNTAIAQLMVFVNAANKEDK 72- 0 Query: 727 LFSDYAKGFVQLIAPFAPHLGEELWQVLTASGQSISYVPWPSYDESKLVENEIEIVVQIK 78- 6 LFSDYAKGFVQLIAPFAPHLGEELWQ LTASG+SISYVPWPSYDESKLVEN++EIVVQIK Sbjct: 721 LFSDYAKGFVQLIAPFAPHLGEELWQALTASGESISYVPWPSYDESKLVENDVEIVVQIK 78- 0 Query: 787 GKVKAKLVVAKDLSREELQDLALANEKVQAEIAGKDIIKVIAVPNKLVNIVVK 839 GKVKAKLVVAKDLSREELQ++ALANEKVQAEIAGKDIIKVIAVPNKLVNIV+K Sbjct: 781 GKVKAKLVVAKDLSREELQEVALANEKVQAEIAGKDIIKVIAVPNKLVNIVIK 833 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2034 A DNA sequence (GBSx2145) was identified in S. agalactiae <SEQ ID 6289> which encodes the amino acid sequence <SEQ ID 6290>. This protein is predicted to be KLAA1074 protein. Analysis of this protein sequence reveals the following: TABLE-US-06224 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8961> which encodes amino acid sequence <SEQ ID 8962> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-06225 Lipop: Possible site: -1 Crend: 7 SRCFLG: 0 McG: Length of UR: 19 Peak Value of UR: 2.86 Net Charge of CR: 4 McG: Discrim Score: 10.27 GvH: Signal Score (-7.5): -3.61 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program Count: 0 value: 2.12 threshold: 0.0 PERIPHERAL Likelihood = 2.12 7 modified ALOM score: -0.92 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 8962 (GBS117) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 29 (lane 8; MW 22.5 kDa). GBS117-His was purified as shown in FIG. 200, lane 7. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2035 A DNA sequence (GBSx2146) was identified in S. agalactiae <SEQ ID 6291> which encodes the amino acid sequence <SEQ ID 6292>. This protein is predicted to be YirC (resE). Analysis of this protein sequence reveals the following: TABLE-US-06226 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.88 Transmembrane 177-193 (173-196) INTEGRAL Likelihood = -4.09 Transmembrane 10-26 (5-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.5352(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06227 >GP:CAB15292 GB:Z99120 similar to two-component sensor histidine kinase [YvqA] [Bacillus subtilis] Identities = 108/379 (28%), Positives = 193/379 (50%), Gaps = 33/379 (8%) Query: 92 DNHKKESHDIIRYLTQKRLWQISKEKDGMFVTIKKKTYYVMTKDYSGILVDGSIKKVPKA 151- +N + S + L+ + ++ K D KKK Y + D +G V IKK Sbjct: 86 ENEEASSDKDLSILSSSFIHKVYKLADKQ--EAKKKRY---SADVNGEKVFFVIKKGLSV 140- Query: 152 QSQLFHVINFS------DITYTQHLITKINHFLIVILVLTYIPMLFIMRKTFTGIRESIQ 20- 5 Q +++++ D+ YT L ++ + V+++L++IP +++ + + + Sbjct: 141 NGQSAMMLSYALDSYRDDLAYT--LFKQLLFIIAVVILLSWIPAIWLAKY----LSRPLV 19- 4 Query: 206 SVQTYISSLWKNQGNHQSSQKEIVFSDFDPLLLESQEMANRIYQAEESQRNFFQNASHEL 26- 5 S + ++ + ++ + K + L +EM ++ Q +E++R QN SH+L Sbjct: 195 SFEKHVKRI--SEQDWDDPVKVDRKDEIGKLGHTIEEMRQKLVQKDETERTLLQNISHDL 25- 2 Query: 266 RTPLMSIQGYTEGVQEGII---DAELAHSVILQESKKMKQLVDDIILLSKLD--SNLSDQ 32- 0 +TP+M I+GYT+ +++GI D K VI E+ K+++ + D++ L+KLD + Q Sbjct: 253 KTPVMVIRGYTQSIKDGIFPKGDLENTVDVIECEALKLEKKIKDLLYLTKLDYLAKQKVQ 31- 2 Query: 321 KDEFSLNELLNSIIAYFKPLANKQKISITYRPDKHEKLLK-GNEELIQRAINNILSNALR 37- 9 D FS+ E+ +I K A K+ +++ D E +L G+ E + + NIL N +R Sbjct: 313 HDMFSIVEVTEEVIERLK-WARKE---LSWEIDVEEDILMPGDPEQWNKLLENILENQIR 36- 8 Query: 380 YAVSHIEISYT----NQKLTISNDGPAISKEDLPYIFDRFYKGHGGQTGIGLAMTKEIIK 43- 5 YA + IEIS N +TI NDGP I E L +++ F KG G+ GIGL++ K I+ Sbjct: 369 YAETKIEISMKQDDRNIVITIKNDGPHIEDEMLSSLYEPFNKGKKGEFGIGLSIVKRILT 42- 8 Query: 436 QHHGNIIAESDSTSTTFTI 454 H +I E+D T ++ I Sbjct: 429 LHKASISIENDKTGVSYRI 447 There is also homology to SEQ ID 1178. SEQ ID 6292 (GBS279) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 52 (lane 7; MW 54.5 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 58 (lane 6; MW 79.4 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2036 A DNA sequence (GBSx2147) was identified in S. agalactiae <SEQ ID 6293> which encodes the amino acid sequence <SEQ ID 6294>. This protein is predicted to be two-component response regulator (mtrA). Analysis of this protein sequence reveals the following: TABLE-US-06228 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1706(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10239> which encodes amino acid sequence <SEQ ID 10240> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06229 >GP:BAB05663 GB:A001513 two-component response regulator [Bacillus halodurans] Identities = 87/220 (39%), Positives = 124/220 (55%), Gaps = 4/220 (1%) Query: 11 IYFADDEKNIRDLVVPFLEHDGFTVRAFETGDLLLEAYKNQKPDLVILDIMMPGTNGLDV 70 - I DDE ++R+LV +L +GF V ETGD ++ + + DLV+LD+MM +G Sbjct: 7 ILIVDDELDLRELVTSYLRKEGFAVYTAETGDEAIKRLEQEPMDLVVLDVMMDEMDGFTA 66 Query: 71 MKSIRQYDNIPIIMLTARDSDVDFITAFNLGTDDYFTKPFSPIKLSLHVKALFKRLDEKA 130- K IR + IPIIMLTAR + D + +G DDY KPFSP +L ++ +R Sbjct: 67 CKEIRAFSQIPIIMLTARGGEDDKVMGLQIGADDYIVKPFSPRELVARIEVALRRTQGIQ 126- Query: 131 IKNDTQYQFLDLTLDTEKRIALLSNEEMPLTKTEFDFLLVLIEKPETAFSRETLLNRIWG 19- 0 +DT Y+F +L + R ++ +E+ LTK E+D L+ L+E F+RE L +R+WG Sbjct: 127 QVDDTGYRFNELRIQPSGRKVFVNGQEISLTKKEYDLLVFLLEHRGRVFTREHLHDRLWG 18- 6 Query: 191 FDDIES--RAVDDTIKRLRKKFKQYHSQVSIKTVWGYGFK 228 D + R VD IK LR K K + IKTVWG G+K Sbjct: 187 MDTQQGTLRTVDTHIKTLRLKLKP--ADRFIKTVWGVGYK 224 There is also homology to SEQ ID 3260. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2037 A DNA sequence (GBSx2148) was identified in S. agalactiae <SEQ ID 6295> which encodes the amino acid sequence <SEQ ID 6296>. Analysis of this protein sequence reveals the following: TABLE-US-06230 Possible Site: 55 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -2.18 Transmembrane 1568-1584 (1568-1585) INTEGRAL Likelihood = -0.16 Transmembrane 338-354 (338-354) ----- Final Results ----- bacterial membrane --- Certainty = 0.1871(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10237> which encodes amino acid sequence <SEQ ID 10238> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06231 >GP:AAG09771 GB:AF243528 cell envelope proteinase [Streptococcus thermophilus] Identities = 797/1594 (50%), Positives = 1056/1594 (66%), Gaps = 39/1594 (2%) Query: 21 MNTKQRFSIRKYKLGAVSVLLGTLFFLGGITNVAADSVINKPSDIAVEQQVKDSPTS-IA 79 - M K+ FS+RKYK+G VSVLLG +F G +VAAD + + + VE V D+ S A Sbjct: 1 MKKKETFSLRKYKIGTVSVLLGAVFLFAGAPSVAADELTSLV-ETKVEATVPDAIVSESA 59 Query: 80 NETPTNN--TSSALASTAQDNLVTKANNSPTETQPVAESHSQATETFSPVANQPVESTQE 137- +E+P +++ +T+ D T ++ + S + ET P P S ++ Sbjct: 60 SESPVVEELVDTSVEATSTDVTTTDNEEETPGSEALENSANTEVETTQPAVETPAISEKK 119- Query: 138 VSKTPLTKQNLAVKSTPAISKET--PQNIDSNKIITVPKVWNTGYKGEGTVVAIIDSGLD 19- 5 V + K ++A ++T ++E PQNIDSN IITVPKVW +GYKGEGTVVAIIDSGLD Sbjct: 120 VEEEE--KLSVADETTAITNQEEAKPQNIDSNTIITVPKVWYSGYKGEGTVVAIIDSGLD 17- 7 Query: 196 INHDALQLNDSTKAKYQNEQQMNAAKAKAGINYGKWYNNKVIFGHNYVDVNTELKEVKST 25- 5 ++HD L ++D + AKY++E+++ AAK AGI YG+W+N+KV+FG+NYVDVNT LKE Sbjct: 178 VDHDVLHISDLSTAKYKSEKEIEAAKEAAGITYGEWFNDKVVFGYNYVDVNTVLKEEDKR 23- 7 Query: 256 SHGMHVTSIATANPSKKDTNELIYGVAPEAQVMFMRVFSDEKRGTGPALYVKAIEDAVKL 31- 5 SHGMHVTSIAT NP++ +L+YGVAPEAQVMFMRVFSD K TG ALYVKAIEDAVKL Sbjct: 238 SHGMHVTSIATGNPTQPVAGQLMYGVAPEAQVMFMRVFSDLKATTGAALYVKAIEDAVKL 29- 7 Query: 316 GADSINLSLGGANGSLVNADDRLIKALEMARLAGVSVVIAAGNDGTFGSGASKPSALYPD 37- 5 GADSINLSLGGANGS+VN ++ + A+E AR AGVSVVIAAGNDGTFGSG S PSA YPD Sbjct: 298 GADSINLSLGGANGSVVNMNENVTAAIEAARRAGVSVVIAAGNDGTFGSGHSNPSADYPD 35- 7 Query: 376 YGLVGSPSTAREAISVASYNNTTLVNKVFNIIGLENNRNLNNGLAAYADPKVSDKTFEVG 43- 5 YGLVG+PSTA +AISVASYNNTT+ +KV NIIGLENN +LN G +++ +P+ S FE+G Sbjct: 358 YGLVGAPSTAHDAISVASYNNTTVGSKVINIIGLENNADLNYGKSSFDNPEKSPVPFEIG 41- 7 Query: 436 KQYDYVFVGKGNDNDYKDKTLNGKIALIERGDITFTKKVVNAINHGAVGAIIFNNKAGEA 49- 5 K+Y+YV+ G G +D+ L GK+ALI+RG ITF++K+ NA GAVG +IFN++ GEA Sbjct: 418 KEYEYVYAGIGQASDFDGLDLTGKLALIKRGTITFSEKIANATAAGAVGVVIFNSRPGEA 47- 7 Query: 496 NLTMSLDPEASAIPAIFTQKEFGDVLAKNNYKIVFNNIKNKQANPNAGVLSDFSSWGLTA 55- 5 N++M LD A AIP++F EFG+ LA N+YKI FNN + + NP AG+LSDFSSWGL+A Sbjct: 478 NVSMQLDDTAIAIPSVFIPLEFGEALAANSYKIAFNNETDIRPNPEAGLLSDFSSWGLSA 53- 7 Query: 556 DGQLKPDLSAPGGSIYAAINDNEYDMMSGTSMASPHVAGATALVKQYLLKEHPELKKGDI 61- 5 DG+LKPDL+APGG+IYAAINDN+Y M GTSMASPHVAGA LVKQYLL +P +I Sbjct: 538 DGELKPDLAAPGGAIYAAINDNDYANMQGTSMASPHVAGAAVLVKQYLLATYPTKSPQEI 59- 7 Query: 616 ERTVKYLLMSTAKAHLNKDTGAYTSPRQQGAGIIDVAAAVQTGLYLTGGENNYGSVTLGN 67- 5 E VK+LLMSTAKAH+NK+T AYTSPRQQGAGIID AAA+ TGLYLT GE+ YGS+TLGN Sbjct: 598 EALVKHLLMSTAKAHVNKETTAYTSPRQQGAGIIDTAAAISTGLYLT-GEDGYGSITLGN 65- 6 Query: 676 IKDKISFDVTVHNINKVAKDLHYTTYLNTDQVKDGFVTLAPQQLGTFTGKTIRIEPGQTQ 73- 5 ++D SF VT+HNI K L+Y+T L TD + L + + + + ++ + Sbjct: 657 VEDTFSFTVTLHNITNEDKTLNYSTQLTTDTAQKRIDHLGSTSISRDSWRKVTVKANSST 71- 6 Query: 736 TITIDIDVSKYHDMLKKVMPNGYFLEGYVRFTDPVDGGEVLSIPYVGFKGEFQNLEVLEK 79- 5 T+TI++D S + + L +M NGY+LEG+VRFTD D G+++SIPYVGF+GEFQNL VLE+ Sbjct: 717 TVTINVDASSFAEELTGLMKNGYYLEGFVRFTDVADDGDIVSIPYVGFRGEFQNLAVLEE 77- 6 Query: 796 SIYKLVANKEKGFYFQP--KQTNEVPGSEDYTALMTTSSEPIYSTDGTSPIQLKALGSYK 85- 3 IY L+A+ + GFYF+P Q N V S YT L+T S+E IYSTD S +K LG++K Sbjct: 777 PIYNLIADGKGGFYFEPVTAQPNTVDISHHYTGLVTGSTELIYSTDKRSDSAIKTLGTFK 83- 6 Query: 854 SIDGKWILQLDQKGQPHLAISPNDDQNQDAVAVKGVFLRNFNNLRAKVYRADDVNLQKPL 91- 3 + G ++L+LD+ G+PHLAISPN D NQD++ KGVFLRN+ +L A VY ADD PL Sbjct: 837 NKAGYFVLELDESGKPHLAISPNGDDNQDSLVFKGVFLRNYTDLVASVYAADDTERTNPL 89- 6 Query: 914 WVSAPQAGDKNYYSGNTENPKSTFLYDTEWKGTTTDGIPLEDGKYKYVLTYYSDVPGSKP 97- 3 W S PQ+GDKN YSGN +NPKS+ +Y TEW GT +DG L DGKY+YVLTY S VPG+ Sbjct: 897 WESQPQSGDKNIYSGNPKNPKSSIIYPTEWNGTDSDGNALADGKYQYVLTYSSKVPGAAV 95- 6 Query: 974 QQMVFDITLDRQAPTLTTATYDKDRRIFKARPAVEHGESGIFREQVFYLKKDKDGHYNSV 10- 33 Q M+FD+ +DR++P +TTATYD+ F RPA+E GESG++REQVFYL D G ++ Sbjct: 957 QTMIFDVIIDRESPVITTATYDETNFTFNPRPAIEKGESGLYREQVFYLVADASG-VTTI 10- 15 Query: 1034 LRQQGEDGILVEDNKVFIKQEKDGSFILPKEVNDFSHVYYTVEDYAGNLVSAKLEDLINI 1- 093 + V DNKVF+ Q DGSF LP ++ D S YYTVEDYAGN+ K+E+LI+I Sbjct: 1016 PSLLKNGDVTVSDNKVFVAQNDDGSFTLPLDLADISKFYYTVEDYAGNISYEKVENLISI 1- 075 Query: 1094 GNKNGLVNVKVFSPELNSNVDIDFSYSVKDDKGNIIKK-QHHGKDLNLLKLPFGTYTFDL 1- 152 GN+ GLV V + + NS V I FSYSV D+ G I+ + + D ++LKLPFGTYTFDL Sbjct: 1076 GNEKGLVTVNILDKDTNSPVPILFSYSVTDETSKIVAELPRYAGDTSVLKLPFGTYTFDL 1- 135 Query: 1153 FLYDEERANLISPKSVTVTISEKDSLKDVLFKVNLLKKAALLVEFDKLLPKGATVQLVTK 1- 212 FLYD E ++L VTI E +S +V F V L KA LL++ D LLP G+T+QLVT Sbjct: 1136 FLYDTEWSSLAGETKAVVTILEDNSTAEVNFYVTLKDKANLLIDIDALLPSGSTIQLVTA 1- 195 Query: 1213 TNTVVDLPKATYSPTDYGKNIPVGDYRLNVTLPSGYSTLENLDDLLVSVKEDQVNLTKLT 1- 272 + LP A YS TDYGK +PVG Y + TLP GY LE LD V+V +Q N+ KLT Sbjct: 1196 DGQAIQLPNAKYSKTDYGKFVPVGTYTILPTLPEGYEFLEELD---VAVLANQSNVKKLT 1- 252 Query: 1273 LINKAPLINALAEQTDIITQPVFYNAGTHLKNNYLANLEKAQTLIKNRVEQTSIDNAIAA 1- 332 LINK L +AE + +YNA L+ Y LE A + N+ Q +D+A+A+ Sbjct: 1253 LINKVALKELIAELAGLEETARYYNASPELQTAYAKALEDANAVYANKHNQAQVDSALAS 1- 312 Query: 1333 LRESRQALNGKETDTSLLAKAILAETEIKGNYQFVNASPLSQSTYINQVQLAKNLLQKPN 1- 392 L +R+ LNG+ TD L + T + N+ + NA Q Y V+ A+ +L + N Sbjct: 1313 LVAAREQLNGQATDKEKLIAEVSNYTPTQANFIYYNAENTKQIAYDTAVRSAQLVLNQEN 1- 372 Query: 1393 VTQSEVDKALENLDIAKNQLNGHETDYSGLHHMIIKANVLKQTSSKYQNASQFAKENYNN 1- 452 VTQ+ V++AL +L AK L+G +TD S L + ++VLK T +KY NAS+ K+ Y+ Sbjct: 1373 VTQAVVNQALADLLAAKANLDGQKTDISALRSAVSVSSVLKATDAKYLNASENVKQAYDQ 1- 432 Query: 1453 LIKKAELLLSNRQATQAQVEELLNQIKATEQELDG----RDRVSSAENYSQSLNDNDSLN 1- 508 ++ A+ +L + A+QA V++ L + + + ELDG + N + D ++ Sbjct: 1433 AVEAAKAILVDESASQASVDQALAVLTSAQAELDGVATSTNDAKEPANTATDKKDEGTVT 1- 492 Query: 1509 TTPIN--------PP-----NQPQALIFKKGMTKESEVAQKRVLGVTSQTDNQKVKTNKL 1- 555 PI+ PP N I +K + + + L + + NQ+ + +L Sbjct: 1493 PPPIDSEIVDVQAPPVKDTGNSEHVPIGQK-PNPQPTLPRPVTLQASLSSPNQEKQVTQL 1- 551 Query: 1556 PKTGESTPKITYTILLFSLSMLGLATIKLKSIKR 1589 P TGE+ K L ++GL T+ L SI+R Sbjct: 1552 PNTCENDTK----YYLVPGVIIGLGTL-LVSIRR 1580 A related GBS gene <SEQ ID 8963> and protein <SEQ ID 8964> were also identified. Analysis of this protein sequence reveals the following:

TABLE-US-06232 Lipop: Possible site: -1 Crend: 10 SRCFLG: 0 McG: Length of UR: 1 Peak Value of UR: 2.55 Net Charge of CR: 4 McG: Discrim Score: 2.60 GvH: Signal Score (-7.5): -0.78 Possible site: 35 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 36 ALOM program count: 1 value: -0.16 threshold: 0.0 INTEGRAL Likelihood = -0.16 Transmembrane 318-334 (318-334) PERIPHERAL Likelihood = 2.54 1161 modified ALOM score: 0.53 icml HYPID: 7 CFP: 0.106 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 1535-1539 The protein has homology with the following sequences in the databases: ##STR00146## ##STR00147## A related GBS nucleic acid sequence <SEQ ID 10965> which encodes amino acid sequence <SEQ ID 10966> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 6297> which encodes the amino acid sequence <SEQ ID 6298>. Analysis of this protein sequence reveals the following: TABLE-US-06233 LPXTG motif: 1614-1619 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.46 Transmembrane 1623-1639 (1621-1641) ----- Final Results ----- bacterial membrane --- Certainty = 0.2784(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06234 >GP:AAG09771 GB:AF243528 cell envelope proteinase [Streptococcus thermophilus] Identities = 465/1125 (41%), Positives = 668/1125 (59%), Gaps = 61/1125 (5%) Query: 1 VEKKQRFSLRKYKSGTFSVLIGSVFLVM-TTTVAADELSTMSEPTITNHAQQQAQHLTNT 59 ++KK+ FSLRKYK GT SVL+G+VFL +VAADEL+++E + T Sbjct: 1 MKKKETFSLRKYKIGTVSVLLGAVFLFAGAPSVAADELTSLVETKVKA-----------T 49 Query: 60 ELSSAESKSQDTSQITLKTNREKEQSQDLVSEPTTTELADTDAASMANTGSDATQKSASL 119- + S+S S + E+ D E T+T++ TD GS+A + SA Sbjct: 50 VPDAIVSESASESPVV-------EELVDTSVEATSTDVTTTDNEE-ETPGSEALENSA-- 99 Query: 120 PPVNTDVHDWVKTKGAWDKGYKGQGKVVAVIDTGIDPAHQSMRISDVSTAKVKSKEDMLA 17- 9 NT+V T+ A + + KV + + ++D +TA +E Sbjct: 100 ----NTEVET---TQPAVETPAISEKKV--------EEEEKLSVADETTAITNQEE---- 14- 0 Query: 180 RQKAAGINYGSWINDKVVFAHNYVENSDNIKE-NQFEDFDEDWENFEFDAEAEPKAIKKH 23- 8 K I+ + I V+ Y + + D D D + + A+ K+ K+ Sbjct: 141 -AKPQNIDSNTIITVPKVWYSGYKGEGTVVAIIDSGLDVDHDVLHISDLSTAKYKSEKEI 19- 9 Query: 239 KIYRPQSTQAPKETVIKTEETDGSHDIDWTQTDDDTKYESHGMHVTGIVAGNSKEAAATG 29- 8 + + + E + G + +D + SHGMHVT I GN + A G Sbjct: 200 EAAKEAAGITYGEW-FNDKVVFGYNYVDVNTVLKEEDKRSHGMHVTSIATGNPTQPVA-G 25- 7 Query: 299 ERFLGIAPEAQVMFMRVFANDIMGSAESLFIKAIEDAVALGADVINLSLGTANGAQLSGS 35- 8 + G+APEAQVMFMRVF++ + +L++KAIEDAV LGAD INLSLG ANG+ ++ + Sbjct: 258 QLMYGVAPEAQVMFMRVFSDLKATTGAALYVKAIEDAVKLGADSINLSLGGANGSVVNMN 31- 7 Query: 359 KPLMEAIEKAKKAGVSVVVAAGNERVYGSDHDDPLATNPDYGLVGSPSTGRTPTSVAAIN 41- 8 + + AIE A++AGVSVV+AAGN+ +GS H +P A PDYGLVG+PST SVA+ N Sbjct: 318 ENVTAAIEAARRAGVSVVIAAGNDGTFGSGHSNFSADYPDYGLVGAPSTAHDAISVASYN 37- 7 Query: 419 SKWVIQRLMTVKELENRADLNHGKAIYSESVDFKDIKDSLGYDKSHQFAYVKESTDAGYN 47- 8 + V +++ + LEN ADLN+GK+ + ++ + + +G + + +A + +++D ++ Sbjct: 378 NTTVGSKVINIIGLENNADLNYGKSSF-DNPEKSPVPFEIGKEYEYVYAGIGQASD--FD 43- 4 Query: 479 AQDVKGKIALIERDPNKTYDEMIALAKKHGALGVLIFNNKPGQSNRSMRLTANGMGIPSA 53- 8 D+ GK+ALI+R T+ E IA A GA+GV+IFN++PG++N SM+L + IPS Sbjct: 435 GLDLTGKLALIKRG-TITFSEKIANATAAGAVGVVIFNSRPGEANVSMQLDDTAIAIPSV 49- 3 Query: 539 FISHEFGKAMSQLNGNGTGSLEFDSVVSKAPSQKGNEMNHFSNWGLTSDGYLKPDITAPG 59- 8 FI EFG+A++ + + F++ P+ + ++ FS+WGL++DG LKPD+ APG Sbjct: 494 FIPLEFGEALAA----NSYKIAFNNETDIRPNPEAGLLSDFSSWGLSADGELKPDLAAPG 54- 9 Query: 599 GDIYSTYNDNHYGSQTGTSMASPQIAGASLLVKQYLEKTQPNLPKEKIADIVKNLLMSNA 65- 8 G IY+ NDN Y + GTSMASP +AGA++LVKQYL T P ++I +VK+LLMS A Sbjct: 550 GAIYAAINDNDYANMQGTSMASPHVAGAAVLVKQYLLATYPTKSPQEIEALVKHLLMSTA 60- 9 Query: 659 QIHVNPETKTTTSPRQQGAGLLNIDGAVTSGLYVTGKDNYGSISLGNITDTMTFDVTVHN 71- 8 + HVN ET TSPRQQOAG+++ A+++GLY+TG+D YGSI+LGN+ DT +F VT+HN Sbjct: 610 KAHVNKETTAYTSPRQQGAGIIDTAAAISTGLYLTGEDGYGSITLGNVEDTFSFTVTLHN 66- 9 Query: 719 LSNKDKTLRYDTELLTDHVDPQKGRFTLTSHSLKTYQGGEVTVPANGKVTVRVTMDVSQF 77- 8 ++N+DKTL Y T+L TD + TS S +++ +VTV AN TV + +D S F Sbjct: 670 ITNEDKTLNYSTQLTTDTAQKRIDHLGSTSISRDSWR--KVTVKANSSTTVTINVDASSF 72- 7 Query: 779 TKELTKQMPNGYYLEGFVRFRDSQDDQLNRVNIPFVGFKGQFENLAVAEESIYRLKSQGK 83- 8 +ELT M NGYYLEGFVRF D DD + V+IP+VGF+G+F+NLAV EE IY L + GK Sbjct: 728 AEELTGLMKNGYYLEGFVRFTDVADDG-DIVSIPYVGFRGEFQNLAVLEEPIYNLIADGK 78- 6 Query: 839 TGFYFDE-SGPKDDIYVGKHFTGLVTLGSETNVSTKTISDNGLHTLGTFKNADGKFILEK 89- 7 GFYF+ + + + + H+TGLVT +E ST SD+ + TLGTFKN G F+LE Sbjct: 787 GGFYFEPVTAQPNTVDISHHYTGLVTGSTELIYSTDKRSDSAIKTLGTFKNKAGYFVLEL 84- 6 Query: 898 NAQGNPVLAISPNGDNNQDFAAFKGVFLRKYQGLKASVYHASDKEHKNPLWVS-PESFKG 95- 6 + G P LAISPNGD+NQD FKGVFLR Y L ASVY A D E NPLW S P+S G Sbjct: 847 DESGKPHLAISPNGDDNQDSLVFKGVFLRNYTDLVASVYAADDTERTNPLWESQPQS--G 90- 4 Query: 957 DKN-FNSDIRFAKSTTLLGTAFSGKSLTGAELPDGHYHYVVSYYPDVVGAKRQEMTFDMI 10- 15 DKN ++ + + KS+ + T ++G G L DG Y YV++Y V GA Q M FD+I Sbjct: 905 DKNIYSGNPKNPKSSIIYPTEWNGTDSDGNALADGKYQYVLTYSSKVPGAAVQTMIFDVI 96- 4 Query: 1016 LDRQKPVLSQATFDPETNRFKPEPLKDRGLAGVRKDSVFYLERKDNKPYTVTINDSYKYV 1- 075 +DR+ PV++ AT+D F P P ++G +G+ ++ VFYL + T+ V Sbjct: 965 IDRESPVITTATYDETNFTFNPRPAIEKGESGLYREQVFYLVADASGVTTIPSLLKNGDV 10- 24 Query: 1076 SVEDNKTFVERQADGSFILPLDKAKLGDFYYMVEDFAGNVAIAKL 1120 +V DNK FV + DGSF LPLD A + FYY VED+AGN++ K+ Sbjct: 1025 TVSDNKVFVAQNDDGSFTLPLDLADISKFYYTVEDYAGNISYEKV 1069 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06235 Identities = 543/1676 (32%), Positives = 821/1676 (48%), Gaps = 158/1676 (9%) Query: 24 KQRFSIRKYKLGAVSVLLGTLFFLGGITNVAAD--SVINKPSDIAVEQQVKDSPTSI--- 78 - KQRFS+RKYK G SVL+G++F + T VAAD S +++P+ QQ T+ Sbjct: 4 KQRFSLRKYKSGTFSVLIGSVFLVM-TTTVAADELSTMSEPTITNHAQQQAQHLTNTELS 62 Query: 79 ANETPTNNTSSALASTAQD-----NLVTKANNSPTETQPVAESHSQATETFSPVANQPVE 133- + E+ + +TS T ++ +LV++ + A + ++ A+ P Sbjct: 63 SAESKSQDTSQITLKTNREKEQSQDLVSEPTTTELADTDAASMANTGSDATQKSASLPPV 122- Query: 134 STQEVSKTPLTKQ--NLAVKSTPAISKETPQNID-SNKIITVPKVWNTGYKGEGTVVAI- 18- 9 +T +V TK + K + ID +++ + + V K + ++A Sbjct: 123 NT-DVHDWVKTKGAWDKGYKGQGKVVAVIDTGIDPAHQSMRISDVSTAKVKSKEDMLARQ 18- 1 Query: 190 ----IDSGLDIN------HDALQLNDSTKAK--------YQNEQQMNAAKAKAGINYGKW 23- 1 I+ G IN H+ ++ +D+ K ++N + A+ KA I K Sbjct: 182 KAAGINYGSWINDKVVFAHNYVENSDNIKENQFEDFDEDWENFEFDAEAEPKA-IKKHKI 24- 0 Query: 232 YN-------------NKVIFGHNYVDVNTELKEVKSTSHGMHVTSIATANPSKKD-TNEL 27- 7 Y + G + +D + K SHGMHVT I N + T E Sbjct: 241 YRPQSTQAPKETVIKTEETDGSHDIDWTQTDDDTKYESHGMHVTGIVAGNSKEAAATGER 30- 0 Query: 278 IYGVAPEAQVMFMRVFSDEKRGTGPALYVKAIEDAVKLGADSINLSLGGANGSLVNADDR 33- 7 C+APEAQVMFMRVF+++ G+ +L++KAIEDAV LGAD INLSLG ANG+ ++ Sbjct: 301 FLGIAPEAQVMFMRVFANDIMGSAESLFIKAIEDAVALGADVINLSLGTANGAQLSGSKP 36- 0 Query: 338 LIKALEMARLAGVSVVIAAGNDGTFGSGASKPSALYPDYGLVGSPSTAREAISVASYNNT 39- 7 L++A+E A+ AGVSVV+AAGN+ +GS P A PDYGLVGSPST R SVA+ N+ Sbjct: 361 LMEAIEKAKKAGVSVVVAAGNERVYGSDHDDPLATNPDYGLVGSPSTGRTPTSVAAINSK 42- 0 Query: 398 TLVNKVFNIIGLENNRNLNNGLAAYA---DPKVSDKTFEVGKQYDYVFVGKGNDNDYKDK 45- 4 ++ ++ + LEN +LN+G A Y+ D K + K + + +V + D Y + Sbjct: 421 WVIQRLMTVKELENRADLNHGKAIYSESVDFKDIKDSLGYDKSHQFAYVKESTDAGYNAQ 48- 0 Query: 455 TLNGKIALIERG-DITFTKKVVNAINHGAVGAIIFNNKAGEANLTMSLDPEASAIPAIFT 51- 3 + GKIALIER + T+ + + A HGA+G +IFNNK G++N +M L IP+ F Sbjct: 481 DVKGKIALIERDPNKTYDEMIALAKKHGALGVLIFNNKPGQSMRSMRLTANGMGIPSAFI 54- 0 Query: 514 QKEFGDVLAKNNYK----IVFNNIKNKQANPNAGVLSDFSSWGLTADGQLKPDLSAPGGS 56- 9 EFG +++ N + F+++ +K + ++ FS+WGLT+DG LKPD++APGG Sbjct: 541 SHEFGKAMSQLNGNGTGSLEFDSVVSKAPSQKGNEMNHFSNWGLTSDGYLKPDITAPGGD 60- 0 Query: 570 IYAAINDNEYDMMSGTSMASPHVAGATALVKQYLLKEHPELKKGDIERTVKYLLMSTAKA 62- 9 IY+ NDN Y +GTSMASP +AGA+ LVKQYL K P L K I VK LLMS A+ Sbjct: 601 IYSTYNDNHYGSQTGTSMASPQIAGASLLVKQYLEKTQPNLPKEKIADIVKNLLMSNAQI 66- 0 Query: 630 HLNKDTGAYTSPRQQGAGIIDVAAAVQTGLYLTGGENNYGSVTLGNIKDKISFDVTVHNI 68- 9 H+N +T TSPRQQGAG++++ AV +GLY+TG ++NYGS++LGNI D ++FDVTVHN+ Sbjct: 661 HVNPETKTTTSPRQQGAGLLNIDGAVTSGLYVTG-KDNYGSISLGNITDTMTFDVTVHNL 71- 9 Query: 690 NKVAKDLHYTTYLNTDQV--KDGFVTLAPQQLGTFTGKTIRIEPGQTQTITIDIDVSKYH 74- 7 + K L Y T L TD V + G TL L T+ G + + T+ + +DVS++ Sbjct: 720 SNKDKTLRYDTELLTDHVDPQKGRFTLTSHSLKTYQGGEVTVPANGKVTVRVTMDVSQFT 77- 9 Query: 748 DMLKKVMPNGYFLEGYVRFTDPVDGG-EVLSIPYVGFKGEFQNLEVLEKSIYKLVANKEK 80- 6 L K MPNGY+LEG+VRF D D ++IP+VGFKG+F+NL V E+SIY+L + + Sbjct: 780 KELTKQMPNGYYLEGFVRFRDSQDDQLNRVNIPFVGFKGQFENLAVAEESIYRLKSQGKT 83- 9 Query: 807 GFYFQPK-QTNEVPGSEDYTALMTTSSEPIYSTDGTSPIQLKALGSYKSIDGKWILQLDQ 86- 5 GEYF +++ + +T L+T SE ST S L LG++K+ DGK+IL+ + Sbjct: 840 GFYFDESGPKDDIYVGKHFTGLVTLGSETNVSTKTISDNGLHTLGTFKNADGKFILEKNA 89- 9 Query: 866 KGQPHLAISPNDDQNQDAVAVKGVFLRNFNNLRAKVYRADDVNLQKPLWVSAPQ-AGDKN 92- 4 +G P LAISPN D NQD A KGVFLR + L+A VY A D + PLWVS GDKN Sbjct: 900 QGNPVLAISPNGDNNQDFAAFKGVFLRKYQGLKASVYHASDKEHKNPLWVSPESFKGDKN 95- 9 Query: 925 YYSGNTENPKSTFLYDTEWKGTTTDGIPLEDGKYKYVLTYYSDVPGSKPQQMVFDITLDR 98- 4 + S + KST L T + G + G L DG Y YV++YY DV G+K Q+M FD+ LDR Sbjct: 960 FNS-DIRFAKSTTLLGTAFSGKSLTGAELPDGHYHYVVSYYPDVVGAKRQEMTFDMILDR 10- 18 Query: 985 QAPTLTTATYDKDRRIFKARPAVEHGESGIFREQVFYLKKDKDGHYNSVLRQQGEDGILV 10- 44 Q P L+ AT+D + FK P + G +G+ ++ VFYL++ KD +V + V Sbjct: 1019 QKPVLSQATFDPETNRFKPEPLKDRGLAGVRKDSVFYLER-KDNKPYTVTINDSYKYVSV 1- 077 Query: 1045 EDNKVFIKQEKDGSFILPKEVNDFSHVYYTVEDYAGNLVSAKLEDLINIGNKNGLVNVKV 1- 104 EDNK F++++ DGSFILP + YY VED+AGN+ AKL D + + +K+ Sbjct: 1078 EDNKTFVERQADGSFILPLDKAKLGDFYYMVEDFAGNVAIAKLGDHLPQTLGKTPIKLKL 1- 137 Query: 1105 FSPELNSNVDIDFSYSVKDDKGNIIKKQ------HHGKDLNLLKLPFGTYTFDLFLYDEE 1- 158 + + + + ++ Q H + + L D F+ E Sbjct: 1138 TDGNYQTKETLKDNLEMTQSDTGLVTNQAQLAVVHRNQPQSQLT----KMNQDFFISFNE 1- 193 Query: 1159 RANLISPKSVTVTISEKDSLKDVLFKVNLLKKAALLVEFDKLLP-----KGATVQLVTKT 1- 213 N K K+++ + L VN+ K + K P GA+V + T Sbjct: 1194 DGN----KDFVAFKGLKNNVYNDL-TVNVYAKD----DHQKQTPIWSSQAGASVSAIEST 1- 244 Query: 1214 NTVVDLPKATYSPTDYGKNIPVGDYRLNVTLPSGYSTLENLDDLLVSVKEDQVNLT--KL 1- 271 A Y T G + GDY+ VT + E+ +SV + + +T Sbjct: 1245 --------AWYGITARGSKVMPGDYQYVVTYRDEHGK-EHQKQYTISVNDKKPMITQGRF 1- 295 Query: 1272 TLINK----APLINALAEQTDIITQPVFYNAGTHLKNNYLANLEKAQTLIKNRVEQTSID 1- 327 IN P + + I+ + VFY A KN ++ + + I T D Sbjct: 1296 DTINGVDHFTPDKTKALDSSGIVREEVFYLA---KKNGRKFDVTEGKDGI------TVSD 1- 346 Query: 1328 NAIAALRESRQALNGKETDTSLLAKAILAETEIKGNYQFVNASPL----SQSTYIN---- 1- 379 N + + + + D L+ + GN F L +N Sbjct: 1347 NKVYIPKNPDGSYTISKRDGVTLSDYYYLVEDRAGNVSFATLRDLKAVGKDKAVVNFGLD 1- 406 Query: 1380 -QVQLAKNLLQKPNVTQSEVDKALENLDIAKNQLNGHETDYS--GLHHMIIKANVLKQTS 1- 436 V K ++ + + K+ ENL+ N N Y + + N K S Sbjct: 1407 LPVPEDKQIVNFTYLVRDADGKPIENLEYYNNSGNSLILPYGKYTVELLTYDTNAAKLES 1- 466 Query: 1437 SKYQNASQFAKSNYNNLIKKAELLLSNR----------QATQAQVEELLNQIKATEQEL- 1- 485 K + + A N+ + K +L +++ + ++ ++ +Q+ EQ L Sbjct: 1467 DKIVSFTLSADNNFQQVTFKITMLATSQITAHFDHLLPEGSRVSLKTAQDQLIPLEQSLY 1- 526 Query: 1486 ----------DGRDRVSSAENYSQSLNDNDSLNTTPINPPNQPQALIFKKGMTKES---- 1- 531 +G V + + N +NT P N ++ + K G +S Sbjct: 1527 VPKAYGKTVQEGTYEVVVSLPKGYRIEGNTKVNTLP-NEVHELSLRLVKVGDASDSTGDH 1- 585 Query: 1532 -----EVAQKRVLGVTSQTDNQKVKTNKLPKTGESTPKITYTILLFSLSMLGLATI 1582 +Q T LP TGE K+ + + L +LGL + Sbjct: 1586 KVMSKNNSQALTASATPTKSTTSATAKALPSTGE---KMGLKLRIVGLVLLGLTCV 1638 SEQ ID 8964 (GBS92) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 31 (lane 2; MW 48 kDa). GBS92-His was purified as shown in FIG. 199, lane 9. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2038 A DNA sequence (GBSx2149) was identified in S. agalactiae <SEQ ID 6299> which encodes the amino acid sequence <SEQ ID 6300>. This protein is predicted to be AzlC family protein. Analysis of this protein sequence reveals the following: TABLE-US-06236 Possible site: 33 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.80 Transmembrane 212-228 (196-230) INTEGRAL Likelihood = -7.27 Transmembrane 167-183 (159-185) INTEGRAL Likelihood = -5.68 Transmembrane 189-205 (188-210) INTEGRAL Likelihood = -2.28 Transmembrane 17-33 (13-34) INTEGRAL Likelihood = -1.06 Transmembrane 135-151 (135-151) INTEGRAL Likelihood = -1.01 Transmembrane 61-77 (60-77) ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10235> which encodes amino acid sequence <SEQ ID 10236> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-06237 >GP:AAF10212 GB:AE001921 AzlC family protein [Deinococcus radiodurans] Identities = 72/224 (32%), Positives = 117/224 (52%), Gaps = 8/224 (3%) Query: 6 FKEGVKDALPTALGYISIGLAFGIVASASDLSAIEVGLMSALVYGGSAQFAMCALLLAKA 65 F +G + +P LG + LA+ + A A+ LS + LMS + G++QFA L A A Sbjct: 7 FWQGFRALVPLWLGTVPFALAYAVTARAAGLSVGDTCLMSLTTFAGASQFAAAGLFGAHA 66 Query: 66 DLMTITMTVFLVNLRNMLMSLHATTIFKSAHLMNQLAIGTLITDESYGV-LLGEALHHKV 124- ++I +T FL+N R++L L + L ++ +TDE+YGV ++ A Sbjct: 67 GGLSIVLTTFLLNARHLLYGLSLARELRLT-LPQRVVAAQFLTDEAYGVAVVSGARLPGG 125- Query: 125 VSPSWMHGNNVMSYLTWVISTIIGTLLGSTIPNPEMFGLDFALVAMFIGLFVFQLFGMLS 18- 4 ++ +++ G + YL+W +ST++G L GS +P PE G+ F+GL V ++ Sbjct: 126 LTFAFLLGAELSLYLSWNVSTLLGALAGSVLPPPEQLGVGVVFPLAFLGLLV----PLVV 18- 1 Query: 185 DGKRLVVYVLASVGLSYFLLATFLSGALSVLLATVVGCSVGVVL 228 D RL + V + GL + L+ L G L +LLA V G +G L Sbjct: 182 D--RLSLLVALAAGLGGWALSRVLPGGLVILLAGVGGALLGAAL 223 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2039 A DNA sequence (GBSx2150) was identified in S. agalactiae <SEQ ID 6301> which encodes the amino acid sequence <SEQ ID 6302>. Analysis of this protein sequence reveals the following: TABLE-US-06238 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3794(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2040 A DNA sequence (GBSx21151) was identified in S. agalactiae <SEQ ID 6303> which encodes the amino acid sequence <SEQ ID 6304>. Analysis of this protein sequence reveals the following: TABLE-US-06239 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5087(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10233> which encodes amino acid sequence <SEQ ID 10234> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06240 >GP:BAB04157 GB:AP001508 homosystein methyl transferase [Bacillus halodurans] Identities = 397/751 (52%), Positives = 519/751 (68%), Gaps = 14/751 (1%) Query: 10 SNLGYPRLGEQREWKQAIEAFWAGNLEQKDLEKQLKQLRINHLKKQKEAGIDLIPVGDFS 69 - SNLGYPR+GE REWK+A+E+FWA + ++ L +K+LR+NHL+ Q+E +DLIPVGDF+ Sbjct: 4 SNLGYPRIGENREWKKALESFWANDTTEEQLLATMKELRLNHLRVQQEQEVDLIPVGDFT 63 Query: 70 CYDHVLDLSFQFNVIPKRFDEY--ERNLDLYFAIARGDKDNVASSMKKWFNTNYHYIVPE 127- YDHVLD++ F +IPKRF + L YFA+ARG K+ A M KW+NTNYHYIVPE Sbjct: 64 LYDHVLDMAVMFGIIPKRFLQQGDTPTLSTYFAMARGSKNAQACEMTKWYNTNYHYIVPE 123- Query: 128 WEVETKPHLQNNYLLDLYLEAREVVGDKAKPVITGPITYVSLSSGIVD--FEATVQRLLP 18- 5 + P L N L+ YLEA+ +G KPVI GP ++V L+ G + + T+Q LLP Sbjct: 124 LH-DAAPRLTKNAPLEAYLEAKNELGIDGKPVILGPYSFVKLAKGYEEDKLQETIQSLLP 18- 2 Query: 186 LYKQVFQDLIDAGATYIQIDEPIFVTDEGELLVDIAKSVYDFFAREVPQAHFIFQTYFES 24- 5 LY QV Q+L+DAGA IQ+DEP VT + + +Y+ + A QTYF++ Sbjct: 183 LYIQVIQELVDAGARSIQVDEPSLVTSISAREMALVTRIYEQINEAIADAPLFLQTYFDA 24- 2 Query: 246 AVCLDKLSKLPVTGFGLDFIHGRAENLAAVKQ-GLFREKELFAGIVNGRNIWAVNLEETL 30- 4 +++ LPV G GLDF+HG A+NL A++ G +K L AGI++GRNIW NL E Sbjct: 243 VTFYEEVVSLPVKGIGLDFVHGGAKNLEALRTFGFPEDKVLAAGIIDGRNIWISNLRERH 30- 2 Query: 305 ALLEEIGPFVK--RLTLQPSSSLLHVPVTTKYETHLDPVLKNGLSFADEKLKELELLASA 36- 2 L+ ++ V RL LQPS SLLHVPVTTK E LDP L L+FA+EKL EL L Sbjct: 303 ELVHQLEQHVAKDRLVLQPSCSLLHVPVTTKREEKLDPTLLGVLAFANEKLTELHTLKQL 36- 2 Query: 363 FDGNKTKGYHEALSR----FSALQAADFRHVALESL-AEVKLERSPYKLRQALQAEKLQL 41- 7 GN++ EAL +AL+ + +R A S E K + R+ LQ EK QL Sbjct: 363 AAGNEAE-VKEALEANDDALAALEKSGWRSGAATSHNLENKKRPQSFNERRPLQEEKWQL 42- 1 Query: 418 PILPTTTIGSFPQSPEIRKKRLAWKRGNLSDSDYKDFIKTEIRRWIAIQEDLDLDVLVHG 47- 7 P+LPTTTIGSFPQ+ ++R+ R W++G LS +Y+ +K+ I +WI IQE+L LDVLVHG Sbjct: 422 PLLPTTTIGSFPQTKDVRRTRSLWRKGELSTVEYERTMKSYIEKWINIQEELGLDVLVHG 48- 1 Query: 478 EFERVDMVEFFGQKLAGFTTTKLGWVQSYGSRAVKPPIIYGDVKHIQPLSLEETVYAQSL 53- 7 EFER DMVEFFG+KL GF T GWVQSYGSR VKPPIIYG+V +P+++ ETVYAQSL Sbjct: 482 EFERNDMVEFFGEKLDGFAFTANGWVQSYGSRCVKPPIIYGNVSFTEPMTVAETVYAQSL 54- 1 Query: 538 TKKPVKGMLTGPITITNWSFERDDISRSDLFNQIALAIKDEIQLLEQSGIAIIQVDEAAL 59- 7 T KPVKGMLTGP+TI NWSF RDD+ + + +QIA A+ E+ LE++GI +IQ+DE A+ Sbjct: 542 TDKPVKGMLTGPVTILNWSFVRDDLPLTVIAHQIAEALTHEVTALEEAGIEMIQIDEPAI 60- 1 Query: 598 REGLPLRQQKQQAYLDDAVAAFKIATSSVKDETQIHTHMCYSKFDEIIDSIRALDADVIS 65- 7 REGLPL+ + QQ YLD AV+AF+ + + VK TQIHTHMCYS+F E+I++I LDADVIS Sbjct: 602 REGLPLKAEDQQEYLDWAVSAFRASCAHVKATTQIHTHMCYSEFHEMIEAIDDLDADVIS 66- 1 Query: 658 IETSRSHGDIIESFETAVYPLGIGLGVYDIHSPRIPTKEEIIVNIQRSLKCLSKEQFWVN 71- 7 IETSRSHG++I +FE Y GIGLGVYDIHSPR+P++EE++ I+R+L L FWVN Sbjct: 662 IETSRSHGEMISAFEKTTYEKGIGLGVYDIHSPRVPSEEEMLNVIRRALTVLPASLFWVN 72- 1 Query: 718 PDCGLKTRREAETIAALEVLVSATKEVRQQL 748 PDCGLKTR E ET+AAL+ +V+A + R++L Sbjct: 722 PDCGLKTRAEKETVAALKNMVAAARAAREEL 752 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2041 A DNA sequence (GBSx2152) was identified in S. agalactiae <SEQ ID 6305> which encodes the amino acid sequence <SEQ ID 6306>. This protein is predicted to be metH. Analysis of this protein sequence reveals the following: TABLE-US-06241 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0753(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06242 >GP:BAB05348 GB:AP001512 unknown conserved protein [Bacillus halodurans] Identities = 301/610 (49%), Positives = 437/610 (71%), Gaps = 9/610 (1%) Query: 1 MSKFLEKLKTDILVADGAMGTLLYTYGLDTCHESYNVTHPEKVLAIHQAYIEAGADVIQT 60 M+ +E LKT+ILV DGAMGTLLY G+D C E NVT PEK++A H AY+EAGADVIQT Sbjct: 1 MTNLVEALKTNILVGDGAMGTLLYEQGIDRCFEELNVTDPEKIVAAHVAYVEAGADVIQT 60 Query: 61 NTYGAQRHRLKNYGLEDQVVSINQAAVNIAHQATLGKETFILGTVGGFRSQRQCDLTLDN 120- NTY A R +L Y L+DQV+ IN+AAV +A +A +ETF+LGT+GG RS + ++ + Sbjct: 61 NTYAANRMKLAKYQLDDQVLEINRAAVRLARKAAK-QETFVLGTIGGIRSVQFEEVEIQE 119- Query: 121 IVEETLEQVEALLATGQLDGLLFETYYDIEEITTVLKIVREMTDLPIITNISLHEAGVTS 18- 0 + + LEQ++AL++ G +DGLL ET+YD+EE + + R +TDLP+I ++S+ E GV Sbjct: 120 VQDVFLEQMKALVSEG-VDGLLLSTFYDLEEAKLAVSLARSLTDLPVIAHLSIAEIGVLQ 17- 8 Query: 181 NGKPIVEALSQLVMLGADVIGLNCHLGPYHMIQSLKQVPLFAQSYLSVYPNASQLSLDGE 24- 0 GK + EA ++L LGAD++G+NC +GPY M++SL+ V L ++Y S YPNAS D Sbjct: 179 GGKLLEEAFAELEGLGADLVGINCRMGPYQMLRSLETVQLLDRAYYSAYPNASLP--DYR 23- 6 Query: 241 NSQYQFSQNSEYFGKSAELLVAEGVRLIGGCCGTTPDHIRAVKRSIRGLKPIERKVVTPI 30- 0 + + + N EYF + + V +GVRL+GGCCGTTP+H+RA + ++GLKP+ K V Sbjct: 237 DGRLYYHSNPEYFYEMGKRFVQQGVRLLGGCCGTTPEHVRAFAKVVKGLKPVVSKPVR-- 29- 4 Query: 301 IPVKDFVRRIRRT---DTLVDKVKKEVTIIAELDPPKHLDIVQFQKAIRAIDQKGIAAIT 35- 7 + +K+ + + + L +KVKK+ +II ELDPPK+L I +F + A+ G+ A+T Sbjct: 295 LEIKETLSSTGQKTAREPLAEKVKKQPSIIVELDPPKNLAIDRFVEGAAALKNAGVDAVT 35- 4 Query: 358 LADNSLSNTRICNLSIASLLKDEISTPFLLHIACRDHNLIGLQSRLLGMELLGFNHILAI 41- 7 +ADNSL++ R+ NL++ ++++ ++ L+H+ CRD NLIGLQS L+G+ LG +LAI Sbjct: 355 MADNSLASPRVDNLALGAIIQQQVGARPLVHVTCRDRNLIGLQSHLMGLHALGMTDLLAI 41- 4 Query: 418 TGDPTKLGDFPGATSVYDVTSFKLLSLIKQLNQGLSYSGASLRRPTDFTVAAAFNPNVKN 47- 7 TGDPTK+GDFPGATSVYDVTSF+L+SLIKQLN+G+S+SG L + +F+V AAFNPNV++ Sbjct: 415 TGDFTKVGDFPGATSVYDVTSFQLISLIKQLNEGISFSGKELGQKANFSVGAAFNPNVRH 47- 4 Query: 478 LTRTVKLIEKKVASGADYFMTQPIFDHSVLKELADLTKTVEQPFFIGIMPITSYNNAVFL 53- 7 L R V+ +EKK+ +GADYFMTQPI++ ++++ + TK +E+P +IGIMP+ + NA FL Sbjct: 475 LERAVQRMEKKIEAGADYFMTQPIYNEKQIEDIYEATKHIEKPIYIGIMPLINGRNAEFL 53- 4 Query: 538 HNEVPGIKLSESFLSALEKVKDDKEACLTLALNESKSLIDEALNYFNGIYLITPFLRYDL 59- 7 HNEVPGIKL++ + + +D++ L +KSL+D A +YFNGIYLITPFLRY + Sbjct: 535 HNEVPGIKLTDQIRERMARAGEDRQKGEREGLAIAKSLLDVATHYFNGIYLITPFLRYGM 59- 4 Query: 598 TLELIDYIQK 607 T++L Y+++ Sbjct: 595 TVDLTHYVKE 604 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2042 A DNA sequence (GBSx2153) was identified in S. agalactiae <SEQ ID 6307> which encodes the amino acid sequence <SEQ ID 6308>. Analysis of this protein sequence reveals the following: TABLE-US-06243 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.55 Transmembrane 127-143 (121-147) INTEGRAL Likelihood = -1.44 Transmembrane 157-173 (155-175) ----- Final Results ----- bacterial membrane --- Certainty = 0.4821(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10231> which encodes amino acid sequence <SEQ ID 10232> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06244 >GP:CAC01354 GB:AL390975 putative integral membrane protein [Streptomyces coelicolor A3(2)] Identities = 38/98 (38%), Positives = 59/98 (59%) Query: 113 RIADDVARFGGSWTFIIVFVSIMAIWMLVNIMKPFGIQFDPYPFILLNLALSTIAAIQAP 17- 2 R+++ VARF G+ FI+ ++ +W++ N+ P G++FD YPFI L L LS A+ AP Sbjct: 47 RLSERVARFLGTGRFIVWMTVVIILWVVWNVSAPSGLRFDEYPFIFLTLMLSLQASYAAP 106- Query: 173 LIMMSQNRAADYDRLQARNDFNVNKTSELEIRLLHEKI 210 LI+++QNR D DR+ D N+ S L +I Sbjct: 107 LILLAQNRQDDRDRVNLEQDRKQNERSIADTEYLTREI 144 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8965> and protein <SEQ ID 8966> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06245 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: -3.84 GvH: Signal Score (-7.5): -5.05 Possible site: 53 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -9.55 threshold: 0.0 INTEGRAL Likelihood = -9.55 Transmembrane 127-143 (121-147) INTEGRAL Likelihood = -1.44 Transmembrane 157-173 (155-175) PERIPHERAL Likelihood = 5.46 27 modified ALOM score: 2.41 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4821(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00148## SEQ ID 8966 (GBS393) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 75 (lane 3; MW 30.8 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 177 (lane 4; MW 56 kDa) and in FIG. 83 (lane 6; MW 56 kDa). GBS393-GST was purified as shown in FIG. 217, lane 5. EXAMPLE 2043 A DNA sequence (GBSx2154) was identified in S. agalactiae <SEQ ID 6309> which encodes the amino acid sequence <SEQ ID 6310>. Analysis of this protein sequence reveals the following: TABLE-US-06246 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.29 Transmembrane 274-290 (271-291) ----- Final Results ---- bacterial membrane --- Certainty = 0.2317(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06247 >GP:AAD35508 GB:AE001721 glycerol dehydrogenase [Thermotoqa maritima] Identities = 94/307 (30%), Positives = 157/307 (50%), Gaps = 21/307 (6%) Query: 63 VYGTDSTQSNIDKLVANPQVQAADAILGFGGGKALDTAKMVAKELGKNSFTIPTICSNCS 122- ++G + + I++L + + D ++G GGGK LDTAK VA +L K +PTI S + Sbjct: 62 IFGGECSDEEIERLSGLVE-EETDVVVGIGGGKTLDTAKAVAYKLKKPVVIVPTIASTDA 120- Query: 123 AGTAIAVVYNDDHSFLRYGY-PESPLHIFINTRIIAQAPSKYFWAGIGDGISKAPEVERA 18- 1 +A++V+Y + F RY + P +P + ++T I+A+AP+++ AG+GD ++ E E Sbjct: 121 PCSALSVIYTPNGEFKRYLFLPRNPDVVLVDTEIVAKAPARFLVAGMGDALATWFEAESC 18- 0 Query: 182 TLEAKTNKLPHT-AVLGQAVALSSKEAFYQFGEQGLKDVEANLASRAVEEI--ALDILIS 23- 8 + N ++ A+A E ++G + VE + A+E+I A +L Sbjct: 181 KQKYAPNMTGRLGSMTAYALARLCYETLLEYGVLAKRSVEEKSVTPALEKIVEANTLLSG 24- 0 Query: 239 TGYASNLVNQPDFYYNSCHAHAFYYGTTAIQRQGEFLHGVVVAFGVLV-LHAYFNELEEL 29- 7 G+ S AHA + G T ++ ++LHG VA GVL L + + Sbjct: 241 LGFESG---------GLAAAHAIHNGLTVLENTHKYLHGEKVAIGVLASLFLTDKPRKMI 29- 1 Query: 298 EKVARFNKSLGLPTTLADVSL---SEKDIPKIVEIAMTTNE---YKNTPFDPKMFAQAIL 35- 1 E+V F + +GLPTTLA++ L S++D+ K+ E A NE + P K A+ Sbjct: 292 EEVYSFCEEVGLPTTLAEIGLDGVSDEDLMKVAEKACDKNETIHNEPQPVTSKDVFFALK 35- 1 Query: 352 AADAFGQ 358 AAD +G+ Sbjct: 352 AADRYGR 358 There is also homology to SEQ ID 3078. SEQ ID 6310 (GBS123) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 29 (lane 7; MW 43.3 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2044 A DNA sequence (GBSx2155) was identified in S. agalactiae <SEQ ID 6311> which encodes the amino acid sequence <SEQ ID 6312>. Analysis of this protein sequence reveals the following: TABLE-US-06248 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0974(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 6313> which encodes the amino acid sequence <SEQ ID 6314>. Analysis of this protein sequence reveals the following: TABLE-US-06249 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2368(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06250 Identities = 92/167 (55%), Positives = 121/167 (72%) Query: 1 MKIAIIGYSGSGKSTLARKLGNYYNCNVLHLDSIHFAPNWEERKYDDMIDDVSNMLEKRT 60 +KIAIIG+SGSGKSTLAR LG +Y+C V HLD +HF+ NW+ER DMI D+S L K+ Sbjct: 1 LKIAIIGHSGSGKSTLARFLGQHYHCEVFHLDQLHFSSNWQERSDHDMIADLSTCLLKQD 60 Query: 61 WIIEGNYKKLLYQERLADADEIIFFDFNRFNCLWRAFKRYCKFRGKTRPDMANGCPEKLD 120- IIEGNY LY+ER+++AD II+ +F+RF+C++RAFKRY +RGKTRPDMA+ C EK D Sbjct: 61 LIIEGNYANCLYEERMSEADYIIYVNFSRFHCVYRAFKRYLNYRGKTRPDMADNCQEKFD 120- Query: 121 FEFISWILKDGRSDKQKSNYKQVVEDYPQKIKILKHQRDLDQYLKEL 167 F+ WIL DGRS Q Y+ VV+ Y K +L +Q+ L Y+ + Sbjct: 121 VAFVKWILLDGRSRNQLKKYQSVVQKYSHKTIVLTNQKQLSHYMNTI 167 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2045 A DNA sequence (GBSx2156) was identified in S. agalactiae <SEQ ID 6315> which encodes the amino acid sequence <SEQ ID 6316>. Analysis of this protein sequence reveals the following: TABLE-US-06251 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3874(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06252 >GP:CAA41941 GB:X59250 initiation factor IF-1 [Lactococcus lactis] Identities = 62/72 (86%), Positives = 70/72 (97%) Query: 1 MAKEDVIEIEGKVVETMPNAMFTVELENGHQILATVSGKIRKNYIRILVGDRVTVEMSPY 60 MAK+DVIE++GKVV+TMPNAMFTVELENGHQ+LAT+SGKIRKNYIRIL GD+V VE+SPY Sbjct: 1 MAKDDVIEVDGKVVDTMPNAMFTVELENGHQVLATISGKIRKNYIRILPGDKVQVELSPY 60 Query: 61 DLTRGRITYRFK 72 DLTRGRITYRFK Sbjct: 61 DLTRGRITYRFK 72 A related DNA sequence was identified in S. pyogenes <SEQ ID 6317> which encodes the amino acid sequence <SEQ ID 6318>. Analysis of this protein sequence reveals the following:

TABLE-US-06253 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3253(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06254 Identities = 67/67 (100%), Positives = 67/67 (100%) Query: 6 VIEIEGKVVETMPNAMFTVELENGHQILATVSGKIRKNYIRILVGDRVTVEMSPYDLTRG 65 VIEIEGKVVETMPNAMFTVELENGHQILATVSGKIRKNYIRILVGDRVTVEMSPYDLTRG Sbjct: 1 VIEIEGKVVETMPNAMFTVELENGHQILATVSGKIRKNYIRILVGDRVTVEMSPYDLTRG 60 Query: 66 RITYRFK 72 RITYRFK Sbjct: 61 RITYRFK 67 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2046 A DNA sequence (GBSx2157) was identified in S. agalactiae <SEQ ID 6319> which encodes the amino acid sequence <SEQ ID 6320>. This protein is predicted to be adenylate kinase (adk). Analysis of this protein sequence reveals the following: TABLE-US-06255 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06256 >GP:CAA41940 GB:X59250 adenylate kinase [Lactococcus lactis] Identities = 146/214 (68%), Positives = 170/214 (79%), Gaps = 6/214 (2%) Query: 1 MNLLIMGLPGAGKGTQAAKIVEEFGVAHISTGDMFRAAMANQTEMGRLAKSYIDKGELVP 60 MNLLIMGLPGAGKGTQA IV+ +GV HISTGDMFRAAM N+TEMG+LAKS+IDKGELVP Sbjct: 1 MNLLIMGLPGAGKGTQAEFIVKNYGVNHISTGDMFRAAMKNETEMGKLAKSFIDKGELVP 60 Query: 61 DEVTNGIVKERLAEDDIAEKGFLLDGYPRTIEQAHALDATLEELGLRLDGVINIKVDPSC 120- DEVTNGIVKERLA+DDI GFLLDGYPRTI+QAHALD LEELG++LD V+NI V+P+ Sbjct: 61 DEVTNGIVKERLAQDDIKASGFLLDGYPRTIDQAHALDTMLEELGIKLDAVVNIVVNPNI 120- Query: 121 LIERLSGRIINRKTGETFHKVFNPPV------DYKEEDYYQREDDKPETVKRRLDVNIAQ 17- 4 L++RLSGR I R G T+HK+FNP D YQR DD PETVK RLDVNI + Sbjct: 121 LVDRLSGRYICRNCGATYHKIFNPTKVEGTCDVCGSHDLYQRADDVPETVKNRLDVNIKE 18- 0 Query: 175 GEPILEHYRKLGLVTDIEGNQEITEVFADVEKAL 208 PI+EHY +LGLV +IEG QEI++V D++K L Sbjct: 181 SAPIIEHYTELGLVKNIEGEQEISQVTDDIKKVL 214 A related DNA sequence was identified in S. pyogenes <SEQ ID 6321> which encodes the amino acid sequence <SEQ ID 6322>. Analysis of this protein sequence reveals the following: TABLE-US-06257 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06258 Identities = 208/212 (98%), Positives = 212/212 (99%) Query: 1 MNLLIMGLPGAGKGTQAAKIVEEFGVAHISTGDMFRAAMANQTEMGRLAKSYIDKGELVP 60 MNLLIMGLPGAGKGTQAAKIVEEFG+AHISTGDMFRAAMANQTEMGRLAKSYIDKGELVP Sbjct: 1 MNLLIMGLPGAGKGTQAAKIVEEFGIAHISTGDMFRAAMANQTEMGRLAKSYIDKGELVP 60 Query: 61 DEVTNGIVKERLAEDDIAEKGFLLDGYPRTIEQAHALDATLEELGLRLDGVINIKVDPSC 120- DEVTNGIVKERLAEDDIAEKGFLLDGYPRTIEQAHALDATLEELGLRLDGVINIKVDPSC Sbjct: 61 DEVTNGIVKERLAEDDIAEKGFLLDGYPRTIEQAHALDATLEELGLRLDGVINIKVDPSC 120- Query: 121 LIERLSGRIINRKTGETFHKVFNPPVDYKEEDYYQREDDKPETVKRRLDVNIAQGEPILE 18- 0 L+ERLSGRIINRKTGETFHKVFNPPVDYKEEDYYQREDDKPETVKRRLDVN+AQGEPILE Sbjct: 121 LVERLSGRIINRKTGETFHKVFNPPVDYKEEDYYQREDDKPETVKRRLDVNMAQGEPILE 18- 0 Query: 181 HYRKLGLVTDIEGNQEITEVFADVEKALLELK 212 HYRKLGLVTDIEGNQEIT+VFADVEKALLELK Sbjct: 181 HYRKLGLVTDIEGNQEITDVFADVEKALLELK 212 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8967> and protein <SEQ ID 8968> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06259 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: -1.04 GvH: Signal Score (-7.5): -1.08 Possible site: 17 >>> Seems to have no N-terminal signal sequence ALOM program count: 0 value: 6.79 threshold: 0.0 PERIPHERAL Likelihood = 6.79 106 modified ALOM score: -1.86 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00149## SEQ ID 8968 (GBS114) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 29 (lane 9; MW 26.9 kDa). The GBS114-His fusion product was purified (FIG. 108A; see also FIG. 200, lane 8) and used to immunise mice (lane 1+2+3 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 108B), FACS (FIG. 108C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. EXAMPLE 2047 A DNA sequence (GBSx2158) was identified in S. agalactiae <SEQ ID 6323> which encodes the amino acid sequence <SEQ ID 6324>. This protein is predicted to be preprotein translocase secy subunit (secY). Analysis of this protein sequence reveals the following: TABLE-US-06260 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.01 Transmembrane 217-233 (209-240) INTEGRAL Likelihood = -8.65 Transmembrane 314-330 (307-334) INTEGRAL Likelihood = -6.16 Transmembrane 369-385 (363-392) INTEGRAL Likelihood = -5.36 Transmembrane 19-35 (17-40) INTEGRAL Likelihood = -3.93 Transmembrane 180-196 (179-199) INTEGRAL Likelihood = -3.03 Transmembrane 395-411 (392-412) INTEGRAL Likelihood = -2.55 Transmembrane 151-167 (151-168) INTEGRAL Likelihood = -2.02 Transmembrane 117-133 (117-133) INTEGRAL Likelihood = -0.64 Transmembrane 270-286 (269-286) ----- Final Results ----- bacterial membrane --- Certainty = 0.6604(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9467> which encodes amino acid sequence <SEQ ID 9468> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06261 >GP:CAA41939 GB:X59250 SecY protein [Lactococcus lactis] Identities = 292/433 (67%), Positives = 361/433 (82%), Gaps = 2/433 (0%) Query: 1 MFLKLLRDALKVKMVRNKILFTIFILLVFRIGTHITVPGINVKSLEQMGELPFLNMLNLV 60 MF K L++A KVK VR +ILFTIFIL VFR+G HIT PG+NV++L+Q+ +LPFL+M+NLV Sbjct: 1 MFFKTLKEAFKVKDVRARILFTIFILFVFRLGAHITAPGVNVQNLQQVADLPFLSMMNLV 60 Query: 61 SGNAMRNFSVFSMGVSPYITASIVVQLLQMDILPKFVEWGKQGEVGRRKLNQATRYISLF 120- SGNAM+N+S+F+MGVSPYITASI+VQLLQMDILPKFVEW KQGE+GRRKLNQATRYI+L Sbjct: 61 SGNAMQNYSLFAMGVSPYITASIIVQLLQMDILPKFVEWSKQGEIGRRKLNQATRYITLV 120- Query: 121 LAFVQSIGITAGFNTLSSVALVKTPNVQTYLLIGAILTTGSMVVTWLGEQITDKGFGNGV 18- 0 LA QSIGITAGF +SS+ +V+ PN Q+YL+IG +LTTGSMVVTW+GEQI +KGFG+GV Sbjct: 121 LAMAQSIGITAGFQAMSSLNIVQNPNWQSYLMIGVLLTTGSMVVTWMGEQINEKGFGSGV 18- 0 Query: 181 SMIIFAGIISSIPSAITTIYEDFFVNVRSSAITNSYIFVGILIVAVLAIVFFTTFIQQAE 24- 0 S+IIFAGI+S IPSAI ++Y++ F+NVR S I S+IFV LI++ + I++ TTF+QQAE Sbjct: 181 SVIIFAGIVSGIPSAIKSVYDEKFLNVRPSEIPMSWIFVIGLILSAIVIIYVTTFVQQAE 24- 0 Query: 241 YKIPIQYTKLVQGAPTSSYLPLKVNPAGVIPVIFASSITTIPSTIIPFFQ--NGKEIPWL 29- 8 K+PIQYTKL QGAPTSSYLPL+VNPAGVIPVIFA SITT P+TI+ F Q G + WL Sbjct: 241 RKVPIQYTKLTQGAPTSSYLPLRVNPAGVIPVIFAGSITTAPATILQFLQRSQGSNVGWL 30- 0 Query: 299 TKLQELLNYQTPVGMIIYAILIILFSFFYTFVQVNPEKTAENLQKNSSYIPSIRPGRETE 35- 8 + LQ L+Y T GM+ YA+LI+LF+FFY+FVQVNPEK AENLQK SYIPS+RPG+ TE Sbjct: 301 STLQNALSYTTWTGMLFYALLIVLFTFFYSFVQVNPEKMAENLQKQGSYIPSVRPGKGTE 36- 0 Query: 359 EYMSSLLKKLATIGSVFLAFISLLPIIAQQALHLSSSIALGGTSLLILIATGIEGMKQLE 41- 8 +Y+S LL +LAT+GS+FL IS++PI AQ L +ALGGTSLLILI I+ +KQLE Sbjct: 361 KYVSRLLMRLATVGSLFLGLISIIPIAAQNVWGLPKIVALGGTSLLILIQVAIQAVKQLE 42- 0 Query: 419 GYLLKRRYVGFMN 431 GYLLKR+Y GFM+ Sbjct: 421 GYLLKRKYAGFMD 433 A related DNA sequence was identified in S. pyogenes <SEQ ID 3987> which encodes the amino acid sequence <SEQ ID 3988>. Analysis of this protein sequence reveals the following: TABLE-US-06262 Possible site: 55 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.70 Transmembrane 233-249 (226-255) INTEGRAL Likelihood = -8.12 Transmembrane 330-346 (323-350) INTEGRAL Likelihood = -6.10 Transmembrane 384-400 (378-403) INTEGRAL Likelihood = -5.20 Transmembrane 35-51 (33-56) INTEGRAL Likelihood = -4.09 Transmembrane 199-215 (195-215) INTEGRAL Likelihood = -3.56 Transmembrane 167-183 (165-184) INTEGRAL Likelihood = -1.65 Transmembrane 411-427 (411-428) INTEGRAL Likelihood = -1.49 Transmembrane 133-149 (133-149) INTEGRAL Likelihood = -0.64 Transmembrane 286-302 (285-302) ----- Final Results ----- bacterial membrane --- Certainty = 0.6880(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06263 Identities = 377/434 (86%), Positives = 417/434 (95%) Query: 1 MFLKLLRDALKVKMVRNKILFTIFILLVFRIGTHITVPGINVKSLEQMGELPFLNMLNLV 60 MFLK+L+DALK+K VRNKI FTIFI+LVFRIGTHITVPG+N KSLEQ+ ELPFLNMLNLV Sbjct: 17 MFLKILKDALKIKTVRNKIFFTIFIILVFRIGTHITVPGVNAKSLEQLSELPFLNMLNLV 76 Query: 61 SGNAMRNFSVFSMGVSPYITASIVVQLLQMDILPKFVEWGKQGEVGRRKLNQATRYISLF 120- SGNAMRNFSVFSMGVSPYITASIVVQLLQMDILPKFVEWGKQGEVGRRKLNQATRYISL Sbjct: 77 SGNAMRNFSVFSMGVSPYITASIVVQLLQMDILPKFVEWGKQGEVGRRKLNQATRYISLV 136- Query: 121 LAFVQSIGITAGFNTLSSVALVKTPNVQTYLLIGAILTTGSMVVTWLGEQITDKGFGNGV 18- 0 LAF QSIGITAGFNTLS+VALVKTP+++TYLLIGA+LTTGS++VTWLGEQITDKGFGNGV Sbjct: 137 LAFAQSIGITAGFNTLSNVALVKTPDIKTYLLIGALLTTGSVIVTWLGEQITDKGFGNGV 19- 6 Query: 181 SMIIFAGIISSIPSAITTIYEDFFVNVRSSAITNSYIFVGILIVAVLAIVFFTTFIQQAE 24- 0 SMIIFAGIISSIPSAI TI ED+FVNV++S + +SY+ VGILI+AVLAIVFFTT++QQAE Sbjct: 197 SMIIFAGIISSIPSAIATIREDYFVNVKASDLHSSYLIVGILIIAVLAIVFFTTYVQQAE 25- 6 Query: 241 YKIPIQYTKLVQGAPTSSYLPLKVNPAGVIPVIFASSITTIPSTIIPFFQNGKEIPWLTK 30- 0 YKIPIQYTKL+QGAPTSSYLPLKVNPAGVIPVIFASSITTIPSTIIPF QNG+++PWL + Sbjct: 257 YKIPIQYTKLMQGAPTSSYLPLKVNPAGVIPVIFASSITTIPSTIIPFVQNGRDLPWLNR 31- 6 Query: 301 LQELLNYQTPVGMIIYAILIILFSFFYTFVQVNPEKTAENLQKNSSYIPSIRPGRETEEY 36- 0 LQE+ NYQTPVGMI+YA+LIILFSFFYTFVQVNPEKTAENLQKNSSYIPS+RPGRETE++ Sbjct: 317 LQEIFNYQTPVGMIVYALLIILFSFFYTFVQVNPEKTAENLQKNSSYIPSVRPGRETEQF 37- 6 Query: 361 MSSLLKKLATIGSVFLAFISLLPIIAQQALHLSSSIALGGTSLLILIATGIEGMKQLEGY 42- 0 MS+LLKKLAT+G++FLAFISL PI AQQAL+LSSSIALGGTSLLILI+TGIEGMKQLEGY Sbjct: 377 MSALLKKLATVGAIFLAFISLAPIAAQQALNLSSSIALGGTSLLILISTGIEGMKQLEGY 43- 6 Query: 421 LLKRRYVGFMNTTE 434 LLKR+YVGFMNT E Sbjct: 437 LLKRKYVGFMNTAE 450 A related GBS gene <SEQ ID 8969> and protein <SEQ ID 8970> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06264 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 6.16 GvH: Signal Score (-7.5): -4.32 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 9 value: -14.01 threshold: 0.0 INTEGRAL Likelihood = -14.01 Transmembrane 217-233 (209-240) INTEGRAL Likelihood = -9.98 Transmembrane 311-327 (307-334) INTEGRAL Likelihood = -6.16 Transmembrane 369-385 (363-392) INTEGRAL Likelihood = -5.36 Transmembrane 19-35 (17-40) INTEGRAL Likelihood = -3.93 Transmembrane 180-196 (179-199) INTEGRAL Likelihood = -3.03 Transmembrane 395-411 (392-412) INTEGRAL Likelihood = -2.55 Transmembrane 151-167 (151-168) INTEGRAL Likelihood = -2.02 Transmembrane 117-133 (117-133) INTEGRAL Likelihood = -0.64 Transmembrane 270-286 (269-286) PERIPHERAL Likelihood = 0.95 69 modified ALOM score: 3.30 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6604(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00150## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2048 A DNA sequence (GBSx2159) was identified in S. agalactiae <SEQ ID 6325> which encodes the amino acid sequence <SEQ ID 6326>. This protein is predicted to be 50S ribosomal protein L15 (rplO). Analysis of this protein sequence reveals the following: TABLE-US-06265 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5259(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06266 >GP:AAB54021 GB:U96620 ribosomal protein L15 [Staphylococcus aureus] Identities = 116/146 (79%), Positives = 128/146 (87%) Query: 1 MKLHELKPAEGSRKVRNRVGRGTSSGNGKTSGRGQKGQKARSGGGVRLGFEGGQTPLFRR 60 MKLHELKPAEGSRK RNRVGRG ++GNGKTSGRG KGQKARSGGGVR GFEGGQ PLFRR Sbjct: 1 MKLHELKPAEGSRKERNRVGRGVATGNGKTSGRGHKGQKARSGGGVRPGFEGGQLPLFRR 60 Query: 61 MPKRGFSNINAKEYALVNLDQLNVFEDGTEVTPVVLKEAGIVRAEKSGVKILGNGELTKK 120- +PKRGF+NIN KEYA+VNLDQLN FEDGTEVTP +L E+G+V+ EKSG+KILGNG L KK Sbjct: 61 LPKRGFTNINRKEYAIVNLDQLNKFEDGTEVTPALLVESGVVKNEKSGIKILGNGSLDKK 120- Query: 121 LSVKAAKFSKSAEAAITAKGGSIEVI 146 L+VKA KFS SA AI AKGG+ EVI Sbjct: 121 LTVKAHKFSASAAEAIDAKGGAHEVI 146 A related DNA sequence was identified in S. pyogenes <SEQ ID 6327> which encodes the amino acid sequence <SEQ ID 6328>. Analysis of this protein sequence reveals the following: TABLE-US-06267 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5329(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06268 Identities = 135/146 (92%), Positives = 142/146 (96%) Query: 1 MKLHELKPAEGSRKVRNRVGRGTSSGNGKTSGRGQKGQKARSGGGVRLGFEGGQTPLFRR 60 MKLHELK AEGSRKVRNRVGRGTSSGNGKTSGRGQKGQKARSGGGVRLGFEGGQTPLFRR Sbjct: 1 MKLHELKAAEGSRKVRNRVGRGTSSGNGKTSGRGQKGQKARSGGGVRLGFEGGQTPLFRR 60 Query: 61 MPKRGFSNINAKEYALVNLDQLNVFEDGTEVTPVVLKEAGIVRAEKSGVKILGNGELTKK 120- +PKRGF+NIN KEYALVNLDQLNVF+DGTEVTP +LK+AGIVRAEKSGVK+LGNGELTKK Sbjct: 61 IPKRGFTNINTKEYALVNLDQLNVFDDGTEVTPAILKDAGIVRAEKSGVKVLGNGELTKK 120- Query: 121 LSVRAAKFSKSAEAAITAKGGSIEVI 146 L+VKAAKFSKSAEAAI AKGGSIEVI Sbjct: 121 LTVKAAKFSKSAEAAIIAKGGSIEVI 146 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2049 A DNA sequence (GBSx2160) was identified in S. agalactiae <SEQ ID 6329> which encodes the amino acid sequence <SEQ ID 6330>. Analysis of this protein sequence reveals the following: TABLE-US-06269 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1162(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06270 >GP:AAB54020 GB:U96620 ribosomal protein L30 [Staphylococcus aureus] Identities = 40/58 (68%), Positives = 46/58 (78%) Query: 1 MAQIKITLTKSPIGRKPEQRKTVVALGLGKLNSSVVKEDNAAIRGMVNAISHLVTVEE 58 MA+++ITLT+S IGR QRKTV ALGL K NSSVV EDN AIRG +N + HLVTVEE Sbjct: 1 MAKLQITLTRSVIGRPETQRKTVEALGLKKTNSSVVVEDNPAIRGQINKVKHLVTVEE 58 A related DNA sequence was identified in S. pyogenes <SEQ ID 6331> which encodes the amino acid sequence <SEQ ID 6332>. Analysis of this protein sequence reveals the following: TABLE-US-06271 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1088(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < suc> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06272 Identities = 56/58 (96%), Positives = 57/58 (97%) Query: 1 MAQIKITLTKSPIGRKPEQRKTVVALGLGKLNSSVVKEDNAAIRGMVNAISHLVTVEE 58 MAQIKITLTKSPIGRKPEQRKTVVALGLGKLNSSVVKEDNAAIRGMV AISHLVTVE+ Sbjct: 1 MAQIKITLTKSPIGRKPEQRKTVVALGLGKLNSSVVKEDNAAIRGMVTAISHLVTVED 58 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2050 A DNA sequence (GBSx2161) was identified in S. agalactiae <SEQ ID 6333> which encodes the amino acid sequence <SEQ ID 6334>. Analysis of this protein sequence reveals the following:

TABLE-US-06273 Possible site: 36 >>> Seems to have no N-terminal signal sequence ---- Final Results ----- bacterial cytoplasm --- Certainty = 0.3226(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2051 A DNA sequence (GBSx2162) was identified in S. agalactiae <SEQ ID 6335> which encodes the amino acid sequence <SEQ ID 6336>. This protein is predicted to be 30S ribosomal protein S5 (rpsE). Analysis of this protein sequence reveals the following: TABLE-US-06274 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3179(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06275 >GP:AAA22699 GB:M57621 ribosomal protein S5 [Bacillus stearothermophilus] Identities = 119/158 (75%), Positives = 139/158 (87%) Query: 6 NAVELEERVVAINRVTKVVKGGRRLRFAALVVVGDRNGRVGFGTGKAQEVPEAIRKAVEA 65 N +ELEERVVA+NRV KVVKGGRRLRF+ALVVVGD+NG VGFGTGKAQEVPEAIRKA+E Sbjct: 7 NKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIED 66 Query: 66 AKKNMVEVPMVGTTIPHEVRSEFGGAKVLLKPAVEGAGVAAGGAVRAVIELAGVADITSK 125- AKKN++EVP+VGTTIPHEV FG +++LKPA EG GV AGG RAV+ELAG++DI SK Sbjct: 67 AKKNLIEVPIVGTTIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSK 126- Query: 126 SLGSNTPINIVRATVEGLKQLKRAEEVAALRGISVSDL 163 S+GSNTPIN+VRAT +GLKQLKRAE+VA LRG +V +L Sbjct: 127 SIGSNTPINMVRATFDGLKQLKRAEDVAKLRGKTVEEL 164 A related DNA sequence was identified in S. pyogenes <SEQ ID 6337> which encodes the amino acid sequence <SEQ ID 6338>. Analysis of this protein sequence reveals the following: TABLE-US-06276 Possible site: 26 >>> Seems to have no N-terminal siqnal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3179(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06277 Identities = 158/164 (96%), Positives = 161/164 (97%) Query: 1 MAFKDNAVELEERVVAINRVTKVVKGGRRLRFAALVVVGDRNGRVGFGTGKAQEVPEAIR 60 MAFKDNAVELEERVVAINRVTKVVKGGRRLRFAALVVVGD NGRVGFGTGKAQEVPEAIR Sbjct: 1 MAFKDNAVELEERVVAINRVTKVVKGGRRLRFAALVVVGDGNGRVGFGTGKAQEVPEAIR 60 Query: 61 KAVEAAKKNMVEVPMVGTTIPHEVRSEFGGAKVLLKPAVEGAGVAAGGAVRAVIELAGVA 120- KAVEAAKKNM+EVPMVGTTIPHEV + FGGAKVLLKPAVEG+GVAAGGAVRAVIELAGVA Sbjct: 61 KAVEAAKKNMIEVPMVGTTIPHEVYTNFGGAKVLLKPAVEGSGVAAGGAVRAVIELAGVA 120- Query: 121 DITSKSLGSNTPINIVRATVEGLKQLKRAEEVAALRGISVSDLA 164 DITSKSLGSNTPINIVRATVEGLKQLKRAEEVAALRGISVSDLA Sbjct: 121 DITSKSLGSNTPINIVRATVEGLKQLKRAEEVAALRGISVSDLA 164 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2052 A DNA sequence (GBSx2163) was identified in S. agalactiae <SEQ ID 6339> which encodes the amino acid sequence <SEQ ID 6340>. This protein is predicted to be 50S ribosomal protein L18 (rplR). Analysis of this protein sequence reveals the following: TABLE-US-06278 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4488(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9465> which encodes amino acid sequence <SEQ ID 9466> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06279 >GP:AAB06815 GB:L47971 ribosomal protein L18 [Bacillus subtilis] Identities = 86/120 (71%), Positives = 97/120 (80%), Gaps = 2/120 (1%) Query: 4 VISKPDKNKIRQKRHRRVRGKLSGTADRPRLNIFRSNTGIYAQVIDDVAGVTLASASTLD 63 +I+K KN R KRH RVR KLSGTA+RPRLN+FRSN IYAQ+IDDV GVTLASASTLD Sbjct: 1 MITKTSKNAARLKRHARVRAKLSGTAERPRLNVFRSNKHIYAQIIDDVNGVTLASASTLD 60 Query: 64 KE--VSNGTKTEQAVVVGKLVAERAVAKGISEVVFDRGGYLYHGRVKALADSARENGLKF 121- K+ V + T A VG+LVA+RA KGIS+VVFDRGGYLYHGRVKALAD+ARE GLKF Sbjct: 61 KDLNVESTGDTSAATKVGELVAKRAAEKGISDVVFDRGGYLYHGRVKALADAAREAGLKF 120- A related DNA sequence was identified in S. pyogenes <SEQ ID 6341> which encodes the amino acid sequence <SEQ ID 6342>. Analysis of this protein sequence reveals the following: TABLE-US-06280 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4488(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06281 Identities = 116/121 (95%), Positives = 120/121 (98%) Query: 1 MKIVISKPDKNKIRQKRHRRVRGKLSGTADRPRLNIFRSNTGIYAQVIDDVAGVTLASAS 60 +KIVISKPDKNKIRQKRHRRVRGKLSGTADRPRLN+FRSNTGIYAQVIDDVAGVTLASAS Sbjct: 1 VKIVISKPDKNKIRQKRHRRVRGKLSGTADRPRLNVFRSNTGIYAQVIDDVAGVTLASAS 60 Query: 61 TLDKEVSNGTKTEQAVVVGKLVAERAVAKGISEVVFDRGGYLYHGRVKALADSARENGLKF 12- 1 TLDK+VS GTKTEQAVVVGKLVAERAVAKGISEVVFDRGGYLYHGRVKALAD+ARENGLKF Sbjct: 61 TLDKDVSKGTKTEQAVVVGKLVAERAVAKGISEVVFDRGGYLYHGRVKALADAARENGLKF 12- 1 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2053 A DNA sequence (GBSx2164) was identified in S. agalactiae <SEQ ID 6343> which encodes the amino acid sequence <SEQ ID 6344>. Analysis of this protein sequence reveals the following: TABLE-US-06282 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1530(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06283 >GP: AAA22700 GB: M57622 ribosomal protein L6 [Bacillus stearothermophilus] Identities = 108/178 (60%), Positives = 133/178 (74%) Query: 1 MSRIGNKVITLPAGVEIINKDNVVTVKGPKGQLTREFNKNIGITVEGTEVTVTRPNDSKE 60 M R+G K I +PAGV + N VTVKGPKG+LTR F+ ++ ITVEG +TVTRP+D K Sbjct: 1 MXRVGKKPIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVTRPSDEKH 60 Query: 61 MKTIHGTTRANLNNMVVGVSEGFKKALEMRGVGYRAQLQGSKLVLSVGKSHQDEVEAPEG 120- + +HGTTR+ L NMV GVS+G++KALE+ GVGYRA QG KLVLSVG SH E+E EG Sbjct: 61 HRALHGTTRSLLANMVEGVSKGYEKALELVGVGYRASKQGKKLVLSVGYSHPVEIEPEEG 120- Query: 121 VTFEVPTPTTINVIGINKESVGQTAAYVRSLRSPEPYKGKGIRYVGEFVRRKEGKTGK 178 + EVP+ T I V G +K+ VG+ AA +R++R PEPYKGKGIRY GE VR KEGKTGK Sbjct: 121 LEIEVPSQTKIIVKGADKQRVGELAANIRAVRPPEPYKGKGIRYEGELVRLKEGKTGK 178 A related DNA sequence was identified in S. pyogenes <SEQ ID 6345> which encodes the amino acid sequence <SEQ ID 6346>. Analysis of this protein sequence reveals the following: TABLE-US-06284 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1704(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06285 Identities = 153/178 (85%), Positives = 166/178 (92%) Query: 1 MSRIGNKVITLPAGVEIINKDNVVTVKGPKGQLTREFNKNIGITVEGTEVTVTRPNDSKE 60 MSRIGNKVIT+PAGVE+ N +NV+TVKGPKG+LTREFNKNI I VEGTE+TV RPNDSKE Sbjct: 1 MSRIGNKVITMPAGVELTNNNNVITVKGPKGELTREFNKNIEIKVEGTEITVVRPNDSKE 60 Query: 61 MKTIHGTTRANLNNMVVGVSEGFKKALEMRGVGYRAQLQGSKLVLSVGKSHQDEVEAPEG 120- MKTIHGTTRANLNNMVVGVSEGFKK LEM+GVGYRAQLQG+KLVLSVGKSHQDEVEAPEG Sbjct: 61 MKTIHGTTRANLNNMVVGVSEGFKKDLEMKGVGYRAQLQGTKLVLSVGKSHQDEVEAPEG 120- Query: 121 VTFEVPTPTTINVIGINKESVGQTAAYVRSLRSPEPYKGKGIRYVGEFVRRKEGKTGK 178 +TF V PT+I+V GINKE VGQTAAY+RSLRSPEPYKGKGIRYVGE+VR KEGKTGK Sbjct: 121 ITFTVANPTSISVEGINKEVVGQTAAYIRSLRSPEPYKGKGIRYVGEYVRLKEGKTGK 178 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2054 A DNA sequence (GBSx2165) was identified in S. agalactiae <SEQ ID 6347> which encodes the amino acid sequence <SEQ ID 6348>. This protein is predicted to be 30S ribosomal protein S8 (rpsH). Analysis of this protein sequence reveals the following: TABLE-US-06286 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4356(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06287 >GP: AAB06813 GB: L47971 ribosomal protein S8 [Bacillus subtilis] Identities = 100/132 (75%), Positives = 116/132 (87%) Query: 1 MVMTDPIADFLTRIRNANQAKHEVLEVPASNIKKGIADILKREGFVKNVEVIEDDKQGII 60 MVMTDPIAD LTRIRNAN +HE LE+PAS +K+ IA+ILKREGF+++VE +ED KQGII Sbjct: 1 MVMTDPIADMLTRIRNANMVRHEKLEIPASKLKREIAEILKREGFIRDVEFVEDSKQGII 60 Query: 61 RVFLKYGQNGERVITNLKRISKPGLRVYTKHEDMPKVLNGLGIAIVSTSEGLLTDKEARQ 120- RVFLKYGQN ERVIT LKRISKPGLRVY K ++P+VLNGLGIAI+STS +G+LTDKEAR Sbjct: 61 RVFLKYGQNNERVITGLKRISKPGLRVYAKSNEVPRVLNGLGIAIISTSQGVLTDKEARA 120- Query: 121 KNIGGEVLAYIW 132 K GGEVLAY+W Sbjct: 121 KQAGGEVLAYVW 132 A related DNA sequence was identified in S. pyogenes <SEQ ID 6349> which encodes the amino acid sequence <SEQ ID 6350>. Analysis of this protein sequence reveals the following: TABLE-US-06288 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4327(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06289 Identities = 122/132 (92%), Positives = 129/132 (97%) Query: 1 MVMTDPIADFLTRIRNANQAKHEVLEVPASNIKKGIADILKREGFVKNVEVIEDDKQGII 60 MVMTDPIADFLTRIRNANQ KHEVLEVPASNIKKGIA+ILKREGFVKNVEVIEDDKQGII Sbjct: 1 MVMTDPIADFLTRIRNANQVKHEVLEVPASNIKKGIAEILKREGFVKNVEVIEDDKQGII 60 Query: 61 RVFLKYGQNGERVITNLKRISKPGLRVYTKHEDMPKVLNGLGIAIVSTSEGLLTDKEARQ 120- RVFLKYG+NGERVITNLKRISKPGLRVY K +DMPKVLNGLGIAI+STSEGLLTDKEARQ Sbjct: 61 RVFLKYGKNGERVITNLKRISKPGLRVYAKRDDMPKVLNGLGIAIISTSEGLLTDKEARQ 120- Query: 121 KNIGGEVLAYIW 132 KN+GGEV+AY+W Sbjct: 121 KNVGGEVIAYVW 132 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2055 A DNA sequence (GBSx2166) was identified in S. agalactiae <SEQ ID 6351> which encodes the amino acid sequence <SEQ ID 6352>. This protein is predicted to be ribosomal protein S14 (rpsN). Analysis of this protein sequence reveals the following: TABLE-US-06290 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3833(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06291 >GP: CAB11905 GB: Z99104 ribosomal protein S14 [Bacillus subtilis] Identities = 47/61 (77%), Positives = 53/61 (86%) Query: 1 MAKKSMIAKNKRPAKFSTQAYTRCEKCGRPHSVYRKFQLCRVCFRDLAYKGQVPGVTKAS 60 MAKKSMIAK +R KF Q YTRCE+CGRPHSV RKF+LCR+CFR+LAYKGQ+PGV KAS Sbjct: 1 MAKKSMIAKQQRTPKFKVQEYTRCERCGRPHSVIRKFKLCRICFRELAYKGQIPGVKKAS 60 Query: 61 W 61 W Sbjct: 61 W 61 A related DNA sequence was identified in S. pyogenes <SEQ ID 6353> which encodes the amino acid sequence <SEQ ID 6354>. Analysis of this protein sequence reveals the following: TABLE-US-06292 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4747(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06293 Identities = 55/61 (90%), Positives = 59/61 (96%) Query: 1 MAKKSMIAKNKRPAKFSTQAYTRCEKCGRPHSVYRKFQLCRVCFRDLAYKGQVPGVTKAS 60 +AKKSMIAKNKRPAK STQAYTRCEKCGRPHSVYRKF+LCRVCFR+LAYKGQ+PGV KAS Sbjct: 1 LAKKSMIAKNKRPAKHSTQAYTRCEKCGRPHSVYRKFKLCRVCFRELAYKGQIPGVVKAS 60 Query: 61 W 61 W Sbjct: 61 W 61 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2056 A DNA sequence (GBSx2167) was identified in S. agalactiae <SEQ ID 6355> which encodes the amino acid sequence <SEQ ID 6356>. This protein is predicted to be 50S ribosomal protein L5 (rplE). Analysis of this protein sequence reveals the following: TABLE-US-06294 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1845(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06295 >GP: BAB03865 GB: AP001507 ribosomal protein L5 (BL6) [Bacillus halodurans] Identities = 143/178 (80%), Positives = 162/178 (90%) Query: 3 NRLKEKYTNEVVPALTEKFNYSSVMAVPKVEKIVLNMGVGDAVSNAKNLEKAAAELALIS 62 NRLKEKY E+VP+LTERFNYSSVMAVPK+EKIV+NMGVGDAV NAK L+KA EL I+ Sbjct: 2 NRLKEKYQKEIVPSLTEKFNYSSVMAVPKLEKIVVNMGVGDAVQNAKALDKAVEELTEIT 61 Query: 63 GQKPLITKAKKSIAGFRLREGVAIGAKVTLRGERMYEFLDKLVSVSLPRVRDFHGVPTKS 122- GQKP+ITKAKKSIAGF+LREG+ IGAKVTLRGERMYEFLDKL+SVSLPRVRDF G+ K+ Sbjct: 62 GQKPIITKAKKSIAGFKLREGMPIGAKVTLRGERMYEFLDKLISVSLPRVRDFRGISKKA 121- Query: 123 FDGRGNYTLGVKEQLIFPEINFDDVDKVRGLDIVIVTTANTDEESRELLKGLGMPFAK 180 FDGRGNYTLGVKEQLIFPEI++D VDKVRG+D+VIVTTA+TDEE+RELL +GMPF K Sbjct: 122 FDGRGNYTLGVKEQLIFPEIDYDKVDKVRGMDVVIVTTASTDEEARELLSQMGMPFQK 179 A related DNA sequence was identified in S. pyogenes <SEQ ID 6357> which encodes the amino acid sequence <SEQ ID 6358>. Analysis of this protein sequence reveals the following: TABLE-US-06296 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1793(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06297 Identities = 177/180 (98%), Positives = 180/180 (99%) Query: 1 MANRLKEKYTNEVVPALTEKFNYSSVMAVPKVEKIVLNMGVGDAVSNAKNLEKAAAELAL 60 MANRLKEKYTNEV+PALTEKFNY+SVMAVPKVEKIVLNMGVGDAVSNAKNLEKAAAELAL Sbjct: 1 MANRLKEKYTNEVIPALTEKFNYTSVMAVPKVEKIVLNMGVGDAVSNAKNLEKAAAELAL 60 Query: 61 ISGQKPLITKAKKSIAGFRLREGVAIGAKVTLRGERMYEFLDKLVSVSLPRVRDFHGVPT 120- ISGQKPLITKAKKSIAGFRLREGVAIGAKVTLRGERMYEFLDKLVSVSLPRVRDFHGVPT Sbjct: 61 ISGQKPLITKAKKSIAGFRLREGVAIGAKVTLRGERMYEFLDKLVSVSLPRVRDFHGVPT 120- Query: 121 KSFDGRGNYTLGVKEQLIFPEINFDDVDKVRGLDIVIVTTANTDEESRELLKGLGMPFAK 18- 0 KSFDGRGNYTLGVKEQLIFPEI+FDDVDKVRGLDIVIVTTANTDEESRELLKGLGMPFAK Sbjct: 121 KSFDGRGNYTLGVKEQLIFPEISFDDVDKVRGLDIVIVTTANTDEESRELLKGLGMPFAK 18- 0 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2057 A DNA sequence (GBSx2169) was identified in S. agalactiae <SEQ ID 6359> which encodes the amino acid sequence <SEQ ID 6360>. This protein is predicted to be 50S ribosomal protein L24 (rplX). Analysis of this protein sequence reveals the following: TABLE-US-06298 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1850(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06299 >GP: AAD33285 GB: AF126061 RpL24 [Streptococcus pneumoniae] Identities = 89/101 (88%), Positives = 94/101 (92%) Query: 1 MFVKKGDKVRVIAGKDKGTEAVVLKALPKVNKVVVEGVALIKKHQKPNNENPQGAIVEKE 60 MFVKKGDKVRVIAGKDKGTEAVVL ALPKVNKV+VEGV ++KKHQ+P NE PQG I+EKE Sbjct: 1 MFVKKGDKVRVIAGKDKGTEAVVLTALPKVNKVIVEGVNIVKKHQRPTNELPQGGIIEKE 60 Query: 61 APIHVSNVQVLDKNGVAGRVGYKVVDGKKVRYNKKSGEVLD 101 A IHVSNVQVLDKNGVAGRVGYK VDGKKVRYNKKSGEVLD Sbjct: 61 AAIHVSNVQVLDKNGVAGRVGYKFVDGKKVRYNKKSGEVLD 101 A related DNA sequence was identified in S. pyogenes <SEQ ID 6361> which encodes the amino acid sequence <SEQ ID 6362>. Analysis of this protein sequence reveals the following:

TABLE-US-06300 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1850(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06301 Identities = 95/101 (94%), Positives = 99/101 (97%) Query: 1 MFVKKGDKVRVIAGKDKGTEAVVLKALPKVNKVVVEGVALIKKHQKPNNENPQGAIVEKE 60 MFVKKGDKVRVIAGKDKGTEAVVLKALFKVNKV+VEGV +IKKHQKPN ENPQGAIVEKE Sbjct: 1 MFVKKGDKVRVIAGKDKGTEAVVLKALPKVNKVIVEGVGMIKKHQKPNTENPQGAIVEKE 60 Query: 61 APIHVSNVQVLDKNGVAGRVGYKVVDGKKVRYNKKSGEVLD 101 APIHVSNVQVLDKNGVAGR+GYKVVDGKKVRY+KKSGEVLD Sbjct: 61 APIHVSNVQVLDKNGVAGRIGYKVVDGKKVRYSKKSGEVLD 101 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2058 A DNA sequence (GBSx2170) was identified in S. agalactiae <SEQ ID 6363> which encodes the amino acid sequence <SEQ ID 6364>. This protein is predicted to be 50S ribosomal protein L14 (rplN). Analysis of this protein sequence reveals the following: TABLE-US-06302 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1004(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06303 >GP: AAD33284 GB: AF126061 RpL14 [Streptococcus pneumoniae] Identities = 116/122 (95%), Positives = 120/122 (98%) Query: 1 MIQQETRLKVADNSGAREILTIKVLGGSGRKFANIGDVIVASVKQATPGGAVKKGDVVKA 60 MIQ ETRLKVADNSGAREILTIKVLGGSGRKFANIGDVIVASVKQATPGGAVKKGDVVKA Sbjct: 1 MIQTETRLKVADNSGAREILTIKVLGGSGRKFANIGDVIVASVKQATPGGAVKKGDVVKA 60 Query: 61 VIVRTKTGARRPDGSYIKFDDNAAVIIRDDKTPRGTRIFGPVARELREGGYMKIVSLAPE 120- VIVRTK+GARR DGSYIKFD+NAAVIIR+DKTPRGTRIFGPVARELREGG+MKIVSLAPE Sbjct: 61 VIVRTKSGARRADGSYIKFDENAAVIIREDKTPRGTRIFGPVARELREGGFMKIVSLAPE 120- Query: 121 VL 122 VL Sbjct: 121 VL 122 A related DNA sequence was identified in S. pyogenes <SEQ ID 6365> which encodes the amino acid sequence <SEQ ID 6366>. Analysis of this protein sequence reveals the following: TABLE-US-06304 Possible site: 16 >>> Seems to have no N-terminal siqnal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1004(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06305 Identities = 122/122 (100%), Positives = 122/122 (100%) Query: 1 MIQQETRLKVADNSGAREILTIKVLGGSGRKFANIGDVIVASVKQATPGGAVKKGDVVKA 60 MIQQETRLKVADNSGAREILTIKVLGGSGRKFANIGDVIVASVKQATPGGAVKKGDVVKA Sbjct: 1 MIQQETRLKVADNSGAREILTIKVLGGSGRKFANIGDVIVASVKQATPGGAVKKGDVVKA 60 Query: 61 VIVRTKTGARRPDGSYIKFDDNAAVIIRDDKTPRGTRIFGPVARELREGGYMKIVSLAPE 120- VIVRTKTGARRPDGSYIKFDDNAAVIIRDDKTPRGTRIFGPVARELREGGYMKIVSLAPE Sbjct: 61 VIVRTKTGARRPDGSYIKFDDNAAVIIRDDKTPRGTRIFGPVARELREGGYMKIVSLAPE 120- Query: 121 VL 122 VL Sbjct: 121 VL 122 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2059 A DNA sequence (GBSx2171) was identified in S. agalactiae <SEQ ID 6367> which encodes the amino acid sequence <SEQ ID 6368>. Analysis of this protein sequence reveals the following: TABLE-US-06306 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3415(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06307 >GP: AAD33283 GB: AF126061 RpS17 [Streptococcus pneumoniae] Identities = 82/86 (95%), Positives = 83/86 (96%) Query: 1 MERNQRKTLYGRVVSDKMDKTITVVVETKRNHPVYGKRINYSKKYKAHDENNVAKEGDIV 60 MERN RK L GRVVSDKMDKTITVVVETKRNHPVYGKRINYSKKYKAHDENNVAKEGDIV Sbjct: 1 MERNNRKVLVGRVVSDKMDKTITVVVETKRNHPVYGKRINYSKKYKAHDENNVAKEGDIV 60 Query: 61 RIMETRPLSATKRFRLVEVVEKAVII 86 RIMETRPLSATKRFRLVEVVE+AVII Sbjct: 61 RIMETRPLSATKRFRLVEVVEKAVII 86 A related DNA sequence was identified in S. pyogenes <SEQ ID 6369> which encodes the amino acid sequence <SEQ ID 6370>. Analysis of this protein sequence reveals the following: TABLE-US-06308 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3415(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06309 Identities = 86/86 (100%), Positives = 86/86 (100%) Query: 1 MERNQRKTLYGRVVSDKMDKTITVVVETKRNHPVYGKRINYSKKYKAHDENNVAKEGDIV 60 MERNQRKTLYGRVVSDKMDKTITVVVETKRNHPVYGKRINYSKKYKAHDENNVAKEGDIV Sbjct: 1 MERNQRKTLYGRVVSDKMDKTITVVVETKRNHPVYGKRINYSKKYKAHDENNVAKEGDIV 60 Query: 61 RIMETRPLSATKRFRLVEVVEKAVII 86 RIMETRPLSATKRFRLVEVVEKAVII Sbjct: 61 RIMETRPLSATKRFRLVEVVEKAVII 86 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2060 A DNA sequence (GBSx2172) was identified in S. agalactiae <SEQ ID 6371> which encodes the amino acid sequence <SEQ ID 6372>. Analysis of this protein sequence reveals the following: TABLE-US-06310 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4329(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06311 >GP: AAD33282 GB: AF126061 RpL29 [Streptococcus pneumoniae] Identities = 58/68 (85%), Positives = 64/68 (93%) Query: 1 MKLQEIKDFVKELRGLSQEELAKKENELKKELFDLRFQAAAGQLEKTARLDEVKKQIARV 60 MKL E+K+FVKELRGLSQEELAK+ENELKKELF+LRFQAA GQLE+TARL EVKKQIAR+ Sbjct: 1 MKLNEVKEFVKELRGLSQEELAKRENELKKELFELRFQAATGQLEQTARLKEVKKQIARI 60 Query: 61 KTVQSEMK 68 KTVQSE K Sbjct: 61 KTVQSEAK 68 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2061 A DNA sequence (GBSx2174) was identified in S. agalactiae <SEQ ID 6373> which encodes the amino acid sequence <SEQ ID 6374>. This protein is predicted to be RpL16 (rplP). Analysis of this protein sequence reveals the following: TABLE-US-06312 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4574(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06313 >GP: AAD33263 GB: AF126059 RpL16 [Streptococcus pneumoniae] Identities = 135/137 (98%), Positives = 137/137 (99%) Query: 1 MLVPKRVKHRREFRGKMRGEAKGGKEVSFGEYGLQATTSHWITNRQIEAARIANTRYMKR 60 MLVPKRVKHRREFRGKMRGEAKGGKEV+FGEYGLQATTSHWITNRQIEAARIANTRYMKR Sbjct: 1 MLVPKRVKHRREFRGKMRGEAKGGKEVAFGEYGLQATTSHWITNRQIEAARIANTRYMKR 60 Query: 61 GGKVWIKIFPHKSYTAKAIGVRMGSGKGAPEGWVAPVKRGKVMFEIAGVSEEVAREALRL 120- GGKVWIKIFPHKSYTAKAIGVRMGSGKGAPEGWVAPVKRGKVMFEIAGVSEE+AREALRL Sbjct: 61 GGKVWIKIFPHKSYTAKAIGVRMGSGKGAPEGWVAPVKRGKVMFEIAGVSEEIAREALRL 120- Query: 121 ASHKLPVKCKFVKREAE 137 ASHKLPVKCKFVKREAE Sbjct: 121 ASHKLPVKCKFVKREAE 137 A related DNA sequence was identified in S. pyogenes <SEQ ID 6375> which encodes the amino acid sequence <SEQ ID 6376>. Analysis of this protein sequence reveals the following: TABLE-US-06314 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4574(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06315 Identities = 136/137 (99%), Positives = 137/137 (99%) Query: 1 MLVPKRVKHRREFRGKMRGEAKGGKEVSFGEYGLQATTSHWITNRQIEAARIAMTRYMKR 60 MLVPKRVKHRREFRGKMRGEAKGGKEVSFGEYGLQATTSHWITNRQIEAARIAMTRYMKR Sbjct: 1 MLVPKRVKHRREFRGRMRGEAKGGKEVSFGEYGLQATTSHWITNRQIEAARIAMTRYMKR 60 Query: 61 GGKVWIKIFPHKSYTAKAIGVRMGSGKGAPEGWVAPVKRGKVMFEIAGVSEEVAREALRL 120- GGKVWIKIFPHKSYTAKAIGVRMGSGKGAPEGWVAPVKRGKVMFEIAGVSEE+AREALRL Sbjct: 61 GGKVWIKIFPHKSYTAKAIGVRMGSGKGAPEGWVAPVKRGKVMFEIAGVSEEIAREALRL 120- Query: 121 ASHKLPVKCKFVKREAE 137 ASHKLPVKCKFVKREAE Sbjct: 121 ASHKLPVKCKFVKREAE 137 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2062 A DNA sequence (GBSx2175) was identified in S. agalactiae <SEQ ID 6377> which encodes the amino acid sequence <SEQ ID 6378>. Analysis of this protein sequence reveals the following: TABLE-US-06316 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3758(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06317 >GP: AAD33280 GB: AF126061 RpS3 [Streptococcus pneumoniae] Identities = 200/208 (96%), Positives = 203/208 (97%) Query: 10 MRVGIIRDWDAKWYAEKEYADYLHEDLAIRKFINKELADASVSTIEIERAVNKVIVSLHT 69 - MRVGIIRDWDAKWYAEKEYADYLHEDLAIRKF+ KELADA+VSTIEIERAVNKV VSLHT Sbjct: 1 MRVGIIRDWDAKWYAEKEYADYLHEDLAIRKFVQKELADAAVSTIEIERAVNKVNVSLHT 60 Query: 70 AKPGMVIGKGGANVDALRGQLNKLTGKQVHINIIEIKQPDLDAHLVGENIARQLEQRVAF 129- AKPGMVIGKGGANVDALR +LNKLTGKQVHINIIEIKQPDLDAHLVGE IARQLEQRVAF Sbjct: 61 AKPGMVIGKGGANVDALRAKLNKLTGKQVHINIIEIKQPDLDAHLVGEGIARQLEQRVAF 120- Query: 130 RRAQKQAIQRTMRAGAKGIKTQVSGRLNGADIARAEGYSEGTVPLHTLRADIDYAWEEAD 18- 9 RRAQKQAIQR MRAGAKGIKTQVSGRLNGADIARAEGYSEGTVPLHTLRADIDYAWEEAD Sbjct: 121 RRAQKQAIQRAMRAGAKGIKTQVSGRLNGADIARAEGYSEGTVPLHTLRADIDYAWEEAD 18- 0 Query: 190 TTYGKLGVKVWIYRGEVLPARKNTKGGK 217 TTYGKLGVKVWIYRGEVLPARKNTKGGK Sbjct: 181 TTYGKLGVKVWIYRGEVLPARKNTKGGK 208 A related DNA sequence was identified in S. pyogenes <SEQ ID 6379> which encodes the amino acid sequence <SEQ ID 6380>. Analysis of this protein sequence reveals the following: TABLE-US-06318 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3758(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2063 A DNA sequence (GBSx2176) was identified in S. agalactiae <SEQ ID 6381> which encodes the amino acid sequence <SEQ ID 6382>. This protein is predicted to be 50S ribosomal protein L22 (rplV). Analysis of this protein sequence reveals the following: TABLE-US-06319 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2704(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06320 >GP: AAD33279 GB: AF126061 RpL22 [Streptococcus pneumoniae] Identities = 99/114 (86%), Positives = 106/114 (92%) Query: 1 MAEITSAKAMARTVRVSPRKTRLVLDLIRGKNVADAIAILKFTPNKAARVIEKTLNSAIA 60 MAEITSAKAMARTVRVSPRK+RLVLD IRGK+VADAIAIL FTPNKAA +I K LNSA+A Sbjct: 1 MAEITSAKAMARTVRVSPRKSRLVLDNIRGKSVADAIAILTFTPNKAAEIILKVLNSAVA 60 Query: 61 NAENNFGLEKANLVVSETFANEGPTMKRFRPRAKGSASPINKRTTHVTVVVSEK 114 NAENNFGL+KANLVVSE FANEGPTMKRFRPRAKGSASPINKRT H+TV V+EK Sbjct: 61 NAENNFGLDKANLVVSEAFANEGPTMKRFRPRAKGSASPINKRTAHITVAVAEK 114 A related DNA sequence was identified in S. pyogenes <SEQ ID 6383> which encodes the amino acid sequence <SEQ ID 6384>. Analysis of this protein sequence reveals the following: TABLE-US-06321 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2794(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06322 Identities = 113/114 (99%), Positives = 113/114 (99%) Query: 1 MAEITSAKAMARTVRVSPRKTRLVLDLIRGKNVADAIAILKFTPNKAARVIEKTLNSAIA 60 MAEITSAKAMARTVRVSPRKTRLVLDLIRGK VADAIAILKFTPNKAARVIEKTLNSAIA Sbjct: 1 MAEITSAKAMARTVRVSPRKTRLVLDLIRGKKVADAIAILKFTPNKAARVIEKTLNSAIA 60 Query: 61 NAENNFGLEKANLVVSETFANEGPTMKRFRPRAKGSASPINKRTTHVTVVVSEK 114 NAENNFGLEKANLVVSETFANEGPTMKRFRPRAKGSASPINKRTTHVTVVVSEK Sbjct: 61 NAENNFGLEKANLVVSETFANEGPTMKRFRPRAKGSASPINKRTTHVTVVVSEK 114 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2064 A DNA sequence (GBSx2177) was identified in S. agalactiae <SEQ ID 6385> which encodes the amino acid sequence <SEQ ID 6386>. This protein is predicted to be 30S ribosomal protein S19 (rpsS). Analysis of this protein sequence reveals the following: TABLE-US-06323 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2991(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein is similar to ribosomal protein S19 from S. pneumoniae. A related DNA sequence was identified in S. pyogenes <SEQ ID 6387> which encodes the amino acid sequence <SEQ ID 6388>. Analysis of this protein sequence reveals the following: TABLE-US-06324 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3319(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06325 Identities = 92/92 (100%), Positives = 92/92 (100%) Query: 1 MGRSLKKGPFVDEHLMKKVEAQANDEKKKVIKTWSRRSTIFPSFIGYTIAVYDGRKHVPV 60 MGRSLKKGPFVDEHLMKKVEAQANDEKKKVIKTWSRRSTIFPSFIGYTIAVYDGRKHVPV Sbjct: 19 MGRSLKKGPFVDEHLMKKVEAQANDEKKKVIKTWSRRSTIFPSFIGYTIAVYDGRKHVPV 78 Query: 61 YIQEDMVGHKLGEFAPTRTYKGHAADDKKTRR 92 YIQEDMVGHKLGEFAPTRTYKGHAADDKKTRR Sbjct: 79 YIQEDMVGHKLGEFAPTRTYKGHAADDKKTRR 110 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2065 A DNA sequence (GBSx2178) was identified in S. agalactiae <SEQ ID 6389> which encodes the amino acid sequence <SEQ ID 6390>. This protein is predicted to be L2 (rplB). Analysis of this protein sequence reveals the following: TABLE-US-06326 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3182(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06327 >GP: AAC45959 GB: U43929 L2 [Bacillus subtilis] Identities = 208/277 (75%), Positives = 239/277 (86%) Query: 1 MGIKVYKPTTNGRRNMTSLDFAEITTNTPEKSLLVSLKNKAGRNNNGRITVRHQGGGHKR 60 M IK YKP++NGRR MT+ DFAEITT+ PEKSLL L K GRNN G++TVRHQGGGHKR Sbjct: 1 MAIKKYKPSSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR 60 Query: 61 HYRLIDFKRNKDGVEAVVKTIEYDPNRTANIALVHYTDGVKAYILAPKGLEVGQRIISGP 120- YR+IDFKR+KDG+ V T+EYDPNR+ANIAL++Y DG K YILAPKG++VG ++SGP Sbjct: 61 QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEVMSGP 120- Query: 121 EADIKVGNALPLANIPVGTVIHNIELQPGKGAELIRAAGASAQVLGQEGKYVLVRLQSGE 18- 0 EADIKVGNALPL NIPVGTV+HNIEL+PGKG +L+R+AG SAQVLG+EGKYVLVRL SGE Sbjct: 121 EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE 18- 0 Query: 181 VRMILGTCRATIGTVGNEQQSLVNIGKAGRNRWKGVRPTVRGSVMNPNDHPHGGGEGKAP 24- 0 VRMIL CRA+IG VGNEQ L+NIGKAGR+RWKG+RPTVRGSVMNPNDHPHGGGEG+AP Sbjct: 181 VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP 24- 0 Query: 241 VGRKAPSTPWGKPALGLKTRNKKAKSDKLIVRRRNQK 277 +GRK+P +PWGKP LG KTR KK KSDK IVRRR K Sbjct: 241 IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK 277 A related DNA sequence was identified in S. pyogenes <SEQ ID 6391> which encodes the amino acid sequence <SEQ ID 6392>. Analysis of this protein sequence reveals the following:

TABLE-US-06328 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2560(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06329 Identities = 264/277 (95%), Positives = 276/277 (99%) Query: 1 MGIKVYKPTTNGRRNMTSLDFAEITTNTPEKSLLVSLKNKAGRNNNGRITVRHQGGGHKR 60 +GIKVYKPTTNGRRNMTSLDFAEITT+TPEKSLLVSLK+KAGRNNNGRITVRHQGGGHKR Sbjct: 1 VGIKVYKPTTNGRRNMTSLDFAEITTSTPEKSLLVSLKSKAGRNNNGRITVRHQGGGHKR 60 Query: 61 HYRLIDFKRNKDGVEAVVKTIEYDPNRTANIALVHYTDGVKAYILAPKGLEVGQRIISGP 120- HYRLIDFKRNKDGVEAVVKTIEYDPNRTANIALVHYTDGVKAYI+APKGLEVGQRI+SGP Sbjct: 61 HYRLIDFKRNKDGVEAVVKTIEYDPNRTANIALVHYTDGVKAYIIAPKGLEVGQRIVSGP 120- Query: 121 EADIKVGNALPLANIPVGTVIHNIELQPGKGAELIRAAGASAQVLGQEGKYVLVRLQSGE 18- 0 +ADIKVGNALPLANIPVGTV+HNIEL+PGKG EL+RAAGASAQVLGQEGKYVLVRLQSGE Sbjct: 121 DADIKVGNALPLANIPVGTVVHNIELKPGKGGELVRAAGASAQVLGQEGKYVLVRLQSGE 18- 0 Query: 181 VRMILGTCRATIGTVGNEQQSLVNIGKAGRNRWKGVRPTVRGSVMNPNDHPHGGGEGKAP 24- 0 VRMILGTCRATIGTVGNEQQSLVNIGKAGR+RWKG+RPTVRGSVMNPNDHPHGGGEGKAP Sbjct: 181 VRMILGTCRATIGTVGNEQQSLVNIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGKAP 24- 0 Query: 241 VGRKAPSTPWGKPALGLKTRNKKAKSDKLIVRRRNQK 277 VGRKAPSTPWGKPALGLKTRNKKAKSDKLIVRRRN+K Sbjct: 241 VGRKAPSTPWGKPALGLKTRNKKAKSDKLIVRRRNEK 277 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2066 A DNA sequence (GBSx2180) was identified in S. agalactiae <SEQ ID 6393> which encodes the amino acid sequence <SEQ ID 6394>. This protein is predicted to be 50S ribosomal protein L23 (rplW). Analysis of this protein sequence reveals the following: TABLE-US-06330 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1669(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06331 >GP: BAB03855 GB: AP001507 ribosomal protein L23 [Bacillus halodurans] Identities = 56/92 (60%), Positives = 67/92 (71%), Gaps = 1/92 (1%) Query: 2 NLYDVIKKPVITEKSMVALEAGKYTFEVDTRAHKLLIKQAVEAAFDGVKVASVNTVTVKP 61 N DVIK+PVITE+S + KYTFEVD RA+K IK A+E FD VKVA VNT+ K Sbjct: 3 NARDVIKRPVITERSTEVMGDKKYTFEVDVRANKTQIKDAIEEIFD-VKVAKVNTMNYKG 61 Query: 62 KAKRVGRYTGFTSKTKKAIITLTADSKAIELF 93 K KR GRYTGFT++ KKAI+TLT DSK ++ F Sbjct: 62 KPKRFGRYTGFTARRKKAIVTLTPDSKELDFF 93 A related DNA sequence was identified in S. pyogenes <SEQ ID 6395> which encodes the amino acid sequence <SEQ ID 6396>. Analysis of this protein sequence reveals the following: TABLE-US-06332 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1617(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06333 Identities = 96/98 (97%), Positives = 97/98 (98%) Query: 1 MNLYDVIKKPVITEKSMVALEAGKYTFEVDTRAHKLLIKQAVEAAFDGVKVASVNTVTVK 60 MNLYDVIKKPVITEKSM+ALEAGKYTFEVDTRAHKLLIKQAVEAAFDGVKVASVNTV VK Sbjct: 1 MNLYDVIKKPVITEKSMIALEAGKYTFEVDTRAHKLLIKQAVEAAFDGVKVASVNTVNVK 60 Query: 61 PKAKRVGRYTGFTSKTKKAIITLTADSKAIELFAAEAE 98 PKAKRVGRYTGFTSKTKKAIITLTADSKAIELFAAEAE Sbjct: 61 PKAKRVGRYTGFTSKTKKAIITLTADSKAIELFAAEAE 98 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2067 A DNA sequence (GBSx2181) was identified in S. agalactiae <SEQ ID 6397> which encodes the amino acid sequence <SEQ ID 6398>. This protein is predicted to be 50S ribosomal protein L4 (rplD). Analysis of this protein sequence reveals the following: TABLE-US-06334 Possible site: 60 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.54 Transmembrane 140-156 (139-156) ----- Final Results ----- bacterial membrane --- Certainty = 0.1617(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06335 >GP: AAC45957 GB: U43929 L4 [Bacillus subtilis] Identities = 130/207 (62%), Positives = 160/207 (76%) Query: 1 MANVKLFDQTGKEVSSVELNEAIFGIEPNESVVFDVVISQRASLRQGTHAVKNRSAVSGG 60 M V L++Q G +ELN ++FGIEPNESVVFD ++ QRASLRQGTH VKNRS V GG Sbjct: 1 MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG 60 Query: 61 GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYGYKLPQKVRRLALKSVYSAKVAE 120- GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSY YKLP+KVRRLA+KSV S+KV + Sbjct: 61 GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID 120- Query: 121 DKFVAVENLSFAAPKTAEFASVLSALSIDSKVLVILEEGNEFAALSARNLPNVTVATATT 18- 0 + + +E+L+ KT E A++L LS++ K L++ + NE ALSARN+P VTV A Sbjct: 121 NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG 18- 0 Query: 181 ASVLDIVNADKLLVTKEAISTIEGVLA 207 +VLD+VN +KLL+TK A+ +E VLA Sbjct: 181 INVLDVVNHEKLLITKAAVEKVEEVLA 207 A related DNA sequence was identified in S. pyogenes <SEQ ID 6399> which encodes the amino acid sequence <SEQ ID 6400>. Analysis of this protein sequence reveals the following: TABLE-US-06336 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2544(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06337 Identities = 199/207 (96%), Positives = 203/207 (97%) Query: 1 MANVKLFDQTGKEVSSVELNEAIFGIEPNESVVFDVVISQRASLRQGTHAVKNRSAVSGG 60 MANVKLFDQTGKEVSSVELN+AIFGIEPNESVVFDVVISQRASLRQGTHAVKNRSAVSGG Sbjct: 1 MANVKLFDQTGKEVSSVELNDAIFGIEPNESVVFDVVISQRASLRQGTHAVKNRSAVSGG 60 Query: 61 GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYGYKLPQRVRRLALKSVYSAKVAE 120- GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYGYKLPQKVRRLALKSVYSAKVAE Sbjct: 61 GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYGYKLPQKVRRLALKSVYSAKVAE 120- Query: 121 DKFVAVENLSFAAPKTAEFASVLSALSIDSKVLVILEEGNEFAALSARNLPNVTVATATT 18- 0 DKFVAVE LSFAAPKTAEFA VLSALSID+KVLV++EEGNEFAALSARNLPNVTVATA T Sbjct: 121 DKFVAVEGLSFAAPKTAEFAKVLSALSIDTKVLVLVEEGNEFAALSARNLPNVTVATAAT 18- 0 Query: 181 ASVLDIVNADKLLVTKEAISTIEGVLA 207 ASVLDIVNADKLLVTKEAISTIE VLA Sbjct: 181 ASVLDIVNADKLLVTKEAISTIEEVLA 207 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2068 A DNA sequence (GBSx2183) was identified in S. agalactiae <SEQ ID 6401> which encodes the amino acid sequence <SEQ ID 6402>. This protein is predicted to be 50S ribosomal protein L3 (rplC). Analysis of this protein sequence reveals the following: TABLE-US-06338 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2090(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06339 >GP: AAC45956 GB: U43929 L3 [Bacillus subtilis] Identities = 157/208 (75%), Positives = 180/208 (86%), Gaps = 2/208 (0%) Query: 1 MTKGILGKKVGMTQIFTESGEFIPVTVIEATPNVVLQVKTVETDGYEAVQVGFDDKREVL 60 MTKGILG+K+GMTQ+F E+G+ IPVTVIEA PNVVLQ KT E DGYEA+Q+GFDDKRE L Sbjct: 1 MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL 60 Query: 61 SNKPAKGHVAKANTAPKRFIREFKNIE--GLEVGAELSVEQFEAGDVVDVTGTSKGKGFQ 118- SNKP KGHVAKA TAPKRF++E + +E EVG E+ VE F AG++VDVTG SKGKGFQ Sbjct: 61 SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ 120- Query: 119 GVIKRHGQSRGPMAHGSRYHRRPGSMGPVAPNRVFKNKRLAGRMGGNRVTVQNLEIVQVI 17- 8 G IKRHGQSRGPM+HGSRYHRRPGSMGPV PNRVFK K L GRMGG ++TVQNLEIV+V Sbjct: 121 GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGPMGGEQITVQNLEIVKVD 18- 0 Query: 179 PEKNVVLIKGNVPGAKKSLITIKSAVKA 206 E+N++LIKGNVPGAKKSLIT+KSAVK+ Sbjct: 181 AERNLLLIKGNVPGAKKSLITVKSAVKS 208 A related DNA sequence was identified in S. pyogenes <SEQ ID 6403> which encodes the amino acid sequence <SEQ ID 6404>. Analysis of this protein sequence reveals the following: TABLE-US-06340 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2090(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06341 Identities = 205/208 (98%), Positives = 207/208 (98%) Query: 1 MTKGILGKKVGMTQIFTESGEFIPVTVIEATPNVVLQVKTVETDGYEAVQVGFDDKREVL 60 MTKGILGKKVGMTQIFTESGEFIPVTVIEATPNVVLQVKTVETDGYEAVQVGFDDKREVL Sbjct: 1 MTKGILGKKVGMTQIFTESGEFIPVTVIEATPNVVLQVKTVETDGYEAVQVGFDDKREVL 60 Query: 61 SNKPAKGHVAKANTAPKRFIREFKNIEGLEVGAELSVEQFEAGDVVDVTGTSKGKGFQGV 120- SNKPAKGHVAKANTAPKRFIREFKNIEGLEVGAELSVEQFEAGDVVDVTG SKGKGFQGV Sbjct: 61 SNKPAKGHVAKANTAPKRFIREFKNIEGLEVGAELSVEQFEAGDVVDVTGISKGKGFQGV 120- Query: 121 IKRHGQSRGPMAHGSRYHRRPGSMGPVAPNRVFKNKRLAGRMGGNRVTVQNLEIVQVIPE 18- 0 IKRHGQSRGPMAHGSRYHRRPGSMGPVAPNRVFKNKRLAGRMGGNRVTVQNLEIVQVIPE Sbjct: 121 IKRHGQSRGPMAHGSRYHRRPGSMGPVAPNRVFKNKRLAGRMGGNRVTVQNLEIVQVIPE 18- 0 Query: 181 KNVVLIKGNVPGAKKSLITIKSAVKAAK 208 KNV+L+KGNVPGAKKSLITIKSAVKAAK Sbjct: 181 KNVILVKGNVPGAKKSLITIKSAVKAAK 208 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2069 A DNA sequence (GBSx2184) was identified in S. agalactiae <SEQ ID 6405> which encodes the amino acid sequence <SEQ ID 6406>. Analysis of this protein sequence reveals the following: TABLE-US-06342 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.43 Transmembrane 5-21 (5-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2070 A DNA sequence (GBSx2185) was identified in S. agalactiae <SEQ ID 6407> which encodes the amino acid sequence <SEQ ID 6408>. This protein is predicted to be 30S ribosomal protein S10 (rpsJ). Analysis of this protein sequence reveals the following: TABLE-US-06343 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3160(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06344 >GP: AAB46363 GB: L29637 S10 ribosomal protein [Streptococcus mutans] Identities = 98/102 (96%), Positives = 102/102 (99%) Query: 1 MANKKIRIRLKAYEHRTLDTAAEKIVETATRTGATVAGPVPLPTERSLYTIIRATHKYKD 60 MANKKIRIRLKAYEHRTLDTAAEKIVETATRTGA+VAGPVPLPTERSLYT+IRATHKYKD Sbjct: 1 MANKKIRIRLKAYEHRTLDTAAEKIVETATRTGASVAGPVPLPTERSLYTVIPATHKYKD 60 Query: 61 SREQFEMRTHKRLVDIINPTQKTVDALMKLDLPSGVNVEIKL 102 SREQFEMRTHKRL+DI+NPTQKTVDALMKLDLPSGVNVEIKL Sbjct: 61 SREQFEMRTHKRLIDIVNPTQKTVDALMKLDLPSGVNVEIKL 102 A related DNA sequence was identified in S. pyogenes <SEQ ID 6409> which encodes the amino acid sequence <SEQ ID 6410>. Analysis of this protein sequence reveals the following: TABLE-US-06345 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3160(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06346 Identities = 102/102 (100%), Positives = 102/102 (100%) Query: 1 MANKKIRIRLKAYEHRTLDTAAEKIVETATRTGATVAGPVPLPTERSLYTIIRATHKYKD 60 MANKKIRIRLKAYEHRTLDTAAEKIVETATRTGATVAGPVPLPTERSLYTIIRATHKYKD Sbjct: 1 MANKKIRIRLKAYEHRTLDTAAEKIVETATRTGATVAGPVPLPTERSLYTIIRATHKYKD 60 Query: 61 SREQFEMRTHKRLVDIINPTQKTVDALMKLDLPSGVNVEIKL 102 SREQFEMRTHKRLVDIINPTQKTVDALMKLDLPSGVNVEIKL Sbjct: 61 SREQFEMRTHKRLVDIINPTQKTVDALMKLDLPSGVNVEIKL 102 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2071 A DNA sequence (GBSx2186) was identified in S. agalactiae <SEQ ID 6411> which encodes the amino acid sequence <SEQ ID 6412>. Analysis of this protein sequence reveals the following: TABLE-US-06347 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2538(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2072 A DNA sequence (GBSx2187) was identified in S. agalactiae <SEQ ID 6413> which encodes the amino acid sequence <SEQ ID 6414>. Analysis of this protein sequence reveals the following: TABLE-US-06348 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.41 Transmembrane 88-104 (79-110) INTEGRAL Likelihood = -8.39 Transmembrane 304-320 (300-324) INTEGRAL Likelihood = -6.58 Transmembrane 185-201 (180-206) INTEGRAL Likelihood = -5.63 Transmembrane 338-354 (331-357) INTEGRAL Likelihood = -5.52 Transmembrane 240-256 (237-259) INTEGRAL Likelihood = -4.99 Transmembrane 383-399 (375-407) INTEGRAL Likelihood = -3.82 Transmembrane 49-65 (48-73) INTEGRAL Likelihood = -2.87 Transmembrane 127-143 (121-144) INTEGRAL Likelihood = -2.81 Transmembrane 159-175 (159-177) INTEGRAL Likelihood = -2.18 Transmembrane 30-46 (30-47) ----- Final Results ----- bacterial membrane --- Certainty = 0.5564(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06349 >GP: BAB06655 GB: AP001517 unknown conserved protein [Bacillus halodurans] Identities = 132/423 (31%), Positives = 210/423 (49%), Gaps = 16/423 (3%) Query: 7 IIQLAIPAMIENILQMLMGVVDNYLVAQLGVVAVSGVSVANNIITIYQAIF--IALGASI 64 + L P IE +L MLMG D +++Q AV+ V V+N I+ + +F +A G SI Sbjct: 11 LFALTWPIFIEILLHMLMGNADTLMLSQYSDDAVAAVGVSNQILAVIIVMFGFVATGTSI 70 Query: 65 ASLLAKSLAGSKKDDAISVCSQAIFLTLLIGAVLGIISIVFGQTFFKLLGTTKSVAQVGG 124- L+A+ L ++++A V +I L+ G VLG++ I FG K + S+ Q Sbjct: 71 --LVAQHLGAKERENAGKVAVVSIGANLIFGIVLGLLLIAFGPPILKAMQLDDSLLQEAT 128- Query: 125 LYLAIVGGGVVTLGMLTTLGSFLRVQGQPRLPMYVSIFVNFLNAVLSGFAIFEWR----Y 18- 0 LYL IVGG V ++ T G+ LR + MYV+I +N LN + + IF Sbjct: 129 LYLQIVGGFSVVQSLIMTAGAILRSHSFTKDVMYVTIGMNILNVIGNYLFIFGPFGIPVL 18- 8 Query: 181 GLVGVAVSTLIARLIGICILAKYL--------PIKKIIKRMTWKISAQIWNLALPSAGER 23- 2 G+ GVA+ST+++R IG+ ++A L P ++KR + + +PSAGE+ Sbjct: 189 GVTGVALSTVVSRTIGLFVIAILLYKRIRGELPFAYLLKRFPRVELRNLLKIGIPSAGEQ 24- 8 Query: 233 LMNRAGDVVIVAIVVQLGTNVVAGNAIGETLTQFNYMPGLGIATATIILTAKYVGQKNRE 29- 2 L A +VI + +GT + + L F ++ + I T IL VG K + Sbjct: 249 LSYNASQLVITYFIAMMGTEALTTKVYTQNLMMFVFLFAVAIGQGTQILIGHQVGAKQIQ 30- 8 Query: 293 SIEETIQSSYYIGLVLMILISSFMLLAGKPLTQLFTNNPSAIKGSLIVILLSFVGVPATI 35- 2 + S +I + + + ++ PL +FT+NP + ++LL+ + P Sbjct: 309 AAYVRCFRSLWIAMTVSVSMAVVFFAFSTPLLGIFTDNPDILSLGTTLLLLTIILEPGRA 36- 8 Query: 353 GTLVYTAAWQGLGNAKLPFYTTTIGMWLIRVVLGYLLGIVFELGLLGVWMATIADNIFRW 41- 2 LV ++ + G+ K P Y + MW I V + YLLG+ LGL+GVW+A IAD FR Sbjct: 369 CNLVVISSLRAAGDVKFPVYLAIVSMWGIAVPIAYLLGLPLGLGLIGVWIAFIADEWFRG 42- 8 Query: 413 LFL 415 L + Sbjct: 429 LLM 431 A related DNA sequence was identified in S. pyogenes <SEQ ID 6415> which encodes the amino acid sequence <SEQ ID 6416>. Analysis of this protein sequence reveals the following:

TABLE-US-06350 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.26 Transmembrane 89-105 (85-108) INTEGRAL Likelihood = -4.35 Transmembrane 305-321 (302-322) INTEGRAL Likelihood = -3.82 Transmembrane 161-177 (161-180) INTEGRAL Likelihood = -3.82 Transmembrane 192-208 (189-208) INTEGRAL Likelihood = -3.77 Transmembrane 129-145 (128-151) INTEGRAL Likelihood = -3.24 Transmembrane 242-258 (240-258) INTEGRAL Likelihood = -2.81 Transmembrane 378-394 (377-394) INTEGRAL Likelihood = -2.66 Transmembrane 339-355 (338-358) INTEGRAL Likelihood = -2.60 Transmembrane 58-74 (58-75) INTEGRAL Likelihood = -2.50 Transmembrane 32-48 (32-49) ----- Final Results ----- bacterial membrane --- Certainty = 0.3102(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06351 >GP: BAB06655 GB: AP001517 unknown conserved protein [Bacillus halodurans] Identities = 119/435 (27%), Positives = 214/435 (48%), Gaps = 14/435 (3%) Query: 9 IFSLALPSMIENILQMLMGMVDNYLVAQIGLVAVSGVSIANNIISIYQSLFIALGAAVSS 68 +F+L P IE +L MLMG D +++Q AV+ V ++N I+++ +F + S Sbjct: 11 LFALTWPIFIEILLHMLMGNADTLMLSQYSDDAVAAVGVSNQILAVIIVMFGFVATGTSI 70 Query: 69 LIARSIGENNQNKQLNYMAGVLQVTLLLSVGLGLLSVAGHHQVLEWLGAEASVTLVGGQY 128- L+A+ +G + + L+ + LGLL +A +L+ + + S+ Y Sbjct: 71 LVAQHLGAKERENAGKVAVVSIGANLIFGIVLGLLLIAFGPPILKAMQLDDSLLQEATLY 130- Query: 129 LSIVGGMIVSLGLLTSLGAIVRAQGYPKIPMQVSLLINVLNAIFSALSIY----VWGFGL 18- 4 L IVGG V L+ + GAI+R+ + K M V++ +N+LN I + L I+ + G+ Sbjct: 131 LQIVGGFSVVQSLIMTAGAILRSHSFTKDVMYVTIGMNILNVIGNYLFIFGPFGIPVLGV 19- 0 Query: 185 LGVAWATVLSRLVGVFLLCQF--------IPIKQVAKRLMRPLDKIIFDLSLPAAGERLM 23- 6 GVA +TV+SR +G+F++ +P + KR R + + + +P+AGE+L Sbjct: 191 TGVALSTVVSRTIGLFVIAILLYKRIRGELPFAYLLKRFPRVELRNLLKIGIPSAGEQLS 25- 0 Query: 237 MRAGDVLIIGIVVRFGTTALAGNAIGETLTQFNYMPGLAMATATIILVARQLGGGKVTEI 29- 6 A ++I + GT AL + L F ++ +A+ T IL+ Q+G ++ Sbjct: 251 YNASQLVITYFIAMMGTEALTTKVYTQNLMMFVFLFAVAIGQGTQILIGHQVGAKQIQAA 31- 0 Query: 297 RYIIREAFILSTLMMLVMGALTYLLGPSLLPLFTQNTDAQRSAMIVLLFSLLGAPATAGT 35- 6 + ++ + + M + + LL +FT N D +LL +++ P A Sbjct: 311 YVRCFRSLWIAMTVSVSMAVVFFAFSTPLLGIFTDNPDILSLGTTLLLLTIILEPGRACN 37- 0 Query: 357 LVYTAVWQGLGKAKLPFYATTIGMWVIRIGLGYVIGVVWQYGLIGVWMATVLDNTSRWFI 41- 6 LV + + G K P Y + MW I + + Y++G+ GLIGVW+A + D R + Sbjct: 371 LVVISSLRAAGDVKFPVYLAIVSMWGIAVPIAYLLGLPLGLGLIGVWIAFIADEWFRGLL 43- 0 Query: 417 LSKHFK--KYQEITF 429 + ++ K+QE++F Sbjct: 431 MIWRWRKGKWQEMSF 445 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06352 Identities = 219/418 (52%), Positives = 316/418 (75%) Query: 5 KEIIQLAIPAMIENILQMLMGVVDNYLVAQLGVVAVSGVSVANNIITIYQAIFIALGASI 64 ++I LA+P+MIENILQMLMG+VDNYLVAQ+G+VAVSGVS+ANNII+IYQ++FIALGA++ Sbjct: 7 RKIFSLALPSMIENILQMLMGMVDNYLVAQIGLVAVSGVSIANNIISIYQSLFIALGAAV 66 Query: 65 ASLLAKSLAGSKKDDAISVCSQAIFLTLLIGAVLGIISIVFGQTFFKLLGTTKSVAQVGG 124- +SL+A+S+ + ++ ++ + + +TLL+ LG++S+ + LG SV VGG Sbjct: 67 SSLIARSIGENNQNKQLNYMAGVLQVTLLLSVGLGLLSVAGHHQVLEWLGAEASVTLVGG 126- Query: 125 LYLAIVGGGVVTLGMLTTLGSFLRVQGQPRLPMYVSIFVNFLNAVLSGFAIFEWRYGLVG 18- 4 YL+IVGG +V+LG+LT+LG+ +R QG P++PM VS+ +N LNA+ S +I+ W +GL+G Sbjct: 127 QYLSIVGGMIVSLGLLTSLGAIVRAQGYPKIPMQVSLLINVLNAIFSALSIYVWGFGLLG 18- 6 Query: 185 VAVSTLIARLIGICILAKYLPIKKIIKRMTWKISAQIWNLALPSAGERLMMRAGDVVIVA 24- 4 VA +T+++RL+G+ +L +++PIK++ KR+ + I++L+LP+AGERLMMRAGDV+I+ Sbjct: 187 VAWATVLSRLVGVFLLCQFIPIKQVAKRLMRPLDKIIFDLSLPAAGERLMMRAGDVLIIG 24- 6 Query: 245 IVVQLGTNVVAGNAIGETLTQFNYMPGLGIATATIILTAKYVGQKNRESIEETIQSSYYI 30- 4 IVV+ GT +AGNAIGETLTQFNYMPGL +ATATIIL A+ +G I I+ ++ + Sbjct: 247 IVVRFGTTALAGNAIGETLTQFNYMPGLAMATATIILVARQLGGGKVTEIRYIIREAFIL 30- 6 Query: 305 GLVLMILISSFMLLAGKPLTQLFTNNPSAIKGSLIVILLSFVGVPATIGTLVYTAAWQGL 36- 4 ++M+++ + L G L LFT N A + ++IV+L S +G PAT GTLVYTA WQGL Sbjct: 307 STLMMLVMGALTYLLGPSLLPLFTQNTDAQRSAMIVLLFSLLGAPATAGTLVYTAVWQGL 36- 6 Query: 365 GNAKLPFYTTTIGMWLIRVVLGYLLGIVFELGLLGVWMATIADNIFRWLFLKVHYHRY 422 G AKLPFY TTIGMW+IR+ LGY++G+V++ GL+GVWMAT+ DN RW L H+ +Y Sbjct: 367 GKAKLPFYATTIGMWVIRIGLGYVIGVVWQYGLIGVWMATVLDNTSRWFILSKHFKKY 424 Identities = 48/211 (22%), Positives = 89/211 (41%), Gaps = 29/211 (13%) Query: 213 MTWKISAQIWNLALPSAGERLMMRAGDVVIVAIVVQLGTNVVAGNAIGETLTQFNYMPGL 27- 2 M + +I++LALPS E ++ +V +V Q+G V+G +I + + Sbjct: 1 MIYNNRRKIFSLALPSMIENILQMLMGMVDNYLVAQIGLVAVSGVSIANNIISIYQSLFI 60 Query: 273 GIATATIILTAKYVGQKNRESIEETIQSSYYIGLVLMILISSFML--------------L 31- 8 + A L A+ +G+ N+ Q +Y G++ + L+ S L L Sbjct: 61 ALGAAVSSLIARSIGENNQNK-----QLNYMAGVLQVTLLLSVGLGLLSVAGHHQVLEWL 115- Query: 319 AGKPLTQLFTNNPSAIKGSLIVILLSFVGVPATIGTLVYTAAWQGLGNAKLPFYTTTIGM 37- 8 + L +I G +IV L G+ ++G +V + G K+P + + + Sbjct: 116 GAEASVTLVGGQYLSIVGGMIVSL----GLLTSLGAIV-----RAQGYPKIPMQVSLL-I 16- 5 Query: 379 WLIRVVLGYLLGIVFELGLLGVWMATIADNI 409 ++ + L V+ GLLGV AT+ + Sbjct: 166 NVLNAIFSALSIYVWGFGLLGVAWATVLSRL 196 A related GBS gene <SEQ ID 8971> and protein <SEQ ID 8972> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06353 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: -0.68 GvH: Signal Score (-7.5): -1.3 Possible site: 46 >>> Seems to have no N-terminal signal sequence ALOM program count: 10 value: -11.41 threshold: 0.0 INTEGRAL Likelihood = -11.41 Transmembrane 88-104 (79-110) INTEGRAL Likelihood = -8.39 Transmembrane 304-320 (300-324) INTEGRAL Likelihood = -6.58 Transmembrane 185-201 (180-206) INTEGRAL Likelihood = -5.63 Transmembrane 338-354 (331-357) INTEGRAL Likelihood = -5.52 Transmembrane 240-256 (237-259) INTEGRAL Likelihood = -4.99 Transmembrane 383-399 (375-407) INTEGRAL Likelihood = -3.82 Transmembrane 49-65 (48-73) INTEGRAL Likelihood = -2.87 Transmembrane 127-143 (121-144) INTEGRAL Likelihood = -2.81 Transmembrane 159-175 (159-177) INTEGRAL Likelihood = -2.18 Transmembrane 30-46 (30-47) PERIPHERAL Likelihood = 0.32 11 modified ALOM score: 2.78 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5564(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00151## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2073 A DNA sequence (GBSx2188) was identified in S. agalactiae <SEQ ID 6417> which encodes the amino acid sequence <SEQ ID 6418>. Analysis of this protein sequence reveals the following: TABLE-US-06354 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2200(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06355 >GP: AAD05671 GB: AE001448 THREONINE SYNTHASE [Helicobacter pylori J99] Identities = 161/479 (33%), Positives = 259/479 (53%), Gaps = 17/479 (3%) Query: 14 KVTASQAILKGLADDGGLFTPITFPKVDLDFTKLKDASYQEVAKLVLSAFFDDFTEQELD 73 - K+ +A+L A GGL+T F L++ SY E+ + V + + L Sbjct: 13 KIDFIEAVLNPNAPKGGLYTLEHFET--LEWQDCLGMSYSELVEHVFELLNLEIPKNLLA 70 Query: 74 YCISQAYDTKFDTTEIAPIVKIGDRYHL-ELFHGPTIAFKDMALSILPYLLTTAAKKQGV 132- + + Y+ + API + +R + EL+HGP++AFKDMAL L L + A G Sbjct: 71 SALKR-YENFDNPKNPAPIFALNERLFVQELYHGPSLAFKDMALQPLASLFSNLAV--GK 127- Query: 133 DNKIVILTATSGDTGKAAMAGFADVPGTEIIVFYPKNGVSYIQELQMITQAGQNTHVVAI 19- 2 + K ++L +TSGDTG A + G A +P ++ YPK+G S +Q+LQM+TQ N V + Sbjct: 128 NEKYLVLVSTSGDTGPATLEGLAGMPNVFVVCLYPKDGTSLVQKLQMVTQNASNLKVFGV 18- 7 Query: 193 EGNFDDAQTSVKEMFNNSLLRLKLSQQHMQLSSANSMNIGRLVPQIVYYIYAYAQLVKSK 25- 2 G+FDDAQ ++K + + L + ++LS ANS+N GR+ QIVY+I+ + +L K Sbjct: 188 SGDFDDAQNALKNLLKDDDFNEALKARQLKLSVANSVNFGRIAFQIVYHIWGFLELYKKG 24- 7 Query: 253 EISIGQPINFSVPTGNFGNILAAYYASQIGLPVTKLICASNDNNVLTDFFKTQTYD-KNR 31- 1 I+ + I ++P+GNFGN L A+YA ++GL + K+ +N N+VL +F +T YD R Sbjct: 248 AINSKEKITLAIPSGNFGNALGAFYAKKMGLNIAKIKVVTNSNDVLREFIETGRYDLTKR 30- 7 Query: 312 EFKVTSSPSMDILVSSNLERLIFHLLGDDAETTKKLMEDLVTTGEYALEARQANIL-ESF 37- 0 K T SP+MDIL SSN+ER +F L G E T +LM+ L YAL+ ++ +L E F Sbjct: 308 SLKQTFSPAMDILKSSNVERALFSLFG--FERTLELMQALEEEKFYALKPKELALLQEHF 36- 5 Query: 371 VAGFATEQFVELDIKHLFDQYQYIEDPHTAVASAVYQAYQTETKDQTPAVIVSTASPYKF 43- 0 +++ I+ ++ ++QY+ DPHTA A K ++ +TAS KF Sbjct: 366 SCASCSDEDCLKTIQEVYAEHQYLIDPHTAT------ALNASLKTHEKTLVSATASYEKF 41- 9 Query: 431 PCVVTKAIT-NKEEIQDFAAISILNDLSGVSLPKAVTDLQKAEVIHRTVVPTSNMRETV 488- P A+ K+ D AA+ L + + + DL + + H+ V+ + ++ ++ Sbjct: 420 PKTTLLALNEQKKNDDDKAALETLKNSYNTPDSQRLDDLFERGIKHQEVLKLNEIKSSI 478- No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2074 A DNA sequence (GBSx2189) was identified in S. agalactiae <SEQ ID 6419> which encodes the amino acid sequence <SEQ ID 6420>. Analysis of this protein sequence reveals the following: TABLE-US-06356 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3153(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9279> which encodes amino acid sequence <SEQ ID 9280> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06357 >GP: AAF40975 GB: AE002410 alcohol dehydrogenase, propanol-preferring [Neisseria meningitidis MC58] Identities = 202/282 (71%), Positives = 228/282 (80%), Gaps = 1/282 (0%) Query: 1 MGHEGIGIVEEIGEGVTSLRVGDRVSIAWFFEGCGHCEYCTTGRETLCRSVKNAGYSVDG 60 +GHEGIG+V+E+ +GV +L+VGDRVSIAW F+ CG CEYC TGRETLCRSV NAGY+ DG Sbjct: 60 LGHEGIGLVKEVADGVKNLKVGDRVSIAWLFQSCGSCEYCNTGRETLCRSVLNAGYTADG 119- Query: 61 GMSEYAIVTADYAVKVPEGLDPAQASSITCAGVTTYKAIKEAGAAPGQWIAVYGAGGLGN 120- GM+ + IV+ADYAVKVPEGLDPAQASSITCAGVTTYKAIK +G PGQWIA+YGAGGLGN Sbjct: 120 GMATHCIVSADYAVKVPEGLDPAQASSITCAGVTTYKAIKVSGVRPGQWIAIYGAGGLGN 17- 9 Query: 121 LAVQYAKKVFNAHVVAVDINADKLQLAKEVGADLTVNGKEIKDVAAYIQEKTGGCHGVVV 18- 0 L VQYAKKVF AHVVA+DIN DKL AKE GADL VN + +D A IQEKTGG H VV Sbjct: 180 LGVQYAKKVFGAHVVAIDINDDKLAFAKETGADLVVNAAK-EDAAKVIQEKTGGAHAAVV 23- 8 Query: 181 TAVSKVAFNQAIDSVRAGGTVVAVGLPSEYMELSIVKTVLDGIRVVGSLVGTRKDLEEAF 24- 0 TAVS AFN A++ VRAGG VVA+GLP E M+LSI + VLDGI VVGSLVGTRKDLEEAF Sbjct: 239 TAVSAAAFNSAVNCVRAGGRVVAIGLPPESMDLSIPRLVLDGIEVVGSLVGTRKDLEEAF 29- 8 Query: 241 AFGAEGLVVPVVEKVPVDTAPQVFDEMERGLIQGRKVLDFTK 282 FGAEGLVVP V+ +D AP +F EM G I GR V+D K Sbjct: 299 QFGAEGLVVPKVQLRALDEAPAIFQEMREGKITGRMVIDMKK 340 A related DNA sequence was identified in S. pyogenes <SEQ ID 6421> which encodes the amino acid sequence <SEQ ID 6422>. Analysis of this protein sequence reveals the following: TABLE-US-06358 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2356(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06359 Identities = 263/280 (93%), Positives = 273/280 (96%) Query: 1 MGHEGIGIVEEIGEGVTSLRVGDRVSIAWFFEGCGHCEYCTTGRETLCRSVKNAGYSVDG 60 +GHEGIGIVEEIGEGVTSL+VGDRVSIAWFFEGCGHCEYCTTGRETLCRSVKNAGYSVDG Sbjct: 76 LGHEGIGIVEEIGEGVTSLKVGDRVSIAWFFEGCGHCEYCTTGRETLCRSVKNAGYSVDG 135- Query: 61 GMSEYAIVTADYAVKVPEGLDPAQASSITCAGVTTYKAIKEAGAAPGQWIAVYGAGGLGN 120- GMSEYA+VTADYAVKVPEGLDPAQASSITCAGVTTYKAIKEAGAAPGQWI ++GAGGLGN Sbjct: 136 GMSEYAVVTADYAVKVPEGLDPAQASSITCAGVTTYKAIKEAGAAPGQWIVIFGAGGLGN 19- 5 Query: 121 LAVQYAKKVFNAHVVAVDINADKLQLAKEVGADLTVNGKEIKDVAAYIQEKTGGCHGVVV 18- 0 LAVQYAKKVFNAHVVAVDIN DKL+LAKEVGAD+ VNGKEI+DV YIQEKTGG HGVVV Sbjct: 196 LAVQYAKKVFNAHVVAVDINNDKLELAKEVGADILVNGKEIEDVPGYIQEKTGGAHGVVV 25- 5 Query: 181 TAVSKVAFNQAIDSVRAGGTVVAVGLPSEYMELSIVKTVLDGIRVVGSLVGTRKDLEEAF 24- 0 TAVSKVAFNQAIDSVRAGGTVVAVGLPSEYMELSIVKTVLDGI+VVGSLVGTRKDLEEAF Sbjct: 256 TAVSKVAFNQAIDSVRAGGTVVAVGLPSEYMELSIVKTVLDGIKVVGSLVGTRKDLEEAF 31- 5 Query: 241 AFGAEGLVVPVVEKVPVDTAPQVFDEMERGLIQGRKVLDF 280 AFGAEGLV PVVEKVPVDTAP+VFDEMERGLIQGRKVLDF Sbjct: 316 AFGAEGLVAPVVEKVPVDTAPEVFDEMERGLIQGRKVLDF 355 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2075 A DNA sequence (GBSx2190) was identified in S. agalactiae <SEQ ID 6423> which encodes the amino acid sequence <SEQ ID 6424>. Analysis of this protein sequence reveals the following: TABLE-US-06360 Possible site: 42 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.82 Transmembrane 83-99 (76-108) INTEGRAL Likelihood = -7.27 Transmembrane 46-62 (43-65) INTEGRAL Likelihood = -7.22 Transmembrane 187-203 (182-209) INTEGRAL Likelihood = -6.00 Transmembrane 243-259 (229-262) INTEGRAL Likelihood = -4.25 Transmembrane 404-420 (402-422) INTEGRAL Likelihood = -3.98 Transmembrane 120-136 (119-136) INTEGRAL Likelihood = -3.88 Transmembrane 308-324 (307-324) INTEGRAL Likelihood = -2.13 Transmembrane 378-394 (376-394) INTEGRAL Likelihood = -1.38 Transmembrane 152-168 (152-168) INTEGRAL Likelihood = -1.17 Transmembrane 271-287 (271-287) ----- Final Results ----- bacterial membrane --- Certainty = 0.4927(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9371> which encodes amino acid sequence <SEQ ID 9372> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06361 >GP: AAC17857 GB: AF026147 YojI [Bacillus subtilis] Identities = 183/432 (42%), Positives = 266/432 (61%), Gaps = 1/432 (0%) Query: 1 MKLFIPVLIYQFANFSATFIDSVMTGQYSQLHLAGVSTASNLWTPFFALLVGMISALVPV 60 + + IP+ I Q TF+D+VM+G+ S LAGV+ S+LWTP + L G++ A+ P+ Sbjct: 15 LHILIPIFITQAGLSLITFLDTVMSGKVSPADLAGVAIGSSLWTPVYTGLAGILMAVTPI 74 Query: 61 VGQHLGRGNKEQIRTEFHQFLYLGLILSLILFLIMQFIAQPVLGSLGLEDEVLAVGRGYL 120- V Q LG K++I Q +Y+ +LS+ + +I +LG L L+ V + + +L Sbjct: 75 VAQLLGAEKKQKIPFTVLQAVYVAALLSIAVLVIGYAAVDLILGRLNLDIHVHQIAKHFL 134- Query: 121 NYMLIGIMPLVLFSICRSFFDALGLTRLSMYLMLLILPFNSFFNYNLIYGKFGMPRLGGA 18- 0 ++ +GI PL ++++ RSF D+LG TR++M + L LP N NY+ I+GKFGMP LGG Sbjct: 135 GFLSLGIFPLFVYTVLRSFIDSLGKTRVTMMITLSSLPINFVLNYVFIFGKFGMPALGGV 19- 4 Query: 181 GAGLGTSLTYWAIFIVIIIVMSLHPQIKTYHIW-TLERIKAPLIIEDIRLGLPIGLQIFA 23- 9 GAGL ++LTYW I I+ ++ + Y I+ T+ + +++GLPIG +F Sbjct: 195 GAGLASALTYWCICIISFFIIHKNAPFSEYGIFLTMYKFSWKACKNLLKIGLPIGFAVFF 25- 4 Query: 240 EVAIFAVVGLFMAKFSSIIIAAHQAAMNFSSLMYAFPLSISTALAITISFEVGAERFQDA 29- 9 E +IFA V L M+ F ++ IA+HQAAMNF+SL+Y PLS+S AL I + FE GA RF+DA Sbjct: 255 ETSIFAAVTLLMSHFHTVTIASHQAAMNFASLLYMLPLSVSMALTIVVGFEAGAARFKDA 31- 4 Query: 300 NTYSRIGRLTAVGITSGTLLFLFLFRENVAAMYNSDPHFVAITAQFLTYSLFFQFADAYA 35- 9 +YS IG + A+G + T + LFRE +A MY SDP + +T FL Y+LFFQ +DA A Sbjct: 315 RSYSLIGIMMAIGFSLFTAACILLFREQIAGMYTSDPDVLRLTQHFLIYALFFQLSDAVA 37- 4 Query: 360 APVQGILRGYKDTTKPFMIGAGSYWLCALPLAVILEKNSQLGPFAYWIGLITGIFVCGLF 41- 9 AP+QG LRGYKD SYW+ LP+ ++ + LG F YWIGLI G+ + Sbjct: 375 APIQGALRGYKDVNYTLAAAFVSYWVIGLPVGYMVGTFTSLGAFGYWIGLIAGLAAGAVG 43- 4 Query: 420 LNQRLQKIKKLY 431 L RL K++K Y Sbjct: 435 LFFRLAKLQKRY 446 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2076 A DNA sequence (GBSx2191) was identified in S. agalactiae <SEQ ID 6425> which encodes the amino acid sequence <SEQ ID 6426>. Analysis of this protein sequence reveals the following: TABLE-US-06362 Possible site: 20 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.60 Transmembrane 23-39 (23-39) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2077 A DNA sequence (GBSx2192) was identified in S. agalactiae <SEQ ID 6427> which encodes the amino acid sequence <SEQ ID 6428>. Analysis of this protein sequence reveals the following:

TABLE-US-06363 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3829(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06364 >GP: AAC06891 GB: AE000703 hypothetical protein [Aquifex aeolicus] Identities = 72/213 (33%), Positives = 115/213 (53%), Gaps = 11/213 (5%) Query: 36 RPKILMHVCCAPCSTYTLEYLSQ---WADVTIYFANSNIHPKDEYYRREYVTQKFVHDFN 92 - + KIL+H+CCAP + Y L+ L + +++ YF + NIHP +EY R T++ + Sbjct: 3 KSKILVHICCAPDAIYFLKKLREDYPESEIIGYFYDPNIHPYEEYRLRYLETERICKELG 62 Query: 93 KNTGYSVQFLSAPYEPNEFFKIVHGLEEEPEGGDRCKVCYDFRLDKTAEKAVELGFDYFG 152- N + Y+ + + V G E+EPE G RC++C+D+RL+K+AE A ELG D Sbjct: 63 IN------LIEGEYDLENWLERVKGYEDEPERGKRCQICFDYRLEKSAEVAKELGCDALT 116- Query: 153 SALTISPHKNSQTINTIGIDVQKIYDTQYLPSDLKKNKGYQRSVEMCKDYDIYRQCYCGC 21- 2 + L +SP K+ + G + K ++L D +K G Q ++ K+ +IY+Q YCGC Sbjct: 117 TTLLMSPKKSIPQLKKAGEEATKRTGIEFLAPDYRKGGGTQEMFKLSKEREIYQQDYCGC 17- 6 Query: 213 IFGAKDQGINLLQIKKDAKAFVSDKDGKEEFPN 245 I+G Q +I D F+ + G +E N Sbjct: 177 IYGLFKQKNG--KIFWDLVGFLGRRPGSKEERN 207 A related DNA sequence was identified in S. pyogenes <SEQ ID 6429> which encodes the amino acid sequence <SEQ ID 6430>. Analysis of this protein sequence reveals the following: TABLE-US-06365 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3498(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> RGD motif: 254-256 The protein has homology with the following sequences in the databases: TABLE-US-06366 >GP: AAC06891 GB: AE000703 hypothetical protein [Aquifex aeolicus] Identities = 65/182 (35%), Positives = 106/182 (57%), Gaps = 9/182 (4%) Query: 39 RPSILMHVCCAPCSTYTLEYLTQF---ADITVYFANSNIHPKDEYHRRAYVTQQFVSEFN 95 - + IL+H+CCAP + Y L+ L + ++I YF + NIHP +EY R T++ E Sbjct: 3 KSKILVHICCAPDAIYFLKKLREDYPESEIIGYFYDPNIHPYEEYRLRYLETERICKELG 62 Query: 96 AKTGNTVQFLEADYVPNEYVRQVRGLEEEPEGGDRCRVCFDYRLDKTAQKAVELGFDYFA 155- + +E +Y ++ +V+G E+EPE G RC++CFDYRL+K+A+ A ELG D Sbjct: 63 ------INLIEGEYDLENWLERVKGYEDEPERGKRCQICFDYRLEKSAEVAKELGCDALT 116- Query: 156 SALTISPHKNSQTINDVGIDVQKVYTTKYLPSDFKKNNGYRRSVEMCEEYDIYRQCYCGC 21- 5 + L +SP K+ + G + K ++L D++K G + ++ +E +IY+Q YCGC Sbjct: 117 TTLLMSPKKSIPQLKKAGEEATKRTGIEFLAPDYRKGGGTQEMFKLSKEREIYQQDYCGC 17- 6 Query: 216 VY 217 +Y Sbjct: 177 IY 178 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06367 Identities = 184/255 (72%), Positives = 219/255 (85%) Query: 1 MIDVENILEKMKPNQKINYDWVMQQMVKQWQASDIRPKILMHVCCAPCSTYTLEYLSQWA 60 MID++ IL M PNQKINYD VMQQM K W+ +RP ILMHVCCAPCSTYTLEYL+Q+A Sbjct: 4 MIDLQEILANMNPNQKINYDRVMQQMAKVWEKESVRPSILMHVCCAPCSTYTLEYLTQFA 63 Query: 61 DVTIYFANSNIHPKDEYYRREYVTQKFVHDFNKNTGYSVQFLSAPYEPNEFFKIVHGLEE 120- D+T+YFANSNIHPKDEY+RR YVTQ+FV +FN TG +VQFL A Y PNE+ + V GLEE Sbjct: 64 DITVYFANSNIHPKDEYHRRAYVTQQFVSEFNAKTGNTVQFLEADYVPNEYVRQVRGLEE 123- Query: 121 EPEGGDRCKVCYDFRLDKTAEKAVELGFDYFGSALTISPHKNSQTINTIGIDVQKIYDTQ 18- 0 EPEGGDRC+VC+D+RLDKTA+KAVELGFDYF SALTISPHKNSQTIN +GIDVQK+Y T+ Sbjct: 124 EPEGGDRCRVCFDYRLDKTAQKAVELGFDYFASALTISPHKNSQTINDVGIDVQKVYTTK 18- 3 Query: 181 YLPSDLKKNKGYQRSVEMCKDYDIYRQCYCGCIFGAKDQGINLLQIKKDAKAFVSDKDGK 24- 0 YLPSD KKN GY+RSVEMC++YDIYRQCYCGC++ AK QGI+L+Q+KKDAKAF++DKD Sbjct: 184 YLPSDFKKNNGYRRSVEMCEEYDIYRQCYCGCVYAAKMQGIDLVQVKKDAKAFMADKDLD 24- 3 Query: 241 EEFPNIRFTFNGKSM 255 +F +IRF++ G M Sbjct: 244 NDFTHIRFSYRGDEM 258 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2078 A DNA sequence (GBSx2193) was identified in S. agalactiae <SEQ ID 6431> which encodes the amino acid sequence <SEQ ID 6432>. Analysis of this protein sequence reveals the following: TABLE-US-06368 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4216(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06369 >GP: CAB14809 GB: Z99118 excinuclease ABC (subunit C) [Bacillus subtilis] Identities = 189/333 (56%), Positives = 244/333 (72%) Query: 1 MNELIKHKLELLPDSPGCYLHKDKNGTIIYVGKAKNLKNRVKSYFHGSHNTKTELLVSEI 60 MN+ +K KL LLPD PGCYL KD+ T+IYVGKAK LKNRV+SYF GSH+ KT+ LV+EI Sbjct: 1 MNKQLKEKLALLPDQPGCYLMKDRQQTVIYVGKAKVLKNRVRSYFTGSHDAKTQRLVTEI 60 Query: 61 EDFEYIVTTSNTEALLLEINLIQENMPKYNIRLKDDKSYPYIKITNERYPRLMITRQVKK 120- EDFEYIVT+SN EAL+LE+NLI+++ PKYN+ LKDDK+YP+IK+T+ER+PRL++TR VKK Sbjct: 61 EDFEYIVTSSNLEALILEMNLIKKHDPKYNVMLKDDKTYPFIKLTHERHPRLIVTRNVKK 120- Query: 121 SDGTYFGPYPDSGAATEIKRLLDRLFPFKKCTNPANKVCFYYHLGQCNAHTVCQTNKAYW 18- 0 G YFGPYP+ AA E K+LLDRL+P +KC+ ++VC YYHLGQC A V ++ Sbjct: 121 DKGRYFGPYPNVQAARETKKLLDRLYPLRKCSKLPDRVCLYYHLGQCLAPCVKDISEETN 18- 0 Query: 181 DSLREDVKQFLNGKDNKIVNGLTEKMKSAAMTMEFERAAEYRDLIEAISLLRTKQRVIHQ 24- 0 L E + +FL G N++ L EKM AA +EFERA E RD I I KQ++ Sbjct: 181 RELVESITRFLRGGYNEVKKELEEKMHEAAENLEFERAKELRDQIAHIESTMEKQKMTMN 24- 0 Query: 241 DMKDRDVFGYFVDKGWMCVQVFFVRNGKLIQRDVNMFPYYNEPEEDFLTYIGQFYQDTKH 30- 0 D+ DRDVF Y DKGWMCVQVFF+R GKLI+RDV+MFP Y E +E+FLT+IGQFY H Sbjct: 241 DLVDRDVFAYAYDKGWMCVQVFFIRQGKLIERDVSMFPLYQEADEEFLTFIGQFYSKNNH 30- 0 Query: 301 FLPKEVFIPQDIDAKSVETIVGCKIVKPQRGKR 333 FLPKE+ +P ID +E ++ + +P++G + Sbjct: 301 FLPKEILVPDSIDQSMIEQLLETNVHQPKKGPK 333 There is also homology to SEQ ID 2568. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2079 A DNA sequence (GBSx2194) was identified in S. agalactiae <SEQ ID 6433> which encodes the amino acid sequence <SEQ ID 6434>. This protein is predicted to be maltose operon transcriptional repressor (rbsR). Analysis of this protein sequence reveals the following: TABLE-US-06370 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3761(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9393> which encodes amino acid sequence <SEQ ID 9394> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06371 >GP: AAD02112 GB: AF039082 putative maltose operon transcriptional repressor [Lactococcus lactis] Identities = 64/166 (38%), Positives = 105/166 (62%), Gaps = 13/166 (7%) Query: 1 MGKSAIDYLYKKGHKSIQFVTDDLNSEVSEERYLGYFKGARKLGLNQKPALLFDRGNPQV 60 +G+ A+ L + H++I FVTD +EV EERY G+ A +LGL+ LLF N + Sbjct: 169 LGREAVRLLAQLNHQNISFVTDTKETEVFEERYQGFKDEAERLGLSHD--LLFMDSNFSL 22- 6 Query: 61 LEEFINRVKEEETTALIVIGDTVSVRVMQFLSFYKLKVPDDISIMTFNNSLFSHLIHPYL 120- E TAL+V+ D +S++V++ L L VP+D+S++T+NNS+F +IHPYL Sbjct: 227 RNE----------TALVVMDDVLSLKVVERLRSQGLNVPEDVSLITYNNSIFGAMIHPYL 27- 6 Query: 121 STFDINVNNLGRTSVRRLIDIIKSPDKVFSETIIVPFTLEERESVR 166 +TFDI++ LG +++++++D+ + + + +TII PF L RES + Sbjct: 277 TTFDIHIEQLGASAIKKILDLRDNKENLPEKTII-PFELIVRESTK 321 There is also homology to SEQ ID 5082. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2080 A DNA sequence (GBSx2195) was identified in S. agalactiae <SEQ ID 6435> which encodes the amino acid sequence <SEQ ID 6436>. This protein is predicted to be 4-alpha-glucanotransferase (malQ). Analysis of this protein sequence reveals the following: TABLE-US-06372 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2003(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06373 >GP: AAA26923 GB: J01796 amylomaltase [Streptococcus pneumoniae] Identities = 250/500 (50%), Positives = 329/500 (65%), Gaps = 4/500 (0%) Query: 1 MKKRASGVLMHITSLPGDLGIGTFGREAYAFVDFLVETDQKFWQILPLTTTSFGDSPYQS 60 MKKR SGVLMHI+SLPG GIG+FG+ AY FVDFLV T Q++WQILPL TS+GDSPYQS Sbjct: 1 MKKRQSGVLMHISSLPGAYGIGSFGQSAYDFVDFLVRTKQRYWQILPLGATSYGDSPYQS 60 Query: 61 FSAVAGNTHLIDFDLLTLEGFISKDDYQNISFGQDPEVVDYAGLFEKRRPVLEKAVKNFL 120- FSA AGNTH ID D+L +G + D + + FG D VDYA ++ RRP+LEKAVK F Sbjct: 61 FSAFAGNTHFIDLDILVEQGLLEASDLEGVDFGSDASEVDYAKIYYARRPLLEKAVKRFF 120- Query: 121 QEERATRMLSDFLQE-EKWVTDFAEFMAIKEHFGNKALQEWDDKAIIRREEEALAGYRQK 17- 9 E + F Q+ + W+ FAE+MAIKE+F N A EW D R+ AL YR++ Sbjct: 121 -EVGDVKDFEKFAQDNQSWLELFAEYMAIKEYFDNLAWTEWPDADARARKASALESYREQ 17- 9 Query: 180 LSEVIKYHEVTQYFFYKQWFELKEYANDKGIQIIGDMPIYVSADSVEVWTMPELFKLDRD 23- 9 L++ + YH VTQYFF++QW +LK YAND I+I+GDMPIYV+ DS ++W P LFK D + Sbjct: 180 LADKLVYHRVTQYFFFQQWLKLKAYANDNHIEIVGDMPIYVAEDSSDMWANPHLFKTDVN 23- 9 Query: 240 KQPLAIAGVPADDFSDDGQLWGNPIYNWDYHKESDFDWWIYRIQSGVKMYDYLRIDHFKG 29- 9 + IAG P D+FS GQLWGNPIY+W+ + + WWI R++ K+YD +RIDHF+G Sbjct: 240 GKATCIAGCPPDEFSVTGQLWGNPIYDWEAMDKDGYKWWIERLRESFKIYDIVRIDHFRG 29- 9 Query: 300 FSDYWEIRGDYQTANDGSWQPAPGPELFATIKEKLGDLPIIAENLGYIDERAERLLAGTG 35- 9 F YWEI TA G W PG +LFA +KE+LG+L IIAE+LG++ + L TG Sbjct: 300 FESYWEIPAGSDTAAPGEWVKGPGYKLFAAVKEELGELNIIAEDLGFMTDEVIELRERTG 35- 9 Query: 360 FPGMKIMEFGFYDTTGNSIDIPHNYTENTIAYAGTHDNEVINGWFEN-LTVEQKAYAENY 41- 8 FPGMKI++F F + SID PH N++ Y GTHDN + GW+ N + + Y Y Sbjct: 360 FPGMKILQFAF-NPEDESIDSPHLAPANSVMYTGTHDNNTVLGWYRNEIDDATREYMARY 41- 8 Query: 419 MRRLPNEPITETVLRTLYATVSQTTITCMQDLLDKPADSRMNMPNTVGGNWQWRMRKEDL 47- 8 R E + +LRT++++VS I MQDLL+ +RMN P+T+GGNW WRM ++ L Sbjct: 419 TNRKEYETVVHAMLRTVFSSVSFMAIATMQDLLELDEAARMNFPSTLGGNWSWRMTEDQL 47- 8 Query: 479 TENRKAFLKEITTIYNRGNK 498 T + L ++TTIY R N+ Sbjct: 479 TPAVEEGLLDLTTIYRRINE 498 A related DNA sequence was identified in S. pyogenes <SEQ ID 6437> which encodes the amino acid sequence <SEQ ID 6438>. Analysis of this protein sequence reveals the following: TABLE-US-06374 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.85 Transmembrane 435-451 (435-451) ----- Final Results ----- bacterial membrane --- Certainty = 0.1341(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06375 Identities = 313/495 (63%), Positives = 387/495 (77%) Query: 1 MKKRASGVLMHITSLPGDLGIGTFGREAYAFVDFLVETDQKFWQILPLTTTSFGDSPYQS 60 M KRASG+LMHI+SLPG GIGTFG+ A+ FVDFL ET Q +WQILPLTTTSFGDSPYQS Sbjct: 1 MNKRASGILMHISSLPGKFGIGTFGKSAFEFVDFLAETKQTYWQILPLTTTSFGDSPYQS 60 Query: 61 FSAVAGNTHLIDFDLLTLEGFISKDDYQNISFGQDPEVVDYAGLFEKRRPVLEKAVKNFL 120- FSA+AGNTH IDF+LL + + D +I+FG +PE VDYA LF+ RRP+LEKAV+ F+ Sbjct: 61 FSAIAGNTHFIDFELLVDDELLEAADLCDITFGTNPEAVDYAQLFQVRRPLLEKAVRAFV 120- Query: 121 QEERATRMLSDFLQEEKWVTDFAEFMAIKEHFGNKALQEWDDKAIIRREEEALAGYRQKL 18- 0 E+ L F W+TDFAEFMA+KE+F NKALQ+WDD+ +I+R+E++L YR+ L Sbjct: 121 AEQENVCKLEAFETASSWLTDFAEFMALKEYFNNKALQDWDDETVIKRQEDSLNNYRELL 18- 0 Query: 181 SEVIKYHEVTQYFFYKQWFELKEYANDKGIQIIGDMPIYVSADSVEVWTMPELFKLDRDK 24- 0 ++ I YH+V QYFFY+QW LK YAN KGI+IIGDMPIYVSADSVEVWTMPELFK+D DK Sbjct: 181 AKKITYHKVCQYFFYQQWSALKTYANHKGIEIIGDMPIYVSADSVEVWTMPELFKVDSDK 24- 0 Query: 241 QPLAIAGVPADDFSDDGQLWGNPIYNWDYHKESDFDWWIYRIQSGVKMYDYLRIDHFKGF 30- 0 +PL IAGVPAD FS+DGQLWGNP YNW H++S+F WWIYRIQ K+YD LRIDHFKGF Sbjct: 241 KPLFIAGVPADGFSEDGQLWGNPTYNWSAHEKSNFAWWIYRIQESFKLYDQLRIDHFKGF 30- 0 Query: 301 SDYWEIRGDYQTANDGSWQPAPGPELFATIKEKLGDLPIIAENLGYIDERAERLLAGTGF 36- 0 SD+WEI +TA +G W APG LF+ ++E LG+LPIIAENLGYIDE+AE+LLA TGF Sbjct: 301 SDFWEIPAGDKTARNGHWASAPGIALFSAVREALGELPIIAENLGYIDEKAEQLLASTGF 36- 0 Query: 361 PGMKIMEFGFYDTTGNSIDIPHNYTENTIAYAGTHDNEVINGWFENLTVEQKAYAENYMR 42- 0 PGMKI+EFG +D T SID+PH Y N +AY GTHDNEV+NGW++NL+ EQ + NY+ Sbjct: 361 PGMKILEFGLFDITSQSIDLPHYYDRNCVAYTGTHDNEVVNGWYDNLSEEQVHFVNNYLH 42- 0 Query: 421 RLPNEPITETVLRTLYATVSQTTITCMQDLLDKPADSRMNMPNTVGGNWQWRMRKEDLTE 48- 0 + +E IT+ +LRT++A+V T I C+QDLLDK SRMNMPNT+GGNWQWRM +L + Sbjct: 421 KHADESITKAMLRTIFASVCDTAILCIQDLLDKDGKSRMNMPNTIGGNWQWRMLDGELNQ 48- 0 Query: 481 NRKAFLKEITTIYNR 495 + K +L +T +Y R Sbjct: 481 DHKDYLIYLTDLYGR 495 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2081 A DNA sequence (GBSx2196) was identified in S. agalactiae <SEQ ID 6439> which encodes the amino acid sequence <SEQ ID 6440>. This protein is predicted to be glycogen phosphorylase (malP). Analysis of this protein sequence reveals the following: TABLE-US-06376 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2678(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06377 >GP: AAC00218 GB: AF008220 glycogen phosphorylase [Bacillus subtilis] Identities = 297/776 (38%), Positives = 452/776 (57%), Gaps = 41/776 (5%) Query: 13 GKVLSELTNEEIYVELLNFVKEEAAA-------KSKNSSQRKVYYISAEFLIGKLLSNNL 65 - GK + + Y L N V+E +A KS+++S ++ YY+S EFL+G+LL NL Sbjct: 21 GKSFKDSAKLDQYKTLGNMVREYISADWIETNEKSRSNSGKQTYYLSIEFLLGQLLEQNL 80 Query: 66 INLGIYKDVKKELELVGKSIAEIEDVEPEPSLGNGGLGRLASCFIDSISSLGINGEGVGL 125- +NLG+ V+ L+ +G ++ EI +E + LGNGGLGRLA+CF+DS++SL + G G+G+ Sbjct: 81 MNLGVRDVVEAGLKEIGINLEEILQIENDAGLGNGGLGRLAACFLDSLASLNLPGHGMGI 140- Query: 126 NYHCGLFKQVFRNNQQEAEANYWIEN-NSWLVPT-DISYDVPF--------RDFTLKSRL 17- 5 Y GLF+Q + Q W++N N W V D + DVPF + L R Sbjct: 141 RYKHGLFEQKIVDGHQVELPEQWLKNGNVWEVRNADQAVDVPFWGEVHMTEKSGRLHFRH 20- 0 Query: 176 DR----------IDVLGYKKDTKNYLNLFDIDGLDYNLIEKGITFDKTEIKKNLTLFLYP 22- 5 ++ I ++GY+ T N L L++ + Y G + ++ FLYP Sbjct: 201 EQATIVTAVPYDIPIIGYETGTVNTLRLWNAE--PYAHYHGGNILSYKRETEAVSEFLYP 25- 8 Query: 226 DDSDKNGELLRIYQQYFMVSNAAQLLIDEAIERGSNLHDLAEYAYVQINDTHPSMVIPEL 28- 5 DD+ G++LR+ QQYF+V + + +++ + +L L + + INDTHP++ +PEL Sbjct: 259 DDTHDEGKILRLKQQYFLVCASLKSIVNNYRKTHKSLSGLHKKVSIHINDTHPALAVPEL 31- 8 Query: 286 IRLLTEKHGFEFDEAVSVVRNMVGYTNHTILAEALEKWPLEYLNEVVPHLVTIIKKLDQM 34- 5 +R+L ++ ++EA + + + YTNHT L+EALEKWP+ ++P + II+++++ Sbjct: 319 MRILLDEENMSWEEAWHITVHTISYTNHTTLSEALEKWPIHLFKPLLPRMYMIIEEINER 37- 8 Query: 346 IRE--------EQTNPEVQIIDEAGRVHMAHMDIHFSTSVNGVAALHTEILKNSELKVFY 39- 7 + E I G V MAH+ I S SVNGVA +H++ILK E++ F+ Sbjct: 379 FCRAVWEKYPGDWKRIENMAITAHGVVKMAHLAIVGSYSVNGVAKIHSDILKEREMRDFH 43- 8 Query: 398 DIYPDKFNNKTNGITFRRWLEFANQDLADYLKELIGDSYLTDATQLEKLLTYADSNEVHD 45- 7 ++P++FNNKTNGI RRWL AN L+ + E IGD ++ L +L YA + Sbjct: 439 LLFPNRFNNKTNGIAHRRWLLKANPGLSAIITEAIGDEWVKQPESLIRLEPYATDPAFIE 49- 8 Query: 458 KLAAIKFKNKLALKRYLKENKGIELDEYSIIDTQIKRFHEYKRQQMNALYVIHKYLEIKR 51- 7 + K K K L + G+ ++ SI D Q+KR H YKRQ +N L++++ Y +K Sbjct: 499 QFQNNKSKKKQELADLIFCTAGVVVNPESIFDVQVKRLHAYKRQLLNVLHIMYLYNRLKE 55- 8 Query: 518 GH-FPSRKLTVIFGGKAAPAYTIAQDIIHLILCLSELINNDPEVNKYLNVHLVENYNVTV 57- 6 F T IFG KA+P+Y A+ II LI ++E +N DP V + + V +ENY V++ Sbjct: 559 DSGFSIYPQTFIFGAKASPSYYYAKKIIKLIHSVAEKVNYDPAVKQLIKVVFLENYRVSM 61- 8 Query: 577 AEKLIPATDISEQISLASKEASGTGNMKFMLNGALTLGTMDGANVEIAELAGKENIYTFG 63- 6 AE++ PA+D+SEQIS ASKEASGTGNMKFM+NGALT+GT DGAN+EI E G + IYTFG Sbjct: 619 AERIFPASDVSEQISTASKEASGTGNMKFMMNGALTIGTHDGANIEILERVGPDCIYTFG 67- 8 Query: 637 KDSDTIINLYETSGYRSKDYYDKDKVIREAVDFIISDDIVSLGNAERLKRLHDELV-GKD 69- 5 +D +++ E GYRS++YY D+ IR+ D +I+ G A+ + + D L+ D Sbjct: 679 LKADEVLSYQENGGYRSREYYQHDRRIRQVADQLINGFFE--GEADEFESIFDSLLPHND 73- 6 Query: 696 WFMTLIDLKEYIAVKEQVLADYEDYESWNKKVIHNIAKAGFFSSDRTIEQYNQDIW 751 + L D Y +E++ ADY + W++ I NIA +G+FSSDRTI +Y +DIW Sbjct: 737 EYFVLKDFSSYADAQERIQADYRERRKWSEHSIVNIAHSGYFSSDRTIREYAKDIW 792 A related DNA sequence was identified in S. pyogenes <SEQ ID 6441> which encodes the amino acid sequence <SEQ ID 6442>. Analysis of this protein sequence reveals the following: TABLE-US-06378 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.71 Transmembrane 538-554 (538-554) ----- Final Results ----- bacterial membrane --- Certainty = 0.2084(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-06379 Identities = 629/754 (83%), Positives = 696/754 (91%), Gaps = 2/754 (0%) Query: 1 MTRNFTTYVGQQ-GKVLSELTNEEIYVELLNFVKEEAAAKSKNSSQRKVYYISAEFLIGK 59 MTR FT YV + GK L++ +NEEIY+ LLNFVKEEA+ K+KNS++RKVYYISAEFLIGK Sbjct: 1 MTR-FTEYVETKLGKSLTQASNEEIYLSLLNFVKEEASHKAKNSAKRKVYYISAEFLIGK 59 Query: 60 LLSNNLINLGIYKDVKKELELVGKSIAEIEDVEPEPSLGNGGLGRLASCFIDSISSLGIN 119- LLSNNLINLGIYKD+K+EL GKSIAE+EDVE EPSLGNGGLGRLASCFIDSI+SLGIN Sbjct: 60 LLSNNLINLGIYKDIKEELAAAGKSIAEVEDVELEPSLGNGGLGRLASCFIDSIASLGIN 119- Query: 120 GEGVGLNYHCGLFKQVFRNNQQEAEANYWIENNSWLVPTDISYDVPFRDFTLKSRLDRID 17- 9 GEGVGLNYHCGLFKQVF++N+QEAE N+WIE++SWLVPTDISYDVPF++FTLKSRLDRID Sbjct: 120 GEGVGLNYHCGLFKQVFKHNEQEAEPNFWIEDDSWLVPTDISYDVPFKNFTLKSRLDRID 17- 9 Query: 180 VLGYKKDTKNYLNLFDIDGLDYNLIEKGITFDKTEIKKNLTLFLYPDDSDKNGELLRIYQ 23- 9 VLGYK+DTKNYLNLFDI+G+DY LI+ GI+FDKT+I KNLTLFLYPDDSDKNGELLRIYQ Sbjct: 180 VLGYKRDTKNYLNLFDIEGVDYGLIKDGISFDKTQIAKNLTLFLYPDDSDKNGELLRIYQ 23- 9 Query: 240 QYFMVSNAAQLLIDEAIERGSNLHDLAEYAYVQINDTHPSMVIPELIRLLTEKHGFEFDE 29- 9 QYFMVSNAAQL+IDEAIERGSNLHDLA+YAYVQINDTHPSMVIPELIRLLTEKHGF+FDE Sbjct: 240 QYFMVSNAAQLIIDEAIERGSNLHDLADYAYVQINDTHPSMVIPELIRLLTEKHGFDFDE 29- 9 Query: 300 AVSVVRNMVGYTNHTILAEALEKWPLEYLNEVVPHLVTIIKKLDQMIREEQTNPEVQIID 35- 9 AV+VV+NMVGYTNHTILAEALEKWP YLNEVVPHLVTII+KLD ++R E ++P VQIID Sbjct: 300 AVAVVKNMVGYTNHTILAEALEKWPTAYLNEVVPHLVTIIEKLDALVRSEVSDPAVQIID 35- 9 Query: 360 EAGRVHMAHMDIHFSTSVNGVAALHTEILKNSELKVFYDIYPDKFNNKTNGITFRRWLEF 41- 9 E+GRVHMAHMDIHF+TSVNGVAALHTEILKNSELK FYD+YP+KFNNKTNGITFRRWLEF Sbjct: 360 ESGRVHMAHMDIHFATSVNGVAALHTEILKNSELKAFYDLYPEKFNNKTNGITFRRWLEF 41- 9 Query: 420 ANQDLADYLKELIGDSYLTDATQLEKLLTYADSNEVHDKLAAIKFKNKLALKRYLKENKG 47- 9 ANQDLADY+KELIGD YLTDAT+LEKL+ +AD VH KLA IKF NKLALKRYLK+NK Sbjct: 420 ANQDLADYIKELIGDEYLTDATKLEKLMAFADDKAVHAKLAEIKFNNKLALKRYLKDNKD 47- 9 Query: 480 IELDEYSIIDTQIKRFHEYKRQQMNALYVIHKYLEIKRGHFPSRKLTVIFGGKAAPAYTI 53- 9 IELDE+SIIDTQIKRFHEYKRQQMNALYVIHKYLEIK+G+ P RK+TVIFGGKAAPAY I Sbjct: 480 IELDEHSIIDTQIKRFHEYKRQQMNALYVIHKYLEIKKGNLPKRKITVIFGGKAAPAYII 53- 9 Query: 540 AQDIIHLILCLSELINNDPEVNKYLNVHLVENYNVTVAEKLIPATDISEQISLASKEASG 59- 9 AQDIIHLILCLSELINNDPEV+ YLNVHLVENYNVTVAE LIPATDISEQISLASKEASG Sbjct: 540 AQDIIHLILCLSELINNDPEVSPYLNVHLVENYNVTVAEHLIPATDISEQISLASKEASG 59- 9 Query: 600 TGNMKFMLNGALTLGTMDGANVEIAELAGKENIYTFGKDSDTIINLYETSGYRSKDYYDK 65- 9 TGNMKFMLNGALTLGTMDGANVEIAELAG ENIYTFGKDSDTIINLY T+ Y +KDYYD Sbjct: 600 TGNMKFMLNGALTLGTMDGANVEIAELAGMENIYTFGKDSDTIINLYATASYVAKDYYDN 65- 9 Query: 660 DKVIREAVDFIISDDIVSLGNAERLKRLHDELVGKDWFMTLIDLKEYIAVKEQVLADYED 71- 9 I+ AV+FIIS ++++ GN ERL RL+ EL+ KDWFMTLIDL+EYI VKE++LADYED Sbjct: 660 HPAIKAAVNFIISPELLAFGNEERLDRLYKELISKDWFMTLIDLEEYIEVKEKMLADYED 71- 9 Query: 720 YESWNKKVIHNIAKAGFFSSDRTIEQYNQDIWHS 753 + W KV+HNIAKAGFFSSDRTIEQYN+DIWHS Sbjct: 720 QDLWMTKVVHNIAKAGFFSSDRTIEQYNEDIWHS 753 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2082 A DNA sequence (GBSx2197) was identified in S. agalactiae <SEQ ID 6443> which encodes the amino acid sequence <SEQ ID 6444>. This protein is predicted to be glycerol-3-phosphatase transporter (glpT). Analysis of this protein sequence reveals the following: TABLE-US-06380 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.88 Transmembrane 339-355 (333-359) INTEGRAL Likelihood = -8.01 Transmembrane 432-448 (426-450) INTEGRAL Likelihood = -6.74 Transmembrane 92-108 (91-127) INTEGRAL Likelihood = -6.69 Transmembrane 194-210 (190-214) INTEGRAL Likelihood = -3.77 Transmembrane 367-383 (364-385) INTEGRAL Likelihood = -2.81 Transmembrane 111-127 (109-127) INTEGRAL Likelihood = -2.28 Transmembrane 407-423 (406-424) INTEGRAL Likelihood = -2.02 Transmembrane 165-181 (165-182) INTEGRAL Likelihood = -0.64 Transmembrane 29-45 (29-45) ----- Final Results ----- bacterial membrane --- Certainty = 0.5352(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06381 >GP: AAC44575 GB: U28354 IS629 ORFB fused with sequences similar to E. coli GlpT and UhpT proteins, Swiss-Prot Accession Number P08194 and P09836; Method: conceptual translation supplied by author [Shig Identities = 174/321 (54%), Positives = 241/321 (74%), Gaps = 4/321 (1%) Query: 109 GVIPSVITSIWLFTIMYLINGWLQGMGYPPGARTLVYWYDNKERIKYATIWNLSHNFGGA 16- 8 GV P V + + + YL+NGW+QGMGYPPGA+TLV+WY+++ERI +AT+WNLSHN GGA Sbjct: 12 GVGP-VCSELHIAPSTYLLNGWIQGMGYPPGAKTLVFWYEHRERISWATLWNLSHNVGGA 70 Query: 169 IAPILTGVGLALAGNDSLNQARAAYWFPGVVACLLAVLVYFLQEDTPESIGLPPIEEYHK 22- 8 +AP+L G G+ +L+ ARAA+ FPGV+ ++VL+YF+Q D P S+GLPPIEE+ Sbjct: 71 LAPVLIGFSFGFFGDSALDHARAAFIFPGVLCMAMSVLIYFIQVDRPVSVGLPPIEEWKG 130- Query: 229 EQYTNVVDSSDILEEPEVLGMGEIIKKYILPNTKLMWASLYSIFVYILRYGIVSWTPKFL 28- 8 ++ E+ L + +II+K+I+ N KL++ +Y FVYILRYGIVSW PKFL Sbjct: 131 NVVSHPAKGR---EQGPRLSIPDIIRKHIIRNNKLIYCCIYGSFVYILRYGIVSWAPKFL 18- 7 Query: 289 ATSVQDGGKGITATAGMGGFSLFEIGGIIGMLTAGYLSAKVFKNSKPLTNVAFLVVAILL 34- 8 + S+ GGK + A MGG S+FEIGG+ GML AGYLS ++F+NSKPLTN FL + I+L Sbjct: 188 SDSLDVGGKDMGKLASMGGGSVFEIGGVAGMLLAGYLSVRLFRNSKPLTNTLFLALTIIL 24- 7 Query: 349 LAAYWFIPAGPQYMALDFIILLGLGASIYGPVMMVGLYAMELVPKAAAGAASGLTGTFSY 40- 8 L AYW++P+G +Y+ L++ IL+ LG ++YGPVM +GLY+MELVPK AAGAASGL+GTFSY Sbjct: 248 LIAYWYVPSGNEYLWLNYTILILLGLAVYGPVMFIGLYSMELVPKEAAGAASGLSGTFSY 30- 7 Query: 409 VGGATIATLAIGIIIDHFGWG 429 + G+ +ATL +G+++D+ GWG Sbjct: 308 IFGSIVATLGMGLVVDYLGWG 328 A related DNA sequence was identified in S. pyogenes <SEQ ID 6445> which encodes the amino acid sequence <SEQ ID 6446>. Analysis of this protein sequence reveals the following: TABLE-US-06382 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.37 Transmembrane 185-201 (175-208) INTEGRAL Likelihood = -9.13 Transmembrane 114-130 (90-134) INTEGRAL Likelihood = -7.75 Transmembrane 322-338 (320-345) INTEGRAL Likelihood = -6.79 Transmembrane 421-437 (419-439) INTEGRAL Likelihood = -6.37 Transmembrane 91-107 (90-113) INTEGRAL Likelihood = -5.36 Transmembrane 163-179 (161-181) INTEGRAL Likelihood = -5.20 Transmembrane 350-366 (347-371) INTEGRAL Likelihood = -4.41 Transmembrane 23-39 (22-41) INTEGRAL Likelihood = -3.77 Transmembrane 257-273 (249-273) INTEGRAL Likelihood = -1.33 Transmembrane 61-77 (61-77) INTEGRAL Likelihood = -1.28 Transmembrane 383-399 (383-399) INTEGRAL Likelihood = -0.90 Transmembrane 299-315 (299-315) ----- Final Results ----- bacterial membrane --- Certainty = 0.5946(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06383 >GP: AAF96050 GB: AE004355 glycerol-3-phosphate transporter [Vibrio cholerae] Identities = 128/438 (29%), Positives = 215/438 (48%), Gaps = 17/438 (3%) Query: 1 LFMEEDYNKREP-EKFTQFLRRQKVVFFVAFF-GYVCAYLVRNNFKLMSNTIMVQNGWDK 58 LF + +R P +K R + F+ F GY YL R NF L + +++ G+ + Sbjct: 21 LFKPAAHTQRLPSDKVDSVYSRLRWQLFIGIFVGYAGYYLGRKNFSL-AMPYLIEQGFSR 79 Query: 59 AQIAILLSCLTVSYGLAKFYMGALGDRVSLRKLFSISLGASALICILIGFF---NSSMVV 115- + + L ++++YGL+KF MG + DR + R S L SAL+ GF S+ Sbjct: 80 GDLGVALGAVSIAYGLSKFLMGNVSDRSNPRYFLSAGLLLSALVMFCFGFMPWATGSITA 139- Query: 116 LGILLVLCGVVQGALAPASQAMIANYFPNKTRGGAIAGWNISQNMGSALLPLTIALLTSM 17- 5 + ILL L G QG PA + +++ K RG ++ WN++ N+G L I + + Sbjct: 140 MFILLFLNGWFQGMGWPACGRTMVHWWSRKERGEIVSVWNVAHNVGGGL----IGPIFLL 19- 5 Query: 176 GLVVPANGNILLAFLIPGVLVFLFALCCWKLGGDNPESEGLDSLRTMYGDAGESAVASEE 23- 5 GL + N + AF +P L A+ W + D P+S GL + D + S E Sbjct: 196 GLWM-FNDDWRTAFYVPAFFAVLVAVFTWLVMRDTPQSCGLPPIEEYKNDYPDDYDKSHE 25- 4 Query: 236 EKHNLSYWQLIWKYVFCNPSLLLVAAVNVALYFVRFGIEDWMPIYLSQVANMSEAHIHFA 29- 5 + ++ ++ +KYVF N L +A N +Y +R+G+ DW P+YL + + + +A Sbjct: 255 NE--MTAKEIFFKYVFNNKLLWSIAIANAFVYLIRYGVLDWAPVYLKEAKHFTVDKSSWA 31- 2 Query: 296 ISMLEWVAIPGSLVFAWLAVR-YPNKMAKVGAIGLFVLAAIVFVYERLTATGAPNYFLLL 35- 4 + EW IPG+L+ W++ + + + A G + + ++ V VY G P + Sbjct: 313 YFLYEWAGIPGTLLCGWISDKVFKGRRAPAGILFMVLVTLAVLVY-WFNPAGNPAVDMAA 37- 1 Query: 355 VIAGILGSLIYGPQLIVNILTINFVPLNVAGTAIGFVGVTAYLIGNMGANWLMPILADGF 41- 4 ++A +G LIYGP +++ + + P AGTA G G+ YL G + AN ++ D F Sbjct: 372 LVA--IGFLIYGPVMLIGLYALELAPKKAAGTAAGLTGLFGYLGGAVAANAILGYTVDHF 42- 9 Query: 415 GWFWSYIVVAALSAFSAV 432 GW ++V+ A S + Sbjct: 430 GWDGGFMVLVASCVLSVL 447 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06384 Identities = 117/439 (26%), Positives = 203/439 (45%), Gaps = 27/439 (6%) Query: 23 KYPRYRVQVLISIFVGYMGYYFVRNTTSILSGILNMS----ATEIGIITCASYIAYGLSK 78 - ++ R + V F GY+ Y VRN ++S + + +I I+ ++YGL+K Sbjct: 17 QFLRRQKVVFFVAFFGYVCAYLVRNNFKLMSNTIMVQNGWDKAQIAILLSCLTVSYGLAK 76 Query: 79 FISGLISDESNSKIFLPVGLFLTGLVNVLIGVIPSVITSIWLFTIMYLINGWLQGHGYPP 138- F G + D + + + L + L+ +LIG S S+ + I+ ++ G +QG P Sbjct: 77 FYMGALGDRVSLRKLFSISLGASALICILIGFFNS---SMVVLGILLVLCGVVQGALAPA 133- Query: 139 GARTLVYWYDNKERIKYATIWNLSHNFGGAIAPI----LTGVGLALAGNDSLNQARAAYW 19- 4 + ++ NK R WN+S N G A+ P+ LT +GL + N ++ A+ Sbjct: 134 SQAMIANYFPNKTRGGAIAGWNISQNMGSALLPLTIALLTSMGLVVPANGNI---LLAFL 19- 0 Query: 195 FPGVVACLLAVLVYFLQEDTPESIGLPPIEEYHKEQYTNVVDSSDILEEPEVLGMGEIIK 25- 4 PGV+ L A+ + L D PES GL + + + + V S EE L ++I Sbjct: 191 IPGVLVFLFALCCWKLGGDNPESEGLDSLRTMYGDAGESAVASE---EEKHNLSYWQLIW 24- 7 Query: 255 KYILPNTKLMWASLYSIFVYILRYGIVSWTPKFLATSVQDGGKGITATAGMGGFSLFEIG 31- 4 KY+ N L+ + ++ +Y +R+GI W P +L+ I S+ E Sbjct: 248 KYVFCNPSLLLVAAVNVALYFVRFGIEDWMPIYLSQVANMSEAHIHFA-----ISMLEWV 30- 2 Query: 315 GIIGMLTAGYLSAKVFKNSKPLTNVAFLVVAILLLAAYWFIPAG-PQYMALDFIILLG-L 37- 2 I G L +L+ + + + V+A ++ G P Y L +++ G L Sbjct: 303 AIPGSLVFAWLAVRYPNKMAKVGAIGLFVLAAIVFVYERLTATGAPNYFLL--LVIAGIL 36- 0 Query: 373 GASIYGPVMMVGLYAMELVPKAAAGAASGLTGTFSYVGGATIATLAIGIIIDHFGWGVAF 43- 2 G+ IYGP ++V + + VP AG A G G +Y+ G A + I+ D FGW ++ Sbjct: 361 GSLIYGPQLIVNILTINFVPLNVAGTAIGFVGVTAYLIGNMGANWLMPILADGFGWFWSY 42- 0 Query: 433 IIF-GISGFAAIVCTLLSR 450 I+ +S F+A+ +L++ Sbjct: 421 IVVAALSAFSAVGYLILAK 439 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2083 A DNA sequence (GBSx2198) was identified in S. agalactiae <SEQ ID 6447> which encodes the amino acid sequence <SEQ ID 6448>. Analysis of this protein sequence reveals the following: TABLE-US-06385 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3202(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 6449> which encodes the amino acid sequence <SEQ ID 6450>. Analysis of this protein sequence reveals the following: TABLE-US-06386 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4473(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06387 Identities = 54/100 (54%), Positives = 67/100 (67%) Query: 1 MTYELCLEYGTYPLRPVDAWADEINTAPAFITEDKKLLELLEEVNTLFHELFLTIECSFH 60 MTYELCLEYGTYPL VDA+ E P FI ED+ L LE +N LFH+LF+TIE FH Sbjct: 1 MTYELCLEYGTYPLSRVDAYWGEDQNPPTFIQEDRLLCHKLETMNHLFHDLFVTIESQFH 60 Query: 61 YIGHDFPEKRAKITQIYHVIIEHLSIHYPEYDIKIESLLM 100 Y+G + PEKRA+I +Y + L Y +Y IKIE+ L+ Sbjct: 61 YVGFNMPEKRAQIRILYQEVATILKSKYKDYPIKIETFLL 100 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2084 A DNA sequence (GBSx2199) was identified in S. agalactiae <SEQ ID 6451> which encodes the amino acid sequence <SEQ ID 6452>. Analysis of this protein sequence reveals the following: TABLE-US-06388 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2369(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06389 >GP: AAB81912 GB: U92974 unknown [Lactococcus lactis] Identities = 213/322 (66%), Positives = 260/322 (80%), Gaps = 5/322 (1%) Query: 1 MSEKIRVLLYYKYVSIENAEEYAAKHLEFCKSIGLKGRILIADEGINGTVSGDYETTQKY 60 M++ RVLLYY+YV IE+ E +A KHL CK +GLKGRIL+ADEGINGTVSG E T Y Sbjct: 1 MTQDYRVLLYYQYVPIEDGETFAQKHLADCKELGLKGRILVADEGINGTVSGTIEQTNAY 60 Query: 61 MDWVHSDERFADLWFKIDEENQQAFRKMFVRYKKEIVHLGLEDNNFDSDINPLETTGEYL 120- M+ + +D RF+ FKIDE Q AF+KM VRY+ E+V+L LED D+NPLE TG YL Sbjct: 61 MELMKNDPRFSSTIFKIDEAEQNAFKKMHVRYRPELVNLSLED-----DVNPLELTGAYL 115- Query: 121 NPKQFKEALLDEDTVVLDTRNDYEYDLGHFRGAIRPDIRNFRELPQWVRDNKDKFMEKRV 18- 0 +PK+F+EA+LDE+TVV+D RNDYE+DLGHFRGAIRP+IR+FRELPQW+RDNK++FMEKRV Sbjct: 116 DPKEFREAMLDENTVVIDARNDYEFDLGHFRGAIRPEIRSFRELPQWIRDNKEQFMEKRV 17- 5 Query: 181 VVYCTGGVRCEKFSGWMVREGFKDVGQLHGGIATYGKDPEVQGELWDGAMYVFDDRISVP 24- 0 + YCTGG+RCEKFSGW+VREGFKDVGQL GGIATYGKDPEVQG+LWDG MYVFD RI+VP Sbjct: 176 LTYCTGGIRCEKFSGWLVREGFKDVGQLLGGIATYGKDPEVQGDLWDGQMYVFDSRIAVP 23- 5 Query: 241 INHVNPTVISKDYFDGTPCERYVNCANPFCNKQIFASEENEAKYVRGCSPECRAHERNRY 30- 0 IN ++ +D+FDG+PCERY+NC NP CN+Q+ ASEENEAKY+ CS ECR H NRY Sbjct: 236 INQKEHVIVGRDWFDGSPCERYINCGNPECNRQMLASEENEAKYLGACSHECRVHPNNRY 29- 5 Query: 301 VQENGLSRQEWAERLEAIGESL 322 ++ + LS QE ERL + + L Sbjct: 296 IKAHQLSNQEVQERLALLEKDL 317 A related DNA sequence was identified in S. pyogenes <SEQ ID 6453> which encodes the amino acid sequence <SEQ ID 6454>. Analysis of this protein sequence reveals the following: TABLE-US-06390 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2443(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06391 Identities = 321/324 (99%), Positives = 323/324 (99%) Query: 1 MSEKIRVLLYYKYVSIENAEEYAAKHLEFCKSIGLKGRILIADEGINGTVSGDYETTQKY 60 MSEKIRVLLYYKYVSIENA+EYAAKHLEFCKSIGLKGRILIADEGINGTVSGDYETTQKY Sbjct: 1 MSEKIRVLLYYKYVSIENAQEYAAKHLEFCKSIGLKGRILIADEGINGTVSGDYETTQKY 60 Query: 61 MDWVHSDERFADLWFKIDEENQQAFRKMFVRYKKEIVHLGLEDNNFDSDINPLETTGEYL 120- MDWVHSDERFADLWFKIDEENQQAFRKMFVRYKKEIVHLGLEDNNFDSDINPLETTGEYL Sbjct: 61 MDWVHSDERFADLWFKIDEENQQAFRKMFVRYKKEIVHLGLEDNNFDSDINPLETTGEYL 120- Query: 121 NPKQFKEALLDEDTVVLDTRNDYEYDLGHFRGAIRPDIRNFRELPQWVRDNKDKFMEKRV 18- 0 NPKQFKEALLDEDTVVLDTRNDYEYDLGHFRGAIRPDIRNFRELPQWVRDNKDKFMEKRV Sbjct: 121 NPKQFKEALLDEDTVVLDTRNDYEYDLGHFRGAIRPDIRNFRELPQWVRDNKDKFMEKRV 18- 0 Query: 181 VVYCTGGVRCEKFSGWMVREGFKDVGQLHGGIATYGKDPEVQGELWDGAMYVFDDRISVP 24- 0 VVYCTGGVRCEKFSGWMVREGFKDVGQLHGGIATYGKDPEVQGELWDGAMYVFDDRISVP Sbjct: 181 VVYCTGGVRCEKFSGWMVREGFKDVGQLHGGIATYGKDPEVQGELWDGAMYVFDDRISVP 24- 0 Query: 241 INHVNPTVISKDYFDGTPCERYVNCANPFCNKQIFASEENEAKYVRGCSPECRAHERNRY 30- 0 INHVNPTVISKDYFDGTPCERYVNCANPFCNKQIFASEENE KYVRGCSPECRAHERNRY Sbjct: 241 INHVNPTVISKDYFDGTPCERYVNCANPFCNKQIFASEENETKYVRGCSPECRAHERNRY 30- 0 Query: 301 VQENGLSRQEWAERLEAIGESLPQ 324 VQENGLSRQEWAERLEAIGESLP+ Sbjct: 301 VQENGLSRQEWAERLEAIGESLPE 324 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2085 A DNA sequence (GBSx2200) was identified in S. agalactiae <SEQ ID 6455> which encodes the amino acid sequence <SEQ ID 6456>. Analysis of this protein sequence reveals the following: TABLE-US-06392 Possible site: 57 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06393 >GP: AAC83954 GB: L47648 putative [Bacillus subtilis] Identities = 54/192 (28%), Positives = 89/192 (46%), Gaps = 14/192 (7%) Query: 5 QTIIIGAGAAGIGFGSAMQRLGLTNFLIIEKGHIGESFLRWPRTTQFITPSFTTNGFGFP 64 + IIIG G G+ ++++G+ + L+IEKG++ S +P F + S Sbjct: 5 KAIIIGGGPCGLSAAIHLKQIGI-DALVIEKGNVVNSIYNYPTHQTFFSSSEKLE----- 58 Query: 65 DLNAVIPDTSPAFSFEKEHLSGVEYARYLQLVAAHYNLPIQNETSVLSIDK-RDSLFVIK 123- I D AF E ++ Y + V N+ + V + K +++ FVI+ Sbjct: 59 -----IGDV--AFITENRKPVRIQALSYYREVVKRKNIRVNAFEMVRKVTKTQNNTFVIE 111- Query: 124 TSKGDFSADYLIMATGEFQNPNTIDIKGADLGMHYGQVDNFHIKSDNPFIIIGGNESACD 18- 3 TSK ++ Y I+ATG + +PN + + G DL + H D ++IGG S+ D Sbjct: 112 TSKETYTTPYCIIATGYYDHPNYMGVPGEDLPKVFHYFKEGHPYFDKDVVVIGGKNSSVD 17- 1 Query: 184 ALTHLVYLGNQV 195 A LV G +V Sbjct: 172 AALELVKSGARV 183 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8973> and protein <SEQ ID 8974> were also identified. Analysis of this protein sequence reveals the following:

TABLE-US-06394 Lipop Possible site: -1 Crend: 2 McG: Discrim Score: 5.05 GvH: Signal Score (-7.5): -3.14 Possible site: 57 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 0 value: 0.26 threshold: 0.0 PERIPHERAL Likelihood = 0.26 6 modified ALOM score: -0.55 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00152## SEQ ID 8974 (GBS284) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 52 (lane 10; MW 42.7 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 58 (lane 9; MW 67.6 kDa). GBS284-GST was purified as shown in FIG. 225, lane 7. EXAMPLE 2086 A DNA sequence (GBSx2201) was identified in S. agalactiae <SEQ ID 6457> which encodes the amino acid sequence <SEQ ID 6458>. This protein is predicted to be NrgA-like protein. Analysis of this protein sequence reveals the following: TABLE-US-06395 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.73 Transmembrane 7-23 (1-31) INTEGRAL Likelihood = -6.42 Transmembrane 86-102 (82-108) INTEGRAL Likelihood = -6.42 Transmembrane 324-340 (318-342) INTEGRAL Likelihood = -5.26 Transmembrane 210-226 (207-229) INTEGRAL Likelihood = -5.10 Transmembrane 113-129 (112-133) INTEGRAL Likelihood = -1.49 Transmembrane 246-262 (246-263) INTEGRAL Likelihood = -1.17 Transmembrane 183-199 (183-199) INTEGRAL Likelihood = -0.43 Transmembrane 41-57 (41-57) INTEGRAL Likelihood = -0.00 Transmembrane 265-281 (265-282) ----- Final Results ----- bacterial membrane --- Certainty = 0.5692(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9997> which encodes amino acid sequence <SEQ ID 9998> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06396 >GP: CAB15668 GB: Z99122 ammonium transporter [Bacillus subtilis] Identities = 105/378 (27%), Positives = 181/378 (47%), Gaps = 41/378 (10%) Query: 3 VKKGLFVFLLLCILSMWLMIFGVAFYYFGSLH-QSLTSRIIYQFVLTVLLTTTAWFMGAY 61- ++ G VF+ C L +WLM G+A +Y G + +++ S ++ F ++ + + W + Y Sbjct: 1 MQMGDTVFMFFCALLVWLMTPGLALFYGGMVKSKNVLSTAMHSFS-SIAIVSIVWVLFGY 59- Query: 62 FLAFEGHFKTVFQFQEADGKQI--------------VNCLFQLCFALYAVVMLIGSIIDR 10- 7 LAF + + A K + + +FQ+ FA+ ++ G+ +R Sbjct: 60 TLAFAPGNSIIGGLEWAGLKGVGFDPGDYSDTIPHSLFMMFQMTFAVLTTAIISGAFAER 11- 9 Query: 108 VQTKRLLLAVVSWLFLVYTPLAYLIWNSEGVFAKMGVLDFSGGMIVHLSAGLSSYILAHV 16- 7 ++ LL V W LVYTP+A+ +W G ++G LDF+GG +VH+S+G++ +LA V Sbjct: 120 MRFGAFLLFSVLWASLVYTPVAHWVWGG-GWIGQLGALDFAGGNVVHISSGVAGLVLAIV 17- 8 Query: 168 IGK-----SEHQHNKVKNDSLFLGMILITFGWFGFNMGPVGEWNSQAIMILLNTIFAIIG 22- 2 +GK + HN + FLG LI FGWFGFN+G + A+ +NT A Sbjct: 179 LGKRKDGTASSPHNLIYT---FLGGALIWFGWFGFNVGSALTLDGVAMYAFINTNTAAAA 23- 5 Query: 223 GGLAWTLAAKWNGEEEKTGSLLNGIIVGLVTSTAGVGYLLTWQLLAVTFFASLFTYFVTD 28- 2 G W L ++ ++G I GLV T G++ + + + ++ Sbjct: 236 GIAGWILVEWIINKKPTMLGAVSGAIAGLVAITPAAGFVTPFASIIIGIIGGAVCFWGVF 29- 5 Query: 283 YVAKAFAIDDVVSSFGMNGIGGLLGSLGVGLFKLSHMP----------------VQLLAL 32- 6 + K F DD + +FG++GIGG G + GLF + + Q++A+ Sbjct: 296 SLKKKFGYDDALDAFGLHGIGGTWGGIATGLFATTSVNSAGADGLFYGDASLIWKQIVAI 35- 5 Query: 327 ATTILLSIIMTYIISKAI 344 A T + I+T++I K + Sbjct: 356 AATYVFVFIVTFVIIKIV 373 No corresponding DNA sequence was identified in S. pyogenes. A related GBS gene <SEQ ID 8975> and protein <SEQ ID 8976> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06397 Lipop: Possible site: -1 Crend: 4 McG: Discrim Score: 17.19 GVH: Signal Score (-7.5): -4.07 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 9 value: -11.73 threshold: 0.0 INTEGRAL Likelihood = -11.73 Transmembrane 7-23 (1-31) INTEGRAL Likelihood = -6.42 Transmembrane 86-102 (82-108) INTEGRAL Likelihood = -6.42 Transmembrane 324-340 (318-342) INTEGRAL Likelihood = -5.26 Transmembrane 210-226 (207-229) INTEGRAL Likelihood = -5.10 Transmembrane 113-129 (112-133) INTEGRAL Likelihood = -1.49 Transmembrane 246-262 (246-263) INTEGRAL Likelihood = -1.17 Transmembrane 183-199 (183-199) INTEGRAL Likelihood = -0.43 Transmembrane 41-57 (41-57) INTEGRAL Likelihood = -0.00 Transmembrane 265-281 (265-282) PERIPHERAL Likelihood = 0.26 152 modified ALOM score: 2.85 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5692(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00153## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2087 A DNA sequence (GBSx2202) was identified in S. agalactiae <SEQ ID 6459> which encodes the amino acid sequence <SEQ ID 6460>. This protein is predicted to be dUTPase (dut). Analysis of this protein sequence reveals the following: TABLE-US-06398 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2731(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9471> which encodes amino acid sequence <SEQ ID 9472> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06399 >GP: CAA72644 GB: Y11901 dUTPase [Lactococcus lactis] Identities = 67/144 (46%), Positives = 90/144 (61%), Gaps = 8/144 (5%) Query: 40 RGFELVSQFSNKELLPKRETAHAAGYDLKVAKKTVIEPGEITLVPTGIKAYMQPGEVLYL 99- RGF+ + +P+R T H+AGYD+ ++ I+P EI +V TG+ + EVL L Sbjct: 3 RGFK---KLDGNATIPERATKHSAGYDISASETVTIQPDEIKMVSTGLAVQLGDDEVLKL 59- Query: 100 YDRSSNPRKKGIVLINSVGVIDGDYYNNQVNEGHIFAQMQNITDQAVILEEGERIVQAVF 15- 9 YDRSSNP K+GI LINSVG+ID DYY + NI+ + V + +G+RI+Q VF Sbjct: 60 YDRSSNPVKRGIALINSVGIIDSDYYPQEFK-----GLFMNISKEPVTISKGQRIMQGVF 11- 4 Query: 160 APFLLADDDQATGMRTGGFGSTGK 183 +L DDD A G RTGGFGSTG+ Sbjct: 115 VKYLTIDDDNANGKRTGGFGSTGE 138 A related DNA sequence was identified in S. pyogenes <SEQ ID 6461> which encodes the amino acid sequence <SEQ ID 6462>. Analysis of this protein sequence reveals the following: TABLE-US-06400 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2519(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06401 Identities = 115/148 (77%), Positives = 125/148 (83%) Query: 36 MSKVRGFELVSQFSNKELLPKRETAHAAGYDLKVAKKTVIEPGEITLVPTGIKAYMQPGE 95 - M+K+RGFELVS F+N +LLPKRET HAAGYDL VA+ I PGEI LVPTG+KAYMQ GE Sbjct: 1 MTKIRGFELVSSFTNPDLLPKRETTHAAGYDLSVAEAVTIAPGEIKLVPTGVKAYMQDGE 60 Query: 96 VLYLYDRSSNPRKKGIVLINSVGVIDGDYYNNQVNEGHIFAQMQNITDQAVILEEGERIV 155- VLYLYDRSSNPRKKGI+LINSVGVID DYY N+ NEGHIFAQMQNITD V L GERIV Sbjct: 61 VLYLYDRSSNPRKKGIILINSVGVIDADYYGNEANEGHIFAQMQNITDHPVTLAVGERIV 120- Query: 156 QAVFAPFLLADDDQATGMRTGGFGSTGK 183 Q VF PFL+AD DQA G RTGGFGSTG+ Sbjct: 121 QGVFMPFLIADGDQARGERTGGFGSTGQ 148 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2088 A DNA sequence (GBSx2203) was identified in S. agalactiae <SEQ ID 6463> which encodes the amino acid sequence <SEQ ID 6464>. This protein is predicted to be RadA homolog (radA). Analysis of this protein sequence reveals the following: TABLE-US-06402 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2628(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06403 >GP: CAB11863 GB: Z99104 DNA repair protein homolog [Bacillus subtilis] Identities = 285/453 (62%), Positives = 358/453 (78%), Gaps = 4/453 (0%) Query: 1 MAKKKSVFTCQECGYQSPKYLGRCPNCSAWSSFVEEVEVQEVKNARVSLNGEKSRPTKLK 60 MAK KS F CQ CGY+SPK++G+CP C AW++ VEE+ + N R + + K Sbjct: 1 MAKTKSKFICQSCGYESPKWMGKCPGCGAWNTMVEEMIKKAPANRRAAFSHSVQTVQKPS 60 Query: 61 DVSSINYS---RTKTDMDEFNRVLGGGVVPGSLVLIGGDPGIGKSTLLLQVSTQLA-NKG 116- ++SI S R KT + EFNRVLGGGVV GSLVLIGGDPGIGKSTLLLQVS QL+ + Sbjct: 61 PITSIETSEEPRVKTQLGEFNRVLGGGVVKGSLVLIGGDPGIGKSTLLLQVSAQLSGSSN 120- Query: 117 TVLYVSGEESAEQIKLRSERLGDIDNEFYLYAETNMQSIRSEIEKIKPDFLIIDSIQTIM 17- 6 +VLY+SGEES +Q KLR++RLG + ++ +ET+M+ I S I+++ P F+++DSIQT+ Sbjct: 121 SVLYISGEESVKQTKLRADRLGINNPSLHVLSETDMEYISSAIQEMNPSFVVVDSIQTVY 18- 0 Query: 177 SPEVSSVQGSVSQVREVTAELMQLAKTNNIATFIVGHVTKEGTLAGPRMLEHMVDTVLYF 23- 6 +++S GSVSQVRE TAELM++AKT I FIVGHVTKEG++AGPR+LEHMVDTVLYF Sbjct: 181 QSDITSAPGSVSQVRECTAELMKIAKTKGIPIFIVGHVTKEGSIAGPRLLEHMVDTVLYF 24- 0 Query: 237 EGERHHTFRILRAVKNRFGSTNEIGIFEMQSGGLVEVLNPSQVFLEERLDGATGSAIVVT 29- 6 EGERHHTFRILRAVKNRFGSTNE+GIFEM+ GL EVLNPS++FLEER G+ GS+I + Sbjct: 241 EGERHHTFRILRAVKNRFGSTNEMGIFEMREEGLTEVLNPSEIFLEERSAGSAGSSITAS 30- 0 Query: 297 MEGTRPILAEVQALVTPTVFGNAKRTTTGLDFNRVSLIMAVLEKRCGLLLQNQDAYLKSA 35- 6 MEGTRPIL E+QAL++PT FGN +R TG+D NRVSL+MAVLEKR GLLLQNQDAYLK A Sbjct: 301 MEGTRPILVEIQALISPTSFGNPRRMATGIDHNRVSLLMAVLEKRVGLLLQNQDAYLKVA 36- 0 Query: 357 GGVKLDEPAIDLAVAVAIASSYKEKPTNPQESFIGEIGLTGEIRRVTRIEQRINEASKLG 41- 6 GGVKLDEPAIDLA+ ++IASS+++ P NP + FIGE+GLTGE+RRV+RIEQR+ EA+KLG Sbjct: 361 GGVKLDEPAIDLAIVISIASSFRDTPPNPADCFIGEVGLTGEVRRVSRIEQRVKEAAKLG 42- 0 Query: 417 FTKIYAPKNSLAGIEIPKGIDVIGVTTVSQVLK 449 F ++ P +L G PKGI+VIGV V++ L+ Sbjct: 421 FKRMIIPAANLDGWTKPKGIEVIGVANVAEALR 453 A related DNA sequence was identified in S. pyogenes <SEQ ID 6465> which encodes the amino acid sequence <SEQ ID 6466>. Analysis of this protein sequence reveals the following: TABLE-US-06404 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2191(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06405 Identities = 416/453 (91%), Positives = 441/453 (96%) Query: 1 MAKKKSVFTCQECGYQSPKYLGRCPNCSAWSSFVEEVEVQEVKNARVSLNGEKSRPTKLK 60 MAKKK+ F CQECGYQSPKYLGRCPNCSAWSSFVEEVEV+EVKNARVSL GEKSRP KLK Sbjct: 1 MAKKKATFICQECGYQSPKYLGRCPNCSAWSSFVEEVEVKEVKNARVSLAGEKSRPVKLK 60 Query: 61 DVSSINYSRTKTDMDEFNRVLGGGVVPGSLVLIGGDPGIGKSTLLLQVSTQLANKGTVLY 120- DV +I+Y RT+TDM EFNRVLGGGVVPGSL+LIGGDPGIGKSTLLLQVSTQLANKGTVLY Sbjct: 61 DVDNISYHRTQTDMSEFNRVLGGGVVPGSLILIGGDPGIGKSTLLLQVSTQLANKGTVLY 120- Query: 121 VSGEESAEQIKLRSERLGDIDNEFYLYAETNMQSIRSEIEKIKPDFLIIDSIQTIMSPEV 18- 0 VSGEESAEQIKLRSERLGDIDNEFYLYAETNMQ+IR+EIE IKPDFLIIDSIQTIMSP++ Sbjct: 121 VSGEESAEQIKLRSERLGDIDNEFYLYAETNMQAIRTEIENIKPDFLIIDSIQTIMSPDI 18- 0 Query: 181 SSVQGSVSQVREVTAELMQLAKTNNIATFIVGHVTKEGTLAGPRMLEHMVDTVLYFEGER 24- 0 + VQGSVSQVREVTAELMQLAKTNNIATFIVGHVTKEGTLAGPRMLEHMVDTVLYFEGER Sbjct: 181 TGVQGSVSQVREVTAELMQLAKTNNIATFIVGHVTKEGTLAGPRMLEHMVDTVLYFEGER 24- 0 Query: 241 HHTFRILRAVKNRFGSTNEIGIFEMQSGGLVEVLNPSQVFLEERLDGATGSAIVVTMEGT 30- 0 HHTFRILRAVKNRFGSTNEIGIFEMQSGGLVEVLNPSQVFLEERLDGATGSA+VVTMEG+ Sbjct: 241 HHTFRILRAVKNRFGSTNEIGIFEMQSGGLVEVLNPSQVFLEERLDGATGSAVVVTMEGS 30- 0 Query: 301 RPILAEVQALVTPTVFGNAKRTTTGLDFNRVSLIMAVLEKRCGLLLQNQDAYLKSAGGVK 36- 0 RPILAEVQ+LVTPTVFGNA+RTTTGLDFNRVSLIMAVLEKRCGLLLQNQDAYLKSAGGVK Sbjct: 301 RPILAEVQSLVTPTVFGNARRTTTGLDFNRVSLIMAVLEKRCGLLLQNQDAYLKSAGGVK 36- 0 Query: 361 LDEPAIDLAVAVAIASSYKEKPTNPQESFIGEIGLTGEIRRVTRIEQRINEASKLGFTKI 42- 0 LDEPAIDLAVAVAIASSYKEKPT+PQE+F+GEIGLTGEIRRVTRIEQRINEA+KLGFTK+ Sbjct: 361 LDEPAIDLAVAVAIASSYKEKPTSPQEAFLGEIGLTGEIRRVTRIEQRINEAAKLGFTKV 42- 0 Query: 421 YAPKNSLAGIEIPKGIDVIGVTTVSQVLKAVFS 453 YAPKN+L GI+IP+GI+V+GVTTV QVL AVFS Sbjct: 421 YAPKNALQGIDIPQGIEVVGVTTVGQVLNAVFS 453 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2089 A DNA sequence (GBSx2204) was identified in S. agalactiae <SEQ ID 6467> which encodes the amino acid sequence <SEQ ID 6468>. Analysis of this protein sequence reveals the following: TABLE-US-06406 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3488(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06407 >GP: CAA97750 GB: Z73419 hypothetical protein Rv1284 [Mycobacterium tuberculosis] Identities = 69/162 (42%), Positives = 100/162 (61%), Gaps = 2/162 (1%) Query: 3 TYFDNFLKTNQAYADLHGTAHLPIKPKTKVAIVTCMDSRLHVAQALGLALGDAHILRNAG 62 T D++L N YA LP+ P AIV CMD+RL V + LG+ G+AH++RNAG Sbjct: 2 TVTDDYLANNVDYASGF-KGPLPMPPSKHIAIVACMDARLDVYRMLGIKEGEAHVIRNAG 60 Query: 63 GRVTDDVLRSLVISQQQLGTREIVVLHHTDCGAQTFTNEAFAAQLQRDLGVDMHGHDFLP 122- VTDDV+RSL ISQ+ LGTREI++LHHTDCG TFT++ F +Q + G+ Sbjct: 61 CVVTDDVIRSLAISQRLLGTREIILLHNTDCGMLTFTDDDFKRAIQDETGIRPTWSP-ES 119- Query: 123 FNDIEESVREDVAKLHASPLIPDDVVISGAIYDVDTGRMVEV 164 + D E VR+ + ++ +P + + G ++DV TG++ EV Sbjct: 120 YPDAVEDVRQSLRRIEVNPFVTKHTSLRGFVFDVATGKLNEV 161 There is also homology to SEQ ID 6470: TABLE-US-06408 Identities = 126/164 (76%), Positives = 146/164 (88%) Query: 1 MTTYFDNFLKTNQAYADLHGTAHLPIKPKTKVAIVTCMDSRLHVAQALGLALGDAHILRN 60 + +YF++F+ NQAY LHGTAHLP+KPKTKVAIVTCMDSRLHVAQALGLALGDAHILRN Sbjct: 1 LMSYFEHFMAANQAYVALHGTAHLPLKPKTKVAIVTCMDSRLHVAQALGLALGDAHILRN 60 Query: 61 AGGRVTDDVLRSLVISQQQLGTREIVVLHHTDCGAQTFTNEAFAAQLQRDLGVDMHGHDF 120- AGGRVT+D++RSLVISQQQ+GTREIVVLHHTDCGAQTFTNE FA + LGVD+ G DF Sbjct: 61 AGGRVTEDMIRSLVISQQQMGTREIVVLHHTDCGAQTFTNEGFAKHIHEHLGVDVSGQDF 120- Query: 121 LPFNDIEESVREDVAKLHASPLIPDDVVISGAIYDVDTGRMVEV 164 LPF D+E+SVRED+AK+ AS LI DDVVI+GA+YDVDTG+M +V Sbjct: 121 LPFQDVSDSVREDMAKIRASSLISDDVVINGAVYDVDTGKMTQV 164 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2090 A DNA sequence (GBSx2205) was identified in S. agalactiae <SEQ ID 6471> which encodes the amino acid sequence <SEQ ID 6472>. Analysis of this protein sequence reveals the following: TABLE-US-06409 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0536(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9473> which encodes amino acid sequence <SEQ ID 9474> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06410 >GP: AAC73407 GB: AE000137 putative oxidoreductase [Escherichia coli K12] Identities = 199/438 (45%), Positives = 286/438 (64%) Query: 1 MKKYDVIVLGFGKAGKTLAAKLATQGKSVAMVEEDDKMYGGTCINIGCIPTKTLLVSASK 60 M KY +++GFGKAGKTLA LA G VA++E+ + MYGGTCINIGCIPTKTL+ A + Sbjct: 10 MNKYQAVIIGFGKAGKTLAVTLAKAGWRVALIEQSNAMYGGTCINIGCIPTKTLVHDAQQ 69 Query: 61 NHDFQEAMTTRNEVTSRLRAKNFAMLDNKDTVDVYNAKARFISNKVVELTGGADKQELTA 120- + DF A+ +NEV + LR KNF L + +DV + +A FI+N + + E+ Sbjct: 70 HTDFVRAIQRKNEVVNFLRNKNFHNLADMPNIDVIDGQAEFINNHSLRVHRPEGNLEIHG 129- Query: 121 DVIIINTGAKSVQLPIPGLADSQHVYDSTAIQELAHLPKRLGIIGGGNIGLEFATLYSEL 18- 0 + I INTGA++V PIPG+ + VYDST + L LP LGI+GGG IG+EFA++++ Sbjct: 130 EKIFINTGAQTVVPPIPGITTTPGVYDSTGLLNLKELPGHLGILGGGYIGVEFASMFANF 18- 9 Query: 181 GSKVTVIDSQSRIFAREEEELSEMAQDYLEEMGISFKLSADIKSVQNEDEDVVISFEDEK 24- 0 GSKVT++++ S RE+ ++++ L + G+ L+A ++ + + + V + E + Sbjct: 190 GSKVTILEAASLFLPREDRDIADNIATILRDQGVDIILNAHVERISHHENQVQVHSEHAQ 24- 9 Query: 241 LSFDAVLYATGRKPNTEGLALENTDIKLTERGAIAVDEYCQTSVENIFAVGDVNGGPQFT 30- 0 L+ DA+L A+GR+P T L EN I + ERGAI VD+ T+ +NI+A+GDV GG QFT Sbjct: 250 LAVDALLIASGRQPATASLHPENAGIAVNERGAIVVDKRLHTTADNIWAMGDVTGGLQFT 30- 9 Query: 301 YISLDDSRIVLNYLNCDKDYSLKNRGAVPTSTFTNPPLATVGLDEKTAKEKGYQVKSNSL 36- 0 YISLDD RIV + L + S +R VP S F PPL+ VG+ E+ A+E G ++ +L Sbjct: 310 YISLDDYRIVRDELLGEGKRSTDDRKNVPYSVFMTPPLSRVGMTEEQARESGADIQVVTL 36- 9 Query: 361 LVSAMPRAHVNNDLRGIFKVVVDTETNLILGARLFGAESHELINIITMAMDNKIPYTYFQ 42- 0 V+A+PRA V ND RG+ K +VD +T +LGA L +SHE+INI+ M MD +PY+ + Sbjct: 370 PVAAIPRARVMNDTRGVLKAIVDNKTQRMLGASLLCVDSHEMINIVKMVMDAGLPYSILR 42- 9 Query: 421 KQIFTHPTMVENFNDLFN 438 QIFTHP+M E+ NDLF+ Sbjct: 430 DQIFTHPSMSESLNDLFS 447 There is also homology to SEQ ID 1820. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2091 A DNA sequence (GBSx2206) was identified in S. agalactiae <SEQ ID 6473> which encodes the amino acid sequence <SEQ ID 6474>. This protein is predicted to be glutamyl-tRNA synthetase (gltX). Analysis of this protein sequence reveals the following:

TABLE-US-06411 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2245(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9475> which encodes amino acid sequence <SEQ ID 9476> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10953> which encodes amino acid sequence <SEQ ID 10954> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06412 >GP: AAC31971 GB: U49789 glutamyl-tRNA synthetase [Bacillus subtilis] Identities = 273/491 (55%), Positives = 353/491 (71%), Gaps = 19/491 (3%) Query: 20 LANKIRVRYAPSPTGLLHIGNARTALFNYLYARHHGGDFVIRIEDTDRKRHVEDGERSQL 79 - + N++RVRYAPSPTG LHIGNARTALFNYL+AR+ GG F+IR+EDTD+KR++E GE+SQL Sbjct: 1 MGNEVRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQL 60 Query: 80 ENLRWLGMDWDESPET---HENYRQSERLELYQRYIDQLLAEGKAYKSYVTEEELAAERE 136- L+WLG+DWDES + + YRQSER ++Y+ Y ++LL +G AYK Y TEEEL ERE Sbjct: 61 NYLKWLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKERE 120- Query: 137 RQELAGETPRYINEFIGMSETEKEAYIAEREAAGIIPTVRLAVNESGIYKWTDMVKGDIE 19- 6 Q GE PRY + +++ E+E +IAE G P++R V E + + D+VKG+I Sbjct: 121 EQIARGEMPRYSGKHRDLTQEEQEKFIAE----GRKPSIRFRVPEGKVIAFNDIVKGEIS 17- 6 Query: 197 FEGSNIGGDWVIQKKDGYPTYNFAVVIDDHDMQISHVIRGDDHIANTPKQLMVYEALGWE 25- 6 FE IG D+VI KKDG PTYNFAV IDD+ M+++HV+RG+DHI+NTPKQ+M+Y+A GW+ Sbjct: 177 FESDGIG-DFVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWD 23- 5 Query: 257 APQFGHMTLIINSETGKKLSKRDTNTLQFIEDYRKKGYMSEAVFNFIALLGWNPGGEEEI 31- 6 PQFGHMTLI+N E+ KKLSKRD + +QFIE Y++ GY+ EA+FNFI LLGW+P GEEE+ Sbjct: 236 IPQFGHMTLIVN-ESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWSPVGEEEL 29- 4 Query: 317 FSREQLINLFDENRLSKSPAAFDQKKMDWMSNDYLKNADFESVFALCKPFLEEAGRL--- 37- 3 F++EQ I +FD NRLSKSPA FD K+ W++N Y+K D + V L P L++AG++ Sbjct: 295 FTKEQFIEIFDVNRLSKSPALFDMHKLKWVNNQYVKKLDLDQVVELTLPHLQKAGKVGTE 35- 4 Query: 374 -----TDKAEKLVELYQPQLKSADEIVPLTDLFFADFPELTEAEKEVMAAETVPTVLSAF 42- 8 + KL+ LY QL EIV LTDLFF D E + K V+ E VP VLS F Sbjct: 355 LSAEEQEWVRKLISLYHEQLSYGAEIVELTDLFFTDEIEYNQEAKAVLEEEQVPEVLSTF 41- 4 Query: 429 KEKLVSLSDEEFTRDTIFPQIKAVQKETGIKGKNLFMPIRIAVSGEMHGPELPDTIYLLG 48- 8 KL L EEFT D I IKAVQKETG KGK LFMPIR+AV+G+ HGPELP +I L+G Sbjct: 415 AAKLEEL--EEFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGPELPQSIELIG 47- 2 Query: 489 KEKSVQHIDNM 499 KE ++Q + N+ Sbjct: 473 KETAIQRLKNI 483 A related DNA sequence was identified in S. pyogenes <SEQ ID 6475> which encodes the amino acid sequence <SEQ ID 6476>. Analysis of this protein sequence reveals the following: TABLE-US-06413 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1966(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06414 Identities = 434/481 (90%), Positives = 459/481 (95%) Query: 20 LANKIRVRYAPSPTGLLHIGNARTALFNYLYARHHGGDFVIRIEDTDRKRHVEDGERSQL 79 - ++ IRVRYAPSPTGLLHIGNARTALFNYLYAR HGG F+IRIEDTDRKRHVEDGERSQL Sbjct: 1 MSKPIRVRYAPSPTGLLHIGNARTALFNYLYARRHGGTFIIRIEDTDRKRHVEDGERSQL 60 Query: 80 ENLRWLGMDWDESPETHENYRQSERLELYQRYIDQLLAEGKAYKSYVTEEELAAERERQE 139- ENL+WLGMDWDESPETHENYRQSERL LYQ+YIDQLLAEGKAYKSYVTEEELAAERERQE Sbjct: 61 ENLKWLGMDWDESPETHENYRQSERLALYQQYIDQLLAEGKAYKSYVTEEELAAERERQE 120- Query: 140 LAGETPRYINEFIGMSETEKEAYIAEREAAGIIPTVRLAVNESGIYKWTDMVKGDIEFEG 19- 9 AGETPRYINEFIGMS EK YIAEREAAGI+PTVRLAVNESGIYKWTDMVKGDIEFEG Sbjct: 121 AAGETPRYINEFIGMSADEKAKYIAEREAAGIVPTVRLAVNESGIYKWTDMVKGDIEFEG 18- 0 Query: 200 SNIGGDWVIQKKDGYPTYNFAVVIDDHDMQISHVIRGDDHIANTPKQLMVYEALGWEAPQ 25- 9 NIGGDWVIQKKDGYPTYNFAVV+DDHDMQISHVIRGDDHIANTPKQLMVYEALGWEAP+ Sbjct: 181 GNIGGDWVIQKKDGYPTYNFAVVVDDHDMQISHVIRGDDHIANTPKQLMVYEALGWEAPE 24- 0 Query: 260 FGHMTLIINSETGKKLSKRDTNTLQFIEDYRKKGYMSEAVFNFIALLGWNPGGEEEIFSR 31- 9 FGHMTLIINSETGKKLSKRDTNTLQFIEDYRKKGYM EAVFNFIALLGWNPGGEEEIFSR Sbjct: 241 FGHMTLIINSETGKKLSKRDTNTLQFIEDYRKKGYMPEAVFNFIALLGWNPGGEEEIFSR 30- 0 Query: 320 EQLINLFDENRLSKSPAAFDQKKMDWMSNDYLKNADFESVFALCKPFLEEAGRLTDKAEK 37- 9 EQLI LFDENRLSKSPAAFDQKKMDWMSN+YLK+ADFE+V+ALCKPFLEEAGRLT+KAEK Sbjct: 301 EQLIALFDENRLSKSPAAFDQKKMDWMSNEYLKHADFETVYALCKPFLEEAGRLTEKAEK 36- 0 Query: 380 LVELYQPQLKSADEIVPLTDLFFADFPELTEAEKEVMAAETVPTVLSAFKEKLVSLSDEE 43- 9 LVELY+PQLKSADEI+PLTDLFF+DFPELTEAEKEVMA ETV TVL AFK KL ++SDE+ Sbjct: 361 LVELYKPQLKSADEIIPLTDLFFSDFPELTEAEKEVMAGETVSTVLQAFKAKLEAMSDED 42- 0 Query: 440 FTRDTIFPQIKAVQKETGIKGKNLFMPIRIAVSGEMHGPELPDTIYLLGKEKSVQHIDNML 5- 00 F + IFPQIKAVQKETGIKGKNLFMPIRIAVSGEMHGPELP+TIYLLG++KS++HI NML Sbjct: 421 FKPENIFPQIKAVQKETGIKGKNLFMPIRIAVSGEMHGPELPNTIYLLGRDKSIEHIKNML 4- 81 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2092 A DNA sequence (GBSx2207) was identified in S. agalactiae <SEQ ID 6477> which encodes the amino acid sequence <SEQ ID 6478>. This protein is predicted to be d-ribose-binding protein precursor, fragment (rbsB). Analysis of this protein sequence reveals the following: TABLE-US-06415 Possible site: 24 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06416 >GP: CAB15613 GB: Z99122 ribose ABC transporter (ribose-binding protein) [Bacillus subtilis] Identities = 143/301 (47%), Positives = 205/301 (67%), Gaps = 1/301 (0%) Query: 14 MSIVLILGACGKTGLGNSSGNSTKNVTKKSAKDLKLGVSISTTNNPYFVAMKDGIDKYAS 73 - +S++L L T K + K+ +G+S+ST NNP+FV++K GI+K A Sbjct: 5 VSVILTLSLFLLTACSLEPPQWAKPSNSGNKKEFTIGLSVSTLNNPFFVSLKKGIEKEAK 64 Query: 74 NKKISIKVADAQDDAARQADDVQNFISQNVDAILINPVDSKAIVTAIKSANNANIPVILM 133- + + + + DAQ+D+++Q DV++ I Q VDA+LINP DS AI TA++SAN +PV+ + Sbjct: 65 KRGMKVIIVDAQNDSSKQTSDVEDLIQQGVDALLINPTDSSAISTAVESANAVGVPVVTI 124- Query: 134 DRGSEGGKVLTTVASDNVAAGKMAADYAVKKLGKKAKAFELSGVPGASATVDRGKGFHSV 19- 3 DR +E GKV T VASDNV G+MAA + KLGK AK EL GVPGASAT +RG GFH++ Sbjct: 125 DRSAEQGKVETLVASDNVKGGEMAAAFIADKLGKGAKVAELEGVPGASATRERGSGFHNI 18- 4 Query: 194 AKSKLDILSSQSANFDRAKALNTTQNMIQGHKDVQIIFAQNDEMALGAAQAVKSAGLQNV 25- 3 A KL +++ QSA+FDR K L +N++QGH D+Q +FA NDEMALGA +A+ S+G +++ Sbjct: 185 ADQKLQVVTKQSADFDRTKGLTVMENLLQGHPDIQAVFAHNDEMALGALEAINSSG-KDI 24- 3 Query: 254 LIVGIDGQPDAHDAIKKGDISATIAQQPAKMGEIAIQAAIDYYKGKKVEKETISPIYLVTK 3- 14 L++G DG DA +IK +SAT+AQQP +G++A +AA D GKKV+K +P+ L T+ Sbjct: 244 LVIGFDGNKDALASIKDRKLSATVAQQPELIGKLATEAADDILHGKKVQKTISAPLKLETQ 3- 04 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 6478 (GBS203) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 52 (lane 12; MW 36.8 kDa). GBS203-His was purified as shown in FIG. 208, lane 8. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2093 A DNA sequence (GBSx2208) was identified in S. agalactiae <SEQ ID 6479> which encodes the amino acid sequence <SEQ ID 6480>. This protein is predicted to be galactoside ABC transporter, permease protein (rbsC). Analysis of this protein sequence reveals the following: TABLE-US-06417 Possible site: 14 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.15 Transmembrane 63-79 (52-85) INTEGRAL Likelihood = -3.66 Transmembrane 111-127 (110-128) INTEGRAL Likelihood = -2.71 Transmembrane 168-184 (168-188) INTEGRAL Likelihood = -2.44 Transmembrane 189-205 (188-205) INTEGRAL Likelihood = -0.80 Transmembrane 17-33 (17-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.5458(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9287> which encodes amino acid sequence <SEQ ID 9288> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06418 22 GP: CAB15612 GB: Z99122 ribose ABC transporter (permease) [Bacillus subtilis] Identities = 144/211 (68%), Positives = 182/211 (86%), Gaps = 1/211 (0%) Query: 1 MGMLNGLFISYGKLAPFIVTLATMTIFRGATLVYSNGNPITAGLSDSFLFQFLGQGYIVG 60 +GM+NGL I+ GK+APFI TLATMT+FRG TLVY++GNPIT GL ++ FQ G+GY +G Sbjct: 113 LGMINGLLITKGKMAPFIATLATMTVFRGLTLVYTDGNPIT-GLGTNYGFQMFGRGYFLG 17- 1 Query: 61 IPFPVILMFLTFIILYILLHKTAFGKSVYALGGNEKAAYISGIKLNKVKIIIYTISGIMA 120- IP P I M L F+IL++LLHKT FG+ YA+GGNEKAA ISGIK+ +VK++IY+++G+++ Sbjct: 172 IPVPAITMVLAFVILWVLLHKTPFGRRTYAIGGNEKAALISGIKVTRVKVMIYSLAGLLS 23- 1 Query: 121 SISGLIITSRLSSAQPTAGASYEMDAIAAVVLGGTSLSGGKGRIIGTLIGALIIGVLNNG 18- 0 +++G I+TSRL SAQPTAG SYE+DAIAAVVLGGTSLSGG+GRI+GTLIG LIIG LNNG Sbjct: 232 ALAGAILTSRLHSAQPTAGESYELDAIAAVVLGGTSLSGGRGRIVGTLIGVLIIGTLNNG 29- 1 Query: 181 LNIIGVSAFWQQVVKGIVILMAVLLDRFKVA 211 LN++GVS+F+Q VVKGIVIL+AVLLDR K A Sbjct: 292 LNLLGVSSFYQLVVKGIVILIAVLLDRKKSA 322 A related GBS gene <SEQ ID 8977> and protein <SEQ ID 8978> were also identified. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2094 A DNA sequence (GBSx2209) was identified in S. agalactiae <SEQ ID 6481> which encodes the amino acid sequence <SEQ ID 6482>. Analysis of this protein sequence reveals the following: TABLE-US-06419 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.12 Transmembrane 75-91 (74-91) INTEGRAL Likelihood = -0.64 Transmembrane 96-112 (96-112) ----- Final Results ----- bacterial membrane --- Certainty = 0.1447(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2095 A DNA sequence (GBSx2210) was identified in S. agalactiae <SEQ ID 6483> which encodes the amino acid sequence <SEQ ID 6484>. This protein is predicted to be ribose transport ATP-binding protein rbsa (rbsA). Analysis of this protein sequence reveals the following: TABLE-US-06420 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.00 Transmembrane 401-417 (401-417) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06421 >GP: CAB15611 GB: Z99122 ribose ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 297/493 (60%), Positives = 375/493 (75%), Gaps = 1/493 (0%) Query: 1 MKIDMRNISKSFGTNKVLEKIDLELQSGQIHALMGENGAGKSTLMNILTGLFPASTGTIY 60 M+I+M++I K+FG N+VL + +L G++HALMGENGAGKSTLMNILTGL A G I Sbjct: 1 MQIEMKDIHKTFGKNQVLSGVSFQLMPGEVHALMGENGAGKSTLMNILTGLHKADKGQIS 60 Query: 61 IDGEERTFSNPQEAEEFGISFIHQEMNTWPEMTVLENLFLGREIKTTFGLLNQKLMRQKA 120- I+G E FSNP+EAE+ GI+FIHQE+N WPEMTVLENLF+G+EI + G+L + M+ A Sbjct: 61 INGNETYFSNPKEAEQHGIAFIHQELNIWPEMTVLENLFIGKEISSKLGVLQTRKMKALA 120- Query: 121 LETFKRLGVTIPLDIPIGNLSVGQQQMIEIAKSLLNQLSILVMDEPTAALTDRETENLFR 18- 0 E F +L V++ LD G SVGQQQMIEIAK+L+ +++MDEPTAALT+RE LF Sbjct: 121 KEQFDKLSVSLSLDQEAGECSVGQQQMIEIAKALMTNAEVIIMDEPTAALTEREISKLFE 18- 0 Query: 181 VIRGLKQEGVGVVYISHRMEEIFKITDFVTVMRDGVIVDTKETSLTNSDELVKKMVGRKL 24- 0 VI LK+ GV +VYISHRMEEIF I D +T+MRDG VDT S T+ DE+VKKMVGR+L Sbjct: 181 VITALKKNGVSIVYISHRMEEIFAICDRITIMRDGKTVDTTNISETDFDEVVKKMVGREL 24- 0 Query: 241 EDYYPEKHSEIGPVAFEVSNL-CGDNFEDVSFYVRKGEILGFSGLMGAGRTEVMRTIFGI 29- 9 + YP++ +G FEV N +FEDVSFYVR GEI+G SGLMGAGRTE+MR +FG+ Sbjct: 241 TERYPKRTPSLGDKVFEVKNASVKGSFEDVSFYVRSGEIVGVSGLMGAGRTEMMRALFGV 30- 0 Query: 300 DKKKSGKVKIDDQEITITTPSQAIKQGIGFLTENRKDEGLILDFNIKDNMTLPSTKDFSK 35- 9 D+ +G++ I ++ I P +A+K+G+GF+TENRKDEGL+LD +I++N+ LP+ FS Sbjct: 301 DRLDTGEIWIAGKKTAIKNPQEAVKKGLGFITENRKDEGLLLDTSIRENIALPNLSSFSP 36- 0 Query: 360 HGFFDEKTSTTFVQQLINRLYIKSGRPDLEVGNLSGGNQQKVVLAKWIGIAPKVLILDEP 41- 9 G D K FV LI RL IK+ P+ +LSGGNQQKVV+AKWIGI PKVLILDEP Sbjct: 361 KGLIDHKREAEFVDLLIKRLTIKTASPETHARHLSGGNQQKVVIAKWIGIGPKVLILDEP 42- 0 Query: 420 TRGVDVGAKREIYQLMNELADRGVPIVMVSSDLPEILGVSDRIMVMHEGRISGELSRKEA 47- 9 TRGVDVGAKREIY LMNEL +RGV I+MVSS+LPEILG+SDRI+V+HEGRISGE+ +EA Sbjct: 421 TRGVDVGAKREIYTLMNELTERGVAIIMVSSELPEILGMSDRIIVVHEGRISGEIHAREA 48- 0 Query: 480 DQEKVMQLATGGK 492 QE++M LATGG+ Sbjct: 481 TQERIMTLATGGR 493 There is also homology to SEQ ID 4678. SEQ ID 6484 (GBS407d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 147 (lane 24; MW 72 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 147 (lane 5 & 6; MW 47 kDa). GBS407d-His was purified as shown in FIG. 235, lane 9-10. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2096 A DNA sequence (GBSx2211) was identified in S. agalactiae <SEQ ID 6485> which encodes the amino acid sequence <SEQ ID 6486>. This protein is predicted to be high affinity ribose transport protein rbsd (rbsD). Analysis of this protein sequence reveals the following: TABLE-US-06422 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2673(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06423 >GP: CAB15610 GB: Z99122 ribose ABC transporter (membrane protein) [Bacillus subtilis] Identities = 74/131 (56%), Positives = 95/131 (72%), Gaps = 1/131 (0%) Query: 1 MKKTGILNSHLAKLADDLGHTDRVCIGDLGLPVPNGIPKIDLSLTSGIPSFQEVLDIYLE 60 MKK GILNSHLAK+ DLGHTD++ I D GLPVP+G+ KIDLSL G+P+FQ+ + E Sbjct: 1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAE 60 Query: 61 NILVEKVILAEEIKEANPDQLSRLLAKLDNSVSIEYVSHNHLKQMTQDVKAVIRTGENTP 120- + VEKVI A EIK +N + ++ L L + IEY+SH K +T+D KAVIRTGE TP Sbjct: 61 EMAVEKVIAAAEIKASNQEN-AKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTP 119- Query: 121 YSNIILQSGVI 131 Y+N ILQ+GV+ Sbjct: 120 YANCILQAGVL 130 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2097 A DNA sequence (GBSx2212) was identified in S. agalactiae <SEQ ID 6487> which encodes the amino acid sequence <SEQ ID 6488>. This protein is predicted to be ribokinase (rbsK). Analysis of this protein sequence reveals the following: TABLE-US-06424 Possible site: 47 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-06425 >GP: CAB15609 GB: Z99122 ribokinase [Bacillus subtilis] Identities = 132/293 (45%), Positives = 177/293 (60%), Gaps = 4/293 (1%) Query: 1 MSNIVIIGSISMDLVMETNRIAKEGETVFGQRFSMVPGGKGANQAVAIGRLSQERDNITI 60 M NI +IGS SMDLV+ +++ K GETV G F VPGGKGANQAVA RL + + + Sbjct: 1 MRNICVIGSCSMDLVVTSDKRPKAGETVLGTSFQTVPGGKGANQAVAAARLGAQ---VFM 57 Query: 61 LGAIGEDSFGPILLDNLNKNHVTTDFVGTIP-SSSGVAQITLYNNDNRIIYCPGANGKVD 119- +G +G+D +G +L+NL N V TD++ + + SG A I L DN I+ GAN + Sbjct: 58 VGKVGDDHYGTAILNNLKANGVRTDYMEPVTHTESGTAHIVLAEGDNSIVVVKGANDDIT 117- Query: 120 TKKWSQEWSIIKEADLVVLQNEIPHQANMKIANFCKEHSIKLLYNPAPSRETDIEMLDKV 17- 9 I++ D+V++Q EIP + ++ +C H I ++ NPAP+R E +D Sbjct: 118 PAYALNALEQIEKVDMVLIQQEIPEETVDEVCKYCHSHDIPIILNPAPARPLKQETIDHA 17- 7 Query: 180 DYFTPNEHECQELFPNQKLEDILATYPEKLIVTLGTKGAIYSDGKESHLIPALETKAVDT 23- 9 Y TPNEHE LFP + + LA YP KL +T G +G YS G + LIP+ + VDT Sbjct: 178 TYLTPNEHEASILFPELTISEALALYPAKLFITEGKQGVRYSAGSKEVLIPSFPVEPVDT 23- 7 Query: 240 TGAGDTFNGAFGYAISKKFKIAKALRFATLAAHLSVQKFGAQGGMPTIKEMED 292 TGAGDTFN AF A+++ I ALRFA AA LSV FGAQGGMPT E+E+ Sbjct: 238 TGAGDTFNAAFAVALAEGKDIEAALRFANRAASLSVCSFGAQGGMPTRNEVEE 290 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2098 A DNA sequence (GBSx2213) was identified in S. agalactiae <SEQ ID 6489> which encodes the amino acid sequence <SEQ ID 6490>. Analysis of this protein sequence reveals the following: TABLE-US-06426 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2272(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9477> which encodes amino acid sequence <SEQ ID 9478> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06427 >GP: CAB15608 GB: Z99122 transcriptional regulator (LacI family) [Bacillus subtilis] Identities = 141/327 (43%), Positives = 204/327 (62%), Gaps = 4/327 (1%) Query: 13 MSTIRQVAEKAGVSTSTVSRYISQNGYVSQKASQKIEQAIRELHYVPNFLAQSLKTKKNQ 72 - M+TI+ VA AGVS +TVSR ++ NGYV ++ ++ A+ +L+Y PN +A+SL ++++ Sbjct: 1 MATIKDVAGAAGVSVATVSRNLNDNGYVHEETRTRVIAAMAKLNYYPNEVARSLYKRESR 60 Query: 73 LVGLLLPDISNPFFPRLARGVEEFLKEQGYRVMLGNTNNKSHLEEEYLNVLLQSNAAGII 132- L+GLLLPDI+NPFFP+LARG E+ L +GYR++ GN++ + E EYL Q++ AGII Sbjct: 61 LIGLLLPDITNPFFPQLARGAEDELNREGYRLIFGNSDEELKKELEYLQTFKQNHVAGII 120- Query: 133 --TTHDFTKNHPEIDIPVVVVDRVNQETQYGVFSDNKEGGKLAAQAIWTAGATNILLIRG 19- 0 T + + + ++ PVV +DR E V SD G KLAAQAI + I L+RG Sbjct: 121 AATNYPDLEEYSGMNYPVVFLDR-TLEGAPSVSSDGYTGVKLAAQAIIHGKSQRITLLRG 17- 9 Query: 191 PLDKADNLNQRFQGSQNYLLNKGACFAIEDSASFDFAEIQIEAKTLLDHHPDIDSIIAPS 25- 0 P RF G+ L F + ++ASF + Q AK L +P D +IA + Sbjct: 180 PA-HLPTAQDRFNGALEILKQAEVDFQVIETASFSIKDAQSMAKELFASYPATDGVIASN 23- 8 Query: 251 DIHAIAYLHEILNRGKRIPEDVQIIGYDDILMSQFIYPSLSTIHQSSYIMGQKAAELIFK 31- 0 DI A A LHE L RGK +PED+QIIGYDDI S ++P LSTI Q +Y MG++AA+L+ Sbjct: 239 DIQAAAVLHEALRRGKNVPEDIQIIGYDDIPQSGLLFPPLSTIKQPAYDMGKEAAKLLLG 29- 8 Query: 311 ITNQLPITNKRIKLPVHYVERETLRRK 337 I + P+ I++PV Y+ R+T R++ Sbjct: 299 IIKKQPLAETAIQMPVTYIGRKTTRKE 325 A related DNA sequence was identified in S. pyogenes <SEQ ID 6491> which encodes the amino acid sequence <SEQ ID 6492>. Analysis of this protein sequence reveals the following: TABLE-US-06428 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1657(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06429 Identities = 232/328 (70%), Positives = 274/328 (82%) Query: 10 GVSMSTIRQVAEKAGVSTSTVSRYISQNGYVSQKASQKIEQAIRELHYVPNFLAQSLKTK 69 - G +M TI+QVAE+AGVS STVSRYISQ GYVS A KI+ AI +LHY PN LAQSLKTK Sbjct: 14 GKAMVTIKQVAEEAGVSRSTVSRYISQKGYVSDDARHKIKAAIAKLHYTPNVLAQSLKTK 73 Query: 70 KNQLVGLLLPDISNPFFPRLARGVEEFLKEQGYRVMLGNTNNKSHLEEEYLNVLLQSNAA 129- KNQLVGLLLPDISNPFFPRLARG EE+LKE+GYRVMLGN ++ LEEEY++VLLQSNAA Sbjct: 74 KNQLVGLLLPDISNPFFPRLARGAEEYLKEKGYRVMLGNISDSEALEEEYVHVLLQSNAA 133- Query: 130 GIITTHDFTKNHPEIDIPVVVVDRVNQETQYGVFSDNKEGGKLAAQAIWTAGATNILLIR 18- 9 GIITTHDFTK +P + IPVVVVDRV+QETQYGVFSDN+ GG LAAQ +W AGA +LLIR Sbjct: 134 GIITTHDFTKRYPTLAIPVVVVDRVDQETQYGVFSDNRAGGLLAAQTVWQAGAKEVLLIR 19- 3 Query: 190 GPLDKADNLNQRFQGSQNYLLNKGACFAIEDSASFDFAEIQIEAKTLLDHHPDIDSIIAP 24- 9 GPLD A+N+N+RF+ S +YL + + DS +FDF IQ+EA L +P IQSIIAP Sbjct: 194 GPLDNAENINERFEASFSYLQKQDVTMYVCDSQNFDFESIQLEASYNLKCYPTIDSIIAP 25- 3 Query: 250 SDIHAIAYLHEILNRGKRIPEDVQIIGYDDILMSQFIYPSLSTIHQSSYIMGQKAAELIF 30- 9 SDIHAIAY+HE+ ++GK+IP+DVQIIGYDDILMSQFIYPSLSTIHQSSY+MG+ AAEL++ Sbjct: 254 SDIHAIAYIHELHSQGKKIPQDVQIIGYDDILMSQFIYPSLSTIHQSSYLMGRYAAELVY 31- 3 Query: 310 KITNQLPITNKRIKLPVHYVERETLRRK 337 I +QL + RIKLPVHYVERET+R++ Sbjct: 314 TIASQLTVKANRIKLPVHYVERETIRKR 341 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2099 A DNA sequence (GBSx2214) was identified in S. agalactiae <SEQ ID 6493> which encodes the amino acid sequence <SEQ ID 6494>. Analysis of this protein sequence reveals the following: TABLE-US-06430 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.80 Transmembrane 27-43 (24-51) INTEGRAL Likelihood = -10.61 Transmembrane 337-353 (329-362) INTEGRAL Likelihood = -9.18 Transmembrane 257-273 (249-276) INTEGRAL Likelihood = -8.92 Transmembrane 302-318 (291-326) ----- Final Results ----- bacterial membrane --- Certainty = 0.6519(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8979> which encodes amino acid sequence <SEQ ID 8980> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-06431 Lipop Possible site: -1 Crend: 6 SRCFLG: 0 McG: Length of UR: 4 Peak Value of UR: 3.20 Net Charge of CR: 1 McG: Discrim Score: 6.06 GvH: Signal Score (-7.5): 0.0500002 Possible site: 46 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition: calculated from 47 ALOM program count: 3 value: -10.61 threshold: 0.0 INTEGRAL Likelihood = -10.61 Transmembrane 326-342 (318-348) INTEGRAL Likelihood = -9.18 Transmembrane 246-262 (238-265) INTEGRAL Likelihood = -8.92 Transmembrane 291-307 (280-315) PERIPHERAL Likelihood = 4.98 152 modified ALOM score: 2.62 icml HYPID: 7 CFP: 0.525 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5246(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06432 >GP: AAF12525 GB: AE001863 hypothetical protein [Deinococcus radiodurans] Identities = 103/352 (29%), Positives = 191/352 (54%), Gaps = 9/352 (2%) Query: 15 AWKELTFYKKKYLLIELLIIVMMFMVVFLSGLANGLGRAVSAAIENNPAQTYILNEGAEQ 74 - A +EL K + LLI ++ ++ FMV L+GL GL R ++ + + PAQ+++ + A+ Sbjct: 4 ALRELQHQKLRSLLIGGIVALIAFMVFMLTGLTRGLSRDSASLLLDTPAQSFVTTKEADG 63 Query: 75 VITSSVLTTKDQTDLNSLNLKDSTTLNIQRSSLTRQGHEKKIDISYFAIDKDSFMAPTLS 134- V+ S L+ + +++L + ++ ++ +K++ +D F+AP +S Sbjct: 64 VLNRSFLSPEQ---VSALQQDNEDAAAFAQTFVSFSHGDKQLSGVLLGVDPRGFLAPDVS 120- Query: 135 EGKQLTSYKKAIILNDSLKAEGIKLGDKVIDKSSSISLTVVGFVHNSMYGHGPVAFIDKD 19- 4 EG+ L A++ ++SL+ +G+K+GD + K S L V GF ++ H P ++ Sbjct: 121 EGQTLRVAGGAVV-DESLREDGVKVGDVLTLKPSGDQLRVSGFTRSARLNHQPGMYVSLA 17- 9 Query: 195 IYTEINKKINPQYQFLPQALVMKNDKSISHLP-TQLEAVSKKDVIQHIPGYSAEQSTLNM 25- 3 + +K+NP+ A+ + + +L L ++ +Q +PGY EQ +L M Sbjct: 180 RW----QKLNPRMHGTVNAVALPAAPAQVNLGGADLSVTNRAQTLQVLPGYKEEQGSLTM 23- 5 Query: 254 ILWVLVVASAGILGVFFYIITLQKRHEFSVMKAIGTKMSEIALFQLSQVIILALFGIIVG 31- 3 I L+ +A +L FFY++TLQK +F ++KAIG +A ++Q++IL L + + Sbjct: 236 IQVFLIAVAAFVLATFFYVMTLQKTAQFGLLKAIGASNRTLAGSVVAQMLILTLLAVAIA 29- 5 Query: 314 DGLAVALSYVLPAQMPFVINWQNIILVSFVFLVIAMISSALSIVKVAKIDPV 365 + + + +LPA MPF + NI S + LV+A ++S LS+ +VAK+DP+ Sbjct: 296 AAVTLGMVQLLPAGMPFHLTAANIASASGLLLVVAALASLLSVRRVAKVDPL 347 A related DNA sequence was identified in S. pyogenes <SEQ ID 6495> which encodes the amino acid sequence <SEQ ID 6496>. Analysis of this protein sequence reveals the following: TABLE-US-06433 Possible site: 58 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.31 Transmembrane 246-262 (233-270) INTEGRAL Likelihood = -8.49 Transmembrane 327-343 (321-351) INTEGRAL Likelihood = -1.01 Transmembrane 301-317 (301-317) ----- Final Results ----- bacterial membrane --- Certainty = 0.5925(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06434 >GP: AAF12525 GB: AE001863 hypothetical protein [Deinococcus radiodurans] Identities = 101/360 (28%), Positives = 175/360 (48%), Gaps = 11/360 (3%) Query: 1 MFLALNEMKQSKLRYGLIAGLLCLVAYLMFFLSGLAFGLMQENRSAVDLWKADSVLLAKD 60 M+LAL E++ KLR LI G++ L+A+++F L+GL GL +++ S + A S + K+ Sbjct: 1 MYLALRELQHQKLRSLLIGGIVALIAFMVFMLTGLTRGLSRDSASLLLDTPAQSFVTTKE 60 Query: 61 ADATLTLSQVSRAQENQITADKVAPLAQLNTVAWSVKNPKDADKVKVSLFGIDSNSFIRP 120- AD L S +S Q + + D A T K V L G+D F+ P Sbjct: 61 ADGVLNRSFLSPEQVSALQQDNEDAAAFAQTFVSFSHGDKQLSGV---LLGVDPRGFLAP 117- Query: 121 NIVKGRLFKTNKEVVLDQSLAKEEAFAIGKDFYTSSSSQALTIVGYTQNARFSVAPVVYM 18- 0 ++ +G+ + V+D+SL +E+ +G S L + G+T++AR + P +Y+ Sbjct: 118 DVSEGQTLRVAGGAVVDESL-REDGVKVGDVLTLKPSGDQLRVSGFTRSARLNHQPGMYV 17- 6 Query: 181 NLEAFETLKYGEPLPKDKQVVNAFITKGS--LTDYPKKDFQKLDIKTFITKLPGYSAQLL 23- 8 +L ++ L P+ VNA + + D + + LPGY + Sbjct: 177 SLARWQKLN-----PRMHGTVNAVALPAAPAQVNLGGADLSVTNRAQTLQVLPGYKEEQG 23- 1 Query: 239 TFGFMISFLVIISAIIIGIFMYILTIQKAPIFGIMKAQGISNKTITTAVLMQTFFLSFLG 29- 8 + + FL+ ++A ++ F Y++T+QK FG++KA G SN+T+ +V+ Q L+ L Sbjct: 232 SLTMIQVFLIAVAAFVLATFFYVMTLQKTAQFGLLKAIGASNRTLAGSVVAQMLILTLLA 29- 1 Query: 299 SGLGLLGTWLTSLLLPTVVPFQSNWFLYLAIFVSMICFALLGTLFSVFNIIRIDPLKAIG 35- 8 + T LLP +PF + ++ A L +L SV + ++DPL A+G Sbjct: 292 VAIAAAVTLGMVQLLPAGMPFHLTAANIASASGLLLVVAALASLLSVRRVAKVDPLIALG 35- 1 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06435 Identities = 96/356 (26%), Positives = 178/356 (49%), Gaps = 4/356 (1%) Query: 15 AWKELTFYKKKYLLIELLIIVMMFMVVFLSGLANGLGRAVSAAIENNPAQTYILNEGAEQ 74 - A E+ K +Y LI L+ ++ +++ FLSGLA GL + +A++ A + +L + A+ Sbjct: 4 ALNEMKQSKLRYGLIAGLLCLVAYLMFFLSGLAFGLMQENRSAVDLWKADSVLLAKDADA 63 Query: 75 VITSSVLTTKDQTDLNSLNLKDSTTLNIQRSSLTRQGHEKKIDISYFAIDKDSFMAPTLS 134- +T S ++ + + + + LN S+ K+ +S F ID +SF+ P + Sbjct: 64 TLTLSQVSRAQENQITADKVAPLAQLNTVAWSVKNPKDADKVKVSLFGIDSNSFIRPNIV 123- Query: 135 EGKQLTSYKKAIILNDSLKAEGIKLGDKVIDKSSSISLTVVGFVHNSMYGHGPVAFIDKD 19- 4 +G+ + K+ ++ K E +G SSS +LT+VG+ N+ + PV +++ + Sbjct: 124 KGRLFKTNKEVVLDQSLAKEEAFAIGKDFYTSSSSQALTIVGYTQNARFSVAPVVYMNLE 18- 3 Query: 195 IYTEIN-KKINPQYQFLPQALVMKNDKSISHLPTQ-LEAVSKKDVIQHIPGYSAEQSTLN 25- 2 + + + P+ + + A + K S++ P + + + K I +PGYSA+ T Sbjct: 184 AFETLKYGEPLPKDKQVVNAFITKG--SLTDYPKKDFQKLDIKTFITKLPGYSAQLLTFG 24- 1 Query: 253 MILWVLVVASAGILGVFFYIITLQKRHEFSVMKAIGTKMSEIALFQLSQVIILALFGIIV 31- 2 ++ LV+ SA I+G+F YI+T+QK F +MKA G I L Q L+ G + Sbjct: 242 FMISFLVIISAIIIGIFMYILTIQKAPIFGIMKAQGISNKTITTAVLMQTFFLSFLGSGL 30- 1 Query: 313 GDGLAVALSYVLPAQMPFVINWQNIILVSFVFLVIAMISSALSIVKVAKIDPVEVI 368 G S +LP +PF NW + + + A++ + S+ + +IDP++ I Sbjct: 302 GLLGTWLTSLLLPTVVPFQSNWFLYLAIFVSMICFALLGTLFSVFNIIRIDPLKAI 357 SEQ ID 8980 (GBS239) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 175 (lane 13; MW 64 kDa). GBS239-GST was purified as shown in FIG. 227, lane 4. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2100 A DNA sequence (GBSx2215) was identified in S. agalactiae <SEQ ID 6497> which encodes the amino acid sequence <SEQ ID 6498>. This protein is predicted to be heterocyst maturation protein (devA) (b0879). Analysis of this protein sequence reveals the following: TABLE-US-06436 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1751(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06437 >GP: CAA05977 GB: AJ003195 ATP-binding subunit [Anabaena variabilis] Identities = 87/225 (38%), Positives = 146/225 (64%), Gaps = 1/225 (0%) Query: 3 AILELKHISKHYPDGDELLSILDNLDLSVSAGEFVAILGPSGSGKSTLLSIAGLLLGADQ 62 A++ +K ++ +Y G IL +++L + GE V + GPSGSGK+TLLS+ G L + Sbjct: 5 AVIAIKSLNHYYGKGALKRQILFDINLEIYPGEIVIMTGPSGSGKTTLLSLIGGLRSVQE 64 Query: 63 GSLYVNHENVTDLSQRQRTQLRREALGFIFQSHQLLPYLTIQEQLQQEARFAKHYDKKTS 122- G+L ++ SQ + Q+RR ++G+IFQ+H LL +LT ++ +Q +H ++ + Sbjct: 65 GNLQFLGVELSGASQNKLVQIRR-SIGYIFQAHNLLGFLTARQNVQMAVELNEHISQEEA 123- Query: 123 LEEINKLLSDLGIEQCAHKYPNQLSGGQKQRAAIARAFINHPKVILADEPTASLDEERGR 18- 2 + + +L +G+E YP+ LSGGQKQR AIARA +N+P ++LADEPTA+LD++ GR Sbjct: 124 IAKAEAMLKAVGLENRVDYYPDNLSGGQKQRVAIARALVNNPPLVLADEPTAALDKQSGR 18- 3 Query: 183 QVTELIRQEVKSHNTAAIMVTHDERVLDLVDTVYRLKDGKLVKEN 227 V E++++ K T+ ++VTHD R+LD+ D + ++DG L +++ Sbjct: 184 DVVEIMQRLAKDQGTSILLVTHDNRILDIADRIVEMEDGILARDS 228 A related DNA sequence was identified in S. pyogenes <SEQ ID 6499> which encodes the amino acid sequence <SEQ ID 6500>. Analysis of this protein sequence reveals the following: TABLE-US-06438 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4181(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06439 Identities = 103/224 (45%), Positives = 149/224 (65%), Gaps = 4/224 (1%) Query: 3 AILELKHISKHYPDGDELLSILDNLDLSVSAGEFVAILGPSGSGKSTLLSIAGLLLGADQ 62 ++L K ++K + DG ++ L D S+ AGEFVAI+GPSGSGKST L+IAG L Sbjct: 3 SVLTFKQVTKTFQDGHHEINALKATDFSIEAGEFVAIIGPSGSGKSTFLTIAGGLQTPSS 62 Query: 63 GSLYVNHENVTDLSQRQRTQLRREALGFIFQSHQLLPYLTIQEQLQQEARFAKHYDKKTS 122- G L ++ + T LS+++R++LR +++GFI Q+ L+P+ T+Q+QL+ H Sbjct: 63 GQLIIDGTDYTHLSEKERSRLRFKSVGFILQASNLIPFSTVQQQLE----LVDHLTGSKE 118- Query: 123 LEEINKLLSDLGIEQCAHKYPNQLSGGQKQRAAIARAFINHPKVILADEPTASLDEERGR 18- 2 + N+L DLGI H+ P +LSGG++QRAAIARA + P +ILADEPTASLD E+ Sbjct: 119 KAKANQLFDDLGITGLKHQLPQELSGGERQRAAIARALYHDPALILADEPTASLDTEKAY 17- 8 Query: 183 QVTELIRQEVKSHNTAAIMVTHDERVLDLVDTVYRLKDGKLVKE 226 +V +L+ +E K N A IMVTHD+R+L D VYR++DG+L +E Sbjct: 179 EVVKLLAKESKEKNKAIIMVTHDDRMLKYCDKVYRMQDGELCQE 222 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2101 A DNA sequence (GBSx2216) was identified in S. agalactiae <SEQ ID 6501> which encodes the amino acid sequence <SEQ ID 6502>. Analysis of this protein sequence reveals the following: TABLE-US-06440 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2645(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06441 >GP: CAB64972 GB: AJ012050 VicR protein [Enterococcus faecalis] Identities = 86/229 (37%), Positives = 132/229 (57%), Gaps = 10/229 (4%) Query: 3 KILVVEDNIVQQKIITTKLTQEGYQFITASNGQEALNCLDTEEVQLIITDIMMPMMDGYQ 62 KILVV+D +I+ L +EGY+ TA +G+EAL ++ E LII D+M+P MDG + Sbjct: 52 KILVVDDEKPISEIVKYNLVKEGYEVFTAYDGEEALEKVEEVEPDLIILDLMLPKMDGLE 111- Query: 63 LIQELRSAAYNVPIIVMTAKSQMEDMTKGFGLGADDYMVKPVQLQELALRIKALLRR--- 119- + +E+R +++PII++TAK D G LGADDY+ KP +EL R+KA LRR Sbjct: 112 VAREVRK-THDMPIIMVTAKDSEIDKVLGLELGADDYVTKPFSNRELVARVKANLRRGAT 17- 0 Query: 120 ----ANIVAQHQLIIGNTCLNEDELSLKYFEQEIIFPQKEFRVLFHLLSYPNRIFTRLEL 17- 5 A + Q +L IG+ ++ D + ++I +EF +L++L + ++ TR L Sbjct: 171 NAKEAEVTTQSELTIGDLTIHPDAYMVSKRGEKIELTHREFELLYYLAKHIGQVMTREHL 23- 0 Query: 176 LDSIWGMDTDLDERVVDACINKIRRKVEHLPDFK--IETVRGVGYRAKN 222 L ++WG D D R VD + ++R K+E P + T RGVGY +N Sbjct: 231 LQTVWGYDYFGDVRTVDVTVRRLREKIEDSPSHPTYLVTRRGVGYYLRN 279 There is also homology to SEQ ID 1182. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2102 A DNA sequence (GBSx2217) was identified in S. agalactiae <SEQ ID 6503> which encodes the amino acid sequence <SEQ ID 6504>. This protein is predicted to be sensor protein. Analysis of this protein sequence reveals the following:

TABLE-US-06442 Possible site: 38 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.97 Transmembrane 53-69 (47-77) ----- Final Results ----- bacterial membrane --- Certainty = 0.4588(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06443 >GP: AAC62214 GB: AF049873 sensor protein [Lactococcus lactis] Identities = 97/307 (31%), Positives = 169/307 (54%), Gaps = 16/307 (5%) Query: 57 SALAVVFLSLVIASISMWYGSYHLTKPILDISHIVSNVADGDFEGHIYRNSNRRKSYEYY 11- 6 + LAV+ +L++ + S++Y + +T+P+L I +A GD + N+ Sbjct: 170 AVLAVI--TLIVTAFSIFYITRTVTRPLLKIKLGTDKIAQGDLSIQLNVNTE-------- 21- 9 Query: 117 NELDELSESINQMIVSLSHMDHMRKDFITNVSHELKTPIAAVANIVELLQDPELDEETQS 17- 6 +EL EL++SI + L M R +F+++V+HEL+TP+ + ++ E ++ Sbjct: 220 DELGELAKSIEDLAEKLDFMKRERNEFLSSVAHELRTPLTFIKGYADIANRSTTSLEDKT 27- 9 Query: 177 ELLGLVKTESLRLTRLCDTMLQMSRVDNQETIGELSSVRVDEQIRQAMISLTERWQAKRI 23- 6 + L +++ ES LT+L + ++ +++++ E V + E I + + ++ + KRI Sbjct: 280 QYLRIIREESRHLTQLMEDLMNLAQLEENGFKVEKHQVLIQELINEVVSKVSGVFSEKRI 33- 9 Query: 237 NFQLDSKPYTVYSNSDLLM--QVWINLLDNAIKYSEDIVDLSVRMEETNNHYLRVIISDK 29- 4 NF L S Y+N D + QV +NLL NA KYS D D+ + ++ +++ISDK Sbjct: 340 NF-LISGEGNFYANIDFMRIEQVLVNLLMNAYKYSADESDIKLAFIPEKENF-KIVISDK 39- 7 Query: 295 GRGISQYDVQHIFDKFYQADQSHNQQ--GNGLGLAIVKRIIVLCKGRISVSSQLEIGTEF 35- 2 G GI + D+ +IF++FY+ D+S + G GLGLAIV+ I+ G+I V S GT F Sbjct: 398 GEGIPEQDLPYIFERFYRVDKSRTRTTGGVGLGLAIVQDIVKKHNGKIIVESIQNQGTTF 45- 7 Query: 353 CVELPLS 359 +ELP S Sbjct: 458 IIELPYS 464 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8981> and protein <SEQ ID 8982> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06444 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 4.84 GvH: Signal Score (-7.5): 0.179999 Possible site: 35 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 1 value: -8.97 threshold: 0.0 INTEGRAL Likelihood = -8.97 Transmembrane 50-66 (47-77) PERIPHERAL Likelihood = 1.27 324 modified ALOM score: 2.29 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4588(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00154## SEQ ID 8982 (GBS170d) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 181 (lane 4; MW 35 kDa) and in FIG. 123 (lane 5-7; MW 35 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 123 (lane 24; MW 60 kDa) and in FIG. 184 (lane 3; MW 60 kDa). Purified GBS170d-GST is shown in FIG. 243, lane 7; purified GBS170d-His is shown in FIG. 234, lanes 5-6. EXAMPLE 2103 A DNA sequence (GBSx2218) was identified in S. agalactiae <SEQ ID 6505> which encodes the amino acid sequence <SEQ ID 6506>. Analysis of this protein sequence reveals the following: TABLE-US-06445 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0502(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06446 >GP: BAB06906 GB: AP001518 argininosuccinate synthase [citrulline-asparate ligase) [Bacillus halodurans] Identities = 262/396 (66%), Positives = 321/396 (80%), Gaps = 1/396 (0%) Query: 1 MGKEKLILAYSGGLDTSVAIAWLK-KDYDVIAVCMDVGEGKDLDFIHDKALTIGAIESYI 59- M K+K++LAYSGGLDTSVAI WL K YDVIAV +DVGEGKDL+F+ +KAL +GAIESY Sbjct: 1 MSKKKVVLAYSGGLDTSVAIKWLSDKGYDVIAVGLDVGEGKDLEFVKEKALKVGAIESYT 60- Query: 60 LDVKDEFAEHFVLPALQAHAMYEQKYPLVSALSRPIIAQKLVEMAHQTGATTIAHGCTGK 11- 9 +D K EFAE FVLPALQAHA+YEQKYPLVSALSRP+I++KLVE+A QTGA +AHGCTGK Sbjct: 61 IDAKKEFAEEFVLPALQAHALYEQKYPLVSALSRPLISKKLVEIAEQTGAQAVAHGCTGK 12- 0 Query: 120 GNDQVRFEVAIAALDPELKVIAPVREWKWHREEEITFAKANGVPIPADLDNPYSIDQNLW 17- 9 GNDQVRFEV+I AL+P L+V+APVREW W R+EEI +AK N +PIP DLDNPYS+DQNLW Sbjct: 121 GNDQVRFEVSIQALNPNLEVLAPVREWAWSRDEEIEYAKKNNIPIPIDLDNPYSVDQNLW 18- 0 Query: 180 GRANECGVLENPWNQAPEEAFGITKSPEEAPDCAEYIDITFQNGKPIAINNQEMTLADLI 23- 9 GR+NECG+LE+PW PE A+ +T + E+APD E ++I F+ G P+ +N + + +LI Sbjct: 181 GRSNECGILEDPWATPPEGAYELTVAIEDAPDQPEIVEIGFEKGIPVTLNGKSYPVHELI 24- 0 Query: 240 LSLNEIAGKHGIGRIDHVENRLVGIKSREIYECPAAMVLLAAHKEIEDLTLVREVSHFKP 29- 9 L LN+IAGKHG+GRIDHVENRLVGIKSRE+YECP AM L+ AHKE+EDLTL +EV+HFKP Sbjct: 241 LELNQIAGKHGVGRIDHVENRLVGIKSREVYECPGAMTLIKAHKELEDLTLTKEVAHFKP 30- 0 Query: 300 ILENELSNLIYNALWFSPATKAIIAYVKETQKVVNGTTKVKLYKGSAQVVARHSSNSLYD 35- 9 ++E +++ LIY LWFSP A+ A++KETQ V G +VKL+KG A V R S SLY+ Sbjct: 301 VVEKKIAELIYEGLWFSPLQPALSAFLKETQSTVTGVVRVKLFKGHAIVEGRKSEYSLYN 36- 0 Query: 360 ENLATYTAADSFDQDAAVGFIKLWGLPTQVNAQVNK 395 E LATYT D FD +AAVGFI LWGLPT+V + VNK Sbjct: 361 EKLATYTPDDEFDHNAAVGFISLWGLPTKVYSMVNK 396 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2104 A DNA sequence (GBSx2219) was identified in S. agalactiae <SEQ ID 6507> which encodes the amino acid sequence <SEQ ID 6508>. This protein is predicted to be argininosuccinate lyase (argH). Analysis of this protein sequence reveals the following: TABLE-US-06447 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2131(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06448 >GP: BAB06905 GB: AP001518 argininosuccinate lyase [Bacillus halodurans] Identities = 284/454 (62%), Positives = 350/454 (76%) Query: 6 KLWGGRFESSLEKWVEEFGASISFDQKLAPYDMKASMAHVTMLGKTDIISQEEAGLIKDG 65- KLWGGRF + E WV+EFGASI FDQ+L D++ S+AHVTML K+ I++ EE IK G Sbjct: 3 KLWGGRFTKTAEAWVDEFGASIGFDQQLVEEDIEGSLAHVTMLEKSGILANEEVEQIKKG 62- Query: 66 LKILQDKYRAGQLTFSISNEDIHMNIESLLTAEIGEVAGKLHTARSRNDQVATDMHLYLK 12- 5 L IL +K + G+L +S++NEDIH+NIE LL EIG V GKLHT RSRNDQVATDMHLYL+ Sbjct: 63 LHILLEKAKKGELNYSVANEDIHLNIEKLLIDEIGPVGGKLHTGRSRNDQVATDMHLYLR 12- 2 Query: 126 DKLQEMMKKLLHLRTTLVNLAENHIYTVMPGYTHLQHAQPISFGHHLMAYYNMFTRDTER 18- 5 + +E+++ + +++ LV A+ H+ T++PGYTHLQ AQPISF HHL+AY+ M RD R Sbjct: 123 KQTKEILQLVKNVQAALVEQAKQHVETLIPGYTHLQRAQPISFAHHLLAYFWMLERDYGR 18- 2 Query: 186 LEFNMKHTNLSPLGAAALAGTTFPIDRHMTTRLLDFEKPYSNSLDAVSDRDFIIEFLSNA 24- 5 E ++K N+SPLGA ALAGTTFPIDR T LL F+ Y NSLDAVSDRDFI+EFLS + Sbjct: 183 YEDSLKRLNVSPLGAGALAGTTFPIDREYTAELLGFDGIYENSLDAVSDRDFIVEFLSAS 24- 2 Query: 246 SILMMHLSRFCEEIINWCSYEYQFITLSDTFSTGSSIMPQKKNPDMAELIRGKTGRVYGN 30- 5 S+LM HLSR CEE+I W S E+QF+ + D F+TGSSIMPQKKNPDMAELIRGKTGRVYG+ Sbjct: 243 SLLMTHLSRLCEELILWSSQEFQFVEMDDAFATGSSIMPQKKNPDMAELIRGKTGRVYGS 30- 2 Query: 306 LFSLLTVMKSLPLAYNKDLQEDKEGMFDSVETVSIAIEIMANMLETMTVNEHIMMTSTET 36- 5 LFSLLTV+K LPLAYNKD+QEDKEGMFD+V+TV ++ I A M++TM V E M + Sbjct: 303 LFSLLTVLKGLPLAYNKDMQEDKEGMFDAVKTVKGSLAIFAGMIQTMKVKEETMTKAVHQ 36- 2 Query: 366 DFSNATELADYLASKGVPFRKAHEIVGKLVLECSKNGSYLQDIPLKYYQEISELIENDIY 42- 5 DFSNATELADYLA+KG+PFR+AHE+VGKLVL C + G YL D+PL Y+ S+L + DIY Sbjct: 363 DFSNATELADYLATKGMPFREAHEVVGKLVLLCIQKGIYLLDLPLSDYKAASDLFDEDIY 42- 2 Query: 426 EILTAKTAVKRRNSLGGTGFDQVKKQILLARKEL 459 ++L KT V RR S GGTGF +VKK I A K L Sbjct: 423 DVLQPKTVVARRTSAGGTGFTEVKKAIAKAEKIL 456 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2105 A DNA sequence (GBSx2220) was identified in S. agalactiae <SEQ ID 6509> which encodes the amino acid sequence <SEQ ID 6510>. This protein is predicted to be class-II aldolase (fba). Analysis of this protein sequence reveals the following: TABLE-US-06449 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2930(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9289> which encodes amino acid sequence <SEQ ID 9290> was also identified. Analysis of this sequence reveals: TABLE-US-06450 GvH: Signal Score (-7.5): -2.92 Possible site: 42 >>> Seems to have no N-terminal signal seq. ALOM program count: 0 value: 0.37 threshold: 0.0 PERIPHERAL Likelihood = 0.37 66 modified ALOM score: -0.57 *** Reasoning Step: 3 ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2930(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06451 >GP:BAB16889 GB:AB050113 class-II aldolase [Streptococcus bovis] Identities = 221/242 (91%), Positives = 234/242 (96%) Query: 1 MAIVSAEKFVQAARDNGYAVGGFNTNNLEWTQAILRAAEAKKAPVLIQTSMGAAKYMGGY 60 MAIVSAEKF++AAR+NGYAVGGFNTNNLEWTQAILRAAEAKKAP+LIQTSMGAAKYMGGY Sbjct: 1 MAIVSAEKFIKAARENGYAVGGFNTNNLEWTQAILRAAEAKKAPILIQTSMGAAKYMGGY 60 Query: 61 KLCKQLIETLVESMGITVPVAIHLDHGHYDDALECIEVGYTSIMFDGSHLPVEENLEKAR 120- KLCK LIE LVESMGITVPVAIHLDHGH++DALECIEVGYTS+MFDGSHLPVEENLEKA+ Sbjct: 61 KLCKTLIENLVESNGITVPVAIHLDHGHFEDALECIEVGYTSVMFDGSHLPVEENLEKAK 120- Query: 121 EVVAKAHAKGISVEAEVGTIGGEEDGIVGKGELAPIEDAKAMVETGIDFLAAGIGNIHGP 18- 0 EVVAKAHAKG+SVEAEVGTIGGEEDGIVG GELAPIEDAKANV TGIDFLAAGIGNIHGP Sbjct: 121 EVVAKAHAKGVSVEAEVGTIGGEEDGIVGGGELAPIEDAKAMVATGIDFLAAGIGNIHGP 18- 0 Query: 181 YPANWEGLDLDHLKKLTEAVPGFPIVLHGGSGIPDDQIQEAIKLGVAKVNVNTECQLAFC 24- 0 YPANW+GL LDHLKKLT AVPGFPIVLHGGSGIPDDQI+ AIKLGVAKVNVNTECQ+AF Sbjct: 181 YPANWQGLHLDHLKKLTAAVPGFPIVLHGGSGIPDDQIKAAIKLGVAKVNVNTECQIAFA 24- 0 Query: 241 QA 242 +A Sbjct: 241 KA 242 A related DNA sequence was identified in S. pyogenes <SEQ ID 6511> which encodes the amino acid sequence <SEQ ID 6512>. Analysis of this protein sequence reveals the following: TABLE-US-06452 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2930(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06453 Identities = 217/242 (89%), Positives = 228/242 (93%) Query: 1 MAIVSAEKFVQAARDNGYAVGGFNTNNLEWTQAILRAAEAKKAPVLIQTSMGAAKYMGGY 60 MAIVSAEKFVQAAR+NGYAVGGFNTNNLEWTQAILRAAEAK+APVLIQTSMGAAKYMGGY Sbjct: 1 MAIVSAEKFVQAARENGYAVGGFNTNNLEWTQAILRAAEAKQAPVLIQTSMGAAKYMGGY 60 Query: 61 KLCKQLIETLVESHGITVPVAIHLDHGHYDDALECIEVGYTSIMFDGSHLPVEENLEKAR 120- K+C+ LI LVESMGITVPVAIHLDHGHY+DALECIEVGYTSIMFDGSHLPVEENL K Sbjct: 61 KVCQSLITNLVESMGITVPVAIHLDHGHYEDALECIEVGYTSIMFDGSHLPVEENLAKTA 120- Query: 121 EVVAKAHAKGISVEAEVGTIGGEEDGIVGKGELAPIEDAKAMVETGIDFLAAGIGNIHGP 18- 0 EVV AHAKG+SVEAEVGTIGGEEDGI+GKGELAPIEDAKAMVETGIDFLAAGIGNIHGP Sbjct: 121 EVVKIAHAKGVSVEAEVGTIGGEEDGIIGKGELAPIEDAKAMVETGIDFLAAGIGNIHGP 18- 0 Query: 181 YPANWEGLDLDHLKKLTEAVPGFPIVLHGGSGIPDDQIQEAIKLGVAKVNVNTECQLAFC 24- 0 YP NWEGL LDHL+KLT AVPGFPIVLHGGSGIPDDQI+EAI+LGVAKVNVNTE Q+AF Sbjct: 181 YPENWEGLALDHLEKLTAAVPGFPIVLHGGSGIPDDQIKEAIRLGVAKVNVNTESQIAFS 24- 0 Query: 241 QA 242 A Sbjct: 241 NA 242 SEQ ID 9290 (GBS683) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 150 (lane 8 & 10; MW 55 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 150 (lane 11-13; MW 30 kDa) and in FIG. 184 (lane 11; MW 30 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2106 A DNA sequence (GBSx2221) was identified in S. agalactiae <SEQ ID 6513> which encodes the amino acid sequence <SEQ ID 6514>. Analysis of this protein sequence reveals the following: TABLE-US-06454 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2775(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06455 >GP:AAA88585 GB:M18954 unknown protein [Streptococcus mutans] Identities = 109/229 (47%), Positives = 156/229 (67%), Gaps = 1/229 (0%) Query: 1 MFSGKRLKKRRITLGYSQSELADKLHINRSSYFNWENEKTKPNQSNLKQLAILLDVPETY 60 MFS ++LK+RR LG SQ++ ADKL I+R SYFNWE KTKPNQ NL +LA LL V Y Sbjct: 1 MFSSQKLKERRKKLGLSQAQTADKLGISRPSYFNWEIGKTKPNQKNLDKLAHLLKVDSAY 60 Query: 61 FESEYKIVNTYLQLSLQNQEKVEKYAEELLQTQKVHEKIVPLFAVEVLSEIQLSAGPGEG 120- F S++ IV Y +L+ N+ K KY++ LL+ Q ++ +LSAG G Sbjct: 61 FLSQHDIVEIYTRLNESNKTKTLKYSQHLLEQQDKKRNLMKNKRYPYRVYEKLSAGTGYS 120- Query: 121 LYDEFETETVYSEDEYTGFDIATWISGNSMEPVYKDGEVALIRSTGFDHDGAVYALNWNG 18- 0 + + +TV+ ++E D A+WI G+SMEP++ +GEVALI+ TGFD+DGA+YA++W+G Sbjct: 121 YFGDGNFDTVFYDEEID-HDFASWIFGDSMEPIFLNGEVALIKQTGFDYDGAIYAIDWDG 17- 9 Query: 181 SLYIKKLYREEDGFRMVSINPDVAERFIPFEDEIRIVGKIVGHFMPVIG 229 YIKK+YREE G R+VS+N A++F P+++ RI+G IVG+F+P+ G Sbjct: 180 QTYIKKVYREETGLRLVSLNKKYADKFAPYDENPRIIGLIVGNFIPLEG 228 A related DNA sequence was identified in S. pyogenes <SEQ ID 6515> which encodes the amino acid sequence <SEQ ID 6516>. Analysis of this protein sequence reveals the following: TABLE-US-06456 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4340(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06457 Identities = 84/209 (40%), Positives = 130/209 (62%), Gaps = 9/209 (4%) Query: 25 LHINRSSYFNWENEKTKPNQSNLKQLAILLDVPETYFESEYKIVNTYLQLSLQNQEKVEK 64 - LH+N+ + NWE K PN+ +L L L +V YF+ Y+++ Y QL++ N+EKV Sbjct: 5 LHVNKMTISNWEKGKNIPNEKHLNALLHLFNVTSDYFDPNYRLLTPYNQLTISNKEKVIG 84 Query: 85 YAEELLQTQ------KVHEKIVPLFAVEVLSEIQLSAGPGEGLYDEFETETVYSEDEYTG 138- Y+E LL Q + +K L+A V LSAG G + + + V+ DE Sbjct: 65 YSERLLNHQIDKKSKDLIDKPSQLYAYRVYES--LSAGTGYSYFGDGNFDVVFY-DEQLE 121- Query: 139 FDIATWISGNSMEPVYKDGEVALIRSTGFDHDGAVYALNWNGSLYIKKLYREEDGFRMVS 19- 8 +D A+W+ G+SMEP Y +GEV LI+ FD+DGA+YA+ W+G YIKK++RE++G R+VS Sbjct: 122 YDFASWVFGDSMEPTYLNGEVVLIKQNSFDYDGAIYAVEWDGQTYIKKVFREDEGLRLVS 18- 1 Query: 199 INPDVAERFIPFEDEIRIVGKIVGHFMPV 227 +N +++F P+ +E RI+GKI+ +F P+ Sbjct: 182 LNKKYSDKFAPYSEEPRIIGKIIANFRPL 210 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2107 A DNA sequence (GBSx2222) was identified in S. agalactiae <SEQ ID 6517> which encodes the amino acid sequence <SEQ ID 6518>. Analysis of this protein sequence reveals the following: TABLE-US-06458 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2387(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) <succ> bacterial outside --- Certainty = 0.0000(Not Clear) <succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2108 A DNA sequence (GBSx2223) was identified in S. agalactiae <SEQ ID 6519> which encodes the amino acid sequence <SEQ ID 6520>. This protein is predicted to be UmuC MucB homolog (uvrX). Analysis of this protein sequence reveals the following:

TABLE-US-06459 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2195(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9925> which encodes amino acid sequence <SEQ ID 9926> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06460 >GP:AAC98439 GB:L29324 UmuC MucB homolog [Streptococcus pneumoniae] Identities = 303/436 (69%), Positives = 360/436 (82%) Query: 39 LHTSLCVMSRADNSAGLILASSPMFKKVFGKGNVGRAYDLPFDVHTRKFNYYRAKISGLP 98 - L LCVMSRADNSAGLILASSPMFKKVFGK NVGR+YDLPFDV TRKF+YY AK GLP Sbjct: 5 LRLRLCVMSRADNSAGLILASSPMFKKVFGKSNVGRSYDLPFDVKTRKFSYYNAKKQGLP 64 Query: 99 TDAKFVSFIENWAKRTFIVPPRMDLYIQKNLEIQKVFQNYADPTDILPYSIDEGFIDLTS 158- T +V +IE WAK T IVP L I N+EIQK+FQ++A P DI PYSIDEGFIDLTS Sbjct: 65 TTIDYVRYIEEWAKSTVIVPREWILTIAVNMEIQKIFQDFAAPDDIYPYSIDEGFIDLTS 124- Query: 159 SLNYFVEDKSLSRKDKLDVVSAKIQHDIWEKTGVYSTVGMSNANPLLAKLALDNEAKTTA 21- 8 SLNYFV DKS+SRKDKLD++SA IQ IW KTG+YSTVGMSNANPLLAKLALDNEAK T Sbjct: 125 SLNYFVPDKSISRKDKLDIISAAIQKKIWRKTGIYSTVGMSNANPLLAKLALDNEAKKTP 18- 4 Query: 219 TMRANWSYEDVETKVWNIPKMTDFWGIGSRTEKRLNKLGIYSIKELANCDPTILKKEFGV 27- 8 TMRANWSYEDVE KVW IPKMTDFWGIG+R EKRL+ LGI+SIKELA +P ++KKE G+ Sbjct: 185 TMRANWSYEDVEKKVWTIPKMTDFWGIGNRMEKRLHNLGIFSIKELAQANPDLIKKELGI 24- 4 Query: 279 IGVQHWFHANGIDESNVHEPYRPKAVGIGNSQVLHKDYTRQSDIELVLREMAEQVAIRLR 33- 8 +G++ WFHANGIDESNVH+PY+PK+ GIGNSQVL KDY +Q DIE++LREMAEQVA+RLR Sbjct: 245 MGLELWFHANGIDESNVHKPYKPKSKGIGNSQVLPKDYIKQRDIEIILREMAEQVAVRLR 30- 4 Query: 339 RRHKKATVVAINVGYSNFENKKSINVQRKINPNNRTLVFQDEVVSLFRSKYDGGAVRSIA 39- 8 R KKATVV+I++GYS E K+SIN Q KI P N+T + + V+ LF +KY GA+R++A Sbjct: 305 RSGKKATVVSIHLGYSKVEQKRSINTQMKIEPTNQTALLTNYVLKLFHTKYTSGAIRNVA 36- 4 Query: 399 VRYDGLVDENFAVISLFDDFEESEKEEKLETTIDSIRDRFGFLAVQKASSLLENSRAISR 45- 8 V Y GLVDE+F +ISLFDD E+ EKEE+L++ ID+IR FGF ++ K ++L + SR I+R Sbjct: 365 VNYSGLVDESFGLISLFDDIEKIEKEERLQSAIDAIRTEFGFTSLLKGNALDQASRTIAR 42- 4 Query: 459 SRLVGGHSAGGLEGLK 474 S+L+GGHSAGGL+GLK Sbjct: 425 SKLIGGHSAGGLDGLK 440 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2109 A DNA sequence (GBSx2224) was identified in S. agalactiae <SEQ ID 6521> which encodes the amino acid sequence <SEQ ID 6522>. Analysis of this protein sequence reveals the following: TABLE-US-06461 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4016(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2110 A DNA sequence (GBSx2225) was identified in S. agalactiae <SEQ ID 6523> which encodes the amino acid sequence <SEQ ID 6524>. Analysis of this protein sequence reveals the following: TABLE-US-06462 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2088(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06463 >GP:AAG13001 GB:AF227520 unknown [Streptococcus pneumoniae] Identities = 68/122 (55%), Positives = 89/122 (72%), Gaps = 6/122 (4%) Query: 1 MIDRSYLPFKVAREYQDRKMAKWMGFFLSEHTAGLDSELNKVDYTSELSISDKLLLLNQL 60- MIDRSYLPF+ AREYQD KM KWMGFFLSEHT+ L + NKV Y S+LS+ KLLLL+Q+ Sbjct: 1 MIDRSYLPFQSAREYQDTKMQKWMGFFLSEHTSALTDDANKVTYMSDLSLEKKLLLLSQV 60- Query: 61 YSNQLNGIIAVPGQ----YYSGKVDNLTFNHVSLKTKTGFVSIPIKDILSIDL--EVEYE 11- 4 Y+ QLN I V + Y+G + +LT + + +KT TG +++ +KDI+SI+L EV YE Sbjct: 61 YAGQLNTRIHVVKKNNQVSYTGTIPSLTKDFILIKTTTGHINLKLKDIVSIELVEEVLYE 12- 0 Query: 115 SA 116 SA Sbjct: 121 SA 122 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2111 A DNA sequence (GBSx2226) was identified in S. agalactiae <SEQ ID 6525> which encodes the amino acid sequence <SEQ ID 6526>. Analysis of this protein sequence reveals the following: TABLE-US-06464 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4025(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9927> which encodes amino acid sequence <SEQ ID 9928> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2112 A DNA sequence (GBSx2227) was identified in S. agalactiae <SEQ ID 6527> which encodes the amino acid sequence <SEQ ID 6528>. This protein is predicted to be soluble transducer HtrXIII. Analysis of this protein sequence reveals the following: TABLE-US-06465 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5246(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2113 A DNA sequence (GBSx2228) was identified in S. agalactiae <SEQ ID 6529> which encodes the amino acid sequence <SEQ ID 6530>. Analysis of this protein sequence reveals the following: TABLE-US-06466 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5131(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2114 A DNA sequence (GBSx2229) was identified in S. agalactiae <SEQ ID 6531> which encodes the amino acid sequence <SEQ ID 6532>. This protein is predicted to be pXO2-78. Analysis of this protein sequence reveals the following: TABLE-US-06467 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2105(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06468 >GP:AAF13682 GB:AF188935 pXO2-78 [Bacillus anthracis] Identities = 101/314 (32%), Positives = 147/314 (46%), Gaps = 46/314 (14%) Query: 27 SGQIYEHPDHDSFRIFADTNTFKWFSRDIQGDVIDFVQLVAGVSFKKALSYLETG--GFE 84- S + Y +HDS I N F W SR + G++I FVQ V SF A+ L G +E Sbjct: 39 SERYYRLTEHDSLIIDRKKNQFYWNSRGVNGNIIKFVQEVEDASFPGAMQRLLDGEQDYE 98- Query: 85 EAKVIEETYQPFQYYLREEP----FQQARTYLKDIRGLSNQTINSFGRQGLLAQATYQAE 14- 0 +A I +P+ Y E+ F +AR YL + R + Q +++ +GL+ Q Y Sbjct: 99 KASEITFVSEPYDYEHFEQKEVSRFDRAREYLIEERKIDPQVVDALHNKGLIKQDKYN-- 15- 6 Query: 141 SVLVFKSFDHNGTLQAASLQGLVKNEEKYDRGYLKKIMKGSHGHVGISFDIGNPKRLIFC 20- 0 +VL G + S QG+VK++ KY RG K I K S + G + G P+ L F Sbjct: 157 NVLFLWKDRETGAVMGGSEQGVVKSD-KYKRGAWKSIQKNSTANYGFNVLNGEPRNLKFY 21- 5 Query: 201 ESVIDMMSYYQLHQKQLSDVRLISMEGLKLSVIAYQTLRLAAEEQGKLAFLDTVKPIRLS 26- 0 ES ID++SY LH+ L D LISMEGLK VI + Sbjct: 216 ESDIDLLSYATLHKHNLKDTHLISMEGLKPQVI-------------------------FN 25- 0 Query: 261 HYLQAIQETTTFFQTHSNVITMAVDNDEAGREFYQKL-------SDKGFPIFQ-DLPPLQ 31- 2 +Y++A + + +++ VDND+AG+ F ++L +D F+ + P Sbjct: 251 YYMKACERIGDV----PDSLSLCVDNDKAGKAFVERLIHFRYEKNDGSIVAFKPEYPQAP 30- 6 Query: 313 RLETKSDWNDIVKR 326 E K DWND KR Sbjct: 307 SEEKKWDWNDECKR 320 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2115 A DNA sequence (GBSx2230) was identified in S. agalactiae <SEQ ID 6533> which encodes the amino acid sequence <SEQ ID 6534>. Analysis of this protein sequence reveals the following: TABLE-US-06469 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.7013(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2116 A DNA sequence (GBSx2231) was identified in S. agalactiae <SEQ ID 6535> which encodes the amino acid sequence <SEQ ID 6536>. Analysis of this protein sequence reveals the following: TABLE-US-06470 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1310(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2117 A DNA sequence (GBSx2232) was identified in S. agalactiae <SEQ ID 6537> which encodes the amino acid sequence <SEQ ID 6538>. Analysis of this protein sequence reveals the following: TABLE-US-06471 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6726(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9373> which encodes amino acid sequence <SEQ ID 9374> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2118 A DNA sequence (GBSx2233) was identified in S. agalactiae <SEQ ID 6539> which encodes the amino acid sequence <SEQ ID 6540>. This protein is predicted to be phosphoglucomutase (manB). Analysis of this protein sequence reveals the following: TABLE-US-06472 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2147(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9355> which encodes amino-acid sequence <SEQ ID 9356> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06473 >GP: CAB96418 GB: AJ243290 phosphoglucomutase [Streptococcus thermophilus] Identities = 391/465 (84%), Positives = 424/465 (91%), Gaps = 1/465 (0%) Query: 1 MAQHGIKSYVFEALRPTPELSFAVRHLNAYAGIMVTASHNPAPFNGYKVYGQDGGQLPPA 60 +A HGIKSYVFE+LRPTPELSFAVRHL+ +AGIM+TASHNPAPFNGYKVYG+DGGQ+PPA Sbjct: 107 LAAHGIKSYVFESLRPTPELSFAVRHLHTFAGIMITASHNPAPFNGYKVYGEDGGQMPPA 16- 6 Query: 61 DADALTDFIRAIENPFAVELADLDESKSSGLIQVIGEDVDIEYLREVKDVNINQDLINNF 120- DADALTD+IRAI+NPF V+LADL++SK+SGLI++IGE+VD EYL+EVKDVNINQDLIN + Sbjct: 167 DADALTDYIRAIDNPFTVKLADLEDSKASGLIEIIGENVDAEYLKEVKDVNINQDLINEY 22- 6 Query: 121 GKDMKIVYTPLHGTGEMLTRRALAQAGFESVVVVESQAKADPDFSTVKSPNPESQAAFAL 18- 0 G+DMKIVYT LHGTGEML RRALAQAGF++V VVE+QA DF TVKSPNPE+Q AFAL Sbjct: 227 GRDMKIVYTSLHGTGEMLVRRALAQAGFDAVQVVEAQAVPHADFLTVKSPNPENQDAFAL 28- 6 Query: 181 AEELGREVDADVLVATDPDADRLGVEIRQPDGSYKNLSGNQIGAIIAKYILEAHKTAGTL 24- 0 AEELGR VDADVLVATDPDADRLGVEIRQPDGSY NLSGNQIGAIIAKYILEAHKTAGTL Sbjct: 287 AEELGRNVDADVLVATDPDADRLGVEIRQPDGSYLNLSGNQIGAIIAKYILEAHKTAGTL 34- 6 Query: 241 PENAALAKSIVSTELVTKIAESYGATMFNVLTGFKFIAEKIQEFEEKHNHTYMFGFEESF 30- 0 P NAAL KSIVSTELVTKIAESYGATMFNVLTGFKFI EKI EFE +HN+TYMFGFEESF Sbjct: 347 PANAALCKSIVSTELVTKIAESYGATMFNVLTGFKFIGEKIHEFETQHNYTYMFGFEESF 40- 6 Query: 301 GYLIKPFVRDKDAIQAVLLVAEIAAYYRSRGLTLADGIDEIYKEYGYFAEKTISVTLSGV 36- 0 GYLIKPFVRDKDAIQAVL+VAEIAAYYRSRG+TLADGI+EIYK+YGYF+EKTISVTLSGV Sbjct: 407 GYLIKPFVRDKDAIQAVLIVAEIAAYYRSRGMTLADGIEEIYKQYGYFSEKTISVTLSGV 46- 6 Query: 361 DGAAEIKKIMDKFRENGPKQFNNTDIVLLEDFQKQTATKNDGTISNLTTPPSNVLKYTLA 42- 0 DGAAEIKKIMDKFR N PKQFNNTDI EDF +QTAT DG + LTTPPSNVLKY LA Sbjct: 467 DGAAEIKKIMDKFRRNAPKQFNNTDIAKTEDFLEQTATTADG-VEKLTTPPSNVLKYILA 52- 5 Query: 421 DDSWIAVRPSGTEPKIKFYIATVGNDLADAETKIANIEKEITTFV 465 DDSW AVRPSGTEPKIKFYIATVG ADA+ KIANIE EI FV Sbjct: 526 DDSWFAVRPSGTEPKIKFYIATVGETEADAKEKIANIEAEINAFV 570 There is also homology to SEQ ID 6156: TABLE-US-06474 Query: 1 MAQHGIKSYVFEALRPTPELSFAVRHLNAYAGIMVTASHNPAPFNGYKVYGQDGGQLPPA 60 +AQHGIKSYVFEALRPTPELSFAVRHLNAYAGIMVTASHNPAPFNGYKVYGQDGGQLPPA Sbjct: 107 LAQHGIKSYVFEALRPTPELSFAVRHLNAYAGIMVTASHNPAPFNGYKVYGQDGGQLPPA 16- 6 Query: 61 DADALTDFIRAIENPFAVELADLDESKSSGLIQVIGEDVDIEYLREVKDVNINQDLINNF 120- DADALTDFIRAIENPFAVELADLDE+KSSGLIQVIGEDVD+EYLREVKDVNINQDLINNF Sbjct: 167 DADALTDFIRAIENPFAVELADLDENKSSGLIQVIGEDVDMEYLREVKDVNINQDLINNF 22- 6 Query: 121 GKDMKIVYTPLHGTGEMLTRRALAQAGFESVVVVESQAKADPDFSTVKSPNPESQAAFAL 18- 0 GKDMKIVYTPLHGTGEMLTRRALAQAGFESVVVVESQAKADPDFSTVKSPNPESQAAFAL Sbjct: 227 GKDMKIVYTPLHGTGEMLTRRALAQAGFESVVVVESQAKADPDFSTVKSPNPESQAAFAL 28- 6 Query: 181 AEELGREVDADVLVATDPDADRLGVEIRQPDGSYKNLSGNQIGAIIAKYILEAHKTAGTL 24- 0 AEELGREV+ADVLVATDPDADRLGVEIRQPDGSYKNLSGNQIGAIIAKYILEAHKTAGTL Sbjct: 287 AEELGREVEADVLVATDPDADRLGVEIRQPDGSYKNLSGNQIGAIIAKYILEAHKTAGTL 34- 6 Query: 241 PENAALAKSIVSTELVTKIAESYGATMFNVLTGFKFIAEKIQEFEEKHNHTYMFGFEESF 30- 0 PENAALAKSIVSTELVTKIAESYGATMFNVLTGFKFIAEKIQEFEEKHNHTYMFGFEESF Sbjct: 347 PENAALAKSIVSTELVTKIAESYGATMFNVLTGFKFIAEKIQEFEEKHNHTYMFGFEESF 40- 6 Query: 301 GYLIKPFVRDKDAIQAVLLVAEIAAYYRSRGLTLADGIDEIYKEYGYFAEKTISVTLSGV 36- 0 GYLIKPFVRDKDAIQAVLLVAEIAAYYRSRGLTLADGIDEIYKEYGYFAEKTISVTLSGV Sbjct: 407 GYLIKPFVRDKDAIQAVLLVAEIAAYYRSRGLTLADGIDEIYKEYGYFAEKTISVTLSGV 46- 6 Query: 361 DGAAEIKKIMDKFRENGPKQFNNTDIVLLEDFQKQTATKNDGTISNLTTPPSNVLKYTLA 42- 0 DGAAEIKKIMDKFRENGPKQFNNTDIVLLEDFQKQTATKNDGTISNLTTPPSNVLKYTLA Sbjct: 467 DGAAEIKKIMDKFRENGPKQFNNTDIVLLEDFQKQTATKNDGTISNLTTPPSNVLKYTLA 52- 6 Query: 421 DDSWIAVRPSGTEPKIKFYIATVGNDLADAETKIANIEKEITTFV 465 DDSWIAVRPSGTEPKIKFYIAT+G+ L A+ KIANIE EI TFV Sbjct: 527 DDSWIAVRPSGTEPKIKFYIATIGDTLDIAQEKIANIETEINTFV 571 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2119 A DNA sequence (GBSx2235) was identified in S. agalactiae <SEQ ID 6541> which encodes the amino acid sequence <SEQ ID 6542>. Analysis of this protein sequence reveals the following: TABLE-US-06475 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1564(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9905> which encodes amino acid sequence <SEQ ID 9906> was also identified. There is also homology to SEQ ID 32. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2120 A DNA sequence (GBSx2236) was identified in S. agalactiae <SEQ ID 6543> which encodes the amino acid sequence <SEQ ID 6544>. This protein is predicted to be ABC transporter, ATP-binding protein (msbA). Analysis of this protein sequence reveals the following: TABLE-US-06476 Possible site: 48 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.92 Transmembrane 162-178 (135-184) INTEGRAL Likelihood = -7.11 Transmembrane 58-74 (56-78) INTEGRAL Likelihood = -6.42 Transmembrane 136-152 (135-161) INTEGRAL Likelihood = -5.20 Transmembrane 23-39 (21-49) INTEGRAL Likelihood = -1.75 Transmembrane 485-501 (485-501) ----- Final Results ----- bacterial membrane --- Certainty = 0.4970(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-06477 >GP: AAD35376 GB: AE001710 ABC transporter, ATP-binding protein [Thermotoga maritima] Identities = 216/552 (39%), Positives = 336/552 (60%), Gaps = 3/552 (0%) Query: 26 MALLGTVVQVCLTVYLPVLIGQAVDVVLSPHSMILLLPIMWKMIAVILANTIIQWINPLL 85 - M + V L V P LIG+ +DVV P LL M + + +++ W+ + Sbjct: 41 MVFVFVTVSSILGVLSPYLIGKTIDVVFVPRRFDLLPRYMLILGTIYALTSLLFWLQGKI 100- Query: 86 YNRLIFHYVASLRKAVMEKLNLLPIAYLDKRGIGDLISRVTTDTEQLSNGLLMVFNQFFV 145- L V LRK + EKL +P+ + D+ GD+ISRV D + ++N L QFF Sbjct: 101 MLTLSQDVVFRLRKELFEKLQRVPVGFFDRTPHGDIISRVINDVDNINNVLGNSIIQFFS 16- 0 Query: 146 GLLTIIVTIFSMAKIDLLMLFLVLFLTPLSLFLARFIAKKSY-HLYQNQTASRGRQTQFI 20- 4 G++T+ + M ++++++ + L + PL++ + + ++ ++ + Y+NQ G+ I Sbjct: 161 GIVTLAGAVIMMFRVNVILSLVTLSIVPLTVLITQIVSSQTRKYFYENQRVL-GQLNGII 21- 9 Query: 205 EEMVSQESLIQAFSAQEESSDHFRTINQEYANFSQSAIFYSSTVNPSTRFINSLIYGFLA 26- 4 EE +S ++I+ F+ +E+ + F +N+ A +S + P +N+L + ++ Sbjct: 220 EEDISGLTVIKLFTREEKEMEKFDRVNESLRKVGTKAQIFSGVLPPLMNMVNNLGFALIS 27- 9 Query: 265 GIGALRIMSGAFSVGQLITFLNYVNQYTKPFNDISSVLSEMQSALACAERLYSILEESSP 32- 4 G G + +VG + TF+ Y Q+T+P N++S+ + +Q ALA AER++ IL+ Sbjct: 280 GFGGWLALKDIITVGTIATFIGYSRQFTRPLNELSNQFNMIQMALASAERIFEILDLEEE 33- 9 Query: 325 NITGTEKLDSSTVKGQIDFKNVVFGYNKSKLLLNGINLHIPAGAKVAIVGPTGAGKSTLI 38- 4 + ++ V+G+I+FKNV F Y+K K +L I HI G KVA+VGPTG+GK+T++ Sbjct: 340 K-DDPDAVELREVRGEIEFKNVWFSYDKKKPVLKDITFHIKPGQKVALVGPTGSGKTTIV 39- 8 Query: 385 NLIMRFYEVDGGNILLDCKPITDYEPSQLRQEIGMVLQETWLKSATIHDNIAYANPKASR 44- 4 NL+MRFY+VD G IL+D I + S LR IG+VLQ+T L S T+ +N+ Y NP A+ Sbjct: 399 NLLMRFYDVDRGQILVDGIDIRKIKRSSLRSSIGIVLQDTILFSTTVKENLKYGNPGATD 45- 8 Query: 445 EEVIEAAKAANADFFIKQLPNGYDTYLEDAGDSLSQGQCQLLTIARIFLKLPRILILDEA 50- 4 EE+ EAAK ++D FIK LP GY+T L D G+ LSQGQ QLL I R FL P+ILILDEA Sbjct: 459 EEIKEAAKLTHSDHFIKHLPEGYETVLTDNGEDLSQGQRQLLAITRAFLANPKILILDEA 51- 8 Query: 505 TSSIDTRTEVLVQEAFQMLMKGRTSFIIAHRLSTIQTADIILVMVSGEIVEVGNHSELMA 56- 4 TS++DT+TE +Q A LM+G+TS IIAHRL+TI+ AD+I+V+ GEIVE+G H EL+ Sbjct: 519 TSNVDTKTEKSIQAAMWKLMEGKTSIIIAHRLNTIKNADLIIVLRDGEIVEMGKHDELIQ 57- 8 Query: 565 QKGIYYQMQNAQ 576 ++G YY++ +Q Sbjct: 579 KRGFYYELFTSQ 590 A related DNA sequence was identified in S. pyogenes <SEQ ID 6545> which encodes the amino acid sequence <SEQ ID 6546>. Analysis of this protein sequence reveals the following: TABLE-US-06478 Possible site: 56 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.07 Transmembrane 162-178 (159-182) INTEGRAL Likelihood = -7.17 Transmembrane 143-159 (137-161) INTEGRAL Likelihood = -5.84 Transmembrane 23-39 (19-45) INTEGRAL Likelihood = -5.68 Transmembrane 68-84 (60-86) INTEGRAL Likelihood = -2.55 Transmembrane 261-277 (256-278) ----- Final Results ----- bacterial membrane --- Certainty = 0.4227(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06479 >GP: AAD35376 GB: AE001710 ABC transporter, ATP-binding protein [Thermotoga maritima] Identities = 206/572 (36%), Positives = 342/572 (59%), Gaps = 5/572 (0%) Query: 2 IKTDHHLLKRVLQDLLKKPLPVCILVIASFVQVG--LSVYLPVLIGKAVDMSLSVNSWQT 59 +K L+R+L L +P ++++ FV V L V P LIGK +D+ + Sbjct: 18 LKNPTATLRRLLGYL--RPHTFTLIMVFVFVTVSSILGVLSPYLIGKTIDVVFVPRRFDL 75 Query: 60 LKWLLGQMLVIIVVNTLIQWVMPLVYSRLLYQYSQQLKDKLLEKIHRLPFAYLDRQTIGD 119- L + + I + +L+ W+ + L +L+ +L EK+ R+P + DR GD Sbjct: 76 LPRYMLILGTIYALTSLLFWLQGKIMLTLSQDVVFRLRKELFEKLQRVPVGFFDRTPHGD 135- Query: 120 LVSRVITDTEQLINGLQMVFNQFILGLLTILCTIIAMAQIDWLMLILVLVLTPSSLFLAR 17- 9 ++SRVI D + + N L QF G++T+ +I M +++ ++ ++ L + P ++ + + Sbjct: 136 IISRVINDVDNINNVLGNSIIQFFSGIVTLAGAVIMMFRVNVILSLVTLSIVPLTVLITQ 19- 5 Query: 180 FIAQKSFHYAQAQTKSRGNLAQFTEEILRQEGLVQLFNAQEQSICDYHVLNKTYCEASQK 23- 9 ++ ++ Y + G L EE + +++LF +E+ + + +N++ + K Sbjct: 196 IVSSQTRKYFYENQRVLGQLNGIIEEDISGLTVIKLFTREEKEMEKFDRVNESLRKVGTK 25- 5 Query: 240 AIFYASTVNPATRFINSVIYALLAGLGAVRIMAGLFSVGQLTTFLNVVVQYTKPFNDISS 29- 9 A ++ + P +N++ +AL++G G + + +VG + TF+ Q+T+P N++S+ Sbjct: 256 AQIFSGVLPPLMNMVNNLGFALISGFGGWLALKDIITVGTIATFIGYSRQFTRPLNELSN 31- 5 Query: 300 VLAEIQSSLACAQRLYDLLDIEIKEQEHFLTFKASAVKGQIDFEEVSFSYQKDRPLLKDI 35- 9 IQ +LA A+R++++LD+E +E++ + V+G+I+F+ V FSY K +P+LKDI Sbjct: 316 QFNMIQMALASAERIFEILDLE-EEKDDPDAVELREVRGEIEFKNVWFSYDKKKPVLKDI 37- 4 Query: 360 NFSVPAGSKVAIVGPTGAGKSTLINLLMRFYELDAGSIKLDKVPIKCYAKEELRSITGIV 41- 9 F + G KVA+VGPTG+GK+T++NLLMRFY++D G I +D + I+ + LRS GIV Sbjct: 375 TFHIKPGQKVALVGPTGSGKTTIVNLLMRFYDVDRGQILVDGIDIRKIKRSSLRSSIGIV 43- 4 Query: 420 LQETWLKDATVHELIAYGSEEASRDEVVAAAKAAHAHFFIMQLPKTYDTYLSASDDALSQ 47- 9 LQ+T L TV E + YG+ A+ +E+ AAK H+ FI LP+ Y+T L+ + + LSQ Sbjct: 435 LQDTILFSTTVKENLKYGNPGATDEEIKEAAKLTHSDHFIKHLPEGYETVLTDNGEDLSQ 49- 4 Query: 480 GQLQLLAIARMFLKKPKVLVLDEATSSIDIRTEAVIQEALKELMRGRTSFIIAHRLSTIQ 53- 9 GQ QLLAI R FL PK+L+LDEATS++D +TE IQ A+ +LM G+TS IIAHRL+TI+ Sbjct: 495 GQRQLLAITRAFLANFKILILDEATSNVDTKTEKSIQAAMWKLMEGKTSIIIAHRLNTIK 55- 4 Query: 540 SADLILVMDQGRLVEWGTHASLMSKNGCYVRL 571 +ADLI+V+ G +VE G H L+ K G Y L Sbjct: 555 NADLIIVLRDGEIVEMGKHDELIQKRGFYYEL 586 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06480 Identities = 340/566 (60%), Positives = 433/566 (76%) Query: 11 KKLVQDLLSKKSLVGMALLGTVVQVCLTVYLPVLIGQAVDVVLSPHSMILLLPIMWKMIA 70 - K+++QDLL K V + ++ + VQV L+VYLPVLIG+AVD+ LS +S L ++ +M+ Sbjct: 10 KRVLQDLLKKPLPVCILVIASFVQVGLSVYLPVLIGKAVDMSLSVNSWQTLKWLLGQMLV 69 Query: 71 VILANTIIQWINPLLYNRLIFHYVASLRKAVMEKLNLLPIAYLDKRGIGDLISRVTTDTE 130- +I+ NT+IQW+ PL+Y+RL++ Y L+ ++EK++ LP AYLD++ IGDL+SRV TDTE Sbjct: 70 IIVVNTLIQWVMPLVYSRLLYQYSQQLKDKLLEKIHRLPFAYLDRQTIGDLVSRVITDTE 129- Query: 131 QLSNGLLMVFNQFFVGLLTIIVTIFSMAKIDLLMLFLVLFLTPLSLFLARFIAKKSYHLY 19- 0 QL NGL MVFNQF +GLLTI+ TI +MA+ID LML LVL LTP SLFLARFIA+KS+H Sbjct: 130 QLINGLQMVFNQFILGLLTILCTIIAMAQIDWLMLILVLVLTPSSLFLARFIAQKSFHYA 18- 9 Query: 191 QNQTASRGRQTQFIEEMVSQESLIQAFSAQEESSDHFRTINQEYANFSQSAIFYSSTVNP 25- 0 Q QT SRG QF EE++ QE L+Q F+AQE+S + +N+ Y SQ AIFY+STVNP Sbjct: 190 QAQTKSRGNLAQFTEEILRQEGLVQLFNAQEQSICDYHVLNKTYCEASQKAIFYASTVNP 24- 9 Query: 251 STRFINSLIYGFLAGIGALRIMSGAFSVGQLITFLNYVNQYTKPFNDISSVLSEMQSALA 31- 0 +TRFINS+IY LAG+GA+RIM+G FSVGQL TFLN V QYTKPFNDISSVL+E+QS+LA Sbjct: 250 ATRFINSVIYALLAGLGAVRIMAGLFSVGQLTTFLNVVVQYTKPFNDISSVLAEIQSSLA 30- 9 Query: 311 CAERLYSILEESSPNITGTEKLDSSTVKGQIDFKNVVFGYNKSKLLLNGINLHIPAGAKV 37- 0 CA+RLY +L+ +S VKGQIDF+ V F Y K + LL IN +PAG+KV Sbjct: 310 CAQRLYDLLDIEIKEQEHFLTFKASAVKGQIDFEEVSFSYQKDRPLLKDINFSVPAGSKV 36- 9 Query: 371 AIVGPTGAGKSTLINLIMRFYEVDGGNILLDCKPITDYEPSQLRQEIGMVLQETWLKSAT 43- 0 AIVGPTGAGKSTLINL+MRFYE+D G+I LD PI Y +LR G+VLQETWLK AT Sbjct: 370 AIVGPTGAGKSTLINLLMRFYELDAGSIKLDKVPIKCYAKEELRSITGIVLQETWLKDAT 42- 9 Query: 431 IHDNIAYANPKASREEVIEAAKAANADFFIKQLPNGYDTYLEDAGDSLSQGQCQLLTIAR 49- 0 +H+ IAY + +ASR+EV+ AAKAA+A FFI QLP YDTYL +D+LSQGQ QLL IAR Sbjct: 430 VHELIAYGSEEASRDEVVAAAKAAHAHFFIMQLPKTYDTYLSASDDALSQGQLQLLAIAR 48- 9 Query: 491 IFLKLPRILILDEATSSIDTRTEVLVQEAFQMLMKGRTSFIIAHRLSTIQTADIILVMVS 55- 0 +FLK P++L+LDEATSSID RTE ++QEA + LM+GRTSFIIAHRLSTIQ+AD+ILVM Sbjct: 490 MFLKKPKVLVLDEATSSIDIRTEAVIQEALKELMRGRTSFIIAHRLSTIQSADLILVMDQ 54- 9 Query: 551 GEIVEVGNHSELMAQKGIYYQMQNAQ 576 G +VE G H+ LM++ G Y ++Q + Sbjct: 550 GRLVEWGTHASLMSKNGCYVRLQKIE 575 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2121 A DNA sequence (GBSx2237) was identified in S. agalactiae <SEQ ID 6547> which encodes the amino acid sequence <SEQ ID 6548>. Analysis of this protein sequence reveals the following: TABLE-US-06481 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1099(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2122 A DNA sequence (GBSx2238) was identified in S. agalactiae <SEQ ID 6549> which encodes the amino acid sequence <SEQ ID 6550>. This protein is predicted to be ABC transporter, ATP-binding protein (msbA). Analysis of this protein sequence reveals the following: TABLE-US-06482 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.69 Transmembrane 157-173 (130-182) INTEGRAL Likelihood = -10.88 Transmembrane 56-72 (49-77) INTEGRAL Likelihood = -7.75 Transmembrane 239-255 (235-258) INTEGRAL Likelihood = -6.42 Transmembrane 133-149 (130-156) INTEGRAL Likelihood = -4.78 Transmembrane 271-287 (270-289) INTEGRAL Likelihood = -1.91 Transmembrane 20-36 (20-37) ----- Final Results ----- bacterial membrane --- Certainty = 0.6477(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06483 >GP: AAD35375 GB: AE001710 ABC transporter, ATP-binding protein [Thermotoga maritima] Identities = 196/570 (34%), Positives = 327/570 (56%), Gaps = 5/570 (0%) Query: 1 MKRLTYYFKGYIKETIFGPLFKLLEASFELLVPIVIAKMIDETIPRGDRSGLLLQIGLIF 60 MK L Y K Y + PLF ++E +L P ++A+++DE I RGD S L+L+ G++ Sbjct: 1 MKTLARYLKPYWIFAVLAPLFMVVEVICDLSQPTLLARIVDEGIARGDFS-LVLKTGILM 59 Query: 61 FLAA-VGVVVAITAQYYSSKAAVGYTRQLTEDLYQKVMSLGKKDRDELGTASLITRLTAD 119- + A +G V I ++S A+ + L DL++KV+S + + T+SLITRLT D Sbjct: 60 LIVALIGAVGGIGCTVFASYASQNFGADLRRDLFRKVLSFSISNVNRFHTSSLITRLTND 119- Query: 120 TFQIQTGLNQFLRLFLRAPIIVFGAIIMAFSISPSLTIWFLVMVVTLFIIVFVMSRLLNP 17- 9 Q+Q + LR+ +RAP++ G I+MA SI+ L+ + ++ + ++ +++ NP Sbjct: 120 VTQLQNLVMMLLRIVVRAPLLFVGGIVMAVSINVKLSSVLIFLIPPIVLLFVWLTKKGNP 17- 9 Query: 180 IYLKIRTSTDYLVKLTRQQLQGVRVIRAFNQVDRESEAFNDINYHYTNLQLKAGRLSSLV 23- 9 ++ KI+ STD + ++ R+ L GVRV+RAF + + E+E F N + A L Sbjct: 180 LFRKIQESTDEVNRVVRENLLGVRVVRAFRREEYENENFRKANESLRRSIISAFSLIVFA 23- 9 Query: 240 TPLTFLVVNITLVVIIWRGNLNIANHLLSQGMLVALINYLLQILVELLKMTMLVTSLNQS 29- 9 PL +VN+ ++ ++W G + + N+ + G ++A NYL+QI+ L+ + ++ + ++ Sbjct: 240 LPLFIFIVNMGMIAVLWFGGVLVRNNQMEIGSIMAYTNYLMQIMFSLMMIGNILNFIVRA 29- 9 Query: 300 YISAKRIIAVF-ERPS-EIIDDKLEPKYSNKALEVQEMAFSYPNSSEKALSDITFSMNVG 35- 7 SAKR++ V E+P+ E D+ L ++ + + F Y +++ LS + FS+ G Sbjct: 300 SASAKRVLEVLNEKPAIEEADNALALPNVEGSVSFENVEFRYFENTDPVLSGVNFSVKPG 35- 9 Query: 358 ETLGIIGGTGSGKSTLINLLLHIYKVQEGDIDIYHQGKSPDTISNWRTLVRVVPQNAQLF 41- 7 + ++G TGSGKSTL+NL+ + + G +++ + + R + VPQ LF Sbjct: 360 SLVAVLGETGSGKSTLMNLIPRLIDPERGRVEVDELDVRTVKLKDLRGHISAVPQETVLF 41- 9 Query: 418 KGTIRSNLSLGLGKVSEEKLWTALEIAQASDFVKEKDGQLDAPVESFGRNFSGGQRQRLT 47- 7 GTI+ NL G +++++ A +IAQ DF+ D+ VE GRNFSGGQ+QRL+ Sbjct: 420 SGTIKENLKWGREDATDDEIVEAAKIAQIHDFIISLPEGYDSRVERGGRNFSGGQKQRLS 47- 9 Query: 478 IARALVQDKIPFLILDDATSALDYLTEARLFKAITKHFNQTNLIIVSQRINSIQNADRIL 53- 7 IARALV+ K LILDD TS++D +TE R+ + ++ I++Q+I + AD+IL Sbjct: 480 IARALVK-KPKVLILDDCTSSVDPITEKRILDGLKRYTKGCTTFIITQKIPTALLADKIL 53- 8 Query: 538 LLDKGKQVGFDNHQSLLAHNKVYKSIYHSQ 567 +L +GK GF H+ LL H K Y+ IY SQ Sbjct: 539 VLHEGKVAGFGTHKELLEHCKPYREIYESQ 568 A related DNA sequence was identified in S. pyogenes <SEQ ID 6551> which encodes the amino acid sequence <SEQ ID 6552>. Analysis of this protein sequence reveals the following: TABLE-US-06484 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.47 Transmembrane 157-173 (149-185) INTEGRAL Likelihood = -7.75 Transmembrane 55-71 (51-74) INTEGRAL Likelihood = -4.25 Transmembrane 239-255 (237-260) INTEGRAL Likelihood = -3.77 Transmembrane 20-36 (19-37) INTEGRAL Likelihood = -3.50 Transmembrane 271-287 (270-288) INTEGRAL Likelihood = -2.55 Transmembrane 133-149 (130-151) ----- Final Results ----- bacterial membrane --- Certainty = 0.5989(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06485 !GB: AL137187 putative ABC transporter [Streptomyces . . . 296 6e-79 >GP: CAB69751 GB: AL137187 putative ABC transporter [Streptomyces coelicolor A3(2)] Identities = 185/569 (32%), Positives = 306/569 (53%), Gaps = 8/569 (1%) Query: 1 MKRLRPYVKGYLKESILGPLFKLLEALFELLVPLLIANMIDISISQHNSQGILRVVLTLF 60 ++ LR Y++ Y K L + L+ L +P L A++ID + + +S IL + Sbjct: 3 IRLLRTYLRPYKKPIALLVALQFLQTCASLYLPTLNAHIIDEGVVKGDSGYILSYGALMI 62 Query: 61 GLATIGLLLSVTAQYFSSKAAVGFTRQMTDDLFKKIMFLSKEDQDHLGYASLLSRLTSDS 120- G++ ++ ++ A ++ ++ A R + +F ++ S + H G SL++R T+D Sbjct: 63 GISLAQVVCNIGAVFYGARTAAALGRDVRGAVFDRVQSFSAREVGHFGAPSLITRTTNDV 122- Query: 121 FQIQTGINQFLRLFLRAPIIVCGAMVMAYWISPSLTLWFVMMVIVLLTLVFVMSHLLGPL 18- 0 Q+Q L + API+ G +VMA + L+ + +V VL V ++ L PL Sbjct: 123 QQVQMLALMTFTLMVSAPIMCVGGIVMALGLDVPLSGVLLGVVPVLAICVTLIVRKLRPL 18- 2 Query: 181 YLLIRRETDHLVRLTSQQLQGIRVIKAFNQTQKELQAFKQQNMLLSRHQYQAATLANVLN 24- 0 + ++ D + R+ +Q+ G RVI+AF + + E Q F++ N L+ L ++ Sbjct: 183 FRKMQVRLDTVNRVLREQITGNRVIRAFVRDEYEQQRFRKANTELTEVALGTGNLLALMF 24- 2 Query: 241 PMTFLVVNLTLLILIWQGSWQVAHRSLSQGMLVALINYLLQILAELLKMTMLMGTINQSV 30- 0 P+ VVNL+ + ++W G+ ++ + G L A + YL+QI+ ++ T + + ++ Sbjct: 243 PVVMTVVNLSSIAVVWFGAHRIDSGGMQIGDLTAFLAYLMQIVMSVMMATFMFMMVPRAE 30- 2 Query: 301 TAAKRINQVFVLADEAPLPLLKDGPISTH-LLTIRHLTFTYPGAAEPSLYDIQLSADQGE 35- 9 A+RI +V P+ + H L IR F YPGA EP L I L A GE Sbjct: 303 VCAERIQEVLETESSVVPPVAPVTELRRHGHLEIREAGFRYPGAEEPVLRHIDLVARPGE 36- 2 Query: 360 WIGIIGGTGAGKTTLIDLICQTYSQYSGEISLNW---QGEVPKTLTEWRNVIALVPQKAQ 41- 6 +IG TG+GK+TL+ L+ + + GE+ +N + PKTL + V++LVPQK Sbjct: 363 TTAVIGSTGSGKSTLLGLVPRLFDATDGEVLVNGVDVRTVDPKTLAK---VVSLVPQKPY 41- 9 Query: 417 LFKGTIRSNLLLGQSMPISDEELWRALELAQAKEFVAALPEQLEAPVEAFGRHFSGGQRQ 47- 6 LF GT+ +NL G + +DEELW AL +AQAKEFV+ L L+AP+ G + SGGQRQ Sbjct: 420 LFAGTVATNLRYG-NPDATDEELWHALAVAQAKEFVSELEGGLDAPIAQGGTNVSGGQRQ 47- 8 Query: 477 RLAIARALLKPKPILILDDASSALDNETRGRLFKALKEELSDVLVILVTQSIKNLQFADK 53- 6 RLAIAR L++ I + DD+ SALD T L L +E ++ V++V Q + ++ AD+ Sbjct: 479 RLAIARTLVQRPEIYLFDDSFSALDYATDAALRAELAQETAEATVVIVAQRVATIRDADR 53- 8 Query: 537 ILVLEQGHQLDFASHDQLKVSNALYQEML 565 I+VL++G + H +L N Y+E++ Sbjct: 539 IVVLDEGRVVGVGRHHELMADNETYREIV 567 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06486 Identities = 313/568 (55%), Positives = 428/568 (75%), Gaps = 9/568 (1%) Query: 1 MKRLTYYFKGYIKETIFGPLFKLLEASFELLVPIVIAKMIDETIPRGDRSGLLLQIGLIF 60 MKRL Y KGY+KE+I GPLFKLLEA FELLVP++IA MID +I + + G+L + +F Sbjct: 1 MKRLRPYVKGYLKESILGPLFKLLEALFELLVPLLIANMIDISISQHNSQGILRVVLTLF 60 Query: 61 FLAAVGVVVAITAQYYSSKAAVGYTRQLTEDLYQKVMSLGKKDRDELGTASLITRLTADT 120- LA +G+++++TAQY+SSKAAVG+TRQ+T+DL++K+M L K+D+D LG ASL++RLT+D+ Sbjct: 61 GLATIGLLLSVTAQYFSSKAAVGFTRQMTDDLFKKIMFLSKEDQDHLGYASLLSRLTSDS 120- Query: 121 FQIQTGLNQFLRLFLRAPIIVFGAIIMAFSISPSLTIWFLVMVVTLFIIVFVMSRLLNPI 18- 0 FQIQTG+NQFLRLFLRAPIIV GA++MA+ ISPSLT+WF++MV+ L +VFVMS LL P+ Sbjct: 121 FQIQTGINQFLRLFLRAPIIVCGAMVMAYWISPSLTLWFVMMVIVLLTLVFVMSHLLGPL 18- 0 Query: 181 YLKIRTSTDYLVKLTRQQLQGVRVIRAFNQVDRESEAFNDINYHYTNLQLKAGRLSSLVT 24- 0 YL IR TD+LV+LT QQLQG+RVI+AFNQ +E +AF N + Q +A L++++ Sbjct: 181 YLLIRRETDHLVRLTSQQLQGIRVIKAFNQTQKELQAFKQQNMLLSRHQYQAATLANVLN 24- 0 Query: 241 PLTFLVVNITLVVIIWRGNLNIANHLLSQGMLVALINYLLQILVELLKMTMLVTSLNQSY 30- 0 P+TFLVVN+TL+++IW+G+ +A+ LSQGMLVALINYLLQIL ELLKMTML+ ++NQS Sbjct: 241 PMTFLVVNLTLLILIWQGSWQVAHRSLSQGMLVALINYLLQILAELLKMTMLMGTINQSV 30- 0 Query: 301 ISAKRIIAVF----ERPSEIIDDKLEPKYSNKALEVQEMAFSYPNSSEKALSDITFSMNV 35- 6 +AKRI VF E P ++ D S L ++ + F+YP ++E +L DI S + Sbjct: 301 TAAKRINQVFVLADEAPLPLLKD---GPISTHLLTIRHLTFTYPGAAEPSLYDIQLSADQ 35- 7 Query: 357 GETLGIIGGTGSGKSTLINLLLHIYKVQEGDIDIYHQGKSPDTISNWRTLVRVVPQNAQL 41- 6 GE +GIIGGTG+GK+TLI+L+ Y G+I + QG+ P T++ WR ++ +VPQ AQL Sbjct: 358 GEWIGIIGGTGAGKTTLIDLICQTYSQYSGEISLNWQGEVPKTLTEWRNVIALVPQKAQL 41- 7 Query: 417 FKGTIRSNLSLGLG-KVSEEKLWTALEIAQASDFVKEKDGQLDAPVESFGRNFSGGQRQR 47- 5 FKGTIRSNL LG +S+E+LW ALE+AQA +FV QL+APVE+FGR+FSGGQRQR Sbjct: 418 FKGTIRSNLLLGQSMPISDEELWRALELAQAKEFVAALPEQLEAPVEAFGRHFSGGQRQR 47- 7 Query: 476 LTIARALVQDKIPFLILDDATSALDYLTEARLFKAITKHFNQTNLIIVSQRINSIQNADR 53- 5 L IARAL++ K P LILDDA+SALD T RLFKA+ + + +I+V+Q I ++Q AD+ Sbjct: 478 LAIARALLKPK-PILILDDASSALDNETRGRLFKALKEELSDVLVILVTQSIKNLQFADK 53- 6 Query: 536 ILLLDKGKQVGFDNHQSLLAHNKVYKSI 563 IL+L++G Q+ F +H L N +Y+ + Sbjct: 537 ILVLEQGHQLDFASHDQLKVSNALYQEM 564 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2123 A DNA sequence (GBSx2239) was identified in S. agalactiae <SEQ ID 6553> which encodes the amino acid sequence <SEQ ID 6554>. Analysis of this protein sequence reveals the following:

TABLE-US-06487 Possible site: 43 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.26 Transmembrane 8-24 (1-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.5904(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06488 >GP: AAB84433 GB: AF027868 RAS-related protein [Bacillus subtilis] Identities = 53/140 (37%), Positives = 78/140 (54%), Gaps = 2/140 (1%) Query: 28 VKKVLQYHDLVQNTLAENGSEANVHLVLSMIYTETKGDAIDVMQSSESISGTTNSITDSH 87 - ++++ Y LV+ L G L+L M+Y E+KG D MQSSES+ N ITD Sbjct: 49 LERLTDYKPLVEEELESQGLSNYTSLILGMMYQESKGKGNDPMQSSESLGLKRNEITDPQ 108- Query: 88 TSIKHGVTLLSQNISQAKKAKVDVWTAVQAYNFGSSYIDYVADHGGENSIELAKNYSKNV 147- S+K G+ + K+ VD+ T +Q+YN G+ YID+VA+HGG ++ ELAK YS+ Sbjct: 109 LSVKQGIKQFTLMYKTGKEKGVDLDTIIQSYNMGAGYIDFVAEHGGTHTEELAKQYSEQQ 16- 8 Query: 148 VA--PSLGNYNGDTYFYYHP 165 V P L G+ + +P Sbjct: 169 VKKNPDLYTCGGNAKNFRYP 188 A related DNA sequence was identified in S. pyogenes <SEQ ID 4143> which encodes the amino acid sequence <SEQ ID 4144>. Analysis of this protein sequence reveals the following: TABLE-US-06489 Possible site: 42 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.66 Transmembrane 8-24 (7-25) ----- Final Results ----- bacterial membrane --- Certainty = 0.2062(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06490 Identities = 134/200 (67%), Positives = 165/200 (82%), Gaps = 1/200 (0%) Query: 1 MFKFLKRLIALIIIIFIGYRLVIIHENVKKVLQYHDLVQNTLAENGSEANVHLVLSMIYT 60 MF+ LKR + +++ F+ Y+ +IH NV++VL Y +V+ TLAEN ++ANV LVL+MIYT Sbjct: 1 MFRLLKRACSFLLL-FVIYQSFVIHHNVQRVLAYKPMVEKTLAENDTKANVDLVLAMIYT 59 Query: 61 ETKGDAIDVMQSSESISGTTNSITDSHTSIKHGVTLLSQNISQAKKAKVDVWTAVQAYNF 120- ETKG DVMQSSES SG NSITDS SI+HGV LLS N++ A++A VD WTAVQAYNF Sbjct: 60 ETKGGEADVMQSSESSSGQKNSITDSQASIEHGVNLLSHNLALAEEAGVDSWTAVQAYNF 119- Query: 121 GSSYIDYVADHGGENSIELAKNYSKNVVAPSLGNYNGDTYFYYHPLALISGGKLYKNGGN 18- 0 G++YIDY+A+HGG+N+++LA YSK VVAPSLGN +G TYFYYHPLALISGGKLYKNGGN Sbjct: 120 GTAYIDYIAEHGGQNTVDLATTYSKTVVAPSLGNTSGQTYFYYHPLALISGGKLYKNGGN 17- 9 Query: 181 IYYSREVQFNLYLIKIMELF 200 IYYSREV FNLYLI++M LF Sbjct: 180 IYYSREVHFNLYLIELMSLF 199 SEQ ID 6554 (GBS244) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 59 (lane 4; MW 23.1 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 67 (lane 2; MW 48 kDa). GBS244-GST was purified as shown in FIG. 211, lane 5. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2124 A DNA sequence (GBSx2240) was identified in S. agalactiae <SEQ ID 6555> which encodes the amino acid sequence <SEQ ID 6556>. Analysis of this protein sequence reveals the following: TABLE-US-06491 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2401(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9837> which encodes amino acid sequence <SEQ ID 9838> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06492 >GP: CAB71302 GB: AJ130879 hypothetical protein [Clostridium sticklandii] Identities = 32/95 (33%), Positives = 53/95 (55%), Gaps = 1/95 (1%) Query: 235 LSPEKLADQLFDDNLTARLTFVDELKDAIPGPVQVSDIDHSRQIKKLENQKLSLSNGIEL 29- 4 LS EK + F++ + + + L A Q+ ++ + +K E QK+ +GIE+ Sbjct: 2 LSVEKALETAFEETDEIKAIYKEALSKAGIENEQI-EVSETALKRKFEIQKIITESGIEV 60 Query: 295 IVPNNVYQDAESVEFIQNPDGTYSILIKNIQDIQN 329 +P N Y D +EF+ N DGT S++IKNI +IQ+ Sbjct: 61 KIPVNYYGDPSKLEFVANGDGTVSLVIKNIGNIQS 95 A related DNA sequence was identified in S. pyogenes <SEQ ID 6557> which encodes the amino acid sequence <SEQ ID 6558>. Analysis of this protein sequence reveals the following: TABLE-US-06493 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3336(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06494 Identities = 246/325 (75%), Positives = 286/325 (87%) Query: 6 MMDFYIKQIIIHQFSPNDTELVLSDTPLTLTPRIDDYFRKKLSKVFSDEAKRGYFGEDNV 65 M+D YIK+I+IHQFSPNDTEL+LSD +++TPRID+YFRKKL+KVFSDEAKRG F +N Sbjct: 1 MLDSYIKRIVIHQFSPNDTELLLSDRLVSITPRIDEYFRKKLAKVFSDEAKRGQFEANNT 60 Query: 66 FMSHLQDDLYVSSCQIAQLWKEEFVISEDQKTNDLVFIQFDKDGMEHFAFLRISLKEQFA 125- F + + DDL +S IAQLWKE FVISEDQKTNDLVF+QFDKDG FAFLRI+LKEQFA Sbjct: 61 FFTTIGDDLLETSVTIAQLWKEAFVISEDQKTNDLVFVQFDKDGEPFFAFLRIALKEQFA 120- Query: 126 HVSENQEQPITITQNNLPSAAQTPDEALVVNKSSKQYYLIEKRIKHNGSFANYFSENLLQ 18- 5 H+S+N E P T+TQNNLPS QTPDEALV+N S QYYLIEKR+KHNGSFANYFSE+LL+ Sbjct: 121 HLSDNYEHPFTVTQNNLPSPTQTPDEALVINLKSGQYYLIEKRVKHNGSFANYFSEHLLK 18- 0 Query: 186 VQPEQSVKKSIKMVEQTAQKIAENFNKDDFSFQSKMKSAIYKNLEEEQELSPEKLADQLF 24- 5 V PEQSVKKSIKM+EQTAQKIAE+FN+DDF+FQSKMKS ++K LE + LSPEKLADQLF Sbjct: 181 VTPEQSVKKSIKMIEQTAQKIAEHFNQDDFTFQSKMKSTLFKQLEADDVLSPEKLADQLF 24- 0 Query: 246 DDNLTARLTFVDELKDAIPGPVQVSDIDHSRQIKKLENQKLSLSNGIELIVPNNVYQDAE 30- 5 DDNLTARLTFVD++KD IP P+++SDI+HSRQIKKLENQKLSLSNGIEL VPN +YQDAE Sbjct: 241 DDNLTARLTFVDQVKDVIPEPIKISDIEHSRQIKKLENQKLSLSNGIELTVPNAIYQDAE 30- 0 Query: 306 SVEFIQNPDGTYSILIKNIQDIQNK 330 +VEF+ N DGTYSILIKNI+DI+ K Sbjct: 301 AVEFLLNDDGTYSILIKNIEDIKTK 325 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2125 A DNA sequence (GBSx2241) was identified in S. agalactiae <SEQ ID 6559> which encodes the amino acid sequence <SEQ ID 6560>. This protein is predicted to be Serine hydroxymethyltransferase (glyA-1). Analysis of this protein sequence reveals the following: TABLE-US-06495 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3876(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06496 >GP: AAD35802 GB: AE001743 serine hydroxymethyltransferase [Thermotoga maritima] Identities = 243/416 (58%), Positives = 307/416 (73%), Gaps = 7/416 (1%) Query: 9 KEFDQELWQAIHDEEIRQQNNIELIASENVVSKAVMAAQGSVLTNKYAEGYPSHRYYGGT 68 K+ D E+++ + +E RQ+ +ELIASEN S AV+ GS+LTNKYAEGYP RYYGG Sbjct: 6 KQVDPEIYEVLVNELKRQEYGLELIASENFASLAVIETMGSMLTNKYAEGYPKKRYYGGC 65 Query: 69 DCVDVVESLAIERAKTLFNAEFANVQPHSGSQANAAAYMALIEPGDTVLGMDLAAGGHLT 128- + VD E AIERAK LF A+FANVQPHSGSQAN A Y+AL +PGDT++GM L+ GGHLT Sbjct: 66 EWVDRAEERAIERAKRLFGAKFANVQPHSGSQANMAVYLALAQPGDTIMGMSLSHGGHLT 125- Query: 129 HGASVSFSGKTYHFVSYSVDPKTEMLDYDNILKIAQETQPKLIVAGASAYSRIIDFEKFR 18- 8 HGA V+FSGK + V Y V+ +TE +DYD + ++A E +PK+IVAG SAY+RIIDF++FR Sbjct: 126 HGAPVNFSGKIFKVVPYGVNLETETIDYDEVRRLALEHKPKIIVAGGSAYARIIDFKRFR 18- 5 Query: 189 QIADAVDAYLMVDMAHIAGLVASGHHPSPIPYAHVTTTTTHKTLRGPRGGLILTNDEAIA 24- 8 +IAD V AYLMVDMAH AGLVA+G HP+P+ YAHV T+TTHKTLRGPRGGLILTND IA Sbjct: 186 EIADEVGAYLMVDMAHFAGLVAAGIHPNPLEYAHVVTSTTHKTLRGPRGGLILTNDPEIA 24- 5 Query: 249 KKINSAVFPGLQGGPLEHVIAAKAVALKEALDPSFKIYGEDIIKNAQAMAKVFKEDDDFH 30- 8 K ++ +FPG+QGGPL HVIAAKAV KEA+ FK Y + ++KNA+ MA+ F++ + Sbjct: 246 KAVDKTIFPGIQGGPLMHVIAAKAVCFKEAMTEEFKEYQKQVVKNAKKMAEEFQK-RGYR 30- 4 Query: 309 LISDGTDNHLFLVDVTKVIENGKKAQNVLEEVNITLNKNSIPFERLSPFKTSGIRIGTPA 36- 8 ++S GTD HLFLVD+T GK A+ LE IT+NKN+IP E+ SPF SGIRIGTPA Sbjct: 305 IVSGGTDTHLFLVDLTPKDITGKAAEKALESCGITVNKNTIPNEKRSPFVASGIRIGTPA 36- 4 Query: 369 ITSRGMGVEESRRIAELMIKALKN--HENQDVLTEVRQE----IKSLTDAFPLYEN 418 +T+RGM EE IAE++ L N EN V EVR+E ++ L + FPLY + Sbjct: 365 VTTRGMKEEEMEEIAEMIDLVLSNVIDENGTVKPEVREEVSKKVRELCERFPLYRD 420 A related DNA sequence was identified in S. pyogenes <SEQ ID 6561> which encodes the amino acid sequence <SEQ ID 6562>. Analysis of this protein sequence reveals the following: TABLE-US-06497 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.00 Transmembrane 196-212 (196-212) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06498 >GP: CAB15707 GB: Z99122 serine hydroxymethyltransferase [Bacillus subtilis] Identities = 250/407 (61%), Positives = 311/407 (75%), Gaps = 2/407 (0%) Query: 14 DKELWDAIHAEEERQEHHIELIASENMVSKAVMAAQGSVLTNKYAEGYPGNRYYGGTECV 73 - D+++++AI E ERQ+ IELIASEN VS+AVM AQGSVLTNKYAEGYPG RYYGG E V Sbjct: 8 DEQVFNAIKNERERQQTKIELIASENFVSEAVMEAQGSVLTNKYAEGYPGKRYYGGCEHV 67 Query: 74 DIVETLAIERAKKLFGAAFANVQAHSGSQANAAAYMALIEAGDTVLGMDLAAGGHLTHGS 133- D+VE +A +RAK++FGA NVQ HSG+QAN A Y ++E GDTVLGM+L+ GGHLTHGS Sbjct: 68 DVVEDIARDRAKEIFGAEHVNVQPHSGAQANMAVYFTILEQGDTVLGMNLSHGGHLTHGS 127- Query: 134 PVNFSGKTYHFVGYSVDTDTEMLNYEAILEQAKAVQPKLIVAGASAYSRSIDFEKFRAIA 19- 3 PVNFSG Y+FV Y VD +T+ ++Y+ + E+A A +PKLIVAGASAY R+IDF+KFR IA Sbjct: 128 PVNFSGVQYNFVEYGVDKETQYIDYDDVREKALAHKPKLIVAGASAYPRTIDFKKFREIA 18- 7 Query: 194 DHVGAYLMVDMAHIAGLVAAGVHPSPVPYAHIVTSTTHKTLRGPRGGLILTNDEALAKKI 25- 3 D VGAY MVDMAHIAGLVAAG+HP+PVPYA VT+TTHKTLRGPRGG+IL +E KKI Sbjct: 188 DEVGAYFMVDMAHIAGLVAAGLHPNPVPYADFVTTTTHKTLRGPRGGMILCREE-FGKKI 24- 6 Query: 254 NSAVFPGLQGGPLEHVIAAKAVAFKEALDPAFKDYAQAIIDNTAAMAAVFAQDDRFRLIS 31- 3 + ++FPG+QGGPL HVIAAKAV+F E L FK YAQ +I N +A ++ +L+S Sbjct: 247 DKSIFPGIQGGPLMHVIAAKAVSFGEVLQDDFKTYAQNVISNAKRLAEALTKEG-IQLVS 30- 5 Query: 314 GGTDNHVFLVDVTKVIANGKLAQNLLDEVNITLNKNAIPFETLSPFKTSGIRIGCAAITS 37- 3 GGTDNH+ LVD+ + GK+A+++LDE+ IT NKNAIP++ PF TSGIR+G AA+TS Sbjct: 306 GGTDNHLILVDLRSLGLTGKVAEHVLDEIGITSNKNAIPYDPEKPFVTSGIRLGTAAVTS 36- 5 Query: 374 RGMGVKESQTIARLIIKALVNHDQETILEEVRQEVRQLTDAFPLYKK 420 RG + + +I AL NH+ E LEE RQ V LTD FPLYK+ Sbjct: 366 RGFDGDALEEVGAIIALALKNHEDEGKLEEARQRVAALTDKFPLYKE 412 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06499 Identities = 330/417 (79%), Positives = 368/417 (88%) Query: 1 MIFDKDNFKEFDQELWQAIHDEEIRQQNNIELIASENVVSKAVMAAQGSVLTNKYAEGYP 60 MIFDK N ++FD+ELW AIH EE RQ+++IELIASEN+VSKAVMAAQGSVLTNKYAEGYP Sbjct: 3 MIFDKGNVEDFDKELWDAIHAEEERQEHHIELIASENMVSKAVMAAQGSVLTNKYAEGYP 62 Query: 61 SHRYYGGTDCVDVVESLAIERAKTLFNAEFANVQPHSGSQANAAAYMALIEPGDTVLGMD 120- +RYYGGT+CVD+VE+LAIERAK LF A FANVQ HSGSQANAAAYMALIE GDTVLGMD Sbjct: 63 GNRYYGGTECVDIVETLAIERAKKLFGAAFANVQAHSGSQANAAAYMALIEAGDTVLGMD 122- Query: 121 LAAGGHLTHGASVSFSGKTYHFVSYSVDPKTEMLDYDNILKIAQETQPKLIVAGASAYSR 18- 0 LAAGGHLTHG+ V+FSGKTYHFV YSVD TEML+Y+ IL+ A+ QPKLIVAGASAYSR Sbjct: 123 LAAGGHLTHGSPVNFSGKTYHFVGYSVDTDTEMLNYEAILEQAKAVQPKLIVAGASAYSR 18- 2 Query: 181 IIDFEKFRQIADAVDAYLMVDMAHIAGLVASGHHPSPIPYAHVTTTTTHKTLRGPRGGLI 24- 0 IDFEKFR IAD V AYLMVDMAHIAGLVA+G HPSP+PYAH+ T+TTHKTLRGPRGGLI Sbjct: 183 SIDFEKFRAIADHVGAYLMVDMAHIAGLVAAGVHPSPVPYAHIVTSTTHKTLRGPRGGLI 24- 2 Query: 241 LTNDEAIAKKINSAVFPGLQGGPLEHVIAAKAVALKEALDPSFKIYGEDIIKNAQAMAKV 30- 0 LTNDEA+AKKINSAVFPGLQGGPLEHVIAAKAVA KEALDP+FK Y + II N AMA V Sbjct: 243 LTNDEALAKKINSAVFPGLQGGPLEHVIAAKAVAFKEALDPAFKDYAQAIIDNTAAMAAV 30- 2 Query: 301 FKEDDDFHLISDGTDNHLFLVDVTKVIENGKKAQNVLEEVNITLNKNSIPFERLSPFKTS 36- 0 F +DD F LIS GTDNH+FLVDVTKVI NGK AQN+L+EVNITLNKN+IPFE LSPFKTS Sbjct: 303 FAQDDRFRLISGGTDNHVFLVDVTKVIANGKLAQNLLDEVNITLNKNAIPFETLSPFKTS 36- 2 Query: 361 GIRIGTPAITSRGMGVEESRRIAELMIKALKNHENQDVLTEVRQEIKSLTDAFPLYE 417 GIRIG AITSRGMGV+ES+ IA L+IKAL NH+ + +L EVRQE++ LTDAFPLY+ Sbjct: 363 GIRIGCAAITSRGMGVKESQTIARLIIKALVNHDQETILEEVRQEVRQLTDAFPLYK 419 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2126 A DNA sequence (GBSx2242) was identified in S. agalactiae <SEQ ID 6563> which encodes the amino acid sequence <SEQ ID 6564>. Analysis of this protein sequence reveals the following: TABLE-US-06500 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2289(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9839> which encodes amino acid sequence <SEQ ID 9840> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06501 >GP: AAD35934 GB: AE001752 conserved hypothetical protein [Thermotoga maritima] Identities = 71/198 (35%), Positives = 114/198 (56%), Gaps = 4/198 (2%) Query: 1 MNDLGQILEDHGAVIMPTETVYGIFAKALSEEAVNHVYELKKRPRDKAMNLNICDFETIL 60 + + ++L + +I PTETVYGI A A +EEA +++LK+RP D + ++I F+ + Sbjct: 17 LKEAAELLRNGEVIIFPTETVYGIGADAYNEEACKKIFKLKERPADNPLIVHIHSFKQLE 76 Query: 61 KYSKNQPTYLKQLYDAFLPGPLTIIL-EASQEVPHWINSGLLSVGFRMPKHPVTLDMIAN 119- + ++ +L L F PGPLT+I + S+++P + + L +V RMP HPV L +I Sbjct: 77 EIAEGYEPHLDFL-KKFWPGPLTVIFRKKSEKIPPVVTADLPTVAVRMPAHPVALKLIEL 135- Query: 120 HG-PLIGPSANISGCDSGRVFSEIQKQFNHQV-LGIEDDKALTGVDSTIIDLSGDRVKIL 17- 7 G P+ PSANISG S + + F +V L I+ G++STI+DL+ ++ +L Sbjct: 136 FGHPIAAPSANISGRPSATNVKHVIEDFMGKVKLIIDAGDTPFGLESTIVDLTKEKPVLL 19- 5 Query: 178 RQGAITQEVLTATIPELI 195 R G + E L PEL+ Sbjct: 196 RPGPVEVERLKELFPELV 213 A related DNA sequence was identified in S. pyogenes <SEQ ID 6565> which encodes the amino acid sequence <SEQ ID 6566>. Analysis of this protein sequence reveals the following: TABLE-US-06502 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0282(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06503 Identities = 127/196 (64%), Positives = 154/196 (77%) Query: 1 MNDLGQILEDHGAVIMPTETVYGIFAKALSEEAVNHVYELKKRPRDKAMNLNICDFETIL 60 M L I+E A+++PTETVYG+FAKAL E+AVN VY+LK+RPRDKAMNLN+ DF +IL Sbjct: 11 MEYLASIIESGDALVLPTETVYGLFAKALDEKAVNAVYDLKQRPRDKAMNLNVADFNSIL 70 Query: 61 KYSKNQPTYLKQLYDAFLPGPLTIILEASQEVPHWINSGLLSVGFRMPKHPVTLDMIANH 120- +SK QP YLK+LY AFLPGPLTIIL+A+ +VP+WINSGL +VGFR+P HP+T +I Sbjct: 71 AFSKEQPRYLKKLYQAFLPGPLTIILKANDQVPYWINSGLSTVGFRLPSHPITAALIQKT 130- Query: 121 GPLIGPSANISGCDSGRVFSEIQKQFNHQVLGIEDDKALTGVDSTIIDLSGDRVKILRQG 18- 0 GPLIGPSAN+SG SGRVF I + F+ QV G DD LTG DSTI+DLSG+R ILRQG Sbjct: 131 GPLIGPSANLSGKASGRVFDHIMQDFDFQVFGYADDPFLTGKDSTILDLSGERAVILRQG 19- 0 Query: 181 AITQEVLTATIPELIF 196 AIT+E L A +PEL F Sbjct: 191 AITKEELLANVPELRF 206 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2127 A DNA sequence (GBSx2243) was identified in S. agalactiae <SEQ ID 6567> which encodes the amino acid sequence <SEQ ID 6568>. This protein is predicted to be protoporphyrinogen oxidase (hemK). Analysis of this protein sequence reveals the following: TABLE-US-06504 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06505 >GP: BAB07493 GB: AP001519 protoporphyrinogen oxidase [Bacillus halodurans] Identities = 94/236 (39%), Positives = 132/236 (55%), Gaps = 12/236 (5%) Query: 49 DTDQQLMENIFQQLKKHRSP---QYITGKAYFRDLIFFVDERVLIPRPETEELVDLILSE 105- + D +L + + + L H S Q++ G F F VD+ VLIPRPETEELV +L E Sbjct: 46 ELDGELFQRLEEDLAAHASGVPVQHLIGVESFYGRQFQVDQHVLIPRPETEELVLAVLKE 105- Query: 106 -----NKVEDCSVLDIGTGSGAIAISLKKERPSWDVLASDISVSALDLAKENANNCDAEV 16- 0 K E+ ++LDIGTGSGAIA++L E +V A DIS AL +A +NA A V Sbjct: 106 IRRQFKKEEEITILDIGTGSGAIAVTLALEEERTNVTAVDISRDALQVAADNARRLGANV 16- 5 Query: 161 TFIESDV---FSNISGKFDIIVSNPPYISYNDKDEVGKNVLASEPHSALFADEEGLAIYR 21- 7 I D+ F +FD+IVSNPPYI +KD + +V EP ALF +GL +YR Sbjct: 166 QLIHGDLGEPFLKTGERFDVIVSNPPYIPTVEKDTLAVHVRDHEPALALFGGVDGLDVYR 22- 5 Query: 218 KIIENSREYL-QPRGKLYFEIGYKQGDDLRSLLKRYFPNNRCRVLKDIFGKDRMVV 272 +++ + +G + EIG QG D+ L++ +P VL D+ GKDR+V+ Sbjct: 226 RLMSQLPALTKEEKGMVALEIGAGQGMDVEKLMQTAYPKAAVDVLYDLNGKDRIVL 281 A related DNA sequence was identified in S. pyogenes <SEQ ID 6569> which encodes the amino acid sequence <SEQ ID 6570>. Analysis of this protein sequence reveals the following:

TABLE-US-06506 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4324(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06507 Identities = 174/274 (63%), Positives = 207/274 (75%) Query: 1 MNYAQLIKHYGQLLEACGEEVENFIYVLKDLKQWSTTDYLLNQNSSVSDTDQQLMENIFQ 60 MNYA LI+ Y LE E+ EN YV +++K+WS+ D L++QN +V+ D L+E+IF Sbjct: 1 MNYATLIRTYEDKLEQIDEDRENLAYVFREIKEWSSLDMLIHQNQAVTPEDAVLLEHIFC 60 Query: 61 QLKKHRSPQYITGKAYFRDLIFFVDERVLIPRPETEELVDLILSENKVEDCSVLDIGTGS 120- L +H SPQYITG AYFRDL VD+RVLIPRPETEELVD+IL+EN +VLDIGTGS Sbjct: 61 SLSQHLSPQYITGNAYFRDLKLAVDKRVLIPRPETEELVDMILAENLDAPLNVLDIGTGS 120- Query: 121 GAIAISLKKERPSWDVLASDISVSALDLAKENANNCDAEVTFIESDVFSNISGKFDIIVS 18- 0 GAIAISLKKERP+W V ASDIS +ALDLAK NA+ ++TFIESDVFS IS FDIIVS Sbjct: 121 GAIAISLKKERPNWQVTASDISRAALDLAKANADAYQLDITFIESDVFSLISETFDIIVS 18- 0 Query: 181 NPPYISYNDKDEVGKNVLASEPHSALFADEEGLAIYRKIIENSREYLQPRGKLYFEIGYK 24- 0 NPPYISY DK+EV NVL SEPH ALFA E G AIYRKIIE + YL GKLYFEIGYK Sbjct: 181 NPPYISYEDKEEVSLNVLQSEPHLALFAKENGYAIYRKIIEQADNYLTKEGKLYFEIGYK 24- 0 Query: 241 QGDDLRSLLKRYFPNNRCRVLKDIFGKDRMVVLD 274 Q + ++ +L+ YFP R + DIFGK+RMVV+D Sbjct: 241 QAEGIKDMLQAYFPQRHIRAVTDIFGKERMVVVD 274 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2128 A DNA sequence (GBSx2244) was identified in S. agalactiae <SEQ ID 6571> which encodes the amino acid sequence <SEQ ID 6572>. This protein is predicted to be peptide chain release factor RF-1 (prfA). Analysis of this protein sequence reveals the following: TABLE-US-06508 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3446(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06509 >GP: CAB15718 GB: Z99122 peptide chain release factor 1 [Bacillus subtilis] Identities = 211/351 (60%), Positives = 280/351 (79%), Gaps = 1/351 (0%) Query: 5 DQLQAVEDRYEELGELLSDPDVVSDTKRFMELSREEASTRETVTAYREYKQVIQNISDAE 64 D+L+++E+RYE+L ELLSDP+VV+D K+ E S+E++ +ETV YR+Y+ + ++DA+ Sbjct: 3 DRLKSIEERYEKLNELLSDPEVVNDPKKLREYSKEQSDIQETVDVYRQYRDASEQLADAK 62 Query: 65 EMIKDASGDAELEEMAKEELKESKAAKEEYEERLKILLLPKDPNDDKNIILEIRGAAGGD 124- M+++ DAE+ +M KEE+ E + E ERLK+LL+PKDPNDDKN+I+EIRGAAGG+ Sbjct: 63 AMLEEKL-DAEMRDMVKEEISELQKETETLSERLKVLLIPKDPNDDKNVIMEIRGAAGGE 121- Query: 125 EAALFAGDLLTMYQKYAETQGWRFEVMESSVNGVGGIKEVVAMVSGQSVYSKLKYESGAH 18- 4 EAALFAG+L MY +YAE QGW+ EVME++V G GG KE++ M++G YSKLKYE+GAH Sbjct: 122 EAALFAGNLYRMYSRYAELQGWKTEVMEANVTGTGGYKEIIFMITGSGAYSKLKYENGAH 18- 1 Query: 185 RVQRVPVTESQGRVHTSTATVLVMPEVEEVEYEIDQKDLRVDIYHASGAGGQNVNKVATA 24- 4 RVQRVP TES GR+HTSTATV +PE EEVE +I +KD+RVD + +SG GGQ+VN +A Sbjct: 182 RVQRVPETESGGRIHTSTATVACLPEAEEVEVDIHEKDIRVDTFASSGPGGQSVNTTMSA 24- 1 Query: 245 VRMVHIPTGIKVEMQEERTQQKNRDKAMKIIRARVADHFAQIAQDEQDAERKSTVGTGDR 30- 4 VR+ H+PTG+ V Q+E++Q KN++KAMK++RAR+ D F Q AQ E D RKS VG+GDR Sbjct: 242 VRLTHLPTGVVVSCQDEKSQIKNKEKAMKVLRARIYDKFQQEAQAEYDQTRKSAVGSGDR 30- 1 Query: 305 SERIRTYNFPQNRVTDHRIGLTLQKLDTILSGKMDEVIDALVMYDQTQKLE 355 SERIRTYNFPQNRVTDHRIGLT+QKLD IL GK+DEV++AL++ DQ KL+ Sbjct: 302 SERIRTYNFPQNRVTDHRIGLTIQKLDQILEGKLDEVVEALIVEDQASKLQ 352 A related DNA sequence was identified in S. pyogenes <SEQ ID 6573> which encodes the amino acid sequence <SEQ ID 6574>. Analysis of this protein sequence reveals the following: TABLE-US-06510 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3446(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06511 Identities = 349/358 (97%), Positives = 354/358 (98%) Query: 1 MNIYDQLQAVEDRYEELGELLSDPDVVSDTKRFMELSREEASTRETVTAYREYKQVIQNI 60 MNIYDQLQAVEDRYEELGELLSDPDVVSDTKRFMELSREE +TRETVTAYREYKQVIQ I Sbjct: 1 MNIYDQLQAVEDRYEELGELLSDPDVVSDTKRFMELSREETNTRETVTAYREYKQVIQTI 60 Query: 61 SDAEEMIKDASGDAELEEMAKEELKESKAAKEEYEERLKILLLPKDPNDDKNIILEIRGA 120- SDAEEMIKDASGD ELEEMAKEELKESKAAKEEYEE+LKILLLPKDPNDDKNIILEIRGA Sbjct: 61 SDAEEMIKDASGDPELEEMAKEELKESKAAKEEYEEKLKILLLPKDPNDDKNIILEIRGA 120- Query: 121 AGGDEAALFAGDLLTMYQKYAETQGWRFEVMESSVNGVGGIKEVVAMVSGQSVYSKLKYE 18- 0 AGGDEAALFAGDLLTMYQKYAETQGWRFEVMESSVNGVGGIKEVVAMVSGQSVYSKLKYE Sbjct: 121 AGGDEAALFAGDLLTMYQKYAETQGWRFEVMESSVNGVGGIKEVVAMVSGQSVYSKLKYE 18- 0 Query: 181 SGAHRVQRVPVTESQGRVHTSTATVLVMPEVEEVEYEIDQKDLRVDIYHASGAGGQNVNK 24- 0 SGAHRVQRVPVTESQGRVHTSTATVLVMPEVEEVEY+ID KDLRVDIYHASGAGGQNVNK Sbjct: 181 SGAHRVQRVPVTESQGRVHTSTATVLVMPEVEEVEYDIDPKDLRVDIYHASGAGGQNVNK 24- 0 Query: 241 VATAVRMVHIPTGIKVEMQEERTQQKNRDKAMKIIRARVADHFAQIAQDEQDAERKSTVG 30- 0 VATAVRMVHIPTGIKVEMQEERTQQKNRDKAMKIIRARVADHFAQIAQDEQDAERKSTVG Sbjct: 241 VATAVRMVHIPTGIKVEMQEERTQQKNRDKAMKIIRARVADHFAQIAQDEQDAERKSTVG 30- 0 Query: 301 TGDRSERIRTYNFPQNRVTDHRIGLTLQKLDTILSGKMDEVIDALVMYDQTQKLEALN 358 TGDRSERIRTYNFPQNRVTDHRIGLTLQKLDTILSGKMDEVIDALVMYDQT+KLE+LN Sbjct: 301 TGDRSERIRTYNFPQNRVTDHRIGLTLQKLDTILSGKMDEVIDALVMYDQTKKLESLN 358 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2129 A DNA sequence (GBSx2245) was identified in S. agalactiae <SEQ ID 6575> which encodes the amino acid sequence <SEQ ID 6576>. This protein is predicted to be thymidine kinase (tdk). Analysis of this protein sequence reveals the following: TABLE-US-06512 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2244(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9841> which encodes amino acid sequence <SEQ ID 9842> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06513 >GP: AAB02289 GB: L40415 thymidine kinase [Streptococcus gordonii] Identities = 158/189 (83%), Positives = 175/189 (91%) Query: 1 MAQLYYKYGTMNSGKTIEILKVAHNYEEQGKPVVIMTSALDTRDEFGVVSSRIGMRREAV 60 MAQLYYKYGTMNSGKTIEILKVAHNYEEQGK VVIMTSA+DTRD G VSSRIGM+R+A+ Sbjct: 1 MAQLYYKYGTMNSGKTIEILKVAHNYEEQGKGVVIMTSAVDTRDGVGYVSSRIGMKRQAM 60 Query: 61 PISDDMDIFSYIQNLPQKPYCVLIDECQFLSKKNVYDLARVVDDLDVPVMAFGLKNDFQN 120- I DD DI YI+NLP+KPYC+LIDE QFL + +VYDLARVVD+LDVPVMAFGLKNDF+N Sbjct: 61 AIEDDTDILGYIKNLPEKPYCILIDEAQFLKRHHVYDLARVVDELDVPVMAFGLKNDFRN 120- Query: 121 NLFEGSKHLLLLADKIDEIKTICQYCSKKATMVLRTENGKPVYEGDQIQIGGNETYIPVC 18- 0 LFEGSKHLLLLADKI+EIKTICQYCS+KATMVLRT++GKPVY+G+QIQIGGNETYIPVC Sbjct: 121 ELFEGSKHLLLLADKIEEIKTICQYCSRKATMVLRTDHGKPVYDGEQIQIGGNETYIPVC 18- 0 Query: 181 RKHYFNPDI 189 RKHYF PDI Sbjct: 181 RKHYFKPDI 189 A related DNA sequence was identified in S. pyogenes <SEQ ID 6577> which encodes the amino acid sequence <SEQ ID 6578>. Analysis of this protein sequence reveals the following: TABLE-US-06514 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2244(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06515 Identities = 174/189 (92%), Positives = 184/189 (97%) Query: 1 MAQLYYKYGTMNSGKTIEILKVAHNYEEQGKPVVIMTSALDTRDEFGVVSSRIGMRREAV 60 +AQLYYKYGTMNSGKTIEILKVAHNYEEQGKPVVIMTSALDTRD FG+VSSRIGMRREA+ Sbjct: 1 LAQLYYKYGTMNSGKTIEILKVAHNYEEQGKPVVIMTSALDTRDGFGIVSSRIGMRREAI 60 Query: 61 PISDDMDIFSYIQNLPQKPYCVLIDECQFLSKKNVYDLARVVDDLDVPVMAFGLKNDFQN 120- PIS+DMDIF++I L +KPYCVLIDE QFLSK+NVYDLARVVD+L+VPVMAFGLKNDFQN Sbjct: 61 PISNDMDIFTFIAQLEEKPYCVLIDESQFLSKQNVYDLARVVDELNVPVMAFGLKNDFQN 120- Query: 121 NLFEGSKHLLLLADKIDEIKTICQYCSKKATMVLRTENGKPVYEGDQIQIGGNETYIPVC 18- 0 NLFEGSKHLLLLADKIDEIKTICQYCSKKATMVLRTENGKPVYEGDQIQIGGNETYIPVC Sbjct: 121 NLFEGSKHLLLLADKIDEIKTICQYCSKKATMVLRTENGKPVYEGDQIQIGGNETYIPVC 18- 0 Query: 181 RKHYFNPDI 189 RKHYFNPDI Sbjct: 181 RKHYFNPDI 189 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2130 A DNA sequence (GBSx2246) was identified in S. agalactiae <SEQ ID 6579> which encodes the amino acid sequence <SEQ ID 6580>. Analysis of this protein sequence reveals the following: TABLE-US-06516 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3995(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06517 >GP: AAA26046 GB: M95650 4-oxalocrotonate tautomerase [Plasmid pWW0] Identities = 27/60 (45%), Positives = 36/60 (60%) Query: 1 MPFVKIDLFEGRSQEQKNELAREVTEVVSRIAKAPKENIHVFINDMPEGTYYPQGELKKK 60 MP +I + EGRS EQK L REV+E +SR AP ++ V I +M +G + GEL K Sbjct: 1 MPIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK 60 A related DNA sequence was identified in S. pyogenes <SEQ ID 6581> which encodes the amino acid sequence <SEQ ID 6582>. Analysis of this protein sequence reveals the following: TABLE-US-06518 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4128(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06519 Identities = 56/60 (93%), Positives = 59/60 (98%) Query: 1 MPFVKIDLFEGRSQEQKNELAREVTEVVSRIAKAPKENIHVFINDMPEGTYYPQGELKKK 60 MPFV IDLFEGRSQEQKN+LAREVTEVVSRIAKAPKENIHVFINDMPEGTYYPQGE+K+K Sbjct: 1 MPFVTIDLFEGRSQEQKNQLAREVTEVVSRIAKAPKENIHVFINDMPEGTYYPQGEMKQK 60 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2131 A DNA sequence (GBSx2247) was identified in S. agalactiae <SEQ ID 6583> which encodes the amino acid sequence <SEQ ID 6584>. Analysis of this protein sequence reveals the following: TABLE-US-06520 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2154(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9843> which encodes amino acid sequence <SEQ ID 9844> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06521 >GP: AAC65759 GB: AE001250 conserved hypothetical protein [Treponema pallidum] Identities = 103/317 (32%), Positives = 163/317 (50%), Gaps = 15/317 (4%) Query: 7 QLSHSLRLMGTTIDIQINSKNAQKQIR----EVIELLELYKNRFSANDFNSELMAINNNA 62 + S + ++GT +++ SK ++ EV LL+ + SAN +S L A+N A Sbjct: 31 EYSRAELVIGTLCRVRVYSKRPAAEVHAALEEVFTLLQQQEMVLSANRDDSALAALNAQA 90 Query: 63 GIKPIQVHPDLFELITIGKEHSLARPSNLNIAIGPLVQTWRIGFSDAKLPSPSEISEAMI 122- G P+ V L+ L+ + N A+G V+ W IGF A +P P + EA+ Sbjct: 91 GSAPVVVDRSLYALLERALFFAEKSGGAFNPALGAXVKLWNIGFDRAAVPDPDALKEALT 150- Query: 123 LSDPTHILLDSN-----KQSVFLNQIGMKIDLGALAKGYIADKIMTYLKNEMIDSAIINL 17- 7 D + L + +V L Q GM++DLGA+AKG++ADKI+ L +DSA+++L Sbjct: 151 RCDFRQVHLRAGVSVGAPHTVQLAQAGMQLDLGAIAKGFLADKIVQLLTAHALDSALVDL 21- 0 Query: 178 GGNV----LVHGDNPNRSEGY--WVIGIQHPKKKRGKNIGTVKIKNQSVVTSGTYERRLI 23- 1 GGN+ L +GD + + W +GI+ P K V +++ SVVTSG YER Sbjct: 211 GGNIFALGLKYGDVRSAAAQRLEWNVGIRDPHGTGQKPALVVSVRDCSVVTSGAYERFFE 27- 0 Query: 232 IDDKEYHHIFDRQTGYPIQTEMASISIVSKQSVDCEIWTTRLFGLSIKEALDILNAVSYI 29- 1 D YHHI D TG+P T++ S+SI + +S D + T F L +++ +L + Sbjct: 271 RDGVRYHHIIDPVTGFPAHTDVDSVSIFAPRSTDADALATACFVLGYEKSCALLREFPGV 33- 0 Query: 292 EGIIITKDDRIYLSDGL 308 + + I D R+ S G+ Sbjct: 331 DALFIFPDKRVRASAGI 347 A related DNA sequence was identified in S. pyogenes <SEQ ID 6585> which encodes the amino acid sequence <SEQ ID 6586>. Analysis of this protein sequence reveals the following: TABLE-US-06522 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1020(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06523 Identities = 182/310 (58%), Positives = 232/310 (74%) Query: 8 LSHSLRLMGTTIDIQINSKNAQKQIREVIELLELYKNRFSANDFNSELMAINNNAGIKPI 67 ++ L+LMGT IDIQI S A +Q+ VI+LL YKNRFSAND NSELMAIN AG+KP+ Sbjct: 3 VTQQLKLMGTVIDIQIESDKACQQLSRVIDLLYTYKNRFSANDSNSELMAINQAAGVKPV 62 Query: 68 QVHPDLFELITIGKEHSLARPSNLNIAIGPLVQTWRIGFSDAKLPSPSEISEAMILSDPT 127- VH DLF LI IGK HSL+ PSNLNIAIGPLVQ WRIGF DA++PS + IS+ + L+DP Sbjct: 63 SVHSDLFNLIQIGKAHSLSTPSNLNIAIGPLVQAWRIGFEDARVPSHNLISQQLALTDPR 122- Query: 128 HILLDSNKQSVFLNQIGMKIDLGALAKGYIADKIMTYLKNEMIDSAIINLGGNVLVHGDN 18- 7 +L+D KQ+VFL Q+GM +DLGALAKGYI DKIM YL + IDSA+INLGGNV VHG N Sbjct: 123 QVLIDDKKQTVFLQQVGMALDLGALAKGYITDKIMAYLIEDGIDSALINLGGNVRVHGPN 18- 2 Query: 188 PNRSEGYWVIGIQHPKKKRGKNIGTVKIKNQSVVTSGTYERRLIIDDKEYHHIFDRQTGY 24- 7 P + + IGIQ P KRG+++G +K+ N SVVTSG YER+ K+YHHI DRQTGY Sbjct: 183 PKSPDKTFRIGIQKPDAKRGQHLGVIKVNNHSVVTSGIYERQFTSKGKQYHHILDRQTGY 24- 2 Query: 248 PIQTEMASISIVSKQSVDCEIWTTRLFGLSIKEALDILNAVSYIEGIIITKDDRIYLSDG 30- 7 PI+T+M S++I++ S C+IWTTRLFGL + +LN IEG+++T+ + +S+G Sbjct: 243 PIETDMLSLTIMAPSSFYCDIWTTRLFGLDSSMIITLLNTFDNIEGLLVTRKHHVLMSNG 30- 2 Query: 308 LKHHFQLFYH 317 L+H+FQ +YH Sbjct: 303 LRHYFQPYYH 312 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2132 A DNA sequence (GBSx2248) was identified in S. agalactiae <SEQ ID 6587> which encodes the amino acid sequence <SEQ ID 6588>. Analysis of this protein sequence reveals the following: TABLE-US-06524 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0966(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06525 >GP: AAG18632 GB: AY007504 unknown [Streptococcus mitis] Identities = 92/160 (57%), Positives = 119/160 (73%), Gaps = 1/160 (0%) Query: 1 MKLIGIVGTNSNKSTNRQLLQYMQQHFADKAEIELIEVKDLPLFNKPADKNVPQVILDIA 60 MKL+ IVGTNSN+STNR+LL++MQ+HF+DKA+IE++E+K LP FN+P D+ P + + Sbjct: 1 MKLVAIVGTNSNRSTNRKLLKFMQKHFSDKADIEVLEIKQLPAFNEPEDEQAPAEVQAFS 60 Query: 61 AKIEETDGVIIGTPEYDHSIPSALMSVLAWLSYGIYPLLNKPVMITGASYGTLGSSRAQL 120- KI DGVII TPEYDH+IP+ L S L W++Y L+NKP MI GAS G LG+SRAQ Sbjct: 61 EKILAADGVIISTPEYDHTIPAPLASALEWIAYTSRALINKPTMIVGASLGLLGTSRAQA 120- Query: 121 QLRQILNAPELKASVLP-DEFLLSHSLQAFDKDGNLHDIE 159 LRQIL+APELKA V+P EF L HS Q D + +L++ E Sbjct: 121 HLRQILDAPELKARVMPGTEFFLGHSEQVLDDECHLNNPE 160 A related DNA sequence was identified in S. pyogenes <SEQ ID 6589> which encodes the amino acid sequence <SEQ ID 6590>. Analysis of this protein sequence reveals the following: TABLE-US-06526 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases:

TABLE-US-06527 >GP: CAB62679 GB: AL133422 putative secreted protein. [Streptomyces coelicolor A3(2)] Identities = 68/192 (35%), Positives = 94/192 (48%), Gaps = 25/192 (13%) Query: 4 ILFIVGSLREGSFNHQLAAQAQK-ALEHQAVVSYLNWKDVPVLNQDIEANAPLPVVDA-- 60 IL +VGSLR GS N QLA A + A E V + ++P N+DI+ +P A Sbjct: 5 ILALVGSLRAGSHNRQLAEAAVRFAPEGAEVQLFEGLAEIPFYNEDIDVEGSVPAAAAKL 64 Query: 61 RQAVQSADAIWIFTPVYNFSIPGSVKNLLDWLSRALDLSDPTGPSAIGGKVVTVSSVANG 120- R+A Q A A +F+P YN +IP +KN +DWLSR P G A GK V V A G Sbjct: 65 REAAQGAQAFLLFSPEYNGTIPAVLKNAIDWLSR------PYGAGAFTGKPVAVVGTAFG 118- Query: 121 GHDQVFDQFKA----------LLPFIRTSVAGEFTK-ATVNP--DAWGTGRLEISKETKA 16- 7 + V+ Q +A ++ I+ S+ G T+ A +P DA +L E A Sbjct: 119 QYGGVWAQDEARKAVGIAGGKVIEDIKLSIPGSVTRFAETHPADDAEVAAQL---TEVVA 17- 5 Query: 168 NLLSQAEALLAA 179 L A+ +AA Sbjct: 176 RLHGHADEAIAA 187 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06528 Identities = 28/90 (31%), Positives = 49/90 (54%) Query: 3 LIGIVGTNSNKSTNRQLLQYMQQHFADKAEIELIEVKDLPLFNKPADKNVPQVILDIAAK 62 ++ IVG+ S N QL Q+ +A + + KD+P+ N+ + N P ++D Sbjct: 4 ILFIVGSLREGSFNHQLAAQAQKALEHQAVVSYLNWKDVPVLNQDIEANAPLPVVDARQA 63 Query: 63 IEETDGVIIGTPEYDHSIPSALMSVLAWLS 92 ++ D + I TP Y+ SIP ++ ++L WLS Sbjct: 64 VQSADAIWIFTPVYNFSIPGSVKNLLDWLS 93 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2133 A DNA sequence (GBSx2249) was identified in S. agalactiae <SEQ ID 6591> which encodes the amino acid sequence <SEQ ID 6592>. Analysis of this protein sequence reveals the following: TABLE-US-06529 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1160(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2134 A DNA sequence (GBSx2250) was identified in S. agalactiae <SEQ ID 6593> which encodes the amino acid sequence <SEQ ID 6594>. Analysis of this protein sequence reveals the following: TABLE-US-06530 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2132(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06531 >GP: AAG18632 GB: AY007504 unknown [Streptococcus mitis] Identities = 80/162 (49%), Positives = 112/162 (68%) Query: 1 MKFVGIVGSNAEQSYNRMLLEFIRKNFKTKFELEVLEIDDIPMFNQDQNWEESFQLRLLN 60 MK V IVG+N+ +S NR LL+F++K+F K ++EVLEI +P FN+ ++ + +++ + Sbjct: 1 MKLVAIVGTNSNRSTNRKLLKFMQKHFSDKADIEVLEIKQLPAFNEPEDEQAPAEVQAFS 60 Query: 61 NKITRADGVIIATPEHNHTITAALKSVLEWLSFAVHPLENKPVMIVGASYYDQGTSRAQI 120- KI ADGVII+TPE++HTI A L S LEW+++ L NKP MIVGAS GTSRAQ Sbjct: 61 EKILAADGVIISTPEYDHTIPAPLASALEWIAYTSRALINKPTMIVGASLGLLGTSRAQA 120- Query: 121 HLRKILDAPGVNAYTLPGNEFLLGKAKEAFDDNGNIINPGTV 162 HLR+ILDAP + A +PG EF LG +++ DD ++ NP V Sbjct: 121 HLRQILDAPELKARVMPGTEFFLGHSEQVLDDECHLNNPEKV 162 There is also homology to SEQ ID 6596. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2135 A DNA sequence (GBSx2251) was identified in S. agalactiae <SEQ ID 6597> which encodes the amino acid sequence <SEQ ID 6598>. Analysis of this protein sequence reveals the following: TABLE-US-06532 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.32 Transmembrane 13-29 (11-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.3930(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2136 A DNA sequence (GBSx2252) was identified in S. agalactiae <SEQ ID 6599> which encodes the amino acid sequence <SEQ ID 6600>. This protein is predicted to be potential nitrite transporter. Analysis of this protein sequence reveals the following: TABLE-US-06533 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.92 Transmembrane 61-77 (54-82) INTEGRAL Likelihood = -5.57 Transmembrane 106-122 (103-126) INTEGRAL Likelihood = -5.15 Transmembrane 160-176 (159-177) INTEGRAL Likelihood = -4.09 Transmembrane 180-196 (179-199) INTEGRAL Likelihood = -1.01 Transmembrane 233-249 (233-249) ----- Final Results ----- bacterial membrane --- Certainty = 0.4970(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06534 >GP: CAB15832 GB: Z99123 alternate gene name: ipa-48r~similar to nitrite transporter [Bacillus subtilis] Identities = 82/253 (32%), Positives = 119/253 (46%), Gaps = 10/253 (3%) Query: 6 EKIAYNCAKKEALYKESLGRYALRSMLAGAYLTMSTAAGIVAADTIGK-ISPALSGFVF- 63 +K+ KK+ ++ S RY LRS+LA ++ GI AA G A S F F Sbjct: 7 QKVEQYALKKQNIFASSKIRYVLRSILASIFIGF----GITAASKTGSYFFMADSPFAFP 62 Query: 64 --AFIFSFGLIYVLIFNGELATSNMLYLTAGAYNKNISWKKAMTILIYCTFFNLVGACIL 121- A F ++ + G+L T N Y T A K ISW+ + + + NL+GA + Sbjct: 63 AAAVTFGAAILMIAYGGGDLFTGNTFYFTYTALRKKISWRDTLYLWMSSYAGNLIGAILF 122- Query: 122 AWLFNQSYSFQHLTNDSFLGHVVAKKLGKPSSGAFLEGIIANMFVNLAILAYMLLKEESA 18- 1 A L + + F+ + SFL H+ K+ P+S F G++ N V LA M LK E A Sbjct: 123 AILISATGLFEEPSVHSFLIHLAEHKMEPPASELFFRGMLCNWLVCLAFFIPMSLKGEGA 18- 2 Query: 182 KMTVILSAIFMFVFLSNEHLIANFASFMLAAFSHIEHIKGFTLLNIIRQWTLVFFGNWIG 24- 1 K+ ++ +F F EH IAN +F ++ IEH TL+ +R V GN Sbjct: 183 KLFTMMLFVFCFFISGFEHSIANMCTFAISLL--IEHPDTVTLMGAVRNLIPVTLGNLTA 24- 0 Query: 242 GGVFIGLAYAWLN 254 G V +G Y LN Sbjct: 241 GIVMMGWMYYTLN 253 A related DNA sequence was identified in S. pyogenes <SEQ ID 6601> which encodes the amino acid sequence <SEQ ID 6602>. Analysis of this protein sequence reveals the following: TABLE-US-06535 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.77 Transmembrane 142-158 (139-171) INTEGRAL Likelihood = -9.34 Transmembrane 95-111 (89-119) INTEGRAL Likelihood = -2.02 Transmembrane 61-77 (61-79) INTEGRAL Likelihood = -1.12 Transmembrane 261-277 (261-279) INTEGRAL Likelihood = -0.53 Transmembrane 191-207 (191-207) ----- Final Results ----- bacterial membrane --- Certainty = 0.4906(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06536 >GP: AAB80864 GB: U93874 formate dehydrogenase [Bacillus subtilis] Identities = 133/258 (51%), Positives = 181/258 (69%) Query: 36 KTPEQILEATIHIGEHKVTKTFLAKSILGFIGGAMISLGYLLYVRIAASGLETFGAFSSI 95 - + P++I EA I G K+ + +LGF+GGA I+LGYLL +R+ + +G+ SS+ Sbjct: 4 RKPDEIAEAAIEAGMKKIKLPLPSLLVLGFLGGAFIALGYLLDIRVIGDLPKEWGSLSSL 63 Query: 96 VGACAFPIGLIIILMAGGELITGNMMAVSAALLAKKIKFSELAKNWLIITLFNVIGAVFV 155- +GA FP+GLI++++AG ELITGNMM+V+ AL ++KI ELA NW I+T+ N+IGA+FV Sbjct: 64 IGAAVFPVGLILVVLAGAELITGNMMSVAMALFSRKISVKELAINWGIVTIMNLIGALFV 123- Query: 156 AFVFGHFLGLTSAGIFKEEVIEVAHAKIAASPLQALVSGIGCNWFVGLALWLCYGANDAA 21- 5 A+ FGH +GLT G + E+ I VA K+ S + L+S IGCNW V LA+WL +GA DAA Sbjct: 124 AYFFGHLVGLTETGPYLEKTIAVAQGKLDMSFGKVLISAIGCNWLVCLAVWLSFGAQDAA 18- 3 Query: 216 GKFLGTWFPVMTFVALGFQHSVANAFVIPAAIFEGGATWLDFVTNFIFVYSGNIIGGAIF 27- 5 GK LG WFP+M FVA+GFQH VAN FVIPAAIF G TW F+ N I + GN+IGGA+F Sbjct: 184 GKILGIWFPIMAFVAIGFQHVVANMFVIPAAIFAGSFTWGQFIGNIIPAFIGNVIGGAVF 24- 3 Query: 276 VSFLYFKVYYHPQKSKTQ 293 V +YF Y+ +S+ + Sbjct: 244 VGLIYFIAYHKKDRSRKE 261 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06537 Identities = 69/240 (28%), Positives = 101/240 (41%), Gaps = 18/240 (7%) Query: 15 KEALYKESLGRYALRSMLAGAYLTMSTAAGIVAADTIGKISPALSGFVFAFIFSFGLIYV 74 - K L K LG + G L + AA +T G A S V A F GLI + Sbjct: 55 KTFLAKSILGFIGGAMISLGYLLYVRIAAS--GLETFG----AFSSIVGACAFPIGLIII 108- Query: 75 LIFNGELATSNMLYLTAGAYNKNISWKKAMTILIYCTFFNLVGACILAWLFNQSYSFQHL 134- L+ GEL T NM+ ++A K I + + + T FN++GA +A++F F L Sbjct: 109 LMAGGELITGNMMAVSAALLAKKIKFSELAKNWLIITLFNVIGAVFVAFVFGH---FLGL 16- 5 Query: 135 TNDSFLGHVVAK----KLGKPSSGAFLEGIIANMFVNLAILAYMLLKEESAKMTVILSAI 19- 0 T+ V + K+ A + GI N FV LA+ + + K + Sbjct: 166 TSAGIFKEEVIEVAHAKIAASPLQALVSGIGCNWFVGLALWLCYGANDAAGKFLGTWFPV 22- 5 Query: 191 FMFVFLSNEHLIANFASFMLAAFSHIEHIKGFTLLNIIRQWTLVFFGNWIGGGVFIGLAY 25- 0 FV L +H +AN A F G T L+ + + V+ GN IGG +F+ Y Sbjct: 226 MTFVALGFQHSVANAFVIPAAIFE-----GGATWLDFVTNFIFVYSGNIIGGAIFVSFLY 28- 0 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2137 A DNA sequence (GBSx2253) was identified in S. agalactiae <SEQ ID 6603> which encodes the amino acid sequence <SEQ ID 6604>. Analysis of this protein sequence reveals the following: TABLE-US-06538 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1342(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2138 A DNA sequence (GBSx2254) was identified in S. agalactiae <SEQ ID 6605> which encodes the amino acid sequence <SEQ ID 6606>. Analysis of this protein sequence reveals the following: TABLE-US-06539 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.22 Transmembrane 44-60 (44-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.1086(Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2139 A DNA sequence (GBSx2255) was identified in S. agalactiae <SEQ ID 6607> which encodes the amino acid sequence <SEQ ID 6608>. This protein is predicted to be xanthine permease (pbuX). Analysis of this protein sequence reveals the following: TABLE-US-06540 Possible site: 23 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.91 Transmembrane 160-176 (156-188) INTEGRAL Likelihood = -6.48 Transmembrane 184-200 (179-211) INTEGRAL Likelihood = -6.21 Transmembrane 101-117 (96-121) INTEGRAL Likelihood = -4.04 Transmembrane 309-325 (306-332) INTEGRAL Likelihood = -3.98 Transmembrane 334-350 (331-353) INTEGRAL Likelihood = -3.88 Transmembrane 400-416 (396-420) INTEGRAL Likelihood = -3.45 Transmembrane 19-35 (18-38) INTEGRAL Likelihood = -2.81 Transmembrane 127-143 (127-146) INTEGRAL Likelihood = -2.71 Transmembrane 228-244 (227-249) INTEGRAL Likelihood = -2.02 Transmembrane 47-63 (47-63) INTEGRAL Likelihood = -1.97 Transmembrane 75-91 (73-92) INTEGRAL Likelihood = -0.85 Transmembrane 368-384 (368-384) ----- Final Results ----- bacterial membrane --- Certainty = 0.4163(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06541 >GP: CAB14123 GB: Z99115 xanthine permease [Bacillus subtilis] Identities = 213/412 (51%), Positives = 292/412 (70%), Gaps = 5/412 (1%) Query: 14 LGLQHLLAMYAGSILVPIMIASALGYNAKQLTYLIATDIFMCGIATLLQLRLSKHFGVGL 73 - LG+QH+LAMYAG+I+VP+++ A+G +QLTYL++ DIFMCG+ATLLQ+ ++ FG+GL Sbjct: 11 LGIQHVLAMYAGAIVVPLIVGKAMGLTVEQLTYLVSIDIFMCGVATLLQVWSNRFFGIGL 70 Query: 74 PVVLGCAFQSVAPLSIIGAQQGSGYMFGALIASGIYVVLVAGIFSKVANFFPPIVTGSVI 133- PVVLGC F +V+P+ IG++ G ++G++IASGI V+L++ F K+ +FFPP+VTGSV+ Sbjct: 71 PVVLGCTFTAVSPMIAIGSEYGVSTVYGSIIASGILVILISFFFGKLVSFFPPVVTGSVV 130- Query: 134 TTIGLTLIPVAMGNMGD---NAKEPSLQSLTLSLVTIGVVLLINIFAKGFLKSISILIGL 19- 0 T IG+TL+PVAM NM +A L +L L+ + +++L+ F KGF+KS+SILIG+ Sbjct: 131 TIIGITLMPVAMNNMAGGEGSADFGDLSNLALAFTVLSIIVLLYRFTKGFIKSVSILIGI 19- 0 Query: 191 ISGTILAAFMGLVDASVVADAPLVHIPKPFYFGAPRFEFTSILMMCIIATVSMVESTGVY 25- 0 + GT +A FMG V V+DA +V + +PFYFGAP F I+ M I+A VS+VESTGVY Sbjct: 191 LIGTFIAYFMGKVQFDNVSDAAVVQMIQPFYFGAPSFHAAPIITMSIVAIVSLVESTGVY 25- 0 Query: 251 LALSDITNDKLDSKRLRNGYRSEGLAVLLGGLFNTFPYTGFSQNVGLVQISGIRTRKPIY 31- 0 AL D+TN +L L GYR+EGLAVLLGG+FN FPYT FSQNVGLVQ++GI+ I Sbjct: 251 FALGDLTNRRLTEIDLSKGYRAEGLAVLLGGIFNAFPYTAFSQNVGLVQLTGIKKNAVIV 31- 0 Query: 311 FTALFLVILGLLPKFGAMAQMIPSPVLGGAMLVLFGMVALQGMKMLNQVDFEHNEHNFII 37- 0 T + L+ GL PK A +IPS VLGGAM+ +FGMV G+KML+++DF E N +I Sbjct: 311 VTGVILMAFGLFPKIAAFTTIIPSAVLGGAMVAMFGMVIAYGIKMLSRIDFAKQE-NLLI 36- 9 Query: 371 AAVSIAAGVGFNGT-NLFISLPNTLQMFLTNGIVISTLTAVVLNIILNGLPK 421 A S+ G+G ++F LP+ L + TNGIV + TAVVLNI+ N K Sbjct: 370 VACSVGLGLGVTVVPDIFKQLPSALTLLTTNGIVAGSFTAVVLNIVYNVFSK 421 A related DNA sequence was identified in S. pyogenes <SEQ ID 6609> which encodes the amino acid sequence <SEQ ID 6610>. Analysis of this protein sequence reveals the following: TABLE-US-06542 Possible site: 29 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.32 Transmembrane 160-176 (158-181) INTEGRAL Likelihood = -6.37 Transmembrane 103-119 (98-124) INTEGRAL Likelihood = -5.84 Transmembrane 130-146 (126-152) INTEGRAL Likelihood = -5.68 Transmembrane 187-203 (182-207) INTEGRAL Likelihood = -3.98 Transmembrane 337-353 (334-356) INTEGRAL Likelihood = -3.82 Transmembrane 232-248 (225-252) INTEGRAL Likelihood = -3.35 Transmembrane 403-419 (399-421) INTEGRAL Likelihood = -2.50 Transmembrane 22-38 (21-41) INTEGRAL Likelihood = -2.07 Transmembrane 312-328 (312-328) INTEGRAL Likelihood = -1.97 Transmembrane 78-94 (76-95) ----- Final Results ----- bacterial membrane --- Certainty = 0.3930(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06543 >GP: CAB15234 GB: Z99120 similar to purine permease [Bacillus subtilis] Identities = 216/421 (51%), Positives = 302/421 (71%), Gaps = 5/421 (1%) Query: 6 KQEHSHSQSAVLGLQHVLSMYAGSILVPIMIAGALGYSARELTYLISTDIFMCGVATFLQ 65 K++H+ Q +LGLQH+L+MYAG+ILVP+++ A+G +A +LTYLI+ D+FMCG AT LQ Sbjct: 2 KEQHNALQLMMLGLQHMLAMYAGAILVPLIVGAAIGLNAGQLTYLIAIDLFMCGAATLLQ 61 Query: 66 LKLTKHTGVGLPVVLGCAFQSVAPLSIIGAQQGSGAMFGALIASGIYVILVAGIFSKIAR 125- L ++ G+GLPVVLGC F +V P+ IG+ G A++GA+IA+G+ V+L AG F K+ R Sbjct: 62 LWRNRYFGIGLPVVLGCTFTAVGPMISIGSTYGVPAIYGAIIAAGLIVVLAAGFFGKLVR 121- Query: 126 FFPPIVTGSVITVIGLSLVGVAMGNM--GDNVKE-PTAQSMMLSLLTIVIILLVQKFTKG 18- 2 FFPP+VTGSV+ +IG+SL+ AM N+ G+ KE + +++L ILL+ F KG Sbjct: 122 FFPPVVTGSVVMIIGISLIPTAMNNLAGGEGSKEFGSLDNVLLGFGVTAFILLLFYFFKG 18- 1 Query: 183 FVKSISILIGLVAGTLVSAMMGLVDTTPVVEASWIHVPTPFYFGMPTFEITSIVMMCIIA 24- 2 F++SI+IL+GL+AGT + MG VD + V+EASW+HVP+ FYFG PTFE+ ++V M ++A Sbjct: 182 FIRSIAILLGLIAGTAAAYFMGKVDFSEVLEASWLHVPSLFYFGPPTFELPAVVTMLLVA 24- 1 Query: 243 TVSMVESTGVYLALSDLTNDQLDEKRLRNGYRSEGIAVFLGGLFNTFPYTGFSQNVGLVQ 30- 2 VS+VESTGVY AL+D+TN +L EK L GYR+EG+A+ LGGLFN FPYT FSQNVG+VQ Sbjct: 242 IVSLVESTGVYFALADITNRRLSEKDLEKGYRAEGLAILLGGLFNAFPYTAFSQNVGIVQ 30- 1 Query: 303 ISGIKTRRPIYYAAGILVVIGLLPKFRAMAQMIPSPVLGGAMLVLFGMVALQGMQMLNRV 36- 2 +S +K+ I ILV IGL+PK A+ +IP+PVLGGAM+V+FGMV G++ML+ V Sbjct: 302 LSKMKSVNVIAITGIILVAIGLVPKAAALTTVIPTPVLGGAMIVMFGMVISYGIKMLSSV 36- 1 Query: 363 DFQKNEYNFIIAAVSISAGLGFNGT-NLFASLPETAQMFLTNGIVIATLTSVVLNLVLNGK 4- 22 D ++ N +I A S+S GLG LF+SL A + +GIVI +LT++ L+ K Sbjct: 362 DLD-SQGNLLIIASSVSLGLGATTVPALFSSLSGAASVLAGSGIVIGSLTAIALHAFFQTK 4- 21 An alignment of the GAS and GBS proteins is shown below.

TABLE-US-06544 Identities = 328/416 (78%), Positives = 380/416 (90%) Query: 7 SNSQAALLGLQHLLAMYAGSILVPIMIASALGYNAKQLTYLIATDIFMCGIATLLQLRLS 66 S+SQ+A+LGLQH+L+MYAGSILVPIMIA ALGY+A++LTYLI+TDIFMCG+AT LQL+L+ Sbjct: 10 SHSQSAVLGLQHVLSMYAGSILVPIMIAGALGYSARELTYLISTDIFMCGVATFLQLKLT 69 Query: 67 KHFGVGLPVVLGCAFQSVAPLSIIGAQQGSGYMFGALIASGIYVVLVAGIFSKVANFFPP 126- KH GVGLPVVLGCAFQSVAPLSIIGAQQGSG MFGALIASGIYV+LVAGIFSK+A FFPP Sbjct: 70 KHTGVGLPVVLGCAFQSVAPLSIIGAQQGSGAMFGALIASGIYVILVAGIFSKIARFFPP 129- Query: 127 IVTGSVITTIGLTLIPVAMGNMGDNAKEPSLQSLTLSLVTIGVVLLINIFAKGFLKSISI 18- 6 IVTGSVIT IGL+L+ VAMGNMGDN KEP+ QS+ LSL+TI ++LL+ F KGF+KSISI Sbjct: 130 IVTGSVITVIGLSLVGVAMGNMGDNVKEPTAQSMMLSLLTIVIILLVQKFTKGFVKSISI 18- 9 Query: 187 LIGLISGTILAAFMGLVDASVVADAPLVHIPKPFYFGAPRFEFTSILMMCIIATVSMVES 24- 6 LIGL++GT+++A MGLVD + V +A +H+P PFYFG P FE TSI+MMCIIATVSMVES Sbjct: 190 LIGLVAGTLVSAMNGLVDTTPVVEASWIHVPTPFYFGMPTFEITSIVMMCIIATVSMVES 24- 9 Query: 247 TGVYLALSDITNDKLDSKRLRNGYRSEGLAVLLGGLFNTFPYTGFSQNVGLVQISGIRTR 30- 6 TGVYLALSD+TND+LD KRLRNGYRSEG+AV LGGLFNTFPYTGFSQNVGLVQISGI+TR Sbjct: 250 TGVYLALSDLTNDQLDEKRLRNGYRSEGIAVFLGGLFNTFPYTGFSQNVGLVQISGIKTR 30- 9 Query: 307 KPIYFTALFLVILGLLPKFGAMAQMIPSPVLGGAMLVLFGMVALQGMKMLNQVDFEHNEH 36- 6 +PIY+ A LV++GLLPKF AMAQMIPSPVLGGAMLVLFGMVALQGM+MLN+VDF+ NE+ Sbjct: 310 RPIYYAAGILVVIGLLPKFRAMAQMIPSPVLGGAMLVLFGMVALQGMQMLNRVDFQKNEY 36- 9 Query: 367 NFIIAAVSIAAGVGFNGTNLFISLPNTLQMFLTNGIVISTLTAVVLNIILNGLPKK 422 NFIIAAVSI+AG+GFNGTNLF SLP T QMFLTNGIVI+TLT+VVLN++LNG K+ Sbjct: 370 NFIIAAVSISAGLGFNGTNLFASLPETAQMFLTNGIVIATLTSVVLNLVLNGKDKQ 425 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2140 A DNA sequence (GBSx2256) was identified in S. agalactiae <SEQ ID 6611> which encodes the amino acid sequence <SEQ ID 6612>. This protein is predicted to be xanthine phosphoribosyltransferase (xpt). Analysis of this protein sequence reveals the following: TABLE-US-06545 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1921(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06546 >GP: CAA13587 GB: AJ233894 xanthine phosphoribosyltransferase [Streptococcus pneumoniae] Identities = 133/162 (82%), Positives = 144/162 (88%) Query: 16 GENILKVDSFLTHQVDFELMQEIGKVFADKYKEAGITKVVTIEASGIAPAVYAAQALGVP 75 - G+NILKVDSFLTHQVDF LM+EIGKVFA+K+ AGITKVVTIEASGIAPA++ A+AL VP Sbjct: 1 GDNILKVDSFLTHQVDFSLMREIGKVFAEKFASAGITKVVTIEASGIAPALFTAEALNVP 60 Query: 76 MIFAKKAKNITMTEGILTAEVYSFTKQVTSQVSIVSRFLSNDDTVLIIDDFLANGQAAKG 135- MIFAKKAKNITM EGILTAEVYSFTKQVTS VSI +FLS +D VLIIDDFLANGQAAKG Sbjct: 61 MIFAKKAKNITMNEGILTAEVYSFTKQVTSTVSIAGKFLSPEDKVLIIDDFLANGQAAKG 120- Query: 136 LLEIIGQAGAKVAGIGIVIEKSFQDGRDLLEKTGVPVTSLAR 177 L++II QAGA V IGIVIEKSFQDGRDLLEK G PV SLAR Sbjct: 121 LIQIIEQAGATVEAIGIVIEKSFQDGRDLLEKAGYPVLSLAR 162 A related DNA sequence was identified in S. pyogenes <SEQ ID 6613> which encodes the amino acid sequence <SEQ ID 6614>. Analysis of this protein sequence reveals the following: TABLE-US-06547 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2576(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06548 Identities = 156/193 (80%), Positives = 172/193 (88%) Query: 1 MKLLEERILKDGDVLGENILKVDSFLTHQVDFELMQEIGKVFADKYKEAGITKVVTIEAS 60 M+LLEERIL DG++LGENILKVD+FLTHQVD+ LM+ IGKVFA KY EAGITKVVTIEAS Sbjct: 1 MQLLEERILTDGNILGENILKVDNFLTHQVDYRLMKAIGKVFAQKYAEAGITKVVTIEAS 60 Query: 61 GIAPAVYAAQALGVPMIFAKKAKNITMTEGILTAEVYSFTKQVTSQVSIVSRFLSNDDTV 120- GIAPAVYAA+A+ VPMIFAKK KNITMTEGILTAEVYSFTKQVTS VSI +FLS +D V Sbjct: 61 GIAPAVYAAEAMDVPMIFAKKHKNITMTEGILTAEVYSFTKQVTSTVSIAGKFLSKEDKV 120- Query: 121 LIIDDFLANGQAAKGLLEIIGQAGAKVAGIGIVIEKSFQDGRDLLEKTGVPVTSLARIKA 18- 0 LIIDDFLANGQAAKGL+EIIGQAGA+V G+GIVIEKSFQDGR L+E G+ VTSLARIK Sbjct: 121 LIIDDFLANGQAAKGLIEIIGQAGAQVVGVGIVIEKSFQDGRRLIEDMGIEVTSLARIKN 18- 0 Query: 181 FENGRVVFAEADA 193 FENG + F EADA Sbjct: 181 FENGNLNFLEADA 193 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2141 A DNA sequence (GBSx2257) was identified in S. agalactiae <SEQ ID 6615> which encodes the amino acid sequence <SEQ ID 6616>. Analysis of this protein sequence reveals the following: TABLE-US-06549 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2546(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06550 >GP: CAB15203 GB: Z99120 similar to GMP reductase [Bacillus subtilis] Identities = 243/321 (75%), Positives = 286/321 (88%), Gaps = 2/321 (0%) Query: 7 VFDYEDIQLIPNKCIISSRSQADTSVKLGNYTFKLPVIPANMQTIIDEEVAETLACEGYF 66 VFDYEDIQLIP KCI++SRS+ DTSV+LG +TFKLPV+PANMQTIIDE++A +LA GYF Sbjct: 4 VFDYEDIQLIPAKCIVNSRSECDTSVRLGGHTFKLPVVPANMQTIIDEKLAISLAENGYF 63 Query: 67 YIMHRFNEEERKPFIKRMHDKGLIASISVGVKDYEYDFVTSLKED--APEFITIDIAHGH 124- Y+MHRF E R FIK M+ +GL +SISVGVKD EY+FV L E+ PE++TIDIAHGH Sbjct: 64 YVMHRFEPETRIDFIKDMNARGLFSSISVGVKDEEYEFVRQLAEENLTPEYVTIDIAHGH 123- Query: 125 SNSVIEMIQHIKQELPETFVIAGNVGTPEAVRELENAGADATKVGIGPGKVCITKVKTGF 18- 4 SN+VIEMIQH+K+ LP++FVIAGNVGTPEAVRELENAGADATKVGIGPGKVCITK+KTGF Sbjct: 124 SNAVIEMIQHLKKHLPDSFVIAGNVGTPEAVRELENAGADATKVGIGPGKVCITKIKTGF 18- 3 Query: 185 GTGGWQLAALRWCSKAARKPIIADGGIRTHGDIAKSIRFGASMVMIGSLFAGHLESPGKL 24- 4 GTGGWQLAALRWC+KAA KPIIADGGIRTHGDIAKSIRFGA+MVMIGSLFAGH ESPG+ Sbjct: 184 GTGGWQLAALRWCAKAASKPIIADGGIRTHGDIAKSIRFGATMVMIGSLFAGHEESPGQT 24- 3 Query: 245 VEVEGQQFKEYYGSASEYQKGEHKNVEGKKILLPVKGRLEDTLTEMQQDLQSSISYAGGK 30- 4 +E +G+ +KEY+GSASE+ KGE KNVEGKK+ + KG ++DTL EM+QDLQSSISYAGG Sbjct: 244 IEKDGKLYKEYFGSASEFPKGEKKNVEGKKMHVAHKGSIKDTLIEMEQDLQSSISYAGGT 30- 3 Query: 305 ELDSLRHVDYVIVKNSIWNGD 325 +L+++R+VDYVIVKNSI+NGD Sbjct: 304 KLNAIRNVDYVIVKNSIFNGD 324 A related DNA sequence was identified in S. pyogenes <SEQ ID 6617> which encodes the amino acid sequence <SEQ ID 6618>. Analysis of this protein sequence reveals the following: TABLE-US-06551 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2405(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06552 Identities = 297/327 (90%), Positives = 311/327 (94%) Query: 1 MFNDIPVFDYEDIQLIPNKCIISSRSQADTSVKLGNYTFKLPVIPANMQTIIDEEVAETL 60 MFNDIPVFDYEDIQLIPNKCII+SRSQADTSV LG Y FKLPVIPANMQTIIDE +AE L Sbjct: 8 MFNDIPVFDYEDIQLIPNKCIITSRSQADTSVTLGKYQFKLPVIPANMQTIIDETIAEQL 67 Query: 61 ACEGYFYIMHRFNEEERKPFIKRMHDKGLIASISVGVKDYEYDFVTSLKEDAPEFITIDI 120- A EGYFYIMHRF+E+ RKPFIKRMH++GLIASISVGVK EY+FVTSLKEDAPEFITIDI Sbjct: 68 AKEGYFYIMHRFDEDSRKPFIKRMHEQGLIASISVGVKACEYEFVTSLKEDAPEFITIDI 127- Query: 121 AHGHSNSVIEMIQHIKQELPETFVIAGNVGTPEAVRELENAGADATKVGIGPGKVCITKV 18- 0 AHGH+NSVI+MI+HIK ELPETFVIAGNVGTPEAVRELENAGADATKVGIGPGKVCITKV Sbjct: 128 AHGHANSVIDMIKHIKTELPETFVIAGNVGTPEAVRELENAGADATKVGIGPGKVCITKV 18- 7 Query: 181 KTGFGTGGWQLAALRWCSKAARKPIIADGGIRTHGDIAKSIRFGASMVMIGSLFAGHLES 24- 0 KTGFGTGGWQLAALRWC+KAARKPIIADGGIRTHGDIAKSIRFGASMVMIGSLFAGH ES Sbjct: 188 KTGFGTGGWQLAALRWCAKAARKPIIADGGIRTHGDIAKSIRFGASMVMIGSLFAGHFES 24- 7 Query: 241 PGKLVEVEGQQFKEYYGSASEYQKGEHKNVEGKKILLPVKGRLEDTLTEMQQDLQSSISY 30- 0 PGK VEV+G+ FKEYYGSASEYQKGEHKNVEGKKILLP KG L DTLTEMQQDLQSSISY Sbjct: 248 PGKTVEVDGETFKEYYGSASEYQKGEHKNVEGKKILLPTKGHLSDTLTEMQQDLQSSISY 30- 7 Query: 301 AGGKELDSLRHVDYVIVKNSIWNGDSI 327 AGGK+LDSLRHVDYVIVKNSIWNGDSI Sbjct: 308 AGGKDLDSLRHVDYVIVKNSIWNGDSI 334 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2142 A DNA sequence (GBSx2258) was identified in S. agalactiae <SEQ ID 6619> which encodes the amino acid sequence <SEQ ID 6620>. Analysis of this protein sequence reveals the following: TABLE-US-06553 Possible site: 57 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -16.98 Transmembrane 421-437 (413-443) INTEGRAL Likelihood = -8.81 Transmembrane 166-182 (159-186) INTEGRAL Likelihood = -8.55 Transmembrane 220-236 (208-238) INTEGRAL Likelihood = -6.69 Transmembrane 322-338 (319-353) INTEGRAL Likelihood = -5.26 Transmembrane 199-215 (196-218) INTEGRAL Likelihood = -4.35 Transmembrane 343-359 (342-361) INTEGRAL Likelihood = -4.09 Transmembrane 291-307 (287-308) INTEGRAL Likelihood = -3.66 Transmembrane 8-24 (8-27) INTEGRAL Likelihood = -3.66 Transmembrane 133-149 (133-151) INTEGRAL Likelihood = -3.19 Transmembrane 254-270 (253-278) INTEGRAL Likelihood = -2.50 Transmembrane 53-69 (53-72) INTEGRAL Likelihood = -1.81 Transmembrane 77-93 (76-95) INTEGRAL Likelihood = -1.33 Transmembrane 109-125 (109-125) ----- Final Results ----- bacterial membrane --- Certainty = 0.7793(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06554 >GP: CAB61253 GB: AJ250422 ORFC [Oenococcus oeni] Identities = 157/447 (35%), Positives = 252/447 (56%), Gaps = 13/447 (2%) Query: 11 AIITTAILGFSGILIETSMNVTFPLLMKEFGVNPAVIQWVTTGNLLAVAVTVPLSAFMIK 70 - AI+ A L F G+LIETSMNVTFP LM++F ++ +QW+TT LL VA T+ ++AF+ K Sbjct: 15 AILGLAGLAFCGVLIETSMNVTFPTLMQQFSISLNKVQWLTTAYLLLVAATISIAAFIEK 74 Query: 71 NLSERQIFTLANVLFLSGVLIDSFAPNLAILLVGRVLQGVGTGLALPLLFHIILTQIPME 130- ++IF A +LF+ GV+ + APN ILL+GR++Q + TGLA+PLL I+ QIP + Sbjct: 75 RFIFKKIFFWAGLLFIIGVICSALAPNFLILLIGRLIQALSTGLAIPLLITEIMQQIPQK 134- Query: 131 RRGLMMGVAAMVTLLAPAVGPTYGGVISGMLGWKMIFMLLAPILIISTFIGLASIPKRQV 19- 0 ++G M + + L P++GPTYGGVI+ L W++IF + PI +I+ IGL+ I ++ Sbjct: 135 KQGSYMELVEWLLLWQPSLGPTYGGVITQDLSWRLIFWFVLPIGLIAWLIGLSFIEQKSS 19- 4 Query: 191 RINDKLNFPAFISLGIGLATLLLAIEKMSIF---------YLLVAIVSFVIFYYL--NKQ 23- 9 + FISL + L ++ +A+ I+ +LL+A++ ++F L N + Sbjct: 195 PSKIPFAWKQFISLILALLSITVAVNNAGIYGWTSIKFYGFLLIAVILLIVFIKLSTNSR 25- 4 Query: 240 LEFLNLNVFKDKDFSILLYGVLAFQMIPLALSFLLPNLLQLVLHQTSTKAGLFMFPGAIA 29- 9 +++++FK +F L Q I L+L+FLLPN QL+L + +G+ + G++ Sbjct: 255 QALISISIFKKWEFVCPLLIYFLIQFIQLSLTFLLPNYAQLILKKGVMISGIMLLCGSLI 31- 4 Query: 300 VVFLSPFAGYLLDKIGAFKPIMIGISLSLIGLIGTAIFIPAKSVVVLLAFDILTKIGMGI 35- 9 L P G +LD P++IG + I IF SV ++ A ++ IG Sbjct: 315 SAILQPLTGRMLDSFSVKIPLVIGAFFLITSTISFTIFQRYLSVFLIAALYVIYMIGFSF 37- 4 Query: 360 GASNMVTTALTKLKPAQSADGNSILNTLQQFAGAFATAVASQIFTIGQVAIPKNGAIIGS 41- 9 +N +T AL KL +DGN++ NTLQQ+AG+ T+VAS + G K GS Sbjct: 375 VFNNSLTYALQKLPLKLISDGNAVFNTLQQYAGSLGTSVASALLANGIGTDGKQSNYTGS 43- 4 Query: 420 Q--FAVLFVIVVVILAIVGLTYLRKRK 444 + F + F+ +++ ++ +K K Sbjct: 435 RHIFILNFISCAIVVILIFSIQRKKNK 461 There is also homology to SEQ ID 46. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2143 A DNA sequence (GBSx2259) was identified in S. agalactiae <SEQ ID 6621> which encodes the amino acid sequence <SEQ ID 6622>. Analysis of this protein sequence reveals the following: TABLE-US-06555 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2151(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 6595> which encodes the amino acid sequence <SEQ ID 6596>. Analysis of this protein sequence reveals the following: TABLE-US-06556 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06557 Identities = 74/214 (34%), Positives = 112/214 (51%), Gaps = 5/214 (2%) Query: 13 NESENNFFITLKTYFNYLFSIQIIT---DISTLNHADFDGSFAFHDIETSIPHLVIDSNY 69 - N+ E F L +F++LF + I+T +I + + F G F+FH+ + +P L ++ Sbjct: 15 NQLEETFIRELSHHFSHLFEVTILTSKANIQSNQLSTFQGIFSFHEHDIDLPTLYFKTSQ 74 Query: 70 LAISQTNSKIEANDIKTFSELSKTMTEFHYMLNFDLFNHLPYRFRLHNKDGQTIYSNHKP 129- ++ + LS+ +T F+ + +LP + RL + +G I NH Sbjct: 75 HGQGFLVTESVFDQATAVLSLSQYLTGFYQKFDGHFLQYLPLQARLSDANGNIIVDNHAF 134- Query: 130 EDPFDIYPEEEYPIDKWVQNSLIEKKAKELHLLLPSASQDYILVQSYKRLENDSGQLVGY 18- 9 F P + I+ W+ L LLPS S D+I +Q Y+ L+N GQLVG Sbjct: 135 NGSF--LPTTDKEIEDWILAELRLSDNPCKTFLLPSGSLDHIYMQHYQALKNPQGQLVGV 19- 2 Query: 190 IEHVHNIKPLLEGYLKESGQAIVGWSDVTSGASI 223 ++ V +IKPLL YL+E+GQAIVGWSDVTSG SI Sbjct: 193 LDTVQDIKPLLNQYLEETGQAIVGWSDVTSGPSI 226 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2144 A DNA sequence (GBSx2260) was identified in S. agalactiae <SEQ ID 6623> which encodes the amino acid sequence <SEQ ID 6624>. Analysis of this protein sequence reveals the following: TABLE-US-06558 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.10 Transmembrane 431-447 (423-452) INTEGRAL Likelihood = -8.92 Transmembrane 149-165 (147-174) INTEGRAL Likelihood = -8.86 Transmembrane 404-420 (402-428) INTEGRAL Likelihood = -7.91 Transmembrane 299-315 (293-318) INTEGRAL Likelihood = -6.42 Transmembrane 380-396 (374-398) INTEGRAL Likelihood = -5.31 Transmembrane 350-366 (347-367) INTEGRAL Likelihood = -4.57 Transmembrane 56-72 (54-74) INTEGRAL Likelihood = -3.24 Transmembrane 172-188 (171-198) INTEGRAL Likelihood = -1.33 Transmembrane 224-240 (224-240) INTEGRAL Likelihood = -0.59 Transmembrane 101-117 (101-117) ----- Final Results ----- bacterial membrane --- Certainty = 0.5840(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06559 >GP: AAF84709 GB: AE004010 potassium uptake protein [Xylella fastidiosa] Identities = 201/570 (35%), Positives 319/570 (55%), Gaps = 34/570 (5%) Query: 1 MAEMQHVNHSSFDKASKAGFII--ALGIVYGDIGTSPLYTMQSLVENQGGISSVTESFIL 58 M+ H + ++ G II A+G+V+GDIGTSPLYT++ G++ ++ +L Sbjct: 1 MSTSSHSGDCTAVPSNSNGTIILSAIGVVFGDIGTSPLYTLKEAFSPNYGLTPNHDT-VL 59 Query: 59 GSISLIIWTLTLITTIKYVLVALKADNHHEGGIFSLYTLVRKMTPW-------LIVPAVI 111- G +SLI W + L+ TIKYV V ++ DN EGGI +L L ++ P+ + + + Sbjct: 60 GILSLIFWAMMLVVTIKYVAVIMRVDNDGEGGIMALTALTQRTMPFGSRSIYIVGILGIF 119- Query: 112 GGATLLSDGALTPAVTVTSAVEGLKVVPSLQHIFQNQSNVIFATLFILLLLFAIQRFGTG 17- 1 G + DG +TPA++V SAVEGL+V F V+ TL +L+LLF QRFGT Sbjct: 120 GTSLFFGDGVITPAISVLSAVEGLEVAEPHMKAF-----VVPITLAVLILLFLCQRFGTE 17- 4 Query: 172 VIGKLFGPIMFIWFAFLGISGLLNSFAHPEVFKAINPYYGLKLLFSPENHKGIFILGSIF 23- 1 +GK FGPI +WF +G+ G+ N PEV AINP +GL F +F+LG++ Sbjct: 175 RVGKTFGPITLLWFIAIGVVGVYNIAQAPEVLHAINPSWGLH-FFLEHGWHSMFVLGAVV 23- 3 Query: 232 LATTGAEALYSDLGHVGRGNIHVSWPFVKVAII-LSYCGQGAWILANKNAGNELNPFFAS 29- 0 LA TG EALY+D+GH G I +W +V + ++ L+Y GQGA +L+N A NPF+ S Sbjct: 234 LAVTGGEALYADMGHFGAKAIRHAWMYVVLPMLALNYLGQGALVLSNPTAIG--NPFYQS 29- 1 Query: 291 IPSQFTMHVVILATLAAIIASQALISGSFTLVSEAMRLKIFPQFRSTYPGDN-IGQTYIP 34- 9 IP ++ LAT AA+IASQALI+GS++L S+AM+L P+ + + IGQ Y+P Sbjct: 292 IPDWGLYPMIALATAAAVIASQALITGSYSLSSQAMQLGYIPRMNVRHTSQSTIGQIYVP 35- 1 Query: 350 VINWFLFAITTSIVLLFKTSAHMEAAYGLAITITMLMTTILLSFFL-IQKGVKRGLVLLM 40- 8 +NW L + V+ F S M +AYG+A+T TM++TT+L+ + V R ++ +M Sbjct: 352 TVNWTLLTLVILTVIGFGDSTSMASAYGVAVTGTMMITTVLMIIYARANPRVPRLMLWMM 41- 1 Query: 409 MIFFGILEGIFFLASAVKFMHGGYVVVIIAVAIIFIMTIWYKGSKIVSRYVKL--LDLKD 46- 6 I F ++G FF A+ +KFM G + +++ V I M W +G K++ ++ ++L + Sbjct: 412 AIVFIAVDGAFFYANIIKFMDGAWFPLLLGVVIFTFMRTWLRGRKLLHEEMRKDGINLDN 47- 1 Query: 467 YIGQLDKLRHDHRYPIYHTNVVYLTNRMEEDMIDKSIMYSILDKRPKKAQVYWFVNIKVT 52- 6 ++ L L + P V+LT + ++ ++M+++ + + F+ +K Sbjct: 472 FLPGL-MLAPPVKVP---GTAVFLT--ADSTVVPHALMHNLKHNKVLHERNV-FLTVKTL 52- 4 Query: 527 DEPYTA---EYKVDMMGTDFIVKVELYLGF 553 PY A K++ + F +V + GF Sbjct: 525 KIPYAANSERLKIEPISNGF-YRVHIRFGF 553 A related DNA sequence was identified in S. pyogenes <SEQ ID 6625> which encodes the amino acid sequence <SEQ ID 6626>. Analysis of this protein sequence reveals the following:

TABLE-US-06560 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.78 Transmembrane 428-444 (421-453) INTEGRAL Likelihood = -8.70 Transmembrane 146-162 (144-171) INTEGRAL Likelihood = -7.64 Transmembrane 404-420 (398-426) INTEGRAL Likelihood = -4.88 Transmembrane 296-312 (294-315) INTEGRAL Likelihood = -4.57 Transmembrane 53-69 (51-71) INTEGRAL Likelihood = -3.93 Transmembrane 347-363 (343-363) INTEGRAL Likelihood = -2.50 Transmembrane 372-388 (371-388) INTEGRAL Likelihood = -1.33 Transmembrane 169-185 (169-185) INTEGRAL Likelihood = -1.33 Transmembrane 221-237 (221-237) ----- Final Results ----- bacterial membrane --- Certainty = 0.5713(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06561 >GP: AAF84709 GB: AE004010 potassium uptake protein [Xylella fastidiosa] Identities = 177/467 (37%), Positives = 270/467 (56%), Gaps = 20/467 (4%) Query: 7 TAFDKASKAGFII-ALGIVYGDIGTSPLYTIQSLVENQGGVNQVSESFILGSISLIIWTL 65- TA S I+A+G+V+GDIGTSPLYT++ G+ ++ +LG +SLI W + Sbjct: 11 TAVPSNSNGTIILSAIGVVFGDIGTSPLYTLKEAFSPNYGLTPNHDT-VLGILSLIFWAM 69- Query: 66 TLITTIKYVLIALKADNHHEGGIFSLFTLVRKMSPW-------LIIPAMIGGATLLSDGA 11- 8 L+ TIKYV + ++ DN EGGI +L L ++ P+ + I + G + DG Sbjct: 70 MLVVTIKYVAVIMRVDNDGEGGIMALTALTQRTMPFGSRSIYIVGILGIFGTSLFFGDGV 12- 9 Query: 119 LTPAVTVTSAIEGLKAVPGLSHIYQNQTNVIITTLVILIVLFGIQRFGTGFIGKIFGPVM 17- 8 +TPA++V SA+EGL+ + V+ TL +LI+LF QRFGT +GK FGP+ Sbjct: 130 ITPAISVLSAVEGLEVAEPHMKAF-----VVPITLAVLILLFLCQRFGTERVGKTFGPIT 18- 4 Query: 179 FIWFSFLGVSGFFNTLGHLEIFKAINPYYALHLLFSPENHRGIFILGSIFLATTGAEALY 23- 8 +WF +GV G +N E+ AINP + LH F +F+LG++ LA TG EALY Sbjct: 185 LLWFIAIGVVGVYNIAQAPEVLHAINPSWGLH-FFLEHGWHSMFVLGAVVLAVTGGEALY 24- 3 Query: 239 SDLGHVGRGNIYVSWPFVKM-CIVLSYCGQAAWILANKHSGIELNPFFASVPSQLRVYLV 29- 7 +D+GH G I +W +V + + L+Y GQ A +L+N + NPF+ S+P ++ Sbjct: 244 ADMGHFGAKAIRHAWMYVVLPMLALNYLGQGALVLSNPTA--IGNPFYQSIPDWGLYPMI 30- 1 Query: 298 SLATLAAIIASQALISGSFTLVSEAMRLKIFPLFRVTYPG-ANLGQLYIPVINWILFAVT 35- 6 +LAT AA+IASQALI+GS++L S+AM+L P V + + +GQ+Y+P +NW L + Sbjct: 302 ALATAAAVIASQALITGSYSLSSQAMQLGYIPRMNVRHTSQSTIGQIYVPTVNWTLLTLV 36- 1 Query: 357 SCTVLAFRTSAHMEAAYGLAITITMLMTTILLKYYLIKKGTRPILAHLVMAF-FALVEFI 41- 5 TV+ F S M +AYG+A+T TM++TT+L+ Y P L +MA F V+ Sbjct: 362 ILTVIGFGDSTSMASAYGVAVTGTMMITTVLMIIYARANPRVPRLMLWMMAIVFIAVDGA 42- 1 Query: 416 FFLASAIKFMHGGYAVVILALAIVFVMFIWHAGTRIVFKYVKSLNLN 462 FF A+ IKFM G + ++L + I M W G +++ + ++ +N Sbjct: 422 FFYANIIKFMDGAWFPLLLGVVIFTFMRTWLRGRKLLHEEMRKDGIN 468 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06562 Identities = 485/651 (74%), Positives = 575/651 (87%) Query: 10 SSFDKASKAGFIIALGIVYGDIGTSPLYTMQSLVENQGGISSVTESFILGSISLIIWTLT 69- ++FDKASKAGFIIALGIVYGDIGTSPLYT+QSLVENQGG++ V+ESFILGSISLIIWTLT Sbjct: 7 TAFDKASKAGFIIALGIVYGDIGTSPLYTIQSLVENQGGVNQVSESFILGSISLIIWTLT 66- Query: 70 LITTIKYVLVALKADNHHEGGIFSLYTLVRKMTPWLIVPAVIGGATLLSDGALTPAVTVT 12- 9 LITTIKYVL+ALKADNHHEGGIFSL+TLVRKN+PWLI+PA+IGGATLLSDGALTPAVTVT Sbjct: 67 LITTIKYVLIALKADNHHEGGIFSLFTLVRKMSPWLIIPAMIGGATLLSDGALTPAVTVT 12- 6 Query: 130 SAVEGLKVVPSLQHIFQNQSNVIFATLFILLLLFAIQRFGTGVIGKLFGPIMFIWFAFLG 18- 9 SA+EGLK VP L HI+QNQ+NVI TL IL++LF IQRFGTG IGK+FGP+MFIWF+FLG Sbjct: 127 SAIEGLKAVPGLSHIYQNQTNVIITTLVILIVLFGIQRFGTGFIGKIFGPVMFIWFSFLG 18- 6 Query: 190 ISGLLNSFAHPEVFKAINPYYGLKLLFSPENHKGIFILGSIFLATTGAEALYSDLGHVGR 24- 9 +SG N+ H E+FKAINPYY L LLFSPENH+GIFILGSIFLATTGAEALYSDLGHVGR Sbjct: 187 VSGFFNTLGHLEIFKAINPYYALHLLFSPENHRGIFILGSIFLATTGAEALYSDLGHVGR 24- 6 Query: 250 GNIHVSWPFVKVAIILSYCGQGAWILANKNAGNELNPFFASIPSQFTMHVVILATLAAII 30- 9 GNI+VSWPFVK+ I+LSYCGQ AWILANK++G ELNPFFAS+PSQ +++V LATLAAII Sbjct: 247 GNIYVSWPFVKMCIVLSYCGQAAWILANKHSGIELNPFFASVPSQLRVYLVSLATLAAII 30- 6 Query: 310 ASQALISGSFTLVSEAMRLKIFPQFRSTYPGDNIGQTYIPVINWFLFAITTSIVLLFKTS 36- 9 ASQALISGSFTLVSEAMRLKIFP FR TYPG N+GQ YIPVINW LFA+T+ VL F+TS Sbjct: 307 ASQALISGSFTLVSEAMRLKIFPLFRVTYPGANLGQLYIPVINWILFAVTSCTVLAFRTS 36- 6 Query: 370 AHMEAAYGLAITITMLMTTILLSFFLIQKGVKRGLVLLMMIFFGILEGIFFLASAVKFMH 42- 9 AHMEAAYGLAITITMLMTTILL ++LI+KG + L L+M FF ++E IFFLASA+KFMH Sbjct: 367 AHMEAAYGLAITITMLMTTILLKYYLIKKGTRPILAHLVMAFFALVEFIFFLASAIKFMH 42- 6 Query: 430 GGYVVVIIAVAIIFIMTIWYKGSKIVSRYVKLLDLKDYIGQLDKLRHDHRYPIYRTNVVY 48- 9 GGY VVI+A+AI+F+M IW+ G++IV +YVK L+L DY Q+ +LR D + +Y TNVVY Sbjct: 427 GGYAVVILALAIVFVMFIWHAGTRIVFKYVKSLNLNDYKEQIKQLRDDVCFDLYQTNVVY 48- 6 Query: 490 LTNRMEEDMIDKSIMYSILDKRPKKAQVYWFVNIKVTDEPYTAEYKVDMMGTDFIVKVEL 54- 9 L+NRM++ MID+SI+YSILDKRPK+AQVYWFVN++VTDEPYTA+YKVDMMGTD++V+V L Sbjct: 487 LSNRMQDHMIDRSILYSILDKRPKRAQVYWFVNVQVTDEPYTAKYKVDMMGTDYMVRVNL 54- 6 Query: 550 YLGFKMRQTVSRYLRTIVEELLESGRLPKQGKTYSVRPDSNVGDFRFIVLDERFSSSQNL 60- 9 YLGF+M QTV RYLRTIV++L+ESGRLPKQ + Y++ P +VGDFRF++++ER S+++ L Sbjct: 547 YLGFRMPQTVPRYLRTIVQDLMESGRLPKQEQEYTITPGRDVGDFRFVLIEERVSNARQL 60- 6 Query: 610 KPGERFVMLMKSSIKHWTATPIRWFGLQFSEVTTEVVPLIFTANRGLPIKE 660 ERF+M K+SIKH TA+P+RWFGLQ+SEVT EVVPLI + LPIKE Sbjct: 607 SNFERFIMQTKASIKHVTASPMRWFGLQYSEVTLEVVPLILSDVLKLPIKE 657 A related GBS gene <SEQ ID 8983> and protein <SEQ ID 8984> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06563 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 5.84 GvH: Signal Score (-7.5): -4.59 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 10 value: -12.10 threshold: 0.0 INTEGRAL Likelihood = -12.10 Transmembrane 431-447 (423-452) INTEGRAL Likelihood = -8.92 Transmembrane 149-165 (147-174) INTEGRAL Likelihood = -8.86 Transmembrane 404-420 (402-428) INTEGRAL Likelihood = -7.91 Transmembrane 299-315 (293-318) INTEGRAL Likelihood = -6.42 Transmembrane 380-396 (374-398) INTEGRAL Likelihood = -5.31 Transmembrane 350-366 (347-367) INTEGRAL Likelihood = -4.57 Transmembrane 56-72 (54-74) INTEGRAL Likelihood = -3.24 Transmembrane 172-188 (171-198) INTEGRAL Likelihood = -1.33 Transmembrane 224-240 (224-240) INTEGRAL Likelihood = -0.59 Transmembrane 101-117 (101-117) PERIPHERAL Likelihood = -0.85 20 modified ALOM score: 2.92 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5840(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00155## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2145 A DNA sequence (GBSx2261) was identified in S. agalactiae <SEQ ID 6627> which encodes the amino acid sequence <SEQ ID 6628>. This protein is predicted to be serine dehydrogenase. Analysis of this protein sequence reveals the following: TABLE-US-06564 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3261(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06565 >GP: AAD07424 GB: AE000552 short chain alcohol dehydrogenase [Helicobacter pylori 26695] Identities = 18/31 (58%), Positives = 25/31 (80%) Query: 3 WVASQPEHININRIEIMPVSQTYGPQPVYRD 33 W+ QP H+NINRIEIMP+SQT+ P P +++ Sbjct: 219 WIYEQPLHVNINRIEIMPISQTFAPLPTHKN 249 A related DNA sequence was identified in S. pyogenes <SEQ ID 6629> which encodes the amino acid sequence <SEQ ID 6630>. Analysis of this protein sequence reveals the following: TABLE-US-06566 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1021(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06567 Identities = 24/33 (72%), Positives = 29/33 (87%) Query: 1 MSWVASQPEHININRIEIMPVSQTYGPQPVYRD 33 +SWV QP H+N+NRIE+MPVSQ+YGPQPV RD Sbjct: 20 VSWVIHQPPHVNVNRIELMPVSQSYGPQPVTRD 52 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2146 A DNA sequence (GBSx2262) was identified in S. agalactiae <SEQ ID 6631> which encodes the amino acid sequence <SEQ ID 6632>. Analysis of this protein sequence reveals the following: TABLE-US-06568 Possible site: 21 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9337> which encodes amino acid sequence <SEQ ID 9338> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10781> which encodes amino acid sequence <SEQ ID 10782> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10951> which encodes amino acid sequence <SEQ ID 10952> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06569 >GP: CAA32349 GB: X14130 ORF (AA 1 to 299) [Lactococcus lactis subsp. cremoris] Identities = 72/215 (33%), Positives = 110/215 (50%), Gaps = 8/215 (3%) Query: 4 RSKLAAGFLTLMSVATLAACSGKTSNGTN--VVTMKGDTITVSDFYDQVKTSKAAQQSML 61- + K+ L + L SG SN T+ V T G +T S FY ++K S + + Sbjct: 2 KKKMRLKVLLASTATALLLLSGCQSNQTDQTVATYSGGKVTESSFYKELKQSPTTKTMLA 61- Query: 62 TLILSRVFDTQYGDKVSDKKVSEAYNKTAKGYGNSFSSALSQAGLTPEGYKQQIRTTMLV 12- 1 +++R + YG VS K V++AY+ + YG +F + LSQ G + +K+ +RT L Sbjct: 62 NMLIYRALNHAYGKSVSTKTVNDAYDSYKQQYGENFDAFLSQNGFSRSSFKESLRTNFLS 12- 1 Query: 122 EYAVKEAAKKELTEANYKEAYKNYTPETSVQVIKLDAEDKAKSVLKDVKADGADFAKIAK 18- 1 E A+K+ K+++E+ K A+K Y P+ +VQ I ED AK V+ D+ A G DFA +AK Sbjct: 122 EVALKKL--KKVSESQLKAAWKTYQPKVTVQHILTSDEDTAKQVISDLAA-GKDFAMLAK 17- 8 Query: 182 E---KTTATDKKVEYKFDSAGTTLPKEVMSAAFKL 213 T D + F+ TL AA+KL Sbjct: 179 TDSIDTATKDNGGKISFELNNKTLDATFKDAAYKL 213 A related DNA sequence was identified in S. pyogenes <SEQ ID 6633> which encodes the amino acid sequence <SEQ ID 6634>. Analysis of this protein sequence reveals the following: TABLE-US-06570 Possible site: 21 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06571 >GP: AAA25247 GB: M83946 maturation protein [Lactobacillus paracasei] Identities = 88/294 (29%), Positives = 146/294 (48%), Gaps = 14/294 (4%) Query: 7 LIASVVTLASVMALAACQSTNDNTKVISMKGDTISVSDFYNETKNTEVSQKAMLNLVISR 66 L+AS T +++ L+ CQS + KV + G ++ S+FY E K + ++ + N++I R Sbjct: 10 LLASTAT--ALLLLSGCQSNQADQKVATYSGGKVTESNFYKELKQSPTTKTMLANMLIYR 67 Query: 67 VFEAQYGDKVSKKEVEKAYHKTAEQYGASFSAALAQSSLTPETFKRQIRSSKLVEYAVKE 126- YG VS K V AY +QYG +F A L+Q+ + +FK +R++ L E A+K+ Sbjct: 68 ALNHAYGKSVSTKTVNDAYDSYKQQYGENFDAFLSQNGFSRSSFKESLRTNFLSEVALKK 127- Query: 127 AAKKELTTQEYKKAYESYTPTMAVEMITLDNEETAKSVLEELKAEGADFTAIAKE---KT 18- 3 K+++ + K +++Y P + V+ I +E+TAK V+ +L A G DF +AK T Sbjct: 128 L--KKVSESQLKAVWKTYQPKVTVQHILTSDEDTAKQVISDL-AAGKDFATLAKTDSIDT 18- 4 Query: 184 TTPEKKVTYKFDSGATNVPTDVVKAASSLNEGGISDVISVLDPTSYQKKFYIVKVTKKAE 24- 3 T + F+S + AA L G + P + ++K+ Sbjct: 185 ATKDNGGKISFESNNKTLDATFKDAAYKLKNGDYTQT-----PVKVTNGYEVIKMINH-P 23- 8 Query: 244 KKSDWQEYKKRLKAIIIAEKSKDMNFQNKVIANALDKANVKIKDKAFANILAQY 297 K + KK L A + A+ S+D + +VI+ L +V IKDK A+ L Y Sbjct: 239 AKGTFTSSKKALTASVYAKWSRDSSIMQRVISQVLKNQHVTIKDKDLADALDSY 292 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06572 Identities = 125/213 (58%), Positives = 168/213 (78%), Gaps = 1/213 (0%) Query: 1 MKTRSKLAAGFLTLMSVATLAACSGKTSNGTNVVTMKGDTITVSDFYDQVKTSKAAQQSM 60 MK +KL A +TL SV LAAC T++ T V++MKGDTI+VSDFY++ K ++ +Q++M Sbjct: 1 MKNSNKLIASVVTLASVMALAACQS-TNDNTKVISMKGDTISVSDFYNETKNTEVSQKAM 59 Query: 61 LTLILSRVFDTQYGDKVSDKKVSEAYNKTAKGYGNSFSSALSQAGLTPEGYKQQIRTTML 120- L L++SRVF+ QYGDKVS K+V +AY+KTA+ YG SFS+AL+Q+ LTPE +K+QIR++ L Sbjct: 60 LNLVISRVFEAQYGDKVSKKEVEKAYHKTAEQYGASFSAALAQSSLTPETFKRQIRSSKL 119- Query: 121 VEYAVKEAAKKELTEANYKEAYKNYTPETSVQVIKLDAEDKAKSVLKDVKADGADFAKIA 18- 0 VEYAVKEAAKKELT YK+AY++YTP +V++I LD E+ AKSVL+++KA+GADF IA Sbjct: 120 VEYAVKEAAKKELTTQEYKKAYESYTPTMAVEMITLDNEETAKSVLEELKAEGADFTAIA 17- 9 Query: 181 KEKTTATDKKVEYKFDSAGTTLPKEVMSAAFKL 213 KEKTT +KKV YKFDS T +P +V+ AA L Sbjct: 180 KEKTTTPEKKVTYKFDSGATNVPTDVVKAASSL 212 SEQ ID 10782 (GBS657) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 143 (lane 8-10; MW 62.8 kDa) and in FIG. 187 (lane 3; MW 63 kDa). Purified GBS657-GST is shown in FIG. 245, lanes 2 & 3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2147 A DNA sequence (GBSx2263) was identified in S. agalactiae <SEQ ID 6635> which encodes the amino acid sequence <SEQ ID 6636>. This protein is predicted to be methyltransferase. Analysis of this protein sequence reveals the following: TABLE-US-06573 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2576(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06574 >GP: CAA68045 GB: X99710 methyltransferase [Lactococcus lactis] Identities = 132/227 (58%), Positives = 169/227 (74%) Query: 1 MVQSYSKNANHNMRRPVVKEEIVQYMRQHQKQNNGCLAELEAFAKQENIPIIPHETATYF 60 MV++Y +N M RPVVK E+V++MR Q Q G LAE+ FAK+ NIP+IPHET YF Sbjct: 1 MVETYKSTSNPMMNRPVVKAELVEWMRSSQTQVTGELAEVLNFAKENNIPVIPHETVLYF 60 Query: 61 RFLMQTLQPKHILEIGTAIGFSALLMAENAPEAKITTIDRNEEMIALAKENFAKYDNHNQ 120- + L+ L+PK ILEIGTAIGFSAL+MA+ PEA+I TIDRN EMI LAK+N AKYD+ NQ Sbjct: 61 QMLLSLLKPKRILEIGTAIGFSALVMAQEVPEAEIVTIDRNPEMIELAKKNLAKYDHRNQ 120- Query: 121 ITLLEGDAVDVLQTLDKSYDFVFMDSAKSKYIVFLPQVLKHLDVGGVVVLDDIFQGGDIA 18- 0 I L EGDA DVLQ L +D VFMDSAKSKY+ FLP+ L+ L G++++DD+FQ G+I Sbjct: 121 IQLKEGDAADVLQELKGPFDLVFMDSAKSKYVEFLPKSLELLSENGLILMDDVFQAGEIL 18- 0 Query: 181 KPIDEVRRGQRTIYRGLQRLFDSTLQHPDLTATLVPLGDGLLMIRKN 227 PI EV+R QR + RGL++LFD +P +++PLGDGLLMI+K+ Sbjct: 181 LPIMEVKRNQRALERGLRKLFDEVFDNPKYMTSVLPLGDGLLMIKKH 227 A related DNA sequence was identified in S. pyogenes <SEQ ID 6637> which encodes the amino acid sequence <SEQ ID 6638>. Analysis of this protein sequence reveals the following: TABLE-US-06575 Possible site: 46 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 153-169 (152-170) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06576 >GP: CAA68045 GB: X99710 methyltransferase [Lactococcus lactis] Identities = 134/227 (59%), Positives = 169/227 (74%) Query: 1 MVKSYSKTANHNMRRPVVKEELVHYMRTRQKQTTGFLAELEQFARQENIPIIQPEVVAYF 60 MV++Y T+N M RPVVK ELV +MR+ Q Q TG LAE+ FA++ NIP+I E V YF Sbjct: 1 MVETYKSTSNPMMNRPVVKAELVEWMRSSQTQVTGELAEVLNFAKENNIPVIPHETVLYF 60 Query: 61 RFLLQSLQPKHILEIGTAIGFSALLMAENAPDATIVTIDRNREMIDFAKANFAKYDSRQQ 120- + LL L+PK ILEIGTAIGFSAL+MA+ P+A IVTIDRN EMI+ AK N AKYD R Q Sbjct: 61 QMLLSLLKPKRILEIGTAIGFSALVMAQEVPEAEIVTIDRNPEMIELAKKNLAKYDHRNQ 120- Query: 121 IRLLEGDAADILSTLEGNFDFVFMDSAKSKYIVFLPEILRLLKVGGVVILDDVFQGGDIT 18- 0 I+L EGDAAD+L L+G FD VFMDSAKSKY+ FLP+ L LL G++++DDVFQ G+I Sbjct: 121 IQLKEGDAADVLQELKGPFDLVFMDSAKSKYVEFLPKSLELLSENGLILMDDVFQAGEIL 18- 0 Query: 181 KPIEDIRRGQRTIYRGLQSLFDATLTHPNLTTSLVPLSDGLLMIRKN 227 PI +++R QR + RGL+ LFD +P TS++PL DGLLMI+K+ Sbjct: 181 LPIMEVKRNQRALERGLRKLFDEVFDNPKYMTSVLPLGDGLLMIKKH 227 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06577 Identities = 177/235 (75%), Positives = 199/235 (84%) Query: 1 MVQSYSKNANHNMRRPVVKEEIVQYMRQHQKQNNGCLAELEAFAKQENIPIIPHETATYF 60 MV+SYSK ANHNMRRPVVKEE+V YMR QKQ G LAELE FA+QENIPII E YF Sbjct: 1 MVKSYSKTANHNMRRPVVKEELVHYMRTRQKQTTGFLAELEQFARQENIPIIQPEVVAYF 60 Query: 61 RFLMQTLQPKHILEIGTAIGFSALLMAENAPEAKITTIDRNEEMIALAKENFAKYDNHNQ 120- RFL+Q+LQPKHILEIGTAIGFSALLMAENAP+A I TIDRN EMI AK NFAKYD+ Q Sbjct: 61 RFLLQSLQPKHILEIGTAIGFSALLMAENAPDATIVTIDRNREMIDFAKANFAKYDSRQQ 120- Query: 121 ITLLEGDAVDVLQTLDKSYDFVFMDSAKSKYIVFLPQVLKHLDVGGVVVLDDIFQGGDIA 18- 0 I LLEGDA D+L TL+ ++DFVFMDSAKSKYIVFLP++L+ L VGGVV+LDD+FQGGDI Sbjct: 121 IRLLEGDAADILSTLEGNFDFVFMDSAKSKYIVFLPEILRLLKVGGVVILDDVFQGGDIT 18- 0 Query: 181 KPIDEVRRGQRTIYRGLQRLFDSTLQHPDLTATLVPLGDGLLMIRKNADHIVLED 235 KPI+++RRGQRTIYRGLQ LFD+TL HP+LT +LVPL DGLLMIRKN IVL D Sbjct: 181 KPIEDIRRGQRTIYRGLQSLFDATLTHPNLTTSLVPLSDGLLMIRKNQADIVLPD 235 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2148 A DNA sequence (GBSx2264) was identified in S. agalactiae <SEQ ID 6639> which encodes the amino acid sequence <SEQ ID 6640>. This protein is predicted to be phosphoglycolate phosphatase. Analysis of this protein sequence reveals the following:

TABLE-US-06578 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2193(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 8985> which encodes amino acid sequence <SEQ ID 8986> was also identified. This protein appears to be a hydrolase i.e. an exposed protein. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06579 >GP: CAA91552 GB: Z67740 unidentified [Streptococcus pneumoniae] Identities = 39/117 (33%), Positives = 67/117 (56%), Gaps = 9/117 (7%) Query: 98 KEQESRDSKIHLM-PYAKEILEWTKEQDIPNFMYTHKGASTHSVLETLQISHYFDEILTG 156- KE E+R+ + ++ ++LE Q +F+ +H+ +LE I+ YF E++T Sbjct: 25 KENEARELEHPILFEGVSDLLEDILNQGGRHFLVSHRNDQVLEILEKTSIAAYFTEVVTS 84 Query: 157 VSGFERKPHPQGINYLVKRYSLDKSMTYYIGDRPLDLEVAQNAGIKS------INLR 207 SGF+RKP+P+ + YL ++Y + + IGDRP+D+E Q AG+ + +NLR Sbjct: 85 SSGFKRKPNPESMLYLREKYQISSGLV--IGDRPIDIEAGQAAGLDTHLFTSIVNLR 139 SEQ ID 8986 (GBS240) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 57 (lane 2; MW 26 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 61 (lane 3; MW 51.5 kDa). GBS240-GST was purified as shown in FIG. 225, lane 12. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2149 A DNA sequence (GBSx2265) was identified in S. agalactiae <SEQ ID 6641> which encodes the amino acid sequence <SEQ ID 6642>. Analysis of this protein sequence reveals the following: TABLE-US-06580 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2620(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 6643> which encodes the amino acid sequence <SEQ ID 6644>. Analysis of this protein sequence reveals the following: TABLE-US-06581 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2967(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06582 Identities = 463/599 (77%), Positives = 541/599 (90%) Query: 1 MSDNRSHIEEKYQWDLTTVFATDELWETEVVELTQAIDNAKGFSGHLLDSSQSLLEITEV 60 M+DNRSH+EEKY WDL+T+FATD+ WE EV +L ++ +KGF+GHLLDSS +LL++T+ Sbjct: 1 MTDNRSHLEEKYTWDLSTIFATDKDWEAEVSDLATEVEASKGFAGHLLDSSANLLKVTKT 60 Query: 61 ELDLSRRLEKVYVYASMKNDQDTTVAKYQEFQAKATALYAKFSETFSFYEPELLQLSESD 120- L+L+RR+EKVYVYA MKNDQDTTVAKYQE+QAKA+ LYAKFSE FSFY+PE++ L + D Sbjct: 61 YLELARRVEKVYVYAHMKNDQDTTVAKYQEYQAKASGLYAKFSEVFSFYDPEVMMLHQED 120- Query: 121 YQSFLLEMPDLQKYDHFFEKIFANKPHVLSQNEEELLAGASEIFGAAGETFEILDNADMV 18- 0 YQ+FL E P+L+ Y+HFF+K+F + HVLSQ EEELLAGA EIF A ETF ILDNAD+V Sbjct: 121 YQAFLTETPELKVYNHFFDKLFQAREHVLSQAEEELLAGAQEIFNGAEETFSILDNADIV 18- 0 Query: 181 FPVVKNAKGEEVELTHGNFISLMESSDRTVRKEAYQAMYSTYEQFQHTYAKTLQTNVKSQ 24- 0 FPVVKN KGE+VELTHGNFISLMES DR+VR+ AY+AMYSTYEQFQHTYAKTLQTNVK Q Sbjct: 181 FPVVKNDKGEDVELTHGNFISLMESKDRSVRQAAYEAMYSTYEQFQHTYAKTLQTNVKVQ 24- 0 Query: 241 NFKARVHHYQSARQSALSANFIPEEVYETLIKTVNHHLPLLHRYMKLRQKVLGLDDLKMY 30- 0 N+KARVH Y SARQ+A++ANFIPE VY+TL++TVN HLPLLHRY+KLRQ+VLGLDDLKMY Sbjct: 241 NYKARVHKYDSARQAAMAANFIPEAVYDTLLETVNKHLPLLHRYLKLRQEVLGLDDLKMY 30- 0 Query: 301 DVYTPLSQMDMSFTYDEALKKSEEVLAIFGEAYSERVHRAFTERWIDVHVNKGKRSGAYS 36- 0 DVYTPLS+ D++ YDEAL+K+E+VLA+FG+ Y++RVHRAFTERWIDVHVNKGKRSGAYS Sbjct: 301 DVYTPLSETDLAIGYDEALEKAEKVLAVFGKDYADRVHRAFTERWIDVHVNKGKRSGAYS 36- 0 Query: 361 GGSYDTNAFMLLNWQDTLDNLYTLVHETGHSLHSTFTRENQPYVYGDYSIFLAEIASTTN 42- 0 GGSYDTNAF+LLNWQDTLDNLYTLVHETGHSLHSTFTRE QPYVYGDYSIFLAEIASTTN Sbjct: 361 GGSYDTNAFILLNWQDTLDNLYTLVHETGHSLHSTFTRETQPYVYGDYSIFLAEIASTTN 42- 0 Query: 421 ENILTETLLKEVKDDKNRFAILNHYLDGFKGTIFRQTQFAEFEHAIHVADQEGQVLTSEY 48- 0 ENI+TE LL EV+D+K RFAILNHYLDGF+GT+FRQTQFAEFEHAIH ADQ+G+VLTSEY Sbjct: 421 ENIMTEALLNEVQDEKERFAILNHYLDGFRGTVFRQTQFAEFEHAIHQADQKGEVLTSEY 48- 0 Query: 481 LNNLYAELNEKYYGLTKEDNHFIQYEWARIPHFYYNYYVFQYATGFAAANYLAERIVNGN 54- 0 LN LYA+LNEKYYGL+K+DNHFIQYEWARIPHFYYNYYV+QYATGFAAA+YLA++IV+G Sbjct: 481 LNQLYADLNEKYYGLSKKDNHFIQYEWARIPHFYYNYYVYQYATGFAAASYLADKIVHGT 54- 0 Query: 541 PEDKEAYLNYLKAGNSDYPLNVIAKAGVDMTSADYLDAAFRVFEERLVELENLVAKGVH 599- +D + YL YLK+GNSDYPL VIAKAGVDM DYL+AAF+VF+ERL ELE LV+KG+H Sbjct: 541 QDDIDHYLAYLKSGNSDYPLEVIAKAGVDMEKGDYLEAAFKVFDERLTELEVLVSKGIH 599- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2150 A DNA sequence (GBSx2266) was identified in S. agalactiae <SEQ ID 6645> which encodes the amino acid sequence <SEQ ID 6646>. This protein is predicted to be competence protein. Analysis of this protein sequence reveals the following: TABLE-US-06583 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2955(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06584 >GP: AAC23746 GB: AF052209 competence protein [Streptococcus pneumoniae] Identities = 127/269 (47%), Positives = 176/269 (65%), Gaps = 8/269 (2%) Query: 1 MLIAKDKQGNLINLLESHPGKGQYFCPTCCSAVRLKAGRIMRRHFAHISLKNCQFYHENE 60 M +A+D +G L+N+LE K Y CP C + L+ G +R HFAH SLK+C F+ ENE Sbjct: 1 MFVARDARGELVNVLEDKLEKQAYTCPACGGQLHLRQGPSVRTHFAHKSLKDCDFFFENE 60 Query: 61 SNEHLQLKAKLYMSLSRENETMLEHHLPEINQIADLFVNETLALE----VQCSRLSEQRL 116- S EHL K LY L +E + LE+ L E+ QIAD+FVN LALE V C + + L Sbjct: 61 SPEHLANKESLYHWLKKETKVQLEYPLSELKQIADVFVNGNLALESSVVVPCLK---KVL 117- Query: 117 RERTKAYLQADFQVRWLLGEKLWLKHRLTNLHKQFLQFSQSIGFHIWELDLRLEVLRLKY 17- 6 +ER++ Y +QV WLLG+KLWLK RLT L FL FSQ++GF++WELD +VLRLKY Sbjct: 118 KERSEGYRSQGYQVLWLLGQKLWLKERLTRLQAGFLYFSQNMGFYVWELDKGKQVLRLKY 17- 7 Query: 177 LIYEDLRGHVYYLSKTCPL-SGDVLAFLKWPYQSKNLNFYKVKQDRNIRDYVRQQLRYGN 23- 5 LIY+DLRG ++Y K G +L L+ PY+ + ++ + V +D++I Y+RQQL Y N Sbjct: 178 LIYQDLRGKLHYQIKEFSYGQGSLLEILRLPYKKQKISHFTVSEDKDICRYIRQQLYYQN 23- 7 Query: 236 QFWLRKQEKAYLSGQNLLTQELMMFFPQI 264 FW+++Q +AY G+N+LT L ++PQI Sbjct: 238 LFWMKEQAEAYQKGENILTYGLKEWYPQI 266 A related DNA sequence was identified in S. pyogenes <SEQ ID 6647> which encodes the amino acid sequence <SEQ ID 6648>. Analysis of this protein sequence reveals the following: TABLE-US-06585 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1034(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06586 Identities = 154/312 (49%), Positives = 204/312 (65%), Gaps = 1/312 (0%) Query: 1 MLIAKDKQGNLINLL-ESHPGKGQYFCPTCCSAVRLKAGRIMRRHFAHISLKNCQFYHEN 59 +L A D + LI+L+ + K + CP C S VRL+ G I R HFAH+ L +CQF EN Sbjct: 4 ILTALDDKNQLISLVTQPISTKPPFRCPACKSPVRLRQGTIRRPHFAHVQLAHCQFQAEN 63 Query: 60 ESNEHLQLKAKLYMSLSRENETMLEHHLPEINQIADLFVNETLALEVQCSRLSEQRLRER 119- ES EHL LKAKLY SL R +E +LPE+ QIADL+VN+ LALE+QCS L +RL++R Sbjct: 64 ESEEHLTLKAKLYTSLVRTEAVCIEKYLPELQQIADLWVNDKLALEIQCSPLPVERLKKR 123- Query: 120 TKAYLQADFQVRWLLGEKLWLKHRLTNLHKQFLQFSQSIGFHIWELDLRLEVLRLKYLIY 17- 9 TKAY + + VRWLLG KLWL LT L KQFL FS S+GFH+WELD +LRLKYLI+ Sbjct: 124 TKAYQEKGYPVRWLLGRKLWLNTHLTALQKQFLYFSSSLGFHLWELDAAANLLRLKYLIH 18- 3 Query: 180 EDLRGHVYYLSKTCPLSGDVLAFLKWPYQSKNLNFYKVKQDRNIRDYVRQQLRYGNQFWL 23- 9 EDL G V YL+KT L +++ + PYQ + L Y+ K N+ +++ L + WL Sbjct: 184 EDLFGKVSYLTKTISLDHNIMEMFRLPYQQEILYSYQKKMTVNLSKRIQRALLARHPKWL 24- 3 Query: 240 RKQEKAYLSGQNLLTQELMMFFPQIQPPRVDTDFCQITNSLTSFYQNFTNYYQKNKNNLD 29- 9 R+QEKAYLSG NLL F+PQ +P + + FCQI +L +Y++F YY+K K+ Sbjct: 244 RRQEKAYLSGYNLLMLTTDAFYPQWRPVQSSSGFCQIKGNLRPYYESFKVYYKKEKDKKV 30- 3 Query: 300 QTLYPPVFYDKI 311 QTL+ P +Y K+ Sbjct: 304 QTLFSPKYYVKM 315 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2151 A DNA sequence (GBSx2267) was identified in S. agalactiae <SEQ ID 6649> which encodes the amino acid sequence <SEQ ID 6650>. This protein is predicted to be bicyclomycin resistance protein. Analysis of this protein sequence reveals the following: TABLE-US-06587 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.33 Transmembrane 78-94 (75-96) INTEGRAL Likelihood = -8.33 Transmembrane 269-285 (267-287) INTEGRAL Likelihood = -7.38 Transmembrane 290-306 (287-314) INTEGRAL Likelihood = -7.06 Transmembrane 203-219 (199-225) INTEGRAL Likelihood = -6.69 Transmembrane 157-173 (143-184) INTEGRAL Likelihood = -6.42 Transmembrane 53-69 (44-73) INTEGRAL Likelihood = -6.42 Transmembrane 362-378 (357-381) INTEGRAL Likelihood = -3.72 Transmembrane 242-258 (240-261) INTEGRAL Likelihood = -3.24 Transmembrane 329-345 (328-346) INTEGRAL Likelihood = -1.28 Transmembrane 107-123 (106-123) ----- Final Results ----- bacterial membrane --- Certainty = 0.4333(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06588 >GP: CAA15047 GB: AJ235272 BICYCLOMYCIN RESISTANCE PROTEIN (bcr1) [Rickettsia prowazekii] Identities = 86/336 (25%), Positives = 159/336 (46%), Gaps = 28/336 (8%) Query: 73 GKKNTVLLGLCLILMSGFISFFTSNFSLAMASRLLLGIGIGLYNSLSISIITDLYEADER 13- 2 G++ VLLGL + ++S IS F+ N + M +R + G+ + + + S+ D Y+ E Sbjct: 70 GRRPIVLLGLFIYIVSSIISIFSFNIEMLMIARFIQAFGVSVGSVIGQSMARDSYQGAEL 12- 9 Query: 133 ASMIGLRTASLNIGKALTTFIVGLVLA-IGVNYIYLVYLLVIPVFF-FFWKNVPEVENQT 19- 0 + + + + L AL ++I G ++ + +Y+++ + L + +++ +PE Sbjct: 130 SYVYAILSPWLLFIPALGSYIGGYIIEYLSWHYVFIFFSLAGTILLALYYQILPETNYYI 18- 9 Query: 191 HTLKASTTFDT-----KAALLMLITFLVGI---AYIGATVKIPTLLVTKYHYATSFSSNM 24- 2 ++S F+ K +L L F++G Y G ++ P +L+ + SF + Sbjct: 190 AFSQSSKYFEVFNIIIKDKMLWLYAFIIGAFNGIYYGFFIEAPFILIDQMRVLPSFYGKL 24- 9 Query: 243 LTLLAFSGILVGSVFGKLVK---VFQEKTLLIMILAMGIGNVLFALANNQIIFIVAS--I 29- 7 LL+F+ I G + G L+K V+ +K + I + G +LFA+ + + FI+ S Sbjct: 250 AFLLSFASIFGGFLGGYLIKKRQVYDKKVMSIGFIFSLCGCILFAVDSFILEFILVSNVF 30- 9 Query: 298 LIGASFVGTM-----SSVFFYISKNYAKEHNNFITSLALTAGNI-GVILTPLI--LTKLP 34- 9 I F+ M S+ I+ YA E +T TAG+I G I +I +T Sbjct: 310 AIAMIFMPMMIHMIGHSLLIAITLRYALEDYATVTG---TAGSIFGAIYYVVIASVTYCV 36- 6 Query: 350 SQLHLEPFMTPFLITSGLMVINV--FVYLVLMSKNK 383 S++H E L+ L + +V F Y+ L+ K K Sbjct: 367 SKIHGETISNFSLLCLVLSISSVISFYYICLLYKKK 402 A related GBS gene <SEQ ID 8987> and protein <SEQ ID 8988> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06589 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: 6.28 GvH: Signal Score (-7.5): -2.45 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 10 value: -8.33 threshold: 0.0 INTEGRAL Likelihood = -8.33 Transmembrane 78-94 (75-96) INTEGRAL Likelihood = -8.33 Transmembrane 269-285 (267-287) INTEGRAL Likelihood = -7.38 Transmembrane 290-306 (287-314) INTEGRAL Likelihood = -7.06 Transmembrane 203-219 (199-225) INTEGRAL Likelihood = -6.69 Transmembrane 157-173 (143-184) INTEGRAL Likelihood = -6.42 Transmembrane 53-69 (44-73) INTEGRAL Likelihood = -6.42 Transmembrane 362-378 (357-381) INTEGRAL Likelihood = -3.72 Transmembrane 242-258 (240-261) INTEGRAL Likelihood = -3.24 Transmembrane 329-345 (328-346) INTEGRAL Likelihood = -1.28 Transmembrane 107-123 (106-123) PERIPHERAL Likelihood = -3.71 140 modified ALOM score: 2.17 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4333(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00156## There is also homology to SEQ ID 4001 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2152 A DNA sequence (GBSx2268) was identified in S. agalactiae <SEQ ID 6651> which encodes the amino acid sequence <SEQ ID 6652>. This protein is predicted to be 16S pseudouridylate synthase (rsuA). Analysis of this protein sequence reveals the following: TABLE-US-06590 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2645(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06591 >GP: BAB06992 GB: AP001518 16S pseudouridylate synthase [Bacillus halodurans] Identities 106/234 (45%), Positives = 141/234 (59%), Gaps = 1/234 (0%) Query: 1 MRLDKLLGQAGFGSRNQVKKLICSRQVSVDGQIVTKDNVIVDSGLQSIFVGKERVCLKES 60- MR+DK L GFGSR VKKL++ V V GQ + + V+ +SI V E V K Sbjct: 1 MRIDKFLANMGFGSRKDVKKLLKTGAVRVQGQPIKDPSTHVEPESESITVYGEEVEYKPY 60- Query: 61 SYYLLYKPSGVVSAVRDSEHKTVIDLISEKDKVEGLYPIGRLDRDTEGLLIVTNNGPLGY 12- 0 Y ++ KP GV+ A D EH+TVIDL+E+++ P+GRLD+DT GLL++TN+G + Sbjct: 61 VYLMMNKPKGVICATEDLEHETVIDLLGEEERHYEPSPVGRLDKDTVGLLLITNDGKFNH 12- 0 Query: 121 RMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTARI 18- 0 ++ PKHHV KTY V G + ++ F GVV DDG KPA L I A +S + Sbjct: 121 WLMSPKHHVPKTYRALVEGHVTEEDVGAFSHGVVLDDGYVTKPATLHILEA-GARSHIEL 17- 9 Query: 181 TITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSEAAIL 234 +TEGKFHQVK+MF A G +V+ L RI G+L LD L G+YR L E A+L Sbjct: 180 ILTEGKFHQVKRMFQAVGKRVLELERIKIGNLLLDPELARGEYRELTKEEIALL 233 A related DNA sequence was identified in S. pyogenes <SEQ ID 6653> which encodes the amino acid sequence <SEQ ID 6654>. Analysis of this protein sequence reveals the following: TABLE-US-06592 Possible Site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3310(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06593 Identities = 111/194 (57%), Positives = 138/194 (70%) Query: 1 MRLDKLLGQAGFGSRNQVKKLICSRQVSVDGQIVTKDNVIVDSGLQSIFVGKERVCLKES 60 MRLDKLL GSR+QVKKLI ++ V VD VD GLQ I V +RV + Sbjct: 1 MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKH 60 Query: 61 SYYLLYKPSGVVSAVRDSEHKTVIDLISEKDKVEGLYPIGRLDRDTEGLLIVTNNGPLGY 120- SY +L KPSGVVSA +D+ + TVID ++E+DK LYP+GRLDRDTEGL+++T+NGPLG+ Sbjct: 61 SYIILNKPSGVVSAKKDTNYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGF 120- Query: 121 RMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTARI 18- 0 RMLHP HHV+KTY V VNG L DA FF G+ F G +C+PA+LTI A+ D+S A + Sbjct: 121 RMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASL 18- 0 Query: 181 TITEGKFHQVKKMF 194 TI+EGKFHQVKK F Sbjct: 181 TISEGKFHQVKKCF 194 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2153 A DNA sequence (GBSx2269) was identified in S. agalactiae <SEQ ID 6655> which encodes the amino acid sequence <SEQ ID 6656>. Analysis of this protein sequence reveals the following:

TABLE-US-06594 Possible site: 42 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9745> which encodes amino acid sequence <SEQ ID 9746> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06595 >GP: BAA18872 GB: D90917 hypothetical protein [Synechocystis sp.] Identities = 197/318 (61%), Positives = 243/318 (75%) Query: 22 MGLLVDGKWVDQWYDTASTGGKFVRTVTQFRHWVTKDGSAGPSGDAGFKAESGRYHLYVS 81 - MGLLV+G W DQWYDT STGG+FVR +QFRHW+T DGS GP+G GFKAE+GRYHLYVS Sbjct: 1 MGLLVNGIWQDQWYDTESTGGRFVRHDSQFRHWITPDGSPGPTGHGGFKAEAGRYHLYVS 60 Query: 82 LACPWASRVLIMRKLKNLESHISISIVNPLMLENGWTFQEYKGVIPDMINQSQYLYQIYQ 141- LACPWA R LI RKLK LE I +S+V+ LM ENGWTF GV+PD + ++YLYQIY Sbjct: 61 LACPWAHRTLIFRKLKGLEGMIDVSVVHWLMRENGWTFAPGPGVMPDPLFNAEYLYQIYT 120- Query: 142 ASQSDYTGRVTVPVLWDKKFHTIVNNESSEIMRMLNTAFNHITGNTDDYYPDSLQGQIDE 20- 1 + + Y+GRVTVP+LWDK+ TIVNNESSEI+R+ N+AF+ + + DYYP +L+ QID Sbjct: 121 RADAQYSGRVTVPILWDKQKQTIVNNESSEIIRIFNSAFDGLGAKSGDYYPKALRTQIDA 18- 0 Query: 202 MNNFIYPKINNGVYKAGFATSQNVYQKEVETLFTALDQLEKHLSDNHYLVGEQFTEADIR 26- 1 +N+ IY INNGVYK GFAT+Q Y++ + LF +LD LE L + YL G++ TEAD R Sbjct: 181 LNDRIYHTINNGVYKCGFATTQTAYEEAIAPLFESLDWLEGILQGHQYLTGDEITEADWR 24- 0 Query: 262 LFTTLVRFDTVYYGHFKCNLKALHDYPHLWHYTKRIYNLPGIAETVNFDHIKKHYYGSHK 32- 1 LFTTL+RFD VY GHFKCNL+ + DYP+LW Y + +Y+ PGIAETVNF HIK HYY SH Sbjct: 241 LFTTLIRFDVVYVGHFKCNLRRIQDYPNLWRYLRDLYHQPGIAETVNFQHIKGHYYESHL 30- 0 Query: 322 TINPTGIIPAGPNLDWTI 339 INPTGI+P GP LD ++ Sbjct: 301 NINPTGIVPMGPALDLSL 318 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 6656 (GBS655) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 143 (lane 24; MW 27 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2154 A DNA sequence (GBSx2270) was identified in S. agalactiae <SEQ ID 6657> which encodes the amino acid sequence <SEQ ID 6658>. Analysis of this protein sequence reveals the following: TABLE-US-06596 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1116(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06597 >GP: CAB12030 GB: Z99105 similar to glucosamine-6-phosphate isomerase [Bacillus subtilis] Identities = 112/243 (46%), Positives = 163/243 (66%), Gaps = 10/243 (4%) Query: 1 MRVITVKNDIEGGKIAFTLLEEKMKAGAQT-LGLATGSSPITFYEEIVKS----NLDFSN 55 M+++ ++ E K++ +++E+++A LGLATGS+P+ Y++++ +DFS Sbjct: 1 MKILIAEHYEELCKLSAAIIKEQIQAKKDAVLGLATGSTPVGLYKQLISDYQAGEIDFSK 60 Query: 56 MVSINLDEYVGIAASNDQSYSYFMHKHLFDAKPFKENNL--PNGLAKDLKEEIKRYDAVI 113- + + NLDEY G++ S+ QSY++FMH+HLF + +++ P G L+ K Y+ +I Sbjct: 61 VTTFNLDEYAGLSPSHPQSYNHFMHEHLFQHINMQPDHIHIPQGDNPQLEAACKVYEDLI 120- Query: 114 N-ANPIDFQILGIGRNGHIGFNEPGTPFDITTHVVDLAPSTIEANSRFFNSIDD-VPKQA 17- 1 A ID QILGIG NGHIGFNEPG+ F+ T VV L+ STI+AN+RFF VP+ A Sbjct: 121 RQAGGIDVQILGIGANGHIGFNEPGSDFEDRTRVVKLSESTIQANARFFGGDPVLVPRLA 18- 0 Query: 172 LSMGIGSIMK-SKTIVLVAYGIEKAEAIASMIKGPITEDMPASILQKHDDVVIIVDEAAA 23- 0 +SMGI +IM+ SK IVL+A G EKA+AI M +GP+T D+PASILQKH+ V +I D AA Sbjct: 181 ISMGIKTIMEFSKHIVLLASGEEKADAIQKMAEGPVTTDVPASILQKHNHVTVIADYKAA 24- 0 Query: 231 SKL 233 KL Sbjct: 241 QKL 243 A related DNA sequence was identified in S. pyogenes <SEQ ID 6659> which encodes the amino acid sequence <SEQ ID 6660>. Analysis of this protein sequence reveals the following: TABLE-US-06598 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.59 Transmembrane 174-190 (174-190) ----- Final Results ----- bacterial membrane --- Certainty = 0.1235(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06599 >GP: CAB12030 GB: Z99105 similar to glucosamine-6-phosphate isomerase [Bacillus subtilis] Identities = 120/244 (49%), Positives = 162/244 (66%), Gaps = 12/244 (4%) Query: 1 MKIIRVQDQIEGGKIAFTLLKDSL-AKGAKTLGLATGSSPISFYQEMVKS----PLDFSD 55 MKI+ + E K++ ++K+ + AK LGLATGS+P+ Y++++ +DFS Sbjct: 1 MKILIAEHYEELCKLSAAIIKEQIQAKKDAVLGLATGSTPVGLYKQLISDYQAGEIDFSK 60 Query: 56 LTSINLDEYVGLSVESDQSYDYFMRQNLF---NAKPFKKNYLPNGLATDVEAEAKRYNQI 112- +T+ NLDEY GLS QSY++FM ++LF N +P ++P G +EA K Y + Sbjct: 61 VTTFNLDEYAGLSPSHPQSYNHFMHEHLFQHINMQP-DHIHIPQGDNPQLEAACKVYEDL 119- Query: 113 IAEHP-IDFQVLGIGRNGHIGFNEPGTSFEEETHVVDLQESTIEANSRFFTSIED-VPKQ 17- 0 I + ID Q+LGIG NGHIGFNEPG+ FE+ T VV L ESTI+AN+RFF VP+ Sbjct: 120 IRQAGGIDVQILGIGANGHIGFNEPGSDFEDRTRVVKLSESTIQANARFFGGDPVLVPRL 17- 9 Query: 171 AISMGIASIMK-SEMIVLLAFGQEKADAIKGMVFGPITEHLPASILQKHDHVIVIVDEAA 22- 9 AISMGI +IM+ S+ IVLLA G+EKADAI+ M GP+T +PASILQKH+HV VI D A Sbjct: 180 AISMGIKTIMEFSKHIVLLASGEEKADAIQKMAEGPVTTDVPASILQKHNHVTVIADYKA 23- 9 Query: 230 ASQL 233 A +L Sbjct: 240 AQKL 243 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06600 Identities = 163/233 (69%), Positives = 201/233 (85%) Query: 1 MRVITVKNDIEGGKIAFTLLEEKMKAGAQTLGLATGSSPITFYEEIVKSNLDFSNMVSIN 60 M++I V++ IEGGKIAFTLL++ + GA+TLGLATGSSPI+FY+E+VKS LDFS++ SIN Sbjct: 1 MKIIRVQDQIEGGKIAFTLLKDSLAKGAKTLGLATGSSPISFYQEMVKSPLDFSDLTSIN 60 Query: 61 LDEYVGIAASNDQSYSYFMHKHLFDAKPFKENNLPNGLAKDLKEEIKRYDAVINANPIDF 120- LDEYVG++ +DQSY YFM ++LF+AKPFK+N LPNGLA D++ E KRY+ +I +PIDF Sbjct: 61 LDEYVGLSVESDQSYDYFMRQNLFNAKPFKKNYLPNGLATDVEAEAKRYNQIIAEHPIDF 120- Query: 121 QILGIGRNGHIGFNEPGTPFDITTHVVDLAPSTIEANSRFFNSIDDVPKQALSMGIGSIM 18- 0 Q+LGIGRNGHIGFNEPGT F+ THVVDL STIEANSRFF SI+DVPKQA+SMGI SIM Sbjct: 121 QVLGIGRNGHIGFNEPGTSFEEETHVVDLQESTIEANSRFFTSIEDVPKQAISMGIASIM 18- 0 Query: 181 KSKTIVLVAYGIEKAEAIASMIKGPITEDMPASILQKHDDVVIIVDEAAASKL 233 KS+ IVL+A+G EKA+AI M+ GPITE +PASILQKHD V++IVDEAAAS+L Sbjct: 181 KSEMIVLLAFGQEKADAIKGMVFGPITEHLPASILQKHDHVIVIVDEAAASQL 233 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2155 A DNA sequence (GBSx2271) was identified in S. agalactiae <SEQ ID 6661> which encodes the amino acid sequence <SEQ ID 6662>. Analysis of this protein sequence reveals the following: TABLE-US-06601 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.12 Transmembrane 169-185 (161-194) INTEGRAL Likelihood = -6.37 Transmembrane 151-167 (145-168) INTEGRAL Likelihood = -5.15 Transmembrane 42-58 (41-62) INTEGRAL Likelihood = -1.59 Transmembrane 207-223 (207-224) INTEGRAL Likelihood = -1.12 Transmembrane 24-40 (23-40) ----- Final Results ----- bacterial membrane --- Certainty = 0.4248(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06602 >GP: AAF13747 GB: AF117351 unknown [Zymomonas mobilis] Identities = 88/216 (40%), Positives = 123/216 (56%) Query: 9 QQLNILRAGVLGANDGIISVAGVVIGVASATHNLWIIFLSAASAILAGAFSMAGGEYVSV 68 +Q+ LRA VLGANDGI+S + ++IGVASA + I L+ S ++AGA SMA GEYVSV Sbjct: 17 RQMGWLRASVLGANDGILSTSSLMIGVASAHGSSGNILLAGMSGLIAGALSMAAGEYVSV 76 Query: 69 STQKDTEQAAVAREEKLLENNPELAKKSLVDIYLAKGESHEHAQWLVDKAFSKNAIEHLV 128- S+Q D EQA VARE L+ NP K L +IY+ +G E A + ++ + NA+E + Sbjct: 77 SSQHDMEQADVAREHAELKANPHAEKHELAEIYVERGLDRELALQVAEQLMAHNALEAHL 136- Query: 129 EEKYGIEFGEYTSPWHAAISSFIAFAIGSIFPTITILLLPFSVRIVGTVIIVIVSLLSTG 18- 8 ++ G+ P AA++S I+F+ G+I P +T L P + + +I I+ L G Sbjct: 137 RDELGLTDSLIARPVQAALASAISFSGGAIVPFLTALFSPPEIINITISLISILCLAVLG 19- 6 Query: 189 YVSAKLGQAPTVPAMRRNVMIGCLTMLATYVIGQLF 224 V A LG A A R G L M+ T IG F Sbjct: 197 MVGAHLGGANVPKAALRVTFCGALAMIGTAAIGSFF 232 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2156 A DNA sequence (GBSx2272) was identified in S. agalactiae <SEQ ID 6663> which encodes the amino acid sequence <SEQ ID 6664>. This protein is predicted to be S-adenosylmethionine tRNA ribosyltransferase (queA). Analysis of this protein sequence reveals the following: TABLE-US-06603 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3438(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06604 >GP: CAB14732 GB: Z99118 S-adenosylmethionine tRNA ribosyltransferase [Bacillus subtilis] Identities = 228/341 (66%), Positives = 279/341 (80%) Query: 1 MNTNDFDFYLPEELIAQTPLEKRDASKLLVIDHKNKTMTDSHFDHILDELKPGDALVMNN 60 M + FDF LPE LIAQ PLE+RDAS+L+V+D +TDS F HI+ GD LV+NN Sbjct: 1 MKVDLFDFELPERLIAQVPLEQRDASRLMVLDKHTGELTDSSFKHIISFFNEGDCLVLNN 60 Query: 61 TRVLPARLYGEKQDTHGHVELLLLKNTEGDQWEVLAKPAKRLRVGTKVSFGDGRLIATVT 120- TRVLPARL+G K+DT VELLLLK GD+WE LAKPAKR++ GT V+FGDGRL A T Sbjct: 61 TRVLPARLFGTKEDTGAKVELLLLKQETGDKWETLAKPAKRVKKGTVVTFGDGRLKAICT 120- Query: 121 KELEHGGRIVEFSYDGIFLEVLESLGEMPLPPYIHEKLEDRDRYQTVYAKENGSAAAPTA 18- 0 +ELEHGGR +EF YDGIF EVLESLGEMPLPPYI E+L+D++RYQTVY+KE GSAAAPTA Sbjct: 121 EELEHGGRKMEFQYDGIFYEVLESLGEMPLPPYIKEQLDDKERYQTVYSKEIGSAAAPTA 18- 0 Query: 181 GLHFTKELLEKIETKGVKLVYLTLHVGLGTFRPVSVDNLDEHEMHSEFYQLSKEAADTLN 24- 0 GLHFT+E+L++++ KGV++ ++TLHVGLGTFRPVS D ++EH MH+EFYQ+S+E A LN Sbjct: 181 GLHFTEEILQQLKDKGVQIEFITLHVGLGTFRPVSADEVEEHNMHAEFYQMSEETAAALN 24- 0 Query: 241 AVKESGGRIVAVGTTSIRTLETIGSKFNGELKADSGWTNIFIKPGYQFKVVDAFSTNFHL 30- 0 V+E+GGRI++VGTTS RTLETI + +G+ KA SGWT+IFI PGY+FK +D TNFHL Sbjct: 241 KVRENGGRIISVGTTSTRTLETIAGEHDGQFKASSGWTSIFIYPGYEFKAIDGMITNFHL 30- 0 Query: 301 PKSTLVMLVSAFAGRDFVLEAYNHAVEERYRFFSFGDAMFV 341 PKS+L+MLVSA AGR+ +L AYNHAVEE YRFFSFGDAM + Sbjct: 301 PKSSLIMLVSALAGRENILRAYNHAVEEEYRFFSFGDAMLI 341 A related DNA sequence was identified in S. pyogenes <SEQ ID 6665> which encodes the amino acid sequence <SEQ ID 6666>. Analysis of this protein sequence reveals the following: TABLE-US-06605 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3864(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06606 Identities = 297/341 (87%), Positives = 322/341 (94%) Query: 1 MNTNDFDFYLPEELIAQTPLEKRDASKLLVIDHKNKTMTDSHFDHILDELKPGDALVMNN 60 MNTN+FDF LPEELIAQTPLEKRD+SKLL+IDH+ KTM DSHFDHI+D+L PGDALVMNN Sbjct: 1 MNTNNFDFELPEELIAQTPLEKRDSSKLLIIDHRQKTMVDSHFDHIIDQLNPGDALVMNN 60 Query: 61 TRVLPARLYGEKQDTHGHVELLLLKNTEGDQWEVLAKPAKRLRVGTKVSFGDGRLIATVT 120- TRVLPARLYGEK DTHGHVELLLLKNT+GDQWEVLAKPAKRL+VG++V+FGDGRL AT+ Sbjct: 61 TRVLPARLYGEKPDTHGHVELLLLKNTQGDQWEVLAKPAKRLKVGSQVNFGDGRLKATII 120- Query: 121 KELEHGGRIVEFSYDGIFLEVLESLGEMPLPPYIHEKLEDRDRYQTVYAKENGSAAAPTA 18- 0 ELEHGGRIVEFSYDGIFLEVLESLGEMPLPPYIHEKLED +RYQTVYAKENGSAAAPTA Sbjct: 121 DELEHGGRIVEFSYDGIFLEVLESLGEMPLPPYIHEKLEDAERYQTVYAKENGSAAAPTA 18- 0 Query: 181 GLHFTKELLEKIETKGVKLVYLTLHVGLGTFRPVSVDNLDEHEMHSEFYQLSKEAADTLN 24- 0 GLHFT +LL+KIE KGV LVYLTLHVGLGTFRPVSVDNLDEH+MHSEFY LS+EAA TL Sbjct: 181 GLHFTTDLLKKIEAKGVHLVYLTLHVGLGTFRPVSVDNLDEHDMHSEFYSLSEEAAQTLR 24- 0 Query: 241 AVKESGGRIVAVGTTSIRTLETIGSKFNGELKADSGWTNIFIKPGYQFKVVDAFSTNFHL 30- 0 VK++GGR+VAVGTTSIRTLETIG KF G+++ADSGWTNIFIKPGYQFKVVDAFSTNFHL Sbjct: 241 DVKQAGGRVVAVGTTSIRTLETIGGKFQGDIQADSGWTNIFIKPGYQFKVVDAFSTNFHL 30- 0 Query: 301 PKSTLVMLVSAFAGRDFVLEAYNHAVEERYRFFSFGDAMFV 341 PKSTLVMLVSAFAGRDFVLEAY HAV+E+YRFFSFGDAMFV Sbjct: 301 PKSTLVMLVSAFAGRDFVLEAYRHAVDEKYRFFSFGDAMFV 341 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2157 A DNA sequence (GBSx2273) was identified in S. agalactiae <SEQ ID 6667> which encodes the amino acid sequence <SEQ ID 6668>. Analysis of this protein sequence reveals the following: TABLE-US-06607 Possible site: 36 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -14.22 Transmembrane 14-30 (6-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.6689(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 6669> which encodes the amino acid sequence <SEQ ID 6670>. Analysis of this protein sequence reveals the following: TABLE-US-06608 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2655(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06609 Identities = 126/195 (64%), Positives = 155/195 (78%), Gaps = 1/195 (0%) Query: 160 MEERFDITETDYEYIGEHNNYVAAFSGAMSIDDMQKYSLVYSENTPAYALAERIGGMDSA 21- 9 M ERFDITETDYEY EH+ YVA F+GAMSI DMQ+YSLVYSENTPAYALAER+GGM+ A Sbjct: 1 MTERFDITETDYEYDQEHHAYVAQFNGAMSIPDMQEYSLVYSENTPAYALAERLGGMNKA 60 Query: 220 YSKFGRYGQSKGDIKNIQKNGNKVTTDYYIQVLDYLWKHRKKYDSLITYLEEAFPTDYYR 27- 9 Y F RYG+ G I I +NGNK+TT YY+QVLDYLW+H+ KY ++ Y+ E+FP YY+ Sbjct: 61 YQLFDRYGKVSGAITTIDRNGNKITTAYYLQVLDYLWQHQDKYKDILYYIGESFPDLYYK 120- Query: 280 ALIPSDVVVAQKPGYVREALNVGAIVKEEVPYIVAIYTAGLGGSTQEDSEINGVGLYQLE 33- 9 +P V V QKPGYVREALNVGAIV EE PY++A+Y++GLGG+TQ E+NG+G QL Sbjct: 121 TYLP-HVKVYQKPGYVREALNVGAIVCEESPYLIALYSSGLGGATQASEEVNGLGYVQLV 17- 9 Query: 340 QLCFVINQWHRVNMN 354 QL +VIN+W+R N+N Sbjct: 180 QLPYVINEWYRGNLN 194 SEQ ID 6668 (GBS680) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 164 (lane 10-12; MW 64 kDa) and in FIG. 239 (lane 9; MW 64 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 164 (lane 15; MW 40 kDa) and in FIG. 188 (lane 9; MW 40 kDa). Purified GBS680-His is shown in FIG. 242, lane 8. Purified GBS680-GST is shown in FIG. 246, lanes 6 & 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2158 A DNA sequence (GBSx2274) was identified in S. agalactiae <SEQ ID 6671> which encodes the amino acid sequence <SEQ ID 6672>. Analysis of this protein sequence reveals the following: TABLE-US-06610 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.57 Transmembrane 8-24 (4-25) INTEGRAL Likelihood = -2.13 Transmembrane 66-82 (65-84) INTEGRAL Likelihood = -1.65 Transmembrane 107-123 (107-125) INTEGRAL Likelihood = -0.69 Transmembrane 36-52 (36-52) INTEGRAL Likelihood = -0.48 Transmembrane 89-105 (89-105) ----- Final Results ----- bacterial membrane --- Certainty = 0.2826(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2159 A DNA sequence (GBSx2275) was identified in S. agalactiae <SEQ ID 6673> which encodes the amino acid sequence <SEQ ID 6674>. Analysis of this protein sequence reveals the following: TABLE-US-06611 Possible site: 59 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.87 Transmembrane 108-124 (97-133) INTEGRAL Likelihood = -9.08 Transmembrane 181-197 (173-201) INTEGRAL Likelihood = -7.43 Transmembrane 220-236 (216-248) INTEGRAL Likelihood = -6.69 Transmembrane 6-22 (3-28) INTEGRAL Likelihood = -3.72 Transmembrane 401-417 (400-417) INTEGRAL Likelihood = -3.35 Transmembrane 279-295 (278-295) INTEGRAL Likelihood = -2.87 Transmembrane 31-47 (30-50) INTEGRAL Likelihood = -2.87 Transmembrane 244-260 (242-264) INTEGRAL Likelihood = -0.80 Transmembrane 62-78 (62-78) ----- Final Results ----- bacterial membrane --- Certainty = 0.4949(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-06612 >GP: AAC21770 GB: U32694 H. influenzae predicted coding region HI0092 [Haemophilus influenzae Rd] Identities = 232/416 (55%), Positives = 314/416 (74%), Gaps = 3/416 (0%) Query: 4 TFTTTGALIGLALAILLIIKKVHPAYSLILGALVGGLIGGGDLVTIVNTMVLGAQGMMSS 63 T + GAL+ L +AI LI+KKV PAY +++GALVGGLIGG DL V+ M+ GAQG+ ++ Sbjct: 3 TVSAIGALVALIVAIFLILKKVSPAYGMLVGALVGGLIGGADLSQTVSLMIGGAQGITTA 62 Query: 64 ILRILTSGILAGALIKTGSAEKIAESIIKKLGQQRAITALAIATMIICAVGVFIDIAVIT 123- ++RIL +G+LAG LI++G+A I E+I KLG+ RA+ ALA+ATMI+ AVGVF+D+AVIT Sbjct: 63 VMRILAAGVLAGVLIESGAANSITETITNKLGETRALLALALATMILTAVGVFVDVAVIT 122- Query: 124 VAPIALAIGKKANLSKSSILLAMIGGGKAGNIISPNPNTIAASEAFKVDLTSLMVQNIIP 18- 3 V+PIALA+ ++++LSK++ILLAMIGGGKAGNI+SPNPN IAA++ F + LTS+M+ IIP Sbjct: 123 VSPIALALSRRSDLSKAAILLAMIGGGKAGNIMSPNPNAIAAADTFHLPLTSVMMAGIIP 18- 2 Query: 184 AIAALVVTIILAKIVSKKNNDISYDSEEQV--GSDLPAFLPAISGPLVVICLLALRPLFG 24- 1 A+ L++T LAK + K + ++ D E V +LP+FL A+ PLV I LLALRPLF Sbjct: 183 ALFGLILTYFLAKRLINKGSKVT-DKEVIVLETQNLPSFLTALVAPLVAILLLALRPLFD 24- 1 Query: 242 ITIDPLIALPLGGLISILATGYLKETVPFVEYGLSKVVGVSILLIGTGTLSGIIKASNLQ 30- 1 I +DPLIALPLGGLI G L+ + GLSK+ V+I+L+GTG L+GII S L+ Sbjct: 242 IKVDPLIALPLGGLIGAFCMGKLRNINSYAINGLSKMTPVAIMLLGTGALAGIIANSGLK 30- 1 Query: 302 FDMIHLLEFLNMPTFILAPLSGIFMGAATASTTSGTTIASQTFAETLIKSGVPAVSGAAM 36- 1 +I LE +P++ILAP+SG+ M ATASTT+GT +AS F+ TL++ GV +++GAAM Sbjct: 302 EVLIQGLEHSGLPSYILAPISGVLMSLATASTTAGTAVASNVFSSTLLELGVSSLAGAAM 36- 1 Query: 362 IHAGATVLDSLPHGSFFHATGGAVNMAIKDRMKLISYEALIGLTSTIVAVVYYCFF 417 IHAGATV D +PHGSFFHATGG+VNM IK+R+KLI YE+ +GL TIV+ + + F Sbjct: 362 IHAGATVFDHMPHGSFFHATGGSVNMDIKERLKLIPYESAVGLMMTIVSTLIFGVF 417 A related DNA sequence was identified in S. pyogenes <SEQ ID 6675> which encodes the amino acid sequence <SEQ ID 6676>. Analysis of this protein sequence reveals the following: TABLE-US-06613 Possible site: 51 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.15 Transmembrane 240-256 (236-265) INTEGRAL Likelihood = -10.88 Transmembrane 3-19 (1-32) INTEGRAL Likelihood = -10.14 Transmembrane 269-285 (263-289) INTEGRAL Likelihood = -7.27 Transmembrane 107-123 (102-141) INTEGRAL Likelihood = -7.17 Transmembrane 307-323 (303-330) INTEGRAL Likelihood = -6.64 Transmembrane 24-40 (23-43) INTEGRAL Likelihood = -5.63 Transmembrane 422-438 (420-442) INTEGRAL Likelihood = -3.77 Transmembrane 124-140 (124-141) INTEGRAL Likelihood = -3.24 Transmembrane 189-205 (184-207) INTEGRAL Likelihood = -2.60 Transmembrane 65-81 (65-82) INTEGRAL Likelihood = -2.34 Transmembrane 393-409 (393-409) INTEGRAL Likelihood = -0.11 Transmembrane 149-165 (149-166) ----- Final Results ----- bacterial membrane --- Certainty = 0.5458(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06614 >GP: BAB07616 GB: AP001520 unknown conserved protein [Bacillus halodurans] Identities = 155/435 (35%), Positives = 248/435 (56%), Gaps = 21/435 (4%) Query: 7 LGVLVGVIVIIYLYVKEVNIIIAAPLATSLVILFNQMDPTTTLLGKEPNQFMGALSTYIL 66 LG+++G+++++ L + +II AP+A +V LF +D LL + +M + Sbjct: 2 LGIVLGLVILMVLAYRGWSIIWVAPIAAGVVALFGGLD----LLPAYTDTYMEGFVNFAK 57 Query: 67 NYFAIFLLGSILAKLMETSGATTSIADYILKKVGHDSPYKVLVAIFLISAILTYGGISLF 126- +F +F+LG+I KLME +GA S+A I K +G + ++ + L A+LTYGGISLF Sbjct: 58 QWFPVFMLGAIFGKLMEDTGAARSVASAITKLIGTK---RAILGVMLGCAVLTYGGISLF 114- Query: 127 VVMFAVLPLARSLFKKMDLAWNLIQVPLWLGIATFTMTILPGTPAIQNVIPIQYLDTSLT 18- 6 VV+FA+ PLA +LF++ +++ LI + LG TFTMT +PGTP IQN+IP Y T+ Sbjct: 115 VVVFAMYPLALALFREANISRRLIPGTIALGAFTFTMTAVPGTPQIQNLIPTSYYGTNAM 17- 4 Query: 187 AAAIPSIVGSIGCVAFGLFYMKYCLAKSMARGETYATYAFDNEIQVKTKNLPHFLASILP 24- 6 AA + ++ ++ G Y+ + K GE + T + E + + + +P+ S LP Sbjct: 175 AAPMMGVIAALIMGIGGYTYLVWREKKLKEAGE-FFTEPKNGEKEEEGEKVPNPWLSFLP 23- 3 Query: 247 LLLLIIIALTGSLFGNDFFKKNIIFIALLAVILTASWLFRQFIPNKIAVFNLGASSSIAP 30- 6 L+ +I+ T +L D I +AL++ I+ L + I N GA S+ Sbjct: 234 LVSVIV---TLNLLQWD------IVLALISGIVLIMLLNVGKVKGFIQSMNQGAGGSVLA 28- 4 Query: 307 IFATASAVAFGAVVMIVPGFTFFSDLILNIPGNPLISLAVLTSSMSAITGSSSGALGIVM 36- 6 I T++AV FG+VV VPGF ++L+L I G+PLIS AV + ++ TGS+SG +GI + Sbjct: 285 IINTSAAVGFGSVVRAVPGFERLTELLLGIQGSPLISQAVAINVLAGATGSASGGMGIAL 34- 4 Query: 367 ----PNFAQYYLDQGLNPEMIHRVATIASNIFTIVPQSGVFLTFLALTGLNHKNAFKETF 42- 2 + Q ++ G++PE HRVA+IAS +P +G LT LA+TGL+HK ++K+ F Sbjct: 345 EALGDRYMQLAMETGMSPEAFHRVASIASGGLDTLPHNGAVLTLLAITGLSHKESYKDIF 40- 4 Query: 423 ITVSVSTFIAQVIVI 437 + V ++ I Sbjct: 405 VVGCVIPIVSVAFAI 419 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06615 Identities = 88/395 (22%), Positives = 167/395 (42%), Gaps = 40/395 (10%) Query: 9 GALIGLALAILLIIKKVHPAYSLILGALVGGLIGGGDLVTIV----NTMVLGAQG--MMS 62 G L+G+ + I L +K+V+ + L + L D T + +GA +++ Sbjct: 8 GVLVGVIVIIYLYVKEVNIIIAAPLATSLVILFNQMDPTTTLLGKEPNQFMGALSTYILN 67 Query: 63 SILRILTSGILAGALIKTGSAEKIAESIIKKLGQQ---RAITALAIATMIICAVGVFIDI 119- L ILA + +G+ IA+ I+KK+G + + A+ + + I+ G+ + + Sbjct: 68 YFAIFLLGSILAKLMETSGATTSIADYILKKVGHDSPYKVLVAIFLISAILTYGGISLFV 127- Query: 120 AVITVAPIALAIGKKANLSKSSILLAMIGGGKAGNII----SPNPNTIAASEAFKVDLTS 17- 5 + V P+A ++ KK +L+ + I + + G + +P + + LT+ Sbjct: 128 VMFAVLPLARSLFKKMDLAWNLIQVPLWLGIATFTMTILPGTPAIQNVIPIQYLDTSLTA 18- 7 Query: 176 LMVQNIIPAIAALVVTII-----LAKIVSKKNNDISY--DSEEQVGS-DLPAFLPAISGP 22- 7 + +I+ +I + + LAK +++ +Y D+E QV + +LP FL +I Sbjct: 188 AAIPSIVGSIGCVAFGLFYMKYCLAKSMARGETYATYAFDNEIQVKTKNLPHFLASILPL 24- 7 Query: 228 LVVICLLALRPLFG-------ITIDPLIALPLGGLISILATGYLKETVPFVEYGLSKVVG 28- 0 L++I + LFG I L+A+ L S L ++ + G S + Sbjct: 248 LLLIIIALTGSLFGNDFFKKNIIFIALLAVIL--TASWLFRQFIPNKIAVFNLGASSSIA 30- 5 Query: 281 ---VSILLIGTGTLSGIIKASNLQFDMIHLLEFLNMPTFILAPLSGIFMGAATASTTSGT 33- 7 + + G + I+ D+I L P LA L+ M A T S++ Sbjct: 306 PIFATASAVAFGAVVMIVPGFTFFSDLI--LNIPGNPLISLAVLTS-SMSAITGSSSGAL 36- 2 Query: 338 TIASQTFAETLIKSGVPAVSGAAMIHAGATVLDSL 372 I FA+ + G+ MIH AT+ ++ Sbjct: 363 GIVMPNFAQYYLDQGL----NPEMIHRVATIASNI 393 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2160 A DNA sequence (GBSx2277) was identified in S. agalactiae <SEQ ID 6677> which encodes the amino acid sequence <SEQ ID 6678>. Analysis of this protein sequence reveals the following: TABLE-US-06616 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.24 Transmembrane 85-101 (84-101) ----- Final Results ----- bacterial membrane --- Certainty = 0.2296(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06617 >GP: CAB16041 GB: Z99124 similar to hypothetical proteins [Bacillus subtilis] Identities = 176/377 (46%), Positives = 234/377 (61%), Gaps = 2/377 (0%) Query: 1 MKVVVAIDSLKGSLSSLEAGNAIKESINEVISGADVEVHPLADGGEGTVEALTLGMGGTI 60 MK+++A DS K SLS+LEA AI+ V GAD P+ADGGEGTV++L G I Sbjct: 1 MKIIIAPDSFKESLSALEAAEAIERGFKSVFPGADYRKLPVADGGEGTVQSLVDATNGRI 60 Query: 61 ETIPVKGPLGEKVHASYGIIPQRQLAIIEMAAAAGITLIATEERNPLHTTTYGVGEMIKD 120- V GPLGE V A +G++ + A+IEMAAA+G+ L+ ++RNPL TTT G GE+I Sbjct: 61 IEQVVTGPLGEPVRAFFGMMGDGRTAVIEMAAASGLHLVPVDKRNPLITTTRGTGELIGA 120- Query: 121 AISKGCRHFIIGIGGSATNDGGAGMLQALGYALLDKDNQEISLGAQGLADLKSISTDKVI 18- 0 A+ G IIGIGGSATNDGGAGM+QALG LLD EI G L+ L SI + Sbjct: 121 ALDAGAERLIIGIGGSATNDGGAGMIQALGGRLLDNSGSEIGPGGGALSQLASIDVSGLD 18- 0 Query: 181 EELKECDFKIACDVTNPLCGAQGCSSIFGPQKGADEDMITKMDTWLSNYATLATSVSEKA 24- 0 L+ ++AC+V NPL G +G +++FGPQKGA DM+ +D +S++A +A Sbjct: 181 SRLRNVKLEVACNVDNPLTGPKGATAVFGPQKGATADMLDVLDQNVSHFADMAEKALGST 24- 0 Query: 241 DATIEGTGAAGGLGFAFLAFTNATLEPGIDIILSEINIEKAISEADLVVTGEGRLDGQTV 30- 0 EG GAAGGLG++ L + A L+ GIDI+L ++ E + +ADLV+TGEGR+D QTV Sbjct: 241 FRDTEGAGAAGGLGWSLLTYLQADLKRGIDIVLEAVDFESIVQDADLVITGEGRIDSQTV 30- 0 Query: 301 MGKAPIGVAKLAKKYGKKVVAFSGSVTEDAILCNQHGIDAFFPIVRRLISLDEAMSKEVA 36- 0 GK PIGVAK AK Y V+ +GS++ D+ QHGIDA F IV + L++A Sbjct: 301 HGKTPIGVAKAAKSYDVPVIGIAGSISRDSNAVYQHGIDALFSIVPGAVPLEDAFEHAAE 36- 0 Query: 361 YKNMKETATQVFRLINL 377 Y M+ TA + I L Sbjct: 361 Y--MERTARDIAASIKL 375 A related DNA sequence was identified in S. pyogenes <SEQ ID 6679> which encodes the amino acid sequence <SEQ ID 6680>. Analysis of this protein sequence reveals the following: TABLE-US-06618 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.27 Transmembrane 360-376 (360-376) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06619 >GP: AAA57927 GB: U18997 ORF_f408 [Escherichia coli] Identities = 115/345 (33%), Positives = 182/345 (52%), Gaps = 25/345 (7%) Query: 24 MKILVAIDSFKGSVTSPELNTSVAQALLSVDKQLVIETRAIADGGEGSLVALSQTVAGRW 83 - MKI++A DS+K S+++ E+ ++ + + + +ADGGEG++ A+ G Sbjct: 28 MKIVIAPDSYKESLSASEVAQAIEKGFREIFPDAQYVSVPVADGGEGTVEAMIAATQGAE 87 Query: 84 HQVKTIDLLRRPIKVAY--YRHAKQAFIESASIIGIDKITSNSVTYAQATSYGLGLAVKD 141- L + ++ K AFIE A+ G++ + + TS G G + Sbjct: 88 RHAWVTGPLGEKVNASWGISGDGKTAFIEMAAASGLELVPAEKRDPLVTTSRGTGELILQ 147- Query: 142 AIQKGATQIEIMLGGTGTSDGGKGFLESLNYDFMT--------GRSYLDTLASPVTLLGL 19- 3 A++ GAT I I +GG+ T+DGG G +++L G L+TL + + + GL Sbjct: 148 ALESGATNIIIGIGGSATNDGGAGMVQALGAKLCDANGNEIGFGGGSLNTL-NDIDISGL 20- 6 Query: 194 T------------DVTNPYHGPQGFAAVFGPQKGGSLSQIEETDQIASNFAKKVFCQTTI 24- 1 DVTNP G G + +FGPQKG S + I E D S++A+ + + Sbjct: 207 DPRLKDCVIRVACDVTNPLVGDNGASRIFGPQKGASEAMIVELDNNLSHYAEVIKKALHV 26- 6 Query: 242 DLQTIPGSGAAGGLGGAIV-LLGGTLTSGFSRIAELLNLDNSLQSCDLVITGEGCLDTQS 30- 0 D++ +PG+GAAGG+G A++ LG L SG + LNL+ + C LVITGEG +D+QS Sbjct: 267 DVKDVPGAGAAGGMGAALMAFLGAELKSGIEIVTTALNLEEHIHDCTLVITGEGRIDSQS 32- 6 Query: 301 QSGKVPVAIARMAKKYQVPTIALCGSVKIETGLAAEDFL-AVFSI 344 GKVP+ +A +AKKY P I + GS+ + G+ + + AVFS+ Sbjct: 327 IHGKVPIGVANVAKKYHKPVIGIAGSLTDDVGVVHQHGIDAVFSV 371 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06620 Identities = 128/379 (33%), Positives = 194/379 (50%), Gaps = 23/379 (6%) Query: 1 MKVVVAIDSLKGSLSSLEAGNAIKESINEVISGADVEVHPLADGGEGTVEALTLGMGGTI 60 MK++VAIDS KGS++S E ++ +++ V +E +ADGGEG++ AL+ + G Sbjct: 24 MKILVAIDSFKGSVTSPELNTSVAQALLSVDKQLVIETRAIADGGEGSLVALSQTVAGRW 83 Query: 61 ETIPVKGPLGEKVHASYGIIPQRQLAIIEMAAAAGITLIATEERNPLHTTTYGVGEMIKD 120- + L + +Y + A IE A+ GI I + T+YG+G +KD Sbjct: 84 HQVKTIDLLRRPIKVAY--YRHAKQAFIESASIIGIDKITSNSVTYAQATSYGLGLAVKD 141- Query: 121 AISKGCRHFIIGIGGSATNDGGAGMLQALGYALLDKDNQEISLGAQGLADLKSISTDKVI 18- 0 AI KG I +GG+ T+DGG G L++L Y + G + L ++++ + Sbjct: 142 AIQKGATQIEIMLGGTGTSDGGKGFLESLNYDFMT-----------GRSYLDTLASPVTL 19- 0 Query: 181 EELKECDFKIACDVTNPLCGAQGCSSIFGPQKGADEDMITKMDTWLSNYATLATSVSEKA 24- 0 L DVTNP G QG +++FGPQKG I + D SN+A + Sbjct: 191 LGLT--------DVTNPYHGPQGFAAVFGPQKGGSLSQIEETDQIASNFAKKVFCQTTID 24- 2 Query: 241 DATIEGTGAAGGLGFAFLAFTNATLEPGIDIILSEINIEKAISEADLVVTGEGRLDGQTV 30- 0 TI G+GAAGGLG A + TL G I +N++ ++ DLV+TGEG LD Q+ Sbjct: 243 LQTIPGSGAAGGLGGA-IVLLGGTLTSGFSRIAELLNLDNSLQSCDLVITGEGCLDTQSQ 30- 1 Query: 301 MGKAPIGVAKLAKKYGKKVVAFSGSVTEDAILCNQHGIDAFFPIVRRLISLDEAMSKEVA 36- 0 GK P+ +A++AKKY +A GSV + L + + A F I ++ ISL+ A+ K Sbjct: 302 SGKVPVAIARMAKKYQVPTIALCGSVKIETGLAAEDFL-AVFSIQQQPISLEAAIDKTTT 36- 0 Query: 361 YKNMKETATQVFRLINLYN 379 N+K A + LI +N Sbjct: 361 LSNIKILAANLMLLIAQFN 379 SEQ ID 6678 (GBS409) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 76 (lane 7; MW 45.4 kDa). GBS409-His was purified as shown in FIG. 214, lane 6. GBS409d was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 166 (lane 3 & 4; MW 35 kDa) and in FIG. 188 (lane 12; MW 35 kDa). Purified protein is shown in FIG. 240, lanes 9-10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2161 A DNA sequence (GBSx2278) was identified in S. agalactiae <SEQ ID 6681> which encodes the amino acid sequence <SEQ ID 6682>. Analysis of this protein sequence reveals the following: TABLE-US-06621 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1886(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06622 >GP: AAC21771 GB: U32695 conserved hypothetical protein [Haemophilus influenzae Rd] Identities = 97/383 (25%), Positives = 175/383 (45%), Gaps = 52/383 (13%) Query: 1 MKLRKQLAQQIVTSIKDVCQQDINFINTKGIIFASTNPKRVGEFHEIGLKVAQTGQMIEV 60 M+L K A++IV + +N ++ G+I AS N R+ + H + + +++E+ Sbjct: 1 MQLDKYTAKKIVKRAMKIIHHSVNVMDHDGVIIASGNSTRLNQRHTGAVLALRENRVVEI 60 Query: 61 TD---QESYFGTQAGINIPFYYNCELLATIGISGNPNQVGKYALLAQKMTRLILKEHE-L 116- Q+ F Q GIN+P +Y + + +GISG P QV +YA L + LI+++ L Sbjct: 61 DQALAQKWNFEAQPGINLPIHYLGKNIGVVGISGEPTQVKQYAELVKMTAELIVEQQALL 120- Query: 117 DYLDFGRKNEASIVLHHLVEGRELDYYYLNQFLNQYHLSEKTDYRLLTFEINSQKQKLLL 17- 6 + + R+ + +L L+ LN + ++ + +F++N + +L+ Sbjct: 121 EQESWHRRYKEEFILQ-----------LLHCNLNWKEMEQQA--KFFSFDLNKSRVVVLI 16- 7 Query: 177 S------QSEMSLLNFFDK-----------LDTAIYTFNYPNQYWLLLSDHMFDYYYPNI 21- 9 + +L+N+ ++ LD + + N +LS M Sbjct: 168 KLLNPALDNLQNLINYLEQSEFAQDVAILSLDQVVVLKTWQNS--TVLSAQM------KT 21- 9 Query: 220 LSKFECEKGLYKVGIGQKSSLSLLKR---SYETSILALK-ALKGQQK--VNLVDDLDLEL 27- 3 L + K YK+ +G +L L ++ S++++ L LK + + + D+ L + Sbjct: 220 LLPADYSKQDYKIAVGACLNLPLFEQLPLSFQSAQSTLSYGLKHHPRKGIYVFDEHRLPV 27- 9 Query: 274 LLTSIDSNIKQYVLNKALVNL-SENDKIL---LNSYFKHNLSLKECSQELFIHKNTVQYR 32- 9 LL + + + L K L L SE + IL L YF N L +++LF+H NT++YR Sbjct: 280 LLAGLSHSWQGNELIKPLSPLFSEENAILYKTLQQYFLSNCDLYLTAEKLFVHPNTLRYR 33- 9 Query: 330 LNKIYESTQLNPRNFKDATLLYL 352 LNKI + T L D LYL Sbjct: 340 LNKIEQITGLFFNKIDDKLTLYL 362 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2162 A DNA sequence (GBSx2279) was identified in S. agalactiae <SEQ ID 6683> which encodes the amino acid sequence <SEQ ID 6684>. Analysis of this protein sequence reveals the following: TABLE-US-06623 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0290(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06624 >GP: AAF89979 GB: AF206272 beta-glucosidase [Streptococcus mutans] Identities = 334/475 (70%), Positives = 392/475 (82%), Gaps = 8/475 (1%) Query: 4 FPKHFLWGGAVAANQVEGAFRTDGKGLSVQDVLPNGGLGD-------FTAKPTPDNLKLE 56 FP++FLWGGA AANQ EGA+ DGKGLSVQDV P GG+ T KPT DNLKL Sbjct: 6 FPENFLWGGATAANQFEGAYNQDGKGLSVQDVTPKGGVAQSGSSSPLITEKPTEDNLKLV 65 Query: 57 AIDFYHNYKNDIKLFAEMGFKVFRTSIAWSRIFPNGDDSAPNEAGLQFYDNLFDELLKYN 116- IDFY+ YK DI LFAEMGFKVFR SIAW+RIFPNGDD PNEAGL FYD +FDEL KY+ Sbjct: 66 GIDFYNRYKEDIALFAEMGFKVFRLSIAWTRIFPNGDDLEPNEAGLAFYDKVFDELAKYD 125- Query: 117 IEPLVTLSHYETPLHLAKTYNGWADRRLIAFFEKFAQTVMERYKDKVKYWLTFNEVNSIL 17- 6 IEPLVTLSHYETPLHLA+ YNGWA+R LIAF+E++A+TV RYKDKVKYWLTFNEVNS+L Sbjct: 126 IEPLVTLSHYETPLHLARKYNGWANRELIAFYERYARTVFTRYKDKVKYWLTFNEVNSVL 18- 5 Query: 177 HMPFTSGAIMTDKSQLSPQELYQAIHHELVASARVTKLGRSINPNFKIGCMILAMPAYPM 23- 6 H PF SG I+TD QLS Q+LYQA+HHELV SA TK+G INP+FKIGCM+LAMPAYPM Sbjct: 186 HAPFMSGGIITDPEQLSKQDLYQAVHHELVVSALATKVGHEINPDFKIGCMVLAMPAYPM 24- 5 Query: 237 TSDPRDVLAARQFEQHNLLFSDIHVRGKYPTYIQSYFKNNGIKIKFEEGDEEVLAQNTVD 29- 6 T+DP D LA R+FE N LFSD+H RGKYP YI+ YFK+N I IK EGD+E++ +NTVD Sbjct: 246 TADPLDQLAVREFENQNYLFSDLHARGKYPNYIKRYFKDNNIDIKMGEGDKELMLENTVD 30- 5 Query: 297 FLSFSYYMSVTQAYDFENYQSGQGNILGGLTNPHLTTSEWGWQIDPIGLRLVLNQYYERY 35- 6 F+SFSYYMSV A++ E+Y SG+GN+LGGL+NP+L SEWGWQIDP+GLRLVLN Y+RY Sbjct: 306 FISFSYYMSVAAAHNPEDYNSGRGNVLGGLSNPYLQASEWGWQIDPVGLRLVLNDSYDRY 36- 5 Query: 357 QIPLFIVENGLGAKDQLIETLDGDYTVEDDYRIDYMNQHLVQVAKAIEDGVEIMGYTSWG 41- 6 Q+PLFIVENGLGAKD L++ DG TVEDDYRIDY+ +HL+QV +A++DGV+++GYT+WG Sbjct: 366 QLPLFIVENGLGAKDVLVQGPDGP-TVEDDYRIDYLQKHLMQVGEALQDGVDLLGYTTWG 42- 4 Query: 417 CIDCVSMSTAQLSKRYGLIYVDRNDDGTGSLQRYKKKSFGWYQKVIKTNGQSLFE 471 ID VS ST +LSKRYG IYV NDDG+GSL RYKKKSF WY+KVI+TNG SL+E Sbjct: 425 PIDLVSESTVELSKRYGFIYVACNDDGSGSLARYKKKSFAWYKKVIETNGASLYE 479 A related DNA sequence was identified in S. pyogenes <SEQ ID 5287> which encodes the amino acid sequence <SEQ ID 5288>. Analysis of this protein sequence reveals the following:

TABLE-US-06625 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0763(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06626 Identities = 390/469 (83%), Positives = 423/469 (90%) Query: 1 MTVFPKHFLWGGAVAANQVEGAFRTDGKGLSVQDVLPNGGLGDFTAKPTPDNLKLEAIDF 60 M +FPK FLWGGAVAANQVEGAF D KGLSVQDVLPNGGLG++T PT DNL LEAIDF Sbjct: 1 MGIFPKDFLWGGAVAANQVEGAFEADAKGLSVQDVLPNGGLGEWTDSPTSDNLTLEAIDF 60 Query: 61 YHNYKNDIKLFAEMGFKVFRTSIAWSRIFPNGDDSAPNEAGLQFYDNLFDELLKYNIEPL 120- YH YK DI LFAEMGFKVFRTSIAWSRIFPNGDD PNEAGLQFYD+LFDELL Y IEPL Sbjct: 61 YHRYKEDIALFAEMGFKVFRTSIAWSRIFPNGDDDQPNEAGLQFYDDLFDELLNYGIEPL 120- Query: 121 VTLSHYETPLHLAKTYNGWADRRLIAFFEKFAQTVMERYKDKVKYWLTFNEVNSILHMPF 18- 0 VTLSHYETPLHLAK YNGW DRRLI FFE+FAQTVMERYKDKVKYWLTFNEVNSILHMPF Sbjct: 121 VTLSHYETPLHLAKAYNGWTDRRLIGFFERFAQTVMERYKDKVKYWLTFNEVNSILHMPF 18- 0 Query: 181 TSGAIMTDKSQLSPQELYQAIHHELVASARVTKLGRSINPNFKIGCMILAMPAYPMTSDP 24- 0 TSG IMT+K +LS Q+LYQAIHHELVASA VTKL INP+ K+GCMILAMPAYPMTSDP Sbjct: 181 TSGGIMTEKEKLSLQDLYQAIHHELVASASVTKLAHEINPDVKVGCMILAMPAYPMTSDP 24- 0 Query: 241 RDVLAARQFEQHNLLFSDIHVRGKYPTYIQSYFKNNGIKIKFEEGDEEVLAQNTVDFLSF 30- 0 RD+LAA FE NLLFSDIHVRGKYP+YI+SYFK NGI+I FE+GD+E+LA++TVDFLSF Sbjct: 241 RDILAAHAFENLNLLFSDIHVRGKYPSYIKSYFKENGIEIVFEDGDKELLAEHTVDFLSF 30- 0 Query: 301 SYYMSVTQAYDFENYQSGQGNILGGLTNPHLTTSEWGWQIDPIGLRLVLNQYYERYQIPL 36- 0 SYYMSVTQA++ E Y SGQGNILGGL+NP+L +SEWGWQIDPIGLRLVLNQYY+RYQIPL Sbjct: 301 SYYMSVTQAHNPEAYTSGQGNILGGLSNPYLESSEWGWQIDPIGLRLVLNQYYDRYQIPL 36- 0 Query: 361 FIVENGLGAKDQLIETLDGDYTVEDDYRIDYMNQHLVQVAKAIEDGVEIMGYTSWGCIDC 42- 0 FIVENGLGAKDQL++T DG TV DDYRIDYM+QHLVQVAKAIEDGVE+MGYTSWGCIDC Sbjct: 361 FIVENGLGAKDQLVQTADGSMTVHDDYRIDYMSQHLVQVAKAIEDGVEVMGYTSWGCIDC 42- 0 Query: 421 VSMSTAQLSKRYGLIYVDRNDDGTGSLQRYKKKSFGWYQKVIKTNGQSL 469 VSMSTAQLSKRYG IYVDRNDDGTG L RYKKKSF WY++VI+TNG+ L Sbjct: 421 VSMSTAQLSKRYGFIYVDRNDDGTGQLTRYKKKSFDWYRQVIQTNGRYL 469 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2163 A DNA sequence (GBSx2280) was identified in S. agalactiae <SEQ ID 6685> which encodes the amino acid sequence <SEQ ID 6686>. Analysis of this protein sequence reveals the following: TABLE-US-06627 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.40 Transmembrane 247-263 (241-273) INTEGRAL Likelihood = -8.55 Transmembrane 429-445 (424-450) INTEGRAL Likelihood = -4.88 Transmembrane 285-301 (280-303) INTEGRAL Likelihood = -3.82 Transmembrane 207-223 (205-225) INTEGRAL Likelihood = -3.40 Transmembrane 113-129 (112-139) INTEGRAL Likelihood = -1.97 Transmembrane 309-325 (305-328) INTEGRAL Likelihood = -1.59 Transmembrane 395-411 (395-411) INTEGRAL Likelihood = -1.49 Transmembrane 174-190 (173-193) ----- Final Results ----- bacterial membrane --- Certainty = 0.5161(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06628 >GP: CAA84286 GB: Z34526 beta-glucoside permease [Bacillus subtilis] Identities = 225/594 (37%), Positives = 351/594 (58%), Gaps = 11/594 (1%) Query: 4 YQETAKAILAAVGGEKNIQHVTHCVTRLRLVLDNDEIVNDQVIKTIPNVIGVMRKNDQYQ 63 Y + +K IL VGGE+N+Q V HC+TRLR L ++ + ++ +P V+G +Q+Q Sbjct: 3 YDKLSKDILQLVGGEENVQRVIHCMTRLRFNLHDNAKADRSQLEQLPGVMGTNISGEQFQ 62 Query: 64 IILGNDVNNYYNAFLALGHFENTTREFSSQKKSSILEKLIETIAGVITPLIPALLGGGML 123- II+GNDV Y A + + + SS +K ++L + + I+GV TP++PA+ G GM+ Sbjct: 63 IIIGNDVPKVYQAIVRHSNLSDEKSAGSSSQKKNVLSAVFDVISGVFTPILPAIAGAGMI 122- Query: 124 KVIGILLPMLGIASSSSQTVAFINFFGDAAYYFMPIMIAYSAASRFKVTPVLAATVGGIL 18- 3 K + L G + SQ + GD A+YF+P+++A SAA +F P +AA + + Sbjct: 123 KGLVALAVTFGWMAEKSQVHVILTAVGDGAFYFLPLLLAMSAARKFGSNPYVAAAIAAAI 18- 2 Query: 184 LHPAFVTMVAEGKPLSLFGAPVTLASYGSSVIPILIMVFLMQYIERWINKIVPSVMKSFL 24- 3 LHP ++ GKP+S G PVT A+Y S+VIPIL+ +++ Y+E+WI++ + +K + Sbjct: 183 LHPDLTALLGAGKPISFIGLPVTAATYSSTVIPILLSIWIASYVEKWIDRFTHASLKLIV 24- 2 Query: 244 QPTLIILISGFLALVVVGPLGVIIGKGLSSAMLSIYHVAPWLALSILGAIMPLVVMTGMH 30- 3 PT +LI L L+ VGPLG I+G+ LSS + ++ A +A+ +L L++MTGMH Sbjct: 243 VPTFTLLIVVPLTLITVGPLGAILGEYLSSGVNYLFDHAGLVAMILLAGTFSLIIMTGMH 30- 2 Query: 304 WAFAPIFLAASVATPDVLILPAMLASNLAQGAASLAVAVKAKQKQTRQVAFAAGLSALLA 36- 3 +AF PI + +LPAM +N+ Q AS AV ++++ K+ + +A ++AL+ Sbjct: 303 YAFVPIMINNIAQNGHDYLLPAMFLANMGQAGASFAVFLRSRNKKFKSLALTTSITALM- 36- 1 Query: 364 GITEPALYGVTLKFKKPLYAAMISGGLVGAYIGLVNIASYTFVVPSIIGLPQYINPQGGN 42- 3 GITEPA+YGV ++ KKP AA+I G GA+ G+ +ASY +V GLP I G Sbjct: 362 GITEPAMYGVNMRLKKPFAAALIGGAAGGAFYGMTGVASY--IVGGNAGLPS-IPVFIGP 41- 8 Query: 424 NFSNAVIAAIATIILTFIITWFLGIDEGENEKSSINAQEHTHIRSGLSKKETLYSPMVGN 48- 3 F A+I + + LG ++ ++ S Q H S +E ++SP+ G Sbjct: 419 TFIYAMIGLVIAFAAETAAAYLLGFEDVPSDGSQ---QPAVHEGS----REIIHSPIKGE 47- 1 Query: 484 VLPLSKVPDETFSSKLLGEGLAITPSVGEVYAPFDGEIISLFPTKHAIALKDDKGVEVLI 54- 3 V LS+V D FS+ ++G+G AI P GEV +P G + ++F TKHAI + D+G E+LI Sbjct: 472 VKALSEVKDGVFSAGVMGKGFAIEPEEGEVVSPVRGSVTTIFKTKHAIGITSDQGAEILI 53- 1 Query: 544 HIGIDTVELNGEGFEQLVKVGDFVKRGQLLLRMDIDFISSKGYSLISPVVVTNS 597 HIG+DTV+L G+ F +K GD V G L+ D++ I + GY +I+PV+VTN+ Sbjct: 532 HIGLDTVKLEGQWFTAHIKEGDKVAPGDPLVSFDLEQIKAAGYDVITPVIVTNT 585 A related DNA sequence was identified in S. pyogenes <SEQ ID 2883> which encodes the amino acid sequence <SEQ ID 2884>. Analysis of this protein sequence reveals the following: TABLE-US-06629 Possible site: 20 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.40 Transmembrane 246-262 (240-271) INTEGRAL Likelihood = -6.26 Transmembrane 284-300 (279-304) INTEGRAL Likelihood = -4.14 Transmembrane 173-189 (172-194) INTEGRAL Likelihood = -3.24 Transmembrane 112-128 (111-137) INTEGRAL Likelihood = -2.39 Transmembrane 428-444 (425-445) INTEGRAL Likelihood = -2.13 Transmembrane 383-399 (380-401) INTEGRAL Likelihood = -1.97 Transmembrane 308-324 (304-327) ----- Final Results ----- bacterial membrane --- Certainty = 0.5161(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06630 Identities = 508/619 (82%), Positives = 561/619 (90%), Gaps = 1/619 (0%) Query: 4 YQETAKAILAAVGGEKNIQHVTHCVTRLRLVLDNDEIVNDQVIKTIPNVIGVMRKNDQYQ 63 YQETAKAILAAVGG+ NIQ VTHCVTRLRLVL NDE V DQ +K I NVIGVMRKN QYQ Sbjct: 3 YQETAKAILAAVGGKTNIQRVTHCVTRLRLVLKNDEKVKDQQVKAISNVIGVMRKNGQYQ 62 Query: 64 IILGNDVNNYYNAFLALGHFENTTREFSSQKKSSILEKLIETIAGVITPLIPALLGGGML 123- IILGNDVNNYY AFL+LGHF+N + SS+ K SILE+LIETIAGVITPLIPALLGGGML Sbjct: 63 IILGNDVNNYYQAFLSLGHFDNQDEDHSSKAKGSILERLIETIAGVITPLIPALLGGGML 122- Query: 124 KVIGILLPMLGIASSSSQTVAFINFFGDAAYYFMPIMIAYSAASRFKVTPVLAATVGGIL 18- 3 KV+GILLPMLG+AS+ SQTVAFINFFGDAAYYFMP+MIAYSAA+RFKVTPVLAAT+ GIL Sbjct: 123 KVVGILLPMLGLASADSQTVAFINFFGDAAYYFMPVMIAYSAAARFKVTPVLAATIAGIL 18- 2 Query: 184 LHPAFVTMVAEGKPLSLFGAPVTLASYGSSVIPILIMVFLMQYIERWINKIVPSVMKSFL 24- 3 LHPAFV MVAEGKPL+LFGAPVT ASYGSSVIPIL+MV+LMQYIE+W+N++VPSVMKSFL Sbjct: 183 LHPAFVAMVAEGKPLTLFGAPVTPASYGSSVIPILMMVYLMQYIEKWVNRLVPSVMKSFL 24- 2 Query: 244 QPTLIILISGFLALVVVGPLGVIIGKGLSSAMLSIYHVAPWLALSILGAIMPLVVMTGMH 30- 3 QPTLIILISGFLALVVVGPLGVIIG+GLS+ ML+IYHVAPWLAL+ILGAIMPLVVMTGMH Sbjct: 243 QPTLIILISGFLALVVVGPLGVIIGQGLSNTMLAIYHVAPWLALAILGAIMPLVVMTGMH 30- 2 Query: 304 WAFAPIFLAASVATPDVLILPAMLASNLAQGAASLAVAVKAKQKQTRQVAFAAGLSALLA 36- 3 WAFAPIFLAASVATPDVLILPAMLASNLAQGAASLAVA K KQKQTRQVA AAG+SALLA Sbjct: 303 WAFAPIFLAASVATPDVLILPAMLASNLAQGAASLAVAFKTKQKQTRQVALAAGISALLA 36- 2 Query: 364 GITEPALYGVTLKFKKPLYAAMISGGLVGAYIGLVNIASYTFVVPSIIGLPQYINPQGGN 42- 3 GITEPALYGVTLKFKKPLYAAMISGGLVGA+IG VNIASYTFVVPSIIGLPQYINP GG Sbjct: 363 GITEPALYGVTLKFKKPLYAAMISGGLVGAFIGFVNIASYTFVVPSIIGLPQYINPSGGA 42- 2 Query: 424 NFSNAVIAAIATIILTFIITWFLGIDEGENEKSSINAQEHTHIRSGLSKKETLYSPMVGN 48- 3 NF+NA+IA ATI+L F +TWF+GIDE E+ K A + + ++SGLS K+TLY+PM G Sbjct: 423 NFTNALIAGTATIVLAFSLTWFMGIDE-ESPKQVSVAADMSQVKSGLSTKQTLYAPMTGE 48- 1 Query: 484 VLPLSKVPDETFSSKLLGEGLAITPSVGEVYAPFDGEIISLFPTKHAIALKDDKGVEVLI 54- 3 +L LS+VPDETFSSKLLGEG AI PS GEVYAPFDGE+I+ FPTKHA+ALK+ +GVEVLI Sbjct: 482 MLFLSEVPDETFSSKLLGEGFAILPSEGEVYAPFDGEVITFFPTKHAVALKNTRGVEVLI 54- 1 Query: 544 HIGIDTVELNGEGFEQLVKVGDFVKRGQLLLRMDIDFISSKGYSLISPVVVTNSIDQLEI 60- 3 H+GIDTVEL G+GFEQLV VGD VKRGQ LL+MDIDFI+SKGYSLISPVVVTNS +QLEI Sbjct: 542 HVGIDTVELKGQGFEQLVSVGDVVKRGQALLKMDIDFITSKGYSLISPVVVTNSAEQLEI 60- 1 Query: 604 IVKDAETMVTNEDDLLVIL 622 I++D + MVT ED LLVIL Sbjct: 602 IIQDDKKMVTKEDALLVIL 620 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2164 A DNA sequence (GBSx2281) was identified in S. agalactiae <SEQ ID 6687> which encodes the amino acid sequence <SEQ ID 6688>. Analysis of this protein sequence reveals the following: TABLE-US-06631 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1148(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Cleat) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06632 >GP: CAB15944 GB: Z99124 transcriptional antiterminator (BglG family) [Bacillus subtilis] Identities = 118/275 (42%), Positives = 183/275 (65%) Query: 1 MIIKRVLNHNAVISVTHQGLDVLLMGKGIAFKKRIGDRINSDAIEKSFVLKNSDNMNRFT 60 M I +V+N+N + V QG ++++MG+G+AF+K+ GD ++ IEK F L N D +F Sbjct: 1 MKIAKVINNNVISVVNEQGKELVVMGRGLAFQKKSGDDVDEARIEKVFTLDNKDVSEKFK 60 Query: 61 ELFITVPEEVVACSERIINLGKIKLGKNLDEILYINLTDHIHSAIERHEQGMVIQNPLRL 120- L +P E + SE II+ K++LGK L++ +Y++LTDHI+ AI+R+++G+ I+N L Sbjct: 61 TLLYDIPIECMEVSEEIIHYAKLQLGKKLNDSIYVSLTDHINFAIQRNQKGLDIKNALLW 120- Query: 121 EIQRYYPDEYSIGMKALELIKDELGICLTIDESAFIAMHFVNAGLDNPFNEAHKITEIVS 18- 0 E +R Y DE++IG +AL ++K++ G+ L DE+ FIA+H VNA L+ IT+++ Sbjct: 121 ETKRLYKDEFAIGKEALVMVKNKTGVSLPEDEAGFIALHIVNAELNEEMPNIINITKVMQ 18- 0 Query: 181 YIEQKVKIDFRTELDESSIDYYRFMTHTKLFAQRVLSGMKYEDDDADLLLVVKKKYPREY 24- 0 I VK F+ E +E S+ YYRF+TH K FAQR+ +G E D LL VK+KY R Y Sbjct: 181 EILSIVKYHFKIEFNEESLHYYRFVTHLKFFAQRLFNGTHMESQDDFLLDTVKEKYHRAY 24- 0 Query: 241 KCVKEIGNNMAIQYQYQLNSSELLYLTVHVKRLVK 275 +C K+I + +Y+++L S ELLYLT+H++R+VK Sbjct: 241 ECTKKIQTYIEREYEHKLTSDELLYLTIHIERVVK 275 A related DNA sequence was identified in S. pyogenes <SEQ ID 6689> which encodes the amino acid sequence <SEQ ID 6690>. Analysis of this protein sequence reveals the following: TABLE-US-06633 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0680(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06634 Identities = 220/279 (78%), Positives = 246/279 (87%) Query: 1 MIIKRVLNHNAVISVTHQGLDVLLMGKGIAFKKRIGDRINSDAIEKSFVLKNSDNMNRFT 60 M+IKRVLNHNA IS HQGLD+LLMGKGI F K++GD I +AIE SFVLKNSDNMNRFT Sbjct: 1 MLIKRVLNHNAAISTNHQGLDILLMGKGITFGKKVGDSIELNAIETSFVLKNSDNMNRFT 60 Query: 61 ELFITVPEEVVACSERIINLGKIKLGKNLDEILYINLTDHIHSAIERHEQGMVIQNPLRL 120- ELFITVP+EVVACSERIINLGKIKLGK LDEILYINLTDHIHSAIERHEQGM+I NPLR Sbjct: 61 ELFITVPQEVVACSERIINLGKIKLGKTLDEILYINLTDHIHSAIERHEQGMLIHNPLRW 120- Query: 121 EIQRYYPDEYSIGMKALELIKDELGICLTIDESAFIAMHFVNAGLDNPFNEAHKITEIVS 18- 0 EIQRYYPDEYS+G+KALELI+ LG+ L IDE+AFIAMHFVNA LD PF E H++TEIVS Sbjct: 121 EIQRYYPDEYSLGVKALELIERNLGVTLAIDEAAFIAMHFVNASLDTPFKEPHRLTEIVS 18- 0 Query: 181 YIEQKVKIDFRTELDESSIDYYRFMTHTKLFAQRVLSGMKYEDDDADLLLVVKKKYPREY 24- 0 YIEQK+K DF+TELD++SIDYYRFMTH KLFAQRVLS M Y+DDDA+LLLVVK KYP+EY Sbjct: 181 YIEQKIKTDFKTELDDTSIDYYRFMTHIKLFAQRVLSQMSYDDDDAELLLVVKTKYPKEY 24- 0 Query: 241 KCVKEIGNNMAIQYQYQLNSSELLYLTVHVKRLVKNLKE 279 +CV +I + +Y Y LNSSELLYLTVHVKRLVK+LKE Sbjct: 241 RCVLDISEEIKKRYNYHLNSSELLYLTVHVKRLVKHLKE 279 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2165 A DNA sequence (GBSx2282) was identified in S. agalactiae <SEQ ID 6691> which encodes the amino acid sequence <SEQ ID 6692>. Analysis of this protein sequence reveals the following: TABLE-US-06635 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1104(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9335> which encodes amino acid sequence <SEQ ID 9336> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 6693> which encodes the amino acid sequence <SEQ ID 6694>. Analysis of this protein sequence reveals the following: TABLE-US-06636 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3314(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06637 Identities = 143/178 (80%), Positives = 161/178 (90%) Query: 1 MTLHHDKHHATYVANANAALEKHPEIGEDLEALLADVSQIPEDIRQAVINNGGGHLNHAL 60 MTLHHDKHHATYVAN NAALEKHPEIGE+LE LLADV++IPEDIRQ +INNGGGHLNHAL Sbjct: 24 MTLHHDKHHATYVANTNAALEKHPEIGENLEELLADVTKIPEDIRQTLINNGGGHLNHAL 83 Query: 61 FWELMSPEETQISQELSEDINATFGSFEDFKAAFTAAATGRFGSGWAWLVVNAEGKLEVL 120- FWEL+SPE+ ++ ++++ I+ FGSF+ FK FTAAATGRFGSGWAWLVVN EG+LE+ Sbjct: 84 FWELLSPEKQDVTPDVAQAIDDAFGSFDAFKEQFTAAATGRFGSGWAWLVVNKEGQLEIT 143- Query: 121 STANQDTPIMEGKKPILGLDVWEHAYYLNYRNVRPNYIKAFFEIINWNKVNELYQAAK 178 STANQDTPI EGKKPIL LDVWEHAYYLNYRNVRPNYIKAFFEI+NW KV+ELYQAAK Sbjct: 144 STANQDTPISEGKKPILALDVWEHAYYLNYRNVRPNYIKAFFEIVNWKKVSELYQAAK 201 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2166 A DNA sequence (GBSx2283) was identified in S. agalactiae <SEQ ID 6695> which encodes the amino acid sequence <SEQ ID 6696>. Analysis of this protein sequence reveals the following: TABLE-US-06638 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3331(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2167 A DNA sequence (GBSx2284) was identified in S. agalactiae <SEQ ID 6697> which encodes the amino acid sequence <SEQ ID 6698>. This protein is predicted to be DNA polymerase III delta subunit. Analysis of this protein sequence reveals the following: TABLE-US-06639 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0511(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9743> which encodes amino acid sequence <SEQ ID 9744> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 6699> which encodes the amino acid sequence <SEQ ID 6700>. Analysis of this protein sequence reveals the following: TABLE-US-06640 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.22 Transmembrane 250-266 (249-266) ----- Final Results ----- bacterial membrane --- Certainty = 0.1489(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-06641 Identities = 222/340 (65%), Positives = 282/340 (82%) Query: 1 MIAIEEIGRITPDNLGLVTVLAGEDLGQYAQMKEKLFQVIGFNKDDLAYSYFDLSEEDYQ 60 MIAIE+I +++ +NLGL+T++ G+D+GQY+Q+K +L + I F+KDDLAYSYFD+SE YQ Sbjct: 1 MIAIEKIEKLSKENLGLITLVTGDDIGQYSQLKSRLMEQIAFDKDDLAYSYFDMSEAAYQ 60 Query: 61 NAELDLESLPFLSDYKVVIFDQFQDITTDKKTYLDEQAMKRFEAYLQNPVDTTRLVICAP 120- +AE+DL SLPF ++ KVVIFD DITT+KK++L E+ +K FEAYL+NP++TTRL+I AP Sbjct: 61 DAEMDLVSLPFFAEQKVVIFDHLLDITTNKKSFLKEKDLKAFEAYLENPLETTRLIIFAP 120- Query: 121 GKLDGKRRLVKLLKRDARVLEANTLKESDLKTYFQKYAHQEGLVFEAGVFDELLIKSNYD 18- 0 GKLD KRRLVKLLKRDA VLEAN LKE++L+TYFQKY+HQ GL FE+G FD+LL+KSN D Sbjct: 121 GKLDSKRRLVKLLKRDALVLEANPLKSAELRTYFQKYSHQLGLGFESGAFDQLLLKSNDD 18- 0 Query: 181 FSDTLTNIAFLKSYKTDGHISSNDVREAIPKSLQDNIFDLTQDVLLGRIDLARDLVRDLR 24- 0 FS + N+AFLK+YK G+IS D+ +AIPKSLQDNIFDLT+ VL G+ID ARDL+ DLR Sbjct: 181 FSQIMKNMAFLKAYKKTGNISLTDIEQAIPKSLQDNIFDLTRLVLGGKIDAARDLIHDLR 24- 0 Query: 241 LQGEDEIKLIAIMLGQFRMFLQVKILASKGKSESQIVSELSHYIGRKINPYQVKFAVRDS 30- 0 L GED+IKLIAIMLGQFR+FLQ+ ILA K+E Q+V LS +GR++NPYQVK+A++DS Sbjct: 241 LSGEDDIKLIAIMLGQFRLFLQLTILARDVKNEQQLVISLSDILGRRVNPYQVKYALKDS 30- 0 Query: 301 RNLPLAFLKEAIRILIETDYAIKRGTYDKDYLFDLALLKI 340 R L LAFL A++ LIETDY IK G Y+K YL D+ALLKI Sbjct: 301 RTLSLAFLTGAVKTLIETDYQIKTGLYEKSYLVDIALLKI 340 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2168 A DNA sequence (GBSx2285) was identified in S. agalactiae <SEQ ID 6701> which encodes the amino acid sequence <SEQ ID 6702>. Analysis of this protein sequence reveals the following: TABLE-US-06642 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3071(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) <succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2169 A DNA sequence (GBSx2286) was identified in S. agalactiae <SEQ ID 6703> which encodes the amino acid sequence <SEQ ID 6704>. This protein is predicted to be esterase. Analysis of this protein sequence reveals the following: TABLE-US-06643 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -0.32 Transmembrane 175-191(175-191) ----- Final Results ----- bacterial membrane --- Certainty = 0.1128(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06644 >GP: AAB17013 GB: L38252 esterase [Acinetobacter lwoffii] Identities = 63/218 (28%), Positives = 107/218 (48%), Gaps = 3/218 (1%) Query: 105 KVIFYVHGGSYIHQASELQYIFVNKLAKKLDAKVVFPIYPKAPTYNYSDAIPKIKKLYQN 16- 4 ++IF++HGG++ + + LA + +V+ YP AP + Y +AI I +YQ Sbjct: 73 QLIFHIHGGAFFLGSLNTHRALMTDLAARTQMQVIHVDYPLAPEHPYPEAIDAIFDVYQA 132- Query: 165 TLASVTSPKQIILVGESAGGGLALGLADNLVTEHIKQPKEIILISPWLDIATNNPKIEKV 22- 4 L PK II+ G+S G LAL L L + P +IL+SP+LD+ + + Sbjct: 133 LLVQGIKPKDIIISGDSCGANLALALCLRLKQQPELMPSGLILMSPYLDLTLTSESLRFN 19- 2 Query: 225 QKKDPLLKAWQLQQVAPYWANGKKNFKNPQVSPLYSSQFNKMAPISFFIGTHDIFYPDNQ 28- 4 QK D LL LQ ++ +P+VSPL+ + + P +G+ +I D++ Sbjct: 193 QKHDALLSIEALQAGIKHYLTDDIQPGDPRVSPLF-DDLDGLPPTLVQVGSKEILLDDSK 25- 1 Query: 285 LLHQKLAKENIKHHYIVGQKMNHVYPVLP--IPEAETA 320 +K + ++K H+ + M H + + PEA+ A Sbjct: 252 RFREKAEQADVKVHFKLYTGMWHNFQMFNAWFPEAKQA 289 There is also homology to SEQ ID 3498. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2170 A DNA sequence (GBSx2287) was identified in S. agalactiae <SEQ ID 6705> which encodes the amino acid sequence <SEQ ID 6706>. This protein is predicted to be purine nucleotide synthesis repressor. Analysis of this protein sequence reveals the following: TABLE-US-06645 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2970(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06646 >GP: CAB16124 GB: Z99124 similar to transcriptional regulator (LacI family) [Bacillus subtilis] Identities = 111/300 (37%), Positives = 175/300 (58%), Gaps = 4/300 (1%) Query: 1 MTSISDIAKKAGVAKSTVSRVINHHPHVSDETRQKVMALITELDYIPNQLARDLSRGKTQ 60 M +I +IA+ A V+ STVSRV+NHHP+VS+E R+ V ++ ELDY PN+ A DL RGKT Sbjct: 1 MANIKEIARLANVSVSTVSRVLNHHPYVSEEKRKLVHQVMKELDYTPNRTAIDLIRGKTH 60 Query: 61 KIGVVIPHTRHPYFTQLINGLLDAAKTTDYQLVMMPSDYNQELELSYLKQLKMEAIDALI 120- +GV++P++ HP F +++NG+ AA +Y ++P++YN ++E+ YL+ L+ + ID LI Sbjct: 61 TVGVILPYSDHPCFDKIVNGITKAAFQHEYATTLLPTNYNPDIEIKYLELLRTKKIDGLI 120- Query: 121 FTSRAISLDIIETYAKYGRIVVCEKLQEYNHLSSAYLDRYSSFLEAFSDMKLRGLEHLVL 18- 0 TSRA D I Y +YG ++ CE + + + A+ DR +++ E+F +K RG E++ Sbjct: 121 ITSRANHWDSILAYQEYGPVIACEDTGDID-VPCAFNDRKTAYAESFRYLKSRGHENIAF 17- 9 Query: 181 LFSRNNESSATYQSALLAYQEVYGQLSSPYMVVGNVHDFNDG-LNLSYQLVKEVSIDGIL 23- 9 R + S + AY+ V G+L +M+ G +D NDG L + + I Sbjct: 180 TCVREADRSPSTADKAAAYKAVCGRLEDRHMLSG-CNDMNDGELAAEHFYMSGRVPTAIY 23- 8 Query: 240 ATSDEVAAGLIKGYEESRKKCPYIIGQECLLVGQLLKLPTIDHKSYYLGKLAFKQALAEK 29- 9 A SDEVAAG I + + IIG+ + ++L P++D LG AF L ++ Sbjct: 239 ANSDEVAAG-IHLFAKKNNWDVEIIGEGNTSISRVLGFPSLDLNLEQLGIAAFSLFLQDE 29- 7 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2171 A DNA sequence (GBSx2288) was identified in S. agalactiae <SEQ ID 6707> which encodes the amino acid sequence <SEQ ID 6708>. Analysis of this protein sequence reveals the following: TABLE-US-06647 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3451(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06648 >GP: AAC21682 GB: U32686 conserved hypothetical protein [Haemophilus influenzae Rd ] Identities = 79/264 (29%), Positives = 134/264 (49%), Gaps = 16/264 (6%) Query: 1 MTIKRIFCDMDGTLLNSEGQVSKSNATLIREAA---IPVTLVSARAPMEMKDAVDALQLG 57 M K +F D +GTLL S+ +S +I+ IP +SAR+P+ + L+ Sbjct: 1 MMYKAVFSDFNGTLLTSQHTISPRTVVVIKRLTANGIPFVPISARSPLGILPYWKQLETN 60 Query: 58 GVQVAFNGGLIYRIGDNNQVLPIHTQIIKKSTVKQLLRGIRFHFPQVSLSYYDLNNWYCD 117- V VAF+G LI N + PI++ I+ + ++ + H P + ++YY N+ + Sbjct: 61 NVLVAFSGALIL----NQNLEPIYSVQIEPKDILEINTVLAEH-PLLGVNYYTNNDCHAR 115- Query: 118 KID-EGIRYEHSLTQQCPTFIHNEDQFLEGHTNTFKIMMITFDEANMLELEKYLQSLELP 17- 6 ++ + + YE S+T+ IH D+ T + + I + ++E+E L+ + P Sbjct: 116 DVENKWVIYERSVTK---IEIHPFDEVA---TRSPHKIQIIGEAEEIIEIEVLLKE-KFP 16- 8 Query: 177 EITIQRSGKAYLEITHLLAKKSKGIAYILQKEQLAREETAAFGDGHNDLPMLEMVGYPIV 23- 6 ++I RS +LE+ H A K + ++ + E AFGD NDL MLE VG + Sbjct: 169 HLSICRSHANFLEVMHKSATKGSAVRFLEDYFGVQTNEVIAFGDNFNDLDMLEHVGLGVA 22- 8 Query: 237 MDNAFDDIKAIAYQLTKSNDEDGV 260 M NA ++IK A +T +N+EDG+ Sbjct: 229 MGNAPNEIKQAANVVTATNNEDGL 252 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2172 A DNA sequence (GBSx2289) was identified in S. agalactiae <SEQ ID 6709> which encodes the amino acid sequence <SEQ ID 6710>. Analysis of this protein sequence reveals the following: TABLE-US-06649 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2854 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2173 A DNA sequence (GBSx2290) was identified in S. agalactiae <SEQ ID 6711> which encodes the amino acid sequence <SEQ ID 6712>. Analysis of this protein sequence reveals the following: TABLE-US-06650 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.51 Transmembrane 392-408 (376-417) INTEGRAL Likelihood = -9.92 Transmembrane 440-456 (433-461) INTEGRAL Likelihood = -6.42 Transmembrane 52-68 (51-70) INTEGRAL Likelihood = -6.32 Transmembrane 29-45 (9-48) INTEGRAL Likelihood = -6.32 Transmembrane 309-325 (308-328) INTEGRAL Likelihood = -4.46 Transmembrane 12-28 (9-29) INTEGRAL Likelihood = -3.29 Transmembrane 463-479 (462-479) INTEGRAL Likelihood = -2.07 Transmembrane 353-369 (352-369) INTEGRAL Likelihood = -1.17 Transmembrane 374-390 (374-390) INTEGRAL Likelihood = -0.85 Transmembrane 247-263 (247-263) INTEGRAL Likelihood = -0.06 Transmembrane 278-294 (278-294) ----- Final Results ----- bacterial membrane --- Certainty = 0.5203(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06651 >GP: AAC23742 GB: AF052208 competence protein [Streptococcus pneumoniae] Identities = 325/705 (46%), Positives = 478/705 (67%), Gaps = 3/705 (0%) Query: 1 MLQLTKYFPLKPIYLALLVFQIYLLVFSWTMLGCAFLLFSFIFLIYQYDRETIFKTIAIV 60 MLQ K F + IYL+ L+ +Y +FS + L +F + L Q+ ++ K + I Sbjct: 1 MLQWIKNFSIPLIYLSFLLLWLYYAIFSASYLALLGFVFLLVCLFIQFPWKSAGKVLIIC 60 Query: 61 IFFLFYFLWQNHNMNVQYQRVPNHISQIKVRIDTISINGDVLSFQADASGNTYQAFYTLK 120- F F+F++QN + Q + + + ++++ DT+ +NGD LSF+ A G +Q +Y L+ Sbjct: 61 GIFGFWFVFQNWQQSQASQNLADSVERVRILPDTVKVNGDSLSFRGKADGRIFQVYYKLQ 120- Query: 121 NKSEKDYFQNLDNNIMIIADIKLEEAEERRHFNGFDYRQYLKRHGIYRIAKVTKIKQIRL 18- 0 ++ EK+ FQ L + I + KL E E +R+F GF+Y+ YLK GIY+ + KI+ ++ Sbjct: 121 SEEEKEAFQALTDLHEIGLEGKLSEPEGQRNFGGFNYQAYLKTQGIYQTLNIKKIQSLQK 18- 0 Query: 181 FQHRSFFALMSKWRRSAIVISQT-FPNPMRHYMSGLLFGYLDKTFDDMSDLYSSLGIIHL 23- 9 +S RR A+V +T FP+PMR+YM+GLL G+LD F++M++LYSSLGIIHL Sbjct: 181 IGSWDIGENLSSLRRKAVVWIKTHFPDPMRNYMTGLLLGHLDTDFEEMNELYSSLGIIHL 24- 0 Query: 240 FALSGMQVGFFLGIFRYICLRIGLRLDHVWLLQIPFSLIYAGLTGFSISVVRALIQSLLS 29- 9 FALSGMQVGFF+ F+ + LR+GL + + L PFSLIYAGLTGFS SV+R+L+Q LL+ Sbjct: 241 FALSGMQVGFFMNGFKKLLLRLGLTQEKLKWLTYPFSLIYAGLTGFSASVIRSLLQKLLA 30- 0 Query: 300 HSGVKKDENFALCLLICLISLPHSLLTTGGVLSFAYAFILTMTSFDHFSSIKKVAIESLT 35- 9 GVK +N AL +L+ I +P+ T GGVLS AYAFILTM S + +K VA ESL Sbjct: 301 QHGVKGLDNCALTVLVLFIVMPNFFFTAGGVLSCAYAFILTMPSKEG-EGLKAVASESLV 35- 9 Query: 360 VSVGILPILTYYFSGFQPISIILTALLSFAFDIIFLPLLTVIFVLSPIVKLSCINSLFEI 41- 9 +S+GILPIL++YF+ FQP SI+LT + SF FD+ FLPLL+++FVLS + + +N +FE Sbjct: 360 ISLGILPILSFYFAEFQPWSILLTFVFSFLFDLTFLPLLSILFVLSFLYPVIQLNFIFEW 41- 9 Query: 420 LEVLLKWTGQLFPRPLIFGKPSLFLLIVMIIILGLLYDYYHSKCFRYCSLLIIFTLFFIT 47- 9 LE +++ Q+ RPL+FG+P+ +LLI+++I L L+YD + L+I LF +T Sbjct: 420 LEGIIRLVSQVTSRPLVFGQPNTWLLILLLISLALVYDLRKNIKKLTVLCLLITGLFLLT 47- 9 Query: 480 KNPITNEVAILDVGQGDSILVRDWLGKTILIDTGGRVR-FEQPEEWKQKVNQSNAKRTLI 53- 8 K+P+ NE+ +LDVGQG+SI +RD GKTILID GG+ +++ ++W++K+ SNA+R+LI Sbjct: 480 KHPLENEITMLDVGQGESIFLRDVTGKTILIDVGGKAESYKKIKKWQEKMTTSNAQRSLI 53- 9 Query: 539 PYLKSRGISKIDDLVITHTDTDHMGDMEVISKHFKVARLITSSGSLTNSQYVKHLSKIGV 59- 8 PYLKSRG++KID L++T+TD +H+GD+ ++K F V ++ S SL ++V L Sbjct: 540 PYLKSRGVAKIDQLILTNTDKEHVGDLSEMTKAFHVGEILVSKDSLKQKEFVAELQATQT 59- 9 Query: 599 AVKSIEAGDKLAVMGSYLQVLYPWHKGDGKNNDSIVLYGHLLGKGFLFTGDLEEEGEKQL 65- 8 V+S+ G+ L + GS L+VL P GDG ++D++VLYG L K FLFTG+LEE+GEK L Sbjct: 600 KVRSMIVGENLPIFGSQLEVLSPRKMGDGGHDDTLVLYGKFLDKQFLFTGNLEEKGEKDL 65- 9 Query: 659 LEAYPNLSVDILKAGHHGSKGSSSLSFLKKLSPSVVLVSAGKNNR 703 L+ YP+L V++LKA HG+K SSS +FL+KL P + L+S GK+NR Sbjct: 660 LKHYPDLKVNVLKASQHGNKKSSSPAFLEKLKPELTLISVGKSNR 704 A related DNA sequence was identified in S. pyogenes <SEQ ID 6713> which encodes the amino acid sequence <SEQ ID 6714>. Analysis of this protein sequence reveals the following: TABLE-US-06652 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.19 Transmembrane 394-410 (380-422) INTEGRAL Likelihood = -8.28 Transmembrane 54-70 (52-72) INTEGRAL Likelihood = -6.32 Transmembrane 356-372 (355-377) INTEGRAL Likelihood = -4.73 Transmembrane 8-24 (7-25) INTEGRAL Likelihood = -4.30 Transmembrane 30-46 (29-50) INTEGRAL Likelihood = -3.88 Transmembrane 249-265 (249-267) INTEGRAL Likelihood = -3.40 Transmembrane 467-483 (465-484) INTEGRAL Likelihood = -2.39 Transmembrane 325-341 (325-347) INTEGRAL Likelihood = -0.43 Transmembrane 441-457 (441-458) ----- Final Results ----- bacterial membrane --- Certainty = 0.5076(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06653 >GP: AAC23742 GB: AF052208 competence protein [Streptococcus pneumoniae] Identities = 311/706 (44%), Positives = 458/706 (64%), Gaps = 10/706 (1%) Query: 5 WTKLVPLSKIQFAFLILVFFYQIHSPSWLTFL-LSLSLICLLVKRLSKK--EFLGVFAIL 61 W K + I +FL+L +Y I S S+L L L+CL ++ K + L + I Sbjct: 4 WIKNFSIPLIYLSFLLLWLYYAIFSASYLALLGFVFLLVCLFIQFPWKSAGKVLIICGIF 63 Query: 62 SFCALFLLYQKQQLVQKLEIQPVQITSVALVPDSIRINGDQLAVLGRHGKHSYQLFYRLK 121- F +F +Q+ Q Q L + V ++PD++++NGD L+ G+ +Q++Y+L+ Sbjct: 64 GFWFVFQNWQQSQASQNLADS---VERVRILPDTVKVNGDSLSFRGKADGRIFQVYYKLQ 120- Query: 122 SQAEAQLFKKEHRWLVMHAKVTLEKAEEVRNFKGFNYQTFLTYQGIYRIGKVEQIEQLEV 18- 1 S+ E + F+ + + L + E RNF GFNYQ +L QGIY+ +++I+ L+ Sbjct: 121 SEEEKEAFQALTDLHEIGLEGKLSEPEGQRNFGGFNYQAYLKTQGIYQTLNIKKIQSLQK 18- 0 Query: 182 ISPESICDYLSSLRRRAIVHCQQHFPRPMSHYLTGLLFGYLDKSFGEMTDYYSQLGIIHL 24- 1 I I + LSSLRR+A+V + HFP PM +Y+TGLL G+LD F EM + YS LGIIHL Sbjct: 181 IGSWDIGENLSSLRRKAVVWIKTHFPDPMRNYMTGLLLGHLDTDFEEMNELYSSLGIIHL 24- 0 Query: 242 FALSGMQVGFFLTCFRRVLLLLAVPLEWIKWIELPFACFYAALTGYSISVIRSLVQSQLR 30- 1 FALSGMQVGFF+ F+++LL L + E +KW+ PF+ YA LTG+S SVIRSL+Q L Sbjct: 241 FALSGMQVGFFMNGFKKLLLRLGLTQEKLKWLTYPFSLIYAGLTGFSASVIRSLLQKLLA 30- 0 Query: 302 HLGIKGLDNLACTFLLVFLWDAHFLMTVGGVLTFSYAFLLTVVTVEELSGAKRQLVQVLT 36- 1 G+KGLDN A T L++F+ +F T GGVL+ +YAF+LT+ + +E G K + L Sbjct: 301 QHGVKGLDNCALTVLVLFIVMPNFFFTAGGVLSCAYAFILTMPS-KEGEGLKAVASESLV 35- 9 Query: 362 ISLGILPFLLFYFSSFNPMSMVLTGLLSYLFDLFILPLLCLVFCLSPLVTVSICNHLFIL 42- 1 ISLGILP L FYF+ F P S++LT + S+LFDL LPLL ++F LS L V N +F Sbjct: 360 ISLGILPILSFYFAEFQPWSILLTFVFSFLFDLTFLPLLSILFVLSFLYPVIQLNFIFEW 41- 9 Query: 422 LEKVIQFLGNTFNSSLVFGSPTSWHLLILVISFAIFYDYRQ-VRQRVITCGLVIALTLLS 48- 0 LE +I+ + + LVFG P +W L++L+IS A+ YD R+ +++ + C L+ L LL+ Sbjct: 420 LEGIIRLVSQVTSRPLVFGQPNTWLLILLLISLALVYDLRKNIKKLTVLCLLITGLFLLT 47- 9 Query: 481 VKYPLTNEVTFIDIGQGDSILVREWTGKNLLIDVGGR-PFFSSKEHWRRGHHVANAQKTL 53- 9 K+PL NE+T +D+GQG+SI +R+ TGK +LIDVGG+ + + W+ +NAQ++L Sbjct: 480 -KHPLENEITMLDVGQGESIFLRDVTGKTILIDVGGKAESYKKIKKWQEKMTTSNAQRSL 53- 8 Query: 540 IPYLKSRGIHTIDQLLVTHADTDHMGDIEVVAKAIRIKEILTSQGSLSHPSFVRRLRRLK 59- 9 IPYLKSRG+ IDQL++T+ D +H+GD+ + KA + EIL S+ SL FV L+ + Sbjct: 539 IPYLKSRGVAKIDQLILTNTDKEHVGDLSEMTKAFHVGEILVSKDSLKQKEFVAELQATQ 59- 8 Query: 600 CHVRVLAAGDQLPIMGSVLQVLYPWQLGDGKNNDSLVLYGRLLNRTFLFTGDLEKEGENE 65- 9 VR + G+ LPI GS L+VL P ++GDG ++D+LVLYG+ L++ FLFTG+LE++GE + Sbjct: 599 TKVRSMIVGENLPIFGSQLEVLSPRKMGDGGHDDTLVLYGKFLDKQFLFTGNLEEKGEKD 65- 8 Query: 660 IIKRYPQLRVDYLKAGHHGSNTSSSAAFLDHIQPKVAFISAGKNNR 705 ++K YP L+V+ LKA HG+ SSS AFL+ ++P++ IS GK+NR Sbjct: 659 LLKHYPDLKVNVLKASQHGNKKSSSPAFLEKLKPELTLISVGKSNR 704 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06654 Identities = 346/743 (46%), Positives = 491/743 (65%), Gaps = 3/743 (0%) Query: 5 TKYFPLKPIYLALLVFQIYLLVFSWTMLGCAFLLFSFIFLIYQYDRETIFKTIAIVIFFL 64 TK PL I A L+ + + S + L L L+ + ++ AI+ F Sbjct: 6 TKLVPLSKIQFAFLILVFFYQIHSPSWLTFLLSLSLICLLVKRLSKKEFLGVFAILSFCA 65 Query: 65 FYFLWQNHNMNVQYQRVPNHISQIKVRIDTISINGDVLSFQADASGNTYQAFYTLKNKSE 124- + L+Q + + + P I+ + + D+I INGD L+ ++YQ FY LK+++E Sbjct: 66 LFLLYQKQQLVQKLEIQPVQITSVALVPDSIRINGDQLAVLGRHGKHSYQLFYRLKSQAE 125- Query: 125 KDYFQNLDNNIMIIADIKLEEAEERRHFNGFDYRQYLKRHGIYRIAKVTKIKQIRLFQHR 18- 4 F+ +++ A + LE+AEE R+F GF+Y+ +L GIYRI KV +I+Q+ + Sbjct: 126 AQLFKKEHRWLVMHAKVTLEKAEEVRNFKGFNYQTFLTYQGIYRIGKVEQIEQLEVISPE 18- 5 Query: 185 SFFALMSKWRRSAIV-ISQTFPNPMRHYMSGLLFGYLDKTFDDMSDLYSSLGIIHLFALS 24- 3 S +S RR AIV Q FP PM HY++GLLFGYLDK+F +M+D YS LGIIHLFALS Sbjct: 186 SICDYLSSLRRRAIVHCQQHFPRPMSHYLTGLLFGYLDKSFGEMTDYYSQLGIIHLFALS 24- 5 Query: 244 GMQVGFFLGIFRYICLRIGLRLDHVWLLQIPFSLIYAGLTGFSISVVRALIQSLLSHSGV 30- 3 GMQVGFFL FR + L + + L+ + +++PF+ YA LTG+SISV+R+L+QS L H G+ Sbjct: 246 GMQVGFFLTCFRRVLLLLAVPLEWIKWIELPFACFYAALTGYSISVIRSLVQSQLRHLGI 30- 5 Query: 304 KKDENFALCLLICLISLPHSLLTTGGVLSFAYAFILTMTSFDHFSSIKKVAIESLTVSVG 36- 3 K +N A L+ + H L+T GGVL+F+YAF+LT+ + + S K+ ++ LT+S+G Sbjct: 306 KGLDNLACTFLLVFLWDAHFLMTVGGVLTFSYAFLLTVVTVEELSGAKRQLVQVLTISLG 36- 5 Query: 364 ILPILTYYFSGFQPISIILTALLSFAFDIIFLPLLTVIFVLSPIVKLSCINSLFEILEVL 42- 3 ILP L +YFS F P+S++LT LLS+ FD+ LPLL ++F LSP+V +S N LF +LE + Sbjct: 366 ILPFLLFYFSSFNPMSMVLTGLLSYLFDLFILPLLCLVFCLSPLVTVSICNHLFILLEKV 42- 5 Query: 424 LKWTGQLFPRPLIFGKPSLFLLIVMIIILGLLYDYYHSKC-FRYCSLLIIFTLFFITKNP 48- 2 +++ G F L+FG P+ + L++++I + YDY + C L+I TL + K P Sbjct: 426 IQFLGNTFNSSLVFGSPTSWHLLILVISFAIFYDYRQVRQRVITCGLVIALTLLSV-KYP 48- 4 Query: 483 ITNEVAILDVGQGDSILVRDWLGKTILIDTGGRVRFEQPEEWKQKVNQSNAKRTLIPYLK 54- 2 +TNEV +D+GQGDSILVR+W GK +LID GGR F E W++ + +NA++TLIPYLK Sbjct: 485 LTNEVTFIDIGQGDSILVREWTGKNLLIDVGGRPFFSSKEHWRRGHHVANAQKTLIPYLK 54- 4 Query: 543 SRGISKIDDLVITHTDTDHMGDMEVISKHFKVARLITSSGSLTNSQYVKHLSKIGVAVKS 60- 2 SRGI ID L++TH DTDHMGD+EV++K ++ ++TS GSL++ +V+ L ++ V+ Sbjct: 545 SRGIHTIDQLLVTHADTDHMGDIEVVAKAIRIKEILTSQGSLSHPSFVRRLRRLKCHVRV 60- 4 Query: 603 IEAGDKLAVMGSYLQVLYPWHKGDGKNNDSIVLYGHLLGKGFLFTGDLEEEGEKQLLEAY 66- 2 + AGD+L +MGS LQVLYPW GDGKNNDS+VLYG LL + FLFTGDLE+EGE ++++ Y Sbjct: 605 LAAGDQLPIMGSVLQVLYPWQLGDGKNNDSLVLYGRLLNRTFLFTGDLEKEGENEIIKRY 66- 4 Query: 663 PNLSVDILKAGHHGSKGSSSLSFLKKLSPSVVLVSAGKNNRYQHPHQETLQRFQKIKSKI 72- 2 P L VD LKAGHHGS SSS +FL + P V +SAGKNNRYQHPH+ETL R + + Sbjct: 665 PQLRVDYLKAGHHGSNTSSSAAFLDHIQPKVAFISAGKNNRYQHPHRETLARLEDRQITY 72- 4 Query: 723 FRTDQSGTIRLTGWWKWHIQTVR 745 +RTD G IRLTG WH++TVR Sbjct: 725 YRTDTQGAIRLTGRTSWHLETVR 747 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2174 A DNA sequence (GBSx2291) was identified in S. agalactiae <SEQ ID 6715> which encodes the amino acid sequence <SEQ ID 6716>. This protein is predicted to be competence protein (comEA). Analysis of this protein sequence reveals the following:

TABLE-US-06655 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.77 Transmembrane 18-34 (14-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.2508(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06656 >GP: AAC23741 GB: AF052208 competence protein [Streptococcus pneumoniae] Identities = 96/217 (44%), Positives = 138/217 (63%), Gaps = 4/217 (1%) Query: 3 EIVLEKIKSHKWETTGIIVGLLLFGILGLNHFG-THHKEDNLNINLEK-KVSTITEKKVP 60 E ++EKIK +K +GLL+ G L T KE NL + ++EK+V Sbjct: 2 EAIIEKIKEYKIIVICTGLGLLVGGFFLLKPAPQTPVKETNLQAEVAAVSKDLVSEKEVN 61 Query: 61 MISHVKDKVSNQVTVDVKGAVNHPGVYSLPSQSRVTDAIKRAGGLSNLADSKSVNLAQKL 120- + + +TVDVKGAV PG+Y LP SR+ DA+++AGGL+ ADSKS+NLAQK+ Sbjct: 62 KEEKEEPLEQDLITVDVKGAVKSPGIYDLPVGSRINDAVQKAGGLTEQADSKSLNLAQKV 121- Query: 121 QDETVIYVAQKGEKITVVEEEKANNIATQGNSKGKINLNKADLSSLQTISGVGAKRAQDI 18- 0 DE ++YV KGE+ V ++ A+ + + K+NLNKA L L+ + G+G KRAQDI Sbjct: 122 SDEALVYVPTKGEE--AVSQQTGLGTASSISKEKKVNLNKASLEELKQVKGLGGKRAQDI 17- 9 Query: 181 LDYRDSQGGFKTIDDLKNVSGIGEKTLEKLRQDVTID 217 +D+R++ G FK++D+LK VSGIG KT+EKL+ VT+D Sbjct: 180 IDHREANGKFKSVDELKKVSGIGGKTIEKLKDYVTVD 216 A related DNA sequence was identified in S. pyogenes <SEQ ID 6717> which encodes the amino acid sequence <SEQ ID 6718>. Analysis of this protein sequence reveals the following: TABLE-US-06657 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.61 Transmembrane 22-38 (16-42) ----- Final Results ----- bacterial membrane --- Certainty = 0.4843(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06658 >GP: AAC23741 GB: AF052208 competence protein [Streptococcus pneumoniae] Identities = 82/179 (45%), Positives = 124/179 (68%), Gaps = 4/179 (2%) Query: 42 NRQSKAAVPALREISPVKQQVSEEKKEIQEDSSILVDLKGAVQKEGVYKLTASSRVRDVI 101- N Q++ A + +++ K+ EEK+E E I VD+KGAV+ G+Y L SR+ D + Sbjct: 42 NLQAEVAAVS-KDLVSEKEVNKEEKEEPLEQDLITVDVKGAVKSPGIYDLPVGSRINDAV 100- Query: 102 ELAGGLTSEADKHAINFAEKLTDEQVVYVPKQGEEISVLPRSLVSGKKETASKDQSKVHI 16- 1 + AGGLT +AD ++N A+K++DE +VYVP +GEE + + G + SK++ KV++ Sbjct: 101 QKAGGLTEQADSKSLNLAQKVSDEALVYVPTKGEE--AVSQQTGLGTASSISKEK-KVNL 15- 7 Query: 162 NKASLEELQHIPGIGAKRAQDIIDMRDKLGGFKALEDLRQVSGIGEKTLEKLKDDIFLD 220- NKASLEEL+ + G+G KRAQDIID R+ G FK++++L++VSGIG KT+EKLKD + +D Sbjct: 158 NKASLEELKQVKGLGGKRAQDIIDHREANGKFKSVDELKKVSGIGGKTIEKLKDYVTVD 216- An alignment of the GAS and GBS proteins is shown below. TABLE-US-06659 Identities = 81/166 (48%), Positives = 111/166 (66%), Gaps = 10/166 (6%) Query: 62 ISHVKDKVSNQ---------VTVDVKGAVNHPGVYSLPSQSRVTDAIKRAGGLSNLADSK 11- 2 IS VK +VS + + VD+KGAV GVY L + SRV D I+ AGGL++ AD Sbjct: 55 ISPVKQQVSEEKKEIQEDSSILVDLKGAVQKEGVYKLTASSRVRDVIELAGGLTSEADKH 11- 4 Query: 113 SVNLAQKLQDETVIYVAQKGEKITVVEEEKANNIA-TQGNSKGKINLNKADLSSLQTISG 17- 1 ++N A+KL DE V+YV ++GE+I+V+ + T + K+++NKA L LQ I G Sbjct: 115 AINFAEKLTDEQVVYVPKQGEEISVLPRSLVSGKKETASKDQSKVHINKASLEELQHIPG 17- 4 Query: 172 VGAKRAQDILDYRDSQGGFKTIDDLKNVSGIGEKTLEKLRQDVTID 217 +GAKRAQDI+D RD GGFK ++DL+ VSGIGEKTLEKL+ D+ +D Sbjct: 175 IGAKRAQDIIDMRDKLGGFKALEDLRQVSGIGEKTLEKLKDDIFLD 220 A related GBS gene <SEQ ID 8989> and protein <SEQ ID 8990> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06660 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 5.70 GvH: Signal Score (-7.5): -2.58 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -3.77 threshold: 0.0 INTEGRAL Likelihood = -3.77 Transmembrane 18-34 (14-36) PERIPHERAL Likelihood = 10.40 73 modified ALOM score: 1.25 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2508(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00157## SEQ ID 8990 (GBS129) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 41 (lane 4; MW 43.8 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2175 A DNA sequence (GBSx2292) was identified in S. agalactiae <SEQ ID 6719> which encodes the amino acid sequence <SEQ ID 6720>. Analysis of this protein sequence reveals the following: TABLE-US-06661 Possible site: 54 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -14.01 Transmembrane 215-231 (208-240) ----- Final Results ----- bacterial membrane --- Certainty = 0.6604(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06662 >GP: CAB12793 GB: Z99109 similar to 1-acylglycerol-3-phosphate O-acyltransferase [Bacillus subtilis] Identities = 66/200 (33%), Positives = 111/200 (55%), Gaps = 10/200 (5%) Query: 3 YTYLRTLVMFLIWVANGNAHYHNEDKMLKDDENYILVAPHRTFWDPVYMAFAARPKQFIF 62- Y + + ++ + G Y+E+ L D +++ H + D + + P Q + Sbjct: 2 YKFCANALKVILSLRGGVKVYNKEN--LPADSGFVIACTHSGWVDVITLGVGILPYQIHY 59- Query: 63 MAKKELFTNRLFGWWIKMCGAFPIDREKPGQDAIRYPVKMLKNSNRSLVMFPSGSRHSKD 12- 2 MAKKELF N+ G ++K AFP+DRE PG +I+ P+K+LK + +FPSG+R S+D Sbjct: 60 MAKKELFQNKWIGSFLKKIHAFPVDRENPGPSSIKTPIKLLK-EGEIVGIFPSGTRTSED 11- 8 Query: 123 V--KGGVAVIAKMAKVRIMPAAYRGPMVFKNLLKGHRVDMNFGNPIDVSDIKRMDA-EGI 17- 9 V K G IA+M K ++PAAY+GP K L K +++ G P+ +D + + E + Sbjct: 119 VPLKRGAVTIAQMGKAPLVPAAYQGPSSGKELFKKGKMKLIIGEPLHQADFAHLPSKERL 17- 8 Query: 180 A----EVSRRIQEEFDRLDR 195 A +++RI+E ++LD+ Sbjct: 179 AAMTEALNQRIKELENKLDQ 198 A related DNA sequence was identified in S. pyogenes <SEQ ID 6721> which encodes the amino acid sequence <SEQ ID 6722>. Analysis of this protein sequence reveals the following: TABLE-US-06663 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.83 Transmembrane 241-257 (234-266) INTEGRAL Likelihood = -4.41 Transmembrane 27-43 (26-44) ----- Final Results ----- bacterial membrane --- Certainty = 0.5734(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06664 >GP: CAB12793 GB: Z99109 similar to 1-acylglycerol-3-phosphate O-acyltransferase [Bacillus subtilis] Identities = 59/198 (29%), Positives = 104/198 (51%), Gaps = 6/198 (3%) Query: 29 YAYLRGLVVFLLWVVNGNAHYHHEEKMLDASENYILVAPHRTFWDPVYHAFAARPKQFIF 88- Y + + +L + G Y+ E L A +++ H + D + + P Q + Sbjct: 2 YKFCANALKVILSLRGGVKVYNKEN--LPADSGFVIACTHSGWVDVITLGVGILPYQIHY 59- Query: 89 MAKKELFANRLFAWWIKMCGAFPIDRDKPSPDAIRYPVNMLKKSNRSLLMFPSGSRHSQE 14- 8 MAKKELF N+ ++K AFP+DR+ P P +I+ P+ +LK+ + +FPSG+R S++ Sbjct: 60 MAKKELFQNKWIGSFLKKIHAFPVDRENPGPSSIKTPIKLLKE-GEIVGIFPSGTRTSED 11- 8 Query: 149 V--KGGVAVIAKLAKVKIMPAAYQGPMSVKGLLAGERVDMTFGNPIDVSDIKRM-NDEGI 20- 5 V K G IA++ K ++PAAYQGP S K L ++ + G P+ +D + + E + Sbjct: 119 VPLKRGAVTIAQMGKAPLVPAAYQGPSSGKELFKKGKMKLIIGEPLHQADFAHLPSKERL 17- 8 Query: 206 AEVANRIQAEFDRIDDEL 223 A + + ++++L Sbjct: 179 AAMTEALNQRIKELENKL 196 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06665 Identities = 186/244 (76%), Positives = 212/244 (86%) Query: 1 MFYTYLRTLVMFLIWVANGNAHYHNSDKMLKDDENYILVAPHRTFWDPVYMAFAARPKQF 60- +FY YLR LV+FL+WV NGNAHYH+E+KML ENYILVAPHRTFWDPVYMAFAARPKQF Sbjct: 27 VFYAYLRGLVVFLLWVVNGNAHYHHEEKMLDASENYILVAPHRTFWDPVYMAFAARPKQF 86- Query: 61 IFMAKKELFTNRLFGWWIKMCGAFPIDREKPGQDAIRYPVKMLKNSNRSLVMFPSGSRHS 12- 0 IFMAKKELF NRLF WWIKMCGAFPIDR+KP DAIRYPV MLK SNRSL+MFPSGSRHS Sbjct: 87 IFMAKKELFANRLFAWWIKMCGAFPIDRDKPSPDAIRYPVNMLKKSNRSLLMFPSGSRHS 14- 6 Query: 121 KDVKGGVAVIAKMAKVRIMPAAYRGPMVFKNLLKGHRVDMNFGNPIDVSDIKRMDAEGIA 18- 0 ++VKGGVAVIAK+AKV+IMPAAY+GPM K LL G RVDM FGNPIDVSDIKRM+ EGIA Sbjct: 147 QEVKGGVAVIAKLAKVKIMPAAYQGPMSVKGLLAGERVDMTFGNPIDVSDIKRMNDEGIA 20- 6 Query: 181 EVSRRIQEEFDRLDRENETYDDGKKLNPLTYIYRLPLAIIAIVLLVLTLIFSYLASFVWD 24- 0 EV+ RIQ EFDR+D E + GK NPLTY+YRLPL ++ +V+L+LT++FSY+ASFVW+ Sbjct: 207 EVANRIQAEFDRIDDELAPFQPGKARNPLTYLYRLPLGLVLVVVLLLTMLFSYIASFVWN 26- 6 Query: 241 PQKH 244 P KH Sbjct: 267 PDKH 270 SEQ ID 6720 (GBS171) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 36 (lane 2; MW 25 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 41 (lane 3; MW 49.8 kDa). Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2176 A DNA sequence (GBSx2293) was identified in S. agalactiae <SEQ ID 6723> which encodes the amino acid sequence <SEQ ID 6724>. Analysis of this protein sequence reveals the following: TABLE-US-06666 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3268(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06667 >GP: CAB11810 GB: Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 113/244 (46%), Positives = 173/244 (70%), Gaps = 2/244 (0%) Query: 6 LKENERIDQLFSTDVKIIQNKEVFSYSIDSVLLSRFPKLP-SRGLIVDLCSGNGAVGLFA 64 L ++ER+D L + D+KIIQ+ VF++S+D+VLLS+F +P +G IVDLC+GNG V L Sbjct: 4 LHDDERLDYLLAEDMKIIQSPTVFAFSLDAVLLSKFAYVPIQKGKIVDLCTGNGIVPLLL 63 Query: 65 STKTNATIIEIELQESLADMAKRSIKLNKLEKQVTMINDDLKNLLDHVQRSNVDLMLCNP 124- ST++ A I+ +E+QE L DMA RS++ NKL+ Q+ +I+DDLKN+ + + + D++ CNP Sbjct: 64 STRSKADILGVEIQERLHDMAVRSVEYNKLDDQIQIIHDDLKNMPEKLGHNRYDVVTCNP 123- Query: 125 PYFKASETSKKNLSPHYLLARHEITTNLREICQIAQHALKTKGRIAMVHRPDRFLEIIDT 18- 4 PYFK + +++N++ H +ARHEI L ++ ++ LK G+ A+VHRP R LEI + Sbjct: 124 PYFKTPKQTEQNMNEHLRIARHEIHCTLEDVISVSSKLLKQGGKAALVHRPGRLLEIFEL 18- 3 Query: 185 MRQFNLAPKRIQFVYPKLGKDANMLLIEAIKDGSTEGMKILPPLVVHQDNGDYTETIFDI 24- 4 M+ + + PKR+QFVYPK GK+AN +L+E IK G + +KILPPL V+ + +YT+ I I Sbjct: 184 MKAYQIEPKRVQFVYPKQGKEANTILVEGIKGGRPD-LKILPPLFVYDEQNEYTKEIRTI 24- 2 Query: 245 YFGE 248 +G+ Sbjct: 243 LYGD 246 A related DNA sequence was identified in S. pyogenes <SEQ ID 6725> which encodes the amino acid sequence <SEQ ID 6726>. Analysis of this protein sequence reveals the following: TABLE-US-06668 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2183(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06669 Identities = 200/257 (77%), Positives = 228/257 (87%), Gaps = 3/257 (1%) Query: 1 MIDTILKENERIDQLFSTDVKIIQNKEVFSYSIDSVLLSRFPKLPSRGLIVDLCSGNGAV 60 MI ILKE ERIDQLFS+DV IIQNK+VFSYSIDSVLLSRFPK+PS+GLIVDLCSGNGAV Sbjct: 1 MIKAILKEGERIDQLFSSDVGIIQNKDVFSYSIDSVLLSRFPKMPSKGLIVDLCSGNGAV 60 Query: 61 GLFASTKTNATIIEIELQESLADMAKRSIKLNKLEKQVTMINDDLKNLLDHVQRSNVDLM 120- GLFAST+T A I+E+ELQE LADM +RSI+LN+LE QVTMI DDLKNLL+HV RS VDLM Sbjct: 61 GLFASTRTKAAIVEVELQERLADMGQRSIQLNQLEDQVTMICDDLKNLLNHVPRSGVDLM 120- Query: 121 LCNPPYFKASETSKKNLSPHYLLARHEITTNLREICQIAQHALKTKGRIAMVHRPDRFLE 18- 0 LCNPPYFK+ E+SKKN+S HYLLARHE+TTNL EICQ+A+HALK+ GR+AMVHRPDRFLE Sbjct: 121 LCNPPYFKSHESSKKNVSEHYLLARHEVTTNLEEICQVARHALKSNGRLAMVHRPDRFLE 18- 0 Query: 181 IIDTMRQFNLAPKRIQFVYPKLGKDANMLLIEAIKDGSTEGMKILPPLVVHQDNGDYTET 24- 0 IID++R LAPKR+QFVYPKLGK ANMLLIEAIKDGS EGM ILPPLVVH++NG+YT+ Sbjct: 181 IIDSLRANGLAPKRVQFVYPKLGKSANMLLIEAIKDGSIEGMTILPPLVVHKENGEYTDH 24- 0 Query: 241 IFDIYFGENGK---SHD 254 IF+IYFG K +HD Sbjct: 241 IFEIYFGAASKGKPNHD 257 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2177 A DNA sequence (GBSx2294) was identified in S. agalactiae <SEQ ID 6727> which encodes the amino acid sequence <SEQ ID 6728>. Analysis of this protein sequence reveals the following: TABLE-US-06670 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1512(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06671 >GP: CAB11811 GB: Z99104 similar to hypothetical proteins [Bacillus subtilis] Identities = 40/82 (48%), Positives = 63/82 (76%) Query: 7 YMYVLECSDGTLYTGYTTDVKRRLNTHNTGKGAKYTRARLPVKLLYSEAFNSKQEAMRAE 66 + YV++C D + Y GYT D+ +R+ THN GKGAKYT+ R PV+L+++E+F++K+EAM+AE Sbjct: 7 FFYVVKCKDNSWYAGYTNDLHKRVKTHNDGKGAKYTKVRRPVELIFAESFSTKREAMQAE 66 Query: 67 ALFKQKTRQAKLTYIKQHKNEQ 88 FK+ TR+ K YI++ +N + Sbjct: 67 YYFKKLTRKKKELYIEEKRNSK 88 A related DNA sequence was identified in S. pyogenes <SEQ ID 6729> which encodes the amino acid sequence <SEQ ID 6730>. Analysis of this protein sequence reveals the following: TABLE-US-06672 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1838(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06673 Identities = 60/84 (71%), Positives = 67/84 (79%), Gaps = 1/84 (1%) Query: 6 AYMYVLECSDGTLYTGYTTDVKRRLNTHNTGKGAKYTRARLPVKLLYSEAFNSKQEAMRA 65 AYMYVLEC D TLYTGYTTD+K+RL THN GKGAKYTR RLPV LLY E F+SK+ AM A Sbjct: 6 AYMYVLECVDKTLYTGYTTDLKKRLATHNAGKGAKYTRYRLPVSLLYYEVFDSREAAMSA 65 Query: 66 EALF-KQKTRQAKLTYIKQHKNEQ 88 EALF K+KTR KL YI H+ E+ Sbjct: 66 EALFKKRKTRSQKLAYIATHQKEK 89 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2178 A DNA sequence (GBSx2295) was identified in S. agalactiae <SEQ ID 6731> which encodes the amino acid sequence <SEQ ID 6732>. This protein is predicted to be autoaggregation-mediating protein (deaD). Analysis of this protein sequence reveals the following:

TABLE-US-06674 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2287(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06675 >GP: AAD20136 GB: AF091502 autoaggregation-mediating protein [Lactobacillus reuteri] Identities = 289/504 (57%), Positives = 366/504 (72%), Gaps = 18/504 (3%) Query: 1 MKFTELNLSQDILSAVEKAGFVEPSPIQEMTIPLALEGKDVIGQAQTGTGKTAAFGLPTL 60 MKF+EL LS +L A++++G+ E +PIQE TIP+ LEGKDVIGQAQTGTGKTAAFGLP + Sbjct: 1 MKFSELGLSDSLLKAIKRSGYEEATPIQEQTIPMVLEGKDVIGQAQTGTGKTAAFGLPII 60 Query: 61 NKIHTEDNTIQALIIAPTRELAVQSQEELFRFGRDKGVKVRSVYGGSSIEKQIKALRSGA 120- + TE+ IQA+II+PTRELA+Q+QEEL+R G+DK V+V+ VYGG+ I +QIK+L+ Sbjct: 61 ENVDTENPNIQAIIISPTRELAIQTQEELYRLGKDKHVRVQVVYGGADIRRQIKSLKQHP 120- Query: 121 HVVVGTPGRLLDLIKRKALKLNHIETLILDEADEMLNMGFLEDIEAIISRVPETRQTLLF 18- 0 ++VGTPGRL D I R +KL+HI+TL+LDEADEMLNMGFLEDIE+II P+ RQTLLF Sbjct: 121 QILVGTPGRLRDHINRHTVKLDHIKTLVLDEADEMLNMGFLEDIESIIKETPDDRQTLLF 18- 0 Query: 181 SATMPDPIKRIGVKFMKDPEHVKIKATELTNVNVDQYYVRVKENEKFDTMTRLMDVDQPE 24- 0 SATMP IKRIGV+FM DPE V+IKA ELT VDQYYVR ++ EKFD MTRL+DV P+ Sbjct: 181 SATMPPEIKRIGVQFMSDPETVRIKAKELTTDLVDQYYVRARDYEKFDIMTRLIDVQDPD 24- 0 Query: 241 LSIVFGRTKRRVDELTRGLKLRGFRAEGIHGDLDQNKRLRVIRDFKNDHIDILVATDVAA 30- 0 L+IVFGRTKRRVDEL++GL RG+ A GIHGDL Q+KR +++ FKN+ +DILVATDVAA Sbjct: 241 LTIVFGRTKRRVDELSKGLIARGYNAAGIHGDLTQDKRSKIMWKFKNNELDILVATDVAA 30- 0 Query: 301 RGLDISGVTHVYNYDIPQDPESYVHRIGRTGRAGKSGQSITFVSPNEMGYLTIIENLTKK 36- 0 RGLDISGVTHVYNYDIP DP+SYVHRIGRTGRAG G S+TFV+PNEM YL IE LT+ Sbjct: 301 RGLDISGVTHVYNYDIPSDPDSYVHRIGRTGRAGHHGVSLTFVTPNEMDYLHEIEKLTRV 36- 0 Query: 361 RMTGMKPATASEAFQAKKKVALKRIARDFED-QELVSK--FDKFKADALELATQYTPEEL 41- 7 RM +KP TA EAF+ ++A F D EL+++ D+++ A +L + +L Sbjct: 361 RMLPLKPPTAEEAFKG-------QVASAFNDIDELIAQDSTDRYEEAAEKLLETHNATDL 41- 3 Query: 418 ALYVLSLTVQDPESLPEVEITREKPLPFKPSGGGFKGKGGRGNGRGGD--RRRNDRGDRR 47- 5 +L+ ++ S V+IT E+PLP + G R N GG+ RR+N R + Sbjct: 414 VAALLNNMTKEAASEVPVKITPERPLPRRNKRN--NRNGNRNNSHGGNHYRRKNFRRHQH 47- 1 Query: 476 GNRDRDDRG----SRCDFKRRDDK 495 G+ D+ G SR F R K Sbjct: 472 GSHRNDNHGKSHSSRHSFNIRHRK 495 A related DNA sequence was identified in S. pyogenes <SEQ ID 6733> which encodes the amino acid sequence <SEQ ID 6734>. Analysis of this protein sequence reveals the following: TABLE-US-06676 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1108(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06677 Identities 430/545 (78%), Positives = 463/545 (84%), Gaps = 24/545 (4%) Query: 1 MKFTELNLSQDILSAVEKAGFVEPSPIQEMTIPLALEGKDVIGQAQTGTGKTAAFGLPTL 60 +KFTE NLSQDI SAV AGF + SPIQEMTIPLALEGKDVIGQAQTGTGKTAAFGLPTL Sbjct: 1 LKFTEFNLSQDIQSAVVTAGFEKASPIQEMTIPLALEGKDVIGQAQTGTGKTAAFGLPTL 60 Query: 61 NKIHTEDNTIQALIIAPTRELAVQSQEELFRFGRDKGVKVRSVYGGSSIEKQIKALRSGA 12- 0 NKI T +N IQAL+IAPTRELAVQSQEELFRFGR+KGVKVRSVYGGSSIEKQIKAL+SGA Sbjct: 61 NKIRTNENIIQALVIAPTRELAVQSQEELFRFGREKGVKVRSVYGGSSIEKQIKALKSGA 12- 0 Query: 121 HVVVGTPGRLLDLIKRKALKLNHIETLILDEADEMLNMGFLEDIEAIISRVPETRQTLLF 18- 0 H+VVGTPGRLLDLIKRKAL L+H+ETLILDEADEMLNMGFLEDIEAIISRVP RQTLLF Sbjct: 121 HIVVGRPGRLLDLIKRKALILDHVETLILDEADEMLNMGFLEDIEAIISRVPADRQTLLF 18- 0 Query: 181 SATMPDPIKRIGVKFMKDPEHVKIKATELTNVNVDQYYVRVKENEKFDTMTRLMDVDQPE 24- 0 SATMP PIK+IGVKFMKDPEHV+IK ELTNVNVDQYYVRVKE EKFDTMTRLMDV+QPE Sbjct: 181 SATMPAPIKQIGVKFMKDPEHVQIKNKELTNVNVDQYYVRVKEQEKFDTMTRLMDVNQPE 24- 0 Query: 241 LSIVFGRTKRRVDELTRGLKLRGFRAEGIHGDLDQNKRLRVIRDFKNDHIDILVATDVAA 30- 0 LSIVFGRTKRRVDE+TRGLKLRGFRAEGIHGDLDQNKRLRVIRDFKND IDILVATDVAA Sbjct: 241 LSIVFGRTKRRVDEITRGLKLRGFRAEGIHGDLDQNKRLRVIRDFKNDQIDILVATDVAA 30- 0 Query: 301 RGLDISGVTHVYNYDIPQDPESYVHRIGRTGRAGKSGQSITFVSPNEMGYLTIIENLTKK 36- 0 RGLDISGVTHVYNYDI QDPESYVHRIGRTGRAGKSG+SITFVSPNEMGYL++IENLTKK Sbjct: 301 RGLDISGVTHVYNYDITQDPESYVHRIGRTGRAGKSGESITFVSPNEMGYLSMIENLTKK 36- 0 Query: 361 RMTGMKPATASEAFQAKKKVALKRIARDFEDQELVSKFDKFKADALELATQYTPEELALY 42- 0 +M ++PATA EAFQAKKKVALK+I RDF D+ + S FDKFK DA++LA ++TPEELALY Sbjct: 361 QMKPLRPATAEEAFQAKKKVALKKIERDFADETIRSNFDKFKGDAVQLAAEFTPEELALY 42- 0 Query: 421 VLSLTVQDPESLPEVEITREKPLPFKPSGGGF---KGKGGRG--NGRGGDRRRNDRGDR- 47- 4 +LSLTVQDP+SLPEVEI REKPLPFK GGG GKGGRG N GDRR RGDR Sbjct: 421 ILSLTVQDPDSLPEVEIAREKPLPFKYVGGGHGNKNGKGGRGRDNRNRGDRRGGYRGDRN 48- 0 Query: 475 ------------RGNRDRDDRGSRCDFKRRDDKFKKDNRRQENKKPHKNTSSEKQTGFVI 52- 2 R RD D DFKR+ + KD +E K SS K TGFVI Sbjct: 481 RDERDGDRRRQKRDKRDGHDGSGNRDFKRKSKRNSKDFFNKEKK------SSAKNTFFVI 53- 4 Query: 523 RNKGD 527 R+KG+ Sbjct: 535 RHKGE 539 A related GBS gene <SEQ ID 8991> and protein <SEQ ID 8992> were also identified. Analysis of this protein sequence reveals the following: RGD motif 471-473 The protein has homology with the following sequences in the databases: ##STR00158## There is also homology to SEQ ID 4454. SEQ ID 8992 (GBS307) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 56 (lane 7; MW 62 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 61 (lane 2; MW 86.7 kDa). The GBS307-GST fusion product was purified (FIG. 208, lane 9; FIG. 225, lane 10-11) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 272), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2179 A DNA sequence (GBSx2296) was identified in S. agalactiae <SEQ ID 6735> which encodes the amino acid sequence <SEQ ID 6736>. This protein is predicted to be outer membrane protein (yaeC). Analysis of this protein sequence reveals the following: TABLE-US-06678 Possible site: 19 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06679 >GP: CAB73036 GB: AL139076 putative periplasmic protein [Campylobacter jejuni] Identities = 89/237 (37%), Positives = 132/237 (55%), Gaps = 3/237 (1%) Query: 40 ITVATYSKPTSTFLDLVKDNVKEKGYTLKVVMVSDYIQANIALENKEHDANLLQHEFFMS 99 IT+ P + L+L+KD+ K KGY LK+V SDYI N ALE KE DANL QH+ F+ Sbjct: 23 ITIGATPNPFGSLLELMKDDFKNKGYELKIVEFSDYILPNRALEEKELDANLYQHKPFLE 82 Query: 100 IFNKENDGHLVSITPIYHSLAGFYGQHLKNIAELKDGAKVAIPSDPANMTRALLLLQEKK 15- 9 +N + +L++ TP+ + G Y + +KN+ LK+GA+VAIP+D N +RAL LL++ K Sbjct: 83 EYNLKKGSNLIATTPVLIAPVGVYSKKIKNLENLKEGARVAIPNDATNESRALELLEKAK 14- 2 Query: 160 LITLKNTSKKTKAIEDIITNPKKLRIEPVALLNLNQAYFEYDLVFNFPGYVTKINLVPKR 21- 9 LI L + KT DI NPKKL+ + L +A + D+ + L P + Sbjct: 143 LIELNKNTLKTPL--DINKNPKKLKFIELKAAQLPRALDDVDIAIINSNFALGAGLNPSK 20- 0 Query: 220 DRLLYEKKPDIRFAGALVAREDNKNSDKIKVLKEVLTSKEIRHYITKEIPSEAAVAF 276 D + E K + + +V R + KNS+K KV+ E+L S + + I + AF Sbjct: 201 DTIFREDK-NSPYVNYVVVRSEGKNSEKTKVIDEILRSDKFKAIINEHYKDILIPAF 256 SEQ ID 6736 (GBS126) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 34 (lane 7; MW 32 kDa). Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2180 A DNA sequence (GBSx2297) was identified in S. agalactiae <SEQ ID 6737> which encodes the amino acid sequence <SEQ ID 6738>. This protein is predicted to be probable permease of ABC transporter. Analysis of this protein sequence reveals the following: TABLE-US-06680 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.99 Transmembrane 190-206 ( 187-215) INTEGRAL Likelihood = -8.44 Transmembrane 25-41 ( 16-45) INTEGRAL Likelihood = -6.48 Transmembrane 69-85 ( 68-90) INTEGRAL Likelihood = -3.77 Transmembrane 90-106 ( 88-109) INTEGRAL Likelihood = -1.44 Transmembrane 145-161 ( 145-161) ----- Final Results ----- bacterial membrane --- Certainty = 0.5798(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06681 >GP: AAG08889 GB: AE004963 probable permease of ABC transporter [Pseudomonas aeruginosa] Identities = 80/206 (38%), Positives = 127/206 (60%), Gaps = 4/206 (1%) Query: 15 SFWETNLMLGLTLILCFLIAFPTGILLFSLRKSYLIKHSLAYQLLNLFLGTLRSVPFLIF 74 +FW MLG +L+ ++ P G+LLF + + Y LL+L + LRS+PF+I Sbjct: 24 TFW----MLGGSLLFTVVLGLPLGVLLFLTGPRQMFEQKAVYTLLSLVVNILRSLPFIIL 79 Query: 75 IFILIPLNRLIFGTSFGTIAAILPLTLVSVSLYARYVEQALLNIPQVVVDRALSLGANKR 13- 4 + IPL LI GTS G AI PL + + +AR VE AL + + +++ ++GA+ R Sbjct: 80 LIVMIPLTVLITGTSLGVAGAIPPLVVGATPFFARLVETALREVDKGIIEATQAMGASTR 13- 9 Query: 135 QIIYYFLIPSIKIDLVLSFTATAISILGYSTIMGVIGAGGLGEYAYRFGYQEYDYPVMYL 19- 4 QII+ L+P + ++ + T TAI+++ Y+ + GV+GAGGLG+ A RFGYQ + VM + Sbjct: 140 QIIWNALLPEARPGIIAAITVTAITLVSYTAMAGVVGAGGLGDLAIRFGYQRFQTDVMVV 19- 9 Query: 195 IVVLFIIYVFILQSLGYFIANRYSRK 220 VV+ +I V ILQ++G + +SRK Sbjct: 200 TVVMLLILVQILQTVGDKLVVHFSRK 225 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2181 A DNA sequence (GBSx2298) was identified in S. agalactiae <SEQ ID 6739> which encodes the amino acid sequence <SEQ ID 6740>. This protein is predicted to be ABC transporter, ATP-binding protein (oppF). Analysis of this protein sequence reveals the following: TABLE-US-06682 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5454(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9333> which encodes amino acid sequence <SEQ ID 9334> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06683 >GP: AAC22280 GB: U32744 ABC transporter, ATP-binding protein [Haemophilus influenzae Rd] Identities = 62/174 (35%), Positives = 104/174 (59%), Gaps = 2/174 (1%) Query: 1 MKMINGLIPYDKGNIYYQGKEVKSFSDNKLRQMRKDIAYIFQNHNLLAGESVYYHLALVY 60 ++ +N L G++ G E+ SD +L R+ I IFQ+ NLL+ +V+ ++AL Sbjct: 48 IRCVNLLEKPTSGSVIVDGVELTKLSDRELVLARRQIGMIFQHFNLLSSRTVFENVALPL 10- 7 Query: 61 KLNHQKVN--HDAINDILDFLGLMDLKQVKCHSLSGGQQQKVAIAMAVLQKPKLILCDEI 11- 8 +L + + I +LD +GL + + +LSGGQ+Q+VAIA A+ PK++LCDE Sbjct: 108 ELESESKAKIQEKITALLDLVGLSEKRDAYPSNLSGGQKQRVAIARALASDPKVLLCDEA 16- 7 Query: 119 SSALDTNSEKEIFNLLSDLREKYGISILMIAHHLSLLKQYCDRVMILDHQTIVD 172 +SALD + + I LL ++ GI+IL+I H + ++KQ CD+V ++D +V+ Sbjct: 168 TSALDPATTQSILKLLKEINRTLGITILLITHEMEVVKQICDQVAVIDQGRLVE 221 There is also homology to SEQ ID 76. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2182 A DNA sequence (GBSx2299) was identified in S. agalactiae <SEQ ID 6741> which encodes the amino acid sequence <SEQ ID 6742>. Analysis of this protein sequence reveals the following: TABLE-US-06684 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2183 A DNA sequence (GBSx2300) was identified in S. agalactiae <SEQ ID 6743> which encodes the amino acid sequence <SEQ ID 6744>. Analysis of this protein sequence reveals the following: TABLE-US-06685 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0904(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9741> which encodes amino acid sequence <SEQ ID 9742> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06686 >GP: AAB87515 GB: AF034138 unknown [Bacillus subtilis] Identities = 74/125 (59%), Positives = 92/125 (73%) Query: 5 MGIFSGLMGNASQMDTDKVENQLSDILISDEQVDLAYTLIRDLIVFTNYRLILVDKQGVT 64 MG GL+GNAS + T V+ +L+ IL+ E+V+ A+ L+RDLIVFT+ RLILVDKQG+T Sbjct: 1 MGFIDGLLGNASTLSTAAVQEELAHILLEGEKVEAAFKLVRDLIVFTDKRLILVDKQGIT 60 Query: 65 GKKVSYNSIPYASISRFTVETSGHFDLDAELKIWISSAIEPAEVLQFKNDRNIVSIQKAL 124- GKK + SIPY SISRF+VET+G FDLD+ELKIWIS A PA QFK D +I IQK L Sbjct: 61 GKKTEFQSIPYKSISRFSVETAGRFDLDSELKIWISGAELPAVSKQFKKDESIYDIQKVL 120- Query: 125 ATAVL 129 A + Sbjct: 121 AAVCM 125 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2184 A DNA sequence (GBSx2301) was identified in S. agalactiae <SEQ ID 6745> which encodes the amino acid sequence <SEQ ID 6746>. Analysis of this protein sequence reveals the following: TABLE-US-06687 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0921(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9331> which encodes amino acid sequence <SEQ ID 9332> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06688 >GP: CAA74739 GB: Y14370 peptide chain release factor 3 [Staphylococcus aureus] Identities = 274/462 (59%), Positives = 349/462 (75%), Gaps = 9/462 (1%) Query: 1 MDIEKQRGISVTSSVMQFDYAGKRVNILDTPGHEDFSEDTYRTLMAVDAAVMVVDSAKGI 60 M +E++RGISVTSSVMQFDY +NILDTPGHEDFSEDTYRTLMAVD+AVMV+D AKG+ Sbjct: 57 MKVEQERGISVTSSVMQFDYDDYEINILDTPGHEDFSEDTYRTLMAVDSAVMVIDCAKGV 116- Query: 61 EAQTKKLFEVVKHRNIPVFTFINKLDRDGREPLDLLEELEEVLGIASYPMNWPIGMGKSF 120- E T KLF+V K R IP+FTFINKLDR G+EP +LL+E+EE L I +YPMNWPIGMG+SF Sbjct: 117 EPPTLKLFKVCKMRGIPIFTFINKLDRVGKEPFELLDEIEETLNIETYPMNWPIGMGQSF 17- 6 Query: 121 EGLYDLHNKRLELYKGDERFASIEDG-----DQLFANNPFYEQVKEDIELLQEAGNDFSE 17- 5 G+ D +K +E ++ +E + D D N+ +EQ E++ L++EAG F Sbjct: 177 FGIIDRKSKTIEPFRDEENILHLNDDFELEEDHAITNDSDFEQAIEELMLVEEAGEAFDN 23- 6 Query: 176 QAILDGDLTPVFFGSALTNFGVQTFLDTFLEFAPEPHGHKTTEGNVIDPLAKDFSGFVFK 23- 5 A+L GDLTPVFFGSAL NFGVQ FL+ +++FAP P+ +T E + P FSGF+FK Sbjct: 237 DALLSGDLTPVFFGSALANFGVQNFLNAYVDFAPMPNARQTKENVEVSPFDDSFSGFIFK 29- 6 Query: 236 IQANMDPRHRDRIAFVRIVSGEFERGMGVNLTRTGKGAKLSNVTQFMAES-RENVTNAVA 29- 4 IQANMDP+HRDRIAF+R+VSG FER + + L +K S+V + + ++ ++ V +AVA Sbjct: 297 IQANMDPKHRDRIAFMRVVSGAFER-VWMLLCNVLIKSKRSHVQRHLWQTIKKLVNHAVA 35- 5 Query: 295 GDIIGVYDTGTYQVGDTLTVGKNKFEFEPLPTFTPELFMKVSAKNVMKQKSFHKGIEQLV 35- 4 GDIIG+YDTG YQ+GDTL GK + F+ LP FTPE+FMKVSAKNVMKQK FHKGIEQLV Sbjct: 356 GDIIGLYDTGNYQIGDTLVGGKQTYSFQDLPQFTPEIFMKVSAKNVMKQKHFHKGIEQLV 41- 5 Query: 355 QEGAIQLYKNYQTGEYMLGAVGQLQFEVFKHRMEGEYNAEVVMTPMGKKTVRW--INSDD 41- 2 QEGAIQ YK T + +LGAVGQLQFEVF+HRM+ EYN +VVM P+G+K RW N D Sbjct: 416 QEGAIQYYKTLHTNQIILGAVGQLQFEVFEHRMKNEYNVDVVMEPVGRKIARWDIENEDQ 47- 5 Query: 413 LDERMSSSRNILAKDRFDQPVFLFENDFALRWFADKYPDVKL 454 + ++M++SR+IL KDR+D VFLFEN+FA RWF +K+P++KL Sbjct: 476 ITDKMNTSRSILVKDRYDDLVFLFENEFATRWFEEKFPEIKL 517 A related DNA sequence was identified in S. pyogenes <SEQ ID 6747> which encodes the amino acid sequence <SEQ ID 6748>. Analysis of this protein sequence reveals the following: TABLE-US-06689 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2070(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-06690 Identities = 447/458 (97%), Positives = 455/458 (98%) Query: 1 MDIEKQRGISVTSSVMQFDYAGKRVNILDTPGHEDFSEDTYRTLMAVDAAVMVVDSAKGI 60 MDIEKQRGISVTSSVMQFDYAGKRVNILDTPGHEDFSEDTYRTLMAVDAAVMVVDSAKGI Sbjct: 57 MDIEKQRGISVTSSVMQFDYAGKRVNILDTPGHEDFSEDTYRTLMAVDAAVMVVDSAKGI 116- Query: 61 EAQTKKLFEVVKHRNIPVFTFINKLDRDGREPLDLLEELEEVLGIASYPMNWPIGMGKSF 120- EAQTKKLFEVVKHRNIPVFTFINKLDRDGREPL+LLEELEEVLGIASYPMNWPIGMG++F Sbjct: 117 EAQTKKLFEVVKHRNIPVFTFINKLDRDGREPLELLEELEEVLGIASYPMNWPIGMGRAF 17- 6 Query: 121 EGLYDLHNKRLELYKGDERFASIEDGDQLFANNPFYEQVKEDIELLQEAGNDFSEQAILD 18- 0 EGLYDLHNKRLELYKGDERFASIEDGDQLFANNPFYEQVKEDIELLQEAGNDFSEQAILD Sbjct: 177 EGLYDLHNKRLELYKGDERFASIEDGDQLFANNPFYEQVKEDIELLQEAGNDFSEQAILD 23- 6 Query: 181 GDLTPVFFGSALTNFGVQTFLDTFLEFAPEPHGHKTTEGNVIDPLAKDFSGFVFKIQANM 24- 0 GDLTPVFFGSALTNFGVQTFLDTFLEFAPEPHGHKTTEGNV+DPLAKDFSGFVFKIQANM Sbjct: 237 GDLTPVFFGSALTNFGVQTFLDTFLEFAPEPHGHKTTEGNVVDPLAKDFSGFVFKIQANM 29- 6 Query: 241 DPRHRDRIAFVRIVSGEFERGMGVNLTRTGKGAKLSNVTQFMAESRENVTNAVAGDIIGV 30- 0 DP+HRDRIAFVRIVSGEFERGMGVNLTRTGKGAKLSNVTQFMAESRENVTNAVAGDIIGV Sbjct: 297 DPKHRDRIAFVRIVSGEFERGMGVNLTRTGKGAKLSNVTQFMAESRENVTNAVAGDIIGV 35- 6 Query: 301 YDTGTYQVGDTLTVGKNKFEFEPLPTFTPELFMKVSAKNVMKQKSFHKGIEQLVQEGAIQ 36- 0 YDTGTYQVGDTLTVGKNKFEFEPLPTFTPE+FMKVS KNVMKQKSFHKGIEQLVQEGAIQ Sbjct: 357 YDTGTYQVGDTLTVGKNKFEFEPLPTFTPEIFMKVSPKNVMKQKSFHKGIEQLVQEGAIQ 41- 6 Query: 361 LYKNYQTGEYMLGAVGQLQFEVFKHRMEGEYNAEVVMTPMGKKTVRWINSDDLDERMSSS 42- 0 LYKNYQTGEYMLGAVGQLQFEVFKHRMEGEYNAEVVMTPMGKKTVRWI+ DDLD+RMSSS Sbjct: 417 LYKNYQTGEYMLGAVGQLQFEVFKHRMEGEYNAEVVMTPMGKKTVRWISEDDLDQRMSSS 47- 6 Query: 421 RNILAKDRFDQPVFLFENDFALRWFADKYPDVKLEEKM 458 RNILAKDRFDQPVFLFENDFALRWFADKYPDV LEEKM Sbjct: 477 RNILAKDRFDQPVFLFENDFALRWFADKYPDVTLEEKM 514 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2185 A DNA sequence (GBSx2302) was identified in S. agalactiae <SEQ ID 6749> which encodes the amino acid sequence <SEQ ID 6750>. Analysis of this protein sequence reveals the following: TABLE-US-06691 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3061(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06692 >GP: AAC38046 GB: AF000954 No definition line found [Streptococcus mutans] Identities = 122/142 (85%), Positives = 138/142 (96%) Query: 1 MLEFAAQKTGKENKEMAVTFVTNERSHELNLEYRDTDRPTDVISLEYKPEVDISFDEEDL 60 +LEFAAQKTGKE+KEMAVTFVTNERSHELNL+YRDT+RPTDVISLEYKPE +SFDEEDL Sbjct: 23 ILEFAAQKTGKEDKEMAVTFVTNERSHELNLKYRDTNRPTDVISLEYKPESSLSFDEEDL 82 Query: 61 AENPELAEMLEDFDSYIGELFISIDKAKEQAEEYGHSYEREMGFLAVHGFLHINGYDHYT 120- A++P+LAE+L +FD+YIGELFIS+DKA+EQA+EYGHS+EREMGFLAVHGFLHINGYDHYT Sbjct: 83 ADDPDLAEVLTEFDAYIGELFISVDKAREQAQEYGHSFEREMGFLAVHGFLHINGYDHYT 142- Query: 121 PEEEKEMFSLQEEILTAYGLKR 142 P+EEKEMFSLQEEIL AYGLKR Sbjct: 143 PQEEKEMFSLQEEILDAYGLKR 164 There is also homology to SEQ ID 120. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2186 A DNA sequence (GBSx2303) was identified in S. agalactiae <SEQ ID 6751> which encodes the amino acid sequence <SEQ ID 6752>. Analysis of this protein sequence reveals the following: TABLE-US-06693 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.39 Transmembrane 108-124 (100-131) INTEGRAL Likelihood = -8.92 Transmembrane 61-77 (52-82) INTEGRAL Likelihood = -5.36 Transmembrane 41-57 (40-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.7156(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06694 >GP: AAC38047 GB: AF000954 diacyglycerol kinase [Streptococcus mutans] Identities = 107/133 (80%), Positives = 121/133 (90%), Gaps = 2/133 (1%) Query: 1 MDLNDN--NHKKWKNRTLTSSMEFAVTGIFTAFKEERNMRKHLVSAILVILAGLTFQVSM 58 MDL DN + KKWKNRTLTSS+EFA+TGIFTAFKEERNM+KH VSA+L ++AGL F+VS+ Sbjct: 3 MDLRDNKQSQKKWKNRTLTSSLEFALTGIFTAFKEERNMKKHAVSALLAVIAGLVFKVSV 62 Query: 59 VEWLFLLLSIFLVITFEIINSAIENVVDLASNYHFSMLAKNAKDMAAGAVLVVSLFAVLV 118- +EWLFLLLSIFLVITFEI+NSAIENVVDLAS+YHFSMLAKNAKDMAAGAVLV+S FA L Sbjct: 63 IEWLFLLLSIFLVITFEIVNSAIENVVDLASDYHFSMLAKNAKDMAAGAVLVISGFAALT 122- Query: 119 GLIIFIPKILALL 131 GLIIF+PKI LL Sbjct: 123 GLIIFVPKIWFLL 135 A related DNA sequence was identified in S. pyogenes <SEQ ID 6753> which encodes the amino acid sequence <SEQ ID 6754>. Analysis of this protein sequence reveals the following: TABLE-US-06695 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.67 Transmembrane 63-79 (41-84) INTEGRAL Likelihood = -7.32 Transmembrane 110-126 (105-129) INTEGRAL Likelihood = -5.41 Transmembrane 43-59 (41-62) ----- Final Results ----- bacterial membrane --- Certainty = 0.5267(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06696 >GP: AAC38047 GB: AF000954 diacyglycerol kinase [Streptococcus mutans] Identities = 104/135 (77%), Positives = 119/135 (88%) Query: 1 MALHDNNTTKRKWKNRTITSSLEFALTGVFTAFKEERNLRSHLLSACLACVAGLFFSISA 60 M L DN +++KWKNRT+TSSLEFALTG+FTAFKEERN++ H +SA LA +AGL F +S Sbjct: 3 MDLRDNKQSQKKWKNRTLTSSLEFALTGIFTAFKEERNMKKHAVSALLAVIAGLVFKVSV 62 Query: 61 IEWLFLLLAIFLVITLEIVNSAIENVVDLASDYHFSMLAKNAKDMAAGAVLMISGYAVLT 120- IEWLFLLL+IFLVIT EIVNSAIENVVDLASDYHFSMLAKNAKDMAAGAVL+ISG+A LT Sbjct: 63 IEWLFLLLSIFLVITFEIVNSAIENVVDLASDYHFSMLAKNAKDMAAGAVLVISGFAALT 122- Query: 121 GLIIFIPKIWNIFVH 135 GLIIF+PKIW + H Sbjct: 123 GLIIFVPKIWFLLFH 137 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06697 Identities = 98/129 (75%), Positives = 115/129 (88%), Gaps = 2/129 (1%) Query: 1 MDLNDNN--HKKWKNRTLTSSMEFAVTGIFTAFKEERNMRKHLVSAILVILAGLTFQVSM 58 M L+DNN +KWKNRT+TSS+EFA+TG+FTAFKEERN+R HL+SA L +AGL F +S Sbjct: 1 MALHDNNTTKRKWKNRTITSSLEFALTGVFTAFKEERNLRSHLLSACLACVAGLFFSISA 60 Query: 59 VEWLFLLLSIFLVITFEIINSAIENVVDLASNYHFSMLAKNAKDMAAGAVLVVSLFAVLV 118- +EWLFLLL+IFLVIT EI+NSAIENVVDLAS+YHFSMLAKNAKDMAAGAVL++S +AVL Sbjct: 61 IEWLFLLLAIFLVITLEIVNSAIENVVDLASDYHFSMLAKNAKDMAAGAVLMISGYAVLT 120- Query: 119 GLIIFIPKI 127 GLIIFIPKI Sbjct: 121 GLIIFIPKI 129 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2187 A DNA sequence (GBSx2304) was identified in S. agalactiae <SEQ ID 6755> which encodes the amino acid sequence <SEQ ID 6756>. This protein is predicted to be GTPase Era (era). Analysis of this protein sequence reveals the following: TABLE-US-06698 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1871(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10017> which encodes amino acid sequence <SEQ ID 10018> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06699 >GP: AAD41632 GB: AF072811 GTPase Era [Streptococcus pneumoniae] Identities = 273/299 (91%), Positives = 290/299 (96%) Query: 16 MTFKSGFVAILGRPNVGKSTFLNHVMGQKIAIMSDKAQTTRNKIMGIYTTETEQIVFIDT 75 - MTFKSGFVAILGRPNVGKSTFLNHVMGQKIAIMSDKAQTTRNKIMGIYTT+ EQIVFIDT Sbjct: 1 MTFKSGFVAILGRPNVGKSTFLNHVMGQKIAIMSDKAQTTRNKIMGIYTTDKEQIVFIDT 60 Query: 76 PGIHKPKTALGDFMVESAYSTLREVETVLFMVPADEKRGKGDDMIIERLKAAKIPVILVI 135- PGIHKPKTALGDFMVESAYSTLREV+TVLFMVPADE RGKGDDMIIERLKAAK+PVILV+ Sbjct: 61 PGIHKPKTALGDFMVESAYSTLREVDTVLFMVPADEARGKGDDMIIERLKAAKVPVILVV 120- Query: 136 NKIDKVHPDQLLEQIDDFRSQMDFKEVVPISALQGNNVPTLIKLLTDNLEEGFQYFPEDQ 19- 5 NKIDKVHPDQLL QIDDFR+QMDFKE+VPISALQGNNV L+ +L++NL+EGFQYFP DQ Sbjct: 121 NKIDKVHPDQLLSQIDDFRNQMDFKEIVPISALQGNNVSRLVDILSENLDEGFQYFPSDQ 18- 0 Query: 196 ITDHPERFLVSEMVREKVLHLTQQEVPHSVAVVVESMKRDEETDKVHIRATIMVERDSQK 25- 5 ITDHPERFLVSEMVREKVLHLT++E+PHSVAVVV+SMKRDEETDKVHIRATIMVERDSQK Sbjct: 181 ITDHPERFLVSEMVREKVLHLTREEIPHSVAVVVDSMKRDEETDKVHIRATIMVERDSQK 24- 0 Query: 256 GIIIGKQGAMLKKIGKMARRDIELMLGDKVYLETWVKVKKNWRDKKLDLADFGYNEKEY 314- GIIIGK GAMLKKIG MARRDIELMLGDKV+LETWVKVKKNWRDKKLDLADFGYNE+EY Sbjct: 241 GIIIGKGGAMLKKIGSMARRDIELMLGDKVFLETWVKVKKNWRDKKLDLADFGYNEREY 299- A related DNA sequence was identified in S. pyogenes <SEQ ID 6757> which encodes the amino acid sequence <SEQ ID 6758>. Analysis of this protein sequence reveals the following: TABLE-US-06700 Possible site: 38 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1088(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06701 Identities = 295/297 (99%), Positives = 296/297 (99%) Query: 18 FKSGFVAILGRPNVGKSTFLNHVMGQKIAIMSDKAQTTRNKIMGIYTTETEQIVFIDTPG 77 - FKSGFVAILGRPNVGKSTFLNHVMGQKIAIMSDKAQTTRNKIMGIYTTETEQIVFIDTPG Sbjct: 2 FKSGFVAILGRPNVGKSTFLNHVMGQKIAIMSDKAQTTRNKIMGIYTTETEQIVFIDTPG 61 Query: 78 IHKPKTALGDFMVESAYSTLREVETVLFMVPADEKRGKGDDMIIERLKAAKIPVILVINK 137- IHKPKTALGDFMVESAYSTLREVETVLFMVPADEKRGKGDDMIIERLKAAKIPVILVINK Sbjct: 62 IHKPKTALGDFMVESAYSTLREVETVLFMVPADEKRGKGDDMIIERLKAAKIPVILVINK 121- Query: 138 IDKVHPDQLLEQIDDFRSQMDFKEVVPISALQGNNVPTLIKLLTDNLEEGFQYFPEDQIT 19- 7 IDKVHPDQLLEQIDDF SQMDFKEVVPISAL+GNNVPTLIKLLTDNLEEGFQYFPEDQIT Sbjct: 122 IDKVHPDQLLEQIDDFHSQMDFKEVVPISALEGNNVPTLIKLLTDNLEEGFQYFPEDQIT 18- 1 Query: 198 DHPERFLVSEMVREKVLHLTQQEVPHSVAVVVESMKRDEETDKVHIRATIMVERDSQKGI 25- 7 DHPERFLVSEMVREKVLHLTQQEVPHSVAVVVESMKRDEETDKVHIRATIMVERDSQKGI Sbjct: 182 DHPERFLVSEMVREKVLHLTQQEVPHSVAVVVESMKRDEETDKVHIRATIMVERDSQKGI 24- 1 Query: 258 IIGKQGAMLKKIGKMARRDIELMLGDKVYLETWVKVKKNWRDKKLDLADFGYNEKEY 314 IIGKQGAMLKKIGKMARRDIELMLGDKVYLETWVKVKKNWRDKKLDLADFGYNEKEY Sbjct: 242 IIGKQGAMLKKIGKMARRDIELMLGDKVYLETWVKVKKNWRDKKLDLADFGYNEKEY 298 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2188 A DNA sequence (GBSx2305) was identified in S. agalactiae <SEQ ID 6759> which encodes the amino acid sequence <SEQ ID 6760>. Analysis of this protein sequence reveals the following: TABLE-US-06702 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2679(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2189 A DNA sequence (GBSx2306) was identified in S. agalactiae <SEQ ID 6761> which encodes the amino acid sequence <SEQ ID 6762>. Analysis of this protein sequence reveals the following: TABLE-US-06703 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06704 >GP: BAA16793 GB: D90900 hypothetical protein [Synechocystis sp.] Identities = 36/119 (30%), Positives = 57/119 (47%), Gaps = 15/119 (12%) Query: 390 TSDYEKAKVIHDHLVNNYTYATEELATTRETASGISIHAPEALYKDKRGVCQAFAVMFKD 44- 9 ++D+E+A++ + + N Y +A TR I PE + +C ++ +++ Sbjct: 153 SNDWEEARLAYSWITQNIAYDVP-MAETRN----IDDLRPETVLARGETICSGYSNLYQA 20- 7 Query: 450 MAATAGLSVWYVTGQAGGG----------NHAWNIVTINGVKYYVDTTWDNNIKSNKYF 498- +A GL V + G A GG NHAWN V I+G Y +DTTW I S+ F Sbjct: 208 LAKELGLDVVIIEGFAKGGDVIVGDDPDVNHAWNGVKIDGQWYLLDTTWGAGIVSDGKF 266- A related DNA sequence was identified in S. pyogenes <SEQ ID 6763> which encodes the amino acid sequence <SEQ ID 6764>. Analysis of this protein sequence reveals the following: TABLE-US-06705 Possible site: 23 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. An alignment of the GAS and GBS proteins is shown below. TABLE-US-06706 Identities = 41/181 (22%), Positives = 79/181 (42%), Gaps = 17/181 (9%) Query: 355 ITITYTLKGDMVGLHKEYKQFVDSFVKENITNKNITSDYEKAKVIHDHLVNNYTYATE-- 41- 2 + +T+ + D ++++ Q + + + N +K+ YE+ K ++ ++ + Y + Sbjct: 124 VFVTFPIPEDAKNIYQDL-QAIGNDIVANTPSKD---RYEQVKYFYEVIIRDTDYNKKAF 17- 9 Query: 413 ELATTRETASGISIHAPEALYKDKRGVCQAFAVMFKDMAATAGLSVWYVTGQAGGGN--- 46- 9 E + A S ++++ D VC +A F+ + AG+ V Y+ G Sbjct: 180 EAYQSGSQAQVASNQDIKSVFIDHLSVCNGYAQAFQFLCQKAGIPVAYIRGTGTSQQPQQ 23- 9 Query: 470 ---HAWNIVTINGVKYYVDTTW-----DNNIKSNKYFLVGKTIMDADHLLDSQYNALAKDI 5- 22 HAWN V IN Y VD TW DN++ K + + + L + + +KDI Sbjct: 240 SFAHAWNAVQINNTYYGVDVTWGDPVFDNHLSHQKQGTINYSFLCLPDYLMALSHQPSKDI 3- 00 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2190 A DNA sequence (GBSx2307) was identified in S. agalactiae <SEQ ID 6765> which encodes the amino acid sequence <SEQ ID 6766>. This protein is predicted to be rgg protein. Analysis of this protein sequence reveals the following: TABLE-US-06707 Possible site: 29 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 187-203 (187-203) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10015> which encodes amino acid sequence <SEQ ID 10016> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06708 >GP: AAA26968 GB: M89776 rgg [Streptococcus gordonii] Identities = 71/273 (26%), Positives = 140/273 (51%), Gaps = 16/273 (5%) Query: 8 KELGKTLRRLRKGKKVSISSLADEHLSKSQISRFERGESEITCSRLLNILDKLNITIDEF 67 K GK L+ +R+ K +S+ +A +S +Q+SR+ERG S +T + L +++++ EF Sbjct: 5 KSSGKILKIIRESKNMSLKEVAAGDISVAQLSRYERGISSLTVDSFYSCLRNMSVSLAEF 64 Query: 68 VSI-HSKAHTHFFILLNRVRKYCAEKNVTKLVALL-----------EDHNHKDYEKIMIK 115- + H+ +L ++ + E N+ KL ++L E N+K I+I+ Sbjct: 65 QYVYHNYREADDVVLSQKLSEAQRENNIVKLESILAGSEAMAQEFPEKKNYK-LNTIVIR 123- Query: 116 ALIFSIDQSIEPNQEELARLTDYLFTVEQWGYYEIILLGNCSRLINYNTLFLLTKEMVNS 17- 5 A + S + + ++ ++LTDYLF+VE+WG YE+ L N L+ TL EM+N Sbjct: 124 ATLTSCNPDYQVSKGDIEFLTDYLFSVEEWGRYELWLFTNSVNLLTLETLETFASEMINR 18- 3 Query: 176 FAYSEQNKTNKILVTQLAINCLIISIDHSYFEHSHYLIDKVRSLLQDEVNFYEKTVFLYV 23- 5 + N+ + ++ +N + I++++ + + ++ + + E + Y++ + Y Sbjct: 184 TQFYNNLPENRRRIIKMLLNVVSACIENNHLQVAMKFLNYIDNTKIPETDLYDRVLIKYH 24- 3 Query: 236 TGYYHLKLGDTSSGKEDMRKALQIFKYLGEDSF 268 Y K+G+ + + D+ + L F+YL DSF Sbjct: 244 KALYSYKVGNPHA-RHDIEQCLSTFEYL--DSF 273 There is also homology to SEQ ID 628. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2191 A DNA sequence (GBSx2308) was identified in S. agalactiae <SEQ ID 6767> which encodes the amino acid sequence <SEQ ID 6768>. Analysis of this protein sequence reveals the following: TABLE-US-06709 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3234(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06710 >GP: BAA05066 GB: D26071 formamidopyrimidine-DNA glycosylase [Streptococcus mutans] Identities = 182/271 (67%), Positives = 217/271 (79%) Query: 1 MPELPEVETVRKGLERLVVNQEIASITIKVPKMVKTDLNDFMISLPGKTIQQVLRRGKYL 60 MPELPEVETVR+GLE L+V ++I S+ ++VPKMVKT + DF + + G+T + + RRGKYL Sbjct: 1 MPELPEVETVRRGLEHLIVGKKIVSVEVRVPKMVKTGVEDFQLDILGQTFESIGRRGKYL 60 Query: 61 LFDFGEMVMVSHLRMEGKYLLFPNKVPDNKHFHLYFKLTNGSTLVYQDVRKFGTFELVRK 120- L + ++SHLRMEGKYLLF ++VPDNKHFHL+F L GSTLVYQDVRKFGTFEL+ K Sbjct: 61 LLNLNRQTIISHLRMEGKYLLFEDEVPDNKHFHLFFGLDGGSTLVYQDVRKFGTFELLPK 120- Query: 121 SSLKDYFTQKKLGPEPTADTFQFEPFSKGLANSKKPIKPLLLDQRLVAGLGNIYVDEVLW 18- 0 S ++ YF QKK+GPEP A F+ +PF +GLA S K IK LLLDQ LVAGLGNIYVDEVLW Sbjct: 121 SQVEAYFVQKKIGPEPNAKDFKLKPFEEGLAKSHKVIKTLLLDQHLVAGLGNIYVDEVLW 18- 0 Query: 181 AAKIHPQRLANQLTESETSLLHKEIIRILTLGIEKGGSTIRTYKNALGEDGTMQKYLQVY 24- 0 AAK+ P+RLA+QL SE +H E IRIL L IEKGGSTIR+YKN+LGEDG+MQ LQVY Sbjct: 181 AAKVDPERLASQLKTSEIKRIHDETIRILQLAIEKGGSTIRSYKNSLGEDGSMQDCLQVY 24- 0 Query: 241 GKTGQPCPRCGCLIKKIKVGGRGTHYCPRCQ 271 GKT QPC RC I+KIKVGGRGTH+CP CQ Sbjct: 241 GKTDQPCARCATPIEKIKVGGRGTHFCPSCQ 271 A related DNA sequence was identified in S. pyogenes <SEQ ID 6769> which encodes the amino acid sequence <SEQ ID 6770>. Analysis of this protein sequence reveals the following:

TABLE-US-06711 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2068(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06712 Identities = 190/271 (70%), Positives = 229/271 (84%) Query: 1 MPELPEVETVRKGLERLVVNQEIASITIKVPKMVKTDLNDFMISLPGKTIQQVLRRGKYL 60- MPELPEVETVR+GLE LV+ QEI ++T+KVPKMVKTDL F ++LPG+ IQ V RRGKYL Sbjct: 1 MPELPEVETVRRGLETLVLGQEIVAVTLKVPKMVKTDLETFALTLPGQIIQSVGRRGKYL 60- Query: 61 LFDFGEMVMVSHLRMEGKYLLFPNKVPDNKHFHLYFKLTNGSTLVYQDVRKFGTFELVRK 12- 0 L D G++V+VSHLRMEGKYLLFP++VPDNKHFH++F+L NGSTLVYQDVRKFGTE+L+ K Sbjct: 61 LIDLGQLVLVSHLRMEGKYLLFPDEVPDNKHFHVFFELKNGSTLVYQDVRKFGTFDLIAK 12- 0 Query: 121 SSLKDYFTQKKLGPEPTADTFQFEPFSKGLANSKKPIKPLLLDQRLVAGLGNIYVDEVLW 18- 0 S L +F ++KLGPEP +TF+ + F L +S+KPIKP LLDQ LVAGLGNIYVDEVLW Sbjct: 121 SQLSAFFAKRKLGPEFKKETFKLKTFEAALLSSQKPIKPHLLDQTLVAGLGNIYVDEVLW 18- 0 Query: 181 AAKIHPQRLANQLTESETSLLHKEIIRILTLGIEKGGSTIRTYKNALGEDGTMQKYLQVY 24- 0 AAK+HP+ +++L ++E LH E IRIL LGIEKGGST+RTY+NALG DGTMQ YLQVY Sbjct: 181 AAKVHPETASSRLNKAEIKRLHDETIRILALGIEKGGSTVRTYRNALGADGTMQDYLQVY 24- 0 Query: 241 GKTGQPCPRCGCLIKKIKVGGRGTHYCPRCQ 271 G+TG+PCPRCG I K+KVGGRGTH CP+CQ Sbjct: 241 GQTGKPCPRCGQAIVKLKVGGRGTHICPKCQ 271 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2192 A DNA sequence (GBSx2309) was identified in S. agalactiae <SEQ ID 6771> which encodes the amino acid sequence <SEQ ID 6772>. Analysis of this protein sequence reveals the following: TABLE-US-06713 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0797(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10013> which encodes amino acid sequence <SEQ ID 10014> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06714 >GP: AAC00353 GB: AF008220 YtaG [Bacillus subtilis] Identities = 80/189 (42%), Positives = 113/189 (59%), Gaps = 1/189 (0%) Query: 8 MTKIIGLTGGIASGKSTVTKIIRESGFKVIDADQVVHKLQAKGGKLYQALLEWLGPEILD 67- MT +IGLTGGIASGKSTV ++ E G VIDAD + + KG Y+ +++ G +IL Sbjct: 1 MTLVIGLTGGIASGKSTVANMLIEKGITVIDADIIAKQAVEKGMPAYRQIIDEFGEDILL 60- Query: 68 ADGELDRPKLSQMIFANPDNMKTSARLQNSIIRQELACQRDQLKQTEEIF-FMDIPLLIE 12- 6 ++G++DR KL ++F N + + +RQE+ +RD+ E F +DIPLL E Sbjct: 61 SNGDIDRKKLGALVFTNEQKRLALNAIVHPAVRQEMLNRRDEAVANREAFVVLDIPLLFE 12- 0 Query: 127 EKYIKWFDEIWLVFVDKEKQLQRLMARNNYSREEAELRLSHQMPLTDKKSFASLIIDNNG 18- 6 K D+I +V V KE QL+RLM RN + EEA R+ QMPL +K + A +IDN+G Sbjct: 121 SKLESLVDKIIVVSVTKELQLERLMKRNQLTEEEAVSRIRSQMPLEEKTARADQVIDNSG 18- 0 Query: 187 DLITLKEQI 195 L K Q+ Sbjct: 181 TLEETKRQL 189 A related sequence was also identified in GAS <SEQ ID 9111> which encodes the amino acid sequence <SEQ ID 9112>. Analysis of this protein sequence reveals the following: TABLE-US-06715 Possible cleavage site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.101(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06716 Identities = 118/191 (61%), Positives = 153/191 (79%) Query: 9 TKIIGLTGGIASGKSTVTKIIRESGFKVIDADQVVHKLQAKGGKLYQALLEWLGPEILDA 68- T IIG+TGGIASGKSTV K+IR++G++VIDADQVVH LQ KGG+LY+AL E G +IL A Sbjct: 9 TMIIGITGGIASGKSTVVKVIRKAGYQVIDADQVVHDLQEKGGRLYEALREAFGNQILKA 68- Query: 69 DGELDRPKLSQMIFANPDNMKTSARLQNSIIRQELACQRDQLKQTEEIFFMDIPLLIEEK 12- 8 DGELDR KLS+M+F+NPDNM TS+ +QN II++ELA +RD L Q++ IFFMDIPLL+E Sbjct: 69 DGELDRTKLSEMLFSNPDNMATSSAIQNQIIKEELAAKRDHLAQSQAIFFMDIPLLMELG 12- 8 Query: 129 YIKWFDEIWLVFVDKEKQLQRLMARNNYSREEAELRLSHQMPLTDKKSFASLIIDNNGDL 18- 8 Y WFD IWLV+VD + QLQRLMARN + +A R++ Q+P+ +KK +ASL+IDN+GD+ Sbjct: 129 YQDWFDAIWLVYVDAQTQLQRLMARNRLDKGKARQRIASQLPIEEKKPYASLVIDNSGDI 18- 8 Query: 189 ITLKEQILDAL 199 L +Q+ AL Sbjct: 189 AALIKQVQSAL 199 A related GBS gene <SEQ ID 8993> and protein <SEQ ID 8994> were also identified. Analysis of this protein sequence reveals a signal peptide at residues 1-16. The protein has homology with the following sequences in the databases: ##STR00159## A related DNA sequence was identified in S. pyogenes <SEQ ID 6773> which encodes amino acid sequence <SEQ ID 6774>. An alignment of the GAS and GBS sequences follows: TABLE-US-06717 Score = 218 bits (550), Expect = 4e-59 Identities = 104/175 (59%), Positives = 138/175 (78%) Query: 25 VVKVIRKAGYQVIDADQVVHDLQEKGGRLYEALREAFGNQILKADGELDRTKLSEMLFSN 84- V K+IR++G++VIDADQVVH LQ KGG+LY+AL E G +IL ADGELDR KLS+M+F+N Sbjct: 20 VTKIIRESGFKVIDADQVVHKLQAKGGKLYQALLEWLGPEILDADGELDRPKLSQMIFAN 79- Query: 85 PDNMATSSAIQNQIIKEELAAKRDHLAQSQAIFFMDIPLLMELGYQDWFDAIWLVYVDAQ 14- 4 PDNM TS+ +QN II++ELA +RD L Q++ IFFMDIPLL+E Y WFD IWLV+VD + Sbjct: 80 PDNMKTSARLQNSIIRQELACQRDQLKQTEEIFFMDIPLLIEEKYIKWFDEIWLVFVDKE 13- 9 Query: 145 TQLQRLMARNRLDKGKARQRIASQLPIEEKKPYASLVIDNSGDIAALIKQVQSAL 199 QLQRLMARN + +A R++ Q+P+ +KK +ASL+IDN+GD+ L +Q+ AL Sbjct: 140 KQLQRLMARNNYSREEAELRLSHQMPLTDKKSFASLIIDNNGDLITLKEQILDAL 194 SEQ ID 8994 (GBS245) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 61 (lane 6; MW 23.7 kDa). It was also expressed in E. coli as a GST-fusion product, and purified GBS245-GST is shown in FIG. 211, lane 6. The purified GST fusion product was used to immunise mice ands the resulting antiserum was used for FACS (FIG. 278). This confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2193 A DNA sequence (GBSx2310) was identified in S. agalactiae <SEQ ID 6775> which encodes the amino acid sequence <SEQ ID 6776>. Analysis of this protein sequence reveals the following: TABLE-US-06718 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4073(Affirmative) < succ> bacterial membrane --- Certainty - 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06719 >GP: BAA30330 GB: AP000005 253aa long hypothetical ATP-binding transport protein [Pyrococcus horikoshii] Identities = 78/240 (32%), Positives = 130/240 (53%), Gaps = 13/240 (5%) Query: 3 LVIRDIRKRFQETEVLRGASYRFYSGKITGVLGRNGAGKTTLFNILYGDLAADNGTICLL 62- +++ ++RK+F EVL+G ++ G+I G+LG NG+GK+T IL G + G + + Sbjct: 2 IIVENLRKKFGSKEVLKGINFTVNDGEIYGLLGPNGSGKSTTMRILSGIITDFEGKVMVA 61- Query: 63 -KDNHEYPLTDKDI-GIVYSENYLPEFLTGYEFVKFYMDLH--PSDDL-MTIDDYLDFME 11- 7 D P+ K+I G V L E LT EF F + P D L + +D Sbjct: 62 GVDVSRDPMKVKEIVGYVPETPALYESLTPAEFFSFIGGVRRIPQDILEERVKRLVDAFG 12- 1 Query: 118 IGQTERHRIIKGYSDGMKSKLSLICLMISKPKVILLDEPLTAVDVVSSIAIKRLLLELSE 17- 7 IG+ +++I S G K K+SLI ++ P+V++LDE + +D S+ + LL E E Sbjct: 122 IGK-YMNQLIGTLSFGTKQKISLISALLHDPQVLILDEAMNGLDPKSARIFRELLFEFKE 18- 0 Query: 178 D-HIIILSTHIMALAEDLCDIVAVLDKGKL---QTLDIDR---KHEQFEERLLQVLKGDE 23- 0 + I+ STHI+ALAE +CD + ++ +G++ T+D R + E+ E+ L++ + E Sbjct: 181 EGKSIVFSTHILALAEVMCDRIGIIYEGRIVAEGTIDELREIAREEKLEDIFLKLTQAKE 24- 0 There is also homology to SEQ ID 2876. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2194 A DNA sequence (GBSx2311) was identified in S. agalactiae <SEQ ID 6777> which encodes the amino acid sequence <SEQ ID 6778>. Analysis of this protein sequence reveals the following: TABLE-US-06720 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6138(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2195 A DNA sequence (GBSx2312) was identified in S. agalactiae <SEQ ID 6779> which encodes the amino acid sequence <SEQ ID 6780>. Analysis of this protein sequence reveals the following: TABLE-US-06721 Possible site: 20 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -15.34 Transmembrane 526-542 (511-546) INTEGRAL Likelihood = -9.61 Transmembrane 340-356 (335-359) INTEGRAL Likelihood = -8.17 Transmembrane 455-471 (451-476) INTEGRAL Likelihood = -8.01 Transmembrane 97-113 (95-121) INTEGRAL Likelihood = -8.01 Transmembrane 216-232 (207-236) INTEGRAL Likelihood = -3.40 Transmembrane 50-66 (46-67) INTEGRAL Likelihood = -1.33 Transmembrane 178-194 (178-194) ----- Final Results ----- bacterial membrane --- Certainty = 0.7135(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10011> which encodes amino acid sequence <SEQ ID 10012> was also identified. The protein has no significant homology with any sequences in the GENPEPT database, but there is homology to SEQ ID 376. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2196 A DNA sequence (GBSx2314) was identified in S. agalactiae <SEQ ID 6781> which encodes the amino acid sequence <SEQ ID 6782>. Analysis of this protein sequence reveals the following: TABLE-US-06722 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.17 Transmembrane 140-156 (134-160) INTEGRAL Likelihood = -6.64 Transmembrane 255-271 (253-274) INTEGRAL Likelihood = -5.79 Transmembrane 345-361 (343-363) INTEGRAL Likelihood = -3.29 Transmembrane 184-200 (183-202) INTEGRAL Likelihood = -2.34 Transmembrane 66-82 (65-83) INTEGRAL Likelihood = -1.65 Transmembrane 221-237 (221-239) INTEGRAL Likelihood = -0.00 Transmembrane 121-137 (121-137) ----- Final Results ----- bacterial membrane --- Certainty = 0.4270(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial Cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9401> which encodes amino acid sequence <SEQ ID 9402> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06723 >GP: CAA07482 GB: AJ007367 multi-drug resistance efflux pump [Streptococcus pneumoniae] Identities = 213/372 (57%), Positives = 295/372 (79%) Query: 1 MPFMVLYVEQLGAPSNKVEWYAGLSVSLSALSSALVAPLWGRLADKYGRKPMMVRAGLMM 60 +PFM ++VE LG S +V +YAGL++S+SA+S+AL +P+WG LADKYGRKPMM+RAGL M Sbjct: 28 VPFMPIFVENLGVGSQQVAFYAGLAISVSAISAALFSPIWGILADKYGRKPMMIRAGLAM 87 Query: 61 TFTMGGLAFIHSVTGLLILRILNGIFAGYVPNSTALIASQAPQEESGYALGTLATGVTGG 120- T TMGGLAF+ ++ L+ LR+LNG+FAG+VPN+TALIASQ P+E+SG ALGTL+TGV G Sbjct: 88 TITMGGLAFVPNIYWLIFLRLLNGVFAGFVPNATALIASQVPKEKSGSALGTLSTGVVAG 147- Query: 121 MLIGPLLGGLLAEWFGIREVFLLVGTILLISTLMTIFMVKEDFKPISNEETMPTTEVFKS 18- 0 L GP +GG +AE FGIR VFLLVG+ L ++ ++TI +KEDF+P++ E+ +PT E+F S Sbjct: 148 TLTGPFIGGFIAELFGIRTVFLLVGSFLFLAAILTICFIKEDFQPVAKEKAIPTKELFTS 20- 7 Query: 181 VKSLQILIGLFVTSMIIQISAQSIAPILTLYIRHLGQTENLMFVSGLIVSGMGFSSILSS 24- 0 VK +L+ LF+TS +IQ SAQSI PIL LY+R LGQTENL+FVSGLIVS MGFSS++S+ Sbjct: 208 VKYPYLLLNLFLTSFVIQFSAQSIGPILALYVRDLGQTENLLFVSGLIVSSMGFSSMMSA 26- 7 Query: 241 PKLGRIGDRIGNHRLLLLALLYSFLMYVLCSLAQTSLQLGVIRFLYGFGTGALMPSINSI 30- 0 +G++GD++GNHRLL++A YS ++Y+LC+ A + LQLG+ RFL+G GTGAL+P +N++ Sbjct: 268 GVMGKLGDKVGNHRLLVVAQFYSVIIYLLCANASSPLQLGLYRFLFGLGTGALIPGVNAL 32- 7 Query: 301 LTKIAPRQGLSRIFSYNQMFSNLGQVLGPFVGSAVSIHLGFRWVFFVTSFIVLANFVWCF 36- 0 L+K+ P+ G+SR+F++NQ+F LG V+GP GSAV+ G+ VF+ TS V + ++ Sbjct: 328 LSKMTPKAGISRVFAFNQVFFYLGGVVGPMAGSAVAGQFGYHAVFYATSLCVAFSCLFNL 38- 7 Query: 361 INFRKYIRVKEI 372 I FR ++VKEI Sbjct: 388 IQFRTLLKVKEI 399 A related DNA sequence was identified in S. pyogenes <SEQ ID 6783> which encodes the amino acid sequence <SEQ ID 6784>. Analysis of this protein sequence reveals the following: TABLE-US-06724 Possible site: 58 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.14 Transmembrane 165-181 (150-185) INTEGRAL Likelihood = -7.43 Transmembrane 371-387 (367-391) INTEGRAL Likelihood = -3.88 Transmembrane 90-106 (86-109) INTEGRAL Likelihood = -3.35 Transmembrane 145-161 (143-162) INTEGRAL Likelihood = -1.70 Transmembrane 279-295 (279-297) INTEGRAL Likelihood = -0.85 Transmembrane 209-225 (209-226) INTEGRAL Likelihood = -0.27 Transmembrane 347-363 (347-363) ----- Final Results ----- bacterial membrane --- Certainty = 0.5055(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06725 >GP: CAA07482 GB: AJ007367 multi-drug resistance efflux pump [Streptococcus pneumoniae] Identities = 236/396 (59%), Positives = 309/396 (77%) Query: 1 VNWRQNLKVAWLGNFFTGASFSLVMPFMALYVENLGTPTELVEYYAGLAVAVTALASALF 60 +NW+ NL++AW GNF TGAS SLV+PFM ++VENLG ++ V +YAGLA++V+A+++ALF Sbjct: 4 INWKDNLRIAWFGNFLTGASISLVVPFMPIFVENLGVGSQQVAFYAGLAISVSAISAALF 63 Query: 61 APVWGKLADRYGRKPMMLRASFVMTFTMGGLAIIPNVFWLLILRLLTGVSAGYVPNATAL 120- +P+WG LAD+YGRKPMM+RA MT TMGGLA +PN++WL+ LRLL GV AG+VPNATAL Sbjct: 64 SPIWGILADKYGRKPMMIRAGLAMTITMGGLAFVPNIYWLIFLRLLNGVFAGFVPNATAL 123- Query: 121 IASQAPKEESGYALGTLATGVTAGALIGPLLGGILAELLGIRQVFLLVGVILFLCSLMTA 18- 0 IASQ PKE+SG ALGTL+TGV AG L GP +GG +AEL GIR VFLLVG LFL +++T Sbjct: 124 IASQVPKEKSGSALGTLSTGVVAGTLTGPFIGGFIAELFGIRTVFLLVGSFLFLAAILTI 18- 3 Query: 181 VYVKEEFKPVRRFEMIPTKVILKQVKSPQIMLGLFVTSMIIQISAQSVAPILSLYIRHLG 24- 0 ++KE+F+PV + + IPTK + VK P ++L LF+TS +IQ SAQS+ PIL+LY+R LG Sbjct: 184 CFIKEDFQPVAKEKAIPTKELFTSVKYPYLLLNLFLTSFVIQFSAQSIGPILALYVRDLG 24- 3 Query: 241 QTHNLMFTSGLVVSAMGFSSLFSSSYLGKLGDRFGNHRLLLAALCYSFIMYFSSALAQTS 30- 0 QT NL+F SGL+VS+MGFSS+ S+ +GKLGD+ GNHRLL+ A YS I+Y A A + Sbjct: 244 QTENLLFVSGLIVSSMGFSSMMSAGVMGKLGDKVGNHRLLVVAQFYSVIIYLLCANASSP 30- 3 Query: 301 FQLGVLRFAYGFGVGALMPSINSLLTKLTPKEGISRVFAYNQMFSNLGQVIGPFIGSNVA 36- 0 QLG+ RF +G G GAL+P +N+LL+K+TPK GISRVFA+NQ+F LG V+GP GS VA Sbjct: 304 LQLGLYRFLFGLGTGALIPGVNALLSKMTPKAGISRVFAFNQVFFYLGGVVGPMAGSAVA 36- 3 Query: 361 VVLGYRSVFYVTSLIVFVNLIWSLIIFRKYIKVKDI 396 GY +VFY TSL V + +++LI FR +KVK+I Sbjct: 364 GQFGYHAVFYATSLCVAFSCLFNLIQFRTLLKVKEI 399 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06726 Identities = 262/373 (70%), Positives = 314/373 (83%) Query: 1 MPFMVLYVEQLGAPSNKVEWYAGLSVSLSALSSALVAPLWGRLADKYGRKPMMVRAGLMM 60 MPFM LYVE LG P+ VE+YAGL+V+++AL+SAL AP+WG+LAD+YGRKPMM+RA +M Sbjct: 25 MPFMALYVENLGTPTELVEYYAGLAVAVTALASALFAPVWGKLADRYGRKPMMLRASFVM 84 Query: 61 TFTMGGLAFIHSVTGLLILRILNGIFAGYVPNSTALIASQAPQEESGYALGTLATGVTGG 120- TFTMGGLA I +V LLILR+L G+ AGYVPN+TALIASQAP+EESGYALGTLATGVT G Sbjct: 85 TFTMGGLAIIPNVFWLLILRLLTGVSAGYVPNATALIASQAPKEESGYALGTLATGVTAG 144- Query: 121 MLIGPLLGGLLAEWFGIREVFLLVGTILLISTLMTIFMVKEDFKPISNEETMPTTEVFKS 18- 0 LIGPLLGG+LAE GIR+VFLLVG IL + +LMT VKE+FKP+ E +PT + K Sbjct: 145 ALIGPLLGGILAELLGIRQVFLLVGVILFLCSLMTAVYVKEEFKPVRRFEMIPTKVILKQ 20- 4 Query: 181 VKSLQILIGLFVTSMIIQISAQSIAPILTLYIRHLGQTENLMFVSGLIVSGMGFSSILSS 24- 0 VKS QI++GLFVTSMIIQISAQS+APIL+LYIRHLGQT NLMF SGL+VS MGFSS+ SS Sbjct: 205 VKSPQIMLGLFVTSMIIQISAQSVAPILSLYIRHLGQTHNLMFTSGLVVSAMGFSSLFSS 26- 4 Query: 241 PKLGRIGDRIGNHRLLLLALLYSFLMYVLCSLAQTSLQLGVIRFLYGFGTGALMPSINSI 30- 0 LG++GDR GNHRLLL AL YSF+MY +LAQTS QLGV+RF YGFG GALMPSINS+ Sbjct: 265 SYLGKLGDRFGNHRLLLAALCYSFIMYFSSALAQTSFQLGVLRFAYGFGVGALMPSINSL 32- 4 Query: 301 LTKIAPRQGLSRIFSYNQMFSNLGQVLGPFVGSAVSIHLGFRWVFFVTSFIVLANFVWCF 36- 0 LTK+ P++G+SR+F+YNQMFSNLGQV+GPF+GS V++ LG+R VF+VTS IV N +W Sbjct: 325 LTKLTPKEGISRVFAYNQMFSNLGQVIGPFIGSNVAVVLGYRSVFYVTSLIVFVNLIWSL 38- 4 Query: 361 INFRKYIRVKEIV 373 I FRKYI+VK+IV Sbjct: 385 IIFRKYIKVKDIV 397 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2197 A DNA sequence (GBSx2315) was identified in S. agalactiae <SEQ ID 6785> which encodes the amino acid sequence <SEQ ID 6786>. Analysis of this protein sequence reveals the following:

TABLE-US-06727 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2343(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06728 >GP: AAB69986 GB: U94356 glycerol kinase [Enterococcus faecalis] Identities = 156/186 (83%), Positives = 167/186 (88%), Gaps = 1/186 (0%) Query: 3 SEEKYIMAIDQGTTSSRAIIFNKKGEKIASSQKEFPQIFPQAGWVEHNANQIWNSVQSVI 62 +EEKYIMAIDQGTTSSRAIIF+KKG KI SSQKEF Q FP AGWVEHNAN+IWNSVQSVI Sbjct: 2 AEEKYIMAIDQGTTSSRAIIFDKKGNKIGSSQKEFTQYFPNAGWVEHNANEIWNSVQSVI 61 Query: 63 AGAFIESSIKPGQIEAIGITNQRETTVVWDKKTGLPIYNAIVWQSRQTAPIADQLKQEGH 122- AG+ IES +KP I IGITNQRETTVVWDK TGLPIYNAIVWQSRQT PIADQLK++G+ Sbjct: 62 AGSLIESGVRPTDIAGIGITNQRETTVVWDKATGLPIYNAIVWQSRQTTPIADQLKEDGY 121- Query: 123 TNMIHEKTGLVIDAYFSATKVRWILDHVPGAQERAEKGELLFGTIDTWLVWKLTDGLVHV 18- 2 + MIHEKTGL+IDAYFSATKVRWILDHV GAQERAE GEL+FGTIDTWLVWKLT G HV Sbjct: 122 SEMIHEKTGLIIDAYFSATKVRWILDHVEGAQERAENGELMFGTIDTWLVWKLT-GDTHV 18- 0 Query: 183 TDYSNA 188 TDYSNA Sbjct: 181 TDYSNA 186 There is also high homology to SEQ ID 2844: TABLE-US-06729 Identities = 174/186 (93%), Positives = 182/186 (97%) Query: 3 SEEKYIMAIDQGTTSSRAIIFNKKGEKIASSQKEFPQIFPQAGWVEHNANQIWNSVQSVI 62 S+EKYIMAIDQGTTSSRAIIFN+KGEK++SSQKEFPQIFP AGWVEHNANQIWNSVQSVI Sbjct: 2 SQEKYIMAIDQGTTSSRAIIFNQKGEKVSSSQKEFPQIFPHAGWVEHNANQIWNSVQSVI 61 Query: 63 AGAFIESSIKPGQIEAIGITNQRETTVVWDKKTGLPIYNAIVWQSRQTAPIADQLKQEGH 122- AGAFIESSIKP QIEAIGITNQRETTVVWDKKTG+PIYNAIVWQSRQTAPIA+QLKQ+GH Sbjct: 62 AGAFIESSIKPSQIEAIGITNQRETTVVWDKKTGVPIYNAIVWQSRQTAPIAEQLKQDGH 121- Query: 123 TNMIHEKTGLVIDAYFSATKVRWILDHVPGAQERAEKGELLFGTIDTWLVWKLTDGLVHV 18- 2 T MIHEKTGLVIDAYFSATK+RWILDHVPGAQERAEKGELLFGTIDTWLVWKLTDG VHV Sbjct: 122 TKMIHEKTGLVIDAYFSATKIRWILDHVPGAQERAEKGELLFGTIDTWLVWKLTDGAVHV 18- 1 Query: 183 TDYSNA 188 TDYSNA Sbjct: 182 TDYSNA 187 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2198 A DNA sequence (GBSx2317) was identified in S. agalactiae <SEQ ID 6787> which encodes the amino acid sequence <SEQ ID 6788>. This protein is predicted to be glycyl-tRNA synthetase beta chain (glyS). Analysis of this protein sequence reveals the following: TABLE-US-06730 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2933(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06731 >GP: CAB14468 GB: Z99117 glycyl-tRNA synthetase (beta subunit) [Bacillus subtilis] Identities = 315/687 (45%), Positives = 447/687 (64%), Gaps = 21/687 (3%) Query: 3 KDLLLELGLEELPAYVVTPSEKQLGQKMVKFLEDHRLSFETVQIFSTPRRLAVRVKGLAD 62 +DLLLE+GLEE+PA + S QLG K+ +L++ ++ V++F+TPRRLAV VK +A+ Sbjct: 4 QDLLLEIGLEEMPARFLNESMVQLGDKLTGWLKEKNITHGEVKLFNTPRRLAVFVKDVAE 63 Query: 63 QQTDLTEDFKGPSKKIALDAEGNFSKAAQGFVRGKGLSVDDIEFREVKGEEYVYVTKHET 122- +Q D+ E+ KGP+KKIALDA+GN++KAA GF +G+G +V+D+ +EVKG EYV+V K + Sbjct: 64 KQDDIKEEAKGPAKKIALDADGNWTKAAIGFSKGQGANVEDLYIKEVKGIEYVFVQKFQA 123- Query: 123 GKSAIDVLASVTEVLTELTFPVNMHWANNSFEYIRPVHTLVVLLDDQALELDFLDIHSGR 18- 2 G+ +L ++ ++T L FP NM W N YIRP+ +V L + ++ SGR Sbjct: 124 GQETKSLLPELSGLITSLHFPKNMRWGNEDLRYIRPIKWIVALFGQDVIPFSITNVESGR 18- 3 Query: 183 ISRGHRFLGSDTEISSASSYEDDLRQQFVIADAKERQQMIVNQIHAIEEKKNISVEIDED 24- 2 ++GHRFLG + I S S+YE+ L+ Q VIAD R+QMI +Q+ + + N S+ +DED Sbjct: 184 TTQGHRFLGHEVSIESPSAYEEQLKGQHVIADPSVRKQMIQSQLETMAAENNWSIPVDED 24- 3 Query: 243 LLNEVLNLVEYPTAFLGSFDEKYLDVPEEVLVTSMKNHQRYFVVRDRDGKLLPNFISVRN 30- 2 LL+EV +LVEYPTA GSF+ ++L +PEEVLVT+MK HQRYF V+D++G LLP+FI+VRN Sbjct: 244 LLDEVNHLVEYPTALYGSFESEFLSIPEEVLVTTMKEHQRYFPVKDKNGDLLPHFITVRN 30- 3 Query: 303 GNAEHIENVIKGNEKVLVARLEDGEFFWQEDQKLNIADLVEKLKQVTFHEKIGSLYEHMD 36- 2 GN+ IENV +GNEKVL ARL D FF++EDQKLNI V+KL+ + FHE++GSL + + Sbjct: 304 GNSHAIENVARGNEKVLRARLSDASFFYKEDQKLNIDANVKKLENIVFHEELGSLADKVR 36- 3 Query: 363 RVKVISQYLAEKADLSDEEKLAVLRAASIYKFDLLTGMVDEFDELQGIMGEKYALLAGEQ 42- 2 RV I++ LA + ++ V RAA I KFDL+T M+ EF ELQGIMGEKYA + GE Sbjct: 364 RVTSIAEKLAVRLQADEDTLKHVKRAAEISKFDLVTHMIYEFPELQGIMGEKYARMLGED 42- 3 Query: 423 PAVAAAIREHYMPTSADGELPETRVGAILALADKFDTLLSFFSVGLIPSGSNDPYALRRA 48- 2 AVAAA+ EHYMP SA GE P T GA++A+ADK DT+ SFFS+G+IP+GS DPY L R Sbjct: 424 EAVAAAVNEHYMPRSAGGETPSTFTGAVVAMADKLDTIASFFSIGVIPTGSQDPYGLPRQ 48- 3 Query: 483 TQGIVRILEAFGWDIPLDELVTNLYGLSFASLDYANQKEVMAFISARIEKMIGS-KVPKD 54- 1 GIV IL W I +EL+T F D N E++ F + R++ ++ + ++ D Sbjct: 484 ASGIVAILLDRNWGISFEELLT------FVQTDKEN--ELLDFFTQRLKYVLNAEQIRHD 53- 5 Query: 542 IREAVLESDTYIVSLILEASQALVQKSKDAQYKVSVESLSRAFNLAEKVTHSVLVDSSLF 60- 1 + +AVLES L +Q L QK +K + E+L R ++++K + LF Sbjct: 536 VIDAVLESSELEPYSALHKAQVLEQKLGAPGFKETAEALGRVISISKKGVRGD-IQPDLF 59- 4 Query: 602 ENNQEKALYQAILSLELTEDMHDNLDK---------LFALSPIINDFFDNTMVMTDDEKM 65- 2 EN E L+ A + + E++ +N K L AL I+ +FD+TMV+ D+E + Sbjct: 595 ENEYEAKLFDAYQTAK--ENLQENFSKKDYEAALASLAALKEPIDAYFDHTMVIADNESL 65- 2 Query: 653 KQNRLAILNSLVAKARTVAAFNLLNTK 679 K NRLA + SL + ++ A N L K Sbjct: 653 KANRLAQMVSLADEIKSFANMNALIVK 679 A related DNA sequence was identified in S. pyogenes <SEQ ID 2835> which encodes the amino acid sequence <SEQ ID 2836>. Analysis of this protein sequence reveals the following: TABLE-US-06732 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.96 Transmembrane 450-466 (450-466) ----- Final Results ----- bacterial membrane --- Certainty = 0.1383(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06733 Identities = 505/679 (74%), Positives = 578/679 (84%) Query: 1 MTKDLLLELGLEELPAYVVTPSEKQLGQKMVKFLEDHRLSFETVQIFSTPRRLAVRVKGL 60 M+K+LL+ELGLEELPAYVVTPSEKQLG+++ FL ++RLSFE +Q FSTPRRLAVRV GL Sbjct: 1 MSKNLLIELGLEELPAYVVTPSEKQLGERLATFLTENRLSFEDIQTFSTPRRLAVRVSGL 60 Query: 61 ADQQTDLTEDFKGPSKKIALDAEGNFSKAAQGFVRGKGLSVDDIEFREVKGEEYVYVTKH 120- ADQQTDLTEDFKGP+KKIALDA+GNFSKAAQGFVRGKGL+ D IEFREVKGEEYVYVTKH Sbjct: 61 ADQQTDLTEDFKGPAKKIALDADGNFSKAAQGFVRGKGLTTDAIEFREVKGEEYVYVTKH 120- Query: 121 ETGKSAIDVLASVTEVLTELTFPVNMHWANNSFEYIRPVHTLVVLLDDQALELDFLDIHS 18- 0 E GK A +VL VTEVL+ +TFPV+MHWANNSFEYIRPVHTL VLL+D+ALELDFLDIHS Sbjct: 121 EAGKPAKEVLLGVTEVLSAMTFPVSMHWANNSFEYIRPVHTLTVLLNDEALELDFLDIHS 18- 0 Query: 181 GRISRGHRFLGSDTEISSASSYEDDLRQQFVIADAKERQQMIVNQIHAIEEKKNISVEID 24- 0 GR+SRGHRFLG++T I+SA SYE DLR QFVIADAKERQ+MIV QI +E ++ + V+ID Sbjct: 181 GRVSRGHRFLGTETTITSADSYEADLRSQFVIADAKERQEMIVEQIKTLEVEQGVQVDID 24- 0 Query: 241 EDLLNEVLNLVEYPTAFLGSFDEKYLDVPEEVLVTSMKNHQRYFVVRDRDGKLLPNFISV 30- 0 EDLLNEVLNLVE+PTAF+GSF+ KYLDVPEEVLVTSMKNHQRYFVVRD+ G L+PNF+SV Sbjct: 241 EDLLNEVLNLVEFPTAFMGSFEAKYLDVPEEVLVTSMKNHQRYFVVRDQAGHLMPNFVSV 30- 0 Query: 301 RNGNAEHIENVIKGNEKVLVARLEDGEFFWQEDQKLNIADLVEKLKQVTFHEKIGSLYEH 36- 0 RNGN + IENVIKGNEKVLVARLEDGEFFW+EDQKL IADLV KL VTFHEKIGSL EH Sbjct: 301 RNGNDQAIENVIKGNEKVLVARLEDGEFFWREDQKLQIADLVAKLTNVTFHEKIGSLAEH 36- 0 Query: 361 MDRVKVISQYLAEKADLSDEEKLAVLRAASIYKFDLLTGMVDEFDELQGIMGEKYALLAG 42- 0 MDR +VI+ LA++A+LS EE AV RAA IYKFDLLTGMV EFDELQGIMGEKYALLAG Sbjct: 361 MDRTRVIAASLAKEANLSAEEVTAVDRAAQIYKFDLLTGMVGEFDELQGIMGEKYALLAG 42- 0 Query: 421 EQPAVAAAIREHYMPTSADGELPETRVGAILALADKFDTLLSFFSVGLIPSGSNDPYALR 48- 0 E AVA AIREHY+P +A G LPET+VGA+LALA K DTLLSFFSVGLIPSGSNDPYALR Sbjct: 421 EDAAVATAIREHYLPDAAGGALPETKVGAVLALAAKLDTLLSFFSVGLIPSGSNDPYALR 48- 0 Query: 481 RATQGIVRILEAFGWDIPLDELVTNLYGLSFASLDYANQKEVMAFISARIEKMIGSKVPK 54- 0 RATQGIVRIL+ FGW IP+D+LV +LY LSF SL YAN+ +VM FI AR++KM+G PK Sbjct: 481 RATQGIVRILDHFGWRIPMDKLVDSLYDLSFDSLTYANKADVMNFIRARVDKMMGKAAPK 54- 0 Query: 541 DIREAVLESDTYIVSLILEASQALVQKSKDAQYKVSVESLSRAFNLAEKVTHSVLVDSSL 60- 0 DIREA+L S T++V +L A++ALV+ S YK +VESLSRAFNLAEK SV VD SL Sbjct: 541 DIREAILASSTFVVPEMLAAAEALVKASHTENYKPAVESLSRAFNLAEKADASVQVDPSL 60- 0 Query: 601 FENNQEKALYQAILSLELTEDMHDNLDKLFALSPIINDFFDNTMVMTDDEKMKQNRLAIL 66- 0 FEN QE L+ AI L L L+++FALSP+INDFFDNTMVM D+ +K NRLAIL Sbjct: 601 FENEQENTLFAAIQGLTLAGSAAQQLEQVFALSPVINDFFDNTMVMAGDQALKNNRLAIL 66- 0 Query: 661 NSLVAKARTVAAFNLLNTK 679 + LV+KA+T+ AFN LNTK Sbjct: 661 SDLVSKAKTIVAFNQLNTK 679 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2199 A DNA sequence (GBSx2318) was identified in S. agalactiae <SEQ ID 6789> which encodes the amino acid sequence <SEQ ID 6790>. Analysis of this protein sequence reveals the following: TABLE-US-06734 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2182(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06735 >GP: AAD24436 GB: AF112858 NAD(P)H dehydrogenase [Bacillus stearothermophilus] Identities = 64/174 (36%), Positives = 98/174 (55%), Gaps = 6/174 (3%) Query: 2 NTLIVNSHPDFSNPYSFTTILQEKFIELYNEHFPNHQLSILNLYDCVLPEITKEVLLSIW 61 N L + +HP + S++ + + FI+ Y + P+H++ L+LY +PEI +V S W Sbjct: 3 NVLYITAHPH-DDTQSYSMAVGKAFIDTYKQVHPDHEVIHLDLYKEYIPEIDVDVF-SGW 60 Query: 62 SKQRKGL---ELTADEIVQAKISKDLLEQFKSHHRIVFVSPMHNYNVTARAKTYIDNIFI 118- K R G EL+ +E + +L EQF S + VFV+PM N++ K YID + + Sbjct: 61 GKLRSGKSFEELSDEEKAKVGRMNELCEQFISADKYVFVTPMWNFSFPPVLKAYIDAVAV 120- Query: 119 AGETFKYTENGSVGLMTDDYRLLMLESAGSIYSKGQYSPYEFPVHYLKAIFKDF 172 AG+TFKYTE G VGL+TD + L +++ G YS+G + E YL I + F Sbjct: 121 AGKTFKYTEQGPVGLLTDK-KALHIQARGGFYSEGPAAEMEMGHRYLSVIMQFF 173 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2200 A DNA sequence (GBSx2319) was identified in S. agalactiae <SEQ ID 6791> which encodes the amino acid sequence <SEQ ID 6792>. This protein is predicted to be glycyl-tRNA synthetase (glyQ). Analysis of this protein sequence reveals the following: TABLE-US-06736 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1364(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9521> which encodes amino acid sequence <SEQ ID 9522> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06737 >GP: BAB05089 GB: AP001511 glycyl-tRNA synthetase (alpha subunit) [Bacillus halodurans] Identities = 222/287 (77%), Positives = 250/287 (86%) Query: 6 LTFQEIILTLQQFWNDQGCMLMQAYDNEKGAGTMSPYTFLRAIGPEPWNAAYVEPSRRPA 65 + Q +ILTLQ++W+ Q C+L+QAYD EKGAGTMSPYT LR IGPEPWN AYVEPSRRPA Sbjct: 1 MNVQTMILTLQEYWSKQNCILLQAYDTEKGAGTMSPYTMLRTIGPEPWNVAYVEPSRRPA 60 Query: 66 DGRYGENPNRLYQHHQFQVVMKPSPSNIQELYLKSLELLGINPLEHDIRFVEDNWENPST 125- DGRYGENPNRLYQHHQFQV+MKPSP+NIQELYL SL LGINPLEHDIRFVEDNWENPS Sbjct: 61 DGRYGENPNRLYQHHQFQVIMKPSPTNIQELYLDSLRALGINPLEHDIRFVEDNWENPSL 120- Query: 126 GSAGLGWEVWLDGMEITQFTYFQQVGGLQTGPVTSEVTYGLERLASYIQEVDSVYDIEWA 18- 5 G AGLGWEVWLDGMEITQFTYFQQVGGL+ PV++E+TYGLERLASYIQ+ ++V+D+EW Sbjct: 121 GCAGLGWEVWLDGMEITQFTYFQQVGGLEANPVSAEITYGLERLASYIQDKENVFDLEWV 18- 0 Query: 186 PGVKYGEIFTQPEYEHSKYSFEISDQVMLLENFEKFEREAKRALEEGLVHPAYDYVLKCS 24- 5 G YG+IFTQPEYEHSKY+FE+SD ML E F +E+EA RALEE LV PAYDYVLKCS Sbjct: 181 EGFTYGDIFTQPEYEHSKYTFEVSDSAMLFELFSTYEKEADRALEENLVFPAYDYVLKCS 24- 0 Query: 246 HTFNLLDARGAVSVTERAGYIARIRNLARVVAKTFVAERKKLGFPLL 292 HTFNLLDARGA+SVTER GYI R+RNLAR AK + ER+KLGFP+L Sbjct: 241 HTFNLLDARGAISVTERTGYIGRVRNLARKCAKKYYEEREKLGFPML 287 A related DNA sequence was identified in S. pyogenes <SEQ ID 6793> which encodes the amino acid sequence <SEQ ID 6794>. Analysis of this protein sequence reveals the following: TABLE-US-06738 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2081(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06739 Identities = 290/304 (95%), Positives = 294/304 (96%) Query: 2 MSKKLTFQEIILTLQQFWNDQGCMLMQAYDNEKGAGTMSPYTFLRAIGPEPWNAAYVEPS 61 MSKKLTFQEIILTLQQ+WNDQGCMLMQAYDNEKGAGTMSPYTFLRAIGPEPWNAAYVEPS Sbjct: 1 MSKKLTFQEIILTLQQYWNDQGCMLMQAYDNEKGAGTMSPYTFLRAIGPEPWNAAYVEPS 60 Query: 62 RRPADGRYGENPNRLYQHHQFQVVMKPSPSNIQELYLKSLELLGINPLEHDIRFVEDNWE 121- RRPADGRYGENPNRLYQHHQFQVVMKPSPSNIQELYL SLE LGINPLEHDIRFVEDNWE Sbjct: 61 RRPADGRYGENPNRLYQHHQFQVVMKPSPSNIQELYLASLEKLGINPLEHDIRFVEDNWE 120- Query: 122 NPSTGSAGLGWEVWLDGMEITQFTYFQQVGGLQTGPVTSEVTYGLERLASYIQEVDSVYD 18- 1 NPSTGSAGLGWEVWLDGMEITQFTYFQQVGGL T PVT+EVTYGLERLASYIQEVDSVYD Sbjct: 121 NPSTGSAGLGWEVWLDGMEITQFTYFQQVGGLATSPVTAEVTYGLERLASYIQEVDSVYD 18- 0 Query: 182 IEWAPGVKYGEIFTQPEYEHSKYSFEISDQVMLLENFEKFEREAKRALEEGLVHPAYDYV 24- 1 IEWAPGVKYGEIF QPEYEHSKYSFEISDQ MLLENFEKFE+EA RALEEGLVHPAYDYV Sbjct: 181 IEWAPGVKYGEIFLQPEYEHSKYSFEISDQDMLLENFEKFEKEASRALEEGLVHPAYDYV 24- 0 Query: 242 LKCSHTFNLLDARGAVSVTERAGYIARIRNLARVVAKTFVAERKKLGFPLLDEETRIKLL 30- 1 LKCSHTFNLLDARGAVSVTERAGYIARIRNLARVVAKTFVAERKKLGFPLLDE TR LL Sbjct: 241 LKCSHTFNLLDARGAVSVTERAGYIARIRNLARVVAKTFVAERKKLGFPLLDEATRAILL 30- 0 Query: 302 AEED 305 AE+D Sbjct: 301 AEDD 304 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2201 A DNA sequence (GBSx2320) was identified in S. agalactiae <SEQ ID 6795> which encodes the amino acid sequence <SEQ ID 6796>. This protein is predicted to be vacB protein (vacB). Analysis of this protein sequence reveals the following: TABLE-US-06740 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2966(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9399> which encodes amino acid sequence <SEQ ID 9400> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06741 >GP: CAB15366 GB: Z99121 similar to hypothetical proteins [Bacillus subtilis] Identities = 338/780 (43%), Positives = 485/780 (61%), Gaps = 47/780 (6%) Query: 4 AKAFPKLIKTISNLESHRQL---RFDDNGSLSLQKKEAKKKEITVRGLFRANKAGFGFL- 59 A+ F +L+K + LE + R D G +K ++G A+ GF FL Sbjct: 36 AEEFKELVKALVALEEKGLIVRTRSDRYG--------IPEKMNLIKGKISAHAKGFAFLL 87 Query: 60 SIDQDEDDMFIGKNDIAYAIDGDTVEAVVKKPADRLNGTAAEARVVNIVERSLKTLVGKF 119- D D+FI N++ A++GD V + + +G+ E V+ I+ER+++ +VG + Sbjct: 88 PEDTSLSDVFIPPNELNTAMNGDIVMVRLNSQS---SGSRQEGTVIRILERAIQRVVGTY 144- Query: 120 VLDDERPKYAGYIKSKNQKINQKIYIRKEPV--VLDGTEIIKVDIDKYPTRGHDYFVASV 17- 7 + G++ ++KI I+I K +G +++ V + YP G V Sbjct: 145 T----ETRNFGFVIPDDKKITSDIFIPKNGKNGAAEGHKVV-VKLTSYP-EGRMNAEGEV 19- 8 Query: 178 RDIVGHQGDVGIDVLEVLESMDIVSEFPEDVIAEANAIPDAPTEKDLIGRVDLRQEVTFT 23- 7 I+GH+ D GID+L V+ + EFP D + +A++ PD EKDL R DLR +V T Sbjct: 199 ETILGHKNDPGIDILSVIHKHGLPGEFPADAMEQASSTPDTIDEKDLKDRRDLRDQVIVT 25- 8 Query: 238 IDGADAKDLDDAVHIKLLDNGHFELGVHIADVSYYVTEGSALNREALSRGTSVYVTDRVV 29- 7 IDGADAKDLDDAV + LD+G ++LGVHIADVS+YVTE S +++EAL RGTSVY+ DRV+ Sbjct: 259 IDGADAKDLDDAVTVTKLDDGSYKLGVHIADVSHYVTENSPIDKEALERGTSVYLVDRVI 31- 8 Query: 298 PMLPERLSNGICSLNPNLDRLTQSCIMEIDQNGRVVNHQITQSVINTTYRMTYTAVNDII 35- 7 PM+P RLSNGICSLNP +DRLT SC M I+ G+V H+I QSVI TT RMTY+ VN I+ Sbjct: 319 PMIPHRLSNGICSLNPKVDRLTLSCEMTINSQGQVTEHEIFQSVIKTTERMTYSDVNKIL 37- 8 Query: 358 A-GDEEICSEYESIVSSVQHMVTLHHTLEAMRTRRGALNFDTSEAKIMVNDKGMPVDIVI 41- 6 DEE+ +YE +V + M L L R RGA++FD EAK++V+D+G D+VI Sbjct: 379 VDDDEELKQKYEPLVPMFKDMERLAQILRDKRMDRGAVDFDFKEAKVLVDDEGAVKDVVI 43- 8 Query: 417 RNRGIAERMIESFMLAANETVAEHYARLKLPFIYRIHEEPKAEKLQKFIDYASVFGVQIQ 47- 6 R R +AE++IE FML ANETVAEH+ + +PFIYRIHEEP AEKLQKF+++ + FG ++ Sbjct: 439 RERSVAEKLIEEFMLVANETVAEHFHWMNVPFIYRIHEEPNAEKLQKFLEFVTTFGYVVK 49- 8 Query: 477 GTATKITQSALQDFMKKVQGQPGSEVLSMMLLRSMQQARYSEHNHGHYGLAAEYYTHFTS 53- 6 GTA I ALQ + V+ +P V+S ++LRSM+QA+Y + GH+GL+ E+YTHFTS Sbjct: 499 GTAGNIHPRALQSILDAVRDRPEETVISTVMLRSMKQAKYDPQSLGHFGLSTEFYTHFTS 55- 8 Query: 537 PIRRYPDLLVHRMIRDY-DDKAMDKA--DHFANLIPEIATQTSSLERRAIDAERIVEAMK 59- 3 PIRRYPDL+VHR+IR Y + +D+A + +A +P+IA TSS+ERRA+DAER + +K Sbjct: 559 PIRRYPDLIVHRLIRTYLINGKVDEATQEKWAERLPDIAEHTSSMERRAVDAERETDDLK 61- 8 Query: 594 KAEYMEEYVGEEFEGVVASVVKFGMFVELPNTIEGLIHVTTL-PEYYHFNERTLTLQGEK 65- 2 KAEYM + +GEEF+G+++SV FGMFVELPNTIEGL+HV+ + +YY F+E+ + GE+ Sbjct: 619 KAEYMLDKIGEEFDGMISSVTNFGMFVELPNTIEGLVHVSFMTDDYYRFDEQHFAMIGER 67- 8 Query: 653 SGKVFRVGQQIKVKLIRSDKETGDIDFDYLPSDFDIVEKVSKSSREGRPNRSSKREHQHR 71- 2 +G VFR+G +I VK++ +K+ +IDF+ + +G P R + + Sbjct: 679 TGNVFRIGDEITVKVVDVNKDERNIDFEIV-------------GMKGTPRRPRELD---- 72- 1 Query: 713 ISDRDNKNKNTSKKKASRKPKRNSDSKSHHHKDDRTTGSTKKKTKKPFYKGVAKKGQKRK 77- 2 S R K ++K+ S + S K + T KKK K+ F +K +K+K Sbjct: 722 -SSRSRKRGKPARKRVQSTNTPVSPAPS-EEKGEWFTKPKKKKKKRGFQNAPKQKRKKKK 77- 9 A related DNA sequence was identified in S. pyogenes <SEQ ID 6797> which encodes the amino acid sequence <SEQ ID 6798>. Analysis of this protein sequence reveals the following:

TABLE-US-06742 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0811(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06743 Identities = 579/773 (74%), Positives = 664/773 (84%), Gaps = 22/773 (2%) Query: 1 MAGAKAFPKLIKTISNLESHRQLRFDDNGSLSLQKKEAKKKEITVRGLFRANKAGFGFLS 60 MAGAK FP LIKTIS +ES LRF D+GSL+L+K+ KKKE TV+G+FRANKAGFGFL Sbjct: 27 MAGAKHFPSLIKTISKMESQSLLRFSDDGSLALRKEREKKKEPTVQGVFRANKAGFGFLH 86 Query: 61 IDQDEDDMFIGKNDIAYAIDGDTVEAVVKKPADRLNGTAAEARVVNIVERSLKTLVGKFV 120- +D++EDDMFIG+ND+ YAIDGDTVE VVKKPADRL GTAAEA+VV IV+RSLKT VG F+ Sbjct: 87 VDENEDDMFIGRNDVGYAIDGDTVEVVVKKPADRLKGTAAEAKVVAIVDRSLKTAVGTFI 146- Query: 121 LDDERPKYAGYIKSKNQKINQKIYIRKEPVVLDGTEIIKVDIDKYPTRGHDYFVASVRDI 18- 0 LDD++PKYAGYI+SKNQKI QKIYI+KEPVVL GTEIIKVDIDKYP RGHDYFVASVRDI Sbjct: 147 LDDDKPKYAGYIRSKNQKIQQKIYIKKEPVVLKGTEIIKVDIDKYPIRGHDYFVASVRDI 20- 6 Query: 181 VGHQGDVGIDVLEVLESMDIVSEFPEDVIAEANAIPDAPTEKDLIGRVDLRQEVTFTIDG 24- 0 VGHQGDVGIDVLEVLESMDIVSEFP +V+AEANAI +APT KDLIGRVDLRQE T TIDG Sbjct: 207 VGHQGDVGIDVLEVLESMDIVSEFPAEVLAEANAISEAPTAKDLIGRVDLRQETTITIDG 26- 6 Query: 241 ADAKDLDDAVHIKLLDNGHFELGVHIADVSYYVTEGSALNREALSRGTSVYVTDRVVPML 30- 0 ADAKDLDDA+HIKLLDNG++ELGVHIADVSYYVTEGSAL++EA++RGTSVYVTDRVVPML Sbjct: 267 ADAKDLDDAIHIKLLDNGNYELGVHIADVSYYVTEGSALDKEAIARGTSVYVTDRVVPML 32- 6 Query: 301 PERLSNGICSLNPNLDRLTQSCIMEIDQNGRVVNHQITQSVINTTYRMTYTAVNDIIAGD 36- 0 PERLSNGICSLNPN+DRLTQS +MEI+ G VVN+QI QSVI TTYRMTY+ VND+IAGD Sbjct: 327 PERLSNGICSLNPNIDRLTQSALMEINSQGHVVNYQICQSVIKTTYRMTYSTVNDMIAGD 38- 6 Query: 361 EEICSEYESIVSSVQHMVTLHHTLEAMRTRRGALNFDTSEAKIMVNDKGMPVDIVIRNRG 42- 0 EE E+ SI V MV LH LEAMR++RGALNFDT EAKI+VNDKGMPVD+V+R RG Sbjct: 387 EEALQEFASIADDVTLMVALHRILEAMRSKRGALNFDTQEAKIIVNDKGMPVDVVLRQRG 44- 6 Query: 421 IAERMIESFMLAANETVAEHYARLKLPFIYRIHEEPKAEKLQKFIDYASVFGVQIQGTAT 48- 0 IAERMIESFMLAANE VAEH+A+ KLPFIYRIHEEPKAEKLQ+FIDYAS FG+ IQGTA Sbjct: 447 IAERMIESFMLAANECVAEHFAKAKLPFIYRIHEEPKAEKLQQFIDYASTFGIHIQGTAN 50- 6 Query: 481 KITQSALQDFMKKVQGQPGSEVLSMMLLRSMQQARYSEHNHGHYGLAAEYYTHFTSPIRR 54- 0 KI+Q ALQ FM KV+GQPG+EVL+MMLLRSMQQARYSEHNHGHYGLAAEYYTHFTSPIRR Sbjct: 507 KISQEALQAFMAKVEGQPGAEVLNMMLLRSMQQARYSEHNHGHYGLAAEYYTHFTSPIRR 56- 6 Query: 541 YPDLLVHRMIRDYDDKAMDKADHFANLIPEIATQTSSLERRAIDAERIVEAMKKAEYMEE 60- 0 YPDLLVHRM+R+Y+ + +K DHFA +IPE+AT +S LERRAIDAER+VEAMKKAEYM E Sbjct: 567 YPDLLVHRMVREYNQPSQEKRDHFAQIIPELATSSSQLERRAIDAERVVEAMKKAEYMAE 62- 6 Query: 601 YVGEEFEGVVASVVKFGMFVELPNTIEGLIHVTTLPEYYHFNERTLTLQGEKSGKVFRVG 66- 0 YVGEEF+G+V+SVVKFG FVELPNTIEGL+H+T+LPEYYHFNERTL+LQGEKSGKVF+VG Sbjct: 627 YVGEEFDGIVSSVVKFGFFVELPNTIEGLVHITSLPEYYHFNERTLSLQGEKSGKVFKVG 68- 6 Query: 661 QQIKVKLIRSDKETGDIDFDYLPSDFDIVEKVSKSSREGRPNRSSKREHQHRISDRDNKN 72- 0 Q I+VKL+++DKETGDIDF+YLPSDFD+VEK+ S + R +R K+ Sbjct: 687 QPIRVKLVKADKETGDIDFEYLPSDFDVVEKIKMSDKASRRDR--------------RKS 73- 2 Query: 721 KNTSKKKASRKPKRNSDSKSHHHKDDRTTGSTKKKTKKPFYKGVAKKGQKRKS 773 +SK ++PK + +K T G TKK +KKPFYK AKK +++S Sbjct: 733 SKSSKGTKKKEPKEVAKAK--------TKGKTKKGSKKPFYKEQAKKKSRKRS 777 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2202 A DNA sequence (GBSx2321) was identified in S. agalactiae <SEQ ID 6799> which encodes the amino acid sequence <SEQ ID 6800>. This protein is predicted to be VacB homolog (smpB). Analysis of this protein sequence reveals the following: TABLE-US-06744 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2988(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06745 >GP: AAC23745 GB: AF052209 VacB homolog [Streptococcus pneumoniae] Identities = 121/155 (78%), Positives = 139/155 (89%) Query: 1 MVKGQGNVVAQNKKAHHDYTIVETIEAGIVLTGTEIKSVRAARITLKDGYAQIKNGEAWL 60 M KG+G VVAQNKKA HDYTIV+T+EAG+VLTGTEIKSVRAARI LKDG+AQ+KNGE WL Sbjct: 1 MAKGEGKVVAQNKKARHDYTIVDTLEAGMVLTGTEIKSVRAARINLKDGFAQVKNGEVWL 60 Query: 61 INVHITPYDQGNIWNQDPDRTRKLLLKKREIEKISNELKGTGMTLVPLKVYLKDGFAKVL 120- NVHI PY++GNIWNQ+P+R RKLLL K++I+K+ E KGTGMTLVPLKVY+KDG+AK+L Sbjct: 61 SNVHIAPYEEGNIWNQEPERRRKLLLHKKQIQKLEQETKGTGMTLVPLKVYIKDGYAKLL 120- Query: 121 LGLAKGKHDYDKRESIKRREQNRDIARQLKNYNSR 155 LGLAKGKHDYDKRESIKRREQNRDIAR +K N R Sbjct: 121 LGLAKGKHDYDKRESIKRREQNRDIARVMKAVNQR 155 A related DNA sequence was identified in S. pyogenes <SEQ ID 6801> which encodes the amino acid sequence <SEQ ID 6802>. Analysis of this protein sequence reveals the following: TABLE-US-06746 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2918(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06747 Identities = 124/155 (80%), Positives = 145/155 (93%) Query: 1 MVKGQGNVVAQNKKAHHDYTIVETIEAGIVLTGTEIKSVRAARITLKDGYAQIKNGEAWL 60 M KG+G+++AQNKKA HDY IVET+EAGIVLTGTEIKSVRAARI LKDG+AQIKNGEAWL Sbjct: 1 MAKGEGHILAQNKKARHDYHIVETVEAGIVLTGTEIKSVRAARIQLKDGFAQIKNGEAWL 60 Query: 61 INVHITPYDQGNIWNQDPDRTRKLLLKKREIEKISNELKGTGMTLVPLKVYLKDGFAKVL 120- +NVHI P++QGNIWN DP+RTRKLLLKKREI ++NELKG+GMTLVPLKVYLKDGFAKVL Sbjct: 61 VNVHIAPFEQGNIWNADPERTRKLLLKKREITHLANELKGSGMTLVPLKVYLKDGFAKVL 120- Query: 121 LGLAKGKHDYDKRESIKRREQNRDIARQLKNYNSR 155 +GLAKGKH+YDKRE+IKRR+Q RDI +Q+K+YN+R Sbjct: 121 IGLAKGKHEYDKRETIKRRDQERDIKKQMKHYNAR 155 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2203 A DNA sequence (GBSx2322) was identified in S. agalactiae <SEQ ID 6803> which encodes the amino acid sequence <SEQ ID 6804>. Analysis of this protein sequence reveals the following: TABLE-US-06748 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6876(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2204 A DNA sequence (GBSx2323) was identified in S. agalactiae <SEQ ID 6805> which encodes the amino acid sequence <SEQ ID 6806>. This protein is predicted to be d-serine/d-alanine/glycine transporter (cycA). Analysis of this protein sequence reveals the following: TABLE-US-06749 Possible site: 55 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.02 Transmembrane 71-87 (62-90) INTEGRAL Likelihood = -8.92 Transmembrane 320-336 (316-344) INTEGRAL Likelihood = -8.33 Transmembrane 254-270 (251-275) INTEGRAL Likelihood = -6.00 Transmembrane 158-174 (154-175) INTEGRAL Likelihood = -2.76 Transmembrane 197-213 (196-213) INTEGRAL Likelihood = -2.50 Transmembrane 117-133 (116-136) INTEGRAL Likelihood = -1.38 Transmembrane 282-298 (279-298) INTEGRAL Likelihood = -0.32 Transmembrane 342-358 (342-360) ----- Final Results ----- bacterial membrane --- Certainty = 0.4609(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9397> which encodes amino acid sequence <SEQ ID 9398> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06750 >GP: CAB14651 GB: Z99117 amino acid permease [Bacillus subtilis] Identities = 165/361 (45%), Positives = 227/361 (62%), Gaps = 17/361 (4%) Query: 1 MGIFLT-LSYWISLIFIGMAEITAVGEYVQFWFPEWPSWIIQIVFLAILSSINLIAVKAF 59 M F+T +YW I + MA++TAVG Y Q+W P+ P W+ ++ L IL +NL VK F Sbjct: 95 MAAFITGWTYWFCWISLAMADLTAVGIYTQYWLPDVPQWLPGLLALIILLIMNLATVKLF 154- Query: 60 GETEFWFAMIKVIAILGLIATGIFMVLTNFDTGHGYHASISNITNHFEWFPKGKLNFFMA 119- GE EFWFA+IKVIAIL LI TGI ++ F G AS++N+ +H FP G F ++ Sbjct: 155 GELEFWFALIKVIAILALIVTGILLIAKGFSAASG-PASLNNLWSHGGMFPNGWHGFILS 21- 3 Query: 120 FQMVFFAYLAIEFVGVTTSETANPRKVLPKAIQEIPMRIILFYAGSLLAIMAIFPWQQLP 17- 9 FQMV FA++ IE VG+T ET NP+KV+PKAI +IP+RI+LFY G+L IM I+PW L Sbjct: 214 FQMVVFAFVGIELVGLTAGETENPQKVIPKAINQIPVRILLFYVGALFVIMCIYPWNVLN 27- 3 Query: 180 VNESPFVTVFKLAGIKWAAALINFVVLTSAASALNSTLYSTGRHLFQLANE--SPNALTK 23- 7 NESPFV VF GI AA+LINFVVLTSAASA NS L+ST R ++ LA + +P L K Sbjct: 274 PNESPFVQVFSAVGIVVAASLINFVVLTSAASAANSALFSTSRMVYSLAKDHHAPGLLKK 33- 3 Query: 238 ALKLDQLSRQSVPSRAIIAS--AVIVGASALISVLPGISDAFSLITASSSGVYISIYVLI 29- 5 L+ +VPS A+ S A+++G S L ++P F+LIT+ S+ +I I+ + Sbjct: 334 ------LTSSNVPSNALFFSSIAILIGVS-LNYLMP--EQVFTLITSVSTICFIFIWGIT 38- 4 Query: 296 MIAHWKYRKS--PDFMEDGYKMPAYKILSPITLLFFLFVFVSLFLQDSTYIGAIGATIWII 3- 54 +I H KYRK+ + + +KMP Y + + +TL F F+ V L L + T I +W + Sbjct: 385 VICHLKYRKTRQHEAKANKFKMPFYPLSNYLTLAFLAFILVILALANDTRIALFVTPVWFV 4- 45 There is also homology to SEQ ID 4070: TABLE-US-06751 Identities = 286/364 (78%), Positives = 322/364 (87%), Gaps = 1/364 (0%) Query: 2 GIFLTLSYWISLIFIGMAEITAVGEYVQFWFPEWPSWIIQIVFLAILSSINLIAVKAFGE 61 G F LSYWISLIFIGMAEITAVG YVQFWFP WP+W+IQ+VFL +LSSINLIAV+ FGE Sbjct: 101 GYFSGLSYWISLIFIGMAEITAVGAYVQFWFPSWPAWLIQLVFLVLLSSINLIAVRVFGE 16- 0 Query: 62 TEFWFAMIKVIAILGLIATGIFMVLTNFDTGHGYHASISNITNHFEWFPKGKLNFFMAFQ 121- TEFWFAMIK++AIL LIAT IFMVLT F+T H HAS+SNI +HF FP GKL FFMAFQ Sbjct: 161 TEFWFAMIKILAILALIATAIFMVLTGFET-HTGHASLSNIFDHFSMFPNGKLKFFMAFQ 21- 9 Query: 122 MVFFAYLAIEFVGVTTSETANPRKVLPKAIQEIPMRIILFYAGSLLAIMAIFPWQQLPVN 18- 1 MVFFAY AIEFVG+TTSETANPRKVLPKAIQEIP RI++FY G+L++IMAI PW QLPV+ Sbjct: 220 MVFFAYQAIEFVGITTSETANPRKVLPKAIQEIPTRIVIFYVGALVSIMAIVPWHQLPVD 27- 9 Query: 182 ESPFVTVFKLAGIKWAAALINFVVLTSAASALNSTLYSTGRHLFQLANESPNALTKALKL 24- 1 ESPFV VFKL GIKWAAALINFVVLTSAASALNSTLYSTGRHL+Q+ANE+PNALT LK+ Sbjct: 280 ESPFVMVFKLIGIKWAAALINFVVLTSAASALNSTLYSTGRHLYQIANETPNALTNRLKI 33- 9 Query: 242 DQLSRQSVPSRAIIASAVIVGASALISVLPGISDAFSLITASSSGVYISIYVLIMIAHWK 30- 1 + LSRQ VPSRAIIASAV+VG SALI++LPG++DAFSLITASSSGVYI+IY L MIAHWK Sbjct: 340 NTLSRQGVPSRAIIASAVVVGISALINILPGVADAFSLITASSSGVYIAIYALTMIAHWK 39- 9 Query: 302 YRKSPDFMEDGYKMPAYKILSPITLLFFLFVFVSLFLQDSTYIGAIGATIWIIGFGLYSH 36- 1 YR+S DFM DGY MP YK+ +P+TL FF FVF+SLFLQ+STYIGAIGATIWII FG+YS+ Sbjct: 400 YRQSKDFMADGYLMPKYKVTTPLTLAFFAFVFISLFLQESTYIGAIGATIWIIIFGIYSN 45- 9 Query: 362 FKHK 365 K K Sbjct: 460 VKFK 463 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2205 A DNA sequence (GBSx2324) was identified in S. agalactiae <SEQ ID 6807> which encodes the amino acid sequence <SEQ ID 6808>. Analysis of this protein sequence reveals the following: TABLE-US-06752 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.33 Transmembrane 194-210 (191-215) INTEGRAL Likelihood = -5.47 Transmembrane 17-33 (14-38) INTEGRAL Likelihood = -5.15 Transmembrane 125-141 (119-144) INTEGRAL Likelihood = -3.88 Transmembrane 155-171 (153-176) INTEGRAL Likelihood = -1.38 Transmembrane 96-112 (94-114) INTEGRAL Likelihood = -0.43 Transmembrane 49-65 (49-65) ----- Final Results ----- bacterial membrane --- Certainty = 0.4333(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06753 >GP: AAC95438 GB: AF068901 unknown [Streptococcus pneumoniae] Identities = 80/214 (37%), Positives = 122/214 (56%), Gaps = 3/214 (1%) Query: 4 FFSNIRTEIPQMPLLIHSLILSVLPFLMWLTLVNRDKPLYKTIWSILLGLQLITIYTWFF 63 FF+ T+ P+ L + + ++L + R+K +Y+ + IL +QLI +Y W++ Sbjct: 7 FFTTQATKPPKFDLFWYVSLFTLLALTFYTAHRYREKKVYQRFFQILQTVQLILLYGWYW 66 Query: 64 WAKLPLSESLPLYHCRIGMFVVLLARPGI--LKDYFALLGVVGGVLAMIHPDFYPYQFLH 121- +PLSESLP YHCR+ MFVVLL PG K YFALLG G + A ++P Y F H Sbjct: 67 VNHMPLSESLPFYHCRMAMFVVLLL-PGQSKYKQYFALLGTFGTLAAFVYPVPDAYPFPH 125- Query: 122 VTNIFFFIGHFALFVLSLLHLMTQSNLDKLNPKLIIQLTLLINMSLIFINLLTGGNYGFM 18- 1 +T + F GH AL SL++L+ Q N L+ K I +T +N + +NL+TGG+YGF+ Sbjct: 126 ITILSFIFGHLALLGNSLVYLLRQYNARLLDVKGIFLMTFALNALIFVVNLVTGGDYGFL 18- 5 Query: 182 MKTPILGITNPFLNLFIVTTLLSFLVLFVKQIFQ 215 K P++G N +V+ +L + K+I + Sbjct: 186 TKPPLVGDHGLVANYLLVSIVLVATISLTKKILE 219 A related DNA sequence was identified in S. pyogenes <SEQ ID 6809> which encodes the amino acid sequence <SEQ ID 6810>. Analysis of this protein sequence reveals the following: TABLE-US-06754 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.25 Transmembrane 16-32 (11-39) INTEGRAL Likelihood = -3.45 Transmembrane 154-170 (153-173) INTEGRAL Likelihood = -3.08 Transmembrane 96-112 (94-112) INTEGRAL Likelihood = -1.91 Transmembrane 191-207 (191-209) INTEGRAL Likelihood = -1.12 Transmembrane 71-87 (71-87) ----- Final Results ----- bacterial membrane --- Certainty = 0.5501(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06755 >GP: AAC95438 GB: AF068901 unknown [Streptococcus pneumoniae] Identities = 90/231 (38%), Positives = 128/231 (54%), Gaps = 7/231 (3%) Query: 3 FFAIDPIGLPHTSLIFYLSSLLIALLLVFLTFQAYRLKS-HRYFFLFLQLSQVIGLYTWY 61 FF P L +Y+S L L L F T YR K ++ FF LQ Q+I LY WY Sbjct: 7 FFTTQATKPPKFDLFWYVS-LFTLLALTFYTAHRYREKKVYQRFFQILQTVQLILLYGWY 65 Query: 62 VLRGFPLDEALPLYHCRIAMLAIFFLPDRNKFKQLFMVLGIGGTFLALL--SPDLYPFRL 119- + PL E+LP YHCR+AM + LP ++K+KQ F +LG GT A + PD YPF Sbjct: 66 WVNHMPLSESLPFYHCRMAMFVVLLLPGQSKYKQYFALLGTFGTLAAFVYPVPDAYPFP- 124- Query: 120 WHVANVSFYFGHYALLVNGLIYLLRFYDASQLRLLSVVRYLATVNFLLLLVSLATKGNYG 17- 9 H+ +SF FGH ALL N L+YLLR Y+A L + + +N L+ +V+L T G+YG Sbjct: 125 -HITILSFIFGHLALLGNSLVYLLRQYNARLLDVKGIFLMTFALNALIFVVNLVTGGDYG 18- 3 Query: 180 FVMDIPVIHTRHLLLNFVIVTSGLTFMVKITEYFYLKFGEAQQLALAFSKE 230 F+ P++ L+ N+++V+ L + +T+ L+F AQ+ KE Sbjct: 184 FLTKPPLVGDHGLVANYLLVSIVLVATISLTKKI-LEFFLAQEAEKMIVKE 233 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06756 Identities = 70/216 (32%), Positives = 117/216 (53%), Gaps = 1/216 (0%) Query: 2 IEFFSNIRTEIPQMPLLIHSLILSVLPFLMWLTLVNRDKPLYKTIWSILLGLQLITIYTW 61 ++FF+ +P L+ + L + L++LT ++ + L Q+I +YTW Sbjct: 1 MDFFAIDPIGLPHTSLIFYLSSLLIALLLVFLTFQAYRLKSHRYFFLFLQLSQVIGLYTW 60 Query: 62 FFWAKLPLSESLPLYHCRIGMFVVL-LARPGILKDYFALLGVVGGVLAMIHPDFYPYQFL 120- + PL E+LPLYHCRI M + L K F +LG+ G LA++ PD YP++ Sbjct: 61 YVLRGFPLDEALPLYHCRIAMLAIFFLPDRNKFKQLFMVLGIGGTFLALLSPDLYPFRLW 120- Query: 121 HVTNIFFFIGHFALFVLSLLHLMTQSNLDKLNPKLIIQLTLLINMSLIFINLLTGGNYGF 18- 0 HV N+ F+ GH+AL V L++L+ + +L +++ +N L+ ++L T GNYGF Sbjct: 121 HVANVSFYFGHYALLVNGLIYLLRFYDASQLRLLSVVRYLATVNFLLLLVSLATKGNYGF 18- 0 Query: 181 MMKTPILGITNPFLNLFIVTTLLSFLVLFVKQIFQK 216 +M P++ + LN IVT+ L+F+V + + K Sbjct: 181 VMDIPVIHTRHLLLNFVIVTSGLTFMVKITEYFYLK 216 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2206 A DNA sequence (GBSx2325) was identified in S. agalactiae <SEQ ID 6811> which encodes the amino acid sequence <SEQ ID 6812>. Analysis of this protein sequence reveals the following:

TABLE-US-06757 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3297(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2207 A DNA sequence (GBSx2326) was identified in S. agalactiae <SEQ ID 6813> which encodes the amino acid sequence <SEQ ID 6814>. This protein is predicted to be oxalate:formate antiporter (oxlT-2). Analysis of this protein sequence reveals the following: TABLE-US-06758 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.80 Transmembrane 380-396 (376-399) INTEGRAL Likelihood = -7.43 Transmembrane 291-307 (284-310) INTEGRAL Likelihood = -5.63 Transmembrane 169-185 (163-186) INTEGRAL Likelihood = -4.99 Transmembrane 226-242 (223-245) INTEGRAL Likelihood = -4.19 Transmembrane 46-62 (39-63) INTEGRAL Likelihood = -4.09 Transmembrane 311-327 (308-329) INTEGRAL Likelihood = -1.49 Transmembrane 261-277 (260-278) INTEGRAL Likelihood = -1.06 Transmembrane 133-149 (133-150) INTEGRAL Likelihood = -0.85 Transmembrane 98-114 (98-114) INTEGRAL Likelihood = -0.06 Transmembrane 77-93 (77-93) ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06759 >GP: AAF36228 GB: AF168363 oxalate: formate antiporter [Lactococcus lactis] Identities = 220/398 (55%), Positives = 306/398 (76%), Gaps = 3/398 (0%) Query: 5 NRYVVAVSGVVLHLMLGSTYAWSVFRNPIISETGWDISSVSFAFSLAIFCLGMSAAFMGH 64- NRYVVA +GV+ HLM+GS YAWSVF NPI + GW SSV+ AFS+AI+ LGMSAAFMG Sbjct: 4 NRYVVAFAGVMFHLMIGSVYAWSVFTNPIAKQNGWAESSVALAFSIAIYFLGMSAAFMGK 63- Query: 65 LVERFGPRIMGMISAILYGAGNVLTGLAIETQQLWLLYVAYGILGGIGLGSGYITPVSTI 12- 4 +VE+ GPR+ G I++ LYG G ++TG AI +WLLY++YG++GG+GLG+GY+TPVSTI Sbjct: 64 VVEKIGPRLTGTIASFLYGTGTIMTGWAIHQNSIWLLYLSYGVIGGLGLGAGYVTPVSTI 12- 3 Query: 125 IKWFPDRRGLATGFAIMGFGFASLVTSPLAQSLMIRIGVGKTFYILGLVYFFVMMIASQF 18- 4 IKWFPD+RGLATG AINGFGFA+++T P+AQ LM +G+ +TFY+LG YF +M++A+QF Sbjct: 124 IKWFPDKRGLATGLAIMGFGFAAMLTGPVAQQLMASVGLEQTFYLLGTFYFVIMLLAAQF 18- 3 Query: 185 IKQPPQEKITILTHDGKKNAMNSQIITG--LKANAAIKSKTFYIIWLTLFINISCGLGLI 24- 2 I + P ++ T + +++ G L AN A+K+K+F +W+ FINI+CG+GL+ Sbjct: 184 IVR-PNLALSSTTENSISQKKGTRLTRGPELTANQALKTKSFTFLWIMFFINITCGIGLV 24- 2 Query: 243 SAASPMAQDLAGYSAESAALLVGVLGIFNGFGRLLWASLSDYIGRPLTFIILFIVNFIMT 30- 2 SAASPMAQ + G S ++AA++VG++G+FNGFGRL+WA+LSDYIGRP TF +FI++ +M Sbjct: 243 SAASPMAQSMTGMSVQTAAIMVGIIGLFNGFGRLIWATLSDYIGRPATFSAIFILDIVML 30- 2 Query: 303 SSLFLSFNAIVFAIAMSILMTCYGAGFSLLPAYLSDIFGTKELATLHGYSLTAWAIAGLF 36- 2 S++ + ++F IA+ +LM+CYGAGFS++PAYL D+FGTKEL +HGY LTAWA AG+ Sbjct: 303 SAILIFKLPLLFVIALCLLMSCYGAGFSVIPAYLGDVFGTKELGAVHGYVLTAWAAAGVV 36- 2 Query: 363 GPLLLSKTYSWGNSYQLTLMVFGFLFLFGLLLSLYLRK 400 GPLLLS T+ ++Y LTL F + L LL+S ++++ Sbjct: 363 GPLLLSLTHQLFHNYTLTLAAFILIDLLALLISFWIQR 400 A related DNA sequence was identified in S. pyogenes <SEQ ID 6815> which encodes the amino acid sequence <SEQ ID 6816>. Analysis of this protein sequence reveals the following: TABLE-US-06760 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.95 Transmembrane 289-305 (282-321) INTEGRAL Likelihood = -11.83 Transmembrane 376-392 (372-397) INTEGRAL Likelihood = -8.55 Transmembrane 163-179 (160-189) INTEGRAL Likelihood = -7.75 Transmembrane 227-243 (221-247) INTEGRAL Likelihood = -5.89 Transmembrane 44-60 (41-67) INTEGRAL Likelihood = -1.38 Transmembrane 310-326 (309-327) INTEGRAL Likelihood = -0.90 Transmembrane 353-369 (353-369) INTEGRAL Likelihood = -0.37 Transmembrane 138-154 (138-154) INTEGRAL Likelihood = -0.06 Transmembrane 98-114 (98-114) INTEGRAL Likelihood = -0.00 Transmembrane 259-275 (259-275) ----- Final Results ----- bacterial membrane --- Certainty = 0.6180(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06761 >GP: AAF36228 GB: AF168363 oxalate: formate antiporter [Lactococcus lactis] Identities = 222/399 (55%), Positives = 305/399 (75%), Gaps = 3/399 (0%) Query: 3 KTKRYIIATAGILLHLMLGSTYAWSVYRNPILQETGWDQAPVAFAFSLAIFCLGLSAAFM 62- KT RY++A AG++ HLM+GS YAWSV+ NPI ++ GW ++ VA AFS+AI+ LG+SAAFM Sbjct: 2 KTNRYVVAFAGVMFHLMIGSVYAWSVFTNPIAKQNGWAESSVALAFSIAIYFLGMSAAFM 61- Query: 63 GNLVEQYGPRLTGTVSAILYASGNMLTGLAIDRKEIWLLYIGYGVIGGLGLGAGYITPIS 12- 2 G +VE+ GPRLTGT+++ LY +G ++TG AI + IWLLY+ YGVIGGLGLGAGY+TP+S Sbjct: 62 GKVVEKIGPRLTGTIASFLYGTGTIMTGWAIHQNSIWLLYLSYGVIGGLGLGAGYVTPVS 12- 1 Query: 123 TIIKWFPDKRGMATGFAIMGFGFASLLTSPIAQWLIETEGLVATFYLLGLIYLIVMLFAS 18- 2 TIIKWFPDKRG+ATG AIMGFGFA++LT P+AQ L+ + GL TFYLLG Y ++ML A+ Sbjct: 122 TIIKWFPDKRGLATGLAIMGFGFAAMLTGPVAQQLMASVGLEQTFYLLGTFYFVIMLLAA 18- 1 Query: 183 QLIIKPTAAEIAILDKKRLQ-NNSYLIEG--MTAKEALKTKSFYCLWVILFINITCGLGL 23- 9 Q I++P A + + Q + L G +TA +ALKTKSF LW++ FINITCG+GL Sbjct: 182 QFIVRPNLALSSTTENSISQKKGTRLTRGPELTANQALKTKSFTFLWIMFFINITCGIGL 24- 1 Query: 240 ISVVAPMAQDLTGMSPEMSAIVVGAMGIFNGFGRLVWASLSDYIGRRVTVILLFLVSIIM 29- 9 +S +PMAQ +TGMS + +AI+VG +G+FNGFGRL+WA+LSDYIGR T F++I+M Sbjct: 242 VSAASPMAQSMTGMSVQTAAIMVGIIGLFNGFGRLIWATLSDYIGRPATFSAIFILDIVM 30- 1 Query: 300 TISLIFAHSSLIFMISIATLMTCYGAGFSLIPPYLSDLFGAKELATLHGYILTAWAIAAL 35- 9 +++ L+F+I++ LM+CYGAGFS+IP YL D+FG KEL +HGY+LTAWA A + Sbjct: 302 LSAILIFKLPLLFVIALCLLMSCYGAGFSVIPAYLGDVFGTKELGAVHGYVLTAWAAAGV 36- 1 Query: 360 TGPMLLSITVEWTHNYLLTLCVFIVLYILGLMVALRLKK 398 GP+LLS+T + HNY LTL FI++ +L L+++ +++ Sbjct: 362 VGPLLLSLTHQLFHNYTLTLAAFILIDLLALLISFWIQR 400 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06762 Identities = 252/400 (63%), Positives = 329/400 (82%), Gaps = 2/400 (0%) Query: 1 MKNLNRYVVAVSGVVLHLMLGSTYAWSVFRNPIISETGWDISSVSFAFSLAIFCLGMSAA 60- M+ RY++A +G++LHLMLGSTYAWSV+RNPI+ ETGWD + V+FAFSLAIFCLG+SAA Sbjct: 1 MEKTKRYIIATAGILLHLMLGSTYAWSVYRNPILQETGWDQAPVAFAFSLAIFCLGLSAA 60- Query: 61 FMGHLVERFGPRIMGMISAILYGAGNVLTGLAIETQQLWLLYVAYGILGGIGLGSGYITP 12- 0 FMG+LVE++GPR+ G +SAlLY +GN+LTGLAI+ +++WLLY+ YG++GG+GLG+GYITP Sbjct: 61 FMGNLVEQYGPRLTGTVSAILYASGNMLTGLAIDRKEIWLLYIGYGVIGGLGLGAGYITP 12- 0 Query: 121 VSTIIKWFPDRRGLATGFAIMGFGFASLVTSPLAQSLMIRIGVGKTFYILGLVYFFVMMI 18- 0 +STIIKWFPD+RG+ATGFAIMGFGFASL+TSP+AQ L+ G+ TFY+LGL+Y VM+ Sbjct: 121 ISTIIKWFPDKRGMATGFAIMGFGFASLLTSPIAQWLIETEGLVATFYLLGLIYLIVMLF 18- 0 Query: 181 ASQFIKQPPQEKITILTHDGKKNAMNSQIITGLKANAAIKSKTFYIIWLTLFINISCGLG 24- 0 ASQ I +P +I IL D K+ NS +I G+ A A+K+K+FY +W+ LFINI+CGLG Sbjct: 181 ASQLIIKPTAAEIAIL--DKKRLQNNSYLIEGMTAKEALKTKSFYCLWVILFINITCGLG 23- 8 Query: 241 LISAASPMAQDLAGYSAESAALLVGVLGIFNGFGRLLWASLSDYIGRPLTFIILFIVNFI 30- 0 LIS +PMAQDL G S E +A++VG +GIFNGFGRL+WASLSDYIGR +T I+LF+V+ I Sbjct: 239 LISVVAPMAQDLTGMSPEMSAIVVGAMGIFNGFGRLVWASLSDYIGRRVTVILLFLVSII 29- 8 Query: 301 MTSSLFLSFNAIVFAIAMSILMTCYGAGFSLLPAYLSDIFGTKELATLHGYSLTAWAIAG 36- 0 MT SL + ++++F I+++ LMTCYGAGFSL+P YLSD+FG KELATLHGY LTAWAIA Sbjct: 299 MTISLIFAHSSLIFMISIATLMTCYGAGFSLIPPYLSDLFGAKELATLHGYILTAWAIAA 35- 8 Query: 361 LFGPLLLSKTYSWGNSYQLTLMVFGFLFLFGLLLSLYLRK 400 L GP+LLS T W ++Y LTL VF L++ GL+++L L+K Sbjct: 359 LTGPMLLSITVEWTHNYLLTLCVFIVLYILGLMVALRLKK 398 A related GBS gene <SEQ ID 8995> and protein <SEQ ID 8996> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06763 Lipop: Possible site: -1 Crend: 5 McG: Discrim Score: 5.06 GvH: Signal Score (-7.5): 4.38 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 10 value: --7.80 threshold: 0.0 INTEGRAL Likelihood = -7.80 Transmembrane 380-396 (376-399) INTEGRAL Likelihood = -7.43 Transmembrane 291-307 (284-310) INTEGRAL Likelihood = -5.63 Transmembrane 169-185 (163-186) INTEGRAL Likelihood = -4.99 Transmembrane 226-242 (223-245) INTEGRAL Likelihood = -4.19 Transmembrane 46-62 (39-63) INTEGRAL Likelihood = -4.09 Transmembrane 311-327 (308-329) INTEGRAL Likelihood = -1.49 Transmembrane 261-277 (260-278) INTEGRAL Likelihood = -1.06 Transmembrane 133-149 (133-150) INTEGRAL Likelihood = -0.85 Transmembrane 98-114 (98-114) INTEGRAL Likelihood = -0.06 Transmembrane 77-93 (77-93) PERIPHERAL Likelihood = -0.42 352 modified ALOM score: 2.06 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00160## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2208 A DNA sequence (GBSx2327) was identified in S. agalactiae <SEQ ID 6817> which encodes the amino acid sequence <SEQ ID 6818>. This protein is predicted to be D-Ala-D-Ala adding enzyme (murF). Analysis of this protein sequence reveals the following: TABLE-US-06764 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1311(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9739> which encodes amino acid sequence <SEQ ID 9740> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06765 >GP: AAC95436 GB: AF068901 D-Ala-D-Ala adding enzyme [Streptococcus pneumoniae] Identities = 313/453 (69%), Positives = 375/453 (82%) Query: 32 MKLSLHEVAKVVGAKNQVSEFEDVPLGNIEFDSRNISEGDLFLPLKGARDGHEFIEMAFD 91 - MKL++HE+A+VVGAKN +S FED L EFDSR I GDLF+PLKGARDGH+FIE AF+ Sbjct: 1 MKLTIHEIAQVVGAKNDISIFEDTQLEKAEFDSRLIGTGDLFVPLKGARDGHDFIETAFE 60 Query: 92 NGAIATISEKEIEGHPYLLVSDALKAFQVLAQYYIEKMNVDVIAVTGSNGKTTTKDMIAA 151- NGA T+SEKE+ HPY+LV D L AFQ LA YY+EK VDV AVTGSNGKTTTKDM+A Sbjct: 61 NGAAVTLSEKEVSNHPYILVDDVLTAFQSLASYYLEKTTVDVFAVTGSNGKTTTKDMLAH 120- Query: 152 ILSTTYKTYKTQGNYNNEIGLPYTVLHMPEDTEKIILEMGQDHLGDIHVLSEIAKPRIAV 21- 1 +LST YKTYKTQGNYNNEIGLPYTVLHMPE TEK++LEMGQDHLGDIH+LSE+A+P+ A+ Sbjct: 121 LLSTRYKTYKTQGNYNNEIGLPYTVLHMPEGTEKLVLEMGQDHLGDIHLLSELARPKTAI 18- 0 Query: 212 VTLIGEAHLEFFGSREKIAEGKMQITDGMSSDGILIAPGDPIIDPYLPANQMTIRFGHDQ 27- 1 VTL+GEAHL FF R +IA+GKMQI DGM+S +L+AP DPI++ YLP ++ +RFG Sbjct: 181 VTLVGEAHLAFFKDRSEIAKGKMQIADGMASGSLLLAPADPIVEDYLPTDKKVVRFGQGA 24- 0 Query: 272 ELQVTELKEEKHSLTFKTNALEHQLRIPVPGKYNATNAMVAAYVGKLLAVAEEDIVDALE 33- 1 EL++T+L E K SLTFK N LE L +PV GKYNATNAM+A+YV V+EE I A + Sbjct: 241 ELEITDLVERKDSLTFKANFLEQVLDLPVTGKYNATNAMIASYVALQEGVSEEQIHQAFQ 30- 0 Query: 332 NLQLTRNRTEWKKSANGADILSDVYNANPTAMRLILETFSAIPNNDGGKKIALLADMKEL 39- 1 +L+LTRNRTEWKK+ANGADILSDVYNANPTAM+LILETFSAIP N+GGKKIA+LADMKEL Sbjct: 301 DLELTRNRTEWKKAANGADILSDVYNANPTAMKLILETFSAIPANEGGKKIAVLADMKEL 36- 0 Query: 392 GEQSVDLHNQMIMSIRPDSIDTLICYGQDIEGLAQLASQMFPIGKVYFFKKNQEVDQFDQ 45- 1 G QSV LHNQMI+S+ PD +DT+I YG+DI LAQLASQMFPIG VY+FKK ++ DQF+ Sbjct: 361 GNQSVQLHNQMILSLSPDVLDTVIFYGEDIAELAQLASQMFPIGHVYYFKKTEDQDQFED 42- 0 Query: 452 LLAKVKDTLKEKDQILLKGSNSMNLSKIVDILE 484 L+ +VK++L DQILLKGSNSMNL+ +V+ LE Sbjct: 421 LVKQVKESLSANDQILLKGSNSMNLAMLVESLE 453 A related DNA sequence was identified in S. pyogenes <SEQ ID 6819> which encodes the amino acid sequence <SEQ ID 6820>. Analysis of this protein sequence reveals the following: TABLE-US-06766 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3299(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06767 Identities = 323/452 (71%), Positives = 387/452 (85%) Query: 32 MKLSLHEVAKVVGAKNQVSEFEDVPLGNIEFDSRNISEGDLFLPLKGARDGHEFIEMAFD 91 - MKL+LHEVAK+V A+N VS+ +DVPL +IEFDSR I++GDLFLPLKG RDGHEFI++AF Sbjct: 1 MKLTLHEVAKIVDAQNNVSDLDDVPLHHIEFDSRKITKGDLFLPLKGQRDGHEFIDLAFQ 60 Query: 92 NGAIATISEKEIEGHPYLLVSDALKAFQVLAQYYIEKMNVDVIAVTGSNGKTTTKDMIAA 151- NGA+AT SEKE+ G P+LLV D LKAFQ LA YYI+KM VDVIAVTGSNGKT+TKDMI A Sbjct: 61 NGAVATFSEKELPGKPHLLVEDCLKAFQKLAHYYIDKMRVDVIAVTGSNGKTSTKDMIGA 120- Query: 152 ILSTTYKTYKTQGNYNNEIGLPYTVLHMPEDTEKIILEMGQDHLGDIHVLSEIAKPRIAV 21- 1 +LSTTYKTYKTQGNYNNEIGLPYTVLHMP+DTEKI+LEMGQDH+GDI +LSEIA+PRIAV Sbjct: 121 VLSTTYKTYKTQGNYNNEIGLPYTVLHMPDDTEKIVLEMGQDHMGDIRLLSEIARPRIAV 18- 0 Query: 212 VTLIGEAHLEFFGSREKIAEGKMQITDGMSSDGILIAPGDPIIDPYLPANQMTIRFGHDQ 27- 1 +TL+GEAHLE+FGSR+KIA+GKMQI DGM+SDGILIAPGDPIIDPYLP NQM IRFG+ Q Sbjct: 181 LTLVGEAHLEYFGSRDKIAQGKMQIVDGMNSDGILIAPGDPIIDPYLPENQMVIRFGNQQ 24- 0 Query: 272 ELQVTELKEEKHSLTFKTNALEHQLRIPVPGKYNATNAMVAAYVGKLLAVAEEDIVDALE 33- 1 E+ VT ++E+K SLTF TN L + +P+PGKYNATNAMVAAYVGKLLAV +EDI+ AL+ Sbjct: 241 EIDVTGIQEDKDSLTFTTNVLATPVSLPLPGKYNATNAMVAAYVGKLLAVTDEDIIAALQ 30- 0 Query: 332 NLQLTRNRTEWKKSANGADILSDVYNANPTAMRLILETFSAIPNNDGGKKIALLADMKEL 39- 1 + LT NRTEWKK+ANGADILSDVYNANPTAMRLILETF+ I N GGKKIA+LADMKEL Sbjct: 301 TVTLTGNRTEWKKAANGADILSDVYNANPTAMRLILETFANIAKNPGGKKIAVLADMKEL 36- 0 Query: 392 GEQSVDLHNQMIMSIRPDSIDTLICYGQDIEGLAQLASQMFPIGKVYFFKKNQEVDQFDQ 45- 1 G+ SV LH+Q+I S+ +ID L+ YG I+ LA+LASQ++P +V++F K ++ DQF+ Sbjct: 361 GKDSVILHSQLIDSLTSGNIDQLVFYGDHIKELARLASQVYPAEQVHYFLKTEQEDQFEA 42- 0 Query: 452 LLAKVKDTLKEKDQILLKGSNSMNLSKIVDIL 483 + V++ L DQILLKGS+SM+L K+VD L Sbjct: 421 MAQYVQNILNPFDQILLKGSHSMSLEKLVDRL 452 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2209 A DNA sequence (GBSx2328) was identified in S. agalactiae <SEQ ID 6821> which encodes the amino acid sequence <SEQ ID 6822>. Analysis of this protein sequence reveals the following: TABLE-US-06768 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1381(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06769 >GP: AAC95435 GB: AF068901 D-Ala-D-Ala ligase [Streptococcus pneumoniae] Identities = 243/346 (70%), Positives = 289/346 (83%) Query: 3 KETLILLYGGRSAEREVSVLSAESVMRAINYDKFFVKTYFITQVGQFIKTQEFDEMPSSD 62 K+T+ILLYGGRSAEREVSVLSAESVMRA+NYD+F VKT+FI+Q G FIKTQEF P + Sbjct: 2 KQTIILLYGGRSAEREVSVLSAESVMRAVNYDRFTVKTFFISQSGDFIKTQEFSHAPGQE 61 Query: 63 EKLMTNQTVDLDKMVRPSDIYDDNAIVFPVLHGPMGEDGSIQGFLEVLRMPYVGTNILSS 122- ++LMTN+T+D DK V PS IY++ A+VFPVLHGPMGEDGS+QGFLEVL+MPYVG NILSS Sbjct: 62 DRLMTNETIDWDKKVAPSAIYEEGAVVFPVLHGPMGEDGSVQGFLEVLKMPYVGCNILSS 121- Query: 123 SVAMDKITTKQVLATVGVPQVAYQTYFEGDDLEHAIKLSLETLSFPIFVKPANMGSSVGI 18- 2 S+AMDKITTK+VL + G+ QV Y EGDD+ I E L++P+F KP+NMGSSVGI Sbjct: 122 SLAMDKITTKRVLESAGIAQVPYVAIVEGDDVTAKIAEVEEKLAYPVFTKPSNMGSSVGI 18- 1 Query: 183 SKATDESSLRSAIDLALKYDSRILIEQGVTAREIEVGILGNNDVKTTFPGEVVKDVDFYD 24- 2 SK+ ++ LR A+ LA +YDSR+L+EQGV AREIEVG+LGN DVK+T PGEVVKDV FYD Sbjct: 182 SKSENQEELRQALKLAFRYDSRVLVEQGVNAREIEVGLLGNYDVKSTLPGEVVKDVAFYD 24- 1 Query: 243 YDAKYIDNKITMDIPAKVDEATMEAMRQYASKAFKAIGACGLSRCDFFLTKDGQIFLNEL 30- 2 YDAKYIDNKITMDIPAK+ + + MRQ A AF+AIG GLSRCDFF T G+IFLNEL Sbjct: 242 YDAKYIDNKITMDIPAKISDDVVAVMRQNAETAFRAIGGLGLSRCDFFYTDKGEIFLNEL 30- 1 Query: 303 NTMPGFTQWSMYPLLWENMGLTYSDLIEKLVMLAKEMFEKRESHLI 348 NTMPGFTQWSMYPLLW+NMG++Y +LIE+LV LAKE F+KRE+HLI Sbjct: 302 NTMPGFTQWSMYPLLWDNMGISYPELIERLVDLAKESFDKREAHLI 347 A related DNA sequence was identified in S. pyogenes <SEQ ID 4559> which encodes the amino acid sequence <SEQ ID 4560>. Analysis of this protein sequence reveals the following: TABLE-US-06770 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1451(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-06771 Identities = 261/348 (75%), Positives = 306/348 (87%) Query: 1 MSKETLILLYGGRSAEREVSVLSAESVMRAINYDKFFVKTYFITQVGQFIKTQEFDEMPS 60 MSK+TL+LLYGGRSAEREVSVLSAESVMRA+NYDKF VKTYFITQ+GQFIKTQ+F E PS Sbjct: 1 MSKQTLVLLYGGRSAEREVSVLSAESVMRAVNYDKFLVKTYFITQMGQFIKTQQFSEKPS 60 Query: 61 SDEKLMTNQTVDLDKMVRPSDIYDDNAIVFPVLHGPMGEDGSIQGFLEVLRMPYVGTNIL 120- E+LMTN+T++L + ++PSDIY++ A+VFPVLHGPMGEDGSIQGFLEVLRMPY+GTN++ Sbjct: 61 ESERLMTNETIELTQKIKPSDIYEEGAVVFPVLHGPMGEDGSIQGFLEVLRMPYIGTNVM 120- Query: 121 SSSVAMDKITTKQVLATVGVPQVAYQTYFEGDDLEHAIKLSLETLSFPIFVKPANMGSSV 18- 0 SSS+AMDKITTK+VL ++G+PQVAY Y +G DLE + +L L+FPIFVKPANMGSSV Sbjct: 121 SSSIAMDKITTKRVLESIGIPQVAYTVYIDGQDLEACLVETLARLTFPIFVKPANMGSSV 18- 0 Query: 181 GISKATDESSLRSAIDLALKYDSRILIEQGVTAREIEVGILGNNDVKTTFPGEVVKDVDF 24- 0 GISKA + LR AI LAL YDSR+LIEQGV AREIEVG+LGN+ VK+T PGEV+KDVDF Sbjct: 181 GISKAQTKVELRKAIQLALTYDSRVLIEQGVVAREIEVGLLGNDKVKSTLPGEVIKDVDF 24- 0 Query: 241 YDYDAKYIDNKITMDIPAKVDEATMEAMRQYASKAFKAIGACGLSRCDFFLTKDGQIFLN 30- 0 YDY AKY+DNKITM IPA VD++ + MR YA AFKA+G CGLSRCDFFLT+DGQ++LN Sbjct: 241 YDYQAKYVDNKITMAIPADVDQSIVTEMRSYAEVAFKALGGCGLSRCDFFLTQDGQVYLN 30- 0 Query: 301 ELNTMPGFTQWSMYPLLWENMGLTYSDLIEKLVMLAKEMFEKRESHLI 348 ELNTMPGFTQWSMYPLLWENMGL Y DLIE+LV LA+EMF++RESHLI Sbjct: 301 ELNTMPGFTQWSMYPLLWENMGLAYPDLIEELVTLAQEMFDQRESHLI 348 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2210 A DNA sequence (GBSx2329) was identified in S. agalactiae <SEQ ID 6823> which encodes the amino acid sequence <SEQ ID 6824>. This protein is predicted to be recombination protein (recR). Analysis of this protein sequence reveals the following: TABLE-US-06772 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2540(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06773 >GP: AAC44615 GB: U58210 RecM [Streptococcus thermophilus] Identities = 181/198 (91%), Positives = 189/198 (95%) Query: 1 MLYPTPIAKLIDSFSKLPGIGTKTATRLAFYTIGMSDEDVNEFAKNLLAAKRELTYCSVC 60 MLYPTPIAKLIDSFSKLPGIG KTATRLAFYTI MSDEDVN+FAKNLLAAKRELTYCSVC Sbjct: 1 MLYPTPIAKLIDSFSKLPGIGAKTATRLAFYTISMSDEDVNDFAKNLLAAKRELTYCSVC 60 Query: 61 GNLTDDDPCLICTDKTRDQSVILVVEDSKDVSAMEKIQEYNGLYHVLHGLISPMNGISPD 120- G LTDDDPC+ICTD+TRD++ ILVVEDSKDVSAMEKIQEY GLYHVL GLISPMNG+ PD Sbjct: 61 GRLTDDDPCIICTDETRDRTKILVVEDSKDVSAMEKIQEYRGLYHVLQGLISPMNGVGPD 120- Query: 121 DINLKSLITRLMDGQVTEVIVATNATADGEATSMYISRVLKPAGIKVTRLARGLAVGSDI 18- 0 DINLKSLITRLMD +V EVI+ATNATADGEATSMYISRVLKPAGIKVTRLARGLAVGSDI Sbjct: 121 DINLKSLITRLMDSEVDEVIIATNATADGEATSMYISRVLKPAGIKVTRLARGLAVGSDI 18- 0 Query: 181 EYADEVTLLRAIENRTEL 198 EYADEVTLLRAIENRTEL Sbjct: 181 EYADEVTLLRAIENRTEL 198 A related DNA sequence was identified in S. pyogenes <SEQ ID 6825> which encodes the amino acid sequence <SEQ ID 6826>. Analysis of this protein sequence reveals the following: TABLE-US-06774 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2652(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06775 Identities = 180/198 (90%), Positives = 192/198 (96%) Query: 1 MLYPTPIAKLIDSFSKLPGIGTKTATRLAFYTIGMSDEDVNEFAKNLLAAKRELTYCSVC 60 +LYPTPIAKLIDS+SKLPGIG KTATRLAFYTIGMS+EDVN+FAKNLLAAKRELTYCS+C Sbjct: 1 VLYPTPIAKLIDSYSKLPGIGIKTATRLAFYTIGMSNEDVNDFAKNLLAAKRELTYCSIC 60 Query: 61 GNLTDDDPCLICTDKTRDQSVILVVEDSKDVSAMEKIQEYNGLYHVLHGLISPMNGISPD 120- GNLTDDDPC ICTD +RDQ+ ILVVED+KDVSAMEKIQEY+G YHVLHGLISPMNG+ PD Sbjct: 61 GNLTDDDPCHICTDTSRDQTTILVVEDAKDVSAMEKIQEYHGYYHVLHGLISPMNGVGPD 120- Query: 121 DINLKSLITRLMDGQVTEVIVATNATADGEATSMYISRVLKPAGIKVTRLARGLAVGSDI 18- 0 DINLKSLITRLMDG+V+EVIVATNATADGEATSMYISRVLKPAGIKVTRLARGLAVGSDI Sbjct: 121 DINLKSLITRLMDGKVSEVIVATNATADGEATSMYISRVLKPAGIKVTRLARGLAVGSDI 18- 0 Query: 181 EYADEVTLLRAIENRTEL 198 EYADEVTLLRAIENRTEL Sbjct: 181 EYADEVTLLRAIENRTEL 198 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2211 A DNA sequence (GBSx2330) was identified in S. agalactiae <SEQ ID 6827> which encodes the amino acid sequence <SEQ ID 6828>. Analysis of this protein sequence reveals the following: TABLE-US-06776 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3144(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2212 A DNA sequence (GBSx2331) was identified in S. agalactiae <SEQ ID 6829> which encodes the amino acid sequence <SEQ ID 6830>. This protein is predicted to be penicillin-binding protein 2b. Analysis of this protein sequence reveals the following: TABLE-US-06777 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.69 Transmembrane 23-39 (17-46) ----- Final Results ----- bacterial membrane --- Certainty = 0.6477(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06778 >GP: AAC44614 GB: U58210 penicillin-binding protein 2b [Streptococcus thermophilus] Identities = 341/683 (49%), Positives = 477/683 (68%), Gaps = 12/683 (1%) Query: 4 RKKRYRLTVKKQNASIPRRLNLLFFIIVLLFTVLILRLEQMQIGQQSFYMKKLTALTSYT 63- ++K R ++ +I RR+ LLF ++ +LF +L RL MQ+ +SFY KKL + YT Sbjct: 18 KRKEKRANKPRKPVNISRRVYLLFGVVFVLFLLLFARLTYMQVYNKSFYTKKLEDNSKYT 77- Query: 64 VKESKARGQIFDAKGVVLVENDERPTVAFSRGNNISSQSIKELANKLSHYITLTEVASSD 12- 3 V+ + RGQIFDAKG+ L N + + F+R N +SS ++K +A +L+ +TLTE +D Sbjct: 78 VRIASERGQIFDAKGIALTTNQSKDVITFTRSNLVSSDTMKSVAERLATLVTLTETKVTD 13- 7 Query: 124 RAKRDYYLADKANYKKVVESLPDSKRYDKFGNHLAESTVYANAVAAVPVSAINYSEDELK 18- 3 R KR++YLAD ANYK+VV LP+ K+ DKFGN LAE+T+Y NA+ AVP A++YSEDELK Sbjct: 138 RQKREFYLADSANYKRVVNDLPNDKKTDKFGNKLAEATIYNNAINAVPDEAVDYSEDELK 19- 7 Query: 184 VVALFNQMNATPTFGSVKLSTGELSDDQIKKLDADKKELLGISVTSNWHRRKKGTSLSDI 24- 3 +V +++ MNA F +V L T +L+ DQI + A +KEL GI V +W R +SLS + Sbjct: 198 IVYIYSHMNAVSNFSTVILKTADLTPDQIAIVAAKQKELNGIRVAKDWERHTSDSSLSPL 25- 7 Query: 244 LGTISTEKAGLPREEVKKYLKKGYSLNDRVGTSYLEKQYEDDLQGIRQIRKVVVNKKGKV 30- 3 +G +S+ +AGLP+E+ K YLKKGY+LNDRVGTSYLEK+YE++LQG +R++ V+K+GKV Sbjct: 258 IGRVSSSEAGLPQEDAKDYLKKGYALNDRVGTSYLEKEYEEELQGKHTVREITVDKEGKV 31- 7 Query: 304 VSDNITQEGKSGRNLKLTIDLNYQNKVESILKQYYGSELSSGRASFSEGMYAVAIEPSTG 36- 3 SD I Q+G G NLKLTIDL++Q VE IL Q SE+S +A++SEGMYAV + TG Sbjct: 318 DSDKIIQKGSKGNNLKLTIDLDFQKGVEDILGQQLSSEISGNKATYSEGMYAVVMNADTG 37- 7 Query: 364 KVLAMAGLKNDHG--NLVDDSLGTIAKNFTPGSVVKGATLSSGWENKVLRGNEVLYDQEI 42- 1 VLAMAG K++ G + D+LGTI FTPGSVVKGATL++GW + + G++VL DQ I Sbjct: 378 AVLAMAGQKHEQGAQDFKADALGTITDVFTPGSVVKGATLTAGWRSGAIYGDQVLTDQPI 43- 7 Query: 422 -----ANIRSWFT-RGLTPISAAQALEYSSNTYMVQVALRLMGQDYNTGDALTDRGYQEA 47- 5 I SWFT +G I+A QALEYSSNTYMVQ+A++ +GQ Y G +L+ ++A Sbjct: 438 NIASSPPITSWFTDKGSRAITATQALEYSSNTYMVQIAIKRLGQQYVPGMSLSTDNMEKA 49- 7 Query: 476 MAKLRKTYGEYGLGVSTGLDLP-ESEGYVPGKYSLGTTLMESFGQYDAYTPMQLGQYIST 53- 4 M LR TY E+G+GVSTGLDLP ESEGY+P Y++ L E+FGQYD+YT +QL QY+++ Sbjct: 498 MTTLRDTYAEFGMGVSTGLDLPGESEGYIPKNYNVANVLTEAFGQYDSYTTIQLAQYVAS 55- 7 Query: 535 IANNGNRLAPHVVSDIYEGNDSNKFAQLVRSITPKTLNKIAISDQELAIIQEGFYNVVNS 59- 4 IAN G R+APH+V IY+ + L ++ + LNK+++ ++L IIQ+GF++VVNS Sbjct: 558 IANGGKRVAPHIVGGIYDAGKNGSLGTLSSTVDTRVLNKLSLDSKQLGIIQQGFHDVVNS 61- 7 Query: 595 GSGYATGTSMRGNVTTISGKTGTAETFAKNVNGQTVSTYNLNAIAYDTNR---KIAVAVM 65- 1 GS ATG +M ++ ISGKTGTAET+A + +G +V+T NLNA+AY T + K+AV +M Sbjct: 618 GSSLATGKAMASSIIPISGKTGTAETYATDGSGNSVTTVNLNAVAYATAKDGTKLAVGIM 67- 7 Query: 652 YPHVTTDTTKSHQLVARDMIDQY 674 YPH +K+HQ + +++ Y Sbjct: 678 YPHALDWKSKAHQNAVKAIMELY 700 A related GBS gene <SEQ ID 8997> and protein <SEQ ID 8998> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06779 Lipop Possible site: -1 Crend: 8 McG: Discrim Score: -12.38 GvH: Signal Score (-7.5): -5.9 Possible site: 35 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -12.42 threshold: 0.0 INTEGRAL Likelihood = -12.42 Transmembrane 23-39 (18-46) PERIPHERAL Likelihood = 4.56 355 modified ALOM score: 2.98 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5967(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00161## SEQ ID 8998 (GBS292) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 68 (lane 9; MW 103 kDa). GBS292-GST was purified as shown in FIG. 211, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2213 A DNA sequence (GBSx2332) was identified in S. agalactiae <SEQ ID 6831> which encodes the amino acid sequence <SEQ ID 6832>. Analysis of this protein sequence reveals the following: TABLE-US-06780 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2644(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06781 >GP: CAB51328 GB: AJ131985 phosphoglyceromutase [Streptococcus pneumoniae] Identities = 219/230 (95%), Positives = 226/230 (98%) Query: 1 MVKLVFARHGESEWNKANLFTGWADVDLSEKGTQQAIDAGKLIQAAGIEFDLAFTSVLKR 60- MVKLVFARHGESEWNKANLFTGWADVDLSEKGTQQAIDAGKLI+ AGI+FD A+TSVLKR Sbjct: 1 MVKLVFARHGESEWNKANLFTGWADVDLSEKGTQQAIDAGKLIKEAGIKFDQAYTSVLKR 60- Query: 61 AIKTTNLALEAADQLWVPVEKSWRLNERHYGGLTGKNKAEAAEQFGDEQVHIWRRSYDVL 12- 0 AIKTTNLALEA+DQLWVPVEKSWRLNERHYGGLTGKNKAEAAEQFGDEQVHIWRRSYDVL Sbjct: 61 AIKTTNLALEASDQLWVPVEKSWRLNERHYGGLTGKNKAEAAEQFGDEQVHIWRRSYDVL 12- 0 Query: 121 PPDMAKDDEHSAHTDRRYASLDDSVIPDAENLKVTLERALPFWEDKIAPALKDGKNVFVG 18- 0 PP+M +DDEHSAHTDRRYASLDDSVIPDAENLKVTLERALPFWEDKIAPALKDGKNVFVG Sbjct: 121 PPNMDRDDEHSAHTDRRYASLDDSVIPDAENLKVTLERALPFWEDKIAPALKDGKNVFVG 18- 0 Query: 181 AHGNSIRALVKHIKQLSDDEIMDVEIPNFPPLVFEFDEKLNLVSEYYLGK 230 AHGNSIRALVKHIK LSDDEIMDVEIPNFPPLVFEFDEKLN+VSEYYLGK Sbjct: 181 AHGNSIRALVKHIKGLSDDEIMDVEIPNFPPLVFEFDEKLNVVSEYYLGK 230 A related DNA sequence was identified in S. pyogenes <SEQ ID 6833> which encodes the amino acid sequence <SEQ ID 6834>. Analysis of this protein sequence reveals the following: TABLE-US-06782 Possible Site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2646(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06783 Identities = 206/229 (89%), Positives = 214/229 (92%) Query: 1 MVKLVFARHGESEWNKANLFTGWADVDLSSKGTQQAIDAGKLIQAAGIEFDLAFTSVLKR 60- MVKLVFARHGESEWNKANLFTGWADVDLSEKGTQQAIDAGKLI+ AGIEFDLAFTSVL R Sbjct: 1 MVKLVFARHGESEWNKANLFTGWADVDLSEKGTQQAIDAGKLIKEAGIEFDLAFTSVLTR 60- Query: 61 AIKTTNLALEAADQLWVPVEKSWRLNERHYGGLTGKNKAEAAEQFGDEQVHIWRRSYDVL 12- 0 AIKTTNLALE A QLWVP EKSWRLNERHYG LTGKNKAEAAEQF DEQVHIWRRSYDVL Sbjct: 61 AIKTTNLALENAGQLWVPTEKSWRLNERHYGALTGKNKAEAAEQFCDEQVHIWRRSYDVL 12- 0 Query: 121 PPDMAKDDEHSAHTDRRYASLDDSVIPDAENLKVTLERALPFWEDKIAPALKDGKNVFVG 18- 0 PP MAKDDE+SAH DRRYA LD ++IPDAENLKVTLERA+P+WE+KIAPAL DGKNVFVG Sbjct: 121 PPAMAKDDEYSAHKDRRYADLDPALIPDAENLKVTLERAMPYWEEKIAPALLDGKNVFVG 18- 0 Query: 181 AHGNSIRALVKHIKQLSDDEIMDVEIPNFPPLVFEFDEKLNLVSEYYLG 229 AHGNSIRALVKHIK LSDDEIMDVEIPNFPPLVFE DEKLN+V EYYLG Sbjct: 181 AHGNSIRALVKHIKGLSDDEIMDVEIPNFPPLVFELDEKLNIVKEYYLG 229 SEQ ID 6832 (GBS110) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 38 (lane 8; MW 28.9 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 41 (lane 10; MW 53.9 kDa). The GBS110-GST fusion product was purified (FIG. 204, lane 5) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 252A), FACS (FIG. 252B), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2214 A DNA sequence (GBSx2333) was identified in S. agalactiae <SEQ ID 6835> which encodes the amino acid sequence <SEQ ID 6836>. This protein is predicted to be triosephosphate isomerase (tpiA). Analysis of this protein sequence reveals the following: TABLE-US-06784 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 36-52 (36-52) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06785 >GP: AAC43268 GB: U07640 triosephosphate isomerase [Lactococcus lactis] Identities = 164/252 (65%), Positives = 202/252 (80%) Query: 1 MSRKPFIAGNWKMNKNPEEAKAFIEAVASKLPSSELVEAGIAAPALTLSTVLEAAKGSEL 60 MSRKP IAGNWKMNK EA+AF+EAV + LPSS+ VE+ I APAL L+ + +GSEL Sbjct: 1 MSRKPIIAGNWKMNKTLSEAQAFVEAVKNNLPSSDNVESVIGAPALFLAPMAYLRQGSEL 60 Query: 61 KIAAQNSYFENSGAFTGENSPKVLAEMGTDYVVIGHSERRDYFHETDQDINKKAKAIFAN 120- K+AA+NSYFEN+GAFTGENSP + ++G +Y++IGHSERR+YFHETD+DINKKAKAIFA Sbjct: 61 KLAAENSYFENAGAFTGENSPAAIVDLGIEYIIIGHSERREYFHETDEDINKKAKAIFAA 120- Query: 121 GLTPIICCGESLETYEAGKAVEFVGAQVSAALAGLSEEQVSSLVIAYEPIWAIGTGKSAT 18- 0 G TPI+CCGE+LET+EAGK E+V Q+ A LAGL+ EQVS+LVIAYEPIWAIGTGK+AT Sbjct: 121 GATPILCCGETLETFEAGKTAEWVSGQIEAGLAGLTAEQVSNLVIAYEPIWAIGTGKTAT 18- 0 Query: 181 QDDAQNMCKAVRDVVAADFGQAVADKVRVQYGGSVKPENVAEYMACPDVDGALVGGASLE 24- 0 + A C VR V +G+ V++ VR+QYGGSVKPE + MA ++DGALVGGASLE Sbjct: 181 NEIADETCGVVRSTVEKLYGKEVSEAVRIQYGGSVKPETIEGLMAKENIDGALVGGASLE 24- 0 Query: 241 AESFLALLDFVK 252 A+SFLALL+ K Sbjct: 241 ADSFLALLEMYK 252 A related DNA sequence was identified in S. pyogenes <SEQ ID 6837> which encodes the amino acid sequence <SEQ ID 6838>. Analysis of this protein sequence reveals the following: TABLE-US-06786 Possible site: 42 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.81 Transmembrane 36-52 (36-52) ----- Final Results ----- bacterial membrane --- Certainty = 0.1723(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06787 Identities = 220/251 (87%), Positives = 237/251 (93%) Query: 1 MSRKPFIAGNWKMNKNPEEAKAFIEAVASKLPSSELVEAGIAAPALTLSTVLEAAKGSEL 60 MSRKP IAGNWKMNKNP+EAKAF+EAVASKLPS++LV+ +AAPA+ L T +EAAK S L Sbjct: 1 MSRKPIIAGNWKMNKNPQEAKAFVEAVASKLPSTDLVDVAVAAPAVDLVTTIEAAKDSVL 60 Query: 61 KIAAQNSYFENSGAFTGENSPKVLAEMGTDYVVIGHSERRDYFHETDQDINKKAKAIFAN 120- K+AAQN YFEN+GAFTGE SPKVLAEMG DYVVIGHSERRDYFHETD+DINKKAKAIFAN Sbjct: 61 KVAAQNCYFENTGAFTGETSPKVLAEMGADYVVIGHSERRDYFHETDEDINKKAKAIFAN 120- Query: 121 GLTPIICCGESLETYEAGKAVEFVGAQVSAALAGLSEEQVSSLVIAYEPIWAIGTGKSAT 18- 0 GLTPI+CCGESLETYEAGKAVEFVGAQVSAALAGLS EQV+SLV+AYEPIWAIGTGKSAT Sbjct: 121 GLTPIVCCGESLETYEAGKAVEFVGAQVSAALAGLSAEQVASLVLAYEPIWAIGTGKSAT 18- 0 Query: 181 QDDAQNMCKAVRDVVAADFGQAVADKVRVQYGGSVKPENVAEYMACPDVDGALVGGASLE 24- 0 QDDAQNMCKAVRDVVAADFGQ VADKVRVQYGGSVKPENV +YMACPDVDGALVGGASLE Sbjct: 181 QDDAQNMCKAVRDVVAADFGQEVADKVRVQYGGSVKPENVKDYMACPDVDGALVGGASLE 24- 0 Query: 241 AESFLALLDFV 251 A+SFLALLDF+ Sbjct: 241 ADSFLALLDFL 251 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2215 A DNA sequence (GBSx2334) was identified in S. agalactiae <SEQ ID 6839> which encodes the amino acid sequence <SEQ ID 6840>. Analysis of this protein sequence reveals the following:

TABLE-US-06788 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3050(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06789 >GP: AAB41198 GB: U75481 elongation factor-Tu [Streptococcus mutans] Identities = 44/45 (97%), Positives = 45/45 (99%) Query: 1 MVMPGDNVTIEVELIHPIAVEQGTTFSIREGGRTVGSGIVSEIEA 45 MVMPGDNVTI+VELIHPIAVEQGTTFSIREGGRTVGSGIVSEIEA Sbjct: 117 MVMPGDNVTIDVELIHPIAVEQGTTFSIREGGRTVGSGIVSEIEA 161 There is also homology to SEQ ID 1022: TABLE-US-06790 Identities = 44/45 (97%), Positives = 44/45 (97%) Query: 1 MVMPGDNVTIEVELIHPIAVEQGTTFSIREGGRTVGSGIVSEIEA 45 MVMPGDNVTI VELIHPIAVEQGTTFSIREGGRTVGSGIVSEIEA Sbjct: 371 MVMPGDNVTINVELIHPIAVEQGTTFSIREGGRTVGSGIVSEIEA 415 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2216 A DNA sequence (GBSx2335) was identified in S. agalactiae <SEQ ID 6841> which encodes the amino acid sequence <SEQ ID 6842>. Analysis of this protein sequence reveals the following: TABLE-US-06791 Possible site: 32 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.66 Transmembrane 81-97 (80-97) INTEGRAL Likelihood = -2.60 Transmembrane 18-34 (17-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.2062(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2217 A DNA sequence (GBSx2336) was identified in S. agalactiae <SEQ ID 6843> which encodes the amino acid sequence <SEQ ID 6844>. Analysis of this protein sequence reveals the following: TABLE-US-06792 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0596(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2218 A DNA sequence (GBSx2337) was identified in S. agalactiae <SEQ ID 6845> which encodes the amino acid sequence <SEQ ID 6846>. Analysis of this protein sequence reveals the following: TABLE-US-06793 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3559(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2219 A DNA sequence (GBSx2338) was identified in S. agalactiae <SEQ ID 6847> which encodes the amino acid sequence <SEQ ID 6848>. Analysis of this protein sequence reveals the following: TABLE-US-06794 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06795 >GP: AAF96286 GB: AE004374 hypothetical protein [Vibrio cholerae] Identities = 56/167 (33%), Positives = 89/167 (52%), Gaps = 12/167 (7%) Query: 18 LAIIKSLPLNDCWLCAGTLRNFVWNKLS-GINETLTSDIDVVFFDKNI---SYEETVVLE 73 - L + L L C++ AG +RN VW+ L + T +DIDV+FFD + YE++ LE Sbjct: 41 LECVYQLELPQCYIAAGFVRNLVWDSLHHNVKLTPLNDIDVIFFDADCLDSDYEKS--LE 98 Query: 74 QQLKDNYPQYDWELKNEFYMNTHSPNTPKYTSSKDAISKFPEKCTAVGARLDDRNQLELY 133- +L + PQ +W++KN+ M+ + + P Y S+ DA+S +PEK TAV R + ++ E Sbjct: 99 LKLSEQMPQLNWQVKNQAKMHLQNGDNP-YQSTLDAMSYWPEKETAVAVRKVEHDRYECI 157- Query: 134 LPYGEEEILNFIVSPTPYFEEDLLRYNVYLKRVDKKKWNNIWPRLTI 180 +G E + ++ P Y ++ RV K W +WP L I Sbjct: 158 SAFGFESLFQGFITHNP-----KRAYGIFENRVKSKGWLAMWPNLRI 199 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2220 A DNA sequence (GBSx2339) was identified in S. agalactiae <SEQ ID 6849> which encodes the amino acid sequence <SEQ ID 6850>. Analysis of this protein sequence reveals the following: TABLE-US-06796 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2779(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06797 >GP: CAB13060 GB: Z99110 yjdF [Bacillus subtilis] Identities = 47/138 (34%), Positives = 93/138 (67%), Gaps = 2/138 (1%) Query: 1 MKMTVYFDGNFWLGLIEYDDDGDYKVFRYFFGKEPKDDDVFNFINHKLNDLIKKYEFVKT 60- MK+T+Y+DG FW+G++E D+G + FR+ FGKEP+D +V F++++L +++ + E + Sbjct: 24 MKLTIYYDGQFWVGVVEVVDNGKLRAFRHLFGKEPRDSEVLEFVHNQLLNMMAQAE--QE 81- Query: 61 DISLKRTNEHKKSPKRMQREINREKRKPVVSTKAQLAMKTIHMSIKNERQLSQKCKKNEL 12- 0 + L+ + K +PKR+QR++++E + V++KAQ A+K + K +++ K ++ + Sbjct: 82 GVRLQGRRQKKINPKRLQRQVSKELKNAGVTSKAQEAIKLELEARKQKKKQIMKEQREHV 14- 1 Query: 121 RKHRYQLKQEKRYQKKKG 138 ++ RY LK++K +K +G Sbjct: 142 KEQRYMLKKQKAKKKHRG 159 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2221 A DNA sequence (GBSx2340) was identified in S. agalactiae <SEQ ID 6851> which encodes the amino acid sequence <SEQ ID 6852>. This protein is predicted to be ComX1. Analysis of this protein sequence reveals the following: TABLE-US-06798 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3143(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9469> which encodes amino acid sequence <SEQ ID 9470> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06799 >GP: AAD50429 GB: AF161701 ComX2 [Streptococcus pneumoniae] Identities = 61/152 (40%), Positives = 95/152 (62%) Query: 5 EELFDKVKPIVMKLRRNYFVQLWEYDDWIQEGRIVLFRLLEEEPYLLDNESKLFIYFKTK 64- +EL+++V+ V K R Y++ LWE DW QEG + L L+ L+D+ +L YFKTK Sbjct: 3 KELYEEVQGTVYKCRNEYYLHLWELSDWDQEGMLCLHELISREEGLVDDIPRLRKYFKTK 62- Query: 65 FSNYLNDVLRHQDCQKRQFNKMPYEEISEVSHYVKSKGLVLDDYIAYRDTLTKVEETLSD 12- 4 F N + D +R Q+ QKR+++K PYEE+ E+SH + GL LDDY + +TL S Sbjct: 63 FRNRILDYIRKQESQKRRYDKEPYEEVGEISHRISEGGLWLDDYYLFHETLRDYRNKQSK 12- 2 Query: 125 IDKEKFEKLISGERFAGKKQFIRDIQPFFNAF 156 +E+ E+++S ERF G+++ +RD++ F F Sbjct: 123 EKQEELERVLSNERFRGRQRVLRDLRIVFKEF 154 A related DNA sequence was identified in S. pyogenes <SEQ ID 6853> which encodes the amino acid sequence <SEQ ID 6854>. Analysis of this protein sequence reveals the following: TABLE-US-06800 Possible site: 39 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.35 Transmembrane 9-25 (7-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.5140(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9163> which encodes the amino acid sequence <SEQ ID 9164>. Analysis of this protein sequence reveals the following: TABLE-US-06801 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.35 Transmembrane 2-18 (1-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.160(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06802 >GP: AAD50429 GB: AF161701 ComX2 [Streptococcus pneumoniae] Identities = 60/149 (40%), Positives = 98/149 (65%) Query: 41 FEKVKPIILKLKRHYYIQLWDRDDWLQEGHIILLQLLERYPELIEEEERLYRYFKTKFSS 10- 0 +E+V+ + K + YY+ LW+ DW QEG + L +L+ R L+++ RL +YFKTKF + Sbjct: 6 YEEVQGTVYKCRNEYYLHLWELSDWDQEGMLCLHELISREEGLVDDIPRLRKYFKTKFRN 65- Query: 101 YLKDLLRRQESQKRQFHKLAYEEIGEVAHAIPSRGLWLDDYVAYQEVIASLENQLNSQER 16- 0 + D +R+QESQKR++ K YEE+GE++H I GLWLDDY + E + N+ + +++ Sbjct: 66 RILDYIRKQESQKRRYDKEPYEEVGEISHRISEGGLWLDDYYLFHETLRDYRNKQSKEKQ 12- 5 Query: 161 MQFQALIRGERFKGRRALLRKISPYFKEF 189 + + ++ ERF+GR+ +LR + FKEF Sbjct: 126 EELERVLSNERFRGRQRVLRDLRIVFKEF 154 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06803 Identities = 78/149 (52%), Positives = 116/149 (77%) Query: 8 FDKVKPIVMKLRRNYFVQLWEYDDWIQEGRIVLFRLLEEHPYLLDNESKLFIYFKTKFSN 67- F+KVKPI++KL+R+Y++QLW+ DDW+QEG I+L +LLE +P L++ E +L+ YFKTKFS+ Sbjct: 41 FEKVKPIILKLKRHYYIQLWDRDDWLQEGHIILLQLLERYPELIEEEERLYRYFKTKFSS 10- 0 Query: 68 YLNDVLRHQDCQKRQFNKMPYEEISEVSHYVKSKGLVLDDYIAYRDTLTKVEETLSDIDK 12- 7 YL D+LR Q+ QKRQF+K+ YEEI EV+H + S+GL LDDY+AY++ + +E L+ ++ Sbjct: 101 YLKDLLRRQESQKRQFHKLAYEEIGEVAEAIPSRGLWLDDYVAYQEVIASLENQLNSQER 16- 0 Query: 128 EKFEKLISGERFAGKKQFIRDIQPFFNAF 156 +F+ LI GERF G++ +R I P+F F Sbjct: 161 MQFQALIRGERFKGRRALLRKISPYFKEF 189 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2222 A DNA sequence (GBSx2341) was identified in S. agalactiae <SEQ ID 6855> which encodes the amino acid sequence <SEQ ID 6856>. Analysis of this protein sequence reveals the following: TABLE-US-06804 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.23 Transmembrane 166-182 (166-182) ----- Final Results ----- bacterial membrane --- Certainty = 0.1893(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06805 >GP: CAA99510 GB: Z75191 ORF YOR283w [Saccharomyces cerevisiae] Identities = 57/226 (25%), Positives = 97/226 (42%), Gaps = 22/226 (9%) Query: 4 VRLYIARHGKTMFNTIGRAQGWSDTPLTTFGELGIKELGLGLKASNISFKEAFSSDSGRT 63- +RL+I RHG+T N QG DT+ GE +LG L++ I F + SSD R Sbjct: 17 IRLFIIRHGQTEHNVKKILQGHKDTSINPTGEEQATKLGHYLRSRGIHFDKVVSSDLKRC 76- Query: 64 LQTMEIILREVQQENIPYTRDKRIREWCFGSLDGGYDGDLFNGVLPRVSNGDMSHLTHEE 12- 3 QT ++L+ +QEN+P + +RE G ++G M E+ Sbjct: 77 RQTTALVLKHSKQENVPTSYTSGLRERYMGVIEG------------------MQITEAEK 11- 8 Query: 124 IANLICQVDTAGWAEPWAILSNRILSGFTAIAKKIEDIGGGNAIVVSHGMTIATFL-WL- 18- 1 A+ + + E R+ + + G N +VSHG I L WL Sbjct: 119 YADKHGSGSFRNFGEKSDDFVARLTGCVEEEVAEASNEGVKNLALVSHGGAIRMILQWLK 17- 8 Query: 182 IDHSTPRSLGLDNGSVSVVDF--EDGTFSIQSIGDMSYREKGREIL 225 ++ + + N SV++VD+ + F ++ +G+ + G ++ Sbjct: 179 YENHQAHKIIVFNTSVTIVDYVKDSKQFIVRRVGNTQHLGDGEFVV 224 A related DNA sequence was identified in S. pyogenes <SEQ ID 6857> which encodes the amino acid sequence <SEQ ID 6858>. Analysis of this protein sequence reveals the following: TABLE-US-06806 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.69 Transmembrane 170-186 (170-186) ----- Final Results ----- bacterial membrane --- Certainty = 0.1277(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06807 >GP: CAA99510 GB: Z75191 ORF YOR283w [Saccharomyces cerevisiae] Identities = 64/231 (27%), Positives = 98/231 (41%), Gaps = 27/231 (11%) Query: 5 RLYIARHGKTMFNTIGRAQGWSDTPLTKKGEEGIRELGLGLKDATIPFKAAFSSDSGRTM 64- RL+I RHG+T N QG DT + GEE +LG L+ I F SSD R Sbjct: 18 RLFIIRHGQTEHNVKKILQGHKDTSINPTGEEQATKLGHYLRSRGIHFDKVVSSDLKRCR 77- Query: 65 QTIEIILRESENEFLPYTKDNRIREWCFGSLEGTYDSELFLGVLPRTKAFENRDNLRDVP 12- 4 QT ++L+ S+ E +P + + +RE G +EG +E Sbjct: 78 QTTALVLKHSKQENVPTSYTSGLRERYMGVIEGMQITEA--------------------- 11- 6 Query: 125 YSELAESIVEVDTANWAEPWEVLRKRIWEGFEAIALSIQNAGGGNALVVSHGMTIGTFL- 18- 3 + A+ E N+ E + R+ E N G N +VSHG I L Sbjct: 117 -EKYADKHGEGSFRNFGEKSDDFVARLTGCVEEEVAEASNEGVKNLALVSHGGAIRMILQ 17- 5 Query: 184 WL--IDPDRDKQYIDNGSVTVVEF--DDGQFTIKTIGDMSYRYRGREIIEE 230 WL + K + N SVT+V++ D QF ++ +G+ + G ++ + Sbjct: 176 WLKYENHQAHKIIVFNTSVTIVDYVKDSKQFIVRRVGNTQHLGDGEFVVSD 226 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06808 Identities = 150/231 (64%), Positives = 182/231 (77%), Gaps = 5/231 (2%) Query: 1 MSKVRLYIARHGKTMFNTIGRAQGWSDTPLTTFGELGIKELGLGLKASNISFKEAFSSDS 60- M+K RLYIARHGRTMFNTIGRAQGWSDTPLT GE GI+ELGLGLK + I FK AFSSDS Sbjct: 1 MTKTRLYIARHGKTMFNTIGRAQGWSDTPLTKKGEEGIRELGLGLKDATIPFKAAFSSDS 60- Query: 61 GRTLQTMEIILREVQQENIPYTRDKRIREWCFGSLDGGYDGDLFNGVLPRV----SNGDM 11- 6 GRT+QT+EIILRE + E +PYT+D RIREWCFGSL+G YD +LF GVLPR + ++ Sbjct: 61 GRTMQTIEIILRESENEFLPYTKDNRIREWCFGSLEGTYDSELFLGVLPRTKAFENRDNL 12- 0 Query: 117 SHLTHEEIANLICQVDTAGWAEPWAILSNRILSGFTAIAKKIEDIGGGNAIVVSHGMTIA 17- 6 + + E+A I +VDTA WAEPW +L RI GF AIA I++ GGGNA+VVSHGMTI Sbjct: 121 RDVPYSELAESIVEVDTANWAEPWEVLRKRIWEGFEAIALSIQNAGGGNALVVSHGMTIG 18- 0 Query: 177 TFLWLIDHSTPRSLGLDNGSVSVVDFEDGTFSIQSIGDMSYREKGREILEK 227 TFLWLID + +DNGSV+VV+F+DG F+I++IGDMSYR +GREI+E+ Sbjct: 181 TFLWLIDPDRDKQY-IDNGSVTVVEFDDGQFTIKTIGDMSYRYRGREIIEE 230 A related GBS gene <SEQ ID 8999> and protein <SEQ ID 9000> were also identified. Analysis of this protein sequence reveals the following: ##STR00162## SEQ ID 9000 (GBS44) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 238 (lane 7; MW 42 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 12 (lane 8; MW 52.4 kDa). Purified Thio-GBS44-His is shown in FIG. 244, lanes 7 & 8. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2223 A DNA sequence (GBSx2342) was identified in S. agalactiae <SEQ ID 6859> which encodes the amino acid sequence <SEQ ID 6860>. This protein is predicted to be d-alanyl-d-alanine carboxypeptidase. Analysis of this protein sequence reveals the following: TABLE-US-06809 Possible Site: 27 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06810 >GP: AAD00280 GB: U78599 putative D,D-carboxypeptidase [Streptococcus mutans] Identities = 108/169 (63%), Positives = 139/169 (81%) Query: 79 ELSPDVVPVENIYLDKRITKQATQFLEAARAIDSREHLISGYRSVAYQEKLFNSYVTQEM 13- 8 E++PDV ++ + +D RI + +FL AA+ IDS EHLISGYRSVAYQE+L+N+Y+ QE Sbjct: 4 EMNPDVTDIDGVKVDSRIAENTRKFLAAAQEIDSSEHLISGYRSVAYQEELYNNYIAQEK 63- Query: 139 TSNPNLTRGQAEKLVKTYSQPAGASEHQTGLAMDMSTVDSLNESDPRVVSQLKKIAPQYG 19- 8 +NP+L++ +A+K V+TYSQP G+SEHQTGLA+DMSTVDSLN+SD VV+++ IAP+YG Sbjct: 64 ANNPSLSQEEAQKQVQTYSQPPGSSEHQTGLAIDMSTVDSLNQSDANVVAKVAAIAPKYG 12- 3 Query: 199 FVLRFPDGKTAETGVGYEDWHYRYVGVESAKYMAKHHLTLEEYITLLKE 247 FVLRFP+GK TG+ YEDWHYRYVGV+SAKYM KH LTLEEY+ LKE Sbjct: 124 FVLRFPEGKKDATGIDYEDWHYRYVGVKSAKYMTKHDLTLEEYLKKLKE 172 A related DNA sequence was identified in S. pyogenes <SEQ ID 6861> which encodes the amino acid sequence <SEQ ID 6862>. Analysis of this protein sequence reveals the following: TABLE-US-06811 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.66 Transmembrane 10-26 (3-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.4864(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases:

TABLE-US-06812 >GP: AAD00280 GB: U78599 putative D,D-carboxypeptidase [Streptococcus mutans] Identities = 118/173 (68%), Positives = 139/173 (80%) Query: 74 ITKEMSPELADINGISVDKRIEQATSDFLAAAQAIDLQEHLISGYRSVDYQTELYQSYIK 13- 3 IT EM+P++ DI+G+ VD RI + T FLAAAQ ID EHLISGYRSV YQ ELY +YI Sbjct: 1 ITAEMNPDVTDIDGVKVDSRIAENTRKFLAAAQEIDSSEHLISGYRSVAYQEELYNNYIA 60- Query: 134 KEMANDPTLTQEAAEALVQTYSQPPGASEHHTGLAIDMSTVDTLNASDPSVAKAVQKIAP 19- 3 +E AN+P+L+QE A+ VQTYSQPPG+SEH TGLAIDHSTVD+LN SD +V V IAP Sbjct: 61 QEKANNPSLSQEEAQKQVQTYSQPPGSSEHQTGLAIDMSTVDSLNQSDANVVAKVAAIAP 12- 0 Query: 194 DYGFVLRFPEGKKTSTGVDYEDWHYRYVGKASARYMAQHNLTLEEYIAALKEK 246 YGFVLRFPEGKK +TG+DYEDWHYRYVG SA+YM +H+LTLEEY+ LKEK Sbjct: 121 KYGFVLRFPEGKKDATGIDYEDWHYRYVGVKSAKYMTKHDLTLEEYLKKLKEK 173 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06813 Identities = 131/235 (55%), Positives = 172/235 (72%), Gaps = 3/235 (1%) Query: 15 LLAILCF--SLFALLKPNSQQSSSQKLRNEDIKKISSQKRNKKLQLPAVSSKDWNLILVN 72- LL ++ F L+ +KP + +Q L ++I++ +K ++ LP VS +DW L+LVN Sbjct: 12 LLIVIVFLGGLYLFIKPEESVTPTQ-LNKKEIQQKDIKKTDRLRALPKVSVEDWELVLVN 70- Query: 73 RDHKHEELSPDVVPVENIYLDKRITKQATQFLEAARAIDSREHLISGYRSVAYQEKLFNS 13- 2 RDH +E+SP++ + I +DKRI + + FL AA+AID +EHLISGYRSV YQ +L+ S Sbjct: 71 RDHITKEMSPELADINGISVDKRIEQATSDFLAAAQAIDLQEHLISGYRSVDYQTELYQS 13- 0 Query: 133 YVTQEMTSNPNLTRGQAEKLVKTYSQPAGASEHQTGLAMDMSTVDSLNESDPRVVSQLKK 19- 2 Y+ +EM ++P LT+ AE LV+TYSQP GASEH TGLA+DMSTVD+LN SDP V ++K Sbjct: 131 YIKKEMANDPTLTQEAAEALVQTYSQPPGASEHHTGLAIDMSTVDTLNASDPSVAKAVQK 19- 0 Query: 193 IAPQYGFVLRFPDGKTAETGVGYEDWHYRYVGVESAKYMAKHHLTLEEYITLLKE 247 IAP YGFVLRFP+GK TGV YEDWHYRYVG SA+YMA+H+LTLEEYI LKE Sbjct: 191 IAPDYGFVLRFPEGKKTSTGVDYEDWHYRYVGKASARYMAQHNLTLEEYIAALKE 245 A related GBS gene <SEQ ID 9001> and protein <SEQ ID 9002> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-06814 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: 14.03 GvH: Signal Score (-7.5): -1.02 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 10.08 threshold: 0.0 PERIPHERAL Likelihood = 10.08 56 modified ALOM score: -2.52 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00163## SEQ ID 6860 (GBS18) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 4 (lane 3; MW 31 kDa). The GBS18-His fusion product was purified (FIG. 93A; see also FIG. 189, lane 11) and used to immunise mice (lane 2 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 93B), FACS (FIG. 93C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. EXAMPLE 2224 A DNA sequence (GBSx2343) was identified in S. agalactiae <SEQ ID 6863> which encodes the amino acid sequence <SEQ ID 6864>. This protein is predicted to be unnamed protein product. Analysis of this protein sequence reveals the following: TABLE-US-06815 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.58 Transmembrane 10-26 (3-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.6031(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 6865> which encodes the amino acid sequence <SEQ ID 6866>. Analysis of this protein sequence reveals the following: TABLE-US-06816 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.83 Transmembrane 10-26 (4-33) ----- Final Result ----- bacterial membrane --- Certainty = 0.5734(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06817 >GP:AAD00279 GB:U78599 putative N-acetyl-muramidase [Streptococcus mutans] Identities = 66/150 (44%), Positives = 97/150 (64%), Gaps = 5/150 (3%) Query: 18 LLLIVCPLLSSQRIASADKEVRVNYSQKQFITKNGKEVKPLAKYYGIRPSILIAQILLET 77 - LL+I+ P+L+S +A A+K++ YS K+F+ ++ + L+K YG+R SI+I Q L++ Sbjct: 3 LLVILLPILASGGLADANKKNPSPYSHKEFVKEIAPTAQKLSKIYGVRSSIIIGQAALDS 62 Query: 78 HDGKTLLASKYHNLFSKKATPGQVAITLKSPKQTN---QNV--RYAIYKDDASAIRDYLR 132- H G TLLASKYHNLFS +A+PGQ A+ LKS + N Q V RY +Y+ ++ DY+ Sbjct: 63 HFGSTLLASKYHNLFSIEASPGQGAVRLKSHEYKNGRWQEVTNRYLVYESWKESLYDYMA 122- Query: 133 MLRQGKEVDKRLYRNLATEKGYKAPAKSLQ 162 +L K DK LY + T GYK A++LQ Sbjct: 123 ILHGNKIWDKALYTTMMTSSGYKTVARALQ 152 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06818 Identities = 67/190 (35%), Positives = 102/190 (53%), Gaps = 1/190 (0%) Query: 1 MRKRFSLLNFIVVTFIFFFWILFPLLNHKGKVDANSRQSVTYTKEEFIQKIVPDAQDLGK 60 MRKR F+ + F I+ PLL+ + A+ V Y++++FI K+ + + L K Sbjct: 1 MRKRLKFPYFLTLLACFLLLIVCPLLSSQRIASADKEVRVNYSQKQFITKMGKEVKPLAK 60 Query: 61 SYGIRPSFIIAQAALDSDFGEKILANKYHNLFGLLAEPGTPSITLNDSSTGKKQEKQFTH 120- YGIRPS +IAQ L++ G+ +LA+KYHNLF A PG +ITL S Q ++ Sbjct: 61 YYGIRPSILIAQILLETHDGKTLLASKYHNLFSKKATPGQVAITLK-SPKQTNQNVRYAI 119- Query: 121 YKSWKYSMYDYLAHIKSGATGKKDSYTIMVSVKNPKTLVQKLQDSGFDNDKKYAKKMTEI 18- 0 YK ++ DYL ++G K Y + + K K + LQ DK YA+++++ Sbjct: 120 YKDDASAIRDYLRMLRQGKEVDKRLYRNLATEKGYKAPAKSLQKYLHYTDKTYARRLIQV 17- 9 Query: 181 IDLYDLTRYD 190 I+ DLT YD Sbjct: 180 IESNDLTNYD 189 SEQ ID 6864 (GBS246) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 61 (lane 7; MW 24.6 kDa). GBS246d was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 154 (lane 14 & 15; MW 21 kDa) and in FIG. 183 (lane 4; MW 21 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 187 (lane 12; MW 46 kDa). Purified GBS246d-GST is shown in FIG. 243, lane 12. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2225 A DNA sequence (GBSx2344) was identified in S. agalactiae <SEQ ID 6867> which encodes the amino acid sequence <SEQ ID 6868>. Analysis of this protein sequence reveals the following: TABLE-US-06819 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2541(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06820 >GP:AAC45610 GB:U78296 repressor of class I heat shock gene expression HrcA [Streptococcus mutans] Identities = 227/345 (65%), Positives = 287/345 (82%), Gaps = 1/345 (0%) Query: 17 VITQRQNDILNLIVELFTQTHEPVGSKALQRTIDSSSATIRNDMAKLEKLGLLEKAHTSS 76 - +ITQRQ DILNLIVELFT+THEP+GSK LQ +I SS ATIRNDMA LEKLGLLEKA T Sbjct: 1 MITQRQKDILNLIVELFTKTHEPIGSKTLQNSIASSRATIRNDMAALEKLGLLEKATTPP 60 Query: 77 GRM-PSPAGFKYFVEHSLRLDSIDEQDIYHVIKAFDFEAFKLEDMLQKASHILSEMTGYT 135- +P +YFVEHSL DS+DEQD+Y VIKAFDFEAF+L D+LQ+AS +L+ +TGYT Sbjct: 61 AVVCPVKKAIRYFVEHSLNPDSLDEQDVYQVIKAFDFEAFRLGDLLQRASDVLANLTGYT 120- Query: 136 SVILDVEPARQRLTGFDVVQLSNHDALAVNTLDESKPVTVQFAIPRNFLTRDLIAFKAIV 19- 5 ++ILDVEP +QRLT FD+V+LSNHDALAV+TLDE+ PVTVQFAIP+NFL DL+ I Sbjct: 121 ALILDVEPKKQRLTTFDIVKLSNHDALAVLTLDEASPVTVQFAIPKNFLDSDLMTVAKIA 18- 0 Query: 196 EERLLDGSVMDIHYKLRTEIPQIVQKYFVTTDNVLQLFDYVFSELFLETVFVAGKVNSLT 25- 5 ER L+ +V+DIHY+LRTE PQI+QKYF TDNVL LFD++F+ +F E VF++GK+ +L Sbjct: 181 RERFLNQTVLDIHYRLRTEPPQIIQKYFPRTDNVLDLFDHIFNPIFQEEVEISGKIKTLE 24- 0 Query: 256 YSDLSTYQFLDNEQQVAISLRQSLKEGEMASVQVADSQEAALADVSVLTHKFLIPYRGFG 31- 5 ++ L TYQFL+N Q VA+ +RQSL E E+ VQVADS+E +LAD++V++ KFLIPYRGFG Sbjct: 241 FAGLDTYQFLENLQSVALEIRQSLPEDELHRVQVADSKEKSLADLTVISQKFLIPYRGFG 30- 0 Query: 316 LLSLIGPIDMDYRRSVSLVNIIGKVLAAKLGDYYRYLNSNHYEVH 360 +L++IGP+D+DY+R++SL+N+I +VLA KLGD+YRYLNSNHYEVH Sbjct: 301 ILTVIGPVDLDYQRTISLINVISRVLAVKLGDFYRYLNSNHYEVH 345 A related DNA sequence was identified in S. pyogenes <SEQ ID 6869> which encodes the amino acid sequence <SEQ ID 6870>. Analysis of this protein sequence reveals the following: TABLE-US-06821 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0695(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06822 Identities = 341/344 (99%), Positives = 343/344 (99%) Query: 17 VITQRQNDILNLIVELFTQTHEPVGSKALQRTIDSSSATIRNDMAKLEKLGLLEKAHTSS 76 - VITQRQNDILNLIVELFTQTHEPVGSKALQRTIDSSSATIRNDMAKLEKLGLLEKAHTSS Sbjct: 1 VITQRQNDILNLIVELFTQTHEPVGSKALQRTIDSSSATIRNDMAKLEKLGLLEKAHTSS 60 Query: 77 GRMPSPAGFKYFVEHSLRLDSIDEQDIYHVIKAFDFEAFKLEDMLQKASHILSEMTGYTS 136- GRMPSPAGFKYFVEHSLRLDSIDEQDIYHVIKAFDFEAFKLEDMLQKASHIL+EMTGYTS Sbjct: 61 GRMPSPAGFKYFVEHSLRLDSIDEQDIYHVIKAFDFEAFKLEDMLQKASHILAEMTGYTS 120- Query: 137 VILDVEPARQRLTGFDVVQLSNHDALAVMTLDESKPVTVQFAIPRNFLTRDLIAFKAIVE 19- 6 VILDVEPARQRLTGFDVVQLSNHDALAVMTLDESKPVTVQFAIPRNFLTRDLIAFKAIVE Sbjct: 121 VILDVEPARQRLTGFDVVQLSNHDALAVMTLDESKPVTVQFAIPRNFLTRDLIAFKAIVE 18- 0 Query: 197 ERLLDGSVMDIHYKLRTEIPQIVQKYFVTTDNVLQLFDYVFSELFLETVFVAGKVNSLTY 25- 6 ERLLD SV+DIHYKLRTEIPQIVQKYFVTTDNVLQLFDYVFSELFLETVFVAGKVNSLTY Sbjct: 181 ERLLDNSVIDIHYKLRTEIPQIVQKYFVTTDNVLQLFDYVFSELFLETVFVAGKVNSLTY 24- 0 Query: 257 SDLSTYQFLDNEQQVAISLRQSLKEGEMASVQVADSQEAALADVSVLTHKFLIPYRGFGL 31- 6 SDLSTYQFLDNEQQVAISLRQSLKEGEMASVQVADSQEAALADVSVLTHKFLIPYRGFGL Sbjct: 241 SDLSTYQFLDNEQQVAISLRQSLKEGEMASVQVADSQEAALADVSVLTHKFLIPYRGFGL 30- 0 Query: 317 LSLIGPIDMDYRRSVSLVNIIGKVLAAKLGDYYRYLNSNHYEVH 360 LSLIGPIDMDYRRSVSLVNIIGKVLAAKLGDYYRYLNSNHYEVH Sbjct: 301 LSLIGPIDMDYRRSVSLVNIIGKVLAAKLGDYYRYLNSNHYEVH 344 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2226 A DNA sequence (GBSx2345) was identified in S. agalactiae <SEQ ID 6871> which encodes the amino acid sequence <SEQ ID 6872>. This protein is predicted to be grpe protein (grpE). Analysis of this protein sequence reveals the following: TABLE-US-06823 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5138(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06824 >GP: AAC45611 GB: U78296 GrpE [Streptococcus mutans] Identities = 130/180 (72%), Positives = 151/180 (83%), Gaps = 3/180 (1%) Query: 14 VSEEIKKDDLQEEVEATE--TEETVEEVIEEIPEKSELELANERADEFENKYLRAHAEM- 70 - +S++ KK++ +EEVEATE TEE+VEEV EE E EL+ A ERA++FENKYLRAHAEM Sbjct: 1 MSKKDKKEEYKEEVEATEPTTEESVEEVAEETSENKELQEALERAEDFENKYLRAHAEMP 60 Query: 71 QNIQRRSSEERQQLQRYRSQDLAKAILPSLDNLERALAVEGLTDDVKKGLEMTRDSLIQA 130- + + + QRYRSQDL KAILPSLDNLERALAVEGLTDDVKKGLEM ++SLIQA Sbjct: 61 KTFSVALMKSDKVCQRYRSQDLRKAILPSLDNLERALAVEGLTDDVKKGLEMVQESLIQA 120- Query: 131 LKEEGVEEVEVDSFDHNFHMAVQTLPADDEHPADSIAEVFQKGYKLHERLLRPAMVVVYN 19- 0 LKEEGVEEVE+++FD N HMAVQTL ADD+HPADSIA+V QKGY+LHERLLRPAMVVVYN Sbjct: 121 LKEEGVEEVELENFDANLHMAVQTLDADDDHPADSIAQVHQKGYQLHERLLRPAMVVVYN 18- 0 A related DNA sequence was identified in S. pyogenes <SEQ ID 6873> which encodes the amino acid sequence <SEQ ID 6874>. Analysis of this protein sequence reveals the following: TABLE-US-06825 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5138(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06826 Identities = 189/190 (99%), Positives = 189/190 (99%) Query: 1 MAVFNKLFKRRHSVSEEIKKDDLQEEVEATETEETVEEVIEEIPEKSELELANERADEFE 60 MAVFNKLFKRRHSVSEEIKKDDLQEEVEATETEETVEEVIEE PEKSELELANERADEFE Sbjct: 1 MAVFNKLFKRRHSVSEEIKKDDLQEEVEATETEETVEEVIEETPEKSELELANERADEFE 60 Query: 61 NKYLRAHAEMQNIQRRSSEERQQLQRYRSQDLAKAILPSLDNLERALAVEGLTDDVKKGL 120- NKYLRAHAEMQNIQRRSSEERQQLQRYRSQDLAKAILPSLDNLERALAVEGLTDDVKKGL Sbjct: 61 NKYLRAHAEMQNIQRRSSEERQQLQRYRSQDLAKAILPSLDNLERALAVEGLTDDVKKGL 120- Query: 121 EMTRDSLIQALKEEGVEEVEVDSFDHNFHMAVQTLPADDEHPADSIAEVFQKGYKLHERL 18- 0 EMTRDSLIQALKEEGVEEVEVDSFDHNFHMAVQTLPADDEHPADSIAEVFQKGYKLHERL Sbjct: 121 EMTRDSLIQALKEEGVEEVEVDSFDHNFHMAVQTLPADDEHPADSIAEVFQKGYKLHERL 18- 0 Query: 181 LRPAMVVVYN 190 LRPAMVVVYN Sbjct: 181 LRPAMVVVYN 190 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2227 A DNA sequence (GBSx2346) was identified in S. agalactiae <SEQ ID 6875> which encodes the amino acid sequence <SEQ ID 6876>. This protein is predicted to be heat shock protein 70 (dnaK). Analysis of this protein sequence reveals the following: TABLE-US-06827 Possible Site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0996(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 6877> which encodes the amino acid sequence <SEQ ID 6878>. Analysis of this protein sequence reveals the following: TABLE-US-06828 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0996(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06829 Identities = 594/609 (97%), Positives = 603/609 (98%), Gaps = 1/609 (0%) Query: 1 MSKIIGIDLGTTNSAVAVLEGTESKIIANPEGNRTTPSVVSFKNGEIIVGDAAKRQAVTN 60 MSKIIGIDLGTTNSAVAVLEGTESKIIANPEGNRTTPSVVSFKNGEIIVGDAAKRQAVTN Sbjct: 1 MSKIIGIDLGTTNSAVAVLEGTESKIIANPEGNRTTPSVVSFKNGEIIVGDAAKRQAVTN 60 Query: 61 PDTVISIKSKMGTSEKVSANGKEYTPQEISAMILQYLKGYAEDYLGEKVEKAVITVPAYF 120- P+TVISIKSKMGTSEKVSANGKEYTPQEISAMILQYLKGYAEDYLGEKVEKAVITVPAYF Sbjct: 61 PETVISIKSKMGTSEKVSANGKEYTPQEISAMILQYLKGYAEDYLGEKVEKAVITVPAYF 120- Query: 121 NDAQRQATKDAGKIAGLEVERIVNEPTAAALAYGMDKTDKDEKILVFDLGGGTFDVSILE 18- 0 NDAQRQATKDAGKIAGLEVERIVNEPTAAALAYGMDKTDKDEKILVFDLGGGTFDVSILE Sbjct: 121 NDAQRQATKDAGKIAGLEVERIVNEPTAAALAYGMDKTDKDEKILVFDLGGGTFDVSILE 18- 0 Query: 181 LGDGVFDVLATAGDNKLGGDDFDQKIIDFLVEEFKKENGIDLSQDKMALQRLKDAAEKAK 24- 0 LGDGVFDVLATAGDNKLGGDDFDQKIIDFLV EFKKENGIDLSQDKMALQRLKDAAEKAK Sbjct: 181 LGDGVFDVLATAGDNKLGGDDFDQKIIDFLVAEFKKENGIDLSQDKMALQRLKDAAEKAK 24- 0 Query: 241 KDLSGVTQTQISLPFITAGSAGPLHLEMSLSRAKFDDLTRDLVERTKTPVRQALSDAGLS 30- 0 KDLSGVTQTQISLPFITAGSAGPLHLEMSLSRAKFDDLTRDLVERTKTPVRQALSDAGLS Sbjct: 241 KDLSGVTQTQISLPFITAGSAGPLHLEMSLSRAKFDDLTRDLVERTKTPVRQALSDAGLS 30- 0 Query: 301 LSEIDEVILVGGSTRIPAVVEAVKAETGKEPNKSVNPDEVVAMGAAIQGGVITGDVKDVV 36- 0 LSEIDEVILVGGSTRIPAVVEAVKAETGKEPNKSVNPDEVVAMGAAIQGGVITGDVKDVV Sbjct: 301 LSEIDEVILVGGSTRIPAVVEAVKAETGKEPNKSVNPDEVVAMGAAIQGGVITGDVKDVV 36- 0 Query: 361 LLDVTPLSLGIETMGGVFTKLIDRNTTIPTSKSQVFSTAADNQPAVDIHVLQGERPMAAD 42- 0 LLDVTPLSLGIETMGGVFTKLIDRNTTIPTSKSQVFSTAADNQPAVDIHVLQGERPMAAD Sbjct: 361 LLDVTPLSLGIETMGGVFTKLIDRNTTIPTSKSQVFSTAADNQPAVDIHVLQGERPMAAD 42- 0 Query: 421 NKTLGRFQLTDIPAAPRGIPQIEVTFDIDKNGIVSVKAKDLGTQKEQHIVIQSNSGLTDE 48- 0 NKTLGRFQLTDIPAAPRGIPQIEVTFDIDKNGIVSVKAKDLGTQKEQHIVI+SN GL++E Sbjct: 421 NKTLGRFQLTDIPAAPRGIPQIEVTFDIDKNGIVSVKAKDLGTQKEQHIVIKSNDGLSEE 48- 0 Query: 481 EIDKMMKDAEANAEADAKRKEEVDLKNEVDQAIFATEKTIKETEGKGFDTERDAAQSALD 54- 0 EID+MMKDAEANAEADAKRKEEVDLKNEVDQAIFATEKTIKETEGKGFDTERDAAQSALD Sbjct: 481 EIDRMMKDAEANAEADAKRKEEVDLKNEVDQAIFATEKTIKETEGKGFDTERDAAQSALD 54- 0 Query: 541 ELKKAQESGNLDDMKAKLEALNEKAQALAVKLYEQAAAAQQAAQGAEGAQSADSSSKGDD 60- 0 ELK AQESGNLDDMKAKLEALNEKAQALAVK+YEQAAAAQQAAQGAEGAQ+ DS++ DD Sbjct: 541 ELKAAQESGNLDDMKAKLEALNEKAQALAVKMYEQAAAAQQAAQGAEGAQANDSAN-NDD 59- 9 Query: 601 VVDGEFTEK 609 VVDGEFTEK Sbjct: 600 VVDGEFTEK 608 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2228 A DNA sequence (GBSx2347) was identified in S. agalactiae <SEQ ID 6879> which encodes the amino acid sequence <SEQ ID 6880>. This protein is predicted to be Streptococcus pneumoniae DnaJ protein homologue (dnaJ). Analysis of this protein sequence reveals the following:

TABLE-US-06830 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4180(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 6881> which encodes the amino acid sequence <SEQ ID 6882>. Analysis of this protein sequence reveals the following: TABLE-US-06831 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1322(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06832 Identities = 330/377 (87%), Positives = 357/377 (94%), Gaps = 1/377 (0%) Query: 1 MNNTEFYDRLGVSKDASQDEIKKAYRRMSKKYHPDINKETGAEEKYKEVQEAYETLSDTQ 60 MNNTE+YDRLGVSKDASQD+IKKAYR+MSKKYHPDINKE GAE+KYK+VQEAYETLSD+Q Sbjct: 19 MNNTEYYDRLGVSKDASQDDIKKAYRKMSKKYHPDINKEAGAEQKYKDVQEAYETLSDSQ 78 Query: 61 KRAAYDQYGAAGANGGFGGFDGGGFGGFDGGGFGGFEDIFSSFFGGGGMRNPNAPRQGDD 120- KRAAYDQYGAAGA GGFGG GGFGGFDGGGFGGFEDIFSSFFGGGG RNPNAPRQGDD Sbjct: 79 KRAAYDQYGAAGAQGGFGG-GAGGFGGFDGGGFGGFEDIFSSFFGGGGSRNPNAPRQGDD 137- Query: 121 LQYRVNLSFEEAIFGAEKEVSYNRESSCHTCSGSGAKPGTSPVTCQKCHGSGVINVDTQT 18- 0 LQYRVNLSFEEA+FG EKEVSYNRE++C TC GSGAKPGT+PVTC+KCHGSGV+ +DTQT Sbjct: 138 LQYRVNLSFEEAVFGVEKEVSYNREATCGTCLGSGAKPGTAPVTCRKCHGSGVMTIDTQT 19- 7 Query: 181 PLGTMRRQVTCDVCQGSGQEIKEKCPTCHGTGHEKKTHKVSVKIPAGVETGQQIRLTGQG 24- 0 PLG MRRQVTCD+C GSG+EIKE C TCHGTGHEK+ HKVSVKIPAGVETGQQIRL GQG Sbjct: 198 PLGMMRRQVTCDICHGSGKEIKEPCQTCHGTGHEKQAHKVSVKIPAGVETGQQIRLQGQG 25- 7 Query: 241 EAGFNGGPYGDLFVIINVLPSQQFERNGSTIYYTLNISFVQAALGDTIDIPTVHGAVEMS 30- 0 EAGFNGGPYGDLFVI+NVLPS+QFERNGSTIYY L+ISF QAALGDT++IPTVHG VEM+ Sbjct: 258 EAGFNGGPYGDLFVILNVLPSKQFERNGSTIYYNLDISFTQAALGDTVEIPTVHGDVEMA 31- 7 Query: 301 IPAGTQTGKTFRLRGKGAPKLRGGGQGDQHVTVNIVTPTKLNDAQKEALHAFAEASGDKM 36- 0 IPAGTQTGKTFRL+GKGAPKLRGGGQGDQHVTVNIVTPTKLNDAQ+EAL AFAEASG+KM Sbjct: 318 IPAGTQTGKTFRLKGKGAPKLRGGGQGDQHVTVNIVTPTKLNDAQREALQAFAEASGEKM 37- 7 Query: 361 VHPKKKGFFDKVKDALD 377 +HPKKKGFFDKVKDAL+ Sbjct: 378 LHPKKKGFFDKVKDALE 394 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2229 A DNA sequence (GBSx2348) was identified in S. agalactiae <SEQ ID 6883> which encodes the amino acid sequence <SEQ ID 6884>. Analysis of this protein sequence reveals the following: TABLE-US-06833 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.22 Transmembrane 281-297 (281-297) ----- Final Results ----- bacterial membrane --- Certainty = 0.1086(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06834 >GP: AAD24445 GB: AF118389 unknown [Streptococcus suis] Identities = 182/373 (48%), Positives = 257/373 (68%), Gaps = 5/373 (1%) Query: 4 KVEEIRSYLIASIQNGKLAPGDRLPSIRQLANQFSCNKDTVQRVLMELRFDNYIYAKPRS 63 K + I ++ I+ + G++LPSIRQL Q+ C+KDTVQ+ ++EL++ N IYA +S Sbjct: 3 KYQVIIQDILTGIEEHRFKRGEKLPSIRQLREQYHCSKDTVQKAMLELKYQNKIYAVEKS 62 Query: 64 GYYVFDSHQEEVEEGVSLPNSEIANIAYDDFRLCLNETLIGREDYLFNYYYRQEGLLDLS 123- GYY+ + + + + ++ I Y+DFR+CL E+LIGRE+YLFNYY++QEGL +L Sbjct: 63 GYYILEDRDFQ-DHTCRAQSYRLSRITYEDFRICLKESLIGRENYLFNYYHQQEGLAELI 121- Query: 124 KAVAKLMEETGVYVPLDDIVITAGTQQALFILTQVTFPNRKSRVLIEEPTYPRMIELIKT 18- 3 +V L+ + VY D +VITAG+QQAL+ILTQ+ K+ +LIE PTY RMIELI+ Sbjct: 122 SSVQSLLMDYHVYTKKDQLVITAGSQQALYILTQMETLAGKTEILIENPTYSRMIELIRH 18- 1 Query: 184 QNLPYETISRGTHGIDFQRLEEIFQTQSIKFFYVIPRMHNPLGTSYNPVEMKRLIEMAEK 24- 3 Q +PY+TI R GID + LE IFQT IKFFY IPR+HNPLG++Y+ ++++A++ Sbjct: 182 QGIPYQTIERNLDGIDLEELESIFQTGKIKFFYTIPRLHNPLGSTYDIATKTAIVKLAKQ 24- 1 Query: 244 YDVYIVEDDYMSDFASQS--PLHYYDTHGRVIYLKSFSKAIFPALRLAAICLPQALKSTF 30- 1 YDVYI+EDDY++DF S PLHY DT RVIY+KSF+ +FPALR+ AI LP L+ F Sbjct: 242 YDVYIIEDDYLADFDSSHSLPLHYLDTDNRVIYIKSFTPTLFPALRIGAISLPNQLRDIF 30- 1 Query: 302 MAYKKLMDYDTNLILQKALALYIENGLYAKNSQYLKYRYQKDLANSKSILADHP-NLPSY 36- 0 + +K L+DYDTNLI+QKAL+LYI+NG++A+N+Q+L + Y K L + N+P Y Sbjct: 302 IKHKSLIDYDTNLIMQKALSLYIDNGMFARNTQHLHHIYHAQWNKIKDCLEKYALNIP-Y 36- 0 Query: 361 SLHHDSVLFDCSK 373 + SV F SK Sbjct: 361 RIPKGSVTFQLSK 373 A related DNA sequence was identified in S. pyogenes <SEQ ID 6885> which encodes the amino acid sequence <SEQ ID 6886>. Analysis of this protein sequence reveals the following: TABLE-US-06835 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3043(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06836 Identities = 176/382 (46%), Positives = 255/382 (66%), Gaps = 7/382 (1%) Query: 1 MVTKVEEIRSYLIASIQNGKLAPGDRLPSIRQLANQFSCNKDTVQRVLMELRFDNYIYAK 60 M TK + I S + IQ +L GD+LPSIR L+ + C+KDTVQR L+EL++ + IYA Sbjct: 1 MTTKYQTIISNIEQDIQKQRLKKGDKLPSIRVLSKVYYCSKDTVQRALLELKYRHLIYAV 60 Query: 61 PRSGYYVFDSHQEEVEEGVSLPNSEIANIAYDDFRLCLNETLIGREDYLFNYYYRQEGLL 120- P+SGYYV + + ++L + N+AY+DFRLCLNE L ++ YLF+YY++ EGL Sbjct: 61 PKSGYYVL-GNVSMPDNVLNLSLEDYNNMAYEDFRLCLNEALSAKDKYLFHYYHKTEGLE 119- Query: 121 DLSKAVAKLMEETGVYVPLDDIVITAGTQQALFILTQVTFPNRKSRVLIEEPTYPRMIEL 18- 0 +L +A+ + E VY D ++IT+GTQQAL+IL+Q+ FPN +L+E+PTY RM + Sbjct: 120 ELREALLLYLAENSVYSNKDQLLITSGTQQALYILSQMPFPNTGKTILLEKPTYHRMEAI 17- 9 Query: 181 IKTQNLPYETISRGTHGIDFQRLEEIFQTQSIKFFYVIPRMHNPLGTSYNPVEMKRLIEM 24- 0 + LPY+TISR +G+D + LE +FQT IKFFY I R +PLG SY+ E + ++ + Sbjct: 180 VAQLGLPYQTISRHFNGLDLELLESLFQTGDIKFFYTISRFSHPLGLSYSTKEKEAIVRL 23- 9 Query: 241 AEKYDVYIVEDDYMSDFA--SQSPLHYYDTHGRVIYLKSFSKAIFPALRLAAICLPQALK 29- 8 A++Y VYI+EDDY+ DF + P+HYYDTH R+IYLKSFS ++FPALR+ A+ LP LK Sbjct: 240 AQRYQVYILEDDYLGDFVKLKEPPIHYYDTHHRIIYLKSFSMSVFPALRIGALVLPSGLK 29- 9 Query: 299 STFMAYKKLMDYDTNLILQKALALYIENGLYAKNSQYLKYRYQKDLANSKSILADHPNLP 35- 8 F+ K L+D DTNL++QKALALY+ENG++ KN +++K RY K ++ N P Sbjct: 300 PHFLTQKSLIDLDTNLLMQKALALYLENGMFQKNLRFIK-RYLKQRERQLALFLKQ-NCP 35- 7 Query: 359 S--YSLHHDSVLFDCSKLDNFK 378 Y L ++ D + D+++ Sbjct: 358 DIHYQLTPTHLVIDYTTSDSYR 379 SEQ ID 6884 (GBS423) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 79 (lane 7; MW 49.3 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 172 (lane 2; MW 74 kDa). GBS423-GST was purified as shown in FIG. 219, lane 2-3. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2230 A DNA sequence (GBSx2349) was identified in S. agalactiae <SEQ ID 6887> which encodes the amino acid sequence <SEQ ID 6888>. This protein is predicted to be pseudouridylate synthase I (truA). Analysis of this protein sequence reveals the following: TABLE-US-06837 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3265(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06838 >GP: BAB03886 GB: AP001507 tRNA pseudouridine synthase A (pseudouridylate synthase I) [Bacillus halodurans] Identities = 105/240 (43%), Positives = 147/240 (60%), Gaps = 2/240 (0%) Query: 1 MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDVGVHAYG 60 M R +++YDG+ F+G+Q QPN RTVQ E+E LK ++ G + + +GRTD GVHA G Sbjct: 1 MKRIGLKVAYDGTDFAGYQIQPNERTVQGELESVLKNIHKGMSIRVTASGRTDTGVHARG 60 Query: 61 QVIHFDLPQARDVEKLRFGLDTQCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIGRP 120- Q++HFD + V++ L++Q P DI +++ V DFH RY K Y + V Sbjct: 61 QIVHFDTSLSFPVDRWPIALNSQLPADICVLEAADVPADFHARYSAKTKEYRYRVLTSAQ 120- Query: 121 KNPMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQFEA 18- 0 + RNY H YP+ +E MQ A L+GTHDF+ F A+ VE+KVRTI D + E Sbjct: 121 ADVFRRNYTYHVRYPLDVEAMQRAAVQLLGTHDFSSFCAAKAEVEDKVRTIEDVALWREG 18- 0 Query: 181 SKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAAGNGL 24- 0 + LIF+ GNGFLY VR +VGTLL+IG G+ ++ IL A++R+ AG TA G+GL Sbjct: 181 DE--LIFSIRGNGFLYNMVRIIVGTLLEIGAGKRSAEEVAKILAARSREAAGKTAPGHGL 23- 8 A related DNA sequence was identified in S. pyogenes <SEQ ID 6889> which encodes the amino acid sequence <SEQ ID 6890>. Analysis of this protein sequence reveals the following: TABLE-US-06839 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2558(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06840 Identities = 184/249 (73%), Positives = 214/249 (85%) Query: 1 MTRYKAQISYDGSAFSGFQRQPNCRTVQEEIERTLKRLNSGNDVIIHGAGRTDVGVHAYG 60 M RYKA ISYDG+ FSGFQRQ + RTVQEEIE+TL +LN+G +IIHGAGRTD GVHAYG Sbjct: 1 MVRYKATISYDGTLFSGFQRQRHLRTVQEEIEKTLYKLNNGTKIIIHGAGRTDAGVHAYG 60 Query: 61 QVIHFDLPQARDVEKLRFGLDTQCPDDIDIVKVEQVSDDFHCRYDKHIKTYEFLVDIGRP 120- QVIHFDLPQ ++VEKLRF LDTQ P+DID+V +E+V+DDFHCRY KH+KTYEFLVD GRP Sbjct: 61 QVIHFDLPQEQEVEKLRFALDTQTPEDIDVVNIEKVADDFHCRYQKHLKTYEFLVDNGRP 120- Query: 121 KNPMMRNYATHYPYPVIIELMQEAIKDLVGTHDFTGFTASGTSVENKVRTIFDAKIQFEA 18- 0 KNPMMR+Y THYPY + I+LMQEAI LVGTHDFTGFTA+GTSV+NKVRTI A + + Sbjct: 121 KNPMMRHYTTHYPYTLNIKLMQEAINGLVGTHDFTGFTAAGTSVQNKVRTITKATVSRDE 18- 0 Query: 181 SKNLLIFTFTGNGFLYKQVRNMVGTLLKIGNGRMPISQIKTILQAKNRDLAGPTAAGNGL 24- 0 + L+FTF+GNGFLYKQVRNMVGTLLKIGNG+MP+ Q+K IL +KNR LAGPT +GNGL Sbjct: 181 KTDFLVFTFSGNGFLYKQVRNMVGTLLKIGNGQMPVEQVKVILSSKNRQLAGPTISGNGL 24- 0 Query: 241 YLKEIIYED 249 YLKEI YE+ Sbjct: 241 YLKEICYEN 249 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2231 A DNA sequence (GBSx2350) was identified in S. agalactiae <SEQ ID 6891> which encodes the amino acid sequence <SEQ ID 6892>. This protein is predicted to be phosphomethypyrimidine kinase (thiD). Analysis of this protein sequence reveals the following: TABLE-US-06841 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2051(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06842 >GP: CAB15828 GB: Z99123 phosphomethylpyrimidine kinase [Bacillus subtilis] Identities = 95/253 (37%), Positives = 150/253 (58%), Gaps = 13/253 (5%) Query: 1 MKTRNVLAISGNDIFSGGGLHADLATYVVNKLHGFVAVTCLTAMSDKG---FEVIPIEAS 57 M L I+G+D G G+ ADL T+ ++G A+T + AM +V PI+ Sbjct: 1 MSMHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWNHQVFPIDTD 60 Query: 58 ILKQQLESLKD-VEFGSIKLGLLPNVETAQVVLEFVKSKQECPVVLDPVLVCKENHDL-- 114- ++ QL ++ D + ++K G+LP V+ ++ + +K KQ VV+DPV+VCK +++ Sbjct: 61 TIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQLKNVVIDPVMVCKGANEVLY 120- Query: 115 --EVSQLREQLIAFFPYADVITPNLVEAQLLTGLS-IENLDQMKIAAEKLYDMGAKHVVI 17- 1 LREQL P A VITPNL EA L+G+ ++ +D M AA+K++ +GA++VVI Sbjct: 121 PEHAQALREQLA---PLATVITPNLFEASQLSGMDELKTVDDMIEAAKKIHALGAQYVVI 17- 7 Query: 172 KGGNRLNAEEATDLYYDGERFETYVFPVVDANNT-GAGCTFASSIASQLAMGKNVEDAVK 23- 0 GG +L E+A D+ YDGE E ++D T GAGCTF++++ ++LA G V++A+ Sbjct: 178 TGGGKLKHEKAVDVLYDGETAEVLESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIY 23- 7 Query: 231 MSKGFVYQAIKAS 243 +K F+ AIK S Sbjct: 238 AAKEFITAAIKES 250 A related DNA sequence was identified in S. pyogenes <SEQ ID 4407> which encodes the amino acid sequence <SEQ ID 4408>. Analysis of this protein sequence reveals the following: TABLE-US-06843 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2029(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06844 Identities = 135/252 (53%), Positives = 174/252 (68%) Query: 1 MKTRNVLAISGNDIFSGGGLHADLATYVVNKLHGFVAVTCLTAMSDKGFEVIPIEASILK 60 MKT ++ ISGNDI SGGGL+ADLATY+ L FVAVTCLT S++GF + P+ I + Sbjct: 1 MKTDYIVTISGNDILSGGGLYADLATYIRYDLQAFVAVTCLTTRSEEGFSLFPVAKEIFR 60 Query: 61 QQLESLKDVEFGSIKLGLLPNVETAQVVLEFVKSKQECPVVLDPVLVCKENHDLEVSQLR 120- QL S + +IK+GLLPN E ++VL+F+K PVVLDPVL CKE D+++ LR Sbjct: 61 DQLNSFTNAPISAIKIGLLPNAEMCEIVLDFIKGHLGIPVVLDPVLACKEIDDVKIVPLR 120- Query: 121 EQLIAFFPYADVITPNLVEAQLLTGLSIENLDQMKIAAEKLYDMGAKHVVIKGGNRLNAE 18- 0 ++++ PY V+TPNLVEAQLL+ I +L M+ AA+ Y +GAK VVIKGGNR + + Sbjct: 121 QEILQLLPYVTVVTPNLVEAQLLSQKEIVSLKDMQEAAKYFYQLGAKQVVIKGGNRFSQK 18- 0 Query: 181 EATDLYYDGERFETYVFPVVDANNTGAGCTFASSIASQLAMGKNVEDAVKMSKGFVYQAI 24- 0 +A DL+YDG+ T PV++ NN GAGCTFASSIASQL K +AVK SK VYQAI Sbjct: 181 KAIDLFYDGKEIVTLECPVLEKNNIGAGCTFASSIASQLVKKKTPLEAVKNSKELVYQAI 24- 0 Query: 241 KASDKYGVVQHF 252 SD+YGV Q + Sbjct: 241 LQSDRYGVKQSY 252 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2232 A DNA sequence (GBSx2351) was identified in S. agalactiae <SEQ ID 6893> which encodes the amino acid sequence <SEQ ID 6894>. Analysis of this protein sequence reveals the following: TABLE-US-06845 Possible site: 45 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.05 Transmembrane 97-113 (96-119) INTEGRAL Likelihood = -0.22 Transmembrane 54-70 (54-70) ----- Final Results ----- bacterial membrane --- Certainty = 0.3421(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06846 >GP: BAA30952 GB: AP000007 202aa long hypothetical protein [Pyrococcus horikoshii] Identities = 48/148 (32%), Positives = 78/148 (52%), Gaps = 9/148 (6%) Query: 10 VQLAIVTAISIVLGMFISIPTPTGFLTLLDAGIFFAAFYFGKKEGAVVGALAGFLIDLLK 69 - V A+VTA+++V+ I IP G+L D I + FG G G + DLL Sbjct: 49 VMAALVTAMTMVIR--IPIPASQGYLNFGDIMIMLTSVLFGPLVGGFAGGVGSAFADLL- 105- Query: 70 GYPNWMFFSLLIHGTQGYLAGLPGR------RRLLGLISATLVMVLGYAIASGLMYGWGA 123- GYP+W F+L+I GT+G + G + + LLG + VMV+GY + ++YG Sbjct: 106 GYPSWALFTLVIKGTEGIIVGYFSKGEANYGKILLGTVLGGSVMVIGYVSVAYVLYGPAG 16- 5 Query: 124 VLPDIPGNIMQNMVGMVVGFALNKSLER 151 + ++ +I+Q + G+V+G L L++ Sbjct: 166 AIGELYNDIVQAVSGIVIGGGLGYILKK 193 A related DNA sequence was identified in S. pyogenes <SEQ ID 6895> which encodes the amino acid sequence <SEQ ID 6896>. Analysis of this protein sequence reveals the following: TABLE-US-06847 Possible site: 54 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.62 Transmembrane 98-114 (97-119) INTEGRAL Likelihood = -0.00 Transmembrane 135-151 (135-151) ----- Final Results ----- bacterial membrane --- Certainty = 0.2848(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06848 >GP: CAB49310 GB: AJ248284 hypothetical protein [Pyrococcus abyssi] Identities = 42/145 (28%), Positives = 73/145 (49%), Gaps = 10/145 (6%) Query: 7 RQMSLTGILTALVVVLGRFVMLPTPT--GFLTLLDAGIYAVSFSFGSAQGAIVGGLSGFL 64 R ++++ + ALV + + +P P G+L D I V+ FG G GG+ + Sbjct: 39 RTVAISAVAAALVTAMTMVIRIPIPASQGYLNFGDIMIMLVAVLFGPLVGGFAGGVGSAI 98 Query: 65 IDLVAGYPQWMFHSLIAHSVQGYFAGWRGR------KRWLGVVIGSFIMIFWYFLGSLML 118- DL+ GYP W +LI +G G+ + K +G V+G FIM+ Y S +L Sbjct: 99 ADLI-GYPSWALFTLIIKGSEGLVVGYFSKGEPNYSKILIGTVLGGFIMVLGYVSVSYVL 157- Query: 119 GYGLSGSLAGIWGNVMQNTLGLFVG 143 YG +G+++ ++ + +Q G+ +G Sbjct: 158 -YGPAGAISELYNDTVQAVSGIVIG 181 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06849 Identities = 77/155 (49%), Positives = 106/155 (67%), Gaps = 1/155 (0%) Query: 1 MRKEKTSQLVQLAIVTAISIVLGMFISIPTFTGFLTLLDAGIFFAAFYFGKKEGAVVGAL 60 M+ K Q+ I+TA+ +VLG F+ +PTPTGFLTLLDAGI+ +F FG +GA+VG L Sbjct: 1 MQNSKIRQMSLTGILTALVVVLGRFVMLPTPTGFLTLLDAGIYAVSFSFGSAQGAIVGGL 60 Query: 61 AGFLIDLLKGYPNWMFFSLLIHGTQGYLAGLPGRRRLLGLISATLVMVLGYAIASGLM-Y 119- +GFLIDL+ GYP WMF SL+ H QGY AG GR+R LG++ + +M+ Y + S ++ Y Sbjct: 61 SGFLIDLVAGYPQWMFHSLIAHSVQGYFAGWRGRKRWLGVVIGSFIMIFWYFLGSLMLGY 120- Query: 120 GWGAVLPDIPGNIMQNMVGMVVGFALNKSLERVKK 154 G L I GN+MQN +G+ VGF + K++ R KK Sbjct: 121 GLSGSLAGIWGNVMQNTLGLFVGFIIFKAILRQKK 155 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2233 A DNA sequence (GBSx2352) was identified in S. agalactiae <SEQ ID 6897> which encodes the amino acid sequence <SEQ ID 6898>. Analysis of this protein sequence reveals the following:

TABLE-US-06850 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0881(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06851 >GP: CAB15708 GB: Z99122 alternate gene name: ipc-33d [Bacillus subtilis] Identities = 91/176 (51%), Positives = 115/176 (64%) Query: 6 NKLKQETKAIVVDIIERSALKKGQIFVLGLSSSEVSGGLIGKNSSSEIGEIIVEVILKEL 65 N+LKQ K ++ + +++ LK+ Q+FVLG S+SEV+G IG + S +I E I + + Sbjct: 2 NELKQTWKTMLSEFQDQAELKQDQLFVLGCSTSEVAGSRIGTSGSVDIAESIYSGLAELR 61 Query: 66 HSRGIYLAVQGCEHVNRALVVEAELAERQQLEVVNVVPNLHAGGSGQVAAFKLMTSPVEV 125- GI+LA Q CEH+NRALVVEAE A+ +L V+ VP AGG+ AFK M SPV V Sbjct: 62 EKTGIHLAFQCCEHLNRALVVEAETAKLFRLPTVSAVPVPKAGGAMASYAFKQMKSPVLV 121- Query: 126 EEIVAHAGIDIGDTSIGMHIKRVQVPLIPISRELGGAHVTALASRPKLIGGARAGY 181 E I A AGIDIGDT IGMH+K V VP+ LG AHVT +RPKLIGG RA Y Sbjct: 122 ETIQADAGIDIGDTFIGMHLKPVAVPVRVSQNSLGSAHVTLARTRPKLIGGVRAVY 177 A related DNA sequence was identified in S. pyogenes <SEQ ID 6899> which encodes the amino acid sequence <SEQ ID 6900>. Analysis of this protein sequence reveals the following: TABLE-US-06852 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2166(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06853 Identities = 132/183 (72%), Positives = 161/183 (87%) Query: 6 NKLKQETKAIVVDIIERSALKKGQIFVLGLSSSEVSGGLIGKNSSSEIGEIIVEVILKEL 65 N L+++T+ IV+D++ERSA++ G +FVLGLSSSE+ G IGK SS E+G+I+VEV+L EL Sbjct: 3 NNLEKQTREIVIDVVERSAIQPGNLFVLGLSSSEILGSRIGKQSSLEVGQIVVEVVLDEL 62 Query: 66 HSRGIYLAVQGCEHVNRALVVEAELAERQQLEVVNVVPNLHAGGSGQVAAFKLMTSPVEV 125- + RG++LAVQGCEHVNRALVVE +AE +QLE+VNVVPNLHAGGS Q+AAF+LM+ PVEV Sbjct: 63 NKRGVHLAVQGCEHVNRALVVERHVAESKQLEIVNVVPNLHAGGSAQMAAFQLMSDPVEV 122- Query: 126 EEIVAHAGIDIGDTSIGMHIKRVQVPLIPISRELGGAHVTALASRPKLIGGARAGYTSDP 18- 5 EE++AHAG+DIGDT+IGMHIKRVQ+PLIP RELGGAHVTALASRPKLIGGARA Y D Sbjct: 123 EEVIAHAGLDIGDTAIGMHIKRVQIPLIPCQRELGGAHVTALASRPKLIGGARADYNMDI 18- 2 Query: 186 IRK 188 IRK Sbjct: 183 IRK 185 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2234 A DNA sequence (GBSx2353) was identified in S. agalactiae <SEQ ID 6901> which encodes the amino acid sequence <SEQ ID 6902>. Analysis of this protein sequence reveals the following: TABLE-US-06854 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.25 Transmembrane 21-37 (13-46) INTEGRAL Likelihood = -4.30 Transmembrane 78-94 (76-113) INTEGRAL Likelihood = -2.07 Transmembrane 96-112 (95-113) ----- Final Results ----- bacterial membrane --- Certainty = 0.5501(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06855 >GP: BAB06385 GB: AP001516 unknown conserved protein [Bacillus halodurans] Identities = 105/261 (40%), Positives = 150/261 (57%), Gaps = 2/261 (0%) Query: 12 NVEEVLFTFFTKLIS--ILLLIIAFVIVRQVINYLFEKTVNRSLAFSRQKVARQKTLAKL 69 - N+ F T +I+ +L+ +IAF+IVR + + + R ++ R TL KL Sbjct: 7 NITSGAFLASTFIIAGKVLVAVIAFLIVRAIGKRIISNSFARMAKNNQLSSGRVVTLEKL 66 Query: 70 SHNVLNYTLYFFLFYWILSILGVPISSLLAGAGIAGVAIGLGAQGFLSDVVNGFFILLEN 129- S N +YTL F +L+I G+ S+L+AGAGI G+AIG GAQG +SD+V GFFILLE Sbjct: 67 SLNAFSYTLMFIFATTLLTIFGLNPSALIAGAGIVGLAIGFGAQGLVSDIVTGFFILLEK 126- Query: 130 QFDVGDIINVGTVSGTVTNVGIRTTQIHDFDGTLHFIPNRNITIVSNKSRSNMRAQIDIP 18- 9 Q DVGD + G V G V VG+RT I FDGTLH+IPNRNI VSN SR NMRA +DI Sbjct: 127 QIDVGDYVTAGGVDGIVEEVGLRTALIRGFDGTLHYIPNRNIANVSNHSRGNMRALVDIS 18- 6 Query: 190 LFVHTNLDQISDIVTKINEEYVSKHPAIVGEPTVFGPTTNANGQFVYRINIFTQNGAQFD 24- 9 + + N+D+ ++ K+ ++ + I+ P V G + V RI T+N Q+ Sbjct: 187 ISYNDNIDEAISVMQKVCDQLAEQDERIIEGPDVIGVQNLGDSDVVIRIIAKTENMEQWS 24- 6 Query: 250 IYAEFYKLYQKAILEEGIDLP 270 + K ++A+ I++P Sbjct: 247 VERLLRKQLKEALEAHNIEIP 267 A related DNA sequence was identified in S. pyogenes <SEQ ID 6903> which encodes the amino acid sequence <SEQ ID 6904>. Analysis of this protein sequence reveals the following: TABLE-US-06856 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.49 Transmembrane 24-40 (15-45) INTEGRAL Likelihood = -4.83 Transmembrane 78-94 (73-99) INTEGRAL Likelihood = -2.07 Transmembrane 96-112 (95-113) ----- Final Results ----- bacterial membrane --- Certainty = 0.4397(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06857 >GP: BAB06385 GB: AP001516 unknown conserved protein [Bacillus halodurans] Identities = 104/249 (41%), Positives = 151/249 (59%), Gaps = 4/249 (1%) Query: 22 KKLVSLIILLLFFAILKRVTNYLFEKTINKSFAYSRQSEARKKTLSKLTHNILNYLLYFL 81 - K LV++I L+ AI KR+ + F + + + S R TL KL+ N +Y L F+ Sbjct: 23 KVLVAVIAFLIVRAIGKRIISNSFARMAKNN----QLSSGRVVTLEKLSLNAFSYTLMFI 78 Query: 82 LIYWILSLFGIPVSSLLAGAGIAGVAIGLGAQGFLSDVVNGFFILFENQFEVGDNVTISD 141- +L++FG+ S+L+AGAGI G+AIG GAQG +SD+V GFFIL E Q +VGD VT Sbjct: 79 FATTLLTIFGLNPSALIAGAGIVGLAIGFGAQGLVSDIVTGFFILLEKQIDVGDYVTAGG 138- Query: 142 IEGSVFGVGIRTTQIRGFDGTLHFIPNRSITVVSNKSRGNMRALIEIPLYSTVNLSQVTR 20- 1 ++G V VG+RT IRGFDGTLH+IPNR+I VSN SRGNMRAL++I + N+ + Sbjct: 139 VDGIVEEVGLRTALIRGFDGTLHYIPNRNIANVSNHSRGNMRALVDISISYNDNIDEAIS 19- 8 Query: 202 IIDEVNQKELPNHPQIVGKPNILGPQNNSNGQFTFRIAIFTENGEQFKIYHTFYRLYQEA 26- 1 ++ +V + +I+ P+++G QN + RI TEN EQ+ + + +EA Sbjct: 199 VMQKVCDQLAEQDERIIEGPDVIGVQNLGDSDVVIRIIAKTENMEQWSVERLLRKQLKEA 25- 8 Query: 262 LLKEGIQLP 270 L I++P Sbjct: 259 LEAHNIEIP 267 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06858 Identities = 164/265 (61%), Positives = 215/265 (80%) Query: 7 FIDHLNVEEVLFTFFTKLISILLLIIAFVIVRQVINYLFEKTVNRSLAFSRQKVARQKTL 66 +++ ++E + T F KL+S+++L++ F I+++V NYLFEKT+N+S A+SRQ AR+KTL Sbjct: 7 YLEQSHIENIGLTIFKKLVSLIILLLFFAILKRVTNYLFEKTINKSFAYSRQSEARKKTL 66 Query: 67 AKLSHNVLNYTLYFFLFYWILSILGVPISSLLAGAGIAGVAIGLGAQGFLSDVVNGFFIL 126- +KL+HN+LNY LYF L YWILS+ G+P+SSLLAGAGIAGVAIGLGAQGFLSDVVNGFFIL Sbjct: 67 SKLTHNILNYLLYFLLIYWILSLFGIPVSSLLAGAGIAGVAIGLGAQGFLSDVVNGFFIL 126- Query: 127 LENQFDVGDIINVGTVSGTVTNVGIRTTQIHDFDGTLHFIPNRNITIVSNKSRSNMRAQI 18- 6 ENQF+VGD + + + G+V VGIRTTQI FDGTLHFIPNR+IT+VSNKSR NMRA I Sbjct: 127 FENQFEVGDNVTISDIEGSVFGVGIRTTQIRGFDGTLHFIPNRSITVVSNKSRGNMRALI 18- 6 Query: 187 DIPLFVHTNLDQISDIVTKINEEYVSKHPAIVGEPTVFGPTTNANGQFVYRINIFTQNGA 24- 6 +IPL+ NL Q++ I+ ++N++ + HP IVG+P + GP N+NGQF +RI IFT+NG Sbjct: 187 EIPLYSTVNLSQVTRIIDEVNQKELPNHPQIVGKPNILGPQNNSNGQFTFRIAIFTENGE 24- 6 Query: 247 QFDIYAEFYKLYQKAILEEGIDLPT 271 QF IY FY+LYQ+A+L+EGI LPT Sbjct: 247 QFKIYHTFYRLYQEALLKEGIQLPT 271 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2235 A DNA sequence (GBSx2354) was identified in S. agalactiae <SEQ ID 6905> which encodes the amino acid sequence <SEQ ID 6906>. This protein is predicted to be RopA (tig). Analysis of this protein sequence reveals the following: TABLE-US-06859 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1785(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9283> which encodes amino acid sequence <SEQ ID 9284> was also identified. A related DNA sequence was identified in S. pyogenes <SEQ ID 6907> which encodes the amino acid sequence <SEQ ID 6908>. Analysis of this protein sequence reveals the following: TABLE-US-06860 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0776(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06861 Identities = 303/354 (85%), Positives = 337/354 (94%) Query: 1 MSTSFENKATNRGIITFTISQDEIKPALDQAFNKVKKDLNVPGFRKGHMPRTVFNQKFGE 60 MSTSFENKATNRG+ITFTISQD+IKPALD+AFNK+KKDLN PGFRKGHMPR VFNQKFGE Sbjct: 30 MSTSFENKATNRGVITFTISQDKIKPALDKAFNKIKKDLNAPGFRKGHMPRPVFNQKFGE 89 Query: 61 EALYENALNLVLPKAYEAAVAELGLDVVAQPKIDVVSMEKGQDWKLTAEVVTKPEVKLGD 120- E LYE+ALN+VLP+AYEAAV ELGLDVVAQPKIDVVSMEKG++W L+AEVVTKPEVKLGD Sbjct: 90 EVLYEDALNIVLPEAYEAAVTELGLDVVAQPKIDVVSMEKGKEWTLSAEVVTKPEVKLGD 149- Query: 121 YKDLSVEVDASKEVSDEEVDAKVERERNNLAELTVKDGEAAQGDTVVIDFVGSVDGVEFD 18- 0 YK+L VEVDASKEVSDE+VDAK+ERER NLAEL +KDGEAAQGDTVVIDFVGSVDGVEFD Sbjct: 150 YKNLVVEVDASKEVSDEDVDAKIERERQNLAELIIKDGEAAQGDTVVIDFVGSVDGVEFD 20- 9 Query: 181 GGKGDNFSLELGSGQFIPGFEEQLVGSKAGQTVDVNVTFPEDYQAEDLAGKDAKFVTTIH 24- 0 GGKGDNFSLELGSGQFIPGFE+QLVG+KAG V+VNVTFPE YQAEDLAGK AKF+TTIH Sbjct: 210 GGKGDNFSLELGSGQFIPGFEDQLVGAKAGDEVEVNVTFPESYQAEDLAGKAAKFMTTIH 26- 9 Query: 241 EVKTKEVPALDDELAKDIDDEVETLDELKAKYRKELESAKEIAFDDAVEGAAIELAVANA 30- 0 EVKTKEVP LDDELAKDID++V+TL++LK KYRKELE+A+E A+DDAVEGAAIELAVANA Sbjct: 270 EVKTKEVPELDDELAKDIDEDVDTLEDLKVKYRKELEAAQETAYDDAVEGAAIELAVANA 32- 9 Query: 301 EIVELPEEMVHDEVHRAMNEFMGNMQRQGISPEMYFQLTGTTEEDLHKQYQADA 354 EIV+LPEEM+H+EV+R++NEFMGNMQRQGISPEMYFQLTGTT+EDLH QY A+A Sbjct: 330 EIVDLPEEMIHEEVNRSVNEFMGNMQRQGISPEMYFQLTGTTQEDLHNQYSAEA 383 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2236 A DNA sequence (GBSx2355) was identified in S. agalactiae <SEQ ID 6909> which encodes the amino acid sequence <SEQ ID 6910>. This protein is predicted to be galactose-6-phosphate isomerase laca subunit (rpiB). Analysis of this protein sequence reveals the following: TABLE-US-06862 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3491(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06863 >GP: AAA25177 GB: M60447 galactose 6-P isomerase [Lactococcus lactis] Identities = 92/141 (65%), Positives = 115/141 (81%) Query: 1 MTIIIGADAHGVELKEVIRQHLTSLGKEIIDLTDTSKDFVDNTLAIVAKVNQKEDNLGIM 60 M I++GAD G LK+V++ L G E+ID+T +DFVD TLA+ ++VN+ E NLGI+ Sbjct: 1 MAIVVGADLKGTRLKDVVKNFLVEEGFEVIDVTKDGQDFVDVTLAVASEVNKDEQNLGIV 60 Query: 61 VDAYGVGPFMVATKVKGMIAAEVSDERSAYMTRAHNNARMITLGSEIVGPGVAKHIVEGF 120- +DAYG GPFMVATK+KGM+AAEVSDERSAYMTR HNNARMIT+G+EIVG +AK+I + F Sbjct: 61 IDAYGAGPFMVATKIKGMVAAEVSDERSAYMTRGHNNARMITVGAEIVGDELAKNIAKAF 120- Query: 121 VDGTYDAGRHQIRVDMLNKMC 141 V+G YD GRHQ+RVDMLNKMC Sbjct: 121 VNGKYDGGRHQVRVDMLNKMC 141 A related DNA sequence was identified in S. pyogenes <SEQ ID 6911> which encodes the amino acid sequence <SEQ ID 6912>. Analysis of this protein sequence reveals the following: TABLE-US-06864 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3224(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06865 Identities = 101/140 (72%), Positives = 117/140 (83%) Query: 1 MTIIIGADAHGVELKEVIRQHLTSLGKEIIDLTDTSKDFVDNTLAIVAKVNQKEDNLGIM 60 M II+GADAHG LKE+I+ L G +IID+TD + DF+DNTLA+ VN+ E LGIM Sbjct: 1 MAIILGADAHGNALKELIKSFLQEEGYDIIDVTDINSDFIDNTLAVAKAVNEAEGRLGIM 60 Query: 61 VDAYGVGPFMVATKVKGMIAAEVSDERSAYMTRAHNNARMITLGSEIVGPGVAKHIVEGF 120- VDAYG GPFMVATK+KGM+AAEVSDERSAYMTR HNNARMIT+G+EIVGP +AK+IV+GF Sbjct: 61 VDAYGAGPFMVATKLKGMVAAEVSDERSAYMTRGHNNARMITIGAEIVGPELAKNIVKGF 120- Query: 121 VDGTYDAGRHQIRVDMLNKM 140 V G YD GRHQIRVDMLNKM Sbjct: 121 VTGPYDGGRHQIRVDMLNKM 140 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2237 A DNA sequence (GBSx2356) was identified in S. agalactiae <SEQ ID 6913> which encodes the amino acid sequence <SEQ ID 6914>. This protein is predicted to be galactose-6-phosphate isomerase lacb subunit (rpiB). Analysis of this protein sequence reveals the following: TABLE-US-06866 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2511(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10189> which encodes amino acid sequence <SEQ ID 10190> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06867 >GP: AAA25178 GB: M60447 galactose 6-P isomerase [Lactococcus lactis] Identities = 138/171 (80%), Positives = 157/171 (91%) Query: 10 MKIAVGCDHIVTYDKIAVVDYLKTKGYEVIDCGTYDNIRTHYPIYGKKVGEAVASGKADL 69 - M+IA+GCDHIVT K+AV ++LK+KGYEV+D GTYD++RTHYPIYGKKVGEAV SG+ADL Sbjct: 1 MRIAIGCDHIVTDVKMAVSEFLKSKGYEVLDFGTYDHVRTHYPIYGKKVGEAVVSGQADL 60 Query: 70 GVCICGTGVGINNAVNKVPGIRSALVRDLTSAIYAKEELNANVIGFGGKITGGLLMTDII 129- GVCICGTGVGINNAVNKVPG+RSALVRD+TSA+YAKEELNANVIGFGG ITGGLLM DII Sbjct: 61 GVCICGTGVGINNAVNKVPGVRSALVRDMTSALYAKEELNANVIGFGGMITGGLLMNDII 120- Query: 130 EAFIRAKYKPTKENKVLIEKIAEVETHNAHQEENDFFTEFLDKWNRGEYHD 180 EAFI A+YKPT+ENK LI KI VETHNAHQ + +FFTEFL+KW+RGEYHD Sbjct: 121 EAFIEAEYKPTEENKKLIAKIEHVETHNAHQADEEFFTEFLEKWDRGEYHD 171 A related DNA sequence was identified in S. pyogenes <SEQ ID 6915> which encodes the amino acid sequence <SEQ ID 6916>. Analysis of this protein sequence reveals the following: TABLE-US-06868 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3048(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06869 Identities = 136/171 (79%), Positives = 160/171 (93%) Query: 10 MKIAVGCDHIVTYDKIAVVDYLKTKGYEVIDCGTYDNIRTHYPIYGKKVGEAVASGKADL 69 - MKIA+GCDHIVT +K+AV D+LK+KGY+VIDCGTYD+ RTHYPI+GKKVGEAV +G+ADL Sbjct: 2 MKIAIGCDHIVTNEKMAVSDFLKSKGYDVIDCGTYDHTRTHYPIFGKKVGEAVVNGQADL 61 Query: 70 GVCICGTGVGINNAVNKVPGIRSALVRDLTSAIYAKEELNANVIGFGGKITGGLLMTDII 129- GVCICGTGVGINNAVNKVPGIRSALVRD+T+A+YAKEELNANVIGFGGKITG LLM DII Sbjct: 62 GVCICGTGVGINNAVNKVPGIRSALVRDMTTALYAKEELNANVIGFGGKITGELLMCDII 121- Query: 130 EAFIRAKYKPTKENKVLIEKIAEVETHNAHQEENDFFTEFLDKWNRGEYHD 180 +AFI+A+YK T+ENK LI KIA +E+H+A+QE+ DFFTEFL+KW+RGEYHD Sbjct: 122 DAFIKAEYKETEENKKLIAKIAHLESHHANQEDPDFFTEFLEKWDRGEYHD 172 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2238 A DNA sequence (GBSx2357) was identified in S. agalactiae <SEQ ID 6917> which encodes the amino acid sequence <SEQ ID 6918>. Analysis of this protein sequence reveals the following: TABLE-US-06870 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10187> which encodes amino acid sequence <SEQ ID 10188> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-06871 >GP: AAA25179 GB: M60447 tagatose 6-P kinase [Lactococcus lactis] Identities = 192/310 (61%), Positives = 236/310 (75%) Query: 11 MILTVTLNPSIDISYCLENFNMDTVNRVTDVSKTPGGKGLNVTRVLSQLGDNVVATGLLG 70 - MILTVTLNPS+DISY LE +DTVNRV DVSKT GGKGLNVTRVL + GD V ATG LG Sbjct: 1 MILTVTLNPSVDISYPLETLKIDTVNRVKDVSKTAGGKGLNVTRVLYESGDKVTATGFLG 60 Query: 71 GDFGDFIRSGLDALEIRHQFLSIGGETRHCIAVLHEGQQTEILEKGPHITKDEADAFLNH 130- G G+FI S L+ + F I G TR+CIA+LHEG QTEILE+GP I+ +EA+ FL+H Sbjct: 61 GKIGEFIESELEQSPVSPAFYKISGNTRNCIAILHEGNQTEILEQGPTISHEEAEGFLDH 120- Query: 131 LKLIFDAATIITVSGSLPKGLPSDYYARLISLANHFNKKVVLDCSGEALRSVLKSSAKPT 19- 0 + + ++T+SGSLP GLP+DYY +LI LA+ VVLDCSG L +VLKSSAKPT Sbjct: 121 YSNLIKQSEVVTISGSLPSGLPNDYYEKLIQLASDEGVAVVLDCSGAPLETVLKSSAKPT 18- 0 Query: 191 VIKPNLEELTQLIGKPISYSLDELKSTLQQDLFRGIDWVIVSLGARGAFAKHGNHYYQVT 25- 0 IKPN EEL+QL+GK ++ ++ELK L++ LF GI+W++VSLG GAFAKHG+ +Y+V Sbjct: 181 AIKPNNEELSQLLGKEVTKDIEELKDVLKESLFSGIEWIVVSLGRNGAFAKHGDVFYKVD 24- 0 Query: 251 IPKIEVINPVGSGDATVAGIASALEHQLDDTNLLKRANVLGMLNAQETLTGHINLTYYQE 31- 0 IP I V+NPVGSGD+TVAGIASAL + D +LLK A LGMLNAQET+TGH+N+T Y+ Sbjct: 241 IPDIPVVNPVGSGDSTVAGIASALNSKKSDADLLKHAMTLGMLNAQETMTGHVNMTNYET 30- 0 Query: 311 LISQIQVKEV 320 L SQI VKEV Sbjct: 301 LNSQIGVKEV 310 A related DNA sequence was identified in S. pyogenes <SEQ ID 6919> which encodes the amino acid sequence <SEQ ID 6920>. Analysis of this protein sequence reveals the following: TABLE-US-06872 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1178(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06873 Identities = 184/310 (59%), Positives = 232/310 (74%), Gaps = 1/310 (0%) Query: 11 MILTVTLNPSIDISYCLENFNMDTVNRVTDVSKTPGGKGLNVTRVLSQLGDNVVATGLLG 70 - +ILTVTLNP+ID+SY L+ DTVNRV DV+KTPGGKGLNV+RVL++ G+ V ATG +G Sbjct: 1 VILTVTLNPAIDVSYPLDELKCDTVNRVVDVTKTPGGKGLNVSRVLNEFGETVKATGCVG 60 Query: 71 GDFGDFIRSGLDALEIRHQFLSIGGETRHCIAVLHEGQQTEILEKGPHITKDEADAFLNH 130- G+ GDFI + L I +F I G+TR CIA+LHEG QTEILEKGP ++ DE D F +H Sbjct: 61 GESGDFIINHLPD-SILSRFYKISGDTRTCIAILHEGNQTEILEKGPMLSVDEIDGFTHH 119- Query: 131 LKLIFDAATIITVSGSLPKGLPSDYYARLISLANHFNKKVVLDCSGEALRSVLKSSAKPT 19- 0 K + + ++T+SGSLP G+P DYY +LI +AN KK VLDCSG AL +VLK +KPT Sbjct: 120 FKYLLNDVDVVTLSGSLPAGMPDDYYQKLIKIANLNGKKTVLDCSGNALEAVLKGDSKPT 17- 9 Query: 191 VIKPNLEELTQLIGKPISYSLDELKSTLQQDLFRGIDWVIVSLGARGAFAKHGNHYYQVT 25- 0 VIKPNLEEL+QL+GK ++ D LK LQ +LF GI+W+IVSLGA G FAKH + +Y V Sbjct: 180 VIKPNLEELSQLLGKEMTKDFDALKEVLQDELFDGIEWIIVSLGADGVFAKHKDTFYNVD 23- 9 Query: 251 IPKIEVINPVGSGDATVAGIASALEHQLDDTNLLKRANVLGMLNAQETLTGHINLTYYQE 31- 0 IPKI++++ VGSGD+TVAGIAS L + DD LL +ANVLGMLNAQE TGH+N+ Y + Sbjct: 240 IPKIKIVSAVGSGDSTVAGIASGLANDEDDRALLTKANVLGMLNAQEKTTGHVNMANYDK 29- 9 Query: 311 LISQIQVKEV 320 L I+VKEV Sbjct: 300 LYQSIKVKEV 309 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2239 A DNA sequence (GBSx2358) was identified in S. agalactiae <SEQ ID 6921> which encodes the amino acid sequence <SEQ ID 6922>. This protein is predicted to be tagatose 1,6-diphosphate aldolase. Analysis of this protein sequence reveals the following: TABLE-US-06874 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0369(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06875 >GP: AAA25180 GB: M60447 tagatose 1,6-diP aldolase [Lactococcus lactis] Identities = 253/325 (77%), Positives = 295/325 (89%) Query: 1 MGLTEQKQKHMEQLSDKNGIISALAFDQRGALKRLMAKYQSEEPTVSQIEALKVLVAEEL 60 M LTEQK+K +E+LSDKNG ISALAFDQRGALKRLMA+YQ EPTV+Q+E LKVLVA+EL Sbjct: 1 MVLTEQKRKSLEKLSDKNGFISALAFDQRGALKRLMAQYQDTEPTVAQMEELKVLVADEL 60 Query: 61 TPYASSMLLDPEYGLPATKVLDDNAGLLLAYEKTGYDTSSTKRLPDCLDIWSAKRIKEEG 120- T YASSMLLDPEYGLPATK LD AGLLLA+EKTGYDTSSTKRLPDCLD+WSAKRIKE+G Sbjct: 61 TKYASSMLLDPEYGLPATKALDKEAGLLLAFEKTGYDTSSTKRLPDCLDVWSAKRIKEQG 120- Query: 121 ADAVKFLLYYDVDSSDEVNEEKEAYIERIGSECVAEDIPFFLEILSYDEKITDSSGIEYA 18- 0 ADAVKFLLYYDVDSSDE+N++K+AYIER+GSECVAEDIPFFLEIL+YDE+I+D+ +EYA Sbjct: 121 ADAVKFLLYYDVDSSDELNQQKQAYIERVGSECVAEDIPFFLEILAYDEEISDAGSVEYA 18- 0 Query: 181 KIKPRKVIEAMKVFSNPRFNIDVLKVEVPVNMDYVEGFAQGETAYNKATAAAYFREQDQA 24- 0 K+KPRKVIEAMKVFS+PRFNIDVLKVEVPVN+ YVEGFA GE Y+KA AA +F+ Q++A Sbjct: 181 KVKPRKVIEAMKVFSDPRFNIDVLKVEVPVNVKYVEGFADGEVVYSKAEAADFFKAQEEA 24- 0 Query: 241 TLLPYIFLSAGVPAQLFQETLVFAKEAGAKFNGVLCGRATWAGSVKEYVEKGEAGARQWL 30- 0 T LPYI+LSAGV A+LFQETL FA ++GAKFNGVLCGRATWAGSV+ Y+++GE AR+WL Sbjct: 241 TNLPYIYLSAGVSAKLFQETLQFAHDSGAKFNGVLCGRATWAGSVEPYIKEGEKAAREWL 30- 0 Query: 301 RTIGFQNIDELNKILQKTATSWKER 325 RT GF+NIDELNK+L KTA+ W ++ Sbjct: 301 RTTGFENIDELNKVLVKTASPWTDK 325 A related DNA sequence was identified in S. pyogenes <SEQ ID 6923> which encodes the amino acid sequence <SEQ ID 6924>. Analysis of this protein sequence reveals the following: TABLE-US-06876 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0600(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06877 Identities = 230/323 (71%), Positives = 276/323 (85%), Gaps = 1/323 (0%) Query: 3 LTEQKQKHMEQLSDKNGIISALAFDQRGALKRLMAKYQSEEPTVSQIEALKVLVAEELTP 62 LTE K+K ME+LS +G+ISALAFDQRGALKR+MA++Q++EPTV QIE LK LV+EELTP Sbjct: 5 LTENKRKSMEKLS-VDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTP 63 Query: 63 YASSMLLDPEYGLPATKVLDDNAGLLLAYEKTGYDTSSTKRLPDCLDIWSAKRIKEEGAD 122- +ASS+LLDPEYGLPA++V + AGLLLAYEKTGYD ++T RLPDCLD+WSAKRIKE GA+ Sbjct: 64 FASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAE 123- Query: 123 AVKFLLYYDVDSSDEVNEEKEAYIERIGSECVAEDIPFFLEILSYDEKITDSSGIEYAKI 18- 2 AVKFLLYYD+D +VNE+K+AYIERIGSEC AEDIPF+LEIL+YDEKI D++ E+AK+ Sbjct: 124 AVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKV 18- 3 Query: 183 KPRKVIEAMKVFSNPRFNIDVLKVEVPVNMDYVEGFAQGETAYNKATAAAYFREQDQATL 24- 2 K KV EAMKVFS RF +DVLKVEVPVNM +VEGFA GE + K AA FR+Q+ +T Sbjct: 184 KAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTD 24- 3 Query: 243 LPYIFLSAGVPAQLFQETLVFAKEAGAKFNGVLCGRATWAGSVKEYVEKGEAGARQWLRT 30- 2 LPYI+LSAGV A+LFQ+TLVFA E+GAKFNGVLCGRATWAGSVK Y+E+G AR+WLRT Sbjct: 244 LPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRT 30- 3 Query: 303 IGFQNIDELNKILQKTATSWKER 325 GF+NIDELNK+L KTA+ W E+ Sbjct: 304 EGFKNIDELNKVLDKTASPWTEK 326 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2240 A DNA sequence (GBSx2359) was identified in S. agalactiae <SEQ ID 6925> which encodes the amino acid sequence <SEQ ID 6926>. This protein is predicted to be lacx protein, chromosomal. Analysis of this protein sequence reveals the following: TABLE-US-06878 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0643(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10185> which encodes amino acid sequence <SEQ ID 10186> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06879 >GP: AAA25184 GB: M60447 ORF [Lactococcus lactis] Identities = 173/298 (58%), Positives = 219/298 (73%) Query: 24 MAITIQNHELQVTLKALGATMTSITDSQGVEYLWQGDATYWGGQAPILFPICGSVRNDCV 83 - M I ++N L V K LG +TSI D G+EYLWQ D YW GQAPILFPICGS+RND Sbjct: 1 MTIELKNEYLTVQFKTLGGQLTSIKDKDGLEYLWQADPEYWNGQAPILFPICGSLRNDWA 60 Query: 84 IYRPAQAPHFTGIIPRHGFVRHKTFDYDYISDSSVRFTIKSSKEMLINYPYRFSLEITYT 143- IYRP + P FTG+I RHGFVR + F + ++++SV F+IK + EML NY Y+F L + YT Sbjct: 61 IYRPQERPFFTGLIRRHGFVRKEEFTLEEVNENSVTFSIKPNAEMLDNYLYQFELRVVYT 120- Query: 144 LRNKSIAITYIVKNLESEKNMPYAIGAHPGFNCPLFEKEVFSDYYLEFEQFETCTIPESF 20- 3 L KSI + V NLE+EK MPY IGAHP FNCPL E E + DY LEF + E+C+IP+SF Sbjct: 121 LNGKSIRTEFQVTNLETEKTMPYFIGAHPAFNCPLVEGEKYEDYSLEFSEVESCSIPKSF 18- 0 Query: 204 PDTGLLDLQARHPFLENQKQLSLNHALFEKDAITLDQLRSKTVYLKSRNHAKGIQLDFDD 26- 3 P+TGLLDLQ R PFLENQK L L+++LF DAITLD+L+S++V L+SR KG+++DFDD Sbjct: 181 PETGLLDLQDRTPFLENQKSLDLDYSLFSHDAITLDRLKSRSVTLRSRKSGKGLRVDFDD 24- 0 Query: 264 FENLILWTSNNGGPFLALEPWSSLSTSIEESDILEDKQNIVRLNPKQSKQHSIRITIL 321 F NLILW++ N PF+ALEPWS LSTS+EE +ILEDK + ++ P + + S ITIL Sbjct: 241 FPNLILWSTTNKSPFIALEPWSGLSTSLEEGNILEDKPQVTKVLPLDTSKKSYDITIL 298 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2241 A DNA sequence (GBSx2361) was identified in S. agalactiae <SEQ ID 6927> which encodes the amino acid sequence <SEQ ID 6928>. This protein is predicted to be ABC transporter. Analysis of this protein sequence reveals the following: TABLE-US-06880 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3272(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 10183> which encodes amino acid sequence <SEQ ID 10184> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06881 >GP: CAA51350 GB: X72832 leucine rich protein [Streptococcus equisimilis] Identities = 101/278 (36%), Positives = 160/278 (57%), Gaps = 1/278 (0%) Query: 10 MDFKELFPEVITKQEVKQSEDYIIVEQDGHVLHFPKSSLTKRELYLLQMTPSLEDASSVD 69 - M+ K+ FPE+ ++++ V++ +HFPKS L+++E LL++ + Sbjct: 1 MELKDYFPEMQVGPHPLGDKEWVSVKEGDQYVHFPKSCLSEKERLLLEVGLGQYEVLQ-P 59 Query: 70 SQNPWYRYLVEGRGRLPQSHSAVQFIFIEHQFTLSEELKDFLSPLVINVETIMTINQTQS 129- +PW RYL++ +G PQ QFI++HQ L +L + L ++ +E I+ I+ TQ+ Sbjct: 60 LGSPWQRYLLDHQGNPPQLFETSQFIYLNHQQVLPADLVELLQQMIAGLEVILPISTTQT 119- Query: 130 VMILNQDNFFNATELLTDILPTIENDFNTRLRCYFGNSWTHLQAVDWKELYEEEYKLFTL 18- 9 + Q L +LPT+E+DF L + GN+W + A +E +EEE +L T Sbjct: 120 AFLCRQATSIKVLRSLEGLLPTLESDFGLALTMFVGNAWYQVAAGTLRECFEEECQLLTA 17- 9 Query: 190 FLSHKAEQHYCRFPKMALWALANQSPMPSIKAKCLQHILDTSDTSAIIKALWQEQGNLAK 24- 9 +L K+ F ++ LW++ + P++ + Q + SD + ++ ALW E GNL + Sbjct: 180 YLKQKSGGKLLTFAEVMLWSILSHQSFPALTRQFHQFLNPQSDMADVVHALWSEHGNLVQ 23- 9 Query: 250 TAKALFIHRNSLQYKLDKFTQSSGLNLKILDDLAYAYL 287 TA+ L+IHRNSLQYKLDKF Q SGL+LK LDDLA+AYL Sbjct: 240 TAQRLYIHRNSLQYKLDKFAQQSGLHLKQLDDLAFAYL 277 A related DNA sequence was identified in S. pyogenes <SEQ ID 6929> which encodes the amino acid sequence <SEQ ID 6930>. Analysis of this protein sequence reveals the following: TABLE-US-06882 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4332(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06883 Identities = 106/287 (36%), Positives = 169/287 (57%), Gaps = 4/287 (1%) Query: 3 KTVVED-AMDFKELFPEVITKQEVKQSEDYIIVEQDGHVLHFPKSSLTKRELYLLQM-TP 60 KTV++ AM+ K+ FPE+ +D++ +++ +HFPKS L+++E LL++ Sbjct: 7 KTVMKGMAMELKDYFPEMQVGPHPLGDKDWMSIKEGDQYVHFPKSCLSEKERLLLEVGLG 66 Query: 61 SLEDASSVDSQNPWYRYLVEGRGRLPQSHSAVQFIFIEHQFTLSEELKDFLSPLVINVET 120- E + S PW RYL++ +G PQ + QFI++ HQ L ++L + L ++ +E Sbjct: 67 QCEVLQPLGS--PWQRYLLDHQGNPPQLYETSQFIYLNHQQALPDDLVELLQQMIAGLEV 124- Query: 121 IMTINQTQSVMILNQDNFFNATELLTDILPTIENDFNTRLRCYFGNSWTHLQAVDWKELY 18- 0 I+ I+ TQ+ + Q L D+LPT+E+DF L + GN+W + A +E + Sbjct: 125 ILPISATQTAFLCRQAISIKVLRWLEDLLPTLESDFGLALTMFVGNAWYQVAAGTLRECF 18- 4 Query: 181 EEEYKLFTLFLSHKAEQHYCRFPKMALWALANQSPMPSIKAKCLQHILDTSDTSAIIKAL 24- 0 EEE +L T +L ++ + F + LW+L + ++ + Q + SD + ++ AL Sbjct: 185 EEECQLLTAYLRQQSGRKLLTFSGLMLWSLLSHHTFLALTRQFHQFLSPQSDMADVVHAL 24- 4 Query: 241 WQEQGNLAKTAKALFIHRNSLQYKLDKFTQSSGLNLKILDDLAYAYL 287 W E GNL +TA+ L+IHRNSLQYKLDKF Q SGL+LK LDDLA+A+L Sbjct: 245 WSEHGNLVQTAQRLYIHRNSLQYKLDKFAQQSGLHLKQLDDLAFAHL 291 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2242 A DNA sequence (GBSx2362) was identified in S. agalactiae <SEQ ID 6931> which encodes the amino acid sequence <SEQ ID 6932>. This protein is predicted to be multiple sugar-binding transport ATP-binding protein msmk (malK). Analysis of this protein sequence reveals the following: TABLE-US-06884 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4392(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06885 >GP: AAA26938 GB: M77351 ATP-binding protein [Streptococcus mutans] Identities = 320/377 (84%), Positives = 359/377 (94%) Query: 1 MVELNLNHIYKKYPSASHYSVEDFDLDIKDKEFIVFVGPSGCGKSTTLRMIAGLEDISEG 60 MVELNLNHIYKKYP++SHYSVEDFDLDIK+KEFIVFVGPSGCGKSTTLRM+AGLEDI++G Sbjct: 1 MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60 Query: 61 ELKIDGEVVNDKSPKDRDIAMVFQNYALYPHMTVYDNMAFGLKLRKFSKQEIDKRVREAA 120- ELKIDGEVVNDK+PKDRDIAMVFQNYALYPHM+VYDNMAFGLKLR +SK+ IDKRV+EAA Sbjct: 61 ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120- Query: 121 ANIGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 18- 0 +GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK Sbjct: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 18- 0 Query: 181 IHQRIGSTTIYVTHDQTEAMTLADRIVIMSATKNPDGDGTIGKIEQVGSPQELYNLPANK 24- 0 IH+RIG+TTIYVTHDQTEAMTLADRIVIMS+TKN DG GTIG++EQVG+PQELYN PANK Sbjct: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANK 24- 0 Query: 241 FVAGFIGSPSMNFFKVKVENGMIISEDGLRIAIPEGQEKLLESRGYKGKELIFGIRPEDI 30- 0 FVAGFIGSP+MNFF V +++G ++S+DGL IA+ EGQ K+LES+G+K K LIFGIRPEDI Sbjct: 241 FVAGFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRPEDI 30- 0 Query: 301 SSNLLVQDTYPNANVEAEVLVSELLGSETMLYVKLGQTEFASRVEARDFHNPGEKVNLTF 36- 0 SS+LLVQ+TYP+A V+AEV+VSELLGSETMLY+KLGQTEFA+RV+ARDFH PGEKV+LTF Sbjct: 301 SSSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTEFAARVDARDFHEPGEKVSLTF 36- 0 Query: 361 NVAKGHFFDADTEQAIR 377 NVAKGHFFDA+TE AIR Sbjct: 361 NVAKGHFFDAETEAAIR 377 A related DNA sequence was identified in S. pyogenes <SEQ ID 6933> which encodes the amino acid sequence <SEQ ID 6934>. Analysis of this protein sequence reveals the following: TABLE-US-06886 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4642(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06887 Identities = 332/377 (88%), Positives = 359/377 (95%) Query: 1 MVELNLNHIYKKYPSASHYSVEDFDLDIKDKEFIVFVGPSGCGKSTTLRMIAGLEDISEG 60 MVELNLNHIYKKYP+ +HY+VEDFDLDIKDKEFIVFVGPSGCGKSTTLRMIAGLEDISEG Sbjct: 1 MVELNLNHIYKKYPNTTHYAVEDFDLDIKDKEFIVFVGPSGCGKSTTLRMIAGLEDISEG 60 Query: 61 ELKIDGEVVNDKSPKDRDIAMVFQNYALYPHMTVYDNMAFGLKLRKFSKQEIDKRVREAA 120- ELKI GEVVNDKSPKDRDIAMVFQNYALYPHMTVYDNMAFGLKLRK+ K +ID+RV+EAA Sbjct: 61 ELKIGGEVVNDKSPKDRDIAMVFQNYALYPHMTVYDNMAFGLKLRKYKKDDIDRRVKEAA 120- Query: 121 ANIGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 18- 0 +GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK Sbjct: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 18- 0 Query: 181 IHQRIGSTTIYVTHDQTEAMTLADRIVIMSATKNPDGDGTIGKIEQVGSPQELYNLPANK 24- 0 IH+RIGSTTIYVTHDQTEAMTLADRIVIMSATKNP G+GTIGKIEQVGSPQELYNLPANK Sbjct: 181 IHRRIGSTTIYVTHDQTEAMTLADRIVIMSATKNPQGNGTIGKIEQVGSPQELYNLPANK 24- 0 Query: 241 FVAGFIGSPSMNFFKVKVENGMIISEDGLRIAIPEGQEKLLESRGYKGKELIFGIRPEDI 30- 0 FVAGFIGSP+MNFF+V+V++G I+SEDGL IAIPEGQ K+LE+ GYKG+++ FGIRPEDI Sbjct: 241 FVAGFIGSPAMNFFEVEVKDGRIVSEDGLDIAIPEGQAKMLEAAGYKGEKVTFGIRPEDI 30- 0 Query: 301 SSNLLVQDTYPNANVEAEVLVSELLGSETMLYVKLGQTEFASRVEARDFHNPGEKVNLTF 36- 0 SS +V DTYP+A V AEVLVSELLGSETMLYVKLGQTEFASRV+ARDFH+PGE+V+LTF Sbjct: 301 SSRQIVHDTYPSATVTAEVLVSELLGSETMLYVKLGQTEFASRVDARDFHSPGEQVSLTF 36- 0 Query: 361 NVAKGHFFDADTEQAIR 377 NVAKGHFFD DTEQAIR Sbjct: 361 NVAKGHFFDRDTEQAIR 377 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2243 A DNA sequence (GBSx2363) was identified in S. agalactiae <SEQ ID 6935> which encodes the amino acid sequence <SEQ ID 6936>. This protein is predicted to be glucan 1,6-alpha-glucosidase (dexB) (treC). Analysis of this protein sequence reveals the following:

TABLE-US-06888 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2525(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06889 >GP: CAA51348 GB: X72832 glucan 1,6-alpha-glucosidase [Streptococcus equisimilis] Identities = 413/535 (77%), Positives = 476/535 (88%), Gaps = 1/535 (0%) Query: 1 MKKHWWHKATIYQIYPRSFMDSDGDGVGDIKGITSKLDYLEKLGITAIWLSPVYQSPMDD 60 M+K WWHKATIYQIYPRSF D+ G+G+GD+KGITS+LDYL+KLGITAIWLSPVYQSPMDD Sbjct: 1 MQKQWWHKATIYQIYPRSFKDTSGNGIGDLKGITSQLDYLQKLGITAIWLSPVYQSPMDD 60 Query: 61 NGYDISDYQAIADIFGDMNDMDQLLQEANQRGIKIIMDLVVNHTSDEHAWFVEARENPNS 120- NGYDISDY+AIA++FG+M+DMD LL AN+RGIKIIMDLVVNHTSDEHAWFVEARENPNS Sbjct: 61 NGYDISDYEAIAEVFGNMDDMDDLLAAANERGIKIIMDLVVNHTSDEHAWFVEARENPNS 120- Query: 121 PERDFYIWRDEPNDLTSIFSGSAWEYDKVSGQYYLHLFSKRQPDLNWENEALRHKIYDMM 18- 0 PERD+YIWRDEPN+L SIFSGSAWE D+ SGQYYLHLFSK+QPDLNWEN +R KIYDMM Sbjct: 121 PERDYYIWRDEPNNLMSIFSGSAWELDEASGQYYLHLFSKKQPDLNWENAHVRQKIYDMM 18- 0 Query: 181 NFWIDKGIGGFRMDVIDLIGKIPDKGITGNGPKLHDYLKEMNRASFGKHDLLTVGETWGA 24- 0 NFWI KGIGGFRMDVIDLIGKIPD ITGNGP+LHDYLKEMN+A+FG HD++TVGETWGA Sbjct: 181 NFWIAKGIGGFRMDVIDLIGKIPDSEITGNGPRLHDYLKEMNQATFGNHDVMTVGETWGA 24- 0 Query: 241 TPDIAKQYSNPDNEELSMVFQFEHVGLQHKPDAPKWDYSDGLDVPALKDIFTKWQTQLEL 30- 0 TP+IA+QYS P+N+ELSMVFQFEHVGLQHKP+APKWDY++ LDVPALK IF+KWQT+L+L Sbjct: 241 TPEIARQYSRPENKELSMVFQFEHVGLQHKPNAPKWDYAEELDVPALKTIFSKWQTELKL 30- 0 Query: 301 GQGWNSLFWNNHDLPRVLSIWGNDSDNRKQSAKALAILLHLMRGTPYIYQGEEIGMTNYP 36- 0 G+GWNSLFWNNHDLPRVLSIWGNDS R++SAKALAILLHLMRGTPYIYQGEEIGMTNYP Sbjct: 301 GEGWNSLFWNNHDLPRVLSIWGNDSIYREKSAKALAILLHLMRGTPYIYQGEEIGMTNYP 36- 0 Query: 361 FECLADVDDIESLNYAKEAMDNGVSEATILDSIRKVGRDNARTPMQWSQEHQAGFTKG-T 41- 9 F+ L +VDDIESLNYAKEAM+NGV A ++ SIRKVGRDNARTPMQWS++ AGF++ Sbjct: 361 FKDLTEVDDIESLNYAKEAMENGVPAARVMSSIRKVGRDNARTPMQWSKDTHAGFSEAQE 42- 0 Query: 420 PWLAVNPNYQEINVEAALNDTESIFYTYQKLVALRKEHDWLVDADFKLLETADKVFAYVR 47- 9 WL VNPNYQEINV AL + +SIFYTYQ+L+ALRK+ DWLV+AD+ LL TADKVFAY R Sbjct: 421 TWLPVNPNYQEINVADALANQDSIFYTYQQLIALRKDQDWLVEADYHLLPTADKVFAYQR 48- 0 Query: 480 QTDKERYLIVANLSDQNQSFEFPEAVKETIISNTEVQEVLSSNTLKPWDAFCIEL 534 Q +E Y+IV N+SDQ Q F A E +I+NT+V +VL + L+PWDAFC++L Sbjct: 481 QFGEETYVIVVNVSDQEQVFAKDLAGAEVVITNTDVDKVLETKHLQPWDAFCVKL 535 A related DNA sequence was identified in S. pyogenes <SEQ ID 6937> which encodes the amino acid sequence <SEQ ID 6938>. Analysis of this protein sequence reveals the following: TABLE-US-06890 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2793(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06891 Identities = 418/535 (78%), Positives = 474/535 (88%), Gaps = 1/535 (0%) Query: 1 MKKHWWHKATIYQIYPRSFMDSDGDGVGDIKGITSKLDYLEKLGITAIWLSPVYQSPMDD 60 M HWWHKATIYQIYPRSF D+ G+G+GD+KGITS+LDYL+KLGITAIWLSPVYQSPMDD Sbjct: 1 MNNHWWHKATIYQIYPRSFKDTSGNGIGDLKGITSQLDYLQKLGITAIWLSPVYQSPMDD 60 Query: 61 NGYDISDYQAIADIFGDMNDMDQLLQEANQRGIKIIMDLVVNHTSDEHAWFVEARENPNS 120- NGYDISDY+AIAD+FGDM DMD+LL AN+RGIKIIMDLVVNHTSDEHAWFVEARENPNS Sbjct: 61 NGYDISDYEAIADVFGDMADMDELLAAANERGIKIIMDLVVNHTSDEHAWFVEARENPNS 120- Query: 121 PERDFYIWRDEPNDLTSIFSGSAWEYDKVSGQYYLHLFSKRQPDLNWENEALRHKIYDMM 18- 0 PERD+YIWRDEPN+L SIFSGSAWE D+ SGQYYLHLFSK+QPDLNWEN LR KIYDMM Sbjct: 121 PERDYYIWRDEPNNLMSIFSGSAWELDEASGQYYLHLFSKKQPDLNWENAQLRQKIYDMM 18- 0 Query: 181 NFWIDKGIGGFRMDVIDLIGKIPDKGITGNGPKLHDYLKEMNRASFGKHDLLTVGETWGA 24- 0 NFWI KGIGGFRMDVIDLIGK+PD ITGNGP+LHDYLKEMN+A+FG HD++TVGETWGA Sbjct: 181 NFWIAKGIGGFRMDVIDLIGKVPDLEITGNGPRLHDYLKEMNQATFGNHDVMTVGETWGA 24- 0 Query: 241 TPDIAKQYSNPDNEELSMVFQFEHVGLQHKPDAPKWDYSDGLDVPALKDIFTKWQTQLEL 30- 0 TP+IA+QYS P+N+ELSMVFQFEHVGLQHKPDAPKWDY+ LDVPALK IF+KWQT+L+L Sbjct: 241 TPEIARQYSRPENKELSMVFQFEHVGLQHKPDAPKWDYAKELDVPALKAIFSKWQTELKL 30- 0 Query: 301 GQGWNSLFWNNHDLPRVLSIWGNDSDNRKQSAKALAILLHLMRGTPYIYQGEEIGMTNYP 36- 0 G+GWNSLFWNNHDLPRVLSIWGNDS R++SAKALAILLHLMRGTPYIYQGEEIGMTNYP Sbjct: 301 GEGWNSLFWNNHDLPRVLSIWGNDSTYREKSAKALAILLHLMRGTPYIYQGEEIGMTNYP 36- 0 Query: 361 FECLADVDDIESLNYAKEAMDNGVSEATILDSIRKVGRDNARTPMQWSQEHQAGFTKG-T 41- 9 F+ L +V+DIESLNYAKEAM NGVS A ++DSIRKVGRDNARTPMQWS++ AGF++ Sbjct: 361 FKDLTEVNDIESLNYAKEAMGNGVSAARVMDSIRKVGRDNARTPMQWSKDTHAGFSEAKE 42- 0 Query: 420 PWLAVNPNYQEINVEAALNDTESIFYTYQKLVALRKEHDWLVDADFKLLETADKVFAYVR 47- 9 WL VNPNYQ+INV AL D +SIFYTYQKL+ALRKE DWLV+AD+ LL TADKVFAY R Sbjct: 421 TWLPVNPNYQDINVADALADPDSIFYTYQKLIALRKEQDWLVEADYHLLPTADKVFAYQR 48- 0 Query: 480 QTDKERYLIVANLSDQNQSFEFPEAVKETIISNTEVQEVLSSNTLKPWDAFCIEL 534 Q +E Y+IV N+SD+ Q F A + II+NT+V VL + L+PWDAFC++L Sbjct: 481 QLGEETYVIVVNVSDEEQVFATDLAGAQVIIANTDVDTVLETKHLQPWDAFCLKL 535 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2244 A DNA sequence (GBSx2364) was identified in S. agalactiae <SEQ ID 6939> which encodes the amino acid sequence <SEQ ID 6940>. Analysis of this protein sequence reveals the following: TABLE-US-06892 Possible site: 44 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06893 >GP:AAB49738 GB:U21942 UDP-galactose 4-epimerase [Streptococcus mutans] Identities = 267/331 (80%), Positives = 306/331 (91%) Query: 1 MAVLILGGAGYIGSHMVDQLITQGKEKVIVVDNLVTGHRQAVHSDAIFYEGDLSDKTFMR 60 MA+L+LGGAGYIGSHMVD+LI +G+E+V+VVD+LVTGHR AVH A FY+GDL+D+ FM Sbjct: 1 MAILVLGGAGYIGSHMVORLIEKGEEEVVVVDSLVTGHRAAVHPAAKFYQGDLADREFMS 60 Query: 61 QVFRENPDVDAVIHFAAFSLVAESMENPLKYFDNNTAGMIKLLEVMNECDIKNIVFSSTA 120- VFRENPDVDAVIHFAA+SLVAESM+ PLKYFDNNTAGMIKLLEVM+E +K IVFSSTA Sbjct: 61 MVFRENPDVDAVIHFAAYSLVAESMKKPLKYFDNNTAGMIKLLEVMSEFGVKYIVFSSTA 120- Query: 121 ATYGIPSQVPILETAFQNPINPYGESKLMMETIMKWADQAYGIKFVALRYFNVAGDKPDG 18- 0 ATYGIP ++PI ET PQ PINPYGESKLMMETIMKW+D+AYGIKFV +RYFNVAG RPDG Sbjct: 121 ATYGIPNEIPIKETTPQRPINPYGESKLMMETIMKWS0RAYGIKFVPVRYFNVAGAKPDG 18- 0 Query: 181 SIGEDHKPETHLLPIILQVAQGVRDKIMIFGDDYNTPDGTNVRDYVHPFDLADAHILAVD 24- 0 SIGEDH PETHLLPIILQVAQGVR+KIMIFGDDYNTPDGTNVRDYVHPFDLAD H+LA++ Sbjct: 181 SIGEDHSPETHLLPIILQVAQGVREKIMIFGDDYNTPDGTNVRDYVHPFDLADRHLLALN 24- 0 Query: 241 YLRQGNESNVFNLGSSTGFSNLQMLEAARRITGKEIPAQKAARRPGDPDTLIASSERARQ 30- 0 YLRQGN S FNLGSSTGFSNLQ+LEAAR++TG++IPA+KAARR GDPDTLIASSEKAR+ Sbjct: 241 YLRQGNPSTAFNLGSSTGFSNLQILEAARRVTGQKIPAEKAARRSGDPDTLIASSEKARE 30- 0 Query: 301 ILGWEPKFDNIDKIISSAWAWHSSHPNGYED 331 ++GW+P+FD+I+KII+SAWAWHSSHP GY+D Sbjct: 301 VVGWKPQFDDIEKIIASAWAWHSSHPKGYDD 331 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2245 A DNA sequence (GBSx2366) was identified in S. agalactiae <SEQ ID 6941> which encodes the amino acid sequence <SEQ ID 6942>. This protein is predicted to be two-component response regulator. Analysis of this protein sequence reveals the following: TABLE-US-06894 Possible Site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3945(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06895 >GP:BAB06470 GB:AP001516 two component response regulator [Bacillus halodurans] Identities = 71/223 (31%), Positives = 139/223 (61%), Gaps = 7/223 (3%) Query: 3 VLIIEDDPMVEFIHRNYLEKLNYFQNIYSTASQTQAIAYLNDIKIQLVLLDIHIKEGNGL 62 VL+IEDDPMV+ ++R ++EKL+ F + +TA+ + + +++ L+LLDI + + +GL Sbjct: 9 VLLIEDDPMVQEVNRMFVEKLSGFTIVGTTATGEEGMVKTRELQPDLILLDIFMPKQDGL 68 Query: 63 ELLKLLRNQHQNTEVIVISAANEANTVKEAFHLGIVDYLIKPFTFERFESSIEKFLNHYH 122- +K +R Q+ + ++I ++AAN+ T+K G++DYL+KPFTFER ++++ ++ + Sbjct: 69 SFIKQIREQYIDVDIIAVTAANDTKTIKTLLRYGVMDYLVKPFTFERLKAALTQYEEMFR 128- Query: 123 TFEAD-KIYQDNIOHFQKIDSGWLEGEVKLDE--KGLSEITYQHILDAIQELEQPFTIQE 17- 9 + + ++ QD++D K + + +D+ KGL T Q +++ ++EL++P + +E Sbjct: 129 KMQKEAELSQDSLDEMIK----QKQAQANMDDLPKGLHAHTLQQVIERLEELDEPKSAEE 18- 4 Query: 180 LAKCSQFSHVSVRKYIAYMEEKGLLTSQQIYTKVGRPYKVYKL 222 + + + V+VR+Y+ Y+E G + Y +GRP + YKL Sbjct: 185 IGRDVGLARVTVRRYLNYLESVGQVEMDLTYGSIGRPIQTYKL 227 A related DNA sequence was identified in S. pyogenes <SEQ ID 6943> which encodes the amino acid sequence <SEQ ID 6944>. Analysis of this protein sequence reveals the following: TABLE-US-06896 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4053(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06897 Identities = 123/220 (55%), Positives = 156/220 (70%) Query: 1 MDVLIIEDDPMVEFIHRNYLEKLNYFQNIYSTASQTQAIAYLNDIKIQLVLLDIHIKEGN 60 M+VLIIEDDPMV+FIHRNYLEKLN F I S+ S + L D I L+LLDIHI +GN Sbjct: 1 MNVLIIEDDPMVDFIHRNYLEKLNLFDRIISSDSMKAVQSILTDYAIDLILLDIHITDGN 60 Query: 61 GLELLKLLRNQHQNTEVIVISAANEAHTVKEAFHLGIVDYLIKPFTFEREESSIEKFLNH 120- G++ L+ R QH EVI+ISAAN+ + +++FHLGI+DYLIKPFTFSRF+ SI++F+ H Sbjct: 61 GIQFLEKWRTQHIPCEVIIISAANDGNIIRDGFHLGIIDYLIKPFTFERFQESIQQFVTH 120- Query: 121 YHTFEADKIYQDNIDHFQKIDSGWLEGEVKLDEKGLSEITYQHILDAIQELEQPFTIQEL 18- 0 ++ Q ID + + S +L EKGLSE T+Q I++ I+ +QPFTIQEL Sbjct: 121 REHLANQQLEQAQIDQLKCLTSKKDTKNRQLLEKGLSESTFQWIMENIKVFDQPFTIQEL 18- 0 Query: 181 AKCSQFSHVSVRKYIAYMEEKGLLTSQQIYTKVGRPYKVY 220 A SHVSVRKYIAY+EE L SQQI+TKVGRPY+VY Sbjct: 181 ASACHLSHVSVRKYIAYLEENKQLNSQQIFTKVGRPYRVY 220 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2246 A DNA sequence (GBSx2367) was identified in S. agalactiae <SEQ ID 6945> which encodes the amino acid sequence <SEQ ID 6946>. Analysis of this protein sequence reveals the following: TABLE-US-06898 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.76 Transmembrane 12-28 ( 6-34) INTEGRAL Likelihood = -7.43 Transmembrane 178-194 ( 173-197) ----- Final Results ----- bacterial membrane --- Certainty = 0.4503(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9003> which encodes amino acid sequence <SEQ ID 9004> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-06899 Lipop: Possible site: -1 Crend: 3 SRCFLG: 0 McG: Length of UR: 27 Peak Value of CR: 2.99 Net Charge of CR: 3 McG: Discrim Score: 12.92 GvH: Signal Score (-7.5): -2.57 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 2 value: -8.76 threshold: 0.0 INTEGRAL Likelihood = -8.76 Transmembrane 10-26 ( 4-32) INTEGRAL Likelihood = -7.43 Transmembrane 176-192 ( 171-195) PERIPHERAL Likelihood = 3.18 149 modified ALOM score: 2.25 icm1 HYPID: 7 CFP: 0.450 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4503(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06900 >GP:CAB15141 GB:Z99120 similar to two-component sensor histidine kinase [YufM] [Bacillus subtilis] Identities = 132/461 (28%), Positives = 245/461 (52%), Gaps = 7/461 (1%) Query: 3 MKKKLSLWAFLSLILVTMTICIFSIFYYVTIHQSYRMVRVQEEKILKNTGYALSRNPQVI 62 MKKLL L L++ + + + I ++ Q+ + +R QE+ T ++ P Sbjct: 1 MKKTLKLQTRLTIFVCIVVLIALLITFWTVGAQTTKRIRDQEKATALQTAEMVAEAPMTA 60 Query: 63 QTLKDNHYDQSLQKQNLFLSKKSNLDYIVLINLKGIRFTHPDSTKIGKPFQGGDEQAVEK 122- L+ + LQ + K + +++V++++ GIR THPD +KIGK F+GGDE V K Sbjct: 61 AALESGKKQKELQSYTKRVQKITGTEFVVVMDMNGIRKTHPDPSKIGKKFRGGDESEVLK 120- Query: 123 GKAINSTAEGSLGKSLRYLIPVY-DHQKQVGAIAVGLKLTTLGDLSQSSIKEFSKPLLIS 18- 1 G +STA G+LGKS R +PVY ++ KQVGA+AVG+ + + ++ S++ ++S Sbjct: 121 GHVHISTASGTLGKSQRAFVPVYAENGKQVGAVAVGITVNEIDEVISHSLRPLYFIICVS 18- 0 Query: 182 ILISLVVTSIISYGLKKQLHNLHPSDIFQHLEERNATLDQIQAAVFVIDQRHIIKRNNPA 24- 1 I + ++ I++ +K ++L P +I LEER+A L+ + + +D+ IK N Sbjct: 181 IFVGVIGAVIVARTVKNIMYGLEPYEIATLLEERSAMLESTKEGILAVDEHGKIKLANAE 24- 0 Query: 242 ASLLFKKEGQRDLFSGKLLESLIP--QLKQDHFSKK--TEQVLHFQGQDYLLSISPITVK 29- 7 A LF K G + ++ ++P +LK+ +KK ++ + G + + + PI +K Sbjct: 241 AKRLFVKMGINTNPIDQDVDDILPKSRLKKVIETKKPLQDRDVRINGLELVFNEVPIQLK 30- 0 Query: 298 TQNRGYVVFLRNVTETLFTLDQLAHTTAYASALQAQTHQFNNQLHVIYGLADIEYYDELK 35- 7 Q G + R+ TE +QL+ YA+AL+AQ+H+FNN+LHVI GL ++ YD+L Sbjct: 301 GQTVGAIATFRDKTEVKHLAEQLSGVKNYANALRAQSHEFNNKLHVILGLVQLKEYDDLG 36- 0 Query: 358 IYLKELLEPQNEFLARLSNLVREPRLASFIIGSREKFAEKHINLSTEILVEIPTKSTVED 41- 7 Y+K++ Q + + V+ LA F++G++ E+ NL E IP + Sbjct: 361 DYIKDIAIQQKSETSEIINDVKSSVLAGFLLGKQSFIREQGANLDIECNGVIPNAADPSV 42- 0 Query: 418 VNNYL-LLHRYINTKILTLLN-STTLVSLRLNYQNNLIETD 456 ++ + ++ IN + + + +++ + + N++++ + Sbjct: 421 IHELITIIGNLINNGLDAVADMPKKQITHSMRFHNSILDIE 461 A related DNA sequence was identified in S. pyogenes <SEQ ID 6947> which encodes the amino acid sequence <SEQ ID 6948>. Analysis of this protein sequence reveals the following: TABLE-US-06901 Possible site: 57 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.03 Transmembrane 174-190 ( 170-195) ----- Final Results ----- bacterial membrane --- Certainty = 0.5012(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06902 Identities = 236/488 (48%), Positives = 337/488 (68%), Gaps = 3/488 (0%) Query: 3 MKKKLSLWAFLSLILVTMTICIFSIFYYVTIHQSYRNVRVQEEKILKNTGYALSRNPQVI 62 MKK L LWA LSLILV+M + S+FY + +H +++ ++ QE +L +TG L+ + + Sbjct: 1 MKKPLRLWASLSLILVSMIVVTTSLFYGIMLHDTHQSIKNQETHLLTSTGKNLASHQAIK 60 Query: 63 QTLKDNHYDQSLQKQMLFLSKKSNLDYIVLINLKGIRFTHPDSTKIGKPFQGGDEQAVFK 122- + L +N + ++ NLDY+V++N+KGIR THP+ IGKPFQGGDE+AV Sbjct: 61 ELLLNNQPNAKTTAYTNSIASIYNLDYVVVMNMKGIRLTNPNPKNIGKPFQGGDEEAVLA 120- Query: 123 GKAIMSTAEGSLGKSLRYLIPVYDHQKQVGAIAVGLKLTTLGDLSQSSIKEFSKPLLISI 18- 2 GK ++STA+G+LGKSLRYL+PV+D KQ+GAIAVG+KLTTL D++ +S + ++ LL+ + Sbjct: 121 GKKVISTAKGTLGKSLRYLVPVFDGDKQIGAIAVGIKLTTLNDVALTSKRNYTLSLLLCL 18- 0 Query: 183 LISLVVTSIISYGLKKQLHNLHPSDIFQHLEERNATLDQIQAAVFVIDQRHIIKRNNPAA 24- 2 LISL+VTS IS+ LK+QLH L PS+I+Q EERNA LDQI+AAVFV+D+ I++ N A Sbjct: 181 LISLLVTSFISFRLKRQLHQLEPSEIYQLFEERNAMLDQIEAAVFVVDKAGILQLCNQAG 24- 0 Query: 243 SLLFKKEGQRDLFSGKLLESLIPQLKQDHFSKKTEQVLHFQGQDYLLSISPITVKTQNRG 30- 2 L ++ Q +G L P + + EQ+ + +DYLL+ISPI VK +RG Sbjct: 241 QKLIARKCQLGKPTGNSFNYLFPOFPKLSLQEGHEQLFRYGEEDYLLAISPICVKNDHRG 30- 0 Query: 303 YVVFLRNVTETLWTLDQLAHTTAYASALQAQTHQFMNQLHVIYGLADIEYYDELKIYLKE 36- 2 +++F+R + + TLDQLA+TTAYASALQAQTH+FMNQLHVIYGL DI YYD+LKIYL Sbjct: 301 HIIFMREAVKAIDTLDQLAYTTAYASALQAQTNKFMNQLHVIYGLVDIAYYDQLKIYLDS 36- 0 Query: 363 LLEPQNEFLARLSNLVREPRLASFIIGEREKFAEKHINLSTEILVEIPTKSTVEDVNNYL 42- 2 +LEP+NE L LS+LV+EP LASF+IGE+EK+ E +++L ++L EIP +T +NN L Sbjct: 361 ILEPENEILTSLSVLVKEPLLASFLIGEQEKYQELNVHLKIDVLSEIPHSATKNQLNNGL 42- 0 Query: 423 LLHRYINTKILTLLNSTTLVSLRLNYQNNLIETDYQWENEKWL-LNOYHQYFNDAYFQQL 48- 1 +++R+I+T +LT L +LV + QN+LI + + W+ L F+ YFQQL Sbjct: 421 MIYRFIHTNLLTTLRPKSLVLSIQHDQNHLI--SHYTLTDNWIDLERVQPIFDLPYFQQL 47- 8 Query: 482 LVDSRATY 489 L D+ + + Sbjct: 479 LTDTNSQF 486 SEQ ID 9004 (GBS130d) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 123 (lane 8-10; MW 63 kDa) and in FIG. 184 (lane 4; MW 63kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 123 (lane 11; MW 38 kDa) and in FIG. 181 (lane 7; MW 38 kDa). GBS130d-GST was purified as shown in FIG. 237, lane 11. GBS130d-His was purified as shown in FIG. 233, lane 9-10. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2247 A DNA sequence (GBSx2368) was identified in S. agalactiae <SEQ ID 6949> which encodes the amino acid sequence <SEQ ID 6950>. Analysis of this protein sequence reveals the following:

TABLE-US-06903 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.52 Transmembrane 364-380 ( 353-386) INTEGRAL Likelihood = -9.66 Transmembrane 33-49 ( 26-57) INTEGRAL Likelihood = -7.80 Transmembrane 87-103 ( 82-105) INTEGRAL Likelihood = -6.85 Transmembrane 153-169 ( 144-174) INTEGRAL Likelihood = -4.41 Transmembrane 301-317 ( 300-318) INTEGRAL Likelihood = -2.81 Transmembrane 216-232 ( 212-235) INTEGRAL Likelihood = -2.39 Transmembrane 120-136 ( 120-136) INTEGRAL Likelihood = -1.65 Transmembrane 57-73 ( 56-73) INTEGRAL Likelihood = -1.17 Transmembrane 428-444 ( 428-444) INTEGRAL Likelihood = -0.32 Transmembrane 276-292 ( 276-292) ----- Final Results ----- bacterial membrane --- Certainty = 0.5607(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06904 >GP:AAB18291 GB:U35658 L-malate permease [Streptococcus bovis] Identities = 329/428 (76%), Positives = 375/428 (86%) Query: 18 DLKAKLFHIKIGSVPLPVYVCLALLILLAGFLQKLPVNMLGGFAVILTMGWFLGTIGASI 77 - D + KL +IGSV LPVY+ A +IL+ L++LPVNMLGGFAVILTMGW LGTIG +I Sbjct: 14 DWRNKLTKTRIGSVTLPVYLVTASIILVTALLEQLPVMMLGGFAVILTMGWLLGTIGGNI 73 Query: 78 PGFKNFGGPAILSLLVPSILVFFNLINKNVLESTNMLMKQANFLYFYIACLVSGSILGMN 137- P K+FGGPAILSLLVPSI+VFFNL+N+NVL+ST++LMKQANFLYFYIACLV GSILGMN Sbjct: 74 PILKHFGGPAILSLLVPSIMVFFNLLNQNVLDSTDILMKQANFLYFYIACLVCGSILGMN 133- Query: 138 RKMLIQGLLPMIFPMLLGMVCAMMVGTFVGVILGLEWRHTLFYIVTPVLAGGIGEGILPL 19- 7 RK+L+QGL+RMI PM LGM+ AM VGT VG +LGL W+H+LEYIVTPVLAGGIGEGILPL Sbjct: 134 RKILVQGLMRMIVPMALGMILAMGVGTLVGTLLGLGWKHSLFYIVTPVLAGGIGEGILPL 19- 3 Query: 198 SLGYSSITGVASEQLVAQLIPATIIGMFFAILCTALLMRLGSKKPHLSGQGQLVRLMKGE 25- 7 SLGYS+ITG+SEQLV QLIPATIIGMWFAI+C+ LL+RLGEK+P LSGQGQL+++ + Sbjct: 194 SLGYSAITGLPSEQLVGQLIPATIIGMFFAIMCSGLLSRLGEKRPELSGQGQLIEITMSD 25- 3 Query: 258 DMSDIIADHSGPIDVKKMGGGVLTACSLFIFGHLLQQLTGFPGPVLMIVAAAILRYINVI 31- 7 D+SD + + PIDVE MG GVL AC+LFI G LLQ LTGFPGPVLMIV AA LKY+NV+ Sbjct: 254 DLSDALEEDKAPIDVKLMGAGVLIACTLFITGGLLQHLTGFPGPVLMIVVAAFLKYLNVV 31- 3 Query: 318 PRETQNGAKQLYKFISGNFTFPLMAGLGLLYIPLKDVVATLSIQYFIVVISVVFTVISVG 37- 7 P+ETQ G+KQLYKFISGNFTFPLM GLG+LYIPLKDVV LS QYF+VVISVVFTVI+ G Sbjct: 314 PKETQRGSKQLYKFISGMFTFPLMVGLGMLYIPLKDVVGMLSWQYFVVVISVVFTVIATG 37- 3 Query: 378 FFVSRFLNMNPVEAGIISACQSGMGGTGDVAILSTADRMNLMPFAQVATRLGGAITVITM 43- 7 FFVSRF+NMMPVEA I+SACQSGMGGTGDVAILSTA+RM LMPFAQVATRLGGAITVITM Sbjct: 374 FFVSRFMNMNPVEAAIVSACQSGMGGTGDVAILSTANRMTLMPFAQVATRLGGAITVITM 43- 3 Query: 438 TAILRMLF 445 TAI RMLF Sbjct: 434 TAIFRMLF 441 A related DNA sequence was identified in S. pyogenes <SEQ ID 6951> which encodes the amino acid sequence <SEQ ID 6952>. Analysis of this protein sequence reveals the following: TABLE-US-06905 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.89 Transmembrane 361-377 ( 350-383) INTEGRAL Likelihood = -7.43 Transmembrane 84-100 ( 79-102) INTEGRAL Likelihood = -6.16 Transmembrane 150-166 ( 137-171) INTEGRAL Likelihood = -4.88 Transmembrane 30-46 ( 24-48) INTEGRAL Likelihood = -4.35 Transmembrane 299-315 ( 297-316) INTEGRAL Likelihood = -4.14 Transmembrane 117-133 ( 115-134) INTEGRAL Likelihood = -3.19 Transmembrane 54-70 ( 51-75) INTEGRAL Likelihood = -2.92 Transmembrane 425-441 ( 425-442) INTEGRAL Likelihood = -2.81 Transmembrane 213-229 ( 209-232) INTEGRAL Likelihood = -2.44 Transmembrane 273-289 ( 271-290) ----- Final Results ----- bacterial membrane --- Certainty = 0.5755(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06906 >GP: AAB18291 GB: U35658 L-malate permease [Streptococcus bovis] Identities = 344/443 (77%), Positives = 394/443 (88%), Gaps = 6/443 (1%) Query: 4 ISKKMPQKDLSEHSKAWQNR----RIGSVPLPVYLVLATLILVTGWLQQLPVNMLGGFAV 59 + KK+P +E W+N+ RIGSV LPVYLV A++ILVT L+QLPVNMLGGFAV Sbjct: 1 MEKKLPATAANETD--WRNKLTKTRIGSVTLPVYLVTASIILVTALLEQLPVNMLGGFAV 58 Query: 60 ILTLGWLLGTIGATIPGLKHFGGPAILSLLVPSILVFFNLLNPNVLEATNVLMKQANFLY 119- ILT+GWLLGTIG IP LKHFGGPAILSLLVPSI+VFFNLLN NVL++T++LMKQANFLY Sbjct: 59 ILTMGWLLGTIGGNIPILKHFGGPAILSLLVPSIMVFFNLLNQNVLDSTDILMKQANFLY 118- Query: 120 FYIACLVCGSILGMNRKILIQGLFRMIIPMLLGMVCAMGVGTLVGVILGLDWQHTLFYVV 17- 9 FYIACLVCGSILGMNRKIL+QGL RMI+PM LGM+ AMGVGTLVG +LGL W+H+LFY+V Sbjct: 119 FYIACLVCGSILGMNRKILVQGLMRMIVPMALGMILAMGVGTLVGTLLGLGWKHSLFYIV 17- 8 Query: 180 TPVLAGGIGEGILPLSLGYSAITGVGSEQLVAQLIPATIIGNFFAILCTALLNRFGEKHP 23- 9 TPVLAGGIGEGILPLSLGYSAITG+ SEQLV QLIPATIIGNFFAI+C+ LL+R GEK P Sbjct: 179 TPVLAGGIGEGILPLSLGYSAITGLPSEQLVGQLIPATIIGNFFAIMCSGLLSRLGEKRP 23- 8 Query: 240 SYSGQGQLVKIGHSEDMSDALKDNSGALDVKLMGAGVLTACSLFIAGGLLQHLTDFPGPV 29- 9 SGQGQL+KI +S+D+SDAL+++ +DVKLMGAGVL AC+LFI GGLLQHLT FPGPV Sbjct: 239 ELSGQGQLIKITNSDDLSDALEEDKAPIDVKLMGAGVLIACTLFITGGLLQHLTGFPGPV 29- 8 Query: 300 LMIILAAFLKYLNVIPQETQNGAKQLYKFISSNFTFPLMAGLGLLYIPLKEVVATLSWQY 35- 9 LMI++AAFLKYLNV+P+ETQ G+KQLYKFIS NFTFPLM GLG+LYIPLK+VV LSWQY Sbjct: 299 LMIVVAAFLKYLNVVPKETQRGSKQLYKFISGNFTFPLMVGLGMLYIPLKDVVGMLSWQY 35- 8 Query: 360 FIVVISVVLTVVSVGFFVSRFLNMSPVEAAIISACQSGMGGTGDVAILSTADRMNLMPFA 41- 9 F+VVISVV TV++ GFFVSRF+NM+PVEAAI+SACQSGMGGTGDVAILSTA+RM LMPFA Sbjct: 359 FVVVISVVFTVIATGFFVSRFMNMNPVEAAIVSACQSGMGGTGDVAILSTANRMTLMPFA 41- 8 Query: 420 QVATRLGGAITVITMTAILRIIF 442 QVATRLGGAITVITMTAI R++F Sbjct: 419 QVATRLGGAITVITMTAIFRMLF 441 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06907 Identities = 356/419 (84%), Positives = 385/419 (90%) Query: 27 KIGSVPLPVYVCLALLILLAGFLQKLPVNMLGGFAVILTMGWFLGTIGASIPGFKNFGGP 86 - +IGSVPLPVY+ LA LIL+ G+LQ+LPVNMLGGFAVILT+GW LGTIGA+IPG K+FGGP Sbjct: 24 RIGSVPLPVYLVLATLILVTGWLQQLPVNMLGGFAVILTLGWLLGTIGATIPGLKHFGGP 83 Query: 87 AILSLLVPSILVFFNLINKNVLESTNMLMKQANFLYFYIACLVSGSILGMNRKMLIQGLL 146- AILSLLVPSILVFFNL+N NVLE+TN+LMKQANFLYFYIACLV GSILGMNRK+LIQGL Sbjct: 84 AILSLLVPSILVFFNLLNPNVLEATNVLMKQANFLYFYIACLVCGSILGMNRKILIQGLF 143- Query: 147 RMIFPMLLGMVCAMMVGTFVGVILGLEWRHTLFYIVTPVLAGGIGEGILPLSLGYSSITG 20- 6 RMI PMLLGMVCAM VGT VGVILGL+W+HTLFY+VTPVLAGGIGEGILPLSLGYS+ITG Sbjct: 144 RMIIPMLLGMVCAMGVGTLVGVILGLDWQHTLFYVVTPVLAGGIGEGILPLSLGYSAITG 20- 3 Query: 207 VASEQLVAQLIPATIIGNFFAILCTALLNRLGEKKPHLSGQGQLVRLNKGEDMSDIIADH 26- 6 V SEQLVAQLIPATIIGNFFAILCTALLNR GEK P SGQGQLV++ EDMSD + D+ Sbjct: 204 VGSEQLVAQLIPATIIGNFFAILCTALLNRFGEKHPSYSGQGQLVKIGHSEDMSDALKDN 26- 3 Query: 267 SGPIDVKKMGGGVLTACSLFIFGHLLQQLTGFPGPVLMIVAAAILKYINVIPRETQNGAK 32- 6 SG +DVK MG GVLTACSLFI G LLQ LT FPGPVLMI+ AA LKY+NVIP+ETQNGAK Sbjct: 264 SGALDVKLMGAGVLTACSLFIAGGLLQHLTDFPGPVLMIILAAFLKYLNVIPQETQNGAK 32- 3 Query: 327 QLYKFISGNFTFPLMAGLGLLYIPLKDVVATLSIQYFIVVISVVFTVISVGFFVSRFLNM 38- 6 QLYKFIS NFTFPLMAGLGLLYIPLK+VVATLS QYFIVVISVV TV+SVGFFVSRFLNM Sbjct: 324 QLYKFISSNFTFPLMAGLGLLYIPLKEVVATLSWQYFIVVISVVLTVVSVGFFVSRFLNM 38- 3 Query: 387 NPVEAGIISACQSGMGGTGDVAILSTADRMNLMPFAQVATRLGGAITVITMTAILRMLF 445- +PVEA IISACQSGMGGTGDVAILSTADRMNLMPFAQVATRLGGAITVITMTAILR++F Sbjct: 384 SPVEAAIISACQSGMGGTGDVAILSTADRMNLMPFAQVATRLGGAITVITMTAILRIIF 442- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2248 A DNA sequence (GBSx2369) was identified in S. agalactiae <SEQ ID 6953> which encodes the amino acid sequence <SEQ ID 6954>. This protein is predicted to be malic enzyme (mae). Analysis of this protein sequence reveals the following: TABLE-US-06908 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.28 Transmembrane 164-180 (164-181) ----- Final Results ----- bacterial membrane --- Certainty = 0.1914(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06909 >GP: AAB07709 GB: U35659 malic enzyme [Streptococcus bovis] Identities = 285/386 (73%), Positives = 332/386 (85%), Gaps = 1/386 (0%) Query: 2 SENLGQLAINQARENGGKLEVISKVKVEDKRDLSIAYTPGVASVSSAIAEDVELAYELTT 61 ++++ +LAI QA++ GGKLEV KV +E K DL IAYTPGVA+VSSAI E E AYELTT Sbjct: 3 TKDVKELAIEQAKKFGGKLEVCPKVPIETKADLGIAYTPGVAAVSSAIYEKKERAYELTT 62 Query: 62 KKNTVAVVSDGSAVLGLGDIGPEAAMPVMEGKAALFKRFANVDAVPIVLKTNDTEEIISI 121- KKNTVAV+SDGSAVLGLG+IGPEAAMPVMEGKAALFKRFA VD++P+VL T DTEEII Sbjct: 63 KKNTVAVISDGSAVLGLGNIGPEAAMPVMEGKAALFKRFAGVDSIPLVLDTQDTEEIIQT 122- Query: 122 VKAISPTFGGINLEDISAPRCFEIEQRLIEECDIPVFHDDQHGTAIVVLAALFNSLKLVK 18- 1 VK ++PTFGGINLEDISAPRCFEIEQRLI+E DIPVFHDDQHGTAIVVLAAL+NSLKL+ Sbjct: 123 VKFLAPTFGGINLEDISAPRCFEIEQRLIDELDIPVFHDDQHGTAIVVLAALYNSLKLIN 18- 2 Query: 182 KDIEDIRVVVNGGGSAGLSITRKLLSAGAKHVTVVDRFGIINDKDRESLAPHHKAIAKLT 24- 1 K IEDI VV+NGGGSAGLSITRK L+AG KH+ +VDR GI+++ D +L PHH IAKLT Sbjct: 183 KKIEDIHVVINGGGSAGLSITRKFLAAGVKHIIIVDRTGILSETD-TALPPHHAEIAKLT 24- 1 Query: 242 NREFQSGSLEDALENADVFIGVSAPEALHAEWISKMADKPIVFAMANPIPEIYPDQALKA 30- 1 NRE ++G L ALE ADVF+GVSAP L EWI +M ++P++FAMANP+PEI+PD+AL A Sbjct: 242 NREHRTGDLATALEGADVFVGVSAPGVLKPEWIQQMNEQPVIFAMANPVPEIFPDEALAA 30- 1 Query: 302 GAYIVGTGRSDFPNQINNVLAFPGIFRGALDARAKTITVEMQIAAARGIASLIPEEELST 36- 1 GAYIVGTGRSDFPNQINNVLAFPGIFRGALDARAK IT+EMQIAAA+GIA LIP+ EL+ Sbjct: 302 GAYIVGTGRSDFPNQINNVLAFPGIFRGALDARAKKITIEMQIAAAKGIAKLIPDNELTP 36- 1 Query: 362 THIIPNAFQNDVADVVAKSVSNAVQK 387 T+IIP+ FQ VA VVA+SV NAV++ Sbjct: 362 TNIIPDPFQEGVAKVVAESVRNAVKE 387 A related DNA sequence was identified in S. pyogenes <SEQ ID 6955> which encodes the amino acid sequence <SEQ ID 6956>. Analysis of this protein sequence reveals the following: TABLE-US-06910 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.44 Transmembrane 164-180 (164-181) INTEGRAL Likelihood = -1.75 Transmembrane 94-110 (94-110) ----- Final Results ----- bacterial membrane --- Certainty = 0.1977(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06911 >GP: AAB07709 GB: U35659 malic enzyme [Streptococcus bovis] Identities = 289/379 (76%), Positives = 334/379 (87%), Gaps = 1/379 (0%) Query: 7 QLALEQAKTFGGKLEVQPKVDIKTKHDLSIAYTPGVASVSSAIAKDKTLAYDLTTKKNTV 66 +LA+EQAK FGGKLEV PKV I+TK DL IAYTPGVA+VSSAI + K AY+LTTKKNTV Sbjct: 8 ELAIEQAKKFGGKLEVCPKVPIETKADLGIAYTPGVAAVSSAIYEKKERAYELTTKKNTV 67 Query: 67 AVISDGTAVLGLGDIGPEAAMPVMEGKAALFKAFAGVDAIPIVLDTKDTEEIISIVKALA 126- AVISDG+AVLGLG+IGPEAAMPVMEGKAALFK FAGVD+IP+VLDT+DTEEII VK LA Sbjct: 68 AVISDGSAVLGLGNIGPEAAMPVMEGKAALFKRFAGVDSIPLVLDTQDTEEIIQTVKFLA 127- Query: 127 PTFGGINLEDISAPRCFEIEQRLIKECHIPVFHDDQHGTAIVVLAAIFNSLKLLKKSLDE 18- 6 PTFGGINLEDISAPRCFEIEQRLI E IPVFHDDQHGTAIVVLAA++NSLKL+ K +++ Sbjct: 128 PTFGGINLEDISAPRCFEIEQRLIDELDIPVFHDDQHGTAIVVLAALYNSLKLINKKIED 18- 7 Query: 187 VSIVVNGGGSAGLSITRKLLAAGATKVTVVDKFGIINEQEAAQLAPHHLDIAKVTNREFK 24- 6 + +V+NGGGSAGLSITRK LAAG + +VD+ GI++E + A L PHH +IAK+TNRE + Sbjct: 188 IHVVINGGGSAGLSITRKFLAAGVKHIIIVDRTGILSETDTA-LPPHHAEIAKLTNREHR 24- 6 Query: 247 SGTLEDALEGADIFIGVSAPGVLKAEWISKMAARPVIFAMANPIPEIYPDEALEAGAYIV 30- 6 +G L ALEGAD+F+GVSAPGVLK EWI +M +PVIFAMANP+PEI+PDEAL AGAYIV Sbjct: 247 TGDLATALEGADVFVGVSAPGVLKPEWIQQMNEQPVIFAMANPVPEIFPDEALAAGAYIV 30- 6 Query: 307 GTGRSDFPNQINNVLAFPGIFRGALDARAKTITVEMQIAAAKGIASLVPDDALSTTNIIP 36- 6 GTGRSDFPNQINNVLAFPGIFRGALDARAK IT+EMQIAAAKGIA L+PD+ L+ TNIIP Sbjct: 307 GTGRSDFPNQINNVLAFPGIFRGALDARAKKITIEMQIAAAKGIAKLIPDNELTPTNIIP 36- 6 Query: 367 DAFKEGVAEIVAKSVRSVV 385 D F+EGVA++VA+SVR+ V Sbjct: 367 DPFQEGVAKVVAESVRNAV 385 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06912 Identities = 306/387 (79%), Positives = 349/387 (90%) Query: 1 MSENLGQLAINQARENGGKLEVISKVKVEDKRDLSIAYTPGVASVSSAIAEDVELAYELT 60 M LGQLA+ QA+ GGKLEV KV ++ K DLSIAYTPGVASVSSAIA+D LAY+LT Sbjct: 1 MKNQLGQLALEQAKTFGGKLEVQPKVDIKTKHDLSIAYTPGVASVSSAIAKDKTLAYDLT 60 Query: 61 TKKNTVAVVSDGSAVLGLGDIGPEAAMPVMEGKAALFKRFANVDAVPIVLKTNDTEEIIS 120- TKKNTVAV+SDG+AVLGLGDIGPEAAMPVMEGKAALFK FA VDA+PIVL T DTEEIIS Sbjct: 61 TKKNTVAVISDGTAVLGLGDIGPEAAMPVMEGKAALFKAFAGVDAIPIVLDTKDTEEIIS 120- Query: 121 IVKAISPTFGGINLEDISAPRCFEIEQRLIEECDIPVFHDDQHGTAIVVLAALFNSLKLV 18- 0 IVKA++PTFGGINLEDISAPRCFEIEQRLI+EC IPVFHDDQHGTAIVVLAA+FNSLKL+ Sbjct: 121 IVKALAPTFGGINLEDISAPRCFEIEQRLIKECHIPVFHDDQHGTAIVVLAAIFNSLKLL 18- 0 Query: 181 KKDIEDIRVVVNGGGSAGLSITRKLLSAGAKHVTVVDRFGIINDKDRESLAPHHKAIAKL 24- 0 KK ++++ +VVNGGGSAGLSITRKLL+AGA VTVVD+FGIIN+++ LAPHH IAK+ Sbjct: 181 KKSLDEVSIVVNGGGSAGLSITRKLLAAGATKVTVVDKFGIINEQEAAQLAPHHLDIAKV 24- 0 Query: 241 TNREFQSGSLEDALENADVFIGVSAPEALHAEWISKMADKPIVFAMANPIPEIYPDQALK 30- 0 TNREF+SG+LEDALE AD+FIGVSAP L AEWISKMA +P++FAMANPIPEIYPD+AL+ Sbjct: 241 TNREFKSGTLEDALEGADIFIGVSAPGVLKAEWISKMAARPVIFAMANPIPEIYPDEALE 30- 0 Query: 301 AGAYIVGTGRSDFPNQINNVLAFPGIFRGALDARAKTITVEMQIAAARGIASLIPEEELS 36- 0 AGAYIVGTGRSDFPNQINNVLAFPGIFRGALDARAKTITVEMQIAAA+GIASL+P++ LS Sbjct: 301 AGAYIVGTGRSDFPNQINNVLAFPGIFRGALDARAKTITVEMQIAAAKGIASLVPDDALS 36- 0 Query: 361 TTHIIPNAFQNDVADVVAKSVSNAVQK 387 TT+IIP+AF+ VA++VAKSV + V K Sbjct: 361 TTNIIPDAFKEGVAEIVAKSVRSVVLK 387 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2249 A DNA sequence (GBSx2370) was identified in S. agalactiae <SEQ ID 6957> which encodes the amino acid sequence <SEQ ID 6958>. This protein is predicted to be Bta. Analysis of this protein sequence reveals the following: TABLE-US-06913 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.02 Transmembrane 29-45 (29-45) ----- Final Results ----- bacterial membrane --- Certainty = 0.1808(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06914 >GP: AAD56628 GB: AF165218 Bta [Streptococcus pneumoniae] Identities = 35/112 (31%), Positives = 63/112 (56%) Query: 1 MYSFEELLATMTLITAAEIEDKIDSNQDFVLFIGRISCPFCHLFVPKIVEVADEDEFELF 60 M F + + + + T ++ +D + FIGR +CP+C F + V E + ++ Sbjct: 1 MEQFLDNIKDLEVTTVVRAQEALDKKETATFFIGRKTCPYCRKFAGTLSGVVAETKAHIY 60 Query: 61 HLDSEDFDHWTANKEFRNKYDIPTVPGLMVVKNGTIKVKCDSKMTKEEIREF 112 ++SE+ + FR++Y IPTVPG + + +G I V+CDS M+ +EI++F Sbjct: 61 FINSEEASQLNDLQAFRSRYGIPTVPGFVHITDGQINVRCDSSMSAQEIKDF 112 A related DNA sequence was identified in S. pyogenes <SEQ ID 6959> which encodes the amino acid sequence <SEQ ID 6960>. Analysis of this protein sequence reveals the following: TABLE-US-06915 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0900(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06916 Identities = 39/111 (35%), Positives = 66/111 (59%) Query: 3 SFEELLATMTLITAAEIEDKIDSNQDFVLFIGRISCPFCHLFVPKIVEVADEDEFELFHL 62 +FEE++A + AE+ I S +D ++F+GR SCP+C F PK+ +VA +++ E++ + Sbjct: 11 TFEEIVANFIPSSVAEVTSAIASGKDMIVFLGRSSCPYCRRFAPKLAQVATDNQKEVYFV 70 Query: 63 DSEDFDHWTANKEFRNKYDIPTVPGLMVVKNGTIKVKCDSKMTKEEIREFI 113 DSE+ FR Y + TVP L+V + + CDS +T ++I F+ Sbjct: 71 DSENAADAAELAAFRENYQLVTVPALLVSYDQHQRAVCDSSLTPDDILAFL 121 SEQ ID 6958 (GBS427) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 80 (lane 5; MW 16.2kDa). GBS427-His was purified as shown in FIG. 214, lane 8. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2250 A DNA sequence (GBSx2371) was identified in S. agalactiae <SEQ ID 6961> which encodes the amino acid sequence <SEQ ID 6962>. Analysis of this protein sequence reveals the following: TABLE-US-06917 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.75 Transmembrane 2-18 (1-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.4100(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9437> which encodes amino acid sequence <SEQ ID 9438> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06918 >GP: BAA11328 GB: D78257 ORF11 [Enterococcus faecalis] Identities = 36/80 (45%), Positives = 58/80 (72%) Query: 1 MSLPIIMLVVMVGMMFFMQRQQKKQAQERQKQLNAVQKGDEIVTIGGLFGVVDEVNTEAQ 60 M L +IML+V+V M F++ R QKKQ +ERQ LN +Q GD +VTIGGL GV+ E++++ + Sbjct: 1 MKLMLIMLLVIVAMYFYLFRTQKKQQKERQDFLNNLQPGDAVVTIGGLHGVISEISSDKK 60 Query: 61 RMVLDVDGVYLTFELAAIKS 80 ++ LD +G + F+ +I++ Sbjct: 61 KVTLDCEGAFFDFDQQSIRT 80 A related DNA sequence was identified in S. pyogenes <SEQ ID 6963> which encodes the amino acid sequence <SEQ ID 6964>. Analysis of this protein sequence reveals the following:

TABLE-US-06919 Possible site: 60 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.10 Transmembrane 3-19 (1-22) INTEGRAL Likelihood = -3.03 Transmembrane 63-79 (63-79) ----- Final Results ----- bacterial membrane --- Certainty = 0.3442(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06920 >GP: BAA11328 GB: D78257 ORF11 [Enterococcus faecalis] Identities = 29/75 (38%), Positives = 52/75 (68%) Query: 6 ILMFVVMLGLIWFMQRQQKKQAQERQNQLNAIEKGDEVVTIGGMFAIVDEVDTTAKKIVL 65 ++M +V++ + +++ R QKKQ +ERQ+ LN ++ GD VVTIGG+ ++ E+ + KK+ L Sbjct: 5 LIMLLVIVAMYFYLFRTQKKQQKERQDFLNNLQPGDAVVTIGGLHGVISEISSDKKKVTL 64 Query: 66 DVDGVFLTFELLAIK 80 D +G F F+ +I+ Sbjct: 65 DCEGAFFDFDQQSIR 79 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06921 Identities = 63/90 (70%), Positives = 80/90 (88%) Query: 4 PIIMLVVMVGMMFFMQRQQKKQAQERQKQLNAVQKGDEIVTIGGLFGVVDEVNTEAQRMV 63 PI+M VVM+G+++FMQRQQKKQAQERQ QLNA++KGDE+VTIGG+F +VDEV+T A+++V Sbjct: 5 PILMFVVMLGLIWFMQRQQKKQAQERQNQLNAIEKGDEVVTIGGMFAIVDEVDTTAKKIV 64 Query: 64 LDVDGVYLTFELAAIKSVVSKAATPTEPVE 93 LDVDGV+LTFEL AIK +V+KA T T VE Sbjct: 65 LDVDGVFLTFELLAIKRIVTKATTETTLVE 94 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2251 A DNA sequence (GBSx2372) was identified in S. agalactiae <SEQ ID 6965> which encodes the amino acid sequence <SEQ ID 6966>. Analysis of this protein sequence reveals the following: TABLE-US-06922 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2252 A DNA sequence (GBSx2373) was identified in S. agalactiae <SEQ ID 6967> which encodes the amino acid sequence <SEQ ID 6968>. Analysis of this protein sequence reveals the following: TABLE-US-06923 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 164-180 (164-180) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06924 >GP: CAB61731 GB: AL133220 putative oxidoreductase. [Streptomyces coelicolor A3(2)] Identities = 72/216 (33%), Positives = 120/216 (55%), Gaps = 1/216 (0%) Query: 14 AQALEARGQKLYSVANRTYDKGLEFATKYGIQKVYDHIDQVFEDPEVDIIYISTPHNTHI 73 - A ++ ++ +VA+RT FA ++GI + Y + + D +VD++Y++TPH+ H Sbjct: 25 ADLVDLPDAEVVAVASRTEASAKTFAERFGIPRAYGGWETLARDEDVDVVYVATPHSAHR 84 Query: 74 SFLRKALANGKHVLCEKSITLNSTELKEAIDLAETNHVVLAEAMTIFHMPIYRQLKTLVD 133- + L G++VLCEK TLN+ E E + LA N V L EAM ++ P+ R+LK LV Sbjct: 85 TAAGLCLEAGRNVLCEKPFTLNAREAAELVALARENGVFLMEAMWMYCNPLVRRLKELVA 144- Query: 134 SGKLGPLKMIQMNFGSYKEYDMTNRFFSRDLAGGALLDIGVYALSCIRWFMSEAPHNITS 19- 3 G +G ++ +Q +FG + +R GGALLD+GVY +S + + E P ++ + Sbjct: 145 DGAIGEVRSLQADFGLAGPFPAAHRLRDPAQGGGALLDLGVYPVSFAQLLLGE-PTDVAA 20- 3 Query: 194 QVTFAPTGVDEQVGILLTNPANEMATVSLSLHAKQP 229 + + GVD Q G LL+ + +A++ S+ P Sbjct: 204 RAVLSEEGVDLQTGALLSYGNDALASIHCSITGGTP 239 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2253 A DNA sequence (GBSx2374) was identified in S. agalactiae <SEQ ID 6969> which encodes the amino acid sequence <SEQ ID 6970>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-06925 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4957(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2254 A DNA sequence (GBSx2375) was identified in S. agalactiae <SEQ ID 6971> which encodes the amino acid sequence <SEQ ID 6972>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-06926 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1892(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2255 A DNA sequence (GBSx2376) was identified in S. agalactiae <SEQ ID 6973> which encodes the amino acid sequence <SEQ ID 6974>. This protein is predicted to be a host cell surface-exposed lipoprotein. Analysis of this protein sequence reveals the following: TABLE-US-06927 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.75 Transmembrane 9-25 (5-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.4100(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9005> which encodes amino acid sequence <SEQ ID 9006> was also identified. Analysis of this protein sequence reveals the following: TABLE-US-06928 Lipop: Possible site: -1 Crend: 3 SRCFLG: 0 McG: Length of UR: 24 Peak Value of UR: 2.84 Net Charge of CR: 2 McG: Discrim Score: 10.29 GvH: Signal Score (-7.5): -4.34 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 1 value: -7.75 threshold: 0.0 INTEGRAL Likelihood = -7.75 Transmembrane 5-21 (1-24) PERIPHERAL Likelihood = 13.31 86 modified ALOM score: 2.05 icml HYPID: 7 CFP: 0.410 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4100(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06929 >GP: AAC03455 GB: AF020798 putative host cell surface-exposed lipoprotein [Streptococcus thermophilus bacteriophage TP-J34] Identities = 40/102 (39%), Positives = 63/102 (61%), Gaps = 10/102 (9%) Query: 101 KNALISAKIYSKTMNLSKQSIFEQLYSESPDKATHSDKFTKEESQYAIDHLKVDFKENAL 16- 0 + A+ AK Y+ T+++SK+ + QL S DK++++ S YA+++ +D+ + AL Sbjct: 51 RTAVSKAKQYASTVHMSKEELRSQLVS--------FDKYSQDASDYAVENSGIDYNKQAL 102- Query: 161 ETAKSYQSSSSLSKEEIYKQLTSTLGDKFTNDEAQYAVDHLK 202 E AK YQ + S+S + I QL S DKFT +EA YAV +LK Sbjct: 103 EKAKQYQDTLSMSPDAIRDQLVSF--DKFTQEEADYAVANLK 142 Identities = 40/112 (35%), Positives = 64/112 (56%), Gaps = 9/112 (8%) Query: 41 KKAKIKFNKTQKKIVKKAREYAKSGHMSKDSIIEKLKKDSKKYRQEDINFVINNLKVDYK 100- + ++ K K + V KA++YA + HMSK+ + +L K Y Q+ ++ + N +DY Sbjct: 40 QSSESKVPKEYRTAVSKAKQYASTVHMSKEELRSQLVSFDK-YSQDASDYAVENSGIDYN 98 Query: 101 KNALISAKIYSKTMNLSKQSIFEQLYSESPDKATHSDKFTKEESQYAIDHLK 152 K AL AK Y T+++S +I +QL S DKFT+EE+ YA+ +LK Sbjct: 99 KQALEKAKQYQDTLSMSPDAIRDQLVS--------FDKFTQEEADYAVANLK 142 No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 9006 (GBS122) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 38 (lane 6; MW 21.9 kDa). GBS122-His was purified as shown in FIG. 202, lane 8. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2256 A DNA sequence (GBSx2377) was identified in S. agalactiae <SEQ ID 6975> which encodes the amino acid sequence <SEQ ID 6976>. This protein is predicted to be transposase (orfA). Analysis of this protein sequence reveals the following: TABLE-US-06930 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2830(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06931 >GP: CAB90833 GB: AJ250837 hypothetical protein [Streptococcus dysgalactiae] Identities = 91/96 (94%), Positives = 93/96 (96%) Query: 1 MSRKVRRHFTDDFKQQIVDLYNVGRKRSSLIKVYELTPSTFDKWVRQAKTTGSFKSIDNL 60 MSRK+RRHFTDDFKQQIVDLYN GRKRSSLIK YELTPSTFDKWVRQAKTTGSFKS+DNL Sbjct: 1 MSRKIRRHFTDDFKQQIVDLYNAGRKRSSLIKEYELTPSTFDKWVRQAKTTGSFKSVDNL 60 Query: 61 TDEQRELIELRKHNKELEMQLDILKQAAVIMAQKGK 96 TDEQRELIELRK NKELEMQLDILKQAAVIMAQKGK Sbjct: 61 TDEQRELIELRKRNKELEMQLDILKQAAVIMAQKGK 96 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2257 A DNA sequence (GBSx2378) was identified in S. agalactiae <SEQ ID 6977> which encodes the amino acid sequence <SEQ ID 6978>. This protein is predicted to be transposase (orfB). Analysis of this protein sequence reveals the following: TABLE-US-06932 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2618(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9915> which encodes amino acid sequence <SEQ ID 9916> was also identified. A related GBS nucleic acid sequence <SEQ ID 9903> which encodes amino acid sequence <SEQ ID 9904> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06933 >GP: CAB90834 GB: AJ250837 putative transposase [Streptococcus dysgalactiae] Identities = 243/259 (93%), Positives = 250/259 (95%) Query: 1 MCRWLNMPHSSYYYQAVESVSETEFEETIKRIFLDSESRYGSRKIKICLNNEGITLSRRR 60 MCRWLN+P SSYYY+AVE VSE E EE+IK IFL+S++RYGSRKIKICLNNEGITLSRRR Sbjct: 1 MCRWLNIPRSSYYYKAVEPVSEAELEESIKAIFLESKARYGSRKIKICLNNEGITLSRRR 60 Query: 61 IRRIMKRLNLVSVYQKATFKPHSRGKNEAPIPNHLDRQFKQERPLQALVTDLTYVRVGNR 120- IRRIMKRLNLVSVYQKATFKPHSRGKNEAPIPNHLDRQFK ERPLQALVTDLTYVRVGNR Sbjct: 61 IRRIMKRLNLVSVYQKATFKPHSRGKNEAPIPNHLDRQFKPERPLQALVTDLTYVRVGNR 120- Query: 121 WAYVCLIIDLYNREIIGLSLGWHKTAELVKQAIQSIPYALTKVKMFHSDRGKEFDNQLID 18- 0 WAYVCLIIDLYNREIIGLSLGWHKTAELVKQAIQSIPY LTKVKMFHSDRGKEF+NQLID Sbjct: 121 WAYVCLIIDLYNREIIGLSLGWHKTAELVKQAIQSIPYPLTKVKMFHSDRGKEFNNQLID 18- 0 Query: 181 EILEAFGITRSLSQAGCPYDNAVAESTYRAFKIEFVYQETFQLLEELALKTKDYVHWWNY 24- 0 EILEAFGITRSLSQAGCPYDNAVAESTYRAFKIEFVYQETFQ LEELALKTK YVHWWNY Sbjct: 181 EILEAFGITRSLSQAGCPYDNAVAESTYRAFKIEFVYQETFQSLEELALKTKAYVHWWNY 24- 0 Query: 241 HRIHGSLNYQTPMTKRLIA 259 HRIHGSLNYQTPMTKRLIA Sbjct: 241 HRIHGSLNYQTPMTKRLIA 259 There is also homology to SEQ ID 32. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2258 A DNA sequence (GBSx2379) was identified in S. agalactiae <SEQ ID 6979> which encodes the amino acid sequence <SEQ ID 6980>. This protein is predicted to be pXO1-128. Analysis of this protein sequence reveals the following: TABLE-US-06934 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3684(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06935 >GP: AAD32432 GB: AF065404 pXO1-128 [Bacillus anthracis] Identities = 45/69 (65%), Positives = 52/69 (75%) Query: 17 MKKAGKSNRVIMETLGIKNNSQIYTWMKWYENEELYRFHQGVGKQYTYGKGLEHLSEVEQ 76 - MKK SNR IME LGIKN SQI TWMKWY ++ YRF Q VGKQY+YGKG + LSE+EQ Sbjct: 1 MKKESYSNRTIMEKLGIKNVSQIKTWMKWYRTDQTYRFQQPVGKQYSYGKGPKELSELEQ 60 Query: 77 LQLQVDLLK 85 L+L+ LK Sbjct: 61 LRLENKHLK 69 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2259 A DNA sequence (GBSx2380) was identified in S. agalactiae <SEQ ID 6981> which encodes the amino acid sequence <SEQ ID 6982>. This protein is predicted to be transposase. Analysis of this protein sequence reveals the following: TABLE-US-06936 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2260 A DNA sequence (GBSx2382) was identified in S. agalactiae <SEQ ID 6985> which encodes the amino acid sequence <SEQ ID 6986>. This protein is predicted to be Lmb. Analysis of this protein sequence reveals the following: TABLE-US-06937 Possible site: 18 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 1595> which encodes the amino acid sequence <SEQ ID 1596>. Analysis of this protein sequence reveals the following: TABLE-US-06938 Possible site: 18 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06939 Identities = 302/306 (98%), Positives = 303/306 (98%) Query: 1 MKKVFFLMAMVVSLVMIAGCDKSANPKQPTQGMSVVTSFYPMYAMTKEVSGDLNDVRMIQ 60 MKK FFLMAMVVSLVMIAGCDKSANPKQPTQGMSVVTSFYPMYAMTKEVSGDLNDVRMIQ Sbjct: 1 MKKGFFLMAMVVSLVMIAGCDKSANPKQPTQGMSVVTSFYPMYAMTKEVSGDLNDVRMIQ 60 Query: 61 SGAGIHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKVNVFEASKPLTLDR 120- SGAGIHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKV+VFEASKPLTLDR Sbjct: 61 SGAGIHSFEPSVNDVAAIYDADLFVYHSHTLEAWARDLDPNLKKSKVDVFEASKPLTLDR 120- Query: 121 VKGLEDMEVTQGIDPATLYDPHTWTDPVLAGEEAVNIAKELGHLDPKHKDSYTKKAKAFK 18- 0 VKGLEDMEVTQGIDPATLYDPHTWTDPVLAGEEAVNIAKELG LDPKHKDSYTK AKAFK Sbjct: 121 VKGLEDMEVTQGIDPATLYDPHTWTDPVLAGEEAVNIAKELGRLDPKHKDSYTKNAKAFK 18- 0 Query: 181 KEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISPEQEPSPRQLKEI 24- 0 KEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISPEQEPSPRQLKEI Sbjct: 181 KEAEQLTEEYTQKFKKVRSKTFVTQHTAFSYLAKRFGLKQLGISGISPEQEPSPRQLKEI 24- 0 Query: 241 QDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEV 30- 0 QDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEV Sbjct: 241 QDFVKEYNVKTIFAEDNVNPKIAHAIAKSTGAKVKTLSPLEAAPSGNKTYLENLRANLEV 30- 0 Query: 301 LYQQLK 306 LYQQLK Sbjct: 301 LYQQLK 306 There is also homology to SEQ ID 4. SEQ ID 6986 (GBS189) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 38 (lane 2; MW 35.2 kDa). The GBS189-His fusion product was purified (FIG. 204, lane 7) and used to immunise mice. The resulting antiserum was used for Western blot (FIG. 248A), FACS (FIG. 248B), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2261 A DNA sequence (GBSx2383) was identified in S. agalactiae <SEQ ID 6987> which encodes the amino acid sequence <SEQ ID 6988>. Analysis of this protein sequence reveals the following:

TABLE-US-06940 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4656(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06941 >GP: AAB41455 GB: U34956 phosphoribosylformylglycinamidine synthase [Mycobacterium tuberculosis] Identities = 73/237 (30%), Positives = 112/237 (46%), Gaps = 25/237 (10%) Query: 43 GAGGVCVAIGELAD----GLEIDLDKVPLKYQGLNGTEIAISESQERMSVVVGPSDVDAF 98 - G G+ A ELA G+ I LD VPL+ + + E+ SESQERM VV P +VDAF Sbjct: 282 GGAGLSCATSELASAGDGGMTIQLDSVPLRAKEMTPAEVLCSESQERMCAVVSPKNVDAF 34- 1 Query: 99 IAACNKENIDAVVVATVTEKPNLVMTWNGETIVDLERCFLDTNG------VRVVVDAKVV 152- +A C K + A V+ VT+ L +TW+GET+VD+ + G V + Sbjct: 342 LAVCRKWEVLATVIGEVTDGDRLQITWHGETVVDVPPRTVAHEGPVYQRPVARPDTQDAL 40- 1 Query: 153 DKDLTVPEARTTSAETLEADMLKVLSDLNHASQKGLQTIFDSSVGRSTV--NHPIGGRYQ 21- 0 + D + +R + + L A +L +L + S+ + +D V +TV H GG + Sbjct: 402 NADRSAKLSRPVTGDELRATLLALLGSPHLCSRAFITEQYDRYVRGNTVLAEHADGGMLR 46- 1 Query: 211 ITPTESSVQKLPVQYGVTTTASVMAQGYNPYIAEWSPYHGAAYAVIEATARLVATGA 267 I ES+ + + V + +++ PY GA A+ EA + TGA Sbjct: 462 I--DESTGRGIAVSTDASGRYTLL-----------DPYAGAQLALAEAYRNVAVTGA 505 There is also homology to SEQ ID 982. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2262 A DNA sequence (GBSx2384) was identified in S. agalactiae <SEQ ID 6989> which encodes the amino acid sequence <SEQ ID 6990>. This protein is predicted to be 30S ribosomal protein S11 (rpsK). Analysis of this protein sequence reveals the following: TABLE-US-06942 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0598(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9281> which encodes amino acid sequence <SEQ ID 9282> was also identified. A further related GBS nucleic acid sequence <SEQ ID 10919> which encodes amino acid sequence <SEQ ID 10920> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06943 >GP: CAB11918 GB: Z99104 ribosomal protein S11 (BS11) [Bacillus subtilis] Identities = 81/92 (88%), Positives = 87/92 (94%) Query: 2 HGNALAWSSAGALGFKGSRKSTPFAAQMAAEAAAKSAQEHGLKTVEVTVKGPGSGRESAI 61 HGNA++WSSAGALGF+GSRKSTPFAAQMAAE AAK + EHGLKT+EVTVKGPGSGRE+AI Sbjct: 40 HGNAISWSSAGALGFRGSRKSTPFAAQMAAETAAKGSIEHGLKTLEVTVKGPGSGREAAI 99 Query: 62 RALAAAGLEVTAIRDVTPVPHNGARPPKRRRV 93 RAL AAGLEVTAIRDVTPVPHNG RPPKRRRV Sbjct: 100 RALQAAGLEVTAIRDVTPVPHNGCRPPKRRRV 131 A related DNA sequence was identified in S. pyogenes <SEQ ID 6991> which encodes the amino acid sequence <SEQ ID 6992>. Analysis of this protein sequence reveals the following: TABLE-US-06944 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0945(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06945 Identities = 92/93 (98%), Positives = 93/93 (99%) Query: 1 MHGNALAWSSAGALGFKGSRKSTPFAAQMAAEAAAKSAQEHGLKTVEVTVKGPGSGRESA 60 +HGNALAWSSAGALGFKGSRKSTPFAAQMAAEAAAKSAQEHGLKTVEVTVKGPGSGRESA Sbjct: 35 VHGNALAWSSAGALGFKGSRKSTPFAAQMAAEAAAKSAQEHGLKTVEVTVKGPGSGRESA 94 Query: 61 IRALAAAGLEVTAIRDVTPVPHNGARPPKRRRV 93 IRALAAAGLEVTAIRDVTPVPHNGARPPKRRRV Sbjct: 95 IRALAAAGLEVTAIRDVTPVPHNGARPPKRRRV 127 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2263 A DNA sequence (GBSx2385) was identified in S. agalactiae <SEQ ID 6993> which encodes the amino acid sequence <SEQ ID 6994>. Analysis of this protein sequence reveals the following: TABLE-US-06946 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2551(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06947 >GP:BAB03881 GB:AP001507 DNAdirected RHA polymerase alpha subunit [Bacillus halodurans] Identities = 190/314 (60%), Positives = 249/314 (78%), Gaps 2/314 (0%) Query: 1 MIEFEKPIITKIDENKD--YGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58 MIE EKP+I I+ ++D YG+FV+EPLERGYGTTLGNSLRR+LLSSLPGAAVTS++IDG Sbjct: 1 MIEIEKPVIETIEISEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60 Query: 59 VLHEFDTIPGVREDVMQIILNVKGLAVRSYVEDERIIELDVEGPAEITAGDILTDSDIEI 118- VLHEF TI GV EDV I+LN+K LA+K Y +++K +E+D +G +TAGD+ DSD+++ Sbjct: 61 VLHEFSTIEGVVEDVTTIVLNLKQLALKIYSDEDKTLEIDTQGEGVVTAGDLTHDSDVDV 120- Query: 119 VNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQV 17- 8 +NPD ++ T+ G L+ +T + RGYVPAEGNK D+ +G + +DSIYTPV +VNYQV Sbjct: 121 LNPDLHIATLTTGAHLRNRITAKRGRGYVPAEGNKSDELAIGVIPIDSIYTPVSRVNYQV 18- 0 Query: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKET 23- 8 E RVG +DKLT+++ T+G+I PE+A+L A++L EHLN+F LT+ A+ E+M E Sbjct: 181 ENTRVGQVTNYDKLTLDVWTDGSIRPEEAVSLGAKILTEHLNIFVGLTDQAQNAEIMVEK 24- 0 Query: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEETEPEMMKVRNLGRKSLEEVK 29- 8 E+ EKVL+ TIEELDLSVRSYNCLKRAGINTV +LT+ETE +MMKVRNLGRKSLEEV+ Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQRTEEDMMKVRNLGRKSLEEVQ 30- 0 Query: 299 IKLADLGLGLENDK 312 KL +LGLGL+ ++ Sbjct: 301 EKLGELGLGLRKEE 314 A related DNA sequence was identified in S. pyogenes <SEQ ID 6995> which encodes the amino acid sequence <SEQ ID 6996>. Analysis of this protein sequence reveals the following: TABLE-US-06948 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2551(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06949 Identities = 305/312 (97%), Positives = 311/312 (98%) Query: 1 MIEFEKPIITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVL 60 MIEFEKPIITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVL Sbjct: 1 MIEFEKPIITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVL 60 Query: 61 HEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEIVN 120- HEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIEL+VEGPAE+TAGDILTDSDIE+VN Sbjct: 61 HEFDTIPGVREDVMQIILNVKGLAVISYVEDEKIIELEVEGPAEVTAGDILTDSDIELVN 120- Query: 121 PDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEP 18- 0 PDHYLFTIAEGHSL+ATMTVAK RGYVPAEGNEKDDAPVGTLAVDSIYTPVEKVNYQVEP Sbjct: 121 PDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKODAPVGTLAVDSIYTPVKKVNYQVEP 18- 0 Query: 181 ARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEK 24- 0 ARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEK Sbjct: 181 ARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEK 24- 0 Query: 241 VNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKIK 30- 0 VNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEK+EPEMMKVRNLGRKSLEEVK+K Sbjct: 241 VNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVKVK 30- 0 Query: 301 LADLGLGLKNDK 312 LADLGLGLKNDK Sbjct: 301 LADLGLGLKNDK 312 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2264 A DNA sequence (GBSx2386) was identified in S. agalactiae <SEQ ID 6997> which encodes the amino acid sequence <SEQ ID 6998>. This protein is predicted to be 50S ribosomal protein L17 (rplQ). Analysis of this protein sequence reveals the following: TABLE-US-06950 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1609(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06951 >GP:CAB11920 GB:Z99104 ribosomal protein L17 (BL15) [Bacillus subtilis] Identities = 95/128 (74%), Positives = 105/128 (81%), Gaps = 8/128 (6%) Query: 1 MAYRKLGRTSSQRKANLRDLTTDLLINESIVTTEARAKEIRKTVEKMITLGKRGDLHARR 60 M+YRKLGRTS+QRKANLRDLTTDL+INE I TTE RAKE+R VEKMITLGKRGDLHARR Sbjct: 1 MSYRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITLGKRGDLHARR 60 Query: 61 QAAAYVRNEIASENYDEASDKYTSTTALQRLFDDIAPRYASRNGGYTRILKTEPRRGDAA 120- QAAAY+RNE+A+E ++ ALQKLF DIA RY ER GGYTRI+K PRRGD A Sbjct: 61 QAAAYIRNEVANEENNQ--------DALQKLFSDIATRYEERQGGYTRIMKLGPRRGDGA 112- Query: 121 PMAIIELV 128 PMAIIELV Sbjct: 113 PMAIIELV 120 A related DNA sequence was identified in S. pyogenes <SEQ ID 6999> which encodes the amino acid sequence <SEQ ID 7000>. Analysis of this protein sequence reveals the following: TABLE-US-06952 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1609(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06953 Identities = 125/128 (97%), Positives = 127/128 (98%) Query: 1 MAYRKLGRTSSQRKAMLRDLTTDLLINESIVTTEARAKEIRKTVEKNITLGKRGDLHARR 60 M+YRKLGRTSSQRKAMLRDLTTDLLINESIVTTEARAKEIRKTVEKMITLGKRGDLHARR Sbjct: 1 MAYRKLGRTSSQRKANLRDLTTDLLINESIVTTEARAKEIRKTVERNITLGKRGDLHARR 60 Query: 61 QAAAYVRNEIASENYDEASDKYTSTTALQKLFDDIAPRYAERNGGYTRILKTEPRRGDAA 120- QAAAYVRNEIASENYDEA+DKYTSTTALQKLF +IAPRYAERNGGYTRILKTEPRRGDAA Sbjct: 61 QAAAYVRNEUASENYDEATDKYTSTTALQKLFSEIAPRYAERNGGYTRILKTEPRRGDAA 120- Query: 121 PMAIIELV 128 PMAIIELV Sbjct: 121 PMAIIELV 128 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2265 A DNA sequence (GBSx2396) was identified in S. agalactiae <SEQ ID 7001> which encodes the amino acid sequence <SEQ ID 7002>. This protein is predicted to be mercuric reductase. Analysis of this protein sequence reveals the following: TABLE-US-06954 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2384(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06955 >GP:AAA83977 GB:AF138877 mercuric reductase MerA [Bacillus sp. RCE07] Identities = 29/33 (87%), Positives = 32/33 (96%) Query: 4 VGLTEEQAKEKGYDVKTSVLPLXAVPRAIVNRE 36 VGLTE+QAKEKGY+VKTSVLPL AVPRA+VNRE Sbjct: 520 VGLTEQQAKEKGYEVKTSVLPLDAVPRALVNRE 552 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2266 A DNA sequence (GBSx2397) was identified in S. agalactiae <SEQ ID 7003> which encodes the amino acid sequence <SEQ ID 7004>. This protein is predicted to be mercuric reductase. Analysis of this protein sequence reveals the following: TABLE-US-06956 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3016(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06957 >GP: CAA70224 GB: Y09024 mercuric reductase [Bacillus cereus] Identities = 146/194 (75%), Positives = 175/194 (89%) Query: 2 PQISGLEKMDYLTSTTLLELKKIPKRLTVIGSGYIGMELGQLFHHLGSEITLMQRSERLL 61 P I GL ++DYLTST+LLELKK+PKRL VIGSGYIGMELGQLFH+LGSE+TL+QRSERLL Sbjct: 226 PNIPGLNEVDYLTSTSLLELKKVPKRLVVIGSGYIGMELGQLFHNLGSEVTLIQRSERLL 28- 5 Query: 62 KEYDPEISESVEKALIEQGINLVKGATFERVEQSGEIKRVYVTVNGSREVIESDQLLVAT 121- KEYDPEISESVEK+L+EQGINLVKGAT+ER+EQ+G+IK+V+V VNG + +IE+DQLLVAT Sbjct: 286 KEYDPEISESVEKSLVEQGINLVKGATYERIEQNGDIKKVHVEVNGKKRIIEADQLLVAT 34- 5 Query: 122 GRKPNTDSLNLSAAGVETGKNNEILINDFGQTSNEKIYAAGDVTLGPQFVYVAAYEGGII 18- 1 GR PNT +LNL AAGVE G EI+I+D+ +T+N +IYAAGDVTLGPQFVYVAAY+GG+ Sbjct: 346 GRTPNTATLNLRAAGVEIGSRGEIIIDDYSRTTNTRIYAAGDVTLGPQFVYVAAYQGGVA 40- 5 Query: 182 TDNAIGGLNKKIDL 195 NAIGGLNKK++L Sbjct: 406 APNAIGGLNKKLNL 419 There is also homology to SEQ ID 1820. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2267 A DNA sequence (GBSx2398) was identified in S. agalactiae <SEQ ID 7005> which encodes the amino acid sequence <SEQ ID 7006>. This protein is predicted to be triacylglycerol acylhydrolase. Analysis of this protein sequence reveals the following: TABLE-US-06958 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3180(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2268 A DNA sequence (GBSx2399) was identified in S. agalactiae <SEQ ID 7007> which encodes the amino acid sequence <SEQ ID 7008>. Analysis of this protein sequence reveals the following: TABLE-US-06959 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0544(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06960 >GP: AAC74453 GB: AE000234 orf, hypothetical protein [Escherichia coli K12] Identities = 45/58 (77%), Positives = 51/58 (87%) Query: 1 MPWQNLLHAGQENLFSGLTALTAEFTVGEGKLMTHDEPCSMAPDDKHDLISGTCSHLP 58 +PWQNLLHAG+ENLFSGLTAL+AEFT+GEG+LM HD P APD+ DLISGTCSHLP Sbjct: 34 LPWQNLLHAGEENLFSGLTALSAEFTIGEGELMAHDVPLGCAPDEYDDLISGTCSHLP 91 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2269 A DNA sequence (GBSx2400) was identified in S. agalactiae <SEQ ID 7009> which encodes the amino acid sequence <SEQ ID 7010>. This protein is predicted to be transposase for insertion sequence element is 5. Analysis of this protein sequence reveals the following: TABLE-US-06961 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2058(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06962 >GP: BAB15497 GB: AK026530 unnamed protein product [Homo sapiens] Identities = 297/299 (99%), Positives = 297/299 (99%) Query: 1 MEQILPWQNMVEVIEPFYPKAGNGRRPYPLETMLRIHCMQHWYNLSDGAMEDALYEIASM 60 MEQILPWQNMVEVIEPFYPKAGNGRRPYPLETMLRIHCMQHWYNLSDGAMEDALYEIASM Sbjct: 40 MEQILPWQNMVEVIEPFYPKAGNGRRPYPLETMLRIHCMQHWYNLSDGAMEDALYEIASM 99 Query: 61 RLFARLSLDSALPDRTTIMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATII 120- RLFARLSLDSALPDRTTIMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATII Sbjct: 100 RLFARLSLDSALPDRTTIMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATII 15- 9 Query: 121 EAPSSTKNKEQQRDPEMHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQLX 18- 0 EAPSSTKNKEQQRDPEMHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQL Sbjct: 160 EAPSSTKNKEQQRDPEMHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQLG 21- 9 Query: 181 NLLHGEEQFVSADAXYQGAPQREELAEVDVDWLIAERPGKVRTLKQHPRKNKTAINIEYM 24- 0 NLLHGEEQFVSADA YQGAPQREELAEVDVDWLIAERPGKVRTLKQHPRKNKTAINIEYM Sbjct: 220 NLLHGEEQFVSADAGYQGAPQREELAEVDVDWLIAERPGKVRTLKQHPRKNKTAINIEYM 27- 9 Query: 241 KASIRARVEHPFRIIKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH 299- KASIRARVEHPFRIIKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH Sbjct: 280 KASIRARVEHPFRIIKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH 338- No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2270 A DNA sequence (GBSx2401) was identified in S. agalactiae <SEQ ID 7011> which encodes the amino acid sequence <SEQ ID 7012>. Analysis of this protein sequence reveals the following:

TABLE-US-06963 Possible site: 16 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06964 >GP: CAB51958 GB: AL109661 putative eukaryotic-type serine/threonine protein kinase [Streptomyces coelicolor A3(2)] Identities = 49/169 (28%), Positives = 90/169 (52%), Gaps = 6/169 (3%) Query: 23 PTTIRVPDVSNKTVAQAKMTLENSGLKVGAIRNIESDSVSEGLVVKTDPAAGRSRREGAK 82 - P T+++PDV+ + +A+ LE+ GL+ G + SD V+ G V+ T P +G + R G+ Sbjct: 469 PDTVKLPDVTGYKLDKARTLLEDEGLEPGMVTRAFSDEVARGFVISTKPGSGTTVRAGSA 52- 8 Query: 83 VNLYIATPNKSFTLGNYKEHNYKDILKDLQGKGVKKSLIKVKRKINNDYTTGTILAQSLP 142- V L + + + + + + +L+G G+K + ++N++Y +G + A+ P Sbjct: 529 VAL-VVSKGSPVDVPDVTGDDLDEARAELEGAGLK--VKTADERVNSEYDSGRV-ARQTP 58- 4 Query: 143 EGTSFNPDGNKKLTLTVAVNDPMI-MPDVTGMTVGEVIETLTDLGLDAD 190 E +G+ +TLTV+ MI +PDV G +V + + L D G + D Sbjct: 585 EPGGRAAEGD-TVTLTVSKGPRMIEVPDVVGDSVDDAKQKLEDAGFEVD 632 Identities = 45/161 (27%), Positives = 80/161 (48%), Gaps = 4/161 (2%) Query: 27 RVPDVSNKTVAQAKMTLENSGLKVGAIRNIESDSVSEGLVVKTDPAAGRSRREGAKVNLY 86 - +VP + +KT AQA+ L+++GL VG +R+ SD+V G V+ TDP G R+ V+L Sbjct: 405 KVPPLLSKTEAQARDRLDDAGLDVGKVRHAYSDTVERGKVISTDPGVGDRIRKNDSVSLT 46- 4 Query: 87 IATPNKSFTLGNYKEHNYKDILKDLQGKGVKKSLIKVKRKINNDYTTGTILAQSLPEGTS 146- ++ + L + + L+ +G++ + V R +++ G +++ GT+ Sbjct: 465 VSDGPDTVKLPDVTGYKLDKARTLLEDEGLEPGM--VTRAFSDEVARGFVISTKPGSGTT 52- 2 Query: 147 FNPDGNKKLTLTVAVNDPMIMPDVTGMTVGEVIETLTDLGL 187 + L V+ P+ +PDVTG + E L GL Sbjct: 523 VR--AGSAVALVVSKGSPVDVPDVTGDDLDEARAELEGAGL 561 There is also homology to SEQ ID 3026. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2271 A DNA sequence (GBSx2402) was identified in S. agalactiae <SEQ ID 7013> which encodes the amino acid sequence <SEQ ID 7014>. Analysis of this protein sequence reveals the following: TABLE-US-06965 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9311> which encodes amino acid sequence <SEQ ID 9312> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06966 >GP: AAB90561 GB: AE001058 glutamine ABC transporter, ATP-binding protein (glnQ) [Archaeoglobus fulgidus] Identities = 142/219 (64%), Positives = 178/219 (80%) Query: 1 MDIHQGEVVVIIGPSGSGKSTFLRTMNLLEVPTKGTVTFEGIDITDKKNDIFKMREKMGM 60 M + +GEVVVIIGPSGSGKST LR +N LE PT G + +G+DIT+ K DI K+R+++G+ Sbjct: 24 MKVEKGEVVVIIGPSGSGKSTLLRCINRLEEPTSGKILLDGVDITNSKIDINKVRQRIGI 83 Query: 61 VFQQFNLFPNMTVLENITLSPIKTKGLSNLDAQTKAYELLEKVGLKEKANTYPASLSGGQ 120- VFQQFNLFP++T L+N+TL+PIK K +S +A+ LLEKVGL++KA+ YPA LSGGQ Sbjct: 84 VFQQFNLFPHLTALQNVTLAPIKIKKMSKREAEELGMRLLEKVGLEDKADYYPAQLSGGQ 143- Query: 121 QQRIAIARGLAMNPDVLLFDEPTSALDPEMVGEVLTVMQDLAKSGMTMVIVTHEMGFARE 18- 0 QQR+AIAR LAMNP+V+LFDE TSALDPE+V EVL VM+ LA+ GMTMV+VTHEMGFARE Sbjct: 144 QQRVAIARALAMNPEVMLFDEVTSALDPELVKEVLDVMKQLARDGMTMVVVTHEMGFARE 20- 3 Query: 181 VADRVIFMDAGIIVEQGAPKEVFEQTKEIRTRDFLSKVL 219 V DRVIFMD G+IVE+G P+++F K RTR FLS +L Sbjct: 204 VGDRVIFMDGGVIVEEGKPEQIFSNPKHERTRKFLSMIL 242 There is also homology to SEQ ID 1186. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2272 A DNA sequence (GBSx2403) was identified in S. agalactiae <SEQ ID 7015> which encodes the amino acid sequence <SEQ ID 7016>. This protein is predicted to be 4-hydroxy-2-oxoglutarate aldolase (kdgA). Analysis of this protein sequence reveals the following: TABLE-US-06967 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1479(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06968 >GP: CAB14127 GB: Z99115 deoxyphosphogluconate aldolase [Bacillus subtilis] Identities = 21/62 (33%), Positives = 38/62 (60%), Gaps = 4/62 (6%) Query: 3 QLMQGKIVAVIRGNSQEEAFQAAQACIKGGISAIEIAYTNSKASQVIEQLVTQYTNQEQV 62 +L + K++AVIR ++EA Q ++ + GI A+E+ YT AS +IE + N+E + Sbjct: 9 RLKEAKLIAVIRSKDKQEACQQIESLLDKGIRAVEVTYTTPGASDIIE----SFRNREDI 64 Query: 63 VV 64 ++ Sbjct: 65 LI 66 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2273 A DNA sequence (GBSx2405) was identified in S. agalactiae <SEQ ID 7017> which encodes the amino acid sequence <SEQ ID 7018>. This protein is predicted to be H repeat-associated protein (rfbQRS) (b1458). Analysis of this protein sequence reveals the following: TABLE-US-06969 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0207(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> There is homology to SEQ ID 504. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2274 A DNA sequence (GBSx2406) was identified in S. agalactiae <SEQ ID 7019> which encodes the amino acid sequence <SEQ ID 7020>. Analysis of this protein sequence reveals the following: TABLE-US-06970 Possible site: 14 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.74 Transmembrane 2-18 (1-21) INTEGRAL Likelihood = -3.03 Transmembrane 73-89 (73-92) ----- Final Results ----- bacterial membrane --- Certainty = 0.3697(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. There is also homology to SEQ ID 3376. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2275 A DNA sequence (GBSx2407) was identified in S. agalactiae <SEQ ID 7021> which encodes the amino acid sequence <SEQ ID 7022>. This protein is predicted to be insertion element IS1 protein InsB (insB.sub.--5). Analysis of this protein sequence reveals the following: TABLE-US-06971 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4280(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2276 A DNA sequence (GBSx2409) was identified in S. agalactiae <SEQ ID 7023> which encodes the amino acid sequence <SEQ ID 7024>. Analysis of this protein sequence reveals the following: TABLE-US-06972 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3937(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2277 A DNA sequence (GBSx2410) was identified in S. agalactiae <SEQ ID 7025> which encodes the amino acid sequence <SEQ ID 7026>. This protein is predicted to be triosephosphate isomerase (tpi). Analysis of this protein sequence reveals the following: TABLE-US-06973 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 35-51 (35-51) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06974 >GP: AAC43268 GB: U07640 triosephosphate isomerase [Lactococcus lactis] Identities = 50/75 (66%), Positives = 61/75 (80%) Query: 6 IAGNWKMNKNPEEAKAFIEAVASKLPSSELVEAGIAAPALTLSTVLEAAKGSELKIAAQN 65 IAGNWKMNK EA+AF+EAV + LPSS+ VE+ I APAL L+ + +GSELK+AA+N Sbjct: 7 IAGNWKMNKTLSEAQAFVEAVKNNLPSSDNVESVIGAPALFLAPMAYLRQGSELKLAAEN 66 Query: 66 SYFENSGAFTGENSP 80 SYFEN+GAFTGENSP Sbjct: 67 SYFENAGAFTGENSP 81 There is also homology to SEQ ID 6838: TABLE-US-06975 Identities = 58/77 (75%), Positives = 68/77 (87%) Query: 6 IAGNWKMNKNPEEAKAFIEAVASKLPSSELVEAGIAAPALTLSTVLEAAKGSELKIAAQN 65 IAGNWKMNKNP+EAKAF+EAVASKLPS++LV+ +AAPA+ L T +EAAK S LK+AAQN Sbjct: 7 IAGNWKMNKNPQEAKAFVEAVASKLPSTDLVDVAVAAPAVDLVTTIEAAKDSVLKVAAQN 66 Query: 66 SYFENSGAFTGENSPKV 82 YFEN-GAFTGE SPKV Sbjct: 67 CYFENTGAFTGETSPKV 83 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2278 A DNA sequence (GBSx2412) was identified in S. agalactiae <SEQ ID 7027> which encodes the amino acid sequence <SEQ ID 7028>. Analysis of this protein sequence reveals the following: TABLE-US-06976 Possible site: 20 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.39 Transmembrane 96-112 (96-112) ----- Final Results ----- bacterial membrane --- Certainty = 0.1956(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06977 >GP: BAA14368 GB: D90354 surface protein antigen precursor [Streptococcus sobrinus] Identities = 60/129 (46%), Positives = 76/129 (58%), Gaps = 18/129 (13%) Query: 3 ISFDNSFLETVSDDSAFQADVYLQMKRIAAGQVENTYLHTVNGYVISSNTVVTHTPQPEE 62 ++F FL +VS DSAFQA+VYLQMKRIA G NTY++TVNG SSNTV T TP+P++ Sbjct: 1442 VTFKEDFLRSVSVDSAFQAEVYLQMKRIAVGTFANTYVNTVNGITYSSNTVRTSTPEPKQ 1- 501 Query: 63 PSPNQP--------TPPQPPIETIEPPVPASILPNTGEQES----LLGLIG--AGILLGT 108- PSP P P Q PP A LP TG+ + LLGL+ AG L Sbjct: 1502 PSPVDPKTTTTVVFQPRQGKAYQPAPPAGAQ-LPATGDSSNAYLPLLGLVSLTAGFSL-- 1- 558 Query: 109 AYGLKKKEE 117 GL++K++ Sbjct: 1559 -LGLRRKQD 1566 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2279 A DNA sequence (GBSx2413) was identified in S. agalactiae <SEQ ID 7029> which encodes the amino acid sequence <SEQ ID 7030>. Analysis of this protein sequence reveals the following: TABLE-US-06978 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3691(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9359> which encodes amino acid sequence <SEQ ID 9360> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06979 >GP: CAB15793 GB: Z99123 phosphotransacetylase [Bacillus subtilis] Identities = 131/221 (59%), Positives = 169/221 (76%), Gaps = 2/221 (0%) Query: 6 LVDPVILGKADEVHDSLARLGFVDQDYSIIDPEQYEKFEEMKEAFVEIRKGKATMEDADR 65 +++P+++G +E+ L I DP YE E++ +AFVE RKGKAT E A + Sbjct: 41 VLNPIVIGNENEIQAKAKELNLTLGGVKIYDPHTYEGMEDLVQAFVERRKGKATEEQARK 100- Query: 66 LLKDVNYFGVMLVKLGLADGMVSGAIHSTADTVRPALQIIKTKPGISRTSGVFLMNRENT 125- L D NYFG MLV GLADG+VSGA HSTADTVRPALQIIKTK G+ +TSGVF+M R Sbjct: 101 ALLDENYFGTMLVYKGLADGLVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMARG-- 15- 8 Query: 126 QERYIFADCAINIDPNAQELAEIAVNTADTAKIFDIDPKIAMLSFSTKGSAKAPQAEKVQ 18- 5 +E+Y+FADCAINI P++Q+LAEIA+ +A+TAK+FDI+P++AMLSFSTKGSAK+ + EKV Sbjct: 159 EEQYVFADCAINIAPDSQDLAEIAIESANTAKMFDIEPRVAMLSFSTKGSAKSDETEKVA 21- 8 Query: 186 EAAKIAKDLSPELAVDGELQFDAAFVPETAEIKAPNSDVAG 226 +A KIAK+ +PEL +DGE QFDAAFVP AE KAP+S++ G Sbjct: 219 DAVKIAKEKAPELTLDGEFQFDAAFVPSVAEKKAPDSEIKG 259 A related DNA sequence was identified in S. pyogenes <SEQ ID 7031> which encodes the amino acid sequence <SEQ ID 7032>. Analysis of this protein sequence reveals the following: TABLE-US-06980 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3182(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06981 Identities = 181/227 (79%), Positives = 211/227 (92%) Query: 1 MKFEGLVDPVILGKADEVHDSLARLGFVDQDYSIIDPEQYEKFEEMKEAFVEIRKGKATM 60 +KFEGL++P+ILG+++EV + L +LGF DQDY+II+P +Y F++MKEAFVE+RKGKAT+ Sbjct: 38 LKFEGLLEPIILGQSEEVRNLLTKLGFADQDYTIINPNEYADFDKMKEAFVEVRKGKATL 97 Query: 61 EDADRLLKDVNYFGVMLVKLGLADGMVSGAIHSTADTVRPALQIIKTKPGISRTSGVFLM 120- EDAD++L+DVNYFGVMLVK+GLADGMVSGAIHSTADTVRPALQIIKTKPGISRTSGVFLM Sbjct: 98 EDADKMLRDVNYFGVMLVKMGLADGMVSGAIHSTADTVRPALQIIKTKPGISRTSGVFLM 157- Query: 121 NRENTQERYIFADCAINIDPNAQELAEIAVNTADTAKIFDIDPKIAMLSFSTKGSAKAPQ 18- 0 NRENT ERY+FADCAINIDP AQELAEIAVNTA+TAKIFDIDPKIAMLSFSTKGS KAPQ Sbjct: 158 NRENTSERYVFADCAINIDPTAQELAEIAVNTAETAKIFDIDPKIAMLSFSTKGSGKAPQ 21- 7 Query: 181 AEKVQEAAKIAKDLSPELAVDGELQFDAAFVPETAEIKAPNSDVAGK 227 +KV+EA +IA L+P+LA+DGELQFDAAFVPETA IKAP+S VAG+ Sbjct: 218 VDKVREATEIATGLNPDLALDGELQFDAAFVPETAAIKAPDSAVAGQ 264 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2280 A DNA sequence (GBSx2414) was identified in S. agalactiae <SEQ ID 7033> which encodes the amino acid sequence <SEQ ID 7034>. This protein is predicted to be lipopolysaccharide biosynthesis protein-related protein. Analysis of this protein sequence reveals the following: TABLE-US-06982 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4076(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06983 >GP: AAG19110 GB: AE005009 Vng0600c [Halobacterium sp. NRC-1] Identities = 57/176 (32%), Positives = 86/176 (48%), Gaps = 20/176 (11%) Query: 1 MKVLLYLEAEEYLKKSGIGRAIKHQEKALQIAGIDYTTNPT------------------- 41 M+ L YLEA E L+ G+ A Q AL+ ++ P Sbjct: 2 MRALNYLEAAEALR-GGMVTATNQQRAALETTDVEVVETPWRAGDPVRSIGSLAAGGSCF 60 Query: 42 DDFDLVHMNTYGIRSWLLMSKAKKTGKKVIMHGHSTEEDFRNSFIGSNLVSPLFKWYLCR 101- FD+ H N G S + A++T +++H H T EDF SF GS+ ++P + YL Sbjct: 61 TAFDVAHCNLVGPGSVAVARHARRTDTPLVLHAHLTREDFAQSFRGSSTIAPALEPYLRW 120- Query: 102 FYQKADAIITPTDYSKQLIKAYGIKKPIFVLSNGIDLSRYQXSEKKESAFRHYFHL 157 FY +AD ++ P++Y+K +++AY + PI LSNG+DL Q E + R F L Sbjct: 121 FYSQADLVLCPSEYTKDVLRAYPVDAPIRQLSNGVDLESMQGYESFRADTRARFDL 176 There is also homology to SEQ ID 1220. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2281 A DNA sequence (GBSx2415) was identified in S. agalactiae <SEQ ID 7035> which encodes the amino acid sequence <SEQ ID 7036>. Analysis of this protein sequence reveals the following: TABLE-US-06984 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2625(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06985 >GP: AAC35010 GB: AF055987 intracellular a-amylase [Streptococcus mutans] Identities = 27/46 (58%), Positives = 33/46 (71%) Query: 1 MEVGEIYAGKTFVDYLGNCEQEVVIGDDGWGDFLVESASISAWVPK 46 M +GE K FVDYL NC +EV++ D GWGDF V+ AS+SAWV K Sbjct: 438 MNMGEFNRNKVFVDYLNNCTEEVILDDQGWGDFPVQEASLSAWVNK 483 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2282 A DNA sequence (GBSx2416) was identified in S. agalactiae <SEQ ID 7037> which encodes the amino acid sequence <SEQ ID 7038>. This protein is predicted to be RopA. Analysis of this protein sequence reveals the following:

TABLE-US-06986 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2082(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> There is also homology to SEQ ID 6908: TABLE-US-06987 Identities = 30/35 (85%), Positives = 33/35 (93%) Query: 1 MEADQVRGLLSADMLKHDIAMKKAVDVITSSATVK 35 M ADQVR LLSADMLKHDIAMKKAV+VITS+A+VK Sbjct: 422 MPADQVRSLLSADMLKHDIAMKKAVEVITSTASVK 456 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2283 A DNA sequence (GBSx2417) was identified in S. agalactiae <SEQ ID 7039> which encodes the amino acid sequence <SEQ ID 7040>. This protein is predicted to be DNA-directed RNA polymerase, subunit delta. Analysis of this protein sequence reveals the following: TABLE-US-06988 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2407(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06989 >GP: CAB15744 GB: Z99123 RNA polymerase (delta subunit) [Bacillus subtilis] Identities = 62/186 (33%), Positives = 102/186 (54%), Gaps = 15/186 (8%) Query: 1 MELEVFAGQEKSELSMIEVARAILEQRGRDNEMYFSDLVNDIQTYLGKSDSAIRESLPFF 60 M ++ ++ +E E++++E+A + E+ + + F +L+N+I + LG + + + F Sbjct: 1 MGIKQYSQEELKEMALVEIAHELFEEHKKP--VPFQELLNEIASLLGVKKEELGDRIAQF 58 Query: 61 YSDLNTDGSFIPLGENKWGLRSWYAIDEIDEEIITLEEDEDGAPKRKKKRVNAFMDGDED 120- Y+DLN DG F+ L + WGLRSWY D++DEE K KKK+ ++ D D Sbjct: 59 YTDLNIDGRFLALSDQTWGLRSWYPYDQLDEE-------TQPTVKAKKKKAKKAVEEDLD 111- Query: 121 AIDYNDDDPEDEDFTEETPSLEYDEENPDDEKSEVESYDSEINEIIPDEDLDEDVEINEE 18- 0 ++ + D +D D E L+ + ++ D+E + + D EI E I DED DED Sbjct: 112 LDEFEEIDEDDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDED-DEDY----- 16- 5 Query: 181 DDEEEE 186 DDEEEE Sbjct: 166 DDEEEE 171 A related DNA sequence was identified in S. pyogenes <SEQ ID 7041> which encodes the amino acid sequence <SEQ ID 7042>. Analysis of this protein sequence reveals the following: TABLE-US-06990 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2263(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-06991 Identities = 162/191 (84%), Positives = 181/191 (93%), Gaps = 1/191 (0%) Query: 1 MELEVFAGQEKSELSMIEVARAILEQRGRDNEMYFSDLVNDIQTYLGKSDSAIRESLPFF 60 ++L+VFAGQEKSELSMIEVARAILE+RGRDNEMYFSDLVN+IQ YLGKSD+ IR +LPFF Sbjct: 12 LKLDVFAGQEKSELSMIEVARAILEERGRDNEMYFSDLVNEIQNYLGKSDAGIRHALPFF 71 Query: 61 YSDLNTDGSFIPLGENKWGLRSWYAIDEIDEEIITLEEDEDGAPKRKKKRVNAFMDGDED 120- Y+DLNTDGSFIPLGENKWGLRSWYAIDEIDEEIITLEEDEDGA KRKKKRVNAFMDGDED Sbjct: 72 YTDLNTDGSFIPLGENKWGLRSWYAIDEIDEEIITLEEDEDGAQKRKKKRVNAFMDGDED 131- Query: 121 AIDYNDDDPEDEDFTEETPSLEYDEENPDDEKSEVESYDSEINEIIPDEDLDEDVEINEE 18- 0 AIDY DDDPEDEDFTEE+ +EYDEE+PDDEKSEVESYDSE+NEIIP++D E+V+INEE Sbjct: 132 AIDYRDDDPEDEDFTEESAEVEYDEEDPDDEKSEVESYDSELNEIIPEDDF-EEVDINEE 19- 0 Query: 181 DDEEEEEEEEV 191 D+E+EE+EE V Sbjct: 191 DEEDEEDEEPV 201 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2284 A DNA sequence (GBSx2418) was identified in S. agalactiae <SEQ ID 7043> which encodes the amino acid sequence <SEQ ID 7044>. This protein is predicted to be CTP synthetase (pyrG). Analysis of this protein sequence reveals the following: TABLE-US-06992 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.11 Transmembrane 5-21 (5-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.1044(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06993 >GP: CAA09021 GB: AJ010153 CTP synthetase [Lactococcus lactis subsp. cremoris] (ver 2) Identities = 421/533 (78%), Positives = 481/533 (89%) Query: 2 TKYIFVTGGVVSSIGKGIVAASLGRLLKNRGLKVTIQKFDPYINIDPGTMSPYQHGEVYV 61 TKYIFVTGG SS+GKGIVAASLGRLLKNRGLKVT+QKFDPY+NIDPGTMSPYQHGEV+V Sbjct: 3 TKYIFVTGGGTSSMGKGIVAASLGRLLKNRGLKVTVQKFDPYLNIDPGTMSPYQHGEVFV 62 Query: 62 TDDGAETDLDLGHYERFIDINLNKYSNVTTGKIYSEVLKKERRGEYLGATVQVIPHVTDA 121- TDDGAETDLDLGHYERFIDINLNKYSNVT+GK+YSE+L+KER+GEYLGATVQ++PHVT+ Sbjct: 63 TDDGAETDLDLGHYERFIDINLNKYSNVTSGKVYSEILRKERKGEYLGATVQMVPHVTNM 122- Query: 122 LKEKIKRAATTTDSDVIITEVGGTVGDIESLPFLEALRQMKADVGSDNVMYIHTTLLPYL 18- 1 LKEKIKRAATTTD+D+IITEVGGTVGD+ESLPF+EALRQMKA+VG+DNVMYIHT + +L Sbjct: 123 LKEKIKRAATTTDADIIITEVGGTVGDMESLPFIEALRQMKAEVGADNVMYIHTVPILHL 18- 2 Query: 182 KAAGEMKTKPTQHSVKELRGLGIQPNMLVIRTEQPAGQSIKNKLAQFCDVAPEAVIESLD 24- 1 +AAGE+KTK Q++ K LR GIQ NMLV+R+E P +++K+A FCDVAPEAVI+SLD Sbjct: 183 RAAGELKTKIAQNATKTLREYGIQANMLVLRSEVPITTEMRDKIAMFCDVAPEAVIQSLD 24- 2 Query: 242 VDHIYQIPLNMQAQNMDQIVCDHLKLETPAADMTEWSAMVDKVMNLEKKVKIALVGKYVE 30- 1 V+H+YQIPLN+QAQNMDQIVCDHLKL+ P ADM EWSAMVD VMNL+KKVKIALVGKYVE Sbjct: 243 VEHLYQIPLNLQAQNMDQIVCDHLKLDAPKADMAEWSAMVDHVMNLKKKVKIALVGKYVE 30- 2 Query: 302 LPDAYLSVVEALKHSGYVNDVAIDLKWVNAAEVTEDNIKELVGDADGIIVPGGFGQRGSE 36- 1 LPDAY+SV EALKH+GY +D +D+ WVNA +VT++N+ ELVGDA GIIVPGGFGQRG+E Sbjct: 303 LPDAYISVTEALKHAGYASDAEVDINWVNANDVTDENVAELVGDAAGIIVPGGFGQRGTE 36- 2 Query: 362 GKIEAIRYARENDVPMLGVCLGMQLTCVEFARNVLNLHGANSAELDPKTPFPIIDIMRDQ 42- 1 GKI AI+YARENDVPMLG+CLGMQLT VEFARNVL L GA+S ELDP+T +P+IDIMRDQ Sbjct: 363 GKIAAIKYARENDVPMLGICLGMQLTAVEFARNVLGLEGAHSFELDPETKYPVIDIMRDQ 42- 2 Query: 422 IDIEDMGGTLRLGLYPCKLKSGSRAAAAYNNQEVVQRRHRHRYEFNTKFREQFEAAGFVF 48- 1 +D+EDMGGTLRLGLYP KLK+GSRA AAYN+ EVVQRRHRHRYEFN K+RE FE AGFVF Sbjct: 423 VDVEDMGGTLRLGLYPAKLKNGSRAKAAYNDAEVVQRRHRHRYEFNNKYREDFEKAGFVF 48- 2 Query: 482 SGVSPDNRLMEVVELPEKKFFVAAQYHPELQSRPNHAEELYTAFVTAAVENMK 534 SGVSPDNRL+E+VEL KKFFVA QYHPELQSRPN EELYT F+ AVEN K Sbjct: 483 SGVSPDNRLVEIVELSGKKFFVACQYHPELQSRPNRPEELYTEFIRVAVENSK 535 A related DNA sequence was identified in S. pyogenes <SEQ ID 7045> which encodes the amino acid sequence <SEQ ID 7046>. Analysis of this protein sequence reveals the following: TABLE-US-06994 Possible site: 23 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.11 Transmembrane 5-21 (5-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.1044(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-06995 >GP: CAA09021 GB: AJ010153 CTP synthetase [Lactococcus lactis subsp. cremoris] (ver 2) Identities = 423/532 (79%), Positives = 483/532 (90%) Query: 2 TKYIFVTGGVVSSIGKGIVAASLGRLLKNRGLKVTIQKFDPYINIDPGTMSPYQHGEVYV 61 TKYIFVTGG SS+GKGIVAASLGRLLKNRGLKVT+QKFDPY+NIDPGTMSPYQHGEV+V Sbjct: 3 TKYIFVTGGGTSSMGKGIVAASLGRLLKNRGLKVTVQKFDPYLNIDPGTMSPYQHGEVFV 62 Query: 62 TDDGAETDLDLGHYERFIDINLNKYSNVTTGKIYSEVLRKERKGEYLGATVQVIPHITDA 121- TDDGAETDLDLGHYERFIDINLNKYSNVT+GK+YSE+LRKERKGEYLGATVQ++PH+T+ Sbjct: 63 TDDGAETDLDLGHYERFIDINLNKYSNVTSGKVYSEILRKERKGEYLGATVQMVPHVTNM 122- Query: 122 LKEKIKRAASTTDSDVIITEVGGTVGDIESLPFLEALRQMKADVGSENVMYIHTTLLPYL 18- 1 LKEKIKRAA+TTD+D+IITEVGGTVGD+ESLPF+EALRQMKA+VG++NVMYIHT + +L Sbjct: 123 LKEKIKRAATTTDADIIITEVGGTVGDMESLPFIEALRQMKAEVGADNVMYIHTVPILHL 18- 2 Query: 182 KAAGEMKTKPTQHSVKELRGLGIQPNMLVIRTEEPVEQGIKNKLAQFCDVNSEAVIESRD 24- 1 +AAGE+KTK Q++ K LR GIQ NMLV+R+E P+ +++K+A FCDV EAVI+S D Sbjct: 183 RAAGELKTKIAQNATKTLREYGIQANMLVLRSEVPITTEMRDKIAMFCDVAPEAVIQSLD 24- 2 Query: 242 VEHLYQIPLNLQAQSMDQIVCDHLKLNAPQADMTEWSAMVDKVMNLRKTTKIALVGKYVE 30- 1 VEHLYQIPLNLQAQ+MDQIVCDHLKL+AP+ADM EWSAMVD VMNL+K KIALVGKYVE Sbjct: 243 VEHLYQIPLNLQAQNMDQIVCDHLKLDAPKADMAEWSAMVDHVMNLKKKVKIALVGKYVE 30- 2 Query: 302 LPDAYLSVVEALKHSGYANDTAIDLKWVNANDVTVDNAADLLGDADGIIVPGGFGQRGTE 36- 1 LPDAY+SV EALKH+GYA+D +D+ WVNANDVT +N A+L+GDA GIIVPGGFGQRGTE Sbjct: 303 LPDAYISVTEALKHAGYASDAEVDINWVNANDVTDENVAELVGDAAGIIVPGGFGQRGTE 36- 2 Query: 362 GKIQAIRYARENDVPMLGICLGMQLTCVEFARHVLNMEGANSFELEPSTKYPIIDIMRDQ 42- 1 GKI AI+YARENDVPMLGICLGMQLT VEFAR+VL +EGA+SFEL+P TKYP+IDIMRDQ Sbjct: 363 GKIAAIKYARENDVPMLGICLGMQLTAVEFARNVLGLEGAHSFELDPETKYPVIDIMRDQ 42- 2 Query: 422 IDIEDMGGTLRLGLYPCKLKPGSKAAMAYNNQEVVQRRHRHRYEFNNKFRPEFEAAGFVF 48- 1 +D+EDMGGTLRLGLYP KLK GS+A AYN+ EVVQRRHRHRYEFNNK+R +FE AGFVF Sbjct: 423 VDVEDMGGTLRLGLYPAKLKNGSRAKAAYNDAEVVQRRHRHRYEFNNKYREDFEKAGFVF 48- 2 Query: 482 SGVSPDNRLVEIVELKEKKFFVAAQYHPELQSRPNRPEELYTAFVTAAIKNS 533 SGVSPDNRLVEIVEL KKFFVA QYHPELQSRPNRPEELYT F+ A++NS Sbjct: 483 SGVSPDNRLVEIVELSGKKFFVACQYHPELQSRPNRPEELYTEFIRVAVENS 534 An alignment of the GAS and GBS proteins is shown below. TABLE-US-06996 Identities = 477/532 (89%), Positives = 503/532 (93%) Query: 1 MTKYIFVTGGVVSSIGKGIVAASLGRLLKNRGLKVTIQKFDPYINIDPGTMSPYQHGEVY 60 MTKYIFVTGGVVSSIGKGIVAASLGRLLKNRGLKVTIQKFDPYINIDPGTMSPYQHGEVY Sbjct: 1 MTKYIFVTGGVVSSIGKGIVAASLGRLLKNRGLKVTIQKFDPYINIDPGTMSPYQHGEVY 60 Query: 61 VTDDGAETDLDLGHYERFIDINLNKYSNVTTGKIYSEVLKKERRGEYLGATVQVIPHVTD 120- VTDDGAETDLDLGHYERFIDINLNKYSNVTTGKIYSEVL+KER+GEYLGATVQVIPH+TD Sbjct: 61 VTDDGAETDLDLGHYERFIDINLNKYSNVTTGKIYSEVLRKERKGEYLGATVQVIPHITD 120- Query: 121 ALKEKIKRAATTTDSDVIITEVGGTVGDIESLPFLEALRQMKADVGSDNVMYIHTTLLPY 18- 0 ALKEKIKRAA+TTDSDVIITEVGGTVGDIESLPFLEALRQMKADVGS+NVMYIHTTLLPY Sbjct: 121 ALKEKIKRAASTTDSDVIITEVGGTVGDIESLPFLEALRQMKADVGSENVMYIHTTLLPY 18- 0 Query: 181 LKAAGEMKTKPTQHSVKELRGLGIQPNMLVIRTEQPAGQSIKNKLAQFCDVAPEAVIESL 24- 0 LKAAGEMKTKPTQHSVKELRGLGIQPNMLVIRTE+P Q IKNKLAQFCDV EAVIES Sbjct: 181 LKAAGEMKTKPTQHSVKELRGLGIQPNMLVIRTEEPVEQGIKNKLAQFCDVNSEAVIESR 24- 0 Query: 241 DVDHIYQIPLNMQAQNMDQIVCDHLKLETPAADMTEWSAMVDKVMNLEKKVKIALVGKYV 30- 0 DV+H+YQIPLN+QAQ+MDQIVCDHLKL P ADMTEWSAMVDKVMNL K KIALVGKYV Sbjct: 241 DVEHLYQIPLNLQAQSMDQIVCDHLKLNAPQADMTEWSAMVDKVMNLRKTTKIALVGKYV 30- 0 Query: 301 ELPDAYLSVVEALKHSGYVNDVAIDLKWVNAAEVTEDNIKELVGDADGIIVPGGFGQRGS 36- 0 ELPDAYLSVVEALKHSGY ND AIDLKWVNA +VT DN +L+GDADGIIVPGGFGQRG+ Sbjct: 301 ELPDAYLSVVEALKHSGYANDTAIDLKWVNANDVTVDNAADLLGDADGIIVPGGFGQRGT 36- 0 Query: 361 EGKIEAIRYARENDVPMLGVCLGMQLTCVEFARNVLNLHGANSAELDPKTPFPIIDIMRD 42- 0 EGKI+AIRYARENDVPMLG+CLGMQLTCVEFAR+VLN+ GANS EL+P T +PIIDIMRD Sbjct: 361 EGKIQAIRYARENDVPMLGICLGMQLTCVEFARHVLNMEGANSFELEPSTKYPIIDIMRD 42- 0 Query: 421 QIDIEDMGGTLRLGLYPCKLKSGSRAAAAYNNQEVVQRRHRHRYEFNTKFREQFEAAGFV 48- 0 QIDIEDMGGTLRLGLYPCKLK GS+AA AYNNQEVVQRRHRHRYEFN KFR +FEAAGFV Sbjct: 421 QIDIEDMGGTLRLGLYPCKLKPGSKAAMAYNNQEVVQRRHRNRYEFNNKFRPEFEAAGFV 48- 0 Query: 481 FSGVSPDNRLMEVVELPEKKFFVAAQYHPELQSRPNHAEELYTAFVTAAVEN 532 FSGVSPDNRL+E+VEL EKKFFVAAQYHPELQSRPN EELYTAFVTAA++N Sbjct: 481 FSGVSPDNRLVEIVELKEKKFFVAAQYHPELQSRPNRPEELYTAFVTAAIKN 532 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2285 A DNA sequence (GBSx2419) was identified in S. agalactiae <SEQ ID 7047> which encodes the amino acid sequence <SEQ ID 7048>. Analysis of this protein sequence reveals the following: TABLE-US-06997 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.92 Transmembrane 13-29 ( 3-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.4970(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9285> which encodes amino acid sequence <SEQ ID 9286> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-06998 >GP:CAB14296 GB:Z99116 yqkD [Bacillus subtilis] Identities = 79/289 (27%), Positives = 139/289 (47%), Gaps = 8/289 (2%) Query: 1 MKKIRLSKFIKMIVVILFLISVAASFYFFHVAQVRDDKSFISNGQRKPGNSLYAYDKSFD 60 MKKI L+ I +V + I+ S + + D+ I + G+ ++ +SF+ Sbjct: 1 MKKILLA--IGALVTAVIAIGIVFSHMILFIKKKTDED--IIKRETDNGHDVF---ESFE 53 Query: 61 KLLKQKIEMTNQNIKQVAWYVPAVKKTHKTAVVVHGFANSKENMKAYGWLFHKLGYNVLM 120- ++ K + + + Y A T T ++ HG + N Y LF LG+NVL+ Sbjct: 54 QMEKTAFVIPSAYGYDIKGYHVAPHDTPNTIIICHGVTMNVLNSLKYMHLFLDLGWNVLI 113- Query: 121 PDNIAHGESHGQLIGYGWNDRENIIKWTEMIVDK-NPSSQITLFGVSMGGATVNMASGEK 17- 9 D+ HG+S G+ YG+ +++++ K ++ +K N I + G SMG T ++ +G Sbjct: 114 YDHRRHGQSGGKTTSYGFYEKDDLNKVVSLLKNKTNHRGLIGIHGESMGAVTALLYAGAH 17- 3 Query: 180 LPSQVVNIIEDCGYSSVWDELKFQAKEMYGLPAFPLLYEVSTISKIRAGFSYGQASSVEQ 23- 9 I DC ++ ++L ++ + Y LP++PLL K+R G+ + S + Sbjct: 174 CSDGADFYIADCPFACFDEQLAYRLRAEYRLPSWPLLPIADFFLKLRGGYRAREVSPLAV 23- 3 Query: 240 LKKNNLPALFIHGDKDNFVFTSMVYDNYKATAGKKELYIVKGAKHAKSF 288 + K P LFIH D+++P S Y+ G K LYI + +HA S+ Sbjct: 234 IDKIEKPVLFIHSKDDDYIPVSSTERLYEKKRGPKALYIAENGEHAMSY 282 A related DNA sequence was identified in S. pyogenes <SEQ ID 7049> which encodes the amino acid sequence <SEQ ID 7050>. Analysis of this protein sequence reveals the following: TABLE-US-06999 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.48 Transmembrane 10-26 ( 3-32) ----- Final Results ----- bacterial membrane --- Certainty = 0.3994(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-07000 >GP:CAB14296 GB:Z99116 yqkD [Bacillus subtilis] Identities = 88/295 (29%), Positives = 145/295 (48%), Gaps = 4/295 (1%) Query: 10 LGILFLLITLISVGASFYFFHVAQIREEKSFINNKKRSTNNPLYPAEQSFDALPYEKRQL 69 - L I L+ +I++G F H+ ++K+ + KR T+N + +SF+ + + Sbjct: 6 LAIGALVTAVIAIG--IVFSHMILFIKKKTDEDIIKRETDNG-HDVFESFEQMEKTAFVI 62 Query: 70 TNRGLKQVGWYLPAAQKTKKTAIVVHGFTNDKEDMKPYAMLFHDLGYNVLMPDNEAHGES 129- + + Y A T T I+ HG T + + Y LF DLG+NVL+D+ HG+S Sbjct: 63 PSAYGYDIKGYHVAPHDTPNTIIICHGVTMNVLNSLKYMHLFLDLGWNVLIYDHRRHGQS 122- Query: 130 EGNLIGYGWNDRLNVMAWTDQLI-KENPESQITLFGLSMGAATVMMASGERLPAQVTSLI 18- 8 G YG+ ++ ++ L K N I + G SMGAT ++ +G I Sbjct: 123 GGKTTSYGFYEKDDLNKVVSLLKNETNHRGLIGIHGESMGAVTALLYAGANCSDGADFYI 18- 2 Query: 189 EDCGYASVWDELKFQAKANYNLPAFPLLYEVSALSKIRAGFSYGEASSVKQLAKNKRPTL 24- 8 DC +A ++L ++ +A Y LP++PLL K+R G+ E S + + K ++P L Sbjct: 183 ADCPFACFDEQLAYRLRAEYRLPSWPLLPIADFFLKLRGGYRAREVSPLAVIDKIEKPVL 24- 2 Query: 249 FIHGDRDDFVPTRMVYDNYKATKGPKEILIVRGAKHAKSFETNPEQYQKKIAAFL 303 FIN DD++P Y+ +GPK + I + +HA S+ N Y+K + FL Sbjct: 243 FIHSKDDDYIPVSSTERLYEKKKGPKALYIAENGEHAMSYTKNRHTYRKTVQEFL 297 An alignment of the GAS and GBS proteins is shown below. TABLE-US-07001 Identities = 203/294 (69%), Positives = 246/294 (83%) Query: 1 MKKIRLSKFIKMIVVILFLISVAASFYFFHVAQVRDDKSFISNGQRKPGNSLYAYDKSFD 60 MK IR++K++ ++ +++ LISV ASFYFFHVAQ+R++KSFI+N +R N LY ++SFD Sbjct: 1 MKTIRIAKYLGILFLLITLISVGASFYFFHVAQIREEKSFINNKKRSTNNPLYPAEQSFD 60 Query: 61 KLLKQKIEMTNQNIKQVAWYVPAVKKTHKTAVVVHGFANSKENMKAYGWLFNKLGYNVLN 120- L +K ++TN+ +KQV WY+PA +KT KTA+VVHGF N KE+NK Y LFH LGYNVLN Sbjct: 61 ALPYEKRQLTNRGLKQVGWYLPAAQKTRKTAIVVHGFTNDKEDNKPYANLFHDLGYNVLN 120- Query: 121 PDNIAHGESNGQLIGYGWNDRENIIKWTEDMVDKNPSSQITLFGVSMGGATVMMASGEKL 18- 0 PDN ANGES G LIGYGWNDR N++WT+ ++ +NP SQITLFG+SMG ATVMMASGE+L Sbjct: 121 PDNEAHGESEGNLIGYGWNDRLNVMAWTDQLIKENPESQITLFGLSMGAATVMNASGERL 18- 0 Query: 181 PSQVVNIIEOCGYSSVWDELKFQAKENYGLPAFPLLYEVSTISKIRAGFSYGQASSVEQL 24- 0 P+QV ++IEDCGY+SVWDELKFQAK MY LPAFPLLYEVS +SKIRAGFSYG+ASSV+QL Sbjct: 181 PAQVTSLIEDCGYASVWDELKFQAKANYNLPAFPLLYEVSALSKIRAGFSYGEASSVKQL 24- 0 Query: 241 KKNNLPALFIHGDKDNFVPTSMVYDNYKATAGKKELYIVKGAKHAKSFETEPEK 294 KN P LFIHGDKD+FVPT MVYDNYKAT G KE+ IVKGAKHAKSWET PE+ Sbjct: 241 AKNKRPTLFIHGDKDDFVPTKMVYDNYKATKGPKEILIVKGAKHAKSFETNPEQ 294 SEQ ID 9286 (GBS662) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 136 (lane 8-10; MW 63 kDa) and in FIG. 187 (lane 4; MW 63 kDa). GBS662-GST was purified as shown in FIG. 237, lane 7. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2286 A DNA sequence (GBSx2420) was identified in S. agalactiae <SEQ ID 7051> which encodes the amino acid sequence <SEQ ID 7052>. This protein is predicted to be aspartate--ammonia ligase (asnA). Analysis of this protein sequence reveals the following: TABLE-US-07002 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2898(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9309> which encodes amino acid sequence <SEQ ID 9310> was also identified. The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-07003 >GP:AAC22222 GB:U32738 aspartate--ammonia ligase (asnA) [Haemophilus influenzae Rd] Identities = 246/300 (82%), Positives = 268/300 (89%) Query: 1 MIDKLEIVEVQGPILSQVGDGMQDNLSGIEHPVSVKVLNIPEAEFEVVHSLAKWKRHTLA 60 +I++L I+EVQGPILSQVG+GMQDNLSGIE V V V IP A FEVVHSLAKWKRHTLA Sbjct: 23 LIEQLGIIEVQGPILSQVGNGMQDNLSGIEKAVQVNVKCIPNAVFEVVHSLAKWKRHTLA 82 Query: 61 RFGFNEGEGLFVHMKALRPDEDSLDPTHSVYVDQWDWEKVIPDGRRNLDYLKETVEKIYK 120- RF F E EGLFVHMKALRPDEDSLDPTHSVYVDQWDWEKVIP+GRRN YLKETV IY+ Sbjct: 83 RFNFKEDEGLFVHMKALRPDEDSLDPTHSVYVDQWDWEKVIPEGRRNFAYLKETVNSIYR 142- Query: 121 AIRLTELAVEARFDIESILPKRITFIHTEELVEKYPDLSPKERENAIAKEYGAVFLIGIG 18- 0 AIRLTELAVEARFDI SILPK+ITF+H+E+LV++YPDLS KERENAI KEYGAVFLIGIG Sbjct: 143 AIRLTELAVEARFDIPSILPKQITFVHSEDLVKRYPDLSSKERENAICKEYGAVFLIGIG 20- 2 Query: 181 GELADGKPHDGRAPDYDDWTTPSENGFKGLNGDILVWNEQLGTAFELSSMGIRVDEDALK 24- 0 G+L+DGKPNDGRAPDYDDWTT SENG+KGLNGDILVWN+QLG AFELSSMGIRVDE AL+ Sbjct: 203 GKLSDGKPHDGRAPDYDDWTTESENGYKGLNGDILVWNDQLGKAFELSSMGIRVDESALR 26- 2 Query: 241 RQVVLTGDEDRLEFEWHKTLLRGFFPLTIGGGIGQSRLAMFLLRKXHIGEVQSSVWPKEV 30- 0 QV LTGDED L+ +WH+ LL G PLTIGGGIGQSRLAM LLRK HIGEVQSSVWPKE+ Sbjct: 263 LQVGLTGDEDHLKMDWHQDLLNGKLPLTIGGGIGQSRLAMLLLRKKHIGEVQSSVWPKEM 32- 2 A related DNA sequence was identified in S. pyogenes <SEQ ID 7053> which encodes the amino acid sequence <SEQ ID 7054>. Analysis of this protein sequence reveals the following: TABLE-US-07004 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 189-205 ( 189-205) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the databases: TABLE-US-07005 >GP:AAC22222 GB:U32738 aspartate--aimnonia ligase (asnA) [Haemophilus influen ae Rd] Identities = 255/330 (77%), Positives = 289/330 (87%) Query: 1 MKKSFIHQQEEISFVKNTFTQYLIAKLDVVEVQGPILSRVGDGMQDNLSGTENPVSVNVL 60 MKK+FI QQ+EISFVKNTFTQ LI +L ++EVQGPILS+VG+GMQDNLSG E V VNV Sbjct: 1 MKKTFILQQQEISFVKNTFTQNLIEQLGIIEVQGPILSQVGNGMQDNLSGIEKAVQVNVK 60 Query: 61 KIPNATFEVVNSLAKWKRHTLARFGFNEGEGLVVNMKALRPDEDSLDQTHSVYVDQWDWE 120- IPNA FEVVHSLAKWKRHTLARF F E EGL V+MKALRPDEDSLD THSVYVDQWDWE Sbjct: 61 CIPNAVFEVVHSLAKWKRHTLARFNFKEDEGLFVHMKALRPDEDSLDPTHSVYVDQWDWE 120- Query: 121 KVIPDGKRNLAYLKETVETIYKVIRLTELAVEARYDIEAVLPKKITFIHTEELVAKYPDL 18- 0 KVIP+G+RN AYLKETV +IY+ IRLTELAVEAR+DI ++LPK+ITF+H+E+LV +YPDL Sbjct: 121 KVIPEGRRNFAYLKETVNSIYRAIRLTELAVEARFDIPSILPKQITFVHSEDLVKRYPDL 18- 0 Query: 181 TPKERENAITKEFGAVFLIGIGGVLPDGKPHDGRAPDYDDWTTETENGYHGLNGDILVWN 24- 0 + KERENAI KE+GAVFLIGIGG L DGKPHDGPAPDYDDWTTE+ENGY GLNGDILVWN Sbjct: 181 SSKERENAICKEYGAVFLIGIGGKLSDGKPHDGRAPDYDDWTTESENGYKGLNGDILVWN 24- 0 Query: 241 DQLGSAFELSSNGIRVDEEALKRQVEMTGDQDRLGFDWHESLLNGLFPLTIGGGIGQSRM 30- 0 DQLG AFELSSNGIRVDE AL+ QV +TGD+D L DWH+ LLNG PLTIGGGIGQSR+ Sbjct: 241 DQLGKAFELSSNGIRVDESALRLQVGLTGDEDHLKNDWHQDLLNGKLPLTIGGGIGQSRL 30- 0 Query: 301 VMFLLREQHIGEVQTSVWPQEVRDSYDNIL 330 M LLRK+HIGEVQ+SVWP+E+ + + NIL Sbjct: 301 ANLLLRKKHIGEVQSSVWPKEMLEEFSNIL 330 An alignment of the GAS and GBS proteins is shown below. TABLE-US-07006 Identities = 254/303 (83%), Positives = 280/303 (91%) Query: 1 MIDKLEIVEVQGPILSQVGDGMQDNLSGIEHPVSVKVLNIPEAEFEVVHSLAKWKRHTLA 60 +I KL++VEVQGPILS+VGDGMQDNLSG E+PVSV VL IF A FEVVHSLAKWKRHTLA Sbjct: 23 LIAKLDVVEVQGPILSRVGDGMQDNLSGTENPVSVNVLKIPNATFEVVHSLAKWKRHTLA 82 Query: 61 RFGFNEGEGLFVHMKALRPDEDSLDPTHSVYVDQWDWEKVIPDGRRNLDYLKETVEKIYK 120- RFGFNEGEGL V+MKALRPDEDSLD THSVYVDQWDWEKVIPDG+RNL YLKETVE IYK Sbjct: 83 RFGFNEGEGLVVNMKALRPDEDSLDQTHSVYVDQWDWEKVIPDGKRNLAYLKETVETIYK 142- Query: 121 AIRLTELAVEARFDIESILPKRITFIHTEELVEKYPDLSPKERENAIAKEYGAVFLIGIG 18- 0 IRLTELAVEAR+DIE++LPK+ITFIHTESLV KYPDL+PKERENAI KE+GAVFLIGIG Sbjct: 143 VIRLTELAVEARYDIEAVLPKKITFIHTEELVAKYPDLTPKERENAITKEFGAVFLIGIG 20- 2 Query: 181 GELADGKPHDGRAPDYDDWTTPSENGFKGLNGDILVWNEQLGTAFELSSMGIRVDEDALK 24- 0 G L DGKPHDGRAPDYDDWTT +ENG+ GLNGDILVWN+QLG+AFELSSMGIRVDE+ALK Sbjct: 203 GVLPDGKPHDGRAPDYDOWTTETENGYHGLNGDILVWNDQLGSAFELSSMGIRVDEEALK 26- 2 Query: 241 RQVVLTGDEDRLEFEWHKTLLRGFFPLTIGGGIGQSRLANFLLRKXHIGEVQSSVWPKEV 30- 0 RQV +TGD+DRL F+WHR+LL G FPLTIGGGIGQSR+ MFLLRK HIGEVQ+SVWP+EV Sbjct: 263 RQVEMTGDQDRLGFDWHKSLLNGLFFLTIGGGIGQSRNVMFLLRKQHIGEVQTSVWPQEV 32- 2 Query: 301 RDT 303 RD+ Sbjct: 323 RDS 325 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2287 A DNA sequence (GBSx2421) was identified in S. agalactiae <SEQ ID 7055> which encodes the amino acid sequence <SEQ ID 7056>. Analysis of this protein sequence reveals the following: TABLE-US-07007 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3163(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2288 A DNA sequence (GBSx2422) was identified in S. agalactiae <SEQ ID 7057> which encodes the amino acid sequence <SEQ ID 7058>. Analysis of this protein sequence reveals the following: TABLE-US-07008 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9007> which encodes amino acid sequence <SEQ ID 9008> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07009 >GP:AAD56628 GB:AF165218 Bta [Streptococcus pneumoniae] Identities = 30/97 (30%), Positives = 50/97 (50%), Gaps = 3/97 (3%) Query: 50 KALVSKSQQSEATIFIGRPTCQYCRAFLPKLLKSQATLHSKIYYLDSQKYKG-KRLKSFF 108- +A + ++ AT FIGR TC YCR F L A + IY+++S++ L++F Sbjct: 18 RAQEALDKKETATFFIGRKTCPYCRKFAGTLSGVVAETKAHIYFINSEEASQLNDLQAFR 77 Query: 109 KKHHITTVPNLAHYQQGKMTKYLVQGSQATPQQIQTW 145 ++ I TVP H G++ + S + Q+I+ F Sbjct: 78 SRYGIPTVPGFVHITDGQIN--VRCDSSMSAQEIKDF 112 SEQ ID 9008 (GBS134) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 40 (lane 2; MW 17 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 46 (lane 4; MW 42 kDa). GBS134-GST was purified as shown in FIG. 204, lane 10. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2289 A DNA sequence (GBSx2423) was identified in S. agalactiae <SEQ ID 7059> which encodes the amino acid sequence <SEQ ID 7060>. Analysis of this protein sequence reveals the following: TABLE-US-07010 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0735(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9603> which encodes amino acid sequence <SEQ ID 9604> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07011 >GP: BAB06309 GB: AP001516 unknown conserved protein [Bacillus halodurans] Identities = 78/178 (43%), Positives = 115/178 (63%), Gaps = 3/178 (1%) Query: 3 MRVVAGTFGGRPLKTLDGKTTRPTTDKVKGAIFNMIGPFFEGGRVLDLFSGSGSLAIEAI 62 MRV+AG G LK + G TRPTTDKVK AIFNMIGPFF+GG LDL+ GSG L IEA+ Sbjct: 1 MRVIAGEQKGLTLKAVPGHKTRPTTDKVKEAIFNMIGPFFDGGIGLDLYGGSGGLGIEAL 60 Query: 63 SRGMDQAVLVEKDRRAQVVIQENIAMTKSPEQFQLLKMEANRALEQLTGQ---FDLVLLD 119- SRG+++ + V++ +RA I++N++ + ++ + +A RAL+ LT + F V LD Sbjct: 61 SRGVERMIFVDQQKRAIETIKQNLSHCGLEGRAEVYRNDAKRALQVLTKRGIVFAYVFLD 120- Query: 120 PPYAKEEIVKQIQIMDSKGLLGDDIMIACETDKSVDLPEEIASFGIWKQKIYGISKVT 177 PPYAK+ I + I+ + GLL + ++ CE D+ LP++I K++ YG + +T Sbjct: 121 PPYAKQTIKNDLAILANHGLLEEGGVVVCEHDRDTMLPDQIEYAVKHKEETYGDTMIT 178 There is also homology to SEQ ID 132. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2290 A DNA sequence (GBSx2424) was identified in S. agalactiae <SEQ ID 7061> which encodes the amino acid sequence <SEQ ID 7062>. Analysis of this protein sequence reveals the following: TABLE-US-07012 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4984(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07013 >GP: CAB96619 GB: AJ400630 hypothetical protein [Streptococcus pneumoniae bacteriophage MM1] Identities = 175/254 (68%), Positives = 219/254 (85%) Query: 2 LRRHIYSMLEEHXHLQPEIKYHQKTNLRKNRVYTVFIEEKVDVILADLKLADAFFGIETG 61 L RH+Y ++ EI++HQ++NLRKNRVYTVF EKV L+DL LAD+FFG+ETG Sbjct: 50 LARHLYESFLHFYEIKSEIRHHQRSNLRKNRVYTVFTDEKVQDLLSDLHLADSFFGLETG 109- Query: 62 IEHSILDNDENGRAYLRGAFLSTGTVREPDSGKYQLEIFSVYLDHAQDLANLMKKFMLDA 121- I+ +IL ++E GRAYL GAFL+ G++R+P+SGKYQLEI SVYLDHAQ +A+L+++F+LDA Sbjct: 110 IDEAILSDEEAGRAYLCGAFLANGSIRDPESGKYQLEISSVYLDHAQGIASLLQQFLLDA 16- 9 Query: 122 KVIEHKHGAVTYLQKAEDIMDFLIVIDAMEARDAFEEIKMIRETRNDINRANNVETANIA 18- 1 KV+E K GAVTYLQ+AEDIMDFLIVI AM+ARD FE +K++RETRND+NRANN ETANIA Sbjct: 170 KVLERKKGAVTYLQRAEDIMDFLIVIGAMQARDDFERVKILRETRNDLNRANNAETANIA 22- 9 Query: 182 RTITASMKTINNIIKIMDTIGFDALPSDLRQVAQVRVAHPDYSIQQIADSLETPLSKSGV 24- 1 RT++ASMKTINNI KI D +G + LP DL++VAQ R+ HPDYSIQQ+ADSL TPL+KSGV Sbjct: 230 RTVSASMKTINNISKIKDIMGLENLPVDLQEVAQLRIQHPDYSIQQLADSLSTPLTKSGV 28- 9 Query: 242 NHRLRKINKIADEL 255 NHRLRKINKIADEL Sbjct: 290 NHRLRKINKIADEL 303 There is also homology to SEQ ID 5540: TABLE-US-07014 Identities = 186/254 (73%), Positives = 227/254 (89%) Query: 2 LRRHIYSMLEEHXHLQPEIKYHQKTNLRKNRVYTVFIEEKVDVILADLKLADAFFGIETG 61 + R+IYS++E+ + PEI+YHQKTNLRKNRVYTV++E+ V+ ILADLKLAD+FFG+ETG Sbjct: 50 IARYIYSLIEDAYVIVPEIRYHQKTNLRKNRVYTVYVEQGVETILADLKLADSFFGLETG 109- Query: 62 IEHSILDNDENGRAYLRGAFLSTGTVREPDSGKYQLEIFSVYLDHAQDLANLMKKFMLDA 121- IE +L +D GR+YL+GAFL+ G++R+P+SGKYQLEI+SVYLDHAQDLA LM+KFMLDA Sbjct: 110 IEPQVLSDDNAGRSYLKGAFLAAGSIRDPESGKYQLEIYSVYLDHAQDLAQLMQKFMLDA 16- 9 Query: 122 KVIEHKHGAVTYLQKAEDIMDFLIVIDAMEARDAFEEIKMIRETRNDINRANNVETANIA 18- 1 K IEHK GAVTYLQKAEDIMDFLI+I AM ++ FE IK++RE RNDINRANN ETANIA Sbjct: 170 KTIEHKSGAVTYLQKAEDIMDFLIIIGAMSCKEDFEAIKLLREARNDINRANNAETANIA 22- 9 Query: 182 RTITASMKTINNIIKIMDTIGFDALPSDLRQVAQVRVAHPDYSIQQIADSLETPLSKSGV 24- 1 +TI+ASMKTINNIIKIMDTIG ++LP +L+QVAQ+RV HPDYSIQQ+AD+LE P++KSGV Sbjct: 230 KTISASMKTINNIIKIMDTIGLESLPIELQQVAQLRVKHPDYSIQQVADALEFPITKSGV 28- 9 Query: 242 NHRLRKINKIADEL 255 NHRLRKINKIAD+L Sbjct: 290 NHRLRKINKIADDL 303 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2291 A DNA sequence (GBSx2425) was identified in S. agalactiae <SEQ ID 7063> which encodes the amino acid sequence <SEQ ID 7064>. Analysis of this protein sequence reveals the following: TABLE-US-07015 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0297(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2292 A DNA sequence (GBSx2428) was identified in S. agalactiae <SEQ ID 7065> which encodes the amino acid sequence <SEQ ID 7066>. Analysis of this protein sequence reveals the following: TABLE-US-07016 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2706(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07017 >GP: CAB54571 GB: AJ006393 response regulator [Streptococcus pneumoniae] Identities = 139/190 (73%), Positives = 166/190 (87%) Query: 8 IKIVLVDDHEMVRLGLKSFLNLQADVEVIGEASNGLEGIKKALELRPDVVVMDLVMPEMD 67 +KI+LVDDHEMVRLGLKS+ +LQ DVEV+GEASNG +GI ALELRPDV+VMD+VMPEM+ Sbjct: 1 MKILLVDDHEMVRLGLKSYFDLQDDVEVVGEASNGSQGIDLALELRPDVIVMDIVMPEMN 60 Query: 68 GVEATLALLKDWPEAAILVLTSYLDNEKIYPVIEAGAKGYMLKTSSAAEILNAIRKVSRG 127- G++ATLA+LK+WPEA IL++TSYLDNEKI PV++AGAKGYMLKTSSA E+L+A+ KV+ G Sbjct: 61 GIDATLAILKEWPEAKILIVTSYLDNEKIMPVLDAGAKGYMLKTSSADELLHAVSKVAAG 120- Query: 128 EQAIENEVDKKIKAHDKCPALHEGLTARERDILNLLAKGYDNQRIADELFISLKTVKTHV 18- 7 E AIE EV KK++ H LHE LTARERD+L L+AKGY+NQRIAD+LFISLKTVKTHV Sbjct: 121 ELAIEQEVSKKVEYHRNHMELHEELTARERDVLQLIAKGYENQRIADDLFISLKTVKTHV 18- 0 Query: 188 SNILGKLNGS 197 SNIL KL S Sbjct: 181 SNILAKLEVS 190 There is also high homology to SEQ ID 2996: TABLE-US-07018 Identities = 158/198 (79%), Positives = 176/198 (88%), Gaps = 1/198 (0%) Query: 5 MDKIKIVLVDDHEMVRLGLKSFLNLQADVEVIGEASNGLEGIKKALELRPDVVVMDLVMP 64 M KIK++LVDDHEMVR+GLKSFLNLQAD++V+GEASNG EG+ AL L+PDV+VMDLVMP Sbjct: 3 MSKIKVILVDDHEMVRMGLKSFLNLQADIDVVGEASNGREGVDLALALKPDVLVMDLVMP 62 Query: 65 EMDGVEATLALLKDWPEAAILVLTSYLDNEKIYPVIEAGAKGYMLKTSSAAEILNAIRKV 124- E+ GVEATL +LK W EA +LVLTSYLDNEKIYPVI+AGAKGYMLKTSSAAEILNAIRKV Sbjct: 63 ELGGVEATLEVLKKWKEAKVLVLTSYLDNEKIYPVIDAGAKGYMLKTSSAAEILNAIRKV 122- Query: 125 SRGEQAIENEVDKKIKAHDKCPALHEGLTARERDILNLLAKGYDNQRIADELFISLKTVK 18- 4 S+GE AIE EVDKKIKAHD+ P LHE LTARE DIL+LLAKGYDNQ IADELFISLKTVK Sbjct: 123 SKGELAIETEVDKKIKAHDQHPDLHEELTAREYDILHLLAKGYDNQTIADELFISLKTVK 18- 2 Query: 185 THVSNILGKLN-GSRSNS 201 THVSNIL KL G R+ + Sbjct: 183 THVSNILAKLEVGDRTQA 200 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2293 A DNA sequence (GBSx2429) was identified in S. agalactiae <SEQ ID 7067> which encodes the amino acid sequence <SEQ ID 7068>. This protein is predicted to be histidine kinase (narQ). Analysis of this protein sequence reveals the following: TABLE-US-07019 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3944(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07020 >GP: CAB54570 GB: AJ006393 histidine kinase [Streptococcus pneumoniae] Identities = 32/55 (58%), Positives = 49/55 (88%) Query: 1 MIDNGIGFDMDSVYDLSYGLKNIEDRVEDLAGNLQLLSQPGKGVAMDIRLPLVNQ 55 ++DNGIGF + S+ DLSYGL+NI++RVED+AG +QLL+ P +G+A+DIR+PL+++ Sbjct: 276 VVDNGIGFQLGSLDDLSYGLRNIKERVEDMAGTVQLLTAPKQGLAVDIRIPLLDK 330 There is also homology to SEQ ID 2992: TABLE-US-07021 Identities = 44/59 (74%), Positives = 51/59 (85%) Query: 1 MIDNGIGFDMDSVYDLSYGLKNIEDRVEDLAGNLQLLSQPGKGVAMDIRLPLVNQSEDK 59 MID+G+GFDMD V DLSYGLKNIEDRV DLAGNL L+SQ GKGV+MDIRLP+V +D+ Sbjct: 276 MIDDGVGFDMDQVRDLSYGLKNIEDRVNDLAGNLHLISQKGKGVSMDIRLPIVKGDDDE 334- Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2294 A DNA sequence (GBSx2430) was identified in S. agalactiae <SEQ ID 7069> which encodes the amino acid sequence <SEQ ID 7070>. This protein is predicted to be RfbQRSO155-1. Analysis of this protein sequence reveals the following: TABLE-US-07022 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1120(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> There is also homology to SEQ ID 7072: TABLE-US-07023 Identities = 171/172 (99%), Positives = 172/172 (99%) Query: 1 MGQVAVEEKSNEIVAIPQLLRTIDIRKSIVTIDAMGTQTAIVDTIIKGKADYCLAVKGNQ 60 +GQVAVEEKSNEIVAIPQLLRTIDIRKSIVTIDAMGTQTAIVDTIIKGKADYCLAVKGNQ Sbjct: 143 LGQVAVEEKSNEIVAIPQLLRTIDIRKSIVTIDAMGTQTAIVDTIIKGKADYCLAVKGNQ 20- 2 Query: 61 ETLYDDIALYFSDVNLLEELQENAQYYQTVEKSRGQIEVREYWVSSDIKWLCQNHPKWHK 120- ETLYDDIALYFSDVNLLEELQENAQYYQTVEKSRGQIEVREYWVSSDIKWLCQNHPKWHK Sbjct: 203 ETLYDDIALYFSDVNLLEELQENAQYYQTVEKSRGQIEVREYWVSSDIKWLCQNHPKWHK 26- 2 Query: 121 LRGIGMTRNTIDKDGQLSQENRYFIFSFKPDVLTFANCVRGHWQIESMHWLL 172 LRGIGMTRNTIDKDGQLSQENRYFIFSFKPDVLTFANCVRGHWQIESMHWLL Sbjct: 263 LRGIGMTRNTIDKDGQLSQENRYFIFSFKPDVLTFANCVRGHWQIESMHWLL 314 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2295 A DNA sequence (GBSx2431) was identified in S. agalactiae <SEQ ID 7073> which encodes the amino acid sequence <SEQ ID 7074>. This protein is predicted to be translation initiation factor if-3 homolog dsg (infC). Analysis of this protein sequence reveals the following:

TABLE-US-07024 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1787(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07025 >GP: CAA68920 GB: Y07640 translation initiation factor, IF3 [Listeria monocytogenes] Identities = 112/169 (66%), Positives = 134/169 (79%) Query: 7 KDLFINDEIRVREVRLVGLEGEQLGIKPLSEAQAIADDANVDLVLIQPQATPPVAKIMDY 66 KD+ +ND IR REVRL+ +GEQLG+K +A IA+ AN+DLVL+ P A PPVA+IMDY Sbjct: 3 KDMLVNDGIRAREVRLIDQDGEQLGVKSKIDALQIAEKANLDLVLVAPTAKPPVARIMDY 62 Query: 67 GKFKFEYQKKQKEQRKKQSVVTVKEVRLSPVIDKGDFETKLRNGRKFLEKGNKVKVSIRF 126- GKF+FE QKK KE RK Q V+ +KEVRLSP ID+ DF+TKLRN RKFLEKG+KVK SIRF Sbjct: 63 GKFRFEQQKKDKEARKNQKVIVMKEVRLSPTIDEHDFDTKLRNARKFLEKGDKVKCSIRF 122- Query: 127 KGRMITHKEIGAKVLAEFAEATQDIAIIEQRAKMDGRQMFMQLAPIPDK 175 KGR ITHKEIG KVL FA+A +D+ IEQR KMDGR MF+ LAP+ +K Sbjct: 123 KGRAITHKEIGQKVLDRFAKACEDLCTIEQRPKMDGRSMFLVLAPLHEK 171 A related DNA sequence was identified in S. pyogenes <SEQ ID 7075> which encodes the amino acid sequence <SEQ ID 7076>. Analysis of this protein sequence reveals the following: TABLE-US-07026 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2247(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-07027 Identities = 167/176 (94%), Positives = 173/176 (97%) Query: 1 MKIIAKKDLFINDEIRVREVRLVGLEGEQLGIKPLSEAQAIADDANVDLVLIQPQATPPV 60 +KIIAKKDLFINDEIRVREVRLVGLEGEQLGIKPLSEAQ++AD +NVDLVLIQPQA PPV Sbjct: 1 VKIIAKKDLFINDEIRVREVRLVGLEGEQLGIKPLSEAQSLADASNVDLVLIQPQAVPPV 60 Query: 61 AKIMDYGKFKFEYQKKQKEQRKKQSVVTVKEVRLSPVIDKGDFETKLRNGRKFLEKGNKV 120- AK+MDYGKFKFEYQKKQKEQRKKQSVVTVKEVRLSPVIDKGDFETKLRNGRKFLEKGNKV Sbjct: 61 AKLMDYGKFKFEYQKKQKEQRKKQSVVTVKEVRLSPVIDKGDFETKLRNGRKFLEKGNKV 120- Query: 121 KVSIRFKGRMITHKEIGAKVLAEFAEATQDIAIIEQRAKMDGRQMFMQLAPIPDKK 176 KVSIRFKGRMITHKEIGAKVLA+FAEATQDIAIIEQRAKNDGRQMFMQLAPI DKK Sbjct: 121 KVSIRFKGRMITHKEIGAKVLADFAEATQDIAIIEQRAKMDGRQMFMQLAPISDKK 176 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2296 A DNA sequence (GBSx2432) was identified in S. agalactiae <SEQ ID 7077> which encodes the amino acid sequence <SEQ ID 7078>. Analysis of this protein sequence reveals the following: TABLE-US-07028 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1807(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07029 >GP: AAC45308 GB: U81957 RNA polymerase beta' subunit [Streptococcus gordonii] Identities = 262/286 (91%), Positives = 276/286 (95%) Query: 1 MAAKVVKAGVEEVXIRSVFTCNTRHGVCRHCYGINLATGDAVEVGEAVGTIAAQSIGEPG 60 MA +VV AGV EV IRSV TCNTRHGVCRHCYGINLATGDAVEVGEAVGTIAAQSIGEPG Sbjct: 122 MARQVVNAGVTEVTIRSVLTCNTRHGVCRHCYGINLATGDAVEVGEAVGTIAAQSIGEPG 18- 1 Query: 61 TQLTMRTFHTGGVASNTDITQGLPRIQEIFEARNPKGEAVITEVKGEVVAIEEDSSTRTK 120- TQLTMRTFHTGGVAS++DITQGLFR+QEIFEARNPKGEAVITEVKGEV AIEED+STRTK Sbjct: 182 TQLTMRTFHTGGVASSSDITQGLPRVQEIFEARNPKGEAVITEVKGEVTAIEEDASTRTK 24- 1 Query: 121 KVFVKGQTGEGEYVVPFTARMKVEVGDEVARGAALTEGSIQPKRLLEVRDTLSVETYLLA 18- 0 KVFVKGQTGEGEYVVPFTARMKVEVGD+V+RGAALTEGSIQPK LL VRD LSVETYLLA Sbjct: 242 KVFVKGQTGEGEYVVPFTARMKVEVGDQVSRGAALTEGSIQPKHLLAVRDVLSVETYLLA 30- 1 Query: 181 EVQKVYRSQGVEIGDKHVEVMVRQMLRKVRVMDPGDTDLLPGTLMDISDFTDANKDIVIS 24- 0 EVQKVYRSQGVEIGDKH+EVMVRQM+RKVRVMDPGDTDLL GTLMDI+DFTDAN+D+VIS Sbjct: 302 EVQKVYRSQGVEIGDKHIEVMVRQMIRKVRVMDPGDTDLLMGTLMDITDFTDANRDVVIS 36- 1 Query: 241 GGIPATSRPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKK 286 GG+PAT+RPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKK Sbjct: 362 GGVPATARPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKK 407 There is also homology to SEQ ID 384. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2297 A DNA sequence (GBSx2434) was identified in S. agalactiae <SEQ ID 7079> which encodes the amino acid sequence <SEQ ID 7080>. Analysis of this protein sequence reveals the following: TABLE-US-07030 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0352(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2298 A DNA sequence (GBSx2435) was identified in S. agalactiae <SEQ ID 7081> which encodes the amino acid sequence <SEQ ID 7082>. This protein is predicted to be acetoin dehydrogenase (TPP-dependent) beta chain (pdhB). Analysis of this protein sequence reveals the following: TABLE-US-07031 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0266(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07032 >GP: BAB04496 GB: AP001509 acetoin dehydrogenase (TPP-dependent) beta chain [Bacillus halodurans] Identities = 37/57 (64%), Positives = 50/57 (86%) Query: 1 MLEEFGAKRVRDTPISEAAIAGSAIGAAQTGLRPIVDLTFMDFVTIAMDAIVDDCIR 57 M+EEFG++RVR+TPISEAAI+G+AIGAA TG+RPI++L F DF+TIAMD +V+ + Sbjct: 44 MIEEFGSERVRNTPISEAAISGTAIGAALTGMRPILELQFSDFITIAMDNMVNQAAK 100 There is also homology to SEQ ID 4272. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2299 A DNA sequence (GBSx2436) was identified in S. agalactiae <SEQ ID 7083> which encodes the amino acid sequence <SEQ ID 7084>. This protein is predicted to be Structural protein. Analysis of this protein sequence reveals the following: TABLE-US-07033 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3015(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07034 >GP: AAB18706 GB: U38906 Structural protein [Bacteriophage rlt] Identities = 57/127 (44%), Positives = 83/127 (64%) Query: 5 IKAGTLFKPELVTEIMSKVKGHSTLAKLSGQTPIPFNGVEQFVFNLDGNAQIVGEGEQKL 64 + GTLF P LVT+++SKV G S++A+LS Q PIPFNG + F F +D +V E +K Sbjct: 3 LNKGTLFDPTLVTDLISKVAGKSSIARLSAQKPIPFNGEKVFTFTMDSEIDVVAESGKKT 62 Query: 65 GNTAKVTSKIIKPLKFVYQARMTDEFKYASEEKRLNFLKHYADGFAKKMAEAFDIAAIHG 124- + + + P+K Y AR++DEF YAS+E+++N L+ + DGFAKK+A D+ A HG Sbjct: 63 HGGVTLAPQTMVPIKVEYGARISDEFMYASDEEKINILQEFNDGFAKKVARGIDLMAFHG 122- Query: 125 LEPRTMT 131 + PR T Sbjct: 123 VNPRLGT 129 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2300 A DNA sequence (GBSx2439) was identified in S. agalactiae <SEQ ID 7085> which encodes the amino acid sequence <SEQ ID 7086>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-07035 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1892(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2301 A DNA sequence (GBSx2440) was identified in S. agalactiae <SEQ ID 7087> which encodes the amino acid sequence <SEQ ID 7088>. Analysis of this protein sequence reveals the following: TABLE-US-07036 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2227(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2302 A DNA sequence (GBSx2441) was identified in S. agalactiae <SEQ ID 7089> which encodes the amino acid sequence <SEQ ID 7090>. This protein is predicted to be integrase. Analysis of this protein sequence reveals the following: TABLE-US-07037 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2948(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9319> which encodes amino acid sequence <SEQ ID 9320> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07038 >GP: CAB96616 GB: AJ400629 integrase [Streptococcus pneumoniae bacteriophage MM1] Identities = 84/238 (35%), Positives = 137/238 (57%), Gaps = 8/238 (3%) Query: 1 MTLDKNSSQAQKKAGLILQEKIEDRLAIRNHSEMTYGELKKEYLKQWIPTVKDSTKRGYL 60 +T++K + QA+ +A ++LQEKI +L+ + +T+ E+ + K W TVK+STK Sbjct: 30 VTMEKKTPQARNQAAILLQEKINKKLSTKQVESITFEEIYNLFYKSWAQTVKESTKHNCK 89 Query: 61 VSDSHIATVLPDDTIINKLTKRDIRLIIDKLLKHNSYHVTHKCRKRLHAIFSYAIQMDYM 120- D + V+P DTI+ L +R ++ I+K+++ N Y K R RL IF+YA+Q Y+ Sbjct: 90 SVDKKMKEVIPSDTILANLDRRFLQEAIEKIIESNGYITAKKVRHRLRGIFNYAVQYSYI 149- Query: 121 TSNPTENVLVP-KPK--DDYKPEKVLYLTSNEV---YDLCNRMIDNDEQTLADIVLFMFL 17- 4 +N + +P KPK ++ + ++ +LT E+ D+ NR Q AD+VL + L Sbjct: 150 ENNEVDYTTIPQKPKTLEELEKKRNNFLTMQEIKALVDVLNRR--EYHQKYADMVLVLTL 20- 7 Query: 175 TGVRYGELSCLTYDKIDFENKEILINATYDFNTRXITTTKTKKSTRKISVSDNILDIV 232 TG+RYGEL+ L IDFEN +I I +D + T KT S R I VS+++++ + Sbjct: 208 TGMRYGELTALQLKNIDFENNKIEITGNFDSVNKIKTLPKTTNSIRTIKVSESVIEAI 265 There is also homology to SEQ ID 578. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2303 A DNA sequence (GBSx2444) was identified in S. agalactiae <SEQ ID 7091> which encodes the amino acid sequence <SEQ ID 7092>. Analysis of this protein sequence reveals the following: TABLE-US-07039 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2518(Aftirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. There is also homology to SEQ ID 4212: TABLE-US-07040 Identities = 92/144 (63%), Positives = 118/144 (81%), Gaps = 1/144 (0%) Query: 1 MPKYSLFELENGRRRLLASAGELQKGNELALPTQFMKFLYLASRYNESKGKPEEIEKKQE 60 +PKYSLFELENGR+R+LASAGELQKGNELALP++++ FLYLAS Y + KG PE+ E+KQ Sbjct: 1198 LPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQL 1- 257 Query: 61 FVNQHVSYFDDILQLINDFSKRVILADANLEKINKLYQDNKENISVDELANNIINLFTFT 120- FV QH Y D+I++ I++FSKRVILADANL+K+ Y +++ + E A NII+LFT T Sbjct: 1258 FVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDK-PIREQAENIIHLFTLT 1- 316 Query: 121 SLGAPAAFKFFDKIVDRKRYTSTQ 144 +LGAPAAFK+FD +DRKRYTST+ Sbjct: 1317 NLGAPAAFKYFDTTIDRKRYTSTK 1340 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2304 A DNA sequence (GBSx2445) was identified in S. agalactiae <SEQ ID 7093> which encodes the amino acid sequence <SEQ ID 7094>. This protein is predicted to be 0. Analysis of this protein sequence reveals the following: TABLE-US-07041 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.57 Transmembrane 239-255 (236-256) ----- Final Results ----- bacterial membrane --- Certainty = 0.2826(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07042 >GP: CAB15253 GB: Z99120 similar to opine catabolism [Bacillus subtilis] Identities = 88/257 (34%), Positives = 129/257 (49%), Gaps = 11/257 (4%) Query: 1 MARLGADFYSKLVTDLQKDGFETKFYQQTGVFLLKKDESQLESLFALADKRRLESPLIGD 60 +A+ GA +Y L+ L+KDG Y++ G + D S+L+ + A KRR ++P IGD Sbjct: 61 LAKGGARYYKDLIHQLEKDGESDTGYKRVGAISIHTDASKLDKMEERAYKRREDAPEIGD 120- Query: 61 LQILNKSEANTHFPEL-DGYEQLLYASGGARVEGADLTRILLEAS---GVNVIKDEVHF- 115- + L+ SE FP L DGYE ++ SG ARV G L R LL A+ G VIK Sbjct: 121 ITRLSASETKKLFPILADGYES-VHISGAARVNGRALCRSLLSAAEKRGATVIKGNASLL 17- 9 Query: 116 ----TITDNGFRVQGIDFDKLVLASGAWLAKILDEHNYQVDVRPQKGQLRDYYFSNINTG 17- 1 T+T + D +++ +GAW +IL V QK Q+ + ++ +TG Sbjct: 180 FENGTVTGVQTDTKQFAADAVIVTAGAWANEILKPLGIHFQVSFQKAQIMHFEMTDADTG 23- 9 Query: 172 KYPVVMPEGELDIIPFDNGKVSVGASHENDMAF-DLNIDFKVLDKFEEQAIGYFPQLKKQ 23- 0 +PVVMP + I+ FDNG++ GA+HEND DL + + +A+ P L Sbjct: 240 SWPVVMPPSDQYILSFDNGRIVAGATHENDAGLDDLRVTAGGQHEVLSKALAVAPGLADA 29- 9 Query: 231 IRLLKRVEFVPIQVIFL 247 + RV F P FL Sbjct: 300 AAVETRVGFRPFTPGFL 316 There is also homology to SEQ ID 2656. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2305 A DNA sequence (GBSx2446) was identified in S. agalactiae <SEQ ID 7095> which encodes the amino acid sequence <SEQ ID 7096>. Analysis of this protein sequence reveals the following: TABLE-US-07043 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2572(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9315> which encodes amino acid sequence <SEQ ID 9316> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07044 >GP: AAC00337 GB: AF008220 YtqI [Bacillus subtilis] Identities = 119/256 (46%), Positives = 174/256 (67%), Gaps = 3/256 (1%) Query: 6 QILDKIKEYDTIIIHRHMRPDPDALGSQIGLRDIIRHNFPKKKVLATGFDEPTLAWIAKM 65 +++ I YDTII+HRH+RPDPDA GSQ GL +I+R +P+K + A G EP+L+++ + Sbjct: 4 ELIRTISLYDTIILHRHVRPDPDAYGSQCGLTEILRETYPEKNIFAVGTPEPSLSFLYSL 63 Query: 66 DQVTDQDYQGALVVVTDTANTPRIDDERYKKGDFLIKIDHHPNDEVYGDLSYVDTNASSA 125- D+V ++ Y+GALV+V DTAN RIDD+RY G L+KIDHHPN++ YGDL +VDT+ASS Sbjct: 64 DEVDNETYEGALVIVCDTANQERIDDQRYPSGAKLMKIDHHPNEDPYGDLLWVDTSASSV 123- Query: 126 SEIVTDFAL---SCDLLLSTSAARVLYNGIVGDTGRFLYPATTSKTLKIASKLREFDFDF 18- 2 SE++ + L L+T AA ++Y GIVGDTGRFL+P TT KTLK A +L ++ F Sbjct: 124 SEMIYELYLEGKEHGWKLNTKAAELIYAGIVGDTGRFLFPNTTEKTLKYAGELIQYPFSS 18- 3 Query: 183 SAMARQMDSFPFKIAKLQGFIFEQLKIDKNGAACVTLTQEDLKRFDVTDAETAAIVGVPG 24- 2 S + Q+ + KL GFIF+ + + +NGAA V + ++ L++F T +E + +VG G Sbjct: 184 SELFNQLYETKLNVVKLNGFIFQNVSLSENGAASVFIKKDTLEKFGTTASEASQLVGTLG 24- 3 Query: 243 KIDIVESWAIFVKQSD 258 I + +W FV++ D Sbjct: 244 NISGIRAWVFFVEEDD 259 A related DNA sequence was identified in S. pyogenes <SEQ ID 7097> which encodes the amino acid sequence <SEQ ID 7098>. Analysis of this protein sequence reveals the following: TABLE-US-07045 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2584(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below.

TABLE-US-07046 Identities = 180/256 (70%), Positives = 215/256 (83%) Query: 4 FQQILDKIKEYDTIIIHRHMRPDPDALGSQIGLRDIIRHNFPKKKVLATGFDEPTLAWIA 63 F+ ILDKIK + TIIIHRH PDPDALGSQ GL++II NFP KKVL TGFDEP+LAWI+ Sbjct: 5 FETILDKIKAHQTIIIHRHQNPDPDALGSQAGLKEIIAQNFPDKKVLMTGFDEPSLAWIS 64 Query: 64 KMDQVTDQDYQGALVVVTDTANTPRIDDERYKKGDFLIKIDHHPNDEVYGDLSYVDTNAS 123- +MDQVTD+DY+ ALV++TDTAN PRIDDERY G LIKIDHHPND+VYGD YVDT+AS Sbjct: 65 QMDQVTDKDYKEALVIITDTANRPRIDDERYTLGKCLIKIDHHPNDDVYGDFYYVDTSAS 124- Query: 124 SASEIVTDFALSCDLLLSTSAARVLYNGIVGDTGRFLYPATTSKTLKIASKLREFDFDFS 18- 3 SASEI+ DFA S +L LS AA++LY GIVGDTGRFLY +TTSKTL IAS+LR F+FDF+ Sbjct: 125 SASEIIADFAFSQNLTLSDKAAKLLYTGIVGDTGRFLYASTTSKTLSIASQLRHFEFDFA 18- 4 Query: 184 AMARQMDSFPFKIAKLQGFIFEQLKIDKNGAACVTLTQEDLKRFDVTDAETAAIVGVPGK 24- 3 A++RQMDSFP KIAELQ ++FE L ID++GAA V ++QE LK FDVT AE++AIV PGK Sbjct: 185 AISRQMDSFPLKIAKLQSYVFEHLTIDESGAAYVLVSQETLKHFDVTLAESSAIVCAPGK 24- 4 Query: 244 IDIVESWAIFVKQSDG 259 ID V++WAIFV+ +DG Sbjct: 245 IDNVQAWAIFVELTDG 260 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2306 A DNA sequence (GBSx2447) was identified in S. agalactiae <SEQ ID 7099> which encodes the amino acid sequence <SEQ ID 7100>. Analysis of this protein sequence reveals the following: TABLE-US-07047 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1846(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07048 >GP: CAB42949 GB: AL049863 putative adenosine deaminase [Streptomyces coelicolor A3(2)] Identities = 123/343 (35%), Positives = 175/343 (50%), Gaps = 26/343 (7%) Query: 6 LKELAKAELHCHLDGSLSLPAIRKLANMADIILPSSDK-ELRKYVIAPAQTESLVDYLKT 64 L+ L KA LH HLDG L + +LA LP++D EL + A + LV Y+ T Sbjct: 11 LRRLPKAVLHDHLDGGLRPATVVELARSVGHTLPTTDPDELAAWYYEAANSGDLVRYIAT 70 Query: 65 FEFIRPLLQTKEALRFAAYDVARQAALENVIYIEIRFAPELSMDKGLTASDTVLAVLEGL 124- FE ++Q +E L AA + A + V+Y E+R+APEL+ GL+ + V V EGL Sbjct: 71 FEHTLAVMQNREGLLRAAEEYVLDLAADGVVYGEVRYAPELNTRGGLSMREVVETVQEGL 130- Query: 125 ADAQKEFNIVAR-----ALVCGMRQSSHKTTKDIIKHIVDLA----PKGLVGFDFAGDEF 17- 5 A + L+CGMR D ++ DLA G+VGFD AG E Sbjct: 131 ATGMAKAAAAGTPVRVGTLLCGMRMF------DRVREAADLAVAFRDAGVVGFDIAGAED 18- 4 Query: 176 SYPTDSLVDLIQEVKRSGYPMTLHAGECGCAKHIADSLNL-GIKRMGHVTALT------- 22- 7 +P +D + ++R P T+HAGE I +L + G +R+GH +T Sbjct: 185 GFPPADHLDAFEHLRRENVPFTIHAGEAHGLPSIHQALQVCGAQRIGHGVRITDDIPDLA 24- 4 Query: 228 -GQRDLIKRFVEEDAVA-EMCLTSNLQTKAASSIQSFPYQELYDAGGKITINTDNRTVSD 28- 5 G+ + +V + +A EMC TSNLQT AA+SI P L D G ++T+NTDNR VS Sbjct: 245 AGKLGRLAAWVRDRRIALEMCPTSNLQTGAATSIAEHPITALKDLGFRVTLNTDNRLVSG 30- 4 Query: 286 TNLTKEYSLFVTYFGTKIEDFLVFNQNAVKASFTSDSEKDTLL 328 T +T+E SL V G +ED NA+K++F E+ L+ Sbjct: 305 TTMTREMSLLVEQAGWSVEDLRTVTVNALKSAFVPFDERTALI 347 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2307 A DNA sequence (GBSx2448) was identified in S. agalactiae <SEQ ID 7101> which encodes the amino acid sequence <SEQ ID 7102>. Analysis of this protein sequence reveals the following: TABLE-US-07049 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2042(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9639> which encodes amino acid sequence <SEQ ID 9640> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07050 >GP: CAB13290 GB: Z99111 similar to sulfite reductase [Bacillus subtilis] Identities = 63/146 (43%), Positives = 87/146 (59%), Gaps = 1/146 (0%) Query: 5 MALAKIVYASMTGNTEEIADIVADKLRDLGLDVEVEECTMVDAAD-FEDADIAIVATYTY 63 MA +VYA+M+GNTE +AD++ L++ +V+ E +D A F D D I+ TYT+ Sbjct: 1 MAKILLVYATMSGNTEAMADLIEKGLQEALAEVDRFEAMDIDDAQLFTDYDHVIMGTYTW 60 Query: 64 GDGDLPDEIVDFYEDLAEVDLSGKVYGVVGSGDTFYDYFCKSVDEFEAQFALTGAQKGAD 123- GDGDLPDE +D ED+ E+D SGK V GSGDT Y++FC +VD EA+ G Sbjct: 61 GDGDLPDEFLDLVEDMEEIDFSGKTCAVFGSGDTAYEFFCGAVDTLEAKIKERGGDIVLP 120- Query: 124 CVKVDLAAEDEDIENLEAFAEEIASK 149 VK++ E E+ E L F + A K Sbjct: 121 SVKIENNPEGEEEEELINFGRQFAKK 146 A related DNA sequence was identified in S. pyogenes <SEQ ID 7103> which encodes the amino acid sequence <SEQ ID 7104>. Analysis of this protein sequence reveals the following: TABLE-US-07051 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1641(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-07052 Identities = 116/147 (78%), Positives = 136/147 (91%) Query: 5 MALAKIVYASMTGNTEEIADIVADKLRDLGLDVEVEECTMVDAADFEDADIAIVATYTYG 64 MALAKIVYASMTGNTEEIADIVA+KL++LG DV+++ECT VDA++FE+ADIA+VATYTYG Sbjct: 1 MALAKIVYASMTGNTEEIADIVANKLQELGHDVDIDECTTVDASEFENADIAVVATYTYG 60 Query: 65 DGDLPDEIVDFYEDLAEVDLSGKVYGVVGSGDTFYDYFCKSVDEFEAQFALTGAQKGADC 124- DGDLPDEIVDFYEDL ++DL GK+YGVVGSGDTFYDYFCKSVD+F QFALTGA KGA+ Sbjct: 61 DGDLPDEIVDFYEDLQDLDLEGKIYGVVGSGDTFYDYFCKSVDDFSEQFALTGAIKGAEP 120- Query: 125 VKVDLAAEDEDIENLEAFAEEIASKLN 151 VKVDLAAEDEDI+ LEAFAE+++ +N Sbjct: 121 VKVDLAAEDEDIDRLEAFAEQLSQAVN 147 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2308 A DNA sequence (GBSx2449) was identified in S. agalactiae <SEQ ID 7105> which encodes the amino acid sequence <SEQ ID 7106>. Analysis of this protein sequence reveals the following: TABLE-US-07053 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3568(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07054 >GP:AAB98234 GB:U67480 chorismate mutase/prephenate dehydratase (pheA) (Methanococcus jannaschii] Identities = 26/85 (30%), Positives = 46/85 (53%), Gaps = 1/85 (1%) Query: 2 ELEEIRQEIDEIDQQLVSLLETRMGLILEVIAFKKKHRLPVLDMNRENEVLNNVLKKVQN 61 +L EIR++IDEID +++L+ R L +V K + +P+ D RE + + + K + Sbjct: 4 KLAEIRKKIDEIDNKILKLIAERNSLAKDVAEIKNQLGIPINDPEREKYIYDRIRKLCKE 63 Query: 62 HQFDDVIRATFKDIMTE-SRVYQKE 85 H D+ I I+ E ++ QK+ Sbjct: 64 HNVDENIGIKIFQILIEHNRALQKQ 88 There is also homology to SEQ ID 1568. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2309 A DNA sequence (GBSx2450) was identified in S. agalactiae <SEQ ID 7107> which encodes the amino acid sequence <SEQ ID 7108>. This protein is predicted to be a minor structural protein. Analysis of this protein sequence reveals the following: TABLE-US-07055 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1828(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07056 >GP:AAC34413 GB:AF158600 putative minor structural protein [Streptococcus thermophilus bacteriophage Sfill] Identities = 39/65 (60%), Positives = 54/65 (83%) Query: 1 MEVETDSQEVLMSTGLKDLKAHAYPAITYEVDGYVDLELGDVVRIQDDGYEPPLILTARV 60 ME++TDS++VL+ST L++L+ YPAITYEVDG++DL++GD V+IQD G+ P L+L ARV Sbjct: 707 MEIDTDSEDVLISTALRNLRKFCYPAITYEVDGFLDLDIGDTVKIQDTGFSPMLMLEARV 76- 6 Query: 61 VEQDI 65 EQ I Sbjct: 767 SEQQI 771 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2310 A DNA sequence (GBSx2451) was identified in S. agalactiae <SEQ ID 7109> which encodes the amino acid sequence <SEQ ID 7110>. This protein is predicted to be phosphomethylpyrimidine kinase (thiD). Analysis of this protein sequence reveals the following: TABLE-US-07057 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2051(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07058 >GP:AAC22074 GB:U32725 phosphomethylpyrimidine kinase (thiD) [Haemophiius influenzae Rd] Identities = 29/78 (37%), Positives = 48/78 (61%), Gaps = 2/78 (2%) Query: 4 RNVLAISGNDIFSGGGLHADLATYVVNKLHGFVAVTCLTANSDKG-FEVIPIEASILKQQ 62 + VL I+G+D G G+ ADL T+ + + G A+T +TA + G F++ PI ++ Q Sbjct: 5 KQVLTIAGSDSGGGAGIQADLKTFQMRGVFGTSAITAVTAQNTLGVFDIHPIPLKTIQAQ 64 Query: 63 LESLK-DVEFGSIKLGLL 79 LE++K D + S K+G+L Sbjct: 65 LEAVKNDFQIASCKIGML 82 There is also homology to SEQ ID 4408. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2311 A DNA sequence (GBSx2452) was identified in S. agalactiae <SEQ ID 7111> which encodes the amino acid sequence <SEQ ID 7112>. Analysis of this protein sequence reveals the following: TABLE-US-07059 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.43 Transmembrane 109-125 ( 102-129) INTEGRAL Likelihood = -1.28 Transmembrane 84-100 ( 84-100) ----- Final Results ----- bacterial membrane --- Certainty = 0.3972(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07060 >GP:CAA22372 GB:AL034446 putative transmembrane protein [Streptomyces coelicolor A3(2)] Identities = 25/93 (26%), Positives = 43/93 (45%), Gaps = 1/93 (1%) Query: 62 SASVEILCRGWLLPVSATKYSKIVSVSISSIFFGLLHSANNNVSLISIFNLCL-FGLFLS 120- +A+ E++ RG L + +++ ++ + FGL+H N +L + + G L+ Sbjct: 143 AATEEVVFRGVLFRIIEENIGTYLALGLTGLVFGLMHLLNEDATLWGALAIAIEAGFMLA 20- 2 Query: 121 LYVILKGNIWGACGIHGAWNCVQGSVFGIEVSG 153 N+W G+H WN G VF VSG Sbjct: 203 AAYAATRNLWLTIGVHFGWNFAAGGVFSTVVSG 235 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2312 A DNA sequence (GBSx2453) was identified in S. agalactiae <SEQ ID 7113> which encodes the amino acid sequence <SEQ ID 7114>. This protein is predicted to be pppL protein. Analysis of this protein sequence reveals the following: TABLE-US-07061 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5796(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07062 >GP:CAA1O712 GB:AJ132604 pppL protein [Lactococcus lactis] Identities = 38/64 (59%), Positives = 51/64 (79%) Query: 1 MEISLLTDIGQRRSNNQDFINQFENKAGVPLIILADGMGGHRAGNIASEMTVTDLGSDWA 60 ME S+L+DIG +RS NQD++ + N+AG L +LADGMGGH+AGN+AS++TV DLG W+ Sbjct: 1 MEYSILSDIGSKRSTNQDYVGTYVNRAGYQLFLLADGMGGHKAGNVASKLTVEDLGKLWS 60 Query: 61 ETDF 64 ET F Sbjct: 61 ETFF 64 There is also homology to SEQ ID 3022: TABLE-US-07063 Identities = 58/74 (78%), Positives = 69/74 (92%) Query: 1 MEISLLTDIGQRRSNNQDFINQFENKAGVPLIILADGMGGHRAGNIASEMTVTDLGSDWA 60 M+ISL TDIGQ+RSNNQDFIN+F+NK G+ L+ILADGMGGHRAGNIASEMTVTDLG +W Sbjct: 1 MKISLKTDIGQKRSNNQDFINKFDNKKGITLVILADGMGGHRAGNIASEMTVTDLGREWV 60 Query: 61 ETDFSELSEIRDWM 74 +TDF+ELS+IRDW+ Sbjct: 61 KTDFTELSQIRDWL 74 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2313 A DNA sequence (GBSx2454) was identified in S. agalactiae <SEQ ID 7115> which encodes the amino acid sequence <SEQ ID 7116>. This protein is predicted to be sunL protein. Analysis of this protein sequence reveals the following: TABLE-US-07064 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1631(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07065 >GP: CAA10711 GB: AJ132604 sunL protein [Lactococcus lactis] Identities = 48/81 (59%), Positives = 67/81 (82%) Query: 1 MSILSSVCQTLRKGGIITYSTCTIFEEENFQVIEKFLENHPNFEQVELSHTQEDIVKRGC 60 + IL+S ++L+K GI+ YSTCTIF+EENF V+ +FLENHPNFEQVE+S+ + +++K GC Sbjct: 342 LEILNSASKSLKKSGIMVYSTCTIFDEENFDVVHEFLENHPNFEQVEISNEKPEVIKEGC 40- 1 Query: 61 ISISPEQYHTDGFFIGQVKRI 81 + I+PE YHTDGFFI + K+I Sbjct: 402 LFITPEMYHTDGFFIAKFKKI 422 There is also homology to SEQ ID 3018: TABLE-US-07066 Identities = 64/82 (78%), Positives = 74/82 (90%) Query: 1 MSILSSVCQTLRKGGIITYSTCTIFEEENFQVIEKFLENHPNFEQVELSHTQEDIVKRGC 60 + ILSSVCQTLRKGGIITYSTCTIF+EEN QVIE FL++HPNFEQV+L+HTQ DIVK G Sbjct: 359 LEILSSVCQTLRKGGIITYSTCTIFDEENRQVIEAFLQSHPNFEQVKLNHTQADIVKDGY 41- 8 Query: 61 ISISPEQYHTDGFFIGQVKRIL 82 + I+PEQY TDGFFIGQV+R+L Sbjct: 419 LIITPEQYQTDGFFIGQVRRVL 440 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2314 A DNA sequence (GBSx2455) was identified in S. agalactiae <SEQ ID 7117> which encodes the amino acid sequence <SEQ ID 7118>. This protein is predicted to be PTS permease for mannose subunit IIPMan. Analysis of this protein sequence reveals the following: TABLE-US-07067 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.18 Transmembrane 32-48 (30-58) INTEGRAL Likelihood = -8.07 Transmembrane 127-143 (122-146) INTEGRAL Likelihood = -2.07 Transmembrane 56-72 (56-72) INTEGRAL Likelihood = -1.44 Transmembrane 87-103 (86-103) INTEGRAL Likelihood = -0.53 Transmembrane 105-121 (105-121) ----- Final Results ----- bacterial membrane --- Certainty = 0.4673(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07068 >GP: AAF81084 GB: AF228498 AgaW [Escherichia coli] Identities = 38/122 (31%), Positives = 68/122 (55%), Gaps = 7/122 (5%) Query: 25 KVPETKSIIRLTALAFLVCSILVVELVSMRELISSISFIGILVGSGPVNSFVHHIPQNLM 84 - ++P T + L A +L L+++ +F+ I G+ + + +PQ L+ Sbjct: 126 RMPRTPILAALNACNYLA-------LLALGNFYFLCAFLPIYFGAEHAKTIIDVLPQRLI 17- 8 Query: 85 NGLSAAGGLLPAVGFAMLMKLLWTNKLAVFYLLGFVLTAYLKLPAVAVAALGAVICVISS 144- +GL AGG++PA+GFA+L+K++ N +++LGFV A+LKLP +A+A + +I Sbjct: 179 DGLGVAGGIMPAIGFAVLLKIMMKNVYIPYFILGFVAAAWLKLPVLAIACPALAMALIDL 23- 8 Query: 145 QR 146 R Sbjct: 239 LR 240 There is also homology to SEQ ID 1636: TABLE-US-07069 Identities = 104/109 (95%), Positives = 108/109 (98%) Query: 56 LISSISFIGILVGSGPVNSFVHHIPQNLMNGLSAAGGLLPAVGFAMLMKLLWTNKLAVFY 115- +I+SISFIGILVGSGPVN+FV HIPQNLMNGLSAAGGLLPAVGFAMLMKLLWTNKLAVFY Sbjct: 149 IIASISFIGILVGSGPVNAFVEHIPQNLMNGLSAAGGLLPAVGFAMLMKLLWTNKLAVFY 20- 8 Query: 116 LLGFVLTAYLKLPAVAVAALGAVICVISSQRDIELDAITRGAISKQTTF 164 LLGFVLTAYLKLPAVAVAALGAVICVISSQRD+ELDAITRGAISKQTTF Sbjct: 209 LLGFVLTAYLKLPAVAVAALGAVICVISSQRDLELDAITRGAISKQTTF 257 Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2315 A DNA sequence (GBSx2456) was identified in S. agalactiae <SEQ ID 7119> which encodes the amino acid sequence <SEQ ID 7120>. Analysis of this protein sequence reveals the following: TABLE-US-07070 Possible site: 50 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -8.12 Transmembrane 121-137 (118-144) INTEGRAL Likelihood = -5.52 Transmembrane 91-107 (89-111) INTEGRAL Likelihood = -5.20 Transmembrane 166-182 (162-192) ----- Final Results ----- bacterial membrane --- Certainty = 0.4248(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database.

TABLE-US-07071 >GP: CAB15963 GB: Z99124 phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component [Bacillus subtilis] Identities = 76/201 (37%), Positives = 122/201 (59%), Gaps = 3/201 (1%) Query: 1 MIKALLALLLVFKILTPSSQTYILLNLFADGVFYFLPILIAITAAQKLKANPILALGTVV 60 MIK L+AL + F + SQ +++L DG FYFLP+L+A++AA+K +NP +A Sbjct: 121 MIKGLVALAVTFGWMAEKSQVHVILTAVGDGAFYFLPLLLAMSAARKFGSNPYVAAAIAA 18- 0 Query: 61 MLLHPNWANLVASGKPVSLFHTIPFTLTNYASSVIPIILIICVQAYIEKYLKQIIPKSLR 120- +LHP+ L+ +GKP+S F +P T Y+S+VIPI+L I + +Y+EK++ + SL+ Sbjct: 181 AILHPDLTALLGAGKPIS-FIGLPVTAATYSSTVIPILLSIWIASYVEKWIDRFTHASLK 23- 9 Query: 121 LVLVPMLIFLSMGILSFSILGPMGTIAGQYLAVIFTFLSKYASW-APAFLVGAFAPILIM 17- 9 L++VP L + L+ +GP+G I G+YL+ +L +A A FL G F+ ++IM Sbjct: 240 LIVVPTFTLLIVVPLTLITVGPLGAILGEYLSSGVNYLFDHAGLVAMIFLAGTFS-LIIM 29- 8 Query: 180 FGVHSGIAALGITQLAKLGVD 200 G+H + I +A+ G D Sbjct: 299 TGMHYAFVPIMINNIAQNGHD 319 There is also homology to SEQ ID 2884. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2316 A DNA sequence (GBSx2457) was identified in S. agalactiae <SEQ ID 7121> which encodes the amino acid sequence <SEQ ID 7122>. This protein is predicted to be glucose kinase. Analysis of this protein sequence reveals the following: TABLE-US-07072 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1180(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07073 >GP: CAB14416 GB: Z99116 glucose kinase [Bacillus subtilis] Identities = 32/57 (56%), Positives = 41/57 (71%) Query: 1 MVIGGGVSAAGEFLRSRVEKYFVTFAFPQVKKSTKIKIAELGNDAGIIGAASLANQQ 57 +V+GGGVS AGE LRS+VEK F AFP+ ++ I IA LGNDAG+IG A +A + Sbjct: 258 IVLGGGVSRAGELLRSKVEKTFRKCAFPRAAQAADISIAALGNDAGVIGGAWIAKNE 314 There is also homology to SEQ ID 198. An alignment of the GAS and GBS proteins is shown below: TABLE-US-07074 Identities = 50/56 (89%), Positives = 53/56 (94%) Query: 1 MVIGGGVSAAGEFLRSRVEKYFVTFAFPQVKKSTKIKIAELGNDAGIIGAASLANQ 56 +VIGGGVSAAGEFLRSR+EKYFVTF FPQV+ STKIKIAELGNDAGIIGAASLA Q Sbjct: 264 VVIGGGVSAAGEFLRSRIEKYFVTFTFPQVRYSTKIKIAELGNDAGIIGAASLARQ 319 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2317 A DNA sequence (GBSx2458) was identified in S. agalactiae <SEQ ID 7123> which encodes the amino acid sequence <SEQ ID 7124>. Analysis of this protein sequence reveals the following: TABLE-US-07075 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07076 >GP: CAB14385 GB: Z99116 similar to hypothetical proteins [Bacillus subtilis] Identities = 37/86 (43%), Positives = 51/86 (59%) Query: 3 MSVILIIVILLAFVAWASWNYWRVRRAAKFLDNESFQKEMSRGQLIDIREAGAFHRKHIL 62 MS +++++I AF+ + +Y +R K L E F+ + QLID+RE F HIL Sbjct: 1 MSNMIVLIIFPAFIIYMIASYVYQQRIMKTLTEEEFRAGYRKAQLIDVREPNEFEGGHIL 60 Query: 63 GARNIPASQFKVALSALRKDKPVLLY 88 GARNIP SQ K + +R DKPV LY Sbjct: 61 GARNIPLSQLKQRKNEIRTDKPVYLY 86 There is also homology to SEQ ID 202. An alignment of the GAS and GBS proteins is shown below: TABLE-US-07077 Identities = 51/108 (47%), Positives = 70/108 (64%) Query: 1 MDMSVILIIVILLAFVAWASWNYWRVRRAAKFLDNESFQKEMSRGQLIDIREAGAFHRKH 60 M +++ ++L+ V + +WNY+ R+ AK +DNE+F+ M +GQLID+RE AF KH Sbjct: 1 MSPITLILWLLLVGIVGYYTWNYFSFRKMAKQVDNETFKDVMRQGQLIDLREPAAFRTKH 60 Query: 61 ILGARNIPASQFKVALSALRKDKPVLLYDASRGQSIPRIVLLLRKERF 108 ILGARN PA QF A+ LRKDKPVL+Y+ R Q V L+K F Sbjct: 61 ILGARNFPAQQFDAAIKGLRKDKPVLIYENMRPQYRVPAVKKLKKAGF 108 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2318 A DNA sequence (GBSx2459) was identified in S. agalactiae <SEQ ID 7125> which encodes the amino acid sequence <SEQ ID 7126>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-07078 Possible site: 24 <<< Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1892(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2319 A DNA sequence (GBSx2460) was identified in S. agalactiae <SEQ ID 7127> which encodes the amino acid sequence <SEQ ID 7128>. Analysis of this protein sequence reveals the following: TABLE-US-07079 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3522(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2320 A DNA sequence (GBSx2461) was identified in S. agalactiae <SEQ ID 7129> which encodes the amino acid sequence <SEQ ID 7130>. Analysis of this protein sequence reveals the following: TABLE-US-07080 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2770(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07081 >GP: AAB18708 GB: U38906 ORF33 [Bacteriophage r1t] Identities = 56/85 (65%), Positives = 66/85 (76%), Gaps = 1/85 (1%) Query: 1 MTNFATTDDVILLWRQLSVDEIKRAEALLETVSDTLRLEASKVGKNLDEMILETP-YFAT 59 M FAT DD+ +LWR L DE +RAE LLE VSD+LR EA KVG++L MI E P YFA+ Sbjct: 1 MNPFATVDDLTMLWRPLKGDEKERAEKLLEIVSDSLREEADKVGRDLYAMIAEKPSYFAS 60 Query: 60 VLKSVTVDIVARTLMTATQGEPMSQ 84 V+KSVTVDIVARTLMT+T EPM+Q Sbjct: 61 VVKSVTVDIVARTLMTSTDQEPMTQ 85 There is also homology to SEQ ID 1432. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2321 A DNA sequence (GBSx2462) was identified in S. agalactiae <SEQ ID 7131> which encodes the amino acid sequence <SEQ ID 7132>. This protein is predicted to be regulatory protein TypA (typA). Analysis of this protein sequence reveals the following: TABLE-US-07082 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2238(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07083 >GP: BAB06351 GB: AP001516 GTP-binding protein TypA/BipA (tyrosine phosphorylated protein A) [Bacillus halodurans] Identities = 175/237 (73%), Positives = 204/237 (85%), Gaps = 1/237 (0%) Query: 1 MEDIFVGETVTPTDAIEPLPVLRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAE 60 ME+I VGETV P D +PLP+LRIDEPTLQMTFLVNNSPFAGREGK +TSRK+EERL AE Sbjct: 281 MEEINVGETVCPVDHQDPLPILRIDEPTLQMTFLVNNSPFAGREGKHVTSRKLEERLRAE 34- 0 Query: 61 LQTDVSLRVDPTDSPDKWTVSGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGVQCE 120- L+TDVSLRV+ TDSPD W VSGRGELHLSILIE MRREGYELQVS+PEVII+EIDGVQCE Sbjct: 341 LETDVSLRVENTDSPDMWVVSGRGELHLSILIENMRREGYELQVSKPEVIIREIDGVQCE 40- 0 Query: 121 PFERVQIDTPEEYQGAIIQSLSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSM 18- 0 P ERVQID PEEY GA+++SL ERKG+ML+M G+GQ RL F++PARGLIGY+TEFLS Sbjct: 401 PVERVQIDVPEEYTGAVMESLGERKGEMLNMTNTGSGQVRLEFMVPARGLIGYTTEFLSQ 46- 0 Query: 181 TRGYGIMNHTFDQYLPVVQGEIGGRHRGALVSIENGKATTYSIMRIEERGNLSFVNP 237 TRGYGI+NH+FD Y PV G++GGR +G LVS+E GKAT Y I+++E+RG + FV P Sbjct: 461 TRGYGIINHSFDSYQPVTPGQVGGRRQGVLVSMETGKATQYGIIQVEDRGTI-FVEP 516 There is also homology to SEQ ID 206. An alignment of the GAS and GBS proteins is shown below: TABLE-US-07084 Identities = 228/237 (96%), Positives = 233/237 (98%), Gaps = 1/237 (0%) Query: 1 MEDIFVGETVTPTDAIEPLPVLRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAE 60 MEDIFVGET+TPTD +E LP+LRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAE Sbjct: 284 MEDIFVGETITPTDCVEALPILRIDEPTLQMTFLVNNSPFAGREGKWITSRKVEERLLAE 34- 3 Query: 61 LQTDVSLRVDPTDSPDKWTVSGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGVQCE 120- LQTDVSLRVDPTDSPDKWTVSGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGV+CE Sbjct: 344 LQTDVSLRVDPTDSPDKWTVSGRGELHLSILIETMRREGYELQVSRPEVIIKEIDGVKCE 40- 3 Query: 121 PFERVQIDTPEEYQGAIIQSLSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSM 18- 0 PFERVQIDTPEEYQGAIIQSLSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSM Sbjct: 404 PFERVQIDTPEEYQGAIIQSLSERKGDMLDMQMVGNGQTRLIFLIPARGLIGYSTEFLSM 46- 3 Query: 181 TRGYGIMNHTFDQYLPVVQGEIGGRHRGALVSIENGKATTYSIMRIEERGNLSFVNP 237 TRGYGIMNHTFDQYLPVVQGEIGGRHRGALVSIENGKATTYSIMRIEERG + FVNP Sbjct: 464 TRGYGIMNHTFDQYLPVVQGEIGGRHRGALVSIENGKATTYSIMRIEERGTI-FVNP 519 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2322 A DNA sequence (GBSx2464) was identified in S. agalactiae <SEQ ID 7133> which encodes the amino acid sequence <SEQ ID 7134>. This protein is predicted to be pseudouridine synthase family 1 protein (rluB). Analysis of this protein sequence reveals the following: TABLE-US-07085 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1950(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07086 >GP: CAB14248 GB: Z99116 similar to hypothetical proteins [Bacillus subtilis] Identities = 59/105 (56%), Positives = 85/105 (80%) Query: 5 VKERIYPVGRLDWDTTGLLILTNDGDFTDKMIHPRNEIDKVYLARVKGIATKENLRPLTR 64 + +RIYP+GRLD+DT+GLL+LTNDG+F +K++HP+ EIDK Y+A+VKGI KE LR L R Sbjct: 91 IPQRIYPIGRLDYDTSGLLLLTNDGEFANKLMHPKYEIDKTYVAKVKGIPPKELLRKLER 150- Query: 65 GVVIDGKKTKPARYTIIKVDHEKNRSVVELTIHEGRNHQVKKMFE 109 G+ ++ KT PA+ ++ +D +K S+++LTIHEGRN QV++MFE Sbjct: 151 GIRLEEGKTAPAKAKLLSLDKKKQTSIIQLTIHEGRNRQVRRMFE 195 There is also homology to SEQ ID 4728: TABLE-US-07087 Identities = 96/109 (88%), Positives = 106/109 (97%) Query: 1 MLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDKMIHPRNEIDKVYLARVKGIATKENLR 60 +LPQVKERIYPVGRLDWDT+G+LILTNDGDFTD MIHPRNEIDKVYLARVKGIATKENLR Sbjct: 94 LLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTMIHPRNEIDKVYLARVKGIATKENLR 153- Query: 61 PLTRGVVIDGKKTKPARYTIIKVDHEKNRSVVELTIHEGRNHQVKKMFE 109 PLTRG+VIDGKKTKPARY I++V+ +K+RS+VELTIHEGRNHQVKKMFE Sbjct: 154 PLTRGIVIDGKKTKPARYNIVRVEADKSRSIVELTIHEGRNHQVKKMFE 202 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2323 A DNA sequence (GBSx2466) was identified in S. agalactiae <SEQ ID 7135> which encodes the amino acid sequence <SEQ ID 7136>. This protein is predicted to be L-ribulose 5-phosphate 4-epimerase. Analysis of this protein sequence reveals the following: TABLE-US-07088 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2827(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07089 >GP: AAD45716 GB: AF160811 L-ribulose 5-phosphate 4-epimerase [Bacillus stearothermophilus] Identities = 68/103 (66%), Positives = 82/103 (79%) Query: 2 QEMRERVCEANKSLPVHSLVKFTWGNVSEVDREAGLIVIKPSGVDYDQLTPENMVVTDLE 61 +E+++ V EAN LP + LV FTWGNVS +DRE GL+VIKPSGV YD+LT ++MVV DL Sbjct: 3 EELKQAVLEANLQLPQYRLVTFTWGNVSGIDRERGLVVIKPSGVAYDKLTIDDMVVVDLT 62 Query: 62 GNIVEGDLNPSSDLPTHVQLYKAWPEVGGIVHTHSTEAVGWAQ 104 GN+VEGDL PSSD PTH+ LYK +P +GGIVHTHST A WAQ Sbjct: 63 GNVVEGDLKPSSDTPTHLWLYKQFPGIGGIVHTHSTWATVWAQ 105 There is also homology to SEQ ID 4600: TABLE-US-07090 Identities = 93/103 (90%), Positives = 96/103 (92%) Query: 2 QEMRERVCEANKSLPVHSLVKFTWGNVSEVDREAGLIVIKPSGVDYDQLTPENMVVTDLE 61 QEMRERVC ANKSLP H LVKFTWGNVSEV RE G IVIKPSGVDYD LTPENMVVTDL+ Sbjct: 6 QEMRERVCAANKSLPQHGLVKFTWGNVSEVCRELGRIVIKPSGVDYDLLTPENMVVTDLD 65 Query: 62 GNIVEGDLNPSSDLPTHVQLYKAWPEVGGIVHTHSTEAVGWAQ 104 GN+VEGDLNPSSDLPTHV+LYKAWPEVGGIVHTHSTEAVGWAQ Sbjct: 66 GNVVEGDLNPSSDLPTHVELYKAWPEVGGIVHTHSTEAVGWAQ 108 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2324 A DNA sequence (GBSx2467) was identified in S. agalactiae <SEQ ID 7137> which encodes the amino acid sequence <SEQ ID 7138>. Analysis of this protein sequence reveals the following: TABLE-US-07091 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3452(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07092 >GP: AAG05712 GB: AE004658 hypothetical protein [Pseudomonas aeruginosa] Identities = 141/200 (70%), Positives = 162/200 (80%), Gaps = 1/200 (0%) Query: 10 LSLGTDYETLANRFRPIFREISAGNVEREKARALPYEPIEWLKKAGFGAVRVPSEYGGAG 69 - LS G DYE LA RFRPIF I+ G VERE+ R LP+E I WLK+AGFGAVRVP E+GGAG Sbjct: 14 LSEGADYELLAQRFRPIFARIAEGAVERERQRELPHEAIAWLKQAGFGAVRVPREHGGAG 73 Query: 70 ASIGQLFQLLIELAEADSNIPQALRAHFAFVEDRLNAPPGVDRDTWFARFVAGDLVGNGW 129- AS+ QL QLLIELAEADSNI QALR HFAFVEDRLNA PG RD W RFV GDLVG W Sbjct: 74 ASLPQLVQLLIELAEADSNITQALRGHFAFVEDRLNAEPGPGRDRWLRRFVEGDLVGCAW 133- Query: 130 TEVGTVKIGDVITKVSAQGDG-FVLNGTKFYSTGSIFADWIDVYAQRADNGADVIAVVNA 18- 8 TEVG+V++G+V+T+VS + DG +V+NG+K+YSTGS+F+DWID+YAQR D GADVIA + Sbjct: 134 TEVGSVRLGEVLTRVSRKDDGRWVVNGSKYYSTGSLFSDWIDLYAQRDDTGADVIAAIRT 19- 3 Query: 189 RHAGVRHSDDWDGFGQRTTG 208 GVR SDDWDGFGQRTTG Sbjct: 194 DQPGVRQSDDWDGFGQRTTG 213 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2325 A DNA sequence (GBSx2468) was identified in S. agalactiae <SEQ ID 7139> which encodes the amino acid sequence <SEQ ID 7140>. Analysis of this protein sequence reveals the following: TABLE-US-07093 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1919(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2326 A DNA sequence (GBSx2474) was identified in S. agalactiae <SEQ ID 7141> which encodes the amino acid sequence <SEQ ID 7142>. Analysis of this protein sequence reveals the following: TABLE-US-07094 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2978(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2327 A DNA sequence (GBSx2476) was identified in S. agalactiae <SEQ ID 7143> which encodes the amino acid sequence <SEQ ID 7144>. Analysis of this protein sequence reveals the following: TABLE-US-07095 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5402(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2328 A DNA sequence (GBSx2477) was identified in S. agalactiae <SEQ ID 7145> which encodes the amino acid sequence <SEQ ID 7146>. This protein is predicted to be mercuric reductase. Analysis of this protein sequence reveals the following:

TABLE-US-07096 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2755(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07097 >GP: CAA70224 GB: Y09024 mercuric reductase [Bacillus cereus] Identities = 190/247 (76%), Positives = 225/247 (90%) Query: 1 MELGQLFHHLGSEITLMQRSERLLKEYDPEISESVEKALIEQGINLVKGATFERVEQSGE 60 MELGQLFH+LGSE+TL+QRSERLLKEYDPEISESVEK+L+EQGINLVKGAT+ER+EQ+G+ Sbjct: 262 MELGQLFHNLGSEVTLIQRSERLLKEYDPEISESVEKSLVEQGINLVKGATYERIEQNGD 32- 1 Query: 61 IKRVYVTVNGSREVIESDQLLVATGRKPNTDSLNLSAAGVETGKNNEILINDFGQTSNEK 120- IK+V+V VNG + +IE+DQLLVATGR PNT +LNL AAGVE G EI+I+D+ +T+N + Sbjct: 322 IKKVHVEVNGKKRIIEADQLLVATGRTPNTATLNLRAAGVEIGSRGEIIIDDYSRTTNTR 38- 1 Query: 121 IYAAGDVTLGPQFVYVAAYEGGIITDNAIGGLNKKIDLSVVPAVTFTNPTVATVGLTEEQ 18- 0 IYAAGDVTLGPQFVYVAAY+GG+ NAIGGLNKK++L VVP VTFT P +ATVGLTE+Q Sbjct: 382 IYAAGDVTLGPQFVYVAAYQGGVAAPNAIGGLNKKLNLEVVPGVTFTAPAIATVGLTEQQ 44- 1 Query: 181 AKEKGYDVKTSVLPLGAVPRAIVNRETTGVFKLVADAETLKVLGVHIVSENAGDVIYAAS 24- 0 AKE GY+VKTSVLPL AVPRA+VNRETTGVFKLVAD++T+KVLG H+V+ENAGDVIYAA+ Sbjct: 442 AKENGYEVKTSVLPLDAVPRALVNRETTGVFKLVADSKTMKVLGAHVVAENAGDVIYAAT 50- 1 Query: 241 LAVKFGL 247 LAVKFGL Sbjct: 502 LAVKFGL 508 There is also homology to SEQ ID 1820. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2329 A DNA sequence (GBSx2478) was identified in S. agalactiae <SEQ ID 7147> which encodes the amino acid sequence <SEQ ID 7148>. Analysis of this protein sequence reveals the following: TABLE-US-07098 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3642(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2330 A DNA sequence (GBSx2479) was identified in S. agalactiae <SEQ ID 7149> which encodes the amino acid sequence <SEQ ID 7150>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-07099 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1936(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2331 A DNA sequence (GBSx2480) was identified in S. agalactiae <SEQ ID 7151> which encodes the amino acid sequence <SEQ ID 7152>. This protein is predicted to be Nra. Analysis of this protein sequence reveals the following: TABLE-US-07100 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1510(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9383> which encodes amino acid sequence <SEQ ID 9384> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. A related DNA sequence was identified in S. pyogenes <SEQ ID 7153> which encodes the amino acid sequence <SEQ ID 7154>. Analysis of this protein sequence reveals the following: TABLE-US-07101 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.64 Transmembrane 22-38 (22-38) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-07102 Identities = 42/157 (26%), Positives = 78/157 (48%), Gaps = 2/157 (1%) Query: 71 LLGREFIDSQHFKDINAYFLRHFICYCYYFIPDFYFLNTSRLSY--SKDLYHLLDKGLAD 128- LLG ++S FK I F R FI +PD + + R +K Y+ L + + Sbjct: 8 LLGNNILNSLPFKRILVSFSRLFISNLQVLLPDIHLFHYLRRQQKRNKSFYNTLKTIVEE 67 Query: 129 IFNLKGGNLTFSKHETVLLTMQLSNLIETFLAPLSVYVISSSNIRLQTYQVMLNQYFTSK 18- 8 + +G + +L T+QL L++T+L P+ VY+++++ L L+ YF Sbjct: 68 WMSAEGIVGKLPSYHLLLFTIQLEELLKTYLPPIPVYLLTNNTAALDLMTNALSIYFPPA 127- Query: 189 IAEFFFVNYQTTQIDEKLLKKADIIIAERRYISSLKN 225 IA VN + + + +K +IIA+R+Y++ +++ Sbjct: 128 IATVMPVNVEIIPFKDIVKEKQSVIIADRQYLNLIQH 164 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2332 A DNA sequence (GBSx2481) was identified in S. agalactiae <SEQ ID 7155> which encodes the amino acid sequence <SEQ ID 7156>. Analysis of this protein sequence reveals the following: TABLE-US-07103 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1383(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2333 A DNA sequence (GBSx2482) was identified in S. agalactiae <SEQ ID 7157> which encodes the amino acid sequence <SEQ ID 7158>. Analysis of this protein sequence reveals the following: TABLE-US-07104 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4145(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2334 A DNA sequence (GBSx2484) was identified in S. agalactiae <SEQ ID 7159> which encodes the amino acid sequence <SEQ ID 7160>. Analysis of this protein sequence reveals the following: TABLE-US-07105 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.02 Transmembrane 34-50 (34-50) ----- Final Results ----- bacterial membrane --- Certainty = 0.1808(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2335 A DNA sequence (GBSx2485) was identified in S. agalactiae <SEQ ID 7161> which encodes the amino acid sequence <SEQ ID 7162>. Analysis of this protein sequence reveals the following: TABLE-US-07106 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3488(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07107 >GP: CAB52002 GB: AL109663 hypothetical protein [Streptomyces coelicolor A3(2)] Identities = 61/141 (43%), Positives = 86/141 (60%), Gaps = 2/141 (1%) Query: 3 TYFDNFLKTNQAYADLHGTAHLPIKPKTKVAIVTCMDSRLHVAQALGLALGDAHILRNAG 62 T D ++ N+ YA + +P +VA+V CMD+RL + ALGL LGD H +RNAG Sbjct: 5 TVTDRLVEANERYAAAFADPGMDARPVQRVAVVACMDARLDLHAALGLKLGDCHTIRNAG 64 Query: 63 GRVTDDVLRSLVISQQQLGTREIVVLHHTDCGAQTFTNEAFAAQLQRDLGVDMHGHDFLP 122- G VTDDV+RSL ISQ+ LGTR + ++HHT CG +T T E F L+ ++G Sbjct: 65 GVVTDDVIRSLTISQRALGTRSVALIHHTGCGMETITEE-FRHDLELEVG-QRPAWAVEA 122- Query: 123 FNDIEESVREDVAKLHASPFL 143 F D ++ VR+ + ++ SPFL Sbjct: 123 FRDADQDVRQSIERVRTSPFL 143 A related DNA sequence was identified in S. pyogenes <SEQ ID 6469> which encodes the amino acid sequence <SEQ ID 6470>. Analysis of this protein sequence reveals the following: TABLE-US-07108 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2295(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-07109 Identities = 109/146 (74%), Positives = 128/146 (87%) Query: 1 MTTYFDNFLKTNQAYADLHGTAHLPIKPKTKVAIVTCMDSRLHVAQALGLALGDAHILRN 60 + +YF++F+ NQAY LHGTAHLP+KPKTKVAIVTCMDSRLHVAQALGLALGDAHILRN Sbjct: 1 LMSYFEHFMAANQAYVALHGTAHLPLKPKTKVAIVTCMDSRLHVAQALGLALGDAHILRN 60 Query: 61 AGGRVTDDVLRSLVISQQQLGTREIVVLHHTDCGAQTFTNEAFAAQLQRDLGVDMHGHDF 120- AGGRVT+D++RSLVISQQQ+GTREIVVLHHTDCGAQTFTNE FA + LGVD+ G DF Sbjct: 61 AGGRVTEDMIRSLVISQQQMGTREIVVLHHTDCGAQTFTNEGFAKHIHEHLGVDVSGQDF 120- Query: 121 LPFNDIEESVREDVAKLHASPFLREE 146 LPF D+E+SVRED+AK+ AS + ++ Sbjct: 121 LPFQDVEDSVREDMAKIRASSLISDD 146 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2336 A DNA sequence (GBSx2486) was identified in S. agalactiae <SEQ ID 7163> which encodes the amino acid sequence <SEQ ID 7164>. Analysis of this protein sequence reveals the following: TABLE-US-07110 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0932(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07111 >GP: AAG08811 GB: AE004955 phosphoribosylaminoimidazole carboxylase, catalytic subunit [Pseudomonas aeruginosa] Identities = 20/27 (74%), Positives = 26/27 (96%) Query: 1 MFKHAEEARGRGIKIIIAGAGGAAHLP 27 +F++AEEA GRG+++IIAGAGGAAHLP Sbjct: 46 LFQYAEEAEGRGLEVIIAGAGGAAHLP 72 There is also homology to SEQ ID 910: TABLE-US-07112 Identities = 27/27 (100%), Positives = 27/27 (100%) Query: 1 MFKHAEEARGRGIKIIIAGAGGAAHLP 27 MFKHAEEARGRGIKIIIAGAGGAAHLP Sbjct: 87 MFKHAEEARGRGIKIIIAGAGGAAHLP 113 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2337 A DNA sequence (GBSx2488) was identified in S. agalactiae <SEQ ID 7165> which encodes the amino acid sequence <SEQ ID 7166>. Analysis of this protein sequence reveals the following: TABLE-US-07113 Possible site: 43 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.85 Transmembrane 58-74 (53-80) INTEGRAL Likelihood = -5.79 Transmembrane 103-119 (101-122) ----- Final Results ----- bacterial membrane --- Certainty = 0.3739(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> There is also homology to SEQ IDs 880 and 9278. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2338 A DNA sequence (GBSx2489) was identified in S. agalactiae <SEQ ID 7167> which encodes the amino acid sequence <SEQ ID 7168>. This protein is predicted to be short chain alcohol dehydrogenase. Analysis of this protein sequence reveals the following: TABLE-US-07114 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1742(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9357> which encodes amino acid sequence <SEQ ID 9358> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07115 >GP: AAD06605 GB: AE001530 putative oxidoreductase [Helicobacter pylori J99] Identities = 68/94 (72%), Positives = 79/94 (83%) Query: 4 IDLLVNNAGLALGLDKSYEADFGDWMTMINTNVVGLIYLTRCILPKMVEVNRGLIINLGS 63 ID L+NNAGLALGL+K+YE + DW MI+TN+ GL++LTR ILP M+E ++G IINLGS Sbjct: 76 IDALINNAGLALGLNKAYECELDDWEVMIDTNIKGLLHLTRLILPSMIEHDQGTIINLGS 135- Query: 64 XAGTIPYPGANVYGASKAFVKQFSLNLRADLAGT 97 AGT YPG NVYGASKAFVKQFSLNLRADLAGT Sbjct: 136 IAGTYAYPGGNVYGASKAFVKQFSLNLRADLAGT 169 A related DNA sequence was identified in S. pyogenes <SEQ ID 7169> which encodes the amino acid sequence <SEQ ID 7170>. Analysis of this protein sequence reveals the following: TABLE-US-07116 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9121> which encodes the amino acid sequence <SEQ ID 9122>. Analysis of this protein sequence reveals the following: TABLE-US-07117 Possible site: 12 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-07118 Identities = 78/96 (81%), Positives = 87/96 (90%) Query: 2 QSIDLLVNNAGLALGLDKSYEADFGDWMTMINTNVVGLIYLTRCILPKMVEVNRGLIINL 61 Q I +LVNNAGLALGLDK+YEADF +WMTMINTN+VGLIYLTR +LP MV + G+IINL Sbjct: 82 QDITILVNNAGLALGLDKAYEADFENWMTMINTNIVGLIYLTRQLLPHMVSKDDGIIINL 141- Query: 62 GSXAGTIPYPGANVYGASKAFVKQFSLNLRADLAGT 97 GS AGTIPYPGAN+YGASKAFVKQFSLNLRADLAG+ Sbjct: 142 GSTAGTIPYPGANIYGASKAFVKQFSLNLRADLAGS 177 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2339 A DNA sequence (GBSx2492) was identified in S. agalactiae <SEQ ID 7171> which encodes the amino acid sequence <SEQ ID 7172>. This protein is predicted to be mercuric reductase. Analysis of this protein sequence reveals the following: TABLE-US-07119 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2115(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07120 >GP: CAC14663 GB: Y10855 mercuric reductase [Bacillus licheniformis] Identities = 68/104 (65%), Positives = 82/104 (78%) Query: 1 MNKFKVNISGMTCTGCEKHVESALEKIGAKNIESSYRRGEAVFELPDDIEVESAIKAIDE 60 M K++VN+ GMTCTGCE+HV ALE +GAK IE YRRGEAVFELP+ +EVE+A KAI E Sbjct: 1 MKKYRVNVQGMTCTGCEEHVAVALENMGAKRIEVDYRRGEAVFELPNGLEVETAKKAIAE 60 Query: 61 ANYQAGEIEEVSSLENVALINEDNYDLLIIGSGAAAFSSAIKAI 104 A YQ GE EEV S E + L +E +YD +IIGSG AAFSSAI+A+ Sbjct: 61 AKYQPGEAEEVQSQELIQLGDEGDYDYIIIGSGGAAFSSAIEAV 104 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2340 A DNA sequence (GBSx2494) was identified in S. agalactiae <SEQ ID 7173> which encodes the amino acid sequence <SEQ ID 7174>. Analysis of this protein sequence reveals the following: TABLE-US-07121 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3341(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2341 A DNA sequence (GBSx2495) was identified in S. agalactiae <SEQ ID 7175> which encodes the amino acid sequence <SEQ ID 7176>. Analysis of this protein sequence reveals the following:

TABLE-US-07122 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4989(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2342 A DNA sequence (GBSx2496) was identified in S. agalactiae <SEQ ID 7177> which encodes the amino acid sequence <SEQ ID 7178>. Analysis of this protein sequence reveals the following: TABLE-US-07123 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2569(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2343 A DNA sequence (GBSx2497) was identified in S. agalactiae <SEQ ID 7179> which encodes the amino acid sequence <SEQ ID 7180>. This protein is predicted to be DNA polymerase III alpha subunit (dnaE). Analysis of this protein sequence reveals the following: TABLE-US-07124 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3124(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related DNA sequence was identified in S. pyogenes <SEQ ID 4095> which encodes the amino acid sequence <SEQ ID 4096>. Analysis of this protein sequence reveals the following: TABLE-US-07125 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2600(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-07126 Identities = 186/237 (78%), Positives = 214/237 (89%) Query: 10 DPVKHNLIFERFLNEERYSMPDIDIDLPDIYRGEFLRYVRNRYGSMHSAQIVTFSTFGAK 69 - DPV+H+L+FERFLN+ERYSMPDIDIDLPDIYR EFLRYVRNRYGS HSAQIVTFSTFG K Sbjct: 321 DPVQHDLLFERFLNKERYSMPDIDIDLPDIYRSEFLRYVRNRYGSDHSAQIVTFSTFGPK 38- 0 Query: 70 QAIRDVFKRFGASEYELTNITKKIHFRDNLTSVYNRNLAFRQIIDSKIEYQKAYDIAKRI 129- QAIRDVFKRFG EYELTN+TKKI F+D+L +VY ++++FRQ+I+S+ E+QKA+ IAKRI Sbjct: 381 QAIRDVFKRFGVPEYELTNLTKKIGFKDSLATVYEKSISFRQVINSRTEFQKAFAIAKRI 44- 0 Query: 130 EGNPRQTSIHAAGVVMSDDLLTDHIPLKNGEDMMITQYDASSVEDNGLLKMDFLGLRNLT 18- 9 EGNPRQTSIHAAG+VMSDD LT+HIPLK+G+DMMITQYDA +VE NGLLKMDFLGLRNLT Sbjct: 441 EGNPRQTSIHAAGIVMSDDALTNHIPLKSGDDMMITQYDAHAVEANGLLKMDFLGLRNLT 50- 0 Query: 190 FVQKMKEKVDKDYGISIQLETIDLEDKETLKLFAAGQTKGIFQFEQSGAINLLRRIR 246 FVQKM+EKV KDYG I + IDLED +TL LFA G TKGIFQFEQ+GAINLL+RI+ Sbjct: 501 FVQKMQEKVAKDYGCQIDITAIDLEDPQTLALFAKGDTKGIFQFEQNGAINLLKRIK 557 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2344 A DNA sequence (GBSx2498) was identified in S. agalactiae <SEQ ID 7181> which encodes the amino acid sequence <SEQ ID 7182>. This protein is predicted to be a methylase. Analysis of this protein sequence reveals the following: TABLE-US-07127 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2121(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07128 >GP: AAG21729 GB: AF116907 putative methylase [Corynebacterium hoagii] Identities = 48/160 (30%), Positives = 85/160 (53%), Gaps = 6/160 (3%) Query: 97 EPDDSENGHNDTDLEETDNQIPEEEVVETIPEIPVTDFYFPEDLTDFYPKTARDKVETNI 156- EP+ + E + + ++E +P TDF D+ P A+ +V NI Sbjct: 1236 EPEAPTQPEAASAAETAEPAVEQQEPRAGPQSVPATDFALGTDV--HVPSGAKARVRANI 1- 293 Query: 157 VAIRLVKNLEVEHRNASPSEQELLAKYVGWGGLANEFFDD---YNPKFSKEREELKSLVT 21- 3 A RLV L+ + R A+ EQ +LA++ GWG + E FD+ + +++ ER L L+ Sbjct: 1294 AAARLVLELDEQQRPATAEEQAVLAQWSGWGAVP-EVFDNRSKFLSEWADERAALLDLLG 1- 352 Query: 214 DKEYSDMKQSSLTAYYTDPSLIRQMWGIVERDGFTGWQIL 253 +K +S ++++L A+YTDP+++ ++W V+R G +L Sbjct: 1353 EKGFSQARETTLNAHYTDPAIVGELWRAVQRAGLPDGALL 1392 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2345 A DNA sequence (GBSx2499) was identified in S. agalactiae <SEQ ID 7183> which encodes the amino acid sequence <SEQ ID 7184>. Analysis of this protein sequence reveals the following: TABLE-US-07129 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1111(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2346 A DNA sequence (GBSx2501) was identified in S. agalactiae <SEQ ID 7185> which encodes the amino acid sequence <SEQ ID 7186>. Analysis of this protein sequence reveals the following: TABLE-US-07130 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4752(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07131 >GP: CAA61516 GB: X89232 DNA-directed RNA polymerase [Pediococcus acidilactici] Identities = 48/53 (90%), Positives = 52/53 (97%) Query: 5 KKPETINYRTLKPEREGLFDEVIFGPTKDWECACGKYKRIRYKGIICDRCGVE 57 KKPETINYRTLKPE++GLFDE IFGPTKD+ECACGKYKRIRYKGI+CDRCGVE Sbjct: 29 KKPETINYRTLKPEKDGLFDERIFGPTKDYECACGKYKRIRYKGIVCDRCGVE 81 There is also homology to SEQ ID 384. Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2347 A DNA sequence (GBSx2502) was identified in S. agalactiae <SEQ ID 7187> which encodes the amino acid sequence <SEQ ID 7188>. Analysis of this protein sequence reveals the following: TABLE-US-07132 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3080(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07133 >GP: AAC00282 GB: AF008220 YtlR [Bacillus subtilis] Identities = 61/216 (28%), Positives = 98/216 (45%), Gaps = 28/216 (12%) Query: 8 IPCTYYPVGSGNDFARALKIPNL---------KETLTAIQTERLKEINCFIYDKGLIL-- 56 I ++ P G+ NDF+R I + K LT +T L +N F+ DK IL Sbjct: 86 IELSFVPAGAYNDFSRGFSIKKIDLIQEIKKVKRPLT--RTFHLGSVN-FLQDKSQILYF 142- Query: 57 -NSLDLGFAAYVVWKASNSKIKNILNRYRLGKITYIVIAIKSLLHSSK------VQVLVE 109- N + +GF AYV KA ++ + RL + Y + S LH+S + E Sbjct: 143 MNHIGIGFDAYVNKKAMEFPLRRVFLFLRLRFLVYPL----SHLHASATFKPFTLACTTE 19- 8 Query: 110 GETGQQIKLNDLYFFALANNTYFGGGITIWPKASALTAELDMVYAKGHTFLKRLSILLSL 16- 9 ET + +D++F ++N+ ++GGG+ P A+ D+V + FLK+ +L + Sbjct: 199 DETRE---FHDVWFAVVSNHPFYGGGMKAAPLANPREKTFDIVIVENQPFLKKYWLLCLM 25- 5 Query: 170 VFKRHTTSKSIKHQTFKAMTVYFPKNSLIEIDGEIV 205 F +HT + K +T Y DGEI+ Sbjct: 256 AFGKHTKMDGVTMFKAKDITFYTKDKIPFHADGEIM 291 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2348 A DNA sequence (GBSx2503) was identified in S. agalactiae <SEQ ID 7189> which encodes the amino acid sequence <SEQ ID 7190>. This protein is predicted to be protease subunit HflC (hflC). Analysis of this protein sequence reveals the following: TABLE-US-07134 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1809(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07135 >GP: AAG08326 GB: AE004907 protease subunit HflC [Pseudomonas aeruginosa] Identities = 182/202 (90%), Positives = 194/202 (95%) Query: 1 MSQTERAVLLQFGKVVQTDVKPGLHVKVPYVNQVRKFDGRLLTLDAPTQRFLTLEKKAVM 60 + QTERAV+L+FG+VV++DVKPGLH K+PYVNQVRKFD RLLTLDAPTQRFLTLEKKAVM Sbjct: 26 VQQTERAVMLRFGRVVESDVKPGLHFKIPYVNQVRKFDARLLTLDAPTQRFLTLEKKAVM 85 Query: 61 VDAYAKWRVKDAERFYTATSGLKQIADERLSRRLESGLRDQFGKRTLHEVVSGERDALMA 120- VDAYAKWRV DAERFYTATSGLKQIADERLSRRLE+GLRDQFGKRTLHEVVSGERDALM Sbjct: 86 VDAYAKWRVADAERFYTATSGLKQIADERLSRRLEAGLRDQFGKRTLHEVVSGERDALMG 145- Query: 121 DITGSLNRMAEKELGIEVLDVRVKAIDLPKEVNRSVFERMSTEREREAREHRAKGNELGE 18- 0 DIT SLNRMA+KELGIEV+DVRVKAIDLPKEVNRSVFERMSTEREREAREHRAKG EL E Sbjct: 146 DITASLNRMAQKELGIEVIDVRVKAIDLPKEVNRSVFERMSTEREREAREHRAKGRELAE 20- 5 Query: 181 GIRADADRQRRVLLAEAYRESE 202 GIRADADRQRRV++AEAYRESE Sbjct: 206 GIRADADRQRRVIVAEAYRESE 227 No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2349 A DNA sequence (GBSx2504) was identified in S. agalactiae <SEQ ID 7191> which encodes the amino acid sequence <SEQ ID 7192>. Analysis of this protein sequence reveals the following: TABLE-US-07136 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2350 A DNA sequence (GBSx2505) was identified in S. agalactiae <SEQ ID 7193> which encodes the amino acid sequence. <SEQ ID 7194>. This protein is predicted to be ABC transporter (ATP-binding; daunorubicin resistance). Analysis of this protein sequence reveals the following: TABLE-US-07137 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1846(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07138 >GP: CAB15892 GB: Z99123 similar to ABC transporter (ATP-binding protein) [Bacillus subtilis] Identities = 88/231 (38%), Positives = 132/231 (57%), Gaps = 13/231 (5%) Query: 10 QVIGYLPDVPKFYDYMTAQEYLQLC---AGLAQNKTSLPIADLLEQVGLADN-QQRISTY 65 - ++IGYLP P FY +MTA E+L +GL++ K I ++LE VGL + +RI Y Sbjct: 69 RLIGYLPQYPAFYSWMTANEFLTFAGRLSGLSKRKCQEKIGEMLEFVGLHEAAHKRIGGY 128- Query: 66 SRGMKQRLGLAQALIHXXKILICDEPTSALDPQGRQEILSIISQLRGQKTVIFSTHILSD 125- S GMKQRLGLAQAL+H K LI DEP SALDP GR E+L ++ +L+ V+FSTH+L D Sbjct: 129 SGGMKQRLGLAQALLHKPKFLILDEPVSALDPTGRFEVLDMMRELKKHMAVLFSTHVLHD 18- 8 Query: 126 VEKVCDQVLILTKSGIH---NLEDLRDKASASVNQLNLLIKVSDNEAQKLALRFPLNQKD 18- 2 E+VCDQV+I+ I L++L+ + +V L++ K+ +K + + + Sbjct: 189 AEQVCDQVVIMKNGEISWKGELQELKQQQQTNVFTLSVKEKLEGWLEEKPYVSAIVYKNP 24- 8 Query: 183 QYYKVHLELSEANNREQALASFYRYLVEQEITPYFIELLEDSLEDFYLEVI 233 + EL + + L+ + + +T E +SLED YL+V+ Sbjct: 249 S--QAVFELPDIHAGRSLLSD----CIRKGLTVTRFEQKTESLEDVYLKVV 293 There is also homology to SEQ ID 686. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2351 A DNA sequence (GBSx2506) was identified in S. agalactiae <SEQ ID 7195> which encodes the amino acid sequence <SEQ ID 7196>. Analysis of this protein sequence reveals the following: TABLE-US-07139 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0679(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has homology with glycine-rich cell wall proteins (e.g. GB:AL161589--the glycine-rich cell wall protein from Arabidopsis thaliania) and to SEQ ID 6882. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2352 A DNA sequence (GBSx2507) was identified in S. agalactiae <SEQ ID 7197> which encodes the amino acid sequence <SEQ ID 7198>. Analysis of this protein sequence reveals the following: TABLE-US-07140 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2890(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2353 A DNA sequence (GBSx2508) was identified in S. agalactiae <SEQ ID 7199> which encodes the amino acid sequence <SEQ ID 7200>. Analysis of this protein sequence reveals the following: TABLE-US-07141 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2410(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9329> which encodes amino acid sequence <SEQ ID 9330> was also identified. The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. SEQ ID 9330 (GBS678) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 163 (lane 18; MW 53 kDa), FIG. 164 (lane 2 & 3; MW 53 kDa) and FIG. 188 (lane 7; MW 53 kDa). Purified protein is shown in FIG. 242, lanes 6 & 7. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2354 A DNA sequence (GBSx2509) was identified in S. agalactiae <SEQ ID 7201> which encodes the amino acid sequence <SEQ ID 7202>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-07142 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2025(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2355 A DNA sequence (GBSx2510) was identified in S. agalactiae <SEQ ID 7203> which encodes the amino acid sequence <SEQ ID 7204>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-07143 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1892(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2356 A DNA sequence (GBSx2511) was identified in S. agalactiae <SEQ ID 7205> which encodes the amino acid sequence <SEQ ID 7206>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-07144 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1892(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2357 A DNA sequence (GBSx2512) was identified in S. agalactiae <SEQ ID 7207> which encodes the amino acid sequence <SEQ ID 7208>. Analysis of this protein sequence reveals the following:

TABLE-US-07145 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0999(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2358 A DNA sequence (GBSx2514) was identified in S. agalactiae <SEQ ID 7209> which encodes the amino acid sequence <SEQ ID 7210>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-07146 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1892(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2359 A DNA sequence (GBSx2515) was identified in S. agalactiae <SEQ ID 7211> which encodes the amino acid sequence <SEQ ID 7212>. Analysis of this protein sequence reveals the following: TABLE-US-07147 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2041(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> The protein has no significant homology with any sequences in the GENPEPT database. No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2360 A DNA sequence (GBSx2516) was identified in S. agalactiae <SEQ ID 7213> which encodes the amino acid sequence <SEQ ID 7214>. This protein is predicted to be 30S ribosomal protein S6 (rpsF). Analysis of this protein sequence reveals the following: TABLE-US-07148 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3607(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> A related GBS nucleic acid sequence <SEQ ID 9423> which encodes amino acid sequence <SEQ ID 9424> was also identified. The protein has homology with the following sequences in the GENPEPT database. TABLE-US-07149 >GP: CAB16128 GB: Z99124 ribosomal protein S6 (BS9) [Bacillus subtilis] Identities = 41/72 (56%), Positives = 58/72 (79%), Gaps = 1/72 (1%) Query: 1 MVARFDSILSDNGATVVESKDWEKRRLAYEIQDFTEGLYHIVNVEAEDAVALNEFDRLSK 60 ++ RF+++L+ NGA + +KDW KRRLAYEI DF +G Y IVNV++ DA A+ EFDRL+K Sbjct: 22 VIERFNNVLTSNGAEITGTKDWGKRRLAYEINDFRDGFYQIVNVQS-DAAAVQEFDRLAK 80 Query: 61 INGDILRHMIVK 72 I+ DI+RH++VK Sbjct: 81 ISDDIIRHIVVK 92 A related DNA sequence was identified in S. pyogenes <SEQ ID 7215> which encodes the amino acid sequence <SEQ ID 7216>. Analysis of this protein sequence reveals the following: TABLE-US-07150 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2720(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> An alignment of the GAS and GBS proteins is shown below. TABLE-US-07151 Identities = 66/74 (89%), Positives = 70/74 (94%) Query: 1 MVARFDSILSDNGATVVESKDWEKRRLAYEIQDFTEGLYHIVNVEAEDAVALNEFDRLSK 60 +VARFDSIL+DNGATVVESKDWEKRRLAYEI DF EGLYHIVN+EA DA ALNEFDRLSK Sbjct: 22 LVARFDSILTDNGATVVESKDWEKRRLAYEINDFREGLYHIVNLEATDAAALNEFDRLSK 81 Query: 61 INGDILRHMIVKVD 74 INGDILRHMIVK+D Sbjct: 82 INGDILRHMIVKLD 95 Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2361 A DNA sequence (GBSx2518) was identified in S. agalactiae <SEQ ID 7219> which encodes the amino acid sequence <SEQ ID 7220>. This protein is predicted to be surface protein Rib. Analysis of this protein sequence reveals the following: TABLE-US-07152 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5289(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. pyogenes. Based on this analysis, it was predicted that this protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2362 A DNA sequence (GASx1R) was identified in S. pyogenes <SEQ ID 7221> which encodes the amino acid sequence <SEQ ID 7222>. Analysis of this protein sequence reveals the following: TABLE-US-07153 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2363 A DNA sequence (GASx5R) was identified in S. pyogenes <SEQ ID 7223> which encodes the amino acid sequence <SEQ ID 7224>. Analysis of this protein sequence reveals the following: TABLE-US-07154 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2364 A DNA sequence (GASx11) was identified in S. pyogenes <SEQ ID 7225> which encodes the amino acid sequence <SEQ ID 7226>. Analysis of this protein sequence reveals the following: TABLE-US-07155 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2614(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2365 A DNA sequence (GASx17) was identified in S. pyogenes <SEQ ID 7227> which encodes the amino acid sequence <SEQ ID 7228>. Analysis of this protein sequence reveals the following: TABLE-US-07156 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2849(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2366 A DNA sequence (GASx18) was identified in S. pyogenes <SEQ ID 7229> which encodes the amino acid sequence <SEQ ID 7230>. Analysis of this protein sequence reveals the following: TABLE-US-07157 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2099(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2367 A DNA sequence (GASx34) was identified in S. pyogenes <SEQ ID 7231> which encodes the amino acid sequence <SEQ ID 7232>. Analysis of this protein sequence reveals the following: TABLE-US-07158 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0801(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2368 A DNA sequence (GASx38) was identified in S. pyogenes <SEQ ID 7233> which encodes the amino acid sequence <SEQ ID 7234>. Analysis of this protein sequence reveals the following: TABLE-US-07159 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07160 >GP: CAB12617 GB: Z99108 similar to protein-tyrosine phosphatase [Bacillus subtilis] Identities = 57/155 (36%), Positives = 88/155 (56%), Gaps = 12/155 (7%) Query: 1 MKKVCFVCLGNICRSPMAEFVMKSIVS----SDVMMIESRATSDWEHGNPIHSGTQSILK 56 M V FVCLGNICRSPMAE + + + + + +S W GNP H GTQ IL+ Sbjct: 1 MISVLFVCLGNICRSPMAEAIFRDLAAKKGLEGKIKADSAGIGGWHIGNPPHEGTQEILR 60 Query: 57 TYQINYDITKCSKQITITDFNTFDYIIGMDSDNVKNLKEMSQHQWDSKIYLFRE------ 110- I++D ++Q++ D + FDYII MD++N+ +L+ M+ + S I + Sbjct: 61 REGISFD-GMLARQVSEQDLDDFDYIIAMDAENIGSLRSMAGFKNTSHIKRLLDYVEDSD 119- Query: 111 -GGVPDPWYTNDFEETYQLVRKGCQDWLSRLMSKE 144 VPDP+YT +FEE QL++ GC+ L+ + ++ Sbjct: 120 LADVPDPYYTGNFEEVCQLIKTGCEQLLASIQKEK 154 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2369 A DNA sequence (GASx42R) was identified in S. pyogenes <SEQ ID 7235> which encodes the amino acid sequence <SEQ ID 7236>. Analysis of this protein sequence reveals the following: TABLE-US-07161 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4753(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2370 A DNA sequence (GASx47R) was identified in S. pyogenes <SEQ ID 7237> which encodes the amino acid sequence <SEQ ID 7238>. Analysis of this protein sequence reveals the following: TABLE-US-07162 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2014(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2371 A DNA sequence (GASx53R) was identified in S. pyogenes <SEQ ID 7239> which encodes the amino acid sequence <SEQ ID 7240>. Analysis of this protein sequence reveals the following: TABLE-US-07163 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.11 Transmembrane 56-72 (56-72) ----- Final Results ----- bacterial membrane --- Certainty = 0.1044(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2372 A DNA sequence (GASx67R) was identified in S. pyogenes <SEQ ID 7241> which encodes the amino acid sequence <SEQ ID 7242>. Analysis of this protein sequence reveals the following: TABLE-US-07164 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1610(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2373 A DNA sequence (GASx75) was identified in S. pyogenes <SEQ ID 7243> which encodes the amino acid sequence <SEQ ID 7244>. Analysis of this protein sequence reveals the following: TABLE-US-07165 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2803(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07166 >GP: CAA41942 GB: X59250 ribosomal protein B [Lactococcus lactis] Identities = 37/38 (97%), Positives = 37/38 (97%) Query: 1 MKVRPSVKPICEYCKVIRRNGRVMVICPTNPKHKQRQG 38 MKVRPSVKPICEYCKVIRRNGRVMVICP NPKHKQRQG Sbjct: 1 MKVRPSVKPICEYCKVIRRNGRVMVICPANPKHKQRQG 38 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2374 A DNA sequence (GASx76) was identified in S. pyogenes <SEQ ID 7245> which encodes the amino acid sequence <SEQ ID 7246>. Analysis of this protein sequence reveals the following: TABLE-US-07167 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0824(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07168 >GP: AAB06824 GB: L47971 ribosomal protein S13 [Bacillus subtilis] Identities = 86/121 (71%), Positives = 103/121 (85%) Query: 1 MARIAGVDIPNDKRVVISLTYVYGIGLATSKKILAAAGISEDIRVKDLTSDQEDAIRREV 60 MARIAGVDIP DKRVVISLTY++GIG T++++L AG+SED RV+DLT ++ IR + Sbjct: 1 MARIAGVDIPRDKRVVISLTYIFGIGRTTAQQVLKEAGVSEDTRVRDLTEEELGKIRDII 60 Query: 61 DAIKVEGDLRREVNMNIKRLMEIGSYRGIRHRRGLPVRGQNTKNNARTRKGKAVAIAGKKK 12- 1 D +KVEGDLRREV++NIKRL+EIGSYRGIRHRRGLPVRGQN+KNNARTRKG +A KKK Sbjct: 61 DKLKVEGDLRREVSLNIKRLIEIGSYRGIRHRRGLPVRGQNSKNNARTRKGPRRTVANKKK 12- 1 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2375 A DNA sequence (GASx81R) was identified in S. pyogenes <SEQ ID 7247> which encodes the amino acid sequence <SEQ ID 7248>. Analysis of this protein sequence reveals the following: TABLE-US-07169 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1842(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2376 A DNA sequence (GASx82) was identified in S. pyogenes <SEQ ID 7249> which encodes the amino acid sequence <SEQ ID 7250>. Analysis of this protein sequence reveals the following:

TABLE-US-07170 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3613(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2377 A DNA sequence (GASx83) was identified in S. pyogenes <SEQ ID 7251> which encodes the amino acid sequence <SEQ ID 7252>. Analysis of this protein sequence reveals the following: TABLE-US-07171 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1141(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2378 A DNA sequence (GASx85) was identified in S. pyogenes <SEQ ID 7253> which encodes the amino acid sequence <SEQ ID 7254>. Analysis of this protein sequence reveals the following: TABLE-US-07172 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2280(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2379 A DNA sequence (GASx89R) was identified in S. pyogenes <SEQ ID 7255> which encodes the amino acid sequence <SEQ ID 7256>. Analysis of this protein sequence reveals the following: TABLE-US-07173 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3040(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2380 A DNA sequence (GASx102) was identified in S. pyogenes <SEQ ID 7257> which encodes the amino acid sequence <SEQ ID 7258>. Analysis of this protein sequence reveals the following: TABLE-US-07174 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.75 Transmembrane 21-37 (12-41) ----- Final Results ----- bacterial membrane --- Certainty = 0.6498(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07175 >GP: AAC45312 GB: U81957 ComYC [Streptococcus gordonii] Identities = 59/104 (56%), Positives = 85/104 (81%), Gaps = 1/104 (0%) Query: 6 NNLRHKKLKGFTLLEMLLVILVISVLMLLFVPNLSKQKDRVTETGNAAVVKLVENQAELY 65 N L+ ++K FTL+EML+V+L+ISVLMLLFVPNL+KQK+ V++TGNAAVVK+VE+QAELY Sbjct: 2 NKLKKLRVKAFTLVEMLVVLLIISVLMLLFVPNLTKQKEAVSDTGNAAVVKVVESQAELY 61 Query: 66 EL-SQGSKPSLSQLKADGSITEKQEKAYQDYYDKHKNEKARLSN 108 EL + G + +LS+L A G+I++KQ +Y+ YY K+ +E ++N Sbjct: 62 ELKNTGDQATLSKLVAAGNISQKQADSYKAYYGKNNSETQAVAN 105 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2381 A DNA sequence (GASx103) was identified in S. pyogenes <SEQ ID 7259> which encodes the amino acid sequence <SEQ ID 7260>. Analysis of this protein sequence reveals the following: TABLE-US-07176 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07177 >GP: AAC23740 GB: AF052207 competence protein [Streptococcus pneumoniae] Identities = 52/131 (39%), Positives = 76/131 (57%) Query: 8 IKAFTLLETLLSLSVMSFIILGLSVPVTKSYQKVEEHLFFSHFEHLYRHQQKLAILQQKQ 67 IKAFT+LE+LL L ++S + LGLS V ++ VEE +FF FE LYR QK ++ Q++ Sbjct: 2 IKAFTMLESLLVLGLVSILALGLSGSVQSTFSAVEEQIFFMEFEELYRETQKRSVASQQK 61 Query: 68 RVLDISSTKIVTEGNSLTVPKSITVNHPYRLVIDQMGGNHSLAKIIFDMTDRRFKYQFYL 127- L++ I LTVPK I + D+ GGN SLAK+ F + +YQ YL Sbjct: 62 TSLNLDGQMISNGSQKLTVPKGIQAPSGQSITFDRAGGNSSLAKVEFQTSKGAIRYQLYL 121- Query: 128 GSGNYQKTSQS 138 G+G ++ ++ Sbjct: 122 GNGKIKRIKET 132 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2382 A DNA sequence (GASx104) was identified in S. pyogenes <SEQ ID 7261> which encodes the amino acid sequence <SEQ ID 7262>. Analysis of this protein sequence reveals the following: TABLE-US-07178 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2383 A DNA sequence (GASx109) was identified in S. pyogenes <SEQ ID 7265> which encodes the amino acid sequence <SEQ ID 7266>. Analysis of this protein sequence reveals the following: TABLE-US-07179 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.51 Transmembrane 37-53 (28-58) INTEGRAL Likelihood = -3.56 Transmembrane 61-77 (60-77) ----- Final Results ----- bacterial membrane --- Certainty = 0.5203(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2384 A DNA sequence (GASx115R) was identified in S. pyogenes <SEQ ID 7267> which encodes the amino acid sequence <SEQ ID 7268>. Analysis of this protein sequence reveals the following: TABLE-US-07180 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.09 Transmembrane 20-36 (13-40) ----- Final Results ----- bacterial membrane --- Certainty = 0.5437(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2385 A DNA sequence (GASx124) was identified in S. pyogenes <SEQ ID 7269> which encodes the amino acid sequence <SEQ ID 7270>. Analysis of this protein sequence reveals the following: TABLE-US-07181 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.17 Transmembrane 31-47 (29-59) INTEGRAL Likelihood = -5.63 Transmembrane 737-753 (734-756) ----- Final Results ----- bacterial membrane --- Certainty = 0.4270(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07182 >GP: AAC97148 GB: U49397 Cpa [Streptococcus pyogenes] Identities = 401/737 (54%), Positives = 517/737 (69%), Gaps = 25/737 (3%) Query: 25 SKNSKR--FTVTLVGVFLMIFALVTSMVGAKTVFGLVESSTPNAINPDSSSEYRWYGYES 82 - S N+KR T+ L+ VFL AL+ + + FG E S PN S +Y WYGY+S Sbjct: 11 SANNKRRQTTIGLLKVFLTFVALIGIVGFSIRAFGAEEQSVPN--RQSSIQDYPWYGYDS 68 Query: 83 YVRGHPYYKQFRVAHDLRVNLEGSRSYQVYCFNLKKAFPLGSDSSVKKWYKKHDGISTKF 142- Y +G+P Y + H+L+VNLEGS+ YQ YCFNL K FP SDS +WYKK +G + F Sbjct: 69 YPKGYPDYSPLKTYHNLKVNLEGSKDYQAYCFNLTKHFPSKSDSVRSQWYKKLEGTNENF 128- Query: 143 EDYAMSPRITGDELNQKLRAVMYNGHPQNANGIMEGLEPLNAIRVTQEAVWYYSDNAPIS 20- 2 A PRI +L Q + ++YNG+P N NGIM+G++PLNAI VTQ A+W Y+D+A I Sbjct: 129 IKLADKPRIEDGQLQQNILRILYNGYPNNRNGIMKGIDPLNAILVTQNAIW-YTDSAQI- 18- 6 Query: 203 NPDESFKRESESNLVSTSQLSLMRQALKQLIDPNLATKMPKQVPDDFQLSIFESEDKGDK 26- 2 NPDESFK E+ SN ++ QL LMR+ALK+LIDPNL +K + P ++L++FES D Sbjct: 187 NPDESFKTEARSNGINDQQLGLMRKALKELIDPNLGSKYSNKTPSGYRLNVFESHD---- 24- 2 Query: 263 YNKGYQNLLSGGLVPTKPPTPGDPPMPPNQPQTTSVLIRKYAIGDYSKLLEGATLQLTGD 32- 2 K +QNLLS VP PP PG+ PP + + TSV+IRKYA GD SKLLEGATL+L+ Sbjct: 243 --KPFQNLLSAEYVPDTPPKPGEE--PPAKTEKTSVIIRKYAEGD-SKLLEGATLKLSQI 29- 7 Query: 323 NVNSFQARVFSSNDIGERIELSDGTYTLTELNSPAGYSIAEPITFKVEAGKVYTI-IDGK 38- 1 + FQ + F SN +GE +EL +GTYTLTE +SP GY IAEPI F+VE KV+ + DG Sbjct: 298 EGSGFQEKDFQSNSLGETVELPNGTYTLTETSSPDGYKIAEPIKFRVENKKVFIVQKDGS 35- 7 Query: 382 QIENPNKEIVEPYSVEAYNDFEEFSVLT-TQNYAKFYYAKNKNGSSQVVYCFNADLKSPP 44- 0 Q+ENPNKE+ EPYSVEAYNDF + VL+ Y KFYYA NK+ SSQVVYCFNADL SPP Sbjct: 358 QVENPNKEVAEPYSVEAYNDFMDEEVLSGFTPYGKFYYATNKDKSSQVVYCFNADLHSPP 41- 7 Query: 441 DSEDGGKTMTPDFTT-GEVKYTHIAGRDLFKYTVKPRDTDPDTFLKHIKKVIEKGYREKG 49- 9 DS D G+T+ PD +T EVKYTH AG DLFKY ++PRDT+P+ FLKHIKKVIEKGY++KG Sbjct: 418 DSYDSGETINPDTSTMKEVKYTHTAGSDLFKYALRPRDTNPEDFLKHIKKVIEKGYKKKG 47- 7 Query: 500 QAIEYSGLTETQLRAATQLAIYYFTDSAELDKDKL----KDYHGFGDMNDSTLAVAKILV 55- 5 + Y+GLTETQ RAATQLAIYYFTDSA+L K K YHGF M++ TLAV K L+ Sbjct: 478 DS--YNGLTETQFRAATQLAIYYFTDSADLKTLKTYNNGKGYHGFESMDEKTLAVTKELI 53- 5 Query: 556 EYAQDSNPPQLTDLDFFIPNNNKYQSLIGTQWHPEDLVDIIRMEDKK-EVIPVTHNLTLR 61- 4 YAQ+ + PQLT+LDFF+PNN+K QSLIGT+ HP+DLVD+IRMEDKK EVIPVTH+LT++ Sbjct: 536 TYAQNGSAPQLTNLDFFVPNNSKDQSLIGTECHPDDLVDVIRMEDKKQEVIPVTHSLTVK 59- 5 Query: 615 KTVTGLAGDRTKDFHFEIELKNNKQELLSQTVKTDKTNLEFKDGKATINLKHGESLTLQG 67- 4 KTV G GD+TK F FE+ELK+ + + T+KT+ +L KDGK + NLKHG+++ ++G Sbjct: 596 KTVVGELGDKTKGFQFELELKDKTGQPIVNTLKTNNQDLVAKDGKYSFNLKHGDTIRIEG 65- 5 Query: 675 LPEGYSYLVKETDSEGYKVKVNSQEVANATVSKTGITSDETLAFENNKEPVVPTGVDQKI 73- 4 LP GYSY +KE +++ Y V V+++ A IT D+ + FEN K+ V PTG+ Sbjct: 656 LPTGYSYTLKEAEAKDYIVTVDNKVSQEAQSVGKDITEDKKVTFENRKDLVPPTGLTTDG 71- 5 Query: 735 NGYLALIVIAGISLGIW 751 YL L+++ + L +W Sbjct: 716 AIYLWLLLLVPLGLLVW 732 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2386 A DNA sequence (GASx125R) was identified in S. pyogenes <SEQ ID 7271> which encodes the amino acid sequence <SEQ ID 7272>. Analysis of this protein sequence reveals the following: TABLE-US-07183 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2604(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2387 A DNA sequence (GASx126) was identified in S. pyogenes <SEQ ID 7273> which encodes the amino acid sequence <SEQ ID 7274>. Analysis of this protein sequence reveals the following: TABLE-US-07184 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1537(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07185 >GP: AAC97149 GB: U49397 LepA [Streptococcus pyogenes] Identities = 59/132 (44%), Positives = 84/132 (62%), Gaps = 5/132 (3%) Query: 1 MIIKRNDMAPSVKAGDAILFYRLSQTYKVEEAVVYEDSKTSITKVGRIIAQAGDEVDLTE 60 MII NDM+P++ AGD +L+YRL+ + + VVYE T KVGRI AQAGDEV+ T+ Sbjct: 42 MIINTNDMSPALSAGDGVLYYRLADRSHINDVVVYEVDNT--LKVGRIAAQAGDEVNFTQ 99 Query: 61 QGELKINGHIQNEG---LTFIKSREANYPYRIADNSYLILNDYYSQESENYLQDAIAKDA 117- +G L INGH + LT+ S N+PY++ +Y ILNDY + ++ A+ + Sbjct: 100 EGGLLINGHPPEKEVPYLTYPHSSGPNFPYKVPTGTYFILNDYREERLDSRYYGALPINQ 15- 9 Query: 118 IKGTINTLIRLR 129 IKG I+TL+R+R Sbjct: 160 IKGKISTLLRVR 171 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2388 A DNA sequence (GASx127) was identified in S. pyogenes <SEQ ID 7275> which encodes the amino acid sequence <SEQ ID 7276>. Analysis of this protein sequence reveals the following: TABLE-US-07186 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -3.93 Transmembrane 312-328 (311-337) ----- Final Results ----- bacterial membrane --- Certainty = 0.2572(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07187 >GP: AAC97152 GB: U49397 unknown [Streptococcus pyogenes] Identities = 125/355 (35%), Positives = 191/355 (53%), Gaps = 26/355 (7%) Query: 1 MKLRHLLLTGAALTSFA-----ATTVHGET--VVNGAKLTVTKNL-DLVNSNALIPNTDF 52 MK LLL A L + + + ET V++G+ L V K + N L+P D+ Sbjct: 1 MKKNKLLLATAILATALGMASMSQNIKAETAGVIDGSTLVVKKTFPSYTDDNVLMPKADY 60 Query: 53 TFKIEPDTTVN---EDGNKFK-GVALNTPMTK-VTYTNSDKGGSNTKTAEFDFSEVTFEK 107- +FK+E D +DG K GV TK + Y+NSDK + K+ F+F+ V F Sbjct: 61 SFKVEADDNAKGKTKDGLDIKPGVIDGLENTKTIRYSNSDKITAKEKSVNFEFANVKFPG 120- Query: 108 PGVYYYKVTEEKIDKVPGVSYDTTSYTVQVHVLWNEEQQKPVATYIVGYKEGS--KVPIQ 16- 5 GVY Y V E +K G++YD+ +TV V+V+ N+E YIV + G K P+ Sbjct: 121 VGVYRYTVAEVNGNKA-GITYDSQQWTVDVYVV-NKEGGGFEVKYIVSTEVGQSEKKPVL 17- 8 Query: 166 FKNSLDSTTLTVKKKVSGTGGDRSKDFNFGLTLKANQYYKASEKVMIEKTTKGGQAPVQT 22- 5 FKNS D+T+L ++K+V+G G+ + F+F L L N+ + EK + +GG+ Sbjct: 179 FKNSFDTTSLKIEKQVTGNTGEHQRLFSFTLLLTPNECF---EKGQVVNILQGGETK--- 23- 2 Query: 226 EASIDQLYHFTLKDGESIKVTNLPVGVDYVVTEDDYKSEKYTTNVEVSPQDGAVKNIAGN 28- 5 + I + Y FTLKD S+ ++ LPVG++Y +TE+D + Y T+ + + + G Sbjct: 233 KVVIGEEYSFTLKDKGSVTLSQLPVGIEYKLTEEDVTKDGYKTSATLKDGEQSSTYELGK 29- 2 Query: 286 STEQETSTDKDMTITFTNKKDFEVPTGVAMTVAPYIALGIVAVGGALYFVKKKNA 340 + + S D+ I TNK+D +VPTGV T+AP+ L IVA+GG +Y K+K A Sbjct: 293 DHKTDKSADE---IVVTNKRDTQVPTGVVGTLAPFAVLSIVAIGGVIYITKRKKA 344 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2389 A DNA sequence (GASx128) was identified in S. pyogenes <SEQ ID 7277> which encodes the amino acid sequence <SEQ ID 7278>. Analysis of this protein sequence reveals the following: TABLE-US-07188 Possible site: 44 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-07189 >GP: AAC97152 GB: U49397 unknown [Streptococcus pyogenes] Identities = 115/240 (47%), Positives = 178/240 (73%), Gaps = 3/240 (1%) Query: 1 MIVRLIKLLDKLINVIVLCFFFLCLLIAALGIYDALTVYQGANATNYQQYKKKGVQ--FD 58 M++ ++++++K I+ ++L F + L +A G++D+ +YQ A+A+N++++K Q F+ Sbjct: 351 MMMTIVQVINKAIDTLILIFCLVVLFLAGFGLWDSYHLYQQADASNFKKFKTAQQQPKFE 41- 0 Query: 59 DLLAINSDVMAWLTVKGTHIDYPIVQGENNLEYINKSVEGEYSLSGSVFLDYRNKVTFED 118- DLLA+N DV+ WL + GTHIDYP+VQG+ NLEYINK+V+G ++SGS+FLD RN F D Sbjct: 411 DLLALNEDVIGWLNIPGTHIDYPLVQGKTNLEYINKAVDGSVAMSGSLFLDTRNHNDFTD 47- 0 Query: 119 KYSLIYAHHMAGNVMFGELPNFRKKSFFNKHKEFSIETKTKQKLKINIFACIQTDAFDSL 17- 8 YSLIY HHMAGN MFGE+P F KK+FFNKH + IETK ++KL + IFAC++TDAFD L Sbjct: 471 DYSLIYGHHMAGNAMFGEIPKFLKKNFFNKHNKAIIETKERKKLTVTIFACLKTDAFDQL 53- 0 Query: 179 LFNPIDV-DISSKNEFLNHIKQKSVQYREILTTNESRFVALSTCEDMTTDGRIIVIGQIE 23- 7 +FNP + + + + +++I ++S Q++ + + ++FVA STCE+ +TD R+IV+G I+ Sbjct: 531 VFNPNAITNQDQQRQLVDYISKRSKQFKPVKLKHHTKFVAFSTCENFSTDNRVIVVGTIQ 59- 0 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2390 A DNA sequence (GASx129) was identified in S. pyogenes <SEQ ID 7279> which encodes the amino acid sequence <SEQ ID 7280>. Analysis of this protein sequence reveals the following: TABLE-US-07190 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.05 Transmembrane 5-21 (4-22) INTEGRAL Likelihood = -5.04 Transmembrane 191-207 (186-209) ----- Final Results ----- bacterial membrane --- Certainty = 0.3421(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial --- cytoplasm Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 181-186 No corresponding DNA sequence was identified in S. agalactiae. TABLE-US-07191 >GP: AAC97151 GB: U49397 unknown [Streptococcus pyogenes] Identities = 64/213 (30%), Positives = 106/213 (49%), Gaps = 20/213 (9%) Query: 1 MKKSILRILAIGYLLMSFCLLDSVEAENLTASINIEVINQVDVATNKQSSDIDETFMFVI 60 M+K + ++ +L +V A++ T +I V N ++ A + F + Sbjct: 1 MRKYWKMLFSVVMMLTMLAFNQTVLAKDSTVQTSISVENVLERAGDSTP------FSIAL 54 Query: 61 EALDKESPLPNSVTTSVKGNGKTSFEQLTFSEVGQYHYKIHQLLGKNSQYHYDETVYEVV 120- E++D + ++ G+GK SF L F+ VGQY Y+++Q +N Y D TV++V+ Sbjct: 55 ESIDAMKTIEE---ITIAGSGKASFSPLNFTTVGQYTYRVYQKPSQNKDYQADTTVFDVL 111- Query: 121 IYVLYNEQSGALETNLVSNKLGETEKSELIFKQEYSEKTPEPHQPDTTEKEKPQKKRNGI 18- 0 +YV Y+E G L ++S + G+ EKS + FK + K P QPD + Sbjct: 112 VYVTYDE-DGTLVAKVISRRAGDEEKSAITFKPKRLVKPIPPRQPDIPKTP--------- 16- 1 Query: 181 LPSTGEMVSYVSALGIVLVATITLYSIYKKLKT 213 LP GE+ S + L IVL+ + L + KKLK+ Sbjct: 162 LPLAGEVKSLLGILSIVLLGLLVLLYV-KKLKS 193 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2391 A DNA sequence (GASx130R) was identified in S. pyogenes <SEQ ID 7281> which encodes the amino acid sequence <SEQ ID 7282>. Analysis of this protein sequence reveals the following: TABLE-US-07192 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1614(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07193 >GP: CAB54046 GB: AJ245436 hypothetical protein, 57.8 kD [Pseudomonas putida] Identities = 128/388 (32%), Positives = 204/388 (51%), Gaps = 21/388 (5%) Query: 4 IGSVVQRQELVFIPAQLKRINHVQHAYKCQTCSDNSLSDKIIKAPVPKAPLAHSLGSASI 63 IG V Q L +P Q++ I HV+ Y C+ C ++ A P + S+ S S+ Sbjct: 126 IGEEVSEQ-LEIVPMQIRVIKHVRKVYGCRDCESAPVT-----ADKPAQMIEKSMASPSV 17- 9 Query: 64 IAHTVHQKFTLKVPNYRQEEDWNKLGLSISRKEIANWHIKSSQYYFEPLYDLLRDILLSQ 123- +A + K+ +P +R E+ + G+ I R+ +A W I+ S++ F+PL +L+R+ LL+ Sbjct: 180 LAMLLTTKYVDGLPLHRFEKVLGRHGIDIPRQTLARWVIQCSEH-FQPLLNLMRESLLNS 23- 8 Query: 124 EVIHADETSYRVLESD----TQLTYYWTFLSGKHEKKGITLYHHDKRRSGLVTQEVLGDY 17- 9 +IH DET +VL+ + ++ W G ++ + L+ + R+ V +L Y Sbjct: 239 RIIHCDETRVQVLKEPGREPSSQSWMWVQTGGPPDRP-VILFDYATSRAQEVPVRLLDGY 29- 7 Query: 180 SGYVHCDMHGAYRQL---EHAKLVGCWAHVRRKFFEATPKQAD-KTSLGRKGLVYCDKLF 23- 5 GYV D + Y L + + +GCWAH RRKF EA Q KT L +KL+ Sbjct: 298 RGYVMTDDYAGYNALAAQDGLERLGCWAHARRKFVEAQKVQPKGKTGRADIALNLINKLY 35- 7 Query: 236 ALEAEWCELPPQERLVKRKEILTPLMTTFFDWCR--EQVVLSGSKLGLAIAYSLKHERTF 29- 3 +E + + ++R V R E PL+T +W + V + + LG AI Y + Sbjct: 358 GVERDLKDSDDEDRKVARMERSLPLLTQLKNWVEKTQPQVTTQNALGKAIGYLASNWSKL 41- 7 Query: 294 RTVLEDGHIVLSNNMAERAIKSLVMGRKNWLFSQSFEGAKAAAIIMSLLETAKRHGLNSE 35- 3 +E G++ + NN AERAI+ V+GRKNWLFS + +GA A+A + SL+ETAK +G Sbjct: 418 ERYVEHGYLPMDNNAAERAIRPFVIGRKNWLFSDTPKGATASAQLYSLVETAKANGQEPY 47- 7 Query: 354 KYISYLLDRLPNEETLAKREVLEAYLPW 381 ++ + L+RLP ++ E EA LPW Sbjct: 478 AWLRHALERLPQACSV---EDYEALLPW 502 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2392 A DNA sequence (GASx131R) was identified in S. pyogenes <SEQ ID 7283> which encodes the amino acid sequence <SEQ ID 7284>. Analysis of this protein sequence reveals the following: TABLE-US-07194 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4465(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2393 A DNA sequence (GASx132R) was identified in S. pyogenes <SEQ ID 7285> which encodes the amino acid sequence <SEQ ID 7286>. Analysis of this protein sequence reveals the following: TABLE-US-07195 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1529(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07196 >GP: BAA84885 GB: AB024946 orf50 [Escherichia coli] Identities = 37/91 (40%), Positives = 53/91 (57%) Query: 10 QVYLVCGKTDMRQGIDSLAYLVKSQHELDLFSGAVYLFCGGRRDRFKALYWDGQGFWLLY 69 - +++LV G TDMR G + LA V++ + D FSG +++F G R D+ K L+ D G L Sbjct: 9 RIWLVAGITDMRNGFNGLASKVQNVLKDDPFSGHLFIFRGRRGDQIKVLWADSDGLCLFT 68 Query: 70 KRFENGKLAWPRNRDEVKCLTAVQVDWLMKG 100 KR E G+ WP RD LT Q+ L++G Sbjct: 69 KRLERGRFVWPVTRDGKVHLTPAQLSMLLEG 99 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2394 A DNA sequence (GASx133R) was identified in S. pyogenes <SEQ ID 7287> which encodes the amino acid sequence <SEQ ID 7288>. Analysis of this protein sequence reveals the following: TABLE-US-07197 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1979(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2395 A DNA sequence (GASx135R) was identified in S. pyogenes <SEQ ID 7289> which encodes the amino acid sequence <SEQ ID 7290>. Analysis of this protein sequence reveals the following: TABLE-US-07198 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2396 A DNA sequence (GASx136) was identified in S. pyogenes <SEQ ID 7291> which encodes the amino acid sequence <SEQ ID 7292>. Analysis of this protein sequence reveals the following: TABLE-US-07199 Possible site: 54 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.73 Transmembrane 222-238 (212-242) INTEGRAL Likelihood = -10.88 Transmembrane 37-53 (32-57) INTEGRAL Likelihood = -9.87 Transmembrane 462-478 (456-478) INTEGRAL Likelihood = -4.25 Transmembrane 119-135 (117-137) INTEGRAL Likelihood = -2.60 Transmembrane 308-324 (306-324) INTEGRAL Likelihood = -1.28 Transmembrane 164-180 (164-180) INTEGRAL Likelihood = -0.06 Transmembrane 137-153 (137-153) INTEGRAL Likelihood = -0.06 Transmembrane 343-359 (343-359) ----- Final Results ----- bacterial membrane --- Certainty = 0.5692(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07200 >GP: BAB04077 GB: AP001508 short-chain fatty acids transporter [Bacillus halodurans] Identities = 158/465 (33%), Positives = 248/465 (52%), Gaps = 41/465 (8%) Query: 15 IKTKKRFMDRYIDGFMKWMPESLFICFILTFLVVTMSVLMTDSPFIGTEKTGGIIYGWVN 74 - I R M RY+ P+ +LTFLV +S++ T+S T T I+ W Sbjct: 5 ISLSNRLMQRYL-------PDPFLFVVLLTFLVFALSLIFTES----TPLT--IVQYWGE 51 Query: 75 GFWGLLSFAMQMTILLATGNAVASSPPAHKMFKSLAKLPQTRTQIFIFSIVVGSIFGFLH 134- GFWGLLSF+MQM ++L TG+ +ASSP K +LA LP + Q + VV + F++ Sbjct: 52 GFWGLLSFSMQMVLVLVTGHVLASSPLFKKGLGALAGLPASPGQAILLVTVVSLVASFIN 111- Query: 135 WGLGMMVAIVFGKELLVQARQKGIKVHTPLFVATLFFTFLPATSGLSGAAVLYSATPDYL 19- 4 WG G+++ +F KEL +K V L +A+ + F+ GLSG+ L ATPD+ Sbjct: 112 WGFGLVIGALFAKELA----KKVDNVDYRLLIASAYSGFMIWHGGLSGSVPLTIATPDHF 16- 7 Query: 195 RNSVADAYKQVVPESVPLTESVL---NLPFISLLVVCMLVPLCFALLAHPKDETKIME-- 24- 9 + +P +E++ NL + L + +PL L+ K +T ++ Sbjct: 168 AQDMIGV--------IPTSETIFAPYNLAIVFALFIA--IPLANRLMMPGKSDTVTVDRS 21- 7 Query: 250 -LDDEIYHHSLDTASHVVIARNTPAEKMNASRLVMYLVGGAIVSYSLYHFSVVGLSGLDL 30- 8 LDD L AS + + TP++++ SR++ LVG + + Y+F+ G L+L Sbjct: 218 LLDDG---RDLQAAS-LELEAMTPSDRLENSRMISLLVGVLGLVFLGYYFATNGFE-LNL 27- 2 Query: 309 NCFNFLFLGLGLLLCGQQGPEYYGSLFKDGVMSSWGLVLQFPFYAGIFGIIQSTGLGLEI 36- 8 + N LFL LG+L G P+ + V + G+++QFPFYAG+ GI+ S+GL + Sbjct: 273 DIVNSLFLFLGILFHGT--PKLFLKAVTSAVKGASGIIIQFPFYAGLMGIMVSSGLATVM 33- 0 Query: 369 SHFFVAISNGTTWPVFAYLYSALLNIAVPSGGSKFVIEAPYIVPATIEVGNDLGKILQAY 42- 8 S FV+ SN T+P+F +L + ++N+ VPSGG ++ ++AP ++ A +G K A Sbjct: 331 SEAFVSFSNEVTFPLFVFLSAGIVNVFVPSGGGQWAVQAPVVLEAAQSLGVPAAKAAMAV 39- 0 Query: 429 QLGDATTNLIVPFWALSYLSNFKLKFNQIVAYTIPCVLVVTGIAI 473 GDA TN+I PFWAL L+ LK I+ + + +LVV+G+ I Sbjct: 391 AWGDAWTNMIQPFWALPALAIAGLKAKDIMGFCV-MILVVSGVVI 434 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2397 A DNA sequence (GASx137R) was identified in S. pyogenes <SEQ ID 7293> which encodes the amino acid sequence <SEQ ID 7294>. Analysis of this protein sequence reveals the following: TABLE-US-07201 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2591(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07202 >GP: AAC22434 GB: U32761 transcriptional regulator [Haemophilus influenzae Rd] Identities = 37/107 (34%), Positives = 56/107 (51%), Gaps = 1/107 (0%) Query: 21 LHRQNLVTFDKTFMINHQLTTLFEEANSLPVVKCYSASWDFLLNCTRYS-SYLTILPRPI 79 - LH+Q + FD+TFMI+H L FE N P + S+ WDFLL+ + + LTILP P+ Sbjct: 205 LHQQKMAIFDQTFMIHHHLKEAFERNNCYPDIVLDSSCWDFLLSAVKTNKELLTILPLPM 26- 4 Query: 80 THFAHMDGLVEVQLTEHPKWEVVLASLKHNKTSHLKHYIKHTILDYF 126 H + ++ W+V L + +HL+ YI +L+ F Sbjct: 265 AELYHSKEFLCRKIESPVPWKVTLCRQRKTVYTHLEEYIFDKLLEAF 311 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2398 A DNA sequence (GASx140) was identified in S. pyogenes <SEQ ID 7295> which encodes the amino acid sequence <SEQ ID 7296>. Analysis of this protein sequence reveals the following: TABLE-US-07203 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3351(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07204 !GB: U32761 acetate CoA-transferase, alpha subunit [H . . . 215 4e-55 Identities = 105/213 (49%), Positives = 146/213 (68%) Query: 22 ENKRIAIAEAISHIKDGDTIMVGGFMANGTPEALIDALVDKGTKDLTLICNDAGFVDRGV 81 - + K + + +A +DG TIMVGGFM GTP L++AL++ G +DLTLI ND FVD G+ Sbjct: 2 KTKLMTLQDATGFFRDGMTIMVGGFMGIGTPSRLVEALLESGVRDLTLIANDTAFVDTGI 61 Query: 82 GKMVANHQFKTIYATHIGLNKEAGRQMTAGETTIELIPQGTFAEKIRIGAYGIGGFYTPT 141- G ++ N + + + A+HIG N E GR+M +GE + L+PQGT E+IR G G+GGF TPT Sbjct: 62 GPLIVNGRVRKVIASHIGTNPETGRRMISGEMDVVLVPQGTLIEQIRCGGAGLGGFLTPT 121- Query: 142 GVGTLVAEGKETKTIKGKTYLLEYPFEADVALIFANQADEMGNLQYSGSENNFNQLMAAC 20- 1 GVGT+V EGK+T T+ GKT+LLE P AD+ALI A++ D +GNL Y S NFN L+A Sbjct: 122 GVGTVVEEGKQTLTLDGKTWLLERPLRADLALIRAHRCDTLGNLTYQLSARNFNPLIALA 18- 1 Query: 202 AKTTIVQAREIVPVGTIQPECVHTPHIFVDYIV 234 A T+V+ E+V G +QP+ + TP +D+I+ Sbjct: 182 ADITLVEPDELVETGELQPDHIVTPGAVIDHII 214 subunit (EC 2.8.3.--). [Escherichia coli] Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2399 A DNA sequence (GASx141) was identified in S. pyogenes <SEQ ID 7297> which encodes the amino acid sequence <SEQ ID 7298>. Analysis of this protein sequence reveals the following: TABLE-US-07205 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4941(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07206 >GP:AAF12248 GB:AE001862 CoA transferase, subunit B [Deinococcus radiodurans] Identities = 114/203 (56%), Positives = 158/203 (77%), Gaps = 3/203 (1%) Query: 11 QNRIAKRVAKELEDGTLVNLGIGLPTKVANFVPEEMTVYFQSENGFIGLGP--KSDDPNS 68 - ++ +A R A+EL+DG VNLGIGLPT VAN +P M+V+ QSENG +G+GP D+ + Sbjct: 5 RDEMAARAAQELQDGYYVNLGIGLPTLVANHIPAGMSVWLQSENGLLGIGPFPTEDEVDP 64 Query: 69 TIVNAGGQPVTVYPGAAFENSADSFGIIRGGHVDLTVLGALEIAENGDIANYLIPGKMVP 128- ++NAG Q VT PGA+FF+SADSF +IRGGHV+L +LGA++++E GD+AN++IPGKMV Sbjct: 65 DLINAGKQTVTALPGASFFSSADSFAMIRGGHVNLAILGAMQVSETGDLANWMIPGKMVK 124- Query: 129 GMGGANDLLVGAKKVIVANEHTNKG-KHKLLKECTLPLTAKGVVDLIITEMGVFKVTPDG 18- 7 GMGGANDL+ G ++V+V MEH KG HK+L+ECTLPLT +GVVD IIT++GV VTP G Sbjct: 125 GMGGANDLVAGVQRVVVLMEHVAKGDAHKILRECTLPLTGQGVVDRIITDLGVLDVTPQG 18- 4 Query: 188 IQVIEISEGFTFDEVQAATGVPL 210 ++++E++ G T DE++ TG + Sbjct: 185 LKLVELAPGVTLDELRQKTGADI 207 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2400 A DNA sequence (GASx144) was identified in S. pyogenes <SEQ ID 7299> which encodes the amino acid sequence <SEQ ID 7300>. Analysis of this protein sequence reveals the following: TABLE-US-07207 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Result ----- bacterial cytoplasm --- Certainty = 0.3227(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-07208 >GP:BAA29948 GB:AP000003 137aa long hypothetical protein [Pyrococcus horikoshii] Identities = 49/113 (43%), Positives = 71/113 (62%), Gaps = 1/113 (0%) Query: 5 PEPMGPYSTYTIEGHFLYTAGQLPLNPVTGQLSDG-FEAQCRQVFVNLQSILAEQKLDLN 63 P+P+GPYS G+FL+ AGQ+P++P TG++ G + Q RQV N+++IL LN Sbjct: 22 PKPIGPYSQAIKAGNFLFIAGQIPIDPKTGEIVKGDIKDQTRQVLENIKAILEAAGYSLN 81 Query: 64 HIYKLNVYLTDVTNVEILNHVMTDLFEEPYPVRTAVQVSALPLQALIEVEAVA 116 + K+ VYL D+ + +N V + F E P R AV+VS LP LIE+EA+A Sbjct: 82 DVIKVTVYLKDMNDFAKMNEVYAEYFGESKPARVAVEVSRLPKDVLIEIEAIA 134 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2401 A DNA sequence (GASx146) was identified in S. pyogenes <SEQ ID 7301> which encodes the amino acid sequence <SEQ ID 7302>. Analysis of this protein sequence reveals the following: TABLE-US-07209 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1238(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2402 A DNA sequence (GASx147) was identified in S. pyogenes <SEQ ID 7303> which encodes the amino acid sequence <SEQ ID 7304>. Analysis of this protein sequence reveals the following: TABLE-US-07210 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.46 Transmembrane 456-472 ( 452-481) INTEGRAL Likelihood = -8.17 Transmembrane 603-619 ( 595-623) INTEGRAL Likelihood = -6.85 Transmembrane 495-511 ( 491-518) INTEGRAL Likelihood = -5.31 Transmembrane 420-436 ( 418-443) INTEGRAL Likelihood = -4.99 Transmembrane 396-412 ( 392-413) INTEGRAL Likelihood = -1.59 Transmembrane 522-538 ( 522-538) INTEGRAL Likelihood = -0.64 Transmembrane 577-593 ( 577-593) INTEGRAL Likelihood = -0.43 Transmembrane 377-393 ( 377-393) ----- Final Results ----- bacterial membrane --- Certainty = 0.5585(Affirmative) < succ> bacterial outside --- Certainty = 0.0000CNot Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07211 >GP:BAA04270 GB:D17462 Na+ -ATPase subunit I [Enterococcus hirae] Identities = 232/681 (34%), Positives = 370/681 (54%), Gaps = 40/681 (5%) Query: 1 MAISQMKKLANVFEKDYLDLVLKTLQQSQLVEVRDMKQLKH---WQDAFNKGNVKLPQIV 57 MA+++M+K+ ++ +K +++L+ +Q VE+RD+ Q W + F P+++ Sbjct: 1 MAVTKMEKVTLISDKKNREILLQAVQGLHAVEIRDLFQESENNQWVETF----FPEPEMI 56 Query: 58 QYDLTHQKPLLDDEALQYLLQSQQELENGLASLSAFLPPIGKLTALRQ--KTPSLSFKQF 115- D K L Y L + + F+ G+ + +Q K LS Sbjct: 57 DKDKELAK-------LSYKLTD-------IRTAIQFIEHHGEKSQKKQHLKRRELSLDTL 102- Query: 116 EERHRQQAAQTALKNMSQKIERLEQLQSKIDQLTEYCQELEKWRSLTVLPQDLAQFHFLS 17- 5 E+ + ++A L+ + E+ EQL + QL + L W++L + P+ Sbjct: 103 EKNYSEEAFSKKLEEVLLLKEQWEQLVOERQQLEDQENWLLNWQNLDLAPKAFDS-QMTK 16- 1 Query: 176 ARVGTIPSTANNHFYHQLKQHKGLFIEEVYH----TEFEYGLVLFWQAQOTIHLQKYQFK 23- 1 +GT+ + F ++ + ++EE+ T F Y ++ +++ +Y F Sbjct: 162 LVIGTVNAKNAESFKAEVAEINEAYLEEINSSPTTTYFAYIVLRADESRMEEIASRYGFV 22- 1 Query: 232 PLLYKEQLLPSEQLRINKELLTNWLAEKDSLLKELRQSQKILAQLQVEIDYVLSQYQRQQ 29- 1 Y + P +QL K+ L ++ L + + + + L++ +R+ Sbjct: 222 KEDYLYEGTPQQQLVAAKQSLQEIKDQQKKLSSAIGACSGYIKDFEWTEEIFLARSEREA 28- 1 Query: 292 TKKQLLGTRHLIALEGWIEADSVNQLKGLMTKTLGDMFYLDSYDVTPDDW--EDVPIKLR 34- 9 K +++ T +LI ++GW++ + +L ++ L ++D D+ E+VP KL+ Sbjct: 282 IKDRIIHTPYLILIQGWVDHEEKQELIHMLQNILASEEVYLTFDEPTDNEIAEEVPTKLK 34- 1 Query: 350 NHRYIAPFELVTEMYALPKYQEKDPTPFLAPLYLTFFGMMVADLGYGLLLYAVTLAALVF 40- 9 NH +APFE++TEMY+LPKY+E DPTP++ P YL FFGMMVAD+GYGLL++ Sbjct: 342 NHPIVAPFEHLTEMYSLPKYEEVDPTPWMNPFYLVFFGMMVADIGYGLLMFLGAFLLQKL 40- 1 Query: 410 FNLQKTSKRLVTFFNILAISVAIWGLIYGSFFG---------FDLPVALLSTKTDVITIL 46- 0 L + +R FF ILAI IWG IY SFFG LP +LST DV TIL Sbjct: 402 VVLPRGMQRFAKFFEILAIPSIIWGFIYSSFFGAALPKEIFGIHLPFPILSTTDDVNTIL 46- 1 Query: 461 VVSLLFGFVTLIEGLLLGAWQQVHMKAYATAYTSSLAWTFILLGLLLFILGKNVSGLAYL 52- 0 ++S++FG + ++ GL + A + ++ KAY A AW +ILLG++L +LG Sbjct: 462 ILSVIFGLIQILVGLFIAAKEHIKRKAYVDAVNDGFAWQWILLGIILILLGTNTLKNNAF 52- 1 Query: 521 SVIGKWLALGNAFGILVVSLLKSKSLL-GLGSGLYNLYGISSYLSDLVSFTRLMALGLSG 57- 9 +G LA+ +A IL++ + +S S G+ G YNLYG++ Y+ DLVS+TRLMALG+SG Sbjct: 522 VYLGGALAVLSAVCILIIPVFQSSSKAKGIAKGAYNLYGLTGYIGDLVSYTRLMALGISG 58- 1 Query: 580 ASIGAAFNMIVGIFPPVTRFTVGIFIFILLHAINIFLSMLSGYVHGARLIFVEFFGKFYE 63- 9 SI AAFNM+V PP RF+VGI + I+L A+N+FL++LS YVHGARL +VEFFGKFY Sbjct: 582 GSIAAAFNMLVAFMPPAARFSVGILLIIVLQALNHFLTLLSAYVHGARLQYVEFFGKFYT 64- 1 Query: 640 GGGKAFNPLKLADNYVNVNEE 660 GGG++F PLK + YVN+N + Sbjct: 642 GGGRSFKPLKTVEKYVNINHK 662 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2403 A DNA sequence (GASx148) was identified in S. pyogenes <SEQ ID 7305> which encodes the amino acid sequence <SEQ ID 7306>. Analysis of this protein sequence reveals the following: TABLE-US-07212 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.80 Transmembrane 28-44 ( 21-51) INTEGRAL Likelihood = -6.85 Transmembrane 148-164 ( 146-170) INTEGRAL Likelihood = -2.81 Transmembrane 105-121 ( 105-123) ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07213 >GP:BAA03841 GB:D16334 Na+-ATPase K subunit [Enterococcus hirae] Identities = 85/150 (56%), Positives = 107/150 (70%) Query: 20 HYFTAHGGVFFAALGIVLAVALSGMGSAYGVGKGGQAAAALLKEEPEKFTSALILQLLPG 79 - + T +GG+ FA L + A SG+GSA GVG G+AAAAL +PEKF ALILQLLPG Sbjct: 4 YLITQNGGMVFAVLAMATATIFSGIGSAKGVGMTGEAAAALTTSQPEKFGQALILQLLPG 63 Query: 80 SQGIYGFAIGILIWMKLTPELSVNQGLAYFLVSLPIAIVGYFSAKHQGNVSVAGMQILAK 139- +QG+YGF I LI++ L ++SV QGL + SLPIA G FS QG V+ AG+QILAK Sbjct: 64 TQGLYGFVIAFLIFINLGSDMSVVQGLNFLGASLPIAFTGLFSGIAQGKVAAAGIQILAK 123- Query: 140 RPKDFNKGVILAAMVETYAILAFVVSFILL 169 +P+ KG+I AAMVETYAIL FV+SF+L+ Sbjct: 124 KPEHATKGIIFAAMVETYAILGFVISFLLV 153 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2404 A DNA sequence (GASx149) was identified in S. pyogenes <SEQ ID 7307> which encodes the amino acid sequence <SEQ ID 7308>. Analysis of this protein sequence reveals the following: TABLE-US-07214 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results----- bacterial cytoplasm --- Certainty = 0.4510(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07215 >GP:BAA04272 GB:017462 Na+ -ATPase subunit E [Enterococcus hirae] Identities = 43/193 (22%), Positives = 95/193 (48%), Gaps = 2/193 (1%) Query: 1 VNDITQLRQNVLEIAHQEGQQCLKIATDSLDTDFEERQQQGLHDLKAERQKELKALEQQF 60 V+ I ++ + E A E ++ +D F+ ++ Q D + ++ +L+ +E+ + Sbjct: 3 VDAIDKIITQINETAQLERASFEEMKRKEIDQKFEVKKWQIEADFQKEKASKLEEIERSY 62 Query: 61 QVAQQQLKNQERQALLALKQDSIKELFEASLEKMTNFSKEEELAFLKQVLSEYP-EQPLQ 119- + + + K Q +Q +L KQ+ ++ LF + ++ N KEE+LA +KQ++ P + Sbjct: 63 RQLRNKQKMQVKQEILNAKQEVLQRLFTEATLQLENEPKEEQLALMKQMIQTLPINGTAR 122- Query: 120 VTFGEKTGQKFSSYDCAELRLAFPQLSYNQELIPQ-EAGFLVSLDQVDDNYLYRYLLESV 17- 8 + GEK+ + AE P ++ + +AG ++ + N+L+ +L++ + Sbjct: 123 LIPGEKSADILTPAVIAEWNEELPFELIREDFTSRAQAGLIIDDAGIQYNFLFSHLIEEI 18- 2 Query: 179 LKEESSRIIDMLF 191 + S+ I LF Sbjct: 183 QETMSAEIAKELF 195 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2405 A DNA sequence (GASx150) was identified in S. pyogenes <SEQ ID 7309> which encodes the amino acid sequence <SEQ ID 7310>. Analysis of this protein sequence reveals the following: TABLE-US-07216 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3095(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07217 >GP: BAA04273 GB: D17462 Na+ -ATPase subunit C [Enterococcus hirae] Identities = 94/326 (28%), Positives = 167/326 (50%), Gaps = 5/326 (1%) Query: 6 ELNTTISVKEKELLTKEQFDKLLQAPNTTTLARLLHQSVYHLTVDDLNDLDRLESILMAE 65 ELN I +E EL++K+ F++++Q + +L +L ++Y + D D D E+ L E Sbjct: 5 ELNPLIRGRELELISKDTFEQMIQTDSIDSLGEILQSTIYQPYIYDGFDKD-FEANLSQE 63 Query: 66 LTKTYRWAFAETPQPDIVQLFTLRYTYHNVKVLLKAKASQADLSHLLLPIGDKPLVALEH 125- +K ++W P+P+IV ++T+RYT+HN+KVL KA+ + +L HL + G L L+ Sbjct: 64 RSKLFQWLKESAPEPEIVWIYTMRYTFHNLKVLTKAEITGQNLDHLYIHDGFYSLEVLKD 123- Query: 126 LIRTMTSDEFPKEVVTEIQSIWAEYQDYQDIRVLEIGTDLAYFKALKQIAQRLEDPVFQQ 18- 5 I T S E P ++ I+ + ++ ++ +++ D + +++ ++L P + Sbjct: 124 AIHTQVSVELPDSLMDYIREVHEYCEESTILQGIDVIYDRCFLTEQRRLGEQLGYPELLE 18- 3 Query: 186 AVLIVIDLYNLITVRRAKSQNKPISFMMQLLSDEASRPSKTFITLEDDKDLMTWFENVTP 24- 5 ++ IDL N+ T R Q++ FM ++S S P T ++ ++ ++ + + Sbjct: 184 EIIAFIDLTNITTTARGILQHRSAGFMTTVISSSGSIPKDTLLSFVRG-EMASFTQFLLT 24- 2 Query: 246 DSYMTALKPYSEKLRQGTLQTTELEYLVDECLYHLFAKAKYQVDGPYVLARFLLAKSFEV 30- 5 Y LK + + + + LE L D+ L + A+ Q GP L FL AK E Sbjct: 243 TDYSELLK---QVIHEEQIDLVSLEQLKDDYLSSFYQVAQTQAFGPLPLLAFLNAKEVES 29- 9 Query: 306 KNLRLLAAALANDLPKERVIERMRPI 331 KNLRLL N E++ ERMR + Sbjct: 300 KNLRLLIIGKRNHFSLEQLKERMRQV 325 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2406 A DNA sequence (GASx151) was identified in S. pyogenes <SEQ ID 7311> which encodes the amino acid sequence <SEQ ID 7312>. Analysis of this protein sequence reveals the following: TABLE-US-07218 Possible Site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0484(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07219 >GP: BAA04274 GB: D17462 Na+ -ATPase subunit G [Enterococcus hirae] Identities = 45/101 (44%), Positives = 65/101 (63%) Query: 6 YKVGVIGNRDVILPFQMIGFQTFPVIKPQDAINQLRQLAMEDFGIIYITEDIAAAIPEAL 65 YK+GV+G++D + PF++ GF + + ++A ++G+IYITE A +PE + Sbjct: 3 YKIGVVGDKDSVSPFRLFGFDVQHGTTKTEIRKTIDEMAKNEYGVIYITEQCANLVPETI 62 Query: 66 THYDNQVLPAVIPLPTHQGAQGIGLSRIQAMVEKAVGQNIL 106 Y Q+ PA+I +P+HQG GIGL IQ VEKAVGQNIL Sbjct: 63 ERYKGQLTPAIILIPSHQGTLGIGLEEIQNSVEKAVGQNIL 103 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2407 A DNA sequence (GASx152R) was identified in S. pyogenes <SEQ ID 7313> which encodes the amino acid sequence <SEQ ID 7314>. Analysis of this protein sequence reveals the following: TABLE-US-07220 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1048(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2408 A DNA sequence (GASx156) was identified in S. pyogenes <SEQ ID 7315> which encodes the amino acid sequence <SEQ ID 7316>: EYSIIPQLKETIHYIELKLEEAERASLVRIMKITS Analysis of this protein sequence reveals the following: TABLE-US-07221 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5026(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07222 >GP: BAA04277 GB: D17462 Na+ -ATPase subunit D [Enterococcus hirae] Identities = 119/201 (59%), Positives = 151/201 (74%), Gaps = 2/201 (0%) Query: 10 RLNVKPTRMELSNLKNRLKTATRGHKLLKDKRDELMRRFVDLIRENNELRQTIEKELAAN 69 - RLNV PTRMEL+ LK +L TATRGHKLLKDK+DELMR+F+ LIR+NNELRQ IEKE Sbjct: 2 RLNVNPTRMELTRLKKQLTTATRGHKLLKDKQDELMRQFILLIRKNNELRQAIEKETQTA 61 Query: 70 MKEFVLAKASENSLMVEELFAVPVHEVTLWIDIENIMSVNVPKFHVQSNTAREQEQGEFA 129- MK+FVLAK++ ++EL A+P V++ + +NIMSV VP + Q + + E Sbjct: 62 MKDFVLAKSTVEEAFIDELLALPAENVSISVVEKNIMSVKVPLMNFQYDETLNETPLE-- 119- Query: 130 YSYLSSNSEMDNTIQKTKELLEKLLRLAEVEKTCQLMADDIEKTRRRVNGLEYSIIPQLK 18- 9 Y YL SN+E+D +I +LL KLL+LAEVEKTCQLMA++IEKTRRRVN LEY IPQL+ Sbjct: 120 YGYLHSNAELDRSIDGFTQLLPKLLKLAEVEKTCQLMAEEIEKTRRRVNALEYMTIPQLE 17- 9 Query: 190 ETIHYIELKLEEAERASLVRI 210 ETI+YI++KLEE ERA + R+ Sbjct: 180 ETIYYIKMKLEENERAEVTRL 200 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2409 A DNA sequence (GASx161R) was identified in S. pyogenes <SEQ ID 7317> which encodes the amino acid sequence <SEQ ID 7318>. Analysis of this protein sequence reveals the following: TABLE-US-07223 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2410 A DNA sequence (GASx164) was identified in S. pyogenes <SEQ ID 7319> which encodes the amino acid sequence <SEQ ID 7320>. Analysis of this protein sequence reveals the following: TABLE-US-07224 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.06 Transmembrane 9-25 (9-25) ----- Final Results ----- bacterial membrane --- Certainty = 0.1426(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified <SEQ ID 9091> which encodes the amino acid sequence <SEQ ID 9092>. Analysis of this protein sequence reveals the following: TABLE-US-07225 Possible cleavage site: 33 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.300(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2411 A DNA sequence (GASx165) was identified in S. pyogenes <SEQ ID 7321> which encodes the amino acid sequence <SEQ ID 7322>. Analysis of this protein sequence reveals the following: TABLE-US-07226 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2251(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2412 A DNA sequence (GASx166) was identified in S. pyogenes <SEQ ID 7323> which encodes the amino acid sequence <SEQ ID 7324>. Analysis of this protein sequence reveals the following:

TABLE-US-07227 Possible site: 34 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2413 A DNA sequence (GASx167) was identified in S. pyogenes <SEQ ID 7325> which encodes the amino acid sequence <SEQ ID 7326>. Analysis of this protein sequence reveals the following: TABLE-US-07228 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2414 A DNA sequence (GASx168R) was identified in S. pyogenes <SEQ ID 7327> which encodes the amino acid sequence <SEQ ID 7328>. Analysis of this protein sequence reveals the following: TABLE-US-07229 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2415 A DNA sequence (GASx169R) was identified in S. pyogenes <SEQ ID 7329> which encodes the amino acid sequence <SEQ ID 7330>. Analysis of this protein sequence reveals the following: TABLE-US-07230 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2416 A DNA sequence (GASx170) was identified in S. pyogenes <SEQ ID 7331> which encodes the amino acid sequence <SEQ ID 7332>. Analysis of this protein sequence reveals the following: TABLE-US-07231 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.34 Transmembrane 154-170 (153-170) INTEGRAL Likelihood = -1.12 Transmembrane 20-36 (19-36) INTEGRAL Likelihood = -0.69 Transmembrane 52-68 (52-68) INTEGRAL Likelihood = -0.53 Transmembrane 399-415 (399-415) ----- Final Results ----- bacterial membrane --- Certainty = 0.1935(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07232 >GP: BAB05347 GB: AP001512 cystathionine beta-lyase [Bacillus halodurans] Identities = 200/384 (52%), Positives = 262/384 (68%), Gaps = 3/384 (0%) Query: 79 IAEVYEMRENTTLLHGYTVIDEFTGAASVPIYQTSTFHNSELYCPSQKHLYTRFSNPTTE 138- ++E Y ++ T LLH +D+ TGA SVPI STFH + + + Y+R NPT + Sbjct: 1 MSEQYSLQ--TKLLHNEHKVDQATGAVSVPIQHASTFHQFD-FDTFGTYDYSRSGNPTRD 57 Query: 139 ALEDGLACLEKATYAVAYASGMAAISTVLMLLKAGDHVIFPLEVYGGTCQFATAILPNYQ 19- 8 ALE +A LE + A+ASGMAAIST MLL GDHV+ +VYGGT + T +L Sbjct: 58 ALEAAIAELEGGNHGFAFASGMAAISTAFMLLSKGDHVVLTKDVYGGTFRLVTEVLTRLG 117- Query: 199 IETSFVDMADLATVKASIRPNTRMIYLETPSNPLLKICDISELVQLAKAYGVLTVADNTF 25- 8 IE +FVDM +LA V A+IRPNTR++Y+ETPSNP L I DI +V LAK + LT DNTF Sbjct: 118 IEHTFVDMTNLAEVAAAIRPNTRVLYMETPSNPTLNITDIRGVVSLAKEHECLTFLDNTF 17- 7 Query: 259 MTSLYQEPLAMGVDIVVESVTKFINGHSDVVAGLAATNNEAIYNQLKLFQKNFGAIVGVE 31- 8 +T Q PL +GVD+V+ S TKFI GHSDVVAGLA T NE + +L Q +FGAI+GV+ Sbjct: 178 LTPALQRPLELGVDVVLHSATKFIGGHSDVVAGLAVTKNEELGKKLAFLQNSFGAILGVQ 23- 7 Query: 319 DAWLILRGMKTMGIRMEQAVKNAQQLANYLAKHPKVLKVHYPGLDSHPNHDTHLQQAKNG 37- 8 D WL+LRG+KT+ +RME K AQQ+A +L P+V +V+YPGL HP H+ +QA+ Sbjct: 238 DVWLVLRGLKTLHVRMEHGEKGAQQIAEWLQGVPEVKRVYYPGLKDHPGHELQKRQAEGF 29- 7 Query: 379 GAVLSFELASKEELMTFTHRIQLPILAVSLGGVESILSHPATMSHACLSPQARLEQGVVD 43- 8 GAVLSFEL ++E + F ++LP+ AVSLG VESILS+PA MSHA + + R +G+ D Sbjct: 298 GAVLSFELENEEAVRRFVEHVKLPVFAVSLGAVESILSYPAKMSHAAMPKEEREARGIRD 35- 7 Query: 439 GLLRLSCGVENIEDLLADFEQALA 462 GLLRLS G+E E+L+ADF+ A A Sbjct: 358 GLLRLSVGLEKPEELMADFKAAFA 381 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2417 A DNA sequence (GASx178) was identified in S. pyogenes <SEQ ID 7333> which encodes the amino acid sequence <SEQ ID 7334>. Analysis of this protein sequence reveals the following: TABLE-US-07233 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1492(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2418 A DNA sequence (GASx182) was identified in S. pyogenes <SEQ ID 7335> which encodes the amino acid sequence <SEQ ID 7336>. Analysis of this protein sequence reveals the following: TABLE-US-07234 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2584(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2419 A DNA sequence (GASx187) was identified in S. pyogenes <SEQ ID 7337> which encodes the amino acid sequence <SEQ ID 7338>. Analysis of this protein sequence reveals the following: TABLE-US-07235 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2084(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2420 A DNA sequence (GASx188) was identified in S. pyogenes <SEQ ID 7339> which encodes the amino acid sequence <SEQ ID 7340>. Analysis of this protein sequence reveals the following: TABLE-US-07236 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2060(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07237 >GP: AAG05515 GB: AE004640 conserved hypothetical protein [Pseudomonas aeruginosa] Identities = 140/442 (31%), Positives = 208/442 (46%), Gaps = 73/442 (16%) Query: 2 KKYLNQNVYDALIERLHFLFNDFPIVYISFSGGKDSGLLLNILLDFRDKYYPDREIG--- 58 K Y + +V+ A + RL +F +F V ++FSGGKDS + L + LD RE+G Sbjct: 4 KHYQDADVHAATLSRLRLVFRNFERVCVAFSGGKDSSVTLQLALDVA------RELGRSP 57 Query: 59 --VFHQDFEAQYSLTTKYVQETFTSLEGRKKVSLYWVCLPMATRTALSSYEMFWYPWDDK 116- V D E QY T +V E GR V +WVCLP+ R A S E +W W+ Sbjct: 58 VDVLFIDLEGQYQATIDHVSEML----GRPDVRPWWVCLPLNLRNASSLEEPYWCCWEPG 113- Query: 117 TEDIWVRPMPSQDYVINLENNSITTYRYKMNQEDLAKQFGRWYKQIHGNQKTVCILGNRA 17- 6 E WVRP+P Q VI+ + YRY+M E+ F W + + T ++G R+ Sbjct: 114 AEADWVRPLPKQRGVIS-DPAFFPFYRYRMEFEEFVAGFNAWLAR---EEPTAFLVGIRS 16- 9 Query: 177 SESLHRYSGFINKKYGYQKEC------------WITKQFKDVWTAS--PLYDWSVEDIWH 22- 2 ESL+RY K+ K+C W + + S P+YDW ED+W Sbjct: 170 DESLNRYLAV--KRRSRAKQCAWTPPGGSAPLAWSARDRANPQAVSFFPIYDWRFEDLWR 22- 7 Query: 223 AYYKFSYSYNELYDLFYKAGLKPSQMRVASPFQDYAVDSLNLYRIIDQETWVKLLGRVQG 28- 2 Y+YN LYD Y+AG+ SQMR+ P+ D L+L+ I+ TW K++ RV G Sbjct: 228 CVADHGYAYNRLYDQMYRAGVPFSQMRICQPYGDDQRKGLDLFHRIEPRTWFKVVRRVAG 28- 7 Query: 283 VNFSNIYGRTKAMGYK-SIALPKGH-SWKSYTQFLLSTLPVRLRNNYVRKFNKSIDFWHK 34- 0 N+ Y R + +GY+ + LP +W+ Y+QFLL ++P LR Y R+ + I +W + Sbjct: 288 ANYGARYCRQRFLGYRGGLGLPPSFGTWREYSQFLLRSMPPPLRGIYQRRIERFILWWKQ 34- 7 Query: 341 TGGGLAEETINELIEKGYRIARNGISNYTSFKHSRVIFLDQ-IPDDTDDIVTTKDIPSWK 39- 9 LA I+ D IP + + PSW+ Sbjct: 348 HDYPLA------------------------------IWPDAGIP----ALENRRKQPSWR 37- 3 Query: 400 RMCFCILKNDHICRTMGFGLTR 421 R+ +LK D + R++ FG ++ Sbjct: 374 RIALSLLKQD-MARSLSFGFSQ 394 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2421 A DNA sequence (GASx189) was identified in S. pyogenes <SEQ ID 7341> which encodes the amino acid sequence <SEQ ID 7342>. Analysis of this protein sequence reveals the following: TABLE-US-07238 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4121(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07239 >GP: AAC73702 GB: AE000165 orf, hypothetical protein [Escherichia coli] Identities = 79/162 (48%), Positives = 110/162 (67%), Gaps = 1/162 (0%) Query: 7 PVYEIKSIPIEKISPNDYNPNSVAPPEMKLLYDSIKSDGYTMPIVCYYDKEEDRYSIVDG 66 PV + + ++ PNDYNPN+VAPPE KLL SI+ DG+T PIV + +++ IVDG Sbjct: 46 PVDCVLWVKNSQLMPNDYNPNNVAPPEKKLLQKSIEIDGFTQPIVVTHT-DKNAMEIVDG 104- Query: 67 FHRYRIMLDYSDIYERESGRLPVSVIDKSLDYRMASTIRHNRARGSHDVDLMSQIVKDLH 126- FHR+ I S + R G LPV+ ++ + + R+A+TIRHNRARG H + MS+IV++L Sbjct: 105 FHRHEIGKGSSSLKLRLKGYLPVTCLEGTRNQRIAATIRHNRARGRHQITAMSEIVRELS 16- 4 Query: 127 ECGRSDNWIAKHLGMDKDEILRLKQITGLASLFKDHEFNQSW 168 + G DN I K LGMD DE+LRLKQI GL LF D +++++W Sbjct: 165 QLGWDDNKIGKELGMDSDEVLRLKQINGLQELFADRQYSRAW 206 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2422 A repeated DNA sequence (GASx192R) was identified in S. pyogenes <SEQ ID 7343> which encodes the amino acid sequence <SEQ ID 7344>. Analysis of this protein sequence reveals the following: TABLE-US-07240 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4301(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07241 >GP: CAA63509 GB: X92946 transposase [Lactococcus lactis] Identities = 23/36 (63%), Positives = 28/36 (76%) Query: 1 MQDKLVTEAFNQAYNREKPKEGVIVHTDQGSQYTGA 36 MQDKLV + F QA +E P+ G+IVHTDQGSQYT + Sbjct: 134 MQDKLVRDCFLQACGKEHPQPGLIVHTDQGSQYTSS 169 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2423 A DNA sequence (GASx194R) was identified in S. pyogenes <SEQ ID 7345> which encodes the amino acid sequence <SEQ ID 7346>. Analysis of this protein sequence reveals the following: TABLE-US-07242 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07243 >GP: CAA63508 GB: X92946 hypothetical protein [Lactococcus lactis] Identities = 64/96 (66%), Positives = 78/96 (80%) Query: 1 MPRKTFDKAFKLSAVKLILEEEQSVKMVSSTLEIHPNSLYQWIQEYEKYGESAFPGHGSA 60 M R+ FDK FK SAVKLILEE SVK VS LE+H NSLY+W+QE E+YGESAFPG+G+A Sbjct: 1 MARRKFDKQFKNSAVKLILEEGYSVKEVSQELEVHANSLYRWVQEVEEYGESAFPGNGTA 60 Query: 61 LRHAQFETKKLEKEHKLLQEELALLKKFQVFLKPNR 96 L +AQ + K LEKE++ LQEEL LLKKF+VFLK ++ Sbjct: 61 LANAQHKIKLLEKENRYLQEELELLKKFRVFLKRSK 96 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2424 A DNA sequence (GASx195R) was identified in S. pyogenes <SEQ ID 7347> which encodes the amino acid sequence <SEQ ID 7348>. Analysis of this protein sequence reveals the following: TABLE-US-07244 Possible site: 13 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -11.30 Transmembrane 179-195 (173-201) INTEGRAL Likelihood = -8.86 Transmembrane 229-245 (224-254) INTEGRAL Likelihood = -8.39 Transmembrane 289-305 (280-307) INTEGRAL Likelihood = -8.23 Transmembrane 417-433 (410-435) INTEGRAL Likelihood = -5.89 Transmembrane 324-340 (323-349) INTEGRAL Likelihood = -4.73 Transmembrane 260-276 (256-278) INTEGRAL Likelihood = -4.51 Transmembrane 96-112 (91-113) INTEGRAL Likelihood = -4.25 Transmembrane 24-40 (20-43) INTEGRAL Likelihood = -2.44 Transmembrane 344-360 (342-360) ----- Final Results ----- bacterial membrane --- Certainty = 0.5522(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07245 >GP: CAB75191 GB: AL139075 putative integral membrane protein [Campylobacter jejuni] Identities = 177/430 (41%), Positives = 274/430 (63%), Gaps = 8/430 (1%) Query: 5 IIISAIALAIGIGYRTKINIGLLAIAFSYLIATTLMGLSPKELLHFWPTSLFFTIFSVSL 64 +IIS+I +AI +GY T+ N+G+ A+ F+Y+I M L+PK+++ FWP S+FF IF+VSL Sbjct: 6 LIISSIIVAIILGYITRHNVGIFAMIFAYIIGAFFMDLAPKKIIAFWPISIFFVIFAVSL 65 Query: 65 FYNVATTNGTLDVLAQHILYRTRTHPNALYMILYLIATLLSALGAGFFTTMAVCCPLAIT 124- FYN AT NGTL+ LA H++YR HP L ++++++ +++ALGAGF+T +A PL Sbjct: 66 FYNFATVNGTLEKLAGHLMYRFANHPYLLPFVIFVVSAIIAALGAGFYTVLAFMAPLTFL 125- Query: 125 LCQKADKHPLIGAQAVNWGASGGANLITSGSGIVFQGLFKQMGWE-EQAFSLGNHIFIVS 18- 3 LC K + GA A+N+GA GGAN ITS SGI+F+GL + G E +AF+ + IF + Sbjct: 126 LCDKIGLSKIAGAMAINYGALGGANFITSQSGIIFRGLMENSGIEANEAFANSSIIFAFT 18- 5 Query: 184 IIYPLIVLLLLSCYIRYSKGRTNSSLT-IDQPPVLSKVQRQTTLLMISSMVLVWLFPLLL 24- 2 II P++VL + ++ + N ++ I +P Q+ T +LM +V+V +FP+L Sbjct: 186 IILPIVVL----SFFVFNAFKNNIKISVISKPDPFDYKQKTTLILMFMMIVVVLIFPVLN 24- 1 Query: 243 LIFPNIAWIATYRQTFDIGFVSILMVCLALRLKLGKQEAILAKVPWAIIIMLCGMSLLMS 30- 2 +IFP+ I+ + + DI ++++ V +AL LKL ++ ++A +PW +IM+CG+ +L+S Sbjct: 242 IIFPHNETISYFNKKIDIAMIAMIFVAIALFLKLADEKQVVALIPWGTLIMICGVGMLIS 30- 1 Query: 303 LAVKSGLVTLIGHLITTTIPHFWLPLFFCVIAGVMSLFSSTLSVVAPTLFPIIATISAQS 36- 2 +AV++G + L L+ I ++PL C IA MSLFSSTL VV P LFPI+ +I+A S Sbjct: 302 IAVEAGAIKLFSDLVENEINVIFIPLIMCAIAAFMSLFSSTLGVVTPALFPIVPSIAASS 36- 1 Query: 363 PHIDIRLLTTATIIGALSTNISPFSSAGSLIQLSLPHIEERSLAFKKQILLGVPISLSLA 42- 2 + LL + ++GA ++ ISPFSS GSLI S P + L FK ++ VPI A Sbjct: 362 -GLSEALLFSCIVVGAQASAISPFSSGGSLILGSCPDKYKEKL-FKDLLIKAVPIGFIAA 41- 9 Query: 423 LLTIWILMLL 432 +L I+ + Sbjct: 420 ILATIIMSFI 429 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2425 A DNA sequence (GASx196) was identified in S. pyogenes <SEQ ID 7349> which encodes the amino acid sequence <SEQ ID 7350>. Analysis of this protein sequence reveals the following:

TABLE-US-07246 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0563(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07247 >GP: AAC45128 GB: U65510 nicotinate-nucleotide pyrophosphorylase [Rhodospirillum rubrum] Identities = 116/277 (41%), Positives = 170/277 (60%), Gaps = 4/277 (1%) Query: 17 LTPFQIDDTLKAALREDV-HSEDYSTNAIFDHHGQAKVSLFAKEAGVLAGLTVFQRVFTL 75 - L+PF ID+ ++ AL ED+ + D ++ A +A A++ G+LAGL + F L Sbjct: 10 LSPFAIDEAVRRALAEDLGRAGDITSTATIPAATRAHARFVARQPGILAGLGCARSAFAL 69 Query: 76 FDTEVTFQNPHQFKDGDRLTSGDLVLEIIGSVRSLLTCERVALNFLQHLSGIASMTAAYV 135- D VTF P +DG + +G V E+ G+ R++L ER ALNFL HLSGIA+ T + Sbjct: 70 LDDTVTFTTP--LEDGAEIAAGQTVAEVAGAARTILAAERTALNFLGHLSGIATRTRRFG 127- Query: 136 EALGDDRIKVFDTRKTTPNLRLFEKYAVRVGGGYNHRFNLSDAIMLKDNHIAAVGSVQKA 19- 5 +A+ R ++ TRKTTP LR EKYAVR GGG NHRF L DA+++KDNHIA G V A Sbjct: 128 DAIAHTRARLTCTRKTTPGLRGLEKYAVRCGGGSNHRFGLDDAVLIKDNHIAVAGGVSAA 18- 7 Query: 196 IAQARAYAPFVKMVEVEVESL-AAAEEAAAAGVDIIMLDNMSLEQIEQAITLIAGRSRIE 25- 4 +++ARA + +E+EV++L AE A G ++++LDNM + +A+ ++AGR E Sbjct: 188 LSRARAGVGHMVRIEIEVDTLEQLAEVLAVGGAEVVLLDNMDAPTLTRAVDMVAGRLVTE 24- 7 Query: 255 CSGNIDMTTISRFRGLAIDYVSSGSLTHSAKSLDFSM 291 SG + + TI+ +DY+S G+LTHS +LD + Sbjct: 248 ASGGVSLDTIAALAESGVDYISVGALTHSVTTLDIGL 284 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2426 A DNA sequence (GASx199) was identified in S. pyogenes <SEQ ID 7351> which encodes the amino acid sequence <SEQ ID 7352>. Analysis of this protein sequence reveals the following: TABLE-US-07248 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1649(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2427 A DNA sequence (GASx201) was identified in S. pyogenes <SEQ ID 7353> which encodes the amino acid sequence <SEQ ID 7354>. Analysis of this protein sequence reveals the following: TABLE-US-07249 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2428 A DNA sequence (GASx203) was identified in S. pyogenes <SEQ ID 7355> which encodes the amino acid sequence <SEQ ID 7356>. Analysis of this protein sequence reveals the following: TABLE-US-07250 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2429 A DNA sequence (GASx210) was identified in S. pyogenes <SEQ ID 7357> which encodes the amino acid sequence <SEQ ID 7358>. Analysis of this protein sequence reveals the following: TABLE-US-07251 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2430 A DNA sequence (GASx211) was identified in S. pyogenes <SEQ ID 7359> which encodes the amino acid sequence <SEQ ID 7360>. Analysis of this protein sequence reveals the following: TABLE-US-07252 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2431 A DNA sequence (GASx213) was identified in S. pyogenes <SEQ ID 7361> which encodes the amino acid sequence <SEQ ID 7362>. Analysis of this protein sequence reveals the following: TABLE-US-07253 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4430(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2432 A DNA sequence (GASx219) was identified in S. pyogenes <SEQ ID 7363> which encodes the amino acid sequence <SEQ ID 7364>. Analysis of this protein sequence reveals the following: TABLE-US-07254 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2433 A DNA sequence (GASx220) was identified in S. pyogenes <SEQ ID 7365> which encodes the amino acid sequence <SEQ ID 7366>. Analysis of this protein sequence reveals the following: TABLE-US-07255 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0530(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2434 A DNA sequence (GASx231R) was identified in S. pyogenes <SEQ ID 7367> which encodes the amino acid sequence <SEQ ID 7368>. Analysis of this protein sequence reveals the following: TABLE-US-07256 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2435 A DNA sequence (GASx237) was identified in S. pyogenes <SEQ ID 7369> which encodes the amino acid sequence <SEQ ID 7370>. Analysis of this protein sequence reveals the following: TABLE-US-07257 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4961(Affirmative) < succ> bacterial membrane --- Certainty = 0.00000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07258 >GP: CAB49143 GB: AJ248283 hypothetical protein [Pyrococcus abyssi] Identities = 79/229 (34%), Positives = 131/229 (56%), Gaps = 11/229 (4%) Query: 18 MRFTIDQNMQFPLVEIDLEHGGSVYLQQGSMVYHTENVTLNTKLNGKGSGLGKLVGAIGR 77 - M + I+ F L+E++L G +V + G+MVY V++ TK G L+GA+ R Sbjct: 1 MEYRIEHRPSFSLLEVNLREGEAVQAEAGAMVYMDPTVSIETKARGG------LLGALKR 54 Query: 78 SMVSGESMFITQAMSNGDGKLALAPNTPGQIVALELGEKQYRLNDGAFLALDGSAQYKME 137- S++ GES F+ + G G++ AP PG I++LEL Y GAFL ++ Sbjct: 55 SVLGGESFFMN--VFRGPGRVGFAPGYPGDIISLELNGTLYA-QSGAFLVASEGIDIDVK 111- Query: 138 RQNIGKALFGGQGGLFVMTTEGLGTLLANSFGSIKKITLDGGTMTIDNAHVVAWSRELDY 19- 7 GK +FG +G +F++ +G G + +S+G+I+KITL G ++ +D H+VA++ +D+ Sbjct: 112 FGG-GKTIFGREG-VFLLELKGKGIVFLSSYGAIEKITLRGESVIVDTGHMVAFTEGIDF 16- 9 Query: 198 DIHLENGFMQSIGTGEGVVNTFRGHGEIYIQSLNLEQFAGTLKRYLPTS 246 I G ++ +GEG+V F GHG++YIQ+ +L+ F + +LP S Sbjct: 170 RIRKIGGLKATLFSGEGLVFEFSGHGDVYIQTRSLDGFLSWILPHLPKS 218 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2436 A DNA sequence (GASx240R) was identified in S. pyogenes <SEQ ID 7371> which encodes the amino acid sequence <SEQ ID 7372>. Analysis of this protein sequence reveals the following: TABLE-US-07259 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2745(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2437 A DNA sequence (GASx241) was identified in S. pyogenes <SEQ ID 7373> which encodes the amino acid sequence <SEQ ID 7374>. Analysis of this protein sequence reveals the following: TABLE-US-07260 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.14 Transmembrane 196-212 (187-215) INTEGRAL Likelihood = -8.01 Transmembrane 160-176 (156-179) INTEGRAL Likelihood = -5.89 Transmembrane 116-132 (110-134) INTEGRAL Likelihood = -4.57 Transmembrane 74-90 (73-97) INTEGRAL Likelihood = -2.66 Transmembrane 51-67 (50-68) INTEGRAL Likelihood = -2.60 Transmembrane 8-24 (7-27) INTEGRAL Likelihood = -1.28 Transmembrane 344-360 (344-360) INTEGRAL Likelihood = -0.22 Transmembrane 30-46 (30-46) ----- Final Results ----- bacterial membrane --- Certainty = 0.5055(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07261 >GP: CAC10175 GB: AJ278302 histidine kinase [Streptococcus pneumoniae] Identities = 136/449 (30%), Positives = 234/449 (51%), Gaps = 26/449 (5%) Query: 8 FLLLSIIVYYMTKIYIFSFLSDITLP---VWKQLTI-LALALFFNQFPYLS-----PLLI 58 ++LL +V + KI IF + I+L ++K + LA+ F Y+ + Sbjct: 5 WILLYTLVTHGLKIVIFFKVDGISLTFERIFKAFLFKILLAVVFGMLGYMVGNVYLSYFM 64 Query: 59 DPL----LFLVVLRQETKQLFSLKALFLAVAPSVLVDLLSRFMGTIVIPYLFLSSGIYLG 114- +PL L ++LR+ K+L LF + P +LV+L R + V+P FL G Sbjct: 65 EPLYGIGLSFLLLRELPKKLL----LFYGLFPMILVNLFYRGVSYFVLP--FLGQGQVYD 118- Query: 115 HIIFDLLAYLLIFPSFAIINYMIGKDYKMIC-QSGYSKRSHNFYQTLLMFVLVYYVDIFV 17- 3 F L ++IF F + ++ DY + G + T + +++ Y + Sbjct: 119 DYSFIWLC-IIIFNFFISLAFLKWLDYDFTSLRKGILDKDFQKSLTQINWIMGAYYLVIQ 17- 7 Query: 174 ILGFTDPFLHFHHSLFVPTPYKLLFLMFILLLVYLLSYFNHSSKEYLKNELRREQQAYMT 23- 3 L + + + + T L+ + ++L + ++ + K+ L L +EQ Sbjct: 178 NLSYFE----YEQGIQSTTVRHLILVFYLLFFMGIIKKLDTYLKDKLHERLNQEQDLRYR 23- 3 Query: 234 NLEIYGKHLEKLYRDVRAFQSDYLSRIERLGQAIKSESITQIQDIYAQTVHEANDYWDDK 29- 3 +E Y +H+E+LY++VR+F+ DY + + L I+ E + QI++IY + ++++ D Sbjct: 234 EMERYSRHIEELYKEVRSFRHDYTNLLTSLRLGIEEEDMEQIKEIYDSVLKDSSEKLQDN 29- 3 Query: 294 HYNISKLRKINISSIKSLLSAKIISAEKSGIDLNVEVPDNIKETYIPELDLLLLMSIFCD 35- 3 Y++ +L + ++KSLL+ K I A I NVEVP+ I+ + LD L ++SI CD Sbjct: 294 KYDLGRLVNVRDRALKSLLAGKFIKARDKNIVFNVEVPEEIQVEGVSLLDFLTVVSILCD 35- 3 Query: 354 NAIEAALEAQQPHMSIAYFLLGDYQMFVVTNTTKKK-VDINKIFEEGYSSKGSERGIGLS 41- 2 NAIEA++EA QPH+SIA+F G + F++ N+ K++ +DI++IF G SSKG ERG+GL Sbjct: 354 NAIEASVEACQPHVSIAFFKNGAQETFIIENSIKEEGIDISEIFSFGASSKGEERGVGLY 41- 3 Query: 413 NAQRILKKYPYLSLRTKSFDKEFSQTLTM 441 +I++ +P SL T D F Q LT+ Sbjct: 414 TVMKIVESHPNTSLNTTCQDHVFRQVLTV 442 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2438 A DNA sequence (GASx242R) was identified in S. pyogenes <SEQ ID 7375> which encodes the amino acid sequence <SEQ ID 7376>. Analysis of this protein sequence reveals the following: TABLE-US-07262 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4165(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2439 A DNA sequence (GASx243) was identified in S. pyogenes <SEQ ID 7377> which encodes the amino acid sequence <SEQ ID 7378>. Analysis of this protein sequence reveals the following: TABLE-US-07263 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.09 Transmembrane 188-204 (182-208) INTEGRAL Likelihood = -7.17 Transmembrane 52-68 (47-69) INTEGRAL Likelihood = -4.73 Transmembrane 119-135 (114-142) INTEGRAL Likelihood = -4.62 Transmembrane 83-99 (77-107) INTEGRAL Likelihood = -1.86 Transmembrane 328-344 (328-345) INTEGRAL Likelihood = -1.65 Transmembrane 7-23 (6-23) INTEGRAL Likelihood = -0.22 Transmembrane 35-51 (35-51) ----- Final Results ----- bacterial membrane --- Certainty = 0.5437(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07264 >GP: CAC10175 GB: AJ278302 histidine kinase [Streptococcus pneumoniae] Identities = 123/438 (28%), Positives = 229/438 (52%), Gaps = 49/438 (11%) Query: 20 VIFAKVSAIKLSWKRVS-------IIGISFVIANMIFDKVIL---IDQLFFIIVSLL--- 66 - VIF KV I L+++R+ ++ + F + + V L ++ L+ I +S L Sbjct: 19 VIFFKVDGISLTFERIFKAFLFKILLAVVFGMLGYMVGNVYLSYFMEPLYGIGLSFLLLR 78 Query: 67 SAPKKKLFEHMFNGFFTILIVELLFRVIGSFFLPAVLGFSIGQINNNLKLLELCYLFVLP 126- PKK L +F G F +++V L +R + F LP + GQ+ ++ + LC + + Sbjct: 79 ELPKKLL---LFYGLFPMILVNLFYRGVSYFVLPFL---GQGQVYDDYSFIWLC-IIIFN 131- Query: 127 IFYLFSYIFSIDL---SLIRFISEDKMKKWVFWMNTAMFSYYFFAHFLVTVQSGFLALYF 18- 3 F +++ +D SL + I + +K + +N M +YY L YF Sbjct: 132 FFISLAFLKWLDYDFTSLRKGILDKDFQKSLTQINWIMGAYYLVIQNLS---------YF 18- 2 Query: 184 QY---------RSILVFIYLAIFIWVIVKLDRFAKDQLSQKLTQAQNERIAYLENYNQSI 23- 4 +Y R +++ YL F+ +I KLD + KD+L ++L Q Q+ R +E Y++ I Sbjct: 183 EYEQGIQSTTVRHLILVFYLLFFMGIIKKLDTYLKDKLHERLNQEQDLRYREMERYSRHI 24- 2 Query: 235 EQLYREIRTVKHDSENILISLKDSIDSGDIDLITRVYDTVIQQSATSMMRTNYEISSLDN 29- 4 E+LY+E+R+ +HD N+L SL+ I+ D++ I +YD+V++ S+ + Y++ L N Sbjct: 243 EELYKEVRSFRHDYTNLLTSLRLGIEEEDMEQIKEIYDSVLKDSSEKLQDNKYDLGRLVN 30- 2 Query: 295 IKEAVIRSIMNSKLLEAQYLGIELYIEIPDVIDHLPIKLIDLIVLFTGLVDNAIETAKGS 35- 4 +++ ++S++ K ++A+ I +E+P+ I + L+D + + + L DNAIE + + Sbjct: 303 VRDRALKSLLAGKFIKARDKNIVFNVEVPEEIQVEGVSLLDFLTVVSILCDNAIEASVEA 36- 2 Query: 355 RRPFLSIAYFKQDNKQLFIIENSTKTNRVDIAKRFDAQQQNSAH--------FLTVLDSY 40- 6 +P +SIA+FK ++ FIIENS K +DI++ F + + +++S+ Sbjct: 363 CQPHVSIAFFKNGAQETFIIENSIKEEGIDISEIFSFGASSKGEERGVGLYTVMKIVESH 42- 2 Query: 407 PQITLSTKSDHYRLRQLL 424 P +L+T + RQ+L Sbjct: 423 PNTSLNTTCQDHVFRQVL 440 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2440 A DNA sequence (GASx248) was identified in S. pyogenes <SEQ ID 7379> which encodes the amino acid sequence <SEQ ID 7380>. Analysis of this protein sequence reveals the following:

TABLE-US-07265 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5665(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2441 A DNA sequence (GASx255) was identified in S. pyogenes <SEQ ID 7381> which encodes the amino acid sequence <SEQ ID 7382>. Analysis of this protein sequence reveals the following: TABLE-US-07266 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1437(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2442 A DNA sequence (GASx270R) was identified in S. pyogenes <SEQ ID 7383> which encodes the amino acid sequence <SEQ ID 7384>. Analysis of this protein sequence reveals the following: TABLE-US-07267 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.89 Transmembrane 20-36 (17-36) ----- Final Results ----- bacterial membrane --- Certainty = 0.3357(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2443 A DNA sequence (GASx272) was identified in S. pyogenes <SEQ ID 7385> which encodes the amino acid sequence <SEQ ID 7386>. Analysis of this protein sequence reveals the following: TABLE-US-07268 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2488(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07269 >GP: CAB11887 GB: Z99104 ribosomal protein S7 (BS7) [Bacillus subtilis] Identities = 117/156 (75%), Positives = 139/156 (89%) Query: 1 MSRKNQAPKREVLPDPLYNSKIVTRLINRVMLDGKRGTAATIVYDAFNAIKEATGNDALE 60 M RK KR+VLPDP+YNSK+V+RLIN++M+DGK+G TI+Y +F+ IKE TGNDA+E Sbjct: 1 MPRKGPVAKRDVLPDPIYNSKLVSRLINKMMIDGKKGKPQTILYKSFDIIKERTGNDAME 60 Query: 61 VFETAMDNIMPVLEVRARRVGGSNYQVPVEVRPERRTTLGLRWLVNASRARGEHTMKDRL 120- VFE A+ NIMPVLEV+ARRVGG+NYQVPVEVRPERRTTLGLRWLVN +R RGE TM++RL Sbjct: 61 VFEQALKNIMPVLEVKARRVGGANYQVPVEVRPERRTTLGLRWLVNYARLRGEKTMEERL 120- Query: 121 AKEIMDAANNTGASVKKREDTHKMAEANRAFAHFRW 156 A EI+DAANNTGA+VKKREDTHKMAEAN+AFAH+RW Sbjct: 121 ANEILDAANNTGAAVKKREDTHKMAEANKAFAHYRW 156 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2444 A DNA sequence (GASx274) was identified in S. pyogenes <SEQ ID 7387> which encodes the amino acid sequence <SEQ ID 7388>. Analysis of this protein sequence reveals the following: TABLE-US-07270 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9095> which encodes the amino acid sequence <SEQ ID 9096>. Analysis of this protein sequence reveals the following: TABLE-US-07271 Possible cleavage site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.291(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2445 A DNA sequence (GASx275R) was identified in S. pyogenes <SEQ ID 7389> which encodes the amino acid sequence <SEQ ID 7390>. Analysis of this protein sequence reveals the following: TABLE-US-07272 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5664(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2446 A DNA sequence (GASx283) was identified in S. pyogenes <SEQ ID 7391> which encodes the amino acid sequence <SEQ ID 7392>. Analysis of this protein sequence reveals the following: TABLE-US-07273 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0724(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2447 A DNA sequence (GASx298) was identified in S. pyogenes <SEQ ID 7393> which encodes the amino acid sequence <SEQ ID 7394>. Analysis of this protein sequence reveals the following: TABLE-US-07274 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2840(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2448 A DNA sequence (GASx300) was identified in S. pyogenes <SEQ ID 7395> which encodes the amino acid sequence <SEQ ID 7396>. Analysis of this protein sequence reveals the following: TABLE-US-07275 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.91 Transmembrane 4-20 (4-20) ----- Final Results ----- bacterial membrane --- Certainty = 0.1765(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2449 A DNA sequence (GASx301) was identified in S. pyogenes <SEQ ID 7397> which encodes the amino acid sequence <SEQ ID 7398>. Analysis of this protein sequence reveals the following: TABLE-US-07276 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4884(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2450 A repeated DNA sequence (GASx302) was identified in S. pyogenes <SEQ ID 7399> which encodes the amino acid sequence <SEQ ID 7400>. Analysis of this protein sequence reveals the following: TABLE-US-07277 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2581(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2451 A DNA sequence (GASx316) was identified in S. pyogenes <SEQ ID 7401> which encodes the amino acid sequence <SEQ ID 7402>. Analysis of this protein sequence reveals the following: TABLE-US-07278 Possible site: 18 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.80 Transmembrane 23-39 (22-39) ----- Final Results ----- bacterial membrane --- Certainty = 0.1319(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2452 A DNA sequence (GASx323R) was identified in S. pyogenes <SEQ ID 7403> which encodes the amino acid sequence <SEQ ID 7404>. Analysis of this protein sequence reveals the following: TABLE-US-07279 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0005(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2453 A DNA sequence (GASx334) was identified in S. pyogenes <SEQ ID 7405> which encodes the amino acid sequence <SEQ ID 7406>. Analysis of this protein sequence reveals the following: TABLE-US-07280 Possible site: 17 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2454 A DNA sequence (GASx336) was identified in S. pyogenes <SEQ ID 7407> which encodes the amino acid sequence <SEQ ID 7408>. Analysis of this protein sequence reveals the following: TABLE-US-07281 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3379(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2455 A DNA sequence (GASx361R) was identified in S. pyogenes <SEQ ID 7409> which encodes the amino acid sequence <SEQ ID 7410>. Analysis of this protein sequence reveals the following: TABLE-US-07282 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2807(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2456 A DNA sequence (GASx387) was identified in S. pyogenes <SEQ ID 7411> which encodes the amino acid sequence <SEQ ID 7412>. Analysis of this protein sequence reveals the following: TABLE-US-07283 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2740(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2457 A DNA sequence (GASx389) was identified in S. pyogenes <SEQ ID 7413> which encodes the amino acid sequence <SEQ ID 7414>. Analysis of this protein sequence reveals the following: TABLE-US-07284 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0744(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2458 A DNA sequence (GASx392) was identified in S. pyogenes <SEQ ID 7415> which encodes the amino acid sequence <SEQ ID 7416>. Analysis of this protein sequence reveals the following: TABLE-US-07285 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2162(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2459 A DNA sequence (GASx393R) was identified in S. pyogenes <SEQ ID 7417> which encodes the amino acid sequence <SEQ ID 7418>. Analysis of this protein sequence reveals the following: TABLE-US-07286 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2520(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2460 A DNA sequence (GASx395) was identified in S. pyogenes <SEQ ID 7419> which encodes the amino acid sequence <SEQ ID 7420>. Analysis of this protein sequence reveals the following:

TABLE-US-07287 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2590(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2461 A DNA sequence (GASx396) was identified in S. pyogenes <SEQ ID 7421> which encodes the amino acid sequence <SEQ ID 7422>. Analysis of this protein sequence reveals the following: TABLE-US-07288 Possible site: 41 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07289 >GP: CAB13373 GB: Z99111 similar to hypothetical proteins [Bacillus subtilis] Identities = 23/88 (26%), Positives = 52/88 (58%) Query: 4 KQERIGLVVYLYYNRDARKLSKFGDLYYHSKRSRYLIIYINKNDLDTKLEEMRRLKCVKD 63 + R G+VVYL+ + ++ L KFG+++Y SKR +Y+++Y + + ++ ++++ VK Sbjct: 2 ENRRQGMVVYLHSLKQSKMLRKFGNVHYVSKRLKYVVLYCDMDQIEKTMDKIASYSFVKK 61 Query: 64 IRPSAFDDIDRQFVGNLHRDETNNHQKG 91 + PS + +F L + + +++ G Sbjct: 62 VEPSYKPFLKLEFESKLDKAKEYDYKIG 89 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2462 A DNA sequence (GASx400) was identified in S. pyogenes <SEQ ID 7423> which encodes the amino acid sequence <SEQ ID 7424>. Analysis of this protein sequence reveals the following: TABLE-US-07290 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2010(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2463 A DNA sequence (GASx401) was identified in S. pyogenes <SEQ ID 7425> which encodes the amino acid sequence <SEQ ID 7426>. Analysis of this protein sequence reveals the following: TABLE-US-07291 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1176(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2464 A DNA sequence (GASx402) was identified in S. pyogenes <SEQ ID 7427> which encodes the amino acid sequence <SEQ ID 7428>. Analysis of this protein sequence reveals the following: TABLE-US-07292 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2938(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2465 A DNA sequence (GASx403R) was identified in S. pyogenes <SEQ ID 7429> which encodes the amino acid sequence <SEQ ID 7430>. Analysis of this protein sequence reveals the following: TABLE-US-07293 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2466 A DNA sequence (GASx406) was identified in S. pyogenes <SEQ ID 7431> which encodes the amino acid sequence <SEQ ID 7432>. Analysis of this protein sequence reveals the following: TABLE-US-07294 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.26 Transmembrane 15-31 (4-36) INTEGRAL Likelihood = -6.64 Transmembrane 96-112 (94-115) ----- Final Results ----- bacterial membrane --- Certainty = 0.5904(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2467 A DNA sequence (GASx408R) was identified in S. pyogenes <SEQ ID 7433> which encodes the amino acid sequence <SEQ ID 7434>. Analysis of this protein sequence reveals the following: TABLE-US-07295 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.23 Transmembrane 17-33 (15-34) INTEGRAL Likelihood = -0.85 Transmembrane 38-54 (38-54) ----- Final Results ----- bacterial membrane --- Certainty = 0.1893(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2468 A DNA sequence (GASx412) was identified in S. pyogenes <SEQ ID 7435> which encodes the amino acid sequence <SEQ ID 7436>. Analysis of this protein sequence reveals the following: TABLE-US-07296 Possible site: 13 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.53 Transmembrane 5-21 (4-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.3612(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2469 A DNA sequence (GASx413) was identified in S. pyogenes <SEQ ID 7437> which encodes the amino acid sequence <SEQ ID 7438>. Analysis of this protein sequence reveals the following: TABLE-US-07297 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3422(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07298 >GP: CAA68903 GB: Y07622 lactate oxidase [Streptococcus iniae] Identities = 328/392 (83%), Positives = 359/392 (90%), Gaps = 4/392 (1%) Query: 3 MAQKTVITEETTDFVMDFKTSSAEGNVDFINVFDLEKMAQQVIPKGAFGYIASGAGDTFT 62 M K+ + TT ++FKTSSAEG+VDF+NVFDLEKMAQ+VIPKGAFGYIASGAGDTFT Sbjct: 1 MENKSEMINATT---IEFKTSSAEGSVDFVNVFDLEKMAQKVIPKGAFGYIASGAGDTFT 57 Query: 63 LHENIRSFNHKLIVPHSLKGVENPSTEITFDGDYLTSPLILAPVAAHKLANEQGEVASAK 122- LHENIRSFNHKLI PH LKGVENPSTEITF GD L SP+ILAPVAAHKLANEQGE+ASAK Sbjct: 58 LHENIRSFNHKLI-PHGLKGVENPSTEITFIGDKLASPIILAPVAAHKLANEQGEIASAK 116- Query: 123 GLKEFGSIYTTSSYSTTDLPEISAALGGTPHWFQFYYSKDDGINRNIMDRVKAQGCKAIV 18- 2 G+KEFG+IYTTSSYSTTDLPEIS LG +PHWFQFYYSKDDGINR+IMDR+KA+G K+IV Sbjct: 117 GVKEFGTIYTTSSYSTTDLPEISQTLGDSPHWFQFYYSKDDGINRHIMDRLKAEGVKSIV 17- 6 Query: 183 LTADATVGGNREVDRRNGFVFPVGMPIVQEYLPDGAGKTMDYVYKSAKQALTSKDIEYIA 24- 2 LT DATVGGNREVD+RNGFVFPVGMPIVQEYLP+GAGKTMDYVYK+ KQAL+ KD+EYIA Sbjct: 177 LTVDATVGGNREVDKRNGFVFPVGMPIVQEYLPNGAGKTMDYVYKATKQALSPKDVEYIA 23- 6 Query: 243 TYSGLPVYVKGPQCAEDTLRALDAGASGIWVTNHGGRQLDGGPAAFDSLQEVAEAVDQKV 30- 2 YSGLPVYVKGPQCAED RAL+AGASGIWVTNHGGRQLDGGPAAFDSLQEVAE+VD++V Sbjct: 237 QYSGLPVYVKGPQCAEDAFRALEAGASGIWVTNHGGRQLDGGPAAFDSLQEVAESVDRRV 29- 6 Query: 303 PIVFDSGIRRGQHIFKALASGADLVALGRPAIYGLAMGGSIGTRQVFEKLNDELKMVMQL 36- 2 PIVFDSG+RRGQH+FKALASGADLVALGRP IYGLAMGGS+GTRQVFEK+NDELKMVMQL Sbjct: 297 PIVFDSGVRRGQHVFKALASGADLVALGRPVIYGLAMGGSVGTRQVFEKINDELKMVMQL 35- 6 Query: 363 AGTQTIQDVKAFNLRHNPYDSSIPFDQNALRL 394 AGTQTI DVK F LRHNPYDSSIPF ++ Sbjct: 357 AGTQTIDDVKHFKLRHNPYDSSIPFSPKCFKI 388 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2470 A DNA sequence (GASx414) was identified in S. pyogenes <SEQ ID 7439> which encodes the amino acid sequence <SEQ ID 7440>. Analysis of this protein sequence reveals the following: TABLE-US-07299 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0682(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2471 A DNA sequence (GASx417R) was identified in S. pyogenes <SEQ ID 7441> which encodes the amino acid sequence <SEQ ID 7442>. Analysis of this protein sequence reveals the following: TABLE-US-07300 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1765(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2472 A DNA sequence (GASx418) was identified in S. pyogenes <SEQ ID 7443> which encodes the amino acid sequence <SEQ ID 7444>. Analysis of this protein sequence reveals the following: TABLE-US-07301 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2532(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2473 A DNA sequence (GASx419) was identified in S. pyogenes <SEQ ID 7445> which encodes the amino acid sequence <SEQ ID 7446>. Analysis of this protein sequence reveals the following: TABLE-US-07302 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3082(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2474 A DNA sequence (GASx423) was identified in S. pyogenes <SEQ ID 7447> which encodes the amino acid sequence <SEQ ID 7448>. Analysis of this protein sequence reveals the following: TABLE-US-07303 Possible site: 52 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.18 Transmembrane 14-30 (13-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.1871(Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2475 A DNA sequence (GASx427R) was identified in S-pyogenes <SEQ ID 7449> which encodes the amino acid sequence <SEQ ID 7450>. Analysis of this protein sequence reveals the following: TABLE-US-07304 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.17 Transmembrane 13-29 (10-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.1468(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9105> which encodes the amino acid sequence <SEQ ID 9106>. Analysis of this protein sequence reveals the following: TABLE-US-07305 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.17 Transmembrane 8-24 ----- Final Results ----- bacterial membrane --- Certainty = 0.1470(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07306 >GP: AAA26616 GB: M63917 epidermal cell differentiation inhibitor [Staphylococcus aureus] Identities = 58/195 (29%), Positives = 106/195 (53%), Gaps = 13/195 (6%) Query: 67 RWGKGLI----YPRAEQEAMAAYTCQQAGPINTSLDKAKGELSQLTPELRDQVAQLDAAT 122- +WG LI Y ++ A+ YT + + IN L A G++++L +D+V +LD++ Sbjct: 49 KWGNKLIKQAKYSSDDKIALYEYT-KDSSKINGPLRLAGGDINKLDSTTQDKVRRLDSSI 107- Query: 123 HRLVIPWNIVVYRYVYETFLRDI-GVSHADLTSYYR--NHQFDPHILCKIK--LGTR-YT 17- 6 + P ++ VYR + +L I G ++ DL + N Q+D +++ K+ + +R Y Sbjct: 108 SKSTTPESVYVYRLLNLDYLTSIVGFTNEDLYKLQQTNNGQYDENLVRKLNNVMNSRIYR 16- 7 Query: 177 KHSFMSTTALKNGAMTHRPVEVRICVKKGAKAAFV--EPYSAVPSEVELLFPRGCQLEVV 23- 4 + + ST + A+ RP+E+R+ + KG KAA++ + +A + E+L PRG + V Sbjct: 168 EDGYSSTQLVSGAAVGGRPIELRLELPKGTKAAYLNSKDLTAYYGQQEVLLPRGTEYAVG 22- 7 Query: 235 GAYVSQDQKKLHIEA 249 +S D+KK+ I A Sbjct: 228 SVELSNDKKKIIITA 242 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2476 A DNA sequence (GASx428) was identified in S. pyogenes <SEQ ID 7451> which encodes the amino acid sequence <SEQ ID 7452>. Analysis of this protein sequence reveals the following: TABLE-US-07307 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3817(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2477 A DNA sequence (GASx429) was identified in S. pyogenes <SEQ ID 7453> which encodes the amino acid sequence <SEQ ID 7454>. Analysis of this protein sequence reveals the following: TABLE-US-07308 Possible site: 32 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2478 A DNA sequence (GASx431) was identified in S. pyogenes <SEQ ID 7455> which encodes the amino acid sequence <SEQ ID 7456>. Analysis of this protein sequence reveals the following:

TABLE-US-07309 Possible site: 43 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.60 Transmembrane 68-84 (66-90) INTEGRAL Likelihood = -6.85 Transmembrane 22-38 (16-42) INTEGRAL Likelihood = -3.29 Transmembrane 44-60 (43-61) ----- Final Results ----- bacterial membrane --- Certainty = 0.4439(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2479 A DNA sequence (GASx432R) was identified in S. pyogenes <SEQ ID 7457> which encodes the amino acid sequence <SEQ ID 7458>. Analysis of this protein sequence reveals the following: TABLE-US-07310 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2480 A DNA sequence (GASx434) was identified in S. pyogenes <SEQ ID 7459> which encodes the amino acid sequence <SEQ ID 7460>. Analysis of this protein sequence reveals the following: TABLE-US-07311 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2481 A DNA sequence (GASx435R) was identified in S. pyogenes <SEQ ID 7461> which encodes the amino acid sequence <SEQ ID 7462>. Analysis of this protein sequence reveals the following: TABLE-US-07312 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.50 Transmembrane 4-20 (3-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.1999(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07313 >GP: AAB59092 GB: M97157 pyrogenic exotoxin C [Streptococcus pyogenes] Identities = 110/229 (48%), Positives = 150/229 (65%), Gaps = 4/229 (1%) Query: 4 IIKTIILVIIIFHGYGS--VKSDSE-NIKDVKLQLNYAYEIIPVDYTNCNIDYLTTHDFY 60 IIK + ++ +I S +KSDS+ +I +VK L YAY I P DY +C +++ TTH Sbjct: 6 IIKIVFIITVILISTISPIIKSDSKKDISNVKSDLLYAYTITPYDYKDCRVNFSTTHTLN 65 Query: 61 IDISSYKKKNFSVDSEVESYITTKFTKNQKVNIFGLPYIFTRYDVYYIYGGVTPSVNSNS 120- ID Y+ K++ + SE+ + KF ++ V++FGL YI + YIYGG+TP+ N N Sbjct: 66 IDTQKYRGKDYYISSEMSYEASQKFKRDDHVDVFGLFYILNSHTGEYIYGGITPAQN-NK 124- Query: 121 ENSKIVGNLLIDGVQQKTLINPIKIDKPIFTIQEFDFKIRQYLMQTYKIYDPNSPYIKGQ 18- 0 N K++GNL I G Q+ L N I ++K I T QE DFKIR YLM YKIYD SPY+ G+ Sbjct: 125 VNHKLLGNLFISGESQQNLNNKIILEKDIVTFQEIDFKIRKYLMDNYKIYDATSPYVSGR 18- 4 Query: 181 LEIAINGNKHESFNLYDATSSSTRSDIFKKYKDNKTINMKDFSHFDIYL 229 +EI KHE +L+D+ + TRSDIF KYKDN+ INMK+FSHFDIYL Sbjct: 185 IEIGTKDGKHEQIDLFDSPNEGTRSDIFAKYKDNRIINMKNFSHFDIYL 233 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2482 A DNA sequence (GASx436R) was identified in S. pyogenes <SEQ ID 7463> which encodes the amino acid sequence <SEQ ID 7464>. Analysis of this protein sequence reveals the following: TABLE-US-07314 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2483 A DNA sequence (GASx446) was identified in S. pyogenes <SEQ ID 7465> which encodes the amino acid sequence <SEQ ID 7466>. Analysis of this protein sequence reveals the following: TABLE-US-07315 Possible site: 20 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2484 A DNA sequence (GASx449) was identified in S. pyogenes <SEQ ID 7467> which encodes the amino acid sequence <SEQ ID 7468>. Analysis of this protein sequence reveals the following: TABLE-US-07316 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.82 Transmembrane 3 - 19 (1 - 20) ----- Final Results ----- bacterial membrane --- Certainty = 0.2529(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2485 A DNA sequence (GASx450R) was identified in S. pyogenes <SEQ ID 7469> which encodes the amino acid sequence <SEQ ID 7470>. Analysis of this protein sequence reveals the following: TABLE-US-07317 Possible site: 30 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.44 Transmembrane 21 - 37 (19 - 37) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2486 A DNA sequence (GASx457R) was identified in S. pyogenes <SEQ ID 7471> which encodes the amino acid sequence <SEQ ID 7472>. Analysis of this protein sequence reveals the following: TABLE-US-07318 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -15.34 Transmembrane 64 - 80 (57 - 86) INTEGRAL Likelihood = -13.43 Transmembrane 97 - 113 (91 - 116) INTEGRAL Likelihood = -5.57 Transmembrane 38 - 54 (32 - 56) ----- Final Results ----- bacterial membrane --- Certainty = 0.7135(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2487 A DNA sequence (GASx476R) was identified in S. pyogenes <SEQ ID 7473> which encodes the amino acid sequence <SEQ ID 7474>. Analysis of this protein sequence reveals the following: TABLE-US-07319 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3013(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2488 A DNA sequence (GASx477) was identified in S. pyogenes <SEQ ID 7475> which encodes the amino acid sequence <SEQ ID 7476>. Analysis of this protein sequence reveals the following: TABLE-US-07320 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1022(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07321 >GP:CAC03521 GB:AJ276410 BlpJ protein [Streptococcus pneumoniae] Identities = 47/77 (61%), Positives = 59/77 (76%) Query: 1 MIKFAEEIQKEELFHIIGGYSATDCKNHLIGGITSGAIAGGVGAGMATLGVGGVAGAFAG 60 M+ E + E L + GGYS+TDC+N LI G+T+G I GG GAG+ATLGV G+AGAF G Sbjct: 5 MLSQLEVMDTEMLAKVEGGYSSTDCQNALITGVTTGIITGGTGAGLATLGVAGLAGAFVG 64 Query: 61 AHVGAIAGGLTCVGGML 77 AH+GAI GGLTC+GGM+ Sbjct: 65 AHIGAIGGGLTCLGGMV 81 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2489 A DNA sequence (GASx478) was identified in S. pyogenes <SEQ ID 7477> which encodes the amino acid sequence <SEQ ID 7478>. Analysis of this protein sequence reveals the following: TABLE-US-07322 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.07 Transmembrane 42 - 58 (41 - 58) INTEGRAL Likelihood = -1.59 Transmembrane 22 - 38 (22 - 38) ----- Final Results ----- bacterial membrane --- Certainty = 0.1829(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07323 >GP:CAC03520 GB:AJ276410 BlpI protein [Streptococcus pneumoniae] Identities = 35/56 (62%), Positives = 44/56 (78%) Query: 1 MDNFLELQFEELVNISGGKGNIGSAIGGCLGGMLIAAAGGPITGGAAAFVCVASGI 56 M+ F + EEL +SGG+GN+GSAIGGC+G +L+AAA GPITGGAA +CV SGI Sbjct: 6 MEQFSVMDNEELEIVSGGRGNLGSAIGGCIGAVLLAAATGPITGGAATLICVGSGI 61 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2490 A DNA sequence (GASx482) was identified in S. pyogenes <SEQ ID 7479> which encodes the amino acid sequence <SEQ ID 7480>. Analysis of this protein sequence reveals the following: TABLE-US-07324 Possible site: 14 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.43 Transmembrane 61 - 77 (61 - 79) ----- Final Results ----- bacterial membrane --- Certainty = 0.1171(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07325 >GP:CAC03524 GB:AJ276410 BlpM protein [Streptococcus pneumoniae] Identities = 22/52 (42%), Positives = 30/52 (57%) Query: 29 MEIKKLETFHQMTIEKLAKVEGGKNNWQANVSGVIAAGSAGAAIGFPVCGVA 80 M+ K +E FH+M I L+ +EGGKNNWQ NV A G +G +C + Sbjct: 1 MDTKIMEQFHEMDITMLSSIEGGKNNWQTNVLEGGGAAFGGWGLGTAICAAS 52 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2491 A DNA sequence (GASx483) was identified in S. pyogenes <SEQ ID 7481> which encodes the amino acid sequence <SEQ ID 7482>. Analysis of this protein sequence reveals the following: TABLE-US-07326 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1832(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2492 A DNA sequence (GASx484) was identified in S. pyogenes <SEQ ID 7483> which encodes the amino acid sequence <SEQ ID 7484>. Analysis of this protein sequence reveals the following: TABLE-US-07327 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2493 A DNA sequence (GASx485) was identified in S. pyogenes <SEQ ID 7485> which encodes the amino acid sequence <SEQ ID 7486>. Analysis of this protein sequence reveals the following: TABLE-US-07328 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1037(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2494 A DNA sequence (GASx487) was identified in S. pyogenes <SEQ ID 7487> which encodes the amino acid sequence <SEQ ID 7488>. Analysis of this protein sequence reveals the following: TABLE-US-07329 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1086(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2495 A DNA sequence (GASx488) was identified in S. pyogenes <SEQ ID 7489> which encodes the amino acid sequence <SEQ ID 7490>. Analysis of this protein sequence reveals the following: TABLE-US-07330 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2176(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2496 A DNA sequence (GASx489R) was identified in S. pyogenes <SEQ ID 7491> which encodes the amino acid sequence <SEQ ID 7492>. Analysis of this protein sequence reveals the following: TABLE-US-07331 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2497 A DNA sequence (GASx490) was identified in S. pyogenes <SEQ ID 7493> which encodes the amino acid sequence <SEQ ID 7494>. Analysis of this protein sequence reveals the following:

TABLE-US-07332 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2547(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2498 A DNA sequence (GASx491R) was identified in S. pyogenes <SEQ ID 7495> which encodes the amino acid sequence <SEQ ID 7496>. Analysis of this protein sequence reveals the following: TABLE-US-07333 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.24 Transmembrane 6 - 22 (3 - 28) ----- Final Results ----- bacterial membrane --- Certainty = 0.5097(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2499 A DNA sequence (GASx492) was identified in S. pyogenes <SEQ ID 7497> which encodes the amino acid sequence <SEQ ID 7498>. Analysis of this protein sequence reveals the following: TABLE-US-07334 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2500 A DNA sequence (GASx493) was identified in S. pyogenes <SEQ ID 7499> which encodes the amino acid sequence <SEQ ID 7500>. Analysis of this protein sequence reveals the following: TABLE-US-07335 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.69 Transmembrane 21 - 37 (21 - 37) ----- Final Results ----- bacterial membrane --- Certainty = 0.1277(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2501 A DNA sequence (GASx495R) was identified in S. pyogenes <SEQ ID 7501> which encodes the amino acid sequence <SEQ ID 7502>. Analysis of this protein sequence reveals the following: TABLE-US-07336 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2891(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2502 A DNA sequence (GASx499R) was identified in S. pyogenes <SEQ ID 7503> which encodes the amino acid sequence <SEQ ID 7504>. Analysis of this protein sequence reveals the following: TABLE-US-07337 Possible site: 15 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.50 Transmembrane 3 - 19 (1 - 20) ----- Final Results ----- bacterial membrane --- Certainty = 0.1999(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2503 A DNA sequence (GASx500) was identified in S. pyogenes <SEQ ID 7505> which encodes the amino acid sequence <SEQ ID 7506>. Analysis of this protein sequence reveals the following: TABLE-US-07338 Possible site: 54 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07339 >GP: AAC77220 GB: AE000497 orf, hypothetical protein [Escherichia coli] Identities = 262/480 (54%), Positives = 338/480 (69%), Gaps = 5/480 (1%) Query: 18 GMLNRHGLIAGATGTGKTVTLKVLAEQLSLAGVPVFLADIKGDLSNLTKAGEVTDKLAAR 77 - GM NRHGLI GATGTGKTVTL+ LAE LS GVPVF+AD+KGDL+ + +AG V++KL AR Sbjct: 20 GMANRHGLITGATGTGKTVTLQKLAESLSEIGVPVFMADVKGDLTGVAQAGTVSEKLLAR 79 Query: 78 LATIGVSDYQPQAFPVRMWDVFGQNGQPLRTTISELGPMMLSRLLNLNDTQTGVLNIVFK 137- L IGV+D+QP A PV +WD+FG+ G P+R T+S+LGP++L+RLLNLND Q+GVLNI+F+ Sbjct: 80 LKNIGVNDWQPHANPVVVWDIFGEKGHPVRATVSDLGPLLLARLLNLNDVQSGVLNIIFR 139- Query: 138 IADEKGWLLIDLKDLQAILKEVGDHASDYSSHYGNIAKQSIGAIQRSLLTLEQEGAHQFF 19- 7 IAD++G LL+D KDL+AI + +GD+A + + YGNI+ S+GAIQR LL+LEQ+GA FF Sbjct: 140 IADDQGLLLLDFKDLRAITQYIGDNAKSFQNQYGNISSASVGAIQRGLLSLEQQGAAHFF 19- 9 Query: 198 GEPALDVADLMQLDVASGYGAINILSATKLFQSPTLYTTFLLWLLSELYKLLPEVGDLDK 25- 7 GEP LD+ D M+ D A+G G INILSA KL+Q P LY LLW+LSELY+ LPE GDL+K Sbjct: 200 GEPMLDIKDWMRTD-ANGKGVINILSAEKLYQMPKLYAASLLWMLSELYEQLPEAGDLEK 25- 8 Query: 258 PKMVFFFDEAHLLFKDAPKVFLEKVEQIVRLIRSKGVGIFFVTQNPLDLPETVLAQLGNR 31- 7 PK+VFFFDEAHLLF DAP+V L+K+EQ++RLIRSKGVG++FV+QNP D+P+ VL QLGNR Sbjct: 259 PKLVFFFDEAHLLFNDAPQVLLDKIEQVIRLIRSKGVGVWFVSQNPSDIPDNVLGQLGNR 31- 8 Query: 318 IQHAFRAYTPKEQKAVRVAADTFRQNPDLDVARVITELEVGEALISVLNDKGQPSIVERA 37- 7 +QHA RA+TPK+QKAV+ AA T R NP D + I EL GEALIS L+ KG PS+VERA Sbjct: 319 VQHALRAFTPKDQKAVKAAAQTMRANPAFDTEKAIQELGTGEALISFLDAKGSPSVVERA 37- 8 Query: 378 YIMPPKSSFAVLSEIESQQLVQSSPFASKYSQSIDRESAYEKLAAKVLEDNRLAQEAIAT 43- 7 ++ P S ++E E L+ SP KY +DRESAYE L K + + Q Sbjct: 379 MVIAPCSRMGPVTEDERNGLINHSPVYGKYEDEVDRESAYEML-QKGFQASTEQQNNPPA 43- 7 Query: 438 AQREKEAKEAIKAQAATKKANRRSVGRSHKTVVEKATDAFISTTVRTIGRELVRGLLGSL 49- 7 +E + I K + + R + ++VRG+LGSL Sbjct: 438 KGKEVAVDDGILGGLKDILFGTTGPRGGKK---DGVVQTMAKSAARQVTNQIVRGMLGSL 49- 4 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2504 A DNA sequence (GASx502) was identified in S. pyogenes <SEQ ID 7507> which encodes the amino acid sequence <SEQ ID 7508>. Analysis of this protein sequence reveals the following: TABLE-US-07340 Possible site: 49 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -13.59 Transmembrane 59-75 (52-77) INTEGRAL Likelihood = -9.34 Transmembrane 4-20 (1-24) ----- Final Results ----- bacterial membrane --- Certainty = 0.6434(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07341 >GP: CAB15368 GB: Z99121 yvaL [Bacillus subtilis] Identities = 28/72 (38%), Positives = 44/72 (60%), Gaps = 2/72 (2%) Query: 1 MYNLLLTILLVLSGLLEIAIFMQPQKNPSSNVFDSSGSEALFERTKARGFEAFMQRFTAV 60 M+ +L+T+L+++S L I + +Q K+ + S G+E LF + KARG + + R T V Sbjct: 1 MHAVLITLLVIVSIALIIVVLLQSSKSAGLSGAISGGAEQLFGKQKARGLDLILHRITVV 60 Query: 61 L--VFFWLAIAL 70 L +FF L IAL Sbjct: 61 LAVLFFVLTIAL 72 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2505 A DNA sequence (GASx505) was identified in S. pyogenes <SEQ ID 7509> which encodes the amino acid sequence <SEQ ID 7510>. Analysis of this protein sequence reveals the following: TABLE-US-07342 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.44 Transmembrane 140-156 (138-156) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07343 >GP: AAF09704 GB: AE001874 glutamine cyclotransferase [Deinococcus radiodurans] Identities = 81/229 (35%), Positives = 128/229 (55%), Gaps = 10/229 (4%) Query: 16 YSYDSNLYTQGLEQLNNNHILLSAGRYGFSKVGVYDL--TQEIFSEKIAFP-DTVFAEGL 72 - Y +D +TQGL+ L H L S G+ G S + V +L + ++S +A F EG Sbjct: 54 YPHDRAAFTQGLQYLGGGHYLESTGQVGESDLRVSELRGAKVLWSTPLAQALPQAFGEGS 113- Query: 73 TVVEDYFWLLTYKEGVAYKFDKATCNCLGAYPFEGDGWGLAYDKENQCLWMTSGNAFLQK 132- T + + LT+++GVA +D T G + ++G+GWGL D ++ L M++G + L Sbjct: 114 TQLGSTVYQLTWQDGVALTYDARTFKETGRHRYQGEGWGLTSDGKS--LIMSNGTSTLVW 17- 1 Query: 133 RDPKDFALLDTVLVAIESVPISMLNELEYVDGYLYANIWQTNTIVKLQPDSGKVVATYDI 19- 2 RDPK FA +V V + P+ LNELEYV G +YAN+W T+ I ++ P +GKV+ D+ Sbjct: 172 RDPKTFAAQRSVQVTDQGQPVRNLNELEYVQGSVYANVWLTDRIARIHPQTGKVLTWIDV 23- 1 Query: 193 SPLLKALNLDKSHYPDL----NVLNGIAHLDQQ-RFLITGKLYPLMLEV 236 S L + ++ + +V NGIA + ++ L+TGK +P + EV Sbjct: 232 SDLTREVSAAATKQGQALTFDDVPNGIAFIPERGTLLLTGKRWPTLFEV 280 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2506 A DNA sequence (GASx506R) was identified in S. pyogenes <SEQ ID 7511> which encodes the amino acid sequence <SEQ ID 7512>. Analysis of this protein sequence reveals the following: TABLE-US-07344 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2800(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2507 A DNA sequence (GASx507R) was identified in S. pyogenes <SEQ ID 7513> which encodes the amino acid sequence <SEQ ID 7514>. Analysis of this protein sequence reveals the following: TABLE-US-07345 Possible site: 53 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.51 Transmembrane 103-119 (97-124) INTEGRAL Likelihood = -9.13 Transmembrane 126-142 (122-145) INTEGRAL Likelihood = -8.65 Transmembrane 290-306 (286-307) INTEGRAL Likelihood = -7.17 Transmembrane 200-216 (198-228) INTEGRAL Likelihood = -7.06 Transmembrane 58-74 (54-82) INTEGRAL Likelihood = -3.19 Transmembrane 223-239 (220-242) INTEGRAL Likelihood = -2.81 Transmembrane 244-260 (244-261) INTEGRAL Likelihood = -2.71 Transmembrane 174-190 (169-191) ----- Final Results ----- bacterial membrane --- Certainty = 0.5203(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07346 >GP: CAB56669 GB: AL121596 putative membrane protein [Streptomyces coelicolor A3(2)] Identities = 119/322 (36%), Positives = 182/322 (55%), Gaps = 24/322 (7%) Query: 9 LETIYILIGLQLFHTAYCTFKDKTNPVYFGTALFWGLLGVTFV------------GGAFL 56 +E +Y LIGL A D++NP + +A FWGLLG+TF GG L Sbjct: 4 VEWLYWLIGLVFVVMAVQMAMDRSNPKRWTSAAFWGLLGLTFPYGTGVANATAGNGGWTL 63 Query: 57 PNKVIGFIVIVLALLTLFKQVRIGTLPAFNEQKAEESAHRIGNWIFLPVMLMAMISLLLA 116- P + +G V+ L +L F + G ++ E +A R+GN IF+P + + +++++ A Sbjct: 64 PAEPLGVAVLALIVLAGFNFLGKGVPVTTTGEQREAAAARLGNKIFVPALTIPLVAIVCA 123- Query: 117 LILPDFSKSAIGIAGILA---------TIAILIITKQKPSALLAENNRMNQQVSTSGILP 16- 7 +L + G A +L + +L+ ++K S + M + + ++ +LP Sbjct: 124 SVLDESGLFETGKATLLGLGLGCVAALVVGMLVTGEKKLSVPIHSGRSMLEAMGSALLLP 18- 3 Query: 168 QLLGALGAIFAAAGVGDVIASLIREIVPADSRFFGVLAYVLGMVIFTMIMGNAFAAFTVI 22- 7 QLL LG+IFAAAGVGD + ++ +++P DS++F VLAY +GM +FT+IMGNAFAAF V+ Sbjct: 184 QLLAVLGSIFAAAGVGDQVGDIMNKVLPDDSKYFAVLAYCVGMFLFTVIMGNAFAAFPVM 24- 3 Query: 228 TTGIGVPFVFAL--GADPIIAGALAMTAGFCGTLLTPMAANFNALPVALMEIKDRNAVIK 28- 5 T IG P + G +P + A+ M AGF GTL TPMAANFN +P L+E+KD+ IK Sbjct: 244 TAAIGWPVLIQQMHGNEPAVL-AIGMLAGFAGTLCTPMAANFNIVPATLLELKDQYGPIK 30- 2 Query: 286 KQAPIALVLIISHIALMYLLAY 307 Q P + L+ +M L A+ Sbjct: 303 AQLPTGIALLGCCTVIMALFAF 324 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2508 A DNA sequence (GASx508R) was identified in S. pyogenes <SEQ ID 7515> which encodes the amino acid sequence <SEQ ID 7516>. Analysis of this protein sequence reveals the following: TABLE-US-07347 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.15 Transmembrane 212-228 (208-235) INTEGRAL Likelihood = -8.81 Transmembrane 23-39 (17-64) INTEGRAL Likelihood = -7.43 Transmembrane 45-61 (40-64) INTEGRAL Likelihood = -1.49 Transmembrane 114-130 (114-130) INTEGRAL Likelihood = -1.49 Transmembrane 3-19 (3-20) INTEGRAL Likelihood = -1.49 Transmembrane 76-92 (76-92) ----- Final Results ----- bacterial membrane --- Certainty = 0.5861(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. TABLE-US-07348 >GP: CAB56670 GB: AL121596 possible integral membrane protein [Streptomyces coelicolor A3(2)] Identities = 77/220 (35%), Positives = 138/220 (62%), Gaps = 2/220 (0%) Query: 23 IKLIGIVIIVLGFILKCDAIATVVVAGLVTALVSGISFIDFLDILGKEFTNQRLLTIFFI 82 - I L+G+V+++LGF+ + + + V VAG+VT L+ ++ ++ L G+ F + R +T++ I Sbjct: 2 IVLLGVVVVILGFVTRRNPVLVVGVAGIVTGLLGKMNPLEVLAAFGRSFADSRSVTVYAI 61 Query: 83 TLPLIGLSETYGLKHRATQLIQRVQALTVGRLLTLYLIIRELAGLFSIR-LGGHPQFVRP 141- LP+IGL E YGL+ +A LI R+ L+ GR LT+YL++R++ F + +GG Q VRP Sbjct: 62 VLPVIGLLERYGLREQARHLIGRLGKLSAGRFLTVYLLVRQVTAAFGLNSIGGPAQTVRP 121- Query: 142 LIQPMGEAAAKANIGEELTDAEKDDIKAMAAANENFGNFFAQNTFVGAGGVLLIAGTLEQ 20- 1 L+ PM EAAA+ + G +L D ++ +++ +A+ + G FF ++ F+ G +LLI G + Sbjct: 122 LVAPMAEAAAERSTGAKLPDKLREKVRSYSASADTVGVFFGEDCFIAIGSILLITGFVNS 18- 1 Query: 202 LGY-DGNQAKIAFSSILIAIISIIIVAIYNYLFEKKMERQ 240 + D ++A +I +A+ + +I L +K++ER+ Sbjct: 182 TYHQDIEPTQLALWAIPLAVCAFLIHGARLLLMDKQLERE 221 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2509 A DNA sequence (GASx520) was identified in S. pyogenes <SEQ ID 7517> which encodes the amino acid sequence <SEQ ID 7518>. Analysis of this protein sequence reveals the following: TABLE-US-07349 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2652(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2510 A DNA sequence (GASx522R) was identified in S. pyogenes <SEQ ID 7519> which encodes the amino acid sequence <SEQ ID 7520>. Analysis of this protein sequence reveals the following: TABLE-US-07350 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2511 A DNA sequence (GASx523) was identified in S. pyogenes <SEQ ID 7521> which encodes the amino acid sequence <SEQ ID 7522>. Analysis of this protein sequence reveals the following:

TABLE-US-07351 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2133(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2512 A DNA sequence (GASx525) was identified in S. pyogenes <SEQ ID 7523> which encodes the amino acid sequence <SEQ ID 7524>. Analysis of this protein sequence reveals the following: TABLE-US-07352 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2364(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2513 A DNA sequence (GASx535) was identified in S. pyogenes <SEQ ID 7525> which encodes the amino acid sequence <SEQ ID 7526>. Analysis of this protein sequence reveals the following: TABLE-US-07353 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4223(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2514 A DNA sequence (GASx536) was identified in S. pyogenes <SEQ ID 7527> which encodes the amino acid sequence <SEQ ID 7528>. Analysis of this protein sequence reveals the following: TABLE-US-07354 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1102(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07355 >GP: AAB85515 GB: AE000874 conserved protein [Methanobacterium thermoautotrophicum] Identities = 82/236 (34%), Positives = 132/236 (55%), Gaps = 11/236 (4%) Query: 9 MNLSIFGLKNIPYLKEGDSIEKLIEESIKTSEFFIEDNDVLCIASKVVSIAEGQVMSLNE 68 M +S+ G++ +P + GD I LI ++ + D D++ IA +VS AEG ++SL E Sbjct: 1 MGISLIGVEGMPLVGAGDDIAYLIISALNEGGEDLLDGDIIVIAETIVSKAEGNIISLEE 60 Query: 69 IQVSDVAKEIHRNIPRKDPRIIEIMLNLVNRDLSRLDIKKNYIGCRLENGLKLTSGGIDR 128- I+ S A +I KDP ++E +L + + ++I +G + GID Sbjct: 61 IKPSPEALDIAERTG-KDPSLVEAILG---ESSEIIRVGHDFIVSETRHGFVCANAGIDE 116- Query: 129 KSVDEVFL--LPNNPDASAKRISEYLKKSLGKNVAVVITDSDGREDKRGATQVAIGIYGI 18- 6 +VD+ LP +PD SA++I L+++ G+ +AV+I+D+ GR + GA VA+G+ G+ Sbjct: 117 SNVDDGLATPLPRDPDGSAEKILRTLQEATGRELAVIISDTQGRPFREGAVGVAVGVAGL 17- 6 Query: 187 HPL--RKTEVIDSQGETIKFQEETLCDMIAACAGLVMGQRGTGIPAVLIRGLDYKW 240 P+ RK E D G +++ + D +AA A LVMGQ G+PAV+IRG Y W Sbjct: 177 SPIWDRKGE-RDLYGRSLETTRVAVADELAAAASLVMGQADEGVPAVIIRG--YPW 229 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2515 A DNA sequence (GASx537) was identified in S. pyogenes <SEQ ID 7529> which encodes the amino acid sequence <SEQ ID 7530>. Analysis of this protein sequence reveals the following: TABLE-US-07356 Possible site: 50 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.12 Transmembrane 174-190 (174-190) ----- Final Results ----- bacterial membrane --- Certainty = 0.1447(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2516 A DNA sequence (GASx538) was identified in S. pyogenes <SEQ ID 7531> which encodes the amino acid sequence <SEQ ID 7532>. Analysis of this protein sequence reveals the following: TABLE-US-07357 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3852(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07358 >GP: AAB99212 GB: U67562 conserved hypothetical protein [Methanococcus jannaschii] Identities = 129/387 (33%), Positives = 208/387 (53%), Gaps = 44/387 (11%) Query: 18 EVVERKGLGHPDTLADGIAEQIEIDYSLYCLDKFGVIPHHNFDKIIIRGGHSVQDFGGSD 77 - E+VERKGLGHPD++ DGIAE + ++KFG I HHN D++ + GGH+ FGG Sbjct: 20 EIVERKGLGHPDSICDGIAESVSRALCKMYMEKFGTILHHNTDQVELVGGHAYPKFGGGV 79 Query: 78 FIEPIKIIFLGRASKKCFNS------SIPLFKIQKKAATKYLNRILPNLDVENYVEFETL 131- + PI I+ GRA+ + + +P+ KAA +YL ++L N+DV+ V + Sbjct: 80 MVSPIYILLSGRATMEILDKEKNEVIKLPVGTTAVKAAKEYLKKVLRNVDVDKDVIID-- 137- Query: 132 TSDFTTKTNWFSPEAIEDLP-EYLDVPKANDTATMISYWPLTISEELALMIEGYFYKLD- 18- 9 + S + ++ + +VP ANDT+ + Y PL+ +E L L E + + Sbjct: 138 -----CRIGQGSMDLVDVFERQKNEVPLANDTSFGVGYAPLSTTERLVLETERFLNSDEL 19- 2 Query: 190 KNELPTPRFTKMGGDIKVMVVRNDLEYSIRINFPLISKFFNNDIESQLYVDKHVEKIKKY 24- 9 KNE+P +G DIKVM +R + ++ I ++ ++ N IE V +EK++K Sbjct: 193 KNEIPA-----VGEDIKVMGLREGKKITLTIAMAVVDRYVKN-IEEYKEV---IEKVRKK 24- 3 Query: 250 IEQKYKNIS--FSIDYH-----------YYLTTTGSCIDFGEEGAVGRGNKTHGIISSFR 29- 6 +E K I+ + ++ H YLT TG+ + G++G+VGRGN+ +G+I+ FR Sbjct: 244 VEDLAKKIADGYEVEIHINTADDYERESVYLTVTGTSAEMGDDGSVGRGNRVNGLITPFR 30- 3 Query: 297 PNTMEAPAGKNCTYFVGKVWGFLSDTIAKEIYEAFNT-PCQIIMQLNIGSKLYRPTHLFI 35- 5 P +MEA +GKN VGK++ L++ IA +I + C + + IG + P L I Sbjct: 304 PMSMEAASGKNPVNHVGKIYNILANLIANDIAKLEGVKECYVRILSQIGKPINEPKALDI 36- 3 Query: 356 Q--TEESVD----QERVLEIVNRHLNN 376 + TE+S D + + EI N+ L+N Sbjct: 364 EIITEDSYDIKDIEPKAKEIANKWLDN 390 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2517 A DNA sequence (GASx539) was identified in S. pyogenes <SEQ ID 7533> which encodes the amino acid sequence <SEQ ID 7534>. Analysis of this protein sequence reveals the following: TABLE-US-07359 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1436(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2518 A DNA sequence (GASx540) was identified in S. pyogenes <SEQ ID 7535> which encodes the amino acid sequence <SEQ ID 7536>. Analysis of this protein sequence reveals the following: TABLE-US-07360 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3956(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07361 >GP: AAD36304 GB: AE001779 conserved hypothetical protein [Thermotoga maritima] Identities = 105/353 (29%), Positives = 173/353 (48%), Gaps = 46/353 (13%) Query: 3 VIGIPTLNEADNISRLVKQIDEYAVNL-GKEIIIINSDSKSTDGTPQIFLETKTYNT-KV 60 V+GIP+ N A+ IS + + + V+ + +I+NSD S DGT + F+ET T+ K Sbjct: 106 VVGIPSYNNAETISHVARTAAQGIVDFFDGDGMIVNSDGGSADGTRERFMETDTFGLPKE 16- 5 Query: 61 SIVSEA-KGKGYNVRNIFEYAINHVPNFSGLILIDGDVVSMKKMWLEKMFIAIESGN-DL 118- S V E GKG +R I E+A+ + ++ +D D+ S+K W+E++ + G D Sbjct: 166 SFVYEGLPGKGSAMRAIMEFALKQ--DAEAVVFLDADLRSVKPWWVERLAGPVLKGEADY 22- 3 Query: 119 IIPNYARKSFEGNATNHFIYPMLVKIFKRDMPYQCISGDFGFSRGLIKDLTLKCN--WHK 17- 6 + P Y R F+G TN+ +PM ++ + + Q I GDFG R L++ K W+ Sbjct: 224 VTPFYLRHRFDGTITNNVCFPMTAVLYGKKVR-QPIGGDFGVGRKLLEIYLGKPKEIWNT 28- 2 Query: 177 YTLGYGIDIFLTLTAILKSYKIKEIDLQSKIH--KKSFEKIEKIFLEVSQSFFETINDNS 23- 4 +GIDI++T TAI +S ++ + L +K+H K + ++ +FL+V + FE + Sbjct: 283 DVARFGIDIWMTTTAINESGRVVQAALGTKVHDVKDPGKHLKGMFLQVVGTLFELV---- 33- 8 Query: 235 LNQDKLRLNINFESHSRQFIKSSDI------------LSSNDIENLKLRALFLLQEEKQY 28- 2 I +E+ ++ K D+ S DI NLK A L+E + Sbjct: 339 ---------ITYENVWKEIWKIEDVPIYGETPQEEVPSMSIDIGNLKKLARETLEEVEYI 38- 9 Query: 283 LHG-LSEVEWDGI--LSNTINNIYRYSSEEHSL-------YLLPLYLLRVYNY 325 G LSEV+ G LS+ ++ +YR + + LLP Y R + Sbjct: 390 DRGILSEVKESGTLSLSSWVDTLYRSAVQYRKTRDKKVVENLLPFYFARTARF 442 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2519 A DNA sequence (GASx542) was identified in S. pyogenes <SEQ ID 7537> which encodes the amino acid sequence <SEQ ID 7538>. Analysis of this protein sequence reveals the following: TABLE-US-07362 Possible site: 20 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -5.31 Transmembrane 3-19 (1-21) ----- Final Results ----- bacterial membrane --- Certainty = 0.3123(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. TABLE-US-07363 >GP: BAB07427 GB: AP001519 nucleotide sugar dehydrogenase [Bacillus halodurans] Identities = 184/388 (47%), Positives = 274/388 (70%), Gaps = 3/388 (0%) Query: 1 MKITVVGIGYVGLSIGLLLAKEHDVTFFDIDNKKIDLINKRQSPLKEAAINKLLC-KAKN 59 M IT+ G GYVGLS +LLA+ +DV +DI +K+D+IN R+SP+ + I + L K N Sbjct: 1 MNITIAGTGYVGLSNAVLLAQHNDVIAYDIVQEKVDMINNRKSPIVDREIEEFLATKELN 60 Query: 60 INATSSEELAYKDATFIILSLPTNL--KFNKLDTSIIEISVSNILKINKKATIVIKSTVP 117- + AT+ +E A+KDA F+++S PTN + N DTS +E +S++L IN A +VIKST+P Sbjct: 61 LTATTDKEKAFKDAQFVVISTPTNYDPEKNYFDTSSVEAVISDVLSINPNAVMVIKSTIP 120- Query: 118 IGFTEYLRNRFHYNDIIFSPEFLREGSTIHDQLYPSRTIVGNESRNSQLFLDILTDISVE 17- 7 +G+T + RF+ +IIFSPEFLREGS ++D L+PSR +VG ++ +++F +L +++ Sbjct: 121 VGYTREVNERFNTKNIIFSPEFLREGSALYDNLHPSRIVVGERTQRAKIFAALLVQGAIK 18- 0 Query: 178 KDSPSLLVGSSEAEAIKLFSNAYLAQKIAFFNELDTFAEMQNLDSKKIIEAMGYDQRIGN 23- 7 ++ L S+EAEAIKLF+N YLA ++AFFNELD++AE++ LD+K+II+ +G D RIG Sbjct: 181 ENIDVLFTDSTEAEAIKLFANTYLAMRVAFFNELDSYAELKGLDAKQIIDGVGLDPRIGT 24- 0 Query: 238 SHNNPSFGFGGYCLPKDIKQLEYHFKEIPAPIITSISESNLLRKIHIAKMILNSSAKTIG 29- 7 +NNPSFG+GGYCLPKD KQL +F+++P II +I ++N RK H+A MIL K +G Sbjct: 241 HYNNPSFGYGGYCLPKDTKQLLANFEDVPNNIIGAIVDANDTRKDHVANMILKREPKVVG 30- 0 Query: 298 IYRINSKKDSDNCRESSTIDVAKLLKSSGKDVIIFEPLINQKKFLGCPLSNDFNEFIKYS 35- 7 IYR+ K SDN R+S+ +DV L ++G +V+++EP ++ +F G + DF EF K S Sbjct: 301 IYRLTMKTGSDNFRQSAILDVMTRLNNAGAEVVVYEPALDATEFDGSKVIEDFAEFKKMS 36- 0 Query: 358 DIIVANRIDDALRKCNSKVFTRDIFQYD 385 D+IVANR+ D L++ KV+TRD++ D Sbjct: 361 DVIVANRLSDDLKEVAEKVYTRDLYTRD 388 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2520 A DNA sequence (GASx544R) was identified in S. pyogenes <SEQ ID 7539> which encodes the amino acid sequence <SEQ ID 7540>. Analysis of this protein sequence reveals the following: TABLE-US-07364 Possible site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.06 Transmembrane 46-62 (46-62) ----- Final Results ----- bacterial membrane --- Certainty = 0.1022(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2521 A DNA sequence (GASx545R) was identified in S. pyogenes <SEQ ID 7541> which encodes the amino acid sequence <SEQ ID 7542>. Analysis of this protein sequence reveals the following: TABLE-US-07365 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.49 Transmembrane 186-202 (186-203) ----- Final Results ----- bacterial membrane --- Certainty = 0.1595(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2522 A DNA sequence (GASx546R) was identified in S. pyogenes <SEQ ID 7543> which encodes the amino acid sequence <SEQ ID 7544>. Analysis of this protein sequence reveals the following: TABLE-US-07366 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2422(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2523 A DNA sequence (GASx547R) was identified in S. pyogenes <SEQ ID 7545> which encodes the amino acid sequence <SEQ ID 7546>. Analysis of this protein sequence reveals the following: TABLE-US-07367 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1612(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2524 A DNA sequence (GASx548) was identified in S. pyogenes <SEQ ID 7547> which encodes the amino acid sequence <SEQ ID 7548>. Analysis of this protein sequence reveals the following: TABLE-US-07368 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5156(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2525 A DNA sequence (GASx549R) was identified in S. pyogenes <SEQ ID 7549> which encodes the amino acid sequence <SEQ ID 7550>. Analysis of this protein sequence reveals the following: TABLE-US-07369 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2526 A DNA sequence (GASx552) was identified in S. pyogenes <SEQ ID 7551> which encodes the amino acid sequence <SEQ ID 7552>. Analysis of this protein sequence reveals the following:

TABLE-US-07370 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.59 Transmembrane 83-99 (83-99) ----- Final Results ----- bacterial membrane --- Certainty = 0.1235(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2527 A DNA sequence (GASx553) was identified in S. pyogenes <SEQ ID 7553> which encodes the amino acid sequence <SEQ ID 7554>. Analysis of this protein sequence reveals the following: TABLE-US-07371 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2781(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2528 A DNA sequence (GASx554) was identified in S. pyogenes <SEQ ID 7555> which encodes the amino acid sequence <SEQ ID 7556>. Analysis of this protein sequence reveals the following: TABLE-US-07372 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2792(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2529 A DNA sequence (GASx555) was identified in S. pyogenes <SEQ ID 7557> which encodes the amino acid sequence <SEQ ID 7558>. Analysis of this protein sequence reveals the following: TABLE-US-07373 Possible site: 35 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.00 Transmembrane 49-65 (49-65) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07374 >GP: BAA36631 GB: AB016282 ORF25 [bacteriophage phi-105] Identities = 43/118 (36%), Positives = 69/118 (58%), Gaps = 2/118 (1%) Query: 3 LLDLIGRKRARDKPQNSYEGQDFSYLFG--RTTSGENVDEFKTMQTTAVYACVRVLAEAV 60 LL+ + KR+ +FG +T SGE V E ++ ++ACV VL++ + Sbjct: 2 LLERMFEKRSGSSDHEDGFNNILLNMFGGRKTASGERVSESNSLVQPDIFACVNVLSDDI 61 Query: 61 ASLPIHIYERTENGKEKKLDHPLYFLLHDEPNPEMSSFIFRETIMSHLLIWGNAYVQI 118 A LPIH Y+RT+ G E+K +H ++ PNP M++F +++ +M+H+L WGNAY I Sbjct: 62 AKLPIHTYKRTDGGIERKPEHKSAHAVYARPNPYMTAFTWKKLMMTHVLTWGNAYSYI 119 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2530 A DNA sequence (GASx556) was identified in S. pyogenes <SEQ ID 7559> which encodes the amino acid sequence <SEQ ID 7560>. Analysis of this protein sequence reveals the following: TABLE-US-07375 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial Cytoplasm --- Certainty = 0.2055(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2531 A DNA sequence (GASx557) was identified in S. pyogenes <SEQ ID 7561> which encodes the amino acid sequence <SEQ ID 7562>. Analysis of this protein sequence reveals the following: TABLE-US-07376 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1696(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2532 A DNA sequence (GASx559) was identified in S. pyogenes <SEQ ID 7563> which encodes the amino acid sequence <SEQ ID 7564>. Analysis of this protein sequence reveals the following: TABLE-US-07377 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1556(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07378 >GP: CAB15798 GB: Z99123 alternate gene name: ipa-83d [Bacillus subtilis] Identities = 70/263 (26%), Positives = 121/263 (45%), Gaps = 25/263 (9%) Query: 68 KTIEQIKELK--YSIDAVACWDEALTHIADDISKELGLNPISSLDSQSFRFKDRMRMVCE 125- + +EQI ++ + DA+ +E + LGL +++ R K++MR Sbjct: 87 EVVEQIVKVAEMFGADAITTNNELFIAPMAKACERLGLRGAGVQAAENARDKNKMRDAFN 146- Query: 126 AGGLKMPKYKIINQFSDTNKIINW-KYPLIVKPTSFLASIGVKKVYNFSELQQAVSQMLN 18- 4 G+K K K + D + PLI+KPT +SIGV + + + +++ + Sbjct: 147 KAGVKSIKNKRVTTLEDFRAALEEIGTPLILKPTYLASSIGVTLITDTETAEDEFNRVND 20- 6 Query: 185 VKFPVYIASGVYELGELYNLEPRVLVEEFIDGE-----------EY-SLESVVRNGIYTP 23- 2 + + V E + EEF+ GE +Y S+E ++ +G Y P Sbjct: 207 YLKSINVPKAV-------TFEAPFIAEEFLQGEYGDWYQTEGYSDYISIEGIMADGEYFP 25- 9 Query: 233 LGITKKIVDEKLFMDEIGHIFPSNLNKEEKSRVYSWAEKLHQILQLNHITTHTEFRIGRN 29- 2 + I K ++ E HI PS L++E K ++ A+K ++ L L + THTE ++ +N Sbjct: 260 IAIHDKT--PQIGFTETSHITPSILDEEAKKKIVEAAKKANEGLGLQNCATHTEIKLMKN 31- 7 Query: 293 GDIILIEIGARIGG-DCIPNLMK 314 + LIE AR G + IPN+ K Sbjct: 318 REPGLIESAARFAGWNMIPNIKK 340 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2533 A DNA sequence (GASx561) was identified in S. pyogenes <SEQ ID 7565> which encodes the amino acid sequence <SEQ ID 7566>. Analysis of this protein sequence reveals the following: TABLE-US-07379 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2602(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2534 A DNA sequence (GASx562) was identified in S. pyogenes <SEQ ID 7567> which encodes the amino acid sequence <SEQ ID 7568>. Analysis of this protein sequence reveals the following: TABLE-US-07380 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07381 >GP: AAD06696 GB: AE001539 HISTIDYL-TRNA SYNTHETASE [Helicobacter pylori J99] Identities = 75/309 (24%), Positives = 129/309 (41%), Gaps = 35/309 (11%) Query: 11 KGYRRQFNQILLGAWGIESAYVDAEIIVATWRGLQRFKGIKVE--FIQLSNKNIFDVLEK 68 - KG R+F Q G ES DAEII L K + +E + ++++ I + + + Sbjct: 115 KGRYREFTQCDFDFIGSESLVCDAEIIQVIIASL---KALDLEDFCVSINHRKILNGICE 17- 1 Query: 69 DLSKKLRFEDISIEAILGKYLCNNDIEIIKCLYEKDKINMELLISLISKISNKLVKQEFI 128- E + I L K N E +K + D ++ L+ ++ N L EF Sbjct: 172 YFGIAQVNEVLRIVDKLEKIGLNGVEEELKKECDLDSNTIKDLLEMVQIKQNDLSHAEFF 23- 1 Query: 129 -KVLVLYEYVKNFLP----VDCIYFSLS------NLY--------GTGHYSSMNYKIFIR 16- 9 K+ L +Y +N ++ +Y L NLY G G+Y+ + Y+ + Sbjct: 232 EKIAYLKDYNENLKKGIQDLERLYQLLGDLQISQNLYKIDFSIARGLGYYTGIVYETTLN 29- 1 Query: 170 TKSGDIFDIADGGRIDDMVSKFNKVNVLGVCMGIGTTVLSQEI-------EYEIEDRIMI 22- 2 + + GGR D + F+K N+ GV IG L + E + +++I Sbjct: 292 DMKS-LGSVCSGGRYDHLTKNFSKENLQGVGASIGIDRLIVALSEMQLLDERSTQAKVLI 35- 0 Query: 223 LVEKIDVKIYKNCLELANKLSGYHCSVFEFPYKKIKKFFKHELYSRHHYIIVRLDGSMEY 28- 2 + Y N L + + SG V+ +KIKK F + + H ++ V G E+ Sbjct: 351 ACMHEEYFSYANRLAESLRQSGIFSEVYP-EAQKIKKPFSYANHKGHEFVAV--IGEEEF 40- 7 Query: 283 RFSSVALKN 291 + +++LKN Sbjct: 408 KSETLSLKN 416 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2535 A DNA sequence (GASx564) was identified in S. pyogenes <SEQ ID 7569> which encodes the amino acid sequence <SEQ ID 7570>. Analysis of this protein sequence reveals the following: TABLE-US-07382 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1264(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2536 A DNA sequence (GASx576) was identified in S. pyogenes <SEQ ID 7571> which encodes the amino acid sequence <SEQ ID 7572>. Analysis of this protein sequence reveals the following: TABLE-US-07383 Possible site: 60 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2537 A DNA sequence (GASx577R) was identified in S. pyogenes <SEQ ID 7573> which encodes the amino acid sequence <SEQ ID 7574>. Analysis of this protein sequence reveals the following: TABLE-US-07384 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.60 Transmembrane 2-18 (1-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2538 A DNA sequence (GASx579) was identified in S. pyogenes <SEQ ID 7575> which encodes the amino acid sequence <SEQ ID 7576>. Analysis of this protein sequence reveals the following: TABLE-US-07385 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3161(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07386 >GP: CAB12286 GB: Z99106 similar to hypothetical proteins [Bacillus subtilis] Identities = 62/140 (44%), Positives = 88/140 (62%), Gaps = 3/140 (2%) Query: 3 LTNYVQEVSLADFGKPLHHKAYWNKRLKTTGGRFFPKDGHLDFNPRMLEEHGELIFRKIV 62 L +++S F KP H+A +N RLKTTGGR+ +++ N + L EHG I+ Sbjct: 6 LQKLTEDISETYFKKPFRHQALFNDRLKTTGGRYLLTSHNIELNRKYLIEHGREELIGII 65 Query: 63 RHELCHYHLYFEGRGYHHKDRDFKDLLAQVNGLRY---VPTSSKSKTNHHYSCQTCGQVY 119- +HELCHYHL+ EG+GY H+DRDF+ LL QVN R+ + +++K + Y C TCGQ Y Sbjct: 66 KHELCHYHLHLEGKGYKHRDRDFRMLLQQVNAPRFCTPLKKKAENKKTYMYICTTCGQQY 125- Query: 120 QRKRRINLAKYVCGNCHGKL 139 +KR +N +Y CG C GK+ Sbjct: 126 IKKRAMNPDRYRCGKCRGKI 145 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2539 A DNA sequence (GASx587R) was identified in S. pyogenes <SEQ ID 7577> which encodes the amino acid sequence <SEQ ID 7578>. Analysis of this protein sequence reveals the following: TABLE-US-07387 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.40 Transmembrane 46-62 (39-89) INTEGRAL Likelihood = -5.36 Transmembrane 65-81 (63-89) ----- Final Results ----- bacterial membrane --- Certainty = 0.5161(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2540 A DNA sequence (GASx590R) was identified in S. pyogenes <SEQ ID 7579> which encodes the amino acid sequence <SEQ ID 7580>. Analysis of this protein sequence reveals the following: TABLE-US-07388 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2036(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2541 A DNA sequence (GASx592R) was identified in S. pyogenes <SEQ ID 7581> which encodes the amino acid sequence <SEQ ID 7582>. Analysis of this protein sequence reveals the following: TABLE-US-07389 Possible site: 23 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.62 Transmembrane 25-41 (24-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.2848(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2542 A DNA sequence (GASx600) was identified in S. pyogenes <SEQ ID 7583> which encodes the amino acid sequence <SEQ ID 7584>. Analysis of this protein sequence reveals the following: TABLE-US-07390 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.18 Transmembrane 3-19(2-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.1871(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2543 A DNA sequence (GASx603R) was identified in S. pyogenes <SEQ ID 7585> which encodes the amino acid sequence <SEQ ID 7586>. Analysis of this protein sequence reveals the following:

TABLE-US-07391 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3027(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07392 >GP: CAA03927 GB: AJ000109 gluthatione peroxidase [Lactococcus lactis] Identities = 79/133 (59%), Positives = 103/133 (77%) Query: 1 VVLVVNTATKCGLTPQYQALQALYDTYHDKGFEVLDFPCNQFLNQAPGDAEEINHFCSLT 60 VV+VVNTA+KCG TPQ++ L+ LY+TY D+G E+L FPCNQF NQ G+ EIN FC L Sbjct: 25 VVIVVNTASKCGFTPQFEGLEKLYETYKDQGLEILGFPCNQFANQDAGENTEINEFCQLN 84 Query: 61 YHTTFPRFAKIKVNGKDADPLFTWLKEEKSGPLGKRIEWNFTKFLIDQNGQVIKRYSSKT 120- Y TF F KIKVNGK+A PL+ +LK+E G L I+WNFTKFLID++GQVI+R++ KT Sbjct: 85 YGVTFTMFQKIKVNGKEAHPLYQFLKKEAKGALSGTIKWNFTKFLIDRDGQVIERFAPKT 144- Query: 121 DPKLIEEDLKALL 133 +P+ +EE++K LL Sbjct: 145 EPEEMEEEIKKLL 157 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2544 A DNA sequence (GASx605) was identified in S. pyogenes <SEQ ID 7587> which encodes the amino acid sequence <SEQ ID 7588>. Analysis of this protein sequence reveals the following: TABLE-US-07393 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3687(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2545 A DNA sequence (GASx608R) was identified in S. pyogenes <SEQ ID 7589> which encodes the amino acid sequence <SEQ ID 7590>. Analysis of this protein sequence reveals the following: TABLE-US-07394 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1327(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2546 A DNA sequence (GASx616) was identified in S. pyogenes <SEQ ID 7591> which encodes the amino acid sequence <SEQ ID 7592>. Analysis of this protein sequence reveals the following: TABLE-US-07395 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2547 A DNA sequence (GASx617R) was identified in S. pyogenes <SEQ ID 7593> which encodes the amino acid sequence <SEQ ID 7594>. Analysis of this protein sequence reveals the following: TABLE-US-07396 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0677(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2548 A DNA sequence (GASx622R) was identified in S. pyogenes <SEQ ID 7595> which encodes the amino acid sequence <SEQ ID 7596>. Analysis of this protein sequence reveals the following: TABLE-US-07397 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.32 Transmembrane 4-20 (1-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.3930(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2549 A DNA sequence (GASx632) was identified in S. pyogenes <SEQ ID 7597> which encodes the amino acid sequence <SEQ ID 7598>. Analysis of this protein sequence reveals the following: TABLE-US-07398 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.40 Transmembrane 83-99 (82-102) INTEGRAL Likelihood = -1.28 Transmembrane 108-124 (108-124) ----- Final Results ----- bacterial membrane --- Certainty = 0.2359(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2550 A DNA sequence (GASx638) was identified in S. pyogenes <SEQ ID 7599> which encodes the amino acid sequence <SEQ ID 7600>. Analysis of this protein sequence reveals the following: TABLE-US-07399 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.64 Transmembrane 12 - 28 (12 - 28) ----- Final Results ----- bacterial membrane --- Certainty = 0.1256(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2551 A DNA sequence (GASx652R) was identified in S. pyogenes <SEQ ID 7601> which encodes the amino acid sequence <SEQ ID 7602>. Analysis of this protein sequence reveals the following: TABLE-US-07400 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2622(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07401 >GP:CAA74610 GB:Y14232 hypothetical protein [Bacteriophage TP901-1] Identities = 225/485 (46%), Positives = 308/485 (63%), Gaps = 20/485 (4%) Query: 2 RKVAIYSRVSTINQAEEGYSIQGQIEALTKYCEAMEWKIYKNYSDAGFSGGKLERPAITE 61 +KVAIY+RVST NQAEEG+SI QI+ LTKY EAM W++ Y+DAGFSG KLERPA+ Sbjct: 3 KKVAIYTRVSTTNQAEEGFSIDEQIDRLTKYAEAMGWQVSDTYTDAGFSGAKLERPAMQR 62 Query: 62 LIEDGKNNKFDTILVYKLDRLSRNVKDTLYLVKDVFTANNIHFVSLKENIDTSSAMGNLF 121- LI D +N FDT+LVYKLDRLSR+V+DTLYLVKDVFT N I F+SL E+IDTSSAMG+LF Sbjct: 63 LINDIENKAFDTVLVYKLDRLSRSVRDTLYLVKDVFTKNKIDFISLNESIDTSSAMGSLF 122- Query: 122 LTLLSAIAEFEREQIKERMQFGVMNRAKSGKTTAWKTPPYGYRYNKDEKTLSVNELEAAN 18- 1 LT+LSAI EFERE IKERM G + RAKSGK+ W +GY +N+ L + L+A Sbjct: 123 LTILSAINEFERENIKERMTMGRLGRAKSGKSMMWTKTAFGYYHNRKTGILEIVPLQATI 18- 2 Query: 182 VRQMFDMIISGCSIMSITNYARDN-FVGN--TWTHVKVKRILENETYKGLVKYREQTFSG 23- 8 V Q+F +SG S+ + + ++ +G W++ +++ L+N Y G +K+++ F G Sbjct: 183 VEQIFTDYLSGISLTKLRDKLNESGHIGKDIPWSYRTLRQTLDNPVYCGYIKFKDSLFEG 24- 2 Query: 239 DHQAIIDEKTYNKAQIALAHRT----DTKTNTRPFQGKYMLSHIAKCGYCGAPLKVCTGR 29- 4 H+ II +TY K Q L R + N RPFQ KYMLS +A+CGYCGAPLK+ G Sbjct: 243 MHKPIIPYETYLKVQKELEERQQQTYERNNNPRPFQAKYMLSGMARCGYCGAPLKIVLGH 30- 2 Query: 295 AKNDGTRRQTYVCVNKTESLARRSVNNYNNQKICNTGRYEKKHIEKYVIDVLYKLQHDKE 35- 4 + DG+R Y C N+ + + YN+ K C++G Y+ ++E VID L Q + + Sbjct: 303 KRKDGSRTMKYHCANRFPR-KTKGITVYNDNKKCDSGTYDLSNLENTVIDNLIGFQENND 36- 1 Query: 355 YLKKIKKDDN--IIDITPLKKEIEIIDKKINRLNDLYINDLIDLPKLKKDIEELNHLKDD 41- 2 L KI +N I+D + KK+I IDKKI + +DLY+ND I + +LK + L K Sbjct: 362 SLLKIINGNNQPILDTSSFKKQISQIDKKIQKNSDLYLNDFITMDELKDRTDSLQAEK-- 41- 9 Query: 413 YNKAIKLNYLDKKNEDSLGML------MDNLDIRKSSYDVQSRIVKQLIDRVEVTNDNID 46- 6 K +K +K DS + + ++ I + SYD + +IV L+ +V+VT DN+D Sbjct: 420 --KLLKAKISENKFNDSTDVFELVKTQLGSIPINELSYDNKKKIVNNLVSKVDVTADNVD 47- 7 Query: 467 IIFKF 471 IIFKF Sbjct: 478 IIFKF 482 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2552 A DNA sequence (GASx653R) was identified in S. pyogenes <SEQ ID 7603> which encodes the amino acid sequence <SEQ ID 7604>. Analysis of this protein sequence reveals the following: TABLE-US-07402 Possible site: 48 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.22 Transmembrane 86 - 102 (86 - 102) ----- Final Results ----- bacterial membrane --- Certainty = 0.1489(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07403 >GP:AAF12707 GB:AF066865 unknown [bacteriophage TPW22] Identities = 45/67 (67%), Positives = 53/67 (78%), Gaps = 2/67 (2%) Query: 57 EKEAVRCPKCKSTNVGFMQQGKKTFSVKKAVAGTLLIG--GTVMGFLGEKGKKQWHCNEC 114- +K A++CPKCKST+V FMQQGKK FSV KAV G +L G GT+ GF G+KGKKQWHCN C Sbjct: 138 DKHAIKCPKCKSTDVVFMQQGKKGFSVGKAVGGAVLTGGIGTLAGFAGKKGKKQWHCNNC 19- 7 Query: 115 SCIFETK 121 +FETK Sbjct: 198 GRVFETK 204 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2553 A DNA sequence (GASx655) was identified in S. pyogenes <SEQ ID 7605> which encodes the amino acid sequence <SEQ ID 7606>. Analysis of this protein sequence reveals the following: TABLE-US-07404 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3956(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07405 >GP:CAB63661 GB:AJ251789 Cro protein [Lactobacilius casei bacteriophage A2] Identities = 43/76 (56%), Positives = 55/76 (71%) Query: 26 MTINLKRLKAERIASGMTQCEVAQSMGWKTRTPYAKRENGIVSIGADELAKITLIFGLPI 85 - MT+NLKRL+AERIA GM Q E+A++MGW TR+ YAKRENGI +I A EL K+ I G Sbjct: 1 MTLNLKRLRAERIAKGMNQDEMAKAMGWHTRSSYAKRENGITTISATELVKMASILGYGT 60 Query: 86 EKIAIFFDKDVPVMER 101 ++ +FF +VP ER Sbjct: 61 NQLDLFFTNNVPDRER 76 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2554 A DNA sequence (GASx656) was identified in S. pyogenes <SEQ ID 7607> which encodes the amino acid sequence <SEQ ID 7608>. Analysis of this protein sequence reveals the following: TABLE-US-07406 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4505(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2555 A DNA sequence (GASx657) was identified in S. pyogenes <SEQ ID 7609> which encodes the amino acid sequence <SEQ ID 7610>. Analysis of this protein sequence reveals the following: TABLE-US-07407 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6593(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2556 A DNA sequence (GASx658) was identified in S. pyogenes <SEQ ID 7611> which encodes the amino acid sequence <SEQ ID 7612>. Analysis of this protein sequence reveals the following: TABLE-US-07408 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5244(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2557 A DNA sequence (GASx660) was identified in S. pyogenes <SEQ ID 7613> which encodes the amino acid sequence <SEQ ID 7614>. Analysis of this protein sequence reveals the following: TABLE-US-07409 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1133(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07410 >GP: AAB99331 GB: U67572 purine NTPase [Methanococcus jannaschii] Identities = 71/346 (20%), Positives = 154/346 (43%), Gaps = 52/346 (15%) Query: 8 MSITINKLEIENVK-----RIKAVKIEPSATGLTIIGGNNNQGKTSVLDAIAWAL--GGN 60 MS+ + ++ + N K RIK K G+ I G N GK+S+ +A+ +AL G+ Sbjct: 1 MSMILKEIRMNNFKSHVNSRIKFEK------GIVAIIGENGSGKSSIFEAVFFALFGAGS 54 Query: 61 KYKPSQAMREGSQ---VPPTLKITMSNGLIVERKGKNASLKVIDPNGQ----------KG 107- + + +G + V ++ +N I+ + NG+ K Sbjct: 55 NFNYDTIITKGKKSVYVELDFEVNGNNYKIIREYDSGRGGAKLYKNGKPYATTISAVNKA 114- Query: 108 GQQLL----DSFVEELAI---NLPKFMDSTPKEKADVLLEIIGVGDQLAELELKEKEIYN 16- 0 ++L + F+ + I + KF+ P EK + + +++G+ D+ + K EI Sbjct: 115 VNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGI-DEFEKCYQKMGEIVK 17- 3 Query: 161 QRHAIGVIADQKEKFAKEMTYYPDAPKQLVS-ISELIQQHQAILAKNGE-NAQKR--QNV 21- 6 + + E+ E+ Y + K+L + +S+L ++++ ++ N + N K+ +++ Sbjct: 174 E------YEKRLERIEGELNYKENYEKELKNKMSQLEEKNKKLMEINDKLNKIKKEFEDI 22- 7 Query: 217 ERIRYDYNQSILEVDRLRKLLADAEAKTNKLSEDLKIANTD------AMDLHDESTAEIE 27- 0 E++ ++ L ++ L + + +++LKI D A + + E E Sbjct: 228 EKLFNEWENKKLLYEKFINKLEERKRALELKNQELKILEYDLNTVVEARETLNRHKDEYE 28- 7 Query: 271 ANIADIDEVNRKVRANFDKDKAE-EDAKQQREQYNILTNDIESIRQ 315 + +DE+ RK+ + + K+ ED + +Q I+ DIE +++ Sbjct: 288 KYKSLVDEI-RKIESRLRELKSHYEDYLKLTKQLEIIKGDIEKLKE 332 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2558 A DNA sequence (GASx661) was identified in S. pyogenes <SEQ ID 7615> which encodes the amino acid sequence <SEQ ID 7616>. Analysis of this protein sequence reveals the following: TABLE-US-07411 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1559(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2559 A DNA sequence (GASx662) was identified in S. pyogenes <SEQ ID 7617> which encodes the amino acid sequence <SEQ ID 7618>. Analysis of this protein sequence reveals the following:

TABLE-US-07412 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3292(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2560 A DNA sequence (GASx663) was identified in S. pyogenes <SEQ ID 7619> which encodes the amino acid sequence <SEQ ID 7620>. Analysis of this protein sequence reveals the following: TABLE-US-07413 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4867(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2561 A DNA sequence (GASx664) was identified in S. pyogenes <SEQ ID 7621> which encodes the amino acid sequence <SEQ ID 7622>. Analysis of this protein sequence reveals the following: TABLE-US-07414 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2141(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2562 A DNA sequence (GASx667) was identified in S. pyogenes <SEQ ID 7623> which encodes the amino acid sequence <SEQ ID 7624>. Analysis of this protein sequence reveals the following: TABLE-US-07415 Possible site: 59 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2614(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07416 >GP: AAF80834 GB: AF165214 Orf78 [Pseudomonas phage D3] Identities = 68/200 (34%), Positives = 109/200 (54%), Gaps = 10/200 (5%) Query: 12 GLRFGSLTVINRNRNNSKGGNARWNCLCDCGNKTVVI-GSKLRSGYTKSCGCARKNDNAK 70 - GLR G + V ++ G + W C CDCGN+ ++ G+ +R+ T SCGC+R + Sbjct: 8 GLRVGKVVV--EAFSHCAGKASHWVCRCDCGNRVIMRRGNLMRNRTTTSCGCSRFSH--- 62 Query: 71 GYSSTRLYRIWKGMMNRCYNHKNDNYKYYGGKGISICDEWLTFINFRTWSLSNGYKESLT 130- G + T Y W M++RC N N Y Y G+GI++C+ W+TF NF G + T Sbjct: 63 GMTGTPTYSSWSNMIDRCTNPSNKRYVDYQGRGITVCERWMTFANFLA---DMGERPDAT 119- Query: 131 -IDRINPKGNYTPLNCRWVSMKMQQNNKTNNRYLSYLGQEYTIAEFSEKLNVTYWTVINQ 18- 9 +DRI+ Y NCRW + Q NN N ++ YLG+ T+++++ +L + T+ ++ Sbjct: 120 SLDRIDNDAGYFKENCRWATALEQMNNTRRNTFVEYLGRRQTVSQWAGQLGIPECTLRSR 17- 9 Query: 190 LKLGWSVERIVEEARMKNDR 209 L GWS+E +++ K R Sbjct: 180 LNRGWSIEDAMQKPISKQRR 199 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2563 A DNA sequence (GASx668) was identified in S. pyogenes <SEQ ID 7625> which encodes the amino acid sequence <SEQ ID 7626>. Analysis of this protein sequence reveals the following: TABLE-US-07417 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1476(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07418 >GP: CAB75598 GB: AJ271879 putative DNA helicase [uncultured eubacterium] Identities = 42/168 (25%), Positives = 75/168 (44%), Gaps = 7/168 (4%) Query: 374 IAGPSKAGKSFALIELSIALAEGQKWLG-WQCEQGKVLYVNLELDRPSALHRFKDVYDAM 43- 2 + P AGKS ++L+ +A G LG + G V+Y+ E D P+A+H A Sbjct: 35 LVSPGGAGKSMLALQLAAQIAGGPDLLGVGELPTGPVIYLPAE-DPPTAIHHRLHALGAH 93 Query: 433 GLPPANVANIDIWNLRGKTVPMDKLAPKLIRRSLKKNYQA---VIIDPIYKVLTGDENSA 48- 9 A D ++ + + +LK+ + +I+D + + +EN++ Sbjct: 94 LSAEERQAVADGLLIQPLIGSLPNIMASNWFEALKRAAEGRRLMILDTLRRFHIEEENAS 153- Query: 490 DQMAHFTNQFDKVATELGCSVIYCHHHSKGS--QGGKKSMDRASGSGV 535 MA + + +A + GCS+++ HH SKG+ G + GS V Sbjct: 154 GPMAQVIGRMEAIAADTGCSIVFLHHASKGATMMGAGDQQQASRGSSV 201 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2564 A DNA sequence (GASx669) was identified in S. pyogenes <SEQ ID 7627> which encodes the amino acid sequence <SEQ ID 7628>. Analysis of this protein sequence reveals the following: TABLE-US-07419 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2555(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2565 A DNA sequence (GASx670) was identified in S. pyogenes <SEQ ID 7629> which encodes the amino acid sequence <SEQ ID 7630>. Analysis of this protein sequence reveals the following: TABLE-US-07420 Possible Site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2921(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07421 >GP: AAF74082 GB: AF212845 ORF129 [Lactococcus lactis bacteriophage u136] Identities = 36/108 (33%), Positives = 63/108 (58%), Gaps = 1/108 (0%) Query: 8 IEFFLPMDKIPTTTHQQKKVTVINGKPHFYEPESLKNARDKFTSLLAQHVPPSKLDGPIR 67 ++F +DK+PTT QQK + + GK FY+ KN K + + + + P++ Sbjct: 1 MKFEFELDKMPTT-QQQKGIKKVKGKLQFYDRRGTKNYSLKAQLMKNKPKECWEKNVPLK 59 Query: 68 LTVKWLFPKIKGSTNGQYKTTKPDTDNLQKLLKDCMTELGFWNDDAQV 115 L+V + + + Q+KT++PD DNL K L+D MT+L +++DD+Q+ Sbjct: 60 LSVTFFYAIKQKKRWWQWKTSRPDLDNLMKNLQDYMTKLRYYSDDSQI 107 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2566 A DNA sequence (GASx671) was identified in S. pyogenes <SEQ ID 7631> which encodes the amino acid sequence <SEQ ID 7632>. Analysis of this protein sequence reveals the following: TABLE-US-07422 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4294(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2567 A DNA sequence (GASx672R) was identified in S. pyogenes <SEQ ID 7633> which encodes the amino acid sequence <SEQ ID 7634>. Analysis of this protein sequence reveals the following: TABLE-US-07423 Possible site: 15 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.37 Transmembrane 106-122 (104-125) ----- Final Results ----- bacterial membrane --- Certainty = 0.3548(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2568 A DNA sequence (GASx673) was identified in S. pyogenes <SEQ ID 7635> which encodes the amino acid sequence <SEQ ID 7636>. Analysis of this protein sequence reveals the following: TABLE-US-07424 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4781(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07425 >GP: AAB18697 GB: U38906 ORF22 [Bacteriophage rlt] Identities = 78/207 (37%), Positives = 123/207 (58%), Gaps = 2/207 (0%) Query: 28 EIHRILGIDEVYKAPKRLTDILFDKDSREDIFRQFLKYETDVSYDWFMQYFEEEQADRKN 87 - + + +L +DE R+ +++FDK RE+ + + L D+ D+F YF A Sbjct: 7 QFYDMLNVDEHMNFTNRIQELVFDKKGREEFYSKILNIHHDMGVDFFRDYFMAHSAVSA- 65 Query: 88 KKQDFTPKSVSTLLSKIISGNQYYEVA-VGTGGILIQAWQEQRLNDSPFTYRPSKYWYHV 146- K Q +TP + L + ++ G+ ++ GTG ++IQ WQ+ R+N F Y PS YWY Sbjct: 66 KGQHYTPDELGKLTALLVGGSGGADLTGAGTGTLIIQKWQDDRMNTDFFNYLPSNYWYQA 125- Query: 147 EELSDKAVPFLLFNMSIRGINGVVVHGDSLTRQVKNIYFLQNTKDDMLSFSDINVMPRTQ 20- 6 ELSD+A+ FL+ +IRG+NGVV+HGD+L VK +YF+QN+ ++ + FS+INV+P ++ Sbjct: 126 LELSDEAISFLIHAFAIRGMNGVVIHGDALEMAVKQVYFIQNSANNPIGFSEINVIPHSK 18- 5 Query: 207 DIEREFNVKEWIGDGIEHIENPLIEWI 233 D + EW IEHIE+ +WI Sbjct: 186 DAMEFLGIHEWTEQAIEHIESKFPDWI 212 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2569 A DNA sequence (GASx674) was identified in S. pyogenes <SEQ ID 7637> which encodes the amino acid sequence <SEQ ID 7638>. Analysis of this protein sequence reveals the following: TABLE-US-07426 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.00 Transmembrane 122-138 (122-138) ----- Final Results ----- bacterial membrane --- Certainty = 0.1001(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07427 >GP: AAF63071 GB: AF158600 gp137 [Streptococcus thermophilus bacteriophage Sfi11] Identities = 66/135 (48%), Positives = 89/135 (65%), Gaps = 2/135 (1%) Query: 5 PEIDIQKTKSNAKRKLREYPRWRRIANDVDTQKVTATYSFEPRQSHGVPSKPVERLALNR 64 PEID + T KRKLREYPRWR IA+D QK+T ++F PR G +KPVE +A+ R Sbjct: 4 PEIDEKATLKRCKRKLREYPRWREIAHDSAEQKITQEFTFMPRG--GGVNKPVENIAVRR 61 Query: 65 VSAEQELDAIEQAVSMILEPERRRILYDKYLAPYKKADKVIYTELCMSESFYYDTLDIAL 124- V A EL+AIEQAV+ + P+ RRIL +KYLA K + I + + + + L+ ++ Sbjct: 62 VDALNELEAIEQAVNGLYRPDYRRILIEKYLAYPPKPNWQIAQSIGFERTAFQELLNNSI 121- Query: 125 LAFAELYREGVLLVE 139 LAFAELYR+G L+VE Sbjct: 122 LAFAELYRDGRLIVE 136 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2570 A DNA sequence (GASx675) was identified in S. pyogenes <SEQ ID 7639> which encodes the amino acid sequence <SEQ ID 7640>. Analysis of this protein sequence reveals the following: TABLE-US-07428 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1865(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2571 A DNA sequence (GASx676) was identified in S. pyogenes <SEQ ID 7641> which encodes the amino acid sequence <SEQ ID 7642>. Analysis of this protein sequence reveals the following: TABLE-US-07429 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4870(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07430 >GP:BAB07254 GB:AP001519 unknown [Bacillus halodurans] Identities = 194/451 (43%), Positives = 262/451 (58%), Gaps = 69/451 (15%) Query: 1 MEFVDKKLSEITPYKNNPRNNDEAVGPVAE----SIKEFGFKVPIVV-DKNGEIVNGHTR 55 + V+KK+ ++ P + NPR + + P E SI+EFG PIV ++ G +V GH R Sbjct: 3 IRIVNKKIDDLVPAEYNPRLDLQPGDPEYEKLKRSIEEFGLVEPIVFNERTGRVVGGHQR 62 Query: 56 YKAAQKLGLETVPVIVADDLSEEQIKAFRLADNKV-GEIAVWDLDLLNEELNDILDLDMS 114- K ++LG E VPV V D L + KA +A NK+ G+ + L L EEL+ L+D++ Sbjct: 63 LKILRELGWEEVPVSVVD-LDDHHEKALNVALNKIEGDWDNFKLKELLEELDSGL-IDVT 120- Query: 115 AFGFDVLDNLDDL-----IEDEKDL--DDF----TGTVPDEPKSKLGDIYQLGSHKLMCG 16- 3 GFD + ++DL +EDE ++ DDF +EP +K GD++ LG H L+ G Sbjct: 121 LTGFDE-EEIEDLMTQFFVEDENEIKEDDFDPDEVAEEIEEPITKPGDLWHLGRHFLLVG 17- 9 Query: 164 DSTNGADVKKLMNGELADLLLTDPPYNVAYEGKTKDSLTIKNDSMDNDSFRQFLVNAFSS 22- 3 DST DVK+LM E AD++ TDPPYNV YEG T + IKND+M++ F QFL +AF + Sbjct: 180 DSTKIEDVKRLMGNEKADMIFTDPPYNVDYEGAT--GMKIKNDNMEDSEFYQFLFDAFVA 23- 7 Query: 224 ANEVMKPGAVFYIWHADSEGYNFRGACFDIGWTVRQCLIWNKNSMVLGRQDYHWKHEPCL 28- 3 +V K G Y+ HADSEG FR A D G+ ++QCLIW KNS+VLGRQDYHW+HEP L Sbjct: 238 MYQVTKEGGPIYVCHADSEGLTFRKAFQDSGFLLKQCLIWVKNSLVLGRQDYHWRHEPIL 29- 7 Query: 284 YGWKDGAGHLWASDRKQTSVID-------------------------------------- 30- 5 YGWK GA H W RKQ++VI+ Sbjct: 298 YGWKPGAAHKWYGGRKQSTVIEDPVDLAITPKVDHVLLTFNNGISSTVVKVPSYEIIHDG 35- 7 Query: 306 ---------YEKPQRNGVHPTMKPVGLFDYQIKNNTKGSDIVLDLFGGSGTTLIACESNG 35- 6 E+P+RN HPTMKP+ L I+N++K + VLD FGGSG+TLIACE G Sbjct: 358 SDEGMTTWRIERPKRNADHPTMKPIALCARAIQNSSKPGERVLDPFGGSGSTLIACEQTG 41- 7 Query: 357 RHARLMEYDPKYVDVIIKRWEELTGESVIQL 387 R +MEYDP Y +VII+RWEE TG++ ++L Sbjct: 418 RICHMMEYDPVYAEVIIRRWEEWTGQNAVKL 448 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2572 A DNA sequence (GASx677) was identified in S. pyogenes <SEQ ID 7643> which encodes the amino acid sequence <SEQ ID 7644>. Analysis of this protein sequence reveals the following: TABLE-US-07431 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4744(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2573 A DNA sequence (GASx678) was identified in S. pyogenes <SEQ ID 7645> which encodes the amino acid sequence <SEQ ID 7646>. Analysis of this protein sequence reveals the following: TABLE-US-07432 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.27 Transmembrane 90 - 106 (90 - 106) ----- Final Results ----- bacterial membrane --- Certainty = 0.1107(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2574 A DNA sequence (GASx679) was identified in S. pyogenes <SEQ ID 7647> which encodes the amino acid sequence <SEQ ID 7648>. Analysis of this protein sequence reveals the following:

TABLE-US-07433 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3408(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07434 >GP:CAA66734 GB:X98106 minor capsid protein [Bacteriophage phigle] Identities = 213/494 (43%), Positives = 323/494 (65%), Gaps = 19/494 (3%) Query: 1 MGVIQKIKNLVTRSKYVM-TTQSLTNITDHPKIAISKLEYDRITTNLKYYKSDWDSVLYL 59 MG+IQ+IK+L + T SL+ ITD P+I+I EY RI T+L YY + Y Sbjct: 1 MGLIQRIKDLFWKGAAATGVTGSLSKITDDPRISIDPDEYVRIQTDLDYYSDKLQYIHYQ 60 Query: 60 NTDGETKKRDLNHLPIARTAAKKIASLVFNEQAEIKV-DDDAANEFISETLKNDRFNKNF 118- +DG KKR N + +A+TAA++IAS+VFNE+AEI V D++ A++F++ L+++ F F Sbjct: 61 ASDGIKKKRLKNTINMAKTAARRIASVVFNEKAEIHVKDNNEADKFLNDVLEDNDFKNKF 120- Query: 119 ERYLESCLALGGLAMRPYVDGDKVRVAFVQAPVFLPLQSNTQDVSSAAVVIKSVKTINGK 17- 8 E LE +ALGG AMRPY+DG+ +++A+V+A F PLQSNT D+S AA+ ++ +T + + Sbjct: 121 EEALEKGVALGGFAMRPYIDGNHIKIAWVRADQFYPLQSNTNDISEAAIASRTQRTESNQ 18- 0 Query: 179 EVYYTLIEFHEWQSSDDYVISNELYRSDDKAKVGSRVPLS--EVYKDLKDEAKVTDVTRP 23- 6 YYTL+EFH+WQ + Y I+NELY+SD VG++VPLS VYK+L + ++ + RP Sbjct: 181 TKYYTLLEFHQWQDNGSYQITNELYKSDSPDIVGNQVPLSTLPVYKELAPQVTISGLQRP 24- 0 Query: 237 IFTYLKTPGMNNKDINSPLGLSIFDNAKTTIDFINTTYDEFMWEVKMGQRRVAVPESLTA 29- 6 +F Y KTPG NN +I SPLGL + DNAK +D IN T+D+F+WE+++GQ+ +AV + Sbjct: 241 LFAYFKTPGANNINIESPLGLGVVDNAKHVLDDINDTHDQFIWEIRLGQKHIAVQPGMLR 30- 0 Query: 297 LTVRTADGDVVPRPRFESDQNVYIRMGGRDLDSSAIQDLTTPIRADDYIKAINEGLSLFE 35- 6 D +P F+++QNVY+ + D + ++D+TTPIR Y AI+ + FE Sbjt: 301 F-------DDEHKPTFDTEQNVYVGVLSDDNNGLGVKDMTTPIRTVQYKDAIDHFIKEFE 353- Query: 357 MQIGVSAGLFSFDGKSMKTATEIVSENSDTYQMRNSIVTLVEQSLKELVISIFEIAKAYD 41- 6 +QIG+S G FS+ +KTATE+VS NS TYQ R+S +T+VE+++ EL SIFE+A A Sbjct: 354 VQIGLSTGTFSYSNDGVKTATEVVSNNSMTYQTRSSYLTMVEKAIDELCQSIFELANAGA 41- 3 Query: 417 LYQSEVP--SMDNISISL------DDGVFTDRDAELDYWIKVVNAGFGTREMAIQKVLNV 46- 8 L+ P ++D+ S L DDGVF ++D +L+ KV+ G +++ +Q+ + Sbjct: 414 LFDDGKPLFTLDSASQPLDIECHFDDGVFVNKDKQLEEDAKVLAIGALSKQTFLQRNYGM 47- 3 Query: 469 TEEKAQEIAAEINT 482 T+E+A E A+I + Sbjct: 474 TDEQAAEELAKIQS 487 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2575 A DNA sequence (GASx680) was identified in S. pyogenes <SEQ ID 7649> which encodes the amino acid sequence <SEQ ID 7650>. Analysis of this protein sequence reveals the following: TABLE-US-07435 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1840(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07436 >GP:CAB53790 GB:AJ242593 gp4 [Bacteriophage A118] Identities = 114/385 (29%), Positives = 187/385 (47%), Gaps = 23/385 (5%) Query: 8 LNDEQLLLEASQLSDMYHQLTLDLFDQVIERIKARGSASLADNPYLWQANKLHDVGLLNA 67 L QL L + D+Y L +LF ++ R+K + + S AND WQ KL+ V L+ Sbjct: 3 LTPRQLDLFVQPIVDVYTGLENELFTLIVRRLKTKKNIS-ADNVLAWQIEKLNQVHALDQ 61 Query: 68 DNIKLIAKYSGIAEAQLRYIIKNEGFKIYKNTSEQLEEALGRESGV-------NSTIQDD 120- I+ I+K SG++ +L ++K+ G+ K + E+G TI D Sbjct: 62 QMIERISKASGVSAKKLFSVVKDAGYSDLKQVDNYFSKLA--EAGAVLPLVSDGQTIVDK 119- Query: 121 LSNYARQAIDDVHNLTNTTLPFSVIGAYQGIIQDAVAGVVTGLKTPDQAINQTVIKWFKK 18- 0 + + + + N T+ Y II + V+ GLKT QA+ +TV K+ + Sbjct: 120 VMRSYFKLAESNYKRINQTMLSQARQIYSDIIHETTQSVLAGLKTHRQALAETVTKFAEN 17- 9 Query: 181 GFYGFTDKAGRKWRADSYARTVINTTTWRVFNEAKEAPAREFGIDTFYYSKKATAREMCA 24- 0 G DKA ++W ++Y RTV TT V+N ++ E+G+D S+ AR C+ Sbjct: 180 GVPALVDKANKRWTPEAYVRTVTRTTVNSVYNSVEDERMNEYGVDLVRISQHVGARPTCS 23- 9 Query: 241 PLQHQIV---TTGEAREEGGIKILALSD----YGHGEPDGCLGINCKHTKTPFVVGVNSK 29- 3 +Q +++ + E R + G K +++ YG+G DG G NC+H + F+ G+N Sbjct: 240 IVQGKVICLLSVEETRSKYGNKYMSIYSPELRYGYG--DGIFGCNCRHHRFAFIEGINIA 29- 7 Query: 294 PELPEHLKNITPAQAKANANAQAKQRAIERSIRKSKELLHVAKQLGDKELIRQYQSDVRS 35- 3 P+ E I + K +QR +ER IR +K L A++LGD+ +++ + VR+ Sbjct: 298 PDESE---LIDEEENKRVYALSQQQRLMERDIRAAKRKLSAAEELGDELAVKKAKQAVRT 35- 4 Query: 354 KQDALNYLINNNAFLHRNQAREKRY 378 KQ L + + L R +REK Y Sbjct: 355 KQSKLRAFVKTHN-LTRQYSREKVY 378 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2576 A DNA sequence (GASx681) was identified in S. pyogenes <SEQ ID 7651> which encodes the amino acid sequence <SEQ ID 7652>. Analysis of this protein sequence reveals the following: TABLE-US-07437 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2756(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2577 A DNA sequence (GASx682) was identified in S. pyogenes <SEQ ID 7653> which encodes the amino acid sequence <SEQ ID 7654>: TABLE-US-07438 TLDNQSVIKAIGDTVDYIKKNYKRKWGK Analysis of this protein sequence reveals the following: TABLE-US-07439 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2578 A DNA sequence (GASx683) was identified in S. pyogenes <SEQ ID 7655> which encodes the amino acid sequence <SEQ ID 7656>. Analysis of this protein sequence reveals the following: TABLE-US-07440 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5288(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2579 A DNA sequence (GASx685) was identified in S. pyogenes <SEQ ID 7657> which encodes the amino acid sequence <SEQ ID 7658>: TABLE-US-07441 GATEVGANRVVSGVYGEVLGVQIVRSRKCPKGTAYMVRKGALRIMLKRNT MVETDRDITKAINQIVANKHYGVYLYKAEKAVKITLRDAAKK Analysis of this protein sequence reveals the following: TABLE-US-07442 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1750(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07443 >GP:CAA59185 GB:X84706 major head protein [Bacteriophage B1] Identities = 138/270 (51%), Positives = 186/270 (68%), Gaps = 6/270 (2%) Query: 1 MAVGTTKMAQMLDPEVLADMIDAEVGKAIRFAPLAEVDTTLEGQPGTTLTVPK-WDYIGD 59 M+ T +A +++PEVLA ++ E+ KA+RFAPLA+VDTTL+GQPG TL P + YIGD Sbjct: 1 MSKQKTTLADLVNPEVLATIVSYELNKALRFAPLAQVDTTLQGQPGNTLKFPDPFTYIGD 60 Query: 60 AEDVAEGEAIPMTQLGFKKTTMTIKKAGKGVEITDEAILSGYGDPVGQAAKQIVEAIDHK 119- A DVAEG I + ++G ++TIKKA KG EITDEA LSGYGDP+G++ KQ+ ++ +K Sbjct: 61 AADVAEGGEISLDKIGTTTKSVTIKKAAKGTEITDEAALSGYGDPIGESNKQLGLSLANK 120- Query: 120 VDADVLDALSKSTQTVEATATVDGVSKALDIFNDEDDAETVIVMNPADASTLRLDAAKEW 17- 9 VD D+L A ++QTV A VDGV ALDIFNDED V+++NP DA+ +R DA + Sbjct: 121 VDDDLLSAAKTTSQTVSTKANVDGVQAALDIFNDEDAQAYVLIVNPKDAAKIRKDANAKN 18- 0 Query: 180 LGATEVGANRVVSGVYGEVLGVQIVRSRKCPKGTAYMVR----KGALRIMLKRNTMVETD 23- 5 +G +EVGAN +++G Y +VLG QIVRS+K +G+A M + AL+++LKR VETD Sbjct: 181 IG-SEVGANALINGTYADVLGAQIVRSKKLAEGSALMFKIVSNSPALKLVLKRGVQVETD 23- 9 Query: 236 RDITKAINQIVANKHYGVYLYKAEKAVKIT 265 RDI I A++HY YLY K V IT Sbjct: 240 RDIVTKTTVITADEHYAAYLYDLTKVVNIT 269 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2580 A DNA sequence (GASx686) was identified in S. pyogenes <SEQ ID 7659> which encodes the amino acid sequence <SEQ ID 7660>. Analysis of this protein sequence reveals the following: TABLE-US-07444 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2581 A DNA sequence (GASx687) was identified in S. pyogenes <SEQ ID 7661> which encodes the amino acid sequence <SEQ ID 7662>. Analysis of this protein sequence reveals the following: TABLE-US-07445 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2942(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2582 A DNA sequence (GASx688) was identified in S. pyogenes <SEQ ID 7663> which encodes the amino acid sequence <SEQ ID 7664>. Analysis of this protein sequence reveals the following: TABLE-US-07446 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2844(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07447 >GP:AAC00538 GB:L02496 unknown protein [Bacteriophage LL-H] Identities = 35/86 (40%), Positives = 48/86 (55%), Gaps = 6/86 (6%) Query: 24 KLIMNNQVMMSMNPYVPYRDGALRGSSRANSVGVTWSGPHARAQFYGGAYNKYKSFKFKK 83 - +L + NQ+ M YVP R G LR S N G+ ++ +ARAQFYG + + Sbjct: 20 RLQVLNQMHQDMEQYVPKRAGFLRSQSFVNDTGIHYTAKYARAQFYGFV----NGHRVRN 75 Query: 84 YTTPGTGKRWDKRALANATIVKDWEK 109 Y+TPGTG+RWD + A A DW+K Sbjct: 76 YSTPGTGRRWDLK--AKAVYKADWQK 99 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2583 A DNA sequence (GASx689) was identified in S. pyogenes <SEQ ID 7665> which encodes the amino acid sequence <SEQ ID 7666>. Analysis of this protein sequence reveals the following: TABLE-US-07448 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2892(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07449 >GP:CAA66741 GB:X98106 minor capsid protein [Bacteriophage phigle] Identities = 36/109 (33%), Positives = 64/109 (58%), Gaps = 2/109 (1%) Query: 17 DLGIKPRLDYLTRQEDLAIYPMPGGKVNNEYMDGTREISLPFEIAIKTKNQELASTVMWT 76 - +L +K L YLT + L++YP+PG +V +E G ++ + +E+ ++TKNQ+ A+T +W Sbjct: 16 NLPMKCTLGYLTAADSLSLYPLPGSRVLDEDYAGNQQWQMNYEVGMRTKNQQQANTTLWL 75 Query: 77 INSALSNFDL-KLPSLNHSYTFISLDVE-KPFLNDLSDQGFYIYVLDIT 123 ++ AL L S N S+ F SL + +P +++ QG+ Y L + Sbjct: 76 VSQALDVLTADDLVSSNGSFEFESLTINGQPSISEQDTQGYSTYQLSFS 124 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2584 A DNA sequence (GASx690) was identified in S. pyogenes <SEQ ID 7667> which encodes the amino acid sequence <SEQ ID 7668>. Analysis of this protein sequence reveals the following: TABLE-US-07450 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1626(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07451 >GP:CAB53798 GB:AJ242593 major tail shaft protein [Bacteriophage A118] Identities = 54/133 (40%), Positives = 77/133 (57%), Gaps = 9/133 (6%) Query: 1 MRQKNALRGHFIAPYVKGEEKTEVTKEKLLELARWIKDISDDTDEKTEDEAYYDGDGTEE 60 MR KNA + +A V G + + + L++WI ++SDD + TE++ YDGDG E+ Sbjct: 1 MRIKNAKTKYSVAEIVAGAGEPDWKR-----LSKWITNVSDDGSDNTEEQGDYDGDGNEK 55 Query: 61 TTVVGVKGAYTFEGTYDPEDKAQAHIASLKYKLGDERKVWHLIVSADGKTQWLGVATVTE 120- T V+G AYTFEGT+D ED+AQ I + K + + R + I D +T +G ATV+E Sbjct: 56 TVVLGYSEAYTFEGTHDREDEAQNLIVA-KRRTPENRSIMFKIEIPDTETA-IGKATVSE 113- Query: 121 I--IAGSGAAARF 131 I AG G A F Sbjct: 114 IKGSAGGGDATEF 126 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2585 A DNA sequence (GASx691) was identified in S. pyogenes <SEQ ID 7669> which encodes the amino acid sequence <SEQ ID 7670>. Analysis of this protein sequence reveals the following: TABLE-US-07452 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3521(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2586 A DNA sequence (GASx692) was identified in S. pyogenes <SEQ ID 7671> which encodes the amino acid sequence <SEQ ID 7672>. Analysis of this protein sequence reveals the following: TABLE-US-07453 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3438(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07454 >GP:CAB53801 GB:AJ242593 gp15 [Bacteriophage A118] Identities = 67/191 (35%), Positives = 110/191 (57%), Gaps = 17/191 (8%) Query: 11 FEFRGEIYPIDLSFNKVLDVFDVIDDDFLNEAEKCFLCLDILLDRTDLPFTYAVD----- 65 - +E+ G+ Y +DL+F+ VL V D+ +D+ L++ + L +D+L D+P+ + + Sbjct: 12 YEYEGKEYKLDLAFDNVLRVIDLTEDNSLSDVFRANLAIDVLF-ADDMPWPRSNEEDEYA 70 Query: 66 -------LWVYIKTNFIDAERPEKPQLDIKGNPMPVVKEKEDNKKVI---DLSLDAEFIY 115- + + I TN+I E + DI GN MP D+ + I L+ DA++IY Sbjct: 71 NIEEKSLVLIDIFTNYIVKENDDGLLYDIDGNKMPSATNNNDDAEEIASYSLTQDADYIY 130- Query: 116 ASFRQAYQINLLKEQNRLSWIEFKALLNALPDDTVMQRIIAIRQWE-DDGEGSKKYRDNM 17- 4 ASF Q Y I+LL + ++ W +F+ALL +L DDT ++ II IRQ E G+G++K R+ + Sbjct: 131 ASFLQDYNIDLLDSRGKMHWYKFRALLESLRDDTTIKTIIGIRQAELPSGKGTEKERNEL 19- 0 Query: 175 RKLKAKYSLDE 185 KLK +Y L + Sbjct: 191 IKLKNRYKLKD 201 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2587 A DNA sequence (GASx694) was identified in S. pyogenes <SEQ ID 7673> which encodes the amino acid sequence <SEQ ID 7674>. Analysis of this protein sequence reveals the following:

TABLE-US-07455 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4143(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07456 >GP:AAG18639 GB:AY007505 unknown [Streptococcus mitis] Identities = 48/157 (30%), Positives = 85/157 (53%), Gaps = 10/157 (6%) Query: 86 DLELSWEPDYIYKATHITPFSIKEVLRNFGRLKINFLIHPIKYLKTGKQEVPLVNG-GTL 144- +LE S+ P+ ++ A H S K + +LKI + P +Y KT E NG GT+ Sbjct: 81 ELEFSYHPESVFYA-HFLTASYKPFGNHAWQLKIKLNMQPFRYQKTVNPES--YNGPGTI 137- Query: 145 QNPGNVQAKPILKIKGTGNGILTINDFETGLENVQSELVIDMERHLVYKDVLSAWDNIVR 20- 4 NPG + ++PI++++G G+ +TI ET NV+++ ID + +++ +A + Sbjct: 138 NNPGTIYSEPIIEVQGDGDVSITIGR-ETMYLNVKTKATIDCRQG--RQNIYNATGAVQN 19- 4 Query: 205 TERHRMPLFDV--GQNKISWTGS-FTITAVPNWGVKV 238 T R R F++ G++ I++TG+ + PNW K+ Sbjct: 195 TLRKRGGFFEIPTGRSGITFTGNVLRLIIRPNWRYKI 231 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2588 A DNA sequence (GASx695R) was identified in S. pyogenes <SEQ ID 7675> which encodes the amino acid sequence <SEQ ID 7676>. Analysis of this protein sequence reveals the following: TABLE-US-07457 Possible site: 15 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.60 Transmembrane 15 - 31 (15 - 31) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2589 A DNA sequence (GASx697) was identified in S. pyogenes <SEQ ID 7677> which encodes the amino acid sequence <SEQ ID 7678>. Analysis of this protein sequence reveals the following: TABLE-US-07458 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3348(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07459 >GP:AAA86895 GB:U28144 hyaluronidase [Streptococcus pyogenes] Identities = 326/337 (96%), Positives = 329/337 (96%) Query: 1 MSENIPLRVQFKRMKAAEWARSDVILLESEIGFETDTGFARAGDGHNRFSDLGYISPLDY 60 MSENIPLRVQFKRMKAAEWARSDVILLESEIGFETDTGFARAGDGHNRFSDLGYISPLDY Sbjct: 1 MSENIPLRVQFKRMKAAEWARSDVILLESEIGFETDTGFARAGDGHNRFSDLGYISPLDY 60 Query: 61 NLLTNKPNIDGLATKVETAQKLQQKADKETVYTKAESKQELDKKLNLKGGVMTGQLKFKP 120- NLLTNKPNIDGLATKVETAQKLQQKADKETVYTKAESKQELDKKLNLKGGVMTGQLKFKP Sbjct: 61 NLLTNKPNIDGLATKVETAQKLQQKADKETVYTKAESKQELDKKLNLKGGVMTGQLKFKP 120- Query: 121 AATVAYSSSTGGAVNIDLSSTRGAGVVVYSDNDTSDGPLMSLRTGKETFNQSALFVDYKG 18- 0 AATVAYSSSTGGAVNIDLSSTRGAGVVVYSDNDTSDGPLMSLRTGKETFNQSALFVDYKG Sbjct: 121 AATVAYSSSTGGAVNIDLSSTRGAGVVVYSDNDTSDGPLMSLRTGKETFNQSALFVDYKG 18- 0 Query: 181 TTNAVNIAMRQPTTPNFSSALNITSGNENGSAMQLRGSEKALGTLKITHENPSIGADYDK 24- 0 TTNAVNIAMR TTPNFSSALNITSGNENGSAMQLRGSEKALGTLKITHENPSIGADYDK Sbjct: 181 TTNAVNIAMRHATTPNFSSALNITSGNENGSAMQLRGSEKALGTLKITHENPSIGADYDK 24- 0 Query: 241 NAAALSIDIVKKTNGAGTAAQGIYINSTSGTTGKLLRIRNLSDDKFYVKSDGGFYAKETS 30- 0 NAA + + K+ NGAGTAAQGIYINSTSGTTGKLLRIRNLSDDKFYVKSDGGFYAKETS Sbjct: 241 NAARYPLILSKRQNGAGTAAQGIYINSTSGTTGKLLRIRNLSDDKFYVKSDGGFYAKETS 30- 0 Query: 301 QIDGNLKLKDPTANDHAATKAYVDKAISELKKLILKK 337 QIDGNLKLKDPTANDHAATKAYVDKAISELKKLILKK Sbjct: 301 QIDGNLKLKDPTANDHAATKAYVDKAISELKKLILKK 337 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2590 A DNA sequence (GASx698) was identified in S. pyogenes <SEQ ID 7679> which encodes the amino acid sequence <SEQ ID 7680>. Analysis of this protein sequence reveals the following: TABLE-US-07460 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4208(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> RGD motif 54-56 No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07461 >GP: AAA98102 GB: M19348 ORF [Streptococcus pyogenes phage H4489A] Identities = 250/648 (38%), Positives = 351/648 (53%), Gaps = 75/648 (11%) Query: 1 MSRDPTLILDESNLVIGKDGRVHYTFTTEDDNPKVRLASKCLGTAHFNQLMIERGDQATS 60 MSRDPT ++E +L DGR + TF + + VRL S CLG +L +E + Sbjct: 1 MSRDPTYTINEHDLSFA-DGRFYVTFKADKSSETVRLNSSCLGNTIIKKLQVEDDNTMHD 59 Query: 61 YVAPVVVEGTGNPTGLFKDLKEISLELTDTANSQLWSKIKLTNRGMLQEYYDGKIKTEIV 12- 0 +V P V T GL + +KE+ L+L D S LW KIK N+ ML EY + ++ + I Sbjct: 60 FVKPKVT--TQQAFGLAQQVKELDLQLKDP-KSDLWGKIKFNNKAMLVEYANKEMSSAIA 11- 6 Query: 121 NSARGVATRISEDTDKKLALINDTIDGIRREYRDADRKLSASYQAGIEGLKATMANDKIG 18- 0 SA + ++ D++ + T++GI++ + Sbjct: 117 QSAEQILLQVKSIDDERYSKFEQTLNGIKQTVKSES------------------------ 15- 2 Query: 181 LQAEIKASAQGLSQKYDDELRKLSAKITTTSSGTTEAYESKLAGLRAEFTRSNQGTRTEL 24- 0 ++++ L+ +D + L K + S T ++ S+L G + L Sbjct: 153 ----VESARTQLASMFDSRISGLDGKYSRLSQ-TIDSLSSRLD--------DGVGNYSTL 19- 9 Query: 241 ESQISGLRAVQQSTASQISQEIRDREGAVSRVQQSLESYQRRMQDAEENYSSLTHTVRGL 30- 0 ++SG I + + VSR+ Q+ + Q ++ +A +NYSSL+ TV+GL Sbjct: 200 SQKVSG-----------IDLRVSNAANDVSRLSQTAQGLQSQITNANQNYSSLSQTVQGL 24- 8 Query: 301 QSDVGSPTGKIQSRLTQLAGQIEQRVTRDGVMSIISGAGDSIKLAIQKAGGINAKMSGNE 36- 0 Q+ V SR+ QL+ I +VT+ V + I+ + D I AI+ + KM+G+E Sbjct: 249 QTTVRDNQSNATSRINQLSDLISTKVTKGDVETTIAQSYDKIAFAIRDKLPAS-KMTGSE 30- 7 Query: 361 IIASINLNSYGVTIAGKHAILDGNTTVNGTFTTKIAEAIKIRADQIIAGTIDAARIRVIN 42- 0 IISAINL+ GV I GK+I LDGN+ ++ K A + A +I G ++A+RI Sbjct: 308 IISAINLDRSGVKITGKNITLDGNSYISNA-VIKDAHIANMDAGKINTGYLNASRIAAEA 36- 6 Query: 421 LNASSIVGLDANFIK--AKIGY---------------AIT---DLLEGKVIKARNGAMLI 46- 0 + I A F K A GY A+T + G V+ A NGA Sbjct: 367 ITGDKIKMDYAFFNKLTANEGYFRTLFAKNIFTTSVQAVTTSASKITGGVLSATNGASRW 42- 6 Query: 461 DLNTAKMDFNSDATINFNSKNNALVRKDGTHTAFVHFSNATPKGYTGSALYASIGITSSG 52- 0 DLN+A +DFN DATINFNSKNNALVRK GT+TAFVHFSNATPKGY GSALYASIGITSSG Sbjct: 427 DLNSANIDFNRDATINFNSKNNALVRKSGTNTAFVHFSNATPKGYRGSALYASIGITSSG 48- 6 Query: 521 DGVNSASSGRFAGLRSFRYATGYNHTAAVDQTEIYGDNVLVVDDFNITRGFKFRPDKMQK 58- 0 DG++SASSGRF G+R FRYA G HTA VDQ EIYGD+++ DDFNI RGFK RP M K Sbjct: 487 DGIDSASSGRFCGVRFFRYAEGLQHTAKVDQAEIYGDDIVFSDDFNIDRGFKMRPSLMPK 54- 6 Query: 581 MLDMNDLYAAVVALGRCWGHLANVGWNTAHSNFTSAVNRELNNYITKI 628 M+D+N +Y A++ALGRCW H N W+ + + SA+ E N +I + Sbjct: 547 MVDLNKMYQAILALGRCWLHANNTAWSW-NFDTRSAIIAEYNAHINNL 593 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2591 A DNA sequence (GASx699) was identified in S. pyogenes <SEQ ID 7681> which encodes the amino acid sequence <SEQ ID 7682>. Analysis of this protein sequence reveals the following: TABLE-US-07462 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3323(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2592 A DNA sequence (GASx701) was identified in S. pyogenes <SEQ ID 7683> which encodes the amino acid sequence <SEQ ID 7684>. Analysis of this protein sequence reveals the following: TABLE-US-07463 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1017(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2593 A DNA sequence (GASx702) was identified in S. pyogenes <SEQ ID 7685> which encodes the amino acid sequence <SEQ ID 7686>. Analysis of this protein sequence reveals the following: TABLE-US-07464 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.03 Transmembrane 2-18 ( 1-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.2211(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2594 A DNA sequence (GASx703) was identified in S. pyogenes <SEQ ID 7687> which encodes the amino acid sequence <SEQ ID 7688>. Analysis of this protein sequence reveals the following: TABLE-US-07465 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -3.45 Transmembrane 36-52 ( 36-55) ----- Final Results ----- bacterial membrane --- Certainty = 0.2381(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07466 >GP: AAC39287 GB: AF115103 orf87 gp [Streptococcus thermophilus bacteriophage Sfi21] Identities = 43/73 (58%), Positives = 61/73 (82%) Query: 1 MINLKLRLQNKVTLMAILGAIFLLAQQLGIKLPSNIADIANTAVTLLVLLGVVTDPTTKG 60 - MIN KLRLQNK TL+A++ A+FL+ QQ G+ +P+NI + NT V +LV+LG++TDPTTKG Sbjct: 8 MINFKLRLQNKATLVALISAVFLMLQQFGLHVPNNIQEGINTLVGILVILGIITDPTTKG 67 Query: 61 LSDSEQALTYHEP 73 ++DSE+AL+Y +P Sbjct: 68 IADSERALSYIQP 80 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2595 A DNA sequence (GASx707R) was identified in S. pyogenes <SEQ ID 7689> which encodes the amino acid sequence <SEQ ID 7690>. Analysis of this protein sequence reveals the following: TABLE-US-07467 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.35 Transmembrane 9-25 ( 1-27) ----- Final Results ----- bacterial membrane --- Certainty = 0.5140(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2596 A DNA sequence (GASx714R) was identified in S. pyogenes <SEQ ID 7691> which encodes the amino acid sequence <SEQ ID 7692>. Analysis of this protein sequence reveals the following: TABLE-US-07468 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1401(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2597 A DNA sequence (GASx715) was identified in S. pyogenes <SEQ ID 7693> which encodes the amino acid sequence <SEQ ID 7694>. Analysis of this protein sequence reveals the following: TABLE-US-07469 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0417(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2598 A DNA sequence (GASx726) was identified in S. pyogenes <SEQ ID 7695> which encodes the amino acid sequence <SEQ ID 7696>. Analysis of this protein sequence reveals the following: TABLE-US-07470 Possible site: 33 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.17 Transmembrane 18-34 ( 18-35) ----- Final Results ----- bacterial membrane --- Certainty = 0.1468(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2599 A DNA sequence (GASx728R) was identified in S. pyogenes <SEQ ID 7697> which encodes the amino acid sequence <SEQ ID 7698>. Analysis of this protein sequence reveals the following: TABLE-US-07471 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1795(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07472 >GP: AAF61314 GB: U96166 unknown [Streptococcus cristatus] Identities = 149/194 (76%), Positives = 162/194 (82%) Query: 1 LSAIIRQSTSKRISDKRGIYLVEKLVSLAKQSYFTVTKTSPMIEEVRYYAKELLRLSERR 60 L IIRQSTSKRIS+KR YL +KL+ LAKQS+ V KTSPM+EEVRYYA+ELLRLSERR Sbjct: 56 LYEIIRQSTSKRISEKRIAYLTDKLIKLAKQSFCAVKKTSPMLEEVRYYAQELLRLSERR 11- 5 Query: 61 QAIFDKMVASAQPLPEDKILRSIPSIVETTATSIIGELGAIRRFQSANQINAFIGIDFRH 12- 0 Q + + MVA AQPLPE ILRSIP I ETTATSIIGELG I RFQS NQ NAFIGID RH Sbjct: 116 QVVLNDMVALAQPLPEYDILRSIPGIAETTATSIIGELGDIHRFQSTNQFNAFIGIDLRH 17- 5 Query: 121 YESGNYLAQEHITKRGNPYAPKILFKCIDHIAFASHTNPCHIADFYEKRKRQSQTASTKP 18- 0 YES N+LA+EHITKRGNPYA KILFKCIH+IA ASHTNPCHIADFYEKRKRQS ASTKP Sbjct: 176 YESRNFLAKEHITKRGNPYARKILFKCIHNIASASHTNPCHIADFYEKRKRQSTIASTKP 23- 5 Query: 181 HTIASRHCLVRQCF 194 TIAS H L+R + Sbjct: 236 LTIASIHRLIRTMY 249 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2600 A DNA sequence (GASx729R) was identified in S. pyogenes <SEQ ID 7699> which encodes the amino acid sequence <SEQ ID 7700>. Analysis of this protein sequence reveals the following: TABLE-US-07473 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2363(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2601 A DNA sequence (GASx730R) was identified in S. pyogenes <SEQ ID 7701> which encodes the amino acid sequence <SEQ ID 7702>. Analysis of this protein sequence reveals the following:

TABLE-US-07474 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2602 A DNA sequence (GASx734) was identified in S. pyogenes <SEQ ID 7703> which encodes the amino acid sequence <SEQ ID 7704>. Analysis of this protein sequence reveals the following: TABLE-US-07475 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4001(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2603 A DNA sequence (GASx735) was identified in S. pyogenes <SEQ ID 7705> which encodes the amino acid sequence <SEQ ID 7706>. Analysis of this protein sequence reveals the following: TABLE-US-07476 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.66 Transmembrane 276-292 ( 274-292) ----- Final Results ----- bacterial membrane --- Certainty = 0.2466(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2604 A DNA sequence (GASx736) was identified in S. pyogenes <SEQ ID 7707> which encodes the amino acid sequence <SEQ ID 7708>. Analysis of this protein sequence reveals the following: TABLE-US-07477 Possible site: 33 >>> Seems to have no N-terminal signal sequence ---- Final Results ---- bacterial cytoplasm --- Certainty = 0.3998(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2605 A DNA sequence (GASx737) was identified in S. pyogenes <SEQ ID 7709> which encodes the amino acid sequence <SEQ ID 7710>. Analysis of this protein sequence reveals the following: TABLE-US-07478 Possible site: 60 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.74 Transmembrane 77-93 ( 69-99) INTEGRAL Likelihood = -4.14 Transmembrane 152-168 ( 151-170) INTEGRAL Likelihood = -1.17 Transmembrane 196-212 ( 194-212) ----- Final Results ----- bacterial membrane --- Certainty = 0.6095(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2606 A DNA sequence (GASx738) was identified in S. pyogenes <SEQ ID 7711> which encodes the amino acid sequence <SEQ ID 7712>. Analysis of this protein sequence reveals the following: TABLE-US-07479 Possible site: 37 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -13.16 Transmembrane 44-60 ( 39-71) INTEGRAL Likelihood = -10.24 Transmembrane 94-110 ( 81-114) INTEGRAL Likelihood = -7.64 Transmembrane 185-201 ( 179-207) INTEGRAL Likelihood = -7.48 Transmembrane 132-148 ( 130-158) INTEGRAL Likelihood = -2.76 Transmenibrane 208-224 ( 204-225) INTEGRAL Likelihood = -0.06 Transmernbrane 153-169 ( 152-169) ----- Final Results ----- bacterial membrane --- Certainty = 0.6265(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2607 A DNA sequence (GASx742) was identified in S. pyogenes <SEQ ID 7713> which encodes the amino acid sequence <SEQ ID 7714>. Analysis of this protein sequence reveals the following: TABLE-US-07480 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.80 Transmembrane 887-903 ( 882-906) INTEGRAL Likelihood = -4.88 Transmembrane 6-22 ( 5-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.4121(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 877-881 No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07481 >GP: CAB46409 GB: AL096743 putative large secreted protein [Streptomyces coelicolor A3(2)] Identities = 231/599 (38%), Positives = 329/599 (54%), Gaps = 43/599 (7%) Query: 278 TSSNSDASSRNIVKIGEIQGASHTSPLLKKAVTVEQVVVTYL---DDSTHFYVQDLNGDG 33- 4 T +++ +++ V+I ++QG++ SP + VT +VT + S F++QD D Sbjct: 28 TPAHAASAAAGPVRIHDVQGSTRLSPYAGEQVTDVAGIVTGVRGYGSSKGFWMQDPLPDA 87 Query: 335 DLATSDGIRVFAKNA-KVQVGDVLTISGEVEEFFGRGYEERKQTDLTITQIVAKAVTK-T 39- 2 D ATS+G+ VF A +V VGD +T+SG V E+ G Q+ +T+I VT + Sbjct: 88 DPATSEGVFVFTSRAPEVAVGDAVTVSGTVSEYVPGGTSSGNQS---LTEITRPTVTVVS 14- 4 Query: 393 GTAQVPSPLVLGKDRIAPANIIDNDGLR-------VFDPEEDAIDYWESMEGMLVAVDDA 44- 5 G +P+ + + A + DG P A+DY+ES+EGM V V DA Sbjct: 145 GGNAIPAATTVSARSVPRAYAPEGDGAANGSVNALPLRPGTYALDYYESLEGMNVRVADA 20- 4 Query: 446 KILGPMKN-KEIYVLPGSSTRPLNNSGGVLLPANSYNTDVIPVLFKKGKQI----IKAGD 50- 0 +++G E++V P G V + NT + + GK GD Sbjct: 205 RVVGASDPYTELWVTVKPWENPNRRGGTVYGSYDDQNTGRLQIQ-SLGKPADFPAADVGD 26- 3 Query: 501 SYKGRLAGPVSYS-YGNYKVFVDDSKNMPSLMDGHLKPEKTNLQKDLSKLSIASYNIENF 55- 9 + G AGP+ Y+ YG Y + + + +L G + E T Q +L++A+YN+EN Sbjct: 264 TLAGTTAGPLDYNQYGGYTLVASE---IGALESGGTERESTRRQS-ARELAVATYNVENL 31- 9 Query: 560 SANPSSTKDEKVKRIAESFIHDLNAPDIIGLIEVQDNNGPTDDGTTDATQSAQRLIDAIK 61- 9 +PS D+ AE+ +H L +PDI+ L E+QDNNG TDDGT A + RLIDAI Sbjct: 320 --DPS---DDTFTAHAETIVHRLKSPDIVSLEEIQDNNGATDDGTVAADATVGRLIDAIV 37- 4 Query: 620 KLGGPTYRYVDIAPENNVDGGQPGGNIRTGFLYQPERVSLSDKPKGGARDA--LTWVNGE 43- 4 GGP Y + I P + DGGQPGGNIR FL+ PERVS +D+ G A A + V G+ Sbjct: 375 AAGGPRYDWRGIDPVDKADGGQPGGNIRQAFLFNPERVSFTDRAGGDATTATGVRKVRGK 43- 4 Query: 678 --LNLSVGRIDPTNAAWKDVRKSLAAEFIFQGRKVVVVANHLNSKRGDNALYGCVQPVTF 73- 5 L S GR+DP N AW+D RK LA EF+F+GR V VVANH NSK GD L QP + Sbjct: 435 AALTHSPGRVDPANEAWEDSRKPLAGEFVFRGRTVFVVANHFNSKGGDQGLTAQYQPPSR 49- 4 Query: 736 KSEQQRHVLANMLAQFAKE--QAKHQANIVMLGDFNDFEFTKTIQLIE-EGDMVNLVSRH 79- 2 SE +RH A ++ F KE A+ A++V LGD NDFEF++T +++E +G + + V Sbjct: 495 GSETQRHAQAKVVNTFVKEILAAQKNADVVALGDINDFEFSRTARILEGDGALWSAVKSL 55- 4 Query: 793 DISDRYSYFHQGNNQTLDNILVSRHLL--DHYEFDMVHVNSPFMEAHGRASDHDPLLLQ 849- S+RYSY +QGN+Q LD ILVS + H +D VHVN+ F H + SDHDP +L+ Sbjct: 555 PRSERYSYVYQGNSQVLDQILVSPSVRRGGHLSYDSVHVNAEF---HDQISDHDPQVLR 610- Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2608 A DNA sequence (GASx743) was identified in S. pyogenes <SEQ ID 7715> which encodes the amino acid sequence <SEQ ID 7716>. Analysis of this protein sequence reveals the following: TABLE-US-07482 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2437(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2609 A DNA sequence (GASx756) was identified in S. pyogenes <SEQ ID 7717> which encodes the amino acid sequence <SEQ ID 7718>. Analysis of this protein sequence reveals the following: TABLE-US-07483 Possible site: 18 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.30 Transmembrane 10-26 ( 8-27) INTEGRAL Likelihood = -3.08 Transmembrane 51-67 ( 50-67) ----- Final Results ----- bacterial membrane --- Certainty = 0.2720(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2610 A repeated DNA sequence (GASx758) was identified in S. pyogenes <SEQ ID 7719> which encodes the amino acid sequence <SEQ ID 7720>. Analysis of this protein sequence reveals the following: TABLE-US-07484 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07485 >GP: CAA38133 GB: X54225 7 kDa protein [Streptococcus pneumoniae] Identities = 31/61 (50%), Positives = 41/61 (66%) Query: 1 MTNGLKYVLEQMLLLFIIAALACLFLAIGLMIGYSFMGDGQSPWHILSMDKWAELVNKFT 60- M YV++++LL+I+ L L L IGLM+GY +G GQ PW ILS KW EL++KFT Sbjct: 3 MNKKSSYVVKRLLLVIIVLILGTLALGIGLMVGYGILGKGQDPWAILSPAKWQELIHKFT 62- Query: 61 G 61 G Sbjct: 63 G 63 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2611 A DNA sequence (GASx764) was identified in S. pyogenes <SEQ ID 7721> which encodes the amino acid sequence <SEQ ID 7722>. Analysis of this protein sequence reveals the following: TABLE-US-07486 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.98 Transmembrane 47-63 ( 46-67) ----- Final Results ----- bacterial membrane --- Certainty = 0.2593(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9149> which encodes the amino acid sequence <SEQ ID 9150>. Analysis of this protein sequence reveals the following: TABLE-US-07487 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.98 Transmembrane 35-51 ( 34-55) ----- Final Results ----- bacterial membrane --- Certainty = 0.2593(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2612 A DNA sequence (GASx783) was identified in S. pyogenes <SEQ ID 7723> which encodes the amino acid sequence <SEQ ID 7724>. Analysis of this protein sequence reveals the following: TABLE-US-07488 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.16 Transmembrane 142-158 ( 132-167) INTEGRAL Likelihood = -12.26 Transmembrane 113-129 ( 101-140) INTEGRAL Likelihood = -10.24 Transmembrane 238-254 ( 233-260) INTEGRAL Likelihood = -2.76 Tramsmembrane 34-50 ( 34-51) ----- Final Results ----- bacterial membrane --- Certainty = 0.6265(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07489 >GP: BAA32091 GB: AB010970 ABC-transporter [Streptococcus mutans] Identities = 173/269 (64%), Positives = 214/269 (79%), Gaps = 2/269 (0%) Query: 1 MNFLTKKNRILLREMVKTDFKLRYQGSAIGYLWSILKPLMMFTIMYLVFIRFLRLGGNVP 60 M+F ++KNRILL+E++KTDFKLRYQGSAIGYLWSILKPLM+F IMY+VF+RFL LGG+VP Sbjct: 1 MDFFSRKNRILLKELIKTDFKLRYQGSAIGYLWSILKPLMLFAIMYIVFVRFLPLGGDVP 60 Query: 61 HFPVALLLANVIWSFFSEATSMGMVSIVSRGDLLRKLNFSKHIIVFSAVLGALINFLINL 12- 0 H+PVALLL LVIW+FF E T MGMVS+V+RGDLLRKLNFSK IVFSAV GA INF IN+ Sbjct: 61 HWPVALLLGNVIWTFFQETTMMGMVSVVTRGDLLRKNLFSKQTIVFSAVSGAAINFGINV 12- 0 Query: 121 VVVLIFALINGVTIS--GYAYLSLFLFIELVVLVLGIALLLSNVFVYYRDLAQVWEVLLQ 17- 8 +VVLIFAL+NGFT + +L + LF+EL++ GIA +LS ++V YRD+ VWEV+LQ Sbjct: 121 IVVLIFALLNGVTFTFRWNLFLLIPLFLELLLGSTGIAFILSTLYVRYRDIGPVWEVILQ 18- 0 Query: 179 AGMYATPIIYPITFVLDSHPLAAKLLMLNPVAQMIQDFRYLLIDRANVTIWQMSTNWFYI 23- 8 G Y TPIIY +T++ + AKLL+L+P+AQ+IQD R++LID ANVTIWQM + Sbjct: 181 GGFYGTPIIYSLTYIARRSVVGAKLLLLSPIAQIIQDMRHILIDPANVTIWQMINHKSIA 24- 0 Query: 239 VIPYLVPFVILFIGIFVFKKNADRFAEII 267 VIPYLVP + IG++VF++NA +FAEII Sbjct: 241 VIPYLVPIFVFIIGFLVFNYNAKKFAEII 269 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2613 A DNA sequence (GASx786) was identified in S. pyogenes <SEQ ID 7725> which encodes the amino acid sequence <SEQ ID 7726>. Analysis of this protein sequence reveals the following: TABLE-US-07490 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3828(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07491 >GP: BAA32094 GB: AB010970 rgpFc [Streptococcus mutans] Identities = 381/582 (65%), Positives = 475/582 (81%), Gaps = 1/582 (0%) Query: 1 MNRILLYVHFNKYNKISAHVYYQLEQMRSLFSKIVFISNSKVSHEDLKRLKNHCLIDEFL 60 M R+LLYVHFNKYN++S+HV YQL QMRSLFSK++FISNS+V+ D+K L+ LID+F+ Sbjct: 1 MKRLLLYVHFNKYNRVSSHVVYQLTQMRSLFSKVIFISNSQVADADVKMLREKHLIDDFI 60 Query: 61 QRKNKGFDFSAWHDGLIIMGFDKLEEFDSLTIMNDTCFGPIWEMAPYFENFEEKETVDFW 120- QR+N GFDF+AW DG++ +GFD+L +DS+T MNDTCFGP+WEM ++ FE K TVDFW Sbjct: 61 QRQNSGFDFAAWRDGMVFVGFDELVTYDSVTTMNDTCFGPLWEMYSIYQEFETKTTVDFW 120- Query: 121 GITNNRGTKAFKEHVQSYFMTFKNQVIQNKVFQQFWQSIIEYENVQEVIQHYETQLTSIL 18- 0 G+TNNR TK+F+EH+QSYF++FK V+++ F+ FW++I EY++VQ+VI YET++T+ L Sbjct: 121 GLTNNRATKSFREHIQSYFISFKASVLRSTAFRDFWENIKEYQDVQKVIDQYETKVTTTL 18- 0 Query: 181 LNEGFSYQTVFDTRKAESSFMPHPDFSYYNPTAILKHHVPFIKVKAIDANQHIAPYLLNL 24- 0 L+ GF Y VFDT K ++S M H DFSYYNPTAIL H VPFIKVKAID NQHI PYLLN Sbjct: 181 LDAGFQYDVVFDTTKEDASHMLHADFSYYNPTAILNHRVPFIKVKAIDNNQHITPYLLND 24- 0 Query: 241 IRETTNYPIDLIVSHMSQISLPDTKYLLSQKYLNCQRLAKQTCQKVAVHLHVFYVDLLDE 30- 0 I++ + YPIDLIVSHMS+I+ PD YLL KY+ + QKVAVHLHVFYVDLL+E Sbjct: 241 IQKNSTYPIDLIVSHMSEINYPDFSYLLGHKYVKKRERVDLKNQKVAVHLHVFYVDLLEE 30- 0 Query: 301 FLTAFENWNFHYDLFITTDSDIKRKEIKEILQRKGKTADIRVTGNRGRDIYPMLLLKDKL 36- 0 FLTAF+ ++F YDLFITTDSD K+ EI+EIL G+ A + VTGN GRD+ PML LK+ L Sbjct: 301 FLTAFKQFHFSYDLFITTDSDDKKAEIEEILSANGQEAQVFVTGNIGRDVLPMLKLKNYL 36- 0 Query: 361 SQYDYIGHFHTKKSKEADFWAGESWRKELIDMLVKPADSILSAFETD-DIGIIIADIPSF 41- 9 S YD++GHFHTKKSKEADFWAG+SWR+ELIDMLVKPAD+IL+ + + IG++IAD+P+F Sbjct: 361 SAYDFVGHFHTKKSKEADFWAGQSWREELIDMLVKPADNILAQLQQNPKIGLVIADMPTF 42- 0 Query: 420 FRFNKIVNAWNEHLIAQEMMSLWRKMDVKKQIDFQAMDTFVMSYGTFVWFKYDALKSLFD 47- 9 FR+NKIV+AWNEHLIA EM +LW+KM + K+IDF A TFVMSYGTFVWFKYDALK LFD Sbjct: 421 FRYNKIVDAWNEHLIAPEMNTLWQKMGMTKKIDFNAFHTFVMSYGTFVWFKYDALKPLFD 48- 0 Query: 480 LELTQNDIPSEPLPQNSILHAIERLLVYIAWGDSYDFRIVKNPYELTPFIDNKLLNLRED 53- 9 L LT +D+P EPLPQNSILHAIERLL+YIAW + YDFRI KNP +LTPFIDNKLLN R + Sbjct: 481 LNLTDDDVPEEPLPQNSILHAIERLLIYIAWNEHYDFRISKNPVDLTPFIDNKLLNERGN 54- 0 Query: 540 EGAHTYVNFNQMGGIKGALKYIIVGPAKAMKYIFLRLMEKLK 581 +T+V+FN MGGIKGA KYI +GPA+A+KYI R ++K+K Sbjct: 541 SAPNTFVDFNYMGGIKGAFKYIFIGPARAVKYILKRSLQKIK 582 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2614 A DNA sequence (GASx787) was identified in S. pyogenes <SEQ ID 7727> which encodes the amino acid sequence <SEQ ID 7728>. Analysis of this protein sequence reveals the following:

TABLE-US-07492 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -15.66 Transmembrane 202-218 (191-224) INTEGRAL Likelihood = -10.03 Transmembrane 340-356 (335-365) INTEGRAL Likelihood = -9.08 Transmembrane 270-286 (263-289) INTEGRAL Likelihood = -8.60 Transmembrane 124-140 (118-145) INTEGRAL Likelihood = -4.94 Transmembrane 377-393 (375-395) INTEGRAL Likelihood = -3.29 Transmembrane 291-307 (290-311) INTEGRAL Likelihood = -2.87 Transmembrane 160-176 (159-180) INTEGRAL Likelihood = -2.66 Transmembrane 50-66 (48-66) INTEGRAL Likelihood = -1.28 Transmembrane 77-93 (76-93) INTEGRAL Likelihood = -0.69 Transmembrane 229-245 (229-245) ----- Final Results ----- bacterial membrane --- Certainty = 0.7262 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07493 >GP: BAA32095 GB: AB010970 ORF7 [Streptococcus mutans] Identities = 374/775 (48%), Positives = 525/775 (67%), Gaps = 7/775 (0%) Query: 53 VSFVGYIISLIGLSYYLSRQVSRQLFLKTSFIVISYLIVSYWVQITQHLNDKRFDIWSLT 112- V V Y++S++GLS+YLS+ + + F++ Y+++SY++ +T+ LN++ F IW L Sbjct: 30 VCLVIYVLSILGLSFYLSKNLKKTFFIELLLGYGLYIVISYFLAVTRELNNESFKIWDLA 89 Query: 113 KNQFYQFQALPSLLIILV----MATLIKILAAYFAIEKDRFGLL-GYQGNTFSVALILAV 16- 7 KN F+Q LP+L++I+ + LI++ + + LL + F + ++ Sbjct: 90 KNHFFQPYFLPTLVLIIACTFALNYLIRVKMKRSHLSRKMTLLLENFSETEFLLTGLIVS 149- Query: 168 VPINDIHLLKLISSRFSELVTAGNSQIALLKISGLLIVLLVIFATIIYVVLNALKHLKSN 22- 7 ++D +KL+ + +LL + LL L++F+ I+ NA + +K N Sbjct: 150 FILSDTLYVKLLQESLRAYYHKPLAYESLLFLYTLLT--LILFSVIVEACFNAYRSIKLN 20- 7 Query: 228 KPSFSVAATTSLFLALVFNYTFQYGVKGDEALLGYYVFPGATLFQIVAITLVALLAYVIT 28- 7 +P+ S+A +SL A +FNY FQYG+K D LLG Y+ PGAT +QI+ +T Y+I Sbjct: 208 RPNLSLAFVSSLLFATIFNYAFQYGLKNDADLLGKYIVPGATAYQILVLTAAGFFLYLII 26- 7 Query: 288 NRYWPTTFFLLILGTIISVVNDLKESMRSEPLLVTDFVWLQELGLVTSFVKKSVIVEMVV 34- 7 NRY TF ++ILG+II+VVN LK MR+EPLLVTDF W+ + L+ V ++I ++ Sbjct: 268 NRYLLVTFLIVILGSIITVVNVLKVGMRNEPLLVTDFAWVTNIRLLARSVNANIIFSTLL 32- 7 Query: 348 GLAICIVVAWYLHGRVLAGKLFMSPVKRASAVLGLFIVSCSMLIPFSYEKEGKILSGLPI 40- 7 LA I++ +L R+L GK+ + + + + ++ S+ I F EK KI++G+P+ Sbjct: 328 ILAALILLYLFLRKRLLQGKITENYRLKVGLISSICLLGFSIFIIFRNEKGSKIVNGIPV 38- 7 Query: 408 ISALNNDNDINWLGFSTNARYKSLAYVWTRQVTKKIMEKPTNYSQETIASIAQKYQKLAE 46- 7 IS +NN DI + GF +NA YKSL YVWT+QVTK IM+KP++YS+E I +A+KY +A Sbjct: 388 ISQVNNWVDIGYQGFYSNASYKSLMYVWTKQVTKSIMDKPSDYSKERILKLAKKYNNVAN 44- 7 Query: 468 DINKDRKNNIADQTVIYLLSESLSDPDRVSNVTVSHDVLPNIKAIKNSTTAGLMQSDSYG 52- 7 INK R NI++QTVIY+LSES SDPDRV V +S DV+PNIK IK TT+GLM SD YG Sbjct: 448 KINKVRTENISNQTVIYILSESFSDPDRVQGVNLSRDVIPNIKQIKEKTTSGLMHSDGYG 50- 7 Query: 528 GGTANMEFQTLTSLPFYNFSSSVSVLYSEVFPKMAKPHTISEFYQGKNRIAMHPASANNF 58- 7 GGTANMEFQ+LT LP+YNF+SSVS LY+EV P M+ +IS ++ KNR+ +HP+SA+N+ Sbjct: 508 GGTANMEFQSLTGLPYYNFNSSVSTLYTEVVPDMSVFPSISNQFKSKNRVVIHPSSASNY 56- 7 Query: 588 NRKTVYSNLGFSKFLALSGSKDKFKNIENVGLLTSDKTVYNNILSLINPSESQFFSVITM 64- 7 +RK VY L F F+A SG+ DK + E VGL SDKT Y NIL INPS+SQFFSV+TM Sbjct: 568 SRKYVYDKLKFPTFVASSGTSDKITHSEKVGLNVSDKTTYQNILDKINPSQSQFFSVMTM 62- 7 Query: 648 QNHIPWSSDYPEEIVAEGKNFTEEENHNLTSYARLLSFTDKETRAFLEKLTQINKPITVV 70- 7 QNH+PW+SD P ++VA GK +T++EN +L+SYARLL++TDKET+ FL +L+Q+ +TVV Sbjct: 628 QNHVPWASDEPSDVVATGKGYTKDENGSLSSYARLLTYTDKETKDFLAQLSQLKHKVTVV 68- 7 Query: 708 FYGDHLPGLYPDSAFNKHIENKYLTDYFIWSNGTNEKKNHPLINSSDFTAALFEHTDSKV 76- 7 FYGDHLPGLYP+SAF K +++Y TDYFIWSN + NH +NSSDFTA L EHT+SKV Sbjct: 688 FYGDHLPGLYPESAFKKDPDSQYQTDYFIWSNYNTKTLNHSYVNSSDFTAELLEHTNSKV 74- 7 Query: 768 SPYYALLTEVLNKASVDKSPDSPEVKAIQNDLKNIQYDVTIGKGYLLKHKTFFKI 822 SPYYALLTEVL+ +V + E K I NDLK IQYD+T+GKGY+ +K FF I Sbjct: 748 SPYYALLTEVLDNTTVGHGKLTKEQKEIANDLKLIQYDITVGKGYIRNYKGFFDI 802 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2615 A DNA sequence (GASx789R) was identified in S. pyogenes <SEQ ID 7729> which encodes the amino acid sequence <SEQ ID 7730>. Analysis of this protein sequence reveals the following: TABLE-US-07494 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.06 Transmembrane 42-58 (42-58) ----- Final Results ----- bacterial membrane --- Certainty = 0.1426 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2616 A DNA sequence (GASx790) was identified in S. pyogenes <SEQ ID 7731> which encodes the amino acid sequence <SEQ ID 7732>. Analysis of this protein sequence reveals the following: TABLE-US-07495 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2617 A DNA sequence (GASx791) was identified in S. pyogenes <SEQ ID 7733> which encodes the amino acid sequence <SEQ ID 7734>. Analysis of this protein sequence reveals the following: TABLE-US-07496 Possible site: 48 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.42 Transmembrane 166-182 (157-188) INTEGRAL Likelihood = -7.32 Transmembrane 85-101 (79-104) INTEGRAL Likelihood = -6.90 Transmembrane 397-413 (386-417) INTEGRAL Likelihood = -6.05 Transmembrane 253-269 (252-273) INTEGRAL Likelihood = -5.26 Transmembrane 301-317 (293-325) INTEGRAL Likelihood = -3.35 Transmembrane 363-379 (362-379) INTEGRAL Likelihood = -3.24 Transmembrane 335-351 (335-351) ----- Final Results ----- bacterial membrane --- Certainty = 0.5967 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07497 >GP: AAA64645 GB: U10927 CapF [Staphylococcus aureus] Identities = 97/419 (23%), Positives = 186/419 (44%), Gaps = 40/419 (9%) Query: 12 FLWNMLGSLSTAVISVILLMVVTRLLTSADSDIYAFAYSFANMMVVVGLFQVRNYQATDI 71 - F + + ++ +A+ ++L+V+ RL T D Y +A + + ++R+ T Sbjct: 5 FNYMFVANILSALCKFLILLVIVRLGTPEDVGRYNYALVITAPIFLFISLKIRSVIVT-- 62 Query: 72 NEKYSFSQYLVARLMTCLLMLAITVIYLTLTKTDSYKSTIVFLVCFYRSTDAFSDLYQGM 131- N+KYS ++Y+ A L ++ L I++ + T + +v + + ++ G+ Sbjct: 63 NDKYSPNEYISAILSLNIITLIFVAIFVYVLGNGDL--TTILIVSLIKLFENIKEVPYGI 120- Query: 132 FQQHERLDIAGKSLAYRNTLIFMVYTAIILYSKNLTLALVAVCIVSLVFIMYYDIGHSKK 19- 1 +Q++E L + G S+ N L +++ I +S NL +AL+ + I + D + K Sbjct: 121 YQKNESLKLLGISMGIYNILSLILFYIIYSFSHNLNMALLFLVISCIFSFAIIDRWYLSK 18- 0 Query: 192 FQKLMFSELLSNISFQNSLKLLKESF----PLFLNGFLIIYIYTQPKYAIELMTTLGEVA 24- 7 + + + + N++ KE F PL + L P+ +E + G+ Sbjct: 181 YYNI-------KLHYNNNIAKFKEIFILTIPLAFSSALGSLNTGIPRIVLENL--FGKYT 23- 1 Query: 248 LGS-QTIFNILFMPAFVMNLLILFFRPHITQMAIALIRGQIK-EFNKIQVQLFAYLGVF- 30- 4 LG TI +L + N + F P + + L + + K EF K+ ++ ++G+F Sbjct: 232 LGIFSTIAYVLVIGGLFANSISQVFLPKLRK----LYKDEKKIEFEKLTRKM-VFIGIFI 28- 6 Query: 305 SLIALVGSGLFGIPFLSILYG-----TNLTDYWVDF-MLIMLGGSIGSFATVIDNILTAM 35- 8 + +++ S G LS+L+G N+ + F +L +L G + Sbjct: 287 GMCSVILSLFLGEALLSLLFGKEYGENNIILIILSFGLLFILSGIFLGTTIIATGKYNVN 34- 6 Query: 359 RKQQLLLIPYTGGFLISLLITNLFVMKYHILGAALSFLITMLVWLGLSIMIYLFIMNRF 417- K L+L+ F I L+ + L + KY +LGAAL+ I+ V L I Y F F Sbjct: 347 YKISLILL-----FCI-LIFSFLLIPKYSLLGAALTITISQFVAL---ISYYYFYKRIF 396- Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2618 A DNA sequence (GASx792) was identified in S. pyogenes <SEQ ID 7735> which encodes the amino acid sequence <SEQ ID 7736>. Analysis of this protein sequence reveals the following: TABLE-US-07498 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.03 Transmembrane 64-80 (60-84) INTEGRAL Likelihood = -9.66 Transmembrane 43-59 (37-63) INTEGRAL Likelihood = -8.70 Transmembrane 232-248 (229-251) INTEGRAL Likelihood = -8.28 Transmembrane 410-426 (402-432) INTEGRAL Likelihood = -6.21 Transmembrane 298-314 (296-322) INTEGRAL Likelihood = -6.21 Transmembrane 478-494 (471-496) INTEGRAL Likelihood = -5.04 Transmembrane 265-281 (256-288) INTEGRAL Likelihood = -3.29 Transmembrane 380-396 (378-397) INTEGRAL Likelihood = -2.92 Transmembrane 210-226 (209-227) INTEGRAL Likelihood = -2.60 Transmembrane 187-203 (187-204) INTEGRAL Likelihood = -2.50 Transmembrane 442-458 (439-458) INTEGRAL Likelihood = -1.65 Transmembrane 18-34 (18-35) INTEGRAL Likelihood = -1.38 Transmembrane 165-181 (165-181) ----- Final Results ----- bacterial membrane --- Certainty = 0.5012 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07499 >GP: BAA19642 GB: AB002668 unnamed protein product [Actinobacillus actinomycetemcomitans] Identities = 116/459 (25%), Positives = 207/459 (44%), Gaps = 60/459 (13%) Query: 69 FILVFGTISAIISPINDIPDEYVHYSRTVYISEGDINLTNNNKKLRISKDVDKLI----- 123- FIL F I II+P PDE+ H+ R IS G I ++ K + K + K++ Sbjct: 16 FILTF-IIGVIITPPYQSPDEFYHFQRGYAISNGQIIPSSTEK---LDKAMMKMLSIYEG 71 Query: 124 ----KQSGKTFITSNLKATKHSTREYSYPYIKGTNAYYSFSYIPQALGILVGNALDLPIL 17- 9 ++ T N +EY TN Y+ Y+PQALG +G+ LDL + Sbjct: 72 IPYRSENKVTHFLENEAQNVAWEKEYILDESANTNVYFPLIYLPQALGSFLGSTLDLSLY 131- Query: 180 LTYYFGRLCN-LISYAMLAFIAIKLSGSFKQVIAVVTLLPMNIYLAASFNQDGFAIGLVL 23- 8 YY ++ L+S A+L F +++ S + ++ LPM ++ S N D ++ Sbjct: 132 NMYYLAKIFTLLVSIAILYFASVQYRLSIP--VLLILSLPMTMFQMGSTNPDS-----II 18- 4 Query: 239 VTIGLFI-NLLSSKDKSNYNTKFFLYLVLCGLL------VLSKFTYFLLVCLPLFIPNEK 29- 1 ++ +FI +LL+ SNYN F + C LL------V KF +L+ LP FI + Sbjct: 185 FSLSVFIGSLLARGLDSNYN---FTHKDFCKLLFSIFLCVTVKFNMLVLLLLPFFISKRR 24- 1 Query: 292 FGKNTKLVILKKLGGLLLIFLFAAMWFRLYGQVKTPYVADFLKEV----NVSQQVKNMLE 34- 7 ++ + + + +L + A K + +F + ++ + KN L Sbjct: 242 EIRHGSMYSIFIIILSILWIVLAMKLTEAQSHFKEGALHNFSYYIFHMDDLFEIFKNTLN 30- 1 Query: 348 SPIVYSSIIIRHMVINLINMNNIFQFGA-LSYGITNLFPLYVCFFFFVYISNASKITINI 40- 6 + Y ++R + L ++ F L +G T+L + F++I N K+ I Sbjct: 302 --LTYLKSLLRMFLGVLGWVDTKFTINEYLFFGSTSLLA-----YIFLFIHNLYKLKYVI 35- 4 Query: 407 VEKM--GIIFVISAIIGATVLAMYLTWTPVGSSTVLGVQSRYLIGIIPLVLLLFSS---- 46- 0 V + G++F+ + I + +T+ +G++ ++GVQ RY IP++L++FSS Sbjct: 355 VSVLLVGVVFLFTHFI------LLITYNEIGTTQIVGVQGRY---FIPIMLIIFSSFILK 40- 5 Query: 461 QQQKFKQIEDILSDKLAIHVSLLFILAMLM--STIFRYY 497 + +K + I + + LFI + + + + RYY Sbjct: 406 KSEKTSNNKTISKYFIIVPFLFLFISSFITINTLVSRYY 444 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2619 A DNA sequence (GASx797) was identified in S. pyogenes <SEQ ID 7737> which encodes the amino acid sequence <SEQ ID 7738>. Analysis of this protein sequence reveals the following: TABLE-US-07500 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1491 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07501 >GP: AAC83961 GB: L47648 cytidine monophosphate kinase [Bacillus subtilis] Identities = 116/220 (52%), Positives = 156/220 (70%), Gaps = 1/220 (0%) Query: 2 KAIKIAIDGPASSGKSTVAKIIAKNLGYTYLDTGAMYRSATYIALTHGYTGKEVALILEE 61 K + IAIDGPA++GKSTVAKI+A+ Y Y+DTGAMYR+ TY AL + + E Sbjct: 3 KKLSIAIDGPAAAGKSTVAKIVAEKKSYIYIDTGAMYRAITYAALQENVDLTDEEKLAEL 62 Query: 62 LEKNPIFFKKAKDGSQLVFLGDEDVTLAIRQNDVTNNVSWISALPEIREELVHQQRRIAQ 121- L++ I KDG Q VF+ DVT AIR ++++N VS + +REE+V +Q+++ + Sbjct: 63 LKRTDIELITTKDG-QKVFVNGTDVTEAIRTDEISNQVSIAAKHRSVREEMVKRQQQLGE 121- Query: 122 AGGIIMDGRDIGTVVLPDAELKIFLVASVEERAERRYKENLEKGIESDFETLKEEIAARD 18- 1 GG++MDGRDIGT VLP+AE+KIFL+ASVEERA+RRY+EN++KG + ++ETL EEIA RD Sbjct: 122 KGGVVMDGRDIGTHVLPNAEVKIFLLASVEERAKRRYEENVKKGFDVNYETLIEEIARRD 18- 1 Query: 182 YKDSHRKVSPLKAAEDALIFDTTGVSIDGVVQFIQEKAEK 221 DS R+VSPL+ AEDAL DTT +SI V I E E+ Sbjct: 182 KLDSEREVSPLRKAEDALEIDTTSLSIQEVADKILEAVEQ 221 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2620 A DNA sequence (GASx799) was identified in S. pyogenes <SEQ ID 7739> which encodes the amino acid sequence <SEQ ID 7740>. Analysis of this protein sequence reveals the following: TABLE-US-07502 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4324 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07503 >GP: CAA34313 GB: X16188 ribosomal protein L35 (AA 1-66) [Bacillus stearothermophilus] Identities = 46/65 (70%), Positives = 51/65 (77%) Query: 1 MPKQKTHRASAKRFKRTGSGGLKRFRAFTSHRFHGKTKKQRRHLRKAGLVSSGDFKRIKA 60 MPK KTHR SAKRFK+T SG LKR A+TSH F KTKKQ+RHLRKA LVS GDFKRI+ Sbjct: 1 MPKMKTHRGSAKRFKKTASGKLKRGHAYTSHLFANKTKKQKRHLRKATLVSPGDFKRIRQ 60 Query: 61 MVTGL 65 M+ L Sbjct: 61 MLDNL 65 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2621 A DNA sequence (GASx806R) was identified in S. pyogenes <SEQ ID 7741> which encodes the amino acid sequence <SEQ ID 7742>. Analysis of this protein sequence reveals the following: TABLE-US-07504 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5361 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2622 A DNA sequence (GASx809R) was identified in S. pyogenes <SEQ ID 7743> which encodes the amino acid sequence <SEQ ID 7744>. Analysis of this protein sequence reveals the following: TABLE-US-07505 Possible site: 52 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.81 Transmembrane 33-49 (28-53) ----- Final Results ----- bacterial membrane --- Certainty = 0.4524 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2623 A DNA sequence (GASx814R) was identified in S. pyogenes <SEQ ID 7745> which encodes the amino acid sequence <SEQ ID 7746>. Analysis of this protein sequence reveals the following: TABLE-US-07506 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0206 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2624 A DNA sequence (GASx817) was identified in S. pyogenes <SEQ ID 7747> which encodes the amino acid sequence <SEQ ID 7748>. Analysis of this protein sequence reveals the following: TABLE-US-07507 Possible site: 13 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.49 Transmembrane 16-32 (15-32) ----- Final Results ----- bacterial membrane --- Certainty = 0.1595 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2625 A DNA sequence (GASx820) was identified in S. pyogenes <SEQ ID 7749> which encodes the amino acid sequence <SEQ ID 7750>. Analysis of this protein sequence reveals the following:

TABLE-US-07508 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.11 Transmembrane 62-78 (59-81) INTEGRAL Likelihood = -6.00 Transmembrane 128-144 (123-147) INTEGRAL Likelihood = -2.50 Transmembrane 5-21 (3-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.3845 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07509 >GP: AAA26653 GB: M83994 prolipoprotein signal peptidase [Staphylococcus aureus] Identities = 57/153 (37%), Positives = 96/153 (62%), Gaps = 6/153 (3%) Query: 1 MKKRLFVLSLILL----VALDQLSKFWIVSHIALGEVKPFIPGIVSLTYLQNNGAAFSIL 56 M K+ F+ + IL+ V DQ++K+ I + + +G+ IP +++T +NNGAA+ IL Sbjct: 1 MHKKYFIGTSILIAVFVVIFDQVTKYIIATTMKIGDSFEVIPHFLNITSHRNNGAAWGIL 60 Query: 57 QDQQWFFVVITVLVIGYAIYYLATHPHLNIWKQLALLLIISGGIGNFIDRLRLAYVIDMI 116- + FF +IT++++ +Y+ N++ Q+A+ L+ +G +GNFIDR+ V+D I Sbjct: 61 SGKMTFFFIITIIILIALVYFFIKDAQYNLFMQVAISLLFAGALGNFIDRILTGEVVDFI 120- Query: 117 HLDF--VDFAIFNVADSYLTVGVILLLICLWKE 147 + DF IFN+ADS LT+GVIL++I L K+ Sbjct: 121 DTNIFGYDFPIFNIADSSLTIGVILIIIALLKD 153 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2626 A DNA sequence (GASx822R) was identified in S. pyogenes <SEQ ID 7751> which encodes the amino acid sequence <SEQ ID 7752>. Analysis of this protein sequence reveals the following: TABLE-US-07510 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2638 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2627 A DNA sequence (GASx823R) was identified in S. pyogenes <SEQ ID 7753> which encodes the amino acid sequence <SEQ ID 7754>. Analysis of this protein sequence reveals the following: TABLE-US-07511 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3452 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2628 A DNA sequence (GASx828) was identified in S. pyogenes <SEQ ID 7755> which encodes the amino acid sequence <SEQ ID 7756>. Analysis of this protein sequence reveals the following: TABLE-US-07512 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2629 A DNA sequence (GASx836) was identified in S. pyogenes <SEQ ID 7757> which encodes the amino acid sequence <SEQ ID 7758>. Analysis of this protein sequence reveals the following: TABLE-US-07513 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4333 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2630 A DNA sequence (GASx853R) was identified in S. pyogenes <SEQ ID 7759> which encodes the amino acid sequence <SEQ ID 7760>. Analysis of this protein sequence reveals the following: TABLE-US-07514 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4906 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2631 A DNA sequence (GASx854R) was identified in S. pyogenes <SEQ ID 7761> which encodes the amino acid sequence <SEQ ID 7762>. Analysis of this protein sequence reveals the following: TABLE-US-07515 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3989 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9147> which encodes the amino acid sequence <SEQ ID 9148>. Analysis of this protein sequence reveals the following: TABLE-US-07516 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.399 (Affirmative) < succ> bacterial membrane --- Certainty = 0.000 (Not Clear) < succ> bacterial outside --- Certainty = 0.000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07517 >GP: AAB59092 GB: M97157 pyrogenic exotoxin C [Streptococcus pyogenes] Identities = 39/67 (58%), Positives = 53/67 (78%) Query: 1 LMESKEIYLTKSPYIRGSLEIHSKNRKHEKINLYDAKPNSTRSDVFKKYKDNKTINMKDF 60 LM++ +IY SPY+ G +EI +K+ KHE+I+L+D+ TRSD+F KYKDN+ INMK+F Sbjct: 167 LMDNYKIYDATSPYVSGRIEIGTKDGKHEQIDLFDSPNEGTRSDIFAKYKDNRIINMKNF 22- 6 Query: 61 SHFDIYL 67 SHFDIYL Sbjct: 227 SHFDIYL 233 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2632 A DNA sequence (GASx855R) was identified in S. pyogenes <SEQ ID 7763> which encodes the amino acid sequence <SEQ ID 7764>. Analysis of this protein sequence reveals the following: TABLE-US-07518 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2633 A DNA sequence (GASx856) was identified in S. pyogenes <SEQ ID 7765> which encodes the amino acid sequence <SEQ ID 7766>. Analysis of this protein sequence reveals the following: TABLE-US-07519 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4145 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2634 A DNA sequence (GASx862) was identified in S. pyogenes <SEQ ID 7767> which encodes the amino acid sequence <SEQ ID 7768>. Analysis of this protein sequence reveals the following: TABLE-US-07520 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6285 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2635 A DNA sequence (GASx863) was identified in S. pyogenes <SEQ ID 7769> which encodes the amino acid sequence <SEQ ID 7770>. Analysis of this protein sequence reveals the following: TABLE-US-07521 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2636 A DNA sequence (GASx878) was identified in S. pyogenes <SEQ ID 7771> which encodes the amino acid sequence <SEQ ID 7772>. Analysis of this protein sequence reveals the following: TABLE-US-07522 Possible site: 21 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2637 A DNA sequence (GASx887R) was identified in S. pyogenes <SEQ ID 7773> which encodes the amino acid sequence <SEQ ID 7774>. Analysis of this protein sequence reveals the following: TABLE-US-07523 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1911 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2638 A DNA sequence (GASx910) was identified in S. pyogenes <SEQ ID 7775> which encodes the amino acid sequence <SEQ ID 7776>. Analysis of this protein sequence reveals the following: TABLE-US-07524 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4511 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2639 A DNA sequence (GASx911) was identified in S. pyogenes <SEQ ID 7777> which encodes the amino acid sequence <SEQ ID 7778>. Analysis of this protein sequence reveals the following: TABLE-US-07525 Possible site: 52 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2993 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07526 >GP: AAC74707 GB: AE000259 glutathionine S-transferase [Escherichia coli] Identities = 29/137 (21%), Positives = 61/137 (44%), Gaps = 9/137 (6%) Query: 1 LPFIAKQTLKSQLIPQDNLLAESRFNEIMDFLTGDFPLVFRPMINPHRYTISQDNQALEK 60 + ++A QL+ N ++ + E ++++ + F P+ P E+ Sbjct: 70 MQYLADSVPDRQLLAPVNSISRYKTIEWLNYIATELHKGFTPLFRP---------DTPEE 120- Query: 61 VKQASYKRMDIAMTHLDSLIGESGHVYRDQQTIADAYAYAMALWSQKTPKSYENYPHLAA 120- K +++ + +++ + + + + TIADAY + + W+ + E H+AA Sbjct: 121 YKPTVRAQLEKKLQYVNEALKDEHWICGQRFTIADAYLFTVLRWAYAVKLNLEGLEHIAA 18- 0 Query: 121 FMAKMVEDSAVQQVLNA 137 FM +M E VQ L+A Sbjct: 181 FMQRMAERPEVQDALSA 197 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2640 A DNA sequence (GASx932R) was identified in S. pyogenes <SEQ ID 7779> which encodes the amino acid sequence <SEQ ID 7780>. Analysis of this protein sequence reveals the following: TABLE-US-07527 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4081 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2641 A DNA sequence (GASx935) was identified in S. pyogenes <SEQ ID 7781> which encodes the amino acid sequence <SEQ ID 7782>. Analysis of this protein sequence reveals the following: TABLE-US-07528 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6304 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2642 A DNA sequence (GASx937) was identified in S. pyogenes <SEQ ID 7783> which encodes the amino acid sequence <SEQ ID 7784>. Analysis of this protein sequence reveals the following: TABLE-US-07529 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3503 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2643 A DNA sequence (GASx938R) was identified in S. pyogenes <SEQ ID 7785> which encodes the amino acid sequence <SEQ ID 7786>. Analysis of this protein sequence reveals the following: TABLE-US-07530 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2884 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2644 A DNA sequence (GASx939) was identified in S. pyogenes <SEQ ID 7787> which encodes the amino acid sequence <SEQ ID 7788>. Analysis of this protein sequence reveals the following: TABLE-US-07531 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2771 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2645 A DNA sequence (GASx941) was identified in S. pyogenes <SEQ ID 7789> which encodes the amino acid sequence <SEQ ID 7790>. Analysis of this protein sequence reveals the following: TABLE-US-07532 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2257 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2646 A DNA sequence (GASx942R) was identified in S. pyogenes <SEQ ID 7791> which encodes the amino acid sequence <SEQ ID 7792>. Analysis of this protein sequence reveals the following:

TABLE-US-07533 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3255 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07534 >GP: AAB91582 GB: AF242881 ymh [Agrobacterium tumefaciens] (ver 2) Identities = 75/223 (33%), Positives = 116/223 (51%), Gaps = 2/223 (0%) Query: 38 DQNSGFNKHKRVHNLVSDILNRTQNTDNIKLVIEYVCNPLRYINEVSIFEQLRTAINIPL 97 - D + K R++N + N + +I I P R+ + FE +R +N L Sbjct: 39 DTDPQMTKRHRLYNAFASDQNSRKQRTHIIAFIRKAMKPERFARDSERFEPMRLNLNRAL 98 Query: 98 SLKGLIVSDSGQIVTTTTSKTLSEAKKRFETLDSRLKELKVHPHVLKFCTQELLQENYFH 157- + GL V SG++ ++TLS+A +R L + L VHP VL+FC +ELL +NYFH Sbjct: 99 AFAGLAVKASGELAAVDAAETLSQATRRALELRADLTSRGVHPDVLRFCREELLVDNYFH 158- Query: 158 AVFEASKGVFHRIRLLTGSAMDSASLIDQCFKPGEPIVIINGNKLQTLDEQSEYKGLKNL 21- 7 AV EA K V +IR TG D A L+D+ F P++ I N+LQ+ E+ E +G NL Sbjct: 159 AVLEAVKSVADKIRQRTGLTDDGAVLVDRAFSGDAPMLAI--NELQSESEKGEQRGFSNL 21- 6 Query: 218 LLAIAHLYRNSKAHKLKYYNPDNLNDALTALTLMSLAHNLLDS 260 + ++RN+ AH + + + DA ++ SL H +D+ Sbjct: 217 VKGTFSMFRNTTAHAPRIHWQMSKEDAEDLFSMFSLMHRRIDA 259 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2647 A DNA sequence (GASx943R) was identified in S. pyogenes <SEQ ID 7793> which encodes the amino acid sequence <SEQ ID 7794>. Analysis of this protein sequence reveals the following: TABLE-US-07535 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1526 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2648 A DNA sequence (GASx944) was identified in S. pyogenes <SEQ ID 7795> which encodes the amino acid sequence <SEQ ID 7796>. Analysis of this protein sequence reveals the following: TABLE-US-07536 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1427 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2649 A DNA sequence (GASx945) was identified in S. pyogenes <SEQ ID 7797> which encodes the amino acid sequence <SEQ ID 7798>. Analysis of this protein sequence reveals the following: TABLE-US-07537 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2578 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07538 >GP: AAC98430 GB: L29324 excisionase [Streptococcus pneumoniae] Identities = 23/54 (42%), Positives = 40/54 (73%) Query: 1 LIQQWEGLTVATAKQWATEMRDHPDFKQFVLNPTHRIVFIDYEGFKLFVQWKSR 54 ++++W+GL T +W EMR++ F +V+NPTH++VFI+ EGF+ F++WK + Sbjct: 21 ILKRWDGLNKYTLNRWIKEMRENRTFSMYVINPTHKLVFINLEGFESFLRWKQK 74 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2650 A DNA sequence (GASx946) was identified in S. pyogenes <SEQ ID 7799> which encodes the amino acid sequence <SEQ ID 7800>. Analysis of this protein sequence reveals the following: TABLE-US-07539 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.99 Transmembrane 3-19 (1-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.2996 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2651 A DNA sequence (GASx950) was identified in S. pyogenes <SEQ ID 7801> which encodes the amino acid sequence <SEQ ID 7802>. Analysis of this protein sequence reveals the following: TABLE-US-07540 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2211 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2652 A DNA sequence (GASx951) was identified in S. pyogenes <SEQ ID 7803> which encodes the amino acid sequence <SEQ ID 7804>. Analysis of this protein sequence reveals the following: TABLE-US-07541 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4258 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2653 A DNA sequence (GASx952) was identified in S. pyogenes <SEQ ID 7805> which encodes the amino acid sequence <SEQ ID 7806>. Analysis of this protein sequence reveals the following: TABLE-US-07542 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2476 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07543 >GP: AAF74110 GB: AF212847 ORF245 [Lactococcus lactis bacteriophage ul36.2] Identities = 82/265 (30%), Positives = 128/265 (47%), Gaps = 27/265 (10%) Query: 1 MANQLSTQQVKRDITTDPTLLTGADIKKYFDPQNLLSEKQVGQALALCKGRNLNPFANEV 60 MAN+L V L IK+Y D S+ ++ + LCK N+NPF EV Sbjct: 1 MANELGIFSVDN--------LNMTTIKQYLDGGGKASDAELVLLINLCKQNNMNPFMKEV 52 Query: 61 YIVAYKNNSGTDFSLIVSKEAFMKRAERCEGYDGFEAGITVM-RNGEMVEIEGSLKLPDD 119- Y + Y N ++VS++ + KRA + + G E G+ V+ ++G + EG+ K + Sbjct: 53 YFIKYGNQPA---QIVVSRDFYRKRAFQNPNFVGIEVGVIVLNKDGVLEHNEGTFKTHEQ 109- Query: 120 VLIGGWAIVYRKDRSHRYKVTVDFNEYVKLDKYGNPRSTWKSMPGTMIRKTALVQTLREA 17- 9 L+G WA V+ K+ V V ++EYV++ K G+P W + P TM+ K A Q LR A Sbjct: 110 ELVGAWARVHLKNTEIPVYVAVSYDEYVQM-KDGHPNKMWTNKPCTMLGKVAESQALRMA 16- 8 Query: 180 FPDELGNMYTDIDGGDTFDAIKDVTPQETQEEVRARK---MAQIEQYKQEQ--TQKQTQK 23- 4 FP E Y + + + P++ EV K AQIE + +E +K + Sbjct: 169 FPAEFSGTYGEEEYPE---------PEKEPREVNGVKEPDRAQIESFDKEDYAAKKIEEL 21- 9 Query: 235 ADTSYPVDEVSEHTDDPVQGELLDG 259 + + P EV E T + + E L+G Sbjct: 220 KEKAQPQKEVVEETGEVIDEEPLEG 244 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2654 A DNA sequence (GASx953) was identified in S. pyogenes <SEQ ID 7807> which encodes the amino acid sequence <SEQ ID 7808>. Analysis of this protein sequence reveals the following: TABLE-US-07544 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3413 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07545 >GP: AAF74111 GB: AF212847 ORF364 [Lactococcus lactis bacteriophage u136.2] Identities = 67/222 (30%), Positives = 120/222 (53%), Gaps = 3/222 (1%) Query: 1 MQELQLKVTQAQVEIIDREKFEQNINEVVAKYQNYAVTAGTIKDDKQVLADLRKLKKQLS 60 ++++++ A + I++ EKF+ +IN+VVA+Y + + + D++ A L KL ++ Sbjct: 19 VKDIEIDFKPAIINILEEEKFKASINQVVAEYTGHVPSVENLTVDRKTRASLNKLITKIE 78 Query: 61 DERIKVKKELSKPADDIDGYIKQASKPLDDTIDKIATDVKEFEDHQKALRLDTVKSYLSN 120- R ++KK ++ P + +G+ K+A P++ I+ I +K+ E QK R V L Sbjct: 79 TRRKEIKKSINVPYAEFEGWYKKAIAPMEKVIETIDAGIKKIEAEQKESRKKVVHELLVE 138- Query: 121 KASEYMLDPRIFDEKAMEYTKAGNFMADGVTLKKVTMKSLEDLVTFEYQKEQEVEKAKAT 18- 0 ++ +D RIF+ ++ K+ NF + + KK + S+ ++ E QK E + AK + Sbjct: 139 LTTDTEVDSRIFENFVDDWAKSSNF--NDIKPKKQLIDSITYVIDGEKQKIAEYKSAKQS 19- 6 Query: 181 ISGQCAEYGMTDQPYIRMLKE-MTLVEVLGQIKADYLAEKQK 221 IS C +T PYIRML T+ E++ I D L EKQ+ Sbjct: 197 ISDFCFGNNITSTPYIRMLDSGKTVSEIMAVITEDVLFEKQR 238 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2655 A DNA sequence (GASx954) was identified in S. pyogenes <SEQ ID 7809> which encodes the amino acid sequence <SEQ ID 7810>. Analysis of this protein sequence reveals the following: TABLE-US-07546 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3884 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2656 A DNA sequence (GASx955) was identified in S. pyogenes <SEQ ID 7811> which encodes the amino acid sequence <SEQ ID 7812>. Analysis of this protein sequence reveals the following: TABLE-US-07547 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1777 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2657 A DNA sequence (GASx956) was identified in S. pyogenes <SEQ ID 7813> which encodes the amino acid sequence <SEQ ID 7814>. Analysis of this protein sequence reveals the following: TABLE-US-07548 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.44 Transmembrane 82-98 (81-98) ----- Final Results ----- bacterial membrane --- Certainty = 0.1977 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2658 A DNA sequence (GASx958) was identified in S. pyogenes <SEQ ID 7815> which encodes the amino acid sequence <SEQ ID 7816>. Analysis of this protein sequence reveals the following: TABLE-US-07549 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3673 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2659 A DNA sequence (GASx960) was identified in S. pyogenes <SEQ ID 7817> which encodes the amino acid sequence <SEQ ID 7818>. Analysis of this protein sequence reveals the following: TABLE-US-07550 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1852 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2660 A DNA sequence (GASx961) was identified in S-pyogenes <SEQ ID 7819> which encodes the amino acid sequence <SEQ ID 7820>. Analysis of this protein sequence reveals the following: TABLE-US-07551 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.7380(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07552 >GP: AAFE3071 GB: AF158600 gp137 [Streptococcus thermophilus bacteriophage Sfill] Identities = 67/136 (49%), Positives = 97/136 (71%), Gaps = 2/136 (1%) Query: 5 PEIDIQKTKSNAKRKLREYPRWRRIANDVDTQKVTATYSFEPRQPHGTPSKPVERLALNR 64 PEID + T KRKLREYPRWR IA+D QK+T ++F PR G +KPVE +A+ R Sbjct: 4 PEIDEKATLKRCKRKLREYPRWREIAHDSAEQKITQEFTFMPRG--GGVNKPVENIAVRR 61 Query: 65 VSAEQELDTIERAVNGIFDPEYRLILIDKYLLTYPKTDCDIYTKLGYEKSQYYNMLDNAL 124- V A EL+ IE+AVNG++ P+YR ILI+KYL PK + I +G+E++ + +L+N++ Sbjct: 62 VDALNELEAIEQAVNGLYRPDYRRILIEKYLAYPPKPNWQIAQSIGFERTAFQELLNNSI 121- Query: 125 LSFSELYKEGMLLVEK 140 L+F+ELY++G L+VE+ Sbjct: 122 LAFAELYRDGRLIVER 137 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2661 A DNA sequence (GASx962) was identified in S. pyogenes <SEQ ID 7821> which encodes the amino acid sequence <SEQ ID 7822>. Analysis of this protein sequence reveals the following: TABLE-US-07553 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3375 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2662 A DNA sequence (GASx963R) was identified in S. pyogenes <SEQ ID 7823> which encodes the amino acid sequence <SEQ ID 7824>. Analysis of this protein sequence reveals the following: TABLE-US-07554 Possible site: 48 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2663 A DNA sequence (GASx964) was identified in S. pyogenes <SEQ ID 7825> which encodes the amino acid sequence <SEQ ID 7826>. Analysis of this protein sequence reveals the following: TABLE-US-07555 Possible site: 51 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.16 Transmembrane 90-106 (89-111) INTEGRAL Likelihood = -5.52 Transmembrane 131-147 (129-150) INTEGRAL Likelihood = -0.43 Transmembrane 53-69 (52-69) ----- Final Results ----- bacterial membrane --- Certainty = 0.3463 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2664 A DNA sequence (GASx965) was identified in S. pyogenes <SEQ ID 7827> which encodes the amino acid sequence <SEQ ID 7828>. Analysis of this protein sequence reveals the following:

TABLE-US-07556 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3944 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07557 >GP: CAA66779 GB: X98106 Rorf172 [Bacteriophage phigle] Identities = 36/82 (43%), Positives = 52/82 (62%), Gaps = 3/82 (3%) Query: 18 ELTEKQQRFVDKYITTFNATESAKQAGYSEKSAYSQGQRLLKNVEIQKAMKERFLEAKDT 77 - +LT KQQ+F D+YI + NA ++A++AGYS++SA S GQ L +I++ + ER + Sbjct: 4 KLTPKQQKFADEYIKSGNAADAARKAGYSKRSARSVGQENLTKPDIKQYIDERM---DEI 60 Query: 78 KGDRIQDVAETLEQDTSIARGE 99 RI D E +E T IARGE Sbjct: 61 ASKRIMDATEAVELLTRIARGE 82 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2665 A DNA sequence (GASx966) was identified in S. pyogenes <SEQ ID 7829> which encodes the amino acid sequence <SEQ ID 7830>. Analysis of this protein sequence reveals the following: TABLE-US-07558 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2389 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07559 >GP: CAB13115 GB: Z99110 PBSX defective prophage terminase (large subunit) [Bacillus subtilis] Identities = 117/417 (28%), Positives = 195/417 (46%), Gaps = 33/417 (7%) Query: 31 YRVVKGSRGSKKSKTTALNFIVRLLKYPWANLLVIRRYSNTNKQSTYTDFKWACNQLKVT 90 - Y+ + G GS KS TAL +++LLK LVIR +T++ ST+ F+ +L +T Sbjct: 21 YQFLVGGYGSSKSYHTALKIVLKLLKEK-RTALVIREVFDTHRDSTFALFQEVIEELGLT 79 Query: 91 HLFKFNESLPEITVKATGQKILFRGLDDELKITSITVDVGALCWAWFEEAYQIETEDKFS 150- S ++ G +I+F+G+D+ K+ S V + W EE +++ E Sbjct: 80 KAVASLSSPLQLRFH-NGSRIMFKGMDNPAKLKS----VHNISLIWIEECSEVKYEG--- 131- Query: 151 TVVESIRGSLDAPDFFKQITVTFNPWSERHWLKRVFFDEETKR 193 + + G L P+ + T NP +W R FF +E K+ Sbjct: 132 --FKELIGRLRHPELKLHMICTTNPVGTSNWTYRHFFRDERKKRFVLDDSELYEKRTIVK 18- 9 Query: 194 ADTFSGTTTFRVNEWLDDVDKRRYEDLYKTNPRRARIVCDGEWGVAEGLVFDNFEVVDFD 25- 3 DT+ +T N +L + ++ + L + +P RI G +GV V FEV+ D Sbjct: 190 GDTYYHHSTANDNLFLPESYVKQLDGLKEYDPDLYRIARKGRFGVNGIRVLPQFEVLPHD 24- 9 Query: 254 -VEKTIQRVKET--SAGMDFGFTQDPTTLICVAVDLANKELWLYNEHYQKAMLTDHIVKM 31- 0 V+K I + + GMDFGF + ++ +AVD K L++Y E+YQ M D + Sbjct: 250 QVKKCIAAISKPIFRTGMDFGFEESYNAVVRLAVDPEKKYLYIYWEYYQNKMTDDRTAEE 30- 9 Query: 311 IRDKNLHRSYIAGDSAEKRLIAEIKSKGVSGIVPSIKGKGSIMQGIQFMQGF-KIYIHPS 36- 9 +R+ + I DSAE + I + +G +V + K GS +Q + ++ F KI+ Sbjct: 310 LREFIETQELIKADSAEPKSIQYFRQQGFR-MVGARKFPGSRLQYTKKVKRFKKIFCSDR 36- 8 Query: 370 CEHTIEEFNTYTFKQDKEGNWLNEPIDKNNHVIDAIRYALEKYHIRSNESNQFEVLR 426 CE+ I E T T+ +DK G + + + H +AI YAL+ Y + + + +R Sbjct: 369 CENVIYELETLTYAKDKNGALIEDEFTIDPHTLSAIWYALDDYEVADMKETAHKRMR 425 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2666 A DNA sequence (GASx967) was identified in S. pyogenes <SEQ ID 7831> which encodes the amino acid sequence <SEQ ID 7832>. Analysis of this protein sequence reveals the following: TABLE-US-07560 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4899 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07561 >GP: AAC34397 GB: AF158600 gp502 [Streptococcus thermophilus bacteriophage Sfill] Identities = 67/114 (58%), Positives = 83/114 (72%) Query: 6 FRDSTGKTKTLEFRFHREARMRYQAESLESLLTEKYKLLREMIEHHDKVQKPRIQELLDY 65 F DSTG+ L RFHRE+R+RY+A++LE L+ ++LL+ I HH Q PRIQELLDY Sbjct: 7 FTDSTGQDLVLNLRFHRESRIRYRADNLEELMVNNWELLKNFINHHKLRQAPRIQELLDY 66 Query: 66 AEGNNHTISEIGRRKDDDMADVRAVHNYGKYISTLKQGYLVGNPIRVEYIDGTE 119 A G NH + + GRRKD++MAD RAVHNYG+ IS K GYL GNPIRVEY D + Sbjct: 67 ARGENHDVLKSGRRKDNEMADKRAVHNYGRMISKFKTGYLAGNPIRVEYDDNED 120 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2667 A DNA sequence (GASx968) was identified in S. pyogenes <SEQ ID 7833> which encodes the amino acid sequence <SEQ ID 7834>. Analysis of this protein sequence reveals the following: TABLE-US-07562 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4007 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07563 >GP: AAC34397 GB: AF158600 gp502 [Streptococcus thermophilus bacteriophage Sfi11] Identities = 172/319 (53%), Positives = 227/319 (70%), Gaps = 9/319 (2%) Query: 1 LIYRSMDDKTEVVRLDPREVFVIYQNNLEQSSLAGVRYYNKNQLDGTTKIVELYTDNKIL 60 +IYRS D+T + RL P E FVIY N+LE +S+A VRYYN+ L +VE+YT+ I Sbjct: 157 VIYRSEYDETRIKRLSPLETFVIYDNSLEDNSIAAVRYYNRGTLQNAKDVVEIYTNQHIY 21- 6 Query: 61 KFEYDGDLTPIGETSSHAFGSVPITEYLNTDDGMGDYETELSLIDLYDAAQSDTANYMQD 120- + I T HAFG+VPITE+LN DG+GDYETEL LIDLYD+A+SDTAN+M D Sbjct: 217 TLDASDSFNEISVTP-HAFGTVPITEFLNNADGIGDYETELYLIDLYDSAESDTANHMSD 27- 5 Query: 121 LSDAILAIIGRVSFPGYVDTAEKAIEYLRKMRKARLLNLEPPVDQDGREGSVDAKYLYKQ 18- 0 ++DAILAI G ++ P + ++ M++ RL+ L+PP DG+EG+V A+YL K Sbjct: 276 MADAILAIYGDLALPQGMQASD--------MKRTRLMQLKPPKSADGKEGTVKAEYLTKS 32- 7 Query: 181 YDVQGTEAYKNRIVSDIHKFTNTPDMTDSKFAGQQSGEALKWKVFGLDQERVDMQALFEQ 24- 0 YDV G EAYK R+ DIH FTNTPDM+D+ F+G SGEALK+K+FGLDQ+RVD Q+F Q Sbjct: 328 YDVSGAEAYKTRLNKDIHVFTNTPDMSDNHFSGNASGEALKYKLFGLDQDRVDTQSQFTQ 38- 7 Query: 241 SLKRRYKLIARVSQLLKEIDDFDISKLKITFTPNLPKSLQEKIEAFKALGGELSQETAMA 30- 0 LKRRY+L AR+ L+ E DFD S+LKITFTPNLPKSL E++ LGG++SQETA++ Sbjct: 388 GLKRRYRLAARIGSLVNEFKDFDESRLKITFTPNLPKSLYEQVSILNDLGGQVSQETALS 44- 7 Query: 301 ITDIVEDAKKEISLINSES 319 ++ +VE+ +E+ IN ES Sbjct: 448 LSGLVENPTEELDKINEES 466 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2668 A DNA sequence (GASx969) was identified in S. pyogenes <SEQ ID 7835> which encodes the amino acid sequence <SEQ ID 7836>. Analysis of this protein sequence reveals the following: TABLE-US-07564 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5307 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07565 >GP: AAC79543 GB: U88974 ORF28 [Streptococcus thermophilus temperate bacteriophage O1205] Identities = 118/309 (38%), Positives = 183/309 (59%), Gaps = 18/309 (5%) Query: 8 YWRDRIKKEMDAK-EADDISLEQSMKQLHDYHFRNIEKEIESFYQRYADKEKIDLSEARK 66 YW R +E +A + + ++ ++ L++ + KE++++ Q+YA+K + +S+A++ Sbjct: 3 YWSKRTLREREASIKKGEAEFKKELEALYNLQLSQLRKELDAYIQKYANKNGLSVSDAKR 62 Query: 67 RASELDISAYQKKAKELVAKAEKLRREGKIVTRDDFTHQENADMSIYNLAMKTNALELLR 126- +A D+ A++ KAK VA DF+ + N ++ YN +M ELL Sbjct: 63 KADSFDVKAFETKAKRYVADK-------------DFSPKANRELQDYNFSMSVGRQELLI 109- Query: 127 LNIDLEMQELANGEHKLTKKFLDEGYRKETEFQAGLLGLSVASQASVKSLADAVINANFK 18- 6 ++LE+ L+ E +LT +L GY+ E + LL +V S +++ A +NANF+ Sbjct: 110 QELELELLALSESERQLTNDYLTNGYKSEV-VRESLLDQTVPSGKTLEKYMKAAVNANFE 16- 8 Query: 187 GAKWSDNIWDRQDKLRSIISQSVQSAILKGKNGLTIARDIRREFDVSASYAKRLAITEHA 24- 6 GA+WS+ IW RQ++LR I+ V A+++G+NGLTIAR IR+ D S + A+RLAITEHA Sbjct: 169 GAEWSERIWKRQEQLRKIVKTEVTRALIRGENGLTIARRIRKHMDASRTEAERLAITEHA 22- 8 Query: 247 RVQMEVGRLSMAENGFAMFDILPEPKACDVCKDIAKH---GPYHLDKWRIGENSPPFHPY 30- 3 RVQ M ENGF F ++PE +ACD+CKDI K P + IG N+PP HPY Sbjct: 229 RVQTLAQESIMKENGFEHFKLMPESRACDICKDIGKETEKNPVKIADMEIGTNAPPIHPY 28- 8 Query: 304 CRCAIVGVD 312 CRCA+V V+ Sbjct: 289 CRCAVVEVE 297 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2669 A DNA sequence (GASx970) was identified in S. pyogenes <SEQ ID 7837> which encodes the amino acid sequence <SEQ ID 7838>. Analysis of this protein sequence reveals the following: TABLE-US-07566 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2091 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2670 A DNA sequence (GASx971) was identified in S. pyogenes <SEQ ID 7839> which encodes the amino acid sequence <SEQ ID 7840>. Analysis of this protein sequence reveals the following: TABLE-US-07567 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2671 A DNA sequence (GASx972) was identified in S. pyogenes <SEQ ID 7841> which encodes the amino acid sequence <SEQ ID 7842>. Analysis of this protein sequence reveals the following: TABLE-US-07568 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3226 (Affirnative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2672 A DNA sequence (GASx973) was identified in S. pyogenes <SEQ ID 7843> which encodes the amino acid sequence <SEQ ID 7844>. Analysis of this protein sequence reveals the following: TABLE-US-07569 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1830 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2673 A DNA sequence (GASx975) was identified in S. pyogenes <SEQ ID 7845> which encodes the amino acid sequence <SEQ ID 7846>. Analysis of this protein sequence reveals the following: TABLE-US-07570 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4757 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07571 >GP: BAB07248 GB: AP001519 unknown [Bacillus halodurans] Identities = 46/134 (34%), Positives = 73/134 (54%) Query: 23 KQPQDEKKYTDADVDAIIDKKFAKWKSEQEAEKSEAKKMAKMNEKEKADYEKQKLLDELQ 82 - K + E+ +T +V+ I+ + A+ ++E EA+K+AKMN ++K +YE +KL E + Sbjct: 66 KPNKTERLFTQEEVNRIVKDRLARALKDKEEAIKEAEKLAKMNAEQKREYELEKLRRENE 125- Query: 83 ELKNDKTRNELTAVARQMFAESEINVNDDVLGLVVTLDAEQTKANVTTLANAFAKVIADD 142- +LK + R EL A +M E+ I +DDVL VV DAEQT+ V T + K+ Sbjct: 126 QLKKAQMRYELGREATKMLGEAGIMADDDVLSFVVRDDAEQTQEAVKTFISLVDKLADMR 18- 5 Query: 143 RKALVRQTTPSTGG 156 K ++ P G Sbjct: 186 MKEKLKGRPPKKDG 199 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2674 A DNA sequence (GASx976) was identified in S. pyogenes <SEQ ID 7847> which encodes the amino acid sequence <SEQ ID 7848>. Analysis of this protein sequence reveals the following: TABLE-US-07572 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2478 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07573 >GP: AAC79545 GB: U88974 ORF30 [Streptococcus thermophilus temperate bacteriophage O1205] Identities = 43/119 (36%), Positives = 66/119 (55%), Gaps = 16/119 (13%) Query: 9 SKEILHNLDYEAISVTLDSNKIG-----KKVVPAGTILAGKDKSIFEDRKQKVETVTNEE 63 + I+ +L Y+A+S T+DS+ G KK + AGT++AG SIF+DR + V Sbjct: 9 TSNIVRSLPYKAVSATVDSSYPGVLVDGKKYIKAGTLVAGNGGSIFDDRTKSV------- 61 Query: 64 VSTKEYVDGILLTDVDLTNGDAVGSCVYRGTINADKLADSSVAENYDDLEEVLPHIVFI 122 V K +GI+L DVDLT + V S +Y G + DK+ + D +++ LP + FI Sbjct: 62 VENKTEPEGIVLYDVDLTIDNTV-SVLYAGEVYKDKVNGGDIT---DTVKKALPLVKFI 116 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2675 A DNA sequence (GASx978) was identified in S. pyogenes <SEQ ID 7849> which encodes the amino acid sequence <SEQ ID 7850>. Analysis of this protein sequence reveals the following: TABLE-US-07574 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4138 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07575 >GP: AAC79546 GB: U88974 ORF31 [Streptococcus thermophilus temperate bacteriophage O1205] Identities = 195/343 (56%), Positives = 256/343 (73%), Gaps = 1/343 (0%) Query: 1 MALIHEIITSENIKGFYNAKNENVENTLGEKAFPPKQQLGLKLSFIKGAAGKPVTLKAAA 60 M LI++ +T+ NI G++NA ENV +TLGE FP ++QLG KLS+IKGA+G+ V LKAAA Sbjct: 1 MGLIYDKVTASNIAGYFNALQENVSSTLGESIFPARKQLGTKLSYIKGASGQSVALKAAA 60 Query: 61 FDTKVPLRDRMAVELIDEEMPFFKEAMLVKEADRQQLNMLAQTKNNELIDTILASIYNDQ 120- FDT V +RDR++ E+ DE+MPFFKEAMLVKE DRQQLN++ + N L++TI+A I+ND Sbjct: 61 FDTNVTIRDRVSAEMHDEQMPFFKEAMLVKENDRQQLNLVKDSGNAVLVNTIVAGIFNDN 120- Query: 121 ATLIAGAKARLEAMRMEVLSKGKIHIQSNGVMKDIDYGLAEDQTTKPDAKWDSAGTATPL 18- 0 TL+ GA+ARLEAMRM+VL+ GKI S+GV KDIDYG+ D + W G ATPL Sbjct: 121 LTLVNGARARLEAMRMQVLATGKIAFTSDGVNKDIDYGVKPDHKKQVSKSWAEPG-ATPL 17- 9 Query: 181 KDIEKAIEKMAERGFVPEAIIMNSKTFSLIKNAESTLDVVKPMAPNGAAVTKRDLNTYLE 24- 0 D+E AIE E G PE +MN+KTF LI+ A ST+ V+KP+A +G+AVTK +L Y+ Sbjct: 180 ADLEDAIETARELGLNPERAVMNAKTFGLIRKAASTVKVIKPLAGDGSAVTKAELENYIA 23- 9 Query: 241 DELQIKVILKDGMFVGDDGESRKYFPDGFATLVPNGNLGYTVFGTTPEQSDLLGGEATDA 30- 0 D + ++L++G + D GE K++PDG TL+PNG LG TVFGTTPE+SDL +A Sbjct: 240 DNFGVSIVLENGTYRNDKGEVSKFYPDGHLTLIPNGPLGNTVFGTTPEESDLFADNTVNA 29- 9 Query: 301 NVSIVETGIAITTTKTTDPVNVQTKVSMIALPSFERLEEVHII 343 V IV+ GIA+TTTKTTDPVNVQTKVSM+ALPSFERL++V+++ Sbjct: 300 EVEIVDNGIAVTTTKTTDPVNVQTKVSMVALPSFERLDDVYML 342 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2676 A DNA sequence (GASx979) was identified in S. pyogenes <SEQ ID 7851> which encodes the amino acid sequence <SEQ ID 7852>. Analysis of this protein sequence reveals the following: TABLE-US-07576 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3319 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2677 A DNA sequence (GASx980) was identified in S. pyogenes <SEQ ID 7853> which encodes the amino acid sequence <SEQ ID 7854>. Analysis of this protein sequence reveals the following:

TABLE-US-07577 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2385 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07578 >GP: AAC34404 GB: AF158600 gp113 [Streptococcus thermophilus bacteriophage Sfill] Identities = 53/109 (48%), Positives = 79/109 (71%), Gaps = 4/109 (3%) Query: 11 IVKNVKLDLGIEDDNQDQLLEMLLNRITDHFKANYGVLEIDNAFSFVLEDCLIARFNRRG 70 - +++NV +DL I DDN LL +LL RI +HFKA YGV E+D+ +F+ EDCL+ RFNRRG Sbjct: 9 VIQNVSVDLNINDDN---LLGILLERIVNHFKAEYGVDEVDDNLAFIFEDCLVKRFNRRG 65 Query: 71 SERAKTEEVEGHKTTYYDHLNEFEPYDAMIMAKLNLIKDKSRKGGLYFL 119 +E A++E ++GH +YYD+ NEF+PYD M+ +L ++++G + FL Sbjct: 66 AEGARSESIDGHSMSYYDNENEFDPYDNMLQ-RLYGTSGQAKEGEVLFL 113 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2678 A DNA sequence (GASx981) was identified in S. pyogenes <SEQ ID 7855> which encodes the amino acid sequence <SEQ ID 7856>. Analysis of this protein sequence reveals the following: TABLE-US-07579 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5714 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07580 >GP: CAA59188 GB: X84706 b3 [Bacteriophage B1] Identities = 28/82 (34%), Positives = 49/82 (59%), Gaps = 2/82 (2%) Query: 1 MRYADRVTFVKTT-DEQYNPDLGEYTHTEVISITKPCFVMDMGMEKSVQIFGDYQKDRKV 59 +RY D VTF+K + D Y+PDLGE+ E + D+G ++SV++FGD +K KV Sbjct: 1 LRYLDEVTFIKESPDSHYDPDLGEWVEKEPTRTVFSANITDIGTDRSVEVFGDIKKGAKV 60 Query: 60 IYLKQPYT-KAFDYCEYEGRRY 80 + + + +DY E++ +++ Sbjct: 61 MRMMPLFNMPKYDYIEFDNKKW 82 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2679 A DNA sequence (GASx982) was identified in S. pyogenes <SEQ ID 7857> which encodes the amino acid sequence <SEQ ID 7858>. Analysis of this protein sequence reveals the following: TABLE-US-07581 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2509 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07582 >GP: AAC34406 GB: AF158600 gp114 [Streptococcus thermophilus bacteriophage Sfill] Identities = 44/103 (42%), Positives = 65/103 (62%), Gaps = 5/103 (4%) Query: 17 GLKKKLELIIKKDAVKK---IVRDNGTQLQRKMINKAVFTKGYSTGATRRSITMQIGDGG 73 - GL + + ++K + +K ++R G++L+ +N+A F KGYSTGATRRSIT+Q+ Sbjct: 8 GLDEMAQSLLKNASPEKRSKVLRKYGSKLKEAAVNRAQFNKGYSTGATRRSITLQVESDK 67 Query: 74 LSVKVKPGTHYAGYLERGTRLMSKQPFVLPALKEQKVKFRKDL 116 +V+ T Y+GYLE GTR M QPF+ PAL E K ++L Sbjct: 68 ATVEAL--TSYSGYLEVGTRKMEAQPFMKPALDEVAPKMVEEL 108 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2680 A DNA sequence (GASx983) was identified in S. pyogenes <SEQ ID 7859> which encodes the amino acid sequence <SEQ ID 7860>. Analysis of this protein sequence reveals the following: TABLE-US-07583 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3098 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07584 >GP: AAA32612 GB: L31366 putative [Bacteriophage Tuc2009] Identities = 88/129 (68%), Positives = 108/129 (83%) Query: 1 MIKTRDQSIFDEMFKRIQSLGFKVYDYKPMTEVPYPFVEMESTDAEYIPNKDDIKGSVEL 60 MIKTRDQSIFDE+FKRIQ+LG+ VYDYKPM EV YPFVE+E+T + NK DIKG+V L Sbjct: 1 MIKTRDQSIFDELFKRIQALGYTVYDYKPMNEVGYPFVELENTQTIHEANKTDIKGTVSL 60 Query: 61 MLSVWGVQKKRKQVSDMASAIFSQALTVESSDVFRWSLNTRQSSIQMLDDTTTVTPLKRA 120- LSVWG+QKKRK+VSDMAS IF+QAL + ++D + W+LN++ S+IQMLDDTTT TPLKRA Sbjct: 61 SLSVWGLQKKRKEVSDMASNIFNQALNISATDGYSWALNSQASTIQMLDDTTTHTPLKRA 120- Query: 121 IVTLRFNLR 129 ++ L F LR Sbjct: 121 LINLEFRLR 129 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2681 A DNA sequence (GASx984R) was identified in S. pyogenes <SEQ ID 7861> which encodes the amino acid sequence <SEQ ID 7862>. Analysis of this protein sequence reveals the following: TABLE-US-07585 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1736 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2682 A DNA sequence (GASx985) was identified in S. pyogenes <SEQ ID 7863> which encodes the amino acid sequence <SEQ ID 7864>. Analysis of this protein sequence reveals the following: TABLE-US-07586 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07587 >GP: AAA32613 GB: L31366 structural protein [Bacteriophage Tuc2009] Identities = 81/185 (43%), Positives = 111/185 (59%), Gaps = 22/185 (11%) Query: 4 QLEAKQGIHSILLFRLLKEASSEAATKLAFQTEHEVGKSRDVDGQKTKDGIIQSVGALEY 63 +L AKQG ILL+RLL +A+ EAA KLAFQTEH K+RD + TKDG I S+ A+EY Sbjct: 3 ELTAKQGKDIILLYRLLSKATKEAAWKLAFQTEHSNEKTRDYNTTATKDGTIGSLAAIEY 62 Query: 64 DFKATSILAKGDVLAAKLEKAMENGELVEIWDIDLEETSKNGDSDNKLANVWGIDKNGTN 123- ATSI A GD +++KA ++GE++++W+ID E Sbjct: 63 SLSATSIAANGDPHLDEMDKAFDDGEIIDVWEIDKAEKG--------------------- 101- Query: 124 RGNGKYLATYYQGYISSFSAKKNAEENIEIEMEFAINGVGQKGFATLTDAQKAAVQYAFK 18- 3 +GKY A Y + Y++SFS + N+E+ +E+ +EF + G QKG ATLT+ Q VQY FK Sbjct: 102 -SDGKYKAKYLRAYLTSFSYEPNSEDALELSLEFGVFGKPQKGQATLTEEQANVVQYVFK 16- 0 Query: 184 DTTKG 188 DT G Sbjct: 161 DTVAG 165 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2683 A DNA sequence (GASx986) was identified in S. pyogenes <SEQ ID 7865> which encodes the amino acid sequence <SEQ ID 7866>. Analysis of this protein sequence reveals the following: TABLE-US-07588 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2273 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07589 >GP: CAA59192 GB: X84706 a2 [Bacteriophage B1] Identities = 54/111 (48%), Positives = 72/111 (64%), Gaps = 1/111 (0%) Query: 1 MQLEIKGKTHNVKFGTRFVAEMDKNHIAERQGFKFGAGLQSSV-PFLIDHSVVTLAEVIY 59 M+L IKGK + KFG +FV E+DKN + E+ G FG L + P L ++ TL+ V++ Sbjct: 1 MELTIKGKQVHFKFGVKFVRELDKNLVIEQNGVSFGLALAVKIIPELEMANIATLSNVLF 60 Query: 60 TGTITEPPRPSLNDIYDYIDEVEDIEKLFDDVLDELRQSNASKLFMAQVEK 110 G TE P+ S DI D+IDE EDIEKLFDDVL E+ +SN KL A++ K Sbjct: 61 LGNRTETPKLSQGDIDDFIDECEDIEKLFDDVLKEITESNTGKLIKAKMTK 111 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2684 A DNA sequence (GASx987) was identified in S. pyogenes <SEQ ID 7867> which encodes the amino acid sequence <SEQ ID 7868>. Analysis of this protein sequence reveals the following: TABLE-US-07590 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2735 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07591 >GP: CAA59193 GB: X84706 c2 [Bacteriophage B1] Identities = 40/111 (36%), Positives = 57/111 (51%), Gaps = 10/111 (9%) Query: 2 IVLNCIRYLGMTDINEIGRLTLYEYDLLMTGKALAAVDESHKAHKQAWINHQVTATKLVG 61 +++ +R G+ D++ R+T+ EY + L +DE ++QAW N QV ATK G Sbjct: 15 MMIRFLRCFGIQDLSVFERMTIREYSIRSIAFQLRTLDEEEFIYEQAWANWQVQATKQQG 74 Query: 62 GKKNKKEVPVYKKFKDFFD---YEEEIRKI-TQEIDEGYDKKGMDLLLKAN 108 K P+Y FK FFD E EI I + E D K +DL+ KAN Sbjct: 75 KK------PLYPTFKKFFDKKKLENEILGIESPENKFKKDNKLIDLMKKAN 119 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2685 A DNA sequence (GASx989) was identified in S. pyogenes <SEQ ID 7869> which encodes the amino acid sequence <SEQ ID 7870>. Analysis of this protein sequence reveals the following: TABLE-US-07592 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2869 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07593 >GP: CAA66560 GB: X97918 gene 19.1 [Bacteriophage SPP1] Identities = 66/232 (28%), Positives = 106/232 (45%), Gaps = 12/232 (5%) Query: 38 FRTLTVSGRDVVDLEHQTTSVLGRNGEYFHNATVEVRKLEIKAKISGKDNKS-MRLQYEK 96 - F V GR V +E ++ G +G ++ R+LE+ A + G ++ +R + E Sbjct: 24 FLVQEVRGRSVYSIEMGKRTIAGVDGGVITTESLPARELEVDAIVFGDGTETDLRRRIEY 83 Query: 97 LNKLIVSHNQVFLSFSDEPDRNYLGIFKSKDVPEEVSNEQIIGLTFICYNPFK-----MS 151- LN L+ V ++FSDEP R Y G ++ +E + L F C +P K + Sbjct: 84 LNFLLHRDTDVPITFSDEPSRTYYGRYEFATEGDEKGGFHKVTLNFYCQDPLKYGPEVTT 143- Query: 152 DVKTKKGTSIQNGGLFQTKPIITLNLSSPTKEIKLLHVESQKYIRLT----GTYTTDEIK 20- 7 DV T T ++N GL T P I S+ E ++ ++ ++ G T D + Sbjct: 144 DV-TTASTPVKNTGLAVTNPTIRCVFSTSATEYEMQLLDGSTVVKFLKVKYGFNTGDTLV 20- 2 Query: 208 IDMATGKITQNGRNILGDLDMINSRYFELLPGNNTLQCANAAITAEFREVYL 259 ID +T NG++I+ L +I S + +L P NT A T F E +L Sbjct: 203 IDCHERSVTLNGQDIMPAL-LIQSDWIQLKPQVNTYLKATQPSTIVFTEKFL 253 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2686 A DNA sequence (GASx990) was identified in S. pyogenes <SEQ ID 7871> which encodes the amino acid sequence <SEQ ID 7872>. Analysis of this protein sequence reveals the following: TABLE-US-07594 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2861 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07595 >GP: BAB04681 GB: AP001510 unknown conserved protein in others [Bacillus halodurans] Identities = 116/449 (25%), Positives = 198/449 (43%), Gaps = 79/449 (17%) Query: 2 IYLFDKLERLVATVG-TDDLLSWHFKVKNNDWDQASFEVPVDYDVEPFVYFGFFNYDPHQ 60 +++FD+ ++L+ T+ + L+ F+ + N F ++ E + + HQ Sbjct: 4 LFIFDREDQLLTTLTESTGLVRALFREELNRVPNQPFAFTIEASSEEAKHV----IEEHQ 59 Query: 61 -----KEDVFKLFKVIDYNLEDSKFYKG------LDKAESDLDTIAIIKDKRFRQSSADA 109- KE +LF + + LED G + A +L I++ Q + +A Sbjct: 60 VVFRDKEGDLRLFVIKE--LEDVDGLDGPQTTAICEPAFMELAEHMIVEQSVVNQPAHEA 117- Query: 110 CIDGALEGTGYQVGKVEGITNVRTLSYYYISPRAALIKIVEAFNCEFNVRYTF-INNKIT 16- 8 ++ AL+GT + G VE T + Y+S A+ I+ + +F TF N+IT Sbjct: 118 -LNVALQGTRW-TGSVEVNLGNATEHFSYVSAIEAVWNILVTWGGDFKDVVTFNAENRIT 17- 5 Query: 169 SRYIDLKKRFGKPTGKQFEHGNNLLKVVYEESTDDIVTCLIGRGKGEEIQHEEAEPKDVE 22- 8 S I + +R G GK+FE +N+ + + VT L GRG +Q E E + Sbjct: 176 SHQIKIVQRRGVDRGKRFEIDHNI-EQIERTILSYPVTALYGRGAS--LQGENGE----D 22- 8 Query: 229 GHLPQEERRQGYGRRIEFTDVVWSVEKGDPIDKPAGQNFVALDSAREEYGLSQNGELKHR 28- 8 G L +F +V W G P+DKP GQ +V A ++YG NG+L HR Sbjct: 229 GSL-------------DFGEVEWRKSAGAPVDKPKGQLWVGDPEALQKYGRKHNGQLLHR 27- 5 Query: 289 WGVFVNEEIEDKTELLKATWEELQRLSIPIRIYKAEILDIGPETWKGDSVAIIYDEVKIA 34- 8 G+F N IED ELL+ TWE+LQ+ S P Y+ + +++ + Sbjct: 276 EGIFQNTNIEDPEELLEKTWEQLQKSSKPEVHYRLSVR LFEHIS-- 319 Query: 349 FETRVDEIDIDKLNFNRSVVTLGDYSVVQNR------ESRSRKEAVQ-NMIDESLETITD 40- 1 + +LGD ++ +R E +SR A++ +++D + + Sbjct: 320 -------------GYEHEQASLGDTAIAIDRQFSRPIEIQSRIIAIEYDLVDIDGTGMVE 36- 6 Query: 402 LGMTFQEFLQGIEKRIETGKKEMEDNWRK 430 +G L G+++R+E +E+E N K Sbjct: 367 MGQFLS--LNGMDERLERIIEEIEKNQGK 393 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2687 A DNA sequence (GASx991) was identified in S. pyogenes <SEQ ID 7873> which encodes the amino acid sequence <SEQ ID 7874>. Analysis of this protein sequence reveals the following: TABLE-US-07596 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2584 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07597 >GP: AAA98101 GB: M19348 hyaluronidase [Streptococcus pyogenes phage H4489A] Identities = 314/371 (84%), Positives = 338/371 (90%), Gaps = 1/371 (0%) Query: 1 MAENIPLRVQFKRMKAAEWASSDVVLLEGEIGFETDTGFAKFGDGQNTFSKLKYLTGPKG 60 M ENIPLRVQFKRM A EWA SDV+LLEGEIGFETDTGFAKFGDGQNTFSKLKYLTGPKG Sbjct: 1 MTENIPLRVQFKRMSADEWARSDVILLEGEIGFETDTGFAKFGDGQNTFSKLKYLTGPKG 60 Query: 61 PKGDTGLQGKTGGTGSRGPAGKPGTTDYDQLQNKPDLGAFAQKEETNSKITKLESSKADK 120- PKGDTGLQGKTGGTG RGPAGKPGTTDYDQLQNKPDLGAFAQKEETNSKITKLESSKADK Sbjct: 61 PKGDTGLQGKTGGTGPRGPAGKPGTTDYDQLQNKPDLGAFAQKEETNSKITKLESSKADK 120- Query: 121 NAVYLKAESNAKLDEKLNLKGGVMTGQLQFKPN-SGIKPSSSVGGAINIDMSKSEGAAMV 17- 9 +AVY KAES +LD+KL+L GG++TGQLQFFCPN SGIKPSSSVGGAINIDMSKSEGAAMV Sbjct: 121 SAVYSKAESKIELDKKLSLTGGIVTGQLQFKPNKSGIKPSSSVGGAINIDMSKSEGAAMV 18- 0 Query: 180 MYTNKDTTDGPLMILRSNKDTFDQSVQFVDYKGTTNAVNIVMRQPTTPNFSSALNITSAN 23- 9 MYTNKDTTDGPLMILRS+KDTFDQS QFVDY G TNAVNIVMRQP+ PNFSSALNITSAN Sbjct: 181 MYTNKDTTDGPLMILRSDKDTFDQSAQFVDYSGKTNAVNIVMRQPSAPNFSSALNITSAN 24- 0 Query: 240 EGGSAMQIRGVEKALGTLKITHENPSVDKEYDKNAAALSIDIVKKQKGGKGTAAQGIYIN 29- 9 EGGSAMQIRGVEKALGTLKITHENP+V+ +YD+NAAALSIDIVKKQKGGKGTAAQGIYIN Sbjct: 241 EGGSAMQIRGVEKALGTLKITHENPNVEAKYDENAAALSIDIVKKQKGGKGTAAQGIYIN 30- 0 Query: 300 STSGTTGKLLRIRNLNDDKFYVKPDGGFYAKETSQIDGNLKLKDPIANDHAATKAYVDGE 35- 9 STSGT GK+LRIRN N+DKFYV PDGGF++ S + GNL +KDP + HAATK YVD + Sbjct: 301 STSGTAGKMLRIRNKNEDKFYVGPDGGFHSGANSTVAGNLTVKDPTSGKHAATKDYVDEK 36- 0 Query: 360 VEKLKALLAAK 370 + +LK L+ K Sbjct: 361 IAELKKLILKK 371 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2688 A DNA sequence (GASx993) was identified in S. pyogenes <SEQ ID 7875> which encodes the amino acid sequence <SEQ ID 7876>. Analysis of this protein sequence reveals the following: TABLE-US-07598 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1358 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2689 A DNA sequence (GASx995) was identified in S. pyogenes <SEQ ID 7877> which encodes the amino acid sequence <SEQ ID 7878>. Analysis of this protein sequence reveals the following: TABLE-US-07599 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0855 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-07600 >GP: AAC34418 GB: AF158600 gp149 [Streptococcus thermophilus bacteriophage Sfill] Identities = 27/95 (28%), Positives = 50/95 (52%), Gaps = 2/95 (2%) Query: 9 KYPQLDGTGAVASTHIIIAAEDGAVIPQLIKQDLTSTNDTEIIKAALEEFKKSEYVEIAM 68 K + D +GA +T +I+ DGA +P + + ++TE++K ALE + + + A Sbjct: 26 KSKEYDASGAAYATKVILKNRDGAYVPVFLPVEKIDLSNTELLKEALEVIYQENFPQRAE 85 Query: 69 GEAVQKVDDLEKISQETAKTAKTAQTAAGLAKVSA 103 E ++D EKI + A + K +T A + + S+ Sbjct: 86 NEKFNELD--EKIKEYEALSKKATETIAKMEEASS 118 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2690 A DNA sequence (GASx996) was identified in S. pyogenes <SEQ ID 7879> which encodes the amino acid sequence <SEQ ID 7880>. Analysis of this protein sequence reveals the following: TABLE-US-07601 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.62 Transmembrane 9-25 (7-26) ----- Final Results ----- bacterial membrane --- Certainty = 0.2848 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2691 A DNA sequence (GASx997) was identified in S. pyogenes <SEQ ID 7881> which encodes the amino acid sequence <SEQ ID 7882>. Analysis of this protein sequence reveals the following: TABLE-US-07602 Possible site: 41 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.66 Transmembrane 38-54 (35-55) ----- Final Results ----- bacterial membrane --- Certainty = 0.2466 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2692 A DNA sequence (GASx998R) was identified in S. pyogenes <SEQ ID 7883> which encodes the amino acid sequence <SEQ ID 7884>. Analysis of this protein sequence reveals the following: TABLE-US-07603 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.87 Transmembrane 47-63 (41-72) ----- Final Results ----- bacterial membrane --- Certainty = 0.4949 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2693 A DNA sequence (GASx999) was identified in S. pyogenes <SEQ ID 7885> which encodes the amino acid sequence <SEQ ID 7886>. Analysis of this protein sequence reveals the following: TABLE-US-07604 Possible site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2694 A DNA sequence (GASx1001) was identified in S. pyogenes <SEQ ID 7887> which encodes the amino acid sequence <SEQ ID 7888>. Analysis of this protein sequence reveals the following: TABLE-US-07605 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.51 Transmembrane 18-34 (16-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.5203 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2695 A DNA sequence (GASx1002) was identified in S. pyogenes <SEQ ID 7889> which encodes the amino acid sequence <SEQ ID 7890>. Analysis of this protein sequence reveals the following: TABLE-US-07606 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.61 Transmembrane 12-28 (11-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.2444 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein is similar to AF186180 from S. equi. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2696 A DNA sequence (GASx1003) was identified in S. pyogenes <SEQ ID 7891> which encodes the amino acid sequence <SEQ ID 7892>. Analysis of this protein sequence reveals the following: TABLE-US-07607 Possible site: 32 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein is similar to See H from S. equi: TABLE-US-07608 >GP: AAF72809 GB: AF186180 SeeH [Streptococcus equi] Length = 236 Identities = 233/236 (98%), Positives = 234/236 (98%) Query: 1 MRYNCRYSHIDKKIYSMIICLSFLLYSNVVQANSYNTTNRHNLESLYKHDSNLIEADSIK 60 MRYNCRYSHIDKKIYSMIICLSFLLYSNVVQANSYNTTNRHNLESLYKHDSNLIEADSIK Sbjct: 1 MRYNCRYSHIDKKIYSMIICLSFLLYSNVVQANSYNTTNRHNLESLYKHDSNLIEADSIK 60 Query: 61 NSPDIVTSHMLKYSVKDKNLSVFFEKDWISQEFKDKEVDIYALSAQEVCECPGKRYEAFG 120- NSPDIVTSHMLKYSVKDKNLSVFFEKDWISQEFKDKEVDIYALSAQE CECPGKRYEAFG Sbjct: 61 NSPDIVTSHMLKYSVKDKNLSVFFEKDWISQEFKDKEVDIYALSAQEACECPGKRYEAFG 120- Query: 121 GITLTNSEKKEIKVPVNVWDKSKQQPPMFITVNKPKVTAQEVDIKVRKLLIKKYDIYNNR 18- 0 GITLTNSEKKEIKVP+NVWDKSKQ PPMFITVNKPKVTAQEVDIKVRKLLIKKYDIYNNR Sbjct: 121 GITLTNSEKKEIKVPINVWDKSKQHPPMFITVNKPKVTAQEVDIKVRKLLIKKYDIYNNR 18- 0 Query: 181 EQKYSKGTVTLDLNSGKDIVFDLYYFGNGDFNSMLKIYSNNERIDSTQFHVDVSIS 236 EQKYSKGTVTLDLNSGKDIVFDLYYFGNGDFNSMLKIYSNNERIDSTQFHVDVSIS Sbjct: 181 EQKYSKGTVTLDLNSGKDIVFDLYYFGNGDFNSMLKIYSNNERIDSTQFHVDVSIS 236 There is also homology to a S. aureus enterotoxin: TABLE-US-07609 >GP: AAA19777 GB: U11702 enterotoxin H [Staphylococcus aureus] Identities = 70/215 (32%), positives = 108/215 (49%), Gaps = 19/215 (8%) Query: 27 SNVVQANSYNTTNRHNLESLYKHDSNLIEADSI-KNSPDIVTSHMLKYSVKDKNLSVFFE 85 - +++ AN+Y N ++ K D E D I +N D +K++ D Sbjct: 34 TDLALANAYGQYNHPFIKENIKSDEISGEKDLIFRNQGDSGNDLRVKFATAD-------- 85 Query: 86 KDWISQEFKDKEVDIYALSAQEVCECPGKRYEA--FGGITLTNSEK--KEIKVPVNVWDK 141- ++Q+FK+K VDIY S CE + +GG TL NSEK +E + NVW Sbjct: 86 ---LAQKFKNKNVDIYGASFYYKCEKISENISECLYGGTTL-NSEKLAQERVIGANVWVD 141- Query: 142 SKQQPPMFITVNKPKVTAQEVDIKVRKLLIKKYDIYNNREQKYSKGTVTLDLNSGKDIVF 20- 1 Q+ I NK VT QE+DIK+RK+L KY IY ++ + SKG + D+ + +D F Sbjct: 142 GIQKETELIRTNKKNVTLQELDIKIRKILSDKYKIY-YKDSEISKGLIEFDMKTPRDYSF 20- 0 Query: 202 DLYYFGNGDFNSMLKIYSNNERIDSTQF-HVDVSI 235 D+Y + + KIY +N+ + S H+DV++ Sbjct: 201 DIYDLKGENDYEIDKIYEDNKTLKSDDISHIDVNL 235 >GP: AAC26661 GB: AF064774 extracellular enterotoxin type I precursor [Staphylococcus aureus] Identities = 68/214 (31%), Positives = 109/214 (50%), Gaps = 27/214 (12%) Query: 42 NLESLY-KHDSNLIEADSIKNSPDIVTSHMLKYSVKDKNLSVFFEKDWIS-QEFKDKEVD 99 - NL + Y KHD ++ + KN P ++ L++S +L + +W +FK K++D Sbjct: 32 NLRNFYTKHDYIDLKGVTDKNLP---IANQLEFSTGTNDL-ISESNNWDEISKFKGKKLD 87 Query: 100 IYALSAQEVCECPGKRYEAFGGITLTNSEKKEI-KVPVNVWDKSKQQPPMF--ITVNKPK 15- 6 I+ + C K +GG TL+ K+P+N+W K + I NK Sbjct: 88 IFGIDYNGPC----KSKYMYGGATLSGQYLNSARKIPINLWVNGKHKTISTDKIATNKKL 143- Query: 157 VTAQEVDIKVRKLLIKKYDIYNNRE--------------QKYSKGTVTLDLNSGKDIVFD 20- 2 VTAQE+D+K+R+ L ++Y+IY + ++ G V LN+ K +D Sbjct: 144 VTAQEIDVKLRRYLQEEYNIYGHNNTGKGKEYGYKSKFYSGFNNGKVLFHLNNEKSFSYD 20- 3 Query: 203 LYYFGNGDFNSMLKIYSNNERIDSTQFHVDVSIS 236 L+Y G+G S LKIY +N+ I+S +FH+DV IS Sbjct: 204 LFYTGDGLPVSFLKIYEDNKIIESEKFHLDVEIS 237 >GP: AAC28968 GB: U93688 enterotoxin [Staphylococcus aureus] Identities = 70/244 (28%), Positives = 127/244 (51%), Gaps = 27/244 (11%) Query: 12 KKIYSMIICLSFLLYSNVVQANSYNTTNRHNLESLYKHDSNLIEADSIKNSPDIVTSHML 71 - KK+ S+++ ++ ++ A++ NL + Y + ++ +K++ D ++ L Sbjct: 2 KKLISILL-INIIILGVSNNASAQGDIGIDNLRNFYTK-KDFVDLKDVKDN-DTPIANQL 58 Query: 72 KYSVKDKNLSVFFEKDWIS-QEFKDKEVDIYALSAQEVCECPGKRYEAFGGITLTNSE-K 129- ++S + +L + KD+ FK K++D++ +S C +Y +GG+T TN Sbjct: 59 QFSNESYDL-ISESKDFNKFSNFKGKKLDVFGISYNGQCNT---KY-IYGGVTATNEYLD 113- Query: 130 KEIKVPVNVW--DKSKQQPPMFITVNKPKVTAQEVDIKVRKLLIKKYDIYNNREQK---- 18- 3 K +P+N+W K ++ NK VTAQE+D+K+RK L ++Y+IY + K Sbjct: 114 KSRNIPINIWINGNHKTISTNKVSTNKKLVTAQEIDVKLRKYLQEEYNIYGHNGTKKGEE 17- 3 Query: 184 ----------YSKGTVTLDLNSGKDIVFDLYYFG-NGDFNSMLKIYSNNERIDSTQFHVD 23- 2 ++ G VT LN+ +DL+Y G +G S LKIY +N+ ++S +FH+D Sbjct: 174 YGHKSKFYSGFNIGKVTFHLNNNDTFSYDLFYTGDDGLPKSFLKIYEDNKTVESEKFHLD 23- 3 Query: 233 VSIS 236 V IS Sbjct: 234 VDIS 237 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2697 A DNA sequence (GASx1004R) was identified in S. pyogenes <SEQ ID 7893> which encodes the amino acid sequence <SEQ ID 7894>. Analysis of this protein sequence reveals the following: TABLE-US-07610 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.18 Transmembrane 12-28 (12-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.1871(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2698 A DNA sequence (GASx1009) was identified in S. pyogenes <SEQ ID 7895> which encodes the amino acid sequence <SEQ ID 7896>. Analysis of this protein sequence reveals the following: TABLE-US-07611 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6391(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2699 A DNA sequence (GASx1010) was identified in S. pyogenes <SEQ ID 7897> which encodes the amino acid sequence <SEQ ID 7898>. Analysis of this protein sequence reveals the following: TABLE-US-07612 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4528(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2700 A DNA sequence (GASx1024) was identified in S. pyogenes <SEQ ID 7899> which encodes the amino acid sequence <SEQ ID 7900>. Analysis of this protein sequence reveals the following: TABLE-US-07613 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2701 A DNA sequence (GASx1033) was identified in S. pyogenes <SEQ ID 7901> which encodes the amino acid sequence <SEQ ID 7902>. Analysis of this protein sequence reveals the following: TABLE-US-07614 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1652(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2702 A DNA sequence (GASx1039) was identified in S. pyogenes <SEQ ID 7903> which encodes the amino acid sequence <SEQ ID 7904>. Analysis of this protein sequence reveals the following: TABLE-US-07615 Possible site: 22 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.06 Transmembrane 15-31 (15-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.1426(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2703 A DNA sequence (GASx1058) was identified in S. pyogenes <SEQ ID 7905> which encodes the amino acid sequence <SEQ ID 7906>. Analysis of this protein sequence reveals the following: TABLE-US-07616 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5484(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2704 A DNA sequence (GASx1077) was identified in S. pyogenes <SEQ ID 7907> which encodes the amino acid sequence <SEQ ID 7908>. Analysis of this protein sequence reveals the following: TABLE-US-07617 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4848(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2705 A DNA sequence (GASx1080) was identified in S. pyogenes <SEQ ID 7909> which encodes the amino acid sequence <SEQ ID 7910>. Analysis of this protein sequence reveals the following: TABLE-US-07618 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.42 Transmembrane 107-123 (93-133) INTEGRAL Likelihood = -11.20 Transmembrane 20-36 (14-44) INTEGRAL Likelihood = -8.39 Transmembrane 226-242 (218-246) INTEGRAL Likelihood = -5.52 Transmembrane 129-145 (126-148) INTEGRAL Likelihood = -4.46 Transmembrane 160-176 (159-183) INTEGRAL Likelihood = -1.44 Transmembrane 55-71 (55-72) ----- Final Results ----- bacterial membrane --- Certainty = 0.5967(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2706 A DNA sequence (GASx1081) was identified in S. pyogenes <SEQ ID 7911> which encodes the amino acid sequence <SEQ ID 7912>. Analysis of this protein sequence reveals the following:

TABLE-US-07619 Possible site: 34 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -13.00 Transmembrane 103-119 (91-129) INTEGRAL Likelihood = -11.46 Transmembrane 208-224 (203-230) INTEGRAL Likelihood = -8.28 Transmembrane 54-70 (46-71) INTEGRAL Likelihood = -5.79 Transmembrane 160-176 (155-181) INTEGRAL Likelihood = -4.25 Transmembrane 127-143 (125-149) ----- Final Results ----- bacterial membrane --- Certainty = 0.6201(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2707 A DNA sequence (GASx1089) was identified in S. pyogenes <SEQ ID 7913> which encodes the amino acid sequence <SEQ ID 7914>. Analysis of this protein sequence reveals the following: TABLE-US-07620 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2999(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2708 A DNA sequence (GASx1109) was identified in S. pyogenes <SEQ ID 7915> which encodes the amino acid sequence <SEQ ID 7916>. Analysis of this protein sequence reveals the following: TABLE-US-07621 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1270 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2709 A DNA sequence (GASx1114R) was identified in S. pyogenes <SEQ ID 7917> which encodes the amino acid sequence <SEQ ID 7918>. Analysis of this protein sequence reveals the following: TABLE-US-07622 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4021 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2710 A DNA sequence (GASx1149) was identified in S. pyogenes <SEQ ID 7919> which encodes the amino acid sequence <SEQ ID 7920>. Analysis of this protein sequence reveals the following: TABLE-US-07623 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.70 Transmembrane 12-28 (12-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2711 A DNA sequence (GASx1150) was identified in S. pyogenes <SEQ ID 7921> which encodes the amino acid sequence <SEQ ID 7922>. Analysis of this protein sequence reveals the following: TABLE-US-07624 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2712 A DNA sequence (GASx1160) was identified in S. pyogenes <SEQ ID 7923> which encodes the amino acid sequence <SEQ ID 7924>. Analysis of this protein sequence reveals the following: TABLE-US-07625 Possible site: 17 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.19 Transmembrane 15-31 (15-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.2275 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2713 A DNA sequence (GASx1167) was identified in S. pyogenes <SEQ ID 7925> which encodes the amino acid sequence <SEQ ID 7926>. Analysis of this protein sequence reveals the following: TABLE-US-07626 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1404 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07627 >GP: AAB99233 GB: U67563 oxaloacetate decarboxylase alpha chain (oadA) [Methanococcus jannaschii] Identities = 250/453 (55%), Positives = 325/453 (71%), Gaps = 7/453 (1%) Query: 13 VAITETVLRDGHQSLMATRLSIEDMLPVLTILDKIGYYSLECWGGATFDACIRFLNEDPW 72 - V I +T RD QSL+ATR+ EDMLP+ +D++G+YS+E WGGATFDACIR+LNEDPW Sbjct: 2 VKIVDTTFRDAQQSLIATRMRTEDMLPIAEKMDEVGFYSMEVWGGATFDACIRYLNEDPW 61 Query: 73 ERLRTLKKGLPNTRLQMLLRGQNLLGYRHYADDIVDKFISLSAQNGIDVFRIFDALNDPR 132- ERLR LKK + NT LQMLLRGQNL+GYRHY DDIV+KF+ + +NGID+FRIFDALND R Sbjct: 62 ERLRALKKRIQNTPLQMLLRGQNLVGYRHYPDDIVEKFVIKAHENGIDIFRIFDALNDVR 121- Query: 133 NIQQALRAVKKTGKEAQLCIAYTTSPVHTLNYYLSLVKELVEMGADSICIKDMAGILTPK 19- 2 N++ A++ KK G E Q I YT SPVHT++ Y+ L K+L EMG DSICIKDMAG+LTP Sbjct: 122 NMETAIKTAKKVGAEVQGAICYTISPVHTIDQYVELAKKLEEMGCDSICIKDMAGLLTPY 18- 1 Query: 193 AAKELVSGIKAMTNLPLIVHTHATSGISQMTYLAAVEAGADRIDTALSPFSEGTSQPATE 25- 2 ELV +K +LP+ VH+H TSG++ MTYL +EAGAD +D A+SPF+ GTSQP TE Sbjct: 182 EGYELVKRLKEEISLPIDVHSHCTSGLAPMTYLKVIEAGADMVDCAISPFAMGTSQPPTE 24- 1 Query: 253 SMYLALKEASYDITLDETLLEQAANHLRQARQKYLADGILDPSLLFPDPRTLQYQVPGGM 31- 2 S+ +ALK YD LD LL + ++ + R+KY + P D R L YQVPGGM Sbjct: 242 SIVVALKGTKYDTGLDLKLLNEIRDYFMKVREKYKM--LFSPISQIVDARVLVYQVPGGM 29- 9 Query: 313 LSNMLSQLKQANAESKLEEVLAEVPRVRKDLGYPPLVTPLSQMVGTQAAMNVILGKPYQM 37- 2 LSN++SQLK+ A K EEVL E+PRVRKDLGYPPLVTP SQ+VGTQA +NV+ + Y++ Sbjct: 300 LSNLVSQLKEQGALDKFEEVLQEIPRVRKDLGYPPLVTPTSQIVGTQAVLNVLTEERYKI 35- 9 Query: 373 VSKEIKQYLAGDYGKTPAPVNEDLKRSQI--GSAPVTTNRPADQLSPEFEVLK--AEVAD 42- 8 ++ E+ Y+ G YGK PAP+N +L + + G P+T RPAD L PE+E +K AE Sbjct: 360 ITNEVVNYVKGFYGKPPAPINPELLKRVLDEGEKPITC-RPADLLPPEWEKVKKEAEEKG 41- 8 Query: 429 LAQTDEDVLTYALFPSVAKPFLTTKYQTDDVIK 461 + + +ED+LTYAL+P +A FL + + + + K Sbjct: 419 IVKKEEDILTYALYPQIAVKFLRGELKAEPIPK 451 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2714 A DNA sequence (GASx1168) was identified in S. pyogenes <SEQ ID 7927> which encodes the amino acid sequence <SEQ ID 7928>. Analysis of this protein sequence reveals the following: TABLE-US-07628 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.11 Transmembrane 16-32 (2-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.3845 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2715 A DNA sequence (GASx1170) was identified in S. pyogenes <SEQ ID 7929> which encodes the amino acid sequence <SEQ ID 7930>. Analysis of this protein sequence reveals the following: TABLE-US-07629 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.06 Transmembrane 211-227 (208-238) INTEGRAL Likelihood = -5.84 Transmembrane 117-133 (110-136) INTEGRAL Likelihood = -5.36 Transmembrane 256-272 (253-274) INTEGRAL Likelihood = -4.67 Transmembrane 44-60 (41-64) INTEGRAL Likelihood = -4.19 Transmembrane 287-303 (287-306) INTEGRAL Likelihood = -3.77 Transmembrane 358-374 (357-375) INTEGRAL Likelihood = -2.18 Transmembrane 20-36 (16-38) INTEGRAL Likelihood = -0.85 Transmembrane 90-106 (90-106) INTEGRAL Likelihood = -0.53 Transmembrane 165-181 (164-181) ----- Final Results ----- bacterial membrane --- Certainty = 0.3824 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07630 >GP: CAA05140 GB: AJ002015 methylmalonyl-CoA decarboxylase, beta-subunit [Propionigenium modestum] Identities = 231/395 (58%), Positives = 293/395 (73%), Gaps = 19/395 (4%) Query: 1 MLDVLNQMVQSSGLAHLTVNNLIMICLASFFLYLGIKKEYEPYLMVPIAFGILLVNLPMA 60 ML + S+G L + ++IM+ +A FLYL I KE+EP L+VPI+FGILL NLP A Sbjct: 1 MLQAILDFYHSTGFYGLNMGSIIMMLVACVFLYLAIAKEFEPLLLVPISFGILLTNLPFA 60 Query: 61 GLMDHP---------ANG---------NPGGLLYYLYKGTSLGIYPPLIFLCLGASTDFG 102- G+M P A+G PGGLLYYL++G LGI+PPLIFL +GA TDFG Sbjct: 61 GMMAEPLLEVHEKLSASGAHLYTAHTAEPGGLLYYLFQGDHLGIFPPLIFLGVGAMTDFG 120- Query: 103 PLIANPKTILLGGAAQVGIFLAFFLAIMLGM-TPQEAASVGIIGGADGPTAIYVTTKLAP 16- 1 PLI+NPK++LLG AAQ GIF+ FF AI G+ T QEAAS+GIIGGADGPTAI++++KLAP Sbjct: 121 PLISNPKSLLLGAAAQFGIFVTFFGAIASGLFTAQEAASIGIIGGADGPTAIFLSSKLAP 18- 0 Query: 162 DLLSTIALAAYSYMALVPIIQPPIIKLLTTKAERQVKMTQARTVSQKEKIIFPIMVTIFV 22- 1 L+ IA+AAYSYMALVPIIQPPI+ LT++ ER++KM+Q R VS++EKIIFPI+VTI V Sbjct: 181 HLMGPIAVAAYSYMALVPIIQPPIMTALTSETERKIKMSQLRLVSKREKIIFPIVVTILV 24- 0 Query: 222 SLLVPSATTLVGCLMLGNLVREIKIVPKIVENLQQVVMFCITIILGLTVGAKANGDLFLS 28- 1 SL+VP A TLVG LMLGN RE +V ++ + + ++ ITI LG+TVGA A + FL Sbjct: 241 SLIVPPAATLVGMLMLGNLFRECGVVGRLEDTAKNALINIITIFLGVTVGATATAEAFLK 30- 0 Query: 282 ATTLKIIALGLIAFAAGTAGGVLMGKVMYYLSGNKVNPMIGAAGVSAVPMAARVVQKIGQ 34- 1 TL I+ LG++AF GT GVL+ K M LS +NP++G+AGVSAVPMAARV Q +GQ Sbjct: 301 VETLAILGLGIVAFGIGTGSGVLLAKFMNKLSKEPINPLLGSAGVSAVPMAARVSQVVGQ 36- 0 Query: 342 EEDPSNFLLMHANGPNVAGVIGSAIASGALLAFFG 376 + DP+NFLLMHAMGPNVAGVIGSA+++G LL+ FG Sbjct: 361 KADPTNFLLMHAMGPNVAGVIGSAVSAGVLLSLFG 395 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2716 A DNA sequence (GASx1171R) was identified in S. pyogenes <SEQ ID 7931> which encodes the amino acid sequence <SEQ ID 7932>. Analysis of this protein sequence reveals the following: TABLE-US-07631 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0851 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07632 >GP: AAF93965 GB: AE004165 citG protein [Vibrio cholerae] Identities = 100/287 (34%), Positives = 154/287 (52%), Gaps = 12/287 (4%) Query: 9 ISQLALKALLYEVSLSPKPGLVDRFDNGAHDDMSFITFIDSMIALSPFFQAYIETGFAYA 68 + LA A++ EV L+PKPGLVD +NGAH DM TFI S A++P+ +++ G+ A Sbjct: 32 VGHLAYHAMMLEVHLTPKPGLVDTANNGAHRDMDLNTFIASAEAIAPYLHSFVSAGWESA 91 Query: 69 KEEPLLLFNRLRQLGQKAEETMFCATQGINTHKGLNFSMALLLGATGAYLARTPHLMTDL 128- L + LR +G +AE+ MF ATQG+NTHKG+ F + L+ G+ G A Sbjct: 92 GNPAAQLLSALRPIGIEAEQAMFAATQGVNTHKGMIFILGLICGSVGWLKANQ------- 144- Query: 129 GRFSKEDTLAICRLVKPMTAHLIQTDLGHLNTKKEFTYGEQLFVTYGIKGPRGEASEGFT 18- 8 K D I ++ L+ +L + T GE+++ YG+ G RGEA+ G Sbjct: 145 ---LKIDAQHTGETIRQACQFLVIDELKAKRDCEPETAGERIYRQYGLTGARGEAASGLA 20- 1 Query: 189 TLTDHALPYFRQMISQN-DPETSQLRLLVYLMSIVEDGNLIHRGGIEAWKGVKAD-MRLL 24- 6 + HALP ++ +++ E + L+ LM+ D NL+ RGG+ V+ +LL Sbjct: 202 MVMIQHALPAYQACLTKGASTEQALWHTLLVLMANNNDSNLVSRGGLAGLHFVQEQAQQLL 2- 61 Query: 247 LQQDLSTTDLRLALSSYNQCLINQHLSPGGAADLLALTFYFAFLEKL 293 + ++ AL++ + LI +HLSPGG+ADLLA T+ L +L Sbjct: 262 AKGGFLYQEIEQALTALDSVLIEKHLSPGGSADLLAATWLIYELVQL 308 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2717 A DNA sequence (GASx1172R) was identified in S. pyogenes <SEQ ID 7933> which encodes the amino acid sequence <SEQ ID 7934>. Analysis of this protein sequence reveals the following: TABLE-US-07633 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2501 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07634 >GP: CAB12389 GB: Z99107 similar to transcriptional regulator (GntR family) [Bacillus subtilis] Identities = 60/205 (29%), Positives = 99/205 (48%), Gaps = 3/205 (1%) Query: 19 PLKIAFYNALKKTIILRQIPVGSRINEKEFSIALNISRTPIRYALGLLSEEHLVEHIPKK 78 - P + FYN LKK I G RINE + + + +SR+PIR A+ LL ++ L++ + Sbjct: 11 PYYLQFYNQLKKMIFNGTFKPGERINETQLAKSFGVSRSPIREAMRLLEKDGLLKADDRN 70 Query: 79 GIIVKGVSIKDACEIFEIRKALETLATVQAMHLMTEEDFKVMHNLLEDCETFI--AEDDT 136- G + ++ KD EI++IR LE LA + EE+ ++ LE+ E I +DT Sbjct: 71 GFSITSLTAKDVDEIYKIRIPLEQLAVELVIDEADEEELTILEKQLEETEKAIHNGTEDT 130- Query: 137 NRILDNFNAFNNLIYSYSQMVRLKEIVTELQAYLVYFRKISISSVERRKRALSEHWMIYR 19- 6 I N F+ L+ +S LK ++ + + + R ++ + R + L EH I+ Sbjct: 131 EIIRLN-QKFHELLVDFSHNRHLKNLLEHVNDLIHFCRILNYTGDHRAETILREHRRIFE 18- 9 Query: 197 GMKNKDHEQITLITHEHLNSSLEFI 221 +K K+ E H N E + Sbjct: 190 EVKKKNKEAAKQHVLAHFNHDCEHL 214 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2718 A DNA sequence (GASx1173R) was identified in S. pyogenes <SEQ ID 7935> which encodes the amino acid sequence <SEQ ID 7936>. Analysis of this protein sequence reveals the following: TABLE-US-07635 Possible site: 16 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.99 Transmembrane 450-466 (445-473) INTEGRAL Likelihood = -9.61 Transmembrane 33-49 (30-55) INTEGRAL Likelihood = -8.55 Transmembrane 326-342 (321-346) INTEGRAL Likelihood = -7.01 Transmembrane 288-304 (286-311) INTEGRAL Likelihood = -6.79 Transmembrane 95-111 (88-114) INTEGRAL Likelihood = -4.99 Transmembrane 265-281 (264-285) INTEGRAL Likelihood = -4.62 Transmembrane 208-224 (204-228) INTEGRAL Likelihood = -3.13 Transmembrane 126-142 (126-145) INTEGRAL Likelihood = -2.81 Transmembrane 366-382 (365-383) INTEGRAL Likelihood = -2.34 Transmembrane 419-435 (417-438) ----- Final Results ----- bacterial membrane --- Certainty = 0.5394 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9169> which encodes the amino acid sequence <SEQ ID 9170>. Analysis of this protein sequence reveals the following: TABLE-US-07636 Possible cleavage site: 39 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.99 Transmembrane 443-459 (438-466) INTEGRAL Likelihood = -8.55 Transmembrane 319-335 (314-339) INTEGRAL Likelihood = -7.01 Transmembrane 281-297 (279-304) INTEGRAL Likelihood = -6.79 Transmembrane 88-104 (81-107) INTEGRAL Likelihood = -4.99 Transmembrane 258-274 (257-278) INTEGRAL Likelihood = -4.62 Transmembrane 201-217 (197-221) INTEGRAL Likelihood = -3.13 Transmembrane 119-135 (119-138) INTEGRAL Likelihood = -2.81 Transmembrane 359-375 (358-376) INTEGRAL Likelihood = -2.34 Transmembrane 412-428 (410-431) ----- Final Results ----- bacterial membrane --- Certainty = 0.539 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-07637 >GP: AAG08853 GB: AE004959 probable citrate transporter [Pseudomonas aeruginosa] Identities = 199/468 (42%), Positives = 296/468 (62%), Gaps = 41/468 (8%) Query: 9 LLTMLAYAMIIVFMYVVMKKKMTPFTALVMIPLIMTIAVILTGSADFNADAKFVAFVGDG 68 +LT+LA+AM+ FM+++M K+++ AL+++P +AF G Sbjct: 1 MLTLLAFAMVATFMFLIMTKRLSALIALILVP---------------------IAFALIG 39 Query: 69 GIAKDLTAIGPMVMYGINNTAKTGIMLLFAILFFSVMLDAGLFDPITEKMIRFAKGDPMK 128- G A L GPM++ GI A TG+ML+FAIL+F++M+D+GLFDP K++R KGDP+K Sbjct: 40 GFAAGL---GPMMLDGIRTLAPTGVMLMFAILYFAIMIDSGLFDPAVRKILRLVKGDPLK 96 Query: 129 VLIATAVVAAAVSLNGDGTTTTLICCSAFLPIYKKLDMKIMNLGVLIILQNTIMNLLPWG 18- 8 V + TA +A VSL+GDG+TT +IC +A LP+Y +L M + + LI+L + ++N+ PWG Sbjct: 97 VSLGTAALAMIVSLDGDGSTTYMICVAAVLPLYSRLGMSPLVMACLIMLSSGVLNMTPWG 156- Query: 189 GPTARAMSVLGVGP-EILGYLAPGMILSLL--YVICWVAPSMGRKERARLGVIDL--SEE 24- 3 GPTARA S L V P +I + P MI LL + I W+ G++ERARLG + L E Sbjct: 157 GPTARAASALHVDPADIFVPMIPAMIAGLLAIFAIAWI---YGKRERARLGELHLPTDHE 21- 3 Query: 244 DMRQLTDITDPDTLFIRRPKNFVFNAILTIGLITWLVAGSFNKSIAMAPLLLFAVGTCIA 30- 3 D+ +++ P+ RRPK FNAILT+ L+ L+AG + M L + A G IA Sbjct: 214 DLAEISVSQYPEA---RRPKLLWFNAILTVVLMATLIAGL----LPMPVLFMIAFG--IA 26- 4 Query: 304 LMVNYPVLKDQSKRIGDNAGDAVQVVILVFAAGIFMGLFQGSGMASALAQSFATIIPKQL 36- 3 ++VNYP +++Q KRIG +A + + VV L+FAAG+F G+ G+GM A+++S +IP L Sbjct: 265 MIVNYPCIQEQKKRIGAHAENILAVVSLIFAAGVFTGILSGTGMVDAMSKSLLAVIPPAL 32- 4 Query: 364 AGFWGLVIALVSAPGTFFISNDGFYYGILPVLAEAGAEYGFSNMAMALASLMGQAFHLLS 42- 3 + + ALVS P TFF+SND FYYG+LP+L +A AEYG + + MA AS++GQ HLLS Sbjct: 325 GPYLATITALVSMPFTFFMSNDAFYYGVLPILTQAAAEYGITPVEMARASIVGQPVHLLS 38- 4 Query: 424 PLVAFIYLLLRLTGLDMGEWQKEAAKYALIIFVIFVVTIIAMGQMPLY 471 PLV YLL+ L +D G+ Q+ K+A+++ + + + +G PL+ Sbjct: 385 PLVPSTYLLVGLAKIDFGDHQRFTLKWAVLVCLAILAMALLLGLFPLF 432 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2719 A DNA sequence (GASx1174) was identified in S. pyogenes <SEQ ID 7937> which encodes the amino acid sequence <SEQ ID 7938>. Analysis of this protein sequence reveals the following: TABLE-US-07638 Possible site: 57 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3948 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2720 A DNA sequence (GASx1175) was identified in S. pyogenes <SEQ ID 7939> which encodes the amino acid sequence <SEQ ID 7940>. Analysis of this protein sequence reveals the following: TABLE-US-07639 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3519 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2721 A DNA sequence (GASx1177) was identified in S. pyogenes <SEQ ID 7941> which encodes the amino acid sequence <SEQ ID 7942>. Analysis of this protein sequence reveals the following: TABLE-US-07640 Possible site: 60 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -9.24 Transmembrane 115-131 (105-137) INTEGRAL Likelihood = -8.92 Transmembrane 208-224 (204-238) INTEGRAL Likelihood = -7.80 Transmembrane 282-298 (273-303) INTEGRAL Likelihood = -4.94 Transmembrane 85-101 (75-102) INTEGRAL Likelihood = -4.04 Transmembrane 10-26 (3-32) INTEGRAL Likelihood = -3.61 Transmembrane 255-271 (253-271) ----- Final Results ----- bacterial membrane --- Certainty = 0.4694 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07641 >GP: AAB89172 GB: AE000960 oxaloacetate decarboxylase, sodium ion pump subunit (oadB) [Archaeoglobus fulgidus] Identities = 190/354 (53%), Positives = 255/354 (71%), Gaps = 8/354 (2%) Query: 16 IVMMVIGALLMYLGIKKEYEPTLLVPMGLGTILVNFPGSGVLTQVVNGVEQEGVFEALFN 75 - +VM+ +G LL+YLGI K+ EP LLVP+G+G ILVN PG G+ E+ +F+ Sbjct: 5 LVMIGVGLLLVYLGIVKKMEPLLLVPIGIGAILVNIPGGGL-------AEEGSIFDLFLK 57 Query: 76 FGIGTELFPLLIFIGIGAMIDFGPLLQNPFMLLFGDAAQFGIFFVVVVAVLAGFDIKEAA 135- + I TE+ PLLIF+G+GA+ DF PLL NP L G AAQ GIF ++ A+ GF +EAA Sbjct: 58 YLIHTEIVPLLIFLGLGALTDFSPLLANPKTFLLGAAAQIGIFAALIAALFLGFTPQEAA 117- Query: 136 SIGIIGAADGPTSIFVANQLAKDLLGPITVAAYSYMALVPIIQPFAIKLVTTKKERRIRM 19- 5 SIGIIG ADGPT+I+ LA LL VAAYSYM+LVPIIQP IK +T+ +ER+I+M Sbjct: 118 SIGIIGGADGPTTIYTTTILAPHLLAATAVAAYSYMSLVPIIQPPIIKALTSSRERKIKM 17- 7 Query: 196 TYKAENVSQMTKILFPIIITLVAGFIAPISLPLVGFLMFGNLLRECGVLDRLSQTAQNEL 25- 5 + VS+ KILFPI +++GF+AP +LPLVG LM GNL RE GV DRL++ A EL Sbjct: 178 R-QLRIVSKKEKILFPIATIIISGFLAPKALPLVGMLMTGNLFRESGVTDRLAKGASEEL 23- 6 Query: 256 VNIISILLGLTISIKMQADLFLNVQTLLIIVFGLLAFIMDSIGGVMFAKFLNLFRKEKIN 31- 5 +NI++I+LGL++ M+A+ FL +TLL++ G++AF + GGV+ AK +NLF KEKIN Sbjct: 237 MNIMTIILGLSVGSTMRAESFLTQKTLLVLALGVVAFAAATAGGVLLAKVMNLFLKEKIN 29- 6 Query: 316 PMIGAAGISAFPMSSRVIQKMATDEDPQNFILMYAVGANVSGQIASVIAGGLLL 369 PMIGAAG+SA PMS+RV+Q++A +EDP N ILM+A+G NV+G I S +A G+L+ Sbjct: 297 PMIGAAGVSAVPMSARVVQRLAIEEDPHNHILMHAMGPNVAGVIGSAVAAGVLI 350 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2722 A DNA sequence (GASx1178) was identified in S. pyogenes <SEQ ID 7943> which encodes the amino acid sequence <SEQ ID 7944>. Analysis of this protein sequence reveals the following: TABLE-US-07642 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.50 Transmembrane 21-37 (8-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.4800 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2723 A DNA sequence (GASx1179) was identified in S. pyogenes <SEQ ID 7945> which encodes the amino acid sequence <SEQ ID 7946>. Analysis of this protein sequence reveals the following: TABLE-US-07643 Possible site: 60 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1906 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07644 >GP: AAF93961 GB: AE004165 citrate lyase, gamma subunit [Vibrio cholerae] Identities = 46/97 (47%), Positives = 64/97 (65%) Query: 1 MDIKQTAVAGSLESSDLMITVSPNDEQTITITLDSSVEKQFGNHIRQLIHQTLVNLKVTA 60 M I A AG+LESSDL + + PN++ I + LDS+VE+QFG+ IRQ++ TL ++V Sbjct: 1 MKIAHPAFAGTLESSDLQVRIEPNNDGGIELVLDSTVEQQFGHAIRQVVLHTLDAMQVRD 60 Query: 61 AKVEAVDKGALDCTIQARTIAAVHRAAGIDQYDWKEI 97 A V DKGALDC I+AR AAV RA + +W ++ Sbjct: 61 ALVTIEDKGALDCVIRARVQAAVMRACDVQNIEWSQL 97 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2724 A DNA sequence (GASx1181) was identified in S. pyogenes <SEQ ID 7947> which encodes the amino acid sequence <SEQ ID 7948>. Analysis of this protein sequence reveals the following: TABLE-US-07645 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.65 Transmembrane 74-90 (74-90) ----- Final Results ----- bacterial membrane --- Certainty = 0.1659 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07646 >GP: CAA71632 GB: Y10621 CILB, citryl-CoA lyase beta subunit [Leuconostoc mesenteroides] Identities = 187/293 (63%), Positives = 237/293 (80%), Gaps = 1/293 (0%) Query: 2 ERLRRTMMFVPGANAAMLRDAPLFGADSIMFDLEDSVSLKEKDTSRALVHFALKTFDYSS 61 ERLRRTMNFVPG N AM++DA +FGADSIMFDLED+VSL EKD++R LV+ AL+T DY S Sbjct: 4 ERLRRTMMFVPGNNPAMVKDAGIFGADSIMFDLEDAVSLAEKDSARYLVYEALQTVDYGS 63 Query: 62 VETVVRVNGLDS-CGALDIEAVVLAGVNVIRLPKTETAQDIIDVEAVIERVERENSIEVG 120- E VVR+NGLD+ DI+A+V AG++VIRLPK ETA + ++E++I E+E VG Sbjct: 64 SELVVRINGLDTPFYKNDIKAMVKAGIDVIRLPKVETAAMMHELESLITDAEKEFGRPVG 123- Query: 121 RTRMMAAIESAEGVLNAREIAKASKRLIGIALGAEDYVTNMKTRRYPDGQELFFARSMIL 18- 0 T MMAAIESA GV+NA EIA AS R+IGIAL AEDY T+MKT RYPDGQEL +AR++IL Sbjct: 124 TTHMMAAIESALGVVNAVEIANASDRMIGIALSAEDYTTDMKTHRYPDGQELLYARNVIL 18- 3 Query: 181 HAARAAGIAAIDTVYSDVNNTEGFQNEVRMIKQLGFDGKSVINPRQIPLVNEIYTPTKKE 24- 0 HAARAAGIAA DTV++++N+ EGF E ++I QLGFDGKS+INPRQI +VN++Y PT+KE Sbjct: 184 HAARAAGIAAFDTVFTNLNDEEGFYRETQLIHQLGFDGKSLINPRQIEMVNKVYAPTEKE 24- 3 Query: 241 IDHAKQVIWAIREAESKGSGVISLNGKMVDKPIVERAERVIALATAAGVLSEE 293 I++A+ VI AI EA+ KGSGVIS+NG+MVD+P+V RA+RV+ LA A ++ E Sbjct: 244 INNAQNVIAAIEEAKQKGSGVISMNGQMVDRPVVLRAQRVMKLANANHLVDSE 296 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2725 A DNA sequence (GASx1182) was identified in S. pyogenes <SEQ ID 7949> which encodes the amino acid sequence <SEQ ID 7950>. Analysis of this protein sequence reveals the following: TABLE-US-07647 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3554 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07648 >GP: CAA71633 GB: Y10621 CILA, citrate CoA-transferase alpha subunit [Leuconostoc mesenteroides] Identities = 294/511 (57%), Positives = 378/511 (73%), Gaps = 7/511 (1%) Query: 4 NKLGRDIPQPYADQY--GVFEGELANIKQYDESSRRIKPVKPGDSKLLGSVREAIEKTGL 61 NK+ D+P +Q VFE + +++ G+SK+ S+ + + T L Sbjct: 3 NRVNIDVPDAILEQLDDSVFESTNYGNPEIQRVGPKVRATT-GESKVQSSIDDVLSNT-L 60 Query: 62 TDGMTISFHHHFREGDFIMNMVLEEIAKMGIKNLSIAPSSIANV-HEPLIDHIKNGVVTN 120- DGMTISFHHHFREGDF+ N V+ +I MG +NL++APSS+ NV ++ +I+ IK GVVTN Sbjct: 61 KDGMTISFHHHFREGDFVFNKVMRKIIDMGYQNLTLAPSSLTNVMNDIVIEAIKKGVVTN 120- Query: 121 ITSSGLRDKVGAAISEGLMENPVVIRSHGGRARAIASGDIHIDVAFLGAPSSDAYGNVNG 18- 0 ITSSG+R +G A+S G+++NPV+ RSHG RARAI SG+I IDVAFLG P+SD GN NG Sbjct: 121 ITSSGMRGTLGDAVSHGILKNPVIFRSHGARARAIESGEIKIDVAFLGVPNSDEMGNANG 18- 0 Query: 181 TKGKATCGSLGYAMIDAKYADQVVILTDNLVPYPNTPISIPQTDVDYVVTVDAIGDPQGI 24- 0 G A GSLGYA+IDA+YAD++V++TD ++PYPNTP SI QT VDYVV VD +GDP I Sbjct: 181 MNGDAAFGSLGYALIDAQYADKLVLITDTIMPYPNTPASIKQTQVDYVVKVDKVGDPDKI 24- 0 Query: 241 AKGATRFTKNPKELLIAEYAAKVITNSPYFKEGFSFQTGTGGASLAVTRFMREAMIKENI 30- 0 GATRFTK+PKEL IA+ VI NS YFK FSFQTG+GGA+LAVTRF+REAM+ +NI Sbjct: 241 GSGATRFTKDPKELKIAKTVNDVIVNSKYFKNDFSFQTGSGGAALAVTRFLREAMMAQNI 30- 0 Query: 301 KASFALGGITNAMVELLEEELVEKILDVQDFDHPSAVSLGKHAEHYEIDANMYASPLSKG 36- 0 ASFALGGIT V+LL E LV +++DVQDFD +A S+ EIDA+ YA P +KG Sbjct: 301 MASFALGGITKPTVDLLNEGLVNRVMDVQDFDKGAASSMKLSPNQQEIDASWYADPANKG 36- 0 Query: 361 AVINQLDTCILSALEVDTNFNVNVMTGSDGVIRGASGGHCDTAFAAKMSLVISPLIRGRI 42- 0 A++++LD ILSALEVDTNFNVNVM+GSDGVIRGA GGH D A AK++++ PL+RGRI Sbjct: 361 AMVDKLDVAILSALEVDTNFNVNVMSGSDGVIRGAIGGHQDAA-TAKLTIISVPLVRGRI 41- 9 Query: 421 PTFVDEVNTVITPGTSVDVIVTEVGIAINPNRQDLVDHFKSL-NVPQFSIEELKEKAYAI 47- 9 T V +VNTVITPG S+DV+VTEVGIAINP R DLV+ K + +P +SIEEL++KA I Sbjct: 420 ATIVPKVNTVITPGDSIDVVVTEVGIAINPKRTDLVEQLKQVPGLPIYSIEELQQKAEKI 47- 9 Query: 480 VGTPERIQYGDKVVALIEYRDGSLMDVVYNV 510 VG P +++ D+VVA+ EYRDGS++D++ V Sbjct: 480 VGQPAPLKFTDRVVAVAEYRDGSVIDIIKEV 510 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2726 A DNA sequence (GASx1183) was identified in S. pyogenes <SEQ ID 7951> which encodes the amino acid sequence <SEQ ID 7952>. Analysis of this protein sequence reveals the following: TABLE-US-07649 Possible site: 13 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07650 >GP: CAA71634 GB: Y10621 CILG, hypothetical protein [Leuconostoc mesenteroides] Identities = 65/176 (36%), Positives = 97/176 (54%), Gaps = 3/176 (1%) Query: 21 DTYFSGEAIQLSDMLRAREERALRQLHLLKEYPEGSLLSVTMNIPGPIKTSPKLLEAFDI 80 - D + GE + L +L RE R Q L+ +P + SV +N+PGPIKTSPKL F I Sbjct: 2 DYFEGGERLNLMQVLDNREWREKYQKQLMASFPTAVITSVKLNLPGPIKTSPKLQSVFQI 61 Query: 81 VIKAIQTALADDKICYQLRLL-PTTGYEYYLITSLPSRDLKLKMIALETELPIGRLMDLD 139- +I + D +I + + TG + + +TS + +K MI E +GRL+DLD Sbjct: 62 IINDLNPVFKDLQIIKEASFVDQITGPDIFFVTSGCLKLVKQIMITFEESHLLGRLLDLD 121- Query: 140 VLVLQNDLPHSISRTVLGGSPRQCFICSKEAKVCGRLRKHSVEEMQTAISKLLHSF 195 V+ D +SR LG +PR+C +C K+AK C + HS+ E + I+K+LH+F Sbjct: 122 VMCQNAD--KQLSREELGFAPRKCLLCGKDAKTCIKEGNHSLAEGYSQINKMLHNF 175 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2727 A DNA sequence (GASx1184) was identified in S. pyogenes <SEQ ID 7953> which encodes the amino acid sequence <SEQ ID 7954>. Analysis of this protein sequence reveals the following: TABLE-US-07651 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3730 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07652 >GP: AAB99233 GB: U67563 oxaloacetate decarboxylase alpha chain (oadA) [Methanococcus jannaschii] Identities = 245/441 (55%), Positives = 336/441 (75%), Gaps = 5/441 (1%) Query: 10 IRITETVLRDGQQSQIATRMTTKEMIPILETLDNAGYHALEMWGGATFDSCLRFLNEDPW 69 - ++I +T RD QQS IATRM T++M+PI E +D G++++E+WGGATFD+C+R+LNEDPW Sbjct: 2 VKIVDTTFRDAQQSLIATRMRTEDMLPIAEKMDEVGFYSMEVWGGATFDACIRYLNEDPW 61 Query: 70 ERLRAIRKAVKKTKLQMLLRGQNLLGYRNYADDVVRSFIQKSIENGIDIVRIFDALNDPR 129- ERLRA++K ++ T LQMLLRGQNL+GYR+Y DD+V F+ K+ ENGIDI RIFDALND R Sbjct: 62 ERLRALKKRIQNTPLQMLLRGQNLVGYRHYPDDIVEKFVIKAHENGIDIFRIFDALNDVR 121- Query: 130 NLQTAVSATKKFGGHAQVAISYTTSPVHTIDYFVELAKAYQAIGADSICIKDMAGVLTPE 18- 9 N++TA+ KK G Q AI YT SPVHTID +VELAK + +G DSICIKDMAG+LTP Sbjct: 122 NMETAIKTAKKVGAEVQGAICYTISPVHTIDQYVELAKKLEEMGCDSICIKDMAGLLTPY 18- 1 Query: 190 IGYQLVKCIKENTTIPLEVHTHATSGISEMTYLKVAEAGADIIDTAISSFSGGTSQPATE 24- 9 GY+LVK +KE ++P++VH+H TSG++ MTYLKV EAGAD++D AIS F+ GTSQP TE Sbjct: 182 EGYELVKRLKEEISLPIDVHSHCTSGLAPMTYLKVIEAGADMVDCAISPFAMGTSQPPTE 24- 1 Query: 250 SMAIALTDLGFDTGLDMQEVAKVAEYFNTIRDHYREIGILNPKVKDTEPKTLIYQVPGGM 30- 9 S+ +AL +DTGLD++ + ++ +YF +R+ Y+ + +P + + + L+YQVPGGM Sbjct: 242 SIVVALKGTKYDTGLDLKLLNEIRDYFMKVREKYKM--LFSPISQIVDARVLVYQVPGGM 29- 9 Query: 310 LSNLLSQLTEQGLTDKYEEVLAEVPKVRADLGYPPLVTPLSQMVGTQALMNIISGERYKV 36- 9 LSNL+SQL EQG DK+EEVL E+P+VR DLGYPPLVTP SQ+VGTQA++N+++ ERYK+ Sbjct: 300 LSNLVSQLKEQGALDKFEEVLQEIPRVRKDLGYPPLVTPTSQIVGTQAVLNVLTEERYKI 35- 9 Query: 370 VPNEIKDYVRGLYGQSPAPLAEGIKEKIIGD-EAVITCRPADLIEPQMIYLRDEIAP--Y 42- 6 + NE+ +YV+G YG+ PAP+ + ++++ + E ITCRPADL+ P+ ++ E Sbjct: 360 ITNEVVNYVKGFYGKPPAPINPELLKRVLDEGEKPITCRPADLLPPEWEKVKKEAEEKGI 41- 9 Query: 427 AHSEEDVLSYASFPQQARDFL 447 EED+L+YA +PQ A FL Sbjct: 420 VKKEEDILTYALYPQIAVKFL 440 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2728 A DNA sequence (GASx1185R) was identified in S. pyogenes <SEQ ID 7955> which encodes the amino acid sequence <SEQ ID 7956>. Analysis of this protein sequence reveals the following:

TABLE-US-07653 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2497 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07654 >GP: AAF93960 GB: AE004165 citrate (pro-3S)-lyase ligase [Vibrio cholerae] Identities = 118/336 (35%), Positives = 183/336 (54%), Gaps = 5/336 (1%) Query: 4 YTISKVFPSDKTTMASVKNLLHQEGIRLDAHLDYTCAIMNAQNDVIATGSYFGNSLRCLC 63 YT S+V ++T + +K L Q + +D +++ + N +IA G G+ L+ + Sbjct: 10 YTFSRVSTKNRTKLLQIKEFLCQHQLTVDDDVEHF-VVAYGTNQIIACGGIAGHVLKSIA 68 Query: 64 VSSAYQGEGLLNRIVSHLIDEEYALGNYHLFVYTKTSSAAFFKDLGFTEIVHIDNHISFL 123- VS A QG G ++++ L + Y +G + LF++TK ++ F+ GF + ++ HI+ L Sbjct: 69 VSPALQGTGFALKLMTELTNFAYEMGRFSLFLFTKPANIDLFRQCGFFLVDKVEPHIALL 128- Query: 124 ENKKTGFQDYLMTLNKPEQTPGKVAAIVINANPFTLGHQFLVEKAARENDWVHLFMVSED 18- 3 EN Y L + + K+ +IV+NANPFTLGHQ+L+E+A + DWVHLF+V + Sbjct: 129 ENSPNRLSVYCKQLQLLKMSGRKIGSIVMNANPFTLGHQYLIEQACEQCDWVHLFVVKAE 18- 8 Query: 184 RSLIPFSVRKRLIQEGLAHLDNVIYHETGPYLISQATFPAYFQKEDNDVIKSQALLDTAI 24- 3 ++ R +I+ G HL N+ H Y+IS+ATFP+YF K+ V +S LD +I Sbjct: 189 NKDFSYADRMAMIKAGSKHLLNLTIHSGSDYIISRATFPSYFIKDQQVVNQSHTALDLSI 24- 8 Query: 244 FL-KIAQTLQITKRYVGEEPTSRVTAIYNEIM---AEQLQQAGILLDILPRKAINQQQDP 29- 9 F IA L IT R+VG EP VT YN+ M E+ A + ++ + Q P Sbjct: 249 FRHSIAPALGITHRFVGSEPICTVTRHYNQAMRRWLEEAHDASAPIQVVEIERSQQASQP 30- 8 Query: 300 ISASTARQALKDNDWDLLAKLLPKTSLDYFCSLKAQ 335 ISAS R LK + +A L+PKT+ Y C A+ Sbjct: 309 ISASRVRYLLKQFGFAAIADLVPKTTYSYLCQHYAE 344 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2729 A DNA sequence (GASx1187) was identified in S. pyogenes <SEQ ID 7957> which encodes the amino acid sequence <SEQ ID 7958>. Analysis of this protein sequence reveals the following: TABLE-US-07655 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4790(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2730 A DNA sequence (GASx1188R) was identified in S. pyogenes <SEQ ID 7959> which encodes the amino acid sequence <SEQ ID 7960>. Analysis of this protein sequence reveals the following: TABLE-US-07656 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3956(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2731 A DNA sequence (GASx1190) was identified in S. pyogenes <SEQ ID 7961> which encodes the amino acid sequence <SEQ ID 7962>. Analysis of this protein sequence reveals the following: TABLE-US-07657 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1274(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2732 A DNA sequence (GASx1196R) was identified in S. pyogenes <SEQ ID 7963> which encodes the amino acid sequence <SEQ ID 7964>. Analysis of this protein sequence reveals the following: TABLE-US-07658 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2733 A DNA sequence (GASx1211) was identified in S. pyogenes <SEQ ID 7965> which encodes the amino acid sequence <SEQ ID 7966>. Analysis of this protein sequence reveals the following: TABLE-US-07659 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1850(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2734 A DNA sequence (GASx1219R) was identified in S. pyogenes <SEQ ID 7967> which encodes the amino acid sequence <SEQ ID 7968>. Analysis of this protein sequence reveals the following: TABLE-US-07660 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2284(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2735 A DNA sequence (GASx1225) was identified in S. pyogenes <SEQ ID 7969> which encodes the amino acid sequence <SEQ ID 7970>. Analysis of this protein sequence reveals the following: TABLE-US-07661 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2062(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2736 A DNA sequence (GASx1229) was identified in S. pyogenes <SEQ ID 7971> which encodes the amino acid sequence <SEQ ID 7972>. Analysis of this protein sequence reveals the following: TABLE-US-07662 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2755(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2737 A DNA sequence (GASx1247R) was identified in S. pyogenes <SEQ ID 7973> which encodes the amino acid sequence <SEQ ID 7974>. Analysis of this protein sequence reveals the following: TABLE-US-07663 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.32 Transmembrane 55-71 (53-81) INTEGRAL Likelihood = -6.00 Transmembrane 74-90 (72-95) INTEGRAL Likelihood = -2.18 Transmembrane 95-111 (95-111) INTEGRAL Likelihood = -1.54 Transmembrane 124-140 (123-141) ----- Final Results ----- bacterial membrane --- Certainty = 0.3527(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07664 >GP: CAB14326 GB: Z99116 yqjA [Bacillus subtilis] Identities = 97/306 (31%), Positives = 154/306 (49%) Query: 6 RTLKMTLATIVAILIAYQLHLDYAMSAGIIALLSVLDTRKSSLVVARNRLLSFFLAFGIA 65 RT+K L T +AI I+ LHL SAGII +L + T+K SL + R + LA + Sbjct: 7 RTIKTALGTALAIYISQLLHLQNFASAGIITILCIQITQKRSLQASWARFWACCLAIAFS 66 Query: 66 MMCFSLFGFTTVGFMCYLLIIIPLLYHFQIEAGLVPITVLVTHLIAKKSIALPILSNEFM 125- + F L G+ LLI IP+ +I G+V +V++ HL I + NE Sbjct: 67 YLFFELIGYHPFVIGALLLIFIPITVLLKINEGIVTSSVIILHLYMSGGITPTFIWNEVQ 126- Query: 126 LFFVGTSVALLFNAYMGPQDQQIRYYHQKVESDLKGILYRFESFLLEGKGQNEGLLIKNL 18- 5 L VG VALL N YM D+++ Y +K+E + I E +LL G+ G I Sbjct: 127 LITVGIGVALLMNLYMPSLDRKLIAYRKKIEDNFAVIFAEIERYLLTGEQDWSGKEIPET 18- 6 Query: 186 DKILDEALKLVYRERHNQLFQQTNYQVHYFEMRRQQNRLLGQMAINVNTLMRQSKESILL 24- 5 +++ EA L YR+ N + + N HYF+MR +Q ++ ++ V ++ + ++ Sbjct: 187 HQLITEAKNLAYRDVQNHILRYENLHYHYFKMREKQFEIIERLLPKVTSISITVDQGKMI 24- 6 Query: 246 SHLFHETACQLSEQNPALTLIDDIEQLLETFRHGDLPQTREEFERRAVLFQLLQDLERFI 30- 5 + H+ + N A + + + + F LP TREEFE RA LF LL ++E+++ Sbjct: 247 AEFIHDLREAIHPGNTAYKFLKRLADMRKEFEEMPLPATREEFEARAALFHLLGEMEQYL 30- 6 Query: 306 LLKVEF 311 ++K F Sbjct: 307 VIKSYF 312 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2738 A DNA sequence (GASx1261) was identified in S. pyogenes <SEQ ID 7975> which encodes the amino acid sequence <SEQ ID 7976>. Analysis of this protein sequence reveals the following: TABLE-US-07665 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6082(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2739 A DNA sequence (GASx1262R) was identified in S. pyogenes <SEQ ID 7977> which encodes the amino acid sequence <SEQ ID 7978>. Analysis of this protein sequence reveals the following: TABLE-US-07666 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.06 Transmembrane 38-54 (37-55) ----- Final Results ----- bacterial membrane --- Certainty = 0.3824(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2740 A DNA sequence (GASx1265R) was identified in S. pyogenes <SEQ ID 7979> which encodes the amino acid sequence <SEQ ID 7980>. Analysis of this protein sequence reveals the following: TABLE-US-07667 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2741 A DNA sequence (GASx1270) was identified in S. pyogenes <SEQ ID 7981> which encodes the amino acid sequence <SEQ ID 7982>. Analysis of this protein sequence reveals the following: TABLE-US-07668 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4063(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2742 A DNA sequence (GASx1290R) was identified in S. pyogenes <SEQ ID 7983> which encodes the amino acid sequence <SEQ ID 7984>. Analysis of this protein sequence reveals the following: TABLE-US-07669 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -12.37 Transmembrane 180-196 (172-207) INTEGRAL Likelihood = -10.19 Transmembrane 34-50 (30-53) INTEGRAL Likelihood = -4.09 Transmembrane 233-249 (232-250) ----- Final Results ----- bacterial membrane --- Certainty = 0.5946(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07670 >GP: AAB88010 GB: L21856 MalA [Streptococcus pneumoniae] Identities = 66/237 (27%), Positives = 105/237 (43%), Gaps = 28/237 (11%) Query: 45 MIPVTLHYANMTTYPLERIVTKSLSPITDKTYQALTQGKIEKD---TFQGQSLIRRD--- 98 - M+P+ + ++ TYPLE + P+TDK Q L++ D T+ G + Sbjct: 1 MVPIAIQNSSQETYPLETFIDNVYEPLTDKVVQDLSEHATIVDGTLTYTGTASQAPSVVI 60 Query: 99 GELVLAVLPTKVDLEQLASESTRQIIVTKKEWRFVTPDGKEL-RAHVRGQQQSLADLTTV 157- G + LP + L T +++++K + KEL R R Q T Sbjct: 61 GPSQIKELPKDLQLHF----DTNELVISK--------ESKELTRISYRAIQ------TEG 102- Query: 158 KAVKDFVNQQWY---DSNKASVLGFLLLTFVLMVCVGTLIVIGLGAFFLTLTKRSRLFMI 21- 4 KD + Q + +N+ + FL+L + + IV L +TK+SRLF Sbjct: 103 FKSKDSLTQAFIRLVPTNRVYISLFLVLGASFLFGLNFFIVSLGACLLLYITKKSRLFSF 16- 2 Query: 215 RNFSEGLGLMVNCLAWPSLLAIALSFFIQDPVLIMNCQVFGTLLMLTWVFYKTQFRD 271 R F E ++NCL P+L+ + L F Q+ ++ Q +L L +FYKT FRD Sbjct: 163 RTFKECYHFILNCLGLPTLITLILGLFGQNMTTLITVQNILFVLYLVTIFYKTHFRD 219 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2743 A DNA sequence (GASx1294) was identified in S. pyogenes <SEQ ID 7985> which encodes the amino acid sequence <SEQ ID 7986>. Analysis of this protein sequence reveals the following: TABLE-US-07671 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2104(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2744 A DNA sequence (GASx1303R) was identified in S. pyogenes <SEQ ID 7987> which encodes the amino acid sequence <SEQ ID 7988>. Analysis of this protein sequence reveals the following: TABLE-US-07672 Possible site: 38 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.07 Transmembrane 13-29 (8-38) ----- Final Results ----- bacterial membrane --- Certainty = 0.4227(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2745 A DNA sequence (GASx1307R) was identified in S. pyogenes <SEQ ID 7989> which encodes the amino acid sequence <SEQ ID 7990>. Analysis of this protein sequence reveals the following:

TABLE-US-07673 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2746 A DNA sequence (GASx1312R) was identified in S. pyogenes <SEQ ID 7991> which encodes the amino acid sequence <SEQ ID 7992>. Analysis of this protein sequence reveals the following: TABLE-US-07674 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1996(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2747 A DNA sequence (GASx1316R) was identified in S. pyogenes <SEQ ID 7993> which encodes the amino acid sequence <SEQ ID 7994>. Analysis of this protein sequence reveals the following: TABLE-US-07675 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3504(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> RGD motif: 271-273 No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07676 >GP: AAC66321 GB: AE000792 outer surface protein, putative [Borrelia burgdorferi] Identities = 127/365 (34%), Positives = 195/365 (52%), Gaps = 14/365 (3%) Query: 1 MVDLGFSLYPERYDVTKSKAYIDLCHSYGAKRLFMSLLQLAPADHQMFHCYAELIAYANQ 60 M ++G S+YP K Y++ +G ++F SLL + + F + EL++ AN+ Sbjct: 1 MKEIGISIYPNVSPKNKIIKYLEKSAHFGFTQVFTSLLYI---NGNEFDIFKELLSIANK 57 Query: 61 LGIRVIADVSPSFISQAGWSDQLIERA------HAFGLAGLRLDEALPLAEIVTLTRNPF 114- G++ I DVSP + G + G +RLD E +T N Sbjct: 58 NGMKPIIDVSPEIFKELGIDLSNLRNCPKLDYFKKLGAWAIRLDNTFTGIEESLMTFNDS 117- Query: 115 GLKIELNMSTDKQLLMSLLATDAERSNIIGCHNFYPHEFTGLSWQHFKDMSRFYHEHDIE 17- 4 LKI+LN+S + + +++ N++GCHNFYPH++TGLS FK+ ++ + + I Sbjct: 118 DLKIQLNISNINKHIDTIMYFKPNIKNLLGCHNFYPHKYTGLSRNFFKETTKIFKHYSIP 17- 7 Query: 175 TAAFITAQSASE-GPWLLAEGLPTVEDHRHLPIGLQVELMKAIGTIDNILISNQFISEEE 23- 3 TAAFI++ +A E EG+PT+E HR I Q + + G ID +LISN F SE E Sbjct: 178 TAAFISSNNAEECARGKEKEGVPTLESHRSKDIETQAKDLFKEG-IDTVLISNCFPSETE 23- 6 Query: 234 LAACTQALARPVTTIKVRPIIDLTEVEEQII-GYPHCYRGDVSDYVIRSTMPRLVYAQES 29- 2 L ++ + R + +K D VE++II H RGD++ Y IRSTMPR+ Y + Sbjct: 237 LKKVSK-VNRNILELKADLNPDANSVEKEIILENLHFNRGDINSYRIRSTMPRVYYNNKK 29- 5 Query: 293 IAPRDQSKEVKRGSIIIDNDRYHRYKGELQIALKNFTVSSKANVVAEVREDYLSLLDDLR 35- 2 P E+K+G I+ID+ Y Y GELQIALK+ + NVV ++ D + LL+ + Sbjct: 296 F-PVHSPNEIKKGDILIDSSEYLGYTGELQIALKDTPNNGLVNVVGKIINDEIYLLEKIE 35- 4 Query: 353 PWQEF 357 PW++F Sbjct: 355 PWEKF 359 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2748 A DNA sequence (GASx1319) was identified in S. pyogenes <SEQ ID 7995> which encodes the amino acid sequence <SEQ ID 7996>. Analysis of this protein sequence reveals the following: TABLE-US-07677 Possible Site: 34 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -9.50 Transmembrane 127-143 (125-151) INTEGRAL Likelihood = -7.43 Transmembrane 17-33 (15-36) INTEGRAL Likelihood = -5.68 Transmembrane 39-55 (36-57) INTEGRAL Likelihood = -1.86 Transmembrane 60-76 (59-77) INTEGRAL Likelihood = -0.59 Transmembrane 85-101 (85-101) ----- Final Results ----- bacterial membrane --- Certainty = 0.4800 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2749 A DNA sequence (GASx1320) was identified in S. pyogenes <SEQ ID 7997> which encodes the amino acid sequence <SEQ ID 7998>. Analysis of this protein sequence reveals the following: TABLE-US-07678 Possible site: 45 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.81 Transmembrane 35-51 (35-51) ----- Final Results ----- bacterial membrane --- Certainty = 0.1723 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2750 A DNA sequence (GASx1321) was identified in S. pyogenes <SEQ ID 7999> which encodes the amino acid sequence <SEQ ID 8000>. Analysis of this protein sequence reveals the following: TABLE-US-07679 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2751 A DNA sequence (GASx1329) was identified in S. pyogenes <SEQ ID 8001> which encodes the amino acid sequence <SEQ ID 8002>. Analysis of this protein sequence reveals the following: TABLE-US-07680 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.28 Transmembrane 64-80 (64-80) ----- Final Results ----- bacterial membrane --- Certainty = 0.1510 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2752 A DNA sequence (GASx1332R) was identified in S. pyogenes <SEQ ID 8003> which encodes the amino acid sequence <SEQ ID 8004>. Analysis of this protein sequence reveals the following: TABLE-US-07681 Possible site: 37 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2753 A DNA sequence (GASx1333) was identified in S. pyogenes <SEQ ID 8005> which encodes the amino acid sequence <SEQ ID 8006>. Analysis of this protein sequence reveals the following: TABLE-US-07682 Possible site: 29 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2754 A DNA sequence (GASx1335R) was identified in S. pyogenes <SEQ ID 8007> which encodes the amino acid sequence <SEQ ID 8008>. Analysis of this protein sequence reveals the following: TABLE-US-07683 Possible site: 37 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07684 >GP: AAF96047 GB: AE004354 uridine phosphorylase [Vibrio cholerae] Identities = 46/167 (27%), Positives = 72/167 (42%), Gaps = 12/167 (7%) Query: 8 GVKEMISTGTCGVLVP-IAENRFLVPVKALRDEGTSYHYVAPSRYIDIDPKMLRLIEKTL 66 G K ++ G+ G + I ++ A+RDEG S Y+ + +++ +++ L Sbjct: 79 GAKAIVRVGSAGAMQSEIGLGELILVEGAVRDEGGSKAYIGAAYPAYSSFELVVEMQRFL 138- Query: 67 LAQGLAYQEVITWSTDGFYR-ETKEKVAHRQEEGCSVVEMECSALAAVAQLRG-----IL 120- Q + I S D FY E E + +G +ME SAL V +LRG +L Sbjct: 139 AEQSVPIHRGIVRSHDSFYTDEEAELCRYWHRKGILAADMETSALLTVGRLRGLQVASVL 19- 8 Query: 121 WGQLLFTADTLADVEVY---DQRNWGADSFSFALHLCLEVLNTLEKD 164 +L+ D A V Y DQR + + A L LN L+ D Sbjct: 199 NNVVLYEQDVQAGVNQYVNADQRMMQGE--TLAARAALHALNALKFD 243 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2755 A DNA sequence (GASx1353) was identified in S. pyogenes <SEQ ID 8009> which encodes the amino acid sequence <SEQ ID 8010>. Analysis of this protein sequence reveals the following: TABLE-US-07685 Possible site: 42 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.79 Transmembrane 241-257 (234-260) INTEGRAL Likelihood = -5.15 Transmembrane 44-60 (43-65) INTEGRAL Likelihood = -4.78 Transmembrane 74-90 (72-92) ----- Final Results ----- bacterial membrane --- Certainty = 0.3314 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2756 A DNA sequence (GASx1354R) was identified in S. pyogenes <SEQ ID 8011> which encodes the amino acid sequence <SEQ ID 8012>. Analysis of this protein sequence reveals the following: TABLE-US-07686 Possible site: 55 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -3.45 Transmembrane 68-84 (65-86) ----- Final Results ----- bacterial membrane --- Certainty = 0.2381 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07687 >GP: CAB83831 GB: AL162753 putative integral membrane protein [Neisseria meningitidis] Identities = 31/72 (43%), Positives = 46/72 (63%), Gaps = 6/72 (8%) Query: 17 FVIYAFDKRKAIKKKRRISERKLLVITVLFGGF-GALLAAKKYHHKTRKWYFVI----TC 71 - F +Y DKR+A++ KRRI E +LL + LFGG+ GA L ++ + HKT K FV+ T Sbjct: 38 FALYGIDKRRAVRGKRRIPEHRLL-LPALFGGWAGAYLGSRIFRHKTAKKRFVVLFRLTV 96 Query: 72 YTSILLTLLVTY 83 ++L TL++ Y Sbjct: 97 SGNVLATLILIY 108 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2757 A DNA sequence (GASx1363R) was identified in S. pyogenes <SEQ ID 8013> which encodes the amino acid sequence <SEQ ID 8014>. Analysis of this protein sequence reveals the following: TABLE-US-07688 Possible Site: 21 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2758 A DNA sequence (GASx1367) was identified in S. pyogenes <SEQ ID 8015> which encodes the amino acid sequence <SEQ ID 8016>. Analysis of this protein sequence reveals the following: TABLE-US-07689 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07690 >GP: CAA63508 GB: X92946 hypothetical protein [Lactococcus lactis] Identities = 64/96 (66%), Positives = 77/96 (79%) Query: 1 MPRKTFDKAFKLSAVKLILEEEQPVKMVSSTLEIHPNSLYQWIQEYEKYGESAFPGHGSA 60 M R+ FDK FK SAVKLILEE VK VS LE+H NSLY+W+QE E+YGESAFPG+G+A Sbjct: 1 MARRKEDKQFKNSAVKLILEEGYSVKEVSQELEVHANSLYRWVQEVEEYGESAFPGNGTA 60 Query: 61 LRHAQFKTKKLEKEHKLLQEELALLKKFQVFLKPNR 96 L +AQ K K LEKE++ LQEEL LLKKF+VFLK ++ Sbjct: 61 LANAQHKIKLLEKENRYLQEELELLKKFRVFLKRSK 96 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2759 A DNA sequence (GASx1374R) was identified in S. pyogenes <SEQ ID 8017> which encodes the amino acid sequence <SEQ ID 8018>. Analysis of this protein sequence reveals the following: TABLE-US-07691 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2585 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2760 A DNA sequence (GASx1382R) was identified in S. pyogenes <SEQ ID 8019> which encodes the amino acid sequence <SEQ ID 8020>. Analysis of this protein sequence reveals the following: TABLE-US-07692 Possible site: 14 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.39 Transmembrane 3-19 (3-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.1956 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2761 A DNA sequence (GASx1391R) was identified in S. pyogenes <SEQ ID 8021> which encodes the amino acid sequence <SEQ ID 8022>. Analysis of this protein sequence reveals the following: TABLE-US-07693 Possible site: 22 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2762 A DNA sequence (GASx1404) was identified in S. pyogenes <SEQ ID 8023> which encodes the amino acid sequence <SEQ ID 8024>. Analysis of this protein sequence reveals the following: TABLE-US-07694 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3046 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2763 A DNA sequence (GASx1412R) was identified in S. pyogenes <SEQ ID 8025> which encodes the amino acid sequence <SEQ ID 8026>. Analysis of this protein sequence reveals the following:

TABLE-US-07695 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1590 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2764 A DNA sequence (GASx1414R) was identified in S. pyogenes <SEQ ID 8027> which encodes the amino acid sequence <SEQ ID 8028>. Analysis of this protein sequence reveals the following: TABLE-US-07696 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2816 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2765 A DNA sequence (GASx1416) was identified in S. pyogenes <SEQ ID 8029> which encodes the amino acid sequence <SEQ ID 8030>. Analysis of this protein sequence reveals the following: TABLE-US-07697 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1744 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2766 A DNA sequence (GASx1417) was identified in S. pyogenes <SEQ ID 8031> which encodes the amino acid sequence <SEQ ID 8032>. Analysis of this protein sequence reveals the following: TABLE-US-07698 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3771 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2767 A DNA sequence (GASx1419R) was identified in S. pyogenes <SEQ ID 8033> which encodes the amino acid sequence <SEQ ID 8034>. Analysis of this protein sequence reveals the following: TABLE-US-07699 Possible site: 13 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -10.93 Transmembrane 4-20 (1-25) ----- Final Results ----- bacterial membrane --- Certainty = 0.5373 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2768 A DNA sequence (GASx1423) was identified in S. pyogenes <SEQ ID 8035> which encodes the amino acid sequence <SEQ ID 8036>. Analysis of this protein sequence reveals the following: TABLE-US-07700 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.97 Transmembrane 30-46 (25-49) INTEGRAL Likelihood = -7.80 Transmembrane 52-68 (50-72) INTEGRAL Likelihood = -6.95 Transmembrane 129-145 (125-146) ----- Final Results ----- bacterial membrane --- Certainty = 0.4588 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2769 A DNA sequence (GASx1426R) was identified in S. pyogenes <SEQ ID 8037> which encodes the amino acid sequence <SEQ ID 8038>. Analysis of this protein sequence reveals the following: TABLE-US-07701 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -3.45 Transmembrane 36-52 (36-55) ----- Final Results ----- bacterial membrane --- Certainty = 0.2381 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07702 >GP: AAC39287 GB: AF115103 orf87 gp [Streptococcus thermophilus bacteriophage Sfi21] Identities = 43/73 (58%), Positives = 61/73 (82%) Query: 1 MINLKLRLQNKVTLMAILGAIFLLAQQLGIKLPSNIADIANTAVTLLVLLGVVTDPTTKG 60 MIN KLRLQNK TL+A++ A+FL+ QQ G+ +P+NI + NT V +LV+LG++TDPTTKG Sbjct: 8 MINFKLRLQNKATLVALISAVFLMLQQFGLHVPNNIQEGINTLVGILVILGIITDPTTKG 67 Query: 61 LSDSEQALTYHEP 73 ++DSE+AL+Y +P Sbjct: 68 IADSERALSYIQP 80 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2770 A DNA sequence (GASx1427R) was identified in S. pyogenes <SEQ ID 8039> which encodes the amino acid sequence <SEQ ID 8040>. Analysis of this protein sequence reveals the following: TABLE-US-07703 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.03 Transmembrane 2-18 (1-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.2211 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2771 A DNA sequence (GASx1428R) was identified in S. pyogenes <SEQ ID 8041> which encodes the amino acid sequence <SEQ ID 8042>. Analysis of this protein sequence reveals the following: TABLE-US-07704 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1017 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2772 A DNA sequence (GASx1429R) was identified in S. pyogenes <SEQ ID 8043> which encodes the amino acid sequence <SEQ ID 8044>. Analysis of this protein sequence reveals the following: TABLE-US-07705 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3097 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2773 A DNA sequence (GASx1431R) was identified in S. pyogenes <SEQ ID 8045> which encodes the amino acid sequence <SEQ ID 8046>. Analysis of this protein sequence reveals the following: TABLE-US-07706 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2584 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07707 >GP: AAA98101 GB: M19348 hyaluronidase [Streptococcus pyogenes phage H4489A] Identities = 337/371 (90%), Positives = 351/371 (93%), Gaps = 1/371 (0%) Query: 1 MAENIPLRVQFKRMKAAEWASSDVVLLEGEIGFETDTGFAKFGDGQNTFSKLKYLTGPKG 60 M ENIPLRVQFKRM A EWA SDV+LLEGEIGFETDTGFAKFGDGQNTFSKLKYLTGPKG Sbjct: 1 MTENIPLRVQFKRMSADEWARSDVILLEGEIGFETDTGFAKFGDGQNTFSKLKYLTGPKG 60 Query: 61 PKGDTGLQGKTGGTGSRGPAGKPGTTDYDQLQNKPDLGAFAQKEETNSKITKLESSKADK 120- PKGDTGLQGKTGGTG RGPAGKPGTTDYDQLQNKPDLGAFAQKEETNSKITKLESSKADK Sbjct: 61 PKGDTGLQGKTGGTGPRGPAGKPGTTDYDQLQNKPDLGAFAQKEETNSKITKLESSKADK 120- Query: 121 NAVYLKAESNAKLDEKLNLKGGVMTGQLQFKPN-SGIKPSSSVGGAINIDMSKSEGAAMV 17- 9 +AVY KAES +LD+KL+L GG++TGQLQFKPN SGIKPSSSVGGAINIDMSKSEGAAMV Sbjct: 121 SAVYSKAESKIELDKKLSLTGGIVTGQLQFKPNKSGIKPSSSVGGAINIDMSKSEGAAMV 18- 0 Query: 180 MYTNKDTTDGPLMILRSNKDTFDQSVQFVDYKGTTNAVNIVMRQPTTPNFSSALNITSAN 23- 9 MYTNKDTTDGPLMILRS+KDTFDQS QFVDY G TNAVNIVMRQP+ PNFSSALNITSAN Sbjct: 181 MYTNKDTTDGPLMILRSDKDTFDQSAQFVDYSGKTNAVNIVMRQPSAPNFSSALNITSAN 24- 0 Query: 240 EGGSAMQIRGVEKALGTLKITHENPSVDKEYDENAAALSIDIVKKQKGGKGTAAQGIYIN 29- 9 EGGSAMQIRGVEKALGTLKITHENP+V+ +YDENAAALSIDIVKKQKGGKGTAAQGIYIN Sbjct: 241 EGGSAMQIRGVEKALGTLKITHENPNVEAKYDENAAALSIDIVKKQKGGKGTAAQGIYIN 30- 0 Query: 300 STSGTAGKMLRIRNKNKDKFYVGPDGDFWSCASSIVDGNLTVKDPTSGKHAATKDYVDEK 35- 9 STSGTAGKMLRIRNKN+DKFYVGPDG F S A+S V GNLTVKDPTSGKHAATKDYVDEK Sbjct: 301 STSGTAGKMLRIRNKNEDKFYVGPDGGFHSGANSTVAGNLTVKDPTSGKHAATKDYVDEK 36- 0 Query: 360 IAELKKLILKK 370 IAELKKLILKK Sbjct: 361 IAELKKLILKK 371 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2774 A DNA sequence (GASx1438R) was identified in S. pyogenes <SEQ ID 8047> which encodes the amino acid sequence <SEQ ID 8048>. Analysis of this protein sequence reveals the following: TABLE-US-07708 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1892 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence <SEQ ID 10439> was identified in GBS which encodes amino acid sequence <SEQ ID 10440>. No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07709 >GP: AAB18711 GB: U38906 ORF36 [Bacteriophage rlt] Identities = 70/111 (63%), Positives = 88/111 (79%) Query: 1 LIEVIIKKYLDEHLDVPSFFEHQKDEPARFIILEKTSGAKQNHLLSSTFAFQSYAESLYE 60 +IE+IIK +LD HL V SF E + + P +I+ EKT +K NHLLSSTFAFQSYA S+YE Sbjct: 1 MIEIIIKNFLDTHLSVSSFLEKKGEMPLSYILFEKTGSSKSNHLLSSTFAFQSYAPSMYE 60 Query: 61 AALLNDKVKQVIEQLDVLPQVSGVHLNADYNFTDTATKRYRYQAVFDINHY 111 AA LN+++K+V+E+L L ++S V LN+DYNFTDT TK YRYQAVFDINHY Sbjct: 61 AAKLNEQLKEVVERLIELNEISNVSLNSDYNFTDTETKEYRYQAVFDINHY 111 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2775 A DNA sequence (GASx1442R) was identified in S. pyogenes <SEQ ID 8049> which encodes the amino acid sequence <SEQ ID 8050>. Analysis of this protein sequence reveals the following: TABLE-US-07710 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1241(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2776 A DNA sequence (GASx1444R) was identified in S. pyogenes <SEQ ID 8051> which encodes the amino acid sequence <SEQ ID 8052>. Analysis of this protein sequence reveals the following: TABLE-US-07711 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4547(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2777 A DNA sequence (GASx1447R) was identified in S. pyogenes <SEQ ID 8053> which encodes the amino acid sequence <SEQ ID 8054>. Analysis of this protein sequence reveals the following: TABLE-US-07712 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2778 A DNA sequence (GASx1448R) was identified in S. pyogenes <SEQ ID 8055> which encodes the amino acid sequence <SEQ ID 8056>. Analysis of this protein sequence reveals the following: TABLE-US-07713 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3221(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2779 A DNA sequence (GASx1449R) was identified in S. pyogenes <SEQ ID 8057> which encodes the amino acid sequence <SEQ ID 8058>. Analysis of this protein sequence reveals the following: TABLE-US-07714 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.6356(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2780 A DNA sequence (GASx1453R) was identified in S. pyogenes <SEQ ID 8059> which encodes the amino acid sequence <SEQ ID 8060>. Analysis of this protein sequence reveals the following: TABLE-US-07715 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2869(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2781 A DNA sequence (GASx1455R) was identified in S. pyogenes <SEQ ID 8061> which encodes the amino acid sequence <SEQ ID 8062>. Analysis of this protein sequence reveals the following: TABLE-US-07716 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1787(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-07717 >GP: AAF43512 GB: AF145054 ORF19 [Streptococcus thermophilus bacteriophage 7201] Identities = 47/126 (37%), Positives = 86/126 (67%), Gaps = 2/126 (1%) Query: 8 LKDLRNLDLYIASLIRRRDKIEASLL--SSPKWSSDKVNGGIKRKQDDVYVELIATAKDI 65 ++ ++ LD YI S I + ++E+ L +S +D V GG ++ +DD+YVELI +++ Sbjct: 7 IQQIKALDRYIESQIEQIKRLESQALKVTSGSMHTDMVQGGKRKGKDDIYVELITAREEV 66 Query: 66 EKKTAEAIRKQRELQNLIDSLENTDSQTILSMVYIDKMTRWQVIDELNCSESTYFRLLRV 125- E+ TAEAI+++ E + I ++E+ D++++L MVYID+++ WQ+ D++ S++TY+ LR Sbjct: 67 ERFTAEAIKQKLEFRRQIANIEDIDARSLLQMVYIDQLSIWQICDKMGISKATYYVKLRQ 126- Query: 126 ATKELN 131 A K L+ Sbjct: 127 AEKYLD 132 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2782 A DNA sequence (GASx1456R) was identified in S. pyogenes <SEQ ID 8063> which encodes the amino acid sequence <SEQ ID 8064>. Analysis of this protein sequence reveals the following: TABLE-US-07718 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2883(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07719 >GP: AAB18697 GB: U38906 ORF22 [Bacteriophage rlt] Identities = 78/207 (37%), Positives = 123/207 (58%), Gaps = 2/207 (0%) Query: 6 EIHRILGIDEVYKAPKRLTDILFDKDSREDIFRQFLKYETDVSYDWFMQYFEEEQADRKN 65 + + +L +DE R+ +++FDK RE+ + + L D+ D+F YF A Sbjct: 7 QFYDMLNVDEHMNFTNRIQELVFDKKGREEFYSKILNIHHDMGVDFFRDYFMAHSAVSA- 65 Query: 66 KKQDFTPKSVSTLLSKIISGNQYYEVA-VGTGGILIQAWQEQRLNDSPFTYRPSKYWYHV 124- K Q +TP + L + ++ G+ ++ GTG ++IQ WQ+ R+N F Y PS YWY Sbjct: 66 KGQHYTPDELGKLTALLVGGSGGADLTGAGTGTLIIQKWQDDRMNTDFFNYLPSNYWYQA 125- Query: 125 EELSDKAVPFLLFNMSIRGINGVVVHGDSLTRQVKNIYFLQNTKDDMLSFSDINVMPRTQ 18- 4 ELSD+A+ FL+ +IRG+NGVV+HGD+L VK +YF+QN+ ++ + FS+INV+P ++ Sbjct: 126 LELSDEAISFLIHAFAIRGMNGVVIHGDALEMAVKQVYFIQNSANNPIGFSEINVIPHSK 18- 5 Query: 185 DIEREFNVKEWIGDGIEHIENPLIEWI 211 D + EW IEHIE+ +WI Sbjct: 186 DAMEFLGIHEWTEQAIEHIESKFPDWI 212 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2783 A DNA sequence (GASx1459R) was identified in S. pyogenes <SEQ ID 8065> which encodes the amino acid sequence <SEQ ID 8066>. Analysis of this protein sequence reveals the following: TABLE-US-07720 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.44 Transmembrane 82-98 (81-98) ----- Final Results ----- bacterial membrane --- Certainty = 0.1977(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2784 A DNA sequence (GASx1460R) was identified in S. pyogenes <SEQ ID 8067> which encodes the amino acid sequence <SEQ ID 8068>. Analysis of this protein sequence reveals the following: TABLE-US-07721 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3368(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2785 A DNA sequence (GASx1461R) was identified in S. pyogenes <SEQ ID 8069> which encodes the amino acid sequence <SEQ ID 8070>. Analysis of this protein sequence reveals the following: TABLE-US-07722 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2834(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2786 A DNA sequence (GASx1462R) was identified in S. pyogenes <SEQ ID 8071> which encodes the amino acid sequence <SEQ ID 8072>. Analysis of this protein sequence reveals the following: TABLE-US-07723 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3531(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2787 A DNA sequence (GASx1463R) was identified in S. pyogenes <SEQ ID 8073> which encodes the amino acid sequence <SEQ ID 8074>. Analysis of this protein sequence reveals the following: TABLE-US-07724 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2483(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07725 >GP: CAB14569 GB: Z99117 similar to phage-related protein [Bacillus subtilis] Identities = 98/252 (38%), Positives = 152/252 (59%); Gaps = 29/252 (11%) Query: 16 SPAVKNRIEQVVGARAEQFTTSLLSIISNNNLLAKATSESIMGAAMKAAVLNLPIEPSLG 75 - SP+V R E+V+G RA QFT S+LS+ ++ +L K S++ +AM AA L+LPI+ +LG Sbjct: 33 SPSVIKRFEEVLGKRATQFTASILSLYNSEQMLQKTDPMSVISSAMVAATLDLPIDKNLG 92 Query: 76 FAYVVPYNRNYKDGNRWITVNEAQFQIGYRGLIQLAQRSGQVRNIEHGIIYEEEFLGYDK 135- +A++VPY +AQFQ+GY+G IQLA R+GQ ++I I+E E ++ Sbjct: 93 YAWIVPYG------------GKAQFQLGYKGYIQLALRTGQYKSINCIPIHEGELQKWNP 140- Query: 136 IRGQLKLTGDYVDSGVVKGYFASLELISGFYKMIFWPKEKVYEHAKKYSKTFDKKTGDFK 19- 5 + ++++ + +S V GY A ELI+GF K ++W K +V +H KK+SK+ DF Sbjct: 141 LTEEIEIDFEKRESDAVIGYAAYFELINGFRKTVYWTKAQVEKHKKKFSKS------DF- 19- 3 Query: 196 PGTPWATEFDPMAIKTLLKELLSKYAPLSVEMQDA-LEADNADSTIVIPKDVTPQETNSL 25- 4 W ++D MA+KT+LK +LSK+ LSVEMQ A +E D I D+T + +S Sbjct: 194 ---GWKNDWDAMALKTVLKAVLSKWGILSVEMQKAVIEEDETRERI----DITNEADSS- 24- 5 Query: 255 DDLIGTQNEKKD 266 ++I ++ KD Sbjct: 246 -EIIDSEPSNKD 256 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2788 A DNA sequence (GASx1464R) was identified in S. pyogenes <SEQ ID 8075> which encodes the amino acid sequence <SEQ ID 8076>. Analysis of this protein sequence reveals the following: TABLE-US-07726 Possible site: 30 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4258(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2789 A DNA sequence (GASx1465R) was identified in S. pyogenes <SEQ ID 8077> which encodes the amino acid sequence <SEQ ID 8078>. Analysis of this protein sequence reveals the following: TABLE-US-07727 Possible site: 51 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2045(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2790 A DNA sequence (GASx1469R) was identified in S. pyogenes <SEQ ID 8079> which encodes the amino acid sequence <SEQ ID 8080>. Analysis of this protein sequence reveals the following: TABLE-US-07728 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2791 A DNA sequence (GASx1470R) was identified in S. pyogenes <SEQ ID 8081> which encodes the amino acid sequence <SEQ ID 8082>. Analysis of this protein sequence reveals the following: TABLE-US-07729 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3577 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07730 >GP: AAC98430 GB: L29324 excisionase [Streptococcus pneumoniae] Identities = 23/56 (41%), Positives = 41/56 (73%) Query: 23 KHLIQQWEGLTVATAKQWATEMRDHPDFKQFVLNPTHRIVFIDYKGFKLFVQWKSR 78 K ++++W+GL T +W EMR++ F +V+NPTH++VFI+ +GF+ F++WK + Sbjct: 19 KGILKRWDGLNKYTLNRWIKEMRENRTFSMYVINPTHKLVFINLEGFESFLRWKQK 74 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2792 A DNA sequence (GASx1473) was identified in S. pyogenes <SEQ ID 8083> which encodes the amino acid sequence <SEQ ID 8084>. Analysis of this protein sequence reveals the following: TABLE-US-07731 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2725 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2793 A DNA sequence (GASx1476) was identified in S. pyogenes <SEQ ID 8085> which encodes the amino acid sequence <SEQ ID 8086>. Analysis of this protein sequence reveals the following: TABLE-US-07732 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1422 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2794 A DNA sequence (GASx1480R) was identified in S. pyogenes <SEQ ID 8087> which encodes the amino acid sequence <SEQ ID 8088>. Analysis of this protein sequence reveals the following: TABLE-US-07733 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.04 Transmembrane 291-307 (290-309) ----- Final Results ----- bacterial membrane --- Certainty = 0.2614 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2795 A DNA sequence (GASx1489R) was identified in S. pyogenes <SEQ ID 8089> which encodes the amino acid sequence <SEQ ID 8090>. Analysis of this protein sequence reveals the following: TABLE-US-07734 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2278 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2796 A DNA sequence (GASx1490R) was identified in S. pyogenes <SEQ ID 8091> which encodes the amino acid sequence <SEQ ID 8092>: TABLE-US-07735 SFITSVLAFRKLLKCEGIDLYLMYGDLMTCFEQLLTQLKDWTDVYFNYDE SGYGRLRDQKAAQFFKKNGIAVHTYQDHYLHGSQEIINQSGQPYKVFTPY YRIWQNYPKETPIKVELSQGRWLNLETPDDVLRTVESFKDEKYQDVATFD EASKQLNRFIQDQLAAYHANRDFPAQLGTSRLSPFLRIGAIGIRTVYHAV RQAPNSLGQATFLKELAWRDFYNMVYVAYPDQKTQPIQKAFSQIEWVNNP DWFQLWKEGKTGYPIVDAAMLQLQKTGWMHNRLRMIVASFLTKDLLCDWR LGEQYFQQQLIDYDAASNIGGWQWAASTGTDAVPYFRIFNPVTQGKRFDP KGEFIKAYLPQLEHVPEKYLHEPWKMPKNLQESVSCIIGTDYPQPIVDHA KQREQAIAKYEWAKEKAKIE Analysis of this protein sequence reveals the following: TABLE-US-07736 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07737 >GP: AAA22361 GB: M94110 DNA photolyase [Bacillus firmus] Identities = 175/338 (51%), Positives = 228/338 (66%), Gaps = 6/338 (1%) Query: 145 EIINQSGQPYKVFTPYYRIWQNYPKETP--IKVELSQGRWLNLETPDDVLRTVES--FKD 20- 0 +++ + G PYKVFTPYY+ W K TP IK ++ G PD T+ + K Sbjct: 2 QVLKKDGTPYKVFTPYYKAWAKERKRTPAVIKRDVLLGSVHKGTAPDREAETLFNNLIKK 61 Query: 201 EKYQDVATFDE-ASKQLNRFIQDQLAAYHANRDFPAQLGTSRLSPFLRIGAIGIRTVY-H 25- 8 Y A +E A K+L F + +L+ Y ANRDFP+ GTSRLSP+++ GA+ R++Y H Sbjct: 62 CSYDWSAIGEEHAIKRLQMFTKKRLSGYKANRDFPSITGTSRLSPYIKTGAVSSRSIYYH 121- Query: 259 AVRQAPNSLGQATFLKELAWRDFYNMVYVAYPDQKTQPIQKAFSQIEWVNNPDWFQLWKE 31- 8 + +S TFLKELAWRDFY MV+ PD K + I + + ++ W ++ D WK Sbjct: 122 ILNAEADSYSAETFLKELAWRDFYRMVHFYEPDCKDREIMEGYRELNWSHDQDDLTSWKR 18- 1 Query: 319 GKTGYPIVDAAMLQLQKTGWMHNRLRMIVASFLTKDLLCDWRLGEQYFQQQLIDYDAASN 37- 8 G+TG+PIVDA M QL GWMHNRLRMI ASFLTKDLL DWRLGE+YF++ LIDYD +SN Sbjct: 182 GETGFPIVDAGMRQLLNEGWMHNRLRMITASFLTKDLLIDWRLGERYFERMLIDYDPSSN 24- 1 Query: 379 IGGWQWAASTGTDAVPYFRIFNPVTQGKRFDPKGEFIKAYLPQLEHVPEKYLHEPWKMPK 43- 8 IGGWQWAAS GTDAVPYFRIFNPVTQ KRFD G +I+ Y+P+L HVP+ Y+HEPWKM + Sbjct: 242 IGGWQWAASVGTDAVPYFRIFNPVTQSKRFDENGTYIRTYIPELNHVPDHYIHEPWKMSE 30- 1 Query: 439 NLQESVSCIIGTDYPQPIVDHAKQREQAIAKYEWAKEK 476 Q C + DYP PIVDH+KQR++A++ ++ E+ Sbjct: 302 EEQVKYKCRLDEDYPLPIVDHSKQRKKALSFFKGDDEE 339 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2797 A DNA sequence (GASx1493R) was identified in S. pyogenes <SEQ ID 8093> which encodes the amino acid sequence <SEQ ID 8094>. Analysis of this protein sequence reveals the following: TABLE-US-07738 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2748 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2798 A DNA sequence (GASx1501R) was identified in S. pyogenes <SEQ ID 8095> which encodes the amino acid sequence <SEQ ID 8096>. Analysis of this protein sequence reveals the following:

TABLE-US-07739 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.27 Transmembrane 64-80 (53-83) ----- Final Results ----- bacterial membrane --- Certainty = 0.3909 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07740 >GP: AAC95443 GB: AF068901 YlmG [Streptococcus pneumoniae] Identities = 35/81 (43%), Positives = 58/81 (71%) Query: 1 MILILSILLRLIKVYTYLLIAYALMSWFPGAYDSKIGRLISGIVEPILKPFRAFNLQFAG 60 MI ++ ++ + +Y+ +L+A+A+MSWFPGAY+S +GR I +V+P+L P + LQ AG Sbjct: 1 MIFLIRMIYNAVDIYSLILVAFAVMSWFPGAYESSLGRWIVALVKPVLAPLQRLPLQIAG 60 Query: 61 LDFTIFVVIISLNFLAQVLVR 81 LD +++V I+ + FL + LVR Sbjct: 61 LDLSVWVAIVLVRFLGENLVR 81 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2799 A DNA sequence (GASx1502) was identified in S. pyogenes <SEQ ID 8097> which encodes the amino acid sequence <SEQ ID 8098>. Analysis of this protein sequence reveals the following: TABLE-US-07741 Possible site: 25 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.39 Transmembrane 17-33 (17-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.1956 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2800 A DNA sequence (GASx1507) was identified in S. pyogenes <SEQ ID 8099> which encodes the amino acid sequence <SEQ ID 8100>. Analysis of this protein sequence reveals the following: TABLE-US-07742 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0865 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2801 A DNA sequence (GASx1511R) was identified in S. pyogenes <SEQ ID 8101> which encodes the amino acid sequence <SEQ ID 8102>. Analysis of this protein sequence reveals the following: TABLE-US-07743 Possible site: 47 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.83 Transmembrane 31-47 (22-53) INTEGRAL Likelihood = -0.96 Transmembrane 2-18 (1-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.5734 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2802 A DNA sequence (GASx1516R) was identified in S. pyogenes <SEQ ID 8103> which encodes the amino acid sequence <SEQ ID 8104>. Analysis of this protein sequence reveals the following: TABLE-US-07744 Possible site: 42 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2729 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07745 >GP: BAA96472 GB: AB036428 Dpr [Streptococcus mutans] Identities = 132/175 (75%), Positives = 153/175 (87%) Query: 1 MTNTLVENIYASVTHNISKKEASKNEKTKAVLNQAVADLSVAASIVHQVHWYMRGPGFLY 60 MTNT+ ENIYAS+ H + KKE S NEKTKAVLNQAVADLS AASIVHQVHWYMRG GFLY Sbjct: 1 MTNTITENIYASIIHQVEKKENSGNEKTKAVLNQAVADLSKAASIVHQVHWYMRGSGFLY 60 Query: 61 LHPKMDELLDSLNANLDEMSERLITIGGAPYSTLAEFSKHSKLDEAKGTYDKTVAQHLAR 120- LHPKMDEL+D+LN +LDE+SERLITIGGAP+STL EF ++S+L+E GT+DK++ HL R Sbjct: 61 LHPKMDELMDALNGHLDEISERLITIGGAPFSTLKEFDENSRLEETVGTWDKSITDHLKR 120- Query: 121 LVEVYLYLSSLYQVGLDITDEEGDAGTNDLFTAAKTEAEKTIWMLQAERGQGPAL 175 LV+VY YLSSLYQVGLD+TDEE DA +ND+FTAA+TEA+KTIWMLQAE GQ P L Sbjct: 121 LVQVYDYLSSLYQVGLDVTDEEDDAVSNDIFTAAQTEAQKTIWMLQAELGQAPGL 175 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2803 A DNA sequence (GASx1517) was identified in S. pyogenes <SEQ ID 8105> which encodes the amino acid sequence <SEQ ID 8106>. Analysis of this protein sequence reveals the following: TABLE-US-07746 Possible site: 46 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.32 Transmembrane 109-125 (106-126) INTEGRAL Likelihood = -5.26 Transmembrane 63-79 (61-81) INTEGRAL Likelihood = -5.20 Transmembrane 154-170 (151-176) INTEGRAL Likelihood = -4.14 Transmembrane 189-205 (189-205) INTEGRAL Likelihood = -3.50 Transmembrane 130-146 (127-147) INTEGRAL Likelihood = -2.92 Transmembrane 6-22 (1-24) INTEGRAL Likelihood = -2.23 Transmembrane 83-99 (83-101) ----- Final Results ----- bacterial membrane --- Certainty = 0.3527 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07747 >GP: BAA96471 GB: AB036428 type IV prepilin peptidase homologue [Streptococcus mutans] Identities = 55/127 (43%), Positives = 78/127 (61%), Gaps = 3/127 (2%) Query: 83 VSASYCYLLLFSLLFSLFDWRSQEYPFILWLFSFVSLLLFYSINYLSLILLLLGLLAHLR 142- ++ S LL +L SL+D + Q YP LW+ L+ Y +N +SLIL L G+ A L+ Sbjct: 91 LTTSQVCLLFMGVLLSLYDLQDQSYPLTLWIGFTFLLMFIYPLNLISLILFLFGIFAALK 150- Query: 143 PFSIGAGDFFYLASLALVLDLTSLIWLIQLASLAGITACLLLGIKRIP--FIPYLSFGLF 20- 0 +IG+GDFFYLA+LAL L+L +IW+IQ+ASL GI LL + P F+P+L G Sbjct: 151 NINIGSGDFFYLATLALSLNLQQIIWIIQIASLLGILYSLLFQKHKEPFAFVPFLFLG-H 20- 9 Query: 201 WIVLLEH 207 I++ H Sbjct: 210 LIIIFSH 216 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2804 A DNA sequence (GASx1538R) was identified in S. pyogenes <SEQ ID 8107> which encodes the amino acid sequence <SEQ ID 8108>. Analysis of this protein sequence reveals the following: TABLE-US-07748 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1186 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2805 A DNA sequence (GASx1539R) was identified in S. pyogenes <SEQ ID 8109> which encodes the amino acid sequence <SEQ ID 8110>. Analysis of this protein sequence reveals the following: TABLE-US-07749 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.73 Transmembrane 6-22 (3-32) ----- Final Results ----- bacterial membrane --- Certainty = 0.5692 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07750 >GP: AAF31453 GB: AF221126 putative histidine kinase [Streptococcus pneumoniae] Identities = 141/301 (46%), Positives = 210/301 (68%), Gaps = 7/301 (2%) Query: 1 MKRYPLLVQLISYVFVIVIALITTLGLLYYQTSSRNIRQLIERDTRQSIRQSSQFIDAYI 60 MKR LLV+++ +F++ + L+ +G YYQ+SS I IE +++ +I Q+S FI +YI Sbjct: 1 MKRSSLLVRMVISIFLVFLILLALVGTFYYQSSSSAIEATIEGNSQTTISQTSHFIQSYI 60 Query: 61 KPLKETTSVLAKNTEIQAFASQIHQENDKQVLQLMKMVLATNSDLQAAVLVTKDGRTVST 120- K L+ T++ L + T++ A+A Q+ + + L +L ++ DL+ VLVTK G+ +ST Sbjct: 61 KKLETTSTGLTQQTDVLAYAENPSQDKVEGIRDLFLTILKSDKDLKTVVLVTKSGQVIST 120- Query: 121 NSQLTMKTSSDMMAEPWYKAAIDRQAMPILTPARQLSLSSKKEWVVSVTQEVVDRAGHNL 18- 0 + + MKTSSDMMAE WY+ AI + AMP+LTPAR+ S +WV+SVTQE+VD G NL Sbjct: 121 DDSVQMKTSSDMMAEDWYQKAIHQGAMPVLTPARK----SDSQWVISVTQELVDAKGANL 17- 6 Query: 181 GVLRLDIAYPTIKASLDQLQLGRQGFAFIVNDKHEFVYHPKKSVYSSSKEMAAMKPYLAI 24- 0 GVLRLDI+Y T++A L+QLQLG+QGFAFI+N+ HEFVYHP+ +VYSSS +M AMKPY+ Sbjct: 177 GVLRLDISYETLEAYLNQLQLGQQGFAFIINENHEFVYHPQHTVYSSSSKMEAMKPYIDT 23- 6 Query: 241 QNGYTKDKTSFVYQKLIPNSQWTLVGVASLDQLHRVQRQIFWSFSWNRASTLSDLWLCNCL 3- 01 GYT S+V Q+ I + WT++GV+SL++L +V+ Q+ W+ ++++ L +C CL Sbjct: 237 GQGYTPGHKSYVSQEKIAGTDWTVLGVSSLEKLDQVRSQLLWTL---LGASVTSLLVCLCL 2- 94 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2806 A DNA sequence (GASx1542R) was identified in S. pyogenes <SEQ ID 8111> which encodes the amino acid sequence <SEQ ID 8112>. Analysis of this protein sequence reveals the following: TABLE-US-07751 Possible site: 39 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07752 >GP: AAC23101 GB: U32823 conserved hypothetical protein [Haemophilus influenzae Rd] Identities = 56/128 (43%), Positives = 87/128 (67%) Query: 73 DFELKGIDGKTYRLSEFKGKKVYLKFWASWCSICLSTLADTEDLAKMSDKDYVVLTVVSP 132- D +LK ++ + LS++KGK VY+K WASWC ICL+ LA+ +DL+ D+++ V+T+VSP Sbjct: 24 DVQLKDLNNQPVTLSQYKGKPVYVKMWASWCPICLAGLAEIDDLSAEKDRNFEVITIVSP 83 Query: 133 GHQGEKSEADFKKWFQGTDYKDLPVLLDPDGKLLEAYGVRSYPTEVFIGSDGVLAKKHIG 19- 2 H+GEK ADF +W++G +YK++ VLLD G++++ VR YP +F+ SD L K G Sbjct: 84 DHKGEKDTADFIEWYKGLEYKNITVLLDEKGEIIDKARVRGYPFNLFLDSDLNLKKTVPG 143- Query: 193 YAKKSDIK 200 + I+ Sbjct: 144 HLGAEQIR 151 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2807 A DNA sequence (GASx1543R) was identified in S. pyogenes <SEQ ID 8113> which encodes the amino acid sequence <SEQ ID 8114>. Analysis of this protein sequence reveals the following: TABLE-US-07753 Possible site: 13 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.75 Transmembrane 171-187 (169-191) INTEGRAL Likelihood = -6.26 Transmembrane 205-221 (203-232) INTEGRAL Likelihood = -5.73 Transmembrane 56-72 (54-81) INTEGRAL Likelihood = -5.36 Transmembrane 92-108 (91-113) INTEGRAL Likelihood = -3.45 Transmembrane 20-36 (14-39) INTEGRAL Likelihood = -1.17 Transmembrane 147-163 (144-163) ----- Final Results ----- bacterial membrane --- Certainty = 0.4100 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07754 >GP: AAC23102 GB: U32823 cytochrome C-type biogenesis protein [Haemophilus influenzae Rd] Identities = 106/224 (47%), Positives = 138/224 (61%), Gaps = 16/224 (7%) Query: 6 VLMVSVFGAGLLSFFSPCIFPVLPVYLGILLDADDSKTITIFGKKLYWYGIVKTLAFIFG 65 +L+ +VF AGL SF SPCIFP++P+Y GIL GKK ++ T FI G Sbjct: 6 LLIGTVFLAGLASFLSPCIFPIIPIYFGILSKG---------GKK-----VLNTFLFILG 51 Query: 66 LSTIFVILGYGAGFLGNILYAVWFRYLLGALVIILGIHQMGLITIKSLQFQKSLTFHNNK 125- LS FV LG+ GFLGNIL++ R + G +VIILGIHQ+G+ I L+ K + + Sbjct: 52 LSLTFVSLGFSFGFLGNILFSNTTRIIAGVIVIILGIHQLGIFKIGLLERTKLVEIKTSG 111- Query: 126 NRNGLFNAFILGLTFSFGWTPCVGPVLSSVLALVASGGNGAWQGGVLMIIYTLGLGIPFL 18- 5 L AF+LGLTFS GWTPC+GP+L+SVLAL G+ A G +M +Y LGL PF+ Sbjct: 112 KSTAL-EAFVLGLTFSLGWTPCIGPILASVLALSGDEGS-ALYGASMMFVYVLGLATPFV 16- 9 Query: 186 LISFASGIVLKQFNKLKPHILLLKKVGGVLIIVMGILLMTGTLN 229 L SF S +LK+ L H+ K GG+LIIVMGILL+T + Sbjct: 170 LFSFFSDSLLKRAKGLNKHLDKFKIGGGILIIVMGILLITNNFS 213 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2808 A DNA sequence (GASx1544) was identified in S. pyogenes <SEQ ID 8115> which encodes the amino acid sequence <SEQ ID 8116>. Analysis of this protein sequence reveals the following: TABLE-US-07755 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1493 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2809 A DNA sequence (GASx1546R) was identified in S. pyogenes <SEQ ID 8117> which encodes the amino acid sequence <SEQ ID 8118>. Analysis of this protein sequence reveals the following: TABLE-US-07756 Possible site: 46 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4658 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07757 >GP: BAB04061 GB: AP001508 unknown conserved protein in others [Bacillus halodurans] Identities = 48/89 (53%), Positives = 61/89 (67%) Query: 1 MMVLVTYDVNTETPAGRKRLRHVAKLCVDYGQRVQNSVFECSVTPAEFVDIKHRLTQIID 60 M+VL+TYDV T + G KRLR VAK C +YGQRVQNSVFEC V + +K LT +ID Sbjct: 1 MLVLITYDVQTSSMGGTKRLRKVAKACQNYGQRVQNSVFECIVDSTQLTSLKLELTSLID 60 Query: 61 EKTDSIRFYLLGKNWQRRVETLGKSDSYD 89 E+ DS+R Y LG N++ +VE +G S D Sbjct: 61 EEKDSLRIYRLGNNYKTKVEHIGARPSID 89 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2810 A DNA sequence (GASx1547R) was identified in S. pyogenes <SEQ ID 8119> which encodes the amino acid sequence <SEQ ID 8120>. Analysis of this protein sequence reveals the following: TABLE-US-07758 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.70 Transmembrane 44-60 (43-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 330-332 No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07759 >GP: BAB04060 GB: AP001508 unknown conserved protein in others [Bacillus halodurans] Identities = 162/341 (47%), Positives = 231/341 (67%), Gaps = 1/341 (0%) Query: 1 MKKLLNTLYLTQEDFYVTKEGDNIVIKQEGKVLKRFPFRIIDGIVCFSYLGVSSALVKLC 60 MKKLLNTLY+TQ D Y++ +GDN+V+ +E + L R P ++ IV F Y G S AL+ C Sbjct: 1 MKKLLNTLYVTQPDTYLSLDGDNVVLLKEQEKLGRLPLHNLEAIVGFGYT>FEATURESALM- GYC 60 Query: 61 TENQINLSFHTPQGRFCGRYIGSTNGNVLLRREHYRLSDRE-ESLEYAKRFILAKISNSR 119- E I+++F T GRF R +G + GNV+LR+ YR+S+ + ES + A+ FI K+ NS+ Sbjct: 61 AERNISITFLTKNGRFLARVVGESRGNVVLRKTQYRISENDQESTKIARNFITGKVYNSK 120- Query: 120 KYLLRFKRDHRQQIDTKLFEAVNDELIWALEMVQAADNKDSLRGIEGQAANQYFRIFNDL 17- 9 L R R+H +++ + F+A + L ++ ++ D+ +SLRG EGQAA Y ++F+ + Sbjct: 121 WMLERMTREHPLRVNVEQFKATSQLLSVMNQEIRNCDSLESLRGWEGQAAINYNKVFDQM 18- 0 Query: 180 VLTDKKTFYFQGRSKRPPLDCVNALLSFGYSLLTFECQSALEAVGLDSYVGFFHTDRPGR 23- 9 +L K+ F F GRS+RPP D VNA+LSF Y+LL + +ALE VGLD+YVGF H DRPGR Sbjct: 181 ILQQKEEFAFHGRSRRPPKDNVNAMLSFAYTLLANDVAAALETVGLDAYVGFMHQDRPGR 24- 0 Query: 240 ASLALDLVEEFRSYIVDRFVFSLINKGQLQKKHFEVKENGSILLTENGRAIFIDLWQKRK 29- 9 ASLALDL+EE R DRFV SLIN+ ++ F KENG++L+T+ R F+ WQ +K Sbjct: 241 ASLALDLMEELRGLYADRFVLSLINRKEMTADGFYKKENGAVLMTDEARKTFLKAWQTKK 30- 0 Query: 300 HTEVEHPFTKEKVKLMLLPYVQAQLLAKAIRGDLESYPPFM 340 ++ HP+ EK+ L+PYVQA LLA+ +RGDL+ YPPF+ Sbjct: 301 QEKITHPYLGEKMSWGLVPYVQALLLARFLRGDLDEYPPFL 341 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2811 A DNA sequence (GASx1548R) was identified in S. pyogenes <SEQ ID 8121> which encodes the amino acid sequence <SEQ ID 8122>. Analysis of this protein sequence reveals the following:

TABLE-US-07760 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2247 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07761 >GP: BAB04059 GB: AP001508 unknown [Bacillus halodurans] Identities = 90/169 (53%), Positives = 111/169 (65%), Gaps = 1/169 (0%) Query: 45 LHTKADNPYIKEKRKELLVSRAMPISSAELGLSGIMDVVEFYKDDQGVSLRGKRGKWLPK 104- +H KAD P++KEKR L RAMPI S L +SGI DVVEF +D +G+ L G G + Sbjct: 1 MHKKADQPFMKEKRGSKLTVRAMPIQSKNLQISGICDVVEFVQDSEGIELSGVSGSYKAF 60 Query: 105 VVEYKRGKPKKDTRDIVQLVAQTMCLEETLDCDINEGCLYYHSVNQRVIVPMTSALRQEV 16- 4 VEYKRGKPKK DIVQLVAQ MCLEE L C I++G L+Y+ + RV VP+T ALR +V Sbjct: 61 PVEYKRGKPKKGDEDIVQLVAQAMCLEEMLVCRIDKGYLFYNEIKHRVEVPITDALRDKV 120- Query: 165 KELAAEMHEVYQSQMLPKAAYFKNCQLCSLVDICKPRLSKKTRSVSRYI 213 ++A EMH Y+++ PK C CSL IC P+L K RSV RYI Sbjct: 121 VQMAKEMHHYYENRHTPKVKTGPFCNNCSLQSICLPKLMNK-RSVKRYI 168 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2812 A DNA sequence (GASx1549R) was identified in S. pyogenes <SEQ ID 8123> which encodes the amino acid sequence <SEQ ID 8124>. Analysis of this protein sequence reveals the following: TABLE-US-07762 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1399 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07763 >GP: BAB04058 GB: AP001508 unknown conserved protein in others [Bacillus halodurans] Identities = 148/290 (51%), Positives = 190/290 (65%), Gaps = 19/290 (6%) Query: 6 MLEHKIDFMVTLEVKEANANGDPLNGNMPRTDAKGYGVMSDVSIKRKIRNRLQDMGKSIF 65 +L+HKIDF V L V +AN NGDPLNGN PR + G+G +SDV+IKRKIRNRL DM + IF Sbjct: 3 ILDHKIDFAVILSVTKANPNGDPLNGNRPRQNYDGHGEISDVAIKRKIRNRLLDMEEPIF 62 Query: 66 VQANERIEDDFRSLEKRFSQH----FTAKTPDKEIEEKANAL---WFDVRAFGQVFTYLK 118- VQ+++R D F+SL R + K + ++E A W DVR+FGQVF + Sbjct: 63 VQSDDRKADSFKSLRDRADSNPELAKMLKAKNASVDEFAKIACQEWMDVRSFGQVFAFKG 122- Query: 119 K--SIGVRGPVSISMAKSLEPIVISSLQITRSTNGMEAKNNSGRSSDTMGTKHFVDYGVY 17- 6 S+GVRGPVSI A S++PI I S QIT+S N + RSSDTMG KH VD+GVY Sbjct: 123 SNLSVGVRGPVSIHTATSIDPIDIVSTQITKSVNSVTGDK---RSSDTMGMKHRVDFGVY 17- 9 Query: 177 VLKGSINAYFAEKTGFSQEDAEAIKEVLVSLFENDASSARPEGSMRVCEVFWFTHSSKLG 23- 6 V KGSIN AEKTGF+ EDAE IK L++LFEND+SSARP+GSM V +V+W+ HSSKLG Sbjct: 180 VFKGSINTQLAEKTGFTNEDAEKIKRALITLFENDSSSARPDGSMEVHKVYWWEHSSKLG 23- 9 Query: 237 NVSSARVFDLLEYHQSIEEKSTYDAYQIHLNQEKLAKYEAKGLTLEILEG 286 SSA+V L+ + ++D Y + L YE GL +E+++G Sbjct: 240 QYSSAKVHRSLKIESKTDTPKSFDDYAVEL-------YELDGLGVEVIDG 282 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2813 A DNA sequence (GASx1550R) was identified in S. pyogenes <SEQ ID 8125> which encodes the amino acid sequence <SEQ ID 8126>. Analysis of this protein sequence reveals the following: TABLE-US-07764 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2882 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07765 >GP: BAB04057 GB: AP001508 unknown [Bacillus halodurans] Identities = 176/671 (26%), Positives = 311/671 (46%), Gaps = 87/671 (12%) Query: 1 MDFFTSLLKTYEKAELADLVDHQKR--NNEPVLLPIYHTSLKSNGKNIISVKLDKDGQFH 58 M + L +TYE A L + K+ + E LLPI HT+ ++ I V LD+DG F Sbjct: 1 MSWLLHLYETYE-ANLDQVGKTVKKGEDREYTLLPISHTTQNAH----IEVTLDEDGDFL 55 Query: 59 KAEFMADKQMIIFPVTADSVARSGSHPAPHPLVDKFAYYSAEM----GQIQ------YDS 108- +A+ + K+ + P T ++ +RSGS AP+PL DK +Y + + G+I+ +D+ Sbjct: 56 RAKALT-KESTLIPCTEEAASRSGSKVAPYPLHDKLSYVAGDFVKYGGKIKNQDDAPFDT 114- Query: 109 FHKQLNNWID--YCEEGDVKKFLTFVQQFILKPEFLTLILDSLIGPDYQHNQLKVTFCDA 16- 6 + K L W + Y E VK T++++ L + + + L NQ + + Sbjct: 115 YIKNLGEWANSPYATE-KVKCIYTYLKKGRLIEDLVDAGVLKL-----DENQQLIEKWEK 16- 8 Query: 167 TGKEKLIDLSACFLEFSIDQ------FQGFKNESVSTF---KALHQSYISFVEANRENLG 21- 7 +E L + A F + DQ F F ES+ K + S+ISF Sbjct: 169 RYEELLGEKPAIFSSGATDQASAFVRFNVFHPESIDDVWKDKEMFDSFISFYNDKLGEED 22- 8 Query: 218 ICNISGREEQLTDKH----RGLMGNAKIISVS-NKREAYKGRFREREDVFSVGYETSEKI 27- 2 IC ++G T++H R AK+IS + N ++GRF+ + + YE S+K Sbjct: 229 ICFVTGNRLPSTERHANKIRHAADKAKLISANDNSGFTFRGRFKTSREAVGISYEVSQKA 28- 8 Query: 273 HLMLKYLLENKNTSTWLGSSQYLINWFSDD-LTNDSRLDIVSPIFDDGLEEDDDDDTPPV 33- 1 H LK+L+ ++ S + + W +D+ L + D V + E + D DT + Sbjct: 289 HNALKWLIHRQSKSI---DDRVFLVWSNDNSLVPNPDEDAVDIMKHANRELERDPDTGQI 34- 5 Query: 332 ITLATEDNKRIGKSFIKGQKLFANDATY----YVAILNKTSNGRIALKYFRQLQASQLLT 38- 7 A E K IG + +D Y ++ +L+ + GR+A+ Y+R L L Sbjct: 346 F--AGEVKKAIGG--------YRSDLNYQPEVHILVLDSATTGRMAVLYYRSLNKELYLN 39- 5 Query: 388 NLNKWQETYSWESRSKFGKSRLRT----PTFHDILNVSYGVDRDRFLELDNDNFKSDQIQ 44- 3 L W ++ +WE R + + + P DI +YG ++ D ++ Sbjct: 396 RLEAWHDSCAWEHRYRRDEKEFISFYGAPATKDIAFAAYGPRA-------SEKVIKDLME 44- 8 Query: 444 KLVASLIDGKPMPQSIVKKL---GNNVKERHRYRKHWYQVEQVCLAILHK---QNGEEFS 49- 7 +++ ++DG+ +P+ IV+ +N R+ W + + A++ K + EE+ Sbjct: 449 RMLPCIVDGRRVPKDIVRSAFQRASNPVSMERWE--WEKTLSITCALIRKMHIEQKEEWG 50- 6 Query: 498 PMLDHTNQNRSYLFGRLLAIFELIETLRYGLDGNNNDRITNAERYWTAYTGQPTKLMMLL 55- 7 LD ++ +RSYLFGRLLA+ +++E G G + R TNA RY +Y+ P + + Sbjct: 507 VPLDKSSTDRSYLFGRLLAVADVLER---GALGKDETRATNAIRYMNSYSKNPGRTWKTI 56- 3 Query: 558 ENKIKPYEEPLKLNRRGSWMKLEKEKEEILELLNPLLETETMEKPLDYRFIFGYYAEKNY 61- 7 + ++PY+ KL + ++ L K +EI + P + PL +++ G+Y+++ Sbjct: 564 QESLQPYQ--AKLGTKATY--LSKLVDEIGDQFEP---GDFNNNPLTEQYLLGFYSQRRE 61- 6 Query: 618 YYTKQNTEVTE 628 Y K+ E + Sbjct: 617 LYKKKEEETNQ 627 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2814 A DNA sequence (GASx1551R) was identified in S. pyogenes <SEQ ID 8127> which encodes the amino acid sequence <SEQ ID 8128>. Analysis of this protein sequence reveals the following: TABLE-US-07766 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3035 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07767 >GP: BAB04056 GB: AP001508 unknown [Bacillus halodurans] Identities = 90/218 (41%), Positives = 127/218 (57%), Gaps = 7/218 (3%) Query: 13 GQRALFTNPATKGGSERSSYSVPTRQALNGIVDAIYYKPTFTNIVTEVKVINQIQTELQG 72 - G ALFT+P TK G E+ SYSVPT QAL GI ++IY+KPT ++ E++V+ IQ E +G Sbjct: 11 GDYALFTDPLTKIGGEKLSYSVPTYQALKGIAESIYWKPTIVFVIDELRVMKPIQMESKG 70 Query: 73 VRALLHDYSADLSYVSYLSDVVYLIKFHFVWNEDRKDLNSDRLPAKHEAIMERSIRKGGR 132- VR + + L++ +YL DV Y +K HF +N R DL DR KH +I++RS++ GGR Sbjct: 71 VRPIEYGGGNTLAHYTYLKDVHYQVKAHFEFNLHRPDLAFDRNEGKHYSILQRSLKAGGR 130- Query: 133 RDVFLGTRECLGLVDDISQEEYETTVSYYNGV-NIDLGIMFHSFAYPKDK-KTPLKSYFT 19- 0 RD+FLG REC G V + E+ + +Y+G LG M H F YP + + L Sbjct: 131 RDIFLGARECQGYV---APCEFGSGDGFYDGQGKYHLGTMVHGFNYPDETGQHQLDVRLW 18- 7 Query: 191 KTVMKNGVITFKAQSECDIVNTLSSYAFKA--PEEIKS 226 VM+NG I F +C IV + K P+ ++S Sbjct: 188 SAVMENGYIQFPRPEDCPIVRPVKEMEPKIFNPDNVQS 225 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2815 A DNA sequence (GASx1552R) was identified in S. pyogenes <SEQ ID 8129> which encodes the amino acid sequence <SEQ ID 8130>. Analysis of this protein sequence reveals the following: TABLE-US-07768 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2770 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07769 >GP: BAB04055 GB: AP001508 unknown conserved protein in others [Bacillus halodurans] Identities = 252/836 (30%), Positives = 404/836 (48%), Gaps = 90/836 (10%) Query: 3 MILAHYDCKKDKKQSLDEHLWHVACSSRQEASIIGQGDVLFLIGLYHDLGKADRTFQD-- 60 M +AH Q+L EHL V C + + + V L GL HDLGK F+D Sbjct: 1 MYIAHIREVDKVIQTLKEHLCGVQCLAETFGAKLRLQHVAGLAGLLHDLGKYTNEFKDYI 60 Query: 61 -------KLLNNPNRHVDHSYAGAKYLCSIIGPHLKNRGVDKNERMTFNEMVGYVISAHH 113- +L VDHS AG + L + L +R +E++ E+VG I +HH Sbjct: 61 YKAVFEPELAEKKRGQVDHSTAGGRLLYQM----LHDRENSFHEKL-LAEVVGNAIISHH 115- Query: 114 GMYDLCYYFDDAEYYGFNKFKNRINRDLDGYHYHEDIKGYALKLEKKLCDYGYK-DLREL 17- 2 +Y N + R L+ +++ Y +E+ + + +L Sbjct: 116 SNLQ--------DYISPTIESNFLTRVLE-----KELPEYESAVERFFQEVMTEAELARY 16- 2 Query: 173 IDKAFDNYQQAMSSLNWQDKSEWDYYQSCMVRLYLSLLKNADILDTVNAYGLKISPMDKT 23- 2 + KA D +Q + Q Y SC++ +AD +T + + + T Sbjct: 163 VAKAVDEIKQFTDNSPTQSFFLTKYIFSCLI--------DADRTNT-RMFDEQAREEEPT 21- 3 Query: 233 ERSFLKHSYLAAIEQKYASFGQPNNQ---LNTIRTEIAERVKERGKRDSKGIYRLDLPTG 28- 9 + L Y + AS + ++ +N +R+ ++E+ + R S GIY L +PTG Sbjct: 214 QPQQLFEHYHQQLLNHLASLKESDSAQKPINVLRSAMSEQCESFAMRPS-GIYTLSIPTG 27- 2 Query: 290 AGKTNLSMRYAFHQLVHHDKSRFFYITPFLSVLEQNASEIRKVTGD-LGVLEHHSNVVKQ 34- 8 GKT S+RYA ++K R YI PF +++EQNA E+R + GD +LEHHSNVV+ Sbjct: 273 GGKTLASLRYALKHAQEYNKQRIIYIVPFTTIIEQNAQEVRNILGDDENILEHHSNVVED 33- 2 Query: 349 ANEDDDDKDSLLSA-----YLSDSWDSQVVLTSMVQFFQTLFKTKSANLRRFSSLINSVV 40- 3 + D+ +D +++ D+WD ++ T++VQF + + N RR +L +SV+ Sbjct: 333 SENGDEQEDGVITKKERLRLARDNWDRPIIFTTLVQFLNVFYAKGNRNTRRLHNLSHSVL 39- 2 Query: 404 ILDEVQSLPIEVTTLFNLTMNFLNKVMDTTIVLCTATQPAYDSSEIDHRICYGGNLGELA 46- 3 I DEVQ +P + +LFN +NFL + +I+LCTATQP ++ + H + + Sbjct: 393 IFDEVQKVPTKCVSLFNEALNFLKEFAHCSILLCTATQPTLEN--VKHSLLKDRD----G 44- 6 Query: 464 EIVELTIEEKQIFSRTELRKFDDSDQKVHLTDVINLILGEE---NSVLAIFNTKKTVHNC 52- 0 EIV+ E + F R E+ D +DQ + + + E S L I NTKK V + Sbjct: 447 EIVQNLTEVSEAFKRVEI--LDKTDQPMTNERLAEWVRDEAPSWGSTLIILNTKKVVKDL 50- 4 Query: 521 YTMLKDMTDRPVYQLSTNMCAQHRLDLIAKIKTELQNNIPIICISTQLIEAGVDVDFHRV 58- 0 Y L+ PV+ LST+MCA HR D + +I+ L+ P IC++TQLIEAGVDV F V Sbjct: 505 YEKLEG-GPLPVFHLSTSMCAAHRKDQLDEIRALLKEGTPFICVTTQLIEAGVDVSFKCV 56- 3 Query: 581 IRSYSGIDSIVQAAGRCNREGKRDKGQVTLVNLTNEEENISRLTEIKTKKEATESILHKI 64- 0 IRS +G+DSI QAAGRCNR G+ V +++ + EE +S+L EI+ +E ++L + Sbjct: 564 IRSLAGLDSIAQAAGRCNRHGEEQLQYVYVID--HAEETLSKLKEIEVGQEIAGNVLARF 62- 1 Query: 641 GSPIDISTLN-------RDFFEYYYANNQGLMDYPLED-----NLSIYDYLSLNIYQTAN 68- 8 + N R++F YYY+ ++Y +++ + + N Y T Sbjct: 622 KKKAEKYEGNLLSQAAMREYFRYYYSKMDANLNYFVKEVDKDMTKLLMSHAVENSYVTYY 68- 1 Query: 689 KKFKGK-----LKQAFKTAGAKMNLINNDMIGILVPYGEAEKKLAYLEELGVSHFLSAKD 74- 3 +K G L ++KTA +I+ + +VPYGE + +A L S + Sbjct: 682 QKNTGTHFPLLLNGSYKTAADHFRVIDQNTTSAIVPYGEGQDIIAQLN--------SGEW 73- 3 Query: 744 YQTIKSLLKELQPFTVNV--RENDPLFE--TTKSYLNGQILVLTSEYYDTERGVKY 795 + +LK+ Q +TVN+ +E D L + +L+G + L +Y + GV + Sbjct: 734 VDDLSKVLKKAQQYTVNLYSQEIDQLKKEGAIVMHLDGMVYELKESWYSHQYGVDF 789 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2816 A DNA sequence (GASx1558) was identified in S. pyogenes <SEQ ID 8131> which encodes the amino acid sequence <SEQ ID 8132>. Analysis of this protein sequence reveals the following: TABLE-US-07770 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1050 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2817 A DNA sequence (GASx1563) was identified in S. pyogenes <SEQ ID 8133> which encodes the amino acid sequence <SEQ ID 8134>. Analysis of this protein sequence reveals the following: TABLE-US-07771 Possible site: 27 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1872 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2818 A DNA sequence (GASx1564R) was identified in S. pyogenes <SEQ ID 8135> which encodes the amino acid sequence <SEQ ID 8136>. Analysis of this protein sequence reveals the following: TABLE-US-07772 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2173 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2819 A DNA sequence (GASx1566R) was identified in S. pyogenes <SEQ ID 8137> which encodes the amino acid sequence <SEQ ID 8138>. Analysis of this protein sequence reveals the following: TABLE-US-07773 Possible site: 43 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3486 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2820 A DNA sequence (GASx1568) was identified in S. pyogenes <SEQ ID 8139> which encodes the amino acid sequence <SEQ ID 8140>. Analysis of this protein sequence reveals the following: TABLE-US-07774 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2711 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2821 A DNA sequence (GASx1569) was identified in S. pyogenes <SEQ ID 8141> which encodes the amino acid sequence <SEQ ID 8142>. Analysis of this protein sequence reveals the following: TABLE-US-07775 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2822 A DNA sequence (GASx1576R) was identified in S. pyogenes <SEQ ID 8143> which encodes the amino acid sequence <SEQ ID 8144>. Analysis of this protein sequence reveals the following:

TABLE-US-07776 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4042 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2823 A DNA sequence (GASx1577R) was identified in S. pyogenes <SEQ ID 8145> which encodes the amino acid sequence <SEQ ID 8146>. Analysis of this protein sequence reveals the following: TABLE-US-07777 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3342 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07778 >GP: BAB04515 GB: AP001509 unknown [Bacillus halodurans] Identities = 36/104 (34%), Positives = 55/104 (52%) Query: 2 HMGAWNTGNNKILYTQESVTDDMIAKRDQSIKDAKESPILGFTVDTKVIKTELSNISNVM 61 +M ++ GN IL E D + + A SP LGF D+ ++TE++ ISNV Sbjct: 392 NMPSFAIGNQLILKLYEDDPQDKWEAFEAFNESAIPSPALGFYFDSNPVRTEIAAISNVT 45- 1 Query: 62 NRYKASINTGTVDPDEALPKLLADLKGAGWDKVQKEVQKQLDDF 105 + + ++ G VDP+E LP L AG KV E+Q+Q D++ Sbjct: 452 SEFSPALLKGAVDPEEYLPLFNDKLNEAGLQKVIDEMQRQFDEW 495 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2824 A DNA sequence (GASx1578R) was identified in S. pyogenes <SEQ ID 8147> which encodes the amino acid sequence <SEQ ID 8148>. Analysis of this protein sequence reveals the following: TABLE-US-07779 Possible site: 27 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07780 >GP: BAB04515 GB: AP001509 unknown [Bacillus halodurans] Identities = 134/346 (38%), Positives = 206/346 (58%), Gaps = 10/346 (2%) Query: 21 AACESKSASKDSDVKLLMYQVGDKPDNFDELMTIANKRIKEKTGATVDLQYIGWGDWDDK 80 - +A E+++ D V L Y +G + + +M N +EK ATVDL+ + WG++D++ Sbjct: 42 SANETEATDLDH-VTLTWYMIGTPQPDLELVMEEVNAYTEEKINATVDLRMLDWGEYDER 100- Query: 81 MSTIIASGENYDIAF----ANNYVVNAQKGAFADLTTLMPKYAKKTYKNLDPAYIKGNTI 136- M I SGE YDIAF ANNY +NA++GAF +L L+ ++ ++ + +DPA+++G + Sbjct: 101 MQVITTSGEAYDIAFTSSWANNYALNARRGAFLELNDLLDEHGQEMKELIDPAFLEGAQV 16- 0 Query: 137 DGKLYAFPVDANVYAQQMLSFNKELVDKYGLDISNIKSYADAENVLKQFHEKEPNTAAFA 19- 6 DGKLYA P + V Q +LSFN ELV+K+ LD+S++ S AD E +L E+E + A Sbjct: 161 DGKLYAVPTNKEVGQQAVLSFNNELVEKHNLDLSSVHSLADLEPLLAVIKEEESDVTPIA 22- 0 Query: 197 IGQVFSMSGDYDYPLTKTQPFAVKIDEGKPTIINQYEDESFKNNLRLMHKWYKEGLIPTD 25- 6 F +D L + PFA +++ +IN+YE++ L+ MH +YK+G I D Sbjct: 221 ---TFDAYLPFDSILQEEMPFAFRLEGNTNEVINKYEEDITMETLKTMHDYYKKGYIRPD 27- 7 Query: 257 AATNTEGYPLEGNTWFMREETQGPMDYGDTILTNAAGKDIVSRPLTKPLKTTSQAQMANF 31- 6 AAT+T+ +PLE WF+R+E P Y + I T AG +I +RPL +P + + Sbjct: 278 AATSTDSWPLETPNWFVRKELYQP--YAELIWTRTAGYEIATRPLHEPYIFNNSVTGSNQ 33- 5 Query: 317 VVSSVSKNKEKAVEVLSLLNSDPELLNGLVYGVEGKAWEKIGDKKI 362 +S+ SKN E+A+ L+LLNSDP L N L G+EG +E++ D I Sbjct: 336 AISATSKNPERAMMFLNLLNSDPYLRNLLDKGIEGVHYEELEDGTI 381 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2825 A DNA sequence (GASx1582) was identified in S. pyogenes <SEQ ID 8149> which encodes the amino acid sequence <SEQ ID 8150>. Analysis of this protein sequence reveals the following: TABLE-US-07781 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0454 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2826 A DNA sequence (GASx1584R) was identified in S. pyogenes <SEQ ID 8151> which encodes the amino acid sequence <SEQ ID 8152>. Analysis of this protein sequence reveals the following: TABLE-US-07782 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3105 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> RGD motif: 3-5 No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07783 >GP: AAG21428 GB: AF307332 meningioma-expressed antigen 5s splice variant [Homo sapiens] Identities = 94/271 (34%), Positives = 148/271 (53%), Gaps = 14/271 (5%) Query: 120 GIIEGFYGTPWTREERLDCLRFIGNKRMNTYMYAPKDDDYQRKLWRDLYPEDWVTYFKEL 17- 9 G++EGFYG PW E+R + R + +NTY+YAPKDD R WR++Y + L Sbjct: 63 GVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTL 122- Query: 180 LAVAKEEGLDFWYMISPGLDFDYTKEADYQLLYQKLQQLLALGVCHFGLLLDDIDYQIVD 23- 9 ++ A+E ++F Y ISPGLD ++ + L +KL Q+ G F LL DDID+ + Sbjct: 123 ISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDIDHNMCA Query: 240 AVERRFKKTAYAQAHLATEVHHFLNQQHAAPELVICPTE------YDNHHDSIYLQELSE 29- 3 A + F A+AQ + E++ +L + + CPTE Y N S YL+ + E Sbjct: 183 ADKEVFSSFAHAQVSITNEIYQYLGEPET---FLFCPTEYCGTFCYPNVSQSPYLRTVGE 23- 9 Query: 294 RIPKEVAFFWTGPSTLASQISQADIETMAAVYQRPIIIWDNIPVNDYQKDPERLFLTPFA 35- 3 ++ + WTGP ++ +I IE ++ + +R +IWDNI NDY D +RLFL P+ Sbjct: 240 KLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDY--DQKRLFLGPYK 29- 7 Query: 354 NRSPFLCQPDYQVKGIVSNPMISWELSKLTL 384 RS L ++KG+++NP +E + + + Sbjct: 298 GRSTELIP---RLKGVLTNPNCEFEANYVAI 325 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2827 A DNA sequence (GASx1585R) was identified in S. pyogenes <SEQ ID 8153> which encodes the amino acid sequence <SEQ ID 8154>. Analysis of this protein sequence reveals the following: TABLE-US-07784 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4469 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2828 A DNA sequence (GASx1587) was identified in S. pyogenes <SEQ ID 8155> which encodes the amino acid sequence <SEQ ID 8156>. Analysis of this protein sequence reveals the following: TABLE-US-07785 Possible site: 47 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3082(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07786 >GP: BAB04509 GB: AP001509 unknown conserved protein in others [Bacillus halodurans] Identities = 221/425 (52%), Positives = 296/425 (69%), Gaps = 4/425 (0%) Query: 12 RPIPTSVSQFMAKVESLCGDQHPDWALNFKTSFTNTLETTLKTYEDGTSFLLTGDIPAMW 71 - + IP S+ +A+V++ D L F+ F NT TT++ E GT F++TGDIPAMW Sbjct: 4 KKIPRSLQAIIAQVKAHYADDQELQTL-FEQCFLNTYLTTIQEDEQGT-FVVTGDIPAMW 61 Query: 72 LRDSTAQMKPYLFLAKEDEEIRKIIAGLVKRQFRYICIDPYANAFNEEANEKGHQTDHTQ 131- LRDS+AQ++PYL + KED ++ ++I G+++RQ+RYI DPYANAFN+ AN++GHQ D T+ Sbjct: 62 LRDSSAQVRPYLTVVKEDADMARMIKGVIERQWRYILHDPYANAFNQTANKQGHQQDRTE 121- Query: 132 MNPWIWERKYEIDCLCYPIQLAYLLYRETGSTDQFNDDFHRGVELILDLWTVEQDH-AQS 19- 0 M+P +WERKYE+D LCYPIQLAYL ++ TG + +E I +W +EQDH A+S Sbjct: 122 MSPLVWERKYELDSLCYPIQLAYLYWKATGDDSVLQPTLKQVLETIYRIWKIEQDHEAKS 18- 1 Query: 191 PYLFERDTWRKEDTLTHAGKGSPVAPTGMTWSGFRPSDDACQYGYLIPSNMFAVVVLSYL 25- 0 Y FERD R DTL GKG PTGMTWSGFRPSDDAC YGYLIP+NMFAVVV +Y Sbjct: 182 SYSFERDDCRVSDTLLRKGKGGYSVPTGMTWSGFRPSDDACLYGYLIPANMFAVVVSNYA 24- 1 Query: 251 EDLYNNLFHNEPVATRAKQLKEAIQSGIADHALVQNSKGETIYAYEVDGLGQFSIMDDAN 31- 0 +L + +A ++L+ I+ GI + + + IY YE DG G+ ++MDDAN Sbjct: 242 VELLTAM-EEIKLAEEFRELEADIRQGIGQYGKMDHPVYGEIYVYETDGNGRVNLMDDAN 30- 0 Query: 311 IPSLLAAPYLGFCTKDDPIYLATRRTILSQENPYYYQGNAAAGIGSSHTPENYIWHIALA 37- 0 +PSLLA PYLG+ T DDP+Y TRR ILS++NPYYY+G+ A G+GS HTP++Y+WHI+LA Sbjct: 301 VPSLLAIPYLGYTTADDPVYQNTRRFILSRDNPYYYEGSYAKGVGSPHTPDHYVWHISLA 36- 0 Query: 371 LQGLTALDQDSKKEMLDLLVATDAGTHLMHEGFDVNDPYQYTREWFSWANMMFCELLLDY 43- 0 +QG+TA+D KK+++ + T A T+ MHEGFDV+ P QYTR WF+WAN MF E LL Sbjct: 361 IQGMTAIDSKEKKQIVAMFKQTHADTYFMHEGFDVDRPEQYTRSWFAWANSMFSEFLLSE 42- 0 Query: 431 LGFSI 435 G + Sbjct: 421 AGIYV 425 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2829 A DNA sequence (GASx1588) was identified in S. pyogenes <SEQ ID 8157> which encodes the amino acid sequence <SEQ ID 8158>. Analysis of this protein sequence reveals the following: TABLE-US-07787 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5250(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07788 >GP: BAB04508 GB: AP001509 unknown conserved protein in others (divided) [Bacillus halodurans] Identities = 312/737 (42%), Positives = 426/737 (57%), Gaps = 21/737 (2%) Query: 123 FPDTFGNMGQTPQLMLKAGLQAAAFGRGIRPTGFNNQVDTSEKYSSQFSEISWQGPDNSR 18- 2 FPDTFG GQ PQL+ +AG++AA FGRG+ PTGFNNQV + YSS FSE+ W+ PD S+ Sbjct: 4 FPDTFGIYGQAPQLLAQAGIRAAVFGRGVTPTGFNNQVQHDD-YSSPFSELIWEAPDGSQ 62 Query: 183 ILGLLFANWYSNGNEIPTTEAEARLFWDKKLADAERFASTKHLLMMNGCDHQPVQLDVTK 24- 2 ++G+L ANWYSNGNEIPT E EA+ FW KKL DAERFAST LL MNGCDHQPVQ DVT+ Sbjct: 63 VIGILLANWYSNGNEIPTDEDEAQTFWVKKLRDAERFASTSQLLFMNGCDHQPVQKDVTQ 122- Query: 243 AIALANQLYPDYEFVHSCFEDYLADLADDLPENLSTVQGEITSQETDGWYTLANTASARI 30- 2 AI +A L+PD F HS F DYL + ++LP+ L + GE+ +Q+TDGW TL NTASARI Sbjct: 123 AIKVAETLFPDVAFKHSNFHDYLTQIKEELPKELQKITGELRNQKTDGWSTLVNTASARI 18- 2 Query: 303 YLKQANTRVSRQLENITEPLAAMAYEVTSTYPHDQLRYAWKTLMQNHPHDSICGCSVDSV 36- 2 YLKQAN R L N+ EP+ + + D Y WK LM+NHPHDSICGCS+D+V Sbjct: 183 YLKQANDRCQTLLTNVLEPMCLLV--ENKSLHRDFSEYYWKLLMENHPHDSICGCSIDAV 24- 0 Query: 363 HREMMTRFEKAYEVGHYLAKEAAKQIADAIDTRDFPMDSQPFVLFNTSGHSKTSVAELSL 42- 2 HREM TRFEK E K+IA I+T ++ P V+ T+G S V + Sbjct: 241 HREMKTRFEKVEAGATTFIAEQGKEIAAQINTLHDSEEAIPLVVLKTNGTSGKRVVRHKV 30- 0 Query: 423 TWKKYHFGQRFPKEVYQEAQEYLARLSQSFQIIDTSGQVRPEAEILGTSIAFDYDLPKRS 48- 2 KK +F + ++ + L + ++ + E+ + F YDLP+ Sbjct: 301 AMKKIYFDEM----DFRHIPDRLKEIVMPTYRLEFPNKGSVPIEVQDAGVRFGYDLPRDG 35- 6 Query: 483 FREPYFAIKVRLRLPITLPAMSWKTLALKLG------NETTPSETVSLYDDSNQCLENGF 53- 6 FR PY+A L +T S L + G + T + + D S LEN Sbjct: 357 FRRPYYA----RELEVTFSYDSDLYLGYECGFLVPVEEKQTEARKELIGDPSMNTLENEA 41- 2 Query: 537 LKVMIQTDGRLTITDKQSGLIYQDLLRFEDCGDIGNEYISRQPNHDQPFYADQGTIKLNI 59- 6 +KVMI +G +I DK +G Y+ L +ED GDIGNEY+ + + + + + I Sbjct: 413 MKVMIHRNGSYSILDKTTGFEYRHLGIYEDVGDIGNEYMFKASSDGVRYTTEACEASIRI 47- 2 Query: 597 ISNTAQVAELEIQQTFAIPISADKLLQAEMEAVIDITERQARRSQEKAELTLTTLIRMEK 65- 6 I N + A +EI QT ++P +AD+ L+ E E ++ +R+A RS+E+ ++TL T + +E+ Sbjct: 473 IENNSLCATVEICQTLSVPAAADERLKEEQERLVWHPDRKAGRSKERTDITLRTELTLEQ 53- 2 Query: 657 NNPRLQFTTRFDNQMTNHRLRVLFPTHLKTDHHLADSIFETVKRPNHPDATFWKNPSNPQ 71- 6 L+ DN +HR+R LFP +H ADSI+E V+RPN PD W+NP+ Sbjct: 533 GAKGLKVNVNIDNTAKDHRMRALFPVERARGNHYADSIYEIVERPNTPDPK-WQNPAFDH 59- 1 Query: 717 HQECFVSLFDGENGVTIGNYGLNEYEILPDTNTIAITLLRSVGEMGDWGYFPTPEAQCLG 77- 6 H + VSL +GE G+TI GL+EYEI+ D +IA+TLLRSVGE+GDWG F TPEAQC G Sbjct: 592 HMQRLVSLDNGEYGLTIATKGLHEYEIVSD--SIAVTLLRSVGELGDWGLFETPEAQCFG 64- 9 Query: 777 KHSLSYSFESITKQTQFAS-YWRAQEGQVPVITTQTNQHEGTLAAEYSYLTGTNDQVALT 83- 5 ++ + A+ Y A + V QT Q G L + + + + LT Sbjct: 650 QNEAQFVLLPHKGDVLSANVYVAAYDDPVEPTVIQTEQSMGPLPHATNLFQWSGEGLVLT 70- 9 Query: 836 AFKRRLADNALITRSYN 852 A K + +I R +N Sbjct: 710 ACKPTMDGRGMILRWFN 726 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2830 A DNA sequence (GASx1589R) was identified in S. pyogenes <SEQ ID 8159> which encodes the amino acid sequence <SEQ ID 8160>. Analysis of this protein sequence reveals the following: TABLE-US-07789 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -11.30 Transmembrane 203-219 (195-221) INTEGRAL Likelihood = -8.17 Transmembrane 61-77 (59-82) INTEGRAL Likelihood = -3.98 Transmembrane 107-123 (107-124) INTEGRAL Likelihood = -3.40 Transmembrane 39-55 (38-58) INTEGRAL Likelihood = -2.34 Transmembrane 129-145 (126-145) INTEGRAL Likelihood = -2.07 Transmembrane 89-105 (87-105) ----- Final Results ----- bacterial membrane --- Certainty = 0.5522(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07790 >GP: CAC10175 GB: AJ278302 histidine kinase [Streptococcus pneumoniae] Identities = 114/432 (26%), Positives = 219/432 (50%), Gaps = 10/432 (2%) Query: 21 LTLKLFSFVSAIPLRLKNIFYLSLSMVLFQVVFWAFFPDHFILDVVMLAQF---LFFALI 77 - L + +F V I L + IF L +L VVF +++ V L+ F L+ + Sbjct: 16 LKIVIFFKVDGISLTFERIFKAFLFKILLAVVFGML---GYMVGNVYLSYFMEPLYGIGL 72 Query: 78 ALYYGKSIKAKFLMFYAFFPLVSISLVKRFIVFFVMPLFGMPYSVVKHNTLLIYSITCFS 137- + + + K L+FY FP++ ++L R + +FV+P G V + + I F+ Sbjct: 73 SFLLLRELPKKLLLFYGLFPMILVNLFYRGVSYFVLPFLGQG-QVYDDYSFIWLCIIIFN 131- Query: 138 IFLIYRCIQVFHFDFSTWRQYFQSHRASKLLVFTNSSMALYYLCVQGIDVMSPSLSGLAT 19- 7 F+ ++ +DF++ R+ K L N M YYL +Q + G+ + Sbjct: 132 FFISLAFLKWLDYDFTSLRKGILDKDFQKSLTQINWIMGAYYLVIQNLSYFEYQ-QGIQS 19- 0 Query: 198 TTARSIIVLFYFILFLTLLIHLERYVKQNSIEAIVQQKE--YRELINYSQHLGLLYQDIQ 25- 5 TT R +I++FY + F+ ++ L+ Y+K E + Q+++ YRE+ YS+H+ LY++++ Sbjct: 191 TTVRHLILVFYLLFFMGIIKKLDTYLKDKLHERLNQEQDLRYREMERYSRHIEELYKEVR 25- 0 Query: 256 ELRRLLTTVSSRLKIGIEQNDISIVRLTYEGILNAEKNNAKDDRLDLTCLDKLQVEAIRH 31- 5 R T + + L++GIE+ D+ ++ Y+ +L +D++ DL L ++ A++ Sbjct: 251 SFRHDYTNLLTSLRLGIEEEDMEQIKEIYDSVLKDSSEKLQDNKYDLGRLVNVRDRALKS 31- 0 Query: 316 IVLAKLIEAKNKKLKVEVSIPNCIATFFLEVVDFTKLLSFLLDNAIEMSLETKQPCLSIA 37- 5 ++ K I+A++K + V +P I + ++DF ++S L DNAIE S+E QP +SIA Sbjct: 311 LLAGKFIKARDKNIVFNVEVPEEIQVEGVSLLDFLTVVSILCDNAIEASVEACQPHVSIA 37- 0 Query: 376 FLDQNHKLVIVIQSSTKQGQDDSQSVFAIPALKKRDDWQFDLRNVTTILNRYDYLTISSQ 43- 5 F + +I++S K+ D +F+ A K ++ L V I+ + ++++ Sbjct: 371 FFKNGAQETFIIENSIKEEGIDISEIFSFGASSKGEERGVGLYTVMKIVESHPNTSLNTT 43- 0 Query: 436 IHDGILTQLIEI 447 D + Q++ + Sbjct: 431 CQDHVFRQVLTV 442 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2831 A DNA sequence (GASx1593R) was identified in S. pyogenes <SEQ ID 8161> which encodes the amino acid sequence <SEQ ID 8162>. Analysis of this protein sequence reveals the following:

TABLE-US-07791 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.28 Transmembrane 2-18 (1-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.1510(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2832 A DNA sequence (GASx1594) was identified in S. pyogenes <SEQ ID 8163> which encodes the amino acid sequence <SEQ ID 8164>. Analysis of this protein sequence reveals the following: TABLE-US-07792 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.93 Transmembrane 76-92 (76-92) ----- Final Results ----- bacterial membrane --- Certainty = 0.2572(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07793 >GP: AAF61313 GB: U96166 unknown [Streptococcus cristatus] Identities = 31/66 (46%), Positives = 40/66 (59%), Gaps = 2/66 (3%) Query: 14 LLGRILSKYVGRLTSCIENETTKIRNHSRQNDTIGLNHLLGNLKTVHNPEIILKTINVYS 73 - + G +SK + + E K+ ++ ND IG N LLG+LKTVHNPEII + VYS Sbjct: 30 VFGMDVSKTSSEVAILVNGE--KVHGYTILNDAIGFNRLLGDLKTVHNPEIIFEATGVYS 87 Query: 74 RRLQVF 79 RRLQ F Sbjct: 88 RRLQAF 93 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2833 A DNA sequence (GASx1598) was identified in S. pyogenes <SEQ ID 8165> which encodes the amino acid sequence <SEQ ID 8166>. Analysis of this protein sequence reveals the following: TABLE-US-07794 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2117(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2834 A DNA sequence (GASx1608) was identified in S. pyogenes <SEQ ID 8167> which encodes the amino acid sequence <SEQ ID 8168>. Analysis of this protein sequence reveals the following: TABLE-US-07795 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2835 A DNA sequence (GASx1619) was identified in S. pyogenes <SEQ ID 8169> which encodes the amino acid sequence <SEQ ID 8170>. Analysis of this protein sequence reveals the following: TABLE-US-07796 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2916(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2836 A DNA sequence (GASx1621) was identified in S. pyogenes <SEQ ID 8171> which encodes the amino acid sequence <SEQ ID 8172>. Analysis of this protein sequence reveals the following: TABLE-US-07797 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1899(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07798 alpha subunit [Escherichia coli] Identities = 110/211 (52%), Positives = 153/211 (72%) Query: 7 KEITIKEAVAHVKDGDTIMVGGFMTNGTPEKLIDALVEKGVKDLTLICNDAGFPDKGVGK 66 K +T+++A +DG TIMVGGFM GTP +L++AL+E GV+DLTLI ND F D G+G Sbjct: 4 KLMTLQDATGFFRDGMTIMVGGFMGIGTPSRLVEALLESGVRDLTLIANDTAFVDTGIGP 63 Query: 67 MVANKQFSTIIASHIGLNREAGRQMTEGETVIDLVPQGTLAERIRSGGFGLGGFLTPTGI 126- ++ N + +IASHIG N E GR+M GE + LVPQGTL E+IR GG GLGGFLTPTG+ Sbjct: 64 LIVNGRVRKVIASHIGTNPETGRRMISGEMDVVLVPQGTLIEQIRCGGAGLGGFLTPTGV 123- Query: 127 GTEVAKGKEVITIDGKDYLLEKPLKADVALIFANKADKNGNLQYAGSENNFNHVMAANAK 18- 6 GT V +GK+ +T+DGK +LLE+PL+AD+ALI A++ D GNL Y S NFN ++A A Sbjct: 124 GTVVEEGKQTLTLDGKTWLLERPLRADLALIRAHRCDTLGNLTYQLSARNFNPLIALAAD 18- 3 Query: 187 TTIVEAREIVDVGQMDPNFVHTPGIFVNYLV 217 T+VE E+V+ G++ P+ + TPG +++++ Sbjct: 184 ITLVEPDELVETGELQPDHIVTPGAVIDHII 214 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2837 A DNA sequence (GASx1622) was identified in S. pyogenes <SEQ ID 8173> which encodes the amino acid sequence <SEQ ID 8174>. Analysis of this protein sequence reveals the following: TABLE-US-07799 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4668(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07800 >GP: AAD54948 GB: AF157306 acetoacetate:butyrate/acetate coenzyme A transferase [Clostridium beijerinckii] Identities = 121/214 (56%), Positives = 161/214 (74%), Gaps = 5/214 (2%) Query: 7 VLSKEEIQTRIAKRVAQELEHNTLVNLGIGLPTKVANYIPEGVTITLQSENGFVGLTGLT 66 VL+KE I AKRVA+EL+ LVNLGIGLPT VANY+P+ + IT +SENG VG+ + Sbjct: 6 VLAKEII----AKRVAKELKKGQLVNLGIGLPTLVANYVPKEMNITFESENGMVGMAQMA 61 Query: 67 DD-HYDPTIVNAGGQPVSIAPGGAFFDSSTSFGIIRGGHVAATVLGALQVDKEASIANYL 125- DP I+NAGG+ V++ P GAFFDSSTSF +IRGGHV VLGAL+VD+E ++AN++ Sbjct: 62 SSGENDPDIINAGGEYVTLLPQGAFFDSSTSFALIRGGHVDVAVLGALEVDEEGNLANWI 121- Query: 126 IPGKMVPGMGGAMDLLVGAKKVIVAMEHTNKGKAKILDKCTLPLTAQNVVNLIITEMGVF 18- 5 +P K+VPGMGGAMDL +GAKK+IVAM+HT KGK KI+ KCTLPLTA+ V+LI+TE+ V Sbjct: 122 VPNKIVPGMGGAMDLAIGAKKIIVAMQHTGKGKPKIVKKCTLPLTAKAQVDLIVTELCVI 18- 1 Query: 186 EYQDEGLCALEINPDYTFEDVQNVTEVTLIDKTN 219 + ++GL EI+ D T ++++ +T+ LI N Sbjct: 182 DVTNDGLLFREIHKDTTIDEIKFLTDADLIIPDN 215 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2838 A DNA sequence (GASx1628R) was identified in S. pyogenes <SEQ ID 8175> which encodes the amino acid sequence <SEQ ID 8176>. Analysis of this protein sequence reveals the following: TABLE-US-07801 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1243(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2839 A DNA sequence (GASx1639R) was identified in S. pyogenes <SEQ ID 8177> which encodes the amino acid sequence <SEQ ID 8178>. Analysis of this protein sequence reveals the following: TABLE-US-07802 Possible site: 34 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.65 Transmembrane 55-71 (44-73) INTEGRAL Likelihood = -7.64 Transmembrane 13-29 (5-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.4461(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2840 A DNA sequence (GASx1643) was identified in S. pyogenes <SEQ ID 8179> which encodes the amino acid sequence <SEQ ID 8180>. Analysis of this protein sequence reveals the following: TABLE-US-07803 Possible site: 35 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0766 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2841 A DNA sequence (GASx1645R) was identified in S. pyogenes <SEQ ID 8181> which encodes the amino acid sequence <SEQ ID 8182>. Analysis of this protein sequence reveals the following: TABLE-US-07804 Possible site: 18 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2842 A DNA sequence (GASx1649R) was identified in S. pyogenes <SEQ ID 8183> which encodes the amino acid sequence <SEQ ID 8184>. Analysis of this protein sequence reveals the following: TABLE-US-07805 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0931 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2843 A DNA sequence (GASx1650) was identified in S. pyogenes <SEQ ID 8185> which encodes the amino acid sequence <SEQ ID 8186>. Analysis of this protein sequence reveals the following: TABLE-US-07806 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5678 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2844 A DNA sequence (GASx1651R) was identified in S. pyogenes <SEQ ID 8187> which encodes the amino acid sequence <SEQ ID 8188>. Analysis of this protein sequence reveals the following: TABLE-US-07807 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2761 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2845 A DNA sequence (GASx1667R) was identified in S. pyogenes <SEQ ID 8189> which encodes the amino acid sequence <SEQ ID 8190>. Analysis of this protein sequence reveals the following: TABLE-US-07808 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2967 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2846 A DNA sequence (GASx1672) was identified in S. pyogenes <SEQ ID 8191> which encodes the amino acid sequence <SEQ ID 8192>. Analysis of this protein sequence reveals the following: TABLE-US-07809 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.82 Transmembrane 3-19 (1-20) ----- Final Results ----- bacterial membrane --- Certainty = 0.2529 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2847 A DNA sequence (GASx1673R) was identified in S. pyogenes <SEQ ID 8193> which encodes the amino acid sequence <SEQ ID 8194>. Analysis of this protein sequence reveals the following: TABLE-US-07810 Possible site: 38 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.86 Transmembrane 51-67 (47-75) INTEGRAL Likelihood = -5.20 Transmembrane 27-43 (24-45) INTEGRAL Likelihood = -3.66 Transmembrane 112-128 (112-131) ----- Final Results ----- bacterial membrane --- Certainty = 0.4545 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07811 >GP: AAF41294 GB: AE002440 conserved hypothetical protein [Neisseria meningitidis MC58] Identities = 61/148 (41%), Positives = 96/148 (64%) Query: 1 LKKSITNEKAILAQGGQEFGAQNTKFLTLLHIMIYVFAVIEALLKQIKFDGISFLGLLLM 60 L SI +EKA++A+G +++G N+ L +H + Y+ + L F+GIS +G L + Sbjct: 19 LAVSIKHEKALIAKGAKQYGKTNSTLLAAVHTLYYLACFVWVWLSDTAFNGISLIGTLTV 78 Query: 61 LLSVAVLYEVTRILGDIWTVKLMLAKDHKYVDHWLFKTIKHPNYFLNIAPELVGIALLCH 120- + S +L + + LG+IWTVK+ + +H+ WLFKT +HPNYFLNI PEL+GIALLC Sbjct: 79 MASFVILSLIIKQLGEIWTVKIYILPNHQINRSWLFKTFRHPNYFLNIIPELIGIALLCQ 138- Query: 121 AKITAMLLFPCYIVVIYLRIREENKLLA 148 A ++ P Y++V++ RIR+E + +A Sbjct: 139 AWYVLLIGLPIYLLVLFKRIRQEEQAMA 166 A related GBS gene <SEQ ID 9009> and protein <SEQ ID 9010> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-07812 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: 5.86 GvH: Signal Score (-7.5): 0.14 Possible site: 60 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 2 value: -8.23 threshold: 0.0 INTEGRAL Likelihood = -8.23 Transmembrane 69-85 (64-89) INTEGRAL Likelihood = -3.29 Transmembrane 142-158 (140-159) PERIPHERAL Likelihood = 1.70 123 modified ALOM score: 2.15 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4291 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00164## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2848 A DNA sequence (GASx1674R) was identified in S. pyogenes <SEQ ID 8195> which encodes the amino acid sequence <SEQ ID 8196>. Analysis of this protein sequence reveals the following:

TABLE-US-07813 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3098(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2849 A DNA sequence (GASx1677R) was identified in S. pyogenes <SEQ ID 8197> which encodes the amino acid sequence <SEQ ID 8198>. Analysis of this protein sequence reveals the following: TABLE-US-07814 Possible site: 33 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.86 Transmembrane 254-270 (248-280) INTEGRAL Likelihood = -7.01 Transmembrane 303-319 (296-322) INTEGRAL Likelihood = -2.39 Transmembrane 74-90 (74-91) INTEGRAL Likelihood = -1.91 Transmembrane 201-217 (199-217) INTEGRAL Likelihood = -1.91 Transmembrane 223-239 (220-240) INTEGRAL Likelihood = -1.65 Transmembrane 118-134 (115-135) INTEGRAL Likelihood = -1.49 Transmembrane 56-72 (55-72) INTEGRAL Likelihood = -0.32 Transmembrane 13-29 (13-30) ----- Final Results ----- bacterial membrane --- Certainty = 0.4545(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07815 >GP: BAB05126 GB: AP001511 unknown conserved protein [Bacillus halodurans] Identities = 249/534 (46%), Positives = 380/534 (70%) Query: 12 QDIAFHFFGGLGLFLFSIKYMGDGLQQAAGDKLRYYIDKYTSNPFFGILVGIAMSALIQS 71 - Q + F FFGGLG+FLF IKYMGDGLQ+ AG++LR +DK+T+NP G+L GI ++ L+Q+ Sbjct: 6 QTLLFMFFGGLGIFLFGIKYMGDGLQKVAGERLRDLLDKFTTNPLMGVLAGIVVTVLLQT 65 Query: 72 SSGVTVITVGLVSAGLLNLRQAIGIVMGANIGTTITSFLIGFKLGDYALPMIFIGAACLF 131- S+G TV+T+GLV+AG + L+QAIG++MGANIGTT+T+F+IG K+ +YALP+I +GAA +F Sbjct: 66 STGTTVLTIGLVNAGFMTLKQAIGVIMGANIGTTVTAFIIGIKISEYALPIIAVGAALIF 125- Query: 132 FTSNKKLNNFGRIIFGVGGIFFSLNLMGDAMDPLKSVSAFQNYLATLGDKPFQGVFIGTA 19- 1 F NKK+NN G++IFG G +F+ LN MG+ ++PL+ + AF + ++ + P GV IGT Sbjct: 126 FIKNKKVNNIGQVIFGFGTLFYGLNTMGEGLNPLRELQAFADLTVSMSENPLLGVLIGTI 18- 5 Query: 192 LTMLIQSSAAIIGILQGLFSGGLLTLQGAIPILLGSNIGTCITAVLAAIGSNIAAKRVAA 25- 1 T +QSS+A IG+LQ L+ G + L A+P+L G NIGT ITAVLAAIG+++AAKR A Sbjct: 186 FTAAVQSSSASIGLLQQLYDQGAMDLFAALPVLFGDNIGTTITAVLAAIGASVAAKRAAL 24- 5 Query: 252 AHVLFNLIGTIIFMIILVPFTSLMLWLQSKLSLTPEMTIAFSHGSFNITNTILLIPFISL 31- 1 HV+FNLIGTII +II++PFT + +L +L MTIAF+HG FN++NTI+ PFI + Sbjct: 246 THVIFNLIGTIIVLIIIIPFTHFIAYLAEVFALNRPMTIAFAHGIFNVSNTIIQFPFIGI 30- 5 Query: 312 LAMIVTRLIPGEDEVVKYEALYLDRLLITQAPSIALGNAHKELVHLASYAIQAFEASYSY 37- 1 LA+IVT+L+PG+D ++Y+A +LD + +P+IALG A +E++ +A ++ + Y Sbjct: 306 LAIIVTKLVPGDDFYIEYKAKHLDPRFVGSSPAIALGQAKQEVLRMAEFSEKGLLEVSKY 36- 5 Query: 372 IMTADGKFGEKVKRYERAVDTIDEELTTYLVDISNEALSPSENEVLAGILDSSRDLERIG 43- 1 + K E ++E A++ +D ++T YL+ IS+ +LS ++++ ++D+ RD+ERIG Sbjct: 366 MENGQKKHAEMAVQFEDAINNLDRKITEYLISISSRSLSAQDSKMHGMLMDTVRDIERIG 42- 5 Query: 432 DHSESLGILIEGIISKQIGFSISARQELTEMYQLTHCLTLDAIRAIVDSDTDLAQTIVTR 49- 1 DH E++ L + + ++ S A +L EM+ LTH +AI ++ D + A++++ + Sbjct: 426 DHIENIVELKDYQKANKVKISEKALHDLQEMFDLTHSTLTEAIMSLETGDLEAARSVIEK 48- 5 Query: 492 HKEIEEKERRLRKTHIKRLNCGECTAQAGINFIDIISHYTRITDHALNLAEKVL 545 + I++ ER+LRK HI R+N G CT AGI F+DI+S+ RI DH++N+AE V+ Sbjct: 486 EEHIDQMERKLRKQHIIRVNEGNCTGAAGIVFVDIVSNLERIGDHSVNIAEAVI 539 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2850 A DNA sequence (GASx1678R) was identified in S. pyogenes <SEQ ID 8199> which encodes the amino acid sequence <SEQ ID 8200>. Analysis of this protein sequence reveals the following: TABLE-US-07816 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2940(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2851 A DNA sequence (GASx1685R) was identified in S. pyogenes <SEQ ID 8201> which encodes the amino acid sequence <SEQ ID 8202>. Analysis of this protein sequence reveals the following: TABLE-US-07817 Possible site: 22 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.11 Transmembrane 13-29 (9-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.3845(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2852 A DNA sequence (GASx1695R) was identified in S. pyogenes <SEQ ID 8203> which encodes the amino acid sequence <SEQ ID 8204>. Analysis of this protein sequence reveals the following: TABLE-US-07818 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1357(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2853 A DNA sequence (GASx1698) was identified in S. pyogenes <SEQ ID 8205> which encodes the amino acid sequence <SEQ ID 8206>. Analysis of this protein sequence reveals the following: TABLE-US-07819 Possible site: 33 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1970(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2854 A DNA sequence (GASx1713) was identified in S. pyogenes <SEQ ID 8207> which encodes the amino acid sequence <SEQ ID 8208>. Analysis of this protein sequence reveals the following: TABLE-US-07820 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3092(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2855 A DNA sequence (GASx1737) was identified in S. pyogenes <SEQ ID 8209> which encodes the amino acid sequence <SEQ ID 8210>. Analysis of this protein sequence reveals the following: TABLE-US-07821 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1878(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2856 A DNA sequence (GASx1748R) was identified in S. pyogenes <SEQ ID 8211> which encodes the amino acid sequence <SEQ ID 8212>. Analysis of this protein sequence reveals the following: TABLE-US-07822 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2841(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2857 A DNA sequence (GASx1750R) was identified in S. pyogenes <SEQ ID 8213> which encodes the amino acid sequence <SEQ ID 8214>. Analysis of this protein sequence reveals the following: TABLE-US-07823 Possible site: 59 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.22 Transmembrane 18-34 (18-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.1489(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2858 A DNA sequence (GASx1754) was identified in S. pyogenes <SEQ ID 8215> which encodes the amino acid sequence <SEQ ID 8216>. Analysis of this protein sequence reveals the following: TABLE-US-07824 Possible site: 44 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2859 A DNA sequence (GASx1759) was identified in S. pyogenes <SEQ ID 8217> which encodes the amino acid sequence <SEQ ID 8218>. Analysis of this protein sequence reveals the following: TABLE-US-07825 Possible site: 36 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1534(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2860 A DNA sequence (GASx1764R) was identified in S. pyogenes <SEQ ID 8219> which encodes the amino acid sequence <SEQ ID 8220>. Analysis of this protein sequence reveals the following: TABLE-US-07826 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.74 Transmembrane 90-106 (87-121) INTEGRAL Likelihood = -4.57 Transmembrane 210-226 (205-229) INTEGRAL Likelihood = -4.19 Transmembrane 43-59 (42-62) INTEGRAL Likelihood = -3.77 Transmembrane 137-153 (137-155) ----- Final Results ----- bacterial membrane --- Certainty = 0.3697(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2861 A DNA sequence (GASx1768R) was identified in S. pyogenes <SEQ ID 8221> which encodes the amino acid sequence <SEQ ID 8222>. Analysis of this protein sequence reveals the following: TABLE-US-07827 Possible site: 17 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.37 Transmembrane 26-42 (17-47) INTEGRAL Likelihood = -7.54 Transmembrane 53-69 (46-73) INTEGRAL Likelihood = -3.29 Transmembrane 209-225 (209-225) INTEGRAL Likelihood = -2.13 Transmembrane 82-98 (82-98) INTEGRAL Likelihood = -1.65 Transmembrane 9-25 (9-25) INTEGRAL Likelihood = -0.85 Transmembrane 117-133 (117-134) ----- Final Results ----- bacterial membrane --- Certainty = 0.5946(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07828 >GP: AAB84959 GB: AE000829 conserved protein [Methanobacterium thermoautotrophicum] Identities = 54/192 (28%), Positives = 90/192 (46%), Gaps = 6/192 (3%) Query: 7 TKLLLLVLANACFFFRVDGFLEFIIVIFLLLLLSALNKKKLA--FKLAVVYLLMIGLSVI 64 +KL ++V A F D L I+ + L++ + A F ++ ++ L++I Sbjct: 32 SKLTVVVSATLLSTFISDLTLLIIMGVIFTALIAHSGSLRFAAPFLSFIILFWLVSLAII 91 Query: 65 PLSIFPSYLDHLLSFVSIAGRLVFPSLLAGLITIKTTTIYELVHGLRKWRFPEVWLLTLA 124- + S H + F+S+ F AGL TT +L LR R P + TL Sbjct: 92 MVL---SGNPHTMGFLSLFFARFFIISAAGLSFAFTTEPQKLAESLRSVRIPGEIVFTLT 148- Query: 125 VMCRFIPMIRQECCVIHRSLKIRGIILTKWSILIRPKQYLEYLMVPLLLSLIRSSQELTI 18- 4 V R+IP + E I SLK+R L+ SI+ RP L++P+++ ++ S E+ I Sbjct: 149 VALRYIPALAVEASSIWDSLKLR-TSLSGSSIIRRPSLLYRGLIIPMIIRTVKISDEVAI 20- 7 Query: 185 ASLTKGLAVNKG 196 A+ T+G +G Sbjct: 208 AAETRGFNPREG 219 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2862 A DNA sequence (GASx1769R) was identified in S. pyogenes <SEQ ID 8223> which encodes the amino acid sequence <SEQ ID 8224>. Analysis of this protein sequence reveals the following: TABLE-US-07829 Possible site: 16 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.32 Transmembrane 164-180 (158-186) INTEGRAL Likelihood = -4.67 Transmembrane 85-101 (84-105) INTEGRAL Likelihood = -3.03 Transmembrane 42-58 (42-61) INTEGRAL Likelihood = -2.76 Transmembrane 118-134 (117-134) INTEGRAL Likelihood = -2.07 Transmembrane 64-80 (64-82) INTEGRAL Likelihood = -1.22 Transmembrane 18-34 (17-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.3930(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2863 A DNA sequence (GASx1776R) was identified in S. pyogenes <SEQ ID 8225> which encodes the amino acid sequence <SEQ ID 8226>. Analysis of this protein sequence reveals the following: TABLE-US-07830 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.37 Transmembrane 4-20 (1-22) INTEGRAL Likelihood = -0.43 Transmembrane 261-277 (261-278) ----- Final Results ----- bacterial membrane --- Certainty = 0.3548(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2864 A DNA sequence (GASx1777R) was identified in S. pyogenes <SEQ ID 8227> which encodes the amino acid sequence <SEQ ID 8228>. Analysis of this protein sequence reveals the following: TABLE-US-07831 Possible site: 24 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.17 Transmembrane 1217-1233 (1215-1235) ----- Final Results ----- bacterial membrane --- Certainty = 0.4270(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-07832 >GP: AAF53254 GB: AE003639 CG16974 gene product [Drosophila melanogaster] Identities = 84/238 (35%), Positives = 133/238 (55%), Gaps = 10/238 (4%) Query: 516 LRLDHYELTDISLL--KHAKNITELHLDGNQITEIPKELFSQMKQLRFLNLRSNHLTYLD 57- 3 L + L++ SLL ++ K + ELHLD +++T +P+ ++ +LR LNL N LT L Sbjct: 232 LEMSGNRLSNCSLLNLQYMKQLQELHLDRSELTYLPQRFLGELSELRMLNLSQNLLTELP 29- 1 Query: 574 KDTFKSNAQLRELYLSSNFIHSLEGGLFQSLHHLEQLDLSKNRIGRLCDNPFEGLSRLTS 63- 3 +D F +L LYLS N + L LFQ+ L+ LDLS NR+ DN F +L Sbjct: 292 RDIFVGALKLERLYLSGNRLSVLPFMLFQTAADLQVLDLSDNRLLSFPDNFFARNGQLRQ 35- 1 Query: 634 LGFAENSLEEIPEKALEPLTSLNFIDLSQNNLALLP-KTIEKLRALSTIVASRNHITRID 69- 2 L N L+ I + +L L L +DLSQN+L+++ K E L L + S N++T + Sbjct: 352 LHLQRNQLKSIGKHSLYSLRELRQLDLSQNSLSVIDRKAFESLDHLLALNVSGNNLTLLS 41- 1 Query: 693 NISFKNLPKLSVLDLSTNEISNLPNGIFKQNNQL-------TKLDFFNNLLTQVEESV 743 +I F++L L LDLS N+ LP+G+F++ L T ++ F+N +++ +ES+ Sbjct: 412 SIIFQSLHALRQLDLSRNQFKQLPSGLFQRQRSLVLLRIDETPIEQFSNWISRYDESL 469 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2865 A DNA sequence (GASx1778R) was identified in S. pyogenes <SEQ ID 8229> which encodes the amino acid sequence <SEQ ID 8230>. Analysis of this protein sequence reveals the following: TABLE-US-07833 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1067(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2866 A DNA sequence (GASx1779) was identified in S. pyogenes <SEQ ID 8231> which encodes the amino acid sequence <SEQ ID 8232>. Analysis of this protein sequence reveals the following: TABLE-US-07834 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1885(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2867 A DNA sequence (GASx1786R) was identified in S. pyogenes <SEQ ID 8233> which encodes the amino acid sequence <SEQ ID 8234>. Analysis of this protein sequence reveals the following: TABLE-US-07835 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0612(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2868 A DNA sequence (GASx1790) was identified in S. pyogenes <SEQ ID 8235> which encodes the amino acid sequence <SEQ ID 8236>. Analysis of this protein sequence reveals the following: TABLE-US-07836 Possible site: 13 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2869 A DNA sequence (GASx1791R) was identified in S. pyogenes <SEQ ID 8237> which encodes the amino acid sequence <SEQ ID 8238>. Analysis of this protein sequence reveals the following: TABLE-US-07837 Possible site: 43 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.90 Transmembrane 28-44 (28-44) ----- Final Results ----- bacterial membrane --- Certainty = 0.1362(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> A related sequence was also identified in GAS <SEQ ID 9155> which encodes the amino acid sequence <SEQ ID 9156>. Analysis of this protein sequence reveals the following: TABLE-US-07838 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.300 (Affirmative) < succ> bacterial membrane --- Certainty = 0.000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07839 >GP: AAA24923 GB: L06331 endoglycosidase [Chryseobacterium meningosepticum] Identities = 105/322 (32%), Positives = 153/322 (46%), Gaps = 53/322 (16%) Query: 106 ADKQAQELAKMKIPEKIPMKPLHGSLYGGYFRTWHDKTSDPTEKDKVNSMGELPKEVDLA 16- 5 A K ++ + + I K + GY+RTW D T + SM LP +D+ Sbjct: 37 AQKSGVTVSAVNLSNLIAYKNSDHQISAGYYRTWRDSA---TASGNLPSMRWLPDSLDMV 93 Query: 166 FIFHDWTKDYSLFWKELATKHVPKLNKQGTRVIRTIPWRFLAGGDNSGIAEDTSKYPNTP 22- 5 +F D+T + +W L T +VP L+K+GT+VI T+ G NS T+ Sbjct: 94 MVFPDYTPPENAYWNTLKTNYVPYLHKRGTKVIITL------GDLNSA----TTTGGQDS 143- Query: 226 EGNKALAKAIVDEYVYKYNLDGLDVDVEHDSIPKVDKKEDTAGVERSIQVFEEIGKLIGP 28- 5 G + AK I D++V +YNLDG+D+D+E A + + + + + K GP Sbjct: 144 IGYSSWAKGIYDKWVGEYNLDGIDIDIE--------SSPSGATLTKFVAATKALSKYFGP 19- 5 Query: 286 KGVDKSRLFIMDSTYMADKNP--LIERGAPYINLLLVQVYGSQGEKGGWEPVSNRPEKTM 34- 3 K + F+ D+ ++NP + AP N + +Q YG R + Sbjct: 196 KS-GTGKTFVYDT----NQNPTNFFIQTAPRYNYVFLQAYG-------------RSTTNL 23- 7 Query: 344 EERWQGYSKYIRPEQYMIGFSFYEENAQEGNLWYDINSRKDEDKANGINTDITGTRAERY 40- 3 Y+ YI +Q++ GFSFYEEN GN W D+ + NG TG RA Y Sbjct: 238 TTVSGLYAPYISMKQFLPGFSFYEENGYPGNYWNDVRYPQ-----NG-----TG-RAYDY 28- 6 Query: 404 ARWQPKTGGVKGGIFSYAIDRD 425 ARWQP T G KGG+FSYAI+RD Sbjct: 287 ARWQPAT-GKKGGVFSYAIERD 307 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2870 A DNA sequence (GASx1803) was identified in S. pyogenes <SEQ ID 8239> which encodes the amino acid sequence <SEQ ID 8240>. Analysis of this protein sequence reveals the following: TABLE-US-07840 Possible Site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2099 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2871 A DNA sequence (GASx1806R) was identified in S. pyogenes <SEQ ID 8241> which encodes the amino acid sequence <SEQ ID 8242>. Analysis of this protein sequence reveals the following: TABLE-US-07841 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2706 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07842 >GP: CAB16126 GB: Z99124 ribosomal protein S18 [Bacillus subtilis] Identities = 51/77 (66%), Positives = 63/77 (81%) Query: 1 MAQQRRGGFKRRKKVDFIAANKIEYVDYKDTELLSRFVSERGKILPRRVTGTSAKNQRKV 60 MA RRGG +R+KV + +N I ++DYKD +LL +FVSERGKILPRRVTGT+AK QRK+ Sbjct: 3 MAGGRRGGRAKRRKVCYFTSNGITHIDYKDVDLLKKFVSERGKILPRRVTGTNAKYQRKL 62 Query: 61 TTAIKRARVMALMPYVN 77 T AIKRAR MAL+PYV+ Sbjct: 63 TAAIKRARQMALLPYVS 79 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2872 A DNA sequence (GASx1809R) was identified in S. pyogenes <SEQ ID 8243> which encodes the amino acid sequence <SEQ ID 8244>. Analysis of this protein sequence reveals the following: TABLE-US-07843 Possible site: 60 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.59 Transmembrane 70-86 (66-92) INTEGRAL Likelihood = -6.42 Transmembrane 13-29 (8-33) INTEGRAL Likelihood = -5.68 Transmembrane 48-64 (43-69) ----- Final Results ----- bacterial membrane --- Certainty = 0.4036 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2873 A DNA sequence (GASx1813R) was identified in S. pyogenes <SEQ ID 8245> which encodes the amino acid sequence <SEQ ID 8246>. Analysis of this protein sequence reveals the following: TABLE-US-07844 Possible site: 56 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.51 Transmembrane 127-143 (113-147) INTEGRAL Likelihood = -10.46 Transmembrane 151-167 (149-167) INTEGRAL Likelihood = -4.41 Transmembrane 59-75 (57-77) ----- Final Results ----- bacterial membrane --- Certainty = 0.5203(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07845 >GP: AAB98363 GB: U67490 lipoprotein B (lppB) [Methanococcus jannaschii] Identities = 43/143 (30%), Positives = 68/143 (47%), Gaps = 7/143 (4%) Query: 25 LLNVLLKIITGVMY--ILYPSFLIFTLWQGMTFQLWLRLLIIPAVGFIALSYIRKRFDFP 82 - + + ++ II+ Y I S +IF + +L L + + F +L Y+ P Sbjct: 181 IFDAIMPIISKTAYPLIAITSLIIFIKNRKFGMKLIFALFLAFMIAF-SLKYLVNE---P 23- 6 Query: 83 RPYEKWNIKPLIDKDTKGRSMPSRHVFSATMISMCLLRYYVYFGIVCLILSALLAICRVI 142- RPY + L+ + S PS H A ++ LL Y GI+ L + ++A RV Sbjct: 237 RPYLVLDNVHLLCNEGNEPSFPSGHTTLAFTLATSLLFYSKKLGILFLSWAIIVAYSRVY 29- 6 Query: 143 AGIHYPKDVIVGYLIGLMLGLCL 165 G+HYP DV+ G +IG+ G CL Sbjct: 297 VGVHYPLDVLAGMIIGIFCG-CL 318 A related GBS gene <SEQ ID 9011> and protein <SEQ ID 9012> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-07846 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: 3.19 GvH: Signal Score (-7.5): -2.18 Possible site: 55 >>> Seems to have a cleavable N-term signal seq. ALOM program Count: 3 value: -11.78 threshold: 0.0 INTEGRAL Likelihood = -11.78 Transmembrane 126-142 (112-147) INTEGRAL Likelihood = -11.30 Transmembrane 150-166 (147-166) INTEGRAL Likelihood = -4.41 Transmembrane 58-74 (56-76) PERIPHERAL Likelihood = 3.29 107 modified ALOM score: 2.86 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5713 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00165## Based on this analysis, it was predicted that these proteins and their epitopes could be useful antigens for vaccines or diagnostics. EXAMPLE 2874 A DNA sequence (GASx1815R) was identified in S. pyogenes <SEQ ID 8247> which encodes the amino acid sequence <SEQ ID 8248>. Analysis of this protein sequence reveals the following: TABLE-US-07847 Possible site: 15 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0888(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2875 A DNA sequence (GASx1825R) was identified in S. pyogenes <SEQ ID 8249> which encodes the amino acid sequence <SEQ ID 8250>. Analysis of this protein sequence reveals the following: TABLE-US-07848 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.16 Transmembrane 7-23 (7-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2876 A DNA sequence (GASx1832) was identified in S. pyogenes <SEQ ID 8251> which encodes the amino acid sequence <SEQ ID 8252>. Analysis of this protein sequence reveals the following: TABLE-US-07849 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0918(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2877 A DNA sequence (GASx1836R) was identified in S. pyogenes <SEQ ID 8253> which encodes the amino acid sequence <SEQ ID 8254>. Analysis of this protein sequence reveals the following: TABLE-US-07850 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4084(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2878 A DNA sequence (GASx1864R) was identified in S. pyogenes <SEQ ID 8255> which encodes the amino acid sequence <SEQ ID 8256>. Analysis of this protein sequence reveals the following: TABLE-US-07851 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5280(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07852 >GP: AAC36810 GB: L12244 ribosomal protein L28 [Bacillus subtilis] Identities = 45/62 (72%), Positives = 52/62 (83%) Query: 1 MAKVCYFTGRKTVSGNNRSHAMNQTKRTVKPNLQKVTILVDGKPKKVWASARALKSGKVE 60 MA+ C TG+KT +GNNRSHAMN +KRT NLQKV ILV+GKPKKV+ SARALKSGKVE Sbjct: 1 MARKCVITGKKTTAGNNRSHAMNASKRTWGANLQKVRILVNGKPKKVYVSARALKSGKVE 60 Query: 61 RI 62 R+ Sbjct: 61 RV 62 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2879 A DNA sequence (GASx1869) was identified in S. pyogenes <SEQ ID 8257> which encodes the amino acid sequence <SEQ ID 8258>. Analysis of this protein sequence reveals the following: TABLE-US-07853 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1858(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2880 A DNA sequence (GASx1881) was identified in S. pyogenes <SEQ ID 8259> which encodes the amino acid sequence <SEQ ID 8260>. Analysis of this protein sequence reveals the following:

TABLE-US-07854 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2752(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> RGD motif 136-138 No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07855 >GP: AAF04356 GB: AF177167 type IC restriction subunit [Streptococcus thermophilus] Identities = 358/1047 (34%), Positives = 571/1047 (54%), Gaps = 91/1047 (8%) Query: 7 TELELEKELIHLLETGESQWTYRKELKTEDALWDNFFKILAQNNTQYLNEEPLTASEKEQ 66 +E +E + I +L E+QWTYR +LK+E+ALW NF L + N L E+PLT E +Q Sbjct: 4 SEQMIENQFIQILSEKENQWTYRPDLKSEEALWQNFRSHLNRINLAVLGEQPLTDKEFKQ 63 Query: 67 IKNQLNFVNY--YEAAKWLAGENGIAKVQVQREDAKLGTIRLEVVKADNVAGGTSVYEIA 124- +K + + + + A++WL GENG+A++ ++RED K + LE + +++GGTS YE+ Sbjct: 64 VKVEFSRLTGTPFLASQWLRGENGVAQILLEREDGK--RVTLEAFRNKDISGGTSSYEVV 121- Query: 125 NQVAFSGSRDRRGDVTLLINGLPMIQIELKSQNHQ--CIEAFNQVKKYDKEGQFRGIFST 18- 2 +QV SR RGDV+LLINGLP+I IELK ++ + ++A+ Q+++Y ++G F+GI++T Sbjct: 122 HQVVPDSSRVDRGDVSLLINGLPIIHIELKKESAKDGFMQAYYQIQRYAEDGFFKGIYAT 18- 1 Query: 183 LQMFVVSNKTDTRYIAAAKENKLNP-----NFLTQWVDQNNKPQKDLFAFAKEVLSIPRA 23- 7 Q+ V+SNK DTRY A E+ FL W ++N+ DLF F + VL IP A Sbjct: 182 TQIMVISNKVDTRYFARPSEDTAEAYARMKKFLFNWRTEDNQTVSDLFDFTRTVLRIPDA 24- 1 Query: 238 HQMVMTYSVIDDDKKA---LILLRPYQIHAIEAVAEASRHRKSGYIWHTTGSGKTLTSYK 29- 4 H+++ Y+++ DD+K L+ LRPYQIHAI + + + + G+IWH TGSGKT+TS+ Sbjct: 242 HELISQYTILVDDQKNQKFLMALRPYQIHAIRKIRQKAAQHEGGFIWHATGSGKTITSFV 30- 1 Query: 295 VARNILQIP-AVEKSIFVIDRKDLDNQTASAFQSYA---------QNDIFD--VDETEDT 34- 2 + + Q V++++ V+DR DLD QT F +A +N + + + ++ Sbjct: 302 ATKLLAQNAIGVDRTVMVVDRTDLDAQTQDEFTKFASEYHTGQTTENSVANTLIVGIKNQ 36- 1 Query: 343 RQLIKNLESS--DRRVVVTTIQKLNAMISQMESYDTPKFKKLKERLAHLNVVFVVDECHR 40- 0 +QL +NL SS + ++VTTIQKL+A + + K E+L ++VF+VDE HR Sbjct: 362 KQLAQNLLSSKNNNTILVTTIQKLSAAMRSAQQESEEKGSNQFEKLRQEHIVFIVDEAHR 42- 1 Query: 401 AVTPERQRYLTNTFRNSRWYGFTGTPIFVENKRAQLGDLAQTTEQQYGKCLHQYTVKEAI 46- 0 AV+ E + + NS W+G TGTPIF ENK+ + G A+TT QQYG LH YT+K A+ Sbjct: 422 AVSDEEMKRIKKILPNSTWFGLTGTPIFEENKKQENGTFARTTSQQYGPLLHSYTIKNAM 48- 1 Query: 461 HDKAVLGFQVEYKTTIPD--------------MPEDS------IPEEAYDHEEHMLAVLD 50- 0 D AVLGFQVEY + I + +P+D+ +P E Y+ +EH+ +L Sbjct: 482 DDGAVLGFQVEYHSLISEEDQEVIVTQLNKGKLPDDALQQEKLLPTELYETDEHIRTMLQ 54- 1 Query: 501 SIINQSR--KKLGFNNGIGQTFEGLLTVKSIARAQAYYDLMKKVKAGETDLVISKKVKEK 55- 8 I N+ KK NG T +LT SIA+A+ Y ++K++K T L+ ++ E+ Sbjct: 542 KIFNRRSVVKKFKVKNGF-PTMSAILTTHSIAQAKHIYRILKEMKDNGT-LLNGRQFDER 59- 9 Query: 559 L----PDFPKVAITYSITENDNASISRQDKMTKNLEDYNHLFGTNFTIDNLQGYNRDLND 61- 4 DFP+VAIT+S + + D++ + +++Y F + D + YN+++N Sbjct: 600 HQLIDKDFPRVAITFSTNPDQLEKNEQDDELVEIMKEYEKQFDASPYQDE-KLYNQNINK 65- 8 Query: 615 RLARKKDKFKDRHEQLDLVIVVDRLLTGFDAPCLSTIFIDRQPMKPQHIIQAFSRTNRIF 67- 4 RLARK+ +++ + LD VIVVDRLLTGFD+P + T++IDR+ M Q ++QAFSRTNRI+ Sbjct: 659 RLARKEKQYQSDGQWLDFVIVVDRLLTGFDSPTIQTLYIDRE-MNYQKLLQAFSRTNRIY 71- 7 Query: 675 ESRKHYGQVVTFQTPLRFKEAVDKALSLYSNGGEN-DVLAP-SWEEEKARFFEKVTVLKN 73- 2 + K G +V+F+ P +E V L+SN +N D L P +EE K F E T+ K Sbjct: 718 -TGKDSGLIVSFRKPFTMRENVRNTFRLFSNEKQNFDQLIPKEYEEVKKEFIECSTLYKQ 77- 6 Query: 733 IVPDPDAFPTIESAQTAFLKQYAKAFQAFDKLFASVQVYSDFNETLLSEVGLSDEVIDTY 79- 2 D P A + Y K +++ L + Q DF E SEV E + Y Sbjct: 777 SEADLSDNPNDLKTMIAQVSAYQKLEKSYKALRSYDQYEEDFEE--FSEV---VEQLPQY 83- 1 Query: 793 KGTYQNVIAEIRKRRED--------DEAIPEINIDYELESVQMDDINYHYILTLIQAFVD 84- 4 +G +N+ +I++ ED ++ + EI +L + D ++ YI L++A Sbjct: 832 QGKTENIKTKIKEMIEDEGHPEEDFEKLLQEIAFSSQLNATHKDVVDSFYINQLLKAIQL 89- 1 Query: 845 QEQEALQERLNDNPMDQYIQDLAKSNPAMADSLAELWQDIQKEPKAYEGKSIVYELDNLI 90- 4 E A+++ + + Q + K + D L ++I + + I Sbjct: 892 NEAGAVEK--FEKEIQQKDPQIQKMYHTLKDQLVNTTEEI----------DVAQLKETSI 93- 9 Query: 905 GDKIQRAIKHFADQWKADPDKLAFVATNYHSANSTKQVGMSTLKE-SLDYQAYKEKQGDS 96- 3 ++IQR ++ A+++ D L Y S T L +L + ++ K G+ Sbjct: 940 QNEIQRQLQKEAEEFGLSFDFLQSAMNEYQSDKKTIPYLTHLLDSMTLSKEEFEAKTGE- 99- 8 Query: 964 AMNKLKYKSQFERELVQFIRDQIQPLK 990 K + +++ E +Q +Q+Q K Sbjct: 999 ---KYRRRTKVLEERLQQNFEQLQKWK 1022 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2881 A DNA sequence (GASx1882) was identified in S. pyogenes <SEQ ID 8261> which encodes the amino acid sequence <SEQ ID 8262>. Analysis of this protein sequence reveals the following: TABLE-US-07856 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3653(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07857 >GP: AAB53491 GB: U35629 unknown [Lactococcus lactis subsp. lactis] Identities = 141/241 (58%), Positives = 178/241 (73%) Query: 3 KSKQPQYRFDGFEGEWEEKELGDIVQITMGQSPSSQNYTTNPSDYILVQGNADIKNGYVF 62 K K P+ RF GF EWE ++LGD V+I MGQSP+S+NYT +P+DYILVQGNAD+KNG V Sbjct: 13 KKKVPELRFKGFTDEWELRKLGDEVRIVMGQSPNSENYTDDPNDYILVQGNADMKNGRVL 72 Query: 63 PRVWTTQITKQADKGDIILSVRAPVGDVGKTNYHVIIGRGVAAIKGNEFIFQILKYLKEI 122- PRVWTTQ+TKQA+K D+ILSVRAPVGD+GKT Y V+IGRGVAAIKGNEFIFQ L +K Sbjct: 73 PRVWTTQVTKQAEKDDLILSVRAPVGDIGKTAYDVVIGRGVAAIKGNEFIFQNLGKMKSD 132- Query: 123 GYWKRISTGSTFDSISSSDIKYAKIQIPSLPEQEAIGELFQMVDQLIQLQDQKLATLKEQ 18- 2 GYW R STGSTF+SI+S+DIK A I +P++ EQ+ IG F+ +D I L +KL LKEQ Sbjct: 133 GYWTRYSTGSTFESINSTDIKEAIISVPAIEEQDKIGSFFKQLDNTIALHQRKLDLLKEQ 19- 2 Query: 183 KQTFLRKMFPAQGQKVPEIRLQGFKGEWEEKKLREVSTHRSGTAIEKYFDSEGEFKVISIG 2- 43 K+ FL+KMFP G KVPE+R GF +WEE+KL +++ +G G++ + G Sbjct: 193 KKGFLQKMFPKNGAKVPELRFAGFADDWEERKLGDITKISTGKLDANAMVENGKYDFYTSG 2- 53 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2882 A DNA sequence (GASx1883) was identified in S. pyogenes <SEQ ID 8263> which encodes the amino acid sequence <SEQ ID 8264>. Analysis of this protein sequence reveals the following: TABLE-US-07858 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4318(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07859 >GP: AAF04357 GB: AF177167 type IC modification subunit [Streptococcus thermophilus] Identities = 293/523 (56%), Positives = 377/523 (72%), Gaps = 6/523 (1%) Query: 6 TSLRQALWHSADQLRGQMDANDYKNYLLGLIFYKHLSDKLLLAVCDNLEKHFNTFTEAQK 65 TSL Q LW SAD LRG+MDA++YKNYLLGLIFYK+LSDK L V + +TF E Sbjct: 3 TSLNQQLWASADILRGKMDASEYKNYLLGLIFYKYLSDKQLREVYEQENGKTDTFPERST 62 Query: 66 I---FEDAYQDEGLKDDLISVVTGDLGYFIEPTLTFEKLIQDVYHNTFQLESLAQGFRDI 122- + F + Y+++ KDDLI + GYFI+P F + F L L GF ++ Sbjct: 63 LYAGFMEWYEED--KDDLIENIQPRQGYFIQPDRLFYHYRIKADNYEFNLTDLQAGFNEL 120- Query: 123 EQSGEDFENLFEDIDLYSKKLGSTPQKQNQTISNVMKTLNEIDFEAVDGDTLGDAYEYLI 18- 2 E+ GE+F LF DIDL S KLGS Q++N TI+ V++ L+EID +GD +GDAYEYLI Sbjct: 121 ERQGEEFSGLFSDIDLNSTKLGSNAQQRNVTITEVLRALDEIDLFEHNGDVIGDAYEYLI 18- 0 Query: 183 GEFASESGKKAGEFYTPQAVSHLMTQIVFLGREDQKGMTLYDPAMGSGSLLLNAKKYSNQ 24- 2 G FA+ +GKKAGEFYTPQAVS +M++I +G+E + +YDPAMGSGSL+LN ++Y Sbjct: 181 GMFAAGAGKKAGEFYTPQAVSRIMSEITSIGQESRVPFHIYDPAMGSGSLMLNIRRYLIH 24- 0 Query: 243 SDTVSYYGQEINTSTYNLARMNMMLHGVAIENQHLSNADTLDADWPTDEPINFDGVLMNP 30- 2 + V Y+GQE+NT+T+NLARMN++LHGV E +L+N DTLDADWP++EP FD V+MNP Sbjct: 241 PNQVHYHGQELNTTTFNLARMNLILHGVDKERMNLNNGDTLDADWPSEEPYQFDSVVMNP 30- 0 Query: 303 PYSLKWSATAGFLTDPRFSSYGVLAPKSKADFAFLLHGFYHLKNTGTMAIVLPHGVLFRG 36- 2 PYS KWSA FL+DPRF +G LAPKSKADFAFLLHGFYHLK +GTM IVLPHGVLFRG Sbjct: 301 PYSAKWSAADKFLSDPRFERFGKLAPKSKADFAFLLHGFYHLKESGTMGIVLPHGVLFRG 36- 0 Query: 363 AAEGKIRQKLLEQGAIDTIIGLPSNIFYNTSIPTTIIILKKNRTNKDVFFIDASKEFDKG 42- 2 AEG IRQ LLE GAID +IGLP+NIF+ TSIPTT+IILKKNR+ +DV FIDAS++F+K Sbjct: 361 GAEGTIRQALLEMGAIDAVIGLPANIFFGTSIPTTVIILKKNRSRRDVLFIDASQDFEKQ 42- 0 Query: 423 KNQNTMTDNHIKKILDAYKSRDNSDKFSYLASFDEIIENDYNLNIPRYVDTFEEVPVKPL 48- 2 KNQN + D HI KI+ YK R++ ++++++ASFDEI END+NLNIPRYVDTFEE L Sbjct: 421 KNQNVLLDEHIDKIVSTYKKREDIERYAHVASFDEIQENDFNLNIPRYVDTFEEEEPVDL 48- 0 Query: 483 PELAKQLSDIDQEIAKTNAKLDQLMKQLVGTTKEAQDELDTFR 525 E+ L I++E+ + L L+ ++E Q +++ R Sbjct: 481 VEVNTNLLKINEELVQQEQTLLSLINDF-SESEENQAMIESMR 522 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2883 A DNA sequence (GASx1886R) was identified in S. pyogenes <SEQ ID 8265> which encodes the amino acid sequence <SEQ ID 8266>. Analysis of this protein sequence reveals the following: TABLE-US-07860 Possible site: 59 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.17 Transmembrane 155-171 (147-173) INTEGRAL Likelihood = -7.22 Transmembrane 14-30 (11-33) INTEGRAL Likelihood = -7.17 Transmembrane 182-198 (179-205) INTEGRAL Likelihood = -5.68 Transmembrane 132-148 (128-152) INTEGRAL Likelihood = -4.14 Transmembrane 46-62 (43-62) INTEGRAL Likelihood = -3.50 Transmembrane 73-89 (73-90) INTEGRAL Likelihood = -0.96 Transmembrane 95-111 (95-111) ----- Final Results ----- bacterial membrane --- Certainty = 0.4270(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2884 A DNA sequence (GASx1890R) was identified in S. pyogenes <SEQ ID 8267> which encodes the amino acid sequence <SEQ ID 8268>. Analysis of this protein sequence reveals the following: TABLE-US-07861 Possible site: 58 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4757(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> RGD motif 339-341 No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07862 >GP: AAA62650 GB: L37110 clyM [Plasmid pAD1] Identities = 127/492 (25%), Positives = 230/492 (45%), Gaps = 30/492 (6%) Query: 46 KLFYSEFENQLFETIMFLSMKTLVLDINHFSKEIENK----SEAYEQYIQQ-IREENGIN 100- K F L + ++ L+ KTLVLD++ F K K S+ + Y+++ + I Sbjct: 135 KEFIINLLENLTQELIHLTSKTLVLDLHTFKKNEPLKGNDSSKRFIYYLKKRFNSKKDII 19- 4 Query: 101 HFFDRYPYLLKQINKEVGLIEESYSLLFDRFLEDLSEIKSCFNI-SEPLSNVAFSLGDSH 15- 9 F+ YP L++ + ++ + R EDL I++CFNI S L++++ S GDSH Sbjct: 195 AFYTCYPELMRITVVRMRYFLDNTKQMLIRVTEDLPSIQNCFNIQSSELNSISESQGDSH 25- 4 Query: 160 SKKQTVVKIAFKE-KSVYYKPKSYHSHSILLELTSLLKSSNIPSFSLPKSLVKADYCWQL 21- 8 S+ +TV + F + K + YKPK +S + L + L + K + + Y ++ Sbjct: 255 SRGKTVSTLTFSDGKKIVYKPK-INSENKLRDFFEFLNKELEADIYIVKKVTRNTYFYEE 31- 3 Query: 219 GVAYTSSNK-DEVAKIYFKYGVLAAFSEIFSITDLHMENVIVSGGDLYLIDVETFFQRKL 27- 7 + N +EV K Y +YG L + +F++TDLH EN+I G +ID ETFFQ+ + Sbjct: 314 YIDNIEINNIEEVKKYYERYGKLIGIAFLFNVTDLHYENIIAHGEYPVIIDNETFFQQNI 37- 3 Query: 278 NVQNQNFEGITVDTYQRIYETSLSNGLFP---VQFEKNSAPNVSGISRKGGKRQKGKYEL 33- 4 ++ N TVD + ++ + GL P ++ + +S +S K Q +++ Sbjct: 374 PIEFGN--SATVDAKYKYLDSIMVTGLVPYLAMKDKSDSKDEGVNLSALNFKEQSVPFKI 43- 1 Query: 335 I---NKNRGDLKLVKVDYFQEDRFNIPTLNGKVVEPLDYANEIISGFRECYIFLLSQRSK 39- 1 + N +++ + + N P +N + + + Y I++G + + + K Sbjct: 432 LKIKNTFTDEMRFEYQTHIMDTAKNTPIMNNEKISFISYEKYIVTGMKSILMKAKDSKKK 49- 1 Query: 392 IKEIV-EGFPELKSRVPFRNTSDYGKFLQASTNPKYLFS----EKKRKNLFSILYETKHI 44- 6 I + L R R T Y L+ S +P + EK N+++ Y+ K + Sbjct: 492 ILAYINNNLQNLIVRNVIRPTQRYADMLEFSYHPNCFSNAIEREKVLHNMWAYPYKNKKV 55- 1 Query: 447 EHFIVDNEIKDLMNGDIP-YFSMDTRGNVYNSVGTLIGNLGDTTSL---FDSITILNDER 50- 2 H+ E DL++GDIP +++ ++ ++ S G L+ + ++L + I L DE Sbjct: 552 VHY----EFSDLIDGDIPIFYNNISKTSLIASDGCLVEDFYQESALNRCLNKINDLCDED 60- 7 Query: 503 LKFTCELLEIVL 514 + LEI L Sbjct: 608 ISIQTVWLEIAL 619 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2885 A DNA sequence (GASx1891R) was identified in S. pyogenes <SEQ ID 8269> which encodes the amino acid sequence <SEQ ID 8270>. Analysis of this protein sequence reveals the following: TABLE-US-07863 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3487(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07864 >GP: AAA02867 GB: L07740 salivaricin A [Streptococcus salivarius] Identities = 46/51 (90%), Positives = 48/51 (93%) Query: 1 MSFMKNSKDILTNAIEEVSEKELMEVAGGKKGSGWFATITDDCPNSVFVCC 51 M+ MKNSKDIL NAIEEVSEKELMEVAGGK+GSGW ATITDDCPNSVFVCC Sbjct: 1 MNAMKNSKDILNNAIEEVSEKELMEVAGGKRGSGWIATITDDCPNSVFVCC 51 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2886 A DNA sequence (GASx1901R) was identified in S. pyogenes <SEQ ID 8271> which encodes the amino acid sequence <SEQ ID 8272>. Analysis of this protein sequence reveals the following: TABLE-US-07865 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.59 Transmembrane 3-19 (1-20) ----- Final Results ----- bacterial membrane --- Certainty = 0.1638(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2887 A DNA sequence (GASx1905R) was identified in S. pyogenes <SEQ ID 8273> which encodes the amino acid sequence <SEQ ID 8274>. Analysis of this protein sequence reveals the following: TABLE-US-07866 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.48 Transmembrane 38-54 (37-54) ----- Final Results ----- bacterial membrane --- Certainty = 0.1192(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2888 A DNA sequence (GASx1911R) was identified in S. pyogenes <SEQ ID 8275> which encodes the amino acid sequence <SEQ ID 8276>. Analysis of this protein sequence reveals the following: TABLE-US-07867 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -10.40 Transmembrane 27-43 (22-48) INTEGRAL Likelihood = -9.82 Transmembrane 52-68 (50-74) INTEGRAL Likelihood = -7.27 Transmembrane 113-129 (111-134) INTEGRAL Likelihood = -1.97 Transmembrane 137-153 (135-153) ----- Final Results ----- bacterial membrane --- Certainty = 0.5161(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2889 A DNA sequence (GASx1915R) was identified in S. pyogenes <SEQ ID 8277> which encodes the amino acid sequence <SEQ ID 8278>. Analysis of this protein sequence reveals the following:

TABLE-US-07868 Possible site: 31 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.77 Transmembrane 242-258 (238-262) ----- Final Results ----- bacterial membrane --- Certainty = 0.5310(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2890 A DNA sequence (GASx1918R) was identified in S. pyogenes <SEQ ID 8279> which encodes the amino acid sequence <SEQ ID 8280>. Analysis of this protein sequence reveals the following: TABLE-US-07869 Possible site: 38 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -7.32 Transmembrane 40-56 (39-60) ----- Final Results ----- bacterial membrane --- Certainty = 0.3930(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2891 A DNA sequence (GASx1923R) was identified in S. pyogenes <SEQ ID 8281> which encodes the amino acid sequence <SEQ ID 8282>. Analysis of this protein sequence reveals the following: TABLE-US-07870 Possible site: 42 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.26 Transmembrane 20-36 (13-42) ----- Final Results ----- bacterial membrane --- Certainty = 0.5904(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2892 A DNA sequence (GASx1926) was identified in S. pyogenes <SEQ ID 8283> which encodes the amino acid sequence <SEQ ID 8284>. Analysis of this protein sequence reveals the following: TABLE-US-07871 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2322(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2893 A DNA sequence (GASx1928R) was identified in S. pyogenes <SEQ ID 8285> which encodes the amino acid sequence <SEQ ID 8286>. Analysis of this protein sequence reveals the following: TABLE-US-07872 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3395(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2894 A DNA sequence (GASx1929R) was identified in S. pyogenes <SEQ ID 8287> which encodes the amino acid sequence <SEQ ID 8288>. Analysis of this protein sequence reveals the following: TABLE-US-07873 Possible site: 16 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.86 Transmembrane 17-33 (15-33) ----- Final Results ----- bacterial membrane --- Certainty = 0.1744(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2895 A DNA sequence (GASx1931R) was identified in S. pyogenes <SEQ ID 8289> which encodes the amino acid sequence <SEQ ID 8290>. Analysis of this protein sequence reveals the following: TABLE-US-07874 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0551(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2896 A DNA sequence (GASx1941R) was identified in S. pyogenes <SEQ ID 8291> which encodes the amino acid sequence <SEQ ID 8292>. Analysis of this protein sequence reveals the following: TABLE-US-07875 Possible site: 16 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2377(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2897 A DNA sequence (GASx1949) was identified in S. pyogenes <SEQ ID 8293> which encodes the amino acid sequence <SEQ ID 8294>. Analysis of this protein sequence reveals the following: TABLE-US-07876 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0262(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2898 A DNA sequence (GASx1951R) was identified in S. pyogenes <SEQ ID 8295> which encodes the amino acid sequence <SEQ ID 8296>. Analysis of this protein sequence reveals the following: TABLE-US-07877 Possible site: 45 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1330(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2899 A DNA sequence (GASx1953) was identified in S. pyogenes <SEQ ID 8297> which encodes the amino acid sequence <SEQ ID 8298>. Analysis of this protein sequence reveals the following: TABLE-US-07878 Possible site: 15 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2900 A DNA sequence (GASx1957) was identified in S. pyogenes <SEQ ID 8299> which encodes the amino acid sequence <SEQ ID 8300>. Analysis of this protein sequence reveals the following: TABLE-US-07879 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2409(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2901 A DNA sequence (GASx1969) was identified in S. pyogenes <SEQ ID 8301> which encodes the amino acid sequence <SEQ ID 8302>. Analysis of this protein sequence reveals the following: TABLE-US-07880 Possible site: 14 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.28 Transmembrane 7-23 (7-23) ----- Final Results ----- bacterial membrane --- Certainty = 0.1914(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2902 A DNA sequence (GASx1971R) was identified in S. pyogenes <SEQ ID 8303> which encodes the amino acid sequence <SEQ ID 8304>. Analysis of this protein sequence reveals the following: TABLE-US-07881 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1545(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2903 A DNA sequence (GASx1973) was identified in S. pyogenes <SEQ ID 8305> which encodes the amino acid sequence <SEQ ID 8306>. Analysis of this protein sequence reveals the following: TABLE-US-07882 Possible site: 49 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.44 Transmembrane 31-47 (31-48) ----- Final Results ----- bacterial membrane --- Certainty = 0.1977(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07883 >GP: CAB51744 GB: AJ245405 speX [Streptococcus pyogenes] Identities = 236/256 (92%), Positives = 243/256 (94%) Query: 3 MIISFESVILKHNKIITPEKRLFMKKTKLIFSFTSIFIAIISRPVFGLEVDNNSLLRNIY 62 MIISFESVILKHNKIITPEKRLFMKKTKLIFSFTSIFIAIISRPVFGLEVDNNSLLRNIY Sbjct: 1 MIISFESVILKHNKIITPEKRLFMKKTKLIFSFTSIFIAIISRPVFGLEVDNNSLLRNIY 60 Query: 63 STIVYEYSDTVIDFKTSHNLVTKKLDVRDARDFFINSEMDEYAANDFKDGDKIAMFSVPF 122- STIVYEYSD VIDFKTSHNLVTKKLDVRDARDFFINSEMDEYAANDFK GDKIA+FSVPF Sbjct: 61 STIVYEYSDIVIDFKTSHNLVTKKLDVRDARDFFINSEMDEYAANDFKTGDKIAVFSVPF 120- Query: 123 DWNYLSEGKVIAYTYGGMTPYQEEPMSKNIPVNLWINRKQIPVPYNQISTNKTTVTAQEI 18- 2 DWNYLS+GKV AYTYGG+TPYQ+ K VNLWIN KQI VPYN+ISTNKTTVTAQEI Sbjct: 121 DWNYLSKGKVTAYTYGGITPYQKLQYLKISLVNLWINGKQISVPYNEISTNKTTVTAQEI 18- 0 Query: 183 DLKVRKFLISQHQLYSSGSSYKSGKLVFHTNDNSDKYSLDLFYVGYRDKESIFKVYKDNK 24- 2 DLKVRKFLI+QHQLYSSGSSYKSG+LVFHTNDNSDKYS DLFYVGYRDKESIFKVYKDNK Sbjct: 181 DLKVRKFLIAQHQLYSSGSSYKSGRLVFHTNDNSDKYSFDLFYVGYRDKESIFKVYKDNK 24- 0 Query: 243 SFNIDKIGHLDIEIDS 258 SFNIDKIGHLDIEIDS Sbjct: 241 SFNIDKIGHLDIEIDS 256 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2904 A DNA sequence (GASx1974R) was identified in S. pyogenes <SEQ ID 8307> which encodes the amino acid sequence <SEQ ID 8308>. Analysis of this protein sequence reveals the following: TABLE-US-07884 Possible site: 53 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2022(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2905 A DNA sequence (GASx1983) was identified in S. pyogenes <SEQ ID 8309> which encodes the amino acid sequence <SEQ ID 8310>. Analysis of this protein sequence reveals the following: TABLE-US-07885 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0989(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2906 A DNA sequence (GASx1987) was identified in S-pyogenes <SEQ ID 8311> which encodes the amino acid sequence <SEQ ID 8312>. Analysis of this protein sequence reveals the following: TABLE-US-07886 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2389(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2907 A DNA sequence (GASx1988) was identified in S. pyogenes <SEQ ID 8313> which encodes the amino acid sequence <SEQ ID 8314>. Analysis of this protein sequence reveals the following: TABLE-US-07887 Possible site: 48 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5904(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07888 >GP: BAB16031 GB: AB030747 transposase [Streptococcus pyogenes] Identities = 22/24 (91%), Positives = 23/24 (95%) Query: 1 LERLFGTAKEYHNLCYTREKGKSK 24 +ERLFGTAKEYHNL YTREKGKSK Sbjct: 399 IERLFGTAKEYHNLRYTREKGKSK 422 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2908 A DNA sequence (GASx1990R) was identified in S. pyogenes <SEQ ID 8315> which encodes the amino acid sequence <SEQ ID 8316>. Analysis of this protein sequence reveals the following: TABLE-US-07889 Possible site: 32 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2909 A DNA sequence (GASx1991) was identified in S. pyogenes <SEQ ID 8317> which encodes the amino acid sequence <SEQ ID 8318>. Analysis of this protein sequence reveals the following: TABLE-US-07890 Possible site: 53 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -0.16 Transmembrane 2-18 (1-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.1065(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2910 A DNA sequence (GASx1994) was identified in S. pyogenes <SEQ ID 8319> which encodes the amino acid sequence <SEQ ID 8320>. Analysis of this protein sequence reveals the following:

TABLE-US-07891 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.44 Transmembrane 28-44 (28-44) ----- Final Results ----- bacterial membrane --- Certainty = 0.1574(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2911 A DNA sequence (GASx1996) was identified in S. pyogenes <SEQ ID 8321> which encodes the amino acid sequence <SEQ ID 8322>. Analysis of this protein sequence reveals the following: TABLE-US-07892 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1076(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2912 A DNA sequence (GASx1997R) was identified in S. pyogenes <SEQ ID 8323> which encodes the amino acid sequence <SEQ ID 8324>. Analysis of this protein sequence reveals the following: TABLE-US-07893 Possible site: 61 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.96 Transmembrane 53-69 (49-75) INTEGRAL Likelihood = -2.34 Transmembrane 24-40 (24-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.4185(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2913 A DNA sequence (GASx2007R) was identified in S. pyogenes <SEQ ID 8325> which encodes the amino acid sequence <SEQ ID 8326>. Analysis of this protein sequence reveals the following: TABLE-US-07894 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -6.64 Transmembrane 46-62 (43-65) ----- Final Results ----- bacterial membrane --- Certainty = 0.3654(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07895 >GP: AAB97959 GB: U96166 ATP-binding cassette lipoprotein [Streptococcus cristatus] Identities = 37/60 (61%), Positives = 42/60 (69%), Gaps = 1/60 (1%) Query: 59 FLTACGTKKDSKKEEVKEIKMSDIKDDAVSKKTKVVDGEEVTEYTTKDGNVIQIPAGNEE 118- FL ACG+K KE + + K D K DAV +KTK VDG+EVTEYT DGNVIQIPA EE Sbjct: 12 FLAACGSKNADNKE-ISDGKKVDFKKDAVDQKTKTVDGKEVTEYTMPDGNVIQIPADGEE 70 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2914 A DNA sequence (GASx2009) was identified in S. pyogenes <SEQ ID 8327> which encodes the amino acid sequence <SEQ ID 8328>. Analysis of this protein sequence reveals the following: TABLE-US-07896 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1246(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2915 A DNA sequence (GASx2010) was identified in S. pyogenes <SEQ ID 8329> which encodes the amino acid sequence <SEQ ID 8330>. Analysis of this protein sequence reveals the following: TABLE-US-07897 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2549(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2916 A DNA sequence (GASx2012R) was identified in S. pyogenes <SEQ ID 8331> which encodes the amino acid sequence <SEQ ID 8332>. Analysis of this protein sequence reveals the following: TABLE-US-07898 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3307(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07899 >GP: AAA27007 GB: L26141 pyrogenic exotoxin B [Streptococcus pyogenes] Identities = 40/102 (39%), Positives = 57/102 (55%), Gaps = 7/102 (6%) Query: 2 EMHFVRTEPEARRIAETFCAENTQTKTPMRVQQLSYPSDTDHSGGEL-----YIYALSPA 56 + +F R E EA+ A TF ++ K R + D + GGEL YIY +S Sbjct: 28 DQNFARNEKEAKDSAITFIQKSAAIKAGARSAE-DIKLDKVNLGGELSGSNMYIYNISTG 86 Query: 57 GFIIVSGDTRAHTILGYSFDNNLDLN-HDNVRSMIEAYQKQI 97 GF+IVSGD R+ ILGYS + D+N +N+ S +E+Y +QI Sbjct: 87 GFVIVSGDKRSPEILGYSTSGSFDVNGKENIASFMESYVEQI 128 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2917 A DNA sequence (GASx2013R) was identified in S. pyogenes <SEQ ID 8333> which encodes the amino acid sequence <SEQ ID 8334>. Analysis of this protein sequence reveals the following: TABLE-US-07900 Possible site: 22 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2918 A DNA sequence (GASx2014R) was identified in S. pyogenes <SEQ ID 8335> which encodes the amino acid sequence <SEQ ID 8336>. Analysis of this protein sequence reveals the following: TABLE-US-07901 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1392(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2919 A DNA sequence (GASx2015) was identified in S. pyogenes <SEQ ID 8337> which encodes the amino acid sequence <SEQ ID 8338>. Analysis of this protein sequence reveals the following: TABLE-US-07902 Possible site: 35 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.75 Transmembrane 18-34 (17-37) ----- Final Results ----- bacterial membrane --- Certainty = 0.1702(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2920 A DNA sequence (GASx2018) was identified in S. pyogenes <SEQ ID 8339> which encodes the amino acid sequence <SEQ ID 8340>. Analysis of this protein sequence reveals the following: TABLE-US-07903 Possible site: 29 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -5.84 Transmembrane 23-39 (22-40) ----- Final Results ----- bacterial membrane --- Certainty = 0.3336(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2921 A DNA sequence (GASx2019) was identified in S. pyogenes <SEQ ID 8341> which encodes the amino acid sequence <SEQ ID 8342>. Analysis of this protein sequence reveals the following: TABLE-US-07904 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0669(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07905 >GP: AAC98898 GB: AW023179 low temperature requirement C protein [Listeria monocytogenes] Identities = 95/144 (65%), Positives = 117/144 (80%) Query: 15 LAERGVSLEAIAELVLFLQNDYIPNLTMAECLESVEAVLAKREVQNAIITGVELDKLAEA 74 - L ERGV ++ IAELVLFLQ Y P L + C ++VE VL KREVQNA++TG++LD +AE Sbjct: 16 LIERGVEIDDIAELVLFLQQKYHPGLELDICRQNVEHVLRKREVQNAVLTGIQLDVMAEK 75 Query: 75 NQLSEPLLSILKTDQGLYGIDEILALSIVNLYGSIGFTNYGYLDKTKPGIVDKLNHKDGY 134- +L +PL +I+ D+GLYG+DEILALSIVN+YGSIGFTNYGY+DK KPGI+ KLN DG Sbjct: 76 GELVQPLQNIISADEGLYGVDEILALSIVNVYGSIGFTNYGYIDKVKPGILAKLNEHDGI 135- Query: 135 SCHTFLDDIVSAIAAAAASRIAHN 158 + HTFLDDIV AIAAAAASR+AH+ Sbjct: 136 AVHTFLDDIVGAIAAAAASRLAHS 159 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2922 A DNA sequence (GASx2030) was identified in S. pyogenes <SEQ ID 8343> which encodes the amino acid sequence <SEQ ID 8344>. Analysis of this protein sequence reveals the following: TABLE-US-07906 Possible site: 18 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0320(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2923 A DNA sequence (GASx2031) was identified in S. pyogenes <SEQ ID 8345> which encodes the amino acid sequence <SEQ ID 8346>. Analysis of this protein sequence reveals the following: TABLE-US-07907 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0583(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2924 A DNA sequence (GASx2032R) was identified in S. pyogenes <SEQ ID 8347> which encodes the amino acid sequence <SEQ ID 8348>. Analysis of this protein sequence reveals the following: TABLE-US-07908 Possible site: 53 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.76 Transmembrane 27-43 (26-43) ----- Final Results ----- bacterial membrane --- Certainty = 0.2105(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. A related GBS gene <SEQ ID 8467> and protein <SEQ ID 8468> were also identified. Analysis of this protein sequence reveals the following: TABLE-US-07909 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: -11.19 GvH: Signal Score (-7.5): -4.94 Possible site: 49 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -4.19 threshold: 0.0 INTEGRAL Likelihood = -4.19 Transmembrane 25-41 (25-42) PERIPHERAL Likelihood = 13.26 41 modified ALOM score: 1.34 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2678 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00166## SEQ ID 8468 (GBS396) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 83 (lane 9; MW 35 kDa). GBS396-GST was purified as shown in FIG. 217, lane 8. EXAMPLE 2925 A DNA sequence (GASx2034R) was identified in S. pyogenes <SEQ ID 8349> which encodes the amino acid sequence <SEQ ID 8350>. Analysis of the protein sequence reveals the following: TABLE-US-07910 Possible site: 21 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.59 Transmembrane 53-69 (53-70) ----- Final Results ----- bacterial membrane --- Certainty = 0.1235 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2926 A DNA sequence (GASx2035) was identified in S. pyogenes <SEQ ID 8351> which encodes the amino acid sequence <SEQ ID 8352>. Analysis of this protein sequence reveals the following: TABLE-US-07911 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2928 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2927 A DNA sequence (GASx2042R) was identified in S. pyogenes <SEQ ID 8353> which encodes the amino acid sequence <SEQ ID 8354>. Analysis of this protein sequence reveals the following: TABLE-US-07912 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2547 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2928 A DNA sequence (GASx2043) was identified in S. pyogenes <SEQ ID 8355> which encodes the amino acid sequence <SEQ ID 8356>. Analysis of this protein sequence reveals the following: TABLE-US-07913 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3289 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2929 A DNA sequence (GASx2049) was identified in S. pyogenes <SEQ ID 8357> which encodes the amino acid sequence <SEQ ID 8358>. Analysis of this protein sequence reveals the following:

TABLE-US-07914 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4014 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2930 A DNA sequence (GASx2052) was identified in S. pyogenes <SEQ ID 8359> which encodes the amino acid sequence <SEQ ID 8360>. Analysis of this protein sequence reveals the following: TABLE-US-07915 Possible site: 40 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2931 A DNA sequence (GASx2055R) was identified in S. pyogenes <SEQ ID 8361> which encodes the amino acid sequence <SEQ ID 8362>. Analysis of this protein sequence reveals the following: TABLE-US-07916 Possible site: 32 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3048 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07917 >GP: BAB05703 GB: AP001513 imidazolonepropionase (imidazolone-5-propionate hydrolase) [Bacillus halodurans] Identities = 203/416 (48%), Positives = 278/416 (66%), Gaps = 4/416 (0%) Query: 11 DVLLTHFNQLFCLNDPGHPLTGQEMKKATIVEDGYIAIKDGLIVALGSGEPDAELVGTQT 70 - D LL + QL + G P G+EM + ++E + I+DG + +G+ Q Sbjct: 6 DTLLVNIGQLLPMESKG-PKRGKEMSELQLLEHAALGIRDGKVAFIGTMVEADTFTANQM 64 Query: 71 IMRSYKGKIATPGIIDCHTHLVYGGSREHEFAKKLAGVSYLDILAQGGGILSTVRATRSA 130- I +GK+ TPG++D HTHL++GGSREHE A K GV YL+IL GGGIL+TV ATR+A Sbjct: 65 I--DCQGKLVTPGLVDPHTHLIFGGSREHEMALKQQGVPYLEILKNGGGILATVEATRAA 122- Query: 131 SFDNLYQKSKRLLDYMLLHGVTTVEAKSGYGLDWETEKRQLDVVAALEKDHPIDLVSTFM 19- 0 S + L K+ L+ ML +GVTT+EAKSGYGLD ETE +QL A+ + HPID+VSTF+ Sbjct: 123 SEEELITKAICHLNRMLSYGVTTIEAKSGYGLDRETEWKQLRAAKAVGEQHPIDIVSTFL 18- 2 Query: 191 AAHAIPEEYKGNPKAYLDVIIKDMLPVVKEENLAEFCDIFCEKNVFTADESRYLLSKAKE 25- 0 AHAIP ++ +P +LD + DML +KE+NLAEF DIF E VFT ++SR L KAKE Sbjct: 183 GAHAIPTSHRNDPDRFLDEMA-DMLGEIKEQNLAEFVDIFTETGVFTVEQSRTFLQKAKE 24- 1 Query: 251 MGFKLRIHADEIASIGGVDVAAELSAVSAEHLMMITDDGIAKLIGAGVIGNLLPATTFSL 31- 0 GF L++HADEI +GG ++A EL A+SA+HL+ +D GI K+ AG I LLP TTF L Sbjct: 242 RGFGLKLHADEIDPLGGAELAGELGAISADHLVGASDQGIQKMAAAGTIACLLPGTTFYL 30- 1 Query: 311 MEDTYAPARKMIDAGMAITLSTDSNPGSCPTANMQFVMQLGCFMLRLTPIEVLNAVTINA 37- 0 +DTYA AR MID G+A+T+STD NPGS PT N+Q +M + L++TP E+ +AVT+N Sbjct: 302 GKDTYARARDMIDQGLAVTISTDFNPGSSPTENLQLIMSIAALRLKMTPEEIWHAVTVNG 36- 1 Query: 371 AYSVNRQERVGSLTVGKEADIAIFDAPNIDYPFYFFATNLIHQVYKKGQLTVDRGR 426 A+++ R + G L VG+ AD+ ++DA N Y Y + N +H V+KKG++ +R R Sbjct: 362 AHAIGRGDTAGQLAVGRAADVVVWDAKNYYYVPYHYGVNHVHSVWKKGEVVYERRR 417 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2932 A DNA sequence (GASx2056) was identified in S. pyogenes <SEQ ID 8363> which encodes the amino acid sequence <SEQ ID 8364>. Analysis of this protein sequence reveals the following: TABLE-US-07918 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1847(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07919 >GP: CAB61139 GB: AL132952 predicted using Genefinder~cDNA EST yk155e6.3 comes from this gene~cDNA EST yk155e6.5 comes from this gene~cDNA EST yk156d6.5 comes from this gene~cDNA EST yk259b10.3 comes fr Identities = 302/649 (46%), Positives = 419/649 (64%), Gaps = 17/649 (2%) Query: 29 EGIRRAPDRGFRLTQAQTEIALKNALRYVPTKFHEEVIPEFLEELKTRGRIYGYRFRPKD 88 - + + AP R LTQ + +A++NALRY+P + H + EF EEL T G IYGYRF P Sbjct: 85 KNVAHAPKRPCNLTQTEKMLAVRNALRYIPKEHHVLLATEFAEELNTYGHIYGYRFMPNF 144- Query: 89 RIYGKPIDEYKGNCTAAKAMQVMIDNNLSFEIALYPYELVTYGETGSVCANWMQYCLIKK 148- ++ P+ E +C A A+ +MI NNL +A +P ELVTYG G V +NW+Q+ L+ + Sbjct: 145 DLFAPPVSEIGAHCEQASAIILMILNNLDKRVAQFPQELVTYGGNGQVFSNWIQFRLVLR 20- 4 Query: 149 YLEVMTDEQTLVVESGHPVGLFKSKPEAPRVIITNGLLVGEYDNMKDWEIAEEMGVTNYG 20- 8 YL MTD QTLV+ SGHP+GLF S P++PR+ +TNG+++ Y + ++ +GVT YG Sbjct: 205 YLYTMTDHQTLVLYSGHPLGLFPSTPDSPRMTVTNGMMIPSYSTKELYDKYFALGVTQYG 26- 4 Query: 209 QMTAGGWMYIGPQGIVHGTFNTLLNAGRLKLGVADDGDLTGKLFISSGLGGMSGAQGKAA 26- 8 QMTAG + YIGPQGIVHGT T+LNAGR ++G+ L GK+F+++GLGGMSGAQ KAA Sbjct: 265 QMTAGSFCYIGPQGIVHGTTITVLNAGR-RMGL---DSLAGKVFVTAGLGGMSGAQPKAA 32- 0 Query: 269 EIAKAVAIIAEVDQSRIKTRHSQGWISQIAESPEEALQLAQKAIDAKESTSIAYHGNIVD 32- 8 +IA + +IAE+ + + RH QGW+ ++ EE + ++ + KE+ SI Y GN+VD Sbjct: 321 KIAGCIGVIAEISDTALLKRHQQGWLDVYSKDLEEIVNWIKEYREKKEAISIGYLGNVVD 38- 0 Query: 329 LLE-YVNDKQIHVDLLSDQTSCHNVYDGGYCPVGISFDERTRLLAEDKDTFHQMVDDTLA 38- 7 L E + + V+L SDQTS HN + GG+ P G++F++ +++ D F ++V ++L Sbjct: 381 LWERLAEEPECLVELGSDQTSLHNPFLGGFYPAGLTFEQSNQMMTSDPVKFKKLVQNSLI 44- 0 Query: 388 RHFEAIKTLTENGTYFFDYGNAFMKSVYDSGITEISKNGRNDKDGFIWPSYVEDIMGPML 44- 7 R AI + G YF+DYGNAF+ +G + ++ ++DK F +PSY++DIMG + Sbjct: 441 RQIAAIDKIAAKGMYFWDYGNAFLLECQRAGANLLREDAQDDK-SFRYPSYMQDIMGD-I 49- 8 Query: 448 FDYGYGPFRWVCLSGNHDDLVATDKAAMEAIDPDR--------RYQDRDNYNWIRDAEKN 49- 9 F G+GPFRWVC SG +DL TD+ A + ID + + Q DN WI +AEKN Sbjct: 499 FSMGFGPFRWVCTSGKPEDLRLTDQTACKIIDELKDTDVPEYVKQQYLDNKKWIEEAEKN 55- 8 Query: 500 QLVVGTQARILYQDCIGRVTIALKFNELVRKGKI-GPVMIGRDHHDVSGTDSPFRETSNI 55- 8 +LVVG+QARILY D GRV +A FNELV+ GK+ ++I RDHHDVSGTDSPFRETSN+ Sbjct: 559 KLVVGSQARILYSDRAGRVALASAFNELVKSGKVSAAIVISRDHHDVSGTDSPFRETSNV 61- 8 Query: 559 KDGSNVTCDMAVQCYAGNAARGMSLVALHNGGGTGIGKAINGGFGLVLDGSERIDEIIKS 61- 8 DGS T DMAVQ G++ RG + VALHNGGG G G INGGFG+VLDGS + Sbjct: 619 YDGSAFTADMAVQNCIGDSFRGATWVALHNGGGVGWGDVINGGFGIVLDGSSDAARRAEG 67- 8 Query: 619 AIAWDTMGGVARRNWARNEHAIETAIEYNRLHAGTDHITIPYLADDDLV 667 + WD GV RR+W+ N A E AI+ +T+P AD++L+ Sbjct: 679 MLNWDVPNGVTRRSWSGNAKAQE-AIQRAEKQVDGLRVTLPVEADEELL 726 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2933 A DNA sequence (GASx2057) was identified in S. pyogenes <SEQ ID 8365> which encodes the amino acid sequence <SEQ ID 8366>. Analysis of this protein sequence reveals the following: TABLE-US-07920 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1887(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07921 >GP: AAD35925 GB: AE001751 formiminotransferase- cyclodeaminase/formiminotetrahydrofolate cyclodeaminase, putative [Thermotoga maritima] Identities = 160/296 (54%), Positives = 214/296 (72%), Gaps = 2/296 (0%) Query: 3 KIVECIPNFSEGQNQAVIDGLVATAKSIPGVTLLDYSSDASHNRSVFTLVGDDQSIQEAA 62 K++E +PNFSEG+ + V++ +VA AK V +LD+S DA HNRSV TLVG+ +++ A Sbjct: 2 KLIESVPNFSEGRRKEVVEKIVAEAKKYDRVWVLDWSMDADHNRSVITLVGEPENLINAL 61 Query: 63 FQLVKYASENIDMTKHHGEHPRMGATDVCPFVPIKDITTQECVEISKQVAERINRELGIP 122- F + K A+E ID+ H G+HPRMGA DV P VP+ + T +ECVE SK + RI ELGIP Sbjct: 62 FDMTKKAAELIDLRNHTGQHPRMGAADVIPLVPLYNTTMEECVEYSKILGRRIGEELGIP 121- Query: 123 IFLYEDSATRPERQNLAKVRKGQFEGMPEKLLEEDWAPDYGDRKIHPTAGVTAVGARMPL 18- 2 ++LYE SATRPERQNLA +RKG+FEG EK+ + W PD+G ++HPTAGVTAVGAR L Sbjct: 122 VYLYEKSATRPERQNLADIRKGEFEGFFEKIKDPLWKPDFGPDRVHPTAGVTAVGAREFL 18- 1 Query: 183 VAFNVNLDTDNIDIAHKIAKIIRGSGGGYKYCKAIGVMLEDRHIAQVSMNMVNFEKCSLY 24- 2 +AFNVNL T ++ IA KIA+ IR S GG +Y KAIGV L+ R + QVS+N+ N +K LY Sbjct: 182 IAFNVNLGTRDVKIAEKIARAIRFSSGGLRYVKAIGVDLKGRGVVQVSINITNHKKTPLY 24- 1 Query: 243 RTFETIKFEARRYGVNVIGSEVIGLAPAKALIDVAEYYLQVEDFDYHKQILENHLL 298 R FE IK EA RYGV V+GSE++GL P ++L+ YYL+ + K+++E++LL Sbjct: 242 RVFELIKMEAERYGVPVLGSEIVGLFPLESLLKTVSYYLRTD--LNAKKVIESNLL 295 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2934 A DNA sequence (GASx2058) was identified in S. pyogenes <SEQ ID 8367> which encodes the amino acid sequence <SEQ ID 8368>. Analysis of this protein sequence reveals the following: TABLE-US-07922 Possible site: 31 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2776(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07923 >GP: AAA62653 GB: L33465 methenyl tetrahydrofolate cyclohydrolase [Methylobacterium extorquens] Identities = 79/198 (39%), Positives = 112/198 (55%) Query: 7 SLTDFAKVLGSDAPAPGGGSAAALSGANGISLTKMVCELTLGKKKYADYQDIITEIHAKS 66 ++ F L S AP PGGG AAA+SGA G +L MVC LT+GKKKY + + + ++ KS Sbjct: 6 TIETFLDGLASSAPTPGGGGAAAISGAMGAALVSMVCNLTIGKKKYVEVEADLMQVLEKS 65 Query: 67 TALQASLLAAIDKDTEAFNLVSAVFDMPKETDEDKAARRTAMQKALKTAAQSPFEMMTLM 126- L+ +L I D EAF+ V + +PK TDE+KAAR +Q+ALKTA P + Sbjct: 66 EGLRRTLTGMIADDVEAFDAVMGAYGLPKNTDEEKAARAAKIQEALKTATDVPLACCRVC 125- Query: 127 VEALEITATAVGKSNTNAASDLGVAALNLKAGLQGAWLNVLINLSGIKDEDFVTDYRQKG 18- 6 E +++ K N N SD GVA L+ AGL+ A LNV +N G+ D F + ++ Sbjct: 126 REVIDLAEIVAEKGNLNVISDAGVAVLSAYAGLRSAALNVYVNAKGLDDRAFAEERLKEL 18- 5 Query: 187 QALLDKGCHLADDIYTKI 204 + LL + L + IY + Sbjct: 186 EGLLAEAGALNERIYETV 203 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2935 A DNA sequence (GASx2061) was identified in S. pyogenes <SEQ ID 8369> which encodes the amino acid sequence <SEQ ID 8370>. Analysis of this protein sequence reveals the following: TABLE-US-07924 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3924(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2936 A DNA sequence (GASx2063) was identified in S. pyogenes <SEQ ID 8371> which encodes the amino acid sequence <SEQ ID 8372>. Analysis of this protein sequence reveals the following: TABLE-US-07925 Possible site: 57 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -1.06 Transmembrane 231-247 (231-247) INTEGRAL Likelihood = -0.53 Transmembrane 2-18 (1-18) ----- Final Results ----- bacterial membrane --- Certainty = 0.1426(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07926 >GP: CAB15971 GB: Z99124 histidase [Bacillus subtilis] Identities = 236/477 (49%), Positives = 321/477 (66%), Gaps = 2/477 (0%) Query: 42 VINLDGESLTIEDVIAIARQGVACHIDDSAIEAVNASRKIVDDIVSEKRVVYGVTTGFGS 101- ++ LDG SLT DV + + ++E V SR V+ IV +++ +YG+ TGFG Sbjct: 1 MVTLDGSSLTTADVARVLFDFEEAAASEESMERVKKSRAAVERIVRDEKTIYGINTGFGK 60 Query: 102 LCNVSISPEDTVQLQENLIRTHASGFGDPLPEDAVRAIMLIRINSLVKGYSGIRLSTIEK 16- 1 +V I ED+ LQ NLI +HA G GDP PE RA++L+R N+L+KG+SG+R IE+ Sbjct: 61 FSDVLIQKEDSAALQLNLILSHACGVGDPFPECVSRAMLLLRANALLKGFSGVRAELIEQ 120- Query: 162 LLELLNKGVHPYIPEKGSLGASGDLAPLAHMVLPMLGLGKAYYKGELLSGQEALDKAGID 22- 1 LL LNK VHP IP++GSLGASGDLAPL+H+ L ++G G+ +++GE + L KAGI Sbjct: 121 LLAFLNKRVHPVIPQQGSLGASGDLAPLSHLALALIGQGEVFFEGERMPAMTGLKKAGIQ 18- 0 Query: 222 KISLAAKEGLALINGTTVLTAVGALATYDAIQLLKLSDLAGALSLEVHNGITSPFEENLH 28- 1 ++L +KEGLALINGT +TA+G +A +A +L ++ +L++E GI F+E++H Sbjct: 181 PVTLTSKEGLALINGTQAMTAMGVVAYIEAEKLAYQTERIASLTIEGLQGIIDAFDEDIH 24- 0 Query: 282 TIRPQSGQLATARNIRNLLEGSQNTTVATQSRVQDPYTLRCMPQIHGASKDSIAYVKSKV 34- 1 R Q+ A IR L S TT + RVQD Y+LRC+PQ+HGA+ ++ YVK K+ Sbjct: 241 LARGYQEQIDVAERIRFYLSDSGLTTSQGELRVQDAYSLRCIPQVHGATWQTLGYVKEKL 30- 0 Query: 342 DIEINSVTDNPIICKDG-HVISGGNFHGEPMAQPFDFLGIAISEIGNVSERRVERLVNSQ 40- 0 +IE+N+ TDNP+I DG VISGGNFHG+P+A DFL IAISE+ N++ERR+ERLVN Q Sbjct: 301 EIEMNAATDNPLIFNDGDKVISGGNFHGQPIAFAMDFLKIAISELANIAERRIERLVNPQ 36- 0 Query: 401 LSKLPSFLVKYPGLNSGFMITQYACASLASENKVLAHPASVDSIPSCENQEDFVSMGTTA 46- 0 L+ LP FL +PGL SG MI QYA ASL SENK LAHPASVDSIPS NQED VSMGT A Sbjct: 361 LNDLPPFLSPHPGLQSGAMIMQYAAASLVSENKTLAHPASVDSIPSSANQEDHVSMGTIA 42- 0 Query: 461 ARKAFEILKNSRRIVATEIMAACQALDLKPENHELGKGTKVAYDLFRKEVNFIEHDK 517 AR A++++ N+RR++A E + A QA++ + H TK + RK V I+ D+ Sbjct: 421 ARHAYQVIANTRRVIAIEAICALQAVEYRGIEH-AASYTKQLFQEMRKVVPSIQQDR 476 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2937 A DNA sequence (GASx2064) was identified in S. pyogenes <SEQ ID 8373> which encodes the amino acid sequence <SEQ ID 8374>. Analysis of this protein sequence reveals the following: TABLE-US-07927 Possible site: 44 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4483(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07928 >GP: AAG06563 GB: AE004741 probable arginase family protein [Pseudomonas aeruginosa] Identities = 99/275 (36%), Positives = 147/275 (53%), Gaps = 9/275 (3%) Query: 53 LIGFKSDKGVYINNGRVGAVESPAAIRTQLAKFPWHLGNQVMVYDVGNIDGPNRSLEQLQ 112- L+GF SD+GV N GR GA P A+R LA WH G Q +YD G+I + LE Q Sbjct: 42 LLGFASDEGVRRNQGRQGARHGPPALRRALANLAWH-GEQA-IYDAGDIVAGD-DLEAAQ 98 Query: 113 NSLSKAIKRMCDLNLKPIVLGGGHETAYGHYLGLRQSLSPSDDL---AVINMDAHFDLRP 16- 9 ++ + + + + LGGGHE AY + GL + LS + L ++N DAHFDLR Sbjct: 99 ECYAQRVADLLACGHRVVGLGGGHEIAYASFAGLARHLSRHERLPRIGILNFDAHFDLRH 158- Query: 170 YDQTGPNSGTGFRQMFDDAVADKRLFKYFVLGIQEHNNNLFLFDFVAKSKGIQFLTGQDI 22- 9 ++ +SGT FRQ+ + A F Y LGI +N LFD A+ G+++L + + Sbjct: 159 AERA--SSGTPFRQIAELCQASDWPFAYCCLGISRLSNTAALFD-QAQRLGVRYLLDRQL 21- 5 Query: 230 YQMGHQKVCRAIDRFLEGQERVYLTIDMDCFSVGAAPGVSAIQSLGVDPNLAVLVLQHIA 28- 9 ++ +D FL+ + +YLT+ +D APGVSA + GV+ + +++ Sbjct: 216 QPWNLERSEAFLDGFLQSVDHLYLTVCLDVLPAAQAPGVSAPSAHGVEMPVVEHLVRRAK 27- 5 Query: 290 ASGKLVGFDVVEVSPPHDIDNHTANLAATFIFYLV 324 ASGKL D+ E++P D D TA +AA + LV Sbjct: 276 ASGKLRLADIAELNPQLDSDQRTARIAARLVDSLV 310 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2938 A DNA sequence (GASx2065R) was identified in S. pyogenes <SEQ ID 8375> which encodes the amino acid sequence <SEQ ID 8376>. Analysis of this protein sequence reveals the following: TABLE-US-07929 Possible site: 27 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.37 Transmembrane 375-391 (375-392) ----- Final Results ----- bacterial membrane --- Certainty = 0.1150(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database:

TABLE-US-07930 >GP: CAB37582 GB: AL035569 putative regulatory protein [Streptomyces coelicolor A3(2)] Identities = 95/437 (21%), Positives = 177/437 (39%), Gaps = 28/437 (6%) Query: 271 EVGALLLIGDTGIGKRTLARQVLANQTQTFQIVTAKCFREEAMDSL--LPWRNILDGLGD 32- 8 E ALLL G+ G+GK L + A + +V E D L P+ L L Sbjct: 95 EPQALLLGGEAGVGKTRLVEEFAAAADRRGAVVALGGCVEIGADGLPFAPFSTALRALRR 154- Query: 329 LVIQNRLLTTKAWKAALKRCFP-VATIFQEDNNQPFIKDHTSLLVSFIVDILQHLAEIKA 38- 7 + + + L R P +A ++ + L +L+ +A Sbjct: 155 HLPEELAAAAAGQEEELARLLPELAEGTPVTGGGRHDEESMARLFELTARLLERVAARHT 21- 4 Query: 388 LVILIEDCHWMDEDSLTLLQRVMNQLVHYPIAFVLT-------KHLGTTPELGLCLNALM 44- 0 +V+++ED HW D + L+ ++ L + + T + P L L+ L Sbjct: 215 VVLVLEDLHWADASTRHLIAYLLRTLRTGRLVVLATYRSDDIHRRHPLRPLLAE-LDRLR 27- 3 Query: 441 SQGRLESICLEPFNRQESLVYINSQLGSQPVTAEEMEHLYQASQGNPFFLSEYTQALLRH 50- 0 + RLE L F R E I L +P +++ +++ S GN FF+ E A R Sbjct: 274 TVRRLE---LGRFTRDEVGRQIAGILAHEP-DQLQVDEIFERSDGNAFFVEELAVA-ARV 32- 8 Query: 501 EKFVPLTPAIKAKLGLKLANLSSRDDALLNYLSCCRRPIPLNTLAQLMLLPLEEVIEMVD 56- 0 LT +++ L +++ L + ++ + LA + L +++IE + Sbjct: 329 GSCTGLTDSLRDLLLVRVEALPESAQRVARIVAEGGSTVEYRLLAAVARLAEDDLIEALR 38- 8 Query: 561 NLGHYYILVEESVGEEVLISFRQRIIQLYSYDRLSLSKRRLLHGQIAKRLEDLLPILTPS 62- 0 + + IL+ G+ FR +++ D L +R L+ + A+ L D P L P+ Sbjct: 389 SAVNANILLPAPDGDG--YRFRHSLVREAVGDDLLPGERSRLNRRYAEAL-DADPTLVPA 44- 5 Query: 621 PHLLDDIAYHYQESRQVIKALEYNLNYLDATLPFQHELFPIYSKSIGSLEKSDRDHQRLM 68- 0 + +A ++ + KAL LDA++ + YS+ + LE++ L Sbjct: 446 AERVMRLASYWYHAHAPAKALP---AVLDASVEARRR--HAYSEQLRLLERA----MELW 49- 6 Query: 681 EEQFDKIRQSIADLELT 697 + D +R ++ ++ T Sbjct: 497 DSAPDDVRATLRPVDCT 513 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2939 A DNA sequence (GASx2072) was identified in S. pyogenes <SEQ ID 8377> which encodes the amino acid sequence <SEQ ID 8378>. Analysis of this protein sequence reveals the following: TABLE-US-07931 Possible site: 14 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3702(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2940 A DNA sequence (GASx2074R) was identified in S. pyogenes <SEQ ID 8379> which encodes the amino acid sequence <SEQ ID 8380>. Analysis of this protein sequence reveals the following: TABLE-US-07932 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.90 Transmembrane 21-37 (21-38) ----- Final Results ----- bacterial membrane --- Certainty = 0.1362(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2941 A DNA sequence (GASx2075R) was identified in S. pyogenes <SEQ ID 8381> which encodes the amino acid sequence <SEQ ID 8382>. Analysis of this protein sequence reveals the following: TABLE-US-07933 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3545(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2942 A DNA sequence (GASx2076R) was identified in S. pyogenes <SEQ ID 8383> which encodes the amino acid sequence <SEQ ID 8384>. Analysis of this protein sequence reveals the following: TABLE-US-07934 Possible site: 34 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2340(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07935 >GP: AAC44494 GB: U44893 orf108; unknown function [Butyrivibrio fibrisolvens] Identities = 42/75 (56%), Positives = 55/75 (73%) Query: 1 LLKGTLRFGQLKSSIGSVSQKVLTAQLRAMEADGLVHREVYAEVPPRVEYSLTETGLSLA 60 LL RF +LK+++ +SQKVLT LR+ME DG++ R VY EVPPRVEYSL+E G S+ Sbjct: 31 LLVRPWRFNELKNNLEGISQKVLTDSLRSMEEDGIITRTVYPEVPPRVEYSLSELGESMR 90 Query: 61 PVIEAMSDWGQTYQE 75 P+I+AM WG Y+E Sbjct: 91 PIIKAMEQWGTEYKE 105 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2943 A DNA sequence (GASx2097) was identified in S. pyogenes <SEQ ID 8385> which encodes the amino acid sequence <SEQ ID 8386>. Analysis of this protein sequence reveals the following: TABLE-US-07936 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.40 Transmembrane 26-42 (23-44) ----- Final Results ----- bacterial membrane --- Certainty = 0.2359(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2944 A DNA sequence (GASx2098) was identified in S. pyogenes <SEQ ID 8387> which encodes the amino acid sequence <SEQ ID 8388>. Analysis of this protein sequence reveals the following: TABLE-US-07937 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1385(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2945 A DNA sequence (GASx2100) was identified in S. pyogenes <SEQ ID 8389> which encodes the amino acid sequence <SEQ ID 8390>. Analysis of this protein sequence reveals the following: TABLE-US-07938 Possible site: 23 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2138(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07939 >GP: AAA98589 GB: L44593 ORF79; putative [Lactococcus lactis phage BK5-T] Identities = 34/62 (54%), Positives = 44/62 (70%) Query: 3 QITLKAARINAGYTLKQVAGAVGKNPQTISKYEKDSSDISLGLLQKLSSLYGVTIDNLFL 62 +I LKAAR NA ++ K+VA VGKN QTI YEKDS++I + L KL+ +Y ID +FL Sbjct: 8 KIKLKAARTNADFSAKEVAEIVGKNYQTILSYEKDSTEIPMSLAIKLAEIYDYPIDFIFL 67 Query: 63 GK 64 GK Sbjct: 68 GK 69 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2946 A DNA sequence (GASx2103) was identified in S. pyogenes <SEQ ID 8391> which encodes the amino acid sequence <SEQ ID 8392>. Analysis of this protein sequence reveals the following: TABLE-US-07940 Possible site: 39 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3316(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2947 A DNA sequence (GASx2104) was identified in S. pyogenes <SEQ ID 8393> which encodes the amino acid sequence <SEQ ID 8394>. Analysis of this protein sequence reveals the following: TABLE-US-07941 Possible site: 55 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4371(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2948 A DNA sequence (GASx2105) was identified in S. pyogenes <SEQ ID 8395> which encodes the amino acid sequence <SEQ ID 8396>. Analysis of this protein sequence reveals the following: TABLE-US-07942 Possible site: 40 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2263(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2949 A DNA sequence (GASx2106) was identified in S. pyogenes <SEQ ID 8397> which encodes the amino acid sequence <SEQ ID 8398>. Analysis of this protein sequence reveals the following: TABLE-US-07943 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.42 Transmembrane 9-25 (6-29) ----- Final Results ----- bacterial membrane --- Certainty = 0.3569(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2950 A DNA sequence (GASx2107) was identified in S. pyogenes <SEQ ID 8399> which encodes the amino acid sequence <SEQ ID 8400>. Analysis of this protein sequence reveals the following: TABLE-US-07944 Possible site: 25 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1355(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2951 A DNA sequence (GASx2108) was identified in S. pyogenes <SEQ ID 8401> which encodes the amino acid sequence <SEQ ID 8402>. Analysis of this protein sequence reveals the following: TABLE-US-07945 Possible site: 26 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3050(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2952 A DNA sequence (GASx2109) was identified in S. pyogenes <SEQ ID 8403> which encodes the amino acid sequence <SEQ ID 8404>. Analysis of this protein sequence reveals the following: TABLE-US-07946 Possible site: 13 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3628(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07947 >GP: CAB46557 GB: AJ242479 putative replication protein [Streptococcus thermophilus] Identities = 143/242 (59%), Positives = 180/242 (74%), Gaps = 2/242 (0%) Query: 1 MAIYEARGFSSYLY--PYKGPLEPFDYIAQFRPLKPPEDIDIEEYKRTQAPYCLSGKVTA 58 MAIYE+RGF + L+ +PF ++A FRP+K P+ DI ++KR APYC+SG+V Sbjct: 1 MAIYESRGFGNILHLNNSNASKDPFKFVATFRPMKVPQGEDIADFKRYHAPYCISGEVKQ 60 Query: 59 EKNGSYKRNNASLVYRDLIFLDYDEIETGVNLPKIVSQTLWEYSYIIYPTIKHTPEKPRY 118- +++G+YKRNNASL+YRDLIFLDYD++E + P+ VS L YSY+IYPTIKHT EKPRY Sbjct: 61 DEDGNYKRNNASLLYRDLIFLDYDKLEASTDFPRAVSNALNGYSYVIYPTIKHTAEKPRY 120- Query: 119 RLVMKPSDVMTEATYKQVVKEIADKIGLPFDLASLTWSQLQGLPVTTGDPEDYQRYVNHG 17- 8 RLV+KP+D M E TYK +EIADKIGLPFD +SLTWSQLQGLPVTTGDPE Y+R VN G Sbjct: 121 RLVVKPTDKMDEQTYKATAQEIADKIGLPFDDSSLTWSQLQGLPVTTGDPEKYERIVNRG 18- 0 Query: 179 LDYPVPKNGSTPNRQVVTTYTPRPRSQRSITMRVIDTLFNGFGNEGGRNVALTKFVGLLF 23- 8 YPV + +TPR +S+TMRV+DTL NGFG+EGGRN+ +T+FVGLL Sbjct: 181 RCYPVANPNTVKANHSPNYHTPRQSGDKSLTMRVVDTLLNGFGDEGGRNIEVTRFVGLLL 24- 0 Query: 239 NK 240 +K Sbjct: 241 SK 242 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2953 A DNA sequence (GASx2110) was identified in S. pyogenes <SEQ ID 8405> which encodes the amino acid sequence <SEQ ID 8406>. Analysis of this protein sequence reveals the following: TABLE-US-07948 Possible site: 28 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.5215(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07949 >GP: CAB46558 GB: AJ242479 putative DNA primase [Streptococcus thermophilus] Identities = 274/548 (50%), Positives = 363/548 (66%), Gaps = 17/548 (3%) Query: 17 DLKNLENEITEARE------NEDKYFSTFKGVRGQLIKECQEMKDEAFKIAYDGVMADSK 70 - DL LE E E+++ +ED Y TFK +R Q I ++ K+ A++ YD M + K Sbjct: 8 DLTKLEEEYNESKKEASTLFDEDGYLKTFKDIRKQFINILEQKKEIAYQKGYDLYMNNPK 67 Query: 71 HLENVKAGRLTEVQHE-------ELAKEKGQEASEKALPKTPLGVAIMLKHYLRFIRVKP 123- L + E E E AK++G++A + A PKTPL A LK Y+RFIR++P Sbjct: 68 VLLKLAKAEKDEENGELIRKTVIEDAKKEGEKAKKNATPKTPLECAEFLKKYIRFIRIRP 127- Query: 124 EAQGQKAPLYFFHPDHGVWLEDNEFLQDLISVIFPNATEKQAFDTLYKIARQSQLKEIQR 18- 3 + +G++ F G++LED+EFL DL+ I PN TE+ D LYKIA LK+ Q Sbjct: 128 KGKGRERLYTFTRQILGIYLEDDEFLHDLMVTIHPNNTERLGNDALYKIAHSVPLKDKQE 18- 7 Query: 184 EYTVIGNQLYNYKTGQFEELTPDITVTRKIKTGYNKKAKEPTIKGWKPTAWLLELFDGDA 24- 3 Y V+G +LYN +TG+F + P I VTRK++ GYN A EP I GWKPT WL LF+GD Sbjct: 188 NYVVVGGELYNNETGEFTQFDPRIIVTRKVRMGYNPDATEPIIDGWKPTVWLKGLFNGDR 24- 7 Query: 244 ELYNLAIQIIKASITGQSLQKIFWLFGEGGTGKGTFQQLLINLVGMDNVASLKITELAKS 30- 3 + Y+LAIQII+A+ITG++L+ IFWL+GEGGTGKGTFQ LL NLVG +NVAS EI + A Sbjct: 248 DSYDLAIQIIRATITGKTLENIFWLYGEGGTGKGTFQTLLENLVGSENVASFKI-DGASG 30- 6 Query: 304 RFTTSILLGKSIVIGDDIQKDAVIKDTSDIFSLATGDIMTIEDKGKRPYSIRLNMTVVQS 36- 3 +F TSIL+GK++VIGDDIQKD VIKDTS +FSLATGD + IEDKGKRPY+ R MTVVQS Sbjct: 307 KFDTSILIGKTVVIGDDIQKDVVIKDTSVVFSLATGDPIRIEDKGKRPYTTRKRMTVVQS 36- 6 Query: 364 SNGLPRMNGDKSAIDRRFRILPFTKVFKGKPNKAIRNDYINRKEVLEYLLKLAIETPITD 42- 3 SNG PRMN D+ AI+RRFR+L F+++ KGK +K I+NDY+ RKEVLEY +KLAIETP D Sbjct: 367 SNGFPRMNADQKAINRRFRVLTFSEL-KGKADKRIKNDYVGRKEVLEYFVKLAIETPFRD 42- 5 Query: 424 INPKASIEILEEHHKEMNPVIDFVSKFFTDE-LTSEFIPNSFVYHVWKGFLEYYDIKQ-I 48- 1 +NP+ SIE L+E +KEMNPV DFV +FF DE + ++PN +V+ +K + E + Sbjct: 426 VNPQKSIEFLDEAYKEMNPVADFVDRFFNDEVIKCNYVPNGYVFECFKAYCEKNQNRNYF 48- 5 Query: 482 KSERGLHKEIKSNLPEGFEAGQKVIPVGRQLHTGFYPKEDLPLFASASYANGRASPEKRK 54- 1 + R LHK+IK LP+ F + I G++ + F P + +Y NGR E ++ Sbjct: 486 LNSRTLHKQIKKILPKTFRPKEVTIKKGQKFYEEFNPHLVSNPWHFDAYDNGRNKKEDQQ 54- 5 Query: 542 KPKNERGY 549 K ERGY Sbjct: 546 DAKKERGY 553 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2954 A DNA sequence (GASx2111) was identified in S. pyogenes <SEQ ID 8407> which encodes the amino acid sequence <SEQ ID 8408>. Analysis of this protein sequence reveals the following:

TABLE-US-07950 Possible site: 41 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.0994(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2955 A DNA sequence (GASx2112) was identified in S. pyogenes <SEQ ID 8409> which encodes the amino acid sequence <SEQ ID 8410>. Analysis of this protein sequence reveals the following: TABLE-US-07951 Possible site: 54 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3058(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2956 A DNA sequence (GASx2114) was identified in S. pyogenes <SEQ ID 8411> which encodes the amino acid sequence <SEQ ID 8412>. Analysis of this protein sequence reveals the following: TABLE-US-07952 Possible site: 37 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2815(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2957 A DNA sequence (GASx2115R) was identified in S. pyogenes <SEQ ID 8413> which encodes the amino acid sequence <SEQ ID 8414>. Analysis of this protein sequence reveals the following: TABLE-US-07953 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2958 A DNA sequence (GASx2116) was identified in S. pyogenes <SEQ ID 8415> which encodes the amino acid sequence <SEQ ID 8416>. Analysis of this protein sequence reveals the following: TABLE-US-07954 Possible site: 56 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4213(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2959 A DNA sequence (GASx2117) was identified in S. pyogenes <SEQ ID 8417> which encodes the amino acid sequence <SEQ ID 8418>. Analysis of this protein sequence reveals the following: TABLE-US-07955 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3091(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2960 A DNA sequence (GASx2118) was identified in S. pyogenes <SEQ ID 8419> which encodes the amino acid sequence <SEQ ID 8420>. Analysis of this protein sequence reveals the following: TABLE-US-07956 Possible site: 41 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2961 A DNA sequence (GASx2119) was identified in S. pyogenes <SEQ ID 8421> which encodes the amino acid sequence <SEQ ID 8422>. Analysis of this protein sequence reveals the following: TABLE-US-07957 Possible site: 22 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2531(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07958 >GP: AAF63071 GB: AF158600 gp137 [Streptococcus thermophilus bacteriophage Sfi11] Identities = 41/121 (33%), Positives = 65/121 (52%), Gaps = 3/121 (2%) Query: 4 KNAIRKLKEFHRWQRIAN-SLDLTYTELYQFDIEYHPTRR--KHLEISRECALEELDAIR 60 K RKL+E+ RW+ IA+ S + T+ + F + +++ + R AL EL+AI Sbjct: 13 KRCKRKLREYPRWREIAHDSAEQKITQEFTFMPRGGGVNKPVENIAVRRVDALNELEAIE 72 Query: 61 YAINQLSKVEYRQILIECYLISEEKTQQDIMEELNGSQSWYYESKKRALLEFVEFYRDGAL 12- 1 A+N L + +YR+ILIE YL K I + + ++ + E ++L F E YRDG L Sbjct: 73 QAVNGLYRPDYRRILIEKYLAYPPKPNWQIAQSIGFERTAFQELLNNSILAFAELYRDGRL 13- 3 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2962 A DNA sequence (GASx2120) was identified in S. pyogenes <SEQ ID 8423> which encodes the amino acid sequence <SEQ ID 8424>. Analysis of this protein sequence reveals the following: TABLE-US-07959 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.2666 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2963 A DNA sequence (GASx21121) was identified in S. pyogenes <SEQ ID 8425> which encodes the amino acid sequence <SEQ ID 8426>. Analysis of this protein sequence reveals the following: TABLE-US-07960 Possible site: 30 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2964 A DNA sequence (GASx2123R) was identified in S. pyogenes <SEQ ID 8427> which encodes the amino acid sequence <SEQ ID 8428>. Analysis of this protein sequence reveals the following: TABLE-US-07961 Possible site: 21 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3441 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2965 A DNA sequence (GASx2132) was identified in S. pyogenes <SEQ ID 8429> which encodes the amino acid sequence <SEQ ID 8430>. Analysis of this protein sequence reveals the following: TABLE-US-07962 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2966 A DNA sequence (GASx2136) was identified in S. pyogenes <SEQ ID 8431> which encodes the amino acid sequence <SEQ ID 8432>. Analysis of this protein sequence reveals the following: TABLE-US-07963 Possible site: 30 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.19 Transmembrane 57-73 (54-78) ----- Final Results ----- bacterial membrane --- Certainty = 0.2275 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07964 >GP: AAB18271 GB: U74623 CadX [Staphylococcus lugdunensis] Identities = 50/110 (45%), Positives = 76/110 (68%) Query: 11 MKKDSICQVGVINQQNVTTATNYLEKEKVQKSLRILSKFTDNKQINIIFYLLAVEELCVC 70 - M ++ C V +++ V A ++LE +K +K L IL K D K++ II L+ +ELCVC Sbjct: 1 MSYENACDVICVHEDKVNNALSFLEDDKSKKLLNILEKICDEKKLKIILSLIKEDELCVC 60 Query: 71 DIACLLNLSMASASHHLRKLANQNILDTRREGKIIYYFIKDEEIRDFFNQ 120 DI+ +L +S+AS SHHLR L ++LD ++GK+ YYFIKD+EIR+FF++ Sbjct: 61 DISLILKMSVASTSHHLRLLYKNDVLDFYKKGKMAYYFIKDDEIREFFSK 110 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2967 A DNA sequence (GASx2137) was identified in S. pyogenes <SEQ ID 8433> which encodes the amino acid sequence <SEQ ID 8434>. Analysis of this protein sequence reveals the following: TABLE-US-07965 Possible site: 49 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4582 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2968 A DNA sequence (GASx2139) was identified in S. pyogenes <SEQ ID 8435> which encodes the amino acid sequence <SEQ ID 8436>. Analysis of this protein sequence reveals the following: TABLE-US-07966 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.89 Transmembrane 63-79 (54-80) ----- Final Results ----- bacterial membrane --- Certainty = 0.3357 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2969 A DNA sequence (GASx2141R) was identified in S. pyogenes <SEQ ID 8437> which encodes the amino acid sequence <SEQ ID 8438>. Analysis of this protein sequence reveals the following: TABLE-US-07967 Possible site: 19 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4663 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2970 A DNA sequence (GASx2142) was identified in S. pyogenes <SEQ ID 8439> which encodes the amino acid sequence <SEQ ID 8440>. Analysis of this protein sequence reveals the following: TABLE-US-07968 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -10.08 Transmembrane 143-159 (135-165) INTEGRAL Likelihood = -7.64 Transmembrane 53-69 (49-79) INTEGRAL Likelihood = -7.17 Transmembrane 252-268 (248-275) INTEGRAL Likelihood = -6.74 Transmembrane 186-202 (183-208) INTEGRAL Likelihood = -5.63 Transmembrane 220-236 (218-240) INTEGRAL Likelihood = -5.26 Transmembrane 116-132 (115-136) INTEGRAL Likelihood = -2.02 Transmembrane 85-101 (85-101) INTEGRAL Likelihood = -0.64 Transmembrane 165-181 (165-181) ----- Final Results ----- bacterial membrane --- Certainty = 0.5034 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07969 >GP: AAD35257 GB: AE001701 conserved hypothetical protein [Thermotoga maritima] Identities = 81/275 (29%), Positives = 137/275 (49%), Gaps = 29/275 (10%) Query: 9 FKGMIIALGFILPGVSGGVLAAILGIYERMISFLAHMRDNFIENVLFFLPVGIG---GIL 65 F G+++ + ++PGVSGG +A ++G+YE++I + ++ +PVG G G+ Sbjct: 7 FSGVLMGIANVVPGVSGGTIAVLMGVYEKLIESVNSFFHGNSRSLKVLIPVGAGVLVGVF 66 Query: 66 GIALFSFPVEFLLKHYQVSVLWGFAGAIVGTIPSLIKESTKQSQRDKADWLWLVLTFVIS 125- GIA F +E L Y V + F G I I S +K TK+ K + + FV+ Sbjct: 67 GIARF---LEIFLSKYPVPTHFFFLGLI---IVSFVK--TKEYFSIKP----VNIFFVLL 114- Query: 126 GLGLYFLNDLIG--TLPANFLTFILAGALIALGVLVPGLSPSNLLLILGLYGPMLIGFKS 18- 3 G+ L F+ G T + +L G + A ++VPG+S S +LLI G+Y +L Sbjct: 115 GMFLIFMLHFSGETTAKESMFLLVLGGFVAATAMVVPGISGSLILLIFGVYDHVLYLVSH 17- 4 Query: 184 LDLLGTFLPIAIGGVLAILAFSKSMDYALQHHHSKVYHFIIGIVLSSTLLILIPNSSSPE 24- 3 L ++G L +IG V IL K M++ L+ + Y FI G++L+S L ++P + Sbjct: 175 L-IIGELLIFSIGVVAGILVSVKIMNFLLKRFREETYSFIGGMILAS-LYEVLPKKMNTN 23- 2 Query: 244 SISYSHAGILTWLMAFVLFALGIWLGLWMSQLEEK 278 + L + + L + LG ++ +E+K Sbjct: 233 VV----------LPSVLSLVLSLTLGFFLLYIEKK 257 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2971 A DNA sequence (GASx2143R) was identified in S. pyogenes <SEQ ID 8441> which encodes the amino acid sequence <SEQ ID 8442>. Analysis of this protein sequence reveals the following: TABLE-US-07970 Possible site: 20 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3964 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07971 >GP: BAB05000 GB: AP001511 unknown conserved protein in others [Bacillus halodurans] Identities = 28/78 (35%), Positives = 37/78 (46%) Query: 44 EVDKVFIVPLRQLLFTDPVYYRLEVTPIETTDFPFDRIRNGKYYQFSQEYRSIPFYENLE 103- EVD VF VP+ + P YR+ V FP +RI N YQ S + FY Sbjct: 127 EVDHVFTVPIDHFISHPPEQYRINVHFEPGAGFPIERIANQSAYQKSTRQITESFYYYQS 18- 6 Query: 104 ETIWGMTAQFTKCLTDIL 121 IWG+TA+ + + IL Sbjct: 187 YVIWGLTAKILRHVITIL 204 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2972 A DNA sequence (GASx2144R) was identified in S. pyogenes <SEQ ID 8443> which encodes the amino acid sequence <SEQ ID 8444>. Analysis of this protein sequence reveals the following:

TABLE-US-07972 Possible site: 17 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4761 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2973 A DNA sequence (GASx2145) was identified in S. pyogenes <SEQ ID 8445> which encodes the amino acid sequence <SEQ ID 8446>. Analysis of this protein sequence reveals the following: TABLE-US-07973 Possible site: 25 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -4.09 Transmembrane 2-18 (1-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.2635 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07974 >GP: CAA49519 GB: X69895 X [Bacillus sphaericus] Identities = 40/97 (41%), Positives = 57/97 (58%), Gaps = 5/97 (5%) Query: 10 IEFLILAIVEKNDSYGYDISQTIKLVAN----IKESTLYPILKKLEKAGFLTTYSQE-HQ 64 - ++ +IL ++ + D YGY+ISQ I N IKE+TLY + ++LEK + Y + Sbjct: 11 LDSIILRLILEKDRYGYEISQEISNRTNNSFQIKEATLYAVFQRLEKKEVIEAYYGDVSD 70 Query: 65 GRKRKYYAVTSSGRAQLIFLKKEWQSYKFALDGIIEG 101 G KRKYY +TS G+A L L KEW K +D +EG Sbjct: 71 GGKRKYYRITSLGKAYLSELVKEWAEVKEIIDLFMEG 107 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2974 A DNA sequence (GASx2146) was identified in S. pyogenes <SEQ ID 8447> which encodes the amino acid sequence <SEQ ID 8448>. Analysis of this protein sequence reveals the following: TABLE-US-07975 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.75 Transmembrane 97-113 (77-143) INTEGRAL Likelihood = -6.85 Transmembrane 116-132 (114-143) INTEGRAL Likelihood = -5.68 Transmembrane 156-172 (149-175) INTEGRAL Likelihood = -5.47 Transmembrane 79-95 (77-96) ----- Final Results ----- bacterial membrane --- Certainty = 0.6901 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2975 A DNA sequence (GASx2147) was identified in S. pyogenes <SEQ ID 8449> which encodes the amino acid sequence <SEQ ID 8450>. Analysis of this protein sequence reveals the following: TABLE-US-07976 Possible site: 31 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -7.11 Transmembrane 8-24 (6-30) ----- Final Results ----- bacterial membrane --- Certainty = 0.3845 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07977 >GP: AAF04457 GB: AF078161 lacunin [Manduca sexta] Identities = 68/310 (21%), Positives = 117/310 (36%), Gaps = 12/310 (3%) Query: 55 DIDSSASTITVETGPVQRPTVTYYTHPKLIDPIVTTVTGKTLSLSQTPKDVVITGGIEIL 114- DI+ + ++ + E+ T++ T + TT T T +S T + I + Sbjct: 1004 DIEGTTASGSTESTFTDETTMSKVTEESSVAEEETTKTTITEEVSGTSESASINSDKTTM 1- 063 Query: 115 GFTLNNSRQEKNYRSIT--ITVPEKTSLNEVKASNVPHTTLSNLT--VQDMQFDGNLTLL 17- 0 ++ + IT +TV E+TS TT+S ++ + T Sbjct: 1064 TTLSEDTGKTSVSEEITTEMTVTEETSETSPTEGTSDKTTMSTVSEETESSSVTEETTTE 1- 123 Query: 171 HTKVKKATITGMLEATKSQLTNLELKADYSFSNLTDSSVE-NGTISLGNGQLTTKDTTLK 22- 9 T V+ AT E T S T + ++ S +++ E T + T T+ K Sbjct: 1124 TTVVENATDISSTEVTASDKTTMTTMSEESEKTTEEATTEITVTKEVTESSSTETATSDK 1- 183 Query: 230 AVNIQSLHPGGIE-AERTTLENVTFTVSKSKEEEENDYYDNDAIFTAHALTLKGTNTITG 28- 8 ++ S G AE +T E VT T + EE T+ +T+K T T Sbjct: 1184 TISTLSEETGKTSVAEESTTEKVTETTVTTMPEETGK------TITSEEITIKTTVTEEP 1- 237 Query: 289 GDIDVDITLTKAKAIAYRARTENGKVSLGSQLTPAKIGKESTSDVISYVAENKAATGNLT 34- 8 D+ +T K A E GK S+ + T E++++ S A T T Sbjct: 1238 TDVGSSEAITSDKTTVSTASEETGKYSVSEEETVKTTVAEASTEPSSTEAITSDKTKMST 1- 297 Query: 349 VNLNKGDITI 358 ++ G ++ Sbjct: 1298 ISEETGKTSV 1307 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2976 A DNA sequence (GASx2148R) was identified in S. pyogenes <SEQ ID 8451> which encodes the amino acid sequence <SEQ ID 8452>. Analysis of this protein sequence reveals the following: TABLE-US-07978 Possible Site: 28 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2977 A DNA sequence (GASx2160) was identified in S. pyogenes <SEQ ID 8453> which encodes the amino acid sequence <SEQ ID 8454>. Analysis of this protein sequence reveals the following: TABLE-US-07979 Possible site: 29 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1630 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2978 A DNA sequence (GASx2170R) was identified in S. pyogenes <SEQ ID 8455> which encodes the amino acid sequence <SEQ ID 8456>. Analysis of this protein sequence reveals the following: TABLE-US-07980 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -13.32 Transmembrane 181-197 (175-203) ----- Final Results ----- bacterial membrane --- Certainty = 0.6328 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2979 A DNA sequence (GASx2174) was identified in S. pyogenes <SEQ ID 8457> which encodes the amino acid sequence <SEQ ID 8458>. Analysis of this protein sequence reveals the following: TABLE-US-07981 Possible site: 28 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.39 Transmembrane 3-19 (3-19) ----- Final Results ----- bacterial membrane --- Certainty = 0.1956 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2980 A DNA sequence (GASx2181R) was identified in S. pyogenes <SEQ ID 8459> which encodes the amino acid sequence <SEQ ID 8460>. Analysis of this protein sequence reveals the following: TABLE-US-07982 Possible site: 24 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3751 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2981 A DNA sequence (GASx2185R) was identified in S. pyogenes <SEQ ID 8461> which encodes the amino acid sequence <SEQ ID 8462>. Analysis of this protein sequence reveals the following: TABLE-US-07983 Possible site: 26 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.90 Transmembrane 18-34 (18-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.1362 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has no significant homology with any sequences in the GENPEPT database. Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2982 A DNA sequence (GASx2186R) was identified in S. pyogenes <SEQ ID 8463> which encodes the amino acid sequence <SEQ ID 8464>. Analysis of this protein sequence reveals the following: TABLE-US-07984 Possible site: 61 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.4803 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07985 >GP: CAA78948 GB: Z17279 transposase [Streptococcus salivarius] Identities = 48/77 (62%), Positives = 55/77 (71%), Gaps = 1/77 (1%) Query: 1 VSMKPIDLSKMVSIRKRSKKVMKTNKKTLGKSIEERPEYINDRSEFGHWEIDLALGKKTK 60 + +K IDL + V IRK+ K T KK LGKSIEERPE IN+RS FG WEID LG KT Sbjct: 150 LEIKVIDLPRAVRIRKKFTKRPST-KKHLGKSIEERPEEINNRSRFGDWEIDSVLGGKTI 20- 8 Query: 61 SEAVMLTLVERQTRYAL 77 E +LTLVERQTRYA+ Sbjct: 209 GEPSILTLVERQTRYAV 225 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2983 A DNA sequence (GASx2187R) was identified in S. pyogenes <SEQ ID 8465> which encodes the amino acid sequence <SEQ ID 8466>. Analysis of this protein sequence reveals the following: TABLE-US-07986 Possible site: 50 >>> Seems to have no N-terminal signal sequence ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.3287 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> No corresponding DNA sequence was identified in S. agalactiae. The protein has homology with the following sequences in the GENPEPT database: TABLE-US-07987 >GP: CAA78948 GB: Z17279 transposase [Streptococcus salivarius] Identities = 48/87 (55%), Positives = 57/87 (65%) Query: 1 MNMSNINSTRKSSYSHLSATERGEIAAYLKMGKKPVEIARLLGSHRSTICREIKRGSVDQ 60 MNMS ST SY HLS ERGEI AYL +G KP EIAR LG +RSTI REI RGS+ Q Sbjct: 1 MNMSTNYSTTNQSYKHLSEAERGEIEAYLSVGLKPAEIARRLGRNRSTITREINRGSITQ 60 Query: 61 VKDKNGKQTFFNAYFADSRQRVYETNR 87 VK NG++ ++ Y+AD+ Y R Sbjct: 61 VKKVNGQKVYYQHYYADAAHNRYRHAR 87 Based on this analysis, it was predicted that this GAS-specific protein and its epitopes, could be useful antigens for vaccines or diagnostics. EXAMPLE 2984 A DNA sequence <SEQ ID 9013> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9014>. Analysis of the amino acid sequence reveals the following: TABLE-US-07988 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 10.50 GvH: Signal Score (-7.5): -5.2 Possible site: 40 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 4 value: -12.26 threshold: 0.0 INTEGRAL Likelihood = -12.26 Transmembrane 98-114 (94-116) INTEGRAL Likelihood = -8.17 Transmembrane 5-21 (1-27) INTEGRAL Likelihood = -6.95 Transmembrane 62-78 (57-80) INTEGRAL Likelihood = -5.84 Transmembrane 37-53 (30-55) PERIPHERAL Likelihood = 17.35 81 modified ALOM score: 2.95 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5904 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00167## Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2985 A DNA sequence <SEQ ID 9015> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9016>. Analysis of the amino acid sequence reveals the following: TABLE-US-07989 Lipop: Possible site: -1 Crend: 10 McG: Discrim Score: 13.20 GvH: Signal Score (-7.5): -2.08 Possible site: 34 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 10.45 threshold: 0.0 PERIPHERAL Likelihood = 10.45 36 modified ALOM score: -2.59 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00168## A related DNA sequence <SEQ ID 10507> was identified in GBS which encodes amino acid sequence <SEQ ID 10508>. SEQ ID 9016 (GBS168) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 33 (lane 9; MW 7.6 kDa) and in FIG. 34 (lane 5; MW 7.6 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 42 (lane 2; MW 32.6 kDa). Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vacc EXAMPLE 2986 A DNA sequence <SEQ ID 9017> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9018>. Analysis of the amino acid sequence reveals the following: TABLE-US-07990 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -2.85 GvH: Signal Score (-7.5): -5.7 Possible site: 21 >>> Seems to have no N-terminal signal sequence ALOM program count: 0 value: 5.25 threshold: 0.0 PERIPHERAL Likelihood = 5.25 103 modified ALOM score: -1.55 *** Reasoning Step: 3 ----- Final Results ----- bacterial cytoplasm --- Certainty = 0.1210 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00169## SEQ ID 9018 (GBS45) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 8 (lane 4; MW 18.6 kDa). The GBS45-His fusion product was purified (FIG. 97A; see also FIG. 191, lane 5) and used to immunise mice (lane 1 product; 20 .mu.g/mouse). The resulting antiserum was used for Western blot (FIG. 97B), FACS (FIG. 97C), and in the in vivo passive protection assay (Table III). These tests confirm that the protein is immunoaccessible on GBS bacteria and that it is an effective protective immunogen. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2987 A DNA sequence <SEQ ID 9019> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9020>. Analysis of the amino acid sequence reveals the following: TABLE-US-07991 Lipop: Possible site: -1 Crend: 3 McG: Discrim Score: 6.84 GvH: Signal Score (-7.5): 2.98 Possible site: 25 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 13.69 threshold: 0.0 PERIPHERAL Likelihood = 13.69 77 modified ALOM score: -3.24 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) A DNA sequence <SEQ ID 10337> was identified in GBS which encodes amino acid sequence <SEQ ID 10338>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. SEQ ID 9020 (GBS55) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 17 (lane 7; MW 11.3 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 33 (lane 5; MW 36.3 kDa). GBS55-GST was purified as shown in FIG. 197, lane 5. GBS671 was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 161 (lane 24; MW 12 kDa) and in FIG. 188 (lane 2; MW 12 kDa). Purified protein is shown in FIG. 242, lane 3. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2988 A DNA sequence <SEQ ID 9021> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9022>. Analysis of the amino acid sequence reveals the following:

TABLE-US-07992 Lipop Possible site: -1 Crend: 3 McG: Discrim Score: -14.35 GvH: Signal Score (-7.5): -2.12 Possible site: 44 >>> Seems to have no N-terminal signal sequence ALOM program count: 4 value: -13.90 threshold: 0.0 INTEGRAL Likelihood = -13.90 Transmembrane 101-117 (92-126) INTEGRAL Likelihood = -7.64 Transmembrane 130-146 (125-148) INTEGRAL Likelihood = -6.64 Transmembrane 24-40 (20-45) INTEGRAL Likelihood = -2.44 Transmembrane 55-71 (55-75) PERIPHERAL Likelihood = 17.40 2 modified ALOM score: 3.28 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6562 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 9022 (GBS215) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 175 (lane 10; MW 45 kDa). Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2989 A DNA sequence <SEQ ID 9023> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9024>. Analysis of the amino acid sequence reveals the following: TABLE-US-07993 Lipop Possible site: -1 Crend: 0 McG: Discrim Score: 11.66 GvH: Signal Score (-7.5): -5.3 Possible site: 61 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 2 value: -14.12 threshold: 0.0 INTEGRAL Likelihood = -14.12 Transmembrane 13-29 (5-35) INTEGRAL Likelihood = -8.17 Transmembrane 44-60 (39-65) PERIPHERAL Likelihood = 39.00 29 modified ALOM score: 3.32 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.6647 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 9024 (GBS217) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 85 (lane 2; MW 36.1 kDa) and in FIG. 156 (lane 1 & 3; MW 36 kDa). GBS217-GST was purified as shown in FIG. 224, lane 5-6. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2990 A DNA sequence <SEQ ID 9025> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9026>. Analysis of the amino acid sequence reveals the following: TABLE-US-07994 Lipop Possible site: -1 Crend: 10 McG: Discrim Score: 8.20 GvH: Signal Score (-7.5): -3.7 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 4 value: -9.98 threshold: 0.0 INTEGRAL Likelihood = -9.98 Transmembrane 22-38 (12-43) INTEGRAL Likelihood = -7.80 Transmembrane 61-77 (56-85) INTEGRAL Likelihood = -5.20 Transmembrane 121-137 (117-148) INTEGRAL Likelihood = -2.97 Transmembrane 99-115 (98-119) PERIPHERAL Likelihood = 10.77 5 modified ALOM score: 2.50 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4991 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> A related DNA sequence <SEQ ID 10701> was identified in GBS which encodes amino acid sequence <SEQ ID 10702>. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2991 A DNA sequence <SEQ ID 9027> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9028>. Analysis of the amino acid sequence reveals the following: TABLE-US-07995 Lipop Possible site: -1 Crend: 7 McG: Discrim Score: 10.61 GvH: Signal Score (-7.5): -4.21 Possible site: 51 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 3 value: -10.99 threshold: 0.0 INTEGRAL Likelihood = -10.99 Transmembrane 38-54 (33-61) INTEGRAL Likelihood = -8.01 Transmembrane 5-21 (1-26) INTEGRAL Likelihood = -7.01 Transmembrane 65-81 (60-87) PERIPHERAL Likelihood = 13.85 99 modified ALOM score: 2.70 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5394 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2992 A DNA sequence <SEQ ID 9029> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9030>. Analysis of the amino acid sequence reveals the following: TABLE-US-07996 Lipop Possible site: -1 Crend: 10 McG: Discrim Score: -21.39 GvH: Signal Score (-7.5): -1.85 Possible site: 57 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -8.44 threshold: 0.0 INTEGRAL Likelihood = -8.44 Transmembrane 38-54 (36-59) PERIPHERAL Likelihood = 19.10 18 modified ALOM score: 2.19 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4376 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2993 A DNA sequence <SEQ ID 9031> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9032>. Analysis of the amino acid sequence reveals the following: TABLE-US-07997 Lipop Possible site: -1 Crend: 5 McG: Discrim Score: 12.87 GvH: Signal Score (-7.5): -3.57 Possible site: 41 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 4 value: -10.30 threshold: 0.0 INTEGRAL Likelihood = -10.30 Transmembrane 69-85 (63-98) INTEGRAL Likelihood = -8.65 Transmembrane 4-20 (1-29) INTEGRAL Likelihood = -2.07 Transmembrane 96-112 (95-118) PERIPHERAL Likelihood = 9.71 113 modified ALOM score: 2.56 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5118 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00170## Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2994 A DNA sequence <SEQ ID 9033> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9034>. Analysis of the amino acid sequence reveals the following: TABLE-US-07998 Lipop Possible site: -1 Crend: 9 McG: Discrim Score: 3.25 GvH: Signal Score (-7.5): -3.39 Possible site: 59 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 4 value: -6.64 threshold: 0.0 INTEGRAL Likelihood = -6.64 Transmembrane 46-62 (43-64) INTEGRAL Likelihood = -5.15 Transmembrane 17-33 (15-34) PERIPHERAL Likelihood = 11.03 100 modified ALOM score: 1.83 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3654 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00171## SEQ ID 9034 (GBS283) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 63 (lane 8; MW 67.6 kDa). Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2995 A DNA sequence <SEQ ID 9035> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9036>. Analysis of the amino acid sequence reveals the following: TABLE-US-07999 Lipop Possible Site: -1 Crend: 2 SRCFLG: 0 McG: Length of UR: 22 Peak Value of UR: 3.86 Net Charge of CR: 2 McG: Discrim Score: 16.84 GvH: Signal Score (-7.5): -4.38 Possible site: 21 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition: calculated from 1 ALOM program count: 1 value: -12.37 threshold: 0.0 INTEGRAL Likelihood = -12.37 Transmembrane 7-23 (1-26) PERIPHERAL Likelihood = 12.84 64 modified ALOM score: 2.97 icm1 HYPID: 7 CFP: 0.595 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5946 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 9036 (GBS286) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 52 (lane 11; MW 16.4 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 59 (lane 2; MW 41.3 kDa) and in FIG. 63 (lane 9; MW 41.4 kDa). The GBS286-GST fusion product was purified (FIG. 210, lane 9; FIG. 225, lane 9) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 274), which confirmed that the protein is immunoaccessible on GBS bacteria. GBS668 was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 139 (lane 2-4; MW 43.5 kDa) and in FIG. 187 (lane 6; MW 43 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 139 (lane 6 & 7; MW 18.6 kDa) and in FIG. 179 (lane 12; MW 19 kDa). GBS668-GST was purified as shown in FIG. 237 (lane 10). GBS668-His was purified as shown in FIG. 231 (lanes 5 & 6). GBS673 was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 161 (lane 8-10; MW 17 kDa) and in FIG. 188 (lane 4; MW 17 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 162 (lane 8; MW 41.5 kDa) and in FIG. 239 (lane 7; MW 41 kDa). Purified GBS673-His is shown in FIG. 242, lane 5. Purified GBS673-GST is shown in FIG. 246, lane 2. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2996 A DNA sequence <SEQ ID 9037> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9038>. Analysis of the amino acid sequence reveals the following: TABLE-US-08000 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: -18.42 GvH: Signal Score (-7.5): -6.16 Possible site: 57 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -8.49 threshold: 0.0 INTEGRAL Likelihood = -8.49 Transmembrane 51-67 (44-95) INTEGRAL Likelihood = -3.08 Transmembrane 70-86 (68-95) PERIPHERAL Likelihood = 12.89 32 modified ALOM score: 2.20 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.4397 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> SEQ ID 9038 (GBS386) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 70 (lane 2; MW 14 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 8; MW 39.5 kDa). GBS386-GST was purified as shown in FIG. 213, lane 8. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2997 A DNA sequence <SEQ ID 9039> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9040>. Analysis of the amino acid sequence reveals the following: TABLE-US-08001 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: -15.47 GvH: Signal Score (-7.5): -6.21 Possible site: 14 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -3.61 threshold: 0.0 INTEGRAL Likelihood = -3.61 Transmembrane 94-110 (94-111) INTEGRAL Likelihood = -1.70 Transmembrane 75-91 (75-91) PERIPHERAL Likelihood = 5.94 139 modified ALOM score: 1.22 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.2444 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00172## SEQ ID 9040 (GBS388) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 70 (lane 3; MW 21 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 72 (lane 9; MW 45.6 kDa). The GBS388-GST fusion product was purified (FIG. 213, lane 10) and used to immunise mice. The resulting antiserum was used for FACS (FIG. 311), which confirmed that the protein is immunoaccessible on GBS bacteria. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2998 A DNA sequence <SEQ ID 9041> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9042>. Analysis of the amino acid sequence reveals the following: TABLE-US-08002 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: -11.81 GvH: Signal Score (-7.5): -7.49 Possible site: 25 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -5.68 threshold: 0.0 INTEGRAL Likelihood = -5.68 Transmembrane 78-94 (77-95) PERIPHERAL Likelihood = 4.61 134 modified ALOM score: 1.64 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3272 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00173## A related DNA sequence <SEQ ID 10589> was identified in GBS which encodes amino acid sequence <SEQ ID 10590>. SEQ ID 9042 (GBS408) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 76 (lane 6; MW 20.4 kDa). It was also expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 171 (lane 5; MW 45.3 kDa). GBS408-GST was purified as shown in FIG. 218, lane 9. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 2999 A DNA sequence <SEQ ID 9043> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9044>. Analysis of the amino acid sequence reveals the following: TABLE-US-08003 Lipop: Possible site: -1 Crend: 9 McG: Discrim Score: -9.62 GvH: Signal Score (-7.5): -4.84 Possible site: 61 >>> Seems to have no N-terminal signal sequence ALOM program count: 2 value: -11.09 threshold: 0.0 INTEGRAL Likelihood = -11.09 Transmembrane 45-61 (37-72) INTEGRAL Likelihood = -8.60 Transmembrane 76-92 (70-97) PERIPHERAL Likelihood = 11.62 95 modified ALOM score: 2.72 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5437 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00174## SEQ ID 9044 (GBS411) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 78 (lane 2; MW 16 kDa). Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3000 A DNA sequence <SEQ ID 9045> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9046>. Analysis of the amino acid sequence reveals the following: TABLE-US-08004 Lipop: Possible site: -1 Crend: 6 McG: Discrim Score: -17.94 GvH: Signal Score (-7.5): -4.63 Possible site: 45 >>> Seems to have no N-terminal signal sequence ALOM program count: 1 value: -6.10 threshold: 0.0 INTEGRAL Likelihood = -6.10 Transmembrane 31-47 (26-49) PERIPHERAL Likelihood = 15.33 3 modified ALOM score: 1.72 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3442 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00175## SEQ ID 9046 (GBS412) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 171 (lane 6; MW 36 kDa). Purified GBS412-GST is shown in FIG. 218, lane 10-11. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3001 A DNA sequence <SEQ ID 9047> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9048>. Analysis of the amino acid sequence reveals the following:

TABLE-US-08005 Lipop: Possible site: -1 Crend: 0 McG: Discrim Score: 3.67 GvH: Signal Score (-7.5): -3.62 Possible site: 41 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 5 value: -7.27 threshold: 0.0 INTEGRAL Likelihood = -7.27 Transmembrane 48-64 (32-68) INTEGRAL Likelihood = -6.26 Transmembrane 87-103 (85-105) INTEGRAL Likelihood = -6.21 Transmembrane 29-45 (26-46) INTEGRAL Likelihood = -3.29 Transmembrane 110-126 (109-130) INTEGRAL Likelihood = -2.87 Transmembrane 2-18 (1-18) PERIPHERAL Likelihood = 4.24 66 modified ALOM score: 1.95 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.3909 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00176## Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3002 A DNA sequence <SEQ ID 9049> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9050>. Analysis of the amino acid sequence reveals the following: TABLE-US-08006 Lipop: Possible site: -1 Crend: 2 McG: Discrim Score: 10.43 GvH: Signal Score (-7.5): -4.39 Possible site: 54 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 4 value: -10.30 threshold: 0.0 INTEGRAL Likelihood = -10.30 Transmembrane 62-78 (59-84) INTEGRAL Likelihood = -6.10 Transmembrane 4-20 (1-22) INTEGRAL Likelihood = -4.25 Transmembrane 128-144 (123-145) INTEGRAL Likelihood = -3.13 Transmembrane 88-104 (87-104) PERIPHERAL Likelihood = 2.01 109 modified ALOM score: 2.56 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5118 (Affirmative) < succ> bacterial outside --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has homology with the following sequences in the databases: ##STR00177## There is also homology to SEQ ID 7750. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vacc EXAMPLE 3003 A DNA sequence <SEQ ID 9051> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9052>. Analysis of the amino acid sequence reveals the following: TABLE-US-08007 Lipop: Possible site: -1 Crend: 7 McG: Discrim Score: 13.24 GvH: Signal Score (-7.5): -2.18 Possible site: 19 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 2.01 threshold: 0.0 PERIPHERAL Likelihood = 2.01 21 modified ALOM score: -0.90 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000 (Affirmative) < succ> bacterial membrane --- Certainty = 0.0000 (Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000 (Not Clear) < succ> The protein has no homology with any sequences in the databases. SEQ ID 9052 (GBS138) was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 19 (lane 2; MW 15 kDa) GBS672 was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 161 (lane 5-7; MW 15 kDa) and in FIG. 188 (lane 3; MW 15 kDa). Purified protein is shown in FIG. 242, lane 4. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3004 A DNA sequence <SEQ ID 9053> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9054>. Analysis of the amino acid sequence reveals the following: TABLE-US-08008 Lipop: Possible site: -1 Crend: 8 McG: Discrim Score: 18.01 GvH: Signal Score (-7.5): -2.35 Possible site: 26 >>> Seems to have a cleavable N-term signal seq. ALOM program count: 0 value: 14.80 threshold: 0.0 PERIPHERAL Likelihood = 14.80 51 modified ALOM score: -3.46 *** Reasoning Step: 3 ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 9054 (GBS143) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 23 (lane 2; MW 33.5 kDa). Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3005 A DNA sequence <SEQ ID 9055> was identified in S. agalactiae which encodes amino acid sequence <SEQ ID 9056>. Analysis of the amino acid sequence reveals the following: TABLE-US-08009 Lipop Possible site: -1 Crend: 0 McG: Discrim Score: 7.43 GvH: Signal Score (-7.5): -6.25 Possible site: 41 >>> Seems to have an uncleavable N-term signal seq ALOM program count: 1 value: -10.77 threshold: 0.0 INTEGRAL Likelihood = -10.77 Transmembrane 2-18 (1-20) PERIPHERAL Likelihood = 5.14 29 modified ALOM score: 2.65 *** Reasoning Step: 3 ----- Final Results ----- bacterial membrane --- Certainty = 0.5310(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> SEQ ID 9056 (GBS229) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 55 (lane 3; MW 35.9 kDa). GBS229-GST was purified as shown in FIG. 206, lane 5. Based on this analysis, it is predicted that this protein from S. agalactiae, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3006 A DNA sequence <SEQ ID 9183> was identified in GAS which encodes amino acid sequence <SEQ ID 9184>. Analysis of the amino acid sequence reveals the following: TABLE-US-08010 Possible site: 29 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3007 A DNA sequence <SEQ ID 9185> was identified in GAS which encodes amino acid sequence <SEQ ID 9186>. Analysis of the amino acid sequence reveals the following: TABLE-US-08011 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3008 A DNA sequence <SEQ ID 9187> was identified in GAS which encodes amino acid sequence <SEQ ID 9188>. Analysis of the amino acid sequence reveals the following: TABLE-US-08012 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.70 Transmembrane 850-866 (850-866) INTEGRAL Likelihood = -1.22 Transmembrane 15-31 (15-31) ----- Final Results ----- bacterial membrane --- Certainty = 0.1680(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3009 A DNA sequence <SEQ ID 9189> was identified in GAS which encodes amino acid sequence <SEQ ID 9190>. Analysis of the amino acid sequence reveals the following: TABLE-US-08013 LPXTG motif: 259-263 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.93 Transmembrane 270-286 (268-288) ----- Final Results ----- bacterial membrane --- Certainty = 0.2572(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3010 A DNA sequence <SEQ ID 9191> was identified in GAS which encodes amino acid sequence <SEQ ID 9192>. Analysis of the amino acid sequence reveals the following: TABLE-US-08014 Possible site: 21 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3011 A DNA sequence <SEQ ID 9193> was identified in GAS which encodes amino acid sequence <SEQ ID 9194>. Analysis of the amino acid sequence reveals the following: TABLE-US-08015 Possible site: 29 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3012 A DNA sequence <SEQ ID 9195> was identified in GAS which encodes amino acid sequence <SEQ ID 9196>. Analysis of the amino acid sequence reveals the following: TABLE-US-08016 Possible site: 34 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3013 A DNA sequence <SEQ ID 9197> was identified in GAS which encodes amino acid sequence <SEQ ID 9198>. Analysis of the amino acid sequence reveals the following: TABLE-US-08017 Possible site: 13 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.50 Transmembrane 346-362 (343-366) INTEGRAL Likelihood = -2.97 Transmembrane 177-193 (176-195) ----- Final Results ----- bacterial membrane --- Certainty = 0.2402(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3014 A DNA sequence <SEQ ID 9199> was identified in GAS which encodes amino acid sequence <SEQ ID 9200>. Analysis of the amino acid sequence reveals the following: TABLE-US-08018 Possible site: 19 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.33 Transmembrane 24-40 (24-40) ----- Final Results ----- bacterial membrane --- Certainty = 0.1532(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3015 A DNA sequence <SEQ ID 9201> was identified in GAS which encodes amino acid sequence <SEQ ID 9202>. Analysis of the amino acid sequence reveals the following: TABLE-US-08019 Possible site: 33 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -6.00 Transmembrane 194-210 (192-214) ----- Final Results ----- bacterial membrane --- Certainty = 0.3399(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 183-187 Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3016 A DNA sequence <SEQ ID 9203> was identified in GAS which encodes amino acid sequence <SEQ ID 9204>. Analysis of the amino acid sequence reveals the following: TABLE-US-08020 Possible site: 32 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -11.25 Transmembrane 9-25 (4-28) ----- Final Results ----- bacterial membrane --- Certainty = 0.5501(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3017 A DNA sequence <SEQ ID 9205> was identified in GAS which encodes amino acid sequence <SEQ ID 9206>. Analysis of the amino acid sequence reveals the following: TABLE-US-08021 Possible site: 37 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -3.03 Transmembrane 462-478 (460-479) INTEGRAL Likelihood = -0.90 Transmembrane 18-34 (18-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.2211(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> LPXTG motif: 450-454 Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3018 A DNA sequence <SEQ ID 9207> was identified in GAS which encodes amino acid sequence <SEQ ID 9208>. Analysis of the amino acid sequence reveals the following: TABLE-US-08022 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.60 Transmembrane 15-31 (12-32) ----- Final Results ----- bacterial membrane --- Certainty = 0.2041(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3019 A DNA sequence <SEQ ID 9209> was identified in GAS which encodes amino acid sequence <SEQ ID 9210>. Analysis of the amino acid sequence reveals the following: TABLE-US-08023 Possible site: 28 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 16-32 (16-32) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3020 A DNA sequence <SEQ ID 9211> was identified in GAS which encodes amino acid sequence <SEQ ID 9212>. Analysis of the amino acid sequence reveals the following: TABLE-US-08024 Possible cleavage site: 24 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.300(Affirmative) < succ> bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3021 A DNA sequence <SEQ ID 9213> was identified in GAS which encodes amino acid sequence <SEQ ID 9214>. Analysis of the amino acid sequence reveals the following: TABLE-US-08025 Possible cleavage site: 23 >>> May be a lipoprotein ----- Final Results ----- bacterial membrane --- Certainty = 0.000(Not Clear) < succ> bacterial outside --- Certainty = 0.000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3022 A DNA sequence <SEQ ID 9215> was identified in GAS which encodes amino acid sequence <SEQ ID 9216>. Analysis of the amino acid sequence reveals the following:

TABLE-US-08026 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -2.76 Transmembrane 3-19 (2-20) ----- Final Results ----- bacterial membrane --- Certainty = 0.2105(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> RGD motif: 396-398 Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3023 A DNA sequence <SEQ ID 9217> was identified in GAS which encodes amino acid sequence <SEQ ID 9218>. Analysis of the amino acid sequence reveals the following: TABLE-US-08027 Possible site: 18 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.80 Transmembrane 251-267 (251-267) INTEGRAL Likelihood = -0.75 Transmembrane 179-195 (179-195) ----- Final Results ----- bacterial membrane --- Certainty = 0.1319(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3024 A DNA sequence <SEQ ID 9219> was identified in GAS which encodes amino acid sequence <SEQ ID 9220>. Analysis of the amino acid sequence reveals the following: TABLE-US-08028 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.22 Transmembrane 52-68 (51-68) ----- Final Results ----- bacterial membrane --- Certainty = 0.1489(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3025 A DNA sequence <SEQ ID 9221> was identified in GAS which encodes amino acid sequence <SEQ ID 9222>. Analysis of the amino acid sequence reveals the following: TABLE-US-08029 Possible site: 52 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -12.58 Transmembrane 39-55 (32-86) INTEGRAL Likelihood = -9.55 Transmembrane 60-76 (56-86) ----- Final Results ----- bacterial membrane --- Certainty = 0.6031(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3026 A DNA sequence <SEQ ID 9223> was identified in GAS which encodes amino acid sequence <SEQ ID 9224>. Analysis of the amino acid sequence reveals the following: TABLE-US-08030 Possible site: 18 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3027 A DNA sequence <SEQ ID 9225> was identified in GAS which encodes amino acid sequence <SEQ ID 9226>. Analysis of the amino acid sequence reveals the following: TABLE-US-08031 Possible site: 26 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3028 A DNA sequence <SEQ ID 9227> was identified in GAS which encodes amino acid sequence <SEQ ID 9228>. Analysis of the amino acid sequence reveals the following: TABLE-US-08032 Possible site: 33 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -8.44 Transmembrane 18-34 (13-40) INTEGRAL Likelihood = -7.86 Transmembrane 59-75 (54-79) ----- Final Results ----- bacterial membrane --- Certainty = 0.4376(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3029 A DNA sequence <SEQ ID 9229> was identified in GAS which encodes amino acid sequence <SEQ ID 9230>. Analysis of the amino acid sequence reveals the following: TABLE-US-08033 Possible site: 27 >>> Seems to have a cleavable N-term signal seq. ----- Final Results ----- bacterial outside --- Certainty = 0.3000(Affirmative) < succ> bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3030 A DNA sequence <SEQ ID 9231> was identified in GAS which encodes amino acid sequence <SEQ ID 9232>. Analysis of the amino acid sequence reveals the following: TABLE-US-08034 Possible site: 24 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3031 A DNA sequence <SEQ ID 9233> was identified in GAS which encodes amino acid sequence <SEQ ID 9234>. Analysis of the amino acid sequence reveals the following: TABLE-US-08035 Possible site: 49 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.87 Transmembrane 58-74 (53-81) ----- Final Results ----- bacterial membrane --- Certainty = 0.4949(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3032 A DNA sequence <SEQ ID 9235> was identified in GAS which encodes amino acid sequence <SEQ ID 9236>. Analysis of the amino acid sequence reveals the following: TABLE-US-08036 Possible site: 16 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.06 Transmembrane 92-108 (92-108) ----- Final Results ----- bacterial membrane --- Certainty = 0.1022(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3033 A DNA sequence <SEQ ID 9237> was identified in GAS which encodes amino acid sequence <SEQ ID 9238>. Analysis of the amino acid sequence reveals the following: TABLE-US-08037 Possible site: 40 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.38 Transmembrane 18-34 (18-34) ----- Final Results ----- bacterial membrane --- Certainty = 0.1553(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3034 A DNA sequence <SEQ ID 9239> was identified in GAS which encodes amino acid sequence <SEQ ID 9240>. Analysis of the amino acid sequence reveals the following: TABLE-US-08038 Possible site: 19 >>> Seems to have an uncleavable N-term signal seq ----- Final Results ----- bacterial membrane --- Certainty = 0.0000(Not Clear) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3035 A DNA sequence <SEQ ID 9241> was identified in GAS which encodes amino acid sequence <SEQ ID 9242>. Analysis of the amino acid sequence reveals the following: TABLE-US-08039 Possible site: 57 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.01 Transmembrane 155-171 (154-171) ----- Final Results ----- bacterial membrane --- Certainty = 0.1404(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3036 A DNA sequence <SEQ ID 9243> was identified in GAS which encodes amino acid sequence <SEQ ID 9244>. Analysis of the amino acid sequence reveals the following: TABLE-US-08040 Possible site: 28 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -4.25 Transmembrane 113-129 (111-131) ----- Final Results ----- bacterial membrane --- Certainty = 0.2699(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3037 A DNA sequence <SEQ ID 9245> was identified in GAS which encodes amino acid sequence <SEQ ID 9246>. Analysis of the amino acid sequence reveals the following: TABLE-US-08041 Possible site: 56 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -0.69 Transmembrane 110-126 (110-126) ----- Final Results ----- bacterial membrane --- Certainty = 0.1277(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3038 A DNA sequence <SEQ ID 9247> was identified in GAS which encodes amino acid sequence <SEQ ID 9248>. Analysis of the amino acid sequence reveals the following: TABLE-US-08042 Possible site: 58 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -1.28 Transmembrane 130-146 (128-146) ----- Final Results ----- bacterial membrane --- Certainty = 0.1510(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3039 A DNA sequence <SEQ ID 9249> was identified in GAS which encodes amino acid sequence <SEQ ID 9250>. Analysis of the amino acid sequence reveals the following: TABLE-US-08043 Possible site: 39 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -4.57 Transmembrane 74-90 (72-92) INTEGRAL Likelihood = -3.13 Transmembrane 169-185 (166-185) INTEGRAL Likelihood = -3.13 Transmembrane 28-44 (27-44) ----- Final Results ----- bacterial membrane --- Certainty = 0.2826(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3040 A DNA sequence <SEQ ID 9251> was identified in GAS which encodes amino acid sequence <SEQ ID 9252>. Analysis of the amino acid sequence reveals the following: TABLE-US-08044 Possible cleavage site: 56 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -12.21 Transmembrane 93-109 (87-114) INTEGRAL Likelihood = -8.65 Transmembrane 227-243 (226-243) ----- Final Results ----- bacterial membrane --- Certainty = 0.588(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3041 A DNA sequence <SEQ ID 9253> was identified in GAS which encodes amino acid sequence <SEQ ID 9254>. Analysis of the amino acid sequence reveals the following: TABLE-US-08045 Possible site: 45 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -6.53 Transmembrane 73-89 (70-94) INTEGRAL Likelihood = -4.41 Transmembrane 32-48 (30-51) INTEGRAL Likelihood = -2.55 Transmembrane 10-26 (10-26) INTEGRAL Likelihood = -2.39 Transmembrane 106-122 (104-123) INTEGRAL Likelihood = -1.75 Transmembrane 153-169 (152-169) ----- Final Results ----- bacterial membrane --- Certainty = 0.3612(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3042 A DNA sequence <SEQ ID 9255> was identified in GAS which encodes amino acid sequence <SEQ ID 9256>. Analysis of the amino acid sequence reveals the following: TABLE-US-08046 Possible site: 44 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.68 Transmembrane 25-41 (15-46) INTEGRAL Likelihood = -9.24 Transmembrane 255-271 (248-276) INTEGRAL Likelihood = -7.59 Transmembrane 82-98 (79-100) INTEGRAL Likelihood = -4.30 Transmembrane 115-131 (113-135) INTEGRAL Likelihood = -0.11 Transmembrane 148-164 (148-164) ----- Final Results ----- bacterial membrane --- Certainty = 0.5670(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3043 A DNA sequence <SEQ ID 9257> was identified in GAS which encodes amino acid sequence <SEQ ID 9258>. Analysis of the amino acid sequence reveals the following: TABLE-US-08047 Possible site: 51 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.04 Transmembrane 137-153 (126-160) INTEGRAL Likelihood = -10.56 Transmembrane 36-52 (29-58) INTEGRAL Likelihood = -10.08 Transmembrane 407-423 (399-426) INTEGRAL Likelihood = -4.94 Transmembrane 230-246 (228-250) INTEGRAL Likelihood = -4.83 Transmembrane 79-95 (77-98) INTEGRAL Likelihood = -4.35 Transmembrane 202-218 (201-220) INTEGRAL Likelihood = -1.12 Transmembrane 293-309 (293-309) ----- Final Results ----- bacterial membrane --- Certainty = 0.5416(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3044 A DNA sequence <SEQ ID 9259> was identified in GAS which encodes amino acid sequence <SEQ ID 9260>. Analysis of the amino acid sequence reveals the following: TABLE-US-08048 Possible site: 31 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -2.76 Transmembrane 137-153 (137-154) ----- Final Results ----- bacterial membrane --- Certainty = 0.2105(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3045 A DNA sequence <SEQ ID 9261> was identified in GAS which encodes amino acid sequence <SEQ ID 9262>. Analysis of the amino acid sequence reveals the following: TABLE-US-08049 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.91 Transmembrane 238-254 (236-264) INTEGRAL Likelihood = -6.16 Transmembrane 69-85 (65-89) INTEGRAL Likelihood = -6.00 Transmembrane 136-152 (134-155) INTEGRAL Likelihood = -4.73 Transmembrane 29-45 (21-48) INTEGRAL Likelihood = -2.97 Transmembrane 194-210 (193-220) ----- Final Results ----- bacterial membrane --- Certainty = 0.4163(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3046 A DNA sequence <SEQ ID 9263> was identified in GAS which encodes amino acid sequence <SEQ ID 9264>. Analysis of the amino acid sequence reveals the following:

TABLE-US-08050 Possible site: 39 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -9.87 Transmembrane 574-590 (568-601) INTEGRAL Likelihood = -9.18 Transmembrane 243-259 (238-262) INTEGRAL Likelihood = -7.11 Transmembrane 66-82 (65-87) INTEGRAL Likelihood = -1.28 Transmembrane 270-286 (270-287) ----- Final Results ----- bacterial membrane --- Certainty = 0.4949(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3047 A DNA sequence <SEQ ID 9265> was identified in GAS which encodes amino acid sequence <SEQ ID 9266>. Analysis of the amino acid sequence reveals the following: TABLE-US-08051 Possible site: 33 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -7.91 Transmembrane 98-114 (92-124) INTEGRAL Likelihood = -6.21 Transmembrane 19-35 (14-37) INTEGRAL Likelihood = -5.36 Transmembrane 170-186 (169-189) INTEGRAL Likelihood = -5.15 Transmembrane 147-163 (136-167) INTEGRAL Likelihood = -1.12 Transmembrane 77-93 (77-93) ----- Final Results ----- bacterial membrane --- Certainty = 0.4163(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3048 A DNA sequence <SEQ ID 9267> was identified in GAS which encodes amino acid sequence <SEQ ID 9268>. Analysis of the amino acid sequence reveals the following: TABLE-US-08052 Possible site: 47 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -11.94 Transmembrane 27-43 (19-51) INTEGRAL Likelihood = -4.83 Transmembrane 152-168 (151-171) INTEGRAL Likelihood = -4.09 Transmembrane 277-293 (276-294) INTEGRAL Likelihood = -3.82 Transmembrane 195-211 (193-217) INTEGRAL Likelihood = -2.50 Transmembrane 120-136 (120-137) INTEGRAL Likelihood = -0.64 Transmembrane 81-97 (81-98) ----- Final Results ----- bacterial membrane --- Certainty = 0.5776(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3049 A DNA sequence <SEQ ID 9269> was identified in GAS which encodes amino acid sequence <SEQ ID 9270>. Analysis of the amino acid sequence reveals the following: TABLE-US-08053 Possible site: 36 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -8.49 Transmembrane 27-43 (14-50) INTEGRAL Likelihood = -8.17 Transmembrane 58-74 (52-79) INTEGRAL Likelihood = -7.38 Transmembrane 165-181 (161-193) INTEGRAL Likelihood = -3.66 Transmembrane 247-263 (246-270) INTEGRAL Likelihood = -1.54 Transmembrane 134-150 (134-150) ----- Final Results ----- bacterial membrane --- Certainty = 0.440(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3050 A DNA sequence <SEQ ID 9271> was identified in GAS which encodes amino acid sequence <SEQ ID 9272>. Analysis of the amino acid sequence reveals the following: TABLE-US-08054 Possible site: 55 >>> Seems to have no N-terminal signal sequence INTEGRAL Likelihood = -14.75 Transmembrane 389-405 (377-413) INTEGRAL Likelihood = -8.44 Transmembrane 31-47 (29-54) INTEGRAL Likelihood = -7.17 Transmembrane 181-197 (179-205) INTEGRAL Likelihood = -7.01 Transmembrane 339-355 (326-360) INTEGRAL Likelihood = -6.58 Transmembrane 105-121 (102-124) INTEGRAL Likelihood = -5.36 Transmembrane 225-241 (222-244) INTEGRAL Likelihood = -0.43 Transmembrane 139-155 (139-155) INTEGRAL Likelihood = -0.16 Transmembrane 283-299 (282-300) ----- Final Results ----- bacterial membrane --- Certainty = 0.6901(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3051 A DNA sequence <SEQ ID 9273> was identified in GAS which encodes amino acid sequence <SEQ ID 9274>. Analysis of the amino acid sequence reveals the following: TABLE-US-08055 Possible cleavage site: 25 >>> Seems to have a cleavable N-term signal seq. INTEGRAL Likelihood = -5.31 Transmembrane 155-171 (154-174) INTEGRAL Likelihood = -3.50 Transmembrane 111-127 (110-128) INTEGRAL Likelihood = -2.07 Transmembrane 80-96 (78-96) INTEGRAL Likelihood = -0.90 Transmembrane 57-73 (57-74) ----- Final Results ----- bacterial membrane --- Certainty = 0.312(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3052 A DNA sequence <SEQ ID 9275> was identified in GAS which encodes amino acid sequence <SEQ ID 9276>. Analysis of the amino acid sequence reveals the following: TABLE-US-08056 Possible site: 27 >>> Seems to have an uncleavable N-term signal seq INTEGRAL Likelihood = -3.93 Transmembrane 463-479 (461-480) ----- Final Results ----- bacterial membrane --- Certainty = 0.2572(Affirmative) < succ> bacterial outside --- Certainty = 0.0000(Not Clear) < succ> bacterial cytoplasm --- Certainty = 0.0000(Not Clear) < succ> Based on this analysis, it is predicted that this GAS protein, and its epitopes, could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3053 A DNA sequence <SEQ ID 8741> was identified in GBS which encodes amino acid sequence <SEQ ID 8742>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3054 A DNA sequence <SEQ ID 8685> was identified in GBS which encodes amino acid sequence <SEQ ID 8686>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3055 A DNA sequence <SEQ ID 10303> was identified in GBS which encodes amino acid sequence <SEQ ID 10304>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3056 A DNA sequence <SEQ ID 10305> was identified in GBS which encodes amino acid sequence <SEQ ID 10306>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3057 A DNA sequence <SEQ ID 10307> was identified in GBS which encodes amino acid sequence <SEQ ID 10308>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3058 A DNA sequence <SEQ ID 10309> was identified in GBS which encodes amino acid sequence <SEQ ID 10310>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3059 A DNA sequence <SEQ ID 10311> was identified in GBS which encodes amino acid sequence <SEQ ID 10312>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3060 A DNA sequence <SEQ ID 10313> was identified in GBS which encodes amino acid sequence <SEQ ID 10314>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3061 A DNA sequence <SEQ ID 10315> was identified in GBS which encodes amino acid sequence <SEQ ID 10316>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3062 A DNA sequence <SEQ ID 10317> was identified in GBS which encodes amino acid sequence <SEQ ID 10318>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3063 A repeated DNA sequence <SEQ ID 10319> was identified in GBS which encodes amino acid sequence <SEQ ID 10320>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3064 A DNA sequence <SEQ ID 10321> was identified in GBS which encodes amino acid sequence <SEQ ID 10322>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3065 A DNA sequence <SEQ ID 10323> was identified in GBS which encodes amino acid sequence <SEQ ID 10324>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3066 A DNA sequence <SEQ ID 10325> was identified in GBS which encodes amino acid sequence <SEQ ID 10326>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3067 A DNA sequence <SEQ ID 10327> was identified in GBS which encodes amino acid sequence <SEQ ID 10328>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3068 A DNA sequence <SEQ ID 10329> was identified in GBS which encodes amino acid sequence <SEQ ID 10330>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3069 A DNA sequence <SEQ ID 10331> was identified in GBS which encodes amino acid sequence <SEQ ID 10332>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3070 A DNA sequence <SEQ ID 10333> was identified in GBS which encodes amino acid sequence <SEQ ID 10334>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3071 A DNA sequence <SEQ ID 10335> was identified in GBS which encodes amino acid sequence <SEQ ID 10336>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3072 A DNA sequence <SEQ ID 10339> was identified in GBS which encodes amino acid sequence <SEQ ID 10340>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3073 A DNA sequence <SEQ ID 10341> was identified in GBS which encodes amino acid sequence <SEQ ID 10342>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3074 A DNA sequence <SEQ ID 10343> was identified in GBS which encodes amino acid sequence <SEQ ID 10344>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3075 A DNA sequence <SEQ ID 10345> was identified in GBS which encodes amino acid sequence <SEQ ID 10346>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3076 A DNA sequence <SEQ ID 10347> was identified in GBS which encodes amino acid sequence <SEQ ID 10348>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3077 A DNA sequence <SEQ ID 10349> was identified in GBS which encodes amino acid sequence <SEQ ID 10350>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3078 A DNA sequence <SEQ ID 10351> was identified in GBS which encodes amino acid sequence <SEQ ID 10352>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3079 A DNA sequence <SEQ ID 10353> was identified in GBS which encodes amino acid sequence <SEQ ID 10354>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3080 A DNA sequence <SEQ ID 10355> was identified in GBS which encodes amino acid sequence <SEQ ID 10356>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3081 A DNA sequence <SEQ ID 10357> was identified in GBS which encodes amino acid sequence <SEQ ID 10358>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3082 A DNA sequence <SEQ ID 10359> was identified in GBS which encodes amino acid sequence <SEQ ID 10360>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3083 A DNA sequence <SEQ ID 10361> was identified in GBS which encodes amino acid sequence <SEQ ID 10362>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3084 A DNA sequence <SEQ ID 10363> was identified in GBS which encodes amino acid sequence <SEQ ID 10364>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3085 A DNA sequence <SEQ ID 10365> was identified in GBS which encodes amino acid sequence <SEQ ID 10366>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3086 A DNA sequence <SEQ ID 10367> was identified in GBS which encodes amino acid sequence <SEQ ID 10368>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3087 A DNA sequence <SEQ ID 10369> was identified in GBS which encodes amino acid sequence <SEQ ID 10370>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3088 A DNA sequence <SEQ ID 10371> was identified in GBS which encodes amino acid sequence <SEQ ID 10372>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3089 A DNA sequence <SEQ ID 10373> was identified in GBS which encodes amino acid sequence <SEQ ID 10374>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3090 A DNA sequence <SEQ ID 10375> was identified in GBS which encodes amino acid sequence <SEQ ID 10376>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3091 A DNA sequence <SEQ ID 10377> was identified in GBS which encodes amino acid sequence <SEQ ID 10378>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3092 A DNA sequence <SEQ ID 10379> was identified in GBS which encodes amino acid sequence <SEQ ID 10380>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3093 A DNA sequence <SEQ ID 10381> was identified in GBS which encodes amino acid sequence <SEQ ID 10382>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3094 A DNA sequence <SEQ ID 10383> was identified in GBS which encodes amino acid sequence <SEQ ID 10384>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3095 A DNA sequence <SEQ ID 10385> was identified in GBS which encodes amino acid sequence <SEQ ID 10386>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3096 A DNA sequence <SEQ ID 10387> was identified in GBS which encodes amino acid sequence <SEQ ID 10388>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3097 A DNA sequence <SEQ ID 10389> was identified in GBS which encodes amino acid sequence <SEQ ID 10390>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3098 A DNA sequence <SEQ ID 10391> was identified in GBS which encodes amino acid sequence <SEQ ID 10392>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3099 A DNA sequence <SEQ ID 10393> was identified in GBS which encodes amino acid sequence <SEQ ID 10394>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3100 A DNA sequence <SEQ ID 10395> was identified in GBS which encodes amino acid sequence <SEQ ID 10396>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3101 A DNA sequence <SEQ ID 10397> was identified in GBS which encodes amino acid sequence <SEQ ID 10398>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3102 A DNA sequence <SEQ ID 10399> was identified in GBS which encodes amino acid sequence <SEQ ID 10400>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3103 A DNA sequence <SEQ ID 10401> was identified in GBS which encodes amino acid sequence <SEQ ID 10402>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3104 A DNA sequence <SEQ ID 10403> was identified in GBS which encodes amino acid sequence <SEQ ID 10404>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3105 A DNA sequence <SEQ ID 10405> was identified in GBS which encodes amino acid sequence <SEQ ID 10406>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3106 A DNA sequence <SEQ ID 10407> was identified in GBS which encodes amino acid sequence <SEQ ID 10408>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3107 A DNA sequence <SEQ ID 10409> was identified in GBS which encodes amino acid sequence <SEQ ID 10410>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3108 A DNA sequence <SEQ ID 10411> was identified in GBS which encodes amino acid sequence <SEQ ID 10412>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3109 A DNA sequence <SEQ ID 10413> was identified in GBS which encodes amino acid sequence <SEQ ID 10414>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3110 A DNA sequence <SEQ ID 10415> was identified in GBS which encodes amino acid sequence <SEQ ID 10416>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3111 A DNA sequence <SEQ ID 10417> was identified in GBS which encodes amino acid sequence <SEQ ID 10418>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3112 A DNA sequence <SEQ ID 10419> was identified in GBS which encodes amino acid sequence <SEQ ID 10420>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3113 A DNA sequence <SEQ ID 10421> was identified in GBS which encodes amino acid sequence <SEQ ID 10422>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3114 A DNA sequence <SEQ ID 10423> was identified in GBS which encodes amino acid sequence <SEQ ID 10424>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics.

EXAMPLE 3115 A DNA sequence <SEQ ID 10425> was identified in GBS which encodes amino acid sequence <SEQ ID 10426>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3116 A DNA sequence <SEQ ID 10427> was identified in GBS which encodes amino acid sequence <SEQ ID 10428>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3117 A DNA sequence <SEQ ID 10429> was identified in GBS which encodes amino acid sequence <SEQ ID 10430>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3118 A DNA sequence <SEQ ID 10431> was identified in GBS which encodes amino acid sequence <SEQ ID 10432>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3119 A DNA sequence <SEQ ID 10433> was identified in GBS which encodes amino acid sequence <SEQ ID 10434>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3120 A DNA sequence <SEQ ID 10435> was identified in GBS which encodes amino acid sequence <SEQ ID 10436>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3121 A DNA sequence <SEQ ID 10437> was identified in GBS which encodes amino acid sequence <SEQ ID 10438>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3122 A DNA sequence <SEQ ID 10441> was identified in GBS which encodes amino acid sequence <SEQ ID 10442>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3123 A DNA sequence <SEQ ID 10443> was identified in GBS which encodes amino acid sequence <SEQ ID 10444>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3124 A DNA sequence <SEQ ID 10445> was identified in GBS which encodes amino acid sequence <SEQ ID 10446>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3125 A DNA sequence <SEQ ID 10447> was identified in GBS which encodes amino acid sequence <SEQ ID 10448>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3126 A DNA sequence <SEQ ID 10449> was identified in GBS which encodes amino acid sequence <SEQ ID 10450>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3127 A DNA sequence <SEQ ID 10451> was identified in GBS which encodes amino acid sequence <SEQ ID 10452>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3128 A DNA sequence <SEQ ID 10453> was identified in GBS which encodes amino acid sequence <SEQ ID 10454>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3129 A DNA sequence <SEQ ID 10455> was identified in GBS which encodes amino acid sequence <SEQ ID 10456>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3130 A DNA sequence <SEQ ID 10457> was identified in GBS which encodes amino acid sequence <SEQ ID 10458>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. A related GBS nucleic acid sequence <SEQ ID 10907> which encodes amino acid sequence <SEQ ID 10908> was also identified. EXAMPLE 3131 A DNA sequence <SEQ ID 10459> was identified in GBS which encodes amino acid sequence <SEQ ID 10460>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3132 A DNA sequence <SEQ ID 10461> was identified in GBS which encodes amino acid sequence <SEQ ID 10462>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3133 A DNA sequence <SEQ ID 10463> was identified in GBS which encodes amino acid sequence <SEQ ID 10464>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3134 A DNA sequence <SEQ ID 10465> was identified in GBS which encodes amino acid sequence <SEQ ID 10466>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3135 A DNA sequence <SEQ ID 10467> was identified in GBS which encodes amino acid sequence <SEQ ID 10468>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3136 A DNA sequence <SEQ ID 10469> was identified in GBS which encodes amino acid sequence <SEQ ID 10470>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3137 A DNA sequence <SEQ ID 10471> was identified in GBS which encodes amino acid sequence <SEQ ID 10472>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3138 A DNA sequence <SEQ ID 10473> was identified in GBS which encodes amino acid sequence <SEQ ID 10474>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3139 A DNA sequence <SEQ ID 10475> was identified in GBS which encodes amino acid sequence <SEQ ID 10476>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3140 A DNA sequence <SEQ ID 10477> was identified in GBS which encodes amino acid sequence <SEQ ID 10478>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3141 A DNA sequence <SEQ ID 10479> was identified in GBS which encodes amino acid sequence <SEQ ID 10480>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3142 A DNA sequence <SEQ ID 10481> was identified in GBS which encodes amino acid sequence <SEQ ID 10482>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3143 A DNA sequence <SEQ ID 10483> was identified in GBS which encodes amino acid sequence <SEQ ID 10484>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3144 A DNA sequence <SEQ ID 10485> was identified in GBS which encodes amino acid sequence <SEQ ID 10486>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3145 A DNA sequence <SEQ ID 10487> was identified in GBS which encodes amino acid sequence <SEQ ID 10488>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3146 A DNA sequence <SEQ ID 10489> was identified in GBS which encodes amino acid sequence <SEQ ID 10490>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3147 A DNA sequence <SEQ ID 10491> was identified in GBS which encodes amino acid sequence <SEQ ID 10492>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3148 A DNA sequence <SEQ ID 10493> was identified in GBS which encodes amino acid sequence <SEQ ID 10494>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3149 A DNA sequence <SEQ ID 10495> was identified in GBS which encodes amino acid sequence <SEQ ID 10496>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3150 A DNA sequence <SEQ ID 10497> was identified in GBS which encodes amino acid sequence <SEQ ID 10498>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3151 A DNA sequence <SEQ ID 10499> was identified in GBS which encodes amino acid sequence <SEQ ID 10500>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3152 A DNA sequence <SEQ ID 10501> was identified in GBS which encodes amino acid sequence <SEQ ID 10502>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3153 A DNA sequence <SEQ ID 10503> was identified in GBS which encodes amino acid sequence <SEQ ID 10504>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3154 A DNA sequence <SEQ ID 10505> was identified in GBS which encodes amino acid sequence <SEQ ID 10506>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3155 A DNA sequence <SEQ ID 10509> was identified in GBS which encodes amino acid sequence <SEQ ID 10510>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3156 A DNA sequence <SEQ ID 10511> was identified in GBS which encodes amino acid sequence <SEQ ID 10512>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3157 A DNA sequence <SEQ ID 10513> was identified in GBS which encodes amino acid sequence <SEQ ID 10514>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3158 A DNA sequence <SEQ ID 10515> was identified in GBS which encodes amino acid sequence <SEQ ID 10516>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3159 A DNA sequence <SEQ ID 10517> was identified in GBS which encodes amino acid sequence <SEQ ID 10518>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3160 A DNA sequence <SEQ ID 10519> was identified in GBS which encodes amino acid sequence <SEQ ID 10520>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3161 A DNA sequence <SEQ ID 10521> was identified in GBS which encodes amino acid sequence <SEQ ID 10522>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3162 A DNA sequence <SEQ ID 10523> was identified in GBS which encodes amino acid sequence <SEQ ID 10524>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3163 A DNA sequence <SEQ ID 10525> was identified in GBS which encodes amino acid sequence <SEQ ID 10526>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3164 A DNA sequence <SEQ ID 10527> was identified in GBS which encodes amino acid sequence <SEQ ID 10528>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3165 A DNA sequence <SEQ ID 10529> was identified in GBS which encodes amino acid sequence <SEQ ID 10530>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3166 A DNA sequence <SEQ ID 10531> was identified in GBS which encodes amino acid sequence <SEQ ID 10532>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3167 A DNA sequence <SEQ ID 10533> was identified in GBS which encodes amino acid sequence <SEQ ID 10534>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3168 A DNA sequence <SEQ ID 10535> was identified in GBS which encodes amino acid sequence <SEQ ID 10536>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3169 A DNA sequence <SEQ ID 10537> was identified in GBS which encodes amino acid sequence <SEQ ID 10538>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3170 A DNA sequence <SEQ ID 10539> was identified in GBS which encodes amino acid sequence <SEQ ID 10540>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3171 A DNA sequence <SEQ ID 10541> was identified in GBS which encodes amino acid sequence <SEQ ID 10542>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3172 A DNA sequence <SEQ ID 10543> was identified in GBS which encodes amino acid sequence <SEQ ID 10544>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3173 A DNA sequence <SEQ ID 10545> was identified in GBS which encodes amino acid sequence <SEQ ID 10546>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. SEQ ID 10546 (GBS665) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 137 (lane 8-10; MW 41 kDa) and in FIG. 187 (lane 5; MW 41 kDa). It was also was expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 137 (lane 11 & 12; MW 16.1 kDa), in FIG. 141 (lane 4; MW 16 kDa) and in FIG. 179 (lane 6; MW 16 kDa). Purified GBS665-GST is shown in FIG. 243, lane 4. GBS665-His was purified as shown in FIG. 230, lane 7-8. EXAMPLE 3174 A DNA sequence <SEQ ID 10547> was identified in GBS which encodes amino acid sequence <SEQ ID 10548>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. A related GBS nucleic acid sequence <SEQ ID 10909> which encodes amino acid sequence <SEQ ID 10910> was also identified. EXAMPLE 3175 A DNA sequence <SEQ ID 10549> was identified in GBS which encodes amino acid sequence <SEQ ID 10550>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3176 A DNA sequence <SEQ ID 10551> was identified in GBS which encodes amino acid sequence <SEQ ID 10552>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3177 A DNA sequence <SEQ ID 10553> was identified in GBS which encodes amino acid sequence <SEQ ID 10554>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3178 A DNA sequence <SEQ ID 10555> was identified in GBS which encodes amino acid sequence <SEQ ID 10556>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3179 A DNA sequence <SEQ ID 10557> was identified in GBS which encodes amino acid sequence <SEQ ID 10558>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3180 A DNA sequence <SEQ ID 10559> was identified in GBS which encodes amino acid sequence <SEQ ID 10560>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3181 A DNA sequence <SEQ ID 10561> was identified in GBS which encodes amino acid sequence <SEQ ID 10562>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3182 A DNA sequence <SEQ ID 10563> was identified in GBS which encodes amino acid sequence <SEQ ID 10564>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3183 A DNA sequence <SEQ ID 10565> was identified in GBS which encodes amino acid sequence <SEQ ID 10566>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3184 A DNA sequence <SEQ ID 10567> was identified in GBS which encodes amino acid sequence <SEQ ID 10568>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3185 A DNA sequence <SEQ ID 10569> was identified in GBS which encodes amino acid sequence <SEQ ID 10570>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3186 A DNA sequence <SEQ ID 10571> was identified in GBS which encodes amino acid sequence <SEQ ID 10572>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3187 A DNA sequence <SEQ ID 10573> was identified in GBS which encodes amino acid sequence <SEQ ID 10574>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3188 A DNA sequence <SEQ ID 10575> was identified in GBS which encodes amino acid sequence <SEQ ID 10576>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3189 A DNA sequence <SEQ ID 10577> was identified in GBS which encodes amino acid sequence <SEQ ID 10578>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3190 A DNA sequence <SEQ ID 10579> was identified in GBS which encodes amino acid sequence <SEQ ID 10580>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3191 A DNA sequence <SEQ ID 10581> was identified in GBS which encodes amino acid sequence <SEQ ID 10582>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3192 A DNA sequence <SEQ ID 10583> was identified in GBS which encodes amino acid sequence <SEQ ID 10584>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3193 A DNA sequence <SEQ ID 10585> was identified in GBS which encodes amino acid sequence <SEQ ID 10586>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3194 A DNA sequence <SEQ ID 10587> was identified in GBS which encodes amino acid sequence <SEQ ID 10588>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3195 A DNA sequence <SEQ ID 10591> was identified in GBS which encodes amino acid sequence <SEQ ID 10592>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3196 A DNA sequence <SEQ ID 10593> was identified in GBS which encodes amino acid sequence <SEQ ID 10594>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3197 A DNA sequence <SEQ ID 10595> was identified in GBS which encodes amino acid sequence <SEQ ID 10596>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3198 A DNA sequence <SEQ ID 10597> was identified in GBS which encodes amino acid sequence <SEQ ID 10598>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. A related GBS nucleic acid sequence <SEQ ID 10797> which encodes amino acid sequence <SEQ ID 10798> was also identified. EXAMPLE 3199 A DNA sequence <SEQ ID 10599> was identified in GBS which encodes amino acid sequence <SEQ ID 10600>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3200 A DNA sequence <SEQ ID 10601> was identified in GBS which encodes amino acid sequence <SEQ ID 10602>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3201 A DNA sequence <SEQ ID 10603> was identified in GBS which encodes amino acid sequence <SEQ ID 10604>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3202 A DNA sequence <SEQ ID 10605> was identified in GBS which encodes amino acid sequence <SEQ ID 10606>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3203 A DNA sequence <SEQ ID 10607> was identified in GBS which encodes amino acid sequence <SEQ ID 10608>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3204 A DNA sequence <SEQ ID 10609> was identified in GBS which encodes amino acid sequence <SEQ ID 10610>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3205 A DNA sequence <SEQ ID 10611> was identified in GBS which encodes amino acid sequence <SEQ ID 10612>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3206 A DNA sequence <SEQ ID 10613> was identified in GBS which encodes amino acid sequence <SEQ ID 10614>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3207 A DNA sequence <SEQ ID 10615> was identified in GBS which encodes amino acid sequence <SEQ ID 10616>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3208 A DNA sequence <SEQ ID 10617> was identified in GBS which encodes amino acid sequence <SEQ ID 10618>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3209 A DNA sequence <SEQ ID 10619> was identified in GBS which encodes amino acid sequence <SEQ ID 10620>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics.

EXAMPLE 3210 A DNA sequence <SEQ ID 10621> was identified in GBS which encodes amino acid sequence <SEQ ID 10622>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3211 A DNA sequence <SEQ ID 10623> was identified in GBS which encodes amino acid sequence <SEQ ID 10624>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3212 A DNA sequence <SEQ ID 10625> was identified in GBS which encodes amino acid sequence <SEQ ID 10626>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3213 A DNA sequence <SEQ ID 10627> was identified in GBS which encodes amino acid sequence <SEQ ID 10628>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3214 A DNA sequence <SEQ ID 10629> was identified in GBS which encodes amino acid sequence <SEQ ID 10630>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3215 A DNA sequence <SEQ ID 10631> was identified in GBS which encodes amino acid sequence <SEQ ID 10632>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3216 A DNA sequence <SEQ ID 10633> was identified in GBS which encodes amino acid sequence <SEQ ID 10634>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. A related GBS nucleic acid sequence <SEQ ID 10939> which encodes amino acid sequence <SEQ ID 10940> was also identified. SEQ ID 10634 (GBS675) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 162 (lane 14 & 15; MW 56 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 163 (lane 2; MW 31 kDa) and in FIG. 188 (lane 5; MW 31 kDa). Purified GBS675-His is shown in FIG. 240, lane 7-8. EXAMPLE 3217 A DNA sequence <SEQ ID 10635> was identified in GBS which encodes amino acid sequence <SEQ ID 10636>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3218 A DNA sequence <SEQ ID 10637> was identified in GBS which encodes amino acid sequence <SEQ ID 10638>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3219 A DNA sequence <SEQ ID 10639> was identified in GBS which encodes amino acid sequence <SEQ ID 10640>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3220 A DNA sequence <SEQ ID 10641> was identified in GBS which encodes amino acid sequence <SEQ ID 10642>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3221 A DNA sequence <SEQ ID 10643> was identified in GBS which encodes amino acid sequence <SEQ ID 10644>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3222 A DNA sequence <SEQ ID 10645> was identified in GBS which encodes amino acid sequence <SEQ ID 10646>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3223 A DNA sequence <SEQ ID 10647> was identified in GBS which encodes amino acid sequence <SEQ ID 10648>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3224 A DNA sequence <SEQ ID 10649> was identified in GBS which encodes amino acid sequence <SEQ ID 10650>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3225 A DNA sequence <SEQ ID 10651> was identified in GBS which encodes amino acid sequence <SEQ ID 10652>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3226 A DNA sequence <SEQ ID 10653> was identified in GBS which encodes amino acid sequence <SEQ ID 10654>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3227 A DNA sequence <SEQ ID 10655> was identified in GBS which encodes amino acid sequence <SEQ ID 10656>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3228 A DNA sequence <SEQ ID 10657> was identified in GBS which encodes amino acid sequence <SEQ ID 10658>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3229 A DNA sequence <SEQ ID 10659> was identified in GBS which encodes amino acid sequence <SEQ ID 10660>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3230 A DNA sequence <SEQ ID 10661> was identified in GBS which encodes amino acid sequence <SEQ ID 10662>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3231 A DNA sequence <SEQ ID 10663> was identified in GBS which encodes amino acid sequence <SEQ ID 10664>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3232 A DNA sequence <SEQ ID 10665> was identified in GBS which encodes amino acid sequence <SEQ ID 10666>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. A related GBS nucleic acid sequence <SEQ ID 10917> which encodes amino acid sequence <SEQ ID 10918> was also identified. A DNA sequence <SEQ ID 10667> was identified in GBS which encodes amino acid sequence <SEQ ID 10668>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3233 A DNA sequence <SEQ ID 10669> was identified in GBS which encodes amino acid sequence <SEQ ID 10670>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3234 A DNA sequence <SEQ ID 10671> was identified in GBS which encodes amino acid sequence <SEQ ID 10672>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3235 A DNA sequence <SEQ ID 10673> was identified in GBS which encodes amino acid sequence <SEQ ID 10674>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3236 A DNA sequence <SEQ ID 10675> was identified in GBS which encodes amino acid sequence <SEQ ID 10676>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3237 A DNA sequence <SEQ ID 10677> was identified in GBS which encodes amino acid sequence <SEQ ID 10678>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3238 A DNA sequence <SEQ ID 10679> was identified in GBS which encodes amino acid sequence <SEQ ID 10680>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3239 A DNA sequence <SEQ ID 10681> was identified in GBS which encodes amino acid sequence <SEQ ID 10682>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3240 A DNA sequence <SEQ ID 10683> was identified in GBS which encodes amino acid sequence <SEQ ID 10684>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3241 A DNA sequence <SEQ ID 10685> was identified in GBS which encodes amino acid sequence <SEQ ID 10686>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3242 A DNA sequence <SEQ ID 10687> was identified in GBS which encodes amino acid sequence <SEQ ID 10688>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3243 A DNA sequence <SEQ ID 10689> was identified in GBS which encodes amino acid sequence <SEQ ID 10690>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3244 A DNA sequence <SEQ ID 10691> was identified in GBS which encodes amino acid sequence <SEQ ID 10692>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. SEQ ID 10692 (GBS676) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 163 (lane 3-5; MW 66 kDa) and in FIG. 239 (lane 8; MW 66 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 163 (lane 7 & 8; MW 41 kDa) and in FIG. 188 (lane 6; MW 41 kDa). Purified GBS676-His is shown in FIG. 240, lane 4-5. Purified GBS676-GST is shown in FIG. 246, lanes 10 & 11. EXAMPLE 3245 A DNA sequence <SEQ ID 10693> was identified in GBS which encodes amino acid sequence <SEQ ID 10694>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3246 A DNA sequence <SEQ ID 10695> was identified in GBS which encodes amino acid sequence <SEQ ID 10696>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3247 A DNA sequence <SEQ ID 10697> was identified in GBS which encodes amino acid sequence <SEQ ID 10698>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3248 A DNA sequence <SEQ ID 10699> was identified in GBS which encodes amino acid sequence <SEQ ID 10700>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3249 A DNA sequence <SEQ ID 10703> was identified in GBS which encodes amino acid sequence <SEQ ID 10704>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3250 A DNA sequence <SEQ ID 10705> was identified in GBS which encodes amino acid sequence <SEQ ID 10706>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3251 A DNA sequence <SEQ ID 10707> was identified in GBS which encodes amino acid sequence <SEQ ID 10708>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3252 A DNA sequence <SEQ ID 10709> was identified in GBS which encodes amino acid sequence <SEQ ID 10710>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. A related GBS nucleic acid sequence <SEQ ID 10803> which encodes amino acid sequence <SEQ ID 10804> was also identified. EXAMPLE 3253 A DNA sequence <SEQ ID 10711> was identified in GBS which encodes amino acid sequence <SEQ ID 10712>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. A related GBS nucleic acid sequence <SEQ ID 10913> which encodes amino acid sequence <SEQ ID 10914> was also identified. EXAMPLE 3254 A DNA sequence <SEQ ID 10713> was identified in GBS which encodes amino acid sequence <SEQ ID 10714>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3255 A DNA sequence <SEQ ID 10715> was identified in GBS which encodes amino acid sequence <SEQ ID 10716>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3256 A DNA sequence <SEQ ID 10717> was identified in GBS which encodes amino acid sequence <SEQ ID 10718>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3257 A DNA sequence <SEQ ID 10719> was identified in GBS which encodes amino acid sequence <SEQ ID 10720>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3258 A DNA sequence <SEQ ID 10721> was identified in GBS which encodes amino acid sequence <SEQ ID 10722>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3259 A DNA sequence <SEQ ID 10723> was identified in GBS which encodes amino acid sequence <SEQ ID 10724>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3260 A DNA sequence <SEQ ID 10725> was identified in GBS which encodes amino acid sequence <SEQ ID 10726>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3261 A DNA sequence <SEQ ID 10727> was identified in GBS which encodes amino acid sequence <SEQ ID 10728>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3262 A DNA sequence <SEQ ID 10729> was identified in GBS which encodes amino acid sequence <SEQ ID 10730>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. SEQ ID 10730 (GBS670) was expressed in E. coli as a GST-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 140 (lane 24; MW 45.3 kDa). It was also expressed in E. coli as a His-fusion product. SDS-PAGE analysis of total cell extract is shown in FIG. 140 (lane 5-7; MW 20.4 kDa) and in FIG. 179 (lane 10; MW 20 kDa). GBS670-His was purified as shown in FIG. 230, lane 9-10. EXAMPLE 3263 A DNA sequence <SEQ ID 10731> was identified in GBS which encodes amino acid sequence <SEQ ID 10732>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3264 A DNA sequence <SEQ ID 10733> was identified in GBS which encodes amino acid sequence <SEQ ID 10734>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3265 A DNA sequence <SEQ ID 10735> was identified in GBS which encodes amino acid sequence <SEQ ID 10736>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3266 A DNA sequence <SEQ ID 10737> was identified in GBS which encodes amino acid sequence <SEQ ID 10738>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3267 A DNA sequence <SEQ ID 10739> was identified in GBS which encodes amino acid sequence <SEQ ID 10740>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3268 A DNA sequence <SEQ ID 10741> was identified in GBS which encodes amino acid sequence <SEQ ID 10742>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3269 A DNA sequence <SEQ ID 10743> was identified in GBS which encodes amino acid sequence <SEQ ID 10744>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3270 A DNA sequence <SEQ ID 10745> was identified in GBS which encodes amino acid sequence <SEQ ID 10746>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3271 A DNA sequence <SEQ ID 10747> was identified in GBS which encodes amino acid sequence <SEQ ID 10748>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3272 A DNA sequence <SEQ ID 10749> was identified in GBS which encodes amino acid sequence <SEQ ID 10750>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3273 A DNA sequence <SEQ ID 10751> was identified in GBS which encodes amino acid sequence <SEQ ID 10752>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3274 A DNA sequence <SEQ ID 10753> was identified in GBS which encodes amino acid sequence <SEQ ID 10754>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3275 A DNA sequence <SEQ ID 10755> was identified in GBS which encodes amino acid sequence <SEQ ID 10756>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3276 A DNA sequence <SEQ ID 10757> was identified in GBS which encodes amino acid sequence <SEQ ID 10758>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3277 A DNA sequence <SEQ ID 10759> was identified in GBS which encodes amino acid sequence <SEQ ID 10760>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3278 A DNA sequence <SEQ ID 10761> was identified in GBS which encodes amino acid sequence <SEQ ID 10762>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3279 A DNA sequence <SEQ ID 10763> was identified in GBS which encodes amino acid sequence <SEQ ID 10764>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3280 A DNA sequence <SEQ ID 10765> was identified in GBS which encodes amino acid sequence <SEQ ID 10766>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3281 A DNA sequence <SEQ ID 10767> was identified in GBS which encodes amino acid sequence <SEQ ID 10768>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3282 A DNA sequence <SEQ ID 10769> was identified in GBS which encodes amino acid sequence <SEQ ID 10770>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3283 A DNA sequence <SEQ ID 10771> was identified in GBS which encodes amino acid sequence <SEQ ID 10772>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3284 A repeated DNA sequence <SEQ ID 10791> was identified in GBS which encodes amino acid sequence <SEQ ID 10792>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3285 A DNA sequence <SEQ ID 10805> was identified in GBS which encodes amino acid sequence <SEQ ID 10806>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3286 A DNA sequence <SEQ ID 10807> was identified in GBS which encodes amino acid sequence <SEQ ID 10808>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3287 A DNA sequence <SEQ ID 10809> was identified in GBS which encodes amino acid sequence <SEQ ID 10810>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3288 A DNA sequence <SEQ ID 10811> was identified in GBS which encodes amino acid sequence <SEQ ID 10812>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3289 A DNA sequence <SEQ ID 10813> was identified in GBS which encodes amino acid sequence <SEQ ID 10814>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3290 A DNA sequence <SEQ ID 10815> was identified in GBS which encodes amino acid sequence <SEQ ID 10816>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3291 A DNA sequence <SEQ ID 10817> was identified in GBS which encodes amino acid sequence <SEQ ID 10818>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3292 A DNA sequence <SEQ ID 10819> was identified in GBS which encodes amino acid sequence <SEQ ID 10820>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3293 A DNA sequence <SEQ ID 10821> was identified in GBS which encodes amino acid sequence <SEQ ID 10822>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3294 A DNA sequence <SEQ ID 10823> was identified in GBS which encodes amino acid sequence <SEQ ID 10824>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3295 A DNA sequence <SEQ ID 10825> was identified in GBS which encodes amino acid sequence <SEQ ID 10826>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3296 A DNA sequence <SEQ ID 10827> was identified in GBS which encodes amino acid sequence <SEQ ID 10828>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3297 A DNA sequence <SEQ ID 10829> was identified in GBS which encodes amino acid sequence <SEQ ID 10830>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3298 A DNA sequence <SEQ ID 10831> was identified in GBS which encodes amino acid sequence <SEQ ID 10832>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3299 A DNA sequence <SEQ ID 10833> was identified in GBS which encodes amino acid sequence <SEQ ID 10834>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3300 A DNA sequence <SEQ ID 10835> was identified in GBS which encodes amino acid sequence <SEQ ID 10836>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3301 A DNA sequence <SEQ ID 10837> was identified in GBS which encodes amino acid sequence <SEQ ID 10838>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3302 A DNA sequence <SEQ ID 10839> was identified in GBS which encodes amino acid sequence <SEQ ID 10840>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3303 A DNA sequence <SEQ ID 10841> was identified in GBS which encodes amino acid sequence <SEQ ID 10842>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3304 A DNA sequence <SEQ ID 10843> was identified in GBS which encodes amino acid sequence <SEQ ID 10844>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3305 A DNA sequence <SEQ ID 10845> was identified in GBS which encodes amino acid sequence <SEQ ID 10846>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3306 A DNA sequence <SEQ ID 10847> was identified in GBS which encodes amino acid sequence <SEQ ID 10848>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3307 A DNA sequence <SEQ ID 10849> was identified in GBS which encodes amino acid sequence <SEQ ID 10850>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3308 A DNA sequence <SEQ ID 10851> was identified in GBS which encodes amino acid sequence <SEQ ID 10852>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3309 A DNA sequence <SEQ ID 10853> was identified in GBS which encodes amino acid sequence <SEQ ID 10854>. Related sequences are <SEQ ID 10855>, <SEQ ID 10856>, <SEQ ID 10857>, <SEQ ID 10858>, <SEQ ID 10859>, <SEQ ID 10860>, <SEQ ID 10861>, <SEQ ID 10862>, <SEQ ID 10863>, <SEQ ID 10864>, <SEQ ID 10865> and <SEQ ID 10866>. These proteins and their epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3310 A DNA sequence <SEQ ID 10867> was identified in GBS which encodes amino acid sequence <SEQ ID 10868>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3311 A DNA sequence <SEQ ID 10869> was identified in GBS which encodes amino acid sequence <SEQ ID 10870>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3312 A DNA sequence <SEQ ID 10871> was identified in GBS which encodes amino acid sequence <SEQ ID 10872>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3313 A DNA sequence <SEQ ID 10873> was identified in GBS which encodes amino acid sequence <SEQ ID 10874>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3314 A DNA sequence <SEQ ID 10875> was identified in GBS which encodes amino acid sequence <SEQ ID 10876>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3315 A DNA sequence <SEQ ID 10877> was identified in GBS which encodes amino acid sequence <SEQ ID 10878>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3316 A DNA sequence <SEQ ID 10879> was identified in GBS which encodes amino acid sequence <SEQ ID 10880>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3317 A DNA sequence <SEQ ID 10881> was identified in GBS which encodes amino acid sequence <SEQ ID 10882>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3318 A DNA sequence <SEQ ID 10883> was identified in GBS which encodes amino acid sequence <SEQ ID 10884>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3319 A DNA sequence <SEQ ID 10885> was identified in GBS which encodes amino acid sequence <SEQ ID 10886>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3320 A DNA sequence <SEQ ID 10887> was identified in GBS which encodes amino acid sequence <SEQ ID 10888>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3321 A DNA sequence <SEQ ID 10889> was identified in GBS which encodes amino acid sequence <SEQ ID 10890>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3322 A DNA sequence <SEQ ID 10891> was identified in GBS which encodes amino acid sequence <SEQ ID 10892>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3323 A DNA sequence <SEQ ID 10893> was identified in GBS which encodes amino acid sequence <SEQ ID 10894>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3324 A DNA sequence <SEQ ID 10895> was identified in GBS which encodes amino acid sequence <SEQ ID 10896>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3325 A DNA sequence <SEQ ID 10897> was identified in GBS which encodes amino acid sequence <SEQ ID 10898>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics.

EXAMPLE 3326 A DNA sequence <SEQ ID 10899> was identified in GBS which encodes amino acid sequence <SEQ ID 10900>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3327 A DNA sequence <SEQ ID 10901> was identified in GBS which encodes amino acid sequence <SEQ ID 10902>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3328 A DNA sequence <SEQ ID 10903> was identified in GBS which encodes amino acid sequence <SEQ ID 10904>. This protein and its epitopes could be useful antigens for vaccines and/or diagnostics. EXAMPLE 3329 Seven rRNA genes were identified in S. agalactiae. These are SEQ IDs 12018 to 12024. These rRNA genes are particularly useful for diagnostic purposes and for phlyogenetic studies. An alignment of the rRNA sequences is shown below:

TABLE-US-08057 12023 ------------------------------------TTTCGAGTCAAAGTCATCAGCGTT 12024 ------------------------------------------------------------ 12019 -----TCCAATCATACTTAATTTCACTAATATCTGGATTTTGACATATTCAGTTAATTCT 12021 . . . ATCGAATTGAACGGACTCAATTTGGTTGTTATGTAATTTT--ACATAATCTATGATTTCT 12020 ------------------------------------------------------------ 12018 ------------------------------------------------------------ 12022 ----------------------------CTTCTTTGTTTTCTTTAGAGATATTAACTGTA 12023 TACTGTTACGGCAGCAGTTCCAAGAGTTACTCCACTCACAAGGACTGCTGATAATATTCT 12024 ------------------------------------------------------------ 12019 TTTTCATGCTTTTTGAGATAAGCTACTTGTTCTTTTTTTATTACTTTTTTACCTTTCTTT 12021 TGCTCATGCTCTTTGAGATAGGCTAATTGTTCTTTTTTTGTCATTTTTTTATCTTTCTTC 12020 ------------------------------------------------------------ 12018 ------------------------------------------------------------ 12022 CCCACTTTGGGCGTTAAAATACCTAAAGTAGCCTTTATTAAAGTTGATTTAGCAGCCCCA 12023 TTTTTTCATTTTTATTAAACTACTCCTTTAC--GATAAGACATTAAATATTTTACCAAAA 12024 ------------------------------------------------------------ 12019 ACTGCTGACTGTTTGCTATTTTTTACTTCGTTTGACTGACTTTTAGATTCACTATTCATT 12021 ACTTCTGATTGCTTGCTATTTTTTACTTCGTTTGACTGAATTTTATGTTCACTATTCATT 12020 ------------------------------------------------------------ 12018 ----------------------------CTTT-GATACAATATTATCAAAATTATATTAA 12022 TTTTCACCTGTTAAGGTAACAAACTCCCCACT-GTCTAAATGGTAATTAACCCCTTCCAG 12023 AATTCACGAAATTATATTACGTCATTGTTACATTTATATTTGAAATCAACTATTTCTAAA 12024 ------------------------------------------------------------ 12019 TGACAGCCTGCTAGTAACATCCCAATAATAGATATGGGAATTAACCATTTTACATATTTT 12021 TGACAGCCTCCAAGTATCATCCCAAAAATTGATATGGGAATTAACCATTTTATATATTTT 12020 ------------------------------------------------------------ 12018 CGGTAAAGATATTGTTAAAGACCAAACTTGGATTATCAATCGT----TATCAAGAAATTA 12022 CA-CAGGATCGCTATCGTACTGAAAAGTAAGACCACTAACTGTAATATATCGCATGATTA 12023 TGAACCATAATCAAATCTAGAAAACGATAACCTTCTTCTATTCACTCT---ATCAATATA 12024 ------------------------------------------------------------ 12019 TTCAACATGCTCTCTTTTCTTAGAAAATAAACTTCCCATGTCAAGTATCTAATAAAAATA 12021 CTCATCATGTTCTCTTTTCTTAGAATATAAATTTTATATATCAAGTATATAATGAAATTA 12020 ------------------------------------------------------------ 12018 TTAGTG---ATTTGTCTTTAGGAAGCACTA--------TTGCAGAAGA---AATTACTCG 12022 CCCTTCT--AATTCTCTAGAGAAAAGATCAAGAAAACGTTCTAAAACG---ACCTTTTCG 12023 ATTACTCCATAGTGAAACTAAAAGAGAAATAAAAAAAGAGTATAATTACTCTTAAAATTA 12024 ------------------------------------------------------------ 12019 ATTATTATTTACCAGTATGTTAAAACTAATATTAGTATAACAAA-TTTTCACGAGTTTAA 12021 ACTATTATTCACCAACATTATAAAATTAATTTTAGTATAACAAAATTTTCACGTATTTTT 12020 ----------ATCAAAAAAACATGACCAGTATGAATTAAAGCAACGTATAATCAATGCCT 12018 CTCTAT--AGAGCAGCTAGCTTCACTTCCCATAGAAAATAATCAGTTTTTAT-ATGAT-- 12022 TCCTTTGAAAAATGATTTACTAATCTTCCGTAAACCCCTAACGTATTGTCATGATGATGT 12023 TAATATTTACGGAGAATAAGGGATTCGAACCCTTGCGCCAGTTACCCGACCTAACGATTT 12024 ------------------------------------------------------------ 12019 TT--TTTTAGTCGTAACATATACACTGAAAAATCTTATTATTTTATACTACCTATCTATC 12021 ATAGTTTTAGTCTTAACATGTAAACAGAAA------A---------------------TC 12020 TAATGCGTAAAGGATACCAGTACGAAGATA----------------------------TC 12018 ---TGTTTTTTAGCAGCCGGTGAAGATA-------------------ACAACGCAAAGTT 12022 GTGTGTTCATCTGCAATGGGTTTAGCAAGT----TCA---------GATAACTCAAAATA 12023 AGCAAACCGTCCTCTTCAGCCTCTTGAG--TAATTCTCCAAATTAATATTAATGGGCACG 12024 ------------------------------------------------------------ 12019 ATTCACAAACACTTTTATTACTTCAGAACCTATGACATTTAGGAGTCCTCTTTGAATTTC 12021 ATTTGTATA-----T----------------------TTTAAATGCCCTAATTAAATT-- 12020 AAAAGTGC------T----------------------TTAAGAGAATATTTATAAGAT-- 12018 AGTTGCA-ACGTTTTTTAATCAAAATGA--CATTCCTGCAAGATATGTTCATCCAAACGA 12022 AGTAATACGAGCATCTTTAGAATCTTTA--TTCGCTTTCAACATATCCTGAGA-AATTAA 12023 AGTGGACTCGAACCACCGACCTCACGCTTATCAGGCGTGCGCTCTAACCACCTGAGCTAC 12024 ------------------------------------------------------------ 12019 ATTTAAATGTTGAGTCTCCACTAACTCTTGAAAAATTTCCTTATTATTTCTGCTTGTTTT 12021 ------------------------------AATAATT-----AATATTTATTATTATATA 12020 ------------------------------AATAACTCTCAGACGATGTATT-TTACAGA 12018 AGCAGGAATTATTGTAACTAAAGAACCATG--TAATGCACGAATTATT--CCAG----GA 12022 ACTTTTTACTGCTTTAGTTACAGCTGCCTGACTAATATTTAACTTCTTAGCTAAATCAGA 12023 GCGCCCAAGCAAATGCTTGGTTTTACTTTTATGTAAAGTAAGCGGGTGACGAGAATCGA- 12024 ------------------------------------------------------------ 12019 AAACCTTCTATAACGATTGCAATAATGAAAAACAAATATAAGTAATTTTCAGTAACTTTT 12021 AATTCTTCTACAATGA----------AAAAAATAAATATAT--A-TTACAAGTAACATT- 12020 AAAT----TATGATAA-----A----CTATAACAGACGTAT--AAATTGTAGAAAGTTG- 12018 AGTTATGATAAGATTGA------GAACTTATGTCTATACAATGAGGTTCTTGTTATCCCT 12022 ATTTGTCAACTGCTCTT------GTGATAAAAGCATCAGAATGTGTTCTTGCGTATTAGT 12023 -ACTCGCGACAACAGCTTGGAAGGCTGTAGTTTTACCACTAAACTACACCCGCTAAAAAC 12024 ------------------------------------------------------------ 12019 TCTCAAAATTACCAGCACAATACAAAAAAGACAAGGCTTCTAAACCTTGTCTTTATAAAT 12021 --TCACAATAAATTATCTAGTAGAAAAAAGACAAGGTTTAGAAACCTTGTCTTTATAAGT 12020 ----GTAGGCTATGAGATTACCTAAAGAAGGCGACTTTATTACAATTCAAAGTTACAAAC 12018 GGATTT---------TTTGG--AGTCACAGAAGATAAC-CAAATTTGTACCTTTTCAAGA 12022 CAATTTAA-CATCACTTTGACAAGTACCAAACAATAATTCATGTTGATTTTCTGCTTTAA 12023 TTATATAATAAATGGCGCGAGACGGAATCGAACCGCCGACACATGGAGCTTCAATCCATT 12024 ------------------------------------------------------------ 12019 ATACCGGCGGCCGGGGTCGAACCGGCACGTCCGTGAGGACACTGGATTTTGAGTCCAGCG 12021 ATACCGGCGGCCGGGGTCGAACCGGCACGTCCGTGAGGACACTGGATTTTGAGTCCAGCG 12020 ATGATGGTAGTTTACACCGAACTTG-----GCGTGACACCA-TGGTATTAAAAACAACCG 12018 GGGGGATCTGACATTACTGGATC--------CCTAATTGC--------AGCAGGCATAAA 12022 GCAAGATTTGAC-TCACTAAATGG-------TCTAATTTTTGTTCTAAAACTGTCATATA 12023 GCTCTACCAACTGAGCTACCGAGCCTATTGCGGGAGCAGGATTTGAACCTACGACCTTCG 12024 ------------------------------------------------------------ 12019 CGTCTGCCAATTCCGCCACGCCGGCTATCTTAAAACTGGGGTAGCTGGATTCGA--ACCA 12021 CGTCTGCCAATTCCGCCACGCCGGCTATCTTAAAACTGGGGTAGCTGGATTCGA--ACCA 12020 AAAATGCC--CTCATTGGTGTTAATGATCAT---ACTTTAGTAACAGAAAATGATGGTCG 12018 AGCAGACCT-TTATGAGAACTTCACAGATGT----TGATGGTATATTTGCAGCACATCCA 12022 TACCT-CTT-TTTTGTTAACCAGTAAATTATATCACGAAGATATAGAAGAATCAATCATA 12023 GGTTA-TGAGCCCGACGAGCTACCTAGCTGCTCCA-------TCCCGCGATATCTTTAAA 12024 ------------------------------------------------------------ 12019 ACGCA-TGAGGGAGTCAAAGTCCCTTGCCTTACCG-------CTTGGCTATACCCCATGA 12021 ACGCA-TGAGGGAGTCAAAGTCCCTTGCCTTACCG-------CTTGGCTATACCCCATGA 12020 ACGC--TGGGTGACACGAGAGCC--TGCAATA---------------GTATACTTTCATA 12018 GGT-------GTAGTTAAGAACCCTCACGCTA----------TCCCTGAGCTTACTTATA 12022 GATAGGTGAAGAAGATAAAACCTTTTATCTCAACAACCTAACTTTATAAACTTCTTTGCA 12023 GGA---------GGATGTGGGATTCGAACCCACGCACGCTTTTACAC--GCCTGACGGTT 12024 ------------------------------------------------------------ 12019 AAAGGCG-----AGTGATGGGAATCGAACCCACGAATGTCAGAGCCACAATCTGATGTGT 12021 AAAGGCG-----AGTGATGGGAATCGAACCCACGAATGTCAGAGCCACAATCTGATGTGT 12020 AAA---------AATACTGG---T------TT--AACATTATCGCTA-----TGATACGT 12018 AAGA--------AATGCGTGAATTAGCCTATGCGGGTTTTTCGGTTT-TACATGATGAA- 12022 AAAACCTTTCATACTATTAAAAACACGATCAGCTTTTTTCTCTGTAG-AACACATTGAAA 12023 TTCAAGACCGTTCCCTTCAGCCGGACTTGGGTAATCCTCCATATAACAAAAAATATGGAC 12024 ------------------------------------------------------------ 12019 TAACCACTTCACCACACCCGCCATATTAGAAAAAACACGGGCAGTAGGAATCGAACCCAC 12021 TAACCACTTCACCACACCCGCCATATTAGAAAAAACACGGGCAGTAGGAATCGAACCCAC 12020 GAAACTGGTGTCTCCTACTATTGTAATCTAGCAAGT-----CCGTATATCTTGGACCC-- 12018 --------GCTTTACTTCCTGCCTATCGTGGCAGAATCCCTCTTGTTATTAAAAATAC-- 12022 AAACAGTTGGTCCACTTCCTGTC-ATTAATGCAACATCGGCTCCAGAATTTAACATAC-- 12023 CTTGTAGGACTCGAACCTACGACCGCTCGGTTATGAGCCGAGTGCTCTAACCAGTTGAGC 12024 ------------------------------------------------------------ 12019 ACTGAAGGTTTTGGAGACCTTAGTTCTACCTTTAAACTATGCCCGTTTACTATGGAGAGA 12021 ACTGAAGGTTTTGGAGACCTTAGTTCTACCTTTAAACTATGCCCGTTTACTATGGAGAGA 12020 --TGAAGCACTCAAGTATATTGACTATGACCTTGATGTCAAAGTATTTGCAGATGGTGAA 12018 ----AAA----TAATCCCCAACAGCCTGGTACAAAAATAGTTTTAAAGCATACTCGTAG- 12022 ----GTTCTTTTATTGTACTTATAACTGGATTTTTAGTAATTGTAATATCCTCGAGTGAA 12023 TAAAGGTCCAAAGTCTCAATAAAATAAATAGCGGCGGAGGGGATCGAACCCCCGACCTCC 12024 ------------------------------------------------------------ 12019 GAGGGATTCGAACCCCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCTCT 12021 GAGGGATTCGAACCCCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCTCT 12020 AAAAGACTACTAGATGTGGACGAATATGAACAGCATAAAGYTCAGATGAACT--ATCCTA 12018 --TAACATAGCAGTAACTGG-GATCGCT--TCTGATAGCCGTTTTGCTAGCATAAACGTA 12022 TTTCCCATAGATTTGACCATTAACTGATAATCTGATGACAAAATAGCAGACTTTAATAAA 12023 CGGGTATG-AACCGGACGCTCTAGCCAGCT--GAGCTACACCGCCATAAAAATATATCCA 12024 ------------------------------------------------------------ 12019 TCGCTATC-TCTCCTAAGGTATAAATGGCGCGAGACGGAATCGAACCGCCGACACATGGA 12021 TCGCTATC-TCTCCTAAGGTATAAATGGCGCGAGACGGAATCGAACCGCCGACACATGGA 12020 CCGATATT-GATTATATATTAAAGGAAAATGTAAAAATATTGGTAGAATGGATAAATGAG 12018 TCTAAAT--ACTTAATGAATAGA---GAAGTAGGTTTCGGCCGAAAAG----TACTACAA 12022 TCAATATCAACTCTACTTATAGACTTACAATCAATATCTCTAAAAATGGATTTAGTTGAA 12023 TCGGGAAGACAGGATTCGAACCTGCGACACCTTGGTCCCAAACCAAGTACTCTACCAAGC 12024 ------------------------------------------------------------ 12019 GCTTCAATCCATTGCTCTACCAACTGAGCTACCGAGCCTATTGCGGGAGCAGGATTTGAA 12021 GCTTCAATCCATTGCTCTACCAACTGAGCTACCGAGCCTATTGCGGGAGCAGGATTTGAA 12020 AATAAAGGCCCCTTTTC-ATCATC--ATATATCAA-TATCTGGTATAAACGGTA------ 12018 ATTTTAGAG---GATTTAAATATT---AGTTTTGAACATATGCCAACTGGCATAGATGAT 12022 ATACCAAAATCCGGCTTAACCAGA---ACTATCCAACATGGTCTCAATGTCGGTAAGGGT 12023 TGAGCTACTTCCCGAAAAATATGCAC--CCTAGAGGAGTCGAACCTCTAACCGCCTGATT 12024 ------------------------------------------------------------ 12019 CCTACGACCTTCGGGTTATGAGCCCG--ACGAGCTACCTAGCTGCTCCATCCCGCGATAT 12021 CCTACGACCTTCGGGTTATGAGCCCG--ACGAGCTACCTAGCTGCTCCATCCCGCGATAT 12020 --------CCTTGAATTGAAA-------AAGCGCTAACTAAC-ACACTAAATAGTG-TGT 12018 CTATCCATTGT---CTTACGTGAAA---AAGAATTGACACCAATCAAAGAACAAGAAATC 12022 TTAACAATTTCACCTTTACCTAATACTAACGAACATCCCCCACCAAGACAATAAGGAACA 12023 CGTAGTCAG---GTACTCTATCCAGTTGAGCTAAGGGTGCTAAATATTATA-----TGCC 12024 ------------------------------------------------------------ 12019 CTTTAAAGGAGGATGTGGGATTCGAACCCACGCACGCTTTTACACGCCTGACG--GTTTT 12021 CTTTAAAGGAGGATGTGGGATTCGAACCCACGCACGCTTTTACACGCCTGACG--GTTTT 12020 TTTTATTA----ATATCAAATTTAATTACA---ATACTATTGCAAAAATAT----ATACT 12018 TTAAATTACCTAACTCGTAAACTAGAAGTAG--ATTACGTTGACATCCAA---------- 12022 TC--ACTACC-AATTTTAAAACCAATAGCAACCATTTCGTCATAGTCCATTTGAAGATTC 12023 GAGGACCGGAATC----GAACCGGTACGATGTTTACCATCGCAGGATTTTAAGTCCTGTG 12024 ------------------------------------------------------------ 12019 CAAGACCGTTCCCTTCAGCCGGACTTGGGTAATCCTCCATATAACAAAAAATAGTCCGTA 12021 CAAGACCGTTCCCTTCAGCCGGACTTGGGTAATCCTCCATATAACAAAAAATAGTCCGTA 12020 TAAAATAAA-------AAAAGTAGAAAGATCACTTTCTACTTTTTTAAGAATAGTCCGTA 12018 CACAATCTATC-------TACAATCGTAATTGTAGGTGAAA-ATATGAAAAGTCAGATTG 12022 CATAATCGATT-------AAGAGCTCTTATTGTAGCAGCAGCATCAGTAGAACCACCCCC 12023 CGTCTGCCAGTTCCGCCACCCCGGCCTCTAACAAGCGAACGACGGGGTTCGAACCCGCGA 12024 ------------------------------------------------------------ 12019 CGGGATTCGAACCCGTGTTACCGCCGTGAAAAGGCGGTGTCTTAACCCCTTGACCAACGG 12021 CGGGATTCGAACCCGTGTTACCGCCGTGAAAAGGCGGTGTCTTAACCCCTTGACCAACGG 12020 CGGGATTCGAACCCGTGTTACCGCCGTGAAAAGGCGGTGTCTTAACCCCTTGACCAACGG 12018 GAGTCACTGCAACAGCGACACAAGCCTTATC------AAGAGAAAAA-----ATCAATAT 12022 CAGTC-CTGCACAGACAGGAATGGATTTTTCTAATCTAATATGAACACCTTTATTAATAC 12023 -CCCTCACCTT-----GGCAAGGTGATGTTCTACCACTGAACTACGTTCGCACTAAAGAC 12024 ------------------------------------------------------------ 12019 -ACCATATTCTTGATGGGCACGAGTGGACTCGAACCACCGACCTCACGCTTATCAGGCGT 12021 -ACCATATTCTTGATGGGCACGAGTGGACTCGAACCACCGACCTCACGCTTATCAGGCGT 12020 -ACCATATTCTTGATGGGCACGAGTGGACTCGAACCACCGACCTCACGCTTATCAGGCGT 12018 CACCATGAT-----ATCACA-----AGGTTCAAGCGAA--GTCTCCATTATGT------- 12022 CATATTGATTTTTGATTATATCTGCAGCTTTAAACACATCATTATCATTATTTAAAGGCA 12023 ACTATTTATCCTATAAAATTGTAATGCCGGC----------------------------- 12024 ------TATCCTATAAAATTGTAATGCCGGC----------------------------- 12019 GCGCTCTAACCACCTGAGCTACGCGCCCAAAATAACTTCTAAAATTATAAAGTTAATGCC 12021 GCGCTCTAACCACCTGAGCTACGCGCCCAAG-------CTA------------------- 12020 GCGCTCTAACCACCTGAGCTACGCGCCCAAG-------CTA------------------- 12018 --TCGTTATAAACAGTAAGGATGAAAAAAGAG------------------------CTAT 12022 TTTTGCTACTATCAGAATCGATAACAATACAAT-----CTT---------------CCTT ** * 12023 ---TACATGACTTGAACACGCGACCCTCTGATTACAAATCAGATGCTCTACCAACTGAGC 12024 ---TACATGACTTGAACACGCGACCCTCTGATTACAAATCAGATGCTCTACCAACTGAGC 12019 GGCTACATGACTTGAACACGCGACCCTCTGATTACAAATCAGATGCTCTACCAACTGAGC 12021 --TTGCTTGGTTT-----T--TACTTTCTTATA-------A------------------- 12020 --TTGCTTGGTTT-----T--TACTTTCTTATA-------------------A------- 12018 TAAAGCACTATATGAA-ACAT--TCTTCCAAA--AATAGTACCTATTACACTACTTACAC 12022 TAGCTCAGAAATGGTA-ACGTAGTCATTAAGATCAATACTAACCATAATCATAGCTAATT * * 12023 TAAGCCGGCAATCTACTAATGCGGGTGAAGGGACTTGAACCCCCACGCCGTTAAGCGCCA 12024 TAAGCCGGCAATCTACTAATGCGGGTGAAGGGACTTGAACCCCCACGCCGTTAAGCGCCA 12019 TAAGCCGGCAATCTACTAATGCGGGTGAAGGGACTTGAACCCCCACGCCGTTAAGCGCCA 12021 ---------AG-----TAAAGCGGGTGACGAGAATCGAACTC------------------ 12020 ---------AG-----TAAAGCGGGTGACGAGAATCGAACTC------------------ 12018 TATTAGATAGATAA--CAAATCGTCCT-----AAGTAAGCTTA-------CTTAGGACGA 12022 CATGATAACCATCGT-CACATCGTCCTTTAATATCTAATCCTAAATTAAGTTTGGCAGGA * ** * * * 12023 GATCCTAAATCTGGTGCGTCTGCCAATTCCGCCACACCCGCATTTCTAAATGACCCGTAC 12024 GATCCTAAATCTGGTGCGTCTGCCAATTCCGCCACACCCGCATTTCTAAATGACCCGTAC 12019 GATCCTAAATCTGGTGCGTCTGCCAATTCCGCCACACCCGCATTTCTAAATGACCCGTAC 12021 ------------------------------GCGACAACAGC------------------- 12020 ------------------------------GCGACAACAGC------------------- 12018 TTTT----ATTTAGAACATAGGATAGTTTTTCCACTTTTAATCGTAA-------CCACTT 12022 GCTT----TCTCAAAAATTTTCATAAAACCTCCCTAATAAAATATAGAA-T-ATCCATAT * 12023 TGGGCTCGAACCAGTGACCCATTGATTAAAAGTCAATTGCTCTACCAACTGAGCTAACGA 12024 TGGGCTCGAACCAGTGACCCATTGATTAAAAGTCAATTGCTCTACCAACTGAGCTAACGA 12019 TGGGCTCGAACCAGTGACCCATTGATTAAAAGTCAATTGCTCTACCAACTGAGCTAACGA 12021 --------------T-----------TGGAAGGCTGTAGTTTTACCA-CTAAACTA---- 12020 -------------------------TTGGAAGGCTGTAGTTTTACCA-CTAAACTA---- 12018 GGTATCA------GTGACA----AATTCGGA--CAATTAAGATGTTAGCCAATCTTAAGG 12022 TATAACATAACAAATGACA----AATTCGGA--CAATTAAGATGCTAGCCAATCTTAAGG * * * * * * * * **

12023 GTCTACGGTCCCGACGGGAATCGAACCCGCGATCTTCGCCGTGACAGGGCGACGTGATAA 12024 GTCTACGGTCCCGACGGGAATCGAACCCGCGATCTTCGCCGTGACAGGGCGACGTGATAA 12019 GTCTACGGTCCCGACGGGAATCGAACCCGCGATCTTCGCCGTGACAGGGCGACGTGATAA 12021 --------------------------------------------CACC------------ 12020 --------------------------------------------CACC------------ 12018 ATA-ATAATTCCAATAAAAA--------------------AAGGCTAACCAAAGTTAGTC 12022 ATA-ATAATTCCAATAAAAA--------------------AAGGCTAACCAAAGTTAGTC * 12023 CCGCTACACTACGGGACCTATGGGAGTTAACGGGATCGAACCGCTGACCCTCTGCTTGTA 12024 CCGCTACACTACGGGACCTATGGGAGTTAACGGGATCGAACCGCTGACCCTCTGCTTGTA 12019 CCGCTACACTACGGGACCTATGGGAGTTAACGGGATCGAACCGCTGACCCTCTGCTTGTA 12021 -CGCT-----------TCTATGGGAGTTAACGGGATCGAACCGCTGACCCTCTGCTTGTA 12020 -CGCT-----------TCTATGGGAGTTAACGGGATCGAACCGCTGACCCTCTGCTTGTA 12018 TCCCTTTA--------TCTACTCCGCCAGTAGGACTCGAACCTACGACATCATGATTAAC 12022 TCCCTTTA--------TCTACTCCGCCAGTAGGACTCGAACCTACGACATCATGATTAAC * ** *** ** ******* *** ** ** 12023 AGGCAGATGCT-CTCCCAGCTGAGCTAAACTCCCTTT--GCTAAGCGACTACCTTATCTC 12024 AGGCAGATGCT-CTCCCAGCTGAGCTAAACTCCCTTT--GCTAAGCGACTACCTTATCTC 12019 AGGCAGATGCT-CTCCCAGCTGAGCTAAACTCCCTTT--GCTAAGCGACTACCTTATCTC 12021 AGGCAGATGCT-CTCCCAGCTGAGCTAAACTCCCTTT--GCTAAGCGACTACCTTATCTC 12020 AGGCAGATGCT-CTCCCAGCTGAGCTAAACTCCCTTT--GCTAAGCGACTACCTTATCTC 12018 AGTCATGCGCTACTACCAACTGAGCTATGGCGGATTATAGCTAAGCGACTACCTTATCTC 12022 AGTCATGCGCTACTACCAACTGAGCTATGGCGGATTATAGCTAAGCGACTACCTTATCTC ** ** *** ** *** ******** ** ********************* 12023 ACAGGGGGCAACCCCCAACTACTTCCGGCGTTCTAGGGCTTAACTTCTGTGTTCGGCATG 12024 ACAGGGGGCAACCCCCAACTACTTCCGGCGTTCTAGGGCTTAACTTCTGTGTTCGGCATG 12019 ACAGGGGGCAACCCCCAACTACTTCCGGCGTTCTAGGGCTTAACTTCTGTGTTCGGCATG 12021 ACAGGGGGCAACCCCCAACTACTTCCGGCGTTCTAGGGCTTAACTTCTGTGTTCGGCATG 12020 ACAGGGGGCAACCCCCAACTACTTCCGGCGTTCTAGGGCTTAACTTCTGTGTTCGGCATG 12018 ACAGGGGGCAACCCCCAACTACTTCCGGCGTTCTAGGGCTTAACTTCTGTGTTCGGCATG 12022 ACAGGGGGCAACCCCCAACTACTTCCGGCGTTCTAGGGCTTAACTTCTGTGTTCGGCATG ************************************************************ 12023 AGAACAGGTGTATCTCCTAGGCAATTATCACTTAACTATTGAGCCTTATTCACTCAAAAT 12024 AGAACAGGTGTATCTCCTAGGCAATTATCACTTAACTATTGAGCCTTATTCACTCAAAAT 12019 AGAACAGGTGTATCTCCTAGGCAATTATCACTTAACTATTGAGCCTTATTCACTCAAAAT 12021 AGAACAGGTGTATCTCCTAGGCAATTATCACTTAACTATTGAGCCTTATTCACTCAAAAT 12020 AGAACAGGTGTATCTCCTAGGCAATTATCACTTAACTATTGAGCCTTATTCACTCAAAAT 12018 AGAACAGGTGTATCTCCTAGGCAATTATCACTTAACTATTGAGCCTTATTCACTCAAAAT 12022 AGAACAGGTGTATCTCCTAGGCAATTATCACTTAACTATTGAGCCTTATTCACTCAAAAT ************************************************************ 12023 TGAATATCTATAGTCTAACAAGAAACCGTAACGTTGTCAATATCTCTTTTTGGATAAGTC 12024 TGAATATCTATAGTCTAACAAGAAACCGTAACGTTGTCAATATCTCTTTTTGGATAAGTC 12019 TGAATATCTATAGTCTAACAAGAAACCGTAACGTTGTCAATATCTCTTTTTGGATAAGTC 12021 TGAATATCTATAGTCTAACAAGAAACCGTAACGTTGTCAATATCTCTTTTTGGATAAGTC 12020 TGAATATCTATAGTCTAACAAGAAACCGTAACGTTGTCAATATCTCTTTTTGGATAAGTC 12018 TGAATATCTATAGTCTAACAAGAAACCGTAACGTTGTCAATATCTCTTTTTGGATAAGTC 12022 TGAATATCTATAGTCTAACAAGAAACCGTAACGTTGTCAATATCTCTTTTTGGATAAGTC ************************************************************ 12023 CTCGAGCTATTAGTATTAGTCCGCTAAATGTGTCACCACAATTACACTCCTAACCTATCT 12024 CTCGAGCTATTAGTATTAGTCCGCTAAATGTGTCACCACAATTACACTCCTAACCTATCT 12019 CTCGAGCTATTAGTATTAGTCCGCTAAATGTGTCACCACAATTACACTCCTAACCTATCT 12021 CTCGAGCTATTAGTATTAGTCCGCTAAATGTGTCACCACAATTACACTCCTAACCTATCT 12020 CTCGAGCTATTAGTATTAGTCCGCTAAATGTGTCACCACAATTACACTCCTAACCTATCT 12018 CTCGAGCTATTAGTATTAGTCCGCTAAATGTGTCACCACAATTACACTCCTAACCTATCT 12022 CTCGAGCTATTAGTATTAGTCCGCTAAATGTGTCACCACAATTACACTCCTAACCTATCT ************************************************************ 12023 ACCTGATCATCTCTCAGGGCTCTTACTGATATAAAATCATGGGAAATCTCATCTTGAGGT 12024 ACCTGATCATCTCTCAGGGCTCTTACTGATATAAAATCATGGGAAATCTCATCTTGAGGT 12019 ACCTGATCATCTCTCAGGGCTCTTACTGATATAAAATCATGGGAAATCTCATCTTGAGGT 12021 ACCTGATCATCTCTCAGGGCTCTTACTGATATAAAATCATGGGAAATCTCATCTTGAGGT 12020 ACCTGATCATCTCTCAGGGCTCTTACTGATATAAAATCATGGGAAATCTCATCTTGAGGT 12018 ACCTGATCATCTCTCAGGGCTCTTACTGATATAAAATCATGGGAAATCTCATCTTGAGGT 12022 ACCTGATCATCTCTCAGGGCTCTTACTGATATAAAATCATGGGAAATCTCATCTTGAGGT ************************************************************ 12023 GGGCTTCGCACTTAGATGCTTTCAGCGCTTATCCCTTCCCTACATAGCTACCCAGCGATG 12024 GGGCTTCGCACTTAGATGCTTTCAGCGCTTATCCCTTCCCTACATAGCTACCCAGCGATG 12019 GGGCTTCGCACTTAGATGCTTTCAGCGCTTATCCCTTCCCTACATAGCTACCCAGCGATG 12021 GGGCTTCGCACTTAGATGCTTTCAGCGCTTATCCCTTCCCTACATAGCTACCCAGCGATG 12020 GGGCTTCGCACTTAGATGCTTTCAGCGCTTATCCCTTCCCTACATAGCTACCCAGCGATG 12018 GGGCTTCGCACTTAGATGCTTTCAGCGCTTATCCCTTCCCTACATAGCTACCCAGCGATG 12022 GGGCTTCGCACTTAGATGCTTTCAGCGCTTATCCCTTCCCTACATAGCTACCCAGCGATG ************************************************************ 12023 CCTTTGGCAAGACAACTGGTACACCAGCGGTAAGTCCACTCTGGTCCTCTCGTACTAGGA 12024 CCTTTGGCAAGACAACTGGTACACCAGCGGTAAGTCCACTCTGGTCCTCTCGTACTAGGA 12019 CCTTTGGCAAGACAACTGGTACACCAGCGGTAAGTCCACTCTGGTCCTCTCGTACTAGGA 12021 CCTTTGGCAAGACAACTGGTACACCAGCGGTAAGTCCACTCTGGTCCTCTCGTACTAGGA 12020 CCTTTGGCAAGACAACTGGTACACCAGCGGTAAGTCCACTCTGGTCCTCTCGTACTAGGA 12018 CCTTTGGCAAGACAACTGGTACACCAGCGGTAAGTCCACTCTGGTCCTCTCGTACTAGGA 12022 CCTTTGGCAAGACAACTGGTACACCAGCGGTAAGTCCACTCTGGTCCTCTCGTACTAGGA ************************************************************ 12023 GCAGATCCTCTCAAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGT 12024 GCAGATCCTCTCAAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGT 12019 GCAGATCCTCTCAAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGT 12021 GCAGATCCTCTCAAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGT 12020 GCAGATCCTCTCAAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGT 12018 GCAGATCCTCTCAAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGT 12022 GCAGATCCTCTCAAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGT ************************************************************ 12023 TCTGAACCCAGCTCGCGTGCCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTA 12024 TCTGAACCCAGCTCGCGTGCCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTA 12019 TCTGAACCCAGCTCGCGTGCCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTA 12021 TCTGAACCCAGCTCGCGTGCCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTA 12020 TCTGAACCCAGCTCGCGTGCCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTA 12018 TCTGAACCCAGCTCGCGTGCCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTA 12022 TCTGAACCCAGCTCGCGTGCCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTA ************************************************************ 12023 CAGCCCCAGGATGCGACGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTC 12024 CAGCCCCAGGATGCGACGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTC 12019 CAGCCCCAGGATGCGACGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTC 12021 CAGCCCCAGGATGCGACGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTC 12020 CAGCCCCAGGATGCGACGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTC 12018 CAGCCCCAGGATGCGACGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTC 12022 CAGCCCCAGGATGCGACGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTC ************************************************************ 12023 TTGGGGGAGATAAGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTC 12024 TTGGGGGAGATAAGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTC 12019 TTGGGGGAGATAAGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTC 12021 TTGGGGGAGATAAGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTC 12020 TTGGGGGAGATAAGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTC 12018 TTGGGGGAGATAAGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTC 12022 TTGGGGGAGATAAGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTC ************************************************************ 12023 CATACGGAACCACCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGAGTTGTAGCTCTCG 12024 CATACGGAACCACCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGAGTTGTAGCTCTCG 12019 CATACGGAACCACCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGAGTTGTAGCTCTCG 12021 CATACGGAACCACCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGAGTTGTAGCTCTCG 12020 CATACGGAACCACCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGAGTTGTAGCTCTCG 12018 CATACGGAACCACCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGAGTTGTAGCTCTCG 12022 CATACGGAACCACCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGAGTTGTAGCTCTCG ************************************************************ 12023 CAGTCAAGCTCCCTTATACCTTTACACTCTACGACTGATTTCCAACCAGTCTGAGGGAAC 12024 CAGTCAAGCTCCCTTATACCTTTACACTCTACGACTGATTTCCAACCAGTCTGAGGGAAC 12019 CAGTCAAGCTCCCTTATACCTTTACACTCTACGACTGATTTCCAACCAGTCTGAGGGAAC 12021 CAGTCAAGCTCCCTTATACCTTTACACTCTACGACTGATTTCCAACCAGTCTGAGGGAAC 12020 CAGTCAAGCTCCCTTATACCTTTACACTCTACGACTGATTTCCAACCAGTCTGAGGGAAC 12018 CAGTCAAGCTCCCTTATACCTTTACACTCTACGACTGATTTCCAACCAGTCTGAGGGAAC 12022 CAGTCAAGCTCCCTTATACCTTTACACTCTACGACTGATTTCCAACCAGTCTGAGGGAAC ************************************************************ 12023 CTTTGGGCGCCTCCGTTACCTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAGAC 12024 CTTTGGGCGCCTCCGTTACCTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAGAC 12019 CTTTGGGCGCCTCCGTTACCTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAGAC 12021 CTTTGGGCGCCTCCGTTACCTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAGAC 12020 CTTTGGGCGCCTCCGTTACCTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAGAC 12018 CTTTGGGCGCCTCCGTTACCTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAGAC 12022 CTTTGGGCGCCTCCGTTACCTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAGAC ************************************************************ 12023 ACTGTCTCCGATAGGGATTGCCTATCTGGGTTAGAGTAGCCATAACACAAGGGTAGTATC 12024 ACTGTCTCCGATAGGGATTGCCTATCTGGGTTAGAGTAGCCATAACACAAGGGTAGTATC 12019 ACTGTCTCCGATAGGGATTGCCTATCTGGGTTAGAGTAGCCATAACACAAGGGTAGTATC 12021 ACTGTCTCCGATAGGGATTGCCTATCTGGGTTAGAGTAGCCATAACACAAGGGTAGTATC 12020 ACTGTCTCCGATAGGGATTGCCTATCTGGGTTAGAGTAGCCATAACACAAGGGTAGTATC 12018 ACTGTCTCCGATAGGGATTGCCTATCTGGGTTAGAGTAGCCATAACACAAGGGTAGTATC 12022 ACTGTCTCCGATAGGGATTGCCTATCTGGGTTAGAGTAGCCATAACACAAGGGTAGTATC ************************************************************ 12023 CCAACAACGCCTCAAACGAAACTGGCGTCCCGTTATCATAGGCTCCTACCTATCCTGTAC 12024 CCAACAACGCCTCAAACGAAACTGGCGTCCCGTTATCATAGGCTCCTACCTATCCTGTAC 12019 CCAACAACGCCTCAAACGAAACTGGCGTCCCGTTATCATAGGCTCCTACCTATCCTGTAC 12021 CCAACAACGCCTCAAACGAAACTGGCGTCCCGTTATCATAGGCTCCTACCTATCCTGTAC 12020 CCAACAACGCCTCAAACGAAACTGGCGTCCCGTTATCATAGGCTCCTACCTATCCTGTAC 12018 CCAACAACGCCTCAAACGAAACTGGCGTCCCGTTATCATAGGCTCCTACCTATCCTGTAC 12022 CCAACAACGCCTCAAACGAAACTGGCGTCCCGTTATCATAGGCTCCTACCTATCCTGTAC ************************************************************ 12023 ATGTGGTACAGATACTCAATATCAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTG 12024 ATGTGGTACAGATACTCAATATCAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTG 12019 ATGTGGTACAGATACTCAATATCAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTG 12021 ATGTGGTACAGATACTCAATATCAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTG 12020 ATGTGGTACAGATACTCAATATCAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTG 12018 ATGTGGTACAGATACTCAATATCAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTG 12022 ATGTGGTACAGATACTCAATATCAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTG ************************************************************ 12023 TCGCGGGTAACCTGCATCTTCACAGGTACTAAAATTTCACCGAGTCTCTCGTTGAGACAG 12024 TCGCGGGTAACCTGCATCTTCACAGGTACTAAAATTTCACCGAGTCTCTCGTTGAGACAG 12019 TCGCGGGTAACCTGCATCTTCACAGGTACTAAAATTTCACCGAGTCTCTCGTTGAGACAG 12021 TCGCGGGTAACCTGCATCTTCACAGGTACTAAAATTTCACCGAGTCTCTCGTTGAGACAG 12020 TCGCGGGTAACCTGCATCTTCACAGGTACTAAAATTTCACCGAGTCTCTCGTTGAGACAG 12018 TCGCGGGTAACCTGCATCTTCACAGGTACTAAAATTTCACCGAGTCTCTCGTTGAGACAG 12022 TCGCGGGTAACCTGCATCTTCACAGGTACTAAAATTTCACCGAGTCTCTCGTTGAGACAG ************************************************************ 12023 TGCCCAAATCATTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTAC 12024 TGCCCAAATCATTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTAC 12019 TGCCCAAATCATTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTAC 12021 TGCCCAAATCATTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTAC 12020 TGCCCAAATCATTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTAC 12018 TGCCCAAATCATTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTAC 12022 TGCCCAAATCATTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTAC ************************************************************ 12023 CTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCATACCTTCGCTTA 12024 CTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCATACCTTCGCTTA 12019 CTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCATACCTTCGCTTA 12021 CTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCATACCTTCGCTTA 12020 CTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCATACCTTCGCTTA 12018 CTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCATACCTTCGCTTA 12022 CTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCATACCTTCGCTTA ************************************************************ 12023 CGCTAAGCACTCCTCTTAACCTTCCAGCACCGGGCAGGCGTCACCCCCTATACATCATCT 12024 CGCTAAGCACTCCTCTTAACCTTCCAGCACCGGGCAGGCGTCACCCCCTATACATCATCT 12019 CGCTAAGCACTCCTCTTAACCTTCCAGCACCGGGCAGGCGTCACCCCCTATACATCATCT 12021 CGCTAAGCACTCCTCTTAACCTTCCAGCACCGGGCAGGCGTCACCCCCTATACATCATCT 12020 CGCTAAGCACTCCTCTTAACCTTCCAGCACCGGGCAGGCGTCACCCCCTATACATCATCT 12018 CGCTAAGCACTCCTCTTAACCTTCCAGCACCGGGCAGGCGTCACCCCCTATACATCATCT 12022 CGCTAAGCACTCCTCTTAACCTTCCAGCACCGGGCAGGCGTCACCCCCTATACATCATCT ************************************************************ 12023 TACGATTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCTTGGGCCTATTCACTGCGGC 12024 TACGATTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCTTGGGCCTATTCACTGCGGC 12019 TACGATTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCTTGGGCCTATTCACTGCGGC 12021 TACGATTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCTTGGGCCTATTCACTGCGGC 12020 TACGATTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCTTGGGCCTATTCACTGCGGC 12018 TACGATTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCTTGGGCCTATTCACTGCGGC 12022 TACGATTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCTTGGGCCTATTCACTGCGGC ************************************************************ 12023 TGATCTAAAATCAGCGCCCCTTCTCCCGAAGTTACGGGGCCATTTTGCCGAGTTCCTTAA 12024 TGATCTAAAATCAGCGCCCCTTCTCCCGAAGTTACGGGGCCATTTTGCCGAGTTCCTTAA 12019 TGATCTAAAATCAGCGCCCCTTCTCCCGAAGTTACGGGGCCATTTTGCCGAGTTCCTTAA 12021 TGATCTAAAATCAGCGCCCCTTCTCCCGAAGTTACGGGGCCATTTTGCCGAGTTCCTTAA 12020 TGATCTAAAATCAGCGCCCCTTCTCCCGAAGTTACGGGGCCATTTTGCCGAGTTCCTTAA 12018 TGATCTAAAATCAGCGCCCCTTCTCCCGAAGTTACGGGGCCATTTTGCCGAGTTCCTTAA 12022 TGATCTAAAATCAGCGCCCCTTCTCCCGAAGTTACGGGGCCATTTTGCCGAGTTCCTTAA ************************************************************ 12023 CGAGAGTTCTCTCGCTCACCTGAGGCTACTCGCCTCGACTACCTGTGTCGGTTTGCGGTA 12024 CGAGAGTTCTCTCGCTCACCTGAGGCTACTCGCCTCGACTACCTGTGTCGGTTTGCGGTA 12019 CGAGAGTTCTCTCGCTCACCTGAGGCTACTCGCCTCGACTACCTGTGTCGGTTTGCGGTA 12021 CGAGAGTTCTCTCGCTCACCTGAGGCTACTCGCCTCGACTACCTGTGTCGGTTTGCGGTA 12020 CGAGAGTTCTCTCGCTCACMTGAGGCTACTCGCCTCGACTACCTGTGTCGGTTTGCGGTA 12018 CGAGAGTTCTCTCGCTCACCTGAGGCTACTCGCCTCGACTACCTGTGTCGGTTTGCGGTA 12022 CGAGAGTTCTCTCGCTCACCTGAGGCTACTCGCCTCGACTACCTGTGTCGGTTTGCGGTA ******************* **************************************** 12023 CGGGTAGAGTATATGTATCGCTAGAAGCTTTTCTTGGCAGTGTGACATCACTAACTTCGC 12024 CGGGTAGAGTATATGTATCGCTAGAAGCTTTTCTTGGCAGTGTGACATCACTAACTTCGC 12019 CGGGTAGAGTATATGTATCGCTAGAAGCTTTTCTTGGCAGTGTGACATCACTAACTTCGC 12021 CGGGTAGAGTATATGTATCGCTAGAAGCTTTTCTTGGCAGTGTGACATCACTAACTTCGC 12020 CGGGTAGAGTATATGTATCGCTAGAAGCTTTTCTTGGCAGTGTGACATCACTAACTTCGC 12018 CGGGTAGAGTATATGTATCGCTAGAAGCTTTTCTTGGCAGTGTGACATCACTAACTTCGC 12022 CGGGTAGAGTATATGTATCGCTAGAAGCTTTTCTTGGCAGTGTGACATCACTAACTTCGC ************************************************************ 12023 TACTAAACTTCGCTCCTCGTCACAGCTCAATGTTAAAGATATAAGCATTTGACTCATATC 12024 TACTAAACTTCGCTCCTCGTCACAGCTCAATGTTAAAGATATAAGCATTTGACTCATATC 12019 TACTAAACTTCGCTCCTCGTCACAGCTCAATGTTAAAGATATAAGCATTTGACTCATATC 12021 TACTAAACTTCGCTCCTCGTCACAGCTCAATGTTAAAGATATAAGCATTTGACTCATATC 12020 TACTAAACTTCGCTCCTCGTCACAGCTCAATGTTAAAGATATAAGCATTTGACTCATATC 12018 TACTAAACTTCGCTCCTCGTCACAGCTCAATGTTAAAGATATAAGCATTTGACTCATATC 12022 TACTAAACTTCGCTCCTCGTCACAGCTCAATGTTAAAGATATAAGCATTTGACTCATATC ************************************************************ 12023 ACACCTCACTGTTTGACCAGACACTTCCAATCGTCTGGTTTAGTTAGCCTACTGCGTCCC 12024 ACACCTCACTGTTTGACCAGACACTTCCAATCGTCTGGTTTAGTTAGCCTACTGCGTCCC 12019 ACACCTCACTGTTTGACCAGACACTTCCAATCGTCTGGTTTAGTTAGCCTACTGCGTCCC 12021 ACACCTCACTGTTTGACCAGACACTTCCAATCGTCTGGTTTAGTTAGCCTACTGCGTCCC 12020 ACACCTCACTGTTTGACCAGACACTTCCAATCGTCTGGTTTAGTTAGCCTACTGCGTCCC 12018 ACACCTCACTGTTTGACCAGACACTTCCAATCGTCTGGTTTAGTTAGCCTACTGCGTCCC 12022 ACACCTCACTGTTTGACCAGACACTTCCAATCGTCTGGTTTAGTTAGCCTACTGCGTCCC ************************************************************ 12023 TCCATCACTATATACTCTAGTACAGGAATATCAACCTGTTGTCCATCGGATACACCTTTC 12024 TCCATCACTATATACTCTAGTACAGGAATATCAACCTGTTGTCCATCGGATACACCTTTC 12019 TCCATCACTATATACTCTAGTACAGGAATATCAACCTGTTGTCCATCGGATACACCTTTC 12021 TCCATCACTATATACTCTAGTACAGGAATATCAACCTGTTGTCCATCGGATACACCTTTC 12020 TCCATCACTATATACTCTAGTACAGGAATATCAACCTGTTGTCCATCGGATACACCTTTC 12018 TCCATCACTATATACTCTAGTACAGGAATATCAACCTGTTGTCCATCGGATACACCTTTC 12022 TCCATCACTATATACTCTAGTACAGGAATATCAACCTGTTGTCCATCGGATACACCTTTC ************************************************************ 12023 GGTCTCTCCTTAGGTCCCGACTAACCCAGGGCGGACGAGCCTTCCCCTGGAAACCTTAGT 12024 GGTCTCTCCTTAGGTCCCGACTAACCCAGGGCGGACGAGCCTTCCCCTGGAAACCTTAGT 12019 GGTCTCTCCTTAGGTCCCGACTAACCCAGGGCGGACGAGCCTTCCCCTGGAAACCTTAGT 12021 GGTCTCTCCTTAGGTCCCGACTAACCCAGGGCGGACGAGCCTTCCCCTGGAAACCTTAGT 12020 GGTCTCTCCTTAGGTCCCGACTAACCCAGGGCGGACGAGCCTTCCCCTGGAAACCTTAGT 12018 GGTCTCTCCTTAGGTCCCGACTAACCCAGGGCGGACGAGCCTTCCCCTGGAAACCTTAGT 12022 GGTCTCTCCTTAGGTCCCGACTAACCCAGGGCGGACGAGCCTTCCCCTGGAAACCTTAGT ************************************************************ 12023 CTTACGGTGGACAGGATTCTCACCTGTCTTGCGCTACTCATACCGGCATTCTCACTTCTA 12024 CTTACGGTGGACAGGATTCTCACCTGTCTTGCGCTACTCATACCGGCATTCTCACTTCTA 12019 CTTACGGTGGACAGGATTCTCACCTGTCTTGCGCTACTCATACCGGCATTCTCACTTCTA 12021 CTTACGGTGGACAGGATTCTCACCTGTCTTGCGCTACTCATACCGGCATTCTCACTTCTA 12020 CTTACGGTGGACAGGATTCTCACCTGTCTTGCGCTACTCATACCGGCATTCTCACTTCTA 12018 CTTACGGTGGACAGGATTCTCACCTGTCTTGCGCTACTCATACCGGCATTCTCACTTCTA 12022 CTTACGGTGGACAGGATTCTCACCTGTCTTGCGCTACTCATACCGGCATTCTCACTTCTA ************************************************************ 12023 TGCGTTCCAGCGCTCCTCACGGTACACCTTCTTCACACATAGAACGCTCTCCTACCATGA 12024 TGCGTTCCAGCGCTCCTCACGGTACACCTTCTTCACACATAGAACGCTCTCCTACCATGA 12019 TGCGTTCCAGCGCTCCTCACGGTACACCTTCTTCACACATAGAACGCTCTCCTACCATGA 12021 TGCGTTCCAGCGCTCCTCACGGTACACCTTCTTCACACATAGAACGCTCTCCTACCATGA 12020 TGCGTTCCAGCGCTCCTCACGGTACACCTTCTTCACACATAGAACGCTCTCCTACCATGA 12018 TGCGTTCCAGCGCTCCTCACGGTACACCTTCTTCACACATAGAACGCTCTCCTACCATGA 12022 TGCGTTCCAGCGCTCCTCACGGTACACCTTCTTCACACATAGAACGCTCTCCTACCATGA ************************************************************ 12023 CACTTTTGTGTCATCCACAGCTTCGGTAATATGTTTTAGCCCCGGTACATTTTCGGCGCA 12024 CACTTTTGTGTCATCCACAGCTTCGGTAATATGTTTTAGCCCCGGTACATTTTCGGCGCA 12019 CACTTTTGTGTCATCCACAGCTTCGGTAATATGTTTTAGCCCCGGTACATTTTCGGCGCA 12021 CACTTTTGTGTCATCCACAGCTTCGGTAATATGTTTTAGCCCCGGTACATTTTCGGCGCA 12020 CACTTTTGTGTCATCCACAGCTTCGGTAATATGTTTTAGCCCCGGTACATTTTCGGCGCA 12018 CACTTTTGTGTCATCCACAGCTTCGGTAATATGTTTTAGCCCCGGTACATTTTCGGCGCA 12022 CACTTTTGTGTCATCCACAGCTTCGGTAATATGTTTTAGCCCCGGTACATTTTCGGCGCA ************************************************************ 12023 GGGTCACTCGACTAGTGAGCTATTACGCACTCTTTGAATGAATAGCTGCTTCTAAGCTAA 12024 GGGTCACTCGACTAGTGAGCTATTACGCACTCTTTGAATGAATAGCTGCTTCTAAGCTAA 12019 GGGTCACTCGACTAGTGAGCTATTACGCACTCTTTGAATGAATAGCTGCTTCTAAGCTAA 12021 GGGTCACTCGACTAGTGAGCTATTACGCACTCTTTGAATGAATAGCTGCTTCTAAGCTAA 12020 GGGTCACTCGACTAGTGAGCTATTACGCACTCTTTGAATGAATAGCTGCTTCTAAGCTAA 12018 GGGTCACTCGACTAGTGAGCTATTACGCACTCTTTGAATGAATAGCTGCTTCTAAGCTAA 12022 GGGTCACTCGACTAGTGAGCTATTACGCACTCTTTGAATGAATAGCTGCTTCTAAGCTAA ************************************************************ 12023 CATCCTAGTTGTCTGTGCAACCCCACATCCTTTTCCACTTAACATATATTTTGGGACCTT 12024 CATCCTAGTTGTCTGTGCAACCCCACATCCTTTTCCACTTAACATATATTTTGGGACCTT 12019 CATCCTAGTTGTCTGTGCAACCCCACATCCTTTTCCACTTAACATATATTTTGGGACCTT 12021 CATCCTAGTTGTCTGTGCAACCCCACATCCTTTTCCACTTAACATATATTTTGGGACCTT 12020 CATCCTAGTTGTCTGTGCAACCCCACATCCTTTTCCACTTAACATATATTTTGGGACCTT 12018 CATCCTAGTTGTCTGTGCAACCCCACATCCTTTTCCACTTAACATATATTTTGGGACCTT 12022 CATCCTAGTTGTCTGTGCAACCCCACATCCTTTTCCACTTAACATATATTTTGGGACCTT ************************************************************ 12023 AGCTGGTGGTCTGGGCTGTTTCCCTTTCGACTACGGATCTTAGCACTCGCAGTCTGACTG 12024 AGCTGGTGGTCTGGGCTGTTTCCCTTTCGACTACGGATCTTAGCACTCGCAGTCTGACTG 12019 AGCTGGTGGTCTGGGCTGTTTCCCTTTCGACTACGGATCTTAGCACTCGCAGTCTGACTG 12021 AGCTGGTGGTCTGGGCTGTTTCCCTTTCGACTACGGATCTTAGCACTCGCAGTCTGACTG 12020 AGCTGGTGGTCTGGGCTGTTTCCCTTTCGACTACGGATCTTAGCACTCGCAGTCTGACTG 12018 AGCTGGTGGTCTGGGCTGTTTCCCTTTCGACTACGGATCTTAGCACTCGCAGTCTGACTG 12022 AGCTGGTGGTCTGGGCTGTTTCCCTTTCGACTACGGATCTTAGCACTCGCAGTCTGACTG ************************************************************ 12023 CCGATTATATCTCGTTGGCATTCGGAGTTTATCTGAGATTGGTAATCCGGGATGGACCCC 12024 CCGATTATATCTCGTTGGCATTCGGAGTTTATCTGAGATTGGTAATCCGGGATGGACCCC 12019 CCGATTATATCTCGTTGGCATTCGGAGTTTATCTGAGATTGGTAATCCGGGATGGACCCC 12021 CCGATTATATCTCGTTGGCATTCGGAGTTTATCTGAGATTGGTAATCCGGGATGGACCCC 12020 CCGATTATATCTCGTTGGCATTCGGAGTTTATCTGAGATTGGTAATCCGGGATGGACCCC 12018 CCGATTATATCTCGTTGGCATTCGGAGTTTATCTGAGATTGGTAATCCGGGATGGACCCC 12022 CCGATTATATCTCGTTGGCATTCGGAGTTTATCTGAGATTGGTAATCCGGGATGGACCCC ************************************************************ 12023 TCACCCAAACAGTGCTCTACCTCCAAGAGACTTAACATCGACGCTAGCCCTAAAGCTATT 12024 TCACCCAAACAGTGCTCTACCTCCAAGAGACTTAACATCGACGCTAGCCCTAAAGCTATT 12019 TCACCCAAACAGTGCTCTACCTCCAAGAGACTTAACATCGACGCTAGCCCTAAAGCTATT 12021 TCACCCAAACAGTGCTCTACCTCCAAGAGACTTAACATCGACGCTAGCCCTAAAGCTATT 12020 TCACCCAAACAGTGCTCTACCTCCAAGAGACTTAACATCGACGCTAGCCCTAAAGCTATT 12018 TCACCCAAACAGTGCTCTACCTCCAAGAGACTTAACATCGACGCTAGCCCTAAAGCTATT 12022 TCACCCAAACAGTGCTCTACCTCCAAGAGACTTAACATCGACGCTAGCCCTAAAGCTATT ************************************************************ 12023 TCGGAGAGAACCAGCTATCTCCAAGTTCGTTTGGAATTTCTCCGCTACCCACAAGTCATC 12024 TCGGAGAGAACCAGCTATCTCCAAGTTCGTTTGGAATTTCTCCGCTACCCACAAGTCATC 12019 TCGGAGAGAACCAGCTATCTCCAAGTTCGTTTGGAATTTCTCCGCTACCCACAAGTCATC 12021 TCGGAGAGAACCAGCTATCTCCAAGTTCGTTTGGAATTTCTCCGCTACCCACAAGTCATC 12020 TCGGAGAGAACCAGCTATCTCCAAGTTCGTTTGGAATTTCTCCGCTACCCACAAGTCATC 12018 TCGGAGAGAACCAGCTATCTCCAAGTTCGTTTGGAATTTCTCCGCTACCCACAAGTCATC 12022 TCGGAGAGAACCAGCTATCTCCAAGTTCGTTTGGAATTTCTCCGCTACCCACAAGTCATC ************************************************************ 12023 CAAGCACTTTTCAACGTGCCCTGGTTCGGTCCTCCAGTGAGTTTTACCTCACCTTCAACC 12024 CAAGCACTTTTCAACGTGCCCTGGTTCGGTCCTCCAGTGAGTTTTACCTCACCTTCAACC 12019 CAAGCACTTTTCAACGTGCCCTGGTTCGGTCCTCCAGTGAGTTTTACCTCACCTTCAACC 12021 CAAGCACTTTTCAACGTGCCCTGGTTCGGTCCTCCAGTGAGTTTTACCTCACCTTCAACC 12020 CAAGCACTTTTCAACGTGCCCTGGTTCGGTCCTCCAGTGAGTTTTACCTCACCTTCAACC 12018 CAAGCACTTTTCAACGTGCCCTGGTTCGGTCCTCCAGTGAGTTTTACCTCACCTTCAACC 12022 CAAGCACTTTTCAACGTGCCCTGGTTCGGTCCTCCAGTGAGTTTTACCTCACCTTCAACC ************************************************************ 12023 TGCTCATGGGTAGGTCACATGGTTTCGGGTCTACAACATGATACTATGACGCCCTATTAA 12024 TGCTCATGGGTAGGTCACATGGTTTCGGGTCTACAACATGATACTATGACGCCCTATTAA 12019 TGCTCATGGGTAGGTCACATGGTTTCGGGTCTACAACATGATACTATGACGCCCTATTAA 12021 TGCTCATGGGTAGGTCACATGGTTTCGGGTCTACAACATGATACTATGACGCCCTATTAA 12020 TGCTCATGGGTAGGTCACATGGTTTCGGGTCTACAACATGATACTATGACGCCCTATTAA 12018 TGCTCATGGGTAGGTCACATGGTTTCGGGTCTACAACATGATACTATGACGCCCTATTAA 12022 TGCTCATGGGTAGGTCACATGGTTTCGGGTCTACAACATGATACTATGACGCCCTATTAA ************************************************************ 12023 GACTCGGTTTCCCTACGGCTCCGTCTCTTCAACTTAACCTCGCATCATATCGTAACTCGC 12024 GACTCGGTTTCCCTACGGCTCCGTCTCTTCAACTTAACCTCGCATCATATCGTAACTCGC 12019 GACTCGGTTTCCCTACGGCTCCGTCTCTTCAACTTAACCTCGCATCATATCGTAACTCGC 12021 GACTCGGTTTCCCTACGGCTCCGTCTCTTCAACTTAACCTCGCATCATATCGTAACTCGC 12020 GACTCGGTTTCCCTACGGCTCCGTCTCTTCAACTTAACCTCGCATCATATCGTAACTCGC 12018 GACTCGGTTTCCCTACGGCTCCGTCTCTTCAACTTAACCTCGCATCATATCGTAACTCGC 12022 GACTCGGTTTCCCTACGGCTCCGTCTCTTCAACTTAACCTCGCATCATATCGTAACTCGC ************************************************************ 12023 CGGTTCATTCTACAAAAGGCACGCTCTCACCCATTAACGGGCTCGAACTTGTTGTAGGCA 12024 CGGTTCATTCTACAAAAGGCACGCTCTCACCCATTAACGGGCTCGAACTTGTTGTAGGCA 12019 CGGTTCATTCTACAAAAGGCACGCTCTCACCCATTAACGGGCTCGAACTTGTTGTAGGCA 12021 CGGTTCATTCTACAAAAGGCACGCTCTCACCCATTAACGGGCTCGAACTTGTTGTAGGCA 12020 CGGTTCATTCTACAAAAGGCACGCTCTCACCCATTAACGGGCTCGAACTTGTTGTAGGCA 12018 CGGTTCATTCTACAAAAGGCACGCTCTCACCCATTAACGGGCTCGAACTTGTTGTAGGCA 12022 CGGTTCATTCTACAAAAGGCACGCTCTCACCCATTAACGGGCTCGAACTTGTTGTAGGCA ************************************************************ 12023 CACGGTTTCAGGTTCTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGT 12024 CACGGTTTCAGGTTCTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGT 12019 CACGGTTTCAGGTTCTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGT 12021 CACGGTTTCAGGTTCTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGT 12020 CACGGTTTCAGGTTCTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGT 12018 CACGGTTTCAGGTTCTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGT 12022 CACGGTTTCAGGTTCTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGT ************************************************************ 12023 ACTGGTTCACTATCGGTCACTAGAGAGTATTTAGGGTTGGGAGATGGTCCTCCCAGATTC 12024 ACTGGTTCACTATCGGTCACTAGAGAGTATTTAGGGTTGGGAGATGGTCCTCCCAGATTC 12019 ACTGGTTCACTATCGGTCACTAGAGAGTATTTAGGGTTGGGAGATGGTCCTCCCAGATTC 12021 ACTGGTTCACTATCGGTCACTAGAGAGTATTTAGGGTTGGGAGATGGTCCTCCCAGATTC 12020 ACTGGTTCACTATCGGTCACTAGAGAGTATTTAGGGTTGGGAGATGGTCCTCCCAGATTC 12018 ACTGGTTCACTATCGGTCACTAGAGAGTATTTAGGGTTGGGAGATGGTCCTCCCAGATTC 12022 ACTGGTTCACTATCGGTCACTAGAGAGTATTTAGGGTTGGGAGATGGTCCTCCCAGATTC ************************************************************ 12023 CGACGAGATTTCGCGTGTCTCGCCGTACTCAGGATACTGCTAAGGTTAATCTATCATTTT 12024 CGACGAGATTTCGCGTGTCTCGCCGTACTCAGGATACTGCTAAGGTTAATCTATCATTTT 12019 CGACGAGATTTCGCGTGTCTCGCCGTACTCAGGATACTGCTAAGGTTAATCTATCATTTT 12021 CGACGAGATTTCGCGTGTCTCGCCGTACTCAGGATACTGCTAAGGTTAATCTATCATTTT 12020 CGACGAGATTTCGCGTGTCTCGCCGTACTCAGGATACTGCTAAGGTTAATCTATCATTTT 12018 CGACGAGATTTCGCGTGTCTCGCCGTACTCAGGATACTGCTAAGGTTAATCTATCATTTT 12022 CGACGAGATTTCGCGTGTCTCGCCGTACTCAGGATACTGCTAAGGTTAATCTATCATTTT ************************************************************ 12023 AAATACGAGGCTGTTACTCTCTTTGGCTTACCTTCCCAGGTAATTCTTCTATAATGATTA 12024 AAATACGAGGCTGTTACTCTCTTTGGCTTACCTTCCCAGGTAATTCTTCTATAATGATTA 12019 AAATACGAGGCTGTTACTCTCTTTGGCTTACCTTCCCAGGTAATTCTTCTATAATGATTA 12021 AAATACGAGGCTGTTACTCTCTTTGGCTTACCTTCCCAGGTAATTCTTCTATAATGATTA 12020 AAATACGAGGCTGTTACTCTCTTTGGCTTACCTTCCCAGGTAATTCTTCTATAATGATTA 12018 AAATACGAGGCTGTTACTCTCTTTGGCTTACCTTCCCAGGTAATTCTTCTATAATGATTA 12022 AAATACGAGGCTGTTACTCTCTTTGGCTTACCTTCCCAGGTAATTCTTCTATAATGATTA ************************************************************ 12023 ATCCTATATCGCAGTCCTACAACCCCGAAGTGTAAACACTTCGGTTTGCCCTCCTGCCGT 12024 ATCCTATATCGCAGTCCTACAACCCCGAAGTGTAAACACTTCGGTTTGCCCTCCTGCCGT 12019 ATCCTATATCGCAGTCCTACAACCCCGAAGTGTAAACACTTCGGTTTGCCCTCCTGCCGT 12021 ATCCTATATCGCAGTCCTACAACCCCGAAGTGTAAACACTTCGGTTTGCCCTCCTGCCGT 12020 ATCCTATATCGCAGTCCTACAACCCCGAAGTGTAAACACTTCGGTTTGCCCTCCTGCCGT 12018 ATCCTATATCGCAGTCCTACAACCCCGAAGTGTAAACACTTCGGTTTGCCCTCCTGCCGT 12022 ATCCTATATCGCAGTCCTACAACCCCGAAGTGTAAACACTTCGGTTTGCCCTCCTGCCGT ************************************************************ 12023 TTCGCTCGCCGCTACTAAGGCAATCGCTTTTGCTTTCTCTTCCTGCAGCTACTTAGATGT 12024 TTCGCTCGCCGCTACTAAGGCAATCGCTTTTGCTTTCTCTTCCTGCAGCTACTTAGATGT 12019 TTCGCTCGCCGCTACTAAGGCAATCGCTTTTGCTTTCTCTTCCTGCAGCTACTTAGATGT 12021 TTCGCTCGCCGCTACTAAGGCAATCGCTTTTGCTTTCTCTTCCTGCAGCTACTTAGATGT 12020 TTCGCTCGCCGCTACTAAGGCAATCGCTTTTGCTTTCTCTTCCTGCAGCTACTTAGATGT 12018 TTCGCTCGCCGCTACTAAGGCAATCGCTTTTGCTTTCTCTTCCTGCAGCTACTTAGATGT 12022 TTCGCTCGCCGCTACTAAGGCAATCGCTTTTGCTTTCTCTTCCTGCAGCTACTTAGATGT ************************************************************ 12023 TTCAGTTCACTGCGTCTTCCTTCTCATATCCTTAACAGATATGGATACTAGTCATTAACT 12024 TTCAGTTCACTGCGTCTTCCTTCTCATATCCTTAACAGATATGGATACTAGTCATTAACT 12019 TTCAGTTCACTGCGTCTTCCTTCTCATATCCTTAACAGATATGGATACTAGTCATTAACT 12021 TTCAGTTCACTGCGTCTTCCTTCTCATATCCTTAACAGATATGGATACTAGTCATTAACT 12020 TTCAGTTCACTGCGTCTTCCTTCTCATATCCTTAACAGATATGGATACTAGTCATTAACT 12018 TTCAGTTCACTGCGTCTTCCTTCTCATATCCTTAACAGATATGGATACTAGTCATTAACT 12022 TTCAGTTCACTGCGTCTTCCTTCTCATATCCTTAACAGATATGGATACTAGTCATTAACT ************************************************************ 12023 AGTGGGTTCCCCCATTCGGACATCTCTGGATCAGCGCTTACTTACAGCTCCCCAAAGCAT 12024 AGTGGGTTCCCCCATTCGGACATCTCTGGATCAGCGCTTACTTACAGCTCCCCAAAGCAT 12019 AGTGGGTTCCCCCATTCGGACATCTCTGGATCAGCGCTTACTTACAGCTCCCCAAAGCAT 12021 AGTGGGTTCCCCCATTCGGACATCTCTGGATCAGCGCTTACTTACAGCTCCCCAAAGCAT 12020 AGTGGGTTCCCCCATTCGGACATCTCTGGATCAGCGCTTACTTACAGCTCCCCAAAGCAT 12018 AGTGGGTTCCCCCATTCGGACATCTCTGGATCAGCGCTTACTTACAGCTCCCCAAAGCAT 12022 AGTGGGTTCCCCCATTCGGACATCTCTGGATCAGCGCTTACTTACAGCTCCCCAAAGCAT ************************************************************ 12023 TTCGTCGTTAGTCACGTCCTTCTTCGGCTTCTAGTGCCAAGGCATCCACCGTGCGCCCTT 12024 TTCGTCGTTAGTCACGTCCTTCTTCGGCTTCTAGTGCCAAGGCATCCACCGTGCGCCCTT 12019 TTCGTCGTTAGTCACGTCCTTCTTCGGCTTCTAGTGCCAAGGCATCCACCGTGCGCCCTT 12021 TTCGTCGTTAGTCACGTCCTTCTTCGGCTTCTAGTGCCAAGGCATCCACCGTGCGCCCTT 12020 TTCGTCGTTAGTCACGTCCTTCTTCGGCTTCTAGTGCCAAGGCATCCACCGTGCGCCCTT 12018 TTCGTCGTTAGTCACGTCCTTCTTCGGCTTCTAGTGCCAAGGCATCCACCGTGCGCCCTT 12022 TTCGTCGTTAGTCACGTCCTTCTTCGGCTTCTAGTGCCAAGGCATCCACCGTGCGCCCTT ************************************************************ 12023 ATTAACTTAACCTTATTAACCTAGTTTCTTTAAAACTAGAAAACTCATTAAATATTCACA 12024 ATTAACTTAACCTTATTAACCTAGTTTCTTTAAAACTAGAAAACTCATTAAATATTCACA 12019 ATTAACTTAACCTTATTAACCTAGTTTCTTTAAAACTAGAAAACTCATTAAATATTCACA 12021 ATTAACTTAACCTTATTAACCTAGTTTCTTTAAAACTAGAAAACTCATTAAATATTCACA 12020 ATTAACTTAACCTTATTAACCTAGTTTCTTTAAAACTAGAAAACTCATTAAATATTCACA 12018 ATTAACTTAACCTTATTAACCTAGTTTCTTTAAAACTAGAAAACTCATTAAATATTCACA 12022 ATTAACTTAACCTTATTAACCTAGTTTCTTTAAAACTAGAAAACTCATTAAATATTCACA ************************************************************ 12023 GCGTTTTCGGTTTATTTTCTTGTTACTTTCTACAATCTATTTCTAGATCGTGGAATTTGA 12024 GCGTTTTCGGTTTATTTTCTTGTTACTTTCTACAATCTATTTCTAGATCGTGGAATTTGA 12019 GCGTTTTCGGTTTATTTTCTTGTTACTTTCTACAATCTATTTCTAGATCGTGGAATTTGA 12021 GCGTTTTCGGTTTATTTTCTTGTTACTTTCTACAATCTATTTCTAGATCGTGGAATTTGA 12020 GCGTTTTCGGTTTATTTTCTTGTTACTTTCTACAATCTATTTCTAGATCGTGGAATTTGA 12018 GCGTTTTCGGTTTATTTTCTTGTTACTTTCTACAATCTATTTCTAGATCGTGGAATTTGA 12022 GCGTTTTCGGTTTATTTTCTTGTTACTTTCTACAATCTATTTCTAGATCGTGGAATTTGA ************************************************************

12023 TATAGATATTCAATTTTCAATGAACAATTTGAACCTTTCGATTCAATGGAGCCTAGCGGG 12024 TATAGATATTCAATTTTCAATGAACAATTTGAACCTTTCGATTCAATGGAGCCTAGCGGG 12019 TATAGATATTCAATTTTCAATGAACAATTTGAACCTTTCGATTCAATGGAGCCTAGCGGG 12021 TATAGATATTCAATTTTCAATGAACAATTTGAACCTTTCGATTCAATGGAGCCTAGCGGG 12020 TATAGATATTCAATTTTCAATGAACAATTTGAACCTTTCGATTCAATGGAGCCTAGCGGG 12018 TATAGATATTCAATTTTCAATGAACAATTTGAACCTTTCGATTCAATGGAGCCTAGCGGG 12022 TATAGATATTCAATTTTCAATGAACAATTTGAACCTTTCGATTCAATGGAGCCTAGCGGG ************************************************************ 12023 ATCGAACCGCTGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTAAGGCCCCA 12024 ATCGAACCGCTGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTAAGGCCCCA 12019 ATCGAACCGCTGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTAAGGCCCCA 12021 ATCGAACCGCTGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTAAGGCCCCA 12020 ATCGAACCGCTGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTAAGGCCCCA 12018 ATCGAACCGCTGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTAAGGCCCCA 12022 ATCGAACCGCTGACCTCCTGCGTGCAAAGCAGGCGCTCTCCCAGCTGAGCTAAGGCCCCA ************************************************************ 12023 CAAGACCTCTCAAAACTAAACAAGACGCAAATGGCAGGTTTCCTTATCCTTAGAAAGGAG 12024 CAAGACCTCTCAAAACTAAACAAGACGCAAATGGCAGGTTTCCTTATCCTTAGAAAGGAG 12019 CAAGACCTCTCAAAACTAAACAAGACGCAAATGGCAGGTTTCCTTATCCTTAGAAAGGAG 12021 CAAGACCTCTCAAAACTAAACAAGACGCAAATGGCAGGTTTCCTTATCCTTAGAAAGGAG 12020 CAAGACCTCTCAAAACTAAACAAGACGCAAATGGCAGGTTTCCTTATCCTTAGAAAGGAG 12018 CAAGACCTCTCAAAACTAAACAAGACGCAAATGGCAGGTTTCCTTATCCTTAGAAAGGAG 12022 CAAGACCTCTCAAAACTAAACAAGACGCAAATGGCAGGTTTCCTTATCCTTAGAAAGGAG ************************************************************ 12023 GTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATCTAT 12024 GTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATCTAT 12019 GTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATCTAT 12021 GTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATCTAT 12020 GTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATCTAT 12018 GTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATCTAT 12022 GTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATCTAT ************************************************************ 12023 CCCACCTTAGGCGGCTGGCTCCTAAAAGGTTACCTCACCGACTTCGGGTGTTACAAACTC 12024 CCCACCTTAGGCGGCTGGCTCCTAAAAGGTTACCTCACCGACTTCGGGTGTTACAAACTC 12019 CCCACCTTAGGCGGCTGGCTCCTAAAAGGTTACCTCACCGACTTCGGGTGTTACAAACTC 12021 CCCACCTTAGGCGGCTGGCTCCTAAAAGGTTACCTCACCGACTTCGGGTGTTACAAACTC 12020 CCCACCTTAGGCGGCTGGCTCCTAAAAGGTTACCTCACCGACTTCGGGTGTTACAAACTC 12018 CCCACCTTAGGCGGCTGGCTCCTAAAAGGTTACCTCACCGACTTCGGGTGTTACAAACTC 12022 CCCACCTTAGGCGGCTGGCTCCTAAAAGGTTACCTCACCGACTTCGGGTGTTACAAACTC ************************************************************ 12023 TCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGAT 12024 TCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGAT 12019 TCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGAT 12021 TCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGAT 12020 TCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGAT 12018 TCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGAT 12022 TCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGAT ************************************************************ 12023 CCGCGATTACTAGCGATTCCGACTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGA 12024 CCGCGATTACTAGCGATTCCGACTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGA 12019 CCGCGATTACTAGCGATTCCGACTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGA 12021 CCGCGATTACTAGCGATTCCGACTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGA 12020 CCGCGATTACTAGCGATTCCGACTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGA 12018 CCGCGATTACTAGCGATTCCGACTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGA 12022 CCGCGATTACTAGCGATTCCGACTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGA ************************************************************ 12023 GATTGGCTTTAAGAGATTAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAACCATTG 12024 GATTGGCTTTAAGAGATTAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAACCATTG 12019 GATTGGCTTTAAGAGATTAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAACCATTG 12021 GATTGGCTTTAAGAGATTAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAACCATTG 12020 GATTGGCTTTAAGAGATTAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAACCATTG 12018 GATTGGCTTTAAGAGATTAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAACCATTG 12022 GATTGGCTTTAAGAGATTAGCTTGCCGTCACCGGCTTGCGACTCGTTGTACCAACCATTG ************************************************************ 12023 TAGCACGTGTGTAGCCCAGGTCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCC 12024 TAGCACGTGTGTAGCCCAGGTCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCC 12019 TAGCACGTGTGTAGCCCAGGTCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCC 12021 TAGCACGTGTGTAGCCCAGGTCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCC 12020 TAGCACGTGTGTAGCCCAGGTCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCC 12018 TAGCACGTGTGTAGCCCAGGTCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCC 12022 TAGCACGTGTGTAGCCCAGGTCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCC ************************************************************ 12023 TCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTTAATGATGGCAACTAACAATA 12024 TCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTTAATGATGGCAACTAACAATA 12019 TCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTTAATGATGGCAACTAACAATA 12021 TCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTTAATGATGGCAACTAACAATA 12020 TCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTTAATGATGGCAACTAACAATA 12018 TCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTTAATGATGGCAACTAACAATA 12022 TCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTTAATGATGGCAACTAACAATA ************************************************************

12023 GGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCA 12024 GGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCA 12019 GGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCA 12021 GGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCA 12020 GGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCA 12018 GGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCA 12022 GGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCA ************************************************************ 12023 TGCACCACCTGTCACTTCTGCTCCGAAGAGAAAGCCTATCTCTAGGCCGGTCAGAAGGAT 12024 TGCACCACCTGTCACTTCTGCTCCGAAGAGAAAGCCTATCTCTAGGCCGGTCAGAAGGAT 12019 TGCACCACCTGTCACTTCTGCTCCGAAGAGAAAGCCTATCTCTAGGCCGGTCAGAAGGAT 12021 TGCACCACCTGTCACTTCTGCTCCGAAGAGAAAGCCTATCTCTAGGCCGGTCAGAAGGAT 12020 TGCACCACCTGTCACTTCTGCTCCGAAGAGAAAGCCTATCTCTAGGCCGGTCAGAAGGAT 12018 TGCACCACCTGTCACTTCTGCTCCGAAGAGAAAGCCTATCTCTAGGCCGGTCAGAAGGAT 12022 TGCACCACCTGTCACTTCTGCTCCGAAGAGAAAGCCTATCTCTAGGCCGGTCAGAAGGAT ************************************************************ 12023 GTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTG 12024 GTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTG 12019 GTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTG 12021 GTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTG 12020 GTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTG 12018 GTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTG 12022 GTCAAGACCTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTG ************************************************************ 12023 TGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGT 12024 TGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGT 12019 TGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGT 12021 TGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGT 12020 TGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGT 12018 TGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGT 12022 TGCGGGCCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGT ************************************************************ 12023 GCTTAATGCGTTAGCTGCGGCACTAAGCCCCGGAAAGGGCCTAACACCTAGCACTCATCG 12024 GCTTAATGCGTTAGCTGCGGCACTAAGCCCCGGAAAGGGCCTAACACCTAGCACTCATCG 12019 GCTTAATGCGTTAGCTGCGGCACTAAGCCCCGGAAAGGGCCTAACACCTAGCACTCATCG 12021 GCTTAATGCGTTAGCTGCGGCACTAAGCCCCGGAAAGGGCCTAACACCTAGCACTCATCG 12020 GCTTAATGCGTTAGCTGCGGCACTAAGCCCCGGAAAGGGCCTAACACCTAGCACTCATCG 12018 GCTTAATGCGTTAGCTGCGGCACTAAGCCCCGGAAAGGGCCTAACACCTAGCACTCATCG 12022 GCTTAATGCGTTAGCTGCGGCACTAAGCCCCGGAAAGGGCCTAACACCTAGCACTCATCG ************************************************************ 12023 TTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCA 12024 TTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCA 12019 TTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCA 12021 TTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCA 12020 TTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCA 12018 TTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCA 12022 TTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCA ************************************************************ 12023 GCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCA 12024 GCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCA 12019 GCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCA 12021 GCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCA 12020 GCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCA 12018 GCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCA 12022 GCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCA ************************************************************ 12023 TTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCCTCCAGTTTCCA 12024 TTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCCTCCAGTTTCCA 12019 TTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCCTCCAGTTTCCA 12021 TTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCCTCCAGTTTCCA 12020 TTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCCTCCAGTTTCCA 12018 TTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCCTCCAGTTTCCA 12022 TTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCCTCCAGTTTCCA ************************************************************ 12023 AAGCGTACAATGGTTAAGCCACTGCCTTTAACTTCAGACTTAAAGAACCGCCTGCGCTCG 12024 AAGCGTACAATGGTTAAGCCACTGCCTTTAACTTCAGACTTAAAGAACCGCCTGCGCTCG 12019 AAGCGTACAATGGTTAAGCCACTGCCTTTAACTTCAGACTTAAAGAACCGCCTGCGCTCG 12021 AAGCGTACAATGGTTAAGCCACTGCCTTTAACTTCAGACTTAAAGAACCGCCTGCGCTCG 12020 AAGCGTACAATGGTTAAGCCACTGCCTTTAACTTCAGACTTAAAGAACCGCCTGCGCTCG 12018 AAGCGTACAATGGTTAAGCCACTGCCTTTAACTTCAGACTTAAAGAACCGCCTGCGCTCG 12022 AAGCGTACAATGGTTAAGCCACTGCCTTTAACTTCAGACTTAAAGAACCGCCTGCGCTCG ************************************************************ 12023 CTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGTATTACCGCGGCTGCTGGCA 12024 CTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGTATTACCGCGGCTGCTGGCA 12019 CTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGTATTACCGCGGCTGCTGGCA 12021 CTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGTATTACCGCGGCTGCTGGCA 12020 CTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGTATTACCGCGGCTGCTGGCA 12018 CTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGTATTACCGCGGCTGCTGGCA 12022 CTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGTATTACCGCGGCTGCTGGCA ************************************************************ 12023 CGTAGTTAGCCGTCCCTTTCTGGTTAGTTACCGTCACTTGGTAGATTTTCCACTCCTACC 12024 CGTAGTTAGCCGTCCCTTTCTGGTTAGTTACCGTCACTTGGTAGATTTTCCACTCCTACC 12019 CGTAGTTAGCCGTCCCTTTCTGGTTAGTTACCGTCACTTGGTAGATTTTCCACTCCTACC 12021 CGTAGTTAGCCGTCCCTTTCTGGTTAGTTACCGTCACTTGGTAGATTTTCCACTCCTACC 12020 CGTAGTTAGCCGTCCCTTTCTGGTTAGTTACCGTCACTTGGTAGATTTTCCACTCCTACC 12018 CGTAGTTAGCCGTCCCTTTCTGGTTAGTTACCGTCACTTGGTAGATTTTCCACTCCTACC 12022 CGTAGTTAGCCGTCCCTTTCTGGTTAGTTACCGTCACTTGGTAGATTTTCCACTCCTACC ************************************************************ 12023 AACGTTCTTCTCTAACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGT 12024 AACGTTCTTCTCTAACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGT 12019 AACGTTCTTCTCTAACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGT 12021 AACGTTCTTCTCTAACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGT 12020 AACGTTCTTCTCTAACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGT 12018 AACGTTCTTCTCTAACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGT 12022 AACGTTCTTCTCTAACAACAGAGCTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGT ************************************************************ 12023 TGCTCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTC 12024 TGCTCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTC 12019 TGCTCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTC 12021 TGCTCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTC 12020 TGCTCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTC 12018 TGCTCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTC 12022 TGCTCGGTCAGACTTCCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTC ************************************************************ 12023 TGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGTATCGTCG 12024 TGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGTATCGTCG 12019 TGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGTATCGTCG 12021 TGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGTATCGTCG 12020 TGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGTATCGTCG 12018 TGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGTATCGTCG 12022 TGGGCCGTGTCTCAGTCCCAGTGTGGCCGATCACCCTCTCAGGTCGGCTATGTATCGTCG ************************************************************ 12023 CCTTGGTGAGCCTTTACCTCACCAACTAGCTAATACAACGCAGGTCCATCTCACAGTGAA 12024 CCTTGGTGAGCCTTTACCTCACCAACTAGCTAATACAACGCAGGTCCATCTCACAGTGAA 12019 CCTTGGTGAGCCTTTACCTCACCAACTAGCTAATACAACGCAGGTCCATCTCACAGTGAA 12021 CCTTGGTGAGCCTTTACCTCACCAACTAGCTAATACAACGCAGGTCCATCTCACAGTGAA 12020 CCTTGGTGAGCCTTTACCTCACCAACTAGCTAATACAACGCAGGTCCATCTCACAGTGAA 12018 CCTTGGTGAGCCTTTACCTCACCAACTAGCTAATACAACGCAGGTCCATCTCACAGTGAA 12022 CCTTGGTGAGCCTTTACCTCACCAACTAGCTAATACAACGCAGGTCCATCTCACAGTGAA ************************************************************ 12023 GCAATTGCTCCTTTTAAATAACTAACATGTGTTAATTACTCTTATGCGGTATTAGCTATC 12024 GCAATTGCTCCTTTTAAATAACTAACATGTGTTAATTACTCTTATGCGGTATTAGCTATC 12019 GCAATTGCTCCTTTTAAATAACTAACATGTGTTAATTACTCTTATGCGGTATTAGCTATC 12021 GCAATTGCTCCTTTTAAATAACTAACATGTGTTAATTACTCTTATGCGGTATTAGCTATC 12020 GCAATTGCTCCTTTTAAATAACTAACATGTGTTAATTACTCTTATGCGGTATTAGCTATC 12018 GCAATTGCTCCTTTTAAATAACTAACATGTGTTAATTACTCTTATGCGGTATTAGCTATC 12022 GCAATTGCTCCTTTTAAATAACTAACATGTGTTAATTACTCTTATGCGGTATTAGCTATC ************************************************************ 12023 GTTTCCAATAGTTATCCCCCGCTATGAGGCAGGTTACCTACGCGTTACTCACCCGTTCGC 12024 GTTTCCAATAGTTATCCCCCGCTATGAGGCAGGTTACCTACGCGTTACTCACCCGTTCGC 12019 GTTTCCAATAGTTATCCCCCGCTATGAGGCAGGTTACCTACGCGTTACTCACCCGTTCGC 12021 GTTTCCAATAGTTATCCCCCGCTATGAGGCAGGTTACCTACGCGTTACTCACCCGTTCGC 12020 GTTTCCAATAGTTATCCCCCGCTATGAGGCAGGTTACCTACGCGTTACTCACCCGTTCGC 12018 GTTTCCAATAGTTATCCCCCGCTATGAGGCAGGTTACCTACGCGTTACTCACCCGTTCGC 12022 GTTTCCAATAGTTATCCCCCGCTATGAGGCAGGTTACCTACGCGTTACTCACCCGTTCGC ************************************************************ 12023 AACTCATCAGTCTAGTGTAAACACCAAACCTCAGCGTTCTACTTGCATGTATTAGGCACG 12024 AACTCATCAGTCTAGTGTAAACACCAAACCTCAGCGTTCTACTTGCATGTATTAGGCACG 12019 AACTCATCAGTCTAGTGTAAACACCAAACCTCAGCGTTCTACTTGCATGTATTAGGCACG 12021 AACTCATCAGTCTAGTGTAAACACCAAACCTCAGCGTTCTACTTGCATGTATTAGGCACG 12020 AACTCATCAGTCTAGTGTAAACACCAAACCTCAGCGTTCTACTTGCATGTATTAGGCACG 12018 AACTCATCAGTCTAGTGTAAACACCAAACCTCAGCGTTCTACTTGCATGTATTAGGCACG 12022 AACTCATCAGTCTAGTGTAAACACCAAACCTCAGCGTTCTACTTGCATGTATTAGGCACG ************************************************************ 12023 CCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCATTAAAAGTTTGAGCTTTGCTCTT 12024 CCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCATTAAAAGTTTGAGCTTTGCTCTT 12019 CCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCATTAAAAGTTTGAGCTTTGCTCTT 12021 CCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCATTAAAAGTTTGAGCTTTGCTCTT 12020 CCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCATTAAAAGTTTGAGCTTTGCTCTT 12018 CCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCATTAAAAGTTTGAGCTTTGCTCTT 12022 CCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCATTAAAAGTTTGAGCTTTGCTCTT ************************************************************ 12023 TTCTGTCTCGCTGACAGATTTATTGTTTTTT-GTCATTGACGGATTTACAATGTAAATCC 12024 TTCTGTCTCGCTGACAGATTTATTGTTTTTTTGTCATTGACGGATTTACAATGTAAATCC 12019 TTCTGTCTCGCTGACAGATTTATTGTTTTTT-GTCATTGACGGATTTACAATGTAAATCC 12021 TTCTGTCTCGCTGACAGATTTATTGTTTTTTTGTCATTGACGGATTTACAATGTAAATCC 12020 TTCTGTCTCGCTGACAGATTTATTGTTTTTTTGTCATTGACGGATTTACAATGTAAATCC 12018 TTCTGTCTCGCTGACAGATTTATTGTTTTTT-GTCATTGACGGATTTACAATGTAAATCC 12022 TTCTGTCTCGCTGACAGATTTATTGTTTTTT-GTCATTGACGGATTTACAATGTAAATCC ******************************* **************************** 12023 ACCCTGCACATTCGTTCGTCTTGTTCAGTTTTCAAAGGTCTAATGATATATCATAAAAAT 12024 ACCCTGCACATTCGTTCGTCTTGTTCAGTTTTCAAAGGTCTTTGCCTCTCTTGAGACAAC 12019 ACCCTGCACATTCGTTCGTCTTGTTCAGTTTTCAAAGGTCTTTGCCTCTCTTGAGACAAC 12021 ACCCTGCACATTCGTTCGTCTTGTTCAGTTTTCAAAGGTCTTTGCCTCTCTTGAGACAAC 12020 ACCCTGCACATTCGTTCGTCTTGTTCAGTTTTCAAAGGTCTTTGCCTCTCTTGAGACAAC 12018 ACCCTGCACATTCGTTCATCTTGTTCAGTTTTCAAAGGTCTTTGCCTCTCTTGAGACAAC 12022 ACCCTGCACATTCGTTCGTCTTGTTCAGTTTTCAAAGGTCTTTGCCTCTCTTGAGACAAC ***************** *********************** * * * * ** 12023 ATATCCATCGGGAAGACAGGATTCGAACCTG-CGACACCTTGGTCCCAAACCAAGTACTC 12024 TTCTATATTCTAGCAAACTTATTCTGCTTTGTCAACTACTTTTTTTTAAGTTGTTAACTA 12019 TTCTATATTCTAGCAAACTTATTCTGCTTTGTCAACTACTTT-TTTTAAGTTGTTAACTA 12021 TTCTATATTCTAGCAAACTTATTCTGCTTTGTCAACTACTTT-TTTTAAGTTGTTAACTA 12020 TTCTATATTCTAGCAAACTTATTCTGCTTTGTCAACTACTTT-TTTTAAGTTGTTAACTA 12018 TTCTATATTCTAGCAAACTTATTCTGCTTTGTCAACTACTTT-TTTTAAGTTGTTTATAA 12022 TTCTATATTCTAGCAAACTTATTCTGCTTTGTCAACTACTTT-TTTTAAGTTGTTAACTA * * ** * **** ** * ** *** * ** * 12023 TACCAAGCTG--A-GCTACT-TCCCGAAAAA---TATGCACC---CTAGAGGAGTCGAAC 12024 CGCGTTACTAGAA-GCTGCTCTCTCGAGACAACTTATTCATTATACTAAATATTTCTACT 12019 CGCGCTAATAGAA-ACTGCTCTCTCGAGACAACTTATTCATTATACTAAATATTTCTACT 12021 CGCGCTAATAGAA-ACTGCTCTCTCGAGACAACTTATTTAGTTTACTACATCATCTCTTA 12020 CGCGCTAATAGAA-ACTGCTCTCTCGAGACAACTTATTTAGTTTACTACATCATCTCTTA 12018 AATGATAATACAATATTAGGTTCGCTTAAGAACTCATTTAGTATACTATAATTTTTTATT 12022 CGCGCTAATAGAA-ACTGCTCTCTCGAGACAACTTATTTAGTTTACTACATCATCTCTTA * * * ** * * * ** * *** * 12023 CTCTAACCGCCTGATTCGTA-GTCAGGTACTCTATCC-------AGTTGA----GCTAAG 12024 TCCTGTCAATACTATTTTTGCATTTTTTCTTTTATTTTTAAA-AAGTTAATATTATTTAT 12019 TCCTGTCAATACTATTTTTGTA---TTTTATAAATTTAGTAT-AGACATAACTATTCCTC 12021 CTTTGTCAACTCTTTTTTCATACT-TTTTCTACATTTTCTGA-AAATGTAGATCAGGCTC 12020 CTTTGTCAACTCTTTTTTCATACT-TTTTCTACATTTTCTGA-AAATGTAGATAGAGCGC 12018 TGTTGTCAATAGGTTTTAAAAA-----------AATCTCAGAGAAAACCCTGAGATTTTT 12022 CTTTGTCAACTCTTTTTTCATACT-TTTTCTACATTTTCTGAAAAAAGTTTCCTGTTGGC * * ** * 12023 GGTGCTAAAT--------ATTATATGCCGA-------GGACCGGAATC-------G---A 12024 AGTAACTAAC--------CTTCTATACTTGTTGA-ATGGATAGCATTT-------T---T 12019 TATATTCAATTAAGAGAAATTATATAACCACTATTGAGAAATGTAGTC-------T---A 12021 AA-GCTTAAC---GATTCTTTTTAAAATCATTA-----AATTTTAAAA-------C---A 12020 AAGAAAAAAAGAGGTCTCACCTCTTTTTATTTCTTAGTAACTACTACA-------A---A 12018 TAAATT--ATGTTACAAAGTT--AATTTCCTT-----TAGCTTCAATT---------AAA 12022 TAACACCAATAACATAGAGTTTAAAATTCCATAC--CTAAATTTATTTTATTAGTAAAAA * 12023 ACCGGTACGATGTTTACC-A--TCGCAGGATTTTAAGTCCTGTGCGTCTGC--CAGTTCC 12024 ACCGTTGTCATGTTCAT--A--TTTCATCTTCTTAATTCACAAATTTAAACTTCATCTTC 12019 GCGATTAAATTCTTTGCTCA--TCGAA-AATATCCAATAAATATAATAATGCATAAAACG 12021 AATTTCAGACATGTTGC------CAAA-GTTTTGATATTATTACTATAAT--ATAGTTTG 12020 TCTATTAGGATCGTTACCTT--CAGAATAACTTTCAACACCCTCTATAGT-TGCAATTGT 12018 CCTAGTTCGCCATCTTCACG-CTTGTAAAGGACATTTGTCGTATTATCTTCTGCATCT-- 12022 AATAAAAGATGGGCTAGCCATCTTTTATAATATTTGTTTTTTATATTCTTCAGCTTCTTG * * 12023 G-CCA--------CCCCGGCCTCTAACAAGCGAACGACGGGGTTCGAA-CCCGCGACCCT 12024 A-TAAAAAATACCCTTCAAATTTTATCTAAATTTGAAGGGTATTTGAAATTTATAAAGTT 12019 C-CTGCTTACGAAATATAAACAAA-ATTGTTTGCAT--TTCGTAAACAAGCGTTACCTAT 12021 T-AGAGGAGAATAATATGGGCCAA-GAACCTATCAT--CGAATATCAAAATAT----CAA 12020 T-TTATGAACAGTTTTTCGCTCACTGTTACTCATAGGATCCATATGGTAAGGTTCATTAG 12018 --GTATAGATAAAGAAATCATGACCTAAAAGTTCCATTTGCAACAATGCTTCCTCAACAT 12022 GGGTGTAGATAAAACAAA-ATGACCAGGGGTAATCTCGTGCATTTGACGTTCTTGTCCGT 12023 CAC--CTTGGCAAGGTGATGTTCTACCACTGAACTACGT-TCGCACTAAAGACACTATT- 12024 CTT--TAAAAATATATGATGACTTATTTTTTATCTTCTTCTTGCATTTTTTCTTTGATTT 12019 TTA--ACAATATATGATGAGTGTTCCCGCTGAGAATAATTCTCAGCGGTAGACCAGAGCT 12021 TAA--AGTGTATGGGGAAAATGTTGCGGTTGAAGACA----TTAACCTTAAAATTTACCC 12020 TCT--CTAAAACACGCCTAGCTATTTTTTTAGAAAAA----TCAATTAAAGTTTCTGTAC 12018 CCA--TTGGTTTTAGATTAACATTCTTAGTACGTACAAT--T-CTTTGGCTTACTGCTTC 12022 CTTGCTCAATAGCTGGATTATACGGCTGGTGAACACGTT--GACGTTCACTCTCCGGATC * 12023 ------------------------------------------------------------ 12024 CATCGTATGATAACGCTCTTGCTTTATCTTCA---TCATTTTCTGTCTCAGGCATTTTAC 12019 AGACTAAGAATCGATTGATTCCATCATCATAACACTCAACAAAATTGATAAAAATTATAC 12021 TGGT---GATTTTGTTTGTTTCATCGGTA-------CGAGTGGATCAGGTAAAACAACAT 12020 GATGCTCAACGTAGTCATGGACATTAATGGA----TACTGAAAAACTCTTAGAAAAGCGG 12018 TTCATCTGGCTCAGCC-----TCAAATTCTGTTGTGAAAAC---TTGACTTGCTGGAATC 12022 TGGTTCTGGAATAGCTGATAATAGACTCTTCGTATAAGGGTGGATTGGATTGTTATAAAC 12023 ------------------------------------------------------------ 12024 CTGTCTCAAAAATCGATTTAATCTGAGCAGCATCAA-----GAGTCTCATATTTTAAGAG 12019 TAATTCA-ATAATTGCCATTGGGGCAGCATCGCCAC--GGCGTGGTTCTGT-TTTAAGAA 12021 TAATGCGTATGGTTAACCATATGTTAAAACCAACAA--ATGGTACTCTATTATTTAAGGG 12020 TCATGAAGATAATT----TTGTGCTAACAACTGCAACGATTTTAATACTTT-TCCATGAT 12018 TTTTCACGATATT--------TTTTCGCAATTTTA--------GTTTTATT-TTTACGA- 12022 ATCATCAGATGTTC---CAACTTCTAACAGTTTCCCCCAATGCATAACACC-GATACGAT 12023 ------------------------------------------------------------ 12024 GGCTTCTGCAATTAATTTATGAGTATCACGGTTTTCGTTGATAATATCAGCTGCC--TTA 12019 TACGAGTGTATCCTCCG--TTACGTTCAGCATAACGAGGTGCGATGTCGTC-AAA--AAG 12021 AAAAGATATTTCTACTA--TTAACCCCATTGAATTAAGACGCAGAATTG---GAT--ATG 12020 AACCAATGATGCGCCCAGCTTCTGGCGTTTCTATTTGGAGATTTATTTGTC-GCT--TAC 12018 ---------ATTTGAC------GCTCAATTTT-----ATCAACAACTAAGTCAAT----- 12022 CTGAAATGTATTTTACC--ATAGACAAATCATGTGCGATAAACAAATAAGTCAATCCTTG 12023 ------------------------------------------------------------ 12024 TTACGTGCTTCATTAAGAAGGTGACGAACTTCATCATCAATAAGTTGTGCAGTTTGAGCA 12019 TTTTTGAAGAGCTGTTGTTGATGTAT-ATTT-ATCAGAAGCTTCATCATAGTTTTCTGAT 12021 TTATCCAAAACATTGGTTTAATGCCTCATATGACCATTTACGAAAATATAGTTCT-TGTA 12020 TTGTCGTAG--TTTCTATTGTTGCAT-CTAAATCCATCTCATAGATGATATTTTC----A 12018 TGACCCATACATATCTTGTGAAACATCTTCTGCTCGTAAAGTAATAGAATCTATTAAG-- 12022 TTCTCTTTGCAATTTTTGCATTAAATTAACAACTTGTGCTTGGATTGAAACATCTAAGGC 12023 ------------------------------------------------------------ 12024 GAATATGATTTTTCAGGTGACATTTGACCA--GCCATCATTGCGTGGTTGCCTTCGTATT 12019 GCAATTTCATTACGTACATAAGCAGCAGCT--TGACGACGAGCATGTAAATCACCACGTT 12021 CCAAAATTATTGAAATGGTCAGAAGAAGCT--AAAAGA-GCTAAAGCAAGGGAACTTATT 12020 ACGTATTTAGTCACCTGAGCAGCTGCTACT--TCAATATTAGGAAGTAGGTCAATTTTTT 12018 ----ATTGTTACTTCAACTTTTGCGGTCTT---CTCTCTGTATACTTTGAGGTTGACTCT 12022 AGATATTGGTTCATCAGCAATGATAAATTTAGGCTCTACTGCTAAAGCACGTGCAATCCC 12023 ------------------------------------------------------------ 12024 GAACTGGTCCAAGTTTCTCGCTCATACCATATTCAGTTACCATAGCGCGGGCCATAGCAG 12019 TACCTAGAGTAATCATTTTTTCAACTGTTTTACGGATTTCTTTAGCACGTGCTTCAGTAG 12021 AAATTAGTTGAATTACCCGAAGAA-TATTTGGATCGCTACCCTAGTGAGTTGTCTGGCGG 12020 CAATAGCTTCACTTGTAGTTACAACGTTTTTATCATCAATTTTTGGAAGT--TCTGGTTG 12018 AGTATCTAATTCTTGTGCTTC-----ATTAAAGTATTTTTCAACTTTAGAGAGTTTGGTC 12022 GATACGTTGTCGTTGTCCACCTGAAAATTCATGCGGATAACGTGTTAAATGATCTTTATT 12023 ------------------------------------------------------------ 12024 TGGCTTGTTCGAAGTCATTTGAGGCACCTGTTGTCTGAGCGTTGAAAATAATTTCTTCCG 12019 TTACAATTGATTCGTTGATAAGAAGATCGGTTGTCAAATCA--CGAAGCATTGCCTTACG 12021 TCAGCAACAACGTATCGGTGTCATTCGCGCTCTTGCAGCAGACCAAGATATTATTTTAAT 12020 T----GATACGTCTTCTTTTTCAAGCGT-TTCATCAACCTCCTCTATATATTCTTCCACC 12018 TCAACATACTCA--CGAATAGCTTCTG----TTACTTCGATGTTTTCACCACGAAT-ACT 12022 TAACCCTACAAGATCTAATAGGGCCTGAACTTTACTATCACGATCTGATTTTGATTTAGC 12023 ------------------------------------------------------------ 12024 CTACACGTCCTCCCATAAGACCTGCTAATTGCTCTTTCATATCATCTTTTGAAAGAAGCA 12019 TTGTGAGCTAGT-------GCGTCCTAGTTTACGGTAAGCCATTATGTCCTCCTATTTTA 12021 GGATGAGCCTTTT-----GGAGCTCTGGATCCTATTACTAGAGAAGGTATTCAAGACTTA 12020 ACATCTACGCTA-------GACGGTACATTCTTAATATTTTTTAACG--CTACCGATTCA 12018 GTATTTAATCAT----ATGAGTACCTCTTTCTTGCGTTGTTAACGCTTTCTATACTCTTA 12022 TAATTTATGTAT----ATCTAAACCT-TCTGCTACGATATCACGAATCTTCATACGGCCG 12023 ------------------------------------------------------------ 12024 TTTGATCTTCTTTAGGT----AAAGCAATCATATATCCACCTGCACGACCACGTGGTACG 12019 TTTATCGTTTTTTAATC----CAAGACCTAGATCGGCAAGTTTGATTTTAACTTCTTCAA 12021 GTCAAGTCTCTTCAGG------AAGAAATGGG--GAAAACTATCATCTTAGTTACT-CAT 12020 TTAATATCAGTTACTT----------CGTCGGT-GATACCTTCTATTTCAACTTTTGCTG 12018 TTATAACC-GCTT-----TCATGAAAA--------------------------------- 12022 TTTAAGCTAGCCTGAGGATCCTGAAAAATCATCTGAGCGTCTTTACGAAAACTATGTAAT 12023 ------------------------------------------------------------ 12024 ATAGTAACTTTATGAACAACTCGCGCATTTGAAAGAATCAAACCGACAATTGTGTGCCCA 12019 GACTCTTACGTCCTAAGTTTCGGACTTTCATCATTTCAGGCTCAGTTTTTTCTG-TTAAA 12021 GA---T-ATGGATGAAGCCCTCAAGTT--AGCAACAAAAATT--ATTGTTATGG-ACAAT 12020 GC---TTTTTACCAAAGCCCAAAAAACCTTTTTTCTCACGTGATACAACTTTTATATGTG 12018 ------------------------------------------------------------ 12022 GCTTTACCTTTCAGATGTGAGATCACTTCTCCATTAAAGGTAATTTCTCCATCAGAAATA 12023 ------------------------------------------------------------ 12024 GCTTCATGGTAAGCAACCATAGCTCTTTCTCTTTCAGAAATAGTACGATCTTTTTTAGAA 12019 TCAAATACTGTATTAATTCCAGCACGTTTTAAACAGTTATATGAGCGCACTGACAAATCA 12021 GGTAAAATGGTCCAAGAAGGGACACCCAATGATCTCTTACATCATCCTGCTA-------- 12020 CCCTCAATCGTGAAATGTTTAACTCTTGTAGTCCTTTTTCAATAGCTTCTTCTACAGTCG 12018 ------------------------------------------------------------ 12022 TCATAAAGTTTTAAAATTGAACGTCCAACGGTTGTCTTTCCTGATCCAGATTCCCCAACT 12023 ------------------------------------------------------------ 12024 GGACCAGCAATTACACGGTCTTCTGCTTCATCAATATCTGAAGCATCAATAACTTTTTTA 12019 AGTTCCTCAATTGTCCGGTCAAGCACTTTCTCATCGTTCACTTTCTCTGTTTCCTTCATT 12021 ------------------------------------------------------------ 12020 CTCCTGTAAATAATACC------------------------------------------- 12018 ------------------------------------------------------------ 12022 AATCCAAACACTTCACCTTCATAAATGTCAAAACTAACATTATCAATTGCTCTCACTTCA 12023 ------------------------------------------------------------ 12024 TTTCGTCGCGCAGCAACTAAAGCAGCTTCATTGAGAACATTCTCCAAATCAGCACCAACA 12019 ACTTCAGTTGCTTTAGCAACCTCTGTTAAATCAGTAAACAAGTTTAAGTGTTCAATTAAG 12021 ------------------------------------------------------------ 12020 ------------------------------------------------------------ 12018 ------------------------------------------------------------ 12022 TTAGCTTTTCCTTTATTGAAGGTCAAAGAAACATTTTTGACTTCAACTAATTTTTTTCGA 12023 ------------------------------------------------------------ 12024 AATCCTGGGGTTTGTTGAGCTACTACTTTTAAGTCAACATTATCTGCTAATGGTTTATTT . . . 12019 ACGCGAGCTGAAAGACCAAGAGCATCCTCAGGAATGA----------------------- 12021 ------------------------------------------------------------ 12020 ------------------------------------------------------------ 12018 ------------------------------------------------------------ 12022 TTTTCAGTCATTAGGCT------------------------------------------- It will be understood that the invention has been described by way of example only and modifications may be made whilst remaining within the scope and spirit of the invention.

TABLE-US-08058 TABLE I THEROETICAL MOLECULAR WEIGHTS FOR GBS PROTEINS exp ct d mol. weight (dalton) GBS # GST-fusion His-fusion Native 1 78425 53460 49720 2 40035 15070 11330 3 90305 65340 61600 4 43115 18150 14410 5 158835 133870 130130 6 39265 14300 10560 7 44985 20020 16280 8 56315 31350 27610 9 50265 25300 21560 10 96465 71500 67760 11 91515 66550 62810 11d 85905 60940 57200 12 64455 39490 35750 13 40475 15510 11770 14 33325 8360 4620 15 44765 19800 16060 16 73475 48510 44770 17 46745 21780 18040 18 54335 29370 25630 19 46085 21120 17380 20 47625 22660 18920 21 56535 31570 27830 21 long 66435 41470 37730 22 60055 35090 31350 23 60165 35200 31460 24 58405 33440 29700 25 50265 25300 21560 26 118245 93280 89540 28 63795 38830 35090 29 50595 25630 21890 30 44215 19250 15510 31 63795 38830 35090 31d 58735 33770 30030 32 40585 15620 11880 33 71495 46530 42790 34 69295 44330 40590 35 56535 31570 27830 36 59065 34100 30360 37 46965 22000 18260 38 61815 36850 33110 39 65225 40260 36520 41 75235 50270 46530 42 46745 21780 18040 43 58955 33990 30250 44 52355 27390 23650 45 43555 18590 14850 46 59835 34870 31130 47 84255 59290 55550 48 86455 61490 57750 48d 106695 81730 77990 49 59615 34650 30910 50 94155 69190 65450 51 47075 22110 18370 52 55435 30470 26730 53 110215 85250 81510 54 73365 48400 44660 55 36295 11330 7590 56 34865 9900 6160 57 51145 26180 22440 58 128805 103840 100100 59 99215 74250 70510 60 63575 38610 34870 61 68085 43120 39380 62 105485 80520 76780 63 64125 39160 35420 64 112745 87780 84040 65 72485 47520 43780 66 49715 24750 21010 67 120335 95370 91630 68 131225 106260 102520 68d 103065 78100 74360 69 53895 28930 25190 70 74465 49500 45760 70d 59725 34760 31020 71 56755 31790 28050 72 75565 50600 46860 73 72815 47850 44110 74 131225 106260 102520 74d 95475 70510 66770 75 114725 89760 86020 76 198875 173910 170170 77 78535 53570 49830 78 48835 23870 20130 79 58185 33220 29480 79d 50815 25850 22110 80 81835 56870 53130 81 89205 64240 60500 82 40475 15510 11770 83 62585 37620 33880 84 122645 97680 93940 85 70175 45210 41470 86 84035 59070 55330 87 44435 19470 15730 88 73365 48400 44660 89 143325 118360 114620 90 93495 68530 64790 91 88325 63360 59620 92 193595 168630 164890 93 95585 70620 66880 94 77435 52470 48730 95 60605 35640 31900 96 57195 32230 28490 97 138375 113410 109670 98 82055 57090 53350 99 60715 35750 32010 100 53015 28050 24310 101 59395 34430 30690 102 40695 15730 11990 103 56975 32010 28270 104 120005 95040 91300 105 179735 154770 151030 105dNterm 127265 102300 98560 105dCterm 81285 56320 52580 106 85795 60830 57090 107 89535 64570 60830 108 64565 39600 35860 109 75125 50160 46420 109d 70725 45760 42020 110 53895 28930 25190 111/190 60165 35200 31460 112 63905 38940 35200 113 59175 34210 30470 114 51915 26950 23210 115 98225 73260 69520 116 73475 48510 44770 117 47515 22550 18810 118 42235 17270 13530 119 109225 84260 80520 120 71385 46420 42680 121 65115 40150 36410 122 46855 21890 18150 123 68305 43340 39600 124 54115 29150 25410 125 57305 32340 28600 126 56865 31900 28160 127 80845 55880 52140 128 39925 14960 11220 129 43775 18810 15070 130 82275 57310 53570 130d 63245 38280 34540 131 89755 64790 61050 132 49055 24090 20350 133 54445 29480 25740 134 42015 17050 13310 135 65225 40260 36520 136 54885 29920 26180 137 63465 38500 34760 138 40145 15180 11440 139 38165 13200 9460 140 43445 18480 14740 141 49935 24970 21230 142 79745 54780 51040 143 33545 8580 4840 144 49165 24200 20460 145 63025 38060 34320 146 107025 82060 78320 147 156965 132000 128260 148 41905 16940 13200 149 62365 37400 33660 150 54665 29700 25960 151 50412 25447 21707 151L 50045 25080 21340 152 45535 20570 16830 153 46965 22000 18260 154 101525 76560 72820 155 62585 37620 33880 156 61265 36300 32560 157 74025 49060 45320 158 52025 27060 23320 159 41025 16060 12320 160 82825 57860 54120 161 95365 70400 66660 162 42015 17050 13310 163 69405 44440 40700 164 42345 17380 13640 165 43555 18590 14850 166 38055 13090 9350 167 50375 25410 21670 168 32555 7590 3850 169 43445 18480 14740 170 64015 39050 35310 170d 59945 34980 31240 171 49825 24860 21120 172 62365 37400 33660 173 96795 71830 68090 174 45095 20130 16390 175 59175 34210 30470 176 55435 30470 26730 177 66215 41250 37510 178 62365 37400 33660 179 58515 33550 29810 180 37615 12650 8910 181 63685 38720 34980 182 90085 65120 61380 182d 87225 62260 58520 183 57855 32890 29150 184 46415 21450 17710 185 40695 15730 11990 186 85685 60720 56980 187 56205 31240 27500 188 61595 36630 32890 189 60165 35200 31460 191 116705 91740 88000 192 69625 44660 40920 193 98005 73040 69300 194 49385 24420 20680 195 81065 56100 52360 195L 147615 122650 118910 195L N-term 91405 66440 62700 196 69515 44550 40810 197 99325 74360 70620 198 73805 48840 45100 199 158285 133320 129580 200 132325 107360 103620 201 74538 49573 45833 202 157295 132330 128590 203 61705 36740 33000 204 39705 14740 11000 205 55985 31020 27280 206 56645 31680 27940 207 44765 19800 16060 208 59725 34760 31020 209 62145 37180 33440 209d 56425 31460 27720 210 60935 35970 32230 210d 53675 28710 24970 211 64895 39930 36190 212 60825 35860 32120 213 45205 20240 16500 214 38935 13970 10230 215 45205 20240 16500 216 91515 66550 62810 217 36075 11110 7370 218 81065 56100 52360 219 56535 31570 27830 220 54555 29590 25850 220 50155 25190 21450 221 41465 16500 12760 222 47405 22440 18700 223 42895 17930 14190 224 45865 20900 17160 225 56645 31680 27940 226 44875 19910 16170 227 46195 21230 17490 228 46525 21560 17820 229 35855 10890 7150 230 51915 26950 23210 231 60935 35970 32230 231d 58735 33770 30030 232 41795 16830 13090 233 35635 10670 6930 234 43115 18150 14410 235 58295 33330 29590 235d 48395 23430 19690 236 46525 21560 17820 237 44215 19250 15510 238 59725 34760 31020 239 63905 38940 35200 240 51475 26510 22770 241 45095 20130 16390 242 43225 18260 14520 243 119455 94490 90750 244 48065 23100 19360 245 48615 23650 19910 246 49605 24640 20900 246d 45975 21010 17270 247 58955 33990 30250 248 92505 67540 63800 248d 70835 45870 42130 249 103835 78870 75130 250 136505 111540 107800 251 52135 27170 23430 252 51695 26730 22990 253 74245 49280 45540 254 59615 34650 30910 255 69075 44110 40370 256 47845 22880 19140 257 60495 35530 31790 258 67975 43010 39270 259 79415 54450 50710 260 48175 23210 19470 261 55765 30800 27060 262 75345 50380 46640 263 63465 38500 34760 264 47185 22220 18480 265 56315 31350 27610 266 51365 26400 22660 267 88655 63690 59950 268 50265 25300 21560 269 60495 35530 31790 270 59285 34320 30580 271 56315 31350 27610 272 118355 93390 89650 272d 98885 73920 70180 273 70945 45980 42240 274 56205 31240 27500 275 47515 22550 18810 276 147945 122980 119240 277 87005 62040 58300 277d 75675 50710 46970 278 52245 27280 23540 279 79415 54450 50710 280 88655 63690 59950 281 74465 49500 45760 281d 71495 46530 42790 282 44765 19800 16060 283 20240 16500 284 67645 42680 38940 285 57525 32560 28820 286 41355 16390 12650 287 61045 36080 32340 287d 57085 32120 28380 288 53675 28710 24970 288d 51035 26070 22330 289 65005 40040 36300 289 long 71825 46860 43120 290 47405 22440 18700 291 63795 38830 35090 292 103505 78540 74800 293 115935 90970 87230 293d N-term 73805 48840 45100 293d C-term 70835 45870 42130 294 75785 50820 47080 295 89425 64460 60720 296 60385 35420 31680 297 100205 75240 71500 298 54335 29370 25630 299 62255 37290 33550 300 130895 105930 102190 301 54885 29920 26180 302 80075 55110 51370 303 53235 28270 24530 304 75125 50160 46420 305 78645 53680 49940 306 67975 43010 39270 307 86675 61710 57970 308 59285 34320 30580 309 62695 37730 33990 310 58845 33880 30140 311 76445 51480 47740 312 64785 39820 36080 313 65995 41030 37290 314 52135 27170 23430 315 51695 26730 22990 316 41795 16830 13090 317 179295 154330 150590 317d N-term 115935 90970 87230 317d C-term 92160 67402 63360 318 70065 45100 41360 319 61925 36960 33220 320 57965 33000 29260 321 83705 58740 55000 322 76628 51663 47923 323 86345 61380 57640 324 86345 61380 57640 325 82605 57640 53900 326 91515 66550 62810 326L 172695 147730 143990 326L N-term 113955 88990 85250 327 279175 254210 250470 327d N-term 139915 114950 111210 327d C-term 167965 143000 139260 328 97602 72637 68897 329 113955 88990 85250 330 83595 58630 54890 331 60825 35860 32120 332 75675 50710 46970 333 63465 38500 34760 333d 57965 33000 29260 334 38275 13310 9570 335 43555 18590 14850 336 67645 42680 38940 337 75235 50270 46530 338 54995 30030 26290 339 76665 51700 47960 339d 72925 47960 44220 340 86565 61600 57860 341 38385 13420 9680 342 61595 36630 32890 343 60385 35420 31680 344 55875 30910 27170 345 40585 15620 11880 346 53895 28930 25190 347 55325 30360 26620 348 58405 33440 29700 349 98335 73370 69630 350 53895 28930 25190 351 82165 57200 53460 352 111315 86350 82610 352d 105485 80520 76780 353 55325 30360 26620 354 42345 17380 13640 355 52135 27170 23430 356 59065 34100 30360 357 40255 15290 11550 358 60495 35530 31790 359 78865 53900 50160 360 73695 48730 44990 361 109005 84040 80300 362 125945 100980 97240 362d N-tem 63355 38390 34650 362d C-term 91295 66330 62590 363 53125 28160 24420 364 75015 50050 46310 365 102075 77110 73370 366 68415 43450 39710 367 76885 51920 48180 368 44765 19800 16060 369 142115 117150 113410 370 94595 69630 65890 371 65555 40590 36850 372 55105 30140 26400 373 50265 25300 21560 374 57525 32560 28820 375 66875 41910 38170 376 48065 23100 19360 377 73805 48840 45100 378 58955 33990 30250 379 68855 43890 40150 380 47405 22440 18700 381 66875 41910 38170 382 50815 25850 22110 383 57085 32120 28380 384 77985 53020 49280 385 75675 50710 46970 386 39485 14520 10780 387 54555 29590 25850 388 45645 20680 16940 389 43005 18040 14300 390 62255 37290 33550 391 54775 29810 26070 392 71385 46420 42680 393 55765 30800 27060 394 59725 34760 31020 395 72375 47410 43670 396 34865 9900 6160 397 113625 88660 84920 397d 100865 3740 72160 398 56755 31790 28050 399 55435 30470 26730 400 74135 49170 45430 401 59395 34430 30690 402 78095 53130 49390 403 64455 39490 35750 404 61595 36630 32890 405 45975 21010 17270 406 36955 11990 8250 407 82715 57750 54010 407d 71715 46750 43010 408 45315 20350 16610 409 70395 45430 41690 409d 59600 34842 30800 410 62475 37510 33770 411 41355 16390 12650 412 35965 11000 7260 413 59175 34210 30470 414 50375 25410 21670 415 46195 21230 17490 416 42455 17490 13750 417 77985 53020 49280 418 42125 17160 13420 419 47515 22550 18810 420 67755 42790 39050 421 62915 37950 34210 422 60165 35200 31460 423 74245 49280 45540 424 89975 65010 61270 424 77325 52360 48620 425 116045 91080 87340 426 83815 58850 55110 427 41135 16170 12430 428 55325 30360 26620 429 59175 34210 30470 430 53785 28820 25080 431 54005 29040 25300 432 65665 40700 36960 433 40915 15950 12210 434 44545 19580 15840 642 91845 66880 63140 643 78975 54010 50270 644 49605 24640 20900 645 59725 34760 31020 646 61595 36630 32890 647 55875 30910 27170 648 59835 34870 31130 649 76115 51150 47410 650 51475 26510 22770 651 53345 28380 24640 652 49715 24750 21010 653 44655 19690 15950 654 51255 26290 22550 655 65995 41030 37290 656 57525 32560 28820 657 62805 37840 34100 658 60165 35200 31460 659 60275 35310 31570 660 71495 46530 42790 661 60605 35640 31900 662 62695 37730 33990 663 89535 64570 60830 664 45315 20350 16610 665 41135 16170 12430 666 47075 22110 18370 667 53162 28197 24457 668 43555 18590 14850 669 48505 23540 19800 670 45315 20350 16610 671 36940 12182 8140 672 40130 15372 11330 673 41450 16692 12650 674 45300 20542 16500 675 55970 31212 27170 676 65650 40892 36850 677 54320 29562 25520 678 77750 52992 48950 679 60480 35722 31680 680 64440 39682 35640 681 93040 68282 64240 682 84790 60032 55990 683 15950 44655 19690 684 11880 40585 15620 685 16280 44985 20020 686 21340 50045 25080 687 9350 38055 13090 689 55105 3740 26400

TABLE-US-08059 TABLE II PRIMERS USED TO AMPLIFY GBSnnn PROTEINS Forward primers begin 5'-GGGGACAAGTTTGTACAAAAAAGCAGGC-3' and continue with the sequences indicated in the table below; reverse primers begin 5'-GGGGACCACTTTGTACAAGAAAGCTGGGTT-3' and continue with the sequences indicated in the table. The primers for GBS1 are thus: Fwd: GGGGACAAGTTTGTACAAAAAAGCAGGCTCTCAATCTCATATTGTTTCAG Rev: GGGGACCACTTTGTACAAGAAAGCTGGGTTATTTTTAGACATCATAGACA The full forward primer sequences are given in the sequence listing as SEQ IDs 10968-11492. The reverse primer sequences are SEQ IDs 11493-12017. GBS Forward Reverse 1 TCTCAATCTCATATTGTTTCAG ATTTTTAGACATCATAGACA 2 TCTAATTACATTATTACATTTTTG GGGAATGCCTACAAA 3 TCTGATACTAGTTCAGGAATATC TTTTTTACTATACTTTTTGT 4 TCTGATACAAGTGATAAGAATACT TTCCTTTTTAGGCTTACT 5 TCTATTTTTCTTCATAGTCCAC ATTAGCTTCATTTGTCAG 6 TCTGAATGGGTGTTATTAACTC AGTTTCTTCTTTAAAATCAT 7 TCTACAAATTCTTATTTTAGCAA CTCTGAAGCTGTAAAACC 8 TCTGTATCAGTTCAGGCGT TTTATCAATGTTTGAAACG 9 TCTGCTGCTCTAGGACAAC TAGTAAATCAAGTTTTTGCA 10 TCTTTTGTTGTTGCCTTATT ATCCCTTCTATTTTCGA 11 TCTCCACCTATGGAACGT ATGTAGTGACGTTTCTGTG 11d TCTCAGAAAGTCTATCGGG ATGTAGTGACGTTTCTGTG 12 TCTAGTGAGAAGAAAGCAAAT ATTGGGTGTAAGCATT 13 TCTTCTTGGAATTATTGGAG CTTAACTCTACCCGTCC 14 TCTGCAATGATTGTAACCAT TTTTCTCTTATTAAAGAATT 15 TCTGCATCTTATACCGTGAA ATACCAGCCGTTACTATT 16 TCTGCCGAGAAGGATAAA TTTAGCTGCTTTTTTAATG 17 TCTGTTTATAAAGTTATTCAAAA AAATACTACATTTACAGGTG 18 TCTAAGCCTAACAGTCAACA TTGGTTATTCTCCTTTAAT 19 TCTGATGATAACTTTGAAATGC ATTATATTTTTGGATATTTC 20 TCTGCAGTGATTGCAAGTC GGGCTTTTTCTTAAAAA 21 TGTGCTGCATCAAAC GTTGGCATCCCTTTT 21 Long + A527 TGTGCTGCATCAAAC CTTTTGATGGGATTGG 22 TGTACTAAACAAAGCCAG TTGATTTAACGATTTGA 23 TGTCAATAACCGATAC TTTATCTCCTCTAAAATAATG 24 TGCTCAAATGATTCAT CTTTGATAAGTCAGACCA 25 TCTAAAAGTTCACAAGTTACTACT GTAACCCCAAGCTGAT 26 TCTAGTCATTATTCCATAAAATT TGATTTTGCAATATCAA 28 TCTAATCATATGCTGATTGAG TTTTTGTAATTTAAGTACTAA 29 TCAGTTTGGATGTTAAC TTCTTTTATATTAAGAGCTT 30 TCAACAAATGCAGATG ATTCGGATAAATGTAGC 31 TGTTTTGTCATTATTGATAG TCCATTTTTATCCTCAC 31d TCTCTAACTTGGTTTTTATTAGA TCCATTTTTATCCTCAC 32 TCTGGTTTAAAAGTGACTGAA ATGACCTCTACTTTCCA 33 TCTCATCATTTAGGTAAGGAA CTTGTAATCACTTGGAC 34 TCTGTTAGTAATCGCTACAATC ATTAATCATGGTATTGGT 35 TCTAATCAAGAAGTTTCAGC CCATTGTGGAATATCA 36 TCTCGAGTTTTAGCGGATA TTTGTAAAGCAGTTCTT 37 TCTGTATTATTTTACCAATCACA ATCATTCATATGATCTCTAGA 38 TTAGGAGTGGTAGTTCAT ATTTTGATTGATTCTACTC 39 TTTTTATTGTTAGTATTAGC TTTTGTTTTTTTCAAATA 41 TCTGTTTATCTAGCGGTTAGA ATCTTCAACGTCCTCC 42 TATAACAGTTTAGTTAGAAGTC AAAGTCAAAGGAAACTT 43 TTTAAAGGGTTTACATATT TTCTTTATCTAATTTATAATAG 44 TTTAATACAATTGGTCG TTGCAATGTTTTTTCT 45 TCTATGGAAAAAATTAGGATT TAAACTTTGGATAATCTGT 46 TCTAGAGATGAGCAAGAAATA GTTGAAATTTTGATATGA 47 TCTCAACAGATAGGTCTTTATAA CTCCTTTACTATATAGCTAACT 48 TTTCTCTATAATTACTTCAAT TTGTTTGTGAAGTAAAAC 49 TCTAATAAGGCATTATTAGAGG TGATAATATCTCCATATTTT 50 TCTACACATTTAGTTGACTTAAC GCATTGGCGCCATA 51 TCTAGTAAACAACACATTTATCTA TTCTACACGACTTTTATTC 52 TCTCAAGAAACTCATCAGTTG AAGACCTCCTCGAGAT 53 TCTGCAGAAGACATTGTTACA TGTTTTTTCTTTCTGTTG 54 TATAATTTTTCGACTAATGA TGGATTAGTTTGACCTG 55 TCTGACACAGTGTCTTATCCT TTTATCGTAAGCACTTAGG 56 TCTGTGGAGCAAGTGGCCA CTCCTTCCAGGCATCG 57 TCTCAAGAACTAAGTAACTTTGA GTAAAAGTATCTTAAATAGTCA 58 TCTACTGAAACGTTTGAAGG TGCCATTCCTCCTCT 59 TCTGATGAAGCAACAACTAA TGTTACCTTTTTATTTTCT 60 TCTAATAAAGATAATCAAAAAACT TTTTTCATGCGATTGA 61 TGTTTCTTTTTTATTCCA GAGACGTTTCTTATACCTT 62 TATTACTTTGATGGTAGTTT TGTACCATATGTTCTCTCT 63 TCTGTTCAATCATTAGCAAA AAAAGTTGGACTACTTTC 64 TTTAAAGGTAATAAGAAGTTG TCGTTTTCCACCC 64d TCTAGTCAAGTTGACTCTGTTA TCGTTTTCCACCC 65 TCTCAAAACCAGGTGACTG ATTTGGGTAAATATAGTAAA 66 TTAAGATTTTATAACAACGA TTTACGACTAACCTCAAC 67 TCTAATGTTTTAGGGGAAA AATTCCTTTTGGTGG 68 TCCCAAAAGACTTTTG GGCAGAATACACCTTC 68d TCCCAAAAGACTTTTG GGCTGACGTCGACGCA 69 TCTAAAGTTTTAGCCTTTGA AACTCTCTTAATATATTCTTCT 70 TCTGAAATGGCTTTAG GTCTTTTTCAATATTCTGT 70d TCTACTAACTTATTGAGTAGAATCA GTCTTTTTCAATATTCTGT 71 TGTAGCTCAAAATCTCAT CTTCTCCTTAGGAGTAACG 72 TCTAGTTTATCTATTAAAGATGCC ATTATTATCAATTAATAACTCTT 73 TCTATCAAAGAGGCGGTAA GTCAAACATACTTCCAAA 74 TCTAAAGAGGATAAAAAGCTAG TTTCGTCGTATAAGCA 74d TCTAGTGTTTCAGGTAGTAGTG TTTCGTCGTATAAGCA 75 TCTAAAAAATTAAAACACTCAA TGTCCTCATTTTTTCAG 76 TCTGATGAAGTTACAACTTCAG AATACTTGCTGGAACAG 77 TTATTCCAAAGTAAAATAAA GTCTTTCTTCAATTTTGG 78 TCTCATAACCATCACTCAGAACACATGT GTCGTGATTTTTATGAGT 79 TCTCCCAAGAATAGGATAAA CCCAAACTGGCATAAC 79d TCTAGTCAGTATGAGTCACAGA CCCAAACTGGCATAAC 80 TCTGCAGAAGTGTCACAAGA TGAAGGACGTTTGTTG 81 TCTTTTGATGGATTTTT TTTTTTTAGTTTAAGGCTA 82 TCTACAAATGAAAAACGAAC GTCCACCTTCCGAT 83 TCTGAAATTAAACTCAAAAATATT AACATTGTTTTTCCTTTC 84 TCTCATACTCAAGAACACAAAA ATGGTGATGATGACCT 85 TCTCCTAAGAAGAAATCAGATAC ATTAACATTTTGAGGGT 86 TCTGCAGAACTAACTCTTTTAA TTTTGCAAAATCAACA 87 TCTGCGGATACATATAATAACTA GAATAAATAACTGTATTTTTT 88 TCTTACCAAAAAATGACG ATTTTCATTAATTTCCTCT 89 TCTGAAGAGCTTACCAAAAC GATAGCTAATTGGTCTGT 90 TCTAGATATACAAATGGAAATTT TAAAAGATGAGCTTCTCG 91 TCTAAAAAAGGACAAGTAAATG AATTTCAATATAGCGACG 92 TCTGATTCTGTCATAAATAAGC CTTGTTTGTCTTTACCTT 93 TCTGAATTTTCACGAGAAA ATTATCCTTCAAAGCTG 94 TACCAATTAGGTAGCTATAA TGTGTCATATAATGTAACCA 95 TCTGTTAATACAAAAACACTTCT TGATCTTAATTTTCGAG 96 TCTGGTCAGTCTAAAAATGAAG CCAAACAGGTTGATCT 97 TCTAGCCAGGAGGTATATG ATTTACATCAGACTGTGAC 98 TCTGAAACTATTAATCCAGAAA TTTATGGCCAATAACA 99 TCTACAAGTATGAACCATCAA TTTTTTAGTAGTTGTCAATT 100 TCTAAGGGGCCAAAAGTAG GTAAGCTGAATTTTCGA 101 TCTATTACTTTAGAAAAATTTATAGA ACGAGAGTGGTTATTGG 102 TCTGCCTTTTACTTTGGCA TTTCTTCACTCTTTCTAGAG 103 TCTATTTTTTCCTTGATCAT CGGCCAGTTTTTTCTT 104 TCTGGTGAAACCCAAGATA AACACCTGGTGGGCGT 105 TTAACAATTCATGGACC ACTATTTCTAATTGCTCTG 105d TTAACAATTCATGGACC TGGTCCCGGTGCGCCA 105d TCTCAAGGACCTCCCGGTG ACTATTTCTAATTGCTCTG 106 TCTCAAAATCAAAATTCACA CTTAGCAGATTCATCCC 107 TCTCTGGAGCCTTTTATTT TTTACTATTTGAAAATTGG 108 TCTGGTAATCGTTCAGATAAG TTTCATAGGAACTTGTATT 109 TCTATCCAGCAGATCAACT GTCCACACCTGCGACT 109d TCTAAACGGGTTCGCTATG GTCCACACCTGCGACT 110 TCTGTAAAATTAGTATTCGCAC TTTACCTAAGTAATATTCTGA 111.19 TCTGTTAGCGTTGATAAGGC TCCCCGTCTTTTTTGT 112 TCTACAATTAAAAATCTCACTG GTCGTAATCATAAAAGCC 113 TCTAGTAAAATCAAAATTGTAACG TTCATAACGAACCATAAC 114 TCTAATCTTTTAATTATGGGTT TTTGAGTTCTAGCAACG 115 TTTCAATACTATTTAAAAGG TTTTTTATCTTCTTCTTGC 116 TCTACCGAGGAGCCATTAA TTTTAAAACCTGGTAAAC 117 TCTGAACAATCACAAAAAACA TCAGCTCGTACTGTTT 118 TCTATGGTGACGGTGCTGG GTCCTCCTCAATTGGT 119 TCTAGTCAGCCGGTAGGGG CTCTTTTATACGCGATG 120 TCTGGTGGAGCATTTGCTA GTTATTTGCTCGTTGTT 121 TCTAATAAAGATAATCAAAAAACT TTTCTCAAATGTTTTCAT 122 TCTGCTGCCACCAAGAAAG TTTCAAATGATCTACAGC 123 TCTACAACAAATGTAATGGC GGCTAGTGTCTGTCCG 124 TCAATGAATTTTTCATTT ACCATCTATTTTTACCCC 125 TCTACAAAATATCAGCGAATG AGAACCCGCACTCTCA 126 TCTACTAAGCAAGCAATGTC GAACGCAACGGCTGCT 127 TCTACAAAAGAATATCAAAATTAT TTTCATATCAAAAACTATCG 128 TCGACTAATTCGTTAAA TTCTTTATCTCTTAATGCTT 129 TTTGAAATAGTATTGGAAA CACAACAGTTATTTTTTCA 130 TCTATATTTTCTATTTTTTATTATGT AGGCCCTTCTGAGTAG 130d TCTAAAAAACAACTTCACAAC AGGCCCTTCTGAGTAG 131 TCTAAAACAGATATTGAAATAGC AAATAATCCAATGGCTG 132 TCTATTAAATATTATCATTTGCA CTTTTCAAGCTTTTTCC 133 TCTGCTTTACGGAACCTTG AAAATGATCAGTTTGAGG 134 TCTACTATTTCTCAACAACAATAC TTTTTGGCTTAAGAAAG 135 TCTGAAAAAAAGAGTAGTTCAAC CTTACGATACATTTTAAATTG 136 TCTAATCAATTATCAGAAATCA TTCTTTTTTTACTTTAGCG 137 TCTCAAGAGTATAAAACAAAAGAG CCATTGCAATCCAGCA 138 TCTGCTGTATTTACACTCGTC ATGTTTATGGCTTGCT 139 TCTGGCGGCAAGATAAAAT TTTTTGATAAATCCCC 140 TCTGATGGGTTAAAGAATAATG ATATGTGTATTCATCCTTT 141 TCTGATGTTGTAATTAGTGGAG TACTTCTATTTTTCCATCTG 142 TTCGAATTAAGAGAAAGA GTAATGCAATAAATCAAAA 143 TCTAGCTTTTTAGTGATTTCA GGATTTTAGTTTCGCA 144 TATACGCATAGTGGAAC CCCATTGATTTCGTCG 145 TCTGTTATTATCAGGGGCG TACCTCTTTCAATACCAC 146 TCTGTTAGTCGTTCTCCGA ATTACCGTTAGGTACTGTA 147 TCTGAGGAGCAAGAATTAAA GGTATGGTTAACAGAATC 148 TCTATTCTAACAAAAGCAAGT ATATACCCTAGACTTTTTGA 149 TCTAGTGGGCGTTCATGGA AGGAGTTTTATTGATGATAT 150 TCTGATACCCCTAATCAACTA AAATGATTGTGGAAAAA 151 TGCAGGAGCTGTCCGC ATCAAAGAAGTTGACATTG 151 Long TCTGTCCGCATTGGTAAAG ATCAAAGAAGTTGACATTG 152 TCTAACTGCTTAGAAAATGAA GTTAGATAAATTAACCAGTG 153 TCTAACAACTCCAGCA CCCTTTGCTTCGTTGT 154 TCTGGAAAGGTCAGTGCAG TTCCACAAGTCCGATT 155 TCTATTTTATTTTCAGATGAAC TTGTTTGATTCGTCCT 156 TCTGCATCAGATGTTCAGA ACTACCAAACTGCTGG 157 TCTAGTGACGTTGACAAATA TTGTGTATTTTTAGTTAGGT 158 TCTATGACCATTTACTTCAATA GTGGATAAAATTCGAAA 159 TCTCAAACTATTTTGACGC CAGACTGACTAGGAGCT 160 TCTGATGAATATCTACGTGTCG GACTTGTAATTGATTCGC 161 TCTGATGAGGTGGACTATAACA GAAGGCACCACCACCT 162 TCTATTTTCTTGCTCTTAGTTG GTTGTATAGATGAGTTAATCTG 163 TCTGAAACTGTCATTCAACTTG ACGGTTTTTAAAGAATG 164 TATTTTTTAACAACAAAAAA TTTTTCTTTATCTTCTGTG 165 TCTCCAATTTTTATTGGTTT CGATTTTGTAAGAGCTT 166 TCTGCATCTTATACCGTGAA CGACGAAGCTATTTCT 167 TCTACAATTTATATTGCTTGG TAAGGCTTGCATTTTG 168 TCTGTTGGATTGATGTTGG TTTTCCTAAAAATTTTCC 169 TGGAAACAAATCACAG GGCATCTCCTAGCTTT 170 TCTGCAATAGTTTTTACTTTTTT TGATAAAGGTAGTTCTACAC 170d TCTGGTTCTTATCATTTAACAA TGATAAAGGTAGTTCTACAC 171 TCTGCTAGACCCAAACAGT TTTTAGATGTTTTTGTGG 172 TACACTCATATTGTTGAAAA ATGATTGATAATTTTAAGC 173 TCTAATAGTACTGAGACAAGTGC TGCTTTTTGATATGCC 174 TCTGCTTATGTCGTCAATTT TAAAATAAAGTTCAGAAAAG 175 TCTGAATTACCTTCGTTTATC TTTCTCCCTTGACTTTC 176 TCTAAACATCCGATACTTAATG CTTTTTCTCAGATGCTT 177 TCTAATTATCCTTTTGCGA GACATTGAAACGGAAT 178 TCTGGACTACGCGGAGTAT TTTTATCAATGATGTTGA 179 TCTGCTATTGGAGCAGCTG CATATGACGCAAACGC 180 TCTGATAAAGAAGGGATAGAGG AGCCTCTTTTCTTGTT 181 TCTAAAGAAAAATCACAAACTG ACGATTATCAACAAAGTT 182 TCTCAAAATAATAAAAAAGTAAAA CATTCTTTTAAATACAAATC 182d TCTCAAAATAATAAAAAAGTAAAA GGGTTTGAAGTTTTC 183 TCAAATGGTCAATCTAGC TTTAACTTTAATTACTGGAAT 184 TCTAAGGATTCAAAAATCCC TTTTTTAATAAGCTTCGA 185 TCTGGGCAACCATCTACAT TTTTTTGTAAACTTCCTG 186 TCTCATTCACAGGATAGCA CTTAGATACATTGTTTTTTTC 187 TCTGGACGAGGAGAAGTATC CTTTCTTTTCTTACTTGC 188 TCACAATCTTCTCAAAA TTTATTATTTTTAATACTTGAA 189 TCTGATAAGTCAGCAAACCC CTTCAACTGTTGATAGAGC 191 TCTATCACGACATTACAGACT TCCTTTAGCAGGAGCT 192 TCTAGATATTTAACTGCTGGT GTTATACATGTTGTCTGAAG 193 TCTATAAAATATCAAGATGATTTT CCAAATAATAACACGTTT 194 TTAGAAGTCAGAGAGCAG GCTATCCCTTTCCAAT 195 TCTATTATGGAGACGGGTA TGTATTTTTAATTTGTTTTC 195L TCTTTGAATAATAAAGGTGTCG TGTATTTTTAATTTGTTTTC 195LN TCTTTGAATAATAAAGGTGTCG CAAACTTTTAACATTTAATG 196 TCTATTTCCTCAAATTTTTACG ATAGTGTAAGCTACCAGC 197 TCTAATTTTTATAAGCTCTTG GTCATCATATTCCTGAAA 198 TCTGCGCTTAAAGAATTAA TGTTCGGCGTAAGATT 199 TTTTTAAAAGAAATTGAAA ATTGGTCATTTCTTGAG 200 TTTCGTAAATATAATTTTGA AACAGATTTATTGGTTGG 201 TCTAGCGATACCTTTAATTTT AGACTCATCAACTTTTTCT 202 TCTATGCTGATTAAGTCGC GAACCCTGAAGGGTAG 203 TGTGGTAAAACTGGACT CCAATTGTATTTTTCAAC 204 TCTAAGACAGGAGCACCCGT ATTTATACTACCTGTTGAATC 205 TGCGAGTCAATTGAGC TTTAAATTTGTAGTCTTTAATA 206 TCTACAAATACTTTGAAAAAAGA CTCTTTTACTTTTCCAAAA 207 TCTAATTTATTTAAACGTTCCT CCCTCCCTTAAGAGAA 208 TCTAAAAAGCGGCTAGTCA TTGACGATGTTGCATC 209 TCTGGACAAAAATCAAAAATA TTTCGAATTATTGTGACT 209d TCTGGACAAAAATCAAAAATA GTATTGTTGTTGCCTG 210 TCTGGAGGAAAATTTCAGAA TTTTTGATTTCCCTTTC 210d TCTACCTCATATCCTTTTATTT TTTATAGTGTGTTTGCAA 211 TGTGGACATCGTGGTG TTTGCTAGGAACTTTGA 212 TCTAAGACTAAAAAAATCATCA TGATTCAATTCCTTTTC 213 TCTAAACACACCAGTAAAGAA TTTTTCCTCTACTTTCTTA 214 TCTAAAAATAAAAAAATCTTATTT TTTGCTCACCTCCACA 215 TTAATAAAAGGATTATTGTCA CAATAACTTCTGTAAAATAAA 216 TCTGCTCGTTTAATACCACA TTCACCCTTAAAATAATT 217 TCTAACACTAACATCCCTAGC TGCATTTTTCCCTTCT 218 TCTAGAGGGAAGGTTATTTAC CTCCAGTAAAGTATTAGTATTT 219 TCTATCAATAAAGTAACAGCTCA GTGAGGTTTTGGTAATT 220 TCTAGAACACTATTTAGAATGATAT TGCATATAAGTTTTTTAGC 220d TACTATGCGAATCACAG TGCATATAAGTTTTTTAGC 221 TCTAGTTTAGCATTGCAAAT CTCATCTAAAGTGCTATCC 222 TCTACATTTTATAAAAAGACGG CTCGTATTTAGGCAACT 223 TCTAAGAAAATACGAAGCTATAC ATTGGATATGCCATAAA 224 TCTGGAGGAAATGAAATATTA GACTTTTTGATGTTTACTTT 225 TCTGGTATGTCTAATAAGGAAAT TTCTTTACTATAAACATCTTCA 226 TCTAACAAACTTATTACAGAAAA AGCATTTAAAGTGAATGT 227 TCTGTTTCATATGAAAAAGTCC GTTAGTCTCTTCAAGATCA 228 TCTAGTAGAGGTATTTTTTTACAA AAGACCTACCGCCCAA 229 TCTGAACGTCGGGTAAGTC TACTTCTTTCTCTTTCAATT 230 TTTTTAATCGATTTTATTT CTTAGTGTTCCGATATGA 231 TCATTAATATTCTTACGGT TCTTGTTTTAAGAGCAGA 231d TCTTTATACGTTGTTAAACA TCTTGTTTTAAGAGCAGA 232 TGGCTAAGTAAGCATGAG ATCATGTTTTCCCTCAA 233 TTCCCAGCTAGCTGTC ATCTGATATATCCGTTTTAT 234 TCTATAGAAATTGCTGTATTAATT TTTTTTGTCTCCTTTTTTA 235 TCTATTCGATTTCTTATTCTTG AAAGACACGATAAACATAAG 235d TCTGACTCAACCACAGTCTC AAAGACACGATAAACATAAG 236 TCTGCAGACCTTACAAGTCA ATTTGCAACTTCTTGTATA 237 TCTATTGTATTTGCTATTGCA TTTAAAAGTATCCTTAAATAAG 238 TCTGATATTTTTTCAGCTATTGA CTTCCTCCTCAATAGTTG 239 TCTGTTAGTGCTGCTATTGAA TTCTCCTCCCCCATTA 240 TCTAAGAAGCTTACTTTTATTTG ATCCAAACGAGTGAAAT 241 TCAAAAGGATATTCAAGA AGGTGTTGTTGTATTTTC 242 TCTCATAATATATTAAGATTTTTAGG CTTTCTAAGTTTATTAAACATA 243 TCTATTCTTGGTCAAGATGT GGCATCTGTTACCTTG 244 TCTCATGAAAATGTTAAAAAAG AAACAACTCCATTATTTTT 245 TCTAAGTCAACGGTAACAAA TAAACGTTGAAGAGCAT 246 AGGAAACGTTTTTCCT CTTATCATATCTTGTTAAATCA 246d TCTAACCATAAGGGAAAAGTA CTTATCATATCTTGTTAAATCA 247 TCTGCTAAACAATTAATTGGT TTGCCATGGGTTATAG 248 TCTTTGATGGTGTTGTTATTC AGAATTAAAATTTTCATGC 248d TCTAAAACTTATTTGTCAAATG AGAATTAAAATTTTCATGC 249 TGGGCTTACCATACTG TTTTTTAGATGTTTTATGTG 250 TCTGGCCTTAATCTTAAGC CTCTTTTACTTTAGCTTCA 251 TCTCAATATTTTTTGAAACAAG TTTCAAACTCCAGCCA 252 TTTATTTCAGGTTATATCAA GGAGTGCCTTTCTACT 253 TCTGAAAATTGGAAGTTTGC TTCATATCGTAAAGCATC 254 TCTATTGAAAAGGGAGTTG ATCGTCAACCTTAACG 255 TCTATTGTTGGTAGAGAAATCA TTTTACTTGACGTCTCAC 256 TATCATGTAAAAATGATCA GTCTTCCATTAATATTCCC 257 TCTGATTTTTTATACAAAGGAGG CCAATTATTTTGAAAGTTC 258 TCTGAACGTTATACAGATAAAATG ATTTTTTTGAATAATATAATCC 259 TCTCTTTCTCGTAAAAAAGAG TTTATTATCAGAAAAGGC 260 TCTACTCTTGTCTTAGTTGTTTAT ATTCAAAAAATTTTTCAA 261 TCTATAAAGAAAGCTGAAAATC CGAAACGTCAGGTAAA 262 TCTATAAAAAATGCTATAGCATA ACTTATTTTTGATAATATTTCTT 263 TCTCAGCCTTCTAAACTACTTC ATCAGCATTTCTACGAA 264 TCTGATTTGTTTAGCATGTTG ATGTAGACTCCTAATGATTT 265 TCTCTTGCTTCCCTGATTT TTTACTGTTCCTTTCGC 266 TCTCATCAATCAAATCATTATC GAGATTAATTTGATTATATTTT 267 TCTATCTTTATTATCGGACAA AACATCATTTCCTCCC 268 TCTAAAGAATTTATTAAAGAATGG GTTGATAGTTCCAAAACG 269 TCTGCAGATGATGGTGGTT TAAATGTGTTCCTACTAAATT 270 TTAAATGATGCAATAACAA CATCAATAGCCGAGCTG 271 TTGCTGGATTATCCTC TTTATTTTCCAAATGACA 272 TCTGTATTTATGGCAAATAAGA TTCACTCGGAGTTGGAG 272d TCTATGAGTTCTCTGGAAGTT TTCACTCGGAGTTGGAG 273 TCTGGTGTCCTCAACTCTG AATGTAAATGACAAAGGTA 274 TCTGTTCATGATTTTGGTGA GTTTTTTAATGGTTTGC 275 TCTGGGGTTTGGTTTTATA TTTATCATAAGCATCTAGAC 276 TCTCAATCAGACATTAAAGCA CTGATCTCTTGTTGATGC 277 TCTATTTGGAGGGGGGAAA AAGCAGGGGAGCAATA 277d TCTACCAAATTTGACTGGG AAGCAGGGGAGCAATA 278 TCTGTTACGTTTTTCTTAT CTGAGCAACACCTGTC 279 TCTAAAAAGAAAAGTTTAATTAGC GGCAATTTTGTGGCAA 280 TTTGATTTTTTTAAGAAAA TTGCTTAGTTAATGGCT 281 TCTAAGAAATTAATTATAGGTATTT AGGCGTTGAATATAATTC 281d TCTGGTTTTTCGTTTTTGA AGGCGTTGAATATAATC 282 TCTCTATTCTCAGATGAAACAA CTTTTCAACTCCAAACA 283 TCTGTTAAATTAAAATCGTACTG GAGTTGTCTTTTTTTGTC 284 TCTATGCAACGATTAGGAC GCAATCACAATTGACAT 285 TTAGGTGAAAGCAAATC CTTTGTCTGCTTCACTT 286 TCTGGAGGATTTTATATGAAAG TTGTATCTTCTCCTGACC 287 TCTGCACACACACCTACTAGT TTGGTTAATCGTCTTG 287d TCTAACAATCGTTCAAAGC TTGGTTAATCGTCTTG 288 TCTAAAAAGTTTTTAAAAGTTTT TTTAGTTACTTTCATAAATGG 288d TGGAATAATCATCAGTCA TTTAGTTACTTTCATAAATGG 289 TCTCAATCTAAAGGGCAAA ATATAATTCCTCTAAAACTAGC 289L TCTCAATCTAAAGGGCAAA CCACTTCAAATTAACTAAC 290 TATTACTTATCAAAAGAAAAGG ATTCCTTGAACACGAA 291 TCTCAAGTATTAAATGACAATGG GTGCCATTCATTCTCT 292 TTGAATCGTAAAAAAAGG TTGTCCTGTGAACTGTG 293 TCTATGGGTCTAGCAACAA AGGGTTTATTTGTTGAAG 293d N-term TCTATGGGTCTAGCAACAA TCCTGATTTATCCACTG 293d C-term TCTGTTACAGCTAAACACGG AGGGTTTATTTGTTGAAG 294 TCTGGTCATTTTAGTGAAAAA CAAAATACCTAAGCTAGC 295 TCTAGCGACATAAAAATCAT ACGAACTTCCATAACC 296 TCTAAAGGTATTATTTTAGCG GGCTTCTCCAATCAAA 297 TCTATTCAGATTGGCAAATT TTGAGTTAATGGATTGTT 298 TCTACTAAATTTATTGTTGATTCA TAGCGTTATTTCACTGTG 299 TTTGAAATACTTAAACCTG TTTCTCCGCCCAGTCA 300 TCTGCTTCTACAAATAATGTTTC CCGTTTATTCTTTCTACTG 301 TCTGTAATTAATATTGAGCAAGC CATATCTGTTGCATCAAT 302 TCTGAAATCAACACTGAAATAG AACTGGCTTTTTAGTCAG 303 TCTACAAGGCATATAAAAATTTC TTTATTATTTAATTCTTCAATA 304 TCTAACGAAATCAAATGCCC GTCTTTTAGAGCATCGA 305 TCTGGACGAGTAATGAAAACA CTCTCCTCTAAGACTTTCG 306 TCTGGGAAAAAAATTGTTTT TCCTTTTGTTACTTTTGC 307 TCTAAATTTACAGAACTTAACTTAT TTTATCGCCTTTGTTG 308 ATGACACAGATGAATTTTA ATGTTCAGGTTCTCCG 309 TTGCAACTTGGAATTG TTCCATTATCTTCAAGTTA 310 TCTGCTAAAGAGAGGGTAGAT CTCTTCTTCATTTTTCTA 311 TCAATTATTACTGATGTTTAC TTTTTTTAAGTTGTAGAATG 312 TCTACTGCAACTAAACAACAT GTTTTTTGATGCTTCTTG 313 TCTAAACGTATTGCTGTTTTA TTTACTACTTTGGTTGGC 314 TCTAAATTTTATCTTGTTAGACAC GTGTGTCATTTTGACCT 315 TCTATAGGGGATTATTCAGTAA TCCTTCAAGATCATTTAA 316 TCTACTGAACGAACATTCGA ACCTCCTTTTCTTTCATT 317 TCTAATAAGCCATATTCAATAG ATCTTCTCCTAACTTACCC 317d N-term TCTAATAAGCCATATTCAATAG ACTAGCTAGATTCTTAACGC 317d C-term TCTGACTTGAATGGCAATAT ATCTTCTCCTAACTTACCC 318 TCTATTGATTTTATTTCTATTG GCCTCTTTCTCCAAAT 319 TTAAAACATTTTGGTAGTAA ATGTCCTGTTATATCTTCTT 320 TCTACTATTTATGACCAAATTG GCGTTGAATAATGGTT 321 TCTAAAAATAAAAAAGATCAGTT TATTTCTTTAGTTTCTTCAA 322 TCTCAAGAAACAGATACGACG TAATAAAAATTATATAAGAACCT 323 TCTGGTAATGAGTCAAAGAAC TTCTGTCTTATAAGCATAAG 324 TCTGGAAGTAAATCAGCTTC TTTTTTATAAGCATGTGTA 325 TCTGCTTGGCAACTTGTTC ATGAGACATAAGGTCTTG 326 TCTGGCATCTCAGACTTACC GTTGGAGCTCCTACTG 326L TCTAAATTCAAATCTGGGG GTTGGAGCTCCTACTG 326L N-term TCTAAATTCAAATCTGGGG CATTTCTTTGGTTAAAGC 327 TCTGGAGGGAAAATGAATC TATCTCGAGTGCTATTTG 327d N-term TCTGGAGGGAAAATGAATC CTCTTCATCGACATAGTAA 327d C-term TCTGGCAACTTCAAAGCAT TATCTCGAGTGCTATTTG 328 TCTGACCAAGTCGGTGTCC ATTTTACAGTAGTGGAGTTT 329 TCTAAATCAAAGACCTCTTCTA TGTCCTCATTTTTTCA 330 TCTAATAAACGCGTAAAAATC TTTAACAGTACGAACACG 331 TCTACCAGAACAGTAGCAAT CCCCCTGTTTTTAAAAT 332 TCTACAAAAAACCTGTTATTAA ACCCTCATATGATTCC 333 TCTATTGATATACAAAAAATAAAA TTTAAAATAATGATACATCTC 333d TCTGGATCATTGAGGGCAA TTTAAAATAATGATACATCTC 334 TCTAATTTAGTAAAAGTGAATAGTG TAACCCCGTCTCAACA 335 TCTGAAGAAGAAAAATATTTTGA TATTTTCGTTTTCTCAAA 336 TCTCAGGTTGAAGTTGACTTA TTTCTCCAAATAATCTCTC 337 TCTGAAACAGATTCGTTTGTA CCTATTTTAGTTTTAGAAGA 338 TCTGCTATAATAGACAAAAAG GAAATCATAGCTTCCC 339 TCGAAACCGATTAAGAT ACCTTTTACTTTTGGTAGT 339d TCTCAAGTCATGCGCTATG ACCTTTTACTTTTGGTAGT 340 TCTGGATTTCTCTATAATTACTTC TTGTTTGTGAAGTAAAACG 341 TCTGGAAAACCATTGTTAAC TAATTTAAAAATTGCATAAA 342 TCTCAGAAAATTGAAGGTATT TTTCGTTACCATATCTAGA 343 TCTGAAATGCAAGTTCAAA TAAATCATGGAAACTAGC 344 TCTGCACAACGCAGAATGT AAAGCCCAACCTTCCG 345 TCTAAAAACCTGAATTGGG GTTTCCACGTCCTTTC 346 TCTAATAAAATAGCTAATACAGAAG AAGTTTATTCAAATCTGG 347 TCTATTGATATTCATTCTCATATC AATGTAATGGTTTTTTAATA 348 TCTACTGGATCTAAAAAATTAGC AGCTAAAATACCTAACCAG 349 TCTAAAGATCGCTTATATAATAAA ATTTTTTAAACGACTCAT 350 TCTGCAAAAGATATAATTAAGGTT AGCGGAACGGTGAATA 351 TCAGAAGATCAAAAACA ATAATCTAAACTATCAGCTCT 352 TCTACTTTTTTTAAAAAGCTAAA ATCTCCTATTGTAATTTTGA 352d TCTGGTACAGATAGTAAATTTGG ATCTCCTATTGTAATTTTGA 353 TCTACAATGTTAAAAATTGAAA CACCTCTTTTGTCAGA 354 TCTATTAAAGAACTAAAAGAATTT TTTGTTAGCGAGTAAGTC 355 TCTCGCTCACTACCTT TTTATCATCCTCCTTAATAA 356 TCTAAATTCTATATTATTGATGATG AAACGTTTTACTCTGTAAAA 357 TTGGAACATTTTTATATTAT AAATAAGAATGTTAAAAGAGC 358 TTTTATACAATTGAAGAGC TTCCCCAAAAATTTCT 359 TCAAGAAATAATTACGGT ACGCAGTCCCATTTTC 360 TCTATAATGAAGGCGGTCT CTGGCATGAGGTCTCA 361 TCTAGCGTATATGTTAGTGGA CCTTTTTTCAATAATAGC 362 TCTACTAAACCACAGGGGG ATCTTTAATCTTACCATCC 362d N-term TCTACTAAACCACAGGGGG TGCTGCTACTGCAATG 362 C-term TCTGGTAATGAAGGAAATATCAC ATCTTTAATCTTACCATCC 363 TCTCTCGAATTAAAAAATATTG TAAATTCCTTTGTTGTAATA 364 TCTAACTATATGGGTATGGGC ACCATCAGTTGTCACC 365 TCTGGAACTGCTACATATAGTAGG TATTGACCAGTGCACG 366 TGGCTTGACATTATTTT TTTTTTTGAATTTGTAAAAG 367 TCTAAGAAATTAAAAATATTCCC AGAGATTATTTTTATTTTAAAT 368 TCTAAAATCATTATTCAACGT TTTATTTTTAGTATCTAAAACG 369 TCTAGTAGAATGATTCCAGG TTTAGAAACTCCAAGTATCTC 370 TCTACCGAATTTAATGACG GTTAATTTGACTATTGATATATT 371 TCTAAAGATAGATATATTTTAGCAG TAAACTCTCAAAAGCTAAAC 372 TCAGAAAAATATTCCACT ACGTTCTTCTCTGGCT 373 TCTGAAATTGGTCAGCAAA ACTTAAATGGAACAACC 374 TCTAAGTTCGAAAATATAATATATG TTTGCCTAAAAAATTAGG 375 TCTGAAAAAGAAACTATTTTAAGT GGCTTTCCTCCCTTCA 376 TCTAAAGAAAAGAAAAATTTGG TTCATCTTTTTCAATATCA 377 TCTGGTAATAAACTGATGTATCA GTGAGAGTGTCTTTGTTT 378 TCTGAAGATCAACTCACTATATTT CAGATTTTTAGCTACTTGTC 379 TCTCAAATTACCCGAGAAG TCTAGAGCGCTTTATAAG 380 TCTCTTAAAAGATTACTTACTGAAG TTTTCTAATAGTTAGAAGCC 381 TCTCTTGGGATAGCTCACA TTTTAAATGTGCAGAGA 382 TCTATAAAGTTTAAATTATTTTTTAA ATTTATAATTTCCTTGGG 383 TCTATTTTACAGACGAATATACTAT TCTATAATATCTCTCTAAAGTGA 384 TCTAGAATAATTGTTGTCGG CCTCGCTAACATATCAC 385 TCTAATGTAAAAAAACGC AGCTCTTACAGTCTTGC 386 TCTCTAGTATCAAAGGAGAAAGC TTGTCTGAGTGACCAA 387 TCTGGTATGTTGTTAGCA ATAATATGAAATATGTTGTTCA 388 TCTCTTATGATAATAAATTCATTCG TCCGCAGAGTAAAAAA 389 TCTATGAATAGTGAACATAAAATT TTCATAAATGTGCCAA 390 TCTAGGGAAACTTACTGGA TTCATCTCTGCTCACC 391 TCTAAAAAAGTCATCGATTTAA TTCTCCTTCAGCTTTTA 392 TCTATTACATATGATTTCACAAG GTCATTTTTTCTAAAGTTTG 393 TCTAATAAATCTTGGTTGAGAA TTTTTGTAGTTGTTTCAAT 394 TCTCCTATGTTGTCTGTTGG TTTCATTAGATAACTATTCAGC 395 TCTACTTATCAAAAAACAGTTG TATAGACTGAAGATAATTAATTAA 396 TTTGTCAAAGGGATTT AAATCGATTAATCAAGTC 397 TCTAAATTATTTGATAAGTTTATAGA TCTAAAGTAGTCCTTTAGACTA 397d TCTAAAACTGCTACAGTTAG TCTAAAGTAGTCCTTTAGACTA 398 TATTTAGAACAATTAAAAGAGG TTTGTCCATAATCATTTC 399 TCTAAAGTTTTAGTAGTTGATGAT GGTAGATATGCCTAACATT 400 TCTAAAATAGTTGAAGGCG GTTTCCTTCCAAAAAA 401 TCTGGAATTGAATTTAAAAATG TCCATGCTTAATAGCC 402 TCTGGAAAATATTTTGGTACAG ATCTAAACCAATTTCTGTAC 403 TCTGAGGTTAGAATGGTAACTC GTCCACAAAAACGTCT 404 TCTAAAATAGATGACCTAAGAAA TAGATGTTCTACGGAGAA 405 TTGAAAATTCAGTATTATCA AAAGATGGCAAGCCAT 406 TCTGATAAAAATAATTTAGAAGACT TCTCTCTCCACACCATA 407 TCTAAAATTGACATGAGGAA CTTACCTCCTGTGGCT 407d TCTAAAATTGACATGAGGAA CTTTTGTTGGTTACCTC 408 TCTAACCACTTACTTAACCTCA TATTGTTAAATATGATGAAATG 409 TCTAAGGTAGTAGTAGCTATTGAT ATGATTATACAAATTGATTAAT 409d TCTACTGAAGAGAGAAATCCT ATGATTATACAAATTGATTAAT 410 TCTGCTTTATTATCAGTTATTGTC TCCCTCTTCCTTGACA 411 TCTAAAGACTATATTAACAGAATATT AACGTTTTTGAGCTTT 412 TCTGGATTTTTTGCACAGC TTTTGTCTTAAACGTTCT 413 TCTATTGTTGGTGAACAAGA TTTAGATAGTCTAGCCATTT 414 TTAAATCAATATTTTCTGC ACGGCTTGGGGCAGAG 415 TCTGAGCGAATTCCTGTTC TACCATTATCCGTGCT 416 TCTGAAGTCATTCGTGAACA ACTATTAAACTCCAATGTTA 417 TCAAAACAATATGATTATATC GCGCATTGTAACAAAT 418 TCTAGCAAGCCTAATGTTG TTTTGGTAAAAGGTCTG 419 TCTGATTTAAATAATTACATCGC TCCTGGAAAGTTCATC 420 TCTAAACGTGAATTACTACTCG TAGTTTATCTAAAGCGTTC 421 TCTATACGCCAGTTTTTAAG TTTATGTATAGAAACAGCAG 422 TTTTCGAGCGATTTTG AATGTACATAACAATAGAGAGC 423 TCTGTAACCAAAGTTGAAGAG CAACGATCCCAAGAAC 424 TCTATGAAAGATTTTATTGAATG GCCATTCTTACCTCCT 424d TCTATGAAAGATTTTATTGAATG ACGTTTTTTCTGACCG 425 TCTATAGCCTTTAATAGTTTATTT TATAAAATAAATTTGAAGATCT 426 TCTD440ACAGTTTATAATATAAACCATG ATCATCTTGTACCAACTC 427 TATTCTTTTGAAGAACTTTT GCCAATAAATTCACGG 428 TCTATAAAAATTTTGATCCC AGTCTGTTTTTTAACAAAAG 429 TCTAATCATTCCATTGAATC TGGTTTTAGAACAACTTTA 430 TTACAAAAAAAATATCGG AATTAAGCTGAAAATGAC 431 TCTGCGGCTCAATTAGCTG ATTATATTCTTTTAATTTGTCA 432 TCTCGTACCTTCAAACCAG CTTACGACGTCCTGGA 433 TCTATTAAAGCAACTTTTACTC GTGTGTCATGACTACTGTAC 434 TCAATTTTTCAGACAACA TGAGTAGAGCACAAGC 642 TCTAGAAAACGTAATGATACATT GAAACGAATACGTTCTT 643 TCTGATTGTCAAATTACACCA ACTACCTACCGTTTTCAC 644 TCTATTTTTCGTGGTGATAA TTTGATGGTAACAGTCG 645 TTTTTTAATATTGAATATCAC AGAAAGGCGCTCTTCT 646 TCTAAGGGAGTCCAATATATG TATCTTTAATAAAGCCCTA 647 TCTCGTCGCATGAATACCA CATCCCATAAATTTGTT 648 TCTATAGAATTTTCAGGGC CAAGACATTTCTTAAAGC 649 TCTGCTACTCACTCTAACTCAG TTTTGTTTTAGCGATG 650 TGCTCTTCTTCAAATACT TTTTAAACCATGCTGT 651 TCTCTAACACCATTTACAAAAG TTTGTAAAGACCTTCTTT 652 TCTCAACAAGGTATTATGGATA TTCCTCGTTTATTAATTT 653 TCTAAAATTTTAGGTACACCA AAAGAAAAGATGTGCC 654 TCTGGAAAAATGGTTAAGAA CTGTGCAGGCTCAAAT 655 TCTAAATTCGTCCGAACCGT AATTGTCCAGTCTAAGTTA 656 TCTGGTCTTCCAACGCAGC ATTTAGTGTTATTTCTCCTG 657 TGCTCAGGTAAAACAT TTTTTTAAGTGATGATGAA 658 TCTGAAAGCAAATCTTTGC CTTTGTCTGCTTCACTT 659 TGTGCTAATTGGATTG TTTTGGGGTTACTTTAC 660 TGTGGAAATGTCGGAG TTTTGCTGAAATAATGTT 661 TGTCAGTCAAACCACA ATCATACGAATGCAAC 662 TCTGCTAGTTTTTATTTTTTCC TTTTTCATATTTTTTCAAA 663 TGTGGAAGTAAATCAGC ATTATTTTTATAAGCATGTG 664 TCTGTTAAATTAAAATCGTTACTG GAGTTGTCTTTTTTTGTC 665 TCTATTGCTGGTCCTAGTG GATAAGCACTTTCCTTAA 666 TTATTTTTTGGAAATTGG GCCTAAAAACCAATCA 667 TCTGCTGTATTTACACTCGTC ATGTTTATGGCTTGCT 668 TTTTATATGAAAGAACAACA TTGTATCTTCTCCTGACC 669 TCAATTATTATTGGGTTAA ATATACCCTAGACTTTTTGA 670 TCTCCTAAATTAACCCTAGTCT GGCTTTAAAGTTCGATA 671 TCTAGTCTTGCGAAGGCAG TTTATCGTAAGCACTTAGG 672 TCTGTATTTACACTCGTCTTACA ATGTTTATGGCTTGCTT 673 TCTGGAGGATTTTATATGAAAG TTGTATCTTCTCCTGACC 674 TCTGTTAAATTAAAATCGTTACTG GAGTTGTCTTTTTTTGTCT 675 TCTGGTTCATCAGACAAACA TTCAACTTGATTGCCA 676 TCTGTAGTTAAAGTTGGTATTAACG TTTTGCAATTTTTGC 677 TCTGTATTAGAAGTACATGCTGA TTTTAATGCTGTTTGAA 678 TCTGAGACACCAGTAATGGC TTTTTTAGCTAAGGCTG 679 TCTGCTAACAAGCAGGATC TTTTGCTAAACCTTCTG 680 TCTAATAAGTCCAGTAACTCTAAG ATTCATATTAACACGATGC 681 TCTGCTTTTGATGTAATTATGC TTTGCGTTTTGGAGGG 682 TCTATTAACTATGAGGTTAAAGC TGCACCTTGATGGCGA 683 TCTGTAATTGTTGAACTTAGTTTG CCATAATATTTGATGCTG 684 TCTCTTAGGAAGTATAAGCAAA TTCTAATCCTACAGCATG 685 TCTAAAATTTGTCTGGTTGG AAAAATTCCTCCTAAATTAA 686 TCTGACTTTTATGATATCAATCTT AAAGTTTTGACTATTACTGATAG 687 TATGCTATTATGCAAAAAG TGGGGGAGATAGTTATG 688 TCTGCAATCGTTTCAGCAG TTGACAGAAAGCTAATTG

TABLE-US-08060 TABLE III RESULTS FOR in vivo GBS CHALLENGE % survival GBS # Pre-immune Post-immune 1 18.7 22.2 4gst 19.4 37.2 4his 25.0 75.0 8 14.3 42.1 10 29.1 36.0 15 30.0 60.9 16 33.3 53.8 18 29.4 50.0 21 5.9 10.0 22 36.8 63.1 24 38.5 41.4 25 28.6 85.7 32 20.0 25.0 35 0.0 17.6 45 26.7 37.5 48 20.0 25.0 52 14.2 17.3 53 23.8 29.2 54 22.7 44.0 55 50.0 52.9 57 33.3 55.6 58 6.7 11.8 62 15.8 36.4 63 21.4 42.9 65 3.7 23.3 67 23.5 27.8 71 13.3 26.7 73 28.6 39.1 80 38.8 56.5 84 33.3 37.5 85 30.8 62.5 90 14.3 22.7 94 25.0 30.0 95 16.7 23.1 98 5.9 11.1 100 26.9 42.9 103 16.7 52.9 106 10.0 18.2 110 11.1 30.0 113 17.6 29.4 114 40.0 52.2 117 27.8 36.8 119 36.4 52.2 139 23.1 26.7 150 21.6 44.4 153 25.0 30.0 155 22.6 36.8 157 14.3 31.8 158 22.6 40.0 163 29.6 37.9 164 25.0 43.8 173 17.9 38.7 176 20.0 38.9 177 21.7 33.3 181 5.0 21.7 186 41.2 52.6 188 11.8 23.5 189 21.4 31.6 195 32.1 64.7 206 33.3 50.0 211 30.8 33.3 232 50.0 57.1 233 34.8 55.2 236 57.1 70.6 243 46.7 52.9 263 15.4 35.7 273 61.5 75.0 276 23.8 44.4 296 25.0 28.6 297 13.3 23.5 298 20.0 22.2 302 30.0 52.2 304 33.3 40.9 305 42.1 70.0 316 38.5 42.9 318 7.1 15.8 TABLE-US-08061 TABLE IV COMPARISON OF GBSnnn NUMBERING AND SEQ ID NUMBER GBS numbering Sequence listing GBS1 SEQ ID 3532 & 8736 GBS2 SEQ ID 4530 & 8818 GBS3 SEQ ID 6266 & 8958 GBS4 SEQ ID 2 & 8786 GBS5 SEQ ID 2598 & 8674 GBS6 SEQ ID 398 & 8496 GBS7 SEQ ID 8790 & 9798 GBS8 SEQ ID 8694 GBS9 SEQ ID 4540 & 8822 GBS10 SEQ ID 8718 GBS11 SEQ ID 5884 & 8930 GBS12 SEQ ID 8764 & 9692 GBS13 SEQ ID 8484 GBS14 SEQ ID 5406 & 8892 GBS15 SEQ ID 4 & 8710 GBS16 SEQ ID 944 & 8538 GBS17 SEQ ID 1770 & 8602 GBS18 SEQ ID 6860 & 9002 GBS19 SEQ ID 4422 & 8812 GBS20 SEQ ID 308 & 8488 GBS21 SEQ ID 8762 GBS22 SEQ ID 8584 GBS23 SEQ ID 8512 GBS24 SEQ ID 1694 & 8598 GBS25 SEQ ID 3180 & 8714 GBS26 SEQ ID 8820 GBS27 SEQ ID 8774 GBS28 SEQ ID 8738 GBS29 SEQ ID 8744 GBS30 SEQ ID 8860 GBS31 SEQ ID 8702 GBS32 SEQ ID 8910 & 10142 GBS33 SEQ ID 5734 & 8912 GBS34 SEQ ID 5750 & 8916 GBS35 SEQ ID 8908 GBS36 SEQ ID 8542 GBS37 SEQ ID 8564 GBS38 SEQ ID 2122 & 8642 GBS39 SEQ ID 8480 GBS40 SEQ ID 8654 GBS41 SEQ ID 1176 & 8562 GBS42 SEQ ID 4856 & 8850 GBS43 SEQ ID 672 & 8520 GBS44 SEQ ID 9000 GBS45 SEQ ID 9018 GBS46 SEQ ID 1834 & 8608 GBS47 SEQ ID 8588 GBS48 SEQ ID 8594 & 8596 GBS49 SEQ ID 8494 & 9490 GBS50 SEQ ID 1236 & 8566 GBS51 SEQ ID 5410 GBS52 SEQ ID 3920 GBS53 SEQ ID 8586 GBS54 SEQ ID 3442 GBS55 SEQ ID 9020 & 10338 GBS56 SEQ ID 2510 & 8668 GBS57 SEQ ID 8854 GBS58 SEQ ID 8664 GBS59 SEQ ID 3744 GBS60 SEQ ID 8760 GBS61 SEQ ID 8776 GBS62 SEQ ID 2244 GBS63 SEQ ID 390 GBS64 SEQ ID 374 GBS65 SEQ ID 8544 GBS66 SEQ ID 3028 GBS67 SEQ ID 3746 GBS68 SEQ ID 4012 GBS69 SEQ ID 4916 GBS70 SEQ ID 3718 GBS71 SEQ ID 8906 GBS72 SEQ ID 1348 GBS73 SEQ ID 220 GBS74 SEQ ID 5872 GBS75 SEQ ID 8926 GBS76 SEQ ID 5862 GBS77 SEQ ID 3256 GBS78 SEQ ID 3262 GBS79 SEQ ID 3264 GBS80 SEQ ID 8780 GBS81 SEQ ID 2706 GBS82 SEQ ID 2898 GBS83 SEQ ID 8772 GBS84 SEQ ID 4182 GBS85 SEQ ID 216 GBS86 SEQ ID 2978 GBS87 SEQ ID 3452 GBS88 SEQ ID 5694 GBS89 SEQ ID 2682 GBS90 SEQ ID 8476 GBS91 SEQ ID 8938 GBS92 SEQ ID 8964 & 10238 GBS93 SEQ ID 2848 GBS94 SEQ ID 1592 GBS95 SEQ ID 2224 GBS96 SEQ ID 2130 GBS97 SEQ ID 800 GBS98 SEQ ID 8746 GBS99 SEQ ID 4240 GBS100 SEQ ID 8782 GBS101 SEQ ID 6902 GBS102 SEQ ID 6894 GBS103 SEQ ID 6 GBS104 SEQ ID 8778 GBS105 SEQ ID 1400 GBS106 SEQ ID 8502 GBS107 SEQ ID 6026 GBS108 SEQ ID 8532 GBS109 SEQ ID 4116 GBS110 SEQ ID 6832 GBS111 SEQ ID 8842 GBS112 SEQ ID 8904 GBS113 SEQ ID 300 GBS114 SEQ ID 8968 GBS115 SEQ ID 5164 GBS116 SEQ ID 5152 GBS117 SEQ ID 8962 GBS118 SEQ ID 2508 GBS119 SEQ ID 8814 GBS120 SEQ ID 8874 GBS121 SEQ ID 3826 GBS122 SEQ ID 9006 GBS123 SEQ ID 6310 GBS124 SEQ ID 260 GBS125 SEQ ID 3872 GBS126 SEQ ID 6736 GBS127 SEQ ID 8816 GBS128 SEQ ID 752 GBS129 SEQ ID 8990 GBS130 SEQ ID 9004 GBS131 SEQ ID 6198 GBS132 SEQ ID 8730 GBS133 SEQ ID 474 GBS134 SEQ ID 9008 GBS135 SEQ ID 8882 GBS136 SEQ ID 1188 GBS137 SEQ ID 3960 GBS138 SEQ ID 9052 GBS139 SEQ ID 884 GBS140 SEQ ID 8632 GBS141 SEQ ID 1768 GBS142 SEQ ID 8600 GBS143 SEQ ID 9054 GBS144 SEQ ID 2238 GBS145 SEQ ID 8700 GBS146 SEQ ID 8696 GBS147 SEQ ID 8526 GBS148 SEQ ID 9010 GBS149 SEQ ID 8732 GBS150 SEQ ID 3736 GBS151 SEQ ID 3188 GBS152 SEQ ID 3952 GBS153 SEQ ID 3904 GBS154 SEQ ID 4024 GBS155 SEQ ID 8796 GBS156 SEQ ID 4646 GBS157 SEQ ID 4812 GBS158 SEQ ID 5504 GBS159 SEQ ID 8628 GBS160 SEQ ID 8924 GBS161 SEQ ID 8922 GBS162 SEQ ID 168 GBS163 SEQ ID 224 GBS164 SEQ ID 1102 GBS165 SEQ ID 3672 GBS166 SEQ ID 8712 GBS167 SEQ ID 4214 GBS168 SEQ ID 9016 GBS169 SEQ ID 4346 GBS170 SEQ ID 8982 GBS171 SEQ ID 6720 GBS172 SEQ ID 6704 GBS173 SEQ ID 8788 GBS174 SEQ ID 6150 GBS175 SEQ ID 62 GBS176 SEQ ID 8478 GBS177 SEQ ID 8876 GBS178 SEQ ID 6078 GBS179 SEQ ID 8848 GBS180 SEQ ID 3062 GBS181 SEQ ID 1924 GBS182 SEQ ID 3774 GBS183 SEQ ID 4796 GBS184 SEQ ID 1978 GBS185 SEQ ID 1046 GBS186 SEQ ID 8470 GBS187 SEQ ID 844 GBS188 SEQ ID 3410 GBS189 SEQ ID 6986 GBS190 SEQ ID 8842 GBS191 SEQ ID 1814 GBS192 SEQ ID 8618 GBS193 SEQ ID 2382 GBS194 SEQ ID 3912 GBS195 SEQ ID 8 GBS196 SEQ ID 4944 GBS197 SEQ ID 5486 GBS198 SEQ ID 8896 GBS199 SEQ ID 1162 GBS200 SEQ ID 8936 GBS201 SEQ ID 4550 GBS202 SEQ ID 8666 GBS203 SEQ ID 6478 GBS204 SEQ ID 1996 GBS205 SEQ ID 18 GBS206 SEQ ID 8552 GBS207 SEQ ID 3822 GBS208 SEQ ID 3916 GBS209 SEQ ID 3918 GBS210 SEQ ID 3738 GBS211 SEQ ID 4680 GBS212 SEQ ID 8750 GBS213 SEQ ID 8500 GBS214 SEQ ID 8498 GBS215 SEQ ID 9022 GBS216 SEQ ID 8606 GBS217 SEQ ID 9024 GBS218 SEQ ID 8652 GBS219 SEQ ID 8646 GBS220 SEQ ID 2730 GBS221 SEQ ID 9028 GBS222 SEQ ID 3842 GBS223 SEQ ID 8794 GBS224 SEQ ID 9026 GBS225 SEQ ID 8834 GBS226 SEQ ID 4966 GBS227 SEQ ID 5030 GBS228 SEQ ID 5050 GBS229 SEQ ID 9056 GBS230 SEQ ID 1296 GBS231 SEQ ID 5810 GBS232 SEQ ID 5830 GBS233 SEQ ID 4722 GBS234 SEQ ID 1106 GBS235 SEQ ID 8560

GBS236 SEQ ID 6162 GBS237 SEQ ID 8706 GBS238 SEQ ID 4246 GBS239 SEQ ID 8980 GBS240 SEQ ID 8986 GBS241 SEQ ID 9030 GBS242 SEQ ID 9032 GBS243 SEQ ID 8678 GBS244 SEQ ID 6554 GBS245 SEQ ID 8994 GBS246 SEQ ID 6864 GBS247 SEQ ID 8856 GBS248 SEQ ID 454 GBS249 SEQ ID 8620 GBS250 SEQ ID 8634 GBS251 SEQ ID 2258 GBS252 SEQ ID 8648 GBS253 SEQ ID 2526 GBS254 SEQ ID 2710 GBS255 SEQ ID 2966 GBS256 SEQ ID 3424 GBS257 SEQ ID 3550 GBS258 SEQ ID 3752 GBS259 SEQ ID 8756 GBS260 SEQ ID 4162 GBS261 SEQ ID 1530 GBS262 SEQ ID 8572 GBS263 SEQ ID 1616 GBS264 SEQ ID 8824 GBS265 SEQ ID 4554 GBS266 SEQ ID 4652 GBS267 SEQ ID 4980 GBS268 SEQ ID 5038 GBS269 SEQ ID 5534 GBS270 SEQ ID 1998 GBS271 SEQ ID 8570 GBS272 SEQ ID 22 GBS273 SEQ ID 5994 GBS274 SEQ ID 774 GBS275 SEQ ID 2308 GBS276 SEQ ID 8942 GBS277 SEQ ID 8954 GBS278 SEQ ID 8524 GBS279 SEQ ID 6292 GBS280 SEQ ID 6254 GBS281 SEQ ID 4458 GBS282 SEQ ID 4444 GBS283 SEQ ID 9034 GBS284 SEQ ID 6456 & 8974 GBS285 SEQ ID 8802 GBS286 SEQ ID 9036 GBS287 SEQ ID 5354 GBS288 SEQ ID 5374 GBS289 SEQ ID 8616 GBS290 SEQ ID 8680 GBS291 SEQ ID 8530 GBS292 SEQ ID 8998 GBS293 SEQ ID 8582 GBS294 SEQ ID 8604 GBS295 SEQ ID 2722 GBS296 SEQ ID 2658 GBS297 SEQ ID 3024 GBS298 SEQ ID 8704 GBS299 SEQ ID 3268 GBS300 SEQ ID 4170 GBS301 SEQ ID 8576 GBS302 SEQ ID 8670 GBS303 SEQ ID 8554 GBS304 SEQ ID 5846 GBS305 SEQ ID 208 GBS306 SEQ ID 212 GBS307 SEQ ID 8992 GBS308 SEQ ID 8880 GBS309 SEQ ID 3386 GBS310 SEQ ID 286 GBS311 SEQ ID 3964 GBS312 SEQ ID 4660 GBS313 SEQ ID 4090 GBS314 SEQ ID 8556 GBS315 SEQ ID 1766 GBS316 SEQ ID 2000 GBS317 SEQ ID 4210 GBS318 SEQ ID 8548 GBS319 SEQ ID 892 GBS320 SEQ ID 916 GBS321 SEQ ID 8846 GBS322 SEQ ID 8540 GBS323 SEQ ID 2102 GBS324 SEQ ID 8490 GBS325 SEQ ID 8900 GBS326 SEQ ID 8630 GBS327 SEQ ID 5856 GBS328 SEQ ID 6016 GBS329 SEQ ID 8928 GBS330 SEQ ID 8792 GBS331 SEQ ID 922 GBS332 SEQ ID 1004 GBS333 SEQ ID 1786 GBS334 SEQ ID 1784 GBS335 SEQ ID 1782 GBS336 SEQ ID 1886 GBS337 SEQ ID 2010 GBS338 SEQ ID 8638 GBS339 SEQ ID 2080 GBS340 SEQ ID 8594 & 8596 GBS341 SEQ ID 2280 GBS342 SEQ ID 2266 GBS343 SEQ ID 8644 GBS344 SEQ ID 8662 GBS345 SEQ ID 2442 GBS346 SEQ ID 2768 GBS347 SEQ ID 2766 GBS348 SEQ ID 8658 GBS349 SEQ ID 2360 GBS350 SEQ ID 8698 GBS351 SEQ ID 2970 GBS352 SEQ ID 8692 GBS353 SEQ ID 3454 GBS354 SEQ ID 8754 GBS355 SEQ ID 8752 GBS356 SEQ ID 8724 GBS357 SEQ ID 8720 GBS358 SEQ ID 3184 GBS359 SEQ ID 3948 GBS360 SEQ ID 3926 GBS361 SEQ ID 8770 GBS362 SEQ ID 8768 GBS363 SEQ ID 3816 GBS364 SEQ ID 1452 GBS365 SEQ ID 1398 GBS366 SEQ ID 8574 GBS367 SEQ ID 1340 GBS368 SEQ ID 1598 GBS369 SEQ ID 4822 GBS370 SEQ ID 8844 GBS371 SEQ ID 4926 GBS372 SEQ ID 4956 GBS373 SEQ ID 5062 GBS374 SEQ ID 8878 GBS375 SEQ ID 326 GBS376 SEQ ID 5380 GBS377 SEQ ID 5468 GBS378 SEQ ID 5570 GBS379 SEQ ID 8918 GBS380 SEQ ID 156 GBS381 SEQ ID 8934 GBS382 SEQ ID 8610 GBS383 SEQ ID 4738 GBS384 SEQ ID 8836 GBS385 SEQ ID 1094 GBS386 SEQ ID 9038 GBS387 SEQ ID 8558 GBS388 SEQ ID 9040 GBS389 SEQ ID 8516 GBS390 SEQ ID 8952 GBS391 SEQ ID 8522 GBS392 SEQ ID 6220 GBS393 SEQ ID 8966 GBS394 SEQ ID 8960 GBS395 SEQ ID 6276 GBS396 SEQ ID 8468 GBS397 SEQ ID 6262 GBS398 SEQ ID 8806 GBS399 SEQ ID 1960 GBS400 SEQ ID 3154 GBS401 SEQ ID 3170 GBS402 SEQ ID 4236 GBS403 SEQ ID 8798 GBS404 SEQ ID 8800 GBS405 SEQ ID 8508 GBS406 SEQ ID 8506 GBS407 SEQ ID 6484 GBS408 SEQ ID 9042 GBS409 SEQ ID 6678 GBS410 SEQ ID 4064 GBS411 SEQ ID 9044 GBS412 SEQ ID 9046 GBS413 SEQ ID 272 GBS414 SEQ ID 8946 GBS415 SEQ ID 8944 GBS416 SEQ ID 6044 GBS417 SEQ ID 1874 GBS418 SEQ ID 5146 GBS419 SEQ ID 2638 GBS420 SEQ ID 2104 GBS421 SEQ ID 2108 GBS422 SEQ ID 714 GBS423 SEQ ID 6884 GBS424 SEQ ID 4874 GBS425 SEQ ID 3978 GBS426 SEQ ID 3976 GBS427 SEQ ID 6958 GBS428 SEQ ID 3398 GBS429 SEQ ID 3402 GBS430 SEQ ID 8840 GBS431 SEQ ID 8902 GBS432 SEQ ID 8534 GBS433 SEQ ID 2558 GBS434 SEQ ID 8590 GBS435 SEQ ID 484 GBS436 SEQ ID 8472 GBS437 SEQ ID 466 GBS438 SEQ ID 362 GBS439 SEQ ID 900 GBS440 SEQ ID 8536 GBS441 SEQ ID 936 GBS442 SEQ ID 940 GBS443 SEQ ID 998 GBS444 SEQ ID 1776 GBS445 SEQ ID 8634 GBS446 SEQ ID 2048 GBS447 SEQ ID 1654 GBS448 SEQ ID 8592 GBS449 SEQ ID 1634 GBS450 SEQ ID 1630 GBS451 SEQ ID 2098 GBS452 SEQ ID 2062 GBS453 SEQ ID 8636 GBS454 SEQ ID 1734 GBS455 SEQ ID 1690 GBS456 SEQ ID 1684 GBS457 SEQ ID 8656 GBS458 SEQ ID 8650 GBS459 SEQ ID 2152 GBS460 SEQ ID 2148 GBS461 SEQ ID 2394 GBS462 SEQ ID 2778 GBS463 SEQ ID 8688 GBS464 SEQ ID 8684 GBS465 SEQ ID 8682 GBS466 SEQ ID 2694 GBS467 SEQ ID 2350 GBS468 SEQ ID 8660 GBS469 SEQ ID 2998 GBS470 SEQ ID 2988 GBS471 SEQ ID 2924 GBS472 SEQ ID 2910 GBS473 SEQ ID 2882 GBS474 SEQ ID 2878 GBS475 SEQ ID 2856 GBS476 SEQ ID 8690 GBS477 SEQ ID 3112 GBS478 SEQ ID 3432 GBS479 SEQ ID 3460 GBS480 SEQ ID 3504 GBS481 SEQ ID 8734 GBS482 SEQ ID 8740 GBS483 SEQ ID 3606 GBS484 SEQ ID 3562 GBS485 SEQ ID 3552 GBS486 SEQ ID 3762 GBS487 SEQ ID 3756 GBS488 SEQ ID 3732 GBS489 SEQ ID 3730 GBS490 SEQ ID 3704 GBS491 SEQ ID 3698 GBS492 SEQ ID 3252 GBS493 SEQ ID 3244 GBS494 SEQ ID 3238 GBS495 SEQ ID 8722 GBS496 SEQ ID 8716 GBS497 SEQ ID 3876 GBS498 SEQ ID 3858 GBS499 SEQ ID 8758 GBS500 SEQ ID 4022 GBS501 SEQ ID 4106 GBS502 SEQ ID 1406 GBS503 SEQ ID 8580 GBS504 SEQ ID 4578 GBS505 SEQ ID 4566 GBS506 SEQ ID 8832 GBS507 SEQ ID 8830 GBS508 SEQ ID 4644 GBS509 SEQ ID 8828 GBS510 SEQ ID 8826 GBS511 SEQ ID 4892 GBS512 SEQ ID 4970 GBS513 SEQ ID 4974 GBS514 SEQ ID 8862 GBS515 SEQ ID 8864 GBS516 SEQ ID 8866 GBS517 SEQ ID 8868 GBS518 SEQ ID 9012 GBS519 SEQ ID 5068 GBS520 SEQ ID 8870 GBS521 SEQ ID 5228 GBS522 SEQ ID 322 GBS523 SEQ ID 8492 GBS524 SEQ ID 8894 GBS525 SEQ ID 5430 GBS526 SEQ ID 5414 GBS527 SEQ ID 5524 GBS528 SEQ ID 8898 GBS529 SEQ ID 5670 GBS530 SEQ ID 5630 GBS531 SEQ ID 5588 GBS532 SEQ ID 1324 GBS533 SEQ ID 8914 GBS534 SEQ ID 8550 GBS535 SEQ ID 8568 GBS536 SEQ ID 1288 GBS537 SEQ ID 5798 GBS538 SEQ ID 8920 GBS539 SEQ ID 158 GBS540 SEQ ID 8482 GBS541 SEQ ID 184 GBS542 SEQ ID 9048 GBS543 SEQ ID 8932 GBS544 SEQ ID 5880 GBS545 SEQ ID 44 GBS546 SEQ ID 9014 GBS547 SEQ ID 12 GBS548 SEQ ID 8614 GBS549 SEQ ID 8612 GBS550 SEQ ID 4720 GBS551 SEQ ID 4710 GBS552 SEQ ID 1086 GBS553 SEQ ID 1088 GBS554 SEQ ID 1138 GBS555 SEQ ID 8748 GBS556 SEQ ID 5968 GBS557 SEQ ID 774 GBS558 SEQ ID 1192 GBS559 SEQ ID 1196 GBS560 SEQ ID 1268 GBS561 SEQ ID 8518 GBS562 SEQ ID 8676 GBS563 SEQ ID 2296 GBS564 SEQ ID 2300 GBS565 SEQ ID 8950 GBS566 SEQ ID 694 GBS567 SEQ ID 680 GBS568 SEQ ID 6300 GBS569 SEQ ID 8956 GBS570 SEQ ID 8972 GBS571 SEQ ID 8970 GBS572 SEQ ID 3300 GBS573 SEQ ID 3304 GBS574 SEQ ID 8726 GBS575 SEQ ID 8810 GBS576 SEQ ID 4418 GBS577 SEQ ID 8808 GBS578 SEQ ID 4382 GBS579 SEQ ID 4378 GBS580 SEQ ID 1932 GBS581 SEQ ID 8622 GBS582 SEQ ID 8624 GBS583 SEQ ID 1962 GBS584 SEQ ID 8708 GBS585 SEQ ID 8672 GBS586 SEQ ID 6444 GBS587 SEQ ID 8976 GBS588 SEQ ID 8804 GBS589 SEQ ID 8514 GBS590 SEQ ID 8510 GBS591 SEQ ID 630 GBS592 SEQ ID 8504 GBS593 SEQ ID 514 GBS594 SEQ ID 8978 GBS595 SEQ ID 6738 GBS596 SEQ ID 6712 GBS597 SEQ ID 6686 GBS598 SEQ ID 6674 GBS599 SEQ ID 6662 GBS600 SEQ ID 8988 GBS601 SEQ ID 8578 GBS602 SEQ ID 8948 GBS603 SEQ ID 6132 GBS604 SEQ ID 5282 GBS605 SEQ ID 5302 GBS606 SEQ ID 8884 GBS607 SEQ ID 5314 GBS608 SEQ ID 8886 GBS609 SEQ ID 8888 GBS610 SEQ ID 8890 GBS611 SEQ ID 6028 GBS612 SEQ ID 8474 GBS613 SEQ ID 5092 GBS614 SEQ ID 8872 GBS615 SEQ ID 6052 GBS616 SEQ ID 8940 GBS617 SEQ ID 1824 GBS618 SEQ ID 6600 GBS619 SEQ ID 6608 GBS620 SEQ ID 6620 GBS621 SEQ ID 864 GBS622 SEQ ID 8640 GBS623 SEQ ID 8996 GBS624 SEQ ID 9050 GBS625 SEQ ID 2812 GBS626 SEQ ID 8858 GBS627 SEQ ID 8852 GBS628 SEQ ID 8784 GBS629 SEQ ID 6950 GBS630 SEQ ID 4502 GBS631 SEQ ID 4492 GBS632 SEQ ID 4488 GBS633 SEQ ID 8728 GBS634 SEQ ID 3066 GBS635 SEQ ID 8838 GBS636 SEQ ID 4772 GBS637 SEQ ID 8626 GBS638 SEQ ID 8984 GBS639 SEQ ID 8546 GBS640 SEQ ID 6780 GBS641 SEQ ID 900 GBS642 1312 GBS643 1772 GBS644 1956 GBS645 2726 GBS646 3348 GBS647 3770 GBS648 4934 GBS649 5076 GBS650 5446 GBS651 5602 GBS652 5610 GBS653 5760 GBS654 6096 GBS655 6656 GBS656 9324 GBS657 10782 GBS658 8802 GBS659 9344 GBS660 9410 GBS661 9428 GBS662 9286 GBS663 9294 GBS664 9034 GBS665 10546 GBS666 10610 GBS667 9052 GBS668 9036 GBS669 9010 GBS670 10730 GBS671 9020 GBS672 9052 GBS673 9036 GBS674 9034 GBS675 10634 GBS676 10692 GBS677 10746 GBS678 9330 GBS679 9404 GBS680 6668 GBS681 4264 GBS682 6762 GBS683 9290 GBS684 9614 GBS685 10454 GBS686 2774 GBS687 4620 GBS688 10224 TABLE-US-08062 TABLE V NUCLEOTIDES DELETED IN EXPRESSION OF GBSnnn PROTEINS GBS Deleted nucleotides 11d 1-153 31d 1-129 64d 1-165 68d 2029-2796 70d 1-402 74d 1-975 79d 1-201 105dN 2689-4119 105dC 1-2688 105d 1-2688 109d 1-120 130d 1-518 170d 1-111 182d 1596-1674 195C 1-1710 195N 1711-3243 209d 757-912 210d 1-99 & 777-879 220d 1-120 231d 1-54 235d 1-270 246d 1-75 248d 1-591 272d 1-531 277d 1-318 281d 1-54 287d 1-108 288d 1-72 293C 1-1229 293N 1230-2379 317N 1729-4107 317C 1-2379 326N 1707-2652 326dN 2326-3927 327N 3034-6831 327C 1-3033 333d 1-150 339d 1-111 352d 1-158 362N 1707-2652 362C 1-1706 397d 1-348 399d 1-111 407d 1174-1473 409d 1-297 424d 1327-1671

TABLE-US-08063 TABLE VI PREDICTED FUNCTIONS FOR CERTAIN SEQ IDs SEQ ID Function 6 manganese ABC transporter, ATP-binding protein (psaB) 12 iron (chelated) ABC transporter, permease protein (psaC) 18 peptidyl-prolyl cis-trans isomerase, cyclophilin-type 26 chorismate binding enzyme (pabB) 30 probable transposase (insertion sequence IS861) 42 peptidase, M20/M25/M40 family 44 drug transporter 50 ribosomal protein L11 (rplK) 54 ribosomal protein L1 (rplA) 62 peptide ABC transporter, permease protein 66 peptide ABC transporter, permease protein 78 uridylate kinase (pyrH) 84 ribosome recycling factor (frr) 104 PhoH family protein (phoH) 110 MutT/nudix family protein superfamily 116 tetracenomycin polyketide synthesis O-methyltransferase TcmP 134 phosphopantetheine adenylyltransferase (coaD) 140 PDZ domain protein 144 5-nucleotidase family protein 156 VanZF-related protein 158 ABC transporter, ATP-binding/permease protein 162 ABC transporter, ATP-binding/permease protein 168 BioY family protein 180 acetyl-CoA acetyltransferase 188 endonuclease III (nth) 196 glucokinase (gki) 200 rhodanese family protein 204 elongation factor Tu family protein (typA) 212 UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide) pyrophosphoryl- 216 cell division protein DivlB 220 cell division protein FtsA (ftsA) 224 cell division protein FtsZ (ftsZ) 236 ylmH protein (ylmH) 240 cell division protein DivIVA (divIVA) 244 isoleucyl-tRNA synthetase (ileS) 252 MutT/nudix family protein 256 ATP-dependent Clp protease, ATP-binding subunit ClpE (clpE) 268 methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cycloh 274 exodeoxyribonuclease VII, large subunit (xseA) 278 exodeoxyribonuclease VII, small subunit (xseB) 282 geranyltranstransferase (ispA) 286 hemolysin A 290 transcriptional repressor 296 DNA repair protein RecN (recN) 300 degV family protein (degV) 322 peptide ABC transporter, permease protein (oppC) 326 peptide ABC transporter, ATP-binding protein (oppD) 328 peptide ABC transporter, ATP-binding protein (oppF) 348 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (ispE) 352 adc operon repressor AdcR (adcR) 356 zinc ABC transporter, ATP-binding protein (adcC) 370 tyrosyl-tRNA synthetase (tyrS) 374 penicillin-binding protein 1B (pbp1B) 378 DNA-directed RNA polymerase, beta subunit (rpoB) 382 dna-directed ma polymerase beta' chain 390 competence protein CglA (cglA) 406 acetate kinase (ackA) 410 transcriptional regulator 418 pyrroline-5-carboxylate reductase (proC) 422 glutamyl-aminopeptidase (pepA) 432 thioredoxin family protein 436 tRNA binding domain protein (pheT) 440 methyltransferase 442 single-strand DNA-binding protein, authentic point mutation (ssbB) 454 GAF domain protein (lytS) 466 lrgB protein (lrgB) 474 oligopeptide ABC transporter, permease protein 476 peptide ABC transporter, ATP-binding protein 480 peptide ABC transporter, ATP-binding protein (oppF) 484 PTS system, IIABC components (treB) 488 alpha amylase family protein (treC) 494 transcriptional regulator, BglG family 506 transcriptional regulator, BglG family 508 PTS system, IIB component 514 PTS system, IIC component 518 transketolase, N-terminal subunit (tktA) 528 ribosomal protein S15 (rpsO) 546 cysteinyl-tRNA synthetase (cysS) 554 RNA methyltransferase, TrmH family, group 3 562 DegV family protein (degV) 572 ribosomal protein S9 (rpsl) 576 integrase, phage family 580 transcriptional regulator 596 recombination protein 626 transcriptional regulator MutR 630 transporter 640 amino acid ABC transporter, permease protein (opuBB) 642 glycine betaine/L-proline transport ATP binding subunit (proV) 654 lectin, alpha subunit precursor 662 transcriptional regulator 664 acetyltransferase, GNAT family 666 acetyltransferase, GNAT family (rimJ) 670 acetyltransferase, GNAT family 676 transcriptional regulator, tetR family domain protein 680 ABC transporter efflux protein, DrrB family 690 IS1381, transposase OrfA/OrfB, truncation 714 magnesium transporter, CorA family 718 oxidoreductase, Gfo/ldh/MocA family 722 valyl-tRNA synthetase (valS) 730 acetyltransferase, GNAT family 746 methyltransferase 750 bacteriophage L54a, integrase 754 DNA-damage-inducible protein J 774 cation efflux system protein 778 oxidoreductase, aldo/keto reductase family 784 alcohol dehydrogenase, zinc-containing 790 3-oxoadipate enol-lactone hydrolase/4-carboxymuconolactone decarboxylas 804 ribonucleoside-diphosphate reductase, alpha subunit (nrdE) 808 nrdI protein (nrdI) 812 Ribonucleotide reductases 824 elaA protein (elaA) 828 RNA methyltransferase, TrmA family 832 RecX family protein 840 -identity (jag) 844 membrane protein, 60 kDa (yidC) 856 UTP-glucose-1-phosphate uridylyltransferase (galU) 864 rhomboid family protein 884 MORN motif family 892 transcriptional regulator 896 adenylosuccinate lyase (purB) 908 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) 912 phosphoribosylamine--glycine ligase (purD) 916 phosphosugar-binding transcriptional regulator 920 acetyl xylan esterase 922 ROK family protein (gki) 926 N-acetylneuraminate lyase (nanA) 936 sugar ABC transporter, permease protein 940 sugar ABC transporter, permease protein (msmF) 952 LysM domain protein, authentic frameshift 956 zoocin A endopeptidase 958 phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydr 962 acetyltransferase, GNAT family family 964 phosphoribosylglycinamide formyltransferase (purN) 968 phosphoribosylformylglycinamidine cyclo-ligase (purM) 972 amidophosphoribosyltransferase (purF) 980 phosphoribosylformylglycinamidine synthase 984 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) 1042 oligoendopeptidase F (pepF) 1060 ebsC protein 1068 hydrolase, haloacid dehalogenase-like family 1076 riboflavin synthase, beta subunit (ribH) 1082 riboflavin biosynthesis protein RibD (ribD) 1086 Mn2+/Fe2+ transporter, NRAMP family 1094 peptidase, U32 family 1116 HPr(Ser) kinase/phosphatase (hprK) 1130 oxidoreductase 1148 signal recognition particle-docking protein FtsY (ftsY) 1152 Cof family protein 1156 Cof family protein 1172 vicX protein (vicX) 1176 sensory box sensor histidine kinase (vicK) 1180 DNA-binding response regulator (vicR) 1184 amino acid ABC transporter, ATP-binding protein 1188 amino acid ABC transporter, amino acid-binding protein (fliY) 1192 amino acid ABC transporter, permease protein 1196 amino acid ABC transporter, permease protein 1208 DNA-binding response regulator (vicR) 1210 threonyl-tRNA synthetase (thrS) 1214 glycosyl transferase, group 1 1218 glycosyl transferase, group 1 (cpoA) 1222 alpha-amylase (amy) 1230 proline dipeptidase (pepQ) 1238 haloacid dehalogenase-like hydrolase superfamily 1244 mannonate dehydratase (uxuA) 1248 glucuronate isomerase 1254 transcriptional regulator, GntR family 1268 sodiumgalactoside symporter family protein 1270 D-isomer specific 2-hydroxyacid dehydrogenase family protein 1282 transcriptional regulator, LysR family 1290 ABC transporter, ATP-binding protein (potA) 1296 DedA family protein 1308 MutT/nudix family protein family 1310 phosphoserine phosphatase SerB (serB) 1312 septation ring formation regulator EzrA 1320 hydrolase, haloacid dehalogenase-like family (gph) 1340 sensor histidine kinase (vncS) 1348 transmembrane protein Vexp3 (vex3) 1352 ABC transporter, ATP-binding protein (vex2) 1358 transmembrane protein Vexp1 (vex1) 1366 transposase 1374 integrase, phage family 1390 holin 2 1398 minor structural protein 1400 host specificity protein 1404 minor structural protein 1406 PblA 1486 homeobox protein drg11 1488 reverse transcriptase 1496 p22 erf-like protein 1498 gp157 1500 tropomyosin 2 1512 gp49 homologous 1526 transcriptional regulator-related protein 1566 chorismate mutase 1572 PTS system component 1576 PTS system, IIB component 1580 PTS system IIA component 1584 lactose phosphotransferase system repressor (lacR) 1594 adhesion lipoprotein (lmb) 1602 GTP pyrophosphokinase (relA) 1606 2',3'-cyclic-nucleotide 2'-phosphodiesterase (cpdB) 1616 iron ABC transporter, iron-binding protein 1620 DNA-binding response regulator 1630 PTS system component 1634 PTS system component (manM) 1638 PTS system component (manL) 1642 PTS system component 1658 response regulator BlpR (blpR) 1676 phosphate transport system regulatory protein PhoU 1680 phosphate ABC transporter, ATP-binding protein (pstB) 1684 phosphate ABC transporter, permease protein (pstA) 1690 phosphate ABC transporter, permease protein (pstC) 1694 probable hemolysin precursor 1704 ribosomal protein L11 methyltransferase (prmA) 1710 transcriptional regulator, MerR family (skgA) 1714 acetyltransferase, GNAT family 1716 MutT/nudix family protein 1722 spermidine N1-acetyltransferase 1726 ATPase, AAA family 1736 ABC transporter domain protein 1738 Helix-turn-helix domain protein 1748 integrase, phage family 1756 Helix-turn-helix domain protein 1762 bacteriophage L54a, integrase 1768 LPXTG-motif cell wall anchor domain protein 1776 membrane protein 1778 conjugal transfer protein 1780 IS1381, transposase OrfA/OrfB, truncation 1802 transcriptional regulator (rstR-1) 1806 transcriptional regulator 1808 FtsK/SpoIIIE family protein 1814 aggregation substance 1818 mercuric reductase 1822 transcriptional regulator, MerR family 1824 Mn2+/Fe2+ transporter, NRAMP family 1830 ABC transporter, ATP-binding protein (epiF) 1848 Helix-turn-helix domain protein 1850 type 2 phosphatidic acid phosphatase(PAP2), family 1858 Abortive infection protein family 1868 aminotransferase, class-V 1874 glutathione reductase (gor) 1882 chorismate synthase (aroC) 1886 3-dehydroquinate synthase (aroB) 1900 sulfatase family protein 1914 ABC transporter, ATP-binding protein 1920 smf protein (Smffamily) 1924 transferrin receptor 1928 iron compound ABC transporter, ATP-binding protein 1932 iron compound ABC transporter, permease protein 1942 acetyltransferase, CysE/LacA/LpxA/NodL family 1952 GTP-binding protein 1958 carbon starvation protein A 1960 response regulator (lytR) 1962 GAF domain protein (lytS) 2000 extracellular protein 2004 diarrheal toxin (yukA) 2024 carbamoyl-phosphate synthase, large subunit (carB) 2028 carbamoyl-phosphate synthase, small subunit (carA) 2032 aspartate carbamoyltransferase (pyrB) 2036 dihydroorotase, multifunctional complex type (pyrC) 2040 orotate phosphoribosyltransferase (pyrE) 2048 membrane protein 2062 phosphate ABC transporter, permease protein (pstA-2) 2064 phosphate ABC transporter, ATP-binding protein (pstB) 2070 phosphate transport system regulatory protein PhoU 2072 aminopeptidase N (pepN) 2076 DNA-binding response regulator (arlR) 2080 sensor histidine kinase (arlS) 2088 signal recognition particle protein (ffh) 2102 peptide ABC transporter, peptide-binding protein 2104 integrase/recombinase, phage integrase family 2108 sensor histidine kinase 2112 DNA-binding response regulator (vicR) 2118 ABC transporter, ATP-binding protein 2122 nisin-resistance protein 2130 lipoprotein 2136 gid protein (gid) 2140 transcriptional regulator, GntR family 2142 GMP synthase (guaA) 2152 branched-chain amino acid ABC transporter, permease protein (livM) 2154 branched-chain amino acid ABC transporter, ATP-binding protein (livG) 2156 branched-chain amino acid ABC transporter, ATP-binding protein (livF) 2160 acetoin utilization protein AcuB 2174 DNA polymerase III, delta prime subunit (holB) 2186 copper homeostasis protein (cutC) 2190 phosphoserine aminotransferase (serC) 2202 methylated-DNA--protein-cysteine S-methyltransferase (ogt) 2208 exodeoxyribonuclease III (xth) 2214 PTS system, IIC component 2224 tellurite resistance protein TehB (tehB) 2246 icaA protein 2250 acetyltransferase, GNAT family 2258 oxidoreductase, short chain dehydrogenase/reductase family (fabG) 2266 oxidoreductase, Gfo/Idh/MocA family family 2268 glyoxalase family protein 2272 UDP-N-acetylglucosamine pyrophosphorylase (glmU) 2276 MutT/nudix family protein 2284 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase (mtf) 2296 phosphatidate cytidylyltransferase (cdsA) 2300 membrane-associated zinc metalloprotease 2308 autolysin (flgJ) 2312 DNA polymerase III, alpha subunit, Gram-positive type 2320 nitroreductase family protein superfamily 2326 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldo 2328 carbohydrate kinase, PfkB family 2336 oxidoreductase, short chain dehydrogenase/reductase family (fabG) 2338 PTS system, IIA component (manL) 2342 glucuronyl hydrolase 2346 PTS system, IIB component (manL) 2350 PTS system, IIC component (manM) 2364 sugar binding transcriptional regulator RegR (regR) 2368 polypeptide deformylase (def) 2380 oxidoreductase, Gfo/Idh/MocA family 2382 endopeptidase O (pepO) 2394 Na+/H+ antiporter 2404 transcriptional regulator 2410 replication initiation protein RepRC 2412 bacteriophage L54a, antirepressor 2416 e11 2422 replicative DNA helicase (dnaB) 2432 GTP-binding protein 2440 arpR protein 2444 gene 17 protein 2458 integrase/recombinase, phage integrase family 2468 bacteriophage L54a, phage D3 terminase 2472 protease 2500 PblB 2504 sensor histidine kinase 2514 N-acetylmuramoyl-L-alanine amidase 2518 KH domain protein 2522 ribosomal protein S16 (rpsP) 2526 permease 2528 ABC transporter, ATP-binding protein 2538 carbamoyl-phosphate synthase, large subunit 2540 carbamoyl-phosphate synthase, small subunit (carA) 2550 transcriptional regulator, LysR family 2554 ribosomal protein L27 (rpmA) 2562 ribosomal protein L21 (rplU) 2572 glycerophosphoryl diester phosphodiesterase 2582 nitroreductase family protein 2586 dipeptidase (pepV) 2614 GTP-binding protein HflX (hflX) 2618 galactose-1-phosphate uridylyltransferase (galT) 2626 oxidoreductase, short chain dehydrogenase/reductase family 2630 single-stranded-DNA-specific exonuclease RecJ (recJ) 2638 adenine phosphoribosyltransferase (apt) 2646 Bcl-2 family protein 2654 oxidoreductase, DadA family protein 2658 glucose-1-phosphate thymidylyltransferase (rfbA) 2664 dTDP-4-dehydrorhamnose 3,5-epimerase (rfbC) 2682 hyaluronidase 2686 mutator MutT protein (mutX) 2690 MutT/nudix family protein 2694 membrane protein 2702 acetolactate synthase (ilvK) 2706 adherence and virulence protein A (pavA) 2714 ABC transporter, permease protein (rbsC) 2722 metallo-beta-lactamase superfamily protein 2734 ribose 5-phosphate isomerase (rpiA) 2738 phosphopentomutase (deoB) 2742 purine nucleoside phosphorylase, family 2 (deoD) 2750 purine nucleoside phosphorylase (deoD) 2762 capsular polysaccharide biosynthesis protein Cps4A (cps4A) 2768 cpsb protein 2770 cpsc protein 2772 CpsE 2774 CpsF 2776 CpsVG 2778 CpsVH 2780 CpsVM 2782 CpsVN 2784 glycosyl transferase domain protein 2786 glycosyl transferase, family 2/glycosyl transferase family 8 2790 CpsVK 2794 CpsL 2796 neuB protein 2798 UDP-N-acetylglucosamine 2-epimerase 2800 hexapeptide transferase family protein 2802 NeuA 2808 uracil-DNA glycosylase (ung) 2818 DNA topoisomerase IV, B subunit (parE) 2822 DNA topoisomerase IV, A subunit (parC) 2826 branched-chain amino acid aminotransferase (ilvE) 2842 glycerol kinase (glpK) 2848 aerobic glycerol-3-phosphate dehydrogenase (glpD) 2874 ABC transporter, ATP-binding protein 2882 PTS system component (bglP) 2886 glutamate 5-kinase (proB) 2890 gamma-glutamyl phosphate reductase (proA) 2898 cell division protein FtsL (ftsL) 2904 penicillin-binding protein 2X (pbpX) 2910 phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) 2914 ATP-dependent RNA helicase, DEAD/DEAH box family (deaD) 2918 ABC transporter, substrate-binding protein 2924 amino acid ABC transporter, permease protein 2928 amino acid ABC transporter, ATP-binding protein 2932 thioredoxin reductase (trxB) 2940 NAD+ synthetase (nadE) 2944 aminopeptidase C (pepC) 2952 recombination protein U (recU) 2966 Uncharacterized protein family UPF0020 family 2974 autoinducer-2 production protein LuxS (luxS) 2978 KH domain protein 2986 ABC transporter, ATP-binding protein 2994 DNA-binding response regulator (vraR) 3000 guanylate kinase (gmk) 3004 DNA-directed RNA polymerase, omega subunit 3008 primosomal protein N (priA) 3012 methionyl-tRNA formyltransferase (fmt) 3016 Sun protein (sun) 3020 protein phosphatase 2C 3032 sensor histidine kinase 3034 DNA-binding response regulator (vraR) 3036 cof family protein/peptidyl-prolyl cis-trans isomerase, cyclophilin typ 3040 S1 RNA binding domain protein (rpsA) 3044 pyruvate formate-lyase-activating enzyme 3062 PTS system, IIB component (celA) 3066 PTS system, cellobiose-specific IIC component (celB) 3068 formate acetyltransferase (pfl) 3072 transaldolase 3080 cysteine synthase A (cysK) 3088 comF operon protein 1 (comFA) 3092 competence protein ComF 3096 ribosomal subunit interface protein (yfiA) 3104 tryptophanyl-tRNA synthetase (trpS) 3108 carbamate kinase (arcC) 3116 ornithine carbamoyltransferase (argF) 3124 arginine deiminase (arcA) 3134 transcriptional regulator, Crp/Fnr family 3138 inosine-5'-monophosphate dehydrogenase (guaB) 3140 MutR 3142 transporter 3146 recF protein (recF) 3158 peptidase, M16 family 3166 ABC transporter, ATP-binding protein 3170 ABC transporter, ATP-binding protein 3178 LysM domain protein (lytN) 3180 immunodominant antigen A (isaA) 3184 L-serine dehydratase, iron-sulfur-dependent, alpha subunit (sdhA) 3188 L-serine dehydratase, iron-sulfur-dependent, beta subunit (sdhB) 3202 DHH subfamily 1 protein 3206 ribosomal protein L9 (rplI) 3210 replicative DNA helicase (dnaB) 3216 ribosomal protein S4 (rpsD) 3224 transcriptional regulator, TetR family 3236 membrane protein 3238 choline transporter (proWX) 3240 glycine betaine/L-proline transport ATP binding subunit (proV) 3242 DNA-binding response regulator 3244 Histidine kinase-, DNA gyrase B-, phytochrome-like ATPase family 3246 ornithine carbamoyltransferase (argF) 3248 carbamate kinase (arcC) 3252 membrane protein 3256 sensory box histidine kinase VicK 3258 DNA-binding response regulator 3268 Helix-turn-helix domain protein 3278 integrase 3284 ribosomal protein L33 (rpmG) 3288 ribosomal protein L32 (rpmF) 3300 YitT family protein 3304 YitT family protein 3320 DNA mismatch repair protein MutS (mutS) 3324 cold-shock domain family protein-related protein 3336 drug transporter 3340 Holliday junction DNA helicase RuvA (ruvA) 3352 recA protein (recA) 3386 oxidoreductase, Gfo/Idh/MocA family 3390 acetyltransferase, GNAT family 3394 anaerobic ribonucleoside-triphosphate reductase activating protein (nrd 3412 ABC transporter, permease protein (rbsC) 3414 ABC transporter, ATP-binding protein (nrtC) 3416 PTS system, mannose-specific IIAB components (manL) 3420 Cof family protein 3432 xanthine/uracil permease family protein 3440 acetyltransferase, GNAT family 3442 transcriptional regulator (cps4A) 3448 HIT family protein (hit) 3460 ABC transporter, permease protein 3472 Uncharacterized BCR, YhbC family COG0779 superfamily 3484 ribosomal protein L7A family 3496 esterase 3500 transcriptional repressor, CopY (copY) 3504 cation-transporting ATPase, E1-E2 family 3508 cation-binding protein-related protein 3520 DNA polymerase I (polA) 3534 DNA-binding response regulator (saeR) 3536 sensor histidine kinase (saeS)

3562 drug resistance transporter, EmrB/QacA subfamily 3566 peptidase M24 family protein 3570 peptidase M24 family protein (pepQ) 3572 cytidine/deoxycytidylate deaminase family protein 3584 translation elongation factor P (efp) 3592 N utilization substance protein B (nusB) 3596 sugar-binding transcriptional regulator, LacI family (scrR) 3600 sucrose-6-phosphate dehydrogenase (scrB) 3606 PTS system IIABC components (scrA) 3610 fructokinase (scrK) 3614 mannose-6-phosphate isomerase, class I (manA) 3622 phospho-2-dehydro-3-deoxyheptonate aldolase (aroH) 3626 holo-(acyl-carrier-protein) synthase (acpS) 3630 alanine racemase (alr) 3634 autolysin (usp45) 3636 ATP-dependent DNA helicase RecG (recG) 3642 shikimate 5-dehydrogenase (aroE) 3652 Cof family protein 3668 ferredoxin-related protein 3676 peptidase t (pepT) 3684 UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (mur 3692 iron compound ABC transporter, substrate-binding protein 3698 FecCD transport family protein (sirB) 3704 iron compound ABC transporter, permease protein (sirB) 3710 inorganic pyrophosphatase, manganese-dependent (ppaC) 3714 pyruvate formate-lyase-activating enzyme (pflA) 3718 CBS domain protein 3730 acid phosphatase 3736 LPXTG-motif cell wall anchor domain protein 3738 LPXTG-site transpeptidase family protein 3742 LPXTG-site transpeptidase family protein 3744 cell wall surface anchor family protein 3746 cell wall surface anchor family protein 3752 glycosyl transferase, group 1 family protein domain protein 3754 EpsQ protein 3756 polysaccharide extrusion protein 3768 dTDP-glucose 4-6-dehydratase 3782 glycosyl transferas domain protein 3788 dTDP-4-dehydrorhamnose reductase (rfbD) 3796 RNA polymerase sigma-70 factor (rpoD) 3802 DNA primase (dnaG) 3816 ABC transporter, ATP-binding protein Vexp2 (vex2) 3818 permease 3820 transmembrane protein Vexp3 3822 transmembrane protein Vexp3 3832 endopeptidase O (pepO) 3834 endopeptidase O (pepO) 3840 serine protease, subtilase family 3842 exotoxin 2 3844 CylK 3854 glycine cleavage system T protein 3856 CylE 3858 ABC transporter homolog CylB 3862 acyl carrier protein homolog AcpC (acpP) 3864 3-oxoacyl-(acyl-carrier-protein) reductase (fabG) 3868 CylD 3876 membrane protein 3912 LPXTG-site transpeptidase family protein 3916 LPXTG-site transpeptidase family protein 3918 LPXTG-site transpeptidase family protein 3920 LPXTG-motif cell wall anchor domain protein 3928 chaperonin, 33 kDa (hslO) 3932 Tn5252, Orf 10 protein 3934 transposase OrfAB, subunit B 3948 psr protein 3952 shikimate kinase (aroK) 3964 enolase (eno) 3972 MutT/nudix family protein 3976 glycosyl transferase, group 1 3978 preprotein translocase, SecA subunit (secA) 3986 preprotein translocase SecY family protein 3990 glycosyl transferase, family 8 3992 glycosyl transferase, family 2 3998 glycosyl transferase, family 8 4000 glycosyl transferase, family 2/glycosyl transferase family 8 4002 glycosyl transferase, family 8 4012 LPXTG-motif cell wall anchor domain protein (clfB) 4016 transcriptional regulator 4018 excinuclease ABC, B subunit (uvrB) 4022 Abortive infection protein family 4024 amino acid ABC transporter, amino acid-binding protein/permease protein 4026 amino acid ABC transporter, ATP-binding protein 4034 GTP-binding protein, GTP1/Obg family (obg) 4042 aminopeptidase PepS (pepS) 4050 ribosomal small subunit pseudouridine synthase A (rsuA) 4060 lactoylglutathione lyase (gloA) 4064 glycosyl transferase family protein 4072 alkylphosphonate utilization operon protein PhnA (phnA) 4078 glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (glmS) 4090 Phosphofructokinase 4094 DNA polymerase III, alpha subunit (dnaE) 4098 transcriptional regulator, GntR family 4102 ABC transporter, ATP-binding protein 4106 ABC transporter, ATP-binding protein 4116 FtsK/SpoIIIE family protein 4122 Helix-turn-helix domain protein 4152 Helix-turn-helix domain protein 4158 excisionase 4160 transposase 4166 chloramphenicol acetyltransferase (cat) 4174 PilB-related protein 4178 acetyltransferase 4182 Leucine Rich Repeat domain protein 4190 nucleoside diphosphate kinase (ndk) 4206 Protein of unknown function superfamily 4218 hydrolase, haloacid dehalogenase-like family (pho2) 4226 oxygen-independent coproporphyrinogen III oxidase 4236 phosphoglucomutase/phosphomannomutase family protein (femD) 4240 Gram-positive signal peptide, YSIRK family domain protein 4256 cobyric acid synthase (cobQ) 4260 lipoate-protein ligase A (lplA) 4264 branched-chain alpha-keto acid dehydrogenase E3 component, lipoamide de 4266 pyruvate dehydrogenase complex, E2 component, dihydrolipoamide acetyltr 4270 pyruvate dehydrogenase complex, E1 component, pyruvate dehydrogenase be 4286 magnesium transporter, CorA family 4294 exonuclease RexB (rexB) 4302 phenylalanyl-tRNA synthetase, beta subunit (pheT) 4324 ATP synthase F1, epsilon subunit (atpC) 4328 ATP synthase F1, beta subunit (atpD) 4332 ATP synthase F1, gamma subunit (atpG) 4338 ATP synthase F1, alpha subunit (atpA) 4342 ATP synthase F1, delta subunit (atpH) 4346 ATP synthase F0, B subunit (atpF) 4350 ATP synthase, F0 subunit A (atpB) 4354 proton-translocating ATPase, c subunit-related protein 4360 glycogen synthase (glgA) 4362 glycogen biosynthesis protein GlgD (glgD) 4366 1,4-alpha-glucan branching enzyme (glgB) 4368 pullulanase 4382 ribonuclease BN 4396 acetyltransferase, GNAT family 4398 UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) 4402 thiamine-phosphate pyrophosphorylase (thiE) 4406 phosphomethylpyrimidine kinase (thiD) 4410 transcriptional regulator, Deg family (tenA) 4414 ABC transporter, ATP-binding protein 4426 S-adenosylmethionine synthetase (metK) 4440 DNA polymerase III, gamma and tau subunits (dnaX) 4444 GAF domain protein 4448 uridine kinase (udk) 4452 ATP-dependent RNA helicase, DEAD/DEAH box family 4458 peptidoglycan GlcNAc deacetylase (pgdA) 4462 glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent (gapN) 4466 phosphoenolpyruvate-protein phosphotransferase (ptsI) 4470 phosphocarrier protein hpr 4474 NrdH-redoxin-related protein 4478 ribonucleoside-diphosphate reductase 2, alpha subunit (nrdE) 4498 glycosyl transferase, family 8 4504 alanyl-tRNA synthetase (alaS) 4512 alkyl hydroperoxide reductase, subunit F (ahpF) 4516 alkyl hydroperoxide reductase, subunit C (ahpC) 4520 ribosomal protein S2 (rpsB) 4524 translation elongation factor Ts (tsf) 4532 transcriptional regulator CtsR (ctsR) 4536 ATP-dependent Clp protease, ATP-binding subunit (clpC) 4540 deoxynucleoside kinase 4544 NifR3/Smm1 family protein 4548 chaperonin, 33 kDa (hslO) 4558 glutamate--cysteine ligase (gshA) 4562 Helix-turn-helix domain, fis-type protein 4566 perfringolysin O regulator protein (pfoR) 4570 adenylosuccinate synthetase (purA) 4578 SgaT protein (sgaT) 4582 PTS system, IIB component (sgaT) 4586 PTS system, IIA component (mtlA) 4590 hexulose-6-phosphate synthase 4594 hexulose-6-phosphate isomerase 4598 L-ribulose-5-phosphate 4-epimerase (araD) 4606 sugar binding transcriptional regulator RegR 4610 D-isomer specific 2-hydroxyacid dehydrogenase family protein (serA) 4622 transcriptional regulator, BglG family 4632 glycine betaine/L-proline transport ATP binding subunit (proV) 4636 amino acid ABC transporter, permease protein 4644 Na+/H+ exchanger family protein (kefB) 4648 glyoxylase family protein 4652 LPXTG-site transpeptidase family protein 4656 DNA gyrase, A subunit (gyrA) 4660 L-lactate dehydrogenase (ldh) 4664 NADH oxidase (nox) 4680 lipoprotein (bmpD) 4690 pantothenate kinase (coaA) 4694 ribosomal protein S20 (rpsT) 4698 amino acid ABC transporter, amino acid-binding protein (aatB) 4702 amino acid ABC transporter, ATP-binding protein 4726 ribosomal large subunit pseudouridine synthase B (rluB) 4734 Uncharacterized ACR, COG1354 4738 integrase/recombinase, phage integrase family (xerD) 4742 CBS domain protein 4746 phosphoesterase 4750 HAM1 protein 4768 transcriptional regulator, biotin repressor family 4792 amino acid ABC transproter, permease protein 4796 amino acid ABC transporter, substrate-binding protein 4798 6-aminohexanoate-cyclic-dimer hydrolase 4800 transcription elongation factor GreA (greA) 4804 Uncharacterized BCR, YceG family COG1559 4812 UDP-N-acetylmuramate--alanine ligase (murC) 4822 Snf2 family protein 4828 GTP-binding protein (b2511) 4832 primosomal protein Dnal (dnal) 4844 sensor histidine kinase (arlS) 4846 DNA-binding response regulator (arlR) 4852 heat shock protein HtpX (htpX) 4870 potassium uptake protein, Trk family 4874 ABC transporter, ATP-binding protein 4888 phosphoglycerate kinase (pgk) 4896 transcriptional regulator, MerR family 4900 glutamine synthetase, type I (glnA) 4904 secreted 45 kd protein (usp45) 4908 metallo-beta-lactamase superfamily protein 4916 glycoprotease family protein 4926 glycoprotease family protein (gcp) 4938 ribosomal protein S14p/S29e (rpsN) 4952 exonuclease (dnaQ) 4956 transcriptional regulator, merR family 4958 cyclopropane-fatty-acyl-phospholipid synthase (cfa) 4970 1,4-dihydroxy-2-naphthoate octaprenyltransferase (menA) 4972 pyridine nucleotide-disulphide oxidoreductase (ndh) 4974 cytochrome d oxidase, subunit I (cydA) 4976 cytochrome d ubiquinol oxidase, subunit II (cydB) 4980 transport ATP-binding protein CydD 4988 polyprenyl synthetase (ispB) 4990 X-pro dipeptidyl-peptidase (pepX) 4998 drug transporter 5002 universal stress protein family 5004 glycerol uptake facilitator protein (glpF) 5012 cppA protein (cppA) 5034 exodeoxyribonuclease V, alpha subunit (recD) 5038 Signal peptidase I 5042 ribonuclease HIII (rnhC) 5062 transcriptional regulator 5068 maltose ABC transporter, permease protein (malD) 5072 maltose ABC transporter, permease protein (malC) 5088 ABC transporter, ATP-binding protein 5092 ABC transporter, permease protein 5106 spspoJ protein (spo0J) 5114 DNA polymerase III, beta subunit (dnaN) 5118 Diacylglycerol kinase catalytic domain (presumed) protein 5138 transcription-repair coupling factor (mfd) 5142 S4 domain protein 5156 MesJ/Ycf62 family protein 5160 hypoxanthine phosphoribosyltransferase (hpt) 5164 cell division protein FtsH (ftsH) 5172 hydrolase, haloacid dehalogenase-like family (b2690) 5178 transcriptional regulator, MarR family 5182 3-oxoacyl-(acyl-carrier-protein) synthase III (fabH) 5190 enoyl-(acyl-carrier-protein) reductase (fabK) 5194 malonyl CoA-acyl carrier protein transacylase (fabD) 5198 3-oxoacyl-[acyl-carrier protein] reductase (fabG) 5200 3-oxoacyl-(acyl-carrier-protein) synthase II (fabF) 5202 acetyl-CoA carboxylase, biotin carboxyl carrier protein (accB) 5206 (3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase (fabZ) 5210 acetyl-CoA carboxylase, biotin carboxylase (accC) 5214 acetyl-CoA carboxylase, carboxyl transferase, beta subunit (accD) 5218 acetyl-CoA carboxylase, carboxyl transferase, alpha subunit (accA) 5224 seryl-tRNA synthetase (serS) 5234 PTS system, mannose-specific IID component 5246 ribosomal large subunit pseudouridine synthase, RluD subfamily (rluD) 5254 GTP pyrophosphokinase (relA) 5266 ribose-phosphate pyrophosphokinase (prsA) 5270 aminotransferase, class-V 5274 DNA-binding protein 5282 Domain of unknown function 5290 platelet activating factor 5296 transcriptional regulator, AraC family 5302 voltage-gated chloride channel family protein 5318 spermidine/putrescine ABC transporter, ATP-binding protein (potA) 5320 UDP-N-acetylenolpyruvoylglucosamine reductase (murB) 5324 bifunctional folate synthesis protein (folK) 5328 dihydroneopterin aldolase (folB) 5332 dihydropteroate synthase (folP) 5336 GTP cyclohydrolase I (folE) 5344 rarD protein (rarD) 5348 homoserine kinase (thrB) 5354 Polysaccharide deacetylase family (icaB) 5362 osmoprotectant transporter, BCCT family (opuD) 5384 thiol peroxidase (psaD) 5388 hydrolase 5390 transcriptional regulator, GntR family 5402 gls24 protein 5424 uncharacterized domain 1 5440 cation efflux family protein 5454 dihydroorotate dehydrogenase A (pyrDa) 5458 beta-lactam resistance factor (fibB) 5462 beta-lactam resistance factor (fibA) 5474 HD domain protein 5482 cation-transporting ATPase, E1-E2 family 5486 fructose-1,6-bisphosphatase (fbp) 5488 iron-sulfur cluster-binding protein 5492 peptide chain release factor 2 (prfB) 5496 cell division ABC transporter, ATP-binding protein FtsE (ftsE) 5504 carboxymethylenebutenolidase-related protein 5506 metallo-beta-lactamase superfamily protein 5514 DNA polymerase III, epsilon subunit/ATP-dependent helicase DinG 5520 asparaginyl-tRNA synthetase (asnS) 5526 inosine-uridine preferring nucleoside hydrolase (iunH) 5528 general stress protein 170 5534 Uncharacterised protein family superfamily 5538 Uncharacterized BCR, COG1481 5546 zinc ABC transporter, zinc-binding adhesion liprotein (adcA) 5560 isochorismatase family protein (entB) 5566 3-hydroxybutyryl-CoA dehydrogenase 5572 pyruvate phosphate dikinase (ppdK) 5574 glutamyl-tRNA(Gln) amidotransferase, C subunit (gatC) 5580 glutamyl-tRNA(Gln) amidotransferase, A subunit (gatA) 5594 GTP-binding protein 5612 iojap-related protein 5626 transcriptional regulator SkgA (skgA) 5630 glycerol uptake facilitator protein (glpF) 5634 dihydroxyacetone kinase family protein 5638 dihydroxyacetone kinase family protein 5640 transcriptional regulator, tetR family 5646 dihydroxyacetone kinase family protein 5654 glutamine amidotransferase, class I 5666 peptidase, M20/M25/M40 family 5668 ABC transporter, ATP-binding protein 5686 pur operon repressor (purR) 5690 cmp-binding-factor 1 (cbf1) 5694 competence-induced protein Ccs50 (ccs50) 5702 ribulose-phosphate 3-epimerase (rpe) 5710 rRNA (guanine-N1-)-methyltransferase (rrmA) 5712 dimethyladenosine transferase (ksgA) 5718 primase-related protein 5726 endosome-associated protein 5728 CG17785 gene product 5734 dltD protein (dltD) 5738 D-alanyl carrier protein-related protein 5742 dltB protein (dltB) 5754 DNA-binding response regulator (arlR) 5756 ribosomal protein L34 (rpmH) 5766 penicillin-binding protein 4 (pbp4) 5770 intein-containing protein 5774 NifU family protein 5778 aminotransferase, class-V 5782 Uncharacterized protein family (UPF0051) family 5786 ABC transporter, ATP-binding protein 5790 glycosyl transferase domain protein (llm) 5794 transcriptional regulator MecA (mecA) 5798 undecaprenol kinase 5806 amino acid ABC transporter, amino acid-binding protein/permease protein 5808 amino acid ABC transporter, ATP-binding protein 5834 riboflavin biosynthesis protein RibF (ribF) 5850 type I restriction-modification system, S subunit 5860 lipoprotein 5862 aggregation substance 5866 ID479 5896 type II DNA modification methyltransferase Spn5252IP (spn5252IMP) 5916 ribosomal protein L10 (rplJ) 5922 ATP-dependent Clp protease, ATP-binding subunit ClpC (clpC) 5926 homocysteine S-methyltransferase (mmuM) 5932 transcriptional regulator, TetR family 5938 GTP-binding protein (cgpA) 5952 thymidylate synthase (thyA) 5956 condensing enzyme, FabH-related 5960 hydroxymethylglutaryl-CoA reductase, degradative 5974 gene_idK21C13.21~pir.parallel.T04769~strong similarity to unknown protein, put 5976 FMN-dependent dehydrogenase family protein 5980 phosphomevalonate kinase 5986 diphosphomevalonate decarboxylase (mvaD) 5990 mevalonate kinase (mvk) 5994 Histidine kinase-, DNA gyrase B-, phytochrome-like ATPase family (PhoR1 6002 GTP pyrophosphokinase (relA) 6006 transposase for insertion sequence element is904 6016 5'-nucleotidase family 6018 polypeptide deformylase (def) 6022 NADP-specific glutamate dehydrogenase (gdhA) 6026 ABC transporter, ATP-binding/permease protein 6028 ABC transporter, ATP-binding/permease protein 6030 acetyltransferase, GNAT family family 6032 ABC transporter, ATP-binding protein 6040 degV family protein (degV) 6056 carbohydrate kinase, PfkB family (fruB) 6064 beta-lactam resistance factor (fibB) 6070 2-dehydropantoate 2-reductase 6076 PTS system component 6078 pyridine nucleotide-disulphide oxidoreductase family protein (trxB) 6082 tRNA (guanine-N1)-methyltransferase (trmD) 6092 c5a peptidase precursor 6100 ParA 6102 transposase family protein (orfA) 6116 Tn5252, relaxase 6120 Tn5252, Orf 10 protein 6124 mercuric reductase 6126 transcriptional regulator, MerR family 6132 cation transport ATPase, E1-E2 family 6138 cation-transporting ATPase, E1-E2 family 6140 cation-transporting ATPase, E1-E2 family 6144 cation-transporting ATPase, E1-E2 family 6146 transcriptional repressor, CopY (copY) 6150 cadmium resistance transporter 6158 membrane protein 6162 flavoprotein (dfp) 6170 lipoate-protein ligase A 6174 FMN oxidoreductase (nemA) 6178 Bacterial luciferase superfamily 6182 glycine cleavage system H protein (gcvH) 6186 Domain of unknown function 6194 lipoate-protein ligase A (lplA) 6198 formate-tetrahydrofolate ligase (fhs) 6202 cardiolipin synthetase (cls) 6220 aminotransferase, class II (aspB) 6222 RNA methyltransferase, TrmH family, group 2 6232 60 kda chaperonin 6242 purine nucleoside phosphorylase (deoD) 6248 deoxyribose-phosphate aldolase (deoC) 6254 Lyme disease proteins of unknown function 6258 ribosomal large subunit pseudouridine synthase, RluD subfamily (rluD) 6262 penicillin-binding protein 2A (pbp2A) 6266 pathenogenicity protein 6268 transcription antitermination protein NusG (nusG) 6272 glycosyl transferase, family 8 6276 glycosyl transferase, family 8 6284 sugar transporter family protein 6292 sensory box histidine kinase 6306 homocysteine S-methyltransferase (metH) 6310 glycerol dehydrogenase 6312 DNA topology modulation protein FlaR 6316 translation initiation factor IF-1 (infA) 6320 adenylate kinase (adk) 6326 ribosomal protein L15 (rplO) 6330 ribosomal protein L30 (rpmD) 6336 ribosomal protein S5 (rpsE) 6344 ribosomal protein L6 (rplF) 6348 ribosomal protein S8 (rpsH) 6352 ribosomal protein S14 (rpsN) 6356 ribosomal protein L5 (rplE) 6360 ribosomal protein L24 (rplX) 6366 ribosomal protein L14 (rplN) 6368 ribosomal protein S17 (rpsQ) 6372 ribosomal protein L29 (rpmC) 6374 ribosomal protein L16 (rplP) 6378 ribosomal protein S3 (rpsC) 6382 ribosomal protein L22 (rplV) 6386 ribosomal protein S19 (rpsS) 6390 ribosomal protein L2 (rplB) 6394 ribosomal protein L23 (rplW) 6398 ribosomal protein L4/L1 family (rplD) 6402 ribosomal protein L3 (rplC) 6408 ribosomal protein S10 (rpsJ) 6414 MATE efflux family protein 6418 threonine synthase (thrC) 6428 Uncharacterized BCR, COG1636 superfamily 6436 4-alpha-glucanotransferase (malQ) 6440 glycogen phosphorylase family protein (malP) 6444 glycerol-3-phosphate transporter (glpT) 6452 rhodanese family protein 6458 ammonium transporter 6464 DNA repair protein RadA (radA) 6472 oxidoreductase, pyridine nucleotide-disulfide, class I 6478 ribose ABC transporter, periplasmic D-ribose-binding protein (rbsB) 6484 ribose ABC transporter, ATP-binding protein (rbsA) 6486 ribose ABC transporter protein (rbsD) 6488 ribokinase (rbsK) 6498 ABC transporter, ATP-binding protein 6502 DNA-binding response regulator (vicR) 6506 argininosuccinate synthase (argG) 6508 argininosuccinate lyase (argH) 6514 bacteriophage L54a, repressor protein 6528 soluble transducer HtrXIII 6542 probable transposase (insertion sequence IS861) 6544 ABC transporter, ATP-binding/permease protein 6550 ABC transporter, ATP-binding/permease protein 6560 Serine hydroxymethyltransferase 6568 HemK protein (hemK) 6572 peptide chain release factor 1 (prfA) 6576 thymidine kinases 6580 4-oxalocrotonate tautomerase (dmpI) 6588 oxidoreductase 6594 oxidoreductase 6600 formate/nitrite transporter family protein 6608 xanthine permease (pbuX) 6612 xanthine phosphoribosyltransferase (xpt) 6616 guanosine monophosphate reductase (guaC) 6620 drug resistance transporter, EmrB/QacA subfamily 6622 oxidoreductase 6624 Kup system potassium uptake protein (kup) 6636 O-methyltransferase 6642 oligoendopeptidase F (pepF) 6646 competence protein CoiA (coiA) 6650 major facilitator superfamily protein superfamily 6652 ribosomal small subunit pseudouridine synthase A (rsuA) 6658 glucosamine-6-phosphate isomerase (nagB) 6662 nodulin-related protein, truncation 6664 S-adenosylmethioninetRNA ribosyltransferase-isomerase (queA) 6674 permease, GntP family 6684 6-phospho-beta-glucosidase (bglA) 6686 PTS system, beta-glucosides-specific IIABC components 6688 transcription antiterminator Lict (licT) 6704 esterase 6706 sugar-binding transcriptional repressor, Lacl family 6708 hydrolase, haloacid dehalogenase-like family

6712 DNA internalization-related competence protein CamEC/Rec2 6716 competence protein CelA (celA) 6720 acyltransferase family protein 6732 ATP-dependent RNA helicase DeaD (deaD) 6736 lipoprotein, YaeC family 6738 ABC transporter, permease protein 6752 diacylglycerol kinase (dgkA) 6768 formamidopyrimidine-DNA glycosylase (mutM) 6776 epidermin immunity protein F 6788 glycyl-tRNA synthetase, beta subunit (glyS) 6790 acyl carrier protein phosphodiesterase 6800 SsrA-binding protein (smpB) 6822 D-alanine--D-alanine ligase 6824 recombination protein RecR (recR) 6830 penicillin-binding protein 2b 6832 phosphoglycerate mutase (gpmA) 6836 triosephosphate isomerase (tpiA) 6856 phosphoglycerate mutase family protein 6860 D-alanyl-D-alanine carboxypeptidase family 6864 autolysin 6868 heat-inducible transcription repressor HrcA (hrcA) 6872 heat shock protein GrpE (grpE) 6876 chaperone protein dnak 6880 dnaJ protein (dnaJ) 6884 transcriptional regulator, gntR family domain protein 6888 tRNA pseudouridine synthase A (truA) 6892 phosphomethylpyrimidine kinase (thiD) 6910 galactose-6-phosphate isomerase, LacA subunit (lacA) 6922 tagatose 1,6-diphosphate aldolase (lacD) 6932 sugar ABC transporter, ATP-binding protein (msmK) 6936 glucan 1,6-alpha-glucosidase (dexB) 6940 UDP-glucose 4-epimerase (galE) 6942 response regulator (citB) 6950 citrate carrier protein (citS) 6954 malate oxidoreductase (tme) 6958 bacterocin transport accessory protein 6976 transposase family protein (orfA) 6980 pXO1-128 6986 adhesion lipoprotein (lmb) 6994 DNA-directed RNA polymerase, alpha subunit (rpoA) 6998 ribosomal protein L17 (rplQ) 7040 probable dna-directed rna polymerase delta subunit 7044 CTP synthase (pyrG) 7058 bacteriocin transport accessory protein 7074 translation initiation factor IF-3 (infC) 7100 adenosine deaminase 8468 preprotein translocase, SecE subunit 8476 antigen, 67 kDa 8486 Lipase/Acylhydrolase 8492 peptide ABC transporter, permease protein (oppB) 8494 competence protein CglB (cglB) 8502 peptide ABC transporter, peptide-binding protein 8504 oxidoreductase 8510 amino acid ABC transporter, permease protein (opuBB) 8522 abc transporter atp-binding protein ybhf 8530 glycerol-3-phosphate dehydrogenase (NAD(P)+) (gpsA) 8538 sugar ABC transporter, sugar-binding protein 8544 secreted 45 kd protein (usp45) 8556 phosphoglycerate mutase family protein 8566 glycosyl hydrolase, family 3 8576 N-acetylmuramoyl-L-alanine amidase 8596 sensory box histidine kinase (withHAMPandPASd) 8608 aminoglycoside 6-adenylyltransferase 8622 iron compound ABC transporter, permease protein (sirB) 8636 phosphate ABC transporter, permease protein (pstC-2) 8650 branched-chain amino acid transport system II carrier protein (brnQ) 8658 PTS system, IID component 8662 replisome organiser-related protein 8674 alkaline amylopullulanase 8676 exfoliative toxin A 8690 glycerol uptake facilitator protein (glpF) 8698 ABC transporter, ATP-binding protein 8706 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (pgs 8708 cobalt transport protein 8730 integral membrane protein 8734 yadS protein 8736 cell wall surface anchor family protein 8748 polysaccharide biosynthesis protein 8752 glycosyl transferase domain protein 8764 endopeptidase O 8770 beta-ketoacyl-acyl carrier protein synthase II 8772 ABC transporter, ATP-binding protein 8776 penicillin-binding protein 8778 cell wall surface anchor family protein 8780 cell wall surface anchor family protein 8786 LPXTG-motif cell wall anchor domain protein 8788 6-aminohexanoate-cyclic-dimer hydrolase 8796 NLP/P60 family protein 8802 DNA/RNA non-specific endonuclease 8806 hydroxyethylthiazole kinase (thiM) 8826 PTS system component 8832 sugar ABC transporter, permease protein 8836 potassium uptake protein, Trk family (trkA) 8850 lemA protein (lemA) 8856 cobalt transport protein 8882 spermidine/putrescine ABC transporter, spermidine/putrescine-binding pr 8884 spermidine/putrescine ABC transporter, permease protein (potC) 8906 ABC transporter, substrate-binding protein 8908 lipoprotein 8916 sensor histidine kinase 8930 TrsK-like protein (traK) 8936 R5 protein 8962 chromosome assembly protein homolog 8978 ribose ABC transporter, permease protein (rbsC) 8980 permease 8982 sensor histidine kinase (arlS) 8986 hydrolase, haloacid dehalogenase-like family (gph) 8994 dephospho-CoA kinase 8996 oxalateformate antiporter 9004 sensory box protein 9006 host cell surface-exposed lipoprotein 9012 PAP2 family protein 9034 GtrA family protein 9050 lipoprotein signal peptidase (lspA) 9280 alcohol dehydrogenase, zinc-containing (adh) 9284 trigger factor (tig) 9290 fructose-bisphosphate aldolase (fba) 9292 DAK2 domain protein 9296 oligopeptide ABC transporter, permease protein 9298 N-acetylglucosamine-6-phosphate deacetylase (nagA) 9300 transcriptional regulator, DeoR family (lacR) 9302 PTS system, mannose-specific IIC component (manM) 9306 Phosphoglucose isomerase 9310 aspartate--ammonia ligase (asnA) 9312 amino acid ABC transporter, ATP-binding protein 9314 DNA-binding protein HU (hup) 9316 DHH subfamily 1 protein 9318 chloride channel 9320 integrase (int) 9324 DNA/RNA non-specific endonuclease 9326 PTS system component 9328 cell division protein, FtsW/RodA/SpoVE family (ftsW) 9330 LPXTG-motif cell wall anchor domain protein 9332 peptide chain release factor 3 (prfC) 9334 ABC transporter, ATP-binding protein 9336 superoxide dismutase [mn-fe] 9340 phenylalanyl-tRNA synthetase, alpha subunit (pheS) 9342 amino acid ABC transporter, permease protein 9344 phosphate ABC transporter, phosphate-binding protein (pstS) 9346 NOL1/NOP2/sun family protein (sun) 9348 Abortive infection protein family 9350 permease 9352 N-acetylmuramoyl-L-alanine amidase domain protein (usp45) 9354 ABC transporter, ATP-binding protein 9356 phosphoglucomutase (pgm) 9358 oxidoreductase, short chain dehydrogenase/reductase family 9360 phosphate acetyltransferase 9362 gls24 protein 9364 ribosomal protein S1 (rpsA) 9368 dTDP-glucose 4,6-dehydratase (rfbB) 9370 excinuclease ABC, C subunit (uvrC) 9372 MATE efflux family protein 9378 amino acid permease (rocE) 9380 DNA-binding response regulator TrcR (trcR) 9382 16S rRNA processing protein RimM (rimM) 9384 transcriptional regulator 9388 ribosomal protein L20 (rplT) 9394 sugar-binding transcriptional repressor, Lacl family (malR) 9396 proton/peptide symporter family protein 9398 amino acid permease 9400 exoribonuclease, VacB/Rnb family (vacB) 9402 multi-drug resistance efflux pump (pmrA) 9404 adhesion lipoprotein (psaA) 9406 iron-dependent transcriptional regulator (sirR) 9410 branched-chain amino acid ABC transporter, amino acid-binding protein ( 9412 amino acid permease 9414 SpoU rRNA Methylase family protein 9416 sodium/dicarboxylate symporter (gltP-2) 9418 branched-chain amino acid transport system II carrier protein (brnQ) 9420 alcohol dehydrogenase, zinc-containing 9422 aminotransferase, class I (aspB) 9424 ribosomal protein S6 (rpsF) 9426 A/G-specific adenine glycosylase (mutY) 9428 acid phosphatase (olpA) 9430 ribosomal protein S12 (rpsL) 9434 microcin immunity protein MccF (mccF-1) 9436 undecaprenyl diphosphate synthase (uppS) 9438 preprotein translocase, YajC subunit (yajC) 9440 chaperonin, 10 kDa (groES) 9444 YitT family protein 9446 seine protease (htrA) 9448 ribose-phosphate pyrophosphokinase (prsA) 9450 aromatic amino acid aminotransferase (araT) 9452 Recombination protein O (recO) 9454 Abortive infection protein family 9456 fatty acid/phospholipid synthesis protein PlsX (plsX) 9458 acyl carrier protein (acpP) 9462 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) 9464 alcohol dehydrogenase, iron-containing 9466 ribosomal protein L18 (rplR) 9468 preprotein translocase, SecY subunit 9470 transcriptional regulator ComX1 (comX1) 9472 deoxyuridine 5'-triphosphate nucleotidohydrolase (dut) 9478 sugar-binding transcriptional regulator, Lacl family (rbsR) 9480 SPFH domain/Band 7 family 9488 zinc ABC transporter, permease protein (adcB) 9492 abortive infection protein 9494 hydrolase, haloacid dehalogenase-like family 9496 response regulator (lytT) 9500 transketolase, C-terminal subunit 9502 polyribonucleotide nucleotidyltransferase (pnp) 9504 serine O-acetyltransferase (cysE) 9508 ribosomal protein L13 (rplM) 9510 replication initiation protein 9518 amino acid ABC transporter, amino acid-binding protein 9522 glycyl-tRNA synthetase, alpha subunit (glyQ) 9524 NADH oxidase 9528 transketolase (tkt) 9534 penicillin-binding protein 1A (pbp1A) 9536 cell division protein DivIVA (divIVA) 9538 sensor histidine kinase 9540 serine/threonine protein kinase (pknB) 9542 transcriptional regulator 9544 PTS system, IIA component (lacF) 9546 glycerol dehydrogenase (gldA) 9548 aspartate kinase (thrA) 9550 enoyl-CoA hydratase/isomerase family protein 9552 acyl carrier protein (acpP) 9564 ABC transporter, ATP-binding protein 9566 N utilization substance protein A (nusA) 9568 ribosome-binding factor A (rbfA) 9570 Cof family protein 9572 CoA binding domain protein (b0965) 9574 transcriptional regulator, Fur family 9578 queuine tRNA-ribosyltransferase (tgt) 9580 ribonuclease P protein component (rnpA) 9582 serine protease, subtilase family 9584 glycosyl transferase domain protein 9586 transcriptional activator, AraC family 9588 transcriptional regulator, TetR family 9590 transcriptional regulator, AraC family 9594 surface protein Rib 9596 transposase, mutator family 9600 acetyltransferase, GNAT family 9602 Transposase, Mutator family 9606 UDP-sugar hydrolase 9610 anthranilate synthase component II (trpG) 9612 biotin synthetase (bioB) 9616 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) 9618 ylmF protein (ylmF) 9620 amino acid ABC transporter, permease protein 9622 phosphoglucomutase (pgm) 9624 YjeF-related protein, C-terminus 9626 FemAB family protein (fibA) 9628 Cof family protein 9630 cell division ABC transporter, permease protein FtsX (ftsX) 9632 oxidoreductase, short-chain dehydrogenase/reductase family (fabG) 9634 aspartate aminotransferase (aspC) 9638 ribosomal protein L31 (rpmE) 9640 nrdI protein (nrdI) 9642 ribosomal protein L19 (rplS) 9644 bacteriophage L54a, repressor protein 9646 bacteriophage L54a, antirepressor 9652 single-strand binding protein (ssb) 9660 pneumococcal surface protein A 9666 DNA-binding response regulator (vncR) 9668 transposase OrfAB, subunit B 9670 cell division protein, FtsW/RodA/SpoVE family (rodA) 9672 DNA gyrase, B subunit (gyrB) 9674 3-phosphoshikimate 1-carboxyvinyltransferase (aroA) 9676 RNA methyltransferase, TrmA family 9680 transcriptional regulator, AraC family 9682 ABC transporter, ATP-binding protein 9690 CylJ 9696 permease 9698 regulatory protein 9700 carbohydrate kinase, pfkB family 9702 beta-glucuronidase 9704 2-deydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldo 9706 3-oxoacyl-(acyl-carrier-protein) reductase 9708 catabolite control protein A (ccpA) 9712 ribonuclease III (rnc) 9714 SMC family, C-terminal domain family 9718 S1 RNA binding domain protein 9722 prolipoprotein diacylglyceryl transferase (lgt) 9724 riboflavin synthase, alpha subunit (ribE) 9726 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II (ri 9728 lysyl-tRNA synthetase (lysS) 9734 Transposase subfamily 9738 translation elongation factor Tu (tuf) 9740 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D- -a 9746 Glutathione S-transferases domain protein 9754 Ribonucleotide reductases 9756 biotin--acetyl-CoA-carboxylase ligase 9760 Uncharacterized protein family SNZ family 9762 methionine aminopeptidase, type I (map) 9764 DNA ligase, NAD-dependent (ligA) 9766 glucose-1-phosphate adenylyltransferase (glgC) 9768 UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) 9770 acetyltransferase, GNAT family 9772 exonuclease RexA (rexA) 9774 tRNA modification GTPase TrmE (trmE) 9776 ABC transporter, ATP-binding protein 9778 pyruvate dehydrogenase complex, E1 component, pyruvate dehydrogenase al 9782 Mur ligase family protein 9786 HD domain protein 9788 translation elongation factor G (fusA) 9796 pyruvate kinase (pyk) 9798 Signal peptidase I 9802 cytidine deaminase (cdd) 9804 sugar ABC transporter, ATP-binding protein 9806 sugar ABC transporter, permease protein 9808 acetyltransferase, GNAT family 9810 ABC transporter, permease protein 9812 SatD 9814 Helix-turn-helix domain, fis-type protein 9816 phosphate ABC transporter, ATP-binding protein (pstB-1) 9818 tRNA pseudouridine synthase B (truB) 9820 Acetyltransferase (GNAT) family 9822 DNA topoisomerase I (topA) 9824 ribonuclease HII (rnhB) 9830 orotidine 5'-phosphate decarboxylase (pyrF) 9832 aspartate-semialdehyde dehydrogenase (asd) 9836 pantothenate metabolism flavoprotein (dfp) 9840 Sua5/YciO/YrdC/YwlC family protein 9844 thiamine biosynthesis protein ApbE 9846 Domain of unknown function 9848 DNA repair protein RadC (radC) 9850 glycosyl hydrolase, family 1 (bglA) 9852 Cof family protein (b0844) 9854 spermidine/putrescine ABC transporter, permease protein (potH) 9856 folylpolyglutamate synthase (folC) 9858 homoserine dehydrogenase (hom) 9860 succinate-semialdehyde dehydrogenase (gabD-1) 9862 membrane protein 9864 ATP-dependent DNA helicase PcrA (pcrA) 9866 uracil permease (uraA) 9868 sodiumalanine symporter family protein 9878 capsular polysaccharide biosynthesis protein Cps4B (cps4B) 9880 transcriptional regulator, LysR family 9882 CpslaS 9884 chloride channel protein 9886 tributyrin esterase (estA) 9888 ABC transporter, ATP-binding protein (potA) 9890 alpha-acetolactate decarboxylase (budA) 9892 TPR domain protein 9896 metallo-beta-lactamase superfamily protein 9898 tRNA delta(2)-isopentenylpyrophosphate transferase (miaA) 9902 glycerophosphoryl diester phosphodiesterase 9904 transposase OrfAB, subunit B 9906 IS3-Spn1, transposase 9908 transposase OrfAB, subunit B (orfB) 9910 reverse transcriptase 9916 transposase OrfAB, subunit B 9918 integrase, phage family (int) 9920 transcription regulator 9922 TnpA 9926 structural gene for ultraviolet resistance (uvra) 9930 Helicases conserved C-terminal domain protein 9932 abortive infection bacteriophage resistance protein (abiEi) 9944 ribosomal protein L7/L12 (rplL) 9948 ATP-dependent Clp protease, ATP-binding subunit ClpX (clpX) 9950 dihydrofolate reductase (folA) 9952 hemolysin 9954 transcriptional regulator, MarR family 9958 polyA polymerase family protein 9960 PTS system, fructose specific IIABC components (fruA-1) 9962 lactose phosphotransferase system repressor (lacR) 9964 choline binding protein D (cbpD) 9968 pyrimidine operon regulatory protein (pyrR) 9970 ribosomal large subunit pseudouridine synthase D (rluD) 9972 thiamine biosynthesis protein ThiI (thiI) 9974 3-dehydroquinate dehydratase, type I (aroD) 9976 iron compound ABC transporter, ATP-binding protein (fepC) 9980 transcriptional regulator 9982 glycosyl transferase domain protein 9984 Cps9H 9988 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (ispD) 9990 licD1 protein (licD1) 9996 large conductance mechanosensitive channel protein (mscL) 10000 maltose ABC transporter, maltose-binding protein 10004 nucleotide sugar synthetase-like protein 10006 transcriptional regulator 10008 oxidoreductase, aldo/keto reductase family 10010 NAD(P)H-flavin oxidoreductase 10016 transcriptional regulator MutR 10018 GTP-binding protein Era (era) 10022 peptide methionine sulfoxide reductase (msrA) 10026 peptide ABC transporter, ATP-binding protein 10028 peptide ABC transporter, ATP-binding protein (amiE) 10030 peptide ABC transporter, peptide-binding protein 10032 transposase, IS30 family 10034 transcriptional regulator, LysR family 10036 spoE family protein (ftsK) 10044 methionyl-tRNA synthetase (metG) 10046 D-isomer specific 2-hydroxyacid dehydrogenase family protein (serA) 10048 acetyltransferase, GNAT family 10050 phosphoserine aminotransferase (serC) 10054 thymidylate kinase (tmk) 10060 branched-chain amino acid ABC transporter, permease protein (livH) 10062 ATP-dependent Clp protease, proteolytic subunit ClpP (clpP) 10064 uracil phosphoribosyltransferase (upp) 10066 potassium uptake protein, Trk family (trkH) 10068 glutamate racemase (murI) 10070 membrane protein 10072 HD domain protein 10074 Acylphosphatase 10076 spoIllJ family protein 10078 acetyltransferase, GNAT family 10080 glucose-inhibited division protein B (gidB) 10082 potassium uptake protein, Trk family 10084 ABC transporter, permease protein 10088 isochorismatase family protein 10092 haloacid dehalogenase-like hydrolase superfamily 10094 membrane protein 10096 glutamyl-tRNA(Gln) amidotransferase, B subunit (gatB) 10098 CBS domain protein protein 10100 transcriptional regulator (codY) 10102 universal stress protein family 10104 L-asparaginase (ansA) 10106 oxidoreductase, aldo/keto reductase 2 family 10108 preprotein translocase, SecA subunit (secA) 10112 excinuclease ABC, A subunit (uvrA) 10114 magnesium transporter, CorA family (corA) 10116 thioredoxin (trx) 10118 MutS2 family protein (mutS2) 10122 DNA-damage inducible protein P (dinP) 10124 formate acetyltransferase (pfl) 10126 transcriptional regulator, Crp family 10128 transport ATP-binding protein CydC 10138 ribosomal-protein-alanine acetyltransferase (rimI) 10140 hydrolase 10144 D-alanine-activating enzyme (dltA) 10148 carbohydrate kinase, FGGY family 10150 transaldolase 10160 Helix-turn-helix domain protein 10164 single-strand binding protein (ssb) 10166 type II DNA modification methyltransferase Spn5252IP (spn5252IMP) 10174 integrase, phage family 10178 Cyclic nucleotide-binding domain protein 10180 transcriptional regulator, MarR family 10182 prolyl-tRNA synthetase (proS) 10184 leucine-rich protein 10186 lacX protein, truncation (lacX) 10188 tagatose-6-phosphate kinase (lacC) 10190 galactose-6-phosphate isomerase, LacB subunit (lacB) 10192 neuraminidase 10198 Histidine kinase-, DNA gyrase B-, phytochrome-like ATPase domain protei 10200 ABC transporter, ATP-binding protein 10202 PTS system, IIABC components (ptsG) 10204 phosphate regulon response regulator PhoB (phoB) 10212 Uncharacterized ACR, COG2161 subfamily 10216 abortive phage resistance protein 10222 TnpA 10226 acetyltransferase, GNAT family 10230 ABC transporter domain protein 10234 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase ( 10236 branched-chain amino acid transport protein AzlC (azlC) 10240 DNA-binding response regulator (srrA) 10242 leucyl-tRNA synthetase (leuS) 10246 NupC family protein 10248 transcriptional regulator, GntR family 10252 glyoxalase family protein 10254 anaerobic ribonucleoside-triphosphate reductase (nrdD) 10256 competence-induced protein Ccs4 10262 competence/damage-inducible protein CinA (cinA) 10264 DNA-3-methyladenine glycosylase I (tag) 10268 DNA mismatch repair protein HexB (hexB) 10270 arginine repressor (argR) 10272 arginyl-tRNA synthetase (argS) 10274 aspartyl-tRNA synthetase (aspS) 10276 histidyl-tRNA synthetase (hisS) 10280 AGR_pAT_51p 10286 hydrolase, alpha/beta hydrolase fold family 10288 phage infection protein 10290 Glucose inhibited division protein A (gidA) 10292 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (trmU) 10296 arginine/ornithine antiporter (arcD) 10298 chromosomal replication initiator protein DnaA (dnaA) 10302 peptidyl-tRNA hydrolase (pth) 10310 phosphotyrosine protein phosphatase 10316 ribosomal protein L36 (rpmJ) 10318 ribosomal protein S13/S18 (rpsM) 10328 L-lactate dehydrogenase (ldh) 10330 ribosomal protein L28 (rpmB) 10362 RNA polymerase sigma-70 factor, ECF subfamily 10384 BioY family protein 10386 AtsA/ElaC family protein 10388 cytidine/deoxycytidylate deaminase family protein 10394 phosphorylase, Pnp/Udp family 10396 transcriptional regulator, MerR family 10402 methyltransferase (ubiE) 10412 type IV prepilin peptidase 10416 ylmG protein (ylmG) 10444 transposase OrfAB, subunit B 10446 IS150-like transposase 10452 Bacterial regulatory proteins, tetR family domain protein 10454 cell wall surface anchor family protein, authentic frameshift (clfB) 10456 transposase OrfAB, subunit A (orfA) 10460 chaperonin, 33 kDa (hslO) 10472 (3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase (fabZ) 10482 sprT protein

10490 transcriptional regulator, MarR family 10498 transcriptional regulator 10504 glycogen biosynthesis protein GlgD (glgD) 10536 ribonucleoside-diphosphate reductase, alpha subunit, truncation (nrdD) 10538 LPXTG-motif cell wall anchor domain 10550 membrane protein 10554 arsenate reductase (arsC) 10564 transposase, authentic frameshift 10570 transposase OrfAB, subunit A (orfA) 10574 Tn5252, Orf 9 protein 10580 IS3-Spn1, transposase 10584 transcriptional regulator, ArsR family 10628 ribosomal protein L35 (rpml) 10630 cytidylate kinase (cmk) 10636 MutT/nudix family protein 10644 preprotein translocase, SecG subunit 10680 ribosomal protein S18 (rpsR) 10682 single-strand binding protein (ssb) 10692 glyceraldehyde 3-phosphate dehydrogenase (gap) 10694 translation elongation factor G (fusA) 10696 ribosomal protein S7 (rpsG) 10704 phosphinothricin N-acetyltransferase (pat) 10730 nrdI protein (nrdI) 10732 accessory gene regulator protein C (blpH) 10744 rhodanese family protein (pspE) 10746 cAMP factor 10758 competence/damage-inducible protein CinA (cinA) 10770 transcriptional regulator, ArgR family (argR) 10772 FliP family family 10794 peptide ABC transporter, peptide-binding protein 10800 ribosomal protein S21 (rpsU) 10802 transposase, IS30 family 10816 mucin 2 precursor, intestinal 10854 SV40-transformed marker protein pG1-related protein 10856 SV40-transformed marker protein pG1-related protein 10858 SV40-transformed marker protein pG1-related protein 10860 SV40-transformed marker protein pG1-related protein 10862 SV40-transformed marker protein pG1-related protein 10864 SV40-transformed marker protein pG1-related protein 10866 SV40-transformed marker protein pG1-related protein 10910 transcriptional regulator 10920 ribosomal protein S11 (rpsK) 10922 elaA protein 10926 5-formyltetrahydrofolate cyclo-ligase family protein 10938 inositol monophosphatase family protein 10940 amino acid ABC transporter, amino acid-binding protein (artI) 10944 Holliday junction DNA helicase RuvB (ruvB) 10946 D-alanyl-D-alanine carboxypeptidase (dacA) 10948 lipoprotein (bmpD) 10950 peptidase, U32 family family 10952 protease maturation protein 10954 glutamyl-tRNA synthetase (gltX) 10956 GTP-binding protein LepA (lepA) 10960 translation initiation factor if-2 10962 phosphoenolpyruvate carboxylase (ppc) 10964 calcium E1-E2-type ATPase 10966 serine protease, subtilase family

SEQUENCE LISTING The patent contains a lengthy "Sequence Listing" section. A copy of the "Sequence Listing" is available in electronic form from the USPTO web site ()- . An electronic copy of the "Sequence Listing" will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

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